Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007744.1 Hibiscus syriacus cultivar Beakdansim tig00110007_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: 4276731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 16
Found at i:1536004 original size:31 final size:31
Alignment explanation
Indices: 1535969--1536046 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
1535959 TCAAAACTAT
*
1535969 TTTTTTAAAAACTATATAATTTTTAAAAATG
1 TTTTTTAAAAACTATATAATTTTCAAAAATG
1536000 TTTTTTAAAAACTATATAATTTTCAAAAATG
1 TTTTTTAAAAACTATATAATTTTCAAAAATG
*
1536031 --TTTTAAAAATTATATA
1 TTTTTTAAAAACTATATA
1536047 TTATATATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 15 0.33
31 30 0.67
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (31 bp):
TTTTTTAAAAACTATATAATTTTCAAAAATG
Found at i:1536047 original size:31 final size:30
Alignment explanation
Indices: 1535947--1536046 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 30
1535937 ACTATATATT
* *
1535947 ATATATAAAATTTCAAAACTATTTTTTTAAAAA
1 ATATAT-AATTTTCAAAA--ATGTTTTTAAAAA
* *
1535980 CTATATAATTTTTAAAAATGTTTTTTAAAAA
1 ATATATAATTTTCAAAAATG-TTTTTAAAAA
*
1536011 CTATATAATTTTCAAAAATG-TTTTAAAAA
1 ATATATAATTTTCAAAAATGTTTTTAAAAA
*
1536040 TTATATA
1 ATATATA
1536047 TTATATATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
29 15 0.25
30 2 0.03
31 29 0.48
32 9 0.15
33 5 0.08
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (30 bp):
ATATATAATTTTCAAAAATGTTTTTAAAAA
Found at i:1536092 original size:38 final size:38
Alignment explanation
Indices: 1536012--1536131 Score: 150
Period size: 40 Copynumber: 3.1 Consensus size: 38
1536002 TTTTAAAAAC
*
1536012 TATATAATTTTCAAAAATGTTTTAAAAATTATATATTA
1 TATATAATTTTCAAAAATGTTTTAAAAACTATATATTA
*
1536050 TATATAAGTTTTCAAAAATGTTTTCAAAAACTATCTATTA
1 TATATAA-TTTTCAAAAATGTTTT-AAAAACTATATATTA
* ** * *
1536090 TATACATATTTTCAAAAATCATTTACAAACTATATAATA
1 TATATA-ATTTTCAAAAATGTTTTAAAAACTATATATTA
1536129 TAT
1 TAT
1536132 GTATATATAT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
38 7 0.10
39 31 0.44
40 32 0.45
41 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (38 bp):
TATATAATTTTCAAAAATGTTTTAAAAACTATATATTA
Found at i:1536639 original size:29 final size:30
Alignment explanation
Indices: 1536582--1536639 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1536572 GTAAATTACA
* *
1536582 AAAAAATAAATATTTATGGATCAATTTTGT
1 AAAAAATAAATATTTAAGGATCAAATTTGT
1536612 AAAAAATATAA-ATTTAAGGA-CAAATTTG
1 AAAAAATA-AATATTTAAGGATCAAATTTG
1536640 AAGAAATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 16 0.64
31 2 0.08
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.34
Consensus pattern (30 bp):
AAAAAATAAATATTTAAGGATCAAATTTGT
Found at i:1537009 original size:2 final size:2
Alignment explanation
Indices: 1537002--1537083 Score: 59
Period size: 2 Copynumber: 42.5 Consensus size: 2
1536992 TTATAATGTA
* *
1537002 AT AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT AA ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT
* *
1537044 TT AT AT -T AT AA ACT AT AT A- AT -T AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1537083 A
1 A
1537084 AATTATGTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
1 6 0.10
2 55 0.87
3 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1537022 original size:17 final size:17
Alignment explanation
Indices: 1537000--1537083 Score: 77
Period size: 17 Copynumber: 4.9 Consensus size: 17
1536990 AATTATAATG
1537000 TAATATATATATATATA
1 TAATATATATATATATA
*
1537017 TAATATA-AGTTTATATA
1 TAATATATA-TATATATA
*
1537034 TAA-ACTATATTTATATTA
1 TAATA-TATATATATA-TA
1537052 TAA-ACTATATA-ATTATA
1 TAATA-TATATATA-TATA
1537069 TAATATATATATATA
1 TAATATATATATATA
1537084 AATTATGTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
16 2 0.03
17 39 0.67
18 17 0.29
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (17 bp):
TAATATATATATATATA
Found at i:1537048 original size:15 final size:15
Alignment explanation
Indices: 1537028--1537180 Score: 94
Period size: 15 Copynumber: 10.5 Consensus size: 15
1537018 AATATAAGTT
1537028 TATATATAAACTATA
1 TATATATAAACTATA
1537043 TTTATATTATAAACTATA
1 --TATA-TATAAACTATA
1537061 TA-ATTATATAA-TATA
1 TATA-TATA-AACTATA
* *
1537076 TATATATAAATTATG
1 TATATATAAACTATA
* *
1537091 TTTATATGAAC-A-A
1 TATATATAAACTATA
*
1537104 CATATATAAACTATA
1 TATATATAAACTATA
*
1537119 TATGTATAAACTATA
1 TATATATAAACTATA
1537134 -A-A-A-AAA-TATA
1 TATATATAAACTATA
*
1537144 TAGTTTATAAACTATA
1 TA-TATATAAACTATA
* *
1537160 -ATTTATTAA-TATA
1 TATATATAAACTATA
1537173 TATATATA
1 TATATATA
1537181 TAATATAAAC
Statistics
Matches: 108, Mismatches: 15, Indels: 29
0.71 0.10 0.19
Matches are distributed among these distances:
10 4 0.04
11 4 0.04
12 1 0.01
13 12 0.11
14 18 0.17
15 45 0.42
16 9 0.08
17 4 0.04
18 11 0.10
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (15 bp):
TATATATAAACTATA
Found at i:1537055 original size:18 final size:17
Alignment explanation
Indices: 1537003--1537097 Score: 67
Period size: 17 Copynumber: 5.6 Consensus size: 17
1536993 TATAATGTAA
*
1537003 TATATATATATATATAA-
1 TATATTTATATATA-AAC
1537020 TATAAGTTTATATATAAAC
1 TAT-A-TTTATATATAAAC
1537039 TATATTTATATTATAAAC
1 TATATTTATA-TATAAAC
*
1537057 TATA-TAAT-TATATAA-
1 TATATTTATATATA-AAC
*
1537072 TATA--TATATATAAAT
1 TATATTTATATATAAAC
*
1537087 TATGTTTATAT
1 TATATTTATAT
1537098 GAACAACATA
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
14 4 0.06
15 15 0.23
16 2 0.03
17 17 0.26
18 15 0.23
19 12 0.18
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TATATTTATATATAAAC
Found at i:1537175 original size:56 final size:53
Alignment explanation
Indices: 1537115--1537235 Score: 140
Period size: 53 Copynumber: 2.2 Consensus size: 53
1537105 ATATATAAAC
1537115 TATATATGTATAAACTATAAA-A-AAATATATAGTTTATAAACTATAATTTATTAATA-
1 TATATATGTAT-AA-TATAAACATAAA-A-ATAG-TT-TAAACTATAATTTATTAATAG
* *
1537171 TATATATATATAATATAAACTATAAAAATAGTTTAAATTATAATTTATTAATAG
1 TATATATGTATAATATAAAC-ATAAAAATAGTTTAAACTATAATTTATTAATAG
1537225 TATATATGTAT
1 TATATATGTAT
1537236 GTATAACTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
53 19 0.33
54 18 0.31
55 6 0.10
56 12 0.21
57 3 0.05
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (53 bp):
TATATATGTATAATATAAACATAAAAATAGTTTAAACTATAATTTATTAATAG
Found at i:1537184 original size:15 final size:15
Alignment explanation
Indices: 1537004--1537187 Score: 72
Period size: 15 Copynumber: 12.3 Consensus size: 15
1536994 ATAATGTAAT
1537004 ATATATATATATATA
1 ATATATATATATATA
*
1537019 ATATAAGTTTATATATAA
1 ATAT-A-TATATATAT-A
*
1537037 ACTATATTTATATTATA
1 A-TATATATATA-TATA
1537054 A-ACTATATAATTATATA
1 ATA-TATAT-A-TATATA
1537071 ATATATATATATA-A
1 ATATATATATATATA
* *
1537085 AT-TATGTTTATATGA
1 ATATATATATATAT-A
* *
1537100 ACA-ACATATATA-A
1 ATATATATATATATA
*
1537113 ACTATATATGTATA-A
1 A-TATATATATATATA
1537128 ACTATA-A-A-A-A-A
1 A-TATATATATATATA
*
1537139 ATATATAGTTTATA-A
1 ATATATA-TATATATA
*
1537154 ACTATA-ATTTAT-TA
1 A-TATATATATATATA
1537168 ATATATATATATATA
1 ATATATATATATATA
1537183 ATATA
1 ATATA
1537188 AACTATAAAA
Statistics
Matches: 132, Mismatches: 14, Indels: 46
0.69 0.07 0.24
Matches are distributed among these distances:
10 4 0.03
11 4 0.03
12 1 0.01
13 14 0.11
14 18 0.14
15 42 0.32
16 10 0.08
17 27 0.20
18 9 0.07
19 3 0.02
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:1537580 original size:20 final size:20
Alignment explanation
Indices: 1537541--1537584 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1537531 TATAGTACAT
* **
1537541 GTATGTATAAACTATGTATA
1 GTATATATAAACTACATATA
1537561 GTATATATAAACTACATATA
1 GTATATATAAACTACATATA
1537581 -TATA
1 GTATA
1537585 ACCTATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (20 bp):
GTATATATAAACTACATATA
Found at i:1537605 original size:13 final size:13
Alignment explanation
Indices: 1537562--1537606 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
1537552 CTATGTATAG
1537562 TATATATAAACTACA
1 TATATATAAAC--CA
1537577 TATATAT-AACCTA
1 TATATATAAACC-A
1537590 TATATATAAACCA
1 TATATATAAACCA
1537603 TATA
1 TATA
1537607 AAGTAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 13 0.46
14 7 0.25
15 7 0.25
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (13 bp):
TATATATAAACCA
Found at i:1537691 original size:7 final size:7
Alignment explanation
Indices: 1537681--1537764 Score: 57
Period size: 7 Copynumber: 12.3 Consensus size: 7
1537671 TAGTTTATAG
1537681 AAACCCT
1 AAACCCT
1537688 AAACCCT
1 AAACCCT
*
1537695 AAACCTT
1 AAACCCT
*
1537702 AAACCAT
1 AAACCCT
*
1537709 AAACCAT
1 AAACCCT
**
1537716 AAACTTT
1 AAACCCT
1537723 AAA-CCT
1 AAACCCT
*
1537729 GAACCCT
1 AAACCCT
* *
1537736 AAAACAT
1 AAACCCT
*
1537743 -AACACAT
1 AAAC-CCT
1537750 AAACCC-
1 AAACCCT
1537756 AAACCCT
1 AAACCCT
1537763 AA
1 AA
1537765 GCATTGTGCA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
6 11 0.18
7 47 0.77
8 3 0.05
ACGTcount: A:0.50, C:0.32, G:0.01, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:1537711 original size:21 final size:21
Alignment explanation
Indices: 1537681--1537760 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
1537671 TAGTTTATAG
*
1537681 AAACCCTAAACCCTAAACCTT
1 AAACCATAAACCCTAAACCTT
* *
1537702 AAACCATAAACCATAAACTTT
1 AAACCATAAACCCTAAACCTT
* * *
1537723 AAACC-TGAACCCTAAAACAT
1 AAACCATAAACCCTAAACCTT
1537743 -AACACATAAACCC-AAACC
1 AAAC-CATAAACCCTAAACC
1537761 CTAAGCATTG
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.06
20 15 0.32
21 29 0.62
ACGTcount: A:0.50, C:0.33, G:0.01, T:0.16
Consensus pattern (21 bp):
AAACCATAAACCCTAAACCTT
Found at i:1537885 original size:57 final size:58
Alignment explanation
Indices: 1537824--1537943 Score: 165
Period size: 57 Copynumber: 2.1 Consensus size: 58
1537814 ACATGTAAAT
* *
1537824 TATATATATAACTTATAGTACATGTATGTATA-AA-CTATGTATA-GTATATATAAACTA
1 TATATATATAACCTATAGTACATGTATATATACAATCTATGTATATGT-TATA-AAACTA
* *
1537881 TATATATATAACCTATAGTATATGTATATATACAATCTATTTATATGTTATAAAACTA
1 TATATATATAACCTATAGTACATGTATATATACAATCTATGTATATGTTATAAAACTA
1537939 TATAT
1 TATAT
1537944 GTAACCTAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
57 29 0.52
58 13 0.23
59 12 0.21
60 2 0.04
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.42
Consensus pattern (58 bp):
TATATATATAACCTATAGTACATGTATATATACAATCTATGTATATGTTATAAAACTA
Found at i:1537888 original size:15 final size:16
Alignment explanation
Indices: 1537863--1537903 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
1537853 ATAAACTATG
1537863 TATAGTATATATAAAC
1 TATAGTATATATAAAC
*
1537879 TATA-TATATATAACC
1 TATAGTATATATAAAC
1537894 TATAGTATAT
1 TATAGTATAT
1537904 GTATATATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (16 bp):
TATAGTATATATAAAC
Found at i:1537920 original size:24 final size:23
Alignment explanation
Indices: 1537881--1537932 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
1537871 ATATAAACTA
*
1537881 TATATATATAACCTATAGTATATG
1 TATATATACAACCTAT-GTATATG
* *
1537905 TATATATACAATCTATTTATATG
1 TATATATACAACCTATGTATATG
1537928 T-TATA
1 TATATA
1537933 AAACTATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.16
23 7 0.28
24 14 0.56
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (23 bp):
TATATATACAACCTATGTATATG
Found at i:1538003 original size:21 final size:21
Alignment explanation
Indices: 1537977--1538029 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1537967 TAGTGTACTA
* *
1537977 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
*
1537998 TATAGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
1538019 TATAGTTTATA
1 TATAGTTTATA
1538030 TTAATGTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:1540310 original size:12 final size:11
Alignment explanation
Indices: 1540282--1540321 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1540272 TTGAATTAAC
1540282 TCAAATGTTAT
1 TCAAATGTTAT
*
1540293 TCAAATTTTAT
1 TCAAATGTTAT
1540304 ATCAAATGTTAT
1 -TCAAATGTTAT
*
1540316 TTAAAT
1 TCAAAT
1540322 TATCGTTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (11 bp):
TCAAATGTTAT
Found at i:1551596 original size:42 final size:38
Alignment explanation
Indices: 1551531--1551615 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 38
1551521 TAGGTGCATT
1551531 AAAAAATTAGAGTCAATTATAAATATAAAAAGTGGGATTG
1 AAAAAATTAGAGTCAATTATAAATAT--AAAGTGGGATTG
* * * *
1551571 AAAAAATTAGGGCCTCAATTCTAAATGTAAAGTGTGATTG
1 AAAAAATTAGAG--TCAATTATAAATATAAAGTGGGATTG
1551611 AAAAA
1 AAAAA
1551616 TTAAGGGTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 27 0.69
42 12 0.31
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (38 bp):
AAAAAATTAGAGTCAATTATAAATATAAAGTGGGATTG
Found at i:1551603 original size:40 final size:40
Alignment explanation
Indices: 1551559--1551641 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
1551549 ATAAATATAA
* *
1551559 AAAGTGGGATTGAAAAAATT-AGGGCCTCAATTCTAAATGT
1 AAAGTGGGATTG-AAAAATTAAGGGCCTCAATTATAAAGGT
* * *
1551599 AAAGTGTGATTGAAAAATTAAGGGTCTCTATTATAAAGGT
1 AAAGTGGGATTGAAAAATTAAGGGCCTCAATTATAAAGGT
1551639 AAA
1 AAA
1551642 ATAATGAGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 7 0.19
40 30 0.81
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29
Consensus pattern (40 bp):
AAAGTGGGATTGAAAAATTAAGGGCCTCAATTATAAAGGT
Found at i:1554208 original size:60 final size:62
Alignment explanation
Indices: 1554111--1554227 Score: 193
Period size: 60 Copynumber: 1.9 Consensus size: 62
1554101 TTCCATGTAT
1554111 ATTTTGCAAGGGCTAGGATACTAAGAATGTCCATTCTTTTG-TCTCATACAAGCTGTTCCAAC
1 ATTTTGCAAGGGCTAGGA-ACTAAGAATGTCCATTCTTTTGTTCTCATACAAGCTGTTCCAAC
* *
1554173 ATTTTGCAAGGGCTAGG-CCTAAGAATGTTCATTCTTTTGTTCTCATACAAGCTGT
1 ATTTTGCAAGGGCTAGGAACTAAGAATGTCCATTCTTTTGTTCTCATACAAGCTGT
1554228 GTTGCAACTC
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
60 20 0.38
61 15 0.29
62 17 0.33
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (62 bp):
ATTTTGCAAGGGCTAGGAACTAAGAATGTCCATTCTTTTGTTCTCATACAAGCTGTTCCAAC
Found at i:1556080 original size:27 final size:28
Alignment explanation
Indices: 1556037--1556090 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 28
1556027 TGAATAAAAT
*
1556037 GAAAGTTTAGTGGCTAAA-GTAATTTGG
1 GAAAGTTTAGTGACTAAAGGTAATTTGG
1556064 GAAAGTTTA-TAGACTAAATGGTAATTT
1 GAAAGTTTAGT-GACTAAA-GGTAATTT
1556091 CAAAAGTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.04
27 15 0.65
29 7 0.30
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (28 bp):
GAAAGTTTAGTGACTAAAGGTAATTTGG
Found at i:1558030 original size:22 final size:24
Alignment explanation
Indices: 1557991--1558037 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
1557981 AATGCATATG
*
1557991 GTGGGCATGACCTTATGT-TATTA
1 GTGGGCACGACCTTATGTGTATTA
1558014 GTGGGCACGA-CTTATGTGTATTA
1 GTGGGCACGACCTTATGTGTATTA
1558037 G
1 G
1558038 CATTTCGTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.36
Consensus pattern (24 bp):
GTGGGCACGACCTTATGTGTATTA
Found at i:1558902 original size:192 final size:191
Alignment explanation
Indices: 1558667--1559058 Score: 734
Period size: 192 Copynumber: 2.0 Consensus size: 191
1558657 ACTATATATT
1558667 CTATGATGTAATATGACTACTAAGTTGCTATTTGAAATCAGATTCAGTTTTGTTGATTAAAAATT
1 CTAT-ATGTAATATGACTACTAAGTTGCTATTTGAAATCAGATTCAGTTTTGTTGATTAAAAATT
1558732 AGAAATTTATGTTACTTGATAAATCGATAAATGATTTAAAATTGAATGATAG-AAATTAGTTTAT
65 AGAAATTTATGTTACTTGATAAATCGATAAATGATTT-AAATTGAATGATAGAAAATTAGTTTAT
1558796 CACATTCTGACTCGTATTTGAGAATTAAATATGGGTAA-GTATTACATTTATTGATATCAGAG
129 CACATTCTGACTCGTATTTGAGAATTAAATATGGGTAAGGTATTACATTTATTGATATCAGAG
1558858 CTATATGTAATAATGAACTACTAAGTTGCTATTTGAAATCAGATTCAGTTTTGTTGATTAAAAAT
1 CTATATGTAAT-ATG-ACTACTAAGTTGCTATTTGAAATCAGATTCAGTTTTGTTGATTAAAAAT
1558923 TAGAAATTTATGTTACTTGATAAATCGATAAATGATTTAAATTGAATGATAGAAAATTAGTTTAT
64 TAGAAATTTATGTTACTTGATAAATCGATAAATGATTTAAATTGAATGATAGAAAATTAGTTTAT
1558988 CACATTCTGACTCGTATTTGAGAATTAAATATGGGTAAGGTATTACATTTATTGATATCAGAG
129 CACATTCTGACTCGTATTTGAGAATTAAATATGGGTAAGGTATTACATTTATTGATATCAGAG
1559051 CTATATGT
1 CTATATGT
1559059 TTAGCCGATT
Statistics
Matches: 197, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
190 7 0.04
191 21 0.11
192 137 0.70
193 32 0.16
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (191 bp):
CTATATGTAATATGACTACTAAGTTGCTATTTGAAATCAGATTCAGTTTTGTTGATTAAAAATTA
GAAATTTATGTTACTTGATAAATCGATAAATGATTTAAATTGAATGATAGAAAATTAGTTTATCA
CATTCTGACTCGTATTTGAGAATTAAATATGGGTAAGGTATTACATTTATTGATATCAGAG
Found at i:1564427 original size:26 final size:26
Alignment explanation
Indices: 1564386--1564436 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1564376 TGGTGCATAC
1564386 GGTGGGCACGACCTTATGTGTATTAT
1 GGTGGGCACGACCTTATGTGTATTAT
* *
1564412 GGTGGGCATGATCTTATGTGTATTA
1 GGTGGGCACGACCTTATGTGTATTA
1564437 GCACTTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.20, C:0.12, G:0.31, T:0.37
Consensus pattern (26 bp):
GGTGGGCACGACCTTATGTGTATTAT
Found at i:1566421 original size:21 final size:21
Alignment explanation
Indices: 1566397--1566454 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1566387 CTAAGCAAAA
*
1566397 GGATCGATCCCTTTGACCTAG
1 GGATTGATCCCTTTGACCTAG
1566418 GGATTGATCCCTTTGACCTAG
1 GGATTGATCCCTTTGACCTAG
*
1566439 GGATTGATCCCCTTGA
1 GGATTGATCCCTTTGA
1566455 ACAACAGTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (21 bp):
GGATTGATCCCTTTGACCTAG
Found at i:1566587 original size:68 final size:68
Alignment explanation
Indices: 1566478--1566611 Score: 259
Period size: 68 Copynumber: 2.0 Consensus size: 68
1566468 CATTGGATTC
1566478 TAGTAGCCATGGATCGATCTCTTCCCTTAAAAGATTAATTACTTCTAGTAATGATCGAATCATTT
1 TAGTAGCCATGGATCGATCTCTTCCCTTAAAAGATTAATTACTTCTAGTAATGATCGAATCATTT
1566543 GGA
66 GGA
*
1566546 TAGTAGCCATGGATCGATCTCTTTCCTTAAAAGATTAATTACTTCTAGTAATGATCGAATCATTT
1 TAGTAGCCATGGATCGATCTCTTCCCTTAAAAGATTAATTACTTCTAGTAATGATCGAATCATTT
1566611 G
66 G
1566612 AAAAAAGACC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (68 bp):
TAGTAGCCATGGATCGATCTCTTCCCTTAAAAGATTAATTACTTCTAGTAATGATCGAATCATTT
GGA
Found at i:1569941 original size:21 final size:21
Alignment explanation
Indices: 1569917--1569956 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1569907 AATTATAATT
1569917 GTGCATCGATGCACTGCTACA
1 GTGCATCGATGCACTGCTACA
*
1569938 GTGCATCGATGCATTGCTA
1 GTGCATCGATGCACTGCTA
1569957 TAGTAATGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (21 bp):
GTGCATCGATGCACTGCTACA
Found at i:1570528 original size:24 final size:24
Alignment explanation
Indices: 1570496--1570541 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1570486 TATTCCATAT
1570496 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
1570520 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
1570542 CATGCCATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:1577792 original size:24 final size:24
Alignment explanation
Indices: 1577759--1577804 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1577749 TCTTCCATAT
1577759 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
*
1577783 GATGTGTAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
1577805 CATGTCATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:1581753 original size:31 final size:31
Alignment explanation
Indices: 1581694--1581788 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 31
1581684 ATAACCATTA
* * *
1581694 AACTTTATATAGAAT-ACTAATTTAACCCCTG
1 AACTTTAGATAAAATAAC-AATTTGACCCCTG
* *
1581725 AACTTTATG-TAAAATAACATTTTGACCCCTA
1 AACTTTA-GATAAAATAACAATTTGACCCCTG
* *
1581756 AACTTTAGATAAAATATCAATTTGACCCTTG
1 AACTTTAGATAAAATAACAATTTGACCCCTG
1581787 AA
1 AA
1581789 TTCGAGCATG
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
30 1 0.02
31 49 0.94
32 2 0.04
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (31 bp):
AACTTTAGATAAAATAACAATTTGACCCCTG
Found at i:1583316 original size:18 final size:17
Alignment explanation
Indices: 1583293--1583327 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
1583283 CAGAACCGAC
1583293 CCGTTGACCGATCGTTGA
1 CCGTTGACCG-TCGTTGA
1583311 CCGTTGACCGTCGTTGA
1 CCGTTGACCGTCGTTGA
1583328 ATATAACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (17 bp):
CCGTTGACCGTCGTTGA
Found at i:1586071 original size:88 final size:89
Alignment explanation
Indices: 1585913--1586155 Score: 339
Period size: 88 Copynumber: 2.7 Consensus size: 89
1585903 CTAAGGATAT
* *
1585913 GGCCCCAAGGAATATTCTTAGGTTGGTTTCCTTTTTGCTGTGTGCTTAAGGTAACCCTACGGATC
1 GGCCCCAAGGAATATCCTTAGGTTGGTTTCC-TTTTGCTGTGTACTTAAGGTAACCCTACGGATC
*
1585978 TAAGGATATCCTTGGGTAGGCCCATA
65 TAAGGATACCCTTGGGTAGG-CCATA
*
1586004 GGCCCC-AGGAATATCCTTAGGTTGGTTTCC-TTTGTTGTGTACTTAAGGTAACCCTACGGATCT
1 GGCCCCAAGGAATATCCTTAGGTTGGTTTCCTTTTGCTGTGTACTTAAGGTAACCCTACGGATCT
1586067 AAGGATACCCTTGGGTAGGCCATA
66 AAGGATACCCTTGGGTAGGCCATA
* * * * *
1586091 GGCCCCAAGGAGTATCCTTAGGTTGGCTCCCTTTTTGCTGTGTGCTT-AGCGTAAGCTCTACGGA
1 GGCCCCAAGGAATATCCTTAGGTTGGTTTCC-TTTTGCTGTGTACTTAAG-GTAA-CCCTACGGA
1586155 T
63 T
1586156 GTAGTTTTAG
Statistics
Matches: 137, Mismatches: 10, Indels: 10
0.87 0.06 0.06
Matches are distributed among these distances:
87 11 0.08
88 70 0.51
89 2 0.01
90 39 0.28
91 15 0.11
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.32
Consensus pattern (89 bp):
GGCCCCAAGGAATATCCTTAGGTTGGTTTCCTTTTGCTGTGTACTTAAGGTAACCCTACGGATCT
AAGGATACCCTTGGGTAGGCCATA
Found at i:1590977 original size:89 final size:88
Alignment explanation
Indices: 1590723--1590999 Score: 337
Period size: 91 Copynumber: 3.1 Consensus size: 88
1590713 GGTAAGACCA
* *
1590723 TACGGATCTAAGGATATCCTTAGGTAGGCCCATAGGCCCCAAGGCATATTCTTAGGTTGGTTTAC
1 TACGGATCTAAGGATATCCTTAGGTAGGCCCATAGG-CCCAAGGCATATCCTTAGGTTGG-TTCC
* *
1590788 TTTTTGCTGTGTACTTAAGGTAAACC
64 TTTTTG-TGTGTGCTTAAGGTAACCC
* *
1590814 TACGGATCTAATGATATCCTTAGGTAGGCCCATAGGCCCTAAGGCATATCCTTAGGTTAGTTTCC
1 TACGGATCTAAGGATATCCTTAGGTAGGCCCATAGGCCC-AAGGCATATCCTTAGGTT-GGTTCC
1590879 TTTGTTGTGTGT--TTAAGGTAACCC
64 TTT-TTGTGTGTGCTTAAGGTAACCC
* * *
1590903 TACGGATCTAAGGATACCCTTGGGTAGG-CCATAGGCTCCAAGG-ACTATCCTTAGGTTGGCTCC
1 TACGGATCTAAGGATATCCTTAGGTAGGCCCATAGGC-CCAAGGCA-TATCCTTAGGTTGGTTCC
* *
1590966 TTTTTTGTGTGTGCTGAGGGTAAGCCC
64 -TTTTTGTGTGTGCTTAAGGTAA-CCC
1590993 TACGGAT
1 TACGGAT
1591000 TTAGTTTTGG
Statistics
Matches: 165, Mismatches: 12, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
87 13 0.08
88 27 0.16
89 45 0.27
90 13 0.08
91 63 0.38
92 4 0.02
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (88 bp):
TACGGATCTAAGGATATCCTTAGGTAGGCCCATAGGCCCAAGGCATATCCTTAGGTTGGTTCCTT
TTTGTGTGTGCTTAAGGTAACCC
Found at i:1592129 original size:18 final size:19
Alignment explanation
Indices: 1592094--1592142 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1592084 ACAAACTTTT
*
1592094 TGTTTATAA-TAT-TGTTA
1 TGTTTATAAGTTTGTGTTA
1592111 TG-TTATAAGTTTGTGTTA
1 TGTTTATAAGTTTGTGTTA
*
1592129 TGTTTATAATTTTG
1 TGTTTATAAGTTTG
1592143 ATTATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 6 0.22
17 4 0.15
18 7 0.26
19 10 0.37
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.59
Consensus pattern (19 bp):
TGTTTATAAGTTTGTGTTA
Found at i:1592147 original size:18 final size:17
Alignment explanation
Indices: 1592094--1592147 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
1592084 ACAAACTTTT
*
1592094 TGTTTATAATATTGTTA
1 TGTTTATAATTTTGTTA
1592111 TG-TTATAAGTTTGTGTTA
1 TGTTTATAA-TTT-TGTTA
1592129 TGTTTATAATTTTGATTA
1 TGTTTATAATTTTG-TTA
1592147 T
1 T
1592148 AAATTTCTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
16 6 0.19
17 6 0.19
18 14 0.44
19 6 0.19
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (17 bp):
TGTTTATAATTTTGTTA
Found at i:1597381 original size:224 final size:225
Alignment explanation
Indices: 1596961--1597405 Score: 562
Period size: 224 Copynumber: 2.0 Consensus size: 225
1596951 AAACTATACA
*
1596961 AAAAATTCAATTATATTAACAGTAAAATAAAATATTAAAAATATACCAATTACCTGGATATTGAA
1 AAAAATTCAATTATATTAACAGTAAAATAAAATATTAAAAATATACCAATTACCTGAATATTGAA
** * * *
1597026 ATTGATGAACCACTTCTAGTACTATAATCTGGTGCAAAATAAAAAAAATTTGCAAAAATAATACA
66 ATTGACAAACCACTTC-A-TACTATAATCTGGAGCAAAACAAAAAAAAATTGCAAAAATAATACA
* * * * * * * *
1597091 ACTCTAAAACAATATTATTTCAAAAGTAAAATACATAAAATAAGATTTCTATTTCACTTTCTTGA
129 ACTCTAAAACAAGATCATCTCAAAAGTAAAATAAAGAAAAGAAAATTTCTATTTCACTTACTTGA
*
1597156 TAATCTTTTTAACCCTAAATCAAATCTTTTAT
194 TAATCTTATTAACCCTAAATCAAATCTTTTAT
* *
1597188 AAAAATTCAATTATATTTATCAGTAAAATAAAAATAAATTAAAAA-A-ACTTAATTA-CTGAATA
1 AAAAATTCAATTATA-TTAACAGTAAAAT-AAAAT--ATTAAAAATATAC-CAATTACCTGAATA
* * *
1597250 TTGAAATTGGCAAACCGCTTC-TACTATAATCTGGAGCAAAACAAAAAAAAATTG-TAAAATAAT
61 TTGAAATTGACAAACCACTTCATACTATAATCTGGAGCAAAACAAAAAAAAATTGCAAAAATAAT
* * *
1597313 AGAATTCTAAAACAAGATCA-CTCAAAAGTAAAATAAAGAGAAGAATAATTT-TATTTCACTTAC
126 ACAACTCTAAAACAAGATCATCTCAAAAGTAAAATAAAGAAAAGAA-AATTTCTATTTCACTTAC
1597376 TTGATAATCTTATTAACCCTAAATCAAATC
190 TTGATAATCTTATTAACCCTAAATCAAATC
1597406 GAATATGTAG
Statistics
Matches: 189, Mismatches: 23, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
224 60 0.32
225 28 0.15
226 30 0.16
227 15 0.08
228 12 0.06
229 30 0.16
230 6 0.03
231 8 0.04
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.32
Consensus pattern (225 bp):
AAAAATTCAATTATATTAACAGTAAAATAAAATATTAAAAATATACCAATTACCTGAATATTGAA
ATTGACAAACCACTTCATACTATAATCTGGAGCAAAACAAAAAAAAATTGCAAAAATAATACAAC
TCTAAAACAAGATCATCTCAAAAGTAAAATAAAGAAAAGAAAATTTCTATTTCACTTACTTGATA
ATCTTATTAACCCTAAATCAAATCTTTTAT
Found at i:1597625 original size:21 final size:21
Alignment explanation
Indices: 1597587--1597626 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1597577 TATTATTAAT
1597587 AAAAATAAAATAGTAAAAAAC
1 AAAAATAAAATAGTAAAAAAC
*
1597608 AAAAA-AAAATATTAAAAAA
1 AAAAATAAAATAGTAAAAAA
1597627 TTAATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.15
Consensus pattern (21 bp):
AAAAATAAAATAGTAAAAAAC
Found at i:1600073 original size:29 final size:30
Alignment explanation
Indices: 1600041--1600116 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
1600031 TTCATTTGAT
*
1600041 AAATATGAAAAATTATAA-TTAATATTA-TA
1 AAATAT-AAAAATTATAATTTAATAATATTA
*
1600070 AAATAATAAAAATTACAATTTAATAATATTA
1 AAAT-ATAAAAATTATAATTTAATAATATTA
*
1600101 AAA-ATAAAAAATATAA
1 AAATATAAAAATTATAA
1600117 ATTTGATTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 25 0.62
30 10 0.25
31 5 0.12
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (30 bp):
AAATATAAAAATTATAATTTAATAATATTA
Found at i:1600111 original size:30 final size:29
Alignment explanation
Indices: 1600048--1600120 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 29
1600038 GATAAATATG
*
1600048 AAAAATTATAA-TTAATATTATAAAATAAT
1 AAAAATTA-AATTTAATAATATAAAATAAT
*
1600077 AAAAATTACAATTTAATAATATTAAA-AAT
1 AAAAATTA-AATTTAATAATATAAAATAAT
1600106 AAAAAATATAAATTT
1 -AAAAAT-TAAATTT
1600121 GATTGTTGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 13 0.34
30 23 0.61
31 2 0.05
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAAATTAAATTTAATAATATAAAATAAT
Found at i:1600206 original size:38 final size:43
Alignment explanation
Indices: 1600153--1600248 Score: 139
Period size: 38 Copynumber: 2.3 Consensus size: 43
1600143 TTGATGTTTT
1600153 TATTTCTAAAAGAATATTAATGATATA-TTA-T-TATGA-TTAA
1 TATTT-TAAAAGAATATTAATGATATATTTATTATATGATTTAA
1600193 TA-TTTAAAAGAATATTAATGATATATTTATTACTATGATTTAA
1 TATTTTAAAAGAATATTAATGATATATTTATTA-TATGATTTAA
1600236 TATTTTAAAAGAA
1 TATTTTAAAAGAA
1600249 GTAGGAGGGT
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
38 21 0.42
39 5 0.10
40 3 0.06
42 5 0.10
43 6 0.12
44 10 0.20
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (43 bp):
TATTTTAAAAGAATATTAATGATATATTTATTATATGATTTAA
Found at i:1603146 original size:21 final size:21
Alignment explanation
Indices: 1603102--1603146 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1603092 AAATTACGTA
*
1603102 TTTAGTATCTAAATTATCAGT
1 TTTAGTATCTAAATTATCAAT
*
1603123 TTTAGTATCTGAACTT-TCAAT
1 TTTAGTATCT-AAATTATCAAT
1603144 TTT
1 TTT
1603147 TTCAAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (21 bp):
TTTAGTATCTAAATTATCAAT
Found at i:1604519 original size:2 final size:2
Alignment explanation
Indices: 1604514--1604543 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1604504 TTAAAATTAC
1604514 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
1604544 TCAATAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1605402 original size:75 final size:75
Alignment explanation
Indices: 1605258--1605475 Score: 323
Period size: 75 Copynumber: 2.9 Consensus size: 75
1605248 GAACCATAAA
*
1605258 CAAATCTCAAGACTCAAACCACAATATTAAGTCT--AACAATAAAATTCATAAACAAACCACAAT
1 CAAATCTCAAGACTCAAACAACAATATTAAGTCTAGAACAATAAAATTCATAAACAAACCACAAT
* *
1605321 ACTAAAATGT
66 ATTAAAATAT
* * * *
1605331 CAAATCTTAAGACTGAAACTACAATATTAAGTCTAGAACAATAAAATTCATAAACAAACCACGAT
1 CAAATCTCAAGACTCAAACAACAATATTAAGTCTAGAACAATAAAATTCATAAACAAACCACAAT
1605396 ATTAAAATAT
66 ATTAAAATAT
* * * *
1605406 CAAATCTCAAGATTCAAACAACAATATTAACTCTAGAACAATAAAATCCATAAACAAACCATAAT
1 CAAATCTCAAGACTCAAACAACAATATTAAGTCTAGAACAATAAAATTCATAAACAAACCACAAT
1605471 ATTAA
66 ATTAA
1605476 GTATAAAACA
Statistics
Matches: 129, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
73 31 0.24
75 98 0.76
ACGTcount: A:0.53, C:0.19, G:0.05, T:0.23
Consensus pattern (75 bp):
CAAATCTCAAGACTCAAACAACAATATTAAGTCTAGAACAATAAAATTCATAAACAAACCACAAT
ATTAAAATAT
Found at i:1605472 original size:40 final size:40
Alignment explanation
Indices: 1605428--1605515 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
1605418 TTCAAACAAC
* * *
1605428 AATATTAACTCTAGAACAATAAAATCCATAAACAAACCAT
1 AATATTAACTATAAAACAATAAAATCCACAAACAAACCAT
*
1605468 AATATTAAGTATAAAACAATAAAATCCACAAACAAACCAT
1 AATATTAACTATAAAACAATAAAATCCACAAACAAACCAT
1605508 AATATTAA
1 AATATTAA
1605516 AGTGTCAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.58, C:0.17, G:0.02, T:0.23
Consensus pattern (40 bp):
AATATTAACTATAAAACAATAAAATCCACAAACAAACCAT
Found at i:1609369 original size:17 final size:18
Alignment explanation
Indices: 1609337--1609370 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1609327 TTGTTTTTCG
*
1609337 TTGATCGACTGTTGACTA
1 TTGATCGACAGTTGACTA
1609355 TTGATCGA-AGTTGACT
1 TTGATCGACAGTTGACT
1609371 TTTTTAGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.38
Consensus pattern (18 bp):
TTGATCGACAGTTGACTA
Found at i:1610210 original size:27 final size:27
Alignment explanation
Indices: 1610180--1610249 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
1610170 AATTGAATGG
* * *
1610180 AATGATCGAAATACCTCTTAA-CTCTAA
1 AATGATCGAAATACCCCTGAATC-CAAA
1610207 AATGATCGAAATACCCCTGAATCCAAA
1 AATGATCGAAATACCCCTGAATCCAAA
*
1610234 AATGATCAAAATACCC
1 AATGATCGAAATACCC
1610250 ATGCTCCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.23
Consensus pattern (27 bp):
AATGATCGAAATACCCCTGAATCCAAA
Found at i:1610269 original size:25 final size:27
Alignment explanation
Indices: 1610205--1610269 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
1610195 TCTTAACTCT
* *
1610205 AAAATGATCGAAATACCCCTGAATCCA
1 AAAATGATCAAAATACCCATGAATCCA
*
1610232 AAAATGATCAAAATACCCATG-CTCC-
1 AAAATGATCAAAATACCCATGAATCCA
*
1610257 AAAATGATAAAAA
1 AAAATGATCAAAA
1610270 GTACGATTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 12 0.35
26 3 0.09
27 19 0.56
ACGTcount: A:0.51, C:0.22, G:0.09, T:0.18
Consensus pattern (27 bp):
AAAATGATCAAAATACCCATGAATCCA
Found at i:1622306 original size:26 final size:26
Alignment explanation
Indices: 1622269--1622318 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1622259 CTTTTTATAA
*
1622269 ATTGCTACTGCTAAAAAAGCTAACAG
1 ATTGCTACTGCTAAAAAACCTAACAG
* *
1622295 ATTGCTATTGCTAAACAACCTAAC
1 ATTGCTACTGCTAAAAAACCTAAC
1622319 TCATATTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (26 bp):
ATTGCTACTGCTAAAAAACCTAACAG
Found at i:1622599 original size:21 final size:21
Alignment explanation
Indices: 1622573--1622613 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1622563 ACAAGTCTTG
*
1622573 GAATTTTAAATTATAATGTCA
1 GAATTTCAAATTATAATGTCA
*
1622594 GAATTTCAAATTATGATGTC
1 GAATTTCAAATTATAATGTC
1622614 TAAATAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (21 bp):
GAATTTCAAATTATAATGTCA
Found at i:1629800 original size:18 final size:19
Alignment explanation
Indices: 1629758--1629800 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1629748 TACTCTATAA
1629758 TTCTAGCTCTCCAACTTGAT
1 TTCTAGCTCTCCAACTT-AT
1629778 TTCTAGCT-TCCAATCTT-T
1 TTCTAGCTCTCCAA-CTTAT
1629796 TTCTA
1 TTCTA
1629801 ATGAACAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.27
19 5 0.23
20 11 0.50
ACGTcount: A:0.19, C:0.28, G:0.07, T:0.47
Consensus pattern (19 bp):
TTCTAGCTCTCCAACTTAT
Found at i:1636718 original size:32 final size:32
Alignment explanation
Indices: 1636682--1636757 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
1636672 AGGGCCACGA
*
1636682 GGCCTACCTAAGAACAT-ATCTTAGGGCCGTAG
1 GGCCTACCTAAGAA-ATGATCTCAGGGCCGTAG
**
1636714 GGCCTACCCGAG-AATGATCTCAGGGCCGTAG
1 GGCCTACCTAAGAAATGATCTCAGGGCCGTAG
*
1636745 AGCCTACCTAAGA
1 GGCCTACCTAAGA
1636758 GTCACATTAG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
30 2 0.06
31 24 0.67
32 10 0.28
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (32 bp):
GGCCTACCTAAGAAATGATCTCAGGGCCGTAG
Found at i:1643070 original size:23 final size:24
Alignment explanation
Indices: 1643044--1643097 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
1643034 AAGTCAAAAT
1643044 GATGGTGAC-TAACAACATCAACC
1 GATGGTGACTTAACAACATCAACC
**
1643067 GATGGTG-CTTGGCAACATCAACC
1 GATGGTGACTTAACAACATCAACC
1643090 GATGGTGA
1 GATGGTGA
1643098 TTGGCAACGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.20
Consensus pattern (24 bp):
GATGGTGACTTAACAACATCAACC
Found at i:1643101 original size:23 final size:23
Alignment explanation
Indices: 1643056--1643105 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1643046 TGGTGACTAA
*
1643056 CAACATCAACCGATGGTGCTTGG
1 CAACATCAACCGATGGTGATTGG
1643079 CAACATCAACCGATGGTGATTGG
1 CAACATCAACCGATGGTGATTGG
1643102 CAAC
1 CAAC
1643106 GATGATGAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (23 bp):
CAACATCAACCGATGGTGATTGG
Found at i:1644374 original size:29 final size:29
Alignment explanation
Indices: 1644332--1644403 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
1644322 GCTTGTACTG
*
1644332 TAATTTGTAGAAAAAAATTGGGATGATATTA
1 TAATTTGT--AAAAAAATTGGGATGATATCA
** * *
1644363 TAATTTGTAAAAAGTTTGGGTTGTTATCA
1 TAATTTGTAAAAAAATTGGGATGATATCA
*
1644392 TAATTTGGAAAA
1 TAATTTGTAAAA
1644404 GTTTGATCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 27 0.77
31 8 0.23
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.39
Consensus pattern (29 bp):
TAATTTGTAAAAAAATTGGGATGATATCA
Found at i:1644424 original size:27 final size:29
Alignment explanation
Indices: 1644358--1644466 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 29
1644348 ATTGGGATGA
*
1644358 TATTATAATTTGTAAAAAGTTTGGGTTGT
1 TATTATAATTTGTAAAAAGTTTGGATTGT
* *
1644387 TATCATAATTTG-GAAAAGTTT-GATCT-T
1 TATTATAATTTGTAAAAAGTTTGGAT-TGT
* *
1644414 TATTATAATTTATAAAAAAGTTTGGGTTGT
1 TATTATAATTTGT-AAAAAGTTTGGATTGT
* * *
1644444 TGTT-TAATATGTAAAATGTTTGG
1 TATTATAATTTGTAAAAAGTTTGG
1644467 CTTCATTATA
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
27 13 0.20
28 19 0.30
29 26 0.41
30 6 0.09
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (29 bp):
TATTATAATTTGTAAAAAGTTTGGATTGT
Found at i:1644444 original size:57 final size:55
Alignment explanation
Indices: 1644358--1644617 Score: 204
Period size: 57 Copynumber: 4.6 Consensus size: 55
1644348 ATTGGGATGA
* * **
1644358 TATTATAATTTGTAAAAAGTTTGGGTTGTTATCATAATTTGGAAAAGTTTGATCTT
1 TATTATAATTTATAAAAAGTTTGGGTTATTAT-ATAATTTGGAAAAGTTTGGGCTT
* * * * *
1644414 TATTATAATTTATAAAAAAGTTTGGGTTGTTGTTTAATATGTAAAATGTTT-GGCTT
1 TATTATAATTTAT-AAAAAGTTTGGGTTATTATATAATTTGGAAAA-GTTTGGGCTT
* * * * *
1644470 CATTATAATTTTTTTTAAATAGTTTTGG-TATTATTGTAATTTATGG-AAAGTTTGGGCATT
1 TATTATAA---TTTATAAAAAGTTTGGGTTATTA-TATAA-TT-TGGAAAAGTTTGGGC-TT
* * *
1644530 TATTATGATTTATAAAAAGTTTGGGTTATTAATATAATTTATGAAAACTTTGGGCTT
1 TATTATAATTTATAAAAAGTTTGGGTTATT-ATATAATTT-GGAAAAGTTTGGGCTT
* * *
1644587 TACTGTAATATATAAAAAGTTTGGGTT-TTAT
1 TATTATAATTTATAAAAAGTTTGGGTTATTAT
1644618 TGCAATTTTA
Statistics
Matches: 162, Mismatches: 28, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
55 2 0.01
56 35 0.22
57 67 0.41
58 36 0.22
59 12 0.07
60 10 0.06
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (55 bp):
TATTATAATTTATAAAAAGTTTGGGTTATTATATAATTTGGAAAAGTTTGGGCTT
Found at i:1644521 original size:28 final size:28
Alignment explanation
Indices: 1644485--1644632 Score: 118
Period size: 29 Copynumber: 5.2 Consensus size: 28
1644475 TAATTTTTTT
* *
1644485 TAAATAGTTTTGGTATTATTGTAATTTA
1 TAAAAAGTTTGGGTATTATTGTAATTTA
** * * *
1644513 TGGAAAGTTTGGGCATTTATTATGATTTA
1 TAAAAAGTTTGGGTA-TTATTGTAATTTA
* *
1644542 TAAAAAGTTTGGGTTATTAATATAATTTA
1 TAAAAAGTTTGGG-TATTATTGTAATTTA
* * * *
1644571 TGAAAACTTTGGGCT-TTACTGTAATATA
1 TAAAAAGTTTGGG-TATTATTGTAATTTA
* *
1644599 TAAAAAGTTTGGGTTTTATTGCAATTTTA
1 TAAAAAGTTTGGGTATTATTGTAA-TTTA
1644628 TAAAA
1 TAAAA
1644633 TTTGTTACTA
Statistics
Matches: 93, Mismatches: 23, Indels: 7
0.76 0.19 0.06
Matches are distributed among these distances:
27 1 0.01
28 38 0.41
29 53 0.57
30 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.45
Consensus pattern (28 bp):
TAAAAAGTTTGGGTATTATTGTAATTTA
Found at i:1644628 original size:57 final size:56
Alignment explanation
Indices: 1644485--1644636 Score: 155
Period size: 57 Copynumber: 2.7 Consensus size: 56
1644475 TAATTTTTTT
* * * * * * *
1644485 TAAATAGTTTTGGTATTATTGTAATTTATGGAAAGTTTGGGCATTTATTATGATTTA
1 TAAAAAGTTTGGGTTTTATTGTAATTTAT-GAAAATTTGGGCATTTACTATAATATA
* * *
1644542 TAAAAAGTTTGGGTTATTAATATAATTTATGAAAACTTTGGGC-TTTACTGTAATATA
1 TAAAAAGTTTGGGTT-TTATTGTAATTTATGAAAA-TTTGGGCATTTACTATAATATA
*
1644599 TAAAAAGTTTGGGTTTTATTGCAATTTTAT-AAAATTTG
1 TAAAAAGTTTGGGTTTTATTGTAA-TTTATGAAAATTTG
1644637 TTACTATCGT
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
55 4 0.05
56 10 0.13
57 46 0.58
58 19 0.24
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (56 bp):
TAAAAAGTTTGGGTTTTATTGTAATTTATGAAAATTTGGGCATTTACTATAATATA
Found at i:1650124 original size:20 final size:20
Alignment explanation
Indices: 1650082--1650121 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1650072 TAAGTGTTAA
*
1650082 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
1650102 TGAATTTTAA-ATTATATAT
1 TGAATTTTAAGATTATATAT
1650121 T
1 T
1650122 TGATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:1652936 original size:3 final size:3
Alignment explanation
Indices: 1652928--1652961 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1652918 CATGTTTTTA
*
1652928 ATT ATT ATT ATT ATT ATT ATT TTT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1652962 GTATCATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:1655258 original size:19 final size:20
Alignment explanation
Indices: 1655219--1655258 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1655209 TAAGTGTTAA
*
1655219 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
1655239 TGAATTTTAA-ATTATATAT
1 TGAATTTTAAGATTATATAT
1655258 T
1 T
1655259 CGATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:1660456 original size:6 final size:6
Alignment explanation
Indices: 1660439--1660501 Score: 108
Period size: 6 Copynumber: 10.5 Consensus size: 6
1660429 GACACGTATT
*
1660439 ACCACG ATCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
1660487 ATCACG ACCACG ACC
1 ACCACG ACCACG ACC
1660502 CGAGACGAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.33, C:0.48, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:1661288 original size:42 final size:42
Alignment explanation
Indices: 1661229--1661480 Score: 278
Period size: 42 Copynumber: 5.9 Consensus size: 42
1661219 TGCGATTTTG
1661229 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1661271 GACTATCACAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * * *
1661313 GACTATCGCAACGCGAATTTGGAATAAATCACAA--CGAATTTG
1 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* * * * *
1661355 GAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGCGAATTTG
1 GACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* * * *
1661399 GAATAAATCGCAACGAATTTGGAATAAATTGCAACGCAAACTTC
1 GACT--ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1661443 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAA
1661481 TTTGGAAAAT
Statistics
Matches: 180, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
42 106 0.59
44 74 0.41
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:1661356 original size:65 final size:65
Alignment explanation
Indices: 1661254--1661494 Score: 341
Period size: 65 Copynumber: 3.8 Consensus size: 65
1661244 CTTGGAATAA
* * *
1661254 ATCGCAACGCGAACTTCGACT--ATCACAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGAATAAATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
1661317 ATCGCAACGCGAATTTGGAATAAATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGAATAAATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* * * *
1661382 ATCGCAACGCGAATTTGGAATAAATCGCAACGAATTTGGAATAAATTGCAACGCAAACTTCGACT
1 ATCGCAACGCGAACTTGGAATAAATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
1661447 ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAATTTGG-A-AAATCGCA
1 ATCGCAACGCGAACTTGGAATAAATCACAA--CGAATTTGGAATAAATCGCA
1661495 TTGCGATAGT
Statistics
Matches: 165, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
63 45 0.27
64 1 0.01
65 119 0.72
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (65 bp):
ATCGCAACGCGAACTTGGAATAAATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:1661365 original size:44 final size:45
Alignment explanation
Indices: 1661282--1661494 Score: 146
Period size: 44 Copynumber: 4.9 Consensus size: 45
1661272 ACTATCACAA
* * * * *
1661282 CGAACTTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACG
1 CGAATTTGGAATAAATCACAAC-CGAATTTGGAATAAATCGCAACG
1661326 CGAATTTGGAATAAATCACAA-CGAATTTGGAATAAATCGCAACG
1 CGAATTTGGAATAAATCACAACCGAATTTGGAATAAATCGCAACG
* * * *
1661370 CGAACTTCGACT--ATCGCAACGCGAATTTGGAATAAATCGCAA--
1 CGAATTTGGAATAAATCACAAC-CGAATTTGGAATAAATCGCAACG
** * * * *
1661412 CGAATTTGGAATAAATTGCAACGCAAACTTCGACT--ATCGCAA--
1 CGAATTTGGAATAAATCACAAC-CGAATTTGGAATAAATCGCAACG
* *
1661454 CGAACTTGGAATAAATCGCAACGCGAATTTGG-A-AAATCGCA
1 CGAATTTGGAATAAATCACAAC-CGAATTTGGAATAAATCGCA
1661495 TTGCGATAGT
Statistics
Matches: 138, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
42 64 0.46
44 74 0.54
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (45 bp):
CGAATTTGGAATAAATCACAACCGAATTTGGAATAAATCGCAACG
Found at i:1661490 original size:21 final size:23
Alignment explanation
Indices: 1661233--1661494 Score: 213
Period size: 21 Copynumber: 12.3 Consensus size: 23
1661223 ATTTTGGACT
*
1661233 ATCGCAA--CGAACTTGGAATAA
1 ATCGCAACGCGAATTTGGAATAA
* * *
1661254 ATCGCAACGCGAACTTCGACT--
1 ATCGCAACGCGAATTTGGAATAA
* *
1661275 ATCACAA--CGAACTTGGAATAA
1 ATCGCAACGCGAATTTGGAATAA
* * *
1661296 ATCGCAACGCGAACTTCGACT--
1 ATCGCAACGCGAATTTGGAATAA
1661317 ATCGCAACGCGAATTTGGAATAA
1 ATCGCAACGCGAATTTGGAATAA
*
1661340 ATCACAA--CGAATTTGGAATAA
1 ATCGCAACGCGAATTTGGAATAA
* * *
1661361 ATCGCAACGCGAACTTCGACT--
1 ATCGCAACGCGAATTTGGAATAA
1661382 ATCGCAACGCGAATTTGGAATAA
1 ATCGCAACGCGAATTTGGAATAA
1661405 ATCGCAA--CGAATTTGGAATAA
1 ATCGCAACGCGAATTTGGAATAA
* * * * *
1661426 ATTGCAACGCAAACTTCGACT--
1 ATCGCAACGCGAATTTGGAATAA
*
1661447 ATCGCAA--CGAACTTGGAATAA
1 ATCGCAACGCGAATTTGGAATAA
1661468 ATCGCAACGCGAATTTGG-A-AA
1 ATCGCAACGCGAATTTGGAATAA
1661489 ATCGCA
1 ATCGCA
1661495 TTGCGATAGT
Statistics
Matches: 194, Mismatches: 29, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
19 19 0.10
21 116 0.60
22 1 0.01
23 58 0.30
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (23 bp):
ATCGCAACGCGAATTTGGAATAA
Found at i:1664290 original size:46 final size:46
Alignment explanation
Indices: 1664229--1664348 Score: 114
Period size: 46 Copynumber: 2.6 Consensus size: 46
1664219 GTAATTGGGA
* *
1664229 TTATCACCCACTAAGGATGCACCAGCCTATAAATCGATAATTAGAT
1 TTATCATCCAGTAAGGATGCACCAGCCTATAAATCGATAATTAGAT
* * * * * ** * * *
1664275 TTATCATCCGGTAAGGTTGCACTAGCATGTATTTTGGTAATTGGAT
1 TTATCATCCAGTAAGGATGCACCAGCCTATAAATCGATAATTAGAT
* *
1664321 TTATCATCTAGTAAGGATACACCAGCCT
1 TTATCATCCAGTAAGGATGCACCAGCCT
1664349 GTATATTGAT
Statistics
Matches: 56, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
46 56 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (46 bp):
TTATCATCCAGTAAGGATGCACCAGCCTATAAATCGATAATTAGAT
Found at i:1668009 original size:16 final size:16
Alignment explanation
Indices: 1667990--1668146 Score: 84
Period size: 16 Copynumber: 9.9 Consensus size: 16
1667980 TTTTGGTTTA
*
1667990 GGTTGCTTTCGATTCG
1 GGTTACTTTCGATTCG
* *
1668006 GGTTATTTTCGATTCA
1 GGTTACTTTCGATTCG
* * *
1668022 GATTACTTTCGGTTTG
1 GGTTACTTTCGATTCG
* *
1668038 GGTTAATTTC-ATTTG
1 GGTTACTTTCGATTCG
**
1668053 ATTTACTTTCGAATT-G
1 GGTTACTTTCG-ATTCG
** **
1668069 GGTTAAATTCGATTTA
1 GGTTACTTTCGATTCG
* * *
1668085 GTTTGCTTTCGGTTCG
1 GGTTACTTTCGATTCG
* ** *
1668101 CGTTGTTTTCGGTTCG
1 GGTTACTTTCGATTCG
*
1668117 GGTTACTTTCGATTTG
1 GGTTACTTTCGATTCG
*
1668133 GGTTAATTTCGATT
1 GGTTACTTTCGATT
1668147 GAATTATTTT
Statistics
Matches: 103, Mismatches: 35, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
15 14 0.14
16 86 0.83
17 3 0.03
ACGTcount: A:0.15, C:0.13, G:0.24, T:0.49
Consensus pattern (16 bp):
GGTTACTTTCGATTCG
Found at i:1668041 original size:32 final size:32
Alignment explanation
Indices: 1667995--1668161 Score: 133
Period size: 32 Copynumber: 5.3 Consensus size: 32
1667985 GTTTAGGTTG
* *
1667995 CTTTCGATTCGGGTTATTTTCGATTCAGATTA
1 CTTTCGATTTGGGTTAATTTCGATTCAGATTA
* *
1668027 CTTTCGGTTTGGGTTAATTTC-ATT-TGATTTA
1 CTTTCGATTTGGGTTAATTTCGATTCAGA-TTA
* * * * *
1668058 CTTTCGAATTGGGTTAAATTCGATTTAGTTTG
1 CTTTCGATTTGGGTTAATTTCGATTCAGATTA
* * * ** * * *
1668090 CTTTCGGTTCGCGTTGTTTTCGGTTCGGGTTA
1 CTTTCGATTTGGGTTAATTTCGATTCAGATTA
*
1668122 CTTTCGATTTGGGTTAATTTCGATTGA-ATTA
1 CTTTCGATTTGGGTTAATTTCGATTCAGATTA
*
1668153 TTTTCGATT
1 CTTTCGATT
1668162 CGAGTCAAAT
Statistics
Matches: 100, Mismatches: 32, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
30 2 0.02
31 35 0.35
32 62 0.62
33 1 0.01
ACGTcount: A:0.16, C:0.13, G:0.22, T:0.50
Consensus pattern (32 bp):
CTTTCGATTTGGGTTAATTTCGATTCAGATTA
Found at i:1668110 original size:95 final size:95
Alignment explanation
Indices: 1667986--1668159 Score: 242
Period size: 95 Copynumber: 1.8 Consensus size: 95
1667976 TTGCTTTTGG
* *
1667986 TTTAGGTTGCTTTCGATTCGGGTTATTTTCGATTCAGATTACTTTCGGTTTGGGTTAATTTC-AT
1 TTTAGGTTGCTTTCGATTCGCGTTATTTTCGATTCAGATTACTTTCGATTTGGGTTAATTTCGA-
*
1668050 TTGATTTACTTTCGAATTGGGTTAAATTCGA
65 TTGAATTACTTTCGAATTGGGTTAAATTCGA
* * * * * *
1668081 TTTAGTTTGCTTTCGGTTCGCGTTGTTTTCGGTTCGGGTTACTTTCGATTTGGGTTAATTTCGAT
1 TTTAGGTTGCTTTCGATTCGCGTTATTTTCGATTCAGATTACTTTCGATTTGGGTTAATTTCGAT
*
1668146 TGAATTATTTTCGA
66 TGAATTACTTTCGA
1668160 TTCGAGTCAA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
95 67 0.99
96 1 0.01
ACGTcount: A:0.16, C:0.12, G:0.22, T:0.49
Consensus pattern (95 bp):
TTTAGGTTGCTTTCGATTCGCGTTATTTTCGATTCAGATTACTTTCGATTTGGGTTAATTTCGAT
TGAATTACTTTCGAATTGGGTTAAATTCGA
Found at i:1668638 original size:2 final size:2
Alignment explanation
Indices: 1668631--1668701 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
1668621 ATTTTTCCTT
1668631 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
1668673 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1668702 GGACTTTTTA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1672080 original size:54 final size:54
Alignment explanation
Indices: 1672004--1672352 Score: 475
Period size: 54 Copynumber: 6.4 Consensus size: 54
1671994 GTAAGTTTTT
* * * * * *
1672004 TGGGTTGCGCACGTAGTACCGATACAATCATTCATAAACTTATTATGAATTTCA
1 TGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCG
** * *
1672058 TGGGTTGCACACTTAGTGCCGATAC-AGTTGTTCCTAAACTTATTATGAATTTTCG
1 TGGGTTGCACACTTAGTGCCGATACGA-TCATTCATAAACTTATTATGAA-TTCCG
1672113 TGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCG
1 TGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCG
* * * **
1672167 TGGGCTGCACACTTAGTGTCGATACGGTCATTCATAAACTTATTATGAATTTTG
1 TGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCG
* * *
1672221 TGGGTTGCACATTTAGTGCCGATACGATCGTTCATAAACTTATTATGAATTCCA
1 TGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCG
* * * *
1672275 TAGATTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCCG
1 TGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCG
1672329 TGGGTTGCACACTTAGTGCCGATA
1 TGGGTTGCACACTTAGTGCCGATA
1672353 GTACATATAG
Statistics
Matches: 261, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.00
54 211 0.81
55 48 0.18
56 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (54 bp):
TGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCG
Found at i:1672272 original size:108 final size:108
Alignment explanation
Indices: 1671999--1672352 Score: 528
Period size: 108 Copynumber: 3.3 Consensus size: 108
1671989 TCATTGTAAG
* * * * * *
1671999 TTTTTTGGGTTGCGCACGTAGTACCGATACAATCATTCATAAACTTATTATGAATTTCATGGGTT
1 TTTTGTGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCATGGGTT
* * *
1672064 GCACACTTAGTGCCGATACAGTTGTTCCTAAACTTATTATGAA
66 GCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA
* *
1672107 TTTTCGTGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCGTGGGC
1 TTTT-GTGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCATGGGT
* *
1672172 TGCACACTTAGTGTCGATACGGTCATTCATAAACTTATTATGAA
65 TGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA
* * * *
1672216 TTTTGTGGGTTGCACATTTAGTGCCGATACGATCGTTCATAAACTTATTATGAATTCCATAGATT
1 TTTTGTGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCATGGGTT
1672281 GCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA
66 GCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA
**
1672324 TTCCGTGGGTTGCACACTTAGTGCCGATA
1 TTTTGTGGGTTGCACACTTAGTGCCGATA
1672353 GTACATATAG
Statistics
Matches: 221, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
108 126 0.57
109 95 0.43
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (108 bp):
TTTTGTGGGTTGCACACTTAGTGCCGATACGATCATTCATAAACTTATTATGAATTCCATGGGTT
GCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA
Found at i:1678530 original size:54 final size:53
Alignment explanation
Indices: 1678459--1678697 Score: 343
Period size: 54 Copynumber: 4.5 Consensus size: 53
1678449 ATAAGTTCTT
* *
1678459 TGGGGTGCACACGTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTGTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATT-TG
* *
1678513 TGGGTTGCACACTTAGTGCCTATACGGTCATTCATAAACTTATTATGAATTTCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTT-G
* * * *
1678567 TGGGTTGCACACTTAGTGTCGATATGGTCGTTCATAAACTTATTATGAATCTA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTG
** *
1678620 TTTGTTGCATACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAA-TTTG
*
1678674 TGGGTTGCACACTTAGTGTCGATA
1 TGGGTTGCACACTTAGTGCCGATA
1678698 GTACACATAG
Statistics
Matches: 162, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
53 45 0.28
54 117 0.72
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (53 bp):
TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTG
Found at i:1678667 original size:107 final size:108
Alignment explanation
Indices: 1678459--1678697 Score: 365
Period size: 107 Copynumber: 2.2 Consensus size: 108
1678449 ATAAGTTCTT
* * * *
1678459 TGGGGTGCACACGTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTGTGTGGGTTGCACA
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGCACA
*
1678524 CTTAGTGCCTATACGGTCATTCATAAACTTATTATGAATTTCG
66 CTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTTCG
* * *
1678567 TGGGTTGCACACTTAGTGTCGATATGGTCGTTCATAAACTTATTATGAATCTAT-T-TGTTGCAT
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAAT-TATGTGGGTTGCAC
* *
1678630 ACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTG
65 ACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTTCG
1678674 TGGGTTGCACACTTAGTGTCGATA
1 TGGGTTGCACACTTAGTGTCGATA
1678698 GTACACATAG
Statistics
Matches: 120, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
107 71 0.59
108 47 0.39
109 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (108 bp):
TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGCACA
CTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTTCG
Found at i:1681327 original size:21 final size:21
Alignment explanation
Indices: 1681301--1681347 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1681291 TATGGATTGA
1681301 TTCTTTGCTAAAATCATATTC
1 TTCTTTGCTAAAATCATATTC
1681322 TTCTTTGCTAAAATCATATTC
1 TTCTTTGCTAAAATCATATTC
1681343 TTCTT
1 TTCTT
1681348 CATGCAGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.51
Consensus pattern (21 bp):
TTCTTTGCTAAAATCATATTC
Found at i:1681642 original size:36 final size:36
Alignment explanation
Indices: 1681602--1682163 Score: 210
Period size: 36 Copynumber: 15.2 Consensus size: 36
1681592 AAGTGAATTG
* *
1681602 AAATTTGTTTTAAGAAATACAATCTCGAGTGAGATA
1 AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
* * *** *
1681638 AAATTTCTTGTTTCAGGTAAAAATTGTCTCAAGTGAGACA
1 AAA--T-TTGTTTTAAG-AAAAACAATCTCAAGTGAGATA
* * * * *
1681678 GAGTTTTTTTTAAGAAAAACAATCCCTAGTGAGATA
1 AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
* * ** * **
1681714 AAATTTGGTTTAGAGTGAAAACTGTATCAAGTGAGACG
1 AAATTTGTTTTA-AG-AAAAACAATCTCAAGTGAGATA
* *
1681752 AAGTTTGTTTTAAGAAAAAAAATCTCAAGTGAGATA
1 AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
** * *** *
1681788 AAATTTTGTTTCGAGTGAAAATTGTCTCAAG-CA-ATA
1 AAA-TTTGTTTTAAG-AAAAACAATCTCAAGTGAGATA
* * * *
1681824 CAAATTTTGTTTTAATAAAAACTATCTCGATTGAGATA
1 -AAA-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
** * ** ** * * *
1681862 AAATTTCGTTTCGAGTGAAAACTGTCTTGAGCGATACA
1 AAATTT-GTTTTAAG-AAAAACAATCTCAAGTGAGATA
* * *
1681900 AAGTTTGTTTTAAGAAAAATAAACTCAAGTGAGATA
1 AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
** * ** * **
1681936 AAATTTTGTTTCGAGTGAAAACTGTCTCAAGCGAGACG
1 AAA-TTTGTTTTAAG-AAAAACAATCTCAAGTGAGATA
* * * * *
1681974 AAGTTTATTTTAAGAATAACTATCTCGAGTGAGATA
1 AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
** * * * * **
1682010 AAATTTCGTTTTGGGTGAAAACTATTTCAAGCGAGACG
1 AAATTT-GTTTTAAG-AAAAACAATCTCAAGTGAGATA
* * **
1682048 AAGTTTGTTTTAAGAAAAACTATCTTGAGTGAGATA
1 AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
* ** * ** * *
1682084 AAATTTCATTTCGAGTTAAAACTGTTTCAAGTGAGACA
1 AAATTT-GTTTTAAG-AAAAACAATCTCAAGTGAGATA
* * *
1682122 AAGTTTGTTTTAAGAAAAACTATCTCGAGTGAGATA
1 AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
1682158 AAATTT
1 AAATTT
1682164 CTGATCTTTG
Statistics
Matches: 364, Mismatches: 143, Indels: 38
0.67 0.26 0.07
Matches are distributed among these distances:
36 136 0.37
37 86 0.24
38 117 0.32
39 8 0.02
40 17 0.05
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (36 bp):
AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATA
Found at i:1681770 original size:74 final size:74
Alignment explanation
Indices: 1681605--1682164 Score: 672
Period size: 74 Copynumber: 7.5 Consensus size: 74
1681595 TGAATTGAAA
* * *
1681605 TTTGTTTTAAGAAATACAATCTCGAGTGAGATAAAATTTCTTGTTTC-AGGTAAAAATTGTCTCA
1 TTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTC--GTTTCGA-GTGAAAACTGTCTCA
* *
1681669 AGTGAGACAGAG
63 AGCGAGACAAAG
* * * * * * *
1681681 TTTTTTTTAAGAAAAACAATCCCTAGTGAGATAAAATTTGGTTTAGAGTGAAAACTGTATCAAGT
1 TTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAGC
*
1681746 GAGACGAAG
66 GAGACAAAG
* * * *
1681755 TTTGTTTTAAGAAAAAAAATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAAATTGTCTCAAGC
1 TTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAGC
* * *
1681820 AATACAAAT
66 GAGACAAAG
* * * **
1681829 TTTGTTTTAATAAAAACTATCTCGATTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTTGAGC
1 TTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAGC
*
1681894 GATACAAAG
66 GAGACAAAG
* * * *
1681903 TTTGTTTTAAGAAAAATAAACTCAAGTGAGATAAAATTTTGTTTCGAGTGAAAACTGTCTCAAGC
1 TTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAGC
*
1681968 GAGACGAAG
66 GAGACAAAG
* * * * * * *
1681977 TTTATTTTAAGAATAACTATCTCGAGTGAGATAAAATTTCGTTTTGGGTGAAAACTATTTCAAGC
1 TTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAGC
*
1682042 GAGACGAAG
66 GAGACAAAG
* * * * * *
1682051 TTTGTTTTAAGAAAAACTATCTTGAGTGAGATAAAATTTCATTTCGAGTTAAAACTGTTTCAAGT
1 TTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAGC
1682116 GAGACAAAG
66 GAGACAAAG
*
1682125 TTTGTTTTAAGAAAAACTATCTCGAGTGAGATAAAATTTC
1 TTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTC
1682165 TGATCTTTGC
Statistics
Matches: 415, Mismatches: 68, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
74 379 0.91
75 1 0.00
76 35 0.08
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (74 bp):
TTTGTTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTCGTTTCGAGTGAAAACTGTCTCAAGC
GAGACAAAG
Found at i:1684317 original size:33 final size:30
Alignment explanation
Indices: 1684283--1684343 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
1684273 CAAAGTGAAC
1684283 AACAAGACAAAAAGAAATCAAGTTAGTAG-A
1 AACAAGACAAAAAG-AATCAAGTTAGTAGAA
*
1684313 AACAAGACAAAAAGAATCAAGTTAGTTGAA
1 AACAAGACAAAAAGAATCAAGTTAGTAGAA
1684343 A
1 A
1684344 TGATTAGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.15
Consensus pattern (30 bp):
AACAAGACAAAAAGAATCAAGTTAGTAGAA
Found at i:1684334 original size:29 final size:30
Alignment explanation
Indices: 1684283--1684343 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
1684273 CAAAGTGAAC
1684283 AACAAGACAAAAAGAAATCAAGTTAGTAGA
1 AACAAGACAAAAAGAAATCAAGTTAGTAGA
*
1684313 AACAAGACAAAAAG-AATCAAGTTAGTTGA
1 AACAAGACAAAAAGAAATCAAGTTAGTAGA
1684342 AA
1 AA
1684344 TGATTAGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.15
Consensus pattern (30 bp):
AACAAGACAAAAAGAAATCAAGTTAGTAGA
Found at i:1688929 original size:39 final size:39
Alignment explanation
Indices: 1688885--1688997 Score: 106
Period size: 39 Copynumber: 2.9 Consensus size: 39
1688875 AGTTAAAAGA
* * *
1688885 AATAATTTGGATTGATATAGTGAAATAATTTTAA-AAATT
1 AATAATTTAGAATGATATAGTGAAACAA-TTTAAGAAATT
*
1688924 AATAATTTAGAATGTTATAGTGAAACAATTTAAGAAATT
1 AATAATTTAGAATGATATAGTGAAACAATTTAAGAAATT
** * * *
1688963 AGGAATTTAAAAT-ATCAT-GTGAAATAATTTGAGAA
1 AATAATTTAGAATGAT-ATAGTGAAACAATTTAAGAA
1688998 TTAGGAATAA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
38 21 0.34
39 41 0.66
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (39 bp):
AATAATTTAGAATGATATAGTGAAACAATTTAAGAAATT
Found at i:1693762 original size:21 final size:20
Alignment explanation
Indices: 1693732--1693770 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1693722 ACTTCAAATC
1693732 CAAGCATCTAGA-AACACAAT
1 CAAGCATCTA-ATAACACAAT
1693752 CAAGCATTCTAATAACACA
1 CAAGCA-TCTAATAACACA
1693771 TTTAAACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.26, G:0.08, T:0.18
Consensus pattern (20 bp):
CAAGCATCTAATAACACAAT
Found at i:1703308 original size:3 final size:3
Alignment explanation
Indices: 1703300--1703541 Score: 299
Period size: 3 Copynumber: 78.7 Consensus size: 3
1703290 ATCACCATTT
* * *
1703300 TTA TTA TTA TTTA TT- TTA TTA TTA TTA TTA TTA TCA TCA TCA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1703345 TTTA TTTA TTA TTA TTG TTG TTA TTA TT- TTA TTA TTA TTA TCTGA TTA
1 -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-T-A TTA
*
1703393 TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1703439 TTA TTTA GTTA TTA TTA TTG TTG TTA TTA TTT TTA TTA TTA TTA TTA
1 TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1703486 TTA TTA TTT TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1703534 TTA TTA TT
1 TTA TTA TT
1703542 TCACTCATAT
Statistics
Matches: 216, Mismatches: 15, Indels: 16
0.87 0.06 0.06
Matches are distributed among these distances:
2 4 0.02
3 189 0.88
4 21 0.10
5 2 0.01
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1704819 original size:27 final size:27
Alignment explanation
Indices: 1704780--1704831 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1704770 TTAACAGAAG
*
1704780 CTCAACCGCTTCCTAACTGCCTAACCT
1 CTCAACAGCTTCCTAACTGCCTAACCT
*
1704807 CTCAACAGTTTCCTAACTGCCTAAC
1 CTCAACAGCTTCCTAACTGCCTAAC
1704832 TTCCTCTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.08, T:0.27
Consensus pattern (27 bp):
CTCAACAGCTTCCTAACTGCCTAACCT
Found at i:1709404 original size:27 final size:27
Alignment explanation
Indices: 1709365--1709416 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1709355 TTAACAGAAG
*
1709365 CTCAACCGCTTCCTAACTGCCTAACCT
1 CTCAACAGCTTCCTAACTGCCTAACCT
*
1709392 CTCAACAGTTTCCTAACTGCCTAAC
1 CTCAACAGCTTCCTAACTGCCTAAC
1709417 TTCCTCTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.08, T:0.27
Consensus pattern (27 bp):
CTCAACAGCTTCCTAACTGCCTAACCT
Found at i:1710975 original size:21 final size:21
Alignment explanation
Indices: 1710951--1710993 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
1710941 CACTTTTAAC
1710951 ATTTGTTCTCTT-AATTTATTT
1 ATTT-TTCTCTTCAATTTATTT
1710972 ATTTTTCTCTTCAATTTATTT
1 ATTTTTCTCTTCAATTTATTT
1710993 A
1 A
1710994 GTATTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTTCTCTTCAATTTATTT
Found at i:1714122 original size:14 final size:14
Alignment explanation
Indices: 1714077--1714126 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 14
1714067 GCAAAAACCA
1714077 AAAAAAGAAAAGAAGC
1 AAAAAAGAAAA-AA-C
1714093 AAAAAAGAAGAAAAC
1 AAAAAAGAA-AAAAC
*
1714108 AAAAAAGAAATAAC
1 AAAAAAGAAAAAAC
1714122 AAAAA
1 AAAAA
1714127 TCAAAAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 9 0.28
15 10 0.31
16 11 0.34
17 2 0.06
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.02
Consensus pattern (14 bp):
AAAAAAGAAAAAAC
Found at i:1715804 original size:106 final size:106
Alignment explanation
Indices: 1715679--1716419 Score: 1223
Period size: 106 Copynumber: 7.0 Consensus size: 106
1715669 GTTCCACTTG
* * * * * *
1715679 AGACAACACAAGTTCAACTTCACAAAGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAATT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
*
1715744 CAGAGCCAATTTCAACTTCACAGGGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * *
1715785 AGACAACACAAGTTTAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
*
1715850 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
1715891 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAACAACTTCAT-AATT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC-TCAATT
*
1715955 TCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
1715997 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAAAAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1716062 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * * *
1716103 AGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTTGTTATCAACAAACAAGTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
*
1716168 CAGAGCCAATTTAAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
1716209 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1716274 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
1716315 AGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
* * *
1716380 CAGAGCCAATTTCAATTTTACAGCGGAGGATATTGGACTC
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
1716420 GGAACAATAT
Statistics
Matches: 592, Mismatches: 41, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
105 1 0.00
106 590 1.00
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
Found at i:1716890 original size:2 final size:2
Alignment explanation
Indices: 1716879--1716911 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1716869 AATATAAAAC
1716879 AT AT -T 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
1716912 TATGTGTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1718390 original size:21 final size:21
Alignment explanation
Indices: 1718366--1718408 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
1718356 CACTTTTAAC
1718366 ATTTGTTCTCTT-AATTTATTT
1 ATTT-TTCTCTTCAATTTATTT
1718387 ATTTTTCTCTTCAATTTATTT
1 ATTTTTCTCTTCAATTTATTT
1718408 A
1 A
1718409 GTATTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTTCTCTTCAATTTATTT
Found at i:1722826 original size:19 final size:19
Alignment explanation
Indices: 1722799--1722850 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
1722789 ATGGTTTAAG
1722799 CCTTCGAGAAGAGAACAAAA
1 CCTT-GAGAAGAGAACAAAA
1722819 CCTTGAGAAGAGAACAAAA
1 CCTTGAGAAGAGAACAAAA
*
1722838 CCTTTAGAA-AGAA
1 CCTTGAGAAGAGAA
1722851 AATAGTTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 4 0.13
19 23 0.74
20 4 0.13
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.13
Consensus pattern (19 bp):
CCTTGAGAAGAGAACAAAA
Found at i:1727477 original size:24 final size:24
Alignment explanation
Indices: 1727445--1727495 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
1727435 CTAGCCCAAA
1727445 AGATAATTTTCCACTGCCTCATAT
1 AGATAATTTTCCACTGCCTCATAT
1727469 AGATAATTTTCCACTGCCTCATAT
1 AGATAATTTTCCACTGCCTCATAT
1727493 AGA
1 AGA
1727496 CACTTTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (24 bp):
AGATAATTTTCCACTGCCTCATAT
Found at i:1731147 original size:118 final size:117
Alignment explanation
Indices: 1730807--1731184 Score: 383
Period size: 119 Copynumber: 3.2 Consensus size: 117
1730797 TTTTATAGAT
* * * * * *
1730807 TCAATCCATCACATAATGACGTGGATCGACATTTTCAATGGAATA-GTTCAAAATGATAAGAACT
1 TCAATCCATCACAGAAAGAGGT-GATCGACATTTCCAATGGAA-AGGTTCATAATGAGAAGAACT
* * * * *
1730871 CATCCG-GAGAGGGAGAATACGTTCATAATGAGAAGAACTAGTTCGACTTTTTGC
64 CATCTGAAAG-GGGAGAATAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGC
* *
1730925 TTATATCCATCACA-AAAGGAGGTTGATCGACATTCCCAATGGAAAGGTTCATAGAT-AGAAGAA
1 TCA-ATCCATCACAGAAA-GAGG-TGATCGACATTTCCAATGGAAAGGTTCATA-ATGAGAAGAA
* ** *
1730988 CTCGTCTGAACA-AAGAGAATAAGTTAATAATGAGAAGAACTTGTTCGACCTTTTGC
62 CTCATCTGAA-AGGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGC
*
1731044 TCAAGTCCATCACAGAAAGAGGTGAATCGACATTTCCAATGG-AGGGTTCATAATGAGAAGAACT
1 TCAA-TCCATCACAGAAAGAGGTG-ATCGACATTTCCAATGGAAAGGTTCATAATGAGAAGAACT
* * * *
1731108 CATCTGAAAGGGGAAAATAAGTTCATAATGAGAAGAACTTATTCAACC-TTTCC
64 CATCTGAAAGGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGC
* * *
1731161 TGAAAACCATCACAGAAGGAGGTG
1 T-CAATCCATCACAGAAAGAGGTG
1731185 GTTCAACACT
Statistics
Matches: 217, Mismatches: 30, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
117 25 0.12
118 67 0.31
119 118 0.54
120 6 0.03
121 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (117 bp):
TCAATCCATCACAGAAAGAGGTGATCGACATTTCCAATGGAAAGGTTCATAATGAGAAGAACTCA
TCTGAAAGGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCGACCTTTTGC
Found at i:1731290 original size:3 final size:3
Alignment explanation
Indices: 1731282--1731396 Score: 110
Period size: 3 Copynumber: 38.7 Consensus size: 3
1731272 TTTTTATCAT
1731282 TTA TTA TTA TTA GTTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
1731327 TTTA TT- TTA TTA TCA TCA TCA TTA TTA TTA TTA TT- TTA TTG TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * * *
1731371 TCG TTG TTG TTG TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1731397 TCACTCTTAT
Statistics
Matches: 99, Mismatches: 8, Indels: 10
0.85 0.07 0.09
Matches are distributed among these distances:
2 6 0.06
3 87 0.88
4 6 0.06
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1731392 original size:41 final size:41
Alignment explanation
Indices: 1731295--1731396 Score: 107
Period size: 41 Copynumber: 2.5 Consensus size: 41
1731285 TTATTATTAG
* * *
1731295 TTATTATTATTATTATTATTATTATTTTATTATTTATTTTA
1 TTATCATTATTATTATTATTATTATTTTATTAGTTATGTTA
* * *
1731336 TTATCATCATCATTATTATTATTATTTTATT-GTTATCGTTG
1 TTATCATTATTATTATTATTATTATTTTATTAGTTAT-GTTA
* **
1731377 TTGTTGTTATTATTATTATT
1 TTATCATTATTATTATTATT
1731397 TCACTCTTAT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
40 4 0.08
41 45 0.92
ACGTcount: A:0.25, C:0.04, G:0.05, T:0.66
Consensus pattern (41 bp):
TTATCATTATTATTATTATTATTATTTTATTAGTTATGTTA
Found at i:1738736 original size:26 final size:25
Alignment explanation
Indices: 1738704--1738784 Score: 110
Period size: 26 Copynumber: 3.2 Consensus size: 25
1738694 CCCTCTTGAA
1738704 TTTTTAACTTTTTCTTTTCTCTTTC
1 TTTTTAACTTTTTCTTTTCTCTTTC
1738729 TTTATTAA-TTTTTCTCTTTCTCTTTC
1 TTT-TTAACTTTTTCT-TTTCTCTTTC
* *
1738755 ATTTTAACTTTTACTTTTTCTCTTTC
1 TTTTTAACTTTTTC-TTTTCTCTTTC
1738781 TTTT
1 TTTT
1738785 ACTCATCTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
25 14 0.29
26 34 0.69
27 1 0.02
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTTAACTTTTTCTTTTCTCTTTC
Found at i:1742719 original size:24 final size:24
Alignment explanation
Indices: 1742692--1742743 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1742682 AACGGATATA
*
1742692 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
1742716 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
1742740 TCAA
1 TCAA
1742744 GTAACATATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:1742744 original size:24 final size:24
Alignment explanation
Indices: 1742712--1742829 Score: 150
Period size: 24 Copynumber: 4.9 Consensus size: 24
1742702 AAACATAAAT
1742712 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCATATCAG-AATC
*
1742736 CAGGTCAAGTAACATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
* *
1742760 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
*
1742784 CATGTC-AGATATCATATCAGAATC
1 CAGGTCAAG-TATCATATCAGAATC
* *
1742808 CATGTCAAGTATCAGATCAGAA
1 CAGGTCAAGTATCATATCAGAA
1742830 ATCAAATCGA
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
23 5 0.06
24 77 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAGAATC
Found at i:1742781 original size:48 final size:48
Alignment explanation
Indices: 1742715--1742833 Score: 170
Period size: 48 Copynumber: 2.5 Consensus size: 48
1742705 CATAAATCAG
*
1742715 GTCAAGTATCATATCAGAAATCAGGTCA-AGTAACATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAGGTCAGA-TAACATATCAGAATCCAA
* * *
1742763 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAGGTCAGATAACATATCAGAATCCAA
1742811 GTCAAGTATCAGATCAGAAATCA
1 GTCAAGTATCAGATCAGAAATCA
1742834 AATCGAAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
47 3 0.05
48 57 0.89
49 4 0.06
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.24
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAAATCAGGTCAGATAACATATCAGAATCCAA
Found at i:1745317 original size:18 final size:18
Alignment explanation
Indices: 1745290--1745366 Score: 74
Period size: 18 Copynumber: 4.6 Consensus size: 18
1745280 CAACGGTCAA
1745290 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1745308 CGGGTGGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
* * *
1745321 CGGGTCAGGTAAATGGGT
1 CGGGTCGGGTCAACGGGT
*
1745339 CCGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1745357 CGGGTCGGGT
1 CGGGTCGGGT
1745367 TATGACCGGT
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
13 10 0.22
18 35 0.78
ACGTcount: A:0.13, C:0.19, G:0.49, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1745321 original size:31 final size:31
Alignment explanation
Indices: 1745284--1745362 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
1745274 TCCGGTCAAC
* *
1745284 GGTCAACGGGTCGGGTCAACGGGTCGGGTGG
1 GGTCAACGGGTCGGGTCAACGGGTCCGGTCG
* * *
1745315 GGTCAACGGGTCAGGTAAATGGGTCCGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCCGGTCG
1745346 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
1745363 GGGTTATGAC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.15, C:0.20, G:0.47, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCCGGTCG
Found at i:1745325 original size:13 final size:13
Alignment explanation
Indices: 1745284--1745312 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1745274 TCCGGTCAAC
1745284 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1745297 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1745310 GGT
1 GGT
1745313 GGGGTCAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1747479 original size:24 final size:24
Alignment explanation
Indices: 1747452--1747503 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1747442 AACGGATATA
*
1747452 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
1747476 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
1747500 TCAA
1 TCAA
1747504 GTAACATATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:1747504 original size:24 final size:24
Alignment explanation
Indices: 1747472--1747589 Score: 150
Period size: 24 Copynumber: 4.9 Consensus size: 24
1747462 AAACATAAAT
*
1747472 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
* *
1747496 CAGGTCAAGTAACATATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
1747520 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
1747544 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
1747568 CATGTCAAGTATCAGATCAGAA
1 CAGGTCAAGTATCAGATCAGAA
1747590 ATCAAATCGA
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
23 5 0.06
24 79 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:1747606 original size:48 final size:47
Alignment explanation
Indices: 1747475--1747606 Score: 142
Period size: 48 Copynumber: 2.7 Consensus size: 47
1747465 CATAAATCAG
* * *
1747475 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAA--AATCAGATCAGAATCCAA
* * *
1747523 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCA-AAATCAGATCAGAATCCAA
*
1747571 GTCAAGTATCAGATCAGAAATCAAATCGAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTC-AAAATCAG
1747607 GTAAAATATT
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
47 4 0.06
48 62 0.87
49 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAATCAGATCAGAATCCAA
Found at i:1750048 original size:7 final size:7
Alignment explanation
Indices: 1750036--1750067 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1750026 TGGTCAACTC
1750036 CGGTCAA
1 CGGTCAA
1750043 CGGTCAA
1 CGGTCAA
1750050 CGGGTCAA
1 C-GGTCAA
1750058 CGGTCAA
1 CGGTCAA
1750065 CGG
1 CGG
1750068 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1750057 original size:8 final size:8
Alignment explanation
Indices: 1750037--1750084 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 8
1750027 GGTCAACTCC
1750037 GGTCAAC-
1 GGTCAACG
1750044 GGTCAACG
1 GGTCAACG
1750052 GGTCAAC-
1 GGTCAACG
1750059 GGTCAACG
1 GGTCAACG
1750067 GGT---CG
1 GGTCAACG
1750072 GGTCAACG
1 GGTCAACG
1750080 GGTCA
1 GGTCA
1750085 GGTAAATGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.39
8 17 0.47
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1750057 original size:15 final size:15
Alignment explanation
Indices: 1750037--1750084 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
1750027 GGTCAACTCC
1750037 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1750052 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1750067 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1750080 GGTCA
1 GGTCA
1750085 GGTAAATGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1752235 original size:24 final size:24
Alignment explanation
Indices: 1752208--1752259 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1752198 AACGGATATA
*
1752208 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
1752232 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
1752256 TCAA
1 TCAA
1752260 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:1752260 original size:24 final size:24
Alignment explanation
Indices: 1752228--1752345 Score: 159
Period size: 24 Copynumber: 4.9 Consensus size: 24
1752218 AAACATAAAT
*
1752228 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
1752252 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
1752276 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
1752300 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
1752324 CATGTCAAGTATCAGATCAGAA
1 CAGGTCAAGTATCAGATCAGAA
1752346 ATCAAATCGA
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
23 5 0.06
24 79 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:1752362 original size:48 final size:47
Alignment explanation
Indices: 1752231--1752362 Score: 151
Period size: 48 Copynumber: 2.7 Consensus size: 47
1752221 CATAAATCAG
* *
1752231 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAA--AATCAGATCAGAATCCAA
* * *
1752279 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCA-AAATCAGATCAGAATCCAA
*
1752327 GTCAAGTATCAGATCAGAAATCAAATCGAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTC-AAAATCAG
1752363 GTAAAATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
47 4 0.06
48 63 0.88
49 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAATCAGATCAGAATCCAA
Found at i:1754804 original size:7 final size:7
Alignment explanation
Indices: 1754792--1754823 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1754782 TGGTCAACTC
1754792 CGGTCAA
1 CGGTCAA
1754799 CGGTCAA
1 CGGTCAA
1754806 CGGGTCAA
1 C-GGTCAA
1754814 CGGTCAA
1 CGGTCAA
1754821 CGG
1 CGG
1754824 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1754813 original size:8 final size:8
Alignment explanation
Indices: 1754793--1754840 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 8
1754783 GGTCAACTCC
1754793 GGTCAAC-
1 GGTCAACG
1754800 GGTCAACG
1 GGTCAACG
1754808 GGTCAAC-
1 GGTCAACG
1754815 GGTCAACG
1 GGTCAACG
1754823 GGT---CG
1 GGTCAACG
1754828 GGTCAACG
1 GGTCAACG
1754836 GGTCA
1 GGTCA
1754841 GGTAAATGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.39
8 17 0.47
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1754813 original size:15 final size:15
Alignment explanation
Indices: 1754793--1754840 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
1754783 GGTCAACTCC
1754793 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1754808 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1754823 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1754836 GGTCA
1 GGTCA
1754841 GGTAAATGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1756991 original size:24 final size:24
Alignment explanation
Indices: 1756964--1757015 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1756954 AACGGATATA
*
1756964 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
1756988 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
1757012 TCAA
1 TCAA
1757016 GTAACATATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:1757016 original size:24 final size:24
Alignment explanation
Indices: 1756984--1757101 Score: 150
Period size: 24 Copynumber: 4.9 Consensus size: 24
1756974 AAACATAAAT
*
1756984 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
* *
1757008 CAGGTCAAGTAACATATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
1757032 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
1757056 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
1757080 CATGTCAAGTATCAGATCAGAA
1 CAGGTCAAGTATCAGATCAGAA
1757102 ATCAAATCGA
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
23 5 0.06
24 79 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:1757118 original size:48 final size:47
Alignment explanation
Indices: 1756987--1757118 Score: 142
Period size: 48 Copynumber: 2.7 Consensus size: 47
1756977 CATAAATCAG
* * *
1756987 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAA--AATCAGATCAGAATCCAA
* * *
1757035 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCA-AAATCAGATCAGAATCCAA
*
1757083 GTCAAGTATCAGATCAGAAATCAAATCGAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTC-AAAATCAG
1757119 GTAAAATATT
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
47 4 0.06
48 62 0.87
49 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAATCAGATCAGAATCCAA
Found at i:1759567 original size:8 final size:7
Alignment explanation
Indices: 1759546--1759577 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1759536 TGGTCAACTC
1759546 CGGTCAA
1 CGGTCAA
1759553 CGGTCAA
1 CGGTCAA
1759560 CGGGTCAA
1 C-GGTCAA
1759568 CGGTCAA
1 CGGTCAA
1759575 CGG
1 CGG
1759578 GTGGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Done.