Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014790.1 Corchorus olitorius cultivar O-4 contig14823, 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: 31092
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:2063 original size:2 final size:2
Alignment explanation
Indices: 2056--2086 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2046 CTCAATTCGA
2056 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2087 GACGCTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2325 original size:19 final size:21
Alignment explanation
Indices: 2290--2330 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2280 TAACACAGAG
2290 AGATTATCAAAAATCAT-GGA
1 AGATTATCAAAAATCATAGGA
*
2310 AGATTA-CAAAATTCATAGGA
1 AGATTATCAAAAATCATAGGA
2330 A
1 A
2331 AGTTTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (21 bp):
AGATTATCAAAAATCATAGGA
Found at i:2427 original size:22 final size:21
Alignment explanation
Indices: 2378--2438 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
2368 CTTATGGAGT
*
2378 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTTATAGGTAA
**
2399 TTATCAAAATTTTATATGGTGG
1 TTATCAAAATTTTATA-GGTAA
* *
2421 TTATCAAAAGTTAATAGG
1 TTATCAAAATTTTATAGG
2439 ATATATAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.41
Consensus pattern (21 bp):
TTATCAAAATTTTATAGGTAA
Found at i:2808 original size:2 final size:2
Alignment explanation
Indices: 2766--2796 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2756 GGAGGGAGTA
2766 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2797 GGATTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:6944 original size:35 final size:34
Alignment explanation
Indices: 6895--7013 Score: 103
Period size: 46 Copynumber: 3.1 Consensus size: 34
6885 AGCAAATCTG
*
6895 AAGCTAAGTTTTCTCCATCAACAAAACAACAACA
1 AAGCAAAGTTTTCTCCATCAACAAAACAACAACA
6929 AAGCAAAGTTCTTCTCCATTTCTTATCCATCAACAAAGCAACAACA
1 AAGCAAAGTT-TTCTCCA--TC--A---A-C-A-AAA-CAACAACA
*
6975 AAGCAAAGTTGTTCTCCATCAACAAAGCAACAACA
1 AAGCAAAGTT-TTCTCCATCAACAAAACAACAACA
7010 AAGC
1 AAGC
7014 CTACGAAAGT
Statistics
Matches: 70, Mismatches: 3, Indels: 23
0.73 0.03 0.24
Matches are distributed among these distances:
34 9 0.13
35 19 0.27
36 2 0.03
37 3 0.04
38 1 0.01
39 2 0.03
42 2 0.03
43 1 0.01
44 3 0.04
45 3 0.04
46 25 0.36
ACGTcount: A:0.44, C:0.27, G:0.08, T:0.21
Consensus pattern (34 bp):
AAGCAAAGTTTTCTCCATCAACAAAACAACAACA
Found at i:7009 original size:46 final size:46
Alignment explanation
Indices: 6913--7013 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 46
6903 TTTTCTCCAT
* ** * * *
6913 CAACAAAACAACAACAAAGCAAAGTTCTTCTCCATTTCTTATCCAT
1 CAACAAAGCAACAACAAAGCAAAGTTCTTCTCCATAACTAAACCAA
* *
6959 CAACAAAGCAACAACAAAGCAAAGTTGTTCTCCATCAAC-AAAGCAA
1 CAACAAAGCAACAACAAAGCAAAGTTCTTCTCCAT-AACTAAACCAA
7005 CAACAAAGC
1 CAACAAAGC
7014 CTACGAAAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.47, C:0.28, G:0.08, T:0.18
Consensus pattern (46 bp):
CAACAAAGCAACAACAAAGCAAAGTTCTTCTCCATAACTAAACCAA
Found at i:7223 original size:42 final size:42
Alignment explanation
Indices: 7160--7252 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
7150 TCAAATCTAG
* *
7160 CAAATCCGACAACGAGGAATAACAAGCCTTCAGCCATTTCTCT
1 CAAATCC-ACAACGAGAAATAACAAGCCTTCAGCCATTCCTCT
**
7203 CAAATCCACAACGAGAAATAACAAGCCTTTGGCCATTCCTCT
1 CAAATCCACAACGAGAAATAACAAGCCTTCAGCCATTCCTCT
*
7245 CATATCCA
1 CAAATCCA
7253 TTTCATCGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 38 0.84
43 7 0.16
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.22
Consensus pattern (42 bp):
CAAATCCACAACGAGAAATAACAAGCCTTCAGCCATTCCTCT
Found at i:10565 original size:44 final size:45
Alignment explanation
Indices: 10466--10589 Score: 187
Period size: 44 Copynumber: 2.7 Consensus size: 45
10456 TTGAAGCAAA
*
10466 AGGTAGAGGGCGATAAAAAAATCAACCCCGCCAAGAAGCCGATGCAG
1 AGGTAGAGGGCGAT-AAATAATCAACCCCGCCAAG-AGCCGATGCAG
*
10513 AGGTAGAGGGCGATAAATAATCAACCCCGCCAAG-GTCGATGCAG
1 AGGTAGAGGGCGATAAATAATCAACCCCGCCAAGAGCCGATGCAG
**
10557 AGGTAGAGGGTAATAAATAATCAACCCCGCCAA
1 AGGTAGAGGGCGATAAATAATCAACCCCGCCAA
10590 TGTTGAAAGG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
44 40 0.55
46 19 0.26
47 14 0.19
ACGTcount: A:0.39, C:0.23, G:0.27, T:0.12
Consensus pattern (45 bp):
AGGTAGAGGGCGATAAATAATCAACCCCGCCAAGAGCCGATGCAG
Found at i:13100 original size:38 final size:35
Alignment explanation
Indices: 13023--13106 Score: 114
Period size: 35 Copynumber: 2.3 Consensus size: 35
13013 TCTCCATTTC
**
13023 TTCTCCATCAACAAAGCAACAACAAAGCAAAGTTG
1 TTCTCCATCAACAAAGCAACAACAAAGCAAAGAAG
*
13058 TTCTCCATCAACAAAGCAACAACAAAGCATACGAAAG
1 TTCTCCATCAACAAAGCAACAACAAAGCA-AAG-AAG
13095 TTTCTCCATCAA
1 -TTCTCCATCAA
13107 ATCCCAGCCG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 29 0.67
36 2 0.05
37 1 0.02
38 11 0.26
ACGTcount: A:0.44, C:0.27, G:0.10, T:0.19
Consensus pattern (35 bp):
TTCTCCATCAACAAAGCAACAACAAAGCAAAGAAG
Found at i:13295 original size:42 final size:42
Alignment explanation
Indices: 13232--13324 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
13222 TCAAATCTAG
* *
13232 CAAATCCGACAACGAGGAATAACAAGCCTTCAGCCATTTCTCT
1 CAAATCC-ACAACGAGAAATAACAAGCCTTCAGCCATTCCTCT
* **
13275 CAAATCCACAACGAGAAATAATAAGCCTTTGGCCATTCCTCT
1 CAAATCCACAACGAGAAATAACAAGCCTTCAGCCATTCCTCT
*
13317 CATATCCA
1 CAAATCCA
13325 TTTCATCGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 37 0.84
43 7 0.16
ACGTcount: A:0.35, C:0.30, G:0.12, T:0.23
Consensus pattern (42 bp):
CAAATCCACAACGAGAAATAACAAGCCTTCAGCCATTCCTCT
Found at i:14339 original size:21 final size:24
Alignment explanation
Indices: 14310--14360 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
14300 TTTTGAACTC
14310 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
14333 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
14356 ATTAT
1 ATTAT
14361 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:14355 original size:25 final size:25
Alignment explanation
Indices: 14310--14358 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
14300 TTTTGAACTC
*
14310 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
14335 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
14359 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:17182 original size:21 final size:21
Alignment explanation
Indices: 17157--17209 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
17147 CTCAGCTTCT
*
17157 CTTAGCCCAAAATTACAAACA
1 CTTAGCCCAAAATCACAAACA
*
17178 CTTAGCCCAAAATCGCAAACA
1 CTTAGCCCAAAATCACAAACA
*
17199 CTTAACCCAAA
1 CTTAGCCCAAA
17210 TTAAATACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.45, C:0.32, G:0.06, T:0.17
Consensus pattern (21 bp):
CTTAGCCCAAAATCACAAACA
Found at i:17428 original size:59 final size:59
Alignment explanation
Indices: 17362--17570 Score: 301
Period size: 59 Copynumber: 3.5 Consensus size: 59
17352 TAATTAAATG
* ** *
17362 GCCCATTATGTGGCAAGACATTGGTGATTGAGCATTATGTCTCTCACCTTGGTCATAAT
1 GCCCACTATGTGGCAAGACATTGGTGATTGAGCATTATGTCTCTCACCTTATTCATAAA
* ** *
17421 GCCCATTATGTGGCAAGATGTTGGTGATTGAGCAATATGTCTCTCACCTTATTCATAAA
1 GCCCACTATGTGGCAAGACATTGGTGATTGAGCATTATGTCTCTCACCTTATTCATAAA
* * * *
17480 GCCCACTATGTGGCAAGACATTGGTGATCGAGCATTATGTATCTCACCTTATTTACAAA
1 GCCCACTATGTGGCAAGACATTGGTGATTGAGCATTATGTCTCTCACCTTATTCATAAA
*
17539 GCCCACTATGTGGCAAGGCATTGGTGATTGAG
1 GCCCACTATGTGGCAAGACATTGGTGATTGAG
17571 AAACCCACTA
Statistics
Matches: 134, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 134 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (59 bp):
GCCCACTATGTGGCAAGACATTGGTGATTGAGCATTATGTCTCTCACCTTATTCATAAA
Found at i:18068 original size:28 final size:28
Alignment explanation
Indices: 18036--18101 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
18026 CTATGTTTTT
*
18036 GGCCTCTGCTAAAAGATTACTATTCATC
1 GGCCTCTACTAAAAGATTACTATTCATC
** *
18064 GGCCTCTACTGGAAGATTACTGTTCATC
1 GGCCTCTACTAAAAGATTACTATTCATC
18092 GGCCTCTACT
1 GGCCTCTACT
18102 GGAGTACCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (28 bp):
GGCCTCTACTAAAAGATTACTATTCATC
Found at i:18102 original size:28 final size:28
Alignment explanation
Indices: 18048--18104 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
18038 CCTCTGCTAA
18048 AAGATTACTATTCATCGGCCTCTACTGG
1 AAGATTACTATTCATCGGCCTCTACTGG
*
18076 AAGATTACTGTTCATCGGCCTCTACTGG
1 AAGATTACTATTCATCGGCCTCTACTGG
18104 A
1 A
18105 GTACCGTGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (28 bp):
AAGATTACTATTCATCGGCCTCTACTGG
Found at i:20982 original size:27 final size:28
Alignment explanation
Indices: 20951--21003 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
20941 CTCGAAACAT
*
20951 ATTC-AATACTCAAA-ACACCAAAACAAG
1 ATTCAAATA-TCAAACAAACCAAAACAAG
20978 ATTCAAATATCAAACAAACCAAAACA
1 ATTCAAATATCAAACAAACCAAAACA
21004 GAAACTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.58, C:0.25, G:0.02, T:0.15
Consensus pattern (28 bp):
ATTCAAATATCAAACAAACCAAAACAAG
Found at i:21791 original size:30 final size:30
Alignment explanation
Indices: 21757--21829 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
21747 CAAGGAGAAA
21757 TAAGGGGAAGTTATTGGGAGTTAATAAGAT
1 TAAGGGGAAGTTATTGGGAGTTAATAAGAT
21787 TAAGGGGAAGTTATTGGGAGTTAATAAGAT
1 TAAGGGGAAGTTATTGGGAGTTAATAAGAT
*
21817 TATGGGGAAGTTA
1 TAAGGGGAAGTTA
21830 AAACAAAAGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.30
Consensus pattern (30 bp):
TAAGGGGAAGTTATTGGGAGTTAATAAGAT
Found at i:22571 original size:21 final size:21
Alignment explanation
Indices: 22547--22599 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
22537 CTCAACTTCT
**
22547 CTTAGCCCAAAATTGCAAACA
1 CTTAGCCCAAAATCACAAACA
22568 CTTAGCCCAAAATCACAAACA
1 CTTAGCCCAAAATCACAAACA
*
22589 CTTAACCCAAA
1 CTTAGCCCAAA
22600 TTAAATACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.45, C:0.32, G:0.06, T:0.17
Consensus pattern (21 bp):
CTTAGCCCAAAATCACAAACA
Found at i:22822 original size:59 final size:59
Alignment explanation
Indices: 22759--22961 Score: 298
Period size: 59 Copynumber: 3.4 Consensus size: 59
22749 AATGGCTCAT
** * *
22759 TATGTGGCAAGACATTGGTGATTGAGCATTATGTCTCTCACCTTGGTCATAATGCCCAT
1 TATGTGGCAAGACATTGGTGATTGAGCATTATGTCTCTCACCTTATTCATAAAGCCCAC
** *
22818 TATGTGGCAAGATGTTGGTGATTGAGCAATATGTCTCTCACCTTATTCATAAAGCCCAC
1 TATGTGGCAAGACATTGGTGATTGAGCATTATGTCTCTCACCTTATTCATAAAGCCCAC
* * * *
22877 TATGTGGCAAGACATTGGTGATCGAGCATTATGTATCTCACCTTATTTACAAAGCCCAC
1 TATGTGGCAAGACATTGGTGATTGAGCATTATGTCTCTCACCTTATTCATAAAGCCCAC
*
22936 TATGTGGCAAGGCATTGGTGATTGAG
1 TATGTGGCAAGACATTGGTGATTGAG
22962 AAACCCACTA
Statistics
Matches: 128, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 128 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (59 bp):
TATGTGGCAAGACATTGGTGATTGAGCATTATGTCTCTCACCTTATTCATAAAGCCCAC
Found at i:23491 original size:28 final size:28
Alignment explanation
Indices: 23426--23493 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
23416 TATGTTTTTT
* *
23426 GCCTCTGTTAGAAGATTATTGTTCATCG
1 GCCTCTGCTGGAAGATTATTGTTCATCG
*
23454 GGCTCTGCTGGAAGATTATTGTTCATCG
1 GCCTCTGCTGGAAGATTATTGTTCATCG
23482 GCCTCTGCTGGA
1 GCCTCTGCTGGA
23494 GTACCGGGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (28 bp):
GCCTCTGCTGGAAGATTATTGTTCATCG
Found at i:23644 original size:21 final size:20
Alignment explanation
Indices: 23619--23660 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
23609 TTCCCTTAAA
23619 TCCATTATGTATTTATCTATT
1 TCCATTATGTATTTAT-TATT
*
23640 TCCATTATTTATTTATTATT
1 TCCATTATGTATTTATTATT
23660 T
1 T
23661 ATTAAAGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.24, C:0.12, G:0.02, T:0.62
Consensus pattern (20 bp):
TCCATTATGTATTTATTATT
Found at i:29115 original size:11 final size:11
Alignment explanation
Indices: 29072--29109 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
29062 TTCCTATATA
*
29072 AAATAAATTAT
1 AAATTAATTAT
29083 CAAA-TAATTAT
1 -AAATTAATTAT
29094 AAATTAATTAT
1 AAATTAATTAT
29105 AAATT
1 AAATT
29110 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
Done.