Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019848.1 Corchorus olitorius cultivar O-4 contig19881, 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: 12431
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:2267 original size:23 final size:23
Alignment explanation
Indices: 2241--2291 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2231 CATGACATGC
* *
2241 AAATTTTTAGTTTCGAGTTTTGA
1 AAATTTTGAGTTTCGACTTTTGA
* *
2264 AAATTTTGATTTTTGACTTTTGA
1 AAATTTTGAGTTTCGACTTTTGA
2287 AAATT
1 AAATT
2292 GACATGCTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.14, T:0.53
Consensus pattern (23 bp):
AAATTTTGAGTTTCGACTTTTGA
Found at i:2325 original size:7 final size:7
Alignment explanation
Indices: 2311--2448 Score: 123
Period size: 7 Copynumber: 19.7 Consensus size: 7
2301 AAATGCAGGT
2311 TTTGAAA
1 TTTGAAA
*
2318 TCTGAAA
1 TTTGAAA
2325 TTTGAAA
1 TTTGAAA
2332 TTTGAAA
1 TTTGAAA
2339 TTTGAAA
1 TTTGAAA
2346 TTTGAAA
1 TTTGAAA
2353 TTTGAAA
1 TTTGAAA
*
2360 TTTGAAT
1 TTTGAAA
*
2367 TTTGAAT
1 TTTGAAA
*
2374 TTTGAAC
1 TTTGAAA
*
2381 TTTGAAC
1 TTTGAAA
* *
2388 GTTGAAC
1 TTTGAAA
*
2395 TTTGAAC
1 TTTGAAA
*
2402 TTTGAAC
1 TTTGAAA
* *
2409 GTTGAAC
1 TTTGAAA
**
2416 TTTGAGT
1 TTTGAAA
**
2423 TTTGAGT
1 TTTGAAA
*
2430 TTTGAAT
1 TTTGAAA
*
2437 TTTGAAT
1 TTTGAAA
2444 TTTGA
1 TTTGA
2449 TTTTTGAGCA
Statistics
Matches: 120, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 120 1.00
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (7 bp):
TTTGAAA
Found at i:2637 original size:33 final size:33
Alignment explanation
Indices: 2595--2673 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
2585 AGAATCTGTG
* * *
2595 GATTTTGAACTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
2628 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
2661 AATTTTGAACTTT
1 GATTTTGAACTTT
2674 TTAATCAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:2784 original size:55 final size:56
Alignment explanation
Indices: 2683--2818 Score: 140
Period size: 55 Copynumber: 2.5 Consensus size: 56
2673 TTTAATCAAT
*
2683 CGCACTGGATT-ATTAAGA-ATTCAAC-CTTGATCATGGAAACATTTCTTGGAACGAC
1 CGCACTGGATTAATTTAGAGA-TCAACTCTTGATCATGGAAACA-TTCTTGGAACGAC
* * *
2738 TGCACTGGATTAATTTAGAGATCAACTC-TGATCATCGTAAAC-TTCTTGGAATGAC
1 CGCACTGGATTAATTTAGAGATCAACTCTTGATCAT-GGAAACATTCTTGGAACGAC
* * *
2793 CACACTGGATCAACTTA-AGATCAACT
1 CGCACTGGATTAATTTAGAGATCAACT
2819 TAGATTTTTG
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
54 9 0.13
55 35 0.51
56 18 0.26
57 7 0.10
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (56 bp):
CGCACTGGATTAATTTAGAGATCAACTCTTGATCATGGAAACATTCTTGGAACGAC
Found at i:2837 original size:54 final size:52
Alignment explanation
Indices: 2776--3033 Score: 304
Period size: 54 Copynumber: 4.8 Consensus size: 52
2766 TGATCATCGT
* * * *
2776 AAACTTCT-TGGAATGACCACACTGGATCAACTTAAGATCAACTTAGATTTTTGA
1 AAACTTCTAT-GAA-GACCACACTGGGTCATCTTAAGATCAACTTAGATCTCT-A
* * * * *
2830 AAACTTCTATGGAAGACCATACAGGGTCATCTGAAGATCAATTTAGACCTCTA
1 AAACTTCTAT-GAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTA
* *
2883 AAAGCTTCTATGAAAGACCACACT-GGTCATCTCAAGATCAACTTTGATCTCTGA
1 AAA-CTTCTATG-AAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCT-A
*
2937 AAACTTCTATAAAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTA
1 AAACTTCTAT-GAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTA
*
2990 AAAGCTTCTATGAAGACCACAGTGGGTCATCTTAAGATCAACTT
1 AAA-CTTCTATGAAGACCACACTGGGTCATCTTAAGATCAACTT
3034 TCTAGAGAGA
Statistics
Matches: 177, Mismatches: 20, Indels: 15
0.83 0.09 0.07
Matches are distributed among these distances:
53 82 0.46
54 90 0.51
55 5 0.03
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28
Consensus pattern (52 bp):
AAACTTCTATGAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTA
Found at i:2945 original size:107 final size:106
Alignment explanation
Indices: 2790--3034 Score: 346
Period size: 107 Copynumber: 2.3 Consensus size: 106
2780 TTCTTGGAAT
* * * * ** *
2790 GACCACACTGGATCAACTTAAGATCAACTTAGATTTTTGAAAACTTCTATGGAAGACCATACAGG
1 GACCACACTGG-TCATCTTAAGATCAACTTTGATCTCTGAAAACTTCTATAAAAGACCACACAGG
*
2855 GTCATCTGAAGATCAATTTAGACCTCTAAAAGCTTCTATGAAA
65 GTCATCTGAAGATCAACTTAGACCTCTAAAAGCTTCTATG-AA
* *
2898 GACCACACTGGTCATCTCAAGATCAACTTTGATCTCTGAAAACTTCTATAAAAGACCACACTGGG
1 GACCACACTGGTCATCTTAAGATCAACTTTGATCTCTGAAAACTTCTATAAAAGACCACACAGGG
* *
2963 TCATCTTAAGATCAACTTAGATCTCTAAAAGCTTCTATGAA
66 TCATCTGAAGATCAACTTAGACCTCTAAAAGCTTCTATGAA
*
3004 GACCACAGTGGGTCATCTTAAGATCAACTTT
1 GACCACACT-GGTCATCTTAAGATCAACTTT
3035 CTAGAGAGAC
Statistics
Matches: 122, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
106 10 0.08
107 101 0.83
108 11 0.09
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (106 bp):
GACCACACTGGTCATCTTAAGATCAACTTTGATCTCTGAAAACTTCTATAAAAGACCACACAGGG
TCATCTGAAGATCAACTTAGACCTCTAAAAGCTTCTATGAA
Found at i:3085 original size:20 final size:18
Alignment explanation
Indices: 3065--3106 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3055 CATTTTAAAC
*
3065 ACAAAACATGAATTTTGA
1 ACAAAAAATGAATTTTGA
* *
3083 ACAAGAAATGGATTTTGA
1 ACAAAAAATGAATTTTGA
3101 ACAAAA
1 ACAAAA
3107 TTTGATAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (18 bp):
ACAAAAAATGAATTTTGA
Found at i:3186 original size:37 final size:37
Alignment explanation
Indices: 3143--3338 Score: 146
Period size: 37 Copynumber: 5.3 Consensus size: 37
3133 TTGAAGAGAC
* *
3143 ACCTAAACATGTACCTTAAATAAGGATTTAATAAGAA
1 ACCTAAACATGAACCTTAAATAAGGATTTGATAAGAA
** * *
3180 ACCTAAACATGAATTTTGAATAA-GATTTTGATGAA-AC
1 ACCTAAACATGAACCTTAAATAAGGA-TTTGAT-AAGAA
* *
3217 ACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAA
1 ACCTAAACATGAACCTTAAATAAGGATTTGATAAGAA
* * * * * *
3254 ACCTAAACAGGGATCTTAAACAA-AATTTTTGACAAGAA
1 ACCTAAACATGAACCTTAAATAAGGA--TTTGATAAGAA
* * * ** *
3292 TCCTAAATAGGCTCTTTAAATAAGGATTTGATAAGAA
1 ACCTAAACATGAACCTTAAATAAGGATTTGATAAGAA
*
3329 AGCTAAACAT
1 ACCTAAACAT
3339 AAATCTTGAA
Statistics
Matches: 123, Mismatches: 29, Indels: 14
0.74 0.17 0.08
Matches are distributed among these distances:
36 5 0.04
37 87 0.71
38 30 0.24
39 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.27
Consensus pattern (37 bp):
ACCTAAACATGAACCTTAAATAAGGATTTGATAAGAA
Found at i:3219 original size:74 final size:74
Alignment explanation
Indices: 3129--3362 Score: 267
Period size: 74 Copynumber: 3.1 Consensus size: 74
3119 GCTAAACTAG
* * * *
3129 GATTTTGAAGAGACACCTAAACATGTACCTTAAATAAGGATTTAATAAGAAACCTAAACATGAAT
1 GATTTTGATGAAACACCTAAACAGGTACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAAT
* *
3194 TTTGAATAA
66 CTTGAACAA
* * *
3203 GATTTTGATGAAACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGAT
1 GATTTTGATGAAACACCTAAACAGGTACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAAT
*
3268 CTTAAACAA
66 CTTGAACAA
* * * * *
3277 AATTTT--TGACAAGAATCCTAAATAGGCT-CTTTAAATAAGGATTTGATAAGAAAGCTAAACAT
1 GATTTTGATGA-AA-CA-CCTAAACAGG-TACCTTAAATAAGGATTTGATAAGAAACCTAAACAT
*
3339 AAATCTTGAACAA
62 GAATCTTGAACAA
3352 GATTTTGATGA
1 GATTTTGATGA
3363 GGCTGAATTT
Statistics
Matches: 133, Mismatches: 21, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
72 3 0.02
73 2 0.02
74 70 0.53
75 55 0.41
77 3 0.02
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.28
Consensus pattern (74 bp):
GATTTTGATGAAACACCTAAACAGGTACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAAT
CTTGAACAA
Found at i:5061 original size:14 final size:13
Alignment explanation
Indices: 4995--5059 Score: 78
Period size: 14 Copynumber: 4.8 Consensus size: 13
4985 ACTCAAAACC
*
4995 TTTTCGAAAACTCA
1 TTTTTGAAAA-TCA
5009 TTTTTGAAAATCA
1 TTTTTGAAAATCA
5022 TTTCTTGAAAAT-A
1 TTT-TTGAAAATCA
5035 GTTTCTTGAAAATCA
1 -TTT-TTGAAAATCA
5050 TTTTTGAAAA
1 TTTTTGAAAA
5060 ATGTTCTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
13 14 0.30
14 32 0.68
15 1 0.02
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (13 bp):
TTTTTGAAAATCA
Done.