Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015378.1 Corchorus capsularis cultivar CVL-1 contig15399, 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: 20405
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:830 original size:28 final size:28
Alignment explanation
Indices: 813--883 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
803 CTTGTTGTGT
813 GATACATCAGAGGGAAGAATTTTCGCCA
1 GATACATCAGAGGGAAGAATTTTCGCCA
*
841 GATACATCAGAGGGAAGAATTTTCGCCT
1 GATACATCAGAGGGAAGAATTTTCGCCA
*
869 GAGACATCAGAGGGA
1 GATACATCAGAGGGA
884 GACGTCATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (28 bp):
GATACATCAGAGGGAAGAATTTTCGCCA
Found at i:8827 original size:147 final size:145
Alignment explanation
Indices: 8546--8832 Score: 373
Period size: 147 Copynumber: 2.0 Consensus size: 145
8536 ACTTGGGGGC
* *
8546 CTAAGGCTGACGAACGAAGGAAGATTTATCAAGTGAAGATTGTCGACATACTCATCTAGAAGATT
1 CTAAGGCCGACGAACGAAGGAAGATTTATCAAGTGAAGATTGTCGACATACTAATCTAGAAGATT
* **
8611 GGTGATTCAAATTGATCTTAGGCGGGTCTCTAAGGTGGATTTGGTCCAACATACAACTAGATTCA
66 GGTGATTCAAATTGATCTTAGGCGGGTCTCAAAGGTGGATTTGAACCAACATACAACTAGATTCA
8676 TATCAGAATTGAGGGT
131 TATCA-AATTGAGGGT
* * *
8692 CTAAGGCCGATGAACGAAGGAGGATTTA-CTTAGTGAAGATTGTCGACATAC-AAGTCTAGAAGA
1 CTAAGGCCGACGAACGAAGGAAGATTTATC-AAGTGAAGATTGTCGACATACTAA-TCTAGAAGA
* * * * **
8755 TTTGGTGATTCAAGTTGATCTTTGGCGGGTTTCAAAGGTGGATTTGAACCGATTTGA-AACTAGA
64 -TTGGTGATTCAAATTGATCTTAGGCGGGTCTCAAAGGTGGATTTGAACCAACAT-ACAACTAGA
*
8819 TTCGTATCAAATTG
127 TTCATATCAAATTG
8833 TTTCCTAGGA
Statistics
Matches: 122, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
145 2 0.02
146 59 0.48
147 60 0.49
148 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (145 bp):
CTAAGGCCGACGAACGAAGGAAGATTTATCAAGTGAAGATTGTCGACATACTAATCTAGAAGATT
GGTGATTCAAATTGATCTTAGGCGGGTCTCAAAGGTGGATTTGAACCAACATACAACTAGATTCA
TATCAAATTGAGGGT
Found at i:10872 original size:18 final size:19
Alignment explanation
Indices: 10849--10887 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
10839 TTCTGGAAAT
*
10849 AATTCTTC-AATTGTCTTC
1 AATTCTTCAAATTATCTTC
10867 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATTATCTTC
10886 AA
1 AA
10888 ATAATCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.46
Consensus pattern (19 bp):
AATTCTTCAAATTATCTTC
Found at i:10886 original size:11 final size:11
Alignment explanation
Indices: 10870--10899 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10860 TGTCTTCAAT
*
10870 TCTTCAAATTA
1 TCTTCAAATAA
10881 TCTTCAAATAA
1 TCTTCAAATAA
10892 TCTTCAAA
1 TCTTCAAA
10900 CACGAACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:13365 original size:12 final size:12
Alignment explanation
Indices: 13334--13367 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13324 CATGACCGGC
13334 CAACGCATGGAG
1 CAACGCATGGAG
**
13346 CATTGCATGGAG
1 CAACGCATGGAG
13358 CAACGCATGG
1 CAACGCATGG
13368 GACAGCCGGC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.24, G:0.32, T:0.15
Consensus pattern (12 bp):
CAACGCATGGAG
Found at i:13396 original size:42 final size:42
Alignment explanation
Indices: 13350--13431 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
13340 ATGGAGCATT
*
13350 GCAT-GGAGCAACGCATGGGACAGCCGGCCACAACCGGCCAAC
1 GCATGGGA-CAACGCACGGGACAGCCGGCCACAACCGGCCAAC
* * *
13392 GCATGGGACATCGCACGGGCCATCCGGCCACAACCGGCCA
1 GCATGGGACAACGCACGGGACAGCCGGCCACAACCGGCCA
13432 CTCGACCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 32 0.91
43 3 0.09
ACGTcount: A:0.26, C:0.38, G:0.30, T:0.06
Consensus pattern (42 bp):
GCATGGGACAACGCACGGGACAGCCGGCCACAACCGGCCAAC
Found at i:14265 original size:14 final size:14
Alignment explanation
Indices: 14256--14291 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
14246 TTCATCAAGT
14256 TTCATCCATCAAAA
1 TTCATCCATCAAAA
*
14270 TTCATCCAGCAAAA
1 TTCATCCATCAAAA
14284 TTCATCCA
1 TTCATCCA
14292 CACTCTTAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.39, C:0.31, G:0.03, T:0.28
Consensus pattern (14 bp):
TTCATCCATCAAAA
Found at i:14438 original size:11 final size:11
Alignment explanation
Indices: 14422--14459 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
14412 AGTTATATCG
14422 AAAAATATAAA
1 AAAAATATAAA
14433 AAAAATAT-AA
1 AAAAATATAAA
*
14443 AAAAATAAAAA
1 AAAAATATAAA
14454 AAAAAT
1 AAAAAT
14460 TCGACCAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATATAAA
Found at i:14457 original size:10 final size:10
Alignment explanation
Indices: 14422--14457 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
14412 AGTTATATCG
14422 AAAAATATAAA
1 AAAAATA-AAA
*
14433 AAAAATATAA
1 AAAAATAAAA
14443 AAAAATAAAA
1 AAAAATAAAA
14453 AAAAA
1 AAAAA
14458 ATTCGACCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:19950 original size:12 final size:12
Alignment explanation
Indices: 19933--19974 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
19923 ACCGACCAAT
19933 GCATGGAGCATC
1 GCATGGAGCATC
19945 GCATGGAGCATC
1 GCATGGAGCATC
*
19957 GCATGGAGCAAC
1 GCATGGAGCATC
19969 GCATGG
1 GCATGG
19975 GGCAACCGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.26, C:0.24, G:0.36, T:0.14
Consensus pattern (12 bp):
GCATGGAGCATC
Found at i:19979 original size:12 final size:12
Alignment explanation
Indices: 19933--19980 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
19923 ACCGACCAAT
*
19933 GCATGGAGCATC
1 GCATGGAGCAAC
*
19945 GCATGGAGCATC
1 GCATGGAGCAAC
19957 GCATGGAGCAAC
1 GCATGGAGCAAC
*
19969 GCATGGGGCAAC
1 GCATGGAGCAAC
19981 CGGCCACAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.35, T:0.12
Consensus pattern (12 bp):
GCATGGAGCAAC
Done.