Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012899.1 Corchorus olitorius cultivar O-4 contig12932, 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: 45473
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1140 original size:111 final size:111
Alignment explanation
Indices: 964--1185 Score: 444
Period size: 111 Copynumber: 2.0 Consensus size: 111
954 ATGAGAAGAT
964 TTATTTTTGTAAAAGAATAATAAAAATATATGAATATAAAAATACATGTTTACCCTTTAAATAAA
1 TTATTTTTGTAAAAGAATAATAAAAATATATGAATATAAAAATACATGTTTACCCTTTAAATAAA
1029 TACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATAATTCAGGTC
66 TACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATAATTCAGGTC
1075 TTATTTTTGTAAAAGAATAATAAAAATATATGAATATAAAAATACATGTTTACCCTTTAAATAAA
1 TTATTTTTGTAAAAGAATAATAAAAATATATGAATATAAAAATACATGTTTACCCTTTAAATAAA
1140 TACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATAATTCAGGTC
66 TACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATAATTCAGGTC
1186 CATGGTTTTG
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (111 bp):
TTATTTTTGTAAAAGAATAATAAAAATATATGAATATAAAAATACATGTTTACCCTTTAAATAAA
TACTAAACTTTTAAAATTAAAAAGGTTATTTTAGATAATTCAGGTC
Found at i:10538 original size:14 final size:15
Alignment explanation
Indices: 10512--10546 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
10502 TCTAAATTGA
10512 AACTTTTTCCAGAAG
1 AACTTTTTCCAGAAG
*
10527 CACTTTTT-CAGAAG
1 AACTTTTTCCAGAAG
10541 AACTTT
1 AACTTT
10547 GAGTTAGGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (15 bp):
AACTTTTTCCAGAAG
Found at i:18110 original size:18 final size:17
Alignment explanation
Indices: 18087--18122 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
18077 CTCAACCTAA
18087 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
18105 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
18122 A
1 A
18123 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:34207 original size:31 final size:34
Alignment explanation
Indices: 34169--34230 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
34159 TTTTCAAAAT
34169 AACTAAACT-AA-A-CTAGAAAACAACTTAATTC
1 AACTAAACTAAAGATCTAGAAAACAACTTAATTC
*
34200 AACTAAACTAAAGATCTAGAAAACAATTTAA
1 AACTAAACTAAAGATCTAGAAAACAACTTAA
34231 GGAAAACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 9 0.33
32 2 0.07
33 1 0.04
34 15 0.56
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.23
Consensus pattern (34 bp):
AACTAAACTAAAGATCTAGAAAACAACTTAATTC
Found at i:34980 original size:20 final size:20
Alignment explanation
Indices: 34955--34992 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34945 AAAAACAACC
*
34955 CTATTTTTATGGCTATTTTA
1 CTATTTTTATGGATATTTTA
34975 CTATTTTTATGGATATTT
1 CTATTTTTATGGATATTT
34993 ATGCTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.08, G:0.11, T:0.61
Consensus pattern (20 bp):
CTATTTTTATGGATATTTTA
Found at i:35176 original size:11 final size:10
Alignment explanation
Indices: 35160--35206 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
35150 AAGTTCGTGT
35160 TTGAAGACTCA
1 TTGAAGA-TCA
*
35171 TTGAAGATGA
1 TTGAAGATCA
35181 TTTGAAGAT--
1 -TTGAAGATCA
35190 TTGAAGATCA
1 TTGAAGATCA
35200 TTGAAGA
1 TTGAAGA
35207 ATAATTTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:35195 original size:19 final size:18
Alignment explanation
Indices: 35171--35206 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
35161 TGAAGACTCA
*
35171 TTGAAGATGATTTGAAGAT
1 TTGAAGATCA-TTGAAGAT
35190 TTGAAGATCATTGAAGA
1 TTGAAGATCATTGAAGA
35207 ATAATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (18 bp):
TTGAAGATCATTGAAGAT
Found at i:38604 original size:19 final size:18
Alignment explanation
Indices: 38571--38606 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
38561 TCGAGATAAT
38571 TCTTCAATAATCTTCAAA
1 TCTTCAATAATCTTCAAA
*
38589 TCTTCAAATCATCTTCAA
1 TCTTC-AATAATCTTCAA
38607 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAA
Found at i:38614 original size:11 final size:10
Alignment explanation
Indices: 38566--38617 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
38556 GCTTCTCGAG
38566 ATAATTCTTCA
1 ATAA-TCTTCA
38577 ATAATCTTC-
1 ATAATCTTCA
38586 A-AATCTTCAA
1 ATAATCTTC-A
*
38596 ATCATCTTCA
1 ATAATCTTCA
38606 ATAAGTCTTCA
1 ATAA-TCTTCA
38617 A
1 A
38618 ACACGAACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 7 0.20
9 1 0.03
10 10 0.29
11 17 0.49
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.38
Consensus pattern (10 bp):
ATAATCTTCA
Found at i:40177 original size:30 final size:29
Alignment explanation
Indices: 40138--40195 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
40128 GTTTATTAAT
40138 GAAACTTGAAAATTAAAGACATAAAATAAAG
1 GAAACTTGAAAATTAAAG-CAT-AAATAAAG
40169 GAAA-TTGAAAATTAAAGCATAAATAAA
1 GAAACTTGAAAATTAAAGCATAAATAAA
40196 ATAACTAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 7 0.26
29 3 0.11
30 13 0.48
31 4 0.15
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.21
Consensus pattern (29 bp):
GAAACTTGAAAATTAAAGCATAAATAAAG
Found at i:41907 original size:32 final size:32
Alignment explanation
Indices: 41860--42016 Score: 152
Period size: 32 Copynumber: 4.9 Consensus size: 32
41850 TAGGAATAGT
** *
41860 GGCGTTTCGTTATTTAAACGCTGCTATTTAGC
1 GGCGTTTCGAAATTTAAACGCCGCTATTTAGC
* * **
41892 GGCGTCTCGAAATTTAGACGCCGCTAAATAGC
1 GGCGTTTCGAAATTTAAACGCCGCTATTTAGC
* ** *
41924 GGCGTTTGGAAATTTAAATACCGCTATTTAGT
1 GGCGTTTCGAAATTTAAACGCCGCTATTTAGC
* * **
41956 GGCATTTTGAAATTTAAACGCCGCTAAATAGC
1 GGCGTTTCGAAATTTAAACGCCGCTATTTAGC
* **
41988 GGCGTTTCTATCTTTAAACGCCGCTATTT
1 GGCGTTTCGAAATTTAAACGCCGCTATTT
42017 TGGCCTTTTA
Statistics
Matches: 96, Mismatches: 29, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 96 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (32 bp):
GGCGTTTCGAAATTTAAACGCCGCTATTTAGC
Found at i:41922 original size:64 final size:64
Alignment explanation
Indices: 41854--42016 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 64
41844 TTGATTTAGG
* * * *
41854 AATAGTGGCGTTTCGTTATTTAAACGCTGCTATTTAGCGGCGTCTCGAAATTTAGACGCCGCTA
1 AATAGCGGCGTTTCGTTATTTAAACGCCGCTATTTAGCGGCATCTCGAAATTTAAACGCCGCTA
* ** ** * * *
41918 AATAGCGGCGTTTGGAAATTTAAATACCGCTATTTAGTGGCATTTTGAAATTTAAACGCCGCTA
1 AATAGCGGCGTTTCGTTATTTAAACGCCGCTATTTAGCGGCATCTCGAAATTTAAACGCCGCTA
*
41982 AATAGCGGCGTTTC-TATCTTTAAACGCCGCTATTT
1 AATAGCGGCGTTTCGT-TATTTAAACGCCGCTATTT
42017 TGGCCTTTTA
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
AATAGCGGCGTTTCGTTATTTAAACGCCGCTATTTAGCGGCATCTCGAAATTTAAACGCCGCTA
Done.