Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009749.1 Corchorus capsularis cultivar CVL-1 contig09770, 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: 18184
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:6260 original size:15 final size:15
Alignment explanation
Indices: 6237--6266 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6227 ATCGGTTGAA
*
6237 ATATTGTGTATCGTG
1 ATATCGTGTATCGTG
6252 ATATCGTGTATCGTG
1 ATATCGTGTATCGTG
6267 GCAGCCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
ATATCGTGTATCGTG
Found at i:8420 original size:128 final size:128
Alignment explanation
Indices: 8280--8536 Score: 496
Period size: 128 Copynumber: 2.0 Consensus size: 128
8270 ATCTAAAATA
8280 CCCTTTTTAATATTATAGACATGAGTTTTAAGCTTTAATGATAAATATGTAATTTAATATATCAA
1 CCCTTTTTAATATTATAGACATGAGTTTTAAGCTTTAATGATAAATATGTAATTTAATATATCAA
8345 ATATAAAATATGTTTAAAATACCATTAATGTTAAACTTGCTTCTAATGATGATGATTGCATAT
66 ATATAAAATATGTTTAAAATACCATTAATGTTAAACTTGCTTCTAATGATGATGATTGCATAT
* *
8408 CCCTTTTTAATATTATAGACATGAGTTTTAAGCTTTAGTGATTAATATGTAATTTAATATATCAA
1 CCCTTTTTAATATTATAGACATGAGTTTTAAGCTTTAATGATAAATATGTAATTTAATATATCAA
8473 ATATAAAATATGTTTAAAATACCATTAATGTTAAACTTGCTTCTAATGATGATGATTGCATAT
66 ATATAAAATATGTTTAAAATACCATTAATGTTAAACTTGCTTCTAATGATGATGATTGCATAT
8536 C
1 C
8537 TATATAATAA
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 127 1.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.42
Consensus pattern (128 bp):
CCCTTTTTAATATTATAGACATGAGTTTTAAGCTTTAATGATAAATATGTAATTTAATATATCAA
ATATAAAATATGTTTAAAATACCATTAATGTTAAACTTGCTTCTAATGATGATGATTGCATAT
Found at i:8957 original size:2 final size:2
Alignment explanation
Indices: 8950--8974 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8940 ATGAAATCCA
8950 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8975 AAATAAATAT
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11829 original size:32 final size:32
Alignment explanation
Indices: 11791--11852 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
11781 TTTTTGTTAC
11791 TAGAGTATACGTAACATACATAATTATTGCTA
1 TAGAGTATACGTAACATACATAATTATTGCTA
* *
11823 TAGAGTATGCGTATCATACATAATTATTGC
1 TAGAGTATACGTAACATACATAATTATTGC
11853 AAATATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (32 bp):
TAGAGTATACGTAACATACATAATTATTGCTA
Found at i:14214 original size:85 final size:84
Alignment explanation
Indices: 14017--14247 Score: 363
Period size: 85 Copynumber: 2.7 Consensus size: 84
14007 AAAATAATAA
* * * *
14017 AATTTGTAAAGATAATATTTTCTAAATCTTACCAAATTGTGGATGGTTTAGGAAATATTTTAATA
1 AATTTGTAAAGATAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
14082 AATAAAATTATAAAGATTT
66 AATAAAATTATAAAGATTT
* *
14101 AATTTGTAAATATAATATTTTCTTAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
1 AATTTGTAAAGATAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
14166 AATAAAAATTATAAAGATTT
66 AAT-AAAATTATAAAGATTT
* * * *
14186 CATTTGTAAAGAGAATATTTTCTGAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTA
1 AATTTGTAAAGATAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTA
14248 CAAAGATTTA
Statistics
Matches: 135, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 62 0.46
85 73 0.54
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (84 bp):
AATTTGTAAAGATAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
AATAAAATTATAAAGATTT
Found at i:15972 original size:21 final size:21
Alignment explanation
Indices: 15948--15988 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
15938 ATTGAGACAA
15948 TCACAAGAAGAAATGAGGCAT
1 TCACAAGAAGAAATGAGGCAT
* *
15969 TCACAAGAAGAGATGCGGCA
1 TCACAAGAAGAAATGAGGCA
15989 AGAACAAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.27, T:0.12
Consensus pattern (21 bp):
TCACAAGAAGAAATGAGGCAT
Found at i:18148 original size:2 final size:2
Alignment explanation
Indices: 18143--18184 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
18133 TGTGTGTGTC
18143 TA TA TA TA TA TA TA 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 TA TA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.