Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014303.1 Corchorus olitorius cultivar O-4 contig14336, 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: 21938
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:605 original size:331 final size:330
Alignment explanation
Indices: 1--1782 Score: 2338
Period size: 331 Copynumber: 5.4 Consensus size: 330
*
1 ATTTGTTTTTACGAGCATCTGAATCTCGTTTCGATTTAACTAAGAAATAAATTCGAAAAAAAATG
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACT-AGAAATAAATTCG-AAAAAAATG
* * * * *
66 AAAAAATGATATTAGACGCGTGAAAAACCATTCAATTTTGTTGATGCTGAATAATATATTTTTTC
64 GAAAAATGATATTAGAAGCGTG-AAAACCCTTCAATTTTTTTGATGCTGAATTATATATTTTTTC
* * * *
131 TGAGTATTGTGGCAAAAAATTGAAGAAAAACTTTTCGGGTCAGGTTATGCAAAATTTTAGCCGAA
128 TGAGTATTGTGGCAAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAA
* * * * *
196 ATCGTGTACTAACCATCACGGTGTTTGGCTAAAAACGCATTCCGGGACCCCGGCTCAATTTTACA
193 ATCGTGTACTAACCATCACGGTGTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTGACA
* * *
261 TGATCTTTGGCAGAAAGACTCATTGAAATATCAATATTCATCTAACCAAATCTCAGCCACAATGG
258 TGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGG
*
326 ATTTAAGG
323 ATTAAAGG
334 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAGAAATAAATTCGAAAAAAATGGA
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAGAAATAAATTCGAAAAAAATGGA
* * *
399 AAAATGATATTAGAAGCGTGAAAACCCATTCAATTTTTTTGATGCTGAATAATATATTGTTTCTA
66 AAAATGATATTAGAAGCGTGAAAACCC-TTCAATTTTTTTGATGCTGAATTATATATTTTTTCTG
* * * *
464 AGTATTTTGGCAAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAATTTTTATCTGAAAT
130 AGTATTGTGGCAAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAAT
*
529 CGTGTACTAACCATCACGATGTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTGACATG
195 CGTGTACTAACCATCACGGTGTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTGACATG
594 ATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGAT
260 ATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGAT
659 TAAAGG
325 TAAAGG
* * *
665 ATTTGTTTTTACGAGCATCTGAATCTTATTTCAATTTAACTTGAAATAAATTCGAAAAAAATGGA
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAGAAATAAATTCGAAAAAAATGGA
* * ***
730 AAAATGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGTGTTGTCCTATATATTTTTTTCT
66 AAAATGATATTAGAAGCGTG-AAAACCCTTCAATTTTTTTGATGCTGAATTATATA-TTTTTTCT
* * ** * * *
795 GTGTATAGTGGCAACGAATTCAGGAAAAAAAATTTT--GGTCAGTTTTTGCAAATTTTTAGCCAA
129 GAGTATTGTGGCAAAAAATTGAGG--AAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGA
* ** * * *
858 AATCGT-T-TTATTCATCACGGTTTTTGGCTAAAAACGCG-TTCCGGACTCCCGGCTCAGTTTTG
192 AATCGTGTACTAACCATCACGGTGTTTGGCTAAAAACGCGTTTCGGGGC-CCCGGCTCAG-TTTG
* *** * * * *
920 A-ATGATTTTTAGC-GTAAAGACTCCAAAAAATATCTATATTCATCGAACCAAACCCCATCCACA
255 ACATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACA
* * *
983 TTGGATTTAACG
319 ATGGATTAAAGG
* * * * *
995 ATTTGTTTTTATGAGCTTTTGAATCTTGTTTCGATTTGATTAGAAATAAATTCCG-AAAAAATGG
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAGAAATAAATT-CGAAAAAAATGG
** * **
1059 AAAACCGATATGAGAATTGTGAAAACCCCTTCAATTTTTTTGATGCTGAATTATATATTTTTTCT
65 AAAAATGATATTAGAAGCGTGAAAA-CCCTTCAATTTTTTTGATGCTGAATTATATATTTTTTCT
* * *
1124 AAGTATTGTGGCAAAAAATTGATGAAAAAATTTTCGGGTCAGTTTTTACAAAATTTTAGCCGAAA
129 GAGTATTGTGGCAAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAA
* * * *
1189 TCGTGTACTAACCATCACGGTGTTTGGCTAAAAACGTGCTTCGGGGCCTCGGCTCAGTTTTACAT
194 TCGTGTACTAACCATCACGGTGTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTGACAT
* **
1254 GATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATTTAACCAAATCTCAGGTA-AATTGG
259 GATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAA-TGG
1318 ATTAAAGG
323 ATTAAAGG
* * *
1326 ATTAGTTTTTACAAGCATCTGAATCTTGTTTCGATTTCAATTAGAAATAAATTCTG--AAAAATG
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT-AACTAGAAATAAATTC-GAAAAAAATG
* * *
1389 GAAAACA-GATATTAGAAGTGTAAAAAAACCCTTC-ATTCTTTT--TGCTGAATTATATA-TTTT
64 GAAAA-ATGATATTAGAAGCGT--GAAAACCCTTCAATTTTTTTGATGCTGAATTATATATTTTT
* * *
1449 TCTGACTATTATGG-AAAAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCG
126 TCTGAGTATTGTGGCAAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCG
* * * * * * *
1513 AAATCGTGTAATAATCATCACGGTGTTTGGCTAAAAACGTGTTTCGGGGGCCCAGCTTAGTTTCA
191 AAATCGTGTACTAACCATCACGGTGTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTGA
* *
1578 CATGATTTTTGGCAGAAAGATTCCTTGAAATATCTATATTCATTTAACCAAATCTCAGCCACAAT
256 CATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAAT
1643 GGATTAAAGG
321 GGATTAAAGG
*
1653 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCTATTTAACTAGAAATAAATTCGAAAAAAATGGA
1 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAGAAATAAATTCGAAAAAAATGGA
* * * * *
1718 AAAATCATCTTAGAAGCGTGAAAAGCCCTTCAATTTTTTTGGTGTTGACTTATATATTTTTTCTG
66 AAAATGATATTAGAAGCGTGAAAA-CCCTTCAATTTTTTTGATGCTGAATTATATATTTTTTCTG
1783 TGTCTAGTGG
Statistics
Matches: 1264, Mismatches: 153, Indels: 67
0.85 0.10 0.05
Matches are distributed among these distances:
325 5 0.00
326 22 0.02
327 247 0.20
328 17 0.01
329 92 0.07
330 212 0.17
331 513 0.41
332 102 0.08
333 44 0.03
334 10 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (330 bp):
ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAGAAATAAATTCGAAAAAAATGGA
AAAATGATATTAGAAGCGTGAAAACCCTTCAATTTTTTTGATGCTGAATTATATATTTTTTCTGA
GTATTGTGGCAAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATC
GTGTACTAACCATCACGGTGTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTGACATGA
TTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATT
AAAGG
Found at i:1388 original size:661 final size:659
Alignment explanation
Indices: 5--1781 Score: 2331
Period size: 661 Copynumber: 2.7 Consensus size: 659
1 ATTT
* * *
5 GTTTTTACGAGCATCTGAATCTCGTTTCGATTTAACTAAGAAATAAATTCGAAAAAAAATGAAAA
1 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTTAGAAATAAATTCG--AAAAAATGGAAA
* * * *
70 AATGATATTAGACGCGTGAAAAACCATTCAATTTTGTTGATGCTG-AATAATATATTTTTTCTGA
64 AATGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGATG-TGTTAT-ATAT-TTTTTTCTGA
* * *
134 GTATTGTGGCAAAAAATT--GAAGAAAAACTTTTCGGGTCAGGTTATGCAAAATTTTAGCCGAAA
126 GTATAGTGGCAAAAAATTAGGAA-AAAAACTTTTC-GGTCAGTTTTTGCAAAATTTTAGCCGAAA
* * * *
197 TCGTGTACTAACCATCACGGTGTTTGGCTAAAAACGCATTCCGGGACCCCGGCTCAATTTTACAT
189 TCGTGTAATAATCATCACGGTGTTTGGCTAAAAACGCGTTCC-GGACCCCGGCTCAGTTTTACAT
* *
262 GATCTTTGGCAGAAAGACT-CATTGAAATATCAATATTCATCTAACCAAATCTCAGCCACAATGG
253 GATTTTTGGCAGAAAGACTCCA-TGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGG
326 ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAGAAATAAATTCGAAA
317 ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAGAAATAAATTCGAAA
* * *
391 AAAATGGAAAAATGATATTAGAAGCGTGAAAACCCATTCAATTTTTTTGATGCTGAATAATATAT
382 AAAATGGAAAAACGATATTAGAAGCGTGAAAACCCCTTCAATTTTTTTGATGCTGAATTATATAT
* * * *
456 TGTTTCTAAGTATTTTGGCAAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAATTTTTA
447 TTTTTCTAAGTATTGTGGCAAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTACAAAATTTTA
* * *
521 TCTGAAATCGTGTACTAACCATCACGATGTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGT
512 GCCGAAATCGTGTACTAACCATCACGATGTTTGGCTAAAAACGCGCTTCGGGGCCCCGGCTCAGT
586 TTGACATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCA
577 TTGACATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCA
*
651 CAATGGATTAAAGGATTT
642 CAATGGATTAAAGGATTA
* *
669 GTTTTTACGAGCATCTGAATCTTATTTCAATTTAACTT-GAAATAAATTCGAAAAAAATGGAAAA
1 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTTAGAAATAAATTCG-AAAAAATGGAAAA
* *
733 ATGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGTGTTGTCCTATATATTTTTTTCTGTG
65 ATGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGATG-TGT--TATATATTTTTTTCTGAG
** * * *
798 TATAGTGGCAACGAATTCAGGAAAAAAAATTTT-GGTCAGTTTTTGCAAATTTTTAGCCAAAATC
127 TATAGTGGCAAAAAATT-AGGAAAAAAACTTTTCGGTCAGTTTTTGCAAAATTTTAGCCGAAATC
* * *
862 GT-T-TTATTCATCACGGTTTTTGGCTAAAAACGCGTTCCGGACTCCCGGCTCAGTTTTGA-ATG
191 GTGTAATAATCATCACGGTGTTTGGCTAAAAACGCGTTCCGGAC-CCCGGCTCAGTTTT-ACATG
* ** * * * * *
924 ATTTTTAGC-GTAAAGACTCCAAAAAATATCTATATTCATCGAACCAAACCCCATCCACATTGGA
254 ATTTTTGGCAG-AAAGACTCCATGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGA
* * * * * *
988 TTTAACGATTTGTTTTTATGAGCTTTTGAATCTTGTTTCGATTTGATTAGAAATAAATTCCG-AA
318 TTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAGAAATAAATT-CGAAA
* * **
1052 AAAATGGAAAACCGATATGAGAATTGTGAAAACCCCTTCAATTTTTTTGATGCTGAATTATATAT
382 AAAATGGAAAAACGATATTAGAAGCGTGAAAACCCCTTCAATTTTTTTGATGCTGAATTATATAT
*
1117 TTTTTCTAAGTATTGTGGCAAAAAATTGATGAAAAAATTTTCGGGTCAGTTTTTACAAAATTTTA
447 TTTTTCTAAGTATTGTGGCAAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTACAAAATTTTA
* * *
1182 GCCGAAATCGTGTACTAACCATCACGGTGTTTGGCTAAAAACGTGCTTCGGGGCCTCGGCTCAGT
512 GCCGAAATCGTGTACTAACCATCACGATGTTTGGCTAAAAACGCGCTTCGGGGCCCCGGCTCAGT
* * **
1247 TTTACATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATTTAACCAAATCTCAGGTA
577 TTGACATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCA
1312 -AATTGGATTAAAGGATTA
642 CAA-TGGATTAAAGGATTA
*
1330 GTTTTTACAAGCATCTGAATCTTGTTTCGATTTCAA-TTAGAAATAAATTCTG-AAAAATGGAAA
1 GTTTTTACGAGCATCTGAATCTTGTTTCGATTT-AACTTAGAAATAAATTC-GAAAAAATGGAAA
* * * **
1393 ACA-GATATTAGAAGTGTAAAAAAACCCTTC-ATTCTTTTTGCTGAATTATATA--TTTTTCTGA
64 A-ATGATATTAGAAGCGT-GAAAAACCCTTCAATT-TTTTTGATGTGTTATATATTTTTTTCTGA
*
1454 CTATTA-TGG-AAAAAATTGAGG--AAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAA
126 GTA-TAGTGGCAAAAAATT-AGGAAAAAAACTTTTC-GGTCAGTTTTTGCAAAATTTTAGCCGAA
* * ** * * *
1515 ATCGTGTAATAATCATCACGGTGTTTGGCTAAAAACGTGTTTCGGGGGCCCAGCTTAGTTTCACA
188 ATCGTGTAATAATCATCACGGTGTTTGGCTAAAAACGCG-TTCCGGACCCCGGCTCAGTTTTACA
* * *
1580 TGATTTTTGGCAGAAAGATTCCTTGAAATATCTATATTCATTTAACCAAATCTCAGCCACAATGG
252 TGATTTTTGGCAGAAAGACTCCATGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGG
* *
1645 ATTAAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCTATTTAACTAGAAATAAATTCGAAA
317 ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAGAAATAAATTCGAAA
* * * * *
1710 AAAATGGAAAAATC-ATCTTAGAAGCGTGAAAAGCCCTTCAATTTTTTTGGTGTTGACTTATATA
382 AAAATGGAAAAA-CGATATTAGAAGCGTGAAAACCCCTTCAATTTTTTTGATGCTGAATTATATA
1774 TTTTTTCT
446 TTTTTTCT
1782 GTGTCTAGTG
Statistics
Matches: 966, Mismatches: 119, Indels: 62
0.84 0.10 0.05
Matches are distributed among these distances:
654 9 0.01
656 40 0.04
657 17 0.02
658 208 0.22
659 13 0.01
660 7 0.01
661 463 0.48
662 91 0.09
663 66 0.07
664 38 0.04
665 11 0.01
666 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (659 bp):
GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTTAGAAATAAATTCGAAAAAATGGAAAAA
TGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGATGTGTTATATATTTTTTTCTGAGTATA
GTGGCAAAAAATTAGGAAAAAAACTTTTCGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA
ATAATCATCACGGTGTTTGGCTAAAAACGCGTTCCGGACCCCGGCTCAGTTTTACATGATTTTTG
GCAGAAAGACTCCATGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGGA
TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAACTAGAAATAAATTCGAAAAAAATGGAA
AAACGATATTAGAAGCGTGAAAACCCCTTCAATTTTTTTGATGCTGAATTATATATTTTTTCTAA
GTATTGTGGCAAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTACAAAATTTTAGCCGAAATC
GTGTACTAACCATCACGATGTTTGGCTAAAAACGCGCTTCGGGGCCCCGGCTCAGTTTGACATGA
TTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATT
AAAGGATTA
Found at i:2877 original size:330 final size:328
Alignment explanation
Indices: 1813--4253 Score: 2338
Period size: 328 Copynumber: 7.5 Consensus size: 328
1803 GTTCCGAGCT
* * *
1813 CCCGGCTCAGTTTTGA-ATGATTTTTAGC-GTAAAGACTCCTTAAAATATCTATATTCAT-TGAA
1 CCCGACTCAGTTTT-ACATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCT-AA
* * * * * * * * *
1875 CCAAACCCCATCCACATTGGATTTAACGATTTGTTTTTATGAGCTTTTGAATCTTGTTTCGATTT
63 CCAAATCTCAGCCACAATGGATTAAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * * *
1940 GATTAAAAATAAATTCGTAAAAAAAAAATGGGAAAACGATATTAGAAGCGT-AAAAATCCTTGAA
128 AATTAGAAATAAATTCG----AAAAAAAT-GGAAAACGATATTAGAAGCGTGAAAAACCCTTCAA
* * ** *
2004 TCTTTTT-GCGTTGAATTATATATTTTTTATGAGTATTAAGGCAAAAACTTGA-GAAAAAGCTTT
188 T-TTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAA-CTTT
** * * ** * *
2067 TCATGTCAG-----G-----TTTTAGCCGAAATCATGTAGTAACATCAATGTATTTGGCTAAAAA
251 TCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACATCACGGTTTTTGTCTAAAAA
* * * **
2122 TGGGTTTCGGATC
316 CGCGATTCGGGGC
* * * * * * * ** ** **
2135 CTCGACTTAGTTTTCCATAAATTTTGACACAAAGACTCCTCCAAATAAT-TATAACCATC-AAAA
1 CCCGACTCAGTTTTACATGATTTTTGGCAGAAAGACTCCTTGAAAT-ATCTATATTCATCTAACC
* * * * * *
2198 AAATCTCAGCCACATTGGATTTAGGGATTAG-ATTTACGAGCATCAGAAT-TTCGTTTCGATTTA
65 AAATCTCAGCCACAATGGATTAAAGGATTTGTTTTTACGAGCATCTGAATCTT-GTTTCGATTTA
* * * * * *
2261 ATAAGATATAAATTCAGGAAAAAA---AAAACGATACTAGAATCGTG-AAAACCCTTTAATTTTT
129 ATTAGAAATAAATTC-GAAAAAAATGGAAAACGATATTAGAAGCGTGAAAAACCCTTCAA-TTTT
* * * * * *
2322 TTGATGCTGAATTATTTA-TTTTTCTAAGTATTGTGG-AAAAAATTGAGGTAAGACTTTTCGGGT
192 TTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGT
* * * * * *
2385 CAGTTTTTGCAAAATTTTAGTCGAAATCGTGTGCTAACCATCACGATTTTAGGCTAAAAACGTGA
257 CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CATCACGGTTTTTGTCTAAAAACGCGA
2450 TTCGGGGC
321 TTCGGGGC
* * *
2458 CCCGGCTCAGTTTAACATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATACTCATCTAACCA
1 CCCGACTCAGTTTTACATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCA
*
2523 AATCAT-AGCCACAATGGATTAAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAA
66 AATC-TCAGCCACAATGGATTAAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
* *
2587 TTAGATATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTG
130 TTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTG
* * * *
2652 GATGCTGAATTATATATTTTTGTCTAAGTATTCTGACAAAAAATTGAGGAAAAACTTTTCGGGTC
195 G-TGTTGAATTATATATTTTT-TCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTC
*
2717 AGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGTCTAAAAATGCGAT
258 AGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CATCACGGTTTTTGTCTAAAAACGCGAT
2782 TCGGGG-
322 TCGGGGC
2788 CCCGACTCAGTTTTACATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCA
1 CCCGACTCAGTTTTACATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCA
* * * *
2853 AATCTCATCCAAAATGGATTAAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAAC
66 AATCTCAGCCACAATGGATTAAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
* * * * *
2918 TAAAAATAAATTCGAAAAAAATGGAAAAATGATCTTAGAAGCGTCAAAAACCCATCAATTTTTTT
131 TAGAAATAAATTCGAAAAAAATGG-AAAACGATATTAGAAGCGTGAAAAACCCTTCAA-TTTTTT
* * * * * * * * * *
2983 CGTGTTGACTTGTGTATTTTTTCTGTGTATAGTGGCAAACAATTTAGGAAAAAATTTTCGGGTCT
194 GGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCA
* * *
3048 GTTTTT-CTAAAATTTTAGCCGAAATCGTTTACT-A-ATAACGGTTTTTGGT-TAAAAACACG-T
259 GTTTTTGC-AAAATTTTAGCCGAAATCGTGTACTAACATCACGGTTTTT-GTCTAAAAACGCGAT
*
3108 TCCGGGGT
322 T-CGGGGC
* * * * ** * * *
3116 CCCGGCTCAGTTTCGA-ATGATTTTTAGC-GTAAAGACTGCGCGAAATATCTACATTTATCGAAC
1 CCCGACTCAGTTT-TACATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAAC
** * * * * * * ** *
3179 CATACCCCCAACCACATTGGATTTAACGATTTGTTTTTATGAGTTTTTGAATCTTGTTTCGATTT
64 CA-AATCTCAGCCACAATGGATTAAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
*
3244 GATTAGGAAA-AAATTCCG-AAAAAATGGAAAACCGATATTAGAAGCGTGAAAAACCCTTCAATA
128 AATTA-GAAATAAATT-CGAAAAAAATGGAAAA-CGATATTAGAAGCGTGAAAAACCCTTCAAT-
* * * * *
3307 TTTTTGGCGTTGAATTATTTATTTTTTCTTAGTATTCTGAC-AAAAATTGAGGAAAAACTTTTCG
189 TTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCG
*
3371 GGTCCGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGTCTAAAAACG
254 GGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CATCACGGTTTTTGTCTAAAAACG
3436 CGATTCGGGG-
318 CGATTCGGGGC
* *
3446 CCCGACTCAGTTTTACATGA-TTATGTGCAAAAAGACTCCTTGAAATATCTATATTCATCTAACC
1 CCCGACTCAGTTTTACATGATTTTTG-GCAGAAAGACTCCTTGAAATATCTATATTCATCTAACC
* * * *
3510 AAATCACAGCCACAATGGATTAAAGGATTTGTTTTTACGACCATCTGAAACTTGTTTCCATTTAA
65 AAATCTCAGCCACAATGGATTAAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
* * *
3575 CTAGAAATAAATTCGAAAAAAATGGACAAATGATATTAGAAGCGTGAAAAATCCTTCAATCTTTT
130 TTAGAAATAAATTCGAAAAAAATGGA-AAACGATATTAGAAGCGTGAAAAACCCTTCAA--TTTT
* * * * * * * *
3640 TTGGCGTTGACTTGTATATTTTTTCTGTGTATAGTGGCAAAGAATTGAGGAAAAATTTTTCAGGT
192 TTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGT
* * * * *
3705 CTGTTTTGGCAAAATTTTA-CCGAAATTGTTTACT--CATCACGGTTTTT-TGCTAAAAACGCGT
257 CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACATCACGGTTTTTGT-CTAAAAACGCGA
*
3766 TTCGGGGT
321 TTCGGGGC
* * * ** * *
3774 CCC-AGCTCAGTTTCGA-ATGATTTTTAGC-GTAAAGACTGCGCGAAATATCTATATTAATCGAA
1 CCCGA-CTCAGTTT-TACATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAA
* * * * * * * * * * *
3836 CCAAACCCCAACCACATTGGATTTAACGATTTGTTTTCATGAGCTTTTGAATCTTTTTTCGATTT
63 CCAAATCTCAGCCACAATGGATTAAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * *
3901 GATTA-AGAATAAATTCCG-AAAAAATGGAAACCCGATATTAAAAGCGTGAAAAACCCTTCAATT
128 AATTAGA-AATAAATT-CGAAAAAAATGGAAA-ACGATATTAGAAGCGTGAAAAACCCTTCAA-T
* * * * * *
3964 TTTTTGATGCTAAATTATATATTTTTTCTGAGTATAGTGGGAAAATATTGAGGAAAAACTTTTCG
189 TTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCG
* ** * *
4029 GGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACT--CATCATGGTTTTTGGATAACAACGT
254 GGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACATCACGGTTTTTGTCTAAAAACGC
*
4092 GTTTCGGGGC
319 GATTCGGGGC
* * * **
4102 CCCGACTCAATTTTACATGATTTTTGGTAGAAAGACTCCTTGAGATATCTATATTCATCTAATTA
1 CCCGACTCAGTTTTACATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCA
* * *
4167 AATCTCAGCCACAATGGATTAAAGGATTTGTTTATATGAGCATCTGAATCTCGTTTCGATTTAAT
66 AATCTCAGCCACAATGGATTAAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
* *
4232 AAGATATAAATTCGGAAAAAAA
131 TAGAAATAAATTC-GAAAAAAA
4254 ATTTATTTAT
Statistics
Matches: 1733, Mismatches: 306, Indels: 153
0.79 0.14 0.07
Matches are distributed among these distances:
312 20 0.01
313 50 0.03
314 12 0.01
317 7 0.00
319 2 0.00
320 35 0.02
321 28 0.02
322 61 0.04
323 70 0.04
324 34 0.02
325 41 0.02
326 5 0.00
327 160 0.09
328 434 0.25
329 244 0.14
330 322 0.19
331 200 0.12
332 8 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (328 bp):
CCCGACTCAGTTTTACATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCA
AATCTCAGCCACAATGGATTAAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
TAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTGG
TGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCAGT
TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACATCACGGTTTTTGTCTAAAAACGCGATTCGG
GGC
Found at i:4255 original size:658 final size:653
Alignment explanation
Indices: 1790--4253 Score: 2797
Period size: 658 Copynumber: 3.8 Consensus size: 653
1780 CTGTGTCTAG
* * * ***
1790 TGGCTAAAAACACGTTCCGAGCTCCCGGCTCAGTTTTGAATGATTTTTAGCGTAAAGACTCCTTA
1 TGGCTAAAAACACGTTCCGGGGTCCCGGCTCAGTTTCGAATGATTTTTAGCGTAAAGACTCCGCG
* *
1855 AAATATCTATATTCATTGAACCAAACCCCATCCACATTGGATTTAACGATTTGTTTTTATGAGCT
66 AAATATCTATATTCATCGAACCAAACCCCAACCACATTGGATTTAACGATTTGTTTTTATGAGCT
*
1920 TTTGAATCTTGTTTCGATTTGATTAAAAATAAATTCGTAAAAAAAAAATGGGAAAACGATATTAG
131 TTTGAATCTTGTTTCGATTTGATTAAGAATAAATTCG----AAAAAAAT-GGAAAACGATATTAG
* * * * * * *
1985 AAGCGT-AAAAATCCTTGAATCTTTTTG-CGTTGAATTATATATTTTTTATGAGTATTA-AGGCA
191 AAGCGTGAAAAACCCTTCAATATTTTTGACGCTGAATTATATATTTTTTCTGAGTA-TACTGACA
** * *
2047 AAAACTTGA-GAAAAAGCTTTTCATGTCAG-----G-----TTTTAGCCGAAATCATGTAGTAAC
255 AAAA-TTGAGGAAAAA-CTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACT-AC
** * * * * ** * * * * * *
2101 ATCAATGTATTTGGCTAAAAATGGGTTTCGGATCCTCGACTTAGTTTTCCATAAATTTTGACACA
317 ATCACGGTTTTTGGCTAAAAACGCGATTCGGGGCC-CGACTCAGTTTTACATGATTTTTGGCAGA
** ** ** * * * *
2166 AAGACTCCTCCAAATAAT-TATAACCATC-AAAAAAATCTCAGCCACATTGGATTTAGGGATTAG
381 AAGACTCCTTGAAAT-ATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATTTG
* * * * *
2229 -ATTTACGAGCATCAGAATTTCGTTTCGATTTAA-TAAGATATAAATTCAGGAAAAAA---AAAA
445 TTTTTACGAGCATCTGAATCTCGTTTCGATTTAACTAAGAAATAAATTC-GAAAAAAATGGAAAA
* * * * * * * * * **
2289 CGATACTAGAATCGTG-AAAACCCTTTAATTTTTTTGATGCTGAATTATTTA-TTTTTCTAAGTA
509 TGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGTGTTGACTTGTATATTTTTTCTGTGTA
* * * * * *
2352 TTGTGG-AAAAAATTGAGGTAAGACTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATCGTG
574 TAGTGGCAAAAAATTGAGGAAAAAATTTTCGGGTCTG-TTTTGCAAAATTTTAGCCGAAAT--TG
* *
2416 TGCTAAC-CATCACGATTTT
636 T--TTACTCATCACGGTTTT
* ** * * *
2435 AGGCTAAAAACGTGATT-CGGGGCCCCGGCTCAGTTT-AACATGATTTTTGGCAG-AAAGACTCC
1 TGGCTAAAAACACG-TTCCGGGGTCCCGGCTCAGTTTCGA-ATGATTTTTAGC-GTAAAGACTCC
** * * * ** * * * * *
2497 TTGAAATATCTATACTCATCTAACCAAATCATAGCCACAATGGATTAAAGGATTTGTTTTTACGA
63 GCGAAATATCTATATTCATCGAACCAAACCCCAACCACATTGGATTTAACGATTTGTTTTTATGA
* * * *
2562 GCATCTAAATCTTGTTTCGATTTAATT-AGATATAAATTCGAAAAAAATGGAAAACGATATTAGA
128 GCTTTTGAATCTTGTTTCGATTTGATTAAGA-ATAAATTCGAAAAAAATGGAAAACGATATTAGA
* * * *
2626 AGCGTGAAAAACCCTTCAATATTTTGGATGCTGAATTATATATTTTTGTCTAAGTATTCTGACAA
192 AGCGTGAAAAACCCTTCAATATTTTTGACGCTGAATTATATATTTTT-TCTGAGTATACTGAC-A
2691 AAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA
255 AAAATTGAGGAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACT-A-CA
* *
2756 TCACGGTTTTTGTCTAAAAATGCGATTCGGGGCCCGACTCAGTTTTACATGATTTTTGGCAGAAA
318 TCACGGTTTTTGGCTAAAAACGCGATTCGGGGCCCGACTCAGTTTTACATGATTTTTGGCAGAAA
* *
2821 GACTCCTTGAAATATCTATATTCATCTAACCAAATCTCATCCAAAATGGATTAAAGGATTTGTTT
383 GACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATTTGTTT
**
2886 TTACGAGCATCTGAATCTTATTTCGATTTAACTAA-AAATAAATTCGAAAAAAATGGAAAAATGA
448 TTACGAGCATCTGAATCTCGTTTCGATTTAACTAAGAAATAAATTCGAAAAAAATGG-AAAATGA
* * * * *
2950 TCTTAGAAGCGTCAAAAACCCATCAATTTTTTTCGTGTTGACTTGTGTATTTTTTCTGTGTATAG
512 TATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGTGTTGACTTGTATATTTTTTCTGTGTATAG
* * * *
3015 TGGCAAACAATTTAGGAAAAAATTTTCGGGTCTGTTTTTCTAAAATTTTAGCCGAAATCGTTTAC
577 TGGCAAAAAATTGAGGAAAAAATTTTCGGGTCTGTTTTGC-AAAATTTTAGCCGAAATTGTTTAC
* *
3080 TAATAACGGTTTT
641 TCATCACGGTTTT
* *
3093 TGGTTAAAAACACGTTCCGGGGTCCCGGCTCAGTTTCGAATGATTTTTAGCGTAAAGACTGCGCG
1 TGGCTAAAAACACGTTCCGGGGTCCCGGCTCAGTTTCGAATGATTTTTAGCGTAAAGACTCCGCG
* * * *
3158 AAATATCTACATTTATCGAACCATACCCCCAACCACATTGGATTTAACGATTTGTTTTTATGAGT
66 AAATATCTATATTCATCGAACCA-AACCCCAACCACATTGGATTTAACGATTTGTTTTTATGAGC
* *
3223 TTTTGAATCTTGTTTCGATTTGATTAGGAAAAAATTCCG-AAAAAATGGAAAACCGATATTAGAA
130 TTTTGAATCTTGTTTCGATTTGATTAAGAATAAATT-CGAAAAAAATGGAAAA-CGATATTAGAA
* * * * *
3287 GCGTGAAAAACCCTTCAATATTTTTGGCGTTGAATTATTTATTTTTTCTTAGTATTCTGACAAAA
193 GCGTGAAAAACCCTTCAATATTTTTGACGCTGAATTATATATTTTTTCTGAGTATACTGACAAAA
*
3352 ATTGAGGAAAAACTTTTCGGGTCCGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
258 ATTGAGGAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACT-A-CATCA
* * *
3417 CGGTTTTTGTCTAAAAACGCGATTCGGGGCCCGACTCAGTTTTACATGA-TTATGTGCAAAAAGA
321 CGGTTTTTGGCTAAAAACGCGATTCGGGGCCCGACTCAGTTTTACATGATTTTTG-GCAGAAAGA
*
3481 CTCCTTGAAATATCTATATTCATCTAACCAAATCACAGCCACAATGGATTAAAGGATTTGTTTTT
385 CTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATTTGTTTTT
* * * *
3546 ACGACCATCTGAAACTTGTTTCCATTTAACT-AGAAATAAATTCGAAAAAAATGGACAAATGATA
450 ACGAGCATCTGAATCTCGTTTCGATTTAACTAAGAAATAAATTCGAAAAAAATGGA-AAATGATA
* *
3610 TTAGAAGCGTGAAAAATCCTTCAATCTTTTTTGGCGTTGACTTGTATATTTTTTCTGTGTATAGT
514 TTAGAAGCGTGAAAAACCCTTCAAT-TTTTTTGGTGTTGACTTGTATATTTTTTCTGTGTATAGT
* * *
3675 GGCAAAGAATTGAGGAAAAATTTTTCAGGTCTGTTTTGGCAAAATTTTA-CCGAAATTGTTTACT
578 GGCAAAAAATTGAGGAAAAAATTTTCGGGTCTGTTTT-GCAAAATTTTAGCCGAAATTGTTTACT
3739 CATCACGGTTTT
642 CATCACGGTTTT
* * * * *
3751 TTGCTAAAAACGCGTTTCGGGGTCCCAGCTCAGTTTCGAATGATTTTTAGCGTAAAGACTGCGCG
1 TGGCTAAAAACACGTTCCGGGGTCCCGGCTCAGTTTCGAATGATTTTTAGCGTAAAGACTCCGCG
* *
3816 AAATATCTATATTAATCGAACCAAACCCCAACCACATTGGATTTAACGATTTGTTTTCATGAGCT
66 AAATATCTATATTCATCGAACCAAACCCCAACCACATTGGATTTAACGATTTGTTTTTATGAGCT
* * *
3881 TTTGAATCTTTTTTCGATTTGATTAAGAATAAATTCCG-AAAAAATGGAAACCCGATATTAAAAG
131 TTTGAATCTTGTTTCGATTTGATTAAGAATAAATT-CGAAAAAAATGGAAA-ACGATATTAGAAG
* * * * **
3945 CGTGAAAAACCCTTCAATTTTTTTGATGCTAAATTATATATTTTTTCTGAGTATAGTGGGAAAAT
194 CGTGAAAAACCCTTCAATATTTTTGACGCTGAATTATATATTTTTTCTGAGTATACTGACAAAA-
*
4010 ATTGAGGAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACT-CATCATG
258 ATTGAGGAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTACATCACG
* * * * * *
4074 GTTTTTGGATAACAACGTGTTTCGGGGCCCCGACTCAATTTTACATGATTTTTGGTAGAAAGACT
323 GTTTTTGGCTAAAAACGCGATTCGGGG-CCCGACTCAGTTTTACATGATTTTTGGCAGAAAGACT
* ** * *
4139 CCTTGAGATATCTATATTCATCTAATTAAATCTCAGCCACAATGGATTAAAGGATTTGTTTATAT
387 CCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATTTGTTTTTAC
*
4204 GAGCATCTGAATCTCGTTTCGATTTAA-TAAGATATAAATTCGGAAAAAAA
452 GAGCATCTGAATCTCGTTTCGATTTAACTAAGAAATAAATTC-GAAAAAAA
4254 ATTTATTTAT
Statistics
Matches: 1555, Mismatches: 212, Indels: 92
0.84 0.11 0.05
Matches are distributed among these distances:
640 21 0.01
641 25 0.02
642 18 0.01
643 23 0.01
644 14 0.01
645 132 0.08
646 3 0.00
648 1 0.00
652 2 0.00
653 65 0.04
654 62 0.04
655 66 0.04
656 124 0.08
657 174 0.11
658 515 0.33
659 193 0.12
660 77 0.05
661 40 0.03
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (653 bp):
TGGCTAAAAACACGTTCCGGGGTCCCGGCTCAGTTTCGAATGATTTTTAGCGTAAAGACTCCGCG
AAATATCTATATTCATCGAACCAAACCCCAACCACATTGGATTTAACGATTTGTTTTTATGAGCT
TTTGAATCTTGTTTCGATTTGATTAAGAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCG
TGAAAAACCCTTCAATATTTTTGACGCTGAATTATATATTTTTTCTGAGTATACTGACAAAAATT
GAGGAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTACATCACGGTT
TTTGGCTAAAAACGCGATTCGGGGCCCGACTCAGTTTTACATGATTTTTGGCAGAAAGACTCCTT
GAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTAAAGGATTTGTTTTTACGAGC
ATCTGAATCTCGTTTCGATTTAACTAAGAAATAAATTCGAAAAAAATGGAAAATGATATTAGAAG
CGTGAAAAACCCTTCAATTTTTTTGGTGTTGACTTGTATATTTTTTCTGTGTATAGTGGCAAAAA
ATTGAGGAAAAAATTTTCGGGTCTGTTTTGCAAAATTTTAGCCGAAATTGTTTACTCATCACGGT
TTT
Found at i:7137 original size:7 final size:7
Alignment explanation
Indices: 7125--7149 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
7115 TAAACTACCA
7125 AAAAAAG
1 AAAAAAG
7132 AAAAAAG
1 AAAAAAG
7139 AAAAAAG
1 AAAAAAG
7146 AAAA
1 AAAA
7150 GAAACCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:12397 original size:12 final size:12
Alignment explanation
Indices: 12380--12407 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
12370 TCATTAAATT
12380 TATAAATATATA
1 TATAAATATATA
12392 TATAAATATATA
1 TATAAATATATA
12404 TATA
1 TATA
12408 TACACACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TATAAATATATA
Found at i:12541 original size:16 final size:16
Alignment explanation
Indices: 12520--12562 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
12510 ATATATTTAT
12520 AAAAAGAAAGATAAAA
1 AAAAAGAAAGATAAAA
*
12536 AAAAAGAAATATAAAA
1 AAAAAGAAAGATAAAA
12552 AGAGAAAGAAA
1 A-A-AAAGAAA
12563 AGGAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 16 0.67
17 1 0.04
18 7 0.29
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (16 bp):
AAAAAGAAAGATAAAA
Found at i:12568 original size:6 final size:6
Alignment explanation
Indices: 12526--12576 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
12516 TTATAAAAAG
* * * *
12526 AAAGATA AAA-AA AAAGAA ATATAA AAAGAG AAAGAA AAGGAA AAAGAA
1 AAAGA-A AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
12574 AAA
1 AAA
12577 TATTCTTATG
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
5 4 0.11
6 28 0.80
7 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:21878 original size:2 final size:2
Alignment explanation
Indices: 21871--21901 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21861 GTTTAGAGAA
21871 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21902 GGTATAGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.