Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013777.1 Corchorus olitorius cultivar O-4 contig13810, 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: 11315
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Found at i:1504 original size:13 final size:13
Alignment explanation
Indices: 1468--1505 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1458 TTATAACCTT
*
1468 ATAAATCATAATC
1 ATAAATCATATTC
1481 ATAAATCATATTC
1 ATAAATCATATTC
1494 ATAAATCATATT
1 ATAAATCATATT
1506 TATTATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAAATCATATTC
Found at i:2298 original size:22 final size:21
Alignment explanation
Indices: 2272--2315 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
2262 TAAAAAATAT
*
2272 ATTTTGAAAAATTTAAGTTTAA
1 ATTTTCAAAAATTTAA-TTTAA
* *
2294 ATTTTCCAAAGTTTAATTTAA
1 ATTTTCAAAAATTTAATTTAA
2315 A
1 A
2316 AAAATTGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
ATTTTCAAAAATTTAATTTAA
Found at i:2432 original size:14 final size:15
Alignment explanation
Indices: 2413--2442 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2403 ACGGAAAGAG
2413 TATTTTT-TTTCTTT
1 TATTTTTCTTTCTTT
2427 TATTTTTCTTTCTTT
1 TATTTTTCTTTCTTT
2442 T
1 T
2443 GATTATAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (15 bp):
TATTTTTCTTTCTTT
Found at i:4027 original size:22 final size:22
Alignment explanation
Indices: 3908--4438 Score: 246
Period size: 22 Copynumber: 24.4 Consensus size: 22
3898 ATTACACAAT
* *
3908 TTTTGATGACCTCCTTATAAAA
1 TTTTGATAACCTCCTTATGAAA
*
3930 TTTTAATAACCTTCC-TATGAAA
1 TTTTGATAACC-TCCTTATGAAA
* * *
3952 CTTTAATAACGATACC--ATCG-AA
1 TTTTGATAAC-CT-CCTTAT-GAAA
* *
3974 TTTTGAGAAACCT-TTTAT-AAA
1 TTTTGA-TAACCTCCTTATGAAA
**
3995 TTTTTTTTAACCTCCTTATGAAA
1 -TTTTGATAACCTCCTTATGAAA
* * *
4018 TTTTGATAACCTCCCTAAGCAA
1 TTTTGATAACCTCCTTATGAAA
*
4040 TTTTGAAAACCTCAC-TATGAAA
1 TTTTGATAACCTC-CTTATGAAA
** **
4062 TTTTGATAAATTCCGAATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * *
4084 TTTTGATAATCAATAC-TATGAGA
1 TTTTGATAA-C-CTCCTTATGAAA
* * *
4107 TGTTGATAACCTCCATATGATA
1 TTTTGATAACCTCCTTATGAAA
* * *
4129 TATTGATAACCACGTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * *
4151 ATTTAAGAACCTCCATT-TG-AA
1 TTTTGATAACCTCC-TTATGAAA
* *
4172 TTGTT-AGTAACCACAC-TCTGAAA
1 TT-TTGA-TAACCTC-CTTATGAAA
* *
4195 TTTTGATAATCACAC-TATGAAA
1 TTTTGATAACCTC-CTTATGAAA
* * *
4217 TTGTGATAACCTTGC-TATAAAA
1 TTTTGATAACC-TCCTTATGAAA
*
4239 TTTTGATAAACCTCCTTATAAAA
1 TTTTGAT-AACCTCCTTATGAAA
4262 TTTTGATAACCTCCTTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* *
4284 TCTTGATAA----C-TA-CAAA
1 TTTTGATAACCTCCTTATGAAA
* * ***
4300 CTTTGATAACCTACTTATGTTT
1 TTTTGATAACCTCCTTATGAAA
*
4322 TTTTGATAACCTCATTATGAAA
1 TTTTGATAACCTCCTTATGAAA
* * *
4344 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTCCTTATGAAA
*
4366 TTTTGATAACC-CTATTATGAAA
1 TTTTGATAACCTC-CTTATGAAA
*
4388 TTTTGA-AA-CTAAAC-TATGAAA
1 TTTTGATAACCT--CCTTATGAAA
* *
4409 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACCTCCTTATGAAA
4431 TTTTGATA
1 TTTTGATA
4439 TTCTCCCTGA
Statistics
Matches: 386, Mismatches: 84, Indels: 78
0.70 0.15 0.14
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 1 0.00
20 2 0.01
21 34 0.09
22 281 0.73
23 54 0.14
24 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TTTTGATAACCTCCTTATGAAA
Found at i:4419 original size:43 final size:43
Alignment explanation
Indices: 4322--4436 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 43
4312 ACTTATGTTT
* **
4322 TTTTGATAA-CCTCATTATGAAATTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCCTCATTATGAAATTTTG--AAACTAACTATGAAA
4366 TTTTGATAACCCT-ATTATGAAATTTTGAAACTAAACTATGAAA
1 TTTTGATAACCCTCATTATGAAATTTTGAAACT-AACTATGAAA
*
4409 TTTTGATAACCTTCA-TATGAAATTTTGA
1 TTTTGATAACCCTCATTATGAAATTTTGA
4437 TATTCTCCCT
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
42 4 0.06
43 33 0.52
44 24 0.38
45 3 0.05
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.42
Consensus pattern (43 bp):
TTTTGATAACCCTCATTATGAAATTTTGAAACTAACTATGAAA
Found at i:4614 original size:22 final size:22
Alignment explanation
Indices: 4540--4687 Score: 120
Period size: 22 Copynumber: 6.7 Consensus size: 22
4530 AAATACCACA
* * *
4540 ATGAAATTTTGGTAATCACATTT
1 ATGAAATTTTGATAACCTC-TTT
* *
4563 -TGAAAATTCGATAACCTCTTT
1 ATGAAATTTTGATAACCTCTTT
4584 ATGAAATTTTGATAACCTCTTT
1 ATGAAATTTTGATAACCTCTTT
* * * * *
4606 ATAAAATTTTGTTGACCCCTCT
1 ATGAAATTTTGATAACCTCTTT
*** *
4628 ATGAAATTTTGATATTTTCATT
1 ATGAAATTTTGATAACCTCTTT
* *
4650 ATGTAATTTTGATAACCTCGCTT
1 ATGAAATTTTGATAACCTC-TTT
4673 -TGAAATTTTGATAAC
1 ATGAAATTTTGATAAC
4688 AATACTATAA
Statistics
Matches: 96, Mismatches: 27, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
21 3 0.03
22 91 0.95
23 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCTTT
Found at i:4658 original size:44 final size:44
Alignment explanation
Indices: 4583--4708 Score: 119
Period size: 44 Copynumber: 2.9 Consensus size: 44
4573 ATAACCTCTT
* * * *
4583 TATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCTCATTATAAAATTTTGATAACCCCGC
*** ** *
4627 TATGAAATTTTGATATTTTCATTATGTAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACCTCATTATAAAATTTTGATAACCCCGC
* * *
4671 TTTGAAATTTTGATAACAAT-ACTATAAAATTTTGATAA
1 TATGAAATTTTGATAAC-CTCATTATAAAATTTTGATAA
4709 TCTTCCTATA
Statistics
Matches: 64, Mismatches: 17, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
44 63 0.98
45 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCATTATAAAATTTTGATAACCCCGC
Found at i:4717 original size:22 final size:23
Alignment explanation
Indices: 4675--4757 Score: 82
Period size: 22 Copynumber: 3.7 Consensus size: 23
4665 CCTCGCTTTG
* *
4675 AAATTTTGATAA-CAATACTATA
1 AAATTTCGATAATCAATCCTATA
* *
4697 AAATTTTGATAATC-TTCCTAT-
1 AAATTTCGATAATCAATCCTATA
*
4718 AAATTTCGATAATCCGATCTCTATA
1 AAATTTCGATAAT-CAATC-CTATA
4743 AAATTTCGATAATCA
1 AAATTTCGATAATCA
4758 CTCTATGAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
21 12 0.24
22 18 0.35
23 3 0.06
24 5 0.10
25 13 0.25
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (23 bp):
AAATTTCGATAATCAATCCTATA
Found at i:4770 original size:22 final size:25
Alignment explanation
Indices: 4692--4756 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 25
4682 GATAACAATA
* *
4692 CTATAAAATTTTGATAAT-C-TTC-
1 CTATAAAATTTCGATAATCCGATCT
4714 CTAT-AAATTTCGATAATCCGATCT
1 CTATAAAATTTCGATAATCCGATCT
4738 CTATAAAATTTCGATAATC
1 CTATAAAATTTCGATAATC
4757 ACTCTATGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
21 12 0.32
22 5 0.14
23 2 0.05
24 4 0.11
25 14 0.38
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (25 bp):
CTATAAAATTTCGATAATCCGATCT
Found at i:4854 original size:22 final size:22
Alignment explanation
Indices: 4825--4965 Score: 96
Period size: 22 Copynumber: 6.5 Consensus size: 22
4815 AAATTAAGAC
*
4825 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTACATATGAAA
**
4846 TTTTGATAACC-ACACTAAAAAA
1 TTTTGATAACCTACA-TATGAAA
*
4868 TTTTAATAACC-ACACTATGAAA
1 TTTTGATAACCTACA-TATGAAA
* *
4890 TTTTGATAACCTCCCTATGAAA
1 TTTTGATAACCTACATATGAAA
* * *
4912 TATT-AGTAACCTCCTTATGAAA
1 TTTTGA-TAACCTACATATGAAA
* *
4934 TTTTGTTAACC-ACACTATAAAA
1 TTTTGATAACCTACA-TATGAAA
4956 TTCTT-ATAAC
1 TT-TTGATAAC
4966 TTTCACGTGC
Statistics
Matches: 96, Mismatches: 17, Indels: 13
0.76 0.13 0.10
Matches are distributed among these distances:
21 8 0.08
22 85 0.89
23 3 0.03
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36
Consensus pattern (22 bp):
TTTTGATAACCTACATATGAAA
Found at i:4887 original size:44 final size:44
Alignment explanation
Indices: 4839--4965 Score: 150
Period size: 44 Copynumber: 2.9 Consensus size: 44
4829 ATAACCTTCA
*
4839 TATGAAATTTTGATAACCACACTAAAAAATTTTAATAACCACAC-
1 TATGAAATTTTGATAACCACACTATAAAATTTTAATAACCAC-CT
* * * * * *
4883 TATGAAATTTTGATAACCTCCCTATGAAATATTAGTAACCTCCT
1 TATGAAATTTTGATAACCACACTATAAAATTTTAATAACCACCT
*
4927 TATGAAATTTTGTTAACCACACTATAAAATTCTT-ATAAC
1 TATGAAATTTTGATAACCACACTATAAAATT-TTAATAAC
4966 TTTCACGTGC
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
43 1 0.01
44 65 0.96
45 2 0.03
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACACTATAAAATTTTAATAACCACCT
Found at i:4922 original size:66 final size:65
Alignment explanation
Indices: 4825--4965 Score: 151
Period size: 66 Copynumber: 2.1 Consensus size: 65
4815 AAATTAAGAC
* * *
4825 TTTTATAACCTTCATATGAAATTTTGATAACCACAC-TAAAAAATTTTAATAACCACACTATGAA
1 TTTTATAACCTCCATATGAAATTTAGATAACCAC-CTTAAAAAATTTTAATAACCACACTATAAA
4889 A
65 A
* * ** **
4890 TTTTGATAACCTCCCTATGAAATATTAG-TAACCTCCTTATGAAATTTTGTTAACCACACTATAA
1 TTTT-ATAACCTCCATATGAAAT-TTAGATAACCACCTTAAAAAATTTTAATAACCACACTATAA
4954 AA
64 AA
4956 TTCTTATAAC
1 TT-TTATAAC
4966 TTTCACGTGC
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
65 5 0.08
66 53 0.84
67 5 0.08
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.36
Consensus pattern (65 bp):
TTTTATAACCTCCATATGAAATTTAGATAACCACCTTAAAAAATTTTAATAACCACACTATAAAA
Found at i:5133 original size:22 final size:23
Alignment explanation
Indices: 5094--5140 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
5084 CCTTATAAAA
* *
5094 TTTTAATAACCTTCCTAT-GAAT
1 TTTTAATAACCATACTATCGAAT
*
5116 TTTTAATAACGATACTATCGAAT
1 TTTTAATAACCATACTATCGAAT
5139 TT
1 TT
5141 CGAGAAACCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.34, C:0.15, G:0.06, T:0.45
Consensus pattern (23 bp):
TTTTAATAACCATACTATCGAAT
Found at i:5511 original size:22 final size:22
Alignment explanation
Indices: 5166--5603 Score: 178
Period size: 22 Copynumber: 20.1 Consensus size: 22
5156 ATATTTTTTT
*
5166 TAACCTCCTTATGAAATTTTGA
1 TAACCTCATTATGAAATTTTGA
* *
5188 TAACCTC-TCTAAGGAATTTTGA
1 TAACCTCAT-TATGAAATTTTGA
* * *
5210 AAATCTCACTATGAAATTTTGA
1 TAACCTCATTATGAAATTTTGA
* *
5232 TAACTTCCA-AATGAAATTTTGA
1 TAACCT-CATTATGAAATTTTGA
* * *
5254 T-A-GTCAATACTATGAGATGTTGA
1 TAACCTC-AT--TATGAAATTTTGA
* *
5277 TAACCTCCA-TATGATATATTGA
1 TAACCT-CATTATGAAATTTTGA
* * *
5299 TAACCACGTTATGATAA-TTTAA
1 TAACCTCATTATGA-AATTTTGA
*
5321 GAACCTCCATT-TG-AATTGTT-A
1 TAACCT-CATTATGAAATT-TTGA
* * *
5342 GTAA-TTACACTCTGAAATTTTGA
1 -TAACCT-CATTATGAAATTTTGA
* * * *
5365 TAATCACACTATGAAATTGTGA
1 TAACCTCATTATGAAATTTTGA
*** *
5387 TAACCTTGCTATAAAATTTTGA
1 TAACCTCATTATGAAATTTTGA
* *
5409 TAAACCTCCTTATAAAATTTTGA
1 T-AACCTCATTATGAAATTTTGA
* *
5432 TAACCTCCTTATGAAATCTTGA
1 TAACCTCATTATGAAATTTTGA
* *
5454 TAA---C--TA-CAAACTTTGA
1 TAACCTCATTATGAAATTTTGA
**
5470 TAACCT-ACTTATGATTTTTTGA
1 TAACCTCA-TTATGAAATTTTGA
*
5492 TAACCTCATTATGAAATTTTGT
1 TAACCTCATTATGAAATTTTGA
* **
5514 TAATCTCCCTATGAAATTTTGA
1 TAACCTCATTATGAAATTTTGA
* * *
5536 TCTACAT-ACTATGAAATTTTGA
1 T-AACCTCATTATGAAATTTTGA
5558 TAACC-CTATTATGAAATTTTGA
1 TAACCTC-ATTATGAAATTTTGA
* * *
5580 -AAACTAAACTATGAAATTTTGA
1 TAACCT-CATTATGAAATTTTGA
5602 TA
1 TA
5604 TTCTCCCTGA
Statistics
Matches: 312, Mismatches: 69, Indels: 69
0.69 0.15 0.15
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
19 2 0.01
20 4 0.01
21 16 0.05
22 229 0.73
23 45 0.14
24 1 0.00
25 2 0.01
26 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TAACCTCATTATGAAATTTTGA
Found at i:5549 original size:44 final size:42
Alignment explanation
Indices: 5501--5622 Score: 126
Period size: 44 Copynumber: 2.9 Consensus size: 42
5491 ATAACCTCAT
*
5501 TATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATAC
1 TATGAAATTTTGATAATCTCCCTATGAAATTTTGATCTA-A-AC
* *
5545 TATGAAATTTTGATAA-C-CCTATTATGAAATTTTGAAAACTAAAC
1 TATGAAATTTTGATAATCTCC--CTATGAAATTTTG--ATCTAAAC
*
5589 TATGAAATTTTGATATTCTCCC--TGAAATTTTGAT
1 TATGAAATTTTGATAATCTCCCTATGAAATTTTGAT
5623 TACTCCATAG
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
40 1 0.02
42 12 0.18
43 1 0.02
44 44 0.67
45 2 0.03
46 6 0.09
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (42 bp):
TATGAAATTTTGATAATCTCCCTATGAAATTTTGATCTAAAC
Found at i:5779 original size:22 final size:22
Alignment explanation
Indices: 5704--5873 Score: 123
Period size: 22 Copynumber: 7.7 Consensus size: 22
5694 TAAATACCAC
* * *
5704 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAACCTC-TT
* *
5727 T-TGAAAATTCGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
5748 TATGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
* * * * *
5770 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCTCTT
*** *
5792 TATGAAATTTTGATATTTTCAT
1 TATGAAATTTTGATAACCTCTT
* *
5814 TATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAACCTC-TT
*
5837 T-TGAAATTTTGATAACAATAC--
1 TATGAAATTTTGATAAC-CT-CTT
5858 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
5874 TCTTCCTATA
Statistics
Matches: 114, Mismatches: 28, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
21 4 0.04
22 105 0.92
23 4 0.04
24 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTT
Found at i:5882 original size:22 final size:23
Alignment explanation
Indices: 5791--5896 Score: 89
Period size: 22 Copynumber: 4.8 Consensus size: 23
5781 GTTGACCCCT
*
5791 CTATGAAATTTTGAT-ATTTTCA
1 CTATGAAATTTTGATAATCTTCA
* * * *
5813 TTATGTAATTTTGATAA-CCTCG
1 CTATGAAATTTTGATAATCTTCA
* *
5835 CTTTGAAATTTTGATAA-CAAT-A
1 CTATGAAATTTTGATAATC-TTCA
5857 CTATGAAATTTTGATAATCTTC-
1 CTATGAAATTTTGATAATCTTCA
*
5879 CTAT-AAATTTCGATAATC
1 CTATGAAATTTTGATAATC
5897 CGATCTCTAT
Statistics
Matches: 67, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
21 13 0.19
22 51 0.76
23 3 0.04
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.44
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCTTCA
Found at i:5888 original size:21 final size:23
Alignment explanation
Indices: 5838--5940 Score: 72
Period size: 22 Copynumber: 4.6 Consensus size: 23
5828 AACCTCGCTT
5838 TGAAATTTTGATAA-CAATACTA
1 TGAAATTTTGATAATCAATACTA
* *
5860 TGAAATTTTGATAATC-TTCCTA
1 TGAAATTTTGATAATCAATACTA
* * *
5882 T-AAATTTCGATAATCCGATCTCTA
1 TGAAATTTTGATAAT-CAAT-ACTA
* * *
5906 TAAAATTTCGATAATCACT-CTA
1 TGAAATTTTGATAATCAATACTA
*
5928 TGAGA-TTTGATAA
1 TGAAATTTTGATAA
5941 CCTTTGATAA
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
21 19 0.29
22 26 0.39
23 2 0.03
24 6 0.09
25 13 0.20
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (23 bp):
TGAAATTTTGATAATCAATACTA
Found at i:6018 original size:22 final size:22
Alignment explanation
Indices: 5989--6150 Score: 95
Period size: 22 Copynumber: 7.4 Consensus size: 22
5979 GAATTAAGAC
*
5989 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTACATATGAAA
**
6010 TTTTGATAACC-ACACTAAAAAA
1 TTTTGATAACCTACA-TATGAAA
*
6032 TTTTAATAACC-ACACTATGAAA
1 TTTTGATAACCTACA-TATGAAA
* *
6054 TTTTGATAACCTCCCTATGAAA
1 TTTTGATAACCTACATATGAAA
* * *
6076 TATT-AGTAACCTCCTTATGAAA
1 TTTTGA-TAACCTACATATGAAA
* * *
6098 TTTTGTTAACC-ACACCATAAAA
1 TTTTGATAACCTACA-TATGAAA
* *
6120 TTCTT-ATAACCT-CGCTATGACA
1 TT-TTGATAACCTAC-ATATGAAA
6142 TTTTGATAA
1 TTTTGATAA
6151 TCTCTTTGAT
Statistics
Matches: 109, Mismatches: 22, Indels: 19
0.73 0.15 0.13
Matches are distributed among these distances:
21 10 0.09
22 96 0.88
23 3 0.03
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (22 bp):
TTTTGATAACCTACATATGAAA
Found at i:6051 original size:44 final size:43
Alignment explanation
Indices: 5989--6150 Score: 166
Period size: 44 Copynumber: 3.7 Consensus size: 43
5979 GAATTAAGAC
* *
5989 TTTT-ATAACCTTCATATGAAATTTTGATAACCACACTAAAAAA
1 TTTTAATAACC-TCCTATGAAATTTTGATAACCACACTATAAAA
* * * *
6032 TTTTAATAACCACACTATGAAATTTTGATAACCTCCCTATGAAA
1 TTTTAATAACCTC-CTATGAAATTTTGATAACCACACTATAAAA
* * * *
6076 TATTAGTAACCTCCTTATGAAATTTTGTTAACCACACCATAAAA
1 TTTTAATAACCTCC-TATGAAATTTTGATAACCACACTATAAAA
*
6120 TTCTT-ATAACCTCGCTATGACATTTTGATAA
1 TT-TTAATAACCTC-CTATGAAATTTTGATAA
6151 TCTCTTTGAT
Statistics
Matches: 96, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
43 6 0.06
44 87 0.91
45 3 0.03
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (43 bp):
TTTTAATAACCTCCTATGAAATTTTGATAACCACACTATAAAA
Found at i:6073 original size:66 final size:65
Alignment explanation
Indices: 5989--6150 Score: 166
Period size: 66 Copynumber: 2.5 Consensus size: 65
5979 GAATTAAGAC
* * * *
5989 TTTTATAACCTTCATATGAAATTTTGATAACCACAC-TAAAAAATTTTAATAACCACACTATGAA
1 TTTTATAACCTCCCTATGAAATTTTGATAACCAC-CTTAAAAAATTTTAATAACCACACCATAAA
6053 A
65 A
* * ** **
6054 TTTTGATAACCTCCCTATGAAATATT-AGTAACCTCCTTATGAAATTTTGTTAACCACACCATAA
1 TTTT-ATAACCTCCCTATGAAATTTTGA-TAACCACCTTAAAAAATTTTAATAACCACACCATAA
6118 AA
64 AA
* *
6120 TTCTTATAACCTCGCTATGACATTTTGATAA
1 TT-TTATAACCTCCCTATGAAATTTTGATAA
6151 TCTCTTTGAT
Statistics
Matches: 79, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
65 6 0.08
66 70 0.89
67 3 0.04
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (65 bp):
TTTTATAACCTCCCTATGAAATTTTGATAACCACCTTAAAAAATTTTAATAACCACACCATAAAA
Found at i:6244 original size:24 final size:22
Alignment explanation
Indices: 6194--6379 Score: 76
Period size: 22 Copynumber: 8.4 Consensus size: 22
6184 ACCACACAAT
*
6194 GAAATTTCAATAACCTTCCTAA
1 GAAATTTTAATAACCTTCCTAA
*
6216 AAAATTTTAATAACCTGATCCTAA
1 GAAATTTTAATAACCT--TCCTAA
** * * *
6240 GAAATTTTGGTAACC-ACATTAT
1 GAAATTTTAATAACCTTC-CTAA
* * *
6262 GAAATTTTGATAACCTTCCCAT
1 GAAATTTTAATAACCTTCCTAA
*
6284 GAAATTTTGATAA-CTT-CTATA
1 GAAATTTTAATAACCTTCCTA-A
** * *
6305 TGAAATTTTGGTAACC-ACACTAT
1 -GAAATTTTAATAACCTTC-CTAA
* * *
6328 GGAATTTTGATAACC-TCCTCAT
1 GAAATTTTAATAACCTTCCT-AA
* * * *
6350 GAAATTATAATAACCATCTTAT
1 GAAATTTTAATAACCTTCCTAA
6372 GAAATTTT
1 GAAATTTT
6380 GATTACCACA
Statistics
Matches: 128, Mismatches: 25, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
20 2 0.02
21 6 0.05
22 94 0.73
23 5 0.04
24 21 0.16
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
GAAATTTTAATAACCTTCCTAA
Found at i:6268 original size:22 final size:21
Alignment explanation
Indices: 6240--6388 Score: 118
Period size: 22 Copynumber: 6.8 Consensus size: 21
6230 CTGATCCTAA
*
6240 GAAATTTTGGTAACCACATTAT
1 GAAATTTTGATAACCAC-TTAT
* **
6262 GAAATTTTGATAACCTTCCCAT
1 GAAATTTTGATAACC-ACTTAT
**
6284 GAAATTTTGATAACTTCTATAT
1 GAAATTTTGATAACCACT-TAT
* *
6306 GAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAACCAC-TTAT
* * *
6328 GGAATTTTGATAACCTCCTCAT
1 GAAATTTTGATAACC-ACTTAT
* *
6350 GAAATTATAATAACCATCTTAT
1 GAAATTTTGATAACCA-CTTAT
*
6372 GAAATTTTGATTACCAC
1 GAAATTTTGATAACCAC
6389 ACAGAGACAA
Statistics
Matches: 98, Mismatches: 24, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
21 3 0.03
22 93 0.95
23 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (21 bp):
GAAATTTTGATAACCACTTAT
Found at i:6307 original size:44 final size:43
Alignment explanation
Indices: 6234--6382 Score: 138
Period size: 44 Copynumber: 3.4 Consensus size: 43
6224 AATAACCTGA
* * * *
6234 TCCTAAGAAATTTTGGTAACCACATTATGAAATTTTGATAACC
1 TCCTATGAAATTTTGATAACCTCCTTATGAAATTTTGATAACC
* * *
6277 TTCCCATGAAATTTTGATAA-CTTCTATATGAAATTTTGGTAACC
1 -TCCTATGAAATTTTGATAACCTCCT-TATGAAATTTTGATAACC
* * * * *
6321 ACACTATGGAATTTTGATAACCTCCTCATGAAATTATAATAACC
1 TC-CTATGAAATTTTGATAACCTCCTTATGAAATTTTGATAACC
*
6365 ATCTTATGAAATTTTGAT
1 -TCCTATGAAATTTTGAT
6383 TACCACACAG
Statistics
Matches: 83, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
43 3 0.04
44 75 0.90
45 5 0.06
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (43 bp):
TCCTATGAAATTTTGATAACCTCCTTATGAAATTTTGATAACC
Found at i:6336 original size:66 final size:66
Alignment explanation
Indices: 6183--6390 Score: 215
Period size: 66 Copynumber: 3.1 Consensus size: 66
6173 AAATCGTGAA
* ** ** * * *
6183 AACCACACAATGAAATTTCAATAACCTTCCT-AAAAAATTTTAATAACCTGATCCTAAGAAATTT
1 AACCACACTATGAAATTTTGATAACC-TCCTCATGAAATTATAATAACC--ATCTTATGAAATTT
6247 TGGT
63 TGGT
* * * *
6251 AACCACATTATGAAATTTTGATAACCTTCC-CATGAAATTTTGATAA-CTTCTATATGAAATTTT
1 AACCACACTATGAAATTTTGATAACC-TCCTCATGAAATTATAATAACCATCT-TATGAAATTTT
6314 GGT
64 GGT
* *
6317 AACCACACTATGGAATTTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAATTTTGA
1 AACCACACTATGAAATTTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAATTTTGG
6382 T
66 T
*
6383 TACCACAC
1 AACCACAC
6391 AGAGACAAGA
Statistics
Matches: 119, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
65 5 0.04
66 71 0.60
67 5 0.04
68 38 0.32
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (66 bp):
AACCACACTATGAAATTTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAATTTTGG
T
Found at i:6591 original size:20 final size:20
Alignment explanation
Indices: 6553--6591 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6543 TATTAACATT
6553 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
6573 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
6592 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:7917 original size:22 final size:22
Alignment explanation
Indices: 7872--7970 Score: 69
Period size: 22 Copynumber: 4.5 Consensus size: 22
7862 TTTAATAAAT
* * *
7872 TTTTTTTAACCTTCTTATGAAA
1 TTTTGTTAACCTTCCTAAGAAA
*
7894 TTTTGTTAACCTTCCTAAGGAA
1 TTTTGTTAACCTTCCTAAGAAA
* *
7916 TTTTG-AAGACC-TCACTATGAAA
1 TTTTGTTA-ACCTTC-CTAAGAAA
* *
7938 TTTTGATAA-CTTCCCAATGAAA
1 TTTTGTTAACCTTCCTAA-GAAA
*
7960 TTTTGGTAACC
1 TTTTGTTAACC
7971 AATACTATGA
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
21 6 0.10
22 52 0.87
23 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.41
Consensus pattern (22 bp):
TTTTGTTAACCTTCCTAAGAAA
Found at i:8111 original size:23 final size:24
Alignment explanation
Indices: 8039--8128 Score: 102
Period size: 22 Copynumber: 4.0 Consensus size: 24
8029 TTAGTAATCA
*
8039 CACTCTAAAATTTTGAT-AA--TT
1 CACTATAAAATTTTGATAAACCTT
* *
8060 ACACTATGAAATTGTGAT-AACC-T
1 -CACTATAAAATTTTGATAAACCTT
8083 CACTATAAAATTTTGATAAACCTT
1 CACTATAAAATTTTGATAAACCTT
8107 C-CTATAAAATTTTGATAAACCT
1 CACTATAAAATTTTGATAAACCT
8129 CCTTATGAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
22 31 0.53
23 26 0.44
24 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (24 bp):
CACTATAAAATTTTGATAAACCTT
Found at i:8144 original size:23 final size:23
Alignment explanation
Indices: 8085--8147 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
8075 GATAACCTCA
**
8085 CTATAAAATTTTGATAAACCTTC
1 CTATAAAAGCTTGATAAACCTTC
**
8108 CTATAAAATTTTGATAAACC-TC
1 CTATAAAAGCTTGATAAACCTTC
*
8130 CTTATGAAAGCTTGATAA
1 C-TATAAAAGCTTGATAA
8148 CTACAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 3 0.08
23 33 0.92
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (23 bp):
CTATAAAAGCTTGATAAACCTTC
Done.