Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000303.1 Corchorus capsularis cultivar CVL-1 contig00303, 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: 9090
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:2369 original size:20 final size:22
Alignment explanation
Indices: 1795--2375 Score: 188
Period size: 22 Copynumber: 26.5 Consensus size: 22
1785 ACCTCCTTAC
1795 GAAATTTTGATAACCTTTC-TAT
1 GAAATTTTGATAACC-TTCATAT
* * **
1817 TAAATTTTAATAACGAT-ACTAT
1 GAAATTTTGATAACCTTCA-TAT
* * * **
1839 GAAATTTCGAGAACATTTTTAT
1 GAAATTTTGATAACCTTCATAT
** *
1861 -AAATTCTTTTTAACCTTCTTAT
1 GAAATT-TTGATAACCTTCATAT
* * * * *
1883 GGAATTTTGTTAACCTCCCTAA
1 GAAATTTTGATAACCTTCATAT
*
1905 GGAATTTTGA-AGACC-TCAATAT
1 GAAATTTTGATA-ACCTTC-ATAT
1927 GAAATTTTGATAA-CTTCCCA-AT
1 GAAATTTTGATAACCTT--CATAT
*
1949 GAAATTTTGATAATCAAC-ACACTAT
1 GAAATTTTGATAA-C--CTTCA-TAT
* * *
1974 GAGATGTTGATAACCTCCATAT
1 GAAATTTTGATAACCTTCATAT
* * *
1996 GATATATTGATAACC-ACATTAT
1 GAAATTTTGATAACCTTCA-TAT
* * * *
2018 GAAAATTTAAAAACCTCCATAT
1 GAAATTTTGATAACCTTCATAT
*
2040 G-AATTATT-AGTAATCACACTC-T-T
1 GAAATT-TTGA-TAA-C-C-TTCATAT
* *
2063 GAAATTTTGATAATC-ACACTAT
1 GAAATTTTGATAACCTTCA-TAT
*
2085 GAAATTGTGATAACC-TCAGTAT
1 GAAATTTTGATAACCTTCA-TAT
*
2107 GAAATTTTGATAAACCTTCCTAT
1 GAAATTTTGAT-AACCTTCATAT
* * *
2130 AAAATTTTGATAAACCTCCCTAT
1 GAAATTTTGAT-AACCTTCATAT
* * * *
2153 AAAAATTTGATAACCTCCTTAT
1 GAAATTTTGATAACCTTCATAT
*
2175 GAAATCTTGATAA----C-TA-
1 GAAATTTTGATAACCTTCATAT
* * *
2191 CAAATTTTGATAACCTCCCTAT
1 GAAATTTTGATAACCTTCATAT
** *
2213 GATTTTTTGATAACC-TCATTAA
1 GAAATTTTGATAACCTTCA-TAT
* * * *
2235 GAAATTTTGTTAATCTCCCTAT
1 GAAATTTTGATAACCTTCATAT
* * *
2257 GAAATTTTGATCTACATAC-TAT
1 GAAATTTTGAT-AACCTTCATAT
* *
2279 GAAATTTTGATAACCCTCTTAT
1 GAAATTTTGATAACCTTCATAT
* * **
2301 AAAATTTTGA-AAACTAAACTAT
1 GAAATTTTGATAACCTTCA-TAT
*
2323 AAAATTTTGATAACCTTCATAT
1 GAAATTTTGATAACCTTCATAT
* *
2345 GAAATTTTGATATCC-TCCT-T
1 GAAATTTTGATAACCTTCATAT
2365 GAAATTTTGAT
1 GAAATTTTGAT
2376 TACTCCATAA
Statistics
Matches: 420, Mismatches: 95, Indels: 90
0.69 0.16 0.15
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
18 1 0.00
19 1 0.00
20 13 0.03
21 29 0.07
22 270 0.64
23 67 0.16
24 11 0.03
25 14 0.03
26 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
GAAATTTTGATAACCTTCATAT
Found at i:2662 original size:25 final size:22
Alignment explanation
Indices: 2455--2671 Score: 94
Period size: 22 Copynumber: 9.8 Consensus size: 22
2445 AGAAATACCA
*
2455 CTATGAAATTTTGGTAATCA-C
1 CTATGAAATTTTGATAATCATC
* * *
2476 ATTTTGAAA-TTTGATAA-CCTC
1 -CTATGAAATTTTGATAATCATC
* *
2497 TTTATGAAATTTTGATAAAC-TC
1 -CTATGAAATTTTGATAATCATC
* * * **
2519 TCTATAAAATTTTGTTGA-CCCC
1 -CTATGAAATTTTGATAATCATC
*
2541 TCTATGAGATTTTGATAATTACAT-
1 -CTATGAAATTTTGATAA-T-CATC
*
2565 -TATGTAATTTTGATAA-CATC
1 CTATGAAATTTTGATAATCATC
* * * *
2585 GCTTTCAGATTTTGATAA-CAAC
1 -CTATGAAATTTTGATAATCATC
*
2607 ACTATGAAATTTTGATAATCTTC
1 -CTATGAAATTTTGATAATCATC
2630 CTAT-AAATTTTGATAATCCGATC
1 CTATGAAATTTTGATAAT-C-ATC
*
2653 TCTATGAAATTTCGATAAT
1 -CTATGAAATTTTGATAAT
2672 TACTGTCTCT
Statistics
Matches: 148, Mismatches: 32, Indels: 27
0.71 0.15 0.13
Matches are distributed among these distances:
19 3 0.02
20 1 0.01
21 29 0.20
22 93 0.63
23 5 0.03
24 4 0.03
25 13 0.09
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCATC
Found at i:2763 original size:22 final size:22
Alignment explanation
Indices: 2748--2895 Score: 112
Period size: 22 Copynumber: 6.7 Consensus size: 22
2738 ATAACCTTCA
2748 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCACAC
*
2770 TA-AAAATTTTTGATAACCACAC
1 TATGAAA-TTTTGATAACCACAC
2792 TATGAAATTTTGATAGACTC-C-C
1 TATGAAATTTTGATA-AC-CACAC
* * *
2814 CATGAAATATT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCACAC
2835 TTATGAAATTTT-ATAAACCACAC
1 -TATGAAATTTTGAT-AACCACAC
* * *
2858 TATGAAATTCTT-ATAAACTCGC
1 TATGAAATT-TTGATAACCACAC
*
2880 TATGACATTTTGATAA
1 TATGAAATTTTGATAA
2896 TCTCTTTGAT
Statistics
Matches: 104, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
20 1 0.01
21 11 0.11
22 80 0.77
23 11 0.11
24 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:3011 original size:22 final size:22
Alignment explanation
Indices: 2981--3059 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
2971 TCACTTGATC
2981 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* *
3003 CTATAAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGGTAAC--CACA
* *
3026 -TATGAAATTTTGGTAAGCACT
1 CTATGAAATTTTGGTAACCACA
*
3047 CTATGGAATTTTG
1 CTATGAAATTTTG
3060 AAAATCTCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 41 0.89
23 2 0.04
24 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:3075 original size:44 final size:43
Alignment explanation
Indices: 2979--3078 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 43
2969 AATCACTTGA
*
2979 TCCTATGAAATTTTGGTAACCACACTATAAAATTTTGATAACT
1 TCCTATGAAATTTTGGTAACCACACTATAAAATTTTGAAAACT
* * **
3022 TCCATATGAAATTTTGGTAAGCACTCTATGGAATTTTGAAAA-T
1 TCC-TATGAAATTTTGGTAACCACACTATAAAATTTTGAAAACT
3065 CTCCTCATGAAATT
1 -TCCT-ATGAAATT
3079 ATAATAATTC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
43 5 0.10
44 44 0.90
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (43 bp):
TCCTATGAAATTTTGGTAACCACACTATAAAATTTTGAAAACT
Found at i:3315 original size:20 final size:20
Alignment explanation
Indices: 3277--3315 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3267 TATTGATATT
3277 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
3297 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
3316 AATAATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:6731 original size:29 final size:29
Alignment explanation
Indices: 6698--6757 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
6688 TAAACCGGTG
6698 AAATTCTAACTTCCACCAAACCTTTTACA
1 AAATTCTAACTTCCACCAAACCTTTTACA
*
6727 AAATTCTAACTTCCACCAAGCCTTTTACA
1 AAATTCTAACTTCCACCAAACCTTTTACA
6756 AA
1 AA
6758 GCGAGCTCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.30, G:0.02, T:0.30
Consensus pattern (29 bp):
AAATTCTAACTTCCACCAAACCTTTTACA
Done.