Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016110.1 Corchorus olitorius cultivar O-4 contig16143, 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: 32297
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2376 original size:2 final size:2
Alignment explanation
Indices: 2371--2417 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
2361 AAAAAAACTA
* *
2371 AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2413 AT AT A
1 AT AT A
2418 ATAAATGAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3518 original size:13 final size:13
Alignment explanation
Indices: 3500--3529 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3490 GGTTTTACTC
3500 TGATTTATGACTT
1 TGATTTATGACTT
*
3513 TGATTTATGATTT
1 TGATTTATGACTT
3526 TGAT
1 TGAT
3530 ATTAACGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.17, T:0.57
Consensus pattern (13 bp):
TGATTTATGACTT
Found at i:12569 original size:2 final size:2
Alignment explanation
Indices: 12562--12596 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12552 ATGAGCAAAA
12562 AT AT 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 AT AT A
12597 CTAGTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12684 original size:22 final size:22
Alignment explanation
Indices: 12659--12735 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
12649 TATTTTTATG
*
12659 AAATTTTGATAATTACCCTATT
1 AAATTTTGATAATTACCCTATA
** * *
12681 AAATTTTGATAACCACCATATG
1 AAATTTTGATAATTACCCTATA
12703 AAATTTTGATAATTA-CCTATA
1 AAATTTTGATAATTACCCTATA
*
12724 AAATTGTGATAA
1 AAATTTTGATAA
12736 ACTTCACAAG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 15 0.33
22 31 0.67
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAATTACCCTATA
Found at i:12754 original size:43 final size:44
Alignment explanation
Indices: 12658--12757 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 44
12648 ATATTTTTAT
* * * * *
12658 GAAATTTTGATAATTACCCTATTAAATTTTGATAACCACCATAT
1 GAAATTTTGATAATTACCCTATAAAATTGTGATAAACACCACAA
**
12702 GAAATTTTGATAATTA-CCTATAAAATTGTGATAAACTTCACAA
1 GAAATTTTGATAATTACCCTATAAAATTGTGATAAACACCACAA
*
12745 GAAACTTTGATAA
1 GAAATTTTGATAA
12758 CCTAACTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 32 0.67
44 16 0.33
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (44 bp):
GAAATTTTGATAATTACCCTATAAAATTGTGATAAACACCACAA
Found at i:12809 original size:20 final size:21
Alignment explanation
Indices: 12784--12823 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12774 TAATAAACTT
12784 TCCTATGAATTTTG-TAATCA
1 TCCTATGAATTTTGATAATCA
*
12804 TCCTATGATTTTTGATAATC
1 TCCTATGAATTTTGATAATC
12824 TTTGTGTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (21 bp):
TCCTATGAATTTTGATAATCA
Found at i:14754 original size:7 final size:7
Alignment explanation
Indices: 14744--14796 Score: 55
Period size: 6 Copynumber: 8.4 Consensus size: 7
14734 AATTTAAAAT
*
14744 TAAATCA
1 TAAATAA
14751 TAAATAA
1 TAAATAA
14758 T-AATAA
1 TAAATAA
14764 T-AATAA
1 TAAATAA
14770 T-AATAA
1 TAAATAA
14776 T-AATAA
1 TAAATAA
14782 T-AATAA
1 TAAATAA
14788 T-AATAA
1 TAAATAA
14794 TAA
1 TAA
14797 CAAGAAGGGC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
6 36 0.82
7 8 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (7 bp):
TAAATAA
Found at i:14761 original size:3 final size:3
Alignment explanation
Indices: 14753--14796 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
14743 TTAAATCATA
14753 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
14797 CAAGAAGGGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:15543 original size:3 final size:3
Alignment explanation
Indices: 15535--15573 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
15525 TATAGCATAT
15535 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
15574 TAGTAGAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17930 original size:105 final size:105
Alignment explanation
Indices: 17812--18023 Score: 406
Period size: 105 Copynumber: 2.0 Consensus size: 105
17802 TACATTAAAC
*
17812 TATCAAATAGAAAGATGTCCATCATAATAACTTTTTAAATTAAAATGGTAAAAATAAAATAACTA
1 TATCAAATAGAAAGATGTCCATCACAATAACTTTTTAAATTAAAATGGTAAAAATAAAATAACTA
17877 TAAAATAATAAATTTAATTAAATGAAAATAGAGTTTTTAA
66 TAAAATAATAAATTTAATTAAATGAAAATAGAGTTTTTAA
*
17917 TATCAAATAGAAAGGTGTCCATCACAATAACTTTTTAAATTAAAATGGTAAAAATAAAATAACTA
1 TATCAAATAGAAAGATGTCCATCACAATAACTTTTTAAATTAAAATGGTAAAAATAAAATAACTA
17982 TAAAATAATAAATTTAATTAAATGAAAATAGAGTTTTTAA
66 TAAAATAATAAATTTAATTAAATGAAAATAGAGTTTTTAA
18022 TA
1 TA
18024 GAATAAAAGT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (105 bp):
TATCAAATAGAAAGATGTCCATCACAATAACTTTTTAAATTAAAATGGTAAAAATAAAATAACTA
TAAAATAATAAATTTAATTAAATGAAAATAGAGTTTTTAA
Found at i:18306 original size:73 final size:72
Alignment explanation
Indices: 18187--18331 Score: 211
Period size: 73 Copynumber: 2.0 Consensus size: 72
18177 TTTGAGAAAT
* * *
18187 ATGTTTGAAAAATAAGGGTATATTGGGCGATTCAAAAGTTTTACAGGTGAA-CATACTTTTTAAT
1 ATGTTTGAAAAATAAGGATATAATGGACGATTCAAAAGTTTTACA-G-GAAGCATACTTTTTAAT
18251 ATAGTATAA
64 ATAGTATAA
* *
18260 ATGTTTGACAAATAAGGATATAATGGACGATTCAAAAGTTTTACAGGAAGTCGTACTTTTTAATA
1 ATGTTTGAAAAATAAGGATATAATGGACGATTCAAAAGTTTTACAGGAAG-CATACTTTTTAATA
18325 TAGTATA
65 TAGTATA
18332 GATTCTTTTC
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
71 3 0.05
72 1 0.02
73 61 0.94
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.35
Consensus pattern (72 bp):
ATGTTTGAAAAATAAGGATATAATGGACGATTCAAAAGTTTTACAGGAAGCATACTTTTTAATAT
AGTATAA
Found at i:19216 original size:7 final size:7
Alignment explanation
Indices: 19200--19296 Score: 64
Period size: 6 Copynumber: 13.7 Consensus size: 7
19190 TGGTAACTAA
19200 ATATAAT
1 ATATAAT
19207 ATATAGTAT
1 ATATA--AT
19216 ATATAGTAT
1 ATATA--AT
19225 ATATAAT
1 ATATAAT
19232 A-ATAAT
1 ATATAAT
19238 A-ATAAT
1 ATATAAT
19244 A-ATAAT
1 ATATAAT
19250 A-ATAAT
1 ATATAAT
19256 A-ATAAT
1 ATATAAT
19262 A-ATAAT
1 ATATAAT
19268 AATCATAAT
1 -AT-ATAAT
19277 CATAATAAT
1 -AT-ATAAT
19286 A-ATAAT
1 ATATAAT
*
19292 CTATA
1 ATATA
19297 CTAATTATAA
Statistics
Matches: 81, Mismatches: 3, Indels: 12
0.84 0.03 0.12
Matches are distributed among these distances:
6 40 0.49
7 12 0.15
8 1 0.01
9 28 0.35
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (7 bp):
ATATAAT
Found at i:19227 original size:11 final size:9
Alignment explanation
Indices: 19205--19229 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
19195 ACTAAATATA
19205 ATATATAGT
1 ATATATAGT
19214 ATATATAGT
1 ATATATAGT
19223 ATATATA
1 ATATATA
19230 ATAATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (9 bp):
ATATATAGT
Found at i:19235 original size:3 final size:3
Alignment explanation
Indices: 19227--19291 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
19217 TATAGTATAT
*
19227 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATC ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
19275 ATC ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
19292 CTATACTAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:21376 original size:25 final size:25
Alignment explanation
Indices: 21344--21391 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
21334 TTTGGCCTCA
*
21344 GGTTACTCAGGTTTTGGGTCATTCG
1 GGTTACTCAGGTTCTGGGTCATTCG
*
21369 GGTTACTCGGGTTCTGGGTCATT
1 GGTTACTCAGGTTCTGGGTCATT
21392 TCAGGTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.10, C:0.17, G:0.33, T:0.40
Consensus pattern (25 bp):
GGTTACTCAGGTTCTGGGTCATTCG
Found at i:24593 original size:13 final size:12
Alignment explanation
Indices: 24554--24596 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
24544 CTTAGGTGCG
*
24554 TTTTCTCTTCTCT
1 TTTTCTTTTCT-T
24567 TTTTCTTTTCTT
1 TTTTCTTTTCTT
*
24579 TTTTTTTTTCATT
1 TTTTCTTTTC-TT
24592 TTTTC
1 TTTTC
24597 CCCAACAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:26772 original size:38 final size:38
Alignment explanation
Indices: 26730--26805 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
26720 TTGTCACTTT
26730 CCTTGTTCCTTTTTAATTGTTCCTCATATTTTCTTTTC
1 CCTTGTTCCTTTTTAATTGTTCCTCATATTTTCTTTTC
*
26768 CCTTGTTCCTTTTTAATTGTTCTTCATATTTTCTTTTC
1 CCTTGTTCCTTTTTAATTGTTCCTCATATTTTCTTTTC
26806 AGAAATATCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.11, C:0.22, G:0.05, T:0.62
Consensus pattern (38 bp):
CCTTGTTCCTTTTTAATTGTTCCTCATATTTTCTTTTC
Found at i:29118 original size:14 final size:13
Alignment explanation
Indices: 29082--29120 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
29072 ATTTTATATT
*
29082 TATAATTATATTTA
1 TATAATTA-ATTAA
29096 TATAATTAATTAA
1 TATAATTAATTAA
29109 TATAATTTAATT
1 TATAA-TTAATT
29121 CTTAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATAATTAATTAA
Found at i:32143 original size:26 final size:23
Alignment explanation
Indices: 32110--32171 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 23
32100 ATTCCTTTAA
32110 TTACATTTATATCCTTT-TTTATAT
1 TTACATTTATAT--TTTATTTATAT
32134 TTCACAATTTATATTTTGATTTATAT
1 TT-AC-ATTTATATTTT-ATTTATAT
32160 TTACATTTATAT
1 TTACATTTATAT
32172 ATTGAATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
24 13 0.38
25 4 0.12
26 17 0.50
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.60
Consensus pattern (23 bp):
TTACATTTATATTTTATTTATAT
Done.