Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013188.1 Corchorus olitorius cultivar O-4 contig13221, 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: 80408
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:5714 original size:16 final size:17
Alignment explanation
Indices: 5682--5714 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5672 GATCAAACGA
5682 AATAAAATAAAAGATAG
1 AATAAAATAAAAGATAG
*
5699 AATAAATTAAAA-ATAG
1 AATAAAATAAAAGATAG
5715 TAATTAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (17 bp):
AATAAAATAAAAGATAG
Found at i:7767 original size:207 final size:207
Alignment explanation
Indices: 7410--7824 Score: 785
Period size: 207 Copynumber: 2.0 Consensus size: 207
7400 AAACAGAATA
7410 TAAGGAAATTGGTCTTGGGCCAAAATCCTTCCTCTTTTTTCCTCAAGTCGACGTTAACCCTCCTT
1 TAAGGAAATTGGTCTTGGGCCAAAATCCTTCCTCTTTTTTCCTCAAGTCGACGTTAACCCTCCTT
*
7475 GGTACCATACTTAACCAAAAATTTCAACAACTTTTCAAGCTCCAATGGCTTCCAAAGATCAAGGT
66 GGTACCATACTAAACCAAAAATTTCAACAACTTTTCAAGCTCCAATGGCTTCCAAAGATCAAGGT
*
7540 AACAACAACAAAAGTCATCAATCAAAGTCCTCCTCCATGCCGAATAATTCAAGCCGCAGCTCCTT
131 AACAACAACAAAAATCATCAATCAAAGTCCTCCTCCATGCCGAATAATTCAAGCCGCAGCTCCTT
7605 GTTCTTGGAGGC
196 GTTCTTGGAGGC
*
7617 TAAGGAAATTGGTCTTGGGCCAAAATCCTTCCTCTTTTTTCCTCTAGTCGACGTTAACCCTCCTT
1 TAAGGAAATTGGTCTTGGGCCAAAATCCTTCCTCTTTTTTCCTCAAGTCGACGTTAACCCTCCTT
* *
7682 GGTACCATACTAAACCGAAAATTTCAGCAACTTTTCAAGCTCCAATGGCTTCCAAAGATCAAGGT
66 GGTACCATACTAAACCAAAAATTTCAACAACTTTTCAAGCTCCAATGGCTTCCAAAGATCAAGGT
7747 AACAACAACAAAAATCATCAATCAAAGTCCTCCTCCATGCCGAATAATTCAAGCCGCAGCTCCTT
131 AACAACAACAAAAATCATCAATCAAAGTCCTCCTCCATGCCGAATAATTCAAGCCGCAGCTCCTT
7812 GTTCTTGGAGGC
196 GTTCTTGGAGGC
7824 T
1 T
7825 TCAAAATCTT
Statistics
Matches: 203, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
207 203 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (207 bp):
TAAGGAAATTGGTCTTGGGCCAAAATCCTTCCTCTTTTTTCCTCAAGTCGACGTTAACCCTCCTT
GGTACCATACTAAACCAAAAATTTCAACAACTTTTCAAGCTCCAATGGCTTCCAAAGATCAAGGT
AACAACAACAAAAATCATCAATCAAAGTCCTCCTCCATGCCGAATAATTCAAGCCGCAGCTCCTT
GTTCTTGGAGGC
Found at i:15836 original size:19 final size:19
Alignment explanation
Indices: 15812--15851 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
15802 TGAAAGATCT
15812 ATAAAGAGATAGATAAGGC
1 ATAAAGAGATAGATAAGGC
15831 ATAAAGAGATAGATAAGGC
1 ATAAAGAGATAGATAAGGC
15850 AT
1 AT
15852 GGTCTTTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.05, G:0.25, T:0.17
Consensus pattern (19 bp):
ATAAAGAGATAGATAAGGC
Found at i:16975 original size:45 final size:45
Alignment explanation
Indices: 16920--17045 Score: 234
Period size: 45 Copynumber: 2.8 Consensus size: 45
16910 CTAAATTCTA
*
16920 CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTTTATTC
1 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTTTATTC
*
16965 TTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTTTATTC
1 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTTTATTC
17010 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
1 CTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
17046 GTTAATTGTT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.37
Consensus pattern (45 bp):
CTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTTTATTC
Found at i:17759 original size:42 final size:44
Alignment explanation
Indices: 17709--17799 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 44
17699 AATGCATTAC
*
17709 CTAA-ATTCTACT-T-CATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
17750 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
17795 CTAAT
1 CTAAT
17800 GTTAATTGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.18
44 1 0.02
45 32 0.71
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:18574 original size:22 final size:23
Alignment explanation
Indices: 18549--18594 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
18539 TAATATCCAC
18549 ACACAATTAAT-ATATAAT-TAAA
1 ACACAATTAATCATA-AATATAAA
*
18571 ACACACTTAATCATAAATATAAA
1 ACACAATTAATCATAAATATAAA
18594 A
1 A
18595 ATACTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (23 bp):
ACACAATTAATCATAAATATAAA
Found at i:20072 original size:2 final size:2
Alignment explanation
Indices: 20067--20112 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
20057 CCTAAATTAG
* *
20067 TA TA TA TA TA -A TA TA TA GTA TA TA TA TA TA TG TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
20109 TA TA
1 TA TA
20113 CATACTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (2 bp):
TA
Found at i:20087 original size:18 final size:18
Alignment explanation
Indices: 20064--20112 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
20054 AGCCCTAAAT
20064 TAGTATATATATAATATA
1 TAGTATATATATAATATA
*
20082 TAGTATATATAT-ATATG
1 TAGTATATATATAATATA
20099 TATGTATATATATA
1 TA-GTATATATATA
20113 CATACTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 22 0.79
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (18 bp):
TAGTATATATATAATATA
Found at i:29025 original size:29 final size:29
Alignment explanation
Indices: 28980--29035 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
28970 TTTTTCTGAT
*
28980 TTTGTTTAAGTGCGGGTTGTGCACTTGTG
1 TTTGTTCAAGTGCGGGTTGTGCACTTGTG
*
29009 TTTGTTCAAGTGTGGGTTGTGCACTTG
1 TTTGTTCAAGTGCGGGTTGTGCACTTG
29036 GGATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.11, C:0.11, G:0.34, T:0.45
Consensus pattern (29 bp):
TTTGTTCAAGTGCGGGTTGTGCACTTGTG
Found at i:39545 original size:21 final size:21
Alignment explanation
Indices: 39519--39574 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
39509 TGTTCGGCAT
39519 CTGGGTGCTCAGGCTTTCTAG
1 CTGGGTGCTCAGGCTTTCTAG
39540 CTGGGTGCTCAGGCTTTCTAG
1 CTGGGTGCTCAGGCTTTCTAG
*
39561 CTGGGTGTTCAGGC
1 CTGGGTGCTCAGGC
39575 AAAGTGCCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.09, C:0.23, G:0.36, T:0.32
Consensus pattern (21 bp):
CTGGGTGCTCAGGCTTTCTAG
Found at i:42501 original size:76 final size:76
Alignment explanation
Indices: 42352--42501 Score: 194
Period size: 76 Copynumber: 2.0 Consensus size: 76
42342 GCTGTCCCCA
* * * * *
42352 ACTCTACCTGGGTGCCCACATGGTTGTTCTGAACACCCATGTGGTTTGCTTGAGGACCCAGGTGG
1 ACTCTACCTAGGTGCCCACATGGTTGTTCTGAACACCCATGTAGTTTGCCTGAGCACCCAGGTAG
*
42417 GCTGTGTCACG
66 GCTATGTCACG
* * *
42428 ACTCTAGCTAGGTGCCCACATGGTT-TGTCTGAAGACCCATGTAGTTTGCCTGATCACCCAGGTA
1 ACTCTACCTAGGTGCCCACATGGTTGT-TCTGAACACCCATGTAGTTTGCCTGAGCACCCAGGTA
*
42492 GGTTATGTCA
65 GGCTATGTCA
42502 TAGCTCATTA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
75 1 0.02
76 62 0.98
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (76 bp):
ACTCTACCTAGGTGCCCACATGGTTGTTCTGAACACCCATGTAGTTTGCCTGAGCACCCAGGTAG
GCTATGTCACG
Found at i:46891 original size:2 final size:2
Alignment explanation
Indices: 46884--46992 Score: 59
Period size: 2 Copynumber: 56.0 Consensus size: 2
46874 CAAATATTTT
* *
46884 TA TA TA TA T- TA TA TA T- TA TA AA TA TT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
46924 T- TA TA -A TT TA TA AA TA TA TCA GA -A AA CA TA AA TCA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA T-A TA TA TA
*
46965 TA TA TA TA TA AA TA CTA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
46993 ATTACTTTAA
Statistics
Matches: 81, Mismatches: 17, Indels: 18
0.70 0.15 0.16
Matches are distributed among these distances:
1 6 0.07
2 70 0.86
3 5 0.06
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:46906 original size:28 final size:25
Alignment explanation
Indices: 46864--46974 Score: 91
Period size: 26 Copynumber: 4.2 Consensus size: 25
46854 TAGGATTTTA
46864 ATATATTATACAAATATTTTTATATATATT
1 ATATATTAT--AAATA--TTTATATATA-T
46894 ATATATTATAAATATTTATATATAT
1 ATATATTATAAATATTTATATATAT
*
46919 ATATATTAT-AAT-TTATAAATATAT
1 ATATATTATAAATATT-TATATATAT
* * **
46943 CAGAAAACATAAATCATTTATATATAT
1 -ATATATTATAAAT-ATTTATATATAT
46970 ATATA
1 ATATA
46975 AATACTATTA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
23 2 0.03
24 11 0.16
25 15 0.22
26 16 0.24
27 8 0.12
28 7 0.10
30 9 0.13
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.47
Consensus pattern (25 bp):
ATATATTATAAATATTTATATATAT
Found at i:46908 original size:18 final size:18
Alignment explanation
Indices: 46887--46993 Score: 73
Period size: 18 Copynumber: 6.0 Consensus size: 18
46877 ATATTTTTAT
46887 ATATATTATATATTATAA
1 ATATATTATATATTATAA
46905 ATAT-TTATATA-TAT--
1 ATATATTATATATTATAA
46919 ATATATTATA-ATTTATAA
1 ATATATTATATA-TTATAA
* * * **
46937 ATATATCAGAAAACATAA
1 ATATATTATATATTATAA
*
46955 ATCATTTATATATATATATAA
1 AT-ATAT-TATATAT-TATAA
46976 ATACTATTATATA-TATAA
1 ATA-TATTATATATTATAA
46994 TTACTTTAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
14 5 0.07
15 5 0.07
16 6 0.09
17 7 0.10
18 23 0.34
19 4 0.06
20 10 0.15
21 8 0.12
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (18 bp):
ATATATTATATATTATAA
Found at i:46988 original size:16 final size:15
Alignment explanation
Indices: 46967--47010 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
46957 CATTTATATA
46967 TATATATAAATACTAT
1 TATATATAAATACT-T
46983 TATATATATAATTACTT
1 TATATATA-AA-TACTT
47000 TA-ATATAAATA
1 TATATATAAATA
47011 GCAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.08
15 2 0.08
16 13 0.50
17 5 0.19
18 4 0.15
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATATAAATACTT
Found at i:46998 original size:18 final size:17
Alignment explanation
Indices: 46965--47006 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
46955 ATCATTTATA
46965 TATATATATAAATACTAT
1 TATATATATAAATACT-T
*
46983 TATATATATAATTACTT
1 TATATATATAAATACTT
47000 TA-ATATA
1 TATATATA
47007 AATAGCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.22
17 3 0.13
18 15 0.65
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATATAAATACTT
Found at i:48926 original size:14 final size:14
Alignment explanation
Indices: 48879--48926 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
48869 TAGTATATTT
48879 AGTGCATATGTGCA
1 AGTGCATATGTGCA
* * *
48893 AGTGAATAGGT-TA
1 AGTGCATATGTGCA
48906 A-TGCATATGTGCA
1 AGTGCATATGTGCA
48919 AGTGCATA
1 AGTGCATA
48927 GGAGGTGAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 7 0.27
13 4 0.15
14 15 0.58
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.29
Consensus pattern (14 bp):
AGTGCATATGTGCA
Found at i:60343 original size:20 final size:21
Alignment explanation
Indices: 60320--60368 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
60310 GTTGGCCAGG
60320 TATATATATGT-GTGTATATA
1 TATATATATGTAGTGTATATA
* * *
60340 TATAT-TTTTTATTGTATATA
1 TATATATATGTAGTGTATATA
60360 TATATATAT
1 TATATATAT
60369 ATATATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.13
20 18 0.78
21 2 0.09
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (21 bp):
TATATATATGTAGTGTATATA
Found at i:68017 original size:42 final size:42
Alignment explanation
Indices: 67958--68040 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
67948 TTTTTTAGAA
* *
67958 CCTTTAGCGTTGCGAATACCATACCATATCGTGAGTACCATT
1 CCTTTAGCGTTGCGAATACCATACCACATCGCGAGTACCATT
*
68000 CCTTTAGTGTTGCGAATACCATACCACATCGCGAGTACCAT
1 CCTTTAGCGTTGCGAATACCATACCACATCGCGAGTACCAT
68041 ATGCCATCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.29
Consensus pattern (42 bp):
CCTTTAGCGTTGCGAATACCATACCACATCGCGAGTACCATT
Done.