Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016172.1 Corchorus capsularis cultivar CVL-1 contig16193, 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: 68111
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1761 original size:18 final size:18
Alignment explanation
Indices: 1740--1790 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
1730 ATTAATTATT
*
1740 GTTAAATAGTTTATTAGG
1 GTTAATTAGTTTATTAGG
* *
1758 GTTAATTATTTTATTAGT
1 GTTAATTAGTTTATTAGG
*
1776 TTTAATTAGTTTATT
1 GTTAATTAGTTTATT
1791 TACGATTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (18 bp):
GTTAATTAGTTTATTAGG
Found at i:1969 original size:16 final size:16
Alignment explanation
Indices: 1926--1970 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
1916 GAGGCTGAGT
*
1926 TTCAGAGGGAGAGAGC
1 TTCAGAGAGAGAGAGC
*
1942 TTTAGAGGGAGAGAGAGC
1 TTCAGA--GAGAGAGAGC
1960 TTCAGAGAGAG
1 TTCAGAGAGAG
1971 GCTCAGATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 10 0.42
18 14 0.58
ACGTcount: A:0.33, C:0.09, G:0.42, T:0.16
Consensus pattern (16 bp):
TTCAGAGAGAGAGAGC
Found at i:9515 original size:2 final size:2
Alignment explanation
Indices: 9508--9532 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9498 TTTGAACCAG
9508 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9533 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9538 original size:3 final size:3
Alignment explanation
Indices: 9530--9565 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
9520 ATATATATAT
9530 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
9566 TCTTTTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11420 original size:2 final size:2
Alignment explanation
Indices: 11413--11447 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11403 GTTCGTTCAC
11413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11448 ACAAAAATGA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15657 original size:16 final size:15
Alignment explanation
Indices: 15636--15666 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
15626 ACTACCCTTC
15636 TTTCTTTCTTTTTTTT
1 TTTCTTT-TTTTTTTT
15652 TTTCTTTTTTTTTTT
1 TTTCTTTTTTTTTTT
15667 GTGAAAATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTCTTTTTTTTTTT
Found at i:15661 original size:11 final size:12
Alignment explanation
Indices: 15640--15666 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
15630 CCCTTCTTTC
15640 TTTCTTTTTTTT
1 TTTCTTTTTTTT
15652 TTTCTTTTTTTT
1 TTTCTTTTTTTT
15664 TTT
1 TTT
15667 GTGAAAATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:16052 original size:29 final size:30
Alignment explanation
Indices: 15988--16052 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
15978 CTAACATGGC
*
15988 TTCAAAATTGCGAATTCAGAAGACAAAACG
1 TTCAAAATTGCAAATTCAGAAGACAAAACG
* * *
16018 TCCAAAATTG-AAATTCATGGA-ACAAAATG
1 TTCAAAATTGCAAATTCA-GAAGACAAAACG
16047 TTCAAA
1 TTCAAA
16053 TCGTACAAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (30 bp):
TTCAAAATTGCAAATTCAGAAGACAAAACG
Found at i:17058 original size:21 final size:21
Alignment explanation
Indices: 17032--17110 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
17022 TGACTTTCAT
17032 ATTTGGGGTTTGATCATTAAG
1 ATTTGGGGTTTGATCATTAAG
* *
17053 ATTTGGGGTTTCA-CAATGGATA-
1 ATTTGGGGTTTGATC-AT-TA-AG
* *
17075 ATTTGGGGTTTGACCATTATG
1 ATTTGGGGTTTGATCATTAAG
17096 ATTTGGGGTTTGATC
1 ATTTGGGGTTTGATC
17111 TAATTACTAG
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 1 0.02
21 29 0.62
22 15 0.32
23 2 0.04
ACGTcount: A:0.22, C:0.08, G:0.29, T:0.42
Consensus pattern (21 bp):
ATTTGGGGTTTGATCATTAAG
Found at i:17158 original size:22 final size:22
Alignment explanation
Indices: 17133--17175 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17123 GGGATTTAAT
*
17133 CATGCTTTACGGTTTCACCATA
1 CATGATTTACGGTTTCACCATA
* *
17155 CATGATTTAGGGTTTGACCAT
1 CATGATTTACGGTTTCACCAT
17176 TACGCTTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (22 bp):
CATGATTTACGGTTTCACCATA
Found at i:17355 original size:29 final size:28
Alignment explanation
Indices: 17296--17355 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
17286 AAATTTGTAT
* ** *
17296 AAAAAAAAAATTTGGGATATAATGTTTC
1 AAAAAAAAAATTTAGGATATAACCTTAC
*
17324 AAAAAAAATTATTTAGGATATAACCTTAC
1 AAAAAAAA-AATTTAGGATATAACCTTAC
17353 AAA
1 AAA
17356 TAAGGAGCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (28 bp):
AAAAAAAAAATTTAGGATATAACCTTAC
Found at i:18590 original size:29 final size:29
Alignment explanation
Indices: 18530--18590 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
18520 TTTAATTATG
* * * *
18530 TTTTATTCTTTTATTATTTTTTTTTCAGA
1 TTTTATTCTTTTATTATATATTTATCAAA
18559 TTTTATTC-TTTAGTTATATATTTATCAAA
1 TTTTATTCTTTTA-TTATATATTTATCAAA
18588 TTT
1 TTT
18591 ATTAATACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTATTCTTTTATTATATATTTATCAAA
Found at i:19030 original size:22 final size:21
Alignment explanation
Indices: 19000--19048 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
18990 ATCCTTTACA
* *
19000 GTTTCACCATACATGATTTGGG
1 GTTTGACCAT-CATGATTTAGG
* *
19022 GTTTGACCATTATGTTTTAGG
1 GTTTGACCATCATGATTTAGG
19043 GTTTGA
1 GTTTGA
19049 TCCCATTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.43
Consensus pattern (21 bp):
GTTTGACCATCATGATTTAGG
Found at i:19116 original size:87 final size:86
Alignment explanation
Indices: 18962--19210 Score: 336
Period size: 87 Copynumber: 2.8 Consensus size: 86
18952 ATTATTTAGC
* *
18962 CCCATTACTAGTAGGGATTTGCCTAATCATCCTTTACAGTTTCACCATACATGATTTGGGGTTTG
1 CCCATTACTAGTAGGG-TTTGCCTAATCATGCTTTA-AATTTCACCATACATGATTTGGGGTTTG
* * *
19027 ACCATTATGTTTTAGGGTTTGAT
64 ACCATTACGATTTAGGGGTTGAT
* *
19050 CCCATTACTAGTAGGAGTTTGCCTACTCATGCTTTAAATTTCACTATACATGATTTGGGGTTTGA
1 CCCATTACTAGTAGG-GTTTGCCTAATCATGCTTTAAATTTCACCATACATGATTTGGGGTTTGA
*
19115 CCATTACGATTTGGGGGTTGAT
65 CCATTACGATTTAGGGGTTGAT
* * * *
19137 CCCATTATTAGTAAGGGTTTACCTAATCATGCTTTAAAATTCACCATGCATGATTTGGGGTTTGA
1 CCCATTACTAGT-AGGGTTTGCCTAATCATGCTTTAAATTTCACCATACATGATTTGGGGTTTGA
19202 TCCAATTAC
65 -CC-ATTAC
19211 TAGTAGGGGT
Statistics
Matches: 143, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
87 100 0.70
88 37 0.26
89 6 0.04
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.38
Consensus pattern (86 bp):
CCCATTACTAGTAGGGTTTGCCTAATCATGCTTTAAATTTCACCATACATGATTTGGGGTTTGAC
CATTACGATTTAGGGGTTGAT
Found at i:19260 original size:65 final size:66
Alignment explanation
Indices: 19122--19266 Score: 184
Period size: 66 Copynumber: 2.2 Consensus size: 66
19112 TGACCATTAC
* * * *
19122 GATTTGGGGGTTGATCCCATTATTAGTAAGGGTTTACCTAATCATGCTTTAAAATTCACCATGCA
1 GATTTGGGGTTTGATCCAATTACTAGTAAGGGTTTACCTAATCATGCTTTAAAATTCACCATACA
19187 T
66 T
* ** * ** *
19188 GATTTGGGGTTTGATCCAATTACTAGTAGGGGTTTGTCTAATTATGCTTT-AAATTCATTATACG
1 GATTTGGGGTTTGATCCAATTACTAGTAAGGGTTTACCTAATCATGCTTTAAAATTCACCATACA
19252 T
66 T
19253 GATTTGGGGTTTGA
1 GATTTGGGGTTTGA
19267 ACATTATGAT
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
65 25 0.37
66 43 0.63
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (66 bp):
GATTTGGGGTTTGATCCAATTACTAGTAAGGGTTTACCTAATCATGCTTTAAAATTCACCATACA
T
Found at i:19303 original size:152 final size:153
Alignment explanation
Indices: 19041--19331 Score: 440
Period size: 152 Copynumber: 1.9 Consensus size: 153
19031 TTATGTTTTA
* *
19041 GGGTTTGATCCCATTACTAGTAGGAGTTTGCCTACTCATGCTTTAAATTTCACTATACATGATTT
1 GGGTTTGATCCAATTACTAGTAGGAGTTTGCCTAATCATGCTTTAAATTTCACTATACATGATTT
* *
19106 GGGGTTTGACCATTACGATTTGGGGGTTGATCCCATTATTAGTAAGGGTTTACCTAATCATGCTT
66 GGGGTTTGAACATTACGATTTGGGGGTTGATCCCATTACTAGTAAGGGTTTACCTAATCATGCTT
19171 TAAAATTCACCATGCATGATTTG
131 TAAAATTCACCATGCATGATTTG
* * * * *
19194 GGGTTTGATCCAATTACTAGTAGGGGTTTGTCTAATTATGCTTTAAA-TTCATTATACGTGATTT
1 GGGTTTGATCCAATTACTAGTAGGAGTTTGCCTAATCATGCTTTAAATTTCACTATACATGATTT
* * ** *
19258 GGGGTTTGAACATTATGATTTGTGTTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTT
66 GGGGTTTGAACATTACGATTTGGGGGTTGATCCCATTACTAGTAAGGGTTTACCTAATCATGCTT
*
19323 TAAATTTCA
131 TAAAATTCA
19332 TGATTTGGGA
Statistics
Matches: 123, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
152 81 0.66
153 42 0.34
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (153 bp):
GGGTTTGATCCAATTACTAGTAGGAGTTTGCCTAATCATGCTTTAAATTTCACTATACATGATTT
GGGGTTTGAACATTACGATTTGGGGGTTGATCCCATTACTAGTAAGGGTTTACCTAATCATGCTT
TAAAATTCACCATGCATGATTTG
Found at i:19376 original size:80 final size:83
Alignment explanation
Indices: 19188--19404 Score: 251
Period size: 80 Copynumber: 2.6 Consensus size: 83
19178 CACCATGCAT
* * * * *
19188 GATTTGGGGTTTGATCCAATTACTAGTAGGGGTTTGTCTAATTATGCTTTAAATTCATTATACGT
1 GATTTGAGATTTGATCCCATTACTAGTAGGGGTTTGCCTAATTATGCTTT-AA-T-ATTATACAT
* *
19253 GATTTGGGGTTTGAACATTAT
63 GATTTGGGATTTGAACATTAC
* * * *
19274 GATTTGTGTTTTGATCCCATTACTAGTAAGGGTTTGCCTAATCATGCTTTAA-ATT-T-CATGAT
1 GATTTGAGATTTGATCCCATTACTAGTAGGGGTTTGCCTAATTATGCTTTAATATTATACATGAT
**
19336 TTGGGATTTGATTATTAC
66 TTGGGATTTGAACATTAC
**
19354 GATTTGAGATTTGATCCCATTACTAGTAGGGGTTTGCGAAATTATGCTTTA
1 GATTTGAGATTTGATCCCATTACTAGTAGGGGTTTGCCTAATTATGCTTTA
19405 CAGTTTGACC
Statistics
Matches: 114, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
80 64 0.56
81 1 0.01
82 3 0.03
85 2 0.02
86 44 0.39
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (83 bp):
GATTTGAGATTTGATCCCATTACTAGTAGGGGTTTGCCTAATTATGCTTTAATATTATACATGAT
TTGGGATTTGAACATTAC
Found at i:19453 original size:21 final size:21
Alignment explanation
Indices: 19407--19474 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
19397 ATGCTTTACA
* **
19407 GTTTGACCATATAAGATTTGTA
1 GTTTGACCAT-TAAAATTTGGG
19429 GTTTGACCATTAAAATTTGGG
1 GTTTGACCATTAAAATTTGGG
* *
19450 GTTTGACCAATAATATTTGGG
1 GTTTGACCATTAAAATTTGGG
19471 GTTT
1 GTTT
19475 AACTTTCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 31 0.76
22 10 0.24
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (21 bp):
GTTTGACCATTAAAATTTGGG
Found at i:20308 original size:8 final size:9
Alignment explanation
Indices: 20295--20327 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
20285 TCTACACTAT
20295 TATTAT-TA
1 TATTATATA
20303 TATTATATA
1 TATTATATA
20312 TATATATATA
1 TAT-TATATA
20322 TATTAT
1 TATTAT
20328 TAAACTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 8 0.35
10 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTATATA
Found at i:21259 original size:9 final size:9
Alignment explanation
Indices: 21244--21277 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
21234 TAATTTTGGC
21244 AATATATTA
1 AATATATTA
*
21253 TATATATTA
1 AATATATTA
*
21262 AATCTATTA
1 AATATATTA
21271 AATATAT
1 AATATAT
21278 AATTTAACGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (9 bp):
AATATATTA
Found at i:22798 original size:16 final size:15
Alignment explanation
Indices: 22772--22813 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 15
22762 TTATAACTAC
22772 CAAACATAATAAATATA
1 CAAACA-AATAAAT-TA
22789 CAAACAAATAAATTA
1 CAAACAAATAAATTA
22804 CAAACTAAAT
1 CAAAC-AAAT
22814 TCACATTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (15 bp):
CAAACAAATAAATTA
Found at i:23698 original size:20 final size:19
Alignment explanation
Indices: 23673--23712 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
23663 AGTCCCACAA
*
23673 ATCTAAACCCACAAATTTTT
1 ATCTAAA-CCACAAATCTTT
*
23693 ATCTAAATCACAAATCTTT
1 ATCTAAACCACAAATCTTT
23712 A
1 A
23713 GATTTGTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (19 bp):
ATCTAAACCACAAATCTTT
Found at i:34987 original size:33 final size:33
Alignment explanation
Indices: 34917--34988 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
34907 GCAGCCACTG
*
34917 CCACCGCAACCACCAACACCACAGCCGCGGCCG
1 CCACCGCAACCACCAACACCACAGCCGCGGCCA
* *
34950 CCACCGCAACCACCACCACCACAGTCGTC-GCCA
1 CCACCGCAACCACCAACACCACAGCCG-CGGCCA
34983 CCACCG
1 CCACCG
34989 TCACAGACTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.26, C:0.56, G:0.15, T:0.03
Consensus pattern (33 bp):
CCACCGCAACCACCAACACCACAGCCGCGGCCA
Found at i:43908 original size:25 final size:25
Alignment explanation
Indices: 43880--43927 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
43870 AATCCAAATC
*
43880 TTGGCAACTTTGGTCTACTTGAATA
1 TTGGCAAATTTGGTCTACTTGAATA
*
43905 TTGGCAAATTTGGTCTGCTTGAA
1 TTGGCAAATTTGGTCTACTTGAA
43928 GTTATTGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (25 bp):
TTGGCAAATTTGGTCTACTTGAATA
Found at i:44043 original size:1 final size:1
Alignment explanation
Indices: 44037--44063 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
44027 TTCAAAATTT
44037 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
44064 CATCTCTACA
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:44980 original size:19 final size:20
Alignment explanation
Indices: 44938--44990 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
44928 TACCTTGTTT
*
44938 TATTTATTTTATTATCTCGC
1 TATTTATTTGATTATCTCGC
*
44958 TATTTATTTGATTTTCT-GC
1 TATTTATTTGATTATCTCGC
*
44977 TATTT-TTTCATTAT
1 TATTTATTTGATTAT
44991 TAATTTTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 7 0.24
19 7 0.24
20 15 0.52
ACGTcount: A:0.19, C:0.11, G:0.06, T:0.64
Consensus pattern (20 bp):
TATTTATTTGATTATCTCGC
Found at i:56017 original size:114 final size:114
Alignment explanation
Indices: 55817--56045 Score: 413
Period size: 114 Copynumber: 2.0 Consensus size: 114
55807 GAATTCTAGG
* *
55817 GGGCGTTTGGTTGGGGGTGATCTTTGATCACCTGTGGTGATCTTGGCAGGTGATCTCAGATCGCC
1 GGGCGTTTGGTTGGGGGTGATCTTTGATCACCTGTGGTGATCTTGGCAGCTGATCTCAGATCACC
* *
55882 CCATTTGGTTACACTTTTTGGTTTGGTGTGGTAATCCGGATTACCCCCT
66 CCATTTGGTTAAACTTTTTGGTTTGGTGTGGTAATCCGAATTACCCCCT
55931 GGGCGTTTGGTTGGGGGTGATCTTTGATCACCTGTGGTGATCTTGGCAGCTGATCTCAGATCACC
1 GGGCGTTTGGTTGGGGGTGATCTTTGATCACCTGTGGTGATCTTGGCAGCTGATCTCAGATCACC
*
55996 CCGTTTGGTTAAACTTTTTGGTTTGGTGTGGTAATCCGAATTACCCCCT
66 CCATTTGGTTAAACTTTTTGGTTTGGTGTGGTAATCCGAATTACCCCCT
56045 G
1 G
56046 ATTACCCCTC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 110 1.00
ACGTcount: A:0.14, C:0.20, G:0.30, T:0.36
Consensus pattern (114 bp):
GGGCGTTTGGTTGGGGGTGATCTTTGATCACCTGTGGTGATCTTGGCAGCTGATCTCAGATCACC
CCATTTGGTTAAACTTTTTGGTTTGGTGTGGTAATCCGAATTACCCCCT
Found at i:56137 original size:17 final size:17
Alignment explanation
Indices: 56106--56147 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
56096 TTTGATTACC
*
56106 GGTGATCTTGCATCATT
1 GGTGATCTTGCATCACT
56123 GGTGATCTTAG-ATCACT
1 GGTGATCTT-GCATCACT
*
56140 AGTGATCT
1 GGTGATCT
56148 GGGGGGCGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (17 bp):
GGTGATCTTGCATCACT
Found at i:56260 original size:112 final size:111
Alignment explanation
Indices: 56061--56279 Score: 357
Period size: 112 Copynumber: 2.0 Consensus size: 111
56051 CCCTCTAAAG
* * * *
56061 GGTGATCTGGATTACCACCATAAACCCATGTAATCTTTGATTACCGGTGATCTTGCATCATTGGT
1 GGTGATCTGGATTACCACAATAAACCCATGTAATCTTTGATCACCGGTGATCATGCATCAGTGGT
* *
56126 GATCTTAGATCACTAGTGATCTGGGGGGCGATCCTAACCAAACATCC
66 GATCTTAGATCACTAGTAATCT-GGGAGCGATCCTAACCAAACATCC
*
56173 GGTGATCTGGATTACCACAATAAATCCATGTAATCTTTGATCACCGGTGATCATGCATCAGTGGT
1 GGTGATCTGGATTACCACAATAAACCCATGTAATCTTTGATCACCGGTGATCATGCATCAGTGGT
*
56238 GATCTTAGATCACTAGTAATCTGGGAGTGATCCTAACCAAAC
66 GATCTTAGATCACTAGTAATCTGGGAGCGATCCTAACCAAAC
56280 GCCCCCTCTA
Statistics
Matches: 99, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
111 18 0.18
112 81 0.82
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (111 bp):
GGTGATCTGGATTACCACAATAAACCCATGTAATCTTTGATCACCGGTGATCATGCATCAGTGGT
GATCTTAGATCACTAGTAATCTGGGAGCGATCCTAACCAAACATCC
Found at i:56372 original size:13 final size:13
Alignment explanation
Indices: 56356--56384 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
56346 TAATTCAATG
56356 TTATAAATATTAT
1 TTATAAATATTAT
56369 TTATAAATATTAT
1 TTATAAATATTAT
56382 TTA
1 TTA
56385 GATTTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATAAATATTAT
Found at i:67603 original size:1 final size:1
Alignment explanation
Indices: 67597--67621 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
67587 ACTTTTCATT
67597 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
67622 GGAGTACCCA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.