Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008674.1 Hibiscus syriacus cultivar Beakdansim tig00111689_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 899125
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:257915 original size:23 final size:23
Alignment explanation
Indices: 257887--257941 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
257877 GTCGTTTAAC
*
257887 ATTCATTTAGTGTTCACGAACAT
1 ATTCATTTAGCGTTCACGAACAT
* *
257910 GTTCATTTAGCGTTCACGAACTT
1 ATTCATTTAGCGTTCACGAACAT
257933 ATTCATTTA
1 ATTCATTTA
257942 TATATTCAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (23 bp):
ATTCATTTAGCGTTCACGAACAT
Found at i:258499 original size:23 final size:23
Alignment explanation
Indices: 258454--258499 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
258444 TTTCCAATAG
* *
258454 AAAATACATATATTTTTTATAAA
1 AAAAAACATATATATTTTATAAA
258477 AAAAAACATATGATATTTT-TAAA
1 AAAAAACATAT-ATATTTTATAAA
258500 TTTTTATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (23 bp):
AAAAAACATATATATTTTATAAA
Found at i:261832 original size:3 final size:3
Alignment explanation
Indices: 261826--261855 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
261816 CGATGACGAC
*
261826 GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
261856 TGAAAGGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:273251 original size:16 final size:17
Alignment explanation
Indices: 273220--273253 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
273210 TCATATTACA
273220 TTAATATTACTATATTTT
1 TTAATATTA-TATATTTT
273238 TTAATATT-TATATTTT
1 TTAATATTATATATTTT
273254 AATTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAATATTATATATTTT
Found at i:273294 original size:27 final size:26
Alignment explanation
Indices: 273235--273294 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
273225 ATTACTATAT
*
273235 TTTTTAATATTTATATTTTAATTTAA
1 TTTTTAATAATTATATTTTAATTTAA
* * *
273261 TTATTTAATAATTATTTGTTTATTTTTA
1 TT-TTTAATAATTATAT-TTTAATTTAA
273289 TTTTTA
1 TTTTTA
273295 GAAATTTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.07
27 16 0.57
28 10 0.36
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTTTAATAATTATATTTTAATTTAA
Found at i:277168 original size:103 final size:103
Alignment explanation
Indices: 276975--277183 Score: 346
Period size: 104 Copynumber: 2.0 Consensus size: 103
276965 GTTTGAAAGC
276975 AATGGCGGTGCCAATAGACATCATTAAAATATGATTTTATCGTATCCCGATCAACAAGTTAACAT
1 AATGGCGGTGCCAATAGACATCATTAAAATATGATTTTATCGTATCCCGATCAACAAGTTAACAT
* *
277040 CCAATTCAGGTGATCATTAATTTTTTAACGGAAAAGAT
66 CCAATTCAGGTGATCATTAATTTTTTAACGAAAAAAAT
* * * *
277078 AATGGCGGTGCCAATAGACATCATTAAAATATGATTTTTCTCGTATCCTGATCAATAAGTTAACG
1 AATGGCGGTGCCAATAGACATCATTAAAATATGA-TTTTATCGTATCCCGATCAACAAGTTAACA
*
277143 TTCAATTCAGGTGATCATTAATTTTTTAACGAAAAAAAT
65 TCCAATTCAGGTGATCATTAATTTTTTAACGAAAAAAAT
277182 AA
1 AA
277184 GTTTAGAACA
Statistics
Matches: 98, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
103 34 0.35
104 64 0.65
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (103 bp):
AATGGCGGTGCCAATAGACATCATTAAAATATGATTTTATCGTATCCCGATCAACAAGTTAACAT
CCAATTCAGGTGATCATTAATTTTTTAACGAAAAAAAT
Found at i:281676 original size:36 final size:36
Alignment explanation
Indices: 281608--281749 Score: 196
Period size: 36 Copynumber: 4.0 Consensus size: 36
281598 TGAATAAGAA
* * * *
281608 GAACGAAAGGTAGCATCGACACGTTCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
* * *
281644 GAACAGAAGGAATCATCGGCACTTTCGGTTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
*
281680 GAACGGAAGGAAGCATCGGCACTTTCAATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
*
281716 GAACGGAAGGAGGCATC-GCACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGT
281750 GTTCATCTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 16 0.17
36 77 0.83
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
Found at i:285696 original size:36 final size:36
Alignment explanation
Indices: 285633--285701 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
285623 TTTAATAAAT
** * *
285633 TTTTAATTTTTAATAATCATATCAATTTGATCTTTA
1 TTTTAATTTGAAATAATCATATAAATTTAATCTTTA
285669 TTTTAATTTGAAATAATTCA-ATAAATTTAATCT
1 TTTTAATTTGAAATAA-TCATATAAATTTAATCT
285702 AACGATACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 25 0.89
37 3 0.11
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (36 bp):
TTTTAATTTGAAATAATCATATAAATTTAATCTTTA
Found at i:285748 original size:30 final size:32
Alignment explanation
Indices: 285690--285748 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 32
285680 AATAATTCAA
*
285690 TAAATTTAATCTAACGATACAAAATTAGGGAT
1 TAAATTTAATCTAAAGATACAAAATTAGGGAT
* *
285722 TAAATTTGAT-TAAAGA-ACAAATTTAGG
1 TAAATTTAATCTAAAGATACAAAATTAGG
285749 TGTAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.42
31 5 0.21
32 9 0.38
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (32 bp):
TAAATTTAATCTAAAGATACAAAATTAGGGAT
Found at i:286912 original size:15 final size:15
Alignment explanation
Indices: 286892--286921 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
286882 TTCTCAATAT
286892 TTTTTTGATTTTTAA
1 TTTTTTGATTTTTAA
*
286907 TTTTTTGGTTTTTAA
1 TTTTTTGATTTTTAA
286922 AAAGGGATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (15 bp):
TTTTTTGATTTTTAA
Found at i:295347 original size:14 final size:14
Alignment explanation
Indices: 295324--295361 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
295314 TCTGTCTATA
*
295324 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
295337 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
295352 TGCAGGGATT
1 TGCAGGGATT
295362 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:298137 original size:2 final size:2
Alignment explanation
Indices: 298125--298186 Score: 69
Period size: 2 Copynumber: 32.5 Consensus size: 2
298115 TTTTTGTCAC
* *
298125 CT CT CT TT CT CT CT -T CT TT C- CT CT CT -T CT -T ACT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT CT CT CT
298164 CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT C
298187 ATTCCACTCG
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
1 4 0.08
2 46 0.90
3 1 0.02
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:300056 original size:29 final size:29
Alignment explanation
Indices: 300023--300091 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
300013 CCTCGCATTA
* *
300023 TACAAAACGTGTTTAAATACATCACTTTT
1 TACAAAACGCGTTTAAATACATCACTTTC
300052 TACAAAACGCGTTTAAATACATCACTTTC
1 TACAAAACGCGTTTAAATACATCACTTTC
300081 TACAAAACGCG
1 TACAAAACGCG
300092 AGACTCATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (29 bp):
TACAAAACGCGTTTAAATACATCACTTTC
Found at i:304404 original size:89 final size:89
Alignment explanation
Indices: 304246--304423 Score: 302
Period size: 89 Copynumber: 2.0 Consensus size: 89
304236 TGTTGAGTCA
* * *
304246 TCTGACTATTAAAAGTTACAAAATAGTTCATCAACTATAGGTTCTGCTTTGTTGAGCTCTTCTAT
1 TCTGACTATTAAAAGTTACAAAATAGTCCATCAACTATAGGTTCTGCTTTGTTGAGCTCTTCGAC
304311 TATTAAAAATTACAAAATGGTGAC
66 TATTAAAAATTACAAAATGGTGAC
* * *
304335 TCTGACTATTAAAAGTTACAAAATAGTCCATCGACTGTAGGTTCTGCTTTGTTGAGTTCTTCGAC
1 TCTGACTATTAAAAGTTACAAAATAGTCCATCAACTATAGGTTCTGCTTTGTTGAGCTCTTCGAC
304400 TATTAAAAATTACAAAATGGTGAC
66 TATTAAAAATTACAAAATGGTGAC
304424 CCAACTATTC
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (89 bp):
TCTGACTATTAAAAGTTACAAAATAGTCCATCAACTATAGGTTCTGCTTTGTTGAGCTCTTCGAC
TATTAAAAATTACAAAATGGTGAC
Found at i:308948 original size:59 final size:59
Alignment explanation
Indices: 308867--309016 Score: 162
Period size: 59 Copynumber: 2.5 Consensus size: 59
308857 ACTTAATCCT
**
308867 TAAACTTTTGAATATT-TCAATTTTGTCTCAAAACTATGA-CTCTCATTCTAAATTAGT-CC
1 TAAACTTTTGAATATTCT-AATTTCATCTCAAAACTATGACCTCTC--TCTAAATTAGTCCC
* * * * *
308926 TAAACTTATGAACATTCTAATTTCATCTCTAGACTATGACCTCTCTCTAAATTGGTCCC
1 TAAACTTTTGAATATTCTAATTTCATCTCAAAACTATGACCTCTCTCTAAATTAGTCCC
* * *
308985 CAAACTTTTGAATATTCCAATTTCATCCCAAA
1 TAAACTTTTGAATATTCTAATTTCATCTCAAA
309017 TTCATCCAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
58 10 0.14
59 58 0.78
60 6 0.08
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (59 bp):
TAAACTTTTGAATATTCTAATTTCATCTCAAAACTATGACCTCTCTCTAAATTAGTCCC
Found at i:313208 original size:2 final size:2
Alignment explanation
Indices: 313201--313251 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
313191 TGATAATAGG
313201 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
313242 TA TA TA TA TA
1 TA TA TA TA TA
313252 GTTTGTATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:320520 original size:24 final size:24
Alignment explanation
Indices: 320495--320558 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
320485 TTTTATCGTA
*
320495 TTTAAGTTTTAGAATAGTTTTATAT
1 TTTAAATTTTA-AATAGTTTTATAT
* *
320520 TTTAAATTTTAAATATTTTTATTT
1 TTTAAATTTTAAATAGTTTTATAT
*
320544 TTTAAAATTTAAATA
1 TTTAAATTTTAAATA
320559 TGCCTCTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
24 25 0.71
25 10 0.29
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (24 bp):
TTTAAATTTTAAATAGTTTTATAT
Found at i:321343 original size:36 final size:37
Alignment explanation
Indices: 321268--321343 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
321258 TTTTTATATT
* *
321268 TTTAATTTTGTAAAAAAATTTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATATATATAAATATTATCAA
* *
321305 TTTAATTTTTTAAAGAAAATATATA-AAATTTTA-CAA
1 TTTAATTTTGTAAA-AAAATATATATAAATATTATCAA
321341 TTT
1 TTT
321344 GTAATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 5 0.15
37 20 0.59
38 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAATATATATAAATATTATCAA
Found at i:327933 original size:16 final size:17
Alignment explanation
Indices: 327883--327934 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
327873 AAAAAAATTA
327883 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
327900 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
327915 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
327931 AATT
1 AATT
327935 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:328837 original size:24 final size:24
Alignment explanation
Indices: 328810--328885 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
328800 TATATCAAAA
*
328810 ATCAAAACATAAAT-CAGGTCAATT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
328834 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
328858 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
328882 ATCA
1 ATCA
328886 GATCAGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.09
24 41 0.91
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:328886 original size:24 final size:24
Alignment explanation
Indices: 328827--328946 Score: 143
Period size: 24 Copynumber: 5.0 Consensus size: 24
328817 CATAAATCAG
* * * *
328827 GTCAATTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAA
328851 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
* *
328875 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAA
* * *
328899 GTC-AGATATCATATCATAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
328923 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
328947 ATCGAAAATC
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.02
24 78 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:330044 original size:42 final size:40
Alignment explanation
Indices: 329985--330062 Score: 120
Period size: 42 Copynumber: 1.9 Consensus size: 40
329975 CGGTATTTCA
* *
329985 ATCTTTTTCCTCTATCCGGTCTTATTATTTAATTCAATTTAT
1 ATCTTTTTCCTCCATCCGATCTTA-T-TTTAATTCAATTTAT
330027 ATCTTTTTCCTCCATCCGATCTTATTTTAATTCAAT
1 ATCTTTTTCCTCCATCCGATCTTATTTTAATTCAAT
330063 CTCATCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 11 0.32
41 1 0.03
42 22 0.65
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.53
Consensus pattern (40 bp):
ATCTTTTTCCTCCATCCGATCTTATTTTAATTCAATTTAT
Found at i:331378 original size:7 final size:7
Alignment explanation
Indices: 331366--331397 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
331356 TGGTCAACGC
331366 CGGTCAA
1 CGGTCAA
331373 CGGTCAA
1 CGGTCAA
331380 CGGGTCAA
1 C-GGTCAA
331388 CGGTCAA
1 CGGTCAA
331395 CGG
1 CGG
331398 GTCGAGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:331387 original size:15 final size:15
Alignment explanation
Indices: 331357--331413 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
331347 GGTCAACAGT
331357 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
331374 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
*
331389 GGTCAACGGGTCGA-
1 GGTCAACGGGTCAAC
331403 -GTCAACGGGTC
1 GGTCAACGGGTC
331414 GGGTCGGGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
13 11 0.28
15 20 0.51
17 8 0.21
ACGTcount: A:0.23, C:0.28, G:0.35, T:0.14
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:331408 original size:13 final size:14
Alignment explanation
Indices: 331375--331414 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
331365 CCGGTCAACG
*
331375 GTCAACGGGTCAAC
1 GTCAACGGGTCGAC
331389 GGTCAACGGGTCGA-
1 -GTCAACGGGTCGAC
331403 GTCAACGGGTCG
1 GTCAACGGGTCG
331415 GGTCGGGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
15 12 0.50
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.15
Consensus pattern (14 bp):
GTCAACGGGTCGAC
Found at i:332458 original size:65 final size:66
Alignment explanation
Indices: 332384--332513 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 66
332374 CTACAGAAAA
*
332384 AAAGAAGCTTTATTTAATAATTACATTTTATTTACAGTTTCATCA-TTTTTTAATCCTAATTTCA
1 AAAGAAGCTTTATTTAATAATTACATTTTATTTAAAGTTTCATCATTTTTTTAATCCTAATTTCA
332448 G
66 G
*
332449 AAAGAAGCTTTATTTAATAGTTACATTTTATTTAAAGTTTCATCATTTTTTTAATCCTAATTTCA
1 AAAGAAGCTTTATTTAATAATTACATTTTATTTAAAGTTTCATCATTTTTTTAATCCTAATTTCA
332514 AATTTAACAC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 43 0.69
66 19 0.31
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (66 bp):
AAAGAAGCTTTATTTAATAATTACATTTTATTTAAAGTTTCATCATTTTTTTAATCCTAATTTCA
G
Found at i:334564 original size:15 final size:15
Alignment explanation
Indices: 334518--334583 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 15
334508 CAACTCCATT
334518 TTCC-TTTCTCTCTTC
1 TTCCTTTTCT-TCTTC
* * * *
334533 TTCATTCTGTTCCTC
1 TTCCTTTTCTTCTTC
334548 TTCCTTTTCTTCTTC
1 TTCCTTTTCTTCTTC
334563 TTCCTCTCTTTCTTCTTC
1 TT-C-CT-TTTCTTCTTC
334581 TTC
1 TTC
334584 ATCTTCCTCA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
15 20 0.51
16 4 0.10
17 3 0.08
18 12 0.31
ACGTcount: A:0.02, C:0.36, G:0.02, T:0.61
Consensus pattern (15 bp):
TTCCTTTTCTTCTTC
Found at i:337208 original size:12 final size:12
Alignment explanation
Indices: 337191--337280 Score: 71
Period size: 12 Copynumber: 7.4 Consensus size: 12
337181 TTTCAATGCA
337191 TCTTCAGCCTTC-
1 TCTTCA-CCTTCT
*
337203 TCTTCATCTTCT
1 TCTTCACCTTCT
*
337215 TCTTTCAAC-TCT
1 TC-TTCACCTTCT
337227 TCTTCAGCCTTCT
1 TCTTCA-CCTTCT
*
337240 TCTTCATCTTCT
1 TCTTCACCTTCT
*
337252 TCTTTCAAC-TCT
1 TC-TTCACCTTCT
337264 TCTTCAGCCTTC-
1 TCTTCA-CCTTCT
337276 TCTTC
1 TCTTC
337281 TTGTTCCTCT
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
11 12 0.18
12 32 0.49
13 21 0.32
ACGTcount: A:0.10, C:0.37, G:0.03, T:0.50
Consensus pattern (12 bp):
TCTTCACCTTCT
Found at i:337210 original size:18 final size:19
Alignment explanation
Indices: 337189--337280 Score: 57
Period size: 18 Copynumber: 5.1 Consensus size: 19
337179 CCTTTCAATG
337189 CATCTTCAGCCTTC-TCTT
1 CATCTTCAGCCTTCATCTT
** * *
337207 CATCTTCTTCTTTCAAC-T
1 CATCTTCAGCCTTCATCTT
* *
337225 CTTCTTCAGCCTTCTTCTT
1 CATCTTCAGCCTTCATCTT
** * *
337244 CATCTTCTTCTTTCAAC-T
1 CATCTTCAGCCTTCATCTT
*
337262 CTTCTTCAGCCTTC-TCTT
1 CATCTTCAGCCTTCATCTT
337280 C
1 C
337281 TTGTTCCTCT
Statistics
Matches: 50, Mismatches: 21, Indels: 6
0.65 0.27 0.08
Matches are distributed among these distances:
17 1 0.02
18 36 0.72
19 13 0.26
ACGTcount: A:0.11, C:0.37, G:0.03, T:0.49
Consensus pattern (19 bp):
CATCTTCAGCCTTCATCTT
Found at i:337253 original size:37 final size:36
Alignment explanation
Indices: 337166--337280 Score: 187
Period size: 36 Copynumber: 3.2 Consensus size: 36
337156 CTCCTTGTTC
* *
337166 CTCTTCATCTTCTCCTTTCAA-TGCATCTTCAGCCTT
1 CTCTTCATCTTCTTCTTTCAACT-CTTCTTCAGCCTT
337202 CTCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTT
1 CTCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTT
337238 CTTCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTT
1 C-TCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTT
337275 CTCTTC
1 CTCTTC
337281 TTGTTCCTCT
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
36 38 0.51
37 37 0.49
ACGTcount: A:0.11, C:0.37, G:0.03, T:0.49
Consensus pattern (36 bp):
CTCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTT
Found at i:346490 original size:11 final size:11
Alignment explanation
Indices: 346474--346498 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
346464 TTAATTTGAA
346474 ATTTTTAATTG
1 ATTTTTAATTG
346485 ATTTTTAATTG
1 ATTTTTAATTG
346496 ATT
1 ATT
346499 AATTAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (11 bp):
ATTTTTAATTG
Found at i:346965 original size:75 final size:78
Alignment explanation
Indices: 346875--347028 Score: 278
Period size: 79 Copynumber: 2.0 Consensus size: 78
346865 AAAATAAAAA
346875 ATTACCACGTCAAGTGTGCCGTTAA-TTTTTAAAGA-GAG-ACTAAATTGAAACAAAAATTAAAC
1 ATTACCACGTCAAGTGTGCCGTTAATTTTTTAAAGACGAGAACTAAATTGAAACAAAAATTAAAC
346937 GTTAAGTACGATT
66 GTTAAGTACGATT
346950 ATTACCACGTCAAGTGTGCCGTTAATTTTTTAAAGACGAGATACTAAATTGAAACAAAAATTAAA
1 ATTACCACGTCAAGTGTGCCGTTAATTTTTTAAAGACGAGA-ACTAAATTGAAACAAAAATTAAA
347015 CGTTAAGTACGATT
65 CGTTAAGTACGATT
347029 TTAAAATAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
75 25 0.33
76 10 0.13
77 3 0.04
79 37 0.49
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (78 bp):
ATTACCACGTCAAGTGTGCCGTTAATTTTTTAAAGACGAGAACTAAATTGAAACAAAAATTAAAC
GTTAAGTACGATT
Found at i:350078 original size:29 final size:30
Alignment explanation
Indices: 350023--350083 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
350013 CATTTTGAGT
* *
350023 AACGGAATGAAATGTTAGGCATCAAACTGG
1 AACGAAATGAAATGTTAGACATCAAACTGG
350053 AACGAAAT-AAATGTTAGACA-CTAAACTGG
1 AACGAAATGAAATGTTAGACATC-AAACTGG
350082 AA
1 AA
350084 AAACGAGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 1 0.04
29 20 0.71
30 7 0.25
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (30 bp):
AACGAAATGAAATGTTAGACATCAAACTGG
Found at i:350599 original size:23 final size:23
Alignment explanation
Indices: 350552--350600 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
350542 TTTAGCTTCC
* * * *
350552 AAATGAACATGTTTGTGAGCGTT
1 AAATAAACATGTTTGCGAACATT
350575 AAATAAACATGTTTGCGAACATT
1 AAATAAACATGTTTGCGAACATT
350598 AAA
1 AAA
350601 CGAACATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (23 bp):
AAATAAACATGTTTGCGAACATT
Found at i:350606 original size:23 final size:23
Alignment explanation
Indices: 350556--350607 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
350546 GCTTCCAAAT
* * * *
350556 GAACATGTTTGTGAGCGTTAAAT
1 GAACATGTTTGCGAACATTAAAC
*
350579 AAACATGTTTGCGAACATTAAAC
1 GAACATGTTTGCGAACATTAAAC
350602 GAACAT
1 GAACAT
350608 ATTCGTTAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (23 bp):
GAACATGTTTGCGAACATTAAAC
Found at i:362622 original size:45 final size:45
Alignment explanation
Indices: 362570--362660 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
362560 ATTTAAAATA
362570 AATGTTGATCGGTCATTATTTTTAAAAAACATCATTTATTTACTC
1 AATGTTGATCGGTCATTATTTTTAAAAAACATCATTTATTTACTC
*
362615 AATGTTGATCGGTCATTATTTTTTAAAAACATCATTTATTTACTC
1 AATGTTGATCGGTCATTATTTTTAAAAAACATCATTTATTTACTC
362660 A
1 A
362661 TTTAATTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (45 bp):
AATGTTGATCGGTCATTATTTTTAAAAAACATCATTTATTTACTC
Found at i:364241 original size:90 final size:90
Alignment explanation
Indices: 364088--364266 Score: 277
Period size: 90 Copynumber: 2.0 Consensus size: 90
364078 TATTTATAAC
* * *
364088 AACTTAGTCATAGGGGCTACAATCATCGAAAAATTCTTGACAAACAGACGATAAAATTCATCATT
1 AACTTAGTCATAAGGGCTACAATCATCGAAAAACTCTTGACAAACAGACGATAAAAGTCATCATT
* * *
364153 TTGATATTTGAATCATTTTTGTTAT
66 ATGATATTAGAATCATGTTTGTTAT
* * *
364178 AACTTAGTCATAAGGGTTACAATCATTGAAAAACTCTTGATAAACAGACGATAAAAGTCATCATT
1 AACTTAGTCATAAGGGCTACAATCATCGAAAAACTCTTGACAAACAGACGATAAAAGTCATCATT
364243 ATGATATTAGAATCATGTTTGTTA
66 ATGATATTAGAATCATGTTTGTTA
364267 CCTTTTATTA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (90 bp):
AACTTAGTCATAAGGGCTACAATCATCGAAAAACTCTTGACAAACAGACGATAAAAGTCATCATT
ATGATATTAGAATCATGTTTGTTAT
Found at i:372057 original size:25 final size:26
Alignment explanation
Indices: 372029--372081 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
372019 AGGTTTAAGG
* *
372029 TTTGATTGTGATTT-TAGGTTATGGT
1 TTTGATTGAGATTTATAGGTTAGGGT
*
372054 TTTGATTGAGATTTATAGTTTAGGGT
1 TTTGATTGAGATTTATAGGTTAGGGT
372080 TT
1 TT
372082 AGTTGAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (26 bp):
TTTGATTGAGATTTATAGGTTAGGGT
Found at i:374980 original size:33 final size:30
Alignment explanation
Indices: 374911--374967 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
374901 TTTGGTGATC
374911 TTGGGGCAGCTGCAGTACCATTTGGAGTAG
1 TTGGGGCAGCTGCAGTACCATTTGGAGTAG
374941 TTGGGGCAGCTGCAGTACCATTTGGAG
1 TTGGGGCAGCTGCAGTACCATTTGGAG
374968 AAGTAGTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.19, C:0.18, G:0.37, T:0.26
Consensus pattern (30 bp):
TTGGGGCAGCTGCAGTACCATTTGGAGTAG
Found at i:388233 original size:20 final size:20
Alignment explanation
Indices: 388196--388233 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
388186 GAAGATAATA
*
388196 TAATTTGAATTTATATATAT
1 TAATTTGAAATTATATATAT
388216 TAATTTGTAAATTA-ATAT
1 TAATTTG-AAATTATATAT
388234 TCTCTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
TAATTTGAAATTATATATAT
Found at i:389267 original size:52 final size:52
Alignment explanation
Indices: 389170--389282 Score: 147
Period size: 52 Copynumber: 2.2 Consensus size: 52
389160 CTTTCATTTT
* * * *
389170 AAGCTCAAAAGTCCCTTTTTTATCTCCAATTAGATAAAATTCTTACTTGATT
1 AAGCTCAAAAGTCCCTTTTTTATCTCCAATTAGACAAAATCCTTACCTGATC
* * *
389222 ACGCTCAAAAGT-CCTATTTTTATCTCCAATTATACCAAATCCTTACCTGATC
1 AAGCTCAAAAGTCCCT-TTTTTATCTCCAATTAGACAAAATCCTTACCTGATC
389274 AAGCTCAAA
1 AAGCTCAAA
389283 TTCAACCCAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
51 3 0.06
52 49 0.94
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.35
Consensus pattern (52 bp):
AAGCTCAAAAGTCCCTTTTTTATCTCCAATTAGACAAAATCCTTACCTGATC
Found at i:390123 original size:16 final size:15
Alignment explanation
Indices: 390094--390153 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
390084 TTAAAAAAAA
**
390094 TTAAATTTTCATATAT
1 TTAAATTTAAATAT-T
390110 TTAAATTTAAATATT
1 TTAAATTTAAATATT
* *
390125 TTTAATTTAGATATT
1 TTAAATTTAAATATT
*
390140 TAAAATTATAAATA
1 TTAAATT-TAAATA
390154 ATTAAAATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 19 0.53
16 17 0.47
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
TTAAATTTAAATATT
Found at i:390146 original size:15 final size:15
Alignment explanation
Indices: 390106--390161 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
390096 AAATTTTCAT
390106 ATATTT-AAATTTAA
1 ATATTTAAAATTTAA
** *
390120 ATATTTTTAATTTAG
1 ATATTTAAAATTTAA
390135 ATATTTAAAATTATAA
1 ATATTTAAAATT-TAA
*
390151 ATAATTAAAAT
1 ATATTTAAAAT
390162 ATTATATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 6 0.18
15 16 0.47
16 12 0.35
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
ATATTTAAAATTTAA
Found at i:394609 original size:60 final size:60
Alignment explanation
Indices: 394535--394649 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
394525 ATTATAAGGT
* * *
394535 ATTATTTTGTTGAGTCCATCGACTATTAAAAATTACAAAATAGTCTCCTAACTATAGGAC
1 ATTACTTTATTGAGTCCATCGACTATTAAAAATTACAAAATAGTCACCTAACTATAGGAC
* * *
394595 ATTACTTTATTGAGTCCCTCGATTATTAAAAATTACAAAATAGTCACCTGACTAT
1 ATTACTTTATTGAGTCCATCGACTATTAAAAATTACAAAATAGTCACCTAACTAT
394650 TCATATTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (60 bp):
ATTACTTTATTGAGTCCATCGACTATTAAAAATTACAAAATAGTCACCTAACTATAGGAC
Found at i:394650 original size:29 final size:28
Alignment explanation
Indices: 394555--394650 Score: 68
Period size: 29 Copynumber: 3.2 Consensus size: 28
394545 TGAGTCCATC
394555 GACTATTAAAAATTACAAAATAGTCTCCT
1 GACTATTAAAAATTACAAAATAGTC-CCT
* * * ** *
394584 AACTA-TAGGACATTACTTTATTGAGTCCCT
1 GACTATTA-AAAATTAC-AAAAT-AGTCCCT
*
394614 CGATTATTAAAAATTACAAAATAGTCACCT
1 -GACTATTAAAAATTACAAAATAGTC-CCT
394644 GACTATT
1 GACTATT
394651 CATATTAATA
Statistics
Matches: 47, Mismatches: 14, Indels: 12
0.64 0.19 0.16
Matches are distributed among these distances:
28 2 0.04
29 20 0.43
30 10 0.21
31 13 0.28
32 2 0.04
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (28 bp):
GACTATTAAAAATTACAAAATAGTCCCT
Found at i:395351 original size:10 final size:11
Alignment explanation
Indices: 395333--395360 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
395323 AAATATATAA
395333 ATAAAAAAAAC
1 ATAAAAAAAAC
395344 ATAAAAAAAAC
1 ATAAAAAAAAC
395355 ATAAAA
1 ATAAAA
395361 CTAATAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (11 bp):
ATAAAAAAAAC
Found at i:405834 original size:22 final size:22
Alignment explanation
Indices: 405809--405856 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
405799 GAGCGCGACC
405809 AAAATAAATGAGTGATAAAAAT
1 AAAATAAATGAGTGATAAAAAT
*
405831 AAAATAAGTGAGTGATAAAAAT
1 AAAATAAATGAGTGATAAAAAT
405853 AAAA
1 AAAA
405857 ACTAAATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.21
Consensus pattern (22 bp):
AAAATAAATGAGTGATAAAAAT
Found at i:408683 original size:16 final size:15
Alignment explanation
Indices: 408645--408693 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
408635 ATCATTTTAA
408645 ATATTTTAAACAAT-T
1 ATATTTTAAA-AATAT
*
408660 AAATTTTACAAAATAT
1 ATATTTTA-AAAATAT
408676 ATATTTTAAAAATCAT
1 ATATTTTAAAAAT-AT
408692 AT
1 AT
408694 CTAACGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 15 0.52
16 14 0.48
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTTTAAAAATAT
Found at i:409084 original size:15 final size:15
Alignment explanation
Indices: 409066--409099 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
409056 TTCTAGTCTA
409066 TAAAATAT-TTAATT
1 TAAAATATATTAATT
*
409080 TTAAATATATTAATT
1 TAAAATATATTAATT
409095 TAAAA
1 TAAAA
409100 AACTAAATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAATATATTAATT
Found at i:409582 original size:33 final size:33
Alignment explanation
Indices: 409540--409605 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
409530 TTCGCGTTTC
409540 TGCCACTCGAAGAGTATTGAACTGTTGACGGAT
1 TGCCACTCGAAGAGTATTGAACTGTTGACGGAT
409573 TGCCACTCGAAGAGTATTGAACTGTTGACGGAT
1 TGCCACTCGAAGAGTATTGAACTGTTGACGGAT
409606 AGCTTGTCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (33 bp):
TGCCACTCGAAGAGTATTGAACTGTTGACGGAT
Found at i:420592 original size:22 final size:22
Alignment explanation
Indices: 420567--420609 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
420557 GTGAGAGTGA
* *
420567 GAGAAGCTGATAATACAGAGAC
1 GAGAAGCGGAAAATACAGAGAC
*
420589 GAGAAGCGGAAAATGCAGAGA
1 GAGAAGCGGAAAATACAGAGA
420610 GAATGGGACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.33, T:0.09
Consensus pattern (22 bp):
GAGAAGCGGAAAATACAGAGAC
Found at i:423181 original size:60 final size:60
Alignment explanation
Indices: 423086--423200 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
423076 GTATATACAT
* * * *
423086 ATAGTTTGGGATGAAATTGGAATATTCAAAAAGTTTTAGGACAAATTTAGAATGAAAGTC
1 ATAGTTTGGAATGAAATTGAAATATTCAAAAAGTTTGAAGACAAATTTAGAATGAAAGTC
* *
423146 ATAGTTTGAGAATGAAATTGAAATGTTC-AAAAGTTTGAAGACTAATTTAGAATGA
1 ATAGTTTG-GAATGAAATTGAAATATTCAAAAAGTTTGAAGACAAATTTAGAATGA
423201 TAACAGAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 32 0.67
61 16 0.33
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (60 bp):
ATAGTTTGGAATGAAATTGAAATATTCAAAAAGTTTGAAGACAAATTTAGAATGAAAGTC
Found at i:433754 original size:6 final size:6
Alignment explanation
Indices: 433743--433797 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
433733 CCCTGATCGG
433743 GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA
1 GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA
*
433791 ATGAGA G
1 GTGAGA G
433798 GGGTGAAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.35, C:0.00, G:0.49, T:0.16
Consensus pattern (6 bp):
GTGAGA
Found at i:434681 original size:2 final size:2
Alignment explanation
Indices: 434674--434701 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
434664 TATACAATAC
434674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
434702 TATTAATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:441242 original size:29 final size:29
Alignment explanation
Indices: 441200--441305 Score: 203
Period size: 29 Copynumber: 3.7 Consensus size: 29
441190 CTTCCCAGCA
441200 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
441229 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
*
441258 TAGGTCGCCATGCACTCCTGGGGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
441287 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
441306 CCTGCTCCTC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.14, C:0.34, G:0.27, T:0.25
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:441661 original size:2 final size:2
Alignment explanation
Indices: 441654--441692 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
441644 CACATATTGC
441654 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
441693 CTCAAATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:443377 original size:19 final size:20
Alignment explanation
Indices: 443339--443378 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
443329 AAGAGATAAT
*
443339 TTATTTTTTAAATCTATTAA
1 TTATTTTATAAATCTATTAA
*
443359 TTATTTTATAATTCT-TTAA
1 TTATTTTATAAATCTATTAA
443378 T
1 T
443379 CGAAAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTTATAAATCTATTAA
Found at i:445331 original size:33 final size:33
Alignment explanation
Indices: 445289--445353 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
445279 CTTATGAACC
**
445289 CAGAATTTAGCAGAGTTTGTGAGTTTAACTCAA
1 CAGAATTTAGCAGAGTTTGTGAGAGTAACTCAA
445322 CAGAATTTAGCAGAGTTTGTGAGAGTAACTCA
1 CAGAATTTAGCAGAGTTTGTGAGAGTAACTCA
445354 GTTTATGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (33 bp):
CAGAATTTAGCAGAGTTTGTGAGAGTAACTCAA
Found at i:451457 original size:49 final size:49
Alignment explanation
Indices: 451385--451562 Score: 304
Period size: 49 Copynumber: 3.6 Consensus size: 49
451375 GGTTACGGTG
*
451385 GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCGATGACTGTTAAATTA
1 GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCGATGACTGTTAAATCA
451434 GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCGATGACTGTTAAATCA
1 GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCGATGACTGTTAAATCA
* * *
451483 GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCAACGACGGTT-AATGCA
1 GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCGATGACTGTTAAAT-CA
451532 GAGACAACATCAAAAGGTAGGCTTGTTTGTG
1 GAGACAACATCAAAAGGTAGGCTTGTTTGTG
451563 TTGACGATGG
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
48 3 0.02
49 121 0.98
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (49 bp):
GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCGATGACTGTTAAATCA
Found at i:451585 original size:49 final size:49
Alignment explanation
Indices: 451385--451590 Score: 288
Period size: 49 Copynumber: 4.2 Consensus size: 49
451375 GGTTACGGTG
* **
451385 GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCGATGACTGTTAAATTA
1 GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCGACGACTGTTAAAGCA
* *
451434 GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCGATGACTGTTAAATCA
1 GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCGACGACTGTTAAAGCA
* * *
451483 GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCAACGACGGTTAATGCA
1 GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCGACGACTGTTAAAGCA
** * *
451532 GAGACAACATCAAAAGGTAGGCTTGTTTGTGTTGACGA-TGGTTAACGCC
1 GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCGACGACT-GTTAAAGCA
451581 GAGACAACAT
1 GAGACAACAT
451591 TAGTCTTGAT
Statistics
Matches: 144, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
49 144 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (49 bp):
GAGACAACATCAAAAGGTAGGCTTGTTTGTGCCGACGACTGTTAAAGCA
Found at i:455236 original size:16 final size:16
Alignment explanation
Indices: 455215--455249 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
455205 GGTATTACCC
455215 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
455231 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
455247 GAC
1 GAC
455250 TTATTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.37
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:455256 original size:16 final size:16
Alignment explanation
Indices: 455215--455264 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
455205 GGTATTACCC
* *
455215 GACCTGTTTTCAACCT
1 GACCTATTTTTAACCT
*
455231 GACCTGTTTTTAACCT
1 GACCTATTTTTAACCT
* *
455247 GACTTATTTTTAGCCT
1 GACCTATTTTTAACCT
455263 GA
1 GA
455265 ACTGTAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (16 bp):
GACCTATTTTTAACCT
Found at i:455564 original size:23 final size:24
Alignment explanation
Indices: 455526--455575 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
455516 TGCAAAAGGA
455526 AAATTAATATAATTTAATTTATAT
1 AAATTAATATAATTTAATTTATAT
*
455550 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAATTTAATTTATAT
455573 AAA
1 AAA
455576 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
AAATTAATATAATTTAATTTATAT
Found at i:456581 original size:233 final size:235
Alignment explanation
Indices: 456170--456616 Score: 609
Period size: 233 Copynumber: 1.9 Consensus size: 235
456160 GAAGGTAGAT
** ** *
456170 TTTCTGCATTAAACAAACATTTAATCAGTGGTAAAGCCAAAGGGAATACGATGGCTAACAGTGCC
1 TTTCTGCATTAAACAAACATGCAATCAGCAGTAAAACCAAAGGGAATACGATGGCTAACAGTGCC
* * *
456235 AAACATTTTCGACTTTATCAAACCCTTACATAATAAAACATTCAACATTGTTTATGAAAATAAAA
66 AAACATTTTCAACTTTACCAAACCCTTACATAATAAAACATTCAACATTGTTTATGAAAACAAAA
* * *
456300 TTAATATCAGGGAAAATCAGAACGTGATACTTTAGACAGAAGCATCCTAC-AAAAA-AAAAACAT
131 TTAATATCAAGCAAAATCAGAACGTGATACTTTAGACAGAAACATCCTACAAAAAACAAAAACAT
*
456363 CAATTAAAATTTGTTTCAGATAAACATAATAAACACAATA
196 CAATAAAAATTTGTTTCAGATAAACATAATAAACACAATA
*
456403 TTTCTGCATTAAACAAACATGCAGTCAGCAGTAAAACCAAAGGGAATACGATGGGC-AACAGTGC
1 TTTCTGCATTAAACAAACATGCAATCAGCAGTAAAACCAAAGGGAATACGAT-GGCTAACAGTGC
* * * * *
456467 CAAATATTTTCAATTTTACCAAACCCTTACATAATTAAGCATTTAACATTGTTTAT-AATAACAG
65 CAAACATTTTCAACTTTACCAAACCCTTACATAATAAAACATTCAACATTGTTTATGAA-AACA-
* * * * *
456531 AAA-TAATATCAAGCAAAATGAGGATGTGTTACTTTGGACTA-AAACATCCTACAAAAAACAAAA
128 AAATTAATATCAAGCAAAATCAGAACGTGATACTTTAGAC-AGAAACATCCTACAAAAAACAAAA
456594 ACATCAATAAAAATTTGTTTCAG
192 ACATCAATAAAAATTTGTTTCAG
456617 TTACTGTTAA
Statistics
Matches: 185, Mismatches: 23, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
232 2 0.01
233 145 0.78
234 12 0.06
235 26 0.14
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.27
Consensus pattern (235 bp):
TTTCTGCATTAAACAAACATGCAATCAGCAGTAAAACCAAAGGGAATACGATGGCTAACAGTGCC
AAACATTTTCAACTTTACCAAACCCTTACATAATAAAACATTCAACATTGTTTATGAAAACAAAA
TTAATATCAAGCAAAATCAGAACGTGATACTTTAGACAGAAACATCCTACAAAAAACAAAAACAT
CAATAAAAATTTGTTTCAGATAAACATAATAAACACAATA
Found at i:456870 original size:55 final size:55
Alignment explanation
Indices: 456786--456899 Score: 210
Period size: 55 Copynumber: 2.1 Consensus size: 55
456776 GTTTTTGATA
* *
456786 AAATGTATGAGAATTGGTGTGATATATCCATCACCGTATCCAATTAAATTCCCTT
1 AAATGTATGAGAATTGGTGTGATATATCCATCACCATAGCCAATTAAATTCCCTT
456841 AAATGTATGAGAATTGGTGTGATATATCCATCACCATAGCCAATTAAATTCCCTT
1 AAATGTATGAGAATTGGTGTGATATATCCATCACCATAGCCAATTAAATTCCCTT
456896 AAAT
1 AAAT
456900 CTGGTTTTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (55 bp):
AAATGTATGAGAATTGGTGTGATATATCCATCACCATAGCCAATTAAATTCCCTT
Found at i:457573 original size:24 final size:25
Alignment explanation
Indices: 457528--457574 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
457518 TGTAATTAAT
*
457528 ATTAATATAAAATATAATCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
457553 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
457575 TGTTATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:457582 original size:31 final size:30
Alignment explanation
Indices: 457521--457705 Score: 135
Period size: 31 Copynumber: 5.8 Consensus size: 30
457511 TATAATTTGT
* *
457521 AATTAATATTAATATAAAATATAATCTATAA
1 AATTAATATTAATATAAACTATAGT-TATAA
457552 AATTAATATTAATATAAACTATATGTTAT-A
1 AATTAATATTAATATAAACTATA-GTTATAA
* *
457582 AATTATATAATATAGTTTATAAACTATAGTTAATAT
1 AATTA-AT-AT-TA--ATATAAACTATAGTT-ATAA
*
457618 AATTAATATTAATAT--AGTATAGTTTATAA
1 AATTAATATTAATATAAACTATAG-TTATAA
*
457647 ACTATATACTATATTAATATAAA-TCATAGTTAATAT
1 A--AT-TA--ATATTAATATAAACT-ATAGTT-ATAA
*
457683 AATTAACATTAATATAAACTATA
1 AATTAATATTAATATAAACTATA
457706 TAGTACATTA
Statistics
Matches: 126, Mismatches: 9, Indels: 38
0.73 0.05 0.22
Matches are distributed among these distances:
29 10 0.08
30 8 0.06
31 47 0.37
32 6 0.05
33 6 0.05
34 17 0.13
35 18 0.14
36 14 0.11
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (30 bp):
AATTAATATTAATATAAACTATAGTTATAA
Found at i:457601 original size:14 final size:15
Alignment explanation
Indices: 457584--457652 Score: 58
Period size: 14 Copynumber: 4.9 Consensus size: 15
457574 ATGTTATAAA
457584 TTATATAA-TATAGT
1 TTATATAACTATAGT
457598 TTATA-AACTATAGT
1 TTATATAACTATAGT
* *
457612 TAATATAATTAATA-T
1 TTATATAACT-ATAGT
* *
457627 TAATAT-AGTATAGT
1 TTATATAACTATAGT
457641 TTATA-AACTATA
1 TTATATAACTATA
457653 TACTATATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 5 0.11
14 27 0.60
15 10 0.22
16 3 0.07
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (15 bp):
TTATATAACTATAGT
Found at i:457631 original size:15 final size:15
Alignment explanation
Indices: 457611--457699 Score: 54
Period size: 15 Copynumber: 5.6 Consensus size: 15
457601 TAAACTATAG
457611 TTAATATAATTAATA
1 TTAATATAATTAATA
* *
457626 TTAATATAGTATAGTTTA
1 TTAATATAAT-TA--ATA
* *
457644 TAAACTATATACT-ATA
1 TTAA-TATA-ATTAATA
* *
457660 TTAATATAAATCATA
1 TTAATATAATTAATA
*
457675 GTTAATATAATTAACA
1 -TTAATATAATTAATA
457691 TTAATATAA
1 TTAATATAA
457700 ACTATATAGT
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
14 2 0.04
15 25 0.45
16 19 0.34
18 5 0.09
19 5 0.09
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:457641 original size:29 final size:29
Alignment explanation
Indices: 457606--457699 Score: 89
Period size: 34 Copynumber: 3.0 Consensus size: 29
457596 GTTTATAAAC
*
457606 TATAGTTAATATAATTAATATTAATATAG
1 TATAGTTAATATAATTAATATTAATATAA
* *
457635 TATAGTTTATAAACTATATACTATATTAATATAAA
1 TATAGTTAATATA--AT-TA--ATATTAATAT-AA
*
457670 TCATAGTTAATATAATTAACATTAATATAA
1 T-ATAGTTAATATAATTAATATTAATATAA
457700 ACTATATAGT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
29 11 0.21
30 2 0.04
31 11 0.21
32 2 0.04
33 2 0.04
34 12 0.23
35 2 0.04
36 10 0.19
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (29 bp):
TATAGTTAATATAATTAATATTAATATAA
Found at i:457647 original size:43 final size:40
Alignment explanation
Indices: 457586--457676 Score: 119
Period size: 43 Copynumber: 2.2 Consensus size: 40
457576 GTTATAAATT
* *
457586 ATATAATATAGTTTATAAACTATAGTTAATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTATA--TAATAT-ATTAATATAA
*
457629 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
1 ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
457669 ATCATAGT
1 AT-ATAGT
457677 TAATATAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 11 0.25
41 10 0.23
43 23 0.52
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (40 bp):
ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
Found at i:457713 original size:22 final size:22
Alignment explanation
Indices: 457688--457789 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
457678 AATATAATTA
457688 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
457710 ACATTAATATAAAC--TATAGT
1 ACATTAATATAAACTATATAGT
** * * *
457730 TTATAAATTATATACTATA-GGT
1 ACATTAA-TATAAACTATATAGT
* *
457752 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
457774 ACACTAATATAAACTA
1 ACATTAATATAAACTA
457790 CTATTTATAA
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
20 10 0.16
21 22 0.34
22 27 0.42
23 5 0.08
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:457746 original size:21 final size:21
Alignment explanation
Indices: 457717--457769 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
457707 AGTACATTAA
* *
457717 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
457738 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
457759 TATAAACTATA
1 TATAAACTATA
457770 TAGTACACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:457863 original size:24 final size:20
Alignment explanation
Indices: 457812--457904 Score: 72
Period size: 20 Copynumber: 4.7 Consensus size: 20
457802 TATAAGTTAC
457812 ATATATAGTTTATATAACAT
1 ATATATAGTTTATATAACAT
*
457832 ATAAATAGATTGTATATATACAT
1 ATATATAG-TT-TATATA-ACAT
*
457855 ATACTATAGGTTATAT---AT
1 ATA-TATAGTTTATATAACAT
457873 A-A-ATAGTTTATATATAC-T
1 ATATATAGTTTATATA-ACAT
*
457891 ATACATAGTTTATA
1 ATATATAGTTTATA
457905 CATACACATA
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
15 10 0.17
17 1 0.02
18 5 0.08
19 1 0.02
20 17 0.29
21 2 0.03
22 11 0.19
23 8 0.14
24 4 0.07
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (20 bp):
ATATATAGTTTATATAACAT
Found at i:457934 original size:35 final size:36
Alignment explanation
Indices: 457895--457968 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
457885 TATACTATAC
457895 ATAGTTT-ATACATACACATACTATAAGTTACATAT
1 ATAGTTTAATACATACACATACTATAAGTTACATAT
** * *
457930 ATAGTTTACATGTATACATATACTATAGGTTACATAT
1 ATAGTTTA-ATACATACACATACTATAAGTTACATAT
457967 AT
1 AT
457969 TAACTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
37 26 0.79
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (36 bp):
ATAGTTTAATACATACACATACTATAAGTTACATAT
Found at i:457946 original size:57 final size:58
Alignment explanation
Indices: 457800--457957 Score: 189
Period size: 57 Copynumber: 2.7 Consensus size: 58
457790 CTATTTATAA
* * *
457800 ACTATAAGTTACATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATAT
1 ACTATAAGTTACATATATAGTTTATATATACATATACATAGATTGTATACATACACAT
* *
457857 ACTATAGGTTATATATAAATAGTTTATATATAC-TATACATAG-TT-TATACATACACAT
1 ACTATAAGTTACATAT--ATAGTTTATATATACATATACATAGATTGTATACATACACAT
*
457914 ACTATAAGTTACATATATAGTTTACATGTATACATATACTATAG
1 ACTATAAGTTACATATATAGTTT--ATATATACATATAC-ATAG
457958 GTTACATATA
Statistics
Matches: 86, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
55 7 0.08
57 46 0.53
58 7 0.08
59 24 0.28
60 2 0.02
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (58 bp):
ACTATAAGTTACATATATAGTTTATATATACATATACATAGATTGTATACATACACAT
Found at i:458102 original size:15 final size:14
Alignment explanation
Indices: 458075--458108 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
458065 TAATTTACTT
458075 TATAT-GGTTTATA
1 TATATAGGTTTATA
458088 TATATAGGTTATATA
1 TATATAGGTT-TATA
458103 TATATA
1 TATATA
458109 CATACTATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 4 0.21
15 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (14 bp):
TATATAGGTTTATA
Found at i:458326 original size:7 final size:7
Alignment explanation
Indices: 458315--458360 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
458305 AGTTTATAAA
458315 GTTTAGG
1 GTTTAGG
*
458322 ATTTAGG
1 GTTTAGG
*
458329 GTTTATG
1 GTTTAGG
*
458336 TTTTAGG
1 GTTTAGG
458343 GTTTAGG
1 GTTTAGG
458350 GTTTAGG
1 GTTTAGG
458357 GTTT
1 GTTT
458361 TATAAACTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (7 bp):
GTTTAGG
Found at i:458420 original size:2 final size:2
Alignment explanation
Indices: 458413--458510 Score: 53
Period size: 2 Copynumber: 49.0 Consensus size: 2
458403 TATTTATTTA
*
458413 AT AT AT AT AT AT AT AT AT -T A- AT A- AT AT AT AA ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * * *
458453 -T TT AT AT ACT -T CAT AC AT AT AT AGT TT AT AT AC AT AC AT AT
1 AT AT AT AT A-T AT -AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
*
458494 AC AT AT AT AT ACT AT AT
1 AT AT AT AT AT A-T AT AT
458511 TAATATAAAT
Statistics
Matches: 73, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
1 5 0.07
2 62 0.85
3 6 0.08
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:458473 original size:24 final size:26
Alignment explanation
Indices: 458446--458503 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
458436 ATATATAAAC
*
458446 TATATATTTTATATAC-TTC-ATACA
1 TATATATTTTATATACATACAATACA
*
458470 TATATAGTTTATATACATACATATACA
1 TATATATTTTATATACATACA-ATACA
458497 TATATAT
1 TATATAT
458504 ACTATATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 15 0.54
25 2 0.07
27 11 0.39
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (26 bp):
TATATATTTTATATACATACAATACA
Found at i:458540 original size:89 final size:83
Alignment explanation
Indices: 458413--458573 Score: 225
Period size: 89 Copynumber: 1.9 Consensus size: 83
458403 TATTTATTTA
*
458413 ATATATATATATATATATTAATAATATATAAACTATATA-TTTTATATACTTCATACATATATAG
1 ATATATATATATATATATAAATAATATATAAACTATATACTTTT-TATACTTCATACATATATAG
458477 TTTATATACATACATATAC
65 TTTATATACATACATATAC
* *
458496 ATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATACATA
1 ATATATATA-TATA-T-ATATAAATAATA---TATAAACTATATACTTTTTATACTTCATACATA
458561 TATAGTTTATATA
60 TATAGTTTATATA
458574 TATATTTCAC
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
83 9 0.13
84 4 0.06
85 1 0.01
86 11 0.16
89 39 0.57
90 4 0.06
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (83 bp):
ATATATATATATATATATAAATAATATATAAACTATATACTTTTTATACTTCATACATATATAGT
TTATATACATACATATAC
Found at i:458566 original size:15 final size:15
Alignment explanation
Indices: 458546--458637 Score: 59
Period size: 15 Copynumber: 6.1 Consensus size: 15
458536 ATATACTTTT
458546 TATAGTTTATACATA
1 TATAGTTTATACATA
458561 TATAGTTTAT--ATA
1 TATAGTTTATACATA
*
458574 TATA-TTT-CACATAAA
1 TATAGTTTATACAT--A
* * *
458589 CATAATTTATATATA
1 TATAGTTTATACATA
*
458604 TATAGCTTATAACAATTA
1 TATAGTTTAT-AC-A-TA
458622 TATAGTTTATA-ATA
1 TATAGTTTATACATA
458636 TA
1 TA
458638 AATATAGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 19
0.68 0.10 0.22
Matches are distributed among these distances:
12 3 0.05
13 9 0.15
14 4 0.07
15 23 0.39
16 4 0.07
17 5 0.08
18 11 0.19
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (15 bp):
TATAGTTTATACATA
Found at i:458655 original size:17 final size:18
Alignment explanation
Indices: 458621--458656 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
458611 TATAACAATT
458621 ATATAGTTTATAATATAA
1 ATATAGTTTATAATATAA
458639 ATATAGTTTAT-ATATAA
1 ATATAGTTTATAATATAA
458656 A
1 A
458657 CTTTAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATAGTTTATAATATAA
Found at i:458756 original size:16 final size:16
Alignment explanation
Indices: 458735--458784 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
458725 CTTTTGTGTT
*
458735 TTTTAATTTATTTCAA
1 TTTTAATGTATTTCAA
*
458751 TTTTAA-GTATTTCAC
1 TTTTAATGTATTTCAA
458766 TTTTATATGTATTT-AA
1 TTTTA-ATGTATTTCAA
458782 TTT
1 TTT
458785 AGTTCTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 12 0.41
16 11 0.38
17 6 0.21
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (16 bp):
TTTTAATGTATTTCAA
Found at i:468473 original size:2 final size:2
Alignment explanation
Indices: 468461--468509 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
468451 GTAATATTGG
468461 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
468502 TA TA TA TA
1 TA TA TA TA
468510 GTGTTAGCAC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:473836 original size:37 final size:36
Alignment explanation
Indices: 473792--473945 Score: 105
Period size: 37 Copynumber: 4.1 Consensus size: 36
473782 ATATGAATGA
*
473792 TTTATCTCACTTGAGATTATTTTTCTTAAAACAAGAT
1 TTTATCTCACTTGAGA-TATTTCTCTTAAAACAAGAT
* * * *
473829 TTTATCTCGCTTGAGATAGTTTCCCTCGAAACATAAGAT
1 TTTATCTCACTTGAGATA-TTTCTCT-TAAA-ACAAGAT
* * * **
473868 TTTGTCTCGCTTGAGATA-GTCTCATTGAATATGAAGGA-
1 TTTATCTCACTTGAGATATTTCTC-TT-AA-AACAA-GAT
* *
473906 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGAT
1 TTTATCTCACTTGAGA-TATTTCTCTTAAAACAAGAT
473943 TTT
1 TTT
473946 GAACAAGATT
Statistics
Matches: 89, Mismatches: 18, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
36 4 0.04
37 29 0.33
38 24 0.27
39 29 0.33
40 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTATCTCACTTGAGATATTTCTCTTAAAACAAGAT
Found at i:473869 original size:75 final size:75
Alignment explanation
Indices: 473746--473884 Score: 167
Period size: 75 Copynumber: 1.9 Consensus size: 75
473736 CAACATTTCC
* * *
473746 AAACAAATTTTGTCTCGCTTGAGATAGTCTCATTGAATATGAATGA-TTTATCTCACTTGAGATT
1 AAACAAATTTTATCTCGCTTGAGATAGTCTCATCGAACATGAATGATTTTATCTCACTTGAGATT
473810 ATTTTTCTTA
66 ATTTTTCTTA
* * * *
473820 AAACAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAT-AA-GATTTTGTCTCGCTTGAG
1 AAACAA-ATTTTATCTCGCTTGAGATAGTCT-CATCG-AACATGAATGATTTTATCTCACTTGAG
473883 AT
63 AT
473885 AGTCTCATTG
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
74 6 0.11
75 24 0.44
76 20 0.37
77 4 0.07
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (75 bp):
AAACAAATTTTATCTCGCTTGAGATAGTCTCATCGAACATGAATGATTTTATCTCACTTGAGATT
ATTTTTCTTA
Found at i:473876 original size:39 final size:39
Alignment explanation
Indices: 473752--474101 Score: 229
Period size: 39 Copynumber: 8.9 Consensus size: 39
473742 TTCCAAACAA
* * *
473752 ATTTTGTCTCGCTTGAGATAGTCT-CATTG-AATATGAATG
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT-AA-G
* * ** *
473791 A-TTTATCTCACTTGAGATTA-TTTTTCTT-AAA-ACAAG
1 ATTTTGTCTCGCTTGAGA-TAGTTTCCCTTGAAACATAAG
* *
473827 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACATAAG
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACATAAG
* * *
473866 ATTTTGTCTCGCTTGAGATAGTCT-CATTG-AATATGAAGG
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACAT-AA-G
* * * ** *
473905 A-TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTTGAACAAG
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAAC---A---T----AAG
* *
473953 ATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAG
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACATAAG
* * * *
473992 ATTTTGCCTCGCTTGAGATAGTTTCTCTCGAAACAGAAG
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACATAAG
*
474031 ATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAAC--AA-
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACATAAG
* *
474067 ATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACA
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACA
474102 CAAAATCTTT
Statistics
Matches: 248, Mismatches: 41, Indels: 46
0.74 0.12 0.14
Matches are distributed among these distances:
36 37 0.15
37 28 0.11
38 43 0.17
39 106 0.43
40 2 0.01
43 1 0.00
46 2 0.01
48 2 0.01
49 27 0.11
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (39 bp):
ATTTTGTCTCGCTTGAGATAGTTTCCCTTGAAACATAAG
Found at i:474071 original size:126 final size:126
Alignment explanation
Indices: 473821--474072 Score: 332
Period size: 126 Copynumber: 2.0 Consensus size: 126
473811 TTTTTCTTAA
* *
473821 AACAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACATAAGATTTTGTCTCGCTTGAGATA
1 AACAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTGCCTCGCTTGAGATA
* * ** **
473886 GTCTCATTGAATATGAAGGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTTG
66 GTCTCATCGAATAAGAAGGATTTATCTCACTTGAGACAGTTTCCCTTAAAACAAGATTTTG
*
473947 AACAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTGCCTCGCTTGAGATA
1 AACAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTGCCTCGCTTGAGATA
* * *
474012 GTTTCTC-TCGAA-ACAGAA-GATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAACAA-ATTTTG
66 G--TCTCATCGAATA-AGAAGGA-TTTATCTCACTTGAGACAGTTTCCCTTAAAACAAGATTTTG
474073 TCTCGCTTGA
Statistics
Matches: 110, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
126 72 0.65
127 34 0.31
128 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (126 bp):
AACAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTGCCTCGCTTGAGATA
GTCTCATCGAATAAGAAGGATTTATCTCACTTGAGACAGTTTCCCTTAAAACAAGATTTTG
Found at i:474184 original size:36 final size:37
Alignment explanation
Indices: 474128--474451 Score: 188
Period size: 39 Copynumber: 9.0 Consensus size: 37
474118 GAATGATTTA
* *
474128 TCTCACTTGAGATTA-TTTTTCTTAAA-ACAAGATTTTG
1 TCTCGCTTGAGA-TAGTTTCTCTTAAACACAA-ATTTTG
* *
474165 TCTCGCTTGAGATAGTTT-TCCTCGAAACATAAGATTTTG
1 TCTCGCTTGAGATAGTTTCT-CT-TAAACACAA-ATTTTG
* *
474204 TCTCGCTTGAGATAGTTTCTCTCGAAACAGAAGATTTTG
1 TCTCGCTTGAGATAGTTTCTCT-TAAACACAA-ATTTTG
* *
474243 TCTCGCTTGAGACAGTTTCTCTTGAAACACAAA----A
1 TCTCGCTTGAGATAGTTTCTCTT-AAACACAAATTTTG
* *
474277 TCT---TTGA-ATATGTTTCTCTTGAA-ATAAATTTTG
1 TCTCGCTTGAGATA-GTTTCTCTTAAACACAAATTTTG
* * * *
474310 TCTCCCTTGAGACAGTTTCCCTTGAA-ACAAATTTTG
1 TCTCGCTTGAGATAGTTTCTCTTAAACACAAATTTTG
* * *
474346 TCTCGCTTGAGACAGTTTCTCTTGAATCACAAA----A
1 TCTCGCTTGAGATAGTTTCTCTT-AAACACAAATTTTG
*
474380 TCT---TTGA-ATATGTTTCTCTTGAA-ACAAATTTTG
1 TCTCGCTTGAGATA-GTTTCTCTTAAACACAAATTTTG
* * *
474413 TCTCCCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTG
1 TCTCGCTTGAGATAGTTTCTCTT-AAACACAAAT-TTTG
474452 AGACCATTTC
Statistics
Matches: 231, Mismatches: 27, Indels: 56
0.74 0.09 0.18
Matches are distributed among these distances:
29 9 0.04
30 7 0.03
31 26 0.11
33 6 0.03
34 6 0.03
36 61 0.26
37 23 0.10
38 14 0.06
39 78 0.34
40 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (37 bp):
TCTCGCTTGAGATAGTTTCTCTTAAACACAAATTTTG
Found at i:474380 original size:103 final size:103
Alignment explanation
Indices: 474193--474443 Score: 412
Period size: 103 Copynumber: 2.4 Consensus size: 103
474183 TCCTCGAAAC
* * *
474193 ATAAGATTTTGTCTCGCTTGAGATAGTTTCTCTCGAAACAGAAGATTTTGTCTCGCTTGAGACAG
1 ATAA-ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC--AA-ATTTTGTCTCGCTTGAGACAG
474258 TTTCTCTTGAAACACAAAATCTTTGAATATGTTTCTCTTGAA
62 TTTCTCTTGAAACACAAAATCTTTGAATATGTTTCTCTTGAA
*
474300 ATAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTC
1 ATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTC
*
474365 TCTTGAATCACAAAATCTTTGAATATGTTTCTCTTGAA
66 TCTTGAAACACAAAATCTTTGAATATGTTTCTCTTGAA
*
474403 ACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAA
1 ATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAA
474444 AATCTTTGAG
Statistics
Matches: 137, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
103 101 0.74
104 2 0.01
106 30 0.22
107 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (103 bp):
ATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTC
TCTTGAAACACAAAATCTTTGAATATGTTTCTCTTGAA
Found at i:474488 original size:66 final size:67
Alignment explanation
Indices: 474316--474506 Score: 253
Period size: 66 Copynumber: 2.9 Consensus size: 67
474306 TTTGTCTCCC
* *
474316 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAATCACAAAAT
1 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAT
474381 CT
66 CT
* *
474383 TTGA-ATATGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAAA
1 TTGAGACA-GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAA
474446 TCT
65 TCT
* * * * * *
474449 TTGAGACCA-TTTCCCTTTAAGCAAATTTTTTCTCTCTTGAGATAGTTTCCCTTGAAAC
1 TTGAGA-CAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
474507 GAGTTTTGTC
Statistics
Matches: 109, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
66 55 0.50
67 53 0.49
68 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (67 bp):
TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAT
CT
Found at i:474498 original size:36 final size:35
Alignment explanation
Indices: 474449--474577 Score: 152
Period size: 36 Copynumber: 3.6 Consensus size: 35
474439 ACAAAAATCT
* *
474449 TTGAGACCA-TTTCCCTTTAAGCAAATTTTTTCTCTC
1 TTGAGA-CAGTTTCCCTTGAAAC-AATTTTTTCTCTC
* * *
474485 TTGAGATAGTTTCCCTTGAAACGAGTTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAAC-AATTTTTTCTCTC
*
474521 TTGAGACAATTTCCCTTGAAACAATTTTTATCTCTC
1 TTGAGACAGTTTCCCTTGAAACAATTTTT-TCTCTC
*
474557 TTAAGACAGTTTCCCTTGAAA
1 TTGAGACAGTTTCCCTTGAAA
474578 GAAGAAACGT
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
35 6 0.08
36 73 0.92
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (35 bp):
TTGAGACAGTTTCCCTTGAAACAATTTTTTCTCTC
Found at i:475064 original size:44 final size:44
Alignment explanation
Indices: 475001--475199 Score: 156
Period size: 44 Copynumber: 4.6 Consensus size: 44
474991 TTGTTTGCTT
*
475001 GATTCTATCACAGAAGAAGGTAGATCAGCACCAACATGTCGCTC
1 GATTCTATCACAGAAGAAGGTAGATCAACACCAACATGTCGCTC
* * * **
475045 GATTCTATCACATAAGAAGGTGGATC--GA-C-ATTTGTTCGCTC
1 GATTCTATCACAGAAGAAGGTAGATCAACACCAACATG-TCGCTC
* * * * * * * * * *
475086 AAATCCATCACAGAATG-AGTTGGATCAACATCAACTTTTAGCTT
1 GATTCTATCACAGAA-GAAGGTAGATCAACACCAACATGTCGCTC
* * *
475130 GATTCTATCACAGAAGGAGGTAGATCAACACCAACATTTCGTTC
1 GATTCTATCACAGAAGAAGGTAGATCAACACCAACATGTCGCTC
* *
475174 GATTCCATCACAGAAGAAGGTTGATC
1 GATTCTATCACAGAAGAAGGTAGATC
475200 GACATTTTTA
Statistics
Matches: 120, Mismatches: 28, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
40 3 0.03
41 26 0.22
42 2 0.02
43 2 0.02
44 84 0.70
45 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (44 bp):
GATTCTATCACAGAAGAAGGTAGATCAACACCAACATGTCGCTC
Found at i:475274 original size:133 final size:133
Alignment explanation
Indices: 474994--475673 Score: 881
Period size: 133 Copynumber: 5.1 Consensus size: 133
474984 TGTTCAATTG
* * * * * * *
474994 TTTGCTTGATTCTATCACAGAAGAAGGTAGATCAGCACCAACATGTCGCTCGATTCTATCACATA
1 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATATCGTTCGATTCCATCACAGA
* * * * * *
475059 AGAAGGTGGATCGACA---TT-TGTTCGCTCAAATCCATCACAGAATGAGTTGGATCAACATCAA
66 AGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAAGAGTTGGATCAGCGTCAA
475120 CTT
131 CTT
* * *
475123 TTAGCTTGATTCTATCACAGAAGGAGGTAGATCAACACCAACATTTCGTTCGATTCCATCACAGA
1 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATATCGTTCGATTCCATCACAGA
* * *
475188 AGAAGGTTGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAAGAATTGGATCAGCGTCAA
66 AGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAAGAGTTGGATCAGCGTCAA
475253 CTT
131 CTT
* * * * * * * * *
475256 TTTGCTTGATTCTATCACAGAAAGAGGTAAATCAGCACCGATATCTCGTTTGATTTCATCACAGA
1 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATATCGTTCGATTCCATCACAGA
* *
475321 AGGAGGTGTATCGACATTTTTAATTTCGCTCAAATCCATCGCA-AAAGGAGTTGGATCAGCGTCA
66 AGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAA-GAGTTGGATCAGCGTCA
475385 ACTT
130 ACTT
* *
475389 TTTGCGCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATATCGTTCGATTTCTATCACAG
1 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATATCGTTCGA-TTCCATCACAG
* * *
475454 AAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCACA-AAAGGAGTTGGATTAGCGTA
65 AAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAA-GAGTTGGATCAGCGTC
475518 AACTT
129 AACTT
* * * *
475523 TTAGCTCGATTCTATCACAGAATGAGGTAGATCAA-ATCGACATATCGTTCGATTTCCATCACAG
1 TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATATCGTTCGA-TTCCATCACAG
* * *
475587 AAGGAGGTGGATCAACATTATTATTTTCGCTCAAATCCATCGCAGAAAGAGTTGGATTAGCGTCA
65 AAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAAGAGTTGGATCAGCGTCA
475652 ACTT
130 ACTT
*
475656 CTTGCTCGATTC-ATCACA
1 TTTGCTCGATTCTATCACA
475674 TATGGAGTTG
Statistics
Matches: 488, Mismatches: 56, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
129 73 0.15
132 11 0.02
133 296 0.61
134 108 0.22
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (133 bp):
TTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATATCGTTCGATTCCATCACAGA
AGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAAGAGTTGGATCAGCGTCAA
CTT
Found at i:475617 original size:267 final size:265
Alignment explanation
Indices: 475001--475673 Score: 887
Period size: 267 Copynumber: 2.5 Consensus size: 265
474991 TTGTTTGCTT
* * * * * *
475001 GATTCTATCACAGAAGAAGGTAGATCAGCACCAACATGTCGCTCGA-TTCTATCACATAAGAAGG
1 GATTCTATCACAGAAG-AGGTAGATCAGCACCGACATATCGTTCGATTTCCATCACAGAAGGAGG
* * * * * *
475065 TGGATCGAC---ATT-TGTTCGCTCAAATCCATCACAGAATGAGTTGGATCAACATCAACTTTTA
65 TGGATCGACATTATTATTTTCGCTCAAATCCATCGCA-AAAGAGTTGGATCAGCGTCAACTTTTT
* *
475126 GCTTGATTCTATCACAGAAGGAGGTAGATCAACACCAACATTTCGTTCGATTCCATCACAGAAGA
129 GCTCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATATCGTTCGATTCCATCACAGAAGA
* * *
475191 AGGTTGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAAGAATTGGATCAGCGTCAACTT
194 AGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCACAGAAAGAATTGGATCAGCGTAAACTT
* *
475256 TTTGCTT
259 TTAGCTC
* * * *
475263 GATTCTATCACAGAAAGAGGTAAATCAGCACCGATATCTCGTTTGATTT-CATCACAGAAGGAGG
1 GATTCTATCACAG-AAGAGGTAGATCAGCACCGACATATCGTTCGATTTCCATCACAGAAGGAGG
* * *
475327 TGTATCGACATTTTTAATTTCGCTCAAATCCATCGCAAAAGGAGTTGGATCAGCGTCAACTTTTT
65 TGGATCGACATTATTATTTTCGCTCAAATCCATCGCAAAA-GAGTTGGATCAGCGTCAACTTTTT
* *
475392 GCGCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATATCGTTCGATTTCTATCACAGAAG
129 GCTCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATATCGTTCGA-TTCCATCACAGAAG
* * *
475457 GAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCACA-AAAGGAGTTGGATTAGCGTAAAC
193 AAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCACAGAAA-GAATTGGATCAGCGTAAAC
475521 TTTTAGCTC
257 TTTTAGCTC
* *
475530 GATTCTATCACAGAATGAGGTAGATCA-AATCGACATATCGTTCGATTTCCATCACAGAAGGAGG
1 GATTCTATCACAGAA-GAGGTAGATCAGCACCGACATATCGTTCGATTTCCATCACAGAAGGAGG
* * *
475594 TGGATCAACATTATTATTTTCGCTCAAATCCATCGCAGAAAGAGTTGGATTAGCGTCAACTTCTT
65 TGGATCGACATTATTATTTTCGCTCAAATCCATCGCA-AAAGAGTTGGATCAGCGTCAACTTTTT
475659 GCTCGATTC-ATCACA
129 GCTCGATTCTATCACA
475674 TATGGAGTTG
Statistics
Matches: 356, Mismatches: 43, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
262 56 0.16
263 5 0.01
265 4 0.01
266 113 0.32
267 175 0.49
268 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (265 bp):
GATTCTATCACAGAAGAGGTAGATCAGCACCGACATATCGTTCGATTTCCATCACAGAAGGAGGT
GGATCGACATTATTATTTTCGCTCAAATCCATCGCAAAAGAGTTGGATCAGCGTCAACTTTTTGC
TCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATATCGTTCGATTCCATCACAGAAGAAG
GTGGATCGACATTTTTATTTTCGCTCAAATCCATCACAGAAAGAATTGGATCAGCGTAAACTTTT
AGCTC
Found at i:477288 original size:2 final size:2
Alignment explanation
Indices: 477276--477312 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
477266 GTAATATTGG
477276 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
477313 GTGTTAGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:480902 original size:24 final size:24
Alignment explanation
Indices: 480875--480921 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
480865 AATTCAGAAA
*
480875 TTTTAAGAT-CTTTTAGTTATGAT
1 TTTTTAGATACTTTTAGTTATGAT
*
480898 TTTTTATATACTTTTAGTTATGAT
1 TTTTTAGATACTTTTAGTTATGAT
480922 CTTTGTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.60
Consensus pattern (24 bp):
TTTTTAGATACTTTTAGTTATGAT
Found at i:480925 original size:14 final size:14
Alignment explanation
Indices: 480881--480925 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
480871 GAAATTTTAA
480881 GATCTTTTAGTTAT
1 GATCTTTTAGTTAT
*
480895 GATTTTTTA--TAT
1 GATCTTTTAGTTAT
480907 -A-CTTTTAGTTAT
1 GATCTTTTAGTTAT
480919 GATCTTT
1 GATCTTT
480926 GTGATTAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
10 5 0.20
11 1 0.04
12 6 0.24
13 1 0.04
14 12 0.48
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.60
Consensus pattern (14 bp):
GATCTTTTAGTTAT
Found at i:481057 original size:23 final size:24
Alignment explanation
Indices: 481012--481073 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
481002 CAAGTTGGGG
* * *
481012 TTTTAAAAAAAATAAATTCAATTT
1 TTTTAAAAAAAATAAAGTAAATTA
*
481036 TTTTAAAAAAGA-AAAGTAAATTA
1 TTTTAAAAAAAATAAAGTAAATTA
481059 TTTTAACAAAAAATA
1 TTTTAA-AAAAAATA
481074 TTGACCAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 14 0.45
24 16 0.52
25 1 0.03
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (24 bp):
TTTTAAAAAAAATAAAGTAAATTA
Found at i:481685 original size:191 final size:193
Alignment explanation
Indices: 481459--481842 Score: 754
Period size: 191 Copynumber: 2.0 Consensus size: 193
481449 AAAGTATATC
481459 CAAAGTTAACTTTAGGTGTCTAAAAAGTTTTTTTTGATAAAAATATATGTCTAACGCTATAAAGG
1 CAAAGTTAACTTTAGGTGTCTAAAAAGTTTTTTTTGATAAAAATATATGTCTAACGCTATAAAGG
481524 TTACCATTTTAGGTGCTCACGTTGTAATTGTCGTTAAAAATTTAATTAGGTGACACATGTCATGT
66 TTACCATTTTAGGTGCTCACGTTGTAATTGTCGTTAAAAATTTAATTAGGTGACACATGTCATGT
481589 TCTTGTAATTTTAAAAAATTATTAAAAAAAATCCTTAACAAACTTTTTATATTTATAAAAAAA
131 TCTTGTAATTTTAAAAAATTATTAAAAAAAATCCTTAACAAACTTTTTATATTTATAAAAAAA
481652 CAAAGTT-ACTTTA-GTGTCTAAAAAGTTTTTTTTGATAAAAATATATGTCTAACGCTATAAAGG
1 CAAAGTTAACTTTAGGTGTCTAAAAAGTTTTTTTTGATAAAAATATATGTCTAACGCTATAAAGG
481715 TTACCATTTTAGGTGCTCACGTTGTAATTGTCGTTAAAAATTTAATTAGGTGACACATGTCATGT
66 TTACCATTTTAGGTGCTCACGTTGTAATTGTCGTTAAAAATTTAATTAGGTGACACATGTCATGT
481780 TCTTGTAATTTTAAAAAATTATTAAAAAAAATCCTTAACAAACTTTTTATATTTATAAAAAAA
131 TCTTGTAATTTTAAAAAATTATTAAAAAAAATCCTTAACAAACTTTTTATATTTATAAAAAAA
481843 ACTTAATTTA
Statistics
Matches: 191, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
191 178 0.93
192 6 0.03
193 7 0.04
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (193 bp):
CAAAGTTAACTTTAGGTGTCTAAAAAGTTTTTTTTGATAAAAATATATGTCTAACGCTATAAAGG
TTACCATTTTAGGTGCTCACGTTGTAATTGTCGTTAAAAATTTAATTAGGTGACACATGTCATGT
TCTTGTAATTTTAAAAAATTATTAAAAAAAATCCTTAACAAACTTTTTATATTTATAAAAAAA
Found at i:492804 original size:18 final size:19
Alignment explanation
Indices: 492762--492804 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
492752 TTATTGTAAA
*
492762 TTATATATTATAACTATAT
1 TTATATATAATAACTATAT
*
492781 TT-TATATAATCA-TATAT
1 TTATATATAATAACTATAT
492798 TTATATA
1 TTATATA
492805 ATATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 7 0.33
18 12 0.57
19 2 0.10
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATATATAATAACTATAT
Found at i:493198 original size:2 final size:2
Alignment explanation
Indices: 493191--493219 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
493181 TATCCATTTC
493191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
493220 CTTACCTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:493891 original size:27 final size:27
Alignment explanation
Indices: 493860--493914 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
493850 GACGAGTTAA
* *
493860 GAATTTATTTAAATCGGATTAACAAAG
1 GAATTGATTTAAATCGGATTAAAAAAG
493887 GAATTGATTTAAATCGGATTAAAAAAG
1 GAATTGATTTAAATCGGATTAAAAAAG
493914 G
1 G
493915 TTTTTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.31
Consensus pattern (27 bp):
GAATTGATTTAAATCGGATTAAAAAAG
Found at i:494411 original size:21 final size:22
Alignment explanation
Indices: 494380--494424 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
494370 GAAATGCTTG
494380 AGGGATACCGATACCCTGCTAC
1 AGGGATACCGATACCCTGCTAC
494402 AGGG-TACCGATACCCTGCTAC
1 AGGGATACCGATACCCTGCTAC
494423 AG
1 AG
494425 TACCTCGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (22 bp):
AGGGATACCGATACCCTGCTAC
Found at i:494483 original size:23 final size:23
Alignment explanation
Indices: 494457--494513 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 23
494447 AACTCATAAA
494457 ATTTAAAACATTCATCAT-TATAC
1 ATTTAAAACATTCA-CATATATAC
* *
494480 ATTT--ACCATTTACATATATAC
1 ATTTAAAACATTCACATATATAC
*
494501 GTTTAAAACATTC
1 ATTTAAAACATTC
494514 CAAAACTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
20 3 0.12
21 14 0.54
23 9 0.35
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTTAAAACATTCACATATATAC
Found at i:495276 original size:32 final size:31
Alignment explanation
Indices: 495185--495277 Score: 91
Period size: 31 Copynumber: 2.9 Consensus size: 31
495175 CCTCGTCAAT
* *
495185 TGTCCATAGGTCCCGAAGAACCTAGGTAAAAC
1 TGTCCATATGTCCCGAAG-ACATAGGTAAAAC
** *
495217 TGTCCATATGTTCCTTAA-ACATAGGT-AATC
1 TGTCCATATG-TCCCGAAGACATAGGTAAAAC
495247 ATGTCCATATGTCCCGAAAGACATAGGTAAA
1 -TGTCCATATGTCCCG-AAGACATAGGTAAA
495278 CCCTCGACTC
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
30 6 0.12
31 19 0.39
32 17 0.35
33 7 0.14
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (31 bp):
TGTCCATATGTCCCGAAGACATAGGTAAAAC
Found at i:504287 original size:30 final size:29
Alignment explanation
Indices: 504228--504293 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
504218 CCCGAAGGAC
*
504228 CTATCCAGAGGTCACACAGACCCCGGTAA
1 CTATCCAGAGGTCACAAAGACCCCGGTAA
* * *
504257 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
504287 CTATCCA
1 CTATCCA
504294 TATGTTCCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 17 0.55
30 14 0.45
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (29 bp):
CTATCCAGAGGTCACAAAGACCCCGGTAA
Found at i:504374 original size:32 final size:32
Alignment explanation
Indices: 504285--504380 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
504275 GATCCTCGGT
* *
504285 AACTATCCATATGTTCCTTAGAACATAGGT-A
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
* *
504316 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGTAA
504348 AACTGTCCATATGTTCCGTAGAACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
504380 A
1 A
504381 CCCTCGACTC
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
30 4 0.07
31 20 0.37
32 26 0.48
33 4 0.07
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (32 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTAA
Found at i:505597 original size:21 final size:21
Alignment explanation
Indices: 505567--505611 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
505557 ATTCTGTCGT
* *
505567 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
505588 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
505609 TTG
1 TTG
505612 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:508810 original size:30 final size:29
Alignment explanation
Indices: 508754--508816 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
508744 GAAGGACCTA
*
508754 TCCAGAGGTCACACAGACCCCGGTAACTG
1 TCCAGAGGTCACAAAGACCCCGGTAACTG
* *
508783 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
508813 TCCA
1 TCCA
508817 TATGTTCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (29 bp):
TCCAGAGGTCACAAAGACCCCGGTAACTG
Found at i:508847 original size:31 final size:30
Alignment explanation
Indices: 508805--508902 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
508795 AAAGATCCTC
*
508805 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
508835 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
508866 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
508898 GGTAA
1 GGTAA
508903 ACCCTCGACT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.44
32 25 0.44
33 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:510129 original size:21 final size:21
Alignment explanation
Indices: 510099--510143 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
510089 ATTCTGTCGT
* *
510099 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
510120 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
510141 TTG
1 TTG
510144 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:526566 original size:23 final size:23
Alignment explanation
Indices: 526540--526587 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
526530 ATAAAGTACA
*
526540 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
526563 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
526586 AT
1 AT
526588 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:527400 original size:23 final size:23
Alignment explanation
Indices: 527338--527400 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
527328 ATATAACCAC
* *
527338 TACCTATTACATTATACAAATGA
1 TACCTATTACATTATATAAACGA
* *
527361 TACCTATTACATTATATAAGCGT
1 TACCTATTACATTATATAAACGA
*
527384 TACCTATTACATCATAT
1 TACCTATTACATTATAT
527401 GTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:528511 original size:17 final size:18
Alignment explanation
Indices: 528489--528531 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
528479 ATATATCCGG
528489 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
528506 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
528526 TATCAT
1 TATCAT
528532 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:528805 original size:20 final size:20
Alignment explanation
Indices: 528777--528814 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
528767 TGCTTTAAAG
528777 TTATGTAATTA-TGTTTCAAT
1 TTATGTAA-TAGTGTTTCAAT
*
528797 TTATTTAATAGTGTTTCA
1 TTATGTAATAGTGTTTCA
528815 TGTTTTCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (20 bp):
TTATGTAATAGTGTTTCAAT
Found at i:532217 original size:174 final size:169
Alignment explanation
Indices: 531882--532233 Score: 643
Period size: 174 Copynumber: 2.1 Consensus size: 169
531872 AGAATGATAT
531882 TTCTATATTTGGTGAAAAGCAAAGCCATCTGCAGTAACCAAAACCTTCGTATTTCGTATTTCAGA
1 TTCTATATTTGGTGAAAAGCAAAGCCATCTGCAGTAACCAAAACCTTCGTATTTCGTATTTCAGA
531947 TATTCTCAAGTAATCGTATTATATAATAATGTCACAATAGATATATGTATTGACAAAATCTAGAA
66 TATTCTCAAGTAATCGTATTATATAATAATGTCACAATAGATATATGTATTGACAAAATCTAGAA
532012 ACCAACAGTTGACAGAAAGACGATTAGGCAAAATTTTAG
131 ACCAACAGTTGACAGAAAGACGATTAGGCAAAATTTTAG
532051 TTCTATATTTGGTGAAAAGCAAAGCCATCTGCAGTAACCAAAACCTTCGTATTTCGTATTTCAGA
1 TTCTATATTTGGTGAAAAGCAAAGCCATCTGCAGTAACCAAAACCTTCGTATTTCGTATTTCAGA
532116 TATTCTCAAGTAAATCGTATTATATATATAATAATGTCACAATAGATATATGTATTGACAAAATC
66 TATTCTCAAGT-AATCG---TAT-TATATAATAATGTCACAATAGATATATGTATTGACAAAATC
532181 TAGAAACCAACAGTTGACAGAAAGACGATTAGGCAAAATTTTAG
126 TAGAAACCAACAGTTGACAGAAAGACGATTAGGCAAAATTTTAG
*
532225 TGCTA-ATTT
1 TTCTATATTT
532234 TCCACTTGCC
Statistics
Matches: 177, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
169 76 0.43
170 5 0.03
173 7 0.04
174 89 0.50
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (169 bp):
TTCTATATTTGGTGAAAAGCAAAGCCATCTGCAGTAACCAAAACCTTCGTATTTCGTATTTCAGA
TATTCTCAAGTAATCGTATTATATAATAATGTCACAATAGATATATGTATTGACAAAATCTAGAA
ACCAACAGTTGACAGAAAGACGATTAGGCAAAATTTTAG
Found at i:535450 original size:28 final size:29
Alignment explanation
Indices: 535410--535484 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
535400 GAGGAGCAGG
*
535410 AGGAGTGCCTGGCGACCTTGTA-GTCGCC
1 AGGAGTGCATGGCGACCTTGTAGGTCGCC
535438 AGGAGTGCATGGCGACCTTGTAGGTCGCC
1 AGGAGTGCATGGCGACCTTGTAGGTCGCC
*
535467 CGGAGTGCATGGCGACCT
1 AGGAGTGCATGGCGACCT
535485 ATGCTGGGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 21 0.48
29 23 0.52
ACGTcount: A:0.16, C:0.27, G:0.37, T:0.20
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTTGTAGGTCGCC
Found at i:540200 original size:22 final size:23
Alignment explanation
Indices: 540165--540211 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
540155 TTTTAATTTA
540165 TAAAAAATTATCTATTTTAAGATT
1 TAAAAAATTATCTA-TTTAAGATT
*
540189 TAAAAAA-T-TCTATTTAAGGTT
1 TAAAAAATTATCTATTTAAGATT
540210 TA
1 TA
540212 GAATTTGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 4 0.18
23 1 0.05
24 7 0.32
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (23 bp):
TAAAAAATTATCTATTTAAGATT
Done.