Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014643.1 Corchorus capsularis cultivar CVL-1 contig14664, 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: 66097
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:4262 original size:40 final size:40
Alignment explanation
Indices: 4207--4283 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
4197 CTCAAAAACA
4207 TTACATTTAATTAGAAATCTTAATTTCAACCATTTTTGGT
1 TTACATTTAATTAGAAATCTTAATTTCAACCATTTTTGGT
* *
4247 TTACATTTAATTAGAAATCTTAATTTCAGCCCTTTTT
1 TTACATTTAATTAGAAATCTTAATTTCAACCATTTTT
4284 TATTCAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.48
Consensus pattern (40 bp):
TTACATTTAATTAGAAATCTTAATTTCAACCATTTTTGGT
Found at i:5024 original size:30 final size:29
Alignment explanation
Indices: 4988--5090 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 29
4978 CGAACTTAAG
*
4988 TCGGGTTCAGGTTAAATTTGTCGGGTTGAT
1 TCGGGTTC-GGTTAAATTTGTCAGGTTGAT
* *
5018 TCGGGTTCGGGTTAAATTGGGTTAGGTTGAT
1 TCGGGTTC-GGTTAAATT-TGTCAGGTTGAT
* * * *
5049 TTGGGTTCGGGTAAATTTTGGTTCAAGTTAAT
1 TCGGGTTCGGTTAAA-TTT-G-TCAGGTTGAT
5081 TCGGGTTCGG
1 TCGGGTTCGG
5091 GCTCAGATTG
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
30 23 0.40
31 19 0.33
32 16 0.28
ACGTcount: A:0.17, C:0.09, G:0.35, T:0.40
Consensus pattern (29 bp):
TCGGGTTCGGTTAAATTTGTCAGGTTGAT
Found at i:5029 original size:16 final size:15
Alignment explanation
Indices: 5008--5060 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
4998 GTTAAATTTG
5008 TCGGGTTGATTCGGGT
1 TCGGGTTGATT-GGGT
*
5024 TCGGGTTAAATTGGGT
1 TCGGGTT-GATTGGGT
*
5040 T-AGGTTGATTTGGGT
1 TCGGGTTGA-TTGGGT
5055 TCGGGT
1 TCGGGT
5061 AAATTTTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 11 0.37
16 15 0.50
17 3 0.10
ACGTcount: A:0.11, C:0.08, G:0.42, T:0.40
Consensus pattern (15 bp):
TCGGGTTGATTGGGT
Found at i:5049 original size:31 final size:30
Alignment explanation
Indices: 4988--5091 Score: 102
Period size: 31 Copynumber: 3.4 Consensus size: 30
4978 CGAACTTAAG
* * **
4988 TCGGGTTCAGGTTAAATTTGTCGGGTTGAT
1 TCGGGTTCGGGTTAAATTGGTTAGGTTGAT
5018 TCGGGTTCGGGTTAAATTGGGTTAGGTTGAT
1 TCGGGTTCGGGTTAAATT-GGTTAGGTTGAT
* * *
5049 TTGGGTTCGGG-TAAATTTTGGTTCAAGTTAAT
1 TCGGGTTCGGGTTAAA--TTGGTT-AGGTTGAT
5081 TCGGGTTCGGG
1 TCGGGTTCGGG
5092 CTCAGATTGG
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
30 21 0.34
31 23 0.37
32 18 0.29
ACGTcount: A:0.16, C:0.09, G:0.36, T:0.39
Consensus pattern (30 bp):
TCGGGTTCGGGTTAAATTGGTTAGGTTGAT
Found at i:5052 original size:15 final size:16
Alignment explanation
Indices: 5011--5088 Score: 50
Period size: 16 Copynumber: 4.9 Consensus size: 16
5001 AAATTTGTCG
* *
5011 GGTTGATTCGGGTTCG
1 GGTTGATTTGGGTTCA
* *
5027 GGTTAAATTGGGTT-A
1 GGTTGATTTGGGTTCA
*
5042 GGTTGATTTGGGTTCG
1 GGTTGATTTGGGTTCA
** *
5058 GGTAAATTTTGGTTCA
1 GGTTGATTTGGGTTCA
* * *
5074 AGTTAATTCGGGTTC
1 GGTTGATTTGGGTTC
5089 GGGCTCAGAT
Statistics
Matches: 46, Mismatches: 15, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
15 12 0.26
16 34 0.74
ACGTcount: A:0.17, C:0.08, G:0.35, T:0.41
Consensus pattern (16 bp):
GGTTGATTTGGGTTCA
Found at i:5298 original size:16 final size:16
Alignment explanation
Indices: 5277--5376 Score: 94
Period size: 16 Copynumber: 6.2 Consensus size: 16
5267 ATTGAATTCA
*
5277 GGTTTTTTCAGGTTCG
1 GGTTTTTTCGGGTTCG
5293 GGTTTTTTCGGGTTTC-
1 GGTTTTTTCGGG-TTCG
* * *
5309 AGATTTTTCGGGTTCT
1 GGTTTTTTCGGGTTCG
* *
5325 GATTTTTTCGGGTTTG
1 GGTTTTTTCGGGTTCG
*
5341 AGTTTTTTCGGGTTCG
1 GGTTTTTTCGGGTTCG
* * *
5357 GATTTTTTTGGTTTCG
1 GGTTTTTTCGGGTTCG
5373 GGTT
1 GGTT
5377 CGGACGGGTT
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
15 3 0.05
16 60 0.91
17 3 0.05
ACGTcount: A:0.06, C:0.10, G:0.30, T:0.54
Consensus pattern (16 bp):
GGTTTTTTCGGGTTCG
Found at i:5316 original size:32 final size:32
Alignment explanation
Indices: 5280--5364 Score: 125
Period size: 32 Copynumber: 2.7 Consensus size: 32
5270 GAATTCAGGT
* *
5280 TTTTTCAGGTTCGGGTTTTTTCGGGTTTCAGA
1 TTTTTCGGGTTCGGATTTTTTCGGGTTTCAGA
* * *
5312 TTTTTCGGGTTCTGATTTTTTCGGGTTTGAGT
1 TTTTTCGGGTTCGGATTTTTTCGGGTTTCAGA
5344 TTTTTCGGGTTCGGATTTTTT
1 TTTTTCGGGTTCGGATTTTTT
5365 TGGTTTCGGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.07, C:0.11, G:0.27, T:0.55
Consensus pattern (32 bp):
TTTTTCGGGTTCGGATTTTTTCGGGTTTCAGA
Found at i:7478 original size:21 final size:21
Alignment explanation
Indices: 7452--7492 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
7442 TTATATAATA
7452 ATAACCCTAATTTTTGTTAAG
1 ATAACCCTAATTTTTGTTAAG
7473 ATAACCCTAATTTTTGTTAA
1 ATAACCCTAATTTTTGTTAA
7493 ACAAAAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.44
Consensus pattern (21 bp):
ATAACCCTAATTTTTGTTAAG
Found at i:9219 original size:156 final size:156
Alignment explanation
Indices: 8935--9404 Score: 904
Period size: 156 Copynumber: 3.0 Consensus size: 156
8925 GGACCAACAT
*
8935 TACCTTCAATGCAGTCCACACTTTACAGCTTTAAACTCCATTTTCAAGCCTCAAGTATTGGATCC
1 TACCTTCAATGCAGTCCACACTTTACAGCTTTAAACTCCATTTTCAAGCATCAAGTATTGGATCC
9000 AAGGATCTCTTGGATGTTTCTAAGCAAGCATTAAAAAGAAATTTCAGTATAAGCAATCAAGCAAT
66 AAGGATCTCTTGGATGTTTCTAAGCAAGCATTAAAAAGAAATTTCAGTATAAGCAATCAAGCAAT
9065 TCAAAAAAGTAAATAATGAAATTACA
131 TCAAAAAAGTAAATAATGAAATTACA
*
9091 TACCTTCAATGCAATCCACACTTTACAGCTTTAAACTCCATTTTCAAGCATCAAGTATTGGATCC
1 TACCTTCAATGCAGTCCACACTTTACAGCTTTAAACTCCATTTTCAAGCATCAAGTATTGGATCC
9156 AAGGATCTCTTGGATGTTTCTAAGCAAGCATTAAAAAGAAATTTCAGTATAAGCAATCAAGCAAT
66 AAGGATCTCTTGGATGTTTCTAAGCAAGCATTAAAAAGAAATTTCAGTATAAGCAATCAAGCAAT
*
9221 TCAAAAAAGTAAATAATGAAACTACA
131 TCAAAAAAGTAAATAATGAAATTACA
9247 TACCTTCAATGCAGTCCACACTTTACAGCTTTAAACTCCATTTTCAAGCATCAAGTATTGGATCC
1 TACCTTCAATGCAGTCCACACTTTACAGCTTTAAACTCCATTTTCAAGCATCAAGTATTGGATCC
*
9312 AAGGATCTCTTGGATGTTTCTAAGCAAGCATTAAAAAGAAATTTCAGTATAAGCAATCAAGTAAT
66 AAGGATCTCTTGGATGTTTCTAAGCAAGCATTAAAAAGAAATTTCAGTATAAGCAATCAAGCAAT
9377 TCAAAAAAGTAAATAATGAAATTACA
131 TCAAAAAAGTAAATAATGAAATTACA
9403 TA
1 TA
9405 ATACATAACC
Statistics
Matches: 308, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
156 308 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.29
Consensus pattern (156 bp):
TACCTTCAATGCAGTCCACACTTTACAGCTTTAAACTCCATTTTCAAGCATCAAGTATTGGATCC
AAGGATCTCTTGGATGTTTCTAAGCAAGCATTAAAAAGAAATTTCAGTATAAGCAATCAAGCAAT
TCAAAAAAGTAAATAATGAAATTACA
Found at i:14412 original size:21 final size:21
Alignment explanation
Indices: 14386--14428 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
14376 CCTTACACTT
14386 GGCGGCTAAGAAACTAACAAG
1 GGCGGCTAAGAAACTAACAAG
14407 GGCGGCTAAGAAACTAACAAG
1 GGCGGCTAAGAAACTAACAAG
14428 G
1 G
14429 AAAGTGCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.30, T:0.09
Consensus pattern (21 bp):
GGCGGCTAAGAAACTAACAAG
Found at i:14616 original size:36 final size:36
Alignment explanation
Indices: 14576--14653 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
14566 TACTGAAACG
* * *
14576 CCGCAATTCCAAATAACGGTGTTTGGCTTTTAGACA
1 CCGCAATTCCAAATAACGGCGTTTGACTTGTAGACA
** *
14612 CCGCAATTCCAAATAGTGGCGTTTGACTTGTAGACG
1 CCGCAATTCCAAATAACGGCGTTTGACTTGTAGACA
14648 CCGCAA
1 CCGCAA
14654 AATAACGGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (36 bp):
CCGCAATTCCAAATAACGGCGTTTGACTTGTAGACA
Found at i:15339 original size:2 final size:2
Alignment explanation
Indices: 15334--15358 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15324 TATAAAAAAA
15334 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
15359 TTTTCGAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16222 original size:12 final size:10
Alignment explanation
Indices: 16195--16226 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
16185 CCTTAGGCCT
16195 CGACACACCC
1 CGACACACCC
16205 CGACACACCC
1 CGACACACCC
16215 CGACACACCC
1 CGACACACCC
16225 CG
1 CG
16227 GCTATCCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.28, C:0.59, G:0.12, T:0.00
Consensus pattern (10 bp):
CGACACACCC
Found at i:30294 original size:21 final size:22
Alignment explanation
Indices: 30244--30294 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
30234 TAATTATTAA
* *
30244 AAAATATAATTCAAATTTTTTT
1 AAAATAAAATTCAAATTTTCTT
* *
30266 TAAA-AAAATTTAAA-TTTCTT
1 AAAATAAAATTCAAATTTTCTT
30286 AAAATAAAA
1 AAAATAAAA
30295 ATATTATAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 8 0.35
21 12 0.52
22 3 0.13
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATAAAATTCAAATTTTCTT
Found at i:30353 original size:6 final size:6
Alignment explanation
Indices: 30342--30374 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
30332 GAACCACTAG
30342 TTTTCT TTTTCT TTTTCT TTTTCT TTTT-T TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
30375 GGCAGAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTCT
Found at i:32081 original size:24 final size:24
Alignment explanation
Indices: 32054--32102 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
32044 TTTATGAGTC
32054 AACAAACCATTTTCTCCAACAATT
1 AACAAACCATTTTCTCCAACAATT
*
32078 AACAAACCCTTTTCTCCAACAATT
1 AACAAACCATTTTCTCCAACAATT
32102 A
1 A
32103 CAATTCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.29
Consensus pattern (24 bp):
AACAAACCATTTTCTCCAACAATT
Found at i:44489 original size:73 final size:73
Alignment explanation
Indices: 44370--44518 Score: 289
Period size: 73 Copynumber: 2.0 Consensus size: 73
44360 TTGGTCAGGG
*
44370 ATGCAGAAATAGTACTTCAAGGTTTCAGAGGGTGAATCTATCAAACTCGATCAACCATTAACAAG
1 ATGCAGAAATAGTACTTCAAGGTTTCAGAGGGCGAATCTATCAAACTCGATCAACCATTAACAAG
44435 TAATCCTA
66 TAATCCTA
44443 ATGCAGAAATAGTACTTCAAGGTTTCAGAGGGCGAATCTATCAAACTCGATCAACCATTAACAAG
1 ATGCAGAAATAGTACTTCAAGGTTTCAGAGGGCGAATCTATCAAACTCGATCAACCATTAACAAG
44508 TAATCCTA
66 TAATCCTA
44516 ATG
1 ATG
44519 TGGGTGGTTT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (73 bp):
ATGCAGAAATAGTACTTCAAGGTTTCAGAGGGCGAATCTATCAAACTCGATCAACCATTAACAAG
TAATCCTA
Found at i:44634 original size:23 final size:23
Alignment explanation
Indices: 44604--44650 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
44594 ATTTCTATTC
44604 TTAAAGTGTTCGGATAACACACG
1 TTAAAGTGTTCGGATAACACACG
44627 TTAAAGTGTTCGGATAACACACG
1 TTAAAGTGTTCGGATAACACACG
44650 T
1 T
44651 GACCAATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (23 bp):
TTAAAGTGTTCGGATAACACACG
Found at i:51828 original size:31 final size:31
Alignment explanation
Indices: 51784--51873 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 31
51774 ATTAAACAAA
* *
51784 TAAGGATATAATAGGAATATTAAAAGTTAAT
1 TAAGGGTACAATAGGAATATTAAAAGTTAAT
*
51815 TAAGGGTACAATAGGAATATTAAAAATTAAT
1 TAAGGGTACAATAGGAATATTAAAAGTTAAT
*
51846 TAAGGGTACAATAGGTAAT-TCAAAAGTT
1 TAAGGGTACAATAGG-AATATTAAAAGTT
51874 TCTCAAAACT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
31 50 0.94
32 3 0.06
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.30
Consensus pattern (31 bp):
TAAGGGTACAATAGGAATATTAAAAGTTAAT
Found at i:52120 original size:31 final size:31
Alignment explanation
Indices: 52076--52165 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 31
52066 ATTAAACAAA
* *
52076 TAAGGATATAATAGGAATATTAAAAGTTAAT
1 TAAGGGTACAATAGGAATATTAAAAGTTAAT
*
52107 TAAGGGTACAATAGGAATATTAAAAATTAAT
1 TAAGGGTACAATAGGAATATTAAAAGTTAAT
*
52138 TAAGGGTACAATAGGTAAT-TCAAAAGTT
1 TAAGGGTACAATAGG-AATATTAAAAGTT
52166 TCTCAAAACT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
31 50 0.94
32 3 0.06
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.30
Consensus pattern (31 bp):
TAAGGGTACAATAGGAATATTAAAAGTTAAT
Found at i:52129 original size:292 final size:292
Alignment explanation
Indices: 51605--52189 Score: 1143
Period size: 292 Copynumber: 2.0 Consensus size: 292
51595 TCTTAATAAA
*
51605 AAATGCAAGTTCTATTCCTTAGGCATTTCTCGGAGAGGACCGGTCAATTGTTTCAGAAGAATCGT
1 AAATGCAAGTTCTATTCCTTAGGCATTTCTCGGAGAGGACCGGTCAATTGTTTCAGAAGAACCGT
51670 AAGATATTCAAGTCGAAGAGTCAAACTATATATTTTGTAAATATAATTAAATGTAAATTAACAAA
66 AAGATATTCAAGTCGAAGAGTCAAACTATATATTTTGTAAATATAATTAAATGTAAATTAACAAA
51735 ATTAAAAATTAATTGTATAATGGCAATTTTTAGAAATATATTAAACAAATAAGGATATAATAGGA
131 ATTAAAAATTAATTGTATAATGGCAATTTTTAGAAATATATTAAACAAATAAGGATATAATAGGA
51800 ATATTAAAAGTTAATTAAGGGTACAATAGGAATATTAAAAATTAATTAAGGGTACAATAGGTAAT
196 ATATTAAAAGTTAATTAAGGGTACAATAGGAATATTAAAAATTAATTAAGGGTACAATAGGTAAT
51865 TCAAAAGTTTCTCAAAACTCGTACTTTTATAT
261 TCAAAAGTTTCTCAAAACTCGTACTTTTATAT
51897 AAATGCAAGTTCTATTCCTTAGGCATTTCTCGGAGAGGACCGGTCAATTGTTTCAGAAGAACCGT
1 AAATGCAAGTTCTATTCCTTAGGCATTTCTCGGAGAGGACCGGTCAATTGTTTCAGAAGAACCGT
51962 AAGATATTCAAGTCGAAGAGTCAAACTATATATTTTGTAAATATAATTAAATGTAAATTAACAAA
66 AAGATATTCAAGTCGAAGAGTCAAACTATATATTTTGTAAATATAATTAAATGTAAATTAACAAA
*
52027 ATTAAAAATTAATTGTATAATGGTAATTTTTAGAAATATATTAAACAAATAAGGATATAATAGGA
131 ATTAAAAATTAATTGTATAATGGCAATTTTTAGAAATATATTAAACAAATAAGGATATAATAGGA
52092 ATATTAAAAGTTAATTAAGGGTACAATAGGAATATTAAAAATTAATTAAGGGTACAATAGGTAAT
196 ATATTAAAAGTTAATTAAGGGTACAATAGGAATATTAAAAATTAATTAAGGGTACAATAGGTAAT
*
52157 TCAAAAGTTTCTCAAAACTCGTATTTTTATAT
261 TCAAAAGTTTCTCAAAACTCGTACTTTTATAT
52189 A
1 A
52190 TAACTAATTT
Statistics
Matches: 290, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
292 290 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (292 bp):
AAATGCAAGTTCTATTCCTTAGGCATTTCTCGGAGAGGACCGGTCAATTGTTTCAGAAGAACCGT
AAGATATTCAAGTCGAAGAGTCAAACTATATATTTTGTAAATATAATTAAATGTAAATTAACAAA
ATTAAAAATTAATTGTATAATGGCAATTTTTAGAAATATATTAAACAAATAAGGATATAATAGGA
ATATTAAAAGTTAATTAAGGGTACAATAGGAATATTAAAAATTAATTAAGGGTACAATAGGTAAT
TCAAAAGTTTCTCAAAACTCGTACTTTTATAT
Found at i:52360 original size:22 final size:22
Alignment explanation
Indices: 52311--52366 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
52301 TTATGATCCC
* *
52311 ATTATGAAATTTTGATAATCTT
1 ATTATGAAATTTTAATAATCAT
** *
52333 CCTATGAAATTTTAATAATGAT
1 ATTATGAAATTTTAATAATCAT
*
52355 ATTATGGAATTT
1 ATTATGAAATTT
52367 CGAGAACCTT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (22 bp):
ATTATGAAATTTTAATAATCAT
Found at i:52775 original size:22 final size:22
Alignment explanation
Indices: 52749--52797 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
52739 GAATTTCGAG
* *
52749 AACCTTTTTAT-AAATTTTTTTT
1 AACCTTCTTATGAAA-TTTTGTT
52771 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
52793 AACCT
1 AACCT
52798 CCCTAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:53008 original size:23 final size:23
Alignment explanation
Indices: 52975--53059 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
52965 GATAACCTCG
*
52975 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* * *
52998 CTACAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
53021 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* *
53043 TTATAAAATCTTGATAA
1 CTATAAAATTTTGATAA
53060 CTAAAAATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
22 17 0.33
23 35 0.67
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:53050 original size:22 final size:22
Alignment explanation
Indices: 52953--53061 Score: 94
Period size: 22 Copynumber: 4.9 Consensus size: 22
52943 AGTAATCACA
* * *
52953 CTATGAAATTGTGATAAC-CTC
1 CTATAAAATTTTGATAACTTTC
* *
52974 GCTATGAAATTTTGATAAATCTTC
1 -CTATAAAATTTTGATAACT-TTC
* * *
52998 CTACAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGAT-AACTTTC
53021 CTATAAAATTTTGATAACTTTC
1 CTATAAAATTTTGATAACTTTC
* *
53043 TTATAAAATCTTGATAACT
1 CTATAAAATTTTGATAACT
53062 AAAAATTTTG
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
22 38 0.54
23 29 0.41
24 4 0.06
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.39
Consensus pattern (22 bp):
CTATAAAATTTTGATAACTTTC
Found at i:53051 original size:45 final size:46
Alignment explanation
Indices: 52958--53059 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 46
52948 TCACACTATG
* * *
52958 AAATTGTGAT-AACCTCGCTATGAAATTTTGATAAATCTTCCTACA
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTACA
* * *
53003 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACT-TTCTTATA
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTACA
*
53048 AAATCTTGATAA
1 AAATTTTGATAA
53060 CTAAAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
45 26 0.53
46 23 0.47
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (46 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTACA
Found at i:53106 original size:21 final size:22
Alignment explanation
Indices: 53067--53107 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
53057 TAACTAAAAA
*
53067 TTTTGATAACCTCCCTATGATT
1 TTTTGATAACCTCACTATGATT
*
53089 TTTTGAT-ACCTCATTATGA
1 TTTTGATAACCTCACTATGA
53108 AATTTTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGATT
Found at i:53113 original size:22 final size:22
Alignment explanation
Indices: 53064--53203 Score: 128
Period size: 22 Copynumber: 6.4 Consensus size: 22
53054 TGATAACTAA
*
53064 AAATTTTGATAA-CCTCCCTATG
1 AAATTTTGATAACCCT-CTTATG
**
53086 ATTTTTTGAT-A-CCTCATTATG
1 AAATTTTGATAACCCTC-TTATG
* * * *
53107 AAATTTTGTTAATCTTCCTATG
1 AAATTTTGATAACCCTCTTATG
* *
53129 AAATTTTGATCTA-CATAC-TATG
1 AAATTTTGAT-AACCCT-CTTATG
53151 AAATTTTGATAACCCTCTTATG
1 AAATTTTGATAACCCTCTTATG
53173 AAATTTTGATAACCCTCTTATG
1 AAATTTTGATAACCCTCTTATG
53195 AAATTTTGA
1 AAATTTTGA
53204 AAACTAAACT
Statistics
Matches: 98, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
20 1 0.01
21 17 0.17
22 75 0.77
23 5 0.05
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (22 bp):
AAATTTTGATAACCCTCTTATG
Found at i:53195 original size:44 final size:42
Alignment explanation
Indices: 52953--53203 Score: 188
Period size: 44 Copynumber: 5.8 Consensus size: 42
52943 AGTAATCACA
* *
52953 CTATGAAATTGTGATAACCTCGCTATGAAATTTTGATAAATCTTC
1 CTATGAAATTTTGATAACCT--CTATGAAATTTTGAT-AACCTTC
** * *
52998 CTACAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTC
1 CTATGAAATTTTGAT-AACCT--CTATGAAATTTTGATAACCTTC
* * * * *
53043 TTATAAAATCTTGATAA---CTA-AAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACCTCTATGAAATTTTGATAACCTTC
** * *
53081 CTATGATTTTTTGAT-ACCTCATTATGAAATTTTGTTAATCTTC
1 CTATGAAATTTTGATAACCTC--TATGAAATTTTGATAACCTTC
* * *
53124 CTATGAAATTTTGATCTACATACTATGAAATTTTGATAACCCTC
1 CTATGAAATTTTGAT-AACCT-CTATGAAATTTTGATAACCTTC
*
53168 TTATGAAATTTTGATAACCCTCTTATGAAATTTTGA
1 CTATGAAATTTTGATAA-CCTC-TATGAAATTTTGA
53204 AAACTAAACT
Statistics
Matches: 164, Mismatches: 30, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
37 1 0.01
38 26 0.16
39 3 0.02
40 1 0.01
42 2 0.01
43 29 0.18
44 49 0.30
45 32 0.20
46 21 0.13
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (42 bp):
CTATGAAATTTTGATAACCTCTATGAAATTTTGATAACCTTC
Found at i:55137 original size:17 final size:16
Alignment explanation
Indices: 55091--55133 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
55081 CCAGATGACT
55091 AGTGATCTAAGATCACC
1 AGTGATC-AAGATCACC
55108 AGTGATGCAAGATCACC
1 AGTGAT-CAAGATCACC
*
55125 GGTGATCAA
1 AGTGATCAA
55134 AGATTACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (16 bp):
AGTGATCAAGATCACC
Found at i:63434 original size:9 final size:9
Alignment explanation
Indices: 63420--63448 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
63410 CCAATTAACT
63420 ATTGGTTAA
1 ATTGGTTAA
63429 ATTGGTTAA
1 ATTGGTTAA
63438 ATTGGTTAA
1 ATTGGTTAA
63447 AT
1 AT
63449 AAATATTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (9 bp):
ATTGGTTAA
Found at i:64964 original size:18 final size:19
Alignment explanation
Indices: 64941--64979 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
64931 AGATTACAGC
64941 CAATTA-AAATTAATAAGT
1 CAATTATAAATTAATAAGT
* *
64959 CAATTATTAATTTATAAGT
1 CAATTATAAATTAATAAGT
64978 CA
1 CA
64980 GAGGAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (19 bp):
CAATTATAAATTAATAAGT
Done.