Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014586.1 Corchorus olitorius cultivar O-4 contig14619, 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: 70098
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3284 original size:331 final size:329
Alignment explanation
Indices: 2404--9205 Score: 3110
Period size: 333 Copynumber: 20.7 Consensus size: 329
2394 CGAGCATCAG
* * * * *
2404 AAATTAAATCGGAAAAATA-AGAAAAATGATATTAGAAGCGTGAAAAGGCCTTCAATCTTTTTGA
1 AAATTAATTCGGAAAAA-AGAGGAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTG-
* * * * * * * *
2468 CGTT-GAAT-TATACATTTTTATGAGTATTTTGGACATAAATTGAGGAAAAAACTTTT-GGG---
64 CATTGGATTATATATATTTTTAAGAGTATTGTGGCCAAAAATT-AGG-AAAAATTTTTCGGGATA
* * * *** *
2527 GTTTTTGCAAAATTATT-GACGAAATCGTG---T-A-CATCATGGTTTTTGGCTAAAAACACGTT
127 GTTTTTACAAAATT-TTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGTT
* * * * * * * *
2586 CCAGATCCCCGGCTCAGTTTTGC-TTATTTTTGGCACTAAGACTCATTGAAATATATATATTCTT
191 CCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC-CTGAAATATCTATATTCAT
* * ** * * * * *
2650 ATTACCAAATCTCAATAACATTGCATTTAAAGATTTGTTTTTACGAGCTTTC-ATAACCGGTTTC
255 CTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGA-AACAGGTTTC
*
2714 GATTTATTTAC
319 GATTTAATTAC
* * * * * * *
2725 AAATTAATTCGGAAAAAAAAGGTAAACTACATTAGAAGCGTGCAAAGCCCTTCAATTTTTTAGCG
1 AAATTAATTCGGAAAAAAGAGGAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTGCA
* * * * *
2790 TTGAATTATATATTTTTTTAAGTAGTATTGTAG-C-AAAA--A--AAAAA-TTTTCGTGTTAGTT
66 TTGGATTATATATATTTTTAAG-AGTATTGTGGCCAAAAATTAGGAAAAATTTTTCGGGATAGTT
* * * * * * * *
2848 TTTGA-AAAATATTAGCCGAAAATCGTGTAGTAGCCATTACGATTTTTGACTAATAACGGGTTCC
130 TTT-ACAAAATTTTAGCC-AAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGTTCC
* * * *
2912 GGGGCCCCGTCTCCGTTTTGCATGATTTTTGGCGCCAAGACTCACTAAAATATCTATATTCATCT
193 GGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC-CTGAAATATCTATATTCATCT
* * * ***
2977 GACAAAATCTTAGCAACATTGGATTTAAGGATTT-TTGAAACGAGC-TCCGAAAACAGGTTTCGA
257 AACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCG-AAACAGGTTTCGA
3040 TTTAATTAC
321 TTTAATTAC
* * * *
3049 AAATTAATTCGGAAAAAAGAGGAAAACAATTTTAGAAGTGTGAAAAGCCCTGCAATCTTTTTTGC
1 AAATTAATTCGGAAAAAAGAGGAAAACGATATTAGAAGCGTGAAAAGCCCTTCAAT-TTTTTTGC
** ** * * * *
3114 ATTTTATTATATATATTTTTACCAGTATCGTGGACAAAAATTGAGGAAAAATTTTTCGGGTTAAT
65 ATTGGATTATATATATTTTTAAGAGTATTGTGGCCAAAAATT-AGGAAAAATTTTTCGGGATAGT
* **** *
3179 TTTTACAAAATTTTAACCAAAATTAAATACTAACCATCACAATTTTTGGCTAATAACGCGTTCCG
129 TTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGTTCCG
* * * * * *
3244 GAGCCCCGACTCAGTTTTGCATGATTTTTGGCGTCAAGACTCGTTGAAATATCTATATTTATATG
194 GAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC-CTGAAATATCTATATTCATCTA
* * * *
3309 ACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGATCATCAGAAACCGTTTTCGATT
258 ACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGGTTTCGATT
3374 TAATTTA-
323 TAA-TTAC
* * * * * *
3381 AAATTAATTCAGAAAATAAGA--AAAACGATATTAAAAGTGTGAAAAGTCTTTCAATCTTTTTGG
1 AAATTAATTCGGAAAA-AAGAGGAAAACGATATTAGAAGCGTGAAAAGCCCTTCAAT-TTTTTTG
* * * *
3444 CGTTGGA-T-TATATATTTTGAAGAGTATTGTGGCCAAAAATTGAGGAAAAATTGTTCGGGACAG
64 CATTGGATTATATATATTTTTAAGAGTATTGTGGCCAAAAATT-AGGAAAAATTTTTCGGGATAG
* * * * * * *
3507 TTTTTGCAAAATTTTGGCCGAAATCGTGTGCCAACCATCACAGTTTTTGGCTAAAAATGCGTTCC
128 TTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGTTCC
* * * *
3572 -TAGGCCCCGGCAT-AGTTTTGGATGATTTTTGGCAG-CAAGACTCCTTGAAATATCAATTTTCA
193 GGA-GCCCCGGC-TCAGTTTTGCATGATTTTTGGC-GCCAAGACTCC-TGAAATATCTATATTCA
* * ** * * ** *
3634 TCTAACCAAATCTCAG-ACACAATGAATTTAAGGATAAGGTTTTACGAGCATCTGAATTATGTTT
254 TCTAACCAAATCTCAGCA-ACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGGTTT
*
3698 CGATTTAATTAG
318 CGATTTAATTAC
* * * * * *
3710 AAATTAATTCGGAAAATAG-GAAAAACGATGTTATAAGCATGAAAAGCCCTTAAATTTTTTTAGC
1 AAATTAATTCGGAAAAAAGAGGAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTT-GC
*
3774 GA-T-GAGTTATATAT-TTTTTATGAGTATTGTGGCCAAAAAGTTAGGAAAAATTTTTCGGGATA
65 -ATTGGA-TTATATATATTTTTAAGAGTATTGTGGCCAAAAA-TTAGGAAAAATTTTTCGGGATA
** * * * * *
3836 GTTTTTGGAAAATTTTGGCCGAAATCGTGTACTAACCATCACGATTTTTGG-AAAAAACGCATTC
127 GTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGTTC
* * *
3900 CGGA-CCCCGGCTCAGTTTTGCTTGATTTTTGGTGCCAAGACTCCTTGACATATCTATATTCATC
192 CGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC-TGAAATATCTATATTCATC
* * * * * * **
3964 TAACCAAATCTCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCCGAATCTTGTTTCGA
256 TAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGGTTTCGA
* *
4029 TTTAAGTAG
321 TTTAATTAC
* * ** *
4038 AAATTAATTCAGAAAAAAAAATAAGGAAAAACGATATTAGAAGCGTGAAAAGCATTTCAATATTT
1 AAATTAATTC-G--GAAAAAA-GAGG-AAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTT
* * * * * * *
4103 TTGGAGTTGAACTATATAT-TTTTTATGAGTATTATAGCCAAGAATT--GAAGGAAATTCTTTC-
61 TTGCA-TTGGATTATATATATTTTTAAGAGTATTGTGGCCAAAAATTAGGAA--AAATT-TTTCG
* ** * * ** * * *
4164 GG---G----T-C-AATTTTTAGCTGAAGTCATGTACT-ACCATCACGGTTTCTAGCAAAAAACG
122 GGATAGTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACG
* * * * * *
4219 CATTCCGGGGCCCCGGCTCAGTTTTGCTTGATTTTTGGTGCCAAGTCTCCTTGACATATCTATAT
187 CGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC-TGAAATATCTATAT
* * * * ** * * **
4284 TCATCTAACCAAAGCTCATCCACATTGGATTTAAGTATTTGACTTTACGAACAT-CTAAATCTTG
251 TCATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAA-CAGG
*
4348 TTTCAATTTAAGTTA-
315 TTTCGATTTAA-TTAC
* * * * * ** * *
4363 AAATTAATTTAGAATAAAAAAAGGAAAAATGATATTAGAAGCTTGAAAAGCTTTTCAATATTTTG
1 AAATTAA-TTCGGA-AAAAAGAGG-AAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTT
* * * * * * * *
4428 GGAGTTGAACTATATA-ATTTTTTAGGAGTATGGTAGCCAAAAATT-GAATAAAATTCTTCTGGG
63 GCA-TTGGATTATATATA-TTTTTAAGAGTATTGTGGCCAAAAATTAGGA-AAAATTTTTC-GGG
* * ** * * * * *
4491 -TCATTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATGACGATTTTTAGCAAAAAACGT
124 AT-AGTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGC
* * * * * * *
4555 ATTCCGGGGCCCCGGCTCAGTTTTGCTTGATTTTTAGTGCCAAGACTACTTGACATATCTATATT
188 GTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACT-CCTGAAATATCTATATT
* * * * * * * * * * * **
4620 CAACTAAGCAAATATCATCCACATTGGATTTAAGAATTTGATTTTAAGAACATCTGAATCTTGTT
252 CATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGGTT
* *
4685 TCGATTTAAGTAG
317 TCGATTTAATTAC
** * * * ** *
4698 AAATTAATTTAGAAAAAACTAGGAAAAACGATCTTAGAAGCATGAAAAGCGTTTCAATATTTTTG
1 AAATTAATTCGGAAAAAA-GAGG-AAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTG
* * * ** *
4763 GAGTT-GA--ACTATATATTTTTAATTAGT-TTCATGGGAAAAAATT--GAAGAAA-ATTTC-GG
64 CA-TTGGATTA-TATATATTTTTAA-GAGTATT-GTGGCCAAAAATTAGGAA-AAATTTTTCGGG
* * * ** * * ** *
4820 TTAAATTTTTGCAAAATTTTAGCTGAAATCGTCTACAAACCATCACGGTTTTTGTCTAAAAACGC
124 AT-AGTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGC
* * * * * * * *
4885 ATTCC-GAGGTCCCGGCTCAGTTTTGCTTGGTTTTTGTCGCCATGACTCCTTGACATATATATAT
188 GTTCCGGA-GCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC-TGAAATATCTATAT
** * * * ** ****
4949 TCATCTAACCAAATCT-ATGCCGCGTTGGATTTAAGAAAATT-TTTTTACGAGCATCTTAATTTT
251 TCATCTAACCAAATCTCA-GCAACATTGGATTTAAG-GATTTGTTTTTACGAGCATCCGAAACAG
*
5012 GTTTCGATTT-ATTAAG
314 GTTTCGATTTAATT-AC
* * ** * * * ** * *
5028 AAATCAATTAC-GAAAATAATAATAAAAAAGATATTACAACCGTGAAAAAACTTTCAATATTTTT
1 AAATTAATT-CGGAAAA-AA-GAGGAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTT
* * * * * *
5092 GGAGTT-AATT-TACATATTTTTTATGAGTATTATGGCCAAGAATT--GAAGGAAATTCTTTC-G
63 GCA-TTGGATTATATATA-TTTTTAAGAGTATTGTGGCCAAAAATTAGGAA--AAATT-TTTCGG
* ** * * * * *
5152 G---G----T-C-AATTTTTAGCTGAAATAGTGTACTAACCATCACAGTTTCTAGCAAAAAACGC
123 GATAGTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGC
* * * * * * *
5208 ATTTCGGGGCCCCGGCTCAGTTTTGCTTGATTTTTGGTGCCAAGACTCGTTGACATATCTATATT
188 GTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC-CTGAAATATCTATATT
* * * * * * * * * **
5273 CATCTAACCCAATCTCATCCACATTGGATTTAAGTATTTGATTTTACAAACATCTGAATCTTGTT
252 CATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGGTT
* * *
5338 TCAATTTAAGTAG
317 TCGATTTAATTAC
* * * * * **
5351 AAATTAATTTAGAAAAAAATAGGAAAAATGATATTAGAAGCATGAAAAGCGTTTCAA--TTTTT-
1 AAATTAA-TTCGGAAAAAAGAGG-AAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTG
* * *
5413 --TTGG-----A-GTA----T--G-GTA-----GCCAAAAATT-GAAGAAAATTATTTTGGG-TC
64 CATTGGATTATATATATTTTTAAGAGTATTGTGGCCAAAAATTAGGA-AAAATT-TTTCGGGAT-
* * * ** * * * * **
5456 ATTTTTTGCAAACTTTTAGCTGAAATCGGGTACTAACCATCACGATTTTTAGCAAAAAACGTATT
126 AGTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGTT
* * * * * * * *
5521 CCGGAGCCCTGGCTTAGTTTTGCTTGATTTTTAGTGCCAAGACTACTTGACATATCTATATTCAA
191 CCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACT-CCTGAAATATCTATATTCAT
* * * * * * * * * * **
5586 CTAAGCAAATATCATCCACATTGGATATAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCG
255 CTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGGTTTCG
* *
5651 ATTTAAGTAG
320 ATTTAATTAC
* * * ** *
5661 AAATTAATTCAGAAAAAAATAGGAAAAACGATCTTAGAAGCGTGAAAAGCGTTTCAATATTTTTG
1 AAATTAATTC-GGAAAAAAGAGG-AAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTG
* * * ** * *
5726 GAGTTGAACTT-TATAT-TTTTTATGAGTATCATGGCAAAAAATT--GAAGAAA--ATTCGGG-T
64 CA-TTGGA-TTATATATATTTTTAAGAGTATTGTGGCCAAAAATTAGGAA-AAATTTTTCGGGAT
* * * ** * * * ** * *
5784 AAATTTTTGCCAAATTTTAGCTGAAGTCGTCTACTAACCATGACGGTTTTTGTCTAAAAACGCAT
126 -AGTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGT
* * * * * * *
5849 TCCGGGGCCCAGGCTCAGTTTTGCTTGGTTTTTGTCACCAAGACTCCTTGACATATCTATATTCA
190 TCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC-TGAAATATCTATATTCA
* ** * * * * * ****
5914 TCTAACAAAATCT-ATGCCGCGTTGGATTTAAGAAATTCTTTTTACGAGCATCTGAATTTTGTTT
254 TCTAACCAAATCTCA-GCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGGTTT
* *
5978 CG-TTTTATTAAG
318 CGATTTAATT-AC
* * * ** ** * *
5990 AAATCAATTTGGAAAATAATAATAATAACGATATTAGAAGCGTGAAAAAACTTTCAATATTTTTG
1 AAATTAATTCGGAAAA-AAGAGGAA-AACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTG
* * * ** * *
6055 GAGTT-AATT-TATATATTTTTTATGAGTATCATGGCCAAGAATT--GAAGGAAATTCGTTT-AG
64 CA-TTGGATTATATATA-TTTTTAAGAGTATTGTGGCCAAAAATTAGGAA--AAATT--TTTCGG
* * * *** * * * *
6115 G-TCAATTTTTGCAAATTTTTAGTTGAAATCGTGTACTAACCATCACAATTTCTGACAAAAAACC
123 GAT-AGTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACG
* * * * * * * *
6179 CATTCCGGGGCCTCGGCCCAGTTATGCCTGATTTTTGGTGCCAAGACTCCTTGACATATCTATAT
187 CGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC-TGAAATATCTATAT
* * * * * * **
6244 TCATCTAACCAAATCTCA-TATACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTG
251 TCATCTAACCAAATCTCAGCA-ACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGG
* * *
6308 TTTCAATTTAAGTAG
315 TTTCGATTTAATTAC
* * * * * ** * **
6323 AAATTAATTTAGAAAAAAAATAGGAAAAATGATATTAGAAGCATGAAAAGCGTTTAAATAATTTT
1 AAATTAA-TTCG-GAAAAAAGAGG-AAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTT
* * * * * * *
6388 GGAGTTGAACTATATA-ATTATTTATGAGTATTGTAGCCAAAAATT-GAATAAAATTCTTTTGGG
63 GCA-TTGGATTATATATATT-TTTAAGAGTATTGTGGCCAAAAATTAGGA-AAAATT-TTTCGGG
* * ** * * *
6451 -TCATTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACAATCACGATTTTTGGCAAAAAAAA
124 AT-A-GTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGC---TAAAA
* * * * * * *
6515 ACGCATTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTAGTGCCAAGACTACTTGACATATATA
184 ACGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACT-CCTGAAATATCTA
** * * * * * * * * *
6580 TATTCATCTAAGAAAATATCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCT
248 TATTCATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACA
* * * *
6645 TGTTTCAATTTAAGTAG
313 GGTTTCGATTTAATTAC
* * * * * ** * *
6662 AAATTAATTTAGAAAAAAATAGGAAAAATGATATTAGAAGCATGAAAAGCGTTTAAATATTTTTG
1 AAATTAA-TTCGGAAAAAAGAGG-AAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTG
* * * * * * *
6727 GAGTTGAACTATATA-ATTATTTATGAGTATTGTAGCCAAAAATT-GAAGAAAATTCTTTTGGG-
64 CA-TTGGATTATATATATT-TTTAAGAGTATTGTGGCCAAAAATTAGGA-AAAATT-TTTCGGGA
* * ** * * *
6789 TCATTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACAATCACGATTTTTGGCAAAAAAAAA
125 T-A-GTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGC---TAAAAA
* * * * * *
6854 CGCATTCCGGGGCCCCGGCTCAGTTTTGCTTGATTTTTGGTGCCAAGACTCCTTCACATATCTAT
185 CGCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC-TGAAATATCTAT
* * * * * * * ** * **
6919 ATTCGTCTAACCAAATATCATCCACATTGGATTTAAGAATTTGATTTTACGAACATTTGAATCTT
249 ATTCATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAG
* *
6984 GTTTCGATTTAAGTAG
314 GTTTCGATTTAATTAC
* * * * * * * *
7000 AAATTAGTTC-AAAAAAAAAGGAAAACAATATTAGAAGCGTAAAAAGCCTTTCAATATTTTTGGA
1 AAATTAATTCGGAAAAAAGAGGAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTGCA
* * * * ** * * *
7064 GTTGAACTATATAT-TTTATATGAGTATCATGGCAAAAAATTGAAGAAAAA--TTT-GGG-TAAA
66 -TTGGATTATATATATTTTTAAGAGTATTGTGGCCAAAAATT-AGGAAAAATTTTTCGGGAT-AG
* * * * ** *
7124 TTTTTGCAACATTTTAGCTAAAATCGTCTACTAACCATCACGGTTTTT-GCTAAAAAAACGCATT
128 TTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCT--AAAAACGCGTT
* * * * **
7188 CCGGGGCCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAAGACTTCTTGGCATATCTATATTCAT
191 CCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGAC-TCCTGAAATATCTATATTCAT
* ** * * * * ** ****
7253 CTAACCAAATCTAAGCCGCGTTGGATTTAAGAAATTCTTTTTACGAGCATTTGAATTTTGTTTCG
255 CTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGGTTTCG
*
7318 ATTT-ATTAAG
320 ATTTAATT-AC
* * * ** * * * * *
7328 AAATCAATTTGGAAAATAATAATAAAAAAGATATTAGAACCGTGAAAAACCTTTCAATATTTTTG
1 AAATTAATTCGGAAAA-AA-GAGGAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTG
* * * ** ** *
7393 GAGTT-AATT-TATATATTTTTTATGAGTATCATGGCCAGGAA-T-CGAAGGAAATTCTTTCGGG
64 CA-TTGGATTATATATA-TTTTTAAGAGTATTGTGGCCAAAAATTAGGAA--AAATT-TTTCGGG
* * * ** * * *
7454 -TCAATTTTTGCAAATTTTTAGCTGAAATCGTGTACTAACCATCACGATTTCTGGCAAAAAACGC
124 AT-AGTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGC
* * * * * * *
7518 ATTTCGGGGCCCCGGGTCAGTTTTGCTTGATTTTTTGCGCCAAGACTCCTTGACATATCTATATT
188 GTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC-TGAAATATCTATATT
* * * ** * * * **
7583 CATCTAACCAAATCTCAACCACATTGGATTTAAGAATTTAATTTTACGAACATCTGAATCTTGTT
252 CATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGGTT
* * *
7648 TCAATTTAAGTAA
317 TCGATTTAATTAC
* * * * ** ** *
7661 AAATTAATTAAGAAAAAAATAGGAAAAATGATATTAGAAGCACGAAAAGCGTTTCAATATTTTTG
1 AAATTAATT-CGGAAAAAAGAGG-AAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTG
* * * * * * * *
7726 GAGTTGAACTATATA-ATTTTTTATGAGTATGGTAGCCAAAAATT-GAAGAAAATTCTTTTGGG-
64 CA-TTGGATTATATATA-TTTTTAAGAGTATTGTGGCCAAAAATTAGGA-AAAATT-TTTCGGGA
* * *** *
7788 TCATTTTTTGCAAAATTTTAGTTGAAATCGTGTACTAACCATCACGATTTTTGGC-AAGAAACGC
125 T-AGTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAA-AAACGC
** * * * * * * ** * *
7852 ACTCCGGGGTCCAGGCTCAATTTTGCTTGATTTTTAGTTCCAAGACTCCTTCACATATCTATATT
188 GTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC-TGAAATATCTATATT
* * * * * * * * * **
7917 CATCTAGCCAAATATCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTT
252 CATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGGTT
* *
7982 TCGATTTAAGTAG
317 TCGATTTAATTAC
* * * ** * *
7995 AAATTAATTCAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAACTTTCAATATTTTTG
1 AAATTAATTC-GGAAAAAA-GAGGAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTG
* * * * ** * * *
8060 GAGTT-GAAT-TATATACTTTTAATGAGTATCGTGGCCAAAAATTGAAAAAAAAATTGTCGAG-T
64 CA-TTGGATTATATATATTTTTAA-GAGTATTGTGGCCAAAAATT-AGGAAAAATTTTTCGGGAT
** * ** * * ** * *
8122 CAAATTTTGCAAAATTTTAGCTGAAATCATGTACTAACTATCACGGTTTTGGGCTAAAAACGCAT
126 -AGTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGT
* * * * * * *
8187 TCTGGGGCCCCGGGTCAGTTTTGCTTGATTTTTTGCGCCAAGACTCCTTGACATATCTATATTCT
190 TCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC-TGAAATATCTATATTCA
* * * * * ** * * ** * *** *
8252 TCTAAGCAAATATCATCCACATTGTATTTAATAATTTGATTTTACGAACATTTGAATCTTATTTT
254 TCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGGTTTC
* * *
8317 GAATTAAATAA
319 GATTTAATTAC
* * ** * *
8328 AAATT-ATT----AAAAA-A--AAAACGATATTAAAAGCGTGAAGAGCGTTTCAATATTTTTGAA
1 AAATTAATTCGGAAAAAAGAGGAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTGCA
* ** *
8385 GTT-GA--ACTATATATTTTTATGAGTATCATGGCCAAAAATTA--AAGATAATTTTGTC-GGCT
66 -TTGGATTA-TATATATTTTTAAGAGTATTGTGGCCAAAAATTAGGAA-A-AATTTT-TCGGGAT
** * ** * * * ** *
8444 AAAATTTTGCAAAATTTTAGCTGAAACCATTTACTAACCATCACGGTTTTTGGC-AAAACACGCA
126 -AGTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAA-ACGCG
* * *
8508 TTCC-GAGGCCCCGGCTCAGTTTTGCTTAATTTTTTGCGCCAAGACTCCTAGAAATATCTATATT
189 TTCCGGA-GCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT-GAAATATCTATATT
* * * * * * ** * * **
8572 CATCTAATCAAATCTCATCCACATTGGATTTAAGAATTAGATTTTACGAATATCTGAATCTTGTT
252 CATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGGTT
**
8637 TCGATTTAAGCA-
317 TCGATTTAATTAC
* * ** *
8649 ACAATTAATTCAGAGAAAAATAGGAAAAAC-AGTATTAGAAGCGTGAAAAGCGTTTCAATATTTT
1 A-AATTAATTCGGA-AAAAAGAGG-AAAACGA-TATTAGAAGCGTGAAAAGCCCTTCAATTTTTT
* * * * * * *
8713 TGGAGTTGAACTATATAT-TTTTTATGGGTATCGTGGCCAAAAAATT-GGTGAAAATTATTTCGG
62 TGCA-TTGGATTATATATATTTTTAAGAGTATTGTGGCC-AAAAATTAGG-AAAAATT-TTTCGG
* * * * ***
8776 G-TCAATTTTTGC-AAATTTTAGCTAAAATCGTGTACATTA-CATCATGGTTTTTGGC-AAAAAC
123 GAT-AGTTTTTACAAAATTTTAGCCAAAATCGTGTAC-TAACCATCACAATTTTTGGCTAAAAAC
* * * * * *
8837 GCATTTCGGGGCCCCAGCTCAGTCTTGCTTGATTTTTGGCGCCAAGACTCCGTGACAA-ATCTAT
186 GCGTTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC-TGA-AATATCTAT
* * * * * * * **
8901 ATTCATCTAACCAAATCTCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTT
249 ATTCATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAG
* *
8966 GTTTCGATTTAAGTAA
314 GTTTCGATTTAATTAC
* * * ** * *
8982 AAATTAATTCAGAAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGG
1 AAATTAATTCGGAAAAAAGAGG-AAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTGC
* * * * * * *
9047 AGTTGAACTATATAT-TTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAACTCTTTCGGG-TCA
65 A-TTGGATTATATATATTTTTAAGAGTATTGTGGCCAAAAATT-AGGAAAAATTTTTCGGGAT-A
* * ** * ** *
9110 ATTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACAATCACGTTTTTTGGCAAAAAACGCGTTC
127 GTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGTTC
* * * **
9175 CGGGGCCCCGACTCAATTTTGTTTGATTTTT
192 CGGAGCCCCGGCTCAGTTTTGCATGATTTTT
9206 AGCTTTAACT
Statistics
Matches: 5401, Mismatches: 816, Indels: 517
0.80 0.12 0.08
Matches are distributed among these distances:
300 17 0.00
301 3 0.00
302 1 0.00
305 3 0.00
306 1 0.00
308 2 0.00
309 3 0.00
310 223 0.04
311 1 0.00
312 5 0.00
313 2 0.00
314 5 0.00
315 7 0.00
316 3 0.00
317 4 0.00
318 14 0.00
319 10 0.00
320 6 0.00
321 75 0.01
322 217 0.04
323 328 0.06
324 204 0.04
325 221 0.04
326 10 0.00
327 17 0.00
328 296 0.05
329 526 0.10
330 410 0.08
331 402 0.07
332 322 0.06
333 676 0.13
334 584 0.11
335 266 0.05
336 66 0.01
337 4 0.00
338 318 0.06
339 148 0.03
340 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (329 bp):
AAATTAATTCGGAAAAAAGAGGAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTGCA
TTGGATTATATATATTTTTAAGAGTATTGTGGCCAAAAATTAGGAAAAATTTTTCGGGATAGTTT
TTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCGTTCCGGA
GCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTGAAATATCTATATTCATCTAACC
AAATCTCAGCAACATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAAACAGGTTTCGATTTAA
TTAC
Found at i:4568 original size:988 final size:986
Alignment explanation
Indices: 3206--9205 Score: 6579
Period size: 988 Copynumber: 6.1 Consensus size: 986
3196 CAAAATTAAA
** * * * * * * * *
3206 TACTAACCATCACAATTTTTGGCTAATAACGCGTTCCGGAGCCCCGACTCAGTTTTGCATGATTT
1 TACTAACCATCACGGTTTCTAGCAAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCTTGATTT
* * * * * * * *
3271 TTGGCGTCAAGACTCGTTGAAATATCTATATTTATATGACCAAATCTCAGCAACATTGGATTTAA
66 TTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCATCCACATTGGATTTAA
* * * * * * * * *
3336 GGATTTGTTTTTACGATCATCAGAAAC-CGTTTTCGATTTAATTTA-AAATTAATTCAG--AAAA
131 GTATTTGATTTTACGAACATCTGAATCTTG-TTTCAATTTAAGTTAGAAATTAATTTAGAAAAAA
* * * ** * * * *
3397 TAAGAAAAACGATATTAAAAGTGTGAAAAGTC-TTTCAATCTTTTTGGCGTTGGATTATATA-TT
195 AAAGAAAAATGATATTAGAAGCATGAAAAG-CGTTTCAATATTTTTGGAGTTGAACTATATATTT
* * * * * * * * *
3460 TTGAAGAGTATTGTGGCCAAAAATTGAGGAAAAATTGTTC-GGGACAGTTTTTGCAAAATTTTGG
259 TTTATGAGTATCGTAGCCAAAAATTGAAG-AAAATTCTTCTGGGTCATTTTTTGCAAAATTTTAG
* * * * * * **
3524 CCGAAATCGTGTGCCAACCATCAC-AGTTTTTGGCTAAAAATGCGTTCCTAGGCCCCGGCAT-AG
323 CTGAAATCGTGTACTAACCATCACGA-TTTTTGGCAAAAAACGCATTCCGGGGCCCCGGC-TCAG
** * * * * * * *
3587 TTTTGGATGATTTTT-G-GCAGCAAGACTCCTTGAAATATCAATTTTCATCTAACCAAATCTCAG
386 TTTTGCTTGATTTTTAGTGC--CAAGACTACTTGACATATCTATATTCATCTAAGCAAATATCAT
* * * * * * * *
3650 ACACAATGAATTTAAGGATAAGGTTTTACGAGCATCTGAAT-TATGTTTCGATTTAATTAGAAAT
449 CCACATTGGATTTAAGAATTAGATTTTACGAACATCTGAATCT-TGTTTCGATTTAAGTAGAAAT
* * * * ** * * * * *
3714 TAATTCG-GAAAATAGGAAAAACGATGTTATAAGCATGAAAAGCCCTTAAATTTTTTTAGCGATG
513 TAATTAGAAAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGTTG
** * *
3778 AGTTATATATTTTTTATGAGTATTGTGGCCAAAAAGTTAGGAAAAATT-TTTCGGGAT-AGTTTT
578 AACTATATATTTTTTATGAGTATTGTGGCCAAAAAATT-GGAAAAATTCTTTCGGG-TCAATTTT
* * * *
3841 TGGAAAATTTTGGCCGAAATCGTGTACTAACCATCACGATTTTTGGAAAAAACGCATTCC-GGAC
641 TGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGATTTTTGGAAAAAACGCATTCCGGGGC
3905 CCCGGCTCAGTTTTGCTTGATTTTTGGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCA
706 CCCGGCTCAGTTTTGCTTGATTTTTGGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCA
*
3970 AATCTCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCCGAATCTTGTTTCGATTTAAG
771 AATCTCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAG
*
4035 TAGAAATTAATTCAGAAAAAAAAATAAGGAAAAACGATATTAGAAGCGTG-AAAAGCATTTCAAT
836 TAGAAATTAATTCAG--AAAAAAATAA-GAAAAACGATATTAGAAGCGTGAAAAAAC-TTTCAAT
* * * *
4099 ATTTTTGGAGTTGAACTATATATTTTTTATGAGTATTATAGCCAAGAATTGAAGGAAATTCTTTC
897 ATTTTTGGAGTTGAACTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTCTTTC
*
4164 GGGTCAATTTTTAGCTGAAGTCATG
962 GGGTCAATTTTTAGCTGAAATCATG
4189 TACT-ACCATCACGGTTTCTAGCAAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCTTGATTT
1 TACTAACCATCACGGTTTCTAGCAAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCTTGATTT
* * *
4253 TTGGTGCCAAGTCTCCTTGACATATCTATATTCATCTAACCAAAGCTCATCCACATTGGATTTAA
66 TTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCATCCACATTGGATTTAA
* *
4318 GTATTTGACTTTACGAACATCTAAATCTTGTTTCAATTTAAGTTA-AAATTAATTTAGAATAAAA
131 GTATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTTAGAAATTAATTTAGAA-AAAA
* * *
4382 AAAGGAAAAATGATATTAGAAGCTTGAAAAGCTTTTCAATATTTTGGGAGTTGAACTATATAATT
195 AAA-GAAAAATGATATTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGTTGAACTATAT-ATT
* * *
4447 TTTTAGGAGTATGGTAGCCAAAAATTGAATAAAATTCTTCTGGGTCATTTTTTGCAAAATTTTAG
258 TTTTATGAGTATCGTAGCCAAAAATTGAAGAAAATTCTTCTGGGTCATTTTTTGCAAAATTTTAG
* * *
4512 CTGAAATCGTGTACTAACCATGACGATTTTTAGCAAAAAACGTATTCCGGGGCCCCGGCTCAGTT
323 CTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTCAGTT
*
4577 TTGCTTGATTTTTAGTGCCAAGACTACTTGACATATCTATATTCAACTAAGCAAATATCATCCAC
388 TTGCTTGATTTTTAGTGCCAAGACTACTTGACATATCTATATTCATCTAAGCAAATATCATCCAC
* *
4642 ATTGGATTTAAGAATTTGATTTTAAGAACATCTGAATCTTGTTTCGATTTAAGTAGAAATTAATT
453 ATTGGATTTAAGAATTAGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAGAAATTAA-T
*
4707 TAGAAAAAACTAGGAAAAACGATCTTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGTTGAAC
517 TAGAAAAAA-TAGGAAAAACGATATTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGTTGAAC
* * * * * * *
4772 TATATATTTTTAATTAGT-TTCATGG-GAAAAAATT-GAAGAAA--ATTTCGGTTAAATTTTTGC
581 TATATATTTTTTATGAGTATT-GTGGCCAAAAAATTGGAA-AAATTCTTTCGGGTCAATTTTTGC
* * * ** * *
4832 AAAATTTTAGCTGAAATCGTCTACAAACCATCACGGTTTTTGTCTAAAAACGCATTCCGAGGTCC
644 AAAATTTTAGCTGAAATCGTGTACTAACCATCACGATTTTTG-GAAAAAACGCATTCCGGGGCCC
* * *
4897 CGGCTCAGTTTTGCTTGGTTTTT-GTCGCCATGACTCCTTGACATATATATATTCATCTAACCAA
708 CGGCTCAGTTTTGCTTGATTTTTGGT-GCCAAGACTCCTTGACATATCTATATTCATCTAACCAA
* * * * *
4961 ATCT-ATGCCGCGTTGGATTTAAGAAAATTT--TTTTACGAGCATCTTAATTTTGTTTCGATTT-
772 ATCTCAT-CCACATTGGATTTAAG--AATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTA
* * * * * * *
5022 ATTAAGAAATCAATT-ACGAAAATAATAATAAAAAAGATATTACAACCGTGAAAAAACTTTCAAT
834 AGT-AGAAATTAATTCA-GAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAACTTTCAAT
* * * * *
5086 ATTTTTGGAGTT-AATTTACATATTTTTTATGAGTATTATGGCCAAGAATTGAAGGAAATTCTTT
897 ATTTTTGGAGTTGAA-CTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTCTTT
5150 CGGGTCAATTTTTAGCTGAAAT-AGTG
961 CGGGTCAATTTTTAGCTGAAATCA-TG
* *
5176 TACTAACCATCACAGTTTCTAGCAAAAAACGCATTTCGGGGCCCCGGCTCAGTTTTGCTTGATTT
1 TACTAACCATCACGGTTTCTAGCAAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCTTGATTT
* * *
5241 TTGGTGCCAAGACTCGTTGACATATCTATATTCATCTAACCCAATCTCATCCACATTGGATTTAA
66 TTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCATCCACATTGGATTTAA
*
5306 GTATTTGATTTTACAAACATCTGAATCTTGTTTCAATTTAAG-TAGAAATTAATTTAGAAAAAAA
131 GTATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTTAGAAATTAATTTAGAAAAAAA
*
5370 TAGGAAAAATGATATTAGAAGCATGAAAAGCGTTTC-A-ATTTTT----TTG-------------
196 -AAGAAAAATGATATTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGTTGAACTATATATTTT
* * * *
5416 ----GAGTATGGTAGCCAAAAATTGAAGAAAATTATTTTGGGTCATTTTTTGCAAACTTTTAGCT
260 TTATGAGTATCGTAGCCAAAAATTGAAGAAAATTCTTCTGGGTCATTTTTTGCAAAATTTTAGCT
* * * * * *
5477 GAAATCGGGTACTAACCATCACGATTTTTAGCAAAAAACGTATTCCGGAGCCCTGGCTTAGTTTT
325 GAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTCAGTTTT
*
5542 GCTTGATTTTTAGTGCCAAGACTACTTGACATATCTATATTCAACTAAGCAAATATCATCCACAT
390 GCTTGATTTTTAGTGCCAAGACTACTTGACATATCTATATTCATCTAAGCAAATATCATCCACAT
* *
5607 TGGATATAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAGAAATTAATTCA
455 TGGATTTAAGAATTAGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAGAAATTAATT-A
* * *
5672 GAAAAAAATAGGAAAAACGATCTTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGTTGAACTT
519 G-AAAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGTTGAACTA
** * * *
5737 TATATTTTTTATGAGTATCATGG-CAAAAAATT-GAAGAAA---ATTCGGGTAAATTTTTGCCAA
583 TATATTTTTTATGAGTATTGTGGCCAAAAAATTGGAA-AAATTCTTTCGGGTCAATTTTTGCAAA
* * * * ** *
5797 ATTTTAGCTGAAGTCGTCTACTAACCATGACGGTTTTTGTCTAAAAACGCATTCCGGGGCCCAGG
647 ATTTTAGCTGAAATCGTGTACTAACCATCACGATTTTTG-GAAAAAACGCATTCCGGGGCCCCGG
* * *
5862 CTCAGTTTTGCTTGGTTTTT-GTCACCAAGACTCCTTGACATATCTATATTCATCTAACAAAATC
711 CTCAGTTTTGCTTGATTTTTGGT-GCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATC
* * * ** * * * *
5926 T-ATGCCGCGTTGGATTTAAGAAATTCTTTTTACGAGCATCTGAATTTTGTTTCG-TTTTATTAA
775 TCAT-CCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGT-A
* ** * * *
5989 GAAATCAATTTGGAAAATAATAATAATAACGATATTAGAAGCGTGAAAAAACTTTCAATATTTTT
838 GAAATTAATTCAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAACTTTCAATATTTTT
* * * *
6054 GGAGTT-AATTTATATATTTTTTATGAGTATCATGGCCAAGAATTGAAGGAAATTCGTTTAGGTC
903 GGAGTTGAA-CTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTC-TTTCGG--
* * *
6118 AATTTTTGCAAATTTTTAGTTGAAATCGTG
964 -----GT-C-AATTTTTAGCTGAAATCATG
** * * * * *
6148 TACTAACCATCACAATTTCT-GACAAAAAACCCATTCCGGGGCCTCGGCCCAGTTATGCCTGATT
1 TACTAACCATCACGGTTTCTAG-CAAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCTTGATT
* **
6212 TTTGGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCATATACATTGGATTTA
65 TTTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCATCCACATTGGATTTA
*
6277 AGAATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAG-TAGAAATTAATTTAGAAAAAA
130 AGTATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTTAGAAATTAATTTAGAAAAAA
* *
6341 AATAGGAAAAATGATATTAGAAGCATGAAAAGCGTTTAAATAATTTTGGAGTTGAACTATATAAT
195 AA-A-GAAAAATGATATTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGTTGAACTATAT-AT
* * * *
6406 TATTTATGAGTATTGTAGCCAAAAATTGAATAAAATTCTTTTGGGTCATTTTTTTGCAAAATTTT
257 TTTTTATGAGTATCGTAGCCAAAAATTGAAGAAAATTCTTCTGGGTCA-TTTTTTGCAAAATTTT
*
6471 AGCTGAAATCGTGTACTAACAATCACGATTTTTGGCAAAAAAAAACGCATTCCGGGGCCCCGGCT
321 AGCTGAAATCGTGTACTAACCATCACGATTTTTGGC---AAAAAACGCATTCCGGGGCCCCGGCT
* * *
6536 CAGTTTTGCATGATTTTTAGTGCCAAGACTACTTGACATATATATATTCATCTAAGAAAATATCA
383 CAGTTTTGCTTGATTTTTAGTGCCAAGACTACTTGACATATCTATATTCATCTAAGCAAATATCA
* *
6601 TCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTAGAAAT
448 TCCACATTGGATTTAAGAATTAGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAGAAAT
* *
6666 TAATTTAGAAAAAAATAGGAAAAATGATATTAGAAGCATGAAAAGCGTTTAAATATTTTTGGAGT
513 TAA-TTAG-AAAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGT
* * * * *
6731 TGAACTATATAATTATTTATGAGTATTGTAGCC-AAAAATTGAAGAAAATTCTTTTGGGTCATTT
576 TGAACTATAT-ATTTTTTATGAGTATTGTGGCCAAAAAATTGGA-AAAATTCTTTCGGGTCA-AT
*
6795 TTTTGCAAAATTTTAGCTGAAATCGTGTACTAACAATCACGATTTTTGGCAAAAAAAAACGCATT
638 TTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGATTTTTGG----AAAAAACGCATT
* *
6860 CCGGGGCCCCGGCTCAGTTTTGCTTGATTTTTGGTGCCAAGACTCCTTCACATATCTATATTCGT
699 CCGGGGCCCCGGCTCAGTTTTGCTTGATTTTTGGTGCCAAGACTCCTTGACATATCTATATTCAT
* *
6925 CTAACCAAATATCATCCACATTGGATTTAAGAATTTGATTTTACGAACATTTGAATCTTGTTTCG
764 CTAACCAAATCTCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCG
* * * *
6990 ATTTAAGTAGAAATTAGTTC--AAAAAAA-AAGGAAAACAATATTAGAAGCGT-AAAAAGCCTTT
829 ATTTAAGTAGAAATTAATTCAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAA-ACTTT
* *
7051 CAATATTTTTGGAGTTGAACTATATATTTTATATGAGTATCATGGCAAAAAATTGAAGAAAAATT
893 CAATATTTTTGGAGTTGAACTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAG-AAAA-T
* *** * * * *
7116 TGGGTAAATTTTTG-CAACATTTTAGCTAAAATCGTC
956 T--CT---TTCGGGTCAA-TTTTTAGCTGAAATCATG
* *
7152 TACTAACCATCACGGTTT-TTGCTAAAAAAACGCATTCCGGGGCCCCGACTCAGTTTTGCTTGAT
1 TACTAACCATCACGGTTTCTAGC--AAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCTTGAT
* * * * * *
7216 TTTTGGCGCCAAGACTTCTTGGCATATCTATATTCATCTAACCAAATCTAAGCCGCGTTGGATTT
64 TTTTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCATCCACATTGGATTT
* * ** * * * * * *
7281 AAGAAATTCTTTTTACGAGCATTTGAATTTTGTTTCGATTT-A-TTAAGAAATCAATTTGGAAAA
129 AAGTATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTT-AGAAATTAATTTAGAAAA
* * * * * * * *
7344 TAATAATAAAAAAGATATTAGAACCGTGAAAAACCTTTCAATATTTTTGGAGTT-AATTTATATA
193 -AAAAAGAAAAATGATATTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGTTGAA-CTATATA
* * ** * * * *
7408 TTTTTTATGAGTATCATGGCCAGGAATCGAAGGAAATTCTT-TCGGGTCAATTTTTGCAAATTTT
256 TTTTTTATGAGTATCGTAGCCAAAAATTGAAGAAAATTCTTCT-GGGTCATTTTTTGCAAAATTT
* * *
7472 TAGCTGAAATCGTGTACTAACCATCACGATTTCTGGCAAAAAACGCATTTCGGGGCCCCGGGTCA
320 TAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTCA
* * * * * *
7537 GTTTTGCTTGATTTTTTGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAAC
385 GTTTTGCTTGATTTTTAGTGCCAAGACTACTTGACATATCTATATTCATCTAAGCAAATATCATC
* *
7602 CACATTGGATTTAAGAATTTA-ATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTAAAAATT
450 CACATTGGATTTAAGAA-TTAGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAGAAATT
* *
7666 AATTAAGAAAAAAATAGGAAAAATGATATTAGAAGCACGAAAAGCGTTTCAATATTTTTGGAGTT
514 AATT-AG-AAAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGTT
* * * * *
7731 GAACTATATAATTTTTTATGAGTATGGTAGCC-AAAAATTGAAGAAAATTCTTTTGGGTCATTTT
577 GAACTATAT-ATTTTTTATGAGTATTGTGGCCAAAAAATTGGA-AAAATTCTTTCGGGTCAATTT
* * *
7795 TTGCAAAATTTTAGTTGAAATCGTGTACTAACCATCACGATTTTTGGCAAGAAACGCACTCCGGG
640 TTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGATTTTTGG-AAAAAACGCATTCCGGG
* * * * * * *
7860 GTCCAGGCTCAATTTTGCTTGATTTTTAGTTCCAAGACTCCTTCACATATCTATATTCATCTAGC
704 GCCCCGGCTCAGTTTTGCTTGATTTTTGGTGCCAAGACTCCTTGACATATCTATATTCATCTAAC
*
7925 CAAATATCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTA
769 CAAATCTCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTA
7990 AGTAGAAATTAATTCAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAACTTTCAATAT
834 AGTAGAAATTAATTCAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAACTTTCAATAT
* * * * * * *
8055 TTTTGGAGTTGAATTATATACTTTTAATGAGTATCGTGGCCAAAAATTGAAAAAAAAAT-TGTCG
899 TTTTGGAGTTGAACTATATATTTTTTATGAGTATCATGGCCAAAAATTG-AAGAAAATTCTTTCG
*
8119 AGTCAAATTTTGCAAAATTTTAGCTGAAATCATG
963 GGTC-AA---T------TTTTAGCTGAAATCATG
* * * * *
8153 TACTAACTATCACGGTTT-TGGGCTAAAAACGCATTCTGGGGCCCCGGGTCAGTTTTGCTTGATT
1 TACTAACCATCACGGTTTCT-AGCAAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCTTGATT
* * * * *
8217 TTTTGCGCCAAGACTCCTTGACATATCTATATTCTTCTAAGCAAATATCATCCACATTGTATTTA
65 TTTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCATCCACATTGGATTTA
* * * * *
8282 A-TAATTTGATTTTACGAACATTTGAATCTTATTTTGAA-TTAA-ATAAAAATT-A-TT------
130 AGT-ATTTGATTTTACGAACATCTGAATCTT-GTTTCAATTTAAGTTAGAAATTAATTTAGAAAA
* * * * *
8336 AAAAA-AAAAACGATATTAAAAGCGTGAAGAGCGTTTCAATATTTTTGAAGTTGAACTATATA-T
193 AAAAAGAAAAATGATATTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGTTGAACTATATATT
* * * * * * * **
8399 TTTTATGAGTATCATGGCCAAAAATTAAAGATAATT-TTGTCGGCTAAAATTTTGCAAAATTTTA
258 TTTTATGAGTATCGTAGCCAAAAATTGAAGAAAATTCTTCT-GGGTCATTTTTTGCAAAATTTTA
* * * * * *
8463 GCTGAAACCATTTACTAACCATCACGGTTTTTGGCAAAACACGCATTCCGAGGCCCCGGCTCAGT
322 GCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTCAGT
* * * * * * * *
8528 TTTGCTTAATTTTTTGCGCCAAGACTCCTAGAAATATCTATATTCATCTAATCAAATCTCATCCA
387 TTTGCTTGATTTTTAGTGCCAAGACTACTTGACATATCTATATTCATCTAAGCAAATATCATCCA
* *
8593 CATTGGATTTAAGAATTAGATTTTACGAATATCTGAATCTTGTTTCGATTTAAGCA-ACAATTAA
452 CATTGGATTTAAGAATTAGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAGA-AATTAA
*
8657 TTCAGAGAAAAATAGGAAAAAC-AGTATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGTTG
516 TT-AGA-AAAAATAGGAAAAACGA-TATTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGTTG
* * * *
8721 AACTATATATTTTTTATGGGTATCGTGGCCAAAAAATTGGTGAAAATTATTTCGGGTCAATTTTT
578 AACTATATATTTTTTATGAGTATTGTGGCCAAAAAATTGG-AAAAATTCTTTCGGGTCAATTTTT
* * * * * *
8786 GC-AAATTTTAGCTAAAATCGTGTACATTA-CATCATGGTTTTTGGCAAAAACGCATTTCGGGGC
642 GCAAAATTTTAGCTGAAATCGTGTAC-TAACCATCACGATTTTTGGAAAAAACGCATTCCGGGGC
* * * * *
8849 CCCAGCTCAGTCTTGCTTGATTTTTGGCGCCAAGACTCCGTGACAAATCTATATTCATCTAACCA
706 CCCGGCTCAGTTTTGCTTGATTTTTGGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCA
8914 AATCTCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAG
771 AATCTCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAG
* * * *
8979 TAAAAATTAATTCAG-AAAAAATAGGAAAAACAATATTAGAAGCGTG-AAAAGCGTTTCAATATT
836 TAGAAATTAATTCAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAAC-TTTCAATATT
* *
9042 TTTGGAGTTGAACTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAACTCTTTCGGG
900 TTTGGAGTTGAACTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTCTTTCGGG
*
9107 TCAATTTTTGCAAAATTTTAGCTGAAATCGTG
965 TCAA----T------TTTTAGCTGAAATCATG
* * * * * * * *
9139 TACTAACAATCACGTTTTTTGGCAAAAAACGCGTTCCGGGGCCCCGACTCAATTTTGTTTGATTT
1 TACTAACCATCACGGTTTCTAGCAAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCTTGATTT
9204 TT
66 TT
9206 AGCTTTAACT
Statistics
Matches: 4359, Mismatches: 506, Indels: 301
0.84 0.10 0.06
Matches are distributed among these distances:
960 4 0.00
961 3 0.00
962 302 0.07
963 336 0.08
964 7 0.00
970 1 0.00
971 3 0.00
972 196 0.04
973 32 0.01
974 1 0.00
975 5 0.00
979 3 0.00
981 3 0.00
982 148 0.03
983 5 0.00
985 26 0.01
986 223 0.05
987 307 0.07
988 498 0.11
989 348 0.08
990 178 0.04
991 71 0.02
992 6 0.00
993 2 0.00
994 1 0.00
995 151 0.03
997 46 0.01
998 179 0.04
999 267 0.06
1000 123 0.03
1001 251 0.06
1002 76 0.02
1003 50 0.01
1004 80 0.02
1005 141 0.03
1006 15 0.00
1007 117 0.03
1008 11 0.00
1009 2 0.00
1010 130 0.03
1011 9 0.00
1013 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (986 bp):
TACTAACCATCACGGTTTCTAGCAAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTGCTTGATTT
TTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCATCCACATTGGATTTAA
GTATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTTAGAAATTAATTTAGAAAAAAA
AAGAAAAATGATATTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGTTGAACTATATATTTTT
TATGAGTATCGTAGCCAAAAATTGAAGAAAATTCTTCTGGGTCATTTTTTGCAAAATTTTAGCTG
AAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTCAGTTTTG
CTTGATTTTTAGTGCCAAGACTACTTGACATATCTATATTCATCTAAGCAAATATCATCCACATT
GGATTTAAGAATTAGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAGAAATTAATTAGA
AAAAATAGGAAAAACGATATTAGAAGCATGAAAAGCGTTTCAATATTTTTGGAGTTGAACTATAT
ATTTTTTATGAGTATTGTGGCCAAAAAATTGGAAAAATTCTTTCGGGTCAATTTTTGCAAAATTT
TAGCTGAAATCGTGTACTAACCATCACGATTTTTGGAAAAAACGCATTCCGGGGCCCCGGCTCAG
TTTTGCTTGATTTTTGGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCATCC
ACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAGAAATTAA
TTCAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAACTTTCAATATTTTTGGAGTTGA
ACTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTCTTTCGGGTCAATTTTTAG
CTGAAATCATG
Found at i:7897 original size:334 final size:333
Alignment explanation
Indices: 5407--9207 Score: 4744
Period size: 333 Copynumber: 11.4 Consensus size: 333
5397 AAGCGTTTCA
* * * * *
5407 ATTTTTT-TGGAGTATGGTAGCCAAAAATTGAAGAAAATTATTTTGGGTCATTTTTTGCAAACTT
1 ATTTTTTAT-GAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTTGGGTCAATTTTTGCAAAATT
* * * * * *
5471 TTAGCTGAAATCGGGTACTAACCATCACGATTTTTAGCAAAAAACGTATTCCGGAGCCCTGGCTT
65 TTAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTC
* * * *
5536 AGTTTTGCTTGATTTTTAGTGCCAAGACTACTTGACATATCTATATTCAACTAAGCAAATATCAT
130 AGTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAT
* *
5601 CCACATTGGATATAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAGAAATT
195 CCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAAAAATT
*
5666 AATTCAGAAAAAAATAGGAAAAACGATCTTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGTT
260 AATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGTT
*
5731 GAACTTTAT
325 GAACTATAT
* * * *
5740 ATTTTTTATGAGTATCATGGCAAAAAATTGAAGAAAATTC----GGGTAAATTTTTGCCAAATTT
1 ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTTGGGTCAATTTTTGCAAAATTT
* * * * * * *
5801 TAGCTGAAGTCGTCTACTAACCATGACGGTTTTTGTCTAAAAACGCATTCCGGGGCCCAGGCTCA
66 TAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTCA
* * *
5866 GTTTTGCTTGGTTTTT-GTCACCAAGACTCCTTGACATATCTATATTCATCTAACAAAATCT-AT
131 GTTTTGCTTGATTTTTAGT-GCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAT
* * * ** * * * *
5929 GCCGCGTTGGATTTAAGAAATTCTTTTTACGAGCATCTGAATTTTGTTTCG-TTTTATTAAGAAA
195 -CCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAA-AAA
* ** * ** * *
5993 TCAATTTGGAAAATAATAATAATAACGATATTAGAAGCGTGAAAAAAC-TTTCAATATTTTTGGA
258 TTAATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTG-AAAAGCGTTTCAATATTTTTGGA
*
6057 GTT-AATTTATAT
322 GTTGAA-CTATAT
* * * * * *
6069 ATTTTTTATGAGTATCATGGCCAAGAATTGAAGGAAATTCGTTTAGGTCAATTTTTGCAAATTTT
1 ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTTGGGTCAATTTTTGCAAAATTT
* * * * * * *
6134 TAGTTGAAATCGTGTACTAACCATCACAATTTCTGACAAAAAACCCATTCCGGGGCCTCGGCCCA
66 TAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTCA
* * * *
6199 GTTATGCCTGATTTTTGGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCATA
131 GTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCATC
* * *
6264 TACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTAGAAATTA
196 CACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAAAAATTA
* * * * *
6329 ATTTAGAAAAAAAATAGGAAAAATGATATTAGAAGCATGAAAAGCGTTTAAATAATTTTGGAGTT
261 ATTCAG-AAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGTT
6394 GAACTATAT
325 GAACTATAT
* * * * *
6403 AATTATTTATGAGTATTGTAGCCAAAAATTGAATAAAATTCTTTTGGGTCATTTTTTTGCAAAAT
1 -ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTTGGGTCA-ATTTTTGCAAAAT
*
6468 TTTAGCTGAAATCGTGTACTAACAATCACGATTTTTGGCAAAAAAAAACGCATTCCGGGGCCCCG
64 TTTAGCTGAAATCGTGTACTAACCATCACGATTTTTGGC---AAAAAACGCATTCCGGGGCCCCG
* * * ** *
6533 GCTCAGTTTTGCATGATTTTTAGTGCCAAGACTACTTGACATATATATATTCATCTAAGAAAATA
126 GCTCAGTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATC
* *
6598 TCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTAGA
191 TCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAAA
* * * *
6663 AATTAATTTAGAAAAAAATAGGAAAAATGATATTAGAAGCATGAAAAGCGTTTAAATATTTTTGG
256 AATTAATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGG
6728 AGTTGAACTATAT
321 AGTTGAACTATAT
* * * *
6741 AATTATTTATGAGTATTGTAGCCAAAAATTGAAGAAAATTCTTTTGGGTCATTTTTTTGCAAAAT
1 -ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTTGGGTCA-ATTTTTGCAAAAT
*
6806 TTTAGCTGAAATCGTGTACTAACAATCACGATTTTTGGCAAAAAAAAACGCATTCCGGGGCCCCG
64 TTTAGCTGAAATCGTGTACTAACCATCACGATTTTTGGC---AAAAAACGCATTCCGGGGCCCCG
* * * *
6871 GCTCAGTTTTGCTTGATTTTTGGTGCCAAGACTCCTTCACATATCTATATTCGTCTAACCAAATA
126 GCTCAGTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATC
* *
6936 TCATCCACATTGGATTTAAGAATTTGATTTTACGAACATTTGAATCTTGTTTCGATTTAAGTAGA
191 TCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAAA
* * * *
7001 AATTAGTTCA-AAAAAAA-AGG-AAAACAATATTAGAAGCGTAAAAAGCCTTTCAATATTTTTGG
256 AATTAATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGG
7063 AGTTGAACTATAT
321 AGTTGAACTATAT
* * * * * *
7076 ATTTTATATGAGTATCATGGCAAAAAATTGAAGAAAA---ATTTGGGTAAATTTTTGCAACATTT
1 ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTTGGGTCAATTTTTGCAAAATTT
* * * *
7138 TAGCTAAAATCGTCTACTAACCATCACGGTTTTT-GCTAAAAAAACGCATTCCGGGGCCCCGACT
66 TAGCTGAAATCGTGTACTAACCATCACGATTTTTGGC--AAAAAACGCATTCCGGGGCCCCGGCT
* * * * *
7202 CAGTTTTGCTTGATTTTTGGCGCCAAGACTTCTTGGCATATCTATATTCATCTAACCAAATCTAA
129 CAGTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCA
* * * * ** * * * *
7267 GCCGCGTTGGATTTAAGAAATTCTTTTTACGAGCATTTGAATTTTGTTTCGATTT-ATTAAGAAA
194 TCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAA-AAA
* ** * ** * * * *
7331 TCAATTTGGAAAATAATAATAAAAAAGATATTAGAACCGTGAAAAACCTTTCAATATTTTTGGAG
258 TTAATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAG
*
7396 TT-AATTTATAT
323 TTGAA-CTATAT
* ** * * * *
7407 ATTTTTTATGAGTATCATGGCCAGGAATCGAAGGAAATTCTTTCGGGTCAATTTTTGCAAATTTT
1 ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTTGGGTCAATTTTTGCAAAATTT
* * *
7472 TAGCTGAAATCGTGTACTAACCATCACGATTTCTGGCAAAAAACGCATTTCGGGGCCCCGGGTCA
66 TAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTCA
* * *
7537 GTTTTGCTTGATTTTTTGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAAC
131 GTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCATC
* *
7602 CACATTGGATTTAAGAATTTAATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTAAAAATTA
196 CACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAAAAATTA
* * **
7667 ATTAAGAAAAAAATAGGAAAAATGATATTAGAAGCACGAAAAGCGTTTCAATATTTTTGGAGTTG
261 ATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGTTG
7732 AACTATAT
326 AACTATAT
* * *
7740 AATTTTTTATGAGTATGGTAGCCAAAAATTGAAGAAAATTCTTTTGGGTCATTTTTTGCAAAATT
1 -ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTTGGGTCAATTTTTGCAAAATT
* * * * *
7805 TTAGTTGAAATCGTGTACTAACCATCACGATTTTTGGCAAGAAACGCACTCCGGGGTCCAGGCTC
65 TTAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTC
* * * * *
7870 AATTTTGCTTGATTTTTAGTTCCAAGACTCCTTCACATATCTATATTCATCTAGCCAAATATCAT
130 AGTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAT
*
7935 CCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAGAAATT
195 CCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAAAAATT
* *
8000 AATTCAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAAC-TTTCAATATTTTTGGAGT
260 AATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTG-AAAAGCGTTTCAATATTTTTGGAGT
*
8064 TGAATTATAT
324 TGAACTATAT
* * * * * * * *
8074 ACTTTTAATGAGTATCGTGGCCAAAAATTGAAAAAAAAAT-TGTCGAGTCAAATTTTGCAAAATT
1 ATTTTTTATGAGTATCGTGGCCAAAAATTG-AAGAAAATTCTTTTGGGTCAATTTTTGCAAAATT
* * * * * * *
8138 TTAGCTGAAATCATGTACTAACTATCACGGTTTTGGGCTAAAAACGCATTCTGGGGCCCCGGGTC
65 TTAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTC
* * * * *
8203 AGTTTTGCTTGATTTTTTGCGCCAAGACTCCTTGACATATCTATATTCTTCTAAGCAAATATCAT
130 AGTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAT
* * * * * * *
8268 CCACATTGTATTTAATAATTTGATTTTACGAACATTTGAATCTTATTTTGAATTAAATAAAAATT
195 CCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAAAAATT
* * *
8333 -ATT------AAAA-A--AAAAACGATATTAAAAGCGTGAAGAGCGTTTCAATATTTTTGAAGTT
260 AATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGTT
8388 GAACTATAT
325 GAACTATAT
* * * * * * *
8397 A-TTTTTATGAGTATCATGGCCAAAAATTAAAGATAATT-TTGTCGGCTAAAATTTTGCAAAATT
1 ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTCTT-TTGGGTCAATTTTTGCAAAATT
* * * * * *
8460 TTAGCTGAAACCATTTACTAACCATCACGGTTTTTGGCAAAACACGCATTCCGAGGCCCCGGCTC
65 TTAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTC
* * * * * *
8525 AGTTTTGCTTAATTTTTTGCGCCAAGACTCCTAGAAATATCTATATTCATCTAATCAAATCTCAT
130 AGTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAT
* * * *
8590 CCACATTGGATTTAAGAATTAGATTTTACGAATATCTGAATCTTGTTTCGATTTAAGCAACAATT
195 CCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAAAAATT
*
8655 AATTCAGAGAAAAATAGGAAAAAC-AGTATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGT
260 AATTCAGAAAAAAATAGGAAAAACGA-TATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGT
8719 TGAACTATAT
324 TGAACTATAT
* ** * *
8729 ATTTTTTATGGGTATCGTGGCCAAAAAATTGGTGAAAATTATTTCGGGTCAATTTTTGC-AAATT
1 ATTTTTTATGAGTATCGTGGCC-AAAAATTGAAGAAAATTCTTTTGGGTCAATTTTTGCAAAATT
* * * * * *
8793 TTAGCTAAAATCGTGTACATTA-CATCATGGTTTTTGGC-AAAAACGCATTTCGGGGCCCCAGCT
65 TTAGCTGAAATCGTGTAC-TAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCT
* * * * *
8856 CAGTCTTGCTTGATTTTTGGCGCCAAGACTCCGTGACAAATCTATATTCATCTAACCAAATCTCA
129 CAGTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCA
8921 TCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAAAAAT
194 TCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAAAAAT
*
8986 TAATTCAG-AAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGT
259 TAATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGT
9050 TGAACTATAT
324 TGAACTATAT
* *
9060 ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAACTCTTTCGGGTCAATTTTTGCAAAATTT
1 ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTTGGGTCAATTTTTGCAAAATTT
* * * *
9125 TAGCTGAAATCGTGTACTAACAATCACGTTTTTTGGCAAAAAACGCGTTCCGGGGCCCCGACTCA
66 TAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTCA
* *
9190 ATTTTGTTTGATTTTTAG
131 GTTTTGCTTGATTTTTAG
9208 CTTTAACTCT
Statistics
Matches: 3002, Mismatches: 410, Indels: 113
0.85 0.12 0.03
Matches are distributed among these distances:
321 7 0.00
322 217 0.07
323 50 0.02
325 1 0.00
326 4 0.00
327 3 0.00
328 150 0.05
329 271 0.09
330 86 0.03
331 205 0.07
332 240 0.08
333 666 0.22
334 472 0.16
335 101 0.03
336 48 0.02
337 7 0.00
338 323 0.11
339 151 0.05
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (333 bp):
ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTTGGGTCAATTTTTGCAAAATTT
TAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTCA
GTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCATC
CACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAAAAATTA
ATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGTTG
AACTATAT
Found at i:8088 original size:667 final size:667
Alignment explanation
Indices: 5407--9207 Score: 4787
Period size: 667 Copynumber: 5.7 Consensus size: 667
5397 AAGCGTTTCA
* * * * * *
5407 ATTTTTT-TGGAGTATGGTAGCCAAAAATTGAAGAAAATTATTTTGGGTCATTTTTTGCAAACTT
1 ATTTTTTAT-GAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTCGGGTCAATTTTTGCAAAATT
* * * * * *
5471 TTAGCTGAAATCGGGTACTAACCATCACGATTTTTAGCAAAAAACGTATTCCGGAGCCCTGGCTT
65 TTAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTC
* * * * *
5536 AGTTTTGCTTGATTTTTAGTGCCAAGACTACTTGACATATCTATATTCAACTAAGCAAATATCAT
130 AGTTTTGCTTGATTTTTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATATCAT
* * *
5601 CCACATTGGATATAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAGAAATT
195 CCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTAAAAATT
*
5666 AATTCAGAAAAAAATAGGAAAAACGATCTTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGTT
260 AATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGTT
* *
5731 GAACTTTATATTTTTTATGAGTATCATGGCAAAAAATTGAAGAAAATTC----GGGTAAATTTTT
325 GAACTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTCTTTTGGGTAAATTTTT
* * * * * *
5792 GCCAAATTTTAGCTGAAGTCGTCTACTAACCATGACGGTTTTTGTC-TAAAAACGCATTCCGGGG
390 GCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAAACGCATTCCGGGG
* * *
5856 CCCAGGCTCAGTTTTGCTTGGTTTTT-GTCACCAAGACTCCTTGACATATCTATATTCATCTAA-
455 CCCCGGCTCAGTTTTGCTTGATTTTTAGT-GCCAAGACTCCTTGACATATCTATATTCATCTAAC
* * * ** * *
5919 CAAA-ATCTATGCCGCGTTGGATTTAAGAAATTCTTTTTACGAGCATCTGAATTTTGTTTCG-TT
519 CAAATATC-AT-CCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATT
* * * * * * *
5982 TTATTAAGAAATCAATTTGGAAAATAATAATAATAACGATATTAGAAGCGTGAAAAAACTTTCAA
582 TAAGT-AGAAATTAATTTAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAACTTTCAA
6047 TATTTTTGGAGTT-AATTTATAT
646 TATTTTTGGAGTTGAA-TTATAT
* * * * *
6069 ATTTTTTATGAGTATCATGGCCAAGAATTGAAGGAAATTCGTTT-AGGTCAATTTTTGCAAATTT
1 ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTC-TTTCGGGTCAATTTTTGCAAAATT
* * * * * * *
6133 TTAGTTGAAATCGTGTACTAACCATCACAATTTCTGACAAAAAACCCATTCCGGGGCCTCGGCCC
65 TTAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTC
* * * *
6198 AGTTATGCCTGATTTTTGGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAT
130 AGTTTTGCTTGATTTTTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATATCAT
** *
6263 ATACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTAGAAATT
195 CCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTAAAAATT
* * * * *
6328 AATTTAGAAAAAAAATAGGAAAAATGATATTAGAAGCATGAAAAGCGTTTAAATAATTTTGGAGT
260 AATTCAG-AAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGT
* ** * * **
6393 TGAACTATATAATTATTTATGAGTATTGTAGCCAAAAATTGAATAAAATTCTTTTGGGTCATTTT
324 TGAACTATAT-ATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTCTTTTGGGT-AAATT
* *
6458 TTTGCAAAATTTTAGCTGAAATCGTGTACTAACAATCACGATTTTTGGCAAAAAAAAACGCATTC
387 TTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGC--AAAAAAACGCATTC
* * *
6523 CGGGGCCCCGGCTCAGTTTTGCATGATTTTTAGTGCCAAGACTACTTGACATATATATATTCATC
450 CGGGGCCCCGGCTCAGTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATC
** *
6588 TAAGAAAATATCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCAA
515 TAACCAAATATCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGA
* * * * *
6653 TTTAAGTAGAAATTAATTTAGAAAAAAATAGGAAAAATGATATTAGAAGCATG-AAAAGCGTTTA
580 TTTAAGTAGAAATTAATTTAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAAC-TTTC
*
6717 AATATTTTTGGAGTTGAACTATAT
644 AATATTTTTGGAGTTGAATTATAT
* * * * *
6741 AATTATTTATGAGTATTGTAGCCAAAAATTGAAGAAAATTCTTTTGGGTCATTTTTTTGCAAAAT
1 -ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTCGGGTCA-ATTTTTGCAAAAT
*
6806 TTTAGCTGAAATCGTGTACTAACAATCACGATTTTTGGCAAAAAAAAACGCATTCCGGGGCCCCG
64 TTTAGCTGAAATCGTGTACTAACCATCACGATTTTTGGC---AAAAAACGCATTCCGGGGCCCCG
* * *
6871 GCTCAGTTTTGCTTGATTTTTGGTGCCAAGACTCCTTCACATATCTATATTCGTCTAACCAAATA
126 GCTCAGTTTTGCTTGATTTTTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATA
* * *
6936 TCATCCACATTGGATTTAAGAATTTGATTTTACGAACATTTGAATCTTGTTTCGATTTAAGTAGA
191 TCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTAAA
* * * *
7001 AATTAGTTCA-AAAAAAA-AGG-AAAACAATATTAGAAGCGTAAAAAGCCTTTCAATATTTTTGG
256 AATTAATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGG
* * *
7063 AGTTGAACTATATATTTTATATGAGTATCATGGCAAAAAATTGAAGAAAA---ATTTGGGTAAAT
321 AGTTGAACTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTCTTTTGGGTAAAT
* * *
7125 TTTTGCAACATTTTAGCTAAAATCGTCTACTAACCATCACGGTTTTT-GCTAAAAAAACGCATTC
386 TTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGC-AAAAAAACGCATTC
* * * * *
7189 CGGGGCCCCGACTCAGTTTTGCTTGATTTTTGGCGCCAAGACTTCTTGGCATATCTATATTCATC
450 CGGGGCCCCGGCTCAGTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATC
* * * * * * ** * * *
7254 TAACCAAATCTAAGCCGCGTTGGATTTAAGAAATTCTTTTTACGAGCATTTGAATTTTGTTTCGA
515 TAACCAAATATCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGA
* * * * * * * *
7319 TTT-ATTAAGAAATCAATTTGGAAAATAATAATAAAAAAGATATTAGAACCGTGAAAAACCTTTC
580 TTTAAGT-AGAAATTAATTTAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAACTTTC
7383 AATATTTTTGGAGTT-AATTTATAT
644 AATATTTTTGGAGTTGAA-TTATAT
* ** * * *
7407 ATTTTTTATGAGTATCATGGCCAGGAATCGAAGGAAATTCTTTCGGGTCAATTTTTGCAAATTTT
1 ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTCGGGTCAATTTTTGCAAAATTT
* * *
7472 TAGCTGAAATCGTGTACTAACCATCACGATTTCTGGCAAAAAACGCATTTCGGGGCCCCGGGTCA
66 TAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTCA
* * *
7537 GTTTTGCTTGATTTTTTGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATCTCAAC
131 GTTTTGCTTGATTTTTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATATCATC
*
7602 CACATTGGATTTAAGAATTTAATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTAAAAATTA
196 CACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTAAAAATTA
* * **
7667 ATTAAGAAAAAAATAGGAAAAATGATATTAGAAGCACGAAAAGCGTTTCAATATTTTTGGAGTTG
261 ATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGTTG
** * * *
7732 AACTATATAATTTTTTATGAGTATGGTAGCCAAAAATTGAAGAAAATTCTTTTGGGTCATTTTTT
326 AACTATAT-ATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTCTTTTGGGTAAATTTTT
* * * *
7797 GCAAAATTTTAGTTGAAATCGTGTACTAACCATCACGATTTTTGGC-AAGAAACGCACTCCGGGG
390 GCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAAACGCATTCCGGGG
* * * * * *
7861 TCCAGGCTCAATTTTGCTTGATTTTTAGTTCCAAGACTCCTTCACATATCTATATTCATCTAGCC
455 CCCCGGCTCAGTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAACC
7926 AAATATCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAA
520 AAATATCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAA
*
7991 GTAGAAATTAATTCAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAACTTTCAATATT
585 GTAGAAATTAATTTAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAACTTTCAATATT
8056 TTTGGAGTTGAATTATAT
650 TTTGGAGTTGAATTATAT
* * * * * * *
8074 ACTTTTAATGAGTATCGTGGCCAAAAATTGAAAAAAAAAT-TGTCGAGTCAAATTTTGCAAAATT
1 ATTTTTTATGAGTATCGTGGCCAAAAATTG-AAGAAAATTCTTTCGGGTCAATTTTTGCAAAATT
* * * * * * *
8138 TTAGCTGAAATCATGTACTAACTATCACGGTTTTGGGCTAAAAACGCATTCTGGGGCCCCGGGTC
65 TTAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTC
* * *
8203 AGTTTTGCTTGATTTTTTGCGCCAAGACTCCTTGACATATCTATATTCTTCTAAGCAAATATCAT
130 AGTTTTGCTTGATTTTTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATATCAT
* * * * * *
8268 CCACATTGTATTTAATAATTTGATTTTACGAACATTTGAATCTTATTTTGAA-TTAAATAAAAAT
195 CCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTT-GTTTCAATTTAAGTAAAAAT
* * *
8332 T-ATT------AAAA-A--AAAAACGATATTAAAAGCGTGAAGAGCGTTTCAATATTTTTGAAGT
259 TAATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGT
* * * * *
8387 TGAACTATATA-TTTTTATGAGTATCATGGCCAAAAATTAAAGATAATT-TTGTCGGCTAAAATT
324 TGAACTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTCTT-TTGGGTAAATTT
* * * * *
8450 TTGCAAAATTTTAGCTGAAACCATTTACTAACCATCACGGTTTTTGGC-AAAACACGCATTCCGA
388 TTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAAACGCATTCCGG
* * * * *
8514 GGCCCCGGCTCAGTTTTGCTTAATTTTTTGCGCCAAGACTCCTAGAAATATCTATATTCATCTAA
453 GGCCCCGGCTCAGTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAA
* * * *
8579 TCAAATCTCATCCACATTGGATTTAAGAATTAGATTTTACGAATATCTGAATCTTGTTTCGATTT
518 CCAAATATCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTT
* * * * *
8644 AAGCA-ACAATTAATTCAGAGAAAAATAGGAAAAAC-AGTATTAGAAGCGTG-AAAAGCGTTTCA
583 AAGTAGA-AATTAATTTAGAAAAAAATAAGAAAAACGA-TATTAGAAGCGTGAAAAAAC-TTTCA
*
8706 ATATTTTTGGAGTTGAACTATAT
645 ATATTTTTGGAGTTGAATTATAT
* ** *
8729 ATTTTTTATGGGTATCGTGGCCAAAAAATTGGTGAAAATTATTTCGGGTCAATTTTTGC-AAATT
1 ATTTTTTATGAGTATCGTGGCC-AAAAATTGAAGAAAATTCTTTCGGGTCAATTTTTGCAAAATT
* * * * * *
8793 TTAGCTAAAATCGTGTACATTA-CATCATGGTTTTTGGC-AAAAACGCATTTCGGGGCCCCAGCT
65 TTAGCTGAAATCGTGTAC-TAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCT
* * * *
8856 CAGTCTTGCTTGATTTTTGGCGCCAAGACTCCGTGACAAATCTATATTCATCTAACCAAATCTCA
129 CAGTTTTGCTTGATTTTTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATATCA
*
8921 TCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAGTAAAAAT
194 TCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTAAAAAT
*
8986 TAATTCAG-AAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGT
259 TAATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGT
* * * *
9050 TGAACTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAACTCTTTCGGGTCAATTTT
324 TGAACTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTCTTTTGGGTAAATTTT
* * *
9115 TGCAAAATTTTAGCTGAAATCGTGTACTAACAATCACGTTTTTTGGC-AAAAAACGCGTTCCGGG
389 TGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAAACGCATTCCGGG
* * *
9179 GCCCCGACTCAATTTTGTTTGATTTTTAG
454 GCCCCGGCTCAGTTTTGCTTGATTTTTAG
9208 CTTTAACTCT
Statistics
Matches: 2699, Mismatches: 382, Indels: 114
0.84 0.12 0.04
Matches are distributed among these distances:
653 4 0.00
654 142 0.05
655 340 0.13
656 26 0.01
657 50 0.02
659 1 0.00
660 8 0.00
661 150 0.06
662 233 0.09
663 121 0.04
664 254 0.09
665 79 0.03
666 190 0.07
667 413 0.15
668 114 0.04
669 54 0.02
671 5 0.00
672 207 0.08
673 101 0.04
674 51 0.02
675 7 0.00
677 149 0.06
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (667 bp):
ATTTTTTATGAGTATCGTGGCCAAAAATTGAAGAAAATTCTTTCGGGTCAATTTTTGCAAAATTT
TAGCTGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCATTCCGGGGCCCCGGCTCA
GTTTTGCTTGATTTTTGGCGCCAAGACTCCTTGACATATCTATATTCATCTAACCAAATATCATC
CACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCAATTTAAGTAAAAATTA
ATTCAGAAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCGTTTCAATATTTTTGGAGTTG
AACTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTCTTTTGGGTAAATTTTTG
CAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAAAACGCATTCCGGGGC
CCCGGCTCAGTTTTGCTTGATTTTTAGTGCCAAGACTCCTTGACATATCTATATTCATCTAACCA
AATATCATCCACATTGGATTTAAGAATTTGATTTTACGAACATCTGAATCTTGTTTCGATTTAAG
TAGAAATTAATTTAGAAAAAAATAAGAAAAACGATATTAGAAGCGTGAAAAAACTTTCAATATTT
TTGGAGTTGAATTATAT
Found at i:11554 original size:30 final size:29
Alignment explanation
Indices: 11498--11554 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
11488 TTAAATATAA
* *
11498 TTTAAAATATTCATTTTATTCTATTTAGT
1 TTTAAAATATTCATTTTATACGATTTAGT
* *
11527 TTTAAATTATTTCTTTTTATACGATTTA
1 TTTAAAATA-TTCATTTTATACGATTTA
11555 ACCCTTCAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 8 0.35
30 15 0.65
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.60
Consensus pattern (29 bp):
TTTAAAATATTCATTTTATACGATTTAGT
Found at i:12096 original size:15 final size:15
Alignment explanation
Indices: 12063--12111 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
12053 TTTTACTATT
*
12063 TTTCTAGGAGAAA-AT
1 TTTCTAGG-GAAAGAC
12078 TTTCTAGGGAAAGAC
1 TTTCTAGGGAAAGAC
**
12093 TTTCTATAGAAAGAC
1 TTTCTAGGGAAAGAC
12108 TTTC
1 TTTC
12112 AACCTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 4 0.13
15 26 0.87
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (15 bp):
TTTCTAGGGAAAGAC
Found at i:12193 original size:16 final size:16
Alignment explanation
Indices: 12174--12216 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
12164 ACTTTTCGAT
12174 GAGAGTGCTTTCTAAG
1 GAGAGTGCTTTCTAAG
* *
12190 GAGAGTG-ATTCTCAG
1 GAGAGTGCTTTCTAAG
*
12205 GAGAGTACTTTC
1 GAGAGTGCTTTC
12217 CATGGAAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (16 bp):
GAGAGTGCTTTCTAAG
Found at i:14802 original size:16 final size:16
Alignment explanation
Indices: 14750--14839 Score: 69
Period size: 16 Copynumber: 5.7 Consensus size: 16
14740 GCTTGAATCA
*
14750 GGTCGGGTTAAATTT-
1 GGTCAGGTTAAATTTG
* *
14765 GGTCAGGTT-GATTCG
1 GGTCAGGTTAAATTTG
*
14780 AGTTCAGGTTAAATTTG
1 -GGTCAGGTTAAATTTG
*
14797 GGTCAGGTT-GATTTG
1 GGTCAGGTTAAATTTG
* * *
14812 GGTTCGGGTCAATTTTG
1 GG-TCAGGTTAAATTTG
14829 GGTCAGGTTAA
1 GGTCAGGTTAA
14840 TTCGGGTTCG
Statistics
Matches: 56, Mismatches: 14, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
14 3 0.05
15 15 0.27
16 28 0.50
17 10 0.18
ACGTcount: A:0.19, C:0.09, G:0.34, T:0.38
Consensus pattern (16 bp):
GGTCAGGTTAAATTTG
Found at i:14849 original size:32 final size:32
Alignment explanation
Indices: 14752--14851 Score: 139
Period size: 32 Copynumber: 3.2 Consensus size: 32
14742 TTGAATCAGG
*
14752 TCGGGTTAAATTT-GGTCAGGTTGATTCGAGT
1 TCGGGTTAAATTTGGGTCAGGTTGATTCGGGT
* *
14783 TCAGGTTAAATTTGGGTCAGGTTGATTTGGGT
1 TCGGGTTAAATTTGGGTCAGGTTGATTCGGGT
* * *
14815 TCGGGTCAATTTTGGGTCAGGTTAATTCGGGT
1 TCGGGTTAAATTTGGGTCAGGTTGATTCGGGT
14847 TCGGG
1 TCGGG
14852 CTGGGTTTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
31 12 0.20
32 48 0.80
ACGTcount: A:0.17, C:0.10, G:0.35, T:0.38
Consensus pattern (32 bp):
TCGGGTTAAATTTGGGTCAGGTTGATTCGGGT
Found at i:15074 original size:16 final size:17
Alignment explanation
Indices: 15053--15098 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
15043 TTCGGGTTCG
*
15053 GTTTTTTCGGATTCT-A
1 GTTTTTTCGAATTCTGA
15069 GTTTTTTCGAATT-TGA
1 GTTTTTTCGAATTCTGA
15085 GTTTTTTCGAATTC
1 GTTTTTTCGAATTC
15099 GGATTCGGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 1 0.04
16 26 0.96
ACGTcount: A:0.15, C:0.11, G:0.17, T:0.57
Consensus pattern (17 bp):
GTTTTTTCGAATTCTGA
Found at i:33252 original size:27 final size:27
Alignment explanation
Indices: 33222--33277 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
33212 ATAATATTAT
33222 CTCTACAATACATAATTTAATCTGTAC
1 CTCTACAATACATAATTTAATCTGTAC
* *
33249 CTCTACAATACCTAATTTGATCTGTAC
1 CTCTACAATACATAATTTAATCTGTAC
33276 CT
1 CT
33278 GCAATCGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (27 bp):
CTCTACAATACATAATTTAATCTGTAC
Found at i:37718 original size:21 final size:20
Alignment explanation
Indices: 37692--37750 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
37682 GCTGCTCTAA
37692 TAATCTCATCTGTACAGTATC
1 TAATCTCATCTGTACAGT-TC
* *
37713 TAATCTAATCTGTACAG-TG
1 TAATCTCATCTGTACAGTTC
37732 TAATCTCATCTGTACAGTT
1 TAATCTCATCTGTACAGTT
37751 GTTATATAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.50
20 1 0.03
21 16 0.47
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTTC
Found at i:40034 original size:7 final size:7
Alignment explanation
Indices: 40022--40049 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
40012 ATAGCCACTA
40022 GACACAT
1 GACACAT
40029 GACACAT
1 GACACAT
40036 GACACAT
1 GACACAT
40043 GACACAT
1 GACACAT
40050 CTCTCCGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.14, T:0.14
Consensus pattern (7 bp):
GACACAT
Found at i:48128 original size:19 final size:20
Alignment explanation
Indices: 48104--48158 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
48094 GTTTAGCAAC
48104 TGTACAGATGAGATTACAT-
1 TGTACAGATGAGATTACATA
* * *
48123 TGTACAAATTAGATTAGATA
1 TGTACAGATGAGATTACATA
48143 CTGTACAG-TGAGATTA
1 -TGTACAGATGAGATTA
48159 TTAGAGCAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 16 0.55
20 7 0.24
21 6 0.21
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (20 bp):
TGTACAGATGAGATTACATA
Done.