Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018259.1 Corchorus olitorius cultivar O-4 contig18292, 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: 41465
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:13198 original size:2 final size:2
Alignment explanation
Indices: 13191--13228 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
13181 AAAAGAACTA
13191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13229 TGTAAAAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22967 original size:1 final size:1
Alignment explanation
Indices: 22933--22960 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
22923 CCCGTCTTGG
22933 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
22961 AATTTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:23419 original size:3 final size:3
Alignment explanation
Indices: 23411--23498 Score: 113
Period size: 3 Copynumber: 29.3 Consensus size: 3
23401 TCGGATGGGG
* * * *
23411 GAA GAA GAA GAA GAG GAA GAG GAA GAG GAT GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* * *
23459 GAA GAA GAA GAA GAA GGA GGA GGA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
23499 CCCATTGATA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.58, C:0.00, G:0.41, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:24903 original size:26 final size:26
Alignment explanation
Indices: 24867--24927 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 26
24857 CAACACAACA
*
24867 GCCGTTCACTCTTCCTTACCCTCACC
1 GCCGCTCACTCTTCCTTACCCTCACC
24893 GCCGCTCACTCTTCCTTACCCTCACC
1 GCCGCTCACTCTTCCTTACCCTCACC
*
24919 GCTGCTCAC
1 GCCGCTCAC
24928 ACTCAAACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.11, C:0.51, G:0.10, T:0.28
Consensus pattern (26 bp):
GCCGCTCACTCTTCCTTACCCTCACC
Found at i:30519 original size:12 final size:12
Alignment explanation
Indices: 30502--30545 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
30492 GGAAGAGGGA
*
30502 GAAGAAAGTGGG
1 GAAGAAAGTGAG
30514 GAAGAAAGTGAG
1 GAAGAAAGTGAG
30526 GAAGAATTAGATGAG
1 GAAGAA--AG-TGAG
30541 GAAGA
1 GAAGA
30546 GGAAGAGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 17 0.61
14 2 0.07
15 9 0.32
ACGTcount: A:0.48, C:0.00, G:0.41, T:0.11
Consensus pattern (12 bp):
GAAGAAAGTGAG
Found at i:31254 original size:26 final size:26
Alignment explanation
Indices: 31213--31263 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
31203 AAACTTTCTG
*
31213 TTTTTTGTTCAAACTTGCTGTTTTTC
1 TTTTTTGCTCAAACTTGCTGTTTTTC
* *
31239 TTTTTTGCTCATACTTGTTGTTTTT
1 TTTTTTGCTCAAACTTGCTGTTTTT
31264 TCTGAAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.10, C:0.14, G:0.12, T:0.65
Consensus pattern (26 bp):
TTTTTTGCTCAAACTTGCTGTTTTTC
Found at i:31377 original size:139 final size:137
Alignment explanation
Indices: 31127--31524 Score: 735
Period size: 139 Copynumber: 2.9 Consensus size: 137
31117 AAGGTTAGTT
31127 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
1 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
*
31192 CAAAGTTGCTGAAACTTTCTGTTTTTTGTTCAAACTTGCTGTTTTTCTTTTTTGCTCATACTTGT
66 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGCTGTTTTTCTTTTTTGCTCATACTTG-
31257 TGTTTTTTC
130 T-TTTTTTC
*
31266 TGAAACTTGCTGAAATTTACTTAATTATTCCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
1 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
31331 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGCTGTTTTTC-TTTTTGCTCATACTTGT
66 CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGCTGTTTTTCTTTTTTGCTCATACTTGT
31395 TTTTTTC
131 TTTTTTC
31402 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
1 TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
31467 CAAAGTTGCTGAAACTTACTTGTTTTTTGTTCAAACTTGCTTGTTTTTCTTTTTTGCT
66 CAAAGTTGCTGAAACTTAC-TGTTTTTTGTTCAAACTTGC-TGTTTTTCTTTTTTGCT
31525 ATATTTCTGT
Statistics
Matches: 253, Mismatches: 3, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
136 90 0.36
137 21 0.08
138 24 0.09
139 118 0.47
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (137 bp):
TGAAACTTGCTGAAATTTACTTAATTATTTCTGTTTTGGGAGGCTAATTCTGAAACTTAATTGCT
CAAAGTTGCTGAAACTTACTGTTTTTTGTTCAAACTTGCTGTTTTTCTTTTTTGCTCATACTTGT
TTTTTTC
Found at i:31392 original size:25 final size:24
Alignment explanation
Indices: 31353--31402 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
31343 AACTTACTGT
*
31353 TTTTTGTTCAAACTTGCTGTTTTTC
1 TTTTTGCTCAAACTTG-TGTTTTTC
* *
31378 TTTTTGCTCATACTTGTTTTTTTC
1 TTTTTGCTCAAACTTGTGTTTTTC
31402 T
1 T
31403 GAAACTTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.10, C:0.16, G:0.10, T:0.64
Consensus pattern (24 bp):
TTTTTGCTCAAACTTGTGTTTTTC
Found at i:34001 original size:21 final size:21
Alignment explanation
Indices: 33977--34023 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
33967 TTCTTATATG
33977 CTACGAGCTTATTTACAGTTA
1 CTACGAGCTTATTTACAGTTA
* *
33998 CTACGAGCTTATTTACATTTG
1 CTACGAGCTTATTTACAGTTA
34019 CTACG
1 CTACG
34024 GACATTATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (21 bp):
CTACGAGCTTATTTACAGTTA
Found at i:36630 original size:33 final size:33
Alignment explanation
Indices: 36588--36662 Score: 104
Period size: 30 Copynumber: 2.4 Consensus size: 33
36578 AATTACATAT
*
36588 TATTTCTAATAATATTTATTGCATATTAAATAAA
1 TATTTCTAATAATATTTATTACATATT-AATAAA
36622 TA-TTC---TAATATTTATTACATATTAATAAA
1 TATTTCTAATAATATTTATTACATATTAATAAA
36651 TATTTCTAATAA
1 TATTTCTAATAA
36663 AATCAAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
29 8 0.22
30 20 0.56
33 6 0.17
34 2 0.06
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.48
Consensus pattern (33 bp):
TATTTCTAATAATATTTATTACATATTAATAAA
Found at i:36633 original size:30 final size:30
Alignment explanation
Indices: 36597--36661 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
36587 TTATTTCTAA
*
36597 TAATATTTATTGCATATTAAATAAATA-TTC
1 TAATATTTATTACATATT-AATAAATATTTC
36627 TAATATTTATTACATATTAATAAATATTTC
1 TAATATTTATTACATATTAATAAATATTTC
36657 TAATA
1 TAATA
36662 AAATCAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 8 0.24
30 25 0.76
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.48
Consensus pattern (30 bp):
TAATATTTATTACATATTAATAAATATTTC
Found at i:36762 original size:12 final size:11
Alignment explanation
Indices: 36733--36774 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
36723 ATTAATGAAC
36733 ATAAACGAGCT
1 ATAAACGAGCT
36744 ATAAACGAGCT
1 ATAAACGAGCT
* *
36755 ATTAAACGAACA
1 A-TAAACGAGCT
36767 ATAAACGA
1 ATAAACGA
36775 ACATTAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.17
Consensus pattern (11 bp):
ATAAACGAGCT
Found at i:39177 original size:21 final size:22
Alignment explanation
Indices: 39151--39192 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
39141 ATTAAAGAAG
39151 TCATTAAACAT-AGTCTGACAA
1 TCATTAAACATAAGTCTGACAA
*
39172 TCATTAAACATAATTCTGACA
1 TCATTAAACATAAGTCTGACA
39193 GCAAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (22 bp):
TCATTAAACATAAGTCTGACAA
Found at i:41264 original size:3 final size:3
Alignment explanation
Indices: 41256--41342 Score: 167
Period size: 3 Copynumber: 29.3 Consensus size: 3
41246 ATATCTACTA
41256 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41304 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41343 TATGATTTAA
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 81 0.98
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.