Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014879.1 Corchorus olitorius cultivar O-4 contig14912, 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: 46209
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:111 original size:70 final size:70
Alignment explanation
Indices: 7--141 Score: 261
Period size: 70 Copynumber: 1.9 Consensus size: 70
1 TATATA
*
7 TATATATATAAACTATATGTAGAAAATGGGATTATACATACATACATTAGTCTACATATATATAT
1 TATATATATAAACTATATGTAGAAAATGGAATTATACATACATACATTAGTCTACATATATATAT
72 GTATG
66 GTATG
77 TATATATATAAACTATATGTAGAAAATGGAATTATACATACATACATTAGTCTACATATATATAT
1 TATATATATAAACTATATGTAGAAAATGGAATTATACATACATACATTAGTCTACATATATATAT
142 ATATATATGT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (70 bp):
TATATATATAAACTATATGTAGAAAATGGAATTATACATACATACATTAGTCTACATATATATAT
GTATG
Found at i:561 original size:26 final size:27
Alignment explanation
Indices: 525--582 Score: 109
Period size: 26 Copynumber: 2.2 Consensus size: 27
515 AAGCTTTTCT
525 AAAAATTGAGTATTGTATTTTCT-AAA
1 AAAAATTGAGTATTGTATTTTCTCAAA
551 AAAAATTGAGTATTGTATTTTCTCAAA
1 AAAAATTGAGTATTGTATTTTCTCAAA
578 AAAAA
1 AAAAA
583 AGAAAAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 23 0.74
27 8 0.26
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (27 bp):
AAAAATTGAGTATTGTATTTTCTCAAA
Found at i:592 original size:27 final size:26
Alignment explanation
Indices: 536--588 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
526 AAAATTGAGT
* **
536 ATTGTATTTTCTAAAAAAAATTGAGT
1 ATTGTATTTTCTAAAAAAAATAGAAA
562 ATTGTATTTTCTCAAAAAAAA-AGAAA
1 ATTGTATTTTCT-AAAAAAAATAGAAA
588 A
1 A
589 ATTGAGTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (26 bp):
ATTGTATTTTCTAAAAAAAATAGAAA
Found at i:1114 original size:20 final size:21
Alignment explanation
Indices: 1048--1150 Score: 68
Period size: 21 Copynumber: 4.7 Consensus size: 21
1038 ACTTAATAAC
*
1048 TTTTTAATTAATCTTATAACAT
1 TTTTTAA-TAATCTTATAATAT
* *
1070 TTTTTATTAATTAGCTTAGT-GTAT
1 TTTTTAATAA-T--CTTA-TAATAT
*
1094 TTTTTAGTAA-CTTATAATAT
1 TTTTTAATAATCTTATAATAT
*
1114 TTATTTAATAATTCTTATAAGA-
1 TT-TTTAATAA-TCTTATAATAT
1136 TTTTTAATTAATCTT
1 TTTTTAA-TAATCTT
1151 TTATAATTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
19 1 0.02
20 9 0.14
21 19 0.29
22 12 0.18
23 8 0.12
24 15 0.23
25 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTTTAATAATCTTATAATAT
Found at i:2321 original size:21 final size:21
Alignment explanation
Indices: 2239--2323 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
2229 ACGTTACTAA
* *
2239 ATTTATAGATAAACATATAAG-
1 ATTTTTAG-TAAACTTATAAGC
* *
2260 GTTTTAAGTAAACTATATAAGC
1 ATTTTTAGTAAACT-TATAAGC
* *
2282 TTTTTTA-CAAACTTCATAAGC
1 ATTTTTAGTAAACTT-ATAAGC
*
2303 ATTTTTAGTAATCTTATAAGC
1 ATTTTTAGTAAACTTATAAGC
2324 CTTAGTTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
20 6 0.12
21 34 0.68
22 10 0.20
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (21 bp):
ATTTTTAGTAAACTTATAAGC
Found at i:2757 original size:2 final size:2
Alignment explanation
Indices: 2750--2779 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2740 AAAATACTAG
2750 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2780 AATTATCGTC
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):
TA
Found at i:3041 original size:46 final size:46
Alignment explanation
Indices: 2974--3067 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
2964 CTCTCTCTAA
2974 GTTGCCTTACACACATTCCTTCATATAATTCCTATAAATTTGAAAG
1 GTTGCCTTACACACATTCCTTCATATAATTCCTATAAATTTGAAAG
*
3020 GTTGCCTTACATACATTCCTTCATATAATTCCTATAAATTTGAAAG
1 GTTGCCTTACACACATTCCTTCATATAATTCCTATAAATTTGAAAG
3066 GT
1 GT
3068 CCGTAATTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (46 bp):
GTTGCCTTACACACATTCCTTCATATAATTCCTATAAATTTGAAAG
Found at i:4350 original size:17 final size:17
Alignment explanation
Indices: 4328--4360 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4318 GTCACTTTAA
4328 AATAAAA-ACAAATAAAT
1 AATAAAATA-AAATAAAT
4345 AATAAAATAAAATAAA
1 AATAAAATAAAATAAA
4361 ATAAAATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
AATAAAATAAAATAAAT
Found at i:4353 original size:5 final size:5
Alignment explanation
Indices: 4325--4367 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
4315 CGGGTCACTT
4325 TAAAA TAAAA -ACAAA TAAATAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TA-AAA T-AA-AA TAAAA TAAAA TAAAA TAAAA T
4368 CTCAAAAGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 1 0.03
5 26 0.76
6 3 0.09
7 4 0.12
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:20315 original size:14 final size:15
Alignment explanation
Indices: 20281--20315 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
20271 TAATTAATTG
*
20281 AACTTTGCAGTTTCA
1 AACTTTGCAATTTCA
20296 AACTTTGCAATTTC-
1 AACTTTGCAATTTCA
20310 AACTTT
1 AACTTT
20316 CAAGAACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (15 bp):
AACTTTGCAATTTCA
Found at i:31715 original size:16 final size:16
Alignment explanation
Indices: 31696--31746 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
31686 CCCAAACCCG
31696 AATTAACCTGACCTGA
1 AATTAACCTGACCTGA
* *
31712 AATTGACCTGAACCCGA
1 AATTAACCTG-ACCTGA
*
31729 AA--AACCTGATCTGA
1 AATTAACCTGACCTGA
31743 AATT
1 AATT
31747 GATTCAAACC
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
14 6 0.22
15 5 0.19
16 9 0.33
17 7 0.26
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (16 bp):
AATTAACCTGACCTGA
Found at i:31757 original size:31 final size:31
Alignment explanation
Indices: 31687--31780 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 31
31677 CAATCCGAAC
*
31687 CCAAACCCGAATTAACCTGACCTGAAATTGA
1 CCAAACCCGAATAAACCTGACCTGAAATTGA
* *
31718 CCTGAACCCGAA-AAACCTGATCTGAAATTGA
1 CC-AAACCCGAATAAACCTGACCTGAAATTGA
* * * * * *
31749 TTCAAACCCTAATTAGCCTGACCCGAACTTGA
1 -CCAAACCCGAATAAACCTGACCTGAAATTGA
31781 AAAAACCTGA
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
31 26 0.53
32 23 0.47
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (31 bp):
CCAAACCCGAATAAACCTGACCTGAAATTGA
Found at i:31969 original size:20 final size:22
Alignment explanation
Indices: 31932--31971 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
31922 CCTTCCTTTT
*
31932 ATTTTCTTCATTTGTCTTTCAC
1 ATTTTCTTCATGTGTCTTTCAC
31954 ATTTTCTTC-TGT-TCTTTC
1 ATTTTCTTCATGTGTCTTTC
31972 TCTCTTCCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.10, C:0.23, G:0.05, T:0.62
Consensus pattern (22 bp):
ATTTTCTTCATGTGTCTTTCAC
Found at i:33460 original size:27 final size:26
Alignment explanation
Indices: 33422--33473 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
33412 ACGGTGGTTT
33422 TTTTAAAAATAA-TATAATATATATTG
1 TTTTAAAAATAACT-TAATATATATTG
* *
33448 TTTTATAATATAACTTATTATATATT
1 TTTTA-AAAATAACTTAATATATATT
33474 ATATAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 5 0.23
27 16 0.73
28 1 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTTAAAAATAACTTAATATATATTG
Found at i:33980 original size:25 final size:25
Alignment explanation
Indices: 33949--34033 Score: 79
Period size: 25 Copynumber: 3.4 Consensus size: 25
33939 GGTATGGCTG
33949 TTTGTTGTCTTGAATTAGTTGTTGT
1 TTTGTTGTCTTGAATTAGTTGTTGT
* *
33974 TTTGTTGTC-T-AA--ACTCTGAAATGT
1 TTTGTTGTCTTGAATTAGT-TG--TTGT
*
33998 TTTGGTTGTGTTGAATTAGTTGTTGT
1 TTT-GTTGTCTTGAATTAGTTGTTGT
34024 TTTGTTGTCT
1 TTTGTTGTCT
34034 GAACTCTAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 16
0.68 0.09 0.24
Matches are distributed among these distances:
21 2 0.04
22 2 0.04
23 2 0.04
24 7 0.15
25 20 0.43
26 7 0.15
27 2 0.04
28 2 0.04
29 2 0.04
ACGTcount: A:0.14, C:0.06, G:0.24, T:0.56
Consensus pattern (25 bp):
TTTGTTGTCTTGAATTAGTTGTTGT
Found at i:34020 original size:50 final size:50
Alignment explanation
Indices: 33952--34076 Score: 207
Period size: 50 Copynumber: 2.5 Consensus size: 50
33942 ATGGCTGTTT
* *
33952 GTTGTCTTGAATTAGTTGTTGTTTTGTTGTCTAAACTCTGAA-ATGTTTTG
1 GTTGTGTTGAATTAGTTGTTGTTTTGTTGTCTAAACTCT-AACATGTTATG
*
34002 GTTGTGTTGAATTAGTTGTTGTTTTGTTGTCTGAACTCTAACATGTTATG
1 GTTGTGTTGAATTAGTTGTTGTTTTGTTGTCTAAACTCTAACATGTTATG
34052 GTTGTGTTGAATTAGTTGTTGTTTT
1 GTTGTGTTGAATTAGTTGTTGTTTT
34077 AGGTAATTCT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
49 2 0.03
50 69 0.97
ACGTcount: A:0.17, C:0.06, G:0.24, T:0.53
Consensus pattern (50 bp):
GTTGTGTTGAATTAGTTGTTGTTTTGTTGTCTAAACTCTAACATGTTATG
Found at i:34755 original size:76 final size:76
Alignment explanation
Indices: 34629--34851 Score: 331
Period size: 76 Copynumber: 2.9 Consensus size: 76
34619 TCTACAGAGC
* *
34629 TCTCTTGGTAAGCGATCTGTAAGTCTAAAATATCCGCAAGTGAAAGTCCAATGGATCCGTAAATC
1 TCTCTTGATAAGCGATCTGTAAGTCTGAAATATCCGCAAGTGAAAGTCCAATGGATCCGTAAATC
* *
34694 TTCAAATGTGT
66 TCCAAATGGGT
* *
34705 TCTCTTGATATGCGATCTGTAAGT-TCGAAATATCCGCAAGTGAAAGTCCAATGGATTCGTAAAT
1 TCTCTTGATAAGCGATCTGTAAGTCT-GAAATATCCGCAAGTGAAAGTCCAATGGATCCGTAAAT
34769 CTCCAAATGGGT
65 CTCCAAATGGGT
* ** *
34781 TCTCTTGATAGGTAATCTGTAAGTCTGAAATATCCGCAAGTGAAAGTACAATGGATCCGTAAATC
1 TCTCTTGATAAGCGATCTGTAAGTCTGAAATATCCGCAAGTGAAAGTCCAATGGATCCGTAAATC
*
34846 ACCAAA
66 TCCAAA
34852 GAGGTTGTCT
Statistics
Matches: 133, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
75 1 0.01
76 131 0.98
77 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (76 bp):
TCTCTTGATAAGCGATCTGTAAGTCTGAAATATCCGCAAGTGAAAGTCCAATGGATCCGTAAATC
TCCAAATGGGT
Found at i:38853 original size:2 final size:2
Alignment explanation
Indices: 38846--38885 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
38836 TATGTACATA
*
38846 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38886 TATTTGAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:40196 original size:11 final size:11
Alignment explanation
Indices: 40182--40219 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
40172 ATTCATAACA
40182 AATTTATAATT
1 AATTTATAATT
40193 AATTTATAATT
1 AATTTATAATT
40204 -ATTTGATAATT
1 AATTT-ATAATT
*
40215 TATTT
1 AATTT
40220 TATATAGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:40384 original size:12 final size:12
Alignment explanation
Indices: 40367--40396 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40357 ACTCATAAAA
40367 TTAATAGTAGGT
1 TTAATAGTAGGT
40379 TTAATAGTAGGT
1 TTAATAGTAGGT
*
40391 ATAATA
1 TTAATA
40397 ATTATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (12 bp):
TTAATAGTAGGT
Found at i:41920 original size:45 final size:45
Alignment explanation
Indices: 41871--41977 Score: 115
Period size: 45 Copynumber: 2.4 Consensus size: 45
41861 GAGAAAGATG
* *
41871 AATCTAAGACAATTGAGAAAGTTGCCAAGGACGAGGAGAGGACCA
1 AATCTAAGACAATTGAGAAAATTGCCAAGGACGAAGAGAGGACCA
* ** * * ***
41916 AATCTGAGACAACCGAGAAAATTGCGAAGGAGGAAGAGAGGATTG
1 AATCTAAGACAATTGAGAAAATTGCCAAGGACGAAGAGAGGACCA
*
41961 AATCCAAGACAATTGAG
1 AATCTAAGACAATTGAG
41978 TCTATTCTCG
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (45 bp):
AATCTAAGACAATTGAGAAAATTGCCAAGGACGAAGAGAGGACCA
Found at i:45728 original size:66 final size:66
Alignment explanation
Indices: 45621--45817 Score: 252
Period size: 66 Copynumber: 3.0 Consensus size: 66
45611 GTAAAGATAA
* * * * *
45621 TGATAACTATAGTGTGAAAATTTGATAACCTCATTATGAAATTTTGATAACCACACTATGAAAAT
1 TGATAACCACAGTGTGAAATTTTGATAATCTCACTATGAAATTTTGATAACCACACTATGAAAAT
45686 T
66 T
* * * *
45687 TGATAACCACATTGTGAAATTTTGATAATCACACTAAGAAATTTTGATAACCACACTATGAAACT
1 TGATAACCACAGTGTGAAATTTTGATAATCTCACTATGAAATTTTGATAACCACACTATGAAAAT
45752 T
66 T
* * * * * *
45753 TGATAACCTCAGTGTGAAATTTTGAGAATCTCCCTATGGAATTTTAATAATCACACTAT-AAAAT
1 TGATAACCACAGTGTGAAATTTTGATAATCTCACTATGAAATTTTGATAACCACACTATGAAAAT
45817 T
66 T
45818 GGTAACTGCA
Statistics
Matches: 112, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
65 5 0.04
66 107 0.96
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (66 bp):
TGATAACCACAGTGTGAAATTTTGATAATCTCACTATGAAATTTTGATAACCACACTATGAAAAT
T
Found at i:45770 original size:22 final size:22
Alignment explanation
Indices: 45635--45889 Score: 203
Period size: 22 Copynumber: 11.6 Consensus size: 22
45625 AACTATAGTG
* * *
45635 TGAAAATTTGATAACCTCATTA
1 TGAAATTTTGATAACCACACTA
45657 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCACACTA
* * *
45679 TGAAAATTTGATAACCACATTG
1 TGAAATTTTGATAACCACACTA
*
45701 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCACACTA
*
45723 AGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCACACTA
* * * *
45745 TGAAACTTTGATAACCTCAGTG
1 TGAAATTTTGATAACCACACTA
* * * *
45767 TGAAATTTTGAGAATCTCCCTA
1 TGAAATTTTGATAACCACACTA
* * *
45789 TGGAATTTTAATAATCACACTA
1 TGAAATTTTGATAACCACACTA
* * **
45811 T-AAA-ATTGGTAACTGCACTA
1 TGAAATTTTGATAACCACACTA
* *
45831 TGAAAATATTGATAACCTC-CTCA
1 TG-AAATTTTGATAACCACACT-A
* *
45854 T-AAGATTTTGATAAGCACACCA
1 TGAA-ATTTTGATAACCACACTA
*
45876 TGAAATTTCGATAA
1 TGAAATTTTGATAA
45890 TATCCCTGTG
Statistics
Matches: 183, Mismatches: 43, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
20 11 0.06
21 4 0.02
22 154 0.84
23 14 0.08
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (22 bp):
TGAAATTTTGATAACCACACTA
Done.