Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012379.1 Corchorus capsularis cultivar CVL-1 contig12400, 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: 19405
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:654 original size:201 final size:201
Alignment explanation
Indices: 273--680 Score: 527
Period size: 201 Copynumber: 2.0 Consensus size: 201
263 TTTTTTGGCA
* * * ** *
273 GAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTTGATCTGAGGATTT
1 GAAAAACTCCTTGAAATATCTACATTTATCGAACCAAATCTCAGCCACATTAAATCTAAGGATTT
* *
338 GTTTTTACTAGCATCTAAATCTTGTTTCGATATAATTAAAAATAAATTCGGAAAAAATGGGAAAC
66 GTTTTTACGAGCATCTAAATCTTGTTTCGATATAATTAAAAATAAATTCGGAAAAAATGGAAAAC
* * * * *
403 CAATATTAGAAGCGTTTAAAATCCTTCAATTTCTTTGTGTTGATTTATATATTTTTCCTGAGTAT
131 CAATATTAGAAGCGATGAAAACCCTTCAATTTCTTTGTGTAGAATTATATATTTTTCCTGAGTAT
*
468 TTTGGT
196 TGTGGT
* * ** * *
474 TAAAAACTCCTTGAAATATCTACATTCT-TGGAACCAAATCTCAGCTGCATTAAATTTAATGATT
1 GAAAAACTCCTTGAAATATCTACATT-TATCGAACCAAATCTCAGCCACATTAAATCTAAGGATT
* *
538 TGTTTTTACGAGCATCTAAATCTTGTTTCGATATAATTAGAAATACATTCGGAAAAAATGGAAAA
65 TGTTTTTACGAGCATCTAAATCTTGTTTCGATATAATTAAAAATAAATTCGGAAAAAATGGAAAA
* **
603 CCAATATTA-AA-CGCATGAAAACCCTTCAATTT-TAATTTTGTAGAATTATATATTTTTGTTGA
130 CCAATATTAGAAGCG-ATGAAAACCCTTCAATTTCT--TTGTGTAGAATTATATATTTTTCCTGA
665 GTATTGTGGT
192 GTATTGTGGT
675 GAAAAA
1 GAAAAA
681 TTGGGAAAAA
Statistics
Matches: 177, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
199 3 0.02
200 17 0.10
201 156 0.88
202 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (201 bp):
GAAAAACTCCTTGAAATATCTACATTTATCGAACCAAATCTCAGCCACATTAAATCTAAGGATTT
GTTTTTACGAGCATCTAAATCTTGTTTCGATATAATTAAAAATAAATTCGGAAAAAATGGAAAAC
CAATATTAGAAGCGATGAAAACCCTTCAATTTCTTTGTGTAGAATTATATATTTTTCCTGAGTAT
TGTGGT
Found at i:3711 original size:322 final size:322
Alignment explanation
Indices: 479--4258 Score: 4455
Period size: 323 Copynumber: 11.7 Consensus size: 322
469 TTGGTTAAAA
** ** * *
479 ACTCCTTGAAATATCTACATTCTTGGAACCAAATCTCAGCTGCATTAAATTTAATGATTTGTTTT
1 ACTCCTTGAAATATCTACATT-TTCTAACCAAATCTCAGCCACATTTAATTTAAGGATTTGTTTT
* * * *
544 TACGAGCATCTAAATCTTGTTTCGATATAATTAGAAATACATTCGGAAAAAATGGAAAACCAATA
65 TACGAGTATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAATA
* * *
609 TTAAACGCATG-AAAACCCTTCAATTTTAATTTTGTAGAATTATATATTTTTGTTGAGTATTGTG
130 TTAAACGCATGAAAAACCCTTCAATTTTATTTTTGTTGAATTATATATTTTTGCTGAGTATTGTG
* * *
673 GTGAAAAATTGGGAAAAAAAAATTTCGGGTCAGTTTTGAGCAGAAATCGTGCACTAATCATCACG
195 GTGAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTGAGCAGAAATCGTGTACTAATCATCACG
** ** * **
738 GTTTTTGGCTAAAAACAAGTTTCGGGGCCCC-TATTAGTTTTGCATGA-TTTTTGGCAGAAAG
260 GTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTTTTTGGCAGAAAG
* * * * * *
799 ACTCCTTGAAATATCTATATTTATCTAATCAAATCTCAGCCACATTTGATTTGAGAATTTGTTTC
1 ACTCCTTGAAATATCTACATTT-TCTAACCAAATCTCAGCCACATTTAATTTAAGGATTTGTTTT
* ** *
864 TACAAAAAATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGAAAAACCAAT
65 TAC-GAGTATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAAT
* *
929 ATTAAACGCATGAAAAACCCTTCAATTTTATTTTTGTCGAATTATATATTTTTGCTGAGAATTGT
129 ATTAAACGCATGAAAAACCCTTCAATTTTATTTTTGTTGAATTATATATTTTTGCTGAGTATTGT
*
994 GGTGAAAAATTGAGAAAAAAATATTTTCGGGTCAGTTTTGAGCAGAAATCGTATACTAATCATCA
194 GGTGAAAAATTGAGAAAAAAA-ATTTTCGGGTCAGTTTTGAGCAGAAATCGTGTACTAATCATCA
* * * *
1059 CGGTATTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTACATGATTTTTTGGCAGAAAA
258 CGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTTTTTGGCAGAAAG
*
1124 ACTCCTTGAAATATCTACATTCTT-TAAACCAAATCTCAGCCACATTAAATTTAAGGATTTGTTT
1 ACTCCTTGAAATATCTACATT-TTCT-AACCAAATCTCAGCCACATTTAATTTAAGGATTTGTTT
* ***
1188 TTACGAGTATCTGAATCTTATTTCGATACAATTA-AAATAAATTCGGAAAAAAATGGAAAAATGA
64 TTACGAGTATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGG-AAAAAATGGAAAACCAA
* * *
1252 TATTTGAA-GCATGAAAAACCCTTCAATTTTTTTTTTGGCATTGAA--ATA-ACTTTTTTCTGAG
128 TA-TTAAACGCATGAAAAACCCTTCAATTTTATTTTT-G--TTGAATTATATA-TTTTTGCTGAG
* * * * * *
1313 TTTTGTGG-CAAAAATTTGAG--AAAAAATCTTCCGGGTCAGTTTTTAGCCGAAATTGTGTACTA
188 TATTGTGGTGAAAAA-TTGAGAAAAAAAAT-TTTCGGGTCAGTTTTGAGCAGAAATCGTGTACTA
* *
1375 ATCATCACGATTTTTGGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTAAATGATTTTTTG
251 ATCATCACGGTTTTT-GGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTTTTTG
1440 GCAGAAAG
315 GCAGAAAG
* * * *
1448 ACTCCTTGAAATATCTATATTTATCTCACCAAATCTCAGCCACATTTGATTTGAA-AATTTGTTT
1 ACTCCTTGAAATATCTACATTT-TCTAACCAAATCTCAGCCACATTTAATTT-AAGGATTTGTTT
* * *
1512 TTACAAGAATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAATACCAAT
64 TTACGAGTATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAAT
* *
1577 ATTAAACACATGAAAAACCCTTCAATTTTATTTTTGTTGAATTATATCTTTTTGCTGAGTATTGT
129 ATTAAACGCATGAAAAACCCTTCAATTTTATTTTTGTTGAATTATATATTTTTGCTGAGTATTGT
* * *
1642 GGTGAAAAATTGAGAAAAAAAAATTTCGGGTCAATTTTGAGCAGAAATCATGTACTAATCATCAC
194 GGTGAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTGAGCAGAAATCGTGTACTAATCATCAC
* * * * *
1707 GATATTTGGCTAAAATCGCGTTTCGGGGCCCCTGCTCAGTTTTATATGATTTTTTGGCAGAAAG
259 GGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTTTTTGGCAGAAAG
* * * *
1771 ACTCCTTGAAATATCTACATTCTT-TAAACGAAATCTCAACCGCATTAAATTTAAGGATTTGTTT
1 ACTCCTTGAAATATCTACATT-TTCT-AACCAAATCTCAGCCACATTTAATTTAAGGATTTGTTT
* *
1835 TTACGAGTATCTGAATCTTATTTCGATACAATTA-AAATAAATTCGGAAAAAATGGAAAA-AAGA
64 TTACGAGTATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCA-A
* * * *
1898 TATTCGAA-GCATGAAAAACCCTTCAATTTT-TGTTTT-TTGCATTGAAATAACTTTTTTCTGAG
128 TATT-AAACGCATGAAAAACCCTTCAATTTTAT-TTTTGTTGAATT-ATAT-A-TTTTTGCTGAG
* ** * * *
1960 TTTTGTGGCAAAAAAATTGAG--AAAAAATTTTACGGGTCAGTTTTTAGCCGAAAAT-ATGTACT
188 TATTGTGG-TGAAAAATTGAGAAAAAAAATTTT-CGGGTCAGTTTTGAGCAG-AAATCGTGTACT
* * *
2022 AATAATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGGCCCAGCTCAGTTTTAAATGATTTTTT
250 AATCATCACGGTTTTT-GGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTTTTT
2087 GGCAGAAAG
314 GGCAGAAAG
* * * * * *
2096 ACTCCTTTAAATATCTATATTTATCTAACCAAATCTCAGCCACATTTGATTTGAGAATTTTTTTT
1 ACTCCTTGAAATATCTACATTT-TCTAACCAAATCTCAGCCACATTTAATTTAAGGA-TTTGTTT
* *
2161 TTACAAGAATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAAT
64 TTACGAGTATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAAT
* * *
2226 ATTAAACACATGAAAAACCCTTCAATTTTATTTTGGTTGAATTATAAATTTTTGCT-ATGTATTG
129 ATTAAACGCATGAAAAACCCTTCAATTTTATTTTTGTTGAATTATATATTTTTGCTGA-GTATTG
*
2290 TGGTGAAAAATTGAGAAAAAAAAATTTCGGGTCAGTTTTGAGCAGAAATCGTGTACTAATCATCA
193 TGGTGAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTGAGCAGAAATCGTGTACTAATCATCA
* * * *
2355 CGGTATTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTACATGATTTTTTGGCAGAAAC
258 CGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTTTTTGGCAGAAAG
* * *
2420 ACTCATTGAAATATCTACATTCTT-TAAACCAAATCTCAGCCGCATTAAATTTAAGGATTTGTTT
1 ACTCCTTGAAATATCTACATT-TTCT-AACCAAATCTCAGCCACATTTAATTTAAGGATTTGTTT
** * ** *
2484 CAACGAGTATCTGAATCTTATTTCGATACAATTA-AAATAAATTCGGAAAAAAATGGAAAAATAG
64 TTACGAGTATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGG-AAAAAATGGAAAACCAA
* * * *
2548 TATTCGAA-GCATGAAAAACCCTTCAAGTTTT-TTTTT-TTGCATTGAAATAACTTTTTTCTGAG
128 TATT-AAACGCATGAAAAACCCTTCAA-TTTTATTTTTGTTGAATT-ATAT-A-TTTTTGCTGAG
* * * * *
2610 T-TT-TGTTGCAAAAAGCTGAG-ATAAAAATTTTCCGGGTCAGTTTTTAG-AGGAAATTGTGTAC
188 TATTGTGGTG-AAAAA-TTGAGAAAAAAAATTTT-CGGGTCAGTTTTGAGCA-GAAATCGTGTAC
* * * *
2671 TAACACCATCACAGTTTTTGGACTAAAAACGCGTGTCGGGGCCCCAGCTCAGTTTTAAATGATTT
249 T-A-ATCATCACGGTTTTTGG-CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTT
2736 TTTGGCAGAAAG
311 TTTGGCAGAAAG
* * * *
2748 ATTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTTGATTTGAGGATTTGTTTT
1 ACTCCTTGAAATATCTACATTT-TCTAACCAAATCTCAGCCACATTTAATTTAAGGATTTGTTTT
* * * *
2813 TACGAGCATCTAAATCTTGTTTTGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAATA
65 TACGAGTATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAATA
* *
2878 TTAAACACATGGAAAACCCTTCAATTTTATTTTTGTTGAATTATATATTTTTGCTGAGTATTGTG
130 TTAAACGCATGAAAAACCCTTCAATTTTATTTTTGTTGAATTATATATTTTTGCTGAGTATTGTG
* * *
2943 GTG-AAAATTGAGAGAAAAAAAATTTCGGGTCAGTTTTGAGTAGAAATCGTGTACTTATCATCAC
195 GTGAAAAATTGAGA-AAAAAAATTTTCGGGTCAGTTTTGAGCAGAAATCGTGTACTAATCATCAC
* * * *** * * *
3007 GGTTTTTGACTAAAAACGCGTTTCGAGACCTTTGCTTACTTTTACATGATTTTTTGGCAGAAAG
259 GGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTTTTTGGCAGAAAG
* * * *
3071 ACTCCTTGAAATATCTGCATTTTTTGAACCAAATCTCAGCCGCATTAAATTTAAGGATTTGTTTT
1 ACTCCTTGAAATATCTACATTTTCT-AACCAAATCTCAGCCACATTTAATTTAAGGATTTGTTTT
* * * ****
3136 TACGAGTATTTGAATCTTATTTCGATAGAATTA-AAATAAATTC-G--AGAATGGAAAAATGTTA
65 TACGAGTATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAATA
* * * * *
3197 TTCGAA-GCATGAAAAACCCTTCAATTTT-TTTTT-TTGCATTGAAATAACTTTTTTCTGAGTTT
130 TT-AAACGCATGAAAAACCCTTCAATTTTATTTTTGTTGAATT-ATAT-A-TTTTTGCTGAGTAT
** * * * *
3259 TGTGGCAAAAAATTGAG--AAAAAATTTTCCGGGTCAGTTTTTAGCCGAAATTGTTTA--AATCA
191 TGTGGTGAAAAATTGAGAAAAAAAATTTT-CGGGTCAGTTTTGAGCAGAAATCGTGTACTAATCA
*
3320 TCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTTAGTTTTAAATGATTTTTTGGCAG
255 TCACGGTTTTT-GGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTTTTTGGCAG
3385 AAAG
319 AAAG
* * * * *
3389 ACTGCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTTGATTTGAGAATTTGTTTT
1 ACTCCTTGAAATATCTACATTT-TCTAACCAAATCTCAGCCACATTTAATTTAAGGATTTGTTTT
* * *
3454 TACAAGAATCTCAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAATA
65 TACGAGTATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAATA
3519 TTAAACGCATGAAAAACCCTTCAATTTTATTTTTGTTGAATTATATATTTTT-CTGAGTATTGTG
130 TTAAACGCATGAAAAACCCTTCAATTTTATTTTTGTTGAATTATATATTTTTGCTGAGTATTGTG
* * * *
3583 GTGAAAAATTGAGAAAAAAAAATTTCGGGTTAGTTTTGAGTAGAAATCGTGTACAAATCATCACG
195 GTGAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTGAGCAGAAATCGTGTACTAATCATCACG
* * * * * *
3648 GTTTTTGGCTAAAAACGTGTTTCGGGGCACCGGCTCAGTATTACATGGTTTTTTGGGAGAAAG
260 GTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTTTTTGGCAGAAAG
* * *
3711 ACTCCTTGAAATATCTCCATTCTT-TGAACCAAATCTCAGCCGCATTCAATTTAAGGATTTGTTT
1 ACTCCTTGAAATATCTACATT-TTCT-AACCAAATCTCAGCCACATTTAATTTAAGGATTTGTTT
* * ****
3775 TTACGAGTATCTGAATCTTATTTCGATACAATTA-AAATAAATTCGGGAAAAATGGAAAAATGTT
64 TTACGAGTATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAAT
* * * *
3839 ATTCGAA-GCATGAAAAACCCTTCAATTTTTTTTTTGCATTGAA--ATA-ACTTTTTTCTGAGTT
129 ATT-AAACGCATGAAAAACCCTTCAATTTTATTTTTG--TTGAATTATATA-TTTTTGCTGAGTA
** * * * * *
3900 TTGTGGCAAAAAATTGAG--AAAAAATTTTCCGAGTCAGTTTTTAGCCGAAATTGTGTACTAAAC
190 TTGTGGTGAAAAATTGAGAAAAAAAATTTT-CGGGTCAGTTTTGAGCAGAAATCGTGTACTAATC
* * *
3963 ATCACGGTTTTTCAGCTAAAAACGCGTTTCGGGGCCCCAGCTCAATTTTAAATGATTTTTTGGCA
254 ATCACGGTTTTT-GGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTTTTTGGCA
4028 GAAAG
318 GAAAG
* * * *
4033 ACTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCATATTTGATTTGAGGATTTGTTTT
1 ACTCCTTGAAATATCTACATTT-TCTAACCAAATCTCAGCCACATTTAATTTAAGGATTTGTTTT
* * * * * *
4098 TACGAGCATTTAAATCTTGTTTCGATATAATTAAAAATAAATTCGGAAAAAATGGGAAACCAATA
65 TACGAGTATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAATA
* * ** * * * *
4163 TTAAAAGCGTTTAAAACCCTTCAA-TTTCTTTGTGTTGAATTATATATTTTTCCTGAGTATTCTG
130 TTAAACGCATGAAAAACCCTTCAATTTTATTTTTGTTGAATTATATATTTTTGCTGAGTATTGTG
**
4227 GCAAAAAATTGAGAAAAAAAATTTTTCGGGTC
195 GTGAAAAATTGAGAAAAAAAA-TTTTCGGGTC
4259 CCTGCTCAGT
Statistics
Matches: 2944, Mismatches: 397, Indels: 234
0.82 0.11 0.07
Matches are distributed among these distances:
317 21 0.01
318 147 0.05
319 71 0.02
320 111 0.04
321 222 0.08
322 533 0.18
323 586 0.20
324 532 0.18
325 330 0.11
326 94 0.03
327 94 0.03
328 184 0.06
329 19 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (322 bp):
ACTCCTTGAAATATCTACATTTTCTAACCAAATCTCAGCCACATTTAATTTAAGGATTTGTTTTT
ACGAGTATCTGAATCTTATTTCGATATAATTAGAAATAAATTCGGAAAAAATGGAAAACCAATAT
TAAACGCATGAAAAACCCTTCAATTTTATTTTTGTTGAATTATATATTTTTGCTGAGTATTGTGG
TGAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTGAGCAGAAATCGTGTACTAATCATCACGG
TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTTTTTGGCAGAAAG
Found at i:4497 original size:260 final size:259
Alignment explanation
Indices: 4002--4517 Score: 820
Period size: 260 Copynumber: 2.0 Consensus size: 259
3992 CGGGGCCCCA
4002 GCTCAATTTTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAAAT
1 GCTCAATTTTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAAAT
* * * * *
4067 CTCAGCCATATTTGATTTGAGGATTTGTTTTTACGAGCATTTAAATCTTGTTTCGATATAATTAA
66 CTCAGCCACATTTGATTTGAGAATTTGTTTTTACAAGAATTTAAATCTTATTTCGATATAATTAA
* * ** *
4132 AAATAAATTCGGAAAAAATGGGAAACCAATATTAAAAGCGTTTAAAACCCTTCAATTTCTTTGTG
131 AAATAAATTCGGAAAAAATGGAAAACCAATATTAAAAGCATGGAAAACCCTTCAATTTATTTGTG
*
4197 TTGAATTATATATTTTTCCTGAGTATTCTGGCAAAAAATTGAGAAAAAAAATTTTTCGGGTCCCT
196 TTGAATTATATATTTTTCCTGAGTATTCTGGCAAAAAATTGAGAAAAAAAA-ATTTCGGGTCCCT
*
4262 GCTCAGTTTTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAAAT
1 GCTCAATTTTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAAAT
* *
4327 CTCAGCCACATTTGATTTGAGAATTTGTTTTTACAAGAATTTGAATCTTATTTCGATATAATTAG
66 CTCAGCCACATTTGATTTGAGAATTTGTTTTTACAAGAATTTAAATCTTATTTCGATATAATTAA
*
4392 AAATAAATTCGGAAAAAATGGAAAACCAATATTAAACA-CATGGAAAACCCTTCAATTTTATTTT
131 AAATAAATTCGGAAAAAATGGAAAACCAATATTAAA-AGCATGGAAAACCCTTCAA-TTTATTTG
* * **
4456 TGTTGAATTATATATTTTTGCTGAGTATTGTGG-TGAAAATTGAGAAAAAAAAATTTCGGGTC
194 TGTTGAATTATATATTTTTCCTGAGTATTCTGGCAAAAAATTGAGAAAAAAAAATTTCGGGTC
4518 AGTTTTGAGC
Statistics
Matches: 235, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
259 9 0.04
260 188 0.80
261 38 0.16
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (259 bp):
GCTCAATTTTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAAAT
CTCAGCCACATTTGATTTGAGAATTTGTTTTTACAAGAATTTAAATCTTATTTCGATATAATTAA
AAATAAATTCGGAAAAAATGGAAAACCAATATTAAAAGCATGGAAAACCCTTCAATTTATTTGTG
TTGAATTATATATTTTTCCTGAGTATTCTGGCAAAAAATTGAGAAAAAAAAATTTCGGGTCCCT
Found at i:4818 original size:582 final size:580
Alignment explanation
Indices: 3680--4833 Score: 1420
Period size: 582 Copynumber: 2.0 Consensus size: 580
3670 CGGGGCACCG
* * * *
3680 GCTCAGTATTACATGGTTTTTTGGGAGAAAGACTCCTTGAAATATCTCCATTCTTTGAACCAAAT
1 GCTCAGTATTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTACATTCTTTGAACCAAAT
* * * *
3745 CTCAGCCGCATTCAATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTATTTCGATACAATTAA
66 CTCAGCCACATTCAATTTAAGAATTTGTTTTTACAAGAATCTGAATCTTATTTCGATACAATTAA
* *** * * *
3810 AATAAATTCGGGAAAAATGGAAAAATGTTATTCGAAGCATGAAAAACCCTTCAATTTTTTTTTTG
131 AATAAATTCGGAAAAAATGGAAAAACAATATTCAAAACATGAAAAACCCTTCAATTTTATTTTTG
* * *
3875 CATTGAAATAACTTTTTTCTGAGTTTTGTGGCAAAAAATTGAGAAAAAATTTTCCGAGTCAGTTT
196 -ATTGAAATAACTTTTTGCTGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTCCGAGTCAGTTT
* * *
3940 TTAGCCGAAATTGTGTACTAAACATCACGGTTTTTCAGCTAAAAACGCGTTTCGGGGCCCCAGCT
260 TGAGCAGAAATCGTGTACTAAACATCACGGTTTTTCAGCTAAAAACGCGTTTCGGGGCCCCAGCT
* *
4005 CAATTTTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCTC
325 CAATATTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTACATTTATCTAACCAAATCTC
* * * * *
4070 AGCCATATTTGATTTGAGGATTTGTTTTTACGAGCATTTAAATCTTGTTTCGATATAATTAAAAA
390 AACCACATTTGATTTAAGGATTCGTTTTTACGAGCATCTAAATCTTGTTTCGATATAATTAAAAA
* * ** *
4135 TAAATTCGGAAAAAATGGGAAACCAATATTAAAAGCGTTTAAAACCCTTCAATTTCTTTGTGTTG
455 TAAATTCGGAAAAAATGGAAAAACAATATTAAAAGCGTGAAAAACCCTTCAATTTCTTTGCGTTG
* *
4200 AATTATATATTTTTCCTGAGTATTCTGGCAAAAAATTGAGAAAAAAAATTTTTCGGGTCCCT
520 AATAATAAATTTTTCCTGAGTATTCTGGCAAAAAATTGAG-AAAAAAATTTTTCGGGTCCCT
* *
4262 GCTCAGTTTTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATT-TATCT-AACCAA
1 GCTCAGTATTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTACATTCT-T-TGAACCAA
** * * *
4325 ATCTCAGCCACATTTGATTTGAGAATTTGTTTTTACAAGAATTTGAATCTTATTTCGATATAATT
64 ATCTCAGCCACATTCAATTTAAGAATTTGTTTTTACAAGAATCTGAATCTTATTTCGATACAATT
* *
4390 AGAAATAAATTCGGAAAAAATGGAAAACCAATATT-AAACACATGGAAAACCCTTCAATTTTATT
129 A-AAATAAATTCGGAAAAAATGGAAAAACAATATTCAAA-ACATGAAAAACCCTTCAATTTTATT
** *
4454 TTTG-TTGAATTATATA-TTTTTGCTGAGTATTGTGG-TGAAAATTGAGAAAAAAAAATTT-CGG
192 TTTGATTGAA--ATA-ACTTTTTGCTGAGTATTGTGGCAAAAAATTGAG--AAAAAAATTTCCGA
* *
4515 GTCAGTTTTGAGCAGAAATCGTGTAC-AAATCATCACGGTTTTT-GGCTAAAAACGTGTTTCGGG
252 GTCAGTTTTGAGCAGAAATCGTGTACTAAA-CATCACGGTTTTTCAGCTAAAAACGCGTTTCGGG
* * * * *
4578 GCCCCGGCTCAGTATTACATGGTTTTTTGGCAGAAAGACTCCTTGAAATATCTCCATTCT-T-TG
316 GCCCCAGCTCAATATTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTACATT-TATCT-
* *
4641 AACCAAATCTCAACCGCA-TTGAATTTAAGGATTCGTTTTTACGAGCATCTGAATCTTGTTTCGA
379 AACCAAATCTCAACCACATTTG-ATTTAAGGATTCGTTTTTACGAGCATCTAAATCTTGTTTCGA
** * * ** *
4705 TATTGTTAGAAATAAATTCGGAAAAAAAATGGAAAAACGATATTCGAAGCGTGAAAAATCCTTCT
443 TATAATTAAAAATAAATTCGG--AAAAAATGGAAAAACAATATTAAAAGCGTGAAAAACCCTTC-
** * * * *
4770 TTTTTTTTTGCGTT-AA-AATAAATTTTTTCTGAGTATTGTGGC-AAAAATTGAGAAAACAATTT
505 AATTTCTTTGCGTTGAATAATAAATTTTTCCTGAGTATTCTGGCAAAAAATTGAGAAAAAAATTT
4832 TT
570 TT
4834 AGGTCAGTTT
Statistics
Matches: 487, Mismatches: 69, Indels: 33
0.83 0.12 0.06
Matches are distributed among these distances:
581 21 0.04
582 275 0.56
583 136 0.28
584 45 0.09
585 10 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (580 bp):
GCTCAGTATTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTACATTCTTTGAACCAAAT
CTCAGCCACATTCAATTTAAGAATTTGTTTTTACAAGAATCTGAATCTTATTTCGATACAATTAA
AATAAATTCGGAAAAAATGGAAAAACAATATTCAAAACATGAAAAACCCTTCAATTTTATTTTTG
ATTGAAATAACTTTTTGCTGAGTATTGTGGCAAAAAATTGAGAAAAAAATTTCCGAGTCAGTTTT
GAGCAGAAATCGTGTACTAAACATCACGGTTTTTCAGCTAAAAACGCGTTTCGGGGCCCCAGCTC
AATATTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTACATTTATCTAACCAAATCTCA
ACCACATTTGATTTAAGGATTCGTTTTTACGAGCATCTAAATCTTGTTTCGATATAATTAAAAAT
AAATTCGGAAAAAATGGAAAAACAATATTAAAAGCGTGAAAAACCCTTCAATTTCTTTGCGTTGA
ATAATAAATTTTTCCTGAGTATTCTGGCAAAAAATTGAGAAAAAAATTTTTCGGGTCCCT
Found at i:5002 original size:321 final size:323
Alignment explanation
Indices: 4264--5051 Score: 1022
Period size: 321 Copynumber: 2.5 Consensus size: 323
4254 GGGTCCCTGC
*
4264 TCAGTTTTAAATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCT
1 TCAGTTTTACATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCT
* * * * *
4329 CAGCCACATTTGATTTGAGAATTTGTTTTTACAAGAATTTGAATCTTATTTCGATATAATTAGAA
66 CAGCCACATTTGATTTGAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTAGAA
* *
4394 ATAAATTCGG--AAAAAATGGAAAACCAATATTAAACACATGGAAAACCCTTCAATTTTATTTTT
131 ATAAATTCGGAAAAAAAATGGAAAAACAATATTAAACACATGAAAAACCCTTC-ATTTTATTTTT
* * ** *
4457 GTTGAATTATATATTTTTGCTGAGTATTGTGGTGAAAATTGAGAAAAAAAAATTTCGGGTCAGTT
195 GTTGAATAATAAATTTTTGCTGAGTATTGTGGCAAAAATTGAGAAAAAAAAATTTCAGGTCAGTT
* * * *
4522 TTGAGCAGAAATCGTGTACAAATCATCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCCCGGC
260 TTGAGCAGAAATCGTGTACAAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGA
* * **
4586 TCAGTATTACATGGTTTTTTGGCAGAAAGACTCCTTGAAATATCTCCATTCT-T-TGAACCAAAT
1 TCAGTTTTACATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATT-TATCT-AACCAAAT
* * * * **
4649 CTCAACCGCA-TTGAATTTAAGGATTCGTTTTTACGAGCATCTGAATCTTGTTTCGATATTGTTA
64 CTCAGCCACATTTG-ATTTGAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTA
* * * * * *
4713 GAAATAAATTCGGAAAAAAAATGGAAAAACGATATTCGAA-GCGTGAAAAATCCTTC-TTTTTTT
128 GAAATAAATTCGGAAAAAAAATGGAAAAACAATATT-AAACACATGAAAAACCCTTCATTTTATT
* * * *
4776 TTTGCGTT-AA-AATAAATTTTTTCTGAGTATTGTGGCAAAAATTGAG-AAAACAATTTTTAGGT
192 TTT--GTTGAATAATAAATTTTTGCTGAGTATTGTGGCAAAAATTGAGAAAAAAAAATTTCAGGT
* * * * *
4838 CAGTTTTTAGCCGAAATTGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCT
255 CAGTTTTGAGCAGAAATCGTGTACAAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCC
*
4903 TGGA
320 CGGA
* * *
4907 TCAGTTTTTCATGATTTTATGGCAGAAAGACTCTTTGAAATATCTATATTTATCTAACCAAATCT
1 TCAGTTTTACATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCT
4972 CAGCCACATTTGATTTGAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTAG-A
66 CAGCCACATTTGATTTGAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTAGAA
5036 ATAAATTCGGAAAAAA
131 ATAAATTCGGAAAAAA
5052 TCGAAAATCG
Statistics
Matches: 399, Mismatches: 56, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
320 18 0.05
321 182 0.46
322 160 0.40
323 3 0.01
324 34 0.09
325 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (323 bp):
TCAGTTTTACATGATTTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCT
CAGCCACATTTGATTTGAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTAGAA
ATAAATTCGGAAAAAAAATGGAAAAACAATATTAAACACATGAAAAACCCTTCATTTTATTTTTG
TTGAATAATAAATTTTTGCTGAGTATTGTGGCAAAAATTGAGAAAAAAAAATTTCAGGTCAGTTT
TGAGCAGAAATCGTGTACAAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGA
Found at i:5324 original size:292 final size:295
Alignment explanation
Indices: 4793--6000 Score: 1148
Period size: 292 Copynumber: 3.9 Consensus size: 295
4783 TAAAATAAAT
* ** *
4793 TTTTTCTGAGTATTGTGGC-AAAAATTGAGAAAACAATTTTTAGGTCAGTTTTTAGCCGAAATTG
1 TTTTTCCGAGTATTGTGGCAAAAAATTGAGAAAACAATTTTCGGGTCAGTTTTTAGCCGAAATCG
* *
4857 TGTACTAACCATCAC-AGTTTTTGGCTAAAAACGCGTTTCGGGGCCTTGGATCAGTTTTTCATGA
66 TGTACTAACCATCACGA-TTTTTGGCTAAAAACGCGTTTCGGGGCCTCGGATCAGTTTTGCATGA
* *
4921 TTTTATGGCAGAAAGACTCTTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTTGAT
130 TTTT-TGGCAAAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTTGAT
* *
4986 TTGAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATATAATT-AGAATAAATTCGGAAAA
194 TTGAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTAAAAATAAATTCGGAAAA
* *
5050 AATCGAAAATCGATATT-A-AAAGCTTGAATTATATA
259 AATGGAAAACCGATATTAATAAAGCTTGAATTATATA
* *
5085 TTTTTCCGAGTATTTTGGC-AAAAATTGAGAATAA-AAATTTCGGGTCAGTTTTTAGCCGAAATC
1 TTTTTCCGAGTATTGTGGCAAAAAATTGAGAA-AACAATTTTCGGGTCAGTTTTTAGCCGAAATC
* * *
5148 GTGTACCTAACCATAACGATTTTTGGCTAAAAACGAGTTTCGGGATCC-C-GACTCAGTTTTGCA
65 GTGTA-CTAACCATCACGATTTTTGGCTAAAAACGCGTTTCGGG-GCCTCGGA-TCAGTTTTGCA
* **
5211 TGATTTTTGGCAAAAAGACTCCTTGAAATATCTACATTTAT-TGAACCAAATCTCAGATACATTT
127 TGATTTTTGGCAAAAAGACTCCTTGAAATATCTATATTTATCT-AACCAAATCTCAGCCACATTT
*
5275 GATTTGAGAATTTGTTTTTACGAGCATCTGAATCTTCTTTCGATATAATTAAAAATAAATTCGGA
191 GATTTGAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTAAAAATAAATTCGG-
5340 AAAAAAATGGAAAACCGATATTAGAAGCGTTTAAAACCCTTCAATATTTTTTGCGTTGAATTATA
255 -AAAAAATGGAAAACCG--A-T---A----TT--AA----T-AA-A------GC-TTGAATTATA
5405 TA
294 TA
* * * *
5407 TTTTTGCTGAGTATTGTGCCAAAAAATTGAGGAAAA-AATTTTCGGGTCAATTTTTAGCCGAATT
1 TTTTT-CCGAGTATTGTGGCAAAAAATTGA-GAAAACAATTTTCGGGTCAGTTTTTAGCCGAAAT
* * * * *
5471 C--GTA-T-A--AT---GGTTTTTGGCTAAAAATGCGTTTCGGAGCCCCGGATCAGTTTTACATG
64 CGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTTCGGGGCCTCGGATCAGTTTTGCATG
*
5527 ATTTTTTGGTAGAAAGACTGACTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACAT
129 A-TTTTTGGCA-AAA-A--GACTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACAT
* ** *
5592 TTGATTTGA-AGA-TT-ATTTTACGAGTTTCTGAATCTTGTTTCGATATGATTAAAAATAAATTC
189 TTGATTTGAGA-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTAAAAATAAATTC
* *
5654 GGAAAAAATGGGAAACCGATATTAGAAGTGTTTAAAGTCCTTCAATTTTTTTACGTTGAATTATA
253 GGAAAAAATGGAAAACCGATATT--AA-----TAAAG--CTT-GA-------A--TT--A-TATA
* * *
5719 TATTTTCCTGAGTGTTGTGGCAAAAAATTGAGAAAACAATTTTCGGGTCAGTTTTTAGCCGACAC
1 T-TTTTCC-GAGTATTGTGGCAAAAAATTGAGAAAACAATTTTCGGGTCAGTTTTTAGCCGAAAT
* * * * *
5784 CGTGTACTAATCATCACTGTTTTTTTTGGCTAAAAACGCGTTTCGGGGCCTCTGCTTAGTTTTGC
64 CGTGTACTAACCATCAC-G--ATTTTTGGCTAAAAACGCGTTTCGGGGCCTCGGATCAGTTTTGC
* * *
5849 ATGATTTTTAGCAGAAAGACTCCTTGAATTATCTATATTTATCTAACCAAATCTCAGCCACATTT
126 ATGATTTTTGGCAAAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTT
* * * *
5914 GATTTGAGAATTTGTTTTTACAAGGATCCGAATCTTGTTTCGATATAATTAGAAATAAATTCGGA
191 GATTTGAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTAAAAATAAATTCGGA
* *
5979 AAAAATGAAAAACTGATATTAA
256 AAAAATGGAAAACCGATATTAA
6001 AAGCGTGAAA
Statistics
Matches: 757, Mismatches: 77, Indels: 136
0.78 0.08 0.14
Matches are distributed among these distances:
291 1 0.00
292 159 0.21
293 65 0.09
294 3 0.00
295 14 0.02
297 1 0.00
298 2 0.00
299 2 0.00
300 2 0.00
301 1 0.00
304 1 0.00
305 9 0.01
306 2 0.00
307 1 0.00
308 1 0.00
309 3 0.00
311 1 0.00
312 12 0.02
313 52 0.07
314 39 0.05
315 29 0.04
316 4 0.01
317 49 0.06
318 3 0.00
319 54 0.07
320 59 0.08
321 5 0.01
322 82 0.11
323 14 0.02
324 44 0.06
325 43 0.06
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (295 bp):
TTTTTCCGAGTATTGTGGCAAAAAATTGAGAAAACAATTTTCGGGTCAGTTTTTAGCCGAAATCG
TGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTTCGGGGCCTCGGATCAGTTTTGCATGAT
TTTTGGCAAAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTTGATTT
GAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATATAATTAAAAATAAATTCGGAAAAAA
TGGAAAACCGATATTAATAAAGCTTGAATTATATA
Found at i:6663 original size:581 final size:578
Alignment explanation
Indices: 5546--6661 Score: 1476
Period size: 581 Copynumber: 1.9 Consensus size: 578
5536 TAGAAAGACT
* * *
5546 GACTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACATTTGATTTGAAGATTATTTT
1 GACTCATTGAAATATCTACATTCATCTAACCAAATCTCAGCCACATTTGATTTGAAGATTATTTT
** * * * *
5611 ACGAGTTTCTGAATCTTGTTTCGATATGATTAAAAATAAATTCGGAAAAAATGGGAAACCGATAT
66 ACGAGCATCTGAATATTGTTTCGATATGATTAAAAATAAATTCGGAAAAAATGGAAAAACAATAT
* ** ** * * *
5676 TAGAAGTGTTTAAAGTCCTTCAATTTTTTTACGTTGAATTATATATTTTCCTGAGTGTTGTGGCA
131 TAGAAGCGTGAAAAACCCTTCAATTTTTTTACATTGAA-TATATATTTTCCTGAGTATTGTAGCA
* * ** * * ** * *
5741 AAAAATTGAGAAAACAATTTTCGGGTCAGTTTTTAGCCGACACCGTGTACTAATCATCACTGTTT
195 AAAAATTAAGAAAAAAATTTTCAAGTCAGTTTTTAACCGAAACCACGTACTAACCATCACAG--T
* * * * *
5806 TTTTTGGCTAAAAACGCGTTTCGGGGCCTCTGCTTAGTTTTGCATGATTTTTAGCAGAAAGACTC
258 TTTTTGGCTAAAAACGCGTTTCGAGACCCCGGCTCAGTTTTGCATGATTTTTAGCAGAAAGACTC
* * *
5871 CTTGAATTATCTATATTTATCTAACCAAATCTCAGCCACATTTGATTTGAGAATTTGTTTTTACA
323 CTTGAAATATCTAAATTTATCTAACCAAATCTCAGCCACATTTCATTTGAGAATTTGTTTTTACA
* *
5936 AGGATCCGAATCTTGTTTCGATATAATTAGAAATAAATTCGGAAAAAATGAAAAACTGATATTAA
388 AGGATCCAAATCTTGTTTCGATATAATTAGAAATAAATTCGGAAAAAATGAAAAACCGATATTAA
*
6001 AAGCGTGAAAAACCCTTCAATTTTATTTGCATTGAATTATATATTTTTTCCGAGTATTGTGGCAA
453 AAGCGTGAAAAACCCTTCAATTTTATTTGCATTGAATAATATATTTTTTCCGAGTATTGTGGCAA
6066 AAAATTAAGAAAAAAAACTTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGACAAAAA
518 AAAATTAAGAAAAAAAACTTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGACAAAAA
*
6127 GACTCATTGAAATATCTACATTCA-CTGAACCAAATCTCAGCCGCA-TTGAATTT-AAGGATTTG
1 GACTCATTGAAATATCTACATTCATCT-AACCAAATCTCAGCCACATTTG-ATTTGAA-GA-TT-
* * *
6189 TTTTTACGAGCATCTGAATATTGTTTCGATATTATTAGAAATAAATTCGGAAAAAAATGGAAAAA
61 ATTTTACGAGCATCTGAATATTGTTTCGATATGATTAAAAATAAATTCGG-AAAAAATGGAAAAA
* * *
6254 CAATATTCA-AAGCGTGAAAAACCCTTCAAATTTTTTTTCATTGAA-ATA-ACTTTTTCTTAGTA
125 CAATATT-AGAAGCGTGAAAAACCCTTC-AATTTTTTTACATTGAATATATA-TTTTCCTGAGTA
** *
6316 TTGTAGCAAAAAATTAAGAAAAAAATTTTCAAGTCAGTTTTTAACCGAAATTACGTAGTAACCAT
187 TTGTAGCAAAAAATTAAGAAAAAAATTTTCAAGTCAGTTTTTAACCGAAACCACGTACTAACCAT
* * *
6381 CACAG-TTTTTGGCTAAAAATGCGTTTCGAGACCCCGGCTCAGTTTTTCATGATTTTATGGCAGA
252 CACAGTTTTTTGGCTAAAAACGCGTTTCGAGACCCCGGCTCAGTTTTGCATGATTTT-TAGCAGA
* *
6445 AAGACTTCTTGAAATATCTAAATTTATCTAACCAAATCTCAGCCACATTTCATTTGAGGATTTGT
316 AAGACTCCTTGAAATATCTAAATTTATCTAACCAAATCTCAGCCACATTTCATTTGAGAATTTGT
* * * * * *
6510 TTTTACGAGTATCTAAATCTTGTTTCGATATAATTAGAATTAAATTCGGAAGAAATGGAAAACCG
381 TTTTACAAGGATCCAAATCTTGTTTCGATATAATTAGAAATAAATTCGGAAAAAATGAAAAACCG
* * * *
6575 ATATTAGAAGCGTGAAAAATCCTTCAATTTTATTTGGATTGAATAATATATTTTTTCTGAGTATT
446 ATATTAAAAGCGTGAAAAACCCTTCAATTTTATTTGCATTGAATAATATATTTTTTCCGAGTATT
*
6640 GTGGC-AAAAATT-GGAAAAAAAA
511 GTGGCAAAAAATTAAGAAAAAAAA
6662 AATCGGGTCA
Statistics
Matches: 461, Mismatches: 64, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
579 9 0.02
580 58 0.13
581 232 0.50
582 3 0.01
583 112 0.24
584 31 0.07
585 16 0.03
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (578 bp):
GACTCATTGAAATATCTACATTCATCTAACCAAATCTCAGCCACATTTGATTTGAAGATTATTTT
ACGAGCATCTGAATATTGTTTCGATATGATTAAAAATAAATTCGGAAAAAATGGAAAAACAATAT
TAGAAGCGTGAAAAACCCTTCAATTTTTTTACATTGAATATATATTTTCCTGAGTATTGTAGCAA
AAAATTAAGAAAAAAATTTTCAAGTCAGTTTTTAACCGAAACCACGTACTAACCATCACAGTTTT
TTGGCTAAAAACGCGTTTCGAGACCCCGGCTCAGTTTTGCATGATTTTTAGCAGAAAGACTCCTT
GAAATATCTAAATTTATCTAACCAAATCTCAGCCACATTTCATTTGAGAATTTGTTTTTACAAGG
ATCCAAATCTTGTTTCGATATAATTAGAAATAAATTCGGAAAAAATGAAAAACCGATATTAAAAG
CGTGAAAAACCCTTCAATTTTATTTGCATTGAATAATATATTTTTTCCGAGTATTGTGGCAAAAA
ATTAAGAAAAAAAACTTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGACAAAAA
Found at i:6680 original size:320 final size:320
Alignment explanation
Indices: 6085--7198 Score: 1368
Period size: 320 Copynumber: 3.5 Consensus size: 320
6075 AAAAAAAACT
* ** * * *
6085 TTTCGGGGCCCCGACTCAGTTTTGCATGA-TTTTTGACAAAAAGACTCATTGAAATATCTACATT
1 TTTC-GGGCCCCGGCTCAGTTTTATATGATTTTTTGACAGAAAGACTCCTTGAAATATCTATATT
* * * *
6149 CA-CTGAACCAAATCTCAGCCGCA-TTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATATTG
65 TATCT-AACCAAATCTCAGCCACATTTG-ATTTGAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * *
6212 TTTCGATATTATTAGAAATAAATTCGGAAAAAAATGGAAAAACAATATTCA-AAGCGTGAAAAAC
128 TTTCGATATAATTAAAAATAAATTCGG-AAAAAATGGAAAACCGATATT-AGAAGCGTGAAAAAC
** * * * *
6276 CCTTCAAATTTTTTTTCATTG-A-AATA-ACTTTTTCTTAGTATTGTAGCAAAAAATTAAGAAAA
191 CCTTCAAATTTTTTTGGATTGAATAATATATTTTTTCTGAGTATTGTGGCAAAAAATT-GGAAAA
** *** * * *
6338 AAATTTTCAAGTCAGTTTTTAACCGAAATTACGTAGTAACCATCACAGTTTTTGGCTAAAAATGC
255 AAATTTTCGGGTCAGTTTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGC
6403 G
320 G
* * * * *
6404 TTTCGAGACCCCGGCTCAGTTTT-TCATGATTTTATGGCAGAAAGACTTCTTGAAATATCTAAAT
1 TTTCG-GGCCCCGGCTCAGTTTTAT-ATGATTTTTTGACAGAAAGACTCCTTGAAATATCTATAT
* * *
6468 TTATCTAACCAAATCTCAGCCACATTTCATTTGAGGATTTGTTTTTACGAGTATCTAAATCTTGT
64 TTATCTAACCAAATCTCAGCCACATTTGATTTGAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
6533 TTCGATATAATTAGAATTAAATTCGGAAGAAATGGAAAACCGATATTAGAAGCGTGAAAAATCCT
129 TTCGATATAATTAAAAATAAATTCGGAAAAAATGGAAAACCGATATTAGAAGCGTGAAAAACCCT
6598 TC-AATTTTATTTGGATTGAATAATATATTTTTTCTGAGTATTGTGGC-AAAAATTGGAAAAAAA
194 TCAAATTTT-TTTGGATTGAATAATATATTTTTTCTGAGTATTGTGGCAAAAAATTGGAAAAAAA
*** * * * *
6661 AAATCGGGTCAGTTTTTAACCGAAATCGTGTACCTAACCATAACGGTTTTTGGATAGAAACACG
258 TTTTCGGGTCAGTTTTTAACCGAAATCGTGTA-CTAACCATCACGGTTTTTGGCTAAAAACGCG
* * * *
6725 TTTCGGGCCCCGTCTCAGTTTTATATAATTTTTTGACAGAATGACTCCTTGAAATATTTATATTT
1 TTTCGGGCCCCGGCTCAGTTTTATATGATTTTTTGACAGAAAGACTCCTTGAAATATCTATATTT
** * *
6790 ATCTAACCAAATCTCAGATATATTTGATTTGAGGATTTGTTTTTACGAGCATCTGAATCTTCTTT
66 ATCTAACCAAATCTCAGCCACATTTGATTTGAGGATTTGTTTTTACGAGCATCTGAATCTTGTTT
** * **
6855 CGATATAATTAAAAATAAATTTTGAAAAAATGGAAAACCGATATTAGAAACGTTTAAAACCCTTC
131 CGATATAATTAAAAATAAATTCGGAAAAAATGGAAAACCGATATTAGAAGCGTGAAAAACCCTTC
* *
6920 AAATTTTTTTGCG-TTGAATTATATATTTTTGCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAT
196 AAATTTTTTTG-GATTGAATAATATATTTTTTCTGAGTATTGTGGCAAAAAATTG-GAAAAAAAT
* * *
6984 TTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAATACGCG
259 TTTCGGGTCAGTTTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCG
* **
7046 TTTCGGGGCCCCGGCTCAATTTTATATGATTTTTTGGTAGAAAGACTCCTTGAAATATCTATATT
1 TTTC-GGGCCCCGGCTCAGTTTTATATGATTTTTTGACAGAAAGACTCCTTGAAATATCTATATT
* * ** *
7111 TATCTAACCAAATCTCAACGACATTTGATTTGAGGATTTGTTTTTATAAGGATCTGAATCTTGTT
65 TATCTAACCAAATCTCAGCCACATTTGATTTGAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
*
7176 TTGATATAATTAAAAATAAATTC
130 TCGATATAATTAAAAATAAATTC
7199 AAAAATAAAA
Statistics
Matches: 681, Mismatches: 97, Indels: 31
0.84 0.12 0.04
Matches are distributed among these distances:
318 8 0.01
319 65 0.10
320 334 0.49
321 89 0.13
322 185 0.27
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Consensus pattern (320 bp):
TTTCGGGCCCCGGCTCAGTTTTATATGATTTTTTGACAGAAAGACTCCTTGAAATATCTATATTT
ATCTAACCAAATCTCAGCCACATTTGATTTGAGGATTTGTTTTTACGAGCATCTGAATCTTGTTT
CGATATAATTAAAAATAAATTCGGAAAAAATGGAAAACCGATATTAGAAGCGTGAAAAACCCTTC
AAATTTTTTTGGATTGAATAATATATTTTTTCTGAGTATTGTGGCAAAAAATTGGAAAAAAATTT
TCGGGTCAGTTTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCG
Found at i:7209 original size:18 final size:17
Alignment explanation
Indices: 7186--7224 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
7176 TTGATATAAT
7186 TAAAAATAAATTCAAAAA
1 TAAAAATAAATT-AAAAA
*
7204 TAAAAATAAATTGAAAA
1 TAAAAATAAATTAAAAA
7221 TAAA
1 TAAA
7225 TTCGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAAATAAATTAAAAA
Found at i:7220 original size:11 final size:11
Alignment explanation
Indices: 7206--7239 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
7196 TTCAAAAATA
7206 AAAATAAATTG
1 AAAATAAATTG
7217 AAAATAAATTCG
1 AAAATAAATT-G
7229 AAAA-AAATTG
1 AAAATAAATTG
7239 A
1 A
7240 TTGCGAAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 15 0.68
12 5 0.23
ACGTcount: A:0.65, C:0.03, G:0.09, T:0.24
Consensus pattern (11 bp):
AAAATAAATTG
Found at i:12172 original size:29 final size:30
Alignment explanation
Indices: 12120--12187 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
12110 TTAGGTTGAT
* *
12120 GGGGCAAAACGTTCTAAAATTGAAGTTCAA
1 GGGGCAAAACGTTCCAAAATTGAAATTCAA
*
12150 GGGGCAAAATG-TCCAAAATTGAAATTCAA
1 GGGGCAAAACGTTCCAAAATTGAAATTCAA
**
12179 AAGGCAAAA
1 GGGGCAAAA
12188 AACCCAAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 23 0.70
30 10 0.30
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.19
Consensus pattern (30 bp):
GGGGCAAAACGTTCCAAAATTGAAATTCAA
Found at i:12194 original size:29 final size:29
Alignment explanation
Indices: 12135--12195 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
12125 AAAACGTTCT
* ** ***
12135 AAAATTGAAGTTCAAGGGGCAAAATGTCC
1 AAAATTGAAATTCAAAAGGCAAAAAACCC
12164 AAAATTGAAATTCAAAAGGCAAAAAACCC
1 AAAATTGAAATTCAAAAGGCAAAAAACCC
12193 AAA
1 AAA
12196 CGCTACAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.52, C:0.15, G:0.16, T:0.16
Consensus pattern (29 bp):
AAAATTGAAATTCAAAAGGCAAAAAACCC
Found at i:15544 original size:15 final size:16
Alignment explanation
Indices: 15510--15542 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
15500 GAAAATTTCA
15510 TTGTTTATATATTTTT
1 TTGTTTATATATTTTT
15526 TTGTTTATATATTTTT
1 TTGTTTATATATTTTT
15542 T
1 T
15543 GTATTTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (16 bp):
TTGTTTATATATTTTT
Found at i:15664 original size:21 final size:21
Alignment explanation
Indices: 15640--15681 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
15630 AATACAGTAA
15640 TTTTATTTAACTCTCTCCTTT
1 TTTTATTTAACTCTCTCCTTT
15661 TTTTATTTAACTCTCTCCTTT
1 TTTTATTTAACTCTCTCCTTT
15682 AATCTGTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTATTTAACTCTCTCCTTT
Found at i:16295 original size:2 final size:2
Alignment explanation
Indices: 16288--16322 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
16278 AAACTTTTAG
16288 AT AT AT AT AT AT AT AT GAT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
16323 TTAAAACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16309 original size:17 final size:17
Alignment explanation
Indices: 16287--16320 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16277 AAAACTTTTA
16287 GATATATATATATATAT
1 GATATATATATATATAT
16304 GATATATATATATATAT
1 GATATATATATATATAT
16321 ATTTAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
GATATATATATATATAT
Found at i:17978 original size:106 final size:104
Alignment explanation
Indices: 17837--18038 Score: 300
Period size: 106 Copynumber: 1.9 Consensus size: 104
17827 TTTTTTAGGA
** *
17837 TTAATCTCCGTATGTATATTTCTTATCTTTCTCTTGAAGTCATTGAAATGATTCTTTATTATTTT
1 TTAATCTCCACATGTATATTTCTTATCTTTCTCTTGAAGTCATGGAAATGATTC---ATTATTTT
*
17902 CATGATGTTTTT-TTTTTT-GGCTATAAAAGATAAATACAGGT
63 CATGATGTTTTTCTTTTTTCGTC-ATAAAAGATAAATACAGGT
*
17943 TTAATCTCCACATGTATATTTCTTATCTTTCTCTTGAAGTCATGGAAATGATTCCTTATTTTCAT
1 TTAATCTCCACATGTATATTTCTTATCTTTCTCTTGAAGTCATGGAAATGATTCATTATTTTCAT
*
18008 GCTGTTTTTCTTTTTTCGTCATAAAAGATAA
66 GATGTTTTTCTTTTTTCGTCATAAAAGATAA
18039 GTTCTTGCAA
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
103 18 0.20
104 17 0.19
105 2 0.02
106 51 0.58
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (104 bp):
TTAATCTCCACATGTATATTTCTTATCTTTCTCTTGAAGTCATGGAAATGATTCATTATTTTCAT
GATGTTTTTCTTTTTTCGTCATAAAAGATAAATACAGGT
Found at i:18518 original size:26 final size:26
Alignment explanation
Indices: 18465--18519 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
18455 TGTTTTGATC
* * * *
18465 ATTATTCTCACTTTTTTTAAAAGGAA
1 ATTATTCTCACTATTATAAAAAGCAA
*
18491 ATTATTCTCACTATTATAAAAATCAA
1 ATTATTCTCACTATTATAAAAAGCAA
18517 ATT
1 ATT
18520 TGGATTAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.44
Consensus pattern (26 bp):
ATTATTCTCACTATTATAAAAAGCAA
Done.