Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008689.1 Hibiscus syriacus cultivar Beakdansim tig00111715_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: 959342
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 3 of 4
Found at i:535755 original size:30 final size:30
Alignment explanation
Indices: 535699--535881 Score: 278
Period size: 30 Copynumber: 6.1 Consensus size: 30
535689 GAAGGACCTA
* * * *
535699 TCCAGAGGTCACACAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
535728 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
535758 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
535788 TCTAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
535818 TCCAGAGGTCATAAAGATCCTCGCTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
** *
535848 TCCAGATATCATAAAGATCCTCGGTAAGTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
535878 TCCA
1 TCCA
535882 TATGTTCCTT
Statistics
Matches: 142, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
29 15 0.11
30 127 0.89
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:535911 original size:31 final size:32
Alignment explanation
Indices: 535876--535965 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
535866 CCTCGGTAAG
* *
535876 TGTCCATATGTTCCTTAGAACATAGGT-ATAC
1 TGTCCATATGTTCCATAGAACATAGGTAAAAC
* *
535907 TGTCCATATGTCTCAAAAG-ACATAGGTAAAAC
1 TGTCCATATGT-TCCATAGAACATAGGTAAAAC
*
535939 TGTCCATATGTTCCGTAGAACATAGGT
1 TGTCCATATGTTCCATAGAACATAGGT
535966 CCTCGACTCT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
31 23 0.47
32 26 0.53
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (32 bp):
TGTCCATATGTTCCATAGAACATAGGTAAAAC
Found at i:537186 original size:21 final size:21
Alignment explanation
Indices: 537160--537201 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
537150 AATTCTGTCG
* *
537160 TTTGAAGGGGTATCGGTTCCC
1 TTTGAAGGGGTACCGATTCCC
*
537181 TTTGAATGGGTACCGATTCCC
1 TTTGAAGGGGTACCGATTCCC
537202 CTTGCCCAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (21 bp):
TTTGAAGGGGTACCGATTCCC
Found at i:539181 original size:30 final size:30
Alignment explanation
Indices: 539125--539307 Score: 314
Period size: 30 Copynumber: 6.1 Consensus size: 30
539115 GAAGGACCTA
* * * *
539125 TCCAGAGGTCACACAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
539154 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
539184 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
539214 TCTAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
539244 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
539274 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
539304 TCCA
1 TCCA
539308 TATGTTCCTT
Statistics
Matches: 147, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 15 0.10
30 132 0.90
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:539338 original size:31 final size:30
Alignment explanation
Indices: 539296--539393 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 30
539286 AAAGATCCTC
*
539296 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* * *
539326 GGTATACTGTCCATATATCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
539357 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
539389 GGTAA
1 GGTAA
539394 ACCCTCGACT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
30 6 0.11
31 24 0.44
32 24 0.44
33 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:539388 original size:32 final size:32
Alignment explanation
Indices: 539299--539394 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
539289 GATCCTCGGT
*
539299 AACTGTCCATATGTTCCTTAGAACATAGGT-A
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
* * *
539330 TACTGTCCATAT-ATCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGTAA
539362 AACTGTCCATATGTTCCGTAGAACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
539394 A
1 A
539395 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
30 4 0.08
31 20 0.38
32 25 0.47
33 4 0.08
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (32 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTAA
Found at i:540621 original size:21 final size:21
Alignment explanation
Indices: 540591--540635 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
540581 ATTCTGTCGT
* *
540591 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
540612 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
540633 TTG
1 TTG
540636 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:541394 original size:12 final size:12
Alignment explanation
Indices: 541377--541435 Score: 62
Period size: 12 Copynumber: 5.6 Consensus size: 12
541367 TCGATGCATC
541377 GATGCATGGACT
1 GATGCATGGACT
541389 GATGCAT---C-
1 GATGCATGGACT
541397 GATGCATGGACT
1 GATGCATGGACT
541409 GATGCAT---C-
1 GATGCATGGACT
541417 GATGCATGGACT
1 GATGCATGGACT
541429 GATGCAT
1 GATGCAT
541436 CGGTGCATGC
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
8 14 0.36
9 2 0.05
11 2 0.05
12 21 0.54
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (12 bp):
GATGCATGGACT
Found at i:541394 original size:20 final size:20
Alignment explanation
Indices: 541369--541444 Score: 143
Period size: 20 Copynumber: 3.8 Consensus size: 20
541359 TTAATTCATC
541369 GATGCATCGATGCATGGACT
1 GATGCATCGATGCATGGACT
541389 GATGCATCGATGCATGGACT
1 GATGCATCGATGCATGGACT
541409 GATGCATCGATGCATGGACT
1 GATGCATCGATGCATGGACT
*
541429 GATGCATCGGTGCATG
1 GATGCATCGATGCATG
541445 CCTTTGAATA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.25
Consensus pattern (20 bp):
GATGCATCGATGCATGGACT
Found at i:544013 original size:59 final size:59
Alignment explanation
Indices: 543950--544288 Score: 488
Period size: 59 Copynumber: 5.8 Consensus size: 59
543940 TGGGACTATA
543950 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGTACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGTACTGAG
*
544009 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATAT-GAGTACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGTACTGAG
* *
544067 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGTACTGAG
* * *
544126 TGTGCTAAAAAGATAAGGAAATCATACTGAGTGTATGGATATCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGTACTGAG
* * * * *
544185 TGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCATTA-T-A-
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCC--ATATGG-AGTACTGAG
* * * *
544244 TGTGCTAAAATGGTAAGGGAGTCATACTGAGTATATGGATTTCCA
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCA
544289 GAAAAAGCAC
Statistics
Matches: 258, Mismatches: 18, Indels: 10
0.90 0.06 0.03
Matches are distributed among these distances:
57 1 0.00
58 58 0.22
59 190 0.74
60 1 0.00
61 6 0.02
62 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.30
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGTACTGAG
Found at i:544289 original size:59 final size:58
Alignment explanation
Indices: 543949--544390 Score: 451
Period size: 59 Copynumber: 7.5 Consensus size: 58
543939 ATGGGACTAT
*
543949 ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGTACTGA
1 ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGG-GCACTGA
* * * *
544008 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATATGAGTACTGA
1 ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGGCACTGA
* *
544066 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGA
1 ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGG-GCACTGA
* * *
544125 GTGTGCTAAAAAGATAAGGAAATCATACTGAGTGTATGGATATCCATATGGAGCACTGA
1 ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGG-GCACTGA
* * * * * *
544184 GTGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCA-TTA
1 ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATAT-GGGCACTGA
* * * * * ***
544242 TATGTGCTAAAATGGTAAGGGAGTCATACTGAGTATATGGATTTCCAGAAAAAGCAC-GA
1 -ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCA-TATGGGCACTGA
* * * * * * * **
544301 AGGGTGCTACAAGGATAAGGAAACCATACT-AATAGTATGGATTTTCATATAGGACACTTT
1 A-TGTGCTAAAATGATAAGGAAATCATACTGAGT-GTATGGATTTCCATAT-GGGCACTGA
*
544361 ATGTGCTAAAAATGGTAAAGG-AATCATACT
1 ATGTGCT-AAAATGAT-AAGGAAATCATACT
544391 AATGGTAAAA
Statistics
Matches: 324, Mismatches: 48, Indels: 21
0.82 0.12 0.05
Matches are distributed among these distances:
58 63 0.19
59 240 0.74
60 17 0.05
61 4 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (58 bp):
ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGGCACTGA
Found at i:544396 original size:20 final size:20
Alignment explanation
Indices: 544371--544417 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
544361 ATGTGCTAAA
*
544371 AATGGTAAAGGAATCATACT
1 AATGGTAAAAGAATCATACT
544391 AATGGTAAAAGAATCATACT
1 AATGGTAAAAGAATCATACT
544411 AATGGTA
1 AATGGTA
544418 TGGATTCTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.26
Consensus pattern (20 bp):
AATGGTAAAAGAATCATACT
Found at i:544673 original size:44 final size:44
Alignment explanation
Indices: 544612--544887 Score: 428
Period size: 44 Copynumber: 6.3 Consensus size: 44
544602 GTAAATTATA
* * *
544612 GTAAGTATATTGGTAAAATAAGATTACGAGCTTATGAAATTATA
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATAATG
* * * * *
544656 GTAAGTAGATTGATAAAATAAGCTTACGAGTTTATGAAATTATA
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATAATG
544700 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT-AGAATAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGA-AATAATG
544744 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATAATG
*
544788 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATAATG
* *
544832 GTAAGTATATTGGTAAAATAAACTTACGAGCTTATGGAATAATG
1 GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATAATG
*
544876 GTATGTATATTG
1 GTAAGTATATTG
544888 ATAAGAAATC
Statistics
Matches: 218, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
43 1 0.00
44 216 0.99
45 1 0.00
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (44 bp):
GTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATAATG
Found at i:545317 original size:21 final size:21
Alignment explanation
Indices: 545291--545351 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
545281 TATAGCAGTT
545291 ATTGTAGCAGTGTATCGATGC
1 ATTGTAGCAGTGTATCGATGC
545312 ATTGTAGCAGTGTATCGATGC
1 ATTGTAGCAGTGTATCGATGC
* * *
545333 ACTGTAACAGTGCATCGAT
1 ATTGTAGCAGTGTATCGAT
545352 ACACAATGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (21 bp):
ATTGTAGCAGTGTATCGATGC
Found at i:545444 original size:2 final size:2
Alignment explanation
Indices: 545437--545496 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
545427 ACTGTTCATA
545437 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
545479 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
545497 TACATTAAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:547052 original size:20 final size:20
Alignment explanation
Indices: 547027--547119 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
547017 TTTTCCCAAT
547027 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
547047 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
547067 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
547088 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
547109 TCGCAATGCGA
1 TCGCAATGCGA
547120 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:547069 original size:41 final size:41
Alignment explanation
Indices: 547024--547119 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
547014 CGATTTTCCC
547024 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
547065 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
547106 AAATCGCAATGCGA
1 AATTCGCAATGCGA
547120 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:547073 original size:21 final size:20
Alignment explanation
Indices: 547027--547119 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
547017 TTTTCCCAAT
*
547027 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
547047 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
547067 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
547088 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
547109 TCGCAATGCGA
1 TCGCAATGCGA
547120 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:547133 original size:20 final size:20
Alignment explanation
Indices: 547108--547201 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
547098 AATTGGGAAA
*
547108 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
547128 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
547149 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
547169 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
547189 TTCGCAACGCGAT
1 ATCGCAACGCGAT
547202 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:547182 original size:41 final size:41
Alignment explanation
Indices: 547105--547182 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
547095 GCGAATTGGG
* * **
547105 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
547146 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
547183 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:547779 original size:19 final size:19
Alignment explanation
Indices: 547755--547799 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
547745 GCAACGAGAT
*
547755 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
547774 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
547793 AATCGCA
1 AATCGCA
547800 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:547817 original size:19 final size:19
Alignment explanation
Indices: 547795--547979 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
547785 GAAACCAAAA
*
547795 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
547814 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
547833 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
547852 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
547872 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
547888 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
547905 TCACGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
547919 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
547938 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
547958 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
547978 TC
1 TC
547980 AACCAAAAGA
Statistics
Matches: 137, Mismatches: 16, Indels: 26
0.77 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
19 60 0.44
20 49 0.36
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:547872 original size:39 final size:38
Alignment explanation
Indices: 547795--547884 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
547785 GAAACCAAAA
* *
547795 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
547833 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
547872 TCGCGTTGCGATT
1 TCGCGTTGCGATT
547885 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:547904 original size:33 final size:33
Alignment explanation
Indices: 547867--547954 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
547857 GTTGCGATTT
* *
547867 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
547900 TCATTTCACGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
547933 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
547955 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:547956 original size:20 final size:20
Alignment explanation
Indices: 547922--547979 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
547912 GCGATTCTCT
**
547922 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
547942 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
547962 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
547980 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:550033 original size:42 final size:42
Alignment explanation
Indices: 549973--550095 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
549963 GCTCGACTCG
* * *
549973 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
550015 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
550057 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
550096 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:550053 original size:21 final size:21
Alignment explanation
Indices: 550029--550095 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
550019 TCATTCCTCG
550029 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
550050 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
550071 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
550092 AGAG
1 AGAG
550096 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:551471 original size:14 final size:14
Alignment explanation
Indices: 551452--551487 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
551442 ATTGTTTAAT
551452 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
551466 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
551480 TGATTTGT
1 TGATTTGT
551488 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:551688 original size:19 final size:19
Alignment explanation
Indices: 551666--551783 Score: 67
Period size: 19 Copynumber: 6.7 Consensus size: 19
551656 CGAAATTAAA
551666 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
551685 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
551700 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
551718 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
551733 -TCTCGTTACGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
551751 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
551770 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
551784 GGACATTAAG
Statistics
Matches: 71, Mismatches: 17, Indels: 21
0.65 0.16 0.19
Matches are distributed among these distances:
14 16 0.23
16 6 0.08
17 6 0.08
19 33 0.46
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:551712 original size:33 final size:33
Alignment explanation
Indices: 551670--551763 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
551660 ATTAAATTCG
551670 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
551703 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
551736 CGTTACGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
551764 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:554075 original size:12 final size:12
Alignment explanation
Indices: 554058--554094 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
554048 TCTTCGGGGA
554058 CTTTTTCTTCTT
1 CTTTTTCTTCTT
554070 CTTTTTCTTCTT
1 CTTTTTCTTCTT
554082 CTTTTTCTTCTT
1 CTTTTTCTTCTT
554094 C
1 C
554095 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:555463 original size:19 final size:19
Alignment explanation
Indices: 555414--555457 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
555404 CAACGAGAAT
555414 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
555433 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
555452 ATCGCA
1 ATCGCA
555458 TTGCGATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:555477 original size:14 final size:15
Alignment explanation
Indices: 555457--555529 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
555447 TGAAAATCGC
555457 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
555472 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
555489 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
555507 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
555523 -TTGCGAT
1 ATTGCGAT
555530 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:555494 original size:19 final size:19
Alignment explanation
Indices: 555453--555519 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
555443 GAAATGAAAA
555453 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
555469 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
555486 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
555504 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
555520 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:555660 original size:14 final size:14
Alignment explanation
Indices: 555641--555677 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
555631 CATCAATTAA
555641 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
555655 ACAAATCATCTTTT
1 ACAAATCAACATTT
555669 ACAAATCAA
1 ACAAATCAA
555678 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:557616 original size:14 final size:14
Alignment explanation
Indices: 557597--557654 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
557587 ATGCGAAATG
*
557597 AAAATCGCAACGAC
1 AAAATCGCAACGAA
557611 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAA
*
557627 ATGAAATCGCAACGAT
1 A--AAATCGCAACGAA
557643 AAAATCGCAACG
1 AAAATCGCAACG
557655 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:557639 original size:32 final size:33
Alignment explanation
Indices: 557581--557671 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
557571 GGAAATGGCT
*
557581 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
557614 ATCGCAACGCGAAATG-AAATCGCAACGATAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
557646 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
557672 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:557665 original size:19 final size:19
Alignment explanation
Indices: 557523--557676 Score: 123
Period size: 19 Copynumber: 8.6 Consensus size: 19
557513 TAGTTTACTT
* *
557523 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
557543 TCGCAACGCGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
557562 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
557582 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
557601 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
557615 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
557633 TCGCAA--CG--AT-AAAA
1 TCGCAACGCGAAATGAAAA
557647 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
557666 TCGCAATGCGA
1 TCGCAACGCGA
557677 TTTGTGTTTC
Statistics
Matches: 110, Mismatches: 12, Indels: 25
0.75 0.08 0.17
Matches are distributed among these distances:
14 21 0.19
15 1 0.01
16 6 0.05
17 2 0.02
18 12 0.11
19 39 0.35
20 29 0.26
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:557707 original size:14 final size:14
Alignment explanation
Indices: 557688--557777 Score: 72
Period size: 14 Copynumber: 5.9 Consensus size: 14
557678 TTGTGTTTCG
557688 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
557702 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
557718 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
557734 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
557750 CGCGTTGCGCTTTTGT
1 --CGTTGCGATTTTGT
*
557766 CGTTGCAATTTT
1 CGTTGCGATTTT
557778 CATTTCGCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 32 0.52
16 8 0.13
18 21 0.34
ACGTcount: A:0.09, C:0.19, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:557722 original size:32 final size:32
Alignment explanation
Indices: 557683--557793 Score: 186
Period size: 32 Copynumber: 3.4 Consensus size: 32
557673 GCGATTTGTG
557683 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
557715 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
* *
557747 TTTCGCGTTGCGCTTTTGTCGTTGCAATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
*
557780 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
557794 AGCCATTTCC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 57 0.77
33 17 0.23
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:557812 original size:20 final size:19
Alignment explanation
Indices: 557778--557832 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
557768 TTGCAATTTT
*
557778 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
557797 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
557817 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
557833 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:558331 original size:18 final size:18
Alignment explanation
Indices: 558305--558349 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
558295 GTCGATCAGA
*
558305 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
558323 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
558341 TGATGGCTC
1 TGATGGCTC
558350 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:560265 original size:20 final size:20
Alignment explanation
Indices: 560159--560273 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
560149 CGCTTTGAAA
*
560159 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
560180 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
** * *
560200 ATCGTGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
560220 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
560241 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
560261 ATCGCATTGCGAT
1 ATCGCATTGCGAT
560274 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 48 0.65
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:560291 original size:21 final size:21
Alignment explanation
Indices: 560262--560337 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
560252 ATAGTCAGTA
560262 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
560283 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
560303 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
560324 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
560338 ACTTATTCGC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:560292 original size:41 final size:41
Alignment explanation
Indices: 560262--560357 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
560252 ATAGTCAGTA
* * *
560262 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
560303 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
*
560344 TCGCATTGTGAATT
1 TCGCATTGCGAATT
560358 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:560306 original size:20 final size:20
Alignment explanation
Indices: 560281--560347 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
560271 GATTTTCCCA
560281 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
560301 ATTCGCATTGCGAATTTCCCA
1 ATTCGCGTTGCG-ATTTACTT
560322 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
560342 ATTCGC
1 ATTCGC
560348 ATTGTGAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:571463 original size:18 final size:16
Alignment explanation
Indices: 571439--571485 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
571429 GGCTATATCA
571439 TCTTTATTATATTCTTC
1 TCTTTATTATATT-TTC
571456 TACTTTATT-TATTTTC
1 T-CTTTATTATATTTTC
*
571472 TCATTATTAT-TTTT
1 TCTTTATTATATTTT
571486 ATTCAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 10 0.37
16 5 0.19
17 5 0.19
18 7 0.26
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (16 bp):
TCTTTATTATATTTTC
Found at i:571509 original size:12 final size:12
Alignment explanation
Indices: 571483--571520 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
571473 CATTATTATT
*
571483 TTTATTCA-ATA
1 TTTATTCATTTA
*
571494 TTTATTTATTTA
1 TTTATTCATTTA
571506 TTTATTCATTTA
1 TTTATTCATTTA
571518 TTT
1 TTT
571521 TCATTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 7 0.30
12 16 0.70
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTCATTTA
Found at i:573543 original size:25 final size:24
Alignment explanation
Indices: 573506--573569 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
573496 TCTCTTCCAT
*
573506 TTTTGCTTTTCTTTCTTTTATTCTA
1 TTTTCCTTTTCTTTCTTTTATT-TA
* *
573531 TTTTCCTTATCTTATCTTTTCTTTA
1 TTTTCCTTTTCTT-TCTTTTATTTA
*
573556 TTTTCTTTTTCTTT
1 TTTTCCTTTTCTTT
573570 TTATTTCTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 1 0.03
25 24 0.73
26 8 0.24
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTTCCTTTTCTTTCTTTTATTTA
Found at i:574271 original size:5 final size:5
Alignment explanation
Indices: 574261--574289 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
574251 CCTTTTCATT
574261 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
574290 CTTCAAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:588415 original size:57 final size:57
Alignment explanation
Indices: 588345--588463 Score: 175
Period size: 57 Copynumber: 2.1 Consensus size: 57
588335 TGGTAGAGAT
* * * *
588345 GGTGATGGATGTTGTGATAATGGATTATGTTAAAGTGATGATGATTGAATAGAGGTA
1 GGTGATGGATGTTGCGATAATGAATTATGTTAAAGTGACGATGATTAAATAGAGGTA
* * *
588402 GGTGATGGATGTTGCGATAATGAATTATGTTAAAGTGGCGATGATTAAATAGGGGTG
1 GGTGATGGATGTTGCGATAATGAATTATGTTAAAGTGACGATGATTAAATAGAGGTA
588459 GGTGA
1 GGTGA
588464 AGGTAGAGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.30, C:0.02, G:0.35, T:0.33
Consensus pattern (57 bp):
GGTGATGGATGTTGCGATAATGAATTATGTTAAAGTGACGATGATTAAATAGAGGTA
Found at i:590553 original size:18 final size:18
Alignment explanation
Indices: 590532--590566 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
590522 CCGTCTCCGG
590532 CTCCACCTCTACCTCCAC
1 CTCCACCTCTACCTCCAC
* *
590550 CTCCTCCTCTATCTCCA
1 CTCCACCTCTACCTCCA
590567 AGAATAACAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.57, G:0.00, T:0.29
Consensus pattern (18 bp):
CTCCACCTCTACCTCCAC
Found at i:592954 original size:402 final size:402
Alignment explanation
Indices: 592210--593823 Score: 2989
Period size: 402 Copynumber: 4.0 Consensus size: 402
592200 GAGCTTAGAG
*
592210 AGTTAAAAGTGCAACTATATGAGTTACTTGATCGAGGCTTTATTAGACTGAGTGTATCTCCAAGG
1 AGTTAAAAGTGCAACTATAGGAGTTACTTGATCGAGGCTTTATTAGACTGAGTGTATCTCCAAGG
592275 ATCGATGATCTGTTTGATCAGCTCAAGGGTGCTTCATTATTTTTGAAGATTGATCTTCGGTCTAG
66 ATCGATGATCTGTTTGATCAGCTCAAGGGTGCTTCATTATTTTTGAAGATTGATCTTCGGTCTAG
592340 ATATCATTAGTTAAAGAATAAAGAAAAAGATATTCCGAAGATGACTTTTAGAACCCGATATGGTC
131 ATATCATTAGTTAAAGAATAAAGAAAAAGATATTCCGAAGATGACTTTTAGAACCCGATATGGTC
*
592405 ATTATGAGTTTAAGGTTATGCCGTTTGGATTGACAAATGCTCCAGCAACATTCATGGATTTAATG
196 ATTATGAGATTAAGGTTATGCCGTTTGGATTGACAAATGCTCCAGCAACATTCATGGATTTAATG
592470 AATCGGGTGTTTCATCCGTATTTGGATTAGTTTATTGTTGCATTCATTGATTATATTTTGGTGTA
261 AATCGGGTGTTTCATCCGTATTTGGATTAGTTTATTGTTGCATTCATTGATTATATTTTGGTGTA
592535 TTTTAAGGCTAAAGAGGATCACGACGTGCATCTTTGCTCTGTACTTCATACGCTGCGGGATAAAA
326 TTTTAAGGCTAAAGAGGATCACGACGTGCATCTTTGCTCTGTACTTCATACGCTGCGGGATAAAA
592600 AGTTATATGCTA
391 AGTTATATGCTA
592612 AGTTAAAAGTGCAACTATAGGAGTTACTTGATCGAGGCTTTATTAGACTGAGTGTATCTCCAAGG
1 AGTTAAAAGTGCAACTATAGGAGTTACTTGATCGAGGCTTTATTAGACTGAGTGTATCTCCAAGG
*
592677 ATCGATGATCTGTTTGATCAGCTCAAGGGTGCTTTATTATTTTTGAAGATTGATCTTCGGTCTAG
66 ATCGATGATCTGTTTGATCAGCTCAAGGGTGCTTCATTATTTTTGAAGATTGATCTTCGGTCTAG
592742 ATATCATTAGTTAAAGAATAAAGAAAAAGATATTCCGAAGATGACTTTTAGAACCCGATATGGTC
131 ATATCATTAGTTAAAGAATAAAGAAAAAGATATTCCGAAGATGACTTTTAGAACCCGATATGGTC
* **
592807 ATTATGAGATTATA-GTTATGTCGTTTGGATTGACAAATGCTCCAGCGGCATTCATGGATTTAAT
196 ATTATGAGATTA-AGGTTATGCCGTTTGGATTGACAAATGCTCCAGCAACATTCATGGATTTAAT
592871 GAATCGGGTGTTTCATCCGTATTTGGATTAGTTTATTGTTGCATTCATTGATTATATTTTGGTGT
260 GAATCGGGTGTTTCATCCGTATTTGGATTAGTTTATTGTTGCATTCATTGATTATATTTTGGTGT
592936 ATTTTAAGGCTAAAGAGGATCACGACGTGCATCTTTGCTCTGTACTTCATACGCTGCGGGATAAA
325 ATTTTAAGGCTAAAGAGGATCACGACGTGCATCTTTGCTCTGTACTTCATACGCTGCGGGATAAA
593001 AAGTTATATGCTA
390 AAGTTATATGCTA
593014 AGTTAAAAGTGCAACTATAGGAGTTACTTGATCGAGGCTTTATTAGACTGAGTGTATCTCCAAGG
1 AGTTAAAAGTGCAACTATAGGAGTTACTTGATCGAGGCTTTATTAGACTGAGTGTATCTCCAAGG
593079 ATCGATGATCTGTTTGATCAGCTCAAGGGTGCTTCATTATTTTTGAAGATTGATCTTCGGTCTAG
66 ATCGATGATCTGTTTGATCAGCTCAAGGGTGCTTCATTATTTTTGAAGATTGATCTTCGGTCTAG
593144 ATATCATTAGTTAAAGAATAAAGAAAAAGATATTCCGAAGATGACTTTTAGAACCCGATATGGTC
131 ATATCATTAGTTAAAGAATAAAGAAAAAGATATTCCGAAGATGACTTTTAGAACCCGATATGGTC
*
593209 ATTATGAGTTTAAGGTTATGCCGTTTGGATTGACAAATGCTCCAGCAACATTCATGGATTTAATG
196 ATTATGAGATTAAGGTTATGCCGTTTGGATTGACAAATGCTCCAGCAACATTCATGGATTTAATG
593274 AATCGGGTGTTTCATCCGTATTTGGATTAGTTTATTGTTGCATTCATTGATTATATTTTGGTGTA
261 AATCGGGTGTTTCATCCGTATTTGGATTAGTTTATTGTTGCATTCATTGATTATATTTTGGTGTA
593339 TTTTAAGGCTAAAGAGGATCACGACGTGCATCTTTGCTCTGTACTTCATACGCTGCGGGATAAAA
326 TTTTAAGGCTAAAGAGGATCACGACGTGCATCTTTGCTCTGTACTTCATACGCTGCGGGATAAAA
593404 AGTTATATGCTA
391 AGTTATATGCTA
593416 AGTTAAAAGTGCAACTATAGGAGTTACTTGATCGAGGCTTTATTAGACTGAGTGTATCTCCAAGG
1 AGTTAAAAGTGCAACTATAGGAGTTACTTGATCGAGGCTTTATTAGACTGAGTGTATCTCCAAGG
*
593481 ATCGATGATCTGTTTGATCAGCTCAAGGGTGCTTTATTATTTTTGAAGATTGATCTTCGGTCTAG
66 ATCGATGATCTGTTTGATCAGCTCAAGGGTGCTTCATTATTTTTGAAGATTGATCTTCGGTCTAG
593546 ATATCATTAGTTAAAGAATAAAGAAAAAGATATTCCGAAGATGACTTTTAGAACCCGATATGGTC
131 ATATCATTAGTTAAAGAATAAAGAAAAAGATATTCCGAAGATGACTTTTAGAACCCGATATGGTC
* **
593611 ATTATGAGATTATA-GTTATGTCGTTTGGATTGACAAATGCTCCAGCGGCATTCATGGATTTAAT
196 ATTATGAGATTA-AGGTTATGCCGTTTGGATTGACAAATGCTCCAGCAACATTCATGGATTTAAT
* * * * * *
593675 GAATAGGGTGTTTTATCTGTATTTGGATTAGTTTGTGGTTGTATTCATTGATTATATTTTGGTGT
260 GAATCGGGTGTTTCATCCGTATTTGGATTAGTTTATTGTTGCATTCATTGATTATATTTTGGTGT
* * * * *
593740 ATTTTAAGGCTAAAGAGGAGCACGACGTGCATCTTCGCACTGTACTTCAGACACTGCGGGATAAA
325 ATTTTAAGGCTAAAGAGGATCACGACGTGCATCTTTGCTCTGTACTTCATACGCTGCGGGAT-AA
593805 AAAGTTATATGCTA
389 AAAGTTATATGCTA
593819 AGTTA
1 AGTTA
593824 TCAAAATGTG
Statistics
Matches: 1181, Mismatches: 27, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
401 1 0.00
402 1157 0.98
403 23 0.02
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (402 bp):
AGTTAAAAGTGCAACTATAGGAGTTACTTGATCGAGGCTTTATTAGACTGAGTGTATCTCCAAGG
ATCGATGATCTGTTTGATCAGCTCAAGGGTGCTTCATTATTTTTGAAGATTGATCTTCGGTCTAG
ATATCATTAGTTAAAGAATAAAGAAAAAGATATTCCGAAGATGACTTTTAGAACCCGATATGGTC
ATTATGAGATTAAGGTTATGCCGTTTGGATTGACAAATGCTCCAGCAACATTCATGGATTTAATG
AATCGGGTGTTTCATCCGTATTTGGATTAGTTTATTGTTGCATTCATTGATTATATTTTGGTGTA
TTTTAAGGCTAAAGAGGATCACGACGTGCATCTTTGCTCTGTACTTCATACGCTGCGGGATAAAA
AGTTATATGCTA
Found at i:605968 original size:6 final size:6
Alignment explanation
Indices: 605959--605998 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
605949 TCTTTCTCAT
*
605959 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CTTCCC CCTC
1 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCTC
605999 TTTTTCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (6 bp):
CCTCCC
Found at i:606924 original size:3 final size:3
Alignment explanation
Indices: 606918--606946 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
606908 GAGGAGGAGG
606918 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
606947 GCCACGTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:610334 original size:30 final size:30
Alignment explanation
Indices: 610293--610372 Score: 151
Period size: 30 Copynumber: 2.7 Consensus size: 30
610283 GATTCAGGTA
*
610293 TCGGGTCGGATCAAATCGGATGGGTTGATT
1 TCGGGTTGGATCAAATCGGATGGGTTGATT
610323 TCGGGTTGGATCAAATCGGATGGGTTGATT
1 TCGGGTTGGATCAAATCGGATGGGTTGATT
610353 TCGGGTTGGATCAAATCGGA
1 TCGGGTTGGATCAAATCGGA
610373 ACGATTAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.21, C:0.12, G:0.36, T:0.30
Consensus pattern (30 bp):
TCGGGTTGGATCAAATCGGATGGGTTGATT
Found at i:610547 original size:20 final size:21
Alignment explanation
Indices: 610509--610547 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
610499 ATATTTTTGT
*
610509 AAAAAAAACATGTCTATTTTA
1 AAAAAAAACATATCTATTTTA
*
610530 AAAAAAAACTTATC-ATTT
1 AAAAAAAACATATCTATTT
610548 GTGTTCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (21 bp):
AAAAAAAACATATCTATTTTA
Found at i:611151 original size:16 final size:16
Alignment explanation
Indices: 611114--611157 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
611104 AATTAAATTA
611114 GGGTTACTTTTGATTC
1 GGGTTACTTTTGATTC
**
611130 AAGTTA-TTTTCGATTC
1 GGGTTACTTTT-GATTC
611146 GGGTTACTTTTG
1 GGGTTACTTTTG
611158 GTTTGACTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
15 4 0.18
16 14 0.64
17 4 0.18
ACGTcount: A:0.16, C:0.11, G:0.23, T:0.50
Consensus pattern (16 bp):
GGGTTACTTTTGATTC
Found at i:617188 original size:40 final size:40
Alignment explanation
Indices: 617138--617276 Score: 106
Period size: 40 Copynumber: 3.3 Consensus size: 40
617128 CGATCTCTAA
617138 TTCGCATTGCGATCTCAACTATCGCAAATTCGCGTTGCAT
1 TTCGCATTGCGATCTCAACTATCGCAAATTCGCGTTGCAT
* * * *
617178 TTCGCGTTGCGATAGTTGACCAACAAAATCGCAAA---GCGATCT-CTAA
1 TTCGCATTGCGAT--CT---CAAC--TATCGCAAATTCGCG-T-TGC-AT
*
617224 TTCGCATTGCGATCTCCACTATCGCAAATTCGCGTTGCAT
1 TTCGCATTGCGATCTCAACTATCGCAAATTCGCGTTGCAT
*
617264 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
617277 AGTTGAAAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
39 8 0.11
40 26 0.35
41 5 0.07
42 4 0.05
44 4 0.05
45 6 0.08
46 14 0.19
47 8 0.11
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (40 bp):
TTCGCATTGCGATCTCAACTATCGCAAATTCGCGTTGCAT
Found at i:617253 original size:86 final size:86
Alignment explanation
Indices: 617108--617282 Score: 332
Period size: 86 Copynumber: 2.0 Consensus size: 86
617098 TTTACGAAAA
*
617108 TGACCAACAAAATCGCAATGCGATCTCTAATTCGCATTGCGATCTCAACTATCGCAAATTCGCGT
1 TGACCAACAAAATCGCAAAGCGATCTCTAATTCGCATTGCGATCTCAACTATCGCAAATTCGCGT
617173 TGCATTTCGCGTTGCGATAGT
66 TGCATTTCGCGTTGCGATAGT
*
617194 TGACCAACAAAATCGCAAAGCGATCTCTAATTCGCATTGCGATCTCCACTATCGCAAATTCGCGT
1 TGACCAACAAAATCGCAAAGCGATCTCTAATTCGCATTGCGATCTCAACTATCGCAAATTCGCGT
617259 TGCATTTCGCGTTGCGATAGT
66 TGCATTTCGCGTTGCGATAGT
617280 TGA
1 TGA
617283 AAATCGCCTT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 87 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (86 bp):
TGACCAACAAAATCGCAAAGCGATCTCTAATTCGCATTGCGATCTCAACTATCGCAAATTCGCGT
TGCATTTCGCGTTGCGATAGT
Found at i:617281 original size:21 final size:21
Alignment explanation
Indices: 617257--617361 Score: 79
Period size: 21 Copynumber: 5.1 Consensus size: 21
617247 GCAAATTCGC
617257 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ** * *
617278 GTTGAAAATCGCCTTGCGCT-
1 GTTGCATTTCGCGTTGCGATA
* *
617298 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ***
617319 GTTGAAAACCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
617339 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
617360 GT
1 GT
617362 CTACAGTTAT
Statistics
Matches: 57, Mismatches: 25, Indels: 4
0.66 0.29 0.05
Matches are distributed among these distances:
20 27 0.47
21 30 0.53
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:617306 original size:41 final size:41
Alignment explanation
Indices: 617261--617361 Score: 175
Period size: 41 Copynumber: 2.5 Consensus size: 41
617251 ATTCGCGTTG
* *
617261 CATTTCGCGTTGCGATAGTTGAAAATCGCCTTGCGCTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAACCGCCTTGCGATTTTC
*
617302 CATTTCGCGTTGCGATAGTTGAAAACCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAACCGCCTTGCGATTTTC
617343 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
617362 CTACAGTTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAACCGCCTTGCGATTTTC
Found at i:617314 original size:20 final size:20
Alignment explanation
Indices: 617286--617358 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
617276 TAGTTGAAAA
* *
617286 TCGCCTTGCGCTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
617306 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
617327 CCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
617347 TCGCGTTGCGAT
1 TCGCGTTGCGAT
617359 AGTCTACAGT
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:617502 original size:6 final size:6
Alignment explanation
Indices: 617491--617546 Score: 70
Period size: 5 Copynumber: 10.3 Consensus size: 6
617481 GACACGTATT
617491 ACCACG ACCACG ACCACG ACCACG A-CACG A-CACG A-CACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
617535 ACC-CG ACC-CG AC
1 ACCACG ACCACG AC
617547 TCGAGACGAG
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 29 0.59
6 20 0.41
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:618048 original size:5 final size:5
Alignment explanation
Indices: 618034--618075 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
618024 CCGCCGCCGC
618034 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
618076 GGTCGTGGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.11
5 33 0.89
ACGTcount: A:0.00, C:0.40, G:0.21, T:0.38
Consensus pattern (5 bp):
CGTCT
Found at i:618083 original size:6 final size:6
Alignment explanation
Indices: 618072--618144 Score: 92
Period size: 6 Copynumber: 12.2 Consensus size: 6
618062 TCGTCTCGTC
* * *
618072 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGT TCGTGT TCGTGT
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* * *
618120 TCGTGA TCGTGA TCGTGA TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
618145 AATACGTGTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.04, C:0.16, G:0.41, T:0.38
Consensus pattern (6 bp):
TCGTGG
Found at i:620576 original size:35 final size:35
Alignment explanation
Indices: 620527--620639 Score: 156
Period size: 35 Copynumber: 3.2 Consensus size: 35
620517 TAAAAAGACA
* * *
620527 GAAATTGAAGTATTTTAGAATTTGAGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGAGGTTTAGAAT
*
620562 GTAATTGAATTATTTTGGAATTT-AGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGA-GGTTTAGAAT
* *
620597 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGAGGTTTAGAAT
620632 GAAATTGA
1 GAAATTGA
620640 GAATTGTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 68 0.99
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (35 bp):
GAAATTGAATTATTTTGGAATTTGAGGTTTAGAAT
Found at i:621249 original size:112 final size:112
Alignment explanation
Indices: 621029--621376 Score: 536
Period size: 112 Copynumber: 3.1 Consensus size: 112
621019 ACATTTCAAC
* * * ** *
621029 AAAGCATCGATACATTTTTATAAAAAGTATTTATACTTTCAACATATCAGGTAAATTTTACCGGT
1 AAAGTATCGAT-CCTTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGT
*
621094 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
65 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTATTATATTGT
*
621142 AAAGTATCGAT-CTTTTGTATAAAAATGATCGATACTTTCAACATATTAGGTAAATTTTACCGGT
1 AAAGTATCGATCCTTTT-TATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGT
* *
621206 TTTGTTATAATGAAACTGGTTTTTTCATATTTTTACCTATTATATTGT
65 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTATTATATTGT
* *
621254 AAAGTATCGATCCTTTTTATAAATAGGATCGATACTTTCAACATATTAGGTAAATTTTATCGGTT
1 AAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTT
* *
621319 TTGTCATAATGAAATTGATTTTGTCATATTTTTACCTATTATATTGT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTATTATATTGT
*
621366 AAAATATCGAT
1 AAAGTATCGAT
621377 ACATATATAT
Statistics
Matches: 215, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
111 4 0.02
112 196 0.91
113 15 0.07
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.44
Consensus pattern (112 bp):
AAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTT
TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTATTATATTGT
Found at i:621983 original size:112 final size:112
Alignment explanation
Indices: 621786--622050 Score: 458
Period size: 112 Copynumber: 2.4 Consensus size: 112
621776 AATTTTACCG
* * *
621786 GTTTTGTTATATTTTTACCTGTTATATTGTAAAGTATCGATCCTTTTTATAAAAAGGATCGATAC
1 GTTTTGTTATATTTTTACCTATTATATTGTAAAGTATCGATCATTTTTATAAAAAGGATCAATAC
* *
621851 TTTCAACATATCAGGTAAATTTTATCGGTTTTGTTATAATAAAACTA
66 TTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATAAAACTA
621898 GTTTTGTTATATTTTTACCTATTATATTGTAAAGTATCGATCATTTTTATAAAAAGGATCAATAC
1 GTTTTGTTATATTTTTACCTATTATATTGTAAAGTATCGATCATTTTTATAAAAAGGATCAATAC
*
621963 TTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACTA
66 TTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATAAAACTA
* *
622010 GTTTTGTCATATTTTTACCTATTATATTATAAAGTATCGAT
1 GTTTTGTTATATTTTTACCTATTATATTGTAAAGTATCGAT
622051 ACTTATATAT
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 145 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (112 bp):
GTTTTGTTATATTTTTACCTATTATATTGTAAAGTATCGATCATTTTTATAAAAAGGATCAATAC
TTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATAAAACTA
Found at i:622017 original size:674 final size:677
Alignment explanation
Indices: 620853--622467 Score: 2598
Period size: 674 Copynumber: 2.4 Consensus size: 677
620843 TACTTTACCC
620853 TATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC
1 TATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC
* *
620918 AAAACAATCAAATAATTTTTTGTGCAAATAAAATTATTAAATTAATATTGTAGGTGGAAAACATG
66 AAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATG
*
620983 AAGCACTATTAAAAAATTTTGAAACATAAATTACAT-ACATTTCAACAAAGCATCGATACATTTT
131 AAGCACTATTAAAAAATTTTGAAACATAAATTACATAAC-TTTCAACAAAGTATCGATACATTTT
*
621047 TAT-AAAAAGTATTTATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAAACT
195 TATAAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACC-G----GT--T--T-----T
*
621111 GGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCTTTTGTATAAAAATGATCGATA
246 -G---TGTCATATTTTTACCTGTTATATTGTAAAGTATCGATCTTTTGTATAAAAAGGATCGATA
* * *
621176 CTTTCAACATATTAGGTAAATTTTACCGGTTTTGTTATAATGAAACTGGTTTTTTCATATTTTTA
307 CTTTCAACATATCAGGTAAATTTTACCGGTTTTGTTATAATAAAACTAGTTTTTTCATATTTTTA
* * * *
621241 CCTATTATATTGTAAAGTATCGATCCTTTTTATAAATAGGATCGATACTTTCAACATATTAGGTA
372 CCTATTATATTGTAAAGTATCGATCATTTTTATAAAAAGGATCAATACTTTCAACATATCAGGTA
* * *
621306 AATTTTATCGGTTTTGTCATAATGAAATTGATTTTGTCATATTTTTACCTATTATATTGTAAAAT
437 AATTTTACCGGTTTTGTCATAATGAAATAGATTTTGTCATATTTTTACCTATTATATTATAAAAT
* *
621371 ATCGATACATATATATAAGTGTCGATAATTATTTCACTGTGAAAAACATTAATTTAAGATTATCT
502 ATCGATACATATATATAAGTGTCGACAATTATTTCACTGTGAAAAACATTAATTTAAGATTATAT
*
621436 TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGCGTCTAATAGTTTATTTTTATGTTAC
567 TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGCGTCTAATAGTTTATTTTTATCTTAC
*
621501 AATATTTATTATAATTAAATTAAAAATAATAAACATAGATATTACA
632 AATATATATTATAATTAAATTAAAAATAATAAACATAGATATTACA
621547 TATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC
1 TATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC
*
621612 AAAACAATCAAATAATTTTTTGTGTAAGTGAAATTATTAAATTAATATTGTAGGTGG-AAACATG
66 AAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATG
* * * * *
621676 AATCACTATTAAAAAAATGTGAAACATAAATTACATAACTTTCAACAAAATATCGATATATTTTT
131 AAGCACTATTAAAAAATTTTGAAACATAAATTACATAACTTTCAACAAAGTATCGATACATTTTT
*
621741 ATAAAAAAATATCTATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGT-T-ATATTTTTAC
196 ATAAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTGTCATATTTTTAC
621804 CTGTTATATTGTAAAGTATCGATCCTTTT-TATAAAAAGGATCGATACTTTCAACATATCAGGTA
261 CTGTTATATTGTAAAGTATCGAT-CTTTTGTATAAAAAGGATCGATACTTTCAACATATCAGGTA
*
621868 AATTTTATCGGTTTTGTTATAATAAAACTAGTTTTGTT-ATATTTTTACCTATTATATTGTAAAG
325 AATTTTACCGGTTTTGTTATAATAAAACTAGTTTT-TTCATATTTTTACCTATTATATTGTAAAG
621932 TATCGATCATTTTTATAAAAAGGATCAATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGT
389 TATCGATCATTTTTATAAAAAGGATCAATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGT
* *
621997 CATAATGAAACTAG-TTTTGTCATATTTTTACCTATTATATTATAAAGTATCGATACTTATATAT
454 CATAATGAAA-TAGATTTTGTCATATTTTTACCTATTATATTATAAAATATCGATACATATATAT
* * *
622061 AAGTGTCGACACTTATTTCACTGTGGAAAACATTAATTTAAGGTTATATTTTGAGTGAGTTTTAA
518 AAGTGTCGACAATTATTTCACTGTGAAAAACATTAATTTAAGATTATATTTTGAGTGAGTTTTAA
* * * *
622126 GATATTAATTTCGTAATTATATGCGTCTAATGGTTTATTTTTATCTTACGATATATATTATTATT
583 GATATTAATTTAGTAATTATATGCGTCTAATAGTTTATTTTTATCTTACAATATATATTATAATT
622191 AAATTAAAAATAATAAACATAGATATTACA
648 AAATTAAAAATAATAAACATAGATATTACA
*
622221 TATTTATTATTATCATTGGTTAAAATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC
1 TATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC
* * *
622286 AAAATAATCAAATAATTTTTTATGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATA
66 AAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATG
622351 AAGCACTATTAAAAAATTTTGAAACATAAATTACATAACTTTCAACAAAGTATCGATACATTTTT
131 AAGCACTATTAAAAAATTTTGAAACATAAATTACATAACTTTCAACAAAGTATCGATACATTTTT
* *
622416 ATAAAAAAGTATCTATACTTTCAACATATCAAGTAAATTTTACCAGTTTTGT
196 ATAAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGT
622468 CATAATGAAA
Statistics
Matches: 866, Mismatches: 49, Indels: 31
0.92 0.05 0.03
Matches are distributed among these distances:
674 508 0.59
675 125 0.14
676 1 0.00
679 1 0.00
680 1 0.00
685 1 0.00
687 1 0.00
689 2 0.00
693 66 0.08
694 160 0.18
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (677 bp):
TATTTATTATTATCTTTGGTTAAAATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC
AAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATG
AAGCACTATTAAAAAATTTTGAAACATAAATTACATAACTTTCAACAAAGTATCGATACATTTTT
ATAAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTGTCATATTTTTAC
CTGTTATATTGTAAAGTATCGATCTTTTGTATAAAAAGGATCGATACTTTCAACATATCAGGTAA
ATTTTACCGGTTTTGTTATAATAAAACTAGTTTTTTCATATTTTTACCTATTATATTGTAAAGTA
TCGATCATTTTTATAAAAAGGATCAATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCA
TAATGAAATAGATTTTGTCATATTTTTACCTATTATATTATAAAATATCGATACATATATATAAG
TGTCGACAATTATTTCACTGTGAAAAACATTAATTTAAGATTATATTTTGAGTGAGTTTTAAGAT
ATTAATTTAGTAATTATATGCGTCTAATAGTTTATTTTTATCTTACAATATATATTATAATTAAA
TTAAAAATAATAAACATAGATATTACA
Found at i:622069 original size:20 final size:22
Alignment explanation
Indices: 622031--622076 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
622021 TTTTTACCTA
*
622031 TTATATTATAAAGTATCGATAC
1 TTATATTATAAAGTATCGACAC
*
622053 TTATA-TAT-AAGTGTCGACAC
1 TTATATTATAAAGTATCGACAC
622073 TTAT
1 TTAT
622077 TTCACTGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 3 0.14
22 5 0.23
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (22 bp):
TTATATTATAAAGTATCGACAC
Found at i:629100 original size:143 final size:143
Alignment explanation
Indices: 628842--629128 Score: 556
Period size: 143 Copynumber: 2.0 Consensus size: 143
628832 CAAGTTGGAA
628842 GCTGAAGATTTAATGTCGGCCCAACTCTCTACCATCACCAATATATTAAAGAATTTGCAAAATTC
1 GCTGAAGATTTAATGTCGGCCCAACTCTCTACCATCACCAATATATTAAAGAATTTGCAAAATTC
628907 TAATGAGGTGAAAGAAGTGAAGGTTGATAGCTTGGCATATCTGTTATGCCAAAGCAATCACCATG
66 TAATGAGGTGAAAGAAGTGAAGGTTGATAGCTTGGCATATCTGTTATGCCAAAGCAATCACCATG
628972 AATGTGAATGCCC
131 AATGTGAATGCCC
628985 GCTGAAGATTTAATGTCGGCCCAACTCTCTACCATCACCAATATATTAAAGAATTTGCAAAATTC
1 GCTGAAGATTTAATGTCGGCCCAACTCTCTACCATCACCAATATATTAAAGAATTTGCAAAATTC
* *
629050 TAATGAGGTGAAAGAAGTGAAGGTTGATAGCTTGGCATGTCTGTTATGCCAAGGCAATCACCATG
66 TAATGAGGTGAAAGAAGTGAAGGTTGATAGCTTGGCATATCTGTTATGCCAAAGCAATCACCATG
629115 AATGTGAATGCCC
131 AATGTGAATGCCC
629128 G
1 G
629129 AACAATTAAA
Statistics
Matches: 142, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 142 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (143 bp):
GCTGAAGATTTAATGTCGGCCCAACTCTCTACCATCACCAATATATTAAAGAATTTGCAAAATTC
TAATGAGGTGAAAGAAGTGAAGGTTGATAGCTTGGCATATCTGTTATGCCAAAGCAATCACCATG
AATGTGAATGCCC
Found at i:630473 original size:15 final size:14
Alignment explanation
Indices: 630449--630490 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
630439 TTAGTGTTTG
630449 TTTGTTTATTTTTA
1 TTTGTTTATTTTTA
630463 TTTGTTTTATTTTT-
1 TTTG-TTTATTTTTA
* *
630477 TATCTTTATTTTTA
1 TTTGTTTATTTTTA
630491 ATATTAGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 9 0.38
14 6 0.25
15 9 0.38
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (14 bp):
TTTGTTTATTTTTA
Found at i:631657 original size:17 final size:15
Alignment explanation
Indices: 631637--631682 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 15
631627 GTAAAAAAGT
631637 GAAAAAGTGAAAAAAAA
1 GAAAAAG-G-AAAAAAA
631654 GAAAAAAGGAAAAAAA
1 G-AAAAAGGAAAAAAA
631670 G-AAAA-GAAAAAAA
1 GAAAAAGGAAAAAAA
631683 ATGTGTACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 8 0.29
14 4 0.14
16 8 0.29
17 2 0.07
18 6 0.21
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (15 bp):
GAAAAAGGAAAAAAA
Found at i:631658 original size:16 final size:14
Alignment explanation
Indices: 631645--631683 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
631635 GTGAAAAAGT
631645 GAAAAAAAAGAAAAAA
1 GAAAAAAAAG--AAAA
*
631661 GGAAAAAAAGAAAA
1 GAAAAAAAAGAAAA
631675 GAAAAAAAA
1 GAAAAAAAA
631684 TGTGTACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
16 9 0.43
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAGAAAA
Found at i:647385 original size:2 final size:2
Alignment explanation
Indices: 647378--647440 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
647368 TTTTATCACT
647378 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
647420 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
647441 CAGATTTAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:648175 original size:13 final size:12
Alignment explanation
Indices: 648159--648197 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
648149 ACAAATAACG
648159 ATATATAATATA
1 ATATATAATATA
648171 TATATATAATA-A
1 -ATATATAATATA
*
648183 AAATATAATATA
1 ATATATAATATA
648195 ATA
1 ATA
648198 AAAAAATAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 9 0.39
12 4 0.17
13 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATATAATATA
Found at i:648193 original size:16 final size:17
Alignment explanation
Indices: 648168--648201 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
648158 GATATATAAT
648168 ATATATATATAATAAAA
1 ATATATATATAATAAAA
648185 ATATA-ATATAATAAAA
1 ATATATATATAATAAAA
648201 A
1 A
648202 AATAGAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATATATATAATAAAA
Found at i:648249 original size:2 final size:2
Alignment explanation
Indices: 648242--648269 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
648232 ATATACTTAA
648242 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
648270 TAATATTAAA
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:650120 original size:21 final size:21
Alignment explanation
Indices: 650094--650160 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 21
650084 AGTAACTGTC
650094 TCAAGGGAGACAAAATTCATT
1 TCAAGGGAGACAAAATTCATT
* *
650115 TCAAGGGAGAC--AACT-ATC
1 TCAAGGGAGACAAAATTCATT
*
650133 TCAAGAGAGA-AAAATTCATT
1 TCAAGGGAGACAAAATTCATT
*
650153 TTAAGGGA
1 TCAAGGGA
650161 AATGTTTTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
18 11 0.31
19 6 0.17
20 8 0.22
21 11 0.31
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.22
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTCATT
Found at i:650149 original size:38 final size:39
Alignment explanation
Indices: 650087--650335 Score: 130
Period size: 37 Copynumber: 6.9 Consensus size: 39
650077 TTTCAAGAGT
* *
650087 AACTGTCTCAAGGGAGACAAAATTCATTTCAAGGGAGAC
1 AACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAGAC
*
650126 AACTATCTCAAGAGAGA-AAAATTCATTTTAAGGGA-A-
1 AACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAGAC
** * * * * *
650162 ATGT-TTTC-A-A-TGTC--TA-T-GTTTCAA--GAGA-
1 AACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAGAC
* * ** *
650190 AACTGTCTCAAGGGAGACAAAATTTTGTTTTAA-GG-GA-
1 AACTATCTCAAGAGAGACAAAA-TTCATTTCAAGGGAGAC
*
650227 AACTATCTCAAGAGAGACAACATTCATTTCAA--GAGA-
1 AACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAGAC
* * * **
650263 AACTGTCTCTAGGGAGACAAAATTTTGTTTCAA--GAGA-
1 AACTATCTCAAGAGAGACAAAA-TTCATTTCAAGGGAGAC
650300 AACTATCTCAAGAGAGACAAAATTCATTTCAAGGGA
1 AACTATCTCAAGAGAGACAAAATTCATTTCAAGGGA
650336 AATGTTTTCA
Statistics
Matches: 158, Mismatches: 36, Indels: 33
0.70 0.16 0.15
Matches are distributed among these distances:
27 2 0.01
28 3 0.02
29 8 0.05
30 2 0.01
31 1 0.01
32 3 0.02
33 1 0.01
34 2 0.01
35 4 0.03
36 38 0.24
37 59 0.37
38 20 0.13
39 15 0.09
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (39 bp):
AACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAGAC
Found at i:650229 original size:37 final size:37
Alignment explanation
Indices: 650178--650489 Score: 285
Period size: 37 Copynumber: 8.8 Consensus size: 37
650168 TCAATGTCTA
*
650178 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
650215 TGTTTTAAGGGAAACTATCTCAAGAGAGACAACA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
** * *
650251 CATTTCAAGAGAAACTGTCTCTAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
*
650288 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
** * * *
650324 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATTT
* *
650352 ATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
650390 T-TTTCAAGGGAAACTATCTCAAGAGAGA-AAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * *
650424 CGTTTCAAGAGAAACTGTCTCTAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
650461 TGTTTCAAGGGAAATTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA
650490 TAATGGTGAG
Statistics
Matches: 214, Mismatches: 44, Indels: 34
0.73 0.15 0.12
Matches are distributed among these distances:
28 2 0.01
29 14 0.07
30 3 0.01
32 1 0.00
33 1 0.00
34 3 0.01
35 29 0.14
36 71 0.33
37 87 0.41
38 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:650243 original size:103 final size:103
Alignment explanation
Indices: 650052--650335 Score: 306
Period size: 103 Copynumber: 2.7 Consensus size: 103
650042 TTTGTGTTTC
* *
650052 AAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTCATTTC
1 AAGGGAAACGTTTTCAAAGTCTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTC
650117 AAGGGAGACAACTATCTCAAGAGAGAAAAATTCATTTT
66 AAGGGAGACAACTATCTCAAGAGAGAAAAATTCATTTT
* * **
650155 AAGGGAAATGTTTTCAATGTCTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTT
1 AAGGGAAACGTTTTCAAAGTCTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTCATTT
* * *
650220 TAA-GG-GA-AACTATCTCAAGAGAGACAACATTCATTTC
65 CAAGGGAGACAACTATCTCAAGAGAGA-AAAATTCATTTT
* * * * * *
650257 AAGAGAAACTGTCTCTAGGGAGACAAAAT-TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAA
1 AAGGGAAAC-GT-T-T------TCAAAGTCTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAA
650321 ATTCATTTCAAGGGA
57 ATTCATTTCAAGGGA
650336 AATGTTTTCA
Statistics
Matches: 148, Mismatches: 20, Indels: 18
0.80 0.11 0.10
Matches are distributed among these distances:
101 17 0.11
102 19 0.13
103 57 0.39
104 8 0.05
105 1 0.01
109 7 0.05
110 35 0.24
111 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (103 bp):
AAGGGAAACGTTTTCAAAGTCTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTC
AAGGGAGACAACTATCTCAAGAGAGAAAAATTCATTTT
Found at i:650302 original size:73 final size:73
Alignment explanation
Indices: 650180--650489 Score: 293
Period size: 73 Copynumber: 4.4 Consensus size: 73
650170 AATGTCTATG
* *
650180 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAGGGAAACTATCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
650245 AACATTCA
66 AAAATTCA
*
650253 TTTCAAGAGAAACTGTCTCTAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
650318 AAAATTCA
66 AAAATTCA
* * * * * *
650326 TTTCAAGGGAAA-TGTTTTCAA---TG------TTTATGTTTCAAGAGAAATTGTCTCAAGGGAG
1 TTTCAAGAGAAACTG-TCTCAAGGGAGACAAAATTT-TGTTTCAAGAGAAACTATCTCAAGAGAG
**
650381 ACAAAATTTT
64 ACAAAATTCA
* * * * * * *
650391 TTTCAAGGGAAACTATCTCAAGAGAGA-AAAA-TTCGTTTCAAGAGAAACTGTCTCTAGGGAGAC
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
**
650454 AAAATTTTG
66 AAAA-TTCA
* * *
650463 TTTCAAGGGAAATTGTCTCAAGAGAGA
1 TTTCAAGAGAAACTGTCTCAAGGGAGA
650490 TAATGGTGAG
Statistics
Matches: 203, Mismatches: 22, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
64 3 0.01
65 50 0.25
66 1 0.00
68 1 0.00
70 1 0.00
71 31 0.15
72 32 0.16
73 84 0.41
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (73 bp):
TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTCA
Found at i:650374 original size:175 final size:172
Alignment explanation
Indices: 650077--650489 Score: 648
Period size: 175 Copynumber: 2.4 Consensus size: 172
650067 AAAGTTTATG
* * **
650077 TTTCAAGAGTAACTGTCTCAAGGGAGACAAAA-TTCATTTCAAGGGAGACAACTATCTCAAGAGA
1 TTTCAAGAGAAACTGTCTCTAGGGAGACAAAATTTTGTTTCAA--GAGA-AACTATCTCAAGAGA
*
650141 GAAAAATTCATTTTAAGGGAAATGTTTTCAATGTCTATGTTTCAAGAGAAACTGTCTCAAGGGAG
63 GAAAAATTCATTTCAAGGGAAATGTTTTCAATGTCTATGTTTCAAGAGAAACTGTCTCAAGGGAG
* *
650206 ACAAAATTTTGTTTTAAGGGAAACTATCTCAAGAGAGACAACATTCA
128 ACAAAATTTT-TTTCAAGGGAAACTATCTCAAGAGAGA-AAAATTCA
650253 TTTCAAGAGAAACTGTCTCTAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCTAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGA-
* *
650318 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGAC
65 AAAATTCATTTCAAGGGAAATGTTTTCAATGTCTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
*
650383 AAAATTTTTTTCAAGGGAAACTATCTCAAGAGAGAAAAATTCG
130 AAAATTTTTTTCAAGGGAAACTATCTCAAGAGAGAAAAATTCA
* * *
650426 TTTCAAGAGAAACTGTCTCTAGGGAGACAAAATTTTGTTTCAAGGGAAATTGTCTCAAGAGAGA
1 TTTCAAGAGAAACTGTCTCTAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGA
650490 TAATGGTGAG
Statistics
Matches: 222, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
173 67 0.30
174 43 0.19
175 74 0.33
176 30 0.14
177 8 0.04
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (172 bp):
TTTCAAGAGAAACTGTCTCTAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAA
AAATTCATTTCAAGGGAAATGTTTTCAATGTCTATGTTTCAAGAGAAACTGTCTCAAGGGAGACA
AAATTTTTTTCAAGGGAAACTATCTCAAGAGAGAAAAATTCA
Found at i:654394 original size:5 final size:5
Alignment explanation
Indices: 654395--654435 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
654385 TGAAATGAAA
*
654395 AAAAT AAAAT AAAAT AAAAT AAAAT GAAAAAG AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT AAAA
654436 GTAATGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:656535 original size:21 final size:19
Alignment explanation
Indices: 656510--656562 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
656500 AACAAATACG
*
656510 ATATAAAACATATATATATAT
1 ATATAAAA-AAATATA-ATAT
656531 ATATAATAAAAATATAATAT
1 ATATAA-AAAAATATAATAT
656551 A-ATAAAAAAATA
1 ATATAAAAAAATA
656563 GAGGAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 7 0.23
19 4 0.13
20 5 0.17
21 12 0.40
22 2 0.07
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
ATATAAAAAAATATAATAT
Found at i:656552 original size:16 final size:17
Alignment explanation
Indices: 656525--656558 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
656515 AAACATATAT
656525 ATATATATATAATAAAA
1 ATATATATATAATAAAA
656542 ATATA-ATATAATAAAA
1 ATATATATATAATAAAA
656558 A
1 A
656559 AATAGAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATATATATAATAAAA
Found at i:658871 original size:36 final size:36
Alignment explanation
Indices: 658831--658915 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 36
658821 AATAGTTTTT
* *
658831 TTTATCATTTTAATA-AAGATATAATTTATAAAACCG
1 TTTATCA-TATAATATAACATATAATTTATAAAACCG
658867 TTTATCATATAATATAACATATAATTTATAAAACCG
1 TTTATCATATAATATAACATATAATTTATAAAACCG
658903 TTTAT-ATATAATA
1 TTTATCATATAATA
658916 AAAGTAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
35 14 0.30
36 32 0.70
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (36 bp):
TTTATCATATAATATAACATATAATTTATAAAACCG
Found at i:658933 original size:145 final size:145
Alignment explanation
Indices: 658728--658995 Score: 527
Period size: 145 Copynumber: 1.8 Consensus size: 145
658718 TATAAAGTAA
*
658728 ATATAATATAACATATAATTTATAAAACCTTTTATATATAATAAAAGTAATATGAATATACATAA
1 ATATAATATAACATATAATTTATAAAACCGTTTATATATAATAAAAGTAATATGAATATACATAA
658793 AAATTAGCGATTATTATTATCGAATTTTAATAGTTTTTTTTATCATTTTAATAAAGATATAATTT
66 AAATTAGCGATTATTATTATCGAATTTTAATAGTTTTTTTTATCATTTTAATAAAGATATAATTT
658858 ATAAAACCGTTTATC
131 ATAAAACCGTTTATC
658873 ATATAATATAACATATAATTTATAAAACCGTTTATATATAATAAAAGTAATATGAATATACATAA
1 ATATAATATAACATATAATTTATAAAACCGTTTATATATAATAAAAGTAATATGAATATACATAA
658938 AAATTAGCGATTATTATTATCGAATTTTAATAGTTTTTTTTATCATTTTAATAAAGAT
66 AAATTAGCGATTATTATTATCGAATTTTAATAGTTTTTTTTATCATTTTAATAAAGAT
658996 TTAAAACACA
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 122 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (145 bp):
ATATAATATAACATATAATTTATAAAACCGTTTATATATAATAAAAGTAATATGAATATACATAA
AAATTAGCGATTATTATTATCGAATTTTAATAGTTTTTTTTATCATTTTAATAAAGATATAATTT
ATAAAACCGTTTATC
Found at i:659611 original size:29 final size:30
Alignment explanation
Indices: 659573--659637 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
659563 TTCTTTAATC
*
659573 ATTAATCAAATCAAAT-TTCTT-TTGAAAAT
1 ATTAACCAAATCAAATATT-TTCTTGAAAAT
659602 ATTAACCAAATCAAATATTTTCTTGAAAAT
1 ATTAACCAAATCAAATATTTTCTTGAAAAT
659632 ATTAAC
1 ATTAAC
659638 TGAATTGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.38
Consensus pattern (30 bp):
ATTAACCAAATCAAATATTTTCTTGAAAAT
Found at i:659773 original size:19 final size:20
Alignment explanation
Indices: 659749--659786 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
659739 TTATTTGAAT
*
659749 TAATTTAATTAG-GTATTGA
1 TAATTTAATGAGTGTATTGA
659768 TAATTTAATGAGTGTATTG
1 TAATTTAATGAGTGTATTG
659787 TGGTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (20 bp):
TAATTTAATGAGTGTATTGA
Found at i:659839 original size:2 final size:2
Alignment explanation
Indices: 659832--659868 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
659822 GTTGAGCTTA
659832 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
659869 ATTTCAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:663699 original size:18 final size:17
Alignment explanation
Indices: 663656--663703 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
663646 GACAAATGTA
663656 TATTTTAAAATTAATTT
1 TATTTTAAAATTAATTT
* * *
663673 TCATGTTAATTATTTATTT
1 T-ATTTTAA-AATTAATTT
663692 TATTTTAAAATT
1 TATTTTAAAATT
663704 TTATATGTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
17 4 0.17
18 12 0.50
19 8 0.33
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTTTAAAATTAATTT
Found at i:666270 original size:24 final size:24
Alignment explanation
Indices: 666234--666280 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
666224 TCAAAGAGGA
*
666234 GATGATGTGGAAAATGAA-TATTAT
1 GATGATGTAGAAAAT-AATTATTAT
*
666258 GATGATTTAGAAAATAATTATTA
1 GATGATGTAGAAAATAATTATTA
666281 ATTTATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (24 bp):
GATGATGTAGAAAATAATTATTAT
Found at i:667908 original size:2 final size:2
Alignment explanation
Indices: 667901--667930 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
667891 GCATGTATTA
667901 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
667931 TAAGGTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:668786 original size:29 final size:29
Alignment explanation
Indices: 668752--668811 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
668742 CCTAAATTAA
668752 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
668781 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
668810 TT
1 TT
668812 GGTGAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:673468 original size:29 final size:29
Alignment explanation
Indices: 673434--673493 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
673424 CCTAAATTAA
673434 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
673463 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
673492 TT
1 TT
673494 GGTGAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:677860 original size:193 final size:192
Alignment explanation
Indices: 677531--677914 Score: 711
Period size: 193 Copynumber: 2.0 Consensus size: 192
677521 ATTTTCATAC
677531 AACTACACAAGTAGAAATCAAATTACCCTGAAAATTTGAATCATTTTTCATATATGGAAGGAATA
1 AACTACACAAGTAGAAATCAAATTACCCTGAAAATTTGAATCATTTTTCATATATGGAAGGAATA
677596 ACAAATGTGAATTTCCTTATTTTAGATATTTTTTCCCTTTTATGTAATTCTTTTGGAATCACTAA
66 ACAAATGTGAATTTCCTTATTTTAGATATTTTTTCCCTTTTATGTAATTCTTTTGGAATCACTAA
677661 GGTGTGTTTGTTTTTGTAGAGGTAAAAGTCTGCAGTCTGCGACCACATCTGC-GGCATCTGCAA
131 GGTGTGTTTGTTTTTGTAGA-GTAAAAGTCTGCAGTCTGC-ACCACATCTGCAGGCATCTGCAA
677724 AACTACACAAGTAGAAATCAAATTACCCTGAAAATTTGAATCATTTTTCATATATGGGAAGGAAT
1 AACTACACAAGTAGAAATCAAATTACCCTGAAAATTTGAATCATTTTTCATATAT-GGAAGGAAT
677789 AACAAATGTGAAATTTCCTTA-TTTAGATATTTTTTCCCTTTTATGTAATTCTTTTGGAA-CACT
65 AACAAATGTG-AATTTCCTTATTTTAGATATTTTTTCCCTTTTATGTAATTCTTTTGGAATCACT
677852 AAGGTGTGTTTGTTTTTGTAGAGTAAAAGTCTGCAGTCTGCACCACATCTGCAGGCATCTGCA
129 AAGGTGTGTTTGTTTTTGTAGAGTAAAAGTCTGCAGTCTGCACCACATCTGCAGGCATCTGCA
677915 GCAGAAGAGG
Statistics
Matches: 188, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
191 11 0.06
192 29 0.15
193 81 0.43
194 57 0.30
195 10 0.05
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (192 bp):
AACTACACAAGTAGAAATCAAATTACCCTGAAAATTTGAATCATTTTTCATATATGGAAGGAATA
ACAAATGTGAATTTCCTTATTTTAGATATTTTTTCCCTTTTATGTAATTCTTTTGGAATCACTAA
GGTGTGTTTGTTTTTGTAGAGTAAAAGTCTGCAGTCTGCACCACATCTGCAGGCATCTGCAA
Found at i:679004 original size:31 final size:31
Alignment explanation
Indices: 678935--679009 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
678925 TTTAAAAAAT
* *
678935 TATAAAA-TACTTATTAAATTTATCAAAAGAT
1 TATAAAATTA-TTAATAAATTTATCAAAAGAC
* * *
678966 TAGAAAATTATTAATAAATTTATCTAAATAC
1 TATAAAATTATTAATAAATTTATCAAAAGAC
*
678997 TATAAAATAATTA
1 TATAAAATTATTA
679010 TTATATTATC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (31 bp):
TATAAAATTATTAATAAATTTATCAAAAGAC
Found at i:682144 original size:18 final size:19
Alignment explanation
Indices: 682121--682158 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
682111 TATGAAGTTC
682121 AGGTGAT-AAATAAATTTT
1 AGGTGATAAAATAAATTTT
682139 AGGTGATAAAATAAATTTT
1 AGGTGATAAAATAAATTTT
682158 A
1 A
682159 CCCTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (19 bp):
AGGTGATAAAATAAATTTT
Found at i:684042 original size:42 final size:42
Alignment explanation
Indices: 683946--684473 Score: 315
Period size: 42 Copynumber: 12.9 Consensus size: 42
683936 GAAAAATAAT
* * **
683946 GTACTTTAGTGGAGTTTTTA-TACAAACGCCGCTAA--AGGTC
1 GTACTTTAGTGGCGTTTTAAGTACAAACGCCGCTAATTA-CAC
* * *
683986 GTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAATTCCAT
1 GTACTTTAGTGGCGTTTTAAGTACAAACGCCGCTAATTACAC
* * *
684028 GTACTTCAGTGGCG-TTTAACGTACAAACGCCACTACTTACAC
1 GTACTTTAGTGGCGTTTTAA-GTACAAACGCCGCTAATTACAC
* * * * ** * **
684070 GCACTATAGTGGCGTTTTTA-TATAAACGCCAATAAATA-TT
1 GTACTTTAGTGGCGTTTTAAGTACAAACGCCGCTAATTACAC
* *
684110 GTAC-ATACGTGGCGTTTT-A-TACAAACGCCGCTAATTACAA
1 GTACTTTA-GTGGCGTTTTAAGTACAAACGCCGCTAATTACAC
* * * * * *
684150 GTAC-ATACGTGGCGTTTTATGCATAAACGCCGATAAATACTA-
1 GTACTTTA-GTGGCGTTTTAAGTACAAACGCCGCTAATTAC-AC
* * *
684192 -TATTTTAGTGGCGTTTTTA-TACAAACGCCGCTAA--AGGAC
1 GTACTTTAGTGGCGTTTTAAGTACAAACGCCGCTAATTA-CAC
*
684231 GTACTTTAATGGCGTTTTAAGTACAAACGCCGCTAATTACAC
1 GTACTTTAGTGGCGTTTTAAGTACAAACGCCGCTAATTACAC
* * * * *
684273 GTTCTTTAGTGGCGTTTTATGCAAAAATGCCGCTAATTACAC
1 GTACTTTAGTGGCGTTTTAAGTACAAACGCCGCTAATTACAC
* * * * * * ** * *
684315 GTACTCTAGTTGCATTTTTA-TATAAACACCGAGAAATATTA-
1 GTACTTTAGTGGCGTTTTAAGTACAAACGCCGCTAATTA-CAC
* ** *
684356 -TACTTTAATGGCGTTGCAAGCACAAACGCCGCTAATTACAC
1 GTACTTTAGTGGCGTTTTAAGTACAAACGCCGCTAATTACAC
* * * *
684397 GTATTTTTGTGGCATTTTACA-CACAAACGCCGC-AATTACAC
1 GTACTTTAGTGGCGTTTTA-AGTACAAACGCCGCTAATTACAC
* * *
684438 GTACTTTAGTGGCATTTTTAA-CATAAACGCCGCTAA
1 GTACTTTAGTGGC-GTTTTAAGTACAAACGCCGCTAA
684474 AGGTAGTCTT
Statistics
Matches: 373, Mismatches: 91, Indels: 46
0.73 0.18 0.09
Matches are distributed among these distances:
38 2 0.01
39 18 0.05
40 90 0.24
41 114 0.31
42 142 0.38
43 7 0.02
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (42 bp):
GTACTTTAGTGGCGTTTTAAGTACAAACGCCGCTAATTACAC
Found at i:684127 original size:40 final size:39
Alignment explanation
Indices: 684078--684226 Score: 129
Period size: 40 Copynumber: 3.7 Consensus size: 39
684068 ACGCACTATA
* * *
684078 GTGGCGTTTTTATATAAACGCCAATAAATATTGTACATAC
1 GTGGCG-TTTTATACAAACGCCGATAAATAATGTACATAC
* * *
684118 GTGGCGTTTTATACAAACGCCGCTAATTACAAGTACATAC
1 GTGGCGTTTTATACAAACGCCGATAAATA-ATGTACATAC
* * * **
684158 GTGGCGTTTTATGCATAAACGCCGATAAATACTATATTTTA-
1 GTGGCGTTTTAT--ACAAACGCCGATAAATAATGTA-CATAC
*
684199 GTGGCGTTTTTATACAAACGCCGCTAAA
1 GTGGCG-TTTTATACAAACGCCGATAAA
684227 GGACGTACTT
Statistics
Matches: 88, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
39 19 0.22
40 39 0.44
41 8 0.09
42 22 0.25
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (39 bp):
GTGGCGTTTTATACAAACGCCGATAAATAATGTACATAC
Found at i:684148 original size:80 final size:81
Alignment explanation
Indices: 684049--684225 Score: 209
Period size: 80 Copynumber: 2.2 Consensus size: 81
684039 GCGTTTAACG
* * * * *
684049 TACAAACGCCACTACTTACACGCACTATA-GTGGCGTTTTTAT-ATAAACGCCAATAAATATTGT
1 TACAAACGCCGCTAATTACAAGCAC-ATACGTGGCG-TTTTATCATAAACGCCAATAAATACTAT
684112 A-CATACGTGGCG-TTTTA
64 ATCATA-GTGGCGTTTTTA
* *
684129 TACAAACGCCGCTAATTACAAGTACATACGTGGCGTTTTATGCATAAACGCCGATAAATACTATA
1 TACAAACGCCGCTAATTACAAGCACATACGTGGCGTTTTAT-CATAAACGCCAATAAATACTATA
**
684194 TTTTAGTGGCGTTTTTA
65 TCATAGTGGCGTTTTTA
684211 TACAAACGCCGCTAA
1 TACAAACGCCGCTAA
684226 AGGACGTACT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
79 9 0.11
80 27 0.33
81 25 0.30
82 22 0.27
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (81 bp):
TACAAACGCCGCTAATTACAAGCACATACGTGGCGTTTTATCATAAACGCCAATAAATACTATAT
CATAGTGGCGTTTTTA
Found at i:684370 original size:245 final size:247
Alignment explanation
Indices: 683915--684395 Score: 619
Period size: 245 Copynumber: 2.0 Consensus size: 247
683905 TATATTTAAC
*
683915 GGCGTTTTATGAGAAAACGCCGAAAAATAATGTACTTTAGTGGAGTTTTTATACAAACGCCGCTA
1 GGCGTTTTATGAGAAAACGCCGAAAAATAATATACTTTAGTGGAGTTTTTATACAAACGCCGCTA
* * * *
683980 AAGGTCGTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAATTCCATGTACTTCAGTGGCGTTT
66 AAGGACGTACTTTAATGGCGTTTTAAGCACAAACGCCGCTAATTACACGTACTTCAGTGGCGTTT
* * * * * *
684045 AACGTACAAACGCCACTACTTACACGCACTATAGTGGCGTTTTTATATAAACGCCAATAAATATT
131 AACGCAAAAACGCCACTAATTACACGCACTATAGTGGCATTTTTATATAAACACCAAGAAATATT
* * ** *
684110 GTACATACGTGGCGTT-TTA-TACAAACGCCGCTAATTACAAGTACATACGT
196 ATACATACATGGCGTTGCAAGCACAAACGCCGCTAATTACAAGTACATACGT
* * * * *
684160 GGCGTTTTATGCA-TAAACGCCGATAAATACTATATTTTAGTGGCGTTTTTATACAAACGCCGCT
1 GGCGTTTTATG-AGAAAACGCCGAAAAATAATATACTTTAGTGGAGTTTTTATACAAACGCCGCT
* * *
684224 AAAGGACGTACTTTAATGGCGTTTTAAGTACAAACGCCGCTAATTACACGTTCTTTAGTGGCGTT
65 AAAGGACGTACTTTAATGGCGTTTTAAGCACAAACGCCGCTAATTACACGTACTTCAGTGGCGTT
* * * * * * * *
684289 TTATGCAAAAATGCCGCTAATTACACGTACTCTAGTTGCATTTTTATATAAACACCGAGAAATAT
130 TAACGCAAAAACGCCACTAATTACACGCACTATAGTGGCATTTTTATATAAACACCAAGAAATAT
*
684354 TATACTTTA-ATGGCGTTGCAAGCACAAACGCCGCTAATTACA
195 TATAC-ATACATGGCGTTGCAAGCACAAACGCCGCTAATTACA
684396 CGTATTTTTG
Statistics
Matches: 199, Mismatches: 33, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
245 176 0.88
246 4 0.02
247 19 0.10
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (247 bp):
GGCGTTTTATGAGAAAACGCCGAAAAATAATATACTTTAGTGGAGTTTTTATACAAACGCCGCTA
AAGGACGTACTTTAATGGCGTTTTAAGCACAAACGCCGCTAATTACACGTACTTCAGTGGCGTTT
AACGCAAAAACGCCACTAATTACACGCACTATAGTGGCATTTTTATATAAACACCAAGAAATATT
ATACATACATGGCGTTGCAAGCACAAACGCCGCTAATTACAAGTACATACGT
Found at i:684388 original size:124 final size:124
Alignment explanation
Indices: 683946--684474 Score: 491
Period size: 124 Copynumber: 4.3 Consensus size: 124
683936 GAAAAATAAT
* * ** * *
683946 GTACTTTAGTGG-AGTTTTTATACAAACGCCGCTAAAGGTCGTACTTTAGTGGCGTTTTAAGCAC
1 GTACTTTAGTGGCA-TTTTTATATAAACGCCGATAAATATTGTACTTTAATGGCGTTTTAAGCAC
* * * * * * *
684010 AAACGCCGCTAATTCCATGTACTTCAGTGGCGTTTAACGTACAAACGCCACTACTTACAC
65 AAACGCCGCTAATTACACGTACTTTAGTGGCGTTTTACGCACAAACGCCGCTAATTACAC
* * * * * * *
684070 GCACTATAGTGGCGTTTTTATATAAACGCCAATAAATATTGTAC-ATACGTGGCGTTTT-A-TAC
1 GTACTTTAGTGGCATTTTTATATAAACGCCGATAAATATTGTACTTTA-ATGGCGTTTTAAGCAC
* * * * * *
684132 AAACGCCGCTAATTACAAGTAC-ATACGTGGCGTTTTATGCATAAACGCCGATAAATACTA-
65 AAACGCCGCTAATTACACGTACTTTA-GTGGCGTTTTACGCACAAACGCCGCTAATTAC-AC
* * * * * * *
684192 -TATTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGGA-CGTACTTTAATGGCGTTTTAAGTAC
1 GTACTTTAGTGGCATTTTTATATAAACGCCGATAAA-TATTGTACTTTAATGGCGTTTTAAGCAC
* * * *
684255 AAACGCCGCTAATTACACGTTCTTTAGTGGCGTTTTATGCAAAAATGCCGCTAATTACAC
65 AAACGCCGCTAATTACACGTACTTTAGTGGCGTTTTACGCACAAACGCCGCTAATTACAC
* * * * * **
684315 GTACTCTAGTTGCATTTTTATATAAACACCGAGAAATATTATACTTTAATGGCGTTGCAAGCACA
1 GTACTTTAGTGGCATTTTTATATAAACGCCGATAAATATTGTACTTTAATGGCGTTTTAAGCACA
* * * *
684380 AACGCCGCTAATTACACGTATTTTTGTGGCATTTTACACACAAACGCCGC-AATTACAC
66 AACGCCGCTAATTACACGTACTTTAGTGGCGTTTTACGCACAAACGCCGCTAATTACAC
* *
684438 GTACTTTAGTGGCATTTTTAACATAAACGCCGCTAAA
1 GTACTTTAGTGGCATTTTT-ATATAAACGCCGATAAA
684475 GGTAGTCTTG
Statistics
Matches: 324, Mismatches: 68, Indels: 26
0.78 0.16 0.06
Matches are distributed among these distances:
121 43 0.13
122 51 0.16
123 81 0.25
124 149 0.46
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (124 bp):
GTACTTTAGTGGCATTTTTATATAAACGCCGATAAATATTGTACTTTAATGGCGTTTTAAGCACA
AACGCCGCTAATTACACGTACTTTAGTGGCGTTTTACGCACAAACGCCGCTAATTACAC
Found at i:685609 original size:20 final size:20
Alignment explanation
Indices: 685586--685631 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
685576 TTCTTCTGAG
685586 ATCAAGGGACTATTTCTATA
1 ATCAAGGGACTATTTCTATA
685606 ATCAAGGGACTATTTCTATA
1 ATCAAGGGACTATTTCTATA
685626 ATCAAG
1 ATCAAG
685632 CAGTTCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
ATCAAGGGACTATTTCTATA
Found at i:687691 original size:21 final size:21
Alignment explanation
Indices: 687667--687725 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
687657 TGATTTATTA
**
687667 TTATGGATTTTATTTTTCTTG
1 TTATGGATTTTAAGTTTCTTG
*
687688 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTTAAGTTTCTTG
* *
687709 TTATGGATGTCAAGTTT
1 TTATGGATTTTAAGTTT
687726 ATTGGAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.03, G:0.20, T:0.58
Consensus pattern (21 bp):
TTATGGATTTTAAGTTTCTTG
Found at i:687941 original size:43 final size:43
Alignment explanation
Indices: 687894--688105 Score: 243
Period size: 43 Copynumber: 5.0 Consensus size: 43
687884 CGTTTGTTCT
* * * *
687894 AAAAAACGCCGCTATATAC-C-AGATCTTTTGCGGTGTTTGT-G
1 AAAAAACGCCGCTAAAT-CTCAAGACCTATTGCGGCGTTTGTGG
* *
687935 AGAAAAATGCCGTTAAATCTCAAGACCTATTGCGGCGTTTGTGG
1 A-AAAAACGCCGCTAAATCTCAAGACCTATTGCGGCGTTTGTGG
*
687979 AAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGG
1 AAAAAACGCCGCTAAATCTCAAGACCTATTGCGGCGTTTGTGG
* * * * *
688022 GAAAAACGCCGCTAAAGCTCAACACCTATTACGGCGTTTATTGG
1 AAAAAACGCCGCTAAATCTCAAGACCTATTGCGGCGTTT-GTGG
* *
688066 -AAAAACGCCGCTAAATATCAAAACCTATTGCGGCGTTTGT
1 AAAAAACGCCGCTAAATCTCAAGACCTATTGCGGCGTTTGT
688106 CAAATGCCGC
Statistics
Matches: 148, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.01
42 15 0.10
43 126 0.85
44 5 0.03
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (43 bp):
AAAAAACGCCGCTAAATCTCAAGACCTATTGCGGCGTTTGTGG
Found at i:692597 original size:22 final size:22
Alignment explanation
Indices: 692571--692618 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
692561 CGCATAGTCT
692571 GACATCTACATTCTTTAGATCC
1 GACATCTACATTCTTTAGATCC
692593 GACATCTACATTCTTTAGATCC
1 GACATCTACATTCTTTAGATCC
692615 GACA
1 GACA
692619 ACTTCCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.33
Consensus pattern (22 bp):
GACATCTACATTCTTTAGATCC
Found at i:694599 original size:90 final size:90
Alignment explanation
Indices: 694446--694707 Score: 319
Period size: 90 Copynumber: 2.9 Consensus size: 90
694436 GTTTATTCAT
* * * * * *
694446 GCTCTAGACCTACTTCCATTGAACCCAATTATAGAACAGATCCAAGCTCTAGACCTTTTTCCATC
1 GCTCTAGACCTACATCCATTGAACCCAATTATAGAGCGGATCCATGCTCTAGACCTGTGTCCATC
*
694511 GAATCCAATTATAGAGCGGATCTAA
66 GAACCCAATTATAGAGCGGATCTAA
* ** * * *
694536 GCTCTAGACCTTCATCCCGTGAACCCAATTATAGAGCGGGTCCATCCTCTAGACCTGCGTCCATC
1 GCTCTAGACCTACATCCATTGAACCCAATTATAGAGCGGATCCATGCTCTAGACCTGTGTCCATC
* * *
694601 GAACCCAGTTATGGAGCGGGTCTAA
66 GAACCCAATTATAGAGCGGATCTAA
* * * * *
694626 CCTCTAGACCTGCATCCATTGACCCCAATTATAGAGTGGATCC-TAGCTCTACACCTGTGTCCAT
1 GCTCTAGACCTACATCCATTGAACCCAATTATAGAGCGGATCCAT-GCTCTAGACCTGTGTCCAT
694690 CGAACCCAATTATAGAGC
65 CGAACCCAATTATAGAGC
694708 TGCACCAGAG
Statistics
Matches: 143, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
89 1 0.01
90 142 0.99
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (90 bp):
GCTCTAGACCTACATCCATTGAACCCAATTATAGAGCGGATCCATGCTCTAGACCTGTGTCCATC
GAACCCAATTATAGAGCGGATCTAA
Found at i:694706 original size:45 final size:45
Alignment explanation
Indices: 694446--694707 Score: 221
Period size: 45 Copynumber: 5.8 Consensus size: 45
694436 GTTTATTCAT
* * * * *
694446 GCTCTAGACCTACT-TCCATTGAACCCAATTATAGAACAGATCCAA
1 GCTCTAGACCT-GTATCCATCGAACCCAATTATAGAGCGGATCCTA
* * *
694491 GCTCTAGACCTTTTTCCATCGAATCCAATTATAGAGCGGAT-CTAA
1 GCTCTAGACCTGTATCCATCGAACCCAATTATAGAGCGGATCCT-A
* *
694536 GCTCTAGACCT-TCATCCCGT-GAACCCAATTATAGAGCGGGTCC-A
1 GCTCTAGACCTGT-AT-CCATCGAACCCAATTATAGAGCGGATCCTA
* ** * * *
694580 TCCTCTAGACCTGCGTCCATCGAACCCAGTTATGGAGCGGGT-CTAA
1 -GCTCTAGACCTGTATCCATCGAACCCAATTATAGAGCGGATCCT-A
* * * * *
694626 CCTCTAGACCTGCATCCATTGACCCCAATTATAGAGTGGATCCTA
1 GCTCTAGACCTGTATCCATCGAACCCAATTATAGAGCGGATCCTA
* *
694671 GCTCTACACCTGTGTCCATCGAACCCAATTATAGAGC
1 GCTCTAGACCTGTATCCATCGAACCCAATTATAGAGC
694708 TGCACCAGAG
Statistics
Matches: 176, Mismatches: 30, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
44 8 0.05
45 161 0.91
46 7 0.04
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (45 bp):
GCTCTAGACCTGTATCCATCGAACCCAATTATAGAGCGGATCCTA
Found at i:697784 original size:20 final size:20
Alignment explanation
Indices: 697737--697788 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
697727 GCTTGGAGCG
697737 TGGGGGGAATCGATACCCCC
1 TGGGGGGAATCGATACCCCC
** * *
697757 TCATGGGGAATCGGTTCCCCC
1 T-GGGGGGAATCGATACCCCC
697778 TGGGGGGAATC
1 TGGGGGGAATC
697789 TGTACCCCTG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.17, C:0.27, G:0.37, T:0.19
Consensus pattern (20 bp):
TGGGGGGAATCGATACCCCC
Found at i:706439 original size:28 final size:28
Alignment explanation
Indices: 706401--706465 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 28
706391 AATTAAACAT
706401 TAAAT-AAATAAATAACAAAAC-AATAGAA
1 TAAATAAAATAAA-AA-AAAACAAATAGAA
*
706429 T-AATAAAATAAAAAAAAACGAAATTGAA
1 TAAATAAAATAAAAAAAAAC-AAATAGAA
706457 TAAATAAAA
1 TAAATAAAA
706466 AAGGTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 5 0.16
27 5 0.16
28 15 0.47
29 7 0.22
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (28 bp):
TAAATAAAATAAAAAAAAACAAATAGAA
Found at i:707725 original size:39 final size:37
Alignment explanation
Indices: 707670--707835 Score: 176
Period size: 39 Copynumber: 4.4 Consensus size: 37
707660 TTTCAAAAAC
* * *
707670 ATATAAATTTTTAAAATGTTTTTTAAAAAACTATATATT
1 ATATATATTTTCAAAATG--TTTTCAAAAACTATATATT
* *
707709 ATATATATTTTCAAAATGGTTTTTAAAAATTATATATT
1 ATATATATTTTCAAAAT-GTTTTCAAAAACTATATATT
* * *
707747 ATATAAATGTTTTCATAATGTTTTCAAAAAGTATATA-T
1 ATAT--ATATTTTCAAAATGTTTTCAAAAACTATATATT
* *
707785 -TATATATTTTAAAAACGTTTTCAAAAACTATATATT
1 ATATATATTTTCAAAATGTTTTCAAAAACTATATATT
707821 ATATA-ATTTTCAAAA
1 ATATATATTTTCAAAA
707836 AATATATTTT
Statistics
Matches: 108, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
35 26 0.24
36 10 0.09
37 7 0.06
38 22 0.20
39 31 0.29
40 12 0.11
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (37 bp):
ATATATATTTTCAAAATGTTTTCAAAAACTATATATT
Found at i:707834 original size:25 final size:25
Alignment explanation
Indices: 707802--707878 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
707792 TTTAAAAACG
*
707802 TTTTCAAAAACTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
* * **
707827 TTTTCAAAAAATATATTTTCAAAATGG
1 TTTTCAAAAAATATATATT--ATATAA
* *
707854 TTTTTAAAAATTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
707879 ATGTTTTCAT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
25 20 0.51
27 19 0.49
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (25 bp):
TTTTCAAAAAATATATATTATATAA
Found at i:707842 original size:126 final size:127
Alignment explanation
Indices: 707711--707945 Score: 429
Period size: 126 Copynumber: 1.9 Consensus size: 127
707701 TATATATTAT
*
707711 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAATGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTC-AAA
*
707776 AGTATATA-T-TATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
65 AGTATATATTATATATATTTTAAAAACGCTTTCAAAAACTATATATTATATAATTTTCAAAAA
707837 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
707902 GTATATATTATATATATTTTAAAAACGCTTTCAAAAACTATATA
66 GTATATATTATATATATTTTAAAAACGCTTTCAAAAACTATATA
707946 ATTTTCAAAA
Statistics
Matches: 105, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
125 11 0.10
126 61 0.58
127 33 0.31
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (127 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
GTATATATTATATATATTTTAAAAACGCTTTCAAAAACTATATATTATATAATTTTCAAAAA
Found at i:707846 original size:15 final size:16
Alignment explanation
Indices: 707821--707850 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
707811 ACTATATATT
707821 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
707837 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
707851 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:707850 original size:40 final size:37
Alignment explanation
Indices: 707690--707836 Score: 167
Period size: 35 Copynumber: 3.9 Consensus size: 37
707680 TTAAAATGTT
*
707690 TTTTAAAAAACTATATATTATATATATTTTC-AAAATGG
1 TTTTCAAAAACTATATATTATATA-ATTTTCAAAAAT-G
* * *
707728 TTTTTAAAAATTATATATTATATAAATGTTTTC-ATAATG
1 TTTTCAAAAACTATATATTATAT-AA--TTTTCAAAAATG
* *
707767 TTTTCAAAAAGTATATATTATAT-ATTTT-AAAAACG
1 TTTTCAAAAACTATATATTATATAATTTTCAAAAATG
707802 TTTTCAAAAACTATATATTATATAATTTTCAAAAA
1 TTTTCAAAAACTATATATTATATAATTTTCAAAAA
707837 ATATATTTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
35 30 0.32
36 5 0.05
37 6 0.06
38 22 0.23
39 23 0.24
40 9 0.09
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTTCAAAAACTATATATTATATAATTTTCAAAAATG
Found at i:707886 original size:40 final size:38
Alignment explanation
Indices: 707855--707945 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 38
707845 TCAAAATGGT
* *
707855 TTTTAAAAATTATATATTATATAAATGTTTTCATAACG
1 TTTTAAAAAGTATATATTATATAAATGTTTTCAAAACG
* * *
707893 TTTTCAAAAGTATATATTATAT--ATATTTTAAAAACG
1 TTTTAAAAAGTATATATTATATAAATGTTTTCAAAACG
* *
707929 CTTTCAAAAACTATATA
1 -TTTTAAAAAGTATATA
707946 ATTTTCAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
36 11 0.25
37 13 0.30
38 20 0.45
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (38 bp):
TTTTAAAAAGTATATATTATATAAATGTTTTCAAAACG
Done.