Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015806.1 Corchorus olitorius cultivar O-4 contig15839, 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: 28791
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:799 original size:15 final size:15
Alignment explanation
Indices: 769--810 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
759 TTACTTTGTT
769 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
785 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
800 TTGTTTTCTGT
1 TTGTTTTCTGT
811 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:7973 original size:15 final size:15
Alignment explanation
Indices: 7943--7984 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
7933 TTACTTTGTT
7943 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
7959 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
7974 TTGTTTTCTGT
1 TTGTTTTCTGT
7985 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:12130 original size:22 final size:23
Alignment explanation
Indices: 12104--12149 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
12094 CGGTGCAAAT
*
12104 GGGTCAGTTTAAACAGTTT-TTG
1 GGGTCAGTGTAAACAGTTTCTTG
* *
12126 GGGTCGGTGTAAACGGTTTCTTG
1 GGGTCAGTGTAAACAGTTTCTTG
12149 G
1 G
12150 TCGGTGGGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.17, C:0.11, G:0.35, T:0.37
Consensus pattern (23 bp):
GGGTCAGTGTAAACAGTTTCTTG
Found at i:12265 original size:13 final size:14
Alignment explanation
Indices: 12247--12337 Score: 53
Period size: 16 Copynumber: 6.3 Consensus size: 14
12237 ATATTTGTTT
12247 TATAATTAATTATA
1 TATAATTAATTATA
12261 T-TAATT-A-TATA
1 TATAATTAATTATA
12272 TATAATATAATTATAA
1 TATAAT-TAATTAT-A
** * *
12288 TATATATTTTGTTTTT
1 TATA-A-TTAATTATA
* *
12304 TATGATTAATCATA
1 TATAATTAATTATA
12318 TATAATATAATTATAA
1 TATAAT-TAATTAT-A
12334 TATA
1 TATA
12338 TAAATTTAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
11 5 0.09
12 5 0.09
13 6 0.11
14 11 0.20
15 10 0.18
16 13 0.23
17 5 0.09
18 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (14 bp):
TATAATTAATTATA
Found at i:12273 original size:23 final size:21
Alignment explanation
Indices: 12224--12273 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
12214 TAAATATTTA
**
12224 TATATATAATTATATATTTGT
1 TATATATAATTATATATTAAT
12245 T-T-TATAATTAATTATATTAAT
1 TATATATAATT-A-TATATTAAT
12266 TATATATA
1 TATATATA
12274 TAATATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
19 7 0.30
20 2 0.09
21 9 0.39
22 1 0.04
23 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TATATATAATTATATATTAAT
Found at i:12334 original size:57 final size:55
Alignment explanation
Indices: 12228--12337 Score: 136
Period size: 57 Copynumber: 2.0 Consensus size: 55
12218 TATTTATATA
*
12228 TATAATTATATATTTGTTTTATAATTAATTATATTAATTATATATATAATATAAT
1 TATAATTATATATTTGTTTTATAATTAATCATATTAATTATATATATAATATAAT
*
12283 TATAA-TATATATTTTGTTTTTTATGATTAATCATATATAA-TATA-ATTATAATATA
1 TATAATTATATA-TTTG--TTTTATAATTAATCATAT-TAATTATATA-TATAATATA
12338 TAAATTTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
54 6 0.12
55 9 0.19
56 1 0.02
57 29 0.60
58 3 0.06
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (55 bp):
TATAATTATATATTTGTTTTATAATTAATCATATTAATTATATATATAATATAAT
Found at i:12359 original size:18 final size:18
Alignment explanation
Indices: 12308--12361 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
12298 GTTTTTTATG
*
12308 ATTAATCATATATAATATAA
1 ATTAAT-ATATA-AATTTAA
*
12328 TTATAATATATAAATTTAA
1 AT-TAATATATAAATTTAA
12347 ATTAATATATAAATT
1 ATTAATATATAAATT
12362 CATTCAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 13 0.43
19 7 0.23
20 6 0.20
21 4 0.13
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTAATATATAAATTTAA
Found at i:14045 original size:16 final size:16
Alignment explanation
Indices: 14026--14077 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
14016 TCGTTTGGTA
14026 TTGTTTTCGTTTTTTT
1 TTGTTTTCGTTTTTTT
* *
14042 TTGTTTTTGTTTATATT
1 TTGTTTTCGTTT-TTTT
*
14059 TCGTTTTCGTTTTATTT
1 TTGTTTTCGTTTT-TTT
14076 TT
1 TT
14078 ATTGCGTTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.77
Consensus pattern (16 bp):
TTGTTTTCGTTTTTTT
Found at i:14064 original size:17 final size:16
Alignment explanation
Indices: 14028--14075 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
14018 GTTTGGTATT
* *
14028 GTTTTCGTTTTTTTTT
1 GTTTTCGTTTTATTTC
*
14044 GTTTTTGTTTATATTTC
1 GTTTTCGTTT-TATTTC
14061 GTTTTCGTTTTATTT
1 GTTTTCGTTTTATTT
14076 TTATTGCGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.75
Consensus pattern (16 bp):
GTTTTCGTTTTATTTC
Found at i:14080 original size:22 final size:23
Alignment explanation
Indices: 14046--14098 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
14036 TTTTTTTTGT
* * *
14046 TTTTGTTTATATTTCGTTTTC-G
1 TTTTATTTATATTGCGTTGTCAG
*
14068 TTTTATTTTTATTGCGTTGTCAG
1 TTTTATTTATATTGCGTTGTCAG
14091 TTTT-TTTA
1 TTTTATTTA
14099 AAAACATTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.11, C:0.08, G:0.13, T:0.68
Consensus pattern (23 bp):
TTTTATTTATATTGCGTTGTCAG
Found at i:14415 original size:42 final size:42
Alignment explanation
Indices: 14356--14436 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
14346 TAAGGATTAG
14356 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
14398 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
14437 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:20070 original size:240 final size:238
Alignment explanation
Indices: 19647--20126 Score: 784
Period size: 240 Copynumber: 2.0 Consensus size: 238
19637 TTTTGCATCA
* * * *
19647 ATTTGGTGCAAAAAAGAAATTTGGGGGAAATATCTTTACACCAAATATTTTTTCTGCAACATTTT
1 ATTTGGTGCAAAAAAGAAATTTGAGAGAAATATCTTTACACCAAATATTTTTTCTCCAACATGTT
* * * *
19712 GCATCAAATTGGTGTTATAATTATTTAACTTTTTATAATATTTTTTATTTTTAGAGTATGATTAC
66 GCACCAAATCGGTATTATAATTATTTAACTTTTTATAATATTTTTTATCTTTAGAGTATGATTAC
* *
19777 AAATTTACCCCTATGTAAATCAAGTCCTTCCATTTTGAAGGTACACCTTTTTCTTTTCAATGTGT
131 AAATTTACCCCTATATAAATCAAGTCCTTCCATTTTGAAGGTACACATTTTTCTTTTCAATGTGT
19842 AAAATAAATTTATATCTATATAATAAAAATAATATTAAATATCT
196 AAAATAAATTTATATCTATATAATAAAAATAATATT-AATATCT
* *
19886 ATTTGGTGCAAAAAAGAAATCTTGAGAG-AATATCTTTGCACCAAATATTTTTTGCTCCAACGTG
1 ATTTGGTGCAAAAAAGAAAT-TTGAGAGAAATATCTTTACACCAAATATTTTTT-CTCCAACATG
*
19950 TTGCACCAAATCGGTATTATAATTATTTAACTTTTTATAACTA-TTTTTATCTTTGGAGTATGAT
64 TTGCACCAAATCGGTATTATAATTATTTAACTTTTTATAA-TATTTTTTATCTTTAGAGTATGAT
*
20014 TACAAATTTACCCCTATATAAGTCAAGTCCTTCCATTTTGAAGGTACACATTTTTCTTTTCAATG
128 TACAAATTTACCCCTATATAAATCAAGTCCTTCCATTTTGAAGGTACACATTTTTCTTTTCAATG
20079 TGTAAAATAAATTTATATCTATATAATAAAAATAATATTAATATCT
193 TGTAAAATAAATTTATATCTATATAATAAAAATAATATTAATATCT
20125 AT
1 AT
20127 ATGATTATTA
Statistics
Matches: 224, Mismatches: 14, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
239 53 0.24
240 169 0.75
241 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (238 bp):
ATTTGGTGCAAAAAAGAAATTTGAGAGAAATATCTTTACACCAAATATTTTTTCTCCAACATGTT
GCACCAAATCGGTATTATAATTATTTAACTTTTTATAATATTTTTTATCTTTAGAGTATGATTAC
AAATTTACCCCTATATAAATCAAGTCCTTCCATTTTGAAGGTACACATTTTTCTTTTCAATGTGT
AAAATAAATTTATATCTATATAATAAAAATAATATTAATATCT
Found at i:20234 original size:22 final size:22
Alignment explanation
Indices: 20203--20362 Score: 112
Period size: 22 Copynumber: 7.2 Consensus size: 22
20193 GAATATTTTC
20203 ATGAAATTTTGATAACTACCCT
1 ATGAAATTTTGATAACTACCCT
* * *
20225 ATTAAATTTTGATAACCACGCT
1 ATGAAATTTTGATAACTACCCT
* *
20247 ATGAAAATTTTTCATAATTA-CCT
1 ATG-AAA-TTTTGATAACTACCCT
* * * *
20270 ATGAAATTGTGATAAATTCCAT
1 ATGAAATTTTGATAACTACCCT
* *
20292 ATGAAACTTTGATAACCTA-ACT
1 ATGAAATTTTGATAA-CTACCCT
* *
20314 ATGAAATTTTAATAAACCT-TCCT
1 ATGAAATTTTGAT-AA-CTACCCT
*
20337 ATGAAATTTTG-TAACCTTCCCT
1 ATGAAATTTTGATAA-CTACCCT
20359 ATGA
1 ATGA
20363 GATCTTGTTA
Statistics
Matches: 107, Mismatches: 24, Indels: 14
0.74 0.17 0.10
Matches are distributed among these distances:
21 13 0.12
22 59 0.55
23 26 0.24
24 9 0.08
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
ATGAAATTTTGATAACTACCCT
Found at i:20362 original size:67 final size:67
Alignment explanation
Indices: 20203--20362 Score: 168
Period size: 67 Copynumber: 2.4 Consensus size: 67
20193 GAATATTTTC
* * * * *
20203 ATGAAATTTTGATAACTACCCTATTAAATTTTGATAACCACGCTATGAAAATTTTTCATAATTAC
1 ATGAAATTTTGATAACTTCCCTATGAAACTTTGATAACCACACTATGAAAATTTTTAATAATTAC
20268 CT
66 CT
* * *
20270 ATGAAATTGTGATAAATTCCATATGAAACTTTGATAACCTA-ACTATG-AAA-TTTTAATAAACC
1 ATGAAATTTTGATAACTTCCCTATGAAACTTTGATAACC-ACACTATGAAAATTTTTAAT-AA--
20332 TT-CCT
62 TTACCT
20337 ATGAAATTTTG-TAACCTTCCCTATGA
1 ATGAAATTTTGATAA-CTTCCCTATGA
20363 GATCTTGTTA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
65 6 0.08
66 8 0.10
67 60 0.78
68 3 0.04
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (67 bp):
ATGAAATTTTGATAACTTCCCTATGAAACTTTGATAACCACACTATGAAAATTTTTAATAATTAC
CT
Found at i:20370 original size:22 final size:21
Alignment explanation
Indices: 20328--20370 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
20318 AATTTTAATA
*
20328 AACCTTCCTATGAAATTTTGT
1 AACCTTCCTATGAAATCTTGT
*
20349 AACCTTCCCTATGAGATCTTGT
1 AACCTT-CCTATGAAATCTTGT
20371 TAATCTCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.40
Consensus pattern (21 bp):
AACCTTCCTATGAAATCTTGT
Found at i:21389 original size:42 final size:43
Alignment explanation
Indices: 21342--21431 Score: 137
Period size: 45 Copynumber: 2.1 Consensus size: 43
21332 CATTATCTTA
* *
21342 ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAAT
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
21384 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
21429 ATT
1 ATT
21432 AATTGTTGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 6 0.14
45 37 0.86
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACTAAT
Found at i:22289 original size:2 final size:2
Alignment explanation
Indices: 22282--22320 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
22272 GGGTTGGCCG
22282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22321 ACATTAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24830 original size:15 final size:15
Alignment explanation
Indices: 24800--24841 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
24790 TTACTTTGCT
24800 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
24816 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
24831 TTGCTTTCTGT
1 TTGTTTTCTGT
24842 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:25274 original size:24 final size:23
Alignment explanation
Indices: 25247--25313 Score: 89
Period size: 25 Copynumber: 2.8 Consensus size: 23
25237 TGTTGTGTCG
25247 AAAAAAAATTTTTTGCGTCATAA
1 AAAAAAAATTTTTTGCGTCATAA
*
25270 AAAAAAAATTGTTTCTGCGTCGTAA
1 AAAAAAAATT-TTT-TGCGTCATAA
*
25295 AAAAAAAGAGTTTTTGCGT
1 AAAAAAA-ATTTTTTGCGT
25314 TTTTCTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 10 0.26
24 8 0.21
25 19 0.49
26 2 0.05
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (23 bp):
AAAAAAAATTTTTTGCGTCATAA
Found at i:28214 original size:15 final size:14
Alignment explanation
Indices: 28194--28223 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
28184 ATCTCTTTAA
28194 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
28209 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
28223 T
1 T
28224 GCTTTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Done.