Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_15618
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: 5910
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Found at i:4301 original size:153 final size:153
Alignment explanation
Indices: 3955--4391 Score: 625
Period size: 153 Copynumber: 2.9 Consensus size: 153
3945 CAAGGTGTCA
* ** * *
3955 GATGTTGGTTGGGATG-C--ATCTGGATGGAATAAAAATGTTGAGGATGTTGACAAATTTGCTGC
1 GATGTTGGTTGGGATGCCTTGTCTGGATGGAATAAAAATGCAGAGGATGGTGACAAATTTGCAGC
* * * * *
4017 AGCTGCGACCAGTTCGGAGAAGCAAAATGAGTGGTCTGGTTGGGGTGTGAGCAAATCTAACTCAC
66 AGCTGCAACCAGTTCGAAGAAGCAAAATGAGTGGTCTGATTGGGGGGTGAGCAAATCTAAATCAC
4082 -A-A-GTTGTCTCTCCAAAAGTG
131 AAGATGTTGTCTCTCCAAAAGTG
* *
4102 GATGTTGGTTGGGATGCTTTGTCTGGATGGAATAAAAATGCGGAGGATGGTGACAAATTTGCAGC
1 GATGTTGGTTGGGATGCCTTGTCTGGATGGAATAAAAATGCAGAGGATGGTGACAAATTTGCAGC
* * * *
4167 TGCTGCAACCAGTTCGAAGAAGAAAAATGAGTGTTCTGATTGGGGGGCGAGCAAATCTAAATCAC
66 AGCTGCAACCAGTTCGAAGAAGCAAAATGAGTGGTCTGATTGGGGGGTGAGCAAATCTAAATCAC
4232 AAGATGTTGTCTCTCCAAAAGTG
131 AAGATGTTGTCTCTCCAAAAGTG
* *
4255 GATGTTGGTTGGGATGCCTTGTCTGCATGGAATAAAAATGCAGAGGATGGTGACAATTTTGCAGC
1 GATGTTGGTTGGGATGCCTTGTCTGGATGGAATAAAAATGCAGAGGATGGTGACAAATTTGCAGC
* * ** *
4320 AGCTGCATCCAGTTCAAAGAAGCAAAGCGAGTGGTCTGATTGGGGGATGAGCAAATCTAAATCAC
66 AGCTGCAACCAGTTCGAAGAAGCAAAATGAGTGGTCTGATTGGGGGGTGAGCAAATCTAAATCAC
4385 AAGATGT
131 AAGATGT
4392 CTCTTCAAAA
Statistics
Matches: 256, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
147 16 0.06
150 96 0.38
151 1 0.00
152 1 0.00
153 142 0.55
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (153 bp):
GATGTTGGTTGGGATGCCTTGTCTGGATGGAATAAAAATGCAGAGGATGGTGACAAATTTGCAGC
AGCTGCAACCAGTTCGAAGAAGCAAAATGAGTGGTCTGATTGGGGGGTGAGCAAATCTAAATCAC
AAGATGTTGTCTCTCCAAAAGTG
Found at i:5042 original size:36 final size:36
Alignment explanation
Indices: 4964--5164 Score: 158
Period size: 36 Copynumber: 5.7 Consensus size: 36
4954 AAGAATAGTG
* ** *
4964 CTTGGGACCAACAAAAGTCA-CAGACAATGAATAATG
1 CTTGGGACCAACAAAAGTCACCTG-CAACAAATAATT
*
5000 CTTGGGACCAACAAAAGTCACCTGCAACAAATAGTT
1 CTTGGGACCAACAAAAGTCACCTGCAACAAATAATT
* * ** * * * **
5036 CCTGGGATCGGCAAAAATCATCTACGGCAAATAATT
1 CTTGGGACCAACAAAAGTCACCTGCAACAAATAATT
* * * *
5072 CTTGGGACCAGCAAAAGCCA-C--CAGCAAATAGTT
1 CTTGGGACCAACAAAAGTCACCTGCAACAAATAATT
* * **
5105 CTTGGGACCAAGAAAAGTCACCTACAATGAATAATT
1 CTTGGGACCAACAAAAGTCACCTGCAACAAATAATT
*
5141 CATGGGACCAACAAAAGTCACCTG
1 CTTGGGACCAACAAAAGTCACCTG
5165 AATGTTCACA
Statistics
Matches: 129, Mismatches: 32, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
33 27 0.21
34 1 0.01
35 1 0.01
36 98 0.76
37 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.18
Consensus pattern (36 bp):
CTTGGGACCAACAAAAGTCACCTGCAACAAATAATT
Found at i:5121 original size:33 final size:33
Alignment explanation
Indices: 5062--5162 Score: 98
Period size: 33 Copynumber: 3.0 Consensus size: 33
5052 ATCATCTACG
5062 GCAAATAATTCTTGGGACCAGCAAAAGCCACCA
1 GCAAATAATTCTTGGGACCAGCAAAAGCCACCA
* *
5095 GCAAATAGTTCTTGGGACCAAG-AAAAGTCACCTA
1 GCAAATAATTCTTGGGACC-AGCAAAAGCCACC-A
* * *
5129 -CAATGAATAATTCATGGGACCAACAAAAGTCACC
1 GC-A--AATAATTCTTGGGACCAGCAAAAGCCACC
5163 TGAATGTTCA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
33 28 0.49
34 4 0.07
35 1 0.02
36 24 0.42
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (33 bp):
GCAAATAATTCTTGGGACCAGCAAAAGCCACCA
Found at i:5140 original size:69 final size:69
Alignment explanation
Indices: 4957--5162 Score: 207
Period size: 69 Copynumber: 2.9 Consensus size: 69
4947 CTGGAGTAAG
* * ** *
4957 AATAGTGCTTGGGACCAACAAAAGTCACAGACAATGAATAATGCTTGGGACCAACAAAAGTCACC
1 AATAGTTCTTGGGACCAAGAAAAGTCACCTACAATGAATAATTCTTGGGACCAACAAAAGTCA-C
5022 TGCAACA
65 --CAACA
* * * * * **** * *
5029 AATAGTTCCTGGGATC-GGCAAAAATCATCTACGGCAAATAATTCTTGGGACCAGCAAAAGCCAC
1 AATAGTTCTTGGGACCAAG-AAAAGTCACCTACAATGAATAATTCTTGGGACCAACAAAAGTCAC
*
5093 CAGCA
65 CAACA
*
5098 AATAGTTCTTGGGACCAAGAAAAGTCACCTACAATGAATAATTCATGGGACCAACAAAAGTCACC
1 AATAGTTCTTGGGACCAAGAAAAGTCACCTACAATGAATAATTCTTGGGACCAACAAAAGTCACC
5163 TGAATGTTCA
Statistics
Matches: 103, Mismatches: 29, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
69 55 0.53
70 1 0.01
71 1 0.01
72 46 0.45
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (69 bp):
AATAGTTCTTGGGACCAAGAAAAGTCACCTACAATGAATAATTCTTGGGACCAACAAAAGTCACC
AACA
Found at i:5858 original size:42 final size:42
Alignment explanation
Indices: 5806--5888 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
5796 TCCAGAGAAT
*
5806 TCTCAAGGGAACCGCGACCAAAGTGTTACTCAAGATGATAAC
1 TCTCAAGGGAACCGCGACCAAAGTGTTACTCAAGACGATAAC
* *
5848 TCTCAAGGGAACCGTGACCAAAGTGTTGCTCAAGACGATAA
1 TCTCAAGGGAACCGCGACCAAAGTGTTACTCAAGACGATAA
5889 TGAGGGGGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (42 bp):
TCTCAAGGGAACCGCGACCAAAGTGTTACTCAAGACGATAAC
Done.