Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021976.1 Corchorus olitorius cultivar O-4 contig22009, 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: 46317
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2031 original size:50 final size:50
Alignment explanation
Indices: 1919--2036 Score: 191
Period size: 50 Copynumber: 2.4 Consensus size: 50
1909 ATGTGTTACA
** *
1919 TATGTGTTTTGGACCTTTTGTGTGCGTTGTATGTATTGCCGATGTGTTTG
1 TATGTGTTTTGGGGCTTTTGTGTGCGTTGTATGTATTGCCCATGTGTTTG
* *
1969 TTTGTGTTTTGGGGCTTTTGTGTGTGTTGTATGTATTGCCCATGTGTTTG
1 TATGTGTTTTGGGGCTTTTGTGTGCGTTGTATGTATTGCCCATGTGTTTG
2019 TATGTGTTTTGGGGCTTT
1 TATGTGTTTTGGGGCTTT
2037 GTTATTGGGT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.08, C:0.08, G:0.31, T:0.53
Consensus pattern (50 bp):
TATGTGTTTTGGGGCTTTTGTGTGCGTTGTATGTATTGCCCATGTGTTTG
Found at i:13397 original size:20 final size:20
Alignment explanation
Indices: 13363--13418 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
13353 AATGGAGGTT
13363 AAGCAATTCAAATTAAATTAAG
1 AAGCAATT-AAATTAAA-TAAG
*
13385 TAG-AATTAAATTAAATAAG
1 AAGCAATTAAATTAAATAAG
13404 AAGCAATTAAATTAA
1 AAGCAATTAAATTAA
13419 GAAAAACAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.19
20 19 0.61
21 4 0.13
22 2 0.06
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.29
Consensus pattern (20 bp):
AAGCAATTAAATTAAATAAG
Found at i:18020 original size:109 final size:110
Alignment explanation
Indices: 17811--18020 Score: 284
Period size: 109 Copynumber: 1.9 Consensus size: 110
17801 TTGGTATATT
* * * *
17811 AATTAAGTGATGAAAATTTCAGTTAGTGACAATTTAAACGCCGGGAAAGGTCTAATAATTTTTAA
1 AATTAAGTAATGAAAATTTCAATTAGTGACAATCTAAACGCCGGGAAAGGTCTAAAAATTTTTAA
*
17876 TTGTGACATTTTAAATGCCGGAAAACTCATATTATATATAGTGAA
66 TTGTGACATTTTAAATGCCGGAAAACCCATATTATATATAGTGAA
*
17921 AATT-AGTAATGAAAATTTCAATTAGTGGCAATCTAAACGCCGGGAAAAGG-C-AAAAGATTTTT
1 AATTAAGTAATGAAAATTTCAATTAGTGACAATCTAAACGCCGGG-AAAGGTCTAAAA-ATTTTT
* * *
17983 ATTTGTGGCATTTTAAATGCCAGG-AAACCCATCTTATA
64 AATTGTGACATTTTAAATGCC-GGAAAACCCATATTATA
18021 AATGTTATAC
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
108 3 0.03
109 74 0.84
110 11 0.12
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32
Consensus pattern (110 bp):
AATTAAGTAATGAAAATTTCAATTAGTGACAATCTAAACGCCGGGAAAGGTCTAAAAATTTTTAA
TTGTGACATTTTAAATGCCGGAAAACCCATATTATATATAGTGAA
Found at i:28974 original size:14 final size:14
Alignment explanation
Indices: 28955--28985 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28945 ACAACAATTA
28955 CAAACATCCAAGTT
1 CAAACATCCAAGTT
*
28969 CAAACATTCAAGTT
1 CAAACATCCAAGTT
28983 CAA
1 CAA
28986 CAACAACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (14 bp):
CAAACATCCAAGTT
Found at i:35532 original size:27 final size:28
Alignment explanation
Indices: 35502--35568 Score: 109
Period size: 27 Copynumber: 2.4 Consensus size: 28
35492 AGCGTATTTG
**
35502 AAATGACCAAAATGCCCCTGGATGTGC-
1 AAATGACCAAAATGCCCCTGGACATGCA
35529 AAATGACCAAAATGCCCCTGGACATGCA
1 AAATGACCAAAATGCCCCTGGACATGCA
35557 AAATGACCAAAA
1 AAATGACCAAAA
35569 GAAGTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 25 0.68
28 12 0.32
ACGTcount: A:0.42, C:0.25, G:0.18, T:0.15
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACATGCA
Found at i:37252 original size:57 final size:57
Alignment explanation
Indices: 37164--37281 Score: 236
Period size: 57 Copynumber: 2.1 Consensus size: 57
37154 ATCTGCTTCA
37164 GTTTGATGTTTCACGAAGAGGAGTTTTAAGAAGAGTATCTTGACAATCGTTAAATAT
1 GTTTGATGTTTCACGAAGAGGAGTTTTAAGAAGAGTATCTTGACAATCGTTAAATAT
37221 GTTTGATGTTTCACGAAGAGGAGTTTTAAGAAGAGTATCTTGACAATCGTTAAATAT
1 GTTTGATGTTTCACGAAGAGGAGTTTTAAGAAGAGTATCTTGACAATCGTTAAATAT
37278 GTTT
1 GTTT
37282 TAGTTTTATG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.36
Consensus pattern (57 bp):
GTTTGATGTTTCACGAAGAGGAGTTTTAAGAAGAGTATCTTGACAATCGTTAAATAT
Found at i:40659 original size:107 final size:105
Alignment explanation
Indices: 40492--40781 Score: 391
Period size: 107 Copynumber: 2.7 Consensus size: 105
40482 TTTCTAACCT
* ** * *
40492 TTAAAATAAAATTTTAATTTTAATTTGGCCTAAACTTAGTGAATTAGTTATATATTTTATTTCTA
1 TTAAAATAAAAATAAAATTTTAATTTGGACTAAACTTAGTGAATTAGTTTTATATTTTATTTCTA
* * **
40557 AAATCCTATAGCAACAAATTATTAATCATGGAATTTACCA
66 AAACCCTATAACAACAAATTATTAATCATAAAATTTACCA
* *
40597 TTAAAATAAAAATAAAATTTTAATTTGCGGCTAAACTTAGTGAAGTTAGTTTTGTATTTTATTTC
1 TTAAAATAAAAATAAAATTTTAATTTG-GACTAAACTTAGTGAA-TTAGTTTTATATTTTATTTC
* ** *
40662 TAAAACCCTATAACAATAAATTATTAATTTTAAAATTTACCC
64 TAAAACCCTATAACAACAAATTATTAATCATAAAATTTACCA
*
40704 TTAAAATGAAAATAAAATTTTAATTTGAGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTC
1 TTAAAATAAAAATAAAATTTTAATTTG-GACTAAACTTAGTG-AATTAGTTTTATATTTTATTTC
*
40769 TAAAACTCTATAA
64 TAAAACCCTATAA
40782 TAAAAAAACC
Statistics
Matches: 163, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
105 24 0.15
106 15 0.09
107 122 0.75
108 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (105 bp):
TTAAAATAAAAATAAAATTTTAATTTGGACTAAACTTAGTGAATTAGTTTTATATTTTATTTCTA
AAACCCTATAACAACAAATTATTAATCATAAAATTTACCA
Found at i:40832 original size:107 final size:107
Alignment explanation
Indices: 40507--40817 Score: 344
Period size: 107 Copynumber: 2.9 Consensus size: 107
40497 ATAAAATTTT
* * * **
40507 AATTTTAATTTG-GCCTAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAAATCCTATAGCA
1 AATTTTAATTTGAGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAAA
* * * * * *
40570 ACAAATTATTAA--TCATGGAATTTACCATTAAAATAAAAATAA
66 AAAAACTATTAATTTCA--AAATTCACCCTTAAAATGAAAATAA
* * * * *
40612 AATTTTAATTTGCGGCTAAACTTAGTGAAGTTAGTTTTGTATTTTATTTCTAAAACCCTATAACA
1 AATTTTAATTTGAGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAAA
* * * *
40677 ATAAATTATTAATTTTAAAATTTACCCTTAAAATGAAAATAA
66 AAAAACTATTAATTTCAAAATTCACCCTTAAAATGAAAATAA
*
40719 AATTTTAATTTGAGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACTCTATAATA
1 AATTTTAATTTGAGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAA-A
* *
40784 AAAAAACCT-TTAATTTCATAATTCACTCTTAAAA
65 AAAAAA-CTATTAATTTCAAAATTCACCCTTAAAA
40818 ATCAAATTTC
Statistics
Matches: 177, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
105 12 0.07
106 13 0.07
107 123 0.69
108 26 0.15
109 3 0.02
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (107 bp):
AATTTTAATTTGAGACTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAAA
AAAAACTATTAATTTCAAAATTCACCCTTAAAATGAAAATAA
Found at i:41522 original size:19 final size:19
Alignment explanation
Indices: 41498--41536 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
41488 TTGATGGATC
41498 TTCTCTTATATAAATAAAT
1 TTCTCTTATATAAATAAAT
41517 TTCTCTTATATAAATAAAT
1 TTCTCTTATATAAATAAAT
41536 T
1 T
41537 AAAGAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (19 bp):
TTCTCTTATATAAATAAAT
Found at i:43800 original size:23 final size:23
Alignment explanation
Indices: 43768--43851 Score: 104
Period size: 23 Copynumber: 3.8 Consensus size: 23
43758 CACAATTGCT
*
43768 TGGCGCCCGACCACTTCCAAACC
1 TGGCGACCGACCACTTCCAAACC
43791 TGGCGACCGACCACTTCC--A--
1 TGGCGACCGACCACTTCCAAACC
* *
43810 TAGCGCCCGACCACTTCCAAACC
1 TGGCGACCGACCACTTCCAAACC
*
43833 TGACGACCGACCACTTCCA
1 TGGCGACCGACCACTTCCA
43852 TATCGCGGCG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
19 16 0.31
21 2 0.04
23 33 0.65
ACGTcount: A:0.24, C:0.45, G:0.17, T:0.14
Consensus pattern (23 bp):
TGGCGACCGACCACTTCCAAACC
Found at i:43829 original size:42 final size:42
Alignment explanation
Indices: 43770--43853 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
43760 CAATTGCTTG
*
43770 GCGCCCGACCACTTCCAAACCTGGCGACCGACCACTTCCATA
1 GCGCCCGACCACTTCCAAACCTGACGACCGACCACTTCCATA
43812 GCGCCCGACCACTTCCAAACCTGACGACCGACCACTTCCATA
1 GCGCCCGACCACTTCCAAACCTGACGACCGACCACTTCCATA
43854 TCGCGGCGCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.45, G:0.15, T:0.14
Consensus pattern (42 bp):
GCGCCCGACCACTTCCAAACCTGACGACCGACCACTTCCATA
Found at i:43839 original size:19 final size:19
Alignment explanation
Indices: 43775--43840 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
43765 GCTTGGCGCC
43775 CGACCACTTCCAAACCTGGCGA
1 CGACCACTTCCAAACCT---GA
* * *
43797 CCGACCACTTCCATAGC-GCC
1 -CGACCACTTCCAAACCTG-A
43817 CGACCACTTCCAAACCTGA
1 CGACCACTTCCAAACCTGA
43836 CGACC
1 CGACC
43841 GACCACTTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 20 0.57
20 1 0.03
23 14 0.40
ACGTcount: A:0.26, C:0.45, G:0.15, T:0.14
Consensus pattern (19 bp):
CGACCACTTCCAAACCTGA
Found at i:44015 original size:26 final size:27
Alignment explanation
Indices: 43954--44021 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
43944 AACCAGCTGG
*
43954 CACC-CCACACGTGACCTCCAAACGTA
1 CACCTCCACACGTGACCTCCAAACGGA
43980 CGACCT-CACACGTGACCTCC-AACGGA
1 C-ACCTCCACACGTGACCTCCAAACGGA
*
44006 CACCTCCACATGTGAC
1 CACCTCCACACGTGAC
44022 ATCGCGCGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 4 0.11
26 16 0.43
27 17 0.46
ACGTcount: A:0.28, C:0.44, G:0.15, T:0.13
Consensus pattern (27 bp):
CACCTCCACACGTGACCTCCAAACGGA
Done.