Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020775.1 Corchorus olitorius cultivar O-4 contig20808, 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: 9464
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:2007 original size:17 final size:17
Alignment explanation
Indices: 1985--2017 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1975 TTGTCACACC
*
1985 AAATCACCTTGATGATT
1 AAATCACCATGATGATT
2002 AAATCACCATGATGAT
1 AAATCACCATGATGAT
2018 CTTGAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (17 bp):
AAATCACCATGATGATT
Found at i:6438 original size:322 final size:324
Alignment explanation
Indices: 5853--6668 Score: 1009
Period size: 322 Copynumber: 2.5 Consensus size: 324
5843 TTTTTTTTGT
* * * * * * * * **
5853 TTTTGCATGATATTTGACGTAAATAATCCTTGAAATATCTACATTTATCGAACAAAATCCCAGCC
1 TTTTGCATGATTTTTGGCG-AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
* * * * * *
5918 ACGTTCGATTTAAGTATTTGCTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
65 ACATTAGATTTAAGGATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * * *
5983 TTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGTCCGTCAATCTTTTTGGCGTTGAA
130 TTCGGAAAAAAATGGAAAAATGATATTAAAAGCATGAAAAGACCATCAATCTTTTTGGCGTTGAA
* **
6048 TTATATATATTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTCTCCGATCAGTTTTTAGC
195 TTATATATATTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAATCTCCGATCAGTTTTTAGC
* * * *
6113 CG-AAATCGTGTACTAACCATCACAGTTTTT-GGCTAAAAACGCG-TTCCCGAGTCTCGACTCAA
260 CGAAAATCATGTACTAACCATCACAGTTTTTGGGATAAAAACGCGTTTCCCGAGCCCCGACTCAA
*
6175 TTTTGCATGATTTTTGGCGCAAAGACTACTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGGCG-AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
* *
6240 ACATTGGATATAAGGATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
65 ACATTAGATTTAAGGATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
*
6305 TTCGGAAAAAAATTGGAAAAATGATATTAAAAGCATGAAAAGACCATCAATCTTTTTGGTGTTGA
130 TTCGGAAAAAAA-TGGAAAAATGATATTAAAAGCATGAAAAGACCATCAATCTTTTTGGCGTTGA
* *
6370 ATTATATAT-TTTATCTGAGTATTGTGGC-AAAAATTCAGAAAAACAAAT-TCGGGTCAGTTTTT
194 ATTATATATATTT-TCTGAGTATTGTGGCAAAAAATTCAGAAAAA-AAATCTCCGATCAGTTTTT
** ** * *
6432 AGCCGAAAATCATGTACTAACCATCATGGTTTTTGGGATAAAAACGCGTTTCGGGGGCCCCGGCT
257 AGCCGAAAATCATGTACTAACCATCACAGTTTTTGGGATAAAAACGCGTTTCCCGAGCCCCGACT
*
6497 CAG
322 CAA
* * *
6500 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCTTCTAACCAATCTCAGGCT
1 TTTTGCATGATTTTTGGC-GAAAGACTCCTTGAAATATCTATATTCATCAAACCAA----ATG-T
* * *
6565 CTAAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGGTTTAATTAG
60 C--AGCCACATTAGATTTAAGGATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* *
6630 AAA-TAGATTCGG-AAAAAATAGAAAAATGATATTTAAAGC
123 AAATTA-ATTCGGAAAAAAATGGAAAAATGATATTAAAAGC
6669 GAGAAAATAT
Statistics
Matches: 427, Mismatches: 52, Indels: 22
0.85 0.10 0.04
Matches are distributed among these distances:
322 157 0.37
323 97 0.23
324 12 0.03
325 63 0.15
326 1 0.00
329 2 0.00
330 21 0.05
331 8 0.02
332 66 0.15
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (324 bp):
TTTTGCATGATTTTTGGCGAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCA
CATTAGATTTAAGGATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAAT
TCGGAAAAAAATGGAAAAATGATATTAAAAGCATGAAAAGACCATCAATCTTTTTGGCGTTGAAT
TATATATATTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAATCTCCGATCAGTTTTTAGCC
GAAAATCATGTACTAACCATCACAGTTTTTGGGATAAAAACGCGTTTCCCGAGCCCCGACTCAA
Found at i:7388 original size:882 final size:884
Alignment explanation
Indices: 5372--8125 Score: 4264
Period size: 882 Copynumber: 3.1 Consensus size: 884
5362 TTCTTGTTTC
* * * * *
5372 GATTTGGTTTTACGAGCATCGGAATCTTGTTTCGATTTAAATAGAAATTAAATCCG-AAAAAATT
1 GATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATT
*
5436 GGAAAAATGATATTATAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTAT
66 GGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTAT
* * *
5501 CTGAGTATTGTGGAAAAAAAGTCAGAAAAA-AAA-TCGGGCCAGTTTTTAGCCGAAAATCGTGTA
131 CTGAGTATTGTGG-CAAAAATTCAGAAAAACAAATTCGGGTCAGTTTTTAGCCGAAAATCGTGTA
5564 CTAACCATCATGGTTTTTGGGATAAAAACGCGTTTCGGGGGCCCC-GCTCAGTTTTGCATGATTT
195 CTAACCATCATGGTTTTTGGGATAAAAACGCGTTTCGGGGGCCCCGGCTCAGTTTTGCATGATTT
* * * *
5628 TTGGCAGAAAGACTCCTAGAAATATCTATATTCATCTAACCAATATCAGGCTCTGAGCCACATTA
260 TTGGCAGAAAGACTCCTTGAAATATCTATATTCTTCTAACCAATCTCAGGCTCTAAGCCACATTA
*
5693 GATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGTTTTAATTAGAAATAGATTCGGA
325 GATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGATTCGG-
5758 AAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAA-TTTTTTTTGCATTGAATTGT
389 AAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTTGCATTGAATTGT
* * * *
5822 GTA-TTTTTTGCCGAAAATATATTTTTTTTGTTTTTGCATGATATTTGACGTAAATAATCCTTGA
454 GTATTTTTTTG-CGGAAA-ATATTTTTTTTATTTTTGCATGATTTTTGACGTAAATACTCCTTGA
* * * *
5886 AATATCTACATTTATCGAACAAAATCCCAGCCACGTTCGATTTAAGTATTTGCTTTTACGAGCAT
517 AATATCTATATTCATCGAACAAAATCCCAGCCACGTTCGATATAAGTATTTGTTTTTACGAGCAT
5951 CTGAATCTTGTTTCAATTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGC
582 CTGAATCTTGTTTCAATTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGC
*
6016 GTGAAAAG-TCCGTCAATCTTTTTGGCGTTGAATTATATATATTTTCTGAGTATTGTGGCAAAAA
647 GTGAAAAGCT-CGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAA
* *
6080 ATTGAGAAAAAACTTCTCCGATCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGG
711 ATTGAGAAAAAACTTTTCCGATCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
* * * *
6145 CTAAAAACGCGTTCCCGAGTCTCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTACTTGAAA
776 CTAAAAACGCGTTCCCGAGCCCCGACTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAA
*
6210 TATCTATATTCATCAAACCAAATGTCAGCCACATTGGATATAAG
841 TATCTATATTCATCAAACCAACTGTCAGCCACATTGGATATAAG
6254 GATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATT
1 GATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATT
*
6319 GGAAAAATGATATTAAAAGCATGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTAT
66 GGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTAT
*
6384 CTGAGTATTGTGGCAAAAATTCAGAAAAACAAATTCGGGTCAGTTTTTAGCCGAAAATCATGTAC
131 CTGAGTATTGTGGCAAAAATTCAGAAAAACAAATTCGGGTCAGTTTTTAGCCGAAAATCGTGTAC
6449 TAACCATCATGGTTTTTGGGATAAAAACGCGTTTCGGGGGCCCCGGCTCAGTTTTGCATGATTTT
196 TAACCATCATGGTTTTTGGGATAAAAACGCGTTTCGGGGGCCCCGGCTCAGTTTTGCATGATTTT
6514 TGGCAGAAAGACTCCTTGAAATATCTATATTCTTCTAACCAATCTCAGGCTCTAAGCCACATTAG
261 TGGCAGAAAGACTCCTTGAAATATCTATATTCTTCTAACCAATCTCAGGCTCTAAGCCACATTAG
*
6579 ATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGGTTTAATTAGAAATAGATTCGG-A
326 ATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGATTCGGAA
*
6643 AAAAATAGAAAAATGATATTTAAAGCGAG-AAAATATTTAAATTTTTTTTTGCATTGAATTGTGT
391 AAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTTGCATTGAATTGTGT
*
6707 ATTTTTTTGCGGAAAATATTTTTTTTATTTTTGCATGATTTTTGACGTAAATACTCTTTGAAATA
456 ATTTTTTTGCGGAAAATATTTTTTTTATTTTTGCATGATTTTTGACGTAAATACTCCTTGAAATA
*
6772 TCTATATTCATCGAACAAAATCCCAGCCACGTTCGATATAAGTATTTGTTTTTACGAGTATCTGA
521 TCTATATTCATCGAACAAAATCCCAGCCACGTTCGATATAAGTATTTGTTTTTACGAGCATCTGA
6837 ATCTTGTTTCAATTTAATTAAAAATTAATTCGG-AAAAAATGGAAAAACGATATTAGAAGCGTGA
586 ATCTTGTTTCAATTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGA
* *
6901 AAAGCTCGTCAATCTTTTTGGCATTGAATTATATATTTTTGTCTGAGTATTGTGGCAAACAATTG
651 AAAGCTCGTCAATCTTTTTGGCGTTGAATTATATATTTTT-TCTGAGTATTGTGGCAAAAAATTG
* *
6966 AGAAAAAACTTTTCCGATCAGTGTTTAGCCGAAATCGTGTACT-ACCATCACGGTTTTTGCCTAA
715 AGAAAAAACTTTTCCGATCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
7030 AAACGCGTTCCCGAGCCCCGACTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
780 AAACGCGTTCCCGAGCCCCGACTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
*
7095 TATATTCATCAAATCAACTGTCAGCCACATTGGATATAAG
845 TATATTCATCAAACCAACTGTCAGCCACATTGGATATAAG
* *
7135 GATTTGATTTTACGAGTATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAATT
1 GATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATT
* * *
7200 GGAAAAATGATATTAAAAGCGTGAAAAG-CTCGTCAATTTTTTTGGCGTTGAATTATATATTTTA
66 GGAAAAATGATATTAAAAGCGTGAAAAGAC-CATCAATCTTTTTGGTGTTGAATTATATATTTTA
7264 TCTGAGTATTGTGGCAAAGAATTCAGAAAAACAAATTCGGGTCAGTTTTTAGCCGAAAATCGTGT
130 TCTGAGTATTGTGGCAAA-AATTCAGAAAAACAAATTCGGGTCAGTTTTTAGCCGAAAATCGTGT
* *
7329 ACTAACCATCATGGTTTTTAGGCTAAAAACGCGTTTCGGGGGCCCCGGCTCAGTTTTGCATGATT
194 ACTAACCATCATGGTTTTTGGGATAAAAACGCGTTTCGGGGGCCCCGGCTCAGTTTTGCATGATT
* *
7394 TTTGGCAGATAGACTCCTTGAAATATCTATATTCTTCTAACCAATCTTAGGCTCTGAA-CCACAT
259 TTTGGCAGAAAGACTCCTTGAAATATCTATATTCTTCTAACCAATCTCAGGCTCT-AAGCCACAT
* * *
7458 TAGATTTAAGGATTTGATTTTACGAGCATTTGAATATTGTTTCGATTTAATTAGAAATAGATACG
323 TAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGATTCG
*
7523 GAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTTGCGTTGAATTG
388 GAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTTGCATTGAATTG
* * * *
7588 TGTATTTTTCTGCGGAAAATATTTTTTTTTATTTTTGCATGATTTTTGGCGCAAAGACTCCTTGA
453 TGTATTTTTTTGCGGAAAATA-TTTTTTTTATTTTTGCATGATTTTTGACGTAAATACTCCTTGA
* * ** * * * *
7653 AATATCTATATTCATCAAACCAAATGTCAGCCACATTGGATATAAGGATTAGTTTTTACGAGCAT
517 AATATCTATATTCATCGAACAAAATCCCAGCCACGTTCGATATAAGTATTTGTTTTTACGAGCAT
* * * * * *
7718 CTGAATCTTGTCTCGATTTAAATAGAAATTAATTCGGAAAAAAATTGGAAAAATGATATTAAAAG
582 CTGAATCTTGTTTCAATTTAATTAAAAATTAATTCGGAAAAAAA-TGGAAAAACGATATTAGAAG
* * *
7783 CGTGAAAAGAC-CATCAATCTTTTTGGTGTTGAATTATATATTTTATCTGAGTATTGTGGCAAAA
646 CGTGAAAAG-CTCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAA
* *** * * *
7847 AATTCAGAAAAAAAAAAAATTCGGGTCAGTTTTTAGCCGAAAATCGTGTACTAACCATCATGGTT
710 AATT--G-AGAAAAAACTTTTCCGATCAGTTTTTAGCCG-AAATCGTGTACTAACCATCACGGTT
** * * *
7912 TTTAGGCTAAAAACGCGTTTCGGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG-TAAGACT
771 TTT-GGCTAAAAACGCG-TTCCCGAGCCCCGACTCAGTTTTGCATGATTTTTGGC-GCAAAGACT
* * * *
7976 CCTTAAAATATCTATATTCATCTAACCAATCTTAGGCTCTGAGCCACATTAGATTTAAG
833 CCTTGAAATATCTATATTCATCAAACCAA-C-T--G-TC--AGCCACATTGGATATAAG
* * *
8035 GATTTGCTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAA-TAGATTC-GAAAAAAAA
1 GATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA-ATTCGGAAAAAAAT
* * * *
8098 TAGAAAAATAATATTTAAAGCGAGAAAA
65 TGGAAAAATGATATTAAAAGCGTGAAAA
8126 ATACTTCAAT
Statistics
Matches: 1729, Mismatches: 110, Indels: 49
0.92 0.06 0.03
Matches are distributed among these distances:
880 1 0.00
881 324 0.19
882 509 0.29
883 177 0.10
884 130 0.08
885 271 0.16
886 28 0.02
887 57 0.03
888 2 0.00
889 24 0.01
890 12 0.01
891 14 0.01
892 12 0.01
893 65 0.04
894 2 0.00
895 1 0.00
897 1 0.00
898 2 0.00
899 34 0.02
900 63 0.04
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (884 bp):
GATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATT
GGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTAT
CTGAGTATTGTGGCAAAAATTCAGAAAAACAAATTCGGGTCAGTTTTTAGCCGAAAATCGTGTAC
TAACCATCATGGTTTTTGGGATAAAAACGCGTTTCGGGGGCCCCGGCTCAGTTTTGCATGATTTT
TGGCAGAAAGACTCCTTGAAATATCTATATTCTTCTAACCAATCTCAGGCTCTAAGCCACATTAG
ATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGATTCGGAA
AAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTTGCATTGAATTGTGT
ATTTTTTTGCGGAAAATATTTTTTTTATTTTTGCATGATTTTTGACGTAAATACTCCTTGAAATA
TCTATATTCATCGAACAAAATCCCAGCCACGTTCGATATAAGTATTTGTTTTTACGAGCATCTGA
ATCTTGTTTCAATTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGA
AAAGCTCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA
GAAAAAACTTTTCCGATCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAA
AACGCGTTCCCGAGCCCCGACTCAGTTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCT
ATATTCATCAAACCAACTGTCAGCCACATTGGATATAAG
Found at i:7816 original size:231 final size:234
Alignment explanation
Indices: 7382--7831 Score: 547
Period size: 231 Copynumber: 1.9 Consensus size: 234
7372 CCCGGCTCAG
* * *
7382 TTTTGCATGATTTTTGGCAGATAGACTCCTTGAAATATCTATATTCTTCTAACCAATCTTAGGCT
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCAAACCAA---TAGGCT
* * * * *
7447 CTGAACCACATTAGATTTAAGGATTTGATTTTACGAGCATTTGAATATTGTTTCGATTTAATTAG
63 C-GAACCACATTAGATATAAGGATTAGATTTTACGAGCATCTGAATATTGTCTCGATTTAAATAG
* * * *
7512 AAATAGATACGGAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTTTT
127 AAATAGATACGGAAAAAAATAGAAAAATGATATTAAAAGCGAGAAAAACA-TTCAATTCTTTTTG
* *
7577 GCGTTGAATTGTGTATTTT-TCTGCGGAAAATATTTTTTTTTAT
191 GCGTTGAATTATATATTTTATCTGCGGAAAATATTTTTTTTTAT
*
7620 TTTTGCATGATTTTTGGC-GCAAAGACTCCTTGAAATATCTATATTCATCAAACCAA-ATG-TC-
1 TTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCAAACCAATAGGCTCG
* * * *
7681 AGCCACATTGGATATAAGGATTAGTTTTTACGAGCATCTGAATCTTGTCTCGATTTAAATAGAAA
65 AACCACATTAGATATAAGGATTAGATTTTACGAGCATCTGAATATTGTCTCGATTTAAATAGAAA
* * *
7746 TTA-ATTCGGAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCA-TCAA-TCTTTTTG
130 -TAGATACGGAAAAAAA-TAGAAAAATGATATTAAAAGCGAGAAAA-A-CATTCAATTCTTTTTG
*
7808 GTGTTGAATTATATATTTTATCTG
191 GCGTTGAATTATATATTTTATCTG
7832 AGTATTGTGG
Statistics
Matches: 183, Mismatches: 23, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
231 90 0.49
232 35 0.19
233 3 0.02
234 3 0.02
237 1 0.01
238 51 0.28
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (234 bp):
TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCAAACCAATAGGCTCGA
ACCACATTAGATATAAGGATTAGATTTTACGAGCATCTGAATATTGTCTCGATTTAAATAGAAAT
AGATACGGAAAAAAATAGAAAAATGATATTAAAAGCGAGAAAAACATTCAATTCTTTTTGGCGTT
GAATTATATATTTTATCTGCGGAAAATATTTTTTTTTAT
Found at i:8127 original size:567 final size:563
Alignment explanation
Indices: 7056--8680 Score: 2418
Period size: 567 Copynumber: 2.9 Consensus size: 563
7046 CCCGACTCAG
* *
7056 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAATCAACTGTCAGCC
1 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
* *
7121 ACATTGGATATAAGGATTTGATTTTACGAGTATCTGAATCTTGTTTCAATTTAATTAGAAATTAA
66 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAA
* *
7186 TTCGGAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGCTCGTCAATTTTTTTGGCGTTGA
131 TTCGGAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGCTCATCAATCTTTTTGGCGTTGA
* *
7251 ATTATATATTTTATCTGAGTATTGTGGCAAAGAATTCAG-AAAAACAAATTCGGGTCAGTTTTTA
196 ATTATATATTTTATCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAAATTCGGGTCAGTTTTTA
7315 GCCGAAAATCGTGTACTAACCATCATGGTTTTTAGGCTAAAAACGCGTTTCGGGGGCCCCGGCTC
261 GCCGAAAATCGTGTACTAACCATCATGGTTTTTAGGCTAAAAACGCGTTTCGGGGGCCCCGGCTC
*
7380 AGTTTTGCATGATTTTTGGCAGATAGACTCCTTGAAATATCTATATTCTTCTAACCAATCTTAGG
326 AGTTTTGCATGATTTTTGGCAGA-AGACTCCTTGAAATATCTATATTCATCTAACCAATCTTAGG
* *
7445 CTCTGAACCACATTAGATTTAAGGATTTGATTTTACGAGCATTTGAATATTGTTTCGATTTAATT
390 CTCTGAGCCACATTAGATTTAAGGATTTGATTTTACGAGCATCTGAATATTGTTTCGATTTAATT
* * *
7510 AGAAATAGATACGGAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTTTT
455 AGAAATAGATTCGAAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATACTTCAATTTTTTT
* * *
7575 TTGCGTTGAATTGTGTATTTTTCTGCGGAAAATATTTTTTTTTAT
520 TTGAGTTGAATTGTGTATTTTT-TGCCGAAAATATTTTATTTTAT
7620 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
* * * *
7685 ACATTGGATATAAGGATTAGTTTTTACGAGCATCTGAATCTTGTCTCGATTTAAATAGAAATTAA
66 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAA
*
7750 TTCGGAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGAC-CATCAATCTTTTTGGTGTTG
131 TTCGGAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAG-CTCATCAATCTTTTTGGCGTTG
7814 AATTATATATTTTATCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAAAAATTCGGGTCAGTTT
195 AATTATATATTTTATCTGAGTATTGTGGCAAAAAATTCAG--AAAAAAAAAATTCGGGTCAGTTT
7879 TTAGCCGAAAATCGTGTACTAACCATCATGGTTTTTAGGCTAAAAACGCGTTTCGGGGGCCCCGG
258 TTAGCCGAAAATCGTGTACTAACCATCATGGTTTTTAGGCTAAAAACGCGTTTCGGGGGCCCCGG
*
7944 CTCAGTTTTGCATGATTTTTGGCAGTAAGACTCCTTAAAATATCTATATTCATCTAACCAATCTT
323 CTCAGTTTTGCATGATTTTTGGCAG-AAGACTCCTTGAAATATCTATATTCATCTAACCAATCTT
*
8009 AGGCTCTGAGCCACATTAGATTTAAGGATTTGCTTTTACGAGCATCTGAATATTGTTTCGATTTA
387 AGGCTCTGAGCCACATTAGATTTAAGGATTTGATTTTACGAGCATCTGAATATTGTTTCGATTTA
*
8074 ATTAGAAATAGATTCGAAAAAAAATAGAAAAATAATATTTAAAGCGAGAAAAATACTTCAATTTT
452 ATTAGAAATAGATTCGAAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATACTTCAATTTT
*
8139 TTTTTGAGTTGAATTGTGTATTTTTTGCCGAAAATATTTTATTTTGT
517 TTTTTGAGTTGAATTGTGTATTTTTTGCCGAAAATATTTTATTTTAT
* * * * * * * **
8186 TTTTGCATGATTTTTGACGTAAATAGTCCTTGAAATATCTATATCCATCGAACAAAATCCCAGCC
1 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
* * * * * *
8251 ACGTTCGATATAAGTATTTGTTTTTACAAGCATCTGAATCTTATTTCAATTTAATTAAAAATTAA
66 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAA
* * *
8316 TTCGGAAAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAGCTCTTCAATCTTTTTGGCGTTGA
131 TTCGGAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGCTCATCAATCTTTTTGGCGTTGA
* *** * * *
8380 ATTATATATTTT-TGACTGAGTATTGTGGCAAAAAATTGAG-AAAAAACTTTTCCGATCAGTGTT
196 ATTATATATTTTAT--CTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAAATTCGGGTCAGTTTT
* * * ** * *
8443 TAGCCG-AAATCGTGTACTAACTATCACGG-TTTTAGGCTAAAAACACG-TTCCCGAGCCCCGAC
259 TAGCCGAAAATCGTGTACTAACCATCATGGTTTTTAGGCTAAAAACGCGTTTCGGGGGCCCCGGC
* * *
8505 TCAGTTTTGTATGATTTTTGGCGCGAAGACTCCTTGAAATATCTATATTCATCAAACCAA----A
324 TCAGTTTTGCATGATTTTTGGC-AGAAGACTCCTTGAAATATCTATATTCATCTAACCAATCTTA
* * * * *
8566 TG-TC--AGACACATTGGATATAAGGATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAA
388 GGCTCTGAGCCACATTAGATTTAAGGATTTGATTTTACGAGCATCTGAATATTGTTTCGATTTAA
* *
8628 TTAGAAATTA-ATTCGAAAAAAAAATAGGAAAAATGATATTAAAAGCGCGAAAA
453 TTAGAAA-TAGATTCG-AAAAAAAATA-GAAAAATGATATTTAAAGCGAGAAAA
8681 GACCATCAAT
Statistics
Matches: 973, Mismatches: 76, Indels: 33
0.90 0.07 0.03
Matches are distributed among these distances:
553 65 0.07
554 12 0.01
555 25 0.03
556 2 0.00
560 65 0.07
561 18 0.02
562 21 0.02
563 23 0.02
564 222 0.23
565 59 0.06
566 166 0.17
567 294 0.30
568 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (563 bp):
TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAA
TTCGGAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGCTCATCAATCTTTTTGGCGTTGA
ATTATATATTTTATCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAAATTCGGGTCAGTTTTTA
GCCGAAAATCGTGTACTAACCATCATGGTTTTTAGGCTAAAAACGCGTTTCGGGGGCCCCGGCTC
AGTTTTGCATGATTTTTGGCAGAAGACTCCTTGAAATATCTATATTCATCTAACCAATCTTAGGC
TCTGAGCCACATTAGATTTAAGGATTTGATTTTACGAGCATCTGAATATTGTTTCGATTTAATTA
GAAATAGATTCGAAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATACTTCAATTTTTTTT
TGAGTTGAATTGTGTATTTTTTGCCGAAAATATTTTATTTTAT
Found at i:9309 original size:886 final size:866
Alignment explanation
Indices: 7620--9464 Score: 3032
Period size: 886 Copynumber: 2.1 Consensus size: 866
7610 TTTTTTTTAT
7620 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
* *
7685 ACATTGGATATAAGGATTAGTTTTTACGAGCATCTGAATCTTGTCTCGATTTAAATAGAAATTAA
66 ACATTGGATATAAGGATTTGATTTTACGAGCATCTGAATCTTGTCTCGATTTAAATAGAAATTAA
* * * *
7750 TTCGGAAAAAAATTGGAAAAATGATATTAAAAGCGTGAAAAGACCATCAATCTTTTTGGTGTTGA
131 TTCGAAAAAAAATAGGAAAAATGATATTAAAAGCGCGAAAAGACCATCAATCTTTTTGGTATTGA
*
7815 ATTATATATTTTATCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAAAAATTCGGGTCAGTTTT
196 ATTATATATTTTATCTGAGTATAGTGGCAAAAAATTCA-AAAAAAAAAAAATTCGGGTCAGTTTT
*
7880 TAGCCGAAAATCGTGTACTAACCATCATGGTTTTTAGGCTAAAAACGCGTTTCGGGGGCCCCGGC
260 TAGCCGAAAATCGTG-A-TAACCACCATGGTTTTTAGGCTAAAAACGCGTTTCGGGGGCCCCGGC
* * *
7945 TCAGTTTTGCATGATTTTTGGCAGTAAGACTCCTTAAAATATCTATATTCATCTAACCAATCTTA
323 TCAGTTTTGCATGATTGTTGGCAGGAAGACTCCTTAAAATATCTATATTCATCTAACCAATCTCA
8010 GGCTCTGAGCCACATTAGATTTAAGGATTTGCTTTTACGAGCATCTGAATATTGTTTCGATTTAA
388 GGCTCTGAGCCACATTAGATTTAAGGATTTGCTTTTACGAGCATCTGAATATTGTTTCGATTTAA
8075 TTAGAAATAGATTCGAAAAAAAATAGAAAAATAATATTTAAAGCGAGAAAAATACTTCAATTTTT
453 TTAGAAATAGATTCGAAAAAAAATAGAAAAATAATATTTAAAGCGAGAAAAATACTTCAATTTTT
** *
8140 TTTTGAGTTGAATTGTGTATTTTTTGCCGAAAATATTTTATTTTGTTTTTGCATGATTTTTGACG
518 TTTTGAGTTGAATTGTGTATTTTTCACCGAAAACATTTTATTTTGTTTTTGCATGATTTTTGACG
*
8205 TAAATAGTCCTTGAAATATCTATATCCATCGAACAAAATCCCAGCCACGTTCGATATAAGTATTT
583 TAAATAGTCCTTGAAATATCTATATCCATCGAACAAAATCCCAACCACGTTCGATATAAGTATTT
* *
8270 GTTTTTACAAGCATCTGAATCTTATTTCAATTTAATTAAAAATTAATTCGGAAAAAAATGGAAAA
648 GTTTTTACAAGCATCTGAATCTTATTACAATTTAATTAAAAATTAATTCAGAAAAAAATGGAAAA
* *
8335 ACGATATTAGAAGCGTGAAAAGCTCTTCAATCTTTTTGGCGTTGAATTATATATTTTTGACTGAG
713 ACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTGACTGAG
8400 TATTGTGGCAAAAAATTGAGAAAAAACTTTTCCGATCAGTGTTTAGCCGAAATCGTGTACTAACT
778 TATTGTGGCAAAAAATTGAGAAAAAACTTTTCCGATCAGTGTTTAGCC---A-CG-G-------T
*
8465 ATCACGGTTTTAGGCTAAAAACACGTTCCCGAGCCCCGACTCAG
831 -T-----TTTT--GCTAAAAACACGTTCCCGAGCCCCGACTCAA
* * *
8509 TTTTGTATGATTTTTGGCGCGAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGAC
1 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
* *
8574 ACATTGGATATAAGGATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
66 ACATTGGATATAAGGATTTGATTTTACGAGCATCTGAATCTTGTCTCGATTTAAATAGAAATTAA
8639 TTCGAAAAAAAAATAGGAAAAATGATATTAAAAGCGCGAAAAGACCATCAATCTTTTTGGTATTG
131 TTCG-AAAAAAAATAGGAAAAATGATATTAAAAGCGCGAAAAGACCATCAATCTTTTTGGTATTG
*
8704 AATTATATATTTTATCTGAGTATAGTGGCAAAAAAATTC-AAGAAAAAAAAATTCGGGTCAGTTT
195 AATTATATATTTTATCTGAGTATAGTGGC-AAAAAATTCAAAAAAAAAAAAATTCGGGTCAGTTT
* *
8768 TTAGCCGAAAATCGTG-T-ACCACCATGGTTTTTGGGCTAAATACGCGTTTCGGGGGCCCCGGCT
259 TTAGCCGAAAATCGTGATAACCACCATGGTTTTTAGGCTAAAAACGCGTTTCGGGGGCCCCGGCT
*
8831 CAGTTTTGCATGATTGTTGGCAGGAAGACTCCTTGAAATATCTATATTCATCTAACCAATCTCAG
324 CAGTTTTGCATGATTGTTGGCAGGAAGACTCCTTAAAATATCTATATTCATCTAACCAATCTCAG
* *
8896 GCTCTGAGCCACATTAGATTTAAGGATTTGGTTTTACGAGCATCTGAATATTGTTTCGATTTAGT
389 GCTCTGAGCCACATTAGATTTAAGGATTTGCTTTTACGAGCATCTGAATATTGTTTCGATTTAAT
* * *
8961 TTGAAATAGATTCGGAAAAAAAATAGAAAAATGATATTTAAAGCGAGAAAAATATTTCAATTTTT
454 TAGAAATAGATTC-GAAAAAAAATAGAAAAATAATATTTAAAGCGAGAAAAATACTTCAATTTTT
* *
9026 TTTTGAGTTGAATTGTGTATTTTTCATCGAAAACATTTTATTTTTGTTTTTGTATGATTTTTGAC
518 TTTTGAGTTGAATTGTGTATTTTTCACCGAAAACATTTTA-TTTTGTTTTTGCATGATTTTTGAC
*
9091 GTAAATAGTCCTTGAAATATCTATATTCATCGAACAAAATCCCAACCACGTTCGATATAAGTATT
582 GTAAATAGTCCTTGAAATATCTATATCCATCGAACAAAATCCCAACCACGTTCGATATAAGTATT
* *
9156 TGTTTTTACGAGCATCTGAATCTTGTTACAATTTAATTAAAAATTAATTCAG-AAAAAATGGAAA
647 TGTTTTTACAAGCATCTGAATCTTATTACAATTTAATTAAAAATTAATTCAGAAAAAAATGGAAA
9220 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTGACTGA
712 AACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTGACTGA
* *
9285 GTATTGTGGCAAAAAATTGAGAAAAAACTTTTCTGATCAGTTTTTAGCCACGGTTTTTTGCTAAA
777 GTATTGTGGCAAAAAATTGAGAAAAAACTTTTCCGATCAGTGTTTAGCCACGGTTTTTTGCTAAA
*
9350 AACGCGTTCCCGAGCCCCGACTCAA
842 AACACGTTCCCGAGCCCCGACTCAA
*
9375 TTTTGCATGATTTTTGGCGCAAAGACTACTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
9440 ACATTGGATATAAGGATTTGATTTT
66 ACATTGGATATAAGGATTTGATTTT
Statistics
Matches: 906, Mismatches: 46, Indels: 31
0.92 0.05 0.03
Matches are distributed among these distances:
866 115 0.13
868 4 0.00
873 1 0.00
874 1 0.00
881 1 0.00
882 2 0.00
883 1 0.00
885 179 0.20
886 208 0.23
887 134 0.15
889 167 0.18
890 84 0.09
891 9 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (866 bp):
TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCC
ACATTGGATATAAGGATTTGATTTTACGAGCATCTGAATCTTGTCTCGATTTAAATAGAAATTAA
TTCGAAAAAAAATAGGAAAAATGATATTAAAAGCGCGAAAAGACCATCAATCTTTTTGGTATTGA
ATTATATATTTTATCTGAGTATAGTGGCAAAAAATTCAAAAAAAAAAAAATTCGGGTCAGTTTTT
AGCCGAAAATCGTGATAACCACCATGGTTTTTAGGCTAAAAACGCGTTTCGGGGGCCCCGGCTCA
GTTTTGCATGATTGTTGGCAGGAAGACTCCTTAAAATATCTATATTCATCTAACCAATCTCAGGC
TCTGAGCCACATTAGATTTAAGGATTTGCTTTTACGAGCATCTGAATATTGTTTCGATTTAATTA
GAAATAGATTCGAAAAAAAATAGAAAAATAATATTTAAAGCGAGAAAAATACTTCAATTTTTTTT
TGAGTTGAATTGTGTATTTTTCACCGAAAACATTTTATTTTGTTTTTGCATGATTTTTGACGTAA
ATAGTCCTTGAAATATCTATATCCATCGAACAAAATCCCAACCACGTTCGATATAAGTATTTGTT
TTTACAAGCATCTGAATCTTATTACAATTTAATTAAAAATTAATTCAGAAAAAAATGGAAAAACG
ATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTGACTGAGTAT
TGTGGCAAAAAATTGAGAAAAAACTTTTCCGATCAGTGTTTAGCCACGGTTTTTTGCTAAAAACA
CGTTCCCGAGCCCCGACTCAA
Done.