Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023743.1 Corchorus olitorius cultivar O-4 contig23776, 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: 40269
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:7588 original size:10 final size:10
Alignment explanation
Indices: 7573--7608 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
7563 AATTATGAAA
7573 AAATCTAATT
1 AAATCTAATT
7583 AAATCTAATT
1 AAATCTAATT
* *
7593 AAGTATAATT
1 AAATCTAATT
7603 AAATCT
1 AAATCT
7609 TAAATAACCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (10 bp):
AAATCTAATT
Found at i:8952 original size:50 final size:50
Alignment explanation
Indices: 8877--8983 Score: 187
Period size: 50 Copynumber: 2.1 Consensus size: 50
8867 AGACCATGGG
* *
8877 CCCAACATGATGGCCCAAGTGGAAACAAAAAAGAAATAGATGGAAATGAA
1 CCCAACATGATGACCCAAGTGGAAACAAAAAAGAAATAGATGAAAATGAA
*
8927 CCCAACATGATGACCCAAGTGGAAACAAAAAAGAAATAGATGAAAATGAG
1 CCCAACATGATGACCCAAGTGGAAACAAAAAAGAAATAGATGAAAATGAA
8977 CCCAACA
1 CCCAACA
8984 ACACAAGAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.50, C:0.19, G:0.20, T:0.11
Consensus pattern (50 bp):
CCCAACATGATGACCCAAGTGGAAACAAAAAAGAAATAGATGAAAATGAA
Found at i:9246 original size:34 final size:33
Alignment explanation
Indices: 9208--9457 Score: 120
Period size: 33 Copynumber: 7.6 Consensus size: 33
9198 TTTACCAATT
*
9208 TTACTTTAATTATCAAATACCAATTTTACTCTTC
1 TTACTTTAATTACCAAATACCAA-TTTACTCTTC
* * *
9242 TTACTATATTTACCAAATACCAATTTACTCTTT
1 TTACTTTAATTACCAAATACCAATTTACTCTTC
* *
9275 TTA-TTCTAATTACCGAATACC-ATTTAACT-TTAG
1 TTACTT-TAATTACCAAATACCAATTT-ACTCTT-C
** * ** * *
9308 TTAC-CAAATT-TCATTTTACCATTTTACTCTTT
1 TTACTTTAATTACCA-AATACCAATTTACTCTTC
**** *
9340 TTACTTTAATCT-CTTTTTACC-ATATTACTCTTT
1 TTACTTTAAT-TACCAAATACCAAT-TTACTCTTC
** * ** * * *
9373 TTGTTTTAATTGCCAAATTTCATTTTTCTCTTT
1 TTACTTTAATTACCAAATACCAATTTACTCTTC
* *
9406 TTACTTTGATTACCAAATACCAATTTACTATT-
1 TTACTTTAATTACCAAATACCAATTTACTCTTC
9438 TCTACTTTAATTACCAAATA
1 T-TACTTTAATTACCAAATA
9458 TATACTATAT
Statistics
Matches: 161, Mismatches: 42, Indels: 27
0.70 0.18 0.12
Matches are distributed among these distances:
31 1 0.01
32 25 0.16
33 113 0.70
34 22 0.14
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.49
Consensus pattern (33 bp):
TTACTTTAATTACCAAATACCAATTTACTCTTC
Found at i:9343 original size:17 final size:17
Alignment explanation
Indices: 9321--9374 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
9311 CCAAATTTCA
9321 TTTTACCATTTTACTCT
1 TTTTACCATTTTACTCT
*
9338 TTTTA-C-TTTAATCTCT
1 TTTTACCATTTTA-CTCT
*
9354 TTTTACCATATTACTCT
1 TTTTACCATTTTACTCT
9371 TTTT
1 TTTT
9375 GTTTTAATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.13
16 10 0.32
17 14 0.45
18 3 0.10
ACGTcount: A:0.19, C:0.20, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTACCATTTTACTCT
Found at i:10768 original size:19 final size:20
Alignment explanation
Indices: 10746--10787 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
10736 ACCATTTAAC
10746 TTTAATTACCAAATTTCA-T
1 TTTAATTACCAAATTTCACT
*
10765 TTTACTTACCAAATTTCACT
1 TTTAATTACCAAATTTCACT
10785 TTT
1 TTT
10788 TTCTTTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAATTACCAAATTTCACT
Found at i:10771 original size:24 final size:22
Alignment explanation
Indices: 10751--10836 Score: 52
Period size: 24 Copynumber: 3.8 Consensus size: 22
10741 TTAACTTTAA
10751 TTACCAAATTTCATTTTAC---
1 TTACCAAATTTCATTTTACTTT
*
10770 TTACCAAATTTCACTTTTTTCTTT
1 TTACCAAATTTCA--TTTTACTTT
* * **
10794 TTACCATATTACTCTTTTTGTTTT
1 TTACCAAATT--TCATTTTACTTT
10818 AATTACCAAATTTCATTTT
1 --TTACCAAATTTCATTTT
10837 TTTATCTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
19 13 0.25
21 5 0.10
24 22 0.43
26 11 0.22
ACGTcount: A:0.26, C:0.19, G:0.01, T:0.55
Consensus pattern (22 bp):
TTACCAAATTTCATTTTACTTT
Found at i:10903 original size:32 final size:31
Alignment explanation
Indices: 10837--10985 Score: 114
Period size: 33 Copynumber: 4.8 Consensus size: 31
10827 ATTTCATTTT
*
10837 TTTATCTTTTACTTTGATTACCAAATACCAA
1 TTTATCTTTTACTTTAATTACCAAATACCAA
*
10868 TTTACTCTTTTAACTTTAATTACCAGATACC-A
1 TTTA-TCTTTT-ACTTTAATTACCAAATACCAA
* ** *
10900 TTTA------ACTTTAGTTACCAAATTTCATT
1 TTTATCTTTTACTTTAATTACCAAATACCA-A
* * *
10926 TTTTTCTTTTTACTTTGATTACCAAATACTAA
1 TTTATC-TTTTACTTTAATTACCAAATACCAA
10958 TTTACTCTTTTTACTTTAATTACCAAAT
1 TTTA-TC-TTTTACTTTAATTACCAAAT
10986 TATTATTACC
Statistics
Matches: 90, Mismatches: 16, Indels: 22
0.70 0.12 0.17
Matches are distributed among these distances:
24 15 0.17
26 3 0.03
31 4 0.04
32 14 0.16
33 54 0.60
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.49
Consensus pattern (31 bp):
TTTATCTTTTACTTTAATTACCAAATACCAA
Found at i:10952 original size:90 final size:91
Alignment explanation
Indices: 10815--10982 Score: 293
Period size: 90 Copynumber: 1.9 Consensus size: 91
10805 CTCTTTTTGT
10815 TTTAATTACCAAATTTCATTTTTTTATCTTTTACTTTGATTACCAAATACCAATTTACTCTTTTA
1 TTTAATTACCAAATTTCATTTTTTTATCTTTTACTTTGATTACCAAATACCAATTTACTCTTTTA
10880 ACTTTAATTACCAGATACCATTTAAC
66 ACTTTAATTACCAGATACCATTTAAC
* * * *
10906 TTTAGTTACCAAATTTCATTTTTTTCT-TTTTACTTTGATTACCAAATACTAATTTACTCTTTTT
1 TTTAATTACCAAATTTCATTTTTTTATCTTTTACTTTGATTACCAAATACCAATTTACTCTTTTA
10970 ACTTTAATTACCA
66 ACTTTAATTACCA
10983 AATTATTATT
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
90 48 0.66
91 25 0.34
ACGTcount: A:0.30, C:0.18, G:0.02, T:0.50
Consensus pattern (91 bp):
TTTAATTACCAAATTTCATTTTTTTATCTTTTACTTTGATTACCAAATACCAATTTACTCTTTTA
ACTTTAATTACCAGATACCATTTAAC
Found at i:11686 original size:18 final size:19
Alignment explanation
Indices: 11659--11700 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
11649 AACACAAGTC
*
11659 ATAAATAGAA-CCCAAATA
1 ATAAACAGAAGCCCAAATA
11677 ATAAACAGAAGCCCAAATA
1 ATAAACAGAAGCCCAAATA
11696 ATAAA
1 ATAAA
11701 AGCCTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.62, C:0.17, G:0.07, T:0.14
Consensus pattern (19 bp):
ATAAACAGAAGCCCAAATA
Found at i:11710 original size:34 final size:35
Alignment explanation
Indices: 11659--11737 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 35
11649 AACACAAGTC
* *
11659 ATAAATAGAA-CCCAAATAAT-AAACAGAAGCCCAA
1 ATAAATAAAAGCCTAAATAATGAAACA-AAGCCCAA
**
11693 AT-AATAAAAGCCTAAATAATGAGCCAAAGCCCAA
1 ATAAATAAAAGCCTAAATAATGAAACAAAGCCCAA
11727 ATAAATAAAAG
1 ATAAATAAAAG
11738 AAAGTATACC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 6 0.16
34 21 0.55
35 11 0.29
ACGTcount: A:0.58, C:0.18, G:0.10, T:0.14
Consensus pattern (35 bp):
ATAAATAAAAGCCTAAATAATGAAACAAAGCCCAA
Found at i:15069 original size:12 final size:12
Alignment explanation
Indices: 15052--15076 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15042 ATCTAATAAC
15052 ACATAATTACTA
1 ACATAATTACTA
15064 ACATAATTACTA
1 ACATAATTACTA
15076 A
1 A
15077 TTTGCGAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
ACATAATTACTA
Found at i:15226 original size:14 final size:14
Alignment explanation
Indices: 15207--15255 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
15197 ATGGCCAAAC
15207 TACTAATGCCTAAT
1 TACTAATGCCTAAT
*
15221 TACTAATG-CAAAT
1 TACTAATGCCTAAT
*
15234 GT--TAATACCTAAT
1 -TACTAATGCCTAAT
15247 TACTAATGC
1 TACTAATGC
15256 GAATGCTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
12 5 0.19
13 8 0.30
14 14 0.52
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (14 bp):
TACTAATGCCTAAT
Found at i:15239 original size:26 final size:26
Alignment explanation
Indices: 15210--15260 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
15200 GCCAAACTAC
*
15210 TAATGCCTAATTACTAATGCAAATGT
1 TAATACCTAATTACTAATGCAAATGT
*
15236 TAATACCTAATTACTAATGCGAATG
1 TAATACCTAATTACTAATGCAAATG
15261 CTATTTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (26 bp):
TAATACCTAATTACTAATGCAAATGT
Found at i:19857 original size:3 final size:3
Alignment explanation
Indices: 19849--19895 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
19839 TACTGGGTTT
19849 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19896 CAATGGTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:22828 original size:18 final size:18
Alignment explanation
Indices: 22805--22840 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
22795 TCATATCTCC
22805 CATTTGCTGTACTTGTGT
1 CATTTGCTGTACTTGTGT
22823 CATTTGCTGTACTTGTGT
1 CATTTGCTGTACTTGTGT
22841 GACTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (18 bp):
CATTTGCTGTACTTGTGT
Found at i:35961 original size:38 final size:38
Alignment explanation
Indices: 35913--35992 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
35903 GCGTAATATG
* *
35913 GATCTTAACATTCAAAT-CATCATTGCATTAAAGACATA
1 GATCTTAACA-TAAAATGCATCATTACATTAAAGACATA
* *
35951 GATCTTAACATAAAATGGATCTTTACATTAAAGACATA
1 GATCTTAACATAAAATGCATCATTACATTAAAGACATA
35989 GATC
1 GATC
35993 CGCCAATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 5 0.14
38 32 0.86
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.31
Consensus pattern (38 bp):
GATCTTAACATAAAATGCATCATTACATTAAAGACATA
Found at i:35992 original size:21 final size:21
Alignment explanation
Indices: 35938--35992 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 21
35928 ATCATCATTG
35938 CATTAAAGACATAGATCTTAA
1 CATTAAAGACATAGATCTTAA
* *
35959 CA-T-AA-A-ATGGATCTTTA
1 CATTAAAGACATAGATCTTAA
35976 CATTAAAGACATAGATC
1 CATTAAAGACATAGATC
35993 CGCCAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
17 11 0.41
18 2 0.07
19 4 0.15
20 2 0.07
21 8 0.30
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (21 bp):
CATTAAAGACATAGATCTTAA
Found at i:39393 original size:35 final size:35
Alignment explanation
Indices: 39328--39394 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
39318 GATCCTCTTT
* *
39328 GATATTGGAGTTAGTAGGATATTAATGTGTTTGGA
1 GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA
* * *
39363 GATATTGAAGTTAGTGGGGTTTTAAGGTGTTT
1 GATATTGAAGTTAGTAGGATATTAAGGTGTTT
39395 AAAGAGCTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (35 bp):
GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA
Done.