Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015696.1 Corchorus capsularis cultivar CVL-1 contig15717, 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: 38679
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:3540 original size:86 final size:85
Alignment explanation
Indices: 3395--3566 Score: 317
Period size: 86 Copynumber: 2.0 Consensus size: 85
3385 ATGGGTAGCA
*
3395 TGGGCATGGCCCCTGCCACTGCCTGCCTCATTTTAATCCGCATTCTGAGTGTAAGAGGTTTTTTT
1 TGGGCATGGCCCCTGCCACTGCCTGCCTCATTTTAATCCGCATTCTGAGTGTAAGAGG-TTCTTT
3460 TAAGGAAAGTTGACAATAAGT
65 TAAGGAAAGTTGACAATAAGT
*
3481 TGGGCATGGCCCCTGCCCCTGCCTGCCTCATTTTAATCCGCATTCTGAGTGTAAGAGGTTCTTTT
1 TGGGCATGGCCCCTGCCACTGCCTGCCTCATTTTAATCCGCATTCTGAGTGTAAGAGGTTCTTTT
3546 AAGGAAAGTTGACAATAAGT
66 AAGGAAAGTTGACAATAAGT
3566 T
1 T
3567 TTGGTGATTA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
85 27 0.32
86 57 0.68
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (85 bp):
TGGGCATGGCCCCTGCCACTGCCTGCCTCATTTTAATCCGCATTCTGAGTGTAAGAGGTTCTTTT
AAGGAAAGTTGACAATAAGT
Found at i:3691 original size:2 final size:2
Alignment explanation
Indices: 3686--3722 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3676 TATGTGTGTG
3686 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3723 CAAGTACTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6106 original size:30 final size:31
Alignment explanation
Indices: 6052--6113 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
6042 AATCAACAAA
*
6052 ACTTAGTTTCCCAAATGGCTATCTCAATACC
1 ACTTAGTTTCCCAAATGACTATCTCAATACC
6083 ACTTAGTTTCCC-AATGACTATCTCAATACC
1 ACTTAGTTTCCCAAATGACTATCTCAATACC
6113 A
1 A
6114 ATTACCAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.32
Consensus pattern (31 bp):
ACTTAGTTTCCCAAATGACTATCTCAATACC
Found at i:17876 original size:13 final size:13
Alignment explanation
Indices: 17858--17884 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17848 CTCTAGAATC
17858 TCATAAATCATAT
1 TCATAAATCATAT
17871 TCATAAATCATAT
1 TCATAAATCATAT
17884 T
1 T
17885 TATTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATAAATCATAT
Found at i:28050 original size:22 final size:22
Alignment explanation
Indices: 28016--28058 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28006 ACATGGTTTT
28016 ATGGGTAATAGGAAATCTGTTG
1 ATGGGTAATAGGAAATCTGTTG
*
28038 ATGGGTTAA-AGGAACTCTGTT
1 ATGGG-TAATAGGAAATCTGTT
28059 TTAGGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (22 bp):
ATGGGTAATAGGAAATCTGTTG
Found at i:29522 original size:13 final size:13
Alignment explanation
Indices: 29504--29545 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
29494 AATAAAACTT
29504 AAATACTAATAAA
1 AAATACTAATAAA
*
29517 AAATAC--ACAAA
1 AAATACTAATAAA
29528 AAATACTAATAAA
1 AAATACTAATAAA
29541 AAATA
1 AAATA
29546 ACAAAAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 10 0.40
13 15 0.60
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (13 bp):
AAATACTAATAAA
Found at i:29531 original size:24 final size:23
Alignment explanation
Indices: 29504--29552 Score: 89
Period size: 24 Copynumber: 2.1 Consensus size: 23
29494 AATAAAACTT
29504 AAATACTAATAAAAAATACACAAA
1 AAATACTAATAAAAAATA-ACAAA
29528 AAATACTAATAAAAAATAACAAA
1 AAATACTAATAAAAAATAACAAA
29551 AA
1 AA
29553 GGAAAAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.16
Consensus pattern (23 bp):
AAATACTAATAAAAAATAACAAA
Found at i:29827 original size:31 final size:33
Alignment explanation
Indices: 29787--29848 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
29777 TTTTAAACCT
*
29787 AATAACCAAAACCGCA-C-CAAAACCGTTTAAC
1 AATAACCAAAACCGCATCGCAAAACCATTTAAC
* *
29818 AATATCCAAATCCGCATCGCAAAACCATTTA
1 AATAACCAAAACCGCATCGCAAAACCATTTA
29849 TTAAGCGGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 14 0.54
32 1 0.04
33 11 0.42
ACGTcount: A:0.45, C:0.31, G:0.06, T:0.18
Consensus pattern (33 bp):
AATAACCAAAACCGCATCGCAAAACCATTTAAC
Found at i:31348 original size:2 final size:2
Alignment explanation
Indices: 31341--31375 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31331 ATATAGTTAA
31341 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31376 CTACATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31677 original size:167 final size:164
Alignment explanation
Indices: 31427--31887 Score: 595
Period size: 167 Copynumber: 2.8 Consensus size: 164
31417 TCCCCACCCC
* * * *
31427 GGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGTCTTTTCCCACTTGGCAGATTACTTAAATG
1 GGATTGATGATGAGCTAGAGAACTAA-TTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATG
* * * *
31492 TCCTAACGTTTGATTCTTGAGGAAATTAAATAACTACACTTTTTGGTTATTTCTCAATTGACTTT
65 TCCTAACTTTTGATTCTTGAGGAGATTAAATAACTA-ACTTTTTGGTCATTTCTCAATTGACTTG
* *
31557 AATAGAGTAGTGGAATTACTAAAAGATTC-CTATCAA
129 AATAGAGTAGTGGAATTAATAAAAGA-TCACCATCAA
* ** * *
31593 -GACTTGCTTTTGGAGTTAGAGAACTTATTTTATTCGTCTTTTCCTACTTGGCAGATTACTTAAA
1 GGA-TTGATGAT-GAGCTAGAGAACTAATTTT-TTCGTCTTTTCCTACTTGGCAGATTACTTAAA
* * * *
31657 TGTCCTAACTTTTAATTCTTGAGGGGATTAAATAAGTAATCTTTTTTGGTCATTTCTCAATGGAC
63 TGTCCTAACTTTTGATTCTTGAGGAGATTAAATAACTAA-C-TTTTTGGTCATTTCTCAATTGAC
*
31722 TTGAATATAGTAGTGGAATTAATAAAAGATCACCATCAA
126 TTGAATAGAGTAGTGGAATTAATAAAAGATCACCATCAA
*
31761 GGATTGATGATGAGCTAGAGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATG
1 GGATTGATGATGAGCTAGAGAACTAAT-TTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATG
* *
31826 TTCTAACTTTTGATTCTT-AGGGTGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGAC
65 TCCTAACTTTTGATTCTTGA-GGAGATTAAATAACT-AACTTTTTGGTCATTTCTCAATTGAC
31888 AAATGACTCA
Statistics
Matches: 254, Mismatches: 31, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
165 2 0.01
166 31 0.12
167 156 0.61
168 63 0.25
169 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (164 bp):
GGATTGATGATGAGCTAGAGAACTAATTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGT
CCTAACTTTTGATTCTTGAGGAGATTAAATAACTAACTTTTTGGTCATTTCTCAATTGACTTGAA
TAGAGTAGTGGAATTAATAAAAGATCACCATCAA
Found at i:32077 original size:17 final size:17
Alignment explanation
Indices: 32045--32077 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
32035 TCTCCTATCA
*
32045 ATTATTTTTTGTAAAAG
1 ATTATTTTTTGAAAAAG
32062 ATTATTTTTTGAAAAA
1 ATTATTTTTTGAAAAA
32078 TATGTATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (17 bp):
ATTATTTTTTGAAAAAG
Found at i:36962 original size:38 final size:38
Alignment explanation
Indices: 36884--36964 Score: 119
Period size: 38 Copynumber: 2.1 Consensus size: 38
36874 TATGTATACA
** *
36884 AAGTTTTGGGCTGTACTTTTTTCTTTTTTTTTTTAGGT
1 AAGTTTTGGGCTGTACTTTTTTCTTTTTTTTGATAAGT
36922 AAGTTTTGGGCTG-ACTTTTTTCTTTTTTTTGGATAAGT
1 AAGTTTTGGGCTGTACTTTTTTCTTTTTTTT-GATAAGT
36960 AAGTT
1 AAGTT
36965 AATTTTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
37 17 0.44
38 22 0.56
ACGTcount: A:0.15, C:0.07, G:0.20, T:0.58
Consensus pattern (38 bp):
AAGTTTTGGGCTGTACTTTTTTCTTTTTTTTGATAAGT
Done.