Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011816.1 Corchorus capsularis cultivar CVL-1 contig11837, 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: 36401
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:11860 original size:1 final size:1
Alignment explanation
Indices: 11854--11886 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
11844 TATGTAAGTC
11854 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11887 ATAATTAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:18039 original size:18 final size:18
Alignment explanation
Indices: 18016--18054 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
18006 GGAAGATCAT
18016 GTGTTTCAAGTAATTAAA
1 GTGTTTCAAGTAATTAAA
18034 GTGTTTCAAGTAATTAAA
1 GTGTTTCAAGTAATTAAA
18052 GTG
1 GTG
18055 ACAGACAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (18 bp):
GTGTTTCAAGTAATTAAA
Found at i:28780 original size:2 final size:2
Alignment explanation
Indices: 28773--28799 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28763 ATAGAAATCC
28773 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 A
28800 ACTAAATGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32089 original size:4 final size:4
Alignment explanation
Indices: 32080--32112 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
32070 ATTCATGCCA
32080 CTTT CTTT CTTT CTTT CTTT CTTT CTTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT
32113 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:32116 original size:8 final size:8
Alignment explanation
Indices: 32081--32127 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
32071 TTCATGCCAC
*
32081 TTTCTTTC
1 TTTCTTTT
*
32089 TTTCTTTC
1 TTTCTTTT
32097 TTTCTTTCT
1 TTTCTTT-T
32106 TTTCTTTT
1 TTTCTTTT
32114 TTT-TTTT
1 TTTCTTTT
32121 TTT-TTTT
1 TTTCTTTT
32128 CAAGAAATGG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
7 11 0.30
8 19 0.51
9 7 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTCTTTT
Found at i:32120 original size:12 final size:12
Alignment explanation
Indices: 32081--32127 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
32071 TTCATGCCAC
* *
32081 TTTCTTTCTTTC
1 TTTCTTTTTTTT
*
32093 TTTCTTTCTTTCT
1 TTTCTTT-TTTTT
32106 TTTCTTTTTTTT
1 TTTCTTTTTTTT
32118 TTT-TTTTTTT
1 TTTCTTTTTTT
32128 CAAGAAATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 7 0.23
12 14 0.47
13 9 0.30
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:34087 original size:139 final size:141
Alignment explanation
Indices: 33766--34097 Score: 526
Period size: 141 Copynumber: 2.4 Consensus size: 141
33756 TTCAACTTTG
* * * *
33766 ATTAGATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAATTAACAACATGTTCAATAAT
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGACATGTTCAATAAT
* ** *
33831 TTATTTTTTTGGTAACATAATTAGTTTTTGATTTATTTATTTATGGTAATCTTTTTGGTGGCGAT
66 TTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTAGCGAT
33896 TTTATGGTAAA
131 TTTATGGTAAA
*
33907 ATTATATAATCATCAATCAATTACAACTTTGATT-GACAAAATTAACTAACGACATGTTCAATAA
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGA-AAAATTAACTAACGACATGTTCAATAA
* *
33971 TTTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGTTAAT-TTTTTTGTAGCGA
65 TTTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTAGCGA
34035 -TTTATGGTAAA
130 TTTTATGGTAAA
*
34046 ATTAAATAATTATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGA
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGA
34098 TCACTAACTT
Statistics
Matches: 177, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
139 58 0.33
140 14 0.08
141 105 0.59
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (141 bp):
ATTAAATAATCATCAATCAATTACAACTTTGATTGGAAAAATTAACTAACGACATGTTCAATAAT
TTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTAGCGAT
TTTATGGTAAA
Found at i:34645 original size:139 final size:138
Alignment explanation
Indices: 34382--34774 Score: 450
Period size: 139 Copynumber: 2.8 Consensus size: 138
34372 TTTTTGGCAA
* * ** * * *
34382 TTAATTAACGACTAATTTTATTCCCTAATTTATTTAGTATGTTCAATCAATCTATTTTTTTTGCT
1 TTAACTAACGACTAATTTGATTCATTTATTTATTTAGCATGTTCAATC-A---ATTTTTTTTGGT
* *
34447 AACATAATTACTAATTGATTCATTTATTTA-TGACAAAATCAAATAATCATCAATCAATTATAAC
62 AACATAA-TACTAATTGATTCATTTATTTATTGA-AAAATTAAATAATCACCAATCAATTATAAC
34511 TTTGATT-GACAAAG
125 TTTGATTGGA-AAAG
*
34525 TTGA-TCAACGACTAATTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTGGTAAC
1 TTAACT-AACGACTAATTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTGGTAAC
* * * * *
34589 ATAAGCACTAATTGATTTATTTATTTATTGAAAAATTAAATAATCACCCATTAATTATAACTTTT
65 ATAA-TACTAATTGATTCATTTATTTATTGAAAAATTAAATAATCACCAATCAATTATAACTTTG
34654 ATTGGAAAAG
129 ATTGGAAAAG
* * * * * *
34664 TTAACTAAGGACTAACTTGATTCATTTACTTATTTTGGATGTTCAATCAATTTATTTTTTTGTAA
1 TTAACTAACGACTAATTTGATTCATTTATTTATTTAGCATGTTCAATCAA-TT-TTTTTTGGTAA
* * *
34729 CATAATACTAATTGATTCATTTATTTGTGGCAAAATTAAATAATCA
64 CATAATACTAATTGATTCATTTATTTATTGAAAAATTAAATAATCA
34775 TTAGCTTTTG
Statistics
Matches: 217, Mismatches: 27, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
139 116 0.53
140 44 0.20
141 15 0.07
142 2 0.01
143 40 0.18
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (138 bp):
TTAACTAACGACTAATTTGATTCATTTATTTATTTAGCATGTTCAATCAATTTTTTTTGGTAACA
TAATACTAATTGATTCATTTATTTATTGAAAAATTAAATAATCACCAATCAATTATAACTTTGAT
TGGAAAAG
Done.