Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009580.1 Corchorus capsularis cultivar CVL-1 contig09601, 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: 43086
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Found at i:679 original size:8 final size:8
Alignment explanation
Indices: 661--726 Score: 64
Period size: 8 Copynumber: 7.9 Consensus size: 8
651 ATAATTATGT
661 GTGA-TTA
1 GTGATTTA
*
668 GTGATATA
1 GTGATTTA
676 GTGATTTTA
1 GTGA-TTTA
685 GTGATTTA
1 GTGATTTA
693 GTGACTTATA
1 GTGA-TT-TA
703 GTCTGA-TTA
1 G--TGATTTA
712 GTGATTTA
1 GTGATTTA
720 GTGATTT
1 GTGATTT
727 TATTTATAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
7 7 0.14
8 24 0.48
9 12 0.24
10 4 0.08
12 3 0.06
ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (8 bp):
GTGATTTA
Found at i:687 original size:17 final size:16
Alignment explanation
Indices: 665--725 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
655 TTATGTGTGA
665 TTAGTGATATAGTGATT
1 TTAGTGAT-TAGTGATT
682 TTAGTGATTTAGTGACTT
1 TTAGTGA-TTAGTGA-TT
*
700 ATAGTCTGATTAGTGA-T
1 TTAG--TGATTAGTGATT
717 TTAGTGATT
1 TTAGTGATT
726 TTATTTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 5 0.13
17 17 0.45
18 6 0.16
19 7 0.18
20 3 0.08
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (16 bp):
TTAGTGATTAGTGATT
Found at i:1111 original size:14 final size:15
Alignment explanation
Indices: 1086--1132 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1076 CGCCCCATTT
*
1086 TTTACACTTTTGCCC
1 TTTACACTTTTGCAC
1101 TTTAC-CTTTTGCAC
1 TTTACACTTTTGCAC
*
1115 TTTTTACACTTTTACAC
1 --TTTACACTTTTGCAC
1132 T
1 T
1133 GAGCCTCCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 8 0.30
15 6 0.22
16 5 0.19
17 8 0.30
ACGTcount: A:0.17, C:0.28, G:0.04, T:0.51
Consensus pattern (15 bp):
TTTACACTTTTGCAC
Found at i:1310 original size:32 final size:32
Alignment explanation
Indices: 1269--1340 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1259 AAAATAGCCG
* * *
1269 AGCCGCCCCACCGGGGCGCCCTGTCGTGGCGA
1 AGCCGCCCCACCGAGGCGCCCTGCCCTGGCGA
* *
1301 AGCCGCCCCACCGAGGCGGCCTGCCCTGGCTA
1 AGCCGCCCCACCGAGGCGCCCTGCCCTGGCGA
1333 AGCCGCCC
1 AGCCGCCC
1341 TCTTGGGACG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.11, C:0.47, G:0.33, T:0.08
Consensus pattern (32 bp):
AGCCGCCCCACCGAGGCGCCCTGCCCTGGCGA
Found at i:7750 original size:27 final size:27
Alignment explanation
Indices: 7713--7767 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
7703 TAATCCTCGT
7713 AGGAATAGTAAAACCT-TTCTGGTAGGAA
1 AGGAATAGTAAAACCTATTCT--TAGGAA
7741 AGGAA-AGTAAAACCTATTCTTAGGAA
1 AGGAATAGTAAAACCTATTCTTAGGAA
7767 A
1 A
7768 AACCATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 7 0.27
27 10 0.38
28 9 0.35
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.24
Consensus pattern (27 bp):
AGGAATAGTAAAACCTATTCTTAGGAA
Found at i:8233 original size:73 final size:73
Alignment explanation
Indices: 8114--8259 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
8104 GTTTTGAAAA
8114 AGATAAATTTCTGGATCAACTCGCTTCGACTCTTCTTCAGCAATCCGTACATATTTCCTAGCCTT
1 AGATAAATTTCTGGATCAACTCGCTTCGACTCTTCTTCAGCAATCCGTACATATTTCCTAGCCTT
8179 GATCGAAC
66 GATCGAAC
*
8187 AGATAAATTTCTGGATCAACTCGCTTCGACTCTTCTTCAGCAATCCGTACATATTTCGTAGCCTT
1 AGATAAATTTCTGGATCAACTCGCTTCGACTCTTCTTCAGCAATCCGTACATATTTCCTAGCCTT
8252 GATCGAAC
66 GATCGAAC
8260 CTCTTTAATA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (73 bp):
AGATAAATTTCTGGATCAACTCGCTTCGACTCTTCTTCAGCAATCCGTACATATTTCCTAGCCTT
GATCGAAC
Found at i:14308 original size:18 final size:18
Alignment explanation
Indices: 14285--14322 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
14275 AACTAAAATC
14285 TGAAATGAAATATAAACA
1 TGAAATGAAATATAAACA
14303 TGAAATGAAATATAAACA
1 TGAAATGAAATATAAACA
14321 TG
1 TG
14323 TAAAAAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.05, G:0.13, T:0.24
Consensus pattern (18 bp):
TGAAATGAAATATAAACA
Found at i:19278 original size:2 final size:2
Alignment explanation
Indices: 19271--19298 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19261 AATCAGAGAA
19271 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
19299 GATTATCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23141 original size:6 final size:7
Alignment explanation
Indices: 23123--23148 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
23113 CACCTCGTTT
23123 TAAAAAA
1 TAAAAAA
23130 TAAAAAA
1 TAAAAAA
23137 TAAAAAA
1 TAAAAAA
23144 TAAAA
1 TAAAA
23149 CAAAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:24100 original size:18 final size:18
Alignment explanation
Indices: 24079--24147 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 18
24069 TGTCCTGACC
24079 CTGACCTTGACCCTGGCT
1 CTGACCTTGACCCTGGCT
* * * * *
24097 CTGATCTTGGCCTTGCCC
1 CTGACCTTGACCCTGGCT
*
24115 CTGATCC-TGACCCTGGTT
1 CTGA-CCTTGACCCTGGCT
* *
24133 TTGTCCTTGACCCTG
1 CTGACCTTGACCCTG
24148 ACCCTGACCC
Statistics
Matches: 36, Mismatches: 13, Indels: 4
0.68 0.25 0.08
Matches are distributed among these distances:
17 2 0.06
18 33 0.92
19 1 0.03
ACGTcount: A:0.09, C:0.36, G:0.22, T:0.33
Consensus pattern (18 bp):
CTGACCTTGACCCTGGCT
Found at i:24204 original size:30 final size:30
Alignment explanation
Indices: 24097--24210 Score: 84
Period size: 30 Copynumber: 3.8 Consensus size: 30
24087 GACCCTGGCT
* * * **
24097 CTGATCTTGGCCTTGCCCCTGATCCTGACC
1 CTGATTTTGCCCTTGGCCCTGGCCCTGACC
* * * *
24127 CTGGTTTTGTCCTTGACCCTGACCCTGACC
1 CTGATTTTGCCCTTGGCCCTGGCCCTGACC
** ** *
24157 CCAACCTTGGCCTTGGCCCTGGCCCTGACC
1 CTGATTTTGCCCTTGGCCCTGGCCCTGACC
* *
24187 CTGATTTTGCCCCTGGCCTTGGCC
1 CTGATTTTGCCCTTGGCCCTGGCC
24211 TTGGCCTTGA
Statistics
Matches: 64, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.09, C:0.40, G:0.22, T:0.29
Consensus pattern (30 bp):
CTGATTTTGCCCTTGGCCCTGGCCCTGACC
Found at i:32945 original size:2 final size:2
Alignment explanation
Indices: 32938--32967 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
32928 TGGGTTATCA
32938 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
32968 TTGAAACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34534 original size:3 final size:3
Alignment explanation
Indices: 34526--34559 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
34516 CATATAATAG
34526 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
34560 TAACAGAAGA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Done.