Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold273
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: 639416
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 15802 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:326097 original size:16 final size:16
Alignment explanation
Indices: 326078--326130 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
326068 TTATTTATTA
326078 TTTTTTTAATTTTAAT
1 TTTTTTTAATTTTAAT
*
326094 TTTTTTTAATTTTTGAT
1 TTTTTTTAA-TTTTAAT
*
326111 TTTTGTTTATTATTTAAT
1 TTTT-TTTAAT-TTTAAT
326129 TT
1 TT
326131 GGGCCGGGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 9 0.29
17 11 0.35
18 11 0.35
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (16 bp):
TTTTTTTAATTTTAAT
Found at i:326098 original size:17 final size:17
Alignment explanation
Indices: 326078--326130 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
326068 TTATTTATTA
326078 TTTTTTTAATTTTAA-T
1 TTTTTTTAATTTTAATT
*
326094 TTTTTTTAATTTTTGATT
1 TTTTTTTAA-TTTTAATT
* *
326112 TTTGTTTATTATTTAATT
1 TTTTTTTAAT-TTTAATT
326130 T
1 T
326131 GGGCCGGGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 9 0.30
17 6 0.20
18 15 0.50
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (17 bp):
TTTTTTTAATTTTAATT
Found at i:328374 original size:7 final size:7
Alignment explanation
Indices: 328337--328388 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
328327 TAAATTATGC
328337 TATTTAT
1 TATTTAT
*
328344 TTTTTAAT
1 TATTT-AT
328352 TATATTAT
1 TAT-TTAT
*
328360 T-TACTAT
1 TAT-TTAT
328367 TATTTAT
1 TATTTAT
328374 TATTTAT
1 TATTTAT
328381 TATTTAT
1 TATTTAT
328388 T
1 T
328389 TAGGGAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
7 28 0.74
8 8 0.21
9 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (7 bp):
TATTTAT
Found at i:328380 original size:4 final size:4
Alignment explanation
Indices: 328337--328390 Score: 51
Period size: 4 Copynumber: 13.5 Consensus size: 4
328327 TAAATTATGC
*
328337 TATT TATT T-TT TAAT TATAT TATT TACTAT TATT TA-T TATT TA-T TATT
1 TATT TATT TATT TATT TAT-T TATT TA-T-T TATT TATT TATT TATT TATT
328385 TATT TA
1 TATT TA
328391 GGGAATAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
3 9 0.21
4 24 0.57
5 6 0.14
6 3 0.07
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (4 bp):
TATT
Found at i:347630 original size:144 final size:144
Alignment explanation
Indices: 347370--347661 Score: 494
Period size: 144 Copynumber: 2.0 Consensus size: 144
347360 CCACTTATGG
*
347370 TGTGTAGGATTGGACGGAGATAGTGTGTAGAGGCTGGTGGGTAGGATTCTGATTTACTGTATCTC
1 TGTGTAGGATTGGACCGAGATAGTGTGTAGAGGCTGGTGGGTAGGATTCTGATTTACTGTATCTC
*
347435 CATTCTGTATCTGATATGGCCCAAGGCCCTAATGTCACTCTGAGACTGTATCTTAACAAGCTAAG
66 CATTCTGTATCTGATATGGCCCAAGGCCCTAATGTCACTCTGAGACTGTATCTGAACAAGCTAAG
347500 GCCCAAACTAATTC
131 GCCCAAACTAATTC
* * * *
347514 TGTGTAGGATTGGACCGAGATGGTGTGTATAGGTTGGTGGGTAGGATTCTGATTTTCTGTATCTC
1 TGTGTAGGATTGGACCGAGATAGTGTGTAGAGGCTGGTGGGTAGGATTCTGATTTACTGTATCTC
* * * *
347579 CATTTTGTATCTGATATGGGCCAAGGCCCTAATGTCATTCTGAGACTGTATCTGAACAGGCTAAG
66 CATTCTGTATCTGATATGGCCCAAGGCCCTAATGTCACTCTGAGACTGTATCTGAACAAGCTAAG
347644 GCCCAAACTAATTC
131 GCCCAAACTAATTC
347658 TGTG
1 TGTG
347662 ATGGGCCCAG
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
144 138 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (144 bp):
TGTGTAGGATTGGACCGAGATAGTGTGTAGAGGCTGGTGGGTAGGATTCTGATTTACTGTATCTC
CATTCTGTATCTGATATGGCCCAAGGCCCTAATGTCACTCTGAGACTGTATCTGAACAAGCTAAG
GCCCAAACTAATTC
Found at i:353880 original size:30 final size:30
Alignment explanation
Indices: 353844--353905 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
353834 CTGTAGCTCC
353844 AGATATAAATAATTTAGGAACAGTGACTCA
1 AGATATAAATAATTTAGGAACAGTGACTCA
* *
353874 AGATATAAATAATTTAGTAACAGTGATTCA
1 AGATATAAATAATTTAGGAACAGTGACTCA
353904 AG
1 AG
353906 TGAACAGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (30 bp):
AGATATAAATAATTTAGGAACAGTGACTCA
Found at i:356171 original size:43 final size:43
Alignment explanation
Indices: 356110--356196 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
356100 TTGCATGAAG
* *
356110 TAGCTAAGGATTGTAAGAATAACCAGTTAAGATAAAACAACTT
1 TAGCTAAGCATTGTAAGAAGAACCAGTTAAGATAAAACAACTT
* *
356153 TAGCTAAGCATTGTAAGAAGAGCCGGTTAAGATAAAACAACTT
1 TAGCTAAGCATTGTAAGAAGAACCAGTTAAGATAAAACAACTT
356196 T
1 T
356197 GCCAGGTAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (43 bp):
TAGCTAAGCATTGTAAGAAGAACCAGTTAAGATAAAACAACTT
Found at i:360961 original size:67 final size:66
Alignment explanation
Indices: 360816--360941 Score: 182
Period size: 67 Copynumber: 1.9 Consensus size: 66
360806 TTGTTTAAAG
* * *
360816 AGAAATTATTTTATGGACCTTTCCCACCATATCATTTATGGTCCCTTTTCAATTATTTCTCAAAA
1 AGAAA-TATTTTATGGACCTTTCCCACCACATCATTCATGGTCCCTTTTCAATTATTTATCAAAA
360881 CA
65 CA
*
360883 AGAAATTATTTTATGGATCC-TTCCCACCGCATCATTCATGGTCCCTTTTCAATTATTTA
1 AGAAA-TATTTTATGGA-CCTTTCCCACCACATCATTCATGGTCCCTTTTCAATTATTTA
360942 ATGAAATTTC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 52 0.96
68 2 0.04
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (66 bp):
AGAAATATTTTATGGACCTTTCCCACCACATCATTCATGGTCCCTTTTCAATTATTTATCAAAAC
A
Found at i:367336 original size:27 final size:27
Alignment explanation
Indices: 367298--367364 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
367288 ATCCTGTCAA
*
367298 CCTTTGTGGCATACTCTGTATGAATCG
1 CCTTTGTGGCATACTCTATATGAATCG
* *
367325 CCTTTTTGGCATACTCTATATGAATTG
1 CCTTTGTGGCATACTCTATATGAATCG
*
367352 TCTTTGTGGCATA
1 CCTTTGTGGCATA
367365 TTTTGTAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (27 bp):
CCTTTGTGGCATACTCTATATGAATCG
Found at i:378398 original size:22 final size:21
Alignment explanation
Indices: 378373--378420 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
378363 TTTATCTTAA
378373 AATTAATTAATTTTAATAATAT
1 AATTAATTAATTTTAAT-ATAT
** *
378395 AATTTTTTAATTTTTATATAT
1 AATTAATTAATTTTAATATAT
378416 AATTA
1 AATTA
378421 TTATTTACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTAATTAATTTTAATATAT
Found at i:378417 original size:21 final size:22
Alignment explanation
Indices: 378379--378419 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
378369 TTAAAATTAA
378379 TTAATTTTAATAATATAATTTT
1 TTAATTTTAATAATATAATTTT
*
378401 TTAATTTTTAT-ATATAATT
1 TTAATTTTAATAATATAATT
378420 ATTATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTAATTTTAATAATATAATTTT
Found at i:384938 original size:88 final size:88
Alignment explanation
Indices: 384786--385322 Score: 716
Period size: 88 Copynumber: 6.1 Consensus size: 88
384776 GTGAAGATAA
*** *
384786 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACACCAACCTTGCCTCCCTGGGTT
* *
384851 GTAGTGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * *
384874 CAGATCTTGCCTTCTTGCGCCGACAGCGAAGCAGATTAAAGACACTAACCTTGCCTCCCGGGGTT
1 CAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACACCAACCTTGCCTCCCTGGGTT
*
384939 GCAGCAGAGCAGGTTTAAAAATAG
66 GCAGCGGAGCAGG-TTAAAAATAG
* * *
384963 CAGATCTTGCCTTCCTGCGCCAACAACGAAACAGATCAAAGACACCAACCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACACCAACCTTGCCTCCCTGGGTT
*
385028 GCAGTGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * *
385051 CAGATCTTGCCTTCCTGCGCCGACAGTGAAGCAGATCGAAA-ACACCAGCCTTACCTCACTGGGT
1 CAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATC-AAAGACACCAACCTTGCCTCCCTGGGT
385115 TGCAGCGGAGCAGGTTAAAAATAG
65 TGCAGCGGAGCAGGTTAAAAATAG
*
385139 CAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACACCAACCTTGCCTCCCTTGGTT
1 CAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACACCAACCTTGCCTCCCTGGGTT
*
385204 GCAGCGGAACAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * ** * * * * * * **
385227 CAGATCTTGCCTTCCTGCACCGATAATGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGGGCA
1 CAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACACCAACCTTGCCTCCCTGGGTT
* * * *
385292 GCAGTGGAGTAGGTTGAAAATTG
66 GCAGCGGAGCAGGTTAAAAATAG
385315 CAGATCTT
1 CAGATCTT
385323 ATCTCCCTAA
Statistics
Matches: 394, Mismatches: 52, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
87 3 0.01
88 309 0.78
89 82 0.21
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACACCAACCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:385084 original size:177 final size:176
Alignment explanation
Indices: 384786--385249 Score: 714
Period size: 177 Copynumber: 2.6 Consensus size: 176
384776 GTGAAGATAA
*** *
384786 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACACCAACCTTGCCTCCCTGGGTT
* * *
384851 GTAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCTTGCGCCGACAGCGAAGCAGAT-TAAAG
66 GCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAA-
* * *
384915 ACACTAACCTTGCCTCCCGGGGTTGCAGCAGAGCAGGTTTAAAAATAG
130 ACACCAACCTTACCTCACGGGGTTGCAGCAGAGCAGG-TTAAAAATAG
* * *
384963 CAGATCTTGCCTTCCTGCGCCAACAACGAAACAGATCAAAGACACCAACCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACACCAACCTTGCCTCCCTGGGTT
*
385028 GCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGTGAAGCAGATCGAAAA
66 GCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAAA
* * *
385093 CACCAGCCTTACCTCACTGGGTTGCAGCGGAGCAGGTTAAAAATAG
131 CACCAACCTTACCTCACGGGGTTGCAGCAGAGCAGGTTAAAAATAG
*
385139 CAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACACCAACCTTGCCTCCCTTGGTT
1 CAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACACCAACCTTGCCTCCCTGGGTT
* * *
385204 GCAGCGGAACAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGA
66 GCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGA
385250 TAATGGAGCA
Statistics
Matches: 262, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
176 114 0.44
177 145 0.55
178 3 0.01
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (176 bp):
CAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCAAAGACACCAACCTTGCCTCCCTGGGTT
GCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCGCCGACAGCGAAGCAGATCGAAAA
CACCAACCTTACCTCACGGGGTTGCAGCAGAGCAGGTTAAAAATAG
Found at i:385330 original size:44 final size:44
Alignment explanation
Indices: 385280--385521 Score: 231
Period size: 44 Copynumber: 5.5 Consensus size: 44
385270 CCCAGCCTTG
** * *
385280 TCTCCCTGGGCAGCAGTGGAGTAGGTTGAAAATTGCAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGATCTTA
* * * * ** * *
385324 TCTCCCTAAGCAGTAGTGGAGCA-GATCAAAGTCCCCAG-CCTTG
1 TCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAAT-TACAGATCTTA
* *
385367 TCTCCCTGAGTAGTAGTGGAGTAGGTTGAAAATTACAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGATCTTA
* * * * ** * *
385411 TCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGTCCCCAG-CCTTG
1 TCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAAT-TACAGATCTTA
*
385454 TCTCCTTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGATCTTA
385498 TCTCCCTAAGCAGTAGTGGAGTAG
1 TCTCCCTAAGCAGTAGTGGAGTAG
385522 ATCGAGGATG
Statistics
Matches: 151, Mismatches: 41, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
43 65 0.43
44 86 0.57
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (44 bp):
TCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTACAGATCTTA
Found at i:385367 original size:87 final size:87
Alignment explanation
Indices: 385253--385526 Score: 476
Period size: 87 Copynumber: 3.1 Consensus size: 87
385243 GCACCGATAA
* * *
385253 TGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGGGCAGCAGTGGAGTAGGTTGAAAATTGCAG
1 TGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATTACAG
385318 ATCTTATCTCCCTAAGCAGTAG
66 ATCTTATCTCCCTAAGCAGTAG
* *
385340 TGGAGCAGATCAAAGTCCCCAGCCTTGTCTCCCTGAGTAGTAGTGGAGTAGGTTGAAAATTACAG
1 TGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATTACAG
385405 ATCTTATCTCCCTAAGCAGTAG
66 ATCTTATCTCCCTAAGCAGTAG
* *
385427 TGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCTTAAGCAGTAGTGGAGTAGGTTGAAAATTACAG
1 TGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATTACAG
385492 ATCTTATCTCCCTAAGCAGTAG
66 ATCTTATCTCCCTAAGCAGTAG
*
385514 TGGAGTAGATCGA
1 TGGAGCAGATCGA
385527 GGATGGTAAA
Statistics
Matches: 177, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 177 1.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (87 bp):
TGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATTACAG
ATCTTATCTCCCTAAGCAGTAG
Found at i:385382 original size:43 final size:43
Alignment explanation
Indices: 385253--385474 Score: 178
Period size: 43 Copynumber: 5.1 Consensus size: 43
385243 GCACCGATAA
* ** *
385253 TGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGGGCAGCAG
1 TGGAGCAGATCAAAGTCCCCAGCCTTGTCTCCCTAAGCAGTAG
* * * * ** * *
385296 TGGAGTAGGTTGAAAAT-TGCAGATCTTATCTCCCTAAGCAGTAG
1 TGGAGCA-GATCAAAGTCCCCAG-CCTTGTCTCCCTAAGCAGTAG
* *
385340 TGGAGCAGATCAAAGTCCCCAGCCTTGTCTCCCTGAGTAGTAG
1 TGGAGCAGATCAAAGTCCCCAGCCTTGTCTCCCTAAGCAGTAG
* * * * ** * *
385383 TGGAGTAGGTTGAAAAT-TACAGATCTTATCTCCCTAAGCAGTAG
1 TGGAGCA-GATCAAAGTCCCCAG-CCTTGTCTCCCTAAGCAGTAG
* *
385427 TGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCTTAAGCAGTAG
1 TGGAGCAGATCAAAGTCCCCAGCCTTGTCTCCCTAAGCAGTAG
385470 TGGAG
1 TGGAG
385475 TAGGTTGAAA
Statistics
Matches: 131, Mismatches: 42, Indels: 12
0.71 0.23 0.06
Matches are distributed among these distances:
43 69 0.53
44 62 0.47
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (43 bp):
TGGAGCAGATCAAAGTCCCCAGCCTTGTCTCCCTAAGCAGTAG
Found at i:385540 original size:44 final size:42
Alignment explanation
Indices: 385318--385545 Score: 145
Period size: 44 Copynumber: 5.2 Consensus size: 42
385308 AAAATTGCAG
* * **
385318 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAG-TCCCCA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGAT--TAA
** * * * * * *
385361 GCCTTGTCTCCCTGAGTAGTAGTGGAGTAGGTTGAAAATTACA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATTA-A
* **
385404 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG-TCCCCA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGAT--TAA
** * * * * *
385448 GCCTTGTCTCCTTAAGCAGTAGTGGAGTAGGTTGAAAATTACA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATTA-A
*
385491 GATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAGGATGGTAA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGAT--TAA
385536 ATCTTATCTC
1 ATCTTATCTC
385546 TCTGAAGTTG
Statistics
Matches: 134, Mismatches: 41, Indels: 19
0.69 0.21 0.10
Matches are distributed among these distances:
43 59 0.44
44 72 0.54
45 1 0.01
46 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (42 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATTAA
Found at i:387221 original size:22 final size:21
Alignment explanation
Indices: 387196--387244 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
387186 TTTATCTTAA
387196 AATTAATTAATTTTAATAATGT
1 AATTAATTAATTTTAAT-ATGT
** *
387218 AATTTTTTTAATTTTTATATGT
1 AA-TTAATTAATTTTAATATGT
387240 AATTA
1 AATTA
387245 TTATTTACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
21 2 0.09
22 8 0.36
23 12 0.55
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
AATTAATTAATTTTAATATGT
Found at i:387279 original size:18 final size:18
Alignment explanation
Indices: 387234--387284 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
387224 TTTAATTTTT
*
387234 ATATGTAATTATTATTTAC
1 ATATGT-ATTATTATGTAC
* * *
387253 ATGTATATTTTTATGTAC
1 ATATGTATTATTATGTAC
387271 ATATGTATTATTAT
1 ATATGTATTATTAT
387285 TTTTTTCAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (18 bp):
ATATGTATTATTATGTAC
Found at i:392197 original size:2 final size:2
Alignment explanation
Indices: 392190--392214 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
392180 ATTCAAAACA
392190 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 A
392215 ATTTCAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:396245 original size:29 final size:28
Alignment explanation
Indices: 396213--396277 Score: 94
Period size: 29 Copynumber: 2.3 Consensus size: 28
396203 TTTATGATTC
*
396213 TTTTTATATTTTTTAATATTTTATATCAA
1 TTTTTATATTTTTTAAAATTTT-TATCAA
* *
396242 TTTTAATATTTTTTAAAATTTTTATGAA
1 TTTTTATATTTTTTAAAATTTTTATCAA
396270 TTTTTATA
1 TTTTTATA
396278 AGTTGTTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 12 0.38
29 20 0.62
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (28 bp):
TTTTTATATTTTTTAAAATTTTTATCAA
Found at i:396264 original size:19 final size:20
Alignment explanation
Indices: 396222--396265 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
396212 CTTTTTATAT
*
396222 TTTTTAATATTTTATATCAA
1 TTTTTAATATTTTATATAAA
*
396242 -TTTTAATATTTTTTA-AAA
1 TTTTTAATATTTTATATAAA
396260 TTTTTA
1 TTTTTA
396266 TGAATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTAATATTTTATATAAA
Found at i:396328 original size:21 final size:21
Alignment explanation
Indices: 396300--396355 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
396290 ATTTTATAGG
396300 TTTA-AAATTTTTTT-TTGAATA
1 TTTATAAATTTTTTTATT-AA-A
396321 TTT-TAAATATGTTTTTATTAAA
1 TTTATAAAT-T-TTTTTATTAAA
396343 TTTATAAATTTTT
1 TTTATAAATTTTT
396356 ATAATTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
21 10 0.33
22 6 0.20
23 12 0.40
24 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTATAAATTTTTTTATTAAA
Found at i:396346 original size:9 final size:9
Alignment explanation
Indices: 396334--396382 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
396324 TAAATATGTT
396334 TTTATTAAA
1 TTTATTAAA
396343 TTTA-TAAA
1 TTTATTAAA
396351 TTT-TTATAA
1 TTTATTA-AA
*
396360 TTTATTAGA
1 TTTATTAAA
*
396369 TTTATTATA
1 TTTATTAAA
396378 TTTAT
1 TTTAT
396383 AATATTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 9 0.26
9 23 0.66
10 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (9 bp):
TTTATTAAA
Found at i:396356 original size:19 final size:18
Alignment explanation
Indices: 396332--396402 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
396322 TTTAAATATG
396332 TTTTTATTAAATTTATAAA
1 TTTTTA-TAAATTTATAAA
*
396351 TTTTTAT-AATTTATTAGA
1 TTTTTATAAATTTA-TAAA
396369 TTTATTAT--ATTTATAATA
1 TTT-TTATAAATTTATAA-A
*
396387 TTTTTATAAGTTTATA
1 TTTTTATAAATTTATA
396403 TCAAATTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
17 12 0.27
18 16 0.36
19 16 0.36
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTTATAAATTTATAAA
Found at i:396363 original size:17 final size:17
Alignment explanation
Indices: 396341--396402 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 17
396331 GTTTTTATTA
396341 AATTTATAAATTTTTAT
1 AATTTATAAATTTTTAT
*
396358 AATTTATTAGATTTATTAT
1 AATTTA-TAAATTT-TTAT
396377 -ATTTATAATATTTTTAT
1 AATTTATAA-ATTTTTAT
396394 AAGTTTATA
1 AA-TTTATA
396403 TCAAATTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 12 0.32
18 16 0.42
19 10 0.26
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
AATTTATAAATTTTTAT
Found at i:396387 original size:9 final size:9
Alignment explanation
Indices: 396334--396394 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
396324 TAAATATGTT
*
396334 TTTATTAAA
1 TTTATTATA
*
396343 TTTA-TAAA
1 TTTATTATA
396351 TTT-TTATAA
1 TTTATTAT-A
*
396360 TTTATTAGA
1 TTTATTATA
396369 TTTATTATA
1 TTTATTATA
*
396378 TTTATAATA
1 TTTATTATA
396387 TTT-TTATA
1 TTTATTATA
396395 AGTTTATATC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
8 13 0.30
9 28 0.64
10 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (9 bp):
TTTATTATA
Found at i:396416 original size:37 final size:34
Alignment explanation
Indices: 396338--396427 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 34
396328 TATGTTTTTA
*
396338 TTAA-ATTTATAA-ATTTTTATAATTTATTAGAT
1 TTAATATTTATAATATTTTTATAATTTATTAAAT
396370 TTATTATATTTATAATATTTTTATAAGTTTATATCAAAT
1 TTA--ATATTTATAATATTTTTATAA-TTTAT-T-AAAT
396409 TTAATATTT-TAAATATTTT
1 TTAATATTTAT-AATATTTT
396428 ATTTTTTAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
32 3 0.06
34 1 0.02
35 8 0.16
36 11 0.22
37 19 0.39
38 1 0.02
39 6 0.12
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (34 bp):
TTAATATTTATAATATTTTTATAATTTATTAAAT
Found at i:396428 original size:36 final size:33
Alignment explanation
Indices: 396338--396429 Score: 89
Period size: 36 Copynumber: 2.6 Consensus size: 33
396328 TATGTTTTTA
*
396338 TTAA-ATTTATAAAT-TTTTATAATTTATTAGAT
1 TTAATATTT-TAAATATTTTATAATTTATTAAAT
*
396370 TTATTATATTTATAATATTTTTATAAGTTTATATCAAAT
1 TTAATAT-TTTA-AATA-TTTTATAA-TTTAT-T-AAAT
396409 TTAATATTTTAAATATTTTAT
1 TTAATATTTTAAATATTTTAT
396430 TTTTTAATCC
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
32 3 0.06
33 4 0.08
34 5 0.10
36 14 0.29
37 9 0.18
38 5 0.10
39 9 0.18
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (33 bp):
TTAATATTTTAAATATTTTATAATTTATTAAAT
Found at i:396640 original size:10 final size:10
Alignment explanation
Indices: 396625--396679 Score: 80
Period size: 10 Copynumber: 5.7 Consensus size: 10
396615 CGGTATATTT
396625 TATTTTTTAA
1 TATTTTTTAA
396635 TATTTTTTAA
1 TATTTTTTAA
396645 TATTTTTTAA
1 TATTTTTTAA
396655 TATTTTTCT-A
1 TATTTTT-TAA
396665 -A-TTTTTAA
1 TATTTTTTAA
396673 TATTTTT
1 TATTTTT
396680 ATAGAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
7 1 0.02
8 5 0.12
9 2 0.05
10 32 0.78
11 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:397261 original size:20 final size:20
Alignment explanation
Indices: 397203--397275 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
397193 TTTGGCATAT
397203 CAAAATTTCTAATG-GATAC
1 CAAAATTTCTAATGCGATAC
* * *
397222 CAAAATTTCTCA-CCAAATAC
1 CAAAATTTCTAATGC-GATAC
*
397242 CAAAATTTTTAATGCGATAC
1 CAAAATTTCTAATGCGATAC
*
397262 CAATATTTCTAATG
1 CAAAATTTCTAATG
397276 AAAATCGTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 11 0.26
20 30 0.71
21 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (20 bp):
CAAAATTTCTAATGCGATAC
Found at i:412926 original size:15 final size:16
Alignment explanation
Indices: 412901--412936 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
412891 AATTGAATCG
*
412901 ATTTTTATAATTTTTA
1 ATTTTTATAATTTTCA
412917 ATTTTT-TAATTTTCA
1 ATTTTTATAATTTTCA
412932 ATTTT
1 ATTTT
412937 CAATAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTTATAATTTTCA
Found at i:416031 original size:28 final size:29
Alignment explanation
Indices: 415972--416031 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
415962 TAAAAATTTA
* *
415972 AAAAAAATTTAAAAATACATAAATACTTT
1 AAAAAAATTTAAAAATACATAAAAACTAT
*
416001 AAAAAAA-TTAAAAGTA-ATAAAAACTCAT
1 AAAAAAATTTAAAAATACATAAAAACT-AT
416029 AAA
1 AAA
416032 CCCAATGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.30
28 12 0.44
29 7 0.26
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.25
Consensus pattern (29 bp):
AAAAAAATTTAAAAATACATAAAAACTAT
Found at i:416761 original size:24 final size:24
Alignment explanation
Indices: 416715--416768 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
416705 GACAAATTTT
* * *
416715 AAAAAAATTCATAGTTGATTGACA
1 AAAAAAATCCATAATTGAGTGACA
* *
416739 AAAAAAATCCATAATTGGGTGACT
1 AAAAAAATCCATAATTGAGTGACA
416763 AAAAAA
1 AAAAAA
416769 GAAAACGACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.24
Consensus pattern (24 bp):
AAAAAAATCCATAATTGAGTGACA
Found at i:418020 original size:20 final size:20
Alignment explanation
Indices: 417995--418037 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
417985 AAAACTTAGA
417995 CTTGTTGATAAAACTCGTTT
1 CTTGTTGATAAAACTCGTTT
418015 CTTGTTGATAAAACTCGTTT
1 CTTGTTGATAAAACTCGTTT
418035 CTT
1 CTT
418038 AAGTTTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (20 bp):
CTTGTTGATAAAACTCGTTT
Found at i:418710 original size:26 final size:27
Alignment explanation
Indices: 418681--418739 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
418671 ATAATGACGC
* *
418681 AGCAAAGCTGCCAGTAACAGTA-ATGT
1 AGCAAAGCTGCCAATAACAATATATGT
**
418707 AGCAGGGCTGCCAATAACAATATATGT
1 AGCAAAGCTGCCAATAACAATATATGT
*
418734 GGCAAA
1 AGCAAA
418740 ACCACCAGTA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (27 bp):
AGCAAAGCTGCCAATAACAATATATGT
Found at i:418923 original size:27 final size:27
Alignment explanation
Indices: 418893--418950 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
418883 ACTCCTAGGG
418893 GTATAACAGTCA-TTTTACCCTTCGAGA
1 GTATAACAGT-AGTTTTACCCTTCGAGA
** * *
418920 GTATTTCGGTAGTTTTACCCTTCGAGG
1 GTATAACAGTAGTTTTACCCTTCGAGA
418947 GTAT
1 GTAT
418951 TTTGGTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (27 bp):
GTATAACAGTAGTTTTACCCTTCGAGA
Found at i:418951 original size:27 final size:27
Alignment explanation
Indices: 418904--419046 Score: 189
Period size: 27 Copynumber: 5.3 Consensus size: 27
418894 TATAACAGTC
*
418904 ATTTTACCCTTCGAGAGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
418931 GTTTTACCCTTCGAGGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* * *
418958 ATTTTGCCCTTCGAGGGTATTTTGATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
418985 ATTTT-CTCCTTCGGGGGTATTTCGATA
1 ATTTTAC-CCTTCGAGGGTATTTCGGTA
*
419012 ATTTTACCCTTCGAGGGTATTTCAGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
419039 ATTTTACC
1 ATTTTACC
419047 ACGAATCGTA
Statistics
Matches: 103, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
26 1 0.01
27 101 0.98
28 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGGTA
Found at i:419450 original size:20 final size:21
Alignment explanation
Indices: 419406--419451 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
419396 TAGTAAAGCT
419406 TAACAACCTATTTAAATAAGA
1 TAACAACCTATTTAAATAAGA
*
419427 -AACAACCTATTTGAATAA-A
1 TAACAACCTATTTAAATAAGA
419446 TAACAA
1 TAACAA
419452 AATATTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.26
Consensus pattern (21 bp):
TAACAACCTATTTAAATAAGA
Found at i:422721 original size:20 final size:20
Alignment explanation
Indices: 422696--422741 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
422686 TAGTAAAGCT
*
422696 TAACAACCTATTTAAATAAG
1 TAACAACCTATTTAAATAAA
*
422716 TAACAACCTATTTGAATAAA
1 TAACAACCTATTTAAATAAA
422736 TAACAA
1 TAACAA
422742 AATATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.28
Consensus pattern (20 bp):
TAACAACCTATTTAAATAAA
Found at i:422747 original size:20 final size:20
Alignment explanation
Indices: 422704--422747 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
422694 CTTAACAACC
* **
422704 TATTTAAATAAGTAACAACC
1 TATTTAAATAAATAACAAAA
*
422724 TATTTGAATAAATAACAAAA
1 TATTTAAATAAATAACAAAA
422744 TATT
1 TATT
422748 AACAGATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (20 bp):
TATTTAAATAAATAACAAAA
Found at i:430016 original size:50 final size:50
Alignment explanation
Indices: 429886--430070 Score: 166
Period size: 50 Copynumber: 3.8 Consensus size: 50
429876 ACATTAAGAG
*
429886 GATGAG-A-TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGA
1 GATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
** ** *
429934 GATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGC-TTGGGCACCGA
1 GATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATT-GGCACCGA
* * * * * * *
429984 TATGAGAACTCCCATATAAGACCATATCTGGGATATGACATT--TACAGTA
1 GATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-A
* *
430033 CAGGA-AACATCCCATGTAAGACCATGTCTGGGACATGG
1 GATGAGAAC-TCCCATGTAAGACCATGTCTGGGACATGG
430071 TTTTCGCATG
Statistics
Matches: 108, Mismatches: 23, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
48 12 0.11
49 31 0.29
50 63 0.58
51 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (50 bp):
GATGAGAACTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:430305 original size:20 final size:20
Alignment explanation
Indices: 430280--430328 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
430270 TGAGTTATTT
430280 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
430300 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
430320 AAG-AAGCAA
1 AAGTAAGCAA
430329 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:434329 original size:20 final size:20
Alignment explanation
Indices: 434304--434342 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
434294 TTACTTCTTC
434304 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
434324 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
434343 AAATAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:434604 original size:49 final size:50
Alignment explanation
Indices: 434544--434730 Score: 150
Period size: 50 Copynumber: 3.8 Consensus size: 50
434534 GATAATAACA
*
434544 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTATAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTATACG
* * *
434593 TGCCAATGCCATATCCCAAATATGGTCTTACATGGGA-G-TT-CTAATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCT-ATA-C-G
* ** * ** ** * * *
434643 TGCCCATGTTATGTCTCAGACATGGTCTTACGGGGGACCTCTCATCT-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTATAC-G
* *
434693 TGCCAACGCCATGTCTCAGACATGGTCTTACATGGGAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT
434731 CTCATCCTCT
Statistics
Matches: 107, Mismatches: 24, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
46 2 0.02
47 5 0.05
48 2 0.02
49 33 0.31
50 62 0.58
52 2 0.02
53 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTATACG
Found at i:436753 original size:18 final size:20
Alignment explanation
Indices: 436703--436755 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
436693 TTGGTGATTT
436703 AATATAAATATAA-ATATATA
1 AATAT-AATATAATATATATA
* *
436723 AATATTATTTAATATATAT-
1 AATATAATATAATATATATA
436742 AAT-TAATATAATAT
1 AATATAATATAATAT
436756 TTTTTATAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 11 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATATAATATAATATATATA
Found at i:436754 original size:28 final size:29
Alignment explanation
Indices: 436699--436761 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
436689 TAAGTTGGTG
436699 ATTTAATATAAATATAAATATATAAATATT
1 ATTTAATAT-AATATAAATATATAAATATT
*
436729 ATTTAATAT-ATATAATTA-ATATAATATT
1 ATTTAATATAATATAAATATATA-AATATT
*
436757 TTTTA
1 ATTTA
436762 TAACATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.10
28 18 0.60
30 9 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTAATATAATATAAATATATAAATATT
Found at i:436917 original size:14 final size:14
Alignment explanation
Indices: 436898--436925 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
436888 CAATCTCTCC
436898 TATTTTAGAGCAGA
1 TATTTTAGAGCAGA
436912 TATTTTAGAGCAGA
1 TATTTTAGAGCAGA
436926 CTTTCGAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
TATTTTAGAGCAGA
Found at i:447097 original size:42 final size:42
Alignment explanation
Indices: 447046--447126 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
447036 GGGAAAACGC
* * * *
447046 CGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAATGT
1 CGCTAAAGATAATAACCTTTAGCGACGCTTATACCACAATGT
*
447088 CGCTAAAGATAATAACTTTTAGCGACGCTTATACCACAA
1 CGCTAAAGATAATAACCTTTAGCGACGCTTATACCACAA
447127 ACGCCACTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (42 bp):
CGCTAAAGATAATAACCTTTAGCGACGCTTATACCACAATGT
Found at i:451017 original size:23 final size:24
Alignment explanation
Indices: 450989--451045 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
450979 GGGGTTTCAA
*
450989 GGGGGAAATTAGGGATTTTAG-GG
1 GGGGGAAATTAGGGATTTCAGAGG
* *
451012 GGGGGAAGTTGGGGATTTCAGAGG
1 GGGGGAAATTAGGGATTTCAGAGG
*
451036 GGGAGAAATT
1 GGGGGAAATT
451046 TATAAAATGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.26, C:0.02, G:0.49, T:0.23
Consensus pattern (24 bp):
GGGGGAAATTAGGGATTTCAGAGG
Found at i:451161 original size:40 final size:40
Alignment explanation
Indices: 451073--451163 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 40
451063 TTTTTAAGGT
* *
451073 AAAATTATTTTTTGTGGCGTTTTTTATAAAAATACCGCTA
1 AAAATTATTTTTTGTGGCGTTTTTCATAAAAACACCGCTA
**** *
451113 TTGCTTATTTTTTGTGGCGTTTTTCATAAAAACGCCG-TAA
1 AAAATTATTTTTTGTGGCGTTTTTCATAAAAACACCGCT-A
451153 AAAATTATTTT
1 AAAATTATTTT
451164 ATTTGGAATA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
39 1 0.03
40 38 0.97
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (40 bp):
AAAATTATTTTTTGTGGCGTTTTTCATAAAAACACCGCTA
Found at i:451637 original size:4 final size:4
Alignment explanation
Indices: 451628--451660 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
451618 AATTTGTTAC
*
451628 ATTT ATTT ATTT ATTT ATTT ATTT ATTT TTTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
451661 AATCTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:452044 original size:20 final size:19
Alignment explanation
Indices: 452011--452056 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
452001 ATTGAATTTT
452011 AATT-AATATAAATAAACA
1 AATTAAATATAAATAAACA
*
452029 AATTAAATAGTAAATAGACA
1 AATTAAATA-TAAATAAACA
*
452049 AATAAAAT
1 AATTAAAT
452057 GTTTTTGCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 16 0.67
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.26
Consensus pattern (19 bp):
AATTAAATATAAATAAACA
Found at i:452212 original size:41 final size:41
Alignment explanation
Indices: 452063--452298 Score: 213
Period size: 41 Copynumber: 5.7 Consensus size: 41
452053 AAATGTTTTT
* *
452063 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCTCTGAGCATTA
* ** ** * * *
452104 GCGGCGCTTCTTGGAAAACACCACTAAAGCCCGGAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCTCTGAGCATTA
* * * * *
452145 GCAGCGCTTCTTGAAAAA-CCCTGCTAAATCTCTGAGCATTA
1 GCGGCGCTTTTTCAAAAATGCC-GCTAAAGCTCTGAGCATTA
* * **
452186 GCGGCGCTTTTTTAAAAATGTCGCTAAATATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCTCTGAGCATTA
* * * * *
452227 GCGACACTTTTTCAAAAACGCAGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAATGCCGCTAAAGCTCTGAGCATTA
* *
452268 GCGGCGCTTTTTTTAAAAATGCCGCTGAAGC
1 GCGGCGC-TTTTTCAAAAATGCCGCTAAAGC
452299 CCCGAAAGGT
Statistics
Matches: 158, Mismatches: 34, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
40 2 0.01
41 137 0.87
42 19 0.12
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAATGCCGCTAAAGCTCTGAGCATTA
Found at i:452885 original size:18 final size:18
Alignment explanation
Indices: 452851--452885 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
452841 TCTTCTACTC
* *
452851 CAATTGGTTCTTTTAATT
1 CAATTGGTTCATCTAATT
452869 CAATTGGTTCATCTAAT
1 CAATTGGTTCATCTAAT
452886 CCTCCTTTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.49
Consensus pattern (18 bp):
CAATTGGTTCATCTAATT
Found at i:454597 original size:114 final size:114
Alignment explanation
Indices: 454456--454891 Score: 431
Period size: 114 Copynumber: 3.8 Consensus size: 114
454446 GTTTTCCAGA
* * *
454456 AAGCGTCGC-AAAAAACCTAAGCCCAACGACACCGTTTTCTTAGCATTCGGGGGTTTAGCGGCAT
1 AAGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTTAGCATTCGGGGATTTAGCGGCGT
** * * *
454520 TTTTATTAAAGTGCCGCTAATACTTAGGGCTTTAGCGGCATTTTTGAAG
66 TTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAAG
* * * *
454569 AAGCGCCGTAAAAAAACCTAAGCCCAACGACACCG-TTTCTAAGCTTTTCAGGGATTTAGCGGCG
1 AAGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTTAGC-ATTCGGGGATTTAGCGGCG
** * *
454633 TTTTTAAGGGAGCGCCGCTAATGCTCATGGCTTTAGCGGCACTTTTGGAA-
65 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCA-TTTTTGAAG
* * * *
454683 AAGCGCCGCAAAATAACCTAAGCCCAACGAC-CCTGTTTTCTGAG-ATTTTGGGGATCTAGCGGC
1 AAGCGCCGCAAAAAAACCTAAGCCCAACGACACC-GTTTTCTTAGCA-TTCGGGGATTTAGCGGC
* * * * * **
454746 GTTTCTCT-AG-AAGCGCCGCTAGTGCTCGGGGATTTAACGGCGTTTTTGGGG
64 GTTT-T-TAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAAG
* * ** *
454797 TAGCGCCGCAAGAAAAA-CTAAGCCCAACGGCGTCGTTTTCTGT-GCTTTCGGGGGATTTAGCGG
1 AAGCGCCGCAA-AAAAACCTAAGCCCAACGACACCGTTTTCT-TAGCATTC-GGGGATTTAGCGG
*
454860 CGTTTTTAGGAAAGCGCCGCTAATGCTCAGGG
63 CGTTTTTAAGAAAGCGCCGCTAATGCTCAGGG
454892 ATTTGAAAAT
Statistics
Matches: 263, Mismatches: 44, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
113 23 0.09
114 181 0.69
115 58 0.22
116 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (114 bp):
AAGCGCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTTAGCATTCGGGGATTTAGCGGCGT
TTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTGAAG
Found at i:455991 original size:31 final size:31
Alignment explanation
Indices: 455928--455989 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
455918 TTATTATTGG
455928 ATAAAAAAATACATTTTTTATACCAAATTTT
1 ATAAAAAAATACATTTTTTATACCAAATTTT
455959 ATAAAAAAATA-ATTTTTTTTATACCAAATTT
1 ATAAAAAAATACA--TTTTTTATACCAAATTT
455990 ATTATACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 1 0.03
31 11 0.38
32 17 0.59
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAAAAAAATACATTTTTTATACCAAATTTT
Found at i:455996 original size:14 final size:14
Alignment explanation
Indices: 455977--456003 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
455967 ATAATTTTTT
455977 TTATACCAAATTTA
1 TTATACCAAATTTA
455991 TTATACCAAATTT
1 TTATACCAAATTT
456004 CATCCGTTTC
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:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (14 bp):
TTATACCAAATTTA
Found at i:456273 original size:18 final size:18
Alignment explanation
Indices: 456250--456287 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
456240 TATGGGGTAA
456250 GGGGATTTAAGGTTTAGG
1 GGGGATTTAAGGTTTAGG
*
456268 GGGGATTTAGGGTTTAGG
1 GGGGATTTAAGGTTTAGG
456286 GG
1 GG
456288 TTATGCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.50, T:0.32
Consensus pattern (18 bp):
GGGGATTTAAGGTTTAGG
Found at i:459147 original size:47 final size:47
Alignment explanation
Indices: 458825--459139 Score: 448
Period size: 47 Copynumber: 6.8 Consensus size: 47
458815 AAAAAACGCA
* *
458825 ATATTCTTAAGCATATATTACATTACTTACATTACTTACCGAAATAT
1 ATATTTTTAAGTATATATTACATTACTTACATTACTTACCGAAATAT
*** * * *
458872 AT-TACATAACTCA-GT-TTACTTTACTTACATTACTT----AAATAT
1 ATATTTTTAAGT-ATATATTACATTACTTACATTACTTACCGAAATAT
*
458913 ATATTCTTAAGTATATATTACATTACTTACATTACTTACCGAAATAT
1 ATATTTTTAAGTATATATTACATTACTTACATTACTTACCGAAATAT
**
458960 ATATTTTTAAGTATATATTACATTACTTACATTACTTACTAAAATAT
1 ATATTTTTAAGTATATATTACATTACTTACATTACTTACCGAAATAT
*
459007 GT-TATTTTAAGTATATATTACATTACTTACATTACTTACCGAAATAT
1 ATAT-TTTTAAGTATATATTACATTACTTACATTACTTACCGAAATAT
459054 ATATTTTTAAGTATATATTACATTACTTACATTACTTACCGAAATAT
1 ATATTTTTAAGTATATATTACATTACTTACATTACTTACCGAAATAT
459101 ATATTTTTAAGTATATATTACATTACTTACATTACTTAC
1 ATATTTTTAAGTATATATTACATTACTTACATTACTTAC
459140 TAAAATATGT
Statistics
Matches: 240, Mismatches: 18, Indels: 20
0.86 0.06 0.07
Matches are distributed among these distances:
41 9 0.04
42 7 0.03
43 19 0.08
45 19 0.08
46 7 0.03
47 178 0.74
48 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (47 bp):
ATATTTTTAAGTATATATTACATTACTTACATTACTTACCGAAATAT
Found at i:459157 original size:18 final size:18
Alignment explanation
Indices: 459131--459220 Score: 94
Period size: 18 Copynumber: 4.8 Consensus size: 18
459121 CATTACTTAC
459131 ATTAC-TTACTAAAATAT
1 ATTACATTACTAAAATAT
* *
459148 GTTACATTACTTAAATAT
1 ATTACATTACTAAAATAT
459166 ATTAC-TTACTAAAATTTAT
1 ATTACATTACTAAAA--TAT
*
459185 AATTTACATTACTTAAATAT
1 -A-TTACATTACTAAAATAT
459205 ATTACATTACTTAAAA
1 ATTACATTAC-TAAAA
459221 CTTACATAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
17 12 0.20
18 24 0.40
19 8 0.13
20 4 0.07
21 4 0.07
22 8 0.13
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.43
Consensus pattern (18 bp):
ATTACATTACTAAAATAT
Found at i:459171 original size:31 final size:31
Alignment explanation
Indices: 459113--459202 Score: 90
Period size: 35 Copynumber: 2.6 Consensus size: 31
459103 ATTTTTAAGT
*
459113 ATATATTACATTACTTACATTACTTACTAAA
1 ATATATTACATTACTTAAATTACTTACTAAA
*
459144 ATATGTTACATTACTTAAATATATTACTTACTAAA
1 ATATATTACATTACTT--A-A-ATTACTTACTAAA
459179 ATTTATAATTTACATTACTTAAAT
1 A--TAT-A-TTACATTACTTAAAT
459203 ATATTACATT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
31 15 0.31
33 1 0.02
35 16 0.33
36 1 0.02
37 4 0.08
39 11 0.23
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.44
Consensus pattern (31 bp):
ATATATTACATTACTTAAATTACTTACTAAA
Found at i:459174 original size:22 final size:22
Alignment explanation
Indices: 459122--459214 Score: 65
Period size: 22 Copynumber: 4.4 Consensus size: 22
459112 TATATATTAC
*
459122 ATTACTTACATTACTTACTAAAAT
1 ATTACTTACATTACTTA--AATAT
*
459146 A-T-GTTACATTACTTAAATAT
1 ATTACTTACATTACTTAAATAT
*
459166 ATTACTTAC--TA---AAATTT
1 ATTACTTACATTACTTAAATAT
* *
459183 ATAATTTACATTACTTAAATAT
1 ATTACTTACATTACTTAAATAT
459205 ATTACATTAC
1 ATTAC-TTAC
459215 TTAAAACTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 17
0.67 0.12 0.22
Matches are distributed among these distances:
17 12 0.23
19 2 0.04
20 7 0.13
21 1 0.02
22 24 0.46
23 5 0.10
24 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.01, T:0.44
Consensus pattern (22 bp):
ATTACTTACATTACTTAAATAT
Found at i:465248 original size:40 final size:40
Alignment explanation
Indices: 465143--465254 Score: 127
Period size: 39 Copynumber: 2.8 Consensus size: 40
465133 GTTTGGACAA
* * *
465143 AAAAACGCCGCTATAAATCGAGCATTAGTGGCGCTCTTAG
1 AAAAACGCCGCTAAAAATAGAGCATTAGAGGCGCTCTTAG
* * * * **
465183 GAAAATGCCGCT-AAAATAGAGCATTAGAGGTGCTTTTTT
1 AAAAACGCCGCTAAAAATAGAGCATTAGAGGCGCTCTTAG
*
465222 AAAAACGCCGCTAAAAATAGAGCATTAGCGGCG
1 AAAAACGCCGCTAAAAATAGAGCATTAGAGGCG
465255 TTTCCTAGGA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
39 30 0.52
40 28 0.48
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATAGAGCATTAGAGGCGCTCTTAG
Found at i:465527 original size:28 final size:30
Alignment explanation
Indices: 465492--465556 Score: 107
Period size: 28 Copynumber: 2.2 Consensus size: 30
465482 TTTATATTAG
*
465492 TTAAAATTCAATTTATTTTTAATTG-ATA-
1 TTAAAATTCAACTTATTTTTAATTGAATAT
465520 TTAAAATTCAACTTATTTTTAATTGAATAT
1 TTAAAATTCAACTTATTTTTAATTGAATAT
465550 TTAAAAT
1 TTAAAAT
465557 ATTCAGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 24 0.71
29 3 0.09
30 7 0.21
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.51
Consensus pattern (30 bp):
TTAAAATTCAACTTATTTTTAATTGAATAT
Found at i:465794 original size:14 final size:14
Alignment explanation
Indices: 465775--465964 Score: 79
Period size: 14 Copynumber: 13.4 Consensus size: 14
465765 TATCACTATA
*
465775 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
465789 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
* *
465803 GTTTAGAGTTTAAG
1 GTTTAGGGTTTATG
*
465817 GTTTAGGTGTTACCAT-
1 GTTTAGG-GTT--TATG
*
465833 -TTTAAGGTTTATG
1 GTTTAGGGTTTATG
*
465846 GATTATGGG-TTATG
1 GTTTA-GGGTTTATG
* *
465860 GTTTATGATTTATG
1 GTTTAGGGTTTATG
* *
465874 GTTTATGGTTTAAAG
1 GTTTAGGGTTT-ATG
* *
465889 G-CT-GTGGTTTAAG
1 GTTTAG-GGTTTATG
465902 GTTTAGAGG-TTATG
1 GTTTAG-GGTTTATG
* *
465916 TGTTAAGGGTTTAGG
1 -GTTTAGGGTTTATG
*
465931 GTTTTAGGATTTA-G
1 G-TTTAGGGTTTATG
** *
465945 GTTTATAGTTTAGG
1 GTTTAGGGTTTATG
465959 GTTTAG
1 GTTTAG
465965 ATTAACTAGT
Statistics
Matches: 131, Mismatches: 30, Indels: 30
0.69 0.16 0.16
Matches are distributed among these distances:
12 2 0.02
13 13 0.10
14 81 0.62
15 34 0.26
17 1 0.01
ACGTcount: A:0.21, C:0.02, G:0.31, T:0.47
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:465882 original size:7 final size:7
Alignment explanation
Indices: 465775--465885 Score: 73
Period size: 7 Copynumber: 15.7 Consensus size: 7
465765 TATCACTATA
*
465775 GTTTAGG
1 GTTTATG
*
465782 GTTTTTG
1 GTTTATG
*
465789 GTTTAGG
1 GTTTATG
*
465796 GTATATG
1 GTTTATG
465803 GTTTA-G
1 GTTTATG
*
465809 AGTTTAAG
1 -GTTTATG
465817 GTTTA-G
1 GTTTATG
**
465823 GTGTTACCA
1 GT-TTA-TG
* *
465832 TTTTAAG
1 GTTTATG
465839 GTTTATG
1 GTTTATG
*
465846 GATTATG
1 GTTTATG
*
465853 GGTTATG
1 GTTTATG
465860 GTTTATG
1 GTTTATG
*
465867 ATTTATG
1 GTTTATG
465874 GTTTATG
1 GTTTATG
465881 GTTTA
1 GTTTA
465886 AAGGCTGTGG
Statistics
Matches: 81, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
6 4 0.05
7 72 0.89
8 4 0.05
9 1 0.01
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.50
Consensus pattern (7 bp):
GTTTATG
Found at i:466092 original size:7 final size:7
Alignment explanation
Indices: 466080--466141 Score: 99
Period size: 7 Copynumber: 8.9 Consensus size: 7
466070 ATCTTAAAGT
466080 TTATGGA
1 TTATGGA
466087 TTATGGA
1 TTATGGA
466094 TTATGGA
1 TTATGGA
466101 TTATGGA
1 TTATGGA
466108 TTATGGA
1 TTATGGA
466115 TTATGGA
1 TTATGGA
466122 TTAT-GA
1 TTATGGA
*
466128 TTTATGGT
1 -TTATGGA
466136 TTATGG
1 TTATGG
466142 TTTAATGGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
6 2 0.04
7 49 0.94
8 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.47
Consensus pattern (7 bp):
TTATGGA
Found at i:466151 original size:8 final size:7
Alignment explanation
Indices: 466003--466151 Score: 79
Period size: 7 Copynumber: 21.1 Consensus size: 7
465993 ATTGAATTAA
466003 TTAT-GT
1 TTATGGT
466009 TTATGGT
1 TTATGGT
*
466016 TTAGGGT
1 TTATGGT
*
466023 ATATGGT
1 TTATGGT
*
466030 TTAGGGT
1 TTATGGT
*
466037 ATATGGT
1 TTATGGT
*
466044 TTAGGGT
1 TTATGGT
* *
466051 TTAAGTT
1 TTATGGT
*
466058 TTAGGAGT
1 TTATG-GT
*
466066 TACTAT--C
1 T--TATGGT
**
466073 TTAAAGT
1 TTATGGT
*
466080 TTATGGA
1 TTATGGT
*
466087 TTATGGA
1 TTATGGT
*
466094 TTATGGA
1 TTATGGT
*
466101 TTATGGA
1 TTATGGT
*
466108 TTATGGA
1 TTATGGT
*
466115 TTATGGA
1 TTATGGT
*
466122 TTATGAT
1 TTATGGT
466129 TTATGGT
1 TTATGGT
466136 TTATGGT
1 TTATGGT
466143 TTAATGGT
1 TT-ATGGT
466151 T
1 T
466152 GGGGTTTAAG
Statistics
Matches: 113, Mismatches: 23, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
5 2 0.02
6 4 0.04
7 97 0.86
8 8 0.07
10 2 0.02
ACGTcount: A:0.24, C:0.01, G:0.27, T:0.48
Consensus pattern (7 bp):
TTATGGT
Found at i:466157 original size:21 final size:21
Alignment explanation
Indices: 466133--466172 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
466123 TATGATTTAT
* *
466133 GGTTTATGGTTTAATGGTTGG
1 GGTTTAAGGTTTAAGGGTTGG
466154 GGTTTAAGGTTTAAGGGTT
1 GGTTTAAGGTTTAAGGGTT
466173 AAGGGCTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (21 bp):
GGTTTAAGGTTTAAGGGTTGG
Found at i:466451 original size:22 final size:22
Alignment explanation
Indices: 466421--466464 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
466411 AGTAACAAAT
466421 AAAAATA-TTACTTAAAATTTA
1 AAAAATATTTACTTAAAATTTA
*
466442 AAAAATTATTTATTTAAAATTTA
1 AAAAA-TATTTACTTAAAATTTA
466465 TATGAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 2 0.10
23 13 0.65
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAAATATTTACTTAAAATTTA
Found at i:470091 original size:42 final size:43
Alignment explanation
Indices: 470045--470279 Score: 165
Period size: 43 Copynumber: 5.7 Consensus size: 43
470035 TGTTTTTAGT
* *
470045 GGCGTTTGTGT-AAAAAGCGTCGCTAAAGGTCAGTTCTATAGC
1 GGCGTTTGTGTGAAAAAGCGCCGCTAAAGATCAGTTCTATAGC
* **
470087 GGCGTTTGTATGAAAAAGCGCCGCTAAAGATTTGTTCTATAGC
1 GGCGTTTGTGTGAAAAAGCGCCGCTAAAGATCAGTTCTATAGC
* * * * **
470130 GGCGTTTGTG-GGAAAAGCACCGCTAAAAATGATGACCTATAGC
1 GGCGTTTGTGTGAAAAAGCGCCGCTAAAGATCA-GTTCTATAGC
**
470173 GGCG---G-G-G--AAAGCGCCGCTAAA-ATTCATGACCTATAGC
1 GGCGTTTGTGTGAAAAAGCGCCGCTAAAGA-TCA-GTTCTATAGC
* *
470210 GGCGTTTGTG-GAAAAAGCGCCGCTAAA-AGTTATGATCT-TAGC
1 GGCGTTTGTGTGAAAAAGCGCCGCTAAAGA-TCA-GTTCTATAGC
* * *
470252 GGCGTTTGTG-GGATAAGCGCCGGTAAAG
1 GGCGTTTGTGTGAAAAAGCGCCGCTAAAG
470280 TTCATGACTT
Statistics
Matches: 162, Mismatches: 21, Indels: 19
0.80 0.10 0.09
Matches are distributed among these distances:
36 1 0.01
37 30 0.19
39 2 0.01
40 2 0.01
41 2 0.01
42 55 0.34
43 70 0.43
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (43 bp):
GGCGTTTGTGTGAAAAAGCGCCGCTAAAGATCAGTTCTATAGC
Found at i:470190 original size:37 final size:37
Alignment explanation
Indices: 470143--470213 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
470133 GTTTGTGGGA
*
470143 AAAGCACCGCTAAAAATGATGACCTATAGCGGCGGGG
1 AAAGCACCGCTAAAAATCATGACCTATAGCGGCGGGG
* *
470180 AAAGCGCCGCTAAAATTCATGACCTATAGCGGCG
1 AAAGCACCGCTAAAAATCATGACCTATAGCGGCG
470214 TTTGTGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.34, C:0.24, G:0.27, T:0.15
Consensus pattern (37 bp):
AAAGCACCGCTAAAAATCATGACCTATAGCGGCGGGG
Found at i:470226 original size:80 final size:78
Alignment explanation
Indices: 470101--470255 Score: 213
Period size: 80 Copynumber: 2.0 Consensus size: 78
470091 TTTGTATGAA
** *
470101 AAAGCGCCGCTAAAGATTTGTTCTATAGCGGCGTTTGTGGGAAAAGCACCGCTAAAAATGATGAC
1 AAAGCGCCGCTAAAGATTTGACCTATAGCGGCGTTTGTGGAAAAAGCACCGCTAAAAATGATGAC
470166 CTATAGCGGCGGGG
66 CT-TAGCGGCGGGG
* * *
470180 AAAGCGCCGCTAAA-ATTCATGACCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTTATG
1 AAAGCGCCGCTAAAGATT--TGACCTATAGCGGCGTTTGTGGAAAAAGCACCGCTAAAAATGATG
*
470244 ATCTTAGCGGCG
64 ACCTTAGCGGCG
470256 TTTGTGGGAT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
78 3 0.04
79 22 0.33
80 42 0.63
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (78 bp):
AAAGCGCCGCTAAAGATTTGACCTATAGCGGCGTTTGTGGAAAAAGCACCGCTAAAAATGATGAC
CTTAGCGGCGGGG
Found at i:499415 original size:74 final size:74
Alignment explanation
Indices: 499264--499443 Score: 227
Period size: 74 Copynumber: 2.4 Consensus size: 74
499254 ATCGAGCATT
* * *
499264 AGCGACTTTTTGAAAAACGTCGCCGTAAAAAGATTAAGCACAACGCCGTCATTTTATGTTGAGCT
1 AGCG-CTTTTTGAAAAA---CGCCG-AAAAAAATTAAACACAACGCCGTCATTCTATGTTGAGCT
499329 TCAGTGGCATTAGC
61 TCAGTGGCATTAGC
* * *
499343 AGCGCTTTTTGAAAAACGCCGCAAAAAAATTAAACACAACGCTGT-GTTCTATGTTGAGCTTTAG
1 AGCGCTTTTTGAAAAACGCCG-AAAAAAATTAAACACAACGCCGTCATTCTATGTTGAGCTTCAG
499407 TGGCATTAGC
65 TGGCATTAGC
* *
499417 GGCTCTTTTTGAAAAACGCCGAAAAAA
1 AGCGCTTTTTGAAAAACGCCGAAAAAA
499444 GCATTTTATC
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
73 6 0.07
74 45 0.49
75 25 0.27
78 12 0.13
79 4 0.04
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (74 bp):
AGCGCTTTTTGAAAAACGCCGAAAAAAATTAAACACAACGCCGTCATTCTATGTTGAGCTTCAGT
GGCATTAGC
Found at i:499841 original size:14 final size:15
Alignment explanation
Indices: 499807--499843 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
499797 ACTATTTTAA
499807 GGTTTATGAATTATG
1 GGTTTATGAATTATG
499822 GGTTTA-GAGATTAT-
1 GGTTTATGA-ATTATG
499836 GGTTTATG
1 GGTTTATG
499844 GTTTAAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (15 bp):
GGTTTATGAATTATG
Found at i:499883 original size:21 final size:22
Alignment explanation
Indices: 499837--499899 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
499827 AGAGATTATG
* * *
499837 GTTTATGGTTTAAGGGTTGGTA
1 GTTTAAGGTTTAGGGGTTAGTA
499859 -TTTAAGGTTTAGGGGTTAG-A
1 GTTTAAGGTTTAGGGGTTAGTA
*
499879 GTTTAAGGATTAGGGGCTTAG
1 GTTTAAGGTTTAGGGG-TTAG
499900 GATTTATGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 30 0.86
22 4 0.11
ACGTcount: A:0.22, C:0.02, G:0.37, T:0.40
Consensus pattern (22 bp):
GTTTAAGGTTTAGGGGTTAGTA
Found at i:501398 original size:27 final size:28
Alignment explanation
Indices: 501366--501423 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
501356 TAGCTAACTT
* *
501366 CTTAACTACTAACCAAC-TTAGTAACCA
1 CTTAACTACTAACAAACTTTAGTAACAA
*
501393 CTTAACTGCTAACAAACTTTAGTAACAA
1 CTTAACTACTAACAAACTTTAGTAACAA
501421 CTT
1 CTT
501424 TGACCATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.29
Consensus pattern (28 bp):
CTTAACTACTAACAAACTTTAGTAACAA
Found at i:505979 original size:27 final size:28
Alignment explanation
Indices: 505947--506004 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
505937 TAGCTAACTT
*
505947 CTTAACTGCTAACCAAC-TTAGTAACCA
1 CTTAACTGCTAACCAACTTTAGTAACAA
**
505974 CTTAACTGCTAACTGACTTTAGTAACAA
1 CTTAACTGCTAACCAACTTTAGTAACAA
506002 CTT
1 CTT
506005 TGACCATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (28 bp):
CTTAACTGCTAACCAACTTTAGTAACAA
Found at i:508778 original size:16 final size:16
Alignment explanation
Indices: 508757--508802 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
508747 CGCTGTATTT
508757 GAATAGAGGCGTAATG
1 GAATAGAGGCGTAATG
*
508773 GAATAGAAGCGTAATG
1 GAATAGAGGCGTAATG
508789 GAATA-AGGCGTAAT
1 GAATAGAGGCGTAAT
508803 AGCAAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 8 0.29
16 20 0.71
ACGTcount: A:0.41, C:0.07, G:0.33, T:0.20
Consensus pattern (16 bp):
GAATAGAGGCGTAATG
Found at i:508854 original size:35 final size:37
Alignment explanation
Indices: 508798--508869 Score: 130
Period size: 35 Copynumber: 2.0 Consensus size: 37
508788 GGAATAAGGC
508798 GTAATAGCAAATCAATTGTTTGGTTGAATGTAATGGA
1 GTAATAGCAAATCAATTGTTTGGTTGAATGTAATGGA
508835 GTAATAGC-AA-CAATTGTTTGGTTGAATGTAATGGA
1 GTAATAGCAAATCAATTGTTTGGTTGAATGTAATGGA
508870 ATAGAGGCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 25 0.71
36 2 0.06
37 8 0.23
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.35
Consensus pattern (37 bp):
GTAATAGCAAATCAATTGTTTGGTTGAATGTAATGGA
Found at i:509092 original size:18 final size:17
Alignment explanation
Indices: 509071--509105 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
509061 TTATTATTAA
*
509071 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
509089 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
509106 TCTNNNNNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:515139 original size:43 final size:43
Alignment explanation
Indices: 515065--515225 Score: 157
Period size: 43 Copynumber: 3.8 Consensus size: 43
515055 TTTCATGACC
* ** * *
515065 TTTAGCGGCGTTTTTGGGAAAAGTGTTGCTAAAAGTCATGTTT
1 TTTAGCGGCGTTTTAGGGAAAAGTGCCGCTAAAAGTTATGTTA
** * *
515108 TTTAATGGCGTTTTAGGGGAAAGTGCCGCTAAAGGTTATGTTA
1 TTTAGCGGCGTTTTAGGGAAAAGTGCCGCTAAAAGTTATGTTA
* * * * *
515151 TTTAGCAGCATCTTTAGGG--AAGCGCCACTAAAAGTTATGTTC
1 TTTAGCGGCGT-TTTAGGGAAAAGTGCCGCTAAAAGTTATGTTA
515193 TTTAGCGGCGTTTGT-GGGAAAAGTGCCGCTAAA
1 TTTAGCGGCGTTT-TAGGGAAAAGTGCCGCTAAA
515226 GATCATGCTC
Statistics
Matches: 93, Mismatches: 21, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
41 5 0.05
42 29 0.31
43 52 0.56
44 7 0.08
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (43 bp):
TTTAGCGGCGTTTTAGGGAAAAGTGCCGCTAAAAGTTATGTTA
Found at i:515238 original size:43 final size:42
Alignment explanation
Indices: 515064--515290 Score: 165
Period size: 42 Copynumber: 5.3 Consensus size: 42
515054 TTTTCATGAC
* **
515064 CTTTAGCGGCGTTTTTGGGAAAAGTGTTGCTAAA-AGTCATGTT
1 CTTTAGCGGC-ATTTTGGGAAAAGTGCCGCTAAAGA-TCATGTT
* ** * * * *
515107 TTTTAATGGCGTTTTAGGGGAAAGTGCCGCTAAAGGTTATGTT
1 CTTTAGCGGCATTTT-GGGAAAAGTGCCGCTAAAGATCATGTT
* * * * *
515150 ATTTAGCAGCATCTTTAGGG--AAGCGCCACTAAA-AGTTATGTT
1 CTTTAGCGGCAT-TTT-GGGAAAAGTGCCGCTAAAGA-TCATGTT
* *
515192 CTTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGATCATGCT
1 CTTTAGCGGCATTT-TGGGAAAAGTGCCGCTAAAGATCATGTT
* * **
515235 CTTTAGCGGCATTTTCGGAAAAGCGTTGCTAAAGATCATGTT
1 CTTTAGCGGCATTTTGGGAAAAGTGCCGCTAAAGATCATGTT
*
515277 CTATAGCGGCATTT
1 CTTTAGCGGCATTT
515291 GTCCACATAA
Statistics
Matches: 145, Mismatches: 31, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
41 5 0.03
42 68 0.47
43 64 0.44
44 8 0.06
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.33
Consensus pattern (42 bp):
CTTTAGCGGCATTTTGGGAAAAGTGCCGCTAAAGATCATGTT
Found at i:515267 original size:85 final size:86
Alignment explanation
Indices: 515064--515292 Score: 223
Period size: 85 Copynumber: 2.7 Consensus size: 86
515054 TTTTCATGAC
* * * * ** *
515064 CTTTAGCGGCGTTTTTGGGAAAAGTGTTGCTAAAAGTCATGTTTTTTAATGGCGTTT-TAGGGGA
1 CTTTAGCGGC-ATTTTAGGAAAAGCGTTGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTAGGGAA
* * *
515128 AAGTGCCGCTAAAGGTTATGTT
65 AAGTGCCGCTAAAGATCATGCT
* * * *** *
515150 ATTTAGCAGCATCTTTAGG-GAAGCGCCACTAAAAGTTATGTTCTTTAGCGGCGTTTGT-GGGAA
1 CTTTAGCGGCAT-TTTAGGAAAAGCGTTGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTAGGGAA
515213 AAGTGCCGCTAAAGATCATGCT
65 AAGTGCCGCTAAAGATCATGCT
* * *
515235 CTTTAGCGGCATTTTCGGAAAAGCGTTGCT-AAAGATCATGTTCTATAGCGGCATTTGT
1 CTTTAGCGGCATTTTAGGAAAAGCGTTGCTAAAAG-TCATGTTCTTTAGCGGCGTTTGT
515293 CCACATAAAT
Statistics
Matches: 112, Mismatches: 27, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
84 9 0.08
85 89 0.79
86 14 0.12
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.34
Consensus pattern (86 bp):
CTTTAGCGGCATTTTAGGAAAAGCGTTGCTAAAAGTCATGTTCTTTAGCGGCGTTTGTAGGGAAA
AGTGCCGCTAAAGATCATGCT
Found at i:517817 original size:13 final size:12
Alignment explanation
Indices: 517795--517824 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
517785 ATGTTAAGTT
517795 ATTTGTGTGAAA
1 ATTTGTGTGAAA
517807 ATTTCGTGTGAAA
1 ATTT-GTGTGAAA
517820 ATTTG
1 ATTTG
517825 ATCGTTTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.43
Consensus pattern (12 bp):
ATTTGTGTGAAA
Found at i:519156 original size:37 final size:37
Alignment explanation
Indices: 519115--519234 Score: 102
Period size: 37 Copynumber: 3.2 Consensus size: 37
519105 GAATATAAAT
*
519115 ATGTATGCATATAATCAAGTTATTGAGTTGGGAATTA
1 ATGTATGCATTTAATCAAGTTATTGAGTTGGGAATTA
* * * * *
519152 ATGTATGAATTTTAT-AA-TTATAGGGAGATT-CGAACATA
1 ATGTATGCATTTAATCAAGTTAT--TGAG-TTGGGAA-TTA
*
519190 TATGTATGCATTTAATCAAGTTATTGAGTTGGAAATTA
1 -ATGTATGCATTTAATCAAGTTATTGAGTTGGGAATTA
*
519228 AAGTATG
1 ATGTATG
519235 TTTCTTATGT
Statistics
Matches: 62, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
35 4 0.06
36 2 0.03
37 24 0.39
38 8 0.13
39 18 0.29
40 2 0.03
41 4 0.06
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (37 bp):
ATGTATGCATTTAATCAAGTTATTGAGTTGGGAATTA
Found at i:519517 original size:41 final size:41
Alignment explanation
Indices: 519456--519599 Score: 236
Period size: 41 Copynumber: 3.5 Consensus size: 41
519446 GGCTTTGTGC
519456 CTAGCAGGCTTAACGCCGGTGAAAAATTTCGGACTATACGT
1 CTAGCAGGCTTAACGCCGGTGAAAAATTTCGGACTATACGT
*
519497 CTAACAGGCTTAACGCCGGTGAAAAATTTCGGACTATACGT
1 CTAGCAGGCTTAACGCCGGTGAAAAATTTCGGACTATACGT
** *
519538 CTAGCAGGCTTAACGCCGGTGAAAAATTTCAAACTATATGT
1 CTAGCAGGCTTAACGCCGGTGAAAAATTTCGGACTATACGT
519579 CTAGCAGGCTTAATC-CCGGTG
1 CTAGCAGGCTTAA-CGCCGGTG
519600 TTCTGAATCA
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
41 96 0.99
42 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTTAACGCCGGTGAAAAATTTCGGACTATACGT
Found at i:524359 original size:38 final size:38
Alignment explanation
Indices: 524317--524389 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
524307 TAAGACCATG
*
524317 TCTGGGACATGGCATTGGCACCGAGATGAGAGGTCTCA
1 TCTGGGACATGACATTGGCACCGAGATGAGAGGTCTCA
*
524355 TCTGGGACATGACATTGGCACTGAGATGAGAGGTC
1 TCTGGGACATGACATTGGCACCGAGATGAGAGGTC
524390 CCCCGTAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (38 bp):
TCTGGGACATGACATTGGCACCGAGATGAGAGGTCTCA
Found at i:524448 original size:50 final size:48
Alignment explanation
Indices: 524355--524522 Score: 169
Period size: 50 Copynumber: 3.4 Consensus size: 48
524345 AGAGGTCTCA
* * ** **
524355 TCTGGGACATGACATTGGCACTGAGATGAGAGGTCCCCCGTAAGACCATG
1 TCTGGGACATGGCATTGGCAC-GACATGA-AACTCCCATGTAAGACCATG
* *
524405 TCTGGGACATGGCATTGGCACCGATATGATAACTCCCATGTAAGACCATA
1 TCTGGGACATGGCATTGGCA-CGACATGA-AACTCCCATGTAAGACCATG
* *
524455 TCTGGGATATGGCATT-GCA-GTACAGGAAACATCCCATGTAAGACCATG
1 TCTGGGACATGGCATTGGCACG-ACATGAAAC-TCCCATGTAAGACCATG
*
524503 TCTGGGACATGGCTTTGGCA
1 TCTGGGACATGGCATTGGCA
524523 TGTTATTATC
Statistics
Matches: 100, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
47 4 0.04
48 34 0.34
49 6 0.06
50 55 0.55
51 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (48 bp):
TCTGGGACATGGCATTGGCACGACATGAAACTCCCATGTAAGACCATG
Found at i:524507 original size:48 final size:49
Alignment explanation
Indices: 524394--524522 Score: 165
Period size: 48 Copynumber: 2.6 Consensus size: 49
524384 GAGGTCCCCC
* *
524394 GTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGATAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CGACAGGATAACTCCCAT
* *
524444 GTAAGACCATATCTGGGATATGGCATT-GCA-GTACAGGA-AACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACG-ACAGGATAAC-TCCCAT
*
524492 GTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
524523 TGTTATTATC
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
47 4 0.06
48 34 0.49
49 6 0.09
50 25 0.36
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.24
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACGACAGGATAACTCCCAT
Found at i:525039 original size:23 final size:23
Alignment explanation
Indices: 525006--525346 Score: 240
Period size: 23 Copynumber: 14.6 Consensus size: 23
524996 TCACACCAAT
* *
525006 AATTGGACAGCATATATATAACA
1 AATTGGGCAGCATATATACAACA
* *
525029 ATTTGGGCAGCATATATACATCA
1 AATTGGGCAGCATATATACAACA
* * *
525052 AATTGAGCAGCAT-TTTAGCATAAA
1 AATTGGGCAGCATATATA-CA-ACA
*
525076 AATTGGACAGCATATATACAACA
1 AATTGGGCAGCATATATACAACA
* * *
525099 ATTTGGGCAGCCTATATATATACCA
1 AATTGGGCAG-C-ATATATACAACA
* * * *
525124 AATTGAGCAGCATTTTTACATCAA
1 AATTGGGCAGCATATATACAAC-A
*
525148 AATTGGACAGCATATATACAACA
1 AATTGGGCAGCATATATACAACA
* *
525171 ATTTGGGCAGCATAAATACAACA
1 AATTGGGCAGCATATATACAACA
* *
525194 AATTGGGTAGCATTTA-AGCATA-A
1 AATTGGGCAGCATATATA-CA-ACA
* *
525217 ACATTGGACAGCATATATGCAACA
1 A-ATTGGGCAGCATATATACAACA
* *
525241 ATTTGGGCAGCATAAATACAACA
1 AATTGGGCAGCATATATACAACA
* * * *
525264 AATTGGACAACAT-TTTAGCATAAA
1 AATTGGGCAGCATATATA-CA-ACA
* * * * *
525288 AATTTGACAGTATATATGCACCA
1 AATTGGGCAGCATATATACAACA
* *
525311 ATTTGGGCAGCATAAATACAACA
1 AATTGGGCAGCATATATACAACA
*
525334 AATTGGACAGCAT
1 AATTGGGCAGCAT
525347 TTAAGCATAA
Statistics
Matches: 239, Mismatches: 65, Indels: 28
0.72 0.20 0.08
Matches are distributed among these distances:
22 6 0.03
23 145 0.61
24 65 0.27
25 23 0.10
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (23 bp):
AATTGGGCAGCATATATACAACA
Found at i:525093 original size:47 final size:47
Alignment explanation
Indices: 525006--525361 Score: 210
Period size: 47 Copynumber: 7.6 Consensus size: 47
524996 TCACACCAAT
* * * *
525006 AATTGGACAGCATATAT--ATAACAATTTGGGCAGCATATATACATCA
1 AATTGGGCAGCATATATACATAA-AAATTGGACAGCATATATACAACA
* *
525052 AATTGAGCAGCAT-TTTAGCATAAAAATTGGACAGCATATATACAACA
1 AATTGGGCAGCATATATA-CATAAAAATTGGACAGCATATATACAACA
* * * * * * *
525099 ATTTGGGCAGCCTATATATATACCAAATT-GAGCAGCATTTTTACATCAA
1 AATTGGGCAGCATATATACATA-AAAATTGGA-CAGCATATATACAAC-A
* * * * *
525148 AATTGGACAGCATATATACA-ACAATTTGGGCAGCATAAATACAACA
1 AATTGGGCAGCATATATACATAAAAATTGGACAGCATATATACAACA
* * * *
525194 AATTGGGTAGCATTTA-AGCATAAACATTGGACAGCATATATGCAACA
1 AATTGGGCAGCATATATA-CATAAAAATTGGACAGCATATATACAACA
* * * * * *
525241 ATTTGGGCAGCATAAATACA-ACAAATTGGACAACAT-TTTAGCATAAA
1 AATTGGGCAGCATATATACATAAAAATTGGACAGCATATATA-CA-ACA
* * * * ** * * *
525288 AATTTGACAGTATATATGCA-CCAATTTGGGCAGCATAAATACAACA
1 AATTGGGCAGCATATATACATAAAAATTGGACAGCATATATACAACA
* *
525334 AATTGGACAGCATTTA-AGCATAAAAATT
1 AATTGGGCAGCATATATA-CATAAAAATT
525362 ACATGAACAT
Statistics
Matches: 230, Mismatches: 64, Indels: 31
0.71 0.20 0.10
Matches are distributed among these distances:
45 5 0.02
46 59 0.26
47 120 0.52
48 29 0.13
49 17 0.07
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (47 bp):
AATTGGGCAGCATATATACATAAAAATTGGACAGCATATATACAACA
Found at i:525099 original size:70 final size:69
Alignment explanation
Indices: 525006--525361 Score: 480
Period size: 70 Copynumber: 5.1 Consensus size: 69
524996 TCACACCAAT
* * *
525006 AATTGGACAGCATATATATAACAATTTGGGCAGCATATATACATCAAATTGAGCAGCATTTTAGC
1 AATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTG-GCAGCATTTTAGC
525071 ATAAA
65 ATAAA
* * *
525076 AATTGGACAGCATATATACAACAATTTGGGCAGCCTATATATATACCAAATTGAGCAGCATTTTT
1 AATTGGACAGCATATATACAACAATTTGGGCAG-C-ATAAATACAACAAATTG-GCAGCA-TTTT
*
525141 A-CATCAA
62 AGCATAAA
* *
525148 AATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGGGTAGCATTTAAGC
1 AATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATT-GGCAGCATTTTAGC
525213 ATAAA
65 ATAAA
* * *
525218 CATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTGGACAACATTTTAGC
1 AATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGG-CAGCATTTTAGC
525283 ATAAA
65 ATAAA
* * * * *
525288 AATTTGACAGTATATATGCACCAATTTGGGCAGCATAAATACAACAAATTGGACAGCATTTAAGC
1 AATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGG-CAGCATTTTAGC
525353 ATAAA
65 ATAAA
525358 AATT
1 AATT
525362 ACATGAACAT
Statistics
Matches: 259, Mismatches: 21, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
69 6 0.02
70 185 0.71
71 3 0.01
72 60 0.23
73 5 0.02
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (69 bp):
AATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGGCAGCATTTTAGCA
TAAA
Found at i:525134 original size:95 final size:95
Alignment explanation
Indices: 525017--525200 Score: 221
Period size: 95 Copynumber: 1.9 Consensus size: 95
525007 ATTGGACAGC
* * *
525017 ATATATATAACAATTTGGGCAGCATATATACATC-AAATT-GAGCAGCAT-TTTAGCATAAAAAT
1 ATATATATAACAAATTGAGCAGCATATATACATCAAAATTGGA-CAGCATATATA-CA-AAAAAT
* *
525079 TGGACAGCATATATACAACAATTTGGGCAGCCT
63 TGGACAGCATAAATACAACAAATTGGGCAGCCT
* * * * *
525112 ATATATATACCAAATTGAGCAGCATTTTTACATCAAAATTGGACAGCATATATACAACAATTTGG
1 ATATATATAACAAATTGAGCAGCATATATACATCAAAATTGGACAGCATATATACAAAAAATTGG
*
525177 GCAGCATAAATACAACAAATTGGG
66 ACAGCATAAATACAACAAATTGGG
525201 TAGCATTTAA
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
95 57 0.76
96 13 0.17
97 5 0.07
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (95 bp):
ATATATATAACAAATTGAGCAGCATATATACATCAAAATTGGACAGCATATATACAAAAAATTGG
ACAGCATAAATACAACAAATTGGGCAGCCT
Found at i:525164 original size:142 final size:140
Alignment explanation
Indices: 524937--525361 Score: 525
Period size: 142 Copynumber: 3.0 Consensus size: 140
524927 TCTACCCTGT
* * * * * ** * *
524937 TTGGACAGCCTTTTTACATCAATTTGGACAGCATTCATATACCAAACT-AGACAGCATTTTCACA
1 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATATACCAAATTGAGACAGCATTTTTACA
* * * *
525001 CCAATAATTGGACAGCATATATATAACAATTTGGGCAGCATATATACATCAAATTGAGCAGCATT
66 TCAA-AATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTG-GCAGCATT
*
525066 TTAGCATAAAAA
129 TAAGCATAAAAA
*
525078 TTGGACAGCATATATACAACAATTTGGGCAGCCTATATATATACCAAATTGAG-CAGCATTTTTA
1 TTGGACAGCATATATACAACAATTTGGGCAG-C-ATAAATATACCAAATTGAGACAGCATTTTTA
*
525142 CATCAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGGGTAGCAT
64 CATCAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATT-GGCAGCAT
*
525207 TTAAGCATAAACA
128 TTAAGCATAAAAA
* * * *
525220 TTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTG-GACAACA-TTTTAGC
1 TTGGACAGCATATATACAACAATTTGGGCAGCATAAATATACCAAATTGAGACAGCATTTTTA-C
* * * * *
525283 ATAAAAATTTGACAGTATATATGCACCAATTTGGGCAGCATAAATACAACAAATTGGACAGCATT
65 ATCAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGG-CAGCATT
525348 TAAGCATAAAAA
129 TAAGCATAAAAA
525360 TT
1 TT
525362 ACATGAACAT
Statistics
Matches: 249, Mismatches: 28, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
139 8 0.03
140 88 0.35
141 27 0.11
142 95 0.38
143 29 0.12
144 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (140 bp):
TTGGACAGCATATATACAACAATTTGGGCAGCATAAATATACCAAATTGAGACAGCATTTTTACA
TCAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGGCAGCATTTA
AGCATAAAAA
Found at i:525564 original size:44 final size:44
Alignment explanation
Indices: 525501--525589 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
525491 AACTATGCTA
*
525501 TACATGCCATATATTTGATAACGATTTAACAAAATACCATAGTG
1 TACATGCCATATATTTGATAACGATTTAACAAAATACAATAGTG
*
525545 TACATGCCATATATTTGATAACGATTTAGCAAAATACAATAGTG
1 TACATGCCATATATTTGATAACGATTTAACAAAATACAATAGTG
525589 T
1 T
525590 GACGAACTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (44 bp):
TACATGCCATATATTTGATAACGATTTAACAAAATACAATAGTG
Found at i:527860 original size:95 final size:96
Alignment explanation
Indices: 527750--527947 Score: 380
Period size: 95 Copynumber: 2.1 Consensus size: 96
527740 TATACTTACT
527750 TATTTTATTTCTTTTTCTTTCATATAGTATTATCAAGCATAGTCGAGATCTTGAAGACGTCAAAG
1 TATTTTATTTCTTTTTCTTTCATATAGTATTATCAAGCATAGTCGAGATCTTGAAGACGTCAAAG
*
527815 AGCGTTCACACTATCAACCACCACAACTCGA
66 AGCGTTCACACTATCAACCACCACAAATCGA
527846 TATTTTATTT-TTTTTCTTTCATATAGTATTATCAAGCATAGTCGAGATCTTGAAGACGTCAAAG
1 TATTTTATTTCTTTTTCTTTCATATAGTATTATCAAGCATAGTCGAGATCTTGAAGACGTCAAAG
527910 AGCGTTCACACTATCAACCACCACAAATCGA
66 AGCGTTCACACTATCAACCACCACAAATCGA
527941 TATTTTA
1 TATTTTA
527948 AGACGATAAA
Statistics
Matches: 101, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
95 91 0.90
96 10 0.10
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (96 bp):
TATTTTATTTCTTTTTCTTTCATATAGTATTATCAAGCATAGTCGAGATCTTGAAGACGTCAAAG
AGCGTTCACACTATCAACCACCACAAATCGA
Found at i:533484 original size:5 final size:5
Alignment explanation
Indices: 533474--533499 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
533464 TATTAAACAA
533474 TAATT TAATT TAATT TAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT T
533500 GAAAGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TAATT
Found at i:541252 original size:15 final size:16
Alignment explanation
Indices: 541232--541261 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
541222 CCATAAGCCA
541232 ACAAAAAA-AAAAAGC
1 ACAAAAAAGAAAAAGC
541247 ACAAAAAAGAAAAAG
1 ACAAAAAAGAAAAAG
541262 AGAAAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (16 bp):
ACAAAAAAGAAAAAGC
Found at i:542302 original size:21 final size:21
Alignment explanation
Indices: 542276--542344 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
542266 ATAGATTTTG
542276 TTTTATAAATTTTAAATATTA
1 TTTTATAAATTTTAAATATTA
542297 TTTTATAAAGTTTTAAAGTATT-
1 TTTTATAAA-TTTTAAA-TATTA
* *
542319 TTGTA-AATATTTCTAAAAATTA
1 TTTTATAA-ATTT-TAAATATTA
542341 TTTT
1 TTTT
542345 TTTAAGCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
21 17 0.43
22 19 0.47
23 4 0.10
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (21 bp):
TTTTATAAATTTTAAATATTA
Found at i:542313 original size:22 final size:22
Alignment explanation
Indices: 542276--542318 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
542266 ATAGATTTTG
542276 TTTTATAAATTTTAAA-TATTA
1 TTTTATAAATTTTAAAGTATTA
542297 TTTTATAAAGTTTTAAAGTATT
1 TTTTATAAA-TTTTAAAGTATT
542319 TTGTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTTATAAATTTTAAAGTATTA
Found at i:542320 original size:20 final size:21
Alignment explanation
Indices: 542276--542326 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
542266 ATAGATTTTG
*
542276 TTTTATAAATTTTAAATATTA
1 TTTTATAAATTTTAAATAGTA
542297 TTTTATAAAGTTTT-AA-AGTA
1 TTTTATAAA-TTTTAAATAGTA
*
542317 TTTTGTAAAT
1 TTTTATAAAT
542327 ATTTCTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 11 0.41
21 11 0.41
22 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (21 bp):
TTTTATAAATTTTAAATAGTA
Found at i:545290 original size:13 final size:13
Alignment explanation
Indices: 545272--545296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
545262 TAATTTAATA
545272 TTATTTTGTGTGT
1 TTATTTTGTGTGT
545285 TTATTTTGTGTG
1 TTATTTTGTGTG
545297 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:557204 original size:26 final size:26
Alignment explanation
Indices: 557133--557205 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
557123 TATTTTCTCG
*
557133 AAATTTTACTAGAGGTAAAATCATCA
1 AAATTTTACTAGGGGTAAAATCATCA
* * * *
557159 AAATTTTACCATGGGCAAAATCTTCA
1 AAATTTTACTAGGGGTAAAATCATCA
*
557185 AAATTTTATTAGGGGTAAAAT
1 AAATTTTACTAGGGGTAAAAT
557206 AGGGATGAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (26 bp):
AAATTTTACTAGGGGTAAAATCATCA
Found at i:559848 original size:34 final size:35
Alignment explanation
Indices: 559804--559870 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
559794 CAGTAAAATA
559804 TTTTCCGTAAAATGATTT-CGGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
559838 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
559871 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:563676 original size:6 final size:6
Alignment explanation
Indices: 563667--563700 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
563657 AAAATAATAA
563667 TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGG
1 TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGG
563701 TATTTGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (6 bp):
TTGGGT
Found at i:566439 original size:13 final size:13
Alignment explanation
Indices: 566421--566445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
566411 AATAGTCTCA
566421 CTTTTTTTTCCTC
1 CTTTTTTTTCCTC
566434 CTTTTTTTTCCT
1 CTTTTTTTTCCT
566446 TACCAAGTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
CTTTTTTTTCCTC
Found at i:584176 original size:20 final size:21
Alignment explanation
Indices: 584144--584183 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
584134 GTTTGTTAGG
*
584144 TAGTTAGTCTTGTTATTAGAA
1 TAGTTAGTCTTGTTAATAGAA
584165 TAGTTAGT-TTGTTAATAGA
1 TAGTTAGTCTTGTTAATAGA
584184 TGGTTAGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (21 bp):
TAGTTAGTCTTGTTAATAGAA
Found at i:590519 original size:46 final size:46
Alignment explanation
Indices: 590454--590553 Score: 184
Period size: 46 Copynumber: 2.2 Consensus size: 46
590444 AATATACCTA
590454 TTATATAA-ACACATATACTTATAATAGCAATGTGTATCATTTTTG
1 TTATATAACACACATATACTTATAATAGCAATGTGTATCATTTTTG
*
590499 TTATATAACACACATATACTTATAATTGCAATGTGTATCATTTTTG
1 TTATATAACACACATATACTTATAATAGCAATGTGTATCATTTTTG
590545 TTATATAAC
1 TTATATAAC
590554 CAACCAAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 8 0.15
46 45 0.85
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (46 bp):
TTATATAACACACATATACTTATAATAGCAATGTGTATCATTTTTG
Found at i:590721 original size:41 final size:41
Alignment explanation
Indices: 590673--590791 Score: 141
Period size: 40 Copynumber: 2.9 Consensus size: 41
590663 ACAAATCCAA
* * *
590673 ATATGATACACTGGCACAAAGCCTGTTAGGCATAAAGCCTG
1 ATATGATACACCGGCATAAAGCCTGCTAGGCATAAAGCCTG
* * *
590714 ATCTGATACACCAGCATAAAG-CTGCTAGGCATAAAGCTTG
1 ATATGATACACCGGCATAAAGCCTGCTAGGCATAAAGCCTG
** * *
590754 ATAAAATTCACCGGCATAAAGCCTGCTAGGCACAAAGC
1 ATATGATACACCGGCATAAAGCCTGCTAGGCATAAAGC
590792 GTGAATATCA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 33 0.51
41 32 0.49
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (41 bp):
ATATGATACACCGGCATAAAGCCTGCTAGGCATAAAGCCTG
Found at i:592810 original size:27 final size:27
Alignment explanation
Indices: 592769--592824 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
592759 ATTCAACCAG
*
592769 TTAAAAAAAATATTAAAATAAAGATGT
1 TTAAAAAAAACATTAAAATAAAGATGT
**
592796 TTAAAAAAAACATTACTATAAAGATGT
1 TTAAAAAAAACATTAAAATAAAGATGT
592823 TT
1 TT
592825 TTATTTTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (27 bp):
TTAAAAAAAACATTAAAATAAAGATGT
Found at i:599561 original size:21 final size:22
Alignment explanation
Indices: 599522--599562 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
599512 GAATAACAAT
*
599522 AGAAAGAAAGAAGAGAAAATGG
1 AGAAAGAAAGAAGAAAAAATGG
*
599544 AGAAGGAAA-AAGAAAAAAT
1 AGAAAGAAAGAAGAAAAAAT
599563 TAGAGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (22 bp):
AGAAAGAAAGAAGAAAAAATGG
Found at i:599587 original size:14 final size:16
Alignment explanation
Indices: 599558--599590 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
599548 GGAAAAAGAA
599558 AAAATTAGAGAAATTG
1 AAAATTAGAGAAATTG
599574 AAAATT-GA-AAATTG
1 AAAATTAGAGAAATTG
599588 AAA
1 AAA
599591 TTTCGAGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 2 0.12
16 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (16 bp):
AAAATTAGAGAAATTG
Found at i:606048 original size:3 final size:3
Alignment explanation
Indices: 606040--606137 Score: 178
Period size: 3 Copynumber: 32.7 Consensus size: 3
606030 TTATCTACAA
* *
606040 TAC TAC TAC TAC TAC TAC TAC TAC CAC TAC TAC TAC TAC TAT TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
606088 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
606136 TA
1 TA
606138 TGGAGCACTC
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.34, C:0.33, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:606933 original size:1 final size:1
Alignment explanation
Indices: 606927--606959 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
606917 ATGTTGCCTC
606927 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
606960 TTTTGTAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:607409 original size:16 final size:16
Alignment explanation
Indices: 607388--607420 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
607378 TGAAGGTGCG
607388 TCAACACTCATGCTGT
1 TCAACACTCATGCTGT
*
607404 TCAACATTCATGCTGT
1 TCAACACTCATGCTGT
607420 T
1 T
607421 TTGTTGACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.36
Consensus pattern (16 bp):
TCAACACTCATGCTGT
Found at i:609095 original size:125 final size:124
Alignment explanation
Indices: 608871--609118 Score: 417
Period size: 125 Copynumber: 2.0 Consensus size: 124
608861 GGAGTCATGA
* * *
608871 ATTCCGAACATAAACCATACAACGGACATGAAGAATGCAAAAAAAAAAAAAAACCCCTTTAACTT
1 ATTCCGAACATAAACCATACAACGAACATGAAGAATGCAAAAAAAAAAAAAAACACCTTTAACAT
*
608936 CGTTATTTCAATCAAAATTTCATTTTAATTTTATAGACATTTAATAAATATATGAGTTG
66 CATTATTTCAATCAAAATTTCATTTTAATTTTATAGACATTTAATAAATATATGAGTTG
608995 ATTCCGAACATAAACCATACAACGAACATGAAGAATGCAAAAACAACAAAAAAAA-ACCTTTAAC
1 ATTCCGAACATAAACCATACAACGAACATGAAGAATGCAAAAA-AA-AAAAAAAACACCTTTAAC
* *
609059 ATCATTATTTCAATCAAAATTTCATTTTAATTTTATAGACTTTTAATAAATATATTAGTT
64 ATCATTATTTCAATCAAAATTTCATTTTAATTTTATAGACATTTAATAAATATATGAGTT
609119 ACCTCTTTCA
Statistics
Matches: 116, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
124 42 0.36
125 66 0.57
126 8 0.07
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (124 bp):
ATTCCGAACATAAACCATACAACGAACATGAAGAATGCAAAAAAAAAAAAAAACACCTTTAACAT
CATTATTTCAATCAAAATTTCATTTTAATTTTATAGACATTTAATAAATATATGAGTTG
Found at i:609478 original size:38 final size:39
Alignment explanation
Indices: 609415--609497 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 39
609405 TATTTAATTA
** **
609415 ATTTTTAAAATTTTAATTTTTTTAAAA-AA-TATAAAACT
1 ATTTTTAAAATTTTAAAATAATTAAAATAATTA-AAAACT
*
609453 ATTTTTAAAATTTTAAAATAATTAAAATAATTAAAAATT
1 ATTTTTAAAATTTTAAAATAATTAAAATAATTAAAAACT
609492 ATTTTT
1 ATTTTT
609498 TTGAAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
38 23 0.61
39 13 0.34
40 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (39 bp):
ATTTTTAAAATTTTAAAATAATTAAAATAATTAAAAACT
Found at i:611377 original size:19 final size:19
Alignment explanation
Indices: 611349--611385 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
611339 TTATAAAACA
611349 AATAACAACAATAATAATT
1 AATAACAACAATAATAATT
* *
611368 AATAATAACAGTAATAAT
1 AATAACAACAATAATAAT
611386 ATCAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (19 bp):
AATAACAACAATAATAATT
Done.