Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020797.1 Corchorus olitorius cultivar O-4 contig20830, 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: 53903
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Found at i:662 original size:21 final size:22
Alignment explanation
Indices: 617--659 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
607 TTTTAATATC
617 CTCATACTTAAAAAAAAAAAAA
1 CTCATACTTAAAAAAAAAAAAA
639 CTCATACTTAAAAAAAAAAAA
1 CTCATACTTAAAAAAAAAAAA
660 CTCTTCCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (22 bp):
CTCATACTTAAAAAAAAAAAAA
Found at i:1600 original size:25 final size:23
Alignment explanation
Indices: 1572--1653 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 23
1562 TATCTTAGAT
1572 ATAATTATATATTATTAAATAA-ATA
1 ATAA-TATATATT-TTAAATAATA-A
1597 ATAA-ATATATTTTAAATAATAA
1 ATAATATATATTTTAAATAATAA
* * **
1619 ATAAT-GA-GTTCAAAATAAATAA
1 ATAATATATATTTTAAAT-AATAA
1641 ATAATATATATTT
1 ATAATATATATTT
1654 AATTACTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
21 6 0.13
22 24 0.53
23 9 0.20
24 2 0.04
25 4 0.09
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (23 bp):
ATAATATATATTTTAAATAATAA
Found at i:5524 original size:54 final size:54
Alignment explanation
Indices: 5442--5547 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 54
5432 TAGATGTACC
* *
5442 GTGCCTGAACCGTGAGGTCCTGGATTCAAGTGTCACGAAATTAATAAGTGTATT
1 GTGCCTGAACCGTGAGGTCCGGGATTCAAGTCTCACGAAATTAATAAGTGTATT
* * *
5496 GTGCCTGAACCGTGAGGTCCGGGATTCAAGTCTCATGAAATTGATAGGTGTA
1 GTGCCTGAACCGTGAGGTCCGGGATTCAAGTCTCACGAAATTAATAAGTGTA
5548 CCTCAAGTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (54 bp):
GTGCCTGAACCGTGAGGTCCGGGATTCAAGTCTCACGAAATTAATAAGTGTATT
Found at i:5564 original size:29 final size:29
Alignment explanation
Indices: 5521--5578 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
5511 GGTCCGGGAT
* *
5521 TCAAGTCTCATGAAATTGATAGGTGTACC
1 TCAAGTCTCACGAAATTGATAAGTGTACC
5550 TCAAGTCTCACGAAATTGATAAGTGTACC
1 TCAAGTCTCACGAAATTGATAAGTGTACC
5579 ATGCTTGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (29 bp):
TCAAGTCTCACGAAATTGATAAGTGTACC
Found at i:10991 original size:12 final size:12
Alignment explanation
Indices: 10974--11002 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
10964 TGGTTGACAC
10974 CTGAAGTTAGGG
1 CTGAAGTTAGGG
10986 CTGAAGTTAGGG
1 CTGAAGTTAGGG
10998 CTGAA
1 CTGAA
11003 TGTGATGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.38, T:0.24
Consensus pattern (12 bp):
CTGAAGTTAGGG
Found at i:12841 original size:21 final size:21
Alignment explanation
Indices: 12815--12857 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12805 TAGTTCAGAA
*
12815 CATGAATGTTATTACTTTGAT
1 CATGAATGTTATTAATTTGAT
*
12836 CATGAATGTTGTTAATTTGAT
1 CATGAATGTTATTAATTTGAT
12857 C
1 C
12858 TCCCTGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (21 bp):
CATGAATGTTATTAATTTGAT
Found at i:13042 original size:9 final size:9
Alignment explanation
Indices: 13024--13055 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
13014 TACGAATTCA
13024 AGAAGAAAG
1 AGAAGAAAG
*
13033 AGAAGGAAG
1 AGAAGAAAG
13042 AGAAGAAAG
1 AGAAGAAAG
13051 AGAAG
1 AGAAG
13056 GGGAAGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (9 bp):
AGAAGAAAG
Found at i:13663 original size:50 final size:50
Alignment explanation
Indices: 13588--13689 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
13578 GTTGTACAAG
13588 TACGGTTCTCCTAACAGTCATGACGCCATCTTCAATCTTCTACTTCTCTT
1 TACGGTTCTCCTAACAGTCATGACGCCATCTTCAATCTTCTACTTCTCTT
*
13638 TACGGTTCTCCTGACAGTCATGACGCCATCTTCAATCTTCTACTTCTCTT
1 TACGGTTCTCCTAACAGTCATGACGCCATCTTCAATCTTCTACTTCTCTT
13688 TA
1 TA
13690 GTTCCGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.20, C:0.31, G:0.11, T:0.38
Consensus pattern (50 bp):
TACGGTTCTCCTAACAGTCATGACGCCATCTTCAATCTTCTACTTCTCTT
Found at i:13995 original size:22 final size:22
Alignment explanation
Indices: 13970--14520 Score: 195
Period size: 22 Copynumber: 25.3 Consensus size: 22
13960 ATTACGCTAT
*
13970 TTTTGATGACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
13992 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* ** * *
14014 TTTTAATAACGATACTATGTAA
1 TTTTGATAACCTTCCTATGAAA
* * * **
14036 TTTCGA-GATCTTTTTAT-AAA
1 TTTTGATAACCTTCCTATGAAA
** **
14056 TTTTTTTAACCTTTTTATGAAA
1 TTTTGATAACCTTCCTATGAAA
** * * *
14078 TTTTTTTAACCTCCCTAAGGAA
1 TTTTGATAACCTTCCTATGAAA
**
14100 TTTT-A-AAGATTTCACTATGAAA
1 TTTTGATAA-CCTTC-CTATGAAA
*
14122 TTTTGATAA-CTTCCCAATGAAA
1 TTTTGATAACCTT-CCTATGAAA
*
14144 TTTTGATAA-CTGAT-CTATGAGA
1 TTTTGATAACCT--TCCTATGAAA
* * **
14166 TGTTGATAA-CTTACATATG-GT
1 TTTTGATAACCTT-CCTATGAAA
* *
14187 TTATTGATAACC-ACATTATGAAAA
1 TT-TTGATAACCTTC-CTATG-AAA
*
14211 TTTT-A-AAACTTCCATATG-AA
1 TTTTGATAACCTTCC-TATGAAA
* ** *
14231 TTGTT-AGTAATCACCCTCTGAAA
1 TT-TTGA-TAACCTTCCTATGAAA
* *
14254 TTTTGATAATC-ACACTATGAAA
1 TTTTGATAACCTTC-CTATGAAA
* * * *
14276 TTGTAATAACC-TCGTTATTAAA
1 TTTTGATAACCTTC-CTATGAAA
*
14298 TTTTGATAAACCTTCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
* *
14321 TTTTGATAAACCTCCCTATAAAA
1 TTTTGAT-AACCTTCCTATGAAA
14344 TTTTGATAACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
* *
14366 TCTTGATAA-----CTA-CAAA
1 TTTTGATAACCTTCCTATGAAA
14382 TTTTGATAACCTCTCCCTATGAAA
1 TTTTGATAACCT-T-CCTATGAAA
* * *
14406 TTTTGATCTA-CATACTATGAAA
1 TTTTGAT-AACCTTCCTATGAAA
* *
14428 TTTTGATAACCCTCTTATGAAA
1 TTTTGATAACCTTCCTATGAAA
* **
14450 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT-TCCTATGAAA
*
14472 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACCTTCCTATGAAA
* *
14494 TTTTGATATCC-TCC-CTGAAA
1 TTTTGATAACCTTCCTATGAAA
14514 TTTTGAT
1 TTTTGAT
14521 TACTCCATAA
Statistics
Matches: 400, Mismatches: 89, Indels: 82
0.70 0.16 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
18 1 0.00
20 24 0.06
21 34 0.09
22 244 0.61
23 65 0.16
24 18 0.05
25 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:14425 original size:62 final size:61
Alignment explanation
Indices: 14318--14437 Score: 161
Period size: 62 Copynumber: 2.0 Consensus size: 61
14308 CCTTCCTATA
* *
14318 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCTTATGAAATCTTGATAACTAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACATACTTATGAAATCTTGATAACTAC
* * * *
14379 AAATTTTGATAACCTCTCCCTATGAAATTTTGATCTACATAC-TATGAAATTTTGATAAC
1 AAATTTTGATAAAC-CTCCCTATAAAATTTTGAT-AACATACTTATGAAATCTTGATAAC
14438 CCTCTTATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
61 13 0.25
62 34 0.67
63 4 0.08
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (61 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAACATACTTATGAAATCTTGATAACTAC
Found at i:14437 original size:84 final size:87
Alignment explanation
Indices: 14295--14501 Score: 237
Period size: 84 Copynumber: 2.4 Consensus size: 87
14285 CCTCGTTATT
* * *
14295 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCCTATAAAATTTTGATAA-CCTCCT
1 AAATTTTGAT-AACCTTCCTATGAAATTTTGATAAACATCACTATAAAATTTTGATAACCCT-CT
14359 TATGAAATCTTG-A-T-AACTA-C
64 TATGAAATCTTGAACTAAACTATC
** *
14379 AAATTTTGATAACCTCTCCCTATGAAATTTTGATCTACAT-ACTATGAAATTTTGATAACCCTCT
1 AAATTTTGATAACCT-T-CCTATGAAATTTTGATAAACATCACTATAAAATTTTGATAACCCTCT
* *
14443 TATGAAATTTTGAAAACTAAACTATG
64 TATGAAATCTTG--AACTAAACTATC
*
14469 AAATTTTGATAACCTTCATATGAAATTTTGATA
1 AAATTTTGATAACCTTCCTATGAAATTTTGATA
14502 TCCTCCCTGA
Statistics
Matches: 104, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
83 5 0.05
84 40 0.38
85 21 0.20
87 1 0.01
88 16 0.15
89 6 0.06
90 15 0.14
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (87 bp):
AAATTTTGATAACCTTCCTATGAAATTTTGATAAACATCACTATAAAATTTTGATAACCCTCTTA
TGAAATCTTGAACTAAACTATC
Found at i:14679 original size:22 final size:22
Alignment explanation
Indices: 14626--15173 Score: 270
Period size: 22 Copynumber: 24.7 Consensus size: 22
14616 AATCACATTT
* *
14626 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
* * *
14648 TGGAACTTTGATAACTTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
14670 TAAAATTTTGTTGACCGCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
14692 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * *
14714 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
**
14736 TGAAATTTTGATAACAACTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
14758 TGAAATTTTGATAA-TTTTCCT-
1 TGAAATTTTGATAACCTCT-CTA
* * *
14779 TTAAATTTTGATAATCCGATCTTTG
1 TGAAATTTTGATAA-CC--TCTCTA
** *
14804 TGAAATTTCAATAACCACTCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
14826 TGAGA-TTTGATAACCTTTTTA
1 TGAAATTTTGATAACCTCTCTA
* *
14847 TCAAATTTTGGT-A-CTC-CTTA
1 TGAAATTTTGATAACCTCTC-TA
* * *
14867 TGAAATTGAGACTTTTATAACCTTTATA
1 TGAAA-T-----TTTGATAACCTCTCTA
* *
14895 TGAAATTTTGATAACCTCCCAA
1 TGAAATTTTGATAACCTCTCTA
*
14917 TGAAATATT-AGTAACCTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* *
14939 TGAAATTTTGTTAA--TAC-ATA
1 TGAAATTTTGATAACCT-CTCTA
*
14959 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCTCTA
**
14981 TGAAATTTCAATAACCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
* * *
15003 AGAAATTTTAATAACCTGATCCTA
1 TGAAATTTTGATAACCT-CT-CTA
* *
15027 TGAAATTTTGGTAA-CTACACTA
1 TGAAATTTTGATAACCT-CTCTA
*
15049 TGAAATTTTGATAACCT-TCCA
1 TGAAATTTTGATAACCTCTCTA
*
15070 TGAAATTTTGATAACTTC-CATA
1 TGAAATTTTGATAACCTCTC-TA
* * *
15092 TGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
*
15114 TGAAAATTTGATAACCTC-CTCA
1 TGAAATTTTGATAACCTCTCT-A
* * *
15136 TAAAATTATAATAACCATCT-TA
1 TGAAATTTTGATAACC-TCTCTA
15158 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
15174 ACACAGAGAC
Statistics
Matches: 393, Mismatches: 95, Indels: 76
0.70 0.17 0.13
Matches are distributed among these distances:
20 21 0.05
21 58 0.15
22 258 0.66
23 9 0.02
24 19 0.05
25 13 0.03
26 4 0.01
27 2 0.01
28 9 0.02
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:14750 original size:88 final size:88
Alignment explanation
Indices: 14601--14767 Score: 228
Period size: 88 Copynumber: 1.9 Consensus size: 88
14591 AGAAATACCA
* * * * **
14601 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTATGGAACTTTGATAACTTC
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAACTTTGATAACAAC
14666 TCTATAAAATTTTGTTGACCGCT
66 TCTATAAAATTTTGTTGACCGCT
* * *
14689 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAACAA
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAACTTTGATAACAA
*
14753 CTCTATGAAATTTTG
65 CTCTATAAAATTTTG
14768 ATAATTTTCC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
88 66 0.97
89 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (88 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCCTTATGAAACTTTGATAACAAC
TCTATAAAATTTTGTTGACCGCT
Found at i:14996 original size:64 final size:64
Alignment explanation
Indices: 14892--15107 Score: 163
Period size: 64 Copynumber: 3.3 Consensus size: 64
14882 TATAACCTTT
* *
14892 ATATGAAATTTTGATAACCTCCCAATGAAATATTAGTAACC-TCCTTATGAAATTTTGTTAATAC
1 ATATGAAATTTTGATAACCTCCCAATGAAATATTAATAACCTTCC-TAAGAAATTTTGTTAATAC
* * **
14956 ATATGAAATTCTT-ATAACCTCGCTATGAAAT-TTCAATAACCTTCCTAAGAAATTTTAATAACC
1 ATATGAAATT-TTGATAACCTCCCAATGAAATATT-AATAACCTTCCTAAGAAATTTTGTTAA--
15019 TGATC
62 T-A-C
* * * * * * * *
15024 CTATGAAATTTTGGTAA-CTACACTATGAAATTTTGATAACCTTCC-ATGAAATTTTGATAACTT
1 ATATGAAATTTTGATAACCT-CCCAATGAAATATTAATAACCTTCCTAAGAAATTTTGTTAA--T
*
15087 CC
63 AC
*
15089 ATATGAAATTTTGGTAACC
1 ATATGAAATTTTGATAACC
15108 ACACTATGAA
Statistics
Matches: 126, Mismatches: 15, Indels: 20
0.78 0.09 0.12
Matches are distributed among these distances:
63 2 0.02
64 45 0.36
65 22 0.17
66 2 0.02
67 20 0.16
68 33 0.26
69 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (64 bp):
ATATGAAATTTTGATAACCTCCCAATGAAATATTAATAACCTTCCTAAGAAATTTTGTTAATAC
Found at i:15107 original size:89 final size:87
Alignment explanation
Indices: 14893--15107 Score: 246
Period size: 89 Copynumber: 2.5 Consensus size: 87
14883 ATAACCTTTA
* * *
14893 TATGAAATTTTGATAACCTCCCA-ATGAAATATTAGTAACCTCCTTATGAAATTTTGTTAATACA
1 TATGAAATTTTGATAACCTTCCATATGAAATTTTAGTAACCTCCTTATGAAATTTTGGTAATACA
14957 TATGAAATTCTTATAACCTCGC
66 TATGAAATTCTTATAACCTCGC
** * *
14979 TATGAAATTTCAATAACCTTCC-TAAGAAATTTTAATAACCTGATCC-TATGAAATTTTGGTAAC
1 TATGAAATTTTGATAACCTTCCATATGAAATTTTAGTAACC---TCCTTATGAAATTTTGGTAA-
15042 TACACTATGAAATT-TTGATAACCTTC-C
62 TACA-TATGAAATTCTT-ATAACC-TCGC
*
15069 -ATGAAATTTTGATAA-CTTCCATATGAAATTTTGGTAACC
1 TATGAAATTTTGATAACCTTCCATATGAAATTTTAGTAACC
15108 ACACTATGAA
Statistics
Matches: 108, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
86 33 0.31
88 20 0.19
89 37 0.34
90 16 0.15
91 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (87 bp):
TATGAAATTTTGATAACCTTCCATATGAAATTTTAGTAACCTCCTTATGAAATTTTGGTAATACA
TATGAAATTCTTATAACCTCGC
Found at i:15130 original size:133 final size:129
Alignment explanation
Indices: 14893--15177 Score: 303
Period size: 133 Copynumber: 2.2 Consensus size: 129
14883 ATAACCTTTA
* * * * *
14893 TATGAAATTTTGATAACCTCCCAATGAAATATT-AGTAACC-TCCTTATGAAATTTTGTTAATAC
1 TATGAAATTTTGATAACCACACTATGAAATTTTGA-TAACCTTCC--ATGAAATTTTGATAATAC
* * *
14956 ATATGAAATTCTTATAACCTCGCTATGAAATTTCAATAACCTTCCT-A-AGAAATTTTAATAACC
63 ATATGAAATTCTTATAACCACACTATGAAATTTCAATAACC-TCCTCATA-AAATTATAATAACC
15019 TGATCC
126 --ATCC
* * *
15025 TATGAAATTTTGGTAACTACACTATGAAATTTTGATAACCTTCCATGAAATTTTGATAACTTCCA
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCATGAAATTTTGATAA--TACA
* *
15090 TATGAAATT-TTGGTAACCACACTATGAAAATTT-GATAACCTCCTCATAAAATTATAATAACCA
64 TATGAAATTCTT-ATAACCACACTATG-AAATTTCAATAACCTCCTCATAAAATTATAATAACCA
*
15153 TCT
127 TCC
15156 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
15178 AGAGACAAGA
Statistics
Matches: 129, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
131 37 0.29
132 38 0.29
133 47 0.36
134 7 0.05
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (129 bp):
TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCATGAAATTTTGATAATACATA
TGAAATTCTTATAACCACACTATGAAATTTCAATAACCTCCTCATAAAATTATAATAACCATCC
Found at i:15652 original size:20 final size:20
Alignment explanation
Indices: 15614--15652 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
15604 TATTGACATT
15614 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
15634 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
15653 AATAATAGAA
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:18486 original size:2 final size:2
Alignment explanation
Indices: 18479--18522 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
18469 TTCGTACTTT
18479 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA -A TA 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
18521 TA
1 TA
18523 CTAGTTTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:18503 original size:19 final size:17
Alignment explanation
Indices: 18479--18522 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
18469 TTCGTACTTT
18479 TATATATAGTAT-ATATA
1 TATATATA-TATAATATA
18496 TATATATATATAATATA
1 TATATATATATAATATA
18513 TATATATATA
1 TATATATATA
18523 CTAGTTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 3 0.12
17 23 0.88
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
TATATATATATAATATA
Found at i:18738 original size:21 final size:21
Alignment explanation
Indices: 18710--18768 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
18700 TAATAAACCT
18710 TCCTTATGAAATTTTGTAACA
1 TCCTTATGAAATTTTGTAACA
* * *
18731 TTCTTATG-ATTTTTGATAACC
1 TCCTTATGAAATTTTG-TAACA
*
18752 TCCCTATGAAATTTTGT
1 TCCTTATGAAATTTTGT
18769 TAATCTCCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 6 0.20
21 18 0.60
22 6 0.20
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.47
Consensus pattern (21 bp):
TCCTTATGAAATTTTGTAACA
Found at i:18776 original size:22 final size:22
Alignment explanation
Indices: 18581--18780 Score: 138
Period size: 22 Copynumber: 9.1 Consensus size: 22
18571 TGAATATTTT
*
18581 TATGAAATTTTGATAA-TTACCC
1 TATGAAATTTTGATAACCT-CCC
* * *
18603 TATTAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCTCCC
* * *
18625 TATGAAATTTTGACAA-TTACC
1 TATGAAATTTTGATAACCTCCC
** * *
18646 TATGAAATCGTGATAAACTCCA
1 TATGAAATTTTGATAACCTCCC
* ***
18668 TATGAAACTTTGATAACCTAAA
1 TATGAAATTTTGATAACCTCCC
* *
18690 TATGAAATTTTAATAAACCTTCCT
1 TATGAAATTTTGAT-AACC-TCCC
* * *
18714 TATGAAATTTTG-TAACATTCT
1 TATGAAATTTTGATAACCTCCC
*
18735 TATG-ATTTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* *
18756 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTCCC
18778 TAT
1 TAT
18781 AATTTTTTGA
Statistics
Matches: 135, Mismatches: 37, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
20 6 0.04
21 31 0.23
22 81 0.60
23 5 0.04
24 12 0.09
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:23353 original size:36 final size:36
Alignment explanation
Indices: 23300--23372 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
23290 ATTGTTTGGA
*
23300 GGCCAGTGTCCTCTATGAATTTGGTGGGTTAAAAAT
1 GGCCAGTATCCTCTATGAATTTGGTGGGTTAAAAAT
*
23336 GGCCAGTATCCTTTATGAATTTGGTGGGTTAAAAAT
1 GGCCAGTATCCTCTATGAATTTGGTGGGTTAAAAAT
23372 G
1 G
23373 CTACATATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.34
Consensus pattern (36 bp):
GGCCAGTATCCTCTATGAATTTGGTGGGTTAAAAAT
Found at i:37317 original size:20 final size:20
Alignment explanation
Indices: 37292--37331 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
37282 TTTTGGTGTT
37292 TTAAGAAGAATTAATGTGAC
1 TTAAGAAGAATTAATGTGAC
37312 TTAAGAAGAATTAATGTGAC
1 TTAAGAAGAATTAATGTGAC
37332 GTTTTCCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (20 bp):
TTAAGAAGAATTAATGTGAC
Done.