Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012889.1 Corchorus capsularis cultivar CVL-1 contig12910, 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: 44526
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1867 original size:14 final size:15
Alignment explanation
Indices: 1843--1871 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1833 ATTTTAATTG
1843 AATTGAATTTTTCTT
1 AATTGAATTTTTCTT
1858 AATT-AATTTTTCTT
1 AATTGAATTTTTCTT
1872 TTTTATATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (15 bp):
AATTGAATTTTTCTT
Found at i:9693 original size:9 final size:10
Alignment explanation
Indices: 9670--9696 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9660 GTGGTTGAGA
9670 AAAAATCATC
1 AAAAATCATC
9680 AAAAATCATC
1 AAAAATCATC
9690 AAAAATC
1 AAAAATC
9697 TCTCTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.19, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAATCATC
Found at i:10755 original size:23 final size:22
Alignment explanation
Indices: 10702--10786 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 22
10692 GATAATCACA
* *
10702 CTATGAAATTGTGAT-AACCTCG
1 CTATAAAATT-TGATAAACCTCC
* * *
10724 CTATGAAATTCTGATAAATCTTC
1 CTATAAAATT-TGATAAACCTCC
10747 CTATAAAATTTCGATAAACCTCC
1 CTATAAAATTT-GATAAACCTCC
*
10770 CTATAATATTTTGATAA
1 CTATAA-AATTTGATAA
10787 CTTTCTTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
22 15 0.29
23 33 0.63
24 4 0.08
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
CTATAAAATTTGATAAACCTCC
Found at i:10863 original size:22 final size:22
Alignment explanation
Indices: 10417--11009 Score: 194
Period size: 22 Copynumber: 27.6 Consensus size: 22
10407 ATGATCCCAT
*
10417 TATGAAATTTTGATAACTTTC-C
1 TATGAAATTTTGATAAC-CTCAC
* *
10439 TATGAAATTTTAATAACGAT-AC
1 TATGAAATTTTGATAAC-CTCAC
* * * * ***
10461 TATGGAATTTCGAGAATCTTTT
1 TATGAAATTTTGATAACCTCAC
** *
10483 TAT-AAATTTTTTTAACCTTC-T
1 TATGAAATTTTGATAACC-TCAC
* *
10504 TATGAAATTTGGTTAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * *
10525 TTAAGGAATTTTGA-AGACCTCAA
1 -TATGAAATTTTGATA-ACCTCAC
* *
10548 TATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCTCAC
* *
10570 CATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* *
10593 TATGAGATGTTGATAACCTCTA-
1 TATGAAATTTTGATAACCTC-AC
* * * **
10615 TATGATATATTGATAACCACGT
1 TATGAAATTTTGATAACCTCAC
* * *
10637 TATGAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
10658 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTCAC
* * * *
10681 TCTAAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* *
10703 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
* *
10725 TATGAAATTCTGATAAATCTTC-C
1 TATGAAATTTTGAT-AA-CCTCAC
* * *
10748 TATAAAATTTCGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
* *
10771 TAT-AATATTTTGATAACTTTC-T
1 TATGAA-ATTTTGATAAC-CTCAC
*
10793 TATGAAATCTTGATAA-CT-AC
1 TATGAAATTTTGATAACCTCAC
*
10813 ----AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
10831 TAT-AATTTTTTGATAACCTCAT
1 TATGAA-ATTTTGATAACCTCAC
* *
10853 TATGAAATTTTGTTAATCTC-C
1 TATGAAATTTTGATAACCTCAC
* * *
10874 -CT---A-TTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCAC
*
10891 TATGAAATTTTGATAACCCTC-T
1 TATGAAATTTTGATAA-CCTCAC
* * *
10913 TGTGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
10935 TATGAAATTTTGATAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
*
10957 TATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
10978 -CTG-AATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCAC
10997 T-TGAAATTTTGAT
1 TATGAAATTTTGAT
11010 TACTCCATAA
Statistics
Matches: 423, Mismatches: 101, Indels: 96
0.68 0.16 0.15
Matches are distributed among these distances:
16 16 0.04
17 6 0.01
18 2 0.00
19 18 0.04
20 15 0.04
21 28 0.07
22 271 0.64
23 63 0.15
24 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:11015 original size:19 final size:20
Alignment explanation
Indices: 10959--11009 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
10949 AACCTTCATA
10959 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
10979 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
10998 TGAAATTTTGAT
1 TGAAATTTTGAT
11010 TACTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:11303 original size:22 final size:22
Alignment explanation
Indices: 11090--11325 Score: 128
Period size: 22 Copynumber: 10.6 Consensus size: 22
11080 AGAAATACTA
11090 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * *
11113 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * *
11134 TTATGAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * * * *
11156 TTATAAAATTTTGTTGACCACT
1 CTATGAAATTTTGATAATCACT
*
11178 CTTTATGAAATTCTGATAAATCACGT
1 C--TATGAAATTTTGAT-AATCAC-T
* *
11204 -TATGTAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATC-ACT
**
11225 CTATGAAATTTTGATAATCTTT
1 CTATGAAATTTTGATAATCACT
11247 CTAT-AAATTTTGATAATCCGATCT
1 CTATGAAATTTTGATAAT-C-A-CT
* *
11271 CTATAAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
11293 CTATGAGA-TTTGATAA-C-CTT
1 CTATGAAATTTTGATAATCAC-T
*
11313 CTATCAAATTTTG
1 CTATGAAATTTTG
11326 GTACTTCTTA
Statistics
Matches: 167, Mismatches: 31, Indels: 32
0.73 0.13 0.14
Matches are distributed among these distances:
19 1 0.01
20 8 0.05
21 30 0.18
22 80 0.48
23 14 0.08
24 17 0.10
25 16 0.10
26 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:11377 original size:22 final size:23
Alignment explanation
Indices: 11348--11402 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
11338 AAATTGAGAC
* *
11348 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACCTACACTATAAAA
11369 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
11391 TTTTGATAACCT
1 TTTTGATAACCT
11403 CCCCATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:11413 original size:22 final size:22
Alignment explanation
Indices: 11363--11413 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
11353 TAACCTTCAT
*
11363 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
11385 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
11407 ATGAAAT
1 ATGAAAT
11414 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:11545 original size:22 final size:22
Alignment explanation
Indices: 11513--11561 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
11503 TTGTGATAAT
* *
11513 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTAAGAAATTTCAA
*
11535 TAACCAACCTAAGAGATTTCAA
1 TAACCAACCTAAGAAATTTCAA
11557 TAACC
1 TAACC
11562 TGATCGTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.27, G:0.06, T:0.24
Consensus pattern (22 bp):
TAACCAACCTAAGAAATTTCAA
Found at i:11593 original size:22 final size:22
Alignment explanation
Indices: 11568--11676 Score: 105
Period size: 22 Copynumber: 5.0 Consensus size: 22
11558 AACCTGATCG
*
11568 TATGAAATTTTGGTATCCACAC
1 TATGAAATTTTGGTAACCACAC
11590 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGGTAACCACAC
* * *
11612 TATGGAATTTTGATAACCTCA-
1 TATGAAATTTTGGTAACCACAC
* ** *
11633 TCATGAAATTATAATAACCA-TC
1 T-ATGAAATTTTGGTAACCACAC
*
11655 TCATGAAATTTTGATAACCACA
1 T-ATGAAATTTTGGTAACCACA
11677 TAGAGAGAAG
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
21 1 0.01
22 71 0.99
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (22 bp):
TATGAAATTTTGGTAACCACAC
Found at i:11871 original size:19 final size:20
Alignment explanation
Indices: 11840--11877 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
11830 TATTGACATT
11840 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
11859 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
11878 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:12214 original size:31 final size:31
Alignment explanation
Indices: 12179--12244 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
12169 TGGTAATTTA
* *
12179 GAAATATGTTTTAAAGAA-AAGGGTACAATTG
1 GAAATATATTTTAAA-AATAAGGGTACAATCG
*
12210 GAAATATATTTTAAAAATAAGGGTATAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
12241 GAAA
1 GAAA
12245 ACATAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.48, C:0.03, G:0.20, T:0.29
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Found at i:12299 original size:21 final size:19
Alignment explanation
Indices: 12273--12317 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
12263 TTCGTACTTT
*
12273 TATATATAGTATAGATATATA
1 TATATATAG-ATA-AAATATA
12294 TATATATAGATAAAATATA
1 TATATATAGATAAAATATA
12313 TATAT
1 TATAT
12318 TTACCTGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.48
20 3 0.13
21 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (19 bp):
TATATATAGATAAAATATA
Found at i:17402 original size:68 final size:69
Alignment explanation
Indices: 17273--17409 Score: 240
Period size: 68 Copynumber: 2.0 Consensus size: 69
17263 TATGTGCGTT
*
17273 GCACGTGATCCATCGTGTTTAAATTAAAAAAAAAAGTTAAATTAATAATTGAAATTATTTATAAG
1 GCACGTGATCCATCGTGTTTAAATT-AAAAAAAAAGTTAAAATAATAATTGAAATTATTTATAAG
17338 TAGAC
65 TAGAC
*
17343 GCACGTGATCCATCGTGTTTAAATT-AAAAGAAAGTTAAAATAATAATTGAAATTATTTATAAGT
1 GCACGTGATCCATCGTGTTTAAATTAAAAAAAAAGTTAAAATAATAATTGAAATTATTTATAAGT
17407 AGA
66 AGA
17410 GTTGTCAAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 40 0.62
70 25 0.38
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (69 bp):
GCACGTGATCCATCGTGTTTAAATTAAAAAAAAAGTTAAAATAATAATTGAAATTATTTATAAGT
AGAC
Found at i:18044 original size:46 final size:46
Alignment explanation
Indices: 17989--18080 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
17979 AAAACTATAA
17989 AAGTATATTTAAAAATTAATTGTATAATGACAGTTTTTAGAAATAT
1 AAGTATATTTAAAAATTAATTGTATAATGACAGTTTTTAGAAATAT
18035 AAGTATATTTAAAAATTAATTGTATAATGACAGTTTTTAGAAATAT
1 AAGTATATTTAAAAATTAATTGTATAATGACAGTTTTTAGAAATAT
18081 GTTAGATAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (46 bp):
AAGTATATTTAAAAATTAATTGTATAATGACAGTTTTTAGAAATAT
Found at i:18125 original size:31 final size:31
Alignment explanation
Indices: 18087--18146 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
18077 ATATGTTAGA
*
18087 TAAATAAGAATATAATTGGCGTTTCAAAAAT
1 TAAATAAGAATATAATAGGCGTTTCAAAAAT
* *
18118 TAAATAAGAGTATAATAGGTGTTTCAAAA
1 TAAATAAGAATATAATAGGCGTTTCAAAA
18147 GTTTTACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.32
Consensus pattern (31 bp):
TAAATAAGAATATAATAGGCGTTTCAAAAAT
Found at i:18175 original size:2 final size:2
Alignment explanation
Indices: 18168--18212 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
18158 CTCGTACTTT
* *
18168 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA -A CA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18210 TA T
1 TA T
18213 TTACCTGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:18198 original size:23 final size:21
Alignment explanation
Indices: 18168--18212 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
18158 CTCGTACTTT
*
18168 TATATATAGTATAGATATATATA
1 TATATATA-TATA-ACATATATA
18191 TATATATATATAACATATATA
1 TATATATATATAACATATATA
18212 T
1 T
18213 TTACCTGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 4 0.19
23 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (21 bp):
TATATATATATAACATATATA
Found at i:27008 original size:16 final size:16
Alignment explanation
Indices: 26966--27022 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
26956 ACCCGAACCC
*
26966 GAACCCGAAAAAGCTCA
1 GAACCCGAAAAA-ATCA
*
26983 -AA-CCTAAAAAATTCA
1 GAACCCGAAAAAA-TCA
*
26998 GAACCCGAAAAAATCC
1 GAACCCGAAAAAATCA
27014 GAACCCGAA
1 GAACCCGAA
27023 TCAAAAAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
15 10 0.30
16 15 0.45
17 8 0.24
ACGTcount: A:0.51, C:0.28, G:0.12, T:0.09
Consensus pattern (16 bp):
GAACCCGAAAAAATCA
Found at i:27192 original size:17 final size:17
Alignment explanation
Indices: 27166--27226 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 17
27156 ATCTAGCCAA
27166 AACCCAAATTGAACCCG
1 AACCCAAATTGAACCCG
* *
27183 AACCCGAATT-AACCTG
1 AACCCAAATTGAACCCG
* *
27199 -ACCCAAATTCAACCCA
1 AACCCAAATTGAACCCG
*
27215 AACCCGAATTGA
1 AACCCAAATTGA
27227 TCTGACCCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
15 8 0.23
16 9 0.26
17 18 0.51
ACGTcount: A:0.41, C:0.34, G:0.10, T:0.15
Consensus pattern (17 bp):
AACCCAAATTGAACCCG
Found at i:27213 original size:32 final size:32
Alignment explanation
Indices: 27167--27243 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
27157 TCTAGCCAAA
* *
27167 ACCCAAATTGAACCCGAACCCGAATTAACCTG
1 ACCCAAATTCAACCCAAACCCGAATTAACCTG
* *
27199 ACCCAAATTCAACCCAAACCCGAATTGATCTG
1 ACCCAAATTCAACCCAAACCCGAATTAACCTG
27231 ACCCAAATTCAAC
1 ACCCAAATTCAAC
27244 TTGACCTGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.39, C:0.35, G:0.09, T:0.17
Consensus pattern (32 bp):
ACCCAAATTCAACCCAAACCCGAATTAACCTG
Found at i:32394 original size:18 final size:18
Alignment explanation
Indices: 32371--32441 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
32361 AAAATCATCT
32371 TCACCATTCTGACCATTC
1 TCACCATTCTGACCATTC
*
32389 TCACCA-TC--AACA-TC
1 TCACCATTCTGACCATTC
* *
32403 TTCACCATTCTTACCATTT
1 -TCACCATTCTGACCATTC
* *
32422 TCACCATTGTGAGCATTC
1 TCACCATTCTGACCATTC
32440 TC
1 TC
32442 TTCACCATCT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
14 2 0.05
15 9 0.22
16 2 0.05
17 2 0.05
18 25 0.61
19 1 0.02
ACGTcount: A:0.24, C:0.35, G:0.06, T:0.35
Consensus pattern (18 bp):
TCACCATTCTGACCATTC
Found at i:32408 original size:33 final size:33
Alignment explanation
Indices: 32366--32428 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
32356 TCAACAAAAT
32366 CATCTTCACCATTCTGACCATTCTCACCATCAA
1 CATCTTCACCATTCTGACCATTCTCACCATCAA
* *
32399 CATCTTCACCATTCTTACCATTTTCACCAT
1 CATCTTCACCATTCTGACCATTCTCACCAT
32429 TGTGAGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.38, G:0.02, T:0.35
Consensus pattern (33 bp):
CATCTTCACCATTCTGACCATTCTCACCATCAA
Found at i:33128 original size:58 final size:59
Alignment explanation
Indices: 33027--33162 Score: 184
Period size: 58 Copynumber: 2.3 Consensus size: 59
33017 ACCAAGTCAG
* *
33027 AAACCCAACACATAAAACAAAGAAAAATTGACTAACTTCCCATATATTATATTTGAATACA
1 AAACCCAACACAT-AAA-AAAGAAAAATTGACCAACTTCCCATATATTATATTCGAATACA
* * * * *
33088 AAACCCAATACATAAAAAA-CAAAATTTACCAACTTTCCATATATTCTATTCGAATACA
1 AAACCCAACACATAAAAAAGAAAAATTGACCAACTTCCCATATATTATATTCGAATACA
33146 AAACCCAACACATAAAA
1 AAACCCAACACATAAAA
33163 CAAAATAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
58 49 0.73
59 3 0.04
60 3 0.04
61 12 0.18
ACGTcount: A:0.51, C:0.22, G:0.03, T:0.24
Consensus pattern (59 bp):
AAACCCAACACATAAAAAAGAAAAATTGACCAACTTCCCATATATTATATTCGAATACA
Found at i:35115 original size:30 final size:30
Alignment explanation
Indices: 35075--35132 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
35065 ATAAGTATGA
*
35075 AGAGGATGAAGACGA-AGAGTTTGTTGATTT
1 AGAGGATGAAGAC-ATAGAGTCTGTTGATTT
*
35105 AGAGGGTGAAGACATAGAGTCTGTTGAT
1 AGAGGATGAAGACATAGAGTCTGTTGAT
35133 ATAAATCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.33, C:0.05, G:0.34, T:0.28
Consensus pattern (30 bp):
AGAGGATGAAGACATAGAGTCTGTTGATTT
Found at i:36768 original size:27 final size:25
Alignment explanation
Indices: 36706--36761 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
36696 CTGCGTTGGG
36706 CATATTCCAAAAAAAATATTTGCAA
1 CATATTCCAAAAAAAATATTTGCAA
36731 CATATTCCAAAAAAAATATTTGCAA
1 CATATTCCAAAAAAAATATTTGCAA
*
36756 CTTATT
1 CATATT
36762 GATCAAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (25 bp):
CATATTCCAAAAAAAATATTTGCAA
Found at i:37946 original size:6 final size:6
Alignment explanation
Indices: 37937--37963 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
37927 TTAATCCCAC
37937 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
37964 TTTCTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:40778 original size:2 final size:2
Alignment explanation
Indices: 40773--40809 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
40763 AAATATATTT
40773 TA TA TA GTA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40810 TGTGATGTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:40783 original size:14 final size:13
Alignment explanation
Indices: 40765--40810 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
40755 TTTTTTCTAA
*
40765 ATATATTTTATAT
1 ATATATTATATAT
*
40778 AGTATAATATATAT
1 A-TATATTATATAT
40792 ATATA-TATATAT
1 ATATATTATATAT
40804 ATATATT
1 ATATATT
40811 GTGATGTCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 12 0.41
13 6 0.21
14 11 0.38
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (13 bp):
ATATATTATATAT
Done.