Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011633.1 Corchorus capsularis cultivar CVL-1 contig11654, 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: 55417
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:661 original size:27 final size:27
Alignment explanation
Indices: 620--680 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
610 ATATCACTTA
*
620 AAAAGAAAACTACCAATTTAAATGTGCC
1 AAAA-AAAACTACCAATTTAAAAGTGCC
*
648 AAAAAAAACTACCAATTTAAAAGTGTC
1 AAAAAAAACTACCAATTTAAAAGTGCC
675 AAAAAA
1 AAAAAA
681 GAAAATTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.57, C:0.15, G:0.08, T:0.20
Consensus pattern (27 bp):
AAAAAAAACTACCAATTTAAAAGTGCC
Found at i:3786 original size:125 final size:125
Alignment explanation
Indices: 3561--3788 Score: 284
Period size: 125 Copynumber: 1.8 Consensus size: 125
3551 ATGTTTCGAA
* * *
3561 AAAAAATTGACAACATAACAAAAACAAAACAAGATTTAAAAAAAAAAAGATGTCAAACGACCCTT
1 AAAAAATTGACAACATAACAAAAACAAAACAAGATTTAAAAAAAAAAAAATGTCAAACAACCCTC
** *
3626 AATTACTGTTTTAACTTCCTTGCAAGCAATCTCACCACGCAAAAAAAATGTTTATGTTTT
66 AATTACTCATTTAACTTCCTTACAAGCAATCTCACCACGCAAAAAAAATGTTTATGTTTT
*
3686 AAAAAATTGACAACATAATAAAAACAAATA-AA-A-TTAAAAAAATTAAAACAATGTCAAACAAC
1 AAAAAATTGACAACATAACAAAAACAAA-ACAAGATTTAAAAAAA--AAAA-AATGTCAAACAAC
* * * * *
3748 CCTCAATT-TTCATTTAAGTTCCTTATAAGTAATTTCACCAC
62 CCTCAATTACTCATTTAACTTCCTTACAAGCAATCTCACCAC
3789 CCAACCAAAC
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
123 9 0.10
124 1 0.01
125 58 0.67
126 19 0.22
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (125 bp):
AAAAAATTGACAACATAACAAAAACAAAACAAGATTTAAAAAAAAAAAAATGTCAAACAACCCTC
AATTACTCATTTAACTTCCTTACAAGCAATCTCACCACGCAAAAAAAATGTTTATGTTTT
Found at i:4464 original size:39 final size:40
Alignment explanation
Indices: 4399--4474 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
4389 AACAAAAATC
* *
4399 TGGCCAAAAAAATTGACTAATTAATAAATTAGAATACTGT
1 TGGCCAAAAAAATAGACTAATAAATAAATTAGAATACTGT
4439 TGGCCAAAAAAAATAGA-TAA-AAATAAATTAGAATAC
1 TGGCC-AAAAAAATAGACTAATAAATAAATTAGAATAC
4475 CAACTCTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 15 0.45
40 8 0.24
41 10 0.30
ACGTcount: A:0.54, C:0.09, G:0.12, T:0.25
Consensus pattern (40 bp):
TGGCCAAAAAAATAGACTAATAAATAAATTAGAATACTGT
Found at i:5081 original size:13 final size:13
Alignment explanation
Indices: 5063--5088 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5053 CTTTGTTAAC
5063 TTTTATTTTTTAT
1 TTTTATTTTTTAT
5076 TTTTATTTTTTAT
1 TTTTATTTTTTAT
5089 AATAGGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:13471 original size:18 final size:18
Alignment explanation
Indices: 13448--13484 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
13438 CTGCATTCAC
13448 ATATTATTTCTATTGGTG
1 ATATTATTTCTATTGGTG
13466 ATATTATTTCTATTGGTG
1 ATATTATTTCTATTGGTG
13484 A
1 A
13485 ACAACATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.54
Consensus pattern (18 bp):
ATATTATTTCTATTGGTG
Found at i:15312 original size:20 final size:21
Alignment explanation
Indices: 15289--15330 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
15279 AAGACAAAAA
15289 TATTA-ACACACCTTCAAACT
1 TATTACACACACCTTCAAACT
*
15309 TATTACTCACACCTTCAAACT
1 TATTACACACACCTTCAAACT
15330 T
1 T
15331 CTTCTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (21 bp):
TATTACACACACCTTCAAACT
Found at i:21994 original size:31 final size:31
Alignment explanation
Indices: 21892--22060 Score: 127
Period size: 31 Copynumber: 5.6 Consensus size: 31
21882 TGTGGCTAAT
*
21892 TGCTCAAATAAGGGTCTAATATTTGCCACAA
1 TGCTCAAATAAGGGTCTAATATTTGCCAAAA
* * * * **
21923 TGCTCATATAAGGG-CATGATCTTT--TAATT
1 TGCTCAAATAAGGGTC-TAATATTTGCCAAAA
* *
21952 TGGC-CAAATAAGGGCCTAATGTTTGCCAAAA
1 T-GCTCAAATAAGGGTCTAATATTTGCCAAAA
* * **
21983 TGCTCAAATAAGGGTCTGATATTT--TAATT
1 TGCTCAAATAAGGGTCTAATATTTGCCAAAA
**
22012 TGAC-CAAATAAGGGTCTAACGTTTGCCAAAA
1 TG-CTCAAATAAGGGTCTAATATTTGCCAAAA
22043 TGCTCAAATAAGGGTCTA
1 TGCTCAAATAAGGGTCTA
22061 GCGTCAGTTT
Statistics
Matches: 103, Mismatches: 25, Indels: 20
0.70 0.17 0.14
Matches are distributed among these distances:
29 38 0.37
30 8 0.08
31 57 0.55
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (31 bp):
TGCTCAAATAAGGGTCTAATATTTGCCAAAA
Found at i:21994 original size:60 final size:60
Alignment explanation
Indices: 21896--22059 Score: 249
Period size: 60 Copynumber: 2.7 Consensus size: 60
21886 GCTAATTGCT
* * * * *
21896 CAAATAAGGGTCTAATATTTGCCACAATGCTCATATAAGGG-CATGATCTTTTAATTTGGC
1 CAAATAAGGGTCTAATGTTTGCCAAAATGCTCAAATAAGGGTC-TGATATTTTAATTTGAC
*
21956 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATATTTTAATTTGAC
1 CAAATAAGGGTCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATATTTTAATTTGAC
*
22016 CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGTCT
1 CAAATAAGGGTCTAATGTTTGCCAAAATGCTCAAATAAGGGTCT
22060 AGCGTCAGTT
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (60 bp):
CAAATAAGGGTCTAATGTTTGCCAAAATGCTCAAATAAGGGTCTGATATTTTAATTTGAC
Found at i:22139 original size:31 final size:30
Alignment explanation
Indices: 22098--22201 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 30
22088 TTTCAACGCC
* *
22098 AGGCCTTTATTTGAGTATTTTCAATAATATT
1 AGGCCCTTATTTGAGTATTTTCAATAACA-T
** *
22129 AGGCCCTTATTTG-GTCAAATT-AA-AAGAT
1 AGGCCCTTATTTGAGT-ATTTTCAATAACAT
* *
22157 CGGACCCTTATTTGAGCATTTTCAATAACACT
1 AGG-CCCTTATTTGAGTATTTTCAATAACA-T
22189 AGGCCCTTATTTG
1 AGGCCCTTATTTG
22202 GCCAAATTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 3 0.05
29 16 0.28
30 7 0.12
31 28 0.49
32 3 0.05
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (30 bp):
AGGCCCTTATTTGAGTATTTTCAATAACAT
Found at i:22197 original size:60 final size:60
Alignment explanation
Indices: 22104--22238 Score: 198
Period size: 60 Copynumber: 2.2 Consensus size: 60
22094 CGCCAGGCCT
* * * *
22104 TTATTTGAGTATTTTCAATAATATTAGGCCCTTATTTGGTCAAATTAAAAGATCGGACCC
1 TTATTTGAGCATTTTCAATAACACTAGGCCCTTATTTGGCCAAATTAAAAGATCGGACCC
* * *
22164 TTATTTGAGCATTTTCAATAACACTAGGCCCTTATTTGGCCAAATTAAAATATTGGGCCC
1 TTATTTGAGCATTTTCAATAACACTAGGCCCTTATTTGGCCAAATTAAAAGATCGGACCC
*
22224 TTATTTAAGCATTTT
1 TTATTTGAGCATTTT
22239 GGCAAACGTT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (60 bp):
TTATTTGAGCATTTTCAATAACACTAGGCCCTTATTTGGCCAAATTAAAAGATCGGACCC
Found at i:22228 original size:29 final size:28
Alignment explanation
Indices: 22123--22229 Score: 90
Period size: 29 Copynumber: 3.6 Consensus size: 28
22113 TATTTTCAAT
22123 AATATTAGGCCCTTATTTGGTCAAATTAA
1 AATATTAGGCCCTTATTTGG-CAAATTAA
* * **
22152 AAGA-TCGGACCCTTATTTGAGCATTTTCAA
1 AATATTAGG-CCCTTATTTG-GCAAATT-AA
* *
22182 TAACACTAGGCCCTTATTTGGCCAAATTAA
1 -AATATTAGGCCCTTATTTGG-CAAATTAA
*
22212 AATATTGGGCCCTTATTT
1 AATATTAGGCCCTTATTT
22230 AAGCATTTTG
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
28 3 0.05
29 32 0.52
30 6 0.10
31 17 0.28
32 3 0.05
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (28 bp):
AATATTAGGCCCTTATTTGGCAAATTAA
Found at i:28592 original size:21 final size:21
Alignment explanation
Indices: 28568--28607 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28558 CTAGATGGAT
*
28568 TCAAGACCACTCTAGGTGAAC
1 TCAAGACCACTATAGGTGAAC
28589 TCAAGACCACTATAGGTGA
1 TCAAGACCACTATAGGTGA
28608 GTTCAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (21 bp):
TCAAGACCACTATAGGTGAAC
Found at i:28613 original size:21 final size:21
Alignment explanation
Indices: 28566--28613 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
28556 CCCTAGATGG
*
28566 ATTCAAGACCACTCTAGGTGA
1 ATTCAAGACCACTATAGGTGA
*
28587 ACTCAAGACCACTATAGGTGA
1 ATTCAAGACCACTATAGGTGA
*
28608 GTTCAA
1 ATTCAA
28614 CAAAAATGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (21 bp):
ATTCAAGACCACTATAGGTGA
Found at i:28630 original size:21 final size:21
Alignment explanation
Indices: 28606--28657 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
28596 CACTATAGGT
28606 GAGTTCAACAAAAATGTGAAA
1 GAGTTCAACAAAAATGTGAAA
* **
28627 GAGTTCAATACGAATGTGAAA
1 GAGTTCAACAAAAATGTGAAA
*
28648 GAGTTGAACA
1 GAGTTCAACA
28658 CCAACTTAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (21 bp):
GAGTTCAACAAAAATGTGAAA
Found at i:33587 original size:19 final size:18
Alignment explanation
Indices: 33550--33588 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
33540 TTCTTGAAAT
*
33550 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
33568 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
33587 AA
1 AA
33589 GAAATCTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.44
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:41572 original size:14 final size:14
Alignment explanation
Indices: 41553--41579 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41543 TAAAAATAAC
41553 AATTATAAACTTTG
1 AATTATAAACTTTG
41567 AATTATAAACTTT
1 AATTATAAACTTT
41580 TTAGCACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
AATTATAAACTTTG
Found at i:42318 original size:14 final size:14
Alignment explanation
Indices: 42299--42329 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42289 ATGAATATAG
42299 TAAATTTTGAGACT
1 TAAATTTTGAGACT
*
42313 TAAATTTTGAGATT
1 TAAATTTTGAGACT
42327 TAA
1 TAA
42330 CATGTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (14 bp):
TAAATTTTGAGACT
Found at i:46119 original size:1 final size:1
Alignment explanation
Indices: 46113--46137 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
46103 ATTGAATACC
46113 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
46138 GTGGAAGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:50293 original size:12 final size:12
Alignment explanation
Indices: 50276--50324 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 12
50266 AGGGTAAAAC
50276 ATTAAATATCTA
1 ATTAAATATCTA
50288 ATT-AA-ATCTA
1 ATTAAATATCTA
50298 ATTAAA-A-C--
1 ATTAAATATCTA
50306 ATTAAATATCTA
1 ATTAAATATCTA
50318 ATTAAAT
1 ATTAAAT
50325 CTAAACCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 6 0.19
9 1 0.03
10 10 0.31
11 5 0.16
12 10 0.31
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (12 bp):
ATTAAATATCTA
Found at i:50306 original size:30 final size:30
Alignment explanation
Indices: 50270--50328 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
50260 TCTAGAAGGG
50270 TAAAACATTAAATATCTAATTAAATCTAAT
1 TAAAACATTAAATATCTAATTAAATCTAAT
50300 TAAAACATTAAATATCTAATTAAATCTAA
1 TAAAACATTAAATATCTAATTAAATCTAA
50329 ACCCTTAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (30 bp):
TAAAACATTAAATATCTAATTAAATCTAAT
Found at i:50318 original size:20 final size:20
Alignment explanation
Indices: 50293--50362 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
50283 ATCTAATTAA
50293 ATCTAATTAAAACATTAAAT
1 ATCTAATTAAAACATTAAAT
*
50313 ATCTAATTAAATC--TAAA-
1 ATCTAATTAAAACATTAAAT
** *
50330 CCCTTAGATTGAAACATTAAAT
1 ATC-TA-ATTAAAACATTAAAT
50352 ATCTAATTAAA
1 ATCTAATTAAA
50363 TCTGAAATAA
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
17 1 0.03
18 6 0.16
19 6 0.16
20 17 0.46
21 6 0.16
22 1 0.03
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.34
Consensus pattern (20 bp):
ATCTAATTAAAACATTAAAT
Found at i:51295 original size:22 final size:22
Alignment explanation
Indices: 51270--51439 Score: 98
Period size: 22 Copynumber: 7.8 Consensus size: 22
51260 ATGATCCCAT
51270 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** **
51292 TATGAAATTTTAATAATGATAT
1 TATGAAATTTTGATAACCTTCC
* * * **
51314 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
51336 TAT--AATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* *
51356 TATAAAATTTTGTTAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * *
51378 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
51400 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
*
51422 AATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
51440 AACACTATAT
Statistics
Matches: 110, Mismatches: 30, Indels: 15
0.71 0.19 0.10
Matches are distributed among these distances:
20 15 0.14
21 4 0.04
22 88 0.80
23 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:51481 original size:22 final size:22
Alignment explanation
Indices: 51360--51486 Score: 89
Period size: 22 Copynumber: 5.6 Consensus size: 22
51350 CCTTCTTATA
* *
51360 AAATTTTGTTAACCTTCC-TAAG
1 AAATTTTGATAACC-TCCATATG
* *
51382 GAATTTTGA-AGACCTCAATATG
1 AAATTTTGATA-ACCTCCATATG
*
51404 AAATTTTGATAACTTCCCA-ATG
1 AAATTTTGATAACCT-CCATATG
*
51426 AAATTTTGATAACCAACACTATATG
1 AAATTTTGATAACC-TC-C-ATATG
* *
51451 AGATGTTGATAACCTCCATATG
1 AAATTTTGATAACCTCCATATG
* *
51473 ATATATTGATAACC
1 AAATTTTGATAACC
51487 ATGTTATGAA
Statistics
Matches: 83, Mismatches: 14, Indels: 16
0.73 0.12 0.14
Matches are distributed among these distances:
21 3 0.04
22 58 0.70
23 5 0.06
24 2 0.02
25 15 0.18
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACCTCCATATG
Found at i:51676 original size:22 final size:22
Alignment explanation
Indices: 51650--51863 Score: 121
Period size: 22 Copynumber: 9.7 Consensus size: 22
51640 ATCCCATTAA
51650 GAAATTTTGATAACCTTCCTAT
1 GAAATTTTGATAACCTTCCTAT
* ** *
51672 GAAATTTTAATAACGATACTAT
1 GAAATTTTGATAACCTTCCTAT
* * * **
51694 GGAATTTCGAGAACCTTTTTAT
1 GAAATTTTGATAACCTTCCTAT
* ** *
51716 AAAATTTTTTTAACCTTCTTAT
1 GAAATTTTGATAACCTTCCTAT
* * *
51738 GAAATTTTGCTAACCTCCCTAA
1 GAAATTTTGATAACCTTCCTAT
* *
51760 GGAATTTTGA-AGACC-TCAATAT
1 GAAATTTTGATA-ACCTTC-CTAT
*
51782 GAAATTTTGATAA-CTTCCCAAT
1 GAAATTTTGATAACCTT-CCTAT
* **
51804 AAAATTTTGATAACCAACACTAT
1 GAAATTTTGATAACCTTC-CTAT
* *
51827 GAGATGTTGATAACC-TCCATAT
1 GAAATTTTGATAACCTTCC-TAT
* *
51849 GATATATTGATAACC
1 GAAATTTTGATAACC
51864 ACGTTATGAA
Statistics
Matches: 141, Mismatches: 43, Indels: 16
0.70 0.22 0.08
Matches are distributed among these distances:
21 4 0.03
22 119 0.84
23 18 0.13
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
GAAATTTTGATAACCTTCCTAT
Found at i:51889 original size:377 final size:376
Alignment explanation
Indices: 51167--52270 Score: 1830
Period size: 377 Copynumber: 3.0 Consensus size: 376
51157 CAGATTTTGT
* *
51167 GTGCGTTGCACGTGGCCCAACGTGTTTAAATGGAATATTCATATGAAATTATGATAACCTCTCTG
1 GTGCGTTGCCCGTGGCCCAACGTGTTT-AATGGAATATTCATATGAAATTATGATAACCTCTCTA
* *
51232 TTAAATTATGTTAATTACACTATTTTTTATGATCCCATTATGAAATTTTGATAACCTTCCTATGA
65 TTAAATTATGATAATTACACTATTTTTTATGATCCCATTAAGAAATTTTGATAACCTTCCTATGA
* *
51297 AATTTTAATAATGATATTATGGAATTTCGAGAACCTTTTTAT--AATTTTTTTAACCTTCTTATA
130 AATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTATAAAATTTTTTTAACCTTCTTATG
*
51360 AAATTTTGTTAACCTTCCTAAGGAATTTTGAAGACCTCAATATGAAATTTTGATAACTTCCCAAT
195 AAATTTTGTTAACCTCCCTAAGGAATTTTGAAGACCTCAATATGAAATTTTGATAACTTCCCAAT
*
51425 GAAATTTTGATAACCAACACTATATGAGATGTTGATAACCTCCATATGATATATTGATAACCATG
260 -AAATTTTGATAACCAACAC--TATGAGATGTTGATAACCTCCATATGATATATTGATAACCACG
*
51490 TTATGAAAATTAAAAAACCTCCATATGAATTGTTAGTAATCACATTAGCTTTCAC
322 TTATGAAAATTTAAAAACCTCCATATGAATTGTTAGTAATCACATTAGCTTTCAC
**
51545 GTGCGTTGCCCGTGGCCCAATTTGTTTAATGGAATATTCATATGAAATTATGATAACCTCTCTAT
1 GTGCGTTGCCCGTGGCCCAACGTGTTTAATGGAATATTCATATGAAATTATGATAACCTCTCTAT
*
51610 TAAATTATGATAATTACACTATATTTTATGATCCCATTAAGAAATTTTGATAACCTTCCTATGAA
66 TAAATTATGATAATTACACTATTTTTTATGATCCCATTAAGAAATTTTGATAACCTTCCTATGAA
*
51675 ATTTTAATAACGATACTATGGAATTTCGAGAACCTTTTTATAAAATTTTTTTAACCTTCTTATGA
131 ATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTATAAAATTTTTTTAACCTTCTTATGA
*
51740 AATTTTGCTAACCTCCCTAAGGAATTTTGAAGACCTCAATATGAAATTTTGATAACTTCCCAATA
196 AATTTTGTTAACCTCCCTAAGGAATTTTGAAGACCTCAATATGAAATTTTGATAACTTCCCAAT-
51805 AAATTTTGATAACCAACACTATGAGATGTTGATAACCTCCATATGATATATTGATAACCACGTTA
260 AAATTTTGATAACCAACACTATGAGATGTTGATAACCTCCATATGATATATTGATAACCACGTTA
51870 TGAAAATTTAAAAACCTCCATATGAATTGTTAGTAATCACATTAGCTTTCAC
325 TGAAAATTTAAAAACCTCCATATGAATTGTTAGTAATCACATTAGCTTTCAC
* * *
51922 GTCCGTTGCCCGTGACCCAACGTCTTTAATGGAATATTCATATGAAATTATGATAACCTCTCTAT
1 GTGCGTTGCCCGTGGCCCAACGTGTTTAATGGAATATTCATATGAAATTATGATAACCTCTCTAT
* *
51987 TAAATTATGATAACTACACTATTTTTTATGATCCCATTAAGAAGTTTTGATAACCTTCCTATGAA
66 TAAATTATGATAATTACACTATTTTTTATGATCCCATTAAGAAATTTTGATAACCTTCCTATGAA
* *
52052 ATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTATAAAAATTTTTTAACATTCTTATGA
131 ATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTATAAAATTTTTTTAACCTTCTTATGA
52117 AATTTTGTTAACCTCCCTAAGGAATTTTGAAGACCTCAATATGAAATTTTGATAACTTCCCAATA
196 AATTTTGTTAACCTCCCTAAGGAATTTTGAAGACCTCAATATGAAATTTTGATAACTTCCCAATA
* *
52182 AA--TT--T---------T-T--GATATTGATAACCTCTATATGATATATTGATAACCACGTTAT
261 AATTTTGATAACCAACACTATGAGATGTTGATAACCTCCATATGATATATTGATAACCACGTTAT
52231 GAAAATTTAAAAACCTCCATATGAATTGTTAGTAATCACA
326 GAAAATTTAAAAACCTCCATATGAATTGTTAGTAATCACA
52271 CTATGAAATT
Statistics
Matches: 695, Mismatches: 29, Indels: 22
0.93 0.04 0.03
Matches are distributed among these distances:
360 80 0.12
362 1 0.00
363 1 0.00
372 1 0.00
374 2 0.00
376 3 0.00
377 481 0.69
378 24 0.03
379 102 0.15
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (376 bp):
GTGCGTTGCCCGTGGCCCAACGTGTTTAATGGAATATTCATATGAAATTATGATAACCTCTCTAT
TAAATTATGATAATTACACTATTTTTTATGATCCCATTAAGAAATTTTGATAACCTTCCTATGAA
ATTTTAATAATGATACTATGGAATTTCGAGAACCTTTTTATAAAATTTTTTTAACCTTCTTATGA
AATTTTGTTAACCTCCCTAAGGAATTTTGAAGACCTCAATATGAAATTTTGATAACTTCCCAATA
AATTTTGATAACCAACACTATGAGATGTTGATAACCTCCATATGATATATTGATAACCACGTTAT
GAAAATTTAAAAACCTCCATATGAATTGTTAGTAATCACATTAGCTTTCAC
Found at i:52008 original size:22 final size:22
Alignment explanation
Indices: 51966--52009 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
51956 TATTCATATG
*
51966 AAATTATGATAACCTCTCTATT
1 AAATTATGATAACCTCACTATT
51988 AAATTATGATAA-CTACACTATT
1 AAATTATGATAACCT-CACTATT
52010 TTTTATGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.39
Consensus pattern (22 bp):
AAATTATGATAACCTCACTATT
Found at i:52056 original size:22 final size:22
Alignment explanation
Indices: 52031--52176 Score: 66
Period size: 22 Copynumber: 6.7 Consensus size: 22
52021 CATTAAGAAG
52031 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *** * *
52053 TTTTAATAATGATACTATGGAA
1 TTTTGATAACCTTCCTATGAAA
* * ** *
52075 TTTCGAGAACCTTTTTATAAAAA
1 TTTTGATAACCTTCCTAT-GAAA
* * *
52098 TTTT-TTAACATTCTTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* * * *
52119 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAACCTTCCTATGAAA
*
52141 TTTTGA-AGACC-TCAATATGAAA
1 TTTTGATA-ACCTTC-CTATGAAA
52163 TTTTGATAA-CTTCC
1 TTTTGATAACCTTCC
52177 CAATAAATTT
Statistics
Matches: 85, Mismatches: 33, Indels: 13
0.65 0.25 0.10
Matches are distributed among these distances:
21 10 0.12
22 69 0.81
23 6 0.07
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:52326 original size:23 final size:23
Alignment explanation
Indices: 52298--52355 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
52288 CATTGCTATG
* *
52298 AAATTTTGATAAATCTTCCTACA
1 AAATTTTGATAAAGCTCCCTACA
*
52321 AAATTTTGATAAAGCTCCCTATA
1 AAATTTTGATAAAGCTCCCTACA
52344 AAATTTTGATAA
1 AAATTTTGATAA
52356 CTTTCTTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAAGCTCCCTACA
Found at i:52385 original size:35 final size:35
Alignment explanation
Indices: 52343--52410 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
52333 AGCTCCCTAT
*
52343 AAAATTTTGATAA-CTTTCTTATGAAATCTTGATAA
1 AAAATTTTGATAATC-TTCCTATGAAATCTTGATAA
* *
52378 AAAATTTTGTTAATCTTCCTATGAAATTTTGAT
1 AAAATTTTGATAATCTTCCTATGAAATCTTGAT
52411 CTACATACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 28 0.97
36 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (35 bp):
AAAATTTTGATAATCTTCCTATGAAATCTTGATAA
Found at i:52404 original size:22 final size:21
Alignment explanation
Indices: 52379--52451 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 21
52369 TCTTGATAAA
*
52379 AAATTTTGTTAATCTTCCTATG
1 AAATTTTGTTAA-CATCCTATG
*
52401 AAATTTTGATCT-ACATACTATG
1 AAATTTTG-T-TAACATCCTATG
* * *
52423 AAATTTTGATAACCCTCTTATG
1 AAATTTTGTTAA-CATCCTATG
52445 AAATTTT
1 AAATTTT
52452 AAAAACTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 36 0.88
23 2 0.05
24 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (21 bp):
AAATTTTGTTAACATCCTATG
Found at i:52724 original size:31 final size:31
Alignment explanation
Indices: 52689--52747 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
52679 TGGCAATTTA
52689 GAAATATGTTTTAAAAAAAAGGGTACAATTG
1 GAAATATGTTTTAAAAAAAAGGGTACAATTG
*
52720 GAAATATGTTTTAAAAATAAGGGTACAA
1 GAAATATGTTTTAAAAAAAAGGGTACAA
52748 ACGGAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTAAAAAAAAGGGTACAATTG
Found at i:52754 original size:31 final size:31
Alignment explanation
Indices: 52689--52754 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
52679 TGGCAATTTA
**
52689 GAAATATGTTTTAAAAAAAAGGGTACAATTG
1 GAAATATGTTTTAAAAAAAAGGGTACAAACG
*
52720 GAAATATGTTTTAAAAATAAGGGTACAAACG
1 GAAATATGTTTTAAAAAAAAGGGTACAAACG
52751 GAAA
1 GAAA
52755 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.26
Consensus pattern (31 bp):
GAAATATGTTTTAAAAAAAAGGGTACAAACG
Found at i:54992 original size:19 final size:21
Alignment explanation
Indices: 54943--54993 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
54933 TTCACATCTA
* *
54943 ATAAGGTTACTAAAAATAACT
1 ATAAGGTTATTAAAAATAAAT
54964 ATAGAGGTTATTAAAAA-AAAT
1 ATA-AGGTTATTAAAAATAAAT
54985 -TAAGGTTAT
1 ATAAGGTTAT
54994 AACTTCAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 7 0.26
20 2 0.07
21 6 0.22
22 12 0.44
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.31
Consensus pattern (21 bp):
ATAAGGTTATTAAAAATAAAT
Done.