Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1705
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: 41195
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:666 original size:41 final size:43
Alignment explanation
Indices: 620--720 Score: 179
Period size: 41 Copynumber: 2.4 Consensus size: 43
610 TTGGTTTTCA
*
620 GCACTAAGTGTGCGGGCAATAAGTGTTCGCGGTTGT-A-ATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
661 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
704 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
721 TTGAAATGCA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
41 35 0.61
42 1 0.02
43 21 0.37
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.27
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:737 original size:29 final size:29
Alignment explanation
Indices: 702--775 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
692 GTTGTGAGAT
* *
702 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
731 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
760 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
776 TGGTTGATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:1139 original size:40 final size:40
Alignment explanation
Indices: 1084--1319 Score: 269
Period size: 40 Copynumber: 5.9 Consensus size: 40
1074 TTGAATGATG
** *
1084 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
*
1124 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* *
1164 TCCGGGCTAAGTCCCGAGGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* *
1204 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* ** * * * *
1244 TCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTATG
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * * *
1284 TCCGAGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
1320 CGTGTATTCG
Statistics
Matches: 171, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
40 158 0.92
41 7 0.04
42 6 0.04
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:1298 original size:120 final size:120
Alignment explanation
Indices: 1084--1319 Score: 296
Period size: 120 Copynumber: 2.0 Consensus size: 120
1074 TTGAATGATG
* **
1084 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGGCTAAGTCCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGGCTTCGTGCTAAGTGACCATATCCGGGCTAAACCCCGAAGAGCATT
* * * *
1149 CATGCTAGTGATGTATCCGGGCTAAGTCCCGAGGAGCATTCATGCTAGTGATGTA
66 CATGCTAGTGATATATCCGAGCTAAGTCCCGAAGAGCAATCATGCTAGTGATGTA
* * *
1204 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCT-AGTGA-TATATCCGTGCTAAACCCCGAAGAGCA
1 TCCGGGCTAAGTCCCGAAG-GC-TTCGTGCTAAGTGACCATATCCGGGCTAAACCCCGAAGAGCA
* * * * * *
1267 TTCGTGCTGGTGTTATGTCCGAGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
64 TTCATGCTAGTGATATATCCGAGCTAAGTCCCGAAGAGCAATCATGCTAGTGA
1320 CGTGTATTCG
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
120 84 0.86
121 7 0.07
122 7 0.07
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCTTCGTGCTAAGTGACCATATCCGGGCTAAACCCCGAAGAGCATT
CATGCTAGTGATATATCCGAGCTAAGTCCCGAAGAGCAATCATGCTAGTGATGTA
Found at i:4873 original size:47 final size:47
Alignment explanation
Indices: 4819--5406 Score: 849
Period size: 47 Copynumber: 12.4 Consensus size: 47
4809 TTCAGCCAAG
* * *
4819 AGTGTATGTATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
4866 AGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTA--TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
4915 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
4966 AGTGTATGTATATGT-ATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTA--TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
5014 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
5061 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
5108 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
5155 AGTGTATATATGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
5202 AGTGTATATGTGTGATAAGGCCTAAT-GCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
5248 AGTGTATATGTGTGATAAGGCCTAAT-GGCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
5294 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * * * * * * * *
5341 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
5388 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
5407 TCCCGAAGGC
Statistics
Matches: 506, Mismatches: 25, Indels: 20
0.92 0.05 0.04
Matches are distributed among these distances:
46 95 0.19
47 278 0.55
48 38 0.08
49 48 0.09
51 43 0.08
53 4 0.01
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
Found at i:5329 original size:280 final size:285
Alignment explanation
Indices: 4819--5406 Score: 882
Period size: 280 Copynumber: 2.1 Consensus size: 285
4809 TTCAGCCAAG
* * *
4819 AGTGTATGTATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATGTGAT
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTA-GTATATGTGAT
* *
4884 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTGATAAGGCCTAATGGCC
65 AAGGCCTAATAGCCGACGTGATGAATGTGAAAG-G-ATGTATATATGTGATAAGGCCTAATGGCC
*
4949 GATGTGATGAATGTGAAAGTGTATGTATATGTATAAGGCCTAATAGCCGATGTGATGAATGTGAA
128 GACGTGATGAATGTGAAAGTGTA-GTATATGTATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * *
5014 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAA
192 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAA
* * *
5079 GGCCTAATAGCCGACGTGATGAATGTGAA
257 GGCCGAATAGCCAACGTAATGAATGTGAA
*
5108 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTA-TATATGTGATA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAGTATATGTGATA
*
5172 AGGCCTAATAGCCGACGTGATGAATGTGAAA-G-TGTATATGTGTGATAAGGCCTAAT-GCCGAC
66 AGGCCTAATAGCCGACGTGATGAATGTGAAAGGATGTATATATGTGATAAGGCCTAATGGCCGAC
* *
5234 GTGATGAATGTGAAAGTGTA-TATGTGTGATAAGGCCTAAT-GGCGATGTGATGAATGTGAAAGT
131 GTGATGAATGTGAAAGTGTAGTATATGT-ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
* *
5297 GTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGC
195 GTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGC
* * *
5362 CGAGTGGCCAACGTAATGGATGTGAA
260 CGAATAGCCAACGTAATGAATGTGAA
* *
5388 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
5407 TCCCGAAGGC
Statistics
Matches: 274, Mismatches: 24, Indels: 11
0.89 0.08 0.04
Matches are distributed among these distances:
280 124 0.45
281 12 0.04
282 25 0.09
283 23 0.08
285 1 0.00
287 40 0.15
289 49 0.18
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (285 bp):
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAGTATATGTGATA
AGGCCTAATAGCCGACGTGATGAATGTGAAAGGATGTATATATGTGATAAGGCCTAATGGCCGAC
GTGATGAATGTGAAAGTGTAGTATATGTATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCC
GAATAGCCAACGTAATGAATGTGAA
Found at i:5580 original size:37 final size:37
Alignment explanation
Indices: 5524--5602 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
5514 CCGAGCTCTA
* * *
5524 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
5561 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
5598 AAGAC
1 AAGAC
5603 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:7252 original size:46 final size:47
Alignment explanation
Indices: 7158--7281 Score: 146
Period size: 46 Copynumber: 2.7 Consensus size: 47
7148 GGCTGTCACA
* * *
7158 ATGCATGTCCCAGACATGTCTTACACTGACT-TACGTCTCGAGGCCG
1 ATGCATGTCCCAGACATGTCTTACACTGGCTCTACATATCGAGGCCG
* *
7204 ATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATAAT-GTGGTCG
1 ATGCATGTCCCAGACATGTCTTACACTGGCTCTACAT-ATCGAGGCCG
* * *
7250 ATGCATGTCACAGACATGTATTACACTAGCTC
1 ATGCATGTCCCAGACATGTCTTACACTGGCTC
7282 ACAATTAAGT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
46 66 0.97
47 2 0.03
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (47 bp):
ATGCATGTCCCAGACATGTCTTACACTGGCTCTACATATCGAGGCCG
Found at i:9497 original size:18 final size:18
Alignment explanation
Indices: 9465--9499 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9455 GGCCAACCTA
* *
9465 GGCGTGTGGGGCCACACG
1 GGCGTGTGAGCCCACACG
9483 GGCGTGTGAGCCCACAC
1 GGCGTGTGAGCCCACAC
9500 AGGCAGACCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.31, G:0.43, T:0.11
Consensus pattern (18 bp):
GGCGTGTGAGCCCACACG
Found at i:11128 original size:21 final size:21
Alignment explanation
Indices: 11104--11152 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
11094 CCCAGGGTTT
*
11104 CACGGG-TGTGTCCCGTGCCCA
1 CACGGGCT-TGTCCCGTGACCA
11125 CACGGGCTTGTCCCGTGACCA
1 CACGGGCTTGTCCCGTGACCA
11146 CACGGGC
1 CACGGGC
11153 ATGTGAGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.12, C:0.39, G:0.33, T:0.16
Consensus pattern (21 bp):
CACGGGCTTGTCCCGTGACCA
Found at i:14239 original size:29 final size:29
Alignment explanation
Indices: 14182--14310 Score: 163
Period size: 29 Copynumber: 4.5 Consensus size: 29
14172 ATAGTAAGTC
* *
14182 CGCACACTTAGTG-TTATATAATAAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
*
14210 CACACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
14239 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
* * * * *
14268 TGCACACTTAGTGCTATGCA-ATTTAAACC
1 CGCACACTTAGTGCT-TACATAATCAAACT
14297 CGCACACTTAGTGC
1 CGCACACTTAGTGC
14311 CAATCTCATG
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
28 12 0.13
29 74 0.83
30 3 0.03
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCAAACT
Found at i:22939 original size:42 final size:43
Alignment explanation
Indices: 22887--23016 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 43
22877 AAAGTCTCTA
*
22887 ACCCTAAGTGCCAATATCATGGCCCAAAGCCAACTCAATG-AC
1 ACCCGAAGTGCCAATATCATGGCCCAAAGCCAACTCAATGAAC
*
22929 ACCCGAAGTGCCAATATCACGGCCCAAAGCCAACTCAATGAATCTCAC
1 ACCCGAAGTGCCAATATCATGGCCCAAAGCCAACTCAATG-A----AC
** * *
22977 ACCCGAAGCACCAATATCATGGCCCGAAGCCAACTTAATG
1 ACCCGAAGTGCCAATATCATGGCCCAAAGCCAACTCAATG
23017 TAACCCCTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
42 38 0.51
48 37 0.49
ACGTcount: A:0.35, C:0.34, G:0.15, T:0.15
Consensus pattern (43 bp):
ACCCGAAGTGCCAATATCATGGCCCAAAGCCAACTCAATGAAC
Found at i:23001 original size:48 final size:42
Alignment explanation
Indices: 22897--23016 Score: 141
Period size: 48 Copynumber: 2.7 Consensus size: 42
22887 ACCCTAAGTG
**
22897 CCAATATCATGGCCCAAAGCCAACTCAATGACACCCGAAGTG
1 CCAATATCATGGCCCAAAGCCAACTCAATGACACCCGAAGCA
*
22939 CCAATATCACGGCCCAAAGCCAACTCAATGAATCTCACACCCGAAGCA
1 CCAATATCATGGCCCAAAGCCAACTCAATG------ACACCCGAAGCA
* *
22987 CCAATATCATGGCCCGAAGCCAACTTAATG
1 CCAATATCATGGCCCAAAGCCAACTCAATG
23017 TAACCCCTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
42 29 0.44
48 37 0.56
ACGTcount: A:0.36, C:0.34, G:0.15, T:0.15
Consensus pattern (42 bp):
CCAATATCATGGCCCAAAGCCAACTCAATGACACCCGAAGCA
Found at i:24277 original size:43 final size:43
Alignment explanation
Indices: 24178--24299 Score: 129
Period size: 43 Copynumber: 2.8 Consensus size: 43
24168 ACCGAGATGT
* * * * *
24178 GATTACATGTAAGACCATGTCTGGGACATTAGCATTGTAATGT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGTATCGTAATGC
*
24221 GATTACGTATAAGACCATGTCTGGGACATTGGTATCGTTAAT-C
1 GATTACGTGTAAGACCATGTCTGGGACATTGGTATCG-TAATGC
** * * *
24264 GATTTTGTGTAAGACCCTGTCTGCGACAATGGTATC
1 GATTACGTGTAAGACCATGTCTGGGACATTGGTATC
24300 AATATGTGAT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 62 0.94
44 4 0.06
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGTATCGTAATGC
Found at i:26318 original size:29 final size:28
Alignment explanation
Indices: 26275--26368 Score: 111
Period size: 27 Copynumber: 3.4 Consensus size: 28
26265 AGATTGGCAG
* *
26275 TAAGTGTGCGGGTTTAAATTGT-TCAGCAC
1 TAAGTGTGCGAGTTT-AATTATAT-AGCAC
*
26304 TAAGTGTGCGAGTTTGATTATATAGCAC
1 TAAGTGTGCGAGTTTAATTATATAGCAC
* *
26332 TAAGTGTGCGAG-TTGATTATATAACAC
1 TAAGTGTGCGAGTTTAATTATATAGCAC
26359 TAAGTGTGCG
1 TAAGTGTGCG
26369 GACTTAATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
27 24 0.40
28 21 0.35
29 15 0.25
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.34
Consensus pattern (28 bp):
TAAGTGTGCGAGTTTAATTATATAGCAC
Found at i:26339 original size:28 final size:27
Alignment explanation
Indices: 26299--26368 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
26289 TAAATTGTTC
26299 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAG-TTGATTATAT
26327 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATAT
*
26354 AACACTAAGTGTGCG
1 AGCACTAAGTGTGCG
26369 GACTTAATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATAT
Found at i:26379 original size:27 final size:27
Alignment explanation
Indices: 26301--26381 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
26291 AATTGTTCAG
* * *
26301 CACTAAGTGTGCGAGTTTGATTATATAG
1 CACTAAGTGTGCGA-CTTGAATATATAA
* *
26329 CACTAAGTGTGCGAGTTGATTATATAA
1 CACTAAGTGTGCGACTTGAATATATAA
26356 CACTAAGTGTGCGGACTT-AATATATA
1 CACTAAGTGTGC-GACTTGAATATATA
26382 TTTTTGAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
27 30 0.62
28 18 0.38
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.33
Consensus pattern (27 bp):
CACTAAGTGTGCGACTTGAATATATAA
Found at i:32666 original size:21 final size:22
Alignment explanation
Indices: 32642--32689 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
32632 TTCGAATGAT
* *
32642 TTCACTATTCTATCAT-TTCAA
1 TTCACTAGTCTATCATCTACAA
* *
32663 TTCAATAGTCTTTCATCTACAA
1 TTCACTAGTCTATCATCTACAA
32685 TTCAC
1 TTCAC
32690 AACAGCATCA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.29, C:0.25, G:0.02, T:0.44
Consensus pattern (22 bp):
TTCACTAGTCTATCATCTACAA
Found at i:34830 original size:13 final size:13
Alignment explanation
Indices: 34796--34824 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
34786 CAACACACAC
34796 ACCCATGTGGCTA
1 ACCCATGTGGCTA
34809 ACCCATGTGGCTA
1 ACCCATGTGGCTA
34822 ACC
1 ACC
34825 TGTGTGCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (13 bp):
ACCCATGTGGCTA
Found at i:38203 original size:13 final size:13
Alignment explanation
Indices: 38185--38209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38175 AGGAGAAAAA
38185 GAAGGAAGTGAAT
1 GAAGGAAGTGAAT
38198 GAAGGAAGTGAA
1 GAAGGAAGTGAA
38210 ATATTGCCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.40, T:0.12
Consensus pattern (13 bp):
GAAGGAAGTGAAT
Done.