Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015286.1 Corchorus capsularis cultivar CVL-1 contig15307, 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: 45538
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--28 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29 CTACATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7145 original size:3 final size:3
Alignment explanation
Indices: 7137--7169 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
7127 CTATGAGTAA
7137 TAT TAT TAT TAT TAT TAT TAT ATAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
7170 ATATACTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:7154 original size:12 final size:13
Alignment explanation
Indices: 7137--7173 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
7127 CTATGAGTAA
7137 TATTATTAT-TAT
1 TATTATTATATAT
7149 TATTATTATATAT
1 TATTATTATATAT
7162 TA-TATTATATAT
1 TATTATTATATAT
7174 ACTATATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 19 0.79
13 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATTATATAT
Found at i:7174 original size:9 final size:8
Alignment explanation
Indices: 7140--7186 Score: 53
Period size: 9 Copynumber: 5.9 Consensus size: 8
7130 TGAGTAATAT
7140 TATTATTA
1 TATTATTA
7148 TTATTATTA
1 -TATTATTA
7157 TA-TATTA
1 TATTATTA
7164 TATTATATA
1 TATTAT-TA
*
7173 TACTA-TA
1 TATTATTA
7180 TATTATT
1 TATTATT
7187 TTTAACTACC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 13 0.39
8 6 0.18
9 14 0.42
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTATTA
Found at i:7735 original size:50 final size:50
Alignment explanation
Indices: 7681--7780 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
7671 ATCCAATTAA
*
7681 CAGTATGTTTTATTACCTCTTTGCACTTCCTATTACTTACAAATAAAAGC
1 CAGTATATTTTATTACCTCTTTGCACTTCCTATTACTTACAAATAAAAGC
7731 CAGTATATTTTATTACCTCTTTGCACTTCCTATTACTTACAAATAAAAGC
1 CAGTATATTTTATTACCTCTTTGCACTTCCTATTACTTACAAATAAAAGC
7781 ATGTTCTTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (50 bp):
CAGTATATTTTATTACCTCTTTGCACTTCCTATTACTTACAAATAAAAGC
Found at i:8061 original size:3 final size:3
Alignment explanation
Indices: 8055--8082 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
8045 TAACTTGTTG
8055 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
8083 ATGATGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11706 original size:21 final size:21
Alignment explanation
Indices: 11669--11708 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11659 AGCCGCTCGA
11669 TGCTTGGCTCAAGGATATGCC
1 TGCTTGGCTCAAGGATATGCC
*
11690 TGCTATGGCTTAA-GATATG
1 TGCT-TGGCTCAAGGATATG
11709 GTCTATGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.33
Consensus pattern (21 bp):
TGCTTGGCTCAAGGATATGCC
Found at i:24345 original size:17 final size:17
Alignment explanation
Indices: 24308--24355 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
24298 GTAATCTTTG
* **
24308 ATCACCGGTGATCTTGC
1 ATCACTGGTGATCTTAA
*
24325 ATCATTGGTGATCTTAA
1 ATCACTGGTGATCTTAA
*
24342 ATCACTAGTGATCT
1 ATCACTGGTGATCT
24356 AGGGGGTGAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (17 bp):
ATCACTGGTGATCTTAA
Found at i:25748 original size:2 final size:2
Alignment explanation
Indices: 25741--25772 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25731 TTCCATCTAG
25741 AT 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 AT
25773 TATGCAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32074 original size:21 final size:21
Alignment explanation
Indices: 32021--32080 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
32011 TTTGGAGCAA
*
32021 GAATATTCCAATCGATTCTAT
1 GAATATTCCAATCGATTCTAG
** * *
32042 GTCTACTACAATCGATTCTAG
1 GAATATTCCAATCGATTCTAG
32063 GAATATTCCAATCGATTC
1 GAATATTCCAATCGATTC
32081 CAAGATATGC
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (21 bp):
GAATATTCCAATCGATTCTAG
Found at i:42124 original size:11 final size:11
Alignment explanation
Indices: 42108--42132 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42098 AATATGAGCT
42108 TGAAAACAATG
1 TGAAAACAATG
42119 TGAAAACAATG
1 TGAAAACAATG
42130 TGA
1 TGA
42133 CTGGCCAATG
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:0.52, C:0.08, G:0.20, T:0.20
Consensus pattern (11 bp):
TGAAAACAATG
Found at i:42218 original size:3 final size:3
Alignment explanation
Indices: 42205--42267 Score: 51
Period size: 3 Copynumber: 21.3 Consensus size: 3
42195 GATGATAAAT
* *
42205 TTA TGTA TTA TTA -TA CTA TTA TTA TTA TTA TTA CGT- TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* *
42250 TTA -TA CTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA T
42268 CATTTCCCTC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
2 5 0.10
3 40 0.82
4 4 0.08
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:42244 original size:18 final size:17
Alignment explanation
Indices: 42204--42267 Score: 69
Period size: 17 Copynumber: 3.6 Consensus size: 17
42194 GGATGATAAA
42204 TTTATGTATTATTA-TAC
1 TTTAT-TATTATTATTAC
42221 TATTATTATTATTATTAC
1 T-TTATTATTATTATTAC
42239 GTTTATTATTATTA-TAC
1 -TTTATTATTATTATTAC
*
42256 TATTATCATTAT
1 T-TTATTATTAT
42268 CATTTCCCTC
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 1 0.02
17 21 0.50
18 19 0.45
19 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTATTATTATTATTAC
Found at i:43774 original size:19 final size:19
Alignment explanation
Indices: 43747--43786 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
43737 AACTATGAGG
43747 GAGTAAGTGGGAGGAGAGA
1 GAGTAAGTGGGAGGAGAGA
* *
43766 GAGTTAGTGGGTGGAGAGA
1 GAGTAAGTGGGAGGAGAGA
43785 GA
1 GA
43787 AGAGGGACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.53, T:0.15
Consensus pattern (19 bp):
GAGTAAGTGGGAGGAGAGA
Done.