Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021612.1 Corchorus olitorius cultivar O-4 contig21645, 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: 26790
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:5981 original size:22 final size:22
Alignment explanation
Indices: 5953--6053 Score: 80
Period size: 22 Copynumber: 4.6 Consensus size: 22
5943 TAAATATTCG
5953 TATAAAATTTTGATAACCACAT
1 TATAAAATTTTGATAACCACAT
* * *
5975 TATAAAATTATGATAACTTA-TT
1 TATAAAATTTTGATAAC-CACAT
* **
5997 TATGAAATTTTGATAACC-TTT
1 TATAAAATTTTGATAACCACAT
* * *
6018 GTATAAAATTTTGATTACGACAC
1 -TATAAAATTTTGATAACCACAT
*
6041 TATGAAATTTTGA
1 TATAAAATTTTGA
6054 GAACTTCTCT
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
21 2 0.03
22 59 0.95
23 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.42
Consensus pattern (22 bp):
TATAAAATTTTGATAACCACAT
Found at i:6165 original size:44 final size:44
Alignment explanation
Indices: 6115--6218 Score: 145
Period size: 44 Copynumber: 2.4 Consensus size: 44
6105 ATCTCTATAC
* * * *
6115 AATTTTGTTAATCTTCCTATGGAATTTTGAAAACCTCACTAAGA
1 AATTTTGATAATCTCCCTATGAAATTTTGAAAACCACACTAAGA
* *
6159 AATTTTGATAATCTCCCTATGAAATTTTGATAACCACACTAGGA
1 AATTTTGATAATCTCCCTATGAAATTTTGAAAACCACACTAAGA
*
6203 AATTTTGATAACCTCC
1 AATTTTGATAATCTCC
6219 TTGTGAATTG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (44 bp):
AATTTTGATAATCTCCCTATGAAATTTTGAAAACCACACTAAGA
Found at i:6188 original size:22 final size:22
Alignment explanation
Indices: 5997--6218 Score: 113
Period size: 22 Copynumber: 10.0 Consensus size: 22
5987 ATAACTTATT
***
5997 TATGAAATTTTGATAACCTTTG
1 TATGAAATTTTGATAACCTCCC
* * ** *
6019 TATAAAATTTTGATTACGACAC
1 TATGAAATTTTGATAACCTCCC
* * *
6041 TATGAAATTTTGAGAACTTCTC
1 TATGAAATTTTGATAACCTCCC
* * * * * *
6063 TATGAAATGTCGAAAATCTGCA
1 TATGAAATTTTGATAACCTCCC
* * * *
6085 TATTGAAACTTTGTTAACATATCTC
1 TA-TGAAATTTTGATAAC--CTCCC
* * *
6110 TAT-ACAATTTTGTTAATCTTCC
1 TATGA-AATTTTGATAACCTCCC
* * *
6132 TATGGAATTTTGAAAACCTCAC
1 TATGAAATTTTGATAACCTCCC
* *
6154 TAAGAAATTTTGATAATCTCCC
1 TATGAAATTTTGATAACCTCCC
* *
6176 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCTCCC
*
6198 TAGGAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
6219 TTGTGAATTG
Statistics
Matches: 141, Mismatches: 54, Indels: 10
0.69 0.26 0.05
Matches are distributed among these distances:
22 117 0.83
23 10 0.07
24 11 0.08
25 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:11057 original size:24 final size:23
Alignment explanation
Indices: 10998--11058 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
10988 TCCCCTGATG
* **
10998 CTTGCCGTGAGCGGGGAGGTTCC
1 CTTGACGTGAGCGGGGAGGCCCC
**
11021 CTTGACGAAAGCGGGGAGGACCCC
1 CTTGACGTGAGCGGGGAGG-CCCC
11045 CTTGACGTGAGCGG
1 CTTGACGTGAGCGG
11059 AAAGGTCGCC
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 16 0.53
24 14 0.47
ACGTcount: A:0.16, C:0.26, G:0.41, T:0.16
Consensus pattern (23 bp):
CTTGACGTGAGCGGGGAGGCCCC
Found at i:12169 original size:327 final size:327
Alignment explanation
Indices: 11569--12200 Score: 1174
Period size: 327 Copynumber: 1.9 Consensus size: 327
11559 TAGGTGCTTC
11569 AATTAATGTTATGCCTTACTCAATTTACATTAATCTTAGCATTGGTCCTTTGATTGAAACTGGCG
1 AATTAATGTTATGCCTTACTCAATTTACATTAATCTTAGCATTGGTCCTTTGATTGAAACTGGCG
* *
11634 TGATTATTCAACTCATCGATCGGTCTAACGTTTATCTCGAAGGGATTGTTGAGGATGTGCTTATG
66 TGATTATTCAACTCACCGATCGGTCTAACGTTTATCCCGAAGGGATTGTTGAGGATGTGCTTATG
*
11699 CAGGTTAATGAGCTTGTTTTCCCAGTTGATTTCTATGTGCTTAAGATGGAGGAGGATGAGCTTGA
131 CAGGTTAATGAGCTTGTTTTCCCAGCTGATTTCTATGTGCTTAAGATGGAGGAGGATGAGCTTGA
11764 TCTTCGACCTATTCTTCTGCTTCTAGGTAGACCATTCCTTCGCACTGCAAGGACTAAAATTGATG
196 TCTTCGACCTATTCTTCTGCTTCTAGGTAGACCATTCCTTCGCACTGCAAGGACTAAAATTGATG
11829 TGTATGAGGGAATCTTGACCATGGAATATGATAACCATATGATCCTCCTCCATCTTAAGCACATA
261 TGTATGAGGGAATCTTGACCATGGAATATGATAACCATATGATCCTCCTCCATCTTAAGCACATA
11894 GA
326 GA
*
11896 AATTAATGTTATGCCTTACTCAATTTACATTAATCTTAGCATTGGTCCTTTGATTGAAATTGGCG
1 AATTAATGTTATGCCTTACTCAATTTACATTAATCTTAGCATTGGTCCTTTGATTGAAACTGGCG
*
11961 TGATTATTCAACTCGCCGATCGGTCTAACGTTTATCCCGAAGGGATTGTTGAGGATGTGCTTATG
66 TGATTATTCAACTCACCGATCGGTCTAACGTTTATCCCGAAGGGATTGTTGAGGATGTGCTTATG
12026 CAGGTTAATGAGCTTGTTTTCCCAGCTGATTTCTATGTGCTTAAGATGGAGGAGGATGAGCTTGA
131 CAGGTTAATGAGCTTGTTTTCCCAGCTGATTTCTATGTGCTTAAGATGGAGGAGGATGAGCTTGA
* * *
12091 TCTTTGACCTATTCTTCTGCTTCTAGGTAGACCATTCCTTCGCACTGCAAGTACTAAGATTGATG
196 TCTTCGACCTATTCTTCTGCTTCTAGGTAGACCATTCCTTCGCACTGCAAGGACTAAAATTGATG
* *
12156 TGTATGGGGGAATCTTGACCATGGAATTTGATAACCATATGATCC
261 TGTATGAGGGAATCTTGACCATGGAATATGATAACCATATGATCC
12201 GGTTTGATAT
Statistics
Matches: 295, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
327 295 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (327 bp):
AATTAATGTTATGCCTTACTCAATTTACATTAATCTTAGCATTGGTCCTTTGATTGAAACTGGCG
TGATTATTCAACTCACCGATCGGTCTAACGTTTATCCCGAAGGGATTGTTGAGGATGTGCTTATG
CAGGTTAATGAGCTTGTTTTCCCAGCTGATTTCTATGTGCTTAAGATGGAGGAGGATGAGCTTGA
TCTTCGACCTATTCTTCTGCTTCTAGGTAGACCATTCCTTCGCACTGCAAGGACTAAAATTGATG
TGTATGAGGGAATCTTGACCATGGAATATGATAACCATATGATCCTCCTCCATCTTAAGCACATA
GA
Found at i:15807 original size:17 final size:17
Alignment explanation
Indices: 15766--15808 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
15756 AAATATATAT
15766 AACGTATGATTTGGATG
1 AACGTATGATTTGGATG
*
15783 AACATATGATTTGGATG
1 AACGTATGATTTGGATG
*
15800 AATGTATGA
1 AACGTATGA
15809 GCTCTAGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.35
Consensus pattern (17 bp):
AACGTATGATTTGGATG
Found at i:23785 original size:17 final size:18
Alignment explanation
Indices: 23765--23798 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23755 AATTAAAAAA
*
23765 ATAAAAA-AATTGTTTTC
1 ATAAAAAGAAGTGTTTTC
23782 ATAAAAAGAAGTGTTTT
1 ATAAAAAGAAGTGTTTT
23799 TCATGATAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (18 bp):
ATAAAAAGAAGTGTTTTC
Found at i:24672 original size:19 final size:18
Alignment explanation
Indices: 24648--24683 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
24638 TGAAGATTTA
24648 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
24667 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
24684 ATTATTTCCA
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:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Done.