Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024190.1 Corchorus olitorius cultivar O-4 contig24223, 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: 20117
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Found at i:1553 original size:18 final size:18
Alignment explanation
Indices: 1530--1566 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1520 TTTCTTGCTT
1530 AATGGAAAGAAATGAAGC
1 AATGGAAAGAAATGAAGC
*
1548 AATGGAAAGAAGTGAAGC
1 AATGGAAAGAAATGAAGC
1566 A
1 A
1567 TTTTTTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.30, T:0.11
Consensus pattern (18 bp):
AATGGAAAGAAATGAAGC
Found at i:2267 original size:10 final size:10
Alignment explanation
Indices: 2247--2305 Score: 65
Period size: 10 Copynumber: 6.3 Consensus size: 10
2237 AGGACCCTCA
2247 TTTCTTTCTTT
1 TTTC-TTCTTT
2258 TTTCTTC--T
1 TTTCTTCTTT
2266 TTT-TTC-TT
1 TTTCTTCTTT
*
2274 TTTCTTTTTT
1 TTTCTTCTTT
2284 TTTCTT-TTT
1 TTTCTTCTTT
2293 TTTCTTCTTT
1 TTTCTTCTTT
2303 TTT
1 TTT
2306 TTTCCTGCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
7 3 0.07
8 8 0.19
9 11 0.26
10 17 0.40
11 4 0.09
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTCTTCTTT
Found at i:2277 original size:16 final size:16
Alignment explanation
Indices: 2251--2309 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
2241 CCCTCATTTC
2251 TTTCTTTTTTCTTCTTT
1 TTTC-TTTTTCTTCTTT
*
2268 TTTCTTTTTCTTTTTT
1 TTTCTTTTTCTTCTTT
*
2284 TTTCTTTTTTTTCTTCT
1 TTTCTTTTTCTTCTT-T
2301 TTT-TTTTTC
1 TTTCTTTTTC
2310 CTGCTTATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 29 0.78
17 8 0.22
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTCTTTTTCTTCTTT
Found at i:2280 original size:23 final size:22
Alignment explanation
Indices: 2251--2305 Score: 83
Period size: 23 Copynumber: 2.5 Consensus size: 22
2241 CCCTCATTTC
2251 TTTCTTTTTTCTTCTTTTTTCTT
1 TTTCTTTTTTCTTCTTTTTT-TT
*
2274 TTTCTTTTTTTTTCTTTTTTTT
1 TTTCTTTTTTCTTCTTTTTTTT
*
2296 CTTCTTTTTT
1 TTTCTTTTTT
2306 TTTCCTGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (22 bp):
TTTCTTTTTTCTTCTTTTTTTT
Found at i:2306 original size:23 final size:25
Alignment explanation
Indices: 2247--2308 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
2237 AGGACCCTCA
*
2247 TTTCTTTCTTTTTTCTTCTTTTTTC
1 TTTCTTTTTTTTTTCTTCTTTTTTC
*
2272 TTTTTCTTTTTTTTTCTT-TTTTTTC
1 TTTCT-TTTTTTTTTCTTCTTTTTTC
2297 -TTCTTTTTTTTT
1 TTTCTTTTTTTTT
2309 CCTGCTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 8 0.24
24 3 0.09
25 11 0.33
26 11 0.33
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (25 bp):
TTTCTTTTTTTTTTCTTCTTTTTTC
Found at i:6373 original size:33 final size:32
Alignment explanation
Indices: 6336--6423 Score: 122
Period size: 33 Copynumber: 2.7 Consensus size: 32
6326 AGAATTTGTT
6336 TCATCACAAACAACAGCTAAAATAGATTTAGTA
1 TCATCACAAACAACA-CTAAAATAGATTTAGTA
* *
6369 TCATCACAAACAACACTCAAATTAGGTTTAGTA
1 TCATCACAAACAACACT-AAAATAGATTTAGTA
*
6402 TCATCACTAACAACATCTAAAA
1 TCATCACAAACAACA-CTAAAA
6424 CACTCTTTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
32 2 0.04
33 45 0.92
34 2 0.04
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.25
Consensus pattern (32 bp):
TCATCACAAACAACACTAAAATAGATTTAGTA
Found at i:10210 original size:44 final size:44
Alignment explanation
Indices: 10128--10410 Score: 331
Period size: 44 Copynumber: 6.5 Consensus size: 44
10118 CGCTATATGA
* * * * *
10128 AAATTTTATTTTCCAAATATAATTTC-TAAACATTTATAATTTCT
1 AAATATTATTTTCTAATTATAATTTCAT-TACATATATAATTTCT
* * *
10172 AGATATCATTTTCTAATTATAATTGCATTACATATATAATTTCT
1 AAATATTATTTTCTAATTATAATTTCATTACATATATAATTTCT
* * * * *
10216 AATTATTATTTTCTAAATATAATTTC-TAAAAATTTATAATTTCT
1 AAATATTATTTTCTAATTATAATTTCAT-TACATATATAATTTCT
10260 AAATATTATTTTCTAATTATAATTTCATTACATATATAATTTCT
1 AAATATTATTTTCTAATTATAATTTCATTACATATATAATTTCT
* *
10304 AAATATTATTTTCTAAATA-ATATTTCATTACATATATAATTTAT
1 AAATATTATTTTCTAATTATA-ATTTCATTACATATATAATTTCT
* * * *
10348 AAATA-TAATTCCTAATTATAATTTCATTACATATATCATATCT
1 AAATATTATTTTCTAATTATAATTTCATTACATATATAATTTCT
*
10391 AAATATTATTTTCTCATTAT
1 AAATATTATTTTCTAATTAT
10411 TTTCTAAATA
Statistics
Matches: 201, Mismatches: 32, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
43 37 0.18
44 162 0.81
45 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.50
Consensus pattern (44 bp):
AAATATTATTTTCTAATTATAATTTCATTACATATATAATTTCT
Found at i:10217 original size:30 final size:29
Alignment explanation
Indices: 10161--10529 Score: 137
Period size: 30 Copynumber: 12.9 Consensus size: 29
10151 TTCTAAACAT
*
10161 TTATAATTTC-TAGATATCAT--TTTCTAA
1 TTATAATTTCTTACATAT-ATAATTTCTAA
*
10188 TTATAATTGCATTACATATATAATTTCTAA
1 TTATAATTTC-TTACATATATAATTTCTAA
*
10218 TTATTATTT-TCTA-A-ATATAATTTCTAAAAA
1 TTATAATTTCT-TACATATATAATTTCT---AA
* *
10248 TTTATAATTTC-TAAATAT-TATTTTCTAA
1 -TTATAATTTCTTACATATATAATTTCTAA
10276 TTATAATTTCATTACATATATAATTTCTAA
1 TTATAATTTC-TTACATATATAATTTCTAA
* * *
10306 ATATTATTT-TCTAAATA-AT-ATTTCATTACA
1 TTATAATTTCT-TACATATATAATTTC--TA-A
* *
10336 TATATAATTT-ATA-A-ATATAATTCCTAA
1 T-TATAATTTCTTACATATATAATTTCTAA
* *
10363 TTATAATTTCATTACATATATCATATCTAA
1 TTATAATTTC-TTACATATATAATTTCTAA
* *
10393 ATATTATTT-TCT-CAT-TAT--TTTCTAA
1 TTATAATTTCT-TACATATATAATTTCTAA
* * *
10418 ATATTATTT-TCTAAATA-AT-ATTTCATTACA
1 TTATAATTTCT-TACATATATAATTTC--TA-A
* *
10448 TATATAATTT-ATA-A-ATATAATTCCTAA
1 T-TATAATTTCTTACATATATAATTTCTAA
* *
10475 TTATAATTTCATTACATATATCATATCTAA
1 TTATAATTTC-TTACATATATAATTTCTAA
* *
10505 ATATTATTT-TCT-CAT-TATAATTTCT
1 TTATAATTTCT-TACATATATAATTTCT
10530 GACCAATTTT
Statistics
Matches: 266, Mismatches: 35, Indels: 82
0.69 0.09 0.21
Matches are distributed among these distances:
25 18 0.07
26 20 0.08
27 54 0.20
28 27 0.10
29 33 0.12
30 82 0.31
31 30 0.11
32 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (29 bp):
TTATAATTTCTTACATATATAATTTCTAA
Found at i:10228 original size:88 final size:87
Alignment explanation
Indices: 10128--10440 Score: 388
Period size: 88 Copynumber: 3.6 Consensus size: 87
10118 CGCTATATGA
* * *
10128 AAATTTTATTTTCCAAATATAATTTCTAAACATTTATAATTTCTAGATATCATTTTCTAATTATA
1 AAATATTATTTTCTAAATATAATTTCTAAACATTTATAATTTCTAAATAT-ATTTTCTAATTATA
*
10193 ATTGCATTACATATATAATTTCT
65 ATTTCATTACATATATAATTTCT
* *
10216 AATTATTATTTTCTAAATATAATTTCTAAAAATTTATAATTTCTAAATATTATTTTCTAATTATA
1 AAATATTATTTTCTAAATATAATTTCTAAACATTTATAATTTCTAAATA-TATTTTCTAATTATA
10281 ATTTCATTACATATATAATTTCT
65 ATTTCATTACATATATAATTTCT
* * * * *
10304 AAATATTATTTTCTAAATA-ATATTTC-ATTACATATATAATTTATAAATATAATTCCTAATTAT
1 AAATATTATTTTCTAAATATA-ATTTCTA-AACATTTATAATTTCTAAATATATTTTCTAATTAT
* *
10367 AATTTCATTACATATATCATATCT
64 AATTTCATTACATATATAATTTCT
* * *
10391 AAATATTATTTTCT-CAT-TATTTTCTAAATA-TTAT--TTTCTAAATAATATTT
1 AAATATTATTTTCTAAATATAATTTCTAAACATTTATAATTTCTAAAT-ATATTT
10441 CATTACATAT
Statistics
Matches: 197, Mismatches: 22, Indels: 17
0.83 0.09 0.07
Matches are distributed among these distances:
82 8 0.04
83 5 0.03
84 3 0.02
85 6 0.03
86 4 0.02
87 50 0.25
88 120 0.61
89 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (87 bp):
AAATATTATTTTCTAAATATAATTTCTAAACATTTATAATTTCTAAATATATTTTCTAATTATAA
TTTCATTACATATATAATTTCT
Found at i:10299 original size:132 final size:131
Alignment explanation
Indices: 10128--10529 Score: 380
Period size: 112 Copynumber: 3.2 Consensus size: 131
10118 CGCTATATGA
* * * * * *
10128 AAATTTTATTTTCCAAATATAATTTCTAAACATTTATAATTTCTAGATATCATTTTCT-AATTAT
1 AAATATTATTTTCTAATTATAATTTCTAAACATATATAATTTCTAAATATCATTTTCTAAATAAT
* * * * *
10192 AATTGCATTACATATATAATTTCTAATTATTATTTTCTAAATATAATTTC-TAAAAATTTATAAT
66 -ATTGCATTACATATATAATTTATAAATA-TAATTCCTAAATATAATTTCAT-AAAATATATAAT
*
10256 TTCT
128 ATCT
* *
10260 AAATATTATTTTCTAATTATAATTTC-ATTACATATATAATTTCTAAATATTATTTTCTAAATAA
1 AAATATTATTTTCTAATTATAATTTCTA-AACATATATAATTTCTAAATATCATTTTCTAAATAA
* * * * *
10324 TATTTCATTACATATATAATTTATAAATATAATTCCTAATTATAATTTCATTACATATATCATAT
65 TATTGCATTACATATATAATTTATAAATATAATTCCTAAATATAATTTCATAAAATATATAATAT
10389 CT
130 CT
* *
10391 AAATATTATTTTCTCATTAT--TTTCT-AA-ATAT-TATTTTCT--A-A--A-----T-AAT-AT
1 AAATATTATTTTCTAATTATAATTTCTAAACATATATAATTTCTAAATATCATTTTCTAAATAAT
* * * *
10439 -TT-CATTACATATATAATTTATAAATATAATTCCTAATTATAATTTCATTACATATATCATATC
66 ATTGCATTACATATATAATTTATAAATATAATTCCTAAATATAATTTCATAAAATATATAATATC
10502 T
131 T
*
10503 AAATATTATTTTCTCATTATAATTTCT
1 AAATATTATTTTCTAATTATAATTTCT
10530 GACCAATTTT
Statistics
Matches: 242, Mismatches: 22, Indels: 30
0.82 0.07 0.10
Matches are distributed among these distances:
112 82 0.34
113 2 0.01
114 7 0.03
115 3 0.01
116 1 0.00
121 1 0.00
123 1 0.00
124 1 0.00
126 7 0.03
127 4 0.02
128 1 0.00
129 4 0.02
131 48 0.20
132 75 0.31
133 5 0.02
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.50
Consensus pattern (131 bp):
AAATATTATTTTCTAATTATAATTTCTAAACATATATAATTTCTAAATATCATTTTCTAAATAAT
ATTGCATTACATATATAATTTATAAATATAATTCCTAAATATAATTTCATAAAATATATAATATC
T
Found at i:10430 original size:112 final size:112
Alignment explanation
Indices: 10299--10522 Score: 448
Period size: 112 Copynumber: 2.0 Consensus size: 112
10289 ACATATATAA
10299 TTTCTAAATATTATTTTCTAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAAT
1 TTTCTAAATATTATTTTCTAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAAT
10364 TATAATTTCATTACATATATCATATCTAAATATTATTTTCTCATTAT
66 TATAATTTCATTACATATATCATATCTAAATATTATTTTCTCATTAT
10411 TTTCTAAATATTATTTTCTAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAAT
1 TTTCTAAATATTATTTTCTAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAAT
10476 TATAATTTCATTACATATATCATATCTAAATATTATTTTCTCATTAT
66 TATAATTTCATTACATATATCATATCTAAATATTATTTTCTCATTAT
10523 AATTTCTGAC
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (112 bp):
TTTCTAAATATTATTTTCTAAATAATATTTCATTACATATATAATTTATAAATATAATTCCTAAT
TATAATTTCATTACATATATCATATCTAAATATTATTTTCTCATTAT
Found at i:10439 original size:17 final size:14
Alignment explanation
Indices: 10211--10440 Score: 109
Period size: 14 Copynumber: 16.1 Consensus size: 14
10201 ACATATATAA
*
10211 TTTCTAATTATTAT
1 TTTCTAAATATTAT
*
10225 TTTCTAAATA-TAA
1 TTTCTAAATATTAT
*
10238 TTTCTAAAAATTTAT
1 TTTCTAAATA-TTAT
10253 AATTTCTAAATATTAT
1 --TTTCTAAATATTAT
* *
10269 TTTCTAATTA-TAA
1 TTTCTAAATATTAT
* *
10282 TTTCATTACATATATAA
1 TTTC--TAAATAT-TAT
10299 TTTCTAAATATTAT
1 TTTCTAAATATTAT
*
10313 TTTCTAAATAATA-
1 TTTCTAAATATTAT
* *
10326 TTTCATTACATATATAA
1 TTTC--TAAATAT-TAT
* *
10343 TTTATAAATA-TAA
1 TTTCTAAATATTAT
* * *
10356 TTCCTAATTA-TAA
1 TTTCTAAATATTAT
*
10369 TTTCATTACATA-TAT
1 TTTC--TAAATATTAT
*
10384 CATATCTAAATATTAT
1 --TTTCTAAATATTAT
*
10400 TTTCT---CATTAT
1 TTTCTAAATATTAT
10411 TTTCTAAATATTAT
1 TTTCTAAATATTAT
*
10425 TTTCTAAATAATAT
1 TTTCTAAATATTAT
10439 TT
1 TT
10441 CATTACATAT
Statistics
Matches: 167, Mismatches: 29, Indels: 40
0.71 0.12 0.17
Matches are distributed among these distances:
11 10 0.06
13 37 0.22
14 56 0.34
15 33 0.20
16 9 0.05
17 22 0.13
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTCTAAATATTAT
Found at i:10486 original size:43 final size:44
Alignment explanation
Indices: 10415--10528 Score: 124
Period size: 43 Copynumber: 2.6 Consensus size: 44
10405 CATTATTTTC
* * * *
10415 TAAATATTATTTTCTAAATA-ATATTTCATTACATATATAATTTA
1 TAAATATTAATTCCTAATTATA-ATTTCATTACATATATAATATA
* *
10459 TAAATA-TAATTCCTAATTATAATTTCATTACATATATCATATC
1 TAAATATTAATTCCTAATTATAATTTCATTACATATATAATATA
* * *
10502 TAAATATTATTTTCTCATTATAATTTC
1 TAAATATTAATTCCTAATTATAATTTC
10529 TGACCAATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
43 35 0.59
44 24 0.41
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (44 bp):
TAAATATTAATTCCTAATTATAATTTCATTACATATATAATATA
Found at i:18330 original size:14 final size:14
Alignment explanation
Indices: 18311--18338 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18301 TATATTAGTA
18311 TTTTCTATTCTATT
1 TTTTCTATTCTATT
18325 TTTTCTATTCTATT
1 TTTTCTATTCTATT
18339 AGTATTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Done.