Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023748.1 Corchorus olitorius cultivar O-4 contig23781, 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: 32354
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:12870 original size:21 final size:22
Alignment explanation
Indices: 12816--12868 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
12806 GAGGAAATCG
* *
12816 CGGAGATTTCAGAGAAAAAGCA
1 CGGAGCTTTGAGAGAAAAAGCA
*
12838 CGGAGCTTTTGAGAGAATAAGCA
1 CGGAGC-TTTGAGAGAAAAAGCA
*
12861 TGGAGCTT
1 CGGAGCTT
12869 GATTTTTTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (22 bp):
CGGAGCTTTGAGAGAAAAAGCA
Found at i:15059 original size:28 final size:28
Alignment explanation
Indices: 15015--15117 Score: 118
Period size: 28 Copynumber: 3.7 Consensus size: 28
15005 GGTCACTTAA
*
15015 AGGGGCATTTTGATCATTTTGCATAACC
1 AGGGGCATTTTGGTCATTTTGCATAACC
* *
15043 AGGGGCATTTTGGTCATTTTGCATGAGC
1 AGGGGCATTTTGGTCATTTTGCATAACC
* * * *
15071 AAGGGCATTTTGGTCATTTTAC-TAGGCT
1 AGGGGCATTTTGGTCATTTTGCATA-ACC
*
15099 AGGGGCATTTCGGTCATTT
1 AGGGGCATTTTGGTCATTT
15118 CAGGGACACC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 1 0.02
28 62 0.98
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTGCATAACC
Found at i:21047 original size:22 final size:22
Alignment explanation
Indices: 21022--21068 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
21012 TTTTTAATTG
*
21022 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
21044 AGTAAAATGATAAAAATGAAAT
1 AGTAAAATGATAAAAATAAAAT
21066 AGT
1 AGT
21069 TATAAGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:21059 original size:93 final size:91
Alignment explanation
Indices: 20945--21129 Score: 239
Period size: 93 Copynumber: 2.0 Consensus size: 91
20935 GCTTTTTAAT
* * * * *
20945 TAAATTAGTAATATGGTAAAAAT-AAATTAGGTT-TAAGGATATTAGATTTAATTAAATAAAAAT
1 TAAAATAGTAAAATGATAAAAATGAAA-TA-GTTATAAGGACATTAGACTTAATTAAATAAAAAT
* *
21008 AGAGTTTTTAATTGAGTAAAACTATAAAAG
64 AGA--TTTTAATTAACTAAAACTATAAAAG
*
21038 TAAAATAGTAAAATGATAAAAATGAAATAGTTATAAGGACATTAGACTTAATTAAATAAAATTAG
1 TAAAATAGTAAAATGATAAAAATGAAATAGTTATAAGGACATTAGACTTAATTAAATAAAAATAG
*
21103 ATTTTAGTTAACTAAAACTATAAAAG
66 ATTTTAATTAACTAAAACTATAAAAG
21129 T
1 T
21130 TTAAATAATG
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
91 23 0.28
92 3 0.04
93 52 0.64
94 3 0.04
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.34
Consensus pattern (91 bp):
TAAAATAGTAAAATGATAAAAATGAAATAGTTATAAGGACATTAGACTTAATTAAATAAAAATAG
ATTTTAATTAACTAAAACTATAAAAG
Found at i:26147 original size:15 final size:15
Alignment explanation
Indices: 26127--26157 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
26117 GCCATCTATC
26127 GTCTATAATGATATT
1 GTCTATAATGATATT
26142 GTCTATAATGATATT
1 GTCTATAATGATATT
26157 G
1 G
26158 ACCAAGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.45
Consensus pattern (15 bp):
GTCTATAATGATATT
Found at i:32173 original size:12 final size:12
Alignment explanation
Indices: 32158--32182 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32148 CAATCTTGAA
32158 GAAAATCATGTC
1 GAAAATCATGTC
32170 GAAAATCATGTC
1 GAAAATCATGTC
32182 G
1 G
32183 GATTTTGTAG
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:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (12 bp):
GAAAATCATGTC
Found at i:32287 original size:10 final size:10
Alignment explanation
Indices: 32272--32350 Score: 55
Period size: 10 Copynumber: 8.5 Consensus size: 10
32262 TTTTATTTTT
32272 TTAATTATTA
1 TTAATTATTA
32282 TTAATTA-T-
1 TTAATTATTA
32290 TTAA--A-TA
1 TTAATTATTA
32297 TTAATTATTA
1 TTAATTATTA
*
32307 TTAATT-TAAA
1 TTAATTAT-TA
*
32317 TT-GTTATTA
1 TTAATTATTA
*
32326 TTAATTATAA
1 TTAATTATTA
* *
32336 TTAATAATAA
1 TTAATTATTA
32346 TTAAT
1 TTAAT
32351 AATT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
6 2 0.04
7 4 0.07
8 4 0.07
9 8 0.14
10 38 0.68
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (10 bp):
TTAATTATTA
Found at i:32288 original size:7 final size:7
Alignment explanation
Indices: 32278--32350 Score: 53
Period size: 7 Copynumber: 10.3 Consensus size: 7
32268 TTTTTTAATT
32278 ATTATTA
1 ATTATTA
32285 ATTATTTA
1 ATTA-TTA
*
32293 AATATTA
1 ATTATTA
32300 ATTATT-
1 ATTATTA
32306 ATTAATTTAA
1 ATT-A-TT-A
*
32316 ATTGTT-
1 ATTATTA
32322 ATTATTA
1 ATTATTA
32329 ATTA-TA
1 ATTATTA
*
32335 ATTAATA
1 ATTATTA
*
32342 ATAATTA
1 ATTATTA
32349 AT
1 AT
32351 AATT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
6 14 0.26
7 26 0.49
8 10 0.19
10 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (7 bp):
ATTATTA
Found at i:32298 original size:18 final size:18
Alignment explanation
Indices: 32271--32308 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
32261 ATTTTATTTT
*
32271 TTTAATTATT-ATTAATTA
1 TTTAAATATTAATT-ATTA
32289 TTTAAATATTAATTATTA
1 TTTAAATATTAATTATTA
32307 TT
1 TT
32309 AATTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAAATATTAATTATTA
Found at i:32325 original size:22 final size:21
Alignment explanation
Indices: 32276--32333 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 21
32266 ATTTTTTTAA
32276 TTATTATTAATTATTTAAATAT
1 TTATTATT-ATTATTTAAATAT
*
32298 TAATTATTATTAATTTAAAT-T
1 TTATTATTATT-ATTTAAATAT
32319 GTTATTATTAATTAT
1 -TTATTATT-ATTAT
32334 AATTAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
21 4 0.13
22 24 0.77
23 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTATTATTATTATTTAAATAT
Done.