Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012571.1 Corchorus olitorius cultivar O-4 contig12604, 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: 42187
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1680 original size:21 final size:21
Alignment explanation
Indices: 1656--1713 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1646 CCTTAGGCAA
*
1656 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGACCTTGAAACCTT
* *
1677 CTCCAATGATCTTGAAACTTT
1 CTCCAATGACCTTGAAACCTT
1698 CTCCAATGACCTTGAA
1 CTCCAATGACCTTGAA
1714 TCTTCTTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (21 bp):
CTCCAATGACCTTGAAACCTT
Found at i:13471 original size:70 final size:69
Alignment explanation
Indices: 13357--13496 Score: 201
Period size: 70 Copynumber: 2.0 Consensus size: 69
13347 AAAACTAACA
* * *
13357 ACTAAGGAAAAAATGGTGGGAGCCCCATTAATTACATCTCAATGCTAAAAATACATATAAAGACA
1 ACTAAGGAAAAAATGGTAGGAACACCATTAATTACATCTCAATGCTAAAAATACATATAAAGACA
13422 ATGC
66 ATGC
* * *
13426 ACTAAGGAAAAAAATGGTAGGAACATCATTAATTATATC-CAAATGCTAAAATTACATATAAAGA
1 ACTAAGG-AAAAAATGGTAGGAACACCATTAATTACATCTC-AATGCTAAAAATACATATAAAGA
13490 CAATGC
64 CAATGC
13496 A
1 A
13497 TTTCAAGCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
69 8 0.13
70 55 0.87
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (69 bp):
ACTAAGGAAAAAATGGTAGGAACACCATTAATTACATCTCAATGCTAAAAATACATATAAAGACA
ATGC
Found at i:14144 original size:29 final size:30
Alignment explanation
Indices: 14080--14148 Score: 113
Period size: 29 Copynumber: 2.3 Consensus size: 30
14070 TCTCTCAAAC
14080 ACTTAATTCCTTCTACTTGGTTCCTTTTATT
1 ACTT-ATTCCTTCTACTTGGTTCCTTTTATT
*
14111 TCTTATTCCTTCTACTTGG-TCCTTTTATT
1 ACTTATTCCTTCTACTTGGTTCCTTTTATT
14140 ACTTATTCC
1 ACTTATTCC
14149 CAACCTCTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 18 0.50
30 15 0.42
31 3 0.08
ACGTcount: A:0.14, C:0.25, G:0.06, T:0.55
Consensus pattern (30 bp):
ACTTATTCCTTCTACTTGGTTCCTTTTATT
Found at i:14219 original size:17 final size:17
Alignment explanation
Indices: 14171--14227 Score: 87
Period size: 17 Copynumber: 3.3 Consensus size: 17
14161 AGTCAGGTAC
14171 TTCCTTTCACCTTAATT
1 TTCCTTTCACCTTAATT
14188 TTCCTCTTCACCTTAATT
1 TTCCT-TTCACCTTAATT
* *
14206 TTCCTTTTACCTTAGTT
1 TTCCTTTCACCTTAATT
14223 TTCCT
1 TTCCT
14228 CTTATAGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 20 0.54
18 17 0.46
ACGTcount: A:0.14, C:0.30, G:0.02, T:0.54
Consensus pattern (17 bp):
TTCCTTTCACCTTAATT
Found at i:15323 original size:21 final size:21
Alignment explanation
Indices: 15299--15415 Score: 182
Period size: 21 Copynumber: 5.6 Consensus size: 21
15289 CTTAGGCATT
* *
15299 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
15320 TCCAATGATCTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
15341 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
15362 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
15383 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAACTTGGAACCTT-C
15404 TCCAATGAACTT
1 TCCAATGAACTT
15416 CTAGCATCTT
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 3 0.03
21 87 0.97
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (21 bp):
TCCAATGAACTTGGAACCTTC
Found at i:17331 original size:33 final size:31
Alignment explanation
Indices: 17258--17403 Score: 123
Period size: 33 Copynumber: 4.5 Consensus size: 31
17248 GCTATGATCA
** *
17258 ACCAAAACAGATTTGTTTACATCACAATTAGC
1 ACCAAAACAGATTTGTTT-CATCACAAACAAC
17290 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
17323 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
** * *
17356 ACTCAAATTAGGTTTAGTATT-ATCGCAAACAAC
1 AC-CAAAACAGATTT-GT-TTCATCACAAACAAC
*
17389 ATCTAAAACAGATTT
1 A-CCAAAACAGATTT
17404 AGAATTACTC
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
32 7 0.07
33 76 0.81
34 11 0.12
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Found at i:19889 original size:21 final size:21
Alignment explanation
Indices: 19865--19981 Score: 182
Period size: 21 Copynumber: 5.6 Consensus size: 21
19855 CTTAGGCATT
* *
19865 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
19886 TCCAATGATCTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
19907 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
19928 TCCAATGAACTTGGAACCTTC
1 TCCAATGAACTTGGAACCTTC
*
19949 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAACTTGGAACCTT-C
19970 TCCAATGAACTT
1 TCCAATGAACTT
19982 CTAGCATCTT
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 3 0.03
21 87 0.97
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (21 bp):
TCCAATGAACTTGGAACCTTC
Found at i:28455 original size:52 final size:52
Alignment explanation
Indices: 28395--29067 Score: 1051
Period size: 52 Copynumber: 13.0 Consensus size: 52
28385 TCCTTCAAAG
*
28395 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCGATTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGGTC
* * *
28447 TTTTCAAAGAGGGAAAGTTCCCATCAAGTTTTCAAAGTTTTCAATTGAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGGTC
* ** *
28499 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAACGTTCAATCTAGGT-
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGGTC
* * **
28550 TTTTCAAAGTGGGAAAGGTCCAATCAAGTTTTCAAAGTGTTCAATTTAACTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGGTC
* * *
28602 TTTTCAAAGTGGAAAAGTTCCCATCAGGTTTTCAAAGTGTTCAATTTAGCTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGGTC
* *
28654 TTTTCAAACTGGGAAAGTTCCCATCAGGTTTTCAAAGTGTTCAATTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGGTC
* * *
28706 TTTTCAAAGTGGGAAAGTTCCCATTAGGTTTTCAAAGTGTTCAATTTAAGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGGTC
* *
28758 TTTTCAAAGTGGGAAAGTTCCCATCAGGTTTTCAAAATGTTCAATTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGGTC
*
28810 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGCTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGGTC
**
28862 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAACTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGGTC
* * *
28914 TTTTCAAAGTGGGAAAGCTCCCATCAAGTTTTCAAAGCGTTCGATTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGGTC
*
28966 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTTAATTTAGGTC
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGGTC
* * *
29018 TTTTCAAAGCGGGAAAGTTCCCATCATGTTTTCAAAGCGTTCAATTTAGG
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGG
29068 GAAAGATCCC
Statistics
Matches: 570, Mismatches: 50, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
51 43 0.08
52 527 0.92
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (52 bp):
TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTGTTCAATTTAGGTC
Found at i:28657 original size:24 final size:24
Alignment explanation
Indices: 28630--28716 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
28620 TCCCATCAGG
28630 TTTTCAAAGTGTTCAATTTAGCTC
1 TTTTCAAAGTGTTCAATTTAGCTC
* *** * **
28654 TTTTCAAACTGGGAAAGTTCCCATC
1 TTTTCAAAGTGTTCAATTTAGC-TC
*
28679 AGGTTTTCAAAGTGTTCAATTTAGGTC
1 ---TTTTCAAAGTGTTCAATTTAGCTC
28706 TTTTCAAAGTG
1 TTTTCAAAGTG
28717 GGAAAGTTCC
Statistics
Matches: 44, Mismatches: 15, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
24 26 0.59
25 2 0.05
27 2 0.05
28 14 0.32
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.40
Consensus pattern (24 bp):
TTTTCAAAGTGTTCAATTTAGCTC
Found at i:28865 original size:24 final size:24
Alignment explanation
Indices: 28838--28924 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
28828 TCCCATCAAG
*
28838 TTTTCAAAGTGTTCAATTTAGCTC
1 TTTTCAAAGTGTTCAATTTAACTC
*** * **
28862 TTTTCAAAGTGGGAAAGTTCCCATC
1 TTTTCAAAGTGTTCAATTTAAC-TC
28887 AAGTTTTCAAAGTGTTCAATTTAACTC
1 ---TTTTCAAAGTGTTCAATTTAACTC
28914 TTTTCAAAGTG
1 TTTTCAAAGTG
28925 GGAAAGCTCC
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
24 27 0.57
25 2 0.04
27 2 0.04
28 16 0.34
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (24 bp):
TTTTCAAAGTGTTCAATTTAACTC
Found at i:33848 original size:21 final size:21
Alignment explanation
Indices: 33824--33873 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
33814 CTTAGGCAAT
33824 TCCAATGAGCTTGAAACCTT-C
1 TCCAATGAGCTTGAAA-CTTGC
*
33845 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGAAACTTGC
33866 TCCAATGA
1 TCCAATGA
33874 TCTCCTAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGAAACTTGC
Found at i:35687 original size:33 final size:31
Alignment explanation
Indices: 35614--35718 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 31
35604 GCTATGATCA
** *
35614 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
35646 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
* *
35679 ACCTAAAACATATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
35712 ACTCAAA
1 AC-CAAA
35719 TTACTAACAA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
32 7 0.11
33 50 0.79
34 6 0.10
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.26
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Found at i:38584 original size:19 final size:18
Alignment explanation
Indices: 38560--38595 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
38550 TGAAGATTTA
38560 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
38579 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
38596 ATAATTTCAA
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:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Done.