Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008504.1 Hibiscus syriacus cultivar Beakdansim tig00111356_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: 2056749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:482940 original size:36 final size:36
Alignment explanation
Indices: 482844--483127 Score: 325
Period size: 38 Copynumber: 7.6 Consensus size: 36
482834 ATTATATGGT
* * *
482844 TTTTTAAAATATATATAATATATAGTTTTGAAAACA
1 TTTTGAAAATTTATATAATATATAGTTTTAAAAACA
* *
482880 TTTTGAAAACATTTATATATTATATAGTTTTTAAAACA
1 TTTTG-AAA-ATTTATATAATATATAGTTTTAAAAACA
*
482918 TTTTGAAAATTTATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATTTATATAATATATAGTTTTAAAAACA
* * *
482954 TTTTGAAAACTTATATAGTATATAGTTTTTTAAAACAA
1 TTTTGAAAATTTATATAATATATAG-TTTTAAAAAC-A
* * *
482992 TTTTGAAAAATTATATAATATATAATTTTAAAAACGTTT
1 TTTTGAAAATTTATATAATATATAGTTTTAAAAAC---A
* * *
483031 TTTTGAAAAATTATATAACACATAGTTTTAAAAACA
1 TTTTGAAAATTTATATAATATATAGTTTTAAAAACA
483067 TTTTTGGAAAATTTATATAATATATAGTTTTAAAAACA
1 -TTTT-GAAAATTTATATAATATATAGTTTTAAAAACA
*
483105 TTTTTTGAAAACTTATATAATAT
1 --TTTTGAAAATTTATATAATAT
483128 TTTTAAAACT
Statistics
Matches: 218, Mismatches: 21, Indels: 16
0.85 0.08 0.06
Matches are distributed among these distances:
36 54 0.25
37 29 0.13
38 98 0.45
39 37 0.17
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TTTTGAAAATTTATATAATATATAGTTTTAAAAACA
Found at i:483142 original size:19 final size:21
Alignment explanation
Indices: 483106--483162 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 21
483096 TTAAAAACAT
483106 TTTTTGAAAACTTATATAATA
1 TTTTTGAAAACTTATATAATA
483127 TTTTT-AAAACTATATAATATATA
1 TTTTTGAAAACT-TAT-ATA-ATA
*
483150 GTTTTGAAAACTT
1 TTTTTGAAAACTT
483163 TTTTAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 6 0.19
21 8 0.26
22 3 0.10
23 8 0.26
24 6 0.19
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (21 bp):
TTTTTGAAAACTTATATAATA
Found at i:483154 original size:24 final size:20
Alignment explanation
Indices: 483106--483146 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 20
483096 TTAAAAACAT
483106 TTTTTGAAAACTTATATAATA
1 TTTTT-AAAACTTATATAATA
483127 TTTTTAAAAC-TATATAATA
1 TTTTTAAAACTTATATAATA
483146 T
1 T
483147 ATAGTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 5 0.25
21 5 0.25
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTTTAAAACTTATATAATA
Found at i:483197 original size:31 final size:31
Alignment explanation
Indices: 483138--483197 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
483128 TTTTAAAACT
** *
483138 ATATAATATATAGTTTTGAAAACTTTTTTAA
1 ATATAATATATAGTTTAAAAAAATTTTTTAA
483169 ATATAATATATAG-TTAAAAAAATATTTTT
1 ATATAATATATAGTTTAAAAAAAT-TTTTT
483198 GAAGAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (31 bp):
ATATAATATATAGTTTAAAAAAATTTTTTAA
Found at i:483236 original size:14 final size:13
Alignment explanation
Indices: 483219--483260 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
483209 ATTATATAAT
483219 TTATATTATTATTA
1 TTAT-TTATTATTA
483233 TTATTTATTCATTA
1 TTATTTATT-ATTA
483247 TCT-TTTATTATTA
1 T-TATTTATTATTA
483260 T
1 T
483261 CTTTTTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 10 0.38
14 15 0.58
15 1 0.04
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:483240 original size:27 final size:24
Alignment explanation
Indices: 483210--483260 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
483200 AGAAAATATA
483210 TTATATAATTTATATTATTATTATTAT
1 TTAT-TAA-TTATATT-TTATTATTAT
* *
483237 TTATTCATTATCTTTTATTATTAT
1 TTATTAATTATATTTTATTATTAT
483261 CTTTTTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 10 0.45
25 6 0.27
26 2 0.09
27 4 0.18
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATTAATTATATTTTATTATTAT
Found at i:483259 original size:13 final size:13
Alignment explanation
Indices: 483224--483265 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
483214 ATAATTTATA
483224 TTATTATTAT-TAT
1 TTATTATTATCT-T
483237 TTATTCATTATCTT
1 TTATT-ATTATCTT
483251 TTATTATTATCTT
1 TTATTATTATCTT
483264 TT
1 TT
483266 TATGTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 15 0.56
14 11 0.41
15 1 0.04
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTATTATCTT
Found at i:483266 original size:14 final size:14
Alignment explanation
Indices: 483224--483268 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
483214 ATAATTTATA
*
483224 TTATTATTAT-TAT
1 TTATTATTATCTTT
483237 TTATTCATTATC-TT
1 TTATT-ATTATCTTT
483251 TTATTATTATCTTT
1 TTATTATTATCTTT
483265 TTAT
1 TTAT
483269 GTTTTTTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 11 0.39
14 17 0.61
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTATTATCTTT
Found at i:489444 original size:21 final size:21
Alignment explanation
Indices: 489420--489501 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
489410 CTAGAACCCC
*
489420 AGGGGGTATCGATTCCCCTAT
1 AGGGGGAATCGATTCCCCTAT
* * *
489441 AGGGGGAATCGGTTCTCCTTCAA
1 AGGGGGAATCGATTC-CCCT-AT
*
489464 AGGGGGAATCGGTTCCCCT-T
1 AGGGGGAATCGATTCCCCTAT
* *
489484 CAAGGGGTATCGATTCCC
1 -AGGGGGAATCGATTCCC
489502 TCTACACTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 27 0.55
22 6 0.12
23 16 0.33
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (21 bp):
AGGGGGAATCGATTCCCCTAT
Found at i:489468 original size:22 final size:22
Alignment explanation
Indices: 489420--489490 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 22
489410 CTAGAACCCC
* *
489420 AGGGGGTATCGATTCCCC-T-A
1 AGGGGGAATCGGTTCCCCTTCA
*
489440 TAGGGGGAATCGGTTCTCCTTCAA
1 -AGGGGGAATCGGTTCCCCTTC-A
489464 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGGTTCCCCTTCA
489486 AGGGG
1 AGGGG
489491 TATCGATTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
21 15 0.35
22 7 0.16
23 20 0.47
24 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.24
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCTTCA
Found at i:500033 original size:165 final size:165
Alignment explanation
Indices: 499777--500599 Score: 972
Period size: 165 Copynumber: 5.0 Consensus size: 165
499767 TCTATCACCA
** * * * * * * * ***
499777 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATAATTTACAACATAACTTAAGTAG
1 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCT
* * * *
499841 AGAAGGGTTATCTGCTAACC-AAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCACATCAT
66 AGAAGGGTTATCTG-TCACCAAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCAT
* * * *
499905 TTGCAGCATAGTTTAAGTCGAGAAAGGCTATCTGCT
130 TTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCC
*
499941 AAAGACCCCCGAGTTCGATTTCACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCT
1 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCT
* * * *
500006 AGAAGAGTTGTCTGTTACCAAAAGACCTTCGAGTTCGACTTTGCTCAGCTCCAAGGCACATCATT
66 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATT
* * *
500071 TGTAACATAGCTTAAGTCGAGAAGGGCTATCTGCC
131 TGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCC
* *
500106 AAAGACCCCCGAGTTCAATTACACTCAGCTTAGAGGGCACATCATTTACAACATAACTCAAGGCT
1 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCT
* * * * * *
500171 AGAAGGATTGTCTGTCACTAAAAGACCTTCGAGTTCGACTTTGCTCAGCTGCAAGGCATATCATT
66 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATT
500236 TGCAG-ATAGCTTAAGTCAAGAAGGGCTATCTGCC
131 TGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCC
* * * * * * * *
500270 AAAGGCCCCCGAGTTTGATTGCACTCAGCTTCAAGGGGATATCATTTACAGCATAACTCAGGGCT
1 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCT
* * *
500335 AGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATT
66 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATT
* * * * *
500399 TGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAAC
131 TGCAGCATAGCTTAAGTCAAGAAGGGCTATCTG-C--C
** * * * * * *
500437 AAAAGACCTTCGAGTTCGATTACGCTCAGC-TCCAAGGCATATCATTTACAGCATAACTCAGGGC
1 -AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGC
* * * *
500501 TAGAAGGGTTATTTGTCACCAGAAGACCTTTGAGTTCGACTATGCTCAGCTCCAAAGCACATCAT
65 TAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCAT
* *
500566 TTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTG
130 TTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTG
500600 TCAATAAAAT
Statistics
Matches: 569, Mismatches: 82, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
163 46 0.08
164 149 0.26
165 235 0.41
167 51 0.09
168 88 0.15
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (165 bp):
AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCT
AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATT
TGCAGCATAGCTTAAGTCAAGAAGGGCTATCTGCC
Found at i:500508 original size:412 final size:409
Alignment explanation
Indices: 499571--500491 Score: 1105
Period size: 412 Copynumber: 2.2 Consensus size: 409
499561 TTAAAGATAA
* * * * *
499571 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGATTAC
*
499636 ACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAAAAC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAAAAC
* * * *
499701 CCCGAGTTCGATTACACTTAGCTTCGAGGGAACATCATTTACAACAACTCAAGGCTAGAAGGGTT
131 CCCGAGTTCAATTACACTCAGCTTAGAGGGAACATCATTTACAACAACTCAAGGCTAGAAGGATT
499766 ATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATAATTTACAACATA
196 ATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATAATTTACAACATA
* ** **
499831 ACTTAAGTAGAGAAGGGTTATCTGCTAACCAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAG
261 ACTTAAGTAGAGAAGGGCTATCTG---ACCAAAGACCCCCGAGTTTGACTACACTCAGCTCCAAG
* ** * * * *
499896 GCACATCATTTGCAGCATAGTTTAAGTCGAGAAAGGCTATCTGCTAAAGACCCCCGAGTTCGATT
323 GCACATCATTTACAGCATAACTCAAGGCGAGAAAGGCTATCTGCCAAAGACCCCCGAGTTCGACT
* * *
499961 TCACTCAGCTTCGAGGGCACAT
388 ACACTCAGCTTCCAAGGCACAT
* * * * * ** *
499983 CATTTACAACATAACTCAAGGCTAGAAGAGTTGTCTGTTACCAAAAGACCTTCGAGTTCGACTT-
1 CATTTGCAGCATAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGA-TTA
* * * * *
500047 TGCTCAGCTCCAAGGCACATCATTTGTAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
65 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAAAA
*
500112 CCCCGAGTTCAATTACACTCAGCTTAGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGG
130 CCCCGAGTTCAATTACACTCAGCTTAGAGGGAACATCATTTACAAC--AACTCAAGGCTAGAAGG
* * * ** * * * *
500177 ATTGTCTGTCACTAAAAGACCTTCGAGTTCGACTTTGCTCAGCTGCAAGGCATATCATTTGC-AG
193 ATTATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATAATTTACAAC
* * * * *
500241 ATAGCTTAAGTCA-AGAAGGGCTATCTG-CCAAAGGCCCCCGAGTTTGATTGCACTCAGCTTCAA
258 ATAACTTAAGT-AGAGAAGGGCTATCTGACCAAAGACCCCCGAGTTTGACTACACTCAGCTCCAA
* * * * * * **
500304 GGGGATATCATTTACAGCATAACTCAGGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTT
322 -GGCACATCATTTACAGCATAACTCAAGGCGAGAAAGGCTATCTG---CCAAAGACCCCCGAGTT
* * *
500369 TGACTACGCTCAGC-TCCAAGGCATAT
383 CGACTACACTCAGCTTCCAAGGCACAT
*
500395 CATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGATTAC
* *
500460 GCTCAGCTCCAAGGCATATCATTTACAGCATA
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATA
500492 ACTCAGGGCT
Statistics
Matches: 422, Mismatches: 78, Indels: 18
0.81 0.15 0.03
Matches are distributed among these distances:
409 28 0.07
410 33 0.08
411 2 0.00
412 239 0.57
413 49 0.12
414 71 0.17
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (409 bp):
CATTTGCAGCATAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGATTAC
GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAAAAC
CCCGAGTTCAATTACACTCAGCTTAGAGGGAACATCATTTACAACAACTCAAGGCTAGAAGGATT
ATCTATCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATAATTTACAACATA
ACTTAAGTAGAGAAGGGCTATCTGACCAAAGACCCCCGAGTTTGACTACACTCAGCTCCAAGGCA
CATCATTTACAGCATAACTCAAGGCGAGAAAGGCTATCTGCCAAAGACCCCCGAGTTCGACTACA
CTCAGCTTCCAAGGCACAT
Found at i:500602 original size:84 final size:83
Alignment explanation
Indices: 499571--500602 Score: 827
Period size: 84 Copynumber: 12.5 Consensus size: 83
499561 TTAAAGATAA
* * * *
499571 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTAC
*
499636 ACTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * * * * *
499655 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-CAAAAAACC-CCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * * *
499717 CTTAGCTTCGAGGGAACAT
66 CTCAGC-TCCAAGGCACAT
* * * *
499736 CATTTACA--ACAACTCAAGGCTAGAAGGGTTATCTATCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTAC
*
499799 GCTCAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * * *** * *
499818 AATTTACAACATAACTTAAGTAGAGAAGGGTTATCTGCTAACCAAAGACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTG-TCACCAAAGACCTTCGAGTTCGACTAC
*
499883 GTTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
** * * * * * ** * * *
499902 CATTTGCAGCATAGTTTAAGTCGAGAAAGGCTATCTG---CTAAAGACCCCCGAGTTCGATTTCA
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* *
499964 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCCAAGGCACAT
* * * * * * **
499983 CATTTACAACATAACTCAAGGCTAGAAGAGTTGTCTGTTACCAAAAGACCTTCGAGTTCGACTTT
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTAC
500048 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * * ** * * *
500067 CATTTGTAACATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCAATTACA
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
*
500129 CTCAGCT-TAGAGGGCACAT
66 CTCAGCTCCA-A-GGCACAT
* * * * * * **
500148 CATTTACAACATAACTCAAGGCTAGAAGGATTGTCTGTCACTAAAAGACCTTCGAGTTCGACTTT
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGTCAC-CAAAGACCTTCGAGTTCGACTAC
* *
500213 GCTCAGCTGCAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * * * * ** * * * *
500232 CATTTGCAG-ATAGCTTAAGTCAAGAAGGGCTATCTG---CCAAAGGCCCCCGAGTTTGATTGCA
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * *
500293 CTCAGCTTCAAGGGGATAT
66 CTCAGCTCCAA-GGCACAT
* * * *
500312 CATTTACAGCATAACTCAGGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTTGACTACG
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
*
500377 CTCAGCTCCAAGGCATAT
66 CTCAGCTCCAAGGCACAT
* * * * * *
500395 CATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTAC
*
500460 GCTCAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * * * * *
500479 CATTTACAGCATAACTCAGGGCTAGAAGGGTTATTTGTCACCAGAAGACCTTTGAGTTCGACTAT
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGTCACCA-AAGACCTTCGAGTTCGACTAC
*
500544 GCTCAGCTCCAAAGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * *
500563 CATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCA
1 CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGTCA
500603 ATAAAATTGT
Statistics
Matches: 743, Mismatches: 178, Indels: 54
0.76 0.18 0.06
Matches are distributed among these distances:
79 46 0.06
80 80 0.11
81 118 0.16
82 21 0.03
83 79 0.11
84 346 0.47
85 52 0.07
86 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (83 bp):
CATTTGCAGCATAACTTAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACAT
Found at i:501186 original size:75 final size:74
Alignment explanation
Indices: 501070--501490 Score: 258
Period size: 75 Copynumber: 5.9 Consensus size: 74
501060 TATATAAATG
* ** * *
501070 TATATAGTTATATAGTTTGTGAAAATGTTTTGACAA-A-ATATAATATATAATTTTTAGAAAACG
1 TATATA-TTATATAGTTT-TTAAAACATTTTGAAAATATATATAATATAT-AGTTTT-GAAAAC-
*
501133 ATTTTCG-AAA-GTT
61 ATTTT-GAAAACATT
* * * *
501146 TGTATATTATATGGTTCTTTAAAATATTTTTAAAATATATATAATATATAGTTTTGAAAACATTT
1 TATATATTATATAGTT-TTTAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACATTT
501211 TGAAAACATT
65 TGAAAACATT
* *
501221 TATATATTATATAGTTTTTAAAACATTTTG--AA-A-A-CT--TATATAGTTTTTAAAACATTTT
1 TATATATTATATAGTTTTTAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACA-TTT
501279 TGAAAAC---
65 TGAAAACATT
* * *
501286 T-TATA-TA-GT--TTTTTAAAACATTTTTGAAAA-ATTATATAATATATAATTTTAAAAACATT
1 TATATATTATATAGTTTTTAAAACA-TTTTGAAAATA-TATATAATATATAGTTTTGAAAACA--
501345 TTTTTGAAAA-A-T
62 -TTTTGAAAACATT
** * * *
501357 TATATAACACATAGTTTTAAAAACATTTTTGGAAAA-ATTATATAATATATAGTTTTAAAAACAT
1 TATATATTATATAGTTTTTAAAACA-TTTT-GAAAATA-TATATAATATATAGTTTTGAAAACA-
501421 TTTTTGAAAAC---
62 -TTTTGAAAACATT
* *
501432 T-TATA-TA-ATA--TTTTAAAACATTTTGAAAA-CTATATAATATATAGTTTTGAAAACTTTTT
1 TATATATTATATAGTTTTTAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACATTTT
501491 TAAATATAAT
Statistics
Matches: 293, Mismatches: 27, Indels: 61
0.77 0.07 0.16
Matches are distributed among these distances:
60 11 0.04
61 5 0.02
62 1 0.00
63 5 0.02
64 4 0.01
65 6 0.02
66 1 0.00
67 40 0.14
68 31 0.11
69 5 0.02
70 20 0.07
71 2 0.01
72 9 0.03
73 3 0.01
74 25 0.09
75 45 0.15
76 38 0.13
77 42 0.14
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (74 bp):
TATATATTATATAGTTTTTAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACATTTT
GAAAACATT
Found at i:501211 original size:11 final size:11
Alignment explanation
Indices: 501197--501221 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
501187 TAATATATAG
501197 TTTTGAAAACA
1 TTTTGAAAACA
501208 TTTTGAAAACA
1 TTTTGAAAACA
501219 TTT
1 TTT
501222 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:501225 original size:38 final size:37
Alignment explanation
Indices: 501107--501491 Score: 298
Period size: 38 Copynumber: 10.8 Consensus size: 37
501097 TTTTGACAAA
* * **
501107 ATATAATATATAATTTTTAGAAAACGATTTTCGAAAGTTT
1 ATATAATATAT-AGTTTTA-AAAAC-ATTTTTGAAAACTT
* * * * *
501147 GTATATTATATGGTTCTTTAAAATATTTTT-AAAA-TAT
1 ATATAATATATAGTT-TTAAAAACATTTTTGAAAACT-T
*
501184 ATATAATATATAGTTTTGAAAACA-TTTTGAAAACATTT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAAC--TT
* *
501222 ATATATTATATAGTTTTTAAAACA-TTTTGAAAAC--
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAACTT
*
501256 ---T--TATATAGTTTTTAAAACATTTTTGAAAACTT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAACTT
* *
501288 ATAT-A-GT-T--TTTT-AAAACATTTTTGAAAAATT
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAACTT
* *
501319 ATATAATATATAATTTTAAAAACATTTTTTTGAAAAATT
1 ATATAATATATAGTTTTAAAAACA--TTTTTGAAAACTT
* * *
501358 ATATAACACATAGTTTTAAAAACATTTTTGGAAAAATT
1 ATATAATATATAGTTTTAAAAACATTTTT-GAAAACTT
501396 ATATAATATATAGTTTTAAAAACATTTTTTGAAAAC-T
1 ATATAATATATAGTTTTAAAAACA-TTTTTGAAAACTT
501433 -TAT-ATA-ATA-TTTT-AAAACA-TTTTGAAAAC-T
1 ATATAATATATAGTTTTAAAAACATTTTTGAAAACTT
* *
501463 ATATAATATATAGTTTTGAAAACTTTTTT
1 ATATAATATATAGTTTTAAAAACATTTTT
501492 AAATATAATA
Statistics
Matches: 291, Mismatches: 25, Indels: 62
0.77 0.07 0.16
Matches are distributed among these distances:
29 18 0.06
30 21 0.07
31 26 0.09
32 14 0.05
33 8 0.03
34 9 0.03
35 14 0.05
36 23 0.08
37 28 0.10
38 73 0.25
39 46 0.16
40 11 0.04
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATAATATATAGTTTTAAAAACATTTTTGAAAACTT
Found at i:501282 original size:30 final size:30
Alignment explanation
Indices: 501227--501323 Score: 169
Period size: 31 Copynumber: 3.2 Consensus size: 30
501217 CATTTATATA
501227 TTATATAGTTTTTAAAACA-TTTTGAAAAC
1 TTATATAGTTTTTAAAACATTTTTGAAAAC
501256 TTATATAGTTTTTAAAACATTTTTGAAAAC
1 TTATATAGTTTTTAAAACATTTTTGAAAAC
*
501286 TTATATAGTTTTTTAAAACATTTTTGAAAAA
1 TTATATAG-TTTTTAAAACATTTTTGAAAAC
501317 TTATATA
1 TTATATA
501324 ATATATAATT
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 19 0.29
30 18 0.28
31 28 0.43
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.47
Consensus pattern (30 bp):
TTATATAGTTTTTAAAACATTTTTGAAAAC
Found at i:501393 original size:77 final size:71
Alignment explanation
Indices: 501257--501491 Score: 288
Period size: 67 Copynumber: 3.3 Consensus size: 71
501247 TTTGAAAACT
* * * *
501257 TATATAGTTTTTAAAACA--TTTTTGAAAACTTATATAGT-TTTTTAAAACATTTTTGAAAAATT
1 TATATAGTTTTAAAAACATTTTTTTGAAAAATTATATAATAGTTTTAAAACATTTTTGAAAAATT
501319 ATATAA
66 ATATAA
*
501325 TATATAATTTTAAAAACATTTTTTTGAAAAATTATATAACACATAGTTTTAAAAACATTTTTGGA
1 TATATAGTTTTAAAAACATTTTTTTGAAAAATTATAT---A-ATAGTTTT-AAAACATTTTT-GA
501390 AAAATTATATAA
60 AAAATTATATAA
* *
501402 TATATAGTTTTAAAAACA-TTTTTTGAAAACTTATATAATA-TTTTAAAACA-TTTTG-AAAACT
1 TATATAGTTTTAAAAACATTTTTTTGAAAAATTATATAATAGTTTTAAAACATTTTTGAAAAATT
501463 ATATAA
66 ATATAA
*
501469 TATATAGTTTTGAAAAC-TTTTTT
1 TATATAGTTTTAAAAACATTTTTT
501492 AAATATAATA
Statistics
Matches: 148, Mismatches: 9, Indels: 21
0.83 0.05 0.12
Matches are distributed among these distances:
67 32 0.22
68 17 0.11
69 4 0.03
70 22 0.15
71 4 0.03
72 3 0.02
73 2 0.01
74 1 0.01
75 4 0.03
76 28 0.19
77 31 0.21
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (71 bp):
TATATAGTTTTAAAAACATTTTTTTGAAAAATTATATAATAGTTTTAAAACATTTTTGAAAAATT
ATATAA
Found at i:501500 original size:31 final size:31
Alignment explanation
Indices: 501396--501508 Score: 106
Period size: 34 Copynumber: 3.5 Consensus size: 31
501386 TGGAAAAATT
501396 ATATAATATATAGTTTTAAAAACATTTTTTGAA
1 ATATAATATATAGTTTT-AAAACATTTTTT-AA
* **
501429 A-ACTTATATAATA-TTTTAAAACATTTTGAAAA
1 ATA-TAATAT-ATAGTTTTAAAACATTTT-TTAA
501461 CTATATAATATATAGTTTTGAAAAC-TTTTTTAA
1 --ATATAATATATAGTTTT-AAAACATTTTTTAA
501494 ATATAATATATAGTT
1 ATATAATATATAGTT
501509 AAAAAAATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
31 15 0.23
32 13 0.20
33 15 0.23
34 17 0.26
35 6 0.09
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.45
Consensus pattern (31 bp):
ATATAATATATAGTTTTAAAACATTTTTTAA
Found at i:501522 original size:31 final size:31
Alignment explanation
Indices: 501396--501522 Score: 80
Period size: 34 Copynumber: 3.9 Consensus size: 31
501386 TGGAAAAATT
*
501396 ATATAATATATAGTTTTAAAAACATTTTTTGAA
1 ATATAATATATAG-TTTAAAAAAATTTTTT-AA
* * * **
501429 A-ACTTATATAATA-TTTTAAAACATTTTGAAAA
1 ATA-TAATAT-ATAGTTTAAAAAAATTTT-TTAA
** *
501461 CTATATAATATATAGTTTTGAAAACTTTTTTAA
1 --ATATAATATATAGTTTAAAAAAATTTTTTAA
501494 ATATAATATATAG-TTAAAAAAATATTTTT
1 ATATAATATATAGTTTAAAAAAAT-TTTTT
501523 GAAGAAAATA
Statistics
Matches: 73, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
30 7 0.10
31 18 0.25
32 16 0.22
33 11 0.15
34 20 0.27
35 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (31 bp):
ATATAATATATAGTTTAAAAAAATTTTTTAA
Found at i:501523 original size:67 final size:68
Alignment explanation
Indices: 501257--501525 Score: 226
Period size: 67 Copynumber: 3.9 Consensus size: 68
501247 TTTGAAAACT
* * * * ** *
501257 TATATAGTTTTTAAAACA-TTTTTGAAAACTTATATAGTTTTTTAAAACATTTTTGAAAAATTAT
1 TATATAGTTTTAAAAACATTTTTTGAAAACTAATATAATATTAAAAAACATTTTTG-AAAACTAT
501321 ATAA
65 ATAA
* * * *
501325 TATATAATTTTAAAAACATTTTTTTGAAAAATTATATAACACATAGTTTTAAAAACATTTTTGGA
1 TATATAGTTTTAAAAACA-TTTTTTG-AAAACTA-AT-ATA-ATA--TTAAAAAACATTTTT-G-
*
501390 AAAATTATATAA
57 AAAACTATATAA
* **
501402 TATATAGTTTTAAAAACATTTTTTGAAAACTTATATAATATTTTAAAACA-TTTTGAAAACTATA
1 TATATAGTTTTAAAAACATTTTTTGAAAACTAATATAATATTAAAAAACATTTTTGAAAACTATA
501466 TAA
66 TAA
* *
501469 TATATAGTTTTGAAAAC-TTTTTT-AAATA-TAATAT-ATAGTTAAAAAAATATTTTTGAA
1 TATATAGTTTTAAAAACATTTTTTGAAA-ACTAATATAATA-TT-AAAAAACATTTTTGAA
501526 GAAAATATAT
Statistics
Matches: 169, Mismatches: 19, Indels: 27
0.79 0.09 0.13
Matches are distributed among these distances:
64 3 0.02
65 10 0.06
66 12 0.07
67 34 0.20
68 17 0.10
69 4 0.02
70 15 0.09
71 5 0.03
72 5 0.03
73 4 0.02
74 3 0.02
75 5 0.03
76 21 0.12
77 31 0.18
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (68 bp):
TATATAGTTTTAAAAACATTTTTTGAAAACTAATATAATATTAAAAAACATTTTTGAAAACTATA
TAA
Found at i:501584 original size:13 final size:14
Alignment explanation
Indices: 501561--501590 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
501551 ATTATTATTA
501561 TTTATTCATTTTCT
1 TTTATTCATTTTCT
501575 TTTATT-ATTTTCT
1 TTTATTCATTTTCT
501588 TTT
1 TTT
501591 TATGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTCATTTTCT
Found at i:503110 original size:14 final size:14
Alignment explanation
Indices: 503091--503132 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
503081 GTTTTATGAT
503091 TTTTATTTATTTAA
1 TTTTATTTATTTAA
503105 TTTTATTTTATTT-A
1 TTTTA-TTTATTTAA
*
503119 TTATTATTTTTTTA
1 TT-TTATTTATTTA
503133 TCTCACATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTTATTTAA
Found at i:504482 original size:32 final size:32
Alignment explanation
Indices: 504446--504506 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
504436 ACTGTTGTGG
**
504446 CACATGTCATGTCATTATTTTTGGTGATGCAA
1 CACATGTCACATCATTATTTTTGGTGATGCAA
*
504478 CACATGTTACATCATTATTTTTGGTGATG
1 CACATGTCACATCATTATTTTTGGTGATG
504507 TGGAACATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.43
Consensus pattern (32 bp):
CACATGTCACATCATTATTTTTGGTGATGCAA
Found at i:505184 original size:28 final size:27
Alignment explanation
Indices: 505138--505192 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
505128 CTATTAAAAG
505138 AAAATTAAATTAAAAATTTATATATTTTT
1 AAAATTAAATTAAAAATTT-TAT-TTTTT
* *
505167 AAAA-TAAATTTAATATTTTATTTTTT
1 AAAATTAAATTAAAAATTTTATTTTTT
505193 CACATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 3 0.12
28 12 0.50
29 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
AAAATTAAATTAAAAATTTTATTTTTT
Found at i:505413 original size:20 final size:23
Alignment explanation
Indices: 505386--505443 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 23
505376 TTTTAATAAA
505386 ATATAAAATCATTAATTAA-ATT
1 ATATAAAATCATTAATTAAGATT
**
505408 A-A-AAAAGAATTAATTAAGATT
1 ATATAAAATCATTAATTAAGATT
*
505429 ATATATAATCATTAA
1 ATATAAAATCATTAA
505444 ATTATAAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 13 0.46
21 5 0.18
22 2 0.07
23 8 0.29
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (23 bp):
ATATAAAATCATTAATTAAGATT
Found at i:507995 original size:6 final size:6
Alignment explanation
Indices: 507984--508017 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
507974 AGTATTTTTA
* *
507984 AATACT AATACT AATACT ACTACT AATAAT AATA
1 AATACT AATACT AATACT AATACT AATACT AATA
508018 ATTTAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (6 bp):
AATACT
Found at i:508429 original size:132 final size:132
Alignment explanation
Indices: 508176--508631 Score: 532
Period size: 132 Copynumber: 3.4 Consensus size: 132
508166 ACTATCACTC
* **
508176 AGGGAATATCATATCTGGA-GATGTTGATCCATTTTGCTGTCACTCAGGGAAGATTGAATCGAGG
1 AGGGAATATCAGATCTGGAGGA-GTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGAGG
508240 TAGACTTGTTCCGCTGTTACTCAGGGAATATCAAATCTT-GAAAGAGATAGATC-TGTTCCGCTT
65 TAGACTTGTTCCGCTGTTACTCAGGGAATATCAAATCTTGGAAA-AGA-AGA-CATGTT-CGCTT
* *
508303 CTTTTAA
126 CTTATGA
* * ** * * * *
508310 AGGGAATATCATATATGG-GG-GTTGATCCATTATGTTGTTACTCAGGGAAGATTGAATCAAGGC
1 AGGGAATATCAGATCTGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGAGGT
* * *
508373 AGACTTGTTCCGCTGTTATTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCACTT-TCT
66 AGACTTGTTCCGCTGTTACTCAGGGAATATCAAATCTTGGAAAAGA-AGACATGTTCGCTTCT-T
*
508437 CTGA
129 ATGA
* * * * * * *
508441 AGGGAATATTAGATCCGGAGGAGTTGATCTATTCCGCTGTCACTTAGAGAAGATTTAATCGGGGT
1 AGGGAATATCAGATCTGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGAGGT
* *
508506 AGACTTGTTCTGCTGTTACTCAGGGAATATCAAATATTGGAAAA-ATA-ACATGTTTCGCTTCTT
66 AGACTTGTTCCGCTGTTACTCAGGGAATATCAAATCTTGGAAAAGA-AGACATG-TTCGCTTCTT
508569 ATGA
129 ATGA
*
508573 AGGGAATATCAGATCTGGAGGAGTTGATCCATTCCGTTGTCACTCAGGGAAGATTGAAT
1 AGGGAATATCAGATCTGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAAT
508632 TGAGTTTGAT
Statistics
Matches: 273, Mismatches: 41, Indels: 18
0.82 0.12 0.05
Matches are distributed among these distances:
130 1 0.00
131 27 0.10
132 149 0.55
133 78 0.29
134 18 0.07
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.32
Consensus pattern (132 bp):
AGGGAATATCAGATCTGGAGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGAGGT
AGACTTGTTCCGCTGTTACTCAGGGAATATCAAATCTTGGAAAAGAAGACATGTTCGCTTCTTAT
GA
Found at i:511052 original size:209 final size:209
Alignment explanation
Indices: 510692--511109 Score: 748
Period size: 209 Copynumber: 2.0 Consensus size: 209
510682 AAGCTTTGGG
* * *
510692 TGAAATTTACCCAATAACATCCATGCCTTATGAGGAGGGATGTGGAGTTTGTCTCATAAATCTGG
1 TGAAATTCACCCAATAACATCCATGCCTCATGAGGAGGGATGTGGAGTTTGTCTCATAAATCTGA
*
510757 CATTTGTGATATTTTATGGCGTAATTGATACAATCGGTTTCCAGGGTCAACCAATAATACCCAAA
66 CATTTGTGATATTTTATGGCGTAATTAATACAATCGGTTTCCAGGGTCAACCAATAATACCCAAA
* *
510822 TCTCATTATTTGTTTATCCATTGTATGTCCATTAGCATGGGTATCGCGTACTCCTTCATACACTT
131 TCTCATTATTTGTTTATCCATTGTATATCCATTAGCATGGGTATCACGTACTCCTTCATACACTT
*
510887 CTTTAATGATAGTT
196 CTTCAATGATAGTT
*
510901 TGAAATTCACCCAATAACATCCATGCCTCATGAGGAGGTATGTGGAGTTTGTCTCAATAAAT-TG
1 TGAAATTCACCCAATAACATCCATGCCTCATGAGGAGGGATGTGGAGTTTGTCTC-ATAAATCTG
510965 ACATTTGTGATATTTTATGGCGTAATTAATACAATCGGTTTCCAGGGTCAACCAATAATACCCAA
65 ACATTTGTGATATTTTATGGCGTAATTAATACAATCGGTTTCCAGGGTCAACCAATAATACCCAA
511030 ATCTCATTATTTGTTTATCCATTGTATATCCATTAGCATGGGTATCACGTACTCCTTCATACACT
130 ATCTCATTATTTGTTTATCCATTGTATATCCATTAGCATGGGTATCACGTACTCCTTCATACACT
511095 TCTTCAATGATAGTT
195 TCTTCAATGATAGTT
511110 CTAGCTTCTT
Statistics
Matches: 200, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
209 194 0.97
210 6 0.03
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (209 bp):
TGAAATTCACCCAATAACATCCATGCCTCATGAGGAGGGATGTGGAGTTTGTCTCATAAATCTGA
CATTTGTGATATTTTATGGCGTAATTAATACAATCGGTTTCCAGGGTCAACCAATAATACCCAAA
TCTCATTATTTGTTTATCCATTGTATATCCATTAGCATGGGTATCACGTACTCCTTCATACACTT
CTTCAATGATAGTT
Found at i:520642 original size:18 final size:18
Alignment explanation
Indices: 520604--520643 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
520594 TATTTTTGTC
**
520604 ATTTTAATAAAAATATTA
1 ATTTTAATAAAAATAAAA
*
520622 ATTTTAATTAAAATAAAA
1 ATTTTAATAAAAATAAAA
520640 ATTT
1 ATTT
520644 GAGGTATGCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTTTAATAAAAATAAAA
Found at i:522600 original size:8 final size:8
Alignment explanation
Indices: 522589--522613 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
522579 TGGGTTGTAA
522589 ATAATAAT
1 ATAATAAT
522597 ATAATAAT
1 ATAATAAT
522605 ATAATAAT
1 ATAATAAT
522613 A
1 A
522614 AAATGTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATAATAAT
Found at i:524406 original size:26 final size:28
Alignment explanation
Indices: 524345--524408 Score: 69
Period size: 31 Copynumber: 2.2 Consensus size: 28
524335 CGAGTATTGC
* *
524345 TGAGCTCGACTCGACTCGAAAACTCTGAAA
1 TGAGCTTGACTCGACTAGAAAACTCTG--A
524375 TGGAGCTTGACTCGACTAGAAAACTC-G-
1 T-GAGCTTGACTCGACTAGAAAACTCTGA
524402 TGAGCTT
1 TGAGCTT
524409 AAAATCTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 6 0.19
27 1 0.03
30 2 0.06
31 22 0.71
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (28 bp):
TGAGCTTGACTCGACTAGAAAACTCTGA
Found at i:524929 original size:31 final size:30
Alignment explanation
Indices: 524877--524934 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
524867 GAGTAAATTA
*
524877 TTTATTTAGTCACCAAGTTATTTTTTAGTT
1 TTTATTTAGTCACCAAGTTATTATTTAGTT
*
524907 TTTATTTTGGTCACTCAA-TTATTATTTA
1 TTTA-TTTAGTCAC-CAAGTTATTATTTA
524935 TTTAAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 4 0.17
31 17 0.71
32 3 0.12
ACGTcount: A:0.24, C:0.10, G:0.09, T:0.57
Consensus pattern (30 bp):
TTTATTTAGTCACCAAGTTATTATTTAGTT
Found at i:535770 original size:19 final size:19
Alignment explanation
Indices: 535710--535772 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
535700 ATGCATTGGG
535710 CTATGAATTTGAAAGTAAGA
1 CTATGAATTTGAAAGTAA-A
* *
535730 -TATGAATTTGAAAATAAG
1 CTATGAATTTGAAAGTAAA
* *
535748 CTATAAATTTGACAGTAAA
1 CTATGAATTTGAAAGTAAA
535767 CTATGA
1 CTATGA
535773 GTCTAAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (19 bp):
CTATGAATTTGAAAGTAAA
Found at i:535782 original size:38 final size:38
Alignment explanation
Indices: 535709--535785 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
535699 TATGCATTGG
* * *
535709 GCTATGAATTTGAAAGTAAGATATGAATTTGAAAATAA
1 GCTATAAATTTGAAAGTAAGATATGAATCTAAAAATAA
* *
535747 GCTATAAATTTGACAGTAA-ACTATGAGTCTAAAAATAA
1 GCTATAAATTTGAAAGTAAGA-TATGAATCTAAAAATAA
535785 G
1 G
535786 TTATGAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.30
Consensus pattern (38 bp):
GCTATAAATTTGAAAGTAAGATATGAATCTAAAAATAA
Found at i:535820 original size:19 final size:19
Alignment explanation
Indices: 535711--535830 Score: 71
Period size: 19 Copynumber: 6.3 Consensus size: 19
535701 TGCATTGGGC
* * *
535711 TATGAATTTGAAAGTAAGA
1 TATGAATATGAAAATAAGT
* *
535730 TATGAATTTGAAAATAAGC
1 TATGAATATGAAAATAAGT
* * * * **
535749 TATAAATTTGACAGTAAAC
1 TATGAATATGAAAATAAGT
* * *
535768 TATGAGTCTAAAAATAAGT
1 TATGAATATGAAAATAAGT
*
535787 TATGAATATGGAAATAAGT
1 TATGAATATGAAAATAAGT
* *
535806 TATGATTCA-GAAAATAAAT
1 TATGAAT-ATGAAAATAAGT
535825 TATGAA
1 TATGAA
535831 ATGTGAAAGT
Statistics
Matches: 78, Mismatches: 22, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
19 77 0.99
20 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (19 bp):
TATGAATATGAAAATAAGT
Found at i:535874 original size:12 final size:12
Alignment explanation
Indices: 535847--535890 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
535837 AAGTGTTTAT
*
535847 TATGAACATGGAA
1 TATGAAAAT-GAA
535860 TATGAAAATGAA
1 TATGAAAATGAA
**
535872 TATGTGAATGAA
1 TATGAAAATGAA
535884 TATGAAA
1 TATGAAA
535891 GTGGAAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.27
Consensus pattern (12 bp):
TATGAAAATGAA
Found at i:541693 original size:20 final size:20
Alignment explanation
Indices: 541668--541719 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
541658 AAATGAACGA
541668 GGGTATCGATACTCACCTTT
1 GGGTATCGATACTCACCTTT
*
541688 GGGTATCGATACTTACCTTT
1 GGGTATCGATACTCACCTTT
541708 GGGTATCGATAC
1 GGGTATCGATAC
541720 CTTAAAGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (20 bp):
GGGTATCGATACTCACCTTT
Found at i:541961 original size:20 final size:20
Alignment explanation
Indices: 541932--542003 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
541922 GAGTTGCCCC
*
541932 AGTATAGATACCAC-CCTACG
1 AGTATCGATACCACTCCTA-G
*
541952 AGTATCGATACCTCTCCTAG
1 AGTATCGATACCACTCCTAG
* * * *
541972 AATATCGATACCCATTGCTTG
1 AGTATCGATA-CCACTCCTAG
541993 AGTATCGATAC
1 AGTATCGATAC
542004 TTCTAGCTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 23 0.55
21 19 0.45
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (20 bp):
AGTATCGATACCACTCCTAG
Found at i:556232 original size:18 final size:18
Alignment explanation
Indices: 556219--556292 Score: 121
Period size: 18 Copynumber: 4.1 Consensus size: 18
556209 TGAATGAATC
556219 AGATTAATTAAATGAACT
1 AGATTAATTAAATGAACT
556237 AGATTAATTAAATGAACT
1 AGATTAATTAAATGAACT
*
556255 AGTTTAATTAAATGAACT
1 AGATTAATTAAATGAACT
**
556273 ATTTTAATTAAATGAACT
1 AGATTAATTAAATGAACT
556291 AG
1 AG
556293 TATACTTAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.36
Consensus pattern (18 bp):
AGATTAATTAAATGAACT
Found at i:556258 original size:54 final size:54
Alignment explanation
Indices: 556190--556292 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
556180 ACCATGCAAC
* *
556190 TTAAATGAATTAGTTTCAA-TGAATGAA-TCAGATTAATTAAATGAACTAGATTAA
1 TTAAATGAACTAGTTT-AATTAAATGAACT-AGATTAATTAAATGAACTAGATTAA
**
556244 TTAAATGAACTAGTTTAATTAAATGAACTATTTTAATTAAATGAACTAG
1 TTAAATGAACTAGTTTAATTAAATGAACTAGATTAATTAAATGAACTAG
556293 TATACTTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
53 2 0.05
54 40 0.93
55 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (54 bp):
TTAAATGAACTAGTTTAATTAAATGAACTAGATTAATTAAATGAACTAGATTAA
Found at i:556293 original size:36 final size:36
Alignment explanation
Indices: 556222--556306 Score: 127
Period size: 36 Copynumber: 2.4 Consensus size: 36
556212 ATGAATCAGA
556222 TTAATTAAATGAACTAGATTAATTAAATGAACTAGT
1 TTAATTAAATGAACTAGATTAATTAAATGAACTAGT
**
556258 TTAATTAAATGAACTATTTTAATTAAATGAACTAGT
1 TTAATTAAATGAACTAGATTAATTAAATGAACTAGT
* *
556294 ATACTT-AATGAAC
1 TTAATTAAATGAAC
556307 CAACATACTT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 7 0.16
36 38 0.84
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (36 bp):
TTAATTAAATGAACTAGATTAATTAAATGAACTAGT
Found at i:556301 original size:18 final size:18
Alignment explanation
Indices: 556223--556306 Score: 109
Period size: 18 Copynumber: 4.7 Consensus size: 18
556213 TGAATCAGAT
556223 TAATTAAATGAACTAG-A
1 TAATTAAATGAACTAGTA
*
556240 TTAATTAAATGAACTAGTT
1 -TAATTAAATGAACTAGTA
* *
556259 TAATTAAATGAACTATTT
1 TAATTAAATGAACTAGTA
556277 TAATTAAATGAACTAGTA
1 TAATTAAATGAACTAGTA
*
556295 TACTT-AATGAAC
1 TAATTAAATGAAC
556307 CAACATACTT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
17 7 0.12
18 53 0.88
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (18 bp):
TAATTAAATGAACTAGTA
Found at i:556360 original size:18 final size:18
Alignment explanation
Indices: 556280--556381 Score: 89
Period size: 18 Copynumber: 5.7 Consensus size: 18
556270 ACTATTTTAA
** *
556280 TTAAATGAACTAGTATAC
1 TTAAATGAACTAACATGC
* *
556298 TT-AATGAACCAACATAC
1 TTAAATGAACTAACATGC
* *
556315 TTAAATAAACTATCATGC
1 TTAAATGAACTAACATGC
556333 TTAAATGAACTAACATGC
1 TTAAATGAACTAACATGC
* *
556351 TTAAACGAACTGAATATGC
1 TTAAATGAACT-AACATGC
* *
556370 TTTAATTAACTA
1 TTAAATGAACTA
556382 GCGTGCTAAT
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
17 14 0.21
18 40 0.59
19 14 0.21
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (18 bp):
TTAAATGAACTAACATGC
Found at i:563697 original size:18 final size:18
Alignment explanation
Indices: 563666--563703 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
563656 AAAATGAACT
*
563666 AAATGTAAACAACATGCAA
1 AAATGTAAAAAACATG-AA
563685 AAAT-TAAAAAACATGAA
1 AAATGTAAAAAACATGAA
563702 AA
1 AA
563704 TAGGACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 10 0.56
19 4 0.22
ACGTcount: A:0.66, C:0.11, G:0.08, T:0.16
Consensus pattern (18 bp):
AAATGTAAAAAACATGAA
Found at i:563847 original size:10 final size:10
Alignment explanation
Indices: 563832--563858 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
563822 GGAGGACTAG
563832 ATTAAAATAA
1 ATTAAAATAA
563842 ATTAAAATAA
1 ATTAAAATAA
563852 ATTAAAA
1 ATTAAAA
563859 CTCTATGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
ATTAAAATAA
Found at i:565687 original size:3 final size:3
Alignment explanation
Indices: 565679--565716 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
565669 ACAGTTATAT
565679 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
565717 TTTGGGATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:566188 original size:137 final size:137
Alignment explanation
Indices: 565891--566427 Score: 774
Period size: 137 Copynumber: 3.9 Consensus size: 137
565881 ATGGGGATGT
* *** *
565891 TGATTCATTCCACTGTTTTTCAGGGAAGATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGG
1 TGATTCATTCCGCTGTCACTCAGGGAAGATTGAATCAGGGTAGACTTGTTCCACTGTCACTCAGG
*
565956 GAATATCAAATCTTGAAGGAGAGGGATTTGTT-CGCTTCTTCTGAAGGGATTATCAGATCTGGAA
66 GAATATCAAATCTTGAAGGAGAGGGATTTGTTCCGCTTCTTCTGAAGGGATTATCAGATCTGGGA
566020 GGAGAGG
131 GGAGAGG
* * *
566027 TGATTTATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGTAGACTTGTTCCACTGTAACTCAGG
1 TGATTCATTCCGCTGTCACTCAGGGAAGATTGAATCAGGGTAGACTTGTTCCACTGTCACTCAGG
* * * *
566092 GAATATCAAATCTT-AGAGGATAGGGATTCGTTCCGCTTCCTCTGAAGGGATTATTAGATCTGGG
66 GAATATCAAATCTTGA-AGGAGAGGGATTTGTTCCGCTTCTTCTGAAGGGATTATCAGATCTGGG
566156 AGGAGAGG
130 AGGAGAGG
*
566164 TGATTCATTCCGCTGTCACTCAGGGAAGATTGAATCAGGGCAGACTTGTTCCACTGTCACTCAGG
1 TGATTCATTCCGCTGTCACTCAGGGAAGATTGAATCAGGGTAGACTTGTTCCACTGTCACTCAGG
* * *
566229 GAATATCAAATCGTGAAGGAGAGGGATTTGTTTCGCTTCTTCTGAAGGGATTATCAGATCTGAGA
66 GAATATCAAATCTTGAAGGAGAGGGATTTGTTCCGCTTCTTCTGAAGGGATTATCAGATCTGGGA
*
566294 GGAAAGG
131 GGAGAGG
* * * * **
566301 TGATTTATTCCGCTGTCATTCAGGGAAGGTTGAATCAAGGTAGACTTGTTCTGCTGTCACTCAGG
1 TGATTCATTCCGCTGTCACTCAGGGAAGATTGAATCAGGGTAGACTTGTTCCACTGTCACTCAGG
* * * * *
566366 GAATATCAAATCCTGGAA-TAGAGGGATATGTTCCGCTTCTTCTAAAGGGAATATCAGATCTG
66 GAATATCAAAT-CTTGAAGGAGAGGGATTTGTTCCGCTTCTTCTGAAGGGATTATCAGATCTG
566428 AGTGAGTTGA
Statistics
Matches: 358, Mismatches: 39, Indels: 7
0.89 0.10 0.02
Matches are distributed among these distances:
135 1 0.00
136 85 0.24
137 267 0.75
138 5 0.01
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (137 bp):
TGATTCATTCCGCTGTCACTCAGGGAAGATTGAATCAGGGTAGACTTGTTCCACTGTCACTCAGG
GAATATCAAATCTTGAAGGAGAGGGATTTGTTCCGCTTCTTCTGAAGGGATTATCAGATCTGGGA
GGAGAGG
Found at i:566475 original size:112 final size:112
Alignment explanation
Indices: 566330--566765 Score: 520
Period size: 112 Copynumber: 3.9 Consensus size: 112
566320 TCAGGGAAGG
* * *
566330 TTGAATCAAGGTAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCCTGGAATAGAGGGATAT
1 TTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCCTGGAAGAGAGGGATAT
* *
566395 GTTCCGCTTCTTCTAAAGGGAATATCAGATCTGAGTGAGTTGATCTA
66 GTTCCGCTTCTTCTAAAGGGAATATCAGATCTGAGAGAGTTGATCCA
* * * *
566442 TTGAATCAGGGTAGATTTGTTCCGTTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGGGATTT
1 TTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCCTGGAAGAGAGGGATAT
* * * *
566507 GTTCCTCTTCTTCTAAAGGGAATATCAGATCTGGAAAAAGATGTGACCCA
66 GTTCCGCTTCTTCTAAAGGGAATATCAGATCT-GAGAGAG-T-TGATCCA
* * * *
566557 TTGAATTAGGGCAGATTTGTTCCGCTGTCACTCAGGGAATATCAAA-CCTTGGAAAAGAGGGATA
1 TTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCC-TGGAAGAGAGGGATA
* * * * * *
566621 TGTTCCACTTTTTCTGAAGGGAATATCAGATATG-GGGGGTTGATCCA
65 TGTTCCGCTTCTTCTAAAGGGAATATCAGATCTGAGAGAGTTGATCCA
* * * * *
566668 TTAAATCGGGGCT-GACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGGGATC
1 TTGAATCAGGG-TAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCCTGGAAGAGAGGGATA
* *
566732 TATTCCGCTTCTT-TGAAAGGGAATATAAGATCTG
65 TGTTCCGCTTCTTCT-AAAGGGAATATCAGATCTG
566766 GGGGAGTGAT
Statistics
Matches: 274, Mismatches: 43, Indels: 15
0.83 0.13 0.05
Matches are distributed among these distances:
110 1 0.00
111 84 0.31
112 91 0.33
113 5 0.02
114 3 0.01
115 90 0.33
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (112 bp):
TTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCCTGGAAGAGAGGGATAT
GTTCCGCTTCTTCTAAAGGGAATATCAGATCTGAGAGAGTTGATCCA
Found at i:566608 original size:115 final size:111
Alignment explanation
Indices: 566330--566766 Score: 518
Period size: 115 Copynumber: 3.9 Consensus size: 111
566320 TCAGGGAAGG
* * * * *
566330 TTGAATCAAGGTAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCC-TGGAATAGAGGGATA
1 TTGAATCAGGGCAGATTTGTTCCGCTGTCACTCAGGGAATATCAAA-CCTTGGAAGAGAGGGATA
* *
566394 TGTTCCGCTTCTTCTAAAGGGAATATCAGATCTGAGTGAGTTGATCTA
65 TGTTCCGCTTCTTCTAAAGGGAATATCAGATCTG-GAGAGTTGATCCA
* * * *
566442 TTGAATCAGGGTAGATTTGTTCCGTTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGGGATTT
1 TTGAATCAGGGCAGATTTGTTCCGCTGTCACTCAGGGAATATCAAACCTTGGAAGAGAGGGATAT
* * *
566507 GTTCCTCTTCTTCTAAAGGGAATATCAGATCTGGAAAAAGATGTGACCCA
66 GTTCCGCTTCTTCTAAAGGGAATATCAGATCTGG--AGAG-T-TGATCCA
* *
566557 TTGAATTAGGGCAGATTTGTTCCGCTGTCACTCAGGGAATATCAAACCTTGGAAAAGAGGGATAT
1 TTGAATCAGGGCAGATTTGTTCCGCTGTCACTCAGGGAATATCAAACCTTGGAAGAGAGGGATAT
* * * * * *
566622 GTTCCACTTTTTCTGAAGGGAATATCAGATATGGGGGGTTGATCCA
66 GTTCCGCTTCTTCTAAAGGGAATATCAGATCTGGAGAGTTGATCCA
* * * * * * *
566668 TTAAATCGGGGCTGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGGGATCT
1 TTGAATCAGGGCAGATTTGTTCCGCTGTCACTCAGGGAATATCAAACCTTGGAAGAGAGGGATAT
* *
566733 ATTCCGCTTCTT-TGAAAGGGAATATAAGATCTGG
66 GTTCCGCTTCTTCT-AAAGGGAATATCAGATCTGG
566767 GGGAGTGATT
Statistics
Matches: 278, Mismatches: 41, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
110 1 0.00
111 90 0.32
112 89 0.32
113 3 0.01
114 1 0.00
115 94 0.34
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (111 bp):
TTGAATCAGGGCAGATTTGTTCCGCTGTCACTCAGGGAATATCAAACCTTGGAAGAGAGGGATAT
GTTCCGCTTCTTCTAAAGGGAATATCAGATCTGGAGAGTTGATCCA
Found at i:566754 original size:226 final size:227
Alignment explanation
Indices: 566346--566766 Score: 625
Period size: 226 Copynumber: 1.9 Consensus size: 227
566336 CAAGGTAGAC
* * *
566346 TTGTTCTGCTGTCACTCAGGGAATATCAAATCCTGGAATAGAGGGATATGTTCCGCTTCTTCTAA
1 TTGTTCCGCTGTCACTCAGGGAATATCAAATCCTGGAAAAGAGGGATATGTTCCACTTCTTCTAA
* * * * * *
566411 AGGGAATATCAGATCTGAGTGAGTTGATCTATTGAATCAGGGTAGATTTGTTCCGTTGTCACTCA
66 AGGGAATATCAGATATGAGGGAGTTGATCCATTAAATCAGGGTAGACTTGTTCCGCTGTCACTCA
* * * *
566476 GGGAATATCAAATCTTGGAAGAGAGGGATTTGTTCCTCTTCTTCTAAAGGGAATATCAGATCTGG
131 GGGAATATCAAATCTTGGAAGAGAGGGATCTATTCCGCTTCTTCTAAAGGGAATATAAGATCTGG
566541 AAAAAGATGTGACCCATTGAATTAGGGCAGAT
196 AAAAAGATGTGACCCATTGAATTAGGGCAGAT
* *
566573 TTGTTCCGCTGTCACTCAGGGAATATCAAA-CCTTGGAAAAGAGGGATATGTTCCACTTTTTCTG
1 TTGTTCCGCTGTCACTCAGGGAATATCAAATCC-TGGAAAAGAGGGATATGTTCCACTTCTTCTA
* * *
566637 AAGGGAATATCAGATATG-GGGGGTTGATCCATTAAATCGGGGCT-GACTTGTTCTGCTGTCACT
65 AAGGGAATATCAGATATGAGGGAGTTGATCCATTAAATCAGGG-TAGACTTGTTCCGCTGTCACT
566700 CAGGGAATATCAAATCTTGGAAGAGAGGGATCTATTCCGCTTCTT-TGAAAGGGAATATAAGATC
129 CAGGGAATATCAAATCTTGGAAGAGAGGGATCTATTCCGCTTCTTCT-AAAGGGAATATAAGATC
566764 TGG
193 TGG
566767 GGGAGTGATT
Statistics
Matches: 173, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
225 1 0.01
226 98 0.57
227 74 0.43
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (227 bp):
TTGTTCCGCTGTCACTCAGGGAATATCAAATCCTGGAAAAGAGGGATATGTTCCACTTCTTCTAA
AGGGAATATCAGATATGAGGGAGTTGATCCATTAAATCAGGGTAGACTTGTTCCGCTGTCACTCA
GGGAATATCAAATCTTGGAAGAGAGGGATCTATTCCGCTTCTTCTAAAGGGAATATAAGATCTGG
AAAAAGATGTGACCCATTGAATTAGGGCAGAT
Found at i:566834 original size:37 final size:37
Alignment explanation
Indices: 566772--566887 Score: 178
Period size: 37 Copynumber: 3.1 Consensus size: 37
566762 TCTGGGGGAG
* *
566772 TGATTTGCTTGACTATTCTTCGGTGAAGGCTTAAGAT
1 TGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
*
566809 TGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGAT
1 TGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
* * *
566846 GGATTTGCTTCACTACTCTTCGGTGACGGCTTAATAT
1 TGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
566883 TGATT
1 TGATT
566888 ACTTCGAAGG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (37 bp):
TGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
Found at i:570989 original size:7 final size:7
Alignment explanation
Indices: 570975--571052 Score: 97
Period size: 7 Copynumber: 11.1 Consensus size: 7
570965 TTATTATTTA
570975 TTCTTTT
1 TTCTTTT
570982 TTCCTTTT
1 TT-CTTTT
*
570990 TTTTTTT
1 TTCTTTT
*
570997 TTTTTTT
1 TTCTTTT
571004 TTCTTTT
1 TTCTTTT
571011 TTCTTTT
1 TTCTTTT
571018 TT-TTTT
1 TTCTTTT
571024 TTC-TTT
1 TTCTTTT
571030 TTCTTTT
1 TTCTTTT
*
571037 TTTTTCTT
1 TTCTT-TT
571045 TTCTTTT
1 TTCTTTT
571052 T
1 T
571053 GCTTCCTTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
6 12 0.19
7 38 0.60
8 13 0.21
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTCTTTT
Found at i:570994 original size:11 final size:10
Alignment explanation
Indices: 570978--571052 Score: 93
Period size: 10 Copynumber: 7.7 Consensus size: 10
570968 TTATTTATTC
*
570978 TTTTTTCCTT
1 TTTTTTTCTT
570988 TTTTTTT-TT
1 TTTTTTTCTT
570997 TTTTTTT-TT
1 TTTTTTTCTT
*
571006 CTTTTTTCTT
1 TTTTTTTCTT
571016 TTTTTTT-TT
1 TTTTTTTCTT
*
571025 TCTTTTTCTT
1 TTTTTTTCTT
571035 TTTTTTTCTT
1 TTTTTTTCTT
571045 TTCTTTTT
1 TT-TTTTT
571053 GCTTCCTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
9 25 0.44
10 27 0.47
11 5 0.09
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:571004 original size:21 final size:20
Alignment explanation
Indices: 570987--571052 Score: 105
Period size: 20 Copynumber: 3.2 Consensus size: 20
570977 CTTTTTTCCT
570987 TTTTTTTTTTTTTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTC
*
571007 TTTTTTCTTTTTTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTC
*
571027 TTTTTCTTTTTTTTTCTTTTC
1 TTTTT-TTTTTTTTTTTTTTC
571048 TTTTT
1 TTTTT
571053 GCTTCCTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 24 0.57
21 18 0.43
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (20 bp):
TTTTTTTTTTTTTTTTTTTC
Found at i:571007 original size:29 final size:30
Alignment explanation
Indices: 570975--571075 Score: 118
Period size: 29 Copynumber: 3.3 Consensus size: 30
570965 TTATTATTTA
570975 TTCTTTTTTCCTTTTTTTTTTTT-TTTTT-T
1 TTCTTTTTT-CTTTTTTTTTTTTCTTTTTCT
571004 TTCTTTTTTCTTTTTTTTTTTTCTTTTTCT
1 TTCTTTTTTCTTTTTTTTTTTTCTTTTTCT
* *
571034 TT-TTTTTTCTTTTCTTTTTGCTTCCTTTTTCA
1 TTCTTTTTTCTTTT-TTTTT--TTTCTTTTTCT
*
571066 TTCCTTTTTC
1 TTCTTTTTTC
571076 GAGTGTAGTA
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
28 13 0.21
29 25 0.40
30 8 0.13
32 11 0.17
33 6 0.10
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.82
Consensus pattern (30 bp):
TTCTTTTTTCTTTTTTTTTTTTCTTTTTCT
Found at i:571062 original size:22 final size:19
Alignment explanation
Indices: 570975--571075 Score: 91
Period size: 21 Copynumber: 5.2 Consensus size: 19
570965 TTATTATTTA
*
570975 TTCTTTTTTCCTTTT-TTT
1 TTCTTTTTTTCTTTTCTTT
570993 TT-TTTTTTT-TTTTCTTTT
1 TTCTTTTTTTCTTTTC-TTT
*
571011 TTCTTTTTTTTTTTTCTTT
1 TTCTTTTTTTCTTTTCTTT
571030 TTCTTTTTTTTTCTTTTCTTT
1 TTC--TTTTTTTCTTTTCTTT
* *
571051 TTGCTTCCTTTTTCATTCCTTT
1 TT-CTT--TTTTTCTTTTCTTT
571073 TTC
1 TTC
571076 GAGTGTAGTA
Statistics
Matches: 70, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
16 4 0.06
17 6 0.09
18 7 0.10
19 13 0.19
20 7 0.10
21 18 0.26
22 15 0.21
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.82
Consensus pattern (19 bp):
TTCTTTTTTTCTTTTCTTT
Found at i:571063 original size:1 final size:1
Alignment explanation
Indices: 570986--571052 Score: 80
Period size: 1 Copynumber: 67.0 Consensus size: 1
570976 TCTTTTTTCC
* * * * * *
570986 TTTTTTTTTTTTTTTTTTTTCTTTTTTCTTTTTTTTTTTTCTTTTTCTTTTTTTTTCTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
571051 TT
1 TT
571053 GCTTCCTTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:571063 original size:41 final size:41
Alignment explanation
Indices: 570978--571075 Score: 124
Period size: 41 Copynumber: 2.3 Consensus size: 41
570968 TTATTTATTC
* * * **
570978 TTTTTTCCTTTTTTTTTTTTTTTTTTTTCTTTTTTCTTTTT
1 TTTTTTCCTTTTTCTTTTTTTTTCTTTTCTTTTTGCTTCCT
*
571019 TTTTTTTCTTTTTCTTTTTTTTTCTTTTCTTTTTGCTTCCT
1 TTTTTTCCTTTTTCTTTTTTTTTCTTTTCTTTTTGCTTCCT
571060 TTTTCATTCCTTTTTC
1 TTTT--TTCCTTTTTC
571076 GAGTGTAGTA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 39 0.81
43 9 0.19
ACGTcount: A:0.01, C:0.15, G:0.01, T:0.83
Consensus pattern (41 bp):
TTTTTTCCTTTTTCTTTTTTTTTCTTTTCTTTTTGCTTCCT
Found at i:574913 original size:42 final size:41
Alignment explanation
Indices: 574861--574962 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 41
574851 TCCAAAATTT
* * *
574861 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT-
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGATG
* ** *
574901 ACTTAAATCCTTCAGATCATCTGTAAGCCTTTCGAGCAAGATG
1 A--TAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGATG
*
574944 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
574963 CATAAGACCT
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
40 1 0.02
41 14 0.29
42 32 0.67
43 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGCAAGATG
Found at i:574974 original size:42 final size:40
Alignment explanation
Indices: 574860--574974 Score: 106
Period size: 42 Copynumber: 2.8 Consensus size: 40
574850 TTCCAAAATT
* *
574860 TATAAGTCCTTCGGGCCAT-CAGTAAGTCTTTCGAGCATGA
1 TATAAGTCCTTCGGGCCATCCA-TAAGCCTTTCGAGCAAGA
* * ** **
574900 TACTTAAATCCTTCAGATCATCTGTAAGCCTTTCGAGCAAGA
1 TA--TAAGTCCTTCGGGCCATCCATAAGCCTTTCGAGCAAGA
574942 TGATAAGTCCTTCGGGCCATCCATAAGACCTTT
1 T-ATAAGTCCTTCGGGCCATCCATAAG-CCTTT
574975 GGGCAGGATG
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
40 2 0.04
41 18 0.32
42 35 0.62
43 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (40 bp):
TATAAGTCCTTCGGGCCATCCATAAGCCTTTCGAGCAAGA
Found at i:575120 original size:20 final size:20
Alignment explanation
Indices: 575095--575164 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
575085 CCAAAAGTTA
575095 TAAGTCCTTCGGGTCATCAG
1 TAAGTCCTTCGGGTCATCAG
* * *
575115 TAAGTCTTTCGAG-CATGATG
1 TAAGTCCTTCGGGTCATCA-G
* *
575135 AATAAATCCTTCGGGTCATCTG
1 --TAAGTCCTTCGGGTCATCAG
575157 TAAG-CCTT
1 TAAGTCCTT
575165 TCAAGCAAGA
Statistics
Matches: 37, Mismatches: 9, Indels: 9
0.67 0.16 0.16
Matches are distributed among these distances:
19 8 0.22
20 15 0.41
22 11 0.30
23 3 0.08
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
TAAGTCCTTCGGGTCATCAG
Found at i:575146 original size:42 final size:42
Alignment explanation
Indices: 575094--575177 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
575084 TCCAAAAGTT
* * * *
575094 ATAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGA
1 ATAAATCCTTCGGGTCATCAGTAAGCCTTTCAAGCAAGATGA
*
575136 ATAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGATGA
1 ATAAATCCTTCGGGTCATCAGTAAGCCTTTCAAGCAAGATGA
575178 CAAGTCCATC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (42 bp):
ATAAATCCTTCGGGTCATCAGTAAGCCTTTCAAGCAAGATGA
Found at i:575192 original size:233 final size:233
Alignment explanation
Indices: 574773--575219 Score: 725
Period size: 233 Copynumber: 1.9 Consensus size: 233
574763 TAATCAAAAA
* *
574773 ATGAGAAAGGTTTCTCATTTAAAACTTAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
1 ATGAGAAAGATTTCTCATTTAAAACTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
*
574838 CTAGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATAC
66 CTAGTAAAATATTTCCAAAAGTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATAC
* * * *
574903 TTAAATCCTTCAGATCATCTGTAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAA
131 ATAAATCCTTCAGATCATCTGTAAGCCTTTCAAGCAAGATGACAAGTCCATCGGGCCATCCATAA
*
574968 GACCTTTGGGCAGGATGTTTTCACATGTCTATCGAAAT
196 GACATTTGGGCAGGATGTTTTCACATGTCTATCGAAAT
* * *
575006 ATGAGAAATATTTCTCATTTAAATCTGAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
1 ATGAGAAAGATTTCTCATTTAAAACTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
* *
575071 CTAGTAAACTATTTCCAAAAGTTATAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGA
66 CTAGTAAAATATTTCCAAAAGTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT-A
* * *
575136 -ATAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGATGACAAGTCCATCGGGCCATTCATA
130 CATAAATCCTTCAGATCATCTGTAAGCCTTTCAAGCAAGATGACAAGTCCATCGGGCCATCCATA
*
575200 AGACATTTGGGCATGATGTT
195 AGACATTTGGGCAGGATGTT
575220 CTCATAGGTC
Statistics
Matches: 196, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
233 195 0.99
234 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (233 bp):
ATGAGAAAGATTTCTCATTTAAAACTGAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
CTAGTAAAATATTTCCAAAAGTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATAC
ATAAATCCTTCAGATCATCTGTAAGCCTTTCAAGCAAGATGACAAGTCCATCGGGCCATCCATAA
GACATTTGGGCAGGATGTTTTCACATGTCTATCGAAAT
Found at i:575815 original size:136 final size:136
Alignment explanation
Indices: 575239--576151 Score: 1116
Period size: 136 Copynumber: 6.8 Consensus size: 136
575229 CCCTCTCTTC
*
575239 CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATCTTCCCTGAAGAA
1 CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATCTTCCCTGAAGAA
* * * * * * *
575304 CAATGGAATGGATCAAC-ATCC-ACAGATCTGATATTCCCTTCAGAAGAACCAGAACAGATCCCT
66 CAGTGGAATGAATCAACTATCCTCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACATATCCAT
575367 CTCCTT
131 CTCCTT
* * * * *
575373 CAAGATTTGATATTCCCTCAATGACAACGGAATAAGTCTACCTTGATTCAATCTTCCCTGAGGAA
1 CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATCTTCCCTGAAGAA
* * * * * * *
575438 CAGCGGAATGAATCACCTCTCTTCTAGATCTGATATTCCCTTCAGAAGAAGCAGAACATATCCCT
66 CAGTGGAATGAATCAACTATCCTCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACATATCCAT
575503 CT-CTT
131 CTCCTT
*** * * * * *
575508 CAAGATTTGATATTCCCT-ATGTGACAATAGAACAAGTCTACCCTAATTCAATATTCACTGAAAA
1 CAAGATTTGATATTCCCTGA-GTGACAGCGGAACAAGTCTACCTTGATTCAATCTTCCCTGAAGA
* * * * * *
575572 ATAGTGGAATGAATCAAC-ATCC-CCATATTTGATATTCCCTT-AGAATAAGCGAAACAGAT-CA
65 ACAGTGGAATGAATCAACTATCCTCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACATATCCA
575633 CTCTCCTT
130 -TCTCCTT
* * * * * *
575641 CAAGATTTGATATTCCCTAAATGACATCGAAACAAGTCTACCTTAATTCAATCTTCCCTGAGGAA
1 CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATCTTCCCTGAAGAA
** * *
575706 CAACGGAATGAATCAACTCTCCTCCAGATCTGATATTCCCTTCAGAAGAAGTGGAACATATCCAT
66 CAGTGGAATGAATCAACTATCCTCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACATATCCAT
*
575771 CTCTTT
131 CTCCTT
*
575777 CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCATGATTCAATCTTCCCTGAAGAA
1 CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATCTTCCCTGAAGAA
* * * * *
575842 CAGTGGAATGGATCAA-TATCC-CCAGATCCGATATTCACTTCAGAAGAAGCGGAACAAATCCCT
66 CAGTGGAATGAATCAACTATCCTCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACATATCCAT
575905 CTCCTT
131 CTCCTT
*
575911 CAAGATTTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATCTTCCCTGAGGA
1 CAAGA-TTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATCTTCCCTGAAGA
** * * * * * *
575976 ACAGCAGAATGAATCACCTCTCCTCCATATATGATATTCCCTTTAGAAGAAGCGAAACATATCCA
65 ACAGTGGAATGAATCAACTATCCTCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACATATCCA
576041 TCT-CTT
130 TCTCCTT
* *
576047 CCAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGCCTACCTTGATTCAATCTTCCCTGAAGA
1 -CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATCTTCCCTGAAGA
*
576112 ACAGTAGAATTG-ATCAAC-ATCCT-CAGATCTGATATTCCCT
65 ACAGTGGAA-TGAATCAACTATCCTCCAGATCTGATATTCCCT
576152 GAGTGACAAC
Statistics
Matches: 664, Mismatches: 100, Indels: 30
0.84 0.13 0.04
Matches are distributed among these distances:
131 1 0.00
132 17 0.03
133 86 0.13
134 141 0.21
135 167 0.25
136 207 0.31
137 45 0.07
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (136 bp):
CAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATCTTCCCTGAAGAA
CAGTGGAATGAATCAACTATCCTCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACATATCCAT
CTCCTT
Found at i:575988 original size:404 final size:403
Alignment explanation
Indices: 575230--576151 Score: 1212
Period size: 404 Copynumber: 2.3 Consensus size: 403
575220 CTCATAGGTC
* *
575230 CCTCTCTTCCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATCTTC
1 CCTCTCTTCCAAGATTTGATATTCCCTGAGTGACAGCGAAACAAGTCTACCTTGATTCAATCTTC
*
575295 CCTGAAGAACAATGGAATGGATCAACATCCACAGATCTGATATTCCCTTCAGAAGAACCAGAACA
66 CCTGAAGAACAATGGAAT-GATCAACATCCTCAGATCTGATATTCCCTTCAGAAGAACCAGAACA
* * *
575360 GATCCCTCTCCTTCAAGATTTGATATTCCCTCAATGACAACGGAATAAGTCTACCTTGATTCAAT
130 GATCCATCTCCTTCAAGATTTGATATTCCCTCAATGACAACGGAACAAGTCTACCATGATTCAAT
* * * * * * *
575425 CTTCCCTGAGGAACAGCGGAATGAATCACCTCTCTTCTAGATCTGATATTCCCTTCAGAAGAAGC
195 CTTCCCTGAAGAACAGCGGAATGAATCACATATCTCCCAGATCCGATATTCACTTCAGAAGAAGC
* *
575490 AGAACATATCCCTCTCTTCAAGATTTGATATTCCCTATGTGACAATAGAACAAGTCTACCCTAAT
260 AGAACAAATCCCTCTCTTCAAGATTTGATATTCCCTATGTGACAACAGAACAAGTCTACCCTAAT
* ** *
575555 TCAATATTCACTGAAAAATAGTGGAATGAATCAAC-ATCC-CCATATTTGATATTCCC-TTAGAA
325 TCAATATTCACTGAAAAACAGCAGAATGAATCAACTATCCTCCATATATGATATTCCCTTTAGAA
*
575617 TAAGCGAAACAGAT
390 GAAGCGAAACAGAT
* * * *
575631 CACTCTCCTT-CAAGATTTGATATTCCCTAAATGACATCGAAACAAGTCTACCTTAATTCAATCT
1 C-CTCT-CTTCCAAGATTTGATATTCCCTGAGTGACAGCGAAACAAGTCTACCTTGATTCAATCT
* * * ***
575695 TCCCTGAGGAACAACGGAATGAATCAACTCTCCTCCAGATCTGATATTCCCTTCAGAAGAAGTGG
64 TCCCTGAAGAACAATGGAATG-ATCAAC-ATCCT-CAGATCTGATATTCCCTTCAGAAGAACCAG
* * * * *
575760 AACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCATGATT
126 AACAGATCCATCTCCTTCAAGATTTGATATTCCCTCAATGACAACGGAACAAGTCTACCATGATT
* *
575825 CAATCTTCCCTGAAGAACAGTGGAATGGATCA-ATATC-CCCAGATCCGATATTCACTTCAGAAG
191 CAATCTTCCCTGAAGAACAGCGGAATGAATCACATATCTCCCAGATCCGATATTCACTTCAGAAG
* * *
575888 AAGCGGAACAAATCCCTCTCCTTCAAGATTTTGATATTCCCTGA-GTGACAGCGGAACAAGTCTA
256 AAGCAGAACAAATCCCTCT-CTTCAAGA-TTTGATATTCCCT-ATGTGACAACAGAACAAGTCTA
* * * * ** * *
575952 CCTTGATTCAATCTTCCCTGAGGAACAGCAGAATGAATCACCTCTCCTCCATATATGATATTCCC
318 CCCTAATTCAATATTCACTGAAAAACAGCAGAATGAATCAACTATCCTCCATATATGATATTCCC
*
576017 TTTAGAAGAAGCGAAACATAT
383 TTTAGAAGAAGCGAAACAGAT
*
576038 CCATCTCTTCCAAGATTTGATATTCCCTGAGTGACAGC-AGAACAAGCCTACCTTGATTCAATCT
1 CC-TCTCTTCCAAGATTTGATATTCCCTGAGTGACAGCGA-AACAAGTCTACCTTGATTCAATCT
* *
576102 TCCCTGAAGAACAGTAGAATTGATCAACATCCTCAGATCTGATATTCCCT
64 TCCCTGAAGAACAATGGAA-TGATCAACATCCTCAGATCTGATATTCCCT
576152 GAGTGACAAC
Statistics
Matches: 447, Mismatches: 59, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
401 2 0.00
402 115 0.26
403 17 0.04
404 175 0.39
405 21 0.05
406 25 0.06
407 90 0.20
408 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (403 bp):
CCTCTCTTCCAAGATTTGATATTCCCTGAGTGACAGCGAAACAAGTCTACCTTGATTCAATCTTC
CCTGAAGAACAATGGAATGATCAACATCCTCAGATCTGATATTCCCTTCAGAAGAACCAGAACAG
ATCCATCTCCTTCAAGATTTGATATTCCCTCAATGACAACGGAACAAGTCTACCATGATTCAATC
TTCCCTGAAGAACAGCGGAATGAATCACATATCTCCCAGATCCGATATTCACTTCAGAAGAAGCA
GAACAAATCCCTCTCTTCAAGATTTGATATTCCCTATGTGACAACAGAACAAGTCTACCCTAATT
CAATATTCACTGAAAAACAGCAGAATGAATCAACTATCCTCCATATATGATATTCCCTTTAGAAG
AAGCGAAACAGAT
Found at i:575999 original size:271 final size:270
Alignment explanation
Indices: 575232--576151 Score: 1351
Period size: 271 Copynumber: 3.4 Consensus size: 270
575222 CATAGGTCCC
*
575232 TCTCTTCCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCCTGATTCAATCTTCCC
1 TCTCTTCCAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCTGATTCAATCTTCCC
* * * *
575297 TGAAGAACAATGGAATGGATCAACATCCACAGATCTGATATTCCCTTCAGAAGAACCAGAACAGA
66 TGAAGAACAGTGGAATGGATCAACATCCCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACAGA
* *
575362 TCCCTCTCCTTCAAGATTTGATATTCCCTCAATGACAACGGAATAAGTCTACCTTGATTCAATCT
131 TCCCTCTCCTTCAAGATTTGATATTCCCTAAATGACAACGGAACAAGTCTACCTTGATTCAATCT
* * *
575427 TCCCTGAGGAACAGCGGAATGAATCACCTCTCTTCTAGATCTGATATTCCCTTCAGAAGAAGCAG
196 TCCCTGAGGAACAGCGGAATGAATCACCTCTCCTCCAGATCTGATATTCCCTTCAGAAGAAGCGG
*
575492 AACATATCCC
261 AACATATCCA
** * * *
575502 TCTCTT-CAAGATTTGATATTCCCT-ATGTGACAATAGAACAAGTCTACCCTAATTCAATATTCA
1 TCTCTTCCAAGATTTGATATTCCCTGA-GTGACAGCAGAACAAGTCTACCCTGATTCAATCTTCC
* * * * * * *
575565 CTGAAAAATAGTGGAATGAATCAACATCCCCATATTTGATATTCCCTT-AGAATAAGCGAAACAG
65 CTGAAGAACAGTGGAATGGATCAACATCCCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACAG
* * * *
575629 ATCACTCTCCTTCAAGATTTGATATTCCCTAAATGACATCGAAACAAGTCTACCTTAATTCAATC
130 ATCCCTCTCCTTCAAGATTTGATATTCCCTAAATGACAACGGAACAAGTCTACCTTGATTCAATC
* * *
575694 TTCCCTGAGGAACAACGGAATGAATCAACTCTCCTCCAGATCTGATATTCCCTTCAGAAGAAGTG
195 TTCCCTGAGGAACAGCGGAATGAATCACCTCTCCTCCAGATCTGATATTCCCTTCAGAAGAAGCG
575759 GAACATATCCA
260 GAACATATCCA
* * *
575770 TCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCATGATTCAATCTTCCC
1 TCTCTTCCAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCTGATTCAATCTTCCC
* * * *
575835 TGAAGAACAGTGGAATGGATCAATATCCCCAGATCCGATATTCACTTCAGAAGAAGCGGAACAAA
66 TGAAGAACAGTGGAATGGATCAACATCCCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACAGA
* * *
575900 TCCCTCTCCTTCAAGATTTTGATATTCCCTGAGTGACAGCGGAACAAGTCTACCTTGATTCAATC
131 TCCCTCTCCTTCAAGA-TTTGATATTCCCTAAATGACAACGGAACAAGTCTACCTTGATTCAATC
* * * *
575965 TTCCCTGAGGAACAGCAGAATGAATCACCTCTCCTCCATATATGATATTCCCTTTAGAAGAAGCG
195 TTCCCTGAGGAACAGCGGAATGAATCACCTCTCCTCCAGATCTGATATTCCCTTCAGAAGAAGCG
*
576030 AAACATATCCA
260 GAACATATCCA
* *
576041 TCTCTTCCAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGCCTACCTTGATTCAATCTTCCC
1 TCTCTTCCAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCTGATTCAATCTTCCC
* * *
576106 TGAAGAACAGTAGAATTGATCAACATCCTCAGATCTGATATTCCCT
66 TGAAGAACAGTGGAATGGATCAACATCCCCAGATCTGATATTCCCT
576152 GAGTGACAAC
Statistics
Matches: 573, Mismatches: 72, Indels: 9
0.88 0.11 0.01
Matches are distributed among these distances:
268 147 0.26
269 178 0.31
270 36 0.06
271 212 0.37
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (270 bp):
TCTCTTCCAAGATTTGATATTCCCTGAGTGACAGCAGAACAAGTCTACCCTGATTCAATCTTCCC
TGAAGAACAGTGGAATGGATCAACATCCCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACAGA
TCCCTCTCCTTCAAGATTTGATATTCCCTAAATGACAACGGAACAAGTCTACCTTGATTCAATCT
TCCCTGAGGAACAGCGGAATGAATCACCTCTCCTCCAGATCTGATATTCCCTTCAGAAGAAGCGG
AACATATCCA
Found at i:583968 original size:3 final size:3
Alignment explanation
Indices: 583960--583992 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
583950 TTTCAATATT
*
583960 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
583993 TGAATATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:587689 original size:18 final size:18
Alignment explanation
Indices: 587666--587703 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
587656 ATTAAATTTT
587666 TTCTAACTTCTAATATGA
1 TTCTAACTTCTAATATGA
587684 TTCTAACTTCTAATATGA
1 TTCTAACTTCTAATATGA
587702 TT
1 TT
587704 TAGGCAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (18 bp):
TTCTAACTTCTAATATGA
Found at i:596943 original size:25 final size:25
Alignment explanation
Indices: 596909--596958 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
596899 TCTTAAGACA
596909 CGTTTAAGGTTATTATGTTCAAGTT
1 CGTTTAAGGTTATTATGTTCAAGTT
596934 CGTTTAAGGTTATTATGTTCAAGTT
1 CGTTTAAGGTTATTATGTTCAAGTT
596959 TCGATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (25 bp):
CGTTTAAGGTTATTATGTTCAAGTT
Found at i:597644 original size:10 final size:10
Alignment explanation
Indices: 597631--597657 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
597621 TTATTTATTA
597631 TAAAATAACT
1 TAAAATAACT
597641 TAAAATAACT
1 TAAAATAACT
597651 TAAAATA
1 TAAAATA
597658 TAAAATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAAATAACT
Found at i:599233 original size:24 final size:24
Alignment explanation
Indices: 599199--599270 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
599189 AAATGGAGAT
*
599199 ATCAGAAATCAAAATAAAATTCAG
1 ATCAGAAATCAAAACAAAATTCAG
* * * *
599223 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAAAATTCAG
*
599247 ATCAGAAATCAGAACAAAATTCAG
1 ATCAGAAATCAAAACAAAATTCAG
599271 GTAATGTATC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAAAATTCAG
Found at i:599281 original size:48 final size:47
Alignment explanation
Indices: 599199--599307 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 47
599189 AAATGGAGAT
* * * *
599199 ATCAGAAATCAAAATAAAATTCAGATCAGATATCATAACAGAATCCA
1 ATCAGAAATCAGAACAAAATTCAGATAAGATATCAAAACAGAATCCA
* * *
599246 GATCAGAAATCAGAACAAAATTCAGGTAATG-TATCAAAATAGAATTCA
1 -ATCAGAAATCAGAACAAAATTCAGATAA-GATATCAAAACAGAATCCA
*
599294 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
599308 TAAAATATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
47 1 0.02
48 49 0.96
49 1 0.02
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.21
Consensus pattern (47 bp):
ATCAGAAATCAGAACAAAATTCAGATAAGATATCAAAACAGAATCCA
Found at i:605567 original size:24 final size:24
Alignment explanation
Indices: 605538--605604 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
605528 GAGATTTCAG
* *
605538 AAATCAAAACAGAATTCATATCAT
1 AAATCAAAACAGAATTCAGATCAA
* * * *
605562 ATATCATAACATAATCCAGATCAA
1 AAATCAAAACAGAATTCAGATCAA
*
605586 AAATCAGAACAGAATTCAG
1 AAATCAAAACAGAATTCAG
605605 GTAATGTATC
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.52, C:0.18, G:0.07, T:0.22
Consensus pattern (24 bp):
AAATCAAAACAGAATTCAGATCAA
Found at i:608808 original size:54 final size:54
Alignment explanation
Indices: 608620--608854 Score: 283
Period size: 54 Copynumber: 4.4 Consensus size: 54
608610 TATGCATCGA
* * *
608620 CACTAAATGTGCAACCCACGAAATTCATAATAAGTTTTATGAACGACCGTATCGG
1 CACTAAGTGTGCAACCCACGTAATTCATAATAAG-TTTATGAACGACCGTATTGG
* * *
608675 CACTAAGTGTGCAACCCACATAATTCATAATAAGTTTATGAACGATCGTATTAG
1 CACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACGACCGTATTGG
*
608729 CACTAAGAGTGCAACCCACGTAATTCATAATAAGTTTATGAACGACCGTATTGG
1 CACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACGACCGTATTGG
** * * * * * * * * *
608783 CTTTAGGTGTGTAACCTACGGAATTCATAATGAGCTTATGAATGACTGTATCGG
1 CACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACGACCGTATTGG
*
608837 CACTACGTGTGC-ACCCAC
1 CACTAAGTGTGCAACCCAC
608855 AAAACTCATA
Statistics
Matches: 153, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
53 5 0.03
54 117 0.76
55 31 0.20
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (54 bp):
CACTAAGTGTGCAACCCACGTAATTCATAATAAGTTTATGAACGACCGTATTGG
Found at i:613042 original size:17 final size:16
Alignment explanation
Indices: 613020--613053 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
613010 TAAAGACAGT
613020 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
613037 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
613053 A
1 A
613054 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:613572 original size:24 final size:24
Alignment explanation
Indices: 613528--613577 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
613518 ATAAAGAACC
*
613528 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
613552 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
613576 AA
1 AA
613578 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:616701 original size:22 final size:22
Alignment explanation
Indices: 616676--616718 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
616666 AACTGAAAGG
*
616676 AGTATCGGTACCATAGTAGGGA
1 AGTATCGGTACCATAGGAGGGA
616698 AGTATCGGTACCATAGGAGGG
1 AGTATCGGTACCATAGGAGGG
616719 GTACCGTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (22 bp):
AGTATCGGTACCATAGGAGGGA
Found at i:617121 original size:54 final size:54
Alignment explanation
Indices: 617035--617347 Score: 421
Period size: 54 Copynumber: 5.8 Consensus size: 54
617025 GCATTTTTAT
617035 GTATCGGCACTAAGTGTGCAACCCAC-GAAATTCATAATAAGTTTATGAACGACC
1 GTATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACC
* * *
617089 GTATCGGCACTAAGTGTGCAACCCATATAATTCATAATAAGTTTATGAACGATC
1 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACC
*
617143 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAATGACC
1 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACC
* * **
617197 GTATCGGCACTCAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACAAAT
1 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACC
* * * * * * * *
617251 GTATCAGCTCTAAGTGTGTAACCCACGGAATTCATAATGAGCTTATGAATGATC
1 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACC
* * * * *
617305 GTATCGGCACTATGTGTGCACCCCATAGAACTCATAATGAGTT
1 GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTT
617348 ATAATAGTTA
Statistics
Matches: 226, Mismatches: 32, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
54 226 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (54 bp):
GTATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACC
Found at i:618591 original size:2 final size:2
Alignment explanation
Indices: 618586--618627 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
618576 TATATTTTAG
*
618586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
618628 TCATTTCATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:622292 original size:20 final size:21
Alignment explanation
Indices: 622267--622322 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
622257 TAACGTACGT
622267 AGTATCGATACTGTTCTT-AC
1 AGTATCGATACTGTTCTTAAC
*
622287 AGTATCGATA-T-TATATTAAC
1 AGTATCGATACTGT-TCTTAAC
*
622307 AGTACCGATACTGTTC
1 AGTATCGATACTGTTC
622323 ATGTGGTACC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
18 1 0.03
19 4 0.14
20 21 0.72
21 2 0.07
22 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (21 bp):
AGTATCGATACTGTTCTTAAC
Found at i:623677 original size:17 final size:17
Alignment explanation
Indices: 623655--623702 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
623645 GTCAGCCACC
623655 CCCGTGACCAGCTCACG
1 CCCGTGACCAGCTCACG
623672 CCCGTGACCAGCTCACG
1 CCCGTGACCAGCTCACG
623689 CCCGTGACCAGCTC
1 CCCGTGACCAGCTC
623703 GCCCTATCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.17, C:0.48, G:0.23, T:0.12
Consensus pattern (17 bp):
CCCGTGACCAGCTCACG
Found at i:628407 original size:14 final size:14
Alignment explanation
Indices: 628375--628401 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
628365 AATGGGTTAT
628375 GGTTTATGATTTAA
1 GGTTTATGATTTAA
628389 GGTTTATGATTTA
1 GGTTTATGATTTA
628402 GAGTTTTAAG
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:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (14 bp):
GGTTTATGATTTAA
Found at i:642848 original size:15 final size:15
Alignment explanation
Indices: 642828--642942 Score: 167
Period size: 15 Copynumber: 7.7 Consensus size: 15
642818 ATGTTGTTAG
*
642828 TATGTGAATATGTTA
1 TATGTGAATATGTTC
*
642843 TATGTGAATATATTC
1 TATGTGAATATGTTC
* *
642858 TACGTGAAAATGTTC
1 TATGTGAATATGTTC
642873 TATGTGAATATGTTC
1 TATGTGAATATGTTC
* *
642888 TACGTGAAAATGTTC
1 TATGTGAATATGTTC
642903 TATGTGAATATGTTC
1 TATGTGAATATGTTC
*
642918 TATGTGAATGTGTTC
1 TATGTGAATATGTTC
642933 TATGTGAATA
1 TATGTGAATA
642943 AATGATACTT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 87 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (15 bp):
TATGTGAATATGTTC
Found at i:648504 original size:15 final size:15
Alignment explanation
Indices: 648484--648567 Score: 114
Period size: 15 Copynumber: 5.6 Consensus size: 15
648474 TTTTATTAGG
* *
648484 ATGTGAAAATGTTTT
1 ATGTGAATATGTTCT
648499 ATGTGAATATGTTCT
1 ATGTGAATATGTTCT
* *
648514 ACGTGAAAATGTTCT
1 ATGTGAATATGTTCT
*
648529 ATGTGAATATGTTTT
1 ATGTGAATATGTTCT
*
648544 ATGTGAATGTGTTCT
1 ATGTGAATATGTTCT
648559 ATGTGAATA
1 ATGTGAATA
648568 AATGATACTT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 59 1.00
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (15 bp):
ATGTGAATATGTTCT
Found at i:648709 original size:23 final size:23
Alignment explanation
Indices: 648683--648744 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
648673 TACGCAGTCC
*
648683 TTCGGGACAATTCTATGTGGTCA
1 TTCGGGACAATTCTATGCGGTCA
* * *
648706 TTCGGGACTATTCTACGCGGTCC
1 TTCGGGACAATTCTATGCGGTCA
* *
648729 TTTGGGACAAATCTAT
1 TTCGGGACAATTCTAT
648745 ATGGCACTTC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (23 bp):
TTCGGGACAATTCTATGCGGTCA
Found at i:648737 original size:46 final size:47
Alignment explanation
Indices: 648670--648769 Score: 125
Period size: 46 Copynumber: 2.1 Consensus size: 47
648660 GAGTCGAGGG
* *
648670 TTCTACGCAGTCCTTCGGGACAATTCTATGTGGTCA-TTCGG-G-ACTA
1 TTCTACGCAGTCCTTCGGGACAAATCTATATGG-CACTTCGGTGCA-TA
* *
648716 TTCTACGCGGTCCTTTGGGACAAATCTATATGGCACTTCGGTGCATA
1 TTCTACGCAGTCCTTCGGGACAAATCTATATGGCACTTCGGTGCATA
648763 TTCTACG
1 TTCTACG
648770 TGGCAATTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
45 2 0.04
46 34 0.72
47 10 0.21
48 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (47 bp):
TTCTACGCAGTCCTTCGGGACAAATCTATATGGCACTTCGGTGCATA
Found at i:648773 original size:24 final size:24
Alignment explanation
Indices: 648746--648798 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
648736 CAAATCTATA
* *
648746 TGGCACTTCGGTGCATATTCTACG
1 TGGCAATTCGGTGCAAATTCTACG
648770 TGGCAATTCGGTGCAAATTCTACG
1 TGGCAATTCGGTGCAAATTCTACG
648794 TGGCA
1 TGGCA
648799 GTTTCGACTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (24 bp):
TGGCAATTCGGTGCAAATTCTACG
Found at i:659606 original size:17 final size:18
Alignment explanation
Indices: 659579--659617 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
659569 TGTAGGACCA
659579 AAGTAGAAAGTGAAAGCC
1 AAGTAGAAAGTGAAAGCC
*
659597 AAGT-GAAAGTGAAATCC
1 AAGTAGAAAGTGAAAGCC
659614 AAGT
1 AAGT
659618 TGATTCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.49, C:0.10, G:0.26, T:0.15
Consensus pattern (18 bp):
AAGTAGAAAGTGAAAGCC
Found at i:673783 original size:44 final size:45
Alignment explanation
Indices: 673692--673789 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
673682 ATACTTTGGG
* *
673692 AATAAGTT-GGTAATGCTGGTAATAGCTCCAATATAGACATAGGA
1 AATAAGTTGGGTAATGCTGGTAATAGCTCCAACATAGACAGAGGA
* ** *
673736 AATAAGTTGGGTAATGCTGGTAATAGCTCCACCATAGTGAGA-TA
1 AATAAGTTGGGTAATGCTGGTAATAGCTCCAACATAGACAGAGGA
673780 AATAAGTTGG
1 AATAAGTTGG
673790 ATTTCCAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 19 0.40
45 28 0.60
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (45 bp):
AATAAGTTGGGTAATGCTGGTAATAGCTCCAACATAGACAGAGGA
Found at i:683333 original size:15 final size:15
Alignment explanation
Indices: 683313--683342 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
683303 TGAAAGTTAT
*
683313 GAAAAGAATCTGAAA
1 GAAAAGAATATGAAA
683328 GAAAAGAATATGAAA
1 GAAAAGAATATGAAA
683343 ATGAAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.03, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAAAGAATATGAAA
Found at i:685351 original size:25 final size:25
Alignment explanation
Indices: 685296--685357 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
685286 ATAAGTCTAG
*
685296 ATTCAATATTTTGATACATGATCACA
1 ATTC-ATATTATGATACATGATCACA
* *
685322 TTTCATATTATGATACATGA-CATGA
1 ATTCATATTATGATACATGATCA-CA
685347 ATTCATATTAT
1 ATTCATATTAT
685358 ATGCATTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 26 0.84
26 3 0.10
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCACA
Found at i:685438 original size:31 final size:30
Alignment explanation
Indices: 685400--685459 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
685390 TTATATAAGA
685400 TATGTGATAAA-GTGATGGAACATGATATGTT
1 TATGTGATAAAGGT-ATGGAA-ATGATATGTT
*
685431 TATGTGATAAAGGTATGGAAATTATATGT
1 TATGTGATAAAGGTATGGAAATGATATGT
685460 CTATACAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 17 0.63
32 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
TATGTGATAAAGGTATGGAAATGATATGTT
Found at i:685716 original size:23 final size:23
Alignment explanation
Indices: 685683--685741 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
685673 AATCTTATAT
*
685683 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
685706 GGTACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
685729 GGCACTTCGGTGC
1 GGCACTTCGGTGC
685742 GTTTATATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:691531 original size:19 final size:19
Alignment explanation
Indices: 691507--691553 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
691497 ATGCCATCAA
691507 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
691526 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
691545 TGCATCGAT
1 TGCATCGAT
691554 ACACCCCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAG
Found at i:692284 original size:23 final size:23
Alignment explanation
Indices: 692252--692297 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
692242 TATGGTACTA
*
692252 TGGTATAATTCTACGCGGCACTT
1 TGGTACAATTCTACGCGGCACTT
*
692275 TGGTACAATTCTACGTGGCACTT
1 TGGTACAATTCTACGCGGCACTT
692298 CGGTGCGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (23 bp):
TGGTACAATTCTACGCGGCACTT
Found at i:694888 original size:2 final size:2
Alignment explanation
Indices: 694881--694906 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
694871 TATATTGAGT
694881 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
694907 GGAAATTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:695261 original size:29 final size:28
Alignment explanation
Indices: 695207--695261 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
695197 AAGAAGATGC
*
695207 AGGATATCATTAAATTGGTATAAATTAA
1 AGGATATCATTAAATTGGTACAAATTAA
*
695235 AGGATCAT-ATTATAATTGGTACGAATT
1 AGGAT-ATCATTA-AATTGGTACAAATT
695262 TGACCAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.36
Consensus pattern (28 bp):
AGGATATCATTAAATTGGTACAAATTAA
Found at i:705381 original size:27 final size:27
Alignment explanation
Indices: 705328--705381 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
705318 ACACGTATTT
*
705328 CATGTTATTACAAAGTTTTTTTATTAA
1 CATGTTATTACAAAGTTTTTGTATTAA
* *
705355 CATGTTATTA-TAAGTTATTTGTCTTAA
1 CATGTTATTACAAAGTT-TTTGTATTAA
705382 AAAGTTAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.52
Consensus pattern (27 bp):
CATGTTATTACAAAGTTTTTGTATTAA
Found at i:706176 original size:59 final size:59
Alignment explanation
Indices: 706086--706310 Score: 188
Period size: 59 Copynumber: 3.8 Consensus size: 59
706076 TGTAACAATT
** *
706086 AACACATACTTACACTGGTGTAAGTATGTACATCTCTCAATATCTTGGTAACTTAAAATA
1 AACACATACTTACACCAGTGTAAATATGTACATCTCTCAATATCTTGGT-ACTTAAAATA
* * * *
706146 AACACATACTTAC-CCAATGTAAATATGTACATCTCTCAATACCTT-GTACCTAATTATA
1 AACACATACTTACACCAGTGTAAATATGTACATCTCTCAATATCTTGGTACTTAA-AATA
* * * * * * * ** * *
706204 GATACATACTTACATCAGTGTGAGTATATACATCTCTCATTATCTTAATTCATAAAAATA
1 AACACATACTTACACCAGTGTAAATATGTACATCTCTCAATATCTTGGTAC-TTAAAATA
* *** *
706264 ATCACATACTTAC-GTGGTGTAAATATGTACATC-CCCAATATCTTGGT
1 AACACATACTTACACCAGTGTAAATATGTACATCTCTCAATATCTTGGT
706311 GTAATAAATA
Statistics
Matches: 127, Mismatches: 34, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
57 5 0.04
58 26 0.20
59 66 0.52
60 28 0.22
61 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (59 bp):
AACACATACTTACACCAGTGTAAATATGTACATCTCTCAATATCTTGGTACTTAAAATA
Found at i:710612 original size:72 final size:72
Alignment explanation
Indices: 710531--710843 Score: 386
Period size: 73 Copynumber: 4.3 Consensus size: 72
710521 TTTTGTTGAA
*
710531 AGAAATTATCTCGAGTGAGACAAAAAATATTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTA
1 AGAAATTATCTCGAGTGAGACAAAAAATATTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTG
*
710596 TTTCGAG
66 TTTCAAG
* * * * * * *
710603 CGAAATTATCTTGAGCGAGACAAAAAAAATTCAAGGGAAAAATATCTCAGGTGAAAT-AATTTTT
1 AGAAATTATCTCGAGTGAGACAAAAAATATTCAAGGG-AAAATATCTCAAGTGAGATGAA-ATTT
*
710667 TTTTTCAA-
64 TGTTTCAAG
* * * * *
710675 TGAAAGTATCTCGAGT-AGAC-GAAAATTTTCAAGGGAAAATATCTCAAGTGAGACGTG-ATTTT
1 AGAAATTATCTCGAGTGAGACAAAAAATATTCAAGGGAAAATATCTCAAGTGAGA--TGAAATTT
710737 TGTTTCAAG
64 TGTTTCAAG
*
710746 AGAAACTT-TCTCGAGTGAGACAAAAAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAACTTT
1 AGAAA-TTATCTCGAGTGAGACAAAAAATATTCAAGGGAAAATATCTCAAGTGAGATGAAA-TTT
710810 TGTTTCAAG
64 TGTTTCAAG
710819 AGAAATTATCTCGAGTGAGACAAAA
1 AGAAATTATCTCGAGTGAGACAAAA
710844 TTTGTTTTAA
Statistics
Matches: 206, Mismatches: 23, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
69 16 0.08
70 23 0.11
71 20 0.10
72 55 0.27
73 92 0.45
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (72 bp):
AGAAATTATCTCGAGTGAGACAAAAAATATTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTG
TTTCAAG
Found at i:710743 original size:38 final size:37
Alignment explanation
Indices: 710701--710874 Score: 149
Period size: 38 Copynumber: 4.7 Consensus size: 37
710691 AGACGAAAAT
* * *
710701 TTTCAAGGGAAAATATCTCAAGTGAGACGTGATTTTTG
1 TTTCAAGAGAAAATATCTCAAGTGAGACG-AAATTTTG
* * * ***
710739 TTTCAAGAGAAACTTTCTCGAGTGAGAC-AAAAAAT-
1 TTTCAAGAGAAAATATCTCAAGTGAGACGAAATTTTG
* *
710774 TTTCAAGGGAAAATATCTCAAGTGAGATGAAACTTTTG
1 TTTCAAGAGAAAATATCTCAAGTGAGACGAAA-TTTTG
* * *
710812 TTTCAAGAGAAATTATCTCGAGTGAGAC-AAAATTTG
1 TTTCAAGAGAAAATATCTCAAGTGAGACGAAATTTTG
* *
710848 TTTTAAGA-AAAACTATCTAAAGTGAGA
1 TTTCAAGAGAAAA-TATCTCAAGTGAGA
710875 TAAAAATTTT
Statistics
Matches: 106, Mismatches: 26, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
35 26 0.25
36 28 0.26
37 4 0.04
38 48 0.45
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (37 bp):
TTTCAAGAGAAAATATCTCAAGTGAGACGAAATTTTG
Found at i:710865 original size:36 final size:36
Alignment explanation
Indices: 710735--710879 Score: 123
Period size: 36 Copynumber: 4.0 Consensus size: 36
710725 AGACGTGATT
* * *
710735 TTTGTTTCAAGAGAAACTTTCTCGAGTGAGACAAAA
1 TTTGTTTCAAGAAAAACTATCTCAAGTGAGACAAAA
** * * *
710771 AAT-TTTCAAGGGAAAA-TATCTCAAGTGAGATGAAACT
1 TTTGTTTCAA-GAAAAACTATCTCAAGTGAGA-CAAA-A
* * *
710808 TTTGTTTCAAGAGAAATTATCTCGAGTGAGACAAAA
1 TTTGTTTCAAGAAAAACTATCTCAAGTGAGACAAAA
* * *
710844 TTTGTTTTAAGAAAAACTATCTAAAGTGAGATAAAA
1 TTTGTTTCAAGAAAAACTATCTCAAGTGAGACAAAA
710880 ATTTTATTTT
Statistics
Matches: 83, Mismatches: 21, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
35 18 0.22
36 38 0.46
37 8 0.10
38 19 0.23
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.30
Consensus pattern (36 bp):
TTTGTTTCAAGAAAAACTATCTCAAGTGAGACAAAA
Found at i:713324 original size:23 final size:23
Alignment explanation
Indices: 713298--713390 Score: 80
Period size: 23 Copynumber: 4.1 Consensus size: 23
713288 GGTTCTACAC
713298 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGGGACAATTCTACGT
* * **
713321 GGTCCTTCTGGACATTTCTACAC
1 GGTCCTTCGGGACAATTCTACGT
* ** *
713344 GGTCGTTCGGGACAACACTATGT
1 GGTCCTTCGGGACAATTCTACGT
* * *
713367 GATCATTCGGGAC-ATTCTATGT
1 GGTCCTTCGGGACAATTCTACGT
713389 GG
1 GG
713391 CACTTTGGTG
Statistics
Matches: 53, Mismatches: 17, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
22 8 0.15
23 45 0.85
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTACGT
Found at i:713380 original size:46 final size:46
Alignment explanation
Indices: 713290--713382 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
713280 GAGTAGAGGG
** * * *
713290 TTCTACACGGTCCTTCGGGACAATTCTACGTGGTCCTTCTGGACAT
1 TTCTACACGGTCCTTCGGGACAACACTACGTGATCATTCGGGACAT
* *
713336 TTCTACACGGTCGTTCGGGACAACACTATGTGATCATTCGGGACAT
1 TTCTACACGGTCCTTCGGGACAACACTACGTGATCATTCGGGACAT
713382 T
1 T
713383 CTATGTGGCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (46 bp):
TTCTACACGGTCCTTCGGGACAACACTACGTGATCATTCGGGACAT
Found at i:713621 original size:2 final size:2
Alignment explanation
Indices: 713614--713659 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
713604 TTGATGTTTC
713614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
713656 AT AT
1 AT AT
713660 GCCTCACTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:739997 original size:21 final size:21
Alignment explanation
Indices: 739971--740010 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
739961 CCCCCTTTGA
*
739971 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
739992 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
740011 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:748403 original size:8 final size:8
Alignment explanation
Indices: 748349--748426 Score: 57
Period size: 8 Copynumber: 10.8 Consensus size: 8
748339 AATTAATATA
*
748349 TATATTAA
1 TATATTAT
748357 TATATT-T
1 TATATTAT
748364 TA-ATTAT
1 TATATTAT
748371 T-TATTAT
1 TATATTAT
*
748378 T-T-TTAA
1 TATATTAT
748384 TA-ATTA-
1 TATATTAT
748390 -ATATTAT
1 TATATTAT
748397 TATATTAT
1 TATATTAT
*
748405 TATTTTAT
1 TATATTAT
748413 T-TATTTAT
1 TATA-TTAT
748421 TATATT
1 TATATT
748427 CATTTAATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
5 1 0.02
6 11 0.19
7 15 0.26
8 28 0.49
9 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATATTAT
Found at i:750618 original size:23 final size:23
Alignment explanation
Indices: 750592--750647 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
750582 AATAAACCAT
750592 CGGTTGATGGACTTTTTTAAAGG
1 CGGTTGATGGACTTTTTTAAAGG
750615 CGGTTGATGGACTTTTTTAAAGG
1 CGGTTGATGGACTTTTTTAAAGG
750638 CGGTTGATGG
1 CGGTTGATGG
750648 GATGATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.09, G:0.34, T:0.38
Consensus pattern (23 bp):
CGGTTGATGGACTTTTTTAAAGG
Found at i:760758 original size:55 final size:55
Alignment explanation
Indices: 760632--760860 Score: 250
Period size: 55 Copynumber: 4.2 Consensus size: 55
760622 GTGCACTATT
* ** *
760632 AGTGCCTATACGA-GAATTCATCAAC-CTATGATGAATT--ATGTGGGATGCACACAT
1 AGTGCCTGTACGATG-ATTCATCAACTC-ATGATGAATTCCATG-GATATGCACACAA
* * * * *
760686 AGTGCTTGTACGTTGATTCATCAACTCATGATGAATTCCGTGAATATTCACACAA
1 AGTGCCTGTACGATGATTCATCAACTCATGATGAATTCCATGGATATGCACACAA
* * * *
760741 AGTGCCTGTACGGTGATTCATGAACTCGTGATGAATTCCTTGGATATGCACACAA
1 AGTGCCTGTACGATGATTCATCAACTCATGATGAATTCCATGGATATGCACACAA
* * * *
760796 AGTACATGTACGATGATTCATCAACTCATGATGAATTTCATGGATATGCACATAA
1 AGTGCCTGTACGATGATTCATCAACTCATGATGAATTCCATGGATATGCACACAA
760851 AGTGCCTGTA
1 AGTGCCTGTA
760861 GTATTGATAA
Statistics
Matches: 145, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
54 30 0.21
55 113 0.78
56 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (55 bp):
AGTGCCTGTACGATGATTCATCAACTCATGATGAATTCCATGGATATGCACACAA
Found at i:760956 original size:20 final size:20
Alignment explanation
Indices: 760931--760973 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
760921 TCTAAGAGCT
760931 CATTTAGGAGCATATAGATG
1 CATTTAGGAGCATATAGATG
*
760951 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
760971 CAT
1 CAT
760974 GTGGTGGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:762497 original size:23 final size:23
Alignment explanation
Indices: 762470--762513 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
762460 AACAAAATTT
*
762470 AATTTGCCAAGACATTTCCATCC
1 AATTTGCCAAGACATATCCATCC
*
762493 AATTTGCCACGACATATCCAT
1 AATTTGCCAAGACATATCCAT
762514 TTGGTACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.30, G:0.09, T:0.30
Consensus pattern (23 bp):
AATTTGCCAAGACATATCCATCC
Found at i:767842 original size:13 final size:13
Alignment explanation
Indices: 767817--767862 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
767807 CTTGGCTTGC
767817 TTTCTCTTTTTCT
1 TTTCTCTTTTTCT
767830 TTTCT-TTTCTTCT
1 TTTCTCTTT-TTCT
**
767843 TTTCTGATTTT-T
1 TTTCTCTTTTTCT
767855 TTTCTCTT
1 TTTCTCTT
767863 CTTTTTGCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 10 0.36
13 16 0.57
14 2 0.07
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTCTCTTTTTCT
Found at i:767844 original size:25 final size:24
Alignment explanation
Indices: 767816--767865 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
767806 CCTTGGCTTG
*
767816 CTTTCTCT-TTTTCTTTTCTTTTCTT
1 CTTT-TCTATTTT-TTTTCTCTTCTT
767841 CTTTTCTGATTTTTTTTCTCTTCTT
1 CTTTTCT-ATTTTTTTTCTCTTCTT
767866 TTTGCACTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 3 0.14
25 15 0.68
26 4 0.18
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (24 bp):
CTTTTCTATTTTTTTTCTCTTCTT
Found at i:774246 original size:23 final size:23
Alignment explanation
Indices: 774215--774258 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
774205 ACATTCAACA
*
774215 CAATTTAATTTGCCAAGACATTT
1 CAATCTAATTTGCCAAGACATTT
*
774238 CAATCTAATTTGCCACGACAT
1 CAATCTAATTTGCCAAGACAT
774259 ATCCATTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (23 bp):
CAATCTAATTTGCCAAGACATTT
Found at i:774987 original size:20 final size:20
Alignment explanation
Indices: 774929--774988 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 20
774919 GATGTTTCCA
* * *
774929 GGTATTGATACCCTTACCAT
1 GGTACTGATACCCCTACTAT
774949 GGTACTGATACTACCCTACTAT
1 GGTACTGATAC--CCCTACTAT
774971 GGTACTGATACCCCTACT
1 GGTACTGATACCCCTACT
774989 GGTATCGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 17 0.49
22 18 0.51
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (20 bp):
GGTACTGATACCCCTACTAT
Found at i:776595 original size:2 final size:2
Alignment explanation
Indices: 776588--776636 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
776578 TTTCGTAAAT
776588 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
776630 TA TA TA T
1 TA TA TA T
776637 TAGGTTGACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:782970 original size:23 final size:23
Alignment explanation
Indices: 782944--782988 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
782934 CACCACAGCT
*
782944 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
782967 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
782989 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:784788 original size:64 final size:63
Alignment explanation
Indices: 784690--784850 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
784680 TAATGAAGGT
* *
784690 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
784753 GG
62 GC
*
784755 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
784819 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
784851 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:786098 original size:23 final size:24
Alignment explanation
Indices: 786061--786108 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
786051 TAAATCATAA
786061 ATAAAAATAAATATTT-T-ATATT
1 ATAAAAATAAATATTTATCATATT
*
786083 ATAAAAATAATTTATTTATCATATT
1 ATAAAAATAA-ATATTTATCATATT
786108 A
1 A
786109 CTTAACGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 5 0.23
24 1 0.05
25 6 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAAAATAAATATTTATCATATT
Done.