Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_483
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: 67500
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:9264 original size:15 final size:15
Alignment explanation
Indices: 9246--9279 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
9236 TATCTGGGCA
*
9246 TCTTTTATCTTTTCT
1 TCTTTAATCTTTTCT
*
9261 TCTTTAATTTTTTCT
1 TCTTTAATCTTTTCT
9276 TCTT
1 TCTT
9280 AAGATGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTTTAATCTTTTCT
Found at i:12617 original size:46 final size:45
Alignment explanation
Indices: 12567--12742 Score: 221
Period size: 46 Copynumber: 3.8 Consensus size: 45
12557 TGGTTGAGCA
12567 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
12613 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
12660 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
12706 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
12743 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 68 0.61
47 33 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:12723 original size:93 final size:93
Alignment explanation
Indices: 12564--12734 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
12554 GGATGGTTGA
* *
12564 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
12629 TGAGTCCGAGTTCGAGAAATGTAACTAG
66 TGAGTCCGAGTTCGAGAAATGTAACTAG
*
12657 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
12722 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
12735 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAAATGTAACTAG
Found at i:14719 original size:39 final size:39
Alignment explanation
Indices: 14662--14754 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 39
14652 TGCATGGTAT
* * *
14662 TGGAAAAATATCCAGACTTGAAGTCCGCAGGCTTTA-TGC
1 TGGAAAAATATCCGGACTTAAAGTCCGCAGGC-TAAGTGC
*
14701 TGGAAATATATCCGGACTTAAAGTCCGCAGGCTAAGTGC
1 TGGAAAAATATCCGGACTTAAAGTCCGCAGGCTAAGTGC
14740 TGGAAAAATATCCGG
1 TGGAAAAATATCCGG
14755 GCTAAGTCCC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 2 0.04
39 46 0.96
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (39 bp):
TGGAAAAATATCCGGACTTAAAGTCCGCAGGCTAAGTGC
Found at i:14779 original size:39 final size:39
Alignment explanation
Indices: 14747--14923 Score: 282
Period size: 39 Copynumber: 4.5 Consensus size: 39
14737 TGCTGGAAAA
14747 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
* * **
14786 ATATCTGGGCTAAGTCCTGAAGGCATTCGTGCTGGTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
**
14825 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGCGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
14864 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
14903 ATATCCGGGCTTAAAGTCCCG
1 ATATCCGGGC-T-AAGTCCCG
14924 CATGCTTTGT
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
39 117 0.93
40 1 0.01
41 8 0.06
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.28
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTATT
Found at i:22938 original size:119 final size:120
Alignment explanation
Indices: 22756--22971 Score: 296
Period size: 119 Copynumber: 1.8 Consensus size: 120
22746 TCCTCGTTCA
*
22756 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
22821 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCTGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCTGGATTTAGTAACTCGCACC
* * **
22876 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
22938 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTA
22972 GCCCGGACAT
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.05
119 60 0.71
120 20 0.24
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCTGGATTTAGTAACTCGCACC
Found at i:22978 original size:40 final size:40
Alignment explanation
Indices: 22754--22978 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
22744 GCTCCTCGTT
* *
22754 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
22794 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
22834 CAAATGCCTTCGGGACTTAACCTGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
22874 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
22913 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
22954 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
22979 CATCATTCAA
Statistics
Matches: 162, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 118 0.73
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:30802 original size:80 final size:80
Alignment explanation
Indices: 30698--30921 Score: 269
Period size: 79 Copynumber: 2.8 Consensus size: 80
30688 GCTCCTCGTT
* *
30698 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
30763 ATTTAGTAACTCGCA
66 AATTAGTAACTCGCA
* * *
30778 CAAATGACTTCGGGACTTAACCCGGATT-TAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* *
30841 AAATTAGTATCTCGCA
65 GAATTAGTAACTCGCA
* * * * *
30857 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTC-GGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
30919 GGA
64 GGA
30922 CATCATTCAA
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
78 6 0.05
79 60 0.49
80 54 0.44
81 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCGCA
Found at i:30863 original size:39 final size:40
Alignment explanation
Indices: 30698--30921 Score: 251
Period size: 40 Copynumber: 5.7 Consensus size: 40
30688 GCTCCTCGTT
* *
30698 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
30738 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
30778 CAAATGACTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * *
30818 CCAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
30857 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
30898 CAAA-GCCTTC-GGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
30922 CATCATTCAA
Statistics
Matches: 161, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.01
39 41 0.25
40 108 0.67
41 10 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:33391 original size:44 final size:42
Alignment explanation
Indices: 33341--33499 Score: 160
Period size: 43 Copynumber: 3.7 Consensus size: 42
33331 TATGTGTTGC
**
33341 CGTGTAAGACCATGTCTGGGATGTTGGCATCAACTTATGATTTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCAA-TT-TGATTTA
* * *
33385 CGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTAATTTT
1 CGTGTAAGACCATGTCTGGGACATTGGCATC-AATTTGATTTA
* * * *
33428 C-TGTAAGACCCTGTCTGGGATAGTGGCATTGATATTTGA-TTA
1 CGTGTAAGACCATGTCTGGGACATTGGCA-TCA-ATTTGATTTA
* *
33470 CATGTAAGACCAAGTCTGGGACATTGGCAT
1 CGTGTAAGACCATGTCTGGGACATTGGCAT
33500 TGTACGAGCT
Statistics
Matches: 95, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 28 0.29
43 35 0.37
44 31 0.33
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCAATTTGATTTA
Found at i:39344 original size:40 final size:40
Alignment explanation
Indices: 39246--39415 Score: 225
Period size: 40 Copynumber: 4.3 Consensus size: 40
39236 TCCTCGTTCA
* * * *
39246 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
39285 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
**
39325 AATGCCTTCGGGAGTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* * * *
39365 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
39405 AAGGCCTTCGG
1 AATGCCTTCGG
39416 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 34 0.29
40 83 0.71
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
Found at i:39428 original size:40 final size:40
Alignment explanation
Indices: 39244--39468 Score: 204
Period size: 40 Copynumber: 5.7 Consensus size: 40
39234 GCTCCTCGTT
* * * * * *
39244 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * *
39284 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * *
39323 CGAATGCCTTCGGGAGTTAACCCGGATTTAATAACTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * *
39363 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
** * * * *
39403 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAAGGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCA
*
39444 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAAGGCCTTCGGGACTTAACCCGGA
39469 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 112 0.70
41 11 0.07
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:39428 original size:80 final size:79
Alignment explanation
Indices: 39244--39468 Score: 227
Period size: 80 Copynumber: 2.8 Consensus size: 79
39234 GCTCCTCGTT
* * * * * * *
39244 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
39309 TTTAACAACTCGCA
66 TTTAACAACTCGCA
* * *
39323 CGAATGCCTTCGGGAGTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCGG
** *
39388 ATTTAGTATCTCGCA
65 ATTTAACAACTCGCA
** * * * * * *
39403 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAAGGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACAATGCCTTCGGGACTTAACCCG
39467 GA
64 GA
39469 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
79 37 0.31
80 79 0.65
81 5 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
TTTAACAACTCGCA
Found at i:39477 original size:41 final size:41
Alignment explanation
Indices: 39400--39477 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
39390 TTAGTATCTC
* * *
39400 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
39441 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
39478 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:47332 original size:40 final size:40
Alignment explanation
Indices: 47150--47372 Score: 227
Period size: 40 Copynumber: 5.6 Consensus size: 40
47140 TCCTCGTTCA
* * * * *
47150 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
47189 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
47229 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * *
47269 AATACCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
47309 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
47349 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
47373 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 37 0.23
40 113 0.72
41 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:47332 original size:80 final size:79
Alignment explanation
Indices: 47113--47372 Score: 240
Period size: 80 Copynumber: 3.3 Consensus size: 79
47103 TCAAATCACG
* * * ** * *
47113 TACCTTCGGGATTTAA-CCGGATATAGCT-CCTCGTTCAAATGCCTTCGGGACATAGCCCGGTTT
1 TACCTTCGGGACTTAACCCGGATTTAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT
* *
47176 TAGTAACTCACACAA
65 TAATAACTCGCACAA
* * ** * *
47191 TGCCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTT
1 TACCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTT
47256 AATAACTCGCACGAA
66 AATAACTCGCAC-AA
* * * *
47271 TACCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATA
1 TACCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATT
* * *
47335 TATTCACTTAGCACAA
65 TAATAAC-TCGCACAA
*
47351 -AGCCTTCGGGACTTAGCCCGGA
1 TA-CCTTCGGGACTTAACCCGGA
47373 CAGCATTCAA
Statistics
Matches: 147, Mismatches: 29, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
78 13 0.09
79 51 0.35
80 78 0.53
81 5 0.03
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (79 bp):
TACCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTT
AATAACTCGCACAA
Found at i:47381 original size:41 final size:41
Alignment explanation
Indices: 47304--47381 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
47294 TTAGTATCTC
* * *
47304 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
47345 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
47382 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:50036 original size:27 final size:27
Alignment explanation
Indices: 49995--50116 Score: 176
Period size: 27 Copynumber: 4.5 Consensus size: 27
49985 AAACATACAT
*
49995 CACATAGGGGCAAAACAGTCA-TCTTAC
1 CACATAAGGGCAAAACAGTCATTC-TAC
* *
50022 CATATAAGGGCAAAACAATCATT-TCAC
1 CACATAAGGGCAAAACAGTCATTCT-AC
*
50049 CACATAAGGGAAAAACAGTCATTCTAC
1 CACATAAGGGCAAAACAGTCATTCTAC
50076 CACATAAGGGCAAAACAGTCATTCTAC
1 CACATAAGGGCAAAACAGTCATTCTAC
50103 CACATAAGGGCAAA
1 CACATAAGGGCAAA
50117 TCGAGAACTT
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
26 1 0.01
27 82 0.96
28 2 0.02
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.18
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTCTAC
Found at i:51731 original size:78 final size:78
Alignment explanation
Indices: 51601--51864 Score: 304
Period size: 78 Copynumber: 3.4 Consensus size: 78
51591 TTCCAACCCA
* * * * *
51601 AATGCCTTCAGAACTTAGCCCGAATATAACATCAGCACGAATGCCTTCGGGACTTAGCCCGGATA
1 AATGCCTTCGGGACTTAGCCCGGATATAAAATCAGCACGAATGCCTTTGGGACTTAGCCCGGATA
*
51666 TACTATCAGCACG
66 TAATATCAGCACG
* * * * *
51679 AATGCCTTCGGGACTTAGCCCGGATATAATACCAACACGAATGCCTTTGGGACTTAACCCAGATA
1 AATGCCTTCGGGACTTAGCCCGGATATAAAATCAGCACGAATGCCTTTGGGACTTAGCCCGGATA
*
51744 TAATATCAGCACT
66 TAATATCAGCACG
* * * *
51757 AATGCCTTCGGGACTGAACCCGGATATAAAATCAGTATGAATGCCTTTGGGACTTAGCCCGGATA
1 AATGCCTTCGGGACTTAGCCCGGATATAAAATCAGCACGAATGCCTTTGGGACTTAGCCCGGATA
*
51822 TAAATCTCA-CAC-
66 T-AATATCAGCACG
* *
51834 AAGGCCTGT-GGGTCTTAGCCCGG-T-TAAAATC
1 AATGCCT-TCGGGACTTAGCCCGGATATAAAATC
51865 CTCAAATATC
Statistics
Matches: 159, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
75 7 0.04
76 1 0.01
77 17 0.11
78 128 0.81
79 6 0.04
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (78 bp):
AATGCCTTCGGGACTTAGCCCGGATATAAAATCAGCACGAATGCCTTTGGGACTTAGCCCGGATA
TAATATCAGCACG
Found at i:51825 original size:39 final size:39
Alignment explanation
Indices: 51601--51824 Score: 295
Period size: 39 Copynumber: 5.7 Consensus size: 39
51591 TTCCAACCCA
* * * *
51601 AATGCCTTCAGAACTTAGCCCGAATATAACATCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
*
51640 AATGCCTTCGGGACTTAGCCCGGATATACTATCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
* *
51679 AATGCCTTCGGGACTTAGCCCGGATATAATACCAACACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
* * * *
51718 AATGCCTTTGGGACTTAACCCAGATATAATATCAGCACT
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
* * * * *
51757 AATGCCTTCGGGACTGAACCCGGATATAAAATCAGTATG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
*
51796 AATGCCTTTGGGACTTAGCCCGGATATAA
1 AATGCCTTCGGGACTTAGCCCGGATATAA
51825 ATCTCACACA
Statistics
Matches: 161, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 161 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
Found at i:53788 original size:29 final size:27
Alignment explanation
Indices: 53770--53839 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
53760 ATATTAAGTC
53770 CACACACTCAGTGCTATATAATCAACT
1 CACACACTCAGTGCTATATAATCAACT
* *
53797 CGCACACTTAGTGCTATATAATCAAACT
1 CACACACTCAGTGCTATATAATC-AACT
* *
53825 CGCACACTTAGTGCT
1 CACACACTCAGTGCT
53840 GTACAATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.33, C:0.29, G:0.11, T:0.27
Consensus pattern (27 bp):
CACACACTCAGTGCTATATAATCAACT
Found at i:53833 original size:28 final size:28
Alignment explanation
Indices: 53772--53867 Score: 131
Period size: 28 Copynumber: 3.4 Consensus size: 28
53762 ATTAAGTCCA
*
53772 CACACTCAGTGCTATATAATC-AACTCG
1 CACACTTAGTGCTATATAATCAAACTCG
53799 CACACTTAGTGCTATATAATCAAACTCG
1 CACACTTAGTGCTATATAATCAAACTCG
* * * *
53827 CACACTTAGTGCTGTACAATTTAAACCCG
1 CACACTTAGTGCTATATAA-TCAAACTCG
53856 CACACTTAGTGC
1 CACACTTAGTGC
53868 CAATCTCATG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 20 0.32
28 23 0.37
29 19 0.31
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CACACTTAGTGCTATATAATCAAACTCG
Found at i:61633 original size:29 final size:27
Alignment explanation
Indices: 61615--61684 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
61605 ATATTAAGTC
61615 CACACACTCAGTGCTATATAATCAACT
1 CACACACTCAGTGCTATATAATCAACT
* *
61642 CGCACACTTAGTGCTATATAATCAAACT
1 CACACACTCAGTGCTATATAATC-AACT
* *
61670 CGCACACTTAGTGCT
1 CACACACTCAGTGCT
61685 GTACAATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.33, C:0.29, G:0.11, T:0.27
Consensus pattern (27 bp):
CACACACTCAGTGCTATATAATCAACT
Found at i:61678 original size:28 final size:28
Alignment explanation
Indices: 61617--61712 Score: 131
Period size: 28 Copynumber: 3.4 Consensus size: 28
61607 ATTAAGTCCA
*
61617 CACACTCAGTGCTATATAATC-AACTCG
1 CACACTTAGTGCTATATAATCAAACTCG
61644 CACACTTAGTGCTATATAATCAAACTCG
1 CACACTTAGTGCTATATAATCAAACTCG
* * * *
61672 CACACTTAGTGCTGTACAATTTAAACCCG
1 CACACTTAGTGCTATATAA-TCAAACTCG
61701 CACACTTAGTGC
1 CACACTTAGTGC
61713 CAATCTCATG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 20 0.32
28 23 0.37
29 19 0.31
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CACACTTAGTGCTATATAATCAAACTCG
Found at i:65289 original size:47 final size:47
Alignment explanation
Indices: 65235--65708 Score: 659
Period size: 47 Copynumber: 10.1 Consensus size: 47
65225 TTAGGATTTT
* * * *
65235 ATGTGATGAATGTGAATC-TGTATATATGAGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAA-CATGCATATGTGTGATAAGGCCGAATGGCCA
** * *
65282 ATGTGATGAATGTGAACCTGTATATATATGCGTGATAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAA-C---ATGCATATGTGTGATAAGGCCGAATGGCCA
*
65333 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
**
65380 ATGTGATGAATGTGAACATGTGTATGTGTGATAA---CGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
**
65424 ATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* *
65471 ATGTGATGAATGTGAACATGCGTATCTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* *
65518 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGACCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
*
65565 ATGTGATGAATGTGAACATGCATATGTGTGATAAGACCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* *
65612 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* * * *
65659 ATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
65706 ATG
1 ATG
65709 CGAAACATGT
Statistics
Matches: 396, Mismatches: 24, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
44 44 0.11
47 311 0.79
50 1 0.00
51 40 0.10
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
Found at i:65748 original size:46 final size:46
Alignment explanation
Indices: 65682--65772 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
65672 GAACATGTAT
* *
65682 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACATGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
* * *
65728 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATG
65773 TGTATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTATGAGATGG
Done.