Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001362.1 Hibiscus syriacus cultivar Beakdansim tig00002655_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: 681426
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 2 of 3
Found at i:325594 original size:32 final size:32
Alignment explanation
Indices: 325530--325596 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
325520 AAACTTCTGA
**
325530 TCTAGAACTTCCACATGAGCTGGCTCGTTCAT
1 TCTAGAACTTCCACATGAGCTGGCTCACTCAT
325562 TCTAGAAC-TCTCACATGAGCT-GCATCACTCAT
1 TCTAGAACTTC-CACATGAGCTGGC-TCACTCAT
325594 TCT
1 TCT
325597 CTCAACAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 4 0.13
32 27 0.87
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (32 bp):
TCTAGAACTTCCACATGAGCTGGCTCACTCAT
Found at i:328130 original size:21 final size:21
Alignment explanation
Indices: 328088--328130 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
328078 TTTCTGGGTT
* * *
328088 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
328109 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
328130 A
1 A
328131 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:328191 original size:67 final size:68
Alignment explanation
Indices: 328110--328261 Score: 270
Period size: 67 Copynumber: 2.2 Consensus size: 68
328100 ACCCATTCAA
*
328110 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
328175 -GG
66 GGG
*
328177 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGGGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
328242 GGG
66 GGG
*
328245 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
328262 ATGAGAAAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
67 63 0.78
68 18 0.22
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:328248 original size:21 final size:21
Alignment explanation
Indices: 328222--328262 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
328212 CAGAATGCTA
*
328222 GGGGGGAATCGATACCCCCAG
1 GGGGGGAACCGATACCCCCAG
*
328243 GGGGGGAACCGATTCCCCCA
1 GGGGGGAACCGATACCCCCA
328263 TGAGAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.32, G:0.37, T:0.10
Consensus pattern (21 bp):
GGGGGGAACCGATACCCCCAG
Found at i:328932 original size:149 final size:149
Alignment explanation
Indices: 328739--329042 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
328729 GGGTAGAGGG
*
328739 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAATATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
328804 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
328869 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
328888 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
328953 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
329018 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
329037 TCTACG
1 TCTACG
329043 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:329065 original size:23 final size:23
Alignment explanation
Indices: 329021--329065 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
329011 ATCATTATAT
*
329021 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
329044 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
329066 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:354679 original size:33 final size:34
Alignment explanation
Indices: 354614--354683 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
354604 TATTAATAAA
*
354614 CCTGAATTACAAAAGATACACATTACACTCTAAC
1 CCTGAAATACAAAAGATACACATTACACTCTAAC
*
354648 CCTGAAATACATAAGATACACA-TACACTCTAAC
1 CCTGAAATACAAAAGATACACATTACACTCTAAC
354681 CCT
1 CCT
354684 CCTAGGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 14 0.41
34 20 0.59
ACGTcount: A:0.43, C:0.29, G:0.06, T:0.23
Consensus pattern (34 bp):
CCTGAAATACAAAAGATACACATTACACTCTAAC
Found at i:369298 original size:21 final size:21
Alignment explanation
Indices: 369272--369316 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
369262 GATTTCTGGG
* *
369272 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
369293 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
369314 CAA
1 CAA
369317 ACGAACAAGA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:371065 original size:22 final size:22
Alignment explanation
Indices: 371000--371057 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
370990 ATCATTATAT
*
371000 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
371022 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
371044 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
371058 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.24
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:374249 original size:21 final size:21
Alignment explanation
Indices: 374223--374267 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
374213 GATTTCTGGG
* *
374223 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
374244 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
374265 CAA
1 CAA
374268 ACGAACAAGA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:376018 original size:22 final size:22
Alignment explanation
Indices: 375953--376010 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
375943 ATCATTATAT
*
375953 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
375975 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
375997 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
376011 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.24
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:378150 original size:60 final size:59
Alignment explanation
Indices: 378076--378220 Score: 152
Period size: 60 Copynumber: 2.4 Consensus size: 59
378066 ATGAATTTGA
* * * *
378076 GGATGAAATTAGAATATTTAAAAGTTTAGGGACCAATTTAGAAA-GAGGGATATAGTATAG
1 GGATGAAATTAGAATATTTAAAAGTTTAAGAACCAATTTA-AAATGAGAG-CATAGTATAG
* * * * *
378136 GGATGGAATTAGAATA-TCAAAGAGTTTAAGAACTAATTTAAAATGAGAGCATAGTTTGG
1 GGATGAAATTAGAATATTTAAA-AGTTTAAGAACCAATTTAAAATGAGAGCATAGTATAG
378195 GGATGAAATT-GAAATATTTAAAAGTT
1 GGATGAAATTAG-AATATTTAAAAGTT
378221 CAAAGGCTAA
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
58 1 0.01
59 31 0.44
60 38 0.54
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.30
Consensus pattern (59 bp):
GGATGAAATTAGAATATTTAAAAGTTTAAGAACCAATTTAAAATGAGAGCATAGTATAG
Found at i:380114 original size:31 final size:31
Alignment explanation
Indices: 380065--380146 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 31
380055 TATTTTTTGG
*
380065 TCAAAATATATATTTAAAGTTATTTTTTTTTA
1 TCAAAATATATATCTAAAG-TATTTTTTTTTA
* *
380097 TCAAAATA-GTATCTAAAGTA-TTTTTTTGA
1 TCAAAATATATATCTAAAGTATTTTTTTTTA
*
380126 -CAAAATAAATA-CTAAAGTATT
1 TCAAAATATATATCTAAAGTATT
380147 CAATTTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
28 15 0.34
29 11 0.25
30 2 0.05
31 8 0.18
32 8 0.18
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (31 bp):
TCAAAATATATATCTAAAGTATTTTTTTTTA
Found at i:381027 original size:67 final size:67
Alignment explanation
Indices: 380950--381080 Score: 262
Period size: 67 Copynumber: 2.0 Consensus size: 67
380940 GGGAATTAGA
380950 TGAGGATGATGAATTCTGGGTTTTTAAGGTAACTGATTTTATTTTCTATAATTAAGCTTTTTTTA
1 TGAGGATGATGAATTCTGGGTTTTTAAGGTAACTGATTTTATTTTCTATAATTAAGCTTTTTTTA
381015 TT
66 TT
381017 TGAGGATGATGAATTCTGGGTTTTTAAGGTAACTGATTTTATTTTCTATAATTAAGCTTTTTTT
1 TGAGGATGATGAATTCTGGGTTTTTAAGGTAACTGATTTTATTTTCTATAATTAAGCTTTTTTT
381081 GGGTTGCTGA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.25, C:0.06, G:0.18, T:0.50
Consensus pattern (67 bp):
TGAGGATGATGAATTCTGGGTTTTTAAGGTAACTGATTTTATTTTCTATAATTAAGCTTTTTTTA
TT
Found at i:382387 original size:21 final size:19
Alignment explanation
Indices: 382357--382404 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
382347 AGAATATAGG
382357 TTTTTAAAAAATATAATAATA
1 TTTTTAAAAAATAT-ATAA-A
*
382378 TTTTTTAAAAATATATAAA
1 TTTTTAAAAAATATATAAA
382397 -TTTTAAAA
1 TTTTTAAAA
382405 TTACCATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 1 0.04
20 4 0.16
21 13 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTTTAAAAAATATATAAA
Found at i:386153 original size:3 final size:3
Alignment explanation
Indices: 386145--386170 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
386135 GAATTGGGTT
386145 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
386171 TATTAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:386583 original size:73 final size:73
Alignment explanation
Indices: 386462--386600 Score: 269
Period size: 73 Copynumber: 1.9 Consensus size: 73
386452 TGTCACTTAC
386462 AGGGTTAATAAAAATAACATGTCTCGTTAAAATTTTATTAAGAGAAAAATTATATAAAAGAAAGT
1 AGGGTTAATAAAAATAACATGTCTCGTTAAAATTTTATTAAGAGAAAAATTATATAAAAGAAAGT
386527 TATTATCG
66 TATTATCG
*
386535 AGGGTTAATAAAAATAACATGTCTCGTTAAAATTTTATTAAGATAAAAATTATATAAAAGAAAGT
1 AGGGTTAATAAAAATAACATGTCTCGTTAAAATTTTATTAAGAGAAAAATTATATAAAAGAAAGT
386600 T
66 T
386601 CTTGTCAAAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (73 bp):
AGGGTTAATAAAAATAACATGTCTCGTTAAAATTTTATTAAGAGAAAAATTATATAAAAGAAAGT
TATTATCG
Found at i:388267 original size:14 final size:14
Alignment explanation
Indices: 388248--388274 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
388238 AGGTTAAACT
388248 ATAATTTAATTATA
1 ATAATTTAATTATA
388262 ATAATTTAATTAT
1 ATAATTTAATTAT
388275 TTTACCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATTTAATTATA
Found at i:391172 original size:25 final size:25
Alignment explanation
Indices: 391138--391193 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
391128 TAAAGCACTT
391138 GAGCAACTCTCGGACTTTGAGAAAA
1 GAGCAACTCTCGGACTTTGAGAAAA
391163 GAGCAACTCTCGGACTTTGAGAAAA
1 GAGCAACTCTCGGACTTTGAGAAAA
391188 GAGCAA
1 GAGCAA
391194 ATTCTAGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.18
Consensus pattern (25 bp):
GAGCAACTCTCGGACTTTGAGAAAA
Found at i:393287 original size:28 final size:28
Alignment explanation
Indices: 393236--393292 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
393226 CTGTCGCTAC
393236 TTTCAAGCACTGACTCGACAACATAATG
1 TTTCAAGCACTGACTCGACAACATAATG
* * *
393264 TTTCAAGCACTGGCTTGACGACATAATG
1 TTTCAAGCACTGACTCGACAACATAATG
393292 T
1 T
393293 AAACAAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (28 bp):
TTTCAAGCACTGACTCGACAACATAATG
Found at i:395111 original size:23 final size:22
Alignment explanation
Indices: 395062--395143 Score: 78
Period size: 24 Copynumber: 3.7 Consensus size: 22
395052 TAGTCTTCTA
*
395062 AATTTTTTAAATTTTATATAATTT
1 AATTTTTTATATTTTATAT--TTT
*
395086 AATTTTTTATGTTTTATATTTAT
1 AATTTTTTATATTTTATATTT-T
* *
395109 AATTATTTATCTTTTA-ATTTT
1 AATTTTTTATATTTTATATTTT
*
395130 -TTTTTTTATATTTT
1 AATTTTTTATATTTT
395144 TTAAATTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 11 0.22
21 1 0.02
22 6 0.12
23 15 0.30
24 17 0.34
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (22 bp):
AATTTTTTATATTTTATATTTT
Found at i:395481 original size:12 final size:12
Alignment explanation
Indices: 395473--395497 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
395463 AAGTTTTAAG
395473 TTTTATTTTATA
1 TTTTATTTTATA
395485 TTTTATTTTATA
1 TTTTATTTTATA
395497 T
1 T
395498 ATATATTTAA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTTTATA
Found at i:395819 original size:3 final size:3
Alignment explanation
Indices: 395811--395839 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
395801 TCCAAAGCAA
395811 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
395840 AAGTAAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:398707 original size:24 final size:22
Alignment explanation
Indices: 398680--398724 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
398670 TATCAAAATC
398680 ATGATCCA-GTAGTATATTGTAAAA
1 ATGAT-CATGTAGT-TATT-TAAAA
398704 ATGATCATGTAGTTATTTAAA
1 ATGATCATGTAGTTATTTAAA
398725 TCAAATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATCATGTAGTTATTTAAAA
Found at i:400222 original size:27 final size:27
Alignment explanation
Indices: 400192--400243 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
400182 TTTTTACAAT
*
400192 ATAAGGGTATTTTCGTAATTTTACCCC
1 ATAAGGGTATTTTCGAAATTTTACCCC
* *
400219 ATAAGTGTATTTTTGAAATTTTACC
1 ATAAGGGTATTTTCGAAATTTTACC
400244 TAACATAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.44
Consensus pattern (27 bp):
ATAAGGGTATTTTCGAAATTTTACCCC
Found at i:404659 original size:20 final size:21
Alignment explanation
Indices: 404606--404667 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
404596 TTCCCCTGTG
404606 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGG-ATCGGTT-CCC-TCAAA
* *
404630 GGGGGAATCGGTTCCCTC-AT
1 GGGGGGATCGGTTCCCTCAAA
*
404650 GGGGGGATCGATTCCCTC
1 GGGGGGATCGGTTCCCTC
404668 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGGATCGGTTCCCTCAAA
Found at i:422167 original size:55 final size:54
Alignment explanation
Indices: 422110--422612 Score: 305
Period size: 51 Copynumber: 9.6 Consensus size: 54
422100 TGACGAGCCT
*
422110 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATAAAACGTGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCATAAAACG-GTCC
* * * *
422165 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATC-TTCATAAAAC-GGTCC
* *
422221 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCA-ATAAACAGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCATA-AAAC-GGTCC
* * * * *
422276 GCTCCCTATTCTTTCAGGGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * *
422327 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ATGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * *
422378 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * ***
422429 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAATGAATTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTC-ATAAAACGGTCC
* * * *
422480 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * *
422531 GCTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ATGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
*
422582 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
422613 AATCTTCAAC
Statistics
Matches: 404, Mismatches: 33, Indels: 25
0.87 0.07 0.05
Matches are distributed among these distances:
50 2 0.00
51 279 0.69
52 2 0.00
54 1 0.00
55 72 0.18
56 47 0.12
57 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (54 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATAAAACGGTCC
Found at i:422332 original size:51 final size:51
Alignment explanation
Indices: 422217--422622 Score: 650
Period size: 51 Copynumber: 7.9 Consensus size: 51
422207 AATAAAACGG
* * * ** **
422217 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAG
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* *
422272 GTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
422323 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
422374 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* *
422425 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAATTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
422476 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
422527 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTT
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
422578 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
1 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAAC
422623 AACGAATTTG
Statistics
Matches: 332, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
51 301 0.91
55 31 0.09
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (51 bp):
GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:422499 original size:153 final size:153
Alignment explanation
Indices: 422160--422622 Score: 665
Period size: 153 Copynumber: 3.0 Consensus size: 153
422150 TCATAAAACG
* * * * * **
422160 TGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCCGCTC
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGAC-T---CAATCTTCAAT-GAACTTGTCCGCTC
* * * * ** *
422225 TCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCCCTATTCTTT
61 CCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAATGAACTTGTCCGCTCCCTATTCATT
*
422290 CAGGGAGTATAGGACTCAATCTTCAACGAACT
122 CAGAGAGTATAGGACTCAATCTTCAACGAACT
422322 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCCGCTCCCTAT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCCGCTCCCTAT
*
422387 TCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTA
66 TCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCCGCTCCCTATTCATTCAGAGAGTA
* *
422452 TAGGACTCAATCTTCAATGAATT
131 TAGGACTCAATCTTCAACGAACT
*
422475 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTAT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCCGCTCCCTAT
*
422540 TCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTA
66 TCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCCGCTCCCTATTCATTCAGAGAGTA
422605 TAGGACTCAATCTTCAAC
131 TAGGACTCAATCTTCAAC
422623 AACGAATTTG
Statistics
Matches: 279, Mismatches: 22, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
153 202 0.72
157 35 0.13
158 10 0.04
161 1 0.00
162 31 0.11
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (153 bp):
TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCCGCTCCCTAT
TCATTCAGAGAGTATAGGACTCAATCTTCAATGAACTTGTCCGCTCCCTATTCATTCAGAGAGTA
TAGGACTCAATCTTCAACGAACT
Found at i:423783 original size:8 final size:8
Alignment explanation
Indices: 423757--423863 Score: 57
Period size: 8 Copynumber: 13.4 Consensus size: 8
423747 CCTCCTTTTA
423757 TTTCTCTT
1 TTTCTCTT
*
423765 TTTTTCATT
1 TTTCTC-TT
423774 TTTCTCTT
1 TTTCTCTT
*
423782 TTTAT-TT
1 TTTCTCTT
*
423789 TTCTTTCTT
1 TT-TCTCTT
*
423798 TTTTTCATT
1 TTTCTC-TT
*
423807 TTTAT-TT
1 TTTCTCTT
423814 TTTCTCATT
1 TTTCTC-TT
423823 TTT-TC-T
1 TTTCTCTT
423829 TTTCT-TCT
1 TTTCTCT-T
423837 TTTCT-TCT
1 TTTCTCT-T
423845 TTT-TCTT
1 TTTCTCTT
423852 TTTCTCATT
1 TTTCTC-TT
423861 TTT
1 TTT
423864 ATTATTATTT
Statistics
Matches: 81, Mismatches: 6, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
6 4 0.05
7 16 0.20
8 34 0.42
9 27 0.33
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTCTCTT
Found at i:423783 original size:14 final size:14
Alignment explanation
Indices: 423766--423884 Score: 53
Period size: 14 Copynumber: 7.9 Consensus size: 14
423756 ATTTCTCTTT
423766 TTTTCATTTTTCTC
1 TTTTCATTTTTCTC
*
423780 TTTTTATTTTTCTTTC
1 TTTTCATTTTTC--TC
* *
423796 TTTTTTTCATTTTTATTT
1 ---TTTTCATTTTT-CTC
423814 TTTCTCATTTTT-TC
1 TTT-TCATTTTTCTC
*
423828 TTTTCTTCTTTTCTTC
1 TTTTCAT-TTTTC-TC
423844 TTTTTC-TTTTTCTC
1 -TTTTCATTTTTCTC
* * * *
423858 ATTTTTATTATTATT
1 -TTTTCATTTTTCTC
423873 TTTTCATTTTTC
1 TTTTCATTTTTC
423885 GTTTTTTTTC
Statistics
Matches: 79, Mismatches: 14, Indels: 24
0.68 0.12 0.21
Matches are distributed among these distances:
13 3 0.04
14 34 0.43
15 13 0.16
16 13 0.16
17 5 0.06
18 1 0.01
19 10 0.13
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCATTTTTCTC
Found at i:423783 original size:15 final size:15
Alignment explanation
Indices: 423752--423884 Score: 82
Period size: 15 Copynumber: 8.8 Consensus size: 15
423742 TGAACCCTCC
* *
423752 TTTT-ATTTCTCTTT
1 TTTTCATTTTTCTCT
423766 TTTTCATTTTTCTCT
1 TTTTCATTTTTCTCT
423781 TTTT-ATTTTTCTTTCTTT
1 TTTTCATTTTTC--TC--T
* *
423799 TTTTCATTTTTATTT
1 TTTTCATTTTTCTCT
423814 TTTCTCATTTTT-TC-
1 TTT-TCATTTTTCTCT
*
423828 TTTTCTTCTTTTCTTCT
1 TTTTCAT-TTTTC-TCT
423845 TTTTC-TTTTTCTCAT
1 TTTTCATTTTTCTC-T
* *
423860 TTTT-ATTATTAT-T
1 TTTTCATTTTTCTCT
423873 TTTTCATTTTTC
1 TTTTCATTTTTC
423885 GTTTTTTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
13 8 0.08
14 25 0.26
15 32 0.34
16 13 0.14
17 6 0.06
18 5 0.05
19 6 0.06
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCATTTTTCTCT
Found at i:423809 original size:40 final size:39
Alignment explanation
Indices: 423761--423866 Score: 132
Period size: 40 Copynumber: 2.7 Consensus size: 39
423751 CTTTTATTTC
423761 TCTT-TTTTTCATTTTTCTC-TTTTTATTTTTCTTTCTTT
1 TCTTCTTTTTCATTTTTCTCATTTTTATTTTTC-TTCTTT
*
423799 TTTTCATTTTT-ATTTTTTCTCATTTTT-TCTTTTCTTCTTT
1 TCTTC-TTTTTCA-TTTTTCTCATTTTTAT-TTTTCTTCTTT
423839 TCTTCTTTTTC-TTTTTCTCATTTTTATT
1 TCTTCTTTTTCATTTTTCTCATTTTTATT
423867 ATTATTTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
38 18 0.31
39 7 0.12
40 24 0.41
41 10 0.17
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (39 bp):
TCTTCTTTTTCATTTTTCTCATTTTTATTTTTCTTCTTT
Found at i:423881 original size:8 final size:8
Alignment explanation
Indices: 423764--423883 Score: 50
Period size: 8 Copynumber: 15.6 Consensus size: 8
423754 TTATTTCTCT
423764 TTTTTTCA
1 TTTTTTCA
423772 TTTTTCTC-
1 TTTTT-TCA
*
423780 TTTTTAT-T
1 TTTTT-TCA
*
423788 TTTCTTTCT
1 TTT-TTTCA
423797 TTTTTTCA
1 TTTTTTCA
423805 -TTTTT-A
1 TTTTTTCA
423811 TTTTTTCTCA
1 -TTTTT-TCA
423821 TTTTTTC-
1 TTTTTTCA
423828 TTTTCTTC-
1 TTTT-TTCA
423836 TTTTCTTC-
1 TTTT-TTCA
423844 -TTTTTC-
1 TTTTTTCA
423850 TTTTTCTCA
1 TTTTT-TCA
423859 -TTTTT-A
1 TTTTTTCA
*
423865 -TTATT-A
1 TTTTTTCA
423871 TTTTTTCA
1 TTTTTTCA
423879 TTTTT
1 TTTTT
423884 CGTTTTTTTT
Statistics
Matches: 94, Mismatches: 4, Indels: 28
0.75 0.03 0.22
Matches are distributed among these distances:
6 10 0.11
7 21 0.22
8 48 0.51
9 14 0.15
10 1 0.01
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:435547 original size:16 final size:16
Alignment explanation
Indices: 435526--435566 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
435516 GAATTAATAT
435526 AAACCTAAATAAGCTA
1 AAACCTAAATAAGCTA
435542 AAACCTAAATAAGCTA
1 AAACCTAAATAAGCTA
435558 AAACCTAAA
1 AAACCTAAA
435567 CTATTTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.59, C:0.20, G:0.05, T:0.17
Consensus pattern (16 bp):
AAACCTAAATAAGCTA
Found at i:455061 original size:19 final size:19
Alignment explanation
Indices: 455037--455078 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
455027 ACTGTTACAG
455037 GTTTTCAATTCAAAAGAAC
1 GTTTTCAATTCAAAAGAAC
455056 GTTTTCAATTCAAAAGAAC
1 GTTTTCAATTCAAAAGAAC
455075 GTTT
1 GTTT
455079 ACATCTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (19 bp):
GTTTTCAATTCAAAAGAAC
Found at i:459445 original size:6 final size:6
Alignment explanation
Indices: 459422--459446 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
459412 TTCCTTTTCC
459422 CCTTCT CCTTCT CCTTCT CCTTCT C
1 CCTTCT CCTTCT CCTTCT CCTTCT C
459447 ACTTTCCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CCTTCT
Found at i:466193 original size:32 final size:32
Alignment explanation
Indices: 466121--466194 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
466111 AGTGTCATTT
* * *
466121 TAGCTTGCAAAATTATAGATTGGTGTTACTCA
1 TAGCGTGCAAAATTACAGATTAGTGTTACTCA
* * *
466153 CAGTGTGCAAAATTGCAGATTAGTGTT-CTCCA
1 TAGCGTGCAAAATTACAGATTAGTGTTACT-CA
466185 TAGCGTGCAA
1 TAGCGTGCAA
466195 TCTGGCACGT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
31 2 0.06
32 31 0.94
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (32 bp):
TAGCGTGCAAAATTACAGATTAGTGTTACTCA
Found at i:471236 original size:26 final size:29
Alignment explanation
Indices: 471176--471240 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 29
471166 ATAATAATGG
* *
471176 TAGTTAAGTAACAAAATTTTATTTATTAA
1 TAGTTAATTAACAAAATTTTATTTATGAA
*
471205 TA-TTAATTAA-AAAA-TTTATTTA-GAT
1 TAGTTAATTAACAAAATTTTATTTATGAA
471230 TAGTTAATTAA
1 TAGTTAATTAA
471241 TAGATCCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 3 0.09
26 16 0.50
27 4 0.12
28 7 0.22
29 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (29 bp):
TAGTTAATTAACAAAATTTTATTTATGAA
Found at i:473763 original size:12 final size:12
Alignment explanation
Indices: 473748--473805 Score: 75
Period size: 12 Copynumber: 4.8 Consensus size: 12
473738 TCTTTCCTTC
473748 TTTCTTCTTCAT
1 TTTCTTCTTCAT
473760 TTTCTTCTTCAT
1 TTTCTTCTTCAT
473772 TTTCTTCATT--T
1 TTTCTTC-TTCAT
473783 TCTTCTTCTTCAT
1 T-TTCTTCTTCAT
*
473796 TTTTTTCTTC
1 TTTCTTCTTC
473806 CATCTTTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
11 4 0.10
12 33 0.80
13 4 0.10
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTCTTCTTCAT
Found at i:473767 original size:15 final size:15
Alignment explanation
Indices: 473749--473805 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 15
473739 CTTTCCTTCT
473749 TTCTTCTTCATTTTC
1 TTCTTCTTCATTTTC
473764 TTCTTCATTTTCTTCATTTTC
1 TTCTTC----T--TCATTTTC
*
473785 TTCTTCTTCATTTTT
1 TTCTTCTTCATTTTC
473800 TTCTTC
1 TTCTTC
473806 CATCTTTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
15 19 0.54
17 1 0.03
19 1 0.03
21 14 0.40
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (15 bp):
TTCTTCTTCATTTTC
Found at i:474915 original size:20 final size:19
Alignment explanation
Indices: 474882--474919 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
474872 ATTGATTGTA
474882 ATTTTAACTATCTATATTTT
1 ATTTTAACTATCTA-ATTTT
474902 ATTTTAA-TATTCTAATTT
1 ATTTTAACTA-TCTAATTT
474920 ACTCTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAACTATCTAATTTT
Found at i:475806 original size:13 final size:14
Alignment explanation
Indices: 475779--475808 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
475769 TTGTGAATAG
475779 ATAATTTTTTCTAA
1 ATAATTTTTTCTAA
475793 ATAATTTTTT-TAA
1 ATAATTTTTTCTAA
475806 ATA
1 ATA
475809 TAACAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
ATAATTTTTTCTAA
Found at i:477962 original size:18 final size:18
Alignment explanation
Indices: 477939--478001 Score: 117
Period size: 18 Copynumber: 3.5 Consensus size: 18
477929 CACAGTCAGA
477939 GCCACCGTTCACCATGCT
1 GCCACCGTTCACCATGCT
477957 GCCACCGTTCACCATGCT
1 GCCACCGTTCACCATGCT
477975 GCCACCGTTCACCATGCT
1 GCCACCGTTCACCATGCT
*
477993 ACCACCGTT
1 GCCACCGTT
478002 GATGACGGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.17, C:0.44, G:0.16, T:0.22
Consensus pattern (18 bp):
GCCACCGTTCACCATGCT
Found at i:484290 original size:24 final size:22
Alignment explanation
Indices: 484263--484311 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
484253 TATTTATTAT
* *
484263 ATATATATTTATGAATATATAAAA
1 ATATATATTCAT-AA-AAATAAAA
*
484287 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
484309 ATA
1 ATA
484312 CTATTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:485666 original size:3 final size:3
Alignment explanation
Indices: 485658--485791 Score: 187
Period size: 3 Copynumber: 43.7 Consensus size: 3
485648 TTATTTATTA
* *
485658 AAT AAT AAT AAT ATAT AAT ATAT AAT ATT AAT AAT AAT AAAT ACT AAT
1 AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT
* **
485706 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT GCT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
485754 AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
485792 AATGGATAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
3 107 0.92
4 9 0.08
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:486240 original size:113 final size:113
Alignment explanation
Indices: 486042--486804 Score: 1152
Period size: 113 Copynumber: 6.7 Consensus size: 113
486032 TCTTGATGAG
486042 TTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-C
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTC
*
486105 TGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
64 TGGAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
486155 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * * * *
486220 GAAAAGATGATTCACCAAATGATGGATTCAGGTAAAAGTTTGAACAAA
66 GAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* *
486268 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
486333 GAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
*
486381 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
486446 GAAATGAATGATCCATCAAGTGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAATG-TTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
486495 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
486560 GAAAAGCTGATCCATCAAATGACGGATTCAAGTAAAAGGTTGAACAAA
66 GAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
*
486608 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
486673 GAACTGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* *
486721 TTCTTCTCATTATGAACTTCTTCTTCTTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
486786 GTAATGAATGATCCATCAA
66 GAAATG-TTGATCCATCAA
486805 GTGGATTTGA
Statistics
Matches: 588, Mismatches: 58, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
112 1 0.00
113 473 0.80
114 114 0.19
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
Found at i:486659 original size:340 final size:340
Alignment explanation
Indices: 486040--486807 Score: 1344
Period size: 340 Copynumber: 2.3 Consensus size: 340
486030 GCTCTTGATG
*
486040 AGTTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC
1 AGTTCTTCTCATTATGAACTTCT-TCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-C
* * *
486104 -CTGGCAATG-TTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTA
64 TCTGGAAATGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTA
*
486167 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATT
129 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATC
* * * *
486232 CACCAAATGATGGATTCAGGTAAAAGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTT
194 CACCAAATGACGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT
486297 CTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAATGTTGATCCATCAAATGATGAATTT
259 CTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAATGTTGATCCATCAAATGATGAATTT
486362 AAACAAAAAGTTGAACA
324 AAACAAAAAGTTGAACA
486379 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * *
486444 TGGAAATGAATGATCCATCAAGTGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATG
66 TGGAAATGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
*
486509 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCA
131 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCA
*
486574 TCAAATGACGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
196 CCAAATGACGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
*
486639 TCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAACTGTTGATCCATCAAATGATGAATTTAA
261 TCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAATGTTGATCCATCAAATGATGAATTTAA
486704 ACAAAAAGTTGAACA
326 ACAAAAAGTTGAACA
*
486719 AGTTCTTCTCATTATGAACTTCTTCTTCTTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
486784 TGGTAATGAATGATCCATCAAGTG
66 TGGAAATGAATGATCCATCAAGTG
486808 GATTTGAAAT
Statistics
Matches: 409, Mismatches: 17, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
338 1 0.00
339 67 0.16
340 341 0.83
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (340 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAATGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCA
CCAAATGACGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
TCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAATGTTGATCCATCAAATGATGAATTTAA
ACAAAAAGTTGAACA
Found at i:489829 original size:11 final size:11
Alignment explanation
Indices: 489813--489838 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
489803 TCAATTTTCC
489813 TTTTTCTTTTT
1 TTTTTCTTTTT
489824 TTTTTCTTTTT
1 TTTTTCTTTTT
489835 TTTT
1 TTTT
489839 CTTCTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:489832 original size:17 final size:17
Alignment explanation
Indices: 489807--489849 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
489797 CTTGATTCAA
*
489807 TTTTCCTTTTTCTTTT-T
1 TTTTTCTTTTT-TTTTCT
489824 TTTTTCTTTTTTTTTCT
1 TTTTTCTTTTTTTTTCT
*
489841 TCTTTCTTT
1 TTTTTCTTT
489850 GCTGGATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTCT
Found at i:493874 original size:15 final size:13
Alignment explanation
Indices: 493844--493881 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
493834 AACTATGACA
493844 AAAT-AAATAATG
1 AAATAAAATAATG
493856 AAATAAAATAATTG
1 AAATAAAATAA-TG
493870 CAAATAAAATAA
1 -AAATAAAATAA
493882 AACATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 2 0.09
15 11 0.48
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (13 bp):
AAATAAAATAATG
Found at i:494634 original size:24 final size:22
Alignment explanation
Indices: 494607--494655 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
494597 TATTTATTAT
* *
494607 ATATATATTTATGAATATATAAAA
1 ATATATATTCAT-AA-AAATAAAA
*
494631 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
494653 ATA
1 ATA
494656 CTATTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:496012 original size:3 final size:3
Alignment explanation
Indices: 496004--496134 Score: 181
Period size: 3 Copynumber: 42.7 Consensus size: 3
495994 TTATTTATTA
* *
496004 AAT AAT AAT AAT ATAT AAT ATAT AAT ATT AAT AAT AAT AAAT ACT AAT
1 AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT
* **
496052 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT GCT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
496100 AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
496135 AATGGATAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
3 104 0.92
4 9 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:497539 original size:29 final size:28
Alignment explanation
Indices: 497488--497659 Score: 220
Period size: 29 Copynumber: 6.0 Consensus size: 28
497478 CCGTTGATCG
*
497488 GGTGCTATTTTCGTAATTATTTTTATAAA
1 GGTGCTATTTTTGTAATTATTTTTA-AAA
497517 GGTGCTA-TTTTGTAATTATTTTTAAAA
1 GGTGCTATTTTTGTAATTATTTTTAAAA
497544 TGGTGCTATTTTTGTAATTATTTTTGAAAA
1 -GGTGCTATTTTTGTAATTATTTTT-AAAA
* * *
497574 TGTGATATTTTTGTAATTATTTTAAAAAA
1 GGTGCTATTTTTGTAATTATTTT-TAAAA
*
497603 GGTGTTATTTTTGTAATTATTTTTAAAA
1 GGTGCTATTTTTGTAATTATTTTTAAAA
* * *
497631 TGGTGTTATTTTCGTAAATATTTTTAAAA
1 -GGTGCTATTTTTGTAATTATTTTTAAAA
497660 ATGTGATAGT
Statistics
Matches: 129, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
27 3 0.02
28 27 0.21
29 95 0.74
30 4 0.03
ACGTcount: A:0.30, C:0.03, G:0.14, T:0.53
Consensus pattern (28 bp):
GGTGCTATTTTTGTAATTATTTTTAAAA
Found at i:497641 original size:87 final size:86
Alignment explanation
Indices: 497493--497676 Score: 269
Period size: 87 Copynumber: 2.1 Consensus size: 86
497483 GATCGGGTGC
* * * *
497493 TATTTTCGTAATTATTTTTATAAAGGTGCTATTTTGTAATTATTTTTAAAATGGTGCTATTTTTG
1 TATTTTTGTAATTATTTTAAAAAAGGTGCTATTTTGTAATTATTTTTAAAATGGTGCTATTTTCG
* *
497558 TAATTATTTTTGAAAATGTGA
66 TAAATATTTTTAAAAATGTGA
* *
497579 TATTTTTGTAATTATTTTAAAAAAGGTGTTATTTTTGTAATTATTTTTAAAATGGTGTTATTTTC
1 TATTTTTGTAATTATTTTAAAAAAGGTGCTA-TTTTGTAATTATTTTTAAAATGGTGCTATTTTC
497644 GTAAATATTTTTAAAAATGTGA
65 GTAAATATTTTTAAAAATGTGA
* *
497666 TAGTTGTGTAA
1 TATTTTTGTAA
497677 AATGGTTGAT
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
86 27 0.31
87 60 0.69
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (86 bp):
TATTTTTGTAATTATTTTAAAAAAGGTGCTATTTTGTAATTATTTTTAAAATGGTGCTATTTTCG
TAAATATTTTTAAAAATGTGA
Found at i:499207 original size:35 final size:35
Alignment explanation
Indices: 499137--499212 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
499127 CTCATATCAT
*
499137 ATATATTATAGCATATACAATAATCACTAACACAC
1 ATATATTATAGCATATACAATAATCACTAAAACAC
* *
499172 ATATATTATATCATATA-ATTCATATCAC-AAAACAC
1 ATATATTATAGCATATACAAT-A-ATCACTAAAACAC
499207 ATATAT
1 ATATAT
499213 ACATCACATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 2 0.06
35 29 0.81
36 5 0.14
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (35 bp):
ATATATTATAGCATATACAATAATCACTAAAACAC
Found at i:507244 original size:18 final size:18
Alignment explanation
Indices: 507207--507245 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
507197 ACCGGTTCCA
*
507207 ACCCGACCCGACCTGCTG
1 ACCCGACCCGACCTACTG
* *
507225 ACCCGACCCTACCTATTG
1 ACCCGACCCGACCTACTG
507243 ACC
1 ACC
507246 GTTGTCCGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.49, G:0.15, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGACCTACTG
Found at i:507504 original size:55 final size:54
Alignment explanation
Indices: 507395--507504 Score: 139
Period size: 54 Copynumber: 2.0 Consensus size: 54
507385 TTTCGTAATT
* * * *
507395 ATTTTTAAAATAGTGCTAAATTTGTAATTATTTTTAAAAAGTGATATTTTTGTA
1 ATTTTTAAAATAGTGCTAAATTCGTAAATATTTTTAAAAAGTGATAATTGTGTA
* * * *
507449 ATTTTTTAAATGGTGTTATATTCGTAAATATTTTTAAAAAGGTGATAATTGTGTA
1 ATTTTTAAAATAGTGCTAAATTCGTAAATATTTTTAAAAA-GTGATAATTGTGTA
507504 A
1 A
507505 AATGGTTGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
54 34 0.72
55 13 0.28
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (54 bp):
ATTTTTAAAATAGTGCTAAATTCGTAAATATTTTTAAAAAGTGATAATTGTGTA
Found at i:507505 original size:29 final size:29
Alignment explanation
Indices: 507261--507492 Score: 278
Period size: 29 Copynumber: 8.1 Consensus size: 29
507251 CCGTTAACCG
507261 GGTGTTATTTTTGTAATTATTTTTAAAAA
1 GGTGTTATTTTTGTAATTATTTTTAAAAA
* * *
507290 GGTGTCATTTGTGTAATTATTTTTAAAAT
1 GGTGTTATTTTTGTAATTATTTTTAAAAA
507319 GGTGTTATTTTTGTAATTATTTTTAAAAA
1 GGTGTTATTTTTGTAATTATTTTTAAAAA
* *
507348 TGTGCTATTTTTGTAATTA-TTTTAAAAA
1 GGTGTTATTTTTGTAATTATTTTTAAAAA
*
507376 AGTGTTATTTTTCGTAATTATTTTTAAAATA
1 GGTGTTATTTTT-GTAATTATTTTTAAAA-A
* **
507407 -GTGCTAAATTTGTAATTATTTTTAAAAA
1 GGTGTTATTTTTGTAATTATTTTTAAAAA
* *
507435 -GTGATATTTTTGTAA-T-TTTTT-AAAT
1 GGTGTTATTTTTGTAATTATTTTTAAAAA
* * *
507460 GGTGTTATATTCGTAAATATTTTTAAAAA
1 GGTGTTATTTTTGTAATTATTTTTAAAAA
507489 GGTG
1 GGTG
507493 ATAATTGTGT
Statistics
Matches: 175, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
25 3 0.02
26 17 0.10
27 2 0.01
28 37 0.21
29 99 0.57
30 16 0.09
31 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (29 bp):
GGTGTTATTTTTGTAATTATTTTTAAAAA
Found at i:508970 original size:24 final size:24
Alignment explanation
Indices: 508931--508977 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
508921 CATATATGGT
*
508931 ATGAACAGTACCGTGAACAGTACC
1 ATGAACAATACCGTGAACAGTACC
*
508955 ATGAACAATACTGTGAACAGTAC
1 ATGAACAATACCGTGAACAGTAC
508978 TATAAACAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (24 bp):
ATGAACAATACCGTGAACAGTACC
Found at i:508978 original size:12 final size:12
Alignment explanation
Indices: 508932--508977 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
508922 ATATATGGTA
508932 TGAACAGTACCG
1 TGAACAGTACCG
*
508944 TGAACAGTACCA
1 TGAACAGTACCG
* *
508956 TGAACAATACTG
1 TGAACAGTACCG
508968 TGAACAGTAC
1 TGAACAGTAC
508978 TATAAACAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (12 bp):
TGAACAGTACCG
Found at i:508985 original size:12 final size:12
Alignment explanation
Indices: 508930--508987 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
508920 ACATATATGG
508930 TATGAACAGTAC
1 TATGAACAGTAC
**
508942 CGTGAACAGTAC
1 TATGAACAGTAC
* *
508954 CATGAACAATAC
1 TATGAACAGTAC
*
508966 TGTGAACAGTAC
1 TATGAACAGTAC
*
508978 TATAAACAGT
1 TATGAACAGT
508988 GAAAAATTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.22
Consensus pattern (12 bp):
TATGAACAGTAC
Found at i:509037 original size:11 final size:11
Alignment explanation
Indices: 509021--509054 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
509011 GGATCGATGC
*
509021 ACTGCTACAGT
1 ACTGCTACAAT
509032 ACTGCTACAAT
1 ACTGCTACAAT
*
509043 ACTACTACAAT
1 ACTGCTACAAT
509054 A
1 A
509055 ACTTCGGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.26
Consensus pattern (11 bp):
ACTGCTACAAT
Found at i:513480 original size:12 final size:12
Alignment explanation
Indices: 513465--513505 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
513455 AAACAAACTT
*
513465 ATAAATGAGTCA
1 ATAAATGAGACA
*
513477 ATAAATGAGACT
1 ATAAATGAGACA
*
513489 ATAAATGAGCCA
1 ATAAATGAGACA
513501 ATAAA
1 ATAAA
513506 CGATCTTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.22
Consensus pattern (12 bp):
ATAAATGAGACA
Found at i:514896 original size:6 final size:6
Alignment explanation
Indices: 514885--514910 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
514875 TCAATTGAAG
514885 CTCAAA CTCAAA CTCAAA CTCAAA CT
1 CTCAAA CTCAAA CTCAAA CTCAAA CT
514911 TGAACCTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (6 bp):
CTCAAA
Found at i:515141 original size:73 final size:73
Alignment explanation
Indices: 515022--515163 Score: 257
Period size: 73 Copynumber: 1.9 Consensus size: 73
515012 TATTTTTTTC
515022 GAGTTGCTCGCGAGTATCAAGTAGCTCGTTTCGACTTGTTAAGAACACGAATCGAGTTCGAGTAC
1 GAGTTGCTCGCGAGTATCAAGTAGCTCGTTTCGACTTGTTAAGAACACGAATCGAGTTCGAGTAC
515087 GACTTGAG
66 GACTTGAG
* * *
515095 GAGTTGCTCGCGAGTATCAAGTAGCTCGTTTTGACTTGTTAAGAACACGAGTCGAGTTCGAGTTC
1 GAGTTGCTCGCGAGTATCAAGTAGCTCGTTTCGACTTGTTAAGAACACGAATCGAGTTCGAGTAC
515160 GACT
66 GACT
515164 CGTATCCTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (73 bp):
GAGTTGCTCGCGAGTATCAAGTAGCTCGTTTCGACTTGTTAAGAACACGAATCGAGTTCGAGTAC
GACTTGAG
Found at i:521234 original size:2 final size:2
Alignment explanation
Indices: 521227--521257 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
521217 AAGAAAATGA
521227 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 A
521258 AAGTCAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:527134 original size:31 final size:32
Alignment explanation
Indices: 527064--527135 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
527054 CTTTCATGAG
*
527064 GAGACATAATGCTTCATCAAGGAATGCTTCCAA
1 GAGACATGATGCTTCATCAAGG-ATGCTTCCAA
* * *
527097 GGGACATGATGTTTCATCAAGG-TGCTTCCGA
1 GAGACATGATGCTTCATCAAGGATGCTTCCAA
527128 GAGACATG
1 GAGACATG
527136 TCCTTTCATC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 15 0.44
33 19 0.56
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (32 bp):
GAGACATGATGCTTCATCAAGGATGCTTCCAA
Found at i:527143 original size:31 final size:32
Alignment explanation
Indices: 527076--527145 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
527066 GACATAATGC
* *
527076 TTCATCAAGGAATGCTTCCAAGGGACATGATGT
1 TTCATCAAGG-ATGCTTCCAAGAGACATGATCT
*
527109 TTCATCAAGG-TGCTTCCGAGAGACATG-TCCT
1 TTCATCAAGGATGCTTCCAAGAGACATGAT-CT
527140 TTCATC
1 TTCATC
527146 TCAAAAGGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 1 0.03
31 22 0.67
33 10 0.30
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (32 bp):
TTCATCAAGGATGCTTCCAAGAGACATGATCT
Found at i:528019 original size:28 final size:28
Alignment explanation
Indices: 527979--528051 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
527969 TCACGTGAGC
527979 TCACCATTTCCAACCCGTGCCAGTGCCT
1 TCACCATTTCCAACCCGTGCCAGTGCCT
528007 TCACCATTTCCAACCCGTGCCAGTGCCT
1 TCACCATTTCCAACCCGTGCCAGTGCCT
*
528035 TCACTATTTCCAACCCG
1 TCACCATTTCCAACCCG
528052 GGCTTACCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.19, C:0.42, G:0.12, T:0.26
Consensus pattern (28 bp):
TCACCATTTCCAACCCGTGCCAGTGCCT
Found at i:531942 original size:21 final size:21
Alignment explanation
Indices: 531929--531988 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
531919 ACGAGAAGAG
*
531929 CATTCATCAAGACGAGAATGT
1 CATTCATCAAGACGAGAATGC
531950 CATTCATCAAGACGAGAATGC
1 CATTCATCAAGACGAGAATGC
531971 CATTCATCAAGACGAGAA
1 CATTCATCAAGACGAGAA
531989 GACTCTTCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (21 bp):
CATTCATCAAGACGAGAATGC
Found at i:531997 original size:21 final size:21
Alignment explanation
Indices: 531918--532014 Score: 101
Period size: 21 Copynumber: 4.6 Consensus size: 21
531908 TCGTACCAAG
*
531918 GACGAGAAGAGCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
531939 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
531960 GACGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
*
531981 GACGAGAAGACTC-TTCATGAA
1 GACGAGAAGAC-CATTCATCAA
* *
532002 AATGAGAAGACCA
1 GACGAGAAGACCA
532015 CATCGCATGG
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.18
Consensus pattern (21 bp):
GACGAGAAGACCATTCATCAA
Found at i:537016 original size:108 final size:108
Alignment explanation
Indices: 536790--537035 Score: 316
Period size: 108 Copynumber: 2.3 Consensus size: 108
536780 TTCACCGGAG
* *
536790 AATAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTGAAGCCTTC
1 AATAGTGAAGCAATCCATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACAATCTGAAGCCTTC
* ** *
536855 ACCGGAGAATAGTGAAGCAAACCATCTGAAGCCTTCATCGGAG
66 ACCAGAGAATAGTGAAGCAAACCATCTGAAGCCTTCATCCAAA
* * * *
536898 AATAGGGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCAT-AAGTCTT
1 AATAGTGAAGCAATCCATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACAATC-TGAAGCCTT
* * *
536962 CACCAGAGAGTAGTGAAGCAAACCATCTTAAGTCTTCA-CCAAA
65 CACCAGAGAATAGTGAAGCAAACCATCTGAAGCCTTCATCCAAA
* *
537005 AAGTAGTGAAGCAGATCCATTTTAAGCCTTC
1 AA-TAGTGAAGCA-ATCCATCTGAAGCCTTC
537036 TCAGAAGAGT
Statistics
Matches: 118, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
107 4 0.03
108 99 0.84
109 15 0.13
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (108 bp):
AATAGTGAAGCAATCCATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACAATCTGAAGCCTTC
ACCAGAGAATAGTGAAGCAAACCATCTGAAGCCTTCATCCAAA
Found at i:537017 original size:36 final size:36
Alignment explanation
Indices: 536775--537001 Score: 339
Period size: 36 Copynumber: 6.3 Consensus size: 36
536765 AGTCAATCCT
536775 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
* *
536811 AAGCCTTCACCGGAGAATAGTGAAGCAATCAATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
536847 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
* * * *
536883 AAGCCTTCATCGGAGAATAGGGAAGCAATCAATCTG
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
536919 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCAT-
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATC-TG
* * * *
536955 AAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCTT
1 AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
*
536991 AAGTCTTCACC
1 AAGCCTTCACC
537002 AAAAAGTAGT
Statistics
Matches: 174, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
35 1 0.01
36 172 0.99
37 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (36 bp):
AAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTG
Found at i:537482 original size:51 final size:51
Alignment explanation
Indices: 537417--537873 Score: 565
Period size: 51 Copynumber: 8.8 Consensus size: 51
537407 AAGATTATTT
* * *
537417 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * * *
537468 GAGTTCCATACTCCCTAGAGAAAGAATGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * *
537519 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTAAAGATGTTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
*
537570 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGA-GATGTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATG-T-TC
* *
537622 TGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGATGTTC
1 -GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* *
537674 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * *
537725 GAGTTCTATACTCCTTAAAGAAGGAAGGAGCGAACCCGTTTGAAAAGATTTTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG--AAGATGTTC
* * ** * *
537778 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCATTTGAAGAATATGTC
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-ATGT-TC
* * * *
537831 TGAGTTCCATACTCCCTAGAGAAATAGGGAGCGAACCCATTTG
1 -GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG
537874 TTGAAGATTG
Statistics
Matches: 363, Mismatches: 34, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
50 1 0.00
51 225 0.62
52 7 0.02
53 90 0.25
54 40 0.11
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (51 bp):
GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
Found at i:537697 original size:155 final size:154
Alignment explanation
Indices: 537417--537868 Score: 638
Period size: 155 Copynumber: 2.9 Consensus size: 154
537407 AAGATTATTT
* * * *
537417 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG-AAGATGTCCGAGTTCCATACTC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAAGATGTCTGAGTTCCATACTC
** * * *
537481 CCTAGAGAAAGAATGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAG
66 CCTAGAGAAAGAGGGAGCGAACCCATTTGAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAG
537546 GAGCGAACCCGTTTAAAGATGTTC
131 GAGCGAACCCGTTTAAAGATGTTC
537570 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTGAGTTCCATACT
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAA-AGATGTCTGAGTTCCATACT
* *
537635 CCCTAAAGAAAGAGGGAGCGAACCCATTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAA
65 CCCTAGAGAAAGAGGGAGCGAACCCATTTGAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAA
*
537700 GGAGCGAACCCGTTTGAAGATGTTC
130 GGAGCGAACCCGTTTAAAGATGTTC
* * * *
537725 GAGTTCTATACTCCTTAAAGAAGGAAGGAGCGAACCCGTTTGAAAAGAT-TTTCGAGTTCTATAC
1 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-AAAGATGTCT-GAGTTCCATAC
* * * *
537789 TCCCTAGAGAAAGGGGGAGCGAACCCATTTGAAGAATATGTCTGAGTTCCATACTCCCTAGAGAA
64 TCCCTAGAGAAAGAGGGAGCGAACCCATTTGAAG-ATAT-TC-GAGTTCTATACTCCTTAAAGAA
* *
537854 ATAGGGAGCGAACCC
126 AGAAGGAGCGAACCC
537869 ATTTGTTGAA
Statistics
Matches: 268, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
153 39 0.15
154 3 0.01
155 187 0.70
156 5 0.02
157 2 0.01
158 32 0.12
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (154 bp):
GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAAGATGTCTGAGTTCCATACTC
CCTAGAGAAAGAGGGAGCGAACCCATTTGAAGATATTCGAGTTCTATACTCCTTAAAGAAAGAAG
GAGCGAACCCGTTTAAAGATGTTC
Found at i:538019 original size:55 final size:53
Alignment explanation
Indices: 537850--538185 Score: 331
Period size: 53 Copynumber: 6.2 Consensus size: 53
537840 TACTCCCTAG
* * * *
537850 AGAAATAGGGAGC-GA-ACCCATTTGTTGAAGATTGTGGGTCTTATACTCACGGA
1 AGAAATAGGGAGCAGACA-CGA-TTGTTGAAGATTGTGAGTCTTATACTCTCTGA
* *
537903 AGAAATAGGGAGCAGACACGATCGTTGAAGATTGTGGGTCTTATACTCTCTGA
1 AGAAATAGGGAGCAGACACGATTGTTGAAGATTGTGAGTCTTATACTCTCTGA
* * * * *
537956 AGATATAGGGGGGAGACACGATAGTTGAAGATTGTTCGAGTATTATACTCTCTGA
1 AGAAATAGGGAGCAGACACGATTGTTGAAGATTG-T-GAGTCTTATACTCTCTGA
* * * *
538011 AGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGAGTCTTATACTCTCTGG
1 AGAAATAGGGAGCAGACACGATTGTTGAAGATTGTGAGTCTTATACTCTCTGA
* * *
538064 AGAAATAGGGAGTAGACCCGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGA
1 AGAAATAGGGAGCAGACACGATTGTTGAAGATTG-T-GAGTCTTATACTCTCTGA
* * * * *
538119 AGGAATAAGGAGCAGACACG-TT-TTCAAAGGATTTTCGAGT-TCTATACTCCCTGA
1 AGAAATAGGGAGCAGACACGATTGTT-GAA-GATTGT-GAGTCT-TATACTCTCTGA
*
538173 AGAAAGAGGGAGC
1 AGAAATAGGGAGC
538186 GAACCTGTAG
Statistics
Matches: 240, Mismatches: 34, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
53 121 0.50
54 37 0.15
55 82 0.34
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (53 bp):
AGAAATAGGGAGCAGACACGATTGTTGAAGATTGTGAGTCTTATACTCTCTGA
Found at i:538026 original size:108 final size:108
Alignment explanation
Indices: 537873--538138 Score: 356
Period size: 108 Copynumber: 2.5 Consensus size: 108
537863 GAACCCATTT
* * * *
537873 GTTGAAGATTG-T-GGGTCTTATACTCACGGAAGAAATAGGGAGCAGACACGATCGTTGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGATGAAGATT
* * *
537936 GTGGGTCTTATACTCTCTGAAGATATAGGGGGGAGACACGATA
66 GTGAGTCTTATACTCTCTGAAGAAATAGGGAGGAGACACGATA
* * * *
537979 GTTGAAGATTGTTCGAGTATTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGATGAAGATT
* * * *
538044 GTGAGTCTTATACTCTCTGGAGAAATAGGGAGTAGACCCGATT
66 GTGAGTCTTATACTCTCTGAAGAAATAGGGAGGAGACACGATA
* * *
538087 GTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAAGGAGCAGACACG
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACG
538139 TTTTCAAAGG
Statistics
Matches: 137, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
106 11 0.08
107 1 0.01
108 125 0.91
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (108 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGATGAAGATT
GTGAGTCTTATACTCTCTGAAGAAATAGGGAGGAGACACGATA
Found at i:538612 original size:10 final size:10
Alignment explanation
Indices: 538597--538625 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
538587 TTCGTCCGAG
538597 CCATTTGAAT
1 CCATTTGAAT
538607 CCATTTGAAT
1 CCATTTGAAT
538617 CCATTTGAA
1 CCATTTGAA
538626 GATGATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (10 bp):
CCATTTGAAT
Found at i:538981 original size:28 final size:28
Alignment explanation
Indices: 538941--539013 Score: 146
Period size: 28 Copynumber: 2.6 Consensus size: 28
538931 TCACGTGAGC
538941 TCACCATTTCCAACCCGTGCCAGTGCCT
1 TCACCATTTCCAACCCGTGCCAGTGCCT
538969 TCACCATTTCCAACCCGTGCCAGTGCCT
1 TCACCATTTCCAACCCGTGCCAGTGCCT
538997 TCACCATTTCCAACCCG
1 TCACCATTTCCAACCCG
539014 GGCTTACCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.19, C:0.44, G:0.12, T:0.25
Consensus pattern (28 bp):
TCACCATTTCCAACCCGTGCCAGTGCCT
Found at i:542003 original size:16 final size:16
Alignment explanation
Indices: 541982--542013 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
541972 TATATGTATA
541982 ATATATATAATATATT
1 ATATATATAATATATT
*
541998 ATATATTTAATATATT
1 ATATATATAATATATT
542014 TAATTATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATATAATATATT
Found at i:547635 original size:20 final size:21
Alignment explanation
Indices: 547596--547639 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
547586 AATAAAATTT
*
547596 ATTTTGATTTAAACAAATAAA
1 ATTTTGATTAAAACAAATAAA
*
547617 ATTTTG-TTAAAATAAATAAA
1 ATTTTGATTAAAACAAATAAA
547637 ATT
1 ATT
547640 GAAATGGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (21 bp):
ATTTTGATTAAAACAAATAAA
Found at i:548070 original size:71 final size:71
Alignment explanation
Indices: 547903--548071 Score: 185
Period size: 71 Copynumber: 2.4 Consensus size: 71
547893 GCTTAGGTTC
* * * *
547903 TCTTTGATCCATCATGGCTTATTATTCCTCCTTGTCTTGGTATAGCATGAACAACAATGCTTTGT
1 TCTTTGATCCATCATGGCTTACTATTCCTCCTTATCTTGGTATAGCACGAACAACAATGCTTTGC
547968 TTAAAT
66 TTAAAT
* * * * * * *
547974 TCTTTGATCCATTACGACTTACTATTCCTCCTTATCTTGGTGTAGCACGAATAATAATGTTTTGC
1 TCTTTGATCCATCATGGCTTACTATTCCTCCTTATCTTGGTATAGCACGAACAACAATGCTTTGC
* *
548039 TTGATT
66 TTAAAT
* * * *
548045 TTTTTTATCTATCATGGCTTGCTATTC
1 TCTTTGATCCATCATGGCTTACTATTC
548072 TTTACACAAC
Statistics
Matches: 78, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
71 78 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.45
Consensus pattern (71 bp):
TCTTTGATCCATCATGGCTTACTATTCCTCCTTATCTTGGTATAGCACGAACAACAATGCTTTGC
TTAAAT
Found at i:548227 original size:39 final size:39
Alignment explanation
Indices: 548123--548233 Score: 107
Period size: 39 Copynumber: 2.8 Consensus size: 39
548113 TTTGACCCAT
* * *
548123 AATGTTACGAAAAATGTAACATTTTTTAA-TTGCCAACCGAA
1 AATGTTACGAAGAATCTAACA--TTTTAAGTTG-TAACCGAA
* * *
548164 AATGTTATGAAGCATCTAACATTTTAGGTTGTAACCGAA
1 AATGTTACGAAGAATCTAACATTTTAAGTTGTAACCGAA
* * *
548203 AATGTTACGTAGAATGTAATATTTTAAGTTG
1 AATGTTACGAAGAATCTAACATTTTAAGTTG
548234 CATACAACCT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
39 37 0.65
40 3 0.05
41 17 0.30
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (39 bp):
AATGTTACGAAGAATCTAACATTTTAAGTTGTAACCGAA
Found at i:551256 original size:32 final size:32
Alignment explanation
Indices: 551215--551280 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
551205 AAATCTACTT
551215 CAGTATTTTTTTTATCATAACTTCCTCTGTTC
1 CAGTATTTTTTTTATCATAACTTCCTCTGTTC
551247 CAGTATTTTTTTTATCATAACTTCCTCTGTTC
1 CAGTATTTTTTTTATCATAACTTCCTCTGTTC
551279 CA
1 CA
551281 ACCTCAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.20, C:0.23, G:0.06, T:0.52
Consensus pattern (32 bp):
CAGTATTTTTTTTATCATAACTTCCTCTGTTC
Found at i:555934 original size:22 final size:20
Alignment explanation
Indices: 555895--555935 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
555885 ATATAATAAT
*
555895 AATAATAGCAAAATAAATAC
1 AATAATAACAAAATAAATAC
555915 AATAGATAACAAAGATAAATA
1 AATA-ATAACAAA-ATAAATA
555936 AAAGTTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (20 bp):
AATAATAACAAAATAAATAC
Found at i:557565 original size:23 final size:23
Alignment explanation
Indices: 557547--557607 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
557537 CTCGTATAAA
557547 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
557570 TGCACCGAAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
557593 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
557608 TATAAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:558471 original size:24 final size:22
Alignment explanation
Indices: 558420--558478 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 22
558410 TTCCCTTGAA
558420 GTGCATCGATGCATTCTACAAT
1 GTGCATCGATGCATTCTACAAT
558442 GT--ATCGATGCATTCTTTA-ACAT
1 GTGCATCGATGCATTC--TACA-AT
*
558464 GTGCATCGATACATT
1 GTGCATCGATGCATT
558479 ACCCATGCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 12 0.39
21 1 0.03
22 8 0.26
24 10 0.32
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (22 bp):
GTGCATCGATGCATTCTACAAT
Found at i:559625 original size:5 final size:6
Alignment explanation
Indices: 559596--559643 Score: 60
Period size: 6 Copynumber: 7.5 Consensus size: 6
559586 GCAAAATGAT
*
559596 TAAAAA TTAATAA TAAAAA TAAAAA TAAAAA TAAATAA TAAATAA TAA
1 TAAAAA -TAAAAA TAAAAA TAAAAA TAAAAA TAAA-AA TAAA-AA TAA
559644 TTTTTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 21 0.55
7 17 0.45
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (6 bp):
TAAAAA
Found at i:560083 original size:84 final size:83
Alignment explanation
Indices: 559899--560564 Score: 744
Period size: 84 Copynumber: 7.9 Consensus size: 83
559889 TTGTTGACAT
* * * * * * ** *
559899 ATAGCCCTTCTCGGCTTGAGCTATGCTGTAAATTTGATTTGCCTCT-GAGTTGAATGTAATCGAA
1 ATAGCCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATATGCCT-TGGAGCTGAGCGTAGTCGAA
*
559963 CTCGAAGGCCTTTTGGTGGCAG
63 CTCGAAGG-TTTTTGGTGGCAG
* * * *
559985 ATAGCCCTTTTAGCCTTGAGCTATGCTGCAAATGATGTGACTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
560050 GAAGGTTTTTGGTTGGCAG
66 GAAGGTTTTTGG-TGGCAG
* * *
560069 ATAACTCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTTAGCGTAGTCGAACTC
1 ATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
* *
560134 GGAGGTCTTTTGGTGGAAG
66 GAAGGT-TTTTGGTGGCAG
* * * * * *
560153 ATAGCCCTTCTAGTCTTGAGCTGTGCTGCAAATGATATGCCTTAGAGCTGAGCGTAATTGAACTC
1 ATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
* * *
560218 GAAGGTATTTGGTTAGAAG
66 GAAGGTTTTTGG-TGGCAG
* * * *
560237 ATAACCCTTTTAGCCTTGAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTAGAACTC
1 ATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
*
560302 GAAGGCCTTTTGGTGGCAG
66 GAAGG-TTTTTGGTGGCAG
* * *
560321 ATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATATACCTTAGAGCTGAGCGTAGTCAAACTC
1 ATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
*
560386 GAAGGTCTTTTGGTGGCAT
66 GAAGGT-TTTTGGTGGCAG
* * *
560405 ATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
* * *
560470 AAAGGTCTTTGTTGGCAG
66 GAAGGTTTTTGGTGGCAG
* * * * * * *
560488 ATAAG-CCTTCTAGCCTTGAGTTATACTGCAAAT-AGTGTACCCTCGAAGCTGAGTGTAATCGAA
1 AT-AGCCCTTCTAGCCTTGAGTTATGCTGCAAATGA-TAT-GCCTTGGAGCTGAGCGTAGTCGAA
*
560551 CTCGAAGGTCTTTG
63 CTCGAAGGTTTTTG
560565 TGTTTCAAGA
Statistics
Matches: 500, Mismatches: 71, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
82 1 0.00
83 52 0.10
84 408 0.82
85 11 0.02
86 28 0.06
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (83 bp):
ATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
GAAGGTTTTTGGTGGCAG
Found at i:560411 original size:252 final size:251
Alignment explanation
Indices: 559887--560520 Score: 844
Period size: 252 Copynumber: 2.5 Consensus size: 251
559877 ACTCGTCAAT
* * * * * * *
559887 TTTTGTTGACATATAGCCCTTCTCGGCTTGAGCTATGCTGTAAATTTGATTTGCCTCT-GAGTTG
1 TTTTGGTGGCATATAGCCCTTCTAGCCTTGAGCTATGCTGCAAA--TGATATGCCT-TAGAGCTG
** * *
559951 AATGTAATCGAACTCGAAGGCCTTTTGG-TGGCAGATAGCCCTTTTAGCCTTGAGCTATGCTGCA
63 AGCGTAATCGAACTCGAAGG--TTTTGGTTGGCAGATAACCCTTTTAGCCTTGAGTTATGCTGCA
* * * *
560015 AATGATGTGACTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTGGTTGGCAGATAACTCTTCT
126 AATGATATGACTTGGAGCTGAGCGTAGTAGAACTCGAAGGCTTTTGGTTGGCAGATAACCCTTCT
* * * * *
560080 AGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTTAGCGTAGTCGAACTCGGAGGTC
191 AGCCTTGAGTTATGCTGCAAATGATATACCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTC
* * * *
560141 TTTTGGTGGAAGATAGCCCTTCTAGTCTTGAGCTGTGCTGCAAATGATATGCCTTAGAGCTGAGC
1 TTTTGGTGGCATATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTAGAGCTGAGC
* * * *
560206 GTAATTGAACTCGAAGGTATTTGGTTAGAAGATAACCCTTTTAGCCTTGAGTTATGCTGTAAATG
66 GTAATCGAACTCGAAGGT-TTTGGTTGGCAGATAACCCTTTTAGCCTTGAGTTATGCTGCAAATG
* *
560271 ATATGCCTTGGAGCTGAGCGTAGTAGAACTCGAAGGCCTTTTGG-TGGCAGATAGCCCTTCTAGC
130 ATATGACTTGGAGCTGAGCGTAGTAGAACTCGAAGG-CTTTTGGTTGGCAGATAACCCTTCTAGC
560335 CTTGAGTTATGCTGCAAATGATATACCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTC
194 CTTGAGTTATGCTGCAAATGATATACCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTC
*
560393 TTTTGGTGGCATATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGC
1 TTTTGGTGGCATATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTAGAGCTGAGC
* * * * *
560458 GTAGTCGAACTCAAAGGTCTTT-GTTGGCAGATAAGCCTTCTAGCCTTGAGTTATACTGCAAAT
66 GTAATCGAACTCGAAGGT-TTTGGTTGGCAGATAACCCTTTTAGCCTTGAGTTATGCTGCAAAT
560521 AGTGTACCCT
Statistics
Matches: 332, Mismatches: 44, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
250 1 0.00
251 41 0.12
252 248 0.75
253 6 0.02
254 36 0.11
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (251 bp):
TTTTGGTGGCATATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTAGAGCTGAGC
GTAATCGAACTCGAAGGTTTTGGTTGGCAGATAACCCTTTTAGCCTTGAGTTATGCTGCAAATGA
TATGACTTGGAGCTGAGCGTAGTAGAACTCGAAGGCTTTTGGTTGGCAGATAACCCTTCTAGCCT
TGAGTTATGCTGCAAATGATATACCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTC
Found at i:560642 original size:33 final size:33
Alignment explanation
Indices: 560562--560679 Score: 193
Period size: 33 Copynumber: 3.5 Consensus size: 33
560552 TCGAAGGTCT
*
560562 TTGTGTTTCAAGAGAAAC-ATTTTCAAAGGTTTTT
1 TTGTGTTTCAAGAGAAACGA-TTTCAAAGG-TTTC
*
560596 TTGTGTTTTAAGAGAAACGATTTCAAAGGTTTC
1 TTGTGTTTCAAGAGAAACGATTTCAAAGGTTTC
560629 TTGTGTTTCAAGAGAAACGATTTCAAAGGTTTC
1 TTGTGTTTCAAGAGAAACGATTTCAAAGGTTTC
560662 TTGTGTTTCAAGAGAAAC
1 TTGTGTTTCAAGAGAAAC
560680 TGTCTCTAGG
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
33 53 0.66
34 26 0.32
35 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (33 bp):
TTGTGTTTCAAGAGAAACGATTTCAAAGGTTTC
Found at i:560752 original size:67 final size:70
Alignment explanation
Indices: 560632--560783 Score: 188
Period size: 67 Copynumber: 2.2 Consensus size: 70
560622 AGGTTTCTTG
* * * *
560632 TGTTTCAAGAGAAACGATTTCAAAGGTTTCTTGTGTTTCAAGAGAAACTGTCTCTAGGGAGGA-A
1 TGTTTCAAGAGAAACGATTTCAAAGGTATCTGGTGTTTCAAGAGAAACTGTCTCAAGAGA-GACA
*
560696 AAATTT
65 AAACTT
560702 TGTTTCAAGAGAAAC-ATATTCAAA-G-AT-TGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
1 TGTTTCAAGAGAAACGAT-TTCAAAGGTATCTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACA
560763 AAACTT
65 AAACTT
* *
560769 TGTTTCCAGGGAAAC
1 TGTTTCAAGAGAAAC
560784 TGTCTCAAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
66 2 0.03
67 46 0.63
68 1 0.01
69 3 0.04
70 21 0.29
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.30
Consensus pattern (70 bp):
TGTTTCAAGAGAAACGATTTCAAAGGTATCTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
AACTT
Found at i:560826 original size:36 final size:36
Alignment explanation
Indices: 560732--561010 Score: 285
Period size: 36 Copynumber: 7.9 Consensus size: 36
560722 CAAAGATTGG
560732 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
560769 TGTTTCCAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
560805 TATTTCAAGAGAAACTGTCTCAAGAGAGA-AAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
560841 AGTTCCAAAAGAAACTATCTCAAGGGAGACGAAAA-T
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATT
* *
560877 TGTTTCAAGTA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAG-AGAAAC-TGTCTCAAGAGAGACAAAATT
*
560906 TGTTTCAAG-GAAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAATT
* * * *
560942 TGTTTCAAGGGAAATTGTCTCAAGAAATACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
560978 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
561011 GACAAAATTT
Statistics
Matches: 200, Mismatches: 25, Indels: 35
0.77 0.10 0.13
Matches are distributed among these distances:
28 4 0.02
29 16 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 2 0.01
35 5 0.03
36 128 0.64
37 37 0.19
38 4 0.02
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:560949 original size:21 final size:21
Alignment explanation
Indices: 560925--560989 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
560915 GAAAACTATC
560925 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
*
560946 TCAAG-G-G---AAA-TTGTC
1 TCAAGAGAGACAAAATTTGTT
* *
560961 TCAAGAAATACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
560982 TCAAGAGA
1 TCAAGAGA
560990 AACTGTCTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
15 9 0.27
16 3 0.09
19 1 0.03
20 4 0.12
21 16 0.48
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:561068 original size:201 final size:206
Alignment explanation
Indices: 560732--561212 Score: 670
Period size: 201 Copynumber: 2.3 Consensus size: 206
560722 CAAAGATTGG
* * *
560732 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCCAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAG
* *
560797 ACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGAAAAACTTAGTTCCAAAAGAAACTATCTC
65 ACAAAA-TGA--TCAAGAGAAACTGTCTCAAGAGAGAAAAACTTAGTTCCAAAAGAAAATATCTC
560862 AAGGGAGACGAAAATTGTTTCAA-GTAAAACATATTCAAAGATTTTGTTTCAAGGAAAACTATCT
127 AAGGGAGACG-AAATTGTTTCAATGTAAAACATATTCAAAGATTTTGTTTCAAGGAAAACTATCT
560926 CAAGAGAGACAAAATT
191 CAAGAGAGACAAAATT
* * *
560942 TGTTTCAAGGGAAATTGTCTCAAGAAATACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
** * *
561007 C-AAA-GA-C-A-A-AATTTGTTTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAG
66 CAAAATGATCAAGAGAAACTGTCTCAAGAGAGA-AAAACTTAGTTCCAAAAGAAAATATCTCAAG
* * * * *
561066 GGAGACGAAATTTTTTTAATGTAAAACATATTCAAAGATTTTGTTTCAAGGGAAATTGTCTCAAG
130 GGAGACGAAATTGTTTCAATGTAAAACATATTCAAAGATTTTGTTTCAAGGAAAACTATCTCAAG
561131 AGAGACAAAATT
195 AGAGACAAAATT
* * *
561143 TATTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGAGAAACTGTCTCAAGAAAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
*
561208 AAAAA
66 CAAAA
561213 CTTTGTTTTG
Statistics
Matches: 244, Mismatches: 24, Indels: 14
0.87 0.09 0.05
Matches are distributed among these distances:
200 25 0.10
201 150 0.61
202 4 0.02
203 1 0.00
206 1 0.00
208 3 0.01
209 30 0.12
210 30 0.12
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (206 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
CAAAATGATCAAGAGAAACTGTCTCAAGAGAGAAAAACTTAGTTCCAAAAGAAAATATCTCAAGG
GAGACGAAATTGTTTCAATGTAAAACATATTCAAAGATTTTGTTTCAAGGAAAACTATCTCAAGA
GAGACAAAATT
Found at i:561156 original size:36 final size:36
Alignment explanation
Indices: 561109--561212 Score: 154
Period size: 36 Copynumber: 2.9 Consensus size: 36
561099 AAAGATTTTG
* *
561109 TTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTA
* *
561145 TTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTA
* *
561181 TTTCAAGAGAAACTGTCTCAAGAAAGAAAAAA
1 TTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
561213 CTTTGTTTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTA
Found at i:564190 original size:22 final size:22
Alignment explanation
Indices: 564163--564204 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
564153 AAACCATTTA
564163 GGGGGGAATCGGTACCCTCTTG
1 GGGGGGAATCGGTACCCTCTTG
*
564185 GGGGGGAATCGGTTCCCTCT
1 GGGGGGAATCGGTACCCTCT
564205 GAGCAATCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCTCTTG
Found at i:569959 original size:23 final size:23
Alignment explanation
Indices: 569933--570001 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
569923 CACCACAGCT
569933 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
569956 CATATAATTGCACCGAAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
569979 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
570002 TATAACAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:570233 original size:121 final size:121
Alignment explanation
Indices: 570006--570250 Score: 418
Period size: 121 Copynumber: 2.0 Consensus size: 121
569996 GTGCCATATA
*
570006 ACAATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTAT
1 ACAATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTAT
* * * *
570071 GTGTCTCACTAGACTTCACACATGTTCCTAAGAATACATATATATCCCGAAGGACC
66 GTGTCTCACCAGACTTCACACATGTTCCAAACAATACATATATACCCCGAAGGACC
*
570127 ACAATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTAT
1 ACAATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTAT
* *
570192 GTGTCTCACCAGACTTCACACATGTTCCAAACAATATATATATGCCCCGAAGGACC
66 GTGTCTCACCAGACTTCACACATGTTCCAAACAATACATATATACCCCGAAGGACC
570248 ACA
1 ACA
570251 TATCATTCCT
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 116 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (121 bp):
ACAATGTCCAGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTAT
GTGTCTCACCAGACTTCACACATGTTCCAAACAATACATATATACCCCGAAGGACC
Found at i:570313 original size:103 final size:103
Alignment explanation
Indices: 570134--570355 Score: 399
Period size: 103 Copynumber: 2.2 Consensus size: 103
570124 ACCACAATGT
* *
570134 CCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTC
1 CCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTC
*
570199 ACCAGACTTCACACATGTTCCAAACAATATATATATGC
66 ACCAGACTTCACACATGTTCCAAACAATACATATATGC
570237 CCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTC
1 CCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTC
* *
570302 ACCAGACTTCACACATGTTCCAAAGAATACATATATGT
66 ACCAGACTTCACACATGTTCCAAACAATACATATATGC
570340 CCCGAAGGACCACATA
1 CCCGAAGGACCACATA
570356 GACCCTTGAC
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 114 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (103 bp):
CCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTC
ACCAGACTTCACACATGTTCCAAACAATACATATATGC
Found at i:571220 original size:64 final size:64
Alignment explanation
Indices: 571107--571327 Score: 216
Period size: 64 Copynumber: 3.5 Consensus size: 64
571097 TAATGAAGGT
* ** * * ** * *
571107 ATGCATCGATGCACTACTGATGCATCGGCGCATAAAATGTATTCAATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTACATTCGATGTT-TCATTATTAATGGG
* * * *
571171 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACAAATTACATTCGATGTTTCATTATTAATGGG
* **
571235 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTACATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTACATTCGATGT-TTCATTATTAATGGG
**
571298 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
571328 ACACCTCCAA
Statistics
Matches: 132, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
63 4 0.03
64 123 0.93
65 5 0.04
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAATTACATTCGATGTTTCATTATTAATGGG
Found at i:575914 original size:23 final size:23
Alignment explanation
Indices: 575888--575965 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
575878 CACCACAGCT
575888 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
575911 CATATAATTGCACCGAAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
575934 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
575957 TATAATAAT
1 CAT-ATAAT
575966 GTCCATAAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
23 42 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:576143 original size:103 final size:103
Alignment explanation
Indices: 575975--576189 Score: 376
Period size: 103 Copynumber: 2.1 Consensus size: 103
575965 TGTCCATAAG
* **
575975 GACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGAATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGAATGTGTCTCACCAGAC
*
576040 TTCACATATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
*
576078 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGAATGTGTCTCACCAGAC
*
576143 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
576181 GACCACATA
1 GACCACATA
576190 GACCCTCGAC
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGAATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:581532 original size:17 final size:17
Alignment explanation
Indices: 581510--581553 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
581500 CTGTCCCCAG
581510 CGGAGTCGTCAAGCTGT
1 CGGAGTCGTCAAGCTGT
*
581527 CGGAGTCGCCAAGCTGT
1 CGGAGTCGTCAAGCTGT
581544 CGGAGTCGTC
1 CGGAGTCGTC
581554 TTTCGGGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.16, C:0.27, G:0.36, T:0.20
Consensus pattern (17 bp):
CGGAGTCGTCAAGCTGT
Found at i:581884 original size:19 final size:20
Alignment explanation
Indices: 581855--581892 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
581845 GTTAGATTAT
*
581855 AAAAAATAGAAATAAATATG
1 AAAAAATAGAAAAAAATATG
581875 AAAAAA-AGAAAAAAATAT
1 AAAAAATAGAAAAAAATAT
581893 TAATATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (20 bp):
AAAAAATAGAAAAAAATATG
Found at i:581942 original size:22 final size:20
Alignment explanation
Indices: 581902--581942 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
581892 TTAATATAAT
581902 AATAATAACAAAATAAATAC
1 AATAATAACAAAATAAATAC
*
581922 AATAGATAATAAAGATAAATA
1 AATA-ATAACAAA-ATAAATA
581943 AAAGTTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (20 bp):
AATAATAACAAAATAAATAC
Found at i:584752 original size:31 final size:31
Alignment explanation
Indices: 584712--584782 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
584702 GTTAACTTTT
* *
584712 AATTTGACCCCTAAACTTTAGATGAAGTATC
1 AATTTGACCCCTAAACTTTAGATAAAGCATC
*
584743 ATTTTGA-CCCTAAACTTTAGATAAAGCATC
1 AATTTGACCCCTAAACTTTAGATAAAGCATC
*
584773 AATTTAACCC
1 AATTTGACCC
584783 ATGAATTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 26 0.76
31 8 0.24
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (31 bp):
AATTTGACCCCTAAACTTTAGATAAAGCATC
Found at i:586351 original size:31 final size:30
Alignment explanation
Indices: 586297--586364 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
586287 AAATTCAGGG
* * * *
586297 GGTCAAATTGATATTTAATCTAAACTTTAGA
1 GGTCAAAATAATATTTAAGCTAAACTTCA-A
* *
586328 GGTCAAAATAATATTTCAGCTAAAGTTCAA
1 GGTCAAAATAATATTTAAGCTAAACTTCAA
586358 GGTCAAA
1 GGTCAAA
586365 TTAGTATTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (30 bp):
GGTCAAAATAATATTTAAGCTAAACTTCAA
Found at i:586492 original size:30 final size:31
Alignment explanation
Indices: 586458--586529 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
586448 TTAACGACTT
* *
586458 AGTGACTAAAATATAAT-GATCAATAATGTA
1 AGTGACTAAAATATAATAAATCAATAACGTA
* *
586488 AGTGA-TCAAAATTTAATAAATCGATAACGTA
1 AGTGACT-AAAATATAATAAATCAATAACGTA
*
586519 AGTGACCAAAA
1 AGTGACTAAAA
586530 CTTATATGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
29 1 0.03
30 14 0.41
31 19 0.56
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (31 bp):
AGTGACTAAAATATAATAAATCAATAACGTA
Found at i:603417 original size:25 final size:26
Alignment explanation
Indices: 603364--603420 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
603354 TAGAATTTTA
*
603364 AAAATTTTATTTAAAATAAAAAACTT
1 AAAATTTTATTTAAAATAAAAAACCT
** *
603390 AAAATTTTATTT-TTATAAAAACCCT
1 AAAATTTTATTTAAAATAAAAAACCT
603415 AAAATT
1 AAAATT
603421 ATAAAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (26 bp):
AAAATTTTATTTAAAATAAAAAACCT
Found at i:605563 original size:20 final size:18
Alignment explanation
Indices: 605538--605576 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
605528 AAAATTAAAG
605538 AATTTAATTAGTTTATTTAT
1 AATTTAATTA--TTATTTAT
605558 AATTTAATTATTATTTAT
1 AATTTAATTATTATTTAT
605576 A
1 A
605577 TCTCTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
AATTTAATTATTATTTAT
Found at i:613401 original size:22 final size:22
Alignment explanation
Indices: 613376--613422 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
613366 CTGTTAGCGC
*
613376 CCGACGATGGAAGTTGTGACTG
1 CCGACGATGGAAGCTGTGACTG
*
613398 CCGACGATGGAGGCTGTGACTG
1 CCGACGATGGAAGCTGTGACTG
613420 CCG
1 CCG
613423 GCGAAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.23, G:0.38, T:0.19
Consensus pattern (22 bp):
CCGACGATGGAAGCTGTGACTG
Found at i:618339 original size:198 final size:197
Alignment explanation
Indices: 618000--618405 Score: 749
Period size: 198 Copynumber: 2.1 Consensus size: 197
617990 GAATCACCAC
*
618000 CCATAAGCAATTAGTTTACATGTATCTACCTTTCAGATAGAAAAACATGTTACATACAGCTGATA
1 CCATAAGCAATTAGTTTACATATATCTACCTTTCAGATAGAAAAACATGTTACATACAGCTGATA
*
618065 AACATACTAGATAAATGAAATTGCAGGAAACAAGGACTCATTGTAAGACTATTATGGATAACTAA
66 AACATACTAGATAAATGAAATTGCAGGAAACAAGGACTCATTGTAAGACTATTATGGATAACCAA
** *
618130 CAATTGTAAATGCATACCTATATGGTATGTGTTTATGAGTTTGAAGATCCCTATACTTTTTGGCA
131 CAACGGTAAATGCATACCTATATGGTATGTG-TTATGAGTTTGAAGATCCCTATACTTTTTAGCA
618195 AGG
195 AGG
618198 CCATAAGCAATTAGTTTACATATATCTACCTTTCAGATAGAAAAACATGTTACATACAGCTGATA
1 CCATAAGCAATTAGTTTACATATATCTACCTTTCAGATAGAAAAACATGTTACATACAGCTGATA
618263 AACATACTAGATAAATGAAATTGCAGGAAACAAGGACTCATTGTAAGACTATTATGGATAACCAA
66 AACATACTAGATAAATGAAATTGCAGGAAACAAGGACTCATTGTAAGACTATTATGGATAACCAA
618328 CAACGGTAAATGCATACCTATATGGTATGTGTTATGAGTTTGAAGATCCCTATACTTTTTAGCAA
131 CAACGGTAAATGCATACCTATATGGTATGTGTTATGAGTTTGAAGATCCCTATACTTTTTAGCAA
618393 GG
196 GG
*
618395 CCATAATCAAT
1 CCATAAGCAAT
618406 GATATACACC
Statistics
Matches: 202, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
197 45 0.22
198 157 0.78
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (197 bp):
CCATAAGCAATTAGTTTACATATATCTACCTTTCAGATAGAAAAACATGTTACATACAGCTGATA
AACATACTAGATAAATGAAATTGCAGGAAACAAGGACTCATTGTAAGACTATTATGGATAACCAA
CAACGGTAAATGCATACCTATATGGTATGTGTTATGAGTTTGAAGATCCCTATACTTTTTAGCAA
GG
Found at i:621954 original size:3 final size:3
Alignment explanation
Indices: 621946--621996 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
621936 AAACGTCACC
621946 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
621994 TTA
1 TTA
621997 ATAGGAGATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:622900 original size:22 final size:21
Alignment explanation
Indices: 622864--622937 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
622854 CAATGAGTGG
622864 CATATGAAATTTGTCCCGAAGGA
1 CATATG-AA-TTGTCCCGAAGGA
*
622887 CATGTGAATATGTCCCGAAGGA
1 CATATGAAT-TGTCCCGAAGGA
* *
622909 CCTATGAGTTGTCCCGAAGGA
1 CATATGAATTGTCCCGAAGGA
*
622930 CCTATGAA
1 CATATGAA
622938 ACCCTCGACT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
21 20 0.44
22 20 0.44
23 5 0.11
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (21 bp):
CATATGAATTGTCCCGAAGGA
Found at i:622923 original size:21 final size:21
Alignment explanation
Indices: 622874--622937 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
622864 CATATGAAAT
* *
622874 TTGTCCCGAAGGACATGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
622895 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
622917 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
622938 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:623423 original size:20 final size:20
Alignment explanation
Indices: 623395--623449 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
623385 TTTCTTTTAG
*
623395 GGGGAATCGATTCCCCCCAA
1 GGGGTATCGATTCCCCCCAA
623415 GGGGTATCGATTCCCCCCAA
1 GGGGTATCGATTCCCCCCAA
623435 GGGGTATCGATTCCC
1 GGGGTATCGATTCCC
623450 TTTGCATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.20
Consensus pattern (20 bp):
GGGGTATCGATTCCCCCCAA
Found at i:639039 original size:54 final size:54
Alignment explanation
Indices: 638981--639138 Score: 194
Period size: 54 Copynumber: 2.9 Consensus size: 54
638971 TCTTTTGCCT
* *
638981 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTTGAAAATCTTCTGCAA
1 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTGAAA
* *
639035 ACGGGTTCGCTCCCACTTTCTTCAGGGAGTATAGAACTCGAAAATCTTTTGAAA
1 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTGAAA
* * * * *
639089 ACGTG-TCTGCTCCCTATTCCTTCAGAGAGTA-CGAGACTCGAACAATCTTC
1 ACGGGTTC-GCTCCCTCTTTCTTCAGGGAGTATAGA-ACTCGAA-AATCTTC
639139 AACAATCGTG
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
53 4 0.04
54 80 0.89
55 6 0.07
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (54 bp):
ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTGAAA
Found at i:639185 original size:109 final size:110
Alignment explanation
Indices: 639051--639300 Score: 332
Period size: 109 Copynumber: 2.3 Consensus size: 110
639041 TCGCTCCCAC
* *
639051 TTTCTTCAGGGAGTATAGAACTCGAAAATCTTTTGAA-AA-CGTGTCTGCTCCCTATTCCTTCAG
1 TTTCTTCAGAGAGTATAG-ACTCGAAAATCTTTTCAACAATCGTGTCTGCTCCCTATTCCTTCAG
* * *
639114 AGAGTACGAGACTCGAACAATCTTCAACAATCGTGTCTACTCCCTA
65 AGAGTACAAGACTCGAACAAACTTCAACAATCGCGTCTACTCCCTA
* *
639160 -TTCTTTCAGAGAGTATGAGACTCGAATATC--TTCAACAATCGTGTCTGCTCCCTATTCTTTCA
1 TTTC-TTCAGAGAGTAT-AGACTCGAAAATCTTTTCAACAATCGTGTCTGCTCCCTATTCCTTCA
* *
639222 GAGAGTATAAGACTCGAACAAACTTCAACAATCGCGTCTGCTCCCTA
64 GAGAGTACAAGACTCGAACAAACTTCAACAATCGCGTCTACTCCCTA
639269 TTTCTTCAGAGAGTATAAGAC-CGAACAATCTT
1 TTTCTTCAGAGAGTAT-AGACTCGAA-AATCTT
639301 CAACGATCGC
Statistics
Matches: 122, Mismatches: 11, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
107 4 0.03
108 9 0.07
109 104 0.85
110 5 0.04
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (110 bp):
TTTCTTCAGAGAGTATAGACTCGAAAATCTTTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
GAGTACAAGACTCGAACAAACTTCAACAATCGCGTCTACTCCCTA
Done.