Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008954.1 Hibiscus syriacus cultivar Beakdansim tig00112282_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: 488355
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:425497 original size:2 final size:2
Alignment explanation
Indices: 425490--425517 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
425480 AATAAAAATA
425490 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
425518 TCGAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:425564 original size:39 final size:38
Alignment explanation
Indices: 425497--425758 Score: 295
Period size: 39 Copynumber: 6.8 Consensus size: 38
425487 ATAATATATA
* *
425497 TATATATATATATATATATATTCGAAAATGTTTTAAAAAC
1 TATATAT-TATATATA-ATTTTCAAAAATGTTTTAAAAAC
425537 TATATATTATATATAAGTTTTCAAAAATGTTTTAAAAAC
1 TATATATTATATATAA-TTTTCAAAAATGTTTTAAAAAC
* *
425576 TGTATATTATATAT-A-TTTCCAAAATGTTTTAAAAAC
1 TATATATTATATATAATTTTCAAAAATGTTTTAAAAAC
*
425612 TATATAATATATATAAGTTTTCAAAAATGTTTTAAAAAC
1 TATATATTATATATAA-TTTTCAAAAATGTTTTAAAAAC
* *
425651 TATATATTATATAT-A-TTTCCAAAATGTTTCAAAAAC
1 TATATATTATATATAATTTTCAAAAATGTTTTAAAAAC
* * *
425687 TATATAATATATATATATATTTTCAAAAATTATTTTCAAACC
1 TATAT-AT-TATATATA-ATTTTCAAAAA-TGTTTTAAAAAC
*
425729 TATATAATATATAT-A-TTT-AAAAATTGTTTT
1 TATATATTATATATAATTTTCAAAAA-TGTTTT
425759 TTGAAACATT
Statistics
Matches: 195, Mismatches: 17, Indels: 24
0.83 0.07 0.10
Matches are distributed among these distances:
36 67 0.34
37 6 0.03
38 11 0.06
39 74 0.38
40 15 0.08
41 9 0.05
42 13 0.07
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (38 bp):
TATATATTATATATAATTTTCAAAAATGTTTTAAAAAC
Found at i:425582 original size:75 final size:75
Alignment explanation
Indices: 425499--425746 Score: 363
Period size: 75 Copynumber: 3.2 Consensus size: 75
425489 AATATATATA
*
425499 TATATATATATATATATATTCGAAAATGTTTTAAAAACTATATATTATATATAAGTTTTCAAAAA
1 TATATAT-TATATATAT-TTCCAAAATGTTTTAAAAACTATATATTATATATAAGTTTTCAAAAA
425564 TGTTTTAAAAAC
64 TGTTTTAAAAAC
* *
425576 TGTATATTATATATATTTCCAAAATGTTTTAAAAACTATATAATATATATAAGTTTTCAAAAATG
1 TATATATTATATATATTTCCAAAATGTTTTAAAAACTATATATTATATATAAGTTTTCAAAAATG
425641 TTTTAAAAAC
66 TTTTAAAAAC
*
425651 TATATATTATATATATTTCCAAAATGTTTCAAAAACTATATAATATATATATATA-TTTTCAAAA
1 TATATATTATATATATTTCCAAAATGTTTTAAAAACTATAT-AT-TATATATA-AGTTTTCAAAA
* * *
425715 ATTATTTTCAAACC
63 A-TGTTTTAAAAAC
*
425729 TATATAATATATATATTT
1 TATATATTATATATATTT
425747 AAAAATTGTT
Statistics
Matches: 157, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
75 96 0.61
76 10 0.06
77 24 0.15
78 27 0.17
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (75 bp):
TATATATTATATATATTTCCAAAATGTTTTAAAAACTATATATTATATATAAGTTTTCAAAAATG
TTTTAAAAAC
Found at i:425825 original size:35 final size:33
Alignment explanation
Indices: 425779--425844 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 33
425769 ATACTTTTTG
*
425779 TATTATATTTTCAAAATCGTTTTCTAAAAATTATA
1 TATTATATTTTCAAAAT-ATTTTC-AAAAATTATA
425814 TATTATATTTTCAAAATATTTTCAAAAATTA
1 TATTATATTTTCAAAATATTTTCAAAAATTA
425845 CGCTATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 8 0.27
34 5 0.17
35 17 0.57
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (33 bp):
TATTATATTTTCAAAATATTTTCAAAAATTATA
Found at i:426711 original size:169 final size:169
Alignment explanation
Indices: 426475--427637 Score: 1325
Period size: 169 Copynumber: 6.9 Consensus size: 169
426465 CAGATAAACA
* * * *
426475 TTCTCGCATTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCAAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAA-TTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* * * * *
426540 TCTTTGATTGACAGATAACCCTTCTCACCTTGAGTTATGT-TATACTGGATATGCCTTTGAGCTG
65 TC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGTGTAAATTGGATGTGCCTTTGAGCTG
* *
426604 AATGTAATAGAACTCGAAGGTCTTTTGTTGCCAGATAGCCC
129 AGTGTAATAGAACTCGAAGGTCTTTTGTTGGCAGATAGCCC
* * *
426645 TTCTTGTCTTGAGCTATGCTGTAAATTGATGTGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGT
1 TTCTCGCCTTGAGCTATGCTGTAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
426710 CTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTGGATGTGCCTTTGAGCTGA
66 CTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATG-TGTAAATTGGATGTGCCTTTGAGCTGA
*
426775 GTGTAATCA-AACTCGAAGGTCTTTTGTTGGCAGATATCCC
130 GTGTAAT-AGAACTCGAAGGTCTTTTGTTGGCAGATAGCCC
* * * * ** * *
426815 TTCTCACCTTGAGCTATGTTGCAAA-TGACGTGCCTTTGATATGAGGGTAATCGAACTTGAAGGT
1 TTCTCGCCTTGAGCTATGCTGTAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
* * *
426879 CTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATACTGTAAATTGGATGTGCCTTTAAGTTGA
66 CTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTAT-GTGTAAATTGGATGTGCCTTTGAGCTGA
*
426944 GTGTAATCA-AACTCAAAGGTCTTTTGTTGGCAGATAGCCC
130 GTGTAAT-AGAACTCGAAGGTCTTTTGTTGGCAGATAGCCC
* *
426984 TTCTTGCCTTGAGCTATGCTGCAAA-TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
1 TTCTCGCCTTGAGCTATGCTGTAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
* *
427048 CTTGGTTGATAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTAGATGTGCCTTTG-GACTG
66 CTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATG-TGTAAATTGGATGTGCCTTTGAG-CTG
* *
427112 AGTGTAATCGAACTCGAAGGTCTTTTGTTGGAAGATAGCCC
129 AGTGTAATAGAACTCGAAGGTCTTTTGTTGGCAGATAGCCC
* * * * *
427153 TTCTTGCCTTAAGTTATGCTGCAAA-TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGT
1 TTCTCGCCTTGAGCTATGCTGTAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
* * * * * * *
427217 ATTGGTTGACAGATAGCCTTTCTCGCCTTGAGCTATG-CTACAAAT-GATGTGCCTTTGAGTTGA
66 CTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGTGTA-AATTGGATGTGCCTTTGAGCTGA
* * * *
427280 GTGTAATCGAACTCGAAGGTC-TTGGTTGACAGATATCCC
130 GTGTAATAGAACTCGAAGGTCTTTTGTTGGCAGATAGCCC
* * * * *
427319 TTATCGCGTTGAGTTATGCTGTAAATTGGTTGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAAG
1 TTCTCGCCTTGAGCTATGCTGTAAATT-GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* * * * * *
427384 TCTTTTGTTGGA-AGATAGCCCTTCACGCCTTGAGCTATG-CTACAAAT-GATGTGCCTTTGAGC
65 TC-TTGGTT-GACAGATAACCCTTCTCGCCTTGAGTTATGTGTA-AATTGGATGTGCCTTTGAGC
* * * * * * *
427446 CGAGTATAATCGAACTCGAAGGTC-TTGGTTGACAGATAACCA
127 TGAGTGTAATAGAACTCGAAGGTCTTTTGTTGGCAGATAGCCC
* * * *
427488 TTCTCACCTTGAGTTATGATGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATT-GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* * * ** * * *
427553 TCCATT-TTTGGCATATCGCCCTTCTTGCCTTGAGTTATGCTGCAAA-TGG-TGCGCCTTTGAGC
65 T-C-TTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATG-TGTAAATTGGATGTGCCTTTGAGC
* *
427615 TGAGTGTAATTGAACTCAAAGGT
127 TGAGTGTAATAGAACTCGAAGGT
427638 TCTCTTGAAT
Statistics
Matches: 875, Mismatches: 100, Indels: 37
0.86 0.10 0.04
Matches are distributed among these distances:
166 34 0.04
167 39 0.04
168 75 0.09
169 618 0.71
170 107 0.12
171 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (169 bp):
TTCTCGCCTTGAGCTATGCTGTAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
CTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGTGTAAATTGGATGTGCCTTTGAGCTGAG
TGTAATAGAACTCGAAGGTCTTTTGTTGGCAGATAGCCC
Found at i:427389 original size:421 final size:419
Alignment explanation
Indices: 426461--427624 Score: 1534
Period size: 421 Copynumber: 2.8 Consensus size: 419
426451 ATAGTTTTTA
* * * * * * *
426461 TTGACAGATAAACATTCTCGCATTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTA
1 TTGACAGATAACCCTTATCGCATTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTA
* * * * * *
426526 ATCGAACTCAAAGGTC-TTTGATTGACAGATAACCCTTCTCACCTTGAGTTATG-TTATACTGGA
66 ATCGAACTCAAAGGTCTTTTG-TTGGCAGATAGCCCTTCTCGCCTTGAGCTATGCTCA-AAT-GA
* * * * * * * *
426589 TATGCCTTTGAGCTGAATGTAATAGAACTCGAAGGTCTTTTGTTGCCAGATAGCCCTTCTTGTCT
128 TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCT
* * * *
426654 TGAGCTATGCTGTAAATTGATGTGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTGGTT-G
192 TGAGTTATGATGTAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGG
* * * *
426718 ACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATC
257 A-AGATAGCCCTTCTTGCCTTGAGTTATGCTGCAAA-T-GATGTGCCTTTGAGCTGAGTGTAATC
* * * * * *
426783 AAACTCGAAGGTCTTTTGTTGGCAGATATCCCTTCTCACCTTGAGCTATGTTGCAAATGACGTGC
319 AAACTCGAAGGTCATTGGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTACAAATGACGTGC
*
426848 CTTTGATATGAGGGTAATCGAACTTGAAGGTCTTGG
384 CTTTGATATGAGGGTAATCGAACTCGAAGGTCTTGG
* * * * *
426884 TTGACAGATAACCCTTCTCGCCTTGAGTTATACTGTAAATTGGATGTGCCTTTAAGTTGAGTGTA
1 TTGACAGATAACCCTTATCGCATTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTA
* *
426949 ATCAAACTCAAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
66 ATCGAACTCAAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATGCT-CAAATGATG
*
427014 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGATAGATAACCCTTCTCGCCTTGA
130 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGA
*
427079 GTTATGTTGTAAATTAGATGTGCCTTTG-GACTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGG
195 GTTATGATGTAAATT-GATGTGCCTTTGAG-CTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGG
*
427143 AAGATAGCCCTTCTTGCCTTAAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
257 AAGATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
* * *
427208 CTCGAAGGT-ATTGGTTGACAGATAGCCTTTCTCGCCTTGAGCTATGCTACAAATGATGTGCCTT
322 CTCGAAGGTCATTGGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTACAAATGACGTGCCTT
*
427272 TGAGT-TGAGTGTAATCGAACTCGAAGGTCTTGG
387 TGA-TATGAGGGTAATCGAACTCGAAGGTCTTGG
* * *
427305 TTGACAGATATCCCTTATCGCGTTGAGTTATGCTGTAAATTGGTTGTGCCTTTGAGCTGAGTGTA
1 TTGACAGATAACCCTTATCGCATTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTA
* *
427370 ATCGAACTCGAAA-GTCTTTTGTTGGAAGATAGCCCTTCACGCCTTGAGCTATGCTACAAATGAT
66 ATCGAACTC-AAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATGCT-CAAATGAT
* * * *
427434 GTGCCTTTGAGCCGAGTATAATCGAACTCGAAGGTCTTGGTTGACAGATAACCATTCTCACCTTG
129 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTG
*
427499 AGTTATGATGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTCCATTT-TTG
194 AGTTATGATGTAAATT-GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT-C-TTTGTTG
* * * * *
427563 GCATATCGCCCTTCTTGCCTTGAGTTATGCTGCAAATGGTGCGCCTTTGAGCTGAGTGTAAT
256 GAAGATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
427625 TGAACTCAAA
Statistics
Matches: 656, Mismatches: 74, Indels: 24
0.87 0.10 0.03
Matches are distributed among these distances:
421 357 0.54
422 85 0.13
423 170 0.26
424 41 0.06
425 3 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (419 bp):
TTGACAGATAACCCTTATCGCATTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTA
ATCGAACTCAAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATGCTCAAATGATGT
GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAG
TTATGATGTAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGAAGA
TAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCG
AAGGTCATTGGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTACAAATGACGTGCCTTTGAT
ATGAGGGTAATCGAACTCGAAGGTCTTGG
Found at i:428547 original size:87 final size:86
Alignment explanation
Indices: 428388--428617 Score: 299
Period size: 87 Copynumber: 2.7 Consensus size: 86
428378 AGCTGAATCT
* * *
428388 ATAAAGCCGGAGCGTTTTAACCAATTGCTCTAGAGGGACATCTCAA---TA-TATAAACACCTTT
1 ATAAAGCCGGGGCG-TTTAACCAATTGCT-TAGAGGGACAACTCAAGCTTATTATAATCACCTTT
** *
428449 ATCAGGTTAGCTGAATCTTGTCC
64 ATCAGACTAGCTGAATCTTATCC
428472 ATAAAGCCGGGGCGTTTAACCAATTGTCTTAGAGGG-CAACTCAAGCTCTATTATAATCACCTTT
1 ATAAAGCCGGGGCGTTTAACCAATTG-CTTAGAGGGACAACTCAAGCT-TATTATAATCACCTTT
428536 ATCAGACTAGCTGAATCTTATCC
64 ATCAGACTAGCTGAATCTTATCC
* *
428559 ATAAAGTCGGGGTGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTATAATC
1 ATAAAGCCGGGGCGTTTAACCAATTGC-TTAGAGGGACAACTCAAGC-TTATTATAATC
428618 TGGGTACACG
Statistics
Matches: 129, Mismatches: 8, Indels: 14
0.85 0.05 0.09
Matches are distributed among these distances:
82 7 0.05
83 19 0.15
84 15 0.12
86 3 0.02
87 64 0.50
88 20 0.16
89 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (86 bp):
ATAAAGCCGGGGCGTTTAACCAATTGCTTAGAGGGACAACTCAAGCTTATTATAATCACCTTTAT
CAGACTAGCTGAATCTTATCC
Found at i:429013 original size:22 final size:23
Alignment explanation
Indices: 428988--429038 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
428978 AGTTTTTTTA
*
428988 TGAATAATGATGAACAGTA-CCG
1 TGAACAATGATGAACAGTACCCG
* *
429010 TGAACAGTGATGAAGAGTACCCG
1 TGAACAATGATGAACAGTACCCG
429033 TGAACA
1 TGAACA
429039 TTGAACAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (23 bp):
TGAACAATGATGAACAGTACCCG
Found at i:429037 original size:23 final size:22
Alignment explanation
Indices: 428995--429038 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
428985 TTATGAATAA
428995 TGATGAACAGTACCGTGAACAG
1 TGATGAACAGTACCGTGAACAG
*
429017 TGATGAAGAGTACCCGTGAACA
1 TGATGAACAGTA-CCGTGAACA
429039 TTGAACAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (22 bp):
TGATGAACAGTACCGTGAACAG
Found at i:429678 original size:46 final size:45
Alignment explanation
Indices: 429613--429712 Score: 146
Period size: 46 Copynumber: 2.2 Consensus size: 45
429603 ATATAAATCT
* * * *
429613 CTTACCGTTTATCCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATACA
429658 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATACA
1 CTTACCATTT-ATACCATAAGCTCGTAAGCTTATTTTACCAATACA
*
429704 CTTGCCATT
1 CTTACCATT
429713 ATTTCATACC
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 9 0.18
46 40 0.82
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAATACA
Found at i:435306 original size:20 final size:20
Alignment explanation
Indices: 435283--435340 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
435273 GAAAAATGGA
435283 AAAAATAAAAAAAGAAATAT
1 AAAAATAAAAAAAGAAATAT
435303 -AAAATAAAATAAA-AAA-AT
1 AAAAATAAAA-AAAGAAATAT
* *
435321 AGTAAATAAAAAACGAAATA
1 A-AAAATAAAAAAAGAAATA
435341 AAATGAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 2 0.06
19 14 0.45
20 14 0.45
21 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.16
Consensus pattern (20 bp):
AAAAATAAAAAAAGAAATAT
Found at i:435311 original size:24 final size:23
Alignment explanation
Indices: 435257--435333 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
435247 ATAAATTTAG
*
435257 TAAAAAGAA-AAAAAAAGAAAAA
1 TAAAAAAAATAAAAAAAGAAAAA
** *
435279 TGGAAAAAATAAAAAAAGAAATA
1 TAAAAAAAATAAAAAAAGAAAAA
* *
435302 TAAAATAAAATAAAAAAATAGTAAA
1 TAAAA-AAAATAAAAAAAGA-AAAA
435327 TAAAAAA
1 TAAAAAA
435334 CGAAATAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
22 6 0.14
23 15 0.35
24 15 0.35
25 7 0.16
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (23 bp):
TAAAAAAAATAAAAAAAGAAAAA
Found at i:435312 original size:33 final size:32
Alignment explanation
Indices: 435259--435321 Score: 74
Period size: 33 Copynumber: 1.9 Consensus size: 32
435249 AAATTTAGTA
*
435259 AAAAGAAAAAAAAAGAAAAATGGAAAAAATAAA
1 AAAAGAAAAAAAAAGAAAAAT-AAAAAAATAAA
* *
435292 AAAAGAAATATAAAA-TAAAATAAAAAAATA
1 AAAAGAAA-AAAAAAGAAAAATAAAAAAATA
435322 GTAAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 8 0.31
33 13 0.50
34 5 0.19
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (32 bp):
AAAAGAAAAAAAAAGAAAAATAAAAAAATAAA
Found at i:435333 original size:27 final size:25
Alignment explanation
Indices: 435284--435353 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 25
435274 AAAAATGGAA
* *
435284 AAAAT-AAAAAAAGAAATATAAAAT
1 AAAATAAAAAAAAGAAATAAAAAAC
435308 AAAATAAAAAAATAGTAAATAAAAAAC
1 AAAATAAAAAAA-AG-AAATAAAAAAC
*
435335 GAAATAAAATGAAAAGAAA
1 AAAATAAAA--AAAAGAAA
435354 AAATAAGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 5 0.13
25 6 0.16
26 2 0.05
27 20 0.53
28 2 0.05
29 3 0.08
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.14
Consensus pattern (25 bp):
AAAATAAAAAAAAGAAATAAAAAAC
Found at i:435749 original size:2 final size:2
Alignment explanation
Indices: 435742--435767 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
435732 TGCCAATTTG
435742 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
435768 TTTCAAATGA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:436630 original size:3 final size:3
Alignment explanation
Indices: 436622--436657 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
436612 TTGATAAAAT
436622 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
436658 TATTATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:436839 original size:36 final size:36
Alignment explanation
Indices: 436772--436934 Score: 227
Period size: 36 Copynumber: 4.4 Consensus size: 36
436762 AAACTATATA
* *
436772 ATATATATATATATATATTCGAAAATGTTTTAAAAACC
1 ATATAT-TATATATAT-TTCCAAAATGTTTTAAAAACT
* *
436810 ATGTATTATATATATTTCCAAAATATTTTAAAAACT
1 ATATATTATATATATTTCCAAAATGTTTTAAAAACT
436846 ATATATTATATATATTTCCAAAATGTTTTAAAAACT
1 ATATATTATATATATTTCCAAAATGTTTTAAAAACT
* *
436882 ATATAATATATATAAGTTTTCAAAAATGTTTTAAAAACT
1 ATATATTATATAT-A--TTTCCAAAATGTTTTAAAAACT
436921 ATATATTATATATA
1 ATATATTATATATA
436935 GAGAAAATCG
Statistics
Matches: 113, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
36 64 0.57
37 10 0.09
38 6 0.05
39 33 0.29
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.43
Consensus pattern (36 bp):
ATATATTATATATATTTCCAAAATGTTTTAAAAACT
Found at i:436921 original size:75 final size:73
Alignment explanation
Indices: 436772--436934 Score: 229
Period size: 75 Copynumber: 2.2 Consensus size: 73
436762 AAACTATATA
* * * *
436772 ATATATATATATATATATTCGAAAATGTTTTAAAAACCATGTATTATATATATTTCCAAAATATT
1 ATATAT-TATATATATATTCCAAAATGTTTTAAAAACCATATAATATATATATTTCAAAAATATT
436837 TTAAAAACT
65 TTAAAAACT
* *
436846 ATATATTATATATAT-TTCCAAAATGTTTTAAAAACTATATAATATATATAAGTTTTCAAAAATG
1 ATATATTATATATATATTCCAAAATGTTTTAAAAACCATATAATATATAT-A--TTTCAAAAATA
436910 TTTTAAAAACT
63 TTTTAAAAACT
436921 ATATATTATATATA
1 ATATATTATATATA
436935 GAGAAAATCG
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
72 30 0.38
73 10 0.12
74 6 0.08
75 34 0.43
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.43
Consensus pattern (73 bp):
ATATATTATATATATATTCCAAAATGTTTTAAAAACCATATAATATATATATTTCAAAAATATTT
TAAAAACT
Found at i:437078 original size:20 final size:20
Alignment explanation
Indices: 437055--437106 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
437045 AACGCGATCC
437055 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
437075 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
437095 CCAAAATCGCAA
1 CCAGAATCGCAA
437107 CGCGATTCTT
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:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:437123 original size:21 final size:20
Alignment explanation
Indices: 437096--437194 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
437086 AATCAGTTTC
437096 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
437117 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
437138 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
437158 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
437179 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
437195 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:437223 original size:20 final size:20
Alignment explanation
Indices: 437161--437354 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
437151 CGATTTTCCA
* ** *
437161 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
437181 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
437201 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
437221 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
437241 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
437261 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
437281 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
437301 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
437321 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
437342 AAATCGCAACGCG
1 AAATCGCAACGCG
437355 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:437245 original size:60 final size:60
Alignment explanation
Indices: 437161--437354 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
437151 CGATTTTCCA
* ** * *
437161 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
437221 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
437281 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
437342 AAATCGCAACGCG
1 AAATCGCAACGCG
437355 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:437775 original size:33 final size:33
Alignment explanation
Indices: 437736--437806 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
437726 TTCACTTAGA
*
437736 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
437769 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
437802 TTTCA
1 TTTCA
437807 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:437946 original size:14 final size:14
Alignment explanation
Indices: 437927--437981 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
437917 AGAATGACTG
437927 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
437941 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
437960 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
437974 TCGCAACG
1 TCGCAACG
437982 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:437994 original size:33 final size:33
Alignment explanation
Indices: 437927--437997 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
437917 AGAATGACTG
***
437927 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
437960 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
437993 TCGCA
1 TCGCA
437998 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:438015 original size:19 final size:19
Alignment explanation
Indices: 437993--438090 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
437983 GAAACCAAAA
*
437993 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
438012 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
438026 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
438045 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
438059 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
438078 TCGCGTTGCGATT
1 TCGCGTTGCGATT
438091 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:438034 original size:14 final size:14
Alignment explanation
Indices: 438015--438104 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
438005 TTTCATTTCG
438015 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
438029 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
438048 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
438062 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
438079 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
438095 CGTTGCGATT
1 CGTTGCGATT
438105 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:438040 original size:33 final size:33
Alignment explanation
Indices: 437998--438112 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
437988 CAAAATCGCA
437998 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
438031 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
438064 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
438097 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
438113 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:440040 original size:185 final size:186
Alignment explanation
Indices: 439810--440191 Score: 748
Period size: 185 Copynumber: 2.1 Consensus size: 186
439800 TAGATTGCTT
439810 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
439875 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
439940 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
439995 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
440060 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
440125 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
440181 AGTAAATTTAT
1 AGTAAATTTAT
440192 CCATTCAAGT
Statistics
Matches: 194, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 154 0.79
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:440124 original size:93 final size:93
Alignment explanation
Indices: 439810--440189 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
439800 TAGATTGCTT
*
439810 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
439875 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
439903 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
439967 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
439995 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
440060 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
440088 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
440153 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
440181 AGTAAATTT
1 AGTAAATTT
440190 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:440273 original size:19 final size:19
Alignment explanation
Indices: 440233--440361 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
440223 TAGTTTACTT
* *
440233 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
440253 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
440272 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
440291 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
440305 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
440324 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
440338 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
440357 TCGCA
1 TCGCA
440362 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:440312 original size:33 final size:32
Alignment explanation
Indices: 440269--440361 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
440259 CGCGAAACCA
**
440269 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
440301 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
440334 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
440362 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:440359 original size:52 final size:52
Alignment explanation
Indices: 440233--440361 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
440223 TAGTTTACTT
**
440233 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
440285 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
440338 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
440362 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:440379 original size:19 final size:19
Alignment explanation
Indices: 440357--440491 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
440347 GAAACCAAAA
*
440357 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
440376 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
440392 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
440409 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
440425 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
440442 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
440461 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
440481 TCGTGTTGCGA
1 TCGCGTTGCGA
440492 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:440398 original size:14 final size:14
Alignment explanation
Indices: 440379--440435 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
440369 TTTCATTTCG
440379 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
440393 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
440410 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
440426 CGTTGCGATT
1 CGTTGCGATT
440436 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:440404 original size:33 final size:33
Alignment explanation
Indices: 440362--440454 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
440352 CAAAATCGCA
*
440362 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
440395 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
440428 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
440455 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:442348 original size:38 final size:38
Alignment explanation
Indices: 442305--442377 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
442295 AATTGATTGT
*
442305 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
442343 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
442378 TGTAAAGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:442364 original size:19 final size:19
Alignment explanation
Indices: 442300--442364 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
442290 AGTTTAATTG
*
442300 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
442319 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
442337 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
442357 ATTGATTT
1 ATTGATTT
442365 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:442384 original size:13 final size:14
Alignment explanation
Indices: 442359--442393 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
442349 ATTGTTTAAT
442359 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
442373 TGATTTGT-AAAGT
1 TGATTTGTAAAAGA
442386 TGATTTGT
1 TGATTTGT
442394 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:442516 original size:19 final size:19
Alignment explanation
Indices: 442500--442601 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
442490 AAAAATGACT
442500 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
442519 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
442538 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
442552 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
442571 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
442591 ATCGCAATGCG
1 ATCGCAATGCG
442602 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:442620 original size:19 final size:19
Alignment explanation
Indices: 442608--442955 Score: 405
Period size: 19 Copynumber: 19.8 Consensus size: 19
442598 TGCGTTTATA
442608 ATTTCGCATTGCGA--TT-
1 ATTTCGCATTGCGATTTTC
*
442624 ATCTCG-A-TGCGATTTTC
1 ATTTCGCATTGCGATTTTC
442641 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
442660 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
442677 -TTTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
442693 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
442712 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
* *
442731 ATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGATTTTC
442750 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
442769 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
442786 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
442802 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
442821 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
442838 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
442854 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
442873 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
442890 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
442906 ATTTCCGCATTGCGATTTTC
1 ATTT-CGCATTGCGATTTTC
*
442926 A--T-G--TTGGGATTTTC
1 ATTTCGCATTGCGATTTTC
*
442940 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
442956 GTATTTTCCG
Statistics
Matches: 287, Mismatches: 14, Indels: 59
0.80 0.04 0.16
Matches are distributed among these distances:
14 40 0.14
15 1 0.00
16 38 0.13
17 33 0.11
18 4 0.01
19 159 0.55
20 12 0.04
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:442665 original size:52 final size:52
Alignment explanation
Indices: 442608--442927 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
442598 TGCGTTTATA
* *
442608 ATTTCGCATTGCGATTATCTCGATGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
442660 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
442712 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
442769 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
442821 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
442873 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
442926 AT
1 AT
442928 GTTGGGATTT
Statistics
Matches: 256, Mismatches: 6, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 181 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:442707 original size:71 final size:72
Alignment explanation
Indices: 442631--442955 Score: 387
Period size: 71 Copynumber: 4.6 Consensus size: 72
442621 ATTATCTCGA
442631 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCAT
442695 TTCGCAT
66 TTCGCAT
* *
442702 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATTT
442767 TCATTTCGCAT
62 TCATTTCGCAT
*
442778 TGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--T
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATTT
*
442836 TC-TCTCG--T
62 TCATTTCGCAT
*
442844 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCAT
442908 TTCCGCAT
66 TT-CGCAT
* *
442916 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
442956 GTATTTTCCG
Statistics
Matches: 226, Mismatches: 11, Indels: 38
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.05
67 25 0.11
68 14 0.06
69 13 0.06
70 3 0.01
71 108 0.48
72 12 0.05
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (72 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCAT
TTCGCAT
Found at i:442873 original size:161 final size:157
Alignment explanation
Indices: 442608--442927 Score: 543
Period size: 161 Copynumber: 2.0 Consensus size: 157
442598 TGCGTTTATA
442608 ATTTCGCATTGCGATTATCTCGATGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGATGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
442673 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
442738 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
* *
442769 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGATGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
442834 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
442899 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
442926 AT
1 AT
442928 GTTGGGATTT
Statistics
Matches: 153, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 115 0.75
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGATGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:442899 original size:33 final size:33
Alignment explanation
Indices: 442649--442955 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
442639 TCATTTCGCA
*
442649 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
442682 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
442718 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
442756 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
442791 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
442827 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
442862 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
442895 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
442929 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
442956 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 87 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:445278 original size:12 final size:12
Alignment explanation
Indices: 445261--445285 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
445251 TTCTTCGGGA
445261 CTTTTTCTTCTT
1 CTTTTTCTTCTT
445273 CTTTTTCTTCTT
1 CTTTTTCTTCTT
445285 C
1 C
445286 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:445494 original size:24 final size:24
Alignment explanation
Indices: 445460--445506 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
445450 CTGAAACATC
445460 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
445484 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
445507 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:446208 original size:20 final size:20
Alignment explanation
Indices: 446180--446548 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
446170 AAATTTCAGT
* * * *
446180 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
446200 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
446220 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
446240 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
446260 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
446280 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
446300 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
446320 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
446340 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
446360 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
446380 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
446400 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
446420 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
446440 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
446460 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
446480 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
446500 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
446520 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
446540 GTTGCGATT
1 GTTGCGATT
446549 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:446804 original size:40 final size:40
Alignment explanation
Indices: 446756--446840 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 40
446746 GATTTTCTCT
* *
446756 TATATATAT-TTCCAAAA-TGTTTTAAAAACTATATAATA
1 TATATATATATTCAAAAATTATTTTAAAAACTATATAATA
*
446794 TATATATATATTCAAAAATTATTTTAAAAGCTATATAATA
1 TATATATATATTCAAAAATTATTTTAAAAACTATATAATA
446834 TATATAT
1 TATATAT
446841 TTAAAAACCG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
38 9 0.21
39 7 0.17
40 26 0.62
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (40 bp):
TATATATATATTCAAAAATTATTTTAAAAACTATATAATA
Found at i:446937 original size:37 final size:35
Alignment explanation
Indices: 446871--446942 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 35
446861 ACAATATACT
* *
446871 TTATGTATTATATTTTCAAAATCCGTTTTCTAAAAAA
1 TTATATATTATATTTTCAAAAT-CATTTTC-AAAAAA
446908 TTATATATTATAGTTTTCAAAAAT-ATTTTCAAAAA
1 TTATATATTATA-TTTTC-AAAATCATTTTCAAAAA
446943 GTACACTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 5 0.16
37 16 0.52
38 5 0.16
39 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (35 bp):
TTATATATTATATTTTCAAAATCATTTTCAAAAAA
Found at i:454041 original size:13 final size:13
Alignment explanation
Indices: 454004--454047 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
453994 AATAAATAAT
454004 AATAATAAACA-AA
1 AATAATAAA-AGAA
*
454017 AATAATACAAGAA
1 AATAATAAAAGAA
454030 AATAATAAAAGAA
1 AATAATAAAAGAA
454043 AATAA
1 AATAA
454048 AATGAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 1 0.04
13 27 0.96
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (13 bp):
AATAATAAAAGAA
Found at i:454057 original size:19 final size:18
Alignment explanation
Indices: 454028--454063 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
454018 ATAATACAAG
*
454028 AAAATAATAAAAGAAAAT
1 AAAATAATAAAACAAAAT
454046 AAAATGAATAAAACAAAA
1 AAAAT-AATAAAACAAAA
454064 AGTAAAGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.14
Consensus pattern (18 bp):
AAAATAATAAAACAAAAT
Found at i:455416 original size:30 final size:31
Alignment explanation
Indices: 455382--455450 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
455372 TTAAAATTAT
*
455382 ATTATATACTTTTTAAAAAATG-TTTT-CAAA
1 ATTATATA-GTTTTAAAAAATGTTTTTACAAA
* *
455412 ATTATATAGTTTTCAAAAATGTTTTTAGAAA
1 ATTATATAGTTTTAAAAAATGTTTTTACAAA
455443 ATTATATA
1 ATTATATA
455451 TTATATATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 11 0.32
30 12 0.35
31 11 0.32
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (31 bp):
ATTATATAGTTTTAAAAAATGTTTTTACAAA
Found at i:455530 original size:36 final size:36
Alignment explanation
Indices: 455489--455731 Score: 193
Period size: 36 Copynumber: 6.9 Consensus size: 36
455479 TATATAATAT
*
455489 ATGTTTTTAAAACTATATATTATATATACTTTCAAA
1 ATGTTTTAAAAACTATATATTATATATACTTTCAAA
* **
455525 ATGTTTTAAAAACTATATAATATATAAATGTTTTCAAAA
1 ATGTTTTAAAAACTATAT-AT-TATATATACTTTC-AAA
* *
455564 ATGTTTT----A-TATA-A-TATATGT--TTTTAAA
1 ATGTTTTAAAAACTATATATTATATATACTTTCAAA
455591 ATGTTTTAAAAACTATATATTATATATACTTTCAAA
1 ATGTTTTAAAAACTATATATTATATATACTTTCAAA
* **
455627 ATGTTTTAAAAACTATATAATATATAAATGTTTTCAAA
1 ATGTTTTAAAAACTATAT-AT-TATATATACTTTCAAA
* * * * * * *
455665 ATATTTTTCAAAACCATATACTATATAGATTTTAAAA
1 AT-GTTTTAAAAACTATATATTATATATACTTTCAAA
*
455702 ACGTTTTCAAAAACTATATA--ATATATACTT
1 ATGTTTT-AAAAACTATATATTATATATACTT
455732 ATTTTCGAAA
Statistics
Matches: 165, Mismatches: 26, Indels: 33
0.74 0.12 0.15
Matches are distributed among these distances:
27 10 0.06
28 3 0.02
30 5 0.03
31 1 0.01
32 5 0.03
33 1 0.01
34 10 0.06
35 9 0.05
36 45 0.27
37 27 0.16
38 26 0.16
39 23 0.14
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
ATGTTTTAAAAACTATATATTATATATACTTTCAAA
Found at i:455574 original size:27 final size:27
Alignment explanation
Indices: 455523--455598 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
455513 TATACTTTCA
* * *
455523 AAATGTTTTAAAAACTATATAATAT-AT
1 AAATGTTTTAAAAA-TGTTTTATATAAT
455550 AAATGTTTTCAAAAATGTTTTATATAAT
1 AAATGTTTT-AAAAATGTTTTATATAAT
* *
455578 ATATGTTTTTAAAATGTTTTA
1 AAATGTTTTAAAAATGTTTTA
455599 AAAACTATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 27 0.64
28 15 0.36
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (27 bp):
AAATGTTTTAAAAATGTTTTATATAAT
Found at i:455607 original size:27 final size:28
Alignment explanation
Indices: 455552--455608 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
455542 TAATATATAA
*
455552 ATGTTTTCAAAAATGTTTTATATAATAT
1 ATGTTTTCAAAAATGTTTTATAAAATAT
*
455580 ATGTTTT-TAAAATGTTTTA-AAAACTAT
1 ATGTTTTCAAAAATGTTTTATAAAA-TAT
455607 AT
1 AT
455609 ATTATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 3 0.12
27 16 0.62
28 7 0.27
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (28 bp):
ATGTTTTCAAAAATGTTTTATAAAATAT
Found at i:455617 original size:75 final size:75
Alignment explanation
Indices: 455538--455728 Score: 199
Period size: 75 Copynumber: 2.5 Consensus size: 75
455528 TTTTAAAAAC
* * * * * *
455538 TATATAATATATAAATGTTTTCAAAAA-TGTTTTATATAATATATGTTTTTAAAAT-GTTTTAAA
1 TATATAATTTA-AAATGTTTTCAAAAACTATATAATAT-ATAAATGTTTTCAAAATAGTTTTAAA
* *
455601 AACTATATATTA
64 AACCATATACTA
* * *
455613 TATATACTTTCAAAATGTTTT-AAAAACTATATAATATATAAATGTTTTCAAAATATTTTTCAAA
1 TATATAATTT-AAAATGTTTTCAAAAACTATATAATATATAAATGTTTTCAAAATAGTTTTAAAA
455677 ACCATATACTA
65 ACCATATACTA
* * *
455688 TATAGATTTTAAAAACGTTTTCAAAAACTATATAATATATA
1 TATATAATTT-AAAATGTTTTCAAAAACTATATAATATATA
455729 CTTATTTTCG
Statistics
Matches: 97, Mismatches: 15, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
74 20 0.21
75 57 0.59
76 20 0.21
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (75 bp):
TATATAATTTAAAATGTTTTCAAAAACTATATAATATATAAATGTTTTCAAAATAGTTTTAAAAA
CCATATACTA
Found at i:455773 original size:76 final size:75
Alignment explanation
Indices: 455594--455808 Score: 186
Period size: 76 Copynumber: 2.8 Consensus size: 75
455584 TTTTAAAATG
* * * * * * *
455594 TTTTAAAAACTATATATTATATATACTTTCAAAATGTTTT-AAAAACTATATAATATATAAATGT
1 TTTTCAAAAC-ATATACTATATATATTTTAAAAACGTTTTCAAAAACTATATAATATATACATAT
455658 TTTCAAAATAT
65 TTTCAAAATAT
* *
455669 TTTTCAAAACCATATACTATATAGATTTTAAAAACGTTTTCAAAAACTATATAATATATACTTAT
1 TTTTCAAAA-CATATACTATATATATTTTAAAAACGTTTTCAAAAACTATATAATATATACATAT
*
455734 TTTCGAAAATCGTT
65 TTTC-AAAAT--AT
* ** * * *
455748 TTTTCGAAAA-TTATAC-AT-TATATTTTGTCAAACATTTTCAAAAACTGTATTACTATATACA
1 TTTTC-AAAACATATACTATATATATTTT-AAAAACGTTTTCAAAAACTATA-TAATATATACA
455809 CATATATATA
Statistics
Matches: 114, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
75 32 0.28
76 33 0.29
77 25 0.22
78 14 0.12
79 6 0.05
80 4 0.04
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (75 bp):
TTTTCAAAACATATACTATATATATTTTAAAAACGTTTTCAAAAACTATATAATATATACATATT
TTCAAAATAT
Found at i:455815 original size:2 final size:2
Alignment explanation
Indices: 455810--455860 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
455800 CTATATACAC
* *
455810 AT AT AT AT AT AT A- AT A- AA AT AT AT AT AT AT AT AT AGG A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
455850 AT AT AT AT AT A
1 AT AT AT AT AT A
455861 AACAAAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 3 0.07
2 39 0.91
3 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (2 bp):
AT
Found at i:455835 original size:20 final size:20
Alignment explanation
Indices: 455810--455860 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
455800 CTATATACAC
455810 ATATATATATATA-ATA-AA
1 ATATATATATATATATAGAA
*
455828 ATATATATATATATATAGGA
1 ATATATATATATATATAGAA
455848 ATATATATATATA
1 ATATATATATATA
455861 AACAAAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 13 0.43
19 3 0.10
20 14 0.47
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (20 bp):
ATATATATATATATATAGAA
Found at i:456589 original size:84 final size:84
Alignment explanation
Indices: 456458--457347 Score: 694
Period size: 84 Copynumber: 10.8 Consensus size: 84
456448 GCTATGTTGT
* * * *
456458 AAATGATGTG-CCTCGCAGTTGAGCGTAGTCGAACTCGAAGGTCCTTTGGAGATAGATAACCCTT
1 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGT-CTTTGGAGACAGATAACCCTT
* * * *
456522 CTAGCCTTGAGTTATATTGT
65 CTAGACTTAAGTTATACTGC
* * * ** * *
456542 AAATGATGTACCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTT-G-G-CAGCTAGCCCTTC
1 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGAGACAGATAACCCTTC
* *
456604 TCGACTTAAGCTATACTGC
66 TAGACTTAAGTTATACTGC
* * * * ** * * *
456623 AAATGATGT-ACCTTGGAGCTGAGCGTAATCGAACTCAAAGGTCTTTCGTTGGCAAATAGCCCTT
1 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTT-GGAGACAGATAACCCTT
* * * * *
456687 CTTGCCTTGAGCTATATTGC
65 CTAGACTTAAGTTATACTGC
* * *
456707 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG-GGAGTCTTT-G-G-CAGATAGCCCTT
1 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAG-GTCTTTGGAGACAGATAACCCTT
* * * *
456768 ATCGACTTAAGCTATGCTGC
65 CTAGACTTAAGTTATACTGC
* * * ** * *
456788 AAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTC-AGAGGTCTTTTGTTGGCAGACAACCCT
1 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGA-AGGTC-TTTGGAGACAGATAACCCT
* *
456851 TCTAGACTTAAGTTGTGCTGC
64 TCTAGACTTAAGTTATACTGC
* * * * * *
456872 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTGACAGATAACCCTTC
1 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGAGACAGATAACCCTTC
* * *
456936 TAGCCTTGAGTTATGA-TGT
66 TAGACTTAAGTTAT-ACTGC
* * * *
456955 AAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGAGGTCTTT-G-G-CAGATAGCCCTTC
1 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGAGACAGATAACCCTTC
* *
457017 TCGACTTAAGTTATGCTGC
66 TAGACTTAAGTTATACTGC
* * * * ** * *
457036 AAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTT
1 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGGAGACAGATAACCCTT
*
457100 CTAGACTTAAGTTGTACTGC
65 CTAGACTTAAGTTATACTGC
* * * * *
457120 AAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTC
1 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGAGACAGATAACCCTTC
* * ** *
457184 TAGCCTTGAGTTATGTTGT
66 TAGACTTAAGTTATACTGC
* * * ** *
457203 AAATGATATGCCCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCTTT-G-G-CAGATAGCCCTTC
1 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGAGACAGATAACCCTTC
* * *
457265 TCGACTTAAGTTATGCTGT
66 TAGACTTAAGTTATACTGC
* * * *
457284 AAATGATATG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTG-G-CAGATAGCCCTT
1 AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTG-GAGACAGATAACCCTT
457346 CT
65 CT
457348 GGCCTTGAGC
Statistics
Matches: 656, Mismatches: 124, Indels: 54
0.79 0.15 0.06
Matches are distributed among these distances:
80 103 0.16
81 153 0.23
82 20 0.03
83 96 0.15
84 229 0.35
85 55 0.08
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
AAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGAGACAGATAACCCTTC
TAGACTTAAGTTATACTGC
Found at i:457006 original size:164 final size:162
Alignment explanation
Indices: 456450--457372 Score: 691
Period size: 165 Copynumber: 5.6 Consensus size: 162
456440 TGCCTTGGGC
* * * * * * *
456450 TATGTTGTAAATGATGTGCCTCGCAGTTGAGCGTAGTCGAACTCGAAGGTCCTTTGGAGATAGAT
1 TATGATGTAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGT-CTTT-G-G-CAGAT
* * ** * * * * * * * *
456515 AACCCTTCTAGCCTTGAGTTATATTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCAAACTCG
62 AACCCTTCTAGACTTAAGTTATGCTGCAAATGATAT-GCCTTGGAGCTGAGCGTAGTCGAACTCG
** * * * *
456580 GGGGTCTTT-G-GCAGCTAGCCCTTCTCGACTTAAGC
126 AAGGTCTTTGGTGCAGATAACCCTTCTAGACTTAAGT
* * * * *
456615 TAT-ACTGCAAATGATGTACCTTGGAGCTGAGCGTAATCGAACTCAAAGGTCTTTCGTTGGCAAA
1 TATGA-TGTAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTC--T--TTGGCAGA
* * * * * ** * * * * *
456679 TAGCCCTTCTTGCCTTGAGCTATATTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC
61 TAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTC
* * * * *
456744 G-GGAGTCTTT-G-GCAGATAGCCCTTATCGACTTAAGC
125 GAAG-GTCTTTGGTGCAGATAACCCTTCTAGACTTAAGT
* * * *
456780 TATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTC-AGAGGTCTTTTGTTGGCAG
1 TATGATGTAAATGATATGCC-TTGGAGCTGAGCGTAATCGAACTCGA-AGGTC---T-TTGGCAG
* *
456843 ACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
60 ATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
* * *
456908 GAAGATCTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
125 GAAGGTCTTTGGTG-CAGATAACCCTTCTAGACTTAAGT
* * * * *
456947 TATGATGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGAGGTCTTTGGCAGATAGC
1 TATGATGTAAATGATATG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAAC
* * *
457012 CCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAG
65 CCTTCTAGACTTAAGTTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
457076 GTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGT
129 GTC-TTTGGT-GCAGATAACCCTTCTAGACTTAAGT
* * *
457112 TGT-ACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
1 TATGA-TGTAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTT-G-G-CAGAT
* * * * * * * * *
457176 AACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGTTGAGTGTAATCGAACTCG
62 AACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCG
** * *
457241 GGGGTCTTT-G-GCAGATAGCCCTTCTCGACTTAAGT
126 AAGGTCTTTGGTGCAGATAACCCTTCTAGACTTAAGT
* *
457276 TATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTGGCAGATAG
1 TATGATGTAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTC-TT-TGGCAGATAA
* * * * *
457341 CCCTTCTGGCCTTGAGCTAAGCTGCAAATGAT
64 CCCTTCTAGACTTAAGTTATGCTGCAAATGAT
457373 TTGTTTAAAA
Statistics
Matches: 629, Mismatches: 99, Indels: 62
0.80 0.13 0.08
Matches are distributed among these distances:
163 33 0.05
164 202 0.32
165 259 0.41
166 11 0.02
167 74 0.12
168 50 0.08
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (162 bp):
TATGATGTAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAGATAACC
CTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
CTTTGGTGCAGATAACCCTTCTAGACTTAAGT
Found at i:457026 original size:248 final size:247
Alignment explanation
Indices: 456598--457347 Score: 1159
Period size: 248 Copynumber: 3.0 Consensus size: 247
456588 TGGCAGCTAG
* * * * * * *
456598 CCCTTCTCGACTTAAGCTATACTGCAAATGATGTACCTTGGAGCTGAGCGTAATCGAACTCAAAG
1 CCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * * * * * * *
456663 GTCTTTCGTTGGCAAATAGCCCTTCTTGCCTTGAGCTAT-ATTGCAAATGATGTGCCCTCGAAGC
66 GTCTTT-GGTGACAGATAACCCTTCTAGCCTTGAGTTATGA-TGTAAATGATATGCCCTCGAAGC
* *
456727 TGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTATCGACTTAAGCTATGCTGCAAAT
129 TGAGTGTAATCGAACTCGGG-GTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAAT
456792 GATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAGAGGTCTTTTGTTGGCAGACAA
193 GATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAGAGGTCTTTTGTTGGCAGACAA
*
456847 CCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
456912 ATCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATATGCCCTCGAAGCTG
66 GTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATATGCCCTCGAAGCTG
456977 AGTGTAATCGAACTCGGAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGA
131 AGTGTAATCGAACTCGG-GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGA
*
457042 TGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAA
195 TGTGCCGTTGAGCTGAGCGTAGTCGAACTCAGAGGTCTTTTGTTGGCAGACAA
457095 CCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* *
457160 GTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGTTG
66 GTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATATGCCCTCGAAGCTG
*
457225 AGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGTAAATGA
131 AGTGTAATCGAACTC-GGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGA
* * * *
457290 TATGCC-TTGGAGCTGAGCGTAATCGAACTC-GAAGGTC-TTTG-TGGCAGATAG
195 TGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAG-AGGTCTTTTGTTGGCAGACAA
457341 CCCTTCT
1 CCCTTCT
457348 GGCCTTGAGC
Statistics
Matches: 466, Mismatches: 30, Indels: 13
0.92 0.06 0.03
Matches are distributed among these distances:
246 15 0.03
247 6 0.01
248 379 0.81
249 66 0.14
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (247 bp):
CCCTTCTAGACTTAAGTTGTACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATATGCCCTCGAAGCTG
AGTGTAATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGAT
GTGCCGTTGAGCTGAGCGTAGTCGAACTCAGAGGTCTTTTGTTGGCAGACAA
Found at i:463965 original size:30 final size:31
Alignment explanation
Indices: 463930--463998 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
463920 GAAATTATAT
*
463930 ATTATATACTTTTTAAAAGATG-TTTT-CAAA
1 ATTATATACTTTTCAAAA-ATGTTTTTACAAA
* *
463960 ATTATATAGTTTTCAAAAATGTTTTTAGAAA
1 ATTATATACTTTTCAAAAATGTTTTTACAAA
463991 ATTATATA
1 ATTATATA
463999 TTATATATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 20 0.59
31 11 0.32
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (31 bp):
ATTATATACTTTTCAAAAATGTTTTTACAAA
Found at i:464078 original size:36 final size:36
Alignment explanation
Indices: 464037--464279 Score: 193
Period size: 36 Copynumber: 6.9 Consensus size: 36
464027 TATATAATAT
*
464037 ATGTTTTTAAAACTATATATTATATATACTTTCAAA
1 ATGTTTTAAAAACTATATATTATATATACTTTCAAA
* **
464073 ATGTTTTAAAAACTATATAATATATAAATGTTTTCAAAA
1 ATGTTTTAAAAACTATAT-AT-TATATATACTTTC-AAA
* *
464112 ATGTTTT----A-TATA-A-TATATGT--TTTTAAA
1 ATGTTTTAAAAACTATATATTATATATACTTTCAAA
464139 ATGTTTTAAAAACTATATATTATATATACTTTCAAA
1 ATGTTTTAAAAACTATATATTATATATACTTTCAAA
* **
464175 ATGTTTTAAAAACTATATAATATATAAATGTTTTCAAA
1 ATGTTTTAAAAACTATAT-AT-TATATATACTTTCAAA
* * * * * * *
464213 ATATTTTTCAAAACCATATACTATATAGATTTTAAAA
1 AT-GTTTTAAAAACTATATATTATATATACTTTCAAA
*
464250 ACGTTTTCAAAAACTATATA--ATATATACTT
1 ATGTTTT-AAAAACTATATATTATATATACTT
464280 ATTTTCGAAA
Statistics
Matches: 165, Mismatches: 26, Indels: 33
0.74 0.12 0.15
Matches are distributed among these distances:
27 10 0.06
28 3 0.02
30 5 0.03
31 1 0.01
32 5 0.03
33 1 0.01
34 10 0.06
35 9 0.05
36 45 0.27
37 27 0.16
38 26 0.16
39 23 0.14
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
ATGTTTTAAAAACTATATATTATATATACTTTCAAA
Found at i:464122 original size:27 final size:27
Alignment explanation
Indices: 464071--464146 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
464061 TATACTTTCA
* * *
464071 AAATGTTTTAAAAACTATATAATAT-AT
1 AAATGTTTTAAAAA-TGTTTTATATAAT
464098 AAATGTTTTCAAAAATGTTTTATATAAT
1 AAATGTTTT-AAAAATGTTTTATATAAT
* *
464126 ATATGTTTTTAAAATGTTTTA
1 AAATGTTTTAAAAATGTTTTA
464147 AAAACTATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 27 0.64
28 15 0.36
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (27 bp):
AAATGTTTTAAAAATGTTTTATATAAT
Found at i:464155 original size:27 final size:28
Alignment explanation
Indices: 464100--464156 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
464090 TAATATATAA
*
464100 ATGTTTTCAAAAATGTTTTATATAATAT
1 ATGTTTTCAAAAATGTTTTATAAAATAT
*
464128 ATGTTTT-TAAAATGTTTTA-AAAACTAT
1 ATGTTTTCAAAAATGTTTTATAAAA-TAT
464155 AT
1 AT
464157 ATTATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 3 0.12
27 16 0.62
28 7 0.27
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (28 bp):
ATGTTTTCAAAAATGTTTTATAAAATAT
Found at i:464165 original size:75 final size:75
Alignment explanation
Indices: 464086--464276 Score: 199
Period size: 75 Copynumber: 2.5 Consensus size: 75
464076 TTTTAAAAAC
* * * * * *
464086 TATATAATATATAAATGTTTTCAAAAA-TGTTTTATATAATATATGTTTTTAAAAT-GTTTTAAA
1 TATATAATTTA-AAATGTTTTCAAAAACTATATAATAT-ATAAATGTTTTCAAAATAGTTTTAAA
* *
464149 AACTATATATTA
64 AACCATATACTA
* * *
464161 TATATACTTTCAAAATGTTTT-AAAAACTATATAATATATAAATGTTTTCAAAATATTTTTCAAA
1 TATATAATTT-AAAATGTTTTCAAAAACTATATAATATATAAATGTTTTCAAAATAGTTTTAAAA
464225 ACCATATACTA
65 ACCATATACTA
* * *
464236 TATAGATTTTAAAAACGTTTTCAAAAACTATATAATATATA
1 TATATAATTT-AAAATGTTTTCAAAAACTATATAATATATA
464277 CTTATTTTCG
Statistics
Matches: 97, Mismatches: 15, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
74 20 0.21
75 57 0.59
76 20 0.21
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (75 bp):
TATATAATTTAAAATGTTTTCAAAAACTATATAATATATAAATGTTTTCAAAATAGTTTTAAAAA
CCATATACTA
Found at i:464321 original size:76 final size:76
Alignment explanation
Indices: 464142--464360 Score: 203
Period size: 75 Copynumber: 2.9 Consensus size: 76
464132 TTTTAAAATG
* * * * * *
464142 TTTTAAAAACTATATATTATATATACTTTCAAAATGTTTT-AAAAACTATATAATATATAAATGT
1 TTTTCAAAACCATATACTATATATATTTTCAAAACGTTTTCAAAAACTATATAATATATAAATAT
464206 TTTCAAAATAT
66 TTTCAAAATAT
* * **
464217 TTTTCAAAACCATATACTATATAGATTTTAAAAACGTTTTCAAAAACTATATAATATATACTTAT
1 TTTTCAAAACCATATACTATATATATTTTCAAAACGTTTTCAAAAACTATATAATATATAAATAT
*
464282 TTTCGAAAATCGT
66 TTTC-AAAAT-AT
* * * * * *
464295 TTTTCTGAAA-CTTATAC-AT-TATATTTTGTCAAAACATTTTCAAAAACTGTATTACTATATAT
1 TTTTC-AAAACCATATACTATATATA-TTT-TCAAAACGTTTTCAAAAACTATA-TAATATATAA
464357 ATAT
62 ATAT
464361 ATAAACAAAA
Statistics
Matches: 117, Mismatches: 20, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
75 33 0.28
76 28 0.24
77 10 0.09
78 32 0.27
79 14 0.12
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (76 bp):
TTTTCAAAACCATATACTATATATATTTTCAAAACGTTTTCAAAAACTATATAATATATAAATAT
TTTCAAAATAT
Found at i:481162 original size:40 final size:41
Alignment explanation
Indices: 481118--481221 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 41
481108 AAGGTTTTTT
481118 AAAAAATAATATAATAATAATAA-ATAAATAAACGAAAATAA
1 AAAAAATAATATAATAATAATAAGATAAAT-AACGAAAATAA
* * * * *
481159 AAAAAATATATATAA-AGTTATAAGATATATTACGTAAAT-A
1 AAAAAATA-ATATAATAATAATAAGATAAATAACGAAAATAA
*
481199 AAAAAATAATCA-AATAAAAATAA
1 AAAAAATAAT-ATAATAATAATAA
481222 TTAAGAATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
39 4 0.08
40 15 0.29
41 21 0.41
42 11 0.22
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.25
Consensus pattern (41 bp):
AAAAAATAATATAATAATAATAAGATAAATAACGAAAATAA
Found at i:481887 original size:36 final size:35
Alignment explanation
Indices: 481841--481940 Score: 161
Period size: 33 Copynumber: 2.9 Consensus size: 35
481831 ATAGTATAAC
481841 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG--AAAT
481878 T-TATCCTATTTTTAGGAGTTTGAATCCT--AAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAT
481910 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
481941 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
32 5 0.08
33 27 0.45
36 27 0.45
37 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAT
Found at i:482761 original size:105 final size:105
Alignment explanation
Indices: 482465--483187 Score: 1024
Period size: 105 Copynumber: 7.0 Consensus size: 105
482455 CATTGTTCCA
* * * * ** * *
482465 AGTCTAATATCCTCCGTCGTGAAGTTGAAATTGGCTGTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGAGAAGTTG-TTGTTGACAA
* * * *
482529 CCAGTC-GTCCCTTCGTTGTGAAGTTGAAC-TGTG-TGTCTCG
64 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
482569 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
*
482629 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
482669 AATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
* *
482734 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTATGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
482774 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
*
482838 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
482878 AGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
482943 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
482983 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
*
483048 AGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
483088 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATTGAGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
* *
483152 AGTC-GT-CCTTCGT-GTGAAGTTTAACTTGTGTTGTCT
66 AG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
483188 CTCGAGTGCC
Statistics
Matches: 569, Mismatches: 39, Indels: 24
0.90 0.06 0.04
Matches are distributed among these distances:
97 1 0.00
98 35 0.06
99 2 0.00
100 44 0.08
101 3 0.01
102 24 0.04
103 9 0.02
104 158 0.28
105 293 0.51
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:482860 original size:209 final size:206
Alignment explanation
Indices: 482470--483179 Score: 983
Period size: 209 Copynumber: 3.4 Consensus size: 206
482460 TTCCAAGTCT
* * * ** * *
482470 AATATCCTCCGTCGTGAAGTTGAAATTGGCTGTG-GAACCGGGAAATTGTTTGTTGACAACCAGT
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGAGAAGTTG-TTGTTGACAACCAGT
* *
482534 CGTCCCTTCGTTGTGAAGTTGAAC-TG-TGTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGA
64 CGTCCCTTCGTCGTGAAGTTGAACTTGCT-TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
** * *
482597 AATTGAATCTGAA-T-GAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
128 AATTGGCTCTGAATTGGAAGTTGTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
*
482660 ATTGTCTGGAATCC
193 GTTGTCTGGAATCC
* * *
482674 AATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAG-CG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAACCAGTC-
*
482738 GTCCCTTCGTCGTGAAGTTGAACTTGCATTGTATGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
65 GTCCCTTCGTCGTGAAGTTGAACTTGC-TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
482803 ATTGGCTCTGAGATTGGGAAGTTGTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
129 ATTGGCTCTGA-ATT-GGAAGTTGTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
482868 CGTTGTCT-GAAGTCC
192 CGTTGTCTGGAA-TCC
* * * *
482883 AATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTGTTGACAAGCAG-CG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAACCAGTC-
482947 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
65 GTCCCTTCGTCGTGAAGTTGAACTTGC-TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
* *
483012 ATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTCCCTTCGCCGTGAAGTTGAACTT
129 ATTGGCTCTG-AATTG-GAAGTTG-TGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
*
483077 GCGTTGTCTGGAGTCC
191 GCGTTGTCTGGAATCC
*
483093 AATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATTGAGAAGTTGTTGTTGACAACCAGTCG
1 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAACCAGTCG
*
483157 T-CCTTCGT-GTGAAGTTTAACTTG
66 TCCCTTCGTCGTGAAGTTGAACTTG
483180 TGTTGTCTCT
Statistics
Matches: 460, Mismatches: 31, Indels: 27
0.89 0.06 0.05
Matches are distributed among these distances:
202 1 0.00
203 35 0.08
204 41 0.09
205 44 0.10
206 2 0.00
207 15 0.03
208 11 0.02
209 224 0.49
210 85 0.18
211 2 0.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (206 bp):
AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGAGAAGTTGTTGTTGACAACCAGTCG
TCCCTTCGTCGTGAAGTTGAACTTGCTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
TGGCTCTGAATTGGAAGTTGTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT
GTCTGGAATCC
Found at i:483018 original size:314 final size:309
Alignment explanation
Indices: 482465--483188 Score: 1068
Period size: 314 Copynumber: 2.3 Consensus size: 309
482455 CATTGTTCCA
* * * * ** *
482465 AGTCTAATATCCTCCGTCGTGAAGTTGAAATTGGCTGTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
482529 CCAGTCGTCCCTTCGTTGTGAAGTTGAAC-TGTG-TGTCTCGAGTCCAATATCCTTCGTTGTGAA
64 CCAGTCGTCCCTTCG-TGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
482592 GTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
128 GTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* *
482657 TGCATTGTCTGGAATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAGTTG
193 TGCATTGTCTGGAATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAAATTGAGAAGTTG
*
482722 TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTATGG
258 TTGTTGACAAGCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCATTGTATGG
*
482774 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
* *
482838 AG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAAGTCCAATATCCTTTGTTGTGAA
66 AGTC-GTCCCTTCGT-GTGAAGTTGAACTTGTGTTGTCTCG-AGTCCAATATCCTTCGTTGTGAA
** *
482901 GTTGAAATTGGCTCTGAAATTAAGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
128 GTTGAAATTGAATCTG-AA-T--GAAATT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
* * *
482966 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGA
188 GAACTTGCATTGTCTGGAATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAAATTGAGA
* * *
483031 AGTTGTTGTTGACAGGCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGG
253 AGTTGTTGTTGACAAGCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCATTGTATGG
* *
483088 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATTGAGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
483152 AGTCGT-CCTTCGTGTGAAGTTTAACTTGTGTTGTCTC
66 AGTCGTCCCTTCGTGTGAAGTTGAACTTGTGTTGTCTC
483189 TCGAGTGCCA
Statistics
Matches: 374, Mismatches: 27, Indels: 24
0.88 0.06 0.06
Matches are distributed among these distances:
306 2 0.01
307 33 0.09
308 4 0.01
309 85 0.23
310 3 0.01
311 1 0.00
312 21 0.06
313 23 0.06
314 201 0.54
315 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (309 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
AGTCGTCCCTTCGTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
ATTGTCTGGAATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAAATTGAGAAGTTGTTG
TTGACAAGCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCATTGTATGG
Found at i:483914 original size:67 final size:65
Alignment explanation
Indices: 483820--483976 Score: 199
Period size: 67 Copynumber: 2.4 Consensus size: 65
483810 AAAGATATCA
* * **
483820 TTGTTTCATGAGAAATGGTCTCAAGGGAAACAAAATTATG-TTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAATTGTCTCAAGGGAAACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
483884 TT
64 TT
* * *
483886 TGTGTTTCAAGAGTAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAATTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
483951 T
65 T
* *
483952 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAATTGTCTCAAG
483977 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 21 0.27
66 6 0.08
67 52 0.66
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.33
Consensus pattern (65 bp):
TTGTTTCAAGAGAAATTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:484002 original size:35 final size:36
Alignment explanation
Indices: 483951--484226 Score: 277
Period size: 36 Copynumber: 7.9 Consensus size: 36
483941 ATTCAAAGAT
* *
483951 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
**
483987 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * *
484022 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * *
484059 TTTGTTTCAA-AGAAAACATAT-TC---A-A-A--TAT
1 TTTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACGAAA
*
484088 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * *
484123 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* *
484159 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* *
484195 TTTTTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
484227 AAAACTCTTC
Statistics
Matches: 197, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 17 0.09
30 1 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 64 0.32
36 77 0.39
37 31 0.16
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
Found at i:484061 original size:137 final size:136
Alignment explanation
Indices: 483903--484211 Score: 406
Period size: 137 Copynumber: 2.3 Consensus size: 136
483893 CAAGAGTAAT
* *
483903 TGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
* * *
483968 TGTCTCAAGATAGACGAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTAGTTCCA
66 TGTCTCAAGAGAGAC-AAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCA
484032 AAAGAAAC
129 AAAGAAAC
* * * * * *
484040 TGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
* * * * * *
484105 TGTCTCAAGAGAGACAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTCAAG
66 TGTCTCAAGAGAGACAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAA
*
484170 AGAAAT
131 AGAAAC
*
484176 TGTCTCAAGAGAGACAAAATTT-TTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTT-AAGGGAAAC
484212 TGTCTCAAGA
Statistics
Matches: 147, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
135 3 0.02
136 43 0.29
137 101 0.69
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (136 bp):
TGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
TGTCTCAAGAGAGACAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAA
AGAAAC
Found at i:484162 original size:100 final size:103
Alignment explanation
Indices: 483987--484174 Score: 283
Period size: 100 Copynumber: 1.9 Consensus size: 103
483977 ATAGACGAAA
*
483987 TTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
484052 GACGAAATTTGTTTCAA-AGAAAACATATTCAAATATT
66 GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
* * * * ** *
484089 TTGTTTCAAGGGAAACTGTCTCAAGAGAGA-CAAATTTA-TTTCAAGGGAAACTGTCTCAAGATA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
484152 GACGAAATTTGTTTCAAGAGAAA
66 GACGAAATTTGTTTCAAGAGAAA
484175 TTGTCTCAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
100 37 0.48
101 11 0.14
102 29 0.38
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (103 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
Found at i:484183 original size:15 final size:16
Alignment explanation
Indices: 484155--484187 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
484145 CAAGATAGAC
*
484155 GAAATTTGTTTCAAGA
1 GAAATTTGTCTCAAGA
484171 GAAA-TTGTCTCAAGA
1 GAAATTTGTCTCAAGA
484186 GA
1 GA
484188 GACAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (16 bp):
GAAATTTGTCTCAAGA
Found at i:484253 original size:71 final size:72
Alignment explanation
Indices: 484093--484264 Score: 215
Period size: 71 Copynumber: 2.4 Consensus size: 72
484083 AATATTTTGT
* *
484093 TTCAAGGGAAACTGTCTCAAGAGAGAC-AAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACGA
** *
484157 AATTTGT
66 AAACTGC
* *
484164 TTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTTTTTCAAGGGAAACTGTCTCAAGAGAGAC-A
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACGA
484228 AAACT-C
66 AAACTGC
* * * *
484234 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAGAG-AAACTGTCTCAAGAGAGACAAA
484265 TCTTGTTTAA
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
70 6 0.07
71 48 0.55
72 33 0.38
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (72 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACGA
AAACTGC
Found at i:484731 original size:18 final size:18
Alignment explanation
Indices: 484704--484739 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
484694 TGTTGAATCC
* *
484704 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
484722 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
484740 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:485175 original size:22 final size:22
Alignment explanation
Indices: 485150--485204 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
485140 TTGTGTTTGG
485150 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
485172 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
485194 TCAAAGGTTTG
1 TCAAAGGTTTG
485205 ATGGGATAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:485845 original size:29 final size:28
Alignment explanation
Indices: 485813--485872 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
485803 TTGCATGTGC
* *
485813 TTTTTGTTCCTCTTTCTTTTTGATTCTTG
1 TTTTTGTTCCTCTTTCCTTTTG-TTCGTG
* * *
485842 TTTTTTTTCTTTTTTCCTTTTGTTCGTG
1 TTTTTGTTCCTCTTTCCTTTTGTTCGTG
485870 TTT
1 TTT
485873 CTCTTTTTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.02, C:0.15, G:0.10, T:0.73
Consensus pattern (28 bp):
TTTTTGTTCCTCTTTCCTTTTGTTCGTG
Found at i:485856 original size:7 final size:7
Alignment explanation
Indices: 485844--485917 Score: 62
Period size: 7 Copynumber: 10.3 Consensus size: 7
485834 GATTCTTGTT
485844 TTTTTTC
1 TTTTTTC
485851 TTTTTTCC
1 TTTTTT-C
485859 TTTTGTTC
1 TTTT-TTC
* *
485867 GTGTTTC
1 TTTTTTC
485874 TCTTTTTC
1 T-TTTTTC
485882 TTTTTTC
1 TTTTTTC
485889 TTTGTTT-
1 TTT-TTTC
*
485896 TTTTTGC
1 TTTTTTC
*
485903 TTCTTT-
1 TTTTTTC
485909 TTTTTTC
1 TTTTTTC
485916 TT
1 TT
485918 CTTGATTGGA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
6 7 0.13
7 27 0.51
8 17 0.32
9 2 0.04
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (7 bp):
TTTTTTC
Found at i:485918 original size:13 final size:13
Alignment explanation
Indices: 485882--485920 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
485872 TCTCTTTTTC
485882 TTTTTTCTT-TGTT
1 TTTTTTCTTCT-TT
485895 TTTTTTGCTTCTTT
1 TTTTTT-CTTCTTT
485909 TTTTTTCTTCTT
1 TTTTTTCTTCTT
485921 GATTGGATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 11 0.46
15 1 0.04
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (13 bp):
TTTTTTCTTCTTT
Done.