Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019067.1 Corchorus olitorius cultivar O-4 contig19100, 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: 7521
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:1042 original size:22 final size:21
Alignment explanation
Indices: 950--1043 Score: 62
Period size: 22 Copynumber: 4.2 Consensus size: 21
940 TTACTAGAAT
* *
950 TTCATTGGGAAATTACCAAAA
1 TTCATAGGAAAATTACCAAAA
* **
971 TCTAATAGGAGTTATTACCAAAA
1 T-TCATAGGA-AAATTACCAAAA
* * * *
994 TATAATAGGAAGATTACTAGAAT
1 T-TCATAGGAAAATTACCA-AAA
1017 TTCATAGGAAAATTACCAAAA
1 TTCATAGGAAAATTACCAAAA
1038 CTTCAT
1 -TTCAT
1044 GTCTTTTTCT
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
21 3 0.05
22 30 0.55
23 22 0.40
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (21 bp):
TTCATAGGAAAATTACCAAAA
Found at i:2647 original size:4 final size:4
Alignment explanation
Indices: 2638--2663 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2628 ACACAAAGAA
2638 TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
2664 CACATTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:2816 original size:2 final size:2
Alignment explanation
Indices: 2811--2837 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2801 CTATTTGGGA
2811 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 A
2838 ACATTTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5048 original size:36 final size:35
Alignment explanation
Indices: 4994--5082 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 35
4984 TAAATTTAAA
* *
4994 ATATATATATTT-T-GATTTTCTGATTATTAATGTT
1 ATATATATATTTATATATTTTCAGATTATTAAT-TT
*
5028 ATATATATATTTATATATTTTCAGATTTTTAATTT
1 ATATATATATTTATATATTTTCAGATTATTAATTT
* *
5063 ATA-AGATATATAATATATTT
1 ATATATATAT-TTATATATTT
5083 AAAATTAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
34 17 0.36
35 15 0.32
36 15 0.32
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (35 bp):
ATATATATATTTATATATTTTCAGATTATTAATTT
Found at i:5527 original size:31 final size:27
Alignment explanation
Indices: 5465--5534 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 27
5455 ACTTGTACAG
*
5465 TTTGGACGTTTTGCCCTAAACTGTAAT
1 TTTGGACGTTTTGCCCTAAACTCTAAT
5492 TTTGGACGTTTTGTCCCCCTAAACTCTCAAT
1 TTTGGACGTTTTG---CCCTAAACTCT-AAT
5523 TTTGGACGTTTT
1 TTTGGACGTTTT
5535 AACCCCTCTC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
27 13 0.34
30 10 0.26
31 15 0.39
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (27 bp):
TTTGGACGTTTTGCCCTAAACTCTAAT
Found at i:5541 original size:30 final size:27
Alignment explanation
Indices: 5465--5534 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 27
5455 ACTTGTACAG
* *
5465 TTTGGACGTTTTGCCCTAAACTGTAAT
1 TTTGGACGTTTTCCCCTAAACTCTAAT
5492 TTTGGACGTTTTGTCCCCCTAAACTCTCAAT
1 TTTGGACG-TTT-T-CCCCTAAACTCT-AAT
5523 TTTGGACGTTTT
1 TTTGGACGTTTT
5535 AACCCCTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 8 0.22
28 3 0.08
29 2 0.05
30 13 0.35
31 11 0.30
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (27 bp):
TTTGGACGTTTTCCCCTAAACTCTAAT
Found at i:5914 original size:29 final size:30
Alignment explanation
Indices: 5865--5930 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
5855 GAAAAAAAAG
* * *
5865 TCCAAAATTAAGAGTTTAGGGGATAAAATA
1 TCCAAAATTAAGAGTTCAGGGGACAAAACA
*
5895 TCCAAAATTAA-AGTTCAGGGGGCAAAACA
1 TCCAAAATTAAGAGTTCAGGGGACAAAACA
5924 TCCAAAA
1 TCCAAAA
5931 CAATACAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.21
Consensus pattern (30 bp):
TCCAAAATTAAGAGTTCAGGGGACAAAACA
Done.