Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007124.1 Corchorus capsularis cultivar CVL-1 contig07145, 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: 36583
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7946 original size:2 final size:2
Alignment explanation
Indices: 7939--7966 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7929 AACGACAATC
7939 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
7967 TCCTTTATCT
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):
AT
Found at i:10282 original size:29 final size:30
Alignment explanation
Indices: 10242--10303 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
10232 TCTCACGGAA
*
10242 TGTGAGTTTTCTTT-AAATTTATTTATTTG
1 TGTGAATTTTCTTTGAAATTTATTTATTTG
* *
10271 TGTGAATTTTCTTTGTAATTTATTTGTTTG
1 TGTGAATTTTCTTTGAAATTTATTTATTTG
10301 TGT
1 TGT
10304 ATTTAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.18, C:0.03, G:0.16, T:0.63
Consensus pattern (30 bp):
TGTGAATTTTCTTTGAAATTTATTTATTTG
Found at i:13054 original size:32 final size:32
Alignment explanation
Indices: 13013--13073 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
13003 TGCTGCAATA
* *
13013 ATTTTGTTCGAATAAAATTAACTTATAAACTG
1 ATTTAGTTCGAATAAAATCAACTTATAAACTG
**
13045 ATTTAGTTCGAATATGATCAACTTATAAA
1 ATTTAGTTCGAATAAAATCAACTTATAAA
13074 TATAAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (32 bp):
ATTTAGTTCGAATAAAATCAACTTATAAACTG
Found at i:13248 original size:22 final size:22
Alignment explanation
Indices: 13216--13372 Score: 114
Period size: 22 Copynumber: 7.2 Consensus size: 22
13206 TAAATATTTT
13216 TATGAAATTTTGATAACTATCC
1 TATGAAATTTTGATAACTATCC
* * *
13238 TATTAAATTTTGATAACCACCC
1 TATGAAATTTTGATAACTATCC
* *
13260 TATGAAGTTTTGATAATTAT-C
1 TATGAAATTTTGATAACTATCC
* *
13281 TATGAAATTGTGATAA--AGGCC
1 TATGAAATTTTGATAACTA-TCC
* *
13302 ATATGAAACTTTGATAACCTA-AC
1 -TATGAAATTTTGATAA-CTATCC
13325 TATGAAATTTT-AGTAAATCT-TCC
1 TATGAAATTTTGA-T-AA-CTATCC
13348 TATGAAATTTTG-TAATCT-TCC
1 TATGAAATTTTGATAA-CTATCC
13369 TATG
1 TATG
13373 TTTTTTTATA
Statistics
Matches: 108, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
19 1 0.01
21 29 0.27
22 60 0.56
23 17 0.16
25 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACTATCC
Found at i:13366 original size:21 final size:21
Alignment explanation
Indices: 13324--13402 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
13314 GATAACCTAA
13324 CTATGAAATTTTAGTAAATCTTC
1 CTATGAAATTTT-GT-AATCTTC
13347 CTATGAAATTTTGTAATCTTC
1 CTATGAAATTTTGTAATCTTC
*** * *
13368 CTATGTTTTTTTATAATCTCC
1 CTATGAAATTTTGTAATCTTC
*
13389 CTATGAGATTTTGT
1 CTATGAAATTTTGT
13403 TAATTTTCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 33 0.70
22 2 0.04
23 12 0.26
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (21 bp):
CTATGAAATTTTGTAATCTTC
Found at i:13421 original size:42 final size:41
Alignment explanation
Indices: 13340--13425 Score: 93
Period size: 42 Copynumber: 2.1 Consensus size: 41
13330 AATTTTAGTA
* **
13340 AATCTTCCTATGAAATTTTGTAATCTTCCTATGTTTTTTTAT
1 AATCTCCCTATGAAATTTTGTAATCTTCCTATGAATTTTT-T
* * *
13382 AATCTCCCTATGAGATTTTGTTAATTTTCTTAT-AATTTTTT
1 AATCTCCCTATGAAATTTTG-TAATCTTCCTATGAATTTTTT
13423 AAT
1 AAT
13426 ACTATAATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.11
42 23 0.62
43 10 0.27
ACGTcount: A:0.26, C:0.13, G:0.07, T:0.55
Consensus pattern (41 bp):
AATCTCCCTATGAAATTTTGTAATCTTCCTATGAATTTTTT
Found at i:16364 original size:2 final size:2
Alignment explanation
Indices: 16357--16385 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16347 GTAGTTAGAA
16357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16386 ACTAGGTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17319 original size:8 final size:8
Alignment explanation
Indices: 17306--17332 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
17296 GGGTTGGTCA
17306 ATAATAAT
1 ATAATAAT
17314 ATAATAAT
1 ATAATAAT
17322 ATAATAAT
1 ATAATAAT
17330 ATA
1 ATA
17333 TATATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATAATAAT
Found at i:18742 original size:7 final size:7
Alignment explanation
Indices: 18727--18761 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
18717 TGTGTATTAT
18727 AAAAA-A
1 AAAAAGA
18733 AAAAAGA
1 AAAAAGA
18740 AAAAAGA
1 AAAAAGA
18747 AAAAAGA
1 AAAAAGA
*
18754 AAAGAGA
1 AAAAAGA
18761 A
1 A
18762 GATGTGGGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:21895 original size:20 final size:20
Alignment explanation
Indices: 21872--21917 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
21862 GATATATCGA
21872 GATATCGAT-AAATATCGACG
1 GATATC-ATGAAATATCGACG
*
21892 GATA-CATGGATATATCGACG
1 GATATCAT-GAAATATCGACG
21912 GATATC
1 GATATC
21918 CCGTGACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 2 0.09
19 1 0.05
20 18 0.82
21 1 0.05
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (20 bp):
GATATCATGAAATATCGACG
Found at i:23151 original size:14 final size:14
Alignment explanation
Indices: 23132--23161 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
23122 ACAAAATTTC
23132 ATTTCTTACCTGAA
1 ATTTCTTACCTGAA
23146 ATTTCTTACCTGAA
1 ATTTCTTACCTGAA
23160 AT
1 AT
23162 GACCTGACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (14 bp):
ATTTCTTACCTGAA
Found at i:24684 original size:21 final size:21
Alignment explanation
Indices: 24660--24700 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24650 CCTATAGCCT
*
24660 AGGAGGCGCCTCCCTGTTTTA
1 AGGAGACGCCTCCCTGTTTTA
**
24681 AGGAGACTTCTCCCTGTTTT
1 AGGAGACGCCTCCCTGTTTT
24701 TTGTATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.27, G:0.24, T:0.34
Consensus pattern (21 bp):
AGGAGACGCCTCCCTGTTTTA
Found at i:30325 original size:16 final size:16
Alignment explanation
Indices: 30304--30338 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
30294 TTCACTCTCC
30304 TTTTCTTT-TCTTTTCT
1 TTTTCTTTGT-TTTTCT
30320 TTTTCTTTGTTTTTCT
1 TTTTCTTTGTTTTTCT
30336 TTT
1 TTT
30339 GGGGCATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.94
17 1 0.06
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (16 bp):
TTTTCTTTGTTTTTCT
Found at i:30915 original size:27 final size:27
Alignment explanation
Indices: 30877--30952 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
30867 TGGACTTGAG
* * **
30877 ATGACCAAAATGCCCATGAATGTGCGA
1 ATGACCAAAATGCCCCTGAATGCGAAA
30904 ATGACCAAAATGCCCCTGAATGCGAAA
1 ATGACCAAAATGCCCCTGAATGCGAAA
*
30931 ATGACCAAAATCCCCCTGAATG
1 ATGACCAAAATGCCCCTGAATG
30953 ACCCTAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.17
Consensus pattern (27 bp):
ATGACCAAAATGCCCCTGAATGCGAAA
Found at i:35270 original size:9 final size:9
Alignment explanation
Indices: 35256--35283 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
35246 GTTGCGCACC
35256 CAACTTCAT
1 CAACTTCAT
35265 CAACTTCAT
1 CAACTTCAT
35274 CAACTTCAT
1 CAACTTCAT
35283 C
1 C
35284 TTGTTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (9 bp):
CAACTTCAT
Done.