Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019759.1 Corchorus olitorius cultivar O-4 contig19792, 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: 69829
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2023 original size:12 final size:13
Alignment explanation
Indices: 1989--2024 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1979 GACAGTGTAT
1989 TATATATAAACCC
1 TATATATAAACCC
2002 TATATATAAACCC
1 TATATATAAACCC
*
2015 T-TGTATAAAC
1 TATATATAAAC
2025 GTAAGCACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.33
Consensus pattern (13 bp):
TATATATAAACCC
Found at i:5740 original size:14 final size:14
Alignment explanation
Indices: 5721--5759 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
5711 AAAGGCCTTC
5721 ACCAAGCCATCACA
1 ACCAAGCCATCACA
5735 ACCAAGCCATCACA
1 ACCAAGCCATCACA
*
5749 ACCGAGCCATC
1 ACCAAGCCATC
5760 CAAGCTCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.38, C:0.44, G:0.10, T:0.08
Consensus pattern (14 bp):
ACCAAGCCATCACA
Found at i:5864 original size:33 final size:32
Alignment explanation
Indices: 5775--5866 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 32
5765 TCTTACAACT
* * *
5775 AATGAAGTTGCGGGCCTTCATCAAGCCGTTTC
1 AATGAAGTTACGGGCCTTCATCACGCAGTTTC
* * *
5807 AATAAAATTGACGGGCCTTCATCACGCATTTTC
1 AATGAAGTT-ACGGGCCTTCATCACGCAGTTTC
5840 AATGAAGTTCACGGGCCTTCATCACGC
1 AATGAAGTT-ACGGGCCTTCATCACGC
5867 CTTTACATGT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 7 0.14
33 43 0.86
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (32 bp):
AATGAAGTTACGGGCCTTCATCACGCAGTTTC
Found at i:13333 original size:33 final size:33
Alignment explanation
Indices: 13280--13370 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
13270 CTCTTACAAC
*
13280 CAATGAAGTT-GCGGGCCTTCATCACACCGTTT
1 CAATGAAGTTCACGGGCCTTCATCACACCGTTT
* *
13312 CAATGAAGTTCACGGGCCTTCATCACGCCTTTT
1 CAATGAAGTTCACGGGCCTTCATCACACCGTTT
* *
13345 CAATGAAATTCACGGGACTTCATCAC
1 CAATGAAGTTCACGGGCCTTCATCAC
13371 GCCTTTACAT
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 10 0.19
33 43 0.81
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (33 bp):
CAATGAAGTTCACGGGCCTTCATCACACCGTTT
Found at i:13371 original size:33 final size:33
Alignment explanation
Indices: 13291--13376 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
13281 AATGAAGTTG
* * *
13291 CGGGCCTTCATCACACCGTTTCAATGAAGTTCA
1 CGGGCCTTCATCACGCCTTTTCAATGAAATTCA
13324 CGGGCCTTCATCACGCCTTTTCAATGAAATTCA
1 CGGGCCTTCATCACGCCTTTTCAATGAAATTCA
*
13357 CGGGACTTCATCACGCCTTT
1 CGGGCCTTCATCACGCCTTT
13377 ACATGTTGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.29
Consensus pattern (33 bp):
CGGGCCTTCATCACGCCTTTTCAATGAAATTCA
Found at i:15910 original size:19 final size:18
Alignment explanation
Indices: 15886--15921 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15876 TGAAGATTTA
15886 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
15905 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
15922 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:25579 original size:19 final size:18
Alignment explanation
Indices: 25555--25590 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25545 TGAAGATTTA
25555 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
25574 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
25591 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:31393 original size:21 final size:21
Alignment explanation
Indices: 31368--31416 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
31358 ATGTGGATTA
31368 TTTGTGGATTTATCTTGAATG
1 TTTGTGGATTTATCTTGAATG
* *
31389 TTTGTGGATTTTTTTTGAATG
1 TTTGTGGATTTATCTTGAATG
*
31410 TATGTGG
1 TTTGTGG
31417 GTTTTGTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.27, T:0.55
Consensus pattern (21 bp):
TTTGTGGATTTATCTTGAATG
Found at i:32352 original size:27 final size:28
Alignment explanation
Indices: 32315--32381 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
32305 TTCCTTAAAC
32315 AACACTCATCTTTATGGC-AAAAAAAAA
1 AACACTCATCTTTATGGCAAAAAAAAAA
32342 AACACTCATCTTTATGGCAAAAAAAAAA
1 AACACTCATCTTTATGGCAAAAAAAAAA
32370 AACACTCATCTT
1 AACACTCATCTT
32382 GATTTGGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
27 18 0.46
28 21 0.54
ACGTcount: A:0.49, C:0.21, G:0.06, T:0.24
Consensus pattern (28 bp):
AACACTCATCTTTATGGCAAAAAAAAAA
Found at i:34293 original size:121 final size:125
Alignment explanation
Indices: 34035--34353 Score: 421
Period size: 122 Copynumber: 2.5 Consensus size: 125
34025 AGAATATATT
*
34035 TTAAAAATTCTAATATATCTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGAT
1 TTAAAAATTCTAATATATCTAAGTTTTTTTAATTAAAATAGTAAAATGGT----A-AAAATACAT
* *
34100 ATAAGGATATTAGATTTAATTAAATAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTATAT
61 ATAAGGATATTAGATTTAATTAAATAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAA
* *
34165 TTAAAAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAAAAGT-CATA-AA-
1 TTAAAAATTCTAATATATCTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATACATATAAG
*
34226 GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAGTTTAA
66 GATATTAGATTTAATTAAATAAAA-TAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAA
* * *
34287 TTAAAATTTTCTAATACATCTAAGTTTTTTTTTTCAATTATAATAGTAAAATGGTAAAAATGACA
1 TTAAAA-ATTCTAATATATCTAAG---TTTTTTT-AATTAAAATAGTAAAATGGTAAAAAT-ACA
34352 TA
60 TA
34354 GTTATAAGAA
Statistics
Matches: 169, Mismatches: 11, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
121 24 0.14
122 41 0.24
123 17 0.10
124 4 0.02
125 1 0.01
127 6 0.04
128 24 0.14
129 26 0.15
130 26 0.15
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.39
Consensus pattern (125 bp):
TTAAAAATTCTAATATATCTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATACATATAAG
GATATTAGATTTAATTAAATAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAA
Found at i:38843 original size:23 final size:23
Alignment explanation
Indices: 38817--38864 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
38807 TATGGTCATG
* *
38817 TGGAAAACAAGTTCATACTCTTT
1 TGGAAAACAAGCTAATACTCTTT
38840 TGGAAAACAAGCTAATACTCTTT
1 TGGAAAACAAGCTAATACTCTTT
38863 TG
1 TG
38865 TTGGTTCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (23 bp):
TGGAAAACAAGCTAATACTCTTT
Found at i:45025 original size:25 final size:26
Alignment explanation
Indices: 44991--45049 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 26
44981 CAAAGTCAAT
44991 CCAAATCAAGAGAA-CTCGACCC-AAC
1 CCAAATCAAGA-AAGCTCGACCCAAAC
45016 CCAAATCAAGAAAGCTCGACCCAAAC
1 CCAAATCAAGAAAGCTCGACCCAAAC
45042 CCAAATCA
1 CCAAATCA
45050 TGCTTCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 2 0.06
25 19 0.59
26 11 0.34
ACGTcount: A:0.46, C:0.36, G:0.10, T:0.08
Consensus pattern (26 bp):
CCAAATCAAGAAAGCTCGACCCAAAC
Found at i:45744 original size:22 final size:23
Alignment explanation
Indices: 45716--45758 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
45706 TCCTAGGAGT
45716 AGGTTTTACT-TTCCTACCAGAA
1 AGGTTTTACTATTCCTACCAGAA
45738 AGGTTTTACTATTCCTACCAG
1 AGGTTTTACTATTCCTACCAG
45759 GATTAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (23 bp):
AGGTTTTACTATTCCTACCAGAA
Found at i:54858 original size:20 final size:20
Alignment explanation
Indices: 54829--54880 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
54819 TAATAAATCG
*
54829 CATAATAATTTGTAATATAA
1 CATAAAAATTTGTAATATAA
* *
54849 CATAAAAATTAGTTATATAA
1 CATAAAAATTTGTAATATAA
*
54869 -A-AAAAAGTTGTA
1 CATAAAAATTTGTA
54881 TTGCTATCAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 8 0.31
19 1 0.04
20 17 0.65
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.35
Consensus pattern (20 bp):
CATAAAAATTTGTAATATAA
Found at i:55920 original size:2 final size:2
Alignment explanation
Indices: 55880--55905 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55870 CAATATGATC
55880 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
55906 TAGGGTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55920 original size:21 final size:21
Alignment explanation
Indices: 55894--55938 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
55884 ATATATATAT
55894 ATATAT-ATATATTAGGGTAGA
1 ATATATCA-ATATTAGGGTAGA
55915 ATATATCAATATTAGGGTAGA
1 ATATATCAATATTAGGGTAGA
55936 ATA
1 ATA
55939 CCTTGAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.36
Consensus pattern (21 bp):
ATATATCAATATTAGGGTAGA
Found at i:56007 original size:29 final size:29
Alignment explanation
Indices: 55965--56028 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
55955 TAATCATTAA
* *
55965 AATTCTGTCTACCAATATACGTGCTACAT
1 AATTCTATCTACCAATAAACGTGCTACAT
*
55994 AATTCTATCTACCAATAAACGTGTTACAT
1 AATTCTATCTACCAATAAACGTGCTACAT
56023 AATTCT
1 AATTCT
56029 TTAGTTTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (29 bp):
AATTCTATCTACCAATAAACGTGCTACAT
Found at i:58615 original size:11 final size:11
Alignment explanation
Indices: 58585--58624 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
58575 CCCTTTCCTA
58585 TATAAAATAAAT
1 TATAAAAT-AAT
**
58597 TACCAAATAAT
1 TATAAAATAAT
58608 TATAAAATAAT
1 TATAAAATAAT
58619 TATAAA
1 TATAAA
58625 TTTGTTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (11 bp):
TATAAAATAAT
Found at i:64117 original size:2 final size:2
Alignment explanation
Indices: 64112--64141 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
64102 ACACACACAC
64112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64142 GGATTAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65734 original size:75 final size:76
Alignment explanation
Indices: 65613--65790 Score: 304
Period size: 75 Copynumber: 2.4 Consensus size: 76
65603 AAAATTGAAT
*
65613 ATTGTACATGCATGGTCAAACTCCAAATGATGATGATCAAACCCCAAAGTTTGATAGTCAAACCA
1 ATTGTACATGCATGGTCAAACCCCAAATGATGATGATCAAACCCCAAAGTTTGATAGTCAAACCA
65678 C-AAAAATATC
66 CAAAAAATATC
* *
65688 ATTGTACATGCATGGTCAAACCCCAAATGATGATGGTCAAATCCCAAAGTTTGATAGTCAAACCA
1 ATTGTACATGCATGGTCAAACCCCAAATGATGATGATCAAACCCCAAAGTTTGATAGTCAAACCA
65753 CAAAAAATATC
66 CAAAAAATATC
* *
65764 ATTTTATATGCATGGTCAAACCCCAAA
1 ATTGTACATGCATGGTCAAACCCCAAA
65791 GTTCGATAGT
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
75 63 0.65
76 34 0.35
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.25
Consensus pattern (76 bp):
ATTGTACATGCATGGTCAAACCCCAAATGATGATGATCAAACCCCAAAGTTTGATAGTCAAACCA
CAAAAAATATC
Found at i:65862 original size:57 final size:56
Alignment explanation
Indices: 65724--65868 Score: 168
Period size: 57 Copynumber: 2.6 Consensus size: 56
65714 ATGATGATGG
* * *
65724 TCAAATCCCAAAGTTTGATAGTCAAACCAC-AAAAAATATCATTTTATATGCATGG
1 TCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAAATATCATTGTATATGCATGA
* * *
65779 TCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATTTTATTGTATAT-CTATGA
1 TCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAA-ATATCATTGTATATGC-ATGA
* * * *
65836 TCAAACCCCAAAATTTAATAGGCAAACCTCAAA
1 TCAAACCCCAAAGTTTGATAGTCAAACCACAAA
65869 GTTTGATATT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
55 28 0.37
56 6 0.08
57 42 0.55
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.26
Consensus pattern (56 bp):
TCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAAATATCATTGTATATGCATGA
Found at i:66940 original size:22 final size:24
Alignment explanation
Indices: 66897--66949 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
66887 ATAAATGTTG
66897 CTGATAA-TCTTCTCTTTAATC-T
1 CTGATAATTCTTCTCTTTAATCTT
66919 CTGATAATTC-TCTCATTT-ATCTT
1 CTGATAATTCTTCTC-TTTAATCTT
*
66942 ATGATAAT
1 CTGATAAT
66950 ATTCACATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (24 bp):
CTGATAATTCTTCTCTTTAATCTT
Found at i:67950 original size:2 final size:2
Alignment explanation
Indices: 67943--67971 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
67933 CATTAGGCAA
67943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
67972 GCTAAAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69258 original size:23 final size:23
Alignment explanation
Indices: 69229--69274 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
69219 TGATTGTTTA
69229 TATTTTTCTG-GTTTAAATGTGTT
1 TATTTTTCTGTGTTT-AATGTGTT
*
69252 TATTTTTCTGTGTTTGATGTGTT
1 TATTTTTCTGTGTTTAATGTGTT
69275 CTTGGTTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.13, C:0.04, G:0.20, T:0.63
Consensus pattern (23 bp):
TATTTTTCTGTGTTTAATGTGTT
Done.