Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018784.1 Corchorus olitorius cultivar O-4 contig18817, 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: 29822
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Found at i:11768 original size:32 final size:32
Alignment explanation
Indices: 11729--11803 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
11719 CACAAAAATT
* **
11729 AAAAACGCA-AAAATCAAATTTTTTTTTTTAGA
1 AAAAACGCAGAAAAT-AAATATTTTTTTAGAGA
*
11761 AAAAACGCAGAAAATATATATTTTTTTAGAGA
1 AAAAACGCAGAAAATAAATATTTTTTTAGAGA
*
11793 AGAAACGCAGA
1 AAAAACGCAGA
11804 GACTAAGAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 32 0.86
33 5 0.14
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.29
Consensus pattern (32 bp):
AAAAACGCAGAAAATAAATATTTTTTTAGAGA
Found at i:24386 original size:13 final size:13
Alignment explanation
Indices: 24368--24393 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24358 GCTTGGCATG
24368 AGTGATGATTTTT
1 AGTGATGATTTTT
24381 AGTGATGATTTTT
1 AGTGATGATTTTT
24394 GTTGTTACCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
AGTGATGATTTTT
Found at i:25986 original size:45 final size:45
Alignment explanation
Indices: 25917--26036 Score: 222
Period size: 45 Copynumber: 2.7 Consensus size: 45
25907 CTTTCTCAGC
* *
25917 AAGGCAAGCCCATTAAATGCTTAAGCCCATGCCGCCCCCTGTATA
1 AAGGGAAGCCCATTAAATGCTTAAGCCCATGCCGCCCCCTATATA
25962 AAGGGAAGCCCATTAAATGCTTAAGCCCATGCCGCCCCCTATATA
1 AAGGGAAGCCCATTAAATGCTTAAGCCCATGCCGCCCCCTATATA
26007 AAGGGAAGCCCATTAAATGCTTAAGCCCAT
1 AAGGGAAGCCCATTAAATGCTTAAGCCCAT
26037 TGGCCACAGT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 73 1.00
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (45 bp):
AAGGGAAGCCCATTAAATGCTTAAGCCCATGCCGCCCCCTATATA
Found at i:29372 original size:35 final size:35
Alignment explanation
Indices: 29329--29598 Score: 420
Period size: 35 Copynumber: 7.8 Consensus size: 35
29319 GAAGATCAAC
*
29329 TCAT-AAAAACTTCTTGAAATGCGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
* *
29363 TCATCAAAAACTTCTTAAAATGTGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
*
29398 TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
* * *
29433 TCACCGAAAACTTCTTGAAACGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
* *
29468 TCATCAAAAGCTTCTTGAAAGGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
29503 TCAT-AAAAACTTCTTGAAATGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
*
29537 TCATAAAAAACTTCTTGAAATGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
*
29572 TCATC-GAAACTTCTTGAAATGAGATCA
1 TCATCAAAAACTTCTTGAAATGAGATCA
29599 CTGGATCATC
Statistics
Matches: 218, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
34 57 0.26
35 161 0.74
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (35 bp):
TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
Found at i:29411 original size:70 final size:70
Alignment explanation
Indices: 29329--29822 Score: 509
Period size: 70 Copynumber: 6.9 Consensus size: 70
29319 GAAGATCAAC
* * * *
29329 TCAT-AAAAACTTCTTGAAATGCGATCAACTCTGATCATCAAAAACTTCTTAAAATGTGATCAAC
1 TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGAGATCAAC
29393 TCTGA
66 TCTGA
* * *
29398 TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCACCGAAAACTTCTTGAAACGAGATCAAC
1 TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGAGATCAAC
29463 TCTGA
66 TCTGA
*
29468 TCATCAAAAGCTTCTTGAAAGGAGATCAACTCTGATCAT-AAAAACTTCTTGAAATGAGATCAAC
1 TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGAGATCAAC
29532 TCTGA
66 TCTGA
* * *
29537 TCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCATC-GAAACTTCTTGAAATGAGATC-AC
1 TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGAGATCAAC
*
29600 T-GGA
66 TCTGA
** * * **
29604 TCATCTGGGATCAACTCTGATCCTCGAAAACTTCTTGAAATGAGATCAACTCTGACCATTGAAAA
1 TCATC----A--AAAACT--T-CTTG-AAA------G----GAGATCAACTCTGATCATCAAAAA
*
29669 CTTCTTGAAACGAGATCAACTCTGA
46 CTTCTTGAAATGAGATCAACTCTGA
* * *
29694 TCATCGAAAACTTCTTAAAAGGAGATCAACTCTGATCAT-AAAAACTTCTTGGAATGAGATC-AC
1 TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGAGATCAAC
*
29757 CCTGA
66 TCTGA
* * * *
29762 TCATCGAAAACTTCTTGAAAGGAGATTAACTCTGAT-ATCGAAAACTTCCTGAAATGAGATC
1 TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGAGATC
Statistics
Matches: 358, Mismatches: 41, Indels: 53
0.79 0.09 0.12
Matches are distributed among these distances:
67 8 0.02
68 62 0.17
69 107 0.30
70 112 0.31
71 1 0.00
73 4 0.01
74 1 0.00
75 1 0.00
76 3 0.01
77 3 0.01
80 3 0.01
81 2 0.01
82 1 0.00
84 4 0.01
87 17 0.05
88 19 0.05
89 3 0.01
90 7 0.02
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (70 bp):
TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGAGATCAAC
TCTGA
Found at i:29643 original size:122 final size:122
Alignment explanation
Indices: 29491--29721 Score: 374
Period size: 122 Copynumber: 1.9 Consensus size: 122
29481 CTTGAAAGGA
*
29491 GATCAACTCTGATCATAAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAACTTCTTGAA
1 GATCAACTCTGATCATAAAAACTTCTTGAAATGAGATCAACTCTGACCATAAAAAACTTCTTGAA
* * *
29556 ATGAGATCAACTCTGATCATCG-AAACTTCTTGAAATGAGATCACTGGATCATCTGG
66 ACGAGATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCACTGGATCATCTGG
* * **
29612 GATCAACTCTGATCCTCGAAAACTTCTTGAAATGAGATCAACTCTGACCATTGAAAACTTCTTGA
1 GATCAACTCTGATCAT-AAAAACTTCTTGAAATGAGATCAACTCTGACCATAAAAAACTTCTTGA
29677 AACGAGATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCA
65 AACGAGATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCA
29722 ACTCTGATCA
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
121 15 0.15
122 66 0.66
123 19 0.19
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (122 bp):
GATCAACTCTGATCATAAAAACTTCTTGAAATGAGATCAACTCTGACCATAAAAAACTTCTTGAA
ACGAGATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCACTGGATCATCTGG
Found at i:29741 original size:157 final size:156
Alignment explanation
Indices: 29456--29756 Score: 469
Period size: 157 Copynumber: 1.9 Consensus size: 156
29446 CTTGAAACGA
*
29456 GATCAACTCTGATCATCAAAAGCTTCTTGAAAGGAGATCAACTCTGATCATAAAAACTTCTTGAA
1 GATCAACTCTGATCATCAAAAGCTTCTTGAAAGGAGATCAACTCTGACCATAAAAACTTCTTGAA
* * * **
29521 ATGAGATCAACTCTGATCATAAAAAACTTCTTGAAATGAGATCAACTCTGATCATCGAAACTTCT
66 ACGAGATCAACTCTGATCATAAAAAACTTCTTAAAAGGAGATCAACTCTGATCATAAAAACTTCT
29586 TGAAATGAGATCACTGGATCATCTGG
131 TGAAATGAGATCACTGGATCATCTGG
* * *
29612 GATCAACTCTGATCCTCGAAAA-CTTCTTGAAATGAGATCAACTCTGACCATTGAAAACTTCTTG
1 GATCAACTCTGATCATC-AAAAGCTTCTTGAAAGGAGATCAACTCTGACCA-TAAAAACTTCTTG
**
29676 AAACGAGATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCAACTCTGATCATAAAAACTT
64 AAACGAGATCAACTCTGATCATAAAAAACTTCTTAAAAGGAGATCAACTCTGATCATAAAAACTT
*
29741 CTTGGAATGAGATCAC
129 CTTGAAATGAGATCAC
29757 CCTGATCATC
Statistics
Matches: 131, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
156 42 0.32
157 89 0.68
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (156 bp):
GATCAACTCTGATCATCAAAAGCTTCTTGAAAGGAGATCAACTCTGACCATAAAAACTTCTTGAA
ACGAGATCAACTCTGATCATAAAAAACTTCTTAAAAGGAGATCAACTCTGATCATAAAAACTTCT
TGAAATGAGATCACTGGATCATCTGG
Found at i:29752 original size:191 final size:191
Alignment explanation
Indices: 29421--29787 Score: 580
Period size: 191 Copynumber: 1.9 Consensus size: 191
29411 CTTGAAAGGA
*
29421 GATCAACTCTGATCACCGAAAACTTCTTGAAACGAGATCAACTCTGATCATCAAAAGCTTCTTGA
1 GATCAACTCTGATCACCGAAAACTTCTTGAAACGAGATCAACTCTGACCATCAAAAGCTTCTTGA
* * *
29486 AAGGAGATCAACTCTGATCATAAAAACTTCTTGAAATGAGATCAACTCTGATCATAAAAAACTTC
66 AACGAGATCAACTCTGATCATAAAAACTTCTTAAAAGGAGATCAACTCTGATCATAAAAAACTTC
* *
29551 TTGAAATGAGATCAACTCTGATCATCG-AAACTTCTTGAAATGAGATCACTGGATCATCTGG
131 TTGAAATGAGATC-ACCCTGATCATCGAAAACTTCTTGAAAGGAGATCACTGGATCATCTGG
* *
29612 GATCAACTCTGATC-CTCGAAAACTTCTTGAAATGAGATCAACTCTGACCATTGAAAA-CTTCTT
1 GATCAACTCTGATCAC-CGAAAACTTCTTGAAACGAGATCAACTCTGACCA-TCAAAAGCTTCTT
*
29675 GAAACGAGATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCAACTCTGATCAT-AAAAAC
64 GAAACGAGATCAACTCTGATCAT-AAAAACTTCTTAAAAGGAGATCAACTCTGATCATAAAAAAC
*
29739 TTCTTGGAATGAGATCACCCTGATCATCGAAAACTTCTTGAAAGGAGAT
128 TTCTTGAAATGAGATCACCCTGATCATCGAAAACTTCTTGAAAGGAGAT
29788 TAACTCTGAT
Statistics
Matches: 162, Mismatches: 10, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
190 13 0.08
191 113 0.70
192 36 0.22
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (191 bp):
GATCAACTCTGATCACCGAAAACTTCTTGAAACGAGATCAACTCTGACCATCAAAAGCTTCTTGA
AACGAGATCAACTCTGATCATAAAAACTTCTTAAAAGGAGATCAACTCTGATCATAAAAAACTTC
TTGAAATGAGATCACCCTGATCATCGAAAACTTCTTGAAAGGAGATCACTGGATCATCTGG
Found at i:29783 original size:68 final size:69
Alignment explanation
Indices: 29612--29822 Score: 291
Period size: 68 Copynumber: 3.1 Consensus size: 69
29602 GATCATCTGG
* * * *
29612 GATCAACTCTGATCCTCGAAAACTTCTTGAAATGAGATCAACTCTGACCATTGAAAACTTCTTGA
1 GATCAACCCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCA-TGAAAACTTCTTGA
*
29677 AACGA
65 AATGA
* * * *
29682 GATCAACTCTGATCATCGAAAACTTCTTAAAAGGAGATCAACTCTGATCATAAAAACTTCTTGGA
1 GATCAACCCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATGAAAACTTCTTGAA
29747 ATGA
66 ATGA
* *
29751 GATC-ACCCTGATCATCGAAAACTTCTTGAAAGGAGATTAACTCTGAT-ATCGAAAACTTCCTGA
1 GATCAACCCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCAT-GAAAACTTCTTGA
29814 AATGA
65 AATGA
29819 GATC
1 GATC
Statistics
Matches: 127, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
67 2 0.02
68 59 0.46
69 20 0.16
70 46 0.36
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (69 bp):
GATCAACCCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATGAAAACTTCTTGAA
ATGA
Found at i:29802 original size:34 final size:35
Alignment explanation
Indices: 29612--29822 Score: 293
Period size: 35 Copynumber: 6.1 Consensus size: 35
29602 GATCATCTGG
*
29612 GATCAACTCTGATCCTCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* * *
29647 GATCAACTCTGACCATTGAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
29682 GATCAACTCTGATCATCGAAAACTTCTTAAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
29717 GATCAACTCTGATCAT-AAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
29751 GATC-ACCCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
* *
29785 GATTAACTCTGAT-ATCGAAAACTTCCTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
29819 GATC
1 GATC
Statistics
Matches: 153, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
33 10 0.07
34 58 0.38
35 85 0.56
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (35 bp):
GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
Done.