Table 1 Sequence analysis of newly retrotransposed SINE copies.
From: Recombinant SINEs are formed at high frequency during induced retrotransposition in vivo
|  |  | Number of mismatches with the best database hits †| |||||||
|---|---|---|---|---|---|---|---|---|---|
|  |  | Full length | 5′-end | Middle | 3′-end | ||||
Sequence number | Number of mismatches with marked SINE (position) | Length matched (bp) | Mismatches | Length matched (bp) | Mismatches | Length matched (bp) | Mismatches | Length matched (bp) | Mismatches |
Set I: Marked SINE1 | |||||||||
1–7 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
8 | 1 (134) | NA | NA | NA | NA | NA | NA | NA | NA |
9 | 1 (274) | NA | NA | NA | NA | NA | NA | NA | NA |
10 | 1 (482) | NA | NA | NA | NA | NA | NA | NA | NA |
|  |  | Number of mismatches with the best database hits †| |||||||
|  |  | Full length | 5′-end | Middle | 3′-end | ||||
Sequence number | Number of mismatches with marked SINE | Length matched (bp) ‡ | Mismatches | Length matched (bp) ‡ | Mismatches | Length matched (bp) ‡ | Mismatches | Length matched (bp) ‡ | Mismatches |
Set II: Genomic SINEs | |||||||||
1 | 22 | 501 | 11 | 340 | 4 | NA | NA | 161 | 0 |
2 | 25 | 503 | 6 | 370 | 4 | NA | NA | 133 | 0 |
3 | 19 | 502 | 5 | 305 | 4 | NA | NA | 197 | 1 |
4 | 24 | 503 | 3 | 325 | 0 | NA | NA | 178 | 1 |
5 | 27 | 502 | 20 | 125 | 2 | 255 | 4 | 122 | 5 |
6 | 24 | 502 | 11 | 350 | 2 | 70 | 3 | 82 | 1 |
7 | 22 | 502 | 10 | 380 | 3 | NA | NA | 122 | 2 |
8 | 19 | 502 | 5 | 214 | 1 | NA | NA | 288 | 1 |
|  |  | Number of mismatches with the best database hits †| |||||||
|  |  | Full length | 5′-end | Middle | 3′-end | ||||
Sequence number | Number of mismatches with marked SINE | Length matched (bp) ‡,§ | Mismatches | Length matched (bp) ‡ | Mismatches | Length matched (bp) | Mismatches | Length matched (bp) ‡ | Mismatches |
Set III: Recombinant SINEs | |||||||||
1 | 22 | 476 | 16 | 196 | 0 | NA | NA | 280 | 5 |
2 | 22 | 476 | 15 | 196 | 0 | NA | NA | 280 | 1 |
3 | 25 | 476 | 18 | 196 | 0 | NA | NA | 280 | 4 |
4 | 24 | 502 | 11 | 222 | 2 | NA | NA | 280 | 4 |
5 | 27 | 450 | 28 | 170 | 1 | NA | NA | 280 | 0 |
