Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012321.1 Corchorus olitorius cultivar O-4 contig12354, 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: 33769
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:19 original size:2 final size:2
Alignment explanation
Indices: 13--43 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3 TATCCCCTCC
13 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44 TTGCAATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3402 original size:32 final size:32
Alignment explanation
Indices: 3366--3433 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
3356 AAAAAACCCA
*
3366 AAATAGCGGCGTTTCCATACAGAAACGCCGCT
1 AAATAGCGGCGTTTCCATACAGAAACGCCACT
* *
3398 AAATAGTGGCGTTTCCGTACAGAAACGCCACT
1 AAATAGCGGCGTTTCCATACAGAAACGCCACT
3430 AAAT
1 AAAT
3434 GGCGTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (32 bp):
AAATAGCGGCGTTTCCATACAGAAACGCCACT
Found at i:3481 original size:32 final size:32
Alignment explanation
Indices: 3401--3538 Score: 138
Period size: 32 Copynumber: 4.4 Consensus size: 32
3391 CGCCGCTAAA
* * *
3401 TAGTGGCGTTTCCGTACAGAAACGCCACTA--
1 TAGTGGCGTTTCTGAACATAAACGCCACTATT
* * *
3431 -AATGGCGTTTTTTGAACATAAATGCCACTATT
1 TAGTGGCG-TTTCTGAACATAAACGCCACTATT
* *
3463 TAGCGGCGTTTCTGAACATAAACGCCGCTATT
1 TAGTGGCGTTTCTGAACATAAACGCCACTATT
* * **
3495 TAGTGGCTTTTCTGAACATAAACGCCCCTAAA
1 TAGTGGCGTTTCTGAACATAAACGCCACTATT
3527 TAGTGGCGTTTC
1 TAGTGGCGTTTC
3539 AGTGAAAAAA
Statistics
Matches: 87, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
29 6 0.07
30 17 0.20
32 59 0.68
33 5 0.06
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (32 bp):
TAGTGGCGTTTCTGAACATAAACGCCACTATT
Found at i:4661 original size:2 final size:2
Alignment explanation
Indices: 4654--4699 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
4644 CATAGATCTA
*
4654 AT AT AT AT AT -T GT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4694 AT AT AT
1 AT AT AT
4700 TCTTTCTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9289 original size:3 final size:3
Alignment explanation
Indices: 9169--9274 Score: 203
Period size: 3 Copynumber: 35.3 Consensus size: 3
9159 TATCTTATAT
9169 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
9217 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9265 ATA ATA ATA A
1 ATA ATA ATA A
9275 AATTTATGTA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 101 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:9436 original size:11 final size:11
Alignment explanation
Indices: 9422--9461 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
9412 CTTAATTAAT
9422 TTAAATTATTG
1 TTAAATTATTG
*
9433 TTAAACTATATG
1 TTAAATTAT-TG
9445 TTTAAATTATTG
1 -TTAAATTATTG
9457 TTAAA
1 TTAAA
9462 CTATATGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 13 0.52
12 4 0.16
13 8 0.32
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (11 bp):
TTAAATTATTG
Found at i:9479 original size:24 final size:24
Alignment explanation
Indices: 9421--9469 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
9411 GCTTAATTAA
9421 TTTAAATTATTGTTAAACTATATG
1 TTTAAATTATTGTTAAACTATATG
9445 TTTAAATTATTGTTAAACTATATG
1 TTTAAATTATTGTTAAACTATATG
9469 T
1 T
9470 ATTTCATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (24 bp):
TTTAAATTATTGTTAAACTATATG
Found at i:9640 original size:5 final size:5
Alignment explanation
Indices: 9627--9661 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
9617 GATGAGACCG
*
9627 TTATG TTATA TTATA TTATTA TTATA TTATA TTAT
1 TTATA TTATA TTATA TTA-TA TTATA TTATA TTAT
9662 CAATAAACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:11632 original size:30 final size:30
Alignment explanation
Indices: 11582--11676 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 30
11572 TTAAGGCATA
* * *
11582 CACGTGGCATGACACATGGACACAAAATGC
1 CACGTGGCAAGCCACGTGGACACAAAATGC
*
11612 CATGTGGCAAGCCACGTGGACACAAAATGC
1 CACGTGGCAAGCCACGTGGACACAAAATGC
* * * **
11642 CACGTGTCATGCCACGTGTACA-AAAAAAC
1 CACGTGGCAAGCCACGTGGACACAAAATGC
11671 CACGTG
1 CACGTG
11677 TCATGGGACC
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 11 0.20
30 44 0.80
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15
Consensus pattern (30 bp):
CACGTGGCAAGCCACGTGGACACAAAATGC
Found at i:17153 original size:106 final size:106
Alignment explanation
Indices: 16992--17319 Score: 439
Period size: 106 Copynumber: 3.1 Consensus size: 106
16982 TTTCAGGAGT
* * * *
16992 AAATTATTAAATTTTATTTTAGGGTTTTAGAATTGAAAA-ATATAACTAATTTCACTAAGTTTAG
1 AAATTAATAACTTTTATTATAGGGTTTTAGAAAT-AAAATATATAACTAATTTCACTAAGTTTAG
17056 CCCCAAATTAAAATTATAATTTTATTTTAAGGGTAAATTCCA
65 CCCCAAATTAAAATTATAATTTTATTTTAAGGGTAAATTCCA
*
17098 AAATTAATAACTTATTATTATAGGGTTTTAGAAAT-AAATATAAAACTAATTTCACTAAGTTTAG
1 AAATTAATAACTT-TTATTATAGGGTTTTAGAAATAAAATATATAACTAATTTCACTAAGTTTAG
* ** *
17162 CCCCAAATTAAAATTTTAA-TTTACGTTAAGGGTGAATTCCA
65 CCCCAAATTAAAATTATAATTTTATTTTAAGGGTAAATTCCA
* * *
17203 AAATTAATAACTTTTTATTATAGGGTTCTAGAAATAAAATATATAACTAA-TTGATTAAGTTTAG
1 AAATTAATAAC-TTTTATTATAGGGTTTTAGAAATAAAATATATAACTAATTTCACTAAGTTTAG
** * * * *
17267 CTTCAAATTAAAATTAAAATTTTATTTTAAGCGTAAATACTA
65 CCCCAAATTAAAATTATAATTTTATTTTAAGGGTAAATTCCA
17309 AAATTAATAAC
1 AAATTAATAAC
17320 ATAGAAAAAA
Statistics
Matches: 194, Mismatches: 23, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
105 80 0.41
106 95 0.49
107 19 0.10
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (106 bp):
AAATTAATAACTTTTATTATAGGGTTTTAGAAATAAAATATATAACTAATTTCACTAAGTTTAGC
CCCAAATTAAAATTATAATTTTATTTTAAGGGTAAATTCCA
Found at i:17235 original size:105 final size:107
Alignment explanation
Indices: 17003--17319 Score: 426
Period size: 105 Copynumber: 3.0 Consensus size: 107
16993 AATTATTAAA
* *
17003 TTTTATTTTAGGGTTTTAGAATTGAAAA-ATATAACTAATTTCACTAAGTTTAGCCCCAAATTAA
1 TTTTATTATAGGGTTTTAGAAAT-AAAATATATAACTAATTTCACTAAGTTTAGCCCCAAATTAA
**
17067 AATTATAATTTTATTTTAAGGGTAAATTCCAAAATTAATAACT
65 AATTATAATTTTACGTTAAGGGTAAATTCCAAAATTAATAACT
* *
17110 TATTATTATAGGGTTTTAGAAAT-AAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAA
1 TTTTATTATAGGGTTTTAGAAATAAAATATATAACTAATTTCACTAAGTTTAGCCCCAAATTAAA
* *
17174 ATTTTAA-TTTACGTTAAGGGTGAATTCCAAAATTAATAACT
66 ATTATAATTTTACGTTAAGGGTAAATTCCAAAATTAATAACT
* * * **
17215 TTTTATTATAGGGTTCTAGAAATAAAATATATAACTAA-TTGATTAAGTTTAGCTTCAAATTAAA
1 TTTTATTATAGGGTTTTAGAAATAAAATATATAACTAATTTCACTAAGTTTAGCCCCAAATTAAA
* ** * * *
17279 ATTAAAATTTTATTTTAAGCGTAAATACTAAAATTAATAAC
66 ATTATAATTTTACGTTAAGGGTAAATTCCAAAATTAATAAC
17320 ATAGAAAAAA
Statistics
Matches: 184, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
105 82 0.45
106 82 0.45
107 20 0.11
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (107 bp):
TTTTATTATAGGGTTTTAGAAATAAAATATATAACTAATTTCACTAAGTTTAGCCCCAAATTAAA
ATTATAATTTTACGTTAAGGGTAAATTCCAAAATTAATAACT
Found at i:17587 original size:29 final size:31
Alignment explanation
Indices: 17552--17615 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
17542 GTCAATGACG
17552 TTTTGCCCTCTGAAC-TTCAA-ATCAGAACA
1 TTTTGCCCTCTGAACTTTCAAGATCAGAACA
* * *
17581 TTTTGCCTTCTGAACTTTCAAGTTCAGAATA
1 TTTTGCCCTCTGAACTTTCAAGATCAGAACA
17612 TTTT
1 TTTT
17616 ATTCCCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 14 0.47
30 5 0.17
31 11 0.37
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (31 bp):
TTTTGCCCTCTGAACTTTCAAGATCAGAACA
Found at i:20037 original size:7 final size:7
Alignment explanation
Indices: 20028--20110 Score: 130
Period size: 7 Copynumber: 11.9 Consensus size: 7
20018 TTTTGAAGAG
*
20028 TTTTGAG
1 TTTTGAA
*
20035 TTTTGAG
1 TTTTGAA
20042 TTTTGAA
1 TTTTGAA
*
20049 TTTTGAG
1 TTTTGAA
20056 TTTTGAA
1 TTTTGAA
20063 TTTTGAA
1 TTTTGAA
20070 TTTTGAA
1 TTTTGAA
20077 TTTTGAA
1 TTTTGAA
20084 TTTTGAA
1 TTTTGAA
20091 TTTTGAA
1 TTTTGAA
*
20098 GTTTGAA
1 TTTTGAA
20105 TTTTGA
1 TTTTGA
20111 GCAATGAAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 71 1.00
ACGTcount: A:0.24, C:0.00, G:0.19, T:0.57
Consensus pattern (7 bp):
TTTTGAA
Found at i:20292 original size:33 final size:33
Alignment explanation
Indices: 20254--20326 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
20244 CTGTGGATTT
* * *
20254 TGAACTTTGAGTTTTGATATGATATGCAAATTC
1 TGAACTTTGAATTTTGAAATGAAATGCAAATTC
* *
20287 TGAACTTTGAATTTTGAAATTAAATGCAAATTT
1 TGAACTTTGAATTTTGAAATGAAATGCAAATTC
20320 TGAACTT
1 TGAACTT
20327 CTTAATTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.42
Consensus pattern (33 bp):
TGAACTTTGAATTTTGAAATGAAATGCAAATTC
Found at i:20544 original size:54 final size:53
Alignment explanation
Indices: 20454--20677 Score: 306
Period size: 54 Copynumber: 4.2 Consensus size: 53
20444 GACCACACTG
* * * *
20454 GATCAACTTAGATTTTTGAAAACTTCTATGGAAGACCACACAGGGTCATCTAAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACAC-GGGTCATCTTAA
* * *
20508 GATCAACTTAAACCTCT-AAAAGCTTATATGAAAGACCACACCGGGTCATCTTAA
1 GATCAACTTAGATCTCTGAAAA-CTTCTATGAAAGACCACA-CGGGTCATCTTAA
* *
20562 GATCAACTTAGATCTCTGAAAACTTTTATGAAAGACCACACTGGGTCATCTTAT
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACAC-GGGTCATCTTAA
* *
20616 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGTCAACTTAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACGGGTCATCTTAA
20669 GATCAACTT
1 GATCAACTT
20678 TCTAGAGATA
Statistics
Matches: 151, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
53 23 0.15
54 123 0.81
55 5 0.03
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (53 bp):
GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACGGGTCATCTTAA
Found at i:20729 original size:20 final size:18
Alignment explanation
Indices: 20700--20750 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
20690 ACACTGGATC
*
20700 ATTTTAAACAAAAAACAGG
1 ATTTTGAACAAAAAA-AGG
* *
20719 AATTTTGAACAAGAAATGG
1 -ATTTTGAACAAAAAAAGG
20738 ATTTTGAACAAAA
1 ATTTTGAACAAAA
20751 TTTTGATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 12 0.44
19 2 0.07
20 13 0.48
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (18 bp):
ATTTTGAACAAAAAAAGG
Found at i:20864 original size:74 final size:74
Alignment explanation
Indices: 20776--21379 Score: 832
Period size: 74 Copynumber: 8.2 Consensus size: 74
20766 TAAACTGGGA
* * * * * *
20776 TTTTGAAGAGACACCTAAACATGTACCTTAAATAAGGATTTGATAAAAAACCTAAACAGGGATCT
1 TTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCT
20841 TGAACAAGG
66 TGAACAAGG
* * *
20850 TTTTGATGACACACCTAAATAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAATCT
1 TTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCT
**
20915 TGAATGAGG
66 TGAACAAGG
*
20924 TTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAACATGAATCT
1 TTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCT
*
20989 TGAACGAGG
66 TGAACAAGG
* * *
20998 TTTTGATGAGACACCTAAACAGGGACTTTAAACAAGGATTTAATAAGAAACCTAAACAAGAATCT
1 TTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCT
21063 TGAACAAGG
66 TGAACAAGG
* * *
21072 ATTTGATGAGACACCTAAAAAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAACAAGAATCT
1 TTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCT
*
21137 TGAACAAGA
66 TGAACAAGG
* * * * * * *
21146 TTTTGATGAGACACCTAAACAGGGATCTTTAACCA-GATTTCGATGAGACACCTAAACAGGGACC
1 TTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTT-GATAAGAAACCTAAACAGGAATC
* *
21210 TTAAATAAGG
65 TTGAACAAGG
* * * *
21220 ATTTAATAAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGACACCTAAACAGGAATCT
1 TTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCT
*
21285 TGAACAAGA
66 TGAACAAGG
* * * * **
21294 TTTTGATGAAATACCTAAACAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACAAAAATCT
1 TTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCT
21359 TGAACAAGG
66 TGAACAAGG
21368 TTTTGATGAGAC
1 TTTTGATGAGAC
21380 TGAATTTTGT
Statistics
Matches: 469, Mismatches: 59, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
73 5 0.01
74 459 0.98
75 5 0.01
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.24
Consensus pattern (74 bp):
TTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAACAGGAATCT
TGAACAAGG
Found at i:21373 original size:37 final size:37
Alignment explanation
Indices: 20784--21379 Score: 581
Period size: 37 Copynumber: 16.1 Consensus size: 37
20774 GATTTTGAAG
* * * *
20784 AGACACCTAAACATGTACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGATCTTAAACAAGGATTTGATA
* * * * *
20821 AAAAACCTAAACAGGGATCTTGAACAAGGTTTTGATG
1 AGACACCTAAACAGGGATCTTAAACAAGGATTTGATA
* * * *
20858 ACACACCTAAATAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGATCTTAAACAAGGATTTGATA
* * * ** * *
20895 AGAAACCTAAACAGGAATCTTGAATGAGGTTTTGATG
1 AGACACCTAAACAGGGATCTTAAACAAGGATTTGATA
*
20932 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
1 AGACACCTAAACAGGGATCTTAAACAAGGATTTGATA
* * * * * * *
20969 AGAAACCTAAACATGAATCTTGAACGAGGTTTTGATG
1 AGACACCTAAACAGGGATCTTAAACAAGGATTTGATA
*
21006 AGACACCTAAACAGGGA-CTTTAAACAAGGATTTAATA
1 AGACACCTAAACAGGGATC-TTAAACAAGGATTTGATA
* * * * *
21043 AGAAACCTAAACAAGAATCTTGAACAAGGATTTGATG
1 AGACACCTAAACAGGGATCTTAAACAAGGATTTGATA
* *
21080 AGACACCTAAAAAGGGACCTTAAACAAGGATTTGATA
1 AGACACCTAAACAGGGATCTTAAACAAGGATTTGATA
* * * * *
21117 AGAAACCTAAACAAGAATCTTGAACAA-GATTTTGATG
1 AGACACCTAAACAGGGATCTTAAACAAGGA-TTTGATA
* * *
21154 AGACACCTAAACAGGGATCTTTAACCA-GATTTCGATG
1 AGACACCTAAACAGGGATCTTAAACAAGGATTT-GATA
* * *
21191 AGACACCTAAACAGGGACCTTAAATAAGGATTTAATA
1 AGACACCTAAACAGGGATCTTAAACAAGGATTTGATA
*
21228 AGACACCTAAACAGGGACCTTAAACAAGGATTTGATA
1 AGACACCTAAACAGGGATCTTAAACAAGGATTTGATA
* *
21265 AGACACCTAAACAGGAATCTTGAACAA-GATTTTGATGA
1 AGACACCTAAACAGGGATCTTAAACAAGGA-TTTGAT-A
* * *
21303 A-ATACCTAAACAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGATCTTAAACAAGGATTTGATA
*** * * *
21339 AGACACCTAAACAAAAATCTTGAACAAGGTTTTGATG
1 AGACACCTAAACAGGGATCTTAAACAAGGATTTGATA
21376 AGAC
1 AGAC
21380 TGAATTTTGT
Statistics
Matches: 450, Mismatches: 100, Indels: 18
0.79 0.18 0.03
Matches are distributed among these distances:
36 10 0.02
37 430 0.96
38 10 0.02
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (37 bp):
AGACACCTAAACAGGGATCTTAAACAAGGATTTGATA
Found at i:22269 original size:87 final size:87
Alignment explanation
Indices: 22123--22291 Score: 268
Period size: 87 Copynumber: 1.9 Consensus size: 87
22113 TGATTGATGC
* * *
22123 CCCAAACCTTCTTCCAATTTGGTCATGTATTGATATTCCCAACTCAATTGATGGTTCTGGATCAA
1 CCCAAACCTCCTTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGGTTCTGGATCAA
22188 TTTCCCACCTTAAGAAATATTT
66 TTTCCCACCTTAAGAAATATTT
*
22210 CCCAAATCCTCCTT-CAATTTGATCATGCATTGATATTCCCAACTCAATTGATGTTTCTGGATCA
1 CCCAAA-CCTCCTTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGGTTCTGGATCA
* *
22274 ATTTCTCATCTTAAGAAA
65 ATTTCCCACCTTAAGAAA
22292 CCTTCAAACA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
87 69 0.92
88 6 0.08
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (87 bp):
CCCAAACCTCCTTCCAATTTGATCATGCATTGATATTCCCAACTCAATTGATGGTTCTGGATCAA
TTTCCCACCTTAAGAAATATTT
Found at i:22485 original size:29 final size:29
Alignment explanation
Indices: 22430--22487 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
22420 TTGATTTTTC
*
22430 TTTCTTTTTCTTTTTCTTTGCTTATTCAT
1 TTTCTTTTTCTTTTTCTTTGATTATTCAT
22459 TTTC-TTTT-TTTTTCTTTAGATTGATTCAT
1 TTTCTTTTTCTTTTTCTTT-GATT-ATTCAT
22488 CATGCACCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 9 0.35
28 7 0.27
29 10 0.38
ACGTcount: A:0.10, C:0.14, G:0.05, T:0.71
Consensus pattern (29 bp):
TTTCTTTTTCTTTTTCTTTGATTATTCAT
Found at i:23172 original size:14 final size:13
Alignment explanation
Indices: 23107--23171 Score: 87
Period size: 14 Copynumber: 4.8 Consensus size: 13
23097 ACTCAAAACC
23107 TTTTTGAAAACTCA
1 TTTTTGAAAA-TCA
23121 TTTTTGAAAATCA
1 TTTTTGAAAATCA
23134 TTTCTTGAAAA-CA
1 TTT-TTGAAAATCA
23147 GTTTCTTGAAAATCA
1 -TTT-TTGAAAATCA
23162 TTTTTGAAAA
1 TTTTTGAAAA
23172 AATCCTTTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
13 15 0.31
14 31 0.65
15 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:23557 original size:14 final size:13
Alignment explanation
Indices: 23492--23556 Score: 78
Period size: 14 Copynumber: 4.8 Consensus size: 13
23482 ACTCAAAACC
23492 TTTTTGAAAACTCA
1 TTTTTGAAAA-TCA
*
23506 TTTTTGAAAATTA
1 TTTTTGAAAATCA
23519 TTTCTTGAAAA-CAA
1 TTT-TTGAAAATC-A
23533 TTTCTTGAAAATCA
1 TTT-TTGAAAATCA
23547 TTTTTGAAAA
1 TTTTTGAAAA
23557 AAATCCTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
13 12 0.26
14 33 0.72
15 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:23557 original size:28 final size:27
Alignment explanation
Indices: 23492--23556 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
23482 ACTCAAAACC
* *
23492 TTTTTGAAAACTCATTTTTGAAAATTA
1 TTTTTGAAAACTAATTTTTGAAAATCA
23519 TTTCTTGAAAAC-AATTTCTTGAAAATCA
1 TTT-TTGAAAACTAATTT-TTGAAAATCA
23547 TTTTTGAAAA
1 TTTTTGAAAA
23557 AAATCCTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 14 0.41
28 20 0.59
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (27 bp):
TTTTTGAAAACTAATTTTTGAAAATCA
Found at i:29156 original size:32 final size:32
Alignment explanation
Indices: 29109--29222 Score: 174
Period size: 32 Copynumber: 3.5 Consensus size: 32
29099 TAAAAGCAAT
** *
29109 TAAATATAGCGGCGTTTTGTAATGTAGACGCTGC
1 TAAATA-AG-GGCGTTTTGTTCTGTAGACGCCGC
29143 TAAATAAGGGCGTTTTGTTCTGTAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTGTAGACGCCGC
*
29175 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTGTAGACGCCGC
29207 TAAATAAGGGCGTTTT
1 TAAATAAGGGCGTTTT
29223 CTTTTCACAC
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 68 0.89
33 2 0.03
34 6 0.08
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (32 bp):
TAAATAAGGGCGTTTTGTTCTGTAGACGCCGC
Found at i:29909 original size:27 final size:27
Alignment explanation
Indices: 29871--29931 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
29861 TCCGCTCGTC
29871 CCACTGCTGGGGTCGAAGTGGGAGGAT
1 CCACTGCTGGGGTCGAAGTGGGAGGAT
29898 CCACTGCTGGGGTCGAAGTGGGAGGAT
1 CCACTGCTGGGGTCGAAGTGGGAGGAT
29925 CCACTGC
1 CCACTGC
29932 GGCAACAGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.18, C:0.23, G:0.41, T:0.18
Consensus pattern (27 bp):
CCACTGCTGGGGTCGAAGTGGGAGGAT
Done.