Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000993.1 Corchorus capsularis cultivar CVL-1 contig00993, 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: 2864
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Found at i:1186 original size:31 final size:30
Alignment explanation
Indices: 1136--1196 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
1126 GGAGAAATTT
*
1136 TATATTTTCCGATTGTACCCATTTTTCTAAAA
1 TATATTTTCCGATTATACCC-TTTTT-TAAAA
1168 TATATTTT-CGATTATACCCTTTTTTAAAA
1 TATATTTTCCGATTATACCCTTTTTTAAAA
1197 AAATATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 5 0.18
30 5 0.18
31 10 0.36
32 8 0.29
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (30 bp):
TATATTTTCCGATTATACCCTTTTTTAAAA
Found at i:1200 original size:32 final size:32
Alignment explanation
Indices: 1136--1206 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
1126 GGAGAAATTT
* **
1136 TATATTTTCCGATTGTACCCATTTTTCTAAAA
1 TATATTTTCCGATTATACCCATTTTTAAAAAA
*
1168 TATATTTT-CGATTATACCCTTTTTTAAAAAAA
1 TATATTTTCCGATTATACCCATTTTT-AAAAAA
1200 TATATTT
1 TATATTT
1207 CTAAATAGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 15 0.44
32 19 0.56
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.49
Consensus pattern (32 bp):
TATATTTTCCGATTATACCCATTTTTAAAAAA
Found at i:1664 original size:130 final size:132
Alignment explanation
Indices: 1510--1774 Score: 480
Period size: 130 Copynumber: 2.0 Consensus size: 132
1500 TATATTCATA
* *
1510 TATATCATAGACATAGAAAATAGAACGGGTATAATATTAGCCTTTTTTTTCTCCATAAACTATTG
1 TATATCATAGACATAAAAAATAGAACGGGTATAATATTAGCCTTTTTTTACTCCATAAACTATTG
1575 TATTAATGTGATGTCAAAAAAAAATATTGTATTAATG-A-TTTTTTTTTTTGCATAAAAGAAAAG
66 TATTAATGTGATGTCAAAAAAAAATATTGTATTAATGAATTTTTTTTTTTTGCATAAAAGAAAAG
1638 TC
131 TC
1640 TATATCATAGACATAAAAAATAGAACGGGTATAATATTAGCCTTTTTTTACTCCATAAACTATTG
1 TATATCATAGACATAAAAAATAGAACGGGTATAATATTAGCCTTTTTTTACTCCATAAACTATTG
1705 TATTAATGTGATGTCAAAAAAAAATATTGTATTAATGATATTTTTTTTTTTTTGCATAAAAGAAA
66 TATTAATGTGATGTCAAAAAAAAATATTGTATTAATGA-A-TTTTTTTTTTTTGCATAAAAGAAA
1770 AGTC
129 AGTC
1774 T
1 T
1775 CTTGCTAGAG
Statistics
Matches: 129, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
130 100 0.78
132 1 0.01
134 28 0.22
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (132 bp):
TATATCATAGACATAAAAAATAGAACGGGTATAATATTAGCCTTTTTTTACTCCATAAACTATTG
TATTAATGTGATGTCAAAAAAAAATATTGTATTAATGAATTTTTTTTTTTTGCATAAAAGAAAAG
TC
Found at i:2520 original size:42 final size:42
Alignment explanation
Indices: 2439--2520 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
2429 AGTACTTTTG
* * **
2439 GGGGACAGGGACGGGGATGGGGATTGTTCTCCATTCCCCGTC
1 GGGGACAGGGACGGGGATGGGGATGGTCCTCCACGCCCCGTC
*
2481 GGGGACGGGGACGGGGATGGGGAATGGTCCTCC-CGCCCCG
1 GGGGACAGGGACGGGGATGGGG-ATGGTCCTCCACGCCCCG
2521 AACGCAGCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 26 0.76
43 8 0.24
ACGTcount: A:0.13, C:0.26, G:0.45, T:0.16
Consensus pattern (42 bp):
GGGGACAGGGACGGGGATGGGGATGGTCCTCCACGCCCCGTC
Found at i:2647 original size:22 final size:22
Alignment explanation
Indices: 2621--2694 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
2611 TTTGATAATT
2621 TACTAATAAATAATAATATATA
1 TACTAATAAATAATAATATATA
* * *
2643 TACTAATAAATATTTACTA-ATT
1 TACTAATAAATA-ATAATATATA
2665 TACTAAT-AAT-ATAA-ATATA
1 TACTAATAAATAATAATATATA
*
2684 TATTAA-AAATA
1 TACTAATAAATA
2695 TATATTTTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
18 1 0.02
19 12 0.29
21 3 0.07
22 21 0.51
23 4 0.10
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
TACTAATAAATAATAATATATA
Found at i:2660 original size:14 final size:15
Alignment explanation
Indices: 2631--2663 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2621 TACTAATAAA
2631 TAATAATATATATAC
1 TAATAATATATATAC
*
2646 TAATAA-ATATTTAC
1 TAATAATATATATAC
2660 TAAT
1 TAAT
2664 TTACTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATAATATATATAC
Found at i:2672 original size:44 final size:40
Alignment explanation
Indices: 2616--2695 Score: 115
Period size: 44 Copynumber: 1.9 Consensus size: 40
2606 TATGTTTTGA
2616 TAATTTACTAATAAATAATAATATATATACTAATAAATATTTAC
1 TAATTTACTAAT-AAT-ATAA-ATATATACTAA-AAATATTTAC
*
2660 TAATTTACTAATAATATAAATATATATTAAAAATAT
1 TAATTTACTAATAATATAAATATATACTAAAAATAT
2696 ATATTTTAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
40 6 0.17
41 10 0.29
42 4 0.11
43 3 0.09
44 12 0.34
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (40 bp):
TAATTTACTAATAATATAAATATATACTAAAAATATTTAC
Done.