Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015127.1 Corchorus capsularis cultivar CVL-1 contig15148, 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: 8696
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:1626 original size:31 final size:31
Alignment explanation
Indices: 1591--1652 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1581 CACAAGAGAA
*
1591 CTCTTGATTCATGAATAATTACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
*
1622 CTCTTGATTCATGAATAATCATAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
1653 TAATGACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (31 bp):
CTCTTGATTCATGAATAATCACAATATTCAT
Found at i:5996 original size:7 final size:7
Alignment explanation
Indices: 5984--6010 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5974 TACAAGGTGA
5984 TTCAAAT
1 TTCAAAT
5991 TTCAAAT
1 TTCAAAT
5998 TTCAAAT
1 TTCAAAT
6005 TTCAAA
1 TTCAAA
6011 GCAAAGCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (7 bp):
TTCAAAT
Found at i:6532 original size:2 final size:2
Alignment explanation
Indices: 6527--6558 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6517 CATTATTCTC
6527 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
6559 TAACTAGCAA
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:7371 original size:3 final size:3
Alignment explanation
Indices: 7363--7387 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
7353 TGGTTGTAAA
7363 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
7388 CAACTTAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:8141 original size:70 final size:70
Alignment explanation
Indices: 8059--8291 Score: 297
Period size: 70 Copynumber: 3.2 Consensus size: 70
8049 TTGTTTAGGT
* * *
8059 TTTTA-TAGTTTTACTCCACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATT
8123 ATTTTA
65 ATTTTA
8129 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTT-T-A-TA
*
8194 TTATATTTTACCA
62 AT-TATTTT---A
* * *
8207 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
8272 TTATA
66 TTTTA
*
8277 TTTTACAATTTTACT
1 TTTTACTATTTTACT
8292 ATTTTAGTTA
Statistics
Matches: 144, Mismatches: 10, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
70 63 0.44
71 5 0.03
72 1 0.01
73 6 0.04
74 5 0.03
75 7 0.05
76 1 0.01
77 2 0.01
78 54 0.38
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:8141 original size:78 final size:77
Alignment explanation
Indices: 8059--8297 Score: 350
Period size: 78 Copynumber: 3.2 Consensus size: 77
8049 TTGTTTAGGT
* * *
8059 TTTTA-TAGTTTTACTCCACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-T
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
*
8119 AAT-TATTTT--A
65 ATTATATTTTACA
8129 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
8194 TTATATTTTACCA
66 TTATATTTTA-CA
*
8207 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
8272 TTATATTTTACAA
66 TTATATTTTAC-A
8285 TTTTACTATTTTA
1 TTTTACTATTTTA
8298 GTTAAAAAAA
Statistics
Matches: 154, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
70 48 0.31
71 5 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 89 0.58
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACA
Done.