Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019086.1 Corchorus olitorius cultivar O-4 contig19119, 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: 14844
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Found at i:331 original size:46 final size:46
Alignment explanation
Indices: 243--492 Score: 143
Period size: 46 Copynumber: 5.3 Consensus size: 46
233 GAAAGTTGTG
* * * * * * *
243 AGCCATTGGATTTTTGGTCAATTTTGGCCTTCGAAATTCGTGATGGAT
1 AGCCTTTGGATTTTCGATC-ATTTT-GCCCTCGAAAGTCGTGATAGTT
291 AGCCTTT-GACTTTTC-ATCAAATTTTGCCC-CGAAAGTCGTGATAGTT
1 AGCCTTTGGA-TTTTCGATC--ATTTTGCCCTCGAAAGTCGTGATAGTT
* * * *
337 ACCCTTTGGATTTTCGATCATTTTTCCCTCGATAGTCGTGATTGTT
1 AGCCTTTGGATTTTCGATCATTTTGCCCTCGAAAGTCGTGATAGTT
* * ** * * * *
383 AGCCTTCGGATTTTAGGCCATTTTTGGCCTCCAAATTTCTTGATAGTT
1 AGCCTTTGGATTTTCGATCA-TTTTGCCCTCGAAA-GTCGTGATAGTT
* * * *
431 AGCCTTAGGAATTTTAGA-CAATTTTGGCACC-C-AAAGTCGTGATGGTC
1 AGCCTTTGG-ATTTTCGATC-ATTTT-GC-CCTCGAAAGTCGTGATAGTT
*
478 AGCATTTGGATTTTC
1 AGCCTTTGGATTTTC
493 CACTAATTTT
Statistics
Matches: 158, Mismatches: 33, Indels: 24
0.73 0.15 0.11
Matches are distributed among these distances:
45 8 0.05
46 60 0.38
47 37 0.23
48 41 0.26
49 10 0.06
50 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (46 bp):
AGCCTTTGGATTTTCGATCATTTTGCCCTCGAAAGTCGTGATAGTT
Found at i:511 original size:47 final size:48
Alignment explanation
Indices: 450--540 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
440 AATTTTAGAC
* * *
450 AATTTTGGCACCCAAA-GTCGTGATGGTCAGCATTTGGATTTTCCACT
1 AATTTTAGCACCCAAATATCATGATGGTCAGCATTTGGATTTTCCACT
* * *
497 AATTTTAGCCCCCAAATATCATTATGGTTAGCATTTGGATTTTC
1 AATTTTAGCACCCAAATATCATGATGGTCAGCATTTGGATTTTC
541 AGCCATTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 14 0.38
48 23 0.62
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (48 bp):
AATTTTAGCACCCAAATATCATGATGGTCAGCATTTGGATTTTCCACT
Found at i:2172 original size:12 final size:13
Alignment explanation
Indices: 2155--2185 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
2145 GTGAGTAGAT
2155 GAAGAAGGA-GAA
1 GAAGAAGGAGGAA
2167 GAAGAAGGAGGAA
1 GAAGAAGGAGGAA
2180 GAAGAA
1 GAAGAA
2186 CCCTAATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (13 bp):
GAAGAAGGAGGAA
Found at i:5648 original size:41 final size:41
Alignment explanation
Indices: 5580--5673 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 41
5570 TCATCATAAT
5580 ATATCCTTCGAAAAATAAATCTCTTAAAAAATACATTATTAA
1 ATATCCTTC-AAAAATAAATCTCTTAAAAAATACATTATTAA
* * * * * *
5622 ATGTCCTTCAAAAATAATTTTTTTAAAAAATATATTCTTAA
1 ATATCCTTCAAAAATAAATCTCTTAAAAAATACATTATTAA
5663 ATATCCTTCAA
1 ATATCCTTCAA
5674 CAATGGAGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 37 0.82
42 8 0.18
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (41 bp):
ATATCCTTCAAAAATAAATCTCTTAAAAAATACATTATTAA
Found at i:6662 original size:33 final size:33
Alignment explanation
Indices: 6625--6700 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
6615 GGGATAACTT
*
6625 TAATATATAGAA-GATATAGATAA-ATAGATAATA
1 TAATATATAGAATAATATA-ATAATATA-ATAATA
* * *
6658 TAATAAATATAATAATATACTAATATAATAATA
1 TAATATATAGAATAATATAATAATATAATAATA
6691 TAATATATAG
1 TAATATATAG
6701 TAGGTTAGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (33 bp):
TAATATATAGAATAATATAATAATATAATAATA
Found at i:6674 original size:8 final size:8
Alignment explanation
Indices: 6638--6699 Score: 74
Period size: 8 Copynumber: 7.6 Consensus size: 8
6628 TATATAGAAG
6638 ATATAGATA
1 ATATA-ATA
6647 A-ATAGATA
1 ATATA-ATA
6655 ATATAATAA
1 ATATAAT-A
6664 ATATAATA
1 ATATAATA
*
6672 ATATACTA
1 ATATAATA
6680 ATATAATA
1 ATATAATA
6688 ATATAAT-
1 ATATAATA
6695 ATATA
1 ATATA
6700 GTAGGTTAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
7 5 0.10
8 32 0.65
9 12 0.24
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (8 bp):
ATATAATA
Found at i:6687 original size:13 final size:13
Alignment explanation
Indices: 6652--6697 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
6642 AGATAAATAG
6652 ATAATATAATAA-
1 ATAATATAATAAT
6664 AT-ATAATAAT-AT
1 ATAAT-ATAATAAT
6676 ACTAATATAATAAT
1 A-TAATATAATAAT
6690 ATAATATA
1 ATAATATA
6698 TAGTAGGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
11 3 0.10
12 8 0.28
13 13 0.45
14 5 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATATAATAAT
Done.