Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001377.1 Corchorus capsularis cultivar CVL-1 contig01377, 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: 6970
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Found at i:196 original size:17 final size:16
Alignment explanation
Indices: 174--349 Score: 93
Period size: 17 Copynumber: 11.8 Consensus size: 16
164 ATTTTCTAAA
174 TATAATTTCTAAACATT
1 TATAATTTCTAAACA-T
* *
191 TATAATTTCTAGATAT
1 TATAATTTCTAAACAT
207 TAT--TTTCT--A-AT
1 TATAATTTCTAAACAT
*
218 TATAATTTC-ATTACAT
1 TATAATTTCTA-AACAT
**
234 ATATAATTTCTAATTAT
1 -TATAATTTCTAAACAT
251 TAT--TTTCT-AA-A-
1 TATAATTTCTAAACAT
*
262 TATAATTTCTAAAAAAT
1 TATAATTTCT-AAACAT
279 TATAATTTCTAAACAT
1 TATAATTTCTAAACAT
295 TAT--TTTCT--A-AT
1 TATAATTTCTAAACAT
*
306 TATAATTTC-ATTACAT
1 TATAATTTCTA-AACAT
*
322 ATATAATTTCTAAATAT
1 -TATAATTTCTAAACAT
339 TAT--TTTCTAAA
1 TATAATTTCTAAA
350 TAATATTTCA
Statistics
Matches: 128, Mismatches: 9, Indels: 47
0.70 0.05 0.26
Matches are distributed among these distances:
11 13 0.10
12 3 0.02
13 14 0.11
14 23 0.18
15 4 0.03
16 23 0.18
17 46 0.36
18 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.51
Consensus pattern (16 bp):
TATAATTTCTAAACAT
Found at i:210 original size:44 final size:44
Alignment explanation
Indices: 162--379 Score: 262
Period size: 44 Copynumber: 4.9 Consensus size: 44
152 TATTCAATTT
* *
162 TTATTTTCTAAATATAATTTC-TAAACATTTATAATTTCTAGATA
1 TTATTTTCTAAATATAATTTCAT-AACATATATAATTTCTAAATA
* * *
206 TTATTTTCTAATTATAATTTCATTACATATATAATTTCTAATTA
1 TTATTTTCTAAATATAATTTCATAACATATATAATTTCTAAATA
* * *
250 TTATTTTCTAAATATAATTTC-TAAAAAATTATAATTTCTAAACA
1 TTATTTTCTAAATATAATTTCATAACATA-TATAATTTCTAAATA
* *
294 TTATTTTCTAATTATAATTTCATTACATATATAATTTCTAAATA
1 TTATTTTCTAAATATAATTTCATAACATATATAATTTCTAAATA
* * *
338 TTATTTTCTAAATA-ATATTTCATTATATAATATAATTCCTAA
1 TTATTTTCTAAATATA-ATTTCATAACAT-ATATAATTTCTAA
380 TTACAATTTC
Statistics
Matches: 150, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
43 5 0.03
44 128 0.85
45 17 0.11
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.50
Consensus pattern (44 bp):
TTATTTTCTAAATATAATTTCATAACATATATAATTTCTAAATA
Found at i:225 original size:14 final size:13
Alignment explanation
Indices: 166--521 Score: 106
Period size: 13 Copynumber: 24.4 Consensus size: 13
156 CAATTTTTAT
*
166 TTTCTAAATATAA
1 TTTCTAATTATAA
179 TTTCTAAACATTTATAA
1 TTTCT--A-A-TTATAA
*
196 TTTCTAGA-TATTAT
1 TTTCTA-ATTA-TAA
210 TTTCTAATTATAA
1 TTTCTAATTATAA
223 TTTCATTACATATATAA
1 TTTC--TA-AT-TATAA
*
240 TTTCTAATTATTAT
1 TTTCTAATTA-TAA
*
254 TTTCTAAATATAA
1 TTTCTAATTATAA
267 TTTCTAAAAAATTATAA
1 TTTCT----AATTATAA
** *
284 TTTCTAAACATTAT
1 TTTCTAATTA-TAA
298 TTTCTAATTATAA
1 TTTCTAATTATAA
311 TTTCATTACATATATAA
1 TTTC--TA-AT-TATAA
* *
328 TTTCTAAATATTAT
1 TTTCTAATTA-TAA
*
342 TTTCTAAATA-ATA
1 TTTCTAATTATA-A
355 TTTCATTATATAATATAA
1 TTTC--TA-AT--TATAA
* *
373 TTCCTAATTACAA
1 TTTCTAATTATAA
*
386 TTTCTTCACATATATAG
1 TTTC-T-A-AT-TATAA
* *
403 TTTCTAAATATTAT
1 TTTCTAATTA-TAA
*
417 TTTCTAAATA-ATA
1 TTTCTAATTATA-A
430 TTTCATTACATTTATAA
1 TTTC--TA-A-TTATAA
* *
447 TTTATAAATATAA
1 TTTCTAATTATAA
*
460 TTCCTAATTATAA
1 TTTCTAATTATAA
*
473 TTTCATTACATATATCA
1 TTTC--TA-AT-TATAA
* *
490 TTTCTAAATATTAT
1 TTTCTAATTA-TAA
*
504 TTTCTCATTATAA
1 TTTCTAATTATAA
517 TTTCT
1 TTTCT
522 GACCAACTTT
Statistics
Matches: 259, Mismatches: 40, Indels: 88
0.67 0.10 0.23
Matches are distributed among these distances:
12 2 0.01
13 78 0.30
14 71 0.27
15 25 0.10
16 14 0.05
17 61 0.24
18 7 0.03
19 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (13 bp):
TTTCTAATTATAA
Found at i:264 original size:88 final size:88
Alignment explanation
Indices: 157--351 Score: 336
Period size: 88 Copynumber: 2.2 Consensus size: 88
147 CGTTATATTC
* * * * *
157 AATTTTTATTTTCTAAATATAATTTCTAAACATTTATAATTTCTAGATATTATTTTCTAATTATA
1 AATTATTATTTTCTAAATATAATTTCTAAAAAATTATAATTTCTAAACATTATTTTCTAATTATA
222 ATTTCATTACATATATAATTTCT
66 ATTTCATTACATATATAATTTCT
245 AATTATTATTTTCTAAATATAATTTCTAAAAAATTATAATTTCTAAACATTATTTTCTAATTATA
1 AATTATTATTTTCTAAATATAATTTCTAAAAAATTATAATTTCTAAACATTATTTTCTAATTATA
310 ATTTCATTACATATATAATTTCT
66 ATTTCATTACATATATAATTTCT
*
333 AAATATTATTTTCTAAATA
1 AATTATTATTTTCTAAATA
352 ATATTTCATT
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 101 1.00
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (88 bp):
AATTATTATTTTCTAAATATAATTTCTAAAAAATTATAATTTCTAAACATTATTTTCTAATTATA
ATTTCATTACATATATAATTTCT
Found at i:334 original size:30 final size:29
Alignment explanation
Indices: 190--343 Score: 126
Period size: 27 Copynumber: 5.3 Consensus size: 29
180 TTCTAAACAT
* *
190 TTATAATTTC-TAGATAT-TATTTTCTAA
1 TTATAATTTCTTACATATATAATTTCTAA
217 TTATAATTTCATTACATATATAATTTCTAA
1 TTATAATTTC-TTACATATATAATTTCTAA
*
247 TTATTATTT-TCTA-A-ATATAATTTCTAAAAAA
1 TTATAATTTCT-TACATATATAATTTCT----AA
*
278 TTATAATTTCTAAACAT-TAT--TTTCTAA
1 TTATAATTTCT-TACATATATAATTTCTAA
305 TTATAATTTCATTACATATATAATTTCTAA
1 TTATAATTTC-TTACATATATAATTTCTAA
* *
335 ATATTATTT
1 TTATAATTT
344 TCTAAATAAT
Statistics
Matches: 103, Mismatches: 9, Indels: 27
0.74 0.06 0.19
Matches are distributed among these distances:
27 37 0.36
28 6 0.06
29 8 0.08
30 31 0.30
31 15 0.15
32 2 0.02
33 4 0.04
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (29 bp):
TTATAATTTCTTACATATATAATTTCTAA
Found at i:984 original size:20 final size:20
Alignment explanation
Indices: 964--1003 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
954 CTTTAAAGTC
*
964 TCAATTTGTTGTTGTAGGTCT
1 TCAATTTATTGTT-TAGGTCT
*
985 TCGATTTATTGTTTAGGTC
1 TCAATTTATTGTTTAGGTC
1004 GAAAATCCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.10, G:0.23, T:0.53
Consensus pattern (20 bp):
TCAATTTATTGTTTAGGTCT
Found at i:3649 original size:67 final size:67
Alignment explanation
Indices: 3564--3730 Score: 289
Period size: 67 Copynumber: 2.5 Consensus size: 67
3554 TGTTCAAGTC
* * *
3564 TTTCAATAGGACCACCACGAGCCATCTCCACCCCTGTTGACAGGATTTCTGCAAACAGATACAGG
1 TTTCAATAGGACCACCACGAGCCATCTCCACCCCTGTCGACAGAATTTCTGCAAACAGATACAGA
3629 TT
66 TT
3631 TTTCAATAGGACCACCACGAGCCATCTCCACCCCTGTCGACAGAATTTCTGCAAACAGATACAGA
1 TTTCAATAGGACCACCACGAGCCATCTCCACCCCTGTCGACAGAATTTCTGCAAACAGATACAGA
3696 TT
66 TT
* *
3698 TTTCAATAGGACTACCAGGAGCCATCTCCACCC
1 TTTCAATAGGACCACCACGAGCCATCTCCACCC
3731 TTGGCTTTCT
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 95 1.00
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (67 bp):
TTTCAATAGGACCACCACGAGCCATCTCCACCCCTGTCGACAGAATTTCTGCAAACAGATACAGA
TT
Found at i:6784 original size:2 final size:2
Alignment explanation
Indices: 6777--6806 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6767 GGGAATTGGG
6777 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6807 TTACAAATAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.