Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001665.1 Corchorus capsularis cultivar CVL-1 contig01665, 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: 3372
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Found at i:420 original size:149 final size:150
Alignment explanation
Indices: 115--479 Score: 486
Period size: 150 Copynumber: 2.4 Consensus size: 150
105 AGATTTTAGC
* * *
115 CTTTATAATAATTTAAATAAAACTAATGCTCATTTTATAATTATAGTTAGCAACATTCTTGGAAA
1 CTTTATAATAATTTAAATAAAACTAATGTTCATTTTATAA-T-TAGTAAGCAACATTCTTAGAAA
* * **
180 CAGATATATGATTTCCGTGTGAAATTTTGTTTCCAAGTGAAAACATTTATAGATGAAATTATTTC
64 CAGAAATATAATTTCCGTGTGAAATTCCGTTTCCAAGTGAAAACATTTATAGATGAAATTATTTC
*
245 TGTAAATATTTTCATTCCTTGT
129 TGTAAATATTTTCACTCCTTGT
** * *
267 CTTTATAATAATTTAAATAAAACTAATGTTCATTTTATAATTAGTAAGCAATGTTTTTAGAAACG
1 CTTTATAATAATTTAAATAAAACTAATGTTCATTTTATAATTAGTAAGCAACATTCTTAGAAACA
* * *
332 GAAATATAATTTCTGTGTGAAATTCCGTTTCCAAGTGAAAA-ATTTATAGATGAAATTGTTTCTT
66 GAAATATAATTTCCGTGTGAAATTCCGTTTCCAAGTGAAAACATTTATAGATGAAATTATTTCTG
396 TAAATA-TTTCTACTCCTTGT
131 TAAATATTTTC-ACTCCTTGT
* *
416 CTTTAT-ATAATAGTCCAAATAAAAATAATGTTCATTTTATAATTAGGT-AGCAACATTCTTAGA
1 CTTTATAATAAT--T-TAAATAAAACTAATGTTCATTTTATAATTA-GTAAGCAACATTCTTAGA
479 A
62 A
480 TATAATTTCT
Statistics
Matches: 188, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
148 9 0.05
149 41 0.22
150 55 0.29
151 42 0.22
152 41 0.22
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (150 bp):
CTTTATAATAATTTAAATAAAACTAATGTTCATTTTATAATTAGTAAGCAACATTCTTAGAAACA
GAAATATAATTTCCGTGTGAAATTCCGTTTCCAAGTGAAAACATTTATAGATGAAATTATTTCTG
TAAATATTTTCACTCCTTGT
Found at i:3178 original size:24 final size:23
Alignment explanation
Indices: 3122--3200 Score: 113
Period size: 23 Copynumber: 3.3 Consensus size: 23
3112 AACCCTAAAC
* *
3122 TTCATTTCTAACAACTTCTTCAAA
1 TTCATTTTTAACAA-ATCTTCAAA
*
3146 CTTCATTTTTAATAAATCTTCAAA
1 -TTCATTTTTAACAAATCTTCAAA
3170 TTCATTTTTAACAAATCTTCAAA
1 TTCATTTTTAACAAATCTTCAAA
3193 TTCATTTT
1 TTCATTTT
3201 CCTTCATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 30 0.60
24 8 0.16
25 12 0.24
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (23 bp):
TTCATTTTTAACAAATCTTCAAA
Found at i:3238 original size:26 final size:26
Alignment explanation
Indices: 3209--3276 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
3199 TTCCTTCATT
3209 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
3235 TTAATAATAAACTAATTATATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
3261 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
3277 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:3276 original size:15 final size:14
Alignment explanation
Indices: 3215--3307 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
3205 CATTTTAATC
3215 ATAAACTAATT-AA
1 ATAAACTAATTAAA
3228 AT--ACTAATTAATA
1 ATAAACTAATTAA-A
3241 ATAAACTAATT---
1 ATAAACTAATTAAA
*
3252 ATATACTAATTAAA
1 ATAAACTAATTAAA
3266 CATAAACTAA-TAAA
1 -ATAAACTAATTAAA
* * **
3280 CT-AAGTAATTTTA
1 ATAAACTAATTAAA
*
3293 ATTAACTAATTAAA
1 ATAAACTAATTAAA
3307 A
1 A
3308 CTAATCATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 19
0.67 0.11 0.21
Matches are distributed among these distances:
11 17 0.28
12 6 0.10
13 9 0.15
14 13 0.22
15 15 0.25
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (14 bp):
ATAAACTAATTAAA
Found at i:3300 original size:52 final size:51
Alignment explanation
Indices: 3209--3312 Score: 122
Period size: 52 Copynumber: 2.0 Consensus size: 51
3199 TTCCTTCATT
* *
3209 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTATATACTAA
1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA
* * *
3261 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA
3312 T
1 T
3313 CATAATCTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
51 11 0.24
52 28 0.62
53 6 0.13
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.36
Consensus pattern (51 bp):
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA
Found at i:3347 original size:10 final size:10
Alignment explanation
Indices: 3329--3358 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
3319 CTCATTAATA
3329 TTAAAAAAATT
1 TTAAAAAAA-T
3340 TTAAAAAAAT
1 TTAAAAAAAT
3350 TTAAAAAAA
1 TTAAAAAAA
3359 AAAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TTAAAAAAAT
Done.