Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013861.1 Corchorus olitorius cultivar O-4 contig13894, 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: 55546
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Found at i:1910 original size:33 final size:33
Alignment explanation
Indices: 1868--1933 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1858 GCTAAAAAAA
* *
1868 GCCTGGTCGCG-ACAGGATCGTGACCTGGCCATG
1 GCCTGGTCGCGCACAGG-TCGCGACCGGGCCATG
*
1901 GCCTGGTCGCGCGCAGGTCGCGACCGGGCCATG
1 GCCTGGTCGCGCACAGGTCGCGACCGGGCCATG
1934 ATCAGGTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.12, C:0.33, G:0.39, T:0.15
Consensus pattern (33 bp):
GCCTGGTCGCGCACAGGTCGCGACCGGGCCATG
Found at i:5129 original size:13 final size:12
Alignment explanation
Indices: 5106--5143 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
5096 TGTCAGTTTA
5106 AACCAAGATAAT
1 AACCAAGATAAT
*
5118 ATACCAATATAA-
1 A-ACCAAGATAAT
5130 AACCAAGATAAT
1 AACCAAGATAAT
5142 AA
1 AA
5144 ACGAAAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 9 0.41
12 4 0.18
13 9 0.41
ACGTcount: A:0.61, C:0.16, G:0.05, T:0.18
Consensus pattern (12 bp):
AACCAAGATAAT
Found at i:5145 original size:13 final size:13
Alignment explanation
Indices: 5104--5145 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
5094 TTTGTCAGTT
5104 TAAACCAAGATAA
1 TAAACCAAGATAA
* *
5117 TATACCAATAT-A
1 TAAACCAAGATAA
5129 -AAACCAAGATAA
1 TAAACCAAGATAA
5141 TAAAC
1 TAAAC
5146 GAAAATACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
11 8 0.35
12 2 0.09
13 13 0.57
ACGTcount: A:0.60, C:0.17, G:0.05, T:0.19
Consensus pattern (13 bp):
TAAACCAAGATAA
Found at i:5532 original size:28 final size:27
Alignment explanation
Indices: 5473--5543 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
5463 CTACCAATTC
* * *
5473 TAGGGTAAAATGGTAATTTCCTCATTA
1 TAGGGTAAAATAGTAATTTCATCATCA
*
5500 TAGGGGTAAAATAGTAATTTTATCAATCA
1 TA-GGGTAAAATAGTAATTTCATC-ATCA
*
5529 -AGGGTAATATAGTAA
1 TAGGGTAAAATAGTAA
5544 ATTTGTCCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 15 0.41
28 19 0.51
29 3 0.08
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (27 bp):
TAGGGTAAAATAGTAATTTCATCATCA
Found at i:5541 original size:27 final size:27
Alignment explanation
Indices: 5503--5561 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
5493 CTCATTATAG
*
5503 GGGTAAAATAGTAATTTTATCAATCAA
1 GGGTAAAATAGTAAATTTATCAATCAA
* * * *
5530 GGGTAATATAGTAAATTTGTCCATCAT
1 GGGTAAAATAGTAAATTTATCAATCAA
5557 GGGTA
1 GGGTA
5562 TTTTGGTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.34
Consensus pattern (27 bp):
GGGTAAAATAGTAAATTTATCAATCAA
Found at i:8860 original size:15 final size:16
Alignment explanation
Indices: 8842--8876 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
8832 ATATCATCAT
*
8842 AATATAT-CTTTCAAA
1 AATATATCCTTTAAAA
8857 AATATATCCTTTAAAA
1 AATATATCCTTTAAAA
8873 AATA
1 AATA
8877 CATTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATATCCTTTAAAA
Found at i:8873 original size:16 final size:15
Alignment explanation
Indices: 8842--8886 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
8832 ATATCATCAT
*
8842 AATATATCTTTCAAA
1 AATATATCTTTAAAA
8857 AATATATCCTTTAAAA
1 AATATAT-CTTTAAAA
* *
8873 AATACATTTTTAAA
1 AATATATCTTTAAA
8887 TATTCTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATATCTTTAAAA
Found at i:9854 original size:3 final size:3
Alignment explanation
Indices: 9841--9869 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
9831 TGATATATAT
9841 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9870 CTTATTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:30026 original size:75 final size:76
Alignment explanation
Indices: 29908--30050 Score: 261
Period size: 75 Copynumber: 1.9 Consensus size: 76
29898 GAACTCACCC
* *
29908 ATGTAACATTGACCAAAAAAGGGCCTGCATGGGGCTAGGCTTTCATCTGAATAAAATGCTTGAAC
1 ATGTAACATTGACCAAAAAAGGGCCTGCATGGGGCTAGACTTTCATCTGAACAAAATGCTTGAAC
29973 CCACCCATGTA
66 CCACCCATGTA
29984 ATGTAACATTGACC-AAAAAGGGCCTGCATGGGGCTAGACTTTCATCTGAACAAAATGCTTGAAC
1 ATGTAACATTGACCAAAAAAGGGCCTGCATGGGGCTAGACTTTCATCTGAACAAAATGCTTGAAC
30048 CCA
66 CCA
30051 ACCGATCTAA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
75 51 0.78
76 14 0.22
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (76 bp):
ATGTAACATTGACCAAAAAAGGGCCTGCATGGGGCTAGACTTTCATCTGAACAAAATGCTTGAAC
CCACCCATGTA
Found at i:31730 original size:84 final size:83
Alignment explanation
Indices: 31624--31791 Score: 250
Period size: 83 Copynumber: 2.0 Consensus size: 83
31614 AAATATATTT
*
31624 TAAAAAATATAATATATATCTAAGTTATGTAATTAAAATAGTAAAAATGGTAAAAGTAAAATAGT
1 TAAAAAATATAATATATATCTAAGTTATGTAATTAAAATAGT-AAAATGGTAAAAATAAAATAGT
*
31689 TATAAAGAGATTAGATTTAA
65 TAAAAAGA-ATTAGATTTAA
* * *
31709 TAAAAAATTCTAATA-A-ATCTAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGT
1 TAAAAAA-TATAATATATATCTAAGTTATGTAATTAAAATAGTAAAATGGTAAAAATAAAATAGT
31772 TAAAAAGAATTAGATTTAA
65 TAAAAAGAATTAGATTTAA
31791 T
1 T
31792 TAAATAAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
82 12 0.16
83 28 0.36
84 23 0.30
85 8 0.10
86 6 0.08
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (83 bp):
TAAAAAATATAATATATATCTAAGTTATGTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTT
AAAAAGAATTAGATTTAA
Found at i:32149 original size:22 final size:22
Alignment explanation
Indices: 32124--32165 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
32114 CCTTTGATTT
*
32124 TTCTTGGATCATTCGGGTTAAC
1 TTCTAGGATCATTCGGGTTAAC
* *
32146 TTCTAGGGTCATTTGGGTTA
1 TTCTAGGATCATTCGGGTTA
32166 TGGGTTTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (22 bp):
TTCTAGGATCATTCGGGTTAAC
Found at i:41057 original size:1 final size:1
Alignment explanation
Indices: 41053--41111 Score: 64
Period size: 1 Copynumber: 59.0 Consensus size: 1
41043 GATCTAAGGG
* * * * * *
41053 TTTTTGTTTTTTGTTTTTTTTTGTTTTTTTGTTTTTTTTTGTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
41112 ACGCGTGCAG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (1 bp):
T
Found at i:41073 original size:17 final size:17
Alignment explanation
Indices: 41053--41109 Score: 89
Period size: 17 Copynumber: 3.3 Consensus size: 17
41043 GATCTAAGGG
41053 TTTTTGTTTTTTGTTTT
1 TTTTTGTTTTTTGTTTT
41070 TTTTTGTTTTTTTGTTTT
1 TTTTTG-TTTTTTGTTTT
41088 TTTTTGTTTTGTT-TTTT
1 TTTTTGTTTT-TTGTTTT
41105 TTTTT
1 TTTTT
41110 TTACGCGTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 19 0.50
18 19 0.50
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (17 bp):
TTTTTGTTTTTTGTTTT
Found at i:41074 original size:10 final size:10
Alignment explanation
Indices: 41059--41111 Score: 76
Period size: 10 Copynumber: 5.5 Consensus size: 10
41049 AGGGTTTTTG
41059 TTTTTTGTTT
1 TTTTTTGTTT
41069 TTTTTTG--T
1 TTTTTTGTTT
41077 TTTTTTGTTT
1 TTTTTTGTTT
41087 TTTTTTGTTT
1 TTTTTTGTTT
41097 TGTTTTT-TTT
1 T-TTTTTGTTT
41107 TTTTT
1 TTTTT
41112 ACGCGTGCAG
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.20
9 4 0.10
10 23 0.57
11 5 0.12
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:41074 original size:18 final size:17
Alignment explanation
Indices: 41053--41110 Score: 89
Period size: 18 Copynumber: 3.3 Consensus size: 17
41043 GATCTAAGGG
*
41053 TTTTTGTTTTTTGTTTT
1 TTTTTGTTTTTTTTTTT
41070 TTTTTGTTTTTTTGTTTT
1 TTTTTGTTTTTTT-TTTT
41088 TTTTTGTTTTGTTTTTTT
1 TTTTTGTTTT-TTTTTTT
41106 TTTTT
1 TTTTT
41111 TACGCGTGCA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
17 12 0.32
18 23 0.61
19 3 0.08
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (17 bp):
TTTTTGTTTTTTTTTTT
Found at i:44887 original size:4 final size:4
Alignment explanation
Indices: 44880--44925 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
44870 CATATCTTCC
44880 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
44926 TTTTTATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:46956 original size:18 final size:21
Alignment explanation
Indices: 46933--46974 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
46923 AAATGAAAAC
46933 ATTCCTC-T-GGATAGCTT-T
1 ATTCCTCTTCGGATAGCTTAT
46951 ATTCCTCTTCGGATAGCTTAT
1 ATTCCTCTTCGGATAGCTTAT
46972 ATT
1 ATT
46975 TATTGGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
20 9 0.43
21 4 0.19
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.45
Consensus pattern (21 bp):
ATTCCTCTTCGGATAGCTTAT
Found at i:50743 original size:126 final size:126
Alignment explanation
Indices: 50518--50768 Score: 475
Period size: 126 Copynumber: 2.0 Consensus size: 126
50508 ATGGAAAAAG
* *
50518 TGGGTTTATGTCCAGCATTTCTGATATTTATTCTTGTGTTCAGCAAGCTTCATTCTTCTTTCTCA
1 TGGGTTTATGTCCAGCATTTCTGATATTTATTCTTGTGTTCAGCAAGCTTCATTCCTCTCTCTCA
50583 TTAGCTGATGCACTAACCTTGCAACACTTTGCTTTCATGTTTGTTCTGTTTAAGGGTTAAA
66 TTAGCTGATGCACTAACCTTGCAACACTTTGCTTTCATGTTTGTTCTGTTTAAGGGTTAAA
50644 TGGGTTTATGTCCAGCATTTCTGATATTTATTCTTGTGTTCAGCAAGCTTCATTCCTCTCTCTCA
1 TGGGTTTATGTCCAGCATTTCTGATATTTATTCTTGTGTTCAGCAAGCTTCATTCCTCTCTCTCA
*
50709 TTAGTTGATGCACTAACCTTGCAACACTTTGCTTTCATGTTTGTTCTGTTTAAGGGTTAA
66 TTAGCTGATGCACTAACCTTGCAACACTTTGCTTTCATGTTTGTTCTGTTTAAGGGTTAA
50769 GGATCATACA
Statistics
Matches: 122, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 122 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.44
Consensus pattern (126 bp):
TGGGTTTATGTCCAGCATTTCTGATATTTATTCTTGTGTTCAGCAAGCTTCATTCCTCTCTCTCA
TTAGCTGATGCACTAACCTTGCAACACTTTGCTTTCATGTTTGTTCTGTTTAAGGGTTAAA
Done.