Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 129 of 172
Found at i:42917582 original size:21 final size:22
Alignment explanation
Indices: 42917540--42917586 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
42917530 TTAATTTATT
**
42917540 TTTAATAACAATCCTATTAAAA
1 TTTAATAACAATAATATTAAAA
42917562 TTTAATAACAATAAT-TTAAAA
1 TTTAATAACAATAATATTAAAA
42917583 TTTA
1 TTTA
42917587 TTTAAGGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAATAACAATAATATTAAAA
Found at i:42920357 original size:10 final size:11
Alignment explanation
Indices: 42920337--42920362 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42920327 ATGTCTTCAC
42920337 AAAAACAAAAA
1 AAAAACAAAAA
42920348 AAAAACAAAAA
1 AAAAACAAAAA
42920359 AAAA
1 AAAA
42920363 GACTATGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:42921818 original size:43 final size:43
Alignment explanation
Indices: 42921757--42921845 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 43
42921747 AGACACATGC
* * * *
42921757 CCATGTTTTTGCCCGTATGGACAAAAATAAGCCATTTGAGAAG
1 CCATGTCTCTGCCCGTATGAACAAAAATAAGCCATTTGAAAAG
42921800 CCATGTCTCTGCCCGTATGAACAAAAATAAGCCATTTGAAAAG
1 CCATGTCTCTGCCCGTATGAACAAAAATAAGCCATTTGAAAAG
42921843 CCA
1 CCA
42921846 ATTTGCCACC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (43 bp):
CCATGTCTCTGCCCGTATGAACAAAAATAAGCCATTTGAAAAG
Found at i:42922763 original size:43 final size:43
Alignment explanation
Indices: 42922697--42922853 Score: 153
Period size: 43 Copynumber: 3.6 Consensus size: 43
42922687 TGCTCGTACA
*
42922697 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAAA-CAAATATCG
1 ATGCC-ACGTCCCAGACAG-GGTCTTACACGTAAATCAAATATCG
42922740 ATGCCACTGTCCCAGACAGGGTCTTACACG-AAATCAAATA-CG
1 ATGCCAC-GTCCCAGACAGGGTCTTACACGTAAATCAAATATCG
* * * * *
42922782 ATGCTAACGTCCCAGACATGATCTTAAACGTAAATCATAA-GTCG
1 ATGC-CACGTCCCAGACAGGGTCTTACACGTAAATCA-AATATCG
* *
42922826 ATGCCAATGTCCCAGACATGGTCTTACA
1 ATGCC-ACGTCCCAGACAGGGTCTTACA
42922854 TGAAAACACA
Statistics
Matches: 96, Mismatches: 10, Indels: 15
0.79 0.08 0.12
Matches are distributed among these distances:
42 30 0.31
43 38 0.40
44 28 0.29
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCACGTCCCAGACAGGGTCTTACACGTAAATCAAATATCG
Found at i:42922839 original size:86 final size:85
Alignment explanation
Indices: 42922697--42922858 Score: 218
Period size: 86 Copynumber: 1.9 Consensus size: 85
42922687 TGCTCGTACA
* * * * *
42922697 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACAAATATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAACGTCCCAGACATGATCTTAAACGTAAACAAATATCGATGCCAATGTCCCAGACAGGGT
42922762 CTTACACGAAATCAAATACG
66 CTTACACGAAATCAAATACG
* * *
42922782 ATGCTAACGTCCCAGACATGATCTTAAACGTAAATCATAA-GTCGATGCCAATGTCCCAGACATG
1 ATGCCAACGTCCCAGACATGATCTTAAACGTAAA-CA-AATATCGATGCCAATGTCCCAGACAGG
*
42922846 GTCTTACATGAAA
64 GTCTTACACGAAA
42922859 ACACATAGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
85 29 0.44
86 35 0.53
87 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (85 bp):
ATGCCAACGTCCCAGACATGATCTTAAACGTAAACAAATATCGATGCCAATGTCCCAGACAGGGT
CTTACACGAAATCAAATACG
Found at i:42923962 original size:13 final size:13
Alignment explanation
Indices: 42923944--42923968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42923934 ACAAACGATT
42923944 AAATTTTCACACG
1 AAATTTTCACACG
42923957 AAATTTTCACAC
1 AAATTTTCACAC
42923969 ATACTAATTC
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:42935878 original size:6 final size:6
Alignment explanation
Indices: 42935869--42935898 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
42935859 AATTAGAACT
42935869 TTGTTA TTGTTA TTGTTA TTGTTA TT-TTA T
1 TTGTTA TTGTTA TTGTTA TTGTTA TTGTTA T
42935899 ATAAATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70
Consensus pattern (6 bp):
TTGTTA
Found at i:42939690 original size:23 final size:23
Alignment explanation
Indices: 42939671--42939715 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
42939661 TTTGGTTCTT
42939671 GGGTTAGTGGT-TATTGGGTTTTA
1 GGGTTAG-GGTATATTGGGTTTTA
42939694 GGGTTAGGGTATATTTGGGTTT
1 GGGTTAGGGTATA-TTGGGTTT
42939716 GATTGTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 3 0.15
23 9 0.45
24 8 0.40
ACGTcount: A:0.13, C:0.00, G:0.40, T:0.47
Consensus pattern (23 bp):
GGGTTAGGGTATATTGGGTTTTA
Found at i:42940638 original size:31 final size:31
Alignment explanation
Indices: 42940603--42940663 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
42940593 GCATTTCAAA
42940603 CATTTAAGAATATAATTCAAGTTACATGAAG
1 CATTTAAGAATATAATTCAAGTTACATGAAG
42940634 CATTTAAGAATATAATTCAAGTTACATGAA
1 CATTTAAGAATATAATTCAAGTTACATGAA
42940664 CTTACCTCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (31 bp):
CATTTAAGAATATAATTCAAGTTACATGAAG
Found at i:42942112 original size:35 final size:35
Alignment explanation
Indices: 42942066--42942139 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
42942056 ATTTGTTACC
42942066 TAAATTATTTCATTGTCGTAATCTAGTTTGATATA
1 TAAATTATTTCATTGTCGTAATCTAGTTTGATATA
*
42942101 TAAATTATTTCATTGTCGTAATCTAGTTTGATATT
1 TAAATTATTTCATTGTCGTAATCTAGTTTGATATA
42942136 TAAA
1 TAAA
42942140 CTCTTGAGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (35 bp):
TAAATTATTTCATTGTCGTAATCTAGTTTGATATA
Found at i:42942389 original size:176 final size:176
Alignment explanation
Indices: 42942095--42942446 Score: 704
Period size: 176 Copynumber: 2.0 Consensus size: 176
42942085 AATCTAGTTT
42942095 GATATATAAATTATTTCATTGTCGTAATCTAGTTTGATATTTAAACTCTTGAGTTCGAATTTAGC
1 GATATATAAATTATTTCATTGTCGTAATCTAGTTTGATATTTAAACTCTTGAGTTCGAATTTAGC
42942160 AAATGAAACAAACGTATACAATAAAAGTTTTGAACAACCCGATTTTCAGTGGTATCAAAAAATGT
66 AAATGAAACAAACGTATACAATAAAAGTTTTGAACAACCCGATTTTCAGTGGTATCAAAAAATGT
42942225 AATTTTGGAACCCATTTCCGTAAATCAAGCCCATAAATATCAAATA
131 AATTTTGGAACCCATTTCCGTAAATCAAGCCCATAAATATCAAATA
42942271 GATATATAAATTATTTCATTGTCGTAATCTAGTTTGATATTTAAACTCTTGAGTTCGAATTTAGC
1 GATATATAAATTATTTCATTGTCGTAATCTAGTTTGATATTTAAACTCTTGAGTTCGAATTTAGC
42942336 AAATGAAACAAACGTATACAATAAAAGTTTTGAACAACCCGATTTTCAGTGGTATCAAAAAATGT
66 AAATGAAACAAACGTATACAATAAAAGTTTTGAACAACCCGATTTTCAGTGGTATCAAAAAATGT
42942401 AATTTTGGAACCCATTTCCGTAAATCAAGCCCATAAATATCAAATA
131 AATTTTGGAACCCATTTCCGTAAATCAAGCCCATAAATATCAAATA
42942447 TGAATATTTA
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 176 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (176 bp):
GATATATAAATTATTTCATTGTCGTAATCTAGTTTGATATTTAAACTCTTGAGTTCGAATTTAGC
AAATGAAACAAACGTATACAATAAAAGTTTTGAACAACCCGATTTTCAGTGGTATCAAAAAATGT
AATTTTGGAACCCATTTCCGTAAATCAAGCCCATAAATATCAAATA
Found at i:42942751 original size:16 final size:16
Alignment explanation
Indices: 42942718--42942761 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
42942708 ATGATTAAAT
42942718 TAATT-AAG-TTAA-G
1 TAATTAAAGATTAATG
42942731 TAATTAAAGATTAATG
1 TAATTAAAGATTAATG
42942747 TAATTAAAGATTAAT
1 TAATTAAAGATTAAT
42942762 TATAGTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.18
14 3 0.11
15 4 0.14
16 16 0.57
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (16 bp):
TAATTAAAGATTAATG
Found at i:42943818 original size:36 final size:38
Alignment explanation
Indices: 42943727--42943819 Score: 109
Period size: 38 Copynumber: 2.5 Consensus size: 38
42943717 AGATTATTAT
* * * *
42943727 AGATTATAACGAGATCTAGTATTTGTTGTAGATTCTTG
1 AGATTATAATGAGATCTAGCATTTGTTGCAGATTCTCG
**
42943765 AGTAACATAATGAGATCTAGCA-TTGTTGCAGATTCTCG
1 AG-ATTATAATGAGATCTAGCATTTGTTGCAGATTCTCG
42943803 -GATTATAATGAGATCTA
1 AGATTATAATGAGATCTA
42943820 ACCTTTTTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
36 14 0.30
37 1 0.02
38 16 0.35
39 15 0.33
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (38 bp):
AGATTATAATGAGATCTAGCATTTGTTGCAGATTCTCG
Found at i:42944690 original size:23 final size:25
Alignment explanation
Indices: 42944663--42944717 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
42944653 CTTAATTAAA
*
42944663 TAAAATATTCA-AAAAT-ATCTTAT
1 TAAAATATTAATAAAATAATCTTAT
*
42944686 TAAAATATTAATAAAATAATGTTAT
1 TAAAATATTAATAAAATAATCTTAT
*
42944711 CAAAATA
1 TAAAATA
42944718 ATGTTATCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 10 0.37
24 5 0.19
25 12 0.44
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.36
Consensus pattern (25 bp):
TAAAATATTAATAAAATAATCTTAT
Found at i:42944733 original size:14 final size:14
Alignment explanation
Indices: 42944698--42944725 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42944688 AAATATTAAT
42944698 AAAATAATGTTATC
1 AAAATAATGTTATC
42944712 AAAATAATGTTATC
1 AAAATAATGTTATC
42944726 TAATTAATTA
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:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
AAAATAATGTTATC
Found at i:42951628 original size:46 final size:46
Alignment explanation
Indices: 42951561--42951742 Score: 240
Period size: 46 Copynumber: 4.0 Consensus size: 46
42951551 GCTCTTTGAA
* *
42951561 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
42951607 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
42951653 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACACGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
42951699 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
42951743 TCAAAGATAA
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.01
46 119 0.99
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:42951723 original size:92 final size:92
Alignment explanation
Indices: 42951561--42951737 Score: 266
Period size: 92 Copynumber: 1.9 Consensus size: 92
42951551 GCTCTTTGAA
* * * * *
42951561 ATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCAT
1 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACACGACATGAAATGAGTAAGACCAT
* *
42951626 GGTTGAAAGATACCATGGCAACGTGAC
66 AGTTGAAAGACACCATGGCAACGTGAC
42951653 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACACGACA-GAAAATGAGTAAGACCA
1 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACACGACATG-AAATGAGTAAGACCA
*
42951717 TAGTTGAAAGACACTATGGCA
65 TAGTTGAAAGACACCATGGCA
42951738 TCATGTCAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
91 1 0.01
92 75 0.99
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (92 bp):
ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACACGACATGAAATGAGTAAGACCAT
AGTTGAAAGACACCATGGCAACGTGAC
Found at i:42953298 original size:20 final size:21
Alignment explanation
Indices: 42953270--42953308 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
42953260 TTTTCTTGAT
42953270 CTAAATTAAT-ACAAATTTCA
1 CTAAATTAATCACAAATTTCA
*
42953290 CTAATTTAATCACAAATTT
1 CTAAATTAATCACAAATTT
42953309 AATCAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (21 bp):
CTAAATTAATCACAAATTTCA
Found at i:42957537 original size:26 final size:26
Alignment explanation
Indices: 42957508--42957615 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
42957498 CGATACAAAT
42957508 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
42957534 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
42957560 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
42957586 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
42957612 TGAT
1 TGAT
42957616 GGGAATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:42963775 original size:21 final size:21
Alignment explanation
Indices: 42963746--42963786 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42963736 AATAATAATA
42963746 ATTTAAAATTTCATT-AAAAAC
1 ATTTAAAATTT-ATTCAAAAAC
*
42963767 ATTTTAAATTTATTCAAAAA
1 ATTTAAAATTTATTCAAAAA
42963787 TAGAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTAAAATTTATTCAAAAAC
Found at i:42968496 original size:32 final size:32
Alignment explanation
Indices: 42968460--42968583 Score: 221
Period size: 32 Copynumber: 3.9 Consensus size: 32
42968450 AATAAAAGTC
*
42968460 CTCTTGCTTGATGTGAGTTTTAAATATTAACA
1 CTCTTGCTTGATGTGAGTTTTACATATTAACA
42968492 CTCTTGCTTGATGTGAGTTTTACATATTAACA
1 CTCTTGCTTGATGTGAGTTTTACATATTAACA
*
42968524 CGCTTGCTTGATGTGAGTTTTACATATTAACA
1 CTCTTGCTTGATGTGAGTTTTACATATTAACA
*
42968556 CTCTTGCTTGATATGAGTTTTACATATT
1 CTCTTGCTTGATGTGAGTTTTACATATT
42968584 TGTTAATTTT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 88 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (32 bp):
CTCTTGCTTGATGTGAGTTTTACATATTAACA
Found at i:42987076 original size:19 final size:19
Alignment explanation
Indices: 42987052--42987091 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
42987042 TTAAGCATTC
42987052 AAAATAAACAAATT-TTTAA
1 AAAATAAA-AAATTATTTAA
*
42987071 AAAATAAAAATTTATTTAA
1 AAAATAAAAAATTATTTAA
42987090 AA
1 AA
42987092 GTTTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATAAAAAATTATTTAA
Found at i:42987865 original size:18 final size:17
Alignment explanation
Indices: 42987844--42987879 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
42987834 ATTTAAATAA
*
42987844 TTTTTATTTTTAAAATT
1 TTTTTAATTTTAAAATT
42987861 TTTTTAATTTTAAAATT
1 TTTTTAATTTTAAAATT
42987878 TT
1 TT
42987880 AATAATCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTAATTTTAAAATT
Found at i:42987885 original size:17 final size:17
Alignment explanation
Indices: 42987851--42987885 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42987841 TAATTTTTAT
**
42987851 TTTTAAAATTTTTTTAA
1 TTTTAAAATTTTAATAA
42987868 TTTTAAAATTTTAATAA
1 TTTTAAAATTTTAATAA
42987885 T
1 T
42987886 CAAGACTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAAAATTTTAATAA
Found at i:42989247 original size:15 final size:14
Alignment explanation
Indices: 42989227--42989287 Score: 67
Period size: 13 Copynumber: 4.5 Consensus size: 14
42989217 TATTCCAGTT
42989227 TTATTATTATTATTA
1 TTATTATTATT-TTA
42989242 TTATTATTATTTTA
1 TTATTATTATTTTA
42989256 TT-TTATT-TTATT-
1 TTATTATTATT-TTA
42989268 TTATT-TTATTTTA
1 TTATTATTATTTTA
*
42989281 TTTTTAT
1 TTATTAT
42989288 AAATTTCGAC
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
12 8 0.20
13 15 0.38
14 6 0.15
15 11 0.28
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTATTATTATTTTA
Found at i:42989287 original size:6 final size:5
Alignment explanation
Indices: 42989230--42989284 Score: 83
Period size: 5 Copynumber: 10.4 Consensus size: 5
42989220 TCCAGTTTTA
42989230 TTATT ATTATT ATTATT ATTATT TTATT TTATT TTATT TTATT TTATT
1 TTATT -TTATT -TTATT -TTATT TTATT TTATT TTATT TTATT TTATT
42989278 TTATT TT
1 TTATT TT
42989285 TATAAATTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 32 0.65
6 17 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:42990091 original size:47 final size:46
Alignment explanation
Indices: 42990022--42990171 Score: 219
Period size: 47 Copynumber: 3.2 Consensus size: 46
42990012 CAATAACAGT
* *
42990022 AACAGTAGCAGTACGGTACACAGAGTACCTCATCGGTACAAATCCAG
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCC-G
* *
42990069 AACAGTAACAGTACGGTACACAGAGTACCTTATTGGAACAAATCCG
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCG
* *
42990115 AAGCAGTAACAATACGGTACACAGAGTACCTCATCGGAACAAATCTG
1 AA-CAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCG
42990162 AAACAGTAAC
1 -AACAGTAAC
42990172 GGTAACAGTA
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
46 3 0.03
47 88 0.95
48 2 0.02
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.17
Consensus pattern (46 bp):
AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCG
Found at i:42991330 original size:5 final size:5
Alignment explanation
Indices: 42991320--42991432 Score: 226
Period size: 5 Copynumber: 22.6 Consensus size: 5
42991310 TTTATATATA
42991320 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
42991370 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
42991420 ATAAT ATAAT ATA
1 ATAAT ATAAT ATA
42991433 CTTAATTATT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 108 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:42996763 original size:27 final size:27
Alignment explanation
Indices: 42996671--42996820 Score: 133
Period size: 27 Copynumber: 5.5 Consensus size: 27
42996661 ATATTGAGCC
*
42996671 CGCACACTCAGTGCTATACA-A-TCAAAT
1 CGCACACTTAGTGC-A-ACATAGTCAAAT
* * *
42996698 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCAACATAGTCA-AAT
** * *
42996726 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAACATAGTCAAAT
* * **
42996753 CGCACACTTAGTGCATCATATTCATTT
1 CGCACACTTAGTGCAACATAGTCAAAT
*
42996780 CGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCAACATAGTCAAAT
*
42996807 CGCACCCTTAGTGC
1 CGCACACTTAGTGC
42996821 TGTACAATTT
Statistics
Matches: 99, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
25 3 0.03
26 1 0.01
27 73 0.74
28 22 0.22
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCAACATAGTCAAAT
Found at i:43004671 original size:18 final size:18
Alignment explanation
Indices: 43004648--43004682 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43004638 TTTATAATAC
*
43004648 TATATATTATGTTATTTT
1 TATATATTATGTAATTTT
43004666 TATATATTATGTAATTT
1 TATATATTATGTAATTT
43004683 ATAACATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TATATATTATGTAATTTT
Found at i:43004740 original size:17 final size:17
Alignment explanation
Indices: 43004708--43004740 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
43004698 AATAAACATA
43004708 TACTAAATATATAATAC
1 TACTAAATATATAATAC
43004725 TACTATAATATA-AATA
1 TACTA-AATATATAATA
43004741 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
TACTAAATATATAATAC
Found at i:43004751 original size:11 final size:11
Alignment explanation
Indices: 43004737--43004807 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
43004727 CTATAATATA
43004737 AATATTAAAAT
1 AATATTAAAAT
*
43004748 AATATTAAGAT
1 AATATTAAAAT
*
43004759 GACTATATAAAA-
1 -AATAT-TAAAAT
43004771 AATA-TAAAA-
1 AATATTAAAAT
*
43004780 AATAATTAACATT
1 AAT-ATTAA-AAT
43004793 AA-ATTAAAAT
1 AATATTAAAAT
43004803 AATAT
1 AATAT
43004808 AAATATTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
9 8 0.17
10 5 0.11
11 23 0.49
12 5 0.11
13 6 0.13
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (11 bp):
AATATTAAAAT
Found at i:43005584 original size:23 final size:23
Alignment explanation
Indices: 43005556--43005603 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
43005546 ATATGGTATT
43005556 AAAAATGGTTTAAAAATTAAATA
1 AAAAATGGTTTAAAAATTAAATA
** * *
43005579 AAAAATTTTTTATAATTTAAATA
1 AAAAATGGTTTAAAAATTAAATA
43005602 AA
1 AA
43005604 CAAAGATTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAAATGGTTTAAAAATTAAATA
Found at i:43008504 original size:21 final size:21
Alignment explanation
Indices: 43008478--43008523 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
43008468 TGAGGATTGC
43008478 GTCAGCAGCTATAAAAAGTAA
1 GTCAGCAGCTATAAAAAGTAA
43008499 GTCAGCAGCTATAAAAAGTAA
1 GTCAGCAGCTATAAAAAGTAA
43008520 GTCA
1 GTCA
43008524 ATCAAATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (21 bp):
GTCAGCAGCTATAAAAAGTAA
Found at i:43012708 original size:23 final size:23
Alignment explanation
Indices: 43012682--43012732 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
43012672 ACAAAACCTA
*
43012682 GAAAACGTGCTACA-TAAGCAGAG
1 GAAAACGAGCTACAGT-AGCAGAG
*
43012705 GAAAACGAGCTATAGTAGCAGAG
1 GAAAACGAGCTACAGTAGCAGAG
43012728 GAAAA
1 GAAAA
43012733 ACTCTCAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.47, C:0.14, G:0.27, T:0.12
Consensus pattern (23 bp):
GAAAACGAGCTACAGTAGCAGAG
Found at i:43015230 original size:58 final size:57
Alignment explanation
Indices: 43015112--43015263 Score: 175
Period size: 58 Copynumber: 2.7 Consensus size: 57
43015102 AATAGTTATG
* * *
43015112 ATTTT-TT-AATT-TATATAATAATAATTATATTAAGAATTTTATTAAATTATATATT
1 ATTTTATTAAATTATATTTAATAATAATTATATTAA-AATATGATTAAATTATATATT
* * * *
43015167 ATTTTATTAAGTTATATTTAATAATAATTATGTTAAAATATGGTTAAATTATTTATT
1 ATTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTATATATT
* * *
43015224 ATTTTTATTAAATTATTTTTAATAGTAATTTTATTAAAAT
1 A-TTTTATTAAATTATATTTAATAATAATTATATTAAAAT
43015264 TTAATAACAA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
55 5 0.06
56 2 0.02
57 21 0.26
58 53 0.65
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (57 bp):
ATTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAAATTATATATT
Found at i:43015439 original size:46 final size:44
Alignment explanation
Indices: 43015354--43015442 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
43015344 AACATTATTC
**
43015354 CATTCAACCAAACACAAGAATACTATTACAGTTCTATTCCATTT
1 CATTCAACCAAACACAAGAATACTATTACAACTCTATTCCATTT
***
43015398 CATTCAACCAAACAGTTGAATTACTGATTACAACTCTATTCCATT
1 CATTCAACCAAACACAAGAA-TACT-ATTACAACTCTATTCCATT
43015443 ACAGCTCTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 17 0.45
45 4 0.11
46 17 0.45
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.33
Consensus pattern (44 bp):
CATTCAACCAAACACAAGAATACTATTACAACTCTATTCCATTT
Found at i:43015470 original size:32 final size:32
Alignment explanation
Indices: 43015424--43015493 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
43015414 TGAATTACTG
*
43015424 ATTACAACTCTATTCCATTACAG-CTCTATTCC
1 ATTACAACTCTATTCAATTACAGCCT-TATTCC
*
43015456 ATTATAACTCTATTCAATTACAGCCTTATTCC
1 ATTACAACTCTATTCAATTACAGCCTTATTCC
43015488 ATTACA
1 ATTACA
43015494 GTGAACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 32 0.94
33 2 0.06
ACGTcount: A:0.31, C:0.27, G:0.03, T:0.39
Consensus pattern (32 bp):
ATTACAACTCTATTCAATTACAGCCTTATTCC
Found at i:43015494 original size:16 final size:16
Alignment explanation
Indices: 43015424--43015494 Score: 90
Period size: 16 Copynumber: 4.4 Consensus size: 16
43015414 TGAATTACTG
*
43015424 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
43015440 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
* * *
43015456 ATTATAACTCTATTCA
1 ATTACAGCTCTATTCC
43015472 ATTACAGC-CTTATTCC
1 ATTACAGCTC-TATTCC
43015488 ATTACAG
1 ATTACAG
43015495 TGAACCAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
15 1 0.02
16 46 0.98
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:43024748 original size:13 final size:13
Alignment explanation
Indices: 43024730--43024756 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43024720 AATAAAGTTA
43024730 TGCATATCAGACG
1 TGCATATCAGACG
43024743 TGCATATCAGACG
1 TGCATATCAGACG
43024756 T
1 T
43024757 TATTCCCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (13 bp):
TGCATATCAGACG
Found at i:43025147 original size:24 final size:25
Alignment explanation
Indices: 43025120--43025168 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
43025110 CTTTTTTTAT
*
43025120 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
43025144 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
43025169 AAACAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:43025161 original size:25 final size:23
Alignment explanation
Indices: 43025132--43025196 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
43025122 AATAAAAAAC
*
43025132 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
43025157 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
*
43025178 -TTAAAACA-AAAAATAAATA
1 TTTAAAACATAAAAACAAATA
43025197 AAAAATAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 1 0.03
23 5 0.14
24 3 0.08
25 11 0.30
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:43025195 original size:19 final size:20
Alignment explanation
Indices: 43025158--43025196 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
43025148 TCAAATACAT
43025158 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
*
43025178 TTAAAACA-AAAAATAAATA
1 TTAAAACATAAAAACAAATA
43025197 AAAAATAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:43037146 original size:42 final size:42
Alignment explanation
Indices: 43037046--43037202 Score: 165
Period size: 43 Copynumber: 3.7 Consensus size: 42
43037036 CAATGTCAAC
** * *
43037046 GTCCCAGATGTGGTCTTACATGTAATCAAATATCGATGCCACT
1 GTCCCAGACATGGTCTTACACGAAATCAAATA-CGATGCCACT
* *
43037089 GTCCCAGACAAGGTCTTACACGAAATCAAATACGATGTCGA-T
1 GTCCCAGACATGGTCTTACACGAAATCAAATACGATG-CCACT
* * *
43037131 GTCCCAAACATGGTCTTACACGTAATTCTCAAAT-CGATGCCAGT
1 GTCCCAGACATGGTCTTACACG-AA--ATCAAATACGATGCCACT
*
43037175 GTCCCAGACGTGGTCTTACACGAAATCA
1 GTCCCAGACATGGTCTTACACGAAATCA
43037203 CATATCGAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
41 3 0.03
42 26 0.27
43 35 0.36
44 26 0.27
45 6 0.06
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACGAAATCAAATACGATGCCACT
Found at i:43037179 original size:44 final size:43
Alignment explanation
Indices: 43037046--43037210 Score: 149
Period size: 42 Copynumber: 3.8 Consensus size: 43
43037036 CAATGTCAAC
** * * *
43037046 GTCCCAGATGTGGTCTTACATGTAATC-AAATATCGATGCCACT
1 GTCCCAGACATGGTCTTACACGTAATCTCAA-ATCGATGCCAGT
* * *
43037089 GTCCCAGACAAGGTCTTACACG-AA-ATCAAATACGATGTC-GAT
1 GTCCCAGACATGGTCTTACACGTAATCTCAAAT-CGATGCCAG-T
*
43037131 GTCCCAAACATGGTCTTACACGTAATTCTCAAATCGATGCCAGT
1 GTCCCAGACATGGTCTTACACGTAA-TCTCAAATCGATGCCAGT
* * * *
43037175 GTCCCAGACGTGGTCTTACACGAAATCACATATCGA
1 GTCCCAGACATGGTCTTACACGTAATCTCAAATCGA
43037211 AATCCTATGT
Statistics
Matches: 98, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
41 2 0.02
42 31 0.32
43 29 0.30
44 29 0.30
45 7 0.07
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGTAATCTCAAATCGATGCCAGT
Found at i:43041095 original size:132 final size:132
Alignment explanation
Indices: 43040935--43041197 Score: 386
Period size: 132 Copynumber: 2.0 Consensus size: 132
43040925 TCTTAAAGGA
* *
43040935 TTTTTAGAAGACATGAGTAAAATTTTGAAGGGATATTTGAACATTTTGAGCAAACGAGGAA-TTG
1 TTTTTAGAAGACATGAGTAAAATTTTGAAGGGACATTTGAACATTTTGAGCAAACG-CGAATTTG
*
43040999 CAACCCAACACGTTAGGGCACGATTCCACGAATTGCCAAATATCAAGCCTCGCCTTCGTTTTCAA
65 CAACCCAACACGTTAGGGCACGATTCCACGAATTGCCAAATATCAAACCTCGCCTTCGTTTTCAA
43041064 GAC
130 GAC
* **
43041067 TTTTTAGAAGACATG-GATGAAATTTTGAAGGGACATTTGATTATTTTGAGCAAACGCGAATTTG
1 TTTTTAGAAGACATGAG-TAAAATTTTGAAGGGACATTTGAACATTTTGAGCAAACGCGAATTTG
* * ** * *
43041131 CAATCCAGCACGTTAGGGCACGATTCTGCGAGTTGCCAAATATCAAATCTCGCCTTCGTTTTCAA
65 CAACCCAACACGTTAGGGCACGATTCCACGAATTGCCAAATATCAAACCTCGCCTTCGTTTTCAA
43041196 GA
130 GA
43041198 AGTTTTAAGT
Statistics
Matches: 117, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
131 4 0.03
132 113 0.97
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (132 bp):
TTTTTAGAAGACATGAGTAAAATTTTGAAGGGACATTTGAACATTTTGAGCAAACGCGAATTTGC
AACCCAACACGTTAGGGCACGATTCCACGAATTGCCAAATATCAAACCTCGCCTTCGTTTTCAAG
AC
Found at i:43045045 original size:20 final size:21
Alignment explanation
Indices: 43045007--43045050 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43044997 AATCACCCTA
* *
43045007 TTTTTATTTTATTTTATTTAT
1 TTTTTATTTTATCTAATTTAT
43045028 TTTTTATTTTA-CTAATTTAT
1 TTTTTATTTTATCTAATTTAT
43045048 TTT
1 TTT
43045051 ATTTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTATTTTATCTAATTTAT
Found at i:43046206 original size:11 final size:12
Alignment explanation
Indices: 43046190--43046218 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
43046180 TGTTGTTCTC
43046190 AAAAAAA-TGAA
1 AAAAAAAGTGAA
43046201 AAAAAAAGTGAA
1 AAAAAAAGTGAA
43046213 AAAAAA
1 AAAAAA
43046219 TGCATTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (12 bp):
AAAAAAAGTGAA
Found at i:43049637 original size:24 final size:24
Alignment explanation
Indices: 43049610--43049664 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 24
43049600 CTATAAAAAC
*
43049610 CAATCAAAAAAACAAGTAGAGAAG
1 CAATCAAAAAAACAAGCAGAGAAG
*
43049634 CAATC-AAAAAATAAGCAGAGAAG
1 CAATCAAAAAAACAAGCAGAGAAG
43049657 CAAT-AAAA
1 CAATCAAAA
43049665 CCAAAATGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.64, C:0.13, G:0.15, T:0.09
Consensus pattern (24 bp):
CAATCAAAAAAACAAGCAGAGAAG
Found at i:43057145 original size:39 final size:40
Alignment explanation
Indices: 43057061--43057145 Score: 111
Period size: 39 Copynumber: 2.1 Consensus size: 40
43057051 CTGTATACAT
* **
43057061 ACTGTATCTGAGATGGGCTAAGGCCCTAAGTTATATCTGA
1 ACTGTATCTGAAATGGGCTAAGGCCCTAAACTATATCTGA
*
43057101 ACTGTATCT-AAATGGGCTAAGG-CCTAAACTGTATCTGA
1 ACTGTATCTGAAATGGGCTAAGGCCCTAAACTATATCTGA
43057139 ATCTGTA
1 A-CTGTA
43057146 ATGGGCTTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 14 0.35
39 17 0.43
40 9 0.22
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (40 bp):
ACTGTATCTGAAATGGGCTAAGGCCCTAAACTATATCTGA
Found at i:43067280 original size:34 final size:34
Alignment explanation
Indices: 43067232--43067298 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
43067222 AATCTTTTAT
*
43067232 ATGAAATAATCTCACCAACGATATCATTAAAAAC
1 ATGAAATAATCTCACCAACGATAACATTAAAAAC
*
43067266 ATGAGATAATCTCACCAACGATAACATTAAAAA
1 ATGAAATAATCTCACCAACGATAACATTAAAAA
43067299 ACAACTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.51, C:0.19, G:0.07, T:0.22
Consensus pattern (34 bp):
ATGAAATAATCTCACCAACGATAACATTAAAAAC
Found at i:43069349 original size:3 final size:3
Alignment explanation
Indices: 43069330--43069840 Score: 177
Period size: 3 Copynumber: 169.3 Consensus size: 3
43069320 TTAGTTAATT
* * * * *
43069330 TTA TTA TTT TTA CTA TTA TTA TTA TTA TAA ATA -TA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
43069377 TTG TTA TTA TTA TTTA CATG TTA TTA TTTC TTT TTC TT- TTA TTA TGGTA
1 TTA TTA TTA TTA -TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA T--TA
* ** * *
43069426 TTA TTA TTA TTG CCA TTA TTA CTT- TTT TTA TTTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA
* * * * *
43069472 TTA TTA TTA -TC TTA TT- TTA TTG TCA TTT TTA CTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * *
43069517 TTT TTA TT- TTT TTA CTA CTA TTA TTA TTA GTA TTA TCA ATA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** * * *
43069564 TTA CTA TTA TT- TT- TTA CAA TTA TTA TT- TCA CATA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * * * **
43069607 CTA TTT TTG TTA TTA TTA TTA TTA TTT TTA CCA -TA TTA TTA TT- TCCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T--TA
* * ** * *
43069655 TTT TTA TATA TTA TTA TTG TTA TTA ACA TATA CTA TCA TTA TTAA TGTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT-A T-TA
* * * * * * * * * *
43069704 CTC TTA TTTC TTC TTC TTC TTA TTA TTA TTA CTA ATA TCA CTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * * *
43069750 CCA TTA TTA TTA TTA TTA TTA TTG TTG TTA TTA TTA TTA -TA CCTTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA --TTA
* * * *
43069796 TTA TTA TTG TTA CTA TT- GTA TTA TTA CTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43069841 AATATTTTCT
Statistics
Matches: 367, Mismatches: 112, Indels: 58
0.68 0.21 0.11
Matches are distributed among these distances:
2 23 0.06
3 316 0.86
4 22 0.06
5 6 0.02
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:43069481 original size:37 final size:37
Alignment explanation
Indices: 43069380--43069545 Score: 97
Period size: 34 Copynumber: 4.6 Consensus size: 37
43069370 GTTATTATTG
* * *
43069380 TTATTATTATT-TACA-TGTTATTATTTCTTTTTCT-T
1 TTATTATTATTAT-CATTATTATTATTACTTTTTTTAT
*
43069415 TTATTATGGTATTATTATTATTGCCATTATTACTTTTTTTAT
1 TTATTAT--TATTATCATTATT---ATTATTACTTTTTTTAT
*
43069457 TTATTATTATTATCATTATTATTA-T-CTTATTTTA-
1 TTATTATTATTATCATTATTATTATTACTTTTTTTAT
* * *
43069491 TTGTCATT-TT-T-ACTATTATTATTA-TTTTTTTAT
1 TTATTATTATTATCATTATTATTATTACTTTTTTTAT
*
43069524 TT-TT-TTACTA-CTATTATTATTA
1 TTATTATTATTATC-ATTATTATTA
43069546 GTATTATCAA
Statistics
Matches: 103, Mismatches: 13, Indels: 31
0.70 0.09 0.21
Matches are distributed among these distances:
31 11 0.11
32 11 0.11
33 4 0.04
34 15 0.15
35 15 0.15
36 1 0.01
37 9 0.09
38 4 0.04
40 12 0.12
41 13 0.13
42 8 0.08
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66
Consensus pattern (37 bp):
TTATTATTATTATCATTATTATTATTACTTTTTTTAT
Found at i:43069492 original size:31 final size:31
Alignment explanation
Indices: 43069426--43069488 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
43069416 TATTATGGTA
* * *
43069426 TTATTATTATTGCCATTATTACTTTTTTTAT
1 TTATTATTATTACCATTATTACTTATCTTAT
*
43069457 TTATTATTATTATCATTATTA-TTATCTTAT
1 TTATTATTATTACCATTATTACTTATCTTAT
43069487 TT
1 TT
43069489 TATTGTCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (31 bp):
TTATTATTATTACCATTATTACTTATCTTAT
Found at i:43069536 original size:31 final size:31
Alignment explanation
Indices: 43069440--43069545 Score: 110
Period size: 34 Copynumber: 3.2 Consensus size: 31
43069430 TATTATTGCC
43069440 ATTATTACTTTTTTTATTTATTATTATTA-TCATT
1 ATTATTA-TTTTTTTATTTATT-TTA-TACT-ATT
43069474 ATTATTATCTTATTTTATTGTCATTTT-TACTATT
1 ATTATTAT-TT-TTTTATT-T-ATTTTATACTATT
43069508 ATTATTATTTTTTTATTT-TTTTACTACTATT
1 ATTATTATTTTTTTATTTATTTTA-TACTATT
43069539 ATTATTA
1 ATTATTA
43069546 GTATTATCAA
Statistics
Matches: 65, Mismatches: 0, Indels: 17
0.79 0.00 0.21
Matches are distributed among these distances:
29 4 0.06
31 15 0.23
32 7 0.11
33 3 0.05
34 22 0.34
35 8 0.12
36 3 0.05
37 3 0.05
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (31 bp):
ATTATTATTTTTTTATTTATTTTATACTATT
Found at i:43069647 original size:23 final size:21
Alignment explanation
Indices: 43069617--43069678 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 21
43069607 CTATTTTTGT
43069617 TATTATTATTATTATTTTTACCA
1 TATTATTATT-TTATTTTTA-CA
*
43069640 TATTATTATTTCCTATTTTTATA
1 TATTATTATTT--TATTTTTACA
43069663 TATTATTATTGTTATT
1 TATTATTATT-TTATT
43069679 AACATATACT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
22 5 0.14
23 21 0.60
24 9 0.26
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (21 bp):
TATTATTATTTTATTTTTACA
Found at i:43069675 original size:58 final size:58
Alignment explanation
Indices: 43069560--43069679 Score: 147
Period size: 58 Copynumber: 2.1 Consensus size: 58
43069550 TATCAATATA
*
43069560 ATTATTACTATTATTTTTTACAATTATTATTTCACATACTATTATTACTATTTTTGTT
1 ATTATTACTATTATTTTTTACAATTATTATTTCACATACTATTATTACTATTATTGTT
* * * *
43069618 ATTATTATTATTA-TTTTTACCATATTATTATTTC-C-TATTTTTATATATTATTATTGTT
1 ATTATTACTATTATTTTTTA-CA-ATTATTATTTCACATACTATTAT-TACTATTATTGTT
43069676 ATTA
1 ATTA
43069680 ACATATACTA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
57 13 0.24
58 30 0.56
59 11 0.20
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (58 bp):
ATTATTACTATTATTTTTTACAATTATTATTTCACATACTATTATTACTATTATTGTT
Found at i:43070056 original size:3 final size:3
Alignment explanation
Indices: 43070048--43070238 Score: 104
Period size: 3 Copynumber: 63.7 Consensus size: 3
43070038 TGTATTTACC
* * *
43070048 ATT ATT ATT ACT ATT A-T ATT CACTT -TT ATT ACT ATT ACTT -TT TTT
1 ATT ATT ATT ATT ATT ATT ATT -A-TT ATT ATT ATT ATT A-TT ATT ATT
* * * * * * *
43070093 ATT -TT TTT ATT TTT TTCT ATT ACT ATT ATC ATT ATT ATT AAT ACT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
43070138 AAT ATT AAT ATT CTT ATT ATT ACTT -TT ATT ATT ATC ATT AGT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
* * * * * **
43070183 ATT ATT TTT ACT ACT ACT ATT ATT ATT ATC AAC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43070231 ATT ATT AT
1 ATT ATT AT
43070239 CGTTTTCATC
Statistics
Matches: 146, Mismatches: 32, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
2 10 0.07
3 127 0.87
4 7 0.05
5 2 0.01
ACGTcount: A:0.30, C:0.09, G:0.01, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:43075375 original size:64 final size:64
Alignment explanation
Indices: 43075296--43075541 Score: 474
Period size: 64 Copynumber: 3.8 Consensus size: 64
43075286 TCATTCATAA
* *
43075296 CACATCTAATTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACACAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTCCGATCATAGCATCCTAATTATTTGACACAAGCAT
43075360 CACATCTAGTTAGGAGCATTTGATTCATTCCGATCATAGCATCCTAATTATTTGACACAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTCCGATCATAGCATCCTAATTATTTGACACAAGCAT
43075424 CACATCTAGTTAGGAGCATTTGATTCATTCCGATCATAGCATCCTAATTATTTGACACAAGCAT
1 CACATCTAGTTAGGAGCATTTGATTCATTCCGATCATAGCATCCTAATTATTTGACACAAGCAT
43075488 CACATCTAGTTAGGAGCATTTGATTCATTCCGATCATAGCATCCTAATTATTTG
1 CACATCTAGTTAGGAGCATTTGATTCATTCCGATCATAGCATCCTAATTATTTG
43075542 GCATAAACAT
Statistics
Matches: 180, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 180 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTGATTCATTCCGATCATAGCATCCTAATTATTTGACACAAGCAT
Found at i:43075678 original size:44 final size:44
Alignment explanation
Indices: 43075629--43075771 Score: 132
Period size: 44 Copynumber: 3.3 Consensus size: 44
43075619 GATCTTATCT
*
43075629 CCCTAAGCGGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACC
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACC
* ** * * * ** *
43075673 CCCTAAGCAGTAG-GGTAACAGGCCGAATTAC--AGA-TCTTGTCT
1 CCCTAAGCAGTAGTGG-AGCAGATCGAA-GACGGTGAGCCTTAACC
* *
43075715 CCCTAAGTAGTGGTGGAGCAGATCGAAGACGGTGAGCCTTAACC
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACC
43075759 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
43075772 GGTAACAGGC
Statistics
Matches: 70, Mismatches: 23, Indels: 12
0.67 0.22 0.11
Matches are distributed among these distances:
41 2 0.03
42 23 0.33
43 8 0.11
44 35 0.50
45 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.29, T:0.19
Consensus pattern (44 bp):
CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACC
Found at i:43075807 original size:42 final size:42
Alignment explanation
Indices: 43075673--43075807 Score: 121
Period size: 42 Copynumber: 3.2 Consensus size: 42
43075663 AGCCTTAACC
43075673 CCCTAAGCAGTAGGGTAACAGGCCGAATTACAGATCTTGTCT
1 CCCTAAGCAGTAGGGTAACAGGCCGAATTACAGATCTTGTCT
* * * ** * * * ** *
43075715 CCCTAAGTAGT-GGTGGAGCAGATCGAA-GACGGTGAGCCTTAACC
1 CCCTAAGCAGTAGG-GTAACAGGCCGAATTAC--AGA-TCTTGTCT
43075759 CCCTAAGCAGTAGGGTAACAGGCCGAATTACAGATCTTGTCT
1 CCCTAAGCAGTAGGGTAACAGGCCGAATTACAGATCTTGTCT
43075801 CCCTAAG
1 CCCTAAG
43075808 TAGTGGTGGA
Statistics
Matches: 65, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
41 4 0.06
42 30 0.46
43 4 0.06
44 23 0.35
45 4 0.06
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.21
Consensus pattern (42 bp):
CCCTAAGCAGTAGGGTAACAGGCCGAATTACAGATCTTGTCT
Found at i:43076042 original size:87 final size:86
Alignment explanation
Indices: 43075609--43076394 Score: 1051
Period size: 87 Copynumber: 9.0 Consensus size: 86
43075599 GCAACATCGG
* * ** * * *
43075609 TGAATTCACAGATCTTATCTCCCTAAGCGGTAGTGG-AGCAGATCGAAGACGGTGAGCCTTAACC
1 TGAATTTACAGATCTTATCACCCTAAGTAGTAG-GGAAACAGATCGAAG-CGATGGGCCTTAACC
*
43075673 CCCTAAGCAGTAGGGTAACAGGC
64 CCCTAAGTAGTAGGGTAACAGGC
* * * * * * *
43075696 CGAA-TTACAGATCTTGTCTCCCTAAGTAGT-GGTGGAGCAGATCGAAGACGGTGAGCCTTAACC
1 TGAATTTACAGATCTTATCACCCTAAGTAGTAGG-GAAACAGATCGAAG-CGATGGGCCTTAACC
*
43075759 CCCTAAGCAGTAGGGTAACAGGC
64 CCCTAAGTAGTAGGGTAACAGGC
* * * * *
43075782 CGAA-TTACAGATCTTGTCTCCCTAAGTAGT-GGTGGAGCAGATCGAAGACGATGGGCCTTAACC
1 TGAATTTACAGATCTTATCACCCTAAGTAGTAGG-GAAACAGATCGAAG-CGATGGGCCTTAACC
* *
43075845 TCCTAAGTAGTAGGGTAACAGGT
64 CCCTAAGTAGTAGGGTAACAGGC
* *
43075868 TGAAATTACAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCGAAGGCCGATGGGCCTTAACC
1 TGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCGAA-G-CGATGGGCCTTAACC
*
43075933 CCCTAGGTAGTAGGGTAACAGGC
64 CCCTAAGTAGTAGGGTAACAGGC
*
43075956 TGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCAAATGCGATGGGCCTTAACCC
1 TGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCGAA-GCGATGGGCCTTAACCC
*
43076021 CCTAGGTAGTAGGGTAACAGGC
65 CCTAAGTAGTAGGGTAACAGGC
*
43076043 TGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCAAATGCGATGGGCCTTAACCC
1 TGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCGAA-GCGATGGGCCTTAACCC
*
43076108 CCTAGGTAGTAGGGTAACAGGC
65 CCTAAGTAGTAGGGTAACAGGC
*
43076130 TGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCAAATGCGATGGGCCTTAACCC
1 TGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCGAA-GCGATGGGCCTTAACCC
*
43076195 CCTAGGTAGTAGGGTAACAGGC
65 CCTAAGTAGTAGGGTAACAGGC
*
43076217 TGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCGAAAGTGATGGGCCTTAACCC
1 TGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCG-AAGCGATGGGCCTTAACCC
*
43076282 CCTAAGCAGTAGGGTAACAGGC
65 CCTAAGTAGTAGGGTAACAGGC
* * * * * *
43076304 TGAATTTACAGATCTTATCACACTAAGCAGTAGGGAAACAGATTGAAGGCAATGAGCCTTGACCC
1 TGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCGAA-GCGATGGGCCTTAACCC
*
43076369 CCTAAGCAGTAGGGTAACAGGC
65 CCTAAGTAGTAGGGTAACAGGC
43076391 TGAA
1 TGAA
43076395 AATTATAGAT
Statistics
Matches: 657, Mismatches: 35, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
84 1 0.00
85 2 0.00
86 159 0.24
87 410 0.62
88 85 0.13
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.22
Consensus pattern (86 bp):
TGAATTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGATCGAAGCGATGGGCCTTAACCCC
CTAAGTAGTAGGGTAACAGGC
Found at i:43076586 original size:68 final size:68
Alignment explanation
Indices: 43076408--43077083 Score: 942
Period size: 68 Copynumber: 9.9 Consensus size: 68
43076398 TATAGATTTT
* * *
43076408 TTCTCTCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAGCTGAT
1 TTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGA-
*
43076473 TCTT
65 TCTC
* * *
43076477 TTCTCCTTGAAATGGCGTTGGAGCAGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCAGAT
1 TTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGAT
43076542 CTC
66 CTC
* * *
43076545 TTCTCCCTGAAATGGCATTGGAACGGCTCGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGAT
1 TTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGAT
43076610 CTC
66 CTC
* * * * * * *
43076613 TTCTCCTTGAAATGGCATTGGAGCGGCTAAAATCCATAACAGATCTCCTTGAAGTTTCAGCGGAT
1 TTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGAT
* *
43076678 TTT
66 CTC
* *
43076681 TTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAGCAGAT
1 TTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGAT
43076746 CT-
66 CTC
* * *
43076748 TTCT-CCTAAAATGGCGTTGGAACGGCTAGAAGCCACAACAGATCTCCTTAAAGTTTCAGCGGAT
1 TTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGAT
43076812 CTC
66 CTC
* * * * * * *
43076815 TTCTCCTTGAAATGGCATTGGAGCGGCTAAAATCCATAACAGATCTCCTTGAAGTTTCAGCGGAT
1 TTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGAT
* *
43076880 TTT
66 CTC
* *
43076883 TTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAGCTGAT
1 TTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGA-
*
43076948 TCTT
65 TCTC
* * *
43076952 TTCTCCTTGAAATGGCGTTGGAGCAGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCAGAT
1 TTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGAT
43077017 CTC
66 CTC
* * *
43077020 TTCTCCCTGAAATGGCATTGGAACGGCTCGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGA
1 TTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGA
43077084 GTAGATTGAA
Statistics
Matches: 540, Mismatches: 64, Indels: 7
0.88 0.10 0.01
Matches are distributed among these distances:
66 57 0.11
67 8 0.01
68 353 0.65
69 122 0.23
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (68 bp):
TTCTCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGAT
CTC
Found at i:43076824 original size:202 final size:202
Alignment explanation
Indices: 43076415--43077083 Score: 1059
Period size: 202 Copynumber: 3.3 Consensus size: 202
43076405 TTTTTCTCTC
* * * *
43076415 TGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAGCTGATTCTTTTC
1 TGAAATGGCATTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGCGGATT-TTTTC
* * *
43076480 TCCTTGAAATGGCGTTGGAGCAGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCAGATCTC
65 TCCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAGCAGATCT-
* *
43076545 TTCTCCCTGAAATGGCATTGGAACGGCTCGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGAT
129 TTCT-CCTGAAATGGCGTTGGAACGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGAT
43076610 CTCTTCTCCT
193 CTCTTCTCCT
* *
43076620 TGAAATGGCATTGGAGCGGCTAAAATCCATAACAGATCTCCTTGAAGTTTCAGCGGATTTTTTCT
1 TGAAATGGCATTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGCGGATTTTTTCT
43076685 CCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAGCAGATCTTT
66 CCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAGCAGATCTTT
* *
43076750 CTCCTAAAATGGCGTTGGAACGGCTAGAAGCCACAACAGATCTCCTTAAAGTTTCAGCGGATCTC
131 CTCCTGAAATGGCGTTGGAACGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGATCTC
43076815 TTCTCCT
196 TTCTCCT
* *
43076822 TGAAATGGCATTGGAGCGGCTAAAATCCATAACAGATCTCCTTGAAGTTTCAGCGGATTTTTTCT
1 TGAAATGGCATTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGCGGATTTTTTCT
*
43076887 CCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAGCTGATTCTT
66 CCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAGCAGA-TC-T
* * *
43076952 TTCTCCTTGAAATGGCGTTGGAGCAGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCAGAT
129 TTCTCC-TGAAATGGCGTTGGAACGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGAT
*
43077017 CTCTTCTCCC
193 CTCTTCTCCT
* ** * *
43077027 TGAAATGGCATTGGAACGGCTCGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGA
1 TGAAATGGCATTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGCGGA
43077084 GTAGATTGAA
Statistics
Matches: 434, Mismatches: 27, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
202 190 0.44
203 6 0.01
204 73 0.17
205 165 0.38
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (202 bp):
TGAAATGGCATTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGCGGATTTTTTCT
CCCTGAAATGGCGTTGGAGCGGCTAGAAGCCACAGCAGATCTCCTTGAAGTTTCAGCAGATCTTT
CTCCTGAAATGGCGTTGGAACGGCTAGAAGCCACAGCAGATCTCCTTAAAGTTTCAGCGGATCTC
TTCTCCT
Found at i:43077183 original size:45 final size:44
Alignment explanation
Indices: 43077062--43077305 Score: 120
Period size: 44 Copynumber: 5.4 Consensus size: 44
43077052 GCCACAGCAG
* * * ** *
43077062 ATCTCCTTAAAGTTTCAGCGGAGTAGATTGAAGTCACAAGTCTT
1 ATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGTCACAAATCTT
* * *
43077106 ATCTCCCTAAAGTTGCAGTGGAGCAAACTGAAGAT-AGCAAATCTT
1 ATCTCCCTAAAGTTGCAGTGGAACAGATTGAAG-TCA-CAAATCTT
* * * *
43077151 ATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATGAATAAACAGATCTT
1 ATCTCCCTAAAGTTGCAGTGGAACAGATTG-A---A-G--T-CACAAATCTT
* * * * * *
43077203 ATCTCTCTGAAGTTGCAGT-AAAGCAGA-TCAA--AACAAACCTT
1 ATCTCCCTAAAGTTGCAGTGGAA-CAGATTGAAGTCACAAATCTT
* * * * ** *
43077244 ATCTCCCTGAAGTTGCAGTGCAGCAGGTTGAAGTTGCAAGTCTT
1 ATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGTCACAAATCTT
43077288 ATCTCCCTAAAGTTGCAG
1 ATCTCCCTAAAGTTGCAG
43077306 CAGAGTAGAT
Statistics
Matches: 156, Mismatches: 29, Indels: 30
0.73 0.13 0.14
Matches are distributed among these distances:
41 29 0.19
42 4 0.03
44 51 0.33
45 33 0.21
46 1 0.01
47 1 0.01
49 1 0.01
50 2 0.01
51 5 0.03
52 28 0.18
53 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (44 bp):
ATCTCCCTAAAGTTGCAGTGGAACAGATTGAAGTCACAAATCTT
Found at i:43077360 original size:85 final size:84
Alignment explanation
Indices: 43077196--43077376 Score: 213
Period size: 85 Copynumber: 2.1 Consensus size: 84
43077186 ATGAATAAAC
* * * * *
43077196 AGATCTTATCTCTCTGAAGTTGCAGTAAAGCAGATCAAAACAAACCTTATCTCCCTGAAGTTGCA
1 AGATCTTATCTCCCTAAAGTTGCAGCAAAGCAGATCAAAACAAACC-TATCTCCCTAAAGTGGCA
* * *
43077261 GTGCAGCAGGTTGAAGTTGCA
65 ATGCAACAGATTGAAGTTG-A
* *
43077282 AG-TCTTATCTCCCTAAAGTTGCAGCAGAGTAGATCAAAACAAATTCC-ATCTCCCTAAAGTGGC
1 AGATCTTATCTCCCTAAAGTTGCAGCAAAGCAGATCAAAACAAA--CCTATCTCCCTAAAGTGGC
*
43077345 AATGGAACAGATTGAAGTTGA
64 AATGCAACAGATTGAAGTTGA
43077366 AGATCTTATCT
1 AGATCTTATCT
43077377 TCTTAAAAGT
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
84 3 0.04
85 74 0.91
86 2 0.02
87 2 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (84 bp):
AGATCTTATCTCCCTAAAGTTGCAGCAAAGCAGATCAAAACAAACCTATCTCCCTAAAGTGGCAA
TGCAACAGATTGAAGTTGA
Found at i:43078010 original size:5 final size:5
Alignment explanation
Indices: 43077979--43078137 Score: 234
Period size: 5 Copynumber: 31.8 Consensus size: 5
43077969 GAAATAAAAG
*
43077979 TTTTA -TTTA TTTTCG TTTT- TGTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTT-A TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA
***
43078029 TTTTGA -ACCA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
43078079 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
43078129 TTTTA TTTT
1 TTTTA TTTT
43078138 GAACCTATTT
Statistics
Matches: 141, Mismatches: 7, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
4 6 0.04
5 129 0.91
6 6 0.04
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:43078468 original size:3 final size:3
Alignment explanation
Indices: 43078446--43078947 Score: 169
Period size: 3 Copynumber: 168.3 Consensus size: 3
43078436 TTAGTTAATT
* * * * * * *
43078446 TTA TTA TTT TTA CTA CTA TTA TTA TAA ATA -TA TTA TTT TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
43078493 TTA TTA TTA TTTA CATG TTA TTA TTTC TTT TTC TT- TTA TTA TGGTA
1 TTA TTA TTA -TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA T--TA
* * ** *
43078539 TTA GTA TTG CCA TTA TTA CTT- TT- TTA TT- TT- TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
43078581 TCA TTA TTA TTA -TC TTA TT- TTA TTG TCA TTT TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
43078627 TTT TTA -TA TT- TT- TTA TT- TT- TTA CTA CTA TTA TTA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * ** *
43078670 TCA ATA TAA TTA TTA CTA TTA GTT- TT- TTA CAA TTA TTA TT- TCA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
43078713 CATA CTA TTA TTA CTA TTT TTG TTA TTA TTA TTA TTA TT- TTT TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * **
43078758 CCA TATA TTA TT- TCCTA TTT TTA TATA TTA TTA TTA TTA TTA ACA TATA
1 TTA T-TA TTA TTA T--TA TTA TTA T-TA TTA TTA TTA TTA TTA TTA T-TA
* * * *
43078807 CTA TCA TTA TTAA TGTA CTA TTA TTA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
43078854 ATA TTA ATA TTC TTA TTA TTA CTT- TTA TTA TTA TCA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * ** *
43078899 TTA TTT TTA CTA CTA CTA TTA TTA TTA TCA ACA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43078947 T
1 T
43078948 CGTTTTCATC
Statistics
Matches: 365, Mismatches: 105, Indels: 58
0.69 0.20 0.11
Matches are distributed among these distances:
2 35 0.10
3 302 0.83
4 23 0.06
5 5 0.01
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:43078624 original size:37 final size:35
Alignment explanation
Indices: 43078568--43078663 Score: 108
Period size: 34 Copynumber: 2.7 Consensus size: 35
43078558 TTTTTTATTT
* *
43078568 TTTATTTTTATTATCATTATTATTATCTTATTTTA
1 TTTATTTTTACTATTATTATTATTATCTTATTTTA
43078603 TTGTCATTTTTACTATTATTATTATT-T-TTATATTT-
1 TT-T-ATTTTTACTATTATTATTATTATCTTAT-TTTA
*
43078638 TTTATTTTTTACTACTATTATTATTA
1 TTTA-TTTTTACTATTATTATTATTA
43078664 GTATTATCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
33 1 0.02
34 20 0.38
35 8 0.15
36 5 0.09
37 19 0.36
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (35 bp):
TTTATTTTTACTATTATTATTATTATCTTATTTTA
Found at i:43078798 original size:59 final size:59
Alignment explanation
Indices: 43078678--43078799 Score: 144
Period size: 59 Copynumber: 2.1 Consensus size: 59
43078668 TATCAATATA
* *
43078678 ATTATTACTATTAGTTTTTTACAATTATTATTTCACATACTATTATTACTATTTTTGTT
1 ATTATTACTATTAGTTTTTTACAATTATTATTTCACATACTATTATTACTATTATTATT
* * * * *
43078737 ATTATTATTATTATTTTTTTACCATATATTATTTC-C-TATTTTTA-TA-TATTATTATT
1 ATTATTACTATTAGTTTTTTACAAT-TATTATTTCACATACTATTATTACTATTATTATT
43078793 ATTATTA
1 ATTATTA
43078800 ACATATACTA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
56 15 0.27
57 2 0.04
58 6 0.11
59 23 0.42
60 9 0.16
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.61
Consensus pattern (59 bp):
ATTATTACTATTAGTTTTTTACAATTATTATTTCACATACTATTATTACTATTATTATT
Found at i:43080584 original size:30 final size:29
Alignment explanation
Indices: 43080535--43080593 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
43080525 GCCCCAAAAT
* *
43080535 TATATTTTATAATTTTTTAACTTTTTTAA
1 TATATTTTATAAATTTTTAAATTTTTTAA
*
43080564 TATATTTTTTAGAATTTTTAAATTTTTTAA
1 TATATTTTATA-AATTTTTAAATTTTTTAA
43080594 AATAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (29 bp):
TATATTTTATAAATTTTTAAATTTTTTAA
Found at i:43080594 original size:9 final size:10
Alignment explanation
Indices: 43080539--43080592 Score: 51
Period size: 9 Copynumber: 5.5 Consensus size: 10
43080529 CAAAATTATA
43080539 TTTTATAATT
1 TTTTATAATT
*
43080549 TTTTA-ACTT
1 TTTTATAATT
43080558 TTTTAATATATT
1 TTTT-ATA-ATT
*
43080570 TTTTAGAA-T
1 TTTTATAATT
43080579 TTTTA-AATT
1 TTTTATAATT
43080588 TTTTA
1 TTTTA
43080593 AAATAAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
8 2 0.05
9 19 0.51
10 7 0.19
11 3 0.08
12 6 0.16
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:43082058 original size:28 final size:28
Alignment explanation
Indices: 43082018--43082074 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
43082008 AGAGATGAAG
43082018 TTAATTTCTCAGACACTGATGGTAACGA
1 TTAATTTCTCAGACACTGATGGTAACGA
43082046 TTAATTTCTCAGACACTGATGGTAACGA
1 TTAATTTCTCAGACACTGATGGTAACGA
43082074 T
1 T
43082075 CCCTAATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (28 bp):
TTAATTTCTCAGACACTGATGGTAACGA
Found at i:43082322 original size:18 final size:18
Alignment explanation
Indices: 43082299--43082336 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43082289 TTTCCGATAA
*
43082299 AACCGAATTAATTCGGTT
1 AACCGAATGAATTCGGTT
*
43082317 AACCGACTGAATTCGGTT
1 AACCGAATGAATTCGGTT
43082335 AA
1 AA
43082337 TCGGTCAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (18 bp):
AACCGAATGAATTCGGTT
Found at i:43083071 original size:37 final size:39
Alignment explanation
Indices: 43083030--43083102 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 39
43083020 TAAAATACAA
*
43083030 TAACTAAATCC-AAAACCATAAAAACT-AATGTAGATTT
1 TAACTAAACCCGAAAACCATAAAAACTAAATGTAGATTT
* *
43083067 TAACTAAACCCGAAAACTATAAAATCTAAATGTAGA
1 TAACTAAACCCGAAAACCATAAAAACTAAATGTAGA
43083103 ATCTGAACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 10 0.32
38 13 0.42
39 8 0.26
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.25
Consensus pattern (39 bp):
TAACTAAACCCGAAAACCATAAAAACTAAATGTAGATTT
Found at i:43088319 original size:302 final size:302
Alignment explanation
Indices: 43087769--43088378 Score: 992
Period size: 302 Copynumber: 2.0 Consensus size: 302
43087759 TAGGTAGGTT
** * * *
43087769 CTTA-TGCATGCCAATATGTACTCTACTTTAAAATTAACACATGTTTTCTGTGTATGGGTTTGCC
1 CTTATTGCATGCCAATACCTACTCTACTCTAAAATTAACACATGTTTTCTATATATGGGTTTGCC
*
43087833 TGCATGGTAGTGCGAACCCACATCGTGCGAGCTCATTAAAGAACGCTAACACCTCATGTATGAAC
66 TGCATGGTAGTGCGAACCCACATCGTGCGAGCTCATTAAAGAACACTAACACCTCATGTATGAAC
* * * *
43087898 TCAGGGTGCGAACAATGTAGGCTACAGGTCGGAATCCGATTAGGTAACTAGGTAGTGCGATGGTA
131 TCAGGGTGCGAACAATGTAGGCTACAGGTCGAAATCCAATCAGGTAACTAGGTAGCGCGATGGTA
*
43087963 ATGATGAATACCATAACAATTTGTCCCCCACCTAGTTCGAATAAGAGTTATAAAGTGACTCTTCT
196 ATGATGAATACCATAACAATTTGTCCCCCACCTAGTTCGAAGAAGAGTTATAAAGTGACTCTTCT
*
43088028 AAGAACTTGGCTTCGCGAGGTGAGAGATTATTGAGAGAGAAA
261 AAGAACTTGGCTTCGCGAGGTGAGAGATTACTGAGAGAGAAA
*
43088070 CTTATTGCATGCCAATACCTA-TCCTACTCTAAAATTAACACGTGTTTTCTATATATGGGTTTGC
1 CTTATTGCATGCCAATACCTACT-CTACTCTAAAATTAACACATGTTTTCTATATATGGGTTTGC
*
43088134 CTGCATGGTAGTGCGAATCCACATCGTGCGAGCTCATTAAA-AGACACTAACACCTCATGTATGA
65 CTGCATGGTAGTGCGAACCCACATCGTGCGAGCTCATTAAAGA-ACACTAACACCTCATGTATGA
* *
43088198 ACTCAGGGTGCGAACAATGTAGGCTACGGGTCGAAATCCAATCAGGTAACTAGGTAGCGGGATGG
129 ACTCAGGGTGCGAACAATGTAGGCTACAGGTCGAAATCCAATCAGGTAACTAGGTAGCGCGATGG
* *
43088263 TACTGATGAATACCATAATAATTTGTCCCCCACCTAGTTCGAAGAAGAGTTATAAAGTGACTCTT
194 TAATGATGAATACCATAACAATTTGTCCCCCACCTAGTTCGAAGAAGAGTTATAAAGTGACTCTT
* * *
43088328 TTGAGAACTTGGCTTCGCGAGGTGCGAGATTACTGAGAGAGAAA
259 CTAAGAACTTGGCTTCGCGAGGTGAGAGATTACTGAGAGAGAAA
43088372 CTTATTG
1 CTTATTG
43088379 TATACACTTT
Statistics
Matches: 285, Mismatches: 21, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
301 6 0.02
302 279 0.98
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (302 bp):
CTTATTGCATGCCAATACCTACTCTACTCTAAAATTAACACATGTTTTCTATATATGGGTTTGCC
TGCATGGTAGTGCGAACCCACATCGTGCGAGCTCATTAAAGAACACTAACACCTCATGTATGAAC
TCAGGGTGCGAACAATGTAGGCTACAGGTCGAAATCCAATCAGGTAACTAGGTAGCGCGATGGTA
ATGATGAATACCATAACAATTTGTCCCCCACCTAGTTCGAAGAAGAGTTATAAAGTGACTCTTCT
AAGAACTTGGCTTCGCGAGGTGAGAGATTACTGAGAGAGAAA
Found at i:43090505 original size:29 final size:30
Alignment explanation
Indices: 43090446--43090503 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
43090436 TCCGAGCCTT
*
43090446 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
43090476 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
43090504 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:43090733 original size:13 final size:13
Alignment explanation
Indices: 43090715--43090746 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
43090705 TTTCCAGCAA
43090715 TTATGAATTTATT
1 TTATGAATTTATT
43090728 TTATGAATTTATT
1 TTATGAATTTATT
*
43090741 TGATGA
1 TTATGA
43090747 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:43090878 original size:26 final size:26
Alignment explanation
Indices: 43090849--43090926 Score: 63
Period size: 26 Copynumber: 3.0 Consensus size: 26
43090839 AAAGAGATCC
43090849 CATGTAAGACCATGTCTGGGACATGG
1 CATGTAAGACCATGTCTGGGACATGG
* ** * **
43090875 CATG--GGCACCATCAC-GAGAACATCC
1 CATGTAAG-ACCATGTCTG-GGACATGG
43090900 CATGTAAGACCATGTCTGGGACATGG
1 CATGTAAGACCATGTCTGGGACATGG
43090926 C
1 C
43090927 TTTGGCATGT
Statistics
Matches: 35, Mismatches: 12, Indels: 10
0.61 0.21 0.18
Matches are distributed among these distances:
24 2 0.06
25 15 0.43
26 16 0.46
27 2 0.06
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.19
Consensus pattern (26 bp):
CATGTAAGACCATGTCTGGGACATGG
Found at i:43097198 original size:15 final size:15
Alignment explanation
Indices: 43097178--43097225 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
43097168 TCAAATATGG
43097178 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
43097193 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
43097207 GTTTATGGATATAAA
1 GTTTATGGATATGAA
43097222 GTTT
1 GTTT
43097226 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:43097241 original size:29 final size:29
Alignment explanation
Indices: 43097174--43097231 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
43097164 GGATTCAAAT
*
43097174 ATGGGTTTATGGATATGAAGTTTATGTAG
1 ATGGGTTTATGGATATAAAGTTTATGTAG
*
43097203 ATGGGTTTATGGATATAAAGTTTTTGTAG
1 ATGGGTTTATGGATATAAAGTTTATGTAG
43097232 GTTTGGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.29, T:0.43
Consensus pattern (29 bp):
ATGGGTTTATGGATATAAAGTTTATGTAG
Found at i:43098852 original size:131 final size:131
Alignment explanation
Indices: 43098612--43099431 Score: 988
Period size: 131 Copynumber: 6.3 Consensus size: 131
43098602 GATCGTATCA
* * * * * * *
43098612 ATAAGAAATCAAATGAACTTAGGCTCTGATCGTTAATCAACAAGCCTTAATAATATTAGGTGTGG
1 ATAAGAAATCAAATGAACTTAGGTTGTGATCATTAATCAACGAGCCTTAATAATATCAGCTGTGA
* * * *
43098677 TATTAAATTAGAGAGCTGTTTGGAGTAGCGATAGAAAATTAACTAACTCAAAGAAAATTGTTCAT
66 TCTTAAATCAGCGAGCTGTTTGGAGTAGCGATAGAAAATCAACTAACTCAAAGAAAATTGTTCAT
43098742 G
131 G
* * * * *
43098743 ATAGGAAATCAAATGAACTTAGGTTGTGATCATTAATCAACGAGCATTCATAATATTAGTTGTGA
1 ATAAGAAATCAAATGAACTTAGGTTGTGATCATTAATCAACGAGCCTTAATAATATCAGCTGTGA
* * * **
43098808 TCTTAAATCAGCGAGCTGTTTGGAGTAGTGATAGAAAATCAACTAACTCAGAGAAAATTATTCGC
66 TCTTAAATCAGCGAGCTGTTTGGAGTAGCGATAGAAAATCAACTAACTCAAAGAAAATTGTTCAT
43098873 G
131 G
* * * * * * *
43098874 ATAAGAAATCAAATGAACATAGGCTGTGATTATTAATCGATGAGGCTTAATAATATCAACTGTGA
1 ATAAGAAATCAAATGAACTTAGGTTGTGATCATTAATCAACGAGCCTTAATAATATCAGCTGTGA
* * * * *
43098939 TCTTAAATC-GACAAGTTGTTTAGAGTAGCGATAGAAAATTAGCTAACTCAAAGAAAATTGTTCA
66 TCTTAAATCAG-CGAGCTGTTTGGAGTAGCGATAGAAAATCAACTAACTCAAAGAAAATTGTTCA
43099003 TG
130 TG
* ** * * *
43099005 AT-AGAAAATCAAATGAACTTAGGCTCAGATCGTTAATTAGCGAGCCTTAATAATATCATG-TGT
1 ATAAG-AAATCAAATGAACTTAGGTTGTGATCATTAATCAACGAGCCTTAATAATATCA-GCTGT
* * * * *
43099068 GATCTTAAATGAGCGAGTTGTTTAGAGTAGCGATACAAAATCAGCTAACTCAAAGAAAATTGTTC
64 GATCTTAAATCAGCGAGCTGTTTGGAGTAGCGATAGAAAATCAACTAACTCAAAGAAAATTGTTC
43099133 ATG
129 ATG
** *
43099136 ATAAGAAATCAAATGAACTTAGGTTGTGATCGCTAATCAACAAGCCTTAATAATATCAGCTGTGA
1 ATAAGAAATCAAATGAACTTAGGTTGTGATCATTAATCAACGAGCCTTAATAATATCAGCTGTGA
* * * *
43099201 TCTTAAATCAGCGAGCTGTTTGGAATAGCGATAGAAAATCAAGTAACTCAAAGAAAATTATTCAC
66 TCTTAAATCAGCGAGCTGTTTGGAGTAGCGATAGAAAATCAACTAACTCAAAGAAAATTGTTCAT
43099266 G
131 G
* * ** * *
43099267 ATAATAAATCAAATGAACATAGGCTT-TGATTTTTAATCAATGAGCCTTAATAATATCAACTGTG
1 ATAAGAAATCAAATGAACTTAGG-TTGTGATCATTAATCAACGAGCCTTAATAATATCAGCTGTG
* * *
43099331 ATAC-TAAATCAACGAGTTGTTTGGAGTAGCGATAGAAAATCAACTAACTCAAA-AAATTTGTTC
65 AT-CTTAAATCAGCGAGCTGTTTGGAGTAGCGATAGAAAATCAACTAACTCAAAGAAAATTGTTC
43099394 ATG
129 ATG
*
43099397 AT-AGTAAATCAAATAAACTTAGGTTGTGATCATTA
1 ATAAG-AAATCAAATGAACTTAGGTTGTGATCATTA
43099432 GGGGTGAGTG
Statistics
Matches: 588, Mismatches: 91, Indels: 21
0.84 0.13 0.03
Matches are distributed among these distances:
129 3 0.01
130 39 0.07
131 540 0.92
132 6 0.01
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.30
Consensus pattern (131 bp):
ATAAGAAATCAAATGAACTTAGGTTGTGATCATTAATCAACGAGCCTTAATAATATCAGCTGTGA
TCTTAAATCAGCGAGCTGTTTGGAGTAGCGATAGAAAATCAACTAACTCAAAGAAAATTGTTCAT
G
Found at i:43099351 original size:393 final size:392
Alignment explanation
Indices: 43098617--43099419 Score: 1212
Period size: 393 Copynumber: 2.0 Consensus size: 392
43098607 TATCAATAAG
* * *
43098617 AAATCAAATGAACTTAGGCTCTGATCGTTAATCAACAAGCCTTAATAATATTAGGTGTGGTATTA
1 AAATCAAATGAACTTAGGCTCAGATCGTTAATCAACAAGCCTTAATAATATCAGGTGTGATATTA
* * * * *
43098682 AATTAGAGAGCTGTTTGGAGTAGCGATAGAAAATTAACTAACTCAAAGAAAATTGTTCATGATAG
66 AATGAGAGAGCTGTTTAGAGTAGCGATACAAAATCAACTAACTCAAAGAAAATTGTTCATGATAA
* * * * *
43098747 GAAATCAAATGAACTTAGGTTGTGATCATTAATCAACGAGCATTCATAATATTAGTTGTGATCTT
131 GAAATCAAATGAACTTAGGTTGTGATCACTAATCAACAAGCATTAATAATATCAGCTGTGATCTT
* * * *
43098812 AAATCAGCGAGCTGTTTGGAGTAGTGATAGAAAATCAACTAACTCAGAGAAAATTATTCGCGATA
196 AAATCAGCGAGCTGTTTGGAATAGCGATAGAAAATCAACTAACTCAAAGAAAATTATTCACGATA
* *
43098877 AGAAATCAAATGAACATAGGCTGTGATTATTAATCGATGAGGCTTAATAATATCAACTGTGATCT
261 AGAAATCAAATGAACATAGGCTGTGATTATTAATCAATGAGCCTTAATAATATCAACTGTGATCT
* * *
43098942 TAAATCGACAAGTTGTTTAGAGTAGCGATAGAAAATTAGCTAACTCAAAGAAAATTGTTCATGAT
326 TAAATCAACAAGTTGTTTAGAGTAGCGATAGAAAATCAACTAACTCAAA-AAAATTGTTCATGAT
43099007 AGA
390 AGA
* * * * *
43099010 AAATCAAATGAACTTAGGCTCAGATCGTTAATTAGCGAGCCTTAATAATATCATGTGTGATCTTA
1 AAATCAAATGAACTTAGGCTCAGATCGTTAATCAACAAGCCTTAATAATATCAGGTGTGATATTA
* * *
43099075 AATGAGCGAGTTGTTTAGAGTAGCGATACAAAATCAGCTAACTCAAAGAAAATTGTTCATGATAA
66 AATGAGAGAGCTGTTTAGAGTAGCGATACAAAATCAACTAACTCAAAGAAAATTGTTCATGATAA
* *
43099140 GAAATCAAATGAACTTAGGTTGTGATCGCTAATCAACAAGCCTTAATAATATCAGCTGTGATCTT
131 GAAATCAAATGAACTTAGGTTGTGATCACTAATCAACAAGCATTAATAATATCAGCTGTGATCTT
*
43099205 AAATCAGCGAGCTGTTTGGAATAGCGATAGAAAATCAAGTAACTCAAAGAAAATTATTCACGATA
196 AAATCAGCGAGCTGTTTGGAATAGCGATAGAAAATCAACTAACTCAAAGAAAATTATTCACGATA
* * *
43099270 ATAAATCAAATGAACATAGGCTTTGATTTTTAATCAATGAGCCTTAATAATATCAACTGTGATAC
261 AGAAATCAAATGAACATAGGCTGTGATTATTAATCAATGAGCCTTAATAATATCAACTGTGAT-C
* * *
43099335 -TAAATCAACGAGTTGTTTGGAGTAGCGATAGAAAATCAACTAACTCAAAAAATTTGTTCATGAT
325 TTAAATCAACAAGTTGTTTAGAGTAGCGATAGAAAATCAACTAACTCAAAAAAATTGTTCATGAT
*
43099399 AGT
390 AGA
*
43099402 AAATCAAATAAACTTAGG
1 AAATCAAATGAACTTAGG
43099420 TTGTGATCAT
Statistics
Matches: 368, Mismatches: 41, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
392 33 0.09
393 334 0.91
394 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (392 bp):
AAATCAAATGAACTTAGGCTCAGATCGTTAATCAACAAGCCTTAATAATATCAGGTGTGATATTA
AATGAGAGAGCTGTTTAGAGTAGCGATACAAAATCAACTAACTCAAAGAAAATTGTTCATGATAA
GAAATCAAATGAACTTAGGTTGTGATCACTAATCAACAAGCATTAATAATATCAGCTGTGATCTT
AAATCAGCGAGCTGTTTGGAATAGCGATAGAAAATCAACTAACTCAAAGAAAATTATTCACGATA
AGAAATCAAATGAACATAGGCTGTGATTATTAATCAATGAGCCTTAATAATATCAACTGTGATCT
TAAATCAACAAGTTGTTTAGAGTAGCGATAGAAAATCAACTAACTCAAAAAAATTGTTCATGATA
GA
Found at i:43099861 original size:19 final size:20
Alignment explanation
Indices: 43099834--43099884 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
43099824 AAATATAAAA
43099834 TTTGAAATTTTT-ATAAA-TAT
1 TTTG-AATTTTTGA-AAATTAT
43099854 TTTGAATTTTTGAAAATTAT
1 TTTGAATTTTTGAAAATTAT
*
43099874 ATTGAATTTTT
1 TTTGAATTTTT
43099885 TTGTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (20 bp):
TTTGAATTTTTGAAAATTAT
Found at i:43105023 original size:47 final size:46
Alignment explanation
Indices: 43104948--43105041 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 46
43104938 CATCCACATA
* *
43104948 AACTGTCCAGTATTTTAGCTTCGTTGTTAGGCTAGTTTGTCCCTATG
1 AACTGTCCAGCATTTTAGCTTCGCTGTTAGGCTAGTTTGT-CCTATG
*
43104995 AACTGTCCAGCATTTTAGCTTTGCTGTTAGGCTAGTTTGTCCTATG
1 AACTGTCCAGCATTTTAGCTTCGCTGTTAGGCTAGTTTGTCCTATG
43105041 A
1 A
43105042 TCAGCTAACT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 7 0.16
47 37 0.84
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.41
Consensus pattern (46 bp):
AACTGTCCAGCATTTTAGCTTCGCTGTTAGGCTAGTTTGTCCTATG
Found at i:43111133 original size:29 final size:28
Alignment explanation
Indices: 43111059--43111133 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
43111049 ATTTTTCAAA
*
43111059 ATTTTAAAATTTAGT-ATATATTCTTTT
1 ATTTTAAAATTTAGTCTTATATTCTTTT
* *
43111086 ATTTCTAAGAATTTAGTCTTTTATTTTTTT
1 ATTT-TAA-AATTTAGTCTTATATTCTTTT
43111116 ATTTTAAAATTTAAGTCT
1 ATTTTAAAATTT-AGTCT
43111134 AATTATTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.10
28 8 0.20
29 16 0.39
30 13 0.32
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (28 bp):
ATTTTAAAATTTAGTCTTATATTCTTTT
Found at i:43116495 original size:25 final size:24
Alignment explanation
Indices: 43116449--43116497 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
43116439 GGGGGCATAA
43116449 TATCAATTTAATTTATATTTTTTT
1 TATCAATTTAATTTATATTTTTTT
43116473 TATCAATTTAATTT-TATTATTTTT
1 TATCAATTTAATTTATATT-TTTTT
43116497 T
1 T
43116498 GAGTTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (24 bp):
TATCAATTTAATTTATATTTTTTT
Found at i:43120340 original size:157 final size:157
Alignment explanation
Indices: 43120150--43120467 Score: 600
Period size: 157 Copynumber: 2.0 Consensus size: 157
43120140 TCTATCACCT
*
43120150 TAAACTAGTTTACAACCTTTAGGAATCAAAATTTCAGCAATAGACTTTAATTCCAAATATTTTCA
1 TAAACTAGTTTACAACCTTTAGGAATCAAAATTTCAGCAATAGACTTTAATTCCAAACATTTTCA
43120215 CAATTAGGTCCTAAAAATCAATTTCTATTGAAATTACCTAATAAAATCATCTCATAAACAAATTA
66 CAATTAGGTCCTAAAAATCAATTTCTATTGAAATTACCTAATAAAATCATCTCATAAACAAATTA
43120280 AAGCTTTAATTTCATTATATTTAATCA
131 AAGCTTTAATTTCATTATATTTAATCA
43120307 TAAACTAGTTTACAACCTTTAGGAATCAAAATTTCAGCAATAGACTTTAATTCCAAACATTTTCA
1 TAAACTAGTTTACAACCTTTAGGAATCAAAATTTCAGCAATAGACTTTAATTCCAAACATTTTCA
* *
43120372 CAATTGGGTCCTAAAAATCATTTTCTATTGAAATTACCTAATAAAATCATCTCATAAACAAATTA
66 CAATTAGGTCCTAAAAATCAATTTCTATTGAAATTACCTAATAAAATCATCTCATAAACAAATTA
*
43120437 AAGCTTTAATTTCATTCTATTTAATCA
131 AAGCTTTAATTTCATTATATTTAATCA
43120464 TAAA
1 TAAA
43120468 ATTACAGAAC
Statistics
Matches: 157, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 157 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (157 bp):
TAAACTAGTTTACAACCTTTAGGAATCAAAATTTCAGCAATAGACTTTAATTCCAAACATTTTCA
CAATTAGGTCCTAAAAATCAATTTCTATTGAAATTACCTAATAAAATCATCTCATAAACAAATTA
AAGCTTTAATTTCATTATATTTAATCA
Found at i:43120802 original size:30 final size:29
Alignment explanation
Indices: 43120766--43120825 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
43120756 ATCAATTTTT
* *
43120766 CTGCTGATTTCATACCCTTGCCGTCCAGC
1 CTGCTGATTTCACACCCTTGCCATCCAGC
*
43120795 NCTGCTGATTTCACGCCCTTGCCATCCAGC
1 -CTGCTGATTTCACACCCTTGCCATCCAGC
43120825 C
1 C
43120826 CAAATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.13, C:0.40, G:0.17, T:0.28
Consensus pattern (29 bp):
CTGCTGATTTCACACCCTTGCCATCCAGC
Found at i:43126822 original size:984 final size:984
Alignment explanation
Indices: 43124909--43126869 Score: 3494
Period size: 984 Copynumber: 2.0 Consensus size: 984
43124899 CCAACACTGG
* * *
43124909 TCACTAATGGAGTAGAAGGTCTTGGATTAGTGCGTTGAGAACCTCGCTCTCTGCCCGAATATCCA
1 TCACTAATGGAGTAGAAGGTCTTGGATTAGTGCGTTGAGAACCTCGCTCTCTACCCAAATACCCA
43124974 GTGGCTGAGGTAGAACGATCCTGATACTCCTTCAATTTCTTTGAAGCAAAAAAATGAGATTTTTC
66 GTGGCTGAGGTAGAACGATCCTGATACTCCTTCAATTTCTTTGAAGCAAAAAAATGAGATTTTTC
* * * * *
43125039 CATCGGTCTTTTACTAAAAATTCTAGCTTTCCTCTTAGCCTGTTTCTTTTCTTTGCTCAATTCTT
131 CATCGGTCTTTTACTAAAAATTCGAGCTTCCCTCTCAGCCTATTTCTTTTCTTTACTCAATTCTT
43125104 CTGCTTTATAAGCTCTTTCTGCCAATGTAGCAAACTCTCAAATTTCAAGAATTCCGATCAGTAGC
196 CTGCTTTATAAGCTCTTTCTGCCAATGTAGCAAACTCTCAAATTTCAAGAATTCCGATCAGTAGC
43125169 TTAATATCTTCATTCAACCCTTCTTCGAATCGTTTGCACATTTCAGATTCTGACTGTACCCATTC
261 TTAATATCTTCATTCAACCCTTCTTCGAATCGTTTGCACATTTCAGATTCTGACTGTACCCATTC
* *
43125234 TCGAGCATATTTACTCAATTGAACAAATTCTCTTTCATACTCAGATACTGATCTGTTACCCTGTT
326 TCGAGCATATTTACTCAATCGAACAAATTCTCTTTCATACTCAAATACTGATCTGTTACCCTGTT
*
43125299 TCAGCTCAAGAAATTCTTTTCTCTTTTGATTGAGAAACCTCTAACTGATATATTTCTTTCTGAAC
391 TCAGCTCAAGAAATTCTTTTCTCTTCTGATTGAGAAACCTCTAACTGATATATTTCTTTCTGAAC
43125364 TCAGTCTGAAAGAATTCCCATGTAATTTCTTCTTACAGAACAACTGAAGCTTTAGTATTCCACCA
456 TCAGTCTGAAAGAATTCCCATGTAATTTCTTCTTACAGAACAACTGAAGCTTTAGTATTCCACCA
43125429 ATGGTAAGCTGTGTCTTTTAGCAGTGAGACGGCACATTTCAGACATTCTTCTGTTGTACAAGATA
521 ATGGTAAGCTGTGTCTTTTAGCAGTGAGACGGCACATTTCAGACATTCTTCTGTTGTACAAGATA
* * *
43125494 ATTCCTCCAAACCCGACTAGTGTTTTTTAACCAGAATTCAGCCTGTTCGGAATCATCATCAACTG
586 ATTCCTCCAAACCCGACTAGTGTTTTCTAACCAGAATTCAGCCCGTTCAGAATCATCATCAACTG
* *
43125559 CTGCTCGAAATTCTTCGACCCTATATTTTTAAATTTTATCTACTGGAGCTTTCCCTTTTCTGATA
651 CTGCTCGAAATTCTTCGACCCCATATTTTCAAATTTTATCTACTGGAGCTTTCCCTTTTCTGATA
* *
43125624 GATTCAGTATCTGTACCCTGTGAAATCTCGGGAACCAGTGGAGGAGTAGGAGGGGGAGTTTGAAC
716 GATTCAGTATCTATACCCTGTGAAATCTCGGGAACCAGTGGAGGAGTAGGAGGGGGAGCTTGAAC
*
43125689 TTGCTGCACTATAGGGTTAGTTCTTAAGTATTAATTAAACCATTCATTCATCATTTTAAAGAAGG
781 TTGCTGCACTATAGGGTTAGTTCTTAAGTATTAATTAAACCATTCATTCATCATTTGAAAGAAGG
* * *
43125754 CTGTTTTTGCCTCCTCCCCTCGTCCCTCTGTCTCGGGCCTTCTACTGGTAGTTTTTTCTCTTTGT
846 CTGTTTTTGCCTCCTCCCCTCGACCCTCTGTCTCGGGCCTTCTACTGCTAGTTTCTTCTCTTTGT
43125819 ACTGAAGCCGGAGCATGACTCCCAGCTTCCTCAGATTGAGCTCTGTCGGTAGACATTTACTATAA
911 ACTGAAGCCGGAGCATGACTCCCAGCTTCCTCAGATTGAGCTCTGTCGGTAGACATTTACTATAA
43125884 GATACTGAA
976 GATACTGAA
*
43125893 TCACTGATGGAGTAGAAGGTCTTGGATTAGTGCGTTGAGAACCTCGCTCTCTACCCAAATACCCA
1 TCACTAATGGAGTAGAAGGTCTTGGATTAGTGCGTTGAGAACCTCGCTCTCTACCCAAATACCCA
* *
43125958 GTGGCTGAGGTAGAACGATCCTGATACTCCTTCAATTTCTTTGAGGCAGAAAAATGAGATTTTTC
66 GTGGCTGAGGTAGAACGATCCTGATACTCCTTCAATTTCTTTGAAGCAAAAAAATGAGATTTTTC
*
43126023 CATTGGTCTTTTACTAAAAATTCGAGCTTCCCTCTCAGCCTATTTCTTTTCTTTACTCAATTCTT
131 CATCGGTCTTTTACTAAAAATTCGAGCTTCCCTCTCAGCCTATTTCTTTTCTTTACTCAATTCTT
* *
43126088 CTGCTTTATAAGCT-TTCTTTGCCAATGTAGCAAACTCTCGAATTTCAAGAATTCCGATCAGTAG
196 CTGCTTTATAAGCTCTT-TCTGCCAATGTAGCAAACTCTCAAATTTCAAGAATTCCGATCAGTAG
*
43126152 TTTAATATCTTCATTCAACCCTTCTTCGAATCGTTTGCACATTTCAGATTCTGACTGTACCCATT
260 CTTAATATCTTCATTCAACCCTTCTTCGAATCGTTTGCACATTTCAGATTCTGACTGTACCCATT
43126217 CTCGAGCATATTTACTCAATCGAACAAATTCTCTTTCATACTCAAATACTGATCTGTTACCCTGT
325 CTCGAGCATATTTACTCAATCGAACAAATTCTCTTTCATACTCAAATACTGATCTGTTACCCTGT
*
43126282 TTCAGCTCAAGAAATTCTTTTCTCTTCTGATTGAGAAACCTCTGACTGATATATTTCTTTCTGAA
390 TTCAGCTCAAGAAATTCTTTTCTCTTCTGATTGAGAAACCTCTAACTGATATATTTCTTTCTGAA
*
43126347 CTCAGTCTGAAAGAATTCCCATGTAATTTCTTCTTACGGAA-AACTGAAGCTTTAGTATTCCACC
455 CTCAGTCTGAAAGAATTCCCATGTAATTTCTTCTTACAGAACAACTGAAGCTTTAGTATTCCACC
* *
43126411 AATGGTAAGCTGTGTCTTTTAGCAGTGAGACGTCACATTTCAGATATTCTTCTGTTGTACAAGAT
520 AATGGTAAGCTGTGTCTTTTAGCAGTGAGACGGCACATTTCAGACATTCTTCTGTTGTACAAGAT
*
43126476 AATTCCTCCAGAACCCGAGTAGTGTTTTCTAACCAGAATTCAGCCCGTTCAGAATCATCATCAAC
585 AATTCCTCCA-AACCCGACTAGTGTTTTCTAACCAGAATTCAGCCCGTTCAGAATCATCATCAAC
* * * *
43126541 TGCTGCTCGAAATTTTTCGGCCCCATATTTTCGAATTTTATCTACTGGAGCTTTCTCTTTTCTGA
649 TGCTGCTCGAAATTCTTCGACCCCATATTTTCAAATTTTATCTACTGGAGCTTTCCCTTTTCTGA
* *
43126606 TAGATTCAGTATCTATACCCTGTGGAATCTCGGGAACCGGTGGAGGAGTAGGAGGGGGAGCTTGA
714 TAGATTCAGTATCTATACCCTGTGAAATCTCGGGAACCAGTGGAGGAGTAGGAGGGGGAGCTTGA
43126671 ACTTGCTGCACTATAGGGTTAGTTCTTAAGTATTAATTAAACCATTCATTCATCATTTGAAAGAA
779 ACTTGCTGCACTATAGGGTTAGTTCTTAAGTATTAATTAAACCATTCATTCATCATTTGAAAGAA
* * *
43126736 GGCTGTTTTTGCCTCCTCCCTTTGACCCTTTGTCTCGGGCCTTCTACTGCTAGTTTCTTCTCTTT
844 GGCTGTTTTTGCCTCCTCCCCTCGACCCTCTGTCTCGGGCCTTCTACTGCTAGTTTCTTCTCTTT
*
43126801 GTACTGAAGCCGGAGCATGACTCCCAGCTTCCTCAGATTGAGCTTTGTCGGTAGACATTTACTAT
909 GTACTGAAGCCGGAGCATGACTCCCAGCTTCCTCAGATTGAGCTCTGTCGGTAGACATTTACTAT
43126866 AAGA
974 AAGA
43126870 AAAACACATT
Statistics
Matches: 931, Mismatches: 44, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
983 98 0.11
984 833 0.89
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.36
Consensus pattern (984 bp):
TCACTAATGGAGTAGAAGGTCTTGGATTAGTGCGTTGAGAACCTCGCTCTCTACCCAAATACCCA
GTGGCTGAGGTAGAACGATCCTGATACTCCTTCAATTTCTTTGAAGCAAAAAAATGAGATTTTTC
CATCGGTCTTTTACTAAAAATTCGAGCTTCCCTCTCAGCCTATTTCTTTTCTTTACTCAATTCTT
CTGCTTTATAAGCTCTTTCTGCCAATGTAGCAAACTCTCAAATTTCAAGAATTCCGATCAGTAGC
TTAATATCTTCATTCAACCCTTCTTCGAATCGTTTGCACATTTCAGATTCTGACTGTACCCATTC
TCGAGCATATTTACTCAATCGAACAAATTCTCTTTCATACTCAAATACTGATCTGTTACCCTGTT
TCAGCTCAAGAAATTCTTTTCTCTTCTGATTGAGAAACCTCTAACTGATATATTTCTTTCTGAAC
TCAGTCTGAAAGAATTCCCATGTAATTTCTTCTTACAGAACAACTGAAGCTTTAGTATTCCACCA
ATGGTAAGCTGTGTCTTTTAGCAGTGAGACGGCACATTTCAGACATTCTTCTGTTGTACAAGATA
ATTCCTCCAAACCCGACTAGTGTTTTCTAACCAGAATTCAGCCCGTTCAGAATCATCATCAACTG
CTGCTCGAAATTCTTCGACCCCATATTTTCAAATTTTATCTACTGGAGCTTTCCCTTTTCTGATA
GATTCAGTATCTATACCCTGTGAAATCTCGGGAACCAGTGGAGGAGTAGGAGGGGGAGCTTGAAC
TTGCTGCACTATAGGGTTAGTTCTTAAGTATTAATTAAACCATTCATTCATCATTTGAAAGAAGG
CTGTTTTTGCCTCCTCCCCTCGACCCTCTGTCTCGGGCCTTCTACTGCTAGTTTCTTCTCTTTGT
ACTGAAGCCGGAGCATGACTCCCAGCTTCCTCAGATTGAGCTCTGTCGGTAGACATTTACTATAA
GATACTGAA
Found at i:43130172 original size:38 final size:39
Alignment explanation
Indices: 43130094--43130259 Score: 156
Period size: 38 Copynumber: 4.3 Consensus size: 39
43130084 ATTTGATGTG
* * ** * *
43130094 TATCCGGGCTTAAAGGCCCACAGGCTTTATGTTGGAATTA
1 TATCCGGG-TTAAAGTCCCGCAGGCTTCGTGCTGGTATTA
43130134 TATCCGGGTTAAA-TCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAAGTCCCGCAGGCTTCGTGCTGGTATTA
* * * *
43130172 TATCCGGGTTAAA-TCCCCCAGGCCTAGTGTTGGTATTA
1 TATCCGGGTTAAAGTCCCGCAGGCTTCGTGCTGGTATTA
* * * *
43130210 TATCTGAGTTTAAAGTCCCGTAGGCTTCGTGCTGGTGTTA
1 TATCCG-GGTTAAAGTCCCGCAGGCTTCGTGCTGGTATTA
* *
43130250 TGTTCGGGTT
1 TATCCGGGTT
43130260 TTATACCTTG
Statistics
Matches: 102, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
38 58 0.57
39 14 0.14
40 30 0.29
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (39 bp):
TATCCGGGTTAAAGTCCCGCAGGCTTCGTGCTGGTATTA
Found at i:43132107 original size:57 final size:59
Alignment explanation
Indices: 43132010--43132121 Score: 165
Period size: 57 Copynumber: 1.9 Consensus size: 59
43132000 CAAAAGATTA
* *
43132010 GAGGCACTGTGTGTGCAAATTCTTTTAACCCAAGCACTATGTGTGCGAAATCGGTAATT
1 GAGGCACTGTGTGGGCAAATTCTTTCAACCCAAGCACTATGTGTGCGAAATCGGTAATT
* * *
43132069 GAGGCACTGTGTGGGCGAGTTC-TTCAA-CCAAGCACTATGTGTGCGAGATCGGT
1 GAGGCACTGTGTGGGCAAATTCTTTCAACCCAAGCACTATGTGTGCGAAATCGGT
43132122 CAGTGGGCAC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 25 0.52
58 4 0.08
59 19 0.40
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.28
Consensus pattern (59 bp):
GAGGCACTGTGTGGGCAAATTCTTTCAACCCAAGCACTATGTGTGCGAAATCGGTAATT
Found at i:43133378 original size:23 final size:23
Alignment explanation
Indices: 43133348--43133392 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
43133338 TACGGAACTC
43133348 CAAATTAAAATCCATTAATTTTT
1 CAAATTAAAATCCATTAATTTTT
*
43133371 CAAATTAAAATCCGTTAATTTT
1 CAAATTAAAATCCATTAATTTT
43133393 CCCTGAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.42
Consensus pattern (23 bp):
CAAATTAAAATCCATTAATTTTT
Found at i:43134900 original size:19 final size:19
Alignment explanation
Indices: 43134876--43134913 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
43134866 TATTCCGATA
* *
43134876 ACATTGAATTTAGGCCATT
1 ACATTGAATCTAGACCATT
43134895 ACATTGAATCTAGACCATT
1 ACATTGAATCTAGACCATT
43134914 TCGGCAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (19 bp):
ACATTGAATCTAGACCATT
Found at i:43136451 original size:63 final size:63
Alignment explanation
Indices: 43136376--43136505 Score: 224
Period size: 63 Copynumber: 2.1 Consensus size: 63
43136366 TTTACCCGGA
43136376 AGAAGTAGGAGTAGTTATAGAAAAACTCCTAAGTAACCCAGAAGAAGTAGGAGCAATCATAGG
1 AGAAGTAGGAGTAGTTATAGAAAAACTCCTAAGTAACCCAGAAGAAGTAGGAGCAATCATAGG
* * * *
43136439 AGAAGTATGAGTAGTTATAGGAAAACTCCTAAGTAACCTAGAAGAAGTAGGAGCAGTCATAGG
1 AGAAGTAGGAGTAGTTATAGAAAAACTCCTAAGTAACCCAGAAGAAGTAGGAGCAATCATAGG
43136502 AGAA
1 AGAA
43136506 CTCCTAAGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.44, C:0.12, G:0.26, T:0.18
Consensus pattern (63 bp):
AGAAGTAGGAGTAGTTATAGAAAAACTCCTAAGTAACCCAGAAGAAGTAGGAGCAATCATAGG
Found at i:43136501 original size:42 final size:42
Alignment explanation
Indices: 43136439--43136532 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
43136429 CAATCATAGG
* * * *
43136439 AGAAGTATGAGTAGTTATAGGAAAACTCCTAAGTAACCTAGA
1 AGAAGTAGGAGCAGTCATAGGAAAACTCCTAAGTAACCCAGA
* *
43136481 AGAAGTAGGAGCAGTCATAGGAGAACTCCTAAGTAACCCGGA
1 AGAAGTAGGAGCAGTCATAGGAAAACTCCTAAGTAACCCAGA
43136523 AGAAGTAGGA
1 AGAAGTAGGA
43136533 CCAGCAGAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.18
Consensus pattern (42 bp):
AGAAGTAGGAGCAGTCATAGGAAAACTCCTAAGTAACCCAGA
Found at i:43136545 original size:42 final size:42
Alignment explanation
Indices: 43136457--43136545 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
43136447 GAGTAGTTAT
* * * *
43136457 AGGAAAACTCCTAAGTAACCTAGAAGAAGTAGGAGCAGTCAT
1 AGGAGAACTCCTAAGTAACCCAGAAGAAGTAGGACCAGTCAA
*
43136499 AGGAGAACTCCTAAGTAACCCGGAAGAAGTAGGACCAG-CAGA
1 AGGAGAACTCCTAAGTAACCCAGAAGAAGTAGGACCAGTCA-A
43136541 AGGAG
1 AGGAG
43136546 TATGAAGAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
41 2 0.05
42 39 0.95
ACGTcount: A:0.42, C:0.18, G:0.28, T:0.12
Consensus pattern (42 bp):
AGGAGAACTCCTAAGTAACCCAGAAGAAGTAGGACCAGTCAA
Found at i:43144842 original size:62 final size:62
Alignment explanation
Indices: 43144741--43144927 Score: 349
Period size: 62 Copynumber: 3.0 Consensus size: 62
43144731 TAATAAAATA
*
43144741 TGTAATAGATAAATCCACTCATCATAGTTTAAT-TCAAACTATTACATTTAATTGATAATTTT
1 TGTAATAGATTAATCCACTCATCATAGTTTAATCT-AAACTATTACATTTAATTGATAATTTT
43144803 TGTAATAGATTAATCCACTCATCATAGTTTAATCTAAACTATTACATTTAATTGATAATTTT
1 TGTAATAGATTAATCCACTCATCATAGTTTAATCTAAACTATTACATTTAATTGATAATTTT
43144865 TGTAATAGATTAATCCACTCATCATAGTTTAATCTAAACTATTACATTTAATTGATAATTTT
1 TGTAATAGATTAATCCACTCATCATAGTTTAATCTAAACTATTACATTTAATTGATAATTTT
43144927 T
1 T
43144928 TTTGAACAGC
Statistics
Matches: 123, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
62 122 0.99
63 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.43
Consensus pattern (62 bp):
TGTAATAGATTAATCCACTCATCATAGTTTAATCTAAACTATTACATTTAATTGATAATTTT
Found at i:43153300 original size:29 final size:27
Alignment explanation
Indices: 43153253--43153307 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
43153243 AAATATAATA
* *
43153253 AAAATTAATTATATTAAAATTAAAAAT
1 AAAATTAAATATATTAAAAATAAAAAT
43153280 AAAATATAAATATGATTAAAAATAAAAA
1 AAAAT-TAAATAT-ATTAAAAATAAAAA
43153308 ATATATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 6 0.25
29 13 0.54
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAATTAAATATATTAAAAATAAAAAT
Found at i:43153317 original size:25 final size:23
Alignment explanation
Indices: 43153271--43153315 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
43153261 TTATATTAAA
43153271 ATTAAAAATAAAATATAAATATG
1 ATTAAAAATAAAATATAAATATG
* *
43153294 ATTAAAAATAAAAAATATATAT
1 ATTAAAAATAAAATATAAATAT
43153316 ATTTAGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
ATTAAAAATAAAATATAAATATG
Found at i:43156452 original size:47 final size:47
Alignment explanation
Indices: 43156401--43156531 Score: 176
Period size: 46 Copynumber: 2.8 Consensus size: 47
43156391 GAATTATGAG
43156401 GCATCCGAACTCGTTGAGTTGCGTTTCGAGTTCACTTATCGATG-CAA
1 GCATCCGAACTCGTTGAGTTGCGTTTCGAGTTCA-TTATCGATGTCAA
* * *
43156448 GCATCCGAACTCGTTGAGTTGTGTTTCGAGTTCATTATGGATGTGAA
1 GCATCCGAACTCGTTGAGTTGCGTTTCGAGTTCATTATCGATGTCAA
* * * *
43156495 -CACCCGAGCTCGTTGAGTTGCGTTCCGATTTCATTAT
1 GCATCCGAACTCGTTGAGTTGCGTTTCGAGTTCATTAT
43156532 GGGTGAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
46 40 0.53
47 35 0.47
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.34
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGCGTTTCGAGTTCATTATCGATGTCAA
Found at i:43159150 original size:6 final size:6
Alignment explanation
Indices: 43159139--43159165 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43159129 TAGAGAGGGT
43159139 TTGGCC TTGGCC TTGGCC TTGGCC TTG
1 TTGGCC TTGGCC TTGGCC TTGGCC TTG
43159166 ATGTAGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.30, G:0.33, T:0.37
Consensus pattern (6 bp):
TTGGCC
Found at i:43171684 original size:15 final size:15
Alignment explanation
Indices: 43171639--43171685 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
43171629 GTAAAAACAC
43171639 ATTTGAATTATATAT
1 ATTTGAATTATATAT
* **
43171654 ATTTTTAATT-GGTAT
1 A-TTTGAATTATATAT
43171669 ATTTGAATTATATAT
1 ATTTGAATTATATAT
43171684 AT
1 AT
43171686 ATATATAACT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 7 0.29
15 10 0.42
16 7 0.29
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (15 bp):
ATTTGAATTATATAT
Found at i:43183096 original size:7 final size:7
Alignment explanation
Indices: 43183084--43183109 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43183074 ATGATGTAAA
43183084 AAATTAT
1 AAATTAT
43183091 AAATTAT
1 AAATTAT
43183098 AAATTAT
1 AAATTAT
43183105 AAATT
1 AAATT
43183110 TTTAAAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTAT
Found at i:43186731 original size:20 final size:20
Alignment explanation
Indices: 43186706--43186746 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
43186696 AAGCAAAACT
43186706 TCAACACGAAGACAATTGCC
1 TCAACACGAAGACAATTGCC
43186726 TCAACACGAAGACAATTGCC
1 TCAACACGAAGACAATTGCC
43186746 T
1 T
43186747 ATCAACATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.29, G:0.15, T:0.17
Consensus pattern (20 bp):
TCAACACGAAGACAATTGCC
Found at i:43187637 original size:97 final size:97
Alignment explanation
Indices: 43187465--43187642 Score: 250
Period size: 97 Copynumber: 1.8 Consensus size: 97
43187455 GAATATAAAC
* *
43187465 TTTTAGTTTTTGCCACTTGTGCATTTATCCAACTACTTTGAAAATTTAATGCTTCATTACTCATG
1 TTTTAGTTTTTGCCACTTATGCATTTATCCAACTACTTTGAAAATTTAATACTTCATTACTCATG
* *
43187530 CTTAATCATCTTCCACGGGGCAAAATCAGAAA
66 CCTAACCATCTTCCACGGGGCAAAATCAGAAA
*** * *
43187562 TTTTAGTTTTT-CTCACTTATGCATTTATCTGTCTACTTTGGAAATTTAATACTTTATTACTCAT
1 TTTTAGTTTTTGC-CACTTATGCATTTATCCAACTACTTTGAAAATTTAATACTTCATTACTCAT
*
43187626 TCCTAACCATCTTCCAC
65 GCCTAACCATCTTCCAC
43187643 AATAGAGGCG
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
96 1 0.01
97 69 0.99
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (97 bp):
TTTTAGTTTTTGCCACTTATGCATTTATCCAACTACTTTGAAAATTTAATACTTCATTACTCATG
CCTAACCATCTTCCACGGGGCAAAATCAGAAA
Found at i:43189767 original size:45 final size:44
Alignment explanation
Indices: 43189669--43189788 Score: 140
Period size: 45 Copynumber: 2.8 Consensus size: 44
43189659 AGACTTTTAT
* *
43189669 TCAT-TCACCGGCATT-TCGCCTGCTAGGCTC-GAGGCTCGATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCTCGATA
* *
43189710 TCATGTCACCGGCATTATAGCCTGCTAAGCTCAAAGGCTCGAATA
1 TCATCTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCTCG-ATA
* *
43189755 GT-ATCTCACCGGCATAATAACCTGCTAGGCTCAA
1 -TCATCTCACCGGCATTATAGCCTGCTAGGCTCAA
43189789 GGCCTGAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
41 4 0.06
42 11 0.16
43 13 0.19
44 7 0.10
45 31 0.46
46 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (44 bp):
TCATCTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCTCGATA
Found at i:43189838 original size:38 final size:38
Alignment explanation
Indices: 43189796--43190055 Score: 308
Period size: 38 Copynumber: 7.1 Consensus size: 38
43189786 CAAGGCCTGA
* * *
43189796 ATATAATACCAGTACTAGGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
43189834 ATATAATACCAGCACGAAGCCTGCAGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* *
43189872 ATATATTATCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
43189910 ATATATTACCAGCACGAAG-C--C-----TT---CCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* *
43189937 ATATAATACCAGCACGAAGCCTACGGGATTTAACTCGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
43189975 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCTGG
1 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
* * *
43190013 ATATATTATCAGCACGAAGCCTGCGGGTCTTTAAGCCCGG
1 ATATAATACCAGCACGAAGCCTGCGGG-ATTTAA-CCCGG
43190053 ATA
1 ATA
43190056 CCCATCAAAT
Statistics
Matches: 192, Mismatches: 17, Indels: 24
0.82 0.07 0.10
Matches are distributed among these distances:
27 22 0.11
28 1 0.01
30 3 0.02
35 3 0.02
37 1 0.01
38 150 0.78
39 5 0.03
40 7 0.04
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:43189946 original size:27 final size:27
Alignment explanation
Indices: 43189906--43189958 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
43189896 GGGATTTAAC
*
43189906 CCGGATATATTACCAGCACGAAGCCTT
1 CCGGATATAATACCAGCACGAAGCCTT
43189933 CCGGATATAATACCAGCACGAAGCCT
1 CCGGATATAATACCAGCACGAAGCCT
43189959 ACGGGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (27 bp):
CCGGATATAATACCAGCACGAAGCCTT
Found at i:43189965 original size:27 final size:27
Alignment explanation
Indices: 43189906--43189965 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
43189896 GGGATTTAAC
* *
43189906 CCGGATATATTACCAGCACGAAGCCTT
1 CCGGATATAATACCAGCACGAAGCCTA
43189933 CCGGATATAATACCAGCACGAAGCCTA
1 CCGGATATAATACCAGCACGAAGCCTA
*
43189960 CGGGAT
1 CCGGAT
43189966 TTAACTCGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (27 bp):
CCGGATATAATACCAGCACGAAGCCTA
Found at i:43189976 original size:65 final size:65
Alignment explanation
Indices: 43189868--43189996 Score: 213
Period size: 65 Copynumber: 2.0 Consensus size: 65
43189858 AGGATTTAAC
* * * *
43189868 CCGGATATATTATCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCACGAAGCCTT
1 CCGGATATAATACCAGCACGAAGCCTACGGGATTTAACCCGGATATAATACCAGCACGAAGCCTT
*
43189933 CCGGATATAATACCAGCACGAAGCCTACGGGATTTAACTCGGATATAATACCAGCACGAAGCCT
1 CCGGATATAATACCAGCACGAAGCCTACGGGATTTAACCCGGATATAATACCAGCACGAAGCCT
43189997 GCGGGATTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (65 bp):
CCGGATATAATACCAGCACGAAGCCTACGGGATTTAACCCGGATATAATACCAGCACGAAGCCTT
Found at i:43190009 original size:103 final size:103
Alignment explanation
Indices: 43189830--43190034 Score: 347
Period size: 103 Copynumber: 2.0 Consensus size: 103
43189820 GGGATTTAAC
* * *
43189830 CCGGATATAATACCAGCACGAAGCCTGCAGGATTTAACCCGGATATATTATCAGCACGAAGCCTG
1 CCGGATATAATACCAGCACGAAGCCTACAGGATTTAACCCGGATATAATACCAGCACGAAGCCTG
43189895 CGGGATTTAACCCGGATATATTACCAGCACGAAGCCTT
66 CGGGATTTAACCCGGATATATTACCAGCACGAAGCCTT
* *
43189933 CCGGATATAATACCAGCACGAAGCCTACGGGATTTAACTCGGATATAATACCAGCACGAAGCCTG
1 CCGGATATAATACCAGCACGAAGCCTACAGGATTTAACCCGGATATAATACCAGCACGAAGCCTG
* *
43189998 CGGGATTTAACCTGGATATATTATCAGCACGAAGCCT
66 CGGGATTTAACCCGGATATATTACCAGCACGAAGCCT
43190035 GCGGGTCTTT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (103 bp):
CCGGATATAATACCAGCACGAAGCCTACAGGATTTAACCCGGATATAATACCAGCACGAAGCCTG
CGGGATTTAACCCGGATATATTACCAGCACGAAGCCTT
Found at i:43199154 original size:20 final size:23
Alignment explanation
Indices: 43199104--43199159 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 23
43199094 AAAGTGAATG
43199104 GAATTATATTGAATTGAAAATATA
1 GAATTA-ATTGAATTGAAAATATA
*
43199128 TAATTAATT-AATT-AAAATAT-
1 GAATTAATTGAATTGAAAATATA
43199148 GAATTAATTGAA
1 GAATTAATTGAA
43199160 AACTGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 8 0.28
21 9 0.31
22 4 0.14
23 3 0.10
24 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (23 bp):
GAATTAATTGAATTGAAAATATA
Found at i:43199197 original size:23 final size:23
Alignment explanation
Indices: 43199171--43199215 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
43199161 ACTGAAAAGT
43199171 AAATTAAATACCCTATTAACTAA
1 AAATTAAATACCCTATTAACTAA
43199194 AAATTAAATACCCTATTAACTA
1 AAATTAAATACCCTATTAACTA
43199216 GTCAGGCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (23 bp):
AAATTAAATACCCTATTAACTAA
Found at i:43199609 original size:18 final size:18
Alignment explanation
Indices: 43199536--43199609 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 18
43199526 AACTGGAAAG
43199536 ATTGACTGTTACTGAATA
1 ATTGACTGTTACTGAATA
* * *
43199554 ATTTAATTGTTACTGTATA
1 A-TTGACTGTTACTGAATA
* * * *
43199573 TTTGATTTTTAGTGAATA
1 ATTGACTGTTACTGAATA
*
43199591 ATTGACTGTTACTGGATA
1 ATTGACTGTTACTGAATA
43199609 A
1 A
43199610 CCGATCAATT
Statistics
Matches: 42, Mismatches: 13, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
18 28 0.67
19 14 0.33
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (18 bp):
ATTGACTGTTACTGAATA
Found at i:43199650 original size:18 final size:18
Alignment explanation
Indices: 43199629--43199681 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
43199619 TGATTGATAC
43199629 TGAATAACTGATTATTAT
1 TGAATAACTGATTATTAT
* *
43199647 TGAATAATTGATTGTTAT
1 TGAATAACTGATTATTAT
* *
43199665 CGAATAACTGACTATTA
1 TGAATAACTGATTATTA
43199682 CTAAATAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.42
Consensus pattern (18 bp):
TGAATAACTGATTATTAT
Found at i:43199689 original size:36 final size:36
Alignment explanation
Indices: 43199616--43199702 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 36
43199606 ATAACCGATC
* * * *
43199616 AATTGATTGATACTGAATAACTGATTATTATTGAAT
1 AATTGATTGTTACTGAATAACTGACTATTACTAAAT
43199652 AATTGATTGTTA-TCGAATAACTGACTATTACTAAAT
1 AATTGATTGTTACT-GAATAACTGACTATTACTAAAT
* *
43199688 AAATAATTGTT-CTGA
1 AATTGATTGTTACTGA
43199703 TTGACTGATC
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
35 3 0.07
36 40 0.93
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (36 bp):
AATTGATTGTTACTGAATAACTGACTATTACTAAAT
Found at i:43200427 original size:35 final size:35
Alignment explanation
Indices: 43200308--43200428 Score: 181
Period size: 35 Copynumber: 3.5 Consensus size: 35
43200298 ACAGGAAATG
*
43200308 CCATACCTACGTTT-ATTAACTCAGTATGGATAATA
1 CCATACCTACGTTTCA-CAACTCAGTATGGATAATA
* *
43200343 CCATACTTACGTTTCACAACTCAGTATGGTTAATA
1 CCATACCTACGTTTCACAACTCAGTATGGATAATA
* *
43200378 CCATACCTACGTTTCGCAACTCAGTATGGATGATA
1 CCATACCTACGTTTCACAACTCAGTATGGATAATA
43200413 CCATACCTACGTTTCA
1 CCATACCTACGTTTCA
43200429 AAATTTTTCT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
35 76 0.99
36 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (35 bp):
CCATACCTACGTTTCACAACTCAGTATGGATAATA
Found at i:43208759 original size:17 final size:17
Alignment explanation
Indices: 43208737--43208770 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43208727 TAAGAAATTT
*
43208737 TTATTTAGTGTCTTTTA
1 TTATTTAGTCTCTTTTA
*
43208754 TTATTTATTCTCTTTTA
1 TTATTTAGTCTCTTTTA
43208771 AGTGATTAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.68
Consensus pattern (17 bp):
TTATTTAGTCTCTTTTA
Found at i:43212466 original size:60 final size:61
Alignment explanation
Indices: 43212393--43212514 Score: 237
Period size: 60 Copynumber: 2.0 Consensus size: 61
43212383 TGAAGAATCA
43212393 TCATCTTTTCTTTCCCATGCAAACCAAGGTGAGAGAGAGGAAGAAG-AAAAAAAGTTTTCT
1 TCATCTTTTCTTTCCCATGCAAACCAAGGTGAGAGAGAGGAAGAAGAAAAAAAAGTTTTCT
43212453 TCATCTTTTCTTTCCCATGCAAACCAAGGTGAGAGAGAGGAAGAAGAAAAAAAAGTTTTCT
1 TCATCTTTTCTTTCCCATGCAAACCAAGGTGAGAGAGAGGAAGAAGAAAAAAAAGTTTTCT
43212514 T
1 T
43212515 TCTTTACAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 46 0.75
61 15 0.25
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (61 bp):
TCATCTTTTCTTTCCCATGCAAACCAAGGTGAGAGAGAGGAAGAAGAAAAAAAAGTTTTCT
Done.