Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012641.1 Corchorus olitorius cultivar O-4 contig12674, 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: 34488
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:7810 original size:21 final size:22
Alignment explanation
Indices: 7769--7810 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
7759 TGGTAAAAGT
7769 CATTTGCAATTCATATAGTATG
1 CATTTGCAATTCATATAGTATG
7791 CATTTGTC-ATTCAT-TAGTAT
1 CATTTG-CAATTCATATAGTAT
7811 ATATGCATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 12 0.63
23 1 0.05
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (22 bp):
CATTTGCAATTCATATAGTATG
Found at i:9414 original size:26 final size:27
Alignment explanation
Indices: 9383--9458 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 27
9373 GGAGAGGGAA
9383 GAAAAAGAAAAATGAAGAAAAGAA-TT
1 GAAAAAGAAAAATGAAGAAAAGAAGTT
*
9409 GAAAAAG-AAAA-GAAAAGAAAGAAGTT
1 GAAAAAGAAAAATGAAGA-AAAGAAGTT
* *
9435 GAAAAAACAAAAGATGGAGAAAAG
1 G-AAAAAGAAAA-ATGAAGAAAAG
9459 GATGAATTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
24 4 0.10
25 10 0.25
26 10 0.25
27 5 0.12
28 3 0.08
29 5 0.12
30 3 0.08
ACGTcount: A:0.68, C:0.01, G:0.22, T:0.08
Consensus pattern (27 bp):
GAAAAAGAAAAATGAAGAAAAGAAGTT
Found at i:9715 original size:42 final size:42
Alignment explanation
Indices: 9630--9715 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
9620 ATGAAAAATA
* ** ** *
9630 TTTTCTTCAAAGTGTGATCTTTTCAAAAGAAAAAGGTTTTTT
1 TTTTCCTCAAAGTGCAATCTTTTCAAAAGAAAAAGAATGTTT
9672 TTTTCCTCAAAGTGCAATCTTTTCAAAAGAGAAAA-AATGTTT
1 TTTTCCTCAAAGTGCAATCTTTTCAAAAGA-AAAAGAATGTTT
9714 TT
1 TT
9716 CAAAAAGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
42 33 0.89
43 4 0.11
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42
Consensus pattern (42 bp):
TTTTCCTCAAAGTGCAATCTTTTCAAAAGAAAAAGAATGTTT
Found at i:10895 original size:52 final size:53
Alignment explanation
Indices: 10827--10963 Score: 143
Period size: 54 Copynumber: 2.6 Consensus size: 53
10817 TCTTTTAAAG
* * * *
10827 TTTTCAGAGATCTAAGTT-AACGTTC-ATGGCTCTGTGCGGTCTTTCATAGAAA
1 TTTTCAGAGATTTAAGTTGAAC-TTCAATGACCCTGCGCGGTCTTTCATAGAAA
* * **
10879 TTTTCAGAGATTTAAGTTGATCTTCAGATGACCCTGCGTGGTCTTTCATAGAGG
1 TTTTCAGAGATTTAAGTTGAACTTCA-ATGACCCTGCGCGGTCTTTCATAGAAA
* *
10933 TTTTCAGAGGTTTAAGTTGATCTTCAGATGA
1 TTTTCAGAGATTTAAGTTGAACTTCA-ATGA
10964 TCTAGTGCGG
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
52 20 0.27
53 2 0.03
54 51 0.70
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (53 bp):
TTTTCAGAGATTTAAGTTGAACTTCAATGACCCTGCGCGGTCTTTCATAGAAA
Found at i:11027 original size:55 final size:55
Alignment explanation
Indices: 10947--11066 Score: 147
Period size: 55 Copynumber: 2.2 Consensus size: 55
10937 CAGAGGTTTA
* * *
10947 AGTTGATCT-TCAGATGATCTAGTGCGGT-TCTTCCGAAGAAGTTTTCGAAGATTAG
1 AGTTGATCTCT-AGATGATCTAGTGCGGTCT-TTCAGAAAAAGTTTTCGAAGATCAG
* *
11002 AGTTTATCTCTAGATGATCCT-GTGCGGTCTTTCAGAAAAAGTTTTCGATGATCAG
1 AGTTGATCTCTAGATGAT-CTAGTGCGGTCTTTCAGAAAAAGTTTTCGAAGATCAG
11057 AGTTGATCTC
1 AGTTGATCTC
11067 ATTTCAAGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
55 52 0.93
56 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (55 bp):
AGTTGATCTCTAGATGATCTAGTGCGGTCTTTCAGAAAAAGTTTTCGAAGATCAG
Found at i:11088 original size:35 final size:35
Alignment explanation
Indices: 11040--11302 Score: 336
Period size: 35 Copynumber: 7.5 Consensus size: 35
11030 CTTTCAGAAA
*
11040 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
1 AAGTTTTCTATGATCAGAGTTGATCTCATTTCAAG
** *
11075 AAACTTTCTATGATCAGAGTTGATCTCGTTTCAAG
1 AAGTTTTCTATGATCAGAGTTGATCTCATTTCAAG
*
11110 AAG-TTT-TATGATCAGAGTTGA-CTCCTTTCAAG
1 AAGTTTTCTATGATCAGAGTTGATCTCATTTCAAG
*
11142 AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG
1 AAGTTTTCTATGATCAGAGTTGATCTCATTTCAAG
* * *
11177 AAGTTTTCGATGATCAGAGTTGATCACCTTTCAAG
1 AAGTTTTCTATGATCAGAGTTGATCTCATTTCAAG
* * * *
11212 AAGTTTTTTATGATCAGAGTTGATTTTATTTGAAG
1 AAGTTTTCTATGATCAGAGTTGATCTCATTTCAAG
*
11247 AAGTTTTCGT-TGATCAGAGTTGATCTCATCTCAAG
1 AAGTTTTC-TATGATCAGAGTTGATCTCATTTCAAG
*
11282 AAGTTTTTTTAATGATCAGAG
1 AAG-TTTTCT-ATGATCAGAG
11303 AAGTTTTTTA
Statistics
Matches: 198, Mismatches: 23, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
32 13 0.07
33 18 0.09
34 17 0.09
35 136 0.69
36 5 0.03
37 9 0.05
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (35 bp):
AAGTTTTCTATGATCAGAGTTGATCTCATTTCAAG
Found at i:11315 original size:19 final size:21
Alignment explanation
Indices: 11280--11321 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
11270 TCTCATCTCA
11280 AGAAGTTTTTTTAATGATCAG
1 AGAAGTTTTTTTAATGATCAG
11301 AGAAG-TTTTTT-ATGATCAG
1 AGAAGTTTTTTTAATGATCAG
11320 AG
1 AG
11322 TTGATCTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.48
20 6 0.29
21 5 0.24
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.40
Consensus pattern (21 bp):
AGAAGTTTTTTTAATGATCAG
Found at i:11319 original size:91 final size:91
Alignment explanation
Indices: 11210--11379 Score: 268
Period size: 91 Copynumber: 1.9 Consensus size: 91
11200 TCACCTTTCA
* * * * *
11210 AGAAGTTTTTTATGATCAGAGTTGATTTTATTTGAAGAAGTTTTCGTTGATCAGAGTTGATCTCA
1 AGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTCCGATGATCAGAGTTGATCTCA
11275 TCTCAAGAAGTTTTTTTAATGATCAG
66 TCTCAAGAAGTTTTTTTAATGATCAG
* *
11301 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTCCGATGATTAGAGTTGATCTCA
1 AGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTCCGATGATCAGAGTTGATCTCA
*
11366 TTTCAAGAAGTTTT
66 TCTCAAGAAGTTTT
11380 CAATAATCAG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 71 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (91 bp):
AGAAGTTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTCCGATGATCAGAGTTGATCTCA
TCTCAAGAAGTTTTTTTAATGATCAG
Found at i:11351 original size:35 final size:35
Alignment explanation
Indices: 11301--11909 Score: 871
Period size: 35 Copynumber: 17.4 Consensus size: 35
11291 TAATGATCAG
** *
11301 AGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
* *
11336 AGAAGTTTCCGATGATTAGAGTTGATCTCATTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
* *
11371 AGAAGTTTTCAATAATCAGAGTTGATCTCATTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
* *
11406 AGAAGTTTTCAATGATCAGAGTTGATCTCGTTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
* *
11441 AGAAGTTTTTGATGATCAGAGTTGATCTCGTTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
* * *
11476 AGAAGTATTT-TATGATCAGATTTGTTCTCATTTCA
1 AGAAGT-TTTCGATGATCAGAGTTGATCTCATTTCA
** *
11511 AGAAGTTTTTTATGA-CTAGAGTTGATCTCGTTTCA
1 AGAAGTTTTCGATGATC-AGAGTTGATCTCATTTCA
*
11546 AGAAGGTTTCGATGATCAGAGTTGATCTCATTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
*
11581 AGAAGTTTTCAATGATCAGAGTTGATCTCATTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
** * * *
11616 AGAAGTTTTTTATGATTAGAGTTGATCTCCTTTCG
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
* *
11651 GGAAGTTTTCAATGATCAGAGTTGATCTCATTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
** *
11686 AGAAGTTTTTTATGATCAGAGTTGATCTCGTTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
* *
11721 AGAAGTTTTTGATGATCAGAGCTGATCTCATTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
*
11756 AGAAGTTTTCAATGATCAGAGTTGATCTCATTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
*
11791 AGAAGTTTTCAATGATCAGAGTTGATCTCATTTCA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
11826 AGGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
1 A-GAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
*
11862 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTTA
1 AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
11897 AGAAGTTTTCGAT
1 AGAAGTTTTCGAT
11910 CAAGTTGGTC
Statistics
Matches: 520, Mismatches: 49, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
34 4 0.01
35 478 0.92
36 38 0.07
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.39
Consensus pattern (35 bp):
AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCA
Found at i:13456 original size:11 final size:11
Alignment explanation
Indices: 13440--13540 Score: 50
Period size: 11 Copynumber: 9.2 Consensus size: 11
13430 TTTATTACAG
13440 TTATTTATCTA
1 TTATTTATCTA
*
13451 TTATTTATTTA
1 TTATTTATCTA
* * *
13462 CTATTTCT-TT
1 TTATTTATCTA
13472 TTATTTA--T-
1 TTATTTATCTA
*
13480 TTATTTAGCTA
1 TTATTTATCTA
* *
13491 TTATCTATTTA
1 TTATTTATCTA
13502 TTTAACTATTATCTA
1 -TT-A-T-TTATCTA
13517 TTTATTTA-CTA
1 -TTATTTATCTA
*
13528 TTATTTATTTA
1 TTATTTATCTA
13539 TT
1 TT
13541 TATGTATTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
8 7 0.10
9 1 0.01
10 14 0.20
11 31 0.44
12 5 0.07
13 2 0.03
14 2 0.03
15 8 0.11
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.65
Consensus pattern (11 bp):
TTATTTATCTA
Found at i:13499 original size:19 final size:18
Alignment explanation
Indices: 13440--13542 Score: 107
Period size: 19 Copynumber: 5.4 Consensus size: 18
13430 TTTATTACAG
*
13440 TTATTTATCTATTATTTAT
1 TTATTTA-CTATTATCTAT
* * *
13459 TTACTATTTCTTTTTATTTAT
1 TTA-T-TTAC-TATTATCTAT
13480 TTATTTAGCTATTATCTAT
1 TTATTTA-CTATTATCTAT
13499 TTATTTAACTATTATCTAT
1 TTATTT-ACTATTATCTAT
*
13518 TTATTTACTATTATTTAT
1 TTATTTACTATTATCTAT
13536 TTATTTA
1 TTATTTA
13543 TGTATTTATT
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
18 18 0.25
19 36 0.49
20 5 0.07
21 14 0.19
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.65
Consensus pattern (18 bp):
TTATTTACTATTATCTAT
Found at i:13560 original size:4 final size:4
Alignment explanation
Indices: 13440--13553 Score: 78
Period size: 4 Copynumber: 29.5 Consensus size: 4
13430 TTTATTACAG
* * *
13440 TTAT TTAT CTA- TTAT TTAT TTA- CTAT TT-C TT-T TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * *
13484 TTAG CTA- TTAT CTAT TTAT TTAA CTA- TTAT CTAT TTAT TTACT ATTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T -TTAT
*
13532 TTAT TTAT TTAT GTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TT
13554 TTATTTACCT
Statistics
Matches: 85, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
3 12 0.14
4 68 0.80
5 2 0.02
6 3 0.04
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (4 bp):
TTAT
Found at i:16619 original size:34 final size:34
Alignment explanation
Indices: 16581--16662 Score: 157
Period size: 34 Copynumber: 2.4 Consensus size: 34
16571 TATTCTCCGT
16581 ATGGCTCGGTGCTTGCCCAGGCCATGGCCTCGGC
1 ATGGCTCGGTGCTTGCCCAGGCCATGGCCTCGGC
16615 ATGGCTCGGTGCTTGCCCAGGCCATGGCCTCGGC
1 ATGGCTCGGTGCTTGCCCAGGCCATGGCCTCGGC
16649 ATGGCT-GGTGCTTG
1 ATGGCTCGGTGCTTG
16663 TCTCGGCATG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 8 0.17
34 40 0.83
ACGTcount: A:0.09, C:0.32, G:0.37, T:0.23
Consensus pattern (34 bp):
ATGGCTCGGTGCTTGCCCAGGCCATGGCCTCGGC
Found at i:16668 original size:21 final size:22
Alignment explanation
Indices: 16643--16684 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
16633 AGGCCATGGC
16643 CTCGGCATGGCT-GGTGCTTGT
1 CTCGGCATGGCTCGGTGCTTGT
16664 CTCGGCATGGCTCGGTGCTTG
1 CTCGGCATGGCTCGGTGCTTG
16685 CCGGCTATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.05, C:0.26, G:0.38, T:0.31
Consensus pattern (22 bp):
CTCGGCATGGCTCGGTGCTTGT
Found at i:26238 original size:8 final size:7
Alignment explanation
Indices: 26235--26279 Score: 54
Period size: 7 Copynumber: 6.0 Consensus size: 7
26225 GATTTTTCAT
26235 TTTTTTC
1 TTTTTTC
26242 TTTTTTC
1 TTTTTTC
26249 TAATTTTTC
1 T--TTTTTC
26258 TTTTCTTC
1 TTTT-TTC
26266 TTTTTTC
1 TTTTTTC
*
26273 ATTTTTC
1 TTTTTTC
26280 ATCAAATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 20 0.59
8 7 0.21
9 7 0.21
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTTC
Found at i:26246 original size:16 final size:15
Alignment explanation
Indices: 26227--26271 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
26217 AATTTTCTGA
26227 TTTTTCATTTTTTTCT
1 TTTTTC-TTTTTTTCT
*
26243 TTTTTCTAATTTTTCT
1 TTTTTCT-TTTTTTCT
26259 TTTCTTCTTTTTT
1 TTT-TTCTTTTTT
26272 CATTTTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 1 0.04
16 20 0.80
17 4 0.16
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTCTTTTTTTCT
Found at i:26277 original size:16 final size:14
Alignment explanation
Indices: 26235--26279 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 14
26225 GATTTTTCAT
26235 TTTTTTCTTTTTTC
1 TTTTTTCTTTTTTC
26249 TAATTTTTCTTTTCTTC
1 T--TTTTTCTTTT-TTC
*
26266 TTTTTTCATTTTTC
1 TTTTTTCTTTTTTC
26280 ATCAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 9 0.33
16 10 0.37
17 4 0.15
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTCTTTTTTC
Done.