Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009125.1 Corchorus capsularis cultivar CVL-1 contig09146, 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: 12761
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:73 original size:2 final size:2
Alignment explanation
Indices: 66--105 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
56 TGAGGGCCGT
66 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
106 TTAATTTAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1146 original size:31 final size:31
Alignment explanation
Indices: 1106--1273 Score: 145
Period size: 31 Copynumber: 5.5 Consensus size: 31
1096 ATAGGCTAAT
*
1106 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAATCTTTGCCAAAA
* * ** * **
1137 TACTCAAATAATGGCCTGGTCTTT--TAATT
1 TGCTCAAATAAGGGCCTAATCTTTGCCAAAA
1166 TGGC-CAAATAAGGGCCTAA-CATTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATC-TTTGCCAAAA
* **
1197 TGCTCAAATAAGGGCCTCATCTTTG--AATT
1 TGCTCAAATAAGGGCCTAATCTTTGCCAAAA
1226 TGGC-CAAATAAGGGCCTAA-CGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATC-TTTGCCAAAA
1257 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
1274 GTCTCATGCG
Statistics
Matches: 105, Mismatches: 21, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
28 2 0.02
29 39 0.37
30 7 0.07
31 56 0.53
32 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATCTTTGCCAAAA
Found at i:1177 original size:60 final size:60
Alignment explanation
Indices: 1110--1274 Score: 267
Period size: 60 Copynumber: 2.8 Consensus size: 60
1100 GCTAATTGCT
* * * * *
1110 CAAATAAGGGCCTAATGTTTGCCAAAATACTCAAATAATGGCCTGGTCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTGAATTTGGC
* *
1170 CAAATAAGGGCCTAACATTTGCCAAAATGCTCAAATAAGGGCCTCATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTGAATTTGGC
1230 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTG
1275 TCTCATGCGT
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 96 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTGAATTTGGC
Found at i:1242 original size:29 final size:28
Alignment explanation
Indices: 1141--1243 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 28
1131 CCAAAATACT
* * *
1141 CAAATAATGGCCTGGTCTTTTAATTTGGC
1 CAAATAAGGGCCT-ATCTTTGAATTTGGC
* **
1170 CAAATAAGGGCCTAACATTTGCCAAAAT-GC
1 CAAATAAGGGCCTATC-TTTG--AATTTGGC
1200 TCAAATAAGGGCCTCATCTTTGAATTTGGC
1 -CAAATAAGGGCCT-ATCTTTGAATTTGGC
1230 CAAATAAGGGCCTA
1 CAAATAAGGGCCTA
1244 ACGTTTGCCA
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
28 2 0.03
29 31 0.53
30 4 0.07
31 20 0.34
32 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (28 bp):
CAAATAAGGGCCTATCTTTGAATTTGGC
Found at i:1339 original size:31 final size:30
Alignment explanation
Indices: 1301--1499 Score: 158
Period size: 31 Copynumber: 6.6 Consensus size: 30
1291 AACTGACACC
1301 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGA-AACGTT
*
1332 AGGCCCTTATTTGAGTATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGA-AACGTT
** * *
1363 AGGCCCTTATTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTCGAAACG-TT
* *
1392 GGGCCCTTATTTGAGCATTTTCGATAATGTT
1 AGGCCCTTATTTGAGCATTTTCGA-AACGTT
** * *
1423 AGGCCCTTATTTG-GCCAAATT--AAAAGAT
1 AGGCCCTTATTTGAG-CATTTTCGAAACGTT
* * *
1451 CGAGCCCTTATTTGAACATTTTGGCAAACGTT
1 AG-GCCCTTATTTGAGCATTTTCG-AAACGTT
1483 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
1500 ATTAGTCAAT
Statistics
Matches: 132, Mismatches: 24, Indels: 24
0.73 0.13 0.13
Matches are distributed among these distances:
28 8 0.06
29 34 0.26
30 3 0.02
31 78 0.59
32 9 0.07
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTCGAAACGTT
Found at i:1405 original size:60 final size:60
Alignment explanation
Indices: 1333--1495 Score: 265
Period size: 60 Copynumber: 2.7 Consensus size: 60
1323 GATAACGTTA
*
1333 GGCCCTTATTTGAGTATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
*
1393 GGCCCTTATTTGAGCATTTTCGATAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
* * *
1453 AGCCCTTATTTGAACATTTTGGCA-AACGTTAGGCCCTTATTTG
1 GGCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
1496 AGCAATTAGT
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
60 95 0.99
61 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:5403 original size:22 final size:23
Alignment explanation
Indices: 5378--5423 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
5368 ATGACACGTA
*
5378 AACCCAAATGACTCGAGAA-ATT
1 AACCCAAACGACTCGAGAATATT
* *
5400 AACCCGAACGACTCGTGAATATT
1 AACCCAAACGACTCGAGAATATT
5423 A
1 A
5424 TAAACTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (23 bp):
AACCCAAACGACTCGAGAATATT
Found at i:7288 original size:16 final size:15
Alignment explanation
Indices: 7263--7302 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
7253 GTTATAAGAC
*
7263 AAAAACAAAATTTATT
1 AAAAA-AAAAATTATT
7279 AAAAAAAAAATTATT
1 AAAAAAAAAATTATT
7294 AGAAAAAAA
1 A-AAAAAAA
7303 GTCATATTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAAAAAAAATTATT
Found at i:10286 original size:21 final size:19
Alignment explanation
Indices: 10262--10305 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
10252 ATTTGTAAAA
10262 TAAATCAAATAATAAATATAT
1 TAAAT-AAAT-ATAAATATAT
* *
10283 TAAATAAATTTAAGTATAT
1 TAAATAAATATAAATATAT
10302 TAAA
1 TAAA
10306 CATTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 4 0.19
21 5 0.24
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
TAAATAAATATAAATATAT
Found at i:12281 original size:21 final size:21
Alignment explanation
Indices: 12255--12299 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
12245 TTATTCTGGA
12255 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
* *
12276 TTGCTATTCACTGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
12297 TTG
1 TTG
12300 ACGCTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.31, G:0.11, T:0.40
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:12551 original size:34 final size:33
Alignment explanation
Indices: 12483--12634 Score: 164
Period size: 32 Copynumber: 4.6 Consensus size: 33
12473 GATGACCCGT
*
12483 GCCGCCCCACTTGGGCGGCTT-ACCATGGGCAG
1 GCCGCCCCACTGGGGCGGCTTCACCATGGGCAG
*
12515 GCCGCCCCACTTGGGCGGCTTCACCATTGGGCAG
1 GCCGCCCCACTGGGGCGGCTTCACCA-TGGGCAG
* ***
12549 GCCGCCCCCACTGGGGCGGCTTCACTATGAATAG
1 GCCG-CCCCACTGGGGCGGCTTCACCATGGGCAG
* * * *
12583 GCCGCCCCAGTGGGGCGGCTTCGCCA-CGGTAG
1 GCCGCCCCACTGGGGCGGCTTCACCATGGGCAG
**
12615 GCCGCCCCGGTGGGGCGGCT
1 GCCGCCCCACTGGGGCGGCT
12635 CGGCTAATTT
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
32 43 0.41
33 23 0.22
34 19 0.18
35 20 0.19
ACGTcount: A:0.11, C:0.38, G:0.36, T:0.15
Consensus pattern (33 bp):
GCCGCCCCACTGGGGCGGCTTCACCATGGGCAG
Found at i:12733 original size:32 final size:32
Alignment explanation
Indices: 12692--12761 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
12682 ATTTTGGTCT
12692 AGCCGCCCCACCAGGGCGGCCTGCCATGGCAA
1 AGCCGCCCCACCAGGGCGGCCTGCCATGGCAA
** * *
12724 AGCCGCCCCATGAGGGCGGCCTGCCTTGGCGA
1 AGCCGCCCCACCAGGGCGGCCTGCCATGGCAA
12756 AGCCGC
1 AGCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.16, C:0.41, G:0.34, T:0.09
Consensus pattern (32 bp):
AGCCGCCCCACCAGGGCGGCCTGCCATGGCAA
Done.