Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007565.1 Corchorus capsularis cultivar CVL-1 contig07586, 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: 29421
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:89 original size:33 final size:34
Alignment explanation
Indices: 47--142 Score: 122
Period size: 34 Copynumber: 2.9 Consensus size: 34
37 CTGCCGTGGC
**
47 GAAGCCGCCCCAGTGGGGCGGCCTATTC-ATAGT
1 GAAGCCGCCCCAGTGGGGCGGCCTACCCAATAGT
* *
80 GAAGCCGCCCCAGTGGGGCGGCCTGCCCAATGGT
1 GAAGCCGCCCCAGTGGGGCGGCCTACCCAATAGT
* * *
114 GAAGCCGGCCAAGTGGGGCGGCCTGCCCA
1 GAAGCCGCCCCAGTGGGGCGGCCTACCCA
143 TGATAAGCCG
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 25 0.45
34 31 0.55
ACGTcount: A:0.17, C:0.33, G:0.38, T:0.12
Consensus pattern (34 bp):
GAAGCCGCCCCAGTGGGGCGGCCTACCCAATAGT
Found at i:129 original size:34 final size:33
Alignment explanation
Indices: 17--155 Score: 156
Period size: 33 Copynumber: 4.2 Consensus size: 33
7 AAAATAGCCG
** * *
17 AGCCGCCCCACCGGGGCGGCCTG-CCGTGGCGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
*** *
49 AGCCGCCCCAGTGGGGCGGCCTATTCATAGTGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
82 AGCCGCCCCAGTGGGGCGGCCTGCCCAATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCC-ATGGTGA
* * *
116 AGCCGGCCAAGTGGGGCGGCCTGCCCATGAT-A
1 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
148 AGCCGCCC
1 AGCCGCCC
156 TCTTGGGGCG
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
32 28 0.31
33 32 0.36
34 30 0.33
ACGTcount: A:0.15, C:0.37, G:0.37, T:0.12
Consensus pattern (33 bp):
AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
Found at i:2208 original size:9 final size:10
Alignment explanation
Indices: 2176--2215 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
2166 CTCTATAAGC
2176 AAACAGAGAAA
1 AAACAGAG-AA
*
2187 GAAACAGAGGA
1 -AAACAGAGAA
2198 AAACAGAGAA
1 AAACAGAGAA
2208 AAACAGAG
1 AAACAGAG
2216 GAGAGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 1 0.04
12 8 0.31
ACGTcount: A:0.65, C:0.10, G:0.25, T:0.00
Consensus pattern (10 bp):
AAACAGAGAA
Found at i:2213 original size:20 final size:22
Alignment explanation
Indices: 2176--2217 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
2166 CTCTATAAGC
2176 AAACAGAGAAAGAAACAGAGGA
1 AAACAGAGAAAGAAACAGAGGA
2198 AAACAGAG-AA-AAACAGAGGA
1 AAACAGAGAAAGAAACAGAGGA
2218 GAGTTTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 2 0.10
22 8 0.40
ACGTcount: A:0.64, C:0.10, G:0.26, T:0.00
Consensus pattern (22 bp):
AAACAGAGAAAGAAACAGAGGA
Found at i:2815 original size:23 final size:24
Alignment explanation
Indices: 2789--2836 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
2779 TTGAAGTTTG
2789 ATGTA-AAAAAAATGTCTATGATT
1 ATGTACAAAAAAATGTCTATGATT
*
2812 ATGTACCAAAAAACTGTCTATGATT
1 ATGTA-CAAAAAAATGTCTATGATT
2837 TTACAGGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
25 17 0.77
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGTACAAAAAAATGTCTATGATT
Found at i:3711 original size:10 final size:10
Alignment explanation
Indices: 3689--3727 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
3679 AAATCTCGAT
*
3689 ATATCCGTAA
1 ATATCCATAA
3699 ATATCCATAA
1 ATATCCATAA
*
3709 ATATCCGTAA
1 ATATCCATAA
3719 ATATCCATA
1 ATATCCATA
3728 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (10 bp):
ATATCCATAA
Found at i:3712 original size:20 final size:20
Alignment explanation
Indices: 3689--3727 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3679 AAATCTCGAT
3689 ATATCCGTAAATATCCATAA
1 ATATCCGTAAATATCCATAA
3709 ATATCCGTAAATATCCATA
1 ATATCCGTAAATATCCATA
3728 TTAAATTAAA
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:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
ATATCCGTAAATATCCATAA
Found at i:4576 original size:12 final size:11
Alignment explanation
Indices: 4554--4582 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
4544 TTCGCAGTAC
4554 AAAAAATAAAA
1 AAAAAATAAAA
4565 AAAAAATAAAA
1 AAAAAATAAAA
4576 AAAAAAT
1 AAAAAAT
4583 GTCTACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:4772 original size:13 final size:12
Alignment explanation
Indices: 4742--4784 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
4732 CATCGATACC
4742 TCGATATATCCG
1 TCGATATATCCG
4754 TCGATATATCCG
1 TCGATATATCCG
4766 TTCGATATATCCG
1 -TCGATATATCCG
4779 TCGATA
1 TCGATA
4785 CCTGTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:5203 original size:16 final size:15
Alignment explanation
Indices: 5182--5238 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 15
5172 GGTGAGTGAG
5182 GGTGAGTATCTCACCA
1 GGTGAGTAT-TCACCA
5198 GGTGAGTATTACACCA
1 GGTGAGTATT-CACCA
* * *
5214 GGTGAATATTTACTA
1 GGTGAGTATTCACCA
5229 GGTGAGTATT
1 GGTGAGTATT
5239 GTACTGGGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 13 0.36
16 23 0.64
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (15 bp):
GGTGAGTATTCACCA
Found at i:5248 original size:16 final size:15
Alignment explanation
Indices: 5182--5296 Score: 62
Period size: 16 Copynumber: 7.7 Consensus size: 15
5172 GGTGAGTGAG
* *
5182 GGTGAGTATCTCACCA
1 GGTGAGTAT-TTACTA
* *
5198 GGTGAGTATTACACCA
1 GGTGAGTATT-TACTA
*
5214 GGTGAATATTTACTA
1 GGTGAGTATTTACTA
*
5229 GGTGAGTATTGTACTG
1 GGTGAGTATT-TACTA
* *
5245 GGTGAG----T-GTG
1 GGTGAGTATTTACTA
*
5255 GGTGAGTATCT-CATCA
1 GGTGAGTATTTAC-T-A
5271 GGTGAGTATTTACTA
1 GGTGAGTATTTACTA
5286 GGTGAGTATTT
1 GGTGAGTATTT
5297 GTATTTGGTG
Statistics
Matches: 81, Mismatches: 9, Indels: 19
0.74 0.08 0.17
Matches are distributed among these distances:
10 8 0.10
11 1 0.01
14 1 0.01
15 26 0.32
16 44 0.54
17 1 0.01
ACGTcount: A:0.24, C:0.11, G:0.30, T:0.34
Consensus pattern (15 bp):
GGTGAGTATTTACTA
Found at i:5259 original size:57 final size:58
Alignment explanation
Indices: 5198--5309 Score: 165
Period size: 57 Copynumber: 1.9 Consensus size: 58
5188 TATCTCACCA
5198 GGTGAGTAT-TACACCAGGTGAATATTTACTAGGTGAGTA-TTGTACTGGGTGAGTGTG
1 GGTGAGTATCT-CACCAGGTGAATATTTACTAGGTGAGTATTTGTACTGGGTGAGTGTG
* * * *
5255 GGTGAGTATCTCATCAGGTGAGTATTTACTAGGTGAGTATTTGTATTTGGTGAGT
1 GGTGAGTATCTCACCAGGTGAATATTTACTAGGTGAGTATTTGTACTGGGTGAGT
5310 AGGGTAGGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
57 35 0.71
58 14 0.29
ACGTcount: A:0.23, C:0.08, G:0.32, T:0.37
Consensus pattern (58 bp):
GGTGAGTATCTCACCAGGTGAATATTTACTAGGTGAGTATTTGTACTGGGTGAGTGTG
Found at i:5510 original size:21 final size:22
Alignment explanation
Indices: 5461--5510 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
5451 ACCCTTATAT
*
5461 TATTATATACATTAATACATGA
1 TATTATATACATTAAAACATGA
*
5483 TAATATATA-ATTAAAATCAT-A
1 TATTATATACATTAAAA-CATGA
5504 TATTATA
1 TATTATA
5511 AGCGTGACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
TATTATATACATTAAAACATGA
Found at i:5714 original size:23 final size:22
Alignment explanation
Indices: 5679--5769 Score: 76
Period size: 23 Copynumber: 4.0 Consensus size: 22
5669 CATGGCTTCT
*
5679 TGGTGAGAGCTCCGCGCAAGAGC
1 TGGTGAG-TCTCCGCGCAAGAGC
*
5702 TGGATGAGTCTCCGCTCAAGAGC
1 TGG-TGAGTCTCCGCGCAAGAGC
* * *
5725 AAGG-GAGTTCTCAGCGCTAGAGC
1 -TGGTGAG-TCTCCGCGCAAGAGC
*
5748 TGGGTGAGCCTCCGCGCAAGAG
1 T-GGTGAGTCTCCGCGCAAGAG
5770 TAAGGGAGTA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
22 3 0.06
23 41 0.77
24 9 0.17
ACGTcount: A:0.22, C:0.25, G:0.36, T:0.16
Consensus pattern (22 bp):
TGGTGAGTCTCCGCGCAAGAGC
Found at i:6233 original size:40 final size:40
Alignment explanation
Indices: 6135--6250 Score: 164
Period size: 38 Copynumber: 3.0 Consensus size: 40
6125 CTAGAGCAGG
* *
6135 GCAAGAGAGTCTCCCTCAGGGGAGTCTCCGCTAGCGCAAA
1 GCAAGAGAGTCTCCCTCAGGGGAGTCTCCCCTAACGCAAA
** **
6175 GC-A-AGAGTCTCCCTCAGGGGAGTCTCTTCTAACGCGTA
1 GCAAGAGAGTCTCCCTCAGGGGAGTCTCCCCTAACGCAAA
6213 GCAAGAGAGTCTCCCTCAGGGGAGTCTCCCCTAACGCA
1 GCAAGAGAGTCTCCCTCAGGGGAGTCTCCCCTAACGCA
6251 CAACCATTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
38 32 0.48
39 2 0.03
40 32 0.48
ACGTcount: A:0.23, C:0.31, G:0.28, T:0.18
Consensus pattern (40 bp):
GCAAGAGAGTCTCCCTCAGGGGAGTCTCCCCTAACGCAAA
Found at i:6532 original size:33 final size:33
Alignment explanation
Indices: 6483--6672 Score: 229
Period size: 33 Copynumber: 5.7 Consensus size: 33
6473 TCTCACCTAG
*
6483 CACGTAGCAAGAGAGTCTCCCCTAAGGGAGTCT
1 CACGTAGCAAGGGAGTCTCCCCTAAGGGAGTCT
* * * *
6516 CGCGTAGCAAGGGAGTCTCCCTTGAGGCAGTCT
1 CACGTAGCAAGGGAGTCTCCCCTAAGGGAGTCT
* * ** *
6549 CGCATAGCAAGGGAGTCTCCTTTGAGGGAGTCT
1 CACGTAGCAAGGGAGTCTCCCCTAAGGGAGTCT
6582 CACGTAGCAAGGGAGTCTCCCCTGAA-GGAGTCT
1 CACGTAGCAAGGGAGTCTCCCCT-AAGGGAGTCT
* * * *
6615 CTCGTAGTAAAGGGAGTCTTCCCTGAGGGAGTCT
1 CACGTAG-CAAGGGAGTCTCCCCTAAGGGAGTCT
6649 CACGTAGCAAGGGAGTCTCCCCTA
1 CACGTAGCAAGGGAGTCTCCCCTA
6673 GCGCACAACA
Statistics
Matches: 133, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
33 105 0.79
34 28 0.21
ACGTcount: A:0.23, C:0.26, G:0.31, T:0.21
Consensus pattern (33 bp):
CACGTAGCAAGGGAGTCTCCCCTAAGGGAGTCT
Found at i:6566 original size:66 final size:66
Alignment explanation
Indices: 6487--6671 Score: 255
Period size: 66 Copynumber: 2.8 Consensus size: 66
6477 ACCTAGCACG
* * * *
6487 TAGCAAGAGAGTCTCCCCTAAGGGAGTCTCGCGTAGCAAGGGAGTCTCCCTTG-AGGCAGTCTCG
1 TAGCAAGGGAGTCTCCCCTGAGGGAGTCTCACGTAGCAAGGGAGTCTCCCCTGAAGG-AGTCTCG
6551 CA
65 CA
** *
6553 TAGCAAGGGAGTCTCCTTTGAGGGAGTCTCACGTAGCAAGGGAGTCTCCCCTGAAGGAGTCTCTC
1 TAGCAAGGGAGTCTCCCCTGAGGGAGTCTCACGTAGCAAGGGAGTCTCCCCTGAAGGAGTCTCGC
*
6618 G
66 A
* *
6619 TAGTAAAGGGAGTCTTCCCTGAGGGAGTCTCACGTAGCAAGGGAGTCTCCCCT
1 TAG-CAAGGGAGTCTCCCCTGAGGGAGTCTCACGTAGCAAGGGAGTCTCCCCT
6672 AGCGCACAAC
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
66 57 0.54
67 48 0.46
ACGTcount: A:0.22, C:0.25, G:0.31, T:0.22
Consensus pattern (66 bp):
TAGCAAGGGAGTCTCCCCTGAGGGAGTCTCACGTAGCAAGGGAGTCTCCCCTGAAGGAGTCTCGC
A
Found at i:6578 original size:15 final size:15
Alignment explanation
Indices: 6525--6582 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
6515 TCGCGTAGCA
*
6525 AGGGAGTCTCCCTTG
1 AGGGAGTCTCCATTG
* *
6540 AGGCAGTCTCGCATAG
1 AGGGAGTCTC-CATTG
*
6556 CAAGGGAGTCTCCTTTG
1 --AGGGAGTCTCCATTG
6573 AGGGAGTCTC
1 AGGGAGTCTC
6583 ACGTAGCAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 19 0.56
16 3 0.09
17 3 0.09
18 9 0.26
ACGTcount: A:0.19, C:0.24, G:0.33, T:0.24
Consensus pattern (15 bp):
AGGGAGTCTCCATTG
Found at i:6795 original size:17 final size:16
Alignment explanation
Indices: 6773--6804 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
6763 TATATATATA
6773 TATATATATTTATTTAT
1 TATATATATTT-TTTAT
6790 TATATATATTTTTTA
1 TATATATATTTTTTA
6805 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATATATATTTTTTAT
Found at i:7951 original size:36 final size:36
Alignment explanation
Indices: 7903--7997 Score: 127
Period size: 36 Copynumber: 2.6 Consensus size: 36
7893 TTATGTATTA
* *
7903 GGCGACTTAGGCCAGCGGCGTTATAGCCAAACATTG
1 GGCGACTAAGGCCAGCGGCATTATAGCCAAACATTG
* **
7939 GGCGACTAAGGCCAGCGGCATTATAGCTAAGTATTG
1 GGCGACTAAGGCCAGCGGCATTATAGCCAAACATTG
* *
7975 GGCGACCAAGGCCAGCAGCATTA
1 GGCGACTAAGGCCAGCGGCATTA
7998 CAACCAAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.18
Consensus pattern (36 bp):
GGCGACTAAGGCCAGCGGCATTATAGCCAAACATTG
Found at i:9007 original size:62 final size:63
Alignment explanation
Indices: 8846--9014 Score: 216
Period size: 67 Copynumber: 2.7 Consensus size: 63
8836 TATGCTTCAA
* * **
8846 GATTTGCTTCAAGGGTAGAATGGTTTGATCTTGAACTTGATGATAATTTGAGAACTTGATTTGAT
1 GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATGATAATTTGAGAAC----TTTGAT
8911 TT
62 TT
* * *
8913 GATTTGATTCAAGGGTCGAACGACTTGATCTTGAACTTTATGGTAATTTGAGAAC-TTGATTT
1 GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATGATAATTTGAGAACTTTGATTT
*
8975 GATTTGATTCAAGGGTCGAATGACTTGGTCTTGAA-TTGAT
1 GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGAT
9015 AATTTAATTC
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
61 4 0.04
62 40 0.43
67 48 0.52
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (63 bp):
GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATGATAATTTGAGAACTTTGATTT
Found at i:9073 original size:94 final size:96
Alignment explanation
Indices: 8971--9149 Score: 238
Period size: 99 Copynumber: 1.9 Consensus size: 96
8961 TGAGAACTTG
* *
8971 ATTTGATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAA-T-TGATAATTTAATTCAAGGGTCT
1 ATTTGATTTGATTCAAGGGTCTG-ATGACTTGATCTCGAATTATGATAATTTAATTCAAGGGTCT
9033 TGACGAATTGATCTTGAATTGATGACTTGGGA
65 TGACGAATTGATCTTGAATTGATGACTTGGGA
* *
9065 ATTTGATTTGATTCGAGGGTCTTTGATGACTTGATCTCGAATTGATGATAATTTGATTCAAGGGT
1 ATTTGATTTGATTCAAGGGTC--TGATGACTTGATCTCGAATT-ATGATAATTTAATTCAAGGGT
** *
9130 CTTGGTGATTTGATCTTGAA
63 CTTGACGAATTGATCTTGAA
9150 CAAACAAAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
94 20 0.28
96 14 0.19
97 2 0.03
99 36 0.50
ACGTcount: A:0.26, C:0.09, G:0.25, T:0.40
Consensus pattern (96 bp):
ATTTGATTTGATTCAAGGGTCTGATGACTTGATCTCGAATTATGATAATTTAATTCAAGGGTCTT
GACGAATTGATCTTGAATTGATGACTTGGGA
Found at i:9304 original size:26 final size:26
Alignment explanation
Indices: 9270--9324 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
9260 TGGATCTTCT
*
9270 TTCAATAATT-TCTCAATAACTGGATC
1 TTCAATAATTCTC-CAATAACTGAATC
*
9296 TTCAATAATTCTCCAATAATTGAATC
1 TTCAATAATTCTCCAATAACTGAATC
9322 TTC
1 TTC
9325 TTTGAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (26 bp):
TTCAATAATTCTCCAATAACTGAATC
Found at i:9432 original size:16 final size:16
Alignment explanation
Indices: 9411--9445 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
9401 ATCTGAAATA
9411 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
9427 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
9443 CTT
1 CTT
9446 TCTGAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:10298 original size:58 final size:59
Alignment explanation
Indices: 10217--10334 Score: 175
Period size: 58 Copynumber: 2.0 Consensus size: 59
10207 TTTTTTGTAC
* * * *
10217 TCTAAGTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCT-TTTTTTTT
1 TCTAACTTTTGCCTAAGCCGTCCTTTACAAGATTTCCAACTTAGCGAGCTCTTTTTTTT
* *
10275 TCTAACTTTTTCCTAAGTCGTCCTTTACAAGATTTCCAACTTAGCGAGCTCTTTTTTTT
1 TCTAACTTTTGCCTAAGCCGTCCTTTACAAGATTTCCAACTTAGCGAGCTCTTTTTTTT
10334 T
1 T
10335 GGGTTGACTG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
58 44 0.83
59 9 0.17
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.46
Consensus pattern (59 bp):
TCTAACTTTTGCCTAAGCCGTCCTTTACAAGATTTCCAACTTAGCGAGCTCTTTTTTTT
Found at i:12223 original size:72 final size:72
Alignment explanation
Indices: 12104--12244 Score: 237
Period size: 72 Copynumber: 2.0 Consensus size: 72
12094 TATGCTTCAA
* * **
12104 GATTTGCTTCAAGGGTCGAATGGTTTGATCTTGAACTTGATGATAATTTGAGAACTTGATTTGAT
1 GATTTGATTCAAGGGTCGAACGACTTGATCTTGAACTTGATGATAATTTGAGAACTTGATTTGAT
12169 TTGACTT
66 TTGACTT
*
12176 GATTTGATTCAAGGGTCGAACGACTTGATCTTGAACTTGATGGTAATTTGAGAACTTGATTTGAT
1 GATTTGATTCAAGGGTCGAACGACTTGATCTTGAACTTGATGATAATTTGAGAACTTGATTTGAT
12241 TTGA
66 TTGA
12245 TTCAAGGGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (72 bp):
GATTTGATTCAAGGGTCGAACGACTTGATCTTGAACTTGATGATAATTTGAGAACTTGATTTGAT
TTGACTT
Found at i:12293 original size:40 final size:40
Alignment explanation
Indices: 12239--12318 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 40
12229 ACTTGATTTG
* * *
12239 ATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTG-ACGACTTGATCTTGAATTGATA
12279 ATTTAATTCAAGGGTCTTGACGACTTGATCTTGAATTGAT
1 ATTTAATTCAAGGGTC-TGACGACTTGATCTTGAATTGAT
12319 GACTTGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 15 0.43
41 19 0.54
42 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (40 bp):
ATTTAATTCAAGGGTCTGACGACTTGATCTTGAATTGATA
Found at i:12332 original size:94 final size:96
Alignment explanation
Indices: 12234--12412 Score: 247
Period size: 99 Copynumber: 1.9 Consensus size: 96
12224 TGAGAACTTG
* *
12234 ATTTGATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAA-T-TGATAATTTAATTCAAGGGTCT
1 ATTTGATTTGATTCAAGGGTCTG-ATGACTTGATCTCGAATTATGATAATTTAATTCAAGGGTCT
12296 TGACGACTTGATCTTGAATTGATGACTTGGGA
65 TGACGACTTGATCTTGAATTGATGACTTGGGA
* *
12328 ATTTGATTTGATTCGAGGGTCTTTGATGACTTGATCTCGAATTGATGATAATTTGATTCAAGGGT
1 ATTTGATTTGATTCAAGGGTC--TGATGACTTGATCTCGAATT-ATGATAATTTAATTCAAGGGT
**
12393 CTTGGTGACTTGATCTTGAA
63 CTTGACGACTTGATCTTGAA
12413 CAAACAAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
94 20 0.27
96 14 0.19
97 2 0.03
99 37 0.51
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.40
Consensus pattern (96 bp):
ATTTGATTTGATTCAAGGGTCTGATGACTTGATCTCGAATTATGATAATTTAATTCAAGGGTCTT
GACGACTTGATCTTGAATTGATGACTTGGGA
Found at i:12567 original size:26 final size:26
Alignment explanation
Indices: 12533--12587 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
12523 TGGATCTTCT
*
12533 TTCAATAATT-TCTCAATAACTGGATC
1 TTCAATAATTCTC-CAATAACTGAATC
*
12559 TTCAATAATTCTCCAATAATTGAATC
1 TTCAATAATTCTCCAATAACTGAATC
12585 TTC
1 TTC
12588 TTTGAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (26 bp):
TTCAATAATTCTCCAATAACTGAATC
Found at i:12696 original size:16 final size:16
Alignment explanation
Indices: 12675--12708 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
12665 TCTGAAATAT
12675 TTCAGAGCTTTTCTGC
1 TTCAGAGCTTTTCTGC
*
12691 TTCAGAGCTTTTTTGC
1 TTCAGAGCTTTTCTGC
12707 TT
1 TT
12709 TCTGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.50
Consensus pattern (16 bp):
TTCAGAGCTTTTCTGC
Found at i:14303 original size:107 final size:105
Alignment explanation
Indices: 14131--14373 Score: 366
Period size: 107 Copynumber: 2.3 Consensus size: 105
14121 AGTTTAGCAT
* *
14131 TAATTTCACCAAGTTTAG-TCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAAT
1 TAATTTCACTAAGTTTAGCT-CCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAAT
*
14195 TAATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
65 TAATAA--TATTGTTATAGGATTTTAGAAATAAAATACAAAAC
*
14238 TAATTTCACTAAGTTTAGCTCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCTCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* * *
14303 AATAATATTGTTATAGGATTTTAGAAATAAAATATATAAT
66 AATAATATTGTTATAGGATTTTAGAAATAAAATACAAAAC
*
14343 TAA-TTCACTAAGTTTAGC-CAAAATTAAAATT
1 TAATTTCACTAAGTTTAGCTCCAAATTAAAATT
14374 AAAATTTATA
Statistics
Matches: 127, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
103 12 0.09
104 15 0.12
105 34 0.27
107 65 0.51
108 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCTCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATATTGTTATAGGATTTTAGAAATAAAATACAAAAC
Found at i:16719 original size:22 final size:21
Alignment explanation
Indices: 16677--16719 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
16667 TTGCTTTTCT
* *
16677 TTTTCCTTTTTCTACTGATAG
1 TTTTCCTTCTTCCACTGATAG
*
16698 TTTTCTCTTCTTCCACTTATAG
1 TTTTC-CTTCTTCCACTGATAG
16720 CATACTCAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.14, C:0.23, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTCCTTCTTCCACTGATAG
Found at i:22989 original size:22 final size:22
Alignment explanation
Indices: 22964--23176 Score: 83
Period size: 22 Copynumber: 9.7 Consensus size: 22
22954 ATGATCCCAT
22964 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
** *** *
22986 TATGAAATTTCAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * * **
23008 TATGCAATTTCGAAAATCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
23030 TAT-AAATTTTTTTCAACCTTCT
1 TATGAAATTTTGAT-AACCTTCC
* * *
23052 TATTAAATTGTGTTAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * **
23073 TAAGGAATTTTGAAAACCTTAA
1 TATGAAATTTTGATAACCTTCC
*
23095 TATGGAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
23117 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
23140 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
23161 ATATGATATATTGATA
1 -TATGAAATTTTGATA
23177 TTAGTAACCT
Statistics
Matches: 139, Mismatches: 45, Indels: 14
0.70 0.23 0.07
Matches are distributed among these distances:
21 23 0.17
22 91 0.65
23 25 0.18
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:23971 original size:21 final size:21
Alignment explanation
Indices: 23928--23972 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
23918 TTGATTTTCT
* *
23928 TATAATTTAATATATGTATTA
1 TATAATCTAATATATCTATTA
23949 TATAATCTAATATATACTA-TA
1 TATAATCTAATATAT-CTATTA
23970 TAT
1 TAT
23973 TATTTTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (21 bp):
TATAATCTAATATATCTATTA
Found at i:24134 original size:74 final size:74
Alignment explanation
Indices: 24056--24212 Score: 262
Period size: 74 Copynumber: 2.1 Consensus size: 74
24046 TGGTCTTTTC
*
24056 ACACTTTTCAGG-TGACTAAAAAGCCCCTCTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCTT
1 ACACTTTTC-GGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTT
24120 TTTCGTAATT
65 TTTCGTAATT
* *
24130 ACACTTTTCGGATGATTAAAAAGCCCTTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
24195 TTCGTAATT
66 TTCGTAATT
*
24204 ACACATTTC
1 ACACTTTTC
24213 CCTTCCTTAA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
73 2 0.03
74 76 0.97
ACGTcount: A:0.21, C:0.29, G:0.09, T:0.41
Consensus pattern (74 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
TTCGTAATT
Found at i:24250 original size:20 final size:21
Alignment explanation
Indices: 24219--24257 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
24209 TTTCCCTTCC
24219 TTAATGGTTTTTAATTAATAT
1 TTAATGGTTTTTAATTAATAT
24240 TTAAT-GTTTTTAATTAAT
1 TTAATGGTTTTTAATTAAT
24258 TGCTTCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (21 bp):
TTAATGGTTTTTAATTAATAT
Found at i:24980 original size:31 final size:31
Alignment explanation
Indices: 24942--25001 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
24932 TGGCAATTTA
*
24942 GAAATATATTTTTTAAAA-AAGGGTACAATTG
1 GAAATATA-TTTTAAAAATAAGGGTACAATTG
24973 GAAATATATTTTAAAAATAAGGGTACAAT
1 GAAATATATTTTAAAAATAAGGGTACAAT
25002 CGAAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.33
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATTG
Found at i:26023 original size:31 final size:31
Alignment explanation
Indices: 25954--26055 Score: 123
Period size: 31 Copynumber: 3.3 Consensus size: 31
25944 TCCTTTTGTG
* **
25954 CACGTGGCATGCCACGTGCCACTTTTTGAAA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
25985 CATGTGGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * **
26016 CACGTGGCGTGACATATGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
26047 CATGTGGCA
1 CACGTGGCA
26056 CAACTTTTTG
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:27756 original size:8 final size:8
Alignment explanation
Indices: 27745--27784 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
27735 CTATGCTGCT
*
27745 ATATATGC
1 ATATATAC
27753 ATATATAC
1 ATATATAC
*
27761 ATATATAT
1 ATATATAC
27769 AGTATATAC
1 A-TATATAC
27778 ATATATA
1 ATATATA
27785 TGGATTTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (8 bp):
ATATATAC
Found at i:28271 original size:2 final size:2
Alignment explanation
Indices: 28264--28289 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28254 GTAAAACAAG
28264 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
28290 TCTATGTATA
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:28412 original size:6 final size:6
Alignment explanation
Indices: 28381--28410 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28371 TAATAATAAT
*
28381 GACAAC GACAAC GACAAC GACAAC AACAAC
1 GACAAC GACAAC GACAAC GACAAC GACAAC
28411 AATAGTGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.53, C:0.33, G:0.13, T:0.00
Consensus pattern (6 bp):
GACAAC
Found at i:29396 original size:2 final size:2
Alignment explanation
Indices: 29391--29421 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29381 CTTCCTCAAA
29391 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 A
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.