Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011647.1 Corchorus capsularis cultivar CVL-1 contig11668, 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: 33965
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:9461 original size:2 final size:2
Alignment explanation
Indices: 9454--9484 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
9444 TATTGTTACA
9454 AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
9485 TATTTTTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21138 original size:12 final size:12
Alignment explanation
Indices: 21121--21147 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
21111 ATTCCTCGCC
21121 ATTTTGTCCTTA
1 ATTTTGTCCTTA
21133 ATTTTGTCCTTA
1 ATTTTGTCCTTA
21145 ATT
1 ATT
21148 GAACAAAATG
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:0.19, C:0.15, G:0.07, T:0.59
Consensus pattern (12 bp):
ATTTTGTCCTTA
Found at i:22681 original size:12 final size:12
Alignment explanation
Indices: 22657--22705 Score: 59
Period size: 11 Copynumber: 4.3 Consensus size: 12
22647 CGACGACGAC
*
22657 AAAAAT-AATAT
1 AAAAATAAAGAT
22668 AAAAATAAAGAT
1 AAAAATAAAGAT
*
22680 -AAAATAAAGCT
1 AAAAATAAAGAT
22691 AAAAATAAA-AT
1 AAAAATAAAGAT
22702 AAAA
1 AAAA
22706 GGATGGAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 21 0.64
12 12 0.36
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (12 bp):
AAAAATAAAGAT
Found at i:22686 original size:17 final size:17
Alignment explanation
Indices: 22657--22705 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
22647 CGACGACGAC
*
22657 AAAAATAATATAAAAAT
1 AAAAATAAAATAAAAAT
* **
22674 AAAGATAAAATAAAGCT
1 AAAAATAAAATAAAAAT
22691 AAAAATAAAATAAAA
1 AAAAATAAAATAAAA
22706 GGATGGAAGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (17 bp):
AAAAATAAAATAAAAAT
Found at i:26656 original size:16 final size:18
Alignment explanation
Indices: 26635--26667 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
26625 AAAATTGGTG
26635 TTTCTTC-C-TCTTTTTA
1 TTTCTTCTCTTCTTTTTA
26651 TTTCTTCTCTTCTTTTT
1 TTTCTTCTCTTCTTTTT
26668 TTTTTCTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCTTCTCTTCTTTTTA
Found at i:27084 original size:11 final size:11
Alignment explanation
Indices: 27068--27092 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27058 TTTTTGTAAA
27068 TATTTGATAAT
1 TATTTGATAAT
27079 TATTTGATAAT
1 TATTTGATAAT
27090 TAT
1 TAT
27093 ATAATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
TATTTGATAAT
Found at i:27356 original size:14 final size:15
Alignment explanation
Indices: 27323--27356 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
27313 GTACTAAAAA
*
27323 TTCAGTACTTAATCT
1 TTCAGCACTTAATCT
27338 TTCAGCACTTAAT-T
1 TTCAGCACTTAATCT
27352 TTCAG
1 TTCAG
27357 TTTTCTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (15 bp):
TTCAGCACTTAATCT
Found at i:28215 original size:24 final size:25
Alignment explanation
Indices: 28188--28234 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
28178 TTAATGTTCA
28188 AATT-TTATTTT-TTATTAAAAATTT
1 AATTATTATTTTGTT-TTAAAAATTT
28212 AATTATTATTTTGTTTTAAAAAT
1 AATTATTATTTTGTTTTAAAAAT
28235 AAATATGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.19
25 15 0.71
26 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
AATTATTATTTTGTTTTAAAAATTT
Found at i:31977 original size:31 final size:31
Alignment explanation
Indices: 31916--32094 Score: 175
Period size: 31 Copynumber: 5.9 Consensus size: 31
31906 ACGGAGTCCG
** * **
31916 ACGTGGCGTGCCACGTGGA-CAAAAAATGAC
1 ACGTGGCACGCCACGTGTACCAAAAGGTGAC
* * *
31946 ATGTGGCACGTCACGTGTATCAAAAGGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAGGTGAC
* *
31977 ACGTGACACGCCATGTGTACCAAAAGGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAGGTGAC
* * *
32008 ACGTGTCACGTCATGTGTACCAAAAGGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAGGTGAC
* * *
32039 ACGTGTCACGCCACGTGTATC-AAACGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAGGTGAC
* *
32069 ACGTGGCATGCCACGTGCA-CAAAAGG
1 ACGTGGCACGCCACGTGTACCAAAAGG
32095 ACACATGCCA
Statistics
Matches: 125, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
29 1 0.01
30 42 0.34
31 82 0.66
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAGGTGAC
Found at i:33836 original size:26 final size:26
Alignment explanation
Indices: 33807--33874 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
33797 TTCCTTCATT
33807 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
33833 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
33859 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
33875 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:33898 original size:52 final size:51
Alignment explanation
Indices: 33807--33924 Score: 122
Period size: 52 Copynumber: 2.4 Consensus size: 51
33797 TTCCTTCATT
* *
33807 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA
* * *
33859 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA
33910 -T---CATAAACTAATTAA
1 TTAAACATAAACTAATTAA
33925 TATTAAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
47 10 0.17
48 3 0.05
50 1 0.02
51 10 0.17
52 28 0.48
53 6 0.10
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (51 bp):
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA
Done.