Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014862.1 Corchorus olitorius cultivar O-4 contig14895, 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: 125552
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:680 original size:24 final size:25
Alignment explanation
Indices: 653--713 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
643 GTTTTAGGCT
* *
653 TGCTCCGTTTCTGGGGTTTGA-GAA
1 TGCTCTGTTTCTGGAGTTTGAGGAA
* *
677 TGCTCTGTTTC-GGAGTTTTAGGCA
1 TGCTCTGTTTCTGGAGTTTGAGGAA
701 TGCTCTGTTTCTG
1 TGCTCTGTTTCTG
714 TTAATTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 7 0.23
24 23 0.74
25 1 0.03
ACGTcount: A:0.10, C:0.18, G:0.30, T:0.43
Consensus pattern (25 bp):
TGCTCTGTTTCTGGAGTTTGAGGAA
Found at i:836 original size:18 final size:18
Alignment explanation
Indices: 813--862 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
803 CTTTCCAATC
813 TCCATACATAAACACCTT
1 TCCATACATAAACACCTT
* *
831 TCCATACAAAAAGACCTT
1 TCCATACATAAACACCTT
849 TCCATACATAAACA
1 TCCATACATAAACA
863 TCCAGTAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.44, C:0.30, G:0.02, T:0.24
Consensus pattern (18 bp):
TCCATACATAAACACCTT
Found at i:3042 original size:13 final size:13
Alignment explanation
Indices: 3024--3054 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3014 AATAACAAGC
*
3024 AAAATCATTTACT
1 AAAATCATTTACA
3037 AAAATCATTTACA
1 AAAATCATTTACA
3050 AAAAT
1 AAAAT
3055 AATTAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATCATTTACA
Found at i:4346 original size:12 final size:12
Alignment explanation
Indices: 4329--4414 Score: 100
Period size: 12 Copynumber: 7.2 Consensus size: 12
4319 TCAGCAACAT
*
4329 CTCTTTCTTGAA
1 CTCTTTCTTCAA
4341 CTCTTTCTTCAA
1 CTCTTTCTTCAA
* *
4353 CCCTTTCTTGAA
1 CTCTTTCTTCAA
4365 CTCTTTCTTCAA
1 CTCTTTCTTCAA
* *
4377 CCCTTTCTTGAA
1 CTCTTTCTTCAA
* *
4389 CTGTTTTTTCAA
1 CTCTTTCTTCAA
*
4401 CCCTTTCTTCAA
1 CTCTTTCTTCAA
4413 CT
1 CT
4415 GGATCTGGAG
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.16, C:0.31, G:0.05, T:0.48
Consensus pattern (12 bp):
CTCTTTCTTCAA
Found at i:4415 original size:24 final size:24
Alignment explanation
Indices: 4331--4414 Score: 141
Period size: 24 Copynumber: 3.5 Consensus size: 24
4321 AGCAACATCT
4331 CTTTCTTGAACTCTTTCTTCAACC
1 CTTTCTTGAACTCTTTCTTCAACC
4355 CTTTCTTGAACTCTTTCTTCAACC
1 CTTTCTTGAACTCTTTCTTCAACC
* *
4379 CTTTCTTGAACTGTTTTTTCAACC
1 CTTTCTTGAACTCTTTCTTCAACC
*
4403 CTTTCTTCAACT
1 CTTTCTTGAACT
4415 GGATCTGGAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.17, C:0.31, G:0.05, T:0.48
Consensus pattern (24 bp):
CTTTCTTGAACTCTTTCTTCAACC
Found at i:4594 original size:24 final size:24
Alignment explanation
Indices: 4563--4608 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
4553 ACTACCTTTT
4563 CAACATTTTCATT-TACATTTTCTA
1 CAACATTTTC-TTCTACATTTTCTA
4587 CAACATTTTCTTCTACATTTTC
1 CAACATTTTCTTCTACATTTTC
4609 AACCAGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (24 bp):
CAACATTTTCTTCTACATTTTCTA
Found at i:4618 original size:24 final size:24
Alignment explanation
Indices: 4563--4621 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
4553 ACTACCTTTT
*
4563 CAACATTTTCATTTACATTTTCTA
1 CAACATTTTCATTTACATTTTCAA
4587 CAACATTTTC-TTCTACATTTTCAA
1 CAACATTTTCATT-TACATTTTCAA
* *
4611 CCAGATTTTCA
1 CAACATTTTCA
4622 GCTAAATCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.07
24 28 0.93
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.46
Consensus pattern (24 bp):
CAACATTTTCATTTACATTTTCAA
Found at i:6983 original size:7 final size:7
Alignment explanation
Indices: 6971--6999 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
6961 TATCTAAATA
6971 ACTGGCT
1 ACTGGCT
6978 ACTGGCT
1 ACTGGCT
6985 ACTGGCT
1 ACTGGCT
6992 ACTGGCT
1 ACTGGCT
6999 A
1 A
7000 GAGAAGAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (7 bp):
ACTGGCT
Found at i:18186 original size:13 final size:14
Alignment explanation
Indices: 18160--18201 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
18150 TCCGAAACCG
18160 ATTG-ACCCGAAAA
1 ATTGTACCCGAAAA
18173 ATTGTACCCGAAAA
1 ATTGTACCCGAAAA
18187 ATTGTA-CCGAAAA
1 ATTGTACCCGAAAA
18200 AT
1 AT
18202 CCGTCGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.46
14 15 0.54
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.21
Consensus pattern (14 bp):
ATTGTACCCGAAAA
Found at i:20517 original size:45 final size:45
Alignment explanation
Indices: 20453--20549 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
20443 AATAACAATT
* *
20453 AATATTAGCATTACTTTGATGAATTATATAGAGATGGAGGAGTAG
1 AATATTAGCATTACTTTGATGAATTACATAGAAATGGAGGAGTAG
* * *
20498 AATATTAGCTTTATTTTGATGAATTACCTAGAAATGGAGGAGTAG
1 AATATTAGCATTACTTTGATGAATTACATAGAAATGGAGGAGTAG
20543 AAT-TTAG
1 AATATTAG
20550 GTAATGCACT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (45 bp):
AATATTAGCATTACTTTGATGAATTACATAGAAATGGAGGAGTAG
Found at i:28425 original size:1 final size:1
Alignment explanation
Indices: 28419--28451 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
28409 TGATTCTACT
28419 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28452 CAAACCTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:43102 original size:3 final size:3
Alignment explanation
Indices: 43094--43139 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
43084 GTATGATATG
43094 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
43140 AGCAAGTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:48448 original size:102 final size:101
Alignment explanation
Indices: 48272--48459 Score: 367
Period size: 102 Copynumber: 1.9 Consensus size: 101
48262 TGAGGGAAAG
48272 GGTTCGAATCACCTTTAAAATCATATATATTTTGCATTATATCTAACGGTTAGGGTAGGGTAGTT
1 GGTTCGAATCACCTTTAAAATCATATATATTTTGCATTATATCTAACGGTTAGGGTAGGGTAGTT
48337 TTCCCTGAGGGAAAGGGGTTCGGGTAGGATACGGGTA
66 TTCCCTGAGGGAAA-GGGTTCGGGTAGGATACGGGTA
48374 GGTTCGAATCACCTTTAAAATCATATATATTTTGCATTATATCTAACGGTTAGGGTAGGGTAGTT
1 GGTTCGAATCACCTTTAAAATCATATATATTTTGCATTATATCTAACGGTTAGGGTAGGGTAGTT
48439 TTCCCTGAGGGAAAGGGTTCG
66 TTCCCTGAGGGAAAGGGTTCG
48460 AATTACCTTT
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 7 0.08
102 79 0.92
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.34
Consensus pattern (101 bp):
GGTTCGAATCACCTTTAAAATCATATATATTTTGCATTATATCTAACGGTTAGGGTAGGGTAGTT
TTCCCTGAGGGAAAGGGTTCGGGTAGGATACGGGTA
Found at i:49651 original size:134 final size:134
Alignment explanation
Indices: 49431--49699 Score: 407
Period size: 134 Copynumber: 2.0 Consensus size: 134
49421 TATTATTTAA
* *
49431 ACTTTTATAGTTTTACTCAATTAAAAACTCTATTTTTTTTATTTAATTAAATCTAATATCCTTAA
1 ACTTTTATAGTTTTACTCAATTAAAAACTCTATATTTTTTATTTAATGAAATCTAATATCCTTAA
* *
49496 AACTATTTAATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATCAGAATTTTTTAA
66 AACTATTTAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATCAGAA-TTTTTAA
49561 AATAT
130 AATAT
*
49566 ACTTTTATAGTTTTACTCAATTAAAAACTCTA-ATTTTTTATTTAATGAAATCTAATATTCTT-A
1 ACTTTTATAGTTTTACTCAATTAAAAACTCTATATTTTTTATTTAATGAAATCTAATATCCTTAA
* * * * * *
49629 TACTTGTTTTATTTTTATCATTTTACTAATTTAATTAAAAAATTTAGATATATTAGAATTTTTAA
66 AAC-TATTTAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATCAGAATTTTTAA
49694 AATAT
130 AATAT
49699 A
1 A
49700 TTTCTTAAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
133 16 0.13
134 74 0.61
135 32 0.26
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (134 bp):
ACTTTTATAGTTTTACTCAATTAAAAACTCTATATTTTTTATTTAATGAAATCTAATATCCTTAA
AACTATTTAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATCAGAATTTTTAAA
ATAT
Found at i:50735 original size:15 final size:16
Alignment explanation
Indices: 50710--50739 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
50700 AGTATTTAGT
50710 ATTGATTCATATAATA
1 ATTGATTCATATAATA
50726 ATTG-TTCATATAAT
1 ATTGATTCATATAAT
50740 GAAGTTTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (16 bp):
ATTGATTCATATAATA
Found at i:51272 original size:29 final size:30
Alignment explanation
Indices: 51233--51293 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
51223 TATAAATAAT
* *
51233 ATAATATAATTAAATAA-TTATATTTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
51262 ATAATAAAATTAAATAATTTATATGTATAC
1 ATAATAAAATTAAATAATTTATATGTATAC
51292 AT
1 AT
51294 TAATCAGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (30 bp):
ATAATAAAATTAAATAATTTATATGTATAC
Found at i:57292 original size:13 final size:14
Alignment explanation
Indices: 57261--57295 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
57251 ACTATAAAAG
*
57261 TTTAAACAATATCA
1 TTTAAAAAATATCA
57275 TTTAAAAAATAT-A
1 TTTAAAAAATATCA
57288 TTTAAAAA
1 TTTAAAAA
57296 GTTCCAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTAAAAAATATCA
Found at i:57608 original size:31 final size:30
Alignment explanation
Indices: 57567--57703 Score: 134
Period size: 31 Copynumber: 4.5 Consensus size: 30
57557 GCCAAATAAT
* * *
57567 CAATTTAGGATATAACGTTTGCTGTCACAAG
1 CAATTAAGGATATAACGTTT-CTATTACAAG
* **
57598 CAATTAAGGATATAACGTTAC-AAAACAAG
1 CAATTAAGGATATAACGTTTCTATTACAAG
* *
57627 CAATTAAGGATATAACGTTTTTTATTTCAAG
1 CAATTAAGGATATAACG-TTTCTATTACAAG
* *
57658 CAATTAAGGATATGACGTTT-TGGATTTCAAG
1 CAATTAAGGATATAACGTTTCT--ATTACAAG
57689 CAATTAAGGATATAA
1 CAATTAAGGATATAA
57704 TCAGTTAGGG
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
29 23 0.26
30 6 0.07
31 61 0.68
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (30 bp):
CAATTAAGGATATAACGTTTCTATTACAAG
Found at i:57857 original size:31 final size:29
Alignment explanation
Indices: 57822--57888 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 29
57812 TTTAACGGAC
*
57822 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCG-TTTT-ATAACGT
*
57853 TATATCCTTAATTGCTTGTTTTATAACGT
1 TATATCCTTAATTGCTCGTTTTATAACGT
57882 TATATCC
1 TATATCC
57889 CAAATTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 13 0.38
30 4 0.12
31 17 0.50
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.48
Consensus pattern (29 bp):
TATATCCTTAATTGCTCGTTTTATAACGT
Found at i:61996 original size:36 final size:37
Alignment explanation
Indices: 61954--62037 Score: 152
Period size: 36 Copynumber: 2.3 Consensus size: 37
61944 AATAATTTAT
61954 TAAAACATTTTATAAAGCATTTAAATAAAAACAATAA
1 TAAAACATTTTATAAAGCATTTAAATAAAAACAATAA
*
61991 -AAAACATTTTATAAAGCATTTAAATAAAAACAGTAA
1 TAAAACATTTTATAAAGCATTTAAATAAAAACAATAA
62027 TAAAACATTTT
1 TAAAACATTTT
62038 CCTCAACGGG
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
36 35 0.78
37 10 0.22
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.31
Consensus pattern (37 bp):
TAAAACATTTTATAAAGCATTTAAATAAAAACAATAA
Found at i:62581 original size:28 final size:30
Alignment explanation
Indices: 62538--62614 Score: 99
Period size: 28 Copynumber: 2.7 Consensus size: 30
62528 ACAAGGTTAA
*
62538 AAGGGTAAAACTGTAAATTTAAC-C-TTCT
1 AAGGGTAAAACGGTAAATTTAACTCATTCT
62566 AAGGGTAAAACGGT-AATTT-ACTCATTCT
1 AAGGGTAAAACGGTAAATTTAACTCATTCT
* *
62594 TAGGGTAAAACGGTAATTTTA
1 AAGGGTAAAACGGTAAATTTA
62615 TGCTTATACA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.05
27 6 0.14
28 30 0.71
29 4 0.10
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (30 bp):
AAGGGTAAAACGGTAAATTTAACTCATTCT
Found at i:70531 original size:28 final size:28
Alignment explanation
Indices: 70474--70591 Score: 125
Period size: 28 Copynumber: 4.2 Consensus size: 28
70464 AATGCACTTG
***
70474 AAATGA-TCAAAATGCCCCCTGGATGCGC
1 AAATGACT-AAAATGCCCCCTGGACATGC
*
70502 AAATGACTAAAATGCCCCCTAGACATGC
1 AAATGACTAAAATGCCCCCTGGACATGC
* * *
70530 AAAATGACCAAAAT-ACCCCTGAACATGC
1 -AAATGACTAAAATGCCCCCTGGACATGC
*
70558 AAATGACTAAAATG-CCCCTGGACATGT
1 AAATGACTAAAATGCCCCCTGGACATGC
70585 AAATGAC
1 AAATGAC
70592 CAATATGGGA
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
27 30 0.39
28 33 0.43
29 13 0.17
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.18
Consensus pattern (28 bp):
AAATGACTAAAATGCCCCCTGGACATGC
Found at i:70569 original size:27 final size:27
Alignment explanation
Indices: 70500--70591 Score: 105
Period size: 27 Copynumber: 3.3 Consensus size: 27
70490 CCCTGGATGC
*
70500 GCAAATGACTAAAATGCCCCCT-AGACAT
1 GCAAATGACTAAAAT-ACCCCTGA-ACAT
*
70528 GCAAAATGACCAAAATACCCCTGAACAT
1 GC-AAATGACTAAAATACCCCTGAACAT
* *
70556 GCAAATGACTAAAATGCCCCTGGACAT
1 GCAAATGACTAAAATACCCCTGAACAT
*
70583 GTAAATGAC
1 GCAAATGAC
70592 CAATATGGGA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 30 0.54
28 13 0.23
29 13 0.23
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.17
Consensus pattern (27 bp):
GCAAATGACTAAAATACCCCTGAACAT
Found at i:74702 original size:21 final size:21
Alignment explanation
Indices: 74664--74704 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
74654 AAATAGTAGG
**
74664 AAAGATTGAAAATGGAAGAAA
1 AAAGATTGAAAAAAGAAGAAA
*
74685 AAAGGTTGAAAAAAGAAGAA
1 AAAGATTGAAAAAAGAAGAA
74705 GAGAGAGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAGATTGAAAAAAGAAGAAA
Found at i:79209 original size:28 final size:29
Alignment explanation
Indices: 79154--79209 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
79144 TGAAACAAAG
*
79154 TGAAAGGAATGAAAAAAGAATAAGGAGAA
1 TGAAAGGAATGAAAAAAGAAAAAGGAGAA
*
79183 TGAAATGAA-GAAAAAA-AAAAAGAGAGA
1 TGAAAGGAATGAAAAAAGAAAAAG-GAGA
79210 GATGTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 11 0.46
29 8 0.33
ACGTcount: A:0.66, C:0.00, G:0.25, T:0.09
Consensus pattern (29 bp):
TGAAAGGAATGAAAAAAGAAAAAGGAGAA
Found at i:95608 original size:21 final size:21
Alignment explanation
Indices: 95582--95694 Score: 174
Period size: 21 Copynumber: 5.4 Consensus size: 21
95572 TGCTAGGAGT
95582 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
95603 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
* *
95624 TCATTGGAGAATGTTCTAAGC
1 TCATTGGAGAAGGTTCCAAGC
95645 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
* *
95666 TCATTGAAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
95687 TCATTGGA
1 TCATTGGA
95695 ATTGTCTAAG
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
20 2 0.02
21 82 0.98
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:96325 original size:25 final size:24
Alignment explanation
Indices: 96289--96335 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
96279 TAAATCTATT
96289 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
96312 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
96336 AATTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:97881 original size:33 final size:33
Alignment explanation
Indices: 97778--97915 Score: 120
Period size: 33 Copynumber: 4.2 Consensus size: 33
97768 TTGCAAAGAG
* * * *
97778 TGTTTTAGATGTTGTTAGTGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
** * * *
97811 TAATTTAAGTGTTGTTTGTGATGACACTAAATT
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
97844 TGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTC
1 TGTTTTAGGTGTTGTTTGTGATGAAACTAAA-TC
* **
97877 TGTTTT-GGATGCTAATTGTGATGAAAAC-AAATC
1 TGTTTTAGG-TGTTGTTTGTGATG-AAACTAAATC
97910 TGTTTT
1 TGTTTT
97916 GGTTGATCAT
Statistics
Matches: 86, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
32 5 0.06
33 74 0.86
34 7 0.08
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
Found at i:99744 original size:21 final size:21
Alignment explanation
Indices: 99718--99809 Score: 141
Period size: 21 Copynumber: 4.4 Consensus size: 21
99708 TGCTAGGAGT
99718 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
* *
99739 TCATTGGAGCATGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
99760 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
99781 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
99802 TCATTGGA
1 TCATTGGA
99810 ATTGCCTAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
20 1 0.02
21 65 0.98
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:103510 original size:11 final size:11
Alignment explanation
Indices: 103494--103519 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
103484 CCTTGCCTAA
103494 AAAACTAGAAG
1 AAAACTAGAAG
103505 AAAACTAGAAG
1 AAAACTAGAAG
103516 AAAA
1 AAAA
103520 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:105763 original size:14 final size:15
Alignment explanation
Indices: 105740--105782 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
105730 CTATGGCTAG
105740 AGAGAAAATATCTAA
1 AGAGAAAATATCTAA
** *
105755 AGA-AAAATAGATGA
1 AGAGAAAATATCTAA
105769 AGAGAAAATATCTA
1 AGAGAAAATATCTA
105783 TGTGAAAAAT
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.60, C:0.05, G:0.16, T:0.19
Consensus pattern (15 bp):
AGAGAAAATATCTAA
Found at i:112348 original size:4 final size:4
Alignment explanation
Indices: 112339--112374 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
112329 ATTTTGGATA
112339 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
112375 ATATTGGTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:112783 original size:29 final size:31
Alignment explanation
Indices: 112719--112783 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 31
112709 AATAAGGTAG
* *
112719 TAAAATGTCCTGAATTTGGAATTTCATGGTA
1 TAAAATGTCCTGAATTTGGAAGTTCATGGGA
112750 TAAAATGTCCTG-ATTT-GAAGTTCATGGGA
1 TAAAATGTCCTGAATTTGGAAGTTCATGGGA
112779 TAAAA
1 TAAAA
112784 CGTCTTTGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 16 0.50
30 4 0.12
31 12 0.38
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.35
Consensus pattern (31 bp):
TAAAATGTCCTGAATTTGGAAGTTCATGGGA
Found at i:113848 original size:2 final size:2
Alignment explanation
Indices: 113841--113875 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
113831 ATCATTAATC
113841 TA TA 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 TA TA T
113876 CTGTGTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:116441 original size:18 final size:18
Alignment explanation
Indices: 116420--116461 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
116410 CTACAAACTT
116420 GCTCCGCGCAAAAAACAA
1 GCTCCGCGCAAAAAACAA
116438 GCTCCGCGCAAAAAACAA
1 GCTCCGCGCAAAAAACAA
116456 GCTCCG
1 GCTCCG
116462 TGCTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.36, G:0.19, T:0.07
Consensus pattern (18 bp):
GCTCCGCGCAAAAAACAA
Found at i:119866 original size:23 final size:23
Alignment explanation
Indices: 119840--119892 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
119830 ATAAGTTGGG
*
119840 TATATTCAATTGAATATTAACGT
1 TATATTCAATTGAATACTAACGT
* *
119863 TATATACCATTGAATACTAACGT
1 TATATTCAATTGAATACTAACGT
119886 TATATTC
1 TATATTC
119893 TTTTGCTCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (23 bp):
TATATTCAATTGAATACTAACGT
Found at i:120010 original size:23 final size:23
Alignment explanation
Indices: 119984--120036 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
119974 ATAAGTTGGG
119984 TATATTCAATTGAATATTAACGT
1 TATATTCAATTGAATATTAACGT
* *
120007 TATATACCATTGAATATTAACGT
1 TATATTCAATTGAATATTAACGT
120030 TATATTC
1 TATATTC
120037 TTTTGCTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (23 bp):
TATATTCAATTGAATATTAACGT
Found at i:120080 original size:12 final size:12
Alignment explanation
Indices: 120056--120088 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
120046 ATTGATTCTA
120056 AACATTA-TATT
1 AACATTATTATT
120067 AACATTATTATT
1 AACATTATTATT
120079 AACATTATTA
1 AACATTATTA
120089 CATAATACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (12 bp):
AACATTATTATT
Found at i:124199 original size:22 final size:21
Alignment explanation
Indices: 124147--124200 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
124137 TGCTTCTCGA
124147 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
124168 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
124187 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
124201 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Done.