Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014004.1 Corchorus capsularis cultivar CVL-1 contig14025, 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: 31461
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:4439 original size:45 final size:45
Alignment explanation
Indices: 4381--4466 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
4371 AAGACCTCAA
* * *
4381 TATGAAATTTTGATAACTTCCCA-ATGAAATTTTGATAACCAATAC
1 TATGAAATGTTGATAACCT-CCATATGAAATATTGATAACCAATAC
* *
4426 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCA
4467 CGTTATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCATATGAAATATTGATAACCAATAC
Found at i:4460 original size:22 final size:22
Alignment explanation
Indices: 4337--4722 Score: 142
Period size: 22 Copynumber: 17.6 Consensus size: 22
4327 TTAATCTTCT
*
4337 TATGAAATTTTGTTAACCT-CA
1 TATGAAATTTTGATAACCTCCA
* * *
4358 CTAAGGAATTTTGA-AGACCTCAA
1 -TATGAAATTTTGATA-ACCTCCA
*
4381 TATGAAATTTTGATAACTTCCCA
1 TATGAAATTTTGATAACCT-CCA
*
4404 -ATGAAATTTTGATAACCAATAC-
1 TATGAAATTTTGATAACC--TCCA
* *
4426 TATGAGATGTTGATAACCTCCA
1 TATGAAATTTTGATAACCTCCA
* * * **
4448 TATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCTCCA
* * * *
4470 TATAAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCA
4492 TATG-AATTGTT-AGTAA--TCACA
1 TATGAAATT-TTGA-TAACCTC-CA
* *
4513 CTCTGAAATTTTGATAA-ATCACAA
1 -TATGAAATTTTGATAACCTC-C-A
**
4537 TATGAAATGGTGATAACCTCGC-
1 TATGAAATTTTGATAACCTC-CA
*
4559 TATGAAATTTTGATAAATCTTCC-
1 TATGAAATTTTGAT-AA-CCTCCA
* *
4582 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCA
* * * * *
4605 TTTAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTCCA
* * *
4627 TAGGAAATCTTGACAA----C-
1 TATGAAATTTTGATAACCTCCA
* *
4644 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCA
**
4665 TATGATTTTTTGATAACCT-CA
1 TATGAAATTTTGATAACCTCCA
* * * *
4686 TTATGTAATTTTGTTAATCTCCC
1 -TATGAAATTTTGATAACCTCCA
4709 TATGAAATTTTGAT
1 TATGAAATTTTGAT
4723 TTACATACTG
Statistics
Matches: 271, Mismatches: 65, Indels: 56
0.69 0.17 0.14
Matches are distributed among these distances:
16 10 0.04
17 2 0.01
18 1 0.00
20 3 0.01
21 12 0.04
22 160 0.59
23 75 0.28
24 8 0.03
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:4532 original size:23 final size:23
Alignment explanation
Indices: 4506--4598 Score: 82
Period size: 23 Copynumber: 4.1 Consensus size: 23
4496 AATTGTTAGT
*
4506 AATCACACTCTGAAATTTTGATA
1 AATCACACTATGAAATTTTGATA
* **
4529 AATCACAATATGAAATGGTGAT-
1 AATCACACTATGAAATTTTGATA
* * *
4551 AACCTCGCTATGAAATTTTGATA
1 AATCACACTATGAAATTTTGATA
* *
4574 AATCTTC-CTATAAAATTTTGATA
1 AATC-ACACTATGAAATTTTGATA
4597 AA
1 AA
4599 CCTCCCTTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
22 16 0.29
23 38 0.68
24 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (23 bp):
AATCACACTATGAAATTTTGATA
Found at i:4596 original size:45 final size:46
Alignment explanation
Indices: 4516--4620 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 46
4506 AATCACACTC
* *
4516 TGAAATTTTGATAAATCACAATATGAAATGGTGAT-AACCTCGCTA
1 TGAAATTTTGATAAATCACAATATAAAATGGTGATAAACCTCCCTA
* * ** *
4561 TGAAATTTTGATAAATCTTC-CTATAAAATTTTGATAAACCTCCCTT
1 TGAAATTTTGATAAATC-ACAATATAAAATGGTGATAAACCTCCCTA
*
4607 TAAAATTTTGATAA
1 TGAAATTTTGATAA
4621 CTTTCTTAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
45 28 0.56
46 22 0.44
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37
Consensus pattern (46 bp):
TGAAATTTTGATAAATCACAATATAAAATGGTGATAAACCTCCCTA
Found at i:4610 original size:23 final size:23
Alignment explanation
Indices: 4547--4620 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 23
4537 TATGAAATGG
* *
4547 TGAT-AACCTCGCTATGAAATTT
1 TGATAAACCTCCCTATAAAATTT
* *
4569 TGATAAATCTTCCTATAAAATTT
1 TGATAAACCTCCCTATAAAATTT
*
4592 TGATAAACCTCCCTTTAAAATTT
1 TGATAAACCTCCCTATAAAATTT
4615 TGATAA
1 TGATAA
4621 CTTTCTTAGG
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 4 0.09
23 40 0.91
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.39
Consensus pattern (23 bp):
TGATAAACCTCCCTATAAAATTT
Found at i:4767 original size:22 final size:22
Alignment explanation
Indices: 4742--4800 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
4732 GTGAACCTCT
4742 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAAACTAAA
* **
4763 GTATGAAATTTTGATAACCTTCA
1 -TATGAAATTTTGATAAACTAAA
4786 TATGAAATTTTGATA
1 TATGAAATTTTGATA
4801 TCCTCCCTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAAACTAAA
Found at i:4992 original size:22 final size:22
Alignment explanation
Indices: 4901--5095 Score: 103
Period size: 22 Copynumber: 8.8 Consensus size: 22
4891 GAAATACCAC
4901 TATGAAATTTTTG-TAATCACAT
1 TATGAAA-TTTTGATAATCACAT
* * * * *
4923 TTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACAT
* * * * *
4945 TATAAAATTTTGTTGACCGC-T
1 TATGAAATTTTGATAATCACAT
*
4966 CTATGAAATTCTGATAATCACAT
1 -TATGAAATTTTGATAATCACAT
* * * *
4989 TATGTAATTTTGATAACCTCGT
1 TATGAAATTTTGATAATCACAT
* ** *
5011 TTTGAAATTTTGATAAGAACAC
1 TATGAAATTTTGATAATCACAT
* *
5033 TATGAAATTTTGATAATCTTC-C
1 TATGAAATTTTGATAATC-ACAT
5055 TAT-AAATTTTGATAATCTGATC-T
1 TATGAAATTTTGATAATC--A-CAT
5078 CTATGAAATTTTGATAAT
1 -TATGAAATTTTGATAAT
5096 TACTCTATGA
Statistics
Matches: 129, Mismatches: 36, Indels: 13
0.72 0.20 0.07
Matches are distributed among these distances:
21 19 0.15
22 91 0.71
23 3 0.02
24 3 0.02
25 13 0.10
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:5036 original size:66 final size:66
Alignment explanation
Indices: 4898--5050 Score: 175
Period size: 66 Copynumber: 2.3 Consensus size: 66
4888 CCAGAAATAC
* * *
4898 CACTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTTTATAAAATTTTGTTGAC
1 CACTATGAAA-TTTTGATAATCACATTATGAAAATTTGATAACCTCTTTATAAAATTTTGATAAC
**
4962 CG
65 AA
* * * * * *
4964 CTCTATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGTTT-TGAAATTTTGATAAG
1 CACTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-TTTATAAAATTTTGATAAC
5028 AA
65 AA
5030 CACTATGAAATTTTGATAATC
1 CACTATGAAATTTTGATAATC
5051 TTCCTATAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
65 4 0.06
66 65 0.90
67 3 0.04
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (66 bp):
CACTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTTTATAAAATTTTGATAACA
A
Found at i:5063 original size:21 final size:24
Alignment explanation
Indices: 5032--5115 Score: 108
Period size: 21 Copynumber: 3.7 Consensus size: 24
5022 GATAAGAACA
5032 CTATGAAATTTTGATAATCT-TC-
1 CTATGAAATTTTGATAATCTATCT
5054 CTAT-AAATTTTGATAATCTGATCT
1 CTATGAAATTTTGATAATCT-ATCT
5078 CTATGAAATTTTGATAAT-TA-CT
1 CTATGAAATTTTGATAATCTATCT
*
5100 CTATGAGA-TTTGATAA
1 CTATGAAATTTTGATAA
5116 CCTTTTATCA
Statistics
Matches: 57, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
21 23 0.40
22 13 0.23
23 3 0.05
24 5 0.09
25 13 0.23
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (24 bp):
CTATGAAATTTTGATAATCTATCT
Found at i:5104 original size:22 final size:22
Alignment explanation
Indices: 4964--5115 Score: 109
Period size: 22 Copynumber: 6.9 Consensus size: 22
4954 TTGTTGACCG
* *
4964 CTCTATGAAATTCTGATAATCA
1 CTCTATGAAATTTTGATAATTA
* *
4986 CAT-TATGTAATTTTGATAA--C
1 C-TCTATGAAATTTTGATAATTA
* **
5006 CTCGTTTTGAAATTTTGATAAGAA
1 CTC--TATGAAATTTTGATAATTA
* *
5030 CACTATGAAATTTTGATAATCTT
1 CTCTATGAAATTTTGATAAT-TA
5053 C-CTAT-AAATTTTGATAATCTGA
1 CTCTATGAAATTTTGATAAT-T-A
5075 TCTCTATGAAATTTTGATAATTA
1 -CTCTATGAAATTTTGATAATTA
*
5098 CTCTATGAGA-TTTGATAA
1 CTCTATGAAATTTTGATAA
5116 CCTTTTATCA
Statistics
Matches: 106, Mismatches: 13, Indels: 23
0.75 0.09 0.16
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 23 0.22
22 57 0.54
23 4 0.04
24 7 0.07
25 13 0.12
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (22 bp):
CTCTATGAAATTTTGATAATTA
Found at i:5222 original size:22 final size:22
Alignment explanation
Indices: 5170--5293 Score: 76
Period size: 22 Copynumber: 5.7 Consensus size: 22
5160 TAACCTTCAT
* *
5170 ATGAAATTTTGATAACTACACT
1 ATGAAATTTTGATAACCACACC
* *
5192 AT-AAATTTTGATAACCGCTCC
1 ATGAAATTTTGATAACCACACC
* *
5213 ATGAAATTTT-AGTAACCTC-CTA
1 ATGAAATTTTGA-TAACCACAC-C
* * *
5235 ATGAAATTTTGTTAATCACACT
1 ATGAAATTTTGATAACCACACC
* * *
5257 ATGAAATTCTT-ATAACCTCGCT
1 ATGAAATT-TTGATAACCACACC
*
5279 ATGACATTTTGATAA
1 ATGAAATTTTGATAA
5294 TCTCTTTGAT
Statistics
Matches: 80, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
21 21 0.26
22 56 0.70
23 3 0.04
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:5240 original size:65 final size:66
Alignment explanation
Indices: 5149--5273 Score: 161
Period size: 65 Copynumber: 1.9 Consensus size: 66
5139 CTTATGAAAT
*
5149 TGAAACTTTTATAACCTTCATATGAAATTTTGATAA-CTACACTAT-AAATT-TTGATAACCGCT
1 TGAAACTTTTATAACCTCCATATGAAATTTTGATAATC-ACACTATGAAATTCTT-ATAACCGCT
5211 CCA
64 CCA
*
5214 TGAAA-TTTTAGTAACCTCC-TAATGAAATTTTGTTAATCACACTATGAAATTCTTATAACC
1 TGAAACTTTTA-TAACCTCCAT-ATGAAATTTTGATAATCACACTATGAAATTCTTATAACC
5274 TCGCTATGAC
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
64 6 0.11
65 33 0.62
66 12 0.23
67 2 0.04
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.38
Consensus pattern (66 bp):
TGAAACTTTTATAACCTCCATATGAAATTTTGATAATCACACTATGAAATTCTTATAACCGCTCC
A
Found at i:5475 original size:22 final size:22
Alignment explanation
Indices: 5329--5536 Score: 115
Period size: 22 Copynumber: 9.4 Consensus size: 22
5319 TTGTGATAAT
**
5329 TAACCATC-CTATGAAATTTCAA
1 TAACCA-CACTATGAAATTTTGA
* *
5351 TAACCA-ATCTAAGAAATTTTAA
1 TAACCACA-CTATGAAATTTTGA
** *
5373 TAACCTGATCTTATGAAATTAT-A
1 TAACCACA-C-TATGAAATTTTGA
* * *
5396 GTAACTACACTATGAAATATTGG
1 -TAACCACACTATGAAATTTTGA
*
5419 TAACCATACTATGAAATTTTGA
1 TAACCACACTATGAAATTTTGA
** *
5441 TGATTTC-CA-TATGAAATTTTGG
1 T-A-ACCACACTATGAAATTTTGA
*
5463 TAACCACACTATGGAATTTTGA
1 TAACCACACTATGAAATTTTGA
* * *
5485 TAACCTC-CTCATGAAATTATAA
1 TAACCACACT-ATGAAATTTTGA
*
5507 TAACCATC-TTATGAAATTTTGA
1 TAACCA-CACTATGAAATTTTGA
5529 TAACCACA
1 TAACCACA
5537 TAGAGACAAG
Statistics
Matches: 142, Mismatches: 31, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
20 1 0.01
21 6 0.04
22 111 0.78
23 9 0.06
24 15 0.11
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (22 bp):
TAACCACACTATGAAATTTTGA
Found at i:5499 original size:44 final size:44
Alignment explanation
Indices: 5406--5533 Score: 134
Period size: 44 Copynumber: 2.9 Consensus size: 44
5396 GTAACTACAC
* * * **
5406 TATGAAATATTGGTAACCATACTATGAAATTTTGATGATTTCCA
1 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCA
*
5450 TATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTCC-
1 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCA
* ** *
5493 TCATGAAATTATAATAACCATC-TTATGAAATTTTGATAACC
1 T-ATGAAATTTTGGTAACCA-CACTATGAAATTTTGATAACC
5534 ACATAGAGAC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
43 1 0.01
44 69 0.97
45 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCA
Found at i:5731 original size:19 final size:20
Alignment explanation
Indices: 5700--5737 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5690 TATTGACATT
5700 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
5719 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
5738 AATAATAGAA
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:5852 original size:25 final size:24
Alignment explanation
Indices: 5810--5858 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
5800 GTCTAAATTG
* *
5810 AAAATTTTAATAATTTTTAAATAAT
1 AAAATTATAATAAATTTT-AATAAT
*
5835 AAAATTATACTAAATTTTAATAAT
1 AAAATTATAATAAATTTTAATAAT
5859 GGAAATTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AAAATTATAATAAATTTTAATAAT
Found at i:7175 original size:31 final size:31
Alignment explanation
Indices: 7139--7201 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
7129 TAATGGTAAT
*
7139 TTAGAAATATGTTTTAAAAATAAGGGTACAA
1 TTAGAAATATGTTTTAAAAATAAAGGTACAA
7170 TTAGAAATATGTTTTAAAAATAAAGGTACAA
1 TTAGAAATATGTTTTAAAAATAAAGGTACAA
7201 T
1 T
7202 CGGAAAACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.33
Consensus pattern (31 bp):
TTAGAAATATGTTTTAAAAATAAAGGTACAA
Found at i:8394 original size:54 final size:54
Alignment explanation
Indices: 8266--8379 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
8256 CCTATAGGAG
*
8266 GGCAGTGGATGG-TTTCAGTTCCCTTTACGGGTCAATCCGTAGCGCCTTTTGGAA
1 GGCAGTGGATGGTTTTC-GTTCCCTTTACGGGTCAATCCGGAGCGCCTTTTGGAA
* * *
8320 GGCAGTGGATGGTTTTCGTTCCCTTTTA-GGGTCTATCCGGAGGGTCTTTTGGAA
1 GGCAGTGGATGGTTTTCGTTCCC-TTTACGGGTCAATCCGGAGCGCCTTTTGGAA
8374 GGCAGT
1 GGCAGT
8380 TGATTTTTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
54 46 0.85
55 8 0.15
ACGTcount: A:0.15, C:0.19, G:0.32, T:0.33
Consensus pattern (54 bp):
GGCAGTGGATGGTTTTCGTTCCCTTTACGGGTCAATCCGGAGCGCCTTTTGGAA
Found at i:9218 original size:16 final size:16
Alignment explanation
Indices: 9197--9230 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
9187 ACAATTCAGA
9197 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
9213 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
9229 AA
1 AA
9231 ATATTTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:18167 original size:21 final size:21
Alignment explanation
Indices: 18143--18182 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18133 GAAATTGAAT
18143 CTTTGAATTCAGT-TTTTTATG
1 CTTTG-ATTCAGTGTTTTTATG
*
18164 CTTTGATTCTGTGTTTTTA
1 CTTTGATTCAGTGTTTTTA
18183 ATGAGAGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.60
Consensus pattern (21 bp):
CTTTGATTCAGTGTTTTTATG
Found at i:18754 original size:2 final size:2
Alignment explanation
Indices: 18749--18834 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
18739 GGAAAAAAAG
18749 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
18791 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
18833 GA
1 GA
18835 CTTTCCTCCT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19570 original size:12 final size:13
Alignment explanation
Indices: 19542--19574 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
19532 CATGGTCATT
19542 TTTATTTAAATTA
1 TTTATTTAAATTA
19555 TTTATTTAAA-TA
1 TTTATTTAAATTA
19567 TTTATTTA
1 TTTATTTA
19575 TTTTTACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATTTAAATTA
Found at i:19677 original size:26 final size:26
Alignment explanation
Indices: 19625--19674 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
19615 AAATTTTTAG
*
19625 ACATTATTATGAAAATACTATTAAAT
1 ACATTATTATGAAAACACTATTAAAT
19651 ACATTATATAT-AAAACA-TATTAAA
1 ACATTAT-TATGAAAACACTATTAAA
19675 ATAAAATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 12 0.55
27 3 0.14
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36
Consensus pattern (26 bp):
ACATTATTATGAAAACACTATTAAAT
Found at i:19776 original size:30 final size:29
Alignment explanation
Indices: 19726--19791 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 29
19716 TTTATTTTAA
* *
19726 TTATTTTAAATAGCATTAATTTATATATATTT
1 TTATTTCAAATA-CATTAATTTA-ATA-ATAT
19758 TTATTTCAAATA-ATTAATTTAATAATAT
1 TTATTTCAAATACATTAATTTAATAATAT
19786 TTATTT
1 TTATTT
19792 TTAACCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 9 0.28
29 3 0.09
30 9 0.28
32 11 0.34
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (29 bp):
TTATTTCAAATACATTAATTTAATAATAT
Found at i:26156 original size:2 final size:2
Alignment explanation
Indices: 26149--26185 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
26139 TCGAATAAAT
*
26149 TA TA TA TA TA TA TA TA T- TA TA TA TA TC TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26186 ATAACTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26169 original size:17 final size:17
Alignment explanation
Indices: 26147--26182 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
26137 ATTCGAATAA
26147 ATTATATATATATATAT
1 ATTATATATATATATAT
*
26164 ATTATATATATCTATAT
1 ATTATATATATATATAT
26181 AT
1 AT
26183 ATAATAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATATATATATATAT
Found at i:27734 original size:21 final size:21
Alignment explanation
Indices: 27705--27765 Score: 90
Period size: 19 Copynumber: 3.0 Consensus size: 21
27695 CCAAAAAAAA
*
27705 TAGTTTGAATTTAAAATATTT
1 TAGTCTGAATTTAAAATATTT
27726 TAGTCTGAATTT--AATATTT
1 TAGTCTGAATTTAAAATATTT
*
27745 TAGCCTGAATTTAAAATATTT
1 TAGTCTGAATTTAAAATATTT
27766 ATTTACCAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 18 0.50
21 18 0.50
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (21 bp):
TAGTCTGAATTTAAAATATTT
Found at i:29750 original size:108 final size:109
Alignment explanation
Indices: 29636--29928 Score: 421
Period size: 108 Copynumber: 2.7 Consensus size: 109
29626 TAAATTAAAA
** *
29636 TGGTAAAAATAAAAAAATATATATA-ATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAG
1 TGGTAAAAATAAAGTAAT-TATAAAGATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAG
29700 AATAAAATTGTATATTAGAAAAAA-TTTAATATATCCAAAATTTT
65 AATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAAATTTT
*
29744 TGGTAAAAATAAAGTAATTATAAAGATATT-AGATTTAATTAAATGAAAACAGAGTTTTTAGTAG
1 TGGTAAAAATAAAGTAATTATAAAGATATTGA-ATTTAATTAAATGAAAATAGAGTTTTTAGTAG
* *
29808 AATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
65 AATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAAATTTT
* * *
29853 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATT-G----AATTTAATTAAATGAAAATAGAGTTTTTA
29918 GTAGAATAAAA
61 GTAGAATAAAA
29929 CTATAATAGT
Statistics
Matches: 166, Mismatches: 10, Indels: 12
0.88 0.05 0.06
Matches are distributed among these distances:
107 6 0.04
108 76 0.46
109 48 0.29
114 35 0.21
115 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAAATTTT
Done.