Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024694.1 Corchorus olitorius cultivar O-4 contig24727, 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: 42983
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:314 original size:24 final size:24
Alignment explanation
Indices: 287--335 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
277 ATGCCACCAA
*
287 TGTCACTCATGATTCAATAGCAAT
1 TGTCACTCATGATTCAAGAGCAAT
311 TGTCACTCATGATTCAAGAGCAAT
1 TGTCACTCATGATTCAAGAGCAAT
335 T
1 T
336 ATAATCGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (24 bp):
TGTCACTCATGATTCAAGAGCAAT
Found at i:554 original size:19 final size:19
Alignment explanation
Indices: 530--569 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
520 ACTCCACTTG
530 TTCTTCTTCTCCTTTGATT
1 TTCTTCTTCTCCTTTGATT
*
549 TTCTTCTTCTCCTTTTATT
1 TTCTTCTTCTCCTTTGATT
568 TT
1 TT
570 TAAGGAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.25, G:0.03, T:0.68
Consensus pattern (19 bp):
TTCTTCTTCTCCTTTGATT
Found at i:1306 original size:24 final size:24
Alignment explanation
Indices: 1274--1322 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1264 TACAATATGT
1274 TTATCGGACTAATATTAACTAATA
1 TTATCGGACTAATATTAACTAATA
1298 TTATCGGACTAATATTAACTAATA
1 TTATCGGACTAATATTAACTAATA
1322 T
1 T
1323 ATTTAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (24 bp):
TTATCGGACTAATATTAACTAATA
Found at i:1310 original size:14 final size:14
Alignment explanation
Indices: 1274--1314 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1264 TACAATATGT
1274 TTATCGGACTAATA
1 TTATCGGACTAATA
1288 TTA----ACTAATA
1 TTATCGGACTAATA
1298 TTATCGGACTAATA
1 TTATCGGACTAATA
1312 TTA
1 TTA
1315 ACTAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
10 10 0.43
14 13 0.57
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (14 bp):
TTATCGGACTAATA
Found at i:1852 original size:36 final size:36
Alignment explanation
Indices: 1805--1873 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
1795 AATTAACAAA
1805 TTTCCTTACCGTCAATTTGACCTGTTGATTTTCAAG
1 TTTCCTTACCGTCAATTTGACCTGTTGATTTTCAAG
1841 TTTCCTTACCGTCAATTTGACCTGTTGATTTTC
1 TTTCCTTACCGTCAATTTGACCTGTTGATTTTC
1874 TTTTGAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.17, C:0.23, G:0.13, T:0.46
Consensus pattern (36 bp):
TTTCCTTACCGTCAATTTGACCTGTTGATTTTCAAG
Found at i:5194 original size:30 final size:30
Alignment explanation
Indices: 5160--5236 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
5150 ATTTGTAGTG
*
5160 TTTGGATGTTTTTGCCCCCTGAACT-TTAAT
1 TTTGGATG-TTTTGCCCCCTGAACTCTCAAT
** **
5190 TTTGGACATTTTGCCCTTTGAACTCTCAAT
1 TTTGGATGTTTTGCCCCCTGAACTCTCAAT
5220 TTTGGATGTTTTGCCCC
1 TTTGGATGTTTTGCCCC
5237 TTATCAAACG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 14 0.37
30 24 0.63
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (30 bp):
TTTGGATGTTTTGCCCCCTGAACTCTCAAT
Found at i:5396 original size:31 final size:30
Alignment explanation
Indices: 5353--5470 Score: 100
Period size: 31 Copynumber: 3.9 Consensus size: 30
5343 TTGAGAAGGC
*
5353 GCAAAAACGTCTAAAATTGAAAATTCAGGGA
1 GCAAAAAAGTCTAAAATT-AAAATTCAGGGA
*
5384 GCAAAAAAGTCTAAAATTGAGAATTCATGGG-
1 GCAAAAAAGTCTAAAATT-AAAATTCA-GGGA
* * *
5415 GC-AAAATGTCCAAAATTAAAGTTCAGAGGA
1 GCAAAAAAGTCTAAAATTAAAATTCAG-GGA
*
5445 -CAAAACA-TCTAAACATTACAAATTCA
1 GCAAAAAAGTCTAAA-ATTA-AAATTCA
5471 AGAGGCAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
28 1 0.01
29 14 0.20
30 20 0.28
31 33 0.46
32 3 0.04
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.21
Consensus pattern (30 bp):
GCAAAAAAGTCTAAAATTAAAATTCAGGGA
Found at i:5730 original size:183 final size:183
Alignment explanation
Indices: 5417--5787 Score: 724
Period size: 183 Copynumber: 2.0 Consensus size: 183
5407 TTCATGGGGC
*
5417 AAAATGTCCAAAATTAAAGTTCAGAGGACAAAACATCTAAACATTACAAATTCAAGAGGCAAAAA
1 AAAAAGTCCAAAATTAAAGTTCAGAGGACAAAACATCTAAACATTACAAATTCAAGAGGCAAAAA
5482 GGGTATTAAACCTCAGATGTTGAGATGATGCCTGGTGATCAGCTAGTCGGATTCGAGCTGTGCAA
66 GGGTATTAAACCTCAGATGTTGAGATGATGCCTGGTGATCAGCTAGTCGGATTCGAGCTGTGCAA
5547 TTTTCTTTATTGGTTTGTAATGGTCTCATTTTCTCCATCTACAACCTGGAAAA
131 TTTTCTTTATTGGTTTGTAATGGTCTCATTTTCTCCATCTACAACCTGGAAAA
*
5600 AAAAAGTCCAAAATTGAAGTTCAGAGGACAAAACATCTAAACATTACAAATTCAAGAGGCAAAAA
1 AAAAAGTCCAAAATTAAAGTTCAGAGGACAAAACATCTAAACATTACAAATTCAAGAGGCAAAAA
5665 GGGTATTAAACCTCAGATGTTGAGATGATGCCTGGTGATCAGCTAGTCGGATTCGAGCTGTGCAA
66 GGGTATTAAACCTCAGATGTTGAGATGATGCCTGGTGATCAGCTAGTCGGATTCGAGCTGTGCAA
5730 TTTTCTTTATTGGTTTGTAATGGTCTCATTTTCTCCATCTACAACCTGGAAAA
131 TTTTCTTTATTGGTTTGTAATGGTCTCATTTTCTCCATCTACAACCTGGAAAA
5783 AAAAA
1 AAAAA
5788 ACACTTAGAC
Statistics
Matches: 186, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 186 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (183 bp):
AAAAAGTCCAAAATTAAAGTTCAGAGGACAAAACATCTAAACATTACAAATTCAAGAGGCAAAAA
GGGTATTAAACCTCAGATGTTGAGATGATGCCTGGTGATCAGCTAGTCGGATTCGAGCTGTGCAA
TTTTCTTTATTGGTTTGTAATGGTCTCATTTTCTCCATCTACAACCTGGAAAA
Found at i:29819 original size:11 final size:11
Alignment explanation
Indices: 29798--29839 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
29788 GTTTTTCTGT
29798 TTTTTGTTTTTG
1 TTTTTG-TTTTG
29810 TTTTTGTTTTG
1 TTTTTGTTTTG
*
29821 TTTTCGTTTTG
1 TTTTTGTTTTG
29832 TTTTTGTT
1 TTTTTGTT
29840 GCATTGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
11 22 0.79
12 6 0.21
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (11 bp):
TTTTTGTTTTG
Found at i:29821 original size:17 final size:16
Alignment explanation
Indices: 29797--29839 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
29787 CGTTTTTCTG
*
29797 TTTTTTGTTTTTGTTT
1 TTTTTTGTTTTCGTTT
29813 TTGTTTTGTTTTCGTTT
1 TT-TTTTGTTTTCGTTT
29830 TGTTTTTGTT
1 T-TTTTTGTT
29840 GCATTGTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 2 0.08
17 21 0.88
18 1 0.04
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.81
Consensus pattern (16 bp):
TTTTTTGTTTTCGTTT
Found at i:29836 original size:6 final size:6
Alignment explanation
Indices: 29798--29839 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
29788 GTTTTTCTGT
*
29798 TTTTTG TTTTTG TTTTTG -TTTTG TTTTCG -TTTTG TTTTTG TT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT
29840 GCATTGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (6 bp):
TTTTTG
Found at i:31914 original size:30 final size:30
Alignment explanation
Indices: 31878--31937 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
31868 TAACTCACTT
31878 GCAGATAAATTAAGATTAGAGTTAGAAAAA
1 GCAGATAAATTAAGATTAGAGTTAGAAAAA
*
31908 GCAGATAAATTAAGATTAGAGTTATAAAAA
1 GCAGATAAATTAAGATTAGAGTTAGAAAAA
31938 AGTTAATCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.25
Consensus pattern (30 bp):
GCAGATAAATTAAGATTAGAGTTAGAAAAA
Found at i:32628 original size:19 final size:19
Alignment explanation
Indices: 32579--32617 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
32569 ATTATACAAA
32579 TTAATTTTAATTTATTCAT
1 TTAATTTTAATTTATTCAT
32598 TTAATTTTAATTTATTCAT
1 TTAATTTTAATTTATTCAT
32617 T
1 T
32618 ATTATTTAAT
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:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
TTAATTTTAATTTATTCAT
Found at i:34871 original size:61 final size:61
Alignment explanation
Indices: 34762--34888 Score: 200
Period size: 61 Copynumber: 2.1 Consensus size: 61
34752 ATAGTACTAA
* * *
34762 TTATAAAACAAGTGGATGATGCATCATCTCATACCTCGTTTGTGTAGTACTCCCTATGTTC
1 TTATTAAACAAGTGGATGATGCATCATCTCATACCTCGTTCGTATAGTACTCCCTATGTTC
* * *
34823 TTATTAAAGAAGTGGATGATGCATCATCTCATACCTCGTTCGTATAGTACTCTCTATGTTT
1 TTATTAAACAAGTGGATGATGCATCATCTCATACCTCGTTCGTATAGTACTCCCTATGTTC
34884 TTATT
1 TTATT
34889 TATAAGTCAC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (61 bp):
TTATTAAACAAGTGGATGATGCATCATCTCATACCTCGTTCGTATAGTACTCCCTATGTTC
Found at i:36164 original size:82 final size:82
Alignment explanation
Indices: 36027--36190 Score: 292
Period size: 82 Copynumber: 2.0 Consensus size: 82
36017 AGGTTGTCAA
36027 TTGCAGGTCTAATTGATCATCTAGGGCCGACAAAAGAAAATTGGATCTTTGGGAAGACTATCAAA
1 TTGCAGGTCTAATTGATCATCTAGGGCCGACAAAAGAAAATTGGATCTTTGGGAAGACTATCAAA
36092 TTCATCAAGTCTAGAAG
66 TTCATCAAGTCTAGAAG
* *
36109 TTGCAGGTCTAATTGATCATCTAGGGCCGACAAAAGAAGATTGGATCTTTGGGAAGACTATCAAG
1 TTGCAGGTCTAATTGATCATCTAGGGCCGACAAAAGAAAATTGGATCTTTGGGAAGACTATCAAA
* *
36174 TTCATCAGGTTTAGAAG
66 TTCATCAAGTCTAGAAG
36191 CTGGAGTTTC
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (82 bp):
TTGCAGGTCTAATTGATCATCTAGGGCCGACAAAAGAAAATTGGATCTTTGGGAAGACTATCAAA
TTCATCAAGTCTAGAAG
Found at i:40722 original size:22 final size:21
Alignment explanation
Indices: 40696--40736 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
40686 ACAATATAAA
40696 TAAAAAACTAATAGAAAAATAT
1 TAAAAAACTAA-AGAAAAATAT
*
40718 TAAAAAATTAAAGAAAAAT
1 TAAAAAACTAAAGAAAAAT
40737 GATGCTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (21 bp):
TAAAAAACTAAAGAAAAATAT
Done.