Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013354.1 Corchorus olitorius cultivar O-4 contig13387, 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: 46367
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:14801 original size:12 final size:12
Alignment explanation
Indices: 14780--14813 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
14770 AACATTTTAC
14780 TTTCTCTTTTGTT
1 TTTCT-TTTTGTT
*
14793 TTTGTTTTTGTT
1 TTTCTTTTTGTT
14805 TTTCTTTTT
1 TTTCTTTTT
14814 AGGGTTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (12 bp):
TTTCTTTTTGTT
Found at i:25330 original size:19 final size:18
Alignment explanation
Indices: 25306--25341 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25296 TGAAGACTTA
25306 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
25325 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
25342 ATTATCTCGA
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:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:30585 original size:17 final size:17
Alignment explanation
Indices: 30563--30597 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
30553 AGCAGTTTTA
*
30563 TCCCAAAATGAAGTCTT
1 TCCCAAAAAGAAGTCTT
*
30580 TCCCAAAAAGAATTCTT
1 TCCCAAAAAGAAGTCTT
30597 T
1 T
30598 TTGCATACTA
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:0.23, G:0.09, T:0.31
Consensus pattern (17 bp):
TCCCAAAAAGAAGTCTT
Found at i:31185 original size:41 final size:41
Alignment explanation
Indices: 31083--31363 Score: 212
Period size: 41 Copynumber: 6.7 Consensus size: 41
31073 CCCAATAACT
* * * * *
31083 AAAGTCCCCAAACACATTTATAACATAGGGGCAATTCTCTTTCT
1 AAAGTCCCCAAACACATTTATAACACAGAGGC-A-TCT-ATACC
* *
31127 AAAGTCCTCAAACACATTTATAACACAGAGACATCTATACC
1 AAAGTCCCCAAACACATTTATAACACAGAGGCATCTATACC
* * * *
31168 AAAGTCCCCAAGA-ACATTTGTAACACATG-GGAAATTTTCT-TTCT
1 AAAGTCCCCAA-ACACATTTATAACACA-GAGG-CA---TCTATACC
* * * *
31212 AAAGTCCTCAAACACATTCATAACATAGAGGCATCTATATC
1 AAAGTCCCCAAACACATTTATAACACAGAGGCATCTATACC
* * *
31253 AAAGTCCCCAAACACAATTATAACACATG-GGCAATCCTCT-CTA
1 AAAGTCCCCAAACACATTTATAACACA-GAGGC-AT-CTATAC-C
* *
31296 AAAGTCCTCAAACACATTTATAACACAGAGGCATCTATACT
1 AAAGTCCCCAAACACATTTATAACACAGAGGCATCTATACC
* *
31337 AAAGTCCCTAAACACAATTATAACACA
1 AAAGTCCCCAAACACATTTATAACACA
31364 AGGGCAATTT
Statistics
Matches: 187, Mismatches: 35, Indels: 33
0.73 0.14 0.13
Matches are distributed among these distances:
40 3 0.02
41 80 0.43
42 13 0.07
43 35 0.19
44 53 0.28
45 3 0.02
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (41 bp):
AAAGTCCCCAAACACATTTATAACACAGAGGCATCTATACC
Found at i:31226 original size:85 final size:85
Alignment explanation
Indices: 31083--31373 Score: 399
Period size: 85 Copynumber: 3.4 Consensus size: 85
31073 CCCAATAACT
* * *
31083 AAAGTCCCCAAACACATTTATAACATAGGGGCAATTCTCTTTCTAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACATTTATAACACATGGGCAATTTTCTTTCTAAAGTCCTCAAACACATTTAT
*
31148 AACACAGAGACATCTATACC
66 AACACAGAGGCATCTATACC
* * *
31168 AAAGTCCCCAAGA-ACATTTGTAACACATGGGAAATTTTCTTTCTAAAGTCCTCAAACACATTCA
1 AAAGTCCCCAA-ACACATTTATAACACATGGGCAATTTTCTTTCTAAAGTCCTCAAACACATTTA
* *
31232 TAACATAGAGGCATCTATATC
65 TAACACAGAGGCATCTATACC
* * *
31253 AAAGTCCCCAAACACAATTATAACACATGGGCAA--TCCTCTCTAAAAGTCCTCAAACACATTTA
1 AAAGTCCCCAAACACATTTATAACACATGGGCAATTTTCTTTCT-AAAGTCCTCAAACACATTTA
*
31316 TAACACAGAGGCATCTATACT
65 TAACACAGAGGCATCTATACC
* * *
31337 AAAGTCCCTAAACACAATTATAACACAAGGGCAATTT
1 AAAGTCCCCAAACACATTTATAACACATGGGCAATTT
31374 CTATATGGTA
Statistics
Matches: 181, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
83 6 0.03
84 70 0.39
85 103 0.57
86 2 0.01
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (85 bp):
AAAGTCCCCAAACACATTTATAACACATGGGCAATTTTCTTTCTAAAGTCCTCAAACACATTTAT
AACACAGAGGCATCTATACC
Found at i:40765 original size:33 final size:33
Alignment explanation
Indices: 40723--40803 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 33
40713 AATTACATAT
**
40723 TATTTCTAATAATATTTATTGTATATTAAATAAA
1 TATTTCTAATAATATTTATTACATATT-AATAAA
40757 TA-TTC---TAATATTTATTACATATTAATAAA
1 TATTTCTAATAATATTTATTACATATTAATAAA
*
40786 TATTTCTAATAAAATTTA
1 TATTTCTAATAATATTTA
40804 AATATTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
29 8 0.20
30 19 0.47
33 11 0.28
34 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (33 bp):
TATTTCTAATAATATTTATTACATATTAATAAA
Found at i:40809 original size:30 final size:29
Alignment explanation
Indices: 40745--40810 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
40735 TATTTATTGT
** *
40745 ATATTAAATAAATATTCTAATATTTATTAC
1 ATATT-AATAAATATTCTAATAAATATTAA
40775 ATATTAATAAATATTTCTAATAAA-ATTTAA
1 ATATTAATAAATA-TTCTAATAAATA-TTAA
40805 ATATTA
1 ATATTA
40811 TTTGAAATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
ATATTAATAAATATTCTAATAAATATTAA
Found at i:40890 original size:22 final size:21
Alignment explanation
Indices: 40864--40926 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
40854 AATCTTAATT
*
40864 AACGAACATAAACGAGCTATTA
1 AACGAACATAAACGAGC-ACTA
*
40886 AACGAACAATAAACGAACACTA
1 AACGAAC-ATAAACGAGCACTA
*
40908 AACGAACATTAATCGAGCA
1 AACGAACA-TAAACGAGCA
40927 TGTTCGTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 25 0.71
23 9 0.26
ACGTcount: A:0.52, C:0.21, G:0.13, T:0.14
Consensus pattern (21 bp):
AACGAACATAAACGAGCACTA
Found at i:40900 original size:11 final size:11
Alignment explanation
Indices: 40864--40915 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
40854 AATCTTAATT
40864 AACGAAC-ATA
1 AACGAACAATA
* *
40874 AACGAGCTATTA
1 AACGAAC-AATA
40886 AACGAACAATA
1 AACGAACAATA
*
40897 AACGAACACTA
1 AACGAACAATA
40908 AACGAACA
1 AACGAACA
40916 TTAATCGAGC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 6 0.17
11 21 0.60
12 8 0.23
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.12
Consensus pattern (11 bp):
AACGAACAATA
Found at i:44602 original size:20 final size:23
Alignment explanation
Indices: 44558--44603 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 23
44548 AACAATCCAC
*
44558 CAAGCAGATATATCTCAACCAAG
1 CAAGCAGATATATCTCAAACAAG
44581 CAAGCAGA-A-ATC-CAAACAAG
1 CAAGCAGATATATCTCAAACAAG
44601 CAA
1 CAA
44604 CAATTAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 3 0.14
22 1 0.05
23 8 0.36
ACGTcount: A:0.50, C:0.26, G:0.13, T:0.11
Consensus pattern (23 bp):
CAAGCAGATATATCTCAAACAAG
Found at i:45931 original size:8 final size:9
Alignment explanation
Indices: 45895--45932 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
45885 CTCAAATTAC
45895 TTATGGAAA
1 TTATGGAAA
*
45904 TTAAGGAAA
1 TTATGGAAA
45913 TTATGGAAA
1 TTATGGAAA
45922 TTAT-GAAA
1 TTATGGAAA
45930 TTA
1 TTA
45933 AATGAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34
Consensus pattern (9 bp):
TTATGGAAA
Done.