Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013774.1 Corchorus olitorius cultivar O-4 contig13807, 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: 12310
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--52 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1 AT AT AT AT AT 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 AT AT AT AT AT
43 AT AT AT AT AT
1 AT AT AT AT AT
53 CAAAAAGCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6798 original size:31 final size:31
Alignment explanation
Indices: 6763--6823 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
6753 AATGGATTTG
*
6763 TTTTTTCTTAAGAAAAAGATCTACTTGTTTT
1 TTTTTTCTTAACAAAAAGATCTACTTGTTTT
* ** *
6794 TTTTTTTTTGCCCAAAAGATCTACTTGTTT
1 TTTTTTCTTAACAAAAAGATCTACTTGTTT
6824 AAAACAAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (31 bp):
TTTTTTCTTAACAAAAAGATCTACTTGTTTT
Found at i:7372 original size:35 final size:35
Alignment explanation
Indices: 7332--7406 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
7322 AGTTCGTTTA
7332 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
7367 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
7402 TGTTC
1 TGTTC
7407 GTTTATATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (35 bp):
TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
Found at i:7469 original size:16 final size:16
Alignment explanation
Indices: 7448--7496 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
7438 TATAATTATT
7448 TATATATTAATAATAA
1 TATATATTAATAATAA
*
7464 TATATATTATTAATAA
1 TATATATTAATAATAA
* *
7480 AAT-TA-TAAAAATAA
1 TATATATTAATAATAA
7494 TAT
1 TAT
7497 TCTATTATCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 9 0.32
15 2 0.07
16 17 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:7474 original size:19 final size:19
Alignment explanation
Indices: 7432--7479 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
7422 AAACGTTCGT
* *
7432 TTATTATATAATTATTTATA
1 TTATTA-ATAATAATATATA
7452 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
7470 TTATTAATAA
1 TTATTAATAA
7480 AATTATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:7486 original size:19 final size:19
Alignment explanation
Indices: 7432--7486 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
7422 AAACGTTCGT
* *
7432 TTATT-ATATAATTATTTA
1 TTATTAATAAAATTATATA
7450 TATATTAATAATAA-TATATA
1 T-TATTAATAA-AATTATATA
7470 TTATTAATAAAATTATA
1 TTATTAATAAAATTATA
7487 AAAATAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
18 3 0.10
19 17 0.55
20 9 0.29
21 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTAATAAAATTATATA
Found at i:7626 original size:18 final size:18
Alignment explanation
Indices: 7599--7633 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
7589 AATTATTACA
7599 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
7617 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
7634 CAGTTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:9929 original size:11 final size:11
Alignment explanation
Indices: 9892--9944 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
9882 TGTGGGATTT
9892 TTAA-TAATAA
1 TTAATTAATAA
9902 TT-ATTCAATAAA
1 TTAATT-AAT-AA
* *
9914 ATAATTAATAT
1 TTAATTAATAA
9925 TTAATTAATAA
1 TTAATTAATAA
9936 TTAATTAAT
1 TTAATTAAT
9945 TTCAGTCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
9 1 0.03
10 3 0.09
11 22 0.63
12 6 0.17
13 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
TTAATTAATAA
Found at i:10325 original size:13 final size:13
Alignment explanation
Indices: 10307--10332 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10297 AAGGTAACAA
10307 CAAAAATCATCAC
1 CAAAAATCATCAC
10320 CAAAAATCATCAC
1 CAAAAATCATCAC
10333 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Done.