Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013484.1 Corchorus capsularis cultivar CVL-1 contig13505, 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: 11624
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Found at i:945 original size:17 final size:16
Alignment explanation
Indices: 923--962 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
913 GAATGGGGAT
923 AAGAGGAAGTAGCTGGC
1 AAGAGG-AGTAGCTGGC
*
940 AAGAGGGGTAGCTGGC
1 AAGAGGAGTAGCTGGC
956 AAG-GGAG
1 AAGAGGAG
963 CAAGTGAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 3 0.14
16 12 0.57
17 6 0.29
ACGTcount: A:0.33, C:0.10, G:0.47, T:0.10
Consensus pattern (16 bp):
AAGAGGAGTAGCTGGC
Found at i:2236 original size:40 final size:39
Alignment explanation
Indices: 2185--2331 Score: 231
Period size: 40 Copynumber: 3.7 Consensus size: 39
2175 CATAGTTAAG
2185 GACTTAATTCATAGAAATTAAGTAAAAACAGCAGTCGAAA
1 GACTTAATTCATAGAAATTAAGTAAAAACAGCAGTC-AAA
*
2225 GACTTAATTCATAGAAATTAAGTAAAAACAGTAGTCAGAA
1 GACTTAATTCATAGAAATTAAGTAAAAACAGCAGTCA-AA
* *
2265 GACTTAATTCATAGAAATTAAGTAAAAACAGCAATCTAAG
1 GACTTAATTCATAGAAATTAAGTAAAAACAGCAGTC-AAA
*
2305 GACTTAATTCATTGAAATTAAGTAAAA
1 GACTTAATTCATAGAAATTAAGTAAAA
2332 GTAAAAAAAA
Statistics
Matches: 100, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
39 1 0.01
40 98 0.98
41 1 0.01
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.26
Consensus pattern (39 bp):
GACTTAATTCATAGAAATTAAGTAAAAACAGCAGTCAAA
Found at i:2411 original size:85 final size:86
Alignment explanation
Indices: 2305--2507 Score: 261
Period size: 85 Copynumber: 2.3 Consensus size: 86
2295 GCAATCTAAG
** *
2305 GACTTAA-TTCATTGAAATTAAGTAAAAGTAAAAAAAAAAAAAGA-AGACTGGCTTAGTTTC-AA
1 GACTTAATTTCAAGGAAATTAAGTAAAA--AAAAAAAAAAAAAGAGAGACTGGCTTAATTTCAAA
2367 GGAAACTAGGTAAAGAAAAGACT
64 GGAAACTAGGTAAAGAAAAGACT
* *
2390 G-CTTAATTTCAAGGAAGTTAAGTGAAAAAAAAAAAAAAAGAGAGAGACTGGCTTAATTTCAAGA
1 GACTTAATTTCAAGGAAATTAAGT-AAAAAAAAAAAAAAAAAGAGAGACTGGCTTAATTTC---A
* *
2454 AAGGAAATTAGGTAAAGAAAAGATT
62 AAGGAAACTAGGTAAAGAAAAGACT
2479 GACTTAATTTCAAGGAAATTAAGTAAAAA
1 GACTTAATTTCAAGGAAATTAAGTAAAAA
2508 GACTGGCTCA
Statistics
Matches: 102, Mismatches: 8, Indels: 12
0.84 0.07 0.10
Matches are distributed among these distances:
84 19 0.19
85 29 0.28
86 4 0.04
89 29 0.28
90 21 0.21
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.23
Consensus pattern (86 bp):
GACTTAATTTCAAGGAAATTAAGTAAAAAAAAAAAAAAAAAGAGAGACTGGCTTAATTTCAAAGG
AAACTAGGTAAAGAAAAGACT
Found at i:2577 original size:41 final size:42
Alignment explanation
Indices: 2525--2603 Score: 133
Period size: 41 Copynumber: 1.9 Consensus size: 42
2515 TCAGTTTTAA
*
2525 GAAAGGAAATTAGGTAAGGATAAGCACAGACTTAATTTCAAG
1 GAAAGGAAATTAGGTAAGGACAAGCACAGACTTAATTTCAAG
*
2567 GAAA-GAAATTAGGTAAGGACCAGCACAGACTTAATTT
1 GAAAGGAAATTAGGTAAGGACAAGCACAGACTTAATTT
2604 AGGGTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 31 0.89
42 4 0.11
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (42 bp):
GAAAGGAAATTAGGTAAGGACAAGCACAGACTTAATTTCAAG
Found at i:2695 original size:71 final size:71
Alignment explanation
Indices: 2609--2742 Score: 225
Period size: 71 Copynumber: 1.9 Consensus size: 71
2599 AATTTAGGGT
*
2609 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAA-TTAGCAAAGACTTAATTT
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAGTCAGCAAAGACTTAATTT
2673 CACAAG
66 CACAAG
* *
2679 AATTAAGTAAAATTAGCAAAGACTTAATTTCATAAGAATTAAGTAAAGTCAGCAAAGATTTAAT
1 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAGTCAGCAAAGACTTAAT
2743 CCAAAGATGA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
70 8 0.14
71 37 0.63
72 14 0.24
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (71 bp):
AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAGTCAGCAAAGACTTAATTT
CACAAG
Found at i:2760 original size:36 final size:35
Alignment explanation
Indices: 2609--2742 Score: 223
Period size: 36 Copynumber: 3.8 Consensus size: 35
2599 AATTTAGGGT
2609 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
2644 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
*
2679 AATTAAGTAAAATTAGCAAAGACTTAATTTCATAAG
1 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAG
* *
2715 AATTAAGTAAAGTCAGCAAAGATTTAAT
1 AATTAAGTAAA-TTAGCAAAGACTTAAT
2743 CCAAAGATGA
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
35 46 0.49
36 48 0.51
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (35 bp):
AATTAAGTAAATTAGCAAAGACTTAATTTCACAAG
Found at i:2817 original size:11 final size:11
Alignment explanation
Indices: 2801--2888 Score: 113
Period size: 11 Copynumber: 7.9 Consensus size: 11
2791 TTAGGCAAAA
2801 GAAAGAAGACT
1 GAAAGAAGACT
*
2812 GAAAGAAAACT
1 GAAAGAAGACT
*
2823 GAAAGAAGATT
1 GAAAGAAGACT
* *
2834 GAAAAAATACT
1 GAAAGAAGACT
2845 GAAAGAAGACT
1 GAAAGAAGACT
*
2856 GAAAAAAGGACT
1 GAAAGAA-GACT
2868 GAAAGAAGACT
1 GAAAGAAGACT
*
2879 GAAAAAAGAC
1 GAAAGAAGAC
2889 AAAAAAAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
11 55 0.85
12 10 0.15
ACGTcount: A:0.59, C:0.08, G:0.23, T:0.10
Consensus pattern (11 bp):
GAAAGAAGACT
Found at i:2826 original size:22 final size:22
Alignment explanation
Indices: 2801--2888 Score: 133
Period size: 22 Copynumber: 4.0 Consensus size: 22
2791 TTAGGCAAAA
2801 GAAAGAAGACTGAAAGAAA-ACT
1 GAAAGAAGACTGAAA-AAAGACT
* *
2823 GAAAGAAGATTGAAAAAATACT
1 GAAAGAAGACTGAAAAAAGACT
2845 GAAAGAAGACTGAAAAAAGGACT
1 GAAAGAAGACTGAAAAAA-GACT
2868 GAAAGAAGACTGAAAAAAGAC
1 GAAAGAAGACTGAAAAAAGAC
2889 AAAAAAAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
21 3 0.05
22 37 0.61
23 21 0.34
ACGTcount: A:0.59, C:0.08, G:0.23, T:0.10
Consensus pattern (22 bp):
GAAAGAAGACTGAAAAAAGACT
Found at i:3146 original size:109 final size:103
Alignment explanation
Indices: 2904--3220 Score: 307
Period size: 109 Copynumber: 3.0 Consensus size: 103
2894 AAAAATACTG
* * * * * *
2904 AAAG-AAGACTAACTTAATTTCAAAGAAATTAAGTAAA-AGAAGACTGGCTTAGTTTCAAGGAAA
1 AAAGAAAGACTGACTTAATTTCAAGGAAACTAGGTAAAGA-AAGACTGGC-TAATTTCAGGGAAA
* * * *
2967 GTAGGTAAAAAGAAGACTGCCTTAATTTCAAGGAAATTAGGT
64 CTAGGT--AAAGAAGACTGGCTTAATTTCAAGGAAATTAAGC
* * * *
3009 AAAGATAGACTGACTTAATTTTAAGGAAATTAGGTAAAGATAGACTGGCTTAATTTCAAGAAAGG
1 AAAGAAAGACTGACTTAATTTCAAGGAAACTAGGTAAAGAAAGACTGGC-TAATTTC-AG---GG
* *
3074 AAATTGGGTAAAGATAGACTGGCTTAATTTCAAGGAAATTAAGC
61 AAACTAGGTAAAGA-AGACTGGCTTAATTTCAAGGAAATTAAGC
* * * *
3118 AAAGAAAAGACTGGC-TAGTTTCAGGGAAACTAGGTAAAGAAAGACTGGCTAGTTTCAGGGAAAC
1 AAAG-AAAGACTGACTTAATTTCAAGGAAACTAGGTAAAGAAAGACTGGCTAATTTCAGGGAAAC
* *
3182 TAGGTAAAGAAAGACTGGCTTAATTTTAAGAAAATTAAG
65 TAGGTAAAG-AAGACTGGCTTAATTTCAAGGAAATTAAG
3221 TAAAAGACAC
Statistics
Matches: 178, Mismatches: 25, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
104 39 0.22
105 5 0.03
106 43 0.24
107 4 0.02
108 11 0.06
109 59 0.33
110 17 0.10
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (103 bp):
AAAGAAAGACTGACTTAATTTCAAGGAAACTAGGTAAAGAAAGACTGGCTAATTTCAGGGAAACT
AGGTAAAGAAGACTGGCTTAATTTCAAGGAAATTAAGC
Found at i:3162 original size:34 final size:35
Alignment explanation
Indices: 2916--3248 Score: 334
Period size: 35 Copynumber: 9.5 Consensus size: 35
2906 AGAAGACTAA
* *
2916 CTTAATTTCAAAGAAATTAAGTAAA-AGAAGACTGG
1 CTTAATTTCAAGGAAATTAGGTAAAGA-AAGACTGG
* * * *
2951 CTTAGTTTCAAGGAAAGTAGGTAAAAAGAAGACTGC
1 CTTAATTTCAAGGAAATTAGGTAAAGA-AAGACTGG
* *
2987 CTTAATTTCAAGGAAATTAGGTAAAGATAGACTGA
1 CTTAATTTCAAGGAAATTAGGTAAAGAAAGACTGG
* *
3022 CTTAATTTTAAGGAAATTAGGTAAAGATAGACTGG
1 CTTAATTTCAAGGAAATTAGGTAAAGAAAGACTGG
* *
3057 CTTAATTTCAAGAAAGGAAATTGGGTAAAGATAGACTGG
1 CTTAATTTC----AAGGAAATTAGGTAAAGAAAGACTGG
* *
3096 CTTAATTTCAAGGAAATTAAGCAAAGAAAAGACTGG
1 CTTAATTTCAAGGAAATTAGGTAAAG-AAAGACTGG
* * *
3132 C-TAGTTTCAGGGAAACTAGGTAAAGAAAGACTGG
1 CTTAATTTCAAGGAAATTAGGTAAAGAAAGACTGG
* * *
3166 C-TAGTTTCAGGGAAACTAGGTAAAGAAAGACTGG
1 CTTAATTTCAAGGAAATTAGGTAAAGAAAGACTGG
* * * * * *
3200 CTTAATTTTAAGAAAATTAAGTAAA-AGACACAGG
1 CTTAATTTCAAGGAAATTAGGTAAAGAAAGACTGG
3234 CTTAATTTC-AGGAAA
1 CTTAATTTCAAGGAAA
3249 GGAAATTAAG
Statistics
Matches: 257, Mismatches: 34, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
33 5 0.02
34 58 0.23
35 118 0.46
36 42 0.16
39 34 0.13
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (35 bp):
CTTAATTTCAAGGAAATTAGGTAAAGAAAGACTGG
Found at i:4288 original size:19 final size:19
Alignment explanation
Indices: 4261--4320 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
4251 ATTGTTTAGG
*
4261 TACTATACATATGAGATTA
1 TACTGTACATATGAGATTA
* *
4280 TACTGTACAGATCA-ACTTA
1 TACTGTACATATGAGA-TTA
*
4299 GGTACTGTACATGTGAGATTA
1 --TACTGTACATATGAGATTA
4320 T
1 T
4321 TAAAGCAGCG
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
21 14 0.45
22 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (19 bp):
TACTGTACATATGAGATTA
Found at i:6906 original size:93 final size:93
Alignment explanation
Indices: 6738--6919 Score: 292
Period size: 93 Copynumber: 2.0 Consensus size: 93
6728 GTACAATCAA
* * *
6738 CCTAGACATTTATAGTCTGTTATCTGTCATCTGCTTCATTGACTAATAAGGGACATTTGTCACTT
1 CCTAGACATATATAGTCTGTCATCTCTCATCTGCTTCATTGACTAATAAGGGACATTTGTCACTT
*
6803 CGTGAGTAGAGTAAGTAAAAACTAGCAG
66 CGTGAATAGAGTAAGTAAAAACTAGCAG
* *
6831 CCTAGACATATATAGTCTGTCATCTCTTATCTGCTTCATTGACTAATTAGGGACATTTGTCACTT
1 CCTAGACATATATAGTCTGTCATCTCTCATCTGCTTCATTGACTAATAAGGGACATTTGTCACTT
* *
6896 GGTGAATAGAGTAAGTAGAAACTA
66 CGTGAATAGAGTAAGTAAAAACTA
6920 ACTGCAGCAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 81 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (93 bp):
CCTAGACATATATAGTCTGTCATCTCTCATCTGCTTCATTGACTAATAAGGGACATTTGTCACTT
CGTGAATAGAGTAAGTAAAAACTAGCAG
Found at i:9476 original size:23 final size:24
Alignment explanation
Indices: 9431--9476 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
9421 AACAAGCAAA
*
9431 AAAAAAAAGAAGCAAACGAACCCC
1 AAAAAAAAGAAGCAAAAGAACCCC
9455 AAAAAAAA-AA-CAAAAGATACCC
1 AAAAAAAAGAAGCAAAAGA-ACCC
9477 TTTAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 6 0.30
24 8 0.40
ACGTcount: A:0.67, C:0.22, G:0.09, T:0.02
Consensus pattern (24 bp):
AAAAAAAAGAAGCAAAAGAACCCC
Found at i:9909 original size:2 final size:2
Alignment explanation
Indices: 9904--9929 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9894 AAAAGAGAAA
9904 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
9930 CGCGTTGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11231 original size:3 final size:3
Alignment explanation
Indices: 11223--11248 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11213 TTTTCATTTT
11223 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
11249 TACTATCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Done.