Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008303.1 Hibiscus syriacus cultivar Beakdansim tig00110989_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: 1196166
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:510826 original size:22 final size:20
Alignment explanation
Indices: 510787--510848 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
510777 AAATAGATTG
510787 TATATATACATA-TATTATAGGT
1 TATATATACATAGT-TTATA--T
*
510809 TATATATATATAGTTTATAT
1 TATATATACATAGTTTATAT
510829 T-TACTATACATAGTTTATAT
1 TATA-TATACATAGTTTATAT
510849 ATACATGTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
19 2 0.06
20 17 0.47
22 16 0.44
23 1 0.03
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (20 bp):
TATATATACATAGTTTATAT
Found at i:510877 original size:35 final size:36
Alignment explanation
Indices: 510829--510911 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 36
510819 TAGTTTATAT
* *
510829 TTACTATACATAGTTT-ATATATACATGTACTATAAG
1 TTAC-ATATATAGTTTAATATATACATATACTATAAG
*
510865 TTACATATATAGTTTACATGTATACATATACTATAAG
1 TTACATATATAGTTTA-ATATATACATATACTATAAG
510902 TTACATATAT
1 TTACATATAT
510912 TAACTATTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 10 0.24
36 4 0.10
37 28 0.67
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (36 bp):
TTACATATATAGTTTAATATATACATATACTATAAG
Found at i:511140 original size:2 final size:2
Alignment explanation
Indices: 511135--511204 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
511125 TTATATAGTT
511135 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
511177 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
511205 ATTTATATGA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:511357 original size:9 final size:9
Alignment explanation
Indices: 511345--511373 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
511335 TAATCTATAG
511345 ATTACTTAT
1 ATTACTTAT
511354 ATTACTTAT
1 ATTACTTAT
511363 ATTACTTAT
1 ATTACTTAT
511372 AT
1 AT
511374 ACATACATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (9 bp):
ATTACTTAT
Found at i:511381 original size:4 final size:4
Alignment explanation
Indices: 511372--512069 Score: 1396
Period size: 4 Copynumber: 174.5 Consensus size: 4
511362 TATTACTTAT
511372 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
511420 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
511468 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
511516 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
511564 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
511612 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
511660 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
511708 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
511756 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
511804 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
511852 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
511900 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
511948 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
511996 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
512044 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
512070 GCATGCATGC
Statistics
Matches: 694, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 694 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:512141 original size:35 final size:36
Alignment explanation
Indices: 512092--512174 Score: 114
Period size: 37 Copynumber: 2.3 Consensus size: 36
512082 GCATTTATAT
* *
512092 TTACTATACATAGTTT-ATATATACATGTACTATAAG
1 TTAC-ATATATAGTTTAATATATACATATACTATAAG
*
512128 TTACATATATAGTTTACATGTATACATATACTATAAG
1 TTACATATATAGTTTA-ATATATACATATACTATAAG
512165 TTACATATAT
1 TTACATATAT
512175 TAACTATTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 10 0.24
36 4 0.10
37 28 0.67
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (36 bp):
TTACATATATAGTTTAATATATACATATACTATAAG
Found at i:512372 original size:2 final size:2
Alignment explanation
Indices: 512365--512577 Score: 426
Period size: 2 Copynumber: 106.5 Consensus size: 2
512355 ATTTCTATGA
512365 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
512407 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
512449 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
512491 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
512533 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
512575 AC A
1 AC A
512578 TACATACTGT
Statistics
Matches: 211, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 211 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:513399 original size:21 final size:20
Alignment explanation
Indices: 513360--513397 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
513350 AGTATGTCTA
513360 GGGGGTATCGATTCCCCCTT
1 GGGGGTATCGATTCCCCCTT
513380 GGGGGTATCGATTCCCCC
1 GGGGGTATCGATTCCCCC
513398 CTAAAGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.32, G:0.32, T:0.26
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTT
Found at i:514060 original size:15 final size:15
Alignment explanation
Indices: 514042--514076 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
514032 CGAGGGTATT
514042 GTAGTCCTTCAGGAC
1 GTAGTCCTTCAGGAC
*
514057 GTAGTCCTTCGGGAC
1 GTAGTCCTTCAGGAC
514072 GTAGT
1 GTAGT
514077 GGTCATACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCAGGAC
Found at i:521667 original size:8 final size:8
Alignment explanation
Indices: 521654--521679 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
521644 GTGTTACACA
521654 TACATACG
1 TACATACG
521662 TACATACG
1 TACATACG
521670 TACATACG
1 TACATACG
521678 TA
1 TA
521680 TATATACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (8 bp):
TACATACG
Found at i:521747 original size:15 final size:14
Alignment explanation
Indices: 521727--521865 Score: 81
Period size: 13 Copynumber: 9.1 Consensus size: 14
521717 ATATACTTTT
521727 TATAGTTTATACATA
1 TATAGTTTATA-ATA
521742 TATAGTTTATAATTAAA
1 TATAGTTTATAA-T--A
521759 TACATAGTTTAT-ATA
1 T--ATAGTTTATAATA
521774 TATAGTTCATATAA-A
1 TATAGTT--TATAATA
* *
521789 CATAATTTAT-ATA
1 TATAGTTTATAATA
521802 TATAGTTTATAATAAGTA
1 TATAG-TT-T-ATAA-TA
521820 TATAGTTTATAATATTAA
1 TATAGTTTAT-A-A-T-A
521838 TATAGTTTAT-ATA
1 TATAGTTTATAATA
521851 TATAGTTTAT-ATA
1 TATAGTTTATAATA
521864 TA
1 TA
521866 AACTTATATT
Statistics
Matches: 102, Mismatches: 5, Indels: 36
0.71 0.03 0.25
Matches are distributed among these distances:
12 1 0.01
13 29 0.28
14 4 0.04
15 27 0.26
16 5 0.05
17 8 0.08
18 19 0.19
19 9 0.09
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.47
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:521780 original size:13 final size:13
Alignment explanation
Indices: 521762--521865 Score: 90
Period size: 13 Copynumber: 8.1 Consensus size: 13
521752 AATTAAATAC
521762 ATAGTTTATATAT
1 ATAGTTTATATAT
* *
521775 ATAGTTCATATAAAC
1 ATAGTT--TATATAT
*
521790 ATAATTTATATAT
1 ATAGTTTATATAT
521803 ATAGTTTATA-AT
1 ATAGTTTATATAT
* *
521815 A-AGTATATAGTTT
1 ATAGTTTATA-TAT
* *
521828 ATAATAT-TA-AT
1 ATAGTTTATATAT
521839 ATAGTTTATATAT
1 ATAGTTTATATAT
521852 ATAGTTTATATAT
1 ATAGTTTATATAT
521865 A
1 A
521866 AACTTATATT
Statistics
Matches: 72, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
11 13 0.18
12 5 0.07
13 40 0.56
14 4 0.06
15 10 0.14
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (13 bp):
ATAGTTTATATAT
Found at i:521791 original size:28 final size:30
Alignment explanation
Indices: 521728--521834 Score: 121
Period size: 28 Copynumber: 3.5 Consensus size: 30
521718 TATACTTTTT
521728 ATAGTTTATACATATATAGTTTATAATTAAATAC
1 ATAGTTTAT--ATATATAGTTTATAA-T-AATAC
*
521762 ATAGTTTATATATATAGTTCAT-ATAA-AC
1 ATAGTTTATATATATAGTTTATAATAATAC
* *
521790 ATAATTTATATATATAGTTTATAATAAGTAT
1 ATAGTTTATATATATAGTTTATAATAA-TAC
521821 ATAGTTTATA-ATAT
1 ATAGTTTATATATAT
521835 TAATATAGTT
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
28 22 0.34
29 6 0.09
30 5 0.08
31 11 0.17
32 12 0.18
34 9 0.14
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (30 bp):
ATAGTTTATATATATAGTTTATAATAATAC
Found at i:521823 original size:18 final size:17
Alignment explanation
Indices: 521800--521848 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
521790 ATAATTTATA
521800 TATATAGTTTATAATAAG
1 TATATAGTTTATAAT-AG
*
521818 TATATAGTTTATAATAT
1 TATATAGTTTATAATAG
521835 TAATATAGTTTATA
1 T-ATATAGTTTATA
521849 TATATAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 2 0.07
18 27 0.93
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (17 bp):
TATATAGTTTATAATAG
Found at i:522029 original size:2 final size:2
Alignment explanation
Indices: 522018--522171 Score: 63
Period size: 2 Copynumber: 78.5 Consensus size: 2
522008 TATGTACTTA
* * * * *
522018 AT AT ACT AT AT AT AT AT AT AT AT AT AA ACT GT AT AC AT AA AT CT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * *
522062 -T AT AT AT -T AT AT AT -T AT AT AT TT AT AT AT AT AA AA AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
522100 AC AT AGT TT AT -T A- AT AA ACT AC AT AT AA ACT AT AT AT AT -T
1 AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT
* * *
522140 AT AT AT TT AT CT TT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
522172 ATTTTTTTCA
Statistics
Matches: 111, Mismatches: 28, Indels: 26
0.67 0.17 0.16
Matches are distributed among these distances:
1 8 0.07
2 98 0.88
3 5 0.05
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:522073 original size:7 final size:7
Alignment explanation
Indices: 522061--522093 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
522051 TACATAAATC
522061 TTATATA
1 TTATATA
522068 TTATATA
1 TTATATA
522075 TTATATA
1 TTATATA
522082 TT-TATA
1 TTATATA
522088 -TATATA
1 TTATATA
522094 AAAATTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 1 0.04
6 8 0.32
7 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTATATA
Found at i:522086 original size:22 final size:22
Alignment explanation
Indices: 521990--522175 Score: 76
Period size: 23 Copynumber: 8.2 Consensus size: 22
521980 GAATGTAATT
* *
521990 TATTTATATAGTA-ATATATATG
1 TATTTATATATTATATAT-TATA
* *
522012 TACTTAATATACTATATATATATA
1 TA-TTTATATATTATATAT-TATA
* * * * *
522036 TATATATAAACTGTATA-CATA
1 TATTTATATATTATATATTATA
*
522057 AATCTTATATATTATATATTATA
1 TAT-TTATATATTATATATTATA
* * *
522080 TATTTATATATATAAAAATTACA
1 TATTTATATAT-TATATATTATA
* * *
522103 TAGTTTAT-TAATAAACTACATATA
1 TA-TTTATATATTATA-TA-TTATA
* *
522127 AACTATATATATTATATATT-TA
1 TA-TTTATATATTATATATTATA
*
522149 TCTTTATATATATATATATTATA
1 TATTTATATAT-TATATATTATA
522172 -ATTT
1 TATTT
522176 TTTTCAATTT
Statistics
Matches: 121, Mismatches: 32, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
21 13 0.11
22 37 0.31
23 41 0.34
24 25 0.21
25 5 0.04
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTTATATATTATATATTATA
Found at i:523233 original size:24 final size:25
Alignment explanation
Indices: 523180--523233 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
523170 GAGAGAATCA
*
523180 TAAAAAATATATAGTTGAAAAACAT
1 TAAAAAATATAGAGTTGAAAAACAT
* *
523205 AAAAAAATATAGA-TTTAATAAA-AT
1 TAAAAAATATAGAGTTGAA-AAACAT
523229 TAAAA
1 TAAAA
523234 TTATATTAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.28
Consensus pattern (25 bp):
TAAAAAATATAGAGTTGAAAAACAT
Found at i:525544 original size:64 final size:64
Alignment explanation
Indices: 525470--525663 Score: 214
Period size: 65 Copynumber: 3.0 Consensus size: 64
525460 CGGTGAACCA
*
525470 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCT-GTGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATA-CCTAGAGTGCATCGATGCATGG
** * **
525534 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTTAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATACCTAGAGTGCATCGATGCATGG
** * * * *
525599 AGAATGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTA-A-TGCATCGATGCAT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATAC-CTAGAGTGCATCGATGCAT
525662 GG
63 GG
525664 TTGATGCATC
Statistics
Matches: 108, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
64 35 0.32
65 67 0.62
66 4 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATACCTAGAGTGCATCGATGCATGG
Found at i:525622 original size:17 final size:19
Alignment explanation
Indices: 525584--525630 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
525574 ATATTTAGAG
525584 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
525603 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
525620 TGCATTCGATG
1 TGCA-TCGATG
525631 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:525873 original size:20 final size:21
Alignment explanation
Indices: 525850--525889 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
525840 GAATCGAATA
525850 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
525870 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
525890 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:526043 original size:15 final size:15
Alignment explanation
Indices: 526023--526053 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
526013 AAACTTACTC
526023 CCCCTTACTATAACA
1 CCCCTTACTATAACA
526038 CCCCTTACTATAACA
1 CCCCTTACTATAACA
526053 C
1 C
526054 ATCTTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.42, G:0.00, T:0.26
Consensus pattern (15 bp):
CCCCTTACTATAACA
Found at i:526059 original size:15 final size:15
Alignment explanation
Indices: 526025--526059 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
526015 ACTTACTCCC
*
526025 CCTTACTATAACACC
1 CCTTACTATAACACA
526040 CCTTACTATAACACA
1 CCTTACTATAACACA
*
526055 TCTTA
1 CCTTA
526060 AATTTTCTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (15 bp):
CCTTACTATAACACA
Found at i:533087 original size:64 final size:64
Alignment explanation
Indices: 533034--533197 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
533024 CGGTGCACCA
*
533034 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * ** *
533098 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATACATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
533163 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
533198 CAATTAATTC
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 32 0.38
65 53 0.62
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:533438 original size:20 final size:21
Alignment explanation
Indices: 533415--533454 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
533405 GAATCGAATA
*
533415 TAAAATTTTAAAA-TCATTTG
1 TAAAATCTTAAAATTCATTTG
533435 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
533455 AACTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:533777 original size:20 final size:20
Alignment explanation
Indices: 533752--533794 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
533742 TCTAAGAGCC
533752 CATTTAGGAT-CATATAGATG
1 CATTTAGG-TGCATATAGATG
*
533772 CATTTAGGTGCATATAGTTG
1 CATTTAGGTGCATATAGATG
533792 CAT
1 CAT
533795 GTGGTGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGGTGCATATAGATG
Found at i:535156 original size:18 final size:18
Alignment explanation
Indices: 535123--535181 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
535113 ATTGCACTAC
535123 ACATAATCCAATTTACCACA
1 ACAT-ATCC-ATTTACCACA
*
535143 ACATATCCATTTACTACCA
1 ACATATCCATTTACCA-CA
*
535162 TCAT-TCCATTT-CCACA
1 ACATATCCATTTACCACA
535178 ACAT
1 ACAT
535182 CCATTTCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 5 0.15
17 2 0.06
18 14 0.41
19 9 0.26
20 4 0.12
ACGTcount: A:0.37, C:0.32, G:0.00, T:0.31
Consensus pattern (18 bp):
ACATATCCATTTACCACA
Found at i:537116 original size:26 final size:23
Alignment explanation
Indices: 537060--537117 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 23
537050 TATTTAAATT
* *
537060 AATTATAATTTTTTTGAATTAAA
1 AATTTTAATTTTTTTAAATTAAA
537083 AATATTTAATTTTTATATAAATTAGAA
1 AAT-TTTAATTTTT-T-TAAATTA-AA
537110 AATTTTAA
1 AATTTTAA
537118 AAATTTTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 3 0.10
24 9 0.31
25 1 0.03
26 11 0.38
27 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (23 bp):
AATTTTAATTTTTTTAAATTAAA
Found at i:537674 original size:20 final size:20
Alignment explanation
Indices: 537645--537687 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
537635 ATTCCACCAC
*
537645 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
537665 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
537685 ATG
1 ATG
537688 AGCTCTTAGA
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:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:538664 original size:96 final size:98
Alignment explanation
Indices: 538465--538672 Score: 278
Period size: 99 Copynumber: 2.1 Consensus size: 98
538455 TTCAAGTAGT
* * * * *
538465 AACCAGTAGATTATATGATCCATAAATCAGGAACGATTATTATTTTTTCCCAGTGAAAACATGAG
1 AACCAGTAGATTACATAATCCATAAATCAGGAACGATTATTA-TTTTTCCCAATGAAAACAGGAA
* *
538530 ACCAAATAACATATTTCAGTAACCATAGTTCATA
65 ACCAAAAAACACATTTCAGTAACCATAGTTCATA
* * *
538564 AACCAGTAGATTCCATAATCTATAAATCAGGAACGATTA-TA-TTTT-CCAATGAAATCAGGAAA
1 AACCAGTAGATTACATAATCCATAAATCAGGAACGATTATTATTTTTCCCAATGAAAACAGGAAA
*
538626 CCAAAAAACACATTTCAGGTAACCATAGTTTATA
66 CCAAAAAACACATTTCA-GTAACCATAGTTCATA
538660 AACCAGTAGATTA
1 AACCAGTAGATTA
538673 GTAAATTAGT
Statistics
Matches: 96, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
95 28 0.29
96 31 0.32
98 2 0.02
99 35 0.36
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (98 bp):
AACCAGTAGATTACATAATCCATAAATCAGGAACGATTATTATTTTTCCCAATGAAAACAGGAAA
CCAAAAAACACATTTCAGTAACCATAGTTCATA
Found at i:539891 original size:31 final size:31
Alignment explanation
Indices: 539824--539883 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
539814 CAATTTAAGG
*
539824 CAAAATGATTTTTGGACTTGAATTGAATTTA
1 CAAAATGATATTTGGACTTGAATTGAATTTA
539855 CAAAATG-TATTTGGACTT-AATTGAATTTA
1 CAAAATGATATTTGGACTTGAATTGAATTTA
539884 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (31 bp):
CAAAATGATATTTGGACTTGAATTGAATTTA
Found at i:539975 original size:19 final size:19
Alignment explanation
Indices: 539948--540008 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
539938 AATGTTTTTA
*
539948 TGAATAGTAATTTACTATT
1 TGAACAGTAATTTACTATT
*
539967 TGAACAGTAAATTACTATT
1 TGAACAGTAATTTACTATT
* *
539986 TGAACAGTAATTCACTGTT
1 TGAACAGTAATTTACTATT
540005 TGAA
1 TGAA
540009 GCCCGGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (19 bp):
TGAACAGTAATTTACTATT
Found at i:542617 original size:46 final size:46
Alignment explanation
Indices: 542545--543003 Score: 742
Period size: 46 Copynumber: 10.0 Consensus size: 46
542535 TTATATTAAC
* * ** *
542545 GAGTTATAGCTTCAAAAATTTATAATAAAGGAAGGAATGATGTTAT
1 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATATTAT
* * *
542591 GAGTTATAACTTCAAAAATTTGTAATAAAGGTAGGAATGATATTAT
1 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATATTAT
* * **
542637 GAATTATAGCTTCGGAAATTTGTAATAAAGGTGATAATGATATTAT
1 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATATTAT
*
542683 GAGTTATAGCTTCGGAAATTTGTAATAAAGGTGGGAATGATATTAT
1 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATATTAT
* *
542729 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATCATATTAC
1 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATATTAT
542775 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATATTAT
1 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATATTAT
542821 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATA-T-T
1 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATATTAT
542865 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATATTAT
1 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATATTAT
*
542911 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTAGGAATGATATTAT
1 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATATTAT
* *
542957 GAGTTACAGCTTCAAAAATTTGTAATAAAGGTGGGAATGATATTAT
1 GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATATTAT
543003 G
1 G
543004 TGTGAGTTTG
Statistics
Matches: 388, Mismatches: 23, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
44 43 0.11
45 2 0.01
46 343 0.88
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (46 bp):
GAGTTATAGCTTCGAAAATTTGTAATAAAGGTGGGAATGATATTAT
Found at i:543263 original size:54 final size:54
Alignment explanation
Indices: 543191--543298 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
543181 ACTCGACTCA
*
543191 ATATATATATATAAGTTTAAAATTTTCATGAGATAACTTTGATGTATCTATGAT
1 ATATATATATATAAGTTTAAAATTTTCATGAGATAACTTTGATATATCTATGAT
*
543245 ATATATATATATAAGTTTAAAATTTTCATGAGATAACTTTGATATATCTCTGAT
1 ATATATATATATAAGTTTAAAATTTTCATGAGATAACTTTGATATATCTATGAT
543299 GGCGGTAGCC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.44
Consensus pattern (54 bp):
ATATATATATATAAGTTTAAAATTTTCATGAGATAACTTTGATATATCTATGAT
Found at i:543635 original size:21 final size:21
Alignment explanation
Indices: 543611--543664 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
543601 CGTAAATATT
** *
543611 CATTTTAGGTAGTGAAATTAA
1 CATTTTAGGTAGAAAAAATAA
*
543632 CATTTCCA-GTAGAAAAAATAA
1 CATTT-TAGGTAGAAAAAATAA
543653 CATTTTAGGTAG
1 CATTTTAGGTAG
543665 CACCCTACCA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (21 bp):
CATTTTAGGTAGAAAAAATAA
Found at i:544227 original size:16 final size:16
Alignment explanation
Indices: 544186--544231 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
544176 TGATAAGTAT
*
544186 TTATTTTA-AAATTCAA
1 TTATTTTATTAATT-AA
*
544202 TT-TTTAATTAATTAA
1 TTATTTTATTAATTAA
544217 TTATTTTATTAATTA
1 TTATTTTATTAATTA
544232 TGTTTATCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTTTATTAATTAA
Found at i:549483 original size:8 final size:8
Alignment explanation
Indices: 549466--549589 Score: 54
Period size: 8 Copynumber: 14.5 Consensus size: 8
549456 CAATCAGAAC
*
549466 AAAAAGAG
1 AAAAAAAG
549474 AAAAAAAG
1 AAAAAAAG
**
549482 AATCAAAG
1 AAAAAAAG
549490 TAAAAAAAG
1 -AAAAAAAG
549499 CAAAAAAA-
1 -AAAAAAAG
* *
549507 AAAGAAAC
1 AAAAAAAG
549515 AAAAAAGAGCG
1 AAAAAA-A--G
*
549526 AAAAAGAG
1 AAAAAAAG
* *
549534 ACAAAGAG
1 AAAAAAAG
*
549542 ACAAAGAGAAA
1 A-AAA-A-AAG
549553 AAAAAAAG
1 AAAAAAAG
*
549561 GAAAAAAG
1 AAAAAAAG
549569 AAAAAGAA-
1 AAAAA-AAG
549577 AAAGAAAAG
1 AAA-AAAAG
549586 AAAA
1 AAAA
549590 GAAAAGGGGA
Statistics
Matches: 88, Mismatches: 17, Indels: 22
0.69 0.13 0.17
Matches are distributed among these distances:
7 6 0.07
8 46 0.52
9 24 0.27
10 5 0.06
11 7 0.08
ACGTcount: A:0.77, C:0.05, G:0.17, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:549507 original size:11 final size:11
Alignment explanation
Indices: 549491--549594 Score: 64
Period size: 12 Copynumber: 8.5 Consensus size: 11
549481 GAATCAAAGT
549491 AAAAAAAGCAAA
1 AAAAAAAG-AAA
549503 AAAAAAAGAAA
1 AAAAAAAGAAA
* **
549514 CAAAAAAGAGCG
1 AAAAAAAGA-AA
*
549526 AAAAAGAGACAA
1 AAAAAAAGA-AA
549538 AGAGACAAAGAGAAA
1 A-A-A-AAA-AGAAA
549553 AAAAAAAGGAAAA
1 AAAAAAA-G-AAA
549566 AAGAAAAAGAAA
1 AA-AAAAAGAAA
*
549578 AAGAAAAGAAA
1 AAAAAAAGAAA
549589 AGAAAA
1 A-AAAA
549595 GGGGACGAGA
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
11 21 0.29
12 28 0.39
13 8 0.11
14 7 0.10
15 5 0.07
16 3 0.04
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:549520 original size:50 final size:50
Alignment explanation
Indices: 549466--549579 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 50
549456 CAATCAGAAC
549466 AAAAAGAGAAAAAAAGA-ATCAAAGTA-A-AAAAAGCAAAAAAAAAA-GAAACA
1 AAAAAGAGAAAAAAAGAGA-CAAAG-AGACAAAAAG-AAAAAAAAAAGGAAA-A
** *
549516 AAAAAGAGCGAAAAAGAGACAAAGAGACAAAGAGAAAAAAAAAAGGAAAA
1 AAAAAGAGAAAAAAAGAGACAAAGAGACAAAAAGAAAAAAAAAAGGAAAA
*
549566 AAGAAAAAGAAAAA
1 AA-AAAGAGAAAAA
549580 GAAAAGAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
49 1 0.02
50 34 0.64
51 18 0.34
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (50 bp):
AAAAAGAGAAAAAAAGAGACAAAGAGACAAAAAGAAAAAAAAAAGGAAAA
Found at i:549565 original size:6 final size:6
Alignment explanation
Indices: 549548--549594 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
549538 AGAGACAAAG
549548 AGAAAA A-AAAA AGGAAAAA AGAAAA AGAAAA AG-AAA AG-AAA AGAAAA
1 AGAAAA AGAAAA A-G-AAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
549595 GGGGACGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 15 0.41
6 16 0.43
7 1 0.03
8 5 0.14
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:549572 original size:19 final size:19
Alignment explanation
Indices: 549493--549584 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 19
549483 ATCAAAGTAA
*
549493 AAAAAGCAAAAA-AAAAAG
1 AAAAAGAAAAAAGAAAAAG
*
549511 AAACAA-AAAAGAGCGAAAAAG
1 AAA-AAGAAAA-A-AGAAAAAG
549532 AGACAAAGAGACAAAGAGAAAAA-
1 A-A-AAAGA-A-AAA-AGAAAAAG
549555 AAAAAGGAAAAAAGAAAAAG
1 AAAAA-GAAAAAAGAAAAAG
549575 AAAAAGAAAA
1 AAAAAGAAAA
549585 GAAAAGAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 21
0.71 0.04 0.25
Matches are distributed among these distances:
18 6 0.10
19 15 0.25
20 8 0.13
21 11 0.18
22 6 0.10
23 3 0.05
24 9 0.15
25 2 0.03
ACGTcount: A:0.77, C:0.05, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAAGAAAAAG
Found at i:549574 original size:27 final size:28
Alignment explanation
Indices: 549504--549594 Score: 69
Period size: 27 Copynumber: 3.1 Consensus size: 28
549494 AAAAGCAAAA
**
549504 AAAAAAGAAACAA-AAAAGAGCGAAAAAGAG
1 AAAAAAGAAA-AAGAAAA-AGAAAAAAAG-G
* * *
549534 ACAAAGAGACAAAGAGAAA-AAAAAAAGG
1 A-AAAAAGAAAAAGAAAAAGAAAAAAAGG
*
549562 AAAAAAGAAAAAGAAAAAGAAAAGAAAAG
1 AAAAAAGAAAAAGAAAAAGAAAA-AAAGG
549591 AAAA
1 AAAA
549595 GGGGACGAGA
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
27 14 0.29
28 6 0.12
29 14 0.29
30 4 0.08
31 10 0.21
ACGTcount: A:0.77, C:0.04, G:0.19, T:0.00
Consensus pattern (28 bp):
AAAAAAGAAAAAGAAAAAGAAAAAAAGG
Found at i:549952 original size:12 final size:12
Alignment explanation
Indices: 549913--549943 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
549903 TAGGGGTTCT
549913 TTGATGACAAAC
1 TTGATGACAAAC
549925 TTGATGACAAAC
1 TTGATGACAAAC
549937 TTGATGA
1 TTGATGA
549944 TAAGCTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (12 bp):
TTGATGACAAAC
Found at i:549985 original size:43 final size:43
Alignment explanation
Indices: 549937--550255 Score: 306
Period size: 43 Copynumber: 7.2 Consensus size: 43
549927 GATGACAAAC
*
549937 TTGATGATAAGCTTGAAGGACCATCGTGATATGTAGGGGTTCT
1 TTGATGATAAGCTTGAAGAACCATCGTGATATGTAGGGGTTCT
*
549980 TTGATGACAAGCTTG-AGAAACCATCGTGATATGTAGGGGTT-T
1 TTGATGATAAGCTTGAAG-AACCATCGTGATATGTAGGGGTTCT
* * * * *
550022 CTTGATGACAATCTTGAGGGACCATCGTGATATGTAAGGGTTCCTTAT
1 -TTGATGATAAGCTTGAAGAACCATCGTGATATGTAGGGGTT-C---T
550070 AACAAACTTGATGATAAGCTTGAAGAACCATCGTGATATGTAGGGGTTCT
1 -------TTGATGATAAGCTTGAAGAACCATCGTGATATGTAGGGGTTCT
* *
550120 TTGATGATAGGCTTG-AGAAACCATTGTGATATGTAGGGGTTCT
1 TTGATGATAAGCTTGAAG-AACCATCGTGATATGTAGGGGTTCT
*
550163 TTGATGATAGGCTTG-AGAAACCATCGTGATATGTAGGGGTT-T
1 TTGATGATAAGCTTGAAG-AACCATCGTGATATGTAGGGGTTCT
* ** * * * *
550205 CTTGATGACAATTTTGAGGGACTATCGTGATATGTAGGGGTTCC
1 -TTGATGATAAGCTTGAAGAACCATCGTGATATGTAGGGGTTCT
550249 TTGATGA
1 TTGATGA
550256 CAGACTTGAT
Statistics
Matches: 236, Mismatches: 22, Indels: 36
0.80 0.07 0.12
Matches are distributed among these distances:
42 6 0.03
43 188 0.80
44 2 0.01
48 1 0.00
50 1 0.00
53 1 0.00
54 37 0.16
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (43 bp):
TTGATGATAAGCTTGAAGAACCATCGTGATATGTAGGGGTTCT
Found at i:550100 original size:97 final size:95
Alignment explanation
Indices: 549980--550313 Score: 343
Period size: 97 Copynumber: 3.6 Consensus size: 95
549970 TAGGGGTTCT
*
549980 TTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGACAATCTTGAGGGACC
1 TTGATGATAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGACAATCTTGAGGGACC
*
550045 ATCGTGATATGTAAGGGTTCCTTATAACAAAC
66 ATCGTGATATGTAGGGGTTCCTTAT-AC-AAC
* ** **
550077 TTGATGATAAGCTTGA-AGAACCATCGTGATATGTAGGGG-TTCTTTGATGATAGGCTTGAGAAA
1 TTGATGATAAGCTTGAGA-AACCATCGTGATATGTAGGGGTTTC-TTGATGACAATCTTGAGGGA
*
550140 CCATTGTGATATGTAGGGGTT-C---T-----
64 CCATCGTGATATGTAGGGGTTCCTTATACAAC
* * *
550163 TTGATGATAGGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGACAATTTTGAGGGACT
1 TTGATGATAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGACAATCTTGAGGGACC
550228 ATCGTGATATGTAGGGGTTCCTTGATGACAGAC
66 ATCGTGATATGTAGGGGTTCCTT-AT-ACA-AC
** * ** * *
550261 TTGATGA-ATA-CTTGAGGGACCAACGTGATAAATAGGGGTTCCTTGGTGACAAT
1 TTGATGATA-AGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGACAAT
550314 TAAGAAACTG
Statistics
Matches: 195, Mismatches: 25, Indels: 34
0.77 0.10 0.13
Matches are distributed among these distances:
86 69 0.35
87 5 0.03
91 1 0.01
93 1 0.01
96 5 0.03
97 107 0.55
98 7 0.04
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (95 bp):
TTGATGATAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGACAATCTTGAGGGACC
ATCGTGATATGTAGGGGTTCCTTATACAAC
Found at i:550186 original size:140 final size:140
Alignment explanation
Indices: 549931--550203 Score: 440
Period size: 140 Copynumber: 1.9 Consensus size: 140
549921 AAACTTGATG
*
549931 ACAAACTTGATGATAAGCTTGAAGGACCATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTGA
1 ACAAACTTGATGATAAGCTTGAAGAACCATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTGA
* **
549996 GAAACCATCGTGATATGTAGGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAAGG
66 GAAACCATCGTGATATGTAGGGGTTTCTTGATGACAAGCTTGAGAAACCATCGTGATATGTAAGG
550061 GTTCCTTATA
131 GTTCCTTATA
* *
550071 ACAAACTTGATGATAAGCTTGAAGAACCATCGTGATATGTAGGGGTTCTTTGATGATAGGCTTGA
1 ACAAACTTGATGATAAGCTTGAAGAACCATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTGA
* * * *
550136 GAAACCATTGTGATATGTAGGGG-TTCTTTGATGATAGGCTTGAGAAACCATCGTGATATGTAGG
66 GAAACCATCGTGATATGTAGGGGTTTC-TTGATGACAAGCTTGAGAAACCATCGTGATATGTAAG
550200 GGTT
130 GGTT
550204 TCTTGATGAC
Statistics
Matches: 122, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
139 3 0.02
140 119 0.98
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (140 bp):
ACAAACTTGATGATAAGCTTGAAGAACCATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTGA
GAAACCATCGTGATATGTAGGGGTTTCTTGATGACAAGCTTGAGAAACCATCGTGATATGTAAGG
GTTCCTTATA
Found at i:550248 original size:183 final size:183
Alignment explanation
Indices: 549937--550301 Score: 547
Period size: 183 Copynumber: 2.0 Consensus size: 183
549927 GATGACAAAC
*
549937 TTGATGATAAGCTTGAAGGACCATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTGAGAAACC
1 TTGATGATAAGCTTGAAGAACCATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTGAGAAACC
550002 ATCGTGATATGTAGGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAAGGGTTCCT
66 ATCGTGATATGTAGGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAAGGGTTCCT
* **
550067 T-ATAACAAACTTGATG-ATAAGCTTGAAGAACCATCGTGATATGTAGGGGTTCT
131 TGATAACAAACTTGATGAAT-A-CTTGAAGAACCAACGTGATAAATAGGGGTTCT
* * * *
550120 TTGATGATAGGCTTG-AGAAACCATTGTGATATGTAGGGGTTCTTTGATGATAGGCTTGAGAAAC
1 TTGATGATAAGCTTGAAG-AACCATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTGAGAAAC
* * *
550184 CATCGTGATATGTAGGGGTTTCTTGATGACAATTTTGAGGGACTATCGTGATATGTAGGGGTTCC
65 CATCGTGATATGTAGGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAAGGGTTCC
* * * *
550249 TTGATGACAGACTTGATGAATACTTGAGGGACCAACGTGATAAATAGGGGTTC
130 TTGATAACAAACTTGATGAATACTTGAAGAACCAACGTGATAAATAGGGGTTC
550302 CTTGGTGACA
Statistics
Matches: 164, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
182 2 0.01
183 146 0.89
184 14 0.09
185 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (183 bp):
TTGATGATAAGCTTGAAGAACCATCGTGATATGTAGGGGTTCTTTGATGACAAGCTTGAGAAACC
ATCGTGATATGTAGGGGTTTCTTGATGACAATCTTGAGGGACCATCGTGATATGTAAGGGTTCCT
TGATAACAAACTTGATGAATACTTGAAGAACCAACGTGATAAATAGGGGTTCT
Found at i:552594 original size:23 final size:23
Alignment explanation
Indices: 552568--552614 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
552558 CACCATTATT
*
552568 TTTTTTAATATATAGAAATTTAG
1 TTTTTTAATACATAGAAATTTAG
552591 TTTTTTAATACATAGAAATTTAG
1 TTTTTTAATACATAGAAATTTAG
552614 T
1 T
552615 AATCTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (23 bp):
TTTTTTAATACATAGAAATTTAG
Found at i:553956 original size:26 final size:28
Alignment explanation
Indices: 553895--553956 Score: 65
Period size: 31 Copynumber: 2.2 Consensus size: 28
553885 GAGTATTGCT
* *
553895 GAGCTCGACTCGACTCGAAAACTTTGAAAT
1 GAGCTCGACTCGACTCGAAAACTTCG--AC
553925 GAAGCTCGACTCGACTCGAAAAC-TCG-C
1 G-AGCTCGACTCGACTCGAAAACTTCGAC
553952 GAGCT
1 GAGCT
553957 TAAAATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 4 0.14
27 1 0.03
30 3 0.10
31 21 0.72
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTTCGAC
Found at i:557697 original size:15 final size:14
Alignment explanation
Indices: 557668--557702 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
557658 ATATTATAAT
557668 ATATTTTTATCAAA
1 ATATTTTTATCAAA
*
557682 ATATTATTTATTAAA
1 ATATT-TTTATCAAA
557697 ATATTT
1 ATATTT
557703 AAAGTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (14 bp):
ATATTTTTATCAAA
Found at i:557747 original size:23 final size:22
Alignment explanation
Indices: 557716--557760 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
557706 GTATATTTAT
557716 TAATATTTTTAATAATATAATA
1 TAATATTTTTAATAATATAATA
*
557738 TAATATTTTTTAATATTATAATA
1 TAATA-TTTTTAATAATATAATA
557761 ATATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATATTTTTAATAATATAATA
Found at i:557763 original size:31 final size:32
Alignment explanation
Indices: 557708--557781 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
557698 TATTTAAAGT
* * *
557708 ATATTTATTAATATTTTTAATAATATAATATA
1 ATATTTTTTAATATTTATAATAATATAAAATA
557740 ATATTTTTTAATA-TTATAATAATATAAAATA
1 ATATTTTTTAATATTTATAATAATATAAAATA
*
557771 TTATATTTTTA
1 ATAT-TTTTTA
557782 TTTTAATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 19 0.51
32 18 0.49
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
ATATTTTTTAATATTTATAATAATATAAAATA
Found at i:560576 original size:30 final size:30
Alignment explanation
Indices: 560540--560608 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
560530 TGATTATGGA
*
560540 CGGTTAACCGTACCATTTAGCTTAAACAGT
1 CGGTTAACCGTACCATTTAGCCTAAACAGT
560570 CGGTTAACCGTACCATTTAGCCTAAACAGT
1 CGGTTAACCGTACCATTTAGCCTAAACAGT
560600 CGGTTAACC
1 CGGTTAACC
560609 ATTATAACGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (30 bp):
CGGTTAACCGTACCATTTAGCCTAAACAGT
Found at i:560828 original size:51 final size:51
Alignment explanation
Indices: 560765--560998 Score: 310
Period size: 51 Copynumber: 4.6 Consensus size: 51
560755 AAAAATGCAA
* * * * *
560765 CACTTAACACATACTTACACCTGTGTAAATGAATAAAATAAACAAGTGTAT
1 CACTTAACACATACTTACACCAGTGTAAGTAAATAAAATAAAAAAGTGTAG
* * * *
560816 CACTTAAGACATACTTACACCAGTGTAACTAAATAAAACAAAAAAGTATAG
1 CACTTAACACATACTTACACCAGTGTAAGTAAATAAAATAAAAAAGTGTAG
* *
560867 CACTTAACACATAC-TACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAG
1 CACTTAACACATACTTACACCAGTGTAAGTAAATAAAATAAAAAAGTGTAG
* * *
560917 CACTTAATACATATTTACAACAGTGTAAGTAAATAAAATAAAAAAGTGTAG
1 CACTTAACACATACTTACACCAGTGTAAGTAAATAAAATAAAAAAGTGTAG
*
560968 CACTTAATACATACTTACACC-GATGTAAGTA
1 CACTTAACACATACTTACACCAG-TGTAAGTA
560999 TGTATATCTC
Statistics
Matches: 160, Mismatches: 21, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
50 44 0.28
51 116 0.73
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (51 bp):
CACTTAACACATACTTACACCAGTGTAAGTAAATAAAATAAAAAAGTGTAG
Found at i:560929 original size:101 final size:102
Alignment explanation
Indices: 560765--560997 Score: 351
Period size: 101 Copynumber: 2.3 Consensus size: 102
560755 AAAAATGCAA
* * * *
560765 CACTTAACACATACTTACACCTGTGTAAATGAATAAAATAAACAAGTGTATCACTTAAGACATAC
1 CACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAAGACATAC
*
560830 TTACACCAGTGTAACTAAATAAAACAAAAAAGTATAG
66 TTACAACAGTGTAACTAAATAAAACAAAAAAGTATAG
* *
560867 CACTTAACACATAC-TACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAATACATAT
1 CACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAAGACATAC
* * *
560931 TTACAACAGTGTAAGTAAATAAAATAAAAAAGTGTAG
66 TTACAACAGTGTAACTAAATAAAACAAAAAAGTATAG
* *
560968 CACTTAATACATACTTACACCGATGTAAGT
1 CACTTAACACATACTTACACCGGTGTAAGT
560998 ATGTATATCT
Statistics
Matches: 118, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 90 0.76
102 28 0.24
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (102 bp):
CACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAAGACATAC
TTACAACAGTGTAACTAAATAAAACAAAAAAGTATAG
Found at i:561739 original size:30 final size:30
Alignment explanation
Indices: 561699--561774 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
561689 TGGTAGATGA
561699 ACTTAATTGATTTTTTGGTTAAGTTCAAGG
1 ACTTAATTGATTTTTTGGTTAAGTTCAAGG
*
561729 ACTTATTTGATTTTTTGGTTAAGTTCAAGG
1 ACTTAATTGATTTTTTGGTTAAGTTCAAGG
*
561759 ACTTACTTGATTTTTT
1 ACTTAATTGATTTTTT
561775 AAAAAGTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.24, C:0.08, G:0.17, T:0.51
Consensus pattern (30 bp):
ACTTAATTGATTTTTTGGTTAAGTTCAAGG
Found at i:561782 original size:29 final size:28
Alignment explanation
Indices: 561719--561805 Score: 84
Period size: 30 Copynumber: 3.0 Consensus size: 28
561709 TTTTTTGGTT
***
561719 AAGTTCAAGGACTTATTTGATTTTTTGGTT
1 AAGTTCAAGGACTTA-TTGATTTTTT-AAA
561749 AAGTTCAAGGACTTACTTGATTTTTTAAA
1 AAGTTCAAGGACTTA-TTGATTTTTTAAA
* * * *
561778 AAGTTTAAAGACTTATTTATATTTTAAA
1 AAGTTCAAGGACTTATTGATTTTTTAAA
561806 GAATAAGAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 11 0.22
29 13 0.27
30 25 0.51
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (28 bp):
AAGTTCAAGGACTTATTGATTTTTTAAA
Found at i:562787 original size:21 final size:21
Alignment explanation
Indices: 562762--562801 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
562752 TCAACTTGAC
*
562762 TCGTTACTTGTTAAGCTCAAT
1 TCGTTACTCGTTAAGCTCAAT
*
562783 TCGTTGCTCGTTAAGCTCA
1 TCGTTACTCGTTAAGCTCA
562802 CTAAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGTTACTCGTTAAGCTCAAT
Found at i:564484 original size:21 final size:22
Alignment explanation
Indices: 564436--564484 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
564426 GGCTATGTAT
*
564436 ACATT-TCACATTTTCATATCC
1 ACATTATCACATTTTCATATAC
* *
564457 CCTTTATCAC-TTTTCATATAC
1 ACATTATCACATTTTCATATAC
564478 ACATTAT
1 ACATTAT
564485 TCACCTCACA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.45
Consensus pattern (22 bp):
ACATTATCACATTTTCATATAC
Found at i:570800 original size:20 final size:20
Alignment explanation
Indices: 570775--570813 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
570765 TCATAAACCT
*
570775 TAAACCTTATAATTT-ATACA
1 TAAACCCTA-AATTTGATACA
570795 TAAACCCTAAATTTGATAC
1 TAAACCCTAAATTTGATAC
570814 CATACAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAACCCTAAATTTGATACA
Found at i:573394 original size:29 final size:29
Alignment explanation
Indices: 573361--573489 Score: 132
Period size: 29 Copynumber: 4.4 Consensus size: 29
573351 TAGGATATGT
* * *
573361 ATATAATCCCATACAAAATAAGGACATAG
1 ATATAATCCCATGCAAAATCAGGACAGAG
** * ** *
573390 ATATAATTTCATGCAGAATCAGGATGGGG
1 ATATAATCCCATGCAAAATCAGGACAGAG
573419 ATATAATCCCATGCAAAATCAGGACAGAG
1 ATATAATCCCATGCAAAATCAGGACAGAG
* * * * *
573448 ATATAATCCCAGGCAGAATTAGGACGGGG
1 ATATAATCCCATGCAAAATCAGGACAGAG
573477 ATATAATCCCATG
1 ATATAATCCCATG
573490 TATAATCAAG
Statistics
Matches: 79, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 79 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (29 bp):
ATATAATCCCATGCAAAATCAGGACAGAG
Found at i:573497 original size:58 final size:58
Alignment explanation
Indices: 573361--573489 Score: 186
Period size: 58 Copynumber: 2.2 Consensus size: 58
573351 TAGGATATGT
* * * ** * *
573361 ATATAATCCCATACAAAATAAGGACATAGATATAATTTCATGCAGAATCAGGATGGGG
1 ATATAATCCCATGCAAAATCAGGACAGAGATATAATCCCAGGCAGAATCAGGACGGGG
*
573419 ATATAATCCCATGCAAAATCAGGACAGAGATATAATCCCAGGCAGAATTAGGACGGGG
1 ATATAATCCCATGCAAAATCAGGACAGAGATATAATCCCAGGCAGAATCAGGACGGGG
573477 ATATAATCCCATG
1 ATATAATCCCATG
573490 TATAATCAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 63 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (58 bp):
ATATAATCCCATGCAAAATCAGGACAGAGATATAATCCCAGGCAGAATCAGGACGGGG
Found at i:575997 original size:2 final size:2
Alignment explanation
Indices: 575992--576018 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
575982 TTATTCTTAT
575992 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 T
576019 TAATCATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:576199 original size:15 final size:15
Alignment explanation
Indices: 576179--576210 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
576169 ATATATTTCA
*
576179 TTTTATCTTTTATTT
1 TTTTATCTTCTATTT
576194 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
576209 TT
1 TT
576211 ATTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATCTTCTATTT
Found at i:576227 original size:20 final size:20
Alignment explanation
Indices: 576180--576233 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
576170 TATATTTCAT
*
576180 TTTATCTTTTATTTTTTTATC
1 TTTAT-TTTTATTTTTGTATC
576201 TTCTATTTTTATTTTTGTAT-
1 TT-TATTTTTATTTTTGTATC
*
576221 TGTTATTGTTATT
1 T-TTATTTTTATT
576234 ATCTTCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 10 0.34
21 16 0.55
22 3 0.10
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (20 bp):
TTTATTTTTATTTTTGTATC
Found at i:576279 original size:33 final size:32
Alignment explanation
Indices: 576206--576281 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
576196 TTATCTTCTA
576206 TTTTTATTTTTGTATTGTTATTGTTATTATCT
1 TTTTTATTTTTGTATTGTTATTGTTATTATCT
* *
576238 TCTTTATTTTATGTATT-TTA-T-TTATATATAT
1 TTTTTATTTT-TGTATTGTTATTGTTAT-TATCT
*
576269 TTTTTATATTTGT
1 TTTTTATTTTTGT
576282 TTTTGTGCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
30 7 0.18
31 13 0.34
32 12 0.32
33 6 0.16
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.71
Consensus pattern (32 bp):
TTTTTATTTTTGTATTGTTATTGTTATTATCT
Found at i:586651 original size:7 final size:7
Alignment explanation
Indices: 586638--586840 Score: 343
Period size: 7 Copynumber: 28.9 Consensus size: 7
586628 GCGTCCTAAG
586638 TAAAAAA
1 TAAAAAA
*
586645 CAAAAAA
1 TAAAAAA
*
586652 CAAAAAA
1 TAAAAAA
*
586659 CAAAAAA
1 TAAAAAA
*
586666 CAAAAAA
1 TAAAAAA
586673 TAAAAAA
1 TAAAAAA
586680 TAAAAAA
1 TAAAAAA
586687 TAAAAAA
1 TAAAAAA
586694 TAAAAAA
1 TAAAAAA
586701 TAAAAAA
1 TAAAAAA
586708 TAAAAAA
1 TAAAAAA
586715 TAAAAAA
1 TAAAAAA
586722 TAAAAAA
1 TAAAAAA
586729 TAAAAAA
1 TAAAAAA
586736 TAAAAAA
1 TAAAAAA
586743 TAAAAAA
1 TAAAAAA
586750 TAAAAAA
1 TAAAAAA
586757 TAAAAAA
1 TAAAAAA
586764 TAAAAAA
1 TAAAAAA
586771 TAAAAAA
1 TAAAAAA
586778 TAAAAAA
1 TAAAAAA
586785 TAAAAAA
1 TAAAAAA
586792 TAAAAAA
1 TAAAAAA
586799 TAAAAAA
1 TAAAAAA
586806 TAAAAAA
1 TAAAAAA
586813 TAAAAAA
1 TAAAAAA
*
586820 AAAAAAA
1 TAAAAAA
*
586827 AAAAAAA
1 TAAAAAA
586834 TGAAAAA
1 T-AAAAA
586841 CGTTTAGAAT
Statistics
Matches: 191, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
7 186 0.97
8 5 0.03
ACGTcount: A:0.86, C:0.02, G:0.00, T:0.11
Consensus pattern (7 bp):
TAAAAAA
Found at i:586840 original size:1 final size:1
Alignment explanation
Indices: 586639--586833 Score: 165
Period size: 1 Copynumber: 195.0 Consensus size: 1
586629 CGTCCTAAGT
* * * * * * * * *
586639 AAAAAACAAAAAACAAAAAACAAAAAACAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * *
586704 AAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
586769 AATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAATAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
586834 TGAAAAACGT
Statistics
Matches: 144, Mismatches: 50, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 144 1.00
ACGTcount: A:0.87, C:0.02, G:0.00, T:0.11
Consensus pattern (1 bp):
A
Found at i:588095 original size:110 final size:110
Alignment explanation
Indices: 587938--588144 Score: 306
Period size: 110 Copynumber: 1.9 Consensus size: 110
587928 GCTTCCCAGT
* * *
587938 TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAAATTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* *
588003 CAATAAAGAGGCGACTGATTGTCAACAAACAACGTTTCAGTTTCA
66 CAACAAAGAGGCGACTGACTGTCAACAAACAACGTTTCAGTTTCA
* *
588048 TTCAGAGTCAAATTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAAATTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * * * *
588113 TAGCGAAGGGGTGACTGACTGTCAACAAACAA
66 CAACAAAGAGGCGACTGACTGTCAACAAACAA
588145 TTTCCAGAGC
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
110 85 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (110 bp):
TTCAGAGCCAAATTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACAAAGAGGCGACTGACTGTCAACAAACAACGTTTCAGTTTCA
Found at i:589305 original size:70 final size:70
Alignment explanation
Indices: 589193--589330 Score: 267
Period size: 70 Copynumber: 2.0 Consensus size: 70
589183 AAATCGGAGC
*
589193 AAAAAACGTGATTCTCGAAGAGGAAAATAAGTAAAAAAGGTAAAAGCTTGTACCTTTATCGCTTT
1 AAAAAACGTGATTCTCGAAGAGGAAAATAAGTAAAAAAGGTAAAACCTTGTACCTTTATCGCTTT
589258 AAGGA
66 AAGGA
589263 AAAAAACGTGATTCTCGAAGAGGAAAATAAGTAAAAAAGGTAAAACCTTGTACCTTTATCGCTTT
1 AAAAAACGTGATTCTCGAAGAGGAAAATAAGTAAAAAAGGTAAAACCTTGTACCTTTATCGCTTT
589328 AAG
66 AAG
589331 TCTTTGCATG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (70 bp):
AAAAAACGTGATTCTCGAAGAGGAAAATAAGTAAAAAAGGTAAAACCTTGTACCTTTATCGCTTT
AAGGA
Found at i:589594 original size:20 final size:20
Alignment explanation
Indices: 589571--589663 Score: 159
Period size: 20 Copynumber: 4.7 Consensus size: 20
589561 CGATAGTCAG
*
589571 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
589591 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
589611 ATTCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
589631 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
589651 ATTCGCATTGCGA
1 ATTCGCATTGCGA
589664 ATTAGGAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:589896 original size:2 final size:2
Alignment explanation
Indices: 589891--589940 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
589881 TTATTCTTAT
*
589891 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
589933 TA TA TA TA
1 TA TA TA TA
589941 ATCATATTCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:590006 original size:2 final size:2
Alignment explanation
Indices: 589999--590036 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
589989 TATCGTTATT
589999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
590037 CTTTTAATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:591335 original size:29 final size:29
Alignment explanation
Indices: 591303--591505 Score: 223
Period size: 29 Copynumber: 7.0 Consensus size: 29
591293 GCAGAAACAT
* * ** *
591303 GACAGGGATATAATCCTATGTAGAGTAAG
1 GACATGGATATAATCCCATACAGAGTCAG
591332 GACATGGATATAATCCCATACAGAGTCAG
1 GACATGGATATAATCCCATACAGAGTCAG
591361 GACATGGATATAATCCCATACAGAGTCAG
1 GACATGGATATAATCCCATACAGAGTCAG
591390 GACATGGATATAATCCCATACAGAGTCAG
1 GACATGGATATAATCCCATACAGAGTCAG
* * * *
591419 GACATGGATATAATCCTATGCAGAATTAG
1 GACATGGATATAATCCCATACAGAGTCAG
* * * *
591448 GACGAT-GATATAATCTCATGCATAATCAG
1 GAC-ATGGATATAATCCCATACAGAGTCAG
* *
591477 G--ATGGTGATATAATCCCTTACAGAATCAG
1 GACAT-G-GATATAATCCCATACAGAGTCAG
591506 AAATACACCA
Statistics
Matches: 153, Mismatches: 17, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
26 2 0.01
29 149 0.97
30 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.24
Consensus pattern (29 bp):
GACATGGATATAATCCCATACAGAGTCAG
Found at i:591421 original size:87 final size:87
Alignment explanation
Indices: 591280--591505 Score: 224
Period size: 87 Copynumber: 2.6 Consensus size: 87
591270 ACATGATGGA
* * * * * * * ** *
591280 GATATGATCCAATGCAGAAACATGACAGGGATATAATCCTATGTAGAGTAAGGACATGGATATAA
1 GATATAATCCCATACAGAATCAGGACATGGATATAATCCCATACAGAGTCAGGACATGGATATAA
*
591345 TCCCATACAGAGTCAGGAC-AT
66 TCCCATACAGAATCAGGACGAT
*
591366 GGATATAATCCCATACAGAGTCAGGACATGGATATAATCCCATACAGAGTCAGGACATGGATATA
1 -GATATAATCCCATACAGAATCAGGACATGGATATAATCCCATACAGAGTCAGGACATGGATATA
* * *
591431 ATCCTATGCAGAATTAGGACGAT
65 ATCCCATACAGAATCAGGACGAT
* * * * *
591454 GATATAATCTCATGCATAATCAGG--ATGGTGATATAATCCCTTACAGAATCAG
1 GATATAATCCCATACAGAATCAGGACAT-G-GATATAATCCCATACAGAGTCAG
591506 AAATACACCA
Statistics
Matches: 115, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
85 2 0.02
86 1 0.01
87 110 0.96
88 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (87 bp):
GATATAATCCCATACAGAATCAGGACATGGATATAATCCCATACAGAGTCAGGACATGGATATAA
TCCCATACAGAATCAGGACGAT
Found at i:593260 original size:6 final size:6
Alignment explanation
Indices: 593243--593274 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
593233 TATATTTTTT
593243 CATATGA CATATA CATATA CATATA CATATA C
1 CATAT-A CATATA CATATA CATATA CATATA C
593275 CATGTAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (6 bp):
CATATA
Found at i:593803 original size:3 final size:3
Alignment explanation
Indices: 593795--593844 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
593785 TTATTCAAGC
593795 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
593843 AT
1 AT
593845 TGTGTTAGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:594630 original size:3 final size:3
Alignment explanation
Indices: 594624--594674 Score: 66
Period size: 3 Copynumber: 16.3 Consensus size: 3
594614 TCTAAAAAAA
* *
594624 TAT TAT TAAT TAT TAT TAC TAT TAT TAAT CAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
594671 TAT T
1 TAT T
594675 GTATTAATAC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 37 0.88
4 5 0.12
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:594648 original size:19 final size:19
Alignment explanation
Indices: 594624--594674 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
594614 TCTAAAAAAA
594624 TATTATTAATTATTATTAC
1 TATTATTAATTATTATTAC
* *
594643 TATTATTAATCATTATTAT
1 TATTATTAATTATTATTAC
594662 TATTATT-ATTATT
1 TATTATTAATTATT
594675 GTATTAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 5 0.17
19 24 0.83
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTATTAATTATTATTAC
Found at i:613999 original size:16 final size:17
Alignment explanation
Indices: 613978--614010 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
613968 ACACACCAAA
613978 TCGGTT-TCGGTTTTTT
1 TCGGTTATCGGTTTTTT
613994 TCGGTTATCGGTTTTTT
1 TCGGTTATCGGTTTTTT
614011 AGATCGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.12, G:0.24, T:0.61
Consensus pattern (17 bp):
TCGGTTATCGGTTTTTT
Found at i:614019 original size:20 final size:17
Alignment explanation
Indices: 613977--614031 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 17
613967 AACACACCAA
613977 ATCGGTTTCGGTTTTTT
1 ATCGGTTTCGGTTTTTT
613994 -TCGGTTATCGGTTTTTT
1 ATCGGTT-TCGGTTTTTT
614011 AGATCGGTTTTCGGTTATTTT
1 --ATCGG-TTTCGGTT-TTTT
614032 TTTGGTTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 6 0.19
17 10 0.31
20 10 0.31
21 6 0.19
ACGTcount: A:0.09, C:0.11, G:0.24, T:0.56
Consensus pattern (17 bp):
ATCGGTTTCGGTTTTTT
Found at i:614266 original size:21 final size:21
Alignment explanation
Indices: 614242--614299 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
614232 GAAAAGAAGA
* *
614242 GAGAGAAGCAGAGAGAGCAGT
1 GAGAGAAGAAGAGAGAGCAGC
*
614263 GAGAGAAGAAGAGAGAGTAGC
1 GAGAGAAGAAGAGAGAGCAGC
*
614284 GAGAGAAGTAGAGAGA
1 GAGAGAAGAAGAGAGA
614300 ATCAACATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.47, C:0.05, G:0.43, T:0.05
Consensus pattern (21 bp):
GAGAGAAGAAGAGAGAGCAGC
Found at i:614979 original size:44 final size:44
Alignment explanation
Indices: 614899--614985 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
614889 ATATCGATAT
** *
614899 ATAACCTGAATTTTAGCGGCGTTTTAGTATACAAATGCCACTAC
1 ATAACCTGAATTTTAGCGGCGTTTTAAAAGACAAATGCCACTAC
*
614943 ATAACCTGACTTTTAGCGGCGTTTTTAAAAGA-AAATGCCACTA
1 ATAACCTGAATTTTAGCGGCG-TTTTAAAAGACAAATGCCACTA
614986 ACAGTTGCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 31 0.82
45 7 0.18
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (44 bp):
ATAACCTGAATTTTAGCGGCGTTTTAAAAGACAAATGCCACTAC
Found at i:629702 original size:21 final size:21
Alignment explanation
Indices: 629673--629746 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
629663 ACGTTGCATT
*
629673 TCGCATTGCGATATTTGAAAA
1 TCGCGTTGCGATATTTGAAAA
* ** **
629694 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATATTTGAAAA
* *
629714 TCGCGTTGCAATAGTTGAAAA
1 TCGCGTTGCGATATTTGAAAA
629735 TCGCGTTGCGAT
1 TCGCGTTGCGAT
629747 TTTCCATTTC
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 14 0.37
21 24 0.63
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATATTTGAAAA
Found at i:629714 original size:41 final size:41
Alignment explanation
Indices: 629669--629778 Score: 177
Period size: 41 Copynumber: 2.7 Consensus size: 41
629659 ATTCACGTTG
* *
629669 CATTTCGCATTGCGATATTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
629710 CATTTCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
629751 CATTTCGCATTGCGATAGTTG-AAATCGC
1 CATTTCGCATTGCGATAGTTGAAAATCGC
629779 AACGCGATCT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 7 0.11
41 56 0.89
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (41 bp):
CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:629934 original size:19 final size:19
Alignment explanation
Indices: 629910--629975 Score: 78
Period size: 19 Copynumber: 3.3 Consensus size: 19
629900 ACTGCAGTTG
629910 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* **
629929 TCGTTGCGATATTCTACAGTT
1 TCGTTGCGAT-TT-TCCAAAT
629950 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
629970 TCGTTG
1 TCGTTG
629976 AAAAAAAAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 16 0.42
20 6 0.16
21 6 0.16
22 10 0.26
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:630062 original size:6 final size:6
Alignment explanation
Indices: 630051--630095 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
630041 GACACGTATT
630051 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
630096 CGAGACGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:630402 original size:22 final size:21
Alignment explanation
Indices: 630374--630445 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 21
630364 AAGAAACAAA
630374 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGA-AACTGTAGACT
* **
630396 ATCGCAACG-AA-TTTAGAAA
1 ATCGCAACGAAACTGTAGACT
630415 ATCGCAACGATAACTGTAGACT
1 ATCGCAACGA-AACTGTAGACT
630437 ATCGCAACG
1 ATCGCAACG
630446 CGAAATGGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 14 0.34
20 2 0.05
21 2 0.05
22 23 0.56
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAAACTGTAGACT
Found at i:630462 original size:20 final size:20
Alignment explanation
Indices: 630437--630526 Score: 120
Period size: 20 Copynumber: 4.8 Consensus size: 20
630427 ACTGTAGACT
630437 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
630457 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATGGAAA
*
630477 ATCGCAACGCG--AT----T
1 ATCGCAACGCGAAATGGAAA
630491 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
630511 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
630527 CAACGCGAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
14 11 0.18
16 2 0.03
18 2 0.03
20 46 0.75
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:630500 original size:34 final size:33
Alignment explanation
Indices: 630455--630535 Score: 128
Period size: 34 Copynumber: 2.5 Consensus size: 33
630445 GCGAAATGGA
630455 AAATCGCAACGCGAAATAGAAAATCGCAACGCG
1 AAATCGCAACGCGAAATAGAAAATCGCAACGCG
* *
630488 ATTATCGCAACGCGAAATGGAAAATCGCAACGCG
1 A-AATCGCAACGCGAAATAGAAAATCGCAACGCG
630522 AAAT-GCAACGCGAA
1 AAATCGCAACGCGAA
630536 TTTGCGATAG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 10 0.23
33 3 0.07
34 31 0.70
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.11
Consensus pattern (33 bp):
AAATCGCAACGCGAAATAGAAAATCGCAACGCG
Found at i:637626 original size:19 final size:19
Alignment explanation
Indices: 637565--637676 Score: 93
Period size: 19 Copynumber: 5.8 Consensus size: 19
637555 TTATTTCCTT
*
637565 ATTTT-GGTTGCAAGCTATA
1 ATTTTAGGTTGCAAGCCA-A
* * *
637584 TTTTTAGGTTGGGAA-CCAG
1 ATTTTAGGTT-GCAAGCCAA
*
637603 GTTTTAGGTTGCAAGCCAA
1 ATTTTAGGTTGCAAGCCAA
* *
637622 ATTTTAGGTTGCAAGTCAT
1 ATTTTAGGTTGCAAGCCAA
* *
637641 ATTTTAGGTTACAAACCAA
1 ATTTTAGGTTGCAAGCCAA
*
637660 ATTTTTAGGTTACAAGC
1 A-TTTTAGGTTGCAAGC
637677 AATGCGATGT
Statistics
Matches: 74, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
18 3 0.04
19 48 0.65
20 20 0.27
21 3 0.04
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (19 bp):
ATTTTAGGTTGCAAGCCAA
Found at i:637744 original size:40 final size:40
Alignment explanation
Indices: 637682--637988 Score: 161
Period size: 40 Copynumber: 7.7 Consensus size: 40
637672 CAAGCAATGC
* * *
637682 GATGTATTGTAGGGGGTGCACACCTAAATATGAAAGTGAT
1 GATGTATTGTATGGGATACACACCTAAATATGAAAGTGAT
* * **
637722 GATTTATTGTATGGGATACACA-CTCAAT-T-ACAAGAAAAGT
1 GATGTATTGTATGGGATACACACCTAAATATGA-AAG-TGA-T
* *
637762 GATGTATCGTATGTGG-TAAACACCTAAATATGAAAGT-AGT
1 GATGTATTGTATG-GGATACACACCTAAATATGAAAGTGA-T
* * * * * * *
637802 GATGCATTTTACGGGATACACACCCAATTACAAGCAAG-G-T
1 GATGTATTGTATGGGATACACACCTAA--ATATGAAAGTGAT
* *
637842 GATGTATCGTATGAGG-TAAACACCTAAATATGAAAGTTG-T
1 GATGTATTGTATG-GGATACACACCTAAATATGAAAG-TGAT
* * * *
637882 GATGTATTGTACGGGATACACACCCAATTAT--AAGTAAGGT
1 GATGTATTGTATGGGATACACACCTAAATATGAAAGT--GAT
** * **
637922 GATGTATCCTACGAGG-TACACACCTAAATATGAAAGTGGC
1 GATGTATTGTATG-GGATACACACCTAAATATGAAAGTGAT
* *
637962 GATGTATTTTATGGGATACATACCTAA
1 GATGTATTGTATGGGATACACACCTAA
637989 TTAATAGAAT
Statistics
Matches: 201, Mismatches: 44, Indels: 44
0.70 0.15 0.15
Matches are distributed among these distances:
37 2 0.01
38 13 0.06
39 13 0.06
40 147 0.73
41 11 0.05
42 14 0.07
43 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (40 bp):
GATGTATTGTATGGGATACACACCTAAATATGAAAGTGAT
Found at i:637818 original size:80 final size:79
Alignment explanation
Indices: 637701--637991 Score: 384
Period size: 80 Copynumber: 3.6 Consensus size: 79
637691 TAGGGGGTGC
* * * *
637701 ACACCTAAATATGAAAGTGATGATTTATTGTATGGGATACACACTCAATTACAAGAAAAGTGATG
1 ACACCTAAATATGAAAGTG-TGATGTATTGTACGGGATACACACCCAATTACAAGAAAGGTGATG
*
637766 TATCGTATGTGGTAA
65 TATCGTATGAGGTAA
* * *
637781 ACACCTAAATATGAAAGTAGTGATGCATTTTACGGGATACACACCCAATTACAAGCAAGGTGATG
1 ACACCTAAATATGAAAGT-GTGATGTATTGTACGGGATACACACCCAATTACAAGAAAGGTGATG
637846 TATCGTATGAGGTAA
65 TATCGTATGAGGTAA
* *
637861 ACACCTAAATATGAAAGTTGTGATGTATTGTACGGGATACACACCCAATTATAAGTAAGGTGATG
1 ACACCTAAATATGAAAG-TGTGATGTATTGTACGGGATACACACCCAATTACAAGAAAGGTGATG
* * *
637926 TATCCTACGAGGTAC
65 TATCGTATGAGGTAA
* * * * *
637941 ACACCTAAATATGAAAGTGGCGATGTATTTTATGGGATACATACCTAATTA
1 ACACCTAAATATGAAAGT-GTGATGTATTGTACGGGATACACACCCAATTA
637992 ATAGAATGTT
Statistics
Matches: 188, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
79 1 0.01
80 185 0.98
81 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.28
Consensus pattern (79 bp):
ACACCTAAATATGAAAGTGTGATGTATTGTACGGGATACACACCCAATTACAAGAAAGGTGATGT
ATCGTATGAGGTAA
Found at i:637947 original size:160 final size:160
Alignment explanation
Indices: 637669--637991 Score: 423
Period size: 160 Copynumber: 2.0 Consensus size: 160
637659 AATTTTTAGG
* * * ** * *
637669 TTACAAGCAATGCGATGTATTGTAGGGGGTGCACACCTAAATATGAAAGTGATGATTTATTGTAT
1 TTACAAGCAAGGCGATGTATCGTAGGAGGTAAACACCTAAATATGAAAGTGATGATGTATTGTAC
* * * *
637734 GGGATACACACTCAATTACAAGAAAAGTGATGTATCGTATGTGGTAAACACCTAAATATGAAAGT
66 GGGATACACACCCAATTACAAGAAAAGTGATGTATCCTACGAGGTAAACACCTAAATATGAAAGT
*
637799 AGTGATGCATTTTACGGGATACACACCCAA
131 AGCGATGCATTTTACGGGATACACACCCAA
* *
637829 TTACAAGCAAGGTGATGTATCGTATGAGGTAAACACCTAAATATGAAAGTTG-TGATGTATTGTA
1 TTACAAGCAAGGCGATGTATCGTAGGAGGTAAACACCTAAATATGAAAG-TGATGATGTATTGTA
* * * *
637893 CGGGATACACACCCAATTATAAGTAAGGTGATGTATCCTACGAGGTACACACCTAAATATGAAAG
65 CGGGATACACACCCAATTACAAGAAAAGTGATGTATCCTACGAGGTAAACACCTAAATATGAAAG
* * * * *
637958 TGGCGATGTATTTTATGGGATACATACCTAA
130 TAGCGATGCATTTTACGGGATACACACCCAA
637989 TTA
1 TTA
637992 ATAGAATGTT
Statistics
Matches: 139, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
160 137 0.99
161 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (160 bp):
TTACAAGCAAGGCGATGTATCGTAGGAGGTAAACACCTAAATATGAAAGTGATGATGTATTGTAC
GGGATACACACCCAATTACAAGAAAAGTGATGTATCCTACGAGGTAAACACCTAAATATGAAAGT
AGCGATGCATTTTACGGGATACACACCCAA
Found at i:645220 original size:19 final size:19
Alignment explanation
Indices: 645181--645222 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
645171 CAGAACGTTC
*
645181 AAAAGTTTGAGATCAATTT
1 AAAAGTTTGAGATCAAATT
645200 AAAAGTTTGAGGAT-AAATT
1 AAAAGTTTGA-GATCAAATT
645219 AAAA
1 AAAA
645223 TATTCAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.31
Consensus pattern (19 bp):
AAAAGTTTGAGATCAAATT
Found at i:651499 original size:34 final size:36
Alignment explanation
Indices: 651459--651529 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 36
651449 AAAACTATAT
651459 ACCAGTATATA-GCAACAACTAAAAAACAG-AAGCA
1 ACCAGTATATATGCAACAACTAAAAAACAGAAAGCA
651493 ACCAGTATATATGCAACAACTAAAAAACAGAAAGCA
1 ACCAGTATATATGCAACAACTAAAAAACAGAAAGCA
651529 A
1 A
651530 TACCAGTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 11 0.31
35 18 0.51
36 6 0.17
ACGTcount: A:0.56, C:0.20, G:0.11, T:0.13
Consensus pattern (36 bp):
ACCAGTATATATGCAACAACTAAAAAACAGAAAGCA
Found at i:652217 original size:22 final size:23
Alignment explanation
Indices: 652180--652226 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
652170 AACCCTAAAC
652180 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCCAAAAATCGTATCTGCTA
* *
652203 AAGCCC-AGAATCGTATCTTCTA
1 AAGCCCAAAAATCGTATCTGCTA
652225 AA
1 AA
652227 CTCGCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (23 bp):
AAGCCCAAAAATCGTATCTGCTA
Found at i:660660 original size:30 final size:30
Alignment explanation
Indices: 660626--660682 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
660616 TTCAAATTAC
*
660626 TTTATATTTGACTTCAATTATA-ATTAAGAA
1 TTTATA-TTGAATTCAATTATATATTAAGAA
660656 TTTATATTGAATTCAATTATATATTAA
1 TTTATATTGAATTCAATTATATATTAA
660683 ATTTGACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (30 bp):
TTTATATTGAATTCAATTATATATTAAGAA
Found at i:660694 original size:28 final size:29
Alignment explanation
Indices: 660633--660698 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
660623 TACTTTATAT
* *
660633 TTGACTTCAATTATAATTAAGAATTTATA
1 TTGAATTCAATTATAATTAAGAATTTACA
660662 TTGAATTCAATTATATATT-A-AATTTGACA
1 TTGAATTCAATTATA-ATTAAGAATTT-ACA
660691 -TGAATTCA
1 TTGAATTCA
660699 TTAATTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 13 0.39
29 17 0.52
30 3 0.09
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (29 bp):
TTGAATTCAATTATAATTAAGAATTTACA
Found at i:661721 original size:15 final size:16
Alignment explanation
Indices: 661701--661732 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
661691 TTTAAAGAAA
661701 ATATATAAATTA-AGT
1 ATATATAAATTATAGT
661716 ATATATAAATTATAGT
1 ATATATAAATTATAGT
661732 A
1 A
661733 GAATTCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
ATATATAAATTATAGT
Found at i:662870 original size:42 final size:42
Alignment explanation
Indices: 662814--663062 Score: 222
Period size: 42 Copynumber: 5.9 Consensus size: 42
662804 ATCAAGGACC
* *
662814 TCAATTATAAAGGTAAAAAATGAGATTAAAAAATTAGAAGCC
1 TCAATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGAAGCA
* * * *
662856 TCGATTTTATAGGTAAAAAGTAAGATTGAAAAAATTAG-AG-A
1 TCAATTATAAAGGTAAAAAGTGAGATT-AAAAAATTAGAAGCA
* * *
662897 ACGAAATTGTATAA-GTAAAAAGTGAGATTAAAAAATTAGGAGCA
1 TC--AATTATA-AAGGTAAAAAGTGAGATTAAAAAATTAGAAGCA
* * * *
662941 TCAATAATAAAGGTAAAAAGTGAGATTAACAAATTA-AGGGCC
1 TCAATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGA-AGCA
* *
662983 TCAATTATAAAGGTGAAAAGTGAGATTAAAAAAATTAGAAAC-
1 TCAATTATAAAGGTAAAAAGTGAGATT-AAAAAATTAGAAGCA
* * *
663025 TTAATTATAAAGATACAAAA-TGAGATTGAAAAACTTAG
1 TCAATTATAAAGGTA-AAAAGTGAGATT-AAAAAATTAG
663063 GGTCAATAAT
Statistics
Matches: 168, Mismatches: 28, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
41 3 0.02
42 117 0.70
43 44 0.26
44 4 0.02
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (42 bp):
TCAATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGAAGCA
Found at i:662954 original size:127 final size:127
Alignment explanation
Indices: 662814--663143 Score: 312
Period size: 127 Copynumber: 2.6 Consensus size: 127
662804 ATCAAGGACC
* * * *
662814 TCAATTATAAAGGTAAAAAATGAGATTAAAAAATT-AGAAGCCTCGATTTTATAGGTAAAAAGTA
1 TCAATAATAAAGGTAAAAAATGAGATTAAAAAATTAAG-AGCCTCAATTATAAAGGTAAAAAGTA
* *
662878 AGATTGAAAAAATTAGAGAACGAAATTGTATAAG-TA-AAAAGTGAGATT-AAAAAATTAGGAGC
65 AGATTAAAAAAATTAGA-AACGAAATTATA-AAGATACAAAA-TGAGATTGAAAAAATTAGGAGC
662940 A
127 A
* * * * *
662941 TCAATAATAAAGGTAAAAAGTGAGATTAACAAATTAAGGGCCTCAATTATAAAGGTGAAAAGTGA
1 TCAATAATAAAGGTAAAAAATGAGATTAAAAAATTAAGAGCCTCAATTATAAAGGTAAAAAGTAA
** *
663006 GATTAAAAAAATTAGAAACTTAATTATAAAGATACAAAATGAGATTGAAAAACTTAGG-GTCAA
66 GATTAAAAAAATTAGAAACGAAATTATAAAGATACAAAATGAGATTGAAAAAATTAGGAG-C-A
* * * * * * *
663069 T-AATTATAAATGTAAAAAAAATGGGATTGAAAAAAAAATTAAGAGCCTTAATAATGAAGATAAA
1 TCAATAATAAAGGT--AAAAAATGAGATT----AAAAAATTAAGAGCCTCAATTATAAAGGTAAA
*
663133 AAATAAGATTA
60 AAGTAAGATTA
663144 CAAATTTAAA
Statistics
Matches: 164, Mismatches: 27, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
125 3 0.02
126 19 0.12
127 93 0.57
128 4 0.02
129 11 0.07
133 34 0.21
ACGTcount: A:0.53, C:0.05, G:0.17, T:0.25
Consensus pattern (127 bp):
TCAATAATAAAGGTAAAAAATGAGATTAAAAAATTAAGAGCCTCAATTATAAAGGTAAAAAGTAA
GATTAAAAAAATTAGAAACGAAATTATAAAGATACAAAATGAGATTGAAAAAATTAGGAGCA
Found at i:663015 original size:85 final size:85
Alignment explanation
Indices: 662793--663057 Score: 261
Period size: 85 Copynumber: 3.1 Consensus size: 85
662783 TAAAAAGGGT
* * *
662793 GATTGAAAAAAATCAAGGACCTCAATTATAAAGGTAAAAAATGAGATTAAAAAATTAGAAGCCTC
1 GATTG-AAAAAATTAAGGACCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGAAGCATC
* ** *
662858 GATTTTATAGGTAAAAAGTAA
65 AATAATAAAGGTAAAAAGTAA
* ** * *
662879 GATTGAAAAAATT-AGAGAACGAAATTGTATAA-GTAAAAAGTGAGATTAAAAAATTAGGAGCAT
1 GATTGAAAAAATTAAG-GACCTCAATTATA-AAGGTAAAAAGTGAGATTAAAAAATTAGAAGCAT
*
662942 CAATAATAAAGGTAAAAAGTGA
64 CAATAATAAAGGTAAAAAGTAA
* * * * *
662964 GATT-AACAAATTAAGGGCCTCAATTATAAAGGTGAAAAGTGAGATTAAAAAAATTAGAAAC-TT
1 GATTGAAAAAATTAAGGACCTCAATTATAAAGGTAAAAAGTGAGATT-AAAAAATTAGAAGCATC
* * *
663027 AATTATAAAGATACAAAA-TGA
65 AATAATAAAGGTA-AAAAGTAA
663048 GATTGAAAAA
1 GATTGAAAAA
663058 CTTAGGGTCA
Statistics
Matches: 146, Mismatches: 26, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
83 2 0.01
84 50 0.34
85 87 0.60
86 7 0.05
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.24
Consensus pattern (85 bp):
GATTGAAAAAATTAAGGACCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGAAGCATCA
ATAATAAAGGTAAAAAGTAA
Found at i:666153 original size:28 final size:29
Alignment explanation
Indices: 666098--666153 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
666088 AAAATATTAC
* *
666098 AAAACATTGTTCAACATAATACAAGTTAA
1 AAAACATGGTTCAAAATAATACAAGTTAA
666127 AAAACATGGTT-AAAAT-ATACATAGTTA
1 AAAACATGGTTCAAAATAATACA-AGTTA
666154 TAGTACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 9 0.38
29 10 0.42
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.29
Consensus pattern (29 bp):
AAAACATGGTTCAAAATAATACAAGTTAA
Found at i:666163 original size:22 final size:22
Alignment explanation
Indices: 666138--666188 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
666128 AAACATGGTT
*
666138 AAAATATACATAGTTATAGTAC
1 AAAATATACATAGTTAAAGTAC
*
666160 AAAAAATACATAGTTAAAGTAC
1 AAAATATACATAGTTAAAGTAC
*
666182 ATAATAT
1 AAAATAT
666189 TTTGTAACGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (22 bp):
AAAATATACATAGTTAAAGTAC
Found at i:671185 original size:58 final size:59
Alignment explanation
Indices: 671094--671235 Score: 162
Period size: 58 Copynumber: 2.4 Consensus size: 59
671084 AATATTAAAT
* * * *
671094 ATTCTAATTTCATCCTTACACTATGACTATCATTCTAAATTAGTCATCAAAC-TTTGAGC
1 ATTCCAATTTCATCC-CAAACTATGACTATCATTCTAAATTAGTCATCAAACTTTTGAAC
* * * *
671153 ATTTCAATTTCATCCCAAACTATGACCT-TCATTCTAAATTGGTCCTCAAACTTTTTTAAC
1 ATTCCAATTTCATCCCAAACTATGA-CTATCATTCTAAATTAGTCATCAAAC-TTTTGAAC
*
671213 ATTCCAATTTCATCGCAAACTAT
1 ATTCCAATTTCATCCCAAACTAT
671236 ATGTATATAA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
58 29 0.41
59 15 0.21
60 26 0.37
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.39
Consensus pattern (59 bp):
ATTCCAATTTCATCCCAAACTATGACTATCATTCTAAATTAGTCATCAAACTTTTGAAC
Found at i:671738 original size:5 final size:5
Alignment explanation
Indices: 671728--671753 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
671718 CCAAAGGGAG
671728 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
671754 ATTACAAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:677227 original size:97 final size:96
Alignment explanation
Indices: 677033--677229 Score: 270
Period size: 97 Copynumber: 2.0 Consensus size: 96
677023 ATTGCCCTTT
* * * *
677033 TAACATAAAAAGATTACTGCTACGACTGTTAGTCACCATAGTTTTTACACCGTTAAAAACTAGTA
1 TAACATAAAAAGATGAATGCTACGACTCTTAGTCACCATAGTTTTTACACCGCTAAAAACTAGTA
* *
677098 GTTTATTGATTCCTCTTTTGTAAGAAGTGTA
66 GTTTATCGACTCCTCTTTTGTAAGAAGTGTA
* * * *
677129 TAACATAAAATGATGAATTCTACGACTCTTAGTCACCATAGTTTTTTTA-ACTGCTAAAGACTAG
1 TAACATAAAAAGATGAATGCTACGACTCTTAGTCACCATAG--TTTTTACACCGCTAAAAACTAG
*
677193 TAGTTTATCGACTCCTTTTTTGTAAGAAGTGTA
64 TAGTTTATCGACTCCTCTTTTGTAAGAAGTGTA
677226 TAAC
1 TAAC
677230 CTACTCTTAA
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
96 36 0.41
97 46 0.52
98 6 0.07
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (96 bp):
TAACATAAAAAGATGAATGCTACGACTCTTAGTCACCATAGTTTTTACACCGCTAAAAACTAGTA
GTTTATCGACTCCTCTTTTGTAAGAAGTGTA
Found at i:680189 original size:104 final size:105
Alignment explanation
Indices: 680053--680264 Score: 417
Period size: 104 Copynumber: 2.0 Consensus size: 105
680043 TTAAAAATTA
680053 GTTGTACCTTAAAATTTTATTTTTTTAAATTAAACTATTATTAATATTAATATTTATATGTTATT
1 GTTGTACCTTAAAATTTTATTTTTTTAAATTAAACTATTATTAATATTAATATTTATATGTTATT
680118 TTTTAAAAGAAAATACTGTTGAAA-TTTTTTGTTCTCTCG
66 TTTTAAAAGAAAATACTGTTGAAATTTTTTTGTTCTCTCG
680157 GTTGTACCTTAAAATTTTATTTTTTTAAATTAAACTATTATTAATATTAATATTTATATGTTATT
1 GTTGTACCTTAAAATTTTATTTTTTTAAATTAAACTATTATTAATATTAATATTTATATGTTATT
680222 TTTTAAAAGAAAATACTGTTGAAATTTTTTTGTTCTCTCG
66 TTTTAAAAGAAAATACTGTTGAAATTTTTTTGTTCTCTCG
680262 GTT
1 GTT
680265 TCAAAGTTTC
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
104 89 0.83
105 18 0.17
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52
Consensus pattern (105 bp):
GTTGTACCTTAAAATTTTATTTTTTTAAATTAAACTATTATTAATATTAATATTTATATGTTATT
TTTTAAAAGAAAATACTGTTGAAATTTTTTTGTTCTCTCG
Found at i:681997 original size:33 final size:34
Alignment explanation
Indices: 681927--681990 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
681917 AAGTAAATAG
*
681927 ATTTTTCTCTGAAATAAAATAAATATATAATAAT
1 ATTTTTCTCTGAAACAAAATAAATATATAATAAT
* *
681961 ATTTTT-TTTGAAACAAAATATATA-ATAATA
1 ATTTTTCTCTGAAACAAAATAAATATATAATA
681991 TCTATTTGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 6 0.22
33 15 0.56
34 6 0.22
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (34 bp):
ATTTTTCTCTGAAACAAAATAAATATATAATAAT
Found at i:685110 original size:21 final size:21
Alignment explanation
Indices: 685084--685140 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
685074 GCTTGTCAGT
685084 TCAGATGCCACCACATCACCC
1 TCAGATGCCACCACATCACCC
* ** *
685105 TCAGATGTCATTACATTACCC
1 TCAGATGCCACCACATCACCC
685126 TCAGATGCCACCACA
1 TCAGATGCCACCACA
685141 ATCTGTTCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.39, G:0.11, T:0.21
Consensus pattern (21 bp):
TCAGATGCCACCACATCACCC
Found at i:686876 original size:42 final size:42
Alignment explanation
Indices: 686796--686876 Score: 96
Period size: 42 Copynumber: 1.9 Consensus size: 42
686786 TGTTGGGACA
* *
686796 TTAATGTATAAATGTGAAATTTCAGTTACTAAATGTTGAATT
1 TTAATGTATAAATGTGAAATTTAAGTTACGAAATGTTGAATT
686838 TTAATG-ATTAAATGATGGAAATTTAAGTTA-GAAA-GTTGA
1 TTAATGTA-TAAATG-T-GAAATTTAAGTTACGAAATGTTGA
686877 TTGGAATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
41 1 0.03
42 17 0.50
43 4 0.12
44 12 0.35
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.40
Consensus pattern (42 bp):
TTAATGTATAAATGTGAAATTTAAGTTACGAAATGTTGAATT
Found at i:692064 original size:55 final size:55
Alignment explanation
Indices: 692003--692199 Score: 272
Period size: 55 Copynumber: 3.6 Consensus size: 55
691993 TTTGTATGAG
* *
692003 TGTGTATTGGTACACTGAGGAGTGTATCGATACACACAAAACATCGAATGCTACT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACACACAAAACATCGAATGCTAAT
* * * * *
692058 TGTGTATCGGTACACTAAGGAATGTATCGATACATACAAAACATCAAATACTAAT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACACACAAAACATCGAATGCTAAT
* * *
692113 TGTGTATCGGTTCACTGAGGAGTGTATCGATAC-C-CTAAAACATCGAGTGCTATT
1 TGTGTATCGGTACACTGAGGAGTGTATCGATACACAC-AAAACATCGAATGCTAAT
*
692167 TGTGTATCGATACACTGAGGAGTGTATCGATAC
1 TGTGTATCGGTACACTGAGGAGTGTATCGATAC
692200 TATCATCTAT
Statistics
Matches: 124, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 45 0.36
55 78 0.63
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (55 bp):
TGTGTATCGGTACACTGAGGAGTGTATCGATACACACAAAACATCGAATGCTAAT
Found at i:692591 original size:21 final size:21
Alignment explanation
Indices: 692549--692592 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
692539 TTGTTATGAA
* *
692549 AATATGAACTTTGAACATGTG
1 AATACGAACTTCGAACATGTG
692570 AATACGAACTTCGAATCA-GTG
1 AATACGAACTTCGAA-CATGTG
692591 AA
1 AA
692593 CGTGAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (21 bp):
AATACGAACTTCGAACATGTG
Found at i:692757 original size:21 final size:22
Alignment explanation
Indices: 692731--692787 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
692721 GTCGAGAGTC
*
692731 TATGTGGTCCTTCGA-GATAAT
1 TATGTGGTCCTTCGAGGATAAA
*
692752 TATGTGGTTCTTC-AGGATAAA
1 TATGTGGTCCTTCGAGGATAAA
692773 TATGTGG-CACTTCGA
1 TATGTGGTC-CTTCGA
692788 TGCAACCCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.37
Consensus pattern (22 bp):
TATGTGGTCCTTCGAGGATAAA
Found at i:692800 original size:23 final size:23
Alignment explanation
Indices: 692773--692817 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
692763 TCAGGATAAA
692773 TATGTGGCACTTCGATGCAACCC
1 TATGTGGCACTTCGATGCAACCC
*
692796 TATGTGGCACTTCGGTGCAACC
1 TATGTGGCACTTCGATGCAACC
692818 TATATGGTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (23 bp):
TATGTGGCACTTCGATGCAACCC
Found at i:692830 original size:22 final size:23
Alignment explanation
Indices: 692777--692832 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
692767 GATAAATATG
* *
692777 TGGCACTTCGATGCAACCCTATG
1 TGGCACTTCGGTGCAACCCTATA
692800 TGGCACTTCGGTGCAA-CCTATA
1 TGGCACTTCGGTGCAACCCTATA
692822 TGGTC-CTTCGG
1 TGG-CACTTCGG
692833 GATAATTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 14 0.47
23 16 0.53
ACGTcount: A:0.18, C:0.29, G:0.25, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAACCCTATA
Found at i:696722 original size:20 final size:20
Alignment explanation
Indices: 696699--696736 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
696689 GTTGGAACTT
696699 GTGTTGTTGGATTGGATCCA
1 GTGTTGTTGGATTGGATCCA
696719 GTGTTGTTGGATTGGATC
1 GTGTTGTTGGATTGGATC
696737 TAGGAGTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.08, G:0.37, T:0.42
Consensus pattern (20 bp):
GTGTTGTTGGATTGGATCCA
Found at i:699037 original size:55 final size:55
Alignment explanation
Indices: 698958--699092 Score: 198
Period size: 55 Copynumber: 2.5 Consensus size: 55
698948 AGTGTGTTTT
* * *
698958 GGTACACTGAGGAGTGTATCGATACATACAAAACAACGAATGCTACTTGTGTATC
1 GGTACACTGAGGAGTGTATCGATACATACAAAACAACGAATACTAATTATGTATC
* * *
699013 GGTACACTGAGGAGTTTATTGATACATACAAAACATCGAATACTAATTATGTATC
1 GGTACACTGAGGAGTGTATCGATACATACAAAACAACGAATACTAATTATGTATC
* *
699068 GGTACAATGAGGAGTGTATCAATAC
1 GGTACACTGAGGAGTGTATCGATAC
699093 CCTCAAACAT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 70 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (55 bp):
GGTACACTGAGGAGTGTATCGATACATACAAAACAACGAATACTAATTATGTATC
Found at i:699711 original size:21 final size:21
Alignment explanation
Indices: 699678--699718 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
699668 GTCGAGGGTC
**
699678 TATGTGGTCCTTCGGGACAAA
1 TATGTGGAACTTCGGGACAAA
*
699699 TATGTGGAACTTCGGTACAA
1 TATGTGGAACTTCGGGACAA
699719 CCCTATGTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (21 bp):
TATGTGGAACTTCGGGACAAA
Done.