Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017823.1 Corchorus olitorius cultivar O-4 contig17856, 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: 33793
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:11865 original size:43 final size:42
Alignment explanation
Indices: 11677--12004 Score: 391
Period size: 41 Copynumber: 7.8 Consensus size: 42
11667 CAATAACCAA
* *
11677 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTAT-TCC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-TCTATATAC
* *
11720 AAAAGTCCTCAAACACATATATAACACAGAGGCACCTATAT-C
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC
* * ** *
11762 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATA-TAC
*
11803 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATAT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC
*
11844 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTAT-TAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC-A-TCTATATAC
* *
11887 AAAGTCCTCAAACACATATATAACACAGAGGCATTTATAT-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC
* *
11928 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATA-TAC
* *
11971 AAAGTCCTCAAACACATATATAACACATAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
12005 TTCTCCTTAT
Statistics
Matches: 247, Mismatches: 26, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
39 19 0.08
40 1 0.00
41 98 0.40
42 11 0.04
43 88 0.36
44 30 0.12
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.21
Consensus pattern (42 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATAC
Found at i:11891 original size:84 final size:84
Alignment explanation
Indices: 11677--12004 Score: 543
Period size: 84 Copynumber: 3.9 Consensus size: 84
11667 CAATAACCAA
* *
11677 AAAGTCCCCAAACACATATATAACACAGGGGCAATTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
*
11742 AACACAGAGGCACCTATATC
65 AACACAGAGGCATCTATATC
* ** *
11762 CAAGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
11825 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
11844 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
11909 ACACAGAGGCATTTATATC
66 ACACAGAGGCATCTATATC
*
11928 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
11993 ACACATAGGCAT
66 ACACAGAGGCAT
12005 TTCTCCTTAT
Statistics
Matches: 227, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
82 54 0.24
83 21 0.09
84 138 0.61
85 14 0.06
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.21
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:12885 original size:22 final size:24
Alignment explanation
Indices: 12860--12905 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
12850 CGAAAATGGC
12860 AATCAA-T-CAACTCTAAGAGAAA
1 AATCAACTACAACTCTAAGAGAAA
12882 AATCAACTAACAACTCTAAGAGAA
1 AATCAACT-ACAACTCTAAGAGAA
12906 GAGAAAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.29
23 1 0.05
25 14 0.67
ACGTcount: A:0.54, C:0.20, G:0.09, T:0.17
Consensus pattern (24 bp):
AATCAACTACAACTCTAAGAGAAA
Found at i:18425 original size:658 final size:654
Alignment explanation
Indices: 17183--19760 Score: 2664
Period size: 658 Copynumber: 3.9 Consensus size: 654
17173 AATATTTCCT
* * ** * *
17183 GTTAATTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTATTTAGCTAAAAACAC
1 GTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTTTTAACCATCACAGTTTTTGGCTAAAAACAC
* * *
17248 ATTTCGGGGTCCCAGCTCAGTTTTGCATTATTTTTTGCACT-AGGACTCCTTGAAATATCTATAT
66 A-TTCCGAGTCCCAGCTCAGTTTTGCATTATTTTTGGCACTGA-GACTCCTTGAAATATCTATAT
* * * *
17312 TCATCTAATCAAATTTCAGTCACATTAGATTTAAGAATATATTTTTATGAGCATTTGAAACCGGT
129 TCATCTAATCAAATTTCAGCCACATTAGATTTAAGAATATGTTTTTACGAGCATCTGAAACCGGT
* *
17377 TTCAATTTAATTAGAAATTAATTTACGAAAAATACAGAAAAGATATTAGAAACGA-GAAAAG-CA
194 TTCAATTTAATTAGAAATTAATTTA-GAAAAATACGGAAAAGATATTAGAAAC-ATGAAAAGCCC
** ** *
17440 TCCAATATTTTTTACATTGAATTATATATTTGTTTTGAGTATATTTTGGGTAAAAATTGAGGAAC
257 TCCAATATTTTTGGCATTGAATTATATATTTGTTTTGAGTA-A-TTTGGCCAAAAATTGAGAAAC
* * *
17505 AATATTTTG-GTTCAATTTTTTCAGAATTGTAGCCGAAATCGTGTAT-TAACCATCACAGTATTT
320 AATATTTCGAG-TCAATTTTTTAAAAATTGTAGCCGAAATCGTGT-TCTAACCATCACAGTATTT
* * *
17568 GGCTAAAAACGCGTTCTTGGGCCCCGGCTCAGTTTTGCATGACTTTTGGCGCCGACACTCCTTGA
383 -GCTAAAAACGCGTTC-CGGGCCCC-GCTAAGTTTTGCATGATTTTTGGCGCCGACACTCCTTGA
* * *
17633 TATATCCATATTTATCTAATAAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTAC-AAGCA
445 AATATCCATATTCATCTAATAAAATCTCAGCCACATTAGATTTAAGGATATGTTCTTACGAA-CA
*
17697 TCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTAGAAAAAATCGGAAAAA--ATATTACAAG
509 TCTGAATCTTGTTTCGATTTAATCAGAAATTAATTTAGAAAAAATAGGAAAAACGATATTACAAG
* *
17760 CGTGAAAATACTTAAATGCTTTATGCGTTGAATTATATATTTTTTATTAGTGTTGTGGTTAAAAA
574 TGTGAAAATACTTAAAT-CTTTCTGCGTTGAATTATATATTTTTTATTAGTGTTGTGG-TAAAAA
* *
17825 TTAAGGAAAAACTTTTCGA
637 TTGAGGAAAAA-TTTTCGG
* * *
17844 ATTAGTTTTTGCAAAATTTTAGCCGAGATCGTGTTTTAACCATCACAGTTTTTGGCTCAAAACAC
1 GTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTTTTAACCATCACAGTTTTTGGCTAAAAACAC
* * * * *
17909 ATTCCGACTCCCAGCTCAGTTTTGTATTATTTTTGGAATTGAGACTCCTTTAAATATCTATATTC
66 ATTCCGAGTCCCAGCTCAGTTTTGCATTATTTTTGGCACTGAGACTCCTTGAAATATCTATATTC
* *
17974 ATCTAATCAAATTTCAGCCACATTGGATTTATA-AATATTTTTTTACGAGCATCTGAAACCGGTT
131 ATCTAATCAAATTTCAGCCACATTAGATTTA-AGAATATGTTTTTACGAGCATCTGAAACCGGTT
18038 TCAATTTAATTAGAAATTAATTTAGAAAAATACGGAAAAGATATTAGAAACATGAAAAGCCCTCC
195 TCAATTTAATTAGAAATTAATTTAGAAAAATACGGAAAAGATATTAGAAACATGAAAAGCCCTCC
* ** *
18103 AATATTTTTGGCAATGAATTATATATTTGTTTCCAGTAATTTGGCCAAAAATTGAGAAATAATAT
260 AATATTTTTGGCATTGAATTATATATTTGTTTTGAGTAATTTGGCCAAAAATTGAGAAACAATAT
* * * *
18168 TTTGAGTCAATTTTTTAAAAATTGTAGCCGAAATCGTGTTCTAACCACCATAGCATTTGACTAAA
325 TTCGAGTCAATTTTTTAAAAATTGTAGCCGAAATCGTGTTCTAACCATCACAGTATTTG-CTAAA
* * * *
18233 AACGCGTTCCGGGGCCCCAGCTAAGTTTTGCATGATTTTTGACTCCGAAACTCCTTGAAATATCT
389 AACGCGTTCC-GGGCCCC-GCTAAGTTTTGCATGATTTTTGGCGCCGACACTCCTTGAAATATCC
* * * * *
18298 ATATTCATCTAATTAAATCTCAACTACATTGGATTTAAGCATATGTTCTTACGAACATCTGAATC
452 ATATTCATCTAATAAAATCTCAGCCACATTAGATTTAAGGATATGTTCTTACGAACATCTGAATC
* *
18363 TTGTTTCGATTTAATCAAAAATTAATTT-GAAAAAA-AGGAAAAACGATATTAGAAGTGTGAAAA
517 TTGTTTCGATTTAATCAGAAATTAATTTAGAAAAAATAGGAAAAACGATATTACAAGTGTGAAAA
* ** *
18426 TCCCTTAAATCCTTTCTTTGTTG-A--AT-TATTTTTTATTAGTGTTGTGGGTAAAAATTGTGGA
582 T-ACTTAAAT-CTTTCTGCGTTGAATTATATATTTTTTATTAGTGTTGT-GGTAAAAATTGAGGA
* *
18487 AAATTTTTTTGG
644 AAA-ATTTTCGG
* * * * *
18499 GTTAGTTTTTGCAATATTTTAGCCGAAATCATGTTTTAATCATTACAGTTTTTGGCTAAAAACAT
1 GTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTTTTAACCATCACAGTTTTTGGCTAAAAACAC
* * * * * * *
18564 GTTCTGAAATCTCGGCTCAGTTTTGCATTATTTTTTGCACTGATACTCCTTGAAATATCTATATT
66 ATTCCG-AGTCCCAGCTCAGTTTTGCATTATTTTTGGCACTGAGACTCCTTGAAATATCTATATT
* * * *
18629 TATCTAGTCAAATTTCAGCCACATT-GAATTTAAGGATATGTTTTTACGAGC-TCCTGAAACCAG
130 CATCTAATCAAATTTCAGCCACATTAG-ATTTAAGAATATGTTTTTACGAGCAT-CTGAAACCGG
* * *
18692 TTTCAATTTAATTAAAAATTAATTTAGAAAAAATAGGGAAAAGATATTAGAAACGTGAAAAGCCC
193 TTTCAATTTAATTAGAAATTAATTTAG-AAAAATACGGAAAAGATATTAGAAACATGAAAAGCCC
* * * * * *
18757 TCCAATATTTTTGGCGTTTAATTATATATTTGCTTTGAGTATTTTGGCCAAAATTTGAGGAACAA
257 TCCAATATTTTTGGCATTGAATTATATATTTGTTTTGAGTAATTTGGCCAAAAATTGAGAAACAA
* * * * *
18822 TATTTCGAGTCTATTTTTTCAAAATTGT-GCCCGAAATCGTATACTAACCATCACGGTATTTG--
322 TATTTCGAGTCAATTTTTTAAAAATTGTAG-CCGAAATCGTGTTCTAACCATCACAGTATTTGCT
* * **
18884 ------GC-TACC--G----GCTTAGTTTCCCATGATTTTTGGCGCCGACACTCCTTGAAATATC
386 AAAAACGCGTTCCGGGCCCCGCTAAGTTTTGCATGATTTTTGGCGCCGACACTCCTTGAAATATC
* * * * * * *
18936 CATTTTCATCTAATCAAATCTCAGCCACATTAGATTTGAGGATATGTTGTTATGAGCATTTGAAT
451 CATATTCATCTAATAAAATCTCAGCCACATTAGATTTAAGGATATGTTCTTACGAACATCTGAAT
* *
19001 CTTGTTTCGATTTAATCAGAAATGAATTTGGAAAAAAATAGGAAAAACGATATTACAAGTGTGAA
516 CTTGTTTCGATTTAATCAGAAATTAATTTAG-AAAAAATAGGAAAAACGATATTACAAGTGTGAA
* * * * * * *
19066 AA-ACCCTTAAATCATTCCTGCGTTCAATTGTATAATTTTCATTAGTGTTGCAGGCAAAAATTGA
580 AATA--CTTAAATC-TTTCTGCGTTGAATTATATATTTTTTATTAGTGTTG-TGGTAAAAATTGA
* * *
19130 TGAAAGTATTTTGGG
641 GGAAA-AATTTTCGG
** * * *
19145 GGCAGATTTTGAAAAATTTTAGCCGAAATCGTGTTTTAACCATCACGGTTTTTGGCTAAAAACAC
1 GTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTTTTAACCATCACAGTTTTTGGCTAAAAACAC
* * ** * * * *
19210 GTTCCGGGGTTTCGGCTCAGTTTTGCATGATTTTTGGCACCGAGACTCCTTGAAGTATCTATATT
66 ATTCC-GAGTCCCAGCTCAGTTTTGCATTATTTTTGGCACTGAGACTCCTTGAAATATCTATATT
* * * * * * *
19275 AATCTAATCAAATCTCAGTCACATTAGATTTATGGATATGTTTTTATGAGCATCTGAAACTGGTT
130 CATCTAATCAAATTTCAGCCACATTAGATTTAAGAATATGTTTTTACGAGCATCTGAAACCGGTT
* ** * * * *
19340 TCAATTTAATTAGATATTAATTCCGAAAGAATATGGAAAATGATATTAGAAGCGTGAAAAACCCT
195 TCAATTTAATTAGAAATTAATTTAGAAA-AATACGGAAAA-GATATTAGAAACATGAAAAGCCCT
* * * * *
19405 CCAATATTTTTGGCTTTGAATTATATATTTATTTTGAGTATTTTGGCCAAAAATT-AAAGAATAA
258 CCAATATTTTTGGCATTGAATTATATATTTGTTTTGAGTAATTTGGCCAAAAATTGAGA-AACAA
* * * * * * * *
19469 TATTTCGGGTCAATTTTTGCAAAAATTTTAGCCGAACTCGTG---T-A-CGTTACGGTATTTGGT
322 TATTTCGAGTCAATTTTT-TAAAAATTGTAGCCGAAATCGTGTTCTAACCATCACAGTATTTGCT
* * * * * *
19529 AAAAACACGTTCAAGGG-CCCGACTCAGTTTTGCATGAATTTTGGCGCCGAGACTCCTTGAAATT
386 AAAAACGCGTTC-CGGGCCCCG-CTAAGTTTTGCATGATTTTTGGCGCCGACACTCCTTGAAATA
** * ** *** * * *
19593 TGTATATTCATCCAACCAAAT-T-----TTTTTGGATTTAAGGATTTGTTTTTAC-AAGCATCTG
449 TCCATATTCATCTAATAAAATCTCAGCCACATTAGATTTAAGGATATGTTCTTACGAA-CATCTG
* * ** * ** *
19651 AATCTTGTTTCAATTTAATTCA-AATTTAATTCGGGAAAAAAAAGGAAAAACGATATTGGAAGCG
513 AATCTTGTTTCGATTTAA-TCAGAAATTAATT-TAGAAAAAATAGGAAAAACGATATTACAAGTG
* * * *
19715 TGAAAA-ACCCTTCAATCTTTTTGACTTTGAATTATATACTTTTTAT
576 TGAAAATA--CTTAAATCTTTCTG-CGTTGAATTATATATTTTTTAT
19761 GATATTTTTG
Statistics
Matches: 1615, Mismatches: 242, Indels: 128
0.81 0.12 0.06
Matches are distributed among these distances:
639 119 0.07
640 1 0.00
641 7 0.00
642 41 0.03
643 13 0.01
644 2 0.00
645 5 0.00
646 230 0.14
647 98 0.06
648 18 0.01
649 1 0.00
651 1 0.00
652 7 0.00
653 106 0.07
654 5 0.00
655 103 0.06
656 139 0.09
657 150 0.09
658 234 0.14
659 104 0.06
660 172 0.11
661 59 0.04
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (654 bp):
GTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTTTTAACCATCACAGTTTTTGGCTAAAAACAC
ATTCCGAGTCCCAGCTCAGTTTTGCATTATTTTTGGCACTGAGACTCCTTGAAATATCTATATTC
ATCTAATCAAATTTCAGCCACATTAGATTTAAGAATATGTTTTTACGAGCATCTGAAACCGGTTT
CAATTTAATTAGAAATTAATTTAGAAAAATACGGAAAAGATATTAGAAACATGAAAAGCCCTCCA
ATATTTTTGGCATTGAATTATATATTTGTTTTGAGTAATTTGGCCAAAAATTGAGAAACAATATT
TCGAGTCAATTTTTTAAAAATTGTAGCCGAAATCGTGTTCTAACCATCACAGTATTTGCTAAAAA
CGCGTTCCGGGCCCCGCTAAGTTTTGCATGATTTTTGGCGCCGACACTCCTTGAAATATCCATAT
TCATCTAATAAAATCTCAGCCACATTAGATTTAAGGATATGTTCTTACGAACATCTGAATCTTGT
TTCGATTTAATCAGAAATTAATTTAGAAAAAATAGGAAAAACGATATTACAAGTGTGAAAATACT
TAAATCTTTCTGCGTTGAATTATATATTTTTTATTAGTGTTGTGGTAAAAATTGAGGAAAAATTT
TCGG
Found at i:19334 original size:646 final size:638
Alignment explanation
Indices: 17183--19513 Score: 2527
Period size: 646 Copynumber: 3.6 Consensus size: 638
17173 AATATTTCCT
* * ** * *
17183 GTTAATTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTATTTAGCTAAAAACAC
1 GTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTTTTAACCATCACAGTTTTTGGCTAAAAACAC
* * * *
17248 ATTTCGGGGTCCCAGCTCAGTTTTGCATTATTTTTTGCA-CTAGGACTCCTTGAAATATCTATAT
66 ATTCCGGAGTCCCAGCTCAGTTTTGCATTATTTTTGGCACCGA-GACTCCTTGAAATATCTATAT
* * * *
17312 TCATCTAATCAAATTTCAGTCACATTAGATTTAAGAATATATTTTTATGAGCATTTGAAACCGGT
130 TCATCTAATCAAATTTCAGCCACATTAGATTTAAGAATATGTTTTTACGAGCATCTGAAACCGGT
* * *
17377 TTCAATTTAATTAGAAATTAATTTACGAAAAATACAGAAAAGATATTAGAAACGAGAAAAG-CAT
195 TTCAATTTAATTAGAAATTAATTTA-GAAAAATACGGAAAAGATATTAGAAACGTGAAAAGCCCT
** **
17441 CCAATATTTTTTACATTGAATTATATATTTGTTTTGAGTATATTTTGGGTAAAAATTGAGGAACA
259 CCAATATTTTTGGCATTGAATTATATATTTGTTTTGAG--TATTTTGGCCAAAAATTGAGGAACA
* * *
17506 ATATTTTG-GTTCAATTTTTTCAGAATTGTAGCCGAAATCGTGTATTAACCATCACAGTATTTGG
322 ATATTTCGAG-TCAATTTTTTCAAAATTGTAGCCGAAATCGTGTACTAACCATCACAGTATTTGG
* * *
17570 CTAAAAACGCGTTCTTGGGCCCCGGCTCAGTTTTGCATGACTTTTGGCGCCGACACTCCTTGATA
386 CT----A--------------CCGGCTAAGTTTTGCATGATTTTTGGCGCCGACACTCCTTGAAA
* *
17635 TATCCATATTT-ATCTAATAAAATCTCAGCCACATTAGATTTAAGGATATGTTTTTACAAGCATC
433 TATCCAT-TTTCATCTAATAAAATCTCAGCCACATTAGATTTAAGGATATGTTCTTACGAGCATC
* *
17699 TGAATCTTGTTTCGATTTAATCAGAAATTAATTTAGAAAAAATCGGAAAAA--ATATTACAAGCG
497 TGAATCTTGTTTCGATTTAATCAGAAATTAATTT-GAAAAAATAGGAAAAACGATATTACAAGTG
* *
17762 TGAAAATA--CTTAAATGCTTTATGCGTTGAATTATATATTTTTTATTAGTGTTGTGGTTAAAAA
561 TGAAAA-ACCCTTAAAT-CTTTCTGCGTTGAATT-TATA-TTTTTATTAGTGTTGAGG-TAAAAA
* * * *
17825 TTAAGGAAAAACTTTTCGA
621 TTGATGAAATA-TTTTCGG
* * *
17844 ATTAGTTTTTGCAAAATTTTAGCCGAGATCGTGTTTTAACCATCACAGTTTTTGGCTCAAAACAC
1 GTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTTTTAACCATCACAGTTTTTGGCTAAAAACAC
* * * ** *
17909 ATTCC-GACTCCCAGCTCAGTTTTGTATTATTTTTGGAATTGAGACTCCTTTAAATATCTATATT
66 ATTCCGGAGTCCCAGCTCAGTTTTGCATTATTTTTGGCACCGAGACTCCTTGAAATATCTATATT
* *
17973 CATCTAATCAAATTTCAGCCACATTGGATTTATA-AATATTTTTTTACGAGCATCTGAAACCGGT
131 CATCTAATCAAATTTCAGCCACATTAGATTTA-AGAATATGTTTTTACGAGCATCTGAAACCGGT
*
18037 TTCAATTTAATTAGAAATTAATTTAGAAAAATACGGAAAAGATATTAGAAACATGAAAAGCCCTC
195 TTCAATTTAATTAGAAATTAATTTAGAAAAATACGGAAAAGATATTAGAAACGTGAAAAGCCCTC
* ** * * *
18102 CAATATTTTTGGCAATGAATTATATATTTGTTTCCAGTAATTTGGCCAAAAATTGAGAAATAATA
260 CAATATTTTTGGCATTGAATTATATATTTGTTTTGAGTATTTTGGCCAAAAATTGAGGAACAATA
* * * * * *
18167 TTTTGAGTCAATTTTTTAAAAATTGTAGCCGAAATCGTGTTCTAACCACCATAGCATTTGACTAA
325 TTTCGAGTCAATTTTTTCAAAATTGTAGCCGAAATCGTGTACTAACCATCACAGTATTTG-----
* * * *
18232 AAACGCGTTCCGGGGCCCCAGCTAAGTTTTGCATGATTTTTGACTCCGAAACTCCTTGAAATATC
385 ----GC-TACC---G-----GCTAAGTTTTGCATGATTTTTGGCGCCGACACTCCTTGAAATATC
* * * * * * * *
18297 TATATTCATCTAATTAAATCTCAACTACATTGGATTTAAGCATATGTTCTTACGAACATCTGAAT
437 CATTTTCATCTAATAAAATCTCAGCCACATTAGATTTAAGGATATGTTCTTACGAGCATCTGAAT
* *
18362 CTTGTTTCGATTTAATCAAAAATTAATTTGAAAAAA-AGGAAAAACGATATTAGAAGTGTGAAAA
502 CTTGTTTCGATTTAATCAGAAATTAATTTGAAAAAATAGGAAAAACGATATTACAAGTGTGAAAA
* ** *
18426 TCCCTTAAATCCTTTCTTTGTTGAA-TTAT-TTTTTATTAGTGTTGTGGGTAAAAATTG-TGGAA
567 ACCCTTAAAT-CTTTCTGCGTTGAATTTATATTTTTATTAGTGTTG-AGGTAAAAATTGAT-G-A
* *
18488 AATTTTTTTGG
628 AATATTTTCGG
* * * * *
18499 GTTAGTTTTTGCAATATTTTAGCCGAAATCATGTTTTAATCATTACAGTTTTTGGCTAAAAACAT
1 GTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTTTTAACCATCACAGTTTTTGGCTAAAAACAC
* * * * * * * * *
18564 GTTCTGAAATCTCGGCTCAGTTTTGCATTATTTTTTGCACTGATACTCCTTGAAATATCTATATT
66 ATTCCGGAGTCCCAGCTCAGTTTTGCATTATTTTTGGCACCGAGACTCCTTGAAATATCTATATT
* * * *
18629 TATCTAGTCAAATTTCAGCCACATT-GAATTTAAGGATATGTTTTTACGAGC-TCCTGAAACCAG
131 CATCTAATCAAATTTCAGCCACATTAG-ATTTAAGAATATGTTTTTACGAGCAT-CTGAAACCGG
* *
18692 TTTCAATTTAATTAAAAATTAATTTAGAAAAAATAGGGAAAAGATATTAGAAACGTGAAAAGCCC
194 TTTCAATTTAATTAGAAATTAATTTAG-AAAAATACGGAAAAGATATTAGAAACGTGAAAAGCCC
* * * *
18757 TCCAATATTTTTGGCGTTTAATTATATATTTGCTTTGAGTATTTTGGCCAAAATTTGAGGAACAA
258 TCCAATATTTTTGGCATTGAATTATATATTTGTTTTGAGTATTTTGGCCAAAAATTGAGGAACAA
* * *
18822 TATTTCGAGTCTATTTTTTCAAAATTGT-GCCCGAAATCGTATACTAACCATCACGGTATTTGGC
323 TATTTCGAGTCAATTTTTTCAAAATTGTAG-CCGAAATCGTGTACTAACCATCACAGTATTTGGC
* ** *
18886 TACCGGCTTAGTTTCCCATGATTTTTGGCGCCGACACTCCTTGAAATATCCATTTTCATCTAATC
387 TACCGGCTAAGTTTTGCATGATTTTTGGCGCCGACACTCCTTGAAATATCCATTTTCATCTAATA
* * * *
18951 AAATCTCAGCCACATTAGATTTGAGGATATGTTGTTATGAGCATTTGAATCTTGTTTCGATTTAA
452 AAATCTCAGCCACATTAGATTTAAGGATATGTTCTTACGAGCATCTGAATCTTGTTTCGATTTAA
*
19016 TCAGAAATGAATTTGGAAAAAAATAGGAAAAACGATATTACAAGTGTGAAAAACCCTTAAATCAT
517 TCAGAAATTAATTT-G-AAAAAATAGGAAAAACGATATTACAAGTGTGAAAAACCCTTAAATC-T
* * * * *
19081 TCCTGCGTTCAATTGTATAATTTTCATTAGTGTTGCAGGCAAAAATTGATGAAAGTATTTTGGG
579 TTCTGCGTTGAATT-TAT-ATTTTTATTAGTGTTG-AGGTAAAAATTGATGAAA-TATTTTCGG
** * * *
19145 GGCAGATTTTGAAAAATTTTAGCCGAAATCGTGTTTTAACCATCACGGTTTTTGGCTAAAAACAC
1 GTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTTTTAACCATCACAGTTTTTGGCTAAAAACAC
* * ** * * *
19210 GTTCCGGGGTTTCGGCTCAGTTTTGCATGATTTTTGGCACCGAGACTCCTTGAAGTATCTATATT
66 ATTCCGGAGTCCCAGCTCAGTTTTGCATTATTTTTGGCACCGAGACTCCTTGAAATATCTATATT
* * * * * * *
19275 AATCTAATCAAATCTCAGTCACATTAGATTTATGGATATGTTTTTATGAGCATCTGAAACTGGTT
131 CATCTAATCAAATTTCAGCCACATTAGATTTAAGAATATGTTTTTACGAGCATCTGAAACCGGTT
* ** * * *
19340 TCAATTTAATTAGATATTAATTCCGAAAGAATATGGAAAATGATATTAGAAGCGTGAAAAACCCT
196 TCAATTTAATTAGAAATTAATTTAGAAA-AATACGGAAAA-GATATTAGAAACGTGAAAAGCCCT
* * * * *
19405 CCAATATTTTTGGCTTTGAATTATATATTTATTTTGAGTATTTTGGCCAAAAATTAAAGAATAAT
259 CCAATATTTTTGGCATTGAATTATATATTTGTTTTGAGTATTTTGGCCAAAAATTGAGGAACAAT
* * * *
19470 ATTTCGGGTCAATTTTTGCAAAAATTTTAGCCGAACTCGTGTAC
324 ATTTCGAGTCAATTTTTTC-AAAATTGTAGCCGAAATCGTGTAC
19514 GTTACGGTAT
Statistics
Matches: 1412, Mismatches: 206, Indels: 117
0.81 0.12 0.07
Matches are distributed among these distances:
639 119 0.08
640 1 0.00
641 7 0.00
642 45 0.03
643 1 0.00
644 4 0.00
645 6 0.00
646 226 0.16
647 101 0.07
648 21 0.01
649 1 0.00
650 2 0.00
653 1 0.00
655 92 0.07
656 140 0.10
657 153 0.11
658 210 0.15
659 51 0.04
660 166 0.12
661 62 0.04
667 2 0.00
668 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (638 bp):
GTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTTTTAACCATCACAGTTTTTGGCTAAAAACAC
ATTCCGGAGTCCCAGCTCAGTTTTGCATTATTTTTGGCACCGAGACTCCTTGAAATATCTATATT
CATCTAATCAAATTTCAGCCACATTAGATTTAAGAATATGTTTTTACGAGCATCTGAAACCGGTT
TCAATTTAATTAGAAATTAATTTAGAAAAATACGGAAAAGATATTAGAAACGTGAAAAGCCCTCC
AATATTTTTGGCATTGAATTATATATTTGTTTTGAGTATTTTGGCCAAAAATTGAGGAACAATAT
TTCGAGTCAATTTTTTCAAAATTGTAGCCGAAATCGTGTACTAACCATCACAGTATTTGGCTACC
GGCTAAGTTTTGCATGATTTTTGGCGCCGACACTCCTTGAAATATCCATTTTCATCTAATAAAAT
CTCAGCCACATTAGATTTAAGGATATGTTCTTACGAGCATCTGAATCTTGTTTCGATTTAATCAG
AAATTAATTTGAAAAAATAGGAAAAACGATATTACAAGTGTGAAAAACCCTTAAATCTTTCTGCG
TTGAATTTATATTTTTATTAGTGTTGAGGTAAAAATTGATGAAATATTTTCGG
Found at i:20038 original size:22 final size:22
Alignment explanation
Indices: 20013--20054 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
20003 ACCCTCCAAT
20013 TAAAATTTTGGTAACCTCACTA
1 TAAAATTTTGGTAACCTCACTA
*
20035 TAAAATTTTGGTAATCTCAC
1 TAAAATTTTGGTAACCTCAC
20055 CGGTAACCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
TAAAATTTTGGTAACCTCACTA
Found at i:20089 original size:22 final size:22
Alignment explanation
Indices: 20056--20527 Score: 245
Period size: 22 Copynumber: 21.9 Consensus size: 22
20046 TAATCTCACC
20056 GGTAACCTCACTATGAAATTTT
1 GGTAACCTCACTATGAAATTTT
20078 GGTAA-CTCCACTATGAAATTTT
1 GGTAACCT-CACTATGAAATTTT
* *
20100 GGTAA-CTCCAGTGTGAAATTTT
1 GGTAACCT-CACTATGAAATTTT
* * *
20122 GCTAAACTCACTATGAAACTTT
1 GGTAACCTCACTATGAAATTTT
*
20144 GGTAACCCTCACTATGAAACTTT
1 GGTAA-CCTCACTATGAAATTTT
**
20167 GGTAACCTC-CTATGAAATTCC
1 GGTAACCTCACTATGAAATTTT
* * *
20188 AGTAACCCTC-TTATGAAATATT
1 GGTAA-CCTCACTATGAAATTTT
*
20210 GGTAACCTCACTATGAGATTTT
1 GGTAACCTCACTATGAAATTTT
20232 GGTAACCTTCA--ATGAAA--TT
1 GGTAACC-TCACTATGAAATTTT
** * *
20251 CCT--CCT-A-TGA--AATTTTG
1 GGTAACCTCACT-ATGAAATTTT
** * *
20268 GAAACTTCACT-A-TGA--AATTTTT
1 GGTA--AC-CTCACT-ATGAAATTTT
* * * *
20290 GGTAATCTCCCTATTAAATTTA
1 GGTAACCTCACTATGAAATTTT
20312 GGTAACCATC-CTATGAAA-TTT
1 GGTAACC-TCACTATGAAATTTT
*
20333 GGTAACCTCATTATGAAATTTT
1 GGTAACCTCACTATGAAATTTT
* *
20355 GGTAACCTCACTGA-AAAATTAT
1 GGTAACCTCACT-ATGAAATTTT
* * *
20377 GGTAACCTCCCTATGATATTCT
1 GGTAACCTCACTATGAAATTTT
*
20399 AGTAACC-CACCTATGAAATTTT
1 GGTAACCTCA-CTATGAAATTTT
* * * * **
20421 TGTAACCCCACTTTAAAATTCG
1 GGTAACCTCACTATGAAATTTT
* *
20443 GGTAACCTCCCTATGAAATTCT
1 GGTAACCTCACTATGAAATTTT
*
20465 GGTAACC-CACTTATGATATTTT
1 GGTAACCTCAC-TATGAAATTTT
**
20487 GGTAATATCACTATGAAATTTT
1 GGTAACCTCACTATGAAATTTT
* * *
20509 AGTAATCTTA-TATGAAATT
1 GGTAACCTCACTATGAAATT
20528 CCAGTGATTC
Statistics
Matches: 351, Mismatches: 71, Indels: 57
0.73 0.15 0.12
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
17 4 0.01
19 5 0.01
20 3 0.01
21 55 0.16
22 246 0.70
23 34 0.10
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (22 bp):
GGTAACCTCACTATGAAATTTT
Found at i:20119 original size:44 final size:43
Alignment explanation
Indices: 20056--20527 Score: 317
Period size: 44 Copynumber: 11.0 Consensus size: 43
20046 TAATCTCACC
20056 GGTAACCTCACTATGAAATTTTGGTAA-CTCCACTATGAAATTTT
1 GGTAACC-CACTATGAAATTTTGGTAACCT-CACTATGAAATTTT
* * * * *
20100 GGTAACTCCAGTGTGAAATTTTGCTAAACTCACTATGAAACTTT
1 GGTAAC-CCACTATGAAATTTTGGTAACCTCACTATGAAATTTT
* **
20144 GGTAACCCTCACTATGAAACTTTGGTAACCTC-CTATGAAATTCC
1 GGTAA-CC-CACTATGAAATTTTGGTAACCTCACTATGAAATTTT
* * * *
20188 AGTAACCCTCTTATGAAATATTGGTAACCTCACTATGAGATTTT
1 GGTAACCCAC-TATGAAATTTTGGTAACCTCACTATGAAATTTT
** *
20232 GGTAACCTTCAATGAAA---T--T--CCTC-CTATGAAATTTT
1 GGTAACCCACTATGAAATTTTGGTAACCTCACTATGAAATTTT
* * * * * *
20267 GGAAACTTCACTATGAAATTTTTGGTAATCTCCCTATTAAATTTA
1 GGTAAC-CCACTATGAAA-TTTTGGTAACCTCACTATGAAATTTT
*
20312 GGTAA-CCATCCTATGAAA-TTTGGTAACCTCATTATGAAATTTT
1 GGTAACCCA--CTATGAAATTTTGGTAACCTCACTATGAAATTTT
* * * * *
20355 GGTAACCTCACTGA-AAAATTATGGTAACCTCCCTATGATATTCT
1 GGTAACC-CACT-ATGAAATTTTGGTAACCTCACTATGAAATTTT
* * * * * **
20399 AGTAACCCACCTATGAAATTTTTGTAACCCCACTTTAAAATTCG
1 GGTAACCCA-CTATGAAATTTTGGTAACCTCACTATGAAATTTT
* * *
20443 GGTAACCTCCCTATGAAATTCTGGTAACC-CACTTATGATATTTT
1 GGTAACC-CACTATGAAATTTTGGTAACCTCAC-TATGAAATTTT
** * * *
20487 GGTAATATCACTATGAAATTTTAGTAATCTTA-TATGAAATT
1 GGTAA-CCCACTATGAAATTTTGGTAACCTCACTATGAAATT
20528 CCAGTGATTC
Statistics
Matches: 329, Mismatches: 71, Indels: 57
0.72 0.16 0.12
Matches are distributed among these distances:
35 16 0.05
36 11 0.03
38 1 0.00
40 2 0.01
42 3 0.01
43 72 0.22
44 176 0.53
45 48 0.15
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (43 bp):
GGTAACCCACTATGAAATTTTGGTAACCTCACTATGAAATTTT
Found at i:20183 original size:66 final size:63
Alignment explanation
Indices: 20058--20507 Score: 307
Period size: 66 Copynumber: 7.0 Consensus size: 63
20048 ATCTCACCGG
*
20058 TAACCTCACTATGAAATTTTGGTAA-CTCCACTATGAAATTTTGGTAA-CTCCAGTGTGAAATTT
1 TAACCTC-CTATGAAA-TTTGGTAACCT-CACTATGAAATTTTGGTAACCTCC--TATGAAATTT
*
20121 TGC
61 AGC
* * *
20124 TAAACTCACTATGAAACTTTGGTAACCCTCACTATGAAACTTTGGTAACCTCCTATGAAATTCCA
1 TAACCTC-CTATGAAA-TTTGGTAA-CCTCACTATGAAATTTTGGTAACCTCCTATGAAATT-TA
20189 G-
62 GC
* * * *
20190 TAACCCTCTTATGAAATATTGGTAACCTCACTATGAGATTTTGGTAACCTTCAATGAAA--T---
1 TAA-CCTCCTATGAAAT-TTGGTAACCTCACTATGAAATTTTGGTAACCTCCTATGAAATTTAGC
* * * *
20250 T--CCTCCTATGAAATTTTGGAAACTTCACTATGAAATTTTTGGTAATCTCCCTATTAAATTTAG
1 TAACCTCCTATGAAA-TTTGGTAACCTCACTATGAAA-TTTTGGTAACCT-CCTATGAAATTTAG
*
20313 G
63 C
* *
20314 TAACCATCCTATGAAATTTGGTAACCTCATTATGAAATTTTGGTAACCT-C-ACTGAAAAATTAT
1 TAACC-TCCTATGAAATTTGGTAACCTCACTATGAAATTTTGGTAACCTCCTA-TG-AAATTTA-
*
20377 GG
62 GC
* * * * * * **
20379 TAACCTCCCTATGATATTCTAGTAACC-CACCTATGAAATTTTTGTAACCCCACTTTAAAATTCG
1 TAACCT-CCTATGAAATT-TGGTAACCTCA-CTATGAAATTTTGGTAACCTC-CTATGAAATTTA
*
20443 GG
62 GC
* **
20445 TAACCTCCCTATGAAATTCTGGTAACC-CACTTATGATATTTTGGTAATATCACTATGAAATTT
1 TAACCT-CCTATGAAATT-TGGTAACCTCAC-TATGAAATTTTGGTAACCTC-CTATGAAATTT
20508 TAGTAATCTT
Statistics
Matches: 310, Mismatches: 47, Indels: 54
0.75 0.11 0.13
Matches are distributed among these distances:
57 28 0.09
58 12 0.04
59 6 0.02
60 1 0.00
61 1 0.00
62 1 0.00
63 2 0.01
64 8 0.03
65 62 0.20
66 145 0.47
67 36 0.12
68 8 0.03
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (63 bp):
TAACCTCCTATGAAATTTGGTAACCTCACTATGAAATTTTGGTAACCTCCTATGAAATTTAGC
Found at i:20266 original size:35 final size:36
Alignment explanation
Indices: 20215--20286 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 36
20205 ATATTGGTAA
* *
20215 CCTCACTATGAGATTTTGGTAACCTTCA-ATGAAATT
1 CCTCACTATGAAATTTTGG-AAACTTCACATGAAATT
20251 CCTC-CTATGAAATTTTGGAAACTTCACTATGAAATT
1 CCTCACTATGAAATTTTGGAAACTTCAC-ATGAAATT
20287 TTTGGTAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 7 0.22
35 13 0.41
36 12 0.38
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (36 bp):
CCTCACTATGAAATTTTGGAAACTTCACATGAAATT
Found at i:20354 original size:123 final size:122
Alignment explanation
Indices: 20132--20370 Score: 313
Period size: 123 Copynumber: 2.0 Consensus size: 122
20122 GCTAAACTCA
* *
20132 CTATGAAACTTTGGTAACCCTCACTATGAAACTTTGGTAACCTCCTATGAAATTCCAGTAACCCT
1 CTATGAAACTTTGGTAAACCTCACTATGAAACTTTGGTAACCTCCTATGAAATTCCAGTAACCAT
* *
20197 CTTATGAAATATTGGTAACCTCACTATGAGATTTTGGTAACCTTCAATGAAATTCCTC
66 CCTATGAAATATTGGTAACCTCACTATGAAATTTTGGTAACC-TCAATGAAATTCCTC
* * * * * *
20255 CTATGAAATTTTGG-AAACTTCACTATGAAATTTTTGGTAATCTCCCTATTAAATT-TAGGTAAC
1 CTATGAAACTTTGGTAAACCTCACTATGAAA-CTTTGGTAACCT-CCTATGAAATTCCA-GTAAC
* *
20318 CATCCTATGAAAT-TTGGTAACCTCATTATGAAATTTTGGTAACCTCACTGAAA
63 CATCCTATGAAATATTGGTAACCTCACTATGAAATTTTGGTAACCTCAATGAAA
20371 AATTATGGTA
Statistics
Matches: 101, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
122 22 0.22
123 53 0.52
124 26 0.26
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (122 bp):
CTATGAAACTTTGGTAAACCTCACTATGAAACTTTGGTAACCTCCTATGAAATTCCAGTAACCAT
CCTATGAAATATTGGTAACCTCACTATGAAATTTTGGTAACCTCAATGAAATTCCTC
Found at i:20380 original size:145 final size:145
Alignment explanation
Indices: 20113--20384 Score: 349
Period size: 145 Copynumber: 1.9 Consensus size: 145
20103 AACTCCAGTG
*
20113 TGAAATTTTGCTAAACTCACTATGAAACTTTGGTAACCCTCACTATGAAACTTTGGTAACCTCCT
1 TGAAATTTTGCGAAACTCACTATGAAACTTTGGTAACCCTCACTATGAAACTTTGGTAACCTCCT
* * *
20178 ATGAAATTCCAGTAACCCTCTTATGAAATATTGGTAACCTCACTATGAGATTTTGGTAACCTTCA
66 ATGAAATTCCAGTAACCCTCTTATGAAATATTGGTAACCTCACTATAAAATTATGGTAACCTTCA
20243 ATGAAATTCCTCCTA
131 ATGAAATTCCTCCTA
* * * *
20258 TGAAATTTTG-GAAACTTCACTATGAAATTTTTGGTAA-TCTCCCTATTAAA-TTTAGGTAACCA
1 TGAAATTTTGCGAAAC-TCACTATGAAA-CTTTGGTAACCCTCACTATGAAACTTT-GGTAACC-
** *
20320 TCCTATGAAATT-TGGTAA-CCTCATTATGAAATTTTGGTAACCTCACTGA-AAAATTATGGTAA
62 TCCTATGAAATTCCAGTAACCCTC-TTATGAAATATTGGTAACCTCACT-ATAAAATTATGGTAA
20382 CCT
125 CCT
20385 CCCTATGATA
Statistics
Matches: 110, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
144 11 0.10
145 78 0.71
146 21 0.19
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (145 bp):
TGAAATTTTGCGAAACTCACTATGAAACTTTGGTAACCCTCACTATGAAACTTTGGTAACCTCCT
ATGAAATTCCAGTAACCCTCTTATGAAATATTGGTAACCTCACTATAAAATTATGGTAACCTTCA
ATGAAATTCCTCCTA
Found at i:20412 original size:87 final size:87
Alignment explanation
Indices: 20256--20419 Score: 208
Period size: 87 Copynumber: 1.9 Consensus size: 87
20246 AAATTCCTCC
* * * * *
20256 TATGAAATTTTGGAAACTTCACTATGAAATTTTTGGTAATCTCCCTATTAAATTTAGGTAACCAT
1 TATGAAATTTTGGAAACCTCACTA-GAAAATTATGGTAACCTCCCTATGAAATTTAGGTAACCAT
20321 CCTATGAAATTTGGTAACCTCAT
65 CCTATGAAATTTGGTAACCTCAT
* *
20344 TATGAAATTTTGGTAACCTCACT-GAAAAATTATGGTAACCTCCCTATGATATTCTA-GTAACCC
1 TATGAAATTTTGGAAACCTCACTAG-AAAATTATGGTAACCTCCCTATGAAATT-TAGGTAA-CC
20407 A-CCTATGAAATTT
63 ATCCTATGAAATTT
20420 TTGTAACCCC
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
86 1 0.02
87 39 0.59
88 26 0.39
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37
Consensus pattern (87 bp):
TATGAAATTTTGGAAACCTCACTAGAAAATTATGGTAACCTCCCTATGAAATTTAGGTAACCATC
CTATGAAATTTGGTAACCTCAT
Found at i:20819 original size:63 final size:64
Alignment explanation
Indices: 20704--20832 Score: 206
Period size: 63 Copynumber: 2.0 Consensus size: 64
20694 ATGAAATTTA
* *
20704 TAATATCTTTCTAAAATTGAAAAAAAAAAGTTTCATGACTAAAAGGATCACTAATAAAATAGTT
1 TAATATCTTTCCAAAATTGAAAAAAAAAAGTTTCATGACTAAAAGGAACACTAATAAAATAGTT
* * *
20768 TAATATCTTTCCATAATTGAAAAAAAAAA-TTTCATGATTGAAAGGAACACTAATAAAATAGTT
1 TAATATCTTTCCAAAATTGAAAAAAAAAAGTTTCATGACTAAAAGGAACACTAATAAAATAGTT
20831 TA
1 TA
20833 TGTTTTTATA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
63 33 0.55
64 27 0.45
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (64 bp):
TAATATCTTTCCAAAATTGAAAAAAAAAAGTTTCATGACTAAAAGGAACACTAATAAAATAGTT
Found at i:21337 original size:21 final size:24
Alignment explanation
Indices: 21308--21358 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
21298 TTTTGAACTC
21308 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
21331 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
21354 ATTAT
1 ATTAT
21359 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:21353 original size:25 final size:25
Alignment explanation
Indices: 21308--21356 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
21298 TTTTGAACTC
*
21308 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
21333 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
21357 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:27534 original size:16 final size:16
Alignment explanation
Indices: 27490--27538 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
27480 GTCTTTGGTA
27490 TCGTTTTCGTTTT-TT
1 TCGTTTTCGTTTTGTT
*
27505 T-GTTTTTTGTTTTTGTT
1 TCG-TTTTCG-TTTTGTT
27522 TCGTTTTCGTTTTGTT
1 TCGTTTTCGTTTTGTT
27538 T
1 T
27539 TTGTTGTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 1 0.04
15 6 0.21
16 12 0.43
17 8 0.29
18 1 0.04
ACGTcount: A:0.00, C:0.08, G:0.16, T:0.76
Consensus pattern (16 bp):
TCGTTTTCGTTTTGTT
Found at i:29495 original size:2 final size:2
Alignment explanation
Indices: 29488--29518 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29478 GATAACTTAC
*
29488 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29519 TCGAATTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:29843 original size:21 final size:21
Alignment explanation
Indices: 29819--29885 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
29809 GTAATATAAA
29819 TAATAACTAAAATACTTACAT
1 TAATAACTAAAATACTTACAT
* ** *
29840 TAATTAAATGTAATA-ATAC-T
1 TAA-TAACTAAAATACTTACAT
*
29860 ATAATAACTAAAACACTTACAT
1 -TAATAACTAAAATACTTACAT
29882 TAAT
1 TAAT
29886 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 8 0.24
21 16 0.48
22 9 0.27
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (21 bp):
TAATAACTAAAATACTTACAT
Found at i:32336 original size:58 final size:58
Alignment explanation
Indices: 32233--32347 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
32223 ATAGCATCAT
*
32233 GTCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
1 GTCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
* * * *
32291 GTCTTGGTCCGAAAACGTCTTTTTTTATGCATCTAAT-AAAGAACATGTCACTTGATA
1 GTCTCGGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATA
32348 TTTGATTAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 35 0.69
59 16 0.31
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (58 bp):
GTCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
Done.