Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023750.1 Corchorus olitorius cultivar O-4 contig23783, 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: 8144
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:418 original size:5 final size:5
Alignment explanation
Indices: 387--416 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
377 AATCTGCTCA
387 TCTTT TCTTT TCTTT TCTTT TCTTT T-TTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
417 TTCATGTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TCTTT
Found at i:2032 original size:22 final size:22
Alignment explanation
Indices: 2007--2053 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
1997 TGTTGAATCT
**
2007 AGTGGCCAAGTGTTTTTCTGCA
1 AGTGGCCAAGTAATTTTCTGCA
*
2029 AGT-GCCAATTAATTTTCTGCA
1 AGTGGCCAAGTAATTTTCTGCA
2050 AGTG
1 AGTG
2054 TTTTTCTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (22 bp):
AGTGGCCAAGTAATTTTCTGCA
Found at i:2220 original size:26 final size:26
Alignment explanation
Indices: 2184--2234 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
2174 AACCCAAGAG
2184 AAGGATGAATCGAAATTGAAAACAAC
1 AAGGATGAATCGAAATTGAAAACAAC
2210 AAGGATGAATCGAAATTGAAAACAA
1 AAGGATGAATCGAAATTGAAAACAA
2235 AAACTGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.55, C:0.10, G:0.20, T:0.16
Consensus pattern (26 bp):
AAGGATGAATCGAAATTGAAAACAAC
Found at i:2483 original size:33 final size:33
Alignment explanation
Indices: 2441--2516 Score: 152
Period size: 33 Copynumber: 2.3 Consensus size: 33
2431 ACCAGCAGAT
2441 AGGGAGAAGATAATGGTAACAGAGGAGAGGAGA
1 AGGGAGAAGATAATGGTAACAGAGGAGAGGAGA
2474 AGGGAGAAGATAATGGTAACAGAGGAGAGGAGA
1 AGGGAGAAGATAATGGTAACAGAGGAGAGGAGA
2507 AGGGAGAAGA
1 AGGGAGAAGA
2517 GACTTAGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.03, G:0.43, T:0.08
Consensus pattern (33 bp):
AGGGAGAAGATAATGGTAACAGAGGAGAGGAGA
Found at i:5573 original size:163 final size:162
Alignment explanation
Indices: 5258--5573 Score: 431
Period size: 163 Copynumber: 1.9 Consensus size: 162
5248 TCCAGTGAGA
5258 AAACGCCGCTATATATTATAGGCGTAGAGTTGAAAAATTTCTTTGTTTTAGTAGGAGGGAATTTT
1 AAACGCCGCTATATATTATAGGCGTAGAGTTGAAAAATTTCTTTGTTTTAGTAGGAGGGAATTTT
* * *
5323 TCCCTCCAAAAAAGGGAAAATAATATCTCTCCCTCGATATATTAAAATAGCGGCGTTTGCTTTTC
66 TCCCTCCAAAAAAGGGAAAATAAAATCTCTCCCTCCATATATTAAAATAGCGGCGTTTGCTTGTC
* * * *
5388 TAGACGCTACTAATTAGCGGCGTTTGAGGTCC
131 AAAACGCCACTAAATAGCGGCGTTTGAGGTCC
* * * *
5420 AAACGCCGCTA-ATATTATAGGTGTAGAGTTGTAAACTTTCTTTGTTTTAGTGGGGAGGGAATTT
1 AAACGCCGCTATATATTATAGGCGTAGAGTTGAAAAATTTCTTTGTTTTAGT-AGGAGGGAATTT
* * *
5484 TTCCCTCCAAAAAAAGGAGAAAA-AAAATCTCTCCCTCCATATATTAATATGGCGGCGTCTTTC-
65 TTCCCTCC-AAAAAAGG-GAAAATAAAATCTCTCCCTCCATATATTAAAATAGCGGCGT-TTGCT
* *
5547 TGTCAAAATGCCACTAAATGGCGGCGT
127 TGTCAAAACGCCACTAAATAGCGGCGT
5574 CTGAAAAAAA
Statistics
Matches: 134, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
161 37 0.28
162 30 0.22
163 59 0.44
164 8 0.06
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (162 bp):
AAACGCCGCTATATATTATAGGCGTAGAGTTGAAAAATTTCTTTGTTTTAGTAGGAGGGAATTTT
TCCCTCCAAAAAAGGGAAAATAAAATCTCTCCCTCCATATATTAAAATAGCGGCGTTTGCTTGTC
AAAACGCCACTAAATAGCGGCGTTTGAGGTCC
Found at i:5591 original size:163 final size:162
Alignment explanation
Indices: 5193--5595 Score: 424
Period size: 162 Copynumber: 2.5 Consensus size: 162
5183 CTTTCTTTCA
* * * * * * *
5193 CTCCATATATTACAATTGCGGCGTTTCCTTCCG-C-AGACGCCGCTAAATAGCGGCGTC-CAGTG
1 CTCCATATATTAAAATAGCGGCGTTTGCTT--GTCAAAACGCCACTAAATAGCGGCGTCTGAG-A
*
5255 AGAAAACGCCGCTATATATTATAGGCGTAGAGTTGAAAAATTTCTTTGTTTTAGTAGGAGGGAAT
63 AAAAAACGCCGCTATATATTATAGGCGTAGAGTTGAAAAATTTCTTTGTTTTAGTAGGAGGGAAT
*
5320 TTTTCCCTCCAAAAAAGGGAAAATAATATCTCTCC
128 TTTTCCCTCCAAAAAAGGGAAAATAAAATCTCTCC
* * * * * * * ****
5355 CTCGATATATTAAAATAGCGGCGTTTGCTTTTCTAGACGCTACTAATTAGCGGCGTTTGAGGTCC
1 CTCCATATATTAAAATAGCGGCGTTTGCTTGTCAAAACGCCACTAAATAGCGGCGTCTGAGAAAA
* * * *
5420 AAACGCCGCTA-ATATTATAGGTGTAGAGTTGTAAACTTTCTTTGTTTTAGTGGGGAGGGAATTT
66 AAACGCCGCTATATATTATAGGCGTAGAGTTGAAAAATTTCTTTGTTTTAGT-AGGAGGGAATTT
5484 TTCCCTCCAAAAAAAGGAGAAAA-AAAATCTCTCC
130 TTCCCTCC-AAAAAAGG-GAAAATAAAATCTCTCC
* * * * *
5518 CTCCATATATTAATATGGCGGCGTCTTTC-TGTCAAAATGCCACTAAATGGCGGCGTCTGA-AAA
1 CTCCATATATTAAAATAGCGGCGT-TTGCTTGTCAAAACGCCACTAAATAGCGGCGTCTGAGAAA
5581 AAAGACGCCGCTATA
65 AAA-ACGCCGCTATA
5596 GTCAATTTCA
Statistics
Matches: 198, Mismatches: 34, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
161 38 0.19
162 78 0.39
163 73 0.37
164 9 0.05
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (162 bp):
CTCCATATATTAAAATAGCGGCGTTTGCTTGTCAAAACGCCACTAAATAGCGGCGTCTGAGAAAA
AAACGCCGCTATATATTATAGGCGTAGAGTTGAAAAATTTCTTTGTTTTAGTAGGAGGGAATTTT
TCCCTCCAAAAAAGGGAAAATAAAATCTCTCC
Found at i:6970 original size:16 final size:16
Alignment explanation
Indices: 6949--6984 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
6939 TCTGAAAATA
6949 CTTTAGAGCTTTTCTG
1 CTTTAGAGCTTTTCTG
*
6965 CTTTAGAGCTTTTTTG
1 CTTTAGAGCTTTTCTG
6981 CTTT
1 CTTT
6985 CTGAATTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.56
Consensus pattern (16 bp):
CTTTAGAGCTTTTCTG
Found at i:7838 original size:69 final size:68
Alignment explanation
Indices: 7693--7871 Score: 199
Period size: 69 Copynumber: 2.7 Consensus size: 68
7683 CAAATTTTGT
* * * * * *
7693 CTAAGCCGTCCTTTGCAGGATTTTCAGCTTAGCGAG----ACTTTTTTTTTTCCGCTCTAACTTT
1 CTAAGCCATCCTTTACAGAATTTTCAACTTAGCGAGCTTTTCTTTTTTTTTTCCACTCTAACTTT
*
7754 TGC
66 TCC
* *
7757 CTAAGCCATCCTTTACAGGATTTTCAACTTAGCGAGCCTTTTCTTTTTTTTTTTCACTCTAACTT
1 CTAAGCCATCCTTTACAGAATTTTCAACTTAGCGAG-CTTTTCTTTTTTTTTTCCACTCTAACTT
7822 TTCC
65 TTCC
* *
7826 CTAATCTC-TCCTTTATAGAATTTTCAACTTAGCGAGCTTTT-TTTTT
1 CTAAGC-CATCCTTTACAGAATTTTCAACTTAGCGAGCTTTTCTTTTT
7872 GTTGGGCAGT
Statistics
Matches: 99, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
64 33 0.33
67 5 0.05
68 5 0.05
69 55 0.56
70 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.46
Consensus pattern (68 bp):
CTAAGCCATCCTTTACAGAATTTTCAACTTAGCGAGCTTTTCTTTTTTTTTTCCACTCTAACTTT
TCC
Done.