Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022910.1 Corchorus olitorius cultivar O-4 contig22943, 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: 25725
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:5488 original size:28 final size:28
Alignment explanation
Indices: 5457--5511 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
5447 ATGTTATAAG
5457 ATTCCAAATCCTTAATATCACCACTCGT
1 ATTCCAAATCCTTAATATCACCACTCGT
5485 ATTCCAAATCCTTAATATCACCACTCG
1 ATTCCAAATCCTTAATATCACCACTCG
5512 AAATGAGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.31
Consensus pattern (28 bp):
ATTCCAAATCCTTAATATCACCACTCGT
Found at i:6431 original size:20 final size:20
Alignment explanation
Indices: 6390--6430 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
6380 TTACCATATA
* *
6390 TATATAATATATTATTATTT
1 TATATAATATACTAGTATTT
6410 TATATAATAATACTAGTATTT
1 TATATAAT-ATACTAGTATTT
6431 ACTTGAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TATATAATATACTAGTATTT
Found at i:7236 original size:12 final size:12
Alignment explanation
Indices: 7221--7246 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7211 TAATGATAAT
7221 AAAGTATGAGAG
1 AAAGTATGAGAG
7233 AAAGTATGAGAG
1 AAAGTATGAGAG
7245 AA
1 AA
7247 TGATTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.31, T:0.15
Consensus pattern (12 bp):
AAAGTATGAGAG
Found at i:11894 original size:10 final size:10
Alignment explanation
Indices: 11856--11894 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
11846 AGTGGGATGG
*
11856 TTTTTTGGTT
1 TTTTTTTGTT
11866 TTTTTTTGTT
1 TTTTTTTGTT
*
11876 TTGTTTTGTT
1 TTTTTTTGTT
11886 TTTTTTTGT
1 TTTTTTTGT
11895 CGCTCGACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:12792 original size:66 final size:66
Alignment explanation
Indices: 12593--12906 Score: 341
Period size: 66 Copynumber: 4.8 Consensus size: 66
12583 GTTCCGCTGG
* * * * *
12593 GGAGACTACA-GGGGGCCAACCAC-TGAGGTCTTAC-GACACACGATCTGATTGAACGTCCCGCC
1 GGAGACTGCAGGGGGGCCAACCACTTGGGGTCTTACAG-CGCACCACCTGATTGAACGTCCCGCC
*
12655 GG
65 GA
* * ** * * * *
12657 GGAGACTGCAGGGGGGGCCAACCACTGGGGGTCTTACGGTACACGACTTGATTTAACGTCCTGCC
1 GGAGACTGCA-GGGGGGCCAACCACTTGGGGTCTTACAGCGCACCACCTGATTGAACGTCCCGCC
12722 GA
65 GA
* * * * * **
12724 GGAAATTGCAGGGGGGGACAACCA-TTGGGGTCTTACAGCGCACCACCAGATTGAACGTTCCGTT
1 GGAGACTGCA-GGGGGGCCAACCACTTGGGGTCTTACAGCGCACCACCTGATTGAACGTCCCGCC
12788 GA
65 GA
*
12790 GGAGACTGCAGGGGGGCCAACCACTT-GGGTCTTACGGCGCACCACCTGATTGAACGTCCCGCCG
1 GGAGACTGCAGGGGGGCCAACCACTTGGGGTCTTACAGCGCACCACCTGATTGAACGTCCCGCCG
*
12854 G
66 A
* *
12855 GGAGACTGCAGGGGGGCCAACCACTAGGGGTCTTACTGCGCACCACCTGATT
1 GGAGACTGCAGGGGGGCCAACCACTTGGGGTCTTACAGCGCACCACCTGATT
12907 CCATCGAGGA
Statistics
Matches: 209, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
64 9 0.04
65 70 0.33
66 77 0.37
67 52 0.25
68 1 0.00
ACGTcount: A:0.22, C:0.28, G:0.32, T:0.18
Consensus pattern (66 bp):
GGAGACTGCAGGGGGGCCAACCACTTGGGGTCTTACAGCGCACCACCTGATTGAACGTCCCGCCG
A
Found at i:12885 original size:131 final size:130
Alignment explanation
Indices: 12572--12906 Score: 370
Period size: 131 Copynumber: 2.5 Consensus size: 130
12562 GGATCGTCAT
* * * * * *
12572 CCTGACTTAACGTTCCGCTGGGGAGACTACA-GGGGGCCAACCACTGAGGTCTTACGACACACGA
1 CCTGA-TTAACGTCCCGCCGGGGAGACTGCAGGGGGGCCAACCACTGGGGTCTTACG-CGCACCA
* * *
12636 TCTGATTGAACGTCCCGCCGGGGAGACTGCAGGGGGGGCCAACCACTGGGGGTCTTACGGTACAC
64 CCTGATTGAACGTCCCGCCGAGGAGACTGCAGGGGGGGCCAACCACTGGGGGTCTTACGGCACAC
*
12701 GA
129 CA
* * * * * * *
12703 CTTGATTTAACGTCCTGCCGAGGAAATTGCAGGGGGGGACAACCATTGGGGTCTTACAGCGCACC
1 CCTGA-TTAACGTCCCGCCGGGGAGACTGCA-GGGGGGCCAACCACTGGGGTCTTAC-GCGCACC
* * ** * *
12768 ACCAGATTGAACGTTCCGTTGAGGAGACTGCA-GGGGGGCCAACCACT-TGGGTCTTACGGCGCA
63 ACCTGATTGAACGTCCCGCCGAGGAGACTGCAGGGGGGGCCAACCACTGGGGGTCTTACGGCACA
12831 CCA
128 CCA
12834 CCTGATTGAACGTCCCGCCGGGGAGACTGCAGGGGGGCCAACCACTAGGGGTCTTACTGCGCACC
1 CCTGATT-AACGTCCCGCCGGGGAGACTGCAGGGGGGCCAACCACT-GGGGTCTTAC-GCGCACC
12899 ACCTGATT
63 ACCTGATT
12907 CCATCGAGGA
Statistics
Matches: 166, Mismatches: 33, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
130 15 0.09
131 84 0.51
132 15 0.09
133 51 0.31
134 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.32, T:0.18
Consensus pattern (130 bp):
CCTGATTAACGTCCCGCCGGGGAGACTGCAGGGGGGCCAACCACTGGGGTCTTACGCGCACCACC
TGATTGAACGTCCCGCCGAGGAGACTGCAGGGGGGGCCAACCACTGGGGGTCTTACGGCACACCA
Found at i:12961 original size:37 final size:37
Alignment explanation
Indices: 12911--13129 Score: 153
Period size: 37 Copynumber: 5.8 Consensus size: 37
12901 CTGATTCCAT
* * *
12911 CGAGGATGCCTCTGGGGGACTTATAGTGCTCGGGGGC
1 CGAGGATGCCTCTGGGGGACTTACAGCGCTCAGGGGC
*
12948 CGAGGATGCCTCTGGGGGACTTACAGCGCTCAGGGGT
1 CGAGGATGCCTCTGGGGGACTTACAGCGCTCAGGGGC
* * * *
12985 CGTGGCTGCCTCT-GGGGACTTAC-G-GCGCA-CGGC
1 CGAGGATGCCTCTGGGGGACTTACAGCGCTCAGGGGC
* * *
13018 C-ATCGCGATTGCCTCTCGGGGACTTACAGCGCGCGACGCATGTTGC
1 CGA--G-GA-TGCCTCTGGGGGACTTACAGCGCTC-A-G---G-GGC
*
13064 CGAGGGATGCCTCT-GGGGACTTACAGCGCTCGGGGGC
1 CGA-GGATGCCTCTGGGGGACTTACAGCGCTCAGGGGC
* * * *
13101 CGTGGCTGTCTCTGGGGGACTTACGGCGC
1 CGAGGATGCCTCTGGGGGACTTACAGCGC
13130 ACGACCGTCG
Statistics
Matches: 145, Mismatches: 21, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
33 3 0.02
34 5 0.03
35 2 0.01
36 25 0.17
37 72 0.50
38 2 0.01
39 4 0.03
40 1 0.01
41 1 0.01
43 16 0.11
44 7 0.05
45 2 0.01
46 4 0.03
47 1 0.01
ACGTcount: A:0.13, C:0.28, G:0.39, T:0.20
Consensus pattern (37 bp):
CGAGGATGCCTCTGGGGGACTTACAGCGCTCAGGGGC
Found at i:13157 original size:117 final size:117
Alignment explanation
Indices: 12946--13251 Score: 438
Period size: 117 Copynumber: 2.6 Consensus size: 117
12936 GTGCTCGGGG
*
12946 GCCGA-GGATGCCTCTGGGGGACTTACAGCGCTCAGGGGTCGTGGCTGCCTCT-GGGGACTTACG
1 GCCGAGGGATGCCTCT-GGGGACTTACAGCGCTCAGGGGCCGTGGCTGCCTCTGGGGGACTTACG
* * **
13009 GCGCACGGCCATCGCGATTGCCTCTCGGGGACTTACAGCGCGCGACGCATGTT
65 GCGCACGACCATCGCGACTGCCTCTCGGGGACTTACAGCGCAAGACGCATGTT
* *
13062 GCCGAGGGATGCCTCTGGGGACTTACAGCGCTCGGGGGCCGTGGCTGTCTCTGGGGGACTTACGG
1 GCCGAGGGATGCCTCTGGGGACTTACAGCGCTCAGGGGCCGTGGCTGCCTCTGGGGGACTTACGG
* * * *
13127 CGCACGACCGTCGTGGCTGCCTC-CGAGGGACTTACGGCGCAAGACGCATGTT
66 CGCACGACCATCGCGACTGCCTCTCG-GGGACTTACAGCGCAAGACGCATGTT
* * * *
13179 ACTGAGGGATGCCTCTGGGGATTTACAGCGCTCAGGGGCCGTGGCTGCCTCTGGGGTACTTACGG
1 GCCGAGGGATGCCTCTGGGGACTTACAGCGCTCAGGGGCCGTGGCTGCCTCTGGGGGACTTACGG
13244 CGCACGAC
66 CGCACGAC
13252 TTGGCTTCGT
Statistics
Matches: 170, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
116 40 0.24
117 130 0.76
ACGTcount: A:0.14, C:0.29, G:0.37, T:0.20
Consensus pattern (117 bp):
GCCGAGGGATGCCTCTGGGGACTTACAGCGCTCAGGGGCCGTGGCTGCCTCTGGGGGACTTACGG
CGCACGACCATCGCGACTGCCTCTCGGGGACTTACAGCGCAAGACGCATGTT
Found at i:13675 original size:56 final size:55
Alignment explanation
Indices: 13583--13742 Score: 173
Period size: 56 Copynumber: 2.8 Consensus size: 55
13573 AGTTAGGGCG
* *
13583 TTGGTGCGCGCTACTTCTCTTAGAGTTCTG-CAACATGGGAAGTGCCGCGTGA-GATGT
1 TTGG-GCGCGCTACTTCT-TTAGAATTCTGTC-ACATGGGAAGTGCCGCGTGATG-CGT
* *
13640 TTGGGCGCGCTAATTCTTTCAGAATTCTGTCACATGGGGAA-TGCCGTGTGATGCGT
1 TTGGGCGCGCTACTTCTTT-AGAATTCTGTCACAT-GGGAAGTGCCGCGTGATGCGT
* * *
13696 TTGGACACGCTACTTCTTTAAGAATTCTGTCACATGGGGAGTGCCGC
1 TTGGGCGCGCTACTTCTTT-AGAATTCTGTCACATGGGAAGTGCCGC
13743 AGAGTTCTGC
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
55 6 0.07
56 71 0.81
57 11 0.12
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (55 bp):
TTGGGCGCGCTACTTCTTTAGAATTCTGTCACATGGGAAGTGCCGCGTGATGCGT
Found at i:14230 original size:100 final size:100
Alignment explanation
Indices: 14105--14395 Score: 408
Period size: 100 Copynumber: 2.9 Consensus size: 100
14095 GCGCATGCCA
* * *
14105 GTCTTACAACCCGTCATGGGGTCTTACGGTCGAGAAAGATGGCACTCGGCCTGATTGCCCCCCAG
1 GTCTTACAGCCCGTCAT-GGGTCTTACGGACGAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAG
* *
14170 TGGGGGAATTATTGCAGAGAATGA-GGCGTCCGTCG
65 TGGGGGAATTATTGCAGAGAATGATAGCGTCCGCCG
*
14205 GTCTTACAGCCCGTCATGGGATCTTACGGACGAGAAAGATGGCGCTCGGCCTGATTGCCTCCCAG
1 GTCTTACAGCCCGTCATGGG-TCTTACGGACGAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAG
* * * *
14270 TGGGGGGATTATTGTAGAGAATGATAGTGTCTGCCG
65 TGGGGGAATTATTGCAGAGAATGATAGCGTCCGCCG
* *
14306 GTCTTAC-GACCCGTCATGAGGTCTTAC-GACTGAGAAAGATGGTGCTCAGCCTGATTGCCCCCC
1 GTCTTACAG-CCCGTCATG-GGTCTTACGGAC-GAGAAAGATGGCGCTCGGCCTGATTGCCCCCC
14369 AGTGGGGGAATTATTGCAGAGAATGAT
63 AGTGGGGGAATTATTGCAGAGAATGAT
14396 CCAAGGGAAG
Statistics
Matches: 171, Mismatches: 15, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
99 3 0.02
100 83 0.49
101 83 0.49
102 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.31, T:0.24
Consensus pattern (100 bp):
GTCTTACAGCCCGTCATGGGTCTTACGGACGAGAAAGATGGCGCTCGGCCTGATTGCCCCCCAGT
GGGGGAATTATTGCAGAGAATGATAGCGTCCGCCG
Found at i:14346 original size:101 final size:99
Alignment explanation
Indices: 14100--14395 Score: 391
Period size: 101 Copynumber: 2.9 Consensus size: 99
14090 TGAGGGCGCA
* * *
14100 TGCCAGTCTTACAACCCGTCATGGGGTCTTACG-GTCGAGAAAGATGGCACTCGGCCTGATTGCC
1 TGCCGGTCTTAC-ACCCGTCAT-GGGTCTTACGACT-GAGAAAGATGGCGCTCGGCCTGATTGCC
*
14164 CCCCAGTGGGGGAATTATTGCAGAGAATGA-GGCGTC
63 CCCCAGTGGGGGAATTATTGCAGAGAATGATAGCGTC
* *
14200 CGTCGGTCTTACAGCCCGTCATGGGATCTTACGGAC-GAGAAAGATGGCGCTCGGCCTGATTGCC
1 TGCCGGTCTTACA-CCCGTCATGGG-TCTTAC-GACTGAGAAAGATGGCGCTCGGCCTGATTGCC
* * * *
14264 TCCCAGTGGGGGGATTATTGTAGAGAATGATAGTGTC
63 CCCCAGTGGGGGAATTATTGCAGAGAATGATAGCGTC
* *
14301 TGCCGGTCTTACGACCCGTCATGAGGTCTTACGACTGAGAAAGATGGTGCTCAGCCTGATTGCCC
1 TGCCGGTCTTAC-ACCCGTCATG-GGTCTTACGACTGAGAAAGATGGCGCTCGGCCTGATTGCCC
14366 CCCAGTGGGGGAATTATTGCAGAGAATGAT
64 CCCAGTGGGGGAATTATTGCAGAGAATGAT
14396 CCAAGGGAAG
Statistics
Matches: 171, Mismatches: 17, Indels: 15
0.84 0.08 0.07
Matches are distributed among these distances:
99 4 0.02
100 80 0.47
101 84 0.49
102 3 0.02
ACGTcount: A:0.22, C:0.23, G:0.31, T:0.24
Consensus pattern (99 bp):
TGCCGGTCTTACACCCGTCATGGGTCTTACGACTGAGAAAGATGGCGCTCGGCCTGATTGCCCCC
CAGTGGGGGAATTATTGCAGAGAATGATAGCGTC
Found at i:22432 original size:21 final size:21
Alignment explanation
Indices: 22406--22449 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
22396 CAAAAATACC
22406 ATGCAACTTACGGTGAACAAA
1 ATGCAACTTACGGTGAACAAA
*
22427 ATGCAACTTACGGTGAACGAA
1 ATGCAACTTACGGTGAACAAA
22448 AT
1 AT
22450 AGAGACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (21 bp):
ATGCAACTTACGGTGAACAAA
Found at i:25007 original size:28 final size:29
Alignment explanation
Indices: 24975--25051 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
24965 AGGGTCATCT
* *
24975 AGGGGCATTTCGATCATTTTCG-AAATTC
1 AGGGGCATTTTGGTCATTTTCGCAAATTC
* *
25003 AGGGGCATTTTGGTCATTTTTGCATATTC
1 AGGGGCATTTTGGTCATTTTCGCAAATTC
*
25032 AGGGGTATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
25052 AAGTTCACAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 19 0.44
29 24 0.56
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.43
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTCGCAAATTC
Done.