Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017417.1 Corchorus olitorius cultivar O-4 contig17450, 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: 55462
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:15835 original size:43 final size:43
Alignment explanation
Indices: 15779--15862 Score: 116
Period size: 46 Copynumber: 1.9 Consensus size: 43
15769 AGTAAATTAC
*
15779 CTAAATTATA-CTCCATCTCTAGGTAATTCATCAAAATAAAAG
1 CTAAATTATACCTCCATCTCTAGATAATTCATCAAAATAAAAG
*
15821 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATA
1 CTAA-ATTATA--CCTCCATCTCTAGATAATTCATCAAAATA
15863 TTAATTGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
42 4 0.11
43 5 0.14
46 27 0.75
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (43 bp):
CTAAATTATACCTCCATCTCTAGATAATTCATCAAAATAAAAG
Found at i:16150 original size:15 final size:16
Alignment explanation
Indices: 16124--16154 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
16114 GCAGAGGTGT
16124 AAGAATATCAATTAAA
1 AAGAATATCAATTAAA
16140 AAGAA-ATCAATTAAA
1 AAGAATATCAATTAAA
16155 CTAAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (16 bp):
AAGAATATCAATTAAA
Found at i:17488 original size:19 final size:17
Alignment explanation
Indices: 17456--17490 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
17446 TTGAAATAAT
17456 TCTTCAAAGTCTTCAAG
1 TCTTCAAAGTCTTCAAG
17473 TCTTCAAATGGTCTTCAA
1 TCTTCAAA--GTCTTCAA
17491 ACACGAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (17 bp):
TCTTCAAAGTCTTCAAG
Found at i:19404 original size:21 final size:21
Alignment explanation
Indices: 19378--19437 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
19368 GGCTCTGAAT
*
19378 GGTGGTGGCACGGGCATAGCC
1 GGTGGTGGCACGGGCATAACC
* * *
19399 GGTGGTGGCACGAGCTTAATC
1 GGTGGTGGCACGGGCATAACC
19420 GGTGGTGGCACGGTGCAT
1 GGTGGTGGCACGG-GCAT
19438 GGATAGCTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.15, C:0.20, G:0.45, T:0.20
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Found at i:22762 original size:32 final size:32
Alignment explanation
Indices: 22715--22792 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
22705 AACACAAAAA
*
22715 TTAAAAACGGA-AAAACAAAATCTTTTTTTTAGG
1 TTAAAAACGCAGAAAACAAAA--TTTTTTTTAGG
22748 -T-AAAACGCAGAAAACAAAATTTTTTTTAGG
1 TTAAAAACGCAGAAAACAAAATTTTTTTTAGG
22778 TTAAAAACGCAGAAA
1 TTAAAAACGCAGAAA
22793 CATAGAAACA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
30 11 0.27
31 8 0.20
32 22 0.54
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (32 bp):
TTAAAAACGCAGAAAACAAAATTTTTTTTAGG
Found at i:24448 original size:29 final size:30
Alignment explanation
Indices: 24411--24469 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
24401 AATTCTTCCT
* *
24411 TCTTGAAATAATTCTTCAAA-GTCTTCAAG
1 TCTTCAAATAAGTCTTCAAAGGTCTTCAAG
24440 TCTTCAAATAAGTCTTCAAATGGTCTTCAA
1 TCTTCAAATAAGTCTTCAAA-GGTCTTCAA
24470 ACACGAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 18 0.69
31 8 0.31
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (30 bp):
TCTTCAAATAAGTCTTCAAAGGTCTTCAAG
Found at i:24467 original size:11 final size:12
Alignment explanation
Indices: 24437--24470 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
24427 CAAAGTCTTC
24437 AAGTCTTCAAAT
1 AAGTCTTCAAAT
24449 AAGTCTTCAAAT
1 AAGTCTTCAAAT
*
24461 -GGTCTTCAAA
1 AAGTCTTCAAA
24471 CACGAACTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (12 bp):
AAGTCTTCAAAT
Found at i:27792 original size:42 final size:42
Alignment explanation
Indices: 27745--27829 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
27735 AACAACAATT
* *
27745 AATATTAGCTTTTTTTTGATGAATTATCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
27787 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
27829 A
1 A
27830 TTTTAGGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
Found at i:30270 original size:7 final size:7
Alignment explanation
Indices: 30258--30290 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
30248 AAATAATATT
30258 TAGTATA
1 TAGTATA
30265 TAGTATA
1 TAGTATA
30272 TAGTATA
1 TAGTATA
30279 TA-TATA
1 TAGTATA
30285 TA-TATA
1 TAGTATA
30291 AATGCTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 10 0.38
7 16 0.62
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (7 bp):
TAGTATA
Found at i:31699 original size:24 final size:24
Alignment explanation
Indices: 31649--31700 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
31639 TTAGACTCCC
* * * *
31649 GGGGATTCCATGGCTCCATGGCGA
1 GGGGACTCCATGACTCCATGACAA
31673 GGGGACTCCATGACTCCATGACAA
1 GGGGACTCCATGACTCCATGACAA
31697 GGGG
1 GGGG
31701 CGCACCTGCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.25, G:0.37, T:0.17
Consensus pattern (24 bp):
GGGGACTCCATGACTCCATGACAA
Found at i:38634 original size:10 final size:9
Alignment explanation
Indices: 38610--38667 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
38600 ATTTCTTACC
*
38610 CTTATCTTT
1 CTTATTTTT
38619 -TTATTTTT
1 CTTATTTTT
38627 CGTTATTTTT
1 C-TTATTTTT
38637 CTT-TTTCTT
1 CTTATTT-TT
38646 -TTATTTTT
1 CTTATTTTT
*
38654 GTTTATTTTT
1 -CTTATTTTT
38664 CTTA
1 CTTA
38668 GTTACTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 14 0.34
9 10 0.24
10 17 0.41
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.76
Consensus pattern (9 bp):
CTTATTTTT
Found at i:38641 original size:16 final size:17
Alignment explanation
Indices: 38616--38653 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
38606 TACCCTTATC
38616 TTTTTATTTTTC-GTTA
1 TTTTTATTTTTCTGTTA
* *
38632 TTTTTCTTTTTCTTTTA
1 TTTTTATTTTTCTGTTA
38649 TTTTT
1 TTTTT
38654 GTTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTTCTGTTA
Found at i:39832 original size:21 final size:21
Alignment explanation
Indices: 39793--39841 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
39783 TCAATGCTTT
**
39793 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
39815 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
39836 A-GAAGC
1 AGGAAGC
39842 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:44835 original size:26 final size:26
Alignment explanation
Indices: 44799--44848 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
44789 CCCTCTGAAA
*
44799 AAAAAAAAAAGAGTGTTAGTAACCTC
1 AAAAAAAAAAGAGAGTTAGTAACCTC
* *
44825 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAAAAAAAAGAGAGTTAGTAACC
44849 CCTAAATCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.10, G:0.20, T:0.16
Consensus pattern (26 bp):
AAAAAAAAAAGAGAGTTAGTAACCTC
Found at i:45907 original size:76 final size:76
Alignment explanation
Indices: 45778--45929 Score: 200
Period size: 76 Copynumber: 2.0 Consensus size: 76
45768 TGATGAGCTA
* * *
45778 TGACACAGCCCATCTGGGTGATCAGGCGAAACACATGGGTCTCCAGACAAACCATGTGGGCACCC
1 TGACACAGCCCACCTGGGTGATCAAGCGAAACACATGGGTCTCAAGACAAACCATGTGGGCACCC
45843 AGCTGGAGTCG
66 AGCTGGAGTCG
* ** *
45854 TGACACTGCCCACCTGGGTTCTCAAGC-AAACCACATGGGTGCTCAAGGC-AACCATGTGGGCAC
1 TGACACAGCCCACCTGGGTGATCAAGCGAAA-CACATGGGT-CTCAAGACAAACCATGTGGGCAC
*
45917 CCAGGTGGAGTCG
64 CCAGCTGGAGTCG
45930 GGGTCCTTGT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
75 3 0.05
76 57 0.86
77 6 0.09
ACGTcount: A:0.25, C:0.30, G:0.29, T:0.16
Consensus pattern (76 bp):
TGACACAGCCCACCTGGGTGATCAAGCGAAACACATGGGTCTCAAGACAAACCATGTGGGCACCC
AGCTGGAGTCG
Found at i:48408 original size:28 final size:29
Alignment explanation
Indices: 48375--48442 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
48365 AAGTTATATC
48375 AAGCATGTTTTGTTAGTT-AAAAAAATTG
1 AAGCATGTTTTGTTAGTTAAAAAAAATTG
48403 AAGCATGTTTTGTTAGTTAAAAAAAATTG
1 AAGCATGTTTTGTTAGTTAAAAAAAATTG
48432 AAGCATGTTTT
1 AAGCATGTTTT
48443 TGTAGTCATG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
28 18 0.46
29 21 0.54
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (29 bp):
AAGCATGTTTTGTTAGTTAAAAAAAATTG
Found at i:49228 original size:19 final size:19
Alignment explanation
Indices: 49191--49229 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
49181 TCGAAAGAAG
*
49191 GGGAAATTCGAAAATAAAA
1 GGGAAATTCGAAAACAAAA
49210 GGGAAA-TCGAAAAGCAAAA
1 GGGAAATTCGAAAA-CAAAA
49229 G
1 G
49230 CAAAAGAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.56, C:0.08, G:0.26, T:0.10
Consensus pattern (19 bp):
GGGAAATTCGAAAACAAAA
Found at i:54132 original size:22 final size:22
Alignment explanation
Indices: 54105--54152 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
54095 AAAATCTTTA
54105 TTTTAAATAAATA-ATTTTAT-AT
1 TTTTAAA-AAATACATTTT-TGAT
54127 TTTTAAAAAATACATTTTTGAT
1 TTTTAAAAAATACATTTTTGAT
54149 TTTT
1 TTTT
54153 TTAATTCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTTAAAAAATACATTTTTGAT
Found at i:54918 original size:13 final size:13
Alignment explanation
Indices: 54902--54937 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
54892 AATCAAAGTC
54902 ATAAACCAAAATA
1 ATAAACCAAAATA
*
54915 ATAAACCAGAATA
1 ATAAACCAAAATA
54928 ATAAACCAAA
1 ATAAACCAAA
54938 CAATTAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.67, C:0.17, G:0.03, T:0.14
Consensus pattern (13 bp):
ATAAACCAAAATA
Done.