Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023946.1 Corchorus olitorius cultivar O-4 contig23979, 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: 5363
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:635 original size:27 final size:27
Alignment explanation
Indices: 597--659 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
587 AAGTGAGCTT
597 AAATGACCAAAATGCCCCTGGACGTGC
1 AAATGACCAAAATGCCCCTGGACGTGC
*
624 AAATGACCAAAATGCCCCTGGACGTGT
1 AAATGACCAAAATGCCCCTGGACGTGC
651 AAATG-CCAA
1 AAATGACCAA
660 TTAAGAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 4 0.11
27 31 0.89
ACGTcount: A:0.37, C:0.27, G:0.21, T:0.16
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGACGTGC
Found at i:1126 original size:50 final size:50
Alignment explanation
Indices: 1051--1216 Score: 287
Period size: 50 Copynumber: 3.3 Consensus size: 50
1041 CATTAAACTC
*
1051 GGCTTATGGAAAAGCCCATGTTGATAATTGACTCGTATGGAAACGAGTTT
1 GGCTTATGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTT
* * *
1101 GGCTTGTGGAAAAGCCTGTGTTGATAATTGACTCGTATGGAAACGAGTTC
1 GGCTTATGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTT
*
1151 GGCTTGTGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTT
1 GGCTTATGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTT
1201 GGCTTATGGAAAAGCC
1 GGCTTATGGAAAAGCC
1217 AAAGGATTCG
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 109 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (50 bp):
GGCTTATGGAAAAGCCTATGTTGATAATTGACTCGTATGGAAACGAGTTT
Found at i:1467 original size:91 final size:91
Alignment explanation
Indices: 1295--1592 Score: 426
Period size: 91 Copynumber: 3.3 Consensus size: 91
1285 AAGAAAATAC
* *
1295 CTTGGAAAATAACTCTGAATCTGATGTTGTAACTGAAAACTTCTTGATTGATGAT-AAAAAGGGA
1 CTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAA-GGA
* *
1359 CCAATGTGCGGTGAACTTGAAAAACAA
65 CCAATTTGCGGTCAACTTGAAAAACAA
* *
1386 CTTGAAAAATAACTCTGAGTCTTATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAGAGGAC
1 CTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGAC
* *
1451 CAATTTGCAGTCAACTTGACAAACAA
66 CAATTTGCGGTCAACTTGAAAAACAA
*
1477 CTTGAAAAATAACTCTGAGTCTGATGTTGTAATTGAAAACTTCTTGATTGATGATGAAAAAGGAC
1 CTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGAC
* **
1542 CAATTTGCGGTCAATTTTG----GTAA
66 CAATTTGCGGTCAA-CTTGAAAAACAA
*
1565 CTTGAAGAATAACTCTGAGTCTGATGTT
1 CTTGAAAAATAACTCTGAGTCTGATGTT
1593 ATGATTAACT
Statistics
Matches: 189, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
88 29 0.15
91 153 0.81
92 7 0.04
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (91 bp):
CTTGAAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGAC
CAATTTGCGGTCAACTTGAAAAACAA
Found at i:2072 original size:50 final size:48
Alignment explanation
Indices: 2010--2147 Score: 174
Period size: 45 Copynumber: 2.9 Consensus size: 48
2000 AATGTCCTTC
*
2010 GAAAAGCGAATTTTGATCTTGGACTGACAAATGGAATGCAATCTTACTTT
1 GAAAAGCGAATTTTGATCTTGGACT-A-AAATGGAAAGCAATCTTACTTT
* * *
2060 GAAAAGC-AAATTTGATCTTGGACT--TATGGAAAGCAATTTTACTTT
1 GAAAAGCGAATTTTGATCTTGGACTAAAATGGAAAGCAATCTTACTTT
*
2105 GAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATC
1 GAAAAGCGAATTTTGATCTTGGACT-A-AAATGGAAAGCAATC
2148 GTATTGTAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
45 25 0.33
46 15 0.20
49 16 0.21
50 19 0.25
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (48 bp):
GAAAAGCGAATTTTGATCTTGGACTAAAATGGAAAGCAATCTTACTTT
Found at i:2756 original size:6 final size:6
Alignment explanation
Indices: 2745--2815 Score: 73
Period size: 6 Copynumber: 12.7 Consensus size: 6
2735 ATCAATTCTC
2745 TTTTGA TTTTGA TTTT-A -TTTGA TTTTGA TTTTGA -TTTGA TTTTG-
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
* *
2789 TTTT-T TTATTGA CTTTGA -TTTGA TTTT
1 TTTTGA TT-TTGA TTTTGA TTTTGA TTTT
2816 TTTTTTGAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
4 3 0.05
5 18 0.32
6 34 0.61
7 1 0.02
ACGTcount: A:0.15, C:0.01, G:0.14, T:0.69
Consensus pattern (6 bp):
TTTTGA
Found at i:2770 original size:22 final size:22
Alignment explanation
Indices: 2745--2815 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 22
2735 ATCAATTCTC
*
2745 TTTTGATTTTGATTTTATTTGA
1 TTTTGATTTTGATTTGATTTGA
2767 TTTTGATTTTGATTTGATTTTG-
1 TTTTGATTTTGATTTGA-TTTGA
*
2789 TTTT-TTTATTGACTTTGATTTGA
1 TTTTGATT-TTGA-TTTGATTTGA
2812 TTTT
1 TTTT
2816 TTTTTTGAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.05
22 28 0.65
23 13 0.30
ACGTcount: A:0.15, C:0.01, G:0.14, T:0.69
Consensus pattern (22 bp):
TTTTGATTTTGATTTGATTTGA
Found at i:2820 original size:28 final size:27
Alignment explanation
Indices: 2746--2821 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 27
2736 TCAATTCTCT
** *
2746 TTTGATTTTGATTTTATTTGATTTTGAT
1 TTTGA-TTTGATTTTATTTTTTTTTGAC
*
2774 TTTGATTTGATTTTGTTTTTTTATTGAC
1 TTTGATTTGATTTTATTTTTTT-TTGAC
2802 TTTGATTTGATTTT-TTTTTT
1 TTTGATTTGATTTTATTTTTT
2822 GAATTTTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 20 0.47
28 23 0.53
ACGTcount: A:0.14, C:0.01, G:0.13, T:0.71
Consensus pattern (27 bp):
TTTGATTTGATTTTATTTTTTTTTGAC
Done.