Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013077.1 Corchorus capsularis cultivar CVL-1 contig13098, 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: 45861
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3234 original size:37 final size:37
Alignment explanation
Indices: 3182--3252 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
3172 ATATAATTAT
* *
3182 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
*
3219 TCATAAAGTTGTGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
3253 GTTGATCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:3923 original size:22 final size:22
Alignment explanation
Indices: 3877--3923 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3867 ATGATCCCAT
* *
3877 TATGAAATTTTGATAACCTTAC
1 TATGAAATTTTAATAACATTAC
3899 TATGAAATTTTAATAACGATT-C
1 TATGAAATTTTAATAAC-ATTAC
3921 TAT
1 TAT
3924 AGAATTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTAATAACATTAC
Found at i:4062 original size:45 final size:45
Alignment explanation
Indices: 4004--4089 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
3994 AAGATCTCAA
* * *
4004 TATGAAATTTTGATAACTTTCCA-ATGAAATTTTGATAACCAACAC
1 TATGAAATGTTGATAAC-CTCCATATGAAATATTGATAACCAACAC
* *
4049 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
4090 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 4 0.11
45 31 0.89
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAACAC
Found at i:4083 original size:22 final size:22
Alignment explanation
Indices: 3960--4496 Score: 158
Period size: 22 Copynumber: 24.9 Consensus size: 22
3950 TTTTTTAACT
* *
3960 TATGAAATTTTGTTAACCTCCT
1 TATGAAATTTTGATAACCTCCA
* * * *
3982 TAAGGAATTTTGA-AGATCTCAA
1 TATGAAATTTTGATA-ACCTCCA
*
4004 TATGAAATTTTGATAACTTTCCA
1 TATGAAATTTTGATAAC-CTCCA
**
4027 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTCCA
* *
4048 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTCCA
* * * **
4071 TATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCTCCA
* * *
4093 TATGAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCA
*
4115 TAT-TAATTGTT-AGTAA--TCACA
1 TATGAAATT-TTGA-TAACCTC-CA
* *
4136 CTTTAAAATTTTGATAATCACT-C-
1 -TATGAAATTTTGATAA-C-CTCCA
* *
4159 TATGAAATTGTGATAATCTCGC-
1 TATGAAATTTTGATAACCTC-CA
**
4181 TATGAAATTTTGATAAATTTCCCA
1 TATGAAATTTTGAT-AACCT-CCA
* *
4205 TA--AAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCTCCA
* * * * *
4226 TATAAAATTTTGTTAACTTTCT
1 TATGAAATTTTGATAACCTCCA
*
4248 TATGAAATCTTGATAA----C-
1 TATGAAATTTTGATAACCTCCA
* * * *
4265 TA-CAAATATTGATAAGCTCCC
1 TATGAAATTTTGATAACCTCCA
**
4286 TATGATTTTTTGATAACCT-CA
1 TATGAAATTTTGATAACCTCCA
* * * *
4307 TTATAAAATTTTGTTAATCTCCC
1 -TATGAAATTTTGATAACCTCCA
* * *
4330 TATGAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTCCA
**
4352 TATGAAA-TTTGATAACC-CTGT
1 TATGAAATTTTGATAACCTC-CA
* **
4373 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTCCA
*
4394 CTATGAAATTTTGATAACCTTCA
1 -TATGAAATTTTGATAACCTCCA
* *
4417 TATGAAATGTTGATATCCTCC-
1 TATGAAATTTTGATAACCTCCA
* * *
4438 -CTG-AATTTTGATATCCTCCC
1 TATGAAATTTTGATAACCTCCA
*
4458 TA--AAATTTTGATTA-CTCCA
1 TATGAAATTTTGATAACCTCCA
* * *
4477 TAATAAAAGTTTAATAACCT
1 T-ATGAAATTTTGATAACCT
4497 TCCTAATTTG
Statistics
Matches: 376, Mismatches: 95, Indels: 87
0.67 0.17 0.16
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
19 20 0.05
20 19 0.05
21 32 0.09
22 235 0.62
23 51 0.14
24 4 0.01
26 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:4261 original size:45 final size:44
Alignment explanation
Indices: 4139--4263 Score: 119
Period size: 45 Copynumber: 2.8 Consensus size: 44
4129 AATCACACTT
** *
4139 TAAAATTTTGAT-AATCACTCTATGAAATTGTGAT-AATCTCGCTA
1 TAAAATTTTGATAAATTTC-CTATGAAATT-TGATAAATCTCCCTA
* * *
4183 TGAAATTTTGATAAATTTCCCATAAAATTTTGATAAATCTCCCTA
1 TAAAATTTTGATAAATTTCCTATGAAA-TTTGATAAATCTCCCTA
* * *
4228 TAAAATTTTGTTAACTTTCTTATGAAATCTTGATAA
1 TAAAATTTTGATAAATTTCCTATGAAAT-TTGATAA
4264 CTACAAATAT
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
44 22 0.34
45 43 0.66
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.42
Consensus pattern (44 bp):
TAAAATTTTGATAAATTTCCTATGAAATTTGATAAATCTCCCTA
Found at i:4450 original size:19 final size:20
Alignment explanation
Indices: 4421--4469 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
4411 CCTTCATATG
*
4421 AAATGTTGATATCCTCCCT-
1 AAATTTTGATATCCTCCCTA
*
4440 GAATTTTGATATCCTCCCTA
1 AAATTTTGATATCCTCCCTA
4460 AAATTTTGAT
1 AAATTTTGAT
4470 TACTCCATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (20 bp):
AAATTTTGATATCCTCCCTA
Found at i:4600 original size:22 final size:22
Alignment explanation
Indices: 4550--4654 Score: 88
Period size: 22 Copynumber: 4.8 Consensus size: 22
4540 AGAAATACCA
* *
4550 TTATGAAATTTTTG-TAATCACAT
1 TTATGAAA-TTTTGATAACCTC-T
*
4573 TT-TGAAAGTTTGATAACCTCT
1 TTATGAAATTTTGATAACCTCT
*
4594 TTATGAAATTTTGATAACCTTT
1 TTATGAAATTTTGATAACCTCT
* * * *
4616 TTATAAAATTTTGTTGACCCCT
1 TTATGAAATTTTGATAACCTCT
* *
4638 CTATGAAATTCTGATAA
1 TTATGAAATTTTGATAA
4655 TCACATTGTG
Statistics
Matches: 65, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
21 7 0.11
22 56 0.86
23 2 0.03
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCTCT
Found at i:4710 original size:22 final size:22
Alignment explanation
Indices: 4679--4734 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
4669 TCTGATAATC
* ** *
4679 AAATTCTGATAACCTCACTTTG
1 AAATTTTGATAACAACACTATG
4701 AAATTTTGATAACAACACTATG
1 AAATTTTGATAACAACACTATG
4723 AAATTTTGATAA
1 AAATTTTGATAA
4735 TCTTCATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACAACACTATG
Found at i:4711 original size:36 final size:36
Alignment explanation
Indices: 4643--4712 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
4633 CCCCTCTATG
*
4643 AAATTCTGATAATCACATTGTGTAATTCTGATAATC
1 AAATTCTGATAATCACATTGTGAAATTCTGATAATC
*
4679 AAATTCTGATAACCTCAC-TT-TGAAATTTTGATAA
1 AAATTCTGATAA--TCACATTGTGAAATTCTGATAA
4713 CAACACTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 24 0.80
37 2 0.07
38 4 0.13
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (36 bp):
AAATTCTGATAATCACATTGTGAAATTCTGATAATC
Found at i:4872 original size:22 final size:22
Alignment explanation
Indices: 4842--4952 Score: 61
Period size: 22 Copynumber: 5.1 Consensus size: 22
4832 AAATTGAGAC
*
4842 TTTT-ATAACCTTCATATGAAA
1 TTTTAATAACCTACATATGAAA
*
4863 TTTTAATAACC-ACACTATAAAA
1 TTTTAATAACCTACA-TATGAAA
* * *
4885 TTTTGATAACCTCCCA-CTGAAA
1 TTTTAATAACCT-ACATATGAAA
* * *
4907 TATTAATAACCT-CCTAATAAAA
1 TTTTAATAACCTACAT-ATGAAA
**
4929 TTTTGTTAACC-ACACTATGAAA
1 TTTTAATAACCTACA-TATGAAA
4951 TT
1 TT
4953 CGTATAACCT
Statistics
Matches: 66, Mismatches: 16, Indels: 15
0.68 0.16 0.15
Matches are distributed among these distances:
20 1 0.02
21 6 0.09
22 56 0.85
23 1 0.02
24 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.36
Consensus pattern (22 bp):
TTTTAATAACCTACATATGAAA
Found at i:4950 original size:44 final size:43
Alignment explanation
Indices: 4856--4951 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 43
4846 ATAACCTTCA
* *
4856 TATGAAATTTTAATAACCACACTATAAAATTTTGATAACCTCC
1 TATGAAATATTAATAACCACACTATAAAATTTTGATAACCACC
* * *
4899 CACTGAAATATTAATAACCTC-CTAATAAAATTTTGTTAACCACAC
1 TA-TGAAATATTAATAACCACACT-ATAAAATTTTGATAACCAC-C
4944 TATGAAAT
1 TATGAAAT
4952 TCGTATAACC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
43 3 0.07
44 39 0.89
45 2 0.05
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (43 bp):
TATGAAATATTAATAACCACACTATAAAATTTTGATAACCACC
Found at i:5087 original size:24 final size:22
Alignment explanation
Indices: 5051--5169 Score: 130
Period size: 22 Copynumber: 5.3 Consensus size: 22
5041 CCAACCTAAA
* * *
5051 AAATTTTAATAACCTGACCCTATA
1 AAATTTTAGTAACC--ACACTATG
* *
5075 AAATTTTGGTAACCACACTACG
1 AAATTTTAGTAACCACACTATG
* *
5097 AAATTTTTGTAACCTCACTATG
1 AAATTTTAGTAACCACACTATG
5119 AAATTTTAGTAACCACACTATG
1 AAATTTTAGTAACCACACTATG
* *
5141 AAATTTTGGTAACCACAATATG
1 AAATTTTAGTAACCACACTATG
*
5163 TAATTTT
1 AAATTTT
5170 GATAACCTCC
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
22 70 0.85
24 12 0.15
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
AAATTTTAGTAACCACACTATG
Found at i:5103 original size:22 final size:22
Alignment explanation
Indices: 5070--5176 Score: 142
Period size: 22 Copynumber: 4.9 Consensus size: 22
5060 TAACCTGACC
*
5070 CTATAAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* * *
5092 CTACGAAATTTTTGTAACCTCA
1 CTATGAAATTTTGGTAACCACA
*
5114 CTATGAAATTTTAGTAACCACA
1 CTATGAAATTTTGGTAACCACA
5136 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* * *
5158 ATATGTAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
5177 TCCTCATGGA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:5135 original size:44 final size:44
Alignment explanation
Indices: 5016--5169 Score: 139
Period size: 44 Copynumber: 3.5 Consensus size: 44
5006 TTGTGATAAT
* * * ** **
5016 TAACCACCCTATGAAATTTCAATAACCA-ACCTAAAAAATTTTAA
1 TAACCACACTATGAAATTTTAGTAACCACA-CTACGAAATTTTGG
* * * *
5060 TAACCTGACCCTATAAAATTTTGGTAACCACACTACGAAATTTTTG
1 TAACC--ACACTATGAAATTTTAGTAACCACACTACGAAATTTTGG
* *
5106 TAACCTCACTATGAAATTTTAGTAACCACACTATGAAATTTTGG
1 TAACCACACTATGAAATTTTAGTAACCACACTACGAAATTTTGG
* *
5150 TAACCACAATATGTAATTTT
1 TAACCACACTATGAAATTTT
5170 GATAACCTCC
Statistics
Matches: 90, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
44 55 0.61
46 34 0.38
47 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (44 bp):
TAACCACACTATGAAATTTTAGTAACCACACTACGAAATTTTGG
Found at i:5176 original size:66 final size:65
Alignment explanation
Indices: 5051--5223 Score: 188
Period size: 66 Copynumber: 2.6 Consensus size: 65
5041 CCAACCTAAA
* *
5051 AAATTTTAATAACCTGACCCTATAAAATTTTGGTAACCACACTACGAAATTTTTGTAACCTCACT
1 AAATTTTAATAACC--A-CCTATGAAATTTTGGTAACCACAATACGAAATTTTTGTAACCTC-CT
5116 -ATG
62 CATG
* * *
5119 AAATTTTAGTAACCACACTATGAAATTTTGGTAACCACAATATGTAA-TTTTGATAACCTCCTCA
1 AAATTTTAATAACCAC-CTATGAAATTTTGGTAACCACAATACGAAATTTTTG-TAACCTCCTCA
5183 TG
64 TG
* * * *
5185 GAATTATAATAACCATCTTATGAAATTTTGATAACCACA
1 AAATTTTAATAACCA-CCTATGAAATTTTGGTAACCACA
5224 TAGAGACAAG
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
65 8 0.09
66 69 0.76
67 1 0.01
68 13 0.14
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.34
Consensus pattern (65 bp):
AAATTTTAATAACCACCTATGAAATTTTGGTAACCACAATACGAAATTTTTGTAACCTCCTCATG
Found at i:5189 original size:22 final size:22
Alignment explanation
Indices: 5116--5221 Score: 69
Period size: 22 Copynumber: 4.8 Consensus size: 22
5106 TAACCTCACT
*
5116 ATGAAATTTT-AGTAACCA-CAC
1 ATGAAATTTTGA-TAACCATCTC
*
5137 TATGAAATTTTGGTAACCA-CAAT-
1 -ATGAAATTTTGATAACCATC--TC
*
5160 ATGTAATTTTGATAACC-TCCTC
1 ATGAAATTTTGATAACCAT-CTC
* * * *
5182 ATGGAATTATAATAACCATCTT
1 ATGAAATTTTGATAACCATCTC
5204 ATGAAATTTTGATAACCA
1 ATGAAATTTTGATAACCA
5222 CATAGAGACA
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
21 1 0.02
22 63 0.95
23 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (22 bp):
ATGAAATTTTGATAACCATCTC
Found at i:5364 original size:6 final size:6
Alignment explanation
Indices: 5353--5384 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
5343 AGTATTGTAC
5353 GTGTTA GTGTTA GTGTTA GTGTTA GTGTTA GT
1 GTGTTA GTGTTA GTGTTA GTGTTA GTGTTA GT
5385 TTAATCTTTT
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:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
GTGTTA
Found at i:5436 original size:19 final size:20
Alignment explanation
Indices: 5405--5442 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5395 TATTAACATT
5405 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
5424 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
5443 AATAATAGTA
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:7302 original size:22 final size:22
Alignment explanation
Indices: 7277--7445 Score: 71
Period size: 22 Copynumber: 7.7 Consensus size: 22
7267 AATCCCATTC
7277 TGAAATTTTGATAACCTTCCAA
1 TGAAATTTTGATAACCTTCCAA
* ** * *
7299 TGAAATTTTAATAACGATACTA
1 TGAAATTTTGATAACCTTCCAA
* * * ***
7321 TGGAATTTCGAGAACCTTTTTA
1 TGAAATTTTGATAACCTTCCAA
* ** **
7343 T-AATTTTTTTTAACCTTCTTA
1 TGAAATTTTGATAACCTTCCAA
* * *
7364 TCAAATTTTGTTAA-TTTCCCTAA
1 TGAAATTTTGATAACCTT-CC-AA
*
7387 -GAAATTTTGA-AGACC-TCAATA
1 TGAAATTTTGATA-ACCTTCCA-A
7408 TGAAATTTTGATAA-CTTCCCAA
1 TGAAATTTTGATAACCTT-CCAA
7430 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
7446 AACACTATGA
Statistics
Matches: 106, Mismatches: 30, Indels: 21
0.68 0.19 0.13
Matches are distributed among these distances:
20 1 0.01
21 20 0.19
22 80 0.75
23 5 0.05
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCCAA
Found at i:7553 original size:22 final size:22
Alignment explanation
Indices: 7528--7772 Score: 115
Period size: 22 Copynumber: 11.1 Consensus size: 22
7518 ATGAAGTTAG
*
7528 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
7550 TAATTACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
7572 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
7594 TAAATCTTC-CTAT-AAGATTTTGA
1 T-AATC-ACACTATGAA-ATTTTGA
* * * **
7617 TAACCTCCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* * * *
7639 TAACCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* * *
7661 TAATCTCCCTACGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
7683 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
* * **
7705 TAA-CCCTCATACAAAATTTTGA
1 TAATCACAC-TATGAAATTTTGA
* * *
7727 -AAACTAAACTATGAAATTTCGA
1 TAATC-ACACTATGAAATTTTGA
* *
7749 TAACCTTCA-TATGAAATTTTGA
1 TAATC-ACACTATGAAATTTTGA
7771 TA
1 TA
7773 TCCTCCCTGA
Statistics
Matches: 169, Mismatches: 43, Indels: 22
0.72 0.18 0.09
Matches are distributed among these distances:
21 7 0.04
22 138 0.82
23 22 0.13
24 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:7588 original size:44 final size:43
Alignment explanation
Indices: 7539--7772 Score: 190
Period size: 44 Copynumber: 5.3 Consensus size: 43
7529 AATCACACTC
* *
7539 TGAAATTTTGATAATTACACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACTACACTATGAAATTTTGATAACCTC-CTA
*
7583 TGAAATTTTGATAAATCTTC-CTAT-AAGATTTTGATAACCTCCCTA
1 TGAAATTTTGAT-AA-CTACACTATGAA-ATTTTGATAACCT-CCTA
** * * *
7628 TGATTTTTTGATAACCT-CATTATGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAA-CTACACTATGAAATTTTGATAACCT-CCTA
* *
7672 CGAAATTTTGAT--CTACATACTATGAAATTTTGATAACCCTCATA
1 TGAAATTTTGATAACTAC--ACTATGAAATTTTGATAA-CCTCCTA
** * * * *
7716 CAAAATTTTGAAAACTAAACTATGAAATTTCGATAACCTTCATA
1 TGAAATTTTGATAACTACACTATGAAATTTTGATAACC-TCCTA
7760 TGAAATTTTGATA
1 TGAAATTTTGATA
7773 TCCTCCCTGA
Statistics
Matches: 154, Mismatches: 23, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
41 2 0.01
42 1 0.01
43 3 0.02
44 107 0.69
45 35 0.23
46 6 0.04
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (43 bp):
TGAAATTTTGATAACTACACTATGAAATTTTGATAACCTCCTA
Found at i:8100 original size:22 final size:23
Alignment explanation
Indices: 8071--8125 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
8061 AAATTGAGAC
* *
8071 TTTT-ATAACTTTCA-TATGAAA
1 TTTTGATAACTTACACTATAAAA
*
8092 TTTTGATAAC-CACACTATAAAA
1 TTTTGATAACTTACACTATAAAA
8114 TTTTGATAACTT
1 TTTTGATAACTT
8126 CCCCATGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (23 bp):
TTTTGATAACTTACACTATAAAA
Found at i:8318 original size:46 final size:45
Alignment explanation
Indices: 8252--8428 Score: 168
Period size: 44 Copynumber: 4.0 Consensus size: 45
8242 TAATTAATCA
*** * *
8252 CCATATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGAT
1 CCATATGAAATTTTGGTAACCACA-CTATGAAATTTTGATAACCT--T
8299 CC-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAA-CTT
1 CCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTT
* *
8342 CCATATGAAGTTTTGGTAACCACACTATGGAATTTTGATAACC-T
1 CCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTT
* ** *
8386 CC-TCATGAAATTATAATAACCATC-TTATGAAATTTTGATAACC
1 CCAT-ATGAAATTTTGGTAACCA-CACTATGAAATTTTGATAACC
8429 ACGTAGAGAC
Statistics
Matches: 112, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
43 4 0.04
44 70 0.62
45 4 0.04
46 31 0.28
47 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (45 bp):
CCATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTT
Found at i:8328 original size:22 final size:22
Alignment explanation
Indices: 8255--8430 Score: 130
Period size: 22 Copynumber: 7.9 Consensus size: 22
8245 TTAATCACCA
**
8255 TATGAAATTTCAATAACCA-ACC
1 TATGAAATTTTGATAACCACA-C
* *
8277 TAAGAAATTTTAATAACCTGATC-C
1 TATGAAATTTTGATAACC--A-CAC
*
8301 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACCACAC
8323 TATGAAATTTTGATAACTTC-CA-
1 TATGAAATTTTGATAAC--CACAC
* *
8345 TATGAAGTTTTGGTAACCACAC
1 TATGAAATTTTGATAACCACAC
* *
8367 TATGGAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCACAC
* * *
8388 TCATGAAATTATAATAACCATC-T
1 T-ATGAAATTTTGATAACCA-CAC
8411 TATGAAATTTTGATAACCAC
1 TATGAAATTTTGATAACCAC
8431 GTAGAGACAA
Statistics
Matches: 124, Mismatches: 19, Indels: 23
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.01
21 6 0.05
22 95 0.77
23 4 0.03
24 18 0.15
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:8728 original size:38 final size:38
Alignment explanation
Indices: 8672--8766 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 38
8662 TCAAGTATCT
* * * *
8672 ATATAATGTTGGAGACAAAGATAAAAAGTAAAA-TTAA
1 ATATAACGTTGGAAACAAAGACAAAAAGAAAAATTTAA
*
8709 ATATAACGATTGGAAACAAAGACAAAAGGAAAAATTTAA
1 ATATAACG-TTGGAAACAAAGACAAAAAGAAAAATTTAA
** *
8748 ATAGGACCTTGGAAACAAA
1 ATATAACGTTGGAAACAAA
8767 AAACCAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
37 7 0.15
38 32 0.67
39 9 0.19
ACGTcount: A:0.56, C:0.07, G:0.17, T:0.20
Consensus pattern (38 bp):
ATATAACGTTGGAAACAAAGACAAAAAGAAAAATTTAA
Found at i:9987 original size:62 final size:62
Alignment explanation
Indices: 9906--10057 Score: 232
Period size: 62 Copynumber: 2.5 Consensus size: 62
9896 ATATTCATAC
* * *
9906 GAAATTATGATAACCTTCCTATTAAATTATAATAATTACACTATTTTTAATGATGTACTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATAATAATTACACTATTTTTAATGACGTACTTAT
* * * * *
9968 GATATTTTGATAACTTTCCTATGAAATTATGATAATTACACTATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATAATAATTACACTATTTTTAATGACGTACTTAT
10030 GAAATTTTGATAACCTTCCTATGAAATT
1 GAAATTTTGATAACCTTCCTATGAAATT
10058 TCAATAACGA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 80 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (62 bp):
GAAATTTTGATAACCTTCCTATGAAATTATAATAATTACACTATTTTTAATGACGTACTTAT
Found at i:10052 original size:22 final size:22
Alignment explanation
Indices: 10027--10197 Score: 103
Period size: 22 Copynumber: 7.8 Consensus size: 22
10017 ATGACGTCCT
10027 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
** ** *
10049 TATGAAATTTCAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * * * **
10071 TGTGGAATTTCGAGAACTTTTT
1 TATGAAATTTTGATAACCTTCC
** *
10093 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGATAACCTTCC
* *
10115 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
10137 TAAGGAATTTTGAAAACC-TCAC
1 TATGAAATTTTGATAACCTTC-C
* *
10159 TATGAAATTTTGATAACTTTCA
1 TATGAAATTTTGATAACCTTCC
*
10181 AATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
10198 AAACACTATA
Statistics
Matches: 110, Mismatches: 35, Indels: 8
0.72 0.23 0.05
Matches are distributed among these distances:
21 3 0.03
22 102 0.93
23 5 0.05
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:10308 original size:22 final size:22
Alignment explanation
Indices: 10283--10351 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
10273 GAATAGTCAG
*
10283 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
10305 TAATCACACTATGAAACTGTGA
1 TAATCACACTATGAAATTTTGA
* *
10327 TAACCTCACTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
10349 TAA
1 TAA
10352 ACCTTCCTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:10393 original size:22 final size:22
Alignment explanation
Indices: 10368--10411 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
10358 CTATATAAAT
*
10368 CTCCCTATAAAATTTTAATAAC
1 CTCCCTATAAAATCTTAATAAC
* * *
10390 CTCCTTATGAAATCTTGATAAC
1 CTCCCTATAAAATCTTAATAAC
10412 TACAAATTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (22 bp):
CTCCCTATAAAATCTTAATAAC
Found at i:10465 original size:22 final size:22
Alignment explanation
Indices: 10415--10512 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
10405 TGATAACTAC
10415 AAATTTTGATAATCTCC-CTATG
1 AAATTTTGATAATC-CCTCTATG
**
10437 ATTTTTTGATAA-CCCTCTTATG
1 AAATTTTGATAATCCCTC-TATG
* ****
10459 AAATTTTGAAAATTAAACTATG
1 AAATTTTGATAATCCCTCTATG
*
10481 AAATTTTGATAA-CCTTCATATG
1 AAATTTTGATAATCCCTC-TATG
10503 AAATTTTGAT
1 AAATTTTGAT
10513 TACTCCATAA
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
20 2 0.03
21 3 0.05
22 52 0.90
23 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (22 bp):
AAATTTTGATAATCCCTCTATG
Found at i:10681 original size:24 final size:22
Alignment explanation
Indices: 10620--10697 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
10610 TCACATTTTG
*
10620 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTCTAT
10641 AAAATTTTGATAACCTCTCTAT
1 AAAATTTTGATAACCTCTCTAT
* * *
10663 AAAATTTTGTTGACCCCTCTAT
1 AAAATTTTGATAACCTCTCTAT
*
10685 GAAATTTTGATAA
1 AAAATTTTGATAA
10698 TCACATTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 4 0.08
22 45 0.92
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTCTAT
Found at i:10707 original size:22 final size:22
Alignment explanation
Indices: 10594--10720 Score: 96
Period size: 22 Copynumber: 5.8 Consensus size: 22
10584 GAAGTATCAC
* *
10594 TATGAAATTTTGGTAATCACAT
1 TATGAAATTTTGATAACCACAT
* * * *
10616 TTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCACAT
* *
10638 TATAAAATTTTGATAACCTC-T
1 TATGAAATTTTGATAACCACAT
* * * *
10659 CTATAAAATTTTGTTGACC-CCT
1 -TATGAAATTTTGATAACCACAT
*
10681 CTATGAAATTTTGATAATCACAT
1 -TATGAAATTTTGATAACCACAT
*
10704 TATGTAATTTTGATAAC
1 TATGAAATTTTGATAAC
10721 ATCGCGCTTT
Statistics
Matches: 84, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
21 2 0.02
22 80 0.95
23 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAT
Found at i:10713 original size:44 final size:44
Alignment explanation
Indices: 10593--10720 Score: 132
Period size: 44 Copynumber: 2.9 Consensus size: 44
10583 AGAAGTATCA
* * * *
10593 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
* * * * * * *
10637 TTATAAAATTTTGATAACCTC-TCTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCCCT
*
10681 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAAC
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAAC
10721 ATCGCGCTTT
Statistics
Matches: 63, Mismatches: 19, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
43 1 0.02
44 61 0.97
45 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCCCT
Found at i:10895 original size:37 final size:37
Alignment explanation
Indices: 10823--10895 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 37
10813 GACGAAGACA
** *
10823 AAAAGCAAAATTAAATACAACGATTGGAAACAAAAAC
1 AAAAGCAAAATTAAATACAACGATCAGAAAAAAAAAC
**
10860 AAAAGACAAAATTAAATAGGACG-TCAGAAAAAAAAA
1 AAAAG-CAAAATTAAATACAACGATCAGAAAAAAAAA
10896 AGTCAAATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 15 0.50
38 15 0.50
ACGTcount: A:0.64, C:0.11, G:0.12, T:0.12
Consensus pattern (37 bp):
AAAAGCAAAATTAAATACAACGATCAGAAAAAAAAAC
Found at i:11053 original size:31 final size:31
Alignment explanation
Indices: 11017--11076 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
11007 TGACAATTTA
*
11017 GAAATATGTTTTAAAAAAAAGGGTACAATTG
1 GAAATATATTTTAAAAAAAAGGGTACAATTG
*
11048 GAAATATATTTTAAAAATAAGGGTACAAT
1 GAAATATATTTTAAAAAAAAGGGTACAAT
11077 CGAAAAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (31 bp):
GAAATATATTTTAAAAAAAAGGGTACAATTG
Found at i:12465 original size:17 final size:17
Alignment explanation
Indices: 12443--12475 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12433 CTCAATATAA
*
12443 AATTTCATCTATATTAG
1 AATTTCATCCATATTAG
12460 AATTTCATCCATATTA
1 AATTTCATCCATATTA
12476 ATGTATAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (17 bp):
AATTTCATCCATATTAG
Found at i:12722 original size:108 final size:108
Alignment explanation
Indices: 12533--12749 Score: 350
Period size: 108 Copynumber: 2.0 Consensus size: 108
12523 ATTAATTGGA
* * *
12533 TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTTTAAGGCTGGGATATTCGGA
1 TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGACTGAGATATTCGGA
12598 AAAAAAGAAAACAAAAAAATTGATTTAAGGATA-T-TTAATTAAT
66 AAAAAAGAAAACAAAAAAATTGA--TAAGGATATTGTTAATTAAT
*
12641 TATATTAATTCTTGAACAAAATAATCCGACTTTACATTATAAATTATAAGACTGAGATATTCGGA
1 TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGACTGAGATATTCGGA
12706 AAAAAA-AAAACAAAAAAAATTGATAAGGATATTGTTAATTAAT
66 AAAAAAGAAAAC-AAAAAAATTGATAAGGATATTGTTAATTAAT
12749 T
1 T
12750 TTTACATTAT
Statistics
Matches: 102, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
106 8 0.08
107 6 0.06
108 88 0.86
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.33
Consensus pattern (108 bp):
TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGACTGAGATATTCGGA
AAAAAAGAAAACAAAAAAATTGATAAGGATATTGTTAATTAAT
Found at i:22425 original size:30 final size:31
Alignment explanation
Indices: 22377--22435 Score: 111
Period size: 30 Copynumber: 1.9 Consensus size: 31
22367 ATATTTTCTG
22377 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCTTATTTTTAAAACATATTTCCA
22408 ATTGTACCCTT-TTTTTAAAACATATTTC
1 ATTGTACCCTTATTTTTAAAACATATTTC
22436 TAAATTGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTCCA
Found at i:22442 original size:31 final size:31
Alignment explanation
Indices: 22377--22443 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 31
22367 ATATTTTCTG
*
22377 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCTTATTTTTAAAACATATTTCAA
22408 ATTGTACCCTT-TTTTTAAAACATATTTCTAA
1 ATTGTACCCTTATTTTTAAAACATATTTC-AA
22439 ATTGT
1 ATTGT
22444 CATTACTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 17 0.50
31 17 0.50
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.48
Consensus pattern (31 bp):
ATTGTACCCTTATTTTTAAAACATATTTCAA
Found at i:22494 original size:18 final size:19
Alignment explanation
Indices: 22445--22497 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
22435 CTAAATTGTC
*
22445 ATTACTAAATAATATTTTTA
1 ATTACTAAATTAT-TTTTTA
* **
22465 ATTATTCCATTATTTTTTA
1 ATTACTAAATTATTTTTTA
22484 ATTA-TAAATTATTT
1 ATTACTAAATTATTT
22498 CATTATATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 8 0.30
19 10 0.37
20 9 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTACTAAATTATTTTTTA
Found at i:22572 original size:22 final size:21
Alignment explanation
Indices: 22534--22610 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 21
22524 TGGTTATTAT
* *
22534 AATTCCATGAGGAGGTTATCAA
1 AATTCCAT-AGGTGGTTACCAA
22556 AATTCCATAGTGTGGTTACCAA
1 AATTCCATAG-GTGGTTACCAA
*
22578 AATTTCATAGAGTGGTTACCAA
1 AATTCCATAG-GTGGTTACCAA
*
22600 AATTTCATAGG
1 AATTCCATAGG
22611 ATCAAGTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
21 3 0.06
22 47 0.94
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (21 bp):
AATTCCATAGGTGGTTACCAA
Found at i:22625 original size:24 final size:22
Alignment explanation
Indices: 22576--22652 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
22566 TGTGGTTACC
* **
22576 AAAATTTCATAGAGT-GGTTACC
1 AAAATTTCATAG-GTAAGTTATT
22598 AAAATTTCATAGGATCAAGTTATT
1 AAAATTTCATAGG-T-AAGTTATT
* *
22622 AAAATTTCTTAGGTTAGTTATT
1 AAAATTTCATAGGTAAGTTATT
*
22644 GAAATTTCA
1 AAAATTTCA
22653 CAGGGTGGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.02
22 27 0.60
23 1 0.02
24 16 0.36
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (22 bp):
AAAATTTCATAGGTAAGTTATT
Found at i:22808 original size:22 final size:22
Alignment explanation
Indices: 22783--23039 Score: 82
Period size: 22 Copynumber: 11.5 Consensus size: 22
22773 CTTCATCGGG
22783 AGGTTATCAAAATTTCATATAA
1 AGGTTATCAAAATTTCATATAA
*
22805 AGGTTAT-AAAAGTTTCAATTTCATA
1 AGGTTATCAAAA-TTTC-ATAT-A-A
* * * *
22830 AGGAGTACCAAAATTTGATA-GA
1 AGG-TTATCAAAATTTCATATAA
* * *
22852 AGGTTATC-AAATCTCATAGAG
1 AGGTTATCAAAATTTCATATAA
* * * *
22873 TGATTATCGAAATTTCATAAAGA
1 AGGTTATCAAAATTTCATATA-A
* *
22896 TATGATTATCAAAATTTCATAGT-G
1 -A-GGTTATCAAAATTTCATA-TAA
** * ***
22920 TTGTTATCAAAATTTCAAAGCG
1 AGGTTATCAAAATTTCATATAA
*
22942 AGGTTATCAAAA-TT-ACATAA
1 AGGTTATCAAAATTTCATATAA
* * *
22962 TGCGATTATCAAAATTTCATAGAG
1 AG-G-TTATCAAAATTTCATATAA
* * *
22986 GGGTCAACAAAATTT--TATAA
1 AGGTTATCAAAATTTCATATAA
23006 AGATGTTATCAAAATTTCATA-AA
1 AG--GTTATCAAAATTTCATATAA
23029 GAGGTTATCAA
1 -AGGTTATCAA
23040 GTTTTCAAAA
Statistics
Matches: 169, Mismatches: 44, Indels: 44
0.66 0.17 0.17
Matches are distributed among these distances:
20 15 0.09
21 16 0.09
22 89 0.53
23 8 0.05
24 9 0.05
25 23 0.14
26 5 0.03
27 4 0.02
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATAA
Found at i:22910 original size:25 final size:23
Alignment explanation
Indices: 22855--23070 Score: 107
Period size: 22 Copynumber: 9.7 Consensus size: 23
22845 TGATAGAAGG
* *
22855 TTATC-AAATCTCATAGAG-TGA
1 TTATCAAAATTTCATAAAGTTGA
*
22876 TTATCGAAATTTCATAAAGATATGA
1 TTATCAAAATTTCATAAAG-T-TGA
**
22901 TTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAAAGTTGA
*
22923 TTATCAAAATTTC--AAAG-CGA
1 TTATCAAAATTTCATAAAGTTGA
* * *
22943 GGTTATCAAAATTACATAATG-CGA
1 --TTATCAAAATTTCATAAAGTTGA
* * *
22967 TTATCAAAATTTCATAGAG-GGG
1 TTATCAAAATTTCATAAAGTTGA
* * * *
22989 TCAACAAAATTTTATAAAGATG-
1 TTATCAAAATTTCATAAAGTTGA
* *
23011 TTATCAAAATTTCATAAAG-AGG
1 TTATCAAAATTTCATAAAGTTGA
**
23033 TTATCAAGTTTTCA-AAA-TCTGA
1 TTATCAAAATTTCATAAAGT-TGA
23055 TTA-CAAAAATTTCATA
1 TTATC-AAAATTTCATA
23071 GTGGTATTTT
Statistics
Matches: 150, Mismatches: 30, Indels: 28
0.72 0.14 0.13
Matches are distributed among these distances:
19 1 0.01
20 2 0.01
21 10 0.07
22 107 0.71
23 4 0.03
24 7 0.05
25 19 0.13
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (23 bp):
TTATCAAAATTTCATAAAGTTGA
Found at i:22997 original size:44 final size:44
Alignment explanation
Indices: 22922--23033 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 44
22912 TCATAGTGTT
* * * * *
22922 GTTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATG-C
1 GTTATCAAAATTTCATAGAGAGGTCAACAAAATTACATAAAGAC
* ** *
22965 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAT
1 G-TTATCAAAATTTCATAGAGAGGTCAACAAAATTACATAAAGAC
*
23010 GTTATCAAAATTTCATAAAGAGGT
1 GTTATCAAAATTTCATAGAGAGGT
23034 TATCAAGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
43 1 0.02
44 54 0.96
45 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (44 bp):
GTTATCAAAATTTCATAGAGAGGTCAACAAAATTACATAAAGAC
Found at i:23037 original size:66 final size:66
Alignment explanation
Indices: 22876--23039 Score: 168
Period size: 66 Copynumber: 2.4 Consensus size: 66
22866 CATAGAGTGA
* * ** * * *
22876 TTATCGAAATTTCATAAAGATATGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGC
1 TTATCAAAATTTCATAAAG--A-GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGA
22941 GAGG
63 GAGG
* * * *
22945 TTATCAAAATTACATAATGCGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAA-AGA
1 TTATCAAAATTTCATAAAGAGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCA-AAGAGA
*
23009 TG
65 GG
*
23011 TTATCAAAATTTCATAAAGAGGTTATCAA
1 TTATCAAAATTTCATAAAGAGATTATCAA
23040 GTTTTCAAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
66 60 0.77
67 2 0.03
69 16 0.21
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (66 bp):
TTATCAAAATTTCATAAAGAGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAG
G
Found at i:23179 original size:20 final size:20
Alignment explanation
Indices: 23154--23202 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
23144 ATGGATTAAT
*
23154 CAAAATTTTAGGGAGGATAC
1 CAAAATTTCAGGGAGGATAC
*
23174 CAAAA-TTCAGGGAGGATAT
1 CAAAATTTCAGGGAGGATAC
23193 CAAAATTTCA
1 CAAAATTTCA
23203 TATGAAGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.24
Consensus pattern (20 bp):
CAAAATTTCAGGGAGGATAC
Found at i:23218 original size:22 final size:22
Alignment explanation
Indices: 23190--23749 Score: 153
Period size: 22 Copynumber: 25.7 Consensus size: 22
23180 TCAGGGAGGA
23190 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
23212 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
23234 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
23256 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
23277 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
23300 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
23322 TATCAAAAAATCATAAGAAGCT
1 TATCAAAATTTCATATGAAGGT
*
23344 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
23360 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
23382 TATCAAAATTTTATAGGGAGGCT
1 TATCAAAATTTCATATGAAGG-T
* * * **
23405 TATTAAAATTTTATATAAATATT
1 TATCAAAATTTCATATGAA-GGT
* *
23428 TATCAAAATTTCATA-GCGATGT
1 TATCAAAATTTCATATG-AAGGT
* * *
23450 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
23472 TATCAAAATTTTAAAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* *
23494 TA-CTAACAA-TTCATATGGAGAT
1 TATC-AA-AATTTCATATGAAGGT
** * *
23516 T-TTTAAATTT-TTATAAAGTGGT
1 TATCAAAATTTCATATGAA--GGT
* * *
23538 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
23560 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
23583 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
23605 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
23627 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * *
23649 TAACAAAATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
23671 T-TAAAAAAATT-ATA-AAAGGAT
1 TAT-CAAAATTTCATATGAAGG-T
* ** * **
23692 TCTTGAAATTCCATA-GTACCGT
1 TATCAAAATTTCATATG-AAGGT
*
23714 TATCAAAATTTCATA-GGAGGT
1 TATCAAAATTTCATATGAAGGT
23735 TATCAAAATTTCATA
1 TATCAAAATTTCATA
23750 ATAGGATCAT
Statistics
Matches: 390, Mismatches: 108, Indels: 81
0.67 0.19 0.14
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
20 11 0.03
21 43 0.11
22 252 0.65
23 66 0.17
24 6 0.02
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:23267 original size:66 final size:65
Alignment explanation
Indices: 23185--23354 Score: 173
Period size: 66 Copynumber: 2.6 Consensus size: 65
23175 AAAATTCAGG
* * ** **
23185 GAGGATATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAG-TTTTCAAAATTTCATA
1 GAGGTTATCAAAATTTCATA-GAAGGTTATCAAAATTTCATAG-GGAGATTAACAAAATTTCATA
23249 A-
64 AT
* * *
23250 GAGGGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATA
1 GA-GGTTATCAAAATTTCATAGAAGGT-TATCAAAATTTCATAGGGAGATTAACAAAATTTCATA
23315 AT
64 AT
** *
23317 GAGGTTATCAAAAAATCATAAGAAGCTTATCAAAATTT
1 GAGGTTATCAAAATTTCAT-AGAAGGTTATCAAAATTT
23355 GTAGTTATCA
Statistics
Matches: 85, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
65 8 0.09
66 71 0.84
67 6 0.07
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (65 bp):
GAGGTTATCAAAATTTCATAGAAGGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAT
Found at i:23588 original size:45 final size:45
Alignment explanation
Indices: 23534--23619 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
23524 TTTTATAAAG
* * *
23534 TGGTTATCAATATATCATAT-GGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCAT-TGGGAAGTTATCAAAATCTCATAGTGT
* *
23579 TGGTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATTGGGAAGTTATCAAAATCTCATA
23620 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATTGGGAAGTTATCAAAATCTCATAGTGT
Found at i:23756 original size:65 final size:66
Alignment explanation
Indices: 23581--23756 Score: 157
Period size: 65 Copynumber: 2.7 Consensus size: 66
23571 CATAGTGTTG
* * *
23581 GTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATATTGAGG--TCTTCAAAATTCCTTAGG
1 GTTATCAAAATTTCA-TAGGAAGTTATCAAAATTTCATAAT-AGGATTCTTCAAAATTCCATAGG
*
23644 GAG
64 GAC
* * * * * *
23647 GTTAACAAAATTTCATAAGAAAGTT-TAAAAAAATT-ATAAAAGGATTCTT-GAAATTCCATA-G
1 GTTATCAAAATTTCAT-AGGAAGTTAT-CAAAATTTCATAATAGGATTCTTCAAAATTCCATAGG
*
23708 TACC
64 GA-C
*
23712 GTTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAATAGGAT
1 GTTATCAAAATTTCATAGGAAGTTATCAAAATTTCATAATAGGAT
23757 CATAAAAAAT
Statistics
Matches: 86, Mismatches: 17, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
64 17 0.20
65 39 0.45
66 30 0.35
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (66 bp):
GTTATCAAAATTTCATAGGAAGTTATCAAAATTTCATAATAGGATTCTTCAAAATTCCATAGGGA
C
Found at i:30988 original size:7 final size:7
Alignment explanation
Indices: 30976--31002 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
30966 AAACCCTTCC
30976 TTGTAAG
1 TTGTAAG
30983 TTGTAAG
1 TTGTAAG
30990 TTGTAAG
1 TTGTAAG
30997 TTGTAA
1 TTGTAA
31003 CCAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (7 bp):
TTGTAAG
Found at i:35774 original size:37 final size:37
Alignment explanation
Indices: 35724--35799 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
35714 GGAATTTATC
35724 TTCCTTGAAATTGCGTTAGAACTTGGTGTAAGGGTGT
1 TTCCTTGAAATTGCGTTAGAACTTGGTGTAAGGGTGT
35761 TTCCTTGAAATTGCGTTAGAACTTGGTGTAAGGGTGT
1 TTCCTTGAAATTGCGTTAGAACTTGGTGTAAGGGTGT
35798 TT
1 TT
35800 AAGTAATCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (37 bp):
TTCCTTGAAATTGCGTTAGAACTTGGTGTAAGGGTGT
Found at i:43521 original size:1 final size:1
Alignment explanation
Indices: 43515--43540 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
43505 ATATAAATGC
43515 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
43541 GCGTATACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.