Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015411.1 Corchorus olitorius cultivar O-4 contig15444, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 105894
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2444 original size:333 final size:327
Alignment explanation
Indices: 1--4636 Score: 5338
Period size: 333 Copynumber: 14.2 Consensus size: 327
** * * * * *
1 CTCGTAAAAAATTATTCTTAAATCCATTGTGGCTGAGATTTGGTTTGATGAATATAAATATTTTA
1 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTTA
* * ** * * *
66 AGGAGTCTTGCTGCCAAAAATCAAGCAAAACTAAGTCGGGGCCCCCAGAATGCGAGTTTTTAGCA
66 AGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGG-CCCAAGAA--CGCGTTTTTAGCC
** * *
131 AAAAAGAGTGATGGTTTGTACACGATTTCGGCCAAAATTTTGCAAAAACTATCCCGAAAAATTTT
128 AAAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTT
* * ** *
196 TCCTCAATTTTTGGCCACAGA-ACTTATAAAAAATATGTAACTCAATACCAATAAAATTTAATGG
193 TCCTCAATTTTTGGCCACA-ATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGG
* *
260 CTTTTCAGGCTTCTAATATAATTTTTCCTATTTTTTCGAATTAATTTCTAATTAAATCGAAACAA
257 CTTTTCAGGCTTCTAAT-T-A--TTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAT
325 AATTCAGATG
318 AATTCAGATG
* *
335 CTCGTAAAACCTTATACTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATCTTTTA
1 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTTA
* * * * *
400 AGGAGTCTTGGTGCCAAAAATCATCCAAAACTGTGTCGGGGCCCAGGAACGCGTTTTTAGCAAAA
66 AGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAGCCAAA
* * * * * *
465 AACTGTGATGGTCAGTACACTATTTCGACCAAAATTTAGCGAAAACTGTCCC-AAAAGATTGTTC
131 AACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAA-ATTTTTC
* * * * ** * *
529 CTCAATTTATGGCCACAACACTCATAAAAAATATAAAATTCAA-ATCAA-AAAAGTCTGAAGGCC
195 CTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAA-T-TTAAGGGC
** * *
592 TTTAGATGCTTC-AATTTTCGTATTTCCTATTTTTTTCCTAATTAATTTCTAATTAAATCGAAAC
258 TTTTCAGGCTTCTAA---T--TATTTCCTA--TTTTTCCGAATTAATTTCTAATTAAATCGAAAC
*
656 ATGATTCAGATG
316 ATAATTCAGATG
* * * * * ** * ***
668 CTCGTAAAAAC-AATTCCTTCAATCCAATGTGGCTGAGAACTGGTTAGATTAGTTTAGATATTTT
1 CTCGTAAAACCTTA-TCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTT
* * * * *
732 AATGACACTTGGC-GCCAAAAATCATGC-AAACTGTGCCGGGGCACAAGAACGCGTTTTTAGCGA
65 AAGGAGACTT-GCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAGCCA
* * * * **
795 AAAACCGTGATAGTTAGTACACGATTTGGGCCAAAATTTTGAAAAAACTGTCGTGAAAAATTTTT
129 AAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTT
* *
860 CCTCAATTTGTGACCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCT
194 CCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCT
* * *
925 TTTCAGGCTTCTAA--A-AT-C-ATTTTTCAGAATTAATTTCTAATTAAATCGAAACATAATTTA
259 TTTCAGGCTTCTAATTATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTCA
985 GATG
324 GATG
* *
989 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAAATTTGGTTAGATTAAAATAGATATTTTA
1 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTTA
* ** * *
1054 AGGA-ATCTTGCTGTCAAAAATCATGCAAAACTAAGTCGGGCCCCCCAGAACGCGAGTTTTTAG-
66 AGGAGA-CTTGCTGCCAAAAATCATGCAAAACTGTGTCGGG-GCCCAAGAACGC--GTTTTTAGC
** * *
1117 CATAAAAGAGTGATGGTTAGTACACGTTTTCGGCCAAAATTTTGCAAAAACTATCCCGAAAAATT
127 CA-AAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATT
* * * * * *
1182 TTTCCTCAATTTTTGGCCACAAAACTTATAAAATATATGTAACTCGACGCCAATAAAATTTAATG
191 TTTCCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGG
* *
1247 GCTTTTCAGGCTTCTAATT-TTTCCTATTTTTTCGAATTAATTTCTAATTAAATCGAAACAAAAT
256 GCTTTTCAGGCTTCTAATTATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAAT
1311 TCAGATG
321 TCAGATG
*
1318 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATCTTTTA
1 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTTA
** * * * *
1383 AGGAGTTTTGGTGCCAAGAATCATCCAAAACTGTGTCGGGGCCCAGGAACGCGTTTTTAGCCAAA
66 AGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAGCCAAA
* * * * *
1448 AACTATGATGGTTAGTACACTATTTCGGCCAAAATTTAGCGAAAACTGTCCCGAAAATTTTTTCC
131 AACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCC
* * * ***
1513 TCAATTTTTGGCTACAATACTCGTAAAAAATATTTAACTCAACGCTTTTCAAAATTTAAGGGCTT
196 TCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAAT-AAAATTTAAGGGCTT
* *
1578 TTCAGGCTTCTAA--A-AT-C-ATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTTAG
260 TTCAGGCTTCTAATTATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTCAG
1638 ATG
325 ATG
*
1641 CTCGTAAAATCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTTA
1 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTTA
* ** * * * *
1706 AGGAGTCTTGAAGCCAAAACTCATGCAAAACTGTGCCGGGGCACAAGAACGCGTTTTTAACCAAA
66 AGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAGCCAAA
** * * * * *
1771 AACTACGATAGTTAGTACTCGATTTGGGCCAAAATTTTGAAAAAACTGTCCCGAAAAAATTTTCC
131 AACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCC
* *
1836 TCAATTTGTGACCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCTTT
196 TCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCTTT
* * *
1901 TCAGGCTTCTAA--A-AT-C-ATTTTTCCTAATTAATTTCTAATTAAATCGAAACATAATTTAGA
261 TCAGGCTTCTAATTATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTCAGA
1961 TG
326 TG
*
1963 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAAATGAAAATAGATATTTTA
1 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTTA
* * *
2028 AGGAGACTTGCTGCC-AAAATCATGCAAAACTATGCCGGGGCCCAAGAACACGTTTTTAGCCAAA
66 AGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAGCCAAA
* * ** * *
2092 AACTGTGATGGTTTAGTACATGATTTCAGCCAAAATTTTGTTAAAACTGTCCTGAAAAATTATTC
131 AACTGTGATGG-TTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTC
* * * * ** * * *
2157 CTCAATTTTTCGCCACAACACTCAAAAAAAATATATAATTCAAATCCTAA-AAGACTGAAGGGCT
195 CTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCC-AATAAAATTTAAGGGCT
** * * * *
2221 TTAGATGCTTC-AATTTTCGTATTTCCTATTTTTTTCCTAATTATTTTCGAATTAAATCGAAACA
259 TTTCAGGCTTCTAA---T--TATTTCCTA--TTTTTCCGAATTAATTTCTAATTAAATCGAAACA
*
2285 TGATTCAGATG
317 TAATTCAGATG
* * * * * * ** *
2296 CTCGTAAAAAC-AATTCCTTCAATCCAATGTGGCTGAGAATTGGTTAGATGAGTATAGATATTTC
1 CTCGTAAAACCTTA-TCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTT
* * * * *
2360 AATGACACTTGGC-GACAAAAATCATGCAAAACTGTGACGGGGCCTAAGAACGCGTTTTTAGCCA
65 AAGGAGACTT-GCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAGCCA
** * * * *
2424 AAAACTGTGATATTTAGTACACGATTTGGGACAAAATTTTGCAAAAACTGTCGCG-AAAAGTTTT
129 AAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTT
*
2488 CCTCAATTTGTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGG-T
194 CCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCT
* *
2552 CTTTCAGGCATCTAA-TA--T-C-ATTTTTCCGAATTAATTTCTAATTAAATCGAAATATAATTC
259 -TTTCAGGCTTCTAATTATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTC
2612 AGATG
323 AGATG
* * * * * *
2617 CTCGTAAAGA-ATTATTCTTAAATCCTTTGTGGT-TGAGATTTGGTTAGATGAATACAAATATTT
1 CTCGTAAA-ACCTTATCCTTAAATCCATTGT-GTCTGAGATTTGGTTAGATGAAAATAGATATTT
* * ** * *
2680 TAAGGAGTCTTGCTGCCAAAAATCATGCAAATCTAAGTCGGGCCCCCAGAACGCGAGTTTTTAGC
64 TAAGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGC--GTTTTTAGC
* * * *
2745 AAAAAACAGTGATGGTTAGTACACGATTTCGGCCAAAATTTTACAAAAACTATCCCGAAAAATTT
127 CAAAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTT
* * * *
2810 TTCCTCAATTTTTGGCCACAATACTTATAAAAAATATGTAATTCAACGCCAATAAAATTTAATGG
192 TTCCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGG
2875 CTTTTCAGGCTTCTAATATAATTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAT
257 CTTTTCAGGCTTCTAAT-T-A--TTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAT
*
2940 AATTTAGATG
318 AATTCAGATG
* * *
2950 CTCGTAAAACCTTATCCTTAAATCGATTGTGTCTGAGATTTGGTTAGATGAAAATTGATCTTTTA
1 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTTA
* *
3015 AGGAGACTTGCTGCCAAGAATCATCCAAAACTGTGTCGGGGCCC-AGAAACGCGTTTTTAGCCAA
66 AGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAG-AACGCGTTTTTAGCCAA
* * * * *
3079 AAACTGTGATAGTTAGTACACTATTTCGGCAAAAATTTAGCGAAAACTGTCCC-AAAAATTTTTC
130 AAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTC
*
3143 CTCAATTTTTTGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCTT
195 CTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCTT
* * *
3208 TTCATGCTTCTAA--A-AT-C-ATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTTAG
260 TTCAGGCTTCTAATTATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTCAG
3268 ATG
325 ATG
*
3271 CTCGTAAAACCTTATCCTTAAATGCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTTA
1 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTTA
* *
3336 AGGAGTCTTGCTGCCAAAAATCATGCAAAACTGTGCCGGGGCCCAAGAACGCGTTTTTAGCCAAA
66 AGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAGCCAAA
*
3401 AAC-----T-G-T-G-ACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAAATTTTCC
131 AACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCC
** * *
3457 TCAA-TTTTGGTTACAATACTCAT-AAAAATATGTAACTTAACGCCAATAAAATTTAAGGGCTTT
196 TCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCTTT
* *
3520 TCAGGCTTCTAA--A-AT-C-ATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTTAGA
261 TCAGGCTTCTAATTATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTCAGA
3580 TG
326 TG
*
3582 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATTGATATTTTA
1 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTTA
* *
3647 AGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGCCGGGGCCCAAGAACGCATTTTTAGCCAAA
66 AGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAGCCAAA
* * * ** *
3712 AACTGTGATGGTTAGTACATGATTTCAGTCAAAATTTTGTTAAAACTGTCCTGAAAAATTTTTCC
131 AACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCC
* * * ** * * * *
3777 TCAATTTTTGGCGACAACACTCATAAAAAATATATAATTCAAATCCTAA-AAGACTGAAGGGCTA
196 TCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCC-AATAAAATTTAAGGGCTT
** * * * *
3841 TAGATGCTTC-AATTTTCGTATTTCCTATTTTTTTCCTAATTATTTTCGAATTAAATCGAAACAT
260 TTCAGGCTTCTAA---T--TATTTCCTA--TTTTTCCGAATTAATTTCTAATTAAATCGAAACAT
*
3905 TATTCAGATG
318 AATTCAGATG
* * * * * * * ** *
3915 CTCGTAAAAAC-AATTCCTTCAATCCAATGTGGCTAAGAATTGGTTAGATGAGTATAGATATTTC
1 CTCGTAAAACCTTA-TCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTT
* * * * * *
3979 AATGACACTTGGC-GACAAAAATCATGCAAAACTGTGACGAGGCCTAAGAACGCGTTTTTAGCCA
65 AAGGAGACTT-GCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAGCCA
* *
4043 AAAACTGTGATGCTTAGTACACGATTT-GAGCCAAAATTTTGCAAAAACTGTCCCGAAAAGTTTT
129 AAAACTGTGATGGTTAGTACACGATTTCG-GCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTT
*
4107 TCCTCAATTTGTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGC
193 TCCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGC
*
4172 TTTTCAGGCTTCTAATATAATTTTCCTATTTTTTCGAATTAATTTCTAATTAAATCGAAACATAA
258 TTTTCAGGCTTCTAAT-T-A-TTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAA
4237 TTCAGATG
320 TTCAGATG
**
4245 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATG-AAATAGACCTTTTA
1 CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTTA
* * * *
4309 AGGAGTCTTGCTGCCAAAAATCATCCAAAACTGTGTTGGGGCCCAGGAACGCGTTTTTAGCCAAA
66 AGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAGCCAAA
* * * *
4374 AACTGTGATGGTTAGTACACTATTTCAGCCAAAATTTAGCGAAAACTGTCCCG-AAAA--TTTCC
131 AACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCC
* * ** * * *
4436 TCAATTTTTGGCCACAACACTCATAAAAAATATATAATTCAAATCCAA-AAAGACTGATGGGCTT
196 TCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAA-ATTTAAGGGCTT
** * * * *
4500 TAGATGCTTC-AATTTTCGTTTTTCCTATTGTTTTCCTAATTAATTTCTAATTAAATCGAACCAT
260 TTCAGGCTTCTAA---T--TATTTCCTA-T-TTTTCCGAATTAATTTCTAATTAAATCGAAACAT
* *
4564 GATTGAGATG
318 AATTCAGATG
* ** * * *
4574 CTCGTAAAAACAAATCCTTCAATCCAATGTAGT-TGAG-TATTGGTTAGATGAATATAGATATTT
1 CTCGTAAAACCTTATCCTTAAATCCATTGT-GTCTGAGAT-TTGGTTAGATGAAAATAGATATTT
4637 CAATGAAACT
Statistics
Matches: 3666, Mismatches: 517, Indels: 242
0.83 0.12 0.05
Matches are distributed among these distances:
311 228 0.06
312 48 0.01
313 16 0.00
314 1 0.00
315 1 0.00
316 2 0.00
317 1 0.00
318 1 0.00
319 1 0.00
320 51 0.01
321 477 0.13
322 305 0.08
323 330 0.09
324 83 0.02
325 144 0.04
326 172 0.05
327 40 0.01
328 20 0.01
329 329 0.09
330 190 0.05
331 186 0.05
332 216 0.06
333 665 0.18
334 159 0.04
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (327 bp):
CTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTTTA
AGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAGCCAAA
AACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCC
TCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCTTT
TCAGGCTTCTAATTATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTCAGA
TG
Found at i:2656 original size:654 final size:650
Alignment explanation
Indices: 1--4636 Score: 5204
Period size: 654 Copynumber: 7.1 Consensus size: 650
* * *
1 CTCGTAAAAAATTATTCTTAAATCCATTGTGGCTGAGATTTGGTTTGATGAATATAAATATTTTA
1 CTCGT-AAAAATTATTCTTAAATCCATTGTGGTTGAGATTTGGTTAGATGAATATAGATATTTTA
* ** * * * *
66 AGGAGTCTTGCTGCCAAAAATCAAGCAAAACTAAGTCGGGGCCCCCAGAATGCGAGTTTTTAGCA
65 AGGAGTCTTGCTGCCAAAAATCATGCAAAACTGTGCCGGGG-CCCAAGAA--CGCGTTTTTAGCC
** * *
131 AAAAAGAGTGATGGTTTGTACACGATTTCGGCCAAAATTTTGCAAAAACTATCCCGAAAAATTTT
127 AAAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTT
* * ** *
196 TCCTCAATTTTTGGCCACAGA-ACTTATAAAAAATATGTAACTCAATACCAATAAAATTTAATGG
192 TCCTCAATTTTTGGCCACA-ATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGG
* * *
260 CTTTTCAGGCTTCTAATATAATTTTTCCTATTTTTTCGAATTAATTTCTAATTAAATCGAAACAA
256 CTTTTCAGGCTTCTAAT-T--TATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAT
* *
325 AATTCAGATGCTCGTAAAACCTTATACTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAAT
318 AATTTAGATGCTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAAT
* * * * *
390 AGATCTTTTAAGGAGTCTTGGTGCCAAAAATCATCCAAAACTGTGTCGGGGCCCAGGAACGCGTT
383 AGATATTTTAAGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTT
* * * * * * *
455 TTTAGCAAAAAACTGTGATGGTCAGTACACTATTTCGACCAAAATTTAGCGAAAACTGTCCCAAA
448 TTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAA
* * * * **
520 AGATTGTTCCTCAATTTATGGCCACAACACTCATAAAAAATATAAAATTCAA-ATCAA-AAAAGT
513 A-ATTTTTCCTCAATTTTTGGCCACAACACTCATAAAAAATATATAACTCAACGCCAATAAAA-T
* * ** * * *
583 CTGAAGGCCTTTAGATGCTTCAATTTTCGT-ATTTCCTATTTTTTTCCTAATTAATTTCTAATTA
576 -TTAAGGGCTTTTCA-G--GC-A---TC-TAATATCCTA--TTTTTCCGAATTAATTTCTAATTA
*
647 AATCGAAACATGATTCAGATG
630 AATCGAAACATAATTCAGATG
** * * * ** * * *
668 CTCGTAAAAACAATTCCTTCAATCCAATGTGGCTGAGAACTGGTTAGATTAGTTTAGATATTTTA
1 CTCGTAAAAATTATT-CTTAAATCCATTGTGGTTGAGATTTGGTTAGATGAATATAGATATTTTA
* ** * *
733 ATGACACTTGGC-GCCAAAAATCATGC-AAACTGTGCCGGGGCACAAGAACGCGTTTTTAGCGAA
65 AGGAGTCTT-GCTGCCAAAAATCATGCAAAACTGTGCCGGGGCCCAAGAACGCGTTTTTAGCCAA
* * * * **
796 AAACCGTGATAGTTAGTACACGATTTGGGCCAAAATTTTGAAAAAACTGTCGTGAAAAATTTTTC
129 AAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTC
* *
861 CTCAATTTGTGACCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCTT
194 CTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCTT
* *
926 TTCAGGCTTCTAA---A-AT-C-ATTTTTCAGAATTAATTTCTAATTAAATCGAAACATAATTTA
259 TTCAGGCTTCTAATTTATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTTA
* *
985 GATGCTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAAATTTGGTTAGATTAAAATAGATAT
324 GATGCTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATAT
* ** * *
1050 TTTAAGGA-ATCTTGCTGTCAAAAATCATGCAAAACTAAGTCGGGCCCCCCAGAACGCGAGTTTT
389 TTTAAGGAGA-CTTGCTGCCAAAAATCATGCAAAACTGTGTCGGG-GCCCAAGAACGC--GTTTT
** * *
1114 TAG-CATAAAAGAGTGATGGTTAGTACACGTTTTCGGCCAAAATTTTGCAAAAACTATCCCGAAA
450 TAGCCA-AAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCG-AA
* * * * *
1178 AATTTTTCCTCAATTTTTGGCCACAAAACTTATAAAATATATGTAACTCGACGCCAATAAAATTT
513 AATTTTTCCTCAATTTTTGGCCACAACACTCATAAAAAATATATAACTCAACGCCAATAAAATTT
* * * * *
1243 AATGGCTTTTCAGGCTTCTAATTTTTCCTATTTTTTCGAATTAATTTCTAATTAAATCGAAACAA
578 AAGGGCTTTTCAGGCATCTAA--TATCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAT
1308 AATTCAGATG
641 AATTCAGATG
* * * *
1318 CTCGTAAAACCTTATCCTTAAATCCATTGT-GTCTGAGATTTGGTTAGATGAAAATAGATCTTTT
1 CTCGTAAAA-ATTATTCTTAAATCCATTGTGGT-TGAGATTTGGTTAGATGAATATAGATATTTT
* * * * * *
1382 AAGGAGTTTTGGTGCCAAGAATCATCCAAAACTGTGTCGGGGCCCAGGAACGCGTTTTTAGCCAA
64 AAGGAGTCTTGCTGCCAAAAATCATGCAAAACTGTGCCGGGGCCCAAGAACGCGTTTTTAGCCAA
* * * * *
1447 AAACTATGATGGTTAGTACACTATTTCGGCCAAAATTTAGCGAAAACTGTCCCGAAAATTTTTTC
129 AAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTC
* * * ***
1512 CTCAATTTTTGGCTACAATACTCGTAAAAAATATTTAACTCAACGCTTTTCAAAATTTAAGGGCT
194 CTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAAT-AAAATTTAAGGGCT
*
1577 TTTCAGGCTTCTAA---A-AT-C-ATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTT
258 TTTCAGGCTTCTAATTTATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTT
*
1636 AGATGCTCGTAAAATCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATA
323 AGATGCTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATA
* ** * * * *
1701 TTTTAAGGAGTCTTGAAGCCAAAACTCATGCAAAACTGTGCCGGGGCACAAGAACGCGTTTTTAA
388 TTTTAAGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAG
** * * * * *
1766 CCAAAAACTACGATAGTTAGTACTCGATTTGGGCCAAAATTTTGAAAAAACTGTCCCGAAAAAAT
453 CCAAAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCG-AAAATT
* * *
1831 TTTCCTCAATTTGTGACCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGG
517 TTTCCTCAATTTTTGGCCACAACACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGG
* * * *
1896 GCTTTTCAGGCTTCTAAAAT-C-ATTTTTCCTAATTAATTTCTAATTAAATCGAAACATAATTTA
582 GCTTTTCAGGCATCTAATATCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTCA
1959 GATG
647 GATG
* * * *
1963 CTCGTAAAACCTTATCCTTAAATCCATTGT-GTCTGAGATTTGGTTAAATGAAAATAGATATTTT
1 CTCGTAAAA-ATTATTCTTAAATCCATTGTGGT-TGAGATTTGGTTAGATGAATATAGATATTTT
* * *
2027 AAGGAGACTTGCTGCC-AAAATCATGCAAAACTATGCCGGGGCCCAAGAACACGTTTTTAGCCAA
64 AAGGAGTCTTGCTGCCAAAAATCATGCAAAACTGTGCCGGGGCCCAAGAACGCGTTTTTAGCCAA
* * ** * *
2091 AAACTGTGATGGTTTAGTACATGATTTCAGCCAAAATTTTGTTAAAACTGTCCTGAAAAATTATT
129 AAACTGTGATGG-TTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTT
* * * * ** * * *
2156 CCTCAATTTTTCGCCACAACACTCAAAAAAAATATATAATTCAAATCCTAA-AAGACTGAAGGGC
193 CCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCC-AATAAAATTTAAGGGC
** * * * *
2220 TTTAGATGCTTC-AATTTTCGTATTTCCTATTTTTTTCCTAATTATTTTCGAATTAAATCGAAAC
257 TTTTCAGGCTTCTAA--TT--TATTTCCTA--TTTTTCCGAATTAATTTCTAATTAAATCGAAAC
* * * * * * * * *
2284 ATGATTCAGATGCTCGTAAAAAC-AATTCCTTCAATCCAATGTGGCTGAGAATTGGTTAGATGAG
316 ATAATTTAGATGCTCGTAAAACCTTA-TCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAA
* * * * * * *
2348 TATAGATATTTCAATGACACTTGGC-GACAAAAATCATGCAAAACTGTGACGGGGCCTAAGAACG
380 AATAGATATTTTAAGGAGACTT-GCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACG
** * * *
2412 CGTTTTTAGCCAAAAACTGTGATATTTAGTACACGATTTGGGACAAAATTTTGCAAAAACTGTCG
444 CGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCC
* * *
2477 CGAAAAGTTTTCCTCAATTTGTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAA
509 CGAAAATTTTTCCTCAATTTTTGGCCACAACACTCATAAAAAATATATAACTCAACGCCAATAAA
2542 ATTTAAGGG-TCTTTCAGGCATCTAATAT-C-ATTTTTCCGAATTAATTTCTAATTAAATCGAAA
574 ATTTAAGGGCT-TTTCAGGCATCTAATATCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAA
*
2604 TATAATTCAGATG
638 CATAATTCAGATG
* * *
2617 CTCGTAAAGAATTATTCTTAAATCCTTTGTGGTTGAGATTTGGTTAGATGAATACAAATATTTTA
1 CTCGTAAA-AATTATTCTTAAATCCATTGTGGTTGAGATTTGGTTAGATGAATATAGATATTTTA
* ** * * * *
2682 AGGAGTCTTGCTGCCAAAAATCATGCAAATCTAAGTCGGGCCCCCAGAACGCGAGTTTTTAGCAA
65 AGGAGTCTTGCTGCCAAAAATCATGCAAAACTGTGCCGGGGCCCAAGAACGC--GTTTTTAGCCA
* * *
2747 AAAACAGTGATGGTTAGTACACGATTTCGGCCAAAATTTTACAAAAACTATCCCGAAAAATTTTT
128 AAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTT
* * * *
2812 CCTCAATTTTTGGCCACAATACTTATAAAAAATATGTAATTCAACGCCAATAAAATTTAATGGCT
193 CCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCT
*
2877 TTTCAGGCTTCTAATATAATTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAA
258 TTTCAGGCTTCTAAT-T--TATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAA
* *
2942 TTTAGATGCTCGTAAAACCTTATCCTTAAATCGATTGTGTCTGAGATTTGGTTAGATGAAAATTG
320 TTTAGATGCTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAG
* * *
3007 ATCTTTTAAGGAGACTTGCTGCCAAGAATCATCCAAAACTGTGTCGGGGCCC-AGAAACGCGTTT
385 ATATTTTAAGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAG-AACGCGTTT
* * * * * *
3071 TTAGCCAAAAACTGTGATAGTTAGTACACTATTTCGGCAAAAATTTAGCGAAAACTGTCCCAAAA
449 TTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAA
* *
3136 ATTTTTCCTCAATTTTTTGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTA
514 ATTTTTCCTCAATTTTTGGCCACAACACTCATAAAAAATATATAACTCAACGCCAATAAAATTTA
* * *
3201 AGGGCTTTTCATGCTTCTAAAAT-C-ATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAAT
579 AGGGCTTTTCAGGCATCTAATATCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAAT
*
3264 TTAGATG
644 TCAGATG
* * * *
3271 CTCGTAAAACCTTATCCTTAAATGCATTGT-GTCTGAGATTTGGTTAGATGAAAATAGATATTTT
1 CTCGTAAAA-ATTATTCTTAAATCCATTGTGGT-TGAGATTTGGTTAGATGAATATAGATATTTT
3335 AAGGAGTCTTGCTGCCAAAAATCATGCAAAACTGTGCCGGGGCCCAAGAACGCGTTTTTAGCCAA
64 AAGGAGTCTTGCTGCCAAAAATCATGCAAAACTGTGCCGGGGCCCAAGAACGCGTTTTTAGCCAA
*
3400 AAAC-----T-G-T-G-ACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAAATTTTC
129 AAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTC
** * *
3456 CTCAA-TTTTGGTTACAATACTCAT-AAAAATATGTAACTTAACGCCAATAAAATTTAAGGGCTT
194 CTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCTT
*
3519 TTCAGGCTTCTAA---A-AT-C-ATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTTA
259 TTCAGGCTTCTAATTTATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTTA
*
3578 GATGCTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATTGATAT
324 GATGCTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATAT
* *
3643 TTTAAGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGCCGGGGCCCAAGAACGCATTTTTAGC
389 TTTAAGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAGC
* * * ** *
3708 CAAAAACTGTGATGGTTAGTACATGATTTCAGTCAAAATTTTGTTAAAACTGTCCTGAAAAATTT
454 CAAAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCG-AAAATTT
* * ** * * *
3773 TTCCTCAATTTTTGGCGACAACACTCATAAAAAATATATAATTCAAATCCTAA-AAGACTGAAGG
518 TTCCTCAATTTTTGGCCACAACACTCATAAAAAATATATAACTCAACGCC-AATAAAATTTAAGG
**** * * * *
3837 GCTATAGATGCTTCAATTTTCGT-ATTTCCTATTTTTTTCCTAATTATTTTCGAATTAAATCGAA
582 GC--T---T--TTCAGGCATC-TAATATCCTA--TTTTTCCGAATTAATTTCTAATTAAATCGAA
*
3901 ACATTATTCAGATG
637 ACATAATTCAGATG
** * * * * * * *
3915 CTCGTAAAAACAATTCCTTCAATCCAATGTGGCTAAGAATTGGTTAGATGAGTATAGATATTTCA
1 CTCGTAAAAATTATT-CTTAAATCCATTGTGGTTGAGATTTGGTTAGATGAATATAGATATTTTA
* ** * * * *
3980 ATGACACTTGGC-GACAAAAATCATGCAAAACTGTGACGAGGCCTAAGAACGCGTTTTTAGCCAA
65 AGGAGTCTT-GCTGCCAAAAATCATGCAAAACTGTGCCGGGGCCCAAGAACGCGTTTTTAGCCAA
* *
4044 AAACTGTGATGCTTAGTACACGATTT-GAGCCAAAATTTTGCAAAAACTGTCCCGAAAAGTTTTT
129 AAACTGTGATGGTTAGTACACGATTTCG-GCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTT
*
4108 CCTCAATTTGTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCT
193 CCTCAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCT
* *
4173 TTTCAGGCTTCTAATATAATTTTCCTATTTTTTCGAATTAATTTCTAATTAAATCGAAACATAAT
258 TTTCAGGCTTCTAAT-TTA-TTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAAT
*
4238 TCAGATGCTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATG-AAATAGA
321 TTAGATGCTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGA
** * * * *
4302 CCTTTTAAGGAGTCTTGCTGCCAAAAATCATCCAAAACTGTGTTGGGGCCCAGGAACGCGTTTTT
386 TATTTTAAGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTT
* * * *
4367 AGCCAAAAACTGTGATGGTTAGTACACTATTTCAGCCAAAATTTAGCGAAAACTGTCCCGAAAA-
451 AGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAT
* ** * * *
4431 -TTTCCTCAATTTTTGGCCACAACACTCATAAAAAATATATAATTCAAATCCAA-AAAGACTGAT
516 TTTTCCTCAATTTTTGGCCACAACACTCATAAAAAATATATAACTCAACGCCAATAAA-ATTTAA
** * * * *
4494 GGGCTTTAGATGCTTCAATTTTCGT-TTTTCCTATTGTTTTCCTAATTAATTTCTAATTAAATCG
580 GGGCTTTTCA-G--GC-A---TC-TAATATCCTA-T-TTTTCCGAATTAATTTCTAATTAAATCG
* * *
4558 AACCATGATTGAGATG
635 AAACATAATTCAGATG
** * * * *
4574 CTCGTAAAAACAAATCCTTCAATCCAATGTAGTTGAG-TATTGGTTAGATGAATATAGATATTT
1 CTCGTAAAAA-TTATTCTTAAATCCATTGTGGTTGAGAT-TTGGTTAGATGAATATAGATATTT
4637 CAATGAAACT
Statistics
Matches: 3404, Mismatches: 464, Indels: 210
0.83 0.11 0.05
Matches are distributed among these distances:
632 209 0.06
633 64 0.02
634 3 0.00
635 1 0.00
638 1 0.00
640 9 0.00
641 51 0.01
642 17 0.00
643 54 0.02
644 218 0.06
645 202 0.06
646 2 0.00
647 2 0.00
649 136 0.04
650 110 0.03
651 142 0.04
652 197 0.06
653 58 0.02
654 765 0.22
655 292 0.09
656 116 0.03
657 128 0.04
658 13 0.00
659 165 0.05
660 3 0.00
661 5 0.00
662 118 0.03
663 232 0.07
665 6 0.00
666 19 0.01
667 64 0.02
668 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (650 bp):
CTCGTAAAAATTATTCTTAAATCCATTGTGGTTGAGATTTGGTTAGATGAATATAGATATTTTAA
GGAGTCTTGCTGCCAAAAATCATGCAAAACTGTGCCGGGGCCCAAGAACGCGTTTTTAGCCAAAA
ACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCT
CAATTTTTGGCCACAATACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCTTTT
CAGGCTTCTAATTTATTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTTAGA
TGCTCGTAAAACCTTATCCTTAAATCCATTGTGTCTGAGATTTGGTTAGATGAAAATAGATATTT
TAAGGAGACTTGCTGCCAAAAATCATGCAAAACTGTGTCGGGGCCCAAGAACGCGTTTTTAGCCA
AAAACTGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGCAAAAACTGTCCCGAAAATTTTTC
CTCAATTTTTGGCCACAACACTCATAAAAAATATATAACTCAACGCCAATAAAATTTAAGGGCTT
TTCAGGCATCTAATATCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATAATTCAGATG
Found at i:5959 original size:345 final size:345
Alignment explanation
Indices: 5321--5965 Score: 755
Period size: 345 Copynumber: 1.9 Consensus size: 345
5311 AAAATTCTGC
* * * * * ** *
5321 AAACTGACCCGAAAAATTTTTTCTCAATTTTTGGCCACAATTGTCATAAAAAGTATATAATTCAA
1 AAACTGACACGAAAAATTCTTCCTCAATTTTTGGACAAAATACTCATAAAAAATATATAATTCAA
* * * * * * * * *
5386 TGATAGAAAGATTGAAGGGTTTTTCACGTTTCTAATATTGTTTTTCATATTTTTTCCAGATTTAT
66 TCAGAGAAAGATTGAAAGGCTTTTCACGCTACTAATATCGTTTTTCATATTTTTTCCAAATTAAT
* ** * * * * * *
5451 TTCTGATTAAATCGAAAACTGATTCTGATGCTCATAATAACAAATCCTTGAATCCAATTTGGCTA
131 TTCTAAAAAAATCGAAAACAGATTCTGATGCTCATAAAAACAAATCCTTAAAACCAATGTGACTA
* * ** *
5516 TGATTTGGTTAAAAGAATATAGATAATTCCAAGAGTTTTGACGGCAAAAATCAAGCAAAACTGGG
196 TGATTTGGTTAAAAGAATATAGATAATTCCAAGAATCTTGACACCAAAAATCAAGCAAAACTGAG
*
5581 TCGGGGCCCAGGAACGCGATTTTAGCCAAAAACCGTGATGGTTTTTAATTCATCATAGTACACGA
261 CCGGGGCCCAGGAACGCGATTTTAGCCAAAAACCGTGATGGTTTTTAATTCATCATAGTACACGA
5646 TTTCGACAAAAATTTAGCAA
326 TTTCGACAAAAATTTAGCAA
* *
5666 AAACTGACACGAAAAATTCTTCCTCAATTTTTGGATAAAATACTCGTAAAAAATATATAATTCAA
1 AAACTGACACGAAAAATTCTTCCTCAATTTTTGGACAAAATACTCATAAAAAATATATAATTCAA
* *
5731 CTCCGA-AAATATTGAAAGGCTTTTCACGCTACTAATATCGTTTTTGC-TATTTTTTTCCAAATT
66 -TCAGAGAAAGATTGAAAGGCTTTTCACGCTACTAATATCGTTTTT-CATA-TTTTTTCCAAATT
*
5794 AATTTCTAAAAAAATC-AAAACAAGATTCTGATGCT-AGTAAAAACAAATTCTTAAAACCAATGT
128 AATTTCTAAAAAAATCGAAAAC-AGATTCTGATGCTCA-TAAAAACAAATCCTTAAAACCAATGT
* * * * * *
5857 GACTGAT-ATTTGGTTAGATGAATATAGAT-ATTTCAAGAATCCTTGGCACCAAAAATTATGCAA
191 GACT-ATGATTTGGTTAAAAGAATATAGATAATTCCAAGAAT-CTTGACACCAAAAATCAAGCAA
* * * *
5920 AACTGAGCCGGGGCCCCGGAACTC-CTTTTAGGCAAAAACCGTGATG
254 AACTGAGCCGGGGCCCAGGAACGCGATTTTAGCCAAAAACCGTGATG
5966 AATTCTTTGT
Statistics
Matches: 246, Mismatches: 47, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
345 125 0.51
346 119 0.48
347 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (345 bp):
AAACTGACACGAAAAATTCTTCCTCAATTTTTGGACAAAATACTCATAAAAAATATATAATTCAA
TCAGAGAAAGATTGAAAGGCTTTTCACGCTACTAATATCGTTTTTCATATTTTTTCCAAATTAAT
TTCTAAAAAAATCGAAAACAGATTCTGATGCTCATAAAAACAAATCCTTAAAACCAATGTGACTA
TGATTTGGTTAAAAGAATATAGATAATTCCAAGAATCTTGACACCAAAAATCAAGCAAAACTGAG
CCGGGGCCCAGGAACGCGATTTTAGCCAAAAACCGTGATGGTTTTTAATTCATCATAGTACACGA
TTTCGACAAAAATTTAGCAA
Found at i:6598 original size:236 final size:235
Alignment explanation
Indices: 6174--6619 Score: 569
Period size: 236 Copynumber: 1.9 Consensus size: 235
6164 AGTGGGCTGG
* ** *
6174 GATTTTGTTAGATGAATATAGATATTTCAAGGAGTTTTGGCGCCAAAAATCATGCAAAACTGAGT
1 GATTTGGTTAGATGAATATAGATATTTCAAAAAGTCTTGGCGCCAAAAATCATGCAAAACTGAGT
* *
6239 CAAAGCCCAAAAACGCATTTTTAGCCAAAAACTGTGATGTTCACTATACGATTTTGGCTAAAATT
66 CAAAGCCCAAAAACG-ATTTTTAGCCAAAAACTGTGATGTTCACTACACGATTTCGGCTAAAATT
*
6304 TAGAAAAAACTGACCCGAAAAAATCTTCCTCAATTTTTAGCCACAATTCTCATAAAAAATACATA
130 TAGAAAAAACTGACCCGAAAAAATCTTCATCAATTTTTAGCCACAATTCTCATAAAAAATACATA
* *
6369 ATTTAACGCCAAAAACAAATCCTTTCATCCAATGTGACTGA
195 ATTCAACCCCAAAAACAAATCCTTTCATCCAATGTGACTGA
6410 GATTTGGTTAGATGAATATAGATATTTCAAAAAGTCTTGGCGCCAAAAATCATGCAAAACTGAGT
1 GATTTGGTTAGATGAATATAGATATTTCAAAAAGTCTTGGCGCCAAAAATCATGCAAAACTGAGT
*** * * *
6475 CGGGGCCTCGGAACACG-TTTTTAGCCAAAAACTGTGATGGTT-AGTACACGATTTCGG-TAAAA
66 CAAAGCC-C-AAAAACGATTTTTAGCCAAAAACTGTGAT-GTTCACTACACGATTTCGGCTAAAA
* * ** * * * * *
6537 GTTTAGCAAAAATTTTCCCGAAAGATTTTTCATCAATTTTTGGCCA-ATATAT-TCGTAAAAAAT
128 -TTTAGAAAAAACTGACCCGAAAAAATCTTCATCAATTTTTAGCCACA-AT-TCTCATAAAAAAT
*
6600 ATATAATTCAACCCCAAAAA
190 ACATAATTCAACCCCAAAAA
6620 TATTGAAGGG
Statistics
Matches: 179, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
235 6 0.03
236 163 0.91
237 5 0.03
238 5 0.03
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (235 bp):
GATTTGGTTAGATGAATATAGATATTTCAAAAAGTCTTGGCGCCAAAAATCATGCAAAACTGAGT
CAAAGCCCAAAAACGATTTTTAGCCAAAAACTGTGATGTTCACTACACGATTTCGGCTAAAATTT
AGAAAAAACTGACCCGAAAAAATCTTCATCAATTTTTAGCCACAATTCTCATAAAAAATACATAA
TTCAACCCCAAAAACAAATCCTTTCATCCAATGTGACTGA
Found at i:10293 original size:26 final size:26
Alignment explanation
Indices: 10268--10316 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
10258 TTAATGTTTA
10268 AATT-TTATTTT-TTATTAAAAAATTT
1 AATTATTATTTTATT-TTAAAAAATTT
10293 AATTATTATTTTATTTTAAAAAAT
1 AATTATTATTTTATTTTAAAAAAT
10317 AAATATGGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.18
26 16 0.73
27 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AATTATTATTTTATTTTAAAAAATTT
Found at i:14329 original size:2 final size:2
Alignment explanation
Indices: 14322--14351 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14312 TTAAAGGTAA
14322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14352 TAATTAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33055 original size:19 final size:20
Alignment explanation
Indices: 33025--33088 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
33015 TTGACACTGT
33025 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
*
33046 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATGAGA
*
33065 TTAAGTACTGTACAGATGAGA
1 TT-AGCACTGTACAGATGAGA
33086 TTA
1 TTA
33089 TTAGAGCAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 16 0.42
20 3 0.08
21 19 0.50
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:44050 original size:27 final size:27
Alignment explanation
Indices: 44012--44067 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
44002 ACTACTTGTC
*
44012 AGAAACTCGAATCTAATGTACGTAATG
1 AGAAACTCGAATCTAATGCACGTAATG
44039 AGAAACTCGAATCTAATGCACGTAATG
1 AGAAACTCGAATCTAATGCACGTAATG
44066 AG
1 AG
44068 GGCCATCCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (27 bp):
AGAAACTCGAATCTAATGCACGTAATG
Found at i:47192 original size:30 final size:30
Alignment explanation
Indices: 47156--47218 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
47146 TATTTACCTT
*
47156 CAAGCAACTTTCCAAAGGAGGCTCAAATAA
1 CAAGCAACTTTCCAAAAGAGGCTCAAATAA
47186 CAAGCAACTTTCCAAAAGAGGCTCAAATAA
1 CAAGCAACTTTCCAAAAGAGGCTCAAATAA
47216 CAA
1 CAA
47219 AAAAGCCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.46, C:0.24, G:0.14, T:0.16
Consensus pattern (30 bp):
CAAGCAACTTTCCAAAAGAGGCTCAAATAA
Found at i:48061 original size:3 final size:3
Alignment explanation
Indices: 48053--48126 Score: 132
Period size: 3 Copynumber: 25.0 Consensus size: 3
48043 CAAATAAATA
48053 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
48100 TTT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
48127 ACATAAAGGG
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 66 0.97
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:48627 original size:10 final size:10
Alignment explanation
Indices: 48612--48639 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
48602 ACGGACGTTA
48612 GTCACGTGCC
1 GTCACGTGCC
48622 GTCACGTGCC
1 GTCACGTGCC
48632 GTCACGTG
1 GTCACGTG
48640 ACTAACAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.36, G:0.32, T:0.21
Consensus pattern (10 bp):
GTCACGTGCC
Found at i:48933 original size:17 final size:16
Alignment explanation
Indices: 48913--48962 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
48903 CCAGATCACT
48913 AGTGATCTAAGATTACC
1 AGTGATC-AAGATTACC
*
48930 AGTGATGCAAGATCACC
1 AGTGAT-CAAGATTACC
*
48947 GGTGATCAAAGATTAC
1 AGTGATC-AAGATTAC
48963 ATGGGTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 1 0.04
17 26 0.93
18 1 0.04
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (16 bp):
AGTGATCAAGATTACC
Found at i:51066 original size:1 final size:1
Alignment explanation
Indices: 51060--51091 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
51050 GTTCTGGTGC
51060 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
51092 CTTGATATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:60134 original size:34 final size:35
Alignment explanation
Indices: 60083--60166 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 35
60073 CATCCAATCA
*
60083 ATTTAATC-CATAAACTCAAAAGATTGAGT-AGTTG
1 ATTTAATCAC-TAAACTCAAAAGATTGAGTCAATTG
* * *
60117 ATTTAATCACTATACTCACAGGATTGAGTCAATTG
1 ATTTAATCACTAAACTCAAAAGATTGAGTCAATTG
*
60152 AGTTCAATCACTAAA
1 A-TTTAATCACTAAA
60167 GCTACAATGA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
34 24 0.59
35 6 0.15
36 11 0.27
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.32
Consensus pattern (35 bp):
ATTTAATCACTAAACTCAAAAGATTGAGTCAATTG
Found at i:78812 original size:13 final size:13
Alignment explanation
Indices: 78794--78821 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
78784 CTGCTTCTGC
78794 TTTGGTTTTTGGT
1 TTTGGTTTTTGGT
78807 TTTGGTTTTTGGT
1 TTTGGTTTTTGGT
78820 TT
1 TT
78822 CACTTTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (13 bp):
TTTGGTTTTTGGT
Found at i:79890 original size:26 final size:26
Alignment explanation
Indices: 79843--79895 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
79833 AATAATTAAT
* **
79843 AGTATATAGTAATTTCTCAAAAAAAA
1 AGTATATAGTAATTACAAAAAAAAAA
79869 AGTATATAGTAATTACAAAAAAAAAA
1 AGTATATAGTAATTACAAAAAAAAAA
79895 A
1 A
79896 AAACAGAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (26 bp):
AGTATATAGTAATTACAAAAAAAAAA
Found at i:81378 original size:20 final size:20
Alignment explanation
Indices: 81353--81392 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
81343 GGGCATAACG
*
81353 TTTGCCAAAATGTTCAAATA
1 TTTGCCAAAATGCTCAAATA
81373 TTTGCCAAAATGCTCAAATA
1 TTTGCCAAAATGCTCAAATA
81393 AGGGTCTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (20 bp):
TTTGCCAAAATGCTCAAATA
Found at i:81517 original size:60 final size:60
Alignment explanation
Indices: 81435--81600 Score: 242
Period size: 60 Copynumber: 2.8 Consensus size: 60
81425 ATTTTCGATG
* * * * *
81435 CCAGGCCCTTATCTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTGAAAGA
1 CCAGACCCTTATTTGAGCATTTTGCCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAAA
* *
81495 TCAGACCCTTATTTGAGCATTTTGCCGAACGTTAGGCCCTTATTTGGCCAAATTCAAAAA
1 CCAGACCCTTATTTGAGCATTTTGCCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAAA
* * *
81555 CCGGGCCCTTATTTGAGCATTTTGCCAAACATTAGGCCCTTATTTG
1 CCAGACCCTTATTTGAGCATTTTGCCAAACGTTAGGCCCTTATTTG
81601 AGCAATTAGC
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 94 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (60 bp):
CCAGACCCTTATTTGAGCATTTTGCCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAAA
Found at i:81613 original size:31 final size:31
Alignment explanation
Indices: 81437--81613 Score: 132
Period size: 31 Copynumber: 5.8 Consensus size: 31
81427 TTTCGATGCC
* * * *
81437 AGGCCCTTATCTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCAATTTGCCAAACATT
* * *
81468 AGGCCCTTATTTG-GCCAAATTG--AAAGATC
1 AGGCCCTTATTTGAG-CAATTTGCCAAACATT
* * * *
81497 AGACCCTTATTTGAGCATTTTGCCGAACGTT
1 AGGCCCTTATTTGAGCAATTTGCCAAACATT
* * **
81528 AGGCCCTTATTTG-GCCAAATT--CAAAAACC
1 AGGCCCTTATTTGAG-CAATTTGCCAAACATT
* *
81557 GGGCCCTTATTTGAGCATTTTGCCAAACATT
1 AGGCCCTTATTTGAGCAATTTGCCAAACATT
*
81588 AGGCCCTTATTTGAGCAATTAGCCAA
1 AGGCCCTTATTTGAGCAATTTGCCAA
81614 GTGGATTGAA
Statistics
Matches: 108, Mismatches: 30, Indels: 16
0.70 0.19 0.10
Matches are distributed among these distances:
29 40 0.37
30 4 0.04
31 64 0.59
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCAATTTGCCAAACATT
Found at i:102023 original size:13 final size:13
Alignment explanation
Indices: 102005--102030 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
101995 AAACAACTGA
102005 AAAGCACTTCTGG
1 AAAGCACTTCTGG
102018 AAAGCACTTCTGG
1 AAAGCACTTCTGG
102031 GTTTTCCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
AAAGCACTTCTGG
Done.