Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018274.1 Corchorus olitorius cultivar O-4 contig18307, 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: 7301
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2689 original size:30 final size:30
Alignment explanation
Indices: 2626--2885 Score: 369
Period size: 30 Copynumber: 8.6 Consensus size: 30
2616 GACAACTTAC
*
2626 ATCATGACAGCTTCTGGTGTCAATTGCAA-
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
2655 ATCATGACAACTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
2685 ATCATGACAGCTTCTGGTGTCAATTGCAAT
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
2715 AGCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
2745 AACATGACAACTTTTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
2775 AGCATGACAAGTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
2805 ATCATTGACAAGTTCTGGTGTCAATTGCAAG
1 ATCA-TGACAACTTCTGGTGTCAATTGCAAG
* **
2836 ACCATGACAACTTCTGGTGTCAATTTTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
2866 ACCATTGACAACTTCTGGTG
1 ATCA-TGACAACTTCTGGTG
2886 ACCATGACAA
Statistics
Matches: 212, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
29 28 0.13
30 140 0.66
31 44 0.21
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:2751 original size:60 final size:60
Alignment explanation
Indices: 2628--3207 Score: 638
Period size: 60 Copynumber: 9.8 Consensus size: 60
2618 CAACTTACAT
* * * * *
2628 CATGACAGCTTCTGGTGTCAATTGCAA-ATCATGACAACTTCTGGTGTCAATTGCAAAAT
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAGAC
* * * * *
2687 CATGACAGCTTCTGGTGTCAATTGCAATAGCATGACAACTTCTGGTGTCAATTGCAAGAA
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAGAC
* * * * *
2747 CATGACAACTTTTGGTGTCAATTGCAAGAGCATGACAAGTTCTGGTGTCAATTGCAAGAT
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAGAC
* *
2807 CATTGACAAGTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTTTAAGAC
1 CA-TGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAGAC
* *
2868 CATTGACAACTTCT-G-G-----T----GACCATGACAATTTCTGGTGTCATTTGTAAGAC
1 CA-TGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAGAC
* * * * *
2918 CATGACAATTTCTGGTGTCATTTGTAAGACCATGACAATTTCTGGTGTCATTTGTAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAGAC
* * * * *
2978 CATGACAACTTTTGTTGTCATTTGTAAGACCATGACAACTTCTGGTGTC-ATTCATAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATT-GTAAGAC
* * *
3038 CATGACAACTTCTGGTGTC-ATTCGTAAGATCATGACAACTTTTGGTGTC-ATTCGTAAGAC
1 CATGACAACTTCTGGTGTCAATT-GCAAGACCATGACAACTTCTGGTGTCAATT-GTAAGAC
* * *
3098 CATGACAACTTCTGATGTC-ATTCGTAAGACCATGACAACTTCTGATGTC-ATTCGTAAGAC
1 CATGACAACTTCTGGTGTCAATT-GCAAGACCATGACAACTTCTGGTGTCAATT-GTAAGAC
*
3158 CATGACAACTTCTGGTGTC-ATTCGTAAGACCATGACAACTTCTGGTGTCA
1 CATGACAACTTCTGGTGTCAATT-GCAAGACCATGACAACTTCTGGTGTCA
3208 TCTTTGAATA
Statistics
Matches: 467, Mismatches: 38, Indels: 30
0.87 0.07 0.06
Matches are distributed among these distances:
49 10 0.02
50 33 0.07
51 1 0.00
54 1 0.00
56 1 0.00
59 32 0.07
60 325 0.70
61 64 0.14
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (60 bp):
CATGACAACTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTGTAAGAC
Found at i:2781 original size:90 final size:89
Alignment explanation
Indices: 2628--3207 Score: 625
Period size: 90 Copynumber: 6.6 Consensus size: 89
2618 CAACTTACAT
* * * * *
2628 CATGACAGCTTCTGGTGTCAATTGCAA-ATCATGACAACTTCTGGTGTCAATTGCAAAATCATGA
1 CATGACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCATGA
* * *
2692 CAGCTTCTGGTGTCAATTGCAATAG
66 CAACTTCTGGTGTC-ATTGCAAGAC
* * * *
2717 CATGACAACTTCTGGTGTCAATTGCAAGAACATGACAACTTTTGGTGTCAATTGCAAGAGCATGA
1 CATGACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCATGA
* *
2782 CAAGTTCTGGTGTCAATTGCAAGAT
66 CAACTTCTGGTGTC-ATTGCAAGAC
* * **
2807 CATTGACAAGTTCTGGTGTCAATTGCAAGACCATGACAACTTCTGGTGTCAATTTTAAGACCATT
1 CA-TGACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCA-T
2872 GACAACTTCT-G-G----T----GAC
64 GACAACTTCTGGTGTCATTGCAAGAC
* * * * *
2888 CATGACAATTTCTGGTGTCATTTGTAAGACCATGACAATTTCTGGTGTCATTTGTAAGACCATGA
1 CATGACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCATGA
* *
2953 CAATTTCTGGTGTCATTTGTAAGAC
66 CAACTTCTGGTGTCA-TTGCAAGAC
* * *
2978 CATGACAACTTTTGTTGTCATTTGTAAGACCATGACAACTTCTGGTGTC-ATT-CATAAGACCAT
1 CATGACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCAATTGC--AAGACCAT
* *
3041 GACAACTTCTGGTGTCATTCGTAAGAT
64 GACAACTTCTGGTGTCATT-GCAAGAC
* * *
3068 CATGACAACTTTTGGTGTC-ATTCGTAAGACCATGACAACTTCTGATGTC-ATTCGTAAGACCAT
1 CATGACAACTTCTGGTGTCAATT-GTAAGACCATGACAACTTCTGGTGTCAATT-GCAAGACCAT
* *
3131 GACAACTTCTGATGTCATTCGTAAGAC
64 GACAACTTCTGGTGTCATT-GCAAGAC
3158 CATGACAACTTCTGGTGTC-ATTCGTAAGACCATGACAACTTCTGGTGTCA
1 CATGACAACTTCTGGTGTCAATT-GTAAGACCATGACAACTTCTGGTGTCA
3208 TCTTTGAATA
Statistics
Matches: 430, Mismatches: 40, Indels: 40
0.84 0.08 0.08
Matches are distributed among these distances:
79 10 0.02
80 55 0.13
81 5 0.01
85 1 0.00
86 1 0.00
89 32 0.07
90 261 0.61
91 55 0.13
92 10 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (89 bp):
CATGACAACTTCTGGTGTCAATTGTAAGACCATGACAACTTCTGGTGTCAATTGCAAGACCATGA
CAACTTCTGGTGTCATTGCAAGAC
Found at i:2895 original size:19 final size:20
Alignment explanation
Indices: 2865--2904 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2855 TCAATTTTAA
2865 GACCATTGACAACTTCTGGT
1 GACCATTGACAACTTCTGGT
*
2885 GACCA-TGACAATTTCTGGT
1 GACCATTGACAACTTCTGGT
2904 G
1 G
2905 TCATTTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (20 bp):
GACCATTGACAACTTCTGGT
Found at i:2921 original size:30 final size:30
Alignment explanation
Indices: 2885--3208 Score: 522
Period size: 30 Copynumber: 10.8 Consensus size: 30
2875 AACTTCTGGT
* *
2885 GACCATGACAATTTCTGGTGTCATTTGTAA
1 GACCATGACAACTTCTGGTGTCATTCGTAA
* *
2915 GACCATGACAATTTCTGGTGTCATTTGTAA
1 GACCATGACAACTTCTGGTGTCATTCGTAA
* *
2945 GACCATGACAATTTCTGGTGTCATTTGTAA
1 GACCATGACAACTTCTGGTGTCATTCGTAA
* * *
2975 GACCATGACAACTTTTGTTGTCATTTGTAA
1 GACCATGACAACTTCTGGTGTCATTCGTAA
*
3005 GACCATGACAACTTCTGGTGTCATTCATAA
1 GACCATGACAACTTCTGGTGTCATTCGTAA
3035 GACCATGACAACTTCTGGTGTCATTCGTAA
1 GACCATGACAACTTCTGGTGTCATTCGTAA
* *
3065 GATCATGACAACTTTTGGTGTCATTCGTAA
1 GACCATGACAACTTCTGGTGTCATTCGTAA
*
3095 GACCATGACAACTTCTGATGTCATTCGTAA
1 GACCATGACAACTTCTGGTGTCATTCGTAA
*
3125 GACCATGACAACTTCTGATGTCATTCGTAA
1 GACCATGACAACTTCTGGTGTCATTCGTAA
3155 GACCATGACAACTTCTGGTGTCATTCGTAA
1 GACCATGACAACTTCTGGTGTCATTCGTAA
3185 GACCATGACAACTTCTGGTGTCAT
1 GACCATGACAACTTCTGGTGTCAT
3209 CTTTGAATAG
Statistics
Matches: 280, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 280 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (30 bp):
GACCATGACAACTTCTGGTGTCATTCGTAA
Found at i:3342 original size:18 final size:18
Alignment explanation
Indices: 3316--3351 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3306 TATCAACTCC
*
3316 TCACCAAACCAAGAAGAT
1 TCACAAAACCAAGAAGAT
*
3334 TCACAAAACCAAGGAGAT
1 TCACAAAACCAAGAAGAT
3352 AGTTTATCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.14, T:0.11
Consensus pattern (18 bp):
TCACAAAACCAAGAAGAT
Found at i:4301 original size:22 final size:24
Alignment explanation
Indices: 4266--4319 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
4256 ATAAATGTTG
* *
4266 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
4288 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
4311 CTTGATAAT
1 C-TGATAAT
4320 ATCTAGCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:4550 original size:80 final size:81
Alignment explanation
Indices: 4415--4578 Score: 240
Period size: 84 Copynumber: 2.0 Consensus size: 81
4405 CTTACCTGAG
*
4415 ATCAATCACTTTTATTTAATCATACTCAATTTAAAATCAATCTTATCA-TTATTTTTTCATTGGG
1 ATCAATCACTTTTATTTAATCATACTCAATTTAAAATCAATCTTACCACTTATTTTTTCATTGGG
*
4479 CCTATGGAACTTGCAC
66 CCTACGGAACTTGCAC
* * * *
4495 ATCAATCACTTTTATTTAATCGTATTCAATTTTAGAATCAATCTTACCACTTTTTTTTTTTCATT
1 ATCAATCACTTTTATTTAATCATACTCAA-TTTAAAATCAATCTTACCAC--TTATTTTTTCATT
4560 GGGCCTACGGAACTTGCAC
63 GGGCCTACGGAACTTGCAC
4579 TTGATTGAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
80 27 0.36
81 17 0.23
84 30 0.41
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (81 bp):
ATCAATCACTTTTATTTAATCATACTCAATTTAAAATCAATCTTACCACTTATTTTTTCATTGGG
CCTACGGAACTTGCAC
Found at i:4992 original size:16 final size:14
Alignment explanation
Indices: 4946--4998 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 14
4936 TCAACCCTAA
* *
4946 TTTTAAAAAGCAC-
1 TTTTCAAAACCACT
*
4959 TTTTCAAAAGCACT
1 TTTTCAAAACCACT
4973 TTTTCAAAACCAAGCT
1 TTTTCAAAACC-A-CT
4989 TTTTCAAAAC
1 TTTTCAAAAC
4999 TTAACCTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
13 12 0.34
14 10 0.29
15 1 0.03
16 12 0.34
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.34
Consensus pattern (14 bp):
TTTTCAAAACCACT
Found at i:6369 original size:33 final size:33
Alignment explanation
Indices: 6328--6391 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
6318 CAATAAACAA
*
6328 AAATTAAAAATGGCCAT-TCTCATACAATTTTAG
1 AAATTAAAAATGACCATAT-TCATACAATTTTAG
*
6361 AAATTAAAAATGACCATATTCATACACTTTT
1 AAATTAAAAATGACCATATTCATACAATTTT
6392 GAGTACCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (33 bp):
AAATTAAAAATGACCATATTCATACAATTTTAG
Found at i:6965 original size:8 final size:8
Alignment explanation
Indices: 6954--6982 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
6944 GTTGTTTTTT
6954 TTTTTTAA
1 TTTTTTAA
6962 TTTTTTAA
1 TTTTTTAA
6970 -TTTTTAA
1 TTTTTTAA
6977 TTTTTT
1 TTTTTT
6983 TTATCCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTAA
Done.