Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009477.1 Corchorus capsularis cultivar CVL-1 contig09498, 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: 37009
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:139 original size:24 final size:24
Alignment explanation
Indices: 112--158 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
102 TTTAGGGTTT
112 GGTGGGAATTTTCAATTTTGGGCC
1 GGTGGGAATTTTCAATTTTGGGCC
*
136 GGTGGGAATTTTTAATTTTGGGC
1 GGTGGGAATTTTCAATTTTGGGC
159 AAAGCCCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.09, G:0.34, T:0.40
Consensus pattern (24 bp):
GGTGGGAATTTTCAATTTTGGGCC
Found at i:441 original size:17 final size:17
Alignment explanation
Indices: 421--454 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
411 AAAGGTACAG
421 ATTTTTCAAAAAATAAT
1 ATTTTTCAAAAAATAAT
438 ATTTTTCAAAAAATAAT
1 ATTTTTCAAAAAATAAT
455 CGACAGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTTTCAAAAAATAAT
Found at i:1087 original size:167 final size:165
Alignment explanation
Indices: 614--1097 Score: 596
Period size: 168 Copynumber: 2.9 Consensus size: 165
604 TGACTCATTT
*
614 GTCAATTGAGAAATGACCAAAAAAGTTTAGTTATTTAATCCCCTCAAGAATTAAAAGTTAGGACA
1 GTCAATTGAGAAATGACC-AAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACA
* * * * **
679 TTTAAGTAATCTGCCAAGTAGGTAAAGATG-AAAAGATTAGTTCTCTAGCTTATCATCAATCCTT
64 TTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAATTCTCTAGCTCCTCATCAATCCTT
** * *
743 TATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
129 GGTGGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * *
780 GTCCATTGAGAAATAACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAATTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
** ** * *
845 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAA-TAAGTTCTCTAATTCCAAAAGCAAGCCT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAA-TTCTCTAGCTCC-TCATCAATCCT
*
909 TGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
128 TGGTGGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * *
947 GTCAATTGAGAAAATGACCAAAAAGTCTAGTTATTTAATCACCTCTAGAATCAAAAGTTAGGGCA
1 GTCAATTGAG-AAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACA
* * * * *
1012 TTTAAGTAATCGGTCAAGT-GTGAAAAGACGAAAAAAATTAATTCTCTCGCTCCTCATTAATCCG
64 TTTAAGTAATCTGCCAAGTAG-GAAAAGACGAAAAAAATTAATTCTCTAGCTCCTCATCAATCCT
*
1076 GGGTGGGGATCTTTTAGTAATT
128 TGGTGGGGATCTTTTAGTAATT
1098 TTTATATGTT
Statistics
Matches: 268, Mismatches: 43, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
165 72 0.27
166 29 0.11
167 76 0.28
168 88 0.33
169 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAATTCTCTAGCTCCTCATCAATCCTTGG
TGGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:12139 original size:14 final size:14
Alignment explanation
Indices: 12120--12148 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12110 TTTGGACTAT
12120 TTAATGAGGAATAG
1 TTAATGAGGAATAG
12134 TTAATGAGGAATAG
1 TTAATGAGGAATAG
12148 T
1 T
12149 GGCTATGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (14 bp):
TTAATGAGGAATAG
Found at i:16081 original size:2 final size:2
Alignment explanation
Indices: 16074--16098 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16064 ATATTTGTAC
16074 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16099 GTTCCATAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23775 original size:107 final size:108
Alignment explanation
Indices: 23589--23806 Score: 393
Period size: 107 Copynumber: 2.0 Consensus size: 108
23579 CAAGACCCGA
** *
23589 ATCGTACCTTGATCCGGATAACAATGGATTAGGTTCTTGAGGGATAGTTCCATTTTTGATGGCAT
1 ATCGTACCTTGATCCGGATAACAATGGATTAGGTTCCCGAGGGAGAGTTCCATTTTTGATGGCAT
23654 AGTCAAGTGCTCGATGACCCCAATTATCAAAAGCCCA-TTAGC
66 AGTCAAGTGCTCGATGACCCCAATTATCAAAAGCCCATTTAGC
*
23696 ATCGTACCTTGATCCGGATAACAATGGATTAGGTTCCCGAGGGAGAGTTTCATTTTTGATGGCAT
1 ATCGTACCTTGATCCGGATAACAATGGATTAGGTTCCCGAGGGAGAGTTCCATTTTTGATGGCAT
23761 AGTCAAGTGCTCGATGACCCCAATTATCAAAAGCCCATTTAGC
66 AGTCAAGTGCTCGATGACCCCAATTATCAAAAGCCCATTTAGC
23804 ATC
1 ATC
23807 TTTAAAGCCA
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
107 98 0.92
108 8 0.08
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (108 bp):
ATCGTACCTTGATCCGGATAACAATGGATTAGGTTCCCGAGGGAGAGTTCCATTTTTGATGGCAT
AGTCAAGTGCTCGATGACCCCAATTATCAAAAGCCCATTTAGC
Found at i:25352 original size:2 final size:2
Alignment explanation
Indices: 25347--25406 Score: 54
Period size: 2 Copynumber: 30.5 Consensus size: 2
25337 TTTTTTGTGT
* * *
25347 TA TA TA TA GTA TA TA T- TA TT TA T- TA CTA TA AA TA TA -A AA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
25388 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
25407 GATTCAATGA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
1 3 0.06
2 41 0.85
3 4 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:26615 original size:24 final size:25
Alignment explanation
Indices: 26579--26638 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
26569 AAAATGAAGG
* *
26579 AAAATTAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
26602 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
*
26627 GAAATGAAGTTT
1 AAAATGAAGTTT
26639 AGGGTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 7 0.22
24 7 0.22
25 18 0.56
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Done.