Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4116
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: 15928
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Found at i:90 original size:46 final size:47
Alignment explanation
Indices: 2--93 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 47
1 A
2 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAG
*
49 GGCCTAGTGGCCGATGTGATG-ATGTGAAAGTGTATATATGTGATA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATA
94 AGTCCGAAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 24 0.55
47 20 0.45
ACGTcount: A:0.28, C:0.09, G:0.33, T:0.30
Consensus pattern (47 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAG
Found at i:293 original size:37 final size:36
Alignment explanation
Indices: 237--314 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 36
227 TCGAGCTCTA
* * *
237 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGT-CGGGT
*
274 AAGACCCGATAACTTCGTGTGGAGATTATGTCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCGGGT
310 AAGAC
1 AAGAC
315 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 10 0.27
37 27 0.73
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (36 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCGGGT
Found at i:2392 original size:40 final size:40
Alignment explanation
Indices: 2164--2509 Score: 323
Period size: 40 Copynumber: 8.7 Consensus size: 40
2154 TCGAATGATG
* **
2164 CCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AGTGA-TGTAT
* * * * *
2204 CCGGACTAAGAT-CCGAAG-GCATTTGTGCGAGTTACT-AATT
1 CCGGGCTAAG-TCCCGAAGAGCATTCGTGCTAGTGA-TGTA-T
* * * **
2244 CCGGGCTAAG--CCGAAG-GCATTGGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA-TGTAT
* * * * * *
2282 CCGGGTTAAGTCCCGAAG-GCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA-TGTAT
* *
2322 CCGGGCTAAGTTCCGAAGAGCATTTGTGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
*
2362 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
2402 CCGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
2442 CCGGGCTAAGTCTCGAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
*
2482 CCGGGCTAAGTTCCGAAGAGCATTCGTG
1 CCGGGCTAAGTCCCGAAGAGCATTCGTG
2510 TAGATTCGCT
Statistics
Matches: 269, Mismatches: 30, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
38 33 0.12
39 3 0.01
40 211 0.78
41 22 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
Found at i:5035 original size:48 final size:49
Alignment explanation
Indices: 4955--5194 Score: 332
Period size: 48 Copynumber: 5.0 Consensus size: 49
4945 GTGAACATGC
4955 ATATATG-AGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTA-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
5004 ATATATGTAATAAGG-CTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
5052 ATATATGTGATAAGGCCTAATGGCCGATGTGATG-ATGTGAAAGTG--T
1 ATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
5098 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
1 ATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * * * * * *
5145 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTAT
1 ATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
5194 A
1 A
5195 AATGTGATAA
Statistics
Matches: 178, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
46 35 0.20
47 51 0.29
48 58 0.33
49 33 0.19
50 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (49 bp):
ATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
Found at i:5104 original size:143 final size:141
Alignment explanation
Indices: 4934--5205 Score: 388
Period size: 143 Copynumber: 1.9 Consensus size: 141
4924 TTAGGATTCT
4934 ATGTGATGGATGTGAACATGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGGATGTGAACATGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
* * * *
4999 TGTATATATATGTAATAAGG-CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
66 TG--TATATATGTAACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATA-A-ATGTGAT
5063 AAGGCCTAATGGCCG
127 AAGGCCTAATGGCCG
* *
5078 ATGTGAT-GATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
* * * *
5141 GTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
65 GTGTATATATGTAACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATAAG
5206 TCCCGAAGGG
Statistics
Matches: 116, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
140 10 0.09
141 14 0.12
142 30 0.26
143 55 0.47
144 7 0.06
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (141 bp):
ATGTGATGGATGTGAACATGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTAACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATAAGG
CCTAATGGCCG
Found at i:5187 original size:47 final size:47
Alignment explanation
Indices: 4934--5205 Score: 370
Period size: 47 Copynumber: 5.7 Consensus size: 47
4924 TTAGGATTCT
* * *
4934 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
*
4981 ATGTGATGAATGTGAAAGTGTATATATATGTAATAAGG-CTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
5029 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
5078 ATGTGATG-ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
5124 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
5171 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
5206 TCCCGAAGGG
Statistics
Matches: 205, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
46 36 0.18
47 80 0.39
48 58 0.28
49 31 0.15
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:5379 original size:37 final size:36
Alignment explanation
Indices: 5323--5400 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 36
5313 CCGAGCTCTA
* * *
5323 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGT-CGGGT
*
5360 AAGACCCGATAACTTCGTGTGGAGATTATGTCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCGGGT
5396 AAGAC
1 AAGAC
5401 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 10 0.27
37 27 0.73
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (36 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCGGGT
Found at i:7387 original size:79 final size:79
Alignment explanation
Indices: 7289--7715 Score: 341
Period size: 79 Copynumber: 5.4 Consensus size: 79
7279 AAGTGACCAT
* *
7289 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATTCCGGGCTAAG-CCTGAAG-GC
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-ACCGGGCTAAGTCC-GAAGAGC
* *
7350 ATTGGTGCGAGTTACTAA
63 ATTCGTGCGAGTGA-TAA
*
7368 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCGAAGAGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCGAAGAGCATT
* **
7433 CGTGCTAGTGATGT
66 CGTGCGAGTGATAA
** * * * *
7447 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TGTATCCGGGCTAAGTTCC-AAGAGCA
1 ATCCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGTTACTATAACCGGGCTAAG-TCCGAAGAGCA
* **
7510 TTCGTGCTAGTGATGT
64 TTCGTGCGAGTGATAA
* ** * * * *
7526 ATCCGGGCTAAGTCTCGAAGAGCATTCATGCTAGTGA-TGTATCCGGGCTAAGTTCCGAAGAGCA
1 ATCCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGTTACTATAACCGGGCTAAG-TCCGAAGAGCA
* **
7590 TTCGTGCTAGTGATGT
64 TTCGTGCGAGTGATAA
** * * * *
7606 ATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGA-TGTATCCGGGCTAAGTTCCGAAGAGCA
1 ATCCGGGCTAAGTCCCGAAG-GCATTTGTGCGAGTTACTATAACCGGGCTAAG-TCCGAAGAGCA
* *
7669 TTCGTGCTAGTGATAT
64 TTCGTGCGAGTGATAA
* ** *
7685 ATCCGTGCTAAACCCCGAAGAGCATTCGTGC
1 ATCCGGGCTAAGTCCCGAAG-GCATTTGTGC
7716 TGGTGTTATA
Statistics
Matches: 318, Mismatches: 22, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
78 1 0.00
79 234 0.74
80 83 0.26
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCGAAGAGCATT
CGTGCGAGTGATAA
Found at i:7491 original size:119 final size:120
Alignment explanation
Indices: 7251--7748 Score: 541
Period size: 119 Copynumber: 4.2 Consensus size: 120
7241 TCGAATGATG
* * *
7251 CCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAG-GCAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AGTGA-TATATCCGGGCTAAGATCCGAAGAGCAT
* * * * * * * * *
7313 TTGTGCGAGTTACT-AATTCCGGGCTAAG-CCTGAAG-GCATTGGTGCGAGTTACTAAAT
64 TCGTGCTAGTGA-TGTA-TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA-TATAT
* * * * *
7370 CCGGGTTAAGTCCCGAAG-GCATTTGTGCGAGTTACTATAACCGGGCTAAG-TCCGAAGAGCATT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA-TATATCCGGGCTAAGATCCGAAGAGCATT
* *
7433 CGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
65 CGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
* *
7489 CCGGGCTAAGTTCC-AAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAG-TCTCGAAGAGCATT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGATC-CGAAGAGCATT
* * *
7552 CATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
65 CGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
* * *
7608 CCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTC
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGATCCGAAGAGCATTC
* * ** * *
7672 GTGCTAGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATAT
66 GTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
* *
7727 CCGTGCTAGGTCCCGAAGAGCA
1 CCGGGCTAAGTCCCGAAGAGCA
7749 ATCATGCTGG
Statistics
Matches: 330, Mismatches: 39, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
118 39 0.12
119 260 0.79
120 31 0.09
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (120 bp):
CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGATCCGAAGAGCATTC
GTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATAT
Found at i:7760 original size:40 final size:40
Alignment explanation
Indices: 7251--7748 Score: 532
Period size: 40 Copynumber: 12.6 Consensus size: 40
7241 TCGAATGATG
* **
7251 CCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AGTGA-TGTAT
* * * * *
7291 CCGGACTAAGAT-CCGAAG-GCATTTGTGCGAGTTACT-AATT
1 CCGGGCTAAG-TCCCGAAGAGCATTCGTGCTAGTGA-TGTA-T
* * * * **
7331 CCGGGCTAAG-CCTGAAG-GCATTGGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA-TGTAT
* * * * * *
7370 CCGGGTTAAGTCCCGAAG-GCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGA-TGTAT
7410 CCGGGCTAAGT-CCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
*
7449 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
*
7489 CCGGGCTAAGTTCC-AAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
7528 CCGGGCTAAGTCTCGAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
*
7568 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
*
7608 CCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
7647 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
* ** * * *
7687 CCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATAT
1 CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
7727 CCGTGCTAGGTCCCGAAGAGCA
1 CCGGGCTAAGTCCCGAAGAGCA
7749 ATCATGCTGG
Statistics
Matches: 408, Mismatches: 40, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
39 127 0.31
40 273 0.67
41 8 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
Found at i:10351 original size:96 final size:93
Alignment explanation
Indices: 10215--10483 Score: 355
Period size: 96 Copynumber: 2.9 Consensus size: 93
10205 TTAGGATTCT
* * * *
10215 ATGTGATGGATGTGACA-TGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
10279 TGTATATATATGTATAAGGCCTAATGGCCG
66 TGTATATATATG-ATAAGG-CTAATGGCCG
10309 ATGTGATGAATGTG-AAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
10373 AGTGTATATATGTGATAAGGCTAATGGCCG
64 AGTGTATATATATGATAAGGCTAATGGCCG
* * * * * * *
10403 ATGTGATGAATGTGAAAGTGTATATATGTGA-CAGGGCGAGTGGCCAACGTGATGGATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
* *
10467 TGTATAAATGTGATAAG
66 TGTATATATATGATAAG
10484 TCCGAAGGGC
Statistics
Matches: 158, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
92 42 0.27
93 12 0.08
94 39 0.25
95 11 0.07
96 54 0.34
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (93 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATATGATAAGGCTAATGGCCG
Found at i:10418 original size:46 final size:47
Alignment explanation
Indices: 10215--10483 Score: 366
Period size: 46 Copynumber: 5.7 Consensus size: 47
10205 TTAGGATTCT
* * * *
10215 ATGTGATGGATGTGACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
10261 ATGTGATGAATGTGAAAGTGTATATATATGTATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTG-ATAAGGCCTAATGGCCG
10309 ATGTGATGAATGTG-AAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
10357 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGG-CTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
10403 ATGTGATGAATGTGAAAGTGTATATATGTGA-CAGGGCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
10449 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
10484 TCCGAAGGGC
Statistics
Matches: 202, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
45 3 0.01
46 91 0.45
47 32 0.16
48 62 0.31
49 14 0.07
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:10655 original size:37 final size:37
Alignment explanation
Indices: 10599--10677 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
10589 CCGAGCTCTA
* * *
10599 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
10636 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
10673 AAGAC
1 AAGAC
10678 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:13876 original size:39 final size:40
Alignment explanation
Indices: 13840--14059 Score: 299
Period size: 40 Copynumber: 5.6 Consensus size: 40
13830 CTTGCACAAG
* *
13840 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCACAGAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
13880 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
13920 GCCTTCGGGTCTTAGCCCGGATATA-TCACTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
13959 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* *
13999 GCC-TCGGATCTTAGTCCGG-TATAGTCACCTAGCACAAA-
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
14037 GCC-TCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
14060 CATTCGAATA
Statistics
Matches: 160, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
38 22 0.14
39 65 0.41
40 73 0.46
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.24
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:13894 original size:40 final size:40
Alignment explanation
Indices: 13804--14059 Score: 289
Period size: 39 Copynumber: 6.5 Consensus size: 40
13794 CTCAAGAAAT
* * * *
13804 CTTCGGGATTTAG-CCGGATATA-ACTACTTGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
13842 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCACAGATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
13882 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
13922 CTTCGGGTCTTAGCCCGGATATA-TCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
13961 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
*
14001 C-TC-GGATCTTAGTCCGG-TATAGTCACCTAGCACAAA-GC
1 CTTCGGGA-CTTAGCCCGGATATAGTCA-CTAGCACAAATGC
14039 C-TCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
14060 CATTCGAATA
Statistics
Matches: 188, Mismatches: 20, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
38 33 0.18
39 80 0.43
40 75 0.40
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:13953 original size:79 final size:78
Alignment explanation
Indices: 13804--14059 Score: 299
Period size: 79 Copynumber: 3.3 Consensus size: 78
13794 CTCAAGAAAT
* * * * * *
13804 CTTCGGGATTTAG-CCGGATATAACTACTTGCAC-AAGGCCTTCGGGTCTTAGCCCGGATATGGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAT-AT
13867 CACTAGCACAGATGC
65 CACTAGCACA-ATGC
*
13882 CTTCGGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAT
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAT
13946 CACTAGCACAAATGC
65 CACTAGCAC-AATGC
* * * * *
13961 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACGAATGCC-TCGGATCTTAGTCCGG-TATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATA-T
*
14024 CACCTAGCACAAAGC
65 CA-CTAGCACAATGC
14039 C-TCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
14060 CATTCGAATA
Statistics
Matches: 157, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
77 23 0.15
78 35 0.22
79 71 0.45
80 28 0.18
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (78 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATATC
ACTAGCACAATGC
Found at i:14697 original size:38 final size:38
Alignment explanation
Indices: 14646--14732 Score: 165
Period size: 38 Copynumber: 2.3 Consensus size: 38
14636 TGCTTACCTA
14646 TGGCCGAACATACACATCAACTTATGTACTCATTCATG
1 TGGCCGAACATACACATCAACTTATGTACTCATTCATG
*
14684 TGGCCGAACATACACATCAACTTATGTGCTCATTCATG
1 TGGCCGAACATACACATCAACTTATGTACTCATTCATG
14722 TGGCCGAACAT
1 TGGCCGAACAT
14733 GCATGTTATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (38 bp):
TGGCCGAACATACACATCAACTTATGTACTCATTCATG
Done.