Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005815.1 Corchorus capsularis cultivar CVL-1 contig05833, 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: 19275
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:52 original size:22 final size:22
Alignment explanation
Indices: 24--108 Score: 107
Period size: 23 Copynumber: 3.8 Consensus size: 22
14 AAATTTGTAG
* *
24 TTATCAAGATTTTATAAGAAAT
1 TTATCAAAATTTTATAGGAAAT
**
46 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATA-GGAAAT
69 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAA-AT
*
92 TTATCAAAATTTCATAG
1 TTATCAAAATTTTATAG
109 CGAGGTTATC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 18 0.33
23 36 0.67
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGAAAT
Found at i:75 original size:23 final size:23
Alignment explanation
Indices: 45--149 Score: 115
Period size: 23 Copynumber: 4.7 Consensus size: 23
35 TTATAAGAAA
*
45 TTTATCAAAATTTTATAGGGAGG
1 TTTATCAAAATTTCATAGGGAGG
* * *
68 TTTATCAAAATTTTATAGGAAGA
1 TTTATCAAAATTTCATAGGGAGG
*
91 TTTATCAAAATTTCATAGCGAGG
1 TTTATCAAAATTTCATAGGGAGG
* * *
114 -TTATCACAATTTCATAGTG-TG
1 TTTATCAAAATTTCATAGGGAGG
*
135 ATTATCAAAATTTCA
1 TTTATCAAAATTTCA
150 GAGTGTGATT
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
21 1 0.01
22 30 0.42
23 40 0.56
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (23 bp):
TTTATCAAAATTTCATAGGGAGG
Found at i:118 original size:45 final size:45
Alignment explanation
Indices: 23--149 Score: 152
Period size: 45 Copynumber: 2.8 Consensus size: 45
13 AAAATTTGTA
* * * *
23 GTTATCAAGATTTTATAAGAA-ATTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAG
67 GTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAG
1 G-TTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAG
* * *
113 GTTATCACAATTTCATAGTG-TGA-TTATCAAAATTTCA
1 GTTATCAAAATTTTATAG-GAAGATTTATCAAAATTTCA
150 GAGTGTGATT
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
44 15 0.21
45 35 0.48
46 23 0.32
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (45 bp):
GTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAG
Found at i:124 original size:22 final size:21
Alignment explanation
Indices: 46--414 Score: 127
Period size: 22 Copynumber: 16.8 Consensus size: 21
36 TATAAGAAAT
*
46 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTCATA-GGAGG
* *
68 TTTATCAAAATTTTATAGGAAGAT
1 -TTATCAAAATTTCATAGG-AG-G
92 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * *
114 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
* * *
136 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAG-GAGG
158 TTA-CTAACAA-TTCATATGGAGG
1 TTATC-AA-AATTTCATA-GGAGG
* * * * *
180 TTTTTAAATTTTCATAACGTGG
1 TTATCAAAATTTCAT-AGGAGG
* *
202 TTATCAATATATCATATGGAGG
1 TTATCAAAATTTCATA-GGAGG
* * *
224 TTA-CAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAG-G-AGG
* *
246 TTATCAAAATTTCATTGGGAAG
1 TTATCAAAATTTCA-TAGGAGG
* *
268 TTATCAAAATTTAATATTGAGG
1 TTATCAAAATTTCATA-GGAGG
* *
290 TCT-TCAAAATTCCTTAAGGAGG
1 T-TATCAAAATTTCAT-AGGAGG
* ** *
312 TTAACCGAATTTCATAAGAAGG
1 TTATCAAAATTTCAT-AGGAGG
** * **
334 TTAAAAAAAATT-ATAAAAAGG
1 TTATCAAAATTTCAT-AGGAGG
* * * **
355 TTCTCGAAATTCCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
* * *
377 TTATTAAAATTTCATAGAAAGA
1 TTATCAAAATTTCATAG-GAGG
399 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
415 ATGGGGTCAT
Statistics
Matches: 255, Mismatches: 71, Indels: 41
0.69 0.19 0.11
Matches are distributed among these distances:
20 1 0.00
21 31 0.12
22 169 0.66
23 51 0.20
24 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:1262 original size:19 final size:20
Alignment explanation
Indices: 1216--1263 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
1206 TGTGGCACAC
*
1216 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
1238 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
1257 CACATGT
1 CACATGT
1264 CACGTCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:1277 original size:53 final size:53
Alignment explanation
Indices: 1183--1285 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
1173 GACGTGGCAC
* ***
1183 GCCACGTGTACCAAAAAGTGACTTGTGGCACACCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACCAAAAAGTCGT
* ** *
1236 GCCACATGTACCAAAAAGTGACACATGTCACGTCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACCAAAAAGT
1286 GACACGTGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.18
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACACCACATGTACCAAAAAGTCGT
Found at i:1313 original size:31 final size:31
Alignment explanation
Indices: 1235--1333 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 31
1225 CAAAAAGTCG
* *
1235 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* * *
1266 CGTCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
** * *
1297 TGCCACATGTTTCAAAAAATGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
1328 TGCCAC
1 TGCCAC
1334 GTGCACAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:1621 original size:2 final size:2
Alignment explanation
Indices: 1614--1645 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1604 ATTAAGGAAA
1614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1646 CCTTGCTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4213 original size:21 final size:22
Alignment explanation
Indices: 4185--4239 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
4175 TTACAGCCAG
4185 TAAAAACAGAAACTAAAAAAC-
1 TAAAAACAGAAACTAAAAAACT
* * *
4206 TGAAAACAGAAACTCAATAACT
1 TAAAAACAGAAACTAAAAAACT
4228 TAAAAACAGAAA
1 TAAAAACAGAAA
4240 GTACATACAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.65, C:0.15, G:0.07, T:0.13
Consensus pattern (22 bp):
TAAAAACAGAAACTAAAAAACT
Found at i:7036 original size:21 final size:21
Alignment explanation
Indices: 7012--7063 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
7002 AATTGACTTC
7012 ATTACAAATTTATCAAAACAG
1 ATTACAAATTTATCAAAACAG
* * * *
7033 ATTAGATATTTATTAAAACAT
1 ATTACAAATTTATCAAAACAG
7054 ATTACAAATT
1 ATTACAAATT
7064 GAAACTTATG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (21 bp):
ATTACAAATTTATCAAAACAG
Found at i:7460 original size:13 final size:13
Alignment explanation
Indices: 7442--7466 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7432 CATATTATAC
7442 ATTAAGAAGCAAA
1 ATTAAGAAGCAAA
7455 ATTAAGAAGCAA
1 ATTAAGAAGCAA
7467 CTTCCTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (13 bp):
ATTAAGAAGCAAA
Found at i:15083 original size:22 final size:20
Alignment explanation
Indices: 15035--15097 Score: 90
Period size: 20 Copynumber: 3.0 Consensus size: 20
15025 TAAATATCTT
15035 TATAAAATTTTGATAATTAC
1 TATAAAATTTTGATAATTAC
* *
15055 TATAAAATTTTAATAATCTCC
1 TATAAAATTTTGATAAT-TAC
15076 ATATAAAATTTTGATAATTAC
1 -TATAAAATTTTGATAATTAC
15097 T
1 T
15098 TTATGAAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 17 0.46
21 4 0.11
22 16 0.43
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (20 bp):
TATAAAATTTTGATAATTAC
Found at i:15172 original size:22 final size:22
Alignment explanation
Indices: 15147--15198 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
15137 CCTTCATATG
15147 AAATTTTGTTA-ACTTCCCTATA
1 AAATTTTGTTACAC-TCCCTATA
15169 AAATTTTGTTACACTCCCTATA
1 AAATTTTGTTACACTCCCTATA
15191 AAATTTTG
1 AAATTTTG
15199 AAAACCTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (22 bp):
AAATTTTGTTACACTCCCTATA
Found at i:15216 original size:22 final size:22
Alignment explanation
Indices: 15191--15249 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
15181 ACTCCCTATA
15191 AAATTTTGAAAACCTCA-ATATG
1 AAATTTTGAAAACCTCATA-ATG
* *
15213 AAATTTT-AATAACCACCTAATG
1 AAATTTTGAA-AACCTCATAATG
*
15235 AAATTTTGATAACCT
1 AAATTTTGAAAACCT
15250 TCCGATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 2 0.07
22 26 0.87
23 2 0.07
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (22 bp):
AAATTTTGAAAACCTCATAATG
Found at i:15381 original size:22 final size:21
Alignment explanation
Indices: 15368--15472 Score: 101
Period size: 22 Copynumber: 5.0 Consensus size: 21
15358 AACTTCCATT
15368 TGAAATTTTGATAACCT-C-A
1 TGAAATTTTGATAACCTCCTA
* *
15387 TG-AATATTTGAAAACCACCTCA
1 TGAAAT-TTTGATAACCTCCT-A
15409 TGAAATTTTGATAA-CTACCTTA
1 TGAAATTTTGATAACCT-CC-TA
*
15431 TGAAATTTTGATAACATCCCTA
1 TGAAATTTTGATAACCT-CCTA
*
15453 TGAATTTTTGATAACCTCCT
1 TGAAATTTTGATAACCTCCT
15473 GTGTTAACCT
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
18 3 0.04
19 11 0.16
20 1 0.01
21 4 0.06
22 44 0.63
23 7 0.10
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:15524 original size:24 final size:24
Alignment explanation
Indices: 15504--15710 Score: 95
Period size: 22 Copynumber: 9.0 Consensus size: 24
15494 TTGATAAGAG
*
15504 TACACTATTAAATTTTGATAACCA
1 TACACTATGAAATTTTGATAACCA
*
15528 TATACTATGAAATTTTGATAACC-
1 TACACTATGAAATTTTGATAACCA
* * *
15551 T-TATTATGAAATTTTG-TTA--A
1 TACACTATGAAATTTTGATAACCA
* * *
15571 T-CTCTATGAAATTGTGATAA--T
1 TACACTATGAAATTTTGATAACCA
*
15592 TACACTATGAAATTTTGGTAA-C-
1 TACACTATGAAATTTTGATAACCA
15614 T-CACT-TGAAATTTTGATAAACTCA
1 TACACTATGAAATTTTGAT-AAC-CA
* * * *
15638 CTTTATCTCACTCTGTAATTTTAATAA--G
1 ---TA---CACTATGAAATTTTGATAACCA
15666 TACACTATGAAATTTTGATAACC-
1 TACACTATGAAATTTTGATAACCA
* *
15689 -ACATTATAAAATTTTGATAACC
1 TACACTATGAAATTTTGATAACC
15711 TCCATATAAT
Statistics
Matches: 143, Mismatches: 22, Indels: 38
0.70 0.11 0.19
Matches are distributed among these distances:
20 23 0.16
21 11 0.08
22 67 0.47
23 2 0.01
24 21 0.15
25 2 0.01
27 1 0.01
31 6 0.04
32 10 0.07
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.41
Consensus pattern (24 bp):
TACACTATGAAATTTTGATAACCA
Found at i:15580 original size:20 final size:21
Alignment explanation
Indices: 15506--15639 Score: 119
Period size: 22 Copynumber: 6.2 Consensus size: 21
15496 GATAAGAGTA
*
15506 CACTATTAAATTTTGATAACCAT
1 CACTATGAAATTTTGATAA-C-T
*
15529 ATACTATGAAATTTTGATAACCT
1 -CACTATGAAATTTTGATAA-CT
* * *
15552 TATTATGAAATTTTGTTAA-T
1 CACTATGAAATTTTGATAACT
* * *
15572 CTCTATGAAATTGTGATAATT
1 CACTATGAAATTTTGATAACT
*
15593 ACACTATGAAATTTTGGTAACT
1 -CACTATGAAATTTTGATAACT
15615 CACT-TGAAATTTTGATAAACT
1 CACTATGAAATTTTGAT-AACT
15636 CACT
1 CACT
15640 TTATCTCACT
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
20 26 0.28
21 13 0.14
22 34 0.37
23 1 0.01
24 19 0.20
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (21 bp):
CACTATGAAATTTTGATAACT
Found at i:15581 original size:42 final size:42
Alignment explanation
Indices: 15531--15632 Score: 120
Period size: 42 Copynumber: 2.4 Consensus size: 42
15521 ATAACCATAT
* *
15531 ACTATGAAATTTTGATAACCTT-ATTATGAAATTTTGTTAA-TC
1 ACTATGAAATTTTGATAA--TTAACTATGAAATTTTGGTAACTC
* *
15573 TCTATGAAATTGTGATAATTACACTATGAAATTTTGGTAACTC
1 ACTATGAAATTTTGATAATTA-ACTATGAAATTTTGGTAACTC
15616 ACT-TGAAATTTTGATAA
1 ACTATGAAATTTTGATAA
15633 ACTCACTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
40 2 0.04
42 45 0.88
43 4 0.08
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (42 bp):
ACTATGAAATTTTGATAATTAACTATGAAATTTTGGTAACTC
Found at i:15901 original size:21 final size:21
Alignment explanation
Indices: 15858--15919 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 21
15848 GAAATTTTGG
15858 TAACC-TCCATATGAAATTTTAA
1 TAACCTTCC-TATGAAA-TTTAA
15880 T-A-CTATCCCTATGAAATTTAA
1 TAACCT-T-CCTATGAAATTTAA
15901 TAACCTTCCTATGAAATTT
1 TAACCTTCCTATGAAATTT
15920 TGATAACATC
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
20 1 0.03
21 19 0.54
22 11 0.31
23 4 0.11
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (21 bp):
TAACCTTCCTATGAAATTTAA
Found at i:15935 original size:21 final size:20
Alignment explanation
Indices: 15805--16054 Score: 146
Period size: 22 Copynumber: 11.5 Consensus size: 20
15795 CTCCCTGTAT
15805 AATTTTGATAACGTTCCTATGAA
1 AATTTTGATAAC--TCCTATG-A
* * *
15828 AATTCTGTTAACCTCTTTATGA
1 AATTTTGATAA-CTC-CTATGA
*
15850 AATTTTGGTAACCTCCATATGA
1 AATTTTGATAA-CTCC-TATGA
*
15872 AATTTTAAT-ACTATCCCTATGA
1 AATTTTGATAAC--T-CCTATGA
*
15894 AA-TTTAATAACCTTCCTATGA
1 AATTTTGATAA-C-TCCTATGA
*
15915 AATTTTGATAACATCCCATGA
1 AATTTTGATAAC-TCCTATGA
* *
15936 AATTGTGATAACTACACTATAA
1 AATTTTGATAACT-C-CTATGA
* *
15958 AATTTTGATATCCTACTTATGA
1 AATTTTGATA-ACT-CCTATGA
*
15980 AATTTTGATAACTACCTATAA
1 AATTTTGATAACT-CCTATGA
*
16001 AATTTTGATAACTACACTATTA
1 AATTTTGATAACT-C-CTATGA
*
16023 AATTTT-AGTAACAATACTATGA
1 AATTTTGA-TAAC--TCCTATGA
16045 AATTTTGATA
1 AATTTTGATA
16055 TCATTCTTAT
Statistics
Matches: 185, Mismatches: 25, Indels: 35
0.76 0.10 0.14
Matches are distributed among these distances:
20 2 0.01
21 60 0.32
22 100 0.54
23 21 0.11
24 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (20 bp):
AATTTTGATAACTCCTATGA
Found at i:15947 original size:43 final size:43
Alignment explanation
Indices: 15778--16012 Score: 169
Period size: 43 Copynumber: 5.4 Consensus size: 43
15768 ATAACCAGAG
*
15778 TATGAAATTTT-AGTAACCTCCC-TGTATAATTTTGATAACGTTCC
1 TATGAAATTTTGA-TAACCTCCCATG-A-AATTTTGATAACCTTCC
* * ** *
15822 TATGAAAATTCTGTTAACCTCTTTATGAAATTTTGGTAACC-TCC
1 TATG-AAATTTTGATAACCTC-CCATGAAATTTTGATAACCTTCC
* * *
15866 ATATGAAATTTTAAT-ACTATCCCTATGAAA-TTTAATAACCTTCC
1 -TATGAAATTTTGATAAC-CTCCC-ATGAAATTTTGATAACCTTCC
* * *
15910 TATGAAATTTTGATAACATCCCATGAAATTGTGATAA-CTACAC
1 TATGAAATTTTGATAACCTCCCATGAAATTTTGATAACCTTC-C
* * ** *
15953 TATAAAATTTTGATATCCTACTTATGAAATTTTGATAA-CTACC
1 TATGAAATTTTGATAACCT-CCCATGAAATTTTGATAACCTTCC
*
15996 TATAAAATTTTGATAAC
1 TATGAAATTTTGATAAC
16013 TACACTATTA
Statistics
Matches: 154, Mismatches: 25, Indels: 25
0.75 0.12 0.12
Matches are distributed among these distances:
42 9 0.06
43 68 0.44
44 46 0.30
45 28 0.18
46 1 0.01
47 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (43 bp):
TATGAAATTTTGATAACCTCCCATGAAATTTTGATAACCTTCC
Found at i:15979 original size:65 final size:63
Alignment explanation
Indices: 15805--16054 Score: 222
Period size: 65 Copynumber: 3.8 Consensus size: 63
15795 CTCCCTGTAT
* *
15805 AATTTTGATAACGTTC-CTATGAAAATTCTGT-TAACCT-CTTTATGAAATTTTGGTAACCTCCA
1 AATTTTGATAAC-TACACTAT-AAAATT-T-TATAACCTAC-TTATGAAATTTTGATAA-CTCC-
15867 TATGA
59 TATGA
* * * * * * *
15872 AATTTTAAT-ACTATCCCTATGAAATTTAATAACCTTCCTATGAAATTTTGATAACATCCCATGA
1 AATTTTGATAACTA-CACTATAAAATTTTATAACCTACTTATGAAATTTTGATAAC-TCCTATGA
* * *
15936 AATTGTGATAACTACACTATAAAATTTTGATATCCTACTTATGAAATTTTGATAACTACCTATAA
1 AATTTTGATAACTACACTATAAAATTTT-ATAACCTACTTATGAAATTTTGATAACT-CCTATGA
* *
16001 AATTTTGATAACTACACTATTAAATTTTAGTAACAATAC-TATGAAATTTTGATA
1 AATTTTGATAACTACACTATAAAATTTTA-TAAC-CTACTTATGAAATTTTGATA
16055 TCATTCTTAT
Statistics
Matches: 152, Mismatches: 21, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
64 25 0.16
65 103 0.68
66 12 0.08
67 12 0.08
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (63 bp):
AATTTTGATAACTACACTATAAAATTTTATAACCTACTTATGAAATTTTGATAACTCCTATGA
Found at i:15990 original size:44 final size:44
Alignment explanation
Indices: 15932--16071 Score: 151
Period size: 44 Copynumber: 3.2 Consensus size: 44
15922 ATAACATCCC
*
15932 ATGAAATTGTGATAACTACACTATAAAATTTTGATATCCTACTT
1 ATGAAATTTTGATAACTACACTATAAAATTTTGATATCCTACTT
* *
15976 ATGAAATTTTGATAACTAC-CTATAAAATTTTGATA-ACTACACT
1 ATGAAATTTTGATAACTACACTATAAAATTTTGATATCCTAC-TT
* * * * * *
16019 ATTAAATTTT-AGTAACAATACTATGAAATTTTGATATCATTCTT
1 ATGAAATTTTGA-TAACTACACTATAAAATTTTGATATCCTACTT
*
16063 ATAAAATTT
1 ATGAAATTT
16072 GGAAAAATTA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
42 5 0.06
43 31 0.39
44 42 0.52
45 2 0.03
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (44 bp):
ATGAAATTTTGATAACTACACTATAAAATTTTGATATCCTACTT
Done.