Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_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: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 41
Found at i:556529 original size:33 final size:33
Alignment explanation
Indices: 556502--556581 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
556492 CTCGGCTTTT
*
556502 CTCGGATTCCCTCGCATAGCTCGCTCGGTTGCC
1 CTCGGATGCCCTCGCATAGCTCGCTCGGTTGCC
* * *
556535 CTCGGATGCCCTCGCATAGCTCGTTCGGATGGC
1 CTCGGATGCCCTCGCATAGCTCGCTCGGTTGCC
*
556568 CTCGGATGCTCTCG
1 CTCGGATGCCCTCG
556582 GATGGCCTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.10, C:0.36, G:0.28, T:0.26
Consensus pattern (33 bp):
CTCGGATGCCCTCGCATAGCTCGCTCGGTTGCC
Found at i:556544 original size:10 final size:10
Alignment explanation
Indices: 556502--556632 Score: 82
Period size: 10 Copynumber: 12.1 Consensus size: 10
556492 CTCGGCTTTT
*
556502 CTCGGATTCC
1 CTCGGATGCC
*
556512 CTCGCATAGCTC
1 CTCGGAT-GC-C
*
556524 GCTCGGTTGCC
1 -CTCGGATGCC
556535 CTCGGATGCC
1 CTCGGATGCC
*
556545 CTCGCATAGCTC
1 CTCGGAT-GC-C
* *
556557 GTTCGGATGGC
1 -CTCGGATGCC
*
556568 CTCGGATGCT
1 CTCGGATGCC
*
556578 CTCGGATGGC
1 CTCGGATGCC
*
556588 CTCGGATGCT
1 CTCGGATGCC
556598 CTCGGATGACC
1 CTCGGATG-CC
*
556609 TCGGTCGGATGGC
1 -C--TCGGATGCC
556622 CTCGGATGCC
1 CTCGGATGCC
556632 C
1 C
556633 AGCGTGTTGG
Statistics
Matches: 92, Mismatches: 19, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
10 61 0.66
11 6 0.07
12 7 0.08
13 11 0.12
14 7 0.08
ACGTcount: A:0.11, C:0.34, G:0.31, T:0.24
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:556572 original size:43 final size:40
Alignment explanation
Indices: 556525--556613 Score: 106
Period size: 43 Copynumber: 2.1 Consensus size: 40
556515 GCATAGCTCG
*
556525 CTCGGTTGCCCTCGGATGCCCTCGCATAGCTCGTTCGGATGGC
1 CTCGGTTGCCCTCGGATGCCCTCGCAT-GCTC--TCGGATGAC
* * * *
556568 CTCGGATGCTCTCGGATGGCCTCGGATGCTCTCGGATGAC
1 CTCGGTTGCCCTCGGATGCCCTCGCATGCTCTCGGATGAC
556608 CTCGGT
1 CTCGGT
556614 CGGATGGCCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
40 13 0.32
42 4 0.10
43 23 0.57
ACGTcount: A:0.10, C:0.33, G:0.31, T:0.26
Consensus pattern (40 bp):
CTCGGTTGCCCTCGGATGCCCTCGCATGCTCTCGGATGAC
Found at i:556584 original size:20 final size:20
Alignment explanation
Indices: 556525--556612 Score: 104
Period size: 20 Copynumber: 4.2 Consensus size: 20
556515 GCATAGCTCG
* * *
556525 CTCGGTTGCCCTCGGATGCC
1 CTCGGATGCTCTCGGATGGC
*
556545 CTCGCATAGCTCGTTCGGATGGC
1 CTCGGAT-GCTC--TCGGATGGC
556568 CTCGGATGCTCTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
*
556588 CTCGGATGCTCTCGGATGAC
1 CTCGGATGCTCTCGGATGGC
556608 CTCGG
1 CTCGG
556613 TCGGATGGCC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
20 38 0.64
21 3 0.05
22 4 0.07
23 14 0.24
ACGTcount: A:0.10, C:0.33, G:0.32, T:0.25
Consensus pattern (20 bp):
CTCGGATGCTCTCGGATGGC
Found at i:556627 original size:54 final size:53
Alignment explanation
Indices: 556525--556630 Score: 149
Period size: 53 Copynumber: 2.0 Consensus size: 53
556515 GCATAGCTCG
* * *
556525 CTCGGTTGCCCTCGGATGCCCTCGCATAGCTCGTTCGGATGGCCTCGGATGCT
1 CTCGGATGCCCTCGGATGCCCTCGCATACCTCGGTCGGATGGCCTCGGATGCT
* * *
556578 CTCGGATGGCCTCGGATGCTCTCGGATGACCTCGGTCGGATGGCCTCGGATGC
1 CTCGGATGCCCTCGGATGCCCTCGCAT-ACCTCGGTCGGATGGCCTCGGATGC
556631 CCAGCGTGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 23 0.50
54 23 0.50
ACGTcount: A:0.10, C:0.32, G:0.33, T:0.25
Consensus pattern (53 bp):
CTCGGATGCCCTCGGATGCCCTCGCATACCTCGGTCGGATGGCCTCGGATGCT
Found at i:556839 original size:2 final size:2
Alignment explanation
Indices: 556832--556872 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
556822 TTTACCAATA
556832 AT AT 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 AT AT A
556873 CACACATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:557089 original size:19 final size:19
Alignment explanation
Indices: 557067--557105 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
557057 AAGATTATTG
557067 GAATATTATAATATTTTGA
1 GAATATTATAATATTTTGA
* *
557086 GAATGTTGTAATATTTTGA
1 GAATATTATAATATTTTGA
557105 G
1 G
557106 TGGTTTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (19 bp):
GAATATTATAATATTTTGA
Found at i:557311 original size:20 final size:20
Alignment explanation
Indices: 557283--557320 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
557273 TTGAGAAAAA
557283 AATACAATTAGCATATAATT
1 AATACAATTAGCATATAATT
* *
557303 AATATAATTAGTATATAA
1 AATACAATTAGCATATAA
557321 ACTTATATTT
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:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
AATACAATTAGCATATAATT
Found at i:560029 original size:7 final size:7
Alignment explanation
Indices: 560017--560059 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
560007 CTTTAAACTT
560017 ATGGAAG
1 ATGGAAG
560024 ATGGAAG
1 ATGGAAG
560031 ATGGAAG
1 ATGGAAG
560038 ATGGAAG
1 ATGGAAG
*
560045 ACGGAAG
1 ATGGAAG
560052 ATGGAAG
1 ATGGAAG
560059 A
1 A
560060 AGAAATAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.44, C:0.02, G:0.42, T:0.12
Consensus pattern (7 bp):
ATGGAAG
Found at i:564195 original size:21 final size:20
Alignment explanation
Indices: 564169--564207 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
564159 AAAAATTTTG
*
564169 AGTTATTCGAGTTACTATTCA
1 AGTTATCCGAGTTA-TATTCA
564190 AGTTATCCGAGTTATATT
1 AGTTATCCGAGTTATATT
564208 TTACAACTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
AGTTATCCGAGTTATATTCA
Found at i:565760 original size:2 final size:2
Alignment explanation
Indices: 565753--565798 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
565743 AAATATCTAT
565753 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
565795 GA GA
1 GA GA
565799 AAGATTTGGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:565983 original size:2 final size:2
Alignment explanation
Indices: 565976--566009 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
565966 TGCTACAGTA
565976 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
566010 TACAAGAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:571308 original size:21 final size:23
Alignment explanation
Indices: 571254--571325 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 23
571244 ACGTTGCTGC
* *
571254 CAAAATCCCTAACT-TTAAATAC-
1 CAAAATCCCTAAATACTAAA-ACT
*
571276 CAAAATCTCTAAAT-C-AAAACT
1 CAAAATCCCTAAATACTAAAACT
*
571297 CTAAATCCCTAAATACTAAAACT
1 CAAAATCCCTAAATACTAAAACT
571320 CAAAAT
1 CAAAAT
571326 TTAAAATCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
20 2 0.05
21 15 0.37
22 13 0.32
23 11 0.27
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (23 bp):
CAAAATCCCTAAATACTAAAACT
Found at i:573652 original size:25 final size:27
Alignment explanation
Indices: 573590--573653 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 27
573580 AAGTTATATA
*
573590 TTTAGTATGTTTTATTTCGTTTTAGTG
1 TTTAATATGTTTTATTTCGTTTTAGTG
* *
573617 TCTAAT-T-TTTTATTT-GTTTTA-TT
1 TTTAATATGTTTTATTTCGTTTTAGTG
573640 TTTAATATGTTTTA
1 TTTAATATGTTTTA
573654 AAATTATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
23 6 0.19
24 7 0.23
25 13 0.42
26 1 0.03
27 4 0.13
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (27 bp):
TTTAATATGTTTTATTTCGTTTTAGTG
Found at i:574703 original size:23 final size:23
Alignment explanation
Indices: 574677--574724 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
574667 ATAAAGTACA
*
574677 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
574700 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
574723 AT
1 AT
574725 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:575131 original size:21 final size:20
Alignment explanation
Indices: 575101--575154 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
575091 GATAGACACT
*
575101 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
575122 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
575145 TTACATTATA
1 TTACATTATA
575155 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:575142 original size:23 final size:23
Alignment explanation
Indices: 575116--575178 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
575106 ATATAACCAT
575116 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
575139 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
575162 TACCTATTACATCATAT
1 TACCTATTACATTATAT
575179 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:578046 original size:184 final size:184
Alignment explanation
Indices: 577737--578408 Score: 1227
Period size: 184 Copynumber: 3.7 Consensus size: 184
577727 TTTTAAATGG
* *
577737 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATACCGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATACAGGTTGTAGACCTATTCGCGCA
577802 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
577867 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
* *
577921 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATACCGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATACAGGTTGTAGACCTATTCGCGCA
577986 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
578051 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTTCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
*
578105 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATACAGGTTGTAGACCTATTCGCGCA
*
578170 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
* *
578235 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
*
578289 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATACAGGTTGTAGACCTATTCGCGCA
* **
578354 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
578409 ATGTTGAAAG
Statistics
Matches: 478, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 478 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATACAGGTTGTAGACCTATTCGCGCA
TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
Found at i:579783 original size:3 final size:3
Alignment explanation
Indices: 579775--579825 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
579765 ACTTGTTTGG
* * * *
579775 ATC ATC ATC TTC ATC ATC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
579823 ATC
1 ATC
579826 GTCAGCTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:579792 original size:12 final size:12
Alignment explanation
Indices: 579775--579837 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
579765 ACTTGTTTGG
579775 ATCATCATCTTC
1 ATCATCATCTTC
*
579787 ATCATCATCGTC
1 ATCATCATCTTC
*
579799 ATCATCATCATC
1 ATCATCATCTTC
*
579811 ATCGTCATCTTC
1 ATCATCATCTTC
* *
579823 ATCGTCAGCTTC
1 ATCATCATCTTC
579835 ATC
1 ATC
579838 TTCTGCGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:579836 original size:18 final size:18
Alignment explanation
Indices: 579779--579840 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
579769 GTTTGGATCA
579779 TCATCTTCATCATCATCG
1 TCATCTTCATCATCATCG
*
579797 TCATCATCATCATCATCG
1 TCATCTTCATCATCATCG
* * *
579815 TCATCTTCATCGTCAGCT
1 TCATCTTCATCATCATCG
579833 TCATCTTC
1 TCATCTTC
579841 TGCGACCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCATCATCG
Found at i:579840 original size:6 final size:6
Alignment explanation
Indices: 579779--579840 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
579769 GTTTGGATCA
* * * * * *
579779 TCATCT TCATCA TCATCG TCATCA TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
579827 TCAGCT TCATCT TC
1 TCATCT TCATCT TC
579841 TGCGACCGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:581698 original size:198 final size:198
Alignment explanation
Indices: 581302--582914 Score: 2851
Period size: 198 Copynumber: 8.1 Consensus size: 198
581292 TTTAAATTAG
* *
581302 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
581367 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *** *
581431 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-GA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGATGCACCTTG-TAAAAATTCATTCTGGAAA
581495 AAAAA
194 AAAAA
581500 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
581565 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *** *
581630 CGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTG-TAAAAATTCATTCTGGAAAA
581694 AAAA
195 AAAA
581698 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
581763 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
581828 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTAAAAATTCATTCTGGAAAAA
581893 AAA
196 AAA
581896 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
581961 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *** *
582026 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGATGCACCTTG-TAAAAATTCATTCTGGAAA
582091 AAAAA
194 AAAAA
582096 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
582161 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
582226 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTAAAAATTCATTCTGGAAAAA
582291 AAA
196 AAA
582294 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
582359 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *** *
582424 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG-GAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTG-TAAAAATTCATTCTGGAAAA
582488 AAAA
195 AAAA
582492 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
582557 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
582622 CGACAC-TTTT-TATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTAAAAATTCATTCTGGAAAAA
582685 AAA
196 AAA
*
582688 TATCGCCACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
582753 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
582818 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTAAAAATTCATTCTGGAAAAA
582883 AAA
196 AAA
*
582886 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
582915 TGACCCTTAA
Statistics
Matches: 1364, Mismatches: 42, Indels: 18
0.96 0.03 0.01
Matches are distributed among these distances:
195 13 0.01
196 170 0.12
197 57 0.04
198 801 0.59
199 168 0.12
200 155 0.11
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTAAAAATTCATTCTGGAAAAA
AAA
Found at i:582432 original size:596 final size:595
Alignment explanation
Indices: 581302--582914 Score: 2925
Period size: 596 Copynumber: 2.7 Consensus size: 595
581292 TTTAAATTAG
* *
581302 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
581367 ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
581432 GACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGG-AA
131 GACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
581496 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
581561 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
* * ***
581626 GGATCGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGG
326 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGG
*
581690 GAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
390 AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
*
581755 CCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
455 CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
*
581820 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATT
520 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAAATTCATT
581884 CTGGAAAAAAAA
585 CTGG-AAAAAAA
581896 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
581961 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
582026 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
130 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
582091 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
*
582156 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
582221 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGG
325 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGG
582286 AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
390 AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAA
582351 CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
455 CCGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGAT
* ***
582416 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATT
520 TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAAATTCATT
*
582481 CTGGGAAAAAA
585 CTGGAAAAAAA
582492 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
582557 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *** *
582622 CGACAC--TTTT-TATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAA
130 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
*
582683 AAAAATATCGCCACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCG
582748 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
582813 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGG
325 GGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGG
*
582878 AAAAAAAATATCGACACAAACTATATTAGTATCGACA
390 AAAAAAAATATCGACACAAACTATATTAGTGTCGACA
582915 TGACCCTTAA
Statistics
Matches: 989, Mismatches: 26, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
592 244 0.25
593 30 0.03
594 84 0.08
595 110 0.11
596 478 0.48
597 43 0.04
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (595 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
TATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGA
AAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAAC
CGGTATAATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATT
TTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTAAAAATTCATTC
TGGAAAAAAA
Found at i:583021 original size:37 final size:38
Alignment explanation
Indices: 582980--583059 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
582970 TCTCATTCAT
*
582980 AATTAT-ATTCACATAAAAAAATATAAATCGTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
** * * *
583017 AATTATAAATCGTATACAAAATTATAAATCTTATACAA
1 AATTATAAATCACATAAAAAAATATAAATCGTATACAA
583055 AATTA
1 AATTA
583060 ACTCGACATT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 6 0.17
38 30 0.83
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.33
Consensus pattern (38 bp):
AATTATAAATCACATAAAAAAATATAAATCGTATACAA
Found at i:583023 original size:19 final size:19
Alignment explanation
Indices: 582996--583059 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
582986 ATTCACATAA
*
582996 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
583015 AAAATTATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
583034 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
583053 AAAATTA
1 AAAATTA
583060 ACTCGACATT
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:0.56, C:0.09, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:584895 original size:33 final size:33
Alignment explanation
Indices: 584858--584923 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
584848 CATCTTAATA
*
584858 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
584891 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
584924 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:587065 original size:24 final size:24
Alignment explanation
Indices: 587028--587080 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
587018 CCGTTCTATC
587028 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
587052 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
587076 TATTT
1 TATTT
587081 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:587272 original size:21 final size:20
Alignment explanation
Indices: 587225--587272 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
587215 TCCGGTATCA
*
587225 TTTTACCGTTTTTATCATTT
1 TTTTACCGGTTTTATCATTT
**
587245 TGATACCGGTTTTATCATATT
1 TTTTACCGGTTTTATCAT-TT
587266 TTTTACC
1 TTTTACC
587273 TGTTATATCG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.19, C:0.17, G:0.08, T:0.56
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATTT
Found at i:587420 original size:20 final size:20
Alignment explanation
Indices: 587393--587439 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
587383 ACACTTTTAA
587393 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
587412 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
587433 TTTTACC
1 TTTTACC
587440 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:588393 original size:17 final size:17
Alignment explanation
Indices: 588350--588393 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
588340 CCTTTTAAAA
588350 ATTTTA-ATTTTTTTAT
1 ATTTTATATTTTTTTAT
*
588366 ATATTAGATATTTTTTTAT
1 AT-TT-TATATTTTTTTAT
588385 ATTTTATAT
1 ATTTTATAT
588394 GAATTATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 2 0.09
17 6 0.26
18 3 0.13
19 12 0.52
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
ATTTTATATTTTTTTAT
Found at i:600475 original size:33 final size:34
Alignment explanation
Indices: 600427--600492 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
600417 TAGATCATCA
**
600427 CGTTGCGATTTTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
600460 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
600493 ATTATCTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.41
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:600494 original size:20 final size:19
Alignment explanation
Indices: 600427--600517 Score: 84
Period size: 20 Copynumber: 4.9 Consensus size: 19
600417 TAGATCATCA
*
600427 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTCTCATTTCG
600446 CGTTGCGATTCTC---T--
1 CGTTGCGATTCTCATTTCG
**
600460 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTT-CG
*
600480 CGTTGCGATTCTCATTATCT
1 CGTTGCGATTCTCATT-TCG
*
600500 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
600518 AACCAAAAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
14 11 0.19
16 1 0.02
17 1 0.02
19 14 0.24
20 30 0.52
21 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTCTCATTTCG
Found at i:602684 original size:42 final size:42
Alignment explanation
Indices: 602608--602696 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
602598 GACTCGCCTG
* * *
602608 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
602650 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
602692 TCATC
1 TCATC
602697 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:604095 original size:14 final size:14
Alignment explanation
Indices: 604076--604111 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
604066 ATTGTTTAAT
604076 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
604090 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
604104 TGATTTGT
1 TGATTTGT
604112 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:604253 original size:14 final size:14
Alignment explanation
Indices: 604236--604292 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
604226 GCAAAATGAA
604236 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
604250 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
604269 AATCGTAACGAGAG
1 AATCGCAACGAGAG
604283 AATCGCAACG
1 AATCGCAACG
604293 CGAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:604266 original size:33 final size:33
Alignment explanation
Indices: 604218--604307 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
604208 AAAAAGTACT
* *
604218 ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
604251 ATCGCAACGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
604284 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
604308 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:604325 original size:19 final size:19
Alignment explanation
Indices: 604303--604453 Score: 62
Period size: 19 Copynumber: 8.7 Consensus size: 19
604293 CGAAATTAAA
604303 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
604322 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
604337 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
604355 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
* *
604369 TTAGCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
604388 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
604403 -TCTCGTTGTGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
604421 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
604440 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
604454 AGACATTAAG
Statistics
Matches: 91, Mismatches: 25, Indels: 31
0.62 0.17 0.21
Matches are distributed among these distances:
14 26 0.29
16 6 0.07
17 6 0.07
19 43 0.47
20 10 0.11
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:604349 original size:33 final size:32
Alignment explanation
Indices: 604307--604433 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
604297 ATTAAATTCG
604307 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
604340 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
604373 CGTTGCAATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
604406 CGTTGTGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
604434 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:604386 original size:66 final size:66
Alignment explanation
Indices: 604300--604432 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
604290 ACGCGAAATT
* *
604300 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
604365 G
66 G
* *
604366 AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCTCTCGTTGTGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
604431 G
66 G
604432 A
1 A
604433 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCAATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:606743 original size:12 final size:12
Alignment explanation
Indices: 606726--606761 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
606716 TCTTCGGGGA
606726 CTTTTTCTTCTT
1 CTTTTTCTTCTT
606738 CTTTTTCTTCTT
1 CTTTTTCTTCTT
606750 CTTTTTCTTCTT
1 CTTTTTCTTCTT
606762 TAGGATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:606971 original size:24 final size:24
Alignment explanation
Indices: 606937--606990 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
606927 CTGAAACATC
*
606937 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
606961 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
606985 ATCAAA
1 ATCAAA
606991 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:607902 original size:20 final size:20
Alignment explanation
Indices: 607813--607905 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 20
607803 TGCGAATTTG
*
607813 GAAAATCGCAATGCGATACT
1 GAAAATCGCAATGAGATACT
** * *
607833 GACTATCGCAACGAGATAAT
1 GAAAATCGCAATGAGATACT
* * *
607853 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAATGAGATACT
** *
607874 GAATTTCGCAATGAGATTCT
1 GAAAATCGCAATGAGATACT
607894 GAAAATCGCAAT
1 GAAAATCGCAAT
607906 CATCTTCAAA
Statistics
Matches: 56, Mismatches: 16, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
20 41 0.73
21 15 0.27
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (20 bp):
GAAAATCGCAATGAGATACT
Found at i:608143 original size:20 final size:20
Alignment explanation
Indices: 608118--608185 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
608108 CAACGGGGAA
608118 ATCGCAACGCGAAAATGGAT
1 ATCGCAACGCGAAAATGGAT
** * *
608138 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GAT
*
608158 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGAT
608178 ATCGCAAC
1 ATCGCAAC
608186 TAGAAAATCG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 5 0.14
20 27 0.73
21 5 0.14
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGAT
Found at i:608197 original size:34 final size:34
Alignment explanation
Indices: 608102--608205 Score: 100
Period size: 40 Copynumber: 2.9 Consensus size: 34
608092 ATTCATTTGA
** *
608102 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
1 CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
*
608136 ATATCGCAATTCGAAATGAAAAATCGCAACGCGAAAATGG
1 CTATCGCAA--C--AA-G-AAAATCGCAACGCGAAAATGG
* *
608176 CTATCGCAACTAGAAAATCGCAATGCGAAA
1 CTATCGCAACAAGAAAATCGCAACGCGAAA
608206 TGAAAATCAC
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
34 24 0.42
35 1 0.02
36 2 0.04
38 1 0.02
39 1 0.02
40 28 0.49
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.15
Consensus pattern (34 bp):
CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
Found at i:608236 original size:14 final size:16
Alignment explanation
Indices: 608216--608289 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
608206 TGAAAATCAC
608216 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
608231 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
608248 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
608267 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
608283 -TTGCGAT
1 ATTGCGAT
608290 AGTCAGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:608253 original size:19 final size:19
Alignment explanation
Indices: 608231--608279 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
608221 GATTTTCTCG
608231 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
608250 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
608269 TTGCGATTTTC
1 TTGCGATTTTC
608280 TCGTTGCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:608435 original size:14 final size:14
Alignment explanation
Indices: 608416--608452 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
608406 CATCAATTAA
608416 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
608430 ACAAATCATCTTTT
1 ACAAATCAACATTT
608444 ACAAATCAA
1 ACAAATCAA
608453 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:610345 original size:20 final size:19
Alignment explanation
Indices: 610322--610389 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
610312 GAAACTTAAA
610322 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
* *
610342 ATCGCAACACGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
610362 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
610381 ATCGCAACG
1 ATCGCAACG
610390 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
19 14 0.36
20 24 0.62
21 1 0.03
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:610397 original size:14 final size:14
Alignment explanation
Indices: 610378--610468 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
610368 ATGCGAAATG
610378 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
610392 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
610411 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
610425 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
610441 ATGAAATTGCAACGAC
1 A--AAATCGCAACGAC
610457 AAAATCGCAACG
1 AAAATCGCAACG
610469 CGAAACACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 9 0.15
19 10 0.16
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:610458 original size:32 final size:33
Alignment explanation
Indices: 610362--610473 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
610352 GGAAATGGCT
610362 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
610395 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
610428 ATCGCAATGCGAAATG-AAATTGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
610460 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
610474 CACAAATCGC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 28 0.36
33 49 0.64
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:610481 original size:65 final size:66
Alignment explanation
Indices: 610362--610484 Score: 196
Period size: 65 Copynumber: 1.9 Consensus size: 66
610352 GGAAATGGCT
* *
610362 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
610427 A
66 A
*
610428 ATCGCAATGCGAAATG-AAATTGCAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
610485 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 1 0.02
65 36 0.68
66 16 0.30
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:610502 original size:19 final size:19
Alignment explanation
Indices: 610480--610562 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
610470 GAAACACAAA
610480 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
610499 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
610515 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
610532 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
610551 TCGCATTGCGAT
1 TCGCATTGCGAT
610563 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 6 0.11
15 3 0.05
16 4 0.07
17 4 0.07
18 3 0.05
19 35 0.64
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:610570 original size:19 final size:19
Alignment explanation
Indices: 610527--610590 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
610517 GTTGCGATTT
**
610527 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
*
610546 TTATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
* *
610565 CCATTTCCGCGTTGCGATAG
1 TCATTT-CGCATTGCGATAG
610585 TCATTT
1 TCATTT
610591 TCGTGTTGCG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:610581 original size:20 final size:20
Alignment explanation
Indices: 610556--610601 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
610546 TTATTTCGCA
610556 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
610576 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
610596 TTGCGA
1 TTGCGA
610602 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:611109 original size:18 final size:18
Alignment explanation
Indices: 611083--611127 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
611073 GTCGATCAGA
*
611083 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
611101 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
611119 TGATGGCTC
1 TGATGGCTC
611128 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:612495 original size:20 final size:20
Alignment explanation
Indices: 612447--612505 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
612437 AATAGTTTCT
** *
612447 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
612467 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
612487 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
612506 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:612779 original size:22 final size:22
Alignment explanation
Indices: 612749--612792 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
612739 GATGGAGATA
*
612749 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
612771 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
612793 TGAGAAAGTG
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:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:612990 original size:21 final size:21
Alignment explanation
Indices: 612960--613074 Score: 82
Period size: 20 Copynumber: 5.7 Consensus size: 21
612950 CGCTTTGAAA
612960 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGATTATGTATT
* * *
612981 ATCGCGTTGCGA--AAGTCAAT
1 ATCGCATTGCGATTATGT-ATT
* * *
613001 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTATT
*
613022 ATCGCATTGCGA-TA-GTAAGT
1 ATCGCATTGCGATTATGT-ATT
*
613042 ATC-CATTGCGA-TA-GTCAGT
1 ATCGCATTGCGATTATGT-ATT
613061 ATCGCATTGCGATT
1 ATCGCATTGCGATT
613075 TTCCCAATTC
Statistics
Matches: 76, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
19 23 0.30
20 27 0.36
21 24 0.32
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (21 bp):
ATCGCATTGCGATTATGTATT
Found at i:613070 original size:20 final size:20
Alignment explanation
Indices: 613021--613073 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
613011 GATTTTGTAT
613021 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
613041 TATC-CATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
613060 TATCGCATTGCGAT
1 TATCGCATTGCGAT
613074 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:613071 original size:60 final size:62
Alignment explanation
Indices: 612960--613076 Score: 150
Period size: 60 Copynumber: 1.9 Consensus size: 62
612950 CGCTTTGAAA
* * * *
612960 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAATATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTGTATT
* *
613022 ATCGCATTGCGA-TA-GTAAGTATC-CATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTCAATATCGCATTGCGATTTT
613077 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 29 0.60
61 7 0.15
62 12 0.25
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (62 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAATATCGCATTGCGATTTTGTATT
Found at i:616153 original size:51 final size:51
Alignment explanation
Indices: 616077--616179 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
616067 AGAATGGTCT
*
616077 TATGAAAACTGTGTCTGGGCAAGAATTTGATGTGGTAAAGGGTTGATAAGA
1 TATGAAAACTGTGTCAGGGCAAGAATTTGATGTGGTAAAGGGTTGATAAGA
616128 TATGAAAACTGTGTCAGGGCAAGAATTTGATGTGGTAAAGGGTTGATAAGA
1 TATGAAAACTGTGTCAGGGCAAGAATTTGATGTGGTAAAGGGTTGATAAGA
616179 T
1 T
616180 GATCAATGCC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.34, C:0.06, G:0.31, T:0.29
Consensus pattern (51 bp):
TATGAAAACTGTGTCAGGGCAAGAATTTGATGTGGTAAAGGGTTGATAAGA
Found at i:617657 original size:23 final size:23
Alignment explanation
Indices: 617631--617678 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
617621 ATAAAGTACA
*
617631 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
617654 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
617677 AT
1 AT
617679 TTACGTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:618463 original size:23 final size:23
Alignment explanation
Indices: 618437--618499 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
618427 ATATAACCAC
618437 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
618460 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
618483 TACCTATTACATCATAT
1 TACCTATTACATTATAT
618500 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:618956 original size:39 final size:39
Alignment explanation
Indices: 618902--618988 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
618892 TCAAGTTGTA
*
618902 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
618941 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
618980 GATTTTGAT
1 GATTTTGAT
618989 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:619269 original size:18 final size:18
Alignment explanation
Indices: 619246--619282 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
619236 CGAAATATAT
619246 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
619264 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
619282 A
1 A
619283 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:619705 original size:25 final size:25
Alignment explanation
Indices: 619671--619721 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
619661 TTTTTCCAAA
*
619671 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
619696 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
619721 T
1 T
619722 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:619931 original size:21 final size:22
Alignment explanation
Indices: 619906--619957 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
619896 ACACTTTACA
*
619906 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
619929 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
619952 ATATAA
1 ATATAA
619958 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:619942 original size:23 final size:23
Alignment explanation
Indices: 619916--619978 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
619906 ATATAACCAC
619916 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
619939 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
619962 TACCTATTACATCATAT
1 TACCTATTACATTATAT
619979 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:620322 original size:25 final size:25
Alignment explanation
Indices: 620265--620330 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
620255 CACTCAAAAG
*
620265 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
620290 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
620315 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
620331 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:622040 original size:183 final size:183
Alignment explanation
Indices: 621732--622249 Score: 937
Period size: 183 Copynumber: 2.8 Consensus size: 183
621722 TTACCGACAC
*
621732 TTTTTAAATGGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAA
1 TTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAA
*
621797 AGTATCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTAC
66 AGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTAC
621862 AAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACT
131 AAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACT
*
621915 TTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTATAA
1 TTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAA
* *
621980 AGTGTTGAGATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTAC
66 AGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTAC
622045 AAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACT
131 AAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACT
622098 TTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAA
1 TTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAA
* *
622163 AGTGTCGATATAGGTTGTAGACCTATTCACGCATAAAACCGGTATATTTATACCGGTTATATTGC
66 AGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTAC
* * **
622228 AAATTTACCTATTTTATTATAA
131 AAAATTATCTATTACATTATAA
622250 TATGTTGAAA
Statistics
Matches: 321, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 321 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
TTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAA
AGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTAC
AAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACT
Found at i:623677 original size:3 final size:3
Alignment explanation
Indices: 623669--623719 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
623659 ACTTGTTTGG
* * * *
623669 ATC ATC ATC TTC ATC ATC ATC ATC ATC GTC ATC ATC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
623717 ATC
1 ATC
623720 GTCAGCTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:623686 original size:12 final size:12
Alignment explanation
Indices: 623673--623731 Score: 82
Period size: 12 Copynumber: 4.9 Consensus size: 12
623663 GTTTGGATCA
*
623673 TCATCTTCATCA
1 TCATCTTCATCG
*
623685 TCATCATCATCG
1 TCATCTTCATCG
*
623697 TCATCATCATCG
1 TCATCTTCATCG
623709 TCATCTTCATCG
1 TCATCTTCATCG
*
623721 TCAGCTTCATC
1 TCATCTTCATC
623732 TTCTGCGACC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.22, C:0.34, G:0.07, T:0.37
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:623692 original size:18 final size:18
Alignment explanation
Indices: 623669--623734 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
623659 ACTTGTTTGG
623669 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
*
623687 ATCATCATCGTCATCATC
1 ATCATCATCTTCATCATC
* *
623705 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
623723 AGCTTCATCTTC
1 ATCATCATCTTC
623735 TGCGACCGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:623734 original size:6 final size:6
Alignment explanation
Indices: 623673--623734 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
623663 GTTTGGATCA
* * * * * *
623673 TCATCT TCATCA TCATCA TCATCG TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
623721 TCAGCT TCATCT TC
1 TCATCT TCATCT TC
623735 TGCGACCGCT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:625535 original size:199 final size:199
Alignment explanation
Indices: 625195--626769 Score: 3150
Period size: 199 Copynumber: 7.9 Consensus size: 199
625185 TTTAAATTAG
625195 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
625260 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
625325 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
625390 CAAA
196 CAAA
625394 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
625459 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
625524 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
625589 CAAA
196 CAAA
625593 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
625658 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
625723 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
625788 CAAA
196 CAAA
625792 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
625857 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
625922 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
625987 CAAA
196 CAAA
625991 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
626056 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
626121 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
626186 CAAA
196 CAAA
626190 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
626255 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
626320 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
626385 CAAA
196 CAAA
626389 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
626454 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
626519 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
626584 CAAA
196 CAAA
626588 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
626653 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
626718 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCAT
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCAT
626770 ATTGTAAATT
Statistics
Matches: 1376, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
199 1376 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
CAAA
Found at i:626928 original size:19 final size:19
Alignment explanation
Indices: 626882--626930 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
626872 TTATATTCAC
*
626882 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
626901 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
626920 ATACAAAATTA
1 ATACAAAATTA
626931 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:628764 original size:33 final size:33
Alignment explanation
Indices: 628727--628792 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
628717 CATCTTAATA
* *
628727 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
* * *
628760 TCACCCCTCAACACCTCTATTTCATTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
628793 CCATCTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCATTCACCACT
Found at i:628866 original size:21 final size:21
Alignment explanation
Indices: 628826--628890 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
628816 CCCCTTATGC
* *
628826 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
628847 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
628868 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
628889 CT
1 CT
628891 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:631143 original size:17 final size:18
Alignment explanation
Indices: 631121--631163 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
631111 ATATATCCGG
631121 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
631138 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
631158 TATCAT
1 TATCAT
631164 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:631181 original size:20 final size:19
Alignment explanation
Indices: 631126--631172 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
631116 TCCGGTATCA
631126 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
631145 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
631166 TTTTACC
1 TTTTACC
631173 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:631320 original size:20 final size:20
Alignment explanation
Indices: 631294--631339 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
631284 CACTTTTAAA
631294 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
631313 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
631334 TTTACC
1 TTTACC
631340 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:639532 original size:2 final size:2
Alignment explanation
Indices: 639527--639555 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
639517 CCCCCCCCCC
639527 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
639556 ACACACACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:639560 original size:2 final size:2
Alignment explanation
Indices: 639555--639580 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
639545 CTCTCTCTCT
639555 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
639581 TAAACGCAAA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:643993 original size:4 final size:4
Alignment explanation
Indices: 643984--644018 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
643974 ATTTCAGTTC
643984 TTAA TTAA TTAA TTAA TTAA TTAA TCTAAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T-T-AA TTAA T
644019 ATCTAGAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 24 0.83
5 2 0.07
6 3 0.10
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (4 bp):
TTAA
Found at i:644442 original size:30 final size:30
Alignment explanation
Indices: 644378--644459 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
644368 GTACATAACT
* * * * * *
644378 TTAATTTTGTACAATTATACACATGAAGTC
1 TTAATTTTGTTCAATTATATAAATAAAATA
644408 TTAATTTTGTTCAATTATATAAATAAAATA
1 TTAATTTTGTTCAATTATATAAATAAAATA
**
644438 TTAATTTAAATTCAATTATATA
1 TTAATTT-TGTTCAATTATATA
644460 GCTCTTAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 31 0.72
31 12 0.28
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (30 bp):
TTAATTTTGTTCAATTATATAAATAAAATA
Found at i:653897 original size:2 final size:2
Alignment explanation
Indices: 653890--653924 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
653880 GTTACAATAC
*
653890 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
653925 ATTTTTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:653925 original size:10 final size:10
Alignment explanation
Indices: 653885--653925 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
653875 AAACAGTTAC
*
653885 AATACATATA
1 AATATATATA
*
653895 TATATATATA
1 AATATATATA
*
653905 TATATATATA
1 AATATATATA
653915 AATATATATA
1 AATATATATA
653925 A
1 A
653926 TTTTTATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATATATA
Found at i:654161 original size:4 final size:4
Alignment explanation
Indices: 654152--654184 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
654142 AAACGTCTTC
654152 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
654185 CATCTATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:663367 original size:60 final size:59
Alignment explanation
Indices: 663197--663374 Score: 203
Period size: 60 Copynumber: 3.0 Consensus size: 59
663187 TCAAACTATA
* * * * ** *
663197 ATCCTCATTTTAAATTGATACTTAAACTTTTGAATATTTTAATTTTATCTATAAATTATT
1 ATCCTC-TTTTAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAATTATG
* * *
663257 ATTCTTATTTTAAATTATTCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAATTATG
1 A-TCCTCTTTTAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAATTATG
* * * *
663317 ATCCTCTTTCTAAATTAATCCTAAAACTTTTGGATATTCCAATTTCATCCCCAAATTA
1 ATCCTCTTT-TAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAATTA
663375 ATCCAAATAT
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
59 6 0.06
60 90 0.91
61 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.03, T:0.47
Consensus pattern (59 bp):
ATCCTCTTTTAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAATTATG
Found at i:663941 original size:21 final size:21
Alignment explanation
Indices: 663890--663942 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
663880 ATTATGACTA
663890 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
663911 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
663932 TCGCAATGCGA
1 TCGCAATGCGA
663943 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:663957 original size:20 final size:21
Alignment explanation
Indices: 663932--663983 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
663922 TTTTCCCAAT
*
663932 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
663952 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
663973 TCGCAATGCGA
1 TCGCAATGCGA
663984 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:663962 original size:41 final size:41
Alignment explanation
Indices: 663917--664126 Score: 122
Period size: 41 Copynumber: 5.1 Consensus size: 41
663907 AATTTCGCGT
*
663917 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * *
663958 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * * **
663999 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCACGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* *
664040 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* **** * * *
664081 CGCGA-TCAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TAAGTAAATCGCAA
664122 TGCGA
1 TGCGA
664127 ATACGTAAAT
Statistics
Matches: 123, Mismatches: 39, Indels: 14
0.70 0.22 0.08
Matches are distributed among these distances:
39 2 0.02
40 24 0.20
41 95 0.77
43 1 0.01
44 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:664027 original size:21 final size:21
Alignment explanation
Indices: 663993--664065 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
663983 ATACTGACTA
* *
663993 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
664014 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
* **
664034 TCACGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
664055 TCGCAATGCGA
1 TCGCAATGCGA
664066 ATACGTAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:664080 original size:20 final size:20
Alignment explanation
Indices: 664055--664148 Score: 118
Period size: 20 Copynumber: 4.7 Consensus size: 20
664045 TTTTCATAAT
664055 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
664075 TCGCAACGCG-ATCAAGTAAA
1 TCGCAATGCGAAT-ACGTAAA
* *
664095 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
664116 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
664136 TTGCAATGCGAAT
1 TCGCAATGCGAAT
664149 CTTACTATCG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 42 0.67
21 18 0.29
22 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:664135 original size:41 final size:41
Alignment explanation
Indices: 664055--664148 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
664045 TTTTCATAAT
*
664055 TCGCAATGCGAA-TACGTAAATCGCAACGCGATCAAGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGATCAAGTAAA
* * *
664095 TCGCAATGCGAATTAGGAAAATCGCAATGCGAAT-ACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCG-ATCAAGTAAA
*
664136 TTGCAATGCGAAT
1 TCGCAATGCGAAT
664149 CTTACTATCG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
40 12 0.26
41 33 0.70
42 2 0.04
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCGATCAAGTAAA
Found at i:664733 original size:19 final size:19
Alignment explanation
Indices: 664684--664754 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
664674 TAGTTTCGAG
664684 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
*
664704 AAT-AACTATCGCAACGCGA
1 AATGAA-AATCGCAACGCGA
*
664723 AATGAAAATCGCAACGAGA
1 AATGAAAATCGCAACGCGA
**
664742 AACCAAAATCGCA
1 AATGAAAATCGCA
664755 TTGCGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 29 0.66
20 15 0.34
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:664829 original size:20 final size:19
Alignment explanation
Indices: 664755--664843 Score: 89
Period size: 20 Copynumber: 4.8 Consensus size: 19
664745 CAAAATCGCA
*
664755 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCTCG
664774 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCTCG
**
664788 TTGCGATAGTCATTTCTGCG
1 TTGCGATTTTCATTTCT-CG
*
664808 TTGCGATTTTTATTATCTCG
1 TTGCGATTTTCATT-TCTCG
664828 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
664844 AACCAAAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 11 0.19
20 28 0.49
21 3 0.05
ACGTcount: A:0.12, C:0.20, G:0.19, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCG
Found at i:666999 original size:42 final size:42
Alignment explanation
Indices: 666940--667059 Score: 116
Period size: 42 Copynumber: 2.9 Consensus size: 42
666930 CCGACTCGCT
* * *
666940 TATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCC
1 TATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCC
* * * *
666982 TATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCAC
1 TATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCC
* ** * *
667024 TGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGA
1 TATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGA
667060 TCCCGATTCA
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
42 59 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.23
Consensus pattern (42 bp):
TATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCC
Found at i:667018 original size:21 final size:21
Alignment explanation
Indices: 666994--667063 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
666984 TCATTCCTCG
666994 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
667015 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
667036 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
667057 AGA-TCCC
1 AGAGTCCC
667064 GATTCACATG
Statistics
Matches: 34, Mismatches: 13, Indels: 5
0.65 0.25 0.10
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 30 0.88
22 1 0.03
ACGTcount: A:0.23, C:0.39, G:0.19, T:0.20
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:668892 original size:12 final size:12
Alignment explanation
Indices: 668875--668899 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
668865 TCTTCGGGGA
668875 CTTTTTCTTCTT
1 CTTTTTCTTCTT
668887 CTTTTTCTTCTT
1 CTTTTTCTTCTT
668899 C
1 C
668900 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:669921 original size:21 final size:21
Alignment explanation
Indices: 669897--669951 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
669887 CGATTTTCCC
*
669897 AATTCGCAATGCGAATAAGTA
1 AATTCGCAATGCGAATAAGGA
**
669918 AATT-GCAATGCGAATTCGGA
1 AATTCGCAATGCGAATAAGGA
*
669938 AAATCGCAATGCGA
1 AATTCGCAATGCGA
669952 TACTGACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
AATTCGCAATGCGAATAAGGA
Found at i:670025 original size:20 final size:20
Alignment explanation
Indices: 669936--670027 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
669926 TGCGAATTCG
*
669936 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGCGATACT
** * *
669956 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGCGATACT
* *
669976 ACAAAATCACAACGCGATACT
1 -GAAAATCGCAACGCGATACT
*** *
669997 GACTTTCGCAACGCGATTCT
1 GAAAATCGCAACGCGATACT
670017 GAAAATCGCAA
1 GAAAATCGCAA
670028 TCATCTTCAA
Statistics
Matches: 51, Mismatches: 20, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
20 37 0.73
21 14 0.27
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
GAAAATCGCAACGCGATACT
Found at i:670336 original size:19 final size:19
Alignment explanation
Indices: 670295--670381 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
670285 GAAATGAAAA
670295 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
670311 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
670328 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
670347 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
670366 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
670382 TTGTTGCGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 49 0.74
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:670365 original size:38 final size:33
Alignment explanation
Indices: 670295--670391 Score: 140
Period size: 38 Copynumber: 2.8 Consensus size: 33
670285 GAAATGAAAA
670295 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
670328 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
*
670366 TCGCATTGCGATTTTCTTGTTGCGAT
1 TCGCATTGCGATTTTCTCGTTGCGAT
670392 AGTCAGTTTC
Statistics
Matches: 58, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
33 23 0.40
35 2 0.03
36 3 0.05
38 30 0.52
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:670406 original size:20 final size:20
Alignment explanation
Indices: 670378--670420 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
670368 GCATTGCGAT
*
670378 TTTCTTGTTGCGATAGTCAG
1 TTTCGTGTTGCGATAGTCAG
*
670398 TTTCGTGTTGCGATAGTCTG
1 TTTCGTGTTGCGATAGTCAG
670418 TTT
1 TTT
670421 TGCCTTCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.49
Consensus pattern (20 bp):
TTTCGTGTTGCGATAGTCAG
Found at i:672020 original size:41 final size:42
Alignment explanation
Indices: 671966--672057 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
671956 CCTCTTCAAC
* *
671966 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
672007 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
672049 GATGACAGG
1 GATGACAGG
672058 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.44
42 25 0.56
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:672022 original size:21 final size:21
Alignment explanation
Indices: 671993--672053 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
671983 GAACGGTGGG
*
671993 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
672014 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
672035 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
672054 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:672420 original size:20 final size:20
Alignment explanation
Indices: 672397--672486 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
672387 AGAATAGTTT
* *
672397 ACTTTCGCAACACGAAACTT
1 ACTTTCGCAACACGAAAATG
*
672417 ACTTTCGCAACGCGAAAATG
1 ACTTTCGCAACACGAAAATG
*
672437 ACTTTCGCAACACGAAAGTG
1 ACTTTCGCAACACGAAAATG
* * *
672457 ACTATCGCAACGCGGAAATG
1 ACTTTCGCAACACGAAAATG
* *
672477 GCTATCGCAA
1 ACTTTCGCAA
672487 TGCGAAATGA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (20 bp):
ACTTTCGCAACACGAAAATG
Found at i:672441 original size:40 final size:40
Alignment explanation
Indices: 672397--672486 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
672387 AGAATAGTTT
* *
672397 ACTTTCGCAACACGAAACTTACTTTCGCAACGCGAAAATG
1 ACTTTCGCAACACGAAACTGACTATCGCAACGCGAAAATG
* *
672437 ACTTTCGCAACACGAAAGTGACTATCGCAACGCGGAAATG
1 ACTTTCGCAACACGAAACTGACTATCGCAACGCGAAAATG
* *
672477 GCTATCGCAA
1 ACTTTCGCAA
672487 TGCGAAATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (40 bp):
ACTTTCGCAACACGAAACTGACTATCGCAACGCGAAAATG
Found at i:672493 original size:40 final size:39
Alignment explanation
Indices: 672421--672507 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 39
672411 AAACTTACTT
* **
672421 TCGCAACGCGAAAATGACTTTCGCAACACGAAAGTGACTA
1 TCGCAACGCGAAAATGACTATCGCAACACGAAA-TGAAAA
* * **
672461 TCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAAATGACTATCGCAACACGAAATGAAAA
672500 TCGCAACG
1 TCGCAACG
672508 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 12 0.30
40 28 0.70
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.16
Consensus pattern (39 bp):
TCGCAACGCGAAAATGACTATCGCAACACGAAATGAAAA
Found at i:672502 original size:19 final size:19
Alignment explanation
Indices: 672480--672538 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
672470 GGAAATGGCT
672480 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
672499 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
672513 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
672532 ATCGCAA
1 ATCGCAA
672539 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:672515 original size:14 final size:14
Alignment explanation
Indices: 672496--672552 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
672486 ATGCGAAATG
672496 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
672510 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
672529 AAAATCGCAACGAC
1 AAAATCGCAACGAC
672543 AAAATCGCAA
1 AAAATCGCAA
672553 TGCGATTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:672522 original size:33 final size:33
Alignment explanation
Indices: 672480--672557 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
672470 GGAAATGGCT
672480 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
672513 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
672546 ATCGCAATGCGA
1 ATCGCAATGCGA
672558 TTTGTGTTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:672615 original size:20 final size:19
Alignment explanation
Indices: 672564--672635 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 19
672554 GCGATTTGTG
**
672564 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATAGTCA
* *
672583 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATAGTCA
672602 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATAGTCA
*
672622 TTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
672636 AAGTAAACTA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.41
20 23 0.52
21 3 0.07
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:673199 original size:18 final size:18
Alignment explanation
Indices: 673176--673223 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
673166 CGGGTCGATC
673176 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
673194 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
673212 AGGTGATGGCTC
1 AGGTGATGGCTC
673224 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:674591 original size:20 final size:20
Alignment explanation
Indices: 674543--674601 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
674533 AATAGTTTCT
* *
674543 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
674563 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
674583 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
674602 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:674635 original size:14 final size:14
Alignment explanation
Indices: 674616--674642 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
674606 AATAAAATCG
674616 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
674630 CGTTGCGATTTTG
1 CGTTGCGATTTTG
674643 ATTTCGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:674891 original size:22 final size:22
Alignment explanation
Indices: 674864--674907 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
674854 GATGGAGATA
674864 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
674886 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
674908 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:675127 original size:20 final size:20
Alignment explanation
Indices: 675094--675166 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
675084 GATTATGTAT
* *
675094 TATCTCGTTACGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
675114 TATTGCGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
* *
675134 TATCGAGTTGCAAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
675154 TATCGCGTTGCGA
1 TATCGCGTTGCGA
675167 TTTTGTATTA
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Done.