Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023891.1 Corchorus olitorius cultivar O-4 contig23924, 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: 10298
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:955 original size:21 final size:21
Alignment explanation
Indices: 931--970 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
921 GGCGCCCACA
*
931 TGGTTTCCTTGAGAACCCATG
1 TGGTTTACTTGAGAACCCATG
952 TGGTTTACTTGAGAACCCA
1 TGGTTTACTTGAGAACCCA
971 AGTGCGCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.33
Consensus pattern (21 bp):
TGGTTTACTTGAGAACCCATG
Found at i:2844 original size:31 final size:30
Alignment explanation
Indices: 2803--2887 Score: 116
Period size: 31 Copynumber: 2.8 Consensus size: 30
2793 ATTCTTAAGC
* *
2803 AAATCCAAAAGAAAATTTTGGAAAATAAGG
1 AAATCCAAAAGAAGATTTTGGAAAATAAAG
*
2833 TAATTCCAAAAGAAGATTTTGGAAAATAAAG
1 -AAATCCAAAAGAAGATTTTGGAAAATAAAG
**
2864 AAATAAAAAAGAAGATTTTGGAAA
1 AAATCCAAAAGAAGATTTTGGAAA
2888 TTAATAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 21 0.44
31 27 0.56
ACGTcount: A:0.56, C:0.05, G:0.16, T:0.22
Consensus pattern (30 bp):
AAATCCAAAAGAAGATTTTGGAAAATAAAG
Found at i:3512 original size:8 final size:8
Alignment explanation
Indices: 3477--3528 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
3467 GAAGTGCACC
*
3477 AAAAAATG
1 AAAAAAAG
*
3485 AAAAAAGG
1 AAAAAAAG
*
3493 AAAAAAGG
1 AAAAAAAG
3501 AAAAAGAA-
1 AAAAA-AAG
3509 AAAAAAAG
1 AAAAAAAG
3517 AAAAAGAAG
1 AAAAA-AAG
3526 AAA
1 AAA
3529 GAATAAAGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
7 2 0.05
8 30 0.77
9 7 0.18
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5217 original size:169 final size:169
Alignment explanation
Indices: 4931--5443 Score: 864
Period size: 169 Copynumber: 3.0 Consensus size: 169
4921 AGTTTCAATA
* *
4931 CGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGTTTAAGTTTAAAATCCTTGGT
1 CGGGTACCATTTCATTTCATCAAGTTTTTCATTAAAAATTCATGTTTAAGTTTAAAATCCTTGGT
*
4996 CAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTA
66 CAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGGTA
* *
5061 TTAATTCTGATAAGTCCTCCGGGCAATCGATAAAACCCC
131 TTAATTCTGATAAGTCCTCCGGGCAATCGGTAAAACCTC
* * * *
5100 CGGGTACCATTTCATTTCATTAAATTTTTCATTAAAAATTCATGTTTAAGTTTAAAATGCTTGTT
1 CGGGTACCATTTCATTTCATCAAGTTTTTCATTAAAAATTCATGTTTAAGTTTAAAATCCTTGGT
5165 CAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGGTA
66 CAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGGTA
*
5230 TTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTC
131 TTAATTCTGATAAGTCCTCCGGGCAATCGGTAAAACCTC
* * * *
5269 CGGGTACCATTTCATTTCATCGAGTTTTTCATTAAAAAATCATGGTTAAGTTTTAAATCCTTGGT
1 CGGGTACCATTTCATTTCATCAAGTTTTTCATTAAAAATTCATGTTTAAGTTTAAAATCCTTGGT
* *
5334 CAAGCTCTCTAGTCAGAGTTTACATTGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGGTA
66 CAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGGTA
* *
5399 TTAATTCTGATAAGTTCTTCGGGCAATCGGTAAAACCTC
131 TTAATTCTGATAAGTCCTCCGGGCAATCGGTAAAACCTC
5438 CGGGTA
1 CGGGTA
5444 TTAATTCTGA
Statistics
Matches: 321, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
169 321 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (169 bp):
CGGGTACCATTTCATTTCATCAAGTTTTTCATTAAAAATTCATGTTTAAGTTTAAAATCCTTGGT
CAAGGTCTCTATTCAGAGTTTACATTGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGGTA
TTAATTCTGATAAGTCCTCCGGGCAATCGGTAAAACCTC
Found at i:5437 original size:45 final size:45
Alignment explanation
Indices: 5386--5488 Score: 197
Period size: 45 Copynumber: 2.3 Consensus size: 45
5376 ACAAATTCAG
*
5386 AAACCTCCGGGTATTAATTCTGATAAGTTCTTCGGGCAATCGGTA
1 AAACCTCCGGGTATTAATTCTGAGAAGTTCTTCGGGCAATCGGTA
5431 AAACCTCCGGGTATTAATTCTGAGAAGTTCTTCGGGCAATCGGTA
1 AAACCTCCGGGTATTAATTCTGAGAAGTTCTTCGGGCAATCGGTA
5476 AAACCTCCGGGTA
1 AAACCTCCGGGTA
5489 CCATTTCATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (45 bp):
AAACCTCCGGGTATTAATTCTGAGAAGTTCTTCGGGCAATCGGTA
Found at i:5483 original size:214 final size:214
Alignment explanation
Indices: 5217--5657 Score: 702
Period size: 214 Copynumber: 2.1 Consensus size: 214
5207 ACAAATTCAG
* *
5217 AAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTCCGGGTACCATTTC
1 AAACCTCCGGGTATTAATTCTGAGAAGTCCTCCGGGCAATCGGTAAAACCTCCGGGTACCATTTC
* * *
5282 ATTTCATCGAGTTTTTCATTAAAAAATCATGGTTAAGTTTTAAATCCTTGGTCAAGCTCTCTAGT
66 ATTTCATCAAGTTTTTCATTAAAAAATCATGGTTAAGTTTAAAATCCTTGCTCAAGCTCTCTAGT
* *
5347 CAGAGTTTACATTGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAA
131 CAGAGTTTACAATGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGCTATTAATTCTGATAA
* *
5412 GTTCTTCGGGCAATCGGTA
196 GTCCTCCGGGCAATCGGTA
* *
5431 AAACCTCCGGGTATTAATTCTGAGAAGTTCTTCGGGCAATCGGTAAAACCTCCGGGTACCATTTC
1 AAACCTCCGGGTATTAATTCTGAGAAGTCCTCCGGGCAATCGGTAAAACCTCCGGGTACCATTTC
* * * * *
5496 ATTTCATTAAGTTTTTCATTAAAAACTCATGTTTAAGTTTAAAATCCTTGCTCAAGGTCTCTATT
66 ATTTCATCAAGTTTTTCATTAAAAAATCATGGTTAAGTTTAAAATCCTTGCTCAAGCTCTCTAGT
* * *
5561 CAGAGTTTACAATGGTAAGTCCTCCGGGCATAAATTTAGAAACCTCCGGCTATTAATTCTGATAA
131 CAGAGTTTACAATGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGCTATTAATTCTGATAA
*
5626 GTCCTCCGGGCAATTGGTA
196 GTCCTCCGGGCAATCGGTA
5645 AAACCTCCGGGTA
1 AAACCTCCGGGTA
5658 CCATTTCATT
Statistics
Matches: 207, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
214 207 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (214 bp):
AAACCTCCGGGTATTAATTCTGAGAAGTCCTCCGGGCAATCGGTAAAACCTCCGGGTACCATTTC
ATTTCATCAAGTTTTTCATTAAAAAATCATGGTTAAGTTTAAAATCCTTGCTCAAGCTCTCTAGT
CAGAGTTTACAATGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGCTATTAATTCTGATAA
GTCCTCCGGGCAATCGGTA
Found at i:5712 original size:169 final size:168
Alignment explanation
Indices: 5431--5964 Score: 687
Period size: 169 Copynumber: 3.2 Consensus size: 168
5421 GCAATCGGTA
* * *
5431 AAACCTCCGGGTATTAATTCTGAGAAGTTCTTCGGGCAATCGGTAAAACCTCCGGGTACCATTTC
1 AAACCTCCGGGTATTAATTCTGATAAG-TCCTCGGGCAATTGGTAAAACCTCCGGGTACCATTTC
* * *
5496 ATTTCATTAAGTTTTTCATTAAAAACTCATGTTTAAGTTTAAAATCCTTGCTCAAGGTCTCTATT
65 ATTTCATCAAGTTTTTCATTAAAAATTCATGTTTAAGTTTAAAATCCTTGTTCAAGGTCTCTATT
* * * * *
5561 CAGAGTTTACAATGGTAAGTCCTCCGGGCATAAATTTAG
130 CAAAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAG
*
5600 AAACCTCCGGCTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTCCGGGTACCATTTC
1 AAACCTCCGGGTATTAATTCTGATAAGTCCT-CGGGCAATTGGTAAAACCTCCGGGTACCATTTC
* * * *
5665 ATTTCATCGAGTTTTTCATTAAAAATTCATGGTTAAGTTTTAAATCCTTGTTCAAGGTCTTTATT
65 ATTTCATCAAGTTTTTCATTAAAAATTCATGTTTAAGTTTAAAATCCTTGTTCAAGGTCTCTATT
* * *** *
5730 CAAAGTTTGCATTTGTAAGACCTCCAAACACAAGTTCAG
130 CAAAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAG
* * * * * * * * *
5769 AAACCTTCGGGTAGTAATTCTGATAAGTCCTCTGGCAATTTGTAAAGCTTCCGAGTATCATTGCA
1 AAACCTCCGGGTATTAATTCTGATAAGTCCTCGGGCAATTGGTAAAACCTCCGGGTACCATTTCA
* * *
5834 TTTTATCAAG-TTTT--TTAAAGATTCATGTTTAAGTTTAAAATCCTTGTTCAAGGTCTCAATTC
66 TTTCATCAAGTTTTTCATTAAAAATTCATGTTTAAGTTTAAAATCCTTGTTCAAGGTCTCTATTC
* *
5896 AAAGCTTGCATTGGTAAGTCCTCCGGGCACAAATTCGG
131 AAAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAG
* *
5934 AAACCTCCGGGTATTAATTTTGATATGTCCT
1 AAACCTCCGGGTATTAATTCTGATAAGTCCT
5965 TCGGACATTT
Statistics
Matches: 313, Mismatches: 51, Indels: 6
0.85 0.14 0.02
Matches are distributed among these distances:
165 100 0.32
167 4 0.01
168 38 0.12
169 171 0.55
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (168 bp):
AAACCTCCGGGTATTAATTCTGATAAGTCCTCGGGCAATTGGTAAAACCTCCGGGTACCATTTCA
TTTCATCAAGTTTTTCATTAAAAATTCATGTTTAAGTTTAAAATCCTTGTTCAAGGTCTCTATTC
AAAGTTTGCATTGGTAAGTCCTCCGGGCACAAATTCAG
Found at i:5770 original size:383 final size:383
Alignment explanation
Indices: 5048--5796 Score: 1246
Period size: 383 Copynumber: 2.0 Consensus size: 383
5038 ACAAATTCAG
*
5048 AAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATCGATAAAACCCCCGGGTACCATTTC
1 AAACCTCCGGGTATTAATTCTGAGAAGTCCTCCGGGCAATCGATAAAACCCCCGGGTACCATTTC
* * *
5113 ATTTCATTAAATTTTTCATTAAAAATTCATGTTTAAGTTTAAAATGCTTGTTCAAGGTCTCTATT
66 ATTTCATTAAATTTTTCATTAAAAACTCATGTTTAAGTTTAAAATCCTTGCTCAAGGTCTCTATT
* *
5178 CAGAGTTTACATTGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAA
131 CAGAGTTTACAATGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGCTATTAATTCTGATAA
5243 GTCCTCCGGGCAATTGGTAAAACCTCCGGGTACCATTTCATTTCATCGAGTTTTTCATTAAAAAA
196 GTCCTCCGGGCAATTGGTAAAACCTCCGGGTACCATTTCATTTCATCGAGTTTTTCATTAAAAAA
* *
5308 TCATGGTTAAGTTTTAAATCCTTGGTCAAGCTCTCTAGTCAGAGTTTACATTGGTAAGTCCTCCA
261 TCATGGTTAAGTTTTAAATCCTTGGTCAAGCTCTCTAGTCAAAGTTTACATTGGTAAGACCTCCA
** *
5373 GGCACAAATTCAGAAACCTCCGGGTATTAATTCTGATAAGTTCTTCGGGCAATCGGTA
326 AACACAAATTCAGAAACCTCCGGGTAGTAATTCTGATAAGTTCTTCGGGCAATCGGTA
* * * *
5431 AAACCTCCGGGTATTAATTCTGAGAAGTTCTTCGGGCAATCGGTAAAACCTCCGGGTACCATTTC
1 AAACCTCCGGGTATTAATTCTGAGAAGTCCTCCGGGCAATCGATAAAACCCCCGGGTACCATTTC
*
5496 ATTTCATTAAGTTTTTCATTAAAAACTCATGTTTAAGTTTAAAATCCTTGCTCAAGGTCTCTATT
66 ATTTCATTAAATTTTTCATTAAAAACTCATGTTTAAGTTTAAAATCCTTGCTCAAGGTCTCTATT
* * *
5561 CAGAGTTTACAATGGTAAGTCCTCCGGGCATAAATTTAGAAACCTCCGGCTATTAATTCTGATAA
131 CAGAGTTTACAATGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGCTATTAATTCTGATAA
*
5626 GTCCTCCGGGCAATTGGTAAAACCTCCGGGTACCATTTCATTTCATCGAGTTTTTCATTAAAAAT
196 GTCCTCCGGGCAATTGGTAAAACCTCCGGGTACCATTTCATTTCATCGAGTTTTTCATTAAAAAA
* * * * * *
5691 TCATGGTTAAGTTTTAAATCCTTGTTCAAGGTCTTTATTCAAAGTTTGCATTTGTAAGACCTCCA
261 TCATGGTTAAGTTTTAAATCCTTGGTCAAGCTCTCTAGTCAAAGTTTACATTGGTAAGACCTCCA
* *
5756 AACACAAGTTCAGAAACCTTCGGGTAGTAATTCTGATAAGT
326 AACACAAATTCAGAAACCTCCGGGTAGTAATTCTGATAAGT
5797 CCTCTGGCAA
Statistics
Matches: 338, Mismatches: 28, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
383 338 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (383 bp):
AAACCTCCGGGTATTAATTCTGAGAAGTCCTCCGGGCAATCGATAAAACCCCCGGGTACCATTTC
ATTTCATTAAATTTTTCATTAAAAACTCATGTTTAAGTTTAAAATCCTTGCTCAAGGTCTCTATT
CAGAGTTTACAATGGTAAGTCCTCCAGGCACAAATTCAGAAACCTCCGGCTATTAATTCTGATAA
GTCCTCCGGGCAATTGGTAAAACCTCCGGGTACCATTTCATTTCATCGAGTTTTTCATTAAAAAA
TCATGGTTAAGTTTTAAATCCTTGGTCAAGCTCTCTAGTCAAAGTTTACATTGGTAAGACCTCCA
AACACAAATTCAGAAACCTCCGGGTAGTAATTCTGATAAGTTCTTCGGGCAATCGGTA
Found at i:6080 original size:33 final size:33
Alignment explanation
Indices: 6037--6102 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
6027 TTAATTTTCG
*
6037 ATCCTGGTTTAGGATCATTACTTTATCAGTTTA
1 ATCCTGGTTTAGGATCATGACTTTATCAGTTTA
* * *
6070 ATCCTTGTTTAGGATCATGGCTTTCTCAGTTTA
1 ATCCTGGTTTAGGATCATGACTTTATCAGTTTA
6103 TTTCAATCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (33 bp):
ATCCTGGTTTAGGATCATGACTTTATCAGTTTA
Found at i:6154 original size:30 final size:30
Alignment explanation
Indices: 6118--6220 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 30
6108 ATCTTGGTTG
*
6118 AGGATCATTGCTTCATTTTAATCCTGATTT
1 AGGATCATTGCTTCATTTTAATCCTGATCT
* * *
6148 AGGATCATTGCTTTATTTTAATCATGGTCT
1 AGGATCATTGCTTCATTTTAATCCTGATCT
* * *
6178 AGGATCATTGTTTCATTAGTTAATCCCGATGT
1 AGGATCATTGCTTCATT--TTAATCCTGATCT
*
6210 AGGATTATTGC
1 AGGATCATTGC
6221 ATTATGAGTT
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 41 0.69
32 18 0.31
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (30 bp):
AGGATCATTGCTTCATTTTAATCCTGATCT
Found at i:6193 original size:60 final size:61
Alignment explanation
Indices: 6099--6225 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 61
6089 GCTTTCTCAG
* * *
6099 TTTATTTCAATCTTGGTTGAGGATCATTGCTTCATT-TTAATCCTGATTTAGGATCATTGC
1 TTTATTTCAATCATGGTTGAGGATCATTGCTTCATTATTAATCCCGATGTAGGATCATTGC
* * *
6159 TTTATTTTAATCATGGTCT-AGGATCATTGTTTCATTAGTTAATCCCGATGTAGGATTATTGC
1 TTTATTTCAATCATGGT-TGAGGATCATTGCTTCATTA-TTAATCCCGATGTAGGATCATTGC
*
6221 ATTAT
1 TTTAT
6226 GAGTTAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
60 31 0.54
61 1 0.02
62 25 0.44
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (61 bp):
TTTATTTCAATCATGGTTGAGGATCATTGCTTCATTATTAATCCCGATGTAGGATCATTGC
Found at i:6332 original size:39 final size:39
Alignment explanation
Indices: 6278--6366 Score: 133
Period size: 39 Copynumber: 2.3 Consensus size: 39
6268 TTTGAATCTT
*
6278 GATTATAGCTTTGTCAGTCTTATTCCAATCCTGATTTAG
1 GATTATTGCTTTGTCAGTCTTATTCCAATCCTGATTTAG
* * *
6317 GATTATTGCTTTGTCAGTTTTATTTCGATCCTGATTTAG
1 GATTATTGCTTTGTCAGTCTTATTCCAATCCTGATTTAG
*
6356 GATCATTGCTT
1 GATTATTGCTT
6367 ACCAGTTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.47
Consensus pattern (39 bp):
GATTATTGCTTTGTCAGTCTTATTCCAATCCTGATTTAG
Found at i:6754 original size:28 final size:27
Alignment explanation
Indices: 6694--6764 Score: 115
Period size: 28 Copynumber: 2.6 Consensus size: 27
6684 GTAAGGTCAC
6694 CTAGGGGCATTTTGGTCATTTTCACAT
1 CTAGGGGCATTTTGGTCATTTTCACAT
*
6721 CCAGGGGCATTTTGGTCATTTTTCACAT
1 CTAGGGGCATTTTGGTCA-TTTTCACAT
*
6749 CTAGGGGAATTTTGGT
1 CTAGGGGCATTTTGGT
6765 AAGTTCACAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 17 0.43
28 23 0.57
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.39
Consensus pattern (27 bp):
CTAGGGGCATTTTGGTCATTTTCACAT
Found at i:9370 original size:28 final size:27
Alignment explanation
Indices: 9339--9426 Score: 95
Period size: 27 Copynumber: 3.2 Consensus size: 27
9329 GGCAGTTCAA
*
9339 TCATTTTCAAAATCTAGGGGCATTTTAG
1 TCATTTGCAAAATC-AGGGGCATTTTAG
* * *
9367 TCATTTGCACATTCAGGGGCATTTTGG
1 TCATTTGCAAAATCAGGGGCATTTTAG
* * * *
9394 TCATTTGCATACTCAGGGGAATTTTGG
1 TCATTTGCAAAATCAGGGGCATTTTAG
9421 TCATTT
1 TCATTT
9427 TGGGCATTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 42 0.79
28 11 0.21
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.40
Consensus pattern (27 bp):
TCATTTGCAAAATCAGGGGCATTTTAG
Found at i:9388 original size:27 final size:27
Alignment explanation
Indices: 9354--9426 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
9344 TTCAAAATCT
* *
9354 AGGGGCATTTTAGTCATTTGCACATTC
1 AGGGGCATTTTGGTCATTTGCACACTC
*
9381 AGGGGCATTTTGGTCATTTGCATACTC
1 AGGGGCATTTTGGTCATTTGCACACTC
*
9408 AGGGGAATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
9427 TGGGCATTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCACACTC
Done.