Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007327.1 Corchorus capsularis cultivar CVL-1 contig07348, 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: 29162
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:2764 original size:36 final size:36
Alignment explanation
Indices: 2723--2829 Score: 198
Period size: 35 Copynumber: 3.0 Consensus size: 36
2713 CAAGTAAGTT
2723 CAAAGACTTAATTTCACAAGAATTAAGTAAAATTAG
1 CAAAGACTTAATTTCACAAGAATTAAGTAAAATTAG
*
2759 CAAAGACTTAATTTCACAAGAATTAAGT-AAATTAT
1 CAAAGACTTAATTTCACAAGAATTAAGTAAAATTAG
2794 CAAAGACTTAATTTCACAAGAATTAAGTAAAATTAG
1 CAAAGACTTAATTTCACAAGAATTAAGTAAAATTAG
2830 GTAAAATTAG
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 34 0.50
36 34 0.50
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.29
Consensus pattern (36 bp):
CAAAGACTTAATTTCACAAGAATTAAGTAAAATTAG
Found at i:2834 original size:45 final size:45
Alignment explanation
Indices: 2779--2871 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
2769 ATTTCACAAG
*
2779 AATTAAGT-AAATTATCAAAGACTTAATTTCACAAGAATTAAGTAA
1 AATTAAGTAAAATTAGCAAAGACTT-ATTTCACAAGAATTAAGTAA
*
2824 AATTAGGTAAAATTAGCAAAGACTTATTTCACAAGAATTAAGTAA
1 AATTAAGTAAAATTAGCAAAGACTTATTTCACAAGAATTAAGTAA
2869 AAT
1 AAT
2872 CAGCAAAGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 30 0.67
46 15 0.33
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.30
Consensus pattern (45 bp):
AATTAAGTAAAATTAGCAAAGACTTATTTCACAAGAATTAAGTAA
Found at i:2955 original size:11 final size:11
Alignment explanation
Indices: 2941--3038 Score: 81
Period size: 11 Copynumber: 8.7 Consensus size: 11
2931 GAAATTAGGC
*
2941 ACTGAAAGAAG
1 ACTGAAATAAG
2952 ACTGACAA-AAG
1 ACTGA-AATAAG
*
2963 ACTAGAAAGTTAG
1 ACT-GAAA-TAAG
*
2976 ACTGAAATCAG
1 ACTGAAATAAG
*
2987 ACTGAAATTAG
1 ACTGAAATAAG
* *
2998 ACTAAAATTAG
1 ACTGAAATAAG
*
3009 ACTGAAAAAAG
1 ACTGAAATAAG
* *
3020 ACTGATATTAG
1 ACTGAAATAAG
3031 ACTGAAAT
1 ACTGAAAT
3039 TGGACTGATA
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
11 59 0.82
12 8 0.11
13 5 0.07
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.20
Consensus pattern (11 bp):
ACTGAAATAAG
Found at i:2978 original size:24 final size:22
Alignment explanation
Indices: 2941--3055 Score: 90
Period size: 22 Copynumber: 5.1 Consensus size: 22
2931 GAAATTAGGC
**
2941 ACTGAAAGAAGACTGACAA-AAG
1 ACTGAAATTAGACTGA-AATAAG
*
2963 ACTAGAAAGTTAGACTGAAATCAG
1 ACT-GAAA-TTAGACTGAAATAAG
* *
2987 ACTGAAATTAGACTAAAATTAG
1 ACTGAAATTAGACTGAAATAAG
** * *
3009 ACTGAAAAAAGACTGATATTAG
1 ACTGAAATTAGACTGAAATAAG
*
3031 ACTGAAATTGGACTGATAA-AAG
1 ACTGAAATTAGACTGA-AATAAG
3053 ACT
1 ACT
3056 AGCTTAATTT
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
22 52 0.69
23 11 0.15
24 12 0.16
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTGAAATTAGACTGAAATAAG
Found at i:3014 original size:33 final size:33
Alignment explanation
Indices: 2932--3055 Score: 124
Period size: 33 Copynumber: 3.6 Consensus size: 33
2922 AATTTCAAGG
* *
2932 AAATTAGGCACTGAAAGAAGACTGACAA-AAGACTA
1 AAATTA-G-ACTGAAAAAAGACTGA-AATTAGACTA
**
2967 GAAAGTTAGACTGAAATCAGACTGAAATTAGACTA
1 -AAA-TTAGACTGAAAAAAGACTGAAATTAGACTA
* *
3002 AAATTAGACTGAAAAAAGACTGATATTAGACTG
1 AAATTAGACTGAAAAAAGACTGAAATTAGACTA
* *
3035 AAATTGGACTGATAAAAGACT
1 AAATTAGACTGAAAAAAGACT
3056 AGCTTAATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
33 45 0.58
34 5 0.06
35 20 0.26
36 4 0.05
37 3 0.04
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.21
Consensus pattern (33 bp):
AAATTAGACTGAAAAAAGACTGAAATTAGACTA
Found at i:3044 original size:11 final size:11
Alignment explanation
Indices: 2961--3046 Score: 100
Period size: 11 Copynumber: 7.6 Consensus size: 11
2951 GACTGACAAA
2961 AGACTAGAAAGTT
1 AGACT-GAAA-TT
*
2974 AGACTGAAATC
1 AGACTGAAATT
2985 AGACTGAAATT
1 AGACTGAAATT
*
2996 AGACTAAAATT
1 AGACTGAAATT
**
3007 AGACTGAAAAA
1 AGACTGAAATT
*
3018 AGACTGATATT
1 AGACTGAAATT
3029 AGACTGAAATT
1 AGACTGAAATT
*
3040 GGACTGA
1 AGACTGA
3047 TAAAAGACTA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
11 53 0.85
12 4 0.06
13 5 0.08
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (11 bp):
AGACTGAAATT
Found at i:3172 original size:36 final size:36
Alignment explanation
Indices: 3048--3313 Score: 262
Period size: 36 Copynumber: 7.6 Consensus size: 36
3038 TTGGACTGAT
3048 AAAAGACTAGCTTAATTTCAAGGAAATT-GAGTAAAG
1 AAAAGACTAGCTTAATTTCAAGGAAATTAG-GTAAAG
* * *
3084 --AAGACTGGCTTAATTGCAAGGAAATTAAGTAAA-
1 AAAAGACTAGCTTAATTTCAAGGAAATTAGGTAAAG
* * * * * *
3117 ACAAGATTGGCTTAGTTTCAGGGAAACTAGGTAAAG
1 AAAAGACTAGCTTAATTTCAAGGAAATTAGGTAAAG
* *
3153 AAAAGACTAGCTTAATTTCAAGAAAATTAAGT-AA-
1 AAAAGACTAGCTTAATTTCAAGGAAATTAGGTAAAG
* * * * *
3187 ACAAGACTGGCTTAGTTTCACGGAAACTAGGTAAAG
1 AAAAGACTAGCTTAATTTCAAGGAAATTAGGTAAAG
*
3223 AAAAGACTAGCTTAATTTCAAGGAAATTAGGTGAAG
1 AAAAGACTAGCTTAATTTCAAGGAAATTAGGTAAAG
* * *
3259 ATAAGACTGGCTTAATTTCAAGGAAATTAAGT--A-
1 AAAAGACTAGCTTAATTTCAAGGAAATTAGGTAAAG
3292 AAAAGACATAGGCTTAATTTCA
1 AAAAGAC-TA-GCTTAATTTCA
3314 GAAAAGGAAA
Statistics
Matches: 187, Mismatches: 35, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
33 6 0.03
34 56 0.30
35 42 0.22
36 83 0.44
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.26
Consensus pattern (36 bp):
AAAAGACTAGCTTAATTTCAAGGAAATTAGGTAAAG
Found at i:3180 original size:105 final size:105
Alignment explanation
Indices: 3048--3310 Score: 339
Period size: 105 Copynumber: 2.5 Consensus size: 105
3038 TTGGACTGAT
* *
3048 AAAAGACTAGCTTAATTTCAAGGAAATTGAGTAAAGAAGACTGGCTTAATTGCAAGGAAATTAAG
1 AAAAGACTAGCTTAATTTCAAGGAAATTAAGTAAA-AAGACTGGCTTAATTGCAAGGAAACTAAG
* * * * *
3113 TAAA-ACAAGATTGGCTTAGTTTCAGGGAAACTAGGTAAAG
65 TAAAGAAAAGACTAGCTTAATTTCAAGGAAACTAGGTAAAG
* * * * *
3153 AAAAGACTAGCTTAATTTCAAGAAAATTAAGTAAACAAGACTGGCTTAGTTTCACGGAAACTAGG
1 AAAAGACTAGCTTAATTTCAAGGAAATTAAGTAAA-AAGACTGGCTTAATTGCAAGGAAACTAAG
* *
3218 TAAAGAAAAGACTAGCTTAATTTCAAGGAAATTAGGTGAAG
65 TAAAGAAAAGACTAGCTTAATTTCAAGGAAACTAGGTAAAG
* *
3259 ATAAGACTGGCTTAATTTCAAGGAAATTAAGTAAAAAGACATAGGCTTAATT
1 AAAAGACTAGCTTAATTTCAAGGAAATTAAGTAAAAAGAC-T-GGCTTAATT
3311 TCAGAAAAGG
Statistics
Matches: 136, Mismatches: 19, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
105 66 0.49
106 62 0.46
107 8 0.06
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (105 bp):
AAAAGACTAGCTTAATTTCAAGGAAATTAAGTAAAAAGACTGGCTTAATTGCAAGGAAACTAAGT
AAAGAAAAGACTAGCTTAATTTCAAGGAAACTAGGTAAAG
Found at i:3212 original size:70 final size:71
Alignment explanation
Indices: 3050--3318 Score: 302
Period size: 70 Copynumber: 3.8 Consensus size: 71
3040 GGACTGATAA
* * * * *
3050 AAGACTAGCTTAATTTCAAGGAAA-TTGAGTAAAG--AAGACTGGCTTAATTGCAAGGAAATTAA
1 AAGACTGGCTTAATTTCAAGGAAACTAG-GTAAAGAAAAGACTAGCTTAATTTCAAGAAAATTAA
3112 GTAAAAC
65 GTAAAAC
* * *
3119 AAGATTGGCTTAGTTTCAGGGAAACTAGGTAAAGAAAAGACTAGCTTAATTTCAAGAAAATTAAG
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTAGCTTAATTTCAAGAAAATTAAG
3184 T-AAAC
66 TAAAAC
* * * *
3189 AAGACTGGCTTAGTTTCACGGAAACTAGGTAAAGAAAAGACTAGCTTAATTTCAAGGAAATTAGG
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTAGCTTAATTTCAAGAAAATTAAG
* *
3254 TGAAGAT
66 T-AAAAC
* *
3261 AAGACTGGCTTAATTTCAAGGAAATTAAGT--A-AAAAGACATAGGCTTAATTTC-AGAAAA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAAAAGAC-TA-GCTTAATTTCAAGAAAA
3319 GGAAATTAAG
Statistics
Matches: 174, Mismatches: 19, Indels: 13
0.84 0.09 0.06
Matches are distributed among these distances:
69 33 0.19
70 76 0.44
71 37 0.21
72 28 0.16
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.25
Consensus pattern (71 bp):
AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAAAAGACTAGCTTAATTTCAAGAAAATTAAG
TAAAAC
Found at i:3369 original size:36 final size:36
Alignment explanation
Indices: 3317--3422 Score: 162
Period size: 36 Copynumber: 2.9 Consensus size: 36
3307 AATTTCAGAA
*
3317 AAGGAAATTAAGTAGAGTCAATAAAAGACTTAATTC
1 AAGGTAATTAAGTAGAGTCAATAAAAGACTTAATTC
3353 AAGGTAATTAAGTAGAGTCAATAAAAGACTTAATTC
1 AAGGTAATTAAGTAGAGTCAATAAAAGACTTAATTC
*
3389 AGGGTAATTAAGT-GAAGTCAAT-AAAGAACTTAAT
1 AAGGTAATTAAGTAG-AGTCAATAAAAG-ACTTAAT
3423 CTAAAAAGAG
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
35 5 0.08
36 61 0.92
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (36 bp):
AAGGTAATTAAGTAGAGTCAATAAAAGACTTAATTC
Found at i:6607 original size:9 final size:9
Alignment explanation
Indices: 6593--6626 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
6583 GTGTGCACCC
6593 AATCAAGCA
1 AATCAAGCA
6602 AATCAAGCA
1 AATCAAGCA
6611 AATCAAGCA
1 AATCAAGCA
*
6620 ATTCAAG
1 AATCAAG
6627 GCATCAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.53, C:0.21, G:0.12, T:0.15
Consensus pattern (9 bp):
AATCAAGCA
Found at i:6877 original size:21 final size:22
Alignment explanation
Indices: 6852--6910 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
6842 GCATAGGTGA
*
6852 CCGGTGGTGGCATGGTGA-TGG
1 CCGGTGGTGGCACGGTGATTGG
*
6873 CCGGTGGTTGCACGGTGATTGG
1 CCGGTGGTGGCACGGTGATTGG
*
6895 CCGGTAGTGGCACGGT
1 CCGGTGGTGGCACGGT
6911 TGTGGTTGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.10, C:0.19, G:0.47, T:0.24
Consensus pattern (22 bp):
CCGGTGGTGGCACGGTGATTGG
Found at i:9689 original size:22 final size:22
Alignment explanation
Indices: 9664--9727 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
9654 TTTATAACGG
*
9664 AAACCCTAATTTTTTTTTTGAA
1 AAACCCAAATTTTTTTTTTGAA
* *
9686 AAACGCAAATTTTTTTTTAGAA
1 AAACCCAAATTTTTTTTTTGAA
*
9708 AAACGCAAAATTTTTTTTTT
1 AAAC-CCAAATTTTTTTTTT
9728 TTTAGAGTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
22 23 0.66
23 12 0.34
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (22 bp):
AAACCCAAATTTTTTTTTTGAA
Found at i:18504 original size:8 final size:8
Alignment explanation
Indices: 18491--18533 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
18481 TAGCTTGTGG
18491 GAATTTAT
1 GAATTTAT
18499 GAATTTAT
1 GAATTTAT
*
18507 GAATTTTT
1 GAATTTAT
*
18515 G--TTGAT
1 GAATTTAT
18521 GAATTTAT
1 GAATTTAT
18529 GAATT
1 GAATT
18534 ATTTATGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 4 0.14
8 25 0.86
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (8 bp):
GAATTTAT
Done.