Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010347.1 Corchorus capsularis cultivar CVL-1 contig10368, 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: 47976
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7144 original size:4 final size:4
Alignment explanation
Indices: 7137--7168 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
7127 AGAAAAAAAA
7137 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
7169 TCTTACCGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:8214 original size:6 final size:6
Alignment explanation
Indices: 8203--8239 Score: 56
Period size: 6 Copynumber: 5.8 Consensus size: 6
8193 TCTATTAATT
8203 AAAAAG AAAAAG AAAAAG AAAAAG AAAGAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG -AA-AAAG AAAAA
8240 TAGAGAACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 21 0.72
7 4 0.14
8 4 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:14445 original size:18 final size:18
Alignment explanation
Indices: 14424--14464 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
14414 TATCAACCAG
14424 ATTCCCATTCT-CATTATC
1 ATTCCCATTCTGC-TTATC
*
14442 ATTCTCATTCTGCTTATC
1 ATTCCCATTCTGCTTATC
14460 ATTCC
1 ATTCC
14465 TATCATCACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.20, C:0.32, G:0.02, T:0.46
Consensus pattern (18 bp):
ATTCCCATTCTGCTTATC
Found at i:17092 original size:181 final size:181
Alignment explanation
Indices: 16788--17150 Score: 726
Period size: 181 Copynumber: 2.0 Consensus size: 181
16778 ATTTGACATT
16788 AAGAAATTATATTGATTTGACTATTTTCATTCATATCAGACTAAATGTGTTAGATAAATAACTGA
1 AAGAAATTATATTGATTTGACTATTTTCATTCATATCAGACTAAATGTGTTAGATAAATAACTGA
16853 TATAAGTTTCATAGAGACATCATAATTGCACAAAAATGTTACAAACCATCTCACTCAAACATTGC
66 TATAAGTTTCATAGAGACATCATAATTGCACAAAAATGTTACAAACCATCTCACTCAAACATTGC
16918 TACTCATAATAGCAAAGTGAAATCTCCATGAATTCAATTGATATTGTTAGG
131 TACTCATAATAGCAAAGTGAAATCTCCATGAATTCAATTGATATTGTTAGG
16969 AAGAAATTATATTGATTTGACTATTTTCATTCATATCAGACTAAATGTGTTAGATAAATAACTGA
1 AAGAAATTATATTGATTTGACTATTTTCATTCATATCAGACTAAATGTGTTAGATAAATAACTGA
17034 TATAAGTTTCATAGAGACATCATAATTGCACAAAAATGTTACAAACCATCTCACTCAAACATTGC
66 TATAAGTTTCATAGAGACATCATAATTGCACAAAAATGTTACAAACCATCTCACTCAAACATTGC
17099 TACTCATAATAGCAAAGTGAAATCTCCATGAATTCAATTGATATTGTTAGG
131 TACTCATAATAGCAAAGTGAAATCTCCATGAATTCAATTGATATTGTTAGG
17150 A
1 A
17151 TTCATTGAAA
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
181 182 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (181 bp):
AAGAAATTATATTGATTTGACTATTTTCATTCATATCAGACTAAATGTGTTAGATAAATAACTGA
TATAAGTTTCATAGAGACATCATAATTGCACAAAAATGTTACAAACCATCTCACTCAAACATTGC
TACTCATAATAGCAAAGTGAAATCTCCATGAATTCAATTGATATTGTTAGG
Found at i:17272 original size:100 final size:99
Alignment explanation
Indices: 17077--17273 Score: 245
Period size: 100 Copynumber: 2.0 Consensus size: 99
17067 AAATGTTACA
* ** *
17077 AACCATCTCACTCAAACATTGCTACTCATAATAGCAAAGTGAAATCTCCATGAATTCAATTGATA
1 AACCATCTCACTCAAACATTACTACTCATAATAAAAAAGTGAAATCTCCACGAATTCAATTGATA
*
17142 TTGTTAGGATTCATTGAAATGAAACTACACTTAT
66 TTGTTAGGAGTCATTGAAATGAAACTACACTTAT
* * * ** *
17176 AACCATCTCACTCAAATATTACTACTTCATGATAAAAAAGTGAAATTTTGACGAGTTCAATTGAT
1 AACCATCTCACTCAAACATTACTAC-TCATAATAAAAAAGTGAAATCTCCACGAATTCAATTGAT
*
17241 CTT-TTGAGGAGTCACTTGAAATGAAAC-ACACTT
65 ATTGTT-AGGAGTCA-TTGAAATGAAACTACACTT
17274 GTTTATATCA
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
99 25 0.30
100 46 0.55
101 12 0.14
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (99 bp):
AACCATCTCACTCAAACATTACTACTCATAATAAAAAAGTGAAATCTCCACGAATTCAATTGATA
TTGTTAGGAGTCATTGAAATGAAACTACACTTAT
Found at i:27958 original size:1 final size:1
Alignment explanation
Indices: 27952--27990 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
27942 CCTTTGATCC
* * *
27952 AAAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
27991 GAAAGAAAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:27991 original size:15 final size:15
Alignment explanation
Indices: 27955--28002 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
27945 TTGATCCAAA
* * *
27955 AAAAAAAAAAAAAAA
1 AAAAAAGAAAGAAAG
27970 AAAAAAGAAAGAAAG
1 AAAAAAGAAAGAAAG
27985 AAAAAAGAAAGAAAG
1 AAAAAAGAAAGAAAG
28000 AAA
1 AAA
28003 CTCTCCCATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAGAAAG
Found at i:27995 original size:4 final size:4
Alignment explanation
Indices: 27973--28002 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
27963 AAAAAAAAAA
27973 AAAG AAAG AAAG AAA- AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
28003 CTCTCCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:45683 original size:2 final size:2
Alignment explanation
Indices: 45651--45675 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45641 CCATGTGAAA
45651 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 A
45676 GTTATATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46738 original size:3 final size:3
Alignment explanation
Indices: 46732--46770 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
46722 TTATTATACT
46732 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
46771 TTTGAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.