Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017290.1 Corchorus olitorius cultivar O-4 contig17323, 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: 56654
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:5203 original size:21 final size:21
Alignment explanation
Indices: 5179--5219 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5169 GGCGGTGGGC
5179 TTCTTCATCTCTACGCTTGAG
1 TTCTTCATCTCTACGCTTGAG
* *
5200 TTCTTCATCTTTGCGCTTGA
1 TTCTTCATCTCTACGCTTGA
5220 TTTCCTCTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.27, G:0.15, T:0.46
Consensus pattern (21 bp):
TTCTTCATCTCTACGCTTGAG
Found at i:8352 original size:29 final size:30
Alignment explanation
Indices: 8293--8352 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
8283 GAAGTTCGTG
* *
8293 TTTGAAGACTCATTGAAAACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAAACTTACTTCAAGA
8324 TTTGAAGA-CATTGAAGAA-TTACTTCAAGA
1 TTTGAAGACCATTGAA-AACTTACTTCAAGA
8353 GGAAAGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 16 0.62
30 2 0.08
31 8 0.31
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (30 bp):
TTTGAAGACCATTGAAAACTTACTTCAAGA
Found at i:9766 original size:15 final size:16
Alignment explanation
Indices: 9733--9772 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
9723 TTGCTTTGTT
9733 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
9749 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
9764 TTGCTTTCT
1 TTGTTTTCT
9773 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:15346 original size:12 final size:12
Alignment explanation
Indices: 15317--15347 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
15307 GAAGTTCGTG
15317 TTTGAAGACTCA
1 TTTGAAGACTCA
15329 -TTGAAGACTCA
1 TTTGAAGACTCA
15340 TTTGAAGA
1 TTTGAAGA
15348 TTTGAAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (12 bp):
TTTGAAGACTCA
Found at i:15376 original size:29 final size:30
Alignment explanation
Indices: 15317--15376 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
15307 GAAGTTCGTG
* * *
15317 TTTGAAGACTCATTGAAGACTCATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATCACTTCAAGA
*
15348 TTTGAAGA-CATTGAAGAATTACTTCAAGA
1 TTTGAAGACCATTGAAGAATCACTTCAAGA
15377 GGAAAGAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 17 0.68
31 8 0.32
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATCACTTCAAGA
Found at i:15840 original size:13 final size:13
Alignment explanation
Indices: 15822--15848 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15812 TTTTAATCTA
15822 ACTATAAATAGCC
1 ACTATAAATAGCC
15835 ACTATAAATAGCC
1 ACTATAAATAGCC
15848 A
1 A
15849 ATTCTTAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.22
Consensus pattern (13 bp):
ACTATAAATAGCC
Found at i:19466 original size:22 final size:22
Alignment explanation
Indices: 19439--20007 Score: 215
Period size: 22 Copynumber: 26.3 Consensus size: 22
19429 ATTAGACTAT
*
19439 TTTTGATGACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
19461 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* ** *
19483 TTTTAATAACGATACTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* * ** *
19505 TTTCGAGAACCTTTTTAT-AGA
1 TTTTGATAACCTTCCTATGAAA
**
19526 TTTTTTTAA-CTT--TATGAAA
1 TTTTGATAACCTTCCTATGAAA
* * * *
19545 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAACCTTCCTATGAAA
19567 TTTTGA-AGACC-TCACTATGAAA
1 TTTTGATA-ACCTTC-CTATGAAA
* *
19589 TTTTGATAA-CTTCCCAAAGAAA
1 TTTTGATAACCTT-CCTATGAAA
** * **
19611 TTTTGATAACCAACATTATGGGA
1 TTTTGATAACCTTC-CTATGAAA
* *
19634 TGTTGATAACC-TCCATATGATA
1 TTTTGATAACCTTCC-TATGAAA
* * *
19656 TATTGATAACC-ACGTTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* * * *
19678 ATTTAAAAATC-TCCATATG-AA
1 TTTTGATAACCTTCC-TATGAAA
* *
19699 TTGTT-AGTAATC-ACACTATGAAA
1 TT-TTGA-TAACCTTC-CTATGAAA
*
19722 TTGTT-ATAATC-TCGCTATGAAA
1 TT-TTGATAACCTTC-CTATGAAA
* *
19744 TTTTGATAAACCTTTCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
* *
19767 TTTTGATAAACCTCCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
19790 TTTTGATAACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
* *
19812 TCTTGATAA-----CTA-CAAA
1 TTTTGATAACCTTCCTATGAAA
* **
19828 TTTTGATAACCTCCCTATGATT
1 TTTTGATAACCTTCCTATGAAA
*
19850 TTTTGATAACC-TCATTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* * *
19872 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
19894 -TTTGATCTACATT-CTATGAAA
1 TTTTGAT-AACCTTCCTATGAAA
* * *
19915 TTTTGATAACCCTCTTATGGAA
1 TTTTGATAACCTTCCTATGAAA
* * ** *
19937 TTTAGA-AAACTAAACTATAAAA
1 TTTTGATAACCT-TCCTATGAAA
*
19959 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
19981 TTTTGATATCCTCCCTA--AAA
1 TTTTGATAACCTTCCTATGAAA
20001 TTTTGAT
1 TTTTGAT
20008 TACTCCACAA
Statistics
Matches: 407, Mismatches: 104, Indels: 74
0.70 0.18 0.13
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
18 4 0.01
19 10 0.02
20 15 0.04
21 41 0.10
22 252 0.62
23 71 0.17
24 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:20003 original size:20 final size:20
Alignment explanation
Indices: 19953--20075 Score: 67
Period size: 22 Copynumber: 6.0 Consensus size: 20
19943 AAACTAAACT
*
19953 ATAAAATTTTGATAACCTTC
1 ATAAAATTTTGATAACCTCC
*
19973 ATATGAAATTTTGATATCCTCC
1 ATA--AAATTTTGATAACCTCC
* *
19995 CTAAAATTTTGATTA-CTCCAC
1 ATAAAATTTTGATAACCT-C-C
* *
20016 AATAAAAGTTTAATAACCTTCC
1 -ATAAAATTTTGATAACC-TCC
* *
20038 -T--AA-TTTGGTAACCATACT
1 ATAAAATTTTGATAACC-T-CC
20056 ATAAAATTTTGATAACCTCC
1 ATAAAATTTTGATAACCTCC
20076 CCAGAAATAA
Statistics
Matches: 76, Mismatches: 15, Indels: 24
0.66 0.13 0.21
Matches are distributed among these distances:
17 9 0.12
18 3 0.04
19 3 0.04
20 16 0.21
21 4 0.05
22 38 0.50
23 2 0.03
24 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (20 bp):
ATAAAATTTTGATAACCTCC
Found at i:20138 original size:22 final size:22
Alignment explanation
Indices: 20113--20240 Score: 109
Period size: 22 Copynumber: 5.8 Consensus size: 22
20103 AATCACATTT
20113 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
20135 TG-AAATTTCGATAACCTCTTTA
1 TGAAAATTT-GATAACCTCTTTA
*
20157 TG-AAATTTCGATAACCTCTCTA
1 TGAAAATTT-GATAACCTCTTTA
* * * *
20179 T-AAAATTTTGTTGACCCCTCTA
1 TGAAAA-TTTGATAACCTCTTTA
* * * *
20201 TGAAATTTTGATAATCACATTA
1 TGAAAATTTGATAACCTCTTTA
* *
20223 TGTAATTTTGATAACCTC
1 TGAAAATTTGATAACCTC
20241 GCTTTGAAAT
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
21 6 0.07
22 76 0.86
23 6 0.07
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:20139 original size:44 final size:44
Alignment explanation
Indices: 20088--20238 Score: 128
Period size: 44 Copynumber: 3.4 Consensus size: 44
20078 AGAAATAACA
* *
20088 CTATGAAATTTTGGTAATCACATTT-TGAAAATTT-GATAACCTCT
1 CTATGAAATTTTGATAACCAC-TTTATG-AAATTTCGATAACCTCT
* * *
20132 TTATGAAATTTCGATAACCTCTTTATGAAATTTCGATAACCTCT
1 CTATGAAATTTTGATAACCACTTTATGAAATTTCGATAACCTCT
* * * * * * * *
20176 CTATAAAATTTTGTTGACCCCTCTATGAAATTTTGATAATCACAT
1 CTATGAAATTTTGATAACCACTTTATGAAATTTCGATAACCTC-T
*
20221 -TATGTAATTTTGATAACC
1 CTATGAAATTTTGATAACC
20239 TCGCTTTGAA
Statistics
Matches: 85, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
43 9 0.11
44 75 0.88
45 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCACTTTATGAAATTTCGATAACCTCT
Found at i:20251 original size:22 final size:21
Alignment explanation
Indices: 20111--20298 Score: 101
Period size: 22 Copynumber: 8.6 Consensus size: 21
20101 GTAATCACAT
* *
20111 TTTGAAAATTTGATAACCTCT
1 TTTGAAATTTTGATAACCTCC
* *
20132 TTATGAAATTTCGATAACCTCT
1 TT-TGAAATTTTGATAACCTCC
*
20154 TTATGAAATTTCGATAACCTCTC
1 TT-TGAAATTTTGATAACCTC-C
* * * *
20177 TATAAAATTTTGTTGACC-CC
1 TTTGAAATTTTGATAACCTCC
* * *
20197 TCTATGAAATTTTGATAATCACA
1 T-T-TGAAATTTTGATAACCTCC
*
20220 TTATGTAATTTTGATAACCTCGC
1 TT-TGAAATTTTGATAACCTC-C
* * **
20243 TTTGAAATTTTAAGAACAACAC
1 TTTGAAATTTTGATAACCTC-C
* * *
20265 TATAAAATTTTGATAATCTTCC
1 TTTGAAATTTTGATAA-CCTCC
20287 TTT-AAATTTTGA
1 TTTGAAATTTTGA
20299 AAATCCGATC
Statistics
Matches: 129, Mismatches: 31, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
20 2 0.02
21 12 0.09
22 108 0.84
23 7 0.05
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.41
Consensus pattern (21 bp):
TTTGAAATTTTGATAACCTCC
Found at i:20416 original size:22 final size:22
Alignment explanation
Indices: 20401--20516 Score: 103
Period size: 22 Copynumber: 5.3 Consensus size: 22
20391 ATAACCTTCA
*
20401 TATGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCACAC
**
20423 TAAAAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
* *
20445 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
* * *
20467 CATGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCACAC
*
20488 T-TGTAAAATTTTGTTAACCACAC
1 TATG--AAATTTTGATAACCACAC
20511 TATGAA
1 TATGAA
20517 GTTCTTATAA
Statistics
Matches: 75, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
20 2 0.03
21 2 0.03
22 67 0.89
23 2 0.03
24 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.34
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:20664 original size:22 final size:22
Alignment explanation
Indices: 20566--20738 Score: 129
Period size: 22 Copynumber: 7.8 Consensus size: 22
20556 GATAACCTTT
* *
20566 CTATAAAATTGTGATAACCACA
1 CTATGAAATTTTGATAACCACA
* ** *
20588 CTACGAAATTTCAATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
* * *
20610 CTAAGAAATTTTAATAACCAAA
1 CTATGAAATTTTGATAACCACA
* *
20632 TCCTATAAAATTTTGGTAACCACA
1 --CTATGAAATTTTGATAACCACA
20656 CTATGAAATTTTGATAACCATC-
1 CTATGAAATTTTGATAACCA-CA
*
20678 CCATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
* *
20701 -TATAAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
20722 CTATGGAATTTTGATAA
1 CTATGAAATTTTGATAA
20739 TCTTCTCATG
Statistics
Matches: 117, Mismatches: 24, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 94 0.80
23 2 0.02
24 18 0.15
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:20709 original size:44 final size:44
Alignment explanation
Indices: 20553--20783 Score: 177
Period size: 44 Copynumber: 5.2 Consensus size: 44
20543 TCATAATCTC
* * *
20553 TTTGATAACCTTTCTATAAAATTGTGATAACCA-CACTACGAAAT
1 TTTGATAACCTTCCTATAAAATTTTGATAACCATC-CTATGAAAT
** * *
20597 TTCAATAACCTTCCTA-AGAAATTTTAATAACCAAATCCTATAAAAT
1 TTTGATAACCTTCCTATA-AAATTTTGATAACC--ATCCTATGAAAT
* * * *
20643 TTTGGTAACC-ACACTATGAAATTTTGATAACCATCCCATGAAAT
1 TTTGATAACCTTC-CTATAAAATTTTGATAACCATCCTATGAAAT
* *
20687 TTTGATAA-CTTCCATATAAAATTTTGGTAACCA-CACTATGGAAT
1 TTTGATAACCTTCC-TATAAAATTTTGATAACCATC-CTATGAAAT
* * * * *
20731 TTTGATAATCTT-CTCATGAAATTATAATAACCATCTTATGAAAT
1 TTTGATAACCTTCCT-ATAAAATTTTGATAACCATCCTATGAAAT
*
20775 TCTGATAAC
1 TTTGATAAC
20784 GTCATAGAGA
Statistics
Matches: 146, Mismatches: 29, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
43 5 0.03
44 104 0.71
45 5 0.03
46 31 0.21
47 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (44 bp):
TTTGATAACCTTCCTATAAAATTTTGATAACCATCCTATGAAAT
Found at i:20726 original size:66 final size:66
Alignment explanation
Indices: 20553--20762 Score: 242
Period size: 66 Copynumber: 3.2 Consensus size: 66
20543 TCATAATCTC
* * * * ** * *
20553 TTTGATAACCTTTCTATAAAATTGTGATAACCACACTACGAAATTTCAATAACCTTCCTAAGAAA
1 TTTGATAACCTTCCTATAAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAA
20618 T
66 T
* * *
20619 TTTAATAACCAAATCCTATAAAATTTTGGTAACCACACTATGAAATTTTGATAACCATCCCATGA
1 TTTGATAACC--TTCCTATAAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGA
20684 AAT
64 AAT
* * *
20687 TTTGATAA-CTTCCATATAAAATTTTGGTAACCACACTATGGAATTTTGATAATCTTCTCATGAA
1 TTTGATAACCTTCC-TATAAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAA
20751 AT
65 AT
* *
20753 TATAATAACC
1 TTTGATAACC
20763 ATCTTATGAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
65 3 0.02
66 63 0.52
67 2 0.02
68 53 0.44
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (66 bp):
TTTGATAACCTTCCTATAAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAA
T
Found at i:20753 original size:22 final size:21
Alignment explanation
Indices: 20658--20783 Score: 76
Period size: 22 Copynumber: 5.8 Consensus size: 21
20648 TAACCACACT
*
20658 ATGAAATTTTGATAACCATCCC
1 ATGAAATTTTGATAA-CATCTC
*
20680 ATGAAATTTTGATAACTTC-C
1 ATGAAATTTTGATAACATCTC
* * *
20700 ATATAAAATTTTGGTAACCA-CAC
1 --ATGAAATTTTGATAA-CATCTC
* *
20723 TATGGAATTTTGATAATCTTCTC
1 -ATGAAATTTTGATAA-CATCTC
* * *
20746 ATGAAATTATAATAACCATCTT
1 ATGAAATTTTGATAA-CATCTC
*
20768 ATGAAATTCTGATAAC
1 ATGAAATTTTGATAAC
20784 GTCATAGAGA
Statistics
Matches: 81, Mismatches: 18, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.01
21 4 0.05
22 72 0.89
23 4 0.05
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (21 bp):
ATGAAATTTTGATAACATCTC
Found at i:22008 original size:2 final size:2
Alignment explanation
Indices: 22001--22054 Score: 65
Period size: 2 Copynumber: 26.5 Consensus size: 2
21991 TTCATACTTT
* *
22001 TA TA TA TA GTA TA AA GTA TA TA TA TA TA TA -A AA 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 TA TA
22044 TA TA TA TA TA T
1 TA TA TA TA TA T
22055 CAGGAGAGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.02
2 42 0.91
3 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:22032 original size:17 final size:17
Alignment explanation
Indices: 22001--22047 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
21991 TTCATACTTT
*
22001 TATATATAGTATAAAGTA
1 TATATATA-TATAAAATA
22019 TATATATATATAAAATA
1 TATATATATATAAAATA
22036 TATATATATATA
1 TATATATATATA
22048 TATATATCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 20 0.71
18 8 0.29
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (17 bp):
TATATATATATAAAATA
Found at i:23094 original size:16 final size:16
Alignment explanation
Indices: 23075--23173 Score: 83
Period size: 16 Copynumber: 6.2 Consensus size: 16
23065 TTCAGATTCA
*
23075 GGTTCGGGTTTTTTCG
1 GGTTCGAGTTTTTTCG
* *
23091 GGTTCGGGTTTTATCG
1 GGTTCGAGTTTTTTCG
* *
23107 GGTTC-AGATTTTTCA
1 GGTTCGAGTTTTTTCG
* * *
23122 GGTTCTAATTTTATCG
1 GGTTCGAGTTTTTTCG
* *
23138 GGTTTGAGCTTTTTCG
1 GGTTCGAGTTTTTTCG
* *
23154 GGTTCGGGTTTTTTTG
1 GGTTCGAGTTTTTTCG
23170 GGTT
1 GGTT
23174 TTGGTTCGGG
Statistics
Matches: 64, Mismatches: 18, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
15 11 0.17
16 53 0.83
ACGTcount: A:0.08, C:0.11, G:0.31, T:0.49
Consensus pattern (16 bp):
GGTTCGAGTTTTTTCG
Found at i:23119 original size:31 final size:32
Alignment explanation
Indices: 23084--23174 Score: 103
Period size: 32 Copynumber: 2.9 Consensus size: 32
23074 AGGTTCGGGT
23084 TTTTTCGGGTTCGGGTTTTATCGGG-TTCAGA
1 TTTTTCGGGTTCGGGTTTTATCGGGTTTCAGA
* *** * *
23115 TTTTTCAGGTTCTAATTTTATCGGGTTTGAGC
1 TTTTTCGGGTTCGGGTTTTATCGGGTTTCAGA
* *
23147 TTTTTCGGGTTCGGGTTTTTTTGGGTTT
1 TTTTTCGGGTTCGGGTTTTATCGGGTTT
23175 TGGTTCGGGC
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 21 0.45
32 26 0.55
ACGTcount: A:0.09, C:0.11, G:0.29, T:0.52
Consensus pattern (32 bp):
TTTTTCGGGTTCGGGTTTTATCGGGTTTCAGA
Found at i:25507 original size:26 final size:26
Alignment explanation
Indices: 25477--25528 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
25467 ATGGAATTAT
*
25477 ACTGGTTCGATTGAAGATAAAGATAA
1 ACTGGTTCGATTGAAAATAAAGATAA
25503 ACTGGTTCGATTGAAAATAAAGATAA
1 ACTGGTTCGATTGAAAATAAAGATAA
25529 GTGATGAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (26 bp):
ACTGGTTCGATTGAAAATAAAGATAA
Found at i:30229 original size:3 final size:3
Alignment explanation
Indices: 30221--30268 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
30211 TATACTTCAG
*
30221 TTA TTA TTA TTA TATA TTA TTA TTA TTA TTA TTA CTA TTA TTA -TA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30266 TTA
1 TTA
30269 ATATAATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:30282 original size:12 final size:11
Alignment explanation
Indices: 30262--30305 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 11
30252 TTACTATTAT
30262 TATAT-TAATA
1 TATATATAATA
30272 TAATATATAATA
1 T-ATATATAATA
30284 T-TATATAGATA
1 TATATATA-ATA
30295 TATATATAATA
1 TATATATAATA
30306 CTAAATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.23
11 11 0.37
12 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TATATATAATA
Found at i:30286 original size:18 final size:18
Alignment explanation
Indices: 30263--30298 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
30253 TACTATTATT
30263 ATATTAATATA-ATATATA
1 ATATT-ATATAGATATATA
30281 ATATTATATAGATATATA
1 ATATTATATAGATATATA
30299 TATAATACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
ATATTATATAGATATATA
Found at i:37938 original size:77 final size:79
Alignment explanation
Indices: 37755--37961 Score: 310
Period size: 77 Copynumber: 2.6 Consensus size: 79
37745 TTGAAGAAGC
* * * *
37755 AAACAAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCAACCTTGGTGTACC
1 AAACAAAACGATCGTCTCCTTAGAGACTTTCGTCACAAACGGCCGAACACCAACCTTGGTGTACC
37820 CCGTAAAAAAAACA
66 CCGTAAAAAAAACA
* * * *
37834 AAATAGAACGATCGTCTCCTTAGAGACTTTCGTCGCAAACGGCCGAGCACCAACCTTGGTGT-CC
1 AAACAAAACGATCGTCTCCTTAGAGACTTTCGTCACAAACGGCCGAACACCAACCTTGGTGTACC
*
37898 CCGT-AAACAAACA
66 CCGTAAAAAAAACA
*
37911 AAACAAAACGATCGTCTCCTTAGAGACTTTCGTCACAAACGGTCGAACACC
1 AAACAAAACGATCGTCTCCTTAGAGACTTTCGTCACAAACGGCCGAACACC
37962 GGCCCAGGTG
Statistics
Matches: 114, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
77 54 0.47
78 6 0.05
79 54 0.47
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.19
Consensus pattern (79 bp):
AAACAAAACGATCGTCTCCTTAGAGACTTTCGTCACAAACGGCCGAACACCAACCTTGGTGTACC
CCGTAAAAAAAACA
Found at i:37990 original size:77 final size:76
Alignment explanation
Indices: 37755--37961 Score: 297
Period size: 79 Copynumber: 2.7 Consensus size: 76
37745 TTGAAGAAGC
* * * *
37755 AAACAAAACGATCGTCTCCTTTGAGACTCTCGTTACGAACGGCCGAACACCAACCTTGGTGTACC
1 AAACAAAACGATCGTCTCCTTAGAGACTTTCGTCACAAACGGCCGAACACCAACCTTGGTGT-CC
37820 CCGTAAAAAAAACA
65 CCGT--AAAAAACA
* * * *
37834 AAATAGAACGATCGTCTCCTTAGAGACTTTCGTCGCAAACGGCCGAGCACCAACCTTGGTGTCCC
1 AAACAAAACGATCGTCTCCTTAGAGACTTTCGTCACAAACGGCCGAACACCAACCTTGGTGTCCC
37899 CGTAAACAAACA
66 CGTAAA-AAACA
*
37911 AAACAAAACGATCGTCTCCTTAGAGACTTTCGTCACAAACGGTCGAACACC
1 AAACAAAACGATCGTCTCCTTAGAGACTTTCGTCACAAACGGCCGAACACC
37962 GGCCCAGGTG
Statistics
Matches: 114, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
76 3 0.03
77 51 0.45
78 6 0.05
79 54 0.47
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.19
Consensus pattern (76 bp):
AAACAAAACGATCGTCTCCTTAGAGACTTTCGTCACAAACGGCCGAACACCAACCTTGGTGTCCC
CGTAAAAAACA
Found at i:47958 original size:29 final size:28
Alignment explanation
Indices: 47882--48047 Score: 154
Period size: 29 Copynumber: 5.7 Consensus size: 28
47872 AGGATCACCT
* *
47882 AGGGGCATTTTGGTCA-TTTTCAAAAAATCC
1 AGGGGCATTTTGGTCATTTTTC---ACATTC
47912 AGGGGCATTTTGGTCATTTTTCACATTC
1 AGGGGCATTTTGGTCATTTTTCACATTC
47940 AGGGAGCATTTTGGTCATTTTTGCACATTC
1 AGGG-GCATTTTGGTCATTTTT-CACATTC
* * **
47970 AGTGGCATTTTGGTCATTTCTGCATGTTC
1 AGGGGCATTTTGGTCATTT-TTCACATTC
* ** *
47999 AGGGGTATTTTGGTTGTTTGTTTACATTC
1 AGGGGCATTTTGGTCATTT-TTCACATTC
* *
48028 GGGGGCATTTTGGTCGTTTT
1 AGGGGCATTTTGGTCATTTT
48048 CTTAATTGAT
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
28 9 0.08
29 73 0.64
30 27 0.24
31 5 0.04
ACGTcount: A:0.17, C:0.14, G:0.25, T:0.43
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTTCACATTC
Found at i:49309 original size:27 final size:27
Alignment explanation
Indices: 49279--49335 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
49269 GGCTCTTGAG
49279 ACACGCTTCAGATTTTTGCTCACAACC
1 ACACGCTTCAGATTTTTGCTCACAACC
49306 ACACGCTTCAGATTTTTGCTCACAACC
1 ACACGCTTCAGATTTTTGCTCACAACC
49333 ACA
1 ACA
49336 GTGATACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.33, G:0.11, T:0.28
Consensus pattern (27 bp):
ACACGCTTCAGATTTTTGCTCACAACC
Found at i:49585 original size:20 final size:21
Alignment explanation
Indices: 49548--49586 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
49538 AGAGACCCTC
49548 TTCATCACACACATCGCACAT
1 TTCATCACACACATCGCACAT
49569 TTCA-CACACAACA-CGCAC
1 TTCATCACAC-ACATCGCAC
49587 TGTTGACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.36, C:0.41, G:0.05, T:0.18
Consensus pattern (21 bp):
TTCATCACACACATCGCACAT
Found at i:53709 original size:28 final size:28
Alignment explanation
Indices: 53677--53733 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
53667 ACATCGTCAG
53677 GGGAACATTTTTGGAAGCATCAAGTGCA
1 GGGAACATTTTTGGAAGCATCAAGTGCA
53705 GGGAACATTTTTGGAAGCATCAAGTGCA
1 GGGAACATTTTTGGAAGCATCAAGTGCA
53733 G
1 G
53734 CATTGAGGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.25
Consensus pattern (28 bp):
GGGAACATTTTTGGAAGCATCAAGTGCA
Found at i:55456 original size:11 final size:12
Alignment explanation
Indices: 55429--55471 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
55419 GCAACTAACC
55429 AAAAAAGAAATG
1 AAAAAAGAAATG
*
55441 AAAAATGAAATG
1 AAAAAAGAAATG
55453 AAAAAATG--ATG
1 AAAAAA-GAAATG
55464 AAAAAAGA
1 AAAAAAGA
55472 GAAATAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 1 0.04
11 9 0.33
12 16 0.59
13 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (12 bp):
AAAAAAGAAATG
Found at i:55457 original size:13 final size:13
Alignment explanation
Indices: 55429--55469 Score: 54
Period size: 11 Copynumber: 3.5 Consensus size: 13
55419 GCAACTAACC
55429 AAAAAA-GAAATG
1 AAAAAATGAAATG
55441 -AAAAATGAAATG
1 AAAAAATGAAATG
55453 AAAAAATG--ATG
1 AAAAAATGAAATG
55464 AAAAAA
1 AAAAAA
55470 GAGAAATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 14 0.52
12 6 0.22
13 7 0.26
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (13 bp):
AAAAAATGAAATG
Done.