Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014364.1 Corchorus olitorius cultivar O-4 contig14397, 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: 53902
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--30 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31 CGTAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1842 original size:21 final size:22
Alignment explanation
Indices: 1813--1860 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
1803 TTCATTTATT
1813 AACAATATTAAAATTAAA-AAA
1 AACAATATTAAAATTAAATAAA
*
1834 AACAGTATTAAAATTAAATTAAA
1 AACAATATTAAAATTAAA-TAAA
1857 AACA
1 AACA
1861 CATTAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 17 0.71
23 7 0.29
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (22 bp):
AACAATATTAAAATTAAATAAA
Found at i:2445 original size:16 final size:16
Alignment explanation
Indices: 2424--2472 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
2414 CAAGGGAAGC
2424 TTCTTTCCTTCCCCAT
1 TTCTTTCCTTCCCCAT
*
2440 TTCTTTCC-ACCCC-T
1 TTCTTTCCTTCCCCAT
2454 CTTCTTTCCTT-CCCAT
1 -TTCTTTCCTTCCCCAT
2470 TTC
1 TTC
2473 CACTCTACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 1 0.04
15 18 0.64
16 9 0.32
ACGTcount: A:0.06, C:0.45, G:0.00, T:0.49
Consensus pattern (16 bp):
TTCTTTCCTTCCCCAT
Found at i:2860 original size:15 final size:15
Alignment explanation
Indices: 2837--2878 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
2827 AAGTAACCTT
*
2837 TTTCCTTCCTTCCCC
1 TTTCTTTCCTTCCCC
2852 TTTCTTTCC-TCCCC
1 TTTCTTTCCTTCCCC
2866 TCTTCTTTCCTTC
1 T-TTCTTTCCTTC
2879 TCATTTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 16 0.67
16 2 0.08
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTCTTTCCTTCCCC
Found at i:24339 original size:1 final size:1
Alignment explanation
Indices: 24335--24361 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
24325 AAAAAAGGTC
24335 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
24362 GACAATCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28623 original size:15 final size:15
Alignment explanation
Indices: 28599--28629 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28589 AGAAATAGAC
*
28599 TTTCTTAAAGCAGTT
1 TTTCTAAAAGCAGTT
28614 TTTCTAAAAGCAGTT
1 TTTCTAAAAGCAGTT
28629 T
1 T
28630 CTGCATAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (15 bp):
TTTCTAAAAGCAGTT
Found at i:30357 original size:18 final size:18
Alignment explanation
Indices: 30336--30370 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
30326 CATTGTAATT
30336 GTTAGGGATTTTGTTTAA
1 GTTAGGGATTTTGTTTAA
30354 GTTAGGGATTTTGTTTA
1 GTTAGGGATTTTGTTTA
30371 GATTAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (18 bp):
GTTAGGGATTTTGTTTAA
Found at i:30629 original size:8 final size:8
Alignment explanation
Indices: 30618--30653 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
30608 AAAACTTAAA
30618 AAAAAAGG
1 AAAAAAGG
30626 AAAAAAGG
1 AAAAAAGG
30634 AAAAAAGG
1 AAAAAAGG
30642 AAAAAAAGG
1 -AAAAAAGG
30651 AAA
1 AAA
30654 GAATGATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:30637 original size:16 final size:17
Alignment explanation
Indices: 30618--30653 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
30608 AAAACTTAAA
30618 AAAAAAGG-AAAAAAGG
1 AAAAAAGGAAAAAAAGG
30634 AAAAAAGGAAAAAAAGG
1 AAAAAAGGAAAAAAAGG
30651 AAA
1 AAA
30654 GAATGATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAAAAGGAAAAAAAGG
Found at i:32597 original size:36 final size:37
Alignment explanation
Indices: 32549--32622 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
32539 ATCGAATCTG
** *
32549 AATTGGAAAACTCTCCTGACGCCTGTTTTCTCCATTC
1 AATTGGAAAACTCTCCCAACGCCTATTTTCTCCATTC
*
32586 AATT-GAAAACTCTCCCAACGCTTATTTTCTCCATTC
1 AATTGGAAAACTCTCCCAACGCCTATTTTCTCCATTC
32622 A
1 A
32623 CTAAGTCCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 29 0.88
37 4 0.12
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.35
Consensus pattern (37 bp):
AATTGGAAAACTCTCCCAACGCCTATTTTCTCCATTC
Found at i:36430 original size:7 final size:7
Alignment explanation
Indices: 36416--36446 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
36406 TTTTACATGA
36416 TTTAACC
1 TTTAACC
*
36423 TCTAACC
1 TTTAACC
36430 TTTAACC
1 TTTAACC
36437 TTTAACC
1 TTTAACC
36444 TTT
1 TTT
36447 CATATAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (7 bp):
TTTAACC
Found at i:37142 original size:17 final size:19
Alignment explanation
Indices: 37112--37147 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
37102 AGTAGTTTTT
37112 GGCAGTTCTTTTTA-AATG
1 GGCAGTTCTTTTTAGAATG
37130 GGCAGTT-TTTTTAGAATG
1 GGCAGTTCTTTTTAGAATG
37148 ATATAAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.22, C:0.08, G:0.25, T:0.44
Consensus pattern (19 bp):
GGCAGTTCTTTTTAGAATG
Found at i:37208 original size:19 final size:20
Alignment explanation
Indices: 37184--37221 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
37174 ATTTATCTTG
*
37184 AAATGGGTAG-TTTTATTTA
1 AAATGGATAGTTTTTATTTA
37203 AAATGGATAGTTTTTATTT
1 AAATGGATAGTTTTTATTT
37222 TGTTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (20 bp):
AAATGGATAGTTTTTATTTA
Found at i:37295 original size:13 final size:13
Alignment explanation
Indices: 37279--37306 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
37269 CACAAACTTT
37279 ATAATTAGTATAG
1 ATAATTAGTATAG
37292 ATAATTAGTATAG
1 ATAATTAGTATAG
37305 AT
1 AT
37307 TCTTTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (13 bp):
ATAATTAGTATAG
Found at i:38362 original size:16 final size:16
Alignment explanation
Indices: 38341--38374 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
38331 GTTCAATTTC
*
38341 AATAAATATGGAACAA
1 AATAAACATGGAACAA
*
38357 AATAAACATGGAAGAA
1 AATAAACATGGAACAA
38373 AA
1 AA
38375 GCTTAAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.15, T:0.15
Consensus pattern (16 bp):
AATAAACATGGAACAA
Found at i:39314 original size:2 final size:2
Alignment explanation
Indices: 39307--39338 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
39297 TAAGTACACT
*
39307 AG AG AG AG AG AG AG AG AG AG AG AC AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39339 TTCAGGTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42155 original size:27 final size:28
Alignment explanation
Indices: 42103--42155 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
42093 CAGTTAGGAA
* *
42103 AAAATATAAAGTCTGCCAAGATAAAAGC
1 AAAATAAAAAGTCTGCCAAGAAAAAAGC
*
42131 AAAATAAAAAGT-TGCCAATAAAAAA
1 AAAATAAAAAGTCTGCCAAGAAAAAA
42156 ATAAAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.17
Consensus pattern (28 bp):
AAAATAAAAAGTCTGCCAAGAAAAAAGC
Found at i:42156 original size:28 final size:28
Alignment explanation
Indices: 42103--42156 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
42093 CAGTTAGGAA
* * *
42103 AAAATATAAAGTCTGCCAAGATAAAAGC
1 AAAATAAAAAGTCTGCCAAAAAAAAAGC
42131 AAAATAAAAAGT-TGCCAATAAAAAAA
1 AAAATAAAAAGTCTGCCAA-AAAAAAA
42157 TAAAAACAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.17
Consensus pattern (28 bp):
AAAATAAAAAGTCTGCCAAAAAAAAAGC
Found at i:42161 original size:27 final size:28
Alignment explanation
Indices: 42103--42161 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
42093 CAGTTAGGAA
* * *
42103 AAAATATAAAGTCTGCCAAGATAAAAGC
1 AAAATAAAAAGTCTGCCAAGAAAAAAAC
* *
42131 AAAATAAAAAGT-TGCCAATAAAAAAAT
1 AAAATAAAAAGTCTGCCAAGAAAAAAAC
42158 AAAA
1 AAAA
42162 ACAATAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.17
Consensus pattern (28 bp):
AAAATAAAAAGTCTGCCAAGAAAAAAAC
Found at i:46004 original size:77 final size:77
Alignment explanation
Indices: 45874--46031 Score: 307
Period size: 77 Copynumber: 2.1 Consensus size: 77
45864 CGTTAATTTA
45874 GAATATAACGTTATTAAATTGTGTCAATTTAATATAAAATGATCTTTAACTTCTGTGCGTTCGGA
1 GAATATAACGTTATTAAATTGTGTCAATTTAATATAAAATGATCTTTAACTTCTGTGCGTTCGGA
45939 CATACTGACTTG
66 CATACTGACTTG
*
45951 GAATATAACGTTATTAAATTGTGTCAATTTAATATAAAATGATCTTTAGCTTCTGTGCGTTCGGA
1 GAATATAACGTTATTAAATTGTGTCAATTTAATATAAAATGATCTTTAACTTCTGTGCGTTCGGA
46016 CATACTGACTTG
66 CATACTGACTTG
46028 GAAT
1 GAAT
46032 GGCAAAGCCA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (77 bp):
GAATATAACGTTATTAAATTGTGTCAATTTAATATAAAATGATCTTTAACTTCTGTGCGTTCGGA
CATACTGACTTG
Found at i:49285 original size:19 final size:20
Alignment explanation
Indices: 49256--49293 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
49246 AATTCAAAAC
49256 AAAATAAAAACTACTCATTT
1 AAAATAAAAACTACTCATTT
49276 AAAA-AAAAACTACTCATT
1 AAAATAAAAACTACTCATT
49294 AGAGGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAAAAACTACTCATTT
Found at i:50286 original size:24 final size:24
Alignment explanation
Indices: 50259--50307 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
50249 TTTTTTATTT
* *
50259 TTTATTCTTTTCTTCTCCGTTTTC
1 TTTATTCTCTTCTTCTCCATTTTC
50283 TTTATTCTCTTCTTCTCCATTTTC
1 TTTATTCTCTTCTTCTCCATTTTC
50307 T
1 T
50308 GCTTCGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.06, C:0.27, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTATTCTCTTCTTCTCCATTTTC
Found at i:52682 original size:21 final size:20
Alignment explanation
Indices: 52666--52706 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
52656 TCCCCAAAGT
52666 AATATA-CT-TTATACCCAA
1 AATATATCTATTATACCCAA
52684 AATATATCTCATTATACCCAA
1 AATATATCT-ATTATACCCAA
52705 AA
1 AA
52707 ACTTATATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 2 0.10
21 12 0.60
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (20 bp):
AATATATCTATTATACCCAA
Found at i:52842 original size:224 final size:220
Alignment explanation
Indices: 52446--53137 Score: 1050
Period size: 224 Copynumber: 3.2 Consensus size: 220
52436 CGACGTGGTA
*
52446 ACTTCATACCCAAAATATATCTCATTATACCCAAAAACTTATATGCACCATCCCCAAATTCAATA
1 ACTTTATACCCAAAATATATCTCATTATACCCAAAAACTTATATGCACCATCCCCAAATTCAATA
*
52511 GTGATTGACATTTTTTTCTCATATATCCAAAATTGGATTTAAAAAGTGCTTCAATCCATATTTTT
66 GTGATTGACA-TTTTTTCTCATATATCCAAAATT-GATTT-AAAAGTGCTTTAATCCATATTTTT
*
52576 CATTCTAATTAATTGAATAAACCCCGTCTATATGGATTTCAGTGCCATTTAATAATTAAACAAAA
128 CATTCTAATTAATTGAATAAACCCCGTCTATAT-GATTTCAGTGCCATCTAATAATTAAACAAAA
*
52641 TGCAAACAAAT-AGTATCCCCAAAGTAATAT
192 TGC-AA-AATTCAGTATCCCCAAAGTAATAT
52671 ACTTTATACCCAAAATATATCTCATTATACCCAAAAACTTATATGCACCATCCCCAAATTCAATA
1 ACTTTATACCCAAAATATATCTCATTATACCCAAAAACTTATATGCACCATCCCCAAATTCAATA
*
52736 GTGATTGGCATTTTTTCTCATATATCCAAAATTGATTTGAAATAGTGCTTTAATCCATATTTTTC
66 GTGATTGACATTTTTTCTCATATATCCAAAATTGATTT-AAA-AGTGCTTTAATCCATATTTTTC
* * *
52801 ATTCTAATTTATTGAATAAAACCCGTCTATATGAATTTCAGTGCCATCTAATAATTAAACATAAT
129 ATTCTAATTAATTGAATAAACCCCGTCTATATG-ATTTCAGTGCCATCTAATAATTAAACAAAAT
52866 GCAAAATTCAGTATCCCCAAAGTAATAT
193 GCAAAATTCAGTATCCCCAAAGTAATAT
*
52894 ACTTTATACCCAAAATATATTTCATTATACCCAAAAACTTATATGC-CCATCCCCAAATTCAATA
1 ACTTTATACCCAAAATATATCTCATTATACCCAAAAACTTATATGCACCATCCCCAAATTCAATA
*
52958 GTGATTGACATTTTTTCTCATATACCCAAAATTGACTTTAAAAGGTG-TTT--T--A-A---TTC
66 GTGATTGACATTTTTTCTCATATATCCAAAATTGA-TTTAAAA-GTGCTTTAATCCATATTTTTC
* * * * *
53014 A-TAT-ATTAATTGAATAAACCCCGTCTATATGATTTTAGTGACATCTAATAATTAACCAAAATA
129 ATTCTAATTAATTGAATAAACCCCGTCTATATGATTTCAGTGCCATCTAATAATTAAACAAAATG
53077 CAAAATTCAGTATCCCCAAAGTAATAT
194 CAAAATTCAGTATCCCCAAAGTAATAT
*
53104 ACTTTATACCCAAAATATATCTCAATATACCCAA
1 ACTTTATACCCAAAATATATCTCATTATACCCAA
53138 GAAAATGACG
Statistics
Matches: 440, Mismatches: 22, Indels: 25
0.90 0.05 0.05
Matches are distributed among these distances:
210 86 0.20
211 25 0.06
212 2 0.00
213 4 0.01
216 1 0.00
217 1 0.00
219 1 0.00
221 4 0.01
222 60 0.14
223 78 0.18
224 105 0.24
225 73 0.17
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.35
Consensus pattern (220 bp):
ACTTTATACCCAAAATATATCTCATTATACCCAAAAACTTATATGCACCATCCCCAAATTCAATA
GTGATTGACATTTTTTCTCATATATCCAAAATTGATTTAAAAGTGCTTTAATCCATATTTTTCAT
TCTAATTAATTGAATAAACCCCGTCTATATGATTTCAGTGCCATCTAATAATTAAACAAAATGCA
AAATTCAGTATCCCCAAAGTAATAT
Done.