Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005052.1 Corchorus capsularis cultivar CVL-1 contig05070, 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: 33724
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:2587 original size:16 final size:17
Alignment explanation
Indices: 2566--2598 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2556 TATTAGATAA
2566 TACTTGTAATAT-TAAT
1 TACTTGTAATATCTAAT
2582 TACTTGTAATATCTAAT
1 TACTTGTAATATCTAAT
2599 AATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (17 bp):
TACTTGTAATATCTAAT
Found at i:3502 original size:33 final size:33
Alignment explanation
Indices: 3460--3532 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 33
3450 AATTACATAT
* *
3460 TATTTCTAATAATATTTATTGCATATTAAATAAA
1 TATTTCTAATAATATTTAGTACATATT-AATAAA
3494 TA-TTC---TAATATTTAGTACATATTAATAAA
1 TATTTCTAATAATATTTAGTACATATTAATAAA
3523 TATTTCTAAT
1 TATTTCTAAT
3533 GAAATCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
29 8 0.24
30 19 0.58
33 4 0.12
34 2 0.06
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (33 bp):
TATTTCTAATAATATTTAGTACATATTAATAAA
Found at i:3505 original size:30 final size:30
Alignment explanation
Indices: 3469--3532 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
3459 TTATTTCTAA
* *
3469 TAATATTTATTGCATATTAAATAAATA-TTC
1 TAATATTTAGTACATATT-AATAAATATTTC
3499 TAATATTTAGTACATATTAATAAATATTTC
1 TAATATTTAGTACATATTAATAAATATTTC
3529 TAAT
1 TAAT
3533 GAAATCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 8 0.26
30 23 0.74
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (30 bp):
TAATATTTAGTACATATTAATAAATATTTC
Found at i:5064 original size:1 final size:1
Alignment explanation
Indices: 5060--5086 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
5050 ACCCTTTTTT
5060 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
5087 TTACCTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9167 original size:42 final size:42
Alignment explanation
Indices: 9120--9201 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
9110 GACCTCATCA
*
9120 AGCCTAATCTACGGTTGGAGTTAATCCAAGTCATGATCGGAC
1 AGCCTAATCCACGGTTGGAGTTAATCCAAGTCATGATCGGAC
9162 AGCCTAATCCACGGTTGGAGTTAATCCAAGTCATGATCGG
1 AGCCTAATCCACGGTTGGAGTTAATCCAAGTCATGATCGG
9202 TAATAGCGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (42 bp):
AGCCTAATCCACGGTTGGAGTTAATCCAAGTCATGATCGGAC
Found at i:9522 original size:2 final size:2
Alignment explanation
Indices: 9515--9544 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9505 GTAACATCAA
*
9515 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9545 GTTTATACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10240 original size:33 final size:33
Alignment explanation
Indices: 10171--10248 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
10161 TGCTAATTAC
*
10171 TACTATAACCCATTAGCAGGGCCTTAAGCTAAT
1 TACTATAACCCATTAGCAGGGCCTTAAGCGAAT
* ** *
10204 TACTATAACCCGTTAGCAGGGCCGTT-TTCGAGT
1 TACTATAACCCATTAGCAGGGCC-TTAAGCGAAT
10237 TACTATAACCCA
1 TACTATAACCCA
10249 CTTGCAAGGC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 36 0.95
34 2 0.05
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (33 bp):
TACTATAACCCATTAGCAGGGCCTTAAGCGAAT
Found at i:11524 original size:39 final size:40
Alignment explanation
Indices: 11450--11528 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
11440 AAATAATTTT
* *
11450 TTGCTCCATGTTTCAATCCCAAAAGGCAAAACCAAAAGTA
1 TTGCTCCATGTTTCAATCCAAAAAGACAAAACCAAAAGTA
*
11490 TTGCTTCC-TGTTTCAATCCAAAAAGAC-AATCCAAAAGTA
1 TTGC-TCCATGTTTCAATCCAAAAAGACAAAACCAAAAGTA
11529 AACCATTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 11 0.31
40 21 0.60
41 3 0.09
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.25
Consensus pattern (40 bp):
TTGCTCCATGTTTCAATCCAAAAAGACAAAACCAAAAGTA
Found at i:12343 original size:7 final size:7
Alignment explanation
Indices: 12327--12565 Score: 67
Period size: 7 Copynumber: 33.7 Consensus size: 7
12317 ACGGCACTGA
*
12327 TTACTCT
1 TTACTTT
12334 TTACTTT
1 TTACTTT
12341 TTACCATTT
1 TTA-C-TTT
12350 TT-C--T
1 TTACTTT
**
12354 TTACTGA
1 TTACTTT
*
12361 TTACTCT
1 TTACTTT
12368 TTACTTT
1 TTACTTT
*
12375 TTACCATT
1 TTA-CTTT
*
12383 TTACTCT
1 TTACTTT
**
12390 TTACTGA
1 TTACTTT
12397 TTACTTT
1 TTACTTT
12404 TTACTTT
1 TTACTTT
* *
12411 TAACCATT
1 TTA-CTTT
*
12419 TTACTCT
1 TTACTTT
**
12426 TTACTGA
1 TTACTTT
*
12433 TTACTCT
1 TTACTTT
*
12440 TTACTCT
1 TTACTTT
12447 TTACCATTT
1 TTA-C-TTT
12456 TT-C--T
1 TTACTTT
**
12460 TTACTGA
1 TTACTTT
12467 TTACTCTT
1 TTACT-TT
12475 TTACTTT
1 TTACTTT
*
12482 TTACTGAT
1 TTACT-TT
**
12490 TGCCTTT
1 TTACTTT
**
12497 TTGTTTT
1 TTACTTT
**
12504 TTACTGA
1 TTACTTT
*
12511 TTACCTT
1 TTACTTT
*
12518 TTACTTC
1 TTACTTT
**
12525 TTACTGA
1 TTACTTT
*
12532 TTACCTT
1 TTACTTT
*
12539 TTACTTC
1 TTACTTT
**
12546 TTACTGA
1 TTACTTT
12553 TTACCTTT
1 TTA-CTTT
12561 TTACT
1 TTACT
12566 CTTATTGATT
Statistics
Matches: 165, Mismatches: 52, Indels: 30
0.67 0.21 0.12
Matches are distributed among these distances:
4 6 0.04
5 2 0.01
7 121 0.73
8 27 0.16
9 9 0.05
ACGTcount: A:0.18, C:0.21, G:0.04, T:0.57
Consensus pattern (7 bp):
TTACTTT
Found at i:12378 original size:21 final size:21
Alignment explanation
Indices: 12353--12724 Score: 125
Period size: 21 Copynumber: 18.3 Consensus size: 21
12343 ACCATTTTTC
12353 TTTACTGATTACTCTTTACTT
1 TTTACTGATTACTCTTTACTT
* *
12374 TTTAC----CA-T-TTTACTC
1 TTTACTGATTACTCTTTACTT
*
12389 TTTACTGATTACTTTTTACTT
1 TTTACTGATTACTCTTTACTT
** *
12410 -TTA---ACCA-T-TTTACTC
1 TTTACTGATTACTCTTTACTT
*
12425 TTTACTGATTACTCTTTACTC
1 TTTACTGATTACTCTTTACTT
*
12446 TTTAC-CA-T--T-TTT-C-T
1 TTTACTGATTACTCTTTACTT
12460 TT-ACTGATTACTCTTTTACTT
1 TTTACTGATTACTC-TTTACTT
* * **
12481 TTTACTGATTGCCTTTTTGTTT
1 TTTACTGATT-ACTCTTTACTT
12503 TTTACTGATTAC-CTTTTACTT
1 TTTACTGATTACTC-TTTACTT
*
12524 CTTACTGATTAC-CTTTTACTT
1 TTTACTGATTACTC-TTTACTT
* *
12545 CTTACTGATTACCTTTTTAC-T
1 TTTACTGATTA-CTCTTTACTT
* * * **
12566 CTTATTGATTACCTTTTTGTTT
1 TTTACTGATTA-CTCTTTACTT
* * *
12588 CTTTACTAATTAC-CGTTTTTCTC
1 -TTTACTGATTACTC--TTTACTT
* * *
12611 TTTACTAATTAC-CGTTTTTCTC
1 TTTACTGATTACTC--TTTACTT
12633 TTTACTGATTACTCTTTACTT
1 TTTACTGATTACTCTTTACTT
** * *
12654 TCTT-CTTCTTCCT-TTTTCTT
1 T-TTACTGATTACTCTTTACTT
12674 TCTTACTGATTAC-CATTTTACTT
1 T-TTACTGATTACTC--TTTACTT
*
12697 TTTACTGATTACTATTTGACTT
1 TTTACTGATTACTCTTT-ACTT
12719 TTTACT
1 TTTACT
12725 AATTGCCACT
Statistics
Matches: 270, Mismatches: 44, Indels: 73
0.70 0.11 0.19
Matches are distributed among these distances:
13 2 0.01
14 3 0.01
15 19 0.07
16 8 0.03
17 5 0.02
19 7 0.03
20 17 0.06
21 101 0.37
22 86 0.32
23 22 0.08
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTACTGATTACTCTTTACTT
Found at i:12398 original size:36 final size:34
Alignment explanation
Indices: 12322--12485 Score: 256
Period size: 36 Copynumber: 4.7 Consensus size: 34
12312 AAAAGACGGC
12322 ACTGATTACTCTTTACTTTTTACCATTTTTCTTT
1 ACTGATTACTCTTTACTTTTTACCATTTTTCTTT
12356 ACTGATTACTCTTTACTTTTTACCATTTTACTCTTT
1 ACTGATTACTCTTTACTTTTTACCATTTT--TCTTT
* *
12392 ACTGATTACTTTTTACTTTTAACCATTTTACTCTTT
1 ACTGATTACTCTTTACTTTTTACCATTTT--TCTTT
*
12428 ACTGATTACTCTTTACTCTTTACCATTTTTCTTT
1 ACTGATTACTCTTTACTTTTTACCATTTTTCTTT
12462 ACTGATTACTCTTTTACTTTTTAC
1 ACTGATTACTC-TTTACTTTTTAC
12486 TGATTGCCTT
Statistics
Matches: 121, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
34 45 0.37
35 11 0.09
36 65 0.54
ACGTcount: A:0.20, C:0.21, G:0.03, T:0.56
Consensus pattern (34 bp):
ACTGATTACTCTTTACTTTTTACCATTTTTCTTT
Found at i:12487 original size:22 final size:22
Alignment explanation
Indices: 12459--12756 Score: 233
Period size: 22 Copynumber: 13.8 Consensus size: 22
12449 ACCATTTTTC
12459 TTTACTGATTA-CTCTTTTACTT
1 TTTACTGATTACCT-TTTTACTT
* **
12481 TTTACTGATTGCCTTTTTGTTT
1 TTTACTGATTACCTTTTTACTT
12503 TTTACTGATTACC-TTTTACTT
1 TTTACTGATTACCTTTTTACTT
*
12524 CTTACTGATTACC-TTTTACTT
1 TTTACTGATTACCTTTTTACTT
*
12545 CTTACTGATTACCTTTTTAC-T
1 TTTACTGATTACCTTTTTACTT
* * **
12566 CTTATTGATTACCTTTTTGTTT
1 TTTACTGATTACCTTTTTACTT
* *
12588 CTTTACTAATTACCGTTTTT-CTC
1 -TTTACTGATTACC-TTTTTACTT
* *
12611 TTTACTAATTACCGTTTTT-CTC
1 TTTACTGATTACC-TTTTTACTT
*
12633 TTTACTGATTA-CTCTTTACTT
1 TTTACTGATTACCTTTTTACTT
**
12654 TCTT-CTTCTT-CCTTTTT-CTT
1 T-TTACTGATTACCTTTTTACTT
*
12674 TCTTACTGATTACCATTTTACTT
1 T-TTACTGATTACCTTTTTACTT
*
12697 TTTACTGATTA-CTATTTGACTT
1 TTTACTGATTACCT-TTTTACTT
* * ** *
12719 TTTACTAATTGCC-ACTTACTC
1 TTTACTGATTACCTTTTTACTT
*
12740 TTTACTGATTGCCTTTT
1 TTTACTGATTACCTTTT
12757 CTTATTGAAC
Statistics
Matches: 227, Mismatches: 35, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
20 11 0.05
21 91 0.40
22 102 0.45
23 18 0.08
24 5 0.02
ACGTcount: A:0.17, C:0.21, G:0.06, T:0.56
Consensus pattern (22 bp):
TTTACTGATTACCTTTTTACTT
Found at i:12643 original size:130 final size:130
Alignment explanation
Indices: 12455--12756 Score: 305
Period size: 130 Copynumber: 2.3 Consensus size: 130
12445 CTTTACCATT
* * * * * *
12455 TTTCTTTACTGATTACTCTTTTACTTTTTACTGATTGCCTTTTTGTTTTTTACTGATTAC-CTTT
1 TTTCTTTACTAATTACTCTTTTACTCTTTACTAATTACCTTTTTGCTCTTTACTGATTACTC-TT
*
12519 TAC-TTCTTACTGATTACCTTTTAC-TTCTTACTGATTACCTTTTTACTCTTATTGATTACCTTT
65 TACTTTCTT-CTGATT-CCTTTTACTTTCTTACTGATTACCATTTTACTCTTATTGATTACCTTT
12582 TTG
128 TTG
*
12585 TTTCTTTACTAATTAC-CGTTTTTCTCTTTACTAATTACCGTTTTT-CTCTTTACTGATTACTCT
1 TTTCTTTACTAATTACTC-TTTTACTCTTTACTAATTACC-TTTTTGCTCTTTACTGATTACTCT
** * * * *
12648 TTACTTTCTTCTTCTTCCTTTTTCTTTCTTACTGATTACCATTTTACTTTTTACTGATTA-CTAT
64 TTACTTTCTTCTGATTCCTTTTACTTTCTTACTGATTACCATTTTAC-TCTTATTGATTACCTTT
12712 TTG
128 TTG
* * ** * *
12715 ACTT-TTTACTAATTGC-CACTTACTCTTTACTGATTGCCTTTT
1 -TTTCTTTACTAATTACTCTTTTACTCTTTACTAATTACCTTTT
12757 CTTATTGAAC
Statistics
Matches: 144, Mismatches: 21, Indels: 16
0.80 0.12 0.09
Matches are distributed among these distances:
128 4 0.03
129 24 0.17
130 93 0.65
131 23 0.16
ACGTcount: A:0.17, C:0.21, G:0.06, T:0.57
Consensus pattern (130 bp):
TTTCTTTACTAATTACTCTTTTACTCTTTACTAATTACCTTTTTGCTCTTTACTGATTACTCTTT
ACTTTCTTCTGATTCCTTTTACTTTCTTACTGATTACCATTTTACTCTTATTGATTACCTTTTTG
Found at i:12832 original size:34 final size:34
Alignment explanation
Indices: 12781--12860 Score: 119
Period size: 36 Copynumber: 2.4 Consensus size: 34
12771 TCACTAATTA
*
12781 CTTTTT-CTTATTGAACTTAATTA-CTGATTACC
1 CTTTTTACTTTTTGAACTTAATTACCTGATTACC
12813 CTTTTTACTTTTTGGAACTTAATTACTCTGATTACC
1 CTTTTTACTTTTT-GAACTTAATTAC-CTGATTACC
12849 CTTTTTACTTTT
1 CTTTTTACTTTT
12861 CTGAGTGACC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
32 6 0.14
33 5 0.12
34 11 0.26
36 21 0.49
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.54
Consensus pattern (34 bp):
CTTTTTACTTTTTGAACTTAATTACCTGATTACC
Found at i:12851 original size:36 final size:33
Alignment explanation
Indices: 12741--12860 Score: 117
Period size: 30 Copynumber: 3.7 Consensus size: 33
12731 CACTTACTCT
* * *
12741 TTACTGATT-GCC-TTTT-CTTATTGAACTTAG
1 TTACTGATTACCCTTTTTACTTTTTGAACTTAA
* * *
12771 TCACTAATTA--CTTTTT-CTTATTGAACTTAA
1 TTACTGATTACCCTTTTTACTTTTTGAACTTAA
12801 TTACTGATTACCCTTTTTACTTTTTGGAACTTAA
1 TTACTGATTACCCTTTTTACTTTTT-GAACTTAA
12835 TTACTCTGATTACCCTTTTTACTTTT
1 TTA--CTGATTACCCTTTTTACTTTT
12861 CTGAGTGACC
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
29 1 0.01
30 32 0.42
32 6 0.08
33 5 0.07
34 11 0.14
36 21 0.28
ACGTcount: A:0.23, C:0.18, G:0.07, T:0.52
Consensus pattern (33 bp):
TTACTGATTACCCTTTTTACTTTTTGAACTTAA
Found at i:13466 original size:26 final size:26
Alignment explanation
Indices: 13393--13458 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 26
13383 CGAAGTTCAC
* **
13393 AAAGCCTAAATGCATAAAACCAA-TA
1 AAAGCCCAAATGCATAAAATAAATTA
*
13418 AAAGCCCAAATGCTTAAAATAAATTA
1 AAAGCCCAAATGCATAAAATAAATTA
13444 AAAGCCCAAATGCAT
1 AAAGCCCAAATGCAT
13459 CAATTAAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
25 19 0.54
26 16 0.46
ACGTcount: A:0.53, C:0.20, G:0.09, T:0.18
Consensus pattern (26 bp):
AAAGCCCAAATGCATAAAATAAATTA
Found at i:21528 original size:19 final size:18
Alignment explanation
Indices: 21504--21539 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
21494 CTTTTTCATA
*
21504 TTTTTTTAATTTGGATTTC
1 TTTTTTCAATTT-GATTTC
21523 TTTTTTCAATTTGATTT
1 TTTTTTCAATTTGATTT
21540 TTATCCTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.17, C:0.06, G:0.08, T:0.69
Consensus pattern (18 bp):
TTTTTTCAATTTGATTTC
Found at i:22910 original size:35 final size:36
Alignment explanation
Indices: 22865--22995 Score: 119
Period size: 35 Copynumber: 3.6 Consensus size: 36
22855 ATTGATTTAC
22865 TTAATTTACCAGTTTACTTAATTGCACCGAATTAAG
1 TTAATTTACCAGTTTACTTAATTGCACCGAATTAAG
* * *
22901 TTAA-TTACCAAACTACTTAACCTAATT--ACCGAATT-AC
1 TTAATTTACC--AGT--TT-ACTTAATTGCACCGAATTAAG
*
22938 TTAATTTTCCAGTTTACTTAATTGCACCGAATTAAG
1 TTAATTTACCAGTTTACTTAATTGCACCGAATTAAG
* * *
22974 TTGA-TTATCAGATTACTTAATT
1 TTAATTTACCAGTTTACTTAATT
22996 TAATTACCAC
Statistics
Matches: 75, Mismatches: 11, Indels: 19
0.71 0.10 0.18
Matches are distributed among these distances:
33 7 0.09
34 2 0.03
35 28 0.37
36 10 0.13
37 7 0.09
38 12 0.16
39 2 0.03
40 7 0.09
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (36 bp):
TTAATTTACCAGTTTACTTAATTGCACCGAATTAAG
Found at i:22926 original size:21 final size:21
Alignment explanation
Indices: 22902--22941 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22892 CGAATTAAGT
22902 TAATTACCAAACTACTTAACC
1 TAATTACCAAACTACTTAACC
* *
22923 TAATTACCGAATTACTTAA
1 TAATTACCAAACTACTTAA
22942 TTTTCCAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.33
Consensus pattern (21 bp):
TAATTACCAAACTACTTAACC
Found at i:22938 original size:73 final size:73
Alignment explanation
Indices: 22861--23016 Score: 224
Period size: 73 Copynumber: 2.1 Consensus size: 73
22851 AATTATTGAT
22861 TTACTTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTACCAAACTACTTAACCTAA
1 TTACTTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTACCAAACTACTTAACCTAA
22926 TTACCGA-A
66 TTACC-ACA
* * * * * **
22934 TTACTTAATTTTCCAGTTTACTTAATTGCACCGAATTAAGTTGATTATCAGATTACTTAATTTAA
1 TTACTTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTACCAAACTACTTAACCTAA
*
22999 TTACCACT
66 TTACCACA
23007 TTACTTAATT
1 TTACTTAATT
23017 GCACCAAATT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 1 0.01
73 73 0.99
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (73 bp):
TTACTTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTACCAAACTACTTAACCTAA
TTACCACA
Found at i:23001 original size:21 final size:21
Alignment explanation
Indices: 22985--23072 Score: 55
Period size: 21 Copynumber: 4.5 Consensus size: 21
22975 TGATTATCAG
22985 ATTACTTAATTTAATTACCAC
1 ATTACTTAATTTAATTACCAC
* **
23006 TTTACTTAA-TT--GCACCA-
1 ATTACTTAATTTAATTACCAC
* * *
23023 A--A-TTAAGTTGATTACCAA
1 ATTACTTAATTTAATTACCAC
* *
23041 ATTACTTAATTTAACTACCAA
1 ATTACTTAATTTAATTACCAC
23062 ATTACTTAATT
1 ATTACTTAATT
23073 GCACCGAATT
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
14 4 0.08
15 3 0.06
17 4 0.08
18 5 0.10
20 3 0.06
21 32 0.63
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.41
Consensus pattern (21 bp):
ATTACTTAATTTAATTACCAC
Found at i:23017 original size:56 final size:56
Alignment explanation
Indices: 22925--23209 Score: 443
Period size: 56 Copynumber: 5.1 Consensus size: 56
22915 ACTTAACCTA
* *
22925 ATTACCGAATTACTTAA-TT--TT-CCAGTTTACTTAATTGCACCGAATTAAGTTG
1 ATTACCAAATTACTTAATTTAATTACCAATTTACTTAATTGCACCGAATTAAGTTG
* * * *
22977 ATTATCAGATTACTTAATTTAATTACCACTTTACTTAATTGCACCAAATTAAGTTG
1 ATTACCAAATTACTTAATTTAATTACCAATTTACTTAATTGCACCGAATTAAGTTG
* *
23033 ATTACCAAATTACTTAATTTAACTACCAAATTACTTAATTGCACCGAATTAAGTTG
1 ATTACCAAATTACTTAATTTAATTACCAATTTACTTAATTGCACCGAATTAAGTTG
*
23089 ATTACCAAATTACTTAATTTAATTACCAAATTACTTAATTGCACCGAATTAAGTTG
1 ATTACCAAATTACTTAATTTAATTACCAATTTACTTAATTGCACCGAATTAAGTTG
*
23145 ATTACCAAATTACTTAATTTAATTACCCAATTTACTTAATTACACCGAATTAAGTTG
1 ATTACCAAATTACTTAATTTAATTA-CCAATTTACTTAATTGCACCGAATTAAGTTG
23202 ATTACCAA
1 ATTACCAA
23210 TTTGTTTTTT
Statistics
Matches: 214, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
52 14 0.07
53 2 0.01
55 2 0.01
56 159 0.74
57 37 0.17
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.38
Consensus pattern (56 bp):
ATTACCAAATTACTTAATTTAATTACCAATTTACTTAATTGCACCGAATTAAGTTG
Found at i:23046 original size:35 final size:35
Alignment explanation
Indices: 22990--23163 Score: 129
Period size: 35 Copynumber: 4.8 Consensus size: 35
22980 ATCAGATTAC
* **
22990 TTAATTTAATTACCACTTTACTTAATTGCACCAAA
1 TTAAGTTAATTACCAAATTACTTAATTGCACCAAA
* *
23025 TTAAGTTGATTACCAAATTACTTAATTTAACTACCAAA
1 TTAAGTTAATTACCAAATTACTTAA-TT-GC-ACCAAA
* * * *
23063 TT-ACTTAATTGCACCGAATTAAGTTGATT--ACCAAATTA
1 TTAAGTTAATT--ACCAAATT-ACTTAATTGCACC-AA--A
* *
23101 CTTAATTTAATTACCAAATTACTTAATTGCACCGAA
1 -TTAAGTTAATTACCAAATTACTTAATTGCACCAAA
*
23137 TTAAGTTGATTACCAAATTACTTAATT
1 TTAAGTTAATTACCAAATTACTTAATT
23164 TAATTACCCA
Statistics
Matches: 109, Mismatches: 17, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
35 49 0.45
36 5 0.05
37 13 0.12
38 17 0.16
39 14 0.13
40 11 0.10
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (35 bp):
TTAAGTTAATTACCAAATTACTTAATTGCACCAAA
Found at i:23065 original size:129 final size:125
Alignment explanation
Indices: 22825--23072 Score: 336
Period size: 129 Copynumber: 2.0 Consensus size: 125
22815 TATTTGATTA
* *
22825 TTTACTTAATTACACCGAATTAAGCTAATTATTGATTTACTTAATTTACCAGTTTACTTAATTGC
1 TTTACTTAATTACACCGAATTAAGCTAATTATAGATTTACTTAATTTACCACTTTACTTAATTGC
* * *
22890 ACCGAATTAAGTTAATTACCAAACTACTTAACCTAATTACCGAATTACTTAATTTTCCAG
66 ACCAAATTAAGTTAATTACCAAACTACTTAACCTAACTACCAAATTACTTAATTTTCCAG
* * *
22950 TTTACTTAATTGCACCGAATTAAGTTGATTATCAGA-TTACTTAATTTAATTACCACTTTACTTA
1 TTTACTTAATTACACCGAATTAAGCTAATTAT-AGATTTACTTAA--T--TTACCACTTTACTTA
* * **
23014 ATTGCACCAAATTAAGTTGATTACCAAATTACTTAATTTAACTACCAAATTACTTAATT
61 ATTGCACCAAATTAAGTTAATTACCAAACTACTTAACCTAACTACCAAATTACTTAATT
23073 GCACCGAATT
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
125 37 0.35
126 2 0.02
127 1 0.01
129 66 0.62
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (125 bp):
TTTACTTAATTACACCGAATTAAGCTAATTATAGATTTACTTAATTTACCACTTTACTTAATTGC
ACCAAATTAAGTTAATTACCAAACTACTTAACCTAACTACCAAATTACTTAATTTTCCAG
Found at i:23100 original size:129 final size:129
Alignment explanation
Indices: 22865--23100 Score: 296
Period size: 129 Copynumber: 1.8 Consensus size: 129
22855 ATTGATTTAC
* * *
22865 TTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTACCAAACTACTTAACCTAATTAC
1 TTAATTTACCACTTTACTTAATTGCACCAAATTAAGTTAATTACCAAACTACTTAACCTAACTAC
* ** * * *
22930 CGAATTACTTAATTTTCCAGTTTACTTAATTGCACCGAATTAAGTTGATTATCAGATTACTTAAT
66 CAAATTACTTAATTCACCAATTAACTTAATT-CACCAAATTAAGTTGATTATCAGATTACTTAAT
* * **
22995 TTAA-TTACCACTTTACTTAATTGCACCAAATTAAGTTGATTACCAAATTACTTAATTTAACTAC
1 TTAATTTACCACTTTACTTAATTGCACCAAATTAAGTTAATTACCAAACTACTTAACCTAACTAC
* *
23059 CAAATTACTTAATTGCACCGAATTAAGTTGATT-ACCAAATTA
66 CAAATTACTTAATT-CACC-AATTAACTTAATTCACCAAATTA
23101 CTTAATTTAA
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
129 74 0.83
130 6 0.07
131 9 0.10
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (129 bp):
TTAATTTACCACTTTACTTAATTGCACCAAATTAAGTTAATTACCAAACTACTTAACCTAACTAC
CAAATTACTTAATTCACCAATTAACTTAATTCACCAAATTAAGTTGATTATCAGATTACTTAAT
Found at i:23113 original size:21 final size:21
Alignment explanation
Indices: 23089--23185 Score: 82
Period size: 21 Copynumber: 4.9 Consensus size: 21
23079 AATTAAGTTG
23089 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
23110 ATTACCAAATTACTTAA-TT-
1 ATTACCAAATTACTTAATTTA
** * * *
23129 -GCACC-GA--A-TTAAGTTG
1 ATTACCAAATTACTTAATTTA
23145 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
*
23166 ATTACCCAATTTACTTAATT
1 ATTA-CCAAATTACTTAATT
23186 ACACCGAATT
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
14 4 0.07
15 3 0.05
17 4 0.07
18 4 0.07
20 3 0.05
21 27 0.46
22 14 0.24
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.40
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:23179 original size:22 final size:21
Alignment explanation
Indices: 23145--23185 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
23135 AATTAAGTTG
23145 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
*
23166 ATTACCCAATTTACTTAATT
1 ATTA-CCAAATTACTTAATT
23186 ACACCGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:24577 original size:12 final size:12
Alignment explanation
Indices: 24538--24576 Score: 64
Period size: 11 Copynumber: 3.4 Consensus size: 12
24528 CCTTCTTTTC
24538 TTTTTCTGTATA
1 TTTTTCTGTATA
24550 TTTTT-TGTATA
1 TTTTTCTGTATA
24561 TTTTTCTGTAT-
1 TTTTTCTGTATA
24572 TTTTT
1 TTTTT
24577 TTGGTATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (12 bp):
TTTTTCTGTATA
Found at i:29745 original size:17 final size:19
Alignment explanation
Indices: 29723--29757 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
29713 CATTGTTGAA
29723 TTTATC-ACTT-ATTTTTG
1 TTTATCTACTTCATTTTTG
29740 TTTATCTACTTCATTTTT
1 TTTATCTACTTCATTTTT
29758 TATTGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.17, C:0.14, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTATCTACTTCATTTTTG
Found at i:32350 original size:32 final size:32
Alignment explanation
Indices: 32295--32361 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
32285 ATCACAACCA
**
32295 ATAAGCAAAATAAAAAATTTTAAATTCAAAAT
1 ATAAGCAAAATAAAAAAAATTAAATTCAAAAT
32327 ATAA-CAAAATAAAAAAAAATTAAATTCAAAAT
1 ATAAGCAAAAT-AAAAAAAATTAAATTCAAAAT
32359 ATA
1 ATA
32362 GCCATTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.25
Consensus pattern (32 bp):
ATAAGCAAAATAAAAAAAATTAAATTCAAAAT
Found at i:32537 original size:30 final size:29
Alignment explanation
Indices: 32470--32541 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
32460 ACACCGAACC
****
32470 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
32499 GCCAAATAAGCCCCTGAACTCTTAAAAAAA
1 GTCAAATAAGCCCCTGAACTATT-AAAAAA
32529 GTCAAATAAGCCC
1 GTCAAATAAGCCC
32542 TATTGCCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.22
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Done.