Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024573.1 Corchorus olitorius cultivar O-4 contig24606, 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: 55950
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:16090 original size:21 final size:21
Alignment explanation
Indices: 16066--16115 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
16056 ATTTTAGATG
16066 TAAT-ATATATTATTAAATAAA
1 TAATAATATATT-TTAAATAAA
16087 TAATAAATATATTTTAAAT-AA
1 TAAT-AATATATTTTAAATAAA
16108 TAAATAAT
1 T-AATAAT
16116 GAGTTCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 10 0.38
22 9 0.35
23 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATAATATATTTTAAATAAA
Found at i:19916 original size:10 final size:12
Alignment explanation
Indices: 19890--19914 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19880 TTTTTCTTAG
19890 TCTTCTTTTTTC
1 TCTTCTTTTTTC
19902 TCTTCTTTTTTC
1 TCTTCTTTTTTC
19914 T
1 T
19915 TCACCCAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTCTTTTTTC
Found at i:28061 original size:27 final size:28
Alignment explanation
Indices: 27994--28066 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
27984 CAGTGAACTT
* *
27994 AAAATGACCGAAATGCCCTTGAATGTGC
1 AAAATGACCAAAATGCCCTTGAACGTGC
28022 AAAATGACCAAAATGCCCTTGAACGTGC
1 AAAATGACCAAAATGCCCTTGAACGTGC
**
28050 -AAATGATTAAAATGCCC
1 AAAATGACCAAAATGCCC
28067 CAAAATGACC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 15 0.37
28 26 0.63
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.21
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCTTGAACGTGC
Found at i:28645 original size:46 final size:44
Alignment explanation
Indices: 28596--28850 Score: 149
Period size: 43 Copynumber: 6.0 Consensus size: 44
28586 AAGGGCATTT
* *
28596 CTCTCTCCCCAAAGTTCC-CAAGCACATATATAACACAGGGGCAA
1 CTCTCTTCCCAAAG-TCCTCAAGCACATATATAACACAGAGGCAA
* * *
28640 CTCTCTTTCTAAAGTCCTCAAGCACATTTATAACACAGAGGC-A
1 CTCTCTTCCCAAAGTCCTCAAGCACATATATAACACAGAGGCAA
* * * *
28683 -TCTATAT--CAAAGTCCCCAAACACA-ATTATAACACAGGGGCAA
1 CTCTCT-TCCCAAAGTCCTCAAGCACATA-TATAACACAGAGGCAA
* * * * *
28725 -TC-CTTCCTAAAAGTCCTTAAACACATTTATAACATAGAGGC-A
1 CTCTCTTCC-CAAAGTCCTCAAGCACATATATAACACAGAGGCAA
* ** * * *
28767 -TC-CATATCAAAGTCCCCAAGAACA-ATTATAACACAGAGGCAT
1 CTCTCTTCCCAAAGTCCTCAAGCACATA-TATAACACAGAGGCAA
* * * * *
28809 CTCTC-TCTCAAAGTCTTGAAGCACATTTATAACACATAGGCA
1 CTCTCTTCCCAAAGTCCTCAAGCACATATATAACACAGAGGCA
28851 TCTATATCTA
Statistics
Matches: 162, Mismatches: 36, Indels: 27
0.72 0.16 0.12
Matches are distributed among these distances:
40 1 0.01
41 53 0.33
42 12 0.07
43 62 0.38
44 34 0.21
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (44 bp):
CTCTCTTCCCAAAGTCCTCAAGCACATATATAACACAGAGGCAA
Found at i:28654 original size:44 final size:42
Alignment explanation
Indices: 28605--28726 Score: 133
Period size: 44 Copynumber: 2.9 Consensus size: 42
28595 TCTCTCTCCC
* *
28605 CAAAGTTCCCAAGCACATATATAACACAGGGGCAACTCTCTTT
1 CAAAGTTCCCAAGCACATATATAACACAGGGGCAA-TCTATAT
* *
28648 CTAAAG-TCCTCAAGCACATTTATAACACAGAGGC-ATCTATAT
1 C-AAAGTTCC-CAAGCACATATATAACACAGGGGCAATCTATAT
* *
28690 CAAAGTCCCCAAACACA-ATTATAACACAGGGGCAATC
1 CAAAGTTCCCAAGCACATA-TATAACACAGGGGCAATC
28727 CTTCCTAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
41 24 0.36
42 11 0.17
43 5 0.08
44 26 0.39
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (42 bp):
CAAAGTTCCCAAGCACATATATAACACAGGGGCAATCTATAT
Found at i:28765 original size:84 final size:83
Alignment explanation
Indices: 28605--28874 Score: 325
Period size: 84 Copynumber: 3.2 Consensus size: 83
28595 TCTCTCTCCC
* * * *
28605 CAAAGTTCCCAAGCAC-ATATATAACACAGGGGCAACTCTCTTTCTAAAGTCCTCAAGCACATTT
1 CAAAGTCCCCAAACACAAT-TATAACACAGGGGCAA-TC-CTTCCTAAAGTCCTTAAGCACATTT
28669 ATAACACAGAGGCATCTATAT
63 ATAACACAGAGGCATCTATAT
*
28690 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATCCTTCCTAAAAGTCCTTAAACACATTTAT
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATCCTTCCT-AAAGTCCTTAAGCACATTTAT
* *
28755 AACATAGAGGCATCCATAT
65 AACACAGAGGCATCTATAT
*
28774 CAAAGTCCCCAAGA-ACAATTATAACACAGAGGC-AT-CTCTCTCTCAAAGT-CTTGAAGCACAT
1 CAAAGTCCCCAA-ACACAATTATAACACAGGGGCAATCCT-TC-CT-AAAGTCCTT-AAGCACAT
*
28835 TTATAACACATAGGCATCTATAT
61 TTATAACACAGAGGCATCTATAT
* *
28858 CTAAGTCCCTAAACACA
1 CAAAGTCCCCAAACACA
28875 TGTAACATAA
Statistics
Matches: 163, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
82 2 0.01
83 13 0.08
84 115 0.71
85 31 0.19
86 2 0.01
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (83 bp):
CAAAGTCCCCAAACACAATTATAACACAGGGGCAATCCTTCCTAAAGTCCTTAAGCACATTTATA
ACACAGAGGCATCTATAT
Found at i:28850 original size:43 final size:43
Alignment explanation
Indices: 28605--28865 Score: 216
Period size: 41 Copynumber: 6.2 Consensus size: 43
28595 TCTCTCTCCC
* * * * *
28605 CAAAGTTCC-CAAGCACATATATAACACAGGGGCAACTCTCTTT
1 CAAAG-TCCTCAAGCACATTTATAACACAGAGGCATCTCTATAT
28648 CTAAAGTCCTCAAGCACATTTATAACACAGAGGCA--TCTATAT
1 C-AAAGTCCTCAAGCACATTTATAACACAGAGGCATCTCTATAT
* * * * *
28690 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATC-CT-TCCT
1 CAAAGTCCTCAAGCACATTTATAACACAGAGGC-ATCTCTAT-AT
* * * *
28733 AAAAGTCCTTAAACACATTTATAACATAGAGGCATC-C-ATAT
1 CAAAGTCCTCAAGCACATTTATAACACAGAGGCATCTCTATAT
* * * * *
28774 CAAAGTCCCCAAGAACAATTATAACACAGAGGCATCTCTCTCT
1 CAAAGTCCTCAAGCACATTTATAACACAGAGGCATCTCTATAT
* * *
28817 CAAAGTCTTGAAGCACATTTATAACACATAGGCA--TCTATAT
1 CAAAGTCCTCAAGCACATTTATAACACAGAGGCATCTCTATAT
*
28858 CTAAGTCC
1 CAAAGTCC
28866 CTAAACACAT
Statistics
Matches: 174, Mismatches: 35, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
41 69 0.40
42 14 0.08
43 64 0.37
44 27 0.16
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (43 bp):
CAAAGTCCTCAAGCACATTTATAACACAGAGGCATCTCTATAT
Found at i:29629 original size:37 final size:37
Alignment explanation
Indices: 29578--29719 Score: 185
Period size: 37 Copynumber: 3.8 Consensus size: 37
29568 GAGAGCTCCA
* *
29578 AAGAGGGTGTTGTCGTAGTAAGGAGAGCTCTGCGGTG
1 AAGAGGGTGCTGTCGCAGTAAGGAGAGCTCTGCGGTG
*
29615 AAGAGGGTGCTGTCGCAGTAAGGAGAGCTGTGCGGTG
1 AAGAGGGTGCTGTCGCAGTAAGGAGAGCTCTGCGGTG
* * * *
29652 AAGAGGGTGCCGCCGCAGTAAGGAGAGCTCTACGGTA
1 AAGAGGGTGCTGTCGCAGTAAGGAGAGCTCTGCGGTG
** * *
29689 AAGAGGGTGCTACCGCGGTAAGGGGAGCTCT
1 AAGAGGGTGCTGTCGCAGTAAGGAGAGCTCT
29720 ACGATGACGA
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 93 1.00
ACGTcount: A:0.23, C:0.16, G:0.42, T:0.18
Consensus pattern (37 bp):
AAGAGGGTGCTGTCGCAGTAAGGAGAGCTCTGCGGTG
Found at i:29782 original size:29 final size:30
Alignment explanation
Indices: 29736--29807 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
29726 ACGAGTGCTA
* *
29736 TCGCAAAGTGGGAT-TTGCTG-TAAAGCGTT
1 TCGCAAAGTGAG-TCTTGCTGCAAAAGCGTT
* *
29765 TGGTAAAGTGAGTCTTGCTGCAAAAGCGTT
1 TCGCAAAGTGAGTCTTGCTGCAAAAGCGTT
29795 TCGCAAAGTGAGT
1 TCGCAAAGTGAGT
29808 TCTGTGGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
28 1 0.03
29 15 0.43
30 19 0.54
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (30 bp):
TCGCAAAGTGAGTCTTGCTGCAAAAGCGTT
Found at i:41926 original size:18 final size:18
Alignment explanation
Indices: 41888--41926 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
41878 ACCCTTGCCT
* *
41888 AAAACTGGAAGAAAAGTA
1 AAAACTAGAAGAAAAGAA
*
41906 AAAACTAGAAGAAGAGAA
1 AAAACTAGAAGAAAAGAA
41924 AAA
1 AAA
41927 TATTTATGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.05, G:0.21, T:0.08
Consensus pattern (18 bp):
AAAACTAGAAGAAAAGAA
Found at i:48513 original size:2 final size:2
Alignment explanation
Indices: 48506--48536 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
48496 TTATTTATTC
48506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48537 TATCAACTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.