Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 126 of 318
Found at i:38819864 original size:20 final size:20
Alignment explanation
Indices: 38819839--38819897 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
38819829 TAAATATGGT
38819839 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
38819859 ATGTATGATACGCACATGAT
1 ATGTATGATATGCACATGAA
38819879 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
38819898 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:38819978 original size:23 final size:24
Alignment explanation
Indices: 38819948--38820042 Score: 124
Period size: 24 Copynumber: 4.0 Consensus size: 24
38819938 GAGGAAGTGA
38819948 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
38819971 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
38819995 GAAAGGGCTT-TGGCCCCAGTTATT
1 AAAAGGGCTTAT-GCCCCAGTTATT
*
38820019 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
38820043 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
23 23 0.36
24 30 0.47
25 11 0.17
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:38820016 original size:47 final size:49
Alignment explanation
Indices: 38819949--38820042 Score: 133
Period size: 47 Copynumber: 2.0 Consensus size: 49
38819939 AGGAAGTGAA
*
38819949 AAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTATTG
1 AAAGGGCTTATGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTATTG
38819996 AAAGGGCTT-TGGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
1 AAAGGGCTTAT-GCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
38820043 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
46 1 0.02
47 19 0.45
48 11 0.26
49 11 0.26
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (49 bp):
AAAGGGCTTATGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTATTG
Found at i:38820285 original size:38 final size:38
Alignment explanation
Indices: 38820234--38820396 Score: 232
Period size: 38 Copynumber: 4.4 Consensus size: 38
38820224 CGTTTACAGT
38820234 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
*
38820272 AAAGGCTTCGGCCCAG-----T--AATATGAAATATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
38820303 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
* *
38820341 AAAGGCTTCGGCCCAGTATTATGAAATATGAAATACGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
*
38820379 AAAGGGCTACGGCCCAGT
1 AAA-GGCTTCGGCCCAGT
38820397 GCATGATTGA
Statistics
Matches: 112, Mismatches: 5, Indels: 15
0.85 0.04 0.11
Matches are distributed among these distances:
31 29 0.26
33 1 0.01
36 1 0.01
38 68 0.61
39 13 0.12
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (38 bp):
AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
Found at i:38820296 original size:31 final size:31
Alignment explanation
Indices: 38820258--38820373 Score: 142
Period size: 31 Copynumber: 3.5 Consensus size: 31
38820248 AGTATTATGA
38820258 AATATGAAACATGAAAAGGCTTCGGCCCAGT
1 AATATGAAACATGAAAAGGCTTCGGCCCAGT
*
38820289 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTAT
1 AATATGAAACATGAAAAGGCTTCGGCCCAG-----T
38820325 GAAATATGAAACATGAAAAGGCTTCGGCCCAGT
1 --AATATGAAACATGAAAAGGCTTCGGCCCAGT
* *
38820358 ATTATGAAATATGAAA
1 AATATGAAACATGAAA
38820374 TACGAAAAGG
Statistics
Matches: 74, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
31 43 0.58
33 1 0.01
36 1 0.01
38 29 0.39
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (31 bp):
AATATGAAACATGAAAAGGCTTCGGCCCAGT
Found at i:38820310 original size:69 final size:69
Alignment explanation
Indices: 38820234--38820373 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 69
38820224 CGTTTACAGT
38820234 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
38820299 ATGA
66 ATGA
*
38820303 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTATTATGAAAT
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
38820368 ATGA
66 ATGA
38820372 AA
1 AA
38820374 TACGAAAAGG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (69 bp):
AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAAT
ATGA
Found at i:38828133 original size:25 final size:25
Alignment explanation
Indices: 38828104--38828151 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
38828094 TTATAATATG
* * *
38828104 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
38828129 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
38828152 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:38828220 original size:20 final size:20
Alignment explanation
Indices: 38828195--38828253 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
38828185 TAAATATGGT
38828195 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
38828215 ATGTATGATACGCACATGAT
1 ATGTATGATATGCACATGAA
38828235 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
38828254 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:38828334 original size:23 final size:24
Alignment explanation
Indices: 38828304--38828397 Score: 131
Period size: 23 Copynumber: 4.0 Consensus size: 24
38828294 GAGGAAGTGA
38828304 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
38828327 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
38828351 GAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
38828374 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
38828398 ATGATAAAGC
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
23 40 0.62
24 16 0.25
25 8 0.12
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:38828377 original size:47 final size:48
Alignment explanation
Indices: 38828305--38828397 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 48
38828295 AGGAAGTGAA
*
38828305 AAAGGGCTTATGCCCCAGTTATAAAAG-GGCTTATGCC-CCAGTTATTG
1 AAAGGGCTTATGCCCCAGTTATAAAAGAGGC-TAGGCCTCCAGTTATTG
38828352 AAAGGGCTT-TGCCCCAGTTATTAAAAGAGGCTAGGCCTCCAGTTAT
1 AAAGGGCTTATGCCCCAGTTA-TAAAAGAGGCTAGGCCTCCAGTTAT
38828398 ATGATAAAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
46 11 0.26
47 20 0.48
48 11 0.26
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (48 bp):
AAAGGGCTTATGCCCCAGTTATAAAAGAGGCTAGGCCTCCAGTTATTG
Found at i:38828640 original size:38 final size:38
Alignment explanation
Indices: 38828589--38828750 Score: 223
Period size: 38 Copynumber: 4.4 Consensus size: 38
38828579 CGTTTACAGT
38828589 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
*
38828627 AAAGGCTTCGGCCCAG-----T--AATATGAAATATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
38828658 AAA-GCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
* *
38828695 AAAGGCTTCGGCCCAGTATTATGAAATATGAAATACGA
1 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
*
38828733 AAAGGGCTACGGCCCAGT
1 AAA-GGCTTCGGCCCAGT
38828751 GCATGATTGA
Statistics
Matches: 110, Mismatches: 5, Indels: 17
0.83 0.04 0.13
Matches are distributed among these distances:
30 12 0.11
31 16 0.15
33 1 0.01
35 1 0.01
37 16 0.15
38 51 0.46
39 13 0.12
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (38 bp):
AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
Found at i:38828667 original size:30 final size:31
Alignment explanation
Indices: 38828613--38828727 Score: 133
Period size: 31 Copynumber: 3.5 Consensus size: 31
38828603 AGTATTATGA
*
38828613 AATATGAAACATGAAAAGGCTTCGGCCCAGT
1 AATATGAAATATGAAAAGGCTTCGGCCCAGT
38828644 AATATGAAATATGAAAA-GCTTCGGCCCAGTATTAT
1 AATATGAAATATGAAAAGGCTTCGGCCCAG-----T
*
38828679 GAAATATGAAACATGAAAAGGCTTCGGCCCAGT
1 --AATATGAAATATGAAAAGGCTTCGGCCCAGT
*
38828712 ATTATGAAATATGAAA
1 AATATGAAATATGAAA
38828728 TACGAAAAGG
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
30 12 0.17
31 30 0.42
33 1 0.01
35 1 0.01
37 16 0.22
38 12 0.17
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (31 bp):
AATATGAAATATGAAAAGGCTTCGGCCCAGT
Found at i:38828667 original size:68 final size:68
Alignment explanation
Indices: 38828593--38828727 Score: 261
Period size: 68 Copynumber: 2.0 Consensus size: 68
38828583 TACAGTAAAG
38828593 GCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAATATGA
1 GCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAATATGA
38828658 AAA
66 AAA
*
38828661 GCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTATTATGAAATATGA
1 GCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAATATGA
38828726 AA
66 AA
38828728 TACGAAAAGG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (68 bp):
GCTTCGGCCCAGTATTATGAAATATGAAACATGAAAAGGCTTCGGCCCAGTAATATGAAATATGA
AAA
Found at i:38830459 original size:68 final size:67
Alignment explanation
Indices: 38830387--38830536 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
38830377 CATCATGTGT
* * * *
38830387 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
38830449 ATGTAG
62 ATGTAG
** * *
38830455 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
38830520 AG
66 AG
38830522 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
38830537 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:38830492 original size:64 final size:64
Alignment explanation
Indices: 38830411--38830594 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
38830401 AGACATTATG
* *
38830411 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
38830475 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
38830540 AA
63 AA
* * * *
38830542 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
38830595 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:38831687 original size:2 final size:2
Alignment explanation
Indices: 38831680--38831714 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
38831670 TCATGACATG
*
38831680 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38831715 GACTAGTCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:38833265 original size:30 final size:31
Alignment explanation
Indices: 38833231--38833327 Score: 85
Period size: 30 Copynumber: 3.2 Consensus size: 31
38833221 TAAACTAAAA
*
38833231 TGAGCTAAGCTTTAGCTCGTGAGCTA-AAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAGAAGT
* * * * *
38833261 TGAGCTGAGATTAAACTCCTAAGC-AGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAGAAGT
* *
38833291 TGAGCCAAGGTTTAGCTCGTGAGCT-GAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTAGAAGT
38833320 ATGAGCTA
1 -TGAGCTA
38833328 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 48 0.96
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (31 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAGAAGT
Found at i:38835165 original size:23 final size:22
Alignment explanation
Indices: 38835109--38835167 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
38835099 CTTGTTCACA
*
38835109 TTCTTTTTCTCTCTCAAATCTTT
1 TTCTTTTTCT-TTTCAAATCTTT
* *
38835132 TTCATTCTCTTTTC-AATCTCATT
1 TTCTTTTTCTTTTCAAATCT--TT
38835155 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
38835168 TCTTTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 5 0.17
22 3 0.10
23 21 0.72
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (22 bp):
TTCTTTTTCTTTTCAAATCTTT
Found at i:38835252 original size:5 final size:5
Alignment explanation
Indices: 38835242--38835308 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
38835232 CTCTTGCCTC
*
38835242 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
38835289 TCTTT TCTTT GT-TTT TCTTT
1 TCTTT TCTTT -TCTTT TCTTT
38835309 ACAAGAATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
4 5 0.10
5 35 0.67
6 7 0.13
7 5 0.10
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:38836224 original size:13 final size:12
Alignment explanation
Indices: 38836206--38836258 Score: 69
Period size: 11 Copynumber: 4.7 Consensus size: 12
38836196 ATTAAACACT
38836206 TTTTTTTTCAGAA
1 TTTTTTTTC-GAA
38836219 TTTTTTTTCGAA
1 TTTTTTTTCGAA
38836231 -TTTTTTT-GAA
1 TTTTTTTTCGAA
38836241 -TTTTTTT-GAA
1 TTTTTTTTCGAA
38836251 TTTTTTTT
1 TTTTTTTT
38836259 ACTTGTATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
10 13 0.33
11 14 0.36
12 3 0.08
13 9 0.23
ACGTcount: A:0.17, C:0.04, G:0.08, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:38836234 original size:10 final size:10
Alignment explanation
Indices: 38836220--38836257 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
38836210 TTTTCAGAAT
38836220 TTTTTTTCGAA
1 TTTTTTT-GAA
38836231 TTTTTTTGAA
1 TTTTTTTGAA
38836241 TTTTTTTGAA
1 TTTTTTTGAA
38836251 TTTTTTT
1 TTTTTTT
38836258 TACTTGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 20 0.74
11 7 0.26
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.74
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:38836258 original size:12 final size:12
Alignment explanation
Indices: 38836205--38836258 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 12
38836195 CATTAAACAC
38836205 TTTTTTTTTCAGAA
1 TTTTTTTTT--GAA
*
38836219 TTTTTTTTCGAA
1 TTTTTTTTTGAA
38836231 --TTTTTTTGAA
1 TTTTTTTTTGAA
38836241 --TTTTTTTGAA
1 TTTTTTTTTGAA
38836251 TTTTTTTT
1 TTTTTTTT
38836259 ACTTGTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 19 0.53
12 9 0.25
14 8 0.22
ACGTcount: A:0.17, C:0.04, G:0.07, T:0.72
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:38837968 original size:30 final size:30
Alignment explanation
Indices: 38837882--38837979 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
38837872 TTAAACTAAA
* *
38837882 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
38837912 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
38837942 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
38837972 ATGAGCTA
1 ATGAGCTA
38837980 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:38838510 original size:63 final size:65
Alignment explanation
Indices: 38838426--38838556 Score: 146
Period size: 67 Copynumber: 2.0 Consensus size: 65
38838416 CTAACTTAAA
*
38838426 TAAATGAACTAACACTTATGCATCA-T-TTAATCC-AGCAACTAGTTTAATTAATAGAAGCAT-T
1 TAAATGAACTAACACTCATGCATCACTATT-ATCCTAGCAACTAGTTTAATTAA-AGAAGCATCT
38838487 AT
64 AT
* * *
38838489 TAAATGAACTTTA-ACTCATGCATCACTAAATTATCCTAGTAACTAGTTTATTTAAAGAAGCATC
1 TAAATGAAC-TAACACTCATGCATCACT--ATTATCCTAGCAACTAGTTTAATTAAAGAAGCATC
38838553 TAT
63 TAT
38838556 T
1 T
38838557 CAAGTTCATA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
63 20 0.35
64 3 0.05
66 12 0.21
67 22 0.39
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (65 bp):
TAAATGAACTAACACTCATGCATCACTATTATCCTAGCAACTAGTTTAATTAAAGAAGCATCTAT
Found at i:38839523 original size:14 final size:14
Alignment explanation
Indices: 38839501--38839532 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
38839491 AAGAAAGAGG
*
38839501 GGTATGAATGAAAT
1 GGTAGGAATGAAAT
38839515 GGTAGGAATGAAAT
1 GGTAGGAATGAAAT
38839529 GGTA
1 GGTA
38839533 TGAACGAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.34, T:0.25
Consensus pattern (14 bp):
GGTAGGAATGAAAT
Found at i:38840669 original size:30 final size:30
Alignment explanation
Indices: 38840575--38840670 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
38840565 AGCTCACTCC
*
38840575 TAGCTC-ACTTTCA-CTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
38840604 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
38840634 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
38840664 TAGCTCA
1 TAGCTCA
38840671 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
29 9 0.18
30 38 0.76
31 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:38842295 original size:1 final size:1
Alignment explanation
Indices: 38842289--38842322 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
38842279 TGTGAAGTTT
* *
38842289 AAAAAAAAAGACAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38842323 GTGAAGTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.94, C:0.03, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:38843238 original size:21 final size:20
Alignment explanation
Indices: 38843204--38843271 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
38843194 ACATTCTTGT
38843204 AAAGAGAAAA-TAAAGAAAAGA
1 AAAGA-AAAAGTAAA-AAAAGA
*
38843225 AAAGAAAAAGTAAAAGAAGAA
1 AAAGAAAAAGTAAAAAAAG-A
* *
38843246 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGTAA-AAAAAGA
38843267 AAAGA
1 AAAGA
38843272 GAGGCAAGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (20 bp):
AAAGAAAAAGTAAAAAAAGA
Found at i:38843239 original size:6 final size:5
Alignment explanation
Indices: 38843215--38843271 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
38843205 AAGAGAAAAT
*
38843215 AAAGA AAAGA AAAGAA AAAGTA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
38843262 AAAGA AAAGA
1 AAAGA AAAGA
38843272 GAGGCAAGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (5 bp):
AAAGA
Found at i:38843246 original size:15 final size:14
Alignment explanation
Indices: 38843215--38843271 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
38843205 AAGAGAAAAT
38843215 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
38843231 AAAGTAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
38843246 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
38843262 AAAGAAAAGA
1 AAAGAAAAGA
38843272 GAGGCAAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:38843344 original size:11 final size:12
Alignment explanation
Indices: 38843312--38843342 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38843302 TTGAGAGAAC
38843312 TTGAAAAAGCCT
1 TTGAAAAAGCCT
38843324 TTGAAAAAGCCT
1 TTGAAAAAGCCT
38843336 TTGAAAA
1 TTGAAAA
38843343 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:38843353 original size:12 final size:12
Alignment explanation
Indices: 38843345--38843369 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38843335 TTTGAAAAGC
38843345 AAAAAGAAAATG
1 AAAAAGAAAATG
38843357 AAAAAGAAAATG
1 AAAAAGAAAATG
38843369 A
1 A
38843370 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:38843366 original size:18 final size:18
Alignment explanation
Indices: 38843339--38843394 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
38843329 AAAGCCTTTG
38843339 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
38843358 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
38843376 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
38843393 AA
1 AA
38843395 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:38843379 original size:30 final size:31
Alignment explanation
Indices: 38843345--38843426 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
38843335 TTTGAAAAGC
*
38843345 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
38843375 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
38843405 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
38843427 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:38845549 original size:30 final size:31
Alignment explanation
Indices: 38845515--38845611 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
38845505 AGCTCACTCC
*
38845515 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
38845545 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
38845575 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
38845605 TAGCTCA
1 TAGCTCA
38845612 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:38846168 original size:17 final size:17
Alignment explanation
Indices: 38846146--38846178 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
38846136 ATAGAGCTCC
38846146 TTGAACATGTTCACACT
1 TTGAACATGTTCACACT
38846163 TTGAACATGTTCACAC
1 TTGAACATGTTCACAC
38846179 ATGCATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (17 bp):
TTGAACATGTTCACACT
Found at i:38847353 original size:30 final size:30
Alignment explanation
Indices: 38847277--38847354 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
38847267 CTTAACTTAC
* *
38847277 GAGCTAAACCTTAGCTCAACTTCAGCTTAG
1 GAGCTAAAGCTTAGCTCAACTTCAGCTCAG
** * * *
38847307 GAG-TTTAGCCTCAGCTCAACTTTAGCTCAT
1 GAGCTAAAG-CTTAGCTCAACTTCAGCTCAG
38847337 GAGCTAAAGCTTAGCTCA
1 GAGCTAAAGCTTAGCTCA
38847355 TTTTAGTTTA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
29 2 0.06
30 31 0.86
31 3 0.08
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (30 bp):
GAGCTAAAGCTTAGCTCAACTTCAGCTCAG
Found at i:38848165 original size:14 final size:14
Alignment explanation
Indices: 38848146--38848190 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
38848136 AACTCATCTT
*
38848146 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
38848160 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
38848173 AATTTAATTTAATG
1 AGTTTAATTTAATG
38848187 AGTT
1 AGTT
38848191 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:38849220 original size:15 final size:15
Alignment explanation
Indices: 38849174--38849221 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
38849164 AAACCTATAA
*
38849174 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
38849189 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
38849203 AAACTTCATATCCAT
1 AAACTTCATATCCAT
38849218 AAAC
1 AAAC
38849222 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:38851680 original size:11 final size:11
Alignment explanation
Indices: 38851664--38851726 Score: 67
Period size: 11 Copynumber: 5.6 Consensus size: 11
38851654 TATACAAGTT
38851664 AAAAAAATTCA
1 AAAAAAATTCA
38851675 AAAAAAATTC-
1 AAAAAAATTCA
38851685 AAAAAAATTCGA
1 AAAAAAATTC-A
**
38851697 AAAAAAA-GAA
1 AAAAAAATTCA
38851707 TAAAAAAATTCGA
1 -AAAAAAATTC-A
38851720 AAAAAAA
1 AAAAAAA
38851727 GTGATTTATG
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
10 11 0.26
11 17 0.40
12 14 0.33
13 1 0.02
ACGTcount: A:0.75, C:0.06, G:0.05, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:38851727 original size:23 final size:23
Alignment explanation
Indices: 38851663--38851727 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
38851653 TTATACAAGT
*
38851663 TAAAAAAATTC--AAAAAAA-AT
1 TAAAAAAATTCGAAAAAAAAGAA
38851683 TCAAAAAAATTCGAAAAAAAAGAA
1 T-AAAAAAATTCGAAAAAAAAGAA
38851707 TAAAAAAATTCGAAAAAAAAG
1 TAAAAAAATTCGAAAAAAAAG
38851728 TGATTTATGC
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
20 1 0.03
21 10 0.25
23 27 0.68
24 2 0.05
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.15
Consensus pattern (23 bp):
TAAAAAAATTCGAAAAAAAAGAA
Found at i:38855650 original size:11 final size:13
Alignment explanation
Indices: 38855625--38855656 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
38855615 ACAAGTTTGA
38855625 AAAAAAAATTCCG
1 AAAAAAAATTCCG
38855638 AAAAAAAA-T-CG
1 AAAAAAAATTCCG
38855649 AAAAAAAA
1 AAAAAAAA
38855657 AAGTGATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.75, C:0.09, G:0.06, T:0.09
Consensus pattern (13 bp):
AAAAAAAATTCCG
Found at i:38865230 original size:19 final size:19
Alignment explanation
Indices: 38865206--38865245 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
38865196 AGCTCCCATG
38865206 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
38865225 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
38865244 TA
1 TA
38865246 TCAGCTCATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:38871520 original size:30 final size:31
Alignment explanation
Indices: 38871486--38871581 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 31
38871476 GCTCACTCCC
*
38871486 AGCTC-ACTTTCAACTCACGAGCTAAACCTT
1 AGCTCAACTTTCAGCTCACGAGCTAAACCTT
* * * * * *
38871516 AGCTCAAC-TTCAGCTTAGGAGTTTAGCCTC
1 AGCTCAACTTTCAGCTCACGAGCTAAACCTT
*
38871546 AGCTCAACTTT-AGCTCACGAGCTAAAGCTT
1 AGCTCAACTTTCAGCTCACGAGCTAAACCTT
38871576 AGCTCA
1 AGCTCA
38871582 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (31 bp):
AGCTCAACTTTCAGCTCACGAGCTAAACCTT
Found at i:38871959 original size:19 final size:19
Alignment explanation
Indices: 38871935--38871974 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
38871925 AGCTCCCATG
38871935 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
38871954 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
38871973 TA
1 TA
38871975 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:38874985 original size:13 final size:12
Alignment explanation
Indices: 38874959--38875024 Score: 82
Period size: 13 Copynumber: 5.5 Consensus size: 12
38874949 ATACAAGTAT
38874959 AAAAAAATTC--
1 AAAAAAATTCAA
38874969 AAAAAAATTCAGA
1 AAAAAAATTCA-A
*
38874982 AAAAAAATTCGA
1 AAAAAAATTCAA
38874994 AAAAAAATTCAA
1 AAAAAAATTCAA
*
38875006 AAAAAAGTTTCAA
1 AAAAAA-ATTCAA
38875019 AAAAAA
1 AAAAAA
38875025 TGATTTGTGC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
10 10 0.20
12 18 0.37
13 21 0.43
ACGTcount: A:0.71, C:0.08, G:0.05, T:0.17
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:38874985 original size:23 final size:22
Alignment explanation
Indices: 38874959--38875023 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 22
38874949 ATACAAGTAT
38874959 AAAAAAATTCAAAAAAATTCAGA
1 AAAAAAATTCAAAAAAATTCA-A
38874982 AAAAAAATTCGAAAAAAAATTCAA
1 AAAAAAATTC--AAAAAAATTCAA
*
38875006 AAAAAAGTTTCAAAAAAA
1 AAAAAA-ATTCAAAAAAA
38875024 ATGATTTGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
23 17 0.45
24 7 0.18
25 14 0.37
ACGTcount: A:0.71, C:0.08, G:0.05, T:0.17
Consensus pattern (22 bp):
AAAAAAATTCAAAAAAATTCAA
Found at i:38875021 original size:25 final size:25
Alignment explanation
Indices: 38874959--38875024 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
38874949 ATACAAGTAT
38874959 AAAAAAATTC--AAAAAAATTCAGA
1 AAAAAAATTCAAAAAAAAATTCAGA
*
38874982 AAAAAAATTCGAAAAAAAATTCA-A
1 AAAAAAATTCAAAAAAAAATTCAGA
*
38875006 AAAAAAGTTTCAAAAAAAA
1 AAAAAA-ATTCAAAAAAAA
38875025 TGATTTGTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 10 0.26
24 7 0.18
25 21 0.55
ACGTcount: A:0.71, C:0.08, G:0.05, T:0.17
Consensus pattern (25 bp):
AAAAAAATTCAAAAAAAAATTCAGA
Found at i:38877269 original size:30 final size:30
Alignment explanation
Indices: 38877184--38877280 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
38877174 TAAACTATAA
* *
38877184 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
38877214 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
38877244 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
38877273 ATGAGCTA
1 -TGAGCTA
38877281 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:38877712 original size:16 final size:17
Alignment explanation
Indices: 38877682--38877726 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
38877672 ACATTCTTGT
38877682 AAAG-AGAAAATAAAG-A
1 AAAGAAGAAAA-AAAGCA
38877698 AAAGAAGAAAAAAAGCA
1 AAAGAAGAAAAAAAGCA
38877715 AAAGAAGAAAAA
1 AAAGAAGAAAAA
38877727 GAAAATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (17 bp):
AAAGAAGAAAAAAAGCA
Found at i:38877727 original size:9 final size:9
Alignment explanation
Indices: 38877697--38877729 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
38877687 GAAAATAAAG
38877697 AAAAGAAGA
1 AAAAGAAGA
*
38877706 AAAA-AAGC
1 AAAAGAAGA
38877714 AAAAGAAGA
1 AAAAGAAGA
38877723 AAAAGAA
1 AAAAGAA
38877730 AATGAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAGAAGA
Found at i:38877727 original size:15 final size:14
Alignment explanation
Indices: 38877693--38877748 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 14
38877683 AAGAGAAAAT
38877693 AAAGAAAAGAAGAAAA
1 AAAGAAAAGAAG--AA
38877709 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
38877724 AAAGAAAATGAA-ATA
1 AAAGAAAA-GAAGA-A
38877739 AAAGAAAAGA
1 AAAGAAAAGA
38877749 GAAGCAAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.19
15 18 0.49
16 4 0.11
17 8 0.22
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:38877752 original size:31 final size:33
Alignment explanation
Indices: 38877682--38877752 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 33
38877672 ACATTCTTGT
*
38877682 AAAGAGAA-AATAAAGAAAAGAAGAAAAAAAGC
1 AAAGAGAAGAATAAAGAAAAGAAGAAAAAAAGA
*
38877714 AAA-AGAAGAA-AAAGAAAATG-A-AATAAAAGA
1 AAAGAGAAGAATAAAGAAAA-GAAGAAAAAAAGA
38877744 AAAGAGAAG
1 AAAGAGAAG
38877753 CAAGAGGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
30 10 0.29
31 18 0.53
32 6 0.18
ACGTcount: A:0.75, C:0.01, G:0.20, T:0.04
Consensus pattern (33 bp):
AAAGAGAAGAATAAAGAAAAGAAGAAAAAAAGA
Found at i:38877998 original size:30 final size:30
Alignment explanation
Indices: 38877976--38878060 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
38877966 GCTCATATTC
38877976 AGCTCACGAGCTAAACCTTAGCTCAACTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTT
* * * * * *
38878006 AGCTTAGGAGTTTAGCCTCAGCTCAACTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTT
* *
38878036 AGCTCATGAGCTAAAGCTTAGCTCA
1 AGCTCACGAGCTAAACCTTAGCTCA
38878061 TTTTAGTTTA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (30 bp):
AGCTCACGAGCTAAACCTTAGCTCAACTTT
Found at i:38878484 original size:30 final size:30
Alignment explanation
Indices: 38878403--38878485 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
38878393 GCTCATATTC
*
38878403 CTCACGAGCTAAACCTTAGCTCAACTTCAG
1 CTCACGAGCTAAAGCTTAGCTCAACTTCAG
* * ** * *
38878433 CTTAGGAG-TTTAGCCTCAGCTCAACTTTAG
1 CTCACGAGCTAAAG-CTTAGCTCAACTTCAG
38878463 CTCACGAGCTAAAGCTTAGCTCA
1 CTCACGAGCTAAAGCTTAGCTCA
38878486 TTTTAGTTTA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 34 0.87
31 3 0.08
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.27
Consensus pattern (30 bp):
CTCACGAGCTAAAGCTTAGCTCAACTTCAG
Found at i:38878596 original size:425 final size:426
Alignment explanation
Indices: 38877804--38878656 Score: 1609
Period size: 425 Copynumber: 2.0 Consensus size: 426
38877794 ACTTGATACG
*
38877804 AGCACGCCCCGCGAAATTCATCGAACAAGTCTGTCAAGCCGAGCATTGACATGTTGGCAAGCTGA
1 AGCACGCCCCGCGAAATTCATCAAACAAGTCTGTCAAGCCGAGCATTGACATGTTGGCAAGCTGA
*
38877869 TCCCAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCAAACTCGATCC
66 TCCAAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCAAACTCGATCC
*
38877934 AACTTGCCTGAGCTAAACCGAGCTCACTCCTAGCTCATATTCAGCTCACGAGCTAAACCTTAGCT
131 AACTTGCCTGAGCTAAACCAAGCTCACTCCTAGCTCATATTCA-CTCACGAGCTAAACCTTAGCT
* *
38877999 CAACTTTAGCTTAGGAGTTTAGCCTCAGCTCAACTTTAGCTCATGAGCTAAAGCTTAGCTCATTT
195 CAACTTCAGCTTAGGAGTTTAGCCTCAGCTCAACTTTAGCTCACGAGCTAAAGCTTAGCTCATTT
*
38878064 TAGTTTAAACTCGGTTTTGTCTTTAATACATTAAATAAAATTTTGCAAATATTCATTTAAGCATT
260 TAGTTTAAACTCGGTTTTGTCTTTAATACATTAAATAAAAATTTGCAAATATTCATTTAAGCATT
38878129 AAACTTGTCTTATATTAATATTTGTTATTAATATGTCATTGTCATTATATAAATTGATTATGTTC
325 AAACTTGTCTTATATTAATATTTGTTATTAATATGTCATTGTCATTATATAAATTGATTATGTTC
38878194 ACATAGCCGAATTAATGCATGACATTAATGTGTTCAC
390 ACATAGCCGAATTAATGCATGACATTAATGTGTTCAC
*
38878231 AGCACGCCCCGCGAACTTCATCAAACAAGTCTGTCAAGCCGAGCATTGACATGTTGGCAAGCTGA
1 AGCACGCCCCGCGAAATTCATCAAACAAGTCTGTCAAGCCGAGCATTGACATGTTGGCAAGCTGA
*
38878296 TCCAAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCAAGCTCGATCC
66 TCCAAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCAAACTCGATCC
38878361 AACTTGCCTGAGCTAAACCAAGCTCACTCCTAGCTCATATTC-CTCACGAGCTAAACCTTAGCTC
131 AACTTGCCTGAGCTAAACCAAGCTCACTCCTAGCTCATATTCACTCACGAGCTAAACCTTAGCTC
38878425 AACTTCAGCTTAGGAGTTTAGCCTCAGCTCAACTTTAGCTCACGAGCTAAAGCTTAGCTCATTTT
196 AACTTCAGCTTAGGAGTTTAGCCTCAGCTCAACTTTAGCTCACGAGCTAAAGCTTAGCTCATTTT
*
38878490 AGTTTAAACTCGGTTTTGTCTTTAATACATTAAATAAAAATTTGCACATATTCATTTAAGCATTA
261 AGTTTAAACTCGGTTTTGTCTTTAATACATTAAATAAAAATTTGCAAATATTCATTTAAGCATTA
38878555 AACTTGTCTTATATTAATATTTGTTATTAATATGTCATTGTCATTATATAAATTGATTATGTTCA
326 AACTTGTCTTATATTAATATTTGTTATTAATATGTCATTGTCATTATATAAATTGATTATGTTCA
38878620 CATAGCCGAATTAATGCATGACATTAATGTGTTCAC
391 CATAGCCGAATTAATGCATGACATTAATGTGTTCAC
38878656 A
1 A
38878657 TCATGCCGAA
Statistics
Matches: 417, Mismatches: 9, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
425 250 0.60
427 167 0.40
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (426 bp):
AGCACGCCCCGCGAAATTCATCAAACAAGTCTGTCAAGCCGAGCATTGACATGTTGGCAAGCTGA
TCCAAGCTCGTTTCCAGCTCCACGAGCTCCGTCCAGCTCAAATCCAGCTTATTCAAACTCGATCC
AACTTGCCTGAGCTAAACCAAGCTCACTCCTAGCTCATATTCACTCACGAGCTAAACCTTAGCTC
AACTTCAGCTTAGGAGTTTAGCCTCAGCTCAACTTTAGCTCACGAGCTAAAGCTTAGCTCATTTT
AGTTTAAACTCGGTTTTGTCTTTAATACATTAAATAAAAATTTGCAAATATTCATTTAAGCATTA
AACTTGTCTTATATTAATATTTGTTATTAATATGTCATTGTCATTATATAAATTGATTATGTTCA
CATAGCCGAATTAATGCATGACATTAATGTGTTCAC
Found at i:38879963 original size:11 final size:12
Alignment explanation
Indices: 38879931--38879961 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38879921 ATATCAGAAC
38879931 TTGAAAAAGCCT
1 TTGAAAAAGCCT
38879943 TTGAAAAAGCCT
1 TTGAAAAAGCCT
38879955 TTGAAAA
1 TTGAAAA
38879962 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:38879972 original size:12 final size:12
Alignment explanation
Indices: 38879964--38879988 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38879954 TTTGAAAAGC
38879964 AAAAAGAAAATG
1 AAAAAGAAAATG
38879976 AAAAAGAAAATG
1 AAAAAGAAAATG
38879988 A
1 A
38879989 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:38879985 original size:18 final size:18
Alignment explanation
Indices: 38879958--38880013 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
38879948 AAAGCCTTTG
38879958 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
38879977 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
38879995 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
38880012 AA
1 AA
38880014 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:38879998 original size:30 final size:31
Alignment explanation
Indices: 38879964--38880045 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
38879954 TTTGAAAAGC
*
38879964 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
38879994 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
38880024 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
38880046 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:38882198 original size:30 final size:30
Alignment explanation
Indices: 38882154--38882249 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
38882144 AGCTCACTCC
*
38882154 TAGCTC-ATTTCAGCTCACGAGCTAAACCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * * *
38882183 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
38882213 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
38882243 TAGCTCA
1 TAGCTCA
38882250 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
29 6 0.12
30 45 0.88
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:38882584 original size:30 final size:30
Alignment explanation
Indices: 38882550--38882646 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
38882540 AGCTCACTCC
38882550 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
38882580 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* *
38882610 CAGCTCAACGTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAAC-TTCAGCTCACGAGCTAAACCT
38882640 TAGCTCA
1 TAGCTCA
38882647 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
29 1 0.02
30 49 0.94
31 2 0.04
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.27
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:38884134 original size:12 final size:12
Alignment explanation
Indices: 38884126--38884150 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38884116 TTTGAAAAGC
38884126 AAAAAGAAAATG
1 AAAAAGAAAATG
38884138 AAAAAGAAAATG
1 AAAAAGAAAATG
38884150 A
1 A
38884151 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:38884147 original size:18 final size:18
Alignment explanation
Indices: 38884120--38884175 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
38884110 AAAGCCTTTG
38884120 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
38884139 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
38884157 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
38884174 AA
1 AA
38884176 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:38884160 original size:30 final size:31
Alignment explanation
Indices: 38884126--38884207 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
38884116 TTTGAAAAGC
*
38884126 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
38884156 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
38884186 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
38884208 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:38893204 original size:30 final size:30
Alignment explanation
Indices: 38893119--38893215 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
38893109 TAAACTAAAA
* *
38893119 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
38893149 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
38893179 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
38893208 ATGAGCTA
1 -TGAGCTA
38893216 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:38895455 original size:26 final size:25
Alignment explanation
Indices: 38895413--38895465 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
38895403 GCAACTAATT
* *
38895413 AATTTGTTCTAATCTAGACACATTA
1 AATTTGTCCTAAACTAGACACATTA
*
38895438 AATTATGTCCTAAACTAGACATATTA
1 AATT-TGTCCTAAACTAGACACATTA
38895464 AA
1 AA
38895466 ACATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.36
Consensus pattern (25 bp):
AATTTGTCCTAAACTAGACACATTA
Found at i:38896366 original size:18 final size:18
Alignment explanation
Indices: 38896343--38896391 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
38896333 TAAAACACAA
*
38896343 TTAATT-ATTTAAGCTGAC
1 TTAATTAATTTAA-CTAAC
38896361 TTAATTAATTTAACTAAC
1 TTAATTAATTTAACTAAC
*
38896379 TTATTTAATTTAA
1 TTAATTAATTTAA
38896392 TCCAGTAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (18 bp):
TTAATTAATTTAACTAAC
Found at i:38899502 original size:12 final size:12
Alignment explanation
Indices: 38899485--38899519 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
38899475 TCTTTTGCTA
38899485 TTTTCTCTTTCT
1 TTTTCTCTTTCT
38899497 TTTTCTCATTT-T
1 TTTTCTC-TTTCT
38899509 TTTTCTCTTTC
1 TTTTCTCTTTC
38899520 ACTTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.14
12 15 0.71
13 3 0.14
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTCTCTTTCT
Found at i:38899517 original size:20 final size:20
Alignment explanation
Indices: 38899473--38899518 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
38899463 GGTTTTCCAC
38899473 TCTCTTTTGCTATTTTCTCT
1 TCTCTTTTGCTATTTTCTCT
* *
38899493 T-TCTTTTTCTCATTTT-TTT
1 TCTCTTTTGCT-ATTTTCTCT
38899512 TCTCTTT
1 TCTCTTT
38899519 CACTTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.72
Consensus pattern (20 bp):
TCTCTTTTGCTATTTTCTCT
Found at i:38899531 original size:24 final size:24
Alignment explanation
Indices: 38899485--38899535 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
38899475 TCTTTTGCTA
* *
38899485 TTTTCTCTTTCTTTTTCTCATTTT
1 TTTTCTCTTTCCTTTTATCATTTT
38899509 TTTTCTCTTTCACTTTTAT-ATTTT
1 TTTTCTCTTTC-CTTTTATCATTTT
38899533 TTT
1 TTT
38899536 CTTTTTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTCTCTTTCCTTTTATCATTTT
Found at i:38906000 original size:40 final size:40
Alignment explanation
Indices: 38905935--38906109 Score: 269
Period size: 40 Copynumber: 4.4 Consensus size: 40
38905925 TCGATGTAAC
* * *
38905935 AACCAGCACGAATGCCTTCGAGACTTAACCCGGTAATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* * *
38905975 AACTCGCACGAATGCCTTCGGGACTTAGCTCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* **
38906015 AACCTGCACGAATGCCTTCGGGACTTAGTCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
38906055 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
38906095 AACCCGCACGAATGC
1 AACCCGCACGAATGC
38906110 TGTGCACATA
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 122 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:38908252 original size:30 final size:30
Alignment explanation
Indices: 38908218--38908315 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
38908208 AGCTCACTTC
38908218 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
38908248 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
38908278 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
38908308 TAGCTCAT
1 TAGCTCAT
38908316 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:38909990 original size:12 final size:13
Alignment explanation
Indices: 38909973--38910030 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
38909963 TATACAAGTT
38909973 AAAAAAAA-TCAAA
1 AAAAAAAATTC-AA
*
38909986 AAAAAAAATT-GA
1 AAAAAAAATTCAA
38909998 AAAAAAAATTCAA
1 AAAAAAAATTCAA
*
38910011 AAAAAAAATTCGA
1 AAAAAAAATTCAA
38910024 AAAAAAA
1 AAAAAAA
38910031 TAAAAAGAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.28
13 28 0.70
14 1 0.03
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:38910031 original size:12 final size:12
Alignment explanation
Indices: 38909986--38910031 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
38909976 AAAAATCAAA
38909986 AAAAAAAATT-G
1 AAAAAAAATTCG
*
38909997 AAAAAAAAATTCAA
1 -AAAAAAAATTC-G
38910011 AAAAAAAATTCG
1 AAAAAAAATTCG
38910023 AAAAAAAAT
1 AAAAAAAAT
38910032 AAAAAGAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 19 0.63
13 11 0.37
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.15
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:38910031 original size:25 final size:26
Alignment explanation
Indices: 38909973--38910030 Score: 93
Period size: 25 Copynumber: 2.3 Consensus size: 26
38909963 TATACAAGTT
38909973 AAAAAAAA-TCAAAAAAAAAAATTGA
1 AAAAAAAATTCAAAAAAAAAAATTGA
38909998 AAAAAAAATTC-AAAAAAAAAATTCGA
1 AAAAAAAATTCAAAAAAAAAAATT-GA
38910024 AAAAAAA
1 AAAAAAA
38910031 TAAAAAGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 20 0.65
26 11 0.35
ACGTcount: A:0.79, C:0.05, G:0.03, T:0.12
Consensus pattern (26 bp):
AAAAAAAATTCAAAAAAAAAAATTGA
Found at i:38910952 original size:9 final size:10
Alignment explanation
Indices: 38910945--38911001 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
38910935 AAGAGAAAAC
38910945 AAAGAAAAGA
1 AAAGAAAAGA
38910955 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
38910967 AAAGAAGA-A
1 AAAGAAAAGA
38910976 AAAGAAAATGA
1 AAAGAAAA-GA
38910987 AATA-AAAAGA
1 AA-AGAAAAGA
38910997 AAAGA
1 AAAGA
38911002 GAGGCAAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:38910968 original size:21 final size:20
Alignment explanation
Indices: 38910934--38911001 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
38910924 ACATTCTTGT
38910934 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
38910955 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
38910976 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
38910997 AAAGA
1 AAAGA
38911002 GAGGCAAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:38910969 original size:6 final size:5
Alignment explanation
Indices: 38910945--38911001 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
38910935 AAGAGAAAAC
*
38910945 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
38910992 AAAGA AAAGA
1 AAAGA AAAGA
38911002 GAGGCAAAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:38910976 original size:15 final size:14
Alignment explanation
Indices: 38910945--38911001 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
38910935 AAGAGAAAAC
38910945 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
38910961 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
38910976 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
38910992 AAAGAAAAGA
1 AAAGAAAAGA
38911002 GAGGCAAAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:38911079 original size:11 final size:12
Alignment explanation
Indices: 38911048--38911078 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
38911038 TTGAGAGAAC
38911048 TTGAAAAAGCCT
1 TTGAAAAAGCCT
*
38911060 TTGAAAAAGTCT
1 TTGAAAAAGCCT
38911072 TTGAAAA
1 TTGAAAA
38911079 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:38911089 original size:12 final size:12
Alignment explanation
Indices: 38911081--38911105 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38911071 TTTGAAAAGC
38911081 AAAAAGAAAATG
1 AAAAAGAAAATG
38911093 AAAAAGAAAATG
1 AAAAAGAAAATG
38911105 A
1 A
38911106 GATTGAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:38911102 original size:18 final size:18
Alignment explanation
Indices: 38911075--38911130 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
38911065 AAAGTCTTTG
38911075 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
38911094 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
38911112 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
38911129 AA
1 AA
38911131 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:38911115 original size:30 final size:31
Alignment explanation
Indices: 38911081--38911162 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
38911071 TTTGAAAAGC
*
38911081 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
38911111 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
38911141 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
38911163 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:38913407 original size:30 final size:30
Alignment explanation
Indices: 38913373--38913470 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
38913363 AGCTCACTCC
38913373 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
38913403 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
38913433 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
38913463 TAGCTCAT
1 TAGCTCAT
38913471 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:38917311 original size:10 final size:10
Alignment explanation
Indices: 38917298--38917332 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
38917288 AAGCTCGGTT
38917298 GAGCTCAAAC
1 GAGCTCAAAC
*
38917308 GAGCTGAAAC
1 GAGCTCAAAC
*
38917318 GAGCTCAAAT
1 GAGCTCAAAC
38917328 GAGCT
1 GAGCT
38917333 GAGTTGAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:38919966 original size:93 final size:93
Alignment explanation
Indices: 38919853--38920023 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
38919843 GCCCATAAGT
* * * *
38919853 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGAACTCAACTCAA
38919918 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
38919946 GAACTCTGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTAAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGAACTCAACTCAA
* *
38920011 CTAGTTCGGATGC
66 CGAGCTCGGATGC
38920024 TCAACCATCC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTAAACTCGAACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:38920017 original size:46 final size:46
Alignment explanation
Indices: 38919845--38920020 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
38919835 TGTAACCCGC
* * *
38919845 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* *
38919891 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-ATTTGCAT
* * *
38919941 CTC-T---CGAACTCTGACTCAACTCAACGAGTTCGGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
* * * *
38919984 CCATAAGTAAACTCGAACTCAACTCAACTAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
38920021 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 1 0.01
43 8 0.08
44 1 0.01
46 61 0.58
47 27 0.25
49 1 0.01
50 6 0.06
51 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTTGCAT
Found at i:38922325 original size:19 final size:19
Alignment explanation
Indices: 38922280--38922325 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
38922270 ATTAACACAC
*
38922280 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
38922299 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
38922317 AATTAATAA
1 AATTAATAA
38922326 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:38922655 original size:19 final size:19
Alignment explanation
Indices: 38922631--38922670 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
38922621 AGCTCCCATA
38922631 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
38922650 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
38922669 TA
1 TA
38922671 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:38924259 original size:10 final size:10
Alignment explanation
Indices: 38924240--38924284 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
38924230 TAAGCTCGTT
38924240 GAGCTCAAAC
1 GAGCTCAAAC
*
38924250 GAGCTGAAAC
1 GAGCTCAAAC
*
38924260 GAGCTCAAAT
1 GAGCTCAAAC
*
38924270 GAGCTCAAAT
1 GAGCTCAAAC
38924280 GAGCT
1 GAGCT
38924285 GAGTTGAGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:38925884 original size:18 final size:19
Alignment explanation
Indices: 38925861--38925899 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
38925851 ATTATCTCAA
*
38925861 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
38925879 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
38925898 TT
1 TT
38925900 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:38925938 original size:18 final size:18
Alignment explanation
Indices: 38925917--38925965 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
38925907 AAACTCTTTT
38925917 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
38925935 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
38925953 TCAATCT-TTTTTC
1 TCATTCTCTTTTTC
38925966 TTTTTCTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.14, C:0.27, G:0.00, T:0.59
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:38925956 original size:24 final size:24
Alignment explanation
Indices: 38925892--38925972 Score: 92
Period size: 24 Copynumber: 3.4 Consensus size: 24
38925882 CTTGTTCACA
*
38925892 TTCTTTTTCTCTCTCAAACTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
* * * * *
38925916 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTTTCTCTCTCAATCTCTTT
*
38925940 TTCTTTTTCACTCTCAATCT-TTT
1 TTCTTTTTCTCTCTCAATCTCTTT
38925963 TTCTTTTTCT
1 TTCTTTTTCT
38925973 TTCATTTCTT
Statistics
Matches: 44, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 11 0.25
24 33 0.75
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (24 bp):
TTCTTTTTCTCTCTCAATCTCTTT
Found at i:38926026 original size:42 final size:42
Alignment explanation
Indices: 38925969--38926065 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
38925959 TTTTTTCTTT
* * * *
38925969 TTCTTTCA-TTTCTTTGTTTCTTTTCTTGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
38926010 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
38926052 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
38926066 CTCATAATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 7 0.14
42 43 0.86
ACGTcount: A:0.14, C:0.23, G:0.05, T:0.58
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:38927102 original size:17 final size:16
Alignment explanation
Indices: 38927067--38927102 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
38927057 ATTACAACTT
*
38927067 GAATTTTTTTTAATTC
1 GAATTTTTTTTAATAC
38927083 GAATTTTTTTTAACTAC
1 GAATTTTTTTTAA-TAC
38927100 GAA
1 GAA
38927103 CCTATTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (16 bp):
GAATTTTTTTTAATAC
Found at i:38930045 original size:14 final size:14
Alignment explanation
Indices: 38930023--38930070 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
38930013 ACCTAAACCG
* *
38930023 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
38930037 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
*
38930051 ATCC-TTTCGTTCCT
1 A-CCATTTTGTTCCT
38930065 ACCATT
1 ACCATT
38930071 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 2 0.07
14 25 0.86
15 2 0.07
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:38930223 original size:10 final size:10
Alignment explanation
Indices: 38930210--38930244 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
38930200 AAGCTTGGTT
38930210 GAGCTCAAAC
1 GAGCTCAAAC
*
38930220 GAGCTGAAAC
1 GAGCTCAAAC
*
38930230 GAGCTCAAAT
1 GAGCTCAAAC
38930240 GAGCT
1 GAGCT
38930245 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:38930253 original size:20 final size:20
Alignment explanation
Indices: 38930207--38930254 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
38930197 AGTAAGCTTG
38930207 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
38930227 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
38930247 GTTGAGCT
1 GTTGAGCT
38930255 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:38930998 original size:14 final size:14
Alignment explanation
Indices: 38930981--38931020 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
38930971 CGAATGGAAT
*
38930981 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
38930995 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
38931009 GATATGAACAAA
1 GGTAGGAACAAA
38931021 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:38935438 original size:10 final size:10
Alignment explanation
Indices: 38935423--38935449 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
38935413 TACTCCTTCA
38935423 AGCTCAAATC
1 AGCTCAAATC
38935433 AGCTCAAATC
1 AGCTCAAATC
38935443 AGCTCAA
1 AGCTCAA
38935450 CTTCAACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:38935471 original size:10 final size:10
Alignment explanation
Indices: 38935423--38935471 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
38935413 TACTCCTTCA
*
38935423 AGCTCAAATC
1 AGCTCAACTC
*
38935433 AGCTCAAATC
1 AGCTCAACTC
38935443 AGCTCAACTTC
1 AGCTCAAC-TC
* *
38935454 AACTCAACTT
1 AGCTCAACTC
38935464 AGCTCAAC
1 AGCTCAAC
38935472 GAGCTCATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 25 0.74
11 9 0.26
ACGTcount: A:0.37, C:0.33, G:0.08, T:0.22
Consensus pattern (10 bp):
AGCTCAACTC
Found at i:38942684 original size:30 final size:30
Alignment explanation
Indices: 38942650--38942746 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
38942640 AGCTCACTCC
38942650 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * ***
38942680 TAGCTCAACTTCAGCTTAGGAGTTTTGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
38942710 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
38942740 TAGCTCA
1 TAGCTCA
38942747 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:38944476 original size:41 final size:41
Alignment explanation
Indices: 38944431--38944511 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
38944421 CAATATAGTA
*
38944431 CAAAAAAAAGTTAT-ACAAGTAAAAAAAAATC-GAAAAAAATT
1 CAAAAAAAA-TTATAAAAAG-AAAAAAAAATCTGAAAAAAATT
*
38944472 CAAAAAAAATTTTCAAAAAGAAAAAAAAATCTGAAAAAAA
1 CAAAAAAAATTAT-AAAAAGAAAAAAAAATCTGAAAAAAA
38944512 GTGTTTAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 3 0.09
41 20 0.57
42 12 0.34
ACGTcount: A:0.70, C:0.07, G:0.06, T:0.16
Consensus pattern (41 bp):
CAAAAAAAATTATAAAAAGAAAAAAAAATCTGAAAAAAATT
Found at i:38944510 original size:21 final size:21
Alignment explanation
Indices: 38944451--38944512 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
38944441 TTATACAAGT
*
38944451 AAAAAAAAATC-GAAAAAAATT
1 AAAAAAAAATCTGAAAAAAA-G
* ***
38944472 CAAAAAAAAT-TTTCAAAAAG
1 AAAAAAAAATCTGAAAAAAAG
38944492 AAAAAAAAATCTGAAAAAAAG
1 AAAAAAAAATCTGAAAAAAAG
38944513 TGTTTAATGC
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 9 0.30
21 21 0.70
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (21 bp):
AAAAAAAAATCTGAAAAAAAG
Found at i:38945439 original size:9 final size:10
Alignment explanation
Indices: 38945432--38945488 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
38945422 AAGAGAAAAC
38945432 AAAGAAAAGA
1 AAAGAAAAGA
38945442 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
38945454 AAAGAAGA-A
1 AAAGAAAAGA
38945463 AAAGAAAATGA
1 AAAGAAAA-GA
38945474 AATA-AAAAGA
1 AA-AGAAAAGA
38945484 AAAGA
1 AAAGA
38945489 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:38945455 original size:21 final size:20
Alignment explanation
Indices: 38945421--38945488 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
38945411 ACATTCTTGT
38945421 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
38945442 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
38945463 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
38945484 AAAGA
1 AAAGA
38945489 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:38945456 original size:6 final size:5
Alignment explanation
Indices: 38945432--38945488 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
38945422 AAGAGAAAAC
*
38945432 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
38945479 AAAGA AAAGA
1 AAAGA AAAGA
38945489 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:38945463 original size:15 final size:14
Alignment explanation
Indices: 38945432--38945488 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
38945422 AAGAGAAAAC
38945432 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
38945448 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
38945463 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
38945479 AAAGAAAAGA
1 AAAGAAAAGA
38945489 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:38945568 original size:11 final size:12
Alignment explanation
Indices: 38945536--38945566 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38945526 TTGAGAGAAC
38945536 TTGAAAAAGCCT
1 TTGAAAAAGCCT
38945548 TTGAAAAAGCCT
1 TTGAAAAAGCCT
38945560 TTGAAAA
1 TTGAAAA
38945567 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:38945643 original size:30 final size:30
Alignment explanation
Indices: 38945569--38945650 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
38945559 TTTGAAAAGC
* ** *
38945569 AAAAAGAAAATGAAAA-AAAAATGAGATTG
1 AAAAAGAAGATGAAAAGAAATTTGAGAGTG
*
38945598 AAAAAG-AGAACGAAAAGAAATTTGAGAGTG
1 AAAAAGAAG-ATGAAAAGAAATTTGAGAGTG
38945628 AAAAAGAAGATGAAAAAGAAATT
1 AAAAAGAAGATG-AAAAGAAATT
38945651 GAAACAAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.02
29 12 0.28
30 18 0.42
31 12 0.28
ACGTcount: A:0.65, C:0.01, G:0.21, T:0.13
Consensus pattern (30 bp):
AAAAAGAAGATGAAAAGAAATTTGAGAGTG
Found at i:38947779 original size:30 final size:30
Alignment explanation
Indices: 38947745--38947841 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
38947735 AGCTCACTCC
*
38947745 TAGCTCATA-TTCAACTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
38947775 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
38947805 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
38947835 TAGCTCA
1 TAGCTCA
38947842 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:38948948 original size:15 final size:15
Alignment explanation
Indices: 38948928--38948975 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
38948918 TCAAAGATGG
38948928 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
38948943 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
38948957 GTTTATGGATATAAA
1 GTTTATGGATATGAA
38948972 GTTT
1 GTTT
38948976 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:38948962 original size:14 final size:14
Alignment explanation
Indices: 38948922--38948965 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
38948912 AAGGATTCAA
38948922 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
38948936 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
38948951 AGATGGGTTTATGG
1 AGATGGGTTTATGG
38948965 A
1 A
38948966 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:38948991 original size:29 final size:29
Alignment explanation
Indices: 38948922--38948981 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
38948912 AAGGATTCAA
*
38948922 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
38948951 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
38948980 AG
1 AG
38948982 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:38950617 original size:18 final size:19
Alignment explanation
Indices: 38950594--38950630 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
38950584 TTTATCTCAA
*
38950594 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
38950612 TTTCTTGTTCACACTCTTT
1 TTTCTTGTTCACACTCTTT
38950631 CTCTCTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.08, C:0.27, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:38950671 original size:18 final size:18
Alignment explanation
Indices: 38950650--38950699 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
38950640 AAACTCTTTT
38950650 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
38950668 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
38950686 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
38950700 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:38950705 original size:24 final size:24
Alignment explanation
Indices: 38950626--38950702 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
38950616 TTGTTCACAC
*
38950626 TCTTTCTCTCTCTCAAACTCTTTT
1 TCTTTCTCTCTCTCAATCTCTTTT
* * * *
38950650 TCATTCTCTTTTTCAATCTCATTT
1 TCTTTCTCTCTCTCAATCTCTTTT
* *
38950674 TCTTTTTCACTCTCAATCTCTTTT
1 TCTTTCTCTCTCTCAATCTCTTTT
38950698 TCTTT
1 TCTTT
38950703 TTCTTTCATT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.13, C:0.29, G:0.00, T:0.58
Consensus pattern (24 bp):
TCTTTCTCTCTCTCAATCTCTTTT
Found at i:38951730 original size:24 final size:25
Alignment explanation
Indices: 38951697--38951748 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
38951687 TCAGATTTTG
*
38951697 TTTTTTTTTTGAATTTTTTTT-AAAC
1 TTTTTTTTTCG-ATTTTTTTTGAAAC
38951722 TTTTTTTTTCGATTTTTTTTGAAAC
1 TTTTTTTTTCGATTTTTTTTGAAAC
38951747 TT
1 TT
38951749 ACTTGATGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTTTTTTTTCGATTTTTTTTGAAAC
Found at i:38952947 original size:14 final size:14
Alignment explanation
Indices: 38952904--38952949 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
38952894 ATTAAAGAAG
38952904 AAACTCATTAAATT
1 AAACTCATTAAATT
* *
38952918 AAATTCATCAAA-T
1 AAACTCATTAAATT
*
38952931 AAACTCATTTAATT
1 AAACTCATTAAATT
38952945 AAACT
1 AAACT
38952950 AAGATGAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (14 bp):
AAACTCATTAAATT
Done.