Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007775.1 Hibiscus syriacus cultivar Beakdansim tig00110056_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: 599510
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:384367 original size:20 final size:21
Alignment explanation
Indices: 384331--384369 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
384321 AGTTTAATTA
*
384331 TTTATTTATTCTATAAAAAAG
1 TTTAGTTATTCTATAAAAAAG
384352 TTTAGTTATT-TATAAAAA
1 TTTAGTTATTCTATAAAAA
384370 TTAATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (21 bp):
TTTAGTTATTCTATAAAAAAG
Found at i:391748 original size:21 final size:21
Alignment explanation
Indices: 391722--391761 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
391712 CAGAACCCCA
*
391722 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
391743 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
391762 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:391796 original size:20 final size:21
Alignment explanation
Indices: 391742--391804 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
391732 GATTCCCCTG
391742 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
391766 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
391786 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
391805 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:399643 original size:24 final size:24
Alignment explanation
Indices: 399616--399687 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
399606 AAACGGAGAT
399616 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
399640 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
*
399664 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
399688 GTAATGTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:399645 original size:12 final size:12
Alignment explanation
Indices: 399618--399687 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
399608 ACGGAGATAT
* *
399618 CAGAAATCAAAA
1 CAGAATTCAGAA
*
399630 CAGAATTCAGAT
1 CAGAATTCAGAA
*
399642 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
399654 CAGAATCCAGAT
1 CAGAATTCAGAA
*
399666 CAGAAATCAGAA
1 CAGAATTCAGAA
399678 CAGAATTCAG
1 CAGAATTCAG
399688 GTAATGTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:399698 original size:48 final size:47
Alignment explanation
Indices: 399616--399724 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 47
399606 AAACGGAGAT
* * *
399616 ATCAGAAATCAAAACAGAATTCAGATCAGATATCATAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCA
* *
399663 GATCAGAAATCAGAACAGAATTCAGGTAATG-TATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAGAACAGAATCCA
*
399711 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
399725 TAAAATATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.96
49 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAGAACAGAATCCA
Found at i:399722 original size:24 final size:25
Alignment explanation
Indices: 399616--399724 Score: 102
Period size: 24 Copynumber: 4.5 Consensus size: 25
399606 AAACGGAGAT
*
399616 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
399640 ATCAGATATCATAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
399664 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
399688 GTAATG-TATCAGAACAGAATTCAAG
1 ATCA-GAAATCAGAACAGAATTCAAG
*
399713 -TCGGAAATCAGA
1 ATCAGAAATCAGA
399725 TAAAATATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.04
24 62 0.89
25 5 0.07
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:407447 original size:45 final size:45
Alignment explanation
Indices: 407396--407631 Score: 373
Period size: 45 Copynumber: 5.2 Consensus size: 45
407386 CATTCATTAT
* * * *
407396 TTTCATTTATGGAATCCTTCCATGCCTTTAATACACAGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
*
407441 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
407486 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * *
407531 TTTTATTTATGACATCCTTTCATGCCTTTAATGCACCTTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
407576 TTTCGTTTATTGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
*
407621 TTTAATTTATG
1 TTTCATTTATG
407632 TAATGAAAAC
Statistics
Matches: 174, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 174 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:408758 original size:19 final size:19
Alignment explanation
Indices: 408720--408759 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
408710 CGAATAATTG
* *
408720 AATCGAATATAATATGTTA
1 AATCAAATATAAAATGTTA
*
408739 AATCAAATATAAAATTTTA
1 AATCAAATATAAAATGTTA
408758 AA
1 AA
408760 ATTACTTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (19 bp):
AATCAAATATAAAATGTTA
Found at i:409727 original size:89 final size:90
Alignment explanation
Indices: 409562--409752 Score: 267
Period size: 89 Copynumber: 2.1 Consensus size: 90
409552 CAGAACTGCA
* * * * *
409562 TCCGTACGGCTTACCCTAAGCACATAGAAAAATAAAGCCAACCTAAGGTTATTCCTTGGGGCCTA
1 TCCGTA-GGGTTACCCTAAGCACACAGAAAAAGAAAGCCAACCTAAGGATATGCCTTGGGGCCTA
* *
409627 TGGGCCTACCCAAGGGTATCCTTAGG
65 TAGGCCAACCCAAGGGTATCCTTAGG
* * *
409653 TCCGTAGGGTTACCCTAAGCACACAGCAAAGGGAA-CCAACCTAAGGATATGCCTTGGGGCCTAT
1 TCCGTAGGGTTACCCTAAGCACACAGAAAAAGAAAGCCAACCTAAGGATATGCCTTGGGGCCTAT
409717 AGGCCAACCCAAGGGTATCCTTAGG
66 AGGCCAACCCAAGGGTATCCTTAGG
*
409742 TCCGTAAGGTT
1 TCCGTAGGGTT
409753 TTACCAGCTG
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
89 60 0.67
90 23 0.26
91 6 0.07
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.21
Consensus pattern (90 bp):
TCCGTAGGGTTACCCTAAGCACACAGAAAAAGAAAGCCAACCTAAGGATATGCCTTGGGGCCTAT
AGGCCAACCCAAGGGTATCCTTAGG
Found at i:414571 original size:89 final size:90
Alignment explanation
Indices: 414447--414617 Score: 272
Period size: 89 Copynumber: 1.9 Consensus size: 90
414437 CTGTAGGGCA
* * * * *
414447 TACCCTAAGCACATAGCAAAAGGGAGCCAACCTAAGGATATTCCTCGGGGCCTATGGGCCTACCC
1 TACCCTAAGCACACAGCAAAAGAGAACCAACCTAAGGACATGCCTCGGGGCCTATGGGCCTACCC
414512 AAGGGTATCCTTAGGTCATTAGGGT
66 AAGGGTATCCTTAGGTCATTAGGGT
*
414537 TACCCTAAGCACACAG-AAAAGAGAACCAACCTAAGGACATGCCTTGGGGCCTATGGGCCTACCC
1 TACCCTAAGCACACAGCAAAAGAGAACCAACCTAAGGACATGCCTCGGGGCCTATGGGCCTACCC
*
414601 AAGGGTATTCTTAGGTC
66 AAGGGTATCCTTAGGTC
414618 CGTAAGGTCT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 59 0.80
90 15 0.20
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (90 bp):
TACCCTAAGCACACAGCAAAAGAGAACCAACCTAAGGACATGCCTCGGGGCCTATGGGCCTACCC
AAGGGTATCCTTAGGTCATTAGGGT
Found at i:417192 original size:17 final size:17
Alignment explanation
Indices: 417166--417198 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
417156 TCAAAAAAAT
417166 AAAATATGACTTTTTGA
1 AAAATATGACTTTTTGA
*
417183 AAAATTTGACTTTTTG
1 AAAATATGACTTTTTG
417199 GTCAAAGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
AAAATATGACTTTTTGA
Found at i:417459 original size:13 final size:13
Alignment explanation
Indices: 417433--417475 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
417423 TAGCGGCTTT
**
417433 GCTCAGTGATTCG
1 GCTCAGTGGCTCG
*
417446 GTTCAGTGGCTCG
1 GCTCAGTGGCTCG
*
417459 GCTCGGTGGCTCG
1 GCTCAGTGGCTCG
417472 GCTC
1 GCTC
417476 GATGGCTCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.07, C:0.28, G:0.37, T:0.28
Consensus pattern (13 bp):
GCTCAGTGGCTCG
Found at i:417476 original size:13 final size:13
Alignment explanation
Indices: 417451--417483 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
417441 ATTCGGTTCA
417451 GTGGCTCGGCTCG
1 GTGGCTCGGCTCG
417464 GTGGCTCGGCTCG
1 GTGGCTCGGCTCG
*
417477 ATGGCTC
1 GTGGCTC
417484 AACTCTGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.03, C:0.30, G:0.42, T:0.24
Consensus pattern (13 bp):
GTGGCTCGGCTCG
Found at i:422526 original size:21 final size:21
Alignment explanation
Indices: 422477--422539 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
422467 GCATATGAAA
* *
422477 TTGTCCTGAAGGACCTGTGAG
1 TTGTCCCGAAGGACCTATGAG
*
422498 TATGTCCCGAAAGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAG
422520 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
422540 AACCCTCGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:429301 original size:22 final size:21
Alignment explanation
Indices: 429275--429331 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
429265 GCATATGAAA
* *
429275 TTGTCCCGAAGGACCTGTGAG
1 TTGTCCCGAAGGACCTATAAG
*
429296 TATGTCCCGAATGACCTATAAG
1 T-TGTCCCGAAGGACCTATAAG
*
429318 TTATCCCGAAGGAC
1 TTGTCCCGAAGGAC
429332 TTATGAAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATAAG
Found at i:437013 original size:15 final size:16
Alignment explanation
Indices: 436969--437013 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
436959 GCCCTAAATT
436969 GAAA-AAAAAAAG-AA
1 GAAAGAAAAAAAGAAA
*
436983 GAAAGAAAAAGAGAAA
1 GAAAGAAAAAAAGAAA
436999 G-AAGAAAAAAAGAAA
1 GAAAGAAAAAAAGAAA
437014 AATAAGATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 4 0.15
15 20 0.74
16 3 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAAAAGAAA
Found at i:437998 original size:60 final size:63
Alignment explanation
Indices: 437849--438011 Score: 206
Period size: 65 Copynumber: 2.6 Consensus size: 63
437839 CTTGAGATTG
* * * * * * *
437849 GATTTTAACTTCACAACGAATGATATCCAACTCAAAGGCAATTTGGTGAAACTTACTCAAGCTTG
1 GATTTCAACTTCACAACGAAGGATATCCAAATCAAAGCCAATTTGGTAAAAC-TAAT-AAGCTTA
*
437914 GATTTCAACTTCACAACGAAGGATATCAAAATCAAAGCCAATTTGGTAAAAC-AAT-A-CTTA
1 GATTTCAACTTCACAACGAAGGATATCCAAATCAAAGCCAATTTGGTAAAACTAATAAGCTTA
*
437974 GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGC
1 GATTTCAACTTCACAACGAAGGATATCCAAATCAAAGC
438012 TCAACTTCAC
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
60 39 0.44
61 1 0.01
63 2 0.02
65 46 0.52
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (63 bp):
GATTTCAACTTCACAACGAAGGATATCCAAATCAAAGCCAATTTGGTAAAACTAATAAGCTTA
Found at i:438767 original size:15 final size:16
Alignment explanation
Indices: 438747--438776 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
438737 ATATTATGTG
438747 TTACAT-TTATAATAT
1 TTACATATTATAATAT
438762 TTACATATTATAATA
1 TTACATATTATAATA
438777 AACATTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (16 bp):
TTACATATTATAATAT
Found at i:439947 original size:18 final size:19
Alignment explanation
Indices: 439897--439948 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
439887 TTTTCTTTCT
*
439897 TTTTATTTTTATTTA-AATA
1 TTTTA-TTTTATTTATTATA
*
439916 TTTTATATTA-TTATTATA
1 TTTTATTTTATTTATTATA
439934 -TTTATTTTATTTATT
1 TTTTATTTTATTTATT
439949 TTAACGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 11 0.39
18 12 0.43
19 5 0.18
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTATTTTATTTATTATA
Found at i:440161 original size:29 final size:29
Alignment explanation
Indices: 440106--440181 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
440096 CTTTTTTTCC
440106 TTTGTTTTTTTTAATTTTTTGGGTTTA-TA
1 TTTGTTTTTTTT-ATTTTTTGGGTTTATTA
*
440135 TTTGTTTTGTTTTATTTTTAT-GTTTTATTA
1 TTTGTTTT-TTTTATTTTT-TGGGTTTATTA
*
440165 TTT-TCTTATTTTATTTT
1 TTTGT-TTTTTTTATTTT
440182 ATTTTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 29 0.71
30 12 0.29
ACGTcount: A:0.13, C:0.01, G:0.09, T:0.76
Consensus pattern (29 bp):
TTTGTTTTTTTTATTTTTTGGGTTTATTA
Found at i:440165 original size:16 final size:15
Alignment explanation
Indices: 440146--440201 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
440136 TTGTTTTGTT
440146 TTATTTTTATGTTTTA
1 TTATTTTTAT-TTTTA
440162 TTATTTTCT-TATTTTA
1 TTATTTT-TAT-TTTTA
*
440178 TTTTATTTTATTTTTA
1 TTAT-TTTTATTTTTA
440194 TCTATTTT
1 T-TATTTT
440202 ACAATGACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
16 26 0.79
17 7 0.21
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.77
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Found at i:440284 original size:38 final size:38
Alignment explanation
Indices: 440212--440284 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
440202 ACAATGACAT
* * *
440212 TTTATTTTAATTATTTATTTATTTTTGTTTTCTTTGTC
1 TTTATTTTAATTATTTAGTTACTTTTGTTATCTTTGTC
*
440250 TTTATTTTATTTATTTTAGTTACTTTT-TTATCTTT
1 TTTATTTTAATTA-TTTAGTTACTTTTGTTATCTTT
440285 ATTTTATCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 19 0.63
39 11 0.37
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.74
Consensus pattern (38 bp):
TTTATTTTAATTATTTAGTTACTTTTGTTATCTTTGTC
Found at i:440310 original size:13 final size:13
Alignment explanation
Indices: 440294--440328 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
440284 TATTTTATCC
440294 TCTTATTTCTTTA
1 TCTTATTTCTTTA
*
440307 TCTTATTTTTTTA
1 TCTTATTTCTTTA
*
440320 TTTTATTTC
1 TCTTATTTC
440329 CCCTACTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (13 bp):
TCTTATTTCTTTA
Found at i:444857 original size:20 final size:22
Alignment explanation
Indices: 444832--444873 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
444822 AAAAAATTAT
444832 CTAAAACATT-AT-TTTTTTAC
1 CTAAAACATTAATGTTTTTTAC
*
444852 CTAAAATATTAATGTTTTTTAC
1 CTAAAACATTAATGTTTTTTAC
444874 ATTTTCGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (22 bp):
CTAAAACATTAATGTTTTTTAC
Found at i:447303 original size:35 final size:34
Alignment explanation
Indices: 447218--447304 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
447208 AAAATAATTT
* *
447218 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGA
* *
447252 TAAATGATAACCAAATTACAATAACTGATATTAAATGA
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGA
447290 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
447305 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 4 0.09
38 10 0.23
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGA
Found at i:449557 original size:16 final size:16
Alignment explanation
Indices: 449533--449579 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
449523 TATATCTGCA
*
449533 AAAAAATTAAATAAGT
1 AAAATATTAAATAAGT
449549 AAAATATTAAATAAGT
1 AAAATATTAAATAAGT
*
449565 TAAATACTTAAATAA
1 AAAATA-TTAAATAA
449580 ATTAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 20 0.71
17 8 0.29
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (16 bp):
AAAATATTAAATAAGT
Found at i:449567 original size:9 final size:9
Alignment explanation
Indices: 449536--449596 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
449526 ATCTGCAAAA
449536 AAATTAAAT
1 AAATTAAAT
*
449545 -AAGTAAA-
1 AAATTAAAT
*
449552 ATATTAAAT
1 AAATTAAAT
*
449561 AAGTTAAAT
1 AAATTAAAT
*
449570 -ACTTAAAT
1 AAATTAAAT
449578 AAATTAAAT
1 AAATTAAAT
449587 AAATTAAAT
1 AAATTAAAT
449596 A
1 A
449597 CAAAATATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
8 18 0.43
9 24 0.57
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:449568 original size:17 final size:17
Alignment explanation
Indices: 449533--449596 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 17
449523 TATATCTGCA
449533 AAAAAATTAAATAAG-T
1 AAAAAATTAAATAAGTT
*
449549 AAAATATTAAATAAGTT
1 AAAAAATTAAATAAGTT
* * *
449566 AAATACTTAAATAAATT
1 AAAAAATTAAATAAGTT
449583 AAATAAATTAAATA
1 AAA-AAATTAAATA
449597 CAAAATATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
16 14 0.36
17 17 0.44
18 8 0.21
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (17 bp):
AAAAAATTAAATAAGTT
Found at i:449593 original size:26 final size:25
Alignment explanation
Indices: 449536--449597 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
449526 ATCTGCAAAA
* *
449536 AAATTAAATAAGTAAAATATTAAAT
1 AAATTAAATACGTAAAAAATTAAAT
* *
449561 AAGTTAAATACTTAAATAAATTAAAT
1 AAATTAAATACGTAAA-AAATTAAAT
449587 AAATTAAATAC
1 AAATTAAATAC
449598 AAAATATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
25 13 0.42
26 18 0.58
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (25 bp):
AAATTAAATACGTAAAAAATTAAAT
Found at i:451797 original size:7 final size:7
Alignment explanation
Indices: 451785--451831 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
451775 AGCTTCTCTC
*
451785 TCACAAG
1 TCACAAA
451792 TCACAAA
1 TCACAAA
451799 TCACAAA
1 TCACAAA
451806 TCACAAA
1 TCACAAA
451813 TCACAAA
1 TCACAAA
451820 TCACAAA
1 TCACAAA
451827 TCACA
1 TCACA
451832 CACCACCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.53, C:0.30, G:0.02, T:0.15
Consensus pattern (7 bp):
TCACAAA
Found at i:457317 original size:19 final size:18
Alignment explanation
Indices: 457278--457318 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
457268 GTATTTTGTT
*
457278 ATTTTAATAAAAATATTA
1 ATTTTAATAAAAATATAA
*
457296 ATTTTAATTAAAATAATAA
1 ATTTTAATAAAAAT-ATAA
457315 ATTT
1 ATTT
457319 GAGGTCTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTAATAAAAATATAA
Found at i:458612 original size:16 final size:16
Alignment explanation
Indices: 458591--458621 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
458581 ATTAGCATAG
458591 TTGAAAGTTGGCAAAT
1 TTGAAAGTTGGCAAAT
458607 TTGAAAGTTGGCAAA
1 TTGAAAGTTGGCAAA
458622 GTTAACATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (16 bp):
TTGAAAGTTGGCAAAT
Found at i:461771 original size:16 final size:16
Alignment explanation
Indices: 461746--461794 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
461736 TGAAAAATTA
*
461746 GCAAAGTTGAAAGTTG
1 GCAAAATTGAAAGTTG
*
461762 GCAAATTTGAAAGTTG
1 GCAAAATTGAAAGTTG
*
461778 GCAAAATTAAAAGTTG
1 GCAAAATTGAAAGTTG
461794 G
1 G
461795 TAAAGTTGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.41, C:0.06, G:0.27, T:0.27
Consensus pattern (16 bp):
GCAAAATTGAAAGTTG
Found at i:463768 original size:9 final size:9
Alignment explanation
Indices: 463754--464059 Score: 64
Period size: 9 Copynumber: 33.0 Consensus size: 9
463744 AAAAGAAAGG
*
463754 TAAAGATAA
1 TAAAGAAAA
463763 TAAAGAAAA
1 TAAAGAAAA
*
463772 TAAATAAAGA
1 TAAAGAAA-A
* *
463782 AAATAAAAAA
1 TAA-AGAAAA
*
463792 CAAATG-AAA
1 TAAA-GAAAA
463801 TAAAGAAAA
1 TAAAGAAAA
*
463810 T---G-AGA
1 TAAAGAAAA
463815 TAAAGAAAA
1 TAAAGAAAA
*
463824 TATAAAAAAGA
1 TA-AAGAAA-A
463835 TAAA-AAAA
1 TAAAGAAAA
*
463843 TAAATAAAGA
1 TAAAGAAA-A
463853 TAAAGTAAAGA
1 TAAAG-AAA-A
463864 TAAA-AAAA
1 TAAAGAAAA
*
463872 GTAAATAAAA
1 -TAAAGAAAA
* *
463882 TAAATAACA
1 TAAAGAAAA
*
463891 T--A-AATA
1 TAAAGAAAA
463897 TAAAGAAAA
1 TAAAGAAAA
463906 TAAAAGGAATAA
1 T-AAA-GAA-AA
* *
463918 AAATACAAATA
1 TAA-AGAAA-A
*
463929 TAGATAAAAAA
1 TA-A-AGAAAA
*
463940 TAAATAAAA
1 TAAAGAAAA
*
463949 TAAAGAAGA
1 TAAAGAAAA
*
463958 TAATA-ATAA
1 TAA-AGAAAA
* * *
463967 TATATATAA
1 TAAAGAAAA
*
463976 TAAA-TAAA
1 TAAAGAAAA
*
463984 TAAATAAAA
1 TAAAGAAAA
*
463993 -AAGAGTGAAA
1 TAA-AG-AAAA
*
464003 TAAAAATAAA
1 TAAAGA-AAA
*
464013 TAAATAAATA
1 TAAAGAAA-A
*
464023 TAAAGGAAA
1 TAAAGAAAA
464032 TAAA-AAAA
1 TAAAGAAAA
464040 TAAAGTAAAGA
1 TAAAG-AAA-A
464051 TAAAGAAAA
1 TAAAGAAAA
464060 AAAATAAAAA
Statistics
Matches: 226, Mismatches: 36, Indels: 70
0.68 0.11 0.21
Matches are distributed among these distances:
5 3 0.01
6 5 0.02
7 1 0.00
8 25 0.11
9 94 0.42
10 53 0.23
11 36 0.16
12 9 0.04
ACGTcount: A:0.72, C:0.01, G:0.09, T:0.18
Consensus pattern (9 bp):
TAAAGAAAA
Found at i:463778 original size:4 final size:4
Alignment explanation
Indices: 463769--464048 Score: 75
Period size: 4 Copynumber: 66.8 Consensus size: 4
463759 ATAATAAAGA
* * * *
463769 AAAT AAAT AAAGA AAAT AAA- AAAC AAAT GAAAT AAAGA AAAT GAGAT
1 AAAT AAAT AAA-T AAAT AAAT AAAT AAAT -AAAT AAA-T AAAT -AAAT
* * * *
463816 AAAG AAA- ATAT AAAA AAGAT AAAA AAAT AAAT AAAGAT AAAGT AAAGAT
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT -AA-AT AAA-T -AA-AT
* *
463865 AAAA AAAGT AAAT AAAAT AAAT AACAT AAAT --AT AAAGA AAAT AAA-
1 AAAT AAA-T AAAT -AAAT AAAT AA-AT AAAT AAAT AAA-T AAAT AAAT
* *
463910 AGGAAT AAA- AATAC AAAT ATAGAT AAA- AAAT AAAT AAAAT AAAG AAGAT
1 A--AAT AAAT AA-AT AAAT A-A-AT AAAT AAAT AAAT -AAAT AAAT AA-AT
* *
463959 -AAT -AAT -AAT ATAT ATAAT AAAT AAAT AAAT AAAA AAGAGT GAAAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AA-A-T -AAAT
* *
464004 -AA- AAAT AAAT AAAT AAAT --AT AAAGG AAAT AAAA AAAT AAAGT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAA-T AAA
464049 GATAAAGAAA
Statistics
Matches: 208, Mismatches: 29, Indels: 77
0.66 0.09 0.25
Matches are distributed among these distances:
2 4 0.02
3 23 0.11
4 108 0.52
5 60 0.29
6 10 0.05
7 3 0.01
ACGTcount: A:0.72, C:0.01, G:0.08, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:463804 original size:38 final size:39
Alignment explanation
Indices: 463761--464072 Score: 147
Period size: 40 Copynumber: 7.6 Consensus size: 39
463751 AGGTAAAGAT
*
463761 AATAAAGAAAAT-AAATAAAGAAAATAAAAAACAAATGA
1 AATAAAGAAAATAAAATAAAGAAAATAAAAAACAAATAA
* * *
463799 AATAAAGAAAATGAGATAAAGAAAATATAAAAA-AGATAA
1 AATAAAGAAAATAAAATAAAGAAAATA-AAAAACAAATAA
* *
463838 AA-AAA-TAAATAAAGATAAAGTAAAGATAAAAAAAGTAAATAA
1 AATAAAGAAAATAAA-ATAAAG-AAA-AT-AAAAAA-CAAATAA
* * *
463880 AATAAATAACATAAATATAAAGAAAATAAAAGGAATAAAAATACA
1 AATAAAGAAAATAAA-ATAAAGAAAAT-AAA--AA-ACAAATA-A
* * * * *
463925 AATATAGATAA-AAAATAAATAAAATAAAGAAGATAATAA
1 AATAAAGAAAATAAAATAAAGAAAATAAAAAACA-AATAA
* * * * *
463964 TAATATATATAAT-AAATAAA-TAAATAAAAAAGAGTGAAATAAA
1 -AATAAAGAAAATAAAATAAAGAAAAT-AAAAA-A--CAAAT-AA
* * *
464007 AATAAA-TAAATAAATATAAAGGAAATAAAAAAATAAAGTAA
1 AATAAAGAAAATAAA-ATAAAGAAAAT-AAAAAACAAA-TAA
*
464048 AGATAAAGAAAA-AAAATAAAAAAAA
1 A-ATAAAGAAAATAAAATAAAGAAAA
464073 ATTATAGTAA
Statistics
Matches: 217, Mismatches: 29, Indels: 53
0.73 0.10 0.18
Matches are distributed among these distances:
37 5 0.02
38 21 0.10
39 29 0.13
40 38 0.18
41 19 0.09
42 35 0.16
43 29 0.13
44 32 0.15
45 9 0.04
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (39 bp):
AATAAAGAAAATAAAATAAAGAAAATAAAAAACAAATAA
Found at i:463812 original size:14 final size:13
Alignment explanation
Indices: 463761--463909 Score: 110
Period size: 14 Copynumber: 11.2 Consensus size: 13
463751 AGGTAAAGAT
463761 AATAAAGAAAATA
1 AATAAAGAAAATA
463774 AATAAAGAAAATA
1 AATAAAGAAAATA
*
463787 AA-AAA-CAAATGA
1 AATAAAGAAAAT-A
463799 AATAAAGAAAATGA
1 AATAAAGAAAAT-A
*
463813 GATAAAGAAAATA
1 AATAAAGAAAATA
* *
463826 TAAAAAAGATAAAAA
1 -AATAAAGA-AAATA
*
463841 AATAAATAAAGATA
1 AATAAAGAAA-ATA
*
463855 AAGTAAAGATAAAAA
1 AA-TAAAGA-AAATA
*
463870 AAGTAAATAAAATA
1 AA-TAAAGAAAATA
*
463884 AATAACA-TAAAT-
1 AATAA-AGAAAATA
463896 -ATAAAGAAAATA
1 AATAAAGAAAATA
463908 AA
1 AA
463910 AGGAATAAAA
Statistics
Matches: 109, Mismatches: 15, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
10 1 0.01
11 12 0.11
12 6 0.06
13 29 0.27
14 40 0.37
15 19 0.17
16 2 0.02
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (13 bp):
AATAAAGAAAATA
Found at i:463865 original size:29 final size:26
Alignment explanation
Indices: 463769--464063 Score: 138
Period size: 29 Copynumber: 10.8 Consensus size: 26
463759 ATAATAAAGA
* *
463769 AAAT-AAATAAAGAAAAT-AAAAAAC
1 AAATAAAATAAATAAAATAAAAAAAT
* * * *
463793 AAATGAAATAAAGAAAAT---GAGAT
1 AAATAAAATAAATAAAATAAAAAAAT
* *
463816 AAAGAAAATATAAAAAAGATAAAAAAAT
1 AAATAAAATA-AATAAA-ATAAAAAAAT
463844 AAATAAAGATAAAGTAAAGATAAAAAAAGT
1 AAATAAA-ATAAA-TAAA-ATAAAAAAA-T
* *
463874 AAATAAAATAAATAACATAAATATAAAGA
1 AAATAAAATAAATAAAATAAA-A-AAA-T
** * *
463903 AAATAAAAGGAATAAAAATACAAATAT
1 AAATAAAATAAAT-AAAATAAAAAAAT
* *
463930 AGATAAAAAATAAATAAAATAAAGAAGAT
1 A-A-ATAAAATAAATAAAATAAA-AAAAT
* * *
463959 -AATAATAATATATATAATAAATAAAT
1 AAATAA-AATAAATAAAATAAAAAAAT
*
463985 AAATAAAA-AAGAGTGAAATAAAAATAAAT
1 AAATAAAATAA-A-TAAAAT-AAAA-AAAT
**
464014 AAATAAATATAAAGGAAATAAAAAAAT
1 AAATAAA-ATAAATAAAATAAAAAAAT
*
464041 AAAGTAAAGATAAAGAAAA-AAAA
1 AAA-TAAA-ATAAATAAAATAAAA
464064 TAAAAAAAAA
Statistics
Matches: 212, Mismatches: 35, Indels: 45
0.73 0.12 0.15
Matches are distributed among these distances:
23 10 0.05
24 9 0.04
25 16 0.08
26 9 0.04
27 40 0.19
28 45 0.21
29 65 0.31
30 16 0.08
31 2 0.01
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (26 bp):
AAATAAAATAAATAAAATAAAAAAAT
Found at i:463882 original size:39 final size:38
Alignment explanation
Indices: 463812--463888 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 38
463802 AAAGAAAATG
463812 AGATAAAG-AAAATATAAAAAAGATAAA-AAAATAAATAA
1 AGATAAAGTAAAATA-AAAAAAG-TAAATAAAATAAATAA
463850 AGATAAAGTAAAGATAAAAAAAGTAAATAAAATAAATAA
1 AGATAAAGTAAA-ATAAAAAAAGTAAATAAAATAAATAA
463889 CATAAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
38 12 0.33
39 21 0.58
40 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (38 bp):
AGATAAAGTAAAATAAAAAAAGTAAATAAAATAAATAA
Found at i:463901 original size:39 final size:38
Alignment explanation
Indices: 463827--463919 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 38
463817 AAGAAAATAT
* *
463827 AAAAAAGATAAA-AAAATAAATAAAGATAAAGTAAAGATA
1 AAAAAAG-TAAATAAAATAAATAAACATAAAATAAAGA-A
463866 AAAAAAGTAAATAAAATAAAT-AACATAAATATAAAGAA
1 AAAAAAGTAAATAAAATAAATAAACATAAA-ATAAAGAA
*
463904 AATAAAAG-GAATAAAA
1 AA-AAAAGTAAATAAAA
463920 ATACAAATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (38 bp):
AAAAAAGTAAATAAAATAAATAAACATAAAATAAAGAA
Found at i:463990 original size:15 final size:15
Alignment explanation
Indices: 463834--464026 Score: 71
Period size: 15 Copynumber: 12.3 Consensus size: 15
463824 TATAAAAAAG
*
463834 ATAAAAAAATAAATA
1 ATAAATAAATAAATA
* *
463849 A-AGATAAAGTAAA-G
1 ATAAATAAA-TAAATA
*
463863 ATAAAAAAAGTAAATAAA
1 ATAAATAAA-TAAAT--A
463881 ATAAATAACATAAAT-
1 ATAAATAA-ATAAATA
* *
463896 ATAAAGAAAATAAAAGGA
1 ATAAA-TAAAT-AAA-TA
*
463914 ATAAA-AATACAAAT-
1 ATAAATAA-ATAAATA
*
463928 ATAGATAAA-AAATAA
1 ATAAATAAATAAAT-A
*
463943 ATAAAATAAAGAAGATA
1 AT-AAATAAATAA-ATA
*
463960 AT-AATAATATATATA
1 ATAAATAA-ATAAATA
463975 ATAAATAAATAAATAA
1 ATAAATAAATAAAT-A
*
463991 AAAAGAGTGAAATAAA-A
1 ATAA-A-T-AAATAAATA
464008 ATAAATAAATAAAT-
1 ATAAATAAATAAATA
464022 ATAAA
1 ATAAA
464027 GGAAATAAAA
Statistics
Matches: 136, Mismatches: 18, Indels: 49
0.67 0.09 0.24
Matches are distributed among these distances:
13 4 0.03
14 23 0.17
15 42 0.31
16 28 0.21
17 11 0.08
18 20 0.15
19 8 0.06
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.21
Consensus pattern (15 bp):
ATAAATAAATAAATA
Found at i:464034 original size:19 final size:17
Alignment explanation
Indices: 464010--464044 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
464000 AAATAAAAAT
464010 AAATAAATAAATATAAAGG
1 AAATAAA-AAA-ATAAAGG
464029 AAATAAAAAAATAAAG
1 AAATAAAAAAATAAAG
464045 TAAAGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
AAATAAAAAAATAAAGG
Found at i:464060 original size:52 final size:52
Alignment explanation
Indices: 463782--464067 Score: 150
Period size: 52 Copynumber: 5.8 Consensus size: 52
463772 TAAATAAAGA
* * * * * *
463782 AAAT-AAAAAACAAATGAA-ATAAAG-AAAATGAGATAAAGAAAATATA-AAA
1 AAATAAAAAAATAAATAAAGATAAAGAAAAAT-AAATAAATAATATATATAAG
* * *
463831 AAGATAAAAAAATAAATAAAGATAAAGTAAAGATAAAAAAAGTAA-ATA-A-AAT
1 AA-ATAAAAAAATAAATAAAGATAAAG-AAAAATAAATAAA-TAATATATATAAG
* * ** * *
463883 AAATAACATAAAT--ATAAAGA-AAA-TAAAAGGAATAAA-AATACAAATATAG
1 AAATAA-AAAAATAAATAAAGATAAAGAAAAATAAATAAATAATATATATA-AG
* *
463932 --AT-AAAAAATAAATAAA-ATAAAG-AAGAT-AAT-AATAATATATATAAT
1 AAATAAAAAAATAAATAAAGATAAAGAAAAATAAATAAATAATATATATAAG
* *
463977 AAATAAATAAATAAA-AAAGAGTGAAATAAAAATAAATAAATAA-ATATA-AAGG
1 AAATAAAAAAATAAATAAAGA-T-AAAGAAAAATAAATAAATAATATATATAA-G
464029 AAATAAAAAAATAAAGTAAAGATAAAGAAAAA-AAATAAA
1 AAATAAAAAAATAAA-TAAAGATAAAGAAAAATAAATAAA
464068 AAAAAATTAT
Statistics
Matches: 182, Mismatches: 27, Indels: 54
0.69 0.10 0.21
Matches are distributed among these distances:
45 10 0.05
46 15 0.08
47 27 0.15
48 11 0.06
49 7 0.04
50 12 0.07
51 29 0.16
52 46 0.25
53 14 0.08
54 11 0.06
ACGTcount: A:0.72, C:0.01, G:0.08, T:0.18
Consensus pattern (52 bp):
AAATAAAAAAATAAATAAAGATAAAGAAAAATAAATAAATAATATATATAAG
Found at i:464067 original size:19 final size:19
Alignment explanation
Indices: 463812--464067 Score: 117
Period size: 20 Copynumber: 13.1 Consensus size: 19
463802 AAAGAAAATG
463812 AGATAAAGAAAATATAAA-AA
1 AGATAAA-AAAATA-AAATAA
463832 AGATAAAAAAAT-AAATAA
1 AGATAAAAAAATAAAATAA
463850 AGATAAAGTAAAGATAAAA-AA
1 AGATAAA--AAA-ATAAAATAA
463871 AG-TAAATAAAAT-AAAT-A
1 AGATAAA-AAAATAAAATAA
* *
463888 ACATAAATATAAAGAAAATAAA
1 AGATAAA-A-AAATAAAAT-AA
* *
463910 AGGA-ATAAAAATACAAATAT
1 A-GATAAAAAAATA-AAATAA
463930 AGAT-AAAAAAT-AAATAA
1 AGATAAAAAAATAAAATAA
*
463947 A-ATAAAGAAGATAATAATAA
1 AGATAAA-AAAATAA-AATAA
* *
463967 TATATATAATAAAT-AAAT-A
1 -AGATA-AAAAAATAAAATAA
*
463986 A-ATAAAAAAGAGTGAAATAA
1 AGATAAAAAA-A-TAAAATAA
* *
464006 AAATAAATAAATAAATATAA
1 AGATAAAAAAATAAA-ATAA
*
464026 AGGAAATAAAAAAATAAAGTAA
1 A-G--ATAAAAAAATAAAATAA
464048 AGATAAAGAAAA-AAAATAA
1 AGATAAA-AAAATAAAATAA
464067 A
1 A
464068 AAAAAATTAT
Statistics
Matches: 187, Mismatches: 18, Indels: 63
0.70 0.07 0.24
Matches are distributed among these distances:
16 6 0.03
17 20 0.11
18 23 0.12
19 41 0.22
20 44 0.24
21 21 0.11
22 17 0.09
23 15 0.08
ACGTcount: A:0.72, C:0.01, G:0.08, T:0.19
Consensus pattern (19 bp):
AGATAAAAAAATAAAATAA
Found at i:467081 original size:85 final size:85
Alignment explanation
Indices: 466966--467232 Score: 329
Period size: 85 Copynumber: 3.1 Consensus size: 85
466956 TCTCGACTTA
* * * * * *
466966 AGTTATGCTATAAATTTAAAATGCCCTTGAGTTGAATGTAATCGAACTCGAAGGTATTTGTTGAC
1 AGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
*
467031 AGATAACCCTTCTTGTCTTG
66 AGATAACCCTTCTTGCCTTG
* * * ** *
467051 AGTTATTCTGTAAGTTTGGTATGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGAT
1 AGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
* *
467116 AGATAGCTCTTCTCT-CCTTG
66 AGATAACCCTTCT-TGCCTTG
* * * *
467136 AGCTATGCTGTAAATTTGATATGCCTTTGAGCTAAATGTAATAGAACTCGAAGGTCTTTGCTGAC
1 AGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
* *
467201 AGATAACCATTCTCGCCTTG
66 AGATAACCCTTCTTGCCTTG
467221 AGTTATGCTGTA
1 AGTTATGCTGTA
467233 CTGGGTTGGG
Statistics
Matches: 150, Mismatches: 30, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
85 149 0.99
86 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (85 bp):
AGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGAC
AGATAACCCTTCTTGCCTTG
Found at i:467526 original size:65 final size:65
Alignment explanation
Indices: 467413--467594 Score: 274
Period size: 65 Copynumber: 2.8 Consensus size: 65
467403 CTTGAATATT
* * *
467413 GTTTAGCTTTGAGTTAGATATCCTTCATTGTGAAGTTGAAATCTAATCTTGTATAAATTTCACCG
1 GTTT-GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCG
467478 A
65 A
* * *
467479 GTTTGCTTTGAGTTGGATATCCTTTGTTGTGAAATTGAAATCCAATCTTATATAAATTTCACCGA
1 GTTTGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCGA
* * *
467544 ATTGGCTTTGAGTTGGATATTCTTCGTTGTGAAGTTGAAATCCAATCTTGT
1 GTTTGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGT
467595 GTAAGTTGAG
Statistics
Matches: 104, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
65 100 0.96
66 4 0.04
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (65 bp):
GTTTGCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTATAAATTTCACCGA
Found at i:469190 original size:99 final size:99
Alignment explanation
Indices: 469007--469202 Score: 252
Period size: 99 Copynumber: 2.0 Consensus size: 99
468997 AGACAACTCA
* * *
469007 ATATTATAACCACCTGTATCAGGCTAGTTGAATCGTATCCATAAAGCCGGGACGTTTAACTAATT
1 ATATTATAACCACCTGTATCAGGCTAGCTGAATCGTATCCATAAAGCAGGGACGTTTAACGAATT
* *
469072 GCTTCAGAGTGACAACTCAAGCTTTATTGTATAG
66 ACTTCAGAGGGACAACTCAAGCTTTATTGTATAG
** * * *
469106 ATATTATAATTACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTCAGGG-TGTTTAACGAAT
1 ATATTATAACCACCTGTATCAGGCTAGCTGAATCGTATCCATAAAG-CAGGGACGTTTAACGAAT
* *
469170 TACATT-ATAGGGACAGCTCAAGCTTTATTGTAT
65 TAC-TTCAGAGGGACAACTCAAGCTTTATTGTAT
469203 GTATATAATA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
99 77 0.93
100 6 0.07
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (99 bp):
ATATTATAACCACCTGTATCAGGCTAGCTGAATCGTATCCATAAAGCAGGGACGTTTAACGAATT
ACTTCAGAGGGACAACTCAAGCTTTATTGTATAG
Found at i:473214 original size:14 final size:14
Alignment explanation
Indices: 473173--473226 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
473163 AAGGTAATAA
473173 AAATAAAGAAAAT-
1 AAATAAAGAAAATG
*
473186 AAA-AAAAACAAATG
1 AAATAAAGA-AAATG
473200 AAATAAAGAAAATG
1 AAATAAAGAAAATG
*
473214 AGATAAAGAAAAT
1 AAATAAAGAAAAT
473227 ATAAAAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 4 0.11
13 7 0.20
14 20 0.57
15 4 0.11
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (14 bp):
AAATAAAGAAAATG
Found at i:473249 original size:4 final size:4
Alignment explanation
Indices: 473240--473399 Score: 63
Period size: 4 Copynumber: 38.8 Consensus size: 4
473230 AAAAAGATAA
*
473240 AAAT AAAT AAAT ACAT AAAT AAAGAT AAAGT AAAGAT AAA- AAAGT AAAT
1 AAAT AAAT AAAT AAAT AAAT -AA-AT AAA-T -AA-AT AAAT AAA-T AAAT
*
473289 AAAAT AAAT AACAT AAAT --AT AAAGA AAAT AAA- AGGAAT -AA- AAAT
1 -AAAT AAAT AA-AT AAAT AAAT AAA-T AAAT AAAT A--AAT AAAT AAAT
*
473333 AAA- AAAT ATAGAT AAA- AAAT AAAT AAAAT AAAG AAGAT -AAT -AAT
1 AAAT AAAT A-A-AT AAAT AAAT AAAT -AAAT AAAT AA-AT AAAT AAAT
*
473377 -AAT ATAT ATAAT AAAT AAAT AAA
1 AAAT AAAT A-AAT AAAT AAAT AAA
473400 AACAAGAGTA
Statistics
Matches: 123, Mismatches: 8, Indels: 50
0.68 0.04 0.28
Matches are distributed among these distances:
2 2 0.02
3 22 0.18
4 57 0.46
5 33 0.27
6 8 0.07
7 1 0.01
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:473355 original size:44 final size:44
Alignment explanation
Indices: 473238--473399 Score: 125
Period size: 44 Copynumber: 3.5 Consensus size: 44
473228 TAAAAAAGAT
* *
473238 AAAAATA-AATAAATACATAAATAAAGATAAAGTAAAGATAAAAAAGTA
1 AAAAATATAATAAATAAATAAAGAAA-ATAAAG--AAGAT-AAAAA-TA
*
473286 AATAAA-ATAAATAACATAAATATAAAGAAAATAAA-AGGAATAAAAATA
1 AA-AAATAT-AATAA-AT-AA-ATAAAGAAAATAAAGAAG-ATAAAAATA
* *
473334 AAAAATATAGATAAA-AAATAAATAAAATAAAGAAGATAATAATA
1 AAAAATATA-ATAAATAAATAAAGAAAATAAAGAAGATAAAAATA
* *
473378 ATATATATAATAAATAAATAAA
1 AAAAATATAATAAATAAATAAA
473400 AACAAGAGTA
Statistics
Matches: 95, Mismatches: 8, Indels: 26
0.74 0.06 0.20
Matches are distributed among these distances:
43 5 0.05
44 35 0.37
45 4 0.04
47 5 0.05
48 13 0.14
49 10 0.11
50 7 0.07
51 2 0.02
52 6 0.06
53 8 0.08
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (44 bp):
AAAAATATAATAAATAAATAAAGAAAATAAAGAAGATAAAAATA
Found at i:473362 original size:9 final size:9
Alignment explanation
Indices: 473172--473467 Score: 115
Period size: 9 Copynumber: 31.2 Consensus size: 9
473162 TAAGGTAATA
*
473172 AAAATAAAG
1 AAAATAAAT
*
473181 AAAATAAAA
1 AAAATAAAT
*
473190 AAAACAAAT
1 AAAATAAAT
* *
473199 GAAATAAAG
1 AAAATAAAT
*
473208 AAAATGAGAT
1 AAAAT-AAAT
473218 AAAGA-AAAT
1 AAA-ATAAAT
*
473227 ATAAAAAAGAT
1 A-AAATAA-AT
473238 AAAAATAAAT
1 -AAAATAAAT
473248 AAATACATAAAT
1 -AA-A-ATAAAT
473260 AAAGATAAAGT
1 AAA-ATAAA-T
473271 AAAGATAAA-
1 AAA-ATAAAT
*
473280 AAAGTAAAT
1 AAAATAAAT
473289 AAAATAAAT
1 AAAATAAAT
*
473298 AACATAAAT
1 AAAATAAAT
*
473307 ATAAAGAAAAT
1 A-AAA-TAAAT
**
473318 AAAAGGAAT
1 AAAATAAAT
473327 AAAAATAAA-
1 -AAAATAAAT
*
473336 AAATATAGATAA
1 AAA-ATA-A-AT
473348 AAAATAAAT
1 AAAATAAAT
*
473357 AAAATAAAG
1 AAAATAAAT
*
473366 AAGAT-AAT
1 AAAATAAAT
*
473374 AATAATATAT
1 AA-AATAAAT
*
473384 ATAATAAAT
1 AAAATAAAT
473393 -AAATAAA-
1 AAAATAAAT
* *
473400 AACAA-GAGT
1 AA-AATAAAT
473409 AAAATAAAAAT
1 AAAAT--AAAT
*
473420 AAATATAAAG
1 AAA-ATAAAT
*
473430 GAAATAAA-
1 AAAATAAAT
473438 AAAATAAAGT
1 AAAATAAA-T
*
473448 AAAGATAAAG
1 AAA-ATAAAT
473458 AAAA-AAAT
1 AAAATAAAT
473466 AA
1 AA
473468 TAGTAAAAAT
Statistics
Matches: 219, Mismatches: 39, Indels: 59
0.69 0.12 0.19
Matches are distributed among these distances:
8 33 0.15
9 87 0.40
10 47 0.21
11 40 0.18
12 12 0.05
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (9 bp):
AAAATAAAT
Found at i:473377 original size:24 final size:23
Alignment explanation
Indices: 473284--473444 Score: 68
Period size: 24 Copynumber: 6.9 Consensus size: 23
473274 GATAAAAAAG
*
473284 TAAATAAAATAAATAACATAA-ATA
1 TAAATAAAATAAA-AAGATAATA-A
* *
473308 TAAAGAAAAT-AAAAG-GAATAA
1 TAAATAAAATAAAAAGATAATAA
* *
473329 -AAATAAAA-AATATAGATAAAAAA
1 TAAATAAAATAA-AAAGAT-AATAA
473352 TAAATAAAATAAAGAAGATAATAA
1 TAAATAAAATAAA-AAGATAATAA
*
473376 TAATATATATAATAAATAA-ATAAAAA
1 TAA-ATA-A-AATAAA-AAGATAATAA
* *
473402 CAAGAGTAAAATAAAAATA-AAT-A
1 TAA-A-TAAAATAAAAAGATAATAA
** *
473425 TAAAGGAAATAAAAAAATAA
1 TAAATAAAATAAAAAGATAA
473445 AGTAAAGATA
Statistics
Matches: 105, Mismatches: 18, Indels: 30
0.69 0.12 0.20
Matches are distributed among these distances:
20 8 0.08
21 16 0.15
22 6 0.06
23 9 0.09
24 29 0.28
25 16 0.15
26 11 0.10
27 10 0.10
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.20
Consensus pattern (23 bp):
TAAATAAAATAAAAAGATAATAA
Found at i:473397 original size:20 final size:19
Alignment explanation
Indices: 473242--473398 Score: 81
Period size: 20 Copynumber: 7.9 Consensus size: 19
473232 AAAGATAAAA
*
473242 ATAAATAAATACATAAATAAAG
1 ATAAATAAA-A-ATAAAT-AAT
*
473264 ATAAAGTAAAGATAAA-AA-
1 ATAAA-TAAAAATAAATAAT
*
473282 AGTAAAT-AAAATAAATAAC
1 A-TAAATAAAAATAAATAAT
*
473301 ATAAATATAAAGA-AAATAAA
1 ATAAATA-AAA-ATAAATAAT
** *
473321 AGGAATAAAAATAAAAAAT
1 ATAAATAAAAATAAATAAT
* *
473340 ATAGATAAAAAATAAATAAA
1 ATAAAT-AAAAATAAATAAT
*
473360 ATAAAGAAGATAAT-AATAAT
1 ATAAATAA-A-AATAAATAAT
*
473380 ATATATAATAAATAAATAA
1 ATAAATAA-AAATAAATAA
473399 AAACAAGAGT
Statistics
Matches: 105, Mismatches: 18, Indels: 26
0.70 0.12 0.17
Matches are distributed among these distances:
17 7 0.07
18 10 0.10
19 23 0.22
20 47 0.45
21 9 0.09
22 5 0.05
23 4 0.04
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.22
Consensus pattern (19 bp):
ATAAATAAAAATAAATAAT
Found at i:473415 original size:40 final size:40
Alignment explanation
Indices: 473328--473446 Score: 127
Period size: 40 Copynumber: 2.9 Consensus size: 40
473318 AAAAGGAATA
*
473328 AAAATAAAAAATATAGATAAAAAATAAATAAAATAAAGAAG
1 AAAAT-AAAAATATATATAAAAAATAAATAAAATAAAGAAG
* * *
473369 ATAATAATAATATATATAATAAATAAATAAAA-ACAAG-AG
1 AAAATAAAAATATATATAAAAAATAAATAAAATA-AAGAAG
*
473408 TAAAATAAAAATAAATATAAAGGAAATAAA-AAAATAAAG
1 -AAAATAAAAATATATATAAA--AAATAAATAAAATAAAG
473447 TAAAGATAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
39 3 0.05
40 43 0.66
41 11 0.17
42 8 0.12
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.20
Consensus pattern (40 bp):
AAAATAAAAATATATATAAAAAATAAATAAAATAAAGAAG
Found at i:473440 original size:23 final size:23
Alignment explanation
Indices: 473393--473467 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
473383 TATAATAAAT
*
473393 AAATAAAA-ACAAGAGTAAA-ATAA
1 AAATAAAATA-AAGAG-AAAGAAAA
*
473416 AAATAAATATAAAG-GAAATAAAA
1 AAATAAA-ATAAAGAGAAAGAAAA
* *
473439 AAATAAAGTAAAGATAAAGAAAA
1 AAATAAAATAAAGAGAAAGAAAA
473462 AAATAA
1 AAATAA
473468 TAGTAAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 8 0.18
23 31 0.70
24 4 0.09
25 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.09, T:0.15
Consensus pattern (23 bp):
AAATAAAATAAAGAGAAAGAAAA
Found at i:473440 original size:28 final size:27
Alignment explanation
Indices: 473409--473475 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 27
473399 AAACAAGAGT
*
473409 AAAATA-AAAATAAATATAAAGGAAATAA
1 AAAATATAAAATAAAGATAAA-GAAA-AA
*
473437 AAAA-ATAAAGTAAAGATAAAGAAAAA
1 AAAATATAAAATAAAGATAAAGAAAAA
473463 AATAATAGTAAAA
1 AA-AATA-TAAAA
473476 ATATATCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 4 0.12
27 7 0.22
28 17 0.53
29 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (27 bp):
AAAATATAAAATAAAGATAAAGAAAAA
Found at i:473603 original size:41 final size:42
Alignment explanation
Indices: 473528--473607 Score: 112
Period size: 41 Copynumber: 1.9 Consensus size: 42
473518 AATGAAAATA
473528 AAAATAAAAGATAATATATATATATATATATATTTAAATGTT
1 AAAATAAAAGATAATATATATATATATATATATTTAAATGTT
*
473570 AAAAT-AAATATAATA-ATA-ATAATATATAGTATTTAAAT
1 AAAATAAAAGATAATATATATAT-ATATATA-TATTTAAAT
473608 AAAAAGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
39 2 0.06
40 10 0.29
41 18 0.51
42 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (42 bp):
AAAATAAAAGATAATATATATATATATATATATTTAAATGTT
Found at i:478510 original size:13 final size:13
Alignment explanation
Indices: 478491--478523 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
478481 GCACAAACTT
478491 GACACAACTTTGA
1 GACACAACTTTGA
*
478504 GAGACAACTTTGA
1 GACACAACTTTGA
478517 GACACAA
1 GACACAA
478524 TTCACAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (13 bp):
GACACAACTTTGA
Found at i:480393 original size:23 final size:23
Alignment explanation
Indices: 480346--480395 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
480336 AATAACATAT
**
480346 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
*
480369 TAGGTAGTGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
480392 TAGG
1 TAGG
480396 CAGTTAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:480458 original size:87 final size:87
Alignment explanation
Indices: 480312--480471 Score: 302
Period size: 87 Copynumber: 1.8 Consensus size: 87
480302 GTTATATCAT
* *
480312 TTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGT
1 TTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGTAGC
480377 GCTTATATAATAAAATAGGCAG
66 GCTTATATAATAAAATAGGCAG
480399 TTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGTAGC
1 TTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGTAGC
480464 GCTTATAT
66 GCTTATAT
480472 TGACCTATTT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (87 bp):
TTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGTAGC
GCTTATATAATAAAATAGGCAG
Found at i:480470 original size:21 final size:23
Alignment explanation
Indices: 480424--480471 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
480414 ATCAAGTACA
*
480424 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
480447 ATAATATAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
480470 AT
1 AT
480472 TGACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:480897 original size:200 final size:196
Alignment explanation
Indices: 480466--480985 Score: 677
Period size: 200 Copynumber: 2.6 Consensus size: 196
480456 TAGGTAGCGC
* * * *
480466 TTATATTGACCTATTTTATAAGT-AAACCGGTATATTTATACCGGTAACATTGCAAATTTACCTA
1 TTATA-TGACCTATTTTCTTA-TAAAACCGGTATATTTATACAGGT-ACATTGTAAATTTACCTA
* * * *
480530 TTACATTATAATTATCGGTTTCGATATTTTTGGATCGATACATTT--TAAATGCATCGACACTTT
63 TTACATTATAATTATCGGTTTCGATGTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
* * * *
480593 ATGCATGCACCTCGTTGGGCATTCATTCTGGAAAAAAATATCGACACAAACTTAAAAAGTGTCGA
128 ATGCATGCACCCCGTTGGGCATTCATTATGGAAAAAAATATCAACAAAAACTTAAAAAGTGTCGA
480658 TACA
193 TACA
* * * *
480662 TTATTTAGACCTATTTTCTTATAAAACCAGTATATTTCTATCGGGTACATTGTAAATTTACCTAT
1 TTATAT-GACCTATTTTCTTATAAAACCGGTATATTTATA-CAGGTACATTGTAAATTTACCTAT
* * * *
480727 CATATTGTAATTATCGGTTTTGATGTTTGTGGGATCGATACTTTTAATAAATGTATCGACACTTT
64 TACATTATAATTATCGGTTTCGATGTTT-TGGGATCGATACTTTTAATAAATGTATCGACACTTT
* * * **
480792 ATGCGTGCACCCCGTTTGGCATTCATTATGGAAAAAAAGTATCAACAAAAATTTAAATGGTGTCG
128 ATGCATGCACCCCGTTGGGCATTCATTATGGAAAAAAA-TATCAACAAAAACTTAAAAAGTGTCG
*
480857 ATACT
192 ATACA
*
480862 TTATGATGACCTATTTTCTTATAAAACCGGTATATTTATACCAGTTACATTGTAAATTTACCTAT
1 TTAT-ATGACCTATTTTCTTATAAAACCGGTATATTTATA-CAGGTACATTGTAAATTTACCTAT
*
480927 TACATTATAATCATCGGTTTCGATGTTATTGGGATCGATACTTTTAATAAATGTATCGA
64 TACATTATAATTATCGGTTTCGATGTT-TTGGGATCGATACTTTTAATAAATGTATCGA
480986 TATTTTATAT
Statistics
Matches: 279, Mismatches: 36, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
195 2 0.01
196 72 0.26
197 18 0.06
199 51 0.18
200 134 0.48
201 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (196 bp):
TTATATGACCTATTTTCTTATAAAACCGGTATATTTATACAGGTACATTGTAAATTTACCTATTA
CATTATAATTATCGGTTTCGATGTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATG
CATGCACCCCGTTGGGCATTCATTATGGAAAAAAATATCAACAAAAACTTAAAAAGTGTCGATAC
A
Found at i:483691 original size:19 final size:19
Alignment explanation
Indices: 483646--483694 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
483636 TTACATTCAC
483646 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCAT
** *
483665 ATGTAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
483684 ATACAAAATTA
1 ATACAAAATTA
483695 ACCCTACATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:487971 original size:20 final size:21
Alignment explanation
Indices: 487943--487984 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
487933 TAAATTCACA
* *
487943 AAGTGTCGATACTTT-AATAT
1 AAGTATCGACACTTTAAATAT
487963 AAGTATCGACACTTTAAATAT
1 AAGTATCGACACTTTAAATAT
487984 A
1 A
487985 TCCGGTCGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (21 bp):
AAGTATCGACACTTTAAATAT
Found at i:488091 original size:182 final size:182
Alignment explanation
Indices: 487777--488630 Score: 1189
Period size: 182 Copynumber: 4.7 Consensus size: 182
487767 TACTCGTATT
* * * * * * *
487777 TATTAAAGTATCGACACTTTATATATATCCGGTAGCGCTTTACCGATTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTAAATATATCCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
* * * *
487842 GTTTTGTCAT-TTTTTACCTGTTATATCATTGTTGACCGATACATTGTTATAAAGTATCAACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
*
487906 TTATAGGCACTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTT-
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* *
487957 TAATATAAGTATCGACACTTTAAATATATCCGGTCGCTCTATATCGGTTTTGTCCTTTAGAGACC
1 TATTA-AAGTATCGACACTTTAAATATATCCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACC
* * * *
488022 AGTTTTGTCATATTTTTACCTGTTATACCGTTTTGGATCAATACATTGTTATAAAGTATCGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACAC
* * *
488087 TTTATGGGCGCTAAAACTGATTCTCTTTTAAATTCACAAAATGTCGATACTTA
130 TTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
** * *
488140 TATTAAAGTATCGACACTTTAAATATATTTGGTCGCTCTATACCGGTTTTTTCCTTTATAGACCG
1 TATTAAAGTATCGACACTTTAAATATATCCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
* * * * **
488205 ATTTTGTCATATTTTTATCTGTTATATCGTTGTGGATCAATACATTGTTGTAAAGTATTAACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
*
488270 TAATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * *
488322 TATTAAAGTATCGACACTTTCAATATATCTGGTCGCTCTATACCGGTTTTGTCCTTTAGAGATCG
1 TATTAAAGTATCGACACTTTAAATATATCCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
* *
488387 GTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATTATTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
* *
488452 TTATGGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTT-
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * * * * *
488503 TATTAAAGTATCGACACTTTCAATATATACGGTAC-CGT-TTTATCGGTTTTGTCTTTTCGAAAC
1 TATTAAAGTATCGACACTTTAAATATATCCGGT-CGC-TCTATACCGGTTTTGTCCTTTAGAGAC
* * *
488566 CGGTTTTGTCATATTTTTACCTGTTATATTGATGTGGACCGATACAGTT-TTATAAAGTATCGAC
64 CGGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACA-TTGTTATAAAGTATCGAC
488630 A
128 A
488631 TAAACCGTCA
Statistics
Matches: 601, Mismatches: 67, Indels: 11
0.89 0.10 0.02
Matches are distributed among these distances:
180 4 0.01
181 170 0.28
182 423 0.70
183 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTAAATATATCCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACACT
TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:489086 original size:21 final size:21
Alignment explanation
Indices: 489061--489116 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
489051 ACGAATAAGT
*
489061 AAATCGCAACGCGAATTGGGA
1 AAATCGCAATGCGAATTGGGA
489082 AAATCGCAATGCGAATTGGGA
1 AAATCGCAATGCGAATTGGGA
489103 AAATCGCAATGCGA
1 AAATCGCAATGCGA
489117 TACTGACTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.18, G:0.27, T:0.16
Consensus pattern (21 bp):
AAATCGCAATGCGAATTGGGA
Found at i:489130 original size:20 final size:19
Alignment explanation
Indices: 489105--489219 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 19
489095 AATTGGGAAA
*
489105 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* * *
489125 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTAC--T
*
489146 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATAC-TACT
*
489166 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* * *
489186 TTCGTAACGCGATAATACAT
1 ATCGCAACGCGATACTAC-T
*
489206 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
489220 TTTCAAAGCG
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.07
20 46 0.61
21 22 0.29
22 3 0.04
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (19 bp):
ATCGCAACGCGATACTACT
Found at i:489147 original size:41 final size:41
Alignment explanation
Indices: 489102--489179 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
489092 GCGAATTGGG
* * *
489102 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
* *
489143 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
489180 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:489415 original size:22 final size:22
Alignment explanation
Indices: 489387--489430 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
489377 CACTCTCTCA
489387 CCCATCTCCGAAGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
**
489409 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
489431 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.43, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGAAGAAATCCGTC
Found at i:489719 original size:20 final size:20
Alignment explanation
Indices: 489694--489731 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
489684 CGATTCTCTC
489694 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
489714 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
489732 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:490803 original size:48 final size:48
Alignment explanation
Indices: 490750--490845 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
490740 AAGACATATG
490750 CAATAAAAACTTCAAATGATATTCCCAGGGCTATTTCCTGGAAGAGGA
1 CAATAAAAACTTCAAATGATATTCCCAGGGCTATTTCCTGGAAGAGGA
490798 CAATAAAAACTTCAAATGATATTCCCAGGGCTATTTCCTGGAAGAGGA
1 CAATAAAAACTTCAAATGATATTCCCAGGGCTATTTCCTGGAAGAGGA
490846 AACGGACCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (48 bp):
CAATAAAAACTTCAAATGATATTCCCAGGGCTATTTCCTGGAAGAGGA
Found at i:491120 original size:18 final size:18
Alignment explanation
Indices: 491099--491143 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
491089 TCCACTTCGG
*
491099 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
491117 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
491135 GAGCCATCA
1 GAGCCATCA
491144 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:491644 original size:20 final size:19
Alignment explanation
Indices: 491619--491684 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 19
491609 TAGTTTACTT
491619 TCGCAACACGAAAATGACTA
1 TCGCAACACG-AAATGACTA
* *
491639 TCGCAACGCGGAAATGGCTA
1 TCGCAACAC-GAAATGACTA
* * **
491659 ACGCAATACGAAATGAAAA
1 TCGCAACACGAAATGACTA
491678 TCGCAAC
1 TCGCAAC
491685 GACAAAATCG
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
19 12 0.34
20 22 0.63
21 1 0.03
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACACGAAATGACTA
Found at i:491693 original size:14 final size:14
Alignment explanation
Indices: 491674--491763 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
491664 ATACGAAATG
491674 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
491688 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
491704 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
* *
491720 AAAATTGCAATGCGAA
1 AAAATCGCAA--CGAC
491736 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
491752 AAAATCGCAACG
1 AAAATCGCAACG
491764 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 29 0.47
16 16 0.26
18 17 0.27
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:491716 original size:32 final size:32
Alignment explanation
Indices: 491660--491773 Score: 192
Period size: 32 Copynumber: 3.5 Consensus size: 32
491650 AAATGGCTAA
*
491660 CGCAATACGAAATGAAAATCGCAACGACAAAAT
1 CGCAATGCGAAATG-AAATCGCAACGACAAAAT
491693 CGCAATGCGAAATGAAATCGCAACGACAAAAT
1 CGCAATGCGAAATGAAATCGCAACGACAAAAT
*
491725 TGCAATGCGAAATGAAATCGCAACGACAAAAT
1 CGCAATGCGAAATGAAATCGCAACGACAAAAT
*
491757 CGCAACGCGAAATGAAA
1 CGCAATGCGAAATGAAA
491774 ATCGTAATGC
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 64 0.83
33 13 0.17
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.12
Consensus pattern (32 bp):
CGCAATGCGAAATGAAATCGCAACGACAAAAT
Found at i:491816 original size:14 final size:14
Alignment explanation
Indices: 491797--491854 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
491787 TTGTGTTTCG
491797 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
491811 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
491827 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
491843 CATTGCGATTTT
1 CGTTGCGATTTT
491855 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:491833 original size:32 final size:33
Alignment explanation
Indices: 491792--491870 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
491782 GCAATTTGTG
*
491792 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
491824 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
*
491857 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
491871 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
Found at i:491867 original size:19 final size:19
Alignment explanation
Indices: 491843--491900 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 19
491833 GCGATTTTGT
**
491843 CATTGCGATTTTCATTTCG
1 CATTGCGATAGTCATTTCG
*
491862 CATTGCGATAGCCATTTCCG
1 CATTGCGATAGTCATTT-CG
*
491882 CGTTGCGATAGTCATTTCG
1 CATTGCGATAGTCATTTCG
491901 TGTTGCGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (19 bp):
CATTGCGATAGTCATTTCG
Found at i:491907 original size:19 final size:19
Alignment explanation
Indices: 491854--491909 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
491844 ATTGCGATTT
*
491854 TCATTTCGCATTGCGATAG
1 TCATTTCGCGTTGCGATAG
*
491873 CCATTTCCGCGTTGCGATAG
1 TCATTT-CGCGTTGCGATAG
*
491893 TCATTTCGTGTTGCGAT
1 TCATTTCGCGTTGCGAT
491910 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:493795 original size:14 final size:14
Alignment explanation
Indices: 493776--493811 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
493766 ATTGTTTAAT
493776 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
493790 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
493804 TGATTTGT
1 TGATTTGT
493812 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:493937 original size:14 final size:14
Alignment explanation
Indices: 493918--493971 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
493908 CGAAATGGCT
493918 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
493932 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
493951 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
493965 ATCGCAA
1 ATCGCAA
493972 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:493989 original size:33 final size:33
Alignment explanation
Indices: 493899--493976 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
493889 AAAACAGATT
* ***
493899 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
493932 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
493965 ATCGCAATGCGA
1 ATCGCAATGCGA
493977 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:494052 original size:20 final size:20
Alignment explanation
Indices: 493995--494052 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
493985 TCGCATTGCG
* *
493995 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
494015 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
494035 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
494053 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:495520 original size:33 final size:33
Alignment explanation
Indices: 495478--495604 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
495468 GGAAATTACT
495478 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
495511 ATCGCAATGCGAAATGAAAATCACAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
495543 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
495577 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
495605 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:495585 original size:66 final size:66
Alignment explanation
Indices: 495479--495611 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
495469 GAAATTACTA
*
495479 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
495544 T
66 T
* *
495545 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
495610 T
66 T
495611 T
1 T
495612 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
T
Found at i:495626 original size:19 final size:20
Alignment explanation
Indices: 495604--495646 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
495594 AAATCGCAAC
*
495604 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCATT
* *
495623 GCGATTTTCATTTTCGCATT
1 GCGAATTTCAATTTCGCATT
495643 GCGA
1 GCGA
495647 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCATT
Found at i:495806 original size:14 final size:14
Alignment explanation
Indices: 495787--495823 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
495777 CATCAATTAA
495787 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
495801 ACAAATCACCTTTT
1 ACAAATCAACTTTT
495815 ACAAATCAA
1 ACAAATCAA
495824 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:497244 original size:21 final size:21
Alignment explanation
Indices: 497178--497244 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
497168 GTGAATCGGG
*
497178 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
497198 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
497220 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
497241 CTCT
1 CTCT
497245 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:497263 original size:42 final size:41
Alignment explanation
Indices: 497178--497302 Score: 117
Period size: 42 Copynumber: 3.0 Consensus size: 41
497168 GTGAATCGGG
* * * * *
497178 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
497220 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
497262 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGGGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGGGG
497303 AGTCGGGCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 60 0.86
43 6 0.09
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:499328 original size:20 final size:19
Alignment explanation
Indices: 499297--499457 Score: 81
Period size: 20 Copynumber: 8.8 Consensus size: 19
499287 TCTTTTGGTT
499297 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
499316 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
499337 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
499356 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
499370 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * * *
499386 -CCA-GACAATCACAACGC
1 GAAATGAAAATCGCAACGA
*
499403 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* * *
499423 GAAATAAAAATCGCAAAGC
1 GAAATGAAAATCGCAACGA
499442 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
499458 TGCGATTTTG
Statistics
Matches: 108, Mismatches: 21, Indels: 26
0.70 0.14 0.17
Matches are distributed among these distances:
14 16 0.15
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 33 0.31
20 47 0.44
21 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:499379 original size:33 final size:33
Alignment explanation
Indices: 499322--499420 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
499312 ACGAGATAAT
*
499322 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
499356 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* * **
499389 GACAATCACAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
499421 GCGAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.40, C:0.26, G:0.22, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:499414 original size:19 final size:19
Alignment explanation
Indices: 499392--499462 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
499382 GCGACCAGAC
*
499392 AATCACAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
499411 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
*
499431 AATCGCAAAGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
499450 AATCGCAATGCGA
1 AATCGCAACGCGA
499463 TTTTGGTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 28 0.61
20 18 0.39
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:499474 original size:19 final size:19
Alignment explanation
Indices: 499458--499521 Score: 101
Period size: 19 Copynumber: 3.4 Consensus size: 19
499448 AAAATCGCAA
*
499458 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
499477 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
499496 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
499515 TGCGATT
1 TGCGATT
499522 ATCTCGTTGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:499511 original size:38 final size:36
Alignment explanation
Indices: 499458--499557 Score: 107
Period size: 38 Copynumber: 2.8 Consensus size: 36
499448 AAAATCGCAA
**
499458 TGCGATTTTGGTTTCGCGTTGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGTTGCGATTTTTA--TCGCGT
*
499496 TGCGATTTTTATTTCGCGTTGCGA---TTATCTCGT
1 TGCGATTTTTATTTCGCGTTGCGATTTTTATCGCGT
**
499529 TGCGATAGTTATTTCCGCGTTGCGATTTT
1 TGCGATTTTTATTT-CGCGTTGCGATTTT
499558 CATTGTCGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
33 17 0.32
34 10 0.19
35 3 0.06
37 1 0.02
38 22 0.42
ACGTcount: A:0.11, C:0.17, G:0.24, T:0.48
Consensus pattern (36 bp):
TGCGATTTTTATTTCGCGTTGCGATTTTTATCGCGT
Found at i:500260 original size:21 final size:21
Alignment explanation
Indices: 500220--500260 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
500210 ACTGTATACC
**
500220 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
500241 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
500261 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:500970 original size:18 final size:18
Alignment explanation
Indices: 500947--500981 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
500937 AATTATGAAA
500947 TATTAAATATAAA-TTTTG
1 TATTAAAT-TAAAGTTTTG
500965 TATTAAATTAAAGTTTT
1 TATTAAATTAAAGTTTT
500982 ATTCGGATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
TATTAAATTAAAGTTTTG
Found at i:503852 original size:64 final size:64
Alignment explanation
Indices: 503799--503961 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 64
503789 CGGTGCACCA
*
503799 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * ** *
503863 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGTATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
503928 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
503962 CAATTAATTC
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 39 0.46
65 45 0.54
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:503933 original size:19 final size:19
Alignment explanation
Indices: 503909--503959 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
503899 GAAAATATTC
*
503909 AGAGTGTATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
503928 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
503947 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
503960 TTCAATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 18 0.64
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:511348 original size:64 final size:64
Alignment explanation
Indices: 511278--511440 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 64
511268 CGGTGCACCA
*
511278 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * ** *
511342 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGTATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
511407 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
511441 CAATTAATTC
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 39 0.46
65 45 0.54
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:511412 original size:19 final size:19
Alignment explanation
Indices: 511388--511438 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
511378 GAAAATATTC
*
511388 AGAGTGTATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
511407 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
511426 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
511439 TTCAATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 18 0.64
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:513266 original size:46 final size:46
Alignment explanation
Indices: 513202--513296 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 46
513192 TGAAACAAAT
* * *
513202 GAAGAAGATGAAGAGGAAGAGTATCAGTTATAGAATG-GGAATAGAA
1 GAAGAAGAAGAAGAGGAAGAGTATCAGTTAGAGAA-GAGGAACAGAA
* * *
513248 GAAGAAGAAGAAGGGGAAGAGTCTCTGTTAGAGAAGAGGAACAGAA
1 GAAGAAGAAGAAGAGGAAGAGTATCAGTTAGAGAAGAGGAACAGAA
513294 GAA
1 GAA
513297 TGGAAAAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 1 0.02
46 41 0.98
ACGTcount: A:0.47, C:0.04, G:0.35, T:0.14
Consensus pattern (46 bp):
GAAGAAGAAGAAGAGGAAGAGTATCAGTTAGAGAAGAGGAACAGAA
Found at i:513294 original size:37 final size:37
Alignment explanation
Indices: 513253--513353 Score: 94
Period size: 37 Copynumber: 2.7 Consensus size: 37
513243 TAGAAGAAGA
* **
513253 AGAAGAAGGGGAAGAGTCTCTGTTAGAGAAGAGGAAC
1 AGAAGAAAGGGAAGAGTCTCTGTTAGAGAAGAAAAAC
* * * * * *
513290 AGAAGAATGGAAAAAGTGTCTATTAGAGAAGAAAAAG
1 AGAAGAAAGGGAAGAGTCTCTGTTAGAGAAGAAAAAC
** *
513327 AGAAGAAAATGAAGAGTCTCGGTTAGA
1 AGAAGAAAGGGAAGAGTCTCTGTTAGA
513354 TTTAGGATTA
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.47, C:0.06, G:0.32, T:0.16
Consensus pattern (37 bp):
AGAAGAAAGGGAAGAGTCTCTGTTAGAGAAGAAAAAC
Found at i:514179 original size:14 final size:14
Alignment explanation
Indices: 514156--514186 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
514146 TAAATTTTGA
514156 TTTAAAATGATTCC
1 TTTAAAATGATTCC
*
514170 TTTAACATGATTCC
1 TTTAAAATGATTCC
514184 TTT
1 TTT
514187 TGTAGGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.48
Consensus pattern (14 bp):
TTTAAAATGATTCC
Found at i:514850 original size:20 final size:21
Alignment explanation
Indices: 514812--514851 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
514802 ACATAATTAT
*
514812 TAAAAAATATGATATAATAAAA
1 TAAAAAATA-GATAAAATAAAA
514834 TAAAAAATA-ATAAAATAA
1 TAAAAAATAGATAAAATAA
514852 TGATAGTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (21 bp):
TAAAAAATAGATAAAATAAAA
Found at i:517760 original size:15 final size:16
Alignment explanation
Indices: 517735--517765 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
517725 CCAAATTATG
517735 TCTTAAAAATGATTTT
1 TCTTAAAAATGATTTT
517751 TCTT-AAAATGATTTT
1 TCTTAAAAATGATTTT
517766 AAAAGACGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (16 bp):
TCTTAAAAATGATTTT
Found at i:520949 original size:13 final size:13
Alignment explanation
Indices: 520882--520942 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
520872 TGCGTCATAA
*
520882 ATTTATGACGCAC
1 ATTTATGACACAC
*
520895 ATTTATGACACGC
1 ATTTATGACACAC
520908 ATTTATGACACAC
1 ATTTATGACACAC
** *
520921 ATTTATGATGCGC
1 ATTTATGACACAC
520934 ATTTATGAC
1 ATTTATGAC
520943 TTACATTGCG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (13 bp):
ATTTATGACACAC
Found at i:520949 original size:26 final size:26
Alignment explanation
Indices: 520882--520942 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
520872 TGCGTCATAA
*
520882 ATTTATGACGCACATTTATGACACGC
1 ATTTATGACACACATTTATGACACGC
**
520908 ATTTATGACACACATTTATGATGCGC
1 ATTTATGACACACATTTATGACACGC
520934 ATTTATGAC
1 ATTTATGAC
520943 TTACATTGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (26 bp):
ATTTATGACACACATTTATGACACGC
Found at i:521096 original size:85 final size:85
Alignment explanation
Indices: 520921--521086 Score: 271
Period size: 85 Copynumber: 2.0 Consensus size: 85
520911 TATGACACAC
**
520921 ATTTATGATGCGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATAAAGATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATAAAGATGA
* *
520986 CACACATTTGTGTGTCATAA
66 CACACAATCGTGTGTCATAA
*
521006 ATTTATGACACGCATTTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATGAAA-ATG
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAAT-AAAGATG
521070 ACACACAATCGTGTGTC
65 ACACACAATCGTGTGTC
521087 GTGATTTTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
85 72 0.96
86 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATAAAGATGA
CACACAATCGTGTGTCATAA
Found at i:521113 original size:2 final size:2
Alignment explanation
Indices: 521106--521149 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
521096 TTTCGTAAAT
521106 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
521147 TA T
1 TA T
521150 TAACAAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:524915 original size:18 final size:18
Alignment explanation
Indices: 524890--524934 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
524880 AAATCAACAA
524890 AGAGAAAAAAGGGAAAAC
1 AGAGAAAAAAGGGAAAAC
* *
524908 ATAGAAAAAAGGGAAAAG
1 AGAGAAAAAAGGGAAAAC
524926 AGAGAAAAA
1 AGAGAAAAA
524935 TGGGGGAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.69, C:0.02, G:0.27, T:0.02
Consensus pattern (18 bp):
AGAGAAAAAAGGGAAAAC
Found at i:526717 original size:44 final size:44
Alignment explanation
Indices: 526648--526743 Score: 158
Period size: 44 Copynumber: 2.2 Consensus size: 44
526638 GAATTTTGTC
*
526648 TCCCTTGAGACAGTTTCTCTCGAAACATCATCTTTGAGATC-GTT
1 TCCCTTGAGACAGTTTCTCTAGAAACATCATCTTTGAG-TCTGTT
*
526692 TCCCTTGAGACAGTTTTTCTAGAAACATCATCTTTGAGTCTGTT
1 TCCCTTGAGACAGTTTCTCTAGAAACATCATCTTTGAGTCTGTT
526736 TCCCTTGA
1 TCCCTTGA
526744 AACAAAGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 2 0.04
44 47 0.96
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.39
Consensus pattern (44 bp):
TCCCTTGAGACAGTTTCTCTAGAAACATCATCTTTGAGTCTGTT
Found at i:526804 original size:110 final size:109
Alignment explanation
Indices: 526609--526807 Score: 312
Period size: 110 Copynumber: 1.8 Consensus size: 109
526599 AACAAAATTT
* *
526609 ATCATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAGTTTCTCTCGAAAC
1 ATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTAAGACAGTTTCTCTCGAAAC
*
526674 ATCATCTTTGAGATCGTTTCCCTTGAGACAGTTTTTCTAGAAAC
66 ATCATCTTTGAGATCATTTCCCTTGAGACAGTTTTTCTAGAAAC
* *
526718 ATCATCTTTGAG-TCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTAAGACAGTTTCTCTTGAA
1 ATCATCTTTGAGATC-GTTTCCCTTGAAACAAA-TTTTGTCTCCCTTAAGACAGTTTCTCTCGAA
526782 ACAATCATCTTTGAG-TCATTTCCCTT
64 AC-ATCATCTTTGAGATCATTTCCCTT
526808 TAAACGAATT
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
108 2 0.02
109 28 0.34
110 40 0.49
111 12 0.15
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.40
Consensus pattern (109 bp):
ATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTAAGACAGTTTCTCTCGAAAC
ATCATCTTTGAGATCATTTCCCTTGAGACAGTTTTTCTAGAAAC
Found at i:526906 original size:36 final size:35
Alignment explanation
Indices: 526866--526978 Score: 116
Period size: 36 Copynumber: 3.3 Consensus size: 35
526856 CTTTGAGTAT
526866 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAA-AAATTTTGTCTCTCTTGAGACAG
*
526902 TTTCCCTTG-AAACA-----TCATCT-TTGAGATC-G
1 TTTCCCTTGAAAAAATTTTGTC-TCTCTTGAGA-CAG
526931 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAA-AAATTTTGTCTCTCTTGAGACAG
*
526967 TTTCTCTTGAAA
1 TTTCCCTTGAAA
526979 CCATTATCCC
Statistics
Matches: 63, Mismatches: 3, Indels: 22
0.72 0.03 0.25
Matches are distributed among these distances:
29 18 0.29
30 6 0.10
31 2 0.03
34 2 0.03
35 6 0.10
36 29 0.46
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (35 bp):
TTTCCCTTGAAAAAATTTTGTCTCTCTTGAGACAG
Found at i:526935 original size:65 final size:64
Alignment explanation
Indices: 526695--526979 Score: 383
Period size: 66 Copynumber: 4.4 Consensus size: 64
526685 GATCGTTTCC
* *
526695 CTTGAGACAGTTTTTCTAGAAACATCATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTC
1 CTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGTC-GTTTCCCTTGAAACAAA-TTTTGTCTC
526760 T
64 T
* * * * * *
526761 CTTAAGACAGTTTCTCTTGAAACAATCATCTTTGAGTCATTTCCCTTTAAACGAATTTTTTTATC
1 CTTGAGACAGTTTCTCTTGAAAC-ATCATCTTTGAGTCGTTTCCCTTGAAAC-AAATTTTGTCTC
526826 T
64 T
* ** *
526827 CTT-AGGACAGTTTCTCTTGAAATAATCATCTTTGAGTATTTTCCCTTGAAATAAATTTTGTCTC
1 CTTGA-GACAGTTTCTCTTGAAA-CATCATCTTTGAGTCGTTTCCCTTGAAACAAATTTTGTCTC
526891 T
64 T
*
526892 CTTGAGACAGTTTCCCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCT
1 CTTGAGACAGTTTCTCTTGAAACATCATCTTTGAG-TCGTTTCCCTTGAAACAAATTTTGTCTCT
526957 CTTGAGACAGTTTCTCTTGAAAC
1 CTTGAGACAGTTTCTCTTGAAAC
526980 CATTATCCCT
Statistics
Matches: 191, Mismatches: 22, Indels: 13
0.85 0.10 0.06
Matches are distributed among these distances:
64 12 0.06
65 78 0.41
66 85 0.45
67 16 0.08
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (64 bp):
CTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGTCGTTTCCCTTGAAACAAATTTTGTCTCT
Found at i:526935 original size:131 final size:131
Alignment explanation
Indices: 526695--526978 Score: 396
Period size: 131 Copynumber: 2.2 Consensus size: 131
526685 GATCGTTTCC
* * * *
526695 CTTGAGACAGTTTTTCTAGAAACATCATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTC
1 CTTGAGACAGTTTCTCTTGAAAAATCATCTTTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTC
* * * *
526760 TCTTAAGACAGTTTCTCTTGAAACAATCATCTTTGAGTCATTTCCCTTTAAACGAATTTTTTTAT
66 TCTTAAGACAGTTTCCCTTGAAACAATCATCTTTGAGTCATTTCCCTTGAAAC-AAATTTTGTAT
526825 CT
130 CT
*
526827 CTT-AGGACAGTTTCTCTTGAAATAATCATCTTTGAGTAT-TTTCCCTTGAAATAAA-TTTTGTC
1 CTTGA-GACAGTTTCTCTTGAAA-AATCATCTTTGAGTATGTTTCCCTTGAAACAAAGTTTTGTC
* *
526889 TCTCTTGAGACAGTTTCCCTTGAAAC-ATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGT
64 TCTCTTAAGACAGTTTCCCTTGAAACAATCATCTTTGAG-TCATTTCCCTTGAAACAAATTTTGT
*
526953 CTCT
128 ATCT
526957 CTTGAGACAGTTTCTCTTGAAA
1 CTTGAGACAGTTTCTCTTGAAA
526979 CCATTATCCC
Statistics
Matches: 136, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
130 42 0.31
131 47 0.35
132 33 0.24
133 14 0.10
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.42
Consensus pattern (131 bp):
CTTGAGACAGTTTCTCTTGAAAAATCATCTTTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTC
TCTTAAGACAGTTTCCCTTGAAACAATCATCTTTGAGTCATTTCCCTTGAAACAAATTTTGTATC
T
Found at i:527199 original size:40 final size:41
Alignment explanation
Indices: 527136--527241 Score: 101
Period size: 43 Copynumber: 2.6 Consensus size: 41
527126 TAGTTTGTCG
* ***
527136 TCCTCATCACGCAGGAACCGTGTCATCCACT-G-ACCATACC-
1 TCCTCATCACGTAGGAGTTGTGTCA-CCACTAGAACCA-ACCA
*
527176 TCCTCATCACGTAGGAGTTGTGTCACCCCTAGATAACCAACCA
1 TCCTCATCACGTAGGAGTTGTGTCACCACTAG--AACCAACCA
*
527219 TCCTCATCGCGTAGGAGTTGTGT
1 TCCTCATCACGTAGGAGTTGTGT
527242 TATCACCATT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
39 4 0.07
40 22 0.40
42 3 0.05
43 26 0.47
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.25
Consensus pattern (41 bp):
TCCTCATCACGTAGGAGTTGTGTCACCACTAGAACCAACCA
Found at i:527226 original size:131 final size:131
Alignment explanation
Indices: 526981--527342 Score: 393
Period size: 131 Copynumber: 2.7 Consensus size: 131
526971 TCTTGAAACC
* * * * *
526981 ATTATCCCTAAAGATGGCTAGTTGTCCTCATCACGTAGGAACTGTGTCATCC-CTCGACTAGACC
1 ATTATCTCTAAAGATGGTTAGTCGTCCTCATCACGTAGGAACCGTGTCATCCACT-GACCAGACC
** * * ** * *
527045 TCCTCATCACGTAGGAGCCGCGTCAACCTTAGATAACCTCCCGTCTTCATCACGTAGGAATCGTG
65 TCCTCATCACGTAGGAGTTGTGTCACCCTTAGATAACCAACCATCCTCATCACGTAGGAATCGTG
527110 TT
130 TT
* * * *
527112 ATTATCTCTAAAGATAGTTTGTCGTCCTCATCACGCAGGAACCGTGTCATCCACTGACCATACCT
1 ATTATCTCTAAAGATGGTTAGTCGTCCTCATCACGTAGGAACCGTGTCATCCACTGACCAGACCT
* * * *
527177 CCTCATCACGTAGGAGTTGTGTCACCCCTAGATAACCAACCATCCTCATCGCGTAGGAGTTGTGT
66 CCTCATCACGTAGGAGTTGTGTCACCCTTAGATAACCAACCATCCTCATCACGTAGGAATCGTGT
527242 T
131 T
* * * * * * * * *
527243 ATCACCATTCCTAAAGATGGTAAATCGTCCTCATCGCATAGGAACCGTGTTATCTACCGACCAGA
1 ATTATC--T-CTAAAGATGGTTAGTCGTCCTCATCACGTAGGAACCGTGTCATCCACTGACCAGA
* *
527308 TCTCCTCATCATGTAGGAGTTGTGTCACCCTTAGA
63 CCTCCTCATCACGTAGGAGTTGTGTCACCCTTAGA
527343 CGACCAGAAC
Statistics
Matches: 190, Mismatches: 37, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
131 111 0.58
132 2 0.01
133 1 0.01
134 76 0.40
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (131 bp):
ATTATCTCTAAAGATGGTTAGTCGTCCTCATCACGTAGGAACCGTGTCATCCACTGACCAGACCT
CCTCATCACGTAGGAGTTGTGTCACCCTTAGATAACCAACCATCCTCATCACGTAGGAATCGTGT
T
Found at i:527529 original size:2 final size:2
Alignment explanation
Indices: 527522--527547 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
527512 TCAGGTCTTA
527522 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
527548 TATTAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:531474 original size:20 final size:23
Alignment explanation
Indices: 531430--531476 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
531420 TATATTATAA
531430 AAATAAGTTATTTGTGTAGTATT
1 AAATAAGTTATTTGTGTAGTATT
531453 AAATAAGTTATTT-T-TA-TATT
1 AAATAAGTTATTTGTGTAGTATT
531473 AAAT
1 AAAT
531477 TTAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.33
21 2 0.08
22 1 0.04
23 13 0.54
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (23 bp):
AAATAAGTTATTTGTGTAGTATT
Done.