Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016000.1 Corchorus capsularis cultivar CVL-1 contig16021, 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: 33797
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:574 original size:13 final size:13
Alignment explanation
Indices: 556--580 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
546 TTGGAATTTC
556 AAATAATATTTAT
1 AAATAATATTTAT
569 AAATAATATTTA
1 AAATAATATTTA
581 GAACATTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:1273 original size:324 final size:324
Alignment explanation
Indices: 684--1331 Score: 1242
Period size: 324 Copynumber: 2.0 Consensus size: 324
674 TCCATTTAAC
684 TTAATTGTTACTATTACATAAGATAATATTTTACTTAGAATTGAAATTACTCAGTTCCAATCATA
1 TTAATTGTTACTATTACATAAGATAATATTTTACTTAGAATTGAAATTACTCAGTTCCAATCATA
* *
749 AACTGAAAAACCCAACGCAAATGCGCGGGGATAATAACTAGTACAAAATTATTTTTAACAATCCC
66 AACCGAAAAACCCAACGCAAATGCGCGGGGATAATAACTAGTACAAAATCATTTTTAACAATCCC
814 CTCAAACTCAAGATGCCAATTCTCAAAATAGAGCGGATAACGGATTGGAATCACACCGAGAATTT
131 CTCAAACTCAAGATGCCAATTCTCAAAATAGAGCGGATAACGGATTGGAATCACACCGAGAATTT
*
879 TCCCAATAGTAATCATGATCTTTGGTCTAGTAATTCTTCAGATGTCAAGGAGTTTAGAAGATGAT
196 TCCCAATAGTAATCAAGATCTTTGGTCTAGTAATTCTTCAGATGTCAAGGAGTTTAGAAGATGAT
*
944 AGAACTCCTTAAGGATGGAAAAATTACTAGATAACAAAAAGCTCTTGAGACAGCAAATAACGGA
261 AGAACTCCTTAAGGATGGAAAAATTACCAGATAACAAAAAGCTCTTGAGACAGCAAATAACGGA
*
1008 TTAATTGTTACTATTACATAAGATAATATTTTACTTATAATTGAAATTACTCAGTTCCAATCATA
1 TTAATTGTTACTATTACATAAGATAATATTTTACTTAGAATTGAAATTACTCAGTTCCAATCATA
*
1073 AACCGAAAAATCCAACGCAAATGCGCGGGGATAATAACTAGTACAAAATCATTTTTAACAATCCC
66 AACCGAAAAACCCAACGCAAATGCGCGGGGATAATAACTAGTACAAAATCATTTTTAACAATCCC
1138 CTCAAACTCAAGATGCCAATTCTCAAAATAGAGCGGATAACGGATTGGAATCACACCGAGAATTT
131 CTCAAACTCAAGATGCCAATTCTCAAAATAGAGCGGATAACGGATTGGAATCACACCGAGAATTT
1203 TCCCAATAGTAATCAAGATCTTTGGTCTAGTAATTCTTCAGATGTCAAGGAGTTTAGAAGATGAT
196 TCCCAATAGTAATCAAGATCTTTGGTCTAGTAATTCTTCAGATGTCAAGGAGTTTAGAAGATGAT
1268 AGAACTCCTTAAGGATGGAAAAATTACCAGATAACAAAAAGCTCTTGAGACAGCAAATAACGGA
261 AGAACTCCTTAAGGATGGAAAAATTACCAGATAACAAAAAGCTCTTGAGACAGCAAATAACGGA
1332 CATCGGACAT
Statistics
Matches: 318, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
324 318 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (324 bp):
TTAATTGTTACTATTACATAAGATAATATTTTACTTAGAATTGAAATTACTCAGTTCCAATCATA
AACCGAAAAACCCAACGCAAATGCGCGGGGATAATAACTAGTACAAAATCATTTTTAACAATCCC
CTCAAACTCAAGATGCCAATTCTCAAAATAGAGCGGATAACGGATTGGAATCACACCGAGAATTT
TCCCAATAGTAATCAAGATCTTTGGTCTAGTAATTCTTCAGATGTCAAGGAGTTTAGAAGATGAT
AGAACTCCTTAAGGATGGAAAAATTACCAGATAACAAAAAGCTCTTGAGACAGCAAATAACGGA
Found at i:1620 original size:44 final size:44
Alignment explanation
Indices: 1557--1641 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
1547 TTAATATGTT
* *
1557 GTTTGGTTGGTAGATCACTCGCACAAACATATGATAGAGGACGG
1 GTTTGATTGGTAGATCACTCACACAAACATATGATAGAGGACGG
1601 GTTTGATTGGTAGATCACTCACACAAACATATGATAGAGGA
1 GTTTGATTGGTAGATCACTCACACAAACATATGATAGAGGA
1642 GGGGAAGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (44 bp):
GTTTGATTGGTAGATCACTCACACAAACATATGATAGAGGACGG
Found at i:2382 original size:3 final size:3
Alignment explanation
Indices: 2374--2398 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2364 TCTGAATCAA
2374 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
2399 TTTTTTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:9466 original size:18 final size:18
Alignment explanation
Indices: 9445--9484 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
9435 TTGTTTTGTT
9445 TTTTTGGTTTTTTTTCTG
1 TTTTTGGTTTTTTTTCTG
* *
9463 TTTTTGTTTTTTTTTTTG
1 TTTTTGGTTTTTTTTCTG
9481 TTTT
1 TTTT
9485 GAAGAATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (18 bp):
TTTTTGGTTTTTTTTCTG
Found at i:11997 original size:6 final size:6
Alignment explanation
Indices: 11986--12021 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
11976 TTGGGCCCAG
* *
11986 CCTCAA CCTCAA CCTCAA CCTCAA CATCAA CATCAA
1 CCTCAA CCTCAA CCTCAA CCTCAA CCTCAA CCTCAA
12022 GTCCAGCCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.39, C:0.44, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTCAA
Found at i:12182 original size:24 final size:24
Alignment explanation
Indices: 12155--12206 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
12145 CAGGCCCAGC
* *
12155 CTCAGTTCCAAACACAACCCCAAT
1 CTCACTTCCAAACACAACCACAAT
** *
12179 CTCACTTCCAGCCACAATCACAAT
1 CTCACTTCCAAACACAACCACAAT
12203 CTCA
1 CTCA
12207 ACCTCAGCGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.42, G:0.04, T:0.19
Consensus pattern (24 bp):
CTCACTTCCAAACACAACCACAAT
Found at i:23720 original size:76 final size:76
Alignment explanation
Indices: 23594--23745 Score: 286
Period size: 76 Copynumber: 2.0 Consensus size: 76
23584 CAAACAAAAT
23594 TCATGCCTGACCAACTAATTGAGATATGTTTCTTTATCCTAGGTGCATTACAATATACAGGAATG
1 TCATGCCTGACCAACTAATTGAGATATGTTTCTTTATCCTAGGTGCATTACAATATACAGGAATG
23659 ACAAAAACAAC
66 ACAAAAACAAC
*
23670 TCATGCCTGACCAACTAATTGAGATATGTTTCTTTATCCTAGGTGCATTACAATATACTGGAATG
1 TCATGCCTGACCAACTAATTGAGATATGTTTCTTTATCCTAGGTGCATTACAATATACAGGAATG
*
23735 ACAATAACAAC
66 ACAAAAACAAC
23746 ATAAGATTAC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (76 bp):
TCATGCCTGACCAACTAATTGAGATATGTTTCTTTATCCTAGGTGCATTACAATATACAGGAATG
ACAAAAACAAC
Found at i:25965 original size:17 final size:16
Alignment explanation
Indices: 25943--25983 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
25933 TAGAGATTCT
25943 AAAATATAATTTACAA-A
1 AAAATAT-ATTTA-AAGA
25960 AAAATAT-TTTAAAGA
1 AAAATATATTTAAAGA
25975 AAAATATAT
1 AAAATATAT
25984 ATACATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.09
15 12 0.55
16 1 0.05
17 7 0.32
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (16 bp):
AAAATATATTTAAAGA
Found at i:30522 original size:3 final size:3
Alignment explanation
Indices: 30514--30547 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
30504 GTATATATAT
30514 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
30548 CCTAATCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:30774 original size:11 final size:11
Alignment explanation
Indices: 30758--30790 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
30748 TTTCATGTTT
30758 TTCCAAAACAC
1 TTCCAAAACAC
30769 TTCCAAAACAC
1 TTCCAAAACAC
*
30780 TTTCAAAACAC
1 TTCCAAAACAC
30791 AGAAACACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.21
Consensus pattern (11 bp):
TTCCAAAACAC
Found at i:30989 original size:33 final size:33
Alignment explanation
Indices: 30947--31028 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
30937 AAACAAAAAA
30947 CCGTCCTAGTGGGGAGGATCCGCCGTGGCTGAG
1 CCGTCCTAGTGGGGAGGATCCGCCGTGGCTGAG
30980 CCGTCCTAGTGGGGAGGATCCGCCGTGGCTGAG
1 CCGTCCTAGTGGGGAGGATCCGCCGTGGCTGAG
31013 CCGTCCTAGTGGGGAG
1 CCGTCCTAGTGGGGAG
31029 ACTCAGTGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.12, C:0.27, G:0.43, T:0.18
Consensus pattern (33 bp):
CCGTCCTAGTGGGGAGGATCCGCCGTGGCTGAG
Found at i:31101 original size:20 final size:21
Alignment explanation
Indices: 31078--31120 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
31068 CAAAAGTGTA
*
31078 AAAAATGGGGC-GTATTTAGC
1 AAAAATAGGGCGGTATTTAGC
*
31098 AAAACTAGGGCGGTATTTAGC
1 AAAAATAGGGCGGTATTTAGC
31119 AA
1 AA
31121 CCCCCGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.23
Consensus pattern (21 bp):
AAAAATAGGGCGGTATTTAGC
Found at i:32189 original size:1 final size:1
Alignment explanation
Indices: 32185--32214 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
32175 ACTTTTTACT
*
32185 CCCCCCCCCCCCCCCCCCCCCCCCTCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
32215 TCCTCCCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:32219 original size:9 final size:9
Alignment explanation
Indices: 32183--32221 Score: 55
Period size: 8 Copynumber: 4.6 Consensus size: 9
32173 CAACTTTTTA
32183 CTCCCCCCC
1 CTCCCCCCC
32192 C-CCCCCCC
1 CTCCCCCCC
32200 C-CCCCCCC
1 CTCCCCCCC
*
32208 CTCCCCCTC
1 CTCCCCCCC
32217 CTCCC
1 CTCCC
32222 TCTATATTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 16 0.57
9 12 0.43
ACGTcount: A:0.00, C:0.90, G:0.00, T:0.10
Consensus pattern (9 bp):
CTCCCCCCC
Done.