Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011142.1 Corchorus capsularis cultivar CVL-1 contig11163, 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: 48336
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:5837 original size:3 final size:3
Alignment explanation
Indices: 5829--5885 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
5819 TGATTAAATA
5829 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
5877 TAT TAT TAT
1 TAT TAT TAT
5886 GTGTTTGAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:14553 original size:60 final size:60
Alignment explanation
Indices: 14479--14640 Score: 191
Period size: 60 Copynumber: 2.7 Consensus size: 60
14469 ACTAATTGCT
* * * * * * *
14479 CAAATAAGAGCCTAACGTT-TACCAAAATGCTTAAATAAGGGTCTGATCGTTTAATTTGGC
1 CAAATGAGAGCCTAATGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCGTTTAATTTGAC
* * * **
14539 CAAATGAGGGCCTAATGTTATTGAAAATGCTCAAATAAGGACCCGATTTTTTAATTTGAC
1 CAAATGAGAGCCTAATGTTATCGAAAATGCTCAAATAAGGGCCCGATCGTTTAATTTGAC
*
14599 CAAATGAGAACCTAATGTTATCGAAAATGCTCAAATAAGGGC
1 CAAATGAGAGCCTAATGTTATCGAAAATGCTCAAATAAGGGC
14641 TTGGCGTCAA
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
60 84 0.99
61 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (60 bp):
CAAATGAGAGCCTAATGTTATCGAAAATGCTCAAATAAGGGCCCGATCGTTTAATTTGAC
Found at i:14574 original size:31 final size:31
Alignment explanation
Indices: 14539--14638 Score: 80
Period size: 31 Copynumber: 3.3 Consensus size: 31
14529 TTAATTTGGC
* *
14539 CAAATGAGGGCCTAATGTTATTGAAAATGCT
1 CAAATAAGGACCTAATGTTATTGAAAATGCT
** * **
14570 CAAATAAGGACCCGAT-TT-TTTAATTTGAC-
1 CAAATAAGGACCTAATGTTATTGAAAATG-CT
* * *
14599 CAAATGAGAACCTAATGTTATCGAAAATGCT
1 CAAATAAGGACCTAATGTTATTGAAAATGCT
14630 CAAATAAGG
1 CAAATAAGG
14639 GCTTGGCGTC
Statistics
Matches: 48, Mismatches: 17, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
29 18 0.38
30 6 0.12
31 24 0.50
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (31 bp):
CAAATAAGGACCTAATGTTATTGAAAATGCT
Found at i:16549 original size:23 final size:23
Alignment explanation
Indices: 16523--16576 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
16513 TTTGGGACTC
16523 GAGTTTTTGGAACTACTTTGTGA
1 GAGTTTTTGGAACTACTTTGTGA
* *
16546 GAGTTTTTGGGACTCCTTTGTGA
1 GAGTTTTTGGAACTACTTTGTGA
16569 GAGTTTTT
1 GAGTTTTT
16577 TCTATTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.17, C:0.09, G:0.28, T:0.46
Consensus pattern (23 bp):
GAGTTTTTGGAACTACTTTGTGA
Found at i:20101 original size:25 final size:27
Alignment explanation
Indices: 20049--20101 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
20039 TTACTCAACT
* **
20049 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTCATTTTAATGTAA
20076 AAAAACTCTATTTTCA-TTTAAT-TAA
1 AAAAACTCTATTTTCATTTTAATGTAA
20101 A
1 A
20102 TCTAATATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 15 0.65
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (27 bp):
AAAAACTCTATTTTCATTTTAATGTAA
Found at i:33707 original size:2 final size:2
Alignment explanation
Indices: 33660--33692 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33650 GAGAGAGTGC
33660 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
33693 ATAGACACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:36750 original size:260 final size:259
Alignment explanation
Indices: 36282--36803 Score: 875
Period size: 260 Copynumber: 2.0 Consensus size: 259
36272 TCCCACATAT
36282 GGAACTAATATTTCATCAAATTGGAGCATCTCAAATATAGAACTCACCATCCATAAGCAACTCTC
1 GGAACTAATATTTCATCAAATTGGAGCATCTCAAATATAGAACTCACCATCCATAAGCAACTCTC
* *
36347 AATACCAAACTTTCTAACAAGGGACAATGGATCAATTTCAACATTAACCTTTGCAAGTCTCAGTG
66 AATACCAAACTTTCTAACAAGGGACAATGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTA
* *
36412 GACTGCAAATTATTCATACAGGTCACTGCATCAATTTGCAAGTCCAGAGGACTGCAAATTATCCG
131 GACTGCAAATTATTCATACAGGACACTGCATCAATCTGCAAGTCCAGAGGACTGCAAATTATCCG
* *
36477 GGACATTGCATCAATTCTAACAATAAACCTTTGCAAGTCTCAGTGGACTGCAAATTATTCGTAAG
196 GGACATTGCATCAATTCCAACAACAAA-CTTTGCAAGTCTCAGTGGACTGCAAATTATTCGTAAG
* *
36542 GGAACTTATATTTCATCAAATTGGAGCCTCTCAAATATAGAACTCACCATCCATAAGCAACTCTC
1 GGAACTAATATTTCATCAAATTGGAGCATCTCAAATATAGAACTCACCATCCATAAGCAACTCTC
* *
36607 AATACC-AACTTTCTAATAAGGGACAATGCATCAATTTCAACATTAACCTTTGCAAGTCTCATTA
66 AATACCAAACTTTCTAACAAGGGACAATGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTA
* * *
36671 GACTGCAAAATTATTCATACGGGACATTGCATCAATCTGCAAGTCCAGAGGACTGCAAATTATTC
131 GACTGC-AAATTATTCATACAGGACACTGCATCAATCTGCAAGTCCAGAGGACTGCAAATTATCC
* * *
36736 GGGGCATTGCATCAATTCCAACAACAAACTTTGCAAGTCTTAGTGGACTGCAAATTTTTCGTAAG
195 GGGACATTGCATCAATTCCAACAACAAACTTTGCAAGTCTCAGTGGACTGCAAATTATTCGTAAG
36801 GGA
1 GGA
36804 CATTGTATCG
Statistics
Matches: 245, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
259 98 0.40
260 147 0.60
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (259 bp):
GGAACTAATATTTCATCAAATTGGAGCATCTCAAATATAGAACTCACCATCCATAAGCAACTCTC
AATACCAAACTTTCTAACAAGGGACAATGCATCAATTTCAACATTAACCTTTGCAAGTCTCAGTA
GACTGCAAATTATTCATACAGGACACTGCATCAATCTGCAAGTCCAGAGGACTGCAAATTATCCG
GGACATTGCATCAATTCCAACAACAAACTTTGCAAGTCTCAGTGGACTGCAAATTATTCGTAAG
Found at i:37057 original size:1 final size:1
Alignment explanation
Indices: 37053--37078 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
37043 ATAAAAAATT
37053 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
37079 CCCATCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:37683 original size:30 final size:31
Alignment explanation
Indices: 37642--37705 Score: 121
Period size: 30 Copynumber: 2.1 Consensus size: 31
37632 ATGAAAGAGG
37642 GAAAAGAACAATAAAACTGGAGAAAGAAAAA
1 GAAAAGAACAATAAAACTGGAGAAAGAAAAA
37673 GAAAA-AACAATAAAACTGGAGAAAGAAAAA
1 GAAAAGAACAATAAAACTGGAGAAAGAAAAA
37703 GAA
1 GAA
37706 GGCGCTCGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 28 0.85
31 5 0.15
ACGTcount: A:0.69, C:0.06, G:0.19, T:0.06
Consensus pattern (31 bp):
GAAAAGAACAATAAAACTGGAGAAAGAAAAA
Found at i:38859 original size:11 final size:11
Alignment explanation
Indices: 38845--38870 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38835 TAGTCAATAA
38845 AAATAAACAAG
1 AAATAAACAAG
38856 AAATAAACAAG
1 AAATAAACAAG
38867 AAAT
1 AAAT
38871 TGTAAGATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.08, G:0.08, T:0.12
Consensus pattern (11 bp):
AAATAAACAAG
Found at i:39084 original size:3 final size:3
Alignment explanation
Indices: 39071--39105 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
39061 CTCTCTTAAT
39071 TTA TGTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
39106 ATACATACGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:41569 original size:17 final size:16
Alignment explanation
Indices: 41523--41565 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
41513 CCAGATGACT
41523 AGTGATCTAAGATCATC
1 AGTGATC-AAGATCATC
*
41540 AGTGATGCAAGATCATT
1 AGTGAT-CAAGATCATC
*
41557 GGTGATCAA
1 AGTGATCAA
41566 AGATTACATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.13
17 19 0.83
18 1 0.04
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (16 bp):
AGTGATCAAGATCATC
Found at i:47114 original size:21 final size:21
Alignment explanation
Indices: 47088--47131 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
47078 TAATTCTGGA
47088 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
47109 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
47130 TT
1 TT
47132 TTATGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:47559 original size:33 final size:33
Alignment explanation
Indices: 47498--47591 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
47488 GGGGCAGCCT
* * *
47498 GCCGTGGC-GAAGCCGCCCCAGTGTGGAGGCTCC
1 GCCGTGGCTG-AGCCTCCCTAGTGGGGAGGCTCC
*
47531 GCCGTGGTTGAGCCTCCCTAGTGGGGAGGCTCC
1 GCCGTGGCTGAGCCTCCCTAGTGGGGAGGCTCC
47564 GCCGTGGCTGAGCCGT-CCTAGTGGGGAG
1 GCCGTGGCTGAGCC-TCCCTAGTGGGGAG
47592 ACTCAGTGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
33 52 0.96
34 2 0.04
ACGTcount: A:0.11, C:0.31, G:0.41, T:0.17
Consensus pattern (33 bp):
GCCGTGGCTGAGCCTCCCTAGTGGGGAGGCTCC
Found at i:47570 original size:16 final size:17
Alignment explanation
Indices: 47520--47570 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
47510 CCGCCCCAGT
47520 GTGGAGGCTCCGCCGTG
1 GTGGAGGCTCCGCCGTG
* * *
47537 GTTGAGCCTCC-CTAGTG
1 GTGGAGGCTCCGC-CGTG
47554 G-GGAGGCTCCGCCGTG
1 GTGGAGGCTCCGCCGTG
47570 G
1 G
47571 CTGAGCCGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.08, C:0.29, G:0.43, T:0.20
Consensus pattern (17 bp):
GTGGAGGCTCCGCCGTG
Done.