Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023219.1 Corchorus olitorius cultivar O-4 contig23252, 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: 73618
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--44 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1 TG
3 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44 T
1 T
45 TACTAATAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13354 original size:37 final size:37
Alignment explanation
Indices: 13304--13378 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
13294 CAAGTTGTTT
*
13304 TCTGGTTGCCTCCCCCACCTTTGTTTTGTAAAATAAA
1 TCTGGTTGCCTCCCCCACCTTTGTATTGTAAAATAAA
*
13341 TCTGGTTGCCTCCCCCGCCTTTGTATTGTAAAATAAA
1 TCTGGTTGCCTCCCCCACCTTTGTATTGTAAAATAAA
13378 T
1 T
13379 GTGGATGGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (37 bp):
TCTGGTTGCCTCCCCCACCTTTGTATTGTAAAATAAA
Found at i:21433 original size:11 final size:11
Alignment explanation
Indices: 21417--21451 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
21407 TTTTTCTGTT
21417 TTTTGTTTTTG
1 TTTTGTTTTTG
*
21428 TTTTGTTTTCG
1 TTTTGTTTTTG
21439 TTTTGTTTTTG
1 TTTTGTTTTTG
21450 TT
1 TT
21452 GTGCTGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:27889 original size:35 final size:35
Alignment explanation
Indices: 27825--28002 Score: 159
Period size: 35 Copynumber: 5.1 Consensus size: 35
27815 TGCATTAAAC
* * *
27825 AAGTCAGT-AATAACTTAATTTAGGGTAATTAAGT
1 AAGTCAGTAAACAACTTAATTCAGGATAATTAAGT
* **
27859 AAGTCACTAAACAACTTAATTCAGGATAATTAAAC
1 AAGTCAGTAAACAACTTAATTCAGGATAATTAAGT
* * *
27894 AAGTCAGT-AATAACTTAATTCA-AAGTAATTAAGC
1 AAGTCAGTAAACAACTTAATTCAGGA-TAATTAAGT
* *
27928 AAG-CTAGTAATCAACTTAATTCAGGGTAATTAAGT
1 AAGTC-AGTAAACAACTTAATTCAGGATAATTAAGT
* * **
27963 AAATCGGTAAGTAACTTAATTCAAGG-TAATTAAGT
1 AAGTCAGTAAACAACTTAATTC-AGGATAATTAAGT
27998 AAGTC
1 AAGTC
28003 TGGTAATTTG
Statistics
Matches: 117, Mismatches: 20, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
33 2 0.02
34 34 0.29
35 77 0.66
36 4 0.03
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (35 bp):
AAGTCAGTAAACAACTTAATTCAGGATAATTAAGT
Found at i:27943 original size:69 final size:69
Alignment explanation
Indices: 27818--28002 Score: 237
Period size: 69 Copynumber: 2.7 Consensus size: 69
27808 GCGTTCATGC
* * *
27818 ATTAAACAAGTCAGTAATAACTTAATTTAGGGTAATTAAGTAAGTCACTAAACAACTTAATTCAG
1 ATTAAACAAGTCAGTAATAACTTAATTCAAGGTAATTAAGCAAGTCACTAAACAACTTAATTCAG
27883 GATA
66 GATA
* * *
27887 ATTAAACAAGTCAGTAATAACTTAATTCAAAGTAATTAAGCAAG-CTAGTAATCAACTTAATTCA
1 ATTAAACAAGTCAGTAATAACTTAATTCAAGGTAATTAAGCAAGTC-ACTAAACAACTTAATTCA
*
27951 GGGTA
65 GGATA
** * * *
27956 ATTAAGTAAATCGGTAAGTAACTTAATTCAAGGTAATTAAGTAAGTC
1 ATTAAACAAGTCAGTAA-TAACTTAATTCAAGGTAATTAAGCAAGTC
28003 TGGTAATTTG
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
68 1 0.01
69 73 0.73
70 25 0.25
71 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.30
Consensus pattern (69 bp):
ATTAAACAAGTCAGTAATAACTTAATTCAAGGTAATTAAGCAAGTCACTAAACAACTTAATTCAG
GATA
Found at i:28047 original size:71 final size:70
Alignment explanation
Indices: 27831--28033 Score: 205
Period size: 69 Copynumber: 2.9 Consensus size: 70
27821 AAACAAGTCA
* ** * * * * **
27831 GTAA-TAACTTAATTTAGGGTAATTAAGTAAG-TCACTAAACAACTTAATTCAGGATAATTAAAC
1 GTAAGTAACTTAATTCAAAGTAATTAAGCAAGCT-AGTAATCAACTTAATTCAGGGTAATTAAGT
* *
27894 AAGTCA
65 AAATCG
27900 GTAA-TAACTTAATTCAAAGTAATTAAGCAAGCTAGTAATCAACTTAATTCAGGGTAATTAAGTA
1 GTAAGTAACTTAATTCAAAGTAATTAAGCAAGCTAGTAATCAACTTAATTCAGGGTAATTAAGTA
27964 AATCG
66 AATCG
* * * *** *
27969 GTAAGTAACTTAATTCAAGGTAATTAAGTAAGTCTGGTAATTTGCTTAATTTAGGGTAATTAAGT
1 GTAAGTAACTTAATTCAAAGTAATTAAGCAAG-CTAGTAATCAACTTAATTCAGGGTAATTAAGT
28034 TAGTTGAGAA
Statistics
Matches: 113, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
69 60 0.53
70 26 0.23
71 27 0.24
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (70 bp):
GTAAGTAACTTAATTCAAAGTAATTAAGCAAGCTAGTAATCAACTTAATTCAGGGTAATTAAGTA
AATCG
Found at i:28125 original size:51 final size:50
Alignment explanation
Indices: 28005--28166 Score: 173
Period size: 51 Copynumber: 3.1 Consensus size: 50
27995 AGTAAGTCTG
* * * *
28005 GTAATTTGCTTAATTTAGGGTAATTAAGTTAGTTGAGAAGTAAAAAGGATAATCG
1 GTAA-TTGCTTAATTCAGAGTAATTAAGTTA----AGAAGTAAAAAGGGTAATCA
28060 GTAAATTG-TATAATTCAGAGTAATTAAGTTAAGAAGTAAAAAGGGTAATCA
1 GT-AATTGCT-TAATTCAGAGTAATTAAGTTAAGAAGTAAAAAGGGTAATCA
* * * *
28111 GTAATTGGCTTAATTCAAAGTAATTAAGTTAAAAAGTAAAAATGGTAATTA
1 GTAATT-GCTTAATTCAGAGTAATTAAGTTAAGAAGTAAAAAGGGTAATCA
28162 GTAAT
1 GTAAT
28167 AATTGACTTA
Statistics
Matches: 95, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
50 4 0.04
51 63 0.66
52 1 0.01
54 1 0.01
55 24 0.25
56 2 0.02
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.33
Consensus pattern (50 bp):
GTAATTGCTTAATTCAGAGTAATTAAGTTAAGAAGTAAAAAGGGTAATCA
Found at i:28272 original size:43 final size:44
Alignment explanation
Indices: 28186--28274 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 44
28176 AATTTAGGGG
** * *
28186 TAGTTAAGTTGGTTAAGAAGTAAAAGAGAAAGTAAAAATTGGCT
1 TAGTTAAGTTAATTAAGAAGAAAAAGAGAAAGTAAAAAATGGCT
*
28230 TAGTTAAGTTAATTAA-AAGAAAAAGAGAGA-TAATAAAATGGCT
1 TAGTTAAGTTAATTAAGAAGAAAAAGAGAAAGTAA-AAAATGGCT
28273 TA
1 TA
28275 CTTCGGGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 3 0.08
43 22 0.56
44 14 0.36
ACGTcount: A:0.49, C:0.02, G:0.21, T:0.27
Consensus pattern (44 bp):
TAGTTAAGTTAATTAAGAAGAAAAAGAGAAAGTAAAAAATGGCT
Found at i:28319 original size:50 final size:52
Alignment explanation
Indices: 28259--28399 Score: 154
Period size: 47 Copynumber: 2.8 Consensus size: 52
28249 AAAAAGAGAG
* * * *
28259 ATAATAAAATGGCTTACTTC-GGGTAAATTGAGTTAG-TAAAAAAAGAAAAA
1 ATAATAAAATGGCATAATTCAAGGTAAATTGAGTCAGTTAAAAAAAGAAAAA
*
28309 ATAATTAAATGGCATAATTCAAGGTAAATTGAGTCAGTTAAAAAAAG-----
1 ATAATAAAATGGCATAATTCAAGGTAAATTGAGTCAGTTAAAAAAAGAAAAA
* *
28356 ATAATCAAATGGCTTAATTC-AGGATAAATTGAGTCAGTTAAAAA
1 ATAATAAAATGGCATAATTCAAGG-TAAATTGAGTCAGTTAAAAA
28400 GGTAAAAGGG
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
46 3 0.04
47 38 0.47
50 17 0.21
51 14 0.17
52 9 0.11
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (52 bp):
ATAATAAAATGGCATAATTCAAGGTAAATTGAGTCAGTTAAAAAAAGAAAAA
Found at i:31548 original size:18 final size:18
Alignment explanation
Indices: 31525--31567 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
31515 GGCTATTGCG
31525 TTGCTTTGATAAATATGA
1 TTGCTTTGATAAATATGA
31543 TTGCTTTGATAAATATGA
1 TTGCTTTGATAAATATGA
31561 TTG-TTTG
1 TTGCTTTG
31568 TGATGATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.49
Consensus pattern (18 bp):
TTGCTTTGATAAATATGA
Found at i:33691 original size:11 final size:11
Alignment explanation
Indices: 33675--33700 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
33665 AGATAATTTC
33675 TTTTCTTCTAG
1 TTTTCTTCTAG
33686 TTTTCTTCTAG
1 TTTTCTTCTAG
33697 TTTT
1 TTTT
33701 AGGCAAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:39054 original size:45 final size:45
Alignment explanation
Indices: 38989--39160 Score: 310
Period size: 45 Copynumber: 3.8 Consensus size: 45
38979 AAGCAATAAT
* *
38989 TAATATTAGGTTTATTTTGATGAATTACCTAGAGATGGAAGAGTAG
1 TAATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGT-G
39035 -AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTG
1 TAATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTG
39079 TAATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTG
1 TAATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTG
39124 TAATATTAGCTTTATTTTGATGAATTACCTAGAGATG
1 TAATATTAGCTTTATTTTGATGAATTACCTAGAGATG
39161 AAGTAGAATT
Statistics
Matches: 123, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
44 1 0.01
45 122 0.99
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (45 bp):
TAATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTG
Found at i:51677 original size:17 final size:17
Alignment explanation
Indices: 51657--51695 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
51647 TTAGTAATAT
51657 TTATTGAATAATAATTA
1 TTATTGAATAATAATTA
** *
51674 TTATTTTATAATTATTA
1 TTATTGAATAATAATTA
51691 TTATT
1 TTATT
51696 TCAGTAGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTATTGAATAATAATTA
Found at i:51696 original size:17 final size:17
Alignment explanation
Indices: 51664--51696 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
51654 TATTTATTGA
51664 ATAATAATTATTATTTT
1 ATAATAATTATTATTTT
*
51681 ATAATTATTATTATTT
1 ATAATAATTATTATTT
51697 CAGTAGATAA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATAATTATTATTTT
Found at i:58375 original size:22 final size:22
Alignment explanation
Indices: 58347--58392 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
58337 TTGGTGATAA
58347 CACACTTTGGTGAGGCATCTAG
1 CACACTTTGGTGAGGCATCTAG
58369 CACACTTTGGTGAGGCATCTAG
1 CACACTTTGGTGAGGCATCTAG
58391 CA
1 CA
58393 TTATTTAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
CACACTTTGGTGAGGCATCTAG
Found at i:64177 original size:31 final size:29
Alignment explanation
Indices: 64138--64227 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 29
64128 ACCATTTTCC
* *
64138 CCCT-TGAACTTGTAACATATGGATATTTTG
1 CCCTCTGAACTT-CAAC-TATGGACATTTTG
*
64168 CCCTCTGAACTTCAACTTTGGACATTTTG
1 CCCTCTGAACTTCAACTATGGACATTTTG
* * * *
64197 CCC-CTGAAGTCTCAATTTTGGACGTTTTG
1 CCCTCTGAACT-TCAACTATGGACATTTTG
64226 CC
1 CC
64228 TCCTCTCAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
28 6 0.12
29 32 0.62
30 7 0.13
31 7 0.13
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (29 bp):
CCCTCTGAACTTCAACTATGGACATTTTG
Found at i:64197 original size:29 final size:29
Alignment explanation
Indices: 64157--64227 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
64147 TTGTAACATA
*
64157 TGGATATTTTGCCCTCTGAACT-TCAACTT
1 TGGACATTTTGCCC-CTGAACTCTCAACTT
* *
64186 TGGACATTTTGCCCCTGAAGTCTCAATTT
1 TGGACATTTTGCCCCTGAACTCTCAACTT
*
64215 TGGACGTTTTGCC
1 TGGACATTTTGCC
64228 TCCTCTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 6 0.16
29 31 0.84
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.39
Consensus pattern (29 bp):
TGGACATTTTGCCCCTGAACTCTCAACTT
Found at i:64903 original size:2 final size:2
Alignment explanation
Indices: 64820--64887 Score: 52
Period size: 2 Copynumber: 34.5 Consensus size: 2
64810 ATTTTACATA
* * *
64820 AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AC AT AT CCT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
* *
64861 CAT AT CT AA AT AT AT AT A- AT AT AT AT A
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT A
64888 ACATCACAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
1 3 0.06
2 46 0.88
3 3 0.06
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:66900 original size:22 final size:22
Alignment explanation
Indices: 66873--66914 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
66863 GACAAACCCG
*
66873 TAACCC-GAATGACCCGAGAAGT
1 TAACCCAG-ATGACCCAAGAAGT
66895 TAACCCAGATGACCCAAGAA
1 TAACCCAGATGACCCAAGAA
66915 TATTATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.40, C:0.29, G:0.19, T:0.12
Consensus pattern (22 bp):
TAACCCAGATGACCCAAGAAGT
Found at i:68285 original size:133 final size:132
Alignment explanation
Indices: 68114--68367 Score: 402
Period size: 133 Copynumber: 1.9 Consensus size: 132
68104 AATATTTTTT
* *
68114 AAAATTATAATATATCTAAGTTTTTTAATTAAATTAGTAAAATGGT-AAAAATAAAATAGGTATA
1 AAAATTATAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAATAAAATAGGTATA
*
68178 AGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAATGTATATT
66 AGGATATTAAATTTAATTAAAT-AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAATGTATATT
68243 TAA
130 TAA
* * * **
68246 AAAATTCTAGTATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAATTAAATATTTAT
1 AAAATTATAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAAAAAATAAAATAGGTAT
*
68311 AAGGATATTAAATTTAATTAAATAAAAATAGATTTTTTAGTTGAGTAAAACTATAAA
65 AAGGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAA
68368 AAGTTTAAAA
Statistics
Matches: 111, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
132 17 0.15
133 58 0.52
134 36 0.32
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.39
Consensus pattern (132 bp):
AAAATTATAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAATAAAATAGGTATA
AGGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAATGTATATTT
AA
Done.