Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015204.1 Corchorus olitorius cultivar O-4 contig15237, 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: 29457
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:439 original size:13 final size:14
Alignment explanation
Indices: 421--459 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
411 AAAAATTCTT
421 TTTGACCCTCCAA-
1 TTTGACCCTCCAAC
*
434 TTTGACCATCCAAC
1 TTTGACCCTCCAAC
448 TTT-ACCCTCCAA
1 TTTGACCCTCCAA
460 ATAATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 20 0.87
14 3 0.13
ACGTcount: A:0.26, C:0.38, G:0.05, T:0.31
Consensus pattern (14 bp):
TTTGACCCTCCAAC
Found at i:754 original size:17 final size:17
Alignment explanation
Indices: 720--754 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
710 GAAATTGAAT
**
720 TGGTGCATATATTTAAA
1 TGGTGCATATATAGAAA
737 TGGTGCATATATAGAAA
1 TGGTGCATATATAGAAA
754 T
1 T
755 TGAATTGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (17 bp):
TGGTGCATATATAGAAA
Found at i:1516 original size:19 final size:18
Alignment explanation
Indices: 1482--1528 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
1472 TAATTAGGAG
* *
1482 TAATTTTAAGTAAAAATT
1 TAATATTAAATAAAAATT
1500 TAATATATAAATAAAAATT
1 TAATAT-TAAATAAAAATT
1519 TAATATTAAA
1 TAATATTAAA
1529 ATAATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TAATATTAAATAAAAATT
Found at i:14419 original size:18 final size:18
Alignment explanation
Indices: 14396--14442 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
14386 AAGGATCAAA
14396 TGAAGTCCTCAGGCCCA-T
1 TGAAGTCCTCAGG-CCAGT
**
14414 TGAAGTTTTCAGGCCAGT
1 TGAAGTCCTCAGGCCAGT
*
14432 TGAATTCCTCA
1 TGAAGTCCTCA
14443 AACACCAAGC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (18 bp):
TGAAGTCCTCAGGCCAGT
Found at i:17159 original size:18 final size:16
Alignment explanation
Indices: 17123--17157 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
17113 GGGACGGAAG
17123 GAGTAAAATAAAAAGA
1 GAGTAAAATAAAAAGA
17139 GAGTAAAATAAAAAGA
1 GAGTAAAATAAAAAGA
17155 GAG
1 GAG
17158 AGATCAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (16 bp):
GAGTAAAATAAAAAGA
Found at i:22578 original size:17 final size:14
Alignment explanation
Indices: 22539--22582 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 14
22529 GGTATAATTT
22539 TTATAAATTAATAC
1 TTATAAATTAATAC
22553 TTGATAAATTAATAATC
1 TT-ATAAATTAAT-A-C
22570 TCTATAAATTAAT
1 T-TATAAATTAAT
22583 TATTTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 2 0.08
15 10 0.38
16 1 0.04
17 12 0.46
18 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (14 bp):
TTATAAATTAATAC
Found at i:22666 original size:76 final size:77
Alignment explanation
Indices: 22540--22686 Score: 233
Period size: 76 Copynumber: 1.9 Consensus size: 77
22530 GTATAATTTT
* * * *
22540 TATAAATTAATACTTGATAAATTAATAATCTCTATAAATTAATTATTTTT-CATAGTCCTAATAT
1 TATAAATTAACACTCGATAAATTAATAATCTCTATAAATTAATAATTTTTCCATAGTCCCAATAT
22604 TATTAAGTTCCA
66 TATTAAGTTCCA
* *
22616 TATAAATTAACACTCGATAAATTAATAATCTCTCTAAATTAATAATTTTTCCATGGTCCCAATAT
1 TATAAATTAACACTCGATAAATTAATAATCTCTATAAATTAATAATTTTTCCATAGTCCCAATAT
22681 TATTAA
66 TATTAA
22687 TTTATAGAGA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
76 46 0.72
77 18 0.28
ACGTcount: A:0.41, C:0.13, G:0.04, T:0.42
Consensus pattern (77 bp):
TATAAATTAACACTCGATAAATTAATAATCTCTATAAATTAATAATTTTTCCATAGTCCCAATAT
TATTAAGTTCCA
Found at i:22911 original size:18 final size:19
Alignment explanation
Indices: 22874--22913 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
22864 TTTTATTAAT
22874 TAAATATATTATTTATTAG
1 TAAATATATTATTTATTAG
22893 TAAATATA-TA-TTATCTAG
1 TAAATATATTATTTAT-TAG
22911 TAA
1 TAA
22914 TCAAAGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 8 0.40
19 8 0.40
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (19 bp):
TAAATATATTATTTATTAG
Found at i:25723 original size:60 final size:58
Alignment explanation
Indices: 25611--25727 Score: 164
Period size: 58 Copynumber: 2.0 Consensus size: 58
25601 ATTAATCAAA
* *
25611 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGATGTTTTCGGACCGAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGACT
* *
25669 TATCGAGTGACATGTT-TTTATTAGATAGCCTTAAAAAAAGAACGTTTTAGGACCGAGAC
1 TATCAAGTGACATGTTCTTTATTAGAT-G-CATAAAAAAAG-ACGTTTTAGGACCGAGAC
25728 ATGATGCTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
57 10 0.19
58 16 0.31
59 10 0.19
60 16 0.31
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCGAGACT
Found at i:27030 original size:36 final size:36
Alignment explanation
Indices: 26983--27052 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
26973 TTCAATAACC
* *
26983 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
27019 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
27053 CAAAATCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:27931 original size:39 final size:40
Alignment explanation
Indices: 27877--27957 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
27867 ATACCTAAGA
*
27877 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
27916 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
27956 AT
1 AT
27958 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:28030 original size:17 final size:18
Alignment explanation
Indices: 27998--28043 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
27988 CGGTAAAAGA
27998 AATTATAAATTTTAATAT
1 AATTATAAATTTTAATAT
* *
28016 AATTATATA-TTTAATTT
1 AATTATAAATTTTAATAT
28033 AATTGATAAAT
1 AATT-ATAAAT
28044 GAAATTACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AATTATAAATTTTAATAT
Found at i:29045 original size:12 final size:13
Alignment explanation
Indices: 29023--29052 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
29013 ATCGGTTCAG
29023 ATATCGAACGGAT
1 ATATCGAACGGAT
29036 ATATCG-ACGGAT
1 ATATCGAACGGAT
29048 ATATC
1 ATATC
29053 AAGGTATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (13 bp):
ATATCGAACGGAT
Done.