Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015542.1 Corchorus olitorius cultivar O-4 contig15575, 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: 63784
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:4529 original size:123 final size:128
Alignment explanation
Indices: 4400--4643 Score: 408
Period size: 123 Copynumber: 1.9 Consensus size: 128
4390 ACTTTTATAA
4400 TTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-TA-ATTTTTACCA
1 TTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATACTATATTTTTACCA
4461 TTTTACTATTTTAATT-AAAAAACTTATATATATTAGAATTTTTTAAATATACTTTTACAGTT
66 TTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTTACAGTT
*
4523 TTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTATTTTATTTTT
1 TTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATA-CTA---TATTTTT
4588 ACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATATA
62 ACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATATA
4644 TTTCTTAAAT
Statistics
Matches: 111, Mismatches: 1, Indels: 9
0.92 0.01 0.07
Matches are distributed among these distances:
123 43 0.39
124 3 0.03
125 2 0.02
127 2 0.02
131 26 0.23
132 35 0.32
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.49
Consensus pattern (128 bp):
TTACTCAACTAAAAAATCTATTTTTATTTAATTAAATCTAATATCCTTATACTATATTTTTACCA
TTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATATACTTTTACAGTT
Found at i:4665 original size:14 final size:13
Alignment explanation
Indices: 4629--4667 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
4619 TATATATTAG
4629 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
4642 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
4656 AATTTTTTAAAT
1 AATTTTTTAAAT
4668 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:8775 original size:60 final size:60
Alignment explanation
Indices: 8702--8830 Score: 231
Period size: 60 Copynumber: 2.1 Consensus size: 60
8692 AAACTGTCAT
*
8702 TTTGCACCCAACTTTTTTATTTTGATCAAAACACATCCTAAAGTTTTATTTTTGTGCCAC
1 TTTGCACCCAACTTTTTTATTTTGATCAAAACACATCCTAAAGTTTTATTTTTGTGCAAC
* *
8762 TTTGCACCCAACTTTTTTATTTTGATCAAAACGCATCCTAAAGTTTTATTTTTGTGCAAT
1 TTTGCACCCAACTTTTTTATTTTGATCAAAACACATCCTAAAGTTTTATTTTTGTGCAAC
8822 TTTGCACCC
1 TTTGCACCC
8831 TCCGTCTAGG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (60 bp):
TTTGCACCCAACTTTTTTATTTTGATCAAAACACATCCTAAAGTTTTATTTTTGTGCAAC
Found at i:24601 original size:626 final size:612
Alignment explanation
Indices: 23502--24622 Score: 1436
Period size: 626 Copynumber: 1.8 Consensus size: 612
23492 ACCATGATGG
* *
23502 TACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCGTCAATTTTTAGCCAC
1 TACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCCTCAATTTTTAGCCAC
*
23567 AATACTTATAAATATATAAAATTCAACGCCAAAAAGATTGGAGGACTTTTCACGCTGTTAATATC
66 AATACTTATAAATATATAAAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTGTTAATATC
* * * *
23632 GTTTTTCATATTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATGCTCGTAAAAATAAATCC
131 GTTTTTCATATTTTCCGAATTAATTTCTAATAAAATCGAAACAAGATGATCGTAAAAACAAATCC
* * *
23697 TTAAATTCAATGTGGCTGACATTTGATTAGATGAATATAGATATTTCAAGGAGTCCCGGCGCCAT
196 TTAAATCCAATGTGGCTGACATTTGATTAGATGAATATAGATATTTCAAGGAGTCCCAGCGCCAA
* * * * * *
23762 AAATCATGCAAAACTAAGCCGGAGCCACGAAACGCGTTTCTAGCCAAAAACCGTGATGGTTAGTA
261 AAATAATGCAAAACTAAGCCGGAGCCACCAAACACGTTTCTAGCCAAAAACCATGATGCTAAGTA
23827 CACAATTTCGGCTAATATTTTGCAAAAAAAATGACCCAAAAAATTTTTCCTCAATTTTTTTTGGC
326 CACAATTTCGGCTAATATTTTG--AAAAAAATGACCCAAAAAATTTTTCCTCAA--TTTTTTGGC
* * * * * *
23892 TAAAATACTGATAATATATATAATTTAATGCCAAAAATATTTGAGGAGTTTTTACGCTATTAATA
387 TAAAATACTCATAATATATATAATTCAATGCCAAAAAGATTGGAGGACTTTTCACGCTATTAATA
23957 TCAATTTTCATATTTTTCTGAATTAATTTCTAATTAAATCTATTGTAGCTGAGATTTGATTAGAT
452 TCAATTTTCATATTTTTCTGAATTAATTTCTAATTAAATCTATTGTAGCTGAGATTTGATTAGAT
24022 GAATATGGATATCTCAAAGACTCTTGACGCCAAAAATCATGCAAAACTTAGCCGGGGTCCCGGAA
517 GAATATGGATATCTCAAAGACTCTTGACGCCAAAAATCATGCAAAACTTAGCCGGGGTCCCGGAA
24087 CGCGTTTTTAGCCAAAAACCGTGATGATTAT
582 CGCGTTTTTAGCCAAAAACCGTGATGATTAT
* *
24118 TACACGATTTCGGCTAAAATTTTGCAAAAATTTACCCAAAAT-TTATTTCCTCAATTTTTAGCCA
1 TACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATATT-TTTCCTCAATTTTTAGCCA
* * *
24182 CAATACTTATATAA-ATTATATAATTCAACGCCAAAAATATTGAAGGACTTTTCATGCT-TCTAA
65 CAATACTTATA-AATA-TATAAAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTGT-TAA
* ** *
24245 TATCGTTTTTCCTATTATTTTCCGAATTAATTTTTAATCAAAATC-AAATCATTATTCAGATCCT
127 TATCGTTTTT-C-A-TATTTTCCGAATTAATTTCTAAT-AAAATCGAAA-CAAGA-T--GAT-CG
*** * *
24309 TATTTTACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGG
183 TA-AAAACAAATCCTTAAATCCAATGTGGCTGACATTTGATTAGATGAATATAGATATTTCAAGG
* * * * * **
24374 AGTCTCAGTGCCAAAAATAATGCAACACTGAA-CCGGGGCC-CCATAACACGTTTTTAGTTAAAA
247 AGTCCCAGCGCCAAAAATAATGCAAAACT-AAGCCGGAGCCACCA-AACACGTTTCTAGCCAAAA
* * * * *
24437 ACCATGATTTCGACTAACGTACACGATTTCGGCTAATATTTTG-TAAAATTGA-TCAGAAATATT
310 ACCATGA--T-G-CTAA-GTACACAATTTCGGCTAATATTTTGAAAAAAATGACCCA-AAAAATT
*
24500 TTTCCTCAA-TTTTTGTCTAAAATACTCATAATATATATAATTCAACT-CCAAAAAGATTGGAGG
369 TTTCCTCAATTTTTTGGCTAAAATACTCATAATATATATAATTCAA-TGCCAAAAAGATTGGAGG
* * *
24563 ACTTTTCACGCTTTTAATATC-GTTGTTCATATTTTTTCTGAATTAGTTTCTAATTAAATC
433 ACTTTTCACGCTATTAATATCAATT-TTCATA-TTTTTCTGAATTAATTTCTAATTAAATC
24623 GAAACAAGAT
Statistics
Matches: 428, Mismatches: 52, Indels: 40
0.82 0.10 0.08
Matches are distributed among these distances:
615 2 0.00
616 70 0.16
617 53 0.12
618 1 0.00
619 1 0.00
620 24 0.06
621 8 0.02
622 1 0.00
624 4 0.01
625 76 0.18
626 134 0.31
627 4 0.01
628 23 0.05
629 1 0.00
630 2 0.00
631 24 0.06
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (612 bp):
TACACAATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCCTCAATTTTTAGCCAC
AATACTTATAAATATATAAAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTGTTAATATC
GTTTTTCATATTTTCCGAATTAATTTCTAATAAAATCGAAACAAGATGATCGTAAAAACAAATCC
TTAAATCCAATGTGGCTGACATTTGATTAGATGAATATAGATATTTCAAGGAGTCCCAGCGCCAA
AAATAATGCAAAACTAAGCCGGAGCCACCAAACACGTTTCTAGCCAAAAACCATGATGCTAAGTA
CACAATTTCGGCTAATATTTTGAAAAAAATGACCCAAAAAATTTTTCCTCAATTTTTTGGCTAAA
ATACTCATAATATATATAATTCAATGCCAAAAAGATTGGAGGACTTTTCACGCTATTAATATCAA
TTTTCATATTTTTCTGAATTAATTTCTAATTAAATCTATTGTAGCTGAGATTTGATTAGATGAAT
ATGGATATCTCAAAGACTCTTGACGCCAAAAATCATGCAAAACTTAGCCGGGGTCCCGGAACGCG
TTTTTAGCCAAAAACCGTGATGATTAT
Found at i:25304 original size:655 final size:658
Alignment explanation
Indices: 23990--25705 Score: 1657
Period size: 655 Copynumber: 2.6 Consensus size: 658
23980 TAATTTCTAA
* * * * * *
23990 TTAAATCTATTGTAGCTGAGATTTGATTAGATGAATATGGATATCTCAAAGACTCTTGACGCCAA
1 TTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTC-AAGAGTCTTGACGCCAA
* * *
24055 AAATCATGCAAAACTTAGCCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTA
65 AAATCATGCAAAACTGAGCCGGGGTCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGATTATTA
* * *
24120 CACGATTTCGGCTAAAATTTTGCAAAAATTTACCCAAAATTTATTTCCTCAATTTTTAGCCACAA
130 CACGATTTCGGCTAAAATTTTGCAAAAA--TA--CAAAA--TAATTCCTCAAATTTTAGCCAAAA
* * * **
24185 TACTTATATAAATTATATAATTCAACGCCAAAAATATTGAAGGACTTTTCATGCTTCTAATATCG
189 TACTCATAGAAATTATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACACTTCTAATATCG
* * * ** * * ***
24250 TTTTTCCTATTATTTTCCGAATTAATTTTTAATCAAAATCAAATCATTATTCAGATCCTTATTTT
254 TTTTTCATATTATTTTCCAAATTAATTTTTAATCAAAATCAAAACAAGATTAAGATCCTCATAAA
* *
24315 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTC
319 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTC
**
24380 AGTGCCAAAAATAATGCAACACTGAACCGGGGCCCCATAACACGTTTTTAGTTAAAAACCATGAT
384 AGTGCCAAAAATAATGCAACACTGAACCGGGGCCCCATAACACGTTTTTAGCCAAAAACCATGA-
* * * * * *
24445 TTCGACTAACGTACACGATTTCGGCTAATATTTTGTAAAATTGATCAGAAATATTTTTCCTCAAT
448 TTC-AATAACGTACACGATTTCGGCTAAAATTTTGCAAAATTGACCAGAAAGATATTTCCTCAAT
* * * *
24510 TTTTGTCTAAAATACTCATAATATATATAATTCAACTCCAAAAAGATTGGAGGACTTTTCACGCT
512 TTTTGGCTAAAATACTCATAAAAAATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACGCT
** * * *
24575 TTTAATATCGTTGTTCATATTTTTTCTGAATTAGTTTCTAATTAAATCGAAACAAGATTTAGATG
577 ACTAATATCGTTGTTCATATCTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATG
24640 CTCGTAAAAACAAATCC
642 CTCGTAAAAACAAATCC
* * *
24657 TTAAATGCAATGTGGCTGAGATTTGATTAGATGTATATAGATATTTCAAGCAGTCTTGACGGCAA
1 TTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAG-AGTCTTGACGCCAA
* ** *
24722 AAATCATGCAAAACTGAGTC-GGG-CCTCGAAACGCGTTTTTAGCAAAAAATTGTGATGGTT-TG
65 AAATCATGCAAAACTGAGCCGGGGTCC-CGAAACGCGTTTTTAGCAAAAAACCGTGATGATTAT-
* * * * * *
24784 TATACGATTTCGGCTAAAGTTTTGTAAAAA-A-AAAA-AATTCCTTAAATTTTGGCTAAAATACT
128 TACACGATTTCGGCTAAAATTTTGCAAAAATACAAAATAATTCCTCAAATTTTAGCCAAAATACT
* * * * *
24846 CAT-GAAATATATATAATTTAATGCCAAAAAGATTGGAGGACTTTTCACACTTTTCATATCGTTT
193 CATAGAAAT-TATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACACTTCTAATATCGTTT
* * * *
24910 TTCATATT-TTTTCTAAATTAATTTTTAAT-TAAATCAAAACAAGATTAAGGTGCTCATAAAAAC
257 TTCATATTATTTTCCAAATTAATTTTTAATCAAAATCAAAACAAGATTAAGATCCTCAT-AAAAC
* *
24973 AAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATGGATATATTCTCAAGAAGTCT
321 AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATAT--AGATATT-TCAAGAAGTCT
** ** * * * **
25038 TGGTGCTGAAAATCATGC-ACAACTG-ACTTGGGG-CCC-TGACACGCGTTTTTAGCCAAAAATT
383 CAGTGCCAAAAATAATGCAAC-ACTGAAC-CGGGGCCCCAT-A-ACACGTTTTTAGCCAAAAACC
* * * *
25099 GTGA-T-AATTA-TTACACGATTTCGGCTAAAATTTTGCAAAACTTGACCCGAAAGATATTTCCT
444 ATGATTCAATAACGTACACGATTTCGGCTAAAATTTTGCAAAA-TTGACCAGAAAGATATTTCCT
* **
25161 CAATTTTTGGCTAAAATACTCATAAAAAAATATAATTCAA-TGCCAAAAATATTGAAGGGTTTTT
508 CAATTTTTGGCTAAAATACTCAT-AAAAAATATAATTCAACT-CCAAAAAGATTGAAGGACTTTT
* * * * *
25225 TACGCTACTAATATGGTTTTTCCTA-CTTTTCCGAATTAATTTCTAATTAAATTGAAACAAGATT
571 CACGCTACTAATATCGTTGTTCATATCTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
* * *
25289 TAGATGCTTGTAAAAATAAATTC
636 TAGATGCTCGTAAAAACAAATCC
* * *
25312 TTAAATCCAATGTGACTGTGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGACGTCAA
1 TTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAA-GAGTCTTGACGCCAA
* * * * *
25377 AAATCAAGTAAAAATGA-CACGGGGTCCCGTAACCCGTTTTTAGCCAAAACAAAAAAACCGTGAT
65 AAATCATGCAAAACTGAGC-CGGGGTCCCGAAACGCGTTTTTAG------C-AAAAAACCGTGAT
* * * ** *
25441 G----GTACACGATTTCGACTAATATTTTGCAAAAATTGACCCGAAATATTTTTTCCTCAATTTT
122 GATTATTACACGATTTCGGCTAAAATTTTGCAAAAA-T-A--C-AAA-A-TAATTCCTCAAATTT
* * * * * * *
25502 TAGCCACAATACTCATAAAAAATATATAATTCAACACCAAAAATATTGAAGG-TTTTTCACTCTT
180 TAGCCAAAATACTCATAGAAATTATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACACTT
* * * ** * * * * * *
25566 TTAATATCATTTTTTC-TATTTTTTTCTGAATTAATTTCTAAT-TAAATCGAAACTAGGTTTAGA
245 CTAATATC-GTTTTTCATATTATTTTCCAAATTAATTTTTAATCAAAATCAAAACAAGATTAAGA
* ** * * * * *
25629 TGCTTGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAGATAAATATAGATGTTT
309 TCCTCAT-AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTT
*
25694 CAAGGAGTCTCA
373 CAAGAAGTCTCA
25706 ACGCGTAAAA
Statistics
Matches: 862, Mismatches: 148, Indels: 79
0.79 0.14 0.07
Matches are distributed among these distances:
654 27 0.03
655 191 0.22
656 136 0.16
657 81 0.09
658 14 0.02
659 75 0.09
660 4 0.00
662 2 0.00
663 13 0.02
665 3 0.00
666 75 0.09
667 76 0.09
668 21 0.02
669 141 0.16
670 3 0.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (658 bp):
TTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGAGTCTTGACGCCAAA
AATCATGCAAAACTGAGCCGGGGTCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGATTATTAC
ACGATTTCGGCTAAAATTTTGCAAAAATACAAAATAATTCCTCAAATTTTAGCCAAAATACTCAT
AGAAATTATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACACTTCTAATATCGTTTTTCA
TATTATTTTCCAAATTAATTTTTAATCAAAATCAAAACAAGATTAAGATCCTCATAAAACAAATC
CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTCAGTGCCA
AAAATAATGCAACACTGAACCGGGGCCCCATAACACGTTTTTAGCCAAAAACCATGATTCAATAA
CGTACACGATTTCGGCTAAAATTTTGCAAAATTGACCAGAAAGATATTTCCTCAATTTTTGGCTA
AAATACTCATAAAAAATATAATTCAACTCCAAAAAGATTGAAGGACTTTTCACGCTACTAATATC
GTTGTTCATATCTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAA
ACAAATCC
Found at i:25337 original size:333 final size:328
Alignment explanation
Indices: 24004--25703 Score: 1580
Period size: 333 Copynumber: 5.1 Consensus size: 328
23994 ATCTATTGTA
* * * **
24004 GCTGAGATTTGATTAGATGAATATGGATATCTCAA-AGACTCTTGACGCCAAAAATCATGCAAAA
1 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGA-AGTCTTGGTG-CAAAAATCATGCAAAA
* * *
24068 CTTAGCCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGGCT
64 CTGA-CCGGGGTCCCTGAACGCGTTTTTAGCCAAAAACCGTGATAATTATTACACGATTTCGGCT
* * * * * * * *
24133 AAAATTTTGCAAAAATTTACCCAAAATTTATTTCCTCAATTTTTAGCCACAATACTTATATAAAT
128 AAAATTTTGC-AAAATTGACCCGAAATATATTTCCTCAATTTTTGGCTAAAATACTCATA-AAAA
* * *
24198 TATATAATTCAACGCCAAAAATATTGAAGGACTTTTCATGCTTCTAATATCGTTTTTCCTATTAT
191 TATATAATTCAATGCCAAAAATATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCCTATT-T
* * * ** * * * ***
24263 TTTCCGAATTAATTTTTAATCAAAATC-AAATCATTATTCAGATCCTTAT-TTTACAAATCCTTA
255 TTTCTGAATTAATTTCTAAT-TAAATCGAAA-CAAGATTTAGATGCTTGTAAAAACAAATCCTTA
*
24326 AATCCAATGTG
318 AATGCAATGTG
* * ** * *
24337 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCAGTGCCAAAAATAATGCAACAC
1 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTTGGTG-CAAAAATCATGCAAAAC
* * ** * * * *
24402 TGAACCGGGGCCCCAT-AACACGTTTTTAGTTAAAAACCATGATTTCGACTAACGTACACGATTT
65 TG-ACCGGGGTCCC-TGAACGCGTTTTTAGCCAAAAACCGTGA--T--AATTA-TTACACGATTT
* * * * * *
24466 CGGCTAATATTTTGTAAAATTGATCAGAAATATTTTTCCTCAATTTTTGTCTAAAATACTCAT-A
123 CGGCTAAAATTTTGCAAAATTGACCCGAAATATATTTCCTCAATTTTTGGCTAAAATACTCATAA
* * * * *
24530 ATATATATAATTCAACT-CCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTGTTCATA
188 AAATATATAATTCAA-TGCCAAAAATATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCCTA
* *
24594 TTTTTTCTGAATTAGTTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTT
252 TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACAAATCCTT
24659 AAATGCAATGTG
317 AAATGCAATGTG
* *
24671 GCTGAGATTTGATTAGATGTATATAGATATTTCAAGCAGTCTTGACG-GCAAAAATCATGCAAAA
1 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTTG--GTGCAAAAATCATGCAAAA
* * ** ** *
24735 CTGAGTC-GGG--CCTCGAAACGCGTTTTTAGCAAAAAATTGTGATGGTT-TGTATACGATTTCG
64 CTGA-CCGGGGTCCCT-G-AACGCGTTTTTAGCCAAAAACCGTGATAATTAT-TACACGATTTCG
* * * * * *
24796 GCTAAAGTTTTGTAAAA---A----AAA-AAAATTCCTTAAATTTTGGCTAAAATACTCATGAAA
125 GCTAAAATTTTGCAAAATTGACCCGAAATATATTTCCTCAATTTTTGGCTAAAATACTCAT-AAA
* * * * * * *
24853 TATATATAATTTAATGCCAAAAAGATTGGAGGACTTTTCACACTTTTCATATCGTTTTTCATATT
189 AATATATAATTCAATGCCAAAAATATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCCTATT
* * * * * **
24918 TTTTCTAAATTAATTTTTAATTAAATCAAAACAAGATTAAGGTGCTCATAAAAACAAATCCTTAA
254 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACAAATCCTTAA
24983 ATGCAATGTG
319 ATGCAATGTG
* * *
24993 GCTGAGATTTGATTAGATGAATATGGATATATTCTCAAGAAGTCTTGGTGCTGAAAATCATGCAC
1 GCTGAGATTTGATTAGATGAATAT--AGATATT-TCAAGAAGTCTTGGTGC-AAAAATCATGCAA
* **
25058 AACTGACTTGGGG-CCCTGACACGCGTTTTTAGCCAAAAATTGTGATAATTATTACACGATTTCG
62 AACTGAC-CGGGGTCCCTGA-ACGCGTTTTTAGCCAAAAACCGTGATAATTATTACACGATTTCG
*
25122 GCTAAAATTTTGCAAAACTTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAA
125 GCTAAAATTTTGCAAAA-TTGACCCGAAATATATTTCCTCAATTTTTGGCTAAAATACTCATAAA
* ** * ** * *
25187 AAAATATAATTCAATGCCAAAAATATTGAAGGGTTTTTTACGCTACTAATATGGTTTTTCCTA-C
189 AATATATAATTCAATGCCAAAAATATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCCTATT
* * * *
25251 TTTTCCGAATTAATTTCTAATTAAATTGAAACAAGATTTAGATGCTTGTAAAAATAAATTCTTAA
254 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACAAATCCTTAA
*
25316 ATCCAATGTG
319 ATGCAATGTG
* * * * *
25326 ACTGTGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGACGT-CAAAAATCAAGTAAAA
1 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTTG--GTGCAAAAATCATGCAAAA
* * *** * *
25390 ATGACACGGGGTCCC-GTAACCCGTTTTTAGCC-AAAA-CAAAAAAACCGTGATGGTACACGATT
64 CTGAC-CGGGGTCCCTG-AACGCGTTTTTAGCCAAAAACCGTGATAA---TTAT--TACACGATT
* * * * * *
25452 TCGACTAATATTTTGCAAAAATTGACCCGAAATATTTTTTCCTCAATTTTTAGCCACAATACTCA
122 TCGGCTAAAATTTTGC-AAAATTGACCCGAAATA-TATTTCCTCAATTTTTGGCTAAAATACTCA
** * * * *
25517 TAAAAAATATATAATTCAACACCAAAAATATTGAAGG-TTTTTCACTCTTTTAATATCATTTTTT
185 T-AAAAATATATAATTCAATGCCAAAAATATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTC
* *
25581 CTATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACTAGGTTTAGATGCTTGTAAAAACAAAT
249 CTA-TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACAAAT
25646 CCTTAAATGCAATGTG
313 CCTTAAATGCAATGTG
* * * * *
25662 GCTAAGATTTTATTAGATAAATATAGATGTTTCAAGGAGTCT
1 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCT
25704 CAACGCGTAA
Statistics
Matches: 1124, Mismatches: 189, Indels: 105
0.79 0.13 0.07
Matches are distributed among these distances:
320 26 0.02
321 4 0.00
322 152 0.14
323 1 0.00
324 8 0.01
325 31 0.03
326 57 0.05
327 4 0.00
328 29 0.03
329 5 0.00
330 47 0.04
331 17 0.02
332 2 0.00
333 246 0.22
334 209 0.19
335 119 0.11
336 105 0.09
337 39 0.03
338 23 0.02
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (328 bp):
GCTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTTGGTGCAAAAATCATGCAAAACT
GACCGGGGTCCCTGAACGCGTTTTTAGCCAAAAACCGTGATAATTATTACACGATTTCGGCTAAA
ATTTTGCAAAATTGACCCGAAATATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAATATAT
AATTCAATGCCAAAAATATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCTG
AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACAAATCCTTAAATGCAAT
GTG
Found at i:25879 original size:2 final size:2
Alignment explanation
Indices: 25874--25904 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
25864 ATATATATAG
*
25874 AC AC AC AC AC AC AC AA AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
25905 TATATATATT
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:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:26746 original size:38 final size:35
Alignment explanation
Indices: 26683--26757 Score: 87
Period size: 38 Copynumber: 2.1 Consensus size: 35
26673 TTTTAATTTT
* * *
26683 AAATATATTATATATGTTATAAATTAAAAATCTGA
1 AAATATATAATATATATTATAAATTAAAAATCAGA
*
26718 AAATATATAAATATATATATATATAATTAATAATCAGA
1 AAATATAT-AATATATAT-TATA-AATTAAAAATCAGA
26756 AA
1 AA
26758 CTCAAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 8 0.24
36 7 0.21
37 4 0.12
38 14 0.42
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (35 bp):
AAATATATAATATATATTATAAATTAAAAATCAGA
Found at i:29467 original size:75 final size:75
Alignment explanation
Indices: 29328--29470 Score: 180
Period size: 75 Copynumber: 1.9 Consensus size: 75
29318 CATTGGGAAG
* * * * **
29328 CTCAAAATTAGAATTCGAAACAGCATCCTGATTAGGAGAATCAGCTTCAAGATGCTGCCTATCAT
1 CTCAAAATTAGAATTCGAAACAGAAACCTGATAAAGAGAATCAGCTTCAAGATGCTGCAAATCAT
29393 CATTATGATT
66 CATTATGATT
* * * *
29403 CTCAAAATTTA-AATTCGAATCAGAAACCTGATAAAGTGAATCAGCTTCAAGTTGTTGCAAATCA
1 CTCAAAA-TTAGAATTCGAAACAGAAACCTGATAAAGAGAATCAGCTTCAAGATGCTGCAAATCA
29467 TCAT
65 TCAT
29471 CAGAAAACTT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
75 54 0.95
76 3 0.05
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (75 bp):
CTCAAAATTAGAATTCGAAACAGAAACCTGATAAAGAGAATCAGCTTCAAGATGCTGCAAATCAT
CATTATGATT
Found at i:29493 original size:75 final size:75
Alignment explanation
Indices: 29409--29581 Score: 161
Period size: 75 Copynumber: 2.3 Consensus size: 75
29399 GATTCTCAAA
* * *
29409 ATTTAAATTCGAATCAGAAACCTGATAAAGTGAATCAGCTTCAAG-TTGTTG-CAAATCATCATC
1 ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATT-TTGCCAAA-CACCATC
*
29472 AGAAAACTTAGT
64 AGAAAACTCAGT
* ** * * * * * *
29484 ATTTGAATTCAAAAGAGGAATCTGGTCAGGTGAATCAACTTCAAGATTTTGCCTAACACCATCAG
1 ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATTTTGCCAAACACCATCAG
* *
29549 CAAACTCATT
66 AAAACTCAGT
* *
29559 ATTTGAATTCGAATTAGCAACCT
1 ATTTGAATTCGAATCAGAAACCT
29582 AAGAAGGAGA
Statistics
Matches: 76, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
75 71 0.93
76 5 0.07
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (75 bp):
ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATTTTGCCAAACACCATCAG
AAAACTCAGT
Found at i:34528 original size:23 final size:22
Alignment explanation
Indices: 34502--34556 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
34492 CAATGAAATT
*
34502 TTGATAACCAACACTATGAGATG
1 TTGATAACCAACA-TATGAGATA
* ** *
34525 TTGATAGCCTCCATATGATATA
1 TTGATAACCAACATATGAGATA
34547 TTGATAACCA
1 TTGATAACCA
34557 CGTTATGAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (22 bp):
TTGATAACCAACATATGAGATA
Found at i:34631 original size:22 final size:22
Alignment explanation
Indices: 34606--34878 Score: 86
Period size: 22 Copynumber: 12.6 Consensus size: 22
34596 AATCACACCC
34606 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAATCACATTA
* * **
34628 TGAAATTATGAT-ATCCTCGCTA
1 TGAAATTTTGATAAT-CACATTA
*
34650 TGAAATTTTGATAAAC-CATCCTA
1 TGAAATTTTGATAATCACAT--TA
* * * **
34673 TAAAATTTTGATAAACTTCCCTA
1 TGAAATTTTGATAATC-ACATTA
* *
34696 TAAAATTTTGATAA-CATCCTTA
1 TGAAATTTTGATAATCA-CATTA
*
34718 TGAAATCTTGAT-A--AC--TA
1 TGAAATTTTGATAATCACATTA
* * * **
34735 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAATCACATTA
** * * *
34756 TGATTTTTTTATAACCTCATTA
1 TGAAATTTTGATAATCACATTA
* * **
34778 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAATCACATTA
34800 TGAAATTTTGAT-AT-ACATACTA
1 TGAAATTTTGATAATCACAT--TA
* *
34822 TGAAATTTTGATAA-CCCTCTTA
1 TGAAATTTTGATAATCAC-ATTA
* * *
34844 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAATC-ACATTA
34866 TGAAATTTTGATA
1 TGAAATTTTGATA
34879 TCCTCCCTGA
Statistics
Matches: 189, Mismatches: 41, Indels: 41
0.70 0.15 0.15
Matches are distributed among these distances:
16 9 0.05
17 3 0.02
19 2 0.01
20 2 0.01
21 10 0.05
22 124 0.66
23 37 0.20
24 1 0.01
25 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAATCACATTA
Found at i:34678 original size:23 final size:22
Alignment explanation
Indices: 34647--34731 Score: 100
Period size: 23 Copynumber: 3.8 Consensus size: 22
34637 GATATCCTCG
*
34647 CTATGAAATTTTGATAAACCATC
1 CTATAAAATTTTGATAAA-CATC
*
34670 CTATAAAATTTTGATAAACTTCC
1 CTATAAAATTTTGATAAACAT-C
34693 CTATAAAATTTTGAT-AACATC
1 CTATAAAATTTTGATAAACATC
* *
34714 CTTATGAAATCTTGATAA
1 C-TATAAAATTTTGATAA
34732 CTACAAATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
21 2 0.04
22 18 0.33
23 34 0.63
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (22 bp):
CTATAAAATTTTGATAAACATC
Found at i:34823 original size:66 final size:67
Alignment explanation
Indices: 34606--34879 Score: 180
Period size: 66 Copynumber: 4.2 Consensus size: 67
34596 AATCACACCC
* * * * *
34606 TGAAATTTTGATA-ATCA-CATTATGAAATTATGAT-ATCCTCGCTATGAAATTTTGATAAACCA
1 TGAAATTTTGATATA-CATCACTATGAAATTTTGATAACCCTC-TTATGAAATTTTGA-AAACTA
**
34668 TCCTA
63 AACTA
* * * * * * *
34673 TAAAATTTTGATAAACTTCCCTATAAAATTTTGATAA-CATCCTTATGAAATCTTG---A-T-AA
1 TGAAATTTTGATATACATCACTATGAAATTTTGATAACCCT-CTTATGAAATTTTGAAAACTAAA
34732 CTA
65 CTA
* * * ** * * * *
34735 -CAAATTTTGATA-ACCTCCCTATGATTTTTTTATAA-CCTCATTATGAAATTTTGTTAATCT-C
1 TGAAATTTTGATATACATCACTATGAAATTTTGATAACCCTC-TTATGAAATTTTG-AAAACTAA
*
34796 CCTA
64 ACTA
34800 TGAAATTTTGATATACAT-ACTATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAAC
1 TGAAATTTTGATATACATCACTATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAAC
34864 TA
66 TA
34866 TGAAATTTTGATAT
1 TGAAATTTTGATAT
34880 CCTCCCTGAA
Statistics
Matches: 160, Mismatches: 33, Indels: 29
0.72 0.15 0.13
Matches are distributed among these distances:
59 1 0.01
60 32 0.20
61 11 0.07
62 3 0.02
64 1 0.01
65 8 0.05
66 55 0.34
67 20 0.12
68 27 0.17
69 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (67 bp):
TGAAATTTTGATATACATCACTATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTAAAC
TA
Found at i:34824 original size:44 final size:43
Alignment explanation
Indices: 34606--34897 Score: 185
Period size: 44 Copynumber: 6.8 Consensus size: 43
34596 AATCACACCC
* ** * * * *
34606 TGAAATTTTGATAATCACATTATGAAATTATGATATCCTCGCTA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACAT-ACTA
* * * *
34650 TGAAATTTTGATAAAC-CATCCTATAAAATTTTGATAAACTTCCCTA
1 TGAAATTTTGATAATCTC--CCTATGAAATTTTGAT-AACAT-ACTA
* * *
34696 TAAAATTTTGATAA-CATCCTTATGAAATCTTGATAAC-TAC--
1 TGAAATTTTGATAATC-TCCCTATGAAATTTTGATAACATACTA
* ** * * *
34736 --AAATTTTGATAACCTCCCTATGATTTTTTTATAACCTCATTA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACAT-ACTA
*
34778 TGAAATTTTGTTAATCTCCCTATGAAATTTTGATATACATACTA
1 TGAAATTTTGATAATCTCCCTATGAAATTTTGATA-ACATACTA
* *
34822 TGAAATTTTGATAA-C-CCTCTTATGAAATTTTGAAAACTAAACTA
1 TGAAATTTTGATAATCTCC-C-TATGAAATTTTGATAAC-ATACTA
34866 TGAAATTTTGAT-ATCCTCCC--TGAAATTTTGAT
1 TGAAATTTTGATAAT-CTCCCTATGAAATTTTGAT
34898 TACTCCATAA
Statistics
Matches: 199, Mismatches: 30, Indels: 40
0.74 0.11 0.15
Matches are distributed among these distances:
38 28 0.14
39 2 0.01
40 1 0.01
42 14 0.07
43 7 0.04
44 93 0.47
45 31 0.16
46 22 0.11
47 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (43 bp):
TGAAATTTTGATAATCTCCCTATGAAATTTTGATAACATACTA
Found at i:35120 original size:25 final size:24
Alignment explanation
Indices: 34978--35130 Score: 96
Period size: 22 Copynumber: 6.8 Consensus size: 24
34968 AGAAATACTA
*
34978 CTATGAAATTTTGTTAATCACAT-T
1 CTATGAAATTTTGATAATC-CATCT
* *
35002 -T-TGAAAATTTGATAA-AC-TCT
1 CTATGAAATTTTGATAATCCATCT
* *
35022 TTATGAAATTTTAATAA-CC-TCT
1 CTATGAAATTTTGATAATCCATCT
* * * *
35044 CTATAAAATTTTGTTGA-CC-CCT
1 CTATGAAATTTTGATAATCCATCT
* *
35066 CTATGAAATTTTGGTAAT-CTTC-
1 CTATGAAATTTTGATAATCCATCT
35088 CTAT-AAATTTTGATAATCCGATCT
1 CTATGAAATTTTGATAATCC-ATCT
*
35112 CTATGAAATTTCGATAATC
1 CTATGAAATTTTGATAATC
35131 AGTCTATGAG
Statistics
Matches: 101, Mismatches: 19, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
19 1 0.01
20 2 0.02
21 13 0.13
22 64 0.63
23 4 0.04
24 4 0.04
25 13 0.13
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (24 bp):
CTATGAAATTTTGATAATCCATCT
Found at i:35275 original size:22 final size:22
Alignment explanation
Indices: 35208--35349 Score: 110
Period size: 22 Copynumber: 6.5 Consensus size: 22
35198 TTCATATGAG
*
35208 ATTTTGATAACCACACTAAAAA
1 ATTTTGATAACCACACTATAAA
*
35230 ATTTTGATAACCACACTATGAA
1 ATTTTGATAACCACACTATAAA
* * *
35252 ATTTTGATAACCTCCCCATAAA
1 ATTTTGATAACCACACTATAAA
* * *
35274 ATATT-AGTAACCTC-CTTATGAA
1 ATTTTGA-TAACCACAC-TATAAA
* *
35296 ATTTTGTTAACCACACTATGAA
1 ATTTTGATAACCACACTATAAA
* * * *
35318 ATTCTT-ATAACCTCGCTATGAC
1 ATT-TTGATAACCACACTATAAA
35340 ATTTTGATAA
1 ATTTTGATAA
35350 TCTCTTTGAT
Statistics
Matches: 98, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
21 4 0.04
22 91 0.93
23 3 0.03
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.35
Consensus pattern (22 bp):
ATTTTGATAACCACACTATAAA
Found at i:35275 original size:44 final size:42
Alignment explanation
Indices: 35188--35349 Score: 153
Period size: 44 Copynumber: 3.7 Consensus size: 42
35178 AAATTGAGAC
* * * *
35188 TTTTATAAGCTTCATATGAGATTTTGATAACCACACTAAAAAA
1 TTTTATAA-CCTCCTATGAAATTTTGATAACCACACTATAAAA
* * * *
35231 TTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATAAAA
1 TTTT-ATAACCTC-CTATGAAATTTTGATAACCACACTATAAAA
* * *
35275 TATTAGTAACCTCCTTATGAAATTTTGTTAACCACACTATGAAA
1 TTTTA-TAACCTCC-TATGAAATTTTGATAACCACACTATAAAA
*
35319 TTCTTATAACCTCGCTATGACATTTTGATAA
1 TT-TTATAACCTC-CTATGAAATTTTGATAA
35350 TCTCTTTGAT
Statistics
Matches: 95, Mismatches: 18, Indels: 11
0.77 0.15 0.09
Matches are distributed among these distances:
43 8 0.08
44 83 0.87
45 4 0.04
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.36
Consensus pattern (42 bp):
TTTTATAACCTCCTATGAAATTTTGATAACCACACTATAAAA
Found at i:35486 original size:22 final size:21
Alignment explanation
Indices: 35458--35578 Score: 116
Period size: 22 Copynumber: 5.5 Consensus size: 21
35448 GTAACCACAC
*
35458 TTTTGATAACCTTCCCATGAAA
1 TTTTGATAACC-TCCTATGAAA
*
35480 TTTTGATAACTTCCTTATGAAA
1 TTTTGATAACCTCC-TATGAAA
* * *
35502 TTTTGGTAACCACACTATGGAA
1 TTTTGATAACCTC-CTATGAAA
*
35524 TTTTGATAACCTCTTCATGAAA
1 TTTTGATAACCTCCT-ATGAAA
* * *
35546 TTATAATAACCATCTTATGAAA
1 TTTTGATAACC-TCCTATGAAA
35568 TTTTGATAACC
1 TTTTGATAACC
35579 ACACAGAGAC
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
21 4 0.05
22 72 0.89
23 5 0.06
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Found at i:35543 original size:66 final size:66
Alignment explanation
Indices: 35458--35582 Score: 173
Period size: 66 Copynumber: 1.9 Consensus size: 66
35448 GTAACCACAC
* * * *
35458 TTTTGATAACCTTCCCATGAAATTTTGATAA-CTTCCTTATGAAATTTTGGTAACCACACTATGG
1 TTTTGATAACCTTCCCATGAAATTATAATAACCAT-CTTATGAAATTTTGATAACCACACTATGG
35522 AA
65 AA
*
35524 TTTTGATAACC-TCTTCATGAAATTATAATAACCATCTTATGAAATTTTGATAACCACAC
1 TTTTGATAACCTTC-CCATGAAATTATAATAACCATCTTATGAAATTTTGATAACCACAC
35583 AGAGACAAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
65 2 0.04
66 48 0.92
67 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (66 bp):
TTTTGATAACCTTCCCATGAAATTATAATAACCATCTTATGAAATTTTGATAACCACACTATGGA
A
Found at i:35556 original size:44 final size:44
Alignment explanation
Indices: 35463--35578 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 44
35453 CACACTTTTG
* * * * *
35463 ATAACCTTCCCATGAAATTTTGATAACTTCCTTATGAAATTTTG
1 ATAACCATCCTATGAAATTTTGATAACCTCCTTATGAAATTATA
* *
35507 GTAACCA-CACTATGGAATTTTGATAACCT-CTTCATGAAATTATA
1 ATAACCATC-CTATGAAATTTTGATAACCTCCTT-ATGAAATTATA
*
35551 ATAACCATCTTATGAAATTTTGATAACC
1 ATAACCATCCTATGAAATTTTGATAACC
35579 ACACAGAGAC
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
43 4 0.07
44 54 0.92
45 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.37
Consensus pattern (44 bp):
ATAACCATCCTATGAAATTTTGATAACCTCCTTATGAAATTATA
Found at i:36736 original size:4 final size:4
Alignment explanation
Indices: 36727--36787 Score: 58
Period size: 4 Copynumber: 15.8 Consensus size: 4
36717 CCCTTAAACA
* *
36727 TAAC TAAC TAAA TAAC TAAC TAAG TAAC TAAC TTAA- TAAC -AA- TCAAC
1 TAAC TAAC TAAC TAAC TAAC TAAC TAAC TAAC -TAAC TAAC TAAC T-AAC
36774 TAAC T-AC TAAC TAA
1 TAAC TAAC TAAC TAA
36788 TTAGTATAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
3 8 0.17
4 35 0.74
5 4 0.09
ACGTcount: A:0.52, C:0.20, G:0.02, T:0.26
Consensus pattern (4 bp):
TAAC
Found at i:36743 original size:12 final size:12
Alignment explanation
Indices: 36726--36766 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
36716 GCCCTTAAAC
36726 ATAACTAACTAA
1 ATAACTAACTAA
36738 ATAACTAACTAA
1 ATAACTAACTAA
* *
36750 GTAACTAACTTA
1 ATAACTAACTAA
36762 ATAAC
1 ATAAC
36767 AATCAACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27
Consensus pattern (12 bp):
ATAACTAACTAA
Found at i:47997 original size:13 final size:13
Alignment explanation
Indices: 47979--48003 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47969 TTGGAATTCC
47979 AAATAATATTTAT
1 AAATAATATTTAT
47992 AAATAATATTTA
1 AAATAATATTTA
48004 GAATATTGAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:48358 original size:13 final size:13
Alignment explanation
Indices: 48340--48364 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48330 TTGGAATTCC
48340 AAATAATATTTAT
1 AAATAATATTTAT
48353 AAATAATATTTA
1 AAATAATATTTA
48365 GAATATTGAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:48516 original size:361 final size:356
Alignment explanation
Indices: 47817--48903 Score: 1451
Period size: 361 Copynumber: 3.1 Consensus size: 356
47807 ATTATAAATC
* * *
47817 GAAAAACCCGATGCGAATGCGCGGGAAAAATATCTAGTA-TTACTATTAAAGTTATCCCCAAACT
1 GAAAAACCCGACGCGAATGCGCAGGAATAATATCTA-TATTTACTATTAAAGTTATCCCCAAACT
47881 GTTATATGCTCAGTATTTGTCTTTTCTCATGTTGACATTTGTCCAAAGTTAATTGGTTGGGAGAA
65 GTTATATGCTCAGTATTTG-CTTTTCTCATGTTGACATTTGTCCAAAGTTAATTGGTTGGGAGAA
*
47946 AACCA-ATATA-TATTATTATATATTTGGAATTCCAAATAATATTTATAAATAATATTTAGAATA
129 AACAATATATATTATTATTATATATTTGGAATTCCAAATAATATTTATAAATAATATTTAGAATA
* * *
48009 TTGAATTATAATTAAAGTAAAACTCCATTTTCTATTTTCCAGTAAATAATTATTTGAATGCATAT
194 TTGAATTATAATCAAAGTAAAACTTCATTTTCTATTTTCCAGTAAATAATTATTTGAATACATAT
*
48074 TAAAATTCTAACAGTATTTCCTTCCATTTAACTTAATTGTTATTACATAAAATAAAATTTTACTT
259 TAAAATTCTAACAGTATTTCCTTCCATTTAACTTAATTGCTATTACATAAAATAAAATTTTACTT
*
48139 AAAATTGAAATTACTCAGTTCCAATCATAAACT
324 AAAATTGAAATTACTCAATTCCAATCATAAACT
*
48172 GAAAAACCCGACGCGAATGTGCAGGAATAATATCTATACTTTTACTATTAAAGTTATCCCCAAAC
1 GAAAAACCCGACGCGAATGCGCAGGAATAATATCTATA--TTTACTATTAAAGTTATCCCCAAAC
*
48237 TGTTATATGCTCAGTATTTGCCTTTTCTCATGTTGACATTTGTCCAAAGTTGATTGGTTGGGAGA
64 TGTTATATGCTCAGTATTTG-CTTTTCTCATGTTGACATTTGTCCAAAGTTAATTGGTTGGGAGA
48302 AAATCAATATATATTTATTATTATATATTTGGAATTCCAAATAATATTTATAAATAATATTTAGA
128 AAA-CAATATATA-TTATTATTATATATTTGGAATTCCAAATAATATTTATAAATAATATTTAGA
*
48367 ATATTGAATTATAATCAAAGTAAAACTTCATTTTCTATTTTCCAGTAAATGATTATTTGAATACA
191 ATATTGAATTATAATCAAAGTAAAACTTCATTTTCTATTTTCCAGTAAATAATTATTTGAATACA
* *
48432 TATTAAAATTCTAACAATATTTTCTTCCATTTAACTTAATTGCTATTACATAAAATAAAATTTTA
256 TATTAAAATTCTAACAGTATTTCCTTCCATTTAACTTAATTGCTATTACATAAAATAAAATTTTA
48497 CTTAAAATTGAAATTACTCAATTCCAATCATAAACT
321 CTTAAAATTGAAATTACTCAATTCCAATCATAAACT
* * * *
48533 GAAAAACCTGACGCGAATGCGC-GAGAATAATATCTA-GTTTCCTATTAAAGTTATCCACAAACT
1 GAAAAACCCGACGCGAATGCGCAG-GAATAATATCTATATTTACTATTAAAGTTATCCCCAAACT
* * * * * * * *
48596 GTTGTATACTCAATATTTGGTTCTTCTCCTGCTGACATTTGTCCAAA-TTTATTGGTCGGGAGAA
65 GTTATATGCTCAGTATTTGCTT-TTCTCATGTTGACATTTGTCCAAAGTTAATTGGTTGGGAGAA
* *
48660 AACCATTATATATTATTATATTATATATTTGAAATTCC-------------AAATAATATTTAG-
129 AA-CAATATATATTA-T-TATTATATATTTGGAATTCCAAATAATATTTATAAATAATATTTAGA
* * *
48711 A-A---CA-TATAATCAAAGTAAAAC-TCTATTTTCTTTTTTCCAGT--ATAATTATTTGAATAG
191 ATATTGAATTATAATCAAAGTAAAACTTC-ATTTTCTATTTTCCAGTAAATAATTATTTGAATAC
* * * * *
48768 ACATTAAAATTCTAACAGTATTTCCTTACATTCAACTTAATTGCTA--ACCTAAGATAAAATTTT
255 ATATTAAAATTCTAACAGTATTTCCTTCCATTTAACTTAATTGCTATTACATAAAATAAAATTTT
* * *
48831 ACTTAGAATTGAAATTACTCAATTCCAATTATAAACC
320 ACTTAAAATTGAAATTACTCAATTCCAATCATAAACT
* * * **
48868 AAAAAACCCTACGTGAATGCGCAGGGTTAATATCTA
1 GAAAAACCCGACGCGAATGCGCAGGAATAATATCTA
48904 GTAGTTTTTA
Statistics
Matches: 668, Mismatches: 51, Indels: 46
0.87 0.07 0.06
Matches are distributed among these distances:
335 77 0.12
336 1 0.00
337 55 0.08
338 2 0.00
339 33 0.05
340 1 0.00
343 1 0.00
344 1 0.00
345 13 0.02
354 2 0.00
355 32 0.05
356 3 0.00
357 118 0.18
358 83 0.12
359 5 0.01
360 1 0.00
361 240 0.36
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (356 bp):
GAAAAACCCGACGCGAATGCGCAGGAATAATATCTATATTTACTATTAAAGTTATCCCCAAACTG
TTATATGCTCAGTATTTGCTTTTCTCATGTTGACATTTGTCCAAAGTTAATTGGTTGGGAGAAAA
CAATATATATTATTATTATATATTTGGAATTCCAAATAATATTTATAAATAATATTTAGAATATT
GAATTATAATCAAAGTAAAACTTCATTTTCTATTTTCCAGTAAATAATTATTTGAATACATATTA
AAATTCTAACAGTATTTCCTTCCATTTAACTTAATTGCTATTACATAAAATAAAATTTTACTTAA
AATTGAAATTACTCAATTCCAATCATAAACT
Found at i:51425 original size:20 final size:20
Alignment explanation
Indices: 51384--51426 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
51374 GATTTTGAAG
**
51384 ATTAGAAAGTTAAATTCCAA
1 ATTAGAAAGTTAAATTAAAA
51404 ATTA-AAAGTTCAAATTAAAA
1 ATTAGAAAGTT-AAATTAAAA
51424 ATT
1 ATT
51427 GCCCACATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (20 bp):
ATTAGAAAGTTAAATTAAAA
Found at i:53187 original size:31 final size:32
Alignment explanation
Indices: 53152--53228 Score: 111
Period size: 31 Copynumber: 2.4 Consensus size: 32
53142 AGACCTAGAC
53152 CTAGACCCAATCTTTTTTTTTTTTGCCA-AAG
1 CTAGACCCAATCTTTTTTTTTTTTGCCATAAG
* *
53183 CTAGACCCAATTTTTTTTTTTTTTGGCATTAAG
1 CTAGACCCAATCTTTTTTTTTTTTGCCA-TAAG
*
53216 CTGGACCCAATCT
1 CTAGACCCAATCT
53229 ATAAAATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 26 0.65
33 14 0.35
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (32 bp):
CTAGACCCAATCTTTTTTTTTTTTGCCATAAG
Found at i:57480 original size:13 final size:13
Alignment explanation
Indices: 57441--57478 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
57431 AATTTACTTT
57441 TTAATTTCAGAAA
1 TTAATTTCAGAAA
57454 TTAATTTCAGAAA
1 TTAATTTCAGAAA
*
57467 TTCATTTC-GAAA
1 TTAATTTCAGAAA
57479 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (13 bp):
TTAATTTCAGAAA
Found at i:62976 original size:6 final size:6
Alignment explanation
Indices: 62965--63001 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
62955 TTTGATAGTA
62965 TATATC TATATC TATATC TATATAC TATATAC TATAT
1 TATATC TATATC TATATC TATAT-C TATAT-C TATAT
63002 AAGTCTAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.49
Consensus pattern (6 bp):
TATATC
Found at i:63002 original size:14 final size:14
Alignment explanation
Indices: 62963--63002 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
62953 ATTTTGATAG
62963 TATATATCTATAT-C
1 TATATA-CTATATAC
62977 TATAT-CTATATAC
1 TATATACTATATAC
62990 TATATACTATATA
1 TATATACTATATA
63003 AGTCTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
14 12 0.50
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (14 bp):
TATATACTATATAC
Found at i:63244 original size:28 final size:27
Alignment explanation
Indices: 63202--63256 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
63192 TTTTTATTTG
*
63202 AGTTTGTTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTTGAGTCAGTTTCGAGTC
63228 AGTTTGTTTTTTCGAGTCAGTTTCGAGTC
1 AGTTTG-TTTTT-GAGTCAGTTTCGAGTC
63257 TAGTCTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 9 0.36
29 5 0.20
ACGTcount: A:0.13, C:0.11, G:0.27, T:0.49
Consensus pattern (27 bp):
AGTTTGTTTTTGAGTCAGTTTCGAGTC
Done.