Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022477.1 Corchorus olitorius cultivar O-4 contig22510, 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: 30796
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6018 original size:72 final size:71
Alignment explanation
Indices: 5931--6072 Score: 239
Period size: 72 Copynumber: 2.0 Consensus size: 71
5921 AAGTTTCAGC
*
5931 TACCTAGCTAAAGCTAATCATGTCAGCTAAAATTTAAGTAAATTTTGGTTGAATGATAGGATTTA
1 TACCTAGCTAAAGCTAATCATGTCAGCTAAAATTTAAGT-AATTTTGGTTGAATGATAGGATGTA
*
5996 ATAAGTA
65 AGAAGTA
* *
6003 TACCTAGCTACAGCTAATCATGTCAGCTAAAATTTAAGTAATTTTGGTTGAATGATTGGATGTAA
1 TACCTAGCTAAAGCTAATCATGTCAGCTAAAATTTAAGTAATTTTGGTTGAATGATAGGATGTAA
6068 GAAGT
66 GAAGT
6073 TGAAGAAAGA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 28 0.42
72 38 0.58
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.35
Consensus pattern (71 bp):
TACCTAGCTAAAGCTAATCATGTCAGCTAAAATTTAAGTAATTTTGGTTGAATGATAGGATGTAA
GAAGTA
Found at i:12876 original size:31 final size:31
Alignment explanation
Indices: 12841--12908 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
12831 TTAATCTTGG
*
12841 TTGATGCCTTGTTAGACTGTTTAGTTGGATT
1 TTGATGCCTTGTTAGACTATTTAGTTGGATT
* *
12872 TTGATGCCTTGTTAGATTATTTGGTTGGATT
1 TTGATGCCTTGTTAGACTATTTAGTTGGATT
12903 TTGATG
1 TTGATG
12909 TTTATGTCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.16, C:0.07, G:0.26, T:0.50
Consensus pattern (31 bp):
TTGATGCCTTGTTAGACTATTTAGTTGGATT
Found at i:13099 original size:7 final size:7
Alignment explanation
Indices: 13087--13111 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13077 ACATCAAGGA
13087 TTTGGAT
1 TTTGGAT
13094 TTTGGAT
1 TTTGGAT
13101 TTTGGAT
1 TTTGGAT
13108 TTTG
1 TTTG
13112 AAATTACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (7 bp):
TTTGGAT
Found at i:18211 original size:14 final size:13
Alignment explanation
Indices: 18192--18227 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
18182 TTTGGGCAAT
18192 AAAAAAAAAAAACC
1 AAAAAAAAAAAA-C
18206 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
18219 AAAACAAAA
1 AAAA-AAAA
18228 CAAAGTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:26712 original size:60 final size:60
Alignment explanation
Indices: 26625--26787 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
26615 GTTAATTGCT
* *
26625 CAAATAAGGGCTTAATGTT-TGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
* * *
26685 CAAATAAGGACCTAATGTTATCGAAAATGCTCAAATAAAGGCTCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
26745 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAATGTTATCGAAAATGCTCAAATAAGGGCC
26788 TGACATCAAT
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
60 92 0.99
61 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAATGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:26780 original size:31 final size:31
Alignment explanation
Indices: 26685--26788 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 31
26675 TTAATTTGGC
* *
26685 CAAATAAGGACCTAATGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * * **
26716 CAAATAAAGGCTCGATC-TT-T-TAATTTGGC-
1 CAAATAAGGGC-CTAACGTTATCGAAAAT-GCT
26745 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
26776 CAAATAAGGGCCT
1 CAAATAAGGGCCT
26789 GACATCAATT
Statistics
Matches: 53, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
28 3 0.06
29 15 0.28
30 6 0.11
31 27 0.51
32 2 0.04
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:26865 original size:31 final size:31
Alignment explanation
Indices: 26827--26930 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 31
26817 TTTTGATGTC
26827 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
** ***
26858 AGGCCCTTATTTG-GACAAATTAAAAAATCG--
1 AGGCCCTTATTTGAG-CATTTTGGCAAA-CGTT
* *
26888 -GACCCTTATTTGAGCATTTTGGCAAACATT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
26918 AGGCCCTTATTTG
1 AGGCCCTTATTTG
26931 GCCAAATGAA
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
28 1 0.02
29 18 0.33
30 2 0.04
31 31 0.57
32 2 0.04
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACGTT
Found at i:26923 original size:60 final size:60
Alignment explanation
Indices: 26830--26994 Score: 260
Period size: 60 Copynumber: 2.8 Consensus size: 60
26820 TGATGTCAGG
* *
26830 CCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGACAAATTAAAAAATCGGA
1 CCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGACAAATGAAAAAATCGGA
* *
26890 CCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATGAAAAGATCGGA
1 CCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGACAAATGAAAAAATCGGA
* * *
26950 CCCTTATTTGAGCATTTTGACAAACATTA-ACCCTTATTTGAACAA
1 CCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGACAA
26995 TTAGGCAATT
Statistics
Matches: 97, Mismatches: 8, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
59 13 0.13
60 84 0.87
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGACAAATGAAAAAATCGGA
Found at i:26985 original size:30 final size:30
Alignment explanation
Indices: 26889--26990 Score: 93
Period size: 30 Copynumber: 3.4 Consensus size: 30
26879 AAAAAATCGG
*
26889 ACCCTTATTTGAGCATTTTGGCAAACATTA
1 ACCCTTATTTGAGCATTTTGACAAACATTA
* ** * **
26919 GGCCCTTATTTG-GCCA-AATGA-AAAGATCGG
1 -ACCCTTATTTGAG-CATTTTGACAAACAT-TA
26949 ACCCTTATTTGAGCATTTTGACAAACATTA
1 ACCCTTATTTGAGCATTTTGACAAACATTA
26979 ACCCTTATTTGA
1 ACCCTTATTTGA
26991 ACAATTAGGC
Statistics
Matches: 53, Mismatches: 13, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
29 17 0.32
30 19 0.36
31 17 0.32
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (30 bp):
ACCCTTATTTGAGCATTTTGACAAACATTA
Done.