Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007197.1 Corchorus capsularis cultivar CVL-1 contig07218, 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: 42958
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:16958 original size:6 final size:6
Alignment explanation
Indices: 16947--16972 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16937 GATTTTCACA
16947 TCATTT TCATTT TCATTT TCATTT TC
1 TCATTT TCATTT TCATTT TCATTT TC
16973 TGAAAATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.65
Consensus pattern (6 bp):
TCATTT
Found at i:20416 original size:12 final size:12
Alignment explanation
Indices: 20399--20423 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20389 AGTCTCTGTT
20399 TTGGAAAGCATA
1 TTGGAAAGCATA
20411 TTGGAAAGCATA
1 TTGGAAAGCATA
20423 T
1 T
20424 AAAGAAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (12 bp):
TTGGAAAGCATA
Found at i:22464 original size:20 final size:20
Alignment explanation
Indices: 22439--22480 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
22429 GTGCATTCAT
22439 ATCGGGTTTTTTGGTTTATG
1 ATCGGGTTTTTTGGTTTATG
22459 ATCGGGTTTTTTGGTTTATG
1 ATCGGGTTTTTTGGTTTATG
22479 AT
1 AT
22481 TGAAACTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.12, C:0.05, G:0.29, T:0.55
Consensus pattern (20 bp):
ATCGGGTTTTTTGGTTTATG
Found at i:22776 original size:45 final size:45
Alignment explanation
Indices: 22725--22814 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
22715 TAATATAATA
22725 GTGGAATTACTAAAAAA-TCTCTATCC-C-GAATTAATGATGAGCTGG
1 GTGGAATTACTAAAAAATTC-CTA-CCTCGGAA-TAATGATGAGCTGG
*
22770 GTGGAATTACTAAAAGATTCCTACCTCGGAATAATGATGAGCTGG
1 GTGGAATTACTAAAAAATTCCTACCTCGGAATAATGATGAGCTGG
22815 AGAAGTAATC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
44 2 0.05
45 34 0.83
46 5 0.12
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (45 bp):
GTGGAATTACTAAAAAATTCCTACCTCGGAATAATGATGAGCTGG
Found at i:23513 original size:13 final size:13
Alignment explanation
Indices: 23495--23519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23485 TTCAATATTC
23495 TAAATATTATTTA
1 TAAATATTATTTA
23508 TAAATATTATTT
1 TAAATATTATTT
23520 GGAATTCCAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:23661 original size:12 final size:12
Alignment explanation
Indices: 23644--23670 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
23634 TAATAGTAAA
23644 AAATAAATATAT
1 AAATAAATATAT
23656 AAATAAATATAT
1 AAATAAATATAT
23668 AAA
1 AAA
23671 GGTATCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATAAATATAT
Found at i:25827 original size:30 final size:30
Alignment explanation
Indices: 25770--25829 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
25760 TCTCTTCTGT
*
25770 AATATAACCCAGATGATATTTTCTTGTTGC
1 AATATAACCCAGATGAGATTTTCTTGTTGC
* *
25800 AATATAACCCCGATGGGATTCTT-TTGTTGC
1 AATATAACCCAGATGAGATT-TTCTTGTTGC
25830 TACAAGAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (30 bp):
AATATAACCCAGATGAGATTTTCTTGTTGC
Found at i:26712 original size:3 final size:3
Alignment explanation
Indices: 26704--26752 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
26694 TTTGTATTGC
26704 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
26750 TAT
1 TAT
26753 AGATAGAAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:27134 original size:217 final size:214
Alignment explanation
Indices: 26748--27180 Score: 604
Period size: 217 Copynumber: 2.0 Consensus size: 214
26738 TTATTATTAT
* * *
26748 ATTATAGATAGAAGTGGGTAGAACTATCAAAAGTTGATACAAAAACCCGAAAACCTGTCCAATCC
1 ATTATAGATAGAAGTGGGGAGAACCATCAAAAGTTGATACAAAAACCCGAAAAACTGTCCAATCC
* * * *
26813 ATCTAACTTGACTTGATAATTAAAAGTGAATGACCTACATGATCTGGAATCCGATTGACCGAGAC
66 ATCCAACTTGACTTAATAATTAAAAGTGAATGACCCACATGATCTGAAATCCGATTGACCGAGAC
* * * *
26878 CAACATGATTCGAGAGCTTATGAACTTAAGACTTAATTGATCCGAAAACCTAAATGATCCAA-AA
131 CAACATGATCCAAGAGCTGATGAACTTAAGACGTAATTGATCCGAAAACCTAAATGATCCAATAA
26942 CTGAAT-AACTATATAACCCA
196 -TGAATGAA-TATATAACCCA
* * *
26962 ATTATAGATAGAAGTGGGGAGAACCGTCAAAAGTTGAT-CCAAAATCCGAAAAACTGTCCAATCC
1 ATTATAGATAGAAGTGGGGAGAACCATCAAAAGTTGATACAAAAACCCGAAAAACTGTCCAATCC
* *
27026 ATCCAACTTGACTTAATAATTAATTAAAAGTGAATGACCCGCATGATCTGAAATTCGATTGACCG
66 ATCCAACTTGAC-T--TAA-TAATTAAAAGTGAATGACCCACATGATCTGAAATCCGATTGACCG
* * *
27091 AGACCAACATGATCCAAGAGCTGATGGA-TGTAGGACGTAATTGATCTGAAAACCTAAATGATCC
127 AGACCAACATGATCCAAGAGCTGATGAACT-TAAGACGTAATTGATCCGAAAACCTAAATGATCC
27155 AATAATGAATGAATATATAACCCA
191 AATAATGAATGAATATATAACCCA
27179 AT
1 AT
27181 GGGGTGAATT
Statistics
Matches: 193, Mismatches: 19, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
213 34 0.18
214 36 0.19
216 3 0.02
217 116 0.60
218 4 0.02
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.24
Consensus pattern (214 bp):
ATTATAGATAGAAGTGGGGAGAACCATCAAAAGTTGATACAAAAACCCGAAAAACTGTCCAATCC
ATCCAACTTGACTTAATAATTAAAAGTGAATGACCCACATGATCTGAAATCCGATTGACCGAGAC
CAACATGATCCAAGAGCTGATGAACTTAAGACGTAATTGATCCGAAAACCTAAATGATCCAATAA
TGAATGAATATATAACCCA
Found at i:37400 original size:15 final size:15
Alignment explanation
Indices: 37380--37415 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
37370 GGGGAGGGGA
37380 AGAAGCTATGAATAT
1 AGAAGCTATGAATAT
37395 AGAAGCTATGAATAT
1 AGAAGCTATGAATAT
*
37410 AAAAGC
1 AGAAGC
37416 CTTGAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.22
Consensus pattern (15 bp):
AGAAGCTATGAATAT
Found at i:37799 original size:33 final size:33
Alignment explanation
Indices: 37762--37865 Score: 141
Period size: 33 Copynumber: 3.4 Consensus size: 33
37752 ACCACCATGA
37762 CATTTGCTTTGCGACTACCATGACAAACTGGGT
1 CATTTGCTTTGCGACTACCATGACAAACTGGGT
37795 CA-----TTTGC--CTACCATGACAAACTGGGT
1 CATTTGCTTTGCGACTACCATGACAAACTGGGT
* *
37821 CATTTGCTTTGCGACTACCATGACAAACCGGAT
1 CATTTGCTTTGCGACTACCATGACAAACTGGGT
37854 CATTTGCTTTGC
1 CATTTGCTTTGC
37866 AAGAAGTTTG
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
26 21 0.34
28 5 0.08
31 5 0.08
33 31 0.50
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (33 bp):
CATTTGCTTTGCGACTACCATGACAAACTGGGT
Found at i:37805 original size:26 final size:26
Alignment explanation
Indices: 37776--37827 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
37766 TGCTTTGCGA
37776 CTACCATGACAAACTGGGTCATTTGC
1 CTACCATGACAAACTGGGTCATTTGC
37802 CTACCATGACAAACTGGGTCATTTGC
1 CTACCATGACAAACTGGGTCATTTGC
37828 TTTGCGACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (26 bp):
CTACCATGACAAACTGGGTCATTTGC
Found at i:42749 original size:20 final size:20
Alignment explanation
Indices: 42724--42763 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42714 TAACGAAACT
42724 GTTATGGTTTTCCGTTAAGC
1 GTTATGGTTTTCCGTTAAGC
42744 GTTATGGTTTTCCGTTAAGC
1 GTTATGGTTTTCCGTTAAGC
42764 ATTAACGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.45
Consensus pattern (20 bp):
GTTATGGTTTTCCGTTAAGC
Done.