Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold164
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: 2248410
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 3 of 15
Found at i:367895 original size:15 final size:15
Alignment explanation
Indices: 367844--367895 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
367834 GGAATAAATG
* *
367844 ATAAAAAAAAAGAGA
1 ATAAAAAAAAATAAA
*
367859 AT-AAATAAAATAAA
1 ATAAAAAAAAATAAA
**
367873 ATCTAAAAAAATAAA
1 ATAAAAAAAAATAAA
367888 ATAAAAAA
1 ATAAAAAA
367896 GTGCGAAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (15 bp):
ATAAAAAAAAATAAA
Found at i:368781 original size:158 final size:160
Alignment explanation
Indices: 368596--368904 Score: 421
Period size: 161 Copynumber: 1.9 Consensus size: 160
368586 ATTAGATGAT
* *
368596 TTTTTTTATTTATGTAGATTTAAATTATTATTTAATTAAAAATTATTTT-TTTACTTTAA-TCAT
1 TTTTTTTATTTATGTAGATTTAAATTATTATTTAATTAAAAATTATTTTATTTAATTTAATTCAA
* * *
368659 AAATA-TAAATATTTATATAAAATTATTTTTATATTTTAATATATTTTAAATAGTAAGATAATTT
66 AAATATTAAATA-TT-TATAAAATTATTTTAATATTTTAATATATTTTAAATAATAAAATAATTT
**
368723 TTTTGATCGAAT-AAATTAAATCAAATTAAAC
129 TTTAAATCGAATCAAATTAAATCAAATTAAAC
** * * * *
368754 TTTTTTTATTTGAT-TCTATTTAGATTATTATTTAATTTAAATTTATTTTATTTAATTTAATTTT
1 TTTTTTTATTT-ATGTAGATTTAAATTATTATTTAATTAAAAATTATTTTATTTAATTTAA-TTC
368818 AAAAATATTTAAATATTTATAAAATTATTTTAATATTTTAATATATTTTAAATAATAAAATAATT
64 AAAAATA-TTAAATATTTATAAAATTATTTTAATATTTTAATATATTTTAAATAATAAAATAATT
368883 TTTTAAATCGAATCAAATTAAA
128 TTTTAAATCGAATCAAATTAAA
368905 CTCCAAATAA
Statistics
Matches: 131, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
158 41 0.31
159 11 0.08
161 63 0.48
162 10 0.08
163 6 0.05
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (160 bp):
TTTTTTTATTTATGTAGATTTAAATTATTATTTAATTAAAAATTATTTTATTTAATTTAATTCAA
AAATATTAAATATTTATAAAATTATTTTAATATTTTAATATATTTTAAATAATAAAATAATTTTT
TAAATCGAATCAAATTAAATCAAATTAAAC
Found at i:368806 original size:20 final size:20
Alignment explanation
Indices: 368781--368818 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
368771 ATTTAGATTA
368781 TTATTTAATTTAAATTTATT
1 TTATTTAATTTAAATTTATT
*
368801 TTATTTAATTTAATTTTA
1 TTATTTAATTTAAATTTA
368819 AAAATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTAATTTAAATTTATT
Found at i:368846 original size:20 final size:19
Alignment explanation
Indices: 368813--368871 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
368803 ATTTAATTTA
368813 ATTTTAAAAATATTTAAAT
1 ATTTTAAAAATATTTAAAT
* *
368832 ATTTATAAAATTATTTTAAT
1 ATTT-TAAAAATATTTAAAT
*
368852 ATTTT-AATATATTTTAAAT
1 ATTTTAAAAATA-TTTAAAT
368871 A
1 A
368872 ATAAAATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 4 0.12
19 12 0.36
20 17 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTAAAAATATTTAAAT
Found at i:368865 original size:10 final size:9
Alignment explanation
Indices: 368813--368871 Score: 57
Period size: 10 Copynumber: 6.1 Consensus size: 9
368803 ATTTAATTTA
*
368813 ATTTTAAAA
1 ATTTTAAAT
368822 ATATTTAAAT
1 AT-TTTAAAT
368832 ATTTATAAAATT
1 ATTT-T-AAA-T
368844 ATTTT-AAT
1 ATTTTAAAT
368852 ATTTTAATAT
1 ATTTTAA-AT
368862 ATTTTAAAT
1 ATTTTAAAT
368871 A
1 A
368872 ATAAAATAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
8 6 0.14
9 10 0.23
10 18 0.42
11 4 0.09
12 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATTTTAAAT
Found at i:368879 original size:19 final size:19
Alignment explanation
Indices: 368836--368890 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 19
368826 TTAAATATTT
368836 ATAAAAT-TATTTT-AATA
1 ATAAAATATATTTTAAATA
* **
368853 TTTTAATATATTTTAAATA
1 ATAAAATATATTTTAAATA
*
368872 ATAAAATAATTTTTTAAAT
1 ATAAAAT-ATATTTTAAAT
368891 CGAATCAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 8 0.29
20 10 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAAAATATATTTTAAATA
Found at i:370750 original size:19 final size:20
Alignment explanation
Indices: 370728--370773 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
370718 ATATAATTTA
*
370728 AATTAAAAA-AAATAACATT
1 AATTAAAAACAAATAAAATT
*
370747 AATTAAAAACAACTAAAATT
1 AATTAAAAACAAATAAAATT
370767 AA-TAAAA
1 AATTAAAA
370774 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.24
Consensus pattern (20 bp):
AATTAAAAACAAATAAAATT
Found at i:370755 original size:20 final size:20
Alignment explanation
Indices: 370728--370773 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
370718 ATATAATTTA
*
370728 AATT-AAAAAAAATAACATT
1 AATTAAAAAAAAATAAAATT
* *
370747 AATTAAAAACAACTAAAATT
1 AATTAAAAAAAAATAAAATT
370767 AA-TAAAA
1 AATTAAAA
370774 TTTAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.24
Consensus pattern (20 bp):
AATTAAAAAAAAATAAAATT
Found at i:372373 original size:2 final size:2
Alignment explanation
Indices: 372366--372406 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
372356 GATATTAACT
372366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
372407 GTTTATTTAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:373146 original size:14 final size:14
Alignment explanation
Indices: 373119--373158 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
373109 AATGTGGAGG
*
373119 ATAAAAA-TAAAAA
1 ATAAAAATTATAAA
373132 ATAAAAATTATAAA
1 ATAAAAATTATAAA
*
373146 ATAATAATTATAA
1 ATAAAAATTATAA
373159 TATTATGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAAAAATTATAAA
Found at i:382934 original size:22 final size:22
Alignment explanation
Indices: 382904--382948 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
382894 ATAATGTATT
*
382904 GATACATGAATAGTGATGAACA
1 GATACATGAATAGTGATAAACA
*
382926 GATATATGAATAGTGATAAACA
1 GATACATGAATAGTGATAAACA
382948 G
1 G
382949 TGATGTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.22, T:0.24
Consensus pattern (22 bp):
GATACATGAATAGTGATAAACA
Found at i:386144 original size:21 final size:21
Alignment explanation
Indices: 386120--386161 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
386110 TTTTCGCCTT
386120 TAATTCA-TTTATTTTCTTTTC
1 TAATTCACTTTA-TTTCTTTTC
386141 TAATTCACTTTATTTCTTTTC
1 TAATTCACTTTATTTCTTTTC
386162 AAGAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (21 bp):
TAATTCACTTTATTTCTTTTC
Found at i:394661 original size:51 final size:51
Alignment explanation
Indices: 394606--394702 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
394596 AAATAACAGG
* * * *
394606 GTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATGGGTGTTTTAGAAATAAAATCGGA
*
394657 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAA
1 GTTGGAGTATCCCCGATTATGAAAAATGGGTGTTTTAGAAATAAAA
394703 CCAGGGTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATGGGTGTTTTAGAAATAAAATCGGA
Found at i:396912 original size:20 final size:19
Alignment explanation
Indices: 396869--396975 Score: 100
Period size: 20 Copynumber: 5.7 Consensus size: 19
396859 AAAATGCCTG
* * *
396869 AATGTATTGATACATTGTAA
1 AATGTATCGATACAATG-AC
396889 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
396909 AATGTATCG-----AT-AC
1 AATGTATCGATACAATGAC
396922 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
*
396942 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AC
396962 AATGTATCGATACA
1 AATGTATCGATACA
396976 TCTGGATAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
13 10 0.14
14 1 0.01
15 2 0.03
18 2 0.03
19 2 0.03
20 56 0.76
21 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (19 bp):
AATGTATCGATACAATGAC
Found at i:396931 original size:33 final size:33
Alignment explanation
Indices: 396889--396958 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
396879 TACATTGTAA
396889 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
396922 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
396955 AATG
1 AATG
396959 CAAAATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAATGAGCAATGTATCGATAC
Found at i:396934 original size:53 final size:51
Alignment explanation
Indices: 396869--397025 Score: 151
Period size: 53 Copynumber: 3.0 Consensus size: 51
396859 AAAATGCCTG
* *
396869 AATGTATTGATACATTGTAAAATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATG-AAAATGTATCGATACAATGA-CAATGTATCGATAC
* *
396922 AATGTATCGATACAATGAGCAATGTATCGATACAATGCAAAATGTATCGATAC
1 AATGTATCGATACAATGA-AAATGTATCGATACAATG-ACAATGTATCGATAC
* * ** *
396975 -A--TCTGGATA-AACCCAGAATGTATCGATACAATGAACAATGTATCGATAC
1 AATGTATCGATACAA-TGAAAATGTATCGATACAATG-ACAATGTATCGATAC
397024 AA
1 AA
397026 ATTGTGAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
49 33 0.37
50 8 0.09
52 2 0.02
53 45 0.51
54 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (51 bp):
AATGTATCGATACAATGAAAATGTATCGATACAATGACAATGTATCGATAC
Found at i:396957 original size:13 final size:13
Alignment explanation
Indices: 396908--396938 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
396898 ATACAATGAG
396908 CAATGTATCGATA
1 CAATGTATCGATA
396921 CAATGTATCGATA
1 CAATGTATCGATA
396934 CAATG
1 CAATG
396939 AGCAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:398892 original size:14 final size:15
Alignment explanation
Indices: 398873--398901 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
398863 GATCATCTTG
398873 ATTATTTT-AACCTA
1 ATTATTTTAAACCTA
398887 ATTATTTTAAACCTA
1 ATTATTTTAAACCTA
398902 CAAGGTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATTTTAAACCTA
Found at i:400733 original size:17 final size:18
Alignment explanation
Indices: 400713--400746 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
400703 AACAAATTCT
400713 AAAAAACAATC-CAAAGA
1 AAAAAACAATCACAAAGA
*
400730 AAAAAAGAATCACAAAG
1 AAAAAACAATCACAAAG
400747 TATAGCAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.71, C:0.15, G:0.09, T:0.06
Consensus pattern (18 bp):
AAAAAACAATCACAAAGA
Found at i:406685 original size:19 final size:19
Alignment explanation
Indices: 406636--406686 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
406626 TCTTTTAATT
**
406636 TTTAAAAAATAACTATCCA
1 TTTAAAAAATATTTATCCA
** *
406655 -TTAAAATCTATTTATTCA
1 TTTAAAAAATATTTATCCA
406673 TTTAAAAAATATTT
1 TTTAAAAAATATTT
406687 TTTATTTCAA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAAAAAATATTTATCCA
Found at i:406888 original size:2 final size:2
Alignment explanation
Indices: 406881--406919 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
406871 AACATTTTTC
406881 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 A
406920 CATACAGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:408945 original size:73 final size:73
Alignment explanation
Indices: 408858--408995 Score: 233
Period size: 73 Copynumber: 1.9 Consensus size: 73
408848 AATAAAAATT
408858 AAACATTAATTAAACTGTTAGGTAAAAGTTCAGT-AATTATTAAATAAACCTATTAATAGTATTT
1 AAACATTAATTAAACTGTTAGGTAAAAGTT-AGTCAATTATTAAATAAACCTATTAATAGTATTT
408922 TGTACAATC
65 TGTACAATC
* * *
408931 AAACATTAATTAAACTGTTAGGTTAAAGTTAGTCAATTATTAAATAAATCTATTAATATTATTTT
1 AAACATTAATTAAACTGTTAGGTAAAAGTTAGTCAATTATTAAATAAACCTATTAATAGTATTTT
408996 TTTTCGTATA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 3 0.05
73 58 0.95
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (73 bp):
AAACATTAATTAAACTGTTAGGTAAAAGTTAGTCAATTATTAAATAAACCTATTAATAGTATTTT
GTACAATC
Found at i:409709 original size:21 final size:21
Alignment explanation
Indices: 409683--409725 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
409673 GTAAATAGGA
409683 TTATTATTACTAATACTAGAG
1 TTATTATTACTAATACTAGAG
409704 TTATTATTACTAATACTAGAG
1 TTATTATTACTAATACTAGAG
409725 T
1 T
409726 GACCCAGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (21 bp):
TTATTATTACTAATACTAGAG
Found at i:412715 original size:2 final size:2
Alignment explanation
Indices: 412708--412774 Score: 57
Period size: 2 Copynumber: 33.5 Consensus size: 2
412698 TAATGTTGAA
* * * * *
412708 AT AT AT AT AT AT AT GAT CT TT AT TT A- AT AC AT AA AT AGT AT AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
412751 A- 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 A
412775 ATAATCAGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
1 2 0.04
2 46 0.88
3 4 0.08
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:416076 original size:16 final size:17
Alignment explanation
Indices: 416047--416084 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
416037 AAAAAAATTA
416047 TATTTTTCACATTATAT
1 TATTTTTCACATTATAT
* *
416064 TATTTTTTA-ATTATTT
1 TATTTTTCACATTATAT
416080 TATTT
1 TATTT
416085 AAATTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTTTCACATTATAT
Found at i:417483 original size:19 final size:18
Alignment explanation
Indices: 417461--417504 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
417451 ACATAAATAT
*
417461 AATATGAAAAAATAATTAA
1 AATATGAAAAAAT-ATAAA
* *
417480 AATATGACATAATATAAA
1 AATATGAAAAAATATAAA
417498 AATATGA
1 AATATGA
417505 CCATAATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (18 bp):
AATATGAAAAAATATAAA
Found at i:417501 original size:18 final size:19
Alignment explanation
Indices: 417478--417522 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
417468 AAAAATAATT
*
417478 AAAATATGA-CATAATATA
1 AAAATATGACCATAATACA
417496 AAAATATGACCATAATACA
1 AAAATATGACCATAATACA
*
417515 AATATATG
1 AAAATATG
417523 TTAGTGTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.27
Consensus pattern (19 bp):
AAAATATGACCATAATACA
Found at i:417706 original size:27 final size:29
Alignment explanation
Indices: 417676--417746 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 29
417666 ATTAACATGA
417676 TATAAATATAAAAAATTAATTAAA-AT-T
1 TATAAATATAAAAAATTAATTAAATATAT
* * *
417703 TATATATATATAATATT--TTAAATATAT
1 TATAAATATAAAAAATTAATTAAATATAT
417730 TAT-AATAT-AAAAATTAA
1 TATAAATATAAAAAATTAA
417747 CATGGATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
25 10 0.29
26 6 0.18
27 18 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
TATAAATATAAAAAATTAATTAAATATAT
Found at i:417882 original size:17 final size:16
Alignment explanation
Indices: 417852--417894 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
417842 TAGCAATTTC
*
417852 AAATATAACGTAAAATA
1 AAATATAA-TTAAAATA
417869 AAATAATAATTAAAATA
1 AAAT-ATAATTAAAATA
*
417886 TAATATAAT
1 AAATATAAT
417895 ATGAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 14 0.61
18 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
AAATATAATTAAAATA
Found at i:417934 original size:28 final size:29
Alignment explanation
Indices: 417882--417941 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
417872 TAATAATTAA
417882 AATATAATATAATATGAAAAATTATAT-T
1 AATATAATATAATATGAAAAATTATATAT
* *
417910 AATATAATATATATAT-TAAATTTATATAT
1 AATATAATATA-ATATGAAAAATTATATAT
417939 AAT
1 AAT
417942 GTGTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (29 bp):
AATATAATATAATATGAAAAATTATATAT
Found at i:420008 original size:16 final size:16
Alignment explanation
Indices: 419987--420020 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
419977 AAAAAAAATT
* *
419987 AAAAATTTTCTATATA
1 AAAAATATTCAATATA
420003 AAAAATATTCAATATA
1 AAAAATATTCAATATA
420019 AA
1 AA
420021 TGTAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAATATTCAATATA
Found at i:422654 original size:15 final size:17
Alignment explanation
Indices: 422623--422660 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
422613 ACTTAAGCCA
422623 ATTTGATATCTAATCTG
1 ATTTGATATCTAATCTG
422640 ATTTGAT-TC-AATCTG
1 ATTTGATATCTAATCTG
*
422655 AGTTGA
1 ATTTGA
422661 CTAAAATGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 2 0.10
17 7 0.35
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (17 bp):
ATTTGATATCTAATCTG
Found at i:422706 original size:18 final size:19
Alignment explanation
Indices: 422679--422715 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
422669 TCAAAGGCTT
422679 GAATTAAAAAAAA-AAATC
1 GAATTAAAAAAAATAAATC
*
422697 GAATTGAAAAAAATAAATC
1 GAATTAAAAAAAATAAATC
422716 CCAAAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.19
Consensus pattern (19 bp):
GAATTAAAAAAAATAAATC
Found at i:422708 original size:19 final size:18
Alignment explanation
Indices: 422679--422715 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
422669 TCAAAGGCTT
422679 GAATTAAAAAAAAAAATC
1 GAATTAAAAAAAAAAATC
*
422697 GAATTGAAAAAAATAAATC
1 GAATT-AAAAAAAAAAATC
422716 CCAAAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.19
Consensus pattern (18 bp):
GAATTAAAAAAAAAAATC
Found at i:423667 original size:10 final size:10
Alignment explanation
Indices: 423645--423679 Score: 54
Period size: 9 Copynumber: 3.5 Consensus size: 10
423635 ATGTACTATG
423645 TTATTTTTT-
1 TTATTTTTTA
423654 TTATTTTTTA
1 TTATTTTTTA
423664 TTATTTTTTAA
1 TTATTTTTT-A
423675 TTATT
1 TTATT
423680 ATATATATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.38
10 9 0.38
11 6 0.25
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTATTTTTTA
Found at i:423672 original size:18 final size:20
Alignment explanation
Indices: 423649--423695 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
423639 ACTATGTTAT
*
423649 TTTTTTTATT-TTTTAT-TA
1 TTTTTTTATTATTATATATA
*
423667 TTTTTTAATTATTATATATA
1 TTTTTTTATTATTATATATA
423687 TTGTTTTTA
1 TT-TTTTTA
423696 CTAAACCGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 9 0.39
19 5 0.22
20 4 0.17
21 5 0.22
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTTTATTATTATATATA
Found at i:426514 original size:15 final size:15
Alignment explanation
Indices: 426494--426532 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
426484 GCATCATGTC
426494 CATCCACCACCCATG
1 CATCCACCACCCATG
* *
426509 CATCCACAACCCGTG
1 CATCCACCACCCATG
*
426524 CATCTACCA
1 CATCCACCA
426533 ACTGTTTATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.49, G:0.08, T:0.15
Consensus pattern (15 bp):
CATCCACCACCCATG
Found at i:430168 original size:21 final size:22
Alignment explanation
Indices: 430122--430168 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
430112 TTTTATTTTT
430122 ATTAT-TTTTATTTATTTAACA
1 ATTATATTTTATTTATTTAACA
430143 A-TATATTTTA-TTATATTAA-A
1 ATTATATTTTATTTAT-TTAACA
430163 ATTATA
1 ATTATA
430169 ATCGTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTATATTTTATTTATTTAACA
Found at i:430949 original size:15 final size:15
Alignment explanation
Indices: 430929--430974 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
430919 TATTCACTAA
430929 ATAATTGATTTTCAT
1 ATAATTGATTTTCAT
*
430944 ATAATTAATTTT-A-
1 ATAATTGATTTTCAT
* *
430957 AAAATTGATATTCAT
1 ATAATTGATTTTCAT
430972 ATA
1 ATA
430975 TTTAAACAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
13 9 0.38
14 2 0.08
15 13 0.54
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (15 bp):
ATAATTGATTTTCAT
Found at i:435724 original size:22 final size:22
Alignment explanation
Indices: 435698--435739 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
435688 TTTAAAAAAT
435698 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
435720 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
435740 AGAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:436730 original size:2 final size:2
Alignment explanation
Indices: 436675--436711 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
436665 AAATCAAGTT
*
436675 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
436712 TTGTTATCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:436991 original size:16 final size:16
Alignment explanation
Indices: 436970--437015 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
436960 AAAATTATAT
436970 ATTTATATAAATTTTA
1 ATTTATATAAATTTTA
*
436986 ATTTAT-TAATAATTTA
1 ATTTATATAA-ATTTTA
437002 ATTTATAT-AATTTT
1 ATTTATATAAATTTT
437016 TGATACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 7 0.27
16 18 0.69
17 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTATATAAATTTTA
Found at i:437058 original size:11 final size:11
Alignment explanation
Indices: 437044--437081 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
437034 TTTATATCAT
437044 ATTATATTTTA-
1 ATTAT-TTTTAC
*
437055 ATTATTTTTAT
1 ATTATTTTTAC
437066 ATTATTTTTAC
1 ATTATTTTTAC
437077 ATTAT
1 ATTAT
437082 ATAATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (11 bp):
ATTATTTTTAC
Found at i:437872 original size:13 final size:15
Alignment explanation
Indices: 437849--437880 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
437839 TTTATGTGAC
437849 ACTTATTTTTCT-AT
1 ACTTATTTTTCTAAT
437863 ACTT-TTTTTCTAAT
1 ACTTATTTTTCTAAT
437877 ACTT
1 ACTT
437881 CATCTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (15 bp):
ACTTATTTTTCTAAT
Found at i:439017 original size:22 final size:21
Alignment explanation
Indices: 438978--439018 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
438968 ATGTTATTAG
438978 TTTTTAGTTAATTAAATTTGA
1 TTTTTAGTTAATTAAATTTGA
* *
438999 TTTTTATGTTCATTTAATTT
1 TTTTTA-GTTAATTAAATTT
439019 TTTGAAAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTTTAGTTAATTAAATTTGA
Found at i:442341 original size:14 final size:14
Alignment explanation
Indices: 442319--442348 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
442309 CTGTTGCGGT
*
442319 AGCAGTTTTTTTAA
1 AGCAATTTTTTTAA
442333 AGCAATTTTTTTAA
1 AGCAATTTTTTTAA
442347 AG
1 AG
442349 AAAATTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (14 bp):
AGCAATTTTTTTAA
Found at i:443284 original size:13 final size:13
Alignment explanation
Indices: 443266--443322 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
443256 CATAAAGTGT
443266 TGTATCGATACAA
1 TGTATCGATACAA
443279 TGTATCGATACATAA
1 TGTATCGATAC--AA
443294 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
443311 TGTATCGATACA
1 TGTATCGATACA
443323 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:443301 original size:32 final size:32
Alignment explanation
Indices: 443246--443343 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
443236 TTCAACGATT
443246 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
443279 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
443311 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
443343 T
1 T
443344 ATAAGCTACT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:443303 original size:19 final size:18
Alignment explanation
Indices: 443244--443341 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
443234 ATTTCAACGA
443244 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
443263 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
443279 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
443295 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
443311 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
443327 TTTTGTATCGATACA
1 -TTTGTATCGATACA
443342 ATATAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:443402 original size:13 final size:13
Alignment explanation
Indices: 443384--443408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
443374 ATTACTCAAA
443384 TGTATCGATACAT
1 TGTATCGATACAT
443397 TGTATCGATACA
1 TGTATCGATACA
443409 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:443462 original size:52 final size:52
Alignment explanation
Indices: 443417--443545 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
443407 CACTGATCTT
* *
443417 TGTATCGATACATGCAGGCAAATTTGCTCAGATGTATCAATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
443469 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
443521 TGTATCGATACATGCAGGTAAATTT
1 TGTATCGATACATGCAGGCAAATTT
443546 TCATATTTTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:448756 original size:24 final size:24
Alignment explanation
Indices: 448729--448807 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
448719 TGGCACAATA
*
448729 TTTGGCATGACTCTTGAAACGTCT
1 TTTGGCATGACTCTTGAAACATCT
* * *
448753 TTTGGCATGACT-TCTGATACAACC
1 TTTGGCATGACTCT-TGAAACATCT
*
448777 TTTGGCA-GAACTCCTGAAACATCT
1 TTTGGCATG-ACTCTTGAAACATCT
448801 TTTGGCA
1 TTTGGCA
448808 CAACTTATGG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (24 bp):
TTTGGCATGACTCTTGAAACATCT
Found at i:448823 original size:48 final size:47
Alignment explanation
Indices: 448729--448875 Score: 126
Period size: 48 Copynumber: 3.1 Consensus size: 47
448719 TGGCACAATA
* * *
448729 TTTGGCATG-ACTCTTGAAACGTCTTTTGGCATGACTTCT-GATACAACC
1 TTTGGCA-GAACTCCTGAAACATCTTTTGGCACGACTT-TGGA-ACAACC
*
448777 TTTGGCAGAACTCCTGAAACATCTTTTGGCACAACTTATGGAACAA-C
1 TTTGGCAGAACTCCTGAAACATCTTTTGGCACGACTT-TGGAACAACC
* * *
448824 -TTGGCATAACTCGT-AGAACATCCTTTGGCACGACTCTTGGAAC-ACAC
1 TTTGGCAGAACTCCTGA-AACATCTTTTGGCACGACT-TTGGAACAAC-C
448871 TTTGG
1 TTTGG
448876 ATCGATTTTC
Statistics
Matches: 83, Mismatches: 9, Indels: 14
0.78 0.08 0.13
Matches are distributed among these distances:
45 2 0.02
46 35 0.42
47 4 0.05
48 40 0.48
49 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (47 bp):
TTTGGCAGAACTCCTGAAACATCTTTTGGCACGACTTTGGAACAACC
Found at i:448866 original size:24 final size:24
Alignment explanation
Indices: 448729--448875 Score: 74
Period size: 24 Copynumber: 6.2 Consensus size: 24
448719 TGGCACAATA
* * *
448729 TTTGGCATGACTCTTGAAACGTCT
1 TTTGGCATGACTCTTGGAACATCC
*
448753 TTTGGCATGACT-TCT-GATACAACC
1 TTTGGCATGACTCT-TGGA-ACATCC
* * *
448777 TTTGGCA-GAACTCCTGAAACATCT
1 TTTGGCATG-ACTCTTGGAACATCC
** *
448801 TTTGGCACAACT-TATGGAACA-AC
1 TTTGGCATGACTCT-TGGAACATCC
* * *
448824 -TTGGCATAACTCGTAGAACATCC
1 TTTGGCATGACTCTTGGAACATCC
*
448847 TTTGGCACGACTCTTGGAACA-CAC
1 TTTGGCATGACTCTTGGAACATC-C
448871 TTTGG
1 TTTGG
448876 ATCGATTTTC
Statistics
Matches: 91, Mismatches: 21, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
22 16 0.18
23 5 0.05
24 69 0.76
25 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (24 bp):
TTTGGCATGACTCTTGGAACATCC
Found at i:457393 original size:17 final size:17
Alignment explanation
Indices: 457371--457434 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
457361 GGATAACAAA
457371 AAAGGGGAGTAGTTATT
1 AAAGGGGAGTAGTTATT
* * * *
457388 AAAGGGAAGTACTAAAATG
1 AAAGGGGAGTAGT--TATT
*
457407 AAAGGGGGGTAGTTATT
1 AAAGGGGAGTAGTTATT
*
457424 AAAGAGGAGTA
1 AAAGGGGAGTA
457435 CTAAAACGAA
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
17 22 0.65
19 12 0.35
ACGTcount: A:0.42, C:0.02, G:0.34, T:0.22
Consensus pattern (17 bp):
AAAGGGGAGTAGTTATT
Found at i:457411 original size:36 final size:36
Alignment explanation
Indices: 457371--457445 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
457361 GGATAACAAA
*
457371 AAAGGGGAGTAGTTATTAAAG-GGAAGTACTAAAATG
1 AAAGGGGAGTAGTTATTAAAGAGG-AGTACTAAAACG
*
457407 AAAGGGGGGTAGTTATTAAAGAGGAGTACTAAAACG
1 AAAGGGGAGTAGTTATTAAAGAGGAGTACTAAAACG
457443 AAA
1 AAA
457446 ATTTTCTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 34 0.94
37 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.31, T:0.20
Consensus pattern (36 bp):
AAAGGGGAGTAGTTATTAAAGAGGAGTACTAAAACG
Found at i:460563 original size:31 final size:31
Alignment explanation
Indices: 460510--461377 Score: 551
Period size: 32 Copynumber: 27.0 Consensus size: 31
460500 GGTGGTAATT
* *
460510 TTTTCAATAGCCCACACTAGTTGGTGGCAACC
1 TTTTCAA-AGTCCACACGAGTTGGTGGCAACC
* *
460542 TTTTCAAAGTCCACACAAGTTGGTGGTAACC
1 TTTTCAAAGTCCACACGAGTTGGTGGCAACC
** * *
460573 TTTTCAAAAACCCATATGAGTTGGTGGCAACC
1 TTTTC-AAAGTCCACACGAGTTGGTGGCAACC
* *
460605 TTTTCAAAAG-CCTACACAAATTGGTGGCAACC
1 TTTTC-AAAGTCC-ACACGAGTTGGTGGCAACC
*
460637 TTTTCAAAGTTCACACGAGTTGGTGGCAACC
1 TTTTCAAAGTCCACACGAGTTGGTGGCAACC
* * * * *
460668 TTTTCGAAGTCCATATGAGTTGGTGG-TACTA
1 TTTTCAAAGTCCACACGAGTTGGTGGCAAC-C
* * * *
460699 TTTTCAAAGTTCACATGAGTTGGTAGTAACC
1 TTTTCAAAGTCCACACGAGTTGGTGGCAACC
* * *
460730 TCTTCAAGAGTCTACACGAGTTAGTGGCAA-C
1 TTTTCAA-AGTCCACACGAGTTGGTGGCAACC
* *
460761 TTCTTCCTAAA-CCCACATGAGTTGGTGGCAA-C
1 TT-TT-C-AAAGTCCACACGAGTTGGTGGCAACC
* * *
460793 TTCTTCCTAAGCCCATACGAGTTGGTGGCATA-C
1 TT-TT-CAAAGTCCACACGAGTTGGTGGCA-ACC
* * **
460826 TTTTCAAAGTCTACACAAGTCAGTGGCAATCAAACC
1 TTTTCAAAGTCCACACGAGTTGGTGG----C-AACC
460862 TTTTCAAAAGTCCACACGAGTTGGTGGCAACC
1 TTTTC-AAAGTCCACACGAGTTGGTGGCAACC
* *
460894 TTTTCAAAAGCCCATACGAGTTGGTGGC-ACAC
1 TTTTC-AAAGTCCACACGAGTTGGTGGCAAC-C
* * *
460926 TTTTCAAAGTCCACACAAGTTAGTGTCAACTAAAC
1 TTTTCAAAGTCCACACGAGTTGGTGGCAAC----C
* *
460961 TTTTTCCAATGTCCACACGAGTTAGTGGCAACC
1 -TTTT-CAAAGTCCACACGAGTTGGTGGCAACC
* * **
460994 TTTTCAAAAG-CCTACGCGAGTTGGTGGTAATT
1 TTTTC-AAAGTCC-ACACGAGTTGGTGGCAACC
* *
461026 TTTTCAAAAG-CCTACACGAGTTGGTAGTAA-C
1 TTTTC-AAAGTCC-ACACGAGTTGGTGGCAACC
* *
461057 TTTTCTTAAAGCCCACATGAGTTGGT-GC-ACC
1 TTTTC--AAAGTCCACACGAGTTGGTGGCAACC
*
461088 TTTTTCAAAGTCCACACGAGTTGCTGGCAACC
1 -TTTTCAAAGTCCACACGAGTTGGTGGCAACC
* * * *
461120 TTTTCAAAATCCCACACGAGTTGCTAGTAACC
1 TTTTCAAAGT-CCACACGAGTTGGTGGCAACC
* * *
461152 TTTTCAAAAGCCCACACGAGTTGATGGCAAAC
1 TTTTC-AAAGTCCACACGAGTTGGTGGCAACC
* **
461184 TTTTCAAAGTCTACATAAGTTGGTGGC-ACAC
1 TTTTCAAAGTCCACACGAGTTGGTGGCAAC-C
* *
461215 TTTTCAAAGTCCACACAAGTCGGTGGCAACGAAACC
1 TTTTCAAAGTCCACACGAGTTGGTGG---C--AACC
* ** *
461251 TTTTCAAAAGTCAACATAAGTTGGTGGTAACC
1 TTTTC-AAAGTCCACACGAGTTGGTGGCAACC
* *
461283 TTTTCAAAAGTCTACACGAGTTGGTGGTAACC
1 TTTTC-AAAGTCCACACGAGTTGGTGGCAACC
* * * * *
461315 TCTTCTTAAG-CTCACACAAGTTAGTGGC-ACAT
1 TTTTC-AAAGTC-CACACGAGTTGGTGGCAAC-C
* * *
461347 TTTTTAAAGTCCACACAAGTTAGTGGCAACC
1 TTTTCAAAGTCCACACGAGTTGGTGGCAACC
461378 AAACCTCTTA
Statistics
Matches: 672, Mismatches: 117, Indels: 95
0.76 0.13 0.11
Matches are distributed among these distances:
30 20 0.03
31 221 0.33
32 334 0.50
33 13 0.02
34 3 0.00
35 4 0.01
36 17 0.03
37 60 0.09
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (31 bp):
TTTTCAAAGTCCACACGAGTTGGTGGCAACC
Found at i:460642 original size:64 final size:63
Alignment explanation
Indices: 460476--461377 Score: 512
Period size: 63 Copynumber: 14.0 Consensus size: 63
460466 GAGCCACAAT
* * * * ** * *
460476 CCTTTTTAAAAGCCCACATGAGTCGGTGGTAATTTTTTCAATAGCCCACACTAGTTGGTGGCAA
1 CCTTTTCAAAAG-CCACACGAGTTGGTGGCAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAA
* * * * *
460540 CCTTTTC-AAAGTCCACACAAGTTGGTGGTAACCTTTTCAAAAACCCATATGAGTTGGTGGCAA
1 CCTTTTCAAAAG-CCACACGAGTTGGTGGCAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAA
* * **
460603 CCTTTTCAAAAGCCTACACAAATTGGTGGCAACCTTTTC-AAAGTTCACACGAGTTGGTGGCAA
1 CCTTTTCAAAAGCC-ACACGAGTTGGTGGCAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAA
* * * * * ** * * *
460666 CCTTTTC-GAAGTCCATATGAGTTGGTGG-TACTATTTTC-AAAGTTCACATGAGTTGGTAGTAA
1 CCTTTTCAAAAG-CCACACGAGTTGGTGGCAAC-CTTTTCAAAAGCCCACACGAGTTGGTGGCAA
* * * * * *
460728 CCTCTTCAAGAGTCTACACGAGTTAGTGGCAA-CTTCTTCCTAAA-CCCACATGAGTTGGTGGCA
1 CCTTTTCAAAAG-CCACACGAGTTGGTGGCAACCTT-TT-CAAAAGCCCACACGAGTTGGTGGCA
460791 A
63 A
** * * * * **
460792 -CTTCTTCCTAAGCCCATACGAGTTGGTGGCATA-CTTTTC-AAAGTCTACACAAGTCAGTGGCA
1 CCTT-TTCAAAAG-CCACACGAGTTGGTGGCA-ACCTTTTCAAAAGCCCACACGAGTTGGTGG--
460854 ATCAAA
61 --C-AA
*
460860 CCTTTTCAAAAGTCCACACGAGTTGGTGGCAACCTTTTCAAAAGCCCATACGAGTTGGTGGC-A
1 CCTTTTCAAAAG-CCACACGAGTTGGTGGCAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAA
* * * * * * *
460923 CACTTTTC-AAAGTCCACACAAGTTAGTGTCAACTAAACTTTTTCCAATGTCCACACGAGTTAGT
1 C-CTTTTCAAAAG-CCACACGAGTTGGTGGCAAC----C-TTTTCAAAAGCCCACACGAGTTGGT
460987 GGCAA
59 GGCAA
* * ** * * *
460992 CCTTTTCAAAAGCCTACGCGAGTTGGTGGTAATTTTTTCAAAAGCCTACACGAGTTGGTAGTAA
1 CCTTTTCAAAAGCC-ACACGAGTTGGTGGCAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAA
* * * *
461056 -CTTTTCTTAAAGCCCACATGAGTTGGT-GC-ACCTTTTTC-AAAGTCCACACGAGTTGCTGGCA
1 CCTTTTC-AAAAG-CCACACGAGTTGGTGGCAACC-TTTTCAAAAGCCCACACGAGTTGGTGGCA
461117 A
63 A
* * * * *
461118 CCTTTTCAAAATCCCACACGAGTTGCTAGTAACCTTTTCAAAAGCCCACACGAGTTGATGGCAA
1 CCTTTTCAAAA-GCCACACGAGTTGGTGGCAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAA
* * ** * * *
461182 ACTTTTC-AAAGTCTACATAAGTTGGTGGC-ACACTTTTC-AAAGTCCACACAAGTCGGTGGCAA
1 CCTTTTCAAAAG-CCACACGAGTTGGTGGCAAC-CTTTTCAAAAGCCCACACGAGTTGGTGG---
461244 CGAAA
61 C--AA
* ** * * * *
461249 CCTTTTCAAAAGTCAACATAAGTTGGTGGTAACCTTTTCAAAAGTCTACACGAGTTGGTGGTAA
1 CCTTTTCAAAAG-CCACACGAGTTGGTGGCAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAA
* ** * * * ** * * *
461313 CCTCTTCTTAAGCTCACACAAGTTAGTGGC-ACATTTTTTAAAGTCCACACAAGTTAGTGGCAA
1 CCTTTTCAAAAGC-CACACGAGTTGGTGGCAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAA
461376 CC
1 CC
461378 AAACCTCTTA
Statistics
Matches: 651, Mismatches: 139, Indels: 97
0.73 0.16 0.11
Matches are distributed among these distances:
61 2 0.00
62 104 0.16
63 210 0.32
64 169 0.26
65 11 0.02
67 11 0.02
68 88 0.14
69 56 0.09
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (63 bp):
CCTTTTCAAAAGCCACACGAGTTGGTGGCAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAA
Found at i:460890 original size:100 final size:97
Alignment explanation
Indices: 460476--461309 Score: 411
Period size: 95 Copynumber: 8.6 Consensus size: 97
460466 GAGCCACAAT
* * * * * * * * *
460476 CCTTTTTAAAAGCCCACATGAGTCGGTGGTAATTTTTTCAATAGCCCACACTAGTTGGTGGCAAC
1 CCTTTTCAAAAGTCCACACGAGTTGGTGGCAACTTTTCCAA-AGCCCATACGAGTTGGTGGCAA-
*
460541 CTTTTCAAAGTCCACACAAGTTGGTGG---T--AA
64 CTTTTCAAAGTCCACACAAG-TAGTGGCAATCAAA
** * * * * * * *
460571 CCTTTTCAAAAACCCATATGAGTTGGTGGCAACCTTTTCAAAAGCCTACACAAATTGGTGGCAAC
1 CCTTTTCAAAAGTCCACACGAGTTGGTGGCAA-CTTTTCCAAAGCCCATACGAGTTGGTGGCAA-
* * *
460636 CTTTTCAAAGTTCACACGAGTTGGTGG----C-AA
64 CTTTTCAAAGTCCACACAAG-TAGTGGCAATCAAA
* * * * * ** * * * *
460666 CCTTTTC-GAAGTCCATATGAGTTGGTGG-TACTATTTTCAAAGTTCACATGAGTTGGTAGTAAC
1 CCTTTTCAAAAGTCCACACGAGTTGGTGGCAACT-TTTCCAAAGCCCATACGAGTTGGTGGCAA-
* * * *
460729 CTCTTCAAGAGTCTACACGAGTTAGTGGCAA-C--T
64 CTTTTCAA-AGTCCACACAAG-TAGTGGCAATCAAA
* * * * * *
460762 TC-TTCCTAAA-CCCACATGAGTTGGTGGCAACTTCTTCCTAAGCCCATACGAGTTGGTGGCATA
1 CCTTTTCAAAAGTCCACACGAGTTGGTGGCAACTT-TTCCAAAGCCCATACGAGTTGGTGGCA-A
*
460825 CTTTTCAAAGTCTACACAAGTCAGTGGCAATCAAA
64 CTTTTCAAAGTCCACACAAGT-AGTGGCAATCAAA
*
460860 CCTTTTCAAAAGTCCACACGAGTTGGTGGCAACCTTTTCAAAAGCCCATACGAGTTGGTGGCACA
1 CCTTTTCAAAAGTCCACACGAGTTGGTGGCAA-CTTTTCCAAAGCCCATACGAGTTGGTGGCA-A
*
460925 CTTTTCAAAGTCCACACAAGTTAGTGTCAA-CTAAA
64 CTTTTCAAAGTCCACACAAG-TAGTGGCAATC-AAA
* * * * * * ** *
460960 CTTTTTCCAATGTCCACACGAGTTAGTGGCAACCTTTTCAAAAGCCTACGCGAGTTGGTGGTAAT
1 CCTTTTCAAAAGTCCACACGAGTTGGTGGCAA-CTTTTCCAAAGCCCATACGAGTTGGTGGCAA-
* * * *
461025 TTTTTCAAAAG-CCTACACGAGT--TGGTAGT--AA
64 CTTTTC-AAAGTCC-ACACAAGTAGTGGCAATCAAA
* * * * * * * *
461056 -CTTTTCTTAAAGCCCACATGAGTTGGT-GCACCTTTTTCAAAGTCCACACGAGTTGCTGGCAAC
1 CCTTTTC-AAAAGTCCACACGAGTTGGTGGCAACTTTTCCAAAGCCCATACGAGTTGGTGGCAA-
* * * *
461119 CTTTTCAAAATCC-CACACG-AGTTGCTAGT--AA
64 CTTTTCAAAGTCCACACAAGTAGTGGC-AATCAAA
* * *
461150 CCTTTTCAAAAGCCCACACGAGTTGATGGCAAACTTTT-CAAAGTCTACATA--AGTTGGTGGCA
1 CCTTTTCAAAAGTCCACACGAGTTGGTGGC-AACTTTTCCAAAG-C-CCATACGAGTTGGTGGCA
*
461212 CACTTTTCAAAGTCCACACAAGTCGGTGGCAA-CGAAA
63 -ACTTTTCAAAGTCCACACAAGT-AGTGGCAATC-AAA
* ** * * * * *
461249 CCTTTTCAAAAGTCAACATAAGTTGGTGGTAACCTTTTCAAAAGTCTACACGAGTTGGTGG
1 CCTTTTCAAAAGTCCACACGAGTTGGTGGCAA-CTTTTCCAAAGCCCATACGAGTTGGTGG
461310 TAACCTCTTC
Statistics
Matches: 577, Mismatches: 117, Indels: 85
0.74 0.15 0.11
Matches are distributed among these distances:
92 6 0.01
93 33 0.06
94 88 0.15
95 162 0.28
96 68 0.12
97 6 0.01
98 12 0.02
99 39 0.07
100 149 0.26
101 14 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (97 bp):
CCTTTTCAAAAGTCCACACGAGTTGGTGGCAACTTTTCCAAAGCCCATACGAGTTGGTGGCAACT
TTTCAAAGTCCACACAAGTAGTGGCAATCAAA
Found at i:460890 original size:132 final size:130
Alignment explanation
Indices: 460443--461438 Score: 585
Period size: 126 Copynumber: 7.7 Consensus size: 130
460433 CCCAAACCTC
* * * * * * * * * * *
460443 CTTTTTAAAGTCCATACAAGTCCG-AGCCACAATCCTTTTTAAAAGCCCACATGAGTCGGTGGTA
1 CTTTTCAAAGTCCACACAAGTCAGTGGCAACAAACCTTTTCAAAAGTCCACACGAGTTGGTGGCA
** * * * * *
460507 ATTTTTTCAATAGCCCACACTAGTTGGTGGCAACCTTTT-CAAAGTCCACACAAGTTGGTGGTA-
66 ACCTTTTCAAAAGCCCACACGAGTTGGTGGCAA-CTTTTCCTAAGCCCACACAAGTTGGTGGCAC
460570 A
130 A
** * ** * *
460571 CCTTTTCAAAAACC-CATATGAGTTGGTGG---C-AACCTTTTCAAAAG-CCTACACAAATTGGT
1 -CTTTTCAAAGTCCACACA--AGTCAGTGGCAACAAACCTTTTCAAAAGTCC-ACACGAGTTGGT
** * * * **
460630 GGCAACCTTTTC-AAAGTTCACACGAGTTGGTGGCAACCTTTT-CGAAGTCCATATGAGTTGGTG
62 GGCAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAA-CTTTTCCTAAGCCCACACAAGTTGGTG
*
460693 GTACTA
126 GCAC-A
* ** * ** * * * *
460699 -TTTTCAAAGTTCACATGAGT---TGG-TAGTAACCTCTTCAAGAGTCTACACGAGTTAGTGGCA
1 CTTTTCAAAGTCCACACAAGTCAGTGGCAACAAACCTTTTCAAAAGTCCACACGAGTTGGTGGCA
* * * *
460759 A-CTTCTTCCTAAA-CCCACATGAGTTGGTGGCAACTTCTTCCTAAGCCCATACGAGTTGGTGGC
66 ACCTT-TT-CAAAAGCCCACACGAGTTGGTGGCAACTT-TTCCTAAGCCCACACAAGTTGGTGGC
*
460822 ATA
128 ACA
*
460825 CTTTTCAAAGTCTACACAAGTCAGTGGCAATCAAACCTTTTCAAAAGTCCACACGAGTTGGTGGC
1 CTTTTCAAAGTCCACACAAGTCAGTGGCAA-CAAACCTTTTCAAAAGTCCACACGAGTTGGTGGC
* * * * *
460890 AACCTTTTCAAAAGCCCATACGAGTTGGTGGCACACTTTT-CAAAGTCCACACAAGTTAGTGTCA
65 AACCTTTTCAAAAGCCCACACGAGTTGGTGGCA-ACTTTTCCTAAGCCCACACAAGTTGGTGGC-
460954 ACTAAA
128 AC---A
* * * *
460960 CTTTTTCCAATGTCCACACGAGTTAGTGG---C-AACCTTTTCAAAAG-CCTACGCGAGTTGGTG
1 C-TTTT-CAAAGTCCACACAAGTCAGTGGCAACAAACCTTTTCAAAAGTCC-ACACGAGTTGGTG
* ** * * * * **
461020 GTAATTTTTTCAAAAGCCTACACGAGTTGGTAGTAACTTTTCTTAAAGCCCACATGAGTTGGT-G
63 GCAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAACTTTTCCT-AAGCCCACACAAGTTGGTGG
461084 CAC-
127 CACA
* * * *
461087 CTTTTTCAAAGTCCACACGAGT-TGCTGG---C-AACCTTTTCAAAA-TCCCACACGAGTTGCTA
1 C-TTTTCAAAGTCCACACAAGTCAG-TGGCAACAAACCTTTTCAAAAGT-CCACACGAGTTGGTG
* * * * * *
461146 GTAACCTTTTCAAAAGCCCACACGAGTTGATGGCAAACTTTT-CAAAGTCTACATAAGTTGGTGG
63 GCAACCTTTTCAAAAGCCCACACGAGTTGGTGGC-AACTTTTCCTAAGCCCACACAAGTTGGTGG
461210 CACA
127 CACA
* * ** *
461214 CTTTTCAAAGTCCACACAAGTCGGTGGCAACGAAACCTTTTCAAAAGTCAACATAAGTTGGTGGT
1 CTTTTCAAAGTCCACACAAGTCAGTGGCAAC-AAACCTTTTCAAAAGTCCACACGAGTTGGTGGC
* * * * * * *
461279 AACCTTTTCAAAAGTCTACACGAGTTGGTGGTAACCTCTTCTTAAGCTCACACAAGTTAGTGGCA
65 AACCTTTTCAAAAGCCCACACGAGTTGGTGGCAA-CTTTTCCTAAGCCCACACAAGTTGGTGGCA
461344 CA
129 CA
* * * * * *
461346 TTTTTTAAAGTCCACACAAGTTAGTGGCAACCAAACCTCTT-AAAAG-CTAGCACGAGTTTGTGG
1 CTTTTCAAAGTCCACACAAGTCAGTGGCAA-CAAACCTTTTCAAAAGTCCA-CACGAGTTGGTGG
* * *
461409 C-A-C--TTAAAAAGCCCACATGAGCTGGTGGCA
64 CAACCTTTTCAAAAGCCCACACGAGTTGGTGGCA
461439 CCCAACCCTT
Statistics
Matches: 681, Mismatches: 135, Indels: 104
0.74 0.15 0.11
Matches are distributed among these distances:
122 3 0.00
124 3 0.00
125 50 0.07
126 175 0.26
127 109 0.16
128 4 0.01
129 12 0.02
130 12 0.02
131 105 0.15
132 161 0.24
133 23 0.03
135 2 0.00
136 4 0.01
137 18 0.03
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (130 bp):
CTTTTCAAAGTCCACACAAGTCAGTGGCAACAAACCTTTTCAAAAGTCCACACGAGTTGGTGGCA
ACCTTTTCAAAAGCCCACACGAGTTGGTGGCAACTTTTCCTAAGCCCACACAAGTTGGTGGCACA
Found at i:461268 original size:68 final size:68
Alignment explanation
Indices: 461183--461309 Score: 177
Period size: 68 Copynumber: 1.9 Consensus size: 68
461173 TGATGGCAAA
*
461183 CTTTTCAAAGTCTACATAAGTTGGTGGC-ACACTTTTC-AAAGTCCACACAAGTCGGTGGCAACG
1 CTTTTCAAAGTCAACATAAGTTGGTGGCAAC-CTTTTCAAAAGTCCACACAAGTCGGTGGCAACG
461246 AAAC
65 AAAC
* * * *
461250 CTTTTCAAAAGTCAACATAAGTTGGTGGTAACCTTTTCAAAAGTCTACACGAGTTGGTGG
1 CTTTTC-AAAGTCAACATAAGTTGGTGGCAACCTTTTCAAAAGTCCACACAAGTCGGTGG
461310 TAACCTCTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
67 6 0.12
68 26 0.50
69 20 0.38
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (68 bp):
CTTTTCAAAGTCAACATAAGTTGGTGGCAACCTTTTCAAAAGTCCACACAAGTCGGTGGCAACGA
AAC
Found at i:461285 original size:289 final size:288
Alignment explanation
Indices: 460484--461319 Score: 883
Period size: 289 Copynumber: 2.9 Consensus size: 288
460474 ATCCTTTTTA
* * * *
460484 AAAGCCCACATGAGTCGGTGGTAATTTTTTCAATAGCCCACACTAGTTGGTGGCAACCTTTTCAA
1 AAAGCCCACATGAGTTGGTGGCAACTTTTTCAA-AGCCCACACGAGTTGGTGGCAACCTTTTCAA
* * * * * *
460549 AGT-CCACACAAGTTGGTGGTAACCTTTTCAAAAACCCATATGAGTTGGTGGCAACCTTTTCAAA
65 AGTCCCACACGAGTTGCTAGTAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAACCTTTTCAAA
* * * *
460613 AGCCTACACAAATTGGTGGCA-ACCTTTTCAAAGTTCACACGAGTTGGTGG---C-AACCTTTTC
130 AG-CTACATAAGTTGGTGGCACA-CTTTTCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTTC
* * * * * *
460673 GAAGTCCATATGAGTTGGTGGT-ACTATTTTC-AAAGTTCACATGAGTTGGTAGTAACCTCTTCA
193 AAAGTCCACATGAGTTGGTGGTAAC-CTTTTCAAAAGCT-ACACGAGTTGGTGGTAACCTCTTCA
* * *
460736 AGAGTCTACACGAGTTAGTGGCAACTTCTTCCT
256 AAAGCCTACACGAGTTAGTAGCAACTTCTTCCT
* * *
460769 AAA-CCCACATGAGTTGGTGGCAACTTCTTCCTAAGCCCATACGAGTTGGTGGCATA-CTTTTCA
1 AAAGCCCACATGAGTTGGTGGCAACTT-TTTCAAAGCCCACACGAGTTGGTGGCA-ACCTTTTCA
* * * * *
460832 AAGTCTACACAAGTCAGTGGC-AATCAAACCTTTTCAAAAGTCCACACGAGTTGGTGGCAACCTT
64 AAGTC-CCACACG--AGTTGCTAGT--AACCTTTTCAAAAGCCCACACGAGTTGGTGGCAACCTT
* * *
460896 TTCAAAAGC-CCATACGAGTTGGTGGCACACTTTTCAAAGTCCACACAAGTTAGTGTCAACTAAA
124 TTCAAAAGCTACATA--AGTTGGTGGCACACTTTTCAAAGTCCACACAAGTTGGTGGCAAC-AAA
* * * * * * *
460960 CTTTTTCCAATGTCCACACGAGTTAGTGGCAACCTTTTCAAAAGCCTACGCGAGTTGGTGGTAAT
186 CCTTTT-CAAAGTCCACATGAGTTGGTGGTAACCTTTTCAAAAG-CTACACGAGTTGGTGGTAAC
* * * * *
461025 TTTTTCAAAAGCCTACACGAGTTGGTAGTAACTT-TTCTT
249 CTCTTCAAAAGCCTACACGAGTTAGTAGCAACTTCTTCCT
* * *
461064 AAAGCCCACATGAGTTGGT-GCACCTTTTTCAAAGTCCACACGAGTTGCTGGCAACCTTTTCAAA
1 AAAGCCCACATGAGTTGGTGGCAACTTTTTCAAAGCCCACACGAGTTGGTGGCAACCTTTTCAAA
* * *
461128 ATCCCACACGAGTTGCTAGTAACCTTTTCAAAAGCCCACACGAGTTGATGGCAAACTTTTC-AAA
66 GTCCCACACGAGTTGCTAGTAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAACCTTTTCAAAA
*
461192 GTCTACATAAGTTGGTGGCACACTTTTCAAAGTCCACACAAGTCGGTGGCAACGAAACCTTTTCA
131 G-CTACATAAGTTGGTGGCACACTTTTCAAAGTCCACACAAGTTGGTGGCAAC-AAACCTTTTC-
* *
461257 AAAGTCAACATAAGTTGGTGGTAACCTTTTCAAAAGTCTACACGAGTTGGTGGTAACCTCTTC
193 AAAGTCCACATGAGTTGGTGGTAACCTTTTCAAAAG-CTACACGAGTTGGTGGTAACCTCTTC
461320 TTAAGCTCAC
Statistics
Matches: 448, Mismatches: 77, Indels: 48
0.78 0.13 0.08
Matches are distributed among these distances:
284 50 0.11
285 8 0.02
286 4 0.01
287 4 0.01
288 6 0.01
289 180 0.40
290 40 0.09
291 9 0.02
292 3 0.01
293 6 0.01
294 40 0.09
295 35 0.08
296 62 0.14
297 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (288 bp):
AAAGCCCACATGAGTTGGTGGCAACTTTTTCAAAGCCCACACGAGTTGGTGGCAACCTTTTCAAA
GTCCCACACGAGTTGCTAGTAACCTTTTCAAAAGCCCACACGAGTTGGTGGCAACCTTTTCAAAA
GCTACATAAGTTGGTGGCACACTTTTCAAAGTCCACACAAGTTGGTGGCAACAAACCTTTTCAAA
GTCCACATGAGTTGGTGGTAACCTTTTCAAAAGCTACACGAGTTGGTGGTAACCTCTTCAAAAGC
CTACACGAGTTAGTAGCAACTTCTTCCT
Found at i:461323 original size:258 final size:256
Alignment explanation
Indices: 460779--461377 Score: 627
Period size: 258 Copynumber: 2.3 Consensus size: 256
460769 AAACCCACAT
* * * * * * * * *
460779 GAGTTGGTGGCAACTTCTTCCTAAGCCCATACGAGTTGGTGGCATACTTTTCAAAGTCTACACAA
1 GAGTTGGTAGTAAC-TCTTCTTAAGCCCACACAAGTTAGTGGCACATTTTTCAAAGTCCACACAA
* * * *
460844 GTCAGTGGCAATCAAACCTTTTCAAAAGTCCACACGAGTTGGTGGCAACCTTTTCAAAAGCCCAT
65 GTTAGTGG----C-AACCTTTTCAAAAGTCCACACGAGTTGCTAGCAACCTTTTCAAAAGCCCAC
* * * *
460909 ACGAGTTGGTGGCACACTTTTCAAAGTCCACACAAGTTAGTGTCAACTAAACTTTTTCCAATGTC
125 ACGAGTTGATGGCAAACTTTTCAAAGTCCACACAAGTTAGTGGCAAC--AACTTTTTCCAAAGTC
* * * * * **
460974 CACACGAGTTAGTGGCAACCTTTTCAAAAGCCTACGCGAGTTGGTGGTAATTTTTTCAAAAGCCT
188 CACACAAGTCAGTGGCAACCTTTTCAAAAGCCAACACAAGTTGGTGGTAACCTTTTCAAAAGCCT
461039 ACAC
253 ACAC
* ** * * *
461043 GAGTTGGTAGTAACTTTTCTTAAAGCCCACATGAGTTGGT-GCACCTTTTTCAAAGTCCACACGA
1 GAGTTGGTAGTAACTCTTCTT-AAGCCCACACAAGTTAGTGGCACATTTTTCAAAGTCCACACAA
*
461107 GTT-GCTGGCAACCTTTTCAAAA-TCCCACACGAGTTGCTAGTAACCTTTTCAAAAGCCCACACG
65 GTTAG-TGGCAACCTTTTCAAAAGT-CCACACGAGTTGCTAGCAACCTTTTCAAAAGCCCACACG
* * *
461170 AGTTGATGGCAAACTTTTCAAAGTCTACATAAGTTGGTGGC-AC-AC-TTTT-CAAAGTCCACAC
128 AGTTGATGGCAAACTTTTCAAAGTCCACACAAGTTAGTGGCAACAACTTTTTCCAAAGTCCACAC
* * * *
461231 AAGTCGGTGGCAACGAAACCTTTTCAAAAGTCAACATAAGTTGGTGGTAACCTTTTCAAAAGTCT
193 AAGTCAGTGG---C--AACCTTTTCAAAAGCCAACACAAGTTGGTGGTAACCTTTTCAAAAGCCT
461296 ACAC
253 ACAC
* * *
461300 GAGTTGGTGGTAACCTCTTCTTAAGCTCACACAAGTTAGTGGCACATTTTTTAAAGTCCACACAA
1 GAGTTGGTAGTAA-CTCTTCTTAAGCCCACACAAGTTAGTGGCACATTTTTCAAAGTCCACACAA
461365 GTTAGTGGCAACC
65 GTTAGTGGCAACC
461378 AAACCTCTTA
Statistics
Matches: 281, Mismatches: 43, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
252 18 0.06
253 4 0.01
254 2 0.01
255 1 0.00
257 74 0.26
258 122 0.43
259 2 0.01
262 1 0.00
263 29 0.10
264 28 0.10
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (256 bp):
GAGTTGGTAGTAACTCTTCTTAAGCCCACACAAGTTAGTGGCACATTTTTCAAAGTCCACACAAG
TTAGTGGCAACCTTTTCAAAAGTCCACACGAGTTGCTAGCAACCTTTTCAAAAGCCCACACGAGT
TGATGGCAAACTTTTCAAAGTCCACACAAGTTAGTGGCAACAACTTTTTCCAAAGTCCACACAAG
TCAGTGGCAACCTTTTCAAAAGCCAACACAAGTTGGTGGTAACCTTTTCAAAAGCCTACAC
Found at i:468323 original size:79 final size:78
Alignment explanation
Indices: 468240--468399 Score: 187
Period size: 79 Copynumber: 2.0 Consensus size: 78
468230 TAATATCTAC
* * * * *
468240 GTTGGAGTATTCCCTCGAAAACAATGGGGTTGGAGTATCCCCGATGGT-AGAAAATTAATGTTTT
1 GTTGGAGTATTCCCTCAAAAACAACGAGCTTGGAGTATCCCCGATGGTGA-AAAATCAATGTTTT
468304 AAAAATAAAACCGAG
65 AAAAAT-AAACCGAG
* * * * *
468319 GTTGGAGTATTCTCTCAAAAATAACGAGCTTGGAGTATTCTCGATGGTGAAAAATCAGTGTTTTA
1 GTTGGAGTATTCCCTCAAAAACAACGAGCTTGGAGTATCCCCGATGGTGAAAAATCAATGTTTTA
* *
468384 GAAATAAATCGAG
66 AAAATAAACCGAG
468397 GTT
1 GTT
468400 AGGGTATCCG
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
78 10 0.15
79 57 0.84
80 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29
Consensus pattern (78 bp):
GTTGGAGTATTCCCTCAAAAACAACGAGCTTGGAGTATCCCCGATGGTGAAAAATCAATGTTTTA
AAAATAAACCGAG
Found at i:468962 original size:20 final size:20
Alignment explanation
Indices: 468939--468993 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
468929 AAGTACCCAG
* *
468939 ATGTATCGTTACATTTTTCA
1 ATGTATCGATACATTTATCA
* * *
468959 ATGTACCGATACATGTATGA
1 ATGTATCGATACATTTATCA
468979 ATGTATCGATACATT
1 ATGTATCGATACATT
468994 CTGTCTTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:472386 original size:79 final size:78
Alignment explanation
Indices: 472224--472368 Score: 204
Period size: 78 Copynumber: 1.8 Consensus size: 78
472214 ACGTCGCGAC
* *
472224 ATCCCCGATAGTGAAAAATTAGCGTTTTAGAAATAAAATCAGGGTTGAAGTTCCCCTCGAAAATA
1 ATCCCCAATAGTGAAAAATTAGCGTTTTAAAAATAAAATCAGGGTTGAAGTTCCCCTCGAAAATA
472289 ACAAGGTTAAAGT
66 ACAAGGTTAAAGT
* * *
472302 ATCCCCAATGGTGGAAAATTAGTGTTTTAAAAATAAAATC-GAGGTT-AGAGTATCCCCTCGAAA
1 ATCCCCAATAGTGAAAAATTAGCGTTTTAAAAATAAAATCAG-GGTTGA-AGT-TCCCCTCGAAA
472365 ATAA
63 ATAA
472369 TGGGATTGGA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
77 2 0.03
78 42 0.71
79 15 0.25
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (78 bp):
ATCCCCAATAGTGAAAAATTAGCGTTTTAAAAATAAAATCAGGGTTGAAGTTCCCCTCGAAAATA
ACAAGGTTAAAGT
Found at i:472405 original size:28 final size:27
Alignment explanation
Indices: 472344--472412 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
472334 ATAAAATCGA
* *
472344 GGTTAGAGTATCCCCTCGAAAATAATG
1 GGTTGGAGTATCCCCTCGAAAATAAAG
472371 GGATTGGAGTATCCCCTC-AGAAATAACAG
1 GG-TTGGAGTATCCCCTCGA-AAATAA-AG
*
472400 GGTTGGAGAATCC
1 GGTTGGAGTATCC
472413 TCGATGGTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.08
28 30 0.83
29 3 0.08
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (27 bp):
GGTTGGAGTATCCCCTCGAAAATAAAG
Found at i:472454 original size:79 final size:79
Alignment explanation
Indices: 472378--472525 Score: 201
Period size: 79 Copynumber: 1.9 Consensus size: 79
472368 ATGGGATTGG
*
472378 AGTATCCCCTCAGAAATAACAGGGTTGGAGAATC-CTCGATGGTGAAAAATC-AGTATTTTAGAA
1 AGTATCCCCTCAGAAATAACAGGGTTGGAGAATCTC-CGATGGTGAAAAATCGA-TAATTTAGAA
472441 ATAAAATCAGGATTAA
64 ATAAAATCAGGATTAA
* * * * * *
472457 AGTGTTCCCTCGGAAATAACGGGGTTGGAGTATCTCCGATGGTGGAAAATCGATAATTTAGAAAT
1 AGTATCCCCTCAGAAATAACAGGGTTGGAGAATCTCCGATGGTGAAAAATCGATAATTTAGAAAT
472522 AAAA
66 AAAA
472526 ACATCAATGA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
79 58 0.97
80 2 0.03
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (79 bp):
AGTATCCCCTCAGAAATAACAGGGTTGGAGAATCTCCGATGGTGAAAAATCGATAATTTAGAAAT
AAAATCAGGATTAA
Found at i:481014 original size:29 final size:28
Alignment explanation
Indices: 480945--481030 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 28
480935 TTTAGTTTTC
*
480945 TTTTTGTATTTTATTTGACTTTTCATTTCT
1 TTTTTGTATTTTATTT-ACTTTT-AATTCT
*
480975 TCTTATG--TTTTAGTTTACTTTTAATTCT
1 T-TTTTGTATTTTA-TTTACTTTTAATTCT
* *
481003 TTTTTGTATTTTAATTAACCTTTAATTC
1 TTTTTGTATTTT-ATTTACTTTTAATTC
481031 CTTAGCATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
27 4 0.09
28 6 0.13
29 27 0.59
30 5 0.11
31 4 0.09
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (28 bp):
TTTTTGTATTTTATTTACTTTTAATTCT
Found at i:492153 original size:27 final size:26
Alignment explanation
Indices: 492105--492158 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
492095 GGAAAGTTAC
* *
492105 TTTATTTATTTATTTTAAATTTTATAT
1 TTTATATATTTATTATAAA-TTTATAT
492132 TTTATATATTTA-TATAAGATTTATAT
1 TTTATATATTTATTATAA-ATTTATAT
492158 T
1 T
492159 ATCGTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTATATATTTATTATAAATTTATAT
Found at i:493288 original size:18 final size:17
Alignment explanation
Indices: 493265--493300 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
493255 TTAAATTACT
493265 ATTTAATTAAATTAAATA
1 ATTTAATTAAA-TAAATA
*
493283 ATTTAATTTAATAAATA
1 ATTTAATTAAATAAATA
493300 A
1 A
493301 AATTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAATTAAATAAATA
Found at i:494378 original size:11 final size:12
Alignment explanation
Indices: 494351--494380 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
494341 GGAGGGATGA
494351 AAAAAATGAAAG
1 AAAAAATGAAAG
*
494363 AAAAAATGAGAG
1 AAAAAATGAAAG
494375 AAAAAA
1 AAAAAA
494381 AAAATGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (12 bp):
AAAAAATGAAAG
Found at i:495218 original size:12 final size:12
Alignment explanation
Indices: 495201--495232 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
495191 TTCAACAAAG
495201 GCTGCCAACTGT
1 GCTGCCAACTGT
495213 GCTGCCAACTGT
1 GCTGCCAACTGT
*
495225 GCCGCCAA
1 GCTGCCAA
495233 TTTTGACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.38, G:0.25, T:0.19
Consensus pattern (12 bp):
GCTGCCAACTGT
Found at i:500009 original size:27 final size:27
Alignment explanation
Indices: 499970--500025 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
499960 CTGTGCCGCC
* *
499970 AATTTTGACATTCAATTTGAAATAGTA
1 AATTATGAAATTCAATTTGAAATAGTA
499997 AATTATGAAATTCAATTTGAAATAGTA
1 AATTATGAAATTCAATTTGAAATAGTA
500024 AA
1 AA
500026 GGTTGCACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (27 bp):
AATTATGAAATTCAATTTGAAATAGTA
Found at i:501813 original size:11 final size:11
Alignment explanation
Indices: 501799--501853 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
501789 ATTAATTTTT
501799 TAAAAATTAAA
1 TAAAAATTAAA
501810 TAAAAA-T-AA
1 TAAAAATTAAA
*
501819 T--ATATTAAA
1 TAAAAATTAAA
501828 TAAAAATTAAAA
1 TAAAAATT-AAA
*
501840 TAATAATTAAA
1 TAAAAATTAAA
501851 TAA
1 TAA
501854 TTTTTAACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
7 2 0.06
8 1 0.03
9 6 0.17
10 1 0.03
11 16 0.44
12 10 0.28
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAAAATTAAA
Found at i:501850 original size:19 final size:19
Alignment explanation
Indices: 501806--501855 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
501796 TTTTAAAAAT
* *
501806 TAAATAAAAA-TAATATAT
1 TAAATAAAAATTAAAATAA
501824 TAAATAAAAATTAAAATAA
1 TAAATAAAAATTAAAATAA
*
501843 TAATTAAATAATT
1 TAAATAAA-AATT
501856 TTTAACATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 10 0.37
19 13 0.48
20 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAATAAAAATTAAAATAA
Found at i:501854 original size:11 final size:11
Alignment explanation
Indices: 501813--501854 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
501803 AATTAAATAA
501813 AAATAATATATT
1 AAATAATA-ATT
*
501825 AAATAAAAATT
1 AAATAATAATT
501836 AAAATAATAATT
1 -AAATAATAATT
501848 AAATAAT
1 AAATAAT
501855 TTTTAACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATT
Found at i:501860 original size:23 final size:24
Alignment explanation
Indices: 501807--501853 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
501797 TTTAAAAATT
*
501807 AAATAAAAATAATATATTAAATAA
1 AAATTAAAATAATATATTAAATAA
501831 AAATTAAAATAATA-ATTAAATAA
1 AAATTAAAATAATATATTAAATAA
501854 TTTTTAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATTAAAATAATATATTAAATAA
Found at i:503186 original size:14 final size:15
Alignment explanation
Indices: 503156--503189 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
503146 ACAAATTATA
503156 TTAATAAAAATAAAT
1 TTAATAAAAATAAAT
*
503171 TTAATAATAA-AAAT
1 TTAATAAAAATAAAT
503185 TTAAT
1 TTAAT
503190 TTTTTTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAATAAAAATAAAT
Found at i:504501 original size:23 final size:23
Alignment explanation
Indices: 504459--504502 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
504449 AAACTCAATT
*
504459 ATAAATCATTTAAAGCTCGTTCA
1 ATAAATCATTTAAAACTCGTTCA
* *
504482 ATAAATTATTTAAAATTCGTT
1 ATAAATCATTTAAAACTCGTT
504503 TAGTGTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (23 bp):
ATAAATCATTTAAAACTCGTTCA
Found at i:504583 original size:35 final size:36
Alignment explanation
Indices: 504513--504602 Score: 94
Period size: 35 Copynumber: 2.5 Consensus size: 36
504503 TAGTGTTCAA
* ** *
504513 TTATGATATAATTAATGTTATTATTTGTATTTTA-T
1 TTATAATATAATTAATAATATTATATGTATTTTATT
504548 TTATAATATAATTAATAATATT-TATGTATTATTATT
1 TTATAATATAATTAATAATATTATATGTATT-TTATT
* *
504584 TTATATTTAAAATTAATAA
1 TTATA-ATATAATTAATAA
504603 GTATATTTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 7 0.15
35 22 0.48
36 6 0.13
37 11 0.24
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (36 bp):
TTATAATATAATTAATAATATTATATGTATTTTATT
Found at i:504743 original size:26 final size:25
Alignment explanation
Indices: 504703--504751 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
504693 ATAAATTTAT
504703 TTAATTTAAACGAATAAATATAAAC
1 TTAATTTAAACGAATAAATATAAAC
*
504728 TTAATTTTAAATGAATAAATATAA
1 TTAA-TTTAAACGAATAAATATAA
504752 CATAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (25 bp):
TTAATTTAAACGAATAAATATAAAC
Found at i:504759 original size:26 final size:26
Alignment explanation
Indices: 504707--504765 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
504697 ATTTATTTAA
* *
504707 TTTAAACGAATAAATATAAACTTAAT
1 TTTAAATGAATAAATATAAACTAAAT
504733 TTTAAATGAATAAATAT-AACATAAAT
1 TTTAAATGAATAAATATAAAC-TAAAT
*
504759 TTAAAAT
1 TTTAAAT
504766 TCTTACAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 3 0.10
26 26 0.90
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (26 bp):
TTTAAATGAATAAATATAAACTAAAT
Found at i:508249 original size:19 final size:19
Alignment explanation
Indices: 508225--508270 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
508215 ATAAATTACT
508225 TTTATTAAACATAAAAAAA
1 TTTATTAAACATAAAAAAA
*
508244 TTTATTAAATATAAAAAAA
1 TTTATTAAACATAAAAAAA
508263 -TTATTAAA
1 TTTATTAAA
508271 TATATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
TTTATTAAACATAAAAAAA
Found at i:508261 original size:18 final size:18
Alignment explanation
Indices: 508225--508274 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
508215 ATAAATTACT
*
508225 TTTATTAAACATAAAAAAA
1 TTTATTAAATAT-AAAAAA
508244 TTTATTAAATATAAAAAA
1 TTTATTAAATATAAAAAA
*
508262 ATTATTAAATATA
1 TTTATTAAATATA
508275 TATTTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 18 0.62
19 11 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TTTATTAAATATAAAAAA
Found at i:508961 original size:38 final size:38
Alignment explanation
Indices: 508910--509033 Score: 117
Period size: 38 Copynumber: 3.2 Consensus size: 38
508900 AAGCTAACGC
** *
508910 ATAAATTTTTTATTAGCTTTTGAAAA-ATATTAATAAT-T
1 ATAAA-TTTTTATTAAATTTT-AAAAGATATGAATAATAT
*
508948 ATAAATTATTTATTAAATTTTAAAAGATGTGAATAATAT
1 ATAAATT-TTTATTAAATTTTAAAAGATATGAATAATAT
* * * * *
508987 ATAAATTTTTATTAAAATTCAAAAGATAAGACTAATAC
1 ATAAATTTTTATTAAATTTTAAAAGATATGAATAATAT
*
509025 ATGAATTTT
1 ATAAATTTT
509034 ATTTTTGATT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
37 6 0.08
38 58 0.81
39 8 0.11
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (38 bp):
ATAAATTTTTATTAAATTTTAAAAGATATGAATAATAT
Found at i:509510 original size:88 final size:89
Alignment explanation
Indices: 509356--509566 Score: 232
Period size: 89 Copynumber: 2.4 Consensus size: 89
509346 GTAATGCATA
* * * *
509356 GATTGTAAATGTCAAACT-AAAGGATTAGATTAATGCATGAATTGTACCTAAGAATCAGA-TTCT
1 GATTGTAAATGTCAAACTGTAAGAATTAGATTAATACATAAATTGTACCTAAGAATCAGATTTCT
* *
509419 TTTTAG-TGGAAAACAAAGTTGATC
66 TTTTAGTTGGAAAA-AAAATTAATC
* * * * *
509443 GATTGTAAATGTCAAACTGTAAGAATTAGATTGATACATAAATTGTATCTGAGAATCATATTTTT
1 GATTGTAAATGTCAAACTGTAAGAATTAGATTAATACATAAATTGTACCTAAGAATCAGATTTCT
* *
509508 TTTTTGTTGGAAAAAAAATTAATT
66 TTTTAGTTGGAAAAAAAATTAATC
* * *
509532 GATTATAAATGTCAGACTGTAA-ATATTAGACTAAT
1 GATTGTAAATGTCAAACTGTAAGA-ATTAGATTAAT
509567 GTATGAATTA
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
87 18 0.17
88 34 0.33
89 44 0.43
90 7 0.07
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (89 bp):
GATTGTAAATGTCAAACTGTAAGAATTAGATTAATACATAAATTGTACCTAAGAATCAGATTTCT
TTTTAGTTGGAAAAAAAATTAATC
Found at i:512350 original size:78 final size:78
Alignment explanation
Indices: 512221--512379 Score: 291
Period size: 78 Copynumber: 2.0 Consensus size: 78
512211 AGCATTATGG
* *
512221 ATTATGTAGAAATGAAGGTTATACTTATAGAAAATATCTTCATCAATTTAGCACATCAGGAGAGA
1 ATTATGTAGAAATGAAGGCTATACCTATAGAAAATATCTTCATCAATTTAGCACATCAGGAGAGA
512286 GCTCATATCAATA
66 GCTCATATCAATA
*
512299 ATTATGTAGAAATGAAGGCTATACCTATAGAAAATATCTTCATCAATTTAGCACATCAGGGGAGA
1 ATTATGTAGAAATGAAGGCTATACCTATAGAAAATATCTTCATCAATTTAGCACATCAGGAGAGA
512364 GCTCATATCAATA
66 GCTCATATCAATA
512377 ATT
1 ATT
512380 TTTGGTTTTT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (78 bp):
ATTATGTAGAAATGAAGGCTATACCTATAGAAAATATCTTCATCAATTTAGCACATCAGGAGAGA
GCTCATATCAATA
Found at i:516324 original size:71 final size:71
Alignment explanation
Indices: 516132--516325 Score: 205
Period size: 71 Copynumber: 2.7 Consensus size: 71
516122 TTTTAAGTTT
*
516132 TATAATCAAATTAAAAAATAAATCTTAAATTTTTATAAATAAAATTAAATTACACCATTAAAAAT
1 TATAATCAAA-TAAAAAATAAAT-TTAAATTTTTACAAATAAAA-TAAATTACACCATTAAAAAT
*
516197 TTAAACTCA
63 TTAAACCCA
* * * **
516206 TATCATACTTAAT-AAAAATACAA-TTAAATTTTTACAAATCAAAATAAATTATA-TTTTAAAAA
1 TATAAT-C-AAATAAAAAATA-AATTTAAATTTTTACAAAT-AAAATAAATTACACCATTAAAAA
516268 TTTAAACCCA
62 TTTAAACCCA
* * *
516278 TATAATCAAATAAAAAATAAATTTAAACTTCTACGAATAGAAATAAAT
1 TATAATCAAATAAAAAATAAATTTAAATTTTTACAAATA-AAATAAAT
516326 AATAACTCTA
Statistics
Matches: 101, Mismatches: 12, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
70 6 0.06
71 29 0.29
72 21 0.21
73 23 0.23
74 16 0.16
75 4 0.04
76 2 0.02
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.34
Consensus pattern (71 bp):
TATAATCAAATAAAAAATAAATTTAAATTTTTACAAATAAAATAAATTACACCATTAAAAATTTA
AACCCA
Found at i:516750 original size:23 final size:22
Alignment explanation
Indices: 516699--516772 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 22
516689 TCACATAATC
516699 AAATAAAAATAAATTTAA--TTA
1 AAATAAAAATAAA-TTAATTTTA
516720 AAAT-AAAATAAATTAATTTTA
1 AAATAAAAATAAATTAATTTTA
*
516741 TAAATAAAAATAAATCATATTTTA
1 -AAATAAAAATAAATTA-ATTTTA
516765 AAATAAAA
1 AAATAAAA
516773 TAACTTTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
19 4 0.09
20 8 0.17
21 7 0.15
22 4 0.09
23 18 0.38
24 6 0.13
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (22 bp):
AAATAAAAATAAATTAATTTTA
Found at i:517643 original size:20 final size:20
Alignment explanation
Indices: 517618--517692 Score: 54
Period size: 16 Copynumber: 4.0 Consensus size: 20
517608 TTTTTATTTT
517618 TATATTAATATTAATAATTA
1 TATATTAATATTAATAATTA
517638 TATATT--T-TT-ATAATTA
1 TATATTAATATTAATAATTA
* * *
517654 AAT-TTAA-ATAAATAATTT
1 TATATTAATATTAATAATTA
*
517672 TATTATTAAATAATAATAATT
1 TA-TATT-AATATTAATAATT
517693 TAAACCGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
15 2 0.05
16 9 0.22
17 3 0.07
18 8 0.20
19 1 0.02
20 8 0.20
21 2 0.05
22 8 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATTAATATTAATAATTA
Found at i:517689 original size:26 final size:26
Alignment explanation
Indices: 517615--517690 Score: 66
Period size: 26 Copynumber: 2.8 Consensus size: 26
517605 TATTTTTTAT
* *
517615 TTTTA-TATTAATATTAATAATTATATAT
1 TTTTATTATTAA-A-TAATAA-TAAATAA
* *
517643 TTTTATAATTAAAT-TTAAATAAATAA
1 TTTTATTATTAAATAAT-AATAAATAA
517669 TTTTATTATTAAATAATAATAA
1 TTTTATTATTAAATAATAATAA
517691 TTTAAACCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
26 24 0.62
27 4 0.10
28 6 0.15
29 5 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTTATTATTAAATAATAATAAATAA
Found at i:518288 original size:23 final size:24
Alignment explanation
Indices: 518262--518317 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
518252 TCTGATCTGC
*
518262 ATATTTTAATTATTAAAATTTT-T
1 ATATTTTAATAATTAAAATTTTAT
* * *
518285 ATATATTAATAATTTATATTTTAT
1 ATATTTTAATAATTAAAATTTTAT
*
518309 AAATTTTAA
1 ATATTTTAA
518318 AATATATTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTTTAATAATTAAAATTTTAT
Found at i:518408 original size:26 final size:29
Alignment explanation
Indices: 518360--518414 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
518350 ATTTTATTTA
* *
518360 TATCATATTTATATATTTATATTTAATAT
1 TATCAAATTTATATATTTATATTAAATAT
518389 TATCAAATTTA-ATA-TT-TATTAAATAT
1 TATCAAATTTATATATTTATATTAAATAT
518415 GTTCAAGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.38
27 2 0.08
28 3 0.12
29 10 0.42
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (29 bp):
TATCAAATTTATATATTTATATTAAATAT
Found at i:519160 original size:27 final size:27
Alignment explanation
Indices: 519082--519200 Score: 99
Period size: 26 Copynumber: 4.5 Consensus size: 27
519072 TCTGCTCTCG
* *
519082 ATTTAATAAT-TTATATATTTAAATTAT
1 ATTT-ATAATATTATATATTTATATAAT
* *
519109 ATTTAT-ATATTTTTTATTT-TAATAAT
1 ATTTATAATATTATATATTTAT-ATAAT
*
519135 ATTTATAATATTATATTTTTATATAA-
1 ATTTATAATATTATATATTTATATAAT
*
519161 ATTT-TAATATGATTATATTTATATTAAT
1 ATTTATAATATTA-TATATTTATA-TAAT
519189 -TTTAT-ATATTAT
1 ATTTATAATATTAT
519201 TTAATATTAT
Statistics
Matches: 74, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
25 9 0.12
26 34 0.46
27 29 0.39
28 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (27 bp):
ATTTATAATATTATATATTTATATAAT
Found at i:519170 original size:12 final size:12
Alignment explanation
Indices: 519123--519226 Score: 58
Period size: 12 Copynumber: 8.6 Consensus size: 12
519113 ATATATTTTT
519123 TATTTTAATA-A
1 TATTTTAATATA
519134 TATTTATAATATTA
1 TATTT-TAATA-TA
*
519148 TATTTTTATATA
1 TATTTTAATATA
*
519160 AATTTTAATATGA
1 TATTTTAATAT-A
519173 TTATATTT-ATAT-
1 -TAT-TTTAATATA
519185 TAATTTT-ATATA
1 T-ATTTTAATATA
519197 T-TATTTAATAT-
1 TAT-TTTAATATA
* * *
519208 TATATTAATTTT
1 TATTTTAATATA
519220 TATTTTA
1 TATTTTA
519227 TAATTTTAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 23
0.71 0.07 0.22
Matches are distributed among these distances:
10 1 0.01
11 23 0.31
12 30 0.41
13 5 0.07
14 12 0.16
15 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (12 bp):
TATTTTAATATA
Found at i:519180 original size:28 final size:28
Alignment explanation
Indices: 519092--519219 Score: 94
Period size: 26 Copynumber: 4.7 Consensus size: 28
519082 ATTTAATAAT
* *
519092 TTATATATTTAAATT-ATATTTATATAT-T
1 TTATAT-TTTATATTAAT-TTTATATATGA
*
519120 TTTTATTTTA-A-TAATATTTATA-AT-A
1 TTATATTTTATATTAAT-TTTATATATGA
*
519145 TTATATTTTTATATAAATTTTA-ATATGA
1 TTATA-TTTTATATTAATTTTATATATGA
*
519173 TTATA-TTTATATTAATTTTATATATTA
1 TTATATTTTATATTAATTTTATATATGA
*
519200 TT-TAATATTATATTAATTTT
1 TTAT-ATTTTATATTAATTTT
519220 TATTTTATAA
Statistics
Matches: 84, Mismatches: 7, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
25 7 0.08
26 31 0.37
27 19 0.23
28 27 0.32
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (28 bp):
TTATATTTTATATTAATTTTATATATGA
Found at i:519195 original size:17 final size:16
Alignment explanation
Indices: 519173--519228 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
519163 TTTAATATGA
519173 TTATATTTATATTAATT
1 TTATATTTAT-TTAATT
*
519190 TTATATATTATTTAATA
1 TTATAT-TTATTTAATT
* *
519207 TTATATTAATTTTTATT
1 TTATATTTA-TTTAATT
519224 TTATA
1 TTATA
519229 ATTTTAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.06
17 27 0.82
18 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATATTTATTTAATT
Found at i:519210 original size:34 final size:33
Alignment explanation
Indices: 519093--519228 Score: 95
Period size: 34 Copynumber: 4.1 Consensus size: 33
519083 TTTAATAATT
*
519093 TATA-TATTTAA-ATTATATTTATA-TATTTTT
1 TATATTATTTAATATTATATTTATATTATTTTA
* *
519123 TATTTTA-ATAATATTTATAATATTATATT-TTTATA
1 TATATTATTTAATA-TTAT-AT-TTATATTATTT-TA
* *
519158 TAAATT-TTAATATGATTATATTTATATTAATTTTA
1 TATATTATTTA-AT-ATTATATTTATATT-ATTTTA
* *
519193 TATATTATTTAATATTATATTAATTTTTATTTTA
1 TATATTATTTAATATTATATTTA-TATTATTTTA
519227 TA
1 TA
519229 ATTTTAAAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
30 6 0.07
31 3 0.04
32 4 0.05
33 2 0.02
34 32 0.40
35 21 0.26
36 12 0.15
37 1 0.01
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (33 bp):
TATATTATTTAATATTATATTTATATTATTTTA
Found at i:519223 original size:15 final size:15
Alignment explanation
Indices: 519179--519233 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
519169 ATGATTATAT
519179 TTATATTAA-TTTTA
1 TTATATTAATTTTTA
*
519193 -TATATT-ATTTAATA
1 TTATATTAATTT-TTA
519207 TTATATTAATTTTTA
1 TTATATTAATTTTTA
*
519222 TTTTA-TAATTTT
1 TTATATTAATTTT
519234 AAAAGTCATG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
12 1 0.03
13 8 0.24
14 9 0.26
15 12 0.35
16 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTAATTTTTA
Found at i:520357 original size:2 final size:2
Alignment explanation
Indices: 520350--520403 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
520340 CTCATGAAAG
520350 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
520392 AT AT AT AT AT AT
1 AT AT AT AT AT AT
520404 GAGTATCTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:526131 original size:16 final size:16
Alignment explanation
Indices: 526107--526155 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
526097 ATTTGAATTG
526107 AAATAACTCAAAATAA
1 AAATAACTCAAAATAA
* *
526123 AATTAACTCATAACTAA
1 AAATAACTCA-AAATAA
*
526140 AAATGACTCAAAATAA
1 AAATAACTCAAAATAA
526156 TAAAAACTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.61, C:0.14, G:0.02, T:0.22
Consensus pattern (16 bp):
AAATAACTCAAAATAA
Found at i:529158 original size:13 final size:13
Alignment explanation
Indices: 529140--529167 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
529130 GTCCAAAAAT
529140 GTGTCGGACATAG
1 GTGTCGGACATAG
529153 GTGTCGGACATAG
1 GTGTCGGACATAG
529166 GT
1 GT
529168 ACTTCAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.39, T:0.25
Consensus pattern (13 bp):
GTGTCGGACATAG
Found at i:531880 original size:18 final size:19
Alignment explanation
Indices: 531847--531882 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
531837 AGTTTAATGG
*
531847 TTTAACCTTTTTTTCTAAT
1 TTTAACCTTGTTTTCTAAT
531866 TTTAA-CTTGTTTTCTAA
1 TTTAACCTTGTTTTCTAA
531883 CCACCCAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.22, C:0.14, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTAACCTTGTTTTCTAAT
Found at i:532888 original size:39 final size:37
Alignment explanation
Indices: 532828--532901 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 37
532818 TATATTTTAA
* *
532828 TTTTAAAAAATTATTAAATTTTGACATTATT-AATTTT
1 TTTTAAAAAATTACTAAATTTT-ACATCATTCAATTTT
*
532865 TTTTAAAAAAATTACCTACATTTTACATCATTCAATT
1 TTTT-AAAAAATTA-CTAAATTTTACATCATTCAATT
532902 AATTTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
37 4 0.13
38 16 0.52
39 11 0.35
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (37 bp):
TTTTAAAAAATTACTAAATTTTACATCATTCAATTTT
Found at i:533542 original size:14 final size:14
Alignment explanation
Indices: 533525--533573 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
533515 TATAATAAAA
533525 ATATTTTAATTTTT
1 ATATTTTAATTTTT
* **
533539 ATATTATAAAATTT
1 ATATTTTAATTTTT
* *
533553 ATTTTTTAATTTAT
1 ATATTTTAATTTTT
533567 ATATTTT
1 ATATTTT
533574 TATATTATTA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATATTTTAATTTTT
Found at i:533589 original size:20 final size:19
Alignment explanation
Indices: 533533--533591 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 19
533523 AAATATTTTA
* *
533533 ATTTTTATATTATAAAATTT
1 ATTTTTATATTAT-TAATAT
*
533553 ATTTTT-TA--ATTTATAT
1 ATTTTTATATTATTAATAT
533569 ATTTTTATATTATTAACTAT
1 ATTTTTATATTATTAA-TAT
533589 ATT
1 ATT
533592 AAAAAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 9 0.29
17 4 0.13
19 6 0.19
20 12 0.39
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTATATTATTAATAT
Found at i:533627 original size:18 final size:19
Alignment explanation
Indices: 533586--533631 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
533576 TATTATTAAC
* *
533586 TATATTAAAAAATTATTTA
1 TATATTATAAAATTATTGA
*
533605 AATATTATAAAA-TATTGA
1 TATATTATAAAATTATTGA
533623 TATATTATA
1 TATATTATA
533632 TGATATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TATATTATAAAATTATTGA
Found at i:534179 original size:23 final size:22
Alignment explanation
Indices: 534146--534189 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
534136 AAAATAAAAA
* *
534146 ATATTTTTATATTTATATTTAT
1 ATATTTTTATAATTAAATTTAT
534168 ATATATTTTATAATTAAATTTA
1 ATAT-TTTTATAATTAAATTTA
534190 AATAATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:535089 original size:16 final size:16
Alignment explanation
Indices: 535070--535100 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
535060 TCTAATAAGG
535070 TTTCTTTTTAATTAGT
1 TTTCTTTTTAATTAGT
535086 TTTCTTTTTAATTAG
1 TTTCTTTTTAATTAG
535101 ATATAACAAT
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:0.19, C:0.06, G:0.06, T:0.68
Consensus pattern (16 bp):
TTTCTTTTTAATTAGT
Found at i:536139 original size:22 final size:22
Alignment explanation
Indices: 536114--536156 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
536104 AGGAGTTAAT
*
536114 CTTTTTAGCCATAGCCAAATAC
1 CTTTTCAGCCATAGCCAAATAC
536136 CTTTTCAGCCATAGCCAAATA
1 CTTTTCAGCCATAGCCAAATA
536157 TCTAGAGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.30
Consensus pattern (22 bp):
CTTTTCAGCCATAGCCAAATAC
Found at i:544251 original size:20 final size:20
Alignment explanation
Indices: 544226--544302 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
544216 GTAAAAAGAC
544226 AGAATGTATCGATACATTAA
1 AGAATGTATCGATACATTAA
* * *
544246 AGAATGTATCAATATATTCAT
1 AGAATGTATCGATACATT-AA
* * *
544267 A-CATATATCGATACATTGA
1 AGAATGTATCGATACATTAA
544286 AGAATGTATCGATACAT
1 AGAATGTATCGATACAT
544303 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.93
21 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTAA
Found at i:544254 original size:51 final size:50
Alignment explanation
Indices: 544178--544334 Score: 138
Period size: 51 Copynumber: 3.3 Consensus size: 50
544168 TTTTAACTAG
* *
544178 ATGTATCGATAAATCGAAA-AATGTATCGATACATCCGGGTAAAAAGACAGA
1 ATGTATCGATACAT-TAAAGAATGTATCGATACAT-CGGGTAAAAAGACAGA
* * * *
544229 ATGTATCGATACATTAAAGAATGTATCAATATAT----T---CATAC---
1 ATGTATCGATACATTAAAGAATGTATCGATACATCGGGTAAAAAGACAGA
* *
544269 ATATATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
1 ATGTATCGATACATTAAAGAATGTATCGATACATC-GGGTAAAAAGACAGA
544320 ATGTATCGATACATT
1 ATGTATCGATACATT
544335 CATACATGTA
Statistics
Matches: 81, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
40 30 0.37
43 3 0.04
45 1 0.01
46 1 0.01
48 3 0.04
50 3 0.04
51 40 0.49
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.28
Consensus pattern (50 bp):
ATGTATCGATACATTAAAGAATGTATCGATACATCGGGTAAAAAGACAGA
Found at i:544321 original size:71 final size:71
Alignment explanation
Indices: 544246--544380 Score: 225
Period size: 71 Copynumber: 1.9 Consensus size: 71
544236 GATACATTAA
*
544246 AGAATGTATCAATATATTCATACATATATCGATACATTGAAGAATGTATCGATACATCTGGGTAA
1 AGAATGTATCAATACATTCATACATATATCGATACATTGAAGAATGTATCGATACATCTGGGTAA
544311 AAAGAC
66 AAAGAC
* * * *
544317 AGAATGTATCGATACATTCATACATGTATCGATGCATTGAAGAATGTATTGATACATCTGGGTA
1 AGAATGTATCAATACATTCATACATATATCGATACATTGAAGAATGTATCGATACATCTGGGTA
544381 CTTTTCCATA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (71 bp):
AGAATGTATCAATACATTCATACATATATCGATACATTGAAGAATGTATCGATACATCTGGGTAA
AAAGAC
Found at i:544363 original size:20 final size:21
Alignment explanation
Indices: 544317--544373 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
544307 GTAAAAAGAC
544317 AGAATGTATCGATACATTCAT
1 AGAATGTATCGATACATTCAT
* * *
544338 A-CATGTATCGATGCATTGA-
1 AGAATGTATCGATACATTCAT
*
544357 AGAATGTATTGATACAT
1 AGAATGTATCGATACAT
544374 CTGGGTACTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (21 bp):
AGAATGTATCGATACATTCAT
Found at i:545400 original size:28 final size:29
Alignment explanation
Indices: 545282--545869 Score: 795
Period size: 28 Copynumber: 20.4 Consensus size: 29
545272 TTAACTTGTA
**
545282 TGGGCTTTGAAAAGAGTTGCCACCAACTTGTG
1 TGGGCTTTGAAAAGAG-TGCCACTGAC-T-TG
*
545314 TGGGCTTTGAAAAGAGTTACCACT-AGCTTG
1 TGGGCTTTGAAAAGAG-TGCCACTGA-CTTG
*
545344 TGGGCTTTGAAAAAAGTGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
*
545373 TGGGCTTTGAAATGA-TGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
545401 TGGGCTTTGAAAAGAGTGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
545430 TGGGCTTTGAAAAG-GTGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
* * *
545458 TGAGTTTTGAAATGAGTGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
545487 TGGGCTTTG-AAAGAGTGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
*
545515 TGGGTTTTGAAAAGAGTGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
* *
545544 TGAGCTTTGAAAGGA-TGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
* *
545572 TGGGCTTTGAAAAG-GTACCAGTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
*
545600 TGGGCTTTGAAAAGAGTGCCACTGATTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
* *
545629 TGGGCTTTG-AAAGGGTGCCACTAACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
545657 CATGGGCTTTG-AAAGAGTGCCACTGACTTG
1 --TGGGCTTTGAAAAGAGTGCCACTGACTTG
*
545687 TGGGCTTTGAAAGGA-TGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
*
545715 TGGGCTTTGAAAAGAGTGCCATTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
*
545744 TGGGCTTTG-AAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
*
545772 TGGGCTTTG-AAAGAAGTGCCACTGACTTA
1 TGGGCTTTGAAAAG-AGTGCCACTGACTTG
* *
545801 TGGGCTTTG-AAAGGGTACCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG
* *
545829 TGGTCTTTGAAAAGAGTTGCCACTGACTCG
1 TGGGCTTTGAAAAGAG-TGCCACTGACTTG
545859 TGGGCTTTGAA
1 TGGGCTTTGAA
545870 GAGATGAACG
Statistics
Matches: 498, Mismatches: 44, Indels: 30
0.87 0.08 0.05
Matches are distributed among these distances:
28 230 0.46
29 178 0.36
30 65 0.13
31 2 0.00
32 23 0.05
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (29 bp):
TGGGCTTTGAAAAGAGTGCCACTGACTTG
Found at i:545405 original size:57 final size:58
Alignment explanation
Indices: 545282--545869 Score: 795
Period size: 57 Copynumber: 10.2 Consensus size: 58
545272 TTAACTTGTA
** *
545282 TGGGCTTTGAAAAGAGTTGCCACCAACTTGTGTGGGCTTTGAAAAGAGTTACCACT-AGCTTG
1 TGGGCTTTGAAAAGAG-TGCCACTGAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGA-CTTG
* *
545344 TGGGCTTTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAATGA-TGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
545401 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
* * *
545458 TGAGTTTTGAAATGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
* * *
545515 TGGGTTTTGAAAAGAGTGCCACTGACTTGTGAGCTTTGAAAGGA-TGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
* * *
545572 TGGGCTTTGAAAAG-GTACCAGTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
* *
545629 TGGGCTTTG-AAAGGGTGCCACTAACTTGCATGGGCTTTG-AAAGAGTGCCACTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTG--TGGGCTTTGAAAAGAGTGCCACTGACTTG
* *
545687 TGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCATTGACTTG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
* *
545744 TGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGAAGTGCCACTGACTTA
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-AGTGCCACTGACTTG
* * * *
545801 TGGGCTTTG-AAAGGGTACCACTGACTTGTGGTCTTTGAAAAGAGTTGCCACTGACTCG
1 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTG
545859 TGGGCTTTGAA
1 TGGGCTTTGAA
545870 GAGATGAACG
Statistics
Matches: 475, Mismatches: 36, Indels: 33
0.87 0.07 0.06
Matches are distributed among these distances:
56 49 0.10
57 305 0.64
58 68 0.14
59 29 0.06
60 1 0.00
61 8 0.02
62 15 0.03
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (58 bp):
TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTG
Found at i:547116 original size:10 final size:10
Alignment explanation
Indices: 547103--547156 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
547093 TTTTTGCTAT
547103 TTTTTTTTGG
1 TTTTTTTTGG
**
547113 -TTTTTTTAA
1 TTTTTTTTGG
547122 TTTTTTTT--
1 TTTTTTTTGG
* *
547130 TGTTTTTTGT
1 TTTTTTTTGG
547140 TTTTTTTTGG
1 TTTTTTTTGG
547150 TTTTTTT
1 TTTTTTT
547157 AGTGCAAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
8 7 0.19
9 7 0.19
10 22 0.61
ACGTcount: A:0.04, C:0.00, G:0.11, T:0.85
Consensus pattern (10 bp):
TTTTTTTTGG
Found at i:548868 original size:20 final size:20
Alignment explanation
Indices: 548845--548916 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
548835 AAGTACCTAG
*
548845 ATGTATCGATATATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
548865 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
548885 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
548905 ATGTATCGATAC
1 ATGTATCGATAC
548917 GTTCTGTCTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:555209 original size:21 final size:21
Alignment explanation
Indices: 555183--555226 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
555173 GGCCTAAGTA
*
555183 ATATACTGTATATATATAGAG
1 ATATACTATATATATATAGAG
555204 ATATACTATATATATATAGAG
1 ATATACTATATATATATAGAG
555225 AT
1 AT
555227 GTTTATAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (21 bp):
ATATACTATATATATATAGAG
Done.