Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012546.1 Corchorus olitorius cultivar O-4 contig12579, 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: 54004
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Found at i:3609 original size:64 final size:64
Alignment explanation
Indices: 3535--3664 Score: 233
Period size: 64 Copynumber: 2.0 Consensus size: 64
3525 GAAGCTTGTC
*
3535 TTCCATTATTGGACTTTGCAGAGCATTATTGAAAGATTCCTTTCAACTTTTAACTTGTTTTGCT
1 TTCCATTATTGAACTTTGCAGAGCATTATTGAAAGATTCCTTTCAACTTTTAACTTGTTTTGCT
* *
3599 TTCCATTATTGAACTTTGCAGAGCATTATTGAAAGATTTCTTTCAACTTTTGACTTGTTTTGCT
1 TTCCATTATTGAACTTTGCAGAGCATTATTGAAAGATTCCTTTCAACTTTTAACTTGTTTTGCT
3663 TT
1 TT
3665 TCTCCCATCT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (64 bp):
TTCCATTATTGAACTTTGCAGAGCATTATTGAAAGATTCCTTTCAACTTTTAACTTGTTTTGCT
Found at i:3698 original size:20 final size:20
Alignment explanation
Indices: 3673--3710 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3663 TTTCTCCCAT
3673 CTTTGCAGAGCATTATTGGA
1 CTTTGCAGAGCATTATTGGA
3693 CTTTGCAGAGCATTATTG
1 CTTTGCAGAGCATTATTG
3711 AAGCTTGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (20 bp):
CTTTGCAGAGCATTATTGGA
Found at i:10208 original size:36 final size:36
Alignment explanation
Indices: 10161--10236 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
10151 TTTACCTCAA
10161 TAAATACAAAATTTTGAAAAATTTCACATTCCAAAC
1 TAAATACAAAATTTTGAAAAATTTCACATTCCAAAC
10197 TAAATACAAAATTTTGAAAAATTTCACATTCCAAAC
1 TAAATACAAAATTTTGAAAAATTTCACATTCCAAAC
10233 TAAA
1 TAAA
10237 ATTCGTTGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (36 bp):
TAAATACAAAATTTTGAAAAATTTCACATTCCAAAC
Found at i:11893 original size:2 final size:2
Alignment explanation
Indices: 11886--11910 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11876 CTAAAAGAGC
11886 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11911 CTAGTTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11982 original size:22 final size:22
Alignment explanation
Indices: 11957--12017 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
11947 TCAAATATTT
11957 TTATGAAATTTTGATAATTACC
1 TTATGAAATTTTGATAATTACC
11979 TTATGAAATTTTGATAATTACC
1 TTATGAAATTTTGATAATTACC
* *
12001 CTATGAAATTATGATAA
1 TTATGAAATTTTGATAA
12018 ACTTCCAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (22 bp):
TTATGAAATTTTGATAATTACC
Found at i:12902 original size:27 final size:27
Alignment explanation
Indices: 12850--12914 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 27
12840 TACCCTTCTT
12850 TTAAATATATATTTCTAAATTGCCATTA
1 TTAAATA-ATATTTCTAAATTGCCATTA
12878 TTAAATAATATTT-TAATTATT-CCATTA
1 TTAAATAATATTTCTAA--ATTGCCATTA
12905 TTAAAATAAT
1 TT-AAATAAT
12915 GGAAATTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 3 0.09
27 14 0.41
28 17 0.50
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.48
Consensus pattern (27 bp):
TTAAATAATATTTCTAAATTGCCATTA
Found at i:13027 original size:16 final size:16
Alignment explanation
Indices: 12993--13047 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
12983 GCTCGGGCGG
* *
12993 GTTCGGGTA-CTTCGG
1 GTTCGGGTATTTTCGA
13008 GTTCGGGCT-TTTTCGA
1 GTTCGGG-TATTTTCGA
*
13024 GTTCGAGTATTTTCGA
1 GTTCGGGTATTTTCGA
*
13040 GCTCGGGT
1 GTTCGGGT
13048 TCGGGTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 8 0.25
16 24 0.75
ACGTcount: A:0.09, C:0.18, G:0.35, T:0.38
Consensus pattern (16 bp):
GTTCGGGTATTTTCGA
Found at i:13291 original size:22 final size:21
Alignment explanation
Indices: 13233--13527 Score: 127
Period size: 22 Copynumber: 13.5 Consensus size: 21
13223 TGTGCTTCCA
* *
13233 GTTAACAAAATTTTATAAGGAA
1 GTTATCAAAATTTTAT-AGGAG
* *
13255 GTTAT-AGAAAATTTATAGGTAT
1 GTTATCA-AAATTTTATAGG-AG
*
13277 GTTATCAAAATTTTATAAGATG
1 GTTATCAAAATTTTATAGGA-G
* *
13299 GATATCAAAATTTCAT--GAG
1 GTTATCAAAATTTTATAGGAG
* *
13318 GTTATCAAAATTTCAAATGGAG
1 GTTATCAAAATTTTATA-GGAG
13340 GTTATCAAAATTTTATAAGGAG
1 GTTATCAAAATTTTAT-AGGAG
*
13362 GTTTAT-AAAATTTTCACAGTGAG
1 G-TTATCAAAATTTT-ATAG-GAG
* *
13385 G-TATCACAATTTCCTGATA--TG
1 GTTATCAAAATTT--T-ATAGGAG
* *
13406 GTTATCAAAATTTTATAATGTG
1 GTTATCAAAATTTTAT-AGGAG
* * * *
13428 ATTACCAATATTTTATCGGAAG
1 GTTATCAAAATTTTATAGG-AG
* * *
13450 GTTATCAAAATTTCATACTGTG
1 GTTATCAAAATTTTATA-GGAG
* * * * *
13472 TGCTACCAACATTTCATTGGGAG
1 -GTTATCAAAATTTTA-TAGGAG
* *
13495 GTTATCAAAATTTCATAGGGTG
1 GTTATCAAAATTTTATA-GGAG
13517 GTTATCAAAAT
1 GTTATCAAAAT
13528 GAAATTTAAA
Statistics
Matches: 208, Mismatches: 42, Indels: 46
0.70 0.14 0.16
Matches are distributed among these distances:
19 17 0.08
20 4 0.02
21 12 0.06
22 145 0.70
23 26 0.12
24 4 0.02
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (21 bp):
GTTATCAAAATTTTATAGGAG
Found at i:13498 original size:45 final size:44
Alignment explanation
Indices: 13405--13511 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 44
13395 TTCCTGATAT
* * *
13405 GGTTATCAAAATTTTATAATGTGATTACCAATATTTTATCGGAA
1 GGTTATCAAAATTTCATAATGTGATTACCAACATTTCATCGGAA
* * *
13449 GGTTATCAAAATTTCATACTGTG-TGCTACCAACATTTCATTGGGA
1 GGTTATCAAAATTTCATAATGTGAT--TACCAACATTTCATCGGAA
13494 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
13512 GGGTGGTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 1 0.02
44 21 0.38
45 33 0.60
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAATGTGATTACCAACATTTCATCGGAA
Found at i:13686 original size:20 final size:20
Alignment explanation
Indices: 13638--13688 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 20
13628 TTATTATGTA
*
13638 ATTATCAAAATTTTATATTG
1 ATTATCAAAATTTTATAGTG
13658 AGGTTATCAAAATTTTATAGTG
1 A--TTATCAAAATTTTATAGTG
13680 ATTATCAAA
1 ATTATCAAA
13689 TTTCATAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 9 0.32
22 19 0.68
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (20 bp):
ATTATCAAAATTTTATAGTG
Found at i:14115 original size:2 final size:2
Alignment explanation
Indices: 14110--14146 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
14100 TTCGTACTTT
14110 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14147 CTAGTATTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14257 original size:22 final size:22
Alignment explanation
Indices: 14209--14264 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
14199 TATTTTTATT
*
14209 AAATTTTGATAACCACACTATG
1 AAATTTTGATAACCACACTATA
* ** *
14231 GAATTTTGATAATTACCCTATA
1 AAATTTTGATAACCACACTATA
*
14253 AAATTCTGATAA
1 AAATTTTGATAA
14265 ACTCCCAATG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:14576 original size:22 final size:22
Alignment explanation
Indices: 14551--14641 Score: 85
Period size: 22 Copynumber: 4.1 Consensus size: 22
14541 TTGAACTTTA
* *
14551 ATAACTACACTATGAAATTCTG
1 ATAACCACACTATGAAATTTTG
**
14573 ATAACCATTCTATGAAATTTTG
1 ATAACCACACTATGAAATTTTG
* * * *
14595 GTCATCACACTCTGAAATTTTG
1 ATAACCACACTATGAAATTTTG
*
14617 ATAACCACAGTAT-AAATTTGTG
1 ATAACCACACTATGAAATTT-TG
14639 ATA
1 ATA
14642 CCCTCTATAT
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
21 6 0.11
22 47 0.89
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (22 bp):
ATAACCACACTATGAAATTTTG
Found at i:14774 original size:22 final size:22
Alignment explanation
Indices: 14726--14914 Score: 125
Period size: 22 Copynumber: 8.5 Consensus size: 22
14716 GATTTGGTAG
* * **
14726 ACTATGAAATTTGGATAATCAA
1 ACTATGAAATTTTGATAACCTC
14748 ACTATGAAATTTTGATAACCTC
1 ACTATGAAATTTTGATAACCTC
* * * *
14770 CCTATGGAATGTTGATAACTTC
1 ACTATGAAATTTTGATAACCTC
* * *
14792 CCTAT-AGAATTTAGTGTTAATCTC
1 ACTATGA-AATTT--TGATAACCTC
*
14816 ACTATGAAATTTTGATAAACAT-
1 ACTATGAAATTTTGAT-AACCTC
* * *
14838 AATATGAAACTTTGATTACCT-
1 ACTATGAAATTTTGATAACCTC
* *
14859 TCTATGAAATTTTTG-TAACCAC
1 ACTATGAAA-TTTTGATAACCTC
* * *
14881 ATTATGAAATTTTGATAGCCAC
1 ACTATGAAATTTTGATAACCTC
14903 ACTATGAAATTT
1 ACTATGAAATTT
14915 CAATAATCTA
Statistics
Matches: 129, Mismatches: 30, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
21 19 0.15
22 90 0.70
23 3 0.02
24 16 0.12
25 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCTC
Found at i:17666 original size:24 final size:24
Alignment explanation
Indices: 17622--17696 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
17612 CTAATAACTC
* *
17622 GGGTAAAAGAA-ATTAGTTTTTATT
1 GGGTAAAAGAATTTTA-CTTTTATT
*
17646 GGGTAAAAGAATTTTACTTTTTTT
1 GGGTAAAAGAATTTTACTTTTATT
*
17670 TGGTACTGAAAGAATTTTACTTTTATT
1 GGGTA---AAAGAATTTTACTTTTATT
17697 TTTTATTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
24 21 0.50
25 3 0.07
27 18 0.43
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (24 bp):
GGGTAAAAGAATTTTACTTTTATT
Found at i:45493 original size:17 final size:17
Alignment explanation
Indices: 45471--45503 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
45461 TTTTATGGAT
45471 ATTTAT-ATTATTAATTA
1 ATTTATAATT-TTAATTA
45488 ATTTATAATTTTAATT
1 ATTTATAATTTTAATT
45504 GATATAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATAATTTTAATTA
Found at i:47632 original size:78 final size:77
Alignment explanation
Indices: 47542--47710 Score: 241
Period size: 78 Copynumber: 2.2 Consensus size: 77
47532 GTTTTTTAAT
* *
47542 TAAAATATTAAAATGGTAAACTGAAATAGTCAT-AAGTATATTAGATTTAATTAAATAAAAATAA
1 TAAAATA-TAAAATGGTAAAATAAAATAGTCATAAAG-ATATTAGATTTAATTAAATAAAAATAA
47606 AGTATTTAGTTGAG
64 AGTATTTAGTTGAG
* * *
47620 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAATATAGA
1 TAAAATA-TAAAATGGTAAAATAAAATAGTCATAAAGATATTAGATTTAATTAAATAAAAATAAA
*
47685 GTTTTTAGTTGAG
65 GTATTTAGTTGAG
47698 TAAAACTATAAAA
1 TAAAA-TATAAAA
47711 GTTTAAACAA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
78 77 0.94
79 5 0.06
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.34
Consensus pattern (77 bp):
TAAAATATAAAATGGTAAAATAAAATAGTCATAAAGATATTAGATTTAATTAAATAAAAATAAAG
TATTTAGTTGAG
Found at i:49367 original size:22 final size:22
Alignment explanation
Indices: 49328--49393 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
49318 AAAATTCAGT
*
49328 GTGTGGTTA-CTAAATTTTATA
1 GTGTGGTTACCAAAATTTTATA
*
49349 GTGT-GTTTCTCAAAATTTTATA
1 GTGTGGTTAC-CAAAATTTTATA
*
49371 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTACCAAAATTTTATA
49393 G
1 G
49394 GTAGGATGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 3 0.08
21 4 0.11
22 27 0.71
23 4 0.11
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (22 bp):
GTGTGGTTACCAAAATTTTATA
Found at i:49431 original size:22 final size:22
Alignment explanation
Indices: 49339--49431 Score: 82
Period size: 22 Copynumber: 4.2 Consensus size: 22
49329 TGTGGTTACT
*
49339 AAATTTTATAGTGT-GTTTCTCA
1 AAATTTTATAGTGTAG-TTATCA
* *
49361 AAATTTTATAGTGTGGTTACCA
1 AAATTTTATAGTGTAGTTATCA
* * * *
49383 AAATTTCATAG-GTAGGATGTTA
1 AAATTTTATAGTGTA-GTTATCA
49405 AAATTTTATAGTGTAGTTATCA
1 AAATTTTATAGTGTAGTTATCA
*
49427 CAATT
1 AAATT
49432 CCTTGTGATG
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
21 2 0.04
22 49 0.89
23 4 0.07
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (22 bp):
AAATTTTATAGTGTAGTTATCA
Found at i:49472 original size:22 final size:22
Alignment explanation
Indices: 49441--49571 Score: 102
Period size: 22 Copynumber: 5.8 Consensus size: 22
49431 TCCTTGTGAT
49441 GTTATCAAAATATCATAAGGAG
1 GTTATCAAAATATCATAAGGAG
* *
49463 GTTATTAAAATAAAATATCATAAGGAT
1 GTTA-T----CAAAATATCATAAGGAG
* *
49490 GTTATCAAAATTTCATATGGAG
1 GTTATCAAAATATCATAAGGAG
* *
49512 GTTATCAAAATTTCATAAGAAG
1 GTTATCAAAATATCATAAGGAG
* ** *
49534 GTTATCGAAAT-TCATGCGAAG
1 GTTATCAAAATATCATAAGGAG
* *
49555 GTTGTCAAAATTTCATA
1 GTTATCAAAATATCATA
49572 TTCTGGTTAT
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
21 17 0.19
22 51 0.57
23 1 0.01
26 1 0.01
27 19 0.21
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (22 bp):
GTTATCAAAATATCATAAGGAG
Found at i:49478 original size:27 final size:27
Alignment explanation
Indices: 49447--49522 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
49437 TGATGTTATC
*
49447 AAAATATCATAAGGAGGTTATTAAAAT
1 AAAATATCATAAGGAGGTTATCAAAAT
*
49474 AAAATATCATAAGGATGTTATCAAAAT
1 AAAATATCATAAGGAGGTTATCAAAAT
*
49501 ----T-TCATATGGAGGTTATCAAAAT
1 AAAATATCATAAGGAGGTTATCAAAAT
49523 TTCATAAGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
22 19 0.42
23 1 0.02
27 25 0.56
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (27 bp):
AAAATATCATAAGGAGGTTATCAAAAT
Found at i:49528 original size:44 final size:43
Alignment explanation
Indices: 49438--50288 Score: 177
Period size: 44 Copynumber: 19.3 Consensus size: 43
49428 AATTCCTTGT
* * *
49438 GATGTTATCAAAATATCATAAGGAGGTTATTAAAATAAAATATCATAAG
1 GATGTTATCAAAATTTCATATGGAGGTTATCAAAAT----T-TCAT-AG
49487 GATGTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAAG
1 GATGTTATCAAAATTTCATATGGAGGTTATCAAAATTTCAT-AG
* * * ** * * *
49531 AAGGTTATCGAAA-TTCATGCGAAGGTTGTCAAAATTTCATAT
1 GATGTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAG
** * * * * * *
49573 TCTGGTTATCAAAATTTCATAGGGCGATCATCGAAATCTT-ATGTG
1 GAT-GTTATCAAAATTTCATATGGAGGTTATCAAAAT-TTCAT-AG
* * * *
49618 GAGGTTATTAAAATTTCATA-GGAAGATTATTAAAATTTCATAG
1 GATGTTATCAAAATTTCATATGG-AGGTTATCAAAATTTCATAG
* *
49661 TG-TGCTTATAAAAATTACATAGTGAGATAGAGTGAGCTTATCAAAATTTCA-AG
1 -GATG-TTATCAAAATTTCATA-T--G---GA--G-G-TTATCAAAATTTCATAG
* * * * * * *
49714 TGTTGTTACCAAAATTGCATAGTGTA-ATAATCACAATTTCATA-
1 -GATGTTATCAAAATTTCATA-TGGAGGTTATCAAAATTTCATAG
* * * * * *
49757 GAGGTTAACAACATTTCAT-GGGAGGTTATCAAAATTTTAGAGGG
1 GATGTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATA--G
* * * *
49801 GATATTATCAAAATTT-A-GT-GTGGTTATCAAAATTTTATA-
1 GATGTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAG
** * * * * *
49840 -ATGTGGT----ATTTCAGAGGGAGAGGTTATGAAATTTTCATTG
1 GATGTTATCAAAATTTCATA-TG-GAGGTTATCAAAATTTCATAG
** * * *
49880 TG-TGGCAGTTAAAATTTCATAAT-GAGTTTATCAAAATTTCATTG
1 -GATGTTA-TCAAAATTTCAT-ATGGAGGTTATCAAAATTTCATAG
** * ***
49924 GGGGTTATCAAAATTTAAT-TGTGTTCTTATCAAAATTT-AGTAG
1 GATGTTATCAAAATTTCATATG-GAGGTTATCAAAATTTCA-TAG
* * * * *
49967 GAGGTTAACAAAATTTTATAAGGAGGTTATAAAAAAATTT-ATAGG
1 GATGTTATCAAAATTTCATATGGAGGTTAT--CAAAATTTCATA-G
*
50012 GATGTTATCAAAATTTCATA-AGATGGTTATCAAAATTTCATGAG
1 GATGTTATCAAAATTTCATATGGA-GGTTATCAAAATTTCAT-AG
* * *
50056 G-TGGTTTTCAAAATTTC-T-T-GAGATTATCAAAATTTTATAAG
1 GAT-GTTATCAAAATTTCATATGGAGGTTATCAAAATTTCAT-AG
* * * *
50097 GAGGTTTATAAAAATTTCATA-GTGAGG-TATCACAATTTTAT-G
1 GATG-TTATCAAAATTTCATATG-GAGGTTATCAAAATTTCATAG
* * * *
50139 GTATGGTTATCAAAATTTCATCATGTGA--TTACCAATATTTTATCG
1 G-AT-GTTATCAAAATTTCAT-ATG-GAGGTTATCAAAATTTCATAG
* * * * * * *
50184 GAAGGTTATCAAAATATCATAATGTGTGCTTACCAACATTTCATTGG
1 G-ATGTTATCAAAATTTCAT-ATG-GAGGTTATCAAAATTTCA-TAG
* * * * *
50231 GATGTTATCAAAATTCCAT-GGGTGGTTATAAAAAATTCATTAG
1 GATGTTATCAAAATTTCATATGGAGGTTATCAAAATTTCA-TAG
*
50274 G-TGGTTATTAAAATT
1 GAT-GTTATCAAAATT
50289 ATTTTAGGGA
Statistics
Matches: 595, Mismatches: 138, Indels: 144
0.68 0.16 0.16
Matches are distributed among these distances:
34 4 0.01
35 1 0.00
38 4 0.01
39 15 0.03
40 2 0.00
41 34 0.06
42 51 0.09
43 151 0.25
44 177 0.30
45 46 0.08
46 33 0.06
47 4 0.01
48 2 0.00
49 33 0.06
50 1 0.00
51 2 0.00
52 1 0.00
53 19 0.03
54 15 0.03
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.37
Consensus pattern (43 bp):
GATGTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAG
Found at i:49563 original size:43 final size:44
Alignment explanation
Indices: 49474--49593 Score: 125
Period size: 43 Copynumber: 2.8 Consensus size: 44
49464 TTATTAAAAT
* * * * *
49474 AAAATATCATAAGGATGTTATCAAAATTTCATATGGAGGTTATC
1 AAAATTTCATAAGAAGGTTATCAAAATTTCATACGAAGGTTATC
* * *
49518 AAAATTTCATAAGAAGGTTATCGAAA-TTCATGCGAAGGTTGTC
1 AAAATTTCATAAGAAGGTTATCAAAATTTCATACGAAGGTTATC
****
49561 AAAATTTCATATTCTGGTTATCAAAATTTCATA
1 AAAATTTCATAAGAAGGTTATCAAAATTTCATA
49594 GGGCGATCAT
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 34 0.56
44 27 0.44
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (44 bp):
AAAATTTCATAAGAAGGTTATCAAAATTTCATACGAAGGTTATC
Found at i:49606 original size:65 final size:66
Alignment explanation
Indices: 49490--49659 Score: 180
Period size: 65 Copynumber: 2.6 Consensus size: 66
49480 TCATAAGGAT
* * *
49490 GTTATCAAAATTTCATATGGAGGTTATCAAAATTTCATAAGAAGGTTATCGAAAT-TCATGCGAA
1 GTTATCAAAATTTCATATGCAGGTTATCAAAATTTCATAAGAAGATCATCGAAATCTCATGCGAA
49554 G
66 G
* * * * ** * * *
49555 GTTGTCAAAATTTCATATTCTGGTTATCAAAATTTCATAGGGCGATCATCGAAATCTTATGTGGA
1 GTTATCAAAATTTCATATGCAGGTTATCAAAATTTCATAAGAAGATCATCGAAATCTCATGCGAA
49620 G
66 G
* * * * *
49621 GTTATTAAAATTTCATAGGAAGATTATTAAAATTTCATA
1 GTTATCAAAATTTCATATGCAGGTTATCAAAATTTCATA
49660 GTGTGCTTAT
Statistics
Matches: 84, Mismatches: 20, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
65 46 0.55
66 38 0.45
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (66 bp):
GTTATCAAAATTTCATATGCAGGTTATCAAAATTTCATAAGAAGATCATCGAAATCTCATGCGAA
G
Found at i:49669 original size:22 final size:23
Alignment explanation
Indices: 49622--49685 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 23
49612 TATGTGGAGG
49622 TTATTAAAATTTCATAG-GAAGA
1 TTATTAAAATTTCATAGTGAAGA
* *
49644 TTATTAAAATTTCATAGTG-TGC
1 TTATTAAAATTTCATAGTGAAGA
* *
49666 TTATAAAAATTACATAGTGA
1 TTATTAAAATTTCATAGTGA
49686 GATAGAGTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 35 0.97
23 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (23 bp):
TTATTAAAATTTCATAGTGAAGA
Found at i:49783 original size:21 final size:20
Alignment explanation
Indices: 49748--49793 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
49738 TAATAATCAC
49748 AATTTCATAGAGGTTAACAA
1 AATTTCATAGAGGTTAACAA
* * *
49768 CATTTCATGGGAGGTTATCAA
1 AATTTCAT-AGAGGTTAACAA
49789 AATTT
1 AATTT
49794 TAGAGGGGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (20 bp):
AATTTCATAGAGGTTAACAA
Found at i:49933 original size:21 final size:21
Alignment explanation
Indices: 49890--50288 Score: 180
Period size: 22 Copynumber: 18.3 Consensus size: 21
49880 TGTGGCAGTT
* *
49890 AAAATTTCATAATGAGTTTATC
1 AAAATTTCAT-AGGAGGTTATC
* *
49912 AAAATTTCATTGGGGGTTATC
1 AAAATTTCATAGGAGGTTATC
* * ***
49933 AAAATTTAATTGTGTTCTTATC
1 AAAATTTCATAG-GAGGTTATC
*
49955 AAAATTT-AGTAGGAGGTTAAC
1 AAAATTTCA-TAGGAGGTTATC
* *
49976 AAAATTTTATAAGGAGGTTATAAA
1 AAAATTTCAT-AGGAGGTTAT--C
*
50000 AAAATTT-ATAGGGATGTTATC
1 AAAATTTCATA-GGAGGTTATC
*
50021 AAAATTTCATAAGATGGTTATC
1 AAAATTTCATAGGA-GGTTATC
* *
50043 AAAATTTCATGAGGTGGTTTTC
1 AAAATTTCAT-AGGAGGTTATC
* *
50065 AAAATTTC-T-TGAGATTATC
1 AAAATTTCATAGGAGGTTATC
* *
50084 AAAATTTTATAAGGAGGTTTATA
1 AAAATTTCAT-AGGAGG-TTATC
50107 AAAATTTCATAGTGAGG-TATC
1 AAAATTTCATAG-GAGGTTATC
* *
50128 ACAATTTTAT-GGTATGGTTATC
1 AAAATTTCATAGG-A-GGTTATC
* * * *
50150 AAAATTTCATCATGTGATTACC
1 AAAATTTCAT-AGGAGGTTATC
* * *
50172 AATATTTTATCGGAAGGTTATC
1 AAAATTTCATAGG-AGGTTATC
* * * *
50194 AAAATATCATAATGTGTGCTTACC
1 AAAATTTCAT-A-G-GAGGTTATC
* * *
50218 AACATTTCATTGGGATGTTATC
1 AAAATTTCA-TAGGAGGTTATC
* * * *
50240 AAAATTCCATGGGTGGTTATA
1 AAAATTTCATAGGAGGTTATC
* * *
50261 AAAAATTCATTAGGTGGTTATT
1 AAAATTTCA-TAGGAGGTTATC
50283 AAAATT
1 AAAATT
50289 ATTTTAGGGA
Statistics
Matches: 280, Mismatches: 71, Indels: 52
0.69 0.18 0.13
Matches are distributed among these distances:
19 14 0.05
20 3 0.01
21 72 0.26
22 138 0.49
23 30 0.11
24 21 0.08
25 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (21 bp):
AAAATTTCATAGGAGGTTATC
Found at i:50024 original size:24 final size:23
Alignment explanation
Indices: 49955--50024 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
49945 TGTTCTTATC
*
49955 AAAATTTAGT-AGGAGGTTA-ACA
1 AAAATTTA-TAAGGAGGTTATAAA
*
49977 AAATTTTATAAGGAGGTTATAAA
1 AAAATTTATAAGGAGGTTATAAA
* * *
50000 AAAATTTATAGGGATGTTATCAA
1 AAAATTTATAAGGAGGTTATAAA
50023 AA
1 AA
50025 TTTCATAAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.03
22 16 0.40
23 23 0.57
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (23 bp):
AAAATTTATAAGGAGGTTATAAA
Found at i:50024 original size:45 final size:45
Alignment explanation
Indices: 49955--50046 Score: 116
Period size: 45 Copynumber: 2.0 Consensus size: 45
49945 TGTTCTTATC
*
49955 AAAATTTAGTAGGAGGTTAACAAAATTTTATAAGGA-GGTTATAAA
1 AAAATTTAGTAGGAGGTTAACAAAATTTCATAA-GATGGTTATAAA
* * *
50000 AAAATTTA-TAGGGATGTTATCAAAATTTCATAAGATGGTTATCAA
1 AAAATTTAGTA-GGAGGTTAACAAAATTTCATAAGATGGTTATAAA
50045 AA
1 AA
50047 TTTCATGAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 4 0.10
45 37 0.90
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (45 bp):
AAAATTTAGTAGGAGGTTAACAAAATTTCATAAGATGGTTATAAA
Found at i:50134 original size:63 final size:63
Alignment explanation
Indices: 50016--50134 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 63
50006 TATAGGGATG
* * *
50016 TTATCAAAATTTCATAAGATGGTTATCAAAATTTCATGAGGTGGTTTTCAAAATTTCTTGAGA
1 TTATCAAAATTTCATAAGATGGTTATAAAAATTTCATGAGGTGGGTATCAAAATTTCTTGAGA
* *
50079 TTATCAAAATTTTATAAGGA-GGTTTATAAAAATTTCAT-A-GTGAGGTATCACAATTT
1 TTATCAAAATTTCATAA-GATGG-TTATAAAAATTTCATGAGGTG-GGTATCAAAATTT
50135 TATGGTATGG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
62 3 0.06
63 29 0.60
64 16 0.33
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39
Consensus pattern (63 bp):
TTATCAAAATTTCATAAGATGGTTATAAAAATTTCATGAGGTGGGTATCAAAATTTCTTGAGA
Found at i:50134 original size:85 final size:85
Alignment explanation
Indices: 49999--50157 Score: 189
Period size: 85 Copynumber: 1.9 Consensus size: 85
49989 GAGGTTATAA
* * * * * *
49999 AAAAATTTATAGGGATGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCATGAG-GTGGTTT
1 AAAAATTTATAAGGAGGTTATAAAAATTTCATAAGATGGGTATCAAAATTTCATG-GTATGGTTA
50063 TCAAAATTTCTTGAGATTATC
65 TCAAAATTTCTTGAGATTATC
* * *
50084 AAAATTTTATAAGGAGGTTTATAAAAATTTCAT-AG-TGAGGTATCACAATTTTATGGTATGGTT
1 AAAAATTTATAAGGAGG-TTATAAAAATTTCATAAGATG-GGTATCAAAATTTCATGGTATGGTT
50147 ATCAAAATTTC
64 ATCAAAATTTC
50158 ATCATGTGAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
84 3 0.05
85 45 0.73
86 14 0.23
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (85 bp):
AAAAATTTATAAGGAGGTTATAAAAATTTCATAAGATGGGTATCAAAATTTCATGGTATGGTTAT
CAAAATTTCTTGAGATTATC
Found at i:50239 original size:46 final size:44
Alignment explanation
Indices: 50143--50244 Score: 114
Period size: 46 Copynumber: 2.3 Consensus size: 44
50133 TTTATGGTAT
* * * *
50143 GGTTATCAAAATTTCATCATGTGATTACCAATATTTTATCGGAA
1 GGTTATCAAAATATCATAATGTGATTACCAACATTTCATCGGAA
* * *
50187 GGTTATCAAAATATCATAATGTGTGCTTACCAACATTTCATTGGGA
1 GGTTATCAAAATATCATAA--TGTGATTACCAACATTTCATCGGAA
*
50233 TGTTATCAAAAT
1 GGTTATCAAAAT
50245 TCCATGGGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 17 0.35
46 31 0.65
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (44 bp):
GGTTATCAAAATATCATAATGTGATTACCAACATTTCATCGGAA
Found at i:50409 original size:22 final size:20
Alignment explanation
Indices: 50379--50445 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 20
50369 ATAGTCATAA
*
50379 AAAACTTTATAGTGTAATTATC
1 AAAATTTTATA-TG-AATTATC
50401 AAAATTTTATATGGAGATTATC
1 AAAATTTTATAT-GA-ATTATC
50423 AAAATTTTATAATG-ATTATC
1 AAAATTTTAT-ATGAATTATC
50443 AAA
1 AAA
50446 TTTCATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
20 9 0.22
21 2 0.05
22 28 0.68
23 2 0.05
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (20 bp):
AAAATTTTATATGAATTATC
Found at i:50448 original size:19 final size:20
Alignment explanation
Indices: 50416--50453 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
50406 TTTATATGGA
*
50416 GATTATCAAAATTTTATAAT
1 GATTATCAAAATTTCATAAT
50436 GATTATC-AAATTTCATAA
1 GATTATCAAAATTTCATAA
50454 AAATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (20 bp):
GATTATCAAAATTTCATAAT
Done.