Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014984.1 Corchorus capsularis cultivar CVL-1 contig15005, 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: 25823
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Found at i:54 original size:10 final size:9
Alignment explanation
Indices: 34--73 Score: 64
Period size: 9 Copynumber: 4.4 Consensus size: 9
24 GTTTAGGCCA
34 TTTTT-ATT
1 TTTTTAATT
42 TTTTTAAATT
1 TTTTT-AATT
52 TTTTTAATT
1 TTTTTAATT
61 TTTTTAATT
1 TTTTTAATT
70 TTTT
1 TTTT
74 AATATTAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 5 0.17
9 17 0.57
10 8 0.27
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTAATT
Found at i:75 original size:8 final size:8
Alignment explanation
Indices: 34--76 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
24 GTTTAGGCCA
*
34 TTTTTATT
1 TTTTTAAT
42 TTTTTAAATT
1 TTTTT-AA-T
52 TTTTTAATT
1 TTTTTAA-T
61 TTTTTAAT
1 TTTTTAAT
69 TTTTTAAT
1 TTTTTAAT
77 ATTAAGTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 14 0.44
9 12 0.38
10 6 0.19
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTAAT
Found at i:148 original size:15 final size:15
Alignment explanation
Indices: 128--189 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 15
118 TACTTAGTTT
128 ATTAGTTTATATTTA
1 ATTAGTTTATATTTA
143 ATTAG----TATTTA
1 ATTAGTTTATATTTA
154 ATTAGTTTATGA-TTA
1 ATTAGTTTAT-ATTTA
169 ATTAG----TATTTA
1 ATTAGTTTATATTTA
180 ATTAGTTTAT
1 ATTAGTTTAT
190 GATTAAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 20
0.65 0.00 0.35
Matches are distributed among these distances:
10 1 0.03
11 20 0.54
15 15 0.41
16 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (15 bp):
ATTAGTTTATATTTA
Found at i:153 original size:11 final size:11
Alignment explanation
Indices: 137--185 Score: 62
Period size: 11 Copynumber: 4.1 Consensus size: 11
127 TATTAGTTTA
137 TATTTAATTAG
1 TATTTAATTAG
148 TATTTAATTAG
1 TATTTAATTAG
159 TTTATGATTAATTAG
1 --TAT--TTAATTAG
174 TATTTAATTAG
1 TATTTAATTAG
185 T
1 T
186 TTATGATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
11 20 0.59
13 6 0.18
15 8 0.24
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (11 bp):
TATTTAATTAG
Found at i:157 original size:26 final size:26
Alignment explanation
Indices: 128--195 Score: 120
Period size: 26 Copynumber: 2.6 Consensus size: 26
118 TACTTAGTTT
128 ATTAGTTTAT-ATTTAATTAGTATTTA
1 ATTAGTTTATGA-TTAATTAGTATTTA
154 ATTAGTTTATGATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATTTA
180 ATTAGTTTATGATTAA
1 ATTAGTTTATGATTAA
196 AATGAAAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 40 0.98
27 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGTATTTA
Found at i:195 original size:15 final size:14
Alignment explanation
Indices: 128--195 Score: 67
Period size: 15 Copynumber: 5.1 Consensus size: 14
118 TACTTAGTTT
128 ATTAGTTTATATTTA
1 ATTAGTTTATA-TTA
143 ATTAG--TAT-TTA
1 ATTAGTTTATATTA
154 ATTAGTTTATGATTA
1 ATTAGTTTAT-ATTA
169 ATTAG--TAT-TTA
1 ATTAGTTTATATTA
180 ATTAGTTTATGATTA
1 ATTAGTTTAT-ATTA
195 A
1 A
196 AATGAAAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
11 16 0.36
13 12 0.27
15 17 0.38
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.54
Consensus pattern (14 bp):
ATTAGTTTATATTA
Found at i:239 original size:24 final size:25
Alignment explanation
Indices: 205--263 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
195 AAATGAAAGA
*
205 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAATTGTTAG
228 AAATGAAGTTTGAAGAAATTGTTAG
1 AAATGAAGTTTGAAGAAATTGTTAG
253 AAATGAAGTTT
1 AAATGAAGTTT
264 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 19 0.58
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAATTGTTAG
Found at i:378 original size:22 final size:22
Alignment explanation
Indices: 347--391 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
337 CGGTGTTTAG
*
347 CAATCGAGTAAAAATAATTCTA
1 CAATCCAGTAAAAATAATTCTA
369 CAATCCAGTAAAAATAATTCTA
1 CAATCCAGTAAAAATAATTCTA
391 C
1 C
392 GCTTATTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.18, G:0.07, T:0.27
Consensus pattern (22 bp):
CAATCCAGTAAAAATAATTCTA
Found at i:3100 original size:13 final size:13
Alignment explanation
Indices: 3082--3109 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3072 GGGGGATTGT
3082 TGGTAGTTTTAGA
1 TGGTAGTTTTAGA
3095 TGGTAGTTTTAGA
1 TGGTAGTTTTAGA
3108 TG
1 TG
3110 TGGTGCTAGT
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:0.21, C:0.00, G:0.32, T:0.46
Consensus pattern (13 bp):
TGGTAGTTTTAGA
Found at i:8128 original size:15 final size:15
Alignment explanation
Indices: 8108--8137 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8098 TATTTATTGG
*
8108 CGAAAACGGGAGGGA
1 CGAAAACGGAAGGGA
8123 CGAAAACGGAAGGGA
1 CGAAAACGGAAGGGA
8138 GATGGAGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.43, T:0.00
Consensus pattern (15 bp):
CGAAAACGGAAGGGA
Found at i:17462 original size:11 final size:11
Alignment explanation
Indices: 17448--17472 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17438 ATTTATGTGT
17448 GTATTTGGCAG
1 GTATTTGGCAG
17459 GTATTTGGCAG
1 GTATTTGGCAG
17470 GTA
1 GTA
17473 GATGGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.08, G:0.36, T:0.36
Consensus pattern (11 bp):
GTATTTGGCAG
Found at i:25440 original size:3 final size:3
Alignment explanation
Indices: 25429--25464 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
25419 TAATAATATA
25429 TAT TA- TAT TAT TAT TA- TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
25465 AATATAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.20
3 24 0.80
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:25443 original size:11 final size:11
Alignment explanation
Indices: 25429--25469 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
25419 TAATAATATA
25429 TATTATATTAT
1 TATTATATTAT
25440 TATTATATTAT
1 TATTATATTAT
25451 TATTAT-TATAT
1 TATTATAT-TAT
*
25462 TATAATAT
1 TATTATAT
25470 AAAACTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 1 0.04
11 25 0.93
12 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTATATTAT
Found at i:25453 original size:14 final size:14
Alignment explanation
Indices: 25434--25464 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
25424 ATATATATTA
25434 TATTATTATTATAT
1 TATTATTATTATAT
25448 TATTATTATTATAT
1 TATTATTATTATAT
25462 TAT
1 TAT
25465 AATATAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATTATTATAT
Done.