Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008169.1 Corchorus capsularis cultivar CVL-1 contig08190, 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: 63808
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:101 original size:13 final size:13
Alignment explanation
Indices: 69--105 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
59 AAAAAAAATG
69 TTTATTCTAGTTTC
1 TTTATTCTA-TTTC
*
83 TATATTCTATTTC
1 TTTATTCTATTTC
96 TTTATTCTAT
1 TTTATTCTAT
106 AATTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.19, C:0.14, G:0.03, T:0.65
Consensus pattern (13 bp):
TTTATTCTATTTC
Found at i:1091 original size:13 final size:13
Alignment explanation
Indices: 1073--1097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1063 CTATCTCATT
1073 TGTATAGACTATA
1 TGTATAGACTATA
1086 TGTATAGACTAT
1 TGTATAGACTAT
1098 TTACCAGCTA
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATAGACTATA
Found at i:2041 original size:2 final size:2
Alignment explanation
Indices: 2034--2070 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2024 ATATAATGTG
2034 TA TA TA TA TA TA T- TA TA TA T- TA TA T- 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
2071 AAAGACAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:3063 original size:109 final size:109
Alignment explanation
Indices: 2867--3143 Score: 459
Period size: 109 Copynumber: 2.5 Consensus size: 109
2857 TAACTATTAT
* *
2867 AATTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTAC
1 AATTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTAC
2932 TTTATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATAC
61 TTTATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATAC
2981 AATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTAT
1 AATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTAT
*
3046 TTTTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATAC
66 TTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATAC
3090 AATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 AATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
3144 TATTTTTTTT
Statistics
Matches: 159, Mismatches: 3, Indels: 8
0.94 0.02 0.05
Matches are distributed among these distances:
108 7 0.04
109 124 0.78
110 3 0.02
111 2 0.01
114 23 0.14
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (109 bp):
AATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTAT
TTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATAC
Found at i:4580 original size:38 final size:37
Alignment explanation
Indices: 4529--4608 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 37
4519 TTCCCTCTAT
4529 TTTTTAGTATAATAATTAAAAGATCACTTCTTTTTTC
1 TTTTTAGTATAATAATTAAAAGATCACTTCTTTTTTC
4566 GTTTTTAGTATAATAATTAAAAGATCACTTCTTTTTTC
1 -TTTTTAGTATAATAATTAAAAGATCACTTCTTTTTTC
4604 TTTTT
1 TTTTT
4609 GGAATTAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 5 0.12
38 37 0.88
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (37 bp):
TTTTTAGTATAATAATTAAAAGATCACTTCTTTTTTC
Found at i:4941 original size:23 final size:23
Alignment explanation
Indices: 4915--4961 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4905 TGTTTTCTTT
4915 GCATCGATACTTTTTATATTTAC
1 GCATCGATACTTTTTATATTTAC
4938 GCATCGATACTTTTTATATTTAC
1 GCATCGATACTTTTTATATTTAC
4961 G
1 G
4962 AGTCATATGC
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:0.26, C:0.17, G:0.11, T:0.47
Consensus pattern (23 bp):
GCATCGATACTTTTTATATTTAC
Found at i:5144 original size:10 final size:10
Alignment explanation
Indices: 5131--5166 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
5121 AAATCTTGAT
*
5131 ATATCTGTAA
1 ATATCCGTAA
5141 ATATCCGTAA
1 ATATCCGTAA
5151 ATATCCGTAA
1 ATATCCGTAA
*
5161 TTATCC
1 ATATCC
5167 ATTTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:5750 original size:3 final size:3
Alignment explanation
Indices: 5731--5792 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
5721 GCTCACGGAA
* * *
5731 GAT G-T GAT GAT GCT GAT GAT GAT GAT AAT GAT GAC GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
5778 GAT GAC GAT GAT GAT
1 GAT GAT GAT GAT GAT
5793 CATTGGGGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:6907 original size:13 final size:12
Alignment explanation
Indices: 6877--6919 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
6867 CATCGATACC
6877 TCGATATATCCG
1 TCGATATATCCG
*
6889 TCGATATATTCG
1 TCGATATATCCG
6901 TTCGATATATCCG
1 -TCGATATATCCG
6914 TCGATA
1 TCGATA
6920 CCTGTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:13363 original size:60 final size:63
Alignment explanation
Indices: 13270--13393 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 63
13260 GTGTATAAAA
*
13270 ATTTGGTGACATCACTTTATGTCACAAATAATTTTATAC-A-A-GACATAAACAATATGTCAT
1 ATTTGGTGACATCACTTTATGTCACAAATAATTTAATACAATACGACATAAACAATATGTCAT
**
13330 ATTTGGTGACATTTCTTTATGTCACAAATAATTTAATACAATACGTGACATAAACAATATGTCA
1 ATTTGGTGACATCACTTTATGTCACAAATAATTTAATACAATAC--GACATAAACAATATGTCA
13394 CGTATAAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
60 36 0.64
61 1 0.02
62 1 0.02
65 18 0.32
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (63 bp):
ATTTGGTGACATCACTTTATGTCACAAATAATTTAATACAATACGACATAAACAATATGTCAT
Found at i:19371 original size:31 final size:31
Alignment explanation
Indices: 19336--19407 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
19326 GCCAAATTAC
* * *
19336 CAATTTGAACCTAAACCTTTCAAAAGTTGCT
1 CAATTTGAACATAAACATTTCAAAAATTGCT
*
19367 CAATTTGAGCATAAACATTTCAAAAATTGCT
1 CAATTTGAACATAAACATTTCAAAAATTGCT
19398 CAATTTGAAC
1 CAATTTGAAC
19408 TTTAAAATAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (31 bp):
CAATTTGAACATAAACATTTCAAAAATTGCT
Found at i:22745 original size:16 final size:16
Alignment explanation
Indices: 22726--22764 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
22716 TGGGTAACCG
22726 AACCCGAAATGACCCA
1 AACCCGAAATGACCCA
* * *
22742 AACCCAAAATGACTCG
1 AACCCGAAATGACCCA
22758 AACCCGA
1 AACCCGA
22765 TCAACCCGAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.36, G:0.13, T:0.08
Consensus pattern (16 bp):
AACCCGAAATGACCCA
Found at i:23401 original size:2 final size:2
Alignment explanation
Indices: 23385--23422 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
23375 GAAAGTCTAT
23385 TA TA CTA TA -A TA TA TA TA TA TA TA TA 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
23423 AACATTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:24225 original size:18 final size:17
Alignment explanation
Indices: 24185--24229 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
24175 TATCATTTAA
*
24185 AAAATAAACTACCTATTT
1 AAAA-AAACTACCCATTT
24203 AAAAAAACTACCCATTT
1 AAAAAAACTACCCATTT
24220 AGAAAAAACT
1 A-AAAAAACT
24230 GTCACAAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.56, C:0.18, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAAAAACTACCCATTT
Found at i:24226 original size:20 final size:19
Alignment explanation
Indices: 24178--24227 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 19
24168 TTATCTATAT
24178 CATTTAAAAAATAAACTACC
1 CATTTAAAAAA-AAACTACC
*
24198 TATTT--AAAAAAACTACC
1 CATTTAAAAAAAAACTACC
24215 CATTTAGAAAAAA
1 CATTTA-AAAAAA
24228 CTGTCACAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 12 0.48
18 4 0.16
20 9 0.36
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.26
Consensus pattern (19 bp):
CATTTAAAAAAAAACTACC
Found at i:25075 original size:21 final size:21
Alignment explanation
Indices: 25049--25105 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
25039 GTTGACTTGG
25049 GCGAAGCGACCGAAGACCTGA
1 GCGAAGCGACCGAAGACCTGA
25070 GCGAAGCGACCGAAGACCTGA
1 GCGAAGCGACCGAAGACCTGA
25091 GCGAAGCGACCGAAG
1 GCGAAGCGACCGAAG
25106 GGACTTGACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.33, C:0.28, G:0.35, T:0.04
Consensus pattern (21 bp):
GCGAAGCGACCGAAGACCTGA
Found at i:30256 original size:28 final size:28
Alignment explanation
Indices: 30216--30271 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
30206 AGAAAAGATC
30216 ATCTAATATTATACCATGATTATTAAAT
1 ATCTAATATTATACCATGATTATTAAAT
* *
30244 ATCTAATATTATACCATGGTTGTTAAAT
1 ATCTAATATTATACCATGATTATTAAAT
30272 CGAGATACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (28 bp):
ATCTAATATTATACCATGATTATTAAAT
Found at i:38600 original size:120 final size:119
Alignment explanation
Indices: 38421--38771 Score: 420
Period size: 120 Copynumber: 3.0 Consensus size: 119
38411 CAACTTCTGC
*
38421 TCATCCAAGGA-TTTCTTCTCTAGCAAGTTTGGATCTCTTCCCACACCATCACATTTTGGTCCTT
1 TCATCCAAGGACTTT-TTCTCTAGCAAGTTTGGATCTCTTCCCACACCATCACATCTTGGTCCTT
*
38485 TCCTAACCCAACATTTAGTTTCTTCACTGAATTTCATCTGACATTCTGGCATGATT
65 TCCTAACCCAATATTTAGTTTCTTCACTGAATTTCATCTGACATTCT-GCATGATT
* ** *
38541 TCATCCAAGGACTTTTT-TACTAGCAAGTTTGAATCTCTTCCCACATGATCATATCTTGGTCCTT
1 TCATCCAAGGACTTTTTCT-CTAGCAAGTTTGGATCTCTTCCCACACCATCACATCTTGGTCCTT
*
38605 TCCTAACCCAATGTTTAGTTTCTTCACTGAATTTCATCTG--A--C-G--T-ATT
65 TCCTAACCCAATATTTAGTTTCTTCACTGAATTTCATCTGACATTCTGCATGATT
* * * * *
38652 TCATCCAAGGACTTTTTCTCTAGTAAGTTCGGATCACTTTCCACACCATTC-CATCTTGGTCCTC
1 TCATCCAAGGACTTTTTCTCTAGCAAGTTTGGATCTCTTCCCACACCA-TCACATCTTGGTCCTT
* * * *
38716 TCCTAACCCAATATTTAGTTTCTTTTA-TCATTTTCATCTGACGTTCTAGCATGATT
65 TCCTAACCCAATATTTAGTTTC-TTCACTGAATTTCATCTGACATTCT-GCATGATT
38772 CATATGATAG
Statistics
Matches: 196, Mismatches: 21, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
111 85 0.43
112 7 0.04
114 1 0.01
115 1 0.01
116 1 0.01
117 1 0.01
118 1 0.01
119 2 0.01
120 94 0.48
121 3 0.02
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (119 bp):
TCATCCAAGGACTTTTTCTCTAGCAAGTTTGGATCTCTTCCCACACCATCACATCTTGGTCCTTT
CCTAACCCAATATTTAGTTTCTTCACTGAATTTCATCTGACATTCTGCATGATT
Found at i:38733 original size:111 final size:111
Alignment explanation
Indices: 38538--38739 Score: 282
Period size: 111 Copynumber: 1.8 Consensus size: 111
38528 TTCTGGCATG
* * ** *
38538 ATTTCATCCAAGGACTTTTTTACTAGCAAGTTTGAATCTCTTCCCACATGATCATATCTTGGTCC
1 ATTTCATCCAAGGACTTTTTTACTAGCAAGTTCGAATCACTTCCCACACCATCACATCTTGGTCC
* *
38603 TTTCCTAACCCAATGTTTAGTTTCTTCACTGAATTTCATCTGACGT
66 TCTCCTAACCCAATATTTAGTTTCTTCACTGAATTTCATCTGACGT
* * *
38649 ATTTCATCCAAGGACTTTTTCT-CTAGTAAGTTCGGATCACTTTCCACACCATTC-CATCTTGGT
1 ATTTCATCCAAGGACTTTTT-TACTAGCAAGTTCGAATCACTTCCCACACCA-TCACATCTTGGT
38712 CCTCTCCTAACCCAATATTTAGTTTCTT
64 CCTCTCCTAACCCAATATTTAGTTTCTT
38740 TTATCATTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
111 76 0.96
112 3 0.04
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (111 bp):
ATTTCATCCAAGGACTTTTTTACTAGCAAGTTCGAATCACTTCCCACACCATCACATCTTGGTCC
TCTCCTAACCCAATATTTAGTTTCTTCACTGAATTTCATCTGACGT
Found at i:40281 original size:17 final size:17
Alignment explanation
Indices: 40241--40307 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
40231 TCAGGTCGTT
*
40241 TTCGGGTTCGGATTTAA
1 TTCGGGTTCGGATTAAA
*
40258 GTCGGGTTCGGATTAAA
1 TTCGGGTTCGGATTAAA
* *
40275 TTTGGG-TCGGATT-GA
1 TTCGGGTTCGGATTAAA
40290 TTCGGGTTCGG-TTAAA
1 TTCGGGTTCGGATTAAA
40306 TT
1 TT
40308 TAGGTCAGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
15 8 0.20
16 14 0.34
17 19 0.46
ACGTcount: A:0.18, C:0.10, G:0.33, T:0.39
Consensus pattern (17 bp):
TTCGGGTTCGGATTAAA
Found at i:40308 original size:31 final size:31
Alignment explanation
Indices: 40259--40362 Score: 129
Period size: 31 Copynumber: 3.3 Consensus size: 31
40249 CGGATTTAAG
*
40259 TCGGGTTCGGATTAAATTTGGGTC-GGATTGAT
1 TCGGGTTCGG-TTAAATTTAGGTCAGG-TTGAT
40291 TCGGGTTCGGTTAAATTTAGGTCAGGTTGAT
1 TCGGGTTCGGTTAAATTTAGGTCAGGTTGAT
* * * * *
40322 TCGTGTTCGGGTCAATTTTGGTCAGGTTAAT
1 TCGGGTTCGGTTAAATTTAGGTCAGGTTGAT
40353 TCGGGTTCGG
1 TCGGGTTCGG
40363 GCTCGGATTG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
31 52 0.81
32 12 0.19
ACGTcount: A:0.16, C:0.12, G:0.34, T:0.38
Consensus pattern (31 bp):
TCGGGTTCGGTTAAATTTAGGTCAGGTTGAT
Found at i:40530 original size:20 final size:20
Alignment explanation
Indices: 40505--40543 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40495 CATACATGAA
40505 ATTTTCAGAA-ATTATTATTT
1 ATTTTCA-AATATTATTATTT
40525 ATTTTCAAATATTATTATT
1 ATTTTCAAATATTATTATT
40544 GAATTCAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTTCAAATATTATTATTT
Found at i:40582 original size:16 final size:16
Alignment explanation
Indices: 40563--40659 Score: 70
Period size: 16 Copynumber: 5.9 Consensus size: 16
40553 TTTTTTCAGG
40563 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
* *
40579 TTCGGGTTTC-AGATTT
1 TTCGGG-TTCGGGTTTT
* * * *
40595 TTCAGATTCTGATTTT
1 TTCGGGTTCGGGTTTT
* *
40611 TTCGGGTTCGAGCTTT
1 TTCGGGTTCGGGTTTT
40627 TTCGGGTTCGGGATTTTT
1 TTCGGGTTCGGG--TTTT
**
40645 TTTTGGTTCGGGTTT
1 TTCGGGTTCGGGTTT
40660 GGACGGGTTC
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
15 3 0.05
16 41 0.68
17 3 0.05
18 13 0.22
ACGTcount: A:0.07, C:0.12, G:0.29, T:0.52
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:40644 original size:32 final size:32
Alignment explanation
Indices: 40563--40644 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
40553 TTTTTTCAGG
*
40563 TTCGGGTTCGGGTTTTTTCGGGTTTCAGATTT
1 TTCGGGTTCGGGATTTTTCGGGTTTCAGATTT
* * * *
40595 TTCAGATTC-TGATTTTTTCGGG-TTCGAGCTTT
1 TTCGGGTTCGGGA-TTTTTCGGGTTTC-AGATTT
40627 TTCGGGTTCGGGATTTTT
1 TTCGGGTTCGGGATTTTT
40645 TTTTGGTTCG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
31 4 0.10
32 33 0.85
33 2 0.05
ACGTcount: A:0.09, C:0.13, G:0.28, T:0.50
Consensus pattern (32 bp):
TTCGGGTTCGGGATTTTTCGGGTTTCAGATTT
Found at i:40645 original size:18 final size:18
Alignment explanation
Indices: 40607--40656 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
40597 CAGATTCTGA
40607 TTTTTTCGGGTTC--GAG
1 TTTTTTCGGGTTCGGGAG
* *
40623 CTTTTTCGGGTTCGGGAT
1 TTTTTTCGGGTTCGGGAG
**
40641 TTTTTTTTGGTTCGGG
1 TTTTTTCGGGTTCGGG
40657 TTTGGACGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 12 0.44
18 15 0.56
ACGTcount: A:0.04, C:0.12, G:0.32, T:0.52
Consensus pattern (18 bp):
TTTTTTCGGGTTCGGGAG
Found at i:42675 original size:12 final size:13
Alignment explanation
Indices: 42656--42692 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
42646 TCTTTGATGC
42656 TATTATATTTATT
1 TATTATATTTATT
42669 T-TTATATTTATT
1 TATTATATTTATT
42681 TATATATATTTA
1 TAT-TATATTTA
42693 GGCTTAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.55
13 2 0.09
14 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATATTTATT
Found at i:48115 original size:14 final size:15
Alignment explanation
Indices: 48092--48130 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
48082 AATATATATT
48092 TATATTATTAGTAAA
1 TATATTATTAGTAAA
*
48107 TAT-TTATTAGTATA
1 TATATTATTAGTAAA
48121 TATATTATTA
1 TATATTATTA
48131 TTTATTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
TATATTATTAGTAAA
Found at i:48129 original size:19 final size:18
Alignment explanation
Indices: 48084--48140 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
48074 ATTTTTTTAA
48084 TATATATTTATATTATTAG
1 TATATATTTAT-TTATTAG
* *
48103 TAAATATTTA-TTAGTA-
1 TATATATTTATTTATTAG
48119 TATATATTATTATTTATTAG
1 TATATA-T-TTATTTATTAG
48139 TA
1 TA
48141 AATTATCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
16 5 0.17
17 6 0.20
18 3 0.10
19 14 0.47
20 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TATATATTTATTTATTAG
Found at i:48188 original size:2 final size:2
Alignment explanation
Indices: 48183--48223 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
48173 TTTATTTAAC
*
48183 AT AT AT AT AT AT AT AC AT A- 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 AT AT AT AT AT
48224 TTTGGGGCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:51570 original size:90 final size:90
Alignment explanation
Indices: 51385--51572 Score: 218
Period size: 90 Copynumber: 2.1 Consensus size: 90
51375 TTCTTAAATA
* *
51385 ACAAAATAACCAACCACAAAATGACCAAAATACCCCTTAACATTTGTTCTTCATTTGGTGAGTTT
1 ACAAAATAACCAACCACAAAATGACCAAAATACCCCTTAACATTTGTTCTTCATTTGGTGACTTG
* * * * * ** *
51450 TTTTGTAATTTCACTTTCTCCCTTT
66 ATATGCAATGTCACCTAATCACTTT
* *
51475 ACAAAATAACCAACCACAAAATGACCCAAATACCCCTTAACATTTGTTCTTCATTT-TTGCACTT
1 ACAAAATAACCAACCACAAAATGACCAAAATACCCCTTAACATTTGTTCTTCATTTGGTG-ACTT
*
51539 GATATGCAATAGTC-CCTAATCAGTTT
65 GATATGCAAT-GTCACCTAATCACTTT
*
51565 TCAAAATA
1 ACAAAATA
51573 TTATTGGTGA
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
89 2 0.02
90 78 0.95
91 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.34
Consensus pattern (90 bp):
ACAAAATAACCAACCACAAAATGACCAAAATACCCCTTAACATTTGTTCTTCATTTGGTGACTTG
ATATGCAATGTCACCTAATCACTTT
Found at i:52200 original size:178 final size:177
Alignment explanation
Indices: 51835--52214 Score: 419
Period size: 178 Copynumber: 2.1 Consensus size: 177
51825 CTATAAGCAC
* * * * * **
51835 AAATTATGTAATATTAAGTAGATCGTCTATTTCCGTTAACTGAAATAATTAATTCTTTAGAAGCA
1 AAATTATATAATATTAAGTAGACCGTCTATTCCCATTAACTGAAACAACAAATTCTTTAGAAGCA
*
51900 TTGTTTATACCTTGAACATTAAATTTACTTTTCGAGTCCTTCATAAAAATTGTAGATCATGGAAC
66 TTGTTTATACCTTGAACATTAAATTTACTTTTCGAGTCCTTCATAAAAATTGTAGATCATGAAAC
* * * * *
51965 AACCTTTCAAAAGACACTTGAATCATCGCAATCAGACATCTGGAACA
131 AACCTTTCAAAAGACACTTAAATCACCGCAATCAGAAACCTAGAACA
* *
52012 AAAGTTATATAATATTAAGTGGACCGTCTATTCCCATTAA-TCGAAACAACAAATT-TTTCGGAA
1 AAA-TTATATAATATTAAGTAGACCGTCTATTCCCATTAACT-GAAACAACAAATTCTTT-AGAA
* * *
52075 GCATT-TTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCAT
63 GCATTGTTT-ATACCTTG-AACATTAAATTTACTTTTCGAGTCCTTCATAAAAATTGTAGATCAT
* * * ** * *
52138 GAAACAATCTTTTAATAGACACTTAAATCACCTTAATCGGATAACCATAG-AGA
126 GAAACAACCTTTCAAAAGACACTTAAATCACCGCAATCAGA-AACC-TAGAACA
* *
52191 AAATTATATAATGTTAAATAGACC
1 AAATTATATAATATTAAGTAGACC
52215 ATTTAGACTA
Statistics
Matches: 168, Mismatches: 28, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
177 14 0.08
178 145 0.86
179 7 0.04
180 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34
Consensus pattern (177 bp):
AAATTATATAATATTAAGTAGACCGTCTATTCCCATTAACTGAAACAACAAATTCTTTAGAAGCA
TTGTTTATACCTTGAACATTAAATTTACTTTTCGAGTCCTTCATAAAAATTGTAGATCATGAAAC
AACCTTTCAAAAGACACTTAAATCACCGCAATCAGAAACCTAGAACA
Found at i:54762 original size:22 final size:22
Alignment explanation
Indices: 54737--54784 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
54727 TAAAAAAATT
54737 ATAGAGAA-ATTAACAAAATCTC
1 ATAGAGAAGATT-ACAAAATCTC
* * *
54759 ATAGGGAAGGTTACAAAATTTC
1 ATAGAGAAGATTACAAAATCTC
54781 ATAG
1 ATAG
54785 CAAGGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (22 bp):
ATAGAGAAGATTACAAAATCTC
Found at i:54791 original size:21 final size:22
Alignment explanation
Indices: 54749--54791 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
54739 AGAGAAATTA
*
54749 ACAAAATCTCATAGGGAAGGTT
1 ACAAAATCTCATAGGCAAGGTT
*
54771 ACAAAATTTCATA-GCAAGGTT
1 ACAAAATCTCATAGGCAAGGTT
54792 TATTAAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (22 bp):
ACAAAATCTCATAGGCAAGGTT
Found at i:57826 original size:15 final size:15
Alignment explanation
Indices: 57808--57848 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
57798 TCGATTATTA
57808 ATAAAAAATAAAATT
1 ATAAAAAATAAAATT
57823 ATAAAAAGA-AAAATT
1 ATAAAAA-ATAAAATT
57838 ATAAAAGAATA
1 ATAAAA-AATA
57849 TATTAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (15 bp):
ATAAAAAATAAAATT
Found at i:59770 original size:626 final size:626
Alignment explanation
Indices: 58579--59831 Score: 2380
Period size: 626 Copynumber: 2.0 Consensus size: 626
58569 GTTACGTAGT
* *
58579 GAGAAGTACCTTTACGAGCAGTGATAACATCCTACGCCACCGACTCGATTGAAGAAACATAGAGT
1 GAGAAGTACCTCTACGAGCAGTGATAACATCCTACGCCACCGACTCGATCGAAGAAACATAGAGT
*
58644 TTTAACTAACCTGAAATCACAACAAGAATTTGAAAGGGTGAGTATTCCTAAGAATACTCCGTGAG
66 TTTAACTAACATGAAATCACAACAAGAATTTGAAAGGGTGAGTATTCCTAAGAATACTCCGTGAG
58709 TGCAGAGAGCTAACTAACACCGCATTAAGAGTGAAGTGCATGGCCAATCTAAAACATGTAATTTC
131 TGCAGAGAGCTAACTAACACCGCATTAAGAGTGAAGTGCATGGCCAATCTAAAACATGTAATTTC
58774 AAATCAAGACCAGAGATTTCATTGGGGCTATTTAGTCATTTACAAAACTAAAGATAATCATCTTC
196 AAATCAAGACCAGAGATTTCATTGGGGCTATTTAGTCATTTACAAAACTAAAGATAATCATCTTC
*
58839 AATCTAGTCAATTTATCAAAATAATATCAAGCTCAAGGCATTTCCAAACAAATACATATACGTCA
261 AATCTAGTCAATTTATCAAAATAATATCAAGCTCAAGGCATTTCCAAACAAATACATATACATCA
58904 AAAGATCATATTTCGTATGTTAATATCGCATGTCAAAAACTGCAGTAAATGCACATTTGAAACGA
326 AAAGATCATATTTCGTATGTTAATATCGCATGTCAAAAACTGCAGTAAATGCACATTTGAAACGA
58969 TAGCCCCAATTTGTATAAAACCAATAATCATCAGTAAAACGCATGCATTCGTACGTAAAATAAAC
391 TAGCCCCAATTTGTATAAAACCAATAATCATCAGTAAAACGCATGCATTCGTACGTAAAATAAAC
* * *
59034 AATCATTTCTATCAAATCAATTATGGCATGTCGAATTAGAAATCCGAGTAAATATCATAAATATC
456 AATCATTTATATCAAATCAATTATGCCATGTCGAAATAGAAATCCGAGTAAATATCATAAATATC
59099 TTTGCCCTTAAAACATGCATGTATATACAATAAGATGTTAAGCCAAACTTTGAGTTGAAAATAAA
521 TTTGCCCTTAAAACATGCATGTATATACAATAAGATGTTAAGCCAAACTTTGAGTTGAAAATAAA
59164 CCCATCAAATGAGCGGCCGAAAACCAAGTCCTGCGGTTGTA
586 CCCATCAAATGAGCGGCCGAAAACCAAGTCCTGCGGTTGTA
* * *
59205 GAGAAGTACCTCTACGAGCAGTGATAACATCCTATGCCACCGACTCGATCGAGGAAACGTAGAGT
1 GAGAAGTACCTCTACGAGCAGTGATAACATCCTACGCCACCGACTCGATCGAAGAAACATAGAGT
59270 TTTAACTAACATGAAATCACAACAAGAATTTGAAAGGGTGAGTATTCCTAAGAATACTCCGTGAG
66 TTTAACTAACATGAAATCACAACAAGAATTTGAAAGGGTGAGTATTCCTAAGAATACTCCGTGAG
59335 TGCAGAGAGCTAACTAACACCGCATTAAGAGTGAAGTGCATGGCCAATCTAAAACATGTAATTTC
131 TGCAGAGAGCTAACTAACACCGCATTAAGAGTGAAGTGCATGGCCAATCTAAAACATGTAATTTC
59400 AAATCAAGACCAGAGATTTCATTGGGGCTATTTAGTCATTTACAAAACTAAAGATAATCATCTTC
196 AAATCAAGACCAGAGATTTCATTGGGGCTATTTAGTCATTTACAAAACTAAAGATAATCATCTTC
59465 AATCTAGTCAATTTATCAAAATAATATCAAGCTCAAGGCATTTCCAAACAAATACATATACATCA
261 AATCTAGTCAATTTATCAAAATAATATCAAGCTCAAGGCATTTCCAAACAAATACATATACATCA
* *
59530 AAAGATCATATTTCGTATGTTAATATCGCATGTCAAAAACTGCAGTAAATGTACATTTGAAATGA
326 AAAGATCATATTTCGTATGTTAATATCGCATGTCAAAAACTGCAGTAAATGCACATTTGAAACGA
*
59595 TAGCCCCAATTTGTATAAAACCAATAATCGTCAGTAAAACGCATGCATTCGTACGTAAAATAAAC
391 TAGCCCCAATTTGTATAAAACCAATAATCATCAGTAAAACGCATGCATTCGTACGTAAAATAAAC
59660 AATCATTTATATCAAATCAATTATGCCATGTCGAAATAGAAATCCGAGTAAATATCATAAATATC
456 AATCATTTATATCAAATCAATTATGCCATGTCGAAATAGAAATCCGAGTAAATATCATAAATATC
*
59725 TTTGGCCTTAAAACATGCATGTATATACAATAAGATGTTAAGCCAAACTTTGAGTTGAAAATAAA
521 TTTGCCCTTAAAACATGCATGTATATACAATAAGATGTTAAGCCAAACTTTGAGTTGAAAATAAA
59790 CCCATCAAATGAGCGGCCGAAAACCAAGTCCTGCGGTTGTA
586 CCCATCAAATGAGCGGCCGAAAACCAAGTCCTGCGGTTGTA
59831 G
1 G
59832 CTAATCAACC
Statistics
Matches: 613, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
626 613 1.00
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (626 bp):
GAGAAGTACCTCTACGAGCAGTGATAACATCCTACGCCACCGACTCGATCGAAGAAACATAGAGT
TTTAACTAACATGAAATCACAACAAGAATTTGAAAGGGTGAGTATTCCTAAGAATACTCCGTGAG
TGCAGAGAGCTAACTAACACCGCATTAAGAGTGAAGTGCATGGCCAATCTAAAACATGTAATTTC
AAATCAAGACCAGAGATTTCATTGGGGCTATTTAGTCATTTACAAAACTAAAGATAATCATCTTC
AATCTAGTCAATTTATCAAAATAATATCAAGCTCAAGGCATTTCCAAACAAATACATATACATCA
AAAGATCATATTTCGTATGTTAATATCGCATGTCAAAAACTGCAGTAAATGCACATTTGAAACGA
TAGCCCCAATTTGTATAAAACCAATAATCATCAGTAAAACGCATGCATTCGTACGTAAAATAAAC
AATCATTTATATCAAATCAATTATGCCATGTCGAAATAGAAATCCGAGTAAATATCATAAATATC
TTTGCCCTTAAAACATGCATGTATATACAATAAGATGTTAAGCCAAACTTTGAGTTGAAAATAAA
CCCATCAAATGAGCGGCCGAAAACCAAGTCCTGCGGTTGTA
Found at i:62527 original size:2 final size:2
Alignment explanation
Indices: 62520--62547 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
62510 CTTGACTTGA
62520 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
62548 TAGTATTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63399 original size:25 final size:25
Alignment explanation
Indices: 63350--63400 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
63340 TTAGTAGAAT
*
63350 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
63375 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
63401 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Done.