Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019203.1 Corchorus olitorius cultivar O-4 contig19236, 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: 98209
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5870 original size:11 final size:11
Alignment explanation
Indices: 5827--5864 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5817 TTCCTATATA
*
5827 AAATAAATTAT
1 AAATTAATTAT
5838 CAAA-TAATTAT
1 -AAATTAATTAT
5849 AAATTAATTAT
1 AAATTAATTAT
5860 AAATT
1 AAATT
5865 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:10849 original size:2 final size:2
Alignment explanation
Indices: 10842--10879 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
10832 AATTTTCTCA
* *
10842 AT AT AT AT AT AT AT AT AT AG AT AT AT AT CT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10880 GTTCATGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38069 original size:66 final size:64
Alignment explanation
Indices: 37964--38149 Score: 186
Period size: 66 Copynumber: 2.9 Consensus size: 64
37954 GGCTTATATG
* * *
37964 TAATTTGCGGTCCA-CGAGACTTGC-AAAGATTGATGGTGAAATTGATGCAATGTCCCTTAT-GA
1 TAATTTGCGGTCCATTGAGACTTGCAAAAGTTTGGT-GTGAAATTGATGCAATGTCCCTT-TCGA
38026 A
64 A
* *
38027 TAATTATTTGCGGTCCATTGAGACTTGCAAAAG-TTGGTGTGAAATCGATACAATGTCCCTTTCG
1 T-A--ATTTGCGGTCCATTGAGACTTGCAAAAGTTTGGTGTGAAATTGATGCAATGTCCCTTTCG
38091 AA
63 AA
* * * *
38093 TAA-TTGCAGTCTATTGAGACTTGCAAAGGTTTATGGT-TGGAATTGATGCAATGTCCC
1 TAATTTGCGGTCCATTGAGACTTGCAAAAG-TT-TGGTGTGAAATTGATGCAATGTCCC
38150 GAAAAATTTG
Statistics
Matches: 104, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
62 23 0.22
63 2 0.02
64 19 0.18
65 6 0.06
66 37 0.36
67 13 0.12
68 4 0.04
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (64 bp):
TAATTTGCGGTCCATTGAGACTTGCAAAAGTTTGGTGTGAAATTGATGCAATGTCCCTTTCGAA
Found at i:38218 original size:105 final size:105
Alignment explanation
Indices: 38090--38285 Score: 322
Period size: 105 Copynumber: 1.9 Consensus size: 105
38080 TGTCCCTTTC
* * *
38090 GAATAATTGCAGTCTATTGAGACTTGCAAAGGTTTATGGTTGGAATTGATGCAATGTCCCGAAAA
1 GAATAATTGCAGTCCACTAAGACTTGCAAAGGTTTATGGTTGGAATTGATGCAATGTCCCGAAAA
**
38155 ATTTGCAGTCCTTTG-GACTTGCAAATTGATGTCCCGTAT
66 ATTTGCAGTCCACTGAGACTTGCAAATTGATGTCCCGTAT
*
38194 GAATAATTTGCAGTCCACTAAGACTTGCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAAA
1 GAATAA-TTGCAGTCCACTAAGACTTGCAAAGGTTTATGGTTGGAATTGATGCAATGTCCCGAAA
38259 AATTTGCAGTCCACTGAGACTTGCAAA
65 AATTTGCAGTCCACTGAGACTTGCAAA
38286 GGTTTATTGT
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
104 6 0.07
105 68 0.81
106 10 0.12
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (105 bp):
GAATAATTGCAGTCCACTAAGACTTGCAAAGGTTTATGGTTGGAATTGATGCAATGTCCCGAAAA
ATTTGCAGTCCACTGAGACTTGCAAATTGATGTCCCGTAT
Found at i:38263 original size:61 final size:61
Alignment explanation
Indices: 38198--38331 Score: 259
Period size: 61 Copynumber: 2.2 Consensus size: 61
38188 CCGTATGAAT
38198 AATTTGCAGTCCACTAAGACTTGCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAAA
1 AATTTGCAGTCCACTAAGACTTGCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAAA
*
38259 AATTTGCAGTCCACTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAAA
1 AATTTGCAGTCCACTAAGACTTGCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAAA
38320 AATTTGCAGTCC
1 AATTTGCAGTCC
38332 TTTGGACTTG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 72 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (61 bp):
AATTTGCAGTCCACTAAGACTTGCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAAA
Found at i:38282 original size:166 final size:166
Alignment explanation
Indices: 38096--38450 Score: 624
Period size: 166 Copynumber: 2.1 Consensus size: 166
38086 TTTCGAATAA
*
38096 TTGCAGTCTATTGAGACTTGCAAAGGTTTATGGTTGGAATTGATGCAATGTCCCGAAAAATTTGC
1 TTGCAGTCCATTGAGACTTGCAAAGGTTTATGGTTGGAATTGATGCAATGTCCCGAAAAATTTGC
38161 AGTCCTTTGGACTTGCAAA-TTGATGTCCCGTATGAATAATTTGCAGTCCACTAAGACTTGCAAA
66 AGTCCTTTGGACTTGCAAACTT-ATGTCCCGTATGAATAATTTGCAGTCCACTAAGACTTGCAAA
38225 GGTTTATTGTTGGAATTGATGCAATGTCCCGAAAAAT
130 GGTTTATTGTTGGAATTGATGCAATGTCCCGAAAAAT
* *
38262 TTGCAGTCCACTGAGACTTGCAAAGGTTTATTGTTGGAATTGATGCAATGTCCCGAAAAATTTGC
1 TTGCAGTCCATTGAGACTTGCAAAGGTTTATGGTTGGAATTGATGCAATGTCCCGAAAAATTTGC
* *
38327 AGTCCTTTGGACTTGCAAACTTATGTCTCGTATGAATAATTTGCAGTCCACTGAGACTTGCAAAG
66 AGTCCTTTGGACTTGCAAACTTATGTCCCGTATGAATAATTTGCAGTCCACTAAGACTTGCAAAG
*
38392 GTTTATTGTTGGAATTGATGCAATGTCCCGAATAAT
131 GTTTATTGTTGGAATTGATGCAATGTCCCGAAAAAT
*
38428 TTGCAGTCCTTTG-GACTTGCAAA
1 TTGCAGTCCATTGAGACTTGCAAA
38451 CTTATGTCTC
Statistics
Matches: 180, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
165 10 0.06
166 168 0.93
167 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (166 bp):
TTGCAGTCCATTGAGACTTGCAAAGGTTTATGGTTGGAATTGATGCAATGTCCCGAAAAATTTGC
AGTCCTTTGGACTTGCAAACTTATGTCCCGTATGAATAATTTGCAGTCCACTAAGACTTGCAAAG
GTTTATTGTTGGAATTGATGCAATGTCCCGAAAAAT
Found at i:38327 original size:105 final size:104
Alignment explanation
Indices: 38231--38627 Score: 468
Period size: 105 Copynumber: 3.8 Consensus size: 104
38221 CAAAGGTTTA
38231 TTGTTGGAATTGATGCAATGTCCCG-A-AA-AATTTGCAGTCCACTGAGACTTGCAAAGGTTTAT
1 TTGTTGGAATTGATGCAATGTCCCGTAGAATAATTTGCAGTCCACTGAGACTTGCAAAGGTTTAT
38293 TGTTGGAATTGATGCAATGTCCCGAAAAATTTGCAG-TC
66 TGTTGGAATTGATGCAATGTCCCGAAAAATTTGCAGTTC
* * ** * *
38331 CT-TTGGACTTGCAAACTTATGTCTCGTATGAATAATTTGCAGTCCACTGAGACTTGCAAAGGTT
1 TTGTTGGAATTG-ATGC-AATGTCCCGTA-GAATAATTTGCAGTCCACTGAGACTTGCAAAGGTT
*
38395 TATTGTTGGAATTGATGCAATGTCCCGAATAATTTGCAG-TC
63 TATTGTTGGAATTGATGCAATGTCCCGAAAAATTTGCAGTTC
* * ** * *
38436 CT-TTGGACTTGCAAACTTATGTCTCGTATGAATAATTTGCAGTCCACTGAGACTTGCAAAGGTT
1 TTGTTGGAATTG-ATGC-AATGTCCCGTA-GAATAATTTGCAGTCCACTGAGACTTGCAAAGGTT
*
38500 TATTGTTGGAATTGATGCAATGTCCCGAATAATTTGCAGTCCTC
63 TATTGTTGGAATTGATGCAATGTCCCGAAAAATTTGCAGT--TC
* *
38544 TGGATTTGCAAATTGATGCAATGTCCCGTATGAATAATTTGCAGTCCACTGAGACTTGCAAA-GT
1 TTG--TTG-GAATTGATGCAATGTCCCGTA-GAATAATTTGCAGTCCACTGAGACTTGCAAAGGT
* *
38608 TTAATGTTGAAATTGATGCA
62 TTATTGTTGGAATTGATGCA
38628 TGGTCCCTTA
Statistics
Matches: 267, Mismatches: 17, Indels: 17
0.89 0.06 0.06
Matches are distributed among these distances:
99 8 0.03
100 3 0.01
101 7 0.03
102 1 0.00
104 2 0.01
105 174 0.65
108 2 0.01
109 20 0.07
110 41 0.15
111 5 0.02
112 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (104 bp):
TTGTTGGAATTGATGCAATGTCCCGTAGAATAATTTGCAGTCCACTGAGACTTGCAAAGGTTTAT
TGTTGGAATTGATGCAATGTCCCGAAAAATTTGCAGTTC
Found at i:38560 original size:45 final size:47
Alignment explanation
Indices: 38509--38605 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 47
38499 TTATTGTTGG
* *
38509 AATTGATGCAATGTCCC-GAATAATTTGCAGTCCTCTG-GATTTGCA
1 AATTGATGCAATGTCCCTGAATAATTTGCAGTCCACTGAGACTTGCA
38554 AATTGATGCAATGTCCCGTATGAATAATTTGCAGTCCACTGAGACTTGCA
1 AATTGATGCAATGTCCC---TGAATAATTTGCAGTCCACTGAGACTTGCA
38604 AA
1 AA
38606 GTTTAATGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
45 17 0.38
49 19 0.42
50 9 0.20
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (47 bp):
AATTGATGCAATGTCCCTGAATAATTTGCAGTCCACTGAGACTTGCA
Found at i:39619 original size:61 final size:63
Alignment explanation
Indices: 39521--39652 Score: 180
Period size: 61 Copynumber: 2.1 Consensus size: 63
39511 ACTTGCAAAC
* * *
39521 TGATGCAATGTCCCGTATGAATGATTTGCAGTCCACTGAGACTTGCAAAGGTTTATTGTTGGAAT
1 TGATGCAATGTCCCGTA-GAATGATTTGCAGTCCACTGACACTTGCAAA-GTTTAATGTTGAAAT
*
39586 TGATGCAATGTCCCG-A-ACT-ATTTGCAGTCCACTGACACTTGCAAAGTTTAATGTTGAAAT
1 TGATGCAATGTCCCGTAGAATGATTTGCAGTCCACTGACACTTGCAAAGTTTAATGTTGAAAT
*
39646 TAATGCA
1 TGATGCA
39653 TGGTCCCTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
60 19 0.31
61 25 0.40
62 2 0.03
64 1 0.02
65 15 0.24
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (63 bp):
TGATGCAATGTCCCGTAGAATGATTTGCAGTCCACTGACACTTGCAAAGTTTAATGTTGAAAT
Found at i:44010 original size:67 final size:67
Alignment explanation
Indices: 43902--44067 Score: 305
Period size: 67 Copynumber: 2.5 Consensus size: 67
43892 GGCTTAAGAA
43902 TAATTTGCTGCCCACTGGGACTTGCAAAGGTTAACGGTGAAATTGATGCAATGTCCCATACGGAT
1 TAATTTGCTGCCCACTGGGACTTGCAAAGGTTAACGGTGAAATTGATGCAATGTCCCATACGGAT
43967 AT
66 AT
43969 TAATTTGCTGCCCACTGGGACTTGCAAAGGTTAACGGTGAAATTGATGCAATGTCCCATACGGAT
1 TAATTTGCTGCCCACTGGGACTTGCAAAGGTTAACGGTGAAATTGATGCAATGTCCCATACGGAT
44034 AT
66 AT
* * *
44036 TAATTTGCGGTCAACTGGGACTTGCAAAGGTT
1 TAATTTGCTGCCCACTGGGACTTGCAAAGGTT
44068 GTTGATGAAA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 96 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (67 bp):
TAATTTGCTGCCCACTGGGACTTGCAAAGGTTAACGGTGAAATTGATGCAATGTCCCATACGGAT
AT
Found at i:45860 original size:37 final size:37
Alignment explanation
Indices: 45817--45964 Score: 278
Period size: 37 Copynumber: 4.0 Consensus size: 37
45807 TTCCTCAATC
45817 ATTCATGCAAGTGCTTTATCTCAAAACTGGTAGTTGT
1 ATTCATGCAAGTGCTTTATCTCAAAACTGGTAGTTGT
45854 ATTCATGCAAGTGCTTTATCTCAAAACTGGTAGTTGT
1 ATTCATGCAAGTGCTTTATCTCAAAACTGGTAGTTGT
*
45891 ATTCATGCAAGTGCTTTATCTCAAAACTGGTACTTGT
1 ATTCATGCAAGTGCTTTATCTCAAAACTGGTAGTTGT
*
45928 ATTTATGCAAGTGCTTTATCTCAAAACTGGTAGTTGT
1 ATTCATGCAAGTGCTTTATCTCAAAACTGGTAGTTGT
45965 CTGAATGTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 108 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (37 bp):
ATTCATGCAAGTGCTTTATCTCAAAACTGGTAGTTGT
Found at i:58684 original size:14 final size:14
Alignment explanation
Indices: 58665--58692 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58655 CCTCGCCCCC
58665 TCCCAAAAATGACT
1 TCCCAAAAATGACT
58679 TCCCAAAAATGACT
1 TCCCAAAAATGACT
58693 CTTGTTATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (14 bp):
TCCCAAAAATGACT
Found at i:79663 original size:13 final size:13
Alignment explanation
Indices: 79645--79669 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
79635 TTCTCCTTTC
79645 TCTTTTCTTATTT
1 TCTTTTCTTATTT
79658 TCTTTTCTTATT
1 TCTTTTCTTATT
79670 AGTAAAAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (13 bp):
TCTTTTCTTATTT
Found at i:83236 original size:15 final size:15
Alignment explanation
Indices: 83216--83246 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
83206 AACGGTCGAT
83216 ATAACTGCTACAAGG
1 ATAACTGCTACAAGG
*
83231 ATAACTTCTACAAGG
1 ATAACTGCTACAAGG
83246 A
1 A
83247 ATTTTAAACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (15 bp):
ATAACTGCTACAAGG
Found at i:89068 original size:21 final size:21
Alignment explanation
Indices: 89042--89090 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
89032 TGTTATGCCA
89042 TGCTATCAGCCAACTAGAACT
1 TGCTATCAGCCAACTAGAACT
89063 TGCTATCAGCCAACTAGAACT
1 TGCTATCAGCCAACTAGAACT
89084 TGCTATC
1 TGCTATC
89091 GACTAGATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.27
Consensus pattern (21 bp):
TGCTATCAGCCAACTAGAACT
Found at i:96612 original size:120 final size:121
Alignment explanation
Indices: 96442--96681 Score: 437
Period size: 120 Copynumber: 2.0 Consensus size: 121
96432 GCCCCCTTCA
* * *
96442 CCACTCCAATTCTTCTGATTACCATCATGAAAATAAATGATGCTTGATTTTCTGTTTAAGAGTCT
1 CCACTCCAATTCTTCTGATTACCACCATGAAAATAAATGATGCTTGATTTTCTGGTTAAGAATCT
96507 TTGTTATTCTCATGTAAGGTGACTTTGTTCGATACATTCTATGAATTATAAAGCAT
66 TTGTTATTCTCATGTAAGGTGACTTTGTTCGATACATTCTATGAATTATAAAGCAT
96563 CCACTCCAA-TCTTCTGATTACCACCATGAAAATAAATGATGCTTGATTTTCTGGTTAAGAATCT
1 CCACTCCAATTCTTCTGATTACCACCATGAAAATAAATGATGCTTGATTTTCTGGTTAAGAATCT
*
96627 TTGTTATTCTCATGTATGGTGACTTTGTTCGATACATTCTATGAATTATAAAGCA
66 TTGTTATTCTCATGTAAGGTGACTTTGTTCGATACATTCTATGAATTATAAAGCA
96682 AATTTCTCAT
Statistics
Matches: 115, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
120 106 0.92
121 9 0.08
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (121 bp):
CCACTCCAATTCTTCTGATTACCACCATGAAAATAAATGATGCTTGATTTTCTGGTTAAGAATCT
TTGTTATTCTCATGTAAGGTGACTTTGTTCGATACATTCTATGAATTATAAAGCAT
Done.