Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011053.1 Corchorus capsularis cultivar CVL-1 contig11074, 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: 99971
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:31 original size:16 final size:16
Alignment explanation
Indices: 6--144 Score: 83
Period size: 15 Copynumber: 8.8 Consensus size: 16
1 TTTTT
* *
6 ATATAATATATTTAAA
1 ATATATTATATATAAA
22 ATATATTATATAT--A
1 ATATATTATATATAAA
* **
36 TTATATTATATAT-GT
1 ATATATTATATATAAA
* *
51 TTTTATTATATAT-AA
1 ATATATTATATATAAA
* * * *
66 ATAAATAAAATTTAAA
1 ATATATTATATATAAA
82 ATATATT-TATATAAA
1 ATATATTATATATAAA
*
97 ATATATTTTATAT-AA
1 ATATATTATATATAAA
*
112 ATATATTTAATATATATTAT
1 ATATA-TT-ATATATA--AA
132 ATATATTATATAT
1 ATATATTATATAT
145 GTTTTTATTA
Statistics
Matches: 96, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
14 13 0.14
15 39 0.41
16 25 0.26
17 5 0.05
18 6 0.06
19 2 0.02
20 6 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (16 bp):
ATATATTATATATAAA
Found at i:79 original size:24 final size:24
Alignment explanation
Indices: 54--177 Score: 74
Period size: 24 Copynumber: 5.2 Consensus size: 24
44 TATATGTTTT
54 TATTATATATAAATAAATAAAAT-
1 TATTATATATAAATAAATAAAATA
* * ** *
77 T-TAAAATATATTTATATAAAATA
1 TATTATATATAAATAAATAAAATA
* * *
100 TATTTTATATAAATATATTTAATATA
1 TATTATATATAAATA-A-ATAAAATA
* * *** *
126 TATTATATAT-ATTATATATGTTTT
1 TATTATATATAAATAAATA-AAATA
150 TATTATATATAAATAAATAAAATA
1 TATTATATATAAATAAATAAAATA
174 TATT
1 TATT
178 TTAAATATAT
Statistics
Matches: 69, Mismatches: 26, Indels: 11
0.65 0.25 0.10
Matches are distributed among these distances:
22 16 0.23
23 4 0.06
24 25 0.36
25 9 0.13
26 15 0.22
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (24 bp):
TATTATATATAAATAAATAAAATA
Found at i:160 original size:2 final size:2
Alignment explanation
Indices: 5--144 Score: 54
Period size: 2 Copynumber: 76.5 Consensus size: 2
1 TTTT
* *
5 TA TA TA -A TA TA TT TA -A AA TA TA T- TA TA TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
42 TA TA TA TG TT TT TA T- TA TA TA TA AA TA AA TA -A AA TT TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
81 AA TA TA TT TA TA TA -A AA TA TA T- TT TA TA TA AA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
121 -A TA TA TA T- TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
145 GTTTTTATTA
Statistics
Matches: 103, Mismatches: 22, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
1 13 0.13
2 90 0.87
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:389 original size:22 final size:22
Alignment explanation
Indices: 364--416 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
354 TGCATAAGGT
364 GGTTATCAAAATTTCA-AATGGA
1 GGTTATCAAAATTTCATAAT-GA
*
386 GGTTAATAAAAATTTCATAATGA
1 GGTT-ATCAAAATTTCATAATGA
*
409 AGTTATCA
1 GGTTATCA
417 CTATTTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 7 0.27
23 16 0.62
24 3 0.12
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAATGA
Found at i:13612 original size:31 final size:31
Alignment explanation
Indices: 13543--13642 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 31
13533 TCCTTTTGTG
* * * **
13543 CATGTGGCATGCCACGTGCCATTTTTTGAAA
1 CATGTGGTATGCCACGTGTCACTTTTTGGTA
13574 CATGTGGTATGCCACGTGTCACTTTTTGGTA
1 CATGTGGTATGCCACGTGTCACTTTTTGGTA
* * ** * *
13605 CACGTGGTGTGAGATGTGTCACTTTTTTGTA
1 CATGTGGTATGCCACGTGTCACTTTTTGGTA
13636 CATGTGG
1 CATGTGG
13643 CATGACTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (31 bp):
CATGTGGTATGCCACGTGTCACTTTTTGGTA
Found at i:13682 original size:31 final size:31
Alignment explanation
Indices: 13647--13705 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
13637 ATGTGGCATG
* *
13647 ACTTTTTAGTATATGTGGCGTGCCACATGTC
1 ACTTTTTAGTACACGTGGCGTGCCACATGTC
*
13678 ACTTTTTGGTACACGTGGCGTGCCACAT
1 ACTTTTTAGTACACGTGGCGTGCCACAT
13706 CGGACACCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.36
Consensus pattern (31 bp):
ACTTTTTAGTACACGTGGCGTGCCACATGTC
Found at i:16511 original size:32 final size:32
Alignment explanation
Indices: 16448--16525 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
16438 GGGTTCGGGC
* **
16448 TTAAGTCAGG-TCGGGTTGAATTTGGGTCAGA
1 TTAATTCAGGTTCGGGTTGAATTTGGACCAGA
*
16479 TTAATTCAGGTTCGGGTTGGATTTGGACCAGA
1 TTAATTCAGGTTCGGGTTGAATTTGGACCAGA
16511 TTAATTC-GAGTTCGG
1 TTAATTCAG-GTTCGG
16526 TCTAGATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
31 10 0.24
32 31 0.76
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.35
Consensus pattern (32 bp):
TTAATTCAGGTTCGGGTTGAATTTGGACCAGA
Found at i:16534 original size:32 final size:32
Alignment explanation
Indices: 16448--16543 Score: 85
Period size: 32 Copynumber: 3.0 Consensus size: 32
16438 GGGTTCGGGC
* * *
16448 TTAAGTCAGG-TCGGGTT-GAATTTGGGTCAGA
1 TTAATTCAGGTTCGGGTTAG-ATTTTGGCCAGA
*
16479 TTAATTCAGGTTCGGGTTGGA-TTTGGACCAGA
1 TTAATTCAGGTTCGGGTTAGATTTTGG-CCAGA
16511 TTAATTC-GAGTTC-GGTCTAGATTTTGGCCAGA
1 TTAATTCAG-GTTCGGGT-TAGATTTTGGCCAGA
16543 T
1 T
16544 CATTTACCCC
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
31 17 0.31
32 32 0.58
33 6 0.11
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.35
Consensus pattern (32 bp):
TTAATTCAGGTTCGGGTTAGATTTTGGCCAGA
Found at i:16736 original size:16 final size:16
Alignment explanation
Indices: 16679--16736 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
16669 AATTTTCGGA
*
16679 TTCGGATTCTGGTTTT
1 TTCGGATTCGGGTTTT
* *
16695 TTCGGGTAT-GAG-TTT
1 TTCGGAT-TCGGGTTTT
16710 TTCGGATTCGGGTTTT
1 TTCGGATTCGGGTTTT
*
16726 TTCGGGTTCGG
1 TTCGGATTCGG
16737 ATTCATACGG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 1 0.03
15 11 0.33
16 20 0.61
17 1 0.03
ACGTcount: A:0.07, C:0.12, G:0.33, T:0.48
Consensus pattern (16 bp):
TTCGGATTCGGGTTTT
Found at i:18849 original size:12 final size:12
Alignment explanation
Indices: 18834--18865 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
18824 TTTGTTTTCA
18834 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
18846 AAAAAGAAAAAG
1 AAAAAAAAAAAG
18858 AAAAAAAA
1 AAAAAAAA
18866 GAAATTGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:31619 original size:3 final size:3
Alignment explanation
Indices: 31613--31665 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
31603 AGAAGAAGAA
* * *
31613 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GGT AAT GGT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
31661 AAT GA
1 GAT GA
31666 CGACGACGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:57708 original size:3 final size:3
Alignment explanation
Indices: 57700--57730 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
57690 CCCTAACAAT
*
57700 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
57731 GATTTGAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:60796 original size:71 final size:71
Alignment explanation
Indices: 60721--60856 Score: 247
Period size: 71 Copynumber: 1.9 Consensus size: 71
60711 TGGTCTTTTC
*
60721 ACACTTTTCAGG-TGACTAAAAAGCCCCTCTATGAGTTTCCCCTATTCCTTTTCCTTCTACCCTT
1 ACACTTTTC-GGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTT
60785 TGTAATT
65 TGTAATT
60792 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
60857 TTCGTAATTA
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
70 2 0.03
71 61 0.97
ACGTcount: A:0.21, C:0.32, G:0.10, T:0.38
Consensus pattern (71 bp):
ACACTTTTCGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
GTAATT
Found at i:69836 original size:74 final size:74
Alignment explanation
Indices: 69733--69997 Score: 431
Period size: 75 Copynumber: 3.5 Consensus size: 74
69723 ATAATAATGG
69733 GAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAATAATAA
1 GAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAATAATAA
69798 TAAAGTTGA
66 TAAAGTTGA
* * *
69807 GAATATTTTATAAATCTTGCCAAATTGTGGGAAATTTAGGAGATATTTGAAGAAATAAAATAATA
1 GAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT-AAATAATA
69872 ATAAAGTTGA
65 ATAAAGTTGA
* *
69882 GAATATTTTCTAAATCTTACCAAATTGTGGAAGATTTAGGAGATATTTTAAGAAATAAATAAATA
1 GAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAT-AATA
*
69947 ATAAAGAATGA
65 ATAAAG-TTGA
*
69958 GAATATTTCTCTAAATCTTGCCAGATTGTGGGAGATTTAG
1 GAATATTT-TCTAAATCTTGCCAAATTGTGGGAGATTTAG
69998 AAAATATCAA
Statistics
Matches: 175, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
74 57 0.33
75 79 0.45
76 11 0.06
77 28 0.16
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.34
Consensus pattern (74 bp):
GAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAATAATAA
TAAAGTTGA
Found at i:71608 original size:11 final size:11
Alignment explanation
Indices: 71580--71611 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
71570 ATTAATATTT
71580 TAATTTTCTTA
1 TAATTTTCTTA
71591 T-ATTTTCTTA
1 TAATTTTCTTA
71601 TAATTTTCTTA
1 TAATTTTCTTA
71612 ACAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (11 bp):
TAATTTTCTTA
Found at i:77569 original size:6 final size:6
Alignment explanation
Indices: 77558--77584 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
77548 GCTGATGATC
77558 AGGGCG AGGGCG AGGGCG AGGGCG AGG
1 AGGGCG AGGGCG AGGGCG AGGGCG AGG
77585 CGGAGGCGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.15, G:0.67, T:0.00
Consensus pattern (6 bp):
AGGGCG
Found at i:77590 original size:6 final size:6
Alignment explanation
Indices: 77581--77605 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
77571 GGGCGAGGGC
77581 GAGGCG GAGGCG GAGGCG GAGGCG G
1 GAGGCG GAGGCG GAGGCG GAGGCG G
77606 TTGCTCTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.68, T:0.00
Consensus pattern (6 bp):
GAGGCG
Found at i:77655 original size:27 final size:27
Alignment explanation
Indices: 77625--77686 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
77615 CATGAACGTG
77625 TCTGCAGGAATTCCGATGACGCATGAT
1 TCTGCAGGAATTCCGATGACGCATGAT
77652 TCTGCAGGAATTCCGATGACGCATGAT
1 TCTGCAGGAATTCCGATGACGCATGAT
77679 TCTG-AGGA
1 TCTGCAGGA
77687 TCTGTTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.11
27 31 0.89
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (27 bp):
TCTGCAGGAATTCCGATGACGCATGAT
Found at i:79886 original size:21 final size:21
Alignment explanation
Indices: 79861--79901 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
79851 TTAAACCTTA
79861 TGCCTTTAATTATAGGGAGAT
1 TGCCTTTAATTATAGGGAGAT
79882 TGCCTTTAATTATAGGGAGA
1 TGCCTTTAATTATAGGGAGA
79902 GGCTGCAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (21 bp):
TGCCTTTAATTATAGGGAGAT
Found at i:81074 original size:6 final size:6
Alignment explanation
Indices: 81063--81102 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
81053 AGCTGATGAT
* * *
81063 GAGGGC GAGGGC GAGGGC GAGGGG GAGGGG GAGGGG GAGG
1 GAGGGC GAGGGC GAGGGC GAGGGC GAGGGC GAGGGC GAGG
81103 CTGTTGCTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.17, C:0.07, G:0.75, T:0.00
Consensus pattern (6 bp):
GAGGGC
Found at i:81080 original size:12 final size:12
Alignment explanation
Indices: 81063--81102 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
81053 AGCTGATGAT
*
81063 GAGGGCGAGGGC
1 GAGGGCGAGGGG
81075 GAGGGCGAGGGG
1 GAGGGCGAGGGG
*
81087 GAGGGGGAGGGG
1 GAGGGCGAGGGG
81099 GAGG
1 GAGG
81103 CTGTTGCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.17, C:0.07, G:0.75, T:0.00
Consensus pattern (12 bp):
GAGGGCGAGGGG
Found at i:82091 original size:115 final size:118
Alignment explanation
Indices: 81881--82143 Score: 433
Period size: 115 Copynumber: 2.3 Consensus size: 118
81871 TTACAATATT
*
81881 GAATTAAAATACAAGTTTGATTAGTTGAAAGGGGTTTTAATTTTTTTTTAATGTTCCTGACTTAT
1 GAATCAAAATACAAGTTTGATTAGTTGAAAGGGGTTTTAATTTTTTTTTAATGTTCCTGACTTAT
* *
81946 TATATCTACAAGTGATTGTCTGATTGTTTGAGAGGTTAAGCAACACCCACATC
66 TATACCTACAAGTGATTGGCTGATTGTTTGAGAGGTTAAGCAACACCCACATC
* *
81999 GAATCAAAATACAAATTTGATTAGTTGGAA-GGGTTTTAA-TTTTTTTT-ATGTTCCTGACTTAT
1 GAATCAAAATACAAGTTTGATTAGTTGAAAGGGGTTTTAATTTTTTTTTAATGTTCCTGACTTAT
* *
82061 TATACCTACAAGTGATTGGCTGATTGTTTGAGAGGTTAAGCGACATCCACATC
66 TATACCTACAAGTGATTGGCTGATTGTTTGAGAGGTTAAGCAACACCCACATC
*
82114 GAGTCAAAATACAAGTTTGATTAGTTGAAA
1 GAATCAAAATACAAGTTTGATTAGTTGAAA
82144 AGATTTTGCA
Statistics
Matches: 135, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
115 91 0.67
116 8 0.06
117 9 0.07
118 27 0.20
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.38
Consensus pattern (118 bp):
GAATCAAAATACAAGTTTGATTAGTTGAAAGGGGTTTTAATTTTTTTTTAATGTTCCTGACTTAT
TATACCTACAAGTGATTGGCTGATTGTTTGAGAGGTTAAGCAACACCCACATC
Found at i:90072 original size:21 final size:21
Alignment explanation
Indices: 90030--90072 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
90020 AAATGTAAAT
*
90030 CATCAAAACAAAAGACAAAAC
1 CATCAAAACAAAAAACAAAAC
*
90051 CATC-AAACATAAAAACATAAC
1 CATCAAAACA-AAAAACAAAAC
90072 C
1 C
90073 TAAAATTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.63, C:0.26, G:0.02, T:0.09
Consensus pattern (21 bp):
CATCAAAACAAAAAACAAAAC
Found at i:93846 original size:8 final size:8
Alignment explanation
Indices: 93813--93846 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
93803 AGGTTTAGCC
*
93813 TTCTTCTC
1 TTCTTCTT
93821 TTCTTCTT
1 TTCTTCTT
*
93829 TTCTTGTT
1 TTCTTCTT
93837 TTCTTCTT
1 TTCTTCTT
93845 TT
1 TT
93847 TTGGGATCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (8 bp):
TTCTTCTT
Done.