Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010461.1 Corchorus capsularis cultivar CVL-1 contig10482, 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: 67414
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2604 original size:20 final size:21
Alignment explanation
Indices: 2569--2609 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2559 AACACGGTAA
2569 TTAAACCGTGTCAATCGTGTC
1 TTAAACCGTGTCAATCGTGTC
*
2590 TTAAA-CGTGTTAATCGTGTC
1 TTAAACCGTGTCAATCGTGTC
2610 GTGACACGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (21 bp):
TTAAACCGTGTCAATCGTGTC
Found at i:2677 original size:42 final size:43
Alignment explanation
Indices: 2599--2679 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
2589 CTTAAACGTG
* *
2599 TTAATCGTGTCGTGACACGATTATGACCCAAAACACGATAATC
1 TTAATCGTGTCGCGACACGATTATGACACAAAACACGATAATC
* *
2642 TTAATCGTGTC-CGACACGATT-TCGACACGACACACGAT
1 TTAATCGTGTCGCGACACGATTAT-GACACAAAACACGAT
2680 TAACCAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 1 0.03
42 21 0.64
43 11 0.33
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (43 bp):
TTAATCGTGTCGCGACACGATTATGACACAAAACACGATAATC
Found at i:3475 original size:13 final size:14
Alignment explanation
Indices: 3431--3476 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
3421 TATGGGGAGA
3431 ATGCAAGAGTTATG
1 ATGCAAGAGTTATG
*
3445 ATGCAAGAGTTATC
1 ATGCAAGAGTTATG
**
3459 ATGCCGGA-TTATG
1 ATGCAAGAGTTATG
3472 ATGCA
1 ATGCA
3477 TGAACACCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 8 0.30
14 19 0.70
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (14 bp):
ATGCAAGAGTTATG
Found at i:8332 original size:30 final size:30
Alignment explanation
Indices: 8292--8356 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
8282 AGCCGGCACT
*
8292 TCAACCTCCACCTCACCTTCTTTAGCAGAC
1 TCAACATCCACCTCACCTTCTTTAGCAGAC
*
8322 TCAACATCCACCTCACCTTCTTTAGCATAC
1 TCAACATCCACCTCACCTTCTTTAGCAGAC
8352 TCAAC
1 TCAAC
8357 TTCAGCTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.26, C:0.42, G:0.05, T:0.28
Consensus pattern (30 bp):
TCAACATCCACCTCACCTTCTTTAGCAGAC
Found at i:9550 original size:9 final size:9
Alignment explanation
Indices: 9536--9571 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
9526 GATCGAGTTC
9536 GAAGAGAGA
1 GAAGAGAGA
*
9545 GAAGAGAAA
1 GAAGAGAGA
*
9554 TAAGAGAGA
1 GAAGAGAGA
9563 GAAGAGAGA
1 GAAGAGAGA
9572 AAAAATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.39, T:0.03
Consensus pattern (9 bp):
GAAGAGAGA
Found at i:13433 original size:22 final size:22
Alignment explanation
Indices: 13404--14007 Score: 233
Period size: 22 Copynumber: 28.0 Consensus size: 22
13394 ATAATCTCAT
13404 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* * *** *
13426 TATAAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * **
13448 TATGAAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** *
13470 TAT-AATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* *
13491 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
13513 TAAGGAATTTTGA-AGACC-TCAG
1 TATGAAATTTTGATA-ACCTTC-C
13535 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
*
13557 AATGAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
13578 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * * *
13601 TATGAAAATTTAAAAACC-TCGA
1 TATGAAATTTTGATAACCTTC-C
* * *
13623 TATG-AATTGTT-AGTAATCATAC
1 TATGAAATT-TTGA-TAACCTTCC
* * *
13645 TCTGAAATTTTGATAATC-ACGC
1 TATGAAATTTTGATAACCTTC-C
*
13667 TATGAAATTTTGATAACCTTGC
1 TATGAAATTTTGATAACCTTCC
*
13689 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
13712 TATAAAATTTTGATAAACC-CCTC
1 TATGAAATTTTGAT-AACCTTC-C
* * *
13735 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
13757 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
13774 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* ** *
13795 TAAGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
*
13817 TATGAAATTTTGTTAATCC--CC
1 TATGAAATTTTGATAA-CCTTCC
*** * *
13838 TATGAAATTTTGATCTGCATAC
1 TATGAAATTTTGATAACCTTCC
*
13860 TATGAAATTTTGATAACCCT-C
1 TATGAAATTTTGATAACCTTCC
* **
13881 TAATGAAATTTTGA-AAACTAAAC
1 T-ATGAAATTTTGATAACCT-TCC
*
13904 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
13925 -CTGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
13945 ATAATAAAAGTTTAATAACCTT-C
1 -T-ATGAAATTTTGATAACCTTCC
* * *
13968 -AT--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
13986 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
14008 CAGAAATACC
Statistics
Matches: 431, Mismatches: 109, Indels: 84
0.69 0.17 0.13
Matches are distributed among these distances:
16 11 0.03
17 11 0.03
18 3 0.01
19 2 0.00
20 22 0.05
21 49 0.11
22 265 0.61
23 67 0.16
24 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:13770 original size:45 final size:46
Alignment explanation
Indices: 13649--13772 Score: 132
Period size: 45 Copynumber: 2.8 Consensus size: 46
13639 TCATACTCTG
* * *
13649 AAATTTTGAT-AATC-ACGCTATGAAATTTTGAT-AACCTTGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATTTTGATAAACCCTGCTATA
*
13693 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCCCT-CTATA
1 AAATTTTGATAAATCTTCCTATGAAATTTTGATAAA-CCCTGCTATA
* * *
13739 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAATTTTGATAA
13773 CTACAAATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
44 10 0.15
45 35 0.51
46 20 0.29
47 3 0.04
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (46 bp):
AAATTTTGATAAATCTTCCTATGAAATTTTGATAAACCCTGCTATA
Found at i:13931 original size:20 final size:20
Alignment explanation
Indices: 13906--13944 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
13896 AACTAAACTA
13906 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
13926 TGAAATTTTGATATCCTCC
1 TGAAATTTTGATATCCTCC
13945 ATAATAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:14071 original size:21 final size:22
Alignment explanation
Indices: 14041--14094 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
14031 TGTAATCACA
14041 TTCTGAAAATTTGATAACCTTT
1 TTCTGAAAATTTGATAACCTTT
*
14063 TTCTG-AAATTTGATAACCTCT
1 TTCTGAAAATTTGATAACCTTT
*
14084 TTAT-AAAATTT
1 TTCTGAAAATTT
14095 TGTTGACCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.46
Consensus pattern (22 bp):
TTCTGAAAATTTGATAACCTTT
Found at i:14180 original size:87 final size:86
Alignment explanation
Indices: 14019--14183 Score: 192
Period size: 87 Copynumber: 1.9 Consensus size: 86
14009 AGAAATACCA
* ** * **
14019 CTATGAAATTTTTGTAATCACATTCTGAAAATTTGATAACCTTTTTCTGAAATTTGATAACCTCT
1 CTATGAAATTCTAATAATCACATTATGAAAATTTGATAACCTGCTTCTGAAATTTGATAA-CTCT
14084 TTATAAAATTTTGTTGACCCCT
65 TTATAAAATTTTGTTGACCCCT
* *
14106 CTATGAAATTCTAATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAA-TC
1 CTATGAAATTCTAATAATCACATTATGAAAATTTGATAACCT-GCTTCTGAAA-TTTGATAACTC
14169 TTCCTAT-AAATTTTG
64 TT--TATAAAATTTTG
14184 GTAATCTGAT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
86 4 0.06
87 49 0.74
88 13 0.20
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (86 bp):
CTATGAAATTCTAATAATCACATTATGAAAATTTGATAACCTGCTTCTGAAATTTGATAACTCTT
TATAAAATTTTGTTGACCCCT
Found at i:14213 original size:25 final size:22
Alignment explanation
Indices: 14129--14214 Score: 68
Period size: 22 Copynumber: 3.8 Consensus size: 22
14119 ATAATCACAT
* *
14129 TATGTAATTTTGATAA-CCTCGC
1 TATGAAATTTTGATAATCTTC-C
*
14151 TTTGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAATCTTCC
*
14173 TAT-AAATTTTGGTAATCTGATCTC
1 TATGAAATTTTGATAATCT--TC-C
* *
14197 TGTGAAATTTCGATAATC
1 TATGAAATTTTGATAATC
14215 ACTCAATAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 14 0.27
22 17 0.33
23 5 0.10
24 3 0.06
25 12 0.24
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAATCTTCC
Found at i:14316 original size:22 final size:22
Alignment explanation
Indices: 14267--14390 Score: 87
Period size: 22 Copynumber: 5.6 Consensus size: 22
14257 CTTATGAAAT
14267 TGAAACTTTT-ATAACCTTCA-TA
1 TGAAA-TTTTGATAACC-TCACTA
* * *
14289 TAAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCTCACTA
*
14311 TGAAATATT-AGTAACCTCA-TAA
1 TGAAATTTTGA-TAACCTCACT-A
* * *
14333 TGAAATTTTGTTAACCACATTA
1 TGAAATTTTGATAACCTCACTA
*
14355 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCACTA
*
14377 TGACATTTTGATAA
1 TGAAATTTTGATAA
14391 TCTCTTTGAT
Statistics
Matches: 79, Mismatches: 15, Indels: 16
0.72 0.14 0.15
Matches are distributed among these distances:
21 9 0.11
22 67 0.85
23 3 0.04
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCACTA
Found at i:14508 original size:22 final size:21
Alignment explanation
Indices: 14428--14588 Score: 124
Period size: 22 Copynumber: 7.2 Consensus size: 21
14418 GTGAAAATTG
* **
14428 ACCACCCTATTAAATTTCAATA
1 ACCA-CCTATGAAATTTTGATA
* *
14450 ACCAACCTAAGAAATTTTAATA
1 ACC-ACCTATGAAATTTTGATA
* *
14472 ACTTGATCCTATGAAATTTTGGTA
1 AC--CA-CCTATGAAATTTTGATA
*
14496 ACCACACTATGAAATTTTGGTA
1 ACCAC-CTATGAAATTTTGATA
*
14518 ACCACGCTATGGAATTTTGATA
1 ACCAC-CTATGAAATTTTGATA
* * *
14540 ACCTCCTCATGAAATTATAATA
1 ACCACCT-ATGAAATTTTGATA
*
14562 ACCATCTTATGAAATTTTGATA
1 ACCA-CCTATGAAATTTTGATA
14584 ACCAC
1 ACCAC
14589 ATAGAGACAA
Statistics
Matches: 113, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.04
22 89 0.79
23 4 0.04
24 16 0.14
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (21 bp):
ACCACCTATGAAATTTTGATA
Found at i:14784 original size:19 final size:20
Alignment explanation
Indices: 14753--14790 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
14743 TATTGACATT
14753 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
14772 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
14791 ATTAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:24857 original size:17 final size:17
Alignment explanation
Indices: 24835--24870 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
24825 TCTTATGGCC
24835 CAAACTAACTTTTGGAT
1 CAAACTAACTTTTGGAT
24852 CAAACTAACTTTTGGAT
1 CAAACTAACTTTTGGAT
24869 CA
1 CA
24871 CTTTTTGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (17 bp):
CAAACTAACTTTTGGAT
Found at i:46210 original size:30 final size:31
Alignment explanation
Indices: 46156--46220 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
46146 AATTTTATGT
* *
46156 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATCGTACCCTTATTTTTAAAACATA
46187 TTTCCAATCGTACCCTT-TTTTTAAAACATA
1 TTTCCAATCGTACCCTTATTTTTAAAACATA
46217 TTTC
1 TTTC
46221 TAAATTGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.46
Consensus pattern (31 bp):
TTTCCAATCGTACCCTTATTTTTAAAACATA
Found at i:47273 original size:38 final size:38
Alignment explanation
Indices: 47176--47273 Score: 124
Period size: 39 Copynumber: 2.6 Consensus size: 38
47166 AATTTGGCTT
47176 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTTGTC
1 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTTGTC
* * ** **
47214 TTTGTTTCAAATCCTTGTATTTAATTTTGTTTTTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCCTTTTTGTC
*
47253 TTTGTCTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
47274 GGGCTTAGTT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
38 17 0.35
39 31 0.65
ACGTcount: A:0.14, C:0.18, G:0.10, T:0.57
Consensus pattern (38 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTTGTC
Found at i:48099 original size:53 final size:52
Alignment explanation
Indices: 48017--48120 Score: 147
Period size: 53 Copynumber: 2.0 Consensus size: 52
48007 GGTGATCTTT
* *
48017 GATCACCTGTGGTGATCTTGGGTGGTGATCTCAGATCA-CCCTATTTGGTTAG
1 GATCACCTGTGGTAATATTGGGTGGTGATCTCAGATCATCCC-ATTTGGTTAG
* *
48069 GATCACCTGTTGGTAATATTGGGTGTTGATCTCAGATCATCCCGTTTGGTTA
1 GATCACCTG-TGGTAATATTGGGTGGTGATCTCAGATCATCCCATTTGGTTA
48121 CACATTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
52 9 0.20
53 34 0.74
54 3 0.07
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (52 bp):
GATCACCTGTGGTAATATTGGGTGGTGATCTCAGATCATCCCATTTGGTTAG
Found at i:48232 original size:17 final size:17
Alignment explanation
Indices: 48202--48259 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
48192 CTGAAACCAG
* *
48202 GTGATCTAAGATCACTA
1 GTGATCTTACATCACTA
* *
48219 GTGATCTTGA-ATCAGTG
1 GTGATCTT-ACATCACTA
*
48236 GTGATCTTACATCACCA
1 GTGATCTTACATCACTA
48253 GTGATCT
1 GTGATCT
48260 CGGGGGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (17 bp):
GTGATCTTACATCACTA
Found at i:48481 original size:13 final size:13
Alignment explanation
Indices: 48463--48501 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
48453 TTAAATTGAC
48463 ATTATTAAAATTT
1 ATTATTAAAATTT
*
48476 ATTATTTAAAATTA
1 ATTA-TTAAAATTT
48490 ATTA-TAAAATTT
1 ATTATTAAAATTT
48502 CAATTTAGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTATTAAAATTT
Found at i:48895 original size:20 final size:20
Alignment explanation
Indices: 48870--48920 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
48860 TTATGGAGTA
*
48870 ATCAAAATTTTAGGGAGGAT
1 ATCAAAATTTCAGGGAGGAT
*
48890 ATCAAAA-TTCAGTGAGGAT
1 ATCAAAATTTCAGGGAGGAT
*
48909 TTCAAAATTTCA
1 ATCAAAATTTCA
48921 TAGTTTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (20 bp):
ATCAAAATTTCAGGGAGGAT
Found at i:48957 original size:22 final size:22
Alignment explanation
Indices: 48932--48988 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
48922 AGTTTAATTT
*
48932 TCAAAATTTCATAATAGGGT-TA
1 TCAAAATTTCATAATA-GGTAGA
* *
48954 TCAAAATTTCATAGTATGTAGA
1 TCAAAATTTCATAATAGGTAGA
48976 TCAAAATTTCATA
1 TCAAAATTTCATA
48989 GGGAATCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 2 0.06
22 29 0.94
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (22 bp):
TCAAAATTTCATAATAGGTAGA
Found at i:49071 original size:23 final size:23
Alignment explanation
Indices: 49043--49145 Score: 111
Period size: 23 Copynumber: 4.5 Consensus size: 23
49033 CATAAGAAAG
49043 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
* *
49066 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGGAGGT
*
49089 TTATCAAAATTTTCATAGCGAGG-
1 TTATCAAAATTTT-ATAGGGAGGT
* * * * *
49112 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGGGAGGT
49134 TTATCAAAATTT
1 TTATCAAAATTT
49146 CAAAGCATGA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.01
22 16 0.24
23 45 0.66
24 6 0.09
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:49095 original size:46 final size:45
Alignment explanation
Indices: 49021--49145 Score: 139
Period size: 46 Copynumber: 2.8 Consensus size: 45
49011 AAATTTGTAA
* * *
49021 TTATCAAGATTTCATAAGAA-AGTTATCAAAATTTT-ATAGGGAGG
1 TTATCAAAATTTCATAGGAAGA-TTATCAAAATTTTCATAGCGAGG
*
49065 TTTATCAAAATTTTATAGGAAGATTTATCAAAATTTTCATAGCGAGG
1 -TTATCAAAATTTCATAGGAAGA-TTATCAAAATTTTCATAGCGAGG
* *
49112 TTATCACAATTTCATAGTG-TGATTATCAAAATTT
1 TTATCAAAATTTCATAG-GAAGATTATCAAAATTT
49146 CAAAGCATGA
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
45 29 0.42
46 31 0.45
47 9 0.13
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (45 bp):
TTATCAAAATTTCATAGGAAGATTATCAAAATTTTCATAGCGAGG
Found at i:49127 original size:22 final size:21
Alignment explanation
Indices: 48994--49147 Score: 102
Period size: 22 Copynumber: 7.1 Consensus size: 21
48984 TCATAGGGAA
48994 TCATACGGAGGTTATCAAAATT
1 TCATA-GGAGGTTATCAAAATT
* *
49016 T-GTA--A--TTATCAAGATT
1 TCATAGGAGGTTATCAAAATT
* *
49032 TCATAAGAAAGTTATCAAAATT
1 TCAT-AGGAGGTTATCAAAATT
*
49054 TTATAGGGAGGTTTATCAAAATT
1 TCATA-GGAGG-TTATCAAAATT
* *
49077 TTATAGGAAGATTTATCAAAATTT
1 TCATAGG-AG-GTTATCAAAA-TT
*
49101 TCATAGCGAGGTTATCACAATT
1 TCATAG-GAGGTTATCAAAATT
* *
49123 TCATAGTGTGATTATCAAAATT
1 TCATAG-GAGGTTATCAAAATT
49145 TCA
1 TCA
49148 AAGCATGATT
Statistics
Matches: 105, Mismatches: 15, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
16 11 0.10
17 1 0.01
18 2 0.02
20 1 0.01
21 3 0.03
22 42 0.40
23 35 0.33
24 9 0.09
25 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (21 bp):
TCATAGGAGGTTATCAAAATT
Found at i:52405 original size:23 final size:24
Alignment explanation
Indices: 52374--52419 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
52364 ACATTTTATT
* *
52374 CCCATCAAAGACTTTCC-TAACAG
1 CCCAACAAAGACTATCCTTAACAG
52397 CCCAACAAAGACTATCCTTAACA
1 CCCAACAAAGACTATCCTTAACA
52420 TCCTCCCAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.39, C:0.35, G:0.07, T:0.20
Consensus pattern (24 bp):
CCCAACAAAGACTATCCTTAACAG
Found at i:57606 original size:135 final size:135
Alignment explanation
Indices: 57364--57638 Score: 550
Period size: 135 Copynumber: 2.0 Consensus size: 135
57354 CCCCCATGAC
57364 ATTTCTTATTTGGAAATCTCTATTGAAGCACAAGCCGTTTTGCATTTGCTTAAGAGTGCCAATGT
1 ATTTCTTATTTGGAAATCTCTATTGAAGCACAAGCCGTTTTGCATTTGCTTAAGAGTGCCAATGT
57429 TGAACTTCACCCACTTGGGAACTTGCTTATTGACTGCAAGAACATGATGGACAACCTAAGTAATG
66 TGAACTTCACCCACTTGGGAACTTGCTTATTGACTGCAAGAACATGATGGACAACCTAAGTAATG
57494 TGAAG
131 TGAAG
57499 ATTTCTTATTTGGAAATCTCTATTGAAGCACAAGCCGTTTTGCATTTGCTTAAGAGTGCCAATGT
1 ATTTCTTATTTGGAAATCTCTATTGAAGCACAAGCCGTTTTGCATTTGCTTAAGAGTGCCAATGT
57564 TGAACTTCACCCACTTGGGAACTTGCTTATTGACTGCAAGAACATGATGGACAACCTAAGTAATG
66 TGAACTTCACCCACTTGGGAACTTGCTTATTGACTGCAAGAACATGATGGACAACCTAAGTAATG
57629 TGAAG
131 TGAAG
57634 ATTTC
1 ATTTC
57639 CCACTGCTAT
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
135 140 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (135 bp):
ATTTCTTATTTGGAAATCTCTATTGAAGCACAAGCCGTTTTGCATTTGCTTAAGAGTGCCAATGT
TGAACTTCACCCACTTGGGAACTTGCTTATTGACTGCAAGAACATGATGGACAACCTAAGTAATG
TGAAG
Found at i:66683 original size:4 final size:4
Alignment explanation
Indices: 66676--66703 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
66666 TGTGTGTGTT
66676 TTTG TTTG TTTG TTTG TTTG TTTG TTTG
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG
66704 CCTTTAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.25, T:0.75
Consensus pattern (4 bp):
TTTG
Done.