Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009693.1 Corchorus capsularis cultivar CVL-1 contig09714, 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: 17505
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:4068 original size:86 final size:86
Alignment explanation
Indices: 3919--4086 Score: 300
Period size: 86 Copynumber: 2.0 Consensus size: 86
3909 ACACCTGGCA
3919 CCTTCAAACCCTTCATGGAGAACACTGCATTACACACTTCCACCATCTCAAGACCATGCGTCACA
1 CCTTCAAACCCTTCATGGAGAACACTGCATTACACACTTCCACCATCTCAAGACCATGCGTCACA
3984 CAACCTTTCACTTCACTGGTG
66 CAACCTTTCACTTCACTGGTG
* * *
4005 CCTTCAAACCCTTCATGGAGAACACTGCATTCCACACTTCCACCATCTCAAGATCATGTGTCACA
1 CCTTCAAACCCTTCATGGAGAACACTGCATTACACACTTCCACCATCTCAAGACCATGCGTCACA
*
4070 CACCCTTTCACTTCACT
66 CAACCTTTCACTTCACT
4087 TCAATCAAGC
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 78 1.00
ACGTcount: A:0.27, C:0.37, G:0.10, T:0.26
Consensus pattern (86 bp):
CCTTCAAACCCTTCATGGAGAACACTGCATTACACACTTCCACCATCTCAAGACCATGCGTCACA
CAACCTTTCACTTCACTGGTG
Found at i:7167 original size:22 final size:22
Alignment explanation
Indices: 7142--7184 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
7132 AAAATGACAT
7142 ATAAAACATATC-AAATACATGC
1 ATAAAACATA-CAAAATACATGC
* *
7164 ATAATAGATACAAAATACATG
1 ATAAAACATACAAAATACATG
7185 TAACATTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.56, C:0.14, G:0.07, T:0.23
Consensus pattern (22 bp):
ATAAAACATACAAAATACATGC
Found at i:7172 original size:232 final size:232
Alignment explanation
Indices: 6759--7203 Score: 669
Period size: 232 Copynumber: 1.9 Consensus size: 232
6749 TTTGACTATG
* * * *
6759 GTCGAAATTCACCATCTTGAGGTCTCTTTTGGGGCTTCAATCCAATTGTGCTCCAAATACCTCCA
1 GTCGAAAATCACCATCTTGAGGTCTCTTTTGGGGCTTCAATCCAATTGTACTCAAAATACCTCAA
*
6824 TTTTGCTCCATTTTAGACCATATTGCAACTTTCTCTCTAAATAGACCTACAAATGCAAAACGCCC
66 TTTAGCTCCATTTTAGACCATATTGCAACTTTCTCTCTAAATAGACCTACAAATGCAAAACGCCC
*
6889 ATTTAGAGGGTAAAATAACATAGAAAACATATCAAATACATGCAAAATAGATACAAAATGCATGT
131 ATTTAGAGGGTAAAATAACATAGAAAACATATCAAATACATGCAAAATAGATACAAAATACATGT
6954 AACATCTTGGTCTCATCAGCAGCCCTAGACATAGGTC
196 AACATCTTGGTCTCATCAGCAGCCCTAGACATAGGTC
* * * *
6991 GTCGAAAATCACCTTCTTGAGGTCTCCTTTT-GGGTTTTAATCCAATTGTACTCAAAATAGCTCA
1 GTCGAAAATCACCATCTTGAGGTCT-CTTTTGGGGCTTCAATCCAATTGTACTCAAAATACCTCA
* * * * * *
7055 ATTTAGCTTCTTTTTAGACCATATTGCAACTTTCTCTTTAAATAGGCCTACAAGTGTAAAACG-C
65 ATTTAGCTCCATTTTAGACCATATTGCAACTTTCTCTCTAAATAGACCTACAAATGCAAAACGCC
* * * *
7119 CTTATTAGAGGGTAAAATGACATATAAAACATATCAAATACATGCATAATAGATACAAAATACAT
130 CAT-TTAGAGGGTAAAATAACATAGAAAACATATCAAATACATGCAAAATAGATACAAAATACAT
*
7184 GTAACATTTTGGTCTCATCA
194 GTAACATCTTGGTCTCATCA
7204 CCCTCAACCA
Statistics
Matches: 190, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
231 3 0.02
232 182 0.96
233 5 0.03
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (232 bp):
GTCGAAAATCACCATCTTGAGGTCTCTTTTGGGGCTTCAATCCAATTGTACTCAAAATACCTCAA
TTTAGCTCCATTTTAGACCATATTGCAACTTTCTCTCTAAATAGACCTACAAATGCAAAACGCCC
ATTTAGAGGGTAAAATAACATAGAAAACATATCAAATACATGCAAAATAGATACAAAATACATGT
AACATCTTGGTCTCATCAGCAGCCCTAGACATAGGTC
Found at i:12488 original size:14 final size:14
Alignment explanation
Indices: 12469--12520 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
12459 TACATAATAC
12469 TAATAATATATATA
1 TAATAATATATATA
12483 TAATAATATA-ATAA
1 TAATAATATATAT-A
* *
12497 GAATAATACTATGTA
1 TAATAATA-TATATA
12512 T-ATAATATA
1 TAATAATATA
12521 AACTTTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 4 0.12
14 24 0.75
15 3 0.09
16 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (14 bp):
TAATAATATATATA
Found at i:12489 original size:17 final size:17
Alignment explanation
Indices: 12469--12518 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
12459 TACATAATAC
12469 TAATAATATATATATAA
1 TAATAATATATATATAA
*
12486 TAAT-ATA-ATA-AGAA
1 TAATAATATATATATAA
* *
12500 TAATACTATGTATATAA
1 TAATAATATATATATAA
12517 TA
1 TA
12519 TAAACTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
14 7 0.27
15 5 0.19
16 5 0.19
17 9 0.35
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (17 bp):
TAATAATATATATATAA
Found at i:13546 original size:8 final size:8
Alignment explanation
Indices: 13533--13566 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
13523 GATTTCGATT
13533 TACATATA
1 TACATATA
13541 TACATATA
1 TACATATA
13549 TACATATA
1 TACATATA
13557 TACATATA
1 TACATATA
13565 TA
1 TA
13567 TAGTCTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (8 bp):
TACATATA
Found at i:13982 original size:28 final size:28
Alignment explanation
Indices: 13925--13982 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
13915 AGGTTTAACT
* ***
13925 TATATCATTTACATTTTTTTTTGGTAAA
1 TATATCATTTACATATTTTTTTACAAAA
13953 TATATCATTTACA-ATTTTTTTACAACAA
1 TATATCATTTACATATTTTTTTACAA-AA
13981 TA
1 TA
13983 CAAAACACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.52
Consensus pattern (28 bp):
TATATCATTTACATATTTTTTTACAAAA
Found at i:15850 original size:22 final size:22
Alignment explanation
Indices: 15825--15902 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 22
15815 AATTTATATT
*
15825 AAATTTTGATAATTACACCATA
1 AAATTTTGATAATCACACCATA
*
15847 AAA-TTT--TAATGACATCCATA
1 AAATTTTGATAATCACA-CCATA
* *
15867 TGAAATTTTGATAATCACACTATG
1 --AAATTTTGATAATCACACCATA
*
15891 AAATTCTGATAA
1 AAATTTTGATAA
15903 CGACATCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
19 7 0.16
20 5 0.11
21 3 0.07
22 17 0.38
23 3 0.07
24 3 0.07
25 7 0.16
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAATCACACCATA
Found at i:16064 original size:22 final size:22
Alignment explanation
Indices: 16039--16099 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
16029 ATAATAAAAC
* * *
16039 TATGAAAATTTAATAAGTTGCT
1 TATGAAAATTTGATAAGCTCCT
*
16061 TATGAAAATTTGATAACCTCCT
1 TATGAAAATTTGATAAGCTCCT
16083 TATG-AAATTTGATAAGC
1 TATGAAAATTTGATAAGC
16100 AGACTATGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 12 0.35
22 22 0.65
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (22 bp):
TATGAAAATTTGATAAGCTCCT
Found at i:16164 original size:44 final size:43
Alignment explanation
Indices: 16131--16296 Score: 153
Period size: 44 Copynumber: 3.9 Consensus size: 43
16121 CTCCATGTGG
16131 AATGTTGGTAAGCACTCTACGAAATTTTGATAACCTTCCTATAA
1 AATGTTGGTAAGCACTCTACGAAATTTTGATAACC-TCCTATAA
* * * * *
16175 AATGCTGGTAAGCACACTAAGAAATTTTGATCACTTTCCTATAA
1 AATGTTGGTAAGCACTCTACGAAATTTTGATAAC-CTCCTATAA
* * *
16219 AATGTTGGTAATCACTAT-C-AAATTTTGATAACCTCATTATAA
1 AATGTTGGTAAGCACTCTACGAAATTTTGATAACCTC-CTATAA
* * *
16261 AATTTTGATAAAC-CTCT--GTAAACTTTTGATAACCTC
1 AATGTTGGTAAGCACTCTACG-AAA-TTTTGATAACCTC
16297 TTTTGAAATT
Statistics
Matches: 100, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
41 5 0.05
42 30 0.30
43 13 0.13
44 52 0.52
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (43 bp):
AATGTTGGTAAGCACTCTACGAAATTTTGATAACCTCCTATAA
Found at i:16287 original size:21 final size:20
Alignment explanation
Indices: 16213--16380 Score: 95
Period size: 22 Copynumber: 8.1 Consensus size: 20
16203 GATCACTTTC
* * * *
16213 CTATAAAATGTTGGTAATCA
1 CTATAAAATTTTGATAACCT
*
16233 CTATCAAATTTTGATAACCT
1 CTATAAAATTTTGATAACCT
16253 CATTATAAAATTTTGATAAACCT
1 C--TATAAAATTTTGAT-AACCT
* *
16276 CTGTAAACTTTTGATAACCT
1 CTATAAAATTTTGATAACCT
* * * *
16296 CTTTTGAAATTTTGTTAATCT
1 C-TATAAAATTTTGATAACCT
* ** * *
16317 C-ATGATGTTTCGATAACCAC
1 CTATAAAATTTTGATAACC-T
*
16337 CTCATGAAATTTTGATAACTACT
1 CT-ATAAAATTTTGATAAC--CT
*
16360 CTATGAAATTTTGATAACCT
1 CTATAAAATTTTGATAACCT
16380 C
1 C
16381 CCTTTTAAAA
Statistics
Matches: 115, Mismatches: 24, Indels: 18
0.73 0.15 0.11
Matches are distributed among these distances:
19 11 0.10
20 26 0.23
21 27 0.23
22 42 0.37
23 8 0.07
24 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.40
Consensus pattern (20 bp):
CTATAAAATTTTGATAACCT
Found at i:16435 original size:22 final size:22
Alignment explanation
Indices: 16385--16426 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16375 AACCTCCCTT
*
16385 TTAAAAACCACACTATGAAAAC
1 TTAATAACCACACTATGAAAAC
*
16407 TTAATAACCACATTATGAAA
1 TTAATAACCACACTATGAAA
16427 TTTTGATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (22 bp):
TTAATAACCACACTATGAAAAC
Done.