Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012542.1 Corchorus olitorius cultivar O-4 contig12575, 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: 17538
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:3049 original size:42 final size:42
Alignment explanation
Indices: 2992--3086 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
2982 ATATCCATTG
** *
2992 ATATATG-TCATACATCC-TCCATGCATCGTCCATGT-CTTTGT
1 ATATATGTTCATACATCCAT-CATGCATCACCCAT-TCCTCTGT
3033 ATATATGTTCATACATCCATCATGCATCACCCATTCCTCTGT
1 ATATATGTTCATACATCCATCATGCATCACCCATTCCTCTGT
3075 ATATATGTTCAT
1 ATATATGTTCAT
3087 GCATAGGTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
41 8 0.17
42 39 0.81
43 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.09, T:0.39
Consensus pattern (42 bp):
ATATATGTTCATACATCCATCATGCATCACCCATTCCTCTGT
Found at i:3206 original size:139 final size:138
Alignment explanation
Indices: 3033--3314 Score: 447
Period size: 139 Copynumber: 2.0 Consensus size: 138
3023 ATGTCTTTGT
* * * *
3033 ATATATGTTCATACATCCATCATGCATCACCCATTCCTCTGTATATATGTTCATGCATAGGTTAT
1 ATATATGTTCATACATCCATCACGCATCACCCATTCCTCTGTATATACGTTCATGCACAGGTCAT
* *
3098 GCATTCTCCCTTCATTACCACATGCATCTATTTTTGCATTATCCTTATCTTTTGTAAATAGATGC
66 GCATTATCCATTCATTACCACATGCATCTA-TTTTGCATTATCCTTATCTTTTGTAAATAGATGC
3163 ATTTTATGC
130 ATTTTATGC
* * *
3172 ATATATGTTCATACATCCATCGCGCATCATCCATTCCTGTGTATATACGTTCATGCACAGGTCAT
1 ATATATGTTCATACATCCATCACGCATCACCCATTCCTCTGTATATACGTTCATGCACAGGTCAT
* *
3237 GCATTATCCATTCATTACTACATGCATTTATTTTGCATTATCCTTATCTTTTGTAAATAGATGCA
66 GCATTATCCATTCATTACCACATGCATCTATTTTGCATTATCCTTATCTTTTGTAAATAGATGCA
*
3302 TTTTGTGC
131 TTTTATGC
3310 ATATA
1 ATATA
3315 GGCAATACAT
Statistics
Matches: 131, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
138 47 0.36
139 84 0.64
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (138 bp):
ATATATGTTCATACATCCATCACGCATCACCCATTCCTCTGTATATACGTTCATGCACAGGTCAT
GCATTATCCATTCATTACCACATGCATCTATTTTGCATTATCCTTATCTTTTGTAAATAGATGCA
TTTTATGC
Found at i:4070 original size:76 final size:75
Alignment explanation
Indices: 3775--4051 Score: 445
Period size: 76 Copynumber: 3.7 Consensus size: 75
3765 ATCTGGACTA
* *
3775 TGAGCAAAGGAATGATGAGT-T-TTAATCAAAA-AGTTTTCAAAATCAGTTTTAATCAAAACTTT
1 TGAGCAAGGGAATGACG-GTGTCTTAATCAAAAGA-TTTTCAAAATCAGTTTTAATCAAAACTTT
3837 GATTTCGAGCTG
64 GATTTCGAGCTG
3849 TGAGCAAGGGAATGACGGTGTCTTAATCAAAA-AGTTTTCAAAATCAGTTTTAATCAAAACTTTG
1 TGAGCAAGGGAATGACGGTGTCTTAATCAAAAGA-TTTTCAAAATCAGTTTTAATCAAAACTTTG
3913 ATTTCGAGCTG
65 ATTTCGAGCTG
*
3924 TGAGCAAGGGAATGACGGTGTCTTAATCAAAAGATGTTTCAAAATCAGTTTTAATCAAAACTTTA
1 TGAGCAAGGGAATGACGGTGTCTTAATCAAAAGAT-TTTCAAAATCAGTTTTAATCAAAACTTTG
3989 ATTTCGAGCTG
65 ATTTCGAGCTG
*
4000 TGAGCAAGGGAATGACGGTGTCTTAATCAAAAGATATTTCAAAATAAGTTTT
1 TGAGCAAGGGAATGACGGTGTCTTAATCAAAAGAT-TTTCAAAATCAGTTTT
4052 GGTCAAAGTC
Statistics
Matches: 194, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
73 2 0.01
74 16 0.08
75 86 0.44
76 90 0.46
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (75 bp):
TGAGCAAGGGAATGACGGTGTCTTAATCAAAAGATTTTCAAAATCAGTTTTAATCAAAACTTTGA
TTTCGAGCTG
Found at i:4479 original size:15 final size:15
Alignment explanation
Indices: 4461--4502 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
4451 CCAAAAAAAT
4461 GAAAATGAAAATGAA
1 GAAAATGAAAATGAA
*
4476 GAAAATAAAAAGTGAA
1 GAAAATGAAAA-TGAA
*
4492 -AAAAGGAAAAT
1 GAAAATGAAAAT
4503 AAAGGCACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.78
16 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (15 bp):
GAAAATGAAAATGAA
Found at i:4901 original size:12 final size:11
Alignment explanation
Indices: 4876--4900 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4866 CTCCATTAAG
4876 AAATTCAAAAA
1 AAATTCAAAAA
4887 AAATTCAAAAA
1 AAATTCAAAAA
4898 AAA
1 AAA
4901 AACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:5712 original size:50 final size:50
Alignment explanation
Indices: 5517--5712 Score: 302
Period size: 50 Copynumber: 3.9 Consensus size: 50
5507 TTAGAATAAG
* * *
5517 ATTGCATTCCATTTATGAGTTCAAGATCAAAATTCGCTGTTCAAAATAAA
1 ATTGCATTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAA
* *
5567 ATTGCTTTCCATTTGAGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAA
1 ATTGCATTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAA
* * *
5617 ATTGCTTTCCATTTGTGAGTTCGAGATCAAAATTTGCTTTTCAAAGTAAA
1 ATTGCATTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAA
* *
5667 ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGATTTTCAAAG
1 ATTGCATTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
5713 GACATTGAAG
Statistics
Matches: 133, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 133 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (50 bp):
ATTGCATTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGTAAA
Found at i:6314 original size:50 final size:50
Alignment explanation
Indices: 6234--6365 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 50
6224 TTCAGAGTTA
*
6234 TTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATCATTAACATAGGC
1 TTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATCATCAACATAGGC
* * * *
6284 TTTTCCACAAGGCAAACTCGTTTCCGTACGAGTCAATTATCAACATGGGC
1 TTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATCATCAACATAGGC
* **
6334 TTTTCCATAAGCCACAGTTCGTTTCCATACGA
1 TTTTCCACAAGCCA-AACTCGTTTCCATACGA
6366 TACATTACCA
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 57 0.80
51 14 0.20
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (50 bp):
TTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATCATCAACATAGGC
Found at i:6427 original size:35 final size:35
Alignment explanation
Indices: 6383--6687 Score: 375
Period size: 35 Copynumber: 8.7 Consensus size: 35
6373 CCATCTTCTT
*
6383 AGATGACTCGGTGTAGCATCTTCAAAGTTATATTT
1 AGATGACTCGGTGTAGCATCTTCAAAGTTATATTC
*
6418 AGATGACTCGGTGTAGCATCTTGAAAGTTATATTC
1 AGATGACTCGGTGTAGCATCTTCAAAGTTATATTC
6453 AGATGACTCGGTGTAGCATCTTCAAAGTTGA-ATTC
1 AGATGACTCGGTGTAGCATCTTCAAAGTT-ATATTC
** *
6488 AGATGACTCGGTGTAGCATCTTCAAAGACAAATTC
1 AGATGACTCGGTGTAGCATCTTCAAAGTTATATTC
* * ** *
6523 AGATGACTCGGTGCAGCATCTTTAAAGACAAATTC
1 AGATGACTCGGTGTAGCATCTTCAAAGTTATATTC
* * **
6558 AGATGACTCGGTGCAGCATCTTCAAAGATGCATTC
1 AGATGACTCGGTGTAGCATCTTCAAAGTTATATTC
* *
6593 AGATGACTCGGTGTAGCATCTTCAAACATGA-ATTC
1 AGATGACTCGGTGTAGCATCTTCAAA-GTTATATTC
*
6628 AGATGACTCGGTGTAGCATCTTCAAA--AATGATCTC
1 AGATGACTCGGTGTAGCATCTTCAAAGTTAT-AT-TC
* *
6663 GGATGACTCGATGTAGCATCTTCAA
1 AGATGACTCGGTGTAGCATCTTCAA
6688 TGTGAACTCA
Statistics
Matches: 245, Mismatches: 19, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.00
34 3 0.01
35 240 0.98
36 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (35 bp):
AGATGACTCGGTGTAGCATCTTCAAAGTTATATTC
Found at i:6565 original size:105 final size:104
Alignment explanation
Indices: 6383--6687 Score: 414
Period size: 105 Copynumber: 2.9 Consensus size: 104
6373 CCATCTTCTT
* * * * *
6383 AGATGACTCGGTGTAGCATCTTCAAAGTTATATTTAGATGACTCGGTGTAGCATCTTGAAAGTTA
1 AGATGACTCGGTGTAGCATCTTCAAAGATAAATTCAGATGACTCGGTGTAGCATCTTCAAAG-AA
* *
6448 TATTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAATTC
65 AATTCAGATGACTCGGTGTAGCATCTTCAAAGATGAATTC
* * *
6488 AGATGACTCGGTGTAGCATCTTCAAAGACAAATTCAGATGACTCGGTGCAGCATCTTTAAAGACA
1 AGATGACTCGGTGTAGCATCTTCAAAGATAAATTCAGATGACTCGGTGTAGCATCTTCAAAGA-A
* *
6553 AATTCAGATGACTCGGTGCAGCATCTTCAAAGATGCATTC
65 AATTCAGATGACTCGGTGTAGCATCTTCAAAGATGAATTC
* *
6593 AGATGACTCGGTGTAGCATCTTCAAACATGAATTCAGATGACTCGGTGTAGCATCTTCAAA-AAT
1 AGATGACTCGGTGTAGCATCTTCAAAGATAAATTCAGATGACTCGGTGTAGCATCTTCAAAGAA-
* * *
6657 GATCTCGGATGACTCGATGTAGCATCTTCAA
65 AAT-TCAGATGACTCGGTGTAGCATCTTCAA
6688 TGTGAACTCA
Statistics
Matches: 177, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
103 1 0.01
104 3 0.02
105 173 0.98
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (104 bp):
AGATGACTCGGTGTAGCATCTTCAAAGATAAATTCAGATGACTCGGTGTAGCATCTTCAAAGAAA
ATTCAGATGACTCGGTGTAGCATCTTCAAAGATGAATTC
Found at i:16583 original size:27 final size:27
Alignment explanation
Indices: 16545--16599 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
16535 GGAGCCAAGA
16545 TTCCAATTTTGGGGGCCAAACTAAAAT
1 TTCCAATTTTGGGGGCCAAACTAAAAT
16572 TTCCAATTTTGGGGGCCAAACTAAAAT
1 TTCCAATTTTGGGGGCCAAACTAAAAT
16599 T
1 T
16600 AAAAATGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (27 bp):
TTCCAATTTTGGGGGCCAAACTAAAAT
Done.