Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012012.1 Corchorus capsularis cultivar CVL-1 contig12033, 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: 43434
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1000 original size:21 final size:20
Alignment explanation
Indices: 936--999 Score: 101
Period size: 21 Copynumber: 3.1 Consensus size: 20
926 TATTAAGGAT
*
936 AATATTACAAATCAAATAATA
1 AATATTACAAAT-AAATAAAA
957 AATATTACAAATTAAATAAAA
1 AATATTACAAA-TAAATAAAA
978 AATATTACAAATAAATAAAA
1 AATATTACAAATAAATAAAA
998 AA
1 AA
1000 AAACAATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
20 11 0.27
21 29 0.71
22 1 0.02
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (20 bp):
AATATTACAAATAAATAAAA
Found at i:4003 original size:29 final size:29
Alignment explanation
Indices: 3964--4040 Score: 118
Period size: 29 Copynumber: 2.6 Consensus size: 29
3954 CTTGTATCGT
3964 TTGGACGTTTTGCCCCCTGAACTTCAATC
1 TTGGACGTTTTGCCCCCTGAACTTCAATC
* *
3993 TTGGACATTTTGCCCCCTGAACTTCAATT
1 TTGGACGTTTTGCCCCCTGAACTTCAATC
*
4022 TTGGGACGTTTTACCCCCT
1 TT-GGACGTTTTGCCCCCT
4041 CAACCTAACG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 29 0.67
30 14 0.33
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (29 bp):
TTGGACGTTTTGCCCCCTGAACTTCAATC
Found at i:4211 original size:30 final size:29
Alignment explanation
Indices: 4176--4251 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
4166 GTTAGGTTGA
*
4176 GGGGCAAAACGTCCCAAAATTGAAGTTCAG
1 GGGGCAAAACGT-CCAAAATTGAAATTCAG
* * *
4206 GGGGCAAAATGTCTAAGATTGAAATTCAG
1 GGGGCAAAACGTCCAAAATTGAAATTCAG
* *
4235 GGGGTAAAACATCCAAA
1 GGGGCAAAACGTCCAAA
4252 CGATACAAGT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 26 0.70
30 11 0.30
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.18
Consensus pattern (29 bp):
GGGGCAAAACGTCCAAAATTGAAATTCAG
Found at i:4826 original size:22 final size:22
Alignment explanation
Indices: 4801--5048 Score: 69
Period size: 22 Copynumber: 11.5 Consensus size: 22
4791 ATTACACTAT
*
4801 TTTTGATGA-CGTCCTTATGAAA
1 TTTTGATAACCGTCC-TATGAAA
*
4823 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCGTCCTATGAAA
* *
4845 TTATGATAA--TTACACTAT----
1 TTTTGATAACCGT-C-CTATGAAA
* *
4863 TTTTTATGA-CGTCCTTATGAAA
1 TTTTGATAACCGTCC-TATGAAA
*
4885 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCGTCCTATGAAA
** * * *
4907 TTTCAATAA-TGATACTATGGAA
1 TTTTGATAACCG-TCCTATGAAA
* * * *
4929 TTTCGAGAACCTTCTTAT--AA
1 TTTTGATAACCGTCCTATGAAA
* * *
4949 TTCTT-TTCAACCTTCTTATGAAA
1 TT-TTGAT-AACCGTCCTATGAAA
* * *
4972 TTTTGTTAACC-TCCCTAAGGAA
1 TTTTGATAACCGT-CCTATGAAA
4994 TTTTGA-AGACC-TCACTATGAAA
1 TTTTGATA-ACCGTC-CTATGAAA
* *
5016 TTTTGATAA-CTTCCAAATGAAA
1 TTTTGATAACCGTCC-TATGAAA
5038 TTTTGATAACC
1 TTTTGATAACC
5049 AACACTATAA
Statistics
Matches: 170, Mismatches: 32, Indels: 47
0.68 0.13 0.19
Matches are distributed among these distances:
17 1 0.01
18 10 0.06
19 1 0.01
20 6 0.04
21 18 0.11
22 118 0.69
23 16 0.09
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (22 bp):
TTTTGATAACCGTCCTATGAAA
Found at i:4854 original size:62 final size:62
Alignment explanation
Indices: 4757--4908 Score: 268
Period size: 62 Copynumber: 2.5 Consensus size: 62
4747 ATATTCATAC
* * *
4757 GAAATTATGATAACCTTCCTATTAAAATATGATAATTACACTATTTTTGATGACGTCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTGATGACGTCCTTAT
*
4819 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTGATGACGTCCTTAT
4881 GAAATTTTGATAACCTTCCTATGAAATT
1 GAAATTTTGATAACCTTCCTATGAAATT
4909 TCAATAATGA
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 86 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (62 bp):
GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTGATGACGTCCTTAT
Found at i:5158 original size:22 final size:22
Alignment explanation
Indices: 5133--5247 Score: 97
Period size: 22 Copynumber: 5.1 Consensus size: 22
5123 GAATCGTCGG
5133 TAATCACACTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
5155 TAATAACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
5177 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * *
5199 TAAAC-CTTCCTATAAAATTTTGA
1 TAATCAC--ACTATGAAATTTTGA
* * *
5222 TAAATCTCCCTATAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
5245 TAA
1 TAA
5248 CCTCCTTATG
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
21 1 0.01
22 43 0.55
23 30 0.38
24 3 0.04
25 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.37
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:5321 original size:22 final size:22
Alignment explanation
Indices: 5271--5454 Score: 146
Period size: 22 Copynumber: 8.5 Consensus size: 22
5261 TAATAACTAC
*
5271 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCACTATG
** * *
5293 ATTTTTTGATAACCTCATTATA
1 AAATTTTGATAACCTCACTATG
* * *
5315 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCACTATG
* *
5337 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGAT-AACCTCACTATG
* *
5359 AAATTTTGATAACCGTC-TTCTG
1 AAATTTTGATAACC-TCACTATG
* *
5381 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATAACCT-CACTATG
5403 AAATTTTGATAACCTTCA-TATG
1 AAATTTTGATAACC-TCACTATG
* *
5425 AAATTTTGATATCCTC-C-CTG
1 AAATTTTGATAACCTCACTATG
5445 AAATTTTGAT
1 AAATTTTGAT
5455 TACTCCATAA
Statistics
Matches: 125, Mismatches: 29, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
20 13 0.10
21 7 0.06
22 98 0.78
23 6 0.05
24 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCACTATG
Found at i:5351 original size:80 final size:81
Alignment explanation
Indices: 5190--5338 Score: 194
Period size: 79 Copynumber: 1.9 Consensus size: 81
5180 CCTCGCTATG
* * * *
5190 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAATCTCCCTATAAAATTTTGATAACCTCCTT
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCT
5255 ATGAATTAATAACTAC
66 ATGAATTAATAACTAC
* ** * * *
5271 AAATTTTGAT-AACCTCCCTATGATTTTTTGAT-AACCTCATTATAAAATTTTGTTAATCTCCCT
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCT
5334 ATGAA
66 ATGAA
5339 ATTTTGATCT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
79 30 0.52
80 18 0.31
81 10 0.17
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.40
Consensus pattern (81 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCT
ATGAATTAATAACTAC
Found at i:5385 original size:66 final size:65
Alignment explanation
Indices: 5332--5453 Score: 167
Period size: 66 Copynumber: 1.9 Consensus size: 65
5322 GTTAATCTCC
*
5332 CTATGAAATTTTGATCTACATAC-TATGAAATTTTGATAACCGTCTTCTGAAATTTTGAAAACTA
1 CTATGAAATTTTGAT-AACATACATATGAAATTTTGATAACC-TCTTCTGAAATTTTGAAAACTA
5396 AA
64 AA
* * * *
5398 CTATGAAATTTTGATAACCTTCATATGAAATTTTGATATCCTC-CCTGAAATTTTGA
1 CTATGAAATTTTGATAACATACATATGAAATTTTGATAACCTCTTCTGAAATTTTGA
5454 TTACTCCATA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
64 12 0.24
65 6 0.12
66 32 0.64
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (65 bp):
CTATGAAATTTTGATAACATACATATGAAATTTTGATAACCTCTTCTGAAATTTTGAAAACTAAA
Found at i:5587 original size:22 final size:22
Alignment explanation
Indices: 5562--5682 Score: 118
Period size: 22 Copynumber: 5.5 Consensus size: 22
5552 AATCACATTT
*
5562 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
5584 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
5606 TCAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
5628 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
*
5650 TGTAATTTTGATAACCTCGTTT-
1 TGAAATTTTGATAACCTC-TTTA
*
5672 TAAAATTTTGA
1 TGAAATTTTGA
5683 AATTAGACCA
Statistics
Matches: 79, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
22 77 0.97
23 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:5657 original size:44 final size:44
Alignment explanation
Indices: 5536--5665 Score: 136
Period size: 44 Copynumber: 2.9 Consensus size: 44
5526 AAAAAAACCA
* * * *
5536 CTATGAAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCT
1 CTATG-AAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * * *
5581 TTATGAAATTTTGATAACCTC-TCTATCAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCCCT
*
5625 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACC
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACC
5666 TCGTTTTAAA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
43 1 0.02
44 60 0.91
45 5 0.08
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
Found at i:5678 original size:44 final size:43
Alignment explanation
Indices: 5541--5682 Score: 124
Period size: 44 Copynumber: 3.2 Consensus size: 43
5531 AACCACTATG
* * *
5541 AAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTAT
1 AAAATTTTGATAATCACATTATGAAATTTTGATAACCTCTTT-T
* * * * * * * *
5585 GAAATTTTGATAACCTC-TCTATCAAATTTTGTTGACCCCTCTAT
1 AAAATTTTGATAATCACAT-TATGAAATTTTGATAACCTCT-TTT
* *
5629 GAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGTTTT
1 AAAATTTTGATAATCACATTATGAAATTTTGATAACCTC-TTTT
5673 AAAATTTTGA
1 AAAATTTTGA
5683 AATTAGACCA
Statistics
Matches: 74, Mismatches: 20, Indels: 8
0.73 0.20 0.08
Matches are distributed among these distances:
43 1 0.01
44 70 0.95
45 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (43 bp):
AAAATTTTGATAATCACATTATGAAATTTTGATAACCTCTTTT
Found at i:5832 original size:37 final size:37
Alignment explanation
Indices: 5740--5837 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 37
5730 ATCTAAGCCC
* * *
5740 AAATAGGACGTTGGAGACGAAGACAAAAAGCAAAATT
1 AAATAGGACGTTGGAAACAAAAACAAAAAGCAAAATT
** * * *
5777 AAATACAACAATTAGAAACAAAAACAAAAGGCAAAATT
1 AAATAGGAC-GTTGGAAACAAAAACAAAAAGCAAAATT
5815 AAATAGGACGTTGGAAACAAAAA
1 AAATAGGACGTTGGAAACAAAAA
5838 GCCAAATTGA
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
37 19 0.40
38 29 0.60
ACGTcount: A:0.58, C:0.11, G:0.17, T:0.13
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAAACAAAAAGCAAAATT
Found at i:6912 original size:18 final size:18
Alignment explanation
Indices: 6889--6950 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
6879 CATTCCCCGT
6889 CGGGGATGGGGATGGGGA
1 CGGGGATGGGGATGGGGA
* *
6907 CGGGGACGGGGATGGGGT
1 CGGGGATGGGGATGGGGA
*
6925 CGGGAAGTCGGGG-TCGGGGA
1 CGGGGA-T-GGGGAT-GGGGA
6945 CGGGGA
1 CGGGGA
6951 ATATACCCCC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 21 0.60
19 1 0.03
20 13 0.37
ACGTcount: A:0.15, C:0.11, G:0.65, T:0.10
Consensus pattern (18 bp):
CGGGGATGGGGATGGGGA
Found at i:6950 original size:6 final size:6
Alignment explanation
Indices: 6889--6950 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
6879 CATTCCCCGT
* * * * * *
6889 CGGGGA TGGGGA TGGGGA CGGGGA CGGGGA TGGGGT CGGGAAGT CGGGGT
1 CGGGGA CGGGGA CGGGGA CGGGGA CGGGGA CGGGGA CGGG--GA CGGGGA
6939 CGGGGA CGGGGA
1 CGGGGA CGGGGA
6951 ATATACCCCC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
6 42 0.88
8 6 0.12
ACGTcount: A:0.15, C:0.11, G:0.65, T:0.10
Consensus pattern (6 bp):
CGGGGA
Found at i:7147 original size:60 final size:61
Alignment explanation
Indices: 7017--7186 Score: 193
Period size: 60 Copynumber: 2.7 Consensus size: 61
7007 GCTAATTGTT
* * *
7017 CAAATAAGGGTCTAACAATT-TACAAAAATGCTTAAATAATTAGGGTCTGATATTTTTAATTTGG
1 CAAATAAGGGCCTAAC-ATTAT-CGAAAATGCTCAAAT-A--AGGGTCTGATATTTTTAATTTGG
7081 C
61 C
** * *
7082 CAAATAAGGGTTTAACGTTTGTC-AAAATGCTCAAATAAGGGTCTGATA-TTTTAATTTGGC
1 CAAATAAGGGCCTAAC-ATTATCGAAAATGCTCAAATAAGGGTCTGATATTTTTAATTTGGC
*
7142 TAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGTCTG
1 CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGTCTG
7187 GCGTCAGTTT
Statistics
Matches: 94, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
59 4 0.04
60 47 0.50
61 11 0.12
63 1 0.01
64 12 0.13
65 18 0.19
66 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (61 bp):
CAAATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGGTCTGATATTTTTAATTTGGC
Found at i:7323 original size:60 final size:60
Alignment explanation
Indices: 7229--7388 Score: 207
Period size: 60 Copynumber: 2.7 Consensus size: 60
7219 ATTCCAAACC
* **
7229 CTTATTTGAGCATTTTCGATAATGTTAGACCCTTATTTGGTCAAATTAAAAGATCAGAC-
1 CTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGACCAAATTAAAAGATCAGACG
* * * *
7288 CATTATTTGAACATTTTCGATAGCGTTAGGCCCTTATTTGACCAAATTAAAAGATCATACG
1 C-TTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGACCAAATTAAAAGATCAGACG
* *
7349 CTTATTTGAGCATTTT-GACAAACGTTAGACCTTTATTTGA
1 CTTATTTGAGCATTTTCGA-TAACGTTAGACCCTTATTTGA
7389 GCAATTACCC
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
59 3 0.03
60 82 0.95
61 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (60 bp):
CTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGACCAAATTAAAAGATCAGACG
Found at i:9145 original size:86 final size:87
Alignment explanation
Indices: 8988--9157 Score: 297
Period size: 86 Copynumber: 2.0 Consensus size: 87
8978 GTCGGATTCG
* * *
8988 GATTAGTCAGAGCAAAGCTTCTTATATTGGATAGGAAAAAAAATTACTAAGAAGAAACTTAAAAT
1 GATTAGTCAGAGCAAAACTCCTTATACTGGATAGGAAAAAAAATTACTAAGAAGAAACTTAAAAT
9053 TACATATCTACCCTTAAAATCA
66 TACATATCTACCCTTAAAATCA
*
9075 GATTAGTCAGAGCAAAACTCCTTATACTGGAT-GGGAAAAAAATTACTAAGAAGAAACTTAAAAT
1 GATTAGTCAGAGCAAAACTCCTTATACTGGATAGGAAAAAAAATTACTAAGAAGAAACTTAAAAT
9139 TACATATCTACCCTTAAAA
66 TACATATCTACCCTTAAAA
9158 GCAATAGGGT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 50 0.63
87 29 0.37
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (87 bp):
GATTAGTCAGAGCAAAACTCCTTATACTGGATAGGAAAAAAAATTACTAAGAAGAAACTTAAAAT
TACATATCTACCCTTAAAATCA
Found at i:11214 original size:229 final size:229
Alignment explanation
Indices: 10813--11275 Score: 856
Period size: 229 Copynumber: 2.0 Consensus size: 229
10803 GCAAACTTGC
10813 ATTTTGTTCATTTAAGGACAACAAGGCGAAATCAATAAAATTGATCTAGCTAGGGGGTGCGGCTC
1 ATTTTGTTCATTTAAGGACAACAAGGCGAAATCAATAAAATTGATCTAGCTAGGGGGTGCGGCTC
10878 CAACATGGGGTTAGATCATGATGACCCTTGGTTCAAGTAGATCATATTGGCTAAGTTTCATCTCA
66 CAACATGGGGTTAGATCATGATGACCCTTGGTTCAAGTAGATCATATTGGCTAAGTTTCATCTCA
10943 AACGGACTTAAGATGAAAAACTTATACTCGTTTTTCAGTTAAGGACAATTTGGGGTGAAAAACCA
131 AACGGACTTAAGATGAAAAACTTATACTCGTTTTTCAGTTAAGGACAATTTGGGGTGAAAAACCA
*
11008 GTTCACTATCAAGGAGAGCTCGGTTTTACTTAGA
196 GTTCACCATCAAGGAGAGCTCGGTTTTACTTAGA
*
11042 ATTTTGTTCATTTAAGGACGAA-AAGGCGAAATCAATAAAATTGATCTGGCTAGGGGGTGCGGCT
1 ATTTTGTTCATTTAAGGAC-AACAAGGCGAAATCAATAAAATTGATCTAGCTAGGGGGTGCGGCT
* *
11106 CCAACATGGGGTTAGATCATGATGACCCTTGGTTCATGTAGATCATCTTGGCTAAGTTTCATCTC
65 CCAACATGGGGTTAGATCATGATGACCCTTGGTTCAAGTAGATCATATTGGCTAAGTTTCATCTC
* *
11171 AAACGGACTTAAGATGAAAAACTTATACTCGTTTTTCAGTTAAGGACAATTTGTGGTGAAAAATC
130 AAACGGACTTAAGATGAAAAACTTATACTCGTTTTTCAGTTAAGGACAATTTGGGGTGAAAAACC
11236 AGTTCACCATCAAGGAGAGCTCGGTTTTACTTAGA
195 AGTTCACCATCAAGGAGAGCTCGGTTTTACTTAGA
11271 ATTTT
1 ATTTT
11276 TTCCATAGTT
Statistics
Matches: 227, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
229 225 0.99
230 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (229 bp):
ATTTTGTTCATTTAAGGACAACAAGGCGAAATCAATAAAATTGATCTAGCTAGGGGGTGCGGCTC
CAACATGGGGTTAGATCATGATGACCCTTGGTTCAAGTAGATCATATTGGCTAAGTTTCATCTCA
AACGGACTTAAGATGAAAAACTTATACTCGTTTTTCAGTTAAGGACAATTTGGGGTGAAAAACCA
GTTCACCATCAAGGAGAGCTCGGTTTTACTTAGA
Found at i:11493 original size:155 final size:153
Alignment explanation
Indices: 11177--11569 Score: 463
Period size: 155 Copynumber: 2.5 Consensus size: 153
11167 TCTCAAACGG
* * * *
11177 ACTTAAGATGAAAAACTTATACTCGTTTTTCAGTTAAGGACAATTTGTGGTGAAAAATCAGTTCA
1 ACTTAAGATGAAAAACTTATACT-GTTTTTCAGTTAAGGACAGTTTGAGGTGAGAAACCAGTTCA
*
11242 CCATCAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTTTTATGGAGATAATCTAAACAT
65 CCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTTTTATGGAGATAATCTAAACA-
* *
11307 ACTGGTGGAAATTCAACCTTAATGGA
129 ACT-GTGGAAATTCAACCTCAATGCA
* * * * *
11333 A-TTAAGATAAAAAACTTATGCATGTTTTTCACTTAAGGACAGTTTAAGGTGAGAAACCGGTTCA
1 ACTTAAGATGAAAAACTTATAC-TGTTTTTCAGTTAAGGACAGTTTGAGGTGAGAAACCAGTTCA
*
11397 CCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATA-TTCTTATGGAGATAATCTAAGTC
65 CCATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTT-TTATGGAGATAATCTAA-AC
* * *
11461 -CCT-TGGAAAAATTTAATCTCAAT-CA
128 AACTGTGG--AAATTCAACCTCAATGCA
* * * *
11486 TACTTAAGATGAAAAACTTATTCTTGTTTTTTAGTTAAGGACAGTTTGGGGTGTGAAACCTAGTT
1 -ACTTAAGATGAAAAACTTATAC-TGTTTTTCAGTTAAGGACAGTTTGAGGTGAGAAACC-AGTT
*
11551 CACCATGAAGGAGGGCTCG
63 CACCATGAAGGAGAGCTCG
11570 AACCCAACCA
Statistics
Matches: 203, Mismatches: 26, Indels: 16
0.83 0.11 0.07
Matches are distributed among these distances:
152 3 0.01
153 1 0.00
154 17 0.08
155 158 0.78
156 24 0.12
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (153 bp):
ACTTAAGATGAAAAACTTATACTGTTTTTCAGTTAAGGACAGTTTGAGGTGAGAAACCAGTTCAC
CATGAAGGAGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTTTTATGGAGATAATCTAAACAAC
TGTGGAAATTCAACCTCAATGCA
Found at i:11945 original size:28 final size:28
Alignment explanation
Indices: 11883--11955 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
11873 CATGTGACAT
*
11883 ATCAGAGGGAAGATGTTCCACCTGATAT
1 ATCAGAGGGAAGATGTTCCACCTGATAC
* ***
11911 A-CTAGAGGGAAGATTTTCCGTGTGATAC
1 ATC-AGAGGGAAGATGTTCCACCTGATAC
11939 ATCAGAGGG-AGATGTTC
1 ATCAGAGGGAAGATGTTC
11956 TGACCTCCTC
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
27 8 0.22
28 28 0.76
29 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (28 bp):
ATCAGAGGGAAGATGTTCCACCTGATAC
Found at i:17081 original size:17 final size:17
Alignment explanation
Indices: 17059--17095 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
17049 ATGACTACTC
*
17059 ATTTTGATAATTTGCTA
1 ATTTTGATAATTTGCCA
*
17076 ATTTTGATGATTTGCCA
1 ATTTTGATAATTTGCCA
17093 ATT
1 ATT
17096 GGGACTATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (17 bp):
ATTTTGATAATTTGCCA
Found at i:21215 original size:18 final size:18
Alignment explanation
Indices: 21192--21228 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
21182 CCTTTATGCA
21192 GCCATCATAT-GATTCCAT
1 GCCATCAT-TGGATTCCAT
21210 GCCATCATTGGATTCCAT
1 GCCATCATTGGATTCCAT
21228 G
1 G
21229 ACAAATTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (18 bp):
GCCATCATTGGATTCCAT
Found at i:28927 original size:2 final size:2
Alignment explanation
Indices: 28916--28949 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
28906 CTCGAGTATT
28916 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28950 TTAGTAACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34289 original size:1 final size:1
Alignment explanation
Indices: 34283--34307 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
34273 TACTACCCTG
34283 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
34308 AAAAGGATCA
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:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:37968 original size:24 final size:25
Alignment explanation
Indices: 37939--37990 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
37929 ATGATTCTTT
*
37939 AAACGAGAAAAACGCGGTCGTT-TA
1 AAACGAGAAAAACGCCGTCGTTGTA
37963 AAACGAGAAAAACGCCGTCGTTGTA
1 AAACGAGAAAAACGCCGTCGTTGTA
37988 AAA
1 AAA
37991 ATTAGTTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (25 bp):
AAACGAGAAAAACGCCGTCGTTGTA
Found at i:41850 original size:3 final size:3
Alignment explanation
Indices: 41842--41877 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
41832 ATATCCATCT
41842 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
41878 CCTTGACATG
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:42917 original size:6 final size:6
Alignment explanation
Indices: 42906--42937 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
42896 AAGCAAGCAT
42906 ATAGAA ATAGAA ATAGAA ATAGAA ATAGAA AT
1 ATAGAA ATAGAA ATAGAA ATAGAA ATAGAA AT
42938 TGCAATTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.19
Consensus pattern (6 bp):
ATAGAA
Done.