Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016384.1 Corchorus olitorius cultivar O-4 contig16417, 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: 156817
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2944 original size:322 final size:321
Alignment explanation
Indices: 1--4504 Score: 5757
Period size: 321 Copynumber: 14.0 Consensus size: 321
* * *
1 AAATAAATTCGGGAAAAAAAAT-GAAAATCGATATTAGAAGCGTGAAAAATCTTTCAATTTTATT
1 AAATAAATTCGGG--AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTATT
* *
65 GGCGTTGAAGTATATATTTTTTAC-GAGTATTATGGAAAAAAATTGAGAAAAAATTCTTCAAGTC
64 GGCGTTGAATTATATATTTTTT-CTGAGTATTATGGAAAAAAATTGAGAAAAAATT-TTCGAGTC
* * * *
129 AGATTTTAGCCGAAATCGTGTACTAACTAACACAGTTTTTTAGATAAAAACGTATTTCGGCGCCT
127 AGATTTTAGCCGAAATCGTGTACTAACTATCAC-GTTTTTTTGCTAAAAACGTATTTCGGCGCCC
* * *
194 CGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATTTTTATCTAACCAAA
191 CGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAA
* * * * *
259 TCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTAGAGTTAAATA
256 TCTCAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATA
324 G
321 G
** *
325 AAATAAATTCGGGAAAAAAATTTAAAAACGATATTAGAAGCGTGAATAACCCTTCAATTTTATTG
1 AAATAAATTCGGG-AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTG
* * * * *
390 GCATTGAATTATATA-TTTTTCCGAGTATCATGGAAAAAAAATTGAGAAAAAATTTTATGTGTCA
65 GCGTTGAATTATATATTTTTTCTGAGTATTATGG-AAAAAAATTGAGAAAAAATTTT-CGAGTCA
* **
454 GATTTTAGCCGAAATCGTGTACTAACTATCACGATTGTTTTGCTAAAAACGTATTTCAGATG-CC
128 GATTTTAGCCGAAATCGTGTACTAACTATCACG-TTTTTTTGCTAAAAACGTATTTC-GGCGCCC
* *
518 CGGCTCAGTTTTGTC-TGATTTTTGGCAGAAAGACTCCTTAAAATATCTATATTCATTGAACCAA
191 CGGCTCAGTTTTG-CATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAA
* *
582 ATCAT-AGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAATTATA
255 ATC-TCAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAA
646 TAG
319 TAG
* * *
649 AAATCAATTCGGGAAAAAAATGGAAAATCGATATTAGAAGCCTGAAAAACCCTTCAATTTTATTG
1 AAATAAATTCGGG-AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTG
* * * *
714 GGGTTGAATTATATATTTTTTCCGAGTATCATGGACAAAAAAATTGAGAATAAATTTTTTCGAGT
65 GCGTTGAATTATATATTTTTTCTGAGTATTATGG--AAAAAAATTGAGAA-AAA-ATTTTCGAGT
779 CAGATTTTAGCCGAAATCGTGTACTAACTATCA-GATTTTTTTGCTAAAAACGTATTTCGGCGCC
126 CAGATTTTAGCCGAAATCGTGTACTAACTATCACG-TTTTTTTGCTAAAAACGTATTTCGGCGCC
*
843 CCGGCTCAGTTTTGCATGATTTTTGGCAAAAAGACTCCTTGAAATATCTATATTCATCGAACCAA
190 CCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAA
* *
908 ATCTTAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTAAAGTTAAAT
255 ATCTCAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAAT
973 AG
320 AG
* *
975 AAATAAATTCGGGAAAAAATGGAAAATCGATATTAGAAGCGTGAAAACCCCTTCAATTTT-TATG
1 AAATAAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTAT-TG
* ** * * * *
1039 GTGTTGAATTATATATTTTTTCAAAGTATTATGGAAAAAAATTGAG-AAAATTTTTCAACTCTGA
65 GCGTTGAATTATATATTTTTTCTGAGTATTATGGAAAAAAATTGAGAAAAAATTTTCGAGTCAGA
* * * * * * *
1103 TTTT-GACCGAAATCGTCTATTAACGATCACGGTTTTTTGGGTAAAAACGCATTTCGGCGCCCGG
130 TTTTAG-CCGAAATCGTGTACTAACTATCAC-GTTTTTTTGCTAAAAACGTATTTCGGCGCCCCG
* * * * * *
1167 GCTCATTTTTGCCTTATTTTTGGCAGAAGGAATCCTTGAAATATCTATATTCATCTAACCAAATC
193 GCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATC
* * * * * *
1232 TCAGCCACAATGGATTTAAGGATTTAT-TTTCACGAGAATCTGAGTCTTGTTTAGAGTTAAATAG
258 TCAGCCACAATGGATTTAAGAATTTGTGTTT-ACGAGCATCTAAATCTTGTTTACAGTTAAATAG
* * *
1296 AAATAAATTCGGG-AAAAATGCAAAAATGATATTAGATGCGTGAAAAACCCTTCAATTTTATTGG
1 AAATAAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTGG
* ** * *** *
1360 GGTTGAATTATATATTTTTTCCAAGTATGATGGAAAAATAATTGAGAAAAAAAAAATCGAGTTAG
66 CGTTGAATTATATATTTTTTCTGAGTATTATGGAAAAA-AATTGAG-AAAAAATTTTCGAGTCAG
* * *
1425 ATTCTAACCGAAATCGTGTACTAACTATTACGATTTTTTTGCTAAAAACGTATTTCGGCGCCCCG
129 ATTTTAGCCGAAATCGTGTACTAACTATCACG-TTTTTTTGCTAAAAACGTATTTCGGCGCCCCG
* * * *
1490 GCTCAGTTTTGTATGATTTTTGGCAGATAGACTCCTTAAAATATCTATATTCA-CTGAACCACAT
193 GCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATC-GAACCAAAT
* *
1554 CTTAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTATATAG
257 CTCAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAG
* * * *
1619 AAATAAATTCGGAAAAAAAATGGAAAATCGATATTAGAAGTGTGAAAGACCCTTCAATTTTATTG
1 AAATAAATTCGG-GAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTG
* * *
1684 GGGTTGAATTATATATTTTTTCTGAGTATCATGGAAAAAAATTGAGAAAAAATTTTCGAGTCAGG
65 GCGTTGAATTATATATTTTTTCTGAGTATTATGGAAAAAAATTGAGAAAAAATTTTCGAGTCAGA
* *
1749 TTTTAGCCGAAATCGTGTAATAACTATCACGATTTTTTTGCTAAGAACGTATTTCGGCGCCCCGG
130 TTTTAGCCGAAATCGTGTACTAACTATCACG-TTTTTTTGCTAAAAACGTATTTCGGCGCCCCGG
* *
1814 CTCAGTTTTGCTTGATTTTTGGCAAAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
194 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * *
1879 CAGCCATAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTAAAGTTAAATGG
259 CAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAG
*
1942 AAATAAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAACCCCTTCAATTATT-TTG
1 AAATAAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATT-TTATTG
* * * * * *
2006 GCGTTGAATTATATATTATTCCTGAGTATTATTGAAAAAAATTGAG-AAAATTTTTCAATTCAGA
65 GCGTTGAATTATATATTTTTTCTGAGTATTATGGAAAAAAATTGAGAAAAAATTTTCGAGTCAGA
* * * * * * * * *
2070 TTTTAGCTGAAATTGTGTAATAACTATCATGGTTTTTGGCTAAAAACGCATTTCGGCGCCGCGGT
130 TTTTAGCCGAAATCGTGTACTAACTATCACGTTTTTTTGCTAAAAACGTATTTCGGCGCCCCGGC
* * * * **
2135 TTAGTTTTGCATAATTTTTGGCAGAAAGACTCCTTGAAATATATATATTCATCCAAGAAAATCTC
195 TCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTC
*
2200 AGCCACAATGGATTTAAGAATTTGTGTTTAAGAGCATCTAAATCTTGTTTACAGTTAAATAG
260 AGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAG
* * * ***
2262 AAAGAAATTCGGGGAAAAAATGGAAACACGATATTAGAAGCTTGAAAATTTCTTCAATTTT-TAT
1 AAATAAATTC-GGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTAT-T
* * * * * *
2326 GGTGTTGAATTATAT-TTTTTT-TTAGTATTATGGGAAAAAATTGAG-AAAATTTTTGGATTCAG
64 GGCGTTGAATTATATATTTTTTCTGAGTATTATGGAAAAAAATTGAGAAAAAATTTTCGAGTCAG
* * * * * * *
2388 ATTTTGGCCGAAATCGTGTACTAACGATCAAGGTTTTTGGGTAAAAAC-TCATTTCGGCGCCCGG
129 ATTTTAGCCGAAATCGTGTACTAACTATCACGTTTTTTTGCTAAAAACGT-ATTTCGGCGCCCCG
* *
2452 GCTCATTTTTGCATGATTTTTGGCA-AAAGGACTCCTTGAAATATCTATATTCATCTAACCAAAT
193 GCTCAGTTTTGCATGATTTTTGGCAGAAA-GACTCCTTGAAATATCTATATTCATCGAACCAAAT
* * * * * *
2516 CTCAGCCACAATGGATTTAAGGATTTATTTTTACGAGAATCTGAATC-TGTTTAGAGTTAAATAG
257 CTCAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAG
* *
2580 AAATAAATTCGGGAAAAAATGTAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTGG
1 AAATAAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTGG
* * *
2645 GGTTGAATTATATATTTTTTC-GAGTATCATGGAAAAAAATTGAGAAAAAAATTTTCGAGTCAAA
66 CGTTGAATTATATATTTTTTCTGAGTATTATGGAAAAAAATTGAG-AAAAAATTTTCGAGTCAGA
* *
2709 TTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTTTGCTAGAAACGTATTTCGGCGCCCCGA
130 TTTTAGCCGAAATCGTGTACTAACTATCAC-GTTTTTTTGCTAAAAACGTATTTCGGCGCCCCGG
* * *
2774 CTCATTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATAT
194 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* *
2839 CAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACTGTTAAGTAG
259 CAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAG
* * *
2902 AAATAAATTCGGGGAAAGATGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAATTTT-TATG
1 AAATAAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTAT-TG
* * * * *
2966 GTGTTGAATTATATTTTTTTTTTCTAAGTATTATGGAAAAAAGTTGAGAAAAAAATTTTCTAGTC
65 GCGTTGAATTATA--TATTTTTTCTGAGTATTATGGAAAAAAATTGAG-AAAAAATTTTCGAGTC
* * * * * *
3031 AGATTTTAGCTGAAATCGTGTACTAACGATCACGGTTTTTGGGTAAAAACGCATTTCGGCGCCCC
127 AGATTTTAGCCGAAATCGTGTACTAACTATCACGTTTTTTTGCTAAAAACGTATTTCGGCGCCCC
* * * * * * * *
3096 GGCTTATTTTTGCCTGATTTTTGGCAGAAGGACTCCTTGTAATATCTATTTTTATCTAACCAAAT
192 GGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAAT
* * * *
3161 CTCAGCCACAATGGATTTAAGGATTTGT-TTTACGAGAATCTGAATCTTGTTTAAAGTTAAATAG
257 CTCAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAG
* * * * * **
3225 AAATAAATTCGGGAAAAAATGTAAAAATGATATTAGAAACGTGATAACCCCTTCAATTTTATTTC
1 AAATAAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTGG
*
3290 CGTTGAATTATATATTTTTTCCGAGTATTATGGAAAAAAA-TGAGAAAAAAATTTTCGAGTCAGA
66 CGTTGAATTATATATTTTTTCTGAGTATTATGGAAAAAAATTGAG-AAAAAATTTTCGAGTCAGA
* *
3354 TTTTAGCCGAAATCGTGTACTAACTATCATGATTTTTTTGCTAAAAACGTATTTCGGCGCCCCGA
130 TTTTAGCCGAAATCGTGTACTAACTATCACG-TTTTTTTGCTAAAAACGTATTTCGGCGCCCCGG
* * *
3419 CTCAGTTTTGCATGATTTTTGGCAAAAAGACTCCTTGAAATATCTACATACATCGAACCAAATCT
194 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* *
3484 CAGCCACAATGGATTTAAGAATTTATGTTTACGAGCATCTAAATCTTGTTTAAAGTTAAATAG
259 CAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAG
* *
3547 AAATAAATTCGGGAAAAAAAATGGAAAATCGATATTAGAAGCATGAAAAACCCTTCAATTTT-TA
1 AAATAAATTCGGG--AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTAT-
* ** * *
3611 TGGTGTTGAATTATATATTTTTTCAAAGTATTATGGAAAAAAATTGAG-AAAATTTTTCGATTCA
63 TGGCGTTGAATTATATATTTTTTCTGAGTATTATGGAAAAAAATTGAGAAAAAATTTTCGAGTCA
* * * * * * * * * ** *
3675 GATTTTGGCTGAAACCGTGTCCTAACGATCACGGTTTTTGGGTAAAAACGCATTTCGGCGTACGG
128 GATTTTAGCCGAAATCGTGTACTAACTATCACGTTTTTTTGCTAAAAACGTATTTCGGCGCCCCG
* * * *
3740 GCTCATTTTTGCATGATTTTTAGCAGAAGGACTCCTTGAAATATCTATATTCATCTAACCAAATC
193 GCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATC
* * * * * * *
3805 TCAGCCATAATAGATTTAAGGATTT-TCTTTTACGAGAATCTGAATCTTGTTTAGAGTTAAATAG
258 TCAGCCACAATGGATTTAAGAATTTGT-GTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAG
* * * * *
3869 AAATAAATTCAGG-AAAAATGTAAAAATGATATTAGAAGAGTGAAAAATCCTTCAATTTTATTGG
1 AAATAAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTGG
* *
3933 CATTGAATTATATATTTTTTCTGAGTATTATGGAAAAAAATTGAGAAAAAATTTTTCAAGTCAGA
66 CGTTGAATTATATATTTTTTCTGAGTATTATGGAAAAAAATTGAGAAAAAA-TTTTCGAGTCAGA
* ** *
3998 TTTTAGCCGAAATCGTGTATTAACTATCACAGTTTTTTTTATAAAAACGTATTTCGGCGCCCTGG
130 TTTTAGCCGAAATCGTGTACTAACTATCAC-GTTTTTTTGCTAAAAACGTATTTCGGCGCCCCGG
* * *
4063 CTCAGTTTTGCATGATTTTGGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATAT
194 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * *
4128 CAGGCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTATTTCCAGTTAAATAG
259 CAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAG
* *
4191 AAATAAATTCGGGAAAAAAATGGAAAAACGATATTATAAGCGTGAAAAATCCTTCAATTTT-TAT
1 AAATAAATTCGGG-AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTAT-T
* * * *
4255 GGTGTTGAATT-T-T-TTTTGTTCTGCGTATTATGGAAAAAAAATTGAG-AAAATTTTTCGATTC
64 GGCGTTGAATTATATATTTT-TTCTGAGTATTATGG-AAAAAAATTGAGAAAAAATTTTCGAGTC
* * * * * * * * * *
4316 AGATTTTGGCCGAAATCGTGTTCTAACGATCATGGTTTGTGGGTAAAAACGCATTTCGGAGCCCC
127 AGATTTTAGCCGAAATCGTGTACTAACTATCACGTTTTTTTGCTAAAAACGTATTTCGGCGCCCC
* * * * *
4381 GGCTCAATTTTGCATGATTTTTGGCAGAAGGACGCCTTGAAATATCTATATTCATCTAACTAAAT
192 GGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAAT
* * * * * * * *
4446 CTCAGCCAAAATTGATTTAAGTATTTGTTTTTACGAGAATTTGAATCTTGTTTAGAGTT
257 CTCAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTT
4505 TTGTAAAAAC
Statistics
Matches: 3642, Mismatches: 471, Indels: 138
0.86 0.11 0.03
Matches are distributed among these distances:
317 58 0.02
318 55 0.02
319 267 0.07
320 502 0.14
321 594 0.16
322 539 0.15
323 571 0.16
324 587 0.16
325 253 0.07
326 173 0.05
327 39 0.01
328 4 0.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (321 bp):
AAATAAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTGG
CGTTGAATTATATATTTTTTCTGAGTATTATGGAAAAAAATTGAGAAAAAATTTTCGAGTCAGAT
TTTAGCCGAAATCGTGTACTAACTATCACGTTTTTTTGCTAAAAACGTATTTCGGCGCCCCGGCT
CAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCA
GCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAG
Found at i:3221 original size:645 final size:643
Alignment explanation
Indices: 1--5130 Score: 7091
Period size: 645 Copynumber: 8.0 Consensus size: 643
** * * *
1 AAATAAATTCGGGAAAAAAAATGAAAATCGATATTAGAAGCGTGAAAAATCTTTCAATTTTATTG
1 AAATAAATTCGGGAAAAAATGTAAAAAT-GATATTAGAAGCGTGAAAAACCCTTCAATTTTATTG
* * *
66 GCGTTGAAGTATATATTTTTTACGAGTATTATGGAAAAAAATTGAG-AAAAAATTCTTCAAGTCA
65 GCGTTGAATTATATATTTTTTCCGAGTATTATGGAAAAAAATTGAGAAAAAAATT-TTCGAGTCA
* * * *
130 GATTTTAGCCGAAATCGTGTACTAACTAACACAGTTTTTTAGATAAAAACGTATTTCGGCGCCTC
129 GATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTTTGCTAAAAACGTATTTCGGCGCCCC
* * *
195 GGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATTTTTATCTAACCAAAT
194 GGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAAT
* * * * *
260 CTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTAGAGTTAAATAG
259 CTCAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAG
** *
325 AAATAAATTCGGGAAAAAAATTTAAAAACGATATTAGAAGCGTGAATAACCCTTCAA-TTTTATT
324 AAATAAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTA-T
** * ** *
389 GGCATTGAATTATA-TATTTTTCCGAGTATCATGGAAAAAAAATTGAGAAAAAATTTTAT-G-TG
388 GGTGTTGAATTATATTTTTTTTCTAAGTATTATGG-AAAAAAATTGAG--AAAATTTT-TCGAT-
* * * * * * **
451 TCAGATTTTAGCCGAAATCGTGTACTAACTATCACGATTGTTTTGCTAAAAACGTATTTCAGATG
448 TCAGATTTTGGCCGAAATCGTGTACTAACGATCACGGTT-TTTGGGTAAAAACGCATTTC-GGCG
* * *
516 -CCCGGCTCAGTTTTGTC-TGATTTTTGGCAGAAAGACTCCTTAAAATATCTATATTCAT-TGAA
511 CCCCGGCTCATTTTTG-CATGATTTTTGGCAGAAGGACTCCTTGAAATATCTATATTCATCT-AA
* * * * *
578 CCAAATCAT-AGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAAT
574 CCAAATC-TCAGCCACAATGGATTTAAGGATTTGT-TTTACGAGAATCTGAATCTTGTTTAGAGT
*
642 TATATAG
637 TAAATAG
* * *
649 AAATCAATTCGGGAAAAAAATG-GAAAATCGATATTAGAAGCCTGAAAAACCCTTCAATTTTATT
1 AAATAAATTCGGG-AAAAAATGTAAAAAT-GATATTAGAAGCGTGAAAAACCCTTCAATTTTATT
* * **
713 GGGGTTGAATTATATATTTTTTCCGAGTATCATGGACAAAAAAATTGAGAATAAATTTTTTCGAG
64 GGCGTTGAATTATATATTTTTTCCGAGTATTATGG--AAAAAAATTGAGAA-AAAAATTTTCGAG
*
778 TCAGATTTTAGCCGAAATCGTGTACTAACTATCAGA-TTTTTTTGCTAAAAACGTATTTCGGCGC
126 TCAGATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTTTGCTAAAAACGTATTTCGGCGC
*
842 CCCGGCTCAGTTTTGCATGATTTTTGGCAAAAAGACTCCTTGAAATATCTATATTCATCGAACCA
191 CCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCA
* *
907 AATCTTAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTAAAGTTAAA
256 AATCTCAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAA
* *
972 TAGAAATAAATTCGGG-AAAAAATGGAAAATCGATATTAGAAGCGTGAAAACCCCTTCAATTTTT
321 TAGAAATAAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTT
* * * * *
1036 ATGGTGTTGAATTATATATTTTTTCAAAGTATTATGGAAAAAAATTGAGAAAATTTTTCAACTCT
386 ATGGTGTTGAATTATATTTTTTTTCTAAGTATTATGGAAAAAAATTGAGAAAATTTTTCGATTCA
* * * *
1101 GATTTTGACCGAAATCGTCTATTAACGATCACGGTTTTTTGGGTAAAAACGCATTTCGGCGCCCG
451 GATTTTGGCCGAAATCGTGTACTAACGATCACGG-TTTTTGGGTAAAAACGCATTTCGGCGCCCC
* * *
1166 GGCTCATTTTTGCCTTATTTTTGGCAGAAGGAATCCTTGAAATATCTATATTCATCTAACCAAAT
515 GGCTCATTTTTGCATGATTTTTGGCAGAAGGACTCCTTGAAATATCTATATTCATCTAACCAAAT
* *
1231 CTCAGCCACAATGGATTTAAGGATTTATTTTCACGAGAATCTGAGTCTTGTTTAGAGTTAAATAG
580 CTCAGCCACAATGGATTTAAGGATTTGTTTT-ACGAGAATCTGAATCTTGTTTAGAGTTAAATAG
* *
1296 AAATAAATTCGGG-AAAAATGCAAAAATGATATTAGATGCGTGAAAAACCCTTCAATTTTATTGG
1 AAATAAATTCGGGAAAAAATGTAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTGG
* * * *** *
1360 GGTTGAATTATATATTTTTTCCAAGTATGATGGAAAAATAATTGAGAAAAAAAAAATCGAGTTAG
66 CGTTGAATTATATATTTTTTCCGAGTATTATGGAAAAA-AATTGAGAAAAAAATTTTCGAGTCAG
* * *
1425 ATTCTAACCGAAATCGTGTACTAACTATTAC-GATTTTTTTGCTAAAAACGTATTTCGGCGCCCC
130 ATTTTAGCCGAAATCGTGTACTAACTATCACAG-TTTTTTTGCTAAAAACGTATTTCGGCGCCCC
* * * *
1489 GGCTCAGTTTTGTATGATTTTTGGCAGATAGACTCCTTAAAATATCTATATTCA-CTGAACCACA
194 GGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATC-GAACCAAA
* *
1553 TCTTAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTATATA
258 TCTCAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATA
* * * *
1618 GAAATAAATTCGGAAAAAAAATGGAAAATCGATATTAGAAGTGTGAAAGACCCTTCAA-TTTTAT
323 GAAATAAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTA-
* * * * * *
1682 TGGGGTTGAATTATATATTTTTTCTGAGTATCATGGAAAAAAATTGAGAAAAAATTTTCGAGTCA
387 TGGTGTTGAATTATATTTTTTTTCTAAGTATTATGGAAAAAAATTGAG-AAAATTTTTCGATTCA
* * * * * * * * *
1747 GGTTTTAGCCGAAATCGTGTAATAACTATCACGATTTTTTTGCTAAGAACGTATTTCGGCGCCCC
451 GATTTTGGCCGAAATCGTGTACTAACGATCACG-GTTTTTGGGTAAAAACGCATTTCGGCGCCCC
* * * * *
1812 GGCTCAGTTTTGCTTGATTTTTGGCAAAAAGACTCCTTGAAATATCTATATTCATCGAACCAAAT
515 GGCTCATTTTTGCATGATTTTTGGCAGAAGGACTCCTTGAAATATCTATATTCATCTAACCAAAT
* * * * * *
1877 CTCAGCCATAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTAAAGTTAAATGG
580 CTCAGCCACAATGGATTTAAGGATTTGT-TTTACGAGAATCTGAATCTTGTTTAGAGTTAAATAG
* * *
1942 AAATAAATTCGGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAACCCCTTCAATTATT-TTG
1 AAATAAATTCGGGAAAAAATGTAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATT-TTATTG
* * * * *
2006 GCGTTGAATTATATA-TTATTCCTGAGTATTATTGAAAAAAATTGAG--AAAATTTTTCAATTCA
65 GCGTTGAATTATATATTTTTTCC-GAGTATTATGGAAAAAAATTGAGAAAAAAATTTTCGAGTCA
* * * * * * * *
2068 GATTTTAGCTGAAATTGTGTAATAACTATCA-TGGTTTTTGGCTAAAAACGCATTTCGGCGCCGC
129 GATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTTTGCTAAAAACGTATTTCGGCGCCCC
* * * * * **
2132 GGTTTAGTTTTGCATAATTTTTGGCAGAAAGACTCCTTGAAATATATATATTCATCCAAGAAAAT
194 GGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAAT
*
2197 CTCAGCCACAATGGATTTAAGAATTTGTGTTTAAGAGCATCTAAATCTTGTTTACAGTTAAATAG
259 CTCAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAG
* * * * ***
2262 AAAGAAATTCGGGGAAAAAATGGAAACACGATATTAGAAGCTTGAAAATTTCTTCAATTTTTATG
324 AAATAAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTATG
* *
2327 GTGTTGAATTATATTTTTTTT-T-AGTATTATGGGAAAAAATTGAGAAAATTTTTGGATTCAGAT
389 GTGTTGAATTATATTTTTTTTCTAAGTATTATGGAAAAAAATTGAGAAAATTTTTCGATTCAGAT
* * *
2390 TTTGGCCGAAATCGTGTACTAACGATCAAGGTTTTTGGGTAAAAACTCATTTCGGCGCCCGGGCT
454 TTTGGCCGAAATCGTGTACTAACGATCACGGTTTTTGGGTAAAAACGCATTTCGGCGCCCCGGCT
*
2455 CATTTTTGCATGATTTTTGGCAAAAGGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCA
519 CATTTTTGCATGATTTTTGGCAGAAGGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCA
*
2520 GCCACAATGGATTTAAGGATTTATTTTTACGAGAATCTGAATC-TGTTTAGAGTTAAATAG
584 GCCACAATGGATTTAAGGATTT-GTTTTACGAGAATCTGAATCTTGTTTAGAGTTAAATAG
2580 AAATAAATTCGGGAAAAAATGTAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTGG
1 AAATAAATTCGGGAAAAAATGTAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTGG
* * *
2645 GGTTGAATTATATATTTTTT-CGAGTATCATGGAAAAAAATTGAGAAAAAAATTTTCGAGTCAAA
66 CGTTGAATTATATATTTTTTCCGAGTATTATGGAAAAAAATTGAGAAAAAAATTTTCGAGTCAGA
* *
2709 TTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTTTGCTAGAAACGTATTTCGGCGCCCCGA
131 TTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTTTGCTAAAAACGTATTTCGGCGCCCCGG
* * *
2774 CTCATTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATAT
196 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* *
2839 CAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACTGTTAAGTAGAA
261 CAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAGAA
* * *
2904 ATAAATTCGGG-GAAAGATGGAAAAACAATATTAGAAGCGTGAAAAACCCTTCAATTTTTATGGT
326 ATAAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTATGGT
* * * *
2968 GTTGAATTATATTTTTTTTTTCTAAGTATTATGGAAAAAAGTTGAGAAAAAAATTTTCTAGTCAG
391 GTTGAATTATA--TTTTTTTTCTAAGTATTATGGAAAAAAATTGAG--AAAATTTTTCGATTCAG
* *
3033 ATTTTAGCTGAAATCGTGTACTAACGATCACGGTTTTTGGGTAAAAACGCATTTCGGCGCCCCGG
452 ATTTTGGCCGAAATCGTGTACTAACGATCACGGTTTTTGGGTAAAAACGCATTTCGGCGCCCCGG
* * * * *
3098 CTTATTTTTGCCTGATTTTTGGCAGAAGGACTCCTTGTAATATCTATTTTTATCTAACCAAATCT
517 CTCATTTTTGCATGATTTTTGGCAGAAGGACTCCTTGAAATATCTATATTCATCTAACCAAATCT
*
3163 CAGCCACAATGGATTTAAGGATTTGTTTTACGAGAATCTGAATCTTGTTTAAAGTTAAATAG
582 CAGCCACAATGGATTTAAGGATTTGTTTTACGAGAATCTGAATCTTGTTTAGAGTTAAATAG
* * * **
3225 AAATAAATTCGGGAAAAAATGTAAAAATGATATTAGAAACGTGATAACCCCTTCAATTTTATTTC
1 AAATAAATTCGGGAAAAAATGTAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTGG
3290 CGTTGAATTATATATTTTTTCCGAGTATTATGGAAAAAAA-TGAGAAAAAAATTTTCGAGTCAGA
66 CGTTGAATTATATATTTTTTCCGAGTATTATGGAAAAAAATTGAGAAAAAAATTTTCGAGTCAGA
*
3354 TTTTAGCCGAAATCGTGTACTAACTATCA-TGATTTTTTTGCTAAAAACGTATTTCGGCGCCCCG
131 TTTTAGCCGAAATCGTGTACTAACTATCACAG-TTTTTTTGCTAAAAACGTATTTCGGCGCCCCG
* * * *
3418 ACTCAGTTTTGCATGATTTTTGGCAAAAAGACTCCTTGAAATATCTACATACATCGAACCAAATC
195 GCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATC
* *
3483 TCAGCCACAATGGATTTAAGAATTTATGTTTACGAGCATCTAAATCTTGTTTAAAGTTAAATAGA
260 TCAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAGA
* *
3548 AATAAATTCGGGAAAAAAAATGGAAAATCGATATTAGAAGCATGAAAAACCCTTCAATTTTTATG
325 AATAAATTCGGG-AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTATG
* *
3613 GTGTTGAATTATATATTTTTTCAAAGTATTATGGAAAAAAATTGAGAAAATTTTTCGATTCAGAT
389 GTGTTGAATTATATTTTTTTTCTAAGTATTATGGAAAAAAATTGAGAAAATTTTTCGATTCAGAT
* * * ** *
3678 TTTGGCTGAAACCGTGTCCTAACGATCACGGTTTTTGGGTAAAAACGCATTTCGGCGTACGGGCT
454 TTTGGCCGAAATCGTGTACTAACGATCACGGTTTTTGGGTAAAAACGCATTTCGGCGCCCCGGCT
*
3743 CATTTTTGCATGATTTTTAGCAGAAGGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCA
519 CATTTTTGCATGATTTTTGGCAGAAGGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCA
* * *
3808 GCCATAATAGATTTAAGGATTTTCTTTTACGAGAATCTGAATCTTGTTTAGAGTTAAATAG
584 GCCACAATGGATTTAAGGA-TTTGTTTTACGAGAATCTGAATCTTGTTTAGAGTTAAATAG
* * *
3869 AAATAAATTCAGG-AAAAATGTAAAAATGATATTAGAAGAGTGAAAAATCCTTCAATTTTATTGG
1 AAATAAATTCGGGAAAAAATGTAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTGG
* * * *
3933 CATTGAATTATATATTTTTTCTGAGTATTATGGAAAAAAATTGAGAAAAAATTTTTCAAGTCAGA
66 CGTTGAATTATATATTTTTTCCGAGTATTATGGAAAAAAATTGAGAAAAAAATTTTCGAGTCAGA
* ** *
3998 TTTTAGCCGAAATCGTGTATTAACTATCACAGTTTTTTTTATAAAAACGTATTTCGGCGCCCTGG
131 TTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTTTGCTAAAAACGTATTTCGGCGCCCCGG
* * *
4063 CTCAGTTTTGCATGATTTTGGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATAT
196 CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * *
4128 CAGGCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTATTTCCAGTTAAATAGAA
261 CAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAGAA
* *
4193 ATAAATTCGGGAAAAAAATGGAAAAACGATATTATAAGCGTGAAAAATCCTTCAATTTTTATGGT
326 ATAAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTATGGT
* **
4258 GTTGAATT-T-TTTTTGTTCTGCGTATTATGGAAAAAAAATTGAGAAAATTTTTCGATTCAGATT
391 GTTGAATTATATTTTTTTTCTAAGTATTATGG-AAAAAAATTGAGAAAATTTTTCGATTCAGATT
* * * *
4321 TTGGCCGAAATCGTGTTCTAACGATCATGGTTTGTGGGTAAAAACGCATTTCGGAGCCCCGGCTC
455 TTGGCCGAAATCGTGTACTAACGATCACGGTTTTTGGGTAAAAACGCATTTCGGCGCCCCGGCTC
* * *
4386 AATTTTGCATGATTTTTGGCAGAAGGACGCCTTGAAATATCTATATTCATCTAACTAAATCTCAG
520 ATTTTTGCATGATTTTTGGCAGAAGGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAG
* * * *
4451 CCAAAATTGATTTAAGTATTTGTTTTTACGAGAATTTGAATCTTGTTT--AG------AG
585 CCACAATGGATTTAAGGATTTG-TTTTACGAGAATCTGAATCTTGTTTAGAGTTAAATAG
* *
4503 ---T---TT----------TGTAAAAACGATATTAGAAGCGTGAAAATA-CCTTCAATTTTTTTG
1 AAATAAATTCGGGAAAAAATGTAAAAATGATATTAGAAGCGTGAAAA-ACCCTTCAATTTTATTG
* *
4551 GCGTTGAATTATATATTTTTT-CGAGTATTATGGAAAAAAATTGATAAAAAACTTTTCGAGTCAG
65 GCGTTGAATTATATATTTTTTCCGAGTATTATGGAAAAAAATTGAGAAAAAAATTTTCGAGTCAG
* * *
4615 ATTTTAGCCGAAATCGTGTACTAACTTTCACGGTTTTTTTGCTAAAAAAGTATTTCGGCGCCCCG
130 ATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTTTGCTAAAAACGTATTTCGGCGCCCCG
** * *
4680 GCTCAGTTTTGGTTGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATA
195 GCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATC
*
4745 TCAGGCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAGA
260 TCAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAGA
* *
4810 AATAAATTCGGGACAAAAATGGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTATGG
325 AATAAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTATGG
** *
4875 TGTTGAATTATATATTTTTTT-TGCGTATTATGGAAAAAAATTGAGAAAATTTTTCGATTCAAAT
390 TGTTGAATTATAT-TTTTTTTCTAAGTATTATGGAAAAAAATTGAGAAAATTTTTCGATTCAGAT
*
4939 TTTGGCCGAAATCGTGTACTAACGATCACGGTTTTTGGGTAAAAACGCATTTCGTCGCCCCGGCT
454 TTTGGCCGAAATCGTGTACTAACGATCACGGTTTTTGGGTAAAAACGCATTTCGGCGCCCCGGCT
*
5004 CATTTTTGCATGATTTTTGGCAGAAGGACTCCTTGAAATATATATATTCATCTAACCAAATCTCA
519 CATTTTTGCATGATTTTTGGCAGAAGGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCA
* *
5069 GCCACAATAGATTTAAGTATTTGTTTTTACGAGAATCTGAATCTTGTTTAGAGTTAAATAG
584 GCCACAATGGATTTAAGGATTTG-TTTTACGAGAATCTGAATCTTGTTTAGAGTTAAATAG
5130 A
1 A
5131 GAATCTGAAT
Statistics
Matches: 4006, Mismatches: 410, Indels: 152
0.88 0.09 0.03
Matches are distributed among these distances:
618 294 0.07
619 258 0.06
620 14 0.00
621 8 0.00
627 2 0.00
628 2 0.00
631 1 0.00
634 2 0.00
637 23 0.01
638 88 0.02
639 225 0.06
640 201 0.05
641 47 0.01
642 191 0.05
643 563 0.14
644 499 0.12
645 654 0.16
646 232 0.06
647 308 0.08
648 87 0.02
649 69 0.02
650 193 0.05
651 40 0.01
652 5 0.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (643 bp):
AAATAAATTCGGGAAAAAATGTAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATTTTATTGG
CGTTGAATTATATATTTTTTCCGAGTATTATGGAAAAAAATTGAGAAAAAAATTTTCGAGTCAGA
TTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTTTGCTAAAAACGTATTTCGGCGCCCCGG
CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT
CAGCCACAATGGATTTAAGAATTTGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAGAA
ATAAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTATGGT
GTTGAATTATATTTTTTTTCTAAGTATTATGGAAAAAAATTGAGAAAATTTTTCGATTCAGATTT
TGGCCGAAATCGTGTACTAACGATCACGGTTTTTGGGTAAAAACGCATTTCGGCGCCCCGGCTCA
TTTTTGCATGATTTTTGGCAGAAGGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGC
CACAATGGATTTAAGGATTTGTTTTACGAGAATCTGAATCTTGTTTAGAGTTAAATAG
Found at i:5100 original size:321 final size:322
Alignment explanation
Indices: 4509--5130 Score: 917
Period size: 321 Copynumber: 1.9 Consensus size: 322
4499 AGAGTTTTGT
*
4509 AAAAACGATATTAGAAGCGTGAAAATACCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCG
1 AAAAACGATATTAGAAGCGTGAAAATACCTTCAATTTTTATGGCGTTGAATTATATATTTTTTCG
*
4574 AGTATTATGGAAAAAAATTGATAAAAAACTTTTCGAGTCAGATTTTAGCCGAAATCGTGTACTAA
66 AGTATTATGGAAAAAAATTGA-AAAAAACTTTTCGAGTCAAATTTTAGCCGAAATCGTGTACTAA
** * * **
4639 CTTTCACGGTTTTTTTGCTAAAAAAGTATTTCGGCGCCCCGGCTCAGTTTTGGTTGATTTTTGGC
130 CGATCACGGTTTTTTGGCTAAAAAAGCATTTCGGCGCCCCGGCTCAGTTTTGCATGATTTTTGGC
* * * *
4704 AGAAAGACTCCTTGAAATATCTATATTCATCGAAGCAAATATCAGGCACAATGGATTTAAGAATT
195 AGAAAGACTCCTTGAAATATATATATTCATCGAACCAAATATCAGCCACAATAGATTTAAGAATT
*
4769 TGTGTTTACGAGCATCTAAATCTTGTTTACAGTTAAATAGAAATAAATTCGGGACAAAAATGG
260 TGTGTTTACGAGAATCTAAATCTTGTTTACAGTTAAATAGAAATAAATTCGGGACAAAAATGG
*
4832 AAAAACGATATTAGAAGCGTGAAAA-ATCCTTCAATTTTTATGGTGTTGAATTATATATTTTTTT
1 AAAAACGATATTAGAAGCGTGAAAATA-CCTTCAATTTTTATGGCGTTGAATTATATA-TTTTTT
* * * * * *
4896 TGCGTATTATGGAAAAAAATTG-AGAAAATTTTTCGATTCAAATTTTGGCCGAAATCGTGTACTA
64 CGAGTATTATGGAAAAAAATTGAAAAAAACTTTTCGAGTCAAATTTTAGCCGAAATCGTGTACTA
* * * *
4960 ACGATCACGG-TTTTTGGGTAAAAACGCATTTCGTCGCCCCGGCTCATTTTTGCATGATTTTTGG
129 ACGATCACGGTTTTTTGGCTAAAAAAGCATTTCGGCGCCCCGGCTCAGTTTTGCATGATTTTTGG
* * * *
5024 CAGAAGGACTCCTTGAAATATATATATTCATCTAACCAAATCTCAGCCACAATAGATTTAAGTAT
194 CAGAAAGACTCCTTGAAATATATATATTCATCGAACCAAATATCAGCCACAATAGATTTAAGAAT
* * *
5089 TTGTTTTTACGAGAATCTGAATCTTGTTTAGAGTTAAATAGA
259 TTGTGTTTACGAGAATCTAAATCTTGTTTACAGTTAAATAGA
5131 GAATCTGAAT
Statistics
Matches: 266, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
321 141 0.53
322 46 0.17
323 53 0.20
324 26 0.10
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (322 bp):
AAAAACGATATTAGAAGCGTGAAAATACCTTCAATTTTTATGGCGTTGAATTATATATTTTTTCG
AGTATTATGGAAAAAAATTGAAAAAAACTTTTCGAGTCAAATTTTAGCCGAAATCGTGTACTAAC
GATCACGGTTTTTTGGCTAAAAAAGCATTTCGGCGCCCCGGCTCAGTTTTGCATGATTTTTGGCA
GAAAGACTCCTTGAAATATATATATTCATCGAACCAAATATCAGCCACAATAGATTTAAGAATTT
GTGTTTACGAGAATCTAAATCTTGTTTACAGTTAAATAGAAATAAATTCGGGACAAAAATGG
Found at i:5536 original size:19 final size:18
Alignment explanation
Indices: 5494--5536 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
5484 CCATAATAAA
5494 GCAAAAAGGGACAATCAG
1 GCAAAAAGGGACAATCAG
* *
5512 GACAAAAATGGACTATCGAG
1 G-CAAAAAGGGACAATC-AG
5532 GCAAA
1 GCAAA
5537 GCTACATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 17 0.81
20 3 0.14
ACGTcount: A:0.49, C:0.16, G:0.26, T:0.09
Consensus pattern (18 bp):
GCAAAAAGGGACAATCAG
Found at i:5995 original size:19 final size:19
Alignment explanation
Indices: 5952--5995 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5942 ACCACAACAA
5952 GGCAAAAAGGGACAATCAG
1 GGCAAAAAGGGACAATCAG
* * * *
5971 GACAAAAATGGACTATCGG
1 GGCAAAAAGGGACAATCAG
5990 GGCAAA
1 GGCAAA
5996 GCTACTTATG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.16, G:0.30, T:0.09
Consensus pattern (19 bp):
GGCAAAAAGGGACAATCAG
Found at i:5996 original size:459 final size:444
Alignment explanation
Indices: 5142--6198 Score: 1569
Period size: 459 Copynumber: 2.4 Consensus size: 444
5132 AATCTGAATC
* *
5142 ATCCAACGCCATATCGGGACTATCGAGAATAAAAGGCTCTATCGGGACAAAATTGGACTATTGGA
1 ATCCAACGCCATATCGGGACTATCGAGAA-AAAAGGGTCTATCGGGACAAAAATGGACTATTGGA
* *
5207 CCACCCATGTGACTCATGGTAACCCACGATT---------GGGCCCCAAGGTGCGGGTCGCCTAG
65 CCACCCATGTGACTCATGG-AACCCACGGTTGAGCCCCAAGGGCCCCAAGGTGCGAGTCGCCTAG
*
5263 GGGGTTTGGCCATCTTTGGCCAAGAGTCATTATTGGCATCCAAAACTCATGATGGTGAACACCTA
129 GGGGGTTGGCCATCTTTGGCCAAGAGTCATTATTGGCATCCAAAACTCATGATGGTGAACACCTA
* *
5328 TGCATTTGGGCCATTTTTCCCACATCCGAGTGTTATTCAGGGGTGTTCCAACGCCATATCGTGAC
194 TGCATTTGGGCCATTTTTCCCACATCCGAGGGTCATTCAGGGGTGTTCCAACGCCATATCGTGAC
*
5393 AAAAAGGGACTATTGGGGCAAAAATCCACTATCAAAGCAAAACAATGTATGTATTTGGGCCATTT
259 AAAAAGGGACTATTGGGGCAAAAATCCACTATCAAAGCAAAACAACGTATGTATTTGGGCCATTT
* * *
5458 TTCCCACATCCGAGGGTCATCCAACGCCATAATAAAGCAAAAAGGGACAATCAGGACAAAAATGG
324 TTCCCACATCCGAGGGTCATCCAACACCACAACAAAGCAAAAAGGGACAATCAGGACAAAAATGG
5523 ACTATCGAGGCAAAGCTACATATGAATTAAGGTCGTCTTCCCGTCATCTGAGGGTCATCTGAGGG
389 ACTATCGAGGCAAAGCTACATATGAATTAAGGTCGTCTTCCCG---TC--A---TC--C-GAGGG
5588 TG
443 TG
*
5590 ATGCAACGCCATATCGGGACTATCGAGAAAAGAAGGGTCTATCGGGACAAAAATGGACTATTGGA
1 ATCCAACGCCATATCGGGACTATCGAGAAAA-AAGGGTCTATCGGGACAAAAATGGACTATTGGA
* *
5655 CCACTCATGTGACTCATGAGAACCCACGGTTGAGCCCCAAGGCGCCCCTAAGGTGCGAGTCACCT
65 CCACCCATGTGACTCATG-GAACCCACGGTTGAGCCCCAAGG-GCCCC-AAGGTGCGAGTCGCCT
* *
5720 AGGGGGGTTGGCCATCTTTGGCCAAGAGTTATTCTTGGCATCCAAAACTCATGATGGTGAACACC
127 AGGGGGGTTGGCCATCTTTGGCCAAGAGTCATTATTGGCATCCAAAACTCATGATGGTGAACACC
5785 TATGCATTTGGGCCATTTTTCCCACATCCGAGGGTCATTCAGGGGTGTTCCAACGCCATATCGTG
192 TATGCATTTGGGCCATTTTTCCCACATCCGAGGGTCATTCAGGGGTGTTCCAACGCCATATCGTG
* * * *
5850 ACAAAAAGGGATTATTGGGGCAAAAATCCACTATCAAAGCAAAGCAACGTATGTATTTGTGCCGT
257 ACAAAAAGGGACTATTGGGGCAAAAATCCACTATCAAAGCAAAACAACGTATGTATTTGGGCCAT
*
5915 TTTTCCCACATCCGAGGGTCATCCAACACCACAACAAGGCAAAAAGGGACAATCAGGACAAAAAT
322 TTTTCCCACATCCGAGGGTCATCCAACACCACAACAAAGCAAAAAGGGACAATCAGGACAAAAAT
* * *
5980 GGACTATCGGGGCAAAGCTACTTATGAATTAGGGTCGTCTTCCCGTCATCCGAGGGTG
387 GGACTATCGAGGCAAAGCTACATATGAATTAAGGTCGTCTTCCCGTCATCCGAGGGTG
* *
6038 ATCCAACGCCATATCGGGACTATCGGGAAAAAAAAGGGTCTATCGGCA-AAAAATGGACTATTGG
1 ATCCAACGCCATATCGGGACTATC--GAGAAAAAAGGGTCTATCGGGACAAAAATGGACTATTGG
* *
6102 ACCACCCGTGTGACTCATGGGAACCCACGGTTGAGCCCCAAAGGGCGCCCAAGATGCGAGGT-GC
64 ACCACCCATGTGACTCAT-GGAACCCACGGTTGAGCCCC-AAGGGC-CCCAAGGTGCGA-GTCGC
*
6166 CTAAGGGGGTTGGCCATCTTTGGCCAAGAGTCA
125 CTAGGGGGGTTGGCCATCTTTGGCCAAGAGTCA
6199 CTCCCCCTTA
Statistics
Matches: 557, Mismatches: 33, Indels: 38
0.89 0.05 0.06
Matches are distributed among these distances:
447 2 0.00
448 209 0.38
449 26 0.05
450 6 0.01
451 2 0.00
454 1 0.00
456 2 0.00
457 2 0.00
458 5 0.01
459 302 0.54
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (444 bp):
ATCCAACGCCATATCGGGACTATCGAGAAAAAAGGGTCTATCGGGACAAAAATGGACTATTGGAC
CACCCATGTGACTCATGGAACCCACGGTTGAGCCCCAAGGGCCCCAAGGTGCGAGTCGCCTAGGG
GGGTTGGCCATCTTTGGCCAAGAGTCATTATTGGCATCCAAAACTCATGATGGTGAACACCTATG
CATTTGGGCCATTTTTCCCACATCCGAGGGTCATTCAGGGGTGTTCCAACGCCATATCGTGACAA
AAAGGGACTATTGGGGCAAAAATCCACTATCAAAGCAAAACAACGTATGTATTTGGGCCATTTTT
CCCACATCCGAGGGTCATCCAACACCACAACAAAGCAAAAAGGGACAATCAGGACAAAAATGGAC
TATCGAGGCAAAGCTACATATGAATTAAGGTCGTCTTCCCGTCATCCGAGGGTG
Found at i:6899 original size:329 final size:323
Alignment explanation
Indices: 6518--7294 Score: 899
Period size: 330 Copynumber: 2.4 Consensus size: 323
6508 AAGGCCCTAG
* * * *
6518 CTCAGTTTTGCATGATTTTTGGGGTAATGACTCTTTGAAATATCTATATTCATTAAACCAAATCT
1 CTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCT
* * *
6583 CAGCCAAATTAGATTTGAGGATTTGTTTTCACGAGCATCTAAATCATGTTTCGATTTAATT-AGA
66 CAGCCACATTGGATTTGAGGATTTGTTTTCACGAGCATCTGAATCATGTTTCGATTTAATTGA-A
** * * *
6647 AATTGATTCGGAAGAAAAAAAA-AAGAAAAACGATATTAGAAGC-ATGAAAAACCCTTTAATCTT
130 AATAAATTC-GAA-AAAAAAAAGAA-AAAAACGATATTACAAGCGA-GAAAAACCCTTCAATCAT
*
6710 TTTGGTGTT-GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGCAAAAAAAAAAAAATT
191 TTTGGT-TTCGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATT--AAAAAAAAAAAAATT
* *
6774 CGGGTC-A-GTTTTTAGCCAAAATCGTGTACTAACCAACACGATTTTTGGCTAAAAACGTGTTTC
253 CGGGTCAATGTTTTTAGCCAAAATCGTGTACT----AACACGATTTTTGGCTAAAAACGCGTTCC
6837 CG-GACCACGA
314 CGAG-CCACGA
* ** * * *
6847 CTCAGTTTTGAATGGCTTTTGGCATAAAGACTCCTAGAAATATCTATATTCATCAAACCAGATCT
1 CTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCT
* * * *
6912 CAACCACATTGGA-TTGAAGGATTTTTTTTTTCACGAGCATCCGAATCTTGTTTCGATTTAATTG
66 CAGCCACATTGGATTTG-AGGA--TTTGTTTTCACGAGCATCTGAATCATGTTTCGATTTAATTG
* *
6976 AAAATAAATTCGAAAAAAAAAATGAAAATAACGATATTACAAGCGAGAAAAGCCCTTCAATCATT
128 AAAATAAATTCGAAAAAAAAAA-GAAAAAAACGATATTACAAGCGAGAAAAACCCTTCAATCATT
* * *
7041 TTGGTTTCGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTTAGAAAAAAAAAATTTGGG
192 TTGGTTTCGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTAAAAAAAAAAAAATTCGGG
* * * *
7106 TCAATTTTTTTAGCCGAAATCGTGTACTAACACGGTTTTTGGCTAAAAACGCGTTCCCGAGCCCC
257 TCAATGTTTTTAGCCAAAATCGTGTACTAACACGATTTTTGGCTAAAAACGCGTTCCCGAGCCAC
7171 GA
322 GA
* *** * * *
7173 CTTAGTTTTGCATGATTTTTTATGTCAAGGCTCCTTTG-AATATCTATATTCATCGAACCAAATC
1 CTCAGTTTTGCATGATTTTTGGCGTAAAGACTCC-TTGAAATATCTATATTCATCAAACCAAATC
* * * * *
7237 TCAGTCACATTGGATTTAAGAATTTGTTTTTACGAGTATCTGAAT-ATTGTTTCGATTT
65 TCAGCCACATTGGATTTGAGGATTTGTTTTCACGAGCATCTGAATCA-TGTTTCGATTT
7295 GAATAAATCA
Statistics
Matches: 378, Mismatches: 56, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
324 30 0.08
326 96 0.25
327 5 0.01
328 21 0.06
329 80 0.21
330 98 0.26
331 47 0.12
332 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (323 bp):
CTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCT
CAGCCACATTGGATTTGAGGATTTGTTTTCACGAGCATCTGAATCATGTTTCGATTTAATTGAAA
ATAAATTCGAAAAAAAAAAGAAAAAAACGATATTACAAGCGAGAAAAACCCTTCAATCATTTTGG
TTTCGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTAAAAAAAAAAAAATTCGGGTCAA
TGTTTTTAGCCAAAATCGTGTACTAACACGATTTTTGGCTAAAAACGCGTTCCCGAGCCACGA
Found at i:7096 original size:330 final size:326
Alignment explanation
Indices: 6518--7294 Score: 898
Period size: 326 Copynumber: 2.4 Consensus size: 326
6508 AAGGCCCTAG
* * * *
6518 CTCAGTTTTGCATGATTTTTGGGGTAATGACTCTTTGAAATATCTATATTCATTAAACCAAATCT
1 CTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCT
* * * * *
6583 CAGCCAAATTAGATTTG-AGGA-TTTGTTTTCACGAGCATCTAAATCATGTTTCGATTTAATTAG
66 CAGCCACATTGGA-TTGAAGGATTTTTTTTTCACGAGCATCTGAATCTTGTTTCGATTTAATTAG
** * * *
6646 AAATTGATTCGGAAGAAAAAAAAAAGAAAAACGATATTAGAAGCATGAAAAACCCTTTAATCTTT
130 AAATAAATTCGGAAGAAAAAAAAAAGAAAAACGATATTACAAGCATGAAAAACCCTTCAATCATT
*
6711 TTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGCAAAAAAAAAAAAATTCG
195 TTGGTGTTGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTGC--AAAAAAAAAAATTCG
* *
6776 GGTC-A-GTTTTTAGCCAAAATCGTGTACTAACCAACACGATTTTTGGCTAAAAACGTGTTTCCG
258 GGTCAATGTTTTTAGCCAAAATCGTGTACT----AACACGATTTTTGGCTAAAAACGCGTTCCCG
6839 -GACCACGA
319 AG-CCACGA
* ** * * *
6847 CTCAGTTTTGAATGGCTTTTGGCATAAAGACTCCTAGAAATATCTATATTCATCAAACCAGATCT
1 CTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCT
* *
6912 CAACCACATTGGATTGAAGGATTTTTTTTTTCACGAGCATCCGAATCTTGTTTCGATTTAATT-G
66 CAGCCACATTGGATTGAAGGA-TTTTTTTTTCACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* *
6976 AAAATAAATTC-GAA-AAAAAAAATGAA-AATAACGATATTACAAGCGA-GAAAAGCCCTTCAAT
130 -AAATAAATTCGGAAGAAAAAAAA--AAGAAAAACGATATTACAAGC-ATGAAAAACCCTTCAAT
*
7037 CATTTTGGT-TTCGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATT-TAGAAAAAAAAAA
191 CATTTTGGTGTT-GAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTGCA-AAAAAAAAAA
* * * *
7100 TTTGGGTCAATTTTTTTAGCCGAAATCGTGTACTAACACGGTTTTTGGCTAAAAACGCGTTCCCG
254 TTCGGGTCAATGTTTTTAGCCAAAATCGTGTACTAACACGATTTTTGGCTAAAAACGCGTTCCCG
*
7165 AGCCCCGA
319 AGCCACGA
* *** * * *
7173 CTTAGTTTTGCATGATTTTTTATGTCAAGGCTCCTTTG-AATATCTATATTCATCGAACCAAATC
1 CTCAGTTTTGCATGATTTTTGGCGTAAAGACTCC-TTGAAATATCTATATTCATCAAACCAAATC
* * * * * *
7237 TCAGTCACATTGGATTTAAGAATTTGTTTTT-ACGAGTATCTGAATATTGTTTCGATTT
65 TCAGCCACATTGGATTGAAGGATTTTTTTTTCACGAGCATCTGAATCTTGTTTCGATTT
7295 GAATAAATCA
Statistics
Matches: 381, Mismatches: 54, Indels: 31
0.82 0.12 0.07
Matches are distributed among these distances:
324 24 0.06
325 8 0.02
326 99 0.26
327 4 0.01
328 20 0.05
329 80 0.21
330 99 0.26
331 47 0.12
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (326 bp):
CTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCT
CAGCCACATTGGATTGAAGGATTTTTTTTTCACGAGCATCTGAATCTTGTTTCGATTTAATTAGA
AATAAATTCGGAAGAAAAAAAAAAGAAAAACGATATTACAAGCATGAAAAACCCTTCAATCATTT
TGGTGTTGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTGCAAAAAAAAAAATTCGGGT
CAATGTTTTTAGCCAAAATCGTGTACTAACACGATTTTTGGCTAAAAACGCGTTCCCGAGCCACG
A
Found at i:7778 original size:39 final size:39
Alignment explanation
Indices: 7637--7807 Score: 166
Period size: 39 Copynumber: 4.4 Consensus size: 39
7627 AATAAAACTC
* * * * *
7637 ACTTTTATCGACAGTTATAAGTACTGGCAAAAGTCACAG
1 ACTTTTACCGACTGTTTTAAGTGCTGACAAAAGTCACAG
* * * *
7676 GCATTTT-CCGACTGTTATAAGTGC-CAGCAAATGTCACAG
1 AC-TTTTACCGACTGTTTTAAGTGCTGA-CAAAAGTCACAG
* * *
7715 ACTTTTACTGTCTGTTTTAAGTGCTGACAAATGTCACAG
1 ACTTTTACCGACTGTTTTAAGTGCTGACAAAAGTCACAG
* ** *
7754 ACTTTTACCGGCTGTTTTAAGTGCTGTTAAAAGTCACAC
1 ACTTTTACCGACTGTTTTAAGTGCTGACAAAAGTCACAG
7793 ACTTTTACCGACTGT
1 ACTTTTACCGACTGT
7808 AAGTGCCAGT
Statistics
Matches: 109, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
38 4 0.04
39 100 0.92
40 5 0.05
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (39 bp):
ACTTTTACCGACTGTTTTAAGTGCTGACAAAAGTCACAG
Found at i:8081 original size:43 final size:44
Alignment explanation
Indices: 8034--8123 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
8024 GACTTCTTCC
* *
8034 CATTTAAGAT-CCGACTTGATGTGACTTCGATTTAATCATGATT
1 CATTTAAGATCCCGACTTGAGGTGACTTCGAGTTAATCATGATT
*
8077 CATTTAAGATCCCCGACTTGGGGTGACTTCGAGTTAATCATGATT
1 CATTTAAGAT-CCCGACTTGAGGTGACTTCGAGTTAATCATGATT
8122 CA
1 CA
8124 GGACCTGCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 10 0.24
45 32 0.76
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (44 bp):
CATTTAAGATCCCGACTTGAGGTGACTTCGAGTTAATCATGATT
Found at i:20988 original size:22 final size:21
Alignment explanation
Indices: 20954--20994 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
20944 AGCTTTGGGC
**
20954 AATATTTTTTAATAGATTTTTT
1 AATATTTGATAATA-ATTTTTT
20976 AATATTTGATAATAATTTT
1 AATATTTGATAATAATTTT
20995 GAGTTTCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
AATATTTGATAATAATTTTTT
Found at i:26110 original size:13 final size:13
Alignment explanation
Indices: 26092--26125 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
26082 TTACTGATTA
26092 GTAACTTCTATAC
1 GTAACTTCTATAC
26105 GTAACTTCTATAC
1 GTAACTTCTATAC
26118 GTATACTT
1 GTA-ACTT
26126 TGCGAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (13 bp):
GTAACTTCTATAC
Found at i:32136 original size:37 final size:37
Alignment explanation
Indices: 32095--32165 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
32085 ACATAAAGAT
* *
32095 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
32132 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
32166 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:33500 original size:26 final size:25
Alignment explanation
Indices: 33462--33513 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
33452 TTTCTTACAA
33462 AAATAATAGAAATAAACATTAGATAT
1 AAATAATAGAAATAAAC-TTAGATAT
* * * *
33488 AAATCATATAAATGAACTTATATAT
1 AAATAATAGAAATAAACTTAGATAT
33513 A
1 A
33514 TATATCTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (25 bp):
AAATAATAGAAATAAACTTAGATAT
Found at i:42469 original size:21 final size:19
Alignment explanation
Indices: 42425--42480 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
42415 GTTTAGCAAT
42425 TGTACAGATGAGATTACAC
1 TGTACAGATGAGATTACAC
* *
42444 TGTACAGATTAGATTAGATGC
1 TGTACAGATGAGATTACA--C
42465 TGTACAGATGAGATTA
1 TGTACAGATGAGATTA
42481 TTAGAGCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (19 bp):
TGTACAGATGAGATTACAC
Found at i:78786 original size:2 final size:2
Alignment explanation
Indices: 78779--78817 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
78769 GTGCAAATAC
78779 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
78818 CCTTGAGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:79788 original size:50 final size:50
Alignment explanation
Indices: 79713--79824 Score: 224
Period size: 50 Copynumber: 2.2 Consensus size: 50
79703 AAGACAAATC
79713 ATCTTCATATATAAGCCTAACAGAGGAAATAACTATTGTTTGGACTTGGA
1 ATCTTCATATATAAGCCTAACAGAGGAAATAACTATTGTTTGGACTTGGA
79763 ATCTTCATATATAAGCCTAACAGAGGAAATAACTATTGTTTGGACTTGGA
1 ATCTTCATATATAAGCCTAACAGAGGAAATAACTATTGTTTGGACTTGGA
79813 ATCTTCATATAT
1 ATCTTCATATAT
79825 GAGGTAAATG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (50 bp):
ATCTTCATATATAAGCCTAACAGAGGAAATAACTATTGTTTGGACTTGGA
Found at i:86249 original size:14 final size:14
Alignment explanation
Indices: 86230--86258 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
86220 TCTAAGTGAA
86230 TCTTAAGAAGAATT
1 TCTTAAGAAGAATT
86244 TCTTAAGAAGAATT
1 TCTTAAGAAGAATT
86258 T
1 T
86259 TCTCACGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (14 bp):
TCTTAAGAAGAATT
Found at i:106784 original size:42 final size:43
Alignment explanation
Indices: 106737--106826 Score: 128
Period size: 45 Copynumber: 2.1 Consensus size: 43
106727 CATTATTTAA
*
106737 ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAACTAAT
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
**
106779 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGTTAAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
106824 ATT
1 ATT
106827 AATTGTTGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 6 0.14
45 36 0.86
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
Found at i:121342 original size:24 final size:23
Alignment explanation
Indices: 121314--121365 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
121304 TTCATATTAA
* *
121314 AAATTGATTTTATGTTATATTTTT
1 AAATTAATTTAAT-TTATATTTTT
121338 AAATTTAATTTAATTTATATTTTT
1 AAA-TTAATTTAATTTATATTTTT
121362 AAAT
1 AAAT
121366 AAATATTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.04
24 16 0.64
25 8 0.32
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
AAATTAATTTAATTTATATTTTT
Found at i:133391 original size:33 final size:33
Alignment explanation
Indices: 133342--133496 Score: 188
Period size: 33 Copynumber: 4.7 Consensus size: 33
133332 GCTGCCTTCG
* * *
133342 TCTTCCTGCTCTTCTTCTTCGTGTTTAG-TTGCT
1 TCTTCATGCTCCTCTTCTTCATGTTT-GCTTGCT
*
133375 TCTTC-TAGCTCCTCTTCTTCATGTTTTCTTGCT
1 TCTTCAT-GCTCCTCTTCTTCATGTTTGCTTGCT
* *
133408 TCCTCATGCTCCTCTTCTTCATGTTTGCTTTCT
1 TCTTCATGCTCCTCTTCTTCATGTTTGCTTGCT
* * * *
133441 TCTTCCTGCTCATCGTCTTCATGTTTGCCTGCT
1 TCTTCATGCTCCTCTTCTTCATGTTTGCTTGCT
133474 TCTTCATGCTCCTCTTCTTCATG
1 TCTTCATGCTCCTCTTCTTCATG
133497 GCTCTTAGGC
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
32 1 0.01
33 102 0.98
34 1 0.01
ACGTcount: A:0.06, C:0.32, G:0.12, T:0.51
Consensus pattern (33 bp):
TCTTCATGCTCCTCTTCTTCATGTTTGCTTGCT
Found at i:133409 original size:18 final size:17
Alignment explanation
Indices: 133387--133445 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 17
133377 TTCTAGCTCC
133387 TCTTCTTCATGTTTTCT
1 TCTTCTTCATGTTTTCT
* * *
133404 TGCTTCCTCATG--CTCC
1 T-CTTCTTCATGTTTTCT
*
133420 TCTTCTTCATGTTTGCTT
1 TCTTCTTCATGTTTTC-T
133438 TCTTCTTC
1 TCTTCTTC
133446 CTGCTCATCG
Statistics
Matches: 31, Mismatches: 7, Indels: 7
0.69 0.16 0.16
Matches are distributed among these distances:
15 9 0.29
16 3 0.10
17 2 0.06
18 17 0.55
ACGTcount: A:0.05, C:0.31, G:0.08, T:0.56
Consensus pattern (17 bp):
TCTTCTTCATGTTTTCT
Found at i:133490 original size:15 final size:15
Alignment explanation
Indices: 133373--133496 Score: 70
Period size: 15 Copynumber: 7.7 Consensus size: 15
133363 TGTTTAGTTG
133373 CTTCTTC-TAGCTCCT
1 CTTCTTCAT-GCTCCT
* *
133388 CTTCTTCATGTTTTCTT
1 CTTCTTCATG--CTCCT
*
133405 GCTTCCTCATGCTCCT
1 -CTTCTTCATGCTCCT
* *
133421 CTTCTTCATGTTTGCTTT
1 CTTCTTCATG-CT-C-CT
* *
133439 CTTCTTCCTGCTCAT
1 CTTCTTCATGCTCCT
* *
133454 CGTCTTCATGTTTGCCT
1 CTTCTTCATG-CT-CCT
133471 GCTTCTTCATGCTCCT
1 -CTTCTTCATGCTCCT
133487 CTTCTTCATG
1 CTTCTTCATG
133497 GCTCTTAGGC
Statistics
Matches: 82, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
15 36 0.44
16 10 0.12
17 8 0.10
18 28 0.34
ACGTcount: A:0.06, C:0.33, G:0.10, T:0.50
Consensus pattern (15 bp):
CTTCTTCATGCTCCT
Found at i:145005 original size:52 final size:53
Alignment explanation
Indices: 144889--145043 Score: 294
Period size: 52 Copynumber: 2.9 Consensus size: 53
144879 ACTATGACCT
144889 GCCATGCAGATGCAGGGTACAATACATGGCCTTATTACACACACACACACATAC
1 GCCATGCAGATGCAGGGTACAATACATGGCCTTATTACACACACACACACA-AC
144943 GCCATGCAGATGCAGGGTACAATACATGGCCTTATTACACACACACACAC-AC
1 GCCATGCAGATGCAGGGTACAATACATGGCCTTATTACACACACACACACAAC
144995 GCCATGCAGATGCAGGGTACAATACATGGCCTTATTACACACACACACA
1 GCCATGCAGATGCAGGGTACAATACATGGCCTTATTACACACACACACA
145044 TATATAACTA
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
52 51 0.50
54 50 0.50
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.18
Consensus pattern (53 bp):
GCCATGCAGATGCAGGGTACAATACATGGCCTTATTACACACACACACACAAC
Found at i:146217 original size:59 final size:59
Alignment explanation
Indices: 146128--146246 Score: 161
Period size: 59 Copynumber: 2.0 Consensus size: 59
146118 TTATACCTCT
* * ** *
146128 TTGATTAATTCTAAAATCACAAGATAGAACCATTTTAATTTGGCTT-TTTTATTGTAAC
1 TTGATTAATTATAAAATCAAAAGATAGAACCATTTTAAAATGACTTGTTTTATTGTAAC
146186 TTGATTAATTAATAAAATCATAAAG-TAGAACCATTTTAAAATGACTTGTTTTATTGTAAC
1 TTGATTAATT-ATAAAATCA-AAAGATAGAACCATTTTAAAATGACTTGTTTTATTGTAAC
146246 T
1 T
146247 ATAATAATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
58 10 0.19
59 27 0.51
60 16 0.30
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (59 bp):
TTGATTAATTATAAAATCAAAAGATAGAACCATTTTAAAATGACTTGTTTTATTGTAAC
Found at i:150340 original size:81 final size:78
Alignment explanation
Indices: 150247--150449 Score: 255
Period size: 81 Copynumber: 2.5 Consensus size: 78
150237 ACGATGTTGT
*
150247 TGGCTTATCGTTCACCATTGGAGGAGCTAATTGATTTTGAGCATCCG-GAATTACTTTCTCCCAT
1 TGGCTTATCGTTCACCATTGGAGGAGC---TTGATTTTGAGCATCCGAG-ACTACTTTCTCCCAT
150311 CTCTCCCAAGTAATTTC
62 CTCTCCCAAGTAATTTC
*
150328 TGGCTTATCGTTCAGTACCATTGGAGGAGCTTGATTTTGAGCATCCGAGACTACTTTTTCCCATC
1 TGGCTTATCGTTC---ACCATTGGAGGAGCTTGATTTTGAGCATCCGAGACTACTTTCTCCCATC
150393 TCTCCCAAGTAATTTC
63 TCTCCCAAGTAATTTC
* * * * * * *
150409 TGGCTTAGCGTTCGCCATAGCATGATCTTGACTTTGAGCAT
1 TGGCTTATCGTTCACCATTGGAGGAGCTTGATTTTGAGCAT
150450 TATATGATTC
Statistics
Matches: 109, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
78 22 0.20
81 72 0.66
82 1 0.01
84 14 0.13
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.35
Consensus pattern (78 bp):
TGGCTTATCGTTCACCATTGGAGGAGCTTGATTTTGAGCATCCGAGACTACTTTCTCCCATCTCT
CCCAAGTAATTTC
Found at i:152235 original size:22 final size:24
Alignment explanation
Indices: 152209--152256 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
152199 ACTTATAAGA
*
152209 ATTGTATTATA-AT-TATTTATAT
1 ATTGTATTATATATATATATATAT
*
152231 ATTGTGTTATATATATATATATAT
1 ATTGTATTATATATATATATATAT
152255 AT
1 AT
152257 ATGTGTGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (24 bp):
ATTGTATTATATATATATATATAT
Found at i:152361 original size:20 final size:20
Alignment explanation
Indices: 152320--152361 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
152310 CTCGACTCGA
* *
152320 GAAAAATTCGAGTTCGGTTC
1 GAAAAATTCGAGTCCGGCTC
152340 GAAAAATTCGAG-CCGAGCTC
1 GAAAAATTCGAGTCCG-GCTC
152360 GA
1 GA
152362 GCTCGAGCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.21
Consensus pattern (20 bp):
GAAAAATTCGAGTCCGGCTC
Found at i:152364 original size:6 final size:6
Alignment explanation
Indices: 152347--152375 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
152337 TTCGAAAAAT
152347 TCGAGC -CGAGC TCGAGC TCGAGC TCGAGC
1 TCGAGC TCGAGC TCGAGC TCGAGC TCGAGC
152376 CCTAATTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.17, C:0.34, G:0.34, T:0.14
Consensus pattern (6 bp):
TCGAGC
Found at i:155636 original size:26 final size:26
Alignment explanation
Indices: 155570--155636 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
155560 TCTTCTTTGA
* *
155570 TAATAATCTTCCTTG--GATCTTCTT
1 TAATAATCCTCCTTGAAAATCTTCTT
*
155594 TAACAATCCT-CTGTGAAAATCTTCTT
1 TAATAATCCTCCT-TGAAAATCTTCTT
155620 TAATAATCCTCCTTGAA
1 TAATAATCCTCCTTGAA
155637 TATTCTGGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 2 0.06
24 10 0.29
26 21 0.60
27 2 0.06
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.42
Consensus pattern (26 bp):
TAATAATCCTCCTTGAAAATCTTCTT
Found at i:156100 original size:441 final size:441
Alignment explanation
Indices: 155271--156140 Score: 1625
Period size: 441 Copynumber: 2.0 Consensus size: 441
155261 GAAAATTTAA
155271 TAATAAGAAATTGTCCTCTGATTCTTCTCCTTTGTAAAATTCTATTTCAAAATTTGCTTCAAGGG
1 TAATAAGAAATTGTCCTCTGATTCTTCTCCTTTGTAAAATTCTATTTCAAAATTTGCTTCAAGGG
155336 TCGAATGACTTATCTTGAACTTGATAATTTGAGAGCTTGATTTTGATAACATGATTCAATTATCT
66 TCGAATGACTTATCTTGAACTTGATAATTTGAGAGCTTGATTTTGATAACATGATTCAATTATCT
155401 TGGTGACTTAATCTTGAATTAATAACTTGAGAGCTTGATAATTTGATTCAAGGGTCTTGAAGACT
131 TGGTGACTTAATCTTGAATTAATAACTTGAGAGCTTGATAATTTGATTCAAGGGTCTTGAAGACT
* *
155466 TGATCTTGAACGGGTACAAATAATCTTTTTCAATTAAGTTGATAAAGATCAAAATAATAATTTCT
196 TGATCTTGAACGGATAAAAATAATCTTTTTCAATTAAGTTGATAAAGATCAAAATAATAATTTCT
155531 TGAAAGCTTCCGAACTTTTGCAATAAATTTCTTCTTTGATAATAATCTTCCTTGGATCTTCTTTA
261 TGAAAGCTTCCGAACTTTTGCAATAAATTTCTTCTTTGATAATAATCTTCCTTGGATCTTCTTTA
*
155596 ACAATCCTCTGTGAAAATCTTCTTTAATAATCCTCCTTGAATATTCTGGAGACTTTGCTCTTCAG
326 ACAATCCTCTGTGAAAATCTTCTTTAATAATCCTCCTTGAATATTCTGGAGACTTTACTCTTCAG
155661 CTTCTCTGCTCTCAATTGTGTGTGAAAAATGATTTTGGAGCTTCTCCTTTG
391 CTTCTCTGCTCTCAATTGTGTGTGAAAAATGATTTTGGAGCTTCTCCTTTG
155712 TAATAAGAAATTGTCCTCTGATTCTTCTCCTTTGTAAAATTCTATTT-AAAGATTTGCTTCAAGG
1 TAATAAGAAATTGTCCTCTGATTCTTCTCCTTTGTAAAATTCTATTTCAAA-ATTTGCTTCAAGG
* *
155776 GTCGAATGACTTATCTTGAACTTGATAATTTGAGAGCTTGATTTTGATAACTTGATTCAATTGTC
65 GTCGAATGACTTATCTTGAACTTGATAATTTGAGAGCTTGATTTTGATAACATGATTCAATTATC
* *
155841 TTGGTGACTTAATCTTGAATTAATAACTTGAGAGCTTGATAATTTGATTCAAGGGTGTTGGAGAC
130 TTGGTGACTTAATCTTGAATTAATAACTTGAGAGCTTGATAATTTGATTCAAGGGTCTTGAAGAC
* *
155906 TTGATCTTGAACGGATAAAAATAATCTTTTTCTATTAAGTTGATGAAGATCAAAATAATAATTTC
195 TTGATCTTGAACGGATAAAAATAATCTTTTTCAATTAAGTTGATAAAGATCAAAATAATAATTTC
*
155971 TTGAAAGCTTCCGAGCTTTTGCAATAAATTTCTTCTTTGATAATAATCTTCCTTGGATCTTCTTT
260 TTGAAAGCTTCCGAACTTTTGCAATAAATTTCTTCTTTGATAATAATCTTCCTTGGATCTTCTTT
*
156036 AACAATCCTCTGTGAAAATCTTCTTTAATAATTCTCCTTGAATATTCTGGAGACTTTACTCTTCA
325 AACAATCCTCTGTGAAAATCTTCTTTAATAATCCTCCTTGAATATTCTGGAGACTTTACTCTTCA
156101 GCTTCTCTGCTCTCAATTGTGTGTGAAAAATGATTTTGGA
390 GCTTCTCTGCTCTCAATTGTGTGTGAAAAATGATTTTGGA
156141 ACTTGGTAAT
Statistics
Matches: 417, Mismatches: 11, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
440 3 0.01
441 414 0.99
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (441 bp):
TAATAAGAAATTGTCCTCTGATTCTTCTCCTTTGTAAAATTCTATTTCAAAATTTGCTTCAAGGG
TCGAATGACTTATCTTGAACTTGATAATTTGAGAGCTTGATTTTGATAACATGATTCAATTATCT
TGGTGACTTAATCTTGAATTAATAACTTGAGAGCTTGATAATTTGATTCAAGGGTCTTGAAGACT
TGATCTTGAACGGATAAAAATAATCTTTTTCAATTAAGTTGATAAAGATCAAAATAATAATTTCT
TGAAAGCTTCCGAACTTTTGCAATAAATTTCTTCTTTGATAATAATCTTCCTTGGATCTTCTTTA
ACAATCCTCTGTGAAAATCTTCTTTAATAATCCTCCTTGAATATTCTGGAGACTTTACTCTTCAG
CTTCTCTGCTCTCAATTGTGTGTGAAAAATGATTTTGGAGCTTCTCCTTTG
Done.