Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold20
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: 3599867
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51021 characters in sequence are not A, C, G, or T
File 8 of 25
Found at i:1086539 original size:94 final size:98
Alignment explanation
Indices: 1086413--1086761 Score: 293
Period size: 101 Copynumber: 3.6 Consensus size: 98
1086403 AAATAAAAAT
* * * *
1086413 GTGCCACGGAGTTATGGACTTAAAATGAAAAAAGGTGCCATGAAGTTATGGACTTTAAAAGGGAA
1 GTGCCACAGAGTTATGGATTTAAAAAGAAAAAAGGTGCCACGAAGTTATGGACTTTAAAAGGGAA
* **
1086478 AAGTGCTACGAAGTTACGGA-T-TTAAG-G-GG
66 AAGTGCTACAAAGTTACGGACTAAAAAGAGAGG
* * * *
1086507 GTGCCACAGAGTTGTGGATTTAAAAAGAAAAAAGGTGCCACGGAGTTGTGGACTTTAAAA-GAAA
1 GTGCCACAGAGTTATGGATTTAAAAAGAAAAAAGGTGCCACGAAGTTATGGACTTTAAAAGGGAA
* **
1086571 AAGGTGCCACAAAGTTGTGGACTCAAAAAGAAGAAGG
66 AA-GTGCTACAAAGTTACGGACT-AAAAAG-AG-AGG
* * *
1086608 GTGCCACATAGTTATGGACTTT-AAAAGAAAAAGGGTGCCACGAAGTTATAGACTTTAAAAGGGA
1 GTGCCACAGAGTTATGGA-TTTAAAAAGAAAAAAGGTGCCACGAAGTTATGGACTTTAAAAGGGA
* *** **
1086672 AAGGTGCTATGGAGTTTGTGGACTTAAAAAGA-ACGAG
65 AAAGTGCTACAAAG-TTACGGAC-TAAAAAGAGA-G-G
* * * * * *
1086709 TTGCCACAGAGTTGTGGACTTAAAAAG--AAAAGGTGCCATGGAGTTGTGGACTT
1 GTGCCACAGAGTTATGGATTTAAAAAGAAAAAAGGTGCCACGAAGTTATGGACTT
1086762 CGTAGACACC
Statistics
Matches: 205, Mismatches: 35, Indels: 25
0.77 0.13 0.09
Matches are distributed among these distances:
93 5 0.02
94 67 0.33
95 1 0.00
97 3 0.01
99 23 0.11
100 3 0.01
101 81 0.40
102 21 0.10
103 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.23
Consensus pattern (98 bp):
GTGCCACAGAGTTATGGATTTAAAAAGAAAAAAGGTGCCACGAAGTTATGGACTTTAAAAGGGAA
AAGTGCTACAAAGTTACGGACTAAAAAGAGAGG
Found at i:1086645 original size:101 final size:101
Alignment explanation
Indices: 1086505--1086761 Score: 308
Period size: 101 Copynumber: 2.6 Consensus size: 101
1086495 GGATTTAAGG
1086505 GGGTGCCACAGAGTTGTGGA-TTTAAAAAGAAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGA
1 GGGTGCCACAGAGTTGTGGACTTT-AAAAG-AAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGA
1086569 AAAAGGTGCCACAAAG-TTGTGGACTCAAAAAGAA-GAA
64 AAAAGGTGCCACAAAGTTTGTGGACTCAAAAAGAACG-A
* * * * * **
1086606 GGGTGCCACATAGTTATGGACTTTAAAAGAAAAAGGGTGCCACGAAGTTATAGACTTTAAAAGGG
1 GGGTGCCACAGAGTTGTGGACTTTAAAAGAAAAA-GGTGCCACGGAGTTGTGGACTTTAAAAGAA
* *** *
1086671 AAAGGTGCTATGGAGTTTGTGGACTTAAAAAGAACGA
65 AAAGGTGCCACAAAGTTTGTGGACTCAAAAAGAACGA
* * *
1086708 -GTTGCCACAGAGTTGTGGACTTAAAAAG-AAAAGGTGCCATGGAGTTGTGGACTT
1 GGGTGCCACAGAGTTGTGGACTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
1086762 CGTAGACACC
Statistics
Matches: 132, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
99 18 0.14
100 9 0.07
101 83 0.63
102 21 0.16
103 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.29, T:0.22
Consensus pattern (101 bp):
GGGTGCCACAGAGTTGTGGACTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGAAA
AAGGTGCCACAAAGTTTGTGGACTCAAAAAGAACGA
Found at i:1087017 original size:21 final size:22
Alignment explanation
Indices: 1086987--1087028 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1086977 AGTCACATTG
1086987 TTCTCTAAATGTATCAATACAT
1 TTCTCTAAATGTATCAATACAT
*
1087009 TTCT-TAAATGTATCGATACA
1 TTCTCTAAATGTATCAATACA
1087029 AGGTCCCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (22 bp):
TTCTCTAAATGTATCAATACAT
Found at i:1092551 original size:13 final size:13
Alignment explanation
Indices: 1092533--1092557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1092523 CATTATGCTT
1092533 TGTATCGATACAA
1 TGTATCGATACAA
1092546 TGTATCGATACA
1 TGTATCGATACA
1092558 TGTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1092554 original size:33 final size:31
Alignment explanation
Indices: 1092512--1092579 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 31
1092502 ACACACCCAG
*
1092512 ATGTATCGATACAT-TATGCTTTGTATCGATACA
1 ATGTATCGATACATGT-T-CATTGTATCGATA-A
1092545 ATGTATCGATACATGTTCATTGTATCGATAA
1 ATGTATCGATACATGTTCATTGTATCGATAA
1092576 ATGT
1 ATGT
1092580 TCATTGCATC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
31 5 0.15
32 12 0.36
33 15 0.45
34 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (31 bp):
ATGTATCGATACATGTTCATTGTATCGATAA
Found at i:1092570 original size:19 final size:19
Alignment explanation
Indices: 1092546--1092617 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
1092536 ATCGATACAA
1092546 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
*
1092565 TGTATCGATAAATGTTCAT
1 TGTATCGATACATGTTCAT
* **
1092584 TGCATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
1092604 TGTATCGATACATG
1 TGTATCGATACATG
1092618 AAACTGGCAG
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 31 0.67
20 15 0.33
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:1092681 original size:13 final size:13
Alignment explanation
Indices: 1092663--1092692 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1092653 GATACATGGC
1092663 ACATTGTATCGAT
1 ACATTGTATCGAT
*
1092676 ACATTGTATTGAT
1 ACATTGTATCGAT
1092689 ACAT
1 ACAT
1092693 GATGAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:1092690 original size:33 final size:32
Alignment explanation
Indices: 1092646--1092714 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
1092636 CTACCATTGT
1092646 TTGTATCGATACATG-GCACATTGTATCGATACA
1 TTGTATCGATACATGAG-A-ATTGTATCGATACA
* *
1092679 TTGTATTGATACATGATGAATTTTATCGATACA
1 TTGTATCGATACATGA-GAATTGTATCGATACA
1092712 TTG
1 TTG
1092715 CTTTAAATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (32 bp):
TTGTATCGATACATGAGAATTGTATCGATACA
Found at i:1095072 original size:13 final size:13
Alignment explanation
Indices: 1095054--1095079 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1095044 ACATAAGTGT
1095054 TGTATCGATACAA
1 TGTATCGATACAA
1095067 TGTATCGATACAA
1 TGTATCGATACAA
1095080 AGCTACTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1108886 original size:10 final size:10
Alignment explanation
Indices: 1108863--1108909 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
1108853 ACCCTCCGTA
1108863 AAAAAAAGAGAC
1 AAAAAAA-A-AC
1108875 AAAAAAAAAC
1 AAAAAAAAAC
1108885 AAAAAATAAA-
1 AAAAAA-AAAC
*
1108895 AAAAAACAAC
1 AAAAAAAAAC
1108905 AAAAA
1 AAAAA
1108910 GGGTCCGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 2 0.06
10 19 0.59
11 4 0.12
12 7 0.22
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:1108888 original size:20 final size:21
Alignment explanation
Indices: 1108865--1108910 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1108855 CCTCCGTAAA
*
1108865 AAAAAGAGACAAAAAAA-AAC
1 AAAAAGAGAAAAAAAAACAAC
*
1108885 AAAAA-ATAAAAAAAAACAAC
1 AAAAAGAGAAAAAAAAACAAC
1108905 AAAAAG
1 AAAAAG
1108911 GGTCCGGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.83, C:0.09, G:0.07, T:0.02
Consensus pattern (21 bp):
AAAAAGAGAAAAAAAAACAAC
Found at i:1108895 original size:17 final size:18
Alignment explanation
Indices: 1108875--1108908 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1108865 AAAAAGAGAC
1108875 AAAAAAAAACAA-AAAAT
1 AAAAAAAAACAACAAAAT
1108892 AAAAAAAAACAACAAAA
1 AAAAAAAAACAACAAAA
1108909 AGGGTCCGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (18 bp):
AAAAAAAAACAACAAAAT
Found at i:1109930 original size:37 final size:37
Alignment explanation
Indices: 1109889--1109969 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
1109879 TGCCACAATC
*
1109889 ATGCATTTATGACACCCATAACATTTCATTTTGCATG
1 ATGCATTTATGACACCCATAACATTTCATTTTGCATA
* ***
1109926 ATGCATTTGTGACTTTCATAACATTTCATTTTGCATA
1 ATGCATTTATGACACCCATAACATTTCATTTTGCATA
1109963 ATGCATT
1 ATGCATT
1109970 CGTGCTTCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (37 bp):
ATGCATTTATGACACCCATAACATTTCATTTTGCATA
Found at i:1113891 original size:52 final size:52
Alignment explanation
Indices: 1113816--1113941 Score: 225
Period size: 52 Copynumber: 2.4 Consensus size: 52
1113806 AATATGAAAT
* *
1113816 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATGTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
1113868 TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
*
1113920 TTTTCCTGCATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
1113942 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
Found at i:1113968 original size:13 final size:13
Alignment explanation
Indices: 1113950--1113974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1113940 CAAAGATCAG
1113950 TGTATCGATACAA
1 TGTATCGATACAA
1113963 TGTATCGATACA
1 TGTATCGATACA
1113975 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1116883 original size:34 final size:33
Alignment explanation
Indices: 1116840--1116906 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 33
1116830 GCCGTTACAA
*
1116840 GCAATGTATCGATACAATT-TCCTCATGTATCGAT
1 GCAATGTATCGATAC-ATTGTAC-CATGTATCGAT
1116874 GCAATGTATCGATACATTGTACCATGTATCGAT
1 GCAATGTATCGATACATTGTACCATGTATCGAT
1116907 ATAAATAGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
33 14 0.45
34 17 0.55
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (33 bp):
GCAATGTATCGATACATTGTACCATGTATCGAT
Found at i:1116964 original size:20 final size:20
Alignment explanation
Indices: 1116939--1116998 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
1116929 CTACCAATCT
1116939 CATGTATCGATACAATTATC
1 CATGTATCGATACAATTATC
* *
1116959 CATGTATCGATACAATGA-G
1 CATGTATCGATACAATTATC
1116978 CATGTATCGATACAATGTATC
1 CATGTATCGATACAAT-TATC
1116999 GATGCAAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTATC
Found at i:1116983 original size:19 final size:20
Alignment explanation
Indices: 1116939--1116994 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
1116929 CTACCAATCT
*
1116939 CATGTATCGATACAATTATC
1 CATGTATCGATACAATGATC
*
1116959 CATGTATCGATACAATGA-G
1 CATGTATCGATACAATGATC
1116978 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1116995 TATCGATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATGATC
Found at i:1125775 original size:19 final size:20
Alignment explanation
Indices: 1125729--1125781 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1125719 CTGCCAATCT
*
1125729 CATGTATCGATACAATTATC
1 CATGTATCGATACAATGATC
* *
1125749 CTTGTATCGATACAATGA-G
1 CATGTATCGATACAATGATC
1125768 CATGTATCGATACA
1 CATGTATCGATACA
1125782 TTGTATCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATGATC
Found at i:1125788 original size:13 final size:13
Alignment explanation
Indices: 1125770--1125794 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1125760 ACAATGAGCA
1125770 TGTATCGATACAT
1 TGTATCGATACAT
1125783 TGTATCGATACA
1 TGTATCGATACA
1125795 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1125814 original size:33 final size:32
Alignment explanation
Indices: 1125750--1125815 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
1125740 ACAATTATCC
* * *
1125750 TTGTATCGATACAATGAGCATGTATCGATACA
1 TTGTATCGATACAAAGAGAATGTATCAATACA
*
1125782 TTGTATCGATACAAAGCATAATGTATCAATACA
1 TTGTATCGATACAAAG-AGAATGTATCAATACA
1125815 T
1 T
1125816 CTAGGTGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACAAAGAGAATGTATCAATACA
Found at i:1132185 original size:20 final size:19
Alignment explanation
Indices: 1132160--1132232 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
1132150 ACATACCAGA
*
1132160 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
*
1132180 TGTATCGATAAATGTTCAT
1 TGTATCGATACATGTTCAT
**
1132199 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
*
1132219 TGTATCAATACATG
1 TGTATCGATACATG
1132233 AGATTGGCAG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.36
20 28 0.62
21 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:1132298 original size:13 final size:13
Alignment explanation
Indices: 1132277--1132307 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1132267 CGATACATGG
*
1132277 TACAATGTATCGA
1 TACATTGTATCGA
1132290 TACATTGTATCGA
1 TACATTGTATCGA
1132303 TACAT
1 TACAT
1132308 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1132303 original size:33 final size:33
Alignment explanation
Indices: 1132261--1132327 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
1132251 CTACCACTGT
*
1132261 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
1132294 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
1132327 T
1 T
1132328 GATGAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:1132318 original size:20 final size:20
Alignment explanation
Indices: 1132293--1132347 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
1132283 GTATCGATAC
1132293 ATTGTATCGATACATGATGA
1 ATTGTATCGATACATGATGA
1132313 ATTGTATCGATACATGATGA
1 ATTGTATCGATACATGATGA
1132333 ATTGTATCGATACAT
1 ATTGTATCGATACAT
1132348 TGCTTGTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGATGA
Found at i:1132606 original size:28 final size:28
Alignment explanation
Indices: 1132575--1132753 Score: 177
Period size: 28 Copynumber: 6.4 Consensus size: 28
1132565 CCCCCCTTGC
*
1132575 AAAGCCTACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * *
1132603 AAAGCCCATAAGTCAGTGGCATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
* * *
1132632 AAAGCCCACAAGTTAATGGC-ACTTTTTC-
1 AAAGCCCACAAGTCAGTGGCAAC--CTTCA
1132660 AAAGCCCACAAGTCAGTGGCAACCTTC-
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* *
1132687 AAAGCCCATAAGGCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* **
1132715 AAAGCACACAAGTTGGT-GCAACCCTTTCA
1 AAAGCCCACAAGTCAGTGGCAA-CC-TTCA
1132744 AAAGCCCACA
1 AAAGCCCACA
1132754 CAAGTTGGTG
Statistics
Matches: 126, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
27 32 0.25
28 53 0.42
29 41 0.33
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:1132888 original size:49 final size:49
Alignment explanation
Indices: 1132816--1132976 Score: 162
Period size: 49 Copynumber: 3.2 Consensus size: 49
1132806 TATTAGCACG
* * * *
1132816 TTTAAGTCCGATGTTGCTCGCCTTGAATCAGCACATTGGCACCTTCATT
1 TTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * *
1132865 TTTAAGTCTAATATTGCTGGCCTTGAATTAGCATATTAGTGC-CTTTGTCATC
1 TTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATT-G-GCAC-CT-TCATC
* ** * *
1132917 TTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTAGCACCTTCACC
1 TTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
1132966 TTTAAGTCCAA
1 TTTAAGTCCAA
1132977 AATCACTAGC
Statistics
Matches: 90, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
49 46 0.51
50 5 0.06
51 4 0.04
52 35 0.39
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (49 bp):
TTTAAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
Found at i:1132983 original size:49 final size:49
Alignment explanation
Indices: 1132835--1133006 Score: 182
Period size: 49 Copynumber: 3.4 Consensus size: 49
1132825 GATGTTGCTC
* * * **
1132835 GCCTTGAATCAGCACATTGGCACCTTCATTTTTAAGTCTAATATTGCTG
1 GCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCCAATATCACTG
* * ** *
1132884 GCCTTGAATTAGCATATTAGTGCCTTTGTCATCTTTAAGTCCAATGTCACTG
1 GCCTTGAATCAGCACATTAGCACC--T-TCATCTTTAAGTCCAATATCACTG
* * *
1132936 GCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAAAATCACTA
1 GCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCCAATATCACTG
* *
1132985 GCATTGAATCAGCATATTAGCA
1 GCCTTGAATCAGCACATTAGCA
1133007 TCTGTAACAT
Statistics
Matches: 100, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
49 59 0.59
50 1 0.01
51 1 0.01
52 39 0.39
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (49 bp):
GCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCCAATATCACTG
Found at i:1132992 original size:101 final size:101
Alignment explanation
Indices: 1132816--1133004 Score: 252
Period size: 101 Copynumber: 1.9 Consensus size: 101
1132806 TATTAGCACG
* ** * ** * * **
1132816 TTTAAGTCCGATGTTGCTCGCCTTGAATCAGCACATTGGCACCTTCATTTTTAAGTCTAATATTG
1 TTTAAGTCCAATGTCACTCGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAAAATCA
* * *
1132881 CTGGCCTTGAATTAGCATATTAGTGCCTTTGTCATC
66 CTAGCATTGAATCAGCATATTAGTGCCTTTGTCATC
*
1132917 TTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAAAATCA
1 TTTAAGTCCAATGTCACTCGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAAAATCA
1132982 CTAGCATTGAATCAGCATATTAG
66 CTAGCATTGAATCAGCATATTAG
1133005 CATCTGTAAC
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 74 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (101 bp):
TTTAAGTCCAATGTCACTCGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAAAATCA
CTAGCATTGAATCAGCATATTAGTGCCTTTGTCATC
Found at i:1133083 original size:52 final size:50
Alignment explanation
Indices: 1132816--1133159 Score: 212
Period size: 52 Copynumber: 6.8 Consensus size: 50
1132806 TATTAGCACG
* * * * * *
1132816 TTTAAGTCCGATGTTGCTCGCCTTGAATCAGCACATTGGCAC-CTTCATT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTCATC
* * * *
1132865 TTTAAGTCTAATATTGCTGGCCTTGAATTAGCATATTAGTGC-CTTTGTCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATT-G-GCACTTT-TCATC
* * * * *
1132917 TTTAAGTCCAATGTCACTGGCCTTGAATCAGCACATTAGCAC-CTTCACC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTCATC
** * * * * **
1132966 TTTAAGTCCAAAATCACTAGCATTGAATCAGCATATTAGCATCTGTAACAT-
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CT-TTTCATC
* **
1133017 TCCTAAACCCAATGTCGCTGGCCTTGAATCAGCATATTGGCATTCTTTTCATC
1 T-TTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA--CTTTTCATC
* * ** * * *
1133070 TTCAAGTCTAATGTCGCT-GATTGTGAATCAGCACATTGACATTCTTTACATC
1 TTTAAGTCCAATGTCGCTGGCCT-TGAATCAGCATATTGGCA--CTTTTCATC
* * ** *
1133122 TTTAAGCCCAATATCATTGGTCTTGAATCAGCATATTG
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
1133160 ACACCTTTAT
Statistics
Matches: 226, Mismatches: 56, Indels: 23
0.74 0.18 0.08
Matches are distributed among these distances:
49 71 0.31
50 6 0.03
51 7 0.03
52 136 0.60
53 6 0.03
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (50 bp):
TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACTTTTCATC
Found at i:1136422 original size:68 final size:69
Alignment explanation
Indices: 1136342--1136493 Score: 227
Period size: 69 Copynumber: 2.2 Consensus size: 69
1136332 TAGAGAAATG
* * *
1136342 GGGTTGGAGTATCCC-GACAATGATAATTTGGACAAAATAAGACTTAAATTTTGATGAGTTTA-A
1 GGGTTGGAGTATCCCTGACAATGACAATTTAGACAAAATAAGACTTAAAATTTGATGAGTTTACA
1136405 AAGCA
66 AA-CA
* *
1136410 GGGTTAGAGTATCCCTGACAATGACAATTTAGACAAAATAAGATTTAAAATTTGATGAGTTTACA
1 GGGTTGGAGTATCCCTGACAATGACAATTTAGACAAAATAAGACTTAAAATTTGATGAGTTTACA
1136475 AACA
66 AACA
*
1136479 GAGTTGGAGTATCCC
1 GGGTTGGAGTATCCC
1136494 CTCGGAGGAA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
68 14 0.19
69 58 0.77
70 3 0.04
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (69 bp):
GGGTTGGAGTATCCCTGACAATGACAATTTAGACAAAATAAGACTTAAAATTTGATGAGTTTACA
AACA
Found at i:1138882 original size:16 final size:17
Alignment explanation
Indices: 1138790--1138886 Score: 69
Period size: 16 Copynumber: 5.6 Consensus size: 17
1138780 ATTGGCCATT
* *
1138790 TTTTTATTTTTTTATTGTT
1 TTTTTAATTTTTTA-T-TA
*
1138809 TTTTTAATTTTTT-TGA
1 TTTTTAATTTTTTATTA
1138825 TTTCTTAA-TTTTTATTA
1 TTT-TTAATTTTTTATTA
*
1138842 TTATATTGAA--TATTATTA
1 TT-T-TT-AATTTTTTATTA
1138860 TTTTTAATTTTTTATTA
1 TTTTTAATTTTTTATTA
1138877 -TTTTAATTTT
1 TTTTTAATTTT
1138887 ATATAAAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
15 2 0.03
16 20 0.31
17 17 0.26
18 12 0.18
19 14 0.22
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTTTAATTTTTTATTA
Found at i:1143683 original size:13 final size:13
Alignment explanation
Indices: 1143665--1143690 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1143655 ATTTTTTTTG
1143665 TGTATCGATACAT
1 TGTATCGATACAT
1143678 TGTATCGATACAT
1 TGTATCGATACAT
1143691 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1144429 original size:21 final size:21
Alignment explanation
Indices: 1144388--1144431 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1144378 CTCCCCTTTA
* *
1144388 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1144409 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1144430 TC
1 TC
1144432 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1146087 original size:21 final size:21
Alignment explanation
Indices: 1146053--1146092 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1146043 GCTGGTTTTG
1146053 ATGAAAAACGAAGTAATTTTAA
1 ATGAAAAACGAAGT-ATTTTAA
1146075 ATGAAAAAC-AAGTATTTT
1 ATGAAAAACGAAGTATTTT
1146093 GCAAAAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 9 0.50
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (21 bp):
ATGAAAAACGAAGTATTTTAA
Found at i:1148337 original size:15 final size:15
Alignment explanation
Indices: 1148317--1148347 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1148307 ATTTCGTTTG
*
1148317 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1148332 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1148347 G
1 G
1148348 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1152433 original size:13 final size:13
Alignment explanation
Indices: 1152415--1152440 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1152405 ATTTTTTTTG
1152415 TGTATCGATACAT
1 TGTATCGATACAT
1152428 TGTATCGATACAT
1 TGTATCGATACAT
1152441 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1153579 original size:20 final size:20
Alignment explanation
Indices: 1153505--1153583 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 20
1153495 ATGTCCAAAA
*
1153505 TGTATCGATACATGTTTCTG
1 TGTATCGATACATTTTTCTG
* **
1153525 TGTATCGATACATCTGGAAATTCAA
1 TGTATCGATACAT-T----TTTCTG
*
1153550 TGTATTGATACATTTTTCTG
1 TGTATCGATACATTTTTCTG
1153570 TGTATCGATACATT
1 TGTATCGATACATT
1153584 GTATCGATAC
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
20 29 0.64
24 1 0.02
25 15 0.33
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTTTTCTG
Found at i:1153588 original size:13 final size:13
Alignment explanation
Indices: 1153570--1153594 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1153560 CATTTTTCTG
1153570 TGTATCGATACAT
1 TGTATCGATACAT
1153583 TGTATCGATACA
1 TGTATCGATACA
1153595 GGGTGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1156171 original size:13 final size:13
Alignment explanation
Indices: 1156153--1156178 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1156143 TACAGCAAGT
1156153 ATGTATCGATACA
1 ATGTATCGATACA
1156166 ATGTATCGATACA
1 ATGTATCGATACA
1156179 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1161723 original size:23 final size:23
Alignment explanation
Indices: 1161692--1161739 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1161682 AAAATGGCTC
* *
1161692 GTATGAGAACTCTATCTAGTTTT
1 GTATAAGAACTCCATCTAGTTTT
*
1161715 GTATAAGAACTCCATCTGGTTTT
1 GTATAAGAACTCCATCTAGTTTT
1161738 GT
1 GT
1161740 CATTCAAGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.42
Consensus pattern (23 bp):
GTATAAGAACTCCATCTAGTTTT
Found at i:1162583 original size:11 final size:11
Alignment explanation
Indices: 1162566--1162598 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1162556 TAGCAAATTA
1162566 AATAATTATTT
1 AATAATTATTT
*
1162577 GATAATTATTT
1 AATAATTATTT
1162588 AATAATT-TTT
1 AATAATTATTT
1162598 A
1 A
1162599 TAGGATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AATAATTATTT
Found at i:1164387 original size:21 final size:21
Alignment explanation
Indices: 1164349--1164388 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1164339 TTAAAAAAAT
*
1164349 TATTTTATATTAATATTTATA
1 TATTTTATAATAATATTTATA
1164370 TATTTTATAAATAA-ATTTA
1 TATTTTAT-AATAATATTTA
1164389 AATAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTATAATAATATTTATA
Found at i:1169250 original size:3 final size:3
Alignment explanation
Indices: 1169242--1169287 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
1169232 TCTCATTTAA
*
1169242 AAT AAT AAT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1169288 GTGATGAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1169492 original size:16 final size:15
Alignment explanation
Indices: 1169448--1169492 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1169438 ATTTTAATAT
1169448 TTATAAAATTTATAA
1 TTATAAAATTTATAA
* *
1169463 TTAAATAAAGTTATAA
1 TTATA-AAATTTATAA
1169479 TTATTAAAATTTAT
1 TTA-TAAAATTTAT
1169493 TTTCAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 4 0.17
16 19 0.79
17 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
TTATAAAATTTATAA
Found at i:1169821 original size:31 final size:32
Alignment explanation
Indices: 1169779--1169841 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
1169769 AACACGGTAA
*
1169779 GAATACATTAATCTGTCAAAATATAGATAAAT
1 GAATACATTAATCTGTAAAAATATAGATAAAT
* * *
1169811 GAATA-ATTAATGTGTAAAAATTTATATAAAT
1 GAATACATTAATCTGTAAAAATATAGATAAAT
1169842 TTGTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.35
Consensus pattern (32 bp):
GAATACATTAATCTGTAAAAATATAGATAAAT
Found at i:1170554 original size:38 final size:37
Alignment explanation
Indices: 1170512--1170589 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 37
1170502 TCTCTCATAT
1170512 ATAAAATA-AAATATACATAAAAATATATATAAAATAAA
1 ATAAAATATAAATATACA-AAAAATATATA-AAAATAAA
* * ** *
1170550 ATAAATTATTAATATGTAAAAAATATATAAAAATATA
1 ATAAAATATAAATATACAAAAAATATATAAAAATAAA
1170587 ATA
1 ATA
1170590 TTTTAAATAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
37 10 0.29
38 18 0.53
39 6 0.18
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (37 bp):
ATAAAATATAAATATACAAAAAATATATAAAAATAAA
Found at i:1170679 original size:8 final size:8
Alignment explanation
Indices: 1170627--1170681 Score: 51
Period size: 8 Copynumber: 7.1 Consensus size: 8
1170617 AACATATACA
*
1170627 TTTTTTAT
1 TTTTTTCT
*
1170635 TTTTTT-A
1 TTTTTTCT
1170642 TTTTTTC-
1 TTTTTTCT
*
1170649 TTCTTTCT
1 TTTTTTCT
* *
1170657 TTCTTTAT
1 TTTTTTCT
1170665 TTTTTTCT
1 TTTTTTCT
1170673 TTTTTTCT
1 TTTTTTCT
1170681 T
1 T
1170682 GAATATTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
7 12 0.30
8 28 0.70
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTCT
Found at i:1171096 original size:153 final size:151
Alignment explanation
Indices: 1170939--1171214 Score: 327
Period size: 153 Copynumber: 1.8 Consensus size: 151
1170929 ATTCATTATT
* *
1170939 TATTTTATATAATTTATCATAATATTTTAATTTAATGAAAAAATTATGTGTTAATAACATATTCA
1 TATTTTACATAATTTATCATAATATTTTAATTCAATGAAAAAATTATGTGTTAATAACATATTCA
* *
1171004 TGTTATTTTTGAAGTGTTAAAAGTATTATAAATTTTTATATAAAATTTTAAATATCAATATCTAG
66 TATTATTTTTGAAGTGTCAAAAGTATTATAAA--TTTATATAAAATTTTAAATATCAATATCTAG
1171069 TGGTCCTATCTTAATTCATCACA
129 TGGTCCTATCTTAATTCATCACA
* * * ** * ** * * **
1171092 TATTTTGCATAATTTTTTATCGTGTTTTAATTCAATGAAAACTTTGTGTGTTCATAATGTATTCA
1 TATTTTACATAATTTATCATAATATTTTAATTCAATGAAAAAATTATGTGTTAATAACATATTCA
* * * * * * *
1171157 TATTGTTTTTTATGTGTCAAAATTATTATAAATTTATATAAATTTTTATATGTCAATA
66 TATTATTTTTGAAGTGTCAAAAGTATTATAAATTTATATAAAATTTTAAATATCAATA
1171215 ATTAGTATTA
Statistics
Matches: 100, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
151 23 0.23
153 77 0.77
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (151 bp):
TATTTTACATAATTTATCATAATATTTTAATTCAATGAAAAAATTATGTGTTAATAACATATTCA
TATTATTTTTGAAGTGTCAAAAGTATTATAAATTTATATAAAATTTTAAATATCAATATCTAGTG
GTCCTATCTTAATTCATCACA
Found at i:1171231 original size:36 final size:36
Alignment explanation
Indices: 1171163--1171231 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
1171153 TTCATATTGT
* * *
1171163 TTTTTATGTGTCAAAATTATTATAAATTTATATAAA
1 TTTTTATATGTCAAAATTAGTATAAATATATATAAA
*
1171199 TTTTTATATGTCAATAATTAGTAT-TATATATAT
1 TTTTTATATGTCAA-AATTAGTATAAATATATAT
1171232 TTTAGTACGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 20 0.71
37 8 0.29
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (36 bp):
TTTTTATATGTCAAAATTAGTATAAATATATATAAA
Found at i:1172020 original size:11 final size:11
Alignment explanation
Indices: 1171992--1172030 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1171982 ATTTATAAAA
*
1171992 AATATAATATA
1 AATATAATATG
*
1172003 AAAATAATATG
1 AATATAATATG
*
1172014 CATATAATATG
1 AATATAATATG
1172025 AATATA
1 AATATA
1172031 TGTATATATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (11 bp):
AATATAATATG
Found at i:1172087 original size:19 final size:20
Alignment explanation
Indices: 1172069--1172114 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1172059 AATAAATTAT
1172069 TAAT-ATATAA-ATTTTTTA
1 TAATAATATAATATTTTTTA
*
1172087 TAATAATATAATATTTTATA
1 TAATAATATAATATTTTTTA
*
1172107 TAAAAATA
1 TAATAATA
1172115 AAAAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 6 0.25
20 14 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATAATATAATATTTTTTA
Found at i:1172103 original size:18 final size:18
Alignment explanation
Indices: 1172069--1172106 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1172059 AATAAATTAT
*
1172069 TAATATATAAATTTTTTA
1 TAATATATAAATATTTTA
1172087 TAATA-ATATAATATTTTA
1 TAATATATA-AATATTTTA
1172105 TA
1 TA
1172107 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATATATAAATATTTTA
Found at i:1172319 original size:15 final size:16
Alignment explanation
Indices: 1172283--1172322 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1172273 TTTAATATTT
*
1172283 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
1172300 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
1172315 ATAAAATT
1 ATAAAATT
1172323 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:1172325 original size:16 final size:17
Alignment explanation
Indices: 1172283--1172325 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
1172273 TTTAATATTT
*
1172283 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
1172300 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
1172315 ATAAAATTTAT
1 ATAAAATTTAT
1172326 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:1172759 original size:23 final size:23
Alignment explanation
Indices: 1172707--1172759 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1172697 GAAACACGAA
* *
1172707 ATGAACACAACATAGAAAATAAT
1 ATGAATACAACATAAAAAATAAT
*
1172730 -TAAAATACAACATAAAAAATAAT
1 AT-GAATACAACATAAAAAATAAT
1172753 ATGAATA
1 ATGAATA
1172760 TAATACAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 1 0.04
23 22 0.92
24 1 0.04
ACGTcount: A:0.64, C:0.09, G:0.06, T:0.21
Consensus pattern (23 bp):
ATGAATACAACATAAAAAATAAT
Found at i:1173391 original size:11 final size:10
Alignment explanation
Indices: 1173359--1173403 Score: 63
Period size: 11 Copynumber: 4.3 Consensus size: 10
1173349 GAATACATAA
1173359 TTTTTTTCTT
1 TTTTTTTCTT
*
1173369 TTTTTCTCCTT
1 TTTTT-TTCTT
1173380 TTTTTTATCTT
1 TTTTTT-TCTT
1173391 TTTTTTTCTT
1 TTTTTTTCTT
1173401 TTT
1 TTT
1173404 CTCTTGACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 13 0.42
11 18 0.58
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:1174427 original size:23 final size:23
Alignment explanation
Indices: 1174391--1174445 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
1174381 AATACAAATA
1174391 TTTTTCTTTGTTTTTTCTCTCTTT
1 TTTTTCTTTGTTTTTTCTCTC-TT
*
1174415 TTTTTCTTT-TTTTTTCTTTCTT
1 TTTTTCTTTGTTTTTTCTCTCTT
*
1174437 TCTTTCTTT
1 TTTTTCTTT
1174446 CTCTCCTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 10 0.34
23 10 0.34
24 9 0.31
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (23 bp):
TTTTTCTTTGTTTTTTCTCTCTT
Found at i:1174434 original size:4 final size:4
Alignment explanation
Indices: 1174393--1174447 Score: 53
Period size: 4 Copynumber: 14.2 Consensus size: 4
1174383 TACAAATATT
* * *
1174393 TTTC TTTG TTT- TTTC TCTC TTTTT TTTC TTT- TTT- TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1174439 TTTC TTTC T
1 TTTC TTTC T
1174448 CTCCTGTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
3 9 0.21
4 32 0.74
5 2 0.05
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:1176878 original size:25 final size:25
Alignment explanation
Indices: 1176852--1176900 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1176842 TAAATAAATA
* * *
1176852 AAATT-TATTTTATTTATTTATTTT
1 AAATTGTAATTTAATTAATTATTTT
1176876 AAATTGTAATTTAATTAATTATTTT
1 AAATTGTAATTTAATTAATTATTTT
1176901 GTTGTAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
AAATTGTAATTTAATTAATTATTTT
Found at i:1178666 original size:78 final size:78
Alignment explanation
Indices: 1178362--1178726 Score: 353
Period size: 79 Copynumber: 4.7 Consensus size: 78
1178352 TGGAGATAAA
* * ** * * * *
1178362 AACGAGGTTGGAGTATCCTTGATAGTGAAAAATCGATGTTTTCGAAATAAAACTAAGGTTGGAGT
1 AACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATATTTTAGAAATAAAACGAA-GTTGGAGT
* *
1178427 ATTACCTCAAAAAT
65 ATTCCCTCGAAAAT
* * * ** *
1178441 AACGGGGTTAGAGTATCCTCGATTGTGAAAAATCGATATTTTAGAAATAAAGTCGGGGTTAGAGT
1 AACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATATTTTAGAAATAAA-ACGAAGTTGGAGT
*
1178506 ATTCTCTCGAAAAT
65 ATTCCCTCGAAAAT
* * * * * * * * *
1178520 AATGGGGTTCGAGTATCTCCGATTGTGAAAAATTGACATTTTGGAAATAAAACTAGGTTTGGAGT
1 AACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATATTTTAGAAATAAAACGAAG-TTGGAGT
*
1178585 ATCCCCTC-AGAAAT
65 ATTCCCTCGA-AAAT
* *
1178599 AACGGGGTTAGAGTATCCCCGATGGT-AAAAATCGATGTTTTAGAAATAACATCGAAGTTGGAGT
1 AACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATATTTTAGAAATAA-AACGAAGTTGGAGT
1178663 A-TCCCTCGAAAAT
65 ATTCCCTCGAAAAT
* * *
1178676 AATGGGGTTGGAGTATCCCCGATGGTGGAAAAAT--ATATTTTGGAAATAAAA
1 AACGGGGTTAGAGTATCCCCGATGGT-GAAAAATCGATATTTTAGAAATAAAA
1178727 ACATCAATGA
Statistics
Matches: 235, Mismatches: 44, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
76 1 0.00
77 46 0.20
78 32 0.14
79 155 0.66
80 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (78 bp):
AACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATATTTTAGAAATAAAACGAAGTTGGAGTA
TTCCCTCGAAAAT
Found at i:1185691 original size:50 final size:52
Alignment explanation
Indices: 1185587--1185702 Score: 139
Period size: 52 Copynumber: 2.2 Consensus size: 52
1185577 GATGGTACGA
*
1185587 TTGGAGTATCCCCAAAGATGAAAAATTCAGTATTATGGAAGTAAAAAATGGGG
1 TTGGAGTATCCCCAAAGATGAAAAATTCAGTATTA-GGAAGTAAAAAATAGGG
* ** *
1185640 TTGGA-TATCCCCAGAGATGAAATTTTGATGTATTA-GAAGT-AAAAATAGGG
1 TTGGAGTATCCCCAAAGATGAAAAATTCA-GTATTAGGAAGTAAAAAATAGGG
*
1185690 TTAGAGTATCCCC
1 TTGGAGTATCCCC
1185703 TCAGACATGA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
50 13 0.24
51 12 0.22
52 19 0.35
53 11 0.20
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (52 bp):
TTGGAGTATCCCCAAAGATGAAAAATTCAGTATTAGGAAGTAAAAAATAGGG
Found at i:1185924 original size:80 final size:78
Alignment explanation
Indices: 1185635--1185943 Score: 284
Period size: 83 Copynumber: 3.8 Consensus size: 78
1185625 AAGTAAAAAA
* ** * *
1185635 TGGGGTTGGA-TATCCCCAGAGATGAAATTTTG-ATGTATTAGAAGTAAAAATAGGGTTAGAGTA
1 TGGGGTTGGAGTATCCCCAAAGATGAAAAATTGAAT-T-TTGGAAGTAAAAATCGGGTTAGAGTA
* *
1185698 TCCCCTCAGACATGA
64 TCCCCTCAGAGATGG
* * * * *
1185713 TGGGGTTGGAGTATCCCCAAAGATGAAAAATTCGATGTTTTGGAAGCAGAAA-CGAGATCAGAGT
1 TGGGGTTGGAGTATCCCCAAAGATGAAAAATT-GA-ATTTTGGAAGTAAAAATCG-GGTTAGAGT
*
1185777 ATCCCCTCGGAGGGGATGG
63 ATCCCCTC--A-GAGATGG
* * * *
1185796 TGGGGTTAGAGTATCCCCAGACATGAAAAATTCAATGTTTTGGAAGTAAAAA-CGGGTTAGAGTA
1 TGGGGTTGGAGTATCCCCAAAGATGAAAAATTGAA--TTTTGGAAGTAAAAATCGGGTTAGAGTA
**
1185860 TCCTTTCAGAGATGG
64 TCCCCTCAGAGATGG
* *
1185875 TGGGGTTGGAATATCCCCAAAGATGAAAAAAATTGACATTTTGGAAGTAAAAATGGGGTTAGAGT
1 TGGGGTTGGAGTATCCCCAAAGATG--AAAAATTGA-ATTTTGGAAGTAAAAATCGGGTTAGAGT
1185940 ATCC
63 ATCC
1185944 TAGAGATTAA
Statistics
Matches: 186, Mismatches: 31, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
78 10 0.05
79 46 0.25
80 42 0.23
81 23 0.12
82 17 0.09
83 48 0.26
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (78 bp):
TGGGGTTGGAGTATCCCCAAAGATGAAAAATTGAATTTTGGAAGTAAAAATCGGGTTAGAGTATC
CCCTCAGAGATGG
Found at i:1185933 original size:53 final size:52
Alignment explanation
Indices: 1185875--1185994 Score: 152
Period size: 51 Copynumber: 2.3 Consensus size: 52
1185865 TCAGAGATGG
* *
1185875 TGGGGTTGGAATATCCCCAAAGATGAAAAAAATTGACATTTTGGAAGTAAAAA
1 TGGGGTTAGAGTATCCCCAAAGAT-AAAAAAATTGACATTTTGGAAGTAAAAA
* * * * *
1185928 TGGGGTTAGAGTAT-CCTAGAGATTAAAAATTTGACATTTTGGAAGTAGAAA
1 TGGGGTTAGAGTATCCCCAAAGATAAAAAAATTGACATTTTGGAAGTAAAAA
*
1185979 TAGGGTTAGAGTATCC
1 TGGGGTTAGAGTATCC
1185995 TCTTAGAGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 38 0.66
52 8 0.14
53 12 0.21
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (52 bp):
TGGGGTTAGAGTATCCCCAAAGATAAAAAAATTGACATTTTGGAAGTAAAAA
Found at i:1185985 original size:132 final size:130
Alignment explanation
Indices: 1185796--1186074 Score: 334
Period size: 132 Copynumber: 2.1 Consensus size: 130
1185786 GAGGGGATGG
**
1185796 TGGGGTTAGAGTATCCCCAGACATGAAAAATTCAATGTTTTGGAAGTAAAAACGGGTTAGAGTAT
1 TGGGGTTAGAGTAT-CCCAGACATGAAAAATTCAACATTTTGGAAGTAAAAACGGGTTAGAGTAT
* * *
1185861 CCT-TTCAGAGATGGTGGGGTTGGAA-TATCCCCAAAGATGAAAAAAATT-GACATTTTGGAAGT
65 CCTCTT-AGAGATGGTGGGGTT-GAAGTATCCCCAAACATG--AAAAATTCAACATTTTAGAAGT
1185923 AAAAA
126 AAAAA
* * * **
1185928 TGGGGTTAGAGTATCCTAGAGATTAAAAATTTGACATTTTGGAAGTAGAAATA-GGGTTAGAGTA
1 TGGGGTTAGAGTATCCCAGACATGAAAAATTCAACATTTTGGAAGTA-AAA-ACGGGTTAGAGTA
* * *
1185992 TCCTCTTAGAGATGGTGGGGTTGAAGTATCCCCAGACATGAAAACTTCAACGTTTTAGAAGTAAA
64 TCCTCTTAGAGATGGTGGGGTTGAAGTATCCCCAAACATGAAAAATTCAACATTTTAGAAGTAAA
1186057 AA
129 AA
*
1186059 T-GGGTTAGATTATCCC
1 TGGGGTTAGAGTATCCC
1186075 TTCAAAGATG
Statistics
Matches: 127, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
130 19 0.15
131 46 0.36
132 59 0.46
133 3 0.02
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.28
Consensus pattern (130 bp):
TGGGGTTAGAGTATCCCAGACATGAAAAATTCAACATTTTGGAAGTAAAAACGGGTTAGAGTATC
CTCTTAGAGATGGTGGGGTTGAAGTATCCCCAAACATGAAAAATTCAACATTTTAGAAGTAAAAA
Found at i:1186064 original size:79 final size:80
Alignment explanation
Indices: 1185964--1186310 Score: 298
Period size: 80 Copynumber: 4.3 Consensus size: 80
1185954 AAATTTGACA
* * * * *
1185964 TTTTGGAAGTAGAAATAGGGTTAGAGTATCCTCTTAGAGATGGTGGGGTTGAAGTATCCCCAGAC
1 TTTTAGAAGTAAAAATAGGGTTAGAGTATCCCCTTAGAGATGGTGGAGTTGAAGTATCCCCAGAG
* *
1186029 ATGAAAACTTCAACG
66 ATGAAAAATTCAGCG
* * *
1186044 TTTTAGAAGTAAAAAT-GGGTTAGATTAT-CCCTTCAAAGATGGTGGAGTTGGAA-TAT-CCCAA
1 TTTTAGAAGTAAAAATAGGGTTAGAGTATCCCCTT-AGAGATGGTGGAGTT-GAAGTATCCCCAG
* * *
1186105 AAATGAATAATTTAGCG
64 AGATGAAAAATTCAGCG
* * * *
1186122 TTTT-GAAAATAAAAATAGGGTTGGAGTATCCCCTT-GAAAATGGTAGGA-TT-AGAGTATCCCT
1 TTTTAG-AAGTAAAAATAGGGTTAGAGTATCCCCTTAG-AGATGGT-GGAGTTGA-AGTATCCCC
*
1186183 AGAGATGAAAAATTCAGTG
62 AGAGATGAAAAATTCAGCG
* * * * ** **
1186202 TTTTGGAAGTAATAATGGGGTTAGAGTATCCCCTCAGAGATATTGGAGTTGGGGTATCCCC-GAA
1 TTTTAGAAGTAAAAATAGGGTTAGAGTATCCCCTTAGAGATGGTGGAGTTGAAGTATCCCCAG-A
*
1186266 GATGAAAAATTCAGTG
65 GATGAAAAATTCAGCG
* *
1186282 TTTTAGAAGTGAAAATAGGGGTTGGAGTA
1 TTTTAGAAGTAAAAATA-GGGTTAGAGTA
1186311 CCCTTTTTGA
Statistics
Matches: 212, Mismatches: 39, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
77 2 0.01
78 34 0.16
79 52 0.25
80 112 0.53
81 12 0.06
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (80 bp):
TTTTAGAAGTAAAAATAGGGTTAGAGTATCCCCTTAGAGATGGTGGAGTTGAAGTATCCCCAGAG
ATGAAAAATTCAGCG
Found at i:1188825 original size:20 final size:20
Alignment explanation
Indices: 1188800--1188847 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1188790 CGTTACAAGC
* * *
1188800 ATGTATCGATGCATTCACTT
1 ATGTATCAATACATTAACTT
1188820 ATGTATCAATACATTAACTT
1 ATGTATCAATACATTAACTT
1188840 ATTGTATC
1 A-TGTATC
1188848 TGTAGACACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (20 bp):
ATGTATCAATACATTAACTT
Found at i:1189012 original size:19 final size:18
Alignment explanation
Indices: 1188988--1189079 Score: 87
Period size: 19 Copynumber: 5.5 Consensus size: 18
1188978 GATTTGTATT
1188988 GATACATAAGTGTTTTATC
1 GATACATAAGTG-TTTATC
1189007 GATAC--AA-TG--TATC
1 GATACATAAGTGTTTATC
1189020 GATACATAAGTGTTGTATC
1 GATACATAAGTGTT-TATC
1189039 GATAC--AA-TG--TATC
1 GATACATAAGTGTTTATC
1189052 GATACATAAGTGTTGTATC
1 GATACATAAGTGTT-TATC
1189071 GATACATAA
1 GATACATAA
1189080 TTAGCTACTG
Statistics
Matches: 61, Mismatches: 0, Indels: 24
0.72 0.00 0.28
Matches are distributed among these distances:
13 18 0.30
15 4 0.07
16 8 0.13
17 4 0.07
19 27 0.44
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (18 bp):
GATACATAAGTGTTTATC
Found at i:1189018 original size:32 final size:32
Alignment explanation
Indices: 1188982--1189076 Score: 172
Period size: 32 Copynumber: 3.0 Consensus size: 32
1188972 TTCAACGATT
* *
1188982 TGTATTGATACATAAGTGTTTTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1189014 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1189046 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
1189077 TAATTAGCTA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1189021 original size:13 final size:13
Alignment explanation
Indices: 1189003--1189057 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
1188993 ATAAGTGTTT
1189003 TATCGATACAATG
1 TATCGATACAATG
1189016 TATCGATACATAAGTGTTG
1 TATCGATAC--AA----TG
1189035 TATCGATACAATG
1 TATCGATACAATG
1189048 TATCGATACA
1 TATCGATACA
1189058 TAAGTGTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 21 0.58
15 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:1194611 original size:79 final size:78
Alignment explanation
Indices: 1194480--1194866 Score: 289
Period size: 79 Copynumber: 4.8 Consensus size: 78
1194470 AACGGGGCTA
*
1194480 GAGTATCCCCGATTATGGAAAATCAGTGTTCTAAAAATAAAATCG-GGATTGGAGTATCCCCTCG
1 GAGTAT-CCCGATTATGGAAAATCAGTGTTTTAAAAATAAAATCGAGG-TTGGAGTATCCCCTCG
*
1194544 GAAATAACAGGGTTG
64 AAAATAACAGGGTTG
** ** **
1194559 GAGTATCCCTGATTATAAAAAATGGGTGTTTTAAAAATAAAATCGAGGTTGGAGTATATCCTCGA
1 GAGTATCCC-GATTATGGAAAATCAGTGTTTTAAAAATAAAATCGAGGTTGGAGTATCCCCTCGA
*
1194624 AAATAACGGGGTTG
65 AAATAACAGGGTTG
* * * * ** * * *
1194638 GAGTATCTCCGATTGTGGAAAATCATTGCTTTAGAAATAAGGTCGAGGTTAGAGTATCCCCGCAA
1 GAGTATC-CCGATTATGGAAAATCAGTGTTTTAAAAATAAAATCGAGGTTGGAGTATCCCCTCGA
1194703 AAATAACAGGGTTG
65 AAATAACAGGGTTG
* * * * * *
1194717 GAGTATCCCCAAT-TGTGAGAAATCAATATTTTAGAAATAAAGCTAGGGTTGGACGGGGTTGGAG
1 GAGTATCCCGATTATG-GA-AAATCAGTGTTTTAAAAATAAA---A----T---CGAGGTTGGAG
1194781 TAT-CCCT-GATGAAATAACAGGGTTG
54 TATCCCCTCGA--AAATAACAGGGTTG
* * * ** *
1194806 GAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATC-AGAGTTAGAGTATCCCC
1 GAGTAT-CCCGATTATGGAAAATCAGTGTTTTAAAAATAAAATCGAG-GTTGGAGTATCCCC
1194867 AATTGTGAAA
Statistics
Matches: 242, Mismatches: 45, Indels: 41
0.74 0.14 0.12
Matches are distributed among these distances:
77 2 0.01
78 10 0.04
79 158 0.65
80 7 0.03
82 1 0.00
86 2 0.01
87 1 0.00
88 3 0.01
89 50 0.21
90 6 0.02
91 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (78 bp):
GAGTATCCCGATTATGGAAAATCAGTGTTTTAAAAATAAAATCGAGGTTGGAGTATCCCCTCGAA
AATAACAGGGTTG
Found at i:1194769 original size:158 final size:158
Alignment explanation
Indices: 1194470--1194757 Score: 337
Period size: 158 Copynumber: 1.8 Consensus size: 158
1194460 TGGAGATAAC
*
1194470 AACGGGGCTAGAGTATCCCCGATTATGGAAAATCAGTGTTCTAAAAATAAAATCGGGATTGGAGT
1 AACGGGGCTAGAGTATCCCCGATTATGGAAAATCAGTGTTCTAAAAATAAAATCGGGATTAGAGT
* ** ** *** *
1194535 ATCCCCTCGGAAATAACAGGGTTGGAGTATCCCTGATTATAAAAAATGGGTGTTTTAAAAATAAA
66 ATCCCCGCAAAAATAACAGGGTTGGAGTATCCCCAATTATAAAAAATCAATATTTTAAAAATAAA
*
1194600 ATCGAGGTTGGAGTATATCCTCGAAAAT
131 ATAGAGGTTGGAGTATATCCTCGAAAAT
* * * * * * **
1194628 AACGGGGTTGGAGTATCTCCGATTGTGGAAAATCATTGCTT-TAGAAATAAGGTCGAGG-TTAGA
1 AACGGGGCTAGAGTATCCCCGATTATGGAAAATCAGTG-TTCTAAAAATAAAATCG-GGATTAGA
* * * *
1194691 GTATCCCCGCAAAAATAACAGGGTTGGAGTATCCCCAATTGTGAGAAATCAATATTTTAGAAATA
64 GTATCCCCGCAAAAATAACAGGGTTGGAGTATCCCCAATTATAAAAAATCAATATTTTAAAAATA
1194756 AA
129 AA
1194758 GCTAGGGTTG
Statistics
Matches: 106, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
158 102 0.96
159 4 0.04
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.27
Consensus pattern (158 bp):
AACGGGGCTAGAGTATCCCCGATTATGGAAAATCAGTGTTCTAAAAATAAAATCGGGATTAGAGT
ATCCCCGCAAAAATAACAGGGTTGGAGTATCCCCAATTATAAAAAATCAATATTTTAAAAATAAA
ATAGAGGTTGGAGTATATCCTCGAAAAT
Found at i:1194864 original size:51 final size:51
Alignment explanation
Indices: 1194806--1194917 Score: 179
Period size: 51 Copynumber: 2.2 Consensus size: 51
1194796 AACAGGGTTG
* **
1194806 GAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCAGAGTTA
1 GAGTATCCCCAATTGTGAAAAATTAGTGTTTTAAAAATAAAATCAGAGTTA
* *
1194857 GAGTATCCCCAATTGTGAAAAATTAGTGTTTTAAAAATAAAATCGGGGTTA
1 GAGTATCCCCAATTGTGAAAAATTAGTGTTTTAAAAATAAAATCAGAGTTA
1194908 GAGTATCCCC
1 GAGTATCCCC
1194918 TTAGAAATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (51 bp):
GAGTATCCCCAATTGTGAAAAATTAGTGTTTTAAAAATAAAATCAGAGTTA
Found at i:1195005 original size:79 final size:79
Alignment explanation
Indices: 1194854--1195054 Score: 237
Period size: 79 Copynumber: 2.5 Consensus size: 79
1194844 AAAATCAGAG
* * *
1194854 TTAGAGTATCCCCAATTGTGAAAAATT-AGTGTTTTAAAAATAAAATCGGGGTTAGAGTATCCCC
1 TTAGAGTATCCCCGATTATGAAAAATTGA-TGTTTTAAAAATAAAATCGAGGTTAGAGTATCCCC
*
1194918 TTAGAAATATCAAGA
65 TTAGAAATAACAAGA
1194933 TTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAAAAATAAAATCGAGGTTAGAGTAT-CCCT
1 TTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAAAAATAAAATCGAGGTTAGAGTATCCCCT
* ** *
1194997 TCGAAAATAACGGGG
66 TAG-AAATAACAAGA
* * * * *
1195012 TTGGAGTATCCTCGATTGA-GAAAAATCGATGCTTTAGAAATAA
1 TTAGAGTATCCCCGATT-ATGAAAAATTGATGTTTTAAAAATAA
1195055 GGCCGGGGTT
Statistics
Matches: 106, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
78 6 0.06
79 98 0.92
80 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (79 bp):
TTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAAAAATAAAATCGAGGTTAGAGTATCCCCT
TAGAAATAACAAGA
Found at i:1196043 original size:16 final size:16
Alignment explanation
Indices: 1196022--1196053 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1196012 AAAACATCAT
1196022 TTTGGAGATTATTTCA
1 TTTGGAGATTATTTCA
1196038 TTTGGAGATTATTTCA
1 TTTGGAGATTATTTCA
1196054 CCATGAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTGGAGATTATTTCA
Found at i:1197466 original size:20 final size:20
Alignment explanation
Indices: 1197441--1197496 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1197431 ATGTACCGAT
*
1197441 ACAATGTATCAATACAATGA
1 ACAATGTATCGATACAATGA
1197461 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
1197481 ACAATGTATCGATACA
1 ACAATGTATCGATACA
1197497 TCTGGGTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.25
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:1198270 original size:61 final size:61
Alignment explanation
Indices: 1198205--1199060 Score: 957
Period size: 61 Copynumber: 14.4 Consensus size: 61
1198195 TAGAAGGTGT
* ** * * *
1198205 CACCAACTTGTATGGGCTTTGCAAGGAGAAA-GTATCCTACTCTTTGAGGACTGAAAGGTGC
1 CACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGC
* *
1198266 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCTTTGAGGA-TAGAAAAGTGC
1 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACT-GAAAAGTGC
* * * * *
1198327 CACCAACTTGTATGGGCTTTAAAAGGAAAAGGCATTCTACTCCTTGAGGACTGAAAAGTGA
1 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGC
* *
1198388 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAATTGC
1 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGC
* * *
1198449 CACCAACTTGTGTGGCCTTTAAAAAGAAAAGGC-GCCTTGCTCTTTGAGGACTAGAAAAGTGC
1 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC-TGCTCTTTGAGGACT-GAAAAGTGC
* * * * * * *
1198511 CACCAACTTATGTGGGCTTTAAAAGGAAAAGGCATCCTGCCCCTTGAAGAATAAAAAGTAC
1 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGC
* * *
1198572 CACCAACTTGTGTGCGCTTTAAAAGGAAAAGGCATCCTGCTCCTTGAAGACTGAAAAGTGC
1 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGC
** * *
1198633 TGCCAACTTGTATGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACT-AAAAGGTGC
1 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGAAAA-GTGC
* *
1198694 CACCAACTTGTGTGGGCTTTAAAAGGAAAAAGCATCCTGCTCTTTGAGGACTG-AAGGTGC
1 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGC
* *
1198754 CACCAGCTTGTGTGGGCCTT-----G-AAAGGCATCCTGCTCTTTGAGGACTGGAAAA-TGC
1 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACT-GAAAAGTGC
* * * * *
1198809 CACCAACTTGTGTGGGCTTTGAAAGGAAAAAGCGTCATGCTCCTTGAGGACTGAAAAGTGC
1 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGC
* * * * *
1198870 CATCAACTTATGTGGGCTTT-----GAAAA-GCGTCCTGCTCTTTGAGGATTGAAAAATGC
1 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGC
*
1198925 CACCAACTTGTGTGGGCTTT-----G-AAAGGCATCCTGCTCTTTGAGGACTGGAAAA-TAC
1 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACT-GAAAAGTGC
* *
1198980 CAACAACTTGTGTGGGCTTT-----G-AAAGGCGTCCTGCTCTTTGAGGACTAGAAAA-TGC
1 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACT-GAAAAGTGC
* *
1199035 CACTAACTTGTGTGGGCTTTGAAAGG
1 CACCAACTTGTGTGGGCTTTAAAAGG
1199061 TGTCCTACTC
Statistics
Matches: 693, Mismatches: 78, Indels: 49
0.85 0.10 0.06
Matches are distributed among these distances:
54 27 0.04
55 158 0.23
56 12 0.02
60 39 0.06
61 405 0.58
62 50 0.07
63 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (61 bp):
CACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGC
Found at i:1198543 original size:245 final size:236
Alignment explanation
Indices: 1198205--1199060 Score: 958
Period size: 245 Copynumber: 3.6 Consensus size: 236
1198195 TAGAAGGTGT
* * * * * *
1198205 CACCAACTTGTATGGGCTTTGCAAGGAGAAA-GTATCCTACTCTTTGAGGACTGAAAGGTGCCAC
1 CACCAACTTGTGTGGGCTTT-AAAAGA-AAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGCCAC
* *
1198269 CAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCTTTGAGGA-TAGAAAAGTGCCACCAA
64 CAACTTGTGTGGGCTTT-----G-AAAGGCATCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAA
* *
1198333 CTTGTATGGGCTTTAAAAGGAAAAGGCATTCTACTCCTTGAGGACTGAAAAGTGACACCAACTTG
122 CTTGTGTGGGCTTTAAAAGGAAAAGGCATTCTGCTCCTTGAGGACTGAAAAGTG-CACCAACTTG
*
1198398 TGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAATTGC
186 TGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAATGC
* *
1198449 CACCAACTTGTGTGGCCTTTAAAAAGAAAAGGC-GCCTTGCTCTTTGAGGACTAGAAAAGTGCCA
1 CACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCATCC-TGCTCTTTGAGGACT-GAAAAGTGCCA
* * * * * *
1198513 CCAACTTATGTGGGCTTTAAAAGGAAAAGGCATCCTGCCCCTTGAAGAATA-AAAAGTACCACCA
63 CCAACTTGTGTGGGCTTT-----G-AAAGGCATCCTGCTCTTTGAGGACTAGAAAA-TGCCACCA
* * * *
1198577 ACTTGTGTGCGCTTTAAAAGGAAAAGGCATCCTGCTCCTTGAAGACTGAAAAGTGCTGCCAACTT
121 ACTTGTGTGGGCTTTAAAAGGAAAAGGCATTCTGCTCCTTGAGGACTGAAAAGTGC-ACCAACTT
* * * *
1198642 GTATGGGCTTTAAAAGGAAAAGGCATCCTACTCTTTGAGGACT-AAAAGGTGC
185 GTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAA-ATGC
* *
1198694 CACCAACTTGTGTGGGCTTTAAAAGGAAAAAGCATCCTGCTCTTTGAGGACTG-AAGGTGCCACC
1 CACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGCCACC
* * *
1198758 AGCTTGTGTGGGCCTTGAAAGGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTG
65 AACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTG
* * * * *
1198823 GGCTTTGAAAGGAAAAAGC-GTCATGCTCCTTGAGGACTGAAAAGTGCCATCAACTTATGTGGGC
130 GGCTTTAAAAGGAAAAGGCATTC-TGCTCCTTGAGGACTGAAAAGTG-CACCAACTTGTGTGGGC
*
1198887 TTT-----GAAAA-GCGTCCTGCTCTTTGAGGATTGAAAAATGC
193 TTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAATGC
* *
1198925 CACCAACTTGTGTGGGCTTT----G-AAAGGCATCCTGCTCTTTGAGGACTGGAAAA-TACCAAC
1 CACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCTGCTCTTTGAGGACT-GAAAAGTGCCACC
* *
1198984 AACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACTAACTTGTGTG
65 AACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTG
*
1199049 GGCTTTGAAAGG
130 GGCTTTAAAAGG
1199061 TGTCCTACTC
Statistics
Matches: 536, Mismatches: 62, Indels: 46
0.83 0.10 0.07
Matches are distributed among these distances:
225 24 0.04
226 79 0.15
227 2 0.00
231 41 0.08
232 9 0.02
236 1 0.00
237 90 0.17
238 6 0.01
243 28 0.05
244 47 0.09
245 205 0.38
246 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (236 bp):
CACCAACTTGTGTGGGCTTTAAAAGAAAAGGCATCCTGCTCTTTGAGGACTGAAAAGTGCCACCA
ACTTGTGTGGGCTTTGAAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGG
GCTTTAAAAGGAAAAGGCATTCTGCTCCTTGAGGACTGAAAAGTGCACCAACTTGTGTGGGCTTT
AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAATGC
Found at i:1200163 original size:1 final size:1
Alignment explanation
Indices: 1200157--1200232 Score: 62
Period size: 1 Copynumber: 76.0 Consensus size: 1
1200147 AAGTAGGTTC
* * * * * * * * *
1200157 TTTTTTTTTCTCTTTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTGTTTTGTTTTGTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
1200222 TTTATTTTTTT
1 TTTTTTTTTTT
1200233 AAAAAAGAAT
Statistics
Matches: 55, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.01, C:0.03, G:0.09, T:0.87
Consensus pattern (1 bp):
T
Found at i:1200181 original size:5 final size:5
Alignment explanation
Indices: 1200169--1200229 Score: 76
Period size: 5 Copynumber: 12.8 Consensus size: 5
1200159 TTTTTTTCTC
1200169 TTTT- TTTTG TTTT- TTTTG TTTT- TTTTG TTTTTG TTTTG TTTTG TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG -TTTTG TTTTG TTTTG TTTTG
*
1200217 TTTT- TTTTA TTTT
1 TTTTG TTTTG TTTT
1200230 TTTAAAAAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
4 16 0.31
5 31 0.60
6 5 0.10
ACGTcount: A:0.02, C:0.00, G:0.11, T:0.87
Consensus pattern (5 bp):
TTTTG
Found at i:1200181 original size:9 final size:9
Alignment explanation
Indices: 1200159--1200232 Score: 94
Period size: 9 Copynumber: 7.8 Consensus size: 9
1200149 GTAGGTTCTT
*
1200159 TTTTTTTCTC
1 TTTTTTT-TG
1200169 TTTTTTTTG
1 TTTTTTTTG
1200178 TTTTTTTTG
1 TTTTTTTTG
1200187 TTTTTTTTG
1 TTTTTTTTG
1200196 TTTTTGTTTTG
1 -TTTT-TTTTG
1200207 TTTTGTTTTG
1 TTTT-TTTTG
*
1200217 TTTTTTTTA
1 TTTTTTTTG
1200226 TTTTTTT
1 TTTTTTT
1200233 AAAAAAGAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
9 30 0.50
10 25 0.42
11 5 0.08
ACGTcount: A:0.01, C:0.03, G:0.09, T:0.86
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1212284 original size:79 final size:78
Alignment explanation
Indices: 1212140--1212922 Score: 552
Period size: 79 Copynumber: 9.9 Consensus size: 78
1212130 TGGGGATAAC
* * * * *
1212140 AACGGGGCTAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAATAAAATCGAGGTTAGAGT
1 AACGGGGTTGGAGTATCCCCGATTAT-GAAAATCGATGTTTTAAAAATAAAATCGAGGTTGGAGT
1212205 ATCCCCTCGAAAAT
65 ATCCCCTCGAAAAT
** * * *
1212219 AATAGGGTTGGATTATCCCTGATTATAGAAAATCGATATTTTAAAAATAAAATCGAGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTAT-GAAAATCGATGTTTTAAAAATAAAATCGAGGTTGGAGT
1212284 ATCCCCTCGAAAAT
65 ATCCCCTCGAAAAT
* * * * ***
1212298 AACGGGGTTGGAGTATCCCTGATTGTGAAAAATCGATGCTTTAGAAATAAGGCCGAGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATG-AAAATCGATGTTTTAAAAATAAAATCGAGGTTGGAGT
* *
1212363 ATCCCCACAAAAAT
65 ATCCCCTCGAAAAT
** * * * * *
1212377 AACGGGGTAAGAGTATCCCTGATTATAGTAAATCGGTGTTTTAAAAATAAAATTGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTAT-GAAAATCGATGTTTTAAAAATAAAATCGAGGTTGGAGT
1212442 ATCCCCTCGAAAAT
65 ATCCCCTCGAAAAT
* * * * *** *
1212456 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATCTATGCTTTAGAAATAAGGCCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATG-AAAATCGATGTTTTAAAAATAAAATCGAGGTTGGAGT
*
1212521 ATCCTCAT-GAAAAT
65 ATCC-CCTCGAAAAT
* * * * *
1212535 AACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAAT-AAAGCCAGGGTTGGAG
1 AACGGGGTTGGAGTATCCCCGATTATGA-AAATCGATGTTTTAAAAATAAAATCGA-GGTTGGAG
*
1212599 TATCCCCTCAAAAAT
64 TATCCCCTCGAAAAT
* * ** * ** *
1212614 AACGGGATTAGAGTATCCCCGA-TA-GAATAA-CAGA-G-TTGGAATATCCCCGATTAT-GAAAA
1 AACGGGGTTGGAGTATCCCCGATTATGAA-AATC-GATGTTTTAAAAAT-----AAAATCG--AG
* * *
1212673 ATTGGTGT-T----TTGAAAAT
57 GTTGGAGTATCCCCTCGAAAAT
** * * * * *
1212690 AAAATTAGAGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTAGAAATAAAA-CTGGGGTT
1 --AA-CGGGGTTGGAGTATCCCCGATTATG-AAAATCGATG-TTTTAAAAATAAAATC-GAGGTT
* * *
1212754 -GAGTATCTCTTCGGAAAT
60 GGAGTATCCCCTCGAAAAT
* * * * *
1212772 AACGGGAATAGGAGTATCCCCGATTATGAGAAATTGATGTTTTGAAAATAAAATCGGGGTTGGAG
1 AACGGG-GTTGGAGTATCCCCGATTATGA-AAATCGATGTTTTAAAAATAAAATCGAGGTTGGAG
1212837 TATCCCCTCGAAAAT
64 TATCCCCTCGAAAAT
* *** * ** *
1212852 AACGGGGTTGGAGTATCCCCGATTGTGGAAAATCGATACATTAGAAATAAAGCCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTAT-GAAAATCGATGTTTTAAAAATAAAATCGAGGTTGGAGT
1212917 ATCCCC
65 ATCCCC
1212923 ACGATGAAAA
Statistics
Matches: 545, Mismatches: 120, Indels: 78
0.73 0.16 0.10
Matches are distributed among these distances:
75 5 0.01
76 8 0.01
77 8 0.01
78 14 0.03
79 424 0.78
80 60 0.11
81 11 0.02
82 10 0.02
84 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (78 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAATCGATGTTTTAAAAATAAAATCGAGGTTGGAGTA
TCCCCTCGAAAAT
Found at i:1212428 original size:158 final size:157
Alignment explanation
Indices: 1212140--1212636 Score: 629
Period size: 158 Copynumber: 3.1 Consensus size: 157
1212130 TGGGGATAAC
* * * * * *** *
1212140 AACGGGGCTAGAGTATCCCCGATTATGGAAAATCGGTG-TTCTAAAAATAAAATCGAGGTTAGAG
1 AACGGGGTTAGAGTATCCCCGATTGTGAAAAATCGATGCTT-TAGAAATAAGGCCGAGGTTGGAG
* ** *
1212204 TATCCCCTCGAAAATAATAGGGTTGGATTATCCCTGATTATAGAAAATCGATATTTTAAAAATAA
65 TATCCCCACGAAAATAACGGGGTTGGAGTATCCCTGATTATAG-AAATCGATATTTTAAAAATAA
1212269 AATCGAGGTTGGAGTATCCCCTCGAAAAT
129 AATCGAGGTTGGAGTATCCCCTCGAAAAT
* *
1212298 AACGGGGTTGGAGTATCCCTGATTGTGAAAAATCGATGCTTTAGAAATAAGGCCGAGGTTGGAGT
1 AACGGGGTTAGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAATAAGGCCGAGGTTGGAGT
* ** * *
1212363 ATCCCCACAAAAATAACGGGGTAAGAGTATCCCTGATTATAGTAAATCGGTGTTTTAAAAATAAA
66 ATCCCCACGAAAATAACGGGGTTGGAGTATCCCTGATTATAG-AAATCGATATTTTAAAAATAAA
* *
1212428 ATTGGGGTTGGAGTATCCCCTCGAAAAT
130 ATCGAGGTTGGAGTATCCCCTCGAAAAT
* * *
1212456 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATCTATGCTTTAGAAATAAGGCCGGGGTTGGAGT
1 AACGGGGTTAGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAATAAGGCCGAGGTTGGAGT
* * * * *
1212521 ATCCTCATGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAAT-AA
66 ATCCCCACGAAAATAACGGGGTTGGAGTATCCCTGATTAT-AGAAATCGATATTTTAAAAATAAA
* * *
1212585 AGCCAGGGTTGGAGTATCCCCTCAAAAAT
130 ATCGA-GGTTGGAGTATCCCCTCGAAAAT
*
1212614 AACGGGATTAGAGTATCCCCGAT
1 AACGGGGTTAGAGTATCCCCGAT
1212637 AGAATAACAG
Statistics
Matches: 293, Mismatches: 43, Indels: 6
0.86 0.13 0.02
Matches are distributed among these distances:
157 3 0.01
158 286 0.98
159 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.26
Consensus pattern (157 bp):
AACGGGGTTAGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAATAAGGCCGAGGTTGGAGT
ATCCCCACGAAAATAACGGGGTTGGAGTATCCCTGATTATAGAAATCGATATTTTAAAAATAAAA
TCGAGGTTGGAGTATCCCCTCGAAAAT
Found at i:1212580 original size:237 final size:236
Alignment explanation
Indices: 1212140--1212636 Score: 649
Period size: 237 Copynumber: 2.1 Consensus size: 236
1212130 TGGGGATAAC
*
1212140 AACGGGGCTAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAATAAAATCGAGGTTAGAGT
1 AACGGGG-TAGAGTATCCCCGATTATAGAAAATCGGTGTTCTAAAAATAAAATCGAGGTTAGAGT
* * * *
1212205 ATCCCCTCGAAAATAATAGGGTTGGATTATCCCTGATTATAGAAAATCGATATTTTAAAAATAAA
65 ATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATTATAGAAAATCGATACTTTAAAAATAAA
* * * * *
1212270 ATCGAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCTGATTGTGAAAAATCGAT
130 ACCGAGGTTGGAGTATCCCATCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT
* *
1212335 GCTTTAGAAATAAGGCC-GAGGTTGGAGTATCCCCACAAAAAT
195 ACTTTAGAAATAAAGCCAG-GGTTGGAGTATCCCCACAAAAAT
* * * * * *
1212377 AACGGGGTAAGAGTATCCCTGATTATAGTAAATCGGTGTTTTAAAAATAAAATTGGGGTTGGAGT
1 AACGGGGT-AGAGTATCCCCGATTATAGAAAATCGGTGTTCTAAAAATAAAATCGAGGTTAGAGT
* * * * *
1212442 ATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGT-GAAAAATCTATGCTTTAGAAATAA
65 ATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATTATAG-AAAATCGATACTTTAAAAATAA
** * *
1212506 GGCCGGGGTTGGAGTATCCTCAT-GAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCA
129 AACCGAGGTTGGAGTATCC-CATCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCA
* *
1212570 ATATTTTAGAAATAAAGCCAGGGTTGGAGTATCCCCTCAAAAAT
193 ATACTTTAGAAATAAAGCCAGGGTTGGAGTATCCCCACAAAAAT
*
1212614 AACGGGATTAGAGTATCCCCGAT
1 AACGGG-GTAGAGTATCCCCGAT
1212637 AGAATAACAG
Statistics
Matches: 224, Mismatches: 31, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
236 2 0.01
237 218 0.97
238 4 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.26
Consensus pattern (236 bp):
AACGGGGTAGAGTATCCCCGATTATAGAAAATCGGTGTTCTAAAAATAAAATCGAGGTTAGAGTA
TCCCCTCGAAAATAACAGGGTTGGAGTATCCCCGATTATAGAAAATCGATACTTTAAAAATAAAA
CCGAGGTTGGAGTATCCCATCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATA
CTTTAGAAATAAAGCCAGGGTTGGAGTATCCCCACAAAAAT
Found at i:1212710 original size:51 final size:52
Alignment explanation
Indices: 1212645--1212745 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 52
1212635 ATAGAATAAC
1212645 AGAGTTGGAATATCCCCGATTATGAAAAATTGGTGTTTTGA-AAATAAAATT
1 AGAGTTGGAATATCCCCGATTATGAAAAATTGGTGTTTTGAGAAATAAAATT
* *
1212696 AGAGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTAGAAATAAAA
1 AGAGTTGGAATATCCCCGATTATGAAAAATTGGTGTTTTGAGAAATAAAA
1212746 CTGGGGTTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 39 0.83
52 8 0.17
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.33
Consensus pattern (52 bp):
AGAGTTGGAATATCCCCGATTATGAAAAATTGGTGTTTTGAGAAATAAAATT
Found at i:1212758 original size:51 final size:51
Alignment explanation
Indices: 1212645--1212760 Score: 171
Period size: 51 Copynumber: 2.3 Consensus size: 51
1212635 ATAGAATAAC
* *
1212645 AGAGTTGGAATATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATT
1 AGAGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAACT
*
1212696 AGAGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTAGAAATAAAACT
1 AGAGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGA-AAATAAAACT
* *
1212748 GGGGTT-GAGTATC
1 AGAGTTGGAGTATC
1212761 TCTTCGGAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 46 0.78
52 13 0.22
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (51 bp):
AGAGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAACT
Found at i:1215239 original size:20 final size:20
Alignment explanation
Indices: 1215211--1215260 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1215201 TGCTTGAATG
1215211 TATCAATACAATGAACAATA
1 TATCAATACAATGAACAATA
* *
1215231 TATCGATACAATGAACAATG
1 TATCAATACAATGAACAATA
1215251 TATCAATACA
1 TATCAATACA
1215261 TCTGGGTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (20 bp):
TATCAATACAATGAACAATA
Found at i:1216584 original size:27 final size:30
Alignment explanation
Indices: 1216539--1216608 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 30
1216529 AAATTATTTT
* *
1216539 TTTTAAAAAAATAATTAAT-TA-AAATTA-
1 TTTTAAAAAAATAAGTAATAAATAAATTAG
*
1216566 TTTTAAAAAAATTAGTAATAAATAAATTAG
1 TTTTAAAAAAATAAGTAATAAATAAATTAG
*
1216596 TTATAAAAAAATA
1 TTTTAAAAAAATA
1216609 TGGAAATAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 17 0.49
28 1 0.03
29 6 0.17
30 11 0.31
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (30 bp):
TTTTAAAAAAATAAGTAATAAATAAATTAG
Found at i:1216587 original size:15 final size:15
Alignment explanation
Indices: 1216569--1216607 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1216559 AAAATTATTT
1216569 TAAAAAAATTAGTAA
1 TAAAAAAATTAGTAA
* *
1216584 TAAATAAATTAGTTA
1 TAAAAAAATTAGTAA
1216599 TAAAAAAAT
1 TAAAAAAAT
1216608 ATGGAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (15 bp):
TAAAAAAATTAGTAA
Found at i:1217068 original size:14 final size:15
Alignment explanation
Indices: 1217049--1217077 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1217039 TTAAATAAAT
1217049 ATAAAAA-ATAATTA
1 ATAAAAATATAATTA
1217063 ATAAAAATATAATTA
1 ATAAAAATATAATTA
1217078 CTTTTTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAAAATATAATTA
Found at i:1220391 original size:31 final size:31
Alignment explanation
Indices: 1220332--1220397 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1220322 TTGGCATCTG
* *
1220332 CATCTAAATTATATCTAGATGTGGATATGAC
1 CATCTAAATTATATCTAGATATGAATATGAC
*
1220363 CATCTAAATTATAT-TCAGATATTAATATGAC
1 CATCTAAATTATATCT-AGATATGAATATGAC
1220394 CATC
1 CATC
1220398 CGAGAATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (31 bp):
CATCTAAATTATATCTAGATATGAATATGAC
Found at i:1223024 original size:6 final size:6
Alignment explanation
Indices: 1222996--1223056 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
1222986 ACGATATGAG
*
1222996 ATTTTAA ATTTTA A-TTTA A-TTTA ATTTT- ATTAGTA TATTTTA ATTTT-
1 ATTTT-A ATTTTA ATTTTA ATTTTA ATTTTA ATT-TTA -ATTTTA ATTTTA
1223043 ATTTTA ATTTTA AT
1 ATTTTA ATTTTA AT
1223057 AAAATTGATA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
5 18 0.38
6 19 0.40
7 7 0.15
8 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (6 bp):
ATTTTA
Found at i:1223141 original size:14 final size:14
Alignment explanation
Indices: 1223122--1223149 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1223112 TTGAGTATGA
1223122 TTATTATAATATTT
1 TTATTATAATATTT
1223136 TTATTATAATATTT
1 TTATTATAATATTT
1223150 AATATTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTATAATATTT
Found at i:1223679 original size:2 final size:2
Alignment explanation
Indices: 1223672--1223710 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1223662 TTTAAACAAT
1223672 TA TA TA TA -A 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
1223711 CACATCTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1224680 original size:18 final size:20
Alignment explanation
Indices: 1224657--1224700 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
1224647 AATATAAAAG
*
1224657 AAAAAAGGA-AAAGGA-CAA
1 AAAAAAGGATAAAAGACCAA
1224675 AAAAAA-GATAAAAGACCAA
1 AAAAAAGGATAAAAGACCAA
1224694 AAAAAAG
1 AAAAAAG
1224701 ACTGGCTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 11 0.50
19 9 0.41
ACGTcount: A:0.75, C:0.07, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAAAGGATAAAAGACCAA
Found at i:1225901 original size:14 final size:14
Alignment explanation
Indices: 1225867--1225904 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1225857 TATTTCGTAT
1225867 ATTTTATTT-TTAC
1 ATTTTATTTATTAC
**
1225880 ATAATATTTATTAC
1 ATTTTATTTATTAC
1225894 ATTTTATTTAT
1 ATTTTATTTAT
1225905 GGCTAATACA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTTATTTATTAC
Found at i:1227049 original size:12 final size:12
Alignment explanation
Indices: 1227034--1227059 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1227024 GCAAAAATAG
1227034 CAGCATAAAAAT
1 CAGCATAAAAAT
1227046 CAGCATAAAAAT
1 CAGCATAAAAAT
1227058 CA
1 CA
1227060 AAAAGTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.19, G:0.08, T:0.15
Consensus pattern (12 bp):
CAGCATAAAAAT
Found at i:1227774 original size:25 final size:24
Alignment explanation
Indices: 1227729--1227775 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
1227719 AAATAGTATT
*
1227729 TTAATAAATAATTTTAAAATATGA
1 TTAATAAATAATATTAAAATATGA
1227753 TTAATATAATAA-ATTAATAATAT
1 TTAATA-AATAATATTAA-AATAT
1227776 TTTAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TTAATAAATAATATTAAAATATGA
Found at i:1231097 original size:52 final size:51
Alignment explanation
Indices: 1230920--1231187 Score: 180
Period size: 52 Copynumber: 5.0 Consensus size: 51
1230910 TTATTTGAAA
* * * * * **
1230920 GATAACTTAAGTTATCTACTTGCATGCTCATAGTCATCAAGCATGTATAAGT
1 GATAACTT-GGTTATCCACTTGTATGCTAATAGTTATCAAGCATGTATGTGT
* ** * * *
1230972 GACAACTTTGGTTATCCTTTTGTATTCTGATAGTTGTCACCTTCGAGCATGTATGTGAT
1 GATAAC-TTGGTTATCCACTTGTATGCTAATAG-T-T-A---TCAAGCATGTATGTG-T
* * **
1231031 -ATAAATTGGGTTATCCACTTGTATGCTAGTAGTGGTCAAGCATGTATGTGT
1 GATAACTT-GGTTATCCACTTGTATGCTAATAGTTATCAAGCATGTATGTGT
* * * * *
1231082 GATAACTTGGATTATCCACTTGTTTTCTAATAGTTATCGAGCACGTATGTGC
1 GATAACTTGG-TTATCCACTTGTATGCTAATAGTTATCAAGCATGTATGTGT
* * *
1231134 GATAACTTAGGTTATCCA-TCTGTATGCTAATAATTTTCTAGCATGTATGTGT
1 GATAACTT-GGTTATCCACT-TGTATGCTAATAGTTATCAAGCATGTATGTGT
1231186 GA
1 GA
1231188 AAACATGGGT
Statistics
Matches: 165, Mismatches: 38, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
51 4 0.02
52 117 0.71
53 5 0.03
55 1 0.01
57 3 0.02
58 34 0.21
59 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (51 bp):
GATAACTTGGTTATCCACTTGTATGCTAATAGTTATCAAGCATGTATGTGT
Found at i:1235994 original size:52 final size:49
Alignment explanation
Indices: 1235877--1236205 Score: 195
Period size: 49 Copynumber: 6.6 Consensus size: 49
1235867 TCGAAGATGC
* * *** **
1235877 GAAGAATGACAATGTGCTGATTCATGGCCAGTTTCATTAGACTT--GAA-
1 GAAG-ATGCCAATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAGAAT
* ** * *
1235924 GAAGAATGCCAACGTGCTGAGACAAGGCCAGCGACATTGGGCTTAAGAAT
1 GAAG-ATGCCAATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAGAAT
* * * *
1235974 GTTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAGGAT
1 G---AAGATGCCAATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAGAAT
* **
1236026 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCG-CTATTAGACTTGAAG-AT
1 GAAGATGCCAATGTGCTGATTCAAGGCCAGCGAC-ATCGGACTT-AAGAAT
* * * * * * *
1236075 AAAGGTGCCAATATGTTGATTCAAGGCTAGTGACATTGGACTTAA-AGAT
1 GAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAGA-AT
* * * * * *
1236124 GGTTGAGGTGCCGATGTGCTAATTCAAGGCCAACGACATCGGTCTTTAAG-AT
1 -G--AAGATGCCAATGTGCTGATTCAAGGCCAGCGACATCGGAC-TTAAGAAT
* *
1236176 GAAGGTGCCAATATGCTGATTCAAGGCCAG
1 GAAGATGCCAATGTGCTGATTCAAGGCCAG
1236206 TGATATTGGG
Statistics
Matches: 219, Mismatches: 47, Indels: 30
0.74 0.16 0.10
Matches are distributed among these distances:
47 34 0.16
48 2 0.01
49 101 0.46
50 5 0.02
51 1 0.00
52 69 0.32
53 7 0.03
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (49 bp):
GAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAGAAT
Found at i:1236047 original size:49 final size:48
Alignment explanation
Indices: 1235946--1236204 Score: 223
Period size: 49 Copynumber: 5.2 Consensus size: 48
1235936 CGTGCTGAGA
* * * *
1235946 CAAGGCCAGCGACATTGGGCTTAAGAATGTTAAAGATGCCAATATGCTGATT
1 CAAGGCCAACGACATCGGACTTAAG-ATG---AAGGTGCCAATATGCTGATT
* *
1235998 CAAGGCCAACGATATCGGACTTAAGGATGAAGGTGCCAATGTGCTGATT
1 CAAGGCCAACGACATCGGACTTAA-GATGAAGGTGCCAATATGCTGATT
* ** * *
1236047 CAAGGCCAGCG-CTATTAGACTTGAAGATAAAGGTGCCAATATGTTGATT
1 CAAGGCCAACGAC-ATCGGACTT-AAGATGAAGGTGCCAATATGCTGATT
* ** * * * * *
1236096 CAAGGCTAGTGACATTGGACTTAAAGATGGTTGAGGTGCCGATGTGCTAATT
1 CAAGGCCAACGACATCGGACTT-AAGAT-G--AAGGTGCCAATATGCTGATT
*
1236148 CAAGGCCAACGACATCGGTCTTTAAGATGAAGGTGCCAATATGCTGATT
1 CAAGGCCAACGACATCGGAC-TTAAGATGAAGGTGCCAATATGCTGATT
1236197 CAAGGCCA
1 CAAGGCCA
1236205 GTGATATTGG
Statistics
Matches: 167, Mismatches: 32, Indels: 19
0.77 0.15 0.09
Matches are distributed among these distances:
49 102 0.61
50 3 0.02
51 1 0.01
52 58 0.35
53 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.25
Consensus pattern (48 bp):
CAAGGCCAACGACATCGGACTTAAGATGAAGGTGCCAATATGCTGATT
Found at i:1236153 original size:101 final size:98
Alignment explanation
Indices: 1235976--1236214 Score: 282
Period size: 101 Copynumber: 2.4 Consensus size: 98
1235966 TTAAGAATGT
* ** * *
1235976 TAAAGATGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAGGATGAAGGTGCCAATGTG
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGGTGCCAATGTG
* * *
1236041 CTGATTCAAGGCCAGCG-CTATTAGACTTGAAGA
66 CTAATTCAAGGCCAACGAC-ATCAGACTTGAAGA
* * * * *
1236074 TAAAGGTGCCAATATGTTGATTCAAGGCTAGTGACATTGGACTTAAAGATGGTTGAGGTGCCGAT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGAT-G--AAGGTGCCAAT
* * *
1236139 GTGCTAATTCAAGGCCAACGACATCGGTCTTTAAGA
63 GTGCTAATTCAAGGCCAACGACATCAGACTTGAAGA
*
1236175 TGAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGG
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGG
1236215 GCTCGTGCCA
Statistics
Matches: 117, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
98 42 0.36
99 1 0.01
101 73 0.62
102 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.26
Consensus pattern (98 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGGTGCCAATGTG
CTAATTCAAGGCCAACGACATCAGACTTGAAGA
Found at i:1236291 original size:87 final size:87
Alignment explanation
Indices: 1236132--1236388 Score: 343
Period size: 87 Copynumber: 2.9 Consensus size: 87
1236122 ATGGTTGAGG
* * * * * * * *
1236132 TGCCGATGTGCTAATTCAAGGCCAACGACATCGGTCTTTAAGATGAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGA-CAAAGTGCCAATATGCTGATT
* *
1236197 CAAGGCCAGTGATATTGGGCTCG
65 CAAGGCCAGCGATATTGGGCTCA
* *
1236220 TGCCAATGTGTTGATTCAAGGCTAGCAACATTGGTCTTAAAGACAAAGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAAGTGCCAATATGCTGATTC
* * *
1236285 AAGGCCAACGAAATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTCA
* *
1236307 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGTGCCAATATACTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAAGTGCCAATATGCTGATTC
*
1236372 AAAGCCAGCGATATTGG
66 AAGGCCAGCGATATTGG
1236389 ACTTAAAAGA
Statistics
Matches: 147, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
87 112 0.76
88 35 0.24
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (87 bp):
TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAAGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGGCTCA
Found at i:1236301 original size:48 final size:48
Alignment explanation
Indices: 1236219--1236395 Score: 176
Period size: 48 Copynumber: 3.9 Consensus size: 48
1236209 TATTGGGCTC
* * *
1236219 GTGCCAATGTGTTGATTCAAGGCTAGC-AACATTGGTCTTAAAGACAAA
1 GTGCCAATATGCTGATTCAAGGCCAGCGAA-ATTGGTCTTAAAGACAAA
* *
1236267 GTGCCAATATGCTGATTCAAGGCCAACGAAATTGGGCTT--------A
1 GTGCCAATATGCTGATTCAAGGCCAGCGAAATTGGTCTTAAAGACAAA
* *
1236307 -TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAA
1 GTGCCAATATGCTGATTCAAGGCCAGCGAAATTGGTCTTAAAGACAAA
* * * *
1236354 GTGCCAATATACTGATTCAAAGCCAGCGATATTGGACTTAAA
1 GTGCCAATATGCTGATTCAAGGCCAGCGAAATTGGTCTTAAA
1236396 AGAAGACGCC
Statistics
Matches: 105, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
39 34 0.32
40 1 0.01
47 1 0.01
48 67 0.64
49 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (48 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGAAATTGGTCTTAAAGACAAA
Found at i:1236322 original size:39 final size:39
Alignment explanation
Indices: 1236268--1236345 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
1236258 AAAGACAAAG
1236268 TGCCAATATGCTGATTCAAGGCCAACGAAATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAACGAAATTGGGCTTA
* * * *
1236307 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA
1 TGCCAATATGCTGATTCAAGGCCAACGAAATTGGGCTTA
1236346 AAGACAAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (39 bp):
TGCCAATATGCTGATTCAAGGCCAACGAAATTGGGCTTA
Found at i:1236504 original size:27 final size:27
Alignment explanation
Indices: 1236467--1236988 Score: 463
Period size: 27 Copynumber: 18.0 Consensus size: 27
1236457 AGGAGAAAGA
*
1236467 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
1236494 TGCCATGGAGTTGTGGACTTAAAAGGAAAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAA-G------G-G
*
1236529 TGCCACGGAGTTGTGGGCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
1236556 TGCCACGGAGTTGTGGGCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
1236583 TGCCACGAAGTTGTGGACTTACAGGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
1236610 TGCCATGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
1236637 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
1236664 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
1236691 TGCCACAGAGTTGTGGACTTAAAAGGAAAAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAGG-------G
*
1236725 TGCCACGGAGTTGTAGG-CCTAAAAGGG
1 TGCCACGGAGTTGT-GGACTTAAAAGGG
* * *
1236752 TGCCATGGAGTTGTGGACTTATAGGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
1236779 TGCCACGGAGTTGTGCG-CTTTGAAGGGAAAAGAG
1 TGCCACGGAGTTGTG-GAC-TT------AAAAGGG
* * *
1236813 TGCCATGGAGTTGTGGGCTTTAAAAAGAAAAAGC
1 TGCCACGGAGTTGTGGAC-TT-AAAAG-----GG
*
1236847 TACCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
1236874 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAA-G-----G-G
* *
1236908 TGCCACGAAGTTGTGGGCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
** *
1236935 TGCCATAGAGTTGTGGACTTACAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
1236962 TGCCACGGAGTTGTGGGCTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
1236989 AAGAGAGTGC
Statistics
Matches: 412, Mismatches: 45, Indels: 76
0.77 0.08 0.14
Matches are distributed among these distances:
26 2 0.00
27 279 0.68
28 7 0.02
29 5 0.01
32 5 0.01
33 5 0.01
34 84 0.20
35 25 0.06
ACGTcount: A:0.29, C:0.14, G:0.35, T:0.22
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:1236533 original size:35 final size:35
Alignment explanation
Indices: 1236487--1237094 Score: 165
Period size: 27 Copynumber: 20.0 Consensus size: 35
1236477 TTGTGGACTT
* *
1236487 AAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGAA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1236522 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAA-G--
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1236554 ----G-GTGCCACGGAGTTGTGGGCTTAAAA-G--
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1236581 ----G-GTGCCACGAAGTTGTGGACTT-ACAGG--
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1236608 ----G-GTGCCATGGAGTTGTGGACTTAAAA-G--
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
1236635 ----G-GTGCCACGGAGTTGTGGACTTAAAA-G--
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
1236662 ----G-GTGCCACGGAGTTGTGGACTTAAAA-G--
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1236689 ----G-GTGCCACAGAGTTGTGGACTTAAAAGGAA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
1236719 AAAA-AGTGCCACGGAGTTGTAGG-CCTAAAA-G--
1 AAAAGAGTGCCACGGAGTTGT-GGACTTAAAAGGAA
* *
1236750 ----G-GTGCCATGGAGTTGTGGACTT-ATAGG--
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
** *
1236777 ----G-GTGCCACGGAGTTGTGCG-CTTTGAAGG-G
1 AAAAGAGTGCCACGGAGTTGTG-GACTTAAAAGGAA
* * *
1236806 AAAAGAGTGCCATGGAGTTGTGGGCTTTAAAAAG-A
1 AAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
* *
1236841 AAAAG-CTACCACGGAGTTGTGGACTTAAAA-G--
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
1236872 ----G-GTGCCACGGAGTTGTGGACTTAAAAGG-A
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
1236901 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAA-G--
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
** *
1236933 ----G-GTGCCATAGAGTTGTGGACTTACAA-G--
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
1236960 ----G-GTGCCACGGAGTTGTGGGCTTTAAAGG-G
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
1236989 AAGAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG-A
1 AAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
1237024 AAAAG-GTGCCACGGAGTTGTGGACTTTGAAAA-G-A
1 AAAAGAGTGCCACGGAGTTGTGGAC-TT-AAAAGGAA
* *
1237058 AAAAGAGTGCCACGGAGTCGTGGACTTAGAAAAGAA
1 AAAAGAGTGCCACGGAGTTGTGGACTTA-AAAGGAA
1237094 A
1 A
1237095 TGCCACTGAG
Statistics
Matches: 481, Mismatches: 48, Indels: 87
0.78 0.08 0.14
Matches are distributed among these distances:
26 6 0.01
27 248 0.52
28 11 0.02
32 1 0.00
33 13 0.03
34 127 0.26
35 73 0.15
36 2 0.00
ACGTcount: A:0.30, C:0.13, G:0.35, T:0.21
Consensus pattern (35 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:1236729 original size:34 final size:32
Alignment explanation
Indices: 1236690--1237145 Score: 247
Period size: 34 Copynumber: 14.7 Consensus size: 32
1236680 ACTTAAAAGG
*
1236690 GTGCCACAGAGTTGTGGACTTAAAAGGAAAAAAA
1 GTGCCACGGAGTTGTGGACTTAAAAGG--AAAAA
*
1236724 GTGCCACGGAGTTGTAGG-CCTAAAAGG-----
1 GTGCCACGGAGTTGT-GGACTTAAAAGGAAAAA
* * *
1236751 GTGCCATGGAGTTGTGGACTT-ATAGG----G
1 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
* *
1236778 GTGCCACGGAGTTGTGCG-CTTTGAAGGGAAAAGA
1 GTGCCACGGAGTTGTG-GAC-TTAAAAGGAAAA-A
* * *
1236812 GTGCCATGGAGTTGTGGGCTTTAAAAAGAAAAA
1 GTGCCACGGAGTTGTGGAC-TTAAAAGGAAAAA
*
1236845 GCTACCACGGAGTTGTGGACTTAAAAGG-----
1 G-TGCCACGGAGTTGTGGACTTAAAAGGAAAAA
1236873 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
1 GTGCCACGGAGTTGTGGACTTAAAAGG-AAAA-A
* *
1236907 GTGCCACGAAGTTGTGGGCTTAAAAGG-----
1 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
** *
1236934 GTGCCATAGAGTTGTGGACTTACAAGG-----
1 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
* * *
1236961 GTGCCACGGAGTTGTGGGCTTTAAAGGGAAGAGA
1 GTGCCACGGAGTTGTGGAC-TTAAAAGGAA-AAA
* *
1236995 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
1 GTGCCACGGAGTTGTGGAC-TTAAAAGGAAAAA
*
1237028 GGTGCCACGGAGTTGTGGACTTTGAAAAGAAAAAGA
1 -GTGCCACGGAGTTGTGGAC-TT-AAAAGGAAAA-A
* *
1237064 GTGCCACGGAGTCGTGGACTTAGAAA--AGAAA
1 GTGCCACGGAGTTGTGGACTTA-AAAGGAAAAA
* * * *
1237095 -TGCCACTGAGTCGCGGACTTTGAAA-GAAAAA
1 GTGCCACGGAGTTGTGGAC-TTAAAAGGAAAAA
* *
1237126 -TGCCACTGAGTCGTGGACTT
1 GTGCCACGGAGTTGTGGACTT
1237146 TGGGAAGAGA
Statistics
Matches: 346, Mismatches: 43, Indels: 70
0.75 0.09 0.15
Matches are distributed among these distances:
26 6 0.02
27 95 0.27
28 10 0.03
29 3 0.01
30 21 0.06
31 24 0.07
32 3 0.01
33 13 0.04
34 142 0.41
35 28 0.08
36 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.33, T:0.21
Consensus pattern (32 bp):
GTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
Found at i:1236763 original size:61 final size:60
Alignment explanation
Indices: 1236663--1236960 Score: 281
Period size: 61 Copynumber: 4.9 Consensus size: 60
1236653 ACTTAAAAGG
**
1236663 GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAAA
1 GTGCCACGGAGTTGTGG-CTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGAAAAAAA
* * *
1236724 GTGCCACGGAGTTGTAGGCCTAAAAGGGTGCCATGGAGTTGTGGACTT-ATAGG------G
1 GTGCCACGGAGTTGT-GGCTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGAAAAAAA
* * *
1236778 GTGCCACGGAGTTGTGCGCTTTGAAGGGAAAAGAGTGCCATGGAGTTGTGGGCTTTAAAA--AGA
1 GTGCCACGGAGTTGTG-GC-TT------AAAAGGGTGCCATGGAGTTGTGGAC-TTAAAAGGAAA
1236841 AAAA
57 AAAA
* * *
1236845 GCTACCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
1 G-TGCCACGGAGTTGTGG-CTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGAAAAAAA
* * *
1236907 GTGCCACGAAGTTGTGGGCTTAAAAGGGTGCCATAGAGTTGTGGACTTACAAGG
1 GTGCCACGGAGTTGT-GGCTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGG
1236961 GTGCCACGGA
Statistics
Matches: 194, Mismatches: 21, Indels: 44
0.75 0.08 0.17
Matches are distributed among these distances:
53 1 0.01
54 17 0.09
55 1 0.01
60 10 0.05
61 132 0.68
62 12 0.06
63 2 0.01
67 4 0.02
68 15 0.08
ACGTcount: A:0.30, C:0.14, G:0.34, T:0.22
Consensus pattern (60 bp):
GTGCCACGGAGTTGTGGCTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGAAAAAAA
Found at i:1236790 original size:88 final size:88
Alignment explanation
Indices: 1236630--1237049 Score: 491
Period size: 88 Copynumber: 4.6 Consensus size: 88
1236620 TTGTGGACTT
* *
1236630 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
*
1236695 ACAGAGTTGTGGACTTAAAAGGA
66 ACGGAGTTGTGGACTTAAAAGGA
* * * * * *
1236718 AAAAAAGTGCCACGGAGTTGTAGGCCTAAAAGGGTGCCATGGAGTTGTGGACTTATAGGGGTGCC
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
** *
1236783 ACGGAGTTGTGCG-CTTTGAAGGG
66 ACGGAGTTGTG-GACTTAAAAGGA
* * *
1236806 AAAAGAGTGCCATGGAGTTGTGGGCTTTAAAAAGAAAAAGCTACCACGGAGTTGTGGACTTAAAA
1 AAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAG-----GGTGCCACGGAGTTGTGGACTTAAAA
1236871 GGGTGCCACGGAGTTGTGGACTTAAAAGGA
59 GGGTGCCACGGAGTTGTGGACTTAAAAGGA
* ** *
1236901 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGGTGCCATAGAGTTGTGGACTTACAAGGGTGCC
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* * *
1236966 ACGGAGTTGTGGGCTTTAAAGGG
66 ACGGAGTTGTGGACTTAAAAGGA
*
1236989 AAGAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAG-----GGTGCCACGGAGTTGTGGACTT
1237050 TGAAAAGAAA
Statistics
Matches: 278, Mismatches: 38, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
88 167 0.60
89 4 0.01
90 10 0.04
93 5 0.02
94 3 0.01
95 89 0.32
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.22
Consensus pattern (88 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
ACGGAGTTGTGGACTTAAAAGGA
Found at i:1236974 original size:183 final size:181
Alignment explanation
Indices: 1236549--1237049 Score: 697
Period size: 183 Copynumber: 2.8 Consensus size: 181
1236539 TTGTGGGCTT
* *
1236549 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCA-CGAAGTTGTGGACTTACAGGGGTGC
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCATAG-AGTTGTGGACTTACAGGGGTGC
* * *
1236613 CATGGAGTTGTGGAC-TT-----AAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAG-----GGT
65 CACGGAGTTGTGG-CTTTAAGGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGT
1236665 GCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
129 GCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
* * * * *
1236718 AAAAAAGTGCCACGGAGTTGTAGGCCTAAAAGGGTGCCATGGAGTTGTGGACTTATAGGGGTGCC
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCATAGAGTTGTGGACTTACAGGGGTGCC
* *
1236783 ACGGAGTTGTGCGCTTTGAAGGGAAAAGAGTGCCATGGAGTTGTGGGCTTTAAAAAGAAAAAGCT
66 ACGGAGTTGTG-GCTTT-AAGGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGT
* *
1236848 ACCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
129 GCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
* *
1236901 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGGTGCCATAGAGTTGTGGACTTACAAGGGTGCC
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCATAGAGTTGTGGACTTACAGGGGTGCC
*
1236966 ACGGAGTTGTGGGCTTTAAAGGGAAGAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGT
66 ACGGAGTTGT-GGCTTT-AAGGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGT
1237031 GCCACGGAGTTGTGGACTT
129 GCCACGGAGTTGTGGACTT
1237050 TGAAAAGAAA
Statistics
Matches: 290, Mismatches: 25, Indels: 20
0.87 0.07 0.06
Matches are distributed among these distances:
169 68 0.23
170 4 0.01
176 22 0.08
177 2 0.01
178 5 0.02
183 188 0.65
184 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.22
Consensus pattern (181 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCATAGAGTTGTGGACTTACAGGGGTGCC
ACGGAGTTGTGGCTTTAAGGGAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGC
CACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
Found at i:1237091 original size:69 final size:65
Alignment explanation
Indices: 1236960--1237145 Score: 195
Period size: 69 Copynumber: 2.9 Consensus size: 65
1236950 GACTTACAAG
* * * * *
1236960 GGTGCCACGGAGTTGTGGGCTTT-AAAGGGAAGAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGA
1 GGTGCCACGGAGTTGTGGACTTTGAAA-AGAAAAGAGTGCCACGGAGTCGTGGAC-TTAAAAAG-
1237024 AAAA
63 -AAA
1237028 GGTGCCACGGAGTTGTGGACTTTGAAAAGAAAAAGAGTGCCACGGAGTCGTGGACTTAGAAAAGA
1 GGTGCCACGGAGTTGTGGACTTTGAAAAG-AAAAGAGTGCCACGGAGTCGTGGACTTA-AAAAGA
1237093 AA
64 AA
* * * *
1237095 --TGCCACTGAGTCGCGGACTTTG-AAAGAAAA-A-TGCCACTGAGTCGTGGACTT
1 GGTGCCACGGAGTTGTGGACTTTGAAAAGAAAAGAGTGCCACGGAGTCGTGGACTT
1237146 TGGGAAGAGA
Statistics
Matches: 106, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
61 19 0.18
62 1 0.01
63 4 0.04
64 4 0.04
65 19 0.18
67 3 0.03
68 26 0.25
69 30 0.28
ACGTcount: A:0.32, C:0.15, G:0.33, T:0.20
Consensus pattern (65 bp):
GGTGCCACGGAGTTGTGGACTTTGAAAAGAAAAGAGTGCCACGGAGTCGTGGACTTAAAAAGAAA
Found at i:1237099 original size:30 final size:30
Alignment explanation
Indices: 1237030--1237213 Score: 165
Period size: 30 Copynumber: 5.9 Consensus size: 30
1237020 AAGAAAAAGG
* *
1237030 TGCCACGGAGTTGTGGACTTTGAAAAGAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAAAG---AA-A
* *
1237064 GTGCCACGGAGTCGTGGACTTAGAAAAGAAA
1 -TGCCACTGAGTCGTGGACTTTGAAAAGAAA
* *
1237095 TGCCACTGAGTCGCGGACTTTGAAAGAAAAA
1 TGCCACTGAGTCGTGGACTTTGAAA-AGAAA
** *
1237126 TGCCACTGAGTCGTGGACTTTGGGAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAAAAGAAA
1237156 TGCCACTGAGTCGTGGAC-TTGTAAGAA-AATGA
1 TGCCACTGAGTCGTGGACTTTG-AA-AAGAA--A
* *
1237188 TGCCATTGAGTCGTGGACTTAGAAAA
1 TGCCACTGAGTCGTGGACTTTGAAAA
1237214 AAGAGATTGG
Statistics
Matches: 127, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
29 3 0.02
30 44 0.35
31 31 0.24
32 22 0.17
33 2 0.02
35 25 0.20
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.22
Consensus pattern (30 bp):
TGCCACTGAGTCGTGGACTTTGAAAAGAAA
Found at i:1237143 original size:61 final size:62
Alignment explanation
Indices: 1237030--1237213 Score: 228
Period size: 61 Copynumber: 2.9 Consensus size: 62
1237020 AAGAAAAAGG
* * *
1237030 TGCCACGGAGTTGTGGACTTTGAAAAGAAAAAGAGTGCCACGGAGTCGTGGACTTAGAAAAGAAA
1 TGCCACTGAGTCGTGGACTTTG-AAAG-AAAAGA-TGCCACTGAGTCGTGGACTTAGAAAAGAAA
* * ** *
1237095 TGCCACTGAGTCGCGGACTTTGAAAGAAAA-ATGCCACTGAGTCGTGGACTTTGGGAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAAAGAAAAGATGCCACTGAGTCGTGGACTTAGAAAAGAAA
* *
1237156 TGCCACTGAGTCGTGGAC-TTGTAAGAAAATGATGCCATTGAGTCGTGGACTTAGAAAA
1 TGCCACTGAGTCGTGGACTTTGAAAGAAAA-GATGCCACTGAGTCGTGGACTTAGAAAA
1237214 AAGAGATTGG
Statistics
Matches: 103, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
60 10 0.10
61 42 0.41
62 24 0.23
63 4 0.04
64 4 0.04
65 19 0.18
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.22
Consensus pattern (62 bp):
TGCCACTGAGTCGTGGACTTTGAAAGAAAAGATGCCACTGAGTCGTGGACTTAGAAAAGAAA
Found at i:1238518 original size:6 final size:6
Alignment explanation
Indices: 1238484--1238533 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
1238474 TGCCTTTGCA
* *
1238484 TTTTT- TTTTTG TGTGTG TATTTT- TTTTTG TTTTTG TTTTTG TTTTT-
1 TTTTTG TTTTTG TTTTTG T-TTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1238530 TTTT
1 TTTT
1238534 CATCATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 13 0.34
6 23 0.61
7 2 0.05
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:1245534 original size:13 final size:13
Alignment explanation
Indices: 1245516--1245543 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1245506 ATAGAAAGAT
1245516 CAATGTATCGATA
1 CAATGTATCGATA
1245529 CAATGTATCGATA
1 CAATGTATCGATA
1245542 CA
1 CA
1245544 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1245540 original size:33 final size:33
Alignment explanation
Indices: 1245498--1245563 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1245488 AAATTCCAAG
*
1245498 ATGTATCGATAGAAAG-ATCAATGTATCGATACA
1 ATGTATCGATACAAAGAAT-AATGTATCGATACA
**
1245531 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
1245564 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:1246788 original size:20 final size:21
Alignment explanation
Indices: 1246755--1246802 Score: 89
Period size: 20 Copynumber: 2.3 Consensus size: 21
1246745 ATAATTTGTT
1246755 TCGATACAATAAGTGAATGTA
1 TCGATACAATAAGTGAATGTA
1246776 TCGATAC-ATAAGTGAATGTA
1 TCGATACAATAAGTGAATGTA
1246796 TCGATAC
1 TCGATAC
1246803 GTGCTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (21 bp):
TCGATACAATAAGTGAATGTA
Found at i:1246888 original size:20 final size:20
Alignment explanation
Indices: 1246861--1246915 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1246851 TCTGCAAAAA
*
1246861 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTCTTC
*
1246881 ATTGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
1246901 AATGTATCGATACAT
1 AATGTATCGATACAT
1246916 ATAGGCAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:1249426 original size:21 final size:21
Alignment explanation
Indices: 1249401--1249441 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1249391 GGTTATCCTA
1249401 AGATA-ATTAGTGACAATTACG
1 AGATACATT-GTGACAATTACG
1249422 AGATACATTGTGACAATTAC
1 AGATACATTGTGACAATTAC
1249442 ACTTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AGATACATTGTGACAATTACG
Done.