Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009750.1 Corchorus capsularis cultivar CVL-1 contig09771, 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: 10553
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:907 original size:52 final size:49
Alignment explanation
Indices: 817--922 Score: 140
Period size: 52 Copynumber: 2.1 Consensus size: 49
807 CATAAAAAAC
* *
817 AAATAAATAAATATAATAAATCGTATATTAATTCGTAATCACAAATCATAAA
1 AAATAAATAAATATAATAAATCGCATAATAATTCGTAAT-A-AAA-CATAAA
* * *
869 AAATAAATAAATATAATAAATCGCATAATCATTTGTAATATAACATAAA
1 AAATAAATAAATATAATAAATCGCATAATAATTCGTAATAAAACATAAA
918 AAATA
1 AAATA
923 TAATCTTCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 11 0.22
50 2 0.04
51 1 0.02
52 35 0.71
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.30
Consensus pattern (49 bp):
AAATAAATAAATATAATAAATCGCATAATAATTCGTAATAAAACATAAA
Found at i:1088 original size:125 final size:124
Alignment explanation
Indices: 844--1094 Score: 457
Period size: 124 Copynumber: 2.0 Consensus size: 124
834 AAATCGTATA
*
844 TTAATTCGTAATCACAAATCATAAAAAATAAATAAATATAATAAATCGCATAATCATTTGTAATA
1 TTAATTCGTAATCACAAATCATAAAAAATAAATAAATATAATAAATCGCATAATAATTTGTAATA
*
909 TAACATAAAAAATATAATCTTCATCTAATAAAACAACAATTAATATTGGAAAATATGTG
66 TAACATAAAAAATATAATCTTCATCTAATAAAACAACAATCAATATTGGAAAATATGTG
* *
968 TTAATTTGTAATCATAAATCATAAAAAATAAATAAATATAATAAATCGCATAATAATTTGTAATA
1 TTAATTCGTAATCACAAATCATAAAAAATAAATAAATATAATAAATCGCATAATAATTTGTAATA
1033 TAACATAAAAAAATATAATCTTCATCTAATAAAACAACAATCAATATTGGAAAATATGTG
66 TAACAT-AAAAAATATAATCTTCATCTAATAAAACAACAATCAATATTGGAAAATATGTG
1093 TT
1 TT
1095 CAAGCTTTCA
Statistics
Matches: 122, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
124 68 0.56
125 54 0.44
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.32
Consensus pattern (124 bp):
TTAATTCGTAATCACAAATCATAAAAAATAAATAAATATAATAAATCGCATAATAATTTGTAATA
TAACATAAAAAATATAATCTTCATCTAATAAAACAACAATCAATATTGGAAAATATGTG
Found at i:3147 original size:38 final size:38
Alignment explanation
Indices: 3096--3173 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
3086 TTTCAACAAA
3096 TTCAACAATCTTACATTCTTACTTAATACTTT-ACATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGA-ATTT
*
3134 TTCAACAATCTTACATTCTTACTTATTACTTTGAATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
3172 TT
1 TT
3174 GGTAATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 37 0.97
39 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.01, T:0.50
Consensus pattern (38 bp):
TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
Found at i:8514 original size:86 final size:87
Alignment explanation
Indices: 8415--8732 Score: 595
Period size: 87 Copynumber: 3.7 Consensus size: 87
8405 AAATTCTTAA
8415 AATAATAATGAGAATA-TTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
1 AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
*
8479 AACAAATAAATAATAAAAGTTG
66 AACAAATAAATAATAAAAATTG
8501 AATAATAATGAGAATA-TTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
1 AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
8565 AACAAATAAATAATAAAAATTG
66 AACAAATAAATAATAAAAATTG
8587 AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
1 AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
8652 AACAAATAAATAATAAAAATTG
66 AACAAATAAATAATAAAAATTG
* *
8674 AATAATAATGAGAATATTTTTCTAAATCTTGCCAGATTGTGGGAGAATTAGGAGATATT
1 AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATT
8733 AAATAACATT
Statistics
Matches: 228, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
86 101 0.44
87 127 0.56
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.33
Consensus pattern (87 bp):
AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
AACAAATAAATAATAAAAATTG
Found at i:8623 original size:173 final size:173
Alignment explanation
Indices: 8415--8732 Score: 593
Period size: 173 Copynumber: 1.8 Consensus size: 173
8405 AAATTCTTAA
8415 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAA
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAA
*
8480 ACAAATAAATAATAAAAGTTGAATAATAATGAGAATA-TTTTCTAAATCTTGCCAAATTGTGGGA
66 ACAAATAAATAATAAAAATTGAATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGA
*
8544 GATTTAGGAGATATTTTAAGAAACAAATAAATAATAAAAATTG
131 GAATTAGGAGATATTTTAAGAAACAAATAAATAATAAAAATTG
8587 AATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
1 AATAATAATGAGAATA-TTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
*
8652 AACAAATAAATAATAAAAATTGAATAATAATGAGAATATTTTTCTAAATCTTGCCAGATTGTGGG
65 AACAAATAAATAATAAAAATTGAATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGG
8717 AGAATTAGGAGATATT
130 AGAATTAGGAGATATT
8733 AAATAACATT
Statistics
Matches: 141, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
172 16 0.11
173 85 0.60
174 40 0.28
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.33
Consensus pattern (173 bp):
AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAA
ACAAATAAATAATAAAAATTGAATAATAATGAGAATATTTTTCTAAATCTTGCCAAATTGTGGGA
GAATTAGGAGATATTTTAAGAAACAAATAAATAATAAAAATTG
Done.