Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012019.1 Corchorus olitorius cultivar O-4 contig12052, 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: 17178
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:923 original size:138 final size:137
Alignment explanation
Indices: 676--937 Score: 418
Period size: 138 Copynumber: 1.9 Consensus size: 137
666 GCTTAATAAC
*
676 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTTATCAATCGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
* * *
741 ATACAGCACATTATTATTATTATACATAAAACTATACCAAAAAAAGTAGTTGAATATTAAAGATC
66 ATACAACACATTACTATTATTATACATAAAACTATACCAAAAAAAGTAGTTGAACATTAAAGATC
806 TGATTTA
131 TGATTTA
*
813 TTTATCAATCGTGAATGTTATTAATTTTTTAAGTTTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATCGTGAATGTTATTAA-TTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* * * *
878 GATACAACACATTACTATTA-TATATATAGAATTATACCAAAAAAAATTAGTTGAACATTA
65 GATACAACACATTACTATTATTATACATAAAACTATACC-AAAAAAAGTAGTTGAACATTA
938 GTGGTTGATT
Statistics
Matches: 114, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
137 38 0.33
138 76 0.67
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (137 bp):
TTTATCAATCGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
ATACAACACATTACTATTATTATACATAAAACTATACCAAAAAAAGTAGTTGAACATTAAAGATC
TGATTTA
Found at i:1777 original size:42 final size:43
Alignment explanation
Indices: 1707--1789 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
1697 CTTAAATGTG
*
1707 TTAATCGTGTCTTGACACGATTAGGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACGATTAGGACACGAAACACGATAATC
*
1750 TTAATCGTGTC-CGACACGATTCA-GACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATT-AGGACACGAAACACGATAA
1790 GTCAAACACG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 25 0.68
43 12 0.32
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTAGGACACGAAACACGATAATC
Found at i:3330 original size:22 final size:21
Alignment explanation
Indices: 3283--3382 Score: 92
Period size: 22 Copynumber: 4.6 Consensus size: 21
3273 TTAATGTTCC
* **
3283 TATGAAATTTCGGTAACTTCCC
1 TATGAAATTTTGGTAAC-TCAT
*
3305 TATGAAATTTTGGTAACTTATT
1 TATGAAATTTTGGTAACTCA-T
* *
3327 TATGAAATTTTGATATCCTCAT
1 TATGAAATTTTGGTA-ACTCAT
* *
3349 TATGAAATTTTGCTAACCTCAA
1 TATGAAATTTTGGTAA-CTCAT
3371 TATGAAATTTTG
1 TATGAAATTTTG
3383 ATATCTAAAC
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
21 1 0.02
22 61 0.94
23 3 0.05
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (21 bp):
TATGAAATTTTGGTAACTCAT
Found at i:15676 original size:2 final size:2
Alignment explanation
Indices: 15664--15704 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
15654 CTCTTCCTTG
15664 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15705 AATGATTTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16806 original size:43 final size:43
Alignment explanation
Indices: 16758--17002 Score: 340
Period size: 41 Copynumber: 5.8 Consensus size: 43
16748 CAATAACCAA
* *
16758 AAAGTCCCCAAACAAATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTAC
*
16801 AAAGTCCTCAAACACATATATAACACAGAGGC-A-TCTA-TATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTA-C
*
16842 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTAC
* *
16885 AAAGTCCTCAAACACATATATAACACAGAGGC-A-TTTA-TATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTA-C
* *
16926 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTAC
*
16969 AAAAGTCCTCAAACACATATATAACACAGAGGCA
1 -AAAGTCCCCAAACACATATATAACACAGAGGCA
17003 TTTCTCCTTA
Statistics
Matches: 179, Mismatches: 14, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
40 4 0.02
41 69 0.39
42 3 0.02
43 68 0.38
44 35 0.20
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.20
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCAACTCTATTAC
Found at i:16853 original size:84 final size:84
Alignment explanation
Indices: 16758--17003 Score: 456
Period size: 84 Copynumber: 2.9 Consensus size: 84
16748 CAATAACCAA
*
16758 AAAGTCCCCAAACAAATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
16823 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
16842 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
16907 ACACAGAGGCATTTATATC
66 ACACAGAGGCATCTATATC
*
16926 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
16991 AACACAGAGGCAT
65 AACACAGAGGCAT
17004 TTCTCCTTAT
Statistics
Matches: 158, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
84 124 0.78
85 34 0.22
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.20
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:17124 original size:2 final size:2
Alignment explanation
Indices: 17112--17156 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
17102 ACCAAATTCC
17112 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17153 TA TA
1 TA TA
17157 CACACACACA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.