Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014079.1 Corchorus capsularis cultivar CVL-1 contig14100, 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: 29063
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:8802 original size:16 final size:15
Alignment explanation
Indices: 8773--8827 Score: 74
Period size: 15 Copynumber: 3.5 Consensus size: 15
8763 TTTGGGTTGG
8773 ATTTGGGTCAGGTTA
1 ATTTGGGTCAGGTTA
*
8788 ATTTGGGTTCGGGTTGA
1 ATTTGGG-TCAGGTT-A
8805 ATTTGGGTCAGGTTA
1 ATTTGGGTCAGGTTA
*
8820 ATTCGGGT
1 ATTTGGGT
8828 TCGGGTTCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 15 0.43
16 12 0.34
17 8 0.23
ACGTcount: A:0.16, C:0.07, G:0.36, T:0.40
Consensus pattern (15 bp):
ATTTGGGTCAGGTTA
Found at i:8809 original size:32 final size:32
Alignment explanation
Indices: 8766--8834 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
8756 AGTCGGATTT
* *
8766 GGGTTGGATTTGGGTCAGGTTAATTTGGGTTC
1 GGGTTGAATTTGGGTCAGGTTAATTCGGGTTC
8798 GGGTTGAATTTGGGTCAGGTTAATTCGGGTTC
1 GGGTTGAATTTGGGTCAGGTTAATTCGGGTTC
8830 GGGTT
1 GGGTT
8835 CTGTTTGGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.13, C:0.07, G:0.41, T:0.39
Consensus pattern (32 bp):
GGGTTGAATTTGGGTCAGGTTAATTCGGGTTC
Found at i:8834 original size:16 final size:16
Alignment explanation
Indices: 8773--8834 Score: 74
Period size: 16 Copynumber: 3.9 Consensus size: 16
8763 TTTGGGTTGG
*
8773 ATTTGGG-TCAGGTTA
1 ATTTGGGTTCGGGTTA
8788 ATTTGGGTTCGGGTTGA
1 ATTTGGGTTCGGGTT-A
*
8805 ATTTGGG-TCAGGTTA
1 ATTTGGGTTCGGGTTA
*
8820 ATTCGGGTTCGGGTT
1 ATTTGGGTTCGGGTT
8835 CTGTTTGGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
15 14 0.35
16 18 0.45
17 8 0.20
ACGTcount: A:0.15, C:0.08, G:0.37, T:0.40
Consensus pattern (16 bp):
ATTTGGGTTCGGGTTA
Found at i:8842 original size:32 final size:32
Alignment explanation
Indices: 8773--8844 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
8763 TTTGGGTTGG
* *
8773 ATTTGGGTCAGGTTAATTTGGGTTCGGGTTGA
1 ATTTGGGTCAGGTTAATTCGGGTTCGGGTTCA
*
8805 ATTTGGGTCAGGTTAATTCGGGTTCGGGTTCT
1 ATTTGGGTCAGGTTAATTCGGGTTCGGGTTCA
*
8837 GTTTGGGT
1 ATTTGGGT
8845 TTTGGCCAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.12, C:0.08, G:0.38, T:0.42
Consensus pattern (32 bp):
ATTTGGGTCAGGTTAATTCGGGTTCGGGTTCA
Found at i:9003 original size:16 final size:16
Alignment explanation
Indices: 8982--9104 Score: 131
Period size: 16 Copynumber: 7.7 Consensus size: 16
8972 TTTTCATAAA
* *
8982 TTTTCGGATTCGGGTT
1 TTTTCGGGTTCGAGTT
* *
8998 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGAGTT
9014 TTTTCGGGTTCG-GATT
1 TTTTCGGGTTCGAG-TT
* *
9030 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGAGTT
*
9046 TTTTCGGGTTCGTGTT
1 TTTTCGGGTTCGAGTT
* *
9062 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGAGTT
*
9078 TTTTCGGGTTCGGGTT
1 TTTTCGGGTTCGAGTT
*
9094 TTTTCAGGTTC
1 TTTTCGGGTTC
9105 AGGTTCAGGC
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
15 1 0.01
16 85 0.98
17 1 0.01
ACGTcount: A:0.05, C:0.13, G:0.31, T:0.51
Consensus pattern (16 bp):
TTTTCGGGTTCGAGTT
Found at i:9026 original size:32 final size:32
Alignment explanation
Indices: 8982--9103 Score: 208
Period size: 32 Copynumber: 3.8 Consensus size: 32
8972 TTTTCATAAA
*
8982 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
*
9014 TTTTCGGGTTCGGATTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
*
9046 TTTTCGGGTTCGTGTTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
*
9078 TTTTCGGGTTCGGGTTTTTTCAGGTT
1 TTTTCGGGTTCGGGTTTTTTCGGGTT
9104 CAGGTTCAGG
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 84 1.00
ACGTcount: A:0.05, C:0.12, G:0.31, T:0.52
Consensus pattern (32 bp):
TTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCT
Found at i:9118 original size:64 final size:64
Alignment explanation
Indices: 8990--9122 Score: 178
Period size: 64 Copynumber: 2.1 Consensus size: 64
8980 AATTTTCGGA
* * ***
8990 TTCGGGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCGGATTTTTTCGGGTTTGAGCTTTTTCGGG
1 TTCGGGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCGGATTTTTTCAGGTTTCAGCTTAGGCGGG
* * *
9054 TTCGTGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTTTTCAGG-TTCAGGTTCAGGCGGG
1 TTCGGGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCGGATTTTTTCAGGTTTCAGCTT-AGGCGGG
9118 TTCGG
1 TTCGG
9123 ATAGTTGACT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 6 0.10
64 53 0.90
ACGTcount: A:0.05, C:0.14, G:0.34, T:0.47
Consensus pattern (64 bp):
TTCGGGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCGGATTTTTTCAGGTTTCAGCTTAGGCGGG
Found at i:13902 original size:22 final size:22
Alignment explanation
Indices: 13874--13919 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
13864 GAGGCTGCCG
* *
13874 AAATTTCATACCGTGGTTATCA
1 AAATTTCATAACATGGTTATCA
*
13896 AAATTTCATAATATGGTTATCA
1 AAATTTCATAACATGGTTATCA
13918 AA
1 AA
13920 GAGGTTATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (22 bp):
AAATTTCATAACATGGTTATCA
Found at i:13972 original size:22 final size:22
Alignment explanation
Indices: 13920--13977 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
13910 GGTTATCAAA
*
13920 GAGGTTATCAGAATTTCATAAC
1 GAGGTTATCATAATTTCATAAC
* **
13942 GAGGCTATCATAATTTCATAGT
1 GAGGTTATCATAATTTCATAAC
*
13964 GTGGTTATCATAAT
1 GAGGTTATCATAAT
13978 AATTTCATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (22 bp):
GAGGTTATCATAATTTCATAAC
Found at i:14017 original size:22 final size:22
Alignment explanation
Indices: 13947--14050 Score: 76
Period size: 22 Copynumber: 4.7 Consensus size: 22
13937 ATAACGAGGC
* *
13947 TATCATAATTTCATAGTGT-GGT
1 TATCAAAATTTCATAG-GTAAGT
*
13969 TATCATAATAATTTCATAAG-AAGGT
1 TATC--AA-AATTTCATAGGTAA-GT
13994 TA-CTAAAATTTCATAGGTAAGT
1 TATC-AAAATTTCATAGGTAAGT
14016 TATCAAAATTT--TAGTGTAA-T
1 TATCAAAATTTCATAG-GTAAGT
14036 TATCAAAATTTCATA
1 TATCAAAATTTCATA
14051 ATGTGATTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
20 15 0.22
21 4 0.06
22 27 0.40
23 6 0.09
24 3 0.04
25 13 0.19
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (22 bp):
TATCAAAATTTCATAGGTAAGT
Found at i:14106 original size:22 final size:22
Alignment explanation
Indices: 14081--14311 Score: 70
Period size: 22 Copynumber: 10.4 Consensus size: 22
14071 TAAAAATCTC
14081 AATTTCATAAGGTGATTATCAA
1 AATTTCATAAGGTGATTATCAA
** * * * *
14103 AATTAAATAGGGAGATTATTAG
1 AATTTCATAAGGTGATTATCAA
* *
14125 AA-TTCTATAATGTGGTTAT-AGA
1 AATTTC-ATAAGGTGATTATCA-A
*
14147 AATTTCATAAGGTGGTT-T-AA
1 AATTTCATAAGGTGATTATCAA
* *
14167 AATTCTTATAAAGTGGCA-TATTACAAA
1 AATT-TCATAAGGT-G-ATTA-T-C-AA
* * *
14194 AATTTCATATGGAGGTTATCAA
1 AATTTCATAAGGTGATTATCAA
*
14216 AATTTCAT-A-GTGTAGTTATCAG
1 AATTTCATAAGGTG-A-TTATCAA
* * *
14238 AATTTTAT-AGGAAGGTTATCAA
1 AATTTCATAAGG-TGATTATCAA
* *
14260 AAATTCA-AAGTGTGTTTATCAA
1 AATTTCATAAG-GTGATTATCAA
*
14282 AAATTCATATAGAG-G-TTATCAA
1 AATTTCATA-AG-GTGATTATCAA
14304 AATTTCAT
1 AATTTCAT
14312 TAGGAGGGAT
Statistics
Matches: 153, Mismatches: 36, Indels: 40
0.67 0.16 0.17
Matches are distributed among these distances:
20 7 0.05
21 11 0.07
22 107 0.70
23 8 0.05
24 6 0.04
25 3 0.02
26 5 0.03
27 6 0.04
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (22 bp):
AATTTCATAAGGTGATTATCAA
Found at i:14257 original size:44 final size:44
Alignment explanation
Indices: 14190--14311 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 44
14180 TGGCATATTA
*
14190 CAAAAATTTCATATGGAGGTTATCAAAATTTCATAGTGTAG-TTAT
1 CAAAAA-TTCATATAGAGGTTATCAAAATTTCATAGTGT-GTTTAT
* * * *
14235 C-AGAATT-TTATAGGAAGGTTATCAAAAATTCAAAGTGTGTTTAT
1 CAAAAATTCATATA-G-AGGTTATCAAAATTTCATAGTGTGTTTAT
14279 CAAAAATTCATATAGAGGTTATCAAAATTTCAT
1 CAAAAATTCATATAGAGGTTATCAAAATTTCAT
14312 TAGGAGGGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
42 3 0.05
43 4 0.06
44 45 0.71
45 7 0.11
46 4 0.06
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (44 bp):
CAAAAATTCATATAGAGGTTATCAAAATTTCATAGTGTGTTTAT
Found at i:14318 original size:22 final size:21
Alignment explanation
Indices: 14192--14334 Score: 119
Period size: 22 Copynumber: 6.6 Consensus size: 21
14182 GCATATTACA
14192 AAAATTTCATATGGAGGTTATC
1 AAAATTTCATA-GGAGGTTATC
14214 AAAATTTCATAGTGTA-GTTATC
1 AAAATTTCATAG-G-AGGTTATC
* *
14236 AGAATTTTATAGGAAGGTTATC
1 AAAATTTCATAGG-AGGTTATC
* * * *
14258 AAAAATTCAAAGTGTGTTTATC
1 AAAATTTCATAG-GAGGTTATC
* *
14280 AAAAATTCATATAGAGGTTATC
1 AAAATTTCATA-GGAGGTTATC
*
14302 AAAATTTCATTAGGAGG-GATC
1 AAAATTTCA-TAGGAGGTTATC
*
14323 AAAATTTGATAG
1 AAAATTTCATAG
14335 CGTCATTATC
Statistics
Matches: 98, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
20 3 0.03
21 14 0.14
22 77 0.79
23 4 0.04
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (21 bp):
AAAATTTCATAGGAGGTTATC
Found at i:14503 original size:22 final size:22
Alignment explanation
Indices: 14478--14529 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
14468 CCACACTATT
*
14478 AAATTTTGATAACCTCCTTATA
1 AAATTTTGATAACCTCCATATA
* *
14500 AAATTTTTATAACCTTCATATA
1 AAATTTTGATAACCTCCATATA
*
14522 AATTTTTG
1 AAATTTTG
14530 GGAACCACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (22 bp):
AAATTTTGATAACCTCCATATA
Found at i:18249 original size:12 final size:13
Alignment explanation
Indices: 18219--18253 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
18209 CTCATGCACC
*
18219 TAAATCAATTTAT
1 TAAAACAATTTAT
18232 TAAAACAATTTA-
1 TAAAACAATTTAT
18244 TAAAACAATT
1 TAAAACAATT
18254 ACATAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAAACAATTTAT
Found at i:19923 original size:25 final size:25
Alignment explanation
Indices: 19895--19944 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
19885 ATATTAGAAC
**
19895 TTTTAAAATATATTCTTTTACAATTT
1 TTTTAAAA-ATAAACTTTTACAATTT
19921 TTTTAAAAATAAACTTTTACAATT
1 TTTTAAAAATAAACTTTTACAATT
19945 ATTCTACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTAAAAATAAACTTTTACAATTT
Found at i:19967 original size:29 final size:29
Alignment explanation
Indices: 19934--19996 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
19924 TAAAAATAAA
19934 CTTTTACAATTATTCTACTAAAACTCTAT
1 CTTTTACAATTATTCTACTAAAACTCTAT
19963 CTTTTACAATTATTCTACTAAAACTCTAT
1 CTTTTACAATTATTCTACTAAAACTCTAT
19992 -TTTTA
1 CTTTTA
19997 TTCGATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (29 bp):
CTTTTACAATTATTCTACTAAAACTCTAT
Found at i:28242 original size:17 final size:17
Alignment explanation
Indices: 28209--28252 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
28199 AAACAATTTT
28209 AAATTTTT--TTTTCCAA
1 AAATTTTTGCTTTTCC-A
28225 AAATTTTTGCTTTT-CA
1 AAATTTTTGCTTTTCCA
28241 AAATTTTTGCTT
1 AAATTTTTGCTT
28253 CTCTAGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 21 0.81
17 1 0.04
18 4 0.15
ACGTcount: A:0.27, C:0.11, G:0.05, T:0.57
Consensus pattern (17 bp):
AAATTTTTGCTTTTCCA
Done.