Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007562.1 Corchorus capsularis cultivar CVL-1 contig07583, 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: 18591
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:1911 original size:110 final size:112
Alignment explanation
Indices: 1700--1923 Score: 425
Period size: 113 Copynumber: 2.0 Consensus size: 112
1690 CCTCTAATTA
1700 ATTATTCGGCTTATAAATTTATGATACTTTTATCTTAGCATTGAAAATTGAATAGCATAATAATG
1 ATTATTCGGCTTATAAATTTATGATACTTTTATCTTAGCATTGAAAATTGAATAGCATAATAAT-
1765 AAGGAGGGATGAACGACTTTTTCATTTTAGGTAAACACATCTGACTTT
65 AAGGAGGGATGAACGACTTTTTCATTTTAGGTAAACACATCTGACTTT
1813 ATTATTCGGCTTATAAATTTATGATACTTTTATCTTAGCATTGAAAATTGAATAGCATAATAAT-
1 ATTATTCGGCTTATAAATTTATGATACTTTTATCTTAGCATTGAAAATTGAATAGCATAATAATA
1877 A-GAGGGATGAACGACTTTTTCATTTTAGGTAAACACATCTGACTTT
66 AGGAGGGATGAACGACTTTTTCATTTTAGGTAAACACATCTGACTTT
1923 A
1 A
1924 ACCTAATTTA
Statistics
Matches: 111, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
110 46 0.41
111 1 0.01
113 64 0.58
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (112 bp):
ATTATTCGGCTTATAAATTTATGATACTTTTATCTTAGCATTGAAAATTGAATAGCATAATAATA
AGGAGGGATGAACGACTTTTTCATTTTAGGTAAACACATCTGACTTT
Found at i:2365 original size:18 final size:18
Alignment explanation
Indices: 2342--2377 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2332 GGCAATTTCC
*
2342 TTTTTACATAAGAAAAGA
1 TTTTTACACAAGAAAAGA
*
2360 TTTTTACACAAGAGAAGA
1 TTTTTACACAAGAAAAGA
2378 AAGAAGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (18 bp):
TTTTTACACAAGAAAAGA
Found at i:4314 original size:14 final size:14
Alignment explanation
Indices: 4295--4322 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4285 TGAATCATTC
4295 ACAAATCTAAAACA
1 ACAAATCTAAAACA
4309 ACAAATCTAAAACA
1 ACAAATCTAAAACA
4323 GATACACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.14
Consensus pattern (14 bp):
ACAAATCTAAAACA
Found at i:4319 original size:49 final size:49
Alignment explanation
Indices: 4128--4308 Score: 353
Period size: 49 Copynumber: 3.7 Consensus size: 49
4118 TTTCATAACT
4128 TGGGAGGTTTTGAATCATTCACAAATCTAAAACAGATATACTAAAGAGG
1 TGGGAGGTTTTGAATCATTCACAAATCTAAAACAGATATACTAAAGAGG
4177 TGGGAGGTTTTGAATCATTCACAAATCTAAAACAGATATACTAAAGAGG
1 TGGGAGGTTTTGAATCATTCACAAATCTAAAACAGATATACTAAAGAGG
*
4226 TGGGAGGTTTTGAATCATTCACAAATCTAAAACAGATACACTAAAGAGG
1 TGGGAGGTTTTGAATCATTCACAAATCTAAAACAGATATACTAAAGAGG
4275 TGGGAGGTTTTGAATCATTCACAAATCTAAAACA
1 TGGGAGGTTTTGAATCATTCACAAATCTAAAACA
4309 ACAAATCTAA
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 131 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (49 bp):
TGGGAGGTTTTGAATCATTCACAAATCTAAAACAGATATACTAAAGAGG
Found at i:6648 original size:26 final size:27
Alignment explanation
Indices: 6608--6679 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
6598 TTTAATTGAC
*
6608 TAAAACTATTAAAGTATATTTAA-AAAA
1 TAAAA-TATTTAAGTATATTTAATAAAA
* *
6635 TATAATATTTAAGT-TTTTTAATTAAAA
1 TAAAATATTTAAGTATATTTAA-TAAAA
*
6662 TAAAATA-TTAAGAATATT
1 TAAAATATTTAAGTATATT
6680 AGACTTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
25 6 0.17
26 13 0.36
27 17 0.47
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (27 bp):
TAAAATATTTAAGTATATTTAATAAAA
Found at i:7241 original size:158 final size:154
Alignment explanation
Indices: 6938--7234 Score: 447
Period size: 158 Copynumber: 1.9 Consensus size: 154
6928 AATTATAAAG
* *
6938 AGTTTATAATTTTTAAAAAAATGAAAAATTGAAAAAGGAAAAAATAGTAGAGAAAAATAGTCAAC
1 AGTTTATAATTTTTAAAAAAACGAAAAATTGAAAAAGGAAAAAATAGAAGAGAAAAATAGTCAAC
*
7003 AGATTAGTAGAGTACTCTTGATAAAAAAAAAAGAAAGATTAGTAGAGTAGAATTTCTCTAAAAAT
66 AGATTAGTAGAGTACTCTTG--AAAAAAAAAAGAAAGATTAGTAGAGTAGAATTTCTCTAAAAAA
7068 TAAATACATTAAAAAATTGATAGTAT
129 TAAATACATTAAAAAATTGATAGTAT
* *
7094 AGTTTATAATTTTTTAAATAAACGAAAAATTGGAAAAAGGAAAAAATAGAAGAGAAAAATAGTCG
1 AGTTTATAA-TTTTTAAAAAAACGAAAAATT-GAAAAAGGAAAAAATAGAAGAGAAAAATAGTCA
* * ** *
7159 GCGGATTAGTAGAGTACTC-TG-GCAAAAAAA-AAAGATTAGTATAGTAGAATTTCTCTAAAAAA
64 ACAGATTAGTAGAGTACTCTTGAAAAAAAAAAGAAAGATTAGTAGAGTAGAATTTCTCTAAAAAA
7221 TAAATACATTAAAA
129 TAAATACATTAAAA
7235 TAAAAAAAAA
Statistics
Matches: 129, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
153 44 0.34
154 7 0.05
156 9 0.07
157 21 0.16
158 48 0.37
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.27
Consensus pattern (154 bp):
AGTTTATAATTTTTAAAAAAACGAAAAATTGAAAAAGGAAAAAATAGAAGAGAAAAATAGTCAAC
AGATTAGTAGAGTACTCTTGAAAAAAAAAAGAAAGATTAGTAGAGTAGAATTTCTCTAAAAAATA
AATACATTAAAAAATTGATAGTAT
Found at i:7817 original size:238 final size:239
Alignment explanation
Indices: 7399--7875 Score: 778
Period size: 238 Copynumber: 2.0 Consensus size: 239
7389 TTAATTGTTT
*
7399 ACTTTCACGTGCCTTGCACGTGACCTAATATGTTTAAATTAAATGAAAATTAAAATCTTAAGTAT
1 ACTTTCACGTGCCTTGCACGTGACCTAATATGTTTAAATTAAATGAAAATTAAAATCTTAAATAT
* *
7464 ACTACTAACTCGACCGCTTGAAACCAAACCTTATCTAACCCGATTCGACCAAAAAATCCGCTCAA
66 ACTACTAACTCGACCGCTTGAAACCAAACCCTATCCAACCCGATTCGACCAAAAAATCCGCTCAA
* *
7529 TTCGAAATCGAAATGACCTATAATCACTGGTGTTAAAGTTATTTTTGCAATTTATGGGTTTTCAG
131 TTCGAAACCGAAATGACCTATAATCACAGGTGTTAAAGTTATTTTTGCAATTTATGGGTTTTCAG
7594 TTTGAGAATGAACATTGAATG-CATTAGGGGACCGGTCAACATC
196 TTTGAGAATGAACATTGAATGTCATTAGGGGACCGGTCAACATC
*
7637 ACTTTCACGTGCCTTGTACGTGACCTAATATGTTTAAATTAAATGAAAATTAAAATCTTAAATAT
1 ACTTTCACGTGCCTTGCACGTGACCTAATATGTTTAAATTAAATGAAAATTAAAATCTTAAATAT
* * * * *
7702 GCTACTAACTCGACTGCTTGAAGCCAAACCCTATCCAACCCGATTCGACCAAAATAATCCGTTTA
66 ACTACTAACTCGACCGCTTGAAACCAAACCCTATCCAACCCGATTCGACCAAAA-AATCCGCTCA
* *
7767 ATTCGAAACCGAAATGACCTATGAT-ACAGGTGTTAAAGTTATTTTTGCAATTTCTGGGTTTTCA
130 ATTCGAAACCGAAATGACCTATAATCACAGGTGTTAAAGTTATTTTTGCAATTTATGGGTTTTCA
* * * *
7831 GTTTTAGAATGAATATTGAATGTTATTAGGTGACCGGTCAACATC
195 GTTTGAGAATGAACATTGAATGTCATTAGGGGACCGGTCAACATC
7876 CCTCAATTTT
Statistics
Matches: 220, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
238 169 0.77
239 51 0.23
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (239 bp):
ACTTTCACGTGCCTTGCACGTGACCTAATATGTTTAAATTAAATGAAAATTAAAATCTTAAATAT
ACTACTAACTCGACCGCTTGAAACCAAACCCTATCCAACCCGATTCGACCAAAAAATCCGCTCAA
TTCGAAACCGAAATGACCTATAATCACAGGTGTTAAAGTTATTTTTGCAATTTATGGGTTTTCAG
TTTGAGAATGAACATTGAATGTCATTAGGGGACCGGTCAACATC
Found at i:8519 original size:60 final size:60
Alignment explanation
Indices: 8432--8591 Score: 241
Period size: 60 Copynumber: 2.7 Consensus size: 60
8422 GCTAATTGCT
* * *
8432 CAAATAAGGGCATAACGTTTGTC-AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAAC-ATTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
* * *
8492 CAAATAAGGGTCTAACATTATTGAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
8552 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGG
1 CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGG
8592 ACCTAACGTT
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 3 0.03
60 87 0.97
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:8530 original size:31 final size:31
Alignment explanation
Indices: 8428--8624 Score: 142
Period size: 31 Copynumber: 6.5 Consensus size: 31
8418 TATGGCTAAT
* *
8428 TGCTCAAATAAGGGCATAACGTT-TGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTAT-TGAAAA
* * **
8459 TGCTCAAATAAGGGCCCGATC-TT-TT-AATT
1 TGCTCAAATAAGGG-CCTAACGTTATTGAAAA
* *
8488 TGGC-CAAATAAGGGTCTAACATTATTGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATTGAAAA
* * **
8519 TGCTCAAATAAGGGCTCGATC-TT-TT-AATT
1 TGCTCAAATAAGGGC-CTAACGTTATTGAAAA
*
8548 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACGTTATTGAAAA
* **
8579 TGCTCAAATAAGGACCTAACGTTATAAAAAA
1 TGCTCAAATAAGGGCCTAACGTTATTGAAAA
8610 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
8625 ATGTTGTCAG
Statistics
Matches: 130, Mismatches: 24, Indels: 24
0.73 0.13 0.13
Matches are distributed among these distances:
28 6 0.05
29 31 0.24
30 14 0.11
31 73 0.56
32 6 0.05
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTATTGAAAA
Found at i:8561 original size:29 final size:29
Alignment explanation
Indices: 8463--8562 Score: 105
Period size: 29 Copynumber: 3.4 Consensus size: 29
8453 TCAAAATGCT
*
8463 CAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCTCGATCTTTTAATTTGGC
* * **
8492 CAAATAAGGG-TCTAACATTATTGAAAAT-GC
1 CAAATAAGGGCTCGATC-TT-TT-AATTTGGC
8522 TCAAATAAGGGCTCGATCTTTTAATTTGGC
1 -CAAATAAGGGCTCGATCTTTTAATTTGGC
8552 CAAATAAGGGC
1 CAAATAAGGGC
8563 CTAACGTTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
28 3 0.05
29 26 0.46
30 8 0.14
31 15 0.27
32 4 0.07
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (29 bp):
CAAATAAGGGCTCGATCTTTTAATTTGGC
Found at i:8697 original size:31 final size:31
Alignment explanation
Indices: 8654--8821 Score: 136
Period size: 31 Copynumber: 5.5 Consensus size: 31
8644 CGCATGAGAC
8654 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
* ** *
8685 AGGCTCTTATTTG-GCCAAATT--CAAA-GATG
1 AGGCCCTTATTTGAG-CATTTTGGCAAACG-TT
*
8714 GGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
* ** * *
8745 AGGCCTTTATTTG-GCCAAATT---AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGCAAACG-TT
* *
8774 AGACCCTTATTTGAGAATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
8805 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
8822 ATTAGCCGAT
Statistics
Matches: 101, Mismatches: 24, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
28 5 0.05
29 35 0.35
30 4 0.04
31 52 0.51
32 5 0.05
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACGTT
Found at i:8728 original size:60 final size:59
Alignment explanation
Indices: 8653--8817 Score: 258
Period size: 60 Copynumber: 2.7 Consensus size: 59
8643 ACGCATGAGA
*
8653 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCTCTTATTTGGCCAAATTCAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGC-CTTATTTGGCCAAATTAAAAGAT
**
8713 GGGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCTTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCC-TTATTTGGCCAAATTAAAAGAT
* *
8773 CAGACCCTTATTTGAGAATTTTGGCAAACGTTAGGCCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGG-CCTTATTTG
8818 AGCAATTAGC
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
59 1 0.01
60 93 0.97
61 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (59 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCTTATTTGGCCAAATTAAAAGAT
Found at i:9082 original size:22 final size:21
Alignment explanation
Indices: 9064--9106 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
9054 ATCAAAAATG
9064 TATTT-TTTAAAATATAAAAA
1 TATTTATTTAAAATATAAAAA
9084 TATTTATTTAAAATA-AATAAA
1 TATTTATTTAAAATATAA-AAA
9105 TA
1 TA
9107 AATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTTATTTAAAATATAAAAA
Found at i:9103 original size:23 final size:23
Alignment explanation
Indices: 9047--9104 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 23
9037 CACATGGAAC
9047 TAAAA-AAATCAAAAATGTATTTTT
1 TAAAATAAAT-AAAAA-GTATTTTT
9071 TAAAAT--ATAAAAA-TATTTATT
1 TAAAATAAATAAAAAGTATTT-TT
9092 TAAAATAAATAAA
1 TAAAATAAATAAA
9105 TAAATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
20 5 0.17
21 8 0.27
22 5 0.17
23 7 0.23
24 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
TAAAATAAATAAAAAGTATTTTT
Found at i:9115 original size:2 final size:2
Alignment explanation
Indices: 9108--9133 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9098 AAATAAATAA
9108 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9134 TACAAACACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10229 original size:22 final size:20
Alignment explanation
Indices: 10187--10236 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
10177 AAAAAAAATC
*
10187 TTTATTTTAAATAAATATTT
1 TTTATTTTAAAAAAATATTT
10207 TTATATTTTAAAAAATATATTT
1 TT-TATTTTAAAAAA-ATATTT
10229 TTTATTTT
1 TTTATTTT
10237 TTTAATTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.07
21 17 0.63
22 8 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTTTAAAAAAATATTT
Found at i:10237 original size:22 final size:20
Alignment explanation
Indices: 10176--10237 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
10166 TGTTTGTTAA
* *
10176 AAAAAAAAATCTTTA-TTTT
1 AAAAAAATATTTTTATTTTT
*
10195 AAATAAATATTTTTATATTTT
1 AAAAAAATATTTTTAT-TTTT
10216 AAAAAATATATTTTTTATTTTT
1 AAAAAA-ATA-TTTTTATTTTT
10238 TTAATTCCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 12 0.34
21 9 0.26
22 7 0.20
23 7 0.20
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
AAAAAAATATTTTTATTTTT
Found at i:12977 original size:167 final size:163
Alignment explanation
Indices: 12801--13234 Score: 507
Period size: 167 Copynumber: 2.6 Consensus size: 163
12791 GAGAATTAAT
*
12801 TTTTTTTCGTCTTTT-CTCACTTGGCAGATTACTTAAATGTCATAACTTTTGATTCTTGAGGGTA
1 TTTTTTTCGTCTTTTCCT-ACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGG-A
* * * *
12865 TTAAATAACTAGACTTTTTGGTTATTTCTCAATTGATTTTAATAGAGTAGTGGAATTACTAAAAG
64 TTAAATAACTA-ACTTTTTGGTTATTTCTCAATTGACTTGAATAGAGTAGTGAAATTAATAAAAG
* * * * * ** *
12930 ATTCCTACTAATGCTTGTTTTTGAAG-TAAGA-AAGCTTA
128 ATCCCCA-TAAGGATTGATGATG-AGCT-AGATAA-CTAA
* * * *
12968 TTTTTTTCGTCTTTTCCTATTTAGTAGATTACTTAAATATCCTAACTTTTGATTCTTGAGGGAAT
1 TTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGG-AT
* * *
13033 TAAATAAGTAATCTTTTT-CTATCATTTCTCAATGGACTTGAATAGAGTAGTGAAATTAATAAAA
65 TAAATAACTAA-CTTTTTGGT-T-ATTTCTCAATTGACTTGAATAGAGTAGTGAAATTAATAAAA
13097 GATCCCCATAAGGATTGATGATGAGCTAGATAACTAA
127 GATCCCCATAAGGATTGATGATGAGCTAGATAACTAA
* *
13134 TCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGAGGAT
1 TTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAG-GGAT
* *
13199 TAAATAACTAAACTTTTCGGTCATTTCTCAATTGAC
65 TAAATAACT-AACTTTTTGGTTATTTCTCAATTGAC
13235 AAATGACTCA
Statistics
Matches: 226, Mismatches: 32, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
165 13 0.06
166 79 0.35
167 90 0.40
168 44 0.19
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.42
Consensus pattern (163 bp):
TTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGATT
AAATAACTAACTTTTTGGTTATTTCTCAATTGACTTGAATAGAGTAGTGAAATTAATAAAAGATC
CCCATAAGGATTGATGATGAGCTAGATAACTAA
Found at i:13678 original size:5 final size:5
Alignment explanation
Indices: 13644--13675 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
13634 CTTCCTGCTC
13644 TTTAT TTTAT TTTAT TTTAT TTTAT TTATAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT-TAT T
13676 ATAATTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:15648 original size:2 final size:2
Alignment explanation
Indices: 15641--15769 Score: 75
Period size: 2 Copynumber: 70.0 Consensus size: 2
15631 AATAATTTAT
* * * *
15641 TA TA TA TA TA TA TA -A TA AA TA TA -A TT TA TA TA T- TT TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
15680 TA TA T- TT TA TA TA TA TCA TA AA TA -A T- TA AA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
* * *
15719 TA AA TA TA T- TA TA TA TA TA TA TA -A TA AA TA TA -A TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15758 TA TA -A TA -A TA TA
1 TA TA TA TA TA TA TA
15770 ATTGGTCGGT
Statistics
Matches: 96, Mismatches: 18, Indels: 26
0.69 0.13 0.19
Matches are distributed among these distances:
1 12 0.12
2 82 0.85
3 2 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:15673 original size:11 final size:11
Alignment explanation
Indices: 15632--15763 Score: 62
Period size: 9 Copynumber: 13.5 Consensus size: 11
15622 ACTAATAAAA
15632 ATAATTTAT-T
1 ATAATTTATAT
*
15642 AT-ATATATAT
1 ATAATTTATAT
*
15652 ATAA--TAAAT
1 ATAATTTATAT
15661 ATAATTTATAT
1 ATAATTTATAT
*
15672 AT--TTTACAT
1 ATAATTTATAT
*
15681 ATATTTTATAT
1 ATAATTTATAT
* *
15692 AT-A-TCATAA
1 ATAATTTATAT
*
15701 ATAA-TTAAAT
1 ATAATTTATAT
15711 AT-A-TTATAT
1 ATAATTTATAT
*
15720 A-AATATAT-T
1 ATAATTTATAT
*
15729 AT-ATATATAT
1 ATAATTTATAT
*
15739 ATAA--TAAAT
1 ATAATTTATAT
15748 ATAATTTATAT
1 ATAATTTATAT
15759 ATAAT
1 ATAAT
15764 AATATAATTG
Statistics
Matches: 93, Mismatches: 15, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
9 51 0.55
10 17 0.18
11 25 0.27
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
ATAATTTATAT
Found at i:15682 original size:29 final size:29
Alignment explanation
Indices: 15624--15683 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
15614 ATTATAAAAC
*
15624 TAATAAAAATAATTTATTATATATATATA
1 TAATAAAAATAATTTATTATATATACATA
* *
15653 TAATAAATATAATTTA-TATATTTTACATA
1 TAATAAAAATAATTTATTATA-TATACATA
15682 TA
1 TA
15684 TTTTATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
TAATAAAAATAATTTATTATATATACATA
Found at i:15695 original size:13 final size:13
Alignment explanation
Indices: 15638--15761 Score: 86
Period size: 13 Copynumber: 10.0 Consensus size: 13
15628 AAAAATAATT
15638 TATTATATATATA
1 TATTATATATATA
* *
15651 TATAATAAATATA
1 TATTATATATATA
15664 -ATT-TATATAT-
1 TATTATATATATA
*
15674 T-TTACATATAT-
1 TATTATATATATA
15685 T-TTATATATATCA
1 TATTATATATAT-A
* *
15698 TA-AATAATTAAATA
1 TATTAT-A-TATATA
*
15712 TATTATATAAATA
1 TATTATATATATA
15725 TATTATATATATA
1 TATTATATATATA
* *
15738 TATAATAAATATA
1 TATTATATATATA
15751 -ATT-TATATATA
1 TATTATATATATA
15762 ATAATATAAT
Statistics
Matches: 89, Mismatches: 14, Indels: 18
0.74 0.12 0.15
Matches are distributed among these distances:
10 2 0.02
11 29 0.33
12 4 0.04
13 43 0.48
14 5 0.06
15 6 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTATATATATA
Found at i:18389 original size:42 final size:42
Alignment explanation
Indices: 18329--18409 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
18319 CCTCTCTCCA
* * *
18329 TTTGCACAAATGAAAGGAGGGTATGAACTAATTAACATTACT
1 TTTGCACAAACGAAAGGAGGGCACGAACTAATTAACATTACT
* *
18371 TTTGCACACACGAGAGGAGGGCACGAACTAATTAACATT
1 TTTGCACAAACGAAAGGAGGGCACGAACTAATTAACATT
18410 TAATTACATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (42 bp):
TTTGCACAAACGAAAGGAGGGCACGAACTAATTAACATTACT
Done.