Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011940.1 Corchorus capsularis cultivar CVL-1 contig11961, 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: 7021
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Found at i:586 original size:27 final size:27
Alignment explanation
Indices: 529--588 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
519 AAGTGATCTT
**
529 AAAATGACCAAAATGCCCCTAAATGTG
1 AAAATGACCAAAATGCCCCTAAATGCA
* *
556 AAAATGACCAAAATGCCCTTGAATGCA
1 AAAATGACCAAAATGCCCCTAAATGCA
583 AAAATG
1 AAAATG
589 CCCCTAGGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAAATGCA
Found at i:1395 original size:14 final size:13
Alignment explanation
Indices: 1376--1433 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 13
1366 CAAGAGACAT
*
1376 TTTTCAAAAAATTG
1 TTTTCAAAAAA-GG
1390 TTTTCAAGAAAAGG
1 TTTTCAA-AAAAGG
*
1404 TTTTCAAAAATGAG
1 TTTTCAAAAAAG-G
*
1418 ATTTCAAAAAA-G
1 TTTTCAAAAAAGG
1430 TTTT
1 TTTT
1434 TAAGTTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
12 4 0.11
13 4 0.11
14 25 0.68
15 4 0.11
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (13 bp):
TTTTCAAAAAAGG
Found at i:2109 original size:10 final size:10
Alignment explanation
Indices: 2083--2125 Score: 68
Period size: 10 Copynumber: 4.1 Consensus size: 10
2073 CAACTCAAAG
2083 AAAAGAAGAAGA
1 AAAAGAA-AA-A
2095 AAAAGAAAAA
1 AAAAGAAAAA
2105 AAAAGAAAAA
1 AAAAGAAAAA
2115 AAAAGAAAAA
1 AAAAGAAAAA
2125 A
1 A
2126 CTTGGACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 22 0.71
11 2 0.06
12 7 0.23
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:2123 original size:17 final size:18
Alignment explanation
Indices: 2079--2125 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
2069 CATTCAACTC
2079 AAAGAAAAGAAGAAGAAAA
1 AAAGAAAA-AAGAAGAAAA
*
2098 AGAAAAAAAAAGAA-AAAA
1 A-AAGAAAAAAGAAGAAAA
2116 AAAGAAAAAA
1 AAAGAAAAAA
2126 CTTGGACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 8 0.32
18 5 0.20
19 6 0.24
20 6 0.24
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAGAAGAAAA
Found at i:3947 original size:54 final size:54
Alignment explanation
Indices: 3829--4143 Score: 445
Period size: 54 Copynumber: 5.8 Consensus size: 54
3819 TCAGAAGAAC
* *
3829 AAGTTTATCTTCAAGTGA-CCAAGTGCGGTCAATCAA-AGAAGTATCCAGTGGTATT
1 AAGTTTATCTTCAAGTGATCC-AGTGCGGTCAATCAAGA-AAGTTTCCAATGGT-TT
* * *
3884 AAGTTTATCTTTAAGTGATCCAGTGCGGTCAATCAAGAAAGCTTCCAATGGTCT
1 AAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTTT
*
3938 AAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATTGTTT
1 AAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTTT
* * * * *
3992 AAATTTATCTTCAAGTGATCTAGTGCGGTCAATTAAGAAAGTTTGCAGTGGTTT
1 AAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTTT
* *
4046 AAGTTTATTTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATTGTTT
1 AAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTTT
* * *
4100 AAATTTATCTTCAAGTGATCTAGTGCGGTCAGTCAAGAAAGTTT
1 AAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTT
4144 GCAGTGCGGT
Statistics
Matches: 232, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
54 186 0.80
55 43 0.19
56 3 0.01
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (54 bp):
AAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATGGTTT
Found at i:4188 original size:108 final size:105
Alignment explanation
Indices: 3829--4188 Score: 395
Period size: 108 Copynumber: 3.3 Consensus size: 105
3819 TCAGAAGAAC
* * * *
3829 AAGTTTATCTTCAAGTGACCAAGTGCGGTCAATCAA-AGAAGTATCCAGTGGTATTAAGTTTATC
1 AAGTTTATCTTCAAGTG----AGTGCGGTCAATCAAGA-AAGTTTCCAATTGT-TTAAATTTATC
* * * * *
3893 TTTAAGTGATCCAGTGCGGTCAATCAAGAAAGCTTCCAATGGTC-T
60 TTCAAGTGATCTAGTGCGGTCAATCAAGAAAGTTTGCAGTGGTCTT
3938 AAGTTTATCTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATTGTTTAAATTTATCTT
1 AAGTTTATCTTCAAGTG----AGTGCGGTCAATCAAGAAAGTTTCCAATTGTTTAAATTTATCTT
*
4003 CAAGTGATCTAGTGCGGTCAATTAAGAAAGTTTGCAGTGGT-TT
62 CAAGTGATCTAGTGCGGTCAATCAAGAAAGTTTGCAGTGGTCTT
*
4046 AAGTTTATTTTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAATTGTTTAAATTTATCTT
1 AAGTTTATCTTCAAGTG----AGTGCGGTCAATCAAGAAAGTTTCCAATTGTTTAAATTTATCTT
*
4111 CAAGTGATCTAGTGCGGTCAGTCAAGAAAGTTTGCAGTGCGGTCAATT
62 CAAGTGATCTAGTGCGGTCAATCAAGAAAGTTTGCAGT--GGTC--TT
* * *
4159 AGGTTTATCTTCAAGTG-GTTCGGTGAATCA
1 AAGTTTATCTTCAAGTGAGTGCGGTCAATCA
4189 GATGACTCGG
Statistics
Matches: 225, Mismatches: 19, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
108 159 0.71
109 45 0.20
110 4 0.02
113 17 0.08
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (105 bp):
AAGTTTATCTTCAAGTGAGTGCGGTCAATCAAGAAAGTTTCCAATTGTTTAAATTTATCTTCAAG
TGATCTAGTGCGGTCAATCAAGAAAGTTTGCAGTGGTCTT
Found at i:4234 original size:42 final size:40
Alignment explanation
Indices: 4165--4254 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 40
4155 AATTAGGTTT
*
4165 ATCTTCAAGTGGTTCGGTGAATCAGATGACTCG-GTGTAGA
1 ATCTTCAAGTGGTTCGGTAAATCAGATGACT-GAGTGTAGA
* *
4205 ATCTTCAAGCTGGATTTGGTAAATCAGATGACTGAGTGTAGC
1 ATCTTCAAG-TGG-TTCGGTAAATCAGATGACTGAGTGTAGA
*
4247 ATTTTCAA
1 ATCTTCAA
4255 AGTTGGAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 9 0.21
41 4 0.09
42 30 0.70
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (40 bp):
ATCTTCAAGTGGTTCGGTAAATCAGATGACTGAGTGTAGA
Found at i:4279 original size:35 final size:35
Alignment explanation
Indices: 4228--4550 Score: 360
Period size: 35 Copynumber: 9.0 Consensus size: 35
4218 ATTTGGTAAA
* *
4228 TCAGATGACT-GAGTGTAGCATTTTCAAAGTTGGAA
1 TCAGATGACTCG-GTGTAGCATCTTCAAAGTTGGAT
* * *
4263 TCAGATGGCTCGGTGTAGCATCTTAAAAGTTAGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* *
4298 TCGGATGACTCGGTGTAGCATCTTCAAAGTTAGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
*
4333 TCAGATGACTCGGTGTAACATCTTCAAAGTTGGATACGGT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGG--A---T
* *
4373 GGATCAGATGACTCGGTGTAACATCTTCAAAGTTAGAT
1 ---TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* *
4411 TCAGATGACTCAGTGTAGCATTTTCAAAGTTGGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* *
4446 TCAGATGACTGGGTGTAACATCTTCAAAGTTGGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* * ***
4481 TCAGATGACTCGATGAAGCATCTTCAAAGTCAAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
* * *
4516 TCAAATGACTCGGCGAAGCATCTTCAAAGTTGGAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
4551 ACGGTGGATC
Statistics
Matches: 246, Mismatches: 33, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
35 209 0.85
36 1 0.00
37 1 0.00
38 1 0.00
40 1 0.00
41 1 0.00
43 32 0.13
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (35 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGTTGGAT
Found at i:4399 original size:113 final size:113
Alignment explanation
Indices: 4262--4480 Score: 366
Period size: 113 Copynumber: 1.9 Consensus size: 113
4252 CAAAGTTGGA
* * * *
4262 ATCAGATGGCTCGGTGTAGCATCTTAAAAGTTAGATTCGGATGACTCGGTGTAGCATCTTCAAAG
1 ATCAGATGACTCGGTGTAACATCTTAAAAGTTAGATTCAGATGACTCAGTGTAGCATCTTCAAAG
4327 TTAGATTCAGATGACTCGGTGTAACATCTTCAAAGTTGGATACGGTGG
66 TTAGATTCAGATGACTCGGTGTAACATCTTCAAAGTTGGATACGGTGG
* *
4375 ATCAGATGACTCGGTGTAACATCTTCAAAGTTAGATTCAGATGACTCAGTGTAGCATTTTCAAAG
1 ATCAGATGACTCGGTGTAACATCTTAAAAGTTAGATTCAGATGACTCAGTGTAGCATCTTCAAAG
* *
4440 TTGGATTCAGATGACTGGGTGTAACATCTTCAAAGTTGGAT
66 TTAGATTCAGATGACTCGGTGTAACATCTTCAAAGTTGGAT
4481 TCAGATGACT
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
113 98 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (113 bp):
ATCAGATGACTCGGTGTAACATCTTAAAAGTTAGATTCAGATGACTCAGTGTAGCATCTTCAAAG
TTAGATTCAGATGACTCGGTGTAACATCTTCAAAGTTGGATACGGTGG
Found at i:4453 original size:148 final size:148
Alignment explanation
Indices: 4186--4510 Score: 424
Period size: 148 Copynumber: 2.2 Consensus size: 148
4176 GTTCGGTGAA
* ** *
4186 TCAGATGACTCGGTGTAGA-ATCTTC-AAGCTGGATTTGGTAAATCAGATGACTGAGTGTAGCAT
1 TCAGATGACTCGGTGTA-ACATCTTCAAAGTTGGATACGGTAAATCAGATGACTGAGTGTAACAT
* * * * *
4249 TTTCAAAGTTGGAATCAGATGGCTCGGTGTAGCATCTTAAAAGTTAGATTCGGATGACTCGGTGT
65 CTTCAAAGTTAGAATCAGATGACTCAGTGTAGCATCTTAAAAGTTAGATTCAGATGACTCGGTGT
*
4314 AGCATCTTCAAAGTTAGAT
130 AACATCTTCAAAGTTAGAT
**
4333 TCAGATGACTCGGTGTAACATCTTCAAAGTTGGATACGGTGGATCAGATGACTCG-GTGTAACAT
1 TCAGATGACTCGGTGTAACATCTTCAAAGTTGGATACGGTAAATCAGATGACT-GAGTGTAACAT
* * * * *
4397 CTTCAAAGTTAGATTCAGATGACTCAGTGTAGCATTTTCAAAGTTGGATTCAGATGACTGGGTGT
65 CTTCAAAGTTAGAATCAGATGACTCAGTGTAGCATCTTAAAAGTTAGATTCAGATGACTCGGTGT
*
4462 AACATCTTCAAAGTTGGAT
130 AACATCTTCAAAGTTAGAT
*
4481 TCAGATGACTCGATG-AAGCATCTTCAAAGT
1 TCAGATGACTCGGTGTAA-CATCTTCAAAGT
4511 CAAATTCAAA
Statistics
Matches: 155, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
146 1 0.01
147 25 0.16
148 128 0.83
149 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (148 bp):
TCAGATGACTCGGTGTAACATCTTCAAAGTTGGATACGGTAAATCAGATGACTGAGTGTAACATC
TTCAAAGTTAGAATCAGATGACTCAGTGTAGCATCTTAAAAGTTAGATTCAGATGACTCGGTGTA
ACATCTTCAAAGTTAGAT
Found at i:4503 original size:183 final size:184
Alignment explanation
Indices: 4228--4571 Score: 539
Period size: 183 Copynumber: 1.9 Consensus size: 184
4218 ATTTGGTAAA
* * *
4228 TCAGATGACTGAGTGTAGCATTTTCAAAGTTGGAATCAGATGGCTCGGTGTAGCATCTTAAAAGT
1 TCAGATGACTCAGTGTAGCATTTTCAAAGTTGGAATCAGATGACTCGGTGTAACATCTTAAAAGT
* * * * * * *
4293 TAGATTCGGATGACTCGGTGTAGCATCTTCAAAGTTAGATTCAGATGACTCGGTGTAA-CATCTT
66 TAGATTCAGATGACTCGATGAAGCATCTTCAAAGTCAAATTCAAATGACTCGGCG-AAGCATCTT
4357 CAAAGTTGGATACGGTGGATCAGA-TGACTCGGTGTAACATCTTCAAAGTTAGAT
130 CAAAGTTGGATACGGTGGATCAGATTGACTCGGTGTAACATCTTCAAAGTTAGAT
* * *
4411 TCAGATGACTCAGTGTAGCATTTTCAAAGTTGGATTCAGATGACTGGGTGTAACATCTTCAAAGT
1 TCAGATGACTCAGTGTAGCATTTTCAAAGTTGGAATCAGATGACTCGGTGTAACATCTTAAAAGT
*
4476 TGGATTCAGATGACTCGATGAAGCATCTTCAAAGTCAAATTCAAATGACTCGGCGAAGCATCTTC
66 TAGATTCAGATGACTCGATGAAGCATCTTCAAAGTCAAATTCAAATGACTCGGCGAAGCATCTTC
4541 AAAGTTGGATACGGTGGATCAGATTGACTCG
131 AAAGTTGGATACGGTGGATCAGATTGACTCG
4572 ATAAAATTTT
Statistics
Matches: 145, Mismatches: 14, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
182 2 0.01
183 136 0.94
184 7 0.05
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (184 bp):
TCAGATGACTCAGTGTAGCATTTTCAAAGTTGGAATCAGATGACTCGGTGTAACATCTTAAAAGT
TAGATTCAGATGACTCGATGAAGCATCTTCAAAGTCAAATTCAAATGACTCGGCGAAGCATCTTC
AAAGTTGGATACGGTGGATCAGATTGACTCGGTGTAACATCTTCAAAGTTAGAT
Found at i:5073 original size:63 final size:62
Alignment explanation
Indices: 4974--5272 Score: 353
Period size: 63 Copynumber: 4.9 Consensus size: 62
4964 AACTCTCGAG
* * *
4974 CAAGATTTTAGATTGAAAC-AGAAACTCTCGGCTAGAGAGCTCAAGCAGGATTTAAAATGAAA
1 CAAGATTTTGGATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATG-AA
* * **
5036 CAAGATTTTGGGTTGAAACAAGAAACTCTCGACTAGAGACCTCGATTAGGATTTGAAAATGAAA
1 CAAGATTTTGGATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTT-AAAATG-AA
* * * * * * *
5100 CAGGACTTAGAATTG-----A-TAACTCTCGACTAGAGACCTCGAGCAGGATTTGAAATGAA
1 CAAGATTTTGGATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAA
*
5156 CAAGA-TTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAA
1 CAAGATTTTGG-ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAA
*
5218 CATGATTTTGGAATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTT
1 CAAGATTTTGG-ATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTT
5273 TAGAATTAAA
Statistics
Matches: 205, Mismatches: 22, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
55 3 0.01
56 10 0.05
57 5 0.02
58 29 0.14
59 1 0.00
61 1 0.00
62 59 0.29
63 78 0.38
64 19 0.09
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.23
Consensus pattern (62 bp):
CAAGATTTTGGATTGAAACAAGAAACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAA
Found at i:5210 original size:120 final size:120
Alignment explanation
Indices: 4996--5272 Score: 344
Period size: 120 Copynumber: 2.3 Consensus size: 120
4986 TTGAAACAGA
* * *
4996 AACTCTCGGCTAGAGAGCTCAAGCAGGATTTAAAATGAAACAAGATTTTGGGTTGAAACAAGAAA
1 AACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAAGATTTTGGATTGAAACAAGAAA
* **
5061 CTCTCGACTAGAGACCTCGATTAGGATTTGAAAATGAAACAGGACTTAGAATTGAT
66 CTCTCGACTAGAGACCTCAAGCAGGATTTG-AAATGAAACAGGACTTAGAATTGAT
* *
5117 AACTCTCGACTAGAGACCTCGAGCAGGATTTGAAATG-AACAAGA-TTTGGAATTGAAACAAGAA
1 AACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAAGATTTTGG-ATTGAAACAAGAA
* * * *
5180 ACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATG-AACATGATTTTGGAATTGAAACAAGA
65 ACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAGGA-CTTAGAATTG-----A-T
5242 AACTCTCGACTAGAGACCTCAAGCAGGATTT
1 AACTCTCGACTAGAGACCTCAAGCAGGATTT
5273 TAGAATTAAA
Statistics
Matches: 135, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
118 6 0.04
119 18 0.13
120 47 0.35
121 33 0.24
124 1 0.01
125 30 0.22
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.23
Consensus pattern (120 bp):
AACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAAGATTTTGGATTGAAACAAGAAA
CTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAAACAGGACTTAGAATTGAT
Found at i:5588 original size:70 final size:69
Alignment explanation
Indices: 5497--5705 Score: 310
Period size: 70 Copynumber: 3.0 Consensus size: 69
5487 TAGACCACCC
* * * * *
5497 TGGATCAACTGGAAACAACTGATGAAAAACCGCCCTGGGTCAACTGAATCGATCATTCTAACATA
1 TGGATAAACTGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATA
5562 AACT
66 AACT
* * *
5566 TGGATAAACGTGGAAACTACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACAC
1 TGGATAAAC-TGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACAT
5631 AAACT
65 AAACT
*
5636 TGGATAAACTTGGAAACAACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACAT
1 TGGATAAAC-TGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACAT
*
5701 GAACT
65 AAACT
5706 GAAGGAAAAC
Statistics
Matches: 125, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
69 8 0.06
70 117 0.94
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.21
Consensus pattern (69 bp):
TGGATAAACTGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATA
AACT
Found at i:5795 original size:119 final size:119
Alignment explanation
Indices: 5584--5852 Score: 423
Period size: 119 Copynumber: 2.3 Consensus size: 119
5574 CGTGGAAACT
* * *
5584 ACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACACAAACTTGGATAAACTTGG
1 ACTGAAGAAAGACCACCCTGGGTCAACTGAATCGATCATTATAACACAAACTTGGATAAACTTGG
* * *
5649 AAACAACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGACATGA
66 AAACAACTAAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGAAATAA
* *
5703 ACTGAAGGAAA-ACCACCCTAGGTCAACTGAATCGATCATTATAACATAAACTTGGATAAACTTG
1 ACTGAA-GAAAGACCACCCTGGGTCAACTGAATCGATCATTATAACACAAACTTGGATAAACTTG
* *
5767 GAAGCTACTAAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGAAATAA
65 GAAACAACTAAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGAAATAA
*
5822 ACTGGAGAAAGACCACCCTGGGTCAACTGAA
1 ACTGAAGAAAGACCACCCTGGGTCAACTGAA
5853 ATAAGCTGAA
Statistics
Matches: 136, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
118 4 0.03
119 128 0.94
120 4 0.03
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (119 bp):
ACTGAAGAAAGACCACCCTGGGTCAACTGAATCGATCATTATAACACAAACTTGGATAAACTTGG
AAACAACTAAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTCTGAAATAA
Found at i:5866 original size:35 final size:35
Alignment explanation
Indices: 5813--5947 Score: 162
Period size: 35 Copynumber: 3.9 Consensus size: 35
5803 ATCGATCATT
* *
5813 CTGAAATAAACTGGAGAAAGACCACCCTGGGTCAA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* *
5848 CTGAAATAAGCTGAAGAAAGACCGCCCTAGGTCAA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * * * *
5883 CTGAATTAAACTCAAGAAATATCGCCCTGGATCAA
1 CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
* * *
5918 TTGAAATTAACTGAAGAAAGATCGCCCTGG
1 CTGAAATAAACTGAAGAAAGACCGCCCTGG
5948 ATTAATTAAC
Statistics
Matches: 84, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 84 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (35 bp):
CTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAA
Found at i:5932 original size:70 final size:64
Alignment explanation
Indices: 5827--5982 Score: 170
Period size: 70 Copynumber: 2.3 Consensus size: 64
5817 AATAAACTGG
* * * *
5827 AGAAAGACCACCCTGGGTCAACTGAAATAAGCTGAAGAAAGACCGCCCTAGGTCAACTGAATTAA
1 AGAAAGATCGCCCTGGATCAATTGAAATAAGCTGAAGAAAGACCGCCCT-GG---A-TGAATT-A
5892 ACTCA
60 ACTCA
* * *
5897 AGAAATATCGCCCTGGATCAATTGAAATTAA-CTGAAGAAAGATCGCCCTGGATTAATTAACTCA
1 AGAAAGATCGCCCTGGATCAATTGAAA-TAAGCTGAAGAAAGACCGCCCTGGATGAATTAACTCA
*
5961 AGAAAGATCGCCTTGGATCAAT
1 AGAAAGATCGCCCTGGATCAAT
5983 AAACATTAAC
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
64 26 0.34
65 5 0.07
66 1 0.01
69 2 0.03
70 39 0.51
71 3 0.04
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (64 bp):
AGAAAGATCGCCCTGGATCAATTGAAATAAGCTGAAGAAAGACCGCCCTGGATGAATTAACTCA
Found at i:5948 original size:35 final size:34
Alignment explanation
Indices: 5814--5982 Score: 136
Period size: 35 Copynumber: 5.0 Consensus size: 34
5804 TCGATCATTC
* * * * *
5814 TGAAATAAACTGGAGAAAGACCACCCTGGGTCAAC
1 TGAAATTAACTGAAGAAAGATCGCCCT-GGTCAAT
* *
5849 TGAAA-TAAGCTGAAGAAAGACCGCCCTAGGTCAAC
1 TGAAATTAA-CTGAAGAAAGATCGCCCT-GGTCAAT
* *
5884 TG-AATTAAACTCAAGAAATATCGCCCTGGATCAAT
1 TGAAATT-AACTGAAGAAAGATCGCCCTGG-TCAAT
5919 TGAAATTAACTGAAGAAAGATCGCCCTGG---AT
1 TGAAATTAACTGAAGAAAGATCGCCCTGGTCAAT
* *
5950 T--AATTAACTCAAGAAAGATCGCCTTGGATCAAT
1 TGAAATTAACTGAAGAAAGATCGCCCTGG-TCAAT
5983 AAACATTAAC
Statistics
Matches: 113, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
29 24 0.21
31 3 0.03
33 2 0.02
34 6 0.05
35 72 0.64
36 6 0.05
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21
Consensus pattern (34 bp):
TGAAATTAACTGAAGAAAGATCGCCCTGGTCAAT
Found at i:5964 original size:29 final size:30
Alignment explanation
Indices: 5886--5978 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 30
5876 AGGTCAACTG
*
5886 AATTAAACTCAAGAAATATCGCCCTGGATCAATTGA
1 AATT-AACTCAAGAAAGATCGCCCTGG----ATT-A
*
5922 AATTAACTGAAGAAAGATCGCCCTGGATT-
1 AATTAACTCAAGAAAGATCGCCCTGGATTA
*
5951 AATTAACTCAAGAAAGATCGCCTTGGAT
1 AATTAACTCAAGAAAGATCGCCCTGGAT
5979 CAATAAACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
29 26 0.49
31 3 0.06
35 20 0.38
36 4 0.08
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (30 bp):
AATTAACTCAAGAAAGATCGCCCTGGATTA
Done.