Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020878.1 Corchorus olitorius cultivar O-4 contig20911, 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: 17163
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Found at i:6953 original size:14 final size:14
Alignment explanation
Indices: 6934--6961 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6924 GTGGTTCACA
6934 GAGTTATTCCACTT
1 GAGTTATTCCACTT
6948 GAGTTATTCCACTT
1 GAGTTATTCCACTT
6962 TTATATAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (14 bp):
GAGTTATTCCACTT
Found at i:9625 original size:14 final size:15
Alignment explanation
Indices: 9599--9627 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9589 TACTAGTACA
9599 TTTGAACGTTTGAAC
1 TTTGAACGTTTGAAC
9614 TTTGAA-GTTTGAAC
1 TTTGAACGTTTGAAC
9628 CCTTGAGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (15 bp):
TTTGAACGTTTGAAC
Found at i:13129 original size:31 final size:31
Alignment explanation
Indices: 13093--13197 Score: 126
Period size: 31 Copynumber: 3.5 Consensus size: 31
13083 TATGGCTAAT
13093 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
* * * **
13124 TGCTCAAATAAGGGCCCAATCTTT--TAATT
1 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
*
13153 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTTGCCAAAA
13184 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
13198 TCCGGTCTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
29 20 0.34
30 4 0.07
31 35 0.59
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
Found at i:13164 original size:60 final size:60
Alignment explanation
Indices: 13097--13319 Score: 365
Period size: 60 Copynumber: 3.7 Consensus size: 60
13087 GCTAATTGCT
* * **
13097 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGC
1 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGGTCTTTTAATTTGGC
* *
13157 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCGGTCTTTTAATTTGGC
1 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGGTCTTTTAATTTGGC
* *
13217 CAAATAAGGATCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCGGTCTTTTAATTTGGC
1 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGGTCTTTTAATTTGGC
*
13277 CAAATAAGGATCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
13320 TGACATCGAA
Statistics
Matches: 156, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 156 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (60 bp):
CAAATAAGGACCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGGTCTTTTAATTTGGC
Found at i:13255 original size:31 final size:31
Alignment explanation
Indices: 13217--13316 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 31
13207 TTAATTTGGC
13217 CAAATAAGGATCTAACGTTTGCCAAAATGCT
1 CAAATAAGGATCTAACGTTTGCCAAAATGCT
* ** **
13248 CAAATAAGGGTC---CGGTCTT-TTAATTTGGC-
1 CAAATAAGGATCTAAC-GT-TTGCCAAAAT-GCT
13277 CAAATAAGGATCTAACGTTTGCCAAAATGCT
1 CAAATAAGGATCTAACGTTTGCCAAAATGCT
13308 CAAATAAGG
1 CAAATAAGG
13317 GCCTGACATC
Statistics
Matches: 51, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
28 1 0.02
29 16 0.31
30 8 0.16
31 25 0.49
32 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (31 bp):
CAAATAAGGATCTAACGTTTGCCAAAATGCT
Found at i:13285 original size:29 final size:29
Alignment explanation
Indices: 13188--13285 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
13178 CCAAAATGCT
13188 CAAATAAGGGTCCGGTCTTTTAATTTGGC
1 CAAATAAGGGTCCGGTCTTTTAATTTGGC
* ** **
13217 CAAATAAGGATCTAAC-GT-TTGCCAAAAT-GC
1 CAAATAAGGGTC---CGGTCTT-TTAATTTGGC
13247 TCAAATAAGGGTCCGGTCTTTTAATTTGGC
1 -CAAATAAGGGTCCGGTCTTTTAATTTGGC
13277 CAAATAAGG
1 CAAATAAGG
13286 ATCTAACGTT
Statistics
Matches: 51, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
28 1 0.02
29 25 0.49
30 8 0.16
31 16 0.31
32 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (29 bp):
CAAATAAGGGTCCGGTCTTTTAATTTGGC
Found at i:13428 original size:29 final size:29
Alignment explanation
Indices: 13390--13491 Score: 91
Period size: 29 Copynumber: 3.4 Consensus size: 29
13380 GGCAAATGTT
13390 AGGCCCTTATTTGGTCAAATTAAAAGATC
1 AGGCCCTTATTTGGTCAAATTAAAAGATC
** *
13419 AGGCCCTTATTTGAGT-ATTTTCAATAACG-TT
1 AGGCCCTTATTTG-GTCAAATT-AA-AA-GATC
* * *
13450 AGGTCCTTATTTGGCCAAATTTAAAGATC
1 AGGCCCTTATTTGGTCAAATTAAAAGATC
*
13479 GGGCCCTTATTTG
1 AGGCCCTTATTTG
13492 AACATTTTGA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 1 0.02
29 30 0.54
30 6 0.11
31 18 0.32
32 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (29 bp):
AGGCCCTTATTTGGTCAAATTAAAAGATC
Found at i:13458 original size:60 final size:59
Alignment explanation
Indices: 13357--13522 Score: 208
Period size: 60 Copynumber: 2.8 Consensus size: 59
13347 CAAACTGATG
* * *
13357 TCAGACCCTTATTTGAGCATTTTGGC-AAATGTTAGGCCCTTATTTGGTCAAATTAAAAGA
1 TCAGGCCCTTATTTGAGCATTTT--CAAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGA
* * *
13417 TCAGGCCCTTATTTGAGTATTTTCAATAACGTTAGGTCCTTATTTGGCCAAATTTAAAGA
1 TCAGGCCCTTATTTGAGCATTTTCAA-AACGTTAGGCCCTTATTTGGCCAAATTAAAAGA
* * *
13477 TCGGGCCCTTATTTGAACATTTTGACAAACGTTAGGCCCTTATTTG
1 TCAGGCCCTTATTTGAGCATTTTCA-AAACGTTAGGCCCTTATTTG
13523 AGCAATTAGC
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 89 0.97
61 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (59 bp):
TCAGGCCCTTATTTGAGCATTTTCAAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGA
Done.