Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008738.1 Corchorus capsularis cultivar CVL-1 contig08759, 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: 8381
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.32
Found at i:1168 original size:16 final size:16
Alignment explanation
Indices: 1147--1177 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1137 AAATTAGGGT
1147 TTTGTTTTGTTGTTTG
1 TTTGTTTTGTTGTTTG
*
1163 TTTGTTTTTTTGTTT
1 TTTGTTTTGTTGTTT
1178 AAAAGTAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (16 bp):
TTTGTTTTGTTGTTTG
Found at i:1727 original size:2 final size:2
Alignment explanation
Indices: 1722--1750 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1712 GATGTGTGTG
1722 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1751 TAAGCAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2576 original size:8 final size:8
Alignment explanation
Indices: 2563--2587 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2553 AAGTAATGGT
2563 AATCAGTA
1 AATCAGTA
2571 AATCAGTA
1 AATCAGTA
2579 AATCAGTA
1 AATCAGTA
2587 A
1 A
2588 TTAAGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (8 bp):
AATCAGTA
Found at i:2594 original size:16 final size:16
Alignment explanation
Indices: 2563--2596 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2553 AAGTAATGGT
*
2563 AATCAGTAAATCAGTA
1 AATCAGTAAATAAGTA
*
2579 AATCAGTAATTAAGTA
1 AATCAGTAAATAAGTA
2595 AA
1 AA
2597 AGGGATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (16 bp):
AATCAGTAAATAAGTA
Found at i:2741 original size:40 final size:42
Alignment explanation
Indices: 2643--2741 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 42
2633 GCAAGAGATT
* * * *
2643 AATCAGTGAAATCAGTAATTAAAGAGTCAAAGTAAAAGAAGT
1 AATCAGTAAAATCGGTAACTAAAGAGTCAAAGTAAAAGAAGC
2685 AATCAGTAAAAT-GGTAACTAAA-AGT-AAGAGTAAAAGAAGC
1 AATCAGTAAAATCGGTAACTAAAGAGTCAA-AGTAAAAGAAGC
2725 AATCAGT-AAATCGGTAA
1 AATCAGTAAAATCGGTAA
2742 AGAGTAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
39 6 0.12
40 26 0.51
41 8 0.16
42 11 0.22
ACGTcount: A:0.53, C:0.08, G:0.19, T:0.20
Consensus pattern (42 bp):
AATCAGTAAAATCGGTAACTAAAGAGTCAAAGTAAAAGAAGC
Found at i:2778 original size:22 final size:22
Alignment explanation
Indices: 2750--2969 Score: 182
Period size: 22 Copynumber: 10.1 Consensus size: 22
2740 AAAGAGTAAA
*
2750 AATCAGTAAAAAGTAAGAA-GGT
1 AATCAGTAAAAAGTAA-AATAGT
*
2772 AATCAGTAAAGAGTAAAATAGT
1 AATCAGTAAAAAGTAAAATAGT
* ** * *
2794 AATCAGT-GAGGGCAAAATGGT
1 AATCAGTAAAAAGTAAAATAGT
* * *
2815 AATCAATAAAGAGTAAAATGGT
1 AATCAGTAAAAAGTAAAATAGT
2837 AATCAGTAAAAAGTAAGAA-AGT
1 AATCAGTAAAAAGTAA-AATAGT
* *
2859 AATGAGTAAAGAGTAAAATAGT
1 AATCAGTAAAAAGTAAAATAGT
* *
2881 AATTAGTAAAAGGT--AATCAGT
1 AATCAGTAAAAAGTAAAAT-AGT
* * *
2902 AA-GAGCAAAATGGTAAAATAGT
1 AATCAGTAAAA-AGTAAAATAGT
*
2924 AATCAGTAAAAAGTAAAATGGT
1 AATCAGTAAAAAGTAAAATAGT
* *
2946 AATCAGTAAAGAGTAAAATCGT
1 AATCAGTAAAAAGTAAAATAGT
2968 AA
1 AA
2970 AAAGTGATAA
Statistics
Matches: 163, Mismatches: 26, Indels: 18
0.79 0.13 0.09
Matches are distributed among these distances:
20 9 0.06
21 28 0.17
22 115 0.71
23 11 0.07
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (22 bp):
AATCAGTAAAAAGTAAAATAGT
Found at i:2844 original size:87 final size:84
Alignment explanation
Indices: 2750--3206 Score: 363
Period size: 78 Copynumber: 5.5 Consensus size: 84
2740 AAAGAGTAAA
* *
2750 AATCAGTAAAAAGTAAGAA-GGTAATCAGTAAAGAGTAAAATAGTAATCAGTGAGGGCAAAATGG
1 AATCAGTAAAAAGTAA-AATGGTAATCAGTAAAGAGTAAAATAGTAAT-AGTAAGGG-ATAAT-G
*
2814 TAATCAATAAAGAGTAAAATGGT
62 TAATCAGTAAAGAGTAAAATGGT
* * *
2837 AATCAGTAAAAAGTAAGAA-AGTAATGAGTAAAGAGTAAAATAGTAATTAGTAAAAGG-TAATCA
1 AATCAGTAAAAAGTAA-AATGGTAATCAGTAAAGAGTAAAATAGTAA-TAGT-AAGGGATAAT--
* * *
2900 GTAA-GAGCAAA-ATGGTAAAATAGT
61 GTAATCAGTAAAGA--GTAAAATGGT
* *
2924 AATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATCGTAA-A--AAGTGATAA--TAAT
1 AATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATAGTAATAGTAAGGGATAATGTAAT
2984 CAGTAAA-AGGTAAAATGGT
66 CAGTAAAGA-GTAAAATGGT
* * * * *
3003 AATCAGT-AAGAGCAAAATGGTAATCAGTAAAGAGTAGAATCGTAA-A--AAGTGATAA--TAAT
1 AATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATAGTAATAGTAAGGGATAATGTAAT
3062 CAGTAAA-AGGTAAAATGGT
66 CAGTAAAGA-GTAAAATGGT
* * * * * *
3081 AATCAGT-AAGAGCAAAATGGTAATCAGTAAAGGGTAAAA-GGTAATCAGTAAGAGCAAAATGGT
1 AATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATAGTAAT-AGTAAG-GGATAAT-GT
3144 AATCAGTAAAGAGT-AAA----
63 AATCAGTAAAGAGTAAAATGGT
* *
3161 AATCAGTAAAAAGTAAGCA-GGTTATCAGTAAAGAGTAAAATAGTAA
1 AATCAGTAAAAAGTAA-AATGGTAATCAGTAAAGAGTAAAATAGTAA
3207 AAAGTAATCA
Statistics
Matches: 317, Mismatches: 33, Indels: 45
0.80 0.08 0.11
Matches are distributed among these distances:
77 4 0.01
78 105 0.33
79 21 0.07
80 13 0.04
81 28 0.09
82 11 0.03
83 3 0.01
84 3 0.01
85 15 0.05
86 10 0.03
87 100 0.32
88 4 0.01
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (84 bp):
AATCAGTAAAAAGTAAAATGGTAATCAGTAAAGAGTAAAATAGTAATAGTAAGGGATAATGTAAT
CAGTAAAGAGTAAAATGGT
Found at i:2925 original size:29 final size:29
Alignment explanation
Indices: 2893--3025 Score: 106
Period size: 28 Copynumber: 4.9 Consensus size: 29
2883 TTAGTAAAAG
2893 GTAATCAGTAAGAGCAAAATGGTAAAATA
1 GTAATCAGTAAGAGCAAAATGGTAAAATA
*
2922 GTAATCAGT---A--AAAA--GTAAAATG
1 GTAATCAGTAAGAGCAAAATGGTAAAATA
* *
2944 GTAATCAGTAAAGAGTAAAATCGTAAAA-A
1 GTAATCAGT-AAGAGCAAAATGGTAAAATA
* * * * *
2973 GTGAT-AATAATCAGTAAAA-GGTAAAATG
1 GTAATCAGTAA-GAGCAAAATGGTAAAATA
3001 GTAATCAGTAAGAGCAAAATGGTAA
1 GTAATCAGTAAGAGCAAAATGGTAA
3026 TCAGTAAAGA
Statistics
Matches: 81, Mismatches: 11, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
22 16 0.20
24 4 0.05
26 2 0.02
27 8 0.10
28 23 0.28
29 22 0.27
30 6 0.07
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.22
Consensus pattern (29 bp):
GTAATCAGTAAGAGCAAAATGGTAAAATA
Found at i:2997 original size:35 final size:35
Alignment explanation
Indices: 2945--3082 Score: 127
Period size: 35 Copynumber: 3.7 Consensus size: 35
2935 AGTAAAATGG
2945 TAATCAGTAAAGAGTAAAATCGTAAAAAGTGATAA
1 TAATCAGTAAAGAGTAAAATCGTAAAAAGTGATAA
* * *
2980 TAATCAGTAAA-AGGTAAAATGGTAATCAGTAAGAGCAAAA
1 TAATCAGTAAAGA-GTAAAATCGTAA--A--AAGTG-ATAA
*
3020 TGGTAATCAGTAAAGAGTAGAATCGTAAAAAGTGATAA
1 ---TAATCAGTAAAGAGTAAAATCGTAAAAAGTGATAA
*
3058 TAATCAGTAAA-AGGTAAAATGGTAA
1 TAATCAGTAAAGA-GTAAAATCGTAA
3083 TCAGTAAGAG
Statistics
Matches: 83, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
34 2 0.02
35 43 0.52
37 1 0.01
38 3 0.04
39 8 0.10
40 3 0.04
41 1 0.01
43 21 0.25
44 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.22
Consensus pattern (35 bp):
TAATCAGTAAAGAGTAAAATCGTAAAAAGTGATAA
Found at i:3007 original size:22 final size:21
Alignment explanation
Indices: 2980--3033 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
2970 AAAGTGATAA
*
2980 TAATCAGTAAAAGGTAAAATGG
1 TAATCAGTAAAA-GCAAAATGG
*
3002 TAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAAAGCAAAATGG
3023 TAATCAGTAAA
1 TAATCAGTAAA
3034 GAGTAGAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.22
Consensus pattern (21 bp):
TAATCAGTAAAAGCAAAATGG
Found at i:3099 original size:21 final size:21
Alignment explanation
Indices: 3084--3161 Score: 104
Period size: 21 Copynumber: 3.7 Consensus size: 21
3074 AAATGGTAAT
*
3084 CAGTAAGAGCAAAATGGTAAT
1 CAGTAAGAGTAAAATGGTAAT
*
3105 CAGTAAAGGGTAAAA-GGTAAT
1 CAGT-AAGAGTAAAATGGTAAT
*
3126 CAGTAAGAGCAAAATGGTAAT
1 CAGTAAGAGTAAAATGGTAAT
3147 CAGTAAAGAGTAAAA
1 CAGT-AAGAGTAAAA
3162 ATCAGTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.16
21 24 0.49
22 17 0.35
ACGTcount: A:0.50, C:0.08, G:0.24, T:0.18
Consensus pattern (21 bp):
CAGTAAGAGTAAAATGGTAAT
Found at i:3126 original size:42 final size:43
Alignment explanation
Indices: 3058--3161 Score: 183
Period size: 42 Copynumber: 2.4 Consensus size: 43
3048 AAAGTGATAA
*
3058 TAATCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAAGGGTAAAATGGTAATCAGTAAGAGCAAAATGG
3101 TAATCAGTAAAGGGTAAAA-GGTAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAAGGGTAAAATGGTAATCAGTAAGAGCAAAATGG
*
3143 TAATCAGTAAAGAGTAAAA
1 TAATCAGTAAAGGGTAAAA
3162 ATCAGTAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
42 41 0.69
43 18 0.31
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.20
Consensus pattern (43 bp):
TAATCAGTAAAGGGTAAAATGGTAATCAGTAAGAGCAAAATGG
Found at i:3166 original size:17 final size:17
Alignment explanation
Indices: 3144--3176 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3134 GCAAAATGGT
*
3144 AATCAGTAAAGAGTAAA
1 AATCAGTAAAAAGTAAA
3161 AATCAGTAAAAAGTAA
1 AATCAGTAAAAAGTAA
3177 GCAGGTTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.15, T:0.18
Consensus pattern (17 bp):
AATCAGTAAAAAGTAAA
Found at i:6024 original size:14 final size:15
Alignment explanation
Indices: 5997--6077 Score: 55
Period size: 15 Copynumber: 5.7 Consensus size: 15
5987 AAGGATATTT
5997 AAGAATATATTTTTA
1 AAGAATATATTTTTA
* *
6012 AAGAATTTATTTTTG
1 AAGAATATATTTTTA
*
6027 AAG--GATA--TTT-
1 AAGAATATATTTTTA
*
6037 AAGAATGTATTTTTA
1 AAGAATATATTTTTA
* * *
6052 AAGGATTTATTTTTT
1 AAGAATATATTTTTA
*
6067 AAGGATATATT
1 AAGAATATATT
6078 ATGATGATAT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
10 3 0.06
11 3 0.06
12 2 0.04
13 2 0.04
14 3 0.06
15 38 0.75
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (15 bp):
AAGAATATATTTTTA
Found at i:6025 original size:40 final size:40
Alignment explanation
Indices: 5980--6074 Score: 163
Period size: 40 Copynumber: 2.4 Consensus size: 40
5970 GTGTTCTTCC
5980 ATTTTTTAAGGATATTTAAGAATATATTTTTAAAGAATTT
1 ATTTTTTAAGGATATTTAAGAATATATTTTTAAAGAATTT
* * *
6020 ATTTTTGAAGGATATTTAAGAATGTATTTTTAAAGGATTT
1 ATTTTTTAAGGATATTTAAGAATATATTTTTAAAGAATTT
6060 ATTTTTTAAGGATAT
1 ATTTTTTAAGGATAT
6075 ATTATGATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (40 bp):
ATTTTTTAAGGATATTTAAGAATATATTTTTAAAGAATTT
Done.