Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008931.1 Corchorus capsularis cultivar CVL-1 contig08952, 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: 25170
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1554 original size:324 final size:323
Alignment explanation
Indices: 1--2245 Score: 2943
Period size: 324 Copynumber: 7.0 Consensus size: 323
*
1 CTTGTAATATCTGTATTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGATTTTTTTTTACA
1 CTTGTAATATCTGTATTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGA-TTTTTTTTACG
* *
66 AGCATCTGAATCTTGTTTCGATATGATTTGAAATAAATTCGGAATAAAAATGGAAAAATCATATT
65 AGCATCTGAATCTTGTTTCGATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATATT
*
131 AGAAGCATGAAAAAACTCTTAATTTTTTTGGTGATGAATAATAAATTT-TTTTTAGTATTCTGGC
130 AGAAGCATGAAAAAAC-CTCAATTTTTTTGGTGATGAATAATAAATTTATTTTTAGTATTCTGGC
* * *
195 AAAAAATTGAG-AAATAAAATTTTCGTGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGG
194 AAAAAATTGAGAAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGG
*
259 TTTTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCATGATTTCTGGCAGAAAGGACT
259 TTTTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCATGATTTTTGGCAGAAA-GACT
324 C
323 C
* * *
325 CTTGTAATATCTG---T-AT---AACAAATCTCAGGCACAATAGATTTAAGAATTTTTTTTACGA
1 CTTGTAATATCTGTATTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGATTTTTTTTACGA
* * *
383 GCATCTGAATCTTATTTCAATATAATTTGAAATATATTCGG-ATAAAAATGGAAAAATGATATTA
66 GCATCTGAATCTTGTTTCGATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATATTA
* *** *
447 GAAGCATAGAAAAAACTCTTAATTTTTTTGGTGATGAATAATAAAAAAAATTTTAGTATTCTGGC
131 GAAGCAT-GAAAAAAC-CTCAATTTTTTTGGTGATGAATAATAAATTTATTTTTAGTATTCTGGC
*
512 -AAAAATTGAGAAAAAAAAAA-TT-GGTTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGG
194 AAAAAATTGAGAAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGG
* * * *
574 TTTTTGGCTAAAAATGCAATTCGGCGCACCGCCTCAGTTTTGCATGATTTTTGGGAGAAAGATTC
259 TTTTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTC
*
639 CTTGTAATATCTTTATTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGATTTTTTTTTCTT
1 CTTGTAATATCTGTATTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGA---TTTTTT-TT
* * * * * *
704 ACAAGCATCTGATTCTTGTTTCGATAGAATATAAAATAAATTCGGAATAAAAATGGAAAACTGAT
62 ACGAGCATCTGAATCTTGTTTCGATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGAT
* * *
769 ATTAG-AGCCGTGAAAAAATCCTCAATTTTTTTGGTGATGAATTATAAAATTTTTTTTTAGTATT
127 ATTAGAAG-CATGAAAAAA-CCTCAATTTTTTTGGTGATGAATAAT-AAATTTATTTTTAGTATT
*
833 GTGGC-AAAAATTGAGAAAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCA
189 CTGGCAAAAAATTGAGAAAAAAAAAA-TTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCA
* * * *
897 TCACGGTTTTTGGCTGAAAATGCATTTCGGCGGACCGGCTCAATTTTGCATGATTCTTGGCAGAA
253 TCACGGTTTTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCATGATTTTTGGCAGAA
* *
962 AGATTA
318 AGACTC
* *
968 TTTGGAATATCTGTATTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGATTTTTTTTACGA
1 CTTGTAATATCTGTATTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGATTTTTTTTACGA
* * * * *
1033 GCATCTGAATCTTATTTTGATATAATTTGAAATATATTCGGAATAGAAATGGAAAAATCATATTA
66 GCATCTGAATCTTGTTTCGATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATATTA
* ** *
1098 GAAGCATGAAAAAACTCTTAATTTTTTTGGTGATGAATAATAAAAAT-TTTTTAATATTCTGGCA
131 GAAGCATGAAAAAAC-CTCAATTTTTTTGGTGATGAATAATAAATTTATTTTTAGTATTCTGGCA
** * * *
1162 AAAAATTGAG-AAATGAAATTTTCGGATCAGTTTTTAGCCGAAATCGTGTACTAATCATCACGGT
195 AAAAATTGAGAAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGT
* *
1226 TTTTGACTAAAAATGCATTTCGGCGGACCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTC
260 TTTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTC
* *
1290 CTTGTAATATTTGTATTCATCAAAACAAATCTCAACCACAATAGG-TTTAAGGATTTTTTTCTAA
1 CTTGTAATATCTGTATTCATCAAAACAAATCTCAGCCACAAT-GGATTTAAGGATTTTTTT-T-A
* * * *
1354 CGAGCATTTCAATCTTGTTTCGATATTATTTGAAATAAATTCGGAATAAAAATGGAAAAATAATA
63 CGAGCATCTGAATCTTGTTTCGATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATA
* * * *
1419 TTAGAAGCGTGAAAAAATCCTCAATTTTTTTTGTGATGAATTAT-AATTTATTTTTAGTATTGTG
128 TTAGAAGCATGAAAAAA-CCTCAATTTTTTTGGTGATGAATAATAAATTTATTTTTAGTATTCTG
* * *
1483 GC-AGAAATTGAGAAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACTATCAA
192 GCAAAAAATTGAGAAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCAC
* * * * * **
1547 TGTTTTTGCCTAAAAATGCATTTCGACGCACCGGCTCAGTTTTGCATGATTTTTGACGGAGGGAC
257 GGTTTTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGAC
1612 TC
322 TC
*
1614 CTTGTAATATCTGTATTCATCAAAACAAATCTCAGACACAATGGATTTAAGGATTTTTTTTTACG
1 CTTGTAATATCTGTATTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGA-TTTTTTTTACG
* *
1679 AGCATCTGAATCTTATTTCAATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATATT
65 AGCATCTGAATCTTGTTTCGATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATATT
* * *** *
1744 AGAAGCATGAAAAAACTCTTAAATTTTTTTGGTAATGAATAATAAAAAAAGTTTTAGTATTCTGG
130 AGAAGCATGAAAAAAC-C-TCAATTTTTTTGGTGATGAATAATAAATTTATTTTTAGTATTCTGG
* *
1809 CAAAAAATTAAGAAAAAAAAAA-TT-GGTTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACG
193 CAAAAAATTGAGAAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACG
* * *
1872 GTTTTTGGCTAAAAATGCAATTCGGCGCACCGCCTCAGTTTTGCATGATTTTTTGCAGAAAGACT
258 GTTTTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACT
*
1937 G
323 C
* * * * * * *
1938 CTTG-AATTAACTATTTTCATC-GAACAAAATCTCGGCCACAATGGTTTTAACGATTTGTTTTTA
1 CTTGTAA-TATCTGTATTCATCAAAAC-AAATCTCAGCCACAATGGATTTAAGGATTT-TTTTTA
* * *
2001 CGAGTATCTAAATCTTGTTTCAATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATA
63 CGAGCATCTGAATCTTGTTTCGATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATA
* ** * * * * * *
2066 TTAGAAGCGTG-AAAAACCTTCAATTATTTAAGG-GTTAAATTATATATTT-TTCTTACTATTAC
128 TTAGAAGCATGAAAAAACC-TCAATT-TTTTTGGTGATGAATAATAAATTTATTTTTAGTATT-C
* *
2128 -GGCAAAAAATTGAG-AAAAAAAAATTT-GGGTTAGTTTTTAGCCGAAATTGTGTACTAACCAAT
190 TGGCAAAAAATTGAGAAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACC-AT
* * *
2190 -ACGGTTTTTGACTAAAAATGCATTTCGGCGC-CTCGGCTTAGTTTAGCATGATTTTT
254 CACGGTTTTTGGCTAAAAATGCATTTCGGCGCAC-CGGCTCAGTTTTGCATGATTTTT
2246 TTTTTGAAAT
Statistics
Matches: 1686, Mismatches: 191, Indels: 91
0.86 0.10 0.05
Matches are distributed among these distances:
314 16 0.01
315 123 0.07
316 97 0.06
317 50 0.03
318 2 0.00
320 12 0.01
321 130 0.08
322 173 0.10
323 133 0.08
324 522 0.31
325 191 0.11
326 89 0.05
328 2 0.00
329 146 0.09
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (323 bp):
CTTGTAATATCTGTATTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGATTTTTTTTACGA
GCATCTGAATCTTGTTTCGATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATATTA
GAAGCATGAAAAAACCTCAATTTTTTTGGTGATGAATAATAAATTTATTTTTAGTATTCTGGCAA
AAAATTGAGAAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTT
TTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTC
Found at i:2034 original size:647 final size:643
Alignment explanation
Indices: 1--2245 Score: 3186
Period size: 647 Copynumber: 3.5 Consensus size: 643
*
1 CTTGTAATATCTGTATTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGATTTTTTTTTACA
1 CTTGTAATATCT-TTTTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGATTTTTTTTTACA
* *
66 AGCATCTGAATCTTGTTTCGATATGATTTGAAATAAATTCGGAATAAAAATGGAAAAATCATATT
65 AGCATCTGAATCTTGTTTCGATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATATT
* * * *
131 AGAAGCATGAAAAAACTCTTAATTTTTTTGGTGATGAATAATAAATTTTTTTTAGTATTCTGGCA
130 AGAAGCGTGAAAAAAC-CTCAATTTTTTTGGTGATGAATTATAAATTTTTTTTAGTATTGTGGCA
* * *
196 AAAAATTGAGAAATAAAATTTTCGTGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTT
194 AAAAATTGAGAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTT
* *
261 TTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCATGATTTCTGGCAGAAAGGACTCC
259 TTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCATGATTTTTGGC-GGAAGGACTCC
* * *
326 TTGTAATATCTG---T-AT---AACAAATCTCAGGCACAATAGATTTAAGAATTTTTTTTACGAG
323 TTGTAATATCTGTATTCATCAAAACAAATCTCAGACACAATGGATTTAAGGATTTTTTTTACGAG
384 CATCTGAATCTTATTTCAATATAATTTGAAATATATTCGG-ATAAAAATGGAAAAATGATATTAG
388 CATCTGAATCTTATTTCAATATAATTTGAAATATATTCGGAATAAAAATGGAAAAATGATATTAG
448 AAGCATAGAAAAAACTCTTAATTTTTTTGGTGATGAATAATAAAAAAAATTTTAGTATTCTGGC-
453 AAGCAT-GAAAAAACTCTTAATTTTTTTGGTGATGAATAATAAAAAAAATTTTAGTATTCTGGCA
512 AAAAATTGAGAAAAAAAAAATTGGTTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
517 AAAAATTGAGAAAAAAAAAATTGGTTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
* *
577 TTGGCTAAAAATGCAATTCGGCGCACCGCCTCAGTTTTGCATGATTTTTGGGAGAAAGATTC
582 TTGGCTAAAAATGCAATTCGGCGCACCGCCTCAGTTTTGCATGATTTTTGGCAGAAAGACTC
639 CTTGTAATATCTTTATTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGATTTTTTTTTCTT
1 CTTGTAATATCTTT-TTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGA--TTTTTTT-TT
* * * * *
704 ACAAGCATCTGATTCTTGTTTCGATAGAATATAAAATAAATTCGGAATAAAAATGGAAAACTGAT
62 ACAAGCATCTGAATCTTGTTTCGATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGAT
769 ATTAG-AGCCGTGAAAAAATCCTCAATTTTTTTGGTGATGAATTATAAAATTTTTTTTTAGTATT
127 ATTAGAAG-CGTGAAAAAA-CCTCAATTTTTTTGGTGATGAATTAT-AAA-TTTTTTTTAGTATT
833 GTGGC-AAAAATTGAGAAAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCA
188 GTGGCAAAAAATTGAG-AAAAAAAAA-TTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCA
* * * * *
897 TCACGGTTTTTGGCTGAAAATGCATTTCGGCGGACCGGCTCAATTTTGCATGATTCTTGGCAGAA
251 TCACGGTTTTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCATGATTTTTGGCGGAA
* * ** * *
962 AGATTATTTGGAATATCTGTATTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGATTTTTT
316 GGACTCCTTGTAATATCTGTATTCATCAAAACAAATCTCAGACACAATGGATTTAAGGATTTTTT
** * *
1027 TTACGAGCATCTGAATCTTATTTTGATATAATTTGAAATATATTCGGAATAGAAATGGAAAAATC
381 TTACGAGCATCTGAATCTTATTTCAATATAATTTGAAATATATTCGGAATAAAAATGGAAAAATG
** *
1092 ATATTAGAAGCATGAAAAAACTCTTAATTTTTTTGGTGATGAATAAT-AAAAATTTTTTAATATT
446 ATATTAGAAGCATGAAAAAACTCTTAATTTTTTTGGTGATGAATAATAAAAAAAATTTTAGTATT
** ** * *
1156 CTGGCAAAAAATTGAGAAATGAAATTTTCGGATCAGTTTTTAGCCGAAATCGTGTACTAATCATC
511 CTGGCAAAAAATTGAGAAAAAAAAAATT-GGTTCAGTTTTTAGCCGAAATCGTGTACTAACCATC
* * * *
1221 ACGGTTTTTGACTAAAAATGCATTTCGGCGGACCGGCTCAGTTTTGCATGATTTTTGGCAGAAAG
575 ACGGTTTTTGGCTAAAAATGCAATTCGGCGCACCGCCTCAGTTTTGCATGATTTTTGGCAGAAAG
1286 ACTC
640 ACTC
* *
1290 CTTGTAATAT-TTGTATTCATCAAAACAAATCTCAACCACAATAGG-TTTAAGGATTTTTTTCTA
1 CTTGTAATATCTT-T-TTCATCAAAACAAATCTCAGCCACAAT-GGATTTAAGGATTTTTTT-TT
* * * * *
1353 ACGAGCATTTCAATCTTGTTTCGATATTATTTGAAATAAATTCGGAATAAAAATGGAAAAATAAT
62 ACAAGCATCTGAATCTTGTTTCGATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGAT
*
1418 ATTAGAAGCGTGAAAAAATCCTCAATTTTTTTTGTGATGAATTAT-AATTTATTTTTAGTATTGT
127 ATTAGAAGCGTGAAAAAA-CCTCAATTTTTTTGGTGATGAATTATAAATTT-TTTTTAGTATTGT
* *
1482 GGC-AGAAATTGAGAAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACTATCA
190 GGCAAAAAATTGAG-AAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCA
** * * * *
1546 ATGTTTTTGCCTAAAAATGCATTTCGACGCACCGGCTCAGTTTTGCATGATTTTTGACGGAGGGA
254 CGGTTTTTGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCATGATTTTTGGCGGAAGGA
1611 CTCCTTGTAATATCTGTATTCATCAAAACAAATCTCAGACACAATGGATTTAAGGATTTTTTTTT
319 CTCCTTGTAATATCTGTATTCATCAAAACAAATCTCAGACACAATGGATTTAAGGA-TTTTTTTT
*
1676 ACGAGCATCTGAATCTTATTTCAATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGAT
383 ACGAGCATCTGAATCTTATTTCAATATAATTTGAAATATATTCGGAATAAAAATGGAAAAATGAT
* *
1741 ATTAGAAGCATGAAAAAACTCTTAAATTTTTTTGGTAATGAATAATAAAAAAAGTTTTAGTATTC
448 ATTAGAAGCATGAAAAAACTCTT-AATTTTTTTGGTGATGAATAATAAAAAAAATTTTAGTATTC
*
1806 TGGCAAAAAATTAAGAAAAAAAAAATTGGTTCAGTTTTTAGCCGAAATCGTGTACTAACCATCAC
512 TGGCAAAAAATTGAGAAAAAAAAAATTGGTTCAGTTTTTAGCCGAAATCGTGTACTAACCATCAC
*
1871 GGTTTTTGGCTAAAAATGCAATTCGGCGCACCGCCTCAGTTTTGCATGATTTTTTGCAGAAAGAC
577 GGTTTTTGGCTAAAAATGCAATTCGGCGCACCGCCTCAGTTTTGCATGATTTTTGGCAGAAAGAC
*
1936 TG
642 TC
* * * * * *
1938 CTTG-AATTAACTATTTTCATC-GAACAAAATCTCGGCCACAATGGTTTTAACGATTTGTTTTTA
1 CTTGTAA-TATCT-TTTTCATCAAAAC-AAATCTCAGCCACAATGGATTTAAGGATTTTTTTTTA
* * * *
2001 CGAGTATCTAAATCTTGTTTCAATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATA
63 CAAGCATCTGAATCTTGTTTCGATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATA
** * * * * * **
2066 TTAGAAGCGTG-AAAAACCTTCAATTATTTAAGG-GTTAAATTATATATTTTTCTTACTATTACG
128 TTAGAAGCGTGAAAAAACC-TCAATT-TTTTTGGTGATGAATTATAAATTTTTTTTAGTATTGTG
* *
2129 GCAAAAAATTGAGAAAAAAAAATTT-GGGTTAGTTTTTAGCCGAAATTGTGTACTAACCAAT-AC
191 GCAAAAAATTGAGAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACC-ATCAC
* * *
2192 GGTTTTTGACTAAAAATGCATTTCGGCGC-CTCGGCTTAGTTTAGCATGATTTTT
255 GGTTTTTGGCTAAAAATGCATTTCGGCGCAC-CGGCTCAGTTTTGCATGATTTTT
2246 TTTTTGAAAT
Statistics
Matches: 1433, Mismatches: 136, Indels: 69
0.87 0.08 0.04
Matches are distributed among these distances:
637 1 0.00
638 50 0.03
640 9 0.01
641 97 0.07
642 14 0.01
643 41 0.03
644 94 0.07
645 80 0.06
646 193 0.13
647 226 0.16
648 157 0.11
649 163 0.11
650 135 0.09
651 171 0.12
652 2 0.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (643 bp):
CTTGTAATATCTTTTTCATCAAAACAAATCTCAGCCACAATGGATTTAAGGATTTTTTTTTACAA
GCATCTGAATCTTGTTTCGATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATATTA
GAAGCGTGAAAAAACCTCAATTTTTTTGGTGATGAATTATAAATTTTTTTTAGTATTGTGGCAAA
AAATTGAGAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT
TGGCTAAAAATGCATTTCGGCGCACCGGCTCAGTTTTGCATGATTTTTGGCGGAAGGACTCCTTG
TAATATCTGTATTCATCAAAACAAATCTCAGACACAATGGATTTAAGGATTTTTTTTACGAGCAT
CTGAATCTTATTTCAATATAATTTGAAATATATTCGGAATAAAAATGGAAAAATGATATTAGAAG
CATGAAAAAACTCTTAATTTTTTTGGTGATGAATAATAAAAAAAATTTTAGTATTCTGGCAAAAA
ATTGAGAAAAAAAAAATTGGTTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
CTAAAAATGCAATTCGGCGCACCGCCTCAGTTTTGCATGATTTTTGGCAGAAAGACTC
Found at i:3005 original size:317 final size:318
Alignment explanation
Indices: 2320--3048 Score: 861
Period size: 317 Copynumber: 2.3 Consensus size: 318
2310 GTGATAAATT
* * * *
2320 TTTTTTGAATATTATGGCAAAAAATTGAGAATAAAAATTTTCGGGTCAATTTTTAGCCGAAAATC
1 TTTTTTAAATATTATGGC-AAAAATTGAGAAAAAAAAATTTCGGGTCAGTTTTTAGCCG-AAATC
* * *
2385 GTGTATTAACCATCACGGTTTTTAGCTAAAAATGCATTTCGGCGCCCCATCTCAGTTTTGCATGA
64 GTGTACTAACCATAACGGTTTTTAGCTAAAAATGCATTT----GCCCCATCTCAGTTTTACATGA
* * *
2450 TTTTTTTGCAGAAAGACTCCTTCAAATATCTTTATTCATCAAACCAAATCTCAGCCAGAATGGAT
125 TTTTTTGGCAGAAAGACTCCTTCAAATATCTATATTCATCAAACCAAATCTCAGCCACAATGGAT
* * * *
2515 TTAAAGATTTGTTTTTACGAGTATCTGAATCTTGTTTCAACATAATTTGAAATAAATTCGGAATA
190 TTAAAGATTTGTATTTACGAGCATCTGAATCTTGTTTCAACATAAATAGAAATAAATTCGG-A-A
* * * * *
2580 AAAATGGAAAAATGATATTAGAAGCATGAAAAAACCTTTAATTTTTTTGGTGATGAATTACATAT
253 AAAATGCAAAAACGATATTAGAAGCATGAAAAAACCTTCAATATTTTTGGTCATGAATTA-ATAT
2645 TA
317 TA
* *
2647 TTTTTTGAATATTATGGTC-AAAATTGAG-GAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCG
1 TTTTTTAAATATTATGG-CAAAAATTGAGAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCG
* * * *
2710 TGTACTAACCATTACGGTTTTTGGCTAAGAATGCATTT-CCCGA-CTCAGTTTTACATGA-TTTT
65 TGTACTAACCATAACGGTTTTTAGCTAAAAATGCATTTGCCCCATCTCAGTTTTACATGATTTTT
* * * *
2772 TGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAG
130 TGGCAGAAAGACTCCTTCAAATATCTATATTCATCAAACCAAATCTCAGCCACAATGGATTTAAA
* ** *
2837 GATTTGTATTTACGAGCATCTGAATCTTGTTTCGAGTTAAATAGAACTAATAACTT-GG-AAAAA
195 GATTTGTATTTACGAGCATCTGAATCTTGTTTCAACATAAATAG-A--AATAAATTCGGAAAAAA
*
2900 TGCAAAAACGATATTAGAAGCGTG-AAAAACCTGTCAATATTTTTGG-CATTGAATT-ATA-TA
257 TGCAAAAACGATATTAGAAGCATGAAAAAACCT-TCAATATTTTTGGTCA-TGAATTAATATTA
* *
2960 TTTTTCTAAATATT-TTGCAAAATATTGAGAAAAAAAAACATTTCGGGTCAGTTTTTAACCGAAA
1 TTTTT-TAAATATTATGGCAAAA-ATTGAG-AAAAAAAA-ATTTCGGGTCAGTTTTTAGCCGAAA
* *
3024 TCATGTACTAATCATAACGGTTTTT
62 TCGTGTACTAACCATAACGGTTTTT
3049 TTTACGAGCA
Statistics
Matches: 352, Mismatches: 38, Indels: 34
0.83 0.09 0.08
Matches are distributed among these distances:
312 1 0.00
313 12 0.03
314 16 0.05
315 9 0.03
316 49 0.14
317 145 0.41
318 15 0.04
319 6 0.02
320 7 0.02
324 40 0.11
325 25 0.07
326 9 0.03
327 17 0.05
328 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (318 bp):
TTTTTTAAATATTATGGCAAAAATTGAGAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGT
GTACTAACCATAACGGTTTTTAGCTAAAAATGCATTTGCCCCATCTCAGTTTTACATGATTTTTT
GGCAGAAAGACTCCTTCAAATATCTATATTCATCAAACCAAATCTCAGCCACAATGGATTTAAAG
ATTTGTATTTACGAGCATCTGAATCTTGTTTCAACATAAATAGAAATAAATTCGGAAAAAATGCA
AAAACGATATTAGAAGCATGAAAAAACCTTCAATATTTTTGGTCATGAATTAATATTA
Found at i:3177 original size:855 final size:846
Alignment explanation
Indices: 1487--3048 Score: 1903
Period size: 854 Copynumber: 1.8 Consensus size: 846
1477 ATTGTGGCAG
* * *
1487 AAATTGAGAAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACTATCAATGTTT
1 AAATTGAGAAAAAAAAAATTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCAAGGTTT
* * **
1552 TTGCCTAAAAATGCATTTCGACGCACCGGCTCAGTTTTGCATGATTTTTGACGGAGGGACTCCTT
66 TTGCCTAAAAATGCATTTCGACGCACCAGCTCAGTTTTGCATGATTTTTGACAGAAAGACTCCTT
** * *
1617 GTAATATCTGTATTCATCAAAACAAATCTCAGACACAATGGATTTAAGGATTTTTTTTTACGAGC
131 CAAATATCTGTATTCATCAAAACAAATCTCAGACACAATGGATTTAAAGATTTGTTTTTACGAGC
*
1682 ATCTGAATCTTATTTCAATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATATTAGA
196 ATCTGAATCTTATTTCAACATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATATTAGA
* * *
1747 AGCATGAAAAAACTCTTAAATTTTTTTGGTAATGAATAATAAAAAAAGTTTTAGTATTCTGGCAA
261 AGCATGAAAAAACTCTTAAATTTTTTTGGTAATGAATAACAAAAAAAGTTTTAATATTATGGC-A
*
1812 AAAATTAAGAAAAAAAAAATTGGTTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT
325 AAAATTAAGAAAAAAAAAATTGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT
* * * *
1877 TGGCTAAAAATGCAATTCGGCGCACCGCCTCAGTTTTGCATGATTTTTTGCAGAAAGACTGCTTG
390 TGGCTAAAAATGCAATT---CGCACCGACTCAGTTTTACATGATTTTTGGCAGAAAGACTCCTTG
* * * * * *
1942 AATTAACTATTTTCATCGAACAAAATCTCGGCCACAATGGTTTTAACGATTTGTTTTTACGAGTA
452 AAATAACTATATTCATCGAACAAAATCTCAGCCACAATGGATTTAACGATTTGTATTTACGAGCA
* * * *
2007 TCTAAATCTTGTTTCAATATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATATTAGAA
517 TCTAAATCTTGTTTCAATATAAATAGAAATAAATTCGG-A-AAAAATGCAAAAACGATATTAGAA
* * *
2072 GCGTGAAAAACCTTCAATTATTTAAGGGTTAAATTATATATTTTTCTTACTATTACGGCAAAAAA
580 GCGTGAAAAACCTTCAATTATTTAAGGATTAAATTATATATTTTTCTAAATATTACGGCAAAAAA
* * **
2137 TTGAGAAAAAAAAATTTGGGTTAGTTTTTAGCCGAAATTGTGTACTAACCAATACGGTTTTTGAC
645 TTGAGAAAAAAAAATTTGGGTCAGTTTTTAACCGAAATCATGTACTAACCAATACGGTTTTT-AC
* * * *** ***** * *
2202 TAAAAATGCATTTCGGCGCCTCGGCTTAGTTTAGCATGATTTTTTTTTTGAAATATTCAAAAAAA
709 TAAAAATGCATTTCGGCGCCTCGGATTAGATTAGCATAATAAATTCGGAAAAAAATACAAAAAAA
** * * ** * *
2267 AATATGTAATTCATCTCCAAAAAAGTATATAATTCGATTTTTTGTGATAAATTTTTTTTGAATAT
774 AATATGTAAACCATATCCAAAAAAGTAGATAAAACGA-TTTCTGAGATAAATTTTTTTTGAATAT
2332 TATGGCAAA
838 TATGGCAAA
* * * *
2341 AAATTGAG-AATAAAAATTTTCGGGTCAATTTTTAGCCGAAAATCGTGTATTAACCATCACGGTT
1 AAATTGAGAAAAAAAAAATTTCGGGTCAATTTTTAGCCG-AAATCGTGTACTAACCATCAAGGTT
* * *
2405 TTTAG-CTAAAAATGCATTTCGGCGCCCCATCTCAGTTTTGCATGATTTTTTTG-CAGAAAGACT
65 TTT-GCCTAAAAATGCATTTCGACGCACCAGCTCAGTTTTGCATGA--TTTTTGACAGAAAGACT
* * * *
2468 CCTTCAAATATCTTTATTCATCAAACCAAATCTCAGCCAGAATGGATTTAAAGATTTGTTTTTAC
127 CCTTCAAATATCTGTATTCATCAAAACAAATCTCAGACACAATGGATTTAAAGATTTGTTTTTAC
* *
2533 GAGTATCTGAATCTTGTTTCAACATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATAT
192 GAGCATCTGAATCTTATTTCAACATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATAT
* * * * ** **
2598 TAGAAGCATGAAAAAAC-CTTTAATTTTTTTGGTGATGAATTACATATTATTTTTTGAATATTAT
257 TAGAAGCATGAAAAAACTCTTAAATTTTTTTGGTAATGAATAACAAAAAAAGTTTT-AATATTAT
* * * *
2662 GGTC-AAAATTGAG-GAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATTAC
321 GG-CAAAAATTAAGAAAAAAAAAATT-GGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCAC
* *
2725 GGTTTTTGGCTAAGAATGC-ATT-TC-CCGACTCAGTTTTACATGATTTTTGGCAGAAAGACTCC
384 GGTTTTTGGCTAAAAATGCAATTCGCACCGACTCAGTTTTACATGATTTTTGGCAGAAAGACTCC
* * * *
2787 TTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTATTTACGA
449 TTGAAATAACTATATTCATCGAACAAAATCTCAGCCACAATGGATTTAACGATTTGTATTTACGA
* * *
2852 GCATCTGAATCTTGTTTCGAGT-TAAATAGAACTAATAACTT-GG-AAAAATGCAAAAACGATAT
514 GCATCTAAATCTTGTTTC-AATATAAATAG-A--AATAAATTCGGAAAAAATGCAAAAACGATAT
** * **
2914 TAGAAGCGTGAAAAACCTGTCAA-TATTTTTGGCATTGAATTATATATTTTTCTAAATATT-TTG
575 TAGAAGCGTGAAAAACCT-TCAATTATTTAAGG-ATTAAATTATATATTTTTCTAAATATTACGG
* *
2977 CAAAATATTGAGAAAAAAAAACATTTCGGGTCAGTTTTTAACCGAAATCATGTACTAATC-ATAA
638 CAAAAAATTGAG-AAAAAAAA-ATTT-GGGTCAGTTTTTAACCGAAATCATGTACTAACCAAT-A
3041 CGGTTTTT
699 CGGTTTTT
3049 TTTACGAGCA
Statistics
Matches: 613, Mismatches: 78, Indels: 38
0.84 0.11 0.05
Matches are distributed among these distances:
847 54 0.09
848 146 0.24
849 10 0.02
850 39 0.06
851 7 0.01
853 39 0.06
854 159 0.26
855 152 0.25
856 7 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (846 bp):
AAATTGAGAAAAAAAAAATTTCGGGTCAATTTTTAGCCGAAATCGTGTACTAACCATCAAGGTTT
TTGCCTAAAAATGCATTTCGACGCACCAGCTCAGTTTTGCATGATTTTTGACAGAAAGACTCCTT
CAAATATCTGTATTCATCAAAACAAATCTCAGACACAATGGATTTAAAGATTTGTTTTTACGAGC
ATCTGAATCTTATTTCAACATAATTTGAAATAAATTCGGAATAAAAATGGAAAAATGATATTAGA
AGCATGAAAAAACTCTTAAATTTTTTTGGTAATGAATAACAAAAAAAGTTTTAATATTATGGCAA
AAATTAAGAAAAAAAAAATTGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT
GGCTAAAAATGCAATTCGCACCGACTCAGTTTTACATGATTTTTGGCAGAAAGACTCCTTGAAAT
AACTATATTCATCGAACAAAATCTCAGCCACAATGGATTTAACGATTTGTATTTACGAGCATCTA
AATCTTGTTTCAATATAAATAGAAATAAATTCGGAAAAAATGCAAAAACGATATTAGAAGCGTGA
AAAACCTTCAATTATTTAAGGATTAAATTATATATTTTTCTAAATATTACGGCAAAAAATTGAGA
AAAAAAAATTTGGGTCAGTTTTTAACCGAAATCATGTACTAACCAATACGGTTTTTACTAAAAAT
GCATTTCGGCGCCTCGGATTAGATTAGCATAATAAATTCGGAAAAAAATACAAAAAAAAATATGT
AAACCATATCCAAAAAAGTAGATAAAACGATTTCTGAGATAAATTTTTTTTGAATATTATGGCAA
A
Found at i:5812 original size:2 final size:2
Alignment explanation
Indices: 5805--5835 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5795 AACATTATTA
5805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5836 AAAGAGATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18288 original size:13 final size:13
Alignment explanation
Indices: 18270--18294 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18260 AAATAGAGAA
18270 CATTTGAAGTTTT
1 CATTTGAAGTTTT
18283 CATTTGAAGTTT
1 CATTTGAAGTTT
18295 GAATTCCGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (13 bp):
CATTTGAAGTTTT
Found at i:18559 original size:19 final size:18
Alignment explanation
Indices: 18526--18561 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18516 ATTTGTTGCA
*
18526 TGATTGTTTTTTTTTTGT
1 TGATTGTTTTGTTTTTGT
18544 TGATTCGTTTTGTTTTTG
1 TGATT-GTTTTGTTTTTG
18562 GTGAATTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.06, C:0.03, G:0.19, T:0.72
Consensus pattern (18 bp):
TGATTGTTTTGTTTTTGT
Done.