Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023868.1 Corchorus olitorius cultivar O-4 contig23901, 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: 138562
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:670 original size:331 final size:331
Alignment explanation
Indices: 1--6005 Score: 6056
Period size: 331 Copynumber: 18.2 Consensus size: 331
* * *
1 TTTCTAATTAAATCCAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * * * * *
66 AAGATTTTATTAGATGAATATAGATATTTGAAGGAGTATCGGCGACAAAAACCATGCAAAACT-A
66 AAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
* * *
130 TGTCGGGGCCCCGAAACGCGTTTTTAG-ACAAAAACCGTGATAGTTAGTACACGATTTTGGCTAA
131 -GCCGGGGCCCCGAAACGCGTTTTTAGCA-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
* * ** * * * ** * *
194 AATTTTGTAAAAAATGACCCGAAATGTTTTCCCCCAATTTTTGGATAAAATAATCATAAAATATA
194 AATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATA
* * * * *
259 TATAATTTAACACCAAAAAAATTGGAGGAATTTTCACTCTTCTAAT-TCCGTTTTTCATATTTTT
259 TATAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATAT-CGTTTTTCATATTTTT
* *
323 GT-GAATTAG
323 -TCTAATTAA
332 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
*
397 GAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
66 AAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
* ** *
462 GCCGGGGCCCCGAAACACAATTTTAGCAAAAAACAGTGATGGTTAGTACACGATTTCGGCTAAAA
131 GCCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
* * * *
527 TTTTGCGAAAAATAACCAGAAAAATTTTTCCTCAAATTTTAGCCATAATACTCATAAAAAATATA
196 TTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATA
* * * * *
592 TAATTCAACGTCAAAAAGATTGAAGGGCTTCTCACGC-TCTAATATCGTTTTTCCTATTTTTTCC
261 TAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATTTTTT-C
656 TAATT-A
325 TAATTAA
* * * *
662 TATTCTAATTAAAACGAAACATGATTCAGATGTTTGT-------AA-----AAA--CAA--TGGC
1 T-TTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGC
* * *
711 T-AGAATTTGGTTAGATGAATATAGATATTTCAAAG-TGTCTC-AGCGCCAAAAATCATTCAAAA
65 TAAG-ATTTGATTAGATGAATATAGATATTTCAAGGAT-TCTCGA-CGCCAAAAATCATGCAAAA
* * * * * * * * * *
773 TTGA-ACGGGGCCCTGGAACGCGTTTTTAGCTAAGAACCGTGAAGATTATTACACGGTTTCGGCT
127 CTGAGCCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCT
* * * * * * * *
837 AAAATTTGGCAAAAATTGAACC-GAAAGAA-GTTTCCTCAACTCTTAGCCATAATACTCGTAGAA
192 AAAATTTTGCAAAAAATG-ACCAGAAA-AATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAA
* * * * * *
900 AATATATAATTCAACGCCAAAAAGATTGAAGGGATTTTCAAGGTTTTCATACCGTTTTTCATATT
255 AATATATAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATT
*
965 TTTTCTGAATTTA
320 TTTTCT-AATTAA
* * * *
978 TTTCTAATTAAATCCAAAAAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * * * *
1043 AAGATTTTATTAGATGAATATAGATATTTGAAGGAATGTCGGCGCCAAAAACCATGCAAAACT-A
66 AAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
* * *
1107 TGTCGGGGCCCCGAAACGCGTTTTTAG-ACAAAAACCGTGATAGTTAGTACACGATTTTGGCTAA
131 -GCCGGGGCCCCGAAACGCGTTTTTAGCA-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
* * ** * * * ** *
1171 ACTTTTGTAAAAAATGATCC-GAAATGTTTTACCCCAATTTTTGGATAAAATACTCATAAAATAT
194 AATTTTGCAAAAAATGA-CCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAAT
* * * * * *
1235 ATATAATTTAACACCAAAAAAATTGGAGGAATTTTCACTCTTCTAATTTCGTTTTTCATATTTTT
258 ATATAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATTTTT
* *
1300 AT-GAATAAA
323 -TCTAATTAA
*
1309 TTTGTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * * *
1374 GAGATTTGATTAGATGAATATAGGTATTTAAAGGATTTTCGACCCCAAAAATCATGCAAAACAT-
66 AAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAAC-TG
* * * * * *
1438 AGCCGGGGCCCCTAAACACGATTTTAGCAAAATACTGTGATGGTAAGTACACGATTTCGGCTAAA
130 AGCCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * * * *
1503 ATTTTGCGAAAAATGACCAGAAAAATTGTTCCTCAAATTTTAGCCACAATACTCATAAAAATTAT
195 ATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATAT
** * * * * *
1568 ATAATTTAACGCCAAAAAGATTGAAAAGATTTTAAGGGTTTTCATATCGTTTTTCATATTTTTTC
260 ATAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATTTTTTC
*
1633 TGAATTAT
325 T-AATTAA
* * * *
1641 TTTCTAATTAAATCCAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGACT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * * * * * * *
1706 AAAATTTTA-TACGATGAATATAGATATTTGAAGGAGTGTCGGCGCCATAAACCATGC-AAACTA
66 AAGATTTGATTA-GATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTG
** * * *
1769 ATTCGGGACCCCGAAACGCGTTTTTAGACAAAAAACCGTGATAGTTAGTACACGATTTTGGCTAA
130 AGCCGGGGCCCCGAAACGCGTTTTTAG-CAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
* ** * * * ** *
1834 AATTTTGTAAAAAATGA-CACGAAATGTTTTCCCCCAATTTTTGGATAAAATACTCATAAAATAT
194 AATTTTGCAAAAAATGACCA-GAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAAT
* * * * * * *
1898 ATATAATTTAACACCAAAAAAACTGGAGGAATTTTCACTCTTCTAATTTCGTTTTTCATATTTTT
258 ATATAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATTTTT
* * *
1963 GCGAATTAG
323 TCTAATTAA
1972 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* *
2037 GAGATTTGATTAGATGAATATAGGTATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
66 AAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
* * * * * * *
2102 GCCGGGGCCCCTAAACACGATTTTATCAAAATACCGTTATGGTTAGTACACGAATTCGGCTAAAA
131 GCCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
* * * * *
2167 TTTTGCGAAAAATGACCAGAAAAATTGTTCCTCAATTTTTAGCCACAATTCTCATAAAAATTATA
196 TTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATA
* *
2232 TAATTCAACGCCAAAAAGATTGAAGGGATTTTCA-G-----------GGTTTTCATATTTTTTCT
261 TAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCT
2285 GAATTAA
326 -AATTAA
* *
2292 TTTCTAATTAAATCGAAACAAGATTTAA-ATGCTCGTAAAAAAAAATCCTTAAATGCAATGTGGC
1 TTTCTAATTAAATCGAAACAAGA-TTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGC
* * * *
2356 TAAGATTTTATTAGATGAATATAGATATTTGAAGGATTGTCGGCGCCAAAAA-CAATGCAAAACT
65 TAAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATC-ATGCAAAACT
* * * * * ** *
2420 AAGTCGAGGCCTCGAAACGCGTTTTTAG-ACAAAAATCGTGATAATTAGTACACGATTTTGGCTA
129 GAGCCGGGGCCCCGAAACGCGTTTTTAGCA-AAAAACCGTGATGGTTAGTACACGATTTCGGCTA
* * ** * * * ** *
2484 AAATTTTGTAAAAAATGACCCGAAATGTTTTCCCCCAATTTTTGGATAAAATACTCATAAAATAT
193 AAATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAAT
* * * * * *
2549 ATATAATTTAACACCAAAAAAATTGGAGGAATTTTCACTCTTCTAATTTCGTTTTTCATATTTTT
258 ATATAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATTTTT
* *
2614 GT-GAATTAG
323 -TCTAATTAA
*
2623 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGACT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* *
2688 GAGATTTGATTAGATCAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
66 AAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
* * ** * *
2753 GTCGGGGCCCCGAAACACGAATTTAGCAAAATACCGTGATGGTTAGTACACGAATTCGGCTAAAA
131 GCCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
* * * *
2818 TTTTGCAAAAAATGACCAGAAAAATTGTTCCTCAATTTTTAGGCACAATACTCATAAAAATTATA
196 TTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATA
* * * * * * *
2883 TAATTCAACGCCAAAAATATTGAAGGGATTTTCAAGGTTTTCATATCATTTTTCATATTTTTTCA
261 TAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATTTTTTC-
*
2948 GAATTAA
325 TAATTAA
* * * * * *
2955 TTTCTAATTAAATCTAAACAAGATTTAGATGCTCGTAAACACAAATCCCTAAACGCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* *
3020 GAGATTTGATTAGATGAATATAGACATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
66 AAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
* * * *
3085 GTCGGGGCCCCGAAACACGATTTTATCAAAAAACCGTGATGGGTTTAGTACACGATTTCGGCTAA
131 GCCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGAT-GG-TTAGTACACGATTTCGGCTAA
* * * * * *** * * ** * *
3150 AAATTTACGAAAAATGACCTGAAAAGTTCCCCCCCAATTTTTGGATAAAATACTCATAAAATACA
194 AATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATA
* * * * *
3215 TATAATTTAACAG-CAAAAAAATTGGAGGAATTTTCACTCTTCTAATTTCGTTTTTCATATTTTT
259 TATAATTTAAC-GCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATTTTT
3279 TCTGAATTAA
323 TCT-AATTAA
* * * *
3289 TTTCTAATTAAATCCAAACAAGATTTAGATGCTCGCAAAAACAAATCCTTAAATGCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * * * * * *
3354 AAGATTTTATTAGATGAATATAGATATTTGAAGGAGTGTCGGCGCCAAAAACCATGGAAAACTAA
66 AAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
* * * * * *
3419 GCCAGGGCCCCGAAAGGCGTTTTTAG-ACAAAAATCGTGATAGTTAGTACATGATTTTGGCTAAA
131 GCCGGGGCCCCGAAACGCGTTTTTAGCA-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * ** * * * ** *
3483 ATTTTGTAAAAAATGACCCGAAATGTTTTCCCCCAATTTTTGGATAAAATACTCATAAAATATAT
195 ATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATAT
* * * *
3548 ATAATTTAACACCAAAAA-ATTGAAGGAATTTTCACTCTTCTAATTTCGTTTTTCATATTTTTGT
260 ATAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATTTTT-T
* *
3612 -GAATTAG
324 CTAATTAA
* * *
3619 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTTAAAACAAATCCTCAAATGCTATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * *
3684 GAGATTTGATGAGATTAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
66 AAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
* * * *
3749 GCCGGGGCCCCGAAACACGATTTTATCAAAAAACCGTGATGGTTAGTACACGAATTCGGCTAAAA
131 GCCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
* * * **
3814 TTTTGCGAAAAATGACCAGAAAAATTGTTCCTCAATTTTTAGCCACAATACTCATAAAATTTATA
196 TTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATA
* * * * * *
3879 TAATTCAACGCCAAAAAGATTGAAGGGATTTCCAGGGTTTTCATATCGTTTTTCATATTTTTTCT
261 TAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCT
3944 GAATTAA
326 -AATTAA
* * *
3951 TTTCTAATTAAATCCAAACAAGATTTAA-ATGCTCGAAAAAACAAATCCTTAAATGCAATGTGGC
1 TTTCTAATTAAATCGAAACAAGA-TTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGC
* * * * * *
4015 TAAGATTTTATTAGATGAATATAGATATTTGAAGGATTGTCGGCGCCAAAAACCATGCAAAACTA
65 TAAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTG
* * * * ** *
4080 AGTCGAGGCCTCGAAACGCGTTTTTAG-ACAAAAATCGTGATAATTAGTACACGATTTTGGCTAA
130 AGCCGGGGCCCCGAAACGCGTTTTTAGCA-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
* * ** * * * **
4144 AATTTTGTAAAAAATGACCCGAAATGTTTTCCCCCAATTTTTGGATAAAATACTCATAAAATATA
194 AATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAA-A-A
* * * * *
4209 TATATAATTTAACACCAAAAAAATTGAAGGAATTTTCACTCTTCTAATTTCGTTTTTCATATTTT
257 TATATAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATTTT
* *
4274 TGT-GAATTAG
322 T-TCTAATTAA
*
4284 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTCAAATG-ATATGTGGC
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCA-ATGTGGC
* * * * *
4348 TGAGATTTGATGAGTTTAATATAGATATTTCAAGGATTCTGGACGCCAAAAATCATGCAAAACTG
65 TAAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTG
* * * * * *
4413 AGCC--GGCCCAGAAACACGATTTTATCAAAAAAACTGTGATGGTTAGTACACGATTTCGGGTAA
130 AGCCGGGGCCCCGAAACGCGTTTTTAGC-AAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
* * *
4476 AATTTTAC-AAAAATGACCA-AAAAATTTTTCCTCAATTTTTAACCAGAATACTCATAAAAAATA
194 AATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATA
* * * * *
4539 TATAATTCAACGTCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCGTTTTTCTTATTTTTT
259 TATAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATA-TTTTT
4604 TCTGAATTAA
323 TCT-AATTAA
* * * *
4614 TTTGTAATTAAAACGAAACATA-ATTCAGATGTTTGT-------AA-----AAA--CAA--TGGC
1 TTTCTAATTAAATCGAAACA-AGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGC
* * * * *
4662 TAGGATTTGGTTAGATGAATATAGATATTTCAAAGAGTT-TCG-CTGCCAAAAATCATTCAAAAT
65 TAAGATTTGATTAGATGAATATAGATATTTCAAGGA-TTCTCGAC-GCCAAAAATCATGCAAAAC
* * * * * * * * * * *
4725 TGAACC-GGACCCTGGAACGCATTTTTAGCTAAAAACCATGAAGATTATTACATGATTTCGGCTA
128 TGAGCCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
* * * * * * *
4789 AAATTTGGCAAAAATTGTATC-GAAAGTAA--TTTCCTTAGTTTTTAGCCATAATACTAATAAAA
193 AAATTTTGCAAAAAATG-ACCAGAAA--AATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAA
* * * ***
4851 AATATATAATTAAATGCCAAAAATATTGAAGCCCTTTTCACGCTT-TCAATATCGTTTTTCATAT
255 AATATATAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCT-AATATCGTTTTTCATAT
*
4915 TTTTT-TAATCAA
319 TTTTTCTAATTAA
* * * * *
4927 TTTTTAATTAAATCGAAACGAGATTTAGATGCTTGAAAAAACAAATCCTTAAATGCACTGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * * * * * * *
4992 AAGATTTTATTAGATGAATATAGATATTTCAAGGAGTGTTGGCGACAAAAACCACGCAAAACCGA
66 AAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
* * * * ** * **
5057 GTCGGGGCCCCGAAATGCGTTTTTATCCAAAAATTGTGATGGTTAGTACATGATTTTTGCTAAAA
131 GCCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
* * * * * ** * *
5122 TTTTGGGAAAAATAT-CCCA-AAAAAATTTTCC-CCATTTTTTGATAAAATACTCATAGAATATA
196 TTTT-GCAAAAA-ATGACCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATA
* * * * *
5184 TATAATTTAACGTCAAAAAGATTGGA-GGACTTTTCATGCTTTTAATATTGTTTTTCATA-TTTT
259 TATAATTTAACGCCAAAAAGATTGAAGGGA-TTTTCACGCTTCTAATATCGTTTTTCATATTTTT
5247 TCTGAATTAA
323 TCT-AATTAA
* * * *
5257 TTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAATTCTTAAGTCCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * * * * *
5322 AAGATTTGATCAGATGAATATGGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAA
66 AAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
* * * * *
5387 GCCGGGACGCC-AGAACGCTTTTTTAGCAAAAAACTGTGATGGTTATTACACGATTTCGGCTAAA
131 GCCGGGGCCCCGA-AACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * * * *
5451 ATTTTGTAAAAATTGACCAGAAAGATATTTCCTCAATTTTT-CCCTAAAATACTCATAAAAAATA
195 ATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTAGCC-AAAATACTCATAAAAAATA
* * * * * *
5515 AATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGTTTCTAATATCGTTTTTCCTATTTTTT
259 TATAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATTTTTT
*
5580 CCAAATTAA
324 -CTAATTAA
** * *
5589 TTTCTAATTAAATCGAAACAAGATTAAGATGCTCATAAAAA-AAATCATTAAATCCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * * * *
5653 AAAATTTGATTAGATGAATATAGATATTT-TAGGTAGTCCTGGA-GCCTAAAATCATGCAAAATT
66 AAGATTTGATTAGATGAATATAGATATTTCAAGG-A-TTCTCGACGCCAAAAATCATGCAAAACT
** * * * * * * *
5716 GAGATGGGTCCCCGGAACGCGTTTTTAGCCAATAACCATGATGGTTTGTTTGTACACAATTTCGG
129 GAGCCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGAT-G---GTTAGTACACGATTTCGG
* * * * * * *
5781 CTAAAATTTTGCAAACATTTACACA-AAAGATTTCTCCTCAATTTTTGGCTAAAATACTCAT-AA
190 CTAAAATTTTGCAAAAAATGAC-CAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAA
* * * * * * * *
5844 AAATATATAATTCAACGCCAAAAAGATTGGAGGGTTTTTTACACTTTTAATATCGTATTTCTTAT
254 AAATATATAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATAT
5909 TTTTTCTAAAATTAA
319 TTTTTCT--AATTAA
* * * * *
5924 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTTGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* *
5989 GAGATTTGGTTAGATGA
66 AAGATTTGATTAGATGA
6006 TGTAAAGTAT
Statistics
Matches: 4659, Mismatches: 859, Indels: 307
0.80 0.15 0.05
Matches are distributed among these distances:
312 1 0.00
313 34 0.01
314 230 0.05
315 147 0.03
316 89 0.02
317 4 0.00
318 5 0.00
319 20 0.00
320 249 0.05
321 4 0.00
322 2 0.00
323 2 0.00
324 2 0.00
325 3 0.00
327 5 0.00
328 62 0.01
329 143 0.03
330 580 0.12
331 1406 0.30
332 1003 0.22
333 128 0.03
334 392 0.08
335 111 0.02
336 37 0.01
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (331 bp):
TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
AAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
GCCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
TTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATA
TAATTTAACGCCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCT
AATTAA
Found at i:1686 original size:663 final size:658
Alignment explanation
Indices: 1--6005 Score: 6149
Period size: 663 Copynumber: 9.1 Consensus size: 658
* * *
1 TTTCTAATTAAATCCAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * * * * * *
66 AAGATTTTATTAGATGAATATAGATATTTGAAGGAGTATCGGCGACAAAAACCATGCAAAACTAT
66 AAGATTTGATTAGATGAATATAGATATTTAAAGGATTCTCGACGCCAAAAATCATGCAAAACTAA
* * *
131 GTCGGGGCCCCGAAACGCGTTTTTAGACAAAAACCGTGATAGTTAGTACACGATTTTGGCTAAAA
131 GCCGGGGCCCCGAAACGCGTTTTTAG-CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
* * ** * * ** *
196 TTTTGTAAAAAATGACCCGAAATGTTTTCCCCCAATTTTTGGATAAAATAATCAT-AAAATATAT
195 TTTTGCAAAAAATGACCAGAAAAATTTT-CCTCAATTTTTAGCCAAAATACTCATAAAAAT-TAT
* * * * * *
260 ATAATTTAACACCAAAAAAATTG-GAGGAATTTTCA-CTCTTC-TAATTCCGTTTTTCATA-TTT
258 ATAATTCAACGCCAAAAAGATTGAAAGG-ATTTTCAGGTTTTCAT-A-T-CGTTTTTCATATTTT
* * * *
321 TTGTGAATTAGTTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAAT
319 TTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAAT
* * *
386 GCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCA
384 GCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGATTGTCGGCGCCAAAAATCA
* * ** *
451 TGCAAAACTGAGCCGGGGCCCCGAAACACAATTTTAG-CAAAAAACAGTGATGGTTAGTACACGA
449 TGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGAC-AAAAACCGTGATGGTTAGTACACGA
* * * * * * ** *
515 TTTCGGCTAAAATTTTGCGAAAAATAACCAGAAAAATTTTTCCTCAAATTTTAGCCATAATACTC
513 TTTCGGCTAAAATTTTGCAAAAAATGACC-G-AAAAGTTTTCCCCAATTTTTGGATAAAATACTC
* * * * ** * * *
580 ATAAAAAATATATAATTCAACGTCAAAAAGATTGAAGGGCTTCTCACGC-TCTAATATCGTTTTT
576 ATAAAATATATATAATTTAACGCCAAAAAGATTGGAGGAATTTTCACTCTTCTAATTTCGTTTTT
*
644 CCTATTTTTTCCT-AATT-A
641 CATA-TTTTT-CTGAATTAA
* * * *
662 TATTCTAATTAAAACGAAACATGATTCAGATGTTTGT-------AA-----AAA--CAA--TGGC
1 T-TTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGC
* *
711 T-AGAATTTGGTTAGATGAATATAGATATTTCAAA-G-TGTCTC-AGCGCCAAAAATCATTCAAA
65 TAAG-ATTTGATTAGATGAATATAGATATTT-AAAGGAT-TCTCGA-CGCCAAAAATCATGCAAA
* * * * * * * *
772 ATTGAA--CGGGGCCCTGGAACGCGTTTTTAGCTAAGAACCGTGAAGATTATTACACGGTTTCGG
126 ACT-AAGCCGGGGCCCCGAAACGCGTTTTTAGC-AAAAACCGTGATGGTTAGTACACGATTTCGG
* * * * * * *
835 CTAAAATTTGGCAAAAATTGAACC-GAAAGAAGTTTCCTCAACTCTTAGCCATAATACTCGTAGA
189 CTAAAATTTTGCAAAAAATG-ACCAGAAA-AATTTTCCTCAATTTTTAGCCAAAATACTCATA-A
* *
899 AAA-TATATAATTCAACGCCAAAAAGATTGAAGGGATTTTCAAGGTTTTCATACCGTTTTTCATA
251 AAATTATATAATTCAACGCCAAAAAGATTGAAAGGATTTTC-AGGTTTTCATATCGTTTTTCATA
* * *
963 TTTTTTCTGAATTTATTTCTAATTAAATCCAAAAAAGATTTAGATGCTCGTAAAAACAAATCCTT
315 TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTT
* * *
1028 AAATGCAATGTGGCTAAGATTTTATTAGATGAATATAGATATTTGAAGGAATGTCGGCGCCAAAA
380 AAATGCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGATTGTCGGCGCCAAAA
* *
1093 ACCATGCAAAACT-ATGTCGGGGCCCCGAAACGCGTTTTTAGACAAAAACCGTGATAGTTAGTAC
445 ATCATGCAAAACTGA-GTCGGGGCCCCGAAACGCGTTTTTAGACAAAAACCGTGATGGTTAGTAC
* * * *
1157 ACGATTTTGGCTAAACTTTTGTAAAAAATGATCCGAAATGTTTTACCCCAATTTTTGGATAAAAT
509 ACGATTTCGGCTAAAATTTTGCAAAAAATGA-CCGAAAAGTTTT-CCCCAATTTTTGGATAAAAT
* *
1222 ACTCATAAAATATATATAATTTAACACCAAAAAAATTGGAGGAATTTTCACTCTTCTAATTTCGT
572 ACTCATAAAATATATATAATTTAACGCCAAAAAGATTGGAGGAATTTTCACTCTTCTAATTTCGT
* *
1287 TTTTCATATTTTTATGAATAAA
637 TTTTCATATTTTTCTGAATTAA
*
1309 TTTGTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * *
1374 GAGATTTGATTAGATGAATATAGGTATTTAAAGGATTTTCGACCCCAAAAATCATGCAAAAC-AT
66 AAGATTTGATTAGATGAATATAGATATTTAAAGGATTCTCGACGCCAAAAATCATGCAAAACTA-
* * * * *
1438 AGCCGGGGCCCCTAAACACGATTTTAGCAAAATACTGTGATGGTAAGTACACGATTTCGGCTAAA
130 AGCCGGGGCCCCGAAACGCGTTTTTAGCAAAA-ACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * *
1503 ATTTTGCGAAAAATGACCAGAAAAATTGTTCCTCAAATTTTAGCCACAATACTCATAAAAATTAT
194 ATTTTGCAAAAAATGACCAGAAAAATT-TTCCTCAATTTTTAGCCAAAATACTCATAAAAATTAT
* * *
1568 ATAATTTAACGCCAAAAAGATTGAAAAGATTTTAAGGGTTTTCATATCGTTTTTCATATTTTTTC
258 ATAATTCAACGCCAAAAAGATTGAAAGGATTTTCA-GGTTTTCATATCGTTTTTCATATTTTTTC
* *
1633 TGAATTATTTTCTAATTAAATCCAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCA
322 TGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCA
* * * * * * *
1698 ATGTGACTAAAATTTTA-TACGATGAATATAGATATTTGAAGGAGTGTCGGCGCCATAAACCATG
387 ATGTGGCTAAGATTTGATTA-GATGAATATAGATATTTCAAGGATTGTCGGCGCCAAAAATCATG
* * * *
1762 C-AAACTAATTCGGGACCCCGAAACGCGTTTTTAGACAAAAAACCGTGATAGTTAGTACACGATT
451 CAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGAC-AAAAACCGTGATGGTTAGTACACGATT
* * *
1826 TTGGCTAAAATTTTGTAAAAAATGACACGAAATGTTTTCCCCCAATTTTTGGATAAAATACTCAT
515 TCGGCTAAAATTTTGCAAAAAATGAC-CGAAAAGTTTT-CCCCAATTTTTGGATAAAATACTCAT
* * *
1891 AAAATATATATAATTTAACACCAAAAAAACTGGAGGAATTTTCACTCTTCTAATTTCGTTTTTCA
578 AAAATATATATAATTTAACGCCAAAAAGATTGGAGGAATTTTCACTCTTCTAATTTCGTTTTTCA
*
1956 TATTTTTGC-GAATTAG
643 TATTTTT-CTGAATTAA
1972 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * *
2037 GAGATTTGATTAGATGAATATAGGTATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
66 AAGATTTGATTAGATGAATATAGATATTTAAAGGATTCTCGACGCCAAAAATCATGCAAAACTAA
* * * * * *
2102 GCCGGGGCCCCTAAACACGATTTTATCAAAATACCGTTATGGTTAGTACACGAATTCGGCTAAAA
131 GCCGGGGCCCCGAAACGCGTTTTTAGCAAAA-ACCGTGATGGTTAGTACACGATTTCGGCTAAAA
* * *
2167 TTTTGCGAAAAATGACCAGAAAAATTGTTCCTCAATTTTTAGCCACAATTCTCATAAAAATTATA
195 TTTTGCAAAAAATGACCAGAAAAATT-TTCCTCAATTTTTAGCCAAAATACTCATAAAAATTATA
*
2232 TAATTCAACGCCAAAAAGATTGAAGGGATTTTCAGG----------G-TTTTCATATTTTTTCTG
259 TAATTCAACGCCAAAAAGATTGAAAGGATTTTCAGGTTTTCATATCGTTTTTCATATTTTTTCTG
* *
2286 AATTAATTTCTAATTAAATCGAAACAAGATTTAAATGCTCGTAAAAAAAAATCCTTAAATGCAAT
324 AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAAT
* *
2351 GTGGCTAAGATTTTATTAGATGAATATAGATATTTGAAGGATTGTCGGCGCCAAAAA-CAATGCA
389 GTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGATTGTCGGCGCCAAAAATC-ATGCA
* * * * ** *
2415 AAACTAAGTCGAGGCCTCGAAACGCGTTTTTAGACAAAAATCGTGATAATTAGTACACGATTTTG
453 AAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGACAAAAACCGTGATGGTTAGTACACGATTTCG
* *
2480 GCTAAAATTTTGTAAAAAATGACCCGAAATGTTTTCCCCCAATTTTTGGATAAAATACTCATAAA
518 GCTAAAATTTTGCAAAAAATGA-CCGAAAAGTTTT-CCCCAATTTTTGGATAAAATACTCATAAA
* *
2545 ATATATATAATTTAACACCAAAAAAATTGGAGGAATTTTCACTCTTCTAATTTCGTTTTTCATAT
581 ATATATATAATTTAACGCCAAAAAGATTGGAGGAATTTTCACTCTTCTAATTTCGTTTTTCATAT
* *
2610 TTTTGTGAATTAG
646 TTTTCTGAATTAA
*
2623 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGACT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * *
2688 GAGATTTGATTAGATCAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCATGCAAAACTGA
66 AAGATTTGATTAGATGAATATAGATATTTAAAGGATTCTCGACGCCAAAAATCATGCAAAACTAA
* * ** *
2753 GTCGGGGCCCCGAAACACGAATTTAGCAAAATACCGTGATGGTTAGTACACGAATTCGGCTAAAA
131 GCCGGGGCCCCGAAACGCGTTTTTAGCAAAA-ACCGTGATGGTTAGTACACGATTTCGGCTAAAA
* *
2818 TTTTGCAAAAAATGACCAGAAAAATTGTTCCTCAATTTTTAGGCACAATACTCATAAAAATTATA
195 TTTTGCAAAAAATGACCAGAAAAATT-TTCCTCAATTTTTAGCCAAAATACTCATAAAAATTATA
* * * *
2883 TAATTCAACGCCAAAAATATTGAAGGGATTTTCAAGGTTTTCATATCATTTTTCATATTTTTTCA
259 TAATTCAACGCCAAAAAGATTGAAAGGATTTTC-AGGTTTTCATATCGTTTTTCATATTTTTTCT
* * * *
2948 GAATTAATTTCTAATTAAATCTAAACAAGATTTAGATGCTCGTAAACACAAATCCCTAAACGCAA
323 GAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAA
* * * *
3013 TGTGGCTGAGATTTGATTAGATGAATATAGACATTTCAAGGATTCTCGACGCCAAAAATCATGCA
388 TGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGATTGTCGGCGCCAAAAATCATGCA
* * *
3078 AAACTGAGTCGGGGCCCCGAAACACGATTTTA-TCAAAAAACCGTGATGGGTTTAGTACACGATT
453 AAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGAC-AAAAACCGTGAT-GG-TTAGTACACGATT
* * * **
3142 TCGGCTAAAAATTTACGAAAAATGACCTGAAAAGTTCCCCCCCAATTTTTGGATAAAATACTCAT
515 TCGGCTAAAATTTTGCAAAAAATGACC-GAAAAGTT-TTCCCCAATTTTTGGATAAAATACTCAT
* *
3207 AAAATACATATAATTTAACAG-CAAAAAAATTGGAGGAATTTTCACTCTTCTAATTTCGTTTTTC
578 AAAATATATATAATTTAAC-GCCAAAAAGATTGGAGGAATTTTCACTCTTCTAATTTCGTTTTTC
3271 ATATTTTTTCTGAATTAA
642 ATA-TTTTTCTGAATTAA
* * * *
3289 TTTCTAATTAAATCCAAACAAGATTTAGATGCTCGCAAAAACAAATCCTTAAATGCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * * * * *
3354 AAGATTTTATTAGATGAATATAGATATTTGAAGGAGTGTCGGCGCCAAAAACCATGGAAAACTAA
66 AAGATTTGATTAGATGAATATAGATATTTAAAGGATTCTCGACGCCAAAAATCATGCAAAACTAA
* * * * * *
3419 GCCAGGGCCCCGAAAGGCGTTTTTAGACAAAAATCGTGATAGTTAGTACATGATTTTGGCTAAAA
131 GCCGGGGCCCCGAAACGCGTTTTTAG-CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
* * ** * * **
3484 TTTTGTAAAAAATGACCCGAAATGTTTTCCCCCAATTTTTGGATAAAATACTCAT-AAAATATAT
195 TTTTGCAAAAAATGACCAGAAAAATTTT-CCTCAATTTTTAGCCAAAATACTCATAAAAAT-TAT
* * * * *
3548 ATAATTTAACACCAAAAA-ATTG-AAGGAATTTTCA-CTCTTCTAATTTCGTTTTTCATA-TTTT
258 ATAATTCAACGCCAAAAAGATTGAAAGG-ATTTTCAGGT-TT-TCATATCGTTTTTCATATTTTT
* * * * * *
3609 TGTGAATTAGTTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTTAAAACAAATCCTCAAATG
320 TCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATG
* * * * * *
3674 CTATGTGGCTGAGATTTGATGAGATTAATATAGATATTTCAAGGATTCTCGACGCCAAAAATCAT
385 CAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGATTGTCGGCGCCAAAAATCAT
* * * * *
3739 GCAAAACTGAGCCGGGGCCCCGAAACACGATTTTA-TCAAAAAACCGTGATGGTTAGTACACGAA
450 GCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGAC-AAAAACCGTGATGGTTAGTACACGAT
* * * * ** *
3803 TTCGGCTAAAATTTTGCGAAAAATGACCAGAAAAATTGTTCCTCAATTTTTAGCCACAATACTCA
514 TTCGGCTAAAATTTTGCAAAAAATGACC-GAAAAGTT-TTCCCCAATTTTTGGATAAAATACTCA
* * * * * *** * * *
3868 TAAAATTTATATAATTCAACGCCAAAAAGATTGAAGGGATTTCCAGGGTTTTCATATCGTTTTTC
577 TAAAATATATATAATTTAACGCCAAAAAGATTGGAGGAATTTTCACTCTTCTAATTTCGTTTTTC
3933 ATATTTTTTCTGAATTAA
642 ATA-TTTTTCTGAATTAA
* * *
3951 TTTCTAATTAAATCCAAACAAGATTTAA-ATGCTCGAAAAAACAAATCCTTAAATGCAATGTGGC
1 TTTCTAATTAAATCGAAACAAGA-TTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGC
* * * * *
4015 TAAGATTTTATTAGATGAATATAGATATTTGAAGGATTGTCGGCGCCAAAAACCATGCAAAACTA
65 TAAGATTTGATTAGATGAATATAGATATTTAAAGGATTCTCGACGCCAAAAATCATGCAAAACTA
* * * * ** *
4080 AGTCGAGGCCTCGAAACGCGTTTTTAGACAAAAATCGTGATAATTAGTACACGATTTTGGCTAAA
130 AGCCGGGGCCCCGAAACGCGTTTTTAG-CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * ** * * **
4145 ATTTTGTAAAAAATGACCCGAAATGTTTTCCCCCAATTTTTGGATAAAATACTCATAAAATATAT
194 ATTTTGCAAAAAATGACCAGAAAAATTTT-CCTCAATTTTTAGCCAAAATACTCATAAAA-AT-T
* * * * * *
4210 ATATAATTTAACACCAAAAAAATTG-AAGGAATTTTCA-CTCTTCTAATTTCGTTTTTCATA-TT
256 ATATAATTCAACGCCAAAAAGATTGAAAGG-ATTTTCAGGT-TT-TCATATCGTTTTTCATATTT
* * * * *
4272 TTTGTGAATTAGTTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTCAAA
318 TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAA
* * * * *
4337 TG-ATATGTGGCTGAGATTTGATGAGTTTAATATAGATATTTCAAGGATTCT-GGACGCCAAAAA
383 TGCA-ATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGATTGTCGG-CGCCAAAAA
* * * * * * *
4400 TCATGCAAAACTGAG-C-CGGCCCAGAAACACGATTTTATCAAAAAAACTGTGATGGTTAGTACA
446 TCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTA-GACAAAAACCGTGATGGTTAGTACA
* * * * * * * *
4463 CGATTTCGGGTAAAATTTTAC-AAAAATGACCAAAAAATTTTTCCTCAATTTTT-AACCAGAATA
510 CGATTTCGGCTAAAATTTTGCAAAAAATGACC-GAAAAGTTTTCCCCAATTTTTGGA-TAAAATA
* * * * ** * * *
4526 CTCATAAAAAATATATAATTCAACGTCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCGTT
573 CTCATAAAATATATATAATTTAACGCCAAAAAGATTGGAGGAATTTTCACTCTTCTAATTTCGTT
*
4591 TTTCTTATTTTTTTCTGAATTAA
638 TTTC--ATATTTTTCTGAATTAA
* * * *
4614 TTTGTAATTAAAACGAAACATA-ATTCAGATGTTTGT-------AA-----AAA--CAA--TGGC
1 TTTCTAATTAAATCGAAACA-AGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGC
* * *
4662 TAGGATTTGGTTAGATGAATATAGATATTTCAAA-GAGTT-TCG-CTGCCAAAAATCATTCAAAA
65 TAAGATTTGATTAGATGAATATAGATATTT-AAAGGA-TTCTCGAC-GCCAAAAATCATGCAAAA
* * * * * * * * * *
4724 TTGAA-CC-GGACCCTGGAACGCATTTTTAGCTAAAAACCATGAAGATTATTACATGATTTCGGC
127 CT-AAGCCGGGGCCCCGAAACGCGTTTTTAGC-AAAAACCGTGATGGTTAGTACACGATTTCGGC
* * * * * * *
4787 TAAAATTTGGCAAAAATTGTATC-GAAAGTAA-TTTCCTTAGTTTTTAGCCATAATACTAATAAA
190 TAAAATTTTGCAAAAAATG-ACCAGAAA--AATTTTCCTCAATTTTTAGCCAAAATACTCATAAA
* * * * ** * *
4850 AAATATATAATTAAATGCCAAAAATATTG-AAGCCCTTTTCACGCTTTCAATATCGTTTTTCATA
252 AATTATATAATTCAACGCCAAAAAGATTGAAAG-GATTTTCAGGTTTTC-ATATCGTTTTTCATA
* * * * *
4914 TTTTTT-T-AATCAATTTTTAATTAAATCGAAACGAGATTTAGATGCTTGAAAAAACAAATCCTT
315 TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTT
* * * * *
4977 AAATGCACTGTGGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGAGTGTTGGCGACAAAA
380 AAATGCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGATTGTCGGCGCCAAAA
* * * * ** **
5042 ACCACGCAAAACCGAGTCGGGGCCCCGAAATGCGTTTTTATCCAAAAATTGTGATGGTTAGTACA
445 ATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGACAAAAACCGTGATGGTTAGTACA
* ** * * * * *
5107 TGATTTTTGCTAAAATTTTGGGAAAAATAT-CCCAAAAAAATTTTCCCC-ATTTTTTGATAAAAT
510 CGATTTCGGCTAAAATTTT-GCAAAAA-ATGACC-GAAAAGTTTTCCCCAATTTTTGGATAAAAT
* * * *
5170 ACTCATAGAATATATATAATTTAACGTCAAAAAGATTGGAGGACTTTTCA-TGCTTTTAATATT-
572 ACTCATAAAATATATATAATTTAACGCCAAAAAGATTGGAGGAATTTTCACT-CTTCTAAT-TTC
5233 GTTTTTCATATTTTTCTGAATTAA
635 GTTTTTCATATTTTTCTGAATTAA
* * * *
5257 TTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAATTCTTAAGTCCAATGTGGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* * * * * * *
5322 AAGATTTGATCAGATGAATATGGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAA
66 AAGATTTGATTAGATGAATATAGATATTTAAAGGATTCTCGACGCCAAAAATCATGCAAAACTAA
* * * * *
5387 GCCGGGACGCC-AGAACGCTTTTTTAGCAAAAAACTGTGATGGTTATTACACGATTTCGGCTAAA
131 GCCGGGGCCCCGA-AACGCGTTTTTAGC-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
* * * * *
5451 ATTTTGTAAAAATTGACCAGAAAGATATTTCCTCAATTTTT-CCCTAAAATACTCATAAAAAATA
194 ATTTTGCAAAAAATGACCAGAAAAAT-TTTCCTCAATTTTTAGCC-AAAATACTCATAAAAATTA
* * * * * * *
5515 AATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACGTTTCTAATATCGTTTTTCCTATTTTTT
257 TATAATTCAACGCCAAAAAGATTGAAAGGATTTTCAGGTTT-TCATATCGTTTTTCATATTTTTT
** * * * *
5580 CCAAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGCTCATAAAAA-AAATCATTAAATCC
321 CTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGC
* * * * *
5644 AATGTGGCTAAAATTTGATTAGATGAATATAGATATTT-TAGG-TAGTCCTGGAGCCTAAAATCA
386 AATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGATTGT-C-GGCGCCAAAAATCA
* * * * * * *
5707 TGCAAAATTGAGAT-GGGTCCCCGGAACGCGTTTTTAGCCAATAACCATGATGGTTTGTTTGTAC
449 TGCAAAACTGAG-TCGGGGCCCCGAAACGCGTTTTTAGACAAAAACCGTGAT-G---GTTAGTAC
* * * * * *
5771 ACAATTTCGGCTAAAATTTTGCAAACATTTACAC-AAAAGATTTCTCCTCAATTTTTGGCTAAAA
509 ACGATTTCGGCTAAAATTTTGCAAAAAATGAC-CGAAAAG-TTT-TCCCCAATTTTTGGATAAAA
* ** * * * *
5835 TACTCATAAAA-ATATATAATTCAACGCCAAAAAGATTGGAGGGTTTTTTACACTTTTAATATCG
571 TACTCATAAAATATATATAATTTAACGCCAAAAAGATTGGAGGAATTTTCACTCTTCTAATTTCG
* * *
5899 TATTTCTTATTTTTTCTAAAATTAA
636 TTTTTCATA-TTTTTCT-GAATTAA
* * * * *
5924 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTTGCT
1 TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
* *
5989 GAGATTTGGTTAGATGA
66 AAGATTTGATTAGATGA
6006 TGTAAAGTAT
Statistics
Matches: 4616, Mismatches: 557, Indels: 336
0.84 0.10 0.06
Matches are distributed among these distances:
642 1 0.00
643 161 0.03
644 89 0.02
645 226 0.05
646 455 0.10
647 95 0.02
648 10 0.00
649 3 0.00
650 6 0.00
651 582 0.13
652 38 0.01
653 2 0.00
655 4 0.00
656 2 0.00
657 3 0.00
658 9 0.00
659 59 0.01
660 153 0.03
661 104 0.02
662 620 0.13
663 970 0.21
664 255 0.06
665 416 0.09
666 266 0.06
667 87 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (658 bp):
TTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCT
AAGATTTGATTAGATGAATATAGATATTTAAAGGATTCTCGACGCCAAAAATCATGCAAAACTAA
GCCGGGGCCCCGAAACGCGTTTTTAGCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAT
TTTGCAAAAAATGACCAGAAAAATTTTCCTCAATTTTTAGCCAAAATACTCATAAAAATTATATA
ATTCAACGCCAAAAAGATTGAAAGGATTTTCAGGTTTTCATATCGTTTTTCATATTTTTTCTGAA
TTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCAATGT
GGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGATTGTCGGCGCCAAAAATCATGCAAAA
CTGAGTCGGGGCCCCGAAACGCGTTTTTAGACAAAAACCGTGATGGTTAGTACACGATTTCGGCT
AAAATTTTGCAAAAAATGACCGAAAAGTTTTCCCCAATTTTTGGATAAAATACTCATAAAATATA
TATAATTTAACGCCAAAAAGATTGGAGGAATTTTCACTCTTCTAATTTCGTTTTTCATATTTTTC
TGAATTAA
Found at i:8255 original size:16 final size:16
Alignment explanation
Indices: 8234--8292 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
8224 AGCGCAGCAA
8234 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
*
8250 AAACAAAAACAAAAAAC-
1 AAAC-AAAAC-GAAAACG
*
8267 AGA-AAAACGAAAACG
1 AAACAAAACGAAAACG
* *
8282 ATACCAAACGA
1 AAACAAAACGA
8293 CCCCTTAGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 10 0.29
17 7 0.21
18 5 0.15
ACGTcount: A:0.69, C:0.19, G:0.10, T:0.02
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:17732 original size:40 final size:40
Alignment explanation
Indices: 17681--17765 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
17671 CATATTTATA
*
17681 ATTA-GGGGCTAAATCTGAATTTAATTTATTACCTTAATT
1 ATTAGGGGGCTAAACCTGAATTTAATTTATTACCTTAATT
*
17720 ATTAGGGGGCTAAACCTGAATTTAATTTATTTCCTTAATT
1 ATTAGGGGGCTAAACCTGAATTTAATTTATTACCTTAATT
17760 ATTAGG
1 ATTAGG
17766 AGGGTCAAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (40 bp):
ATTAGGGGGCTAAACCTGAATTTAATTTATTACCTTAATT
Found at i:26407 original size:34 final size:34
Alignment explanation
Indices: 26364--26434 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
26354 TCCCTATTTC
26364 ACAAGCAAGAATTCAATACTTATGTAAGCCAAAA
1 ACAAGCAAGAATTCAATACTTATGTAAGCCAAAA
26398 ACAAGCAAGAATTCAATACTTATGTAAGCCAAAA
1 ACAAGCAAGAATTCAATACTTATGTAAGCCAAAA
26432 ACA
1 ACA
26435 TCTGATATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (34 bp):
ACAAGCAAGAATTCAATACTTATGTAAGCCAAAA
Found at i:31226 original size:16 final size:16
Alignment explanation
Indices: 31194--31227 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
31184 TATTATTATC
*
31194 ACATTAAAAATTAAAA
1 ACATTAAAAAATAAAA
31210 ACATTAAAAAAATAAAA
1 ACATT-AAAAAATAAAA
31227 A
1 A
31228 TGAAAATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (16 bp):
ACATTAAAAAATAAAA
Found at i:32228 original size:99 final size:99
Alignment explanation
Indices: 32107--32287 Score: 249
Period size: 99 Copynumber: 1.8 Consensus size: 99
32097 TATAAATTTC
* ** *
32107 AAATGATTTCTTACCATATTTGTATTTTCCCACATGTGTAAATTTTAATTGATG-ACTTAATTAC
1 AAATGATTTCCTACCATATTTGTATTTTCCCACATGTG-AAACGTAAATTGATGAACTTAATTAC
*
32171 ATT-TTAAAATTCATTAATAGTTTTCATTGGAAAT
65 ATTCTTAAAATTAATTAATAGTTTTCATTGGAAAT
* * *
32205 AAATGATCTTCCTACCATATTTGTATTTTTCCACATGTGCAACGTAAATTGATGAACTTGATTAC
1 AAATGAT-TTCCTACCATATTTGTATTTTCCCACATGTGAAACGTAAATTGATGAACTTAATTAC
*
32270 ATTCTTTAAATTAATTAA
65 ATTCTTAAAATTAATTAA
32288 AAATTTTCTT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
98 18 0.25
99 41 0.58
100 12 0.17
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (99 bp):
AAATGATTTCCTACCATATTTGTATTTTCCCACATGTGAAACGTAAATTGATGAACTTAATTACA
TTCTTAAAATTAATTAATAGTTTTCATTGGAAAT
Found at i:32431 original size:70 final size:69
Alignment explanation
Indices: 32312--32446 Score: 200
Period size: 70 Copynumber: 1.9 Consensus size: 69
32302 ATTTCAAATA
* *
32312 ATCTACTTACCATATTTTATTTATTTTCCCACGTGTAAGAGTAGTATAATAAAATTTTAGTCAAT
1 ATCTACTTACCATATTTTATGTATTTTCCCACGTGTAAAAGTAGTATAATAAAATTTTAGTCAAT
32377 GTTG
66 GTTG
* * *
32381 ATCTTCTTACTATATTTT-TGTATTTTCCCACATGTGTAAAAGTATTATAATAAAATTTTAGTCA
1 ATCTACTTACCATATTTTATGTATTTTCCCAC--GTGTAAAAGTAGTATAATAAAATTTTAGTCA
32445 AT
64 AT
32447 TATCTCAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
68 12 0.20
69 16 0.27
70 31 0.53
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.45
Consensus pattern (69 bp):
ATCTACTTACCATATTTTATGTATTTTCCCACGTGTAAAAGTAGTATAATAAAATTTTAGTCAAT
GTTG
Found at i:34721 original size:2 final size:2
Alignment explanation
Indices: 34710--34751 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
34700 TTAGAGATCC
34710 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34750 TA
1 TA
34752 ACTTTAATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45369 original size:13 final size:13
Alignment explanation
Indices: 45351--45375 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45341 GGAAGAAGGT
45351 AAGAAGAAGAAAG
1 AAGAAGAAGAAAG
45364 AAGAAGAAGAAA
1 AAGAAGAAGAAA
45376 AGGAAAGGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAAG
Found at i:49661 original size:8 final size:8
Alignment explanation
Indices: 49645--49694 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
49635 GAACATTCTT
49645 AAAAA-AA
1 AAAAAGAA
49652 AAAAAGAA
1 AAAAAGAA
49660 AAAAA-AGA
1 AAAAAGA-A
49668 AAAAAGAA
1 AAAAAGAA
*
49676 AGAAAGAA
1 AAAAAGAA
*
49684 AGAAAGAA
1 AAAAAGAA
49692 AAA
1 AAA
49695 CCTAGTGTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
7 6 0.16
8 31 0.82
9 1 0.03
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:49670 original size:16 final size:16
Alignment explanation
Indices: 49645--49694 Score: 68
Period size: 15 Copynumber: 3.2 Consensus size: 16
49635 GAACATTCTT
49645 AAAAAA-AAAAAAGAA
1 AAAAAAGAAAAAAGAA
49660 AAAAAAGAAAAAAG-A
1 AAAAAAGAAAAAAGAA
*
49675 AAGAAAGAAAGAAAGAA
1 AAAAAAGAAA-AAAGAA
49692 AAA
1 AAA
49695 CCTAGTGTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 16 0.53
16 11 0.37
17 3 0.10
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAGAA
Found at i:49677 original size:4 final size:4
Alignment explanation
Indices: 49663--49692 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
49653 AAAAGAAAAA
49663 AAAG AAA- AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
49693 AACCTAGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:57372 original size:47 final size:47
Alignment explanation
Indices: 57303--57399 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
57293 ATGCAGTCCT
*
57303 TTACTTTTCAGAAAGAAAATGAAGATTGAAGAGATTACTTCCAAGTC
1 TTACTTTTCAAAAAGAAAATGAAGATTGAAGAGATTACTTCCAAGTC
57350 TTACTTTTCAAAAAGAAAATGAAGATTGAAGAGATTACTTCCAAGTC
1 TTACTTTTCAAAAAGAAAATGAAGATTGAAGAGATTACTTCCAAGTC
57397 TTA
1 TTA
57400 GACATTACAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.31
Consensus pattern (47 bp):
TTACTTTTCAAAAAGAAAATGAAGATTGAAGAGATTACTTCCAAGTC
Found at i:67788 original size:20 final size:22
Alignment explanation
Indices: 67740--67789 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
67730 CAGAGGTAAT
*
67740 TTTTAATCATCTCTATGTTTTAA
1 TTTTAATCATCTC-ATGTATTAA
67763 -TTTAATCATCTC-TG-ATTAA
1 TTTTAATCATCTCATGTATTAA
67782 TTTTAATC
1 TTTTAATC
67790 TGGAAATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 9 0.36
22 12 0.48
ACGTcount: A:0.28, C:0.14, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTTAATCATCTCATGTATTAA
Found at i:69611 original size:48 final size:48
Alignment explanation
Indices: 69555--69662 Score: 198
Period size: 48 Copynumber: 2.2 Consensus size: 48
69545 TTTTGGTTTT
* *
69555 TCTTTTTCCTTTTGTTTGATATTACTAGATTTCTTTATAAAAATGTCA
1 TCTTTTTCCTTTTGTTGGATATTACAAGATTTCTTTATAAAAATGTCA
69603 TCTTTTTCCTTTTGTTGGATATTACAAGATTTCTTTATAAAAATGTCA
1 TCTTTTTCCTTTTGTTGGATATTACAAGATTTCTTTATAAAAATGTCA
69651 TCTTTTTCCTTT
1 TCTTTTTCCTTT
69663 CCTGCATTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.23, C:0.14, G:0.08, T:0.55
Consensus pattern (48 bp):
TCTTTTTCCTTTTGTTGGATATTACAAGATTTCTTTATAAAAATGTCA
Found at i:79705 original size:18 final size:18
Alignment explanation
Indices: 79682--79722 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
79672 TGCCAAATTT
*
79682 GCCAAAACACACTCTCAA
1 GCCAAAACAAACTCTCAA
* *
79700 GCCAAAACAAACTTTTAA
1 GCCAAAACAAACTCTCAA
79718 GCCAA
1 GCCAA
79723 CCCTACTTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.32, G:0.07, T:0.15
Consensus pattern (18 bp):
GCCAAAACAAACTCTCAA
Found at i:90685 original size:2 final size:2
Alignment explanation
Indices: 90680--90713 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
90670 TCTATTCCCA
90680 AT AT 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 AT AT
90714 CTTTAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97689 original size:14 final size:14
Alignment explanation
Indices: 97670--97696 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
97660 CACCTTTTAG
97670 TTTATTTATTTATA
1 TTTATTTATTTATA
97684 TTTATTTATTTAT
1 TTTATTTATTTAT
97697 GTACTAGTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTATTTATA
Found at i:100791 original size:19 final size:19
Alignment explanation
Indices: 100767--100803 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
100757 TCTACCGGGT
100767 GTCAATCTCCGGTCCGATG
1 GTCAATCTCCGGTCCGATG
*
100786 GTCAATCTCTGGTCCGAT
1 GTCAATCTCCGGTCCGAT
100804 TTTGATAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.30, G:0.24, T:0.30
Consensus pattern (19 bp):
GTCAATCTCCGGTCCGATG
Found at i:101306 original size:11 final size:12
Alignment explanation
Indices: 101285--101313 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
101275 TGTTCGTAGG
101285 ATTAGAAAAAAA
1 ATTAGAAAAAAA
101297 ATTA-AAAAAAA
1 ATTAGAAAAAAA
101308 ATTAGA
1 ATTAGA
101314 CCAGTACTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (12 bp):
ATTAGAAAAAAA
Found at i:107630 original size:15 final size:15
Alignment explanation
Indices: 107606--107640 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
107596 TATTTCAGTA
* *
107606 TTTCTTTTATTTTCT
1 TTTCTGTTATTTTAT
107621 TTTCTGTTATTTTAT
1 TTTCTGTTATTTTAT
107636 TTTCT
1 TTTCT
107641 TTTTCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.11, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTGTTATTTTAT
Found at i:116956 original size:24 final size:24
Alignment explanation
Indices: 116929--116978 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
116919 CCACGTAATC
116929 AGGTCTTACTAGTAGACATACTCG
1 AGGTCTTACTAGTAGACATACTCG
116953 AGGTCTTACTAGTAGACATACTCG
1 AGGTCTTACTAGTAGACATACTCG
116977 AG
1 AG
116979 TCTGTGGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (24 bp):
AGGTCTTACTAGTAGACATACTCG
Found at i:119912 original size:25 final size:25
Alignment explanation
Indices: 119884--119938 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
119874 TTTCAGGATC
119884 TATTAACCGATTGG-TCCATATGAAT
1 TATTAA-CGATTGGATCCATATGAAT
* **
119909 TATTTACTTTTGGTATCCATATGAAT
1 TATTAACGATTGG-ATCCATATGAAT
119935 TATT
1 TATT
119939 TACTTACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 5 0.20
25 5 0.20
26 15 0.60
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (25 bp):
TATTAACGATTGGATCCATATGAAT
Found at i:119921 original size:24 final size:25
Alignment explanation
Indices: 119894--119943 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
119884 TATTAACCGA
119894 TTGG-TCCATATGAATTATTTACTT
1 TTGGATCCATATGAATTATTTACTT
119918 TTGGTATCCATATGAATTATTTACTT
1 TTGG-ATCCATATGAATTATTTACTT
119944 ACTAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 4 0.17
26 20 0.83
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (25 bp):
TTGGATCCATATGAATTATTTACTT
Found at i:120239 original size:31 final size:31
Alignment explanation
Indices: 120202--120412 Score: 205
Period size: 31 Copynumber: 6.9 Consensus size: 31
120192 GTGTTCGACA
*
120202 TGGCACGCCATGTGTACCAAAAAGCGACATG
1 TGGCACGCCACGTGTACCAAAAAGCGACATG
* *
120233 TGGCACGCCATGTGTACAAAAAAGCGACATG
1 TGGCACGCCACGTGTACCAAAAAGCGACATG
* *
120264 TGGCACGTCACGTGTACCAAAAAGCGACATA
1 TGGCACGCCACGTGTACCAAAAAGCGACATG
* * * *
120295 TGACACGCCACATGTACCAAAAAGTGACACG
1 TGGCACGCCACGTGTACCAAAAAGCGACATG
* ** * *
120326 TGACACATCACATGTACCAAAAAGTGACATG
1 TGGCACGCCACGTGTACCAAAAAGCGACATG
* ** *
120357 T--CACGCCATGTGTACCAAAAAGTAACACG
1 TGGCACGCCACGTGTACCAAAAAGCGACATG
* * *
120386 TGGCATGCCTCGTGCA-CAAAAAG-GACA
1 TGGCACGCCACGTGTACCAAAAAGCGACA
120413 CGTGCTACGT
Statistics
Matches: 153, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
29 26 0.17
30 7 0.05
31 120 0.78
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (31 bp):
TGGCACGCCACGTGTACCAAAAAGCGACATG
Found at i:120292 original size:62 final size:61
Alignment explanation
Indices: 120202--120390 Score: 227
Period size: 62 Copynumber: 3.1 Consensus size: 61
120192 GTGTTCGACA
* * * *
120202 TGGCACGCCATGTGTACCAAAAAGCGACATGTGGCACGCCATGTGTACAAAAAAGCGACATG
1 TGGCACGTCACGTGTACCAAAAAGCGACATGT-GCACGCCATGTGTACCAAAAAGCGACACG
* ** *
120264 TGGCACGTCACGTGTACCAAAAAGCGACATATGACACGCCACATGTACCAAAAAGTGACACG
1 TGGCACGTCACGTGTACCAAAAAGCGACATGTG-CACGCCATGTGTACCAAAAAGCGACACG
* * * * **
120326 TGACACATCACATGTACCAAAAAGTGACATGT-CACGCCATGTGTACCAAAAAGTAACACG
1 TGGCACGTCACGTGTACCAAAAAGCGACATGTGCACGCCATGTGTACCAAAAAGCGACACG
120386 TGGCA
1 TGGCA
120391 TGCCTCGTGC
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
60 29 0.27
61 1 0.01
62 79 0.72
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (61 bp):
TGGCACGTCACGTGTACCAAAAAGCGACATGTGCACGCCATGTGTACCAAAAAGCGACACG
Found at i:125039 original size:19 final size:19
Alignment explanation
Indices: 125015--125129 Score: 74
Period size: 19 Copynumber: 5.8 Consensus size: 19
125005 TTGTTTAGCA
125015 ACTGTACAGATGAGATTAG
1 ACTGTACAGATGAGATTAG
*
125034 ACTGTACAGATTAGATTAG
1 ACTGTACAGATGAGATTAG
** * *
125053 --TGTGATTGA-CACTGTTTAG
1 ACTGT-ACAGATGA--GATTAG
*
125072 CAACTATACAGATGAGATTAG
1 --ACTGTACAGATGAGATTAG
* *
125093 ACTGTTCAGATTAGATTAG
1 ACTGTACAGATGAGATTAG
125112 TTACTGTACAGATGAGAT
1 --ACTGTACAGATGAGAT
125130 GATTAGAGCA
Statistics
Matches: 71, Mismatches: 15, Indels: 18
0.68 0.14 0.17
Matches are distributed among these distances:
17 4 0.06
18 3 0.04
19 39 0.55
21 19 0.27
22 3 0.04
23 3 0.04
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAG
Found at i:125083 original size:59 final size:59
Alignment explanation
Indices: 124991--125112 Score: 208
Period size: 59 Copynumber: 2.1 Consensus size: 59
124981 GGTGTGGTAG
* *
124991 TAGTGCGATTGACATTGTTTAGCAACTGTACAGATGAGATTAGACTGTACAGATTAGAT
1 TAGTGCGATTGACACTGTTTAGCAACTATACAGATGAGATTAGACTGTACAGATTAGAT
* *
125050 TAGTGTGATTGACACTGTTTAGCAACTATACAGATGAGATTAGACTGTTCAGATTAGAT
1 TAGTGCGATTGACACTGTTTAGCAACTATACAGATGAGATTAGACTGTACAGATTAGAT
125109 TAGT
1 TAGT
125113 TACTGTACAG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (59 bp):
TAGTGCGATTGACACTGTTTAGCAACTATACAGATGAGATTAGACTGTACAGATTAGAT
Found at i:125092 original size:21 final size:19
Alignment explanation
Indices: 125078--125129 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
125068 TTAGCAACTA
125078 TACAGATGAGATTAGACTG
1 TACAGATGAGATTAGACTG
* *
125097 TTCAGATTAGATTAGTTACTG
1 TACAGATGAGATTAG--ACTG
125118 TACAGATGAGAT
1 TACAGATGAGAT
125130 GATTAGAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 13 0.48
21 14 0.52
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (19 bp):
TACAGATGAGATTAGACTG
Found at i:127834 original size:12 final size:12
Alignment explanation
Indices: 127817--127858 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
127807 AGTTGTAGAG
127817 TCTCAGCATACT
1 TCTCAGCATACT
127829 TCTCAGC--A-T
1 TCTCAGCATACT
*
127838 TCTCCGCATACT
1 TCTCAGCATACT
127850 TCTCAGCAT
1 TCTCAGCAT
127859 TCTCAGCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 7 0.28
10 1 0.04
11 1 0.04
12 16 0.64
ACGTcount: A:0.21, C:0.36, G:0.10, T:0.33
Consensus pattern (12 bp):
TCTCAGCATACT
Found at i:127846 original size:21 final size:21
Alignment explanation
Indices: 127817--127866 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
127807 AGTTGTAGAG
127817 TCTCAGCATACTTCTCAGCAT
1 TCTCAGCATACTTCTCAGCAT
*
127838 TCTCCGCATACTTCTCAGCAT
1 TCTCAGCATACTTCTCAGCAT
127859 TCTCAGCA
1 TCTCAGCA
127867 GACAGGGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.36, G:0.10, T:0.32
Consensus pattern (21 bp):
TCTCAGCATACTTCTCAGCAT
Found at i:130642 original size:20 final size:20
Alignment explanation
Indices: 130617--130656 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
130607 TTTTTCCTTT
130617 TTCCCTCGAGTTATTATTAA
1 TTCCCTCGAGTTATTATTAA
130637 TTCCCTCGAGTTATTATTAA
1 TTCCCTCGAGTTATTATTAA
130657 AGGTGGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (20 bp):
TTCCCTCGAGTTATTATTAA
Found at i:132149 original size:15 final size:15
Alignment explanation
Indices: 132129--132157 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
132119 ATATAACAAT
132129 AAAAAAAATTTAAAG
1 AAAAAAAATTTAAAG
132144 AAAAAAAATTTAAA
1 AAAAAAAATTTAAA
132158 ACCATAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAAAAAATTTAAAG
Done.