Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 14 of 214
Found at i:3931784 original size:46 final size:46
Alignment explanation
Indices: 3931661--3931785 Score: 139
Period size: 46 Copynumber: 2.7 Consensus size: 46
3931651 AATATTCCTA
* * **
3931661 TATTCTCAAGTCAACAACACATGTAGAAGCTTGGAACCTAAACATG
1 TATTCTCAAGTCCACAACATATGTAGAAGCTCAGAACCTAAACATG
* * *
3931707 TATTCTCGAGTCCGCAACACT-TGCTAG-AGCTCAGAACCTATAC-TGG
1 TATTCTCAAGTCCACAACA-TATG-TAGAAGCTCAGAACCTAAACAT-G
3931753 TATTCTCAAGTCCACAACATATGTAGAAGCTCA
1 TATTCTCAAGTCCACAACATATGTAGAAGCTCA
3931786 AACTTGGGCA
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
45 5 0.08
46 57 0.88
47 3 0.05
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.26
Consensus pattern (46 bp):
TATTCTCAAGTCCACAACATATGTAGAAGCTCAGAACCTAAACATG
Found at i:3939743 original size:29 final size:30
Alignment explanation
Indices: 3939694--3939752 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
3939684 AAAATTTTTA
* * *
3939694 ATTTATTTTTACTATTTTAAATA-TAAAAT
1 ATTTATTTTTACTACTATAAAAATTAAAAT
3939723 ATTTATTTCTTAC-ACTATAAAAATTAAAAT
1 ATTTATTT-TTACTACTATAAAAATTAAAAT
3939753 TAATAATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTTATTTTTACTACTATAAAAATTAAAAT
Found at i:3947305 original size:18 final size:18
Alignment explanation
Indices: 3947282--3947316 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3947272 ATTTCTCATA
3947282 AAAAAACTATAAAAAATT
1 AAAAAACTATAAAAAATT
*
3947300 AAAAAACTTTAAAAAAT
1 AAAAAACTATAAAAAAT
3947317 ATATTAAAAA
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:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAAACTATAAAAAATT
Found at i:3947337 original size:15 final size:16
Alignment explanation
Indices: 3947312--3947341 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3947302 AAAACTTTAA
3947312 AAAATATATTAAAAAT
1 AAAATATATTAAAAAT
3947328 AAAA-ATATTAAAAA
1 AAAATATATTAAAAA
3947342 CTTTCTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATATATTAAAAAT
Found at i:3947380 original size:20 final size:20
Alignment explanation
Indices: 3947357--3947403 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
3947347 TATAAACTTT
3947357 TAAAAAA-TATAAAAGATTCA
1 TAAAAAAGT-TAAAAGATTCA
*
3947377 TAAAAAAGTTATAAGATTCA
1 TAAAAAAGTTAAAAGATTCA
3947397 TAAAAAA
1 TAAAAAA
3947404 AAAAGTATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (20 bp):
TAAAAAAGTTAAAAGATTCA
Found at i:3949497 original size:2 final size:2
Alignment explanation
Indices: 3949490--3949515 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3949480 CCTCCCTCCT
3949490 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
3949516 TTAGTGGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3952220 original size:16 final size:16
Alignment explanation
Indices: 3952199--3952230 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3952189 AATAACAAGT
3952199 ACCATATAACTATATA
1 ACCATATAACTATATA
3952215 ACCATATAACTATATA
1 ACCATATAACTATATA
3952231 TATATCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (16 bp):
ACCATATAACTATATA
Found at i:3954946 original size:25 final size:25
Alignment explanation
Indices: 3954909--3954964 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
3954899 CATATATGAA
* *
3954909 ATAATCTTGTTGTTTAATGTATTGG
1 ATAATCTTATTGTTTAATGTATAGG
*
3954934 ATAATCTTATTGTTTGATGTATAGG
1 ATAATCTTATTGTTTAATGTATAGG
3954959 ATAATC
1 ATAATC
3954965 ATTTCTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.48
Consensus pattern (25 bp):
ATAATCTTATTGTTTAATGTATAGG
Found at i:3958856 original size:17 final size:17
Alignment explanation
Indices: 3958819--3958857 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3958809 AATATTGTTC
*
3958819 TATTGTTGGAATTGAAT
1 TATTGTTGGAATTGAAA
3958836 TATTGTTGGAATT-ATAA
1 TATTGTTGGAATTGA-AA
3958853 TATTG
1 TATTG
3958858 AATTGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (17 bp):
TATTGTTGGAATTGAAA
Found at i:3959022 original size:21 final size:21
Alignment explanation
Indices: 3958996--3959102 Score: 110
Period size: 21 Copynumber: 5.2 Consensus size: 21
3958986 GTGTTTTACT
3958996 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
3959017 TTCTGTTCAACTCTAATGAGT
1 TTCTGTTCAGCTCTTATGAGC
* *
3959038 TTCTGTTTAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
3959059 TTCTATTAAGCT-TT-CGAGC
1 TTCTGTTCAGCTCTTATGAGC
* *
3959078 TTCTATTCAGCTTTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
3959099 TTCT
1 TTCT
3959103 ATTAAGCTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
19 16 0.22
20 4 0.06
21 52 0.72
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:3959078 original size:19 final size:19
Alignment explanation
Indices: 3959054--3959121 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
3959044 TTAGCTCTTA
3959054 CGAGCTTCTATTAAGCTTT
1 CGAGCTTCTATTAAGCTTT
*
3959073 CGAGCTTCTATTCAGCTTTT
1 CGAGCTTCTATTAAGC-TTT
*
3959093 ATGAGCTTCTATTAAGCTTT
1 -CGAGCTTCTATTAAGCTTT
*
3959113 CAAGCTTCT
1 CGAGCTTCT
3959122 GTTGGCATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 22 0.52
20 6 0.14
21 14 0.33
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.43
Consensus pattern (19 bp):
CGAGCTTCTATTAAGCTTT
Found at i:3959102 original size:40 final size:40
Alignment explanation
Indices: 3959046--3959121 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
3959036 GTTTCTGTTT
*
3959046 AGCTCTTACGAGCTTCTATTAAGCTTTCGAGCTTCTATTC
1 AGCTCTTACGAGCTTCTATTAAGCTTTCAAGCTTCTATTC
* *
3959086 AGCTTTTATGAGCTTCTATTAAGCTTTCAAGCTTCT
1 AGCTCTTACGAGCTTCTATTAAGCTTTCAAGCTTCT
3959122 GTTGGCATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.42
Consensus pattern (40 bp):
AGCTCTTACGAGCTTCTATTAAGCTTTCAAGCTTCTATTC
Found at i:3962432 original size:21 final size:20
Alignment explanation
Indices: 3962405--3962453 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
3962395 AATAGAACTT
*
3962405 ATGAATGACAGGAAATTGTC
1 ATGAATGACAGGAAATTGAC
*
3962425 AGTGAATGACAGGGAATTGAC
1 A-TGAATGACAGGAAATTGAC
3962446 ATGAATGA
1 ATGAATGA
3962454 TTTTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.41, C:0.08, G:0.29, T:0.22
Consensus pattern (20 bp):
ATGAATGACAGGAAATTGAC
Found at i:3964745 original size:21 final size:22
Alignment explanation
Indices: 3964686--3964749 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
3964676 CAGAAACAGT
* *
3964686 ATACGACACATAAAGTTCCTGA
1 ATACGACACATATAGTGCCTGA
** *
3964708 A-ACGACACACGTGGTGCCT-A
1 ATACGACACATATAGTGCCTGA
3964728 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
3964750 TCGGCAAAGC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:3967552 original size:17 final size:18
Alignment explanation
Indices: 3967518--3967553 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3967508 TGAACTTTTA
3967518 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
3967536 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
3967553 T
1 T
3967554 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:3968322 original size:14 final size:17
Alignment explanation
Indices: 3968303--3968340 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
3968293 ATTTATTTCT
3968303 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
3968317 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
3968334 TAATATA
1 TAATATA
3968341 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:3971541 original size:90 final size:88
Alignment explanation
Indices: 3971439--3971716 Score: 349
Period size: 90 Copynumber: 3.0 Consensus size: 88
3971429 TTTTTTTAAT
*
3971439 TTTTTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAGATTGTTTGTATTTAGTTTAGTG
1 TTTTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATA-ATTGTTTGTATTTAGTTTAGTG
3971504 TTTTGTGATTTTTTATAAATGTAA
65 TTTTGTGATTTTTTATAAATGTAA
* *
3971528 TTTTTTCAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATTAATCGTTTGTGTTTAGTTTAGT
1 TTTTTT-AAAGTTATTTTGTTAGTAATTTATGATTAGGTTA-TAATTGTTTGTATTTAGTTTAGT
* *
3971593 GTTTTGTGATTTGTTATGAATATATTTTTATA
64 GTTTTGTGATTT-TT-T--ATA-A-ATGTA-A
* * * *
3971625 TTATTTTAAAGTCATTTTGTTAGTAATTTATGGTTAGGTTATAAATTATTTGTATTTAGTTTAAT
1 TT-TTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTAT-AATTGTTTGTATTTAGTTTAGT
3971690 GTTTATTGTGATTTTTTATAAATGTAA
64 G-TT-TTGTGATTTTTTATAAATGTAA
3971717 AATTTTTTGT
Statistics
Matches: 163, Mismatches: 13, Indels: 23
0.82 0.07 0.12
Matches are distributed among these distances:
89 6 0.04
90 64 0.39
91 4 0.02
92 2 0.01
93 3 0.02
94 4 0.02
95 4 0.02
96 4 0.02
97 55 0.34
98 8 0.05
99 9 0.06
ACGTcount: A:0.26, C:0.01, G:0.16, T:0.57
Consensus pattern (88 bp):
TTTTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAATTGTTTGTATTTAGTTTAGTGT
TTTGTGATTTTTTATAAATGTAA
Found at i:3971754 original size:112 final size:111
Alignment explanation
Indices: 3971617--3971844 Score: 350
Period size: 112 Copynumber: 2.0 Consensus size: 111
3971607 TATGAATATA
* *
3971617 TTTTTATATTATTTTAAAGTCATTTTGTTAGTAATTTATGGTTAGGTTATAAATTATTTGTATTT
1 TTTTTATATTATTTTAAAGTCATTTTGTTAATAATTTATGATTAGGTTATAAATTATTTGTATTT
* * *
3971682 AGTTTAATGTTTATTGTGATTTTTTATAAATGTAAAATTTTTTGT-T
66 AGTTTAATGTTTATTGTGAATTGTCATAAATGT-AAATTTTTTGTAT
* * *
3971728 TTTTTATAATTATTTTAAAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTGTTTGTGTT
1 TTTTTAT-ATTATTTTAAAGTCATTTTGTTAATAATTTATGATTAGGTTATAAATTATTTGTATT
*
3971793 TAGTTTAATGTTTATTGTGAATTGTCATAAATGTAATTTTTTTGTAT
65 TAGTTTAATGTTTATTGTGAATTGTCATAAATGTAAATTTTTTGTAT
3971840 TTTTT
1 TTTTT
3971845 TGTTAGTAAT
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
111 17 0.16
112 89 0.84
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.59
Consensus pattern (111 bp):
TTTTTATATTATTTTAAAGTCATTTTGTTAATAATTTATGATTAGGTTATAAATTATTTGTATTT
AGTTTAATGTTTATTGTGAATTGTCATAAATGTAAATTTTTTGTAT
Found at i:3971846 original size:91 final size:87
Alignment explanation
Indices: 3971751--3971930 Score: 261
Period size: 91 Copynumber: 2.0 Consensus size: 87
3971741 TTTAAAGTTA
* **
3971751 TTTTGTTAATAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTTAATGTTTATTGTGAATT
1 TTTTGTTAATAATTTATGATTAGGTTATAAATT-ATT-TGTTTAGTTTAATGTAAATTGTGAATT
*
3971816 GTCATAAATGTAATTTTTTTGTATTT
64 GTCAT-AATGTAATTTTATT-TATTT
* *
3971842 TTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTTTAGTTTAATGTAAATTGTGATTTGT
1 TTTTGTTAATAATTTATGATTAGGTTATAAATTATTTGTTTAGTTTAATGTAAATTGTGAATTGT
*
3971907 TATAATGTAATTTTATTTATTT
66 CATAATGTAATTTTATTTATTT
3971929 TT
1 TT
3971931 GATTTATTTC
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
87 7 0.09
88 13 0.16
89 28 0.34
90 2 0.02
91 32 0.39
ACGTcount: A:0.27, C:0.01, G:0.14, T:0.58
Consensus pattern (87 bp):
TTTTGTTAATAATTTATGATTAGGTTATAAATTATTTGTTTAGTTTAATGTAAATTGTGAATTGT
CATAATGTAATTTTATTTATTT
Found at i:3972490 original size:21 final size:21
Alignment explanation
Indices: 3972464--3972519 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
3972454 CATCATTGTT
*
3972464 TCTAATCTCACTGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
3972485 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
*
3972506 ACTAATCTCACCGC
1 TCTAATCTCACCGC
3972520 CACCGCTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.34, G:0.09, T:0.29
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAGTA
Found at i:3976979 original size:54 final size:54
Alignment explanation
Indices: 3976831--3976981 Score: 143
Period size: 54 Copynumber: 2.9 Consensus size: 54
3976821 AACTAATAAT
* * * *
3976831 TAATTTATAATACTTACTAACAAAATAACTTTAAAATAAATTAAAAATTAATAAA
1 TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATT-AAAATAAACAAA
* * * *
3976886 -AATTTATATTAATAACCTAAC-AAATCAC---AATAA-ACATTAAACTAAACAAA
1 TAATTTATAATAATAA-CTAACAAAATAACTTTAA-AATAAATTAAAATAAACAAA
* *
3976936 TAATTTATAATAGTAACTAACAAAATGACTTTAAAATAAATTAAAA
1 TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAA
3976982 ACAACATAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 17
0.71 0.12 0.16
Matches are distributed among these distances:
50 14 0.19
51 25 0.33
52 2 0.03
53 2 0.03
54 27 0.36
55 5 0.07
ACGTcount: A:0.58, C:0.10, G:0.01, T:0.31
Consensus pattern (54 bp):
TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAATAAACAAA
Found at i:3976984 original size:51 final size:51
Alignment explanation
Indices: 3976831--3976990 Score: 137
Period size: 51 Copynumber: 3.1 Consensus size: 51
3976821 AACTAATAAT
* * *
3976831 TAATTTATAATACTTACTAACAAAATAACTTTAAAATAAATTAAAAATTAATAA
1 TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAAA--CA-AA
* * * ** *
3976885 AAATTTATATTAATAACCTAAC-AAATCACAATAAACATTAAACT--AAACAAA
1 TAATTTATAATAATAA-CTAACAAAATAACTTTAAA-A-TAAATTAAAAACAAA
* *
3976936 TAATTTATAATAGTAACTAACAAAATGACTTTAAAATAAATTAAAAACAACA
1 TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAAACAA-A
3976988 TAA
1 TAA
3976991 AAACAACAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
49 5 0.06
50 6 0.07
51 31 0.37
52 5 0.06
54 25 0.30
55 6 0.07
56 5 0.06
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (51 bp):
TAATTTATAATAATAACTAACAAAATAACTTTAAAATAAATTAAAAACAAA
Found at i:3977121 original size:18 final size:17
Alignment explanation
Indices: 3977079--3977126 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
3977069 AAATACATTA
*
3977079 TCCTTCTTTTTTTCTTC
1 TCCTTCTTTCTTTCTTC
*
3977096 TCATTTCTTTCTTTCTTC
1 TC-CTTCTTTCTTTCTTC
3977114 TTCCTTCTCTTCT
1 -TCCTTCT-TTCT
3977127 CCTATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 2 0.08
18 17 0.68
19 6 0.24
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (17 bp):
TCCTTCTTTCTTTCTTC
Found at i:3977308 original size:24 final size:25
Alignment explanation
Indices: 3977278--3977326 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
3977268 ACCATTAAAT
*
3977278 AAAATAAATTTTA-TAAAAATATAA
1 AAAATAAATTTTATTAAAAAAATAA
3977302 AAAATAAATTTTATTAAAAAAATAA
1 AAAATAAATTTTATTAAAAAAATAA
3977327 TGGTATTGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAATAAATTTTATTAAAAAAATAA
Found at i:3980478 original size:3 final size:3
Alignment explanation
Indices: 3980470--3980502 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3980460 ATTCCGTTCT
3980470 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3980503 CCTCACGCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3986568 original size:17 final size:19
Alignment explanation
Indices: 3986533--3986572 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
3986523 TTAAAACGTG
3986533 AATTAATGTTATGTTTAAA
1 AATTAATGTTATGTTTAAA
3986552 AATT-ATGTTAT-TTTAAA
1 AATTAATGTTATGTTTAAA
3986569 AATT
1 AATT
3986573 TTAAAAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.48
18 7 0.33
19 4 0.19
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (19 bp):
AATTAATGTTATGTTTAAA
Found at i:3993252 original size:21 final size:22
Alignment explanation
Indices: 3993226--3993267 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3993216 CACTATTTCA
*
3993226 TTAAAAA-ATAATTTTAATCCC
1 TTAAAAAGATAATTTCAATCCC
*
3993247 TTAAAAAGTTAATTTCAATCC
1 TTAAAAAGATAATTTCAATCC
3993268 TACATTGGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.38
Consensus pattern (22 bp):
TTAAAAAGATAATTTCAATCCC
Found at i:3993525 original size:68 final size:67
Alignment explanation
Indices: 3993412--3993538 Score: 166
Period size: 68 Copynumber: 1.9 Consensus size: 67
3993402 ATAAATAAGT
* * ** *
3993412 ACATTGACTAAAGAATACTCTTATTGCTCACTTATCACTATTTTCATTTAAAAGTTAATTTTAAT
1 ACATTAACTAAAGAATACTCTCATAACTCACTTATCACTATTTTCA-TTAAAAATTAATTTTAAT
3993477 CTC
65 CTC
* *
3993480 ACATTAACTAGAGAATACTCTCATAACTCACTTCTTCACTA-TTTCATTAAAAATTAATT
1 ACATTAACTAAAGAATACTCTCATAACTCACTT-ATCACTATTTTCATTAAAAATTAATT
3993539 AATTTTGTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 12 0.24
68 33 0.65
69 6 0.12
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (67 bp):
ACATTAACTAAAGAATACTCTCATAACTCACTTATCACTATTTTCATTAAAAATTAATTTTAATC
TC
Found at i:3996081 original size:65 final size:65
Alignment explanation
Indices: 3995944--3996081 Score: 165
Period size: 65 Copynumber: 2.1 Consensus size: 65
3995934 CACTCACATG
* * * * *
3995944 CTCACACTTACTCTATAAATAAGTGTCAGTTTCTTAACTATTTTCTTTAACAACTTAGTTTTAAT
1 CTCACATTTACTCTATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAACTTAATTTTAAT
* *
3996009 C-CTACATTTA-TCTGATAAATAAGTGAT-AATTTCTTCACTATTTTCATTAAAAATTTAATTTT
1 CTC-ACATTTACTCT-ATAAATAAGTG-TCAATTTCTTAACTATTTTCATTAAAAACTTAATTTT
3996071 AAT
63 AAT
3996074 CTCACATT
1 CTCACATT
3996082 GATTAGAGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
64 4 0.06
65 56 0.90
66 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (65 bp):
CTCACATTTACTCTATAAATAAGTGTCAATTTCTTAACTATTTTCATTAAAAACTTAATTTTAAT
Found at i:3996126 original size:69 final size:68
Alignment explanation
Indices: 3996042--3996219 Score: 216
Period size: 69 Copynumber: 2.6 Consensus size: 68
3996032 TGATAATTTC
* * *
3996042 TTCACTATTTTCATTAAAAATTTAATTTTAATCTCACATTGATTAGAGA-ATACTCTCATAGTTA
1 TTCACTATTTTCATTAAAAA-TTAATTTTAATCTCACATTGACTA-AAATATACTCTCATAGCTA
* *
3996106 ACTTT
64 ACGTA
* * * *
3996111 TTTACTATTTTCATTAAAAAGTTAATTTTAATCTCACACTAACTAAAATATACTCTCATAGCTCA
1 TTCACTATTTTCATTAAAAA-TTAATTTTAATCTCACATTGACTAAAATATACTCTCATAGCTAA
3996176 CGTA
65 CGTA
*
3996180 TTCACAATTTTCATTAAAAATTAATTTTAAT-TCCACATTG
1 TTCACTATTTTCATTAAAAATTAATTTTAATCT-CACATTG
3996220 GCTAGACAAC
Statistics
Matches: 93, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
67 1 0.01
68 18 0.19
69 74 0.80
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (68 bp):
TTCACTATTTTCATTAAAAATTAATTTTAATCTCACATTGACTAAAATATACTCTCATAGCTAAC
GTA
Found at i:3999437 original size:69 final size:69
Alignment explanation
Indices: 3999349--3999497 Score: 201
Period size: 69 Copynumber: 2.2 Consensus size: 69
3999339 AAGTGACAAT
* ** * * *
3999349 TTCTTCACTATTTTTATTAAAAAATTAATTTTAATCCTATATTGACTAGAGAATACTCTCATAGA
1 TTCTTCACTATATCCATTAAAAAATCAATTTTAATCCCAAATTGACTAGAGAATACTCTCATA-A
3999414 -TAAC
65 CTAAC
* *
3999418 TTCTTCACTATATCCATTAAAAAGTCAATTTTAATCCCAAATTGACTAGAGAATACTTTCATAAC
1 TTCTTCACTATATCCATTAAAAAATCAATTTTAATCCCAAATTGACTAGAGAATACTCTCATAAC
*
3999483 TCAC
66 TAAC
3999487 TTCTTCACTAT
1 TTCTTCACTAT
3999498 TAAAAATTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
68 1 0.01
69 69 0.99
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (69 bp):
TTCTTCACTATATCCATTAAAAAATCAATTTTAATCCCAAATTGACTAGAGAATACTCTCATAAC
TAAC
Found at i:3999520 original size:21 final size:22
Alignment explanation
Indices: 3999494--3999537 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3999484 CACTTCTTCA
3999494 CTATTAAAAATT-AATTTTAAT
1 CTATTAAAAATTAAATTTTAAT
*
3999515 CTATTAAAACTTAAATTTTAAT
1 CTATTAAAAATTAAATTTTAAT
3999537 C
1 C
3999538 CCACATTAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (22 bp):
CTATTAAAAATTAAATTTTAAT
Found at i:4009514 original size:23 final size:23
Alignment explanation
Indices: 4009487--4009606 Score: 159
Period size: 23 Copynumber: 5.2 Consensus size: 23
4009477 TGTTATTGAT
* **
4009487 CAGTGGTAGCTTCGGCTACGTTT
1 CAGTGGTAGCTTCGGCTACATAA
*
4009510 TAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
* **
4009533 CAGTGGTAGCTTCAGCTACATTT
1 CAGTGGTAGCTTCGGCTACATAA
*
4009556 TAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
*
4009579 CAGTGGTAGCTTCGGCTACATAT
1 CAGTGGTAGCTTCGGCTACATAA
4009602 CAGTG
1 CAGTG
4009607 TTGCACTTAT
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (23 bp):
CAGTGGTAGCTTCGGCTACATAA
Found at i:4009540 original size:46 final size:46
Alignment explanation
Indices: 4009487--4009599 Score: 208
Period size: 46 Copynumber: 2.5 Consensus size: 46
4009477 TGTTATTGAT
*
4009487 CAGTGGTAGCTTCGGCTACGTTTTAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTTAGTGGTAGCTTCGGCTACATAA
*
4009533 CAGTGGTAGCTTCAGCTACATTTTAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTTAGTGGTAGCTTCGGCTACATAA
4009579 CAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACAT
4009600 ATCAGTGTTG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (46 bp):
CAGTGGTAGCTTCGGCTACATTTTAGTGGTAGCTTCGGCTACATAA
Found at i:4012315 original size:46 final size:46
Alignment explanation
Indices: 4012248--4012499 Score: 393
Period size: 46 Copynumber: 5.5 Consensus size: 46
4012238 TAAGTACTTT
* * **
4012248 TGATCAAGAGATAAAGTGATAAGTGGTAGTTTTAGCTACACTTATC
1 TGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATC
*
4012294 TGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTATC
1 TGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATC
* *
4012340 TGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATT
1 TGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATC
*
4012386 TGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTACC
1 TGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATC
4012432 TGATCAAGTGACAAAGTGATAAGTGGTAGCC-TAGCTACACTTATC
1 TGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATC
* *
4012477 TGAT-TAGGGAC-AAGTGATAAGTG
1 TGATCAAGTGACAAAGTGATAAGTG
4012500 ATCATACGTA
Statistics
Matches: 193, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
43 12 0.06
44 5 0.03
45 17 0.09
46 159 0.82
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (46 bp):
TGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATC
Found at i:4024873 original size:9 final size:9
Alignment explanation
Indices: 4024856--4024931 Score: 93
Period size: 9 Copynumber: 8.4 Consensus size: 9
4024846 TTTGGTTAAA
4024856 AATTAACCG
1 AATTAACCG
*
4024865 AATTGACCG
1 AATTAACCG
4024874 AATT-ACCTG
1 AATTAACC-G
4024883 AATTAACCG
1 AATTAACCG
4024892 AATT-ACTCG
1 AATTAAC-CG
*
4024901 AATTACCCG
1 AATTAACCG
4024910 AATTAACCG
1 AATTAACCG
*
4024919 AATTAACCA
1 AATTAACCG
4024928 AATT
1 AATT
4024932 GAATCACTAC
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
8 5 0.08
9 50 0.85
10 4 0.07
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:4024931 original size:27 final size:26
Alignment explanation
Indices: 4024856--4024923 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 26
4024846 TTTGGTTAAA
*
4024856 AATTAACCGAATTGACCGAATTACCTG
1 AATTAACCGAATT-ACCGAATTACCCG
4024883 AATTAACCGAATTACTCGAATTACCCG
1 AATTAACCGAATTAC-CGAATTACCCG
4024910 AATTAACCGAATTA
1 AATTAACCGAATTA
4024924 ACCAAATTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 2 0.05
27 37 0.95
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (26 bp):
AATTAACCGAATTACCGAATTACCCG
Found at i:4025078 original size:18 final size:18
Alignment explanation
Indices: 4025038--4025081 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4025028 TAATTTTATG
**
4025038 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
4025056 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
4025074 CTTGGGTT
1 ATTGGGTT
4025082 TAGATGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:4027716 original size:20 final size:20
Alignment explanation
Indices: 4027694--4027730 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4027684 AATTTTAGGT
4027694 TTTTTAAG-AATATTTTATA
1 TTTTTAAGAAATATTTTATA
*
4027713 TTTTTATGAAATATTTTA
1 TTTTTAAGAAATATTTTA
4027731 ATAATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTTAAGAAATATTTTATA
Found at i:4027740 original size:21 final size:20
Alignment explanation
Indices: 4027702--4027740 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
4027692 GTTTTTTAAG
*
4027702 AATATTTTATATTTTTATGA
1 AATATTTTATAATTTTATGA
4027722 AATATTTTAATAATTTTAT
1 AATATTTT-ATAATTTTAT
4027741 AGTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
AATATTTTATAATTTTATGA
Found at i:4028731 original size:9 final size:9
Alignment explanation
Indices: 4028717--4028865 Score: 61
Period size: 10 Copynumber: 15.4 Consensus size: 9
4028707 ATATCAGGAC
4028717 AAAATTATA
1 AAAATTATA
4028726 AAAATTATTA
1 AAAATTA-TA
*
4028736 AATATTA-A
1 AAAATTATA
* *
4028744 AATATTATT
1 AAAATTATA
*
4028753 ATAATTAATA
1 AAAATT-ATA
*
4028763 TAAGATTATA
1 -AAAATTATA
4028773 AAAATGT-TA
1 AAAAT-TATA
* *
4028782 ATAGTTAT-
1 AAAATTATA
*
4028790 AAAATTTTA
1 AAAATTATA
4028799 TAAAATTAATA
1 -AAAATT-ATA
*
4028810 AAACATATTTA
1 AAA-AT-TATA
4028821 AAATATTATAA
1 AAA-ATTAT-A
*
4028832 AAAACGTATA
1 AAAA-TTATA
*
4028842 AAAATTCTTA
1 AAAATT-ATA
4028852 AAAACTTATA
1 AAAA-TTATA
4028862 AAAA
1 AAAA
4028866 ATAAAAAAAA
Statistics
Matches: 104, Mismatches: 21, Indels: 29
0.68 0.14 0.19
Matches are distributed among these distances:
8 14 0.13
9 22 0.21
10 43 0.41
11 24 0.23
12 1 0.01
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (9 bp):
AAAATTATA
Found at i:4029511 original size:10 final size:9
Alignment explanation
Indices: 4029490--4029746 Score: 54
Period size: 10 Copynumber: 26.8 Consensus size: 9
4029480 TTTATGATTT
4029490 TTTTTATAA
1 TTTTTATAA
4029499 TTTTTATACA
1 TTTTTATA-A
*
4029509 TTTATATCAA
1 TTTTTAT-AA
*
4029519 TTTTAAT-A
1 TTTTTATAA
*
4029527 -TTTTAAATA
1 TTTTTATA-A
*
4029536 TTTTTATGA
1 TTTTTATAA
4029545 TTTATTATAA
1 TTT-TTATAA
4029555 TTGTTT-TAAGA
1 TT-TTTAT-A-A
*
4029566 ATTTTA-AA
1 TTTTTATAA
4029574 CGTTTTTATGAA
1 --TTTTTAT-AA
*
4029586 ATTTTA-AA
1 TTTTTATAA
4029594 TTTTTTATTAA
1 -TTTTTA-TAA
4029605 TTTTTTATAA
1 -TTTTTATAA
4029615 TTTATTA-AA
1 TTT-TTATAA
*
4029624 -GTTTACTAGA
1 TTTTTA-TA-A
4029634 TTTTTAATAA
1 TTTTT-ATAA
*
4029644 TATTTATAA
1 TTTTTATAA
*
4029653 GTATATGT-TAA
1 -T-T-TTTATAA
*
4029664 TTTTAATAGTA
1 TTTTTATA--A
*
4029675 TTTTTAAAAAA
1 TTTTT--ATAA
4029686 TATTTT-TAA
1 T-TTTTATAA
4029695 TTTTTTATAA
1 -TTTTTATAA
*
4029705 TTTTTATAC
1 TTTTTATAA
4029714 TTTTCT-T--
1 TTTT-TATAA
4029721 TTTTTATATA
1 TTTTTATA-A
4029731 TTTTTA-ATA
1 TTTTTATA-A
4029740 TTTTTAT
1 TTTTTAT
4029747 GAGAAAATAT
Statistics
Matches: 185, Mismatches: 23, Indels: 79
0.64 0.08 0.28
Matches are distributed among these distances:
6 1 0.01
7 12 0.06
8 6 0.03
9 61 0.33
10 66 0.36
11 28 0.15
12 9 0.05
13 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:4029717 original size:25 final size:27
Alignment explanation
Indices: 4029684--4029745 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 27
4029674 ATTTTTAAAA
*
4029684 AATATTTTTAATTTTTTATA-ATTTTT
1 AATACTTTTAATTTTTTATATATTTTT
**
4029710 -ATACTTTTCTTTTTTTATATATTTTT
1 AATACTTTTAATTTTTTATATATTTTT
*
4029736 AATATTTTTA
1 AATACTTTTA
4029746 TGAGAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 16 0.55
26 6 0.21
27 7 0.24
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (27 bp):
AATACTTTTAATTTTTTATATATTTTT
Found at i:4029735 original size:27 final size:25
Alignment explanation
Indices: 4029695--4029744 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
4029685 ATATTTTTAA
*
4029695 TTTTTTATAATTTTTATACTTTTCT
1 TTTTTTATAATTTTAATACTTTTCT
*
4029720 TTTTTTATATATTTTTAATATTTTT
1 TTTTTTATA-A-TTTTAATACTTTT
4029745 ATGAGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 1 0.05
27 11 0.52
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTTTATAATTTTAATACTTTTCT
Found at i:4039360 original size:243 final size:243
Alignment explanation
Indices: 4038932--4039423 Score: 885
Period size: 243 Copynumber: 2.0 Consensus size: 243
4038922 ATCTTCTTGT
*
4038932 CATTCCAGTGGATGGAGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
1 CATTCCAGTAGATGGAGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
* *
4038997 CCCAGCTGCAATTTCTTCAGGAAGACTCCGCTGAAATGTTTTGGGGAGATCCTTTCCAACCCACC
66 CCCAGCTGCAATTTCTTCAGGAAGACTCCACTGAAATGTTTCGGGGAGATCCTTTCCAACCCACC
*
4039062 TACAAGGAGAATGAAAGAAAGGATAGTGCTGTTGATTCAGGAGTTAAATCAAGCTTATCTGCAGA
131 TACAAGGAGAATGAAAGAAAGGATAGTGCTGCTGATTCAGGAGTTAAATCAAGCTTATCTGCAGA
4039127 AGAGATGAATTCATCAACAGCGGATATCTTCAGGGTATGGGATTTGGA
196 AGAGATGAATTCATCAACAGCGGATATCTTCAGGGTATGGGATTTGGA
*
4039175 CATTCCAGTAGATGGGGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
1 CATTCCAGTAGATGGAGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
** * * *
4039240 CTGAGCTGCAATTTCTTCAGGAAGATTCCACTGAAGTGTTTCGGGGAGATCCTTTCCGACCCACC
66 CCCAGCTGCAATTTCTTCAGGAAGACTCCACTGAAATGTTTCGGGGAGATCCTTTCCAACCCACC
4039305 TACAAGGAGAATGAAAGAAAGGATAGTGCTGCTGATTCAGGAGTTAAATCAAGCTTATCTGCAGA
131 TACAAGGAGAATGAAAGAAAGGATAGTGCTGCTGATTCAGGAGTTAAATCAAGCTTATCTGCAGA
*
4039370 AGAGATGAATTCATCAACAGTGGATATCTTCAGGGTATGGGATTTGGA
196 AGAGATGAATTCATCAACAGCGGATATCTTCAGGGTATGGGATTTGGA
4039418 CATTCC
1 CATTCC
4039424 GGATGAGGAA
Statistics
Matches: 238, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
243 238 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (243 bp):
CATTCCAGTAGATGGAGACAATGGAATAAACACCAACAACATTCCTATCAAAAAGAGGACTGGTA
CCCAGCTGCAATTTCTTCAGGAAGACTCCACTGAAATGTTTCGGGGAGATCCTTTCCAACCCACC
TACAAGGAGAATGAAAGAAAGGATAGTGCTGCTGATTCAGGAGTTAAATCAAGCTTATCTGCAGA
AGAGATGAATTCATCAACAGCGGATATCTTCAGGGTATGGGATTTGGA
Found at i:4040733 original size:31 final size:31
Alignment explanation
Indices: 4040693--4040759 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
4040683 AAAACTTAAG
* *
4040693 TAGTCCAATGACTTAAATAAAAACTTTCGAC
1 TAGTTCAATGACTTAAATAAAAACTTTCGAA
*
4040724 TAGTTCAATGACTTAAATGAAAACTTTCGAA
1 TAGTTCAATGACTTAAATAAAAACTTTCGAA
4040755 TAGTT
1 TAGTT
4040760 TAGTGATCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (31 bp):
TAGTTCAATGACTTAAATAAAAACTTTCGAA
Found at i:4041226 original size:21 final size:21
Alignment explanation
Indices: 4041188--4041227 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4041178 AAATTTCTAG
*
4041188 ATTTTTAATTTTGAAAATCGA
1 ATTTTTAATTTGGAAAATCGA
* *
4041209 ATTTTTAGTTTGGTAAATC
1 ATTTTTAATTTGGAAAATC
4041228 ATGCGATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (21 bp):
ATTTTTAATTTGGAAAATCGA
Found at i:4044092 original size:27 final size:25
Alignment explanation
Indices: 4044057--4044114 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
4044047 AGTGTCAAAT
* *
4044057 TTAAATATCTAATCTAATTAAAAAAAA
1 TTAAATATCAAAT-T-AGTAAAAAAAA
*
4044084 TTAAGTATCAAATTAGTAAAAAAAA
1 TTAAATATCAAATTAGTAAAAAAAA
*
4044109 TCAAAT
1 TTAAAT
4044115 TCAGGTACTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 14 0.54
26 1 0.04
27 11 0.42
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (25 bp):
TTAAATATCAAATTAGTAAAAAAAA
Found at i:4056393 original size:12 final size:13
Alignment explanation
Indices: 4056376--4056409 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
4056366 TAAATTGAAA
4056376 TAAAATAAAA-AC
1 TAAAATAAAACAC
*
4056388 TAAAATAAAACCC
1 TAAAATAAAACAC
4056401 TAAAATAAA
1 TAAAATAAA
4056410 CTAAGTGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.18
Consensus pattern (13 bp):
TAAAATAAAACAC
Found at i:4061231 original size:12 final size:11
Alignment explanation
Indices: 4061214--4061247 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
4061204 ACCTTGTGTG
4061214 TGTTCTTTCTGT
1 TGTTCTTT-TGT
4061226 TGTTCTTTTGT
1 TGTTCTTTTGT
4061237 TGCTTCTTTTG
1 TG-TTCTTTTG
4061248 GCATAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.00, C:0.15, G:0.18, T:0.68
Consensus pattern (11 bp):
TGTTCTTTTGT
Found at i:4068023 original size:21 final size:20
Alignment explanation
Indices: 4067987--4068025 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4067977 CTTTGACCGA
*
4067987 TCATTGACTAGTGTTGACTG
1 TCATTGACTAGCGTTGACTG
4068007 TCATTGACTACGCGTTGAC
1 TCATTGACTA-GCGTTGAC
4068026 CAACCACGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
TCATTGACTAGCGTTGACTG
Found at i:4072583 original size:13 final size:13
Alignment explanation
Indices: 4072565--4072594 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
4072555 TATTTGGTAG
4072565 TACAAATTGTAAT
1 TACAAATTGTAAT
4072578 TACAAATTGTAAT
1 TACAAATTGTAAT
4072591 TACA
1 TACA
4072595 CAGTTACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (13 bp):
TACAAATTGTAAT
Found at i:4076702 original size:15 final size:16
Alignment explanation
Indices: 4076672--4076704 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4076662 TAGTTACTTA
*
4076672 TTTGGGTCATTTCGAG
1 TTTGGATCATTTCGAG
4076688 TTTGGATCA-TTCGAG
1 TTTGGATCATTTCGAG
4076703 TT
1 TT
4076705 AGTTTTGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.15, C:0.12, G:0.27, T:0.45
Consensus pattern (16 bp):
TTTGGATCATTTCGAG
Found at i:4078364 original size:18 final size:18
Alignment explanation
Indices: 4078338--4078588 Score: 103
Period size: 18 Copynumber: 14.2 Consensus size: 18
4078328 CGATCACATC
*
4078338 AAAATACGAGAATTTTTA
1 AAAACACGAGAATTTTTA
4078356 AAAACACGA-AGATTTTT-
1 AAAACACGAGA-ATTTTTA
* ** ** *
4078373 GAAACATTTA-TTTTTTTG
1 AAAACA-CGAGAATTTTTA
*
4078391 AAAACACGAAAAATTTTT-
1 AAAACACG-AGAATTTTTA
4078409 AAAACACGAGAA-TTTTA
1 AAAACACGAGAATTTTTA
* * * *
4078426 GAGACACGAAAATTCTTA
1 AAAACACGAGAATTTTTA
* * * *
4078444 AAAATATGAAAATTTTTG
1 AAAACACGAGAATTTTTA
4078462 AAAACACG-GAAATTTTT-
1 AAAACACGAG-AATTTTTA
* *
4078479 AAAACACGGGAATTTTTG
1 AAAACACGAGAATTTTTA
* *
4078497 AAAACATGAAAATTTTT-
1 AAAACACGAGAATTTTTA
* *
4078514 GAAACACCG-GAATTTTGA
1 AAAACA-CGAGAATTTTTA
* * *
4078532 AAATACA--AGGATTCTTG
1 AAA-ACACGAGAATTTTTA
*
4078549 AAAACACGA-AGATTTTTT
1 AAAACACGAGA-ATTTTTA
*
4078567 AAAACACGAAAATTTTTGA
1 AAAACACGAGAATTTTT-A
4078586 AAA
1 AAA
4078589 TACGGAAATT
Statistics
Matches: 173, Mismatches: 41, Indels: 37
0.69 0.16 0.15
Matches are distributed among these distances:
16 7 0.04
17 57 0.33
18 97 0.56
19 12 0.07
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.31
Consensus pattern (18 bp):
AAAACACGAGAATTTTTA
Found at i:4078433 original size:35 final size:35
Alignment explanation
Indices: 4078338--4078588 Score: 190
Period size: 35 Copynumber: 7.1 Consensus size: 35
4078328 CGATCACATC
* * *
4078338 AAAATACGAGAATTTTTAAAAACACGAAGATTTTT
1 AAAACACGAGAATTTTTGAAAACACGAAAATTTTT
* ** **
4078373 GAAACATTTA-TTTTTTTGAAAACACGAAAAATTTTT
1 AAAACA-CGAGAATTTTTGAAAACACG-AAAATTTTT
* * *
4078409 AAAACACGAGAATTTTAG-AGACACGAAAATTCTTA
1 AAAACACGAGAATTTTTGAAAACACGAAAATT-TTT
* * * *
4078444 AAAATATGAAAATTTTTGAAAACACGGAAATTTTT
1 AAAACACGAGAATTTTTGAAAACACGAAAATTTTT
* *
4078479 AAAACACGGGAATTTTTGAAAACATGAAAATTTTT
1 AAAACACGAGAATTTTTGAAAACACGAAAATTTTT
* * * *
4078514 GAAACACCG-GAA-TTTTGAAAATAC-AAGGATTCTTG
1 AAAACA-CGAGAATTTTTGAAAACACGAA-AATT-TTT
*
4078549 AAAACACGA-AGATTTTTTAAAACACGAAAATTTTT
1 AAAACACGAGA-ATTTTTGAAAACACGAAAATTTTT
4078584 GAAAA
1 -AAAA
4078589 TACGGAAATT
Statistics
Matches: 164, Mismatches: 39, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
33 2 0.01
34 22 0.13
35 89 0.54
36 49 0.30
37 2 0.01
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.31
Consensus pattern (35 bp):
AAAACACGAGAATTTTTGAAAACACGAAAATTTTT
Found at i:4078581 original size:53 final size:53
Alignment explanation
Indices: 4078388--4078588 Score: 162
Period size: 53 Copynumber: 3.8 Consensus size: 53
4078378 ATTTATTTTT
* * *
4078388 TTGAAAACACGAAAAATTTTTAAAACACGAGAATTTT-AGAGACACGAA-AATTC
1 TTGAAAACACGAAAAATTTTTAAAACACGAAAATTTTGA-AAACAC-AAGGATTC
* * * * * * *
4078441 TTAAAAATATG-AAAATTTTTGAAAACACGGAAATTTTTAAAACAC-GGGAATTT
1 TTGAAAACACGAAAAATTTTT-AAAACACGAAAATTTTGAAAACACAAGG-ATTC
* * * *
4078494 TTGAAAACATG-AAAATTTTTGAAACACCG-GAATTTTGAAAATACAAGGATTC
1 TTGAAAACACGAAAAATTTTTAAAACA-CGAAAATTTTGAAAACACAAGGATTC
* *
4078546 TTGAAAACACGAAGATTTTTTAAAACACGAAAATTTTTGAAAA
1 TTGAAAACACGAAAAATTTTTAAAACACGAAAA-TTTTGAAAA
4078589 TACGGAAATT
Statistics
Matches: 117, Mismatches: 22, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
52 41 0.35
53 66 0.56
54 10 0.09
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.29
Consensus pattern (53 bp):
TTGAAAACACGAAAAATTTTTAAAACACGAAAATTTTGAAAACACAAGGATTC
Found at i:4078597 original size:18 final size:18
Alignment explanation
Indices: 4078385--4078599 Score: 153
Period size: 18 Copynumber: 12.2 Consensus size: 18
4078375 AACATTTATT
*
4078385 TTTTTGAAAACACGAAAAA
1 TTTTTGAAAACACG-GAAA
4078404 TTTTT-AAAACAC-GAGAA
1 TTTTTGAAAACACGGA-AA
* * *
4078421 TTTTAG-AGACACGAAAA
1 TTTTTGAAAACACGGAAA
* * * * *
4078438 TTCTTAAAAATATGAAAA
1 TTTTTGAAAACACGGAAA
4078456 TTTTTGAAAACACGGAAA
1 TTTTTGAAAACACGGAAA
*
4078474 TTTTT-AAAACACGGGAA
1 TTTTTGAAAACACGGAAA
* *
4078491 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGGAAA
4078509 TTTTTG-AAACACCGG-AA
1 TTTTTGAAAACA-CGGAAA
*
4078526 -TTTTGAAAATAC--AAGGA
1 TTTTTGAAAACACGGAA--A
*
4078543 TTCTTGAAAACAC-GAAGA
1 TTTTTGAAAACACGGAA-A
* *
4078561 TTTTTTAAAACACGAAAA
1 TTTTTGAAAACACGGAAA
*
4078579 TTTTTGAAAATACGGAAA
1 TTTTTGAAAACACGGAAA
4078597 TTT
1 TTT
4078600 GAAATACGGA
Statistics
Matches: 153, Mismatches: 30, Indels: 27
0.73 0.14 0.13
Matches are distributed among these distances:
15 1 0.01
16 7 0.05
17 44 0.29
18 92 0.60
19 9 0.06
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACGGAAA
Found at i:4078606 original size:15 final size:16
Alignment explanation
Indices: 4078581--4078613 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
4078571 CACGAAAATT
4078581 TTTGAAAATACGGAAA
1 TTTGAAAATACGGAAA
4078597 TTTG-AAATACGGAAA
1 TTTGAAAATACGGAAA
4078612 TT
1 TT
4078614 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (16 bp):
TTTGAAAATACGGAAA
Found at i:4078617 original size:18 final size:19
Alignment explanation
Indices: 4078453--4078617 Score: 53
Period size: 18 Copynumber: 9.5 Consensus size: 19
4078443 AAAAATATGA
*
4078453 AAATT-TTTGAAAACACGG
1 AAATTATTTGAAAATACGG
*
4078471 AAATT-TTT-AAAACACGG
1 AAATTATTTGAAAATACGG
* * * *
4078488 GAATT-TTTGAAAACATGA
1 AAATTATTTGAAAATACGG
*
4078506 AAATT-TTTGAAACA-CCGG
1 AAATTATTTGAAA-ATACGG
4078524 -AA-T-TTTGAAAATAC--
1 AAATTATTTGAAAATACGG
* *
4078538 AAGGATT-CTTGAAAACAC-G
1 AA--ATTATTTGAAAATACGG
* * *
4078557 AAGATT-TTTTAAAACACGA
1 AA-ATTATTTGAAAATACGG
4078576 AAATT-TTTGAAAATACGG
1 AAATTATTTGAAAATACGG
4078594 -AA--ATTTG-AAATACGG
1 AAATTATTTGAAAATACGG
4078609 AAATTATTT
1 AAATTATTT
4078618 TTAAAAAACA
Statistics
Matches: 118, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
15 10 0.08
16 15 0.13
17 21 0.18
18 67 0.57
19 5 0.04
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.31
Consensus pattern (19 bp):
AAATTATTTGAAAATACGG
Found at i:4079373 original size:18 final size:19
Alignment explanation
Indices: 4079350--4079385 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
4079340 TGGGCCTGGC
4079350 CTGCTGCTATTT-TTTTTG
1 CTGCTGCTATTTCTTTTTG
4079368 CTGCTGCTATTTCTTTTT
1 CTGCTGCTATTTCTTTTT
4079386 TTTTTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.06, C:0.19, G:0.14, T:0.61
Consensus pattern (19 bp):
CTGCTGCTATTTCTTTTTG
Found at i:4079509 original size:8 final size:8
Alignment explanation
Indices: 4079496--4079553 Score: 62
Period size: 8 Copynumber: 7.0 Consensus size: 8
4079486 TTTCTTTTTC
*
4079496 TTTTATTT
1 TTTTCTTT
*
4079504 TTTTATTT
1 TTTTCTTT
4079512 TTTTCTTCT
1 TTTTCTT-T
4079521 TTTTCTTT
1 TTTTCTTT
*
4079529 CTTTCTTT
1 TTTTCTTT
*
4079537 TTCTCTTTT
1 TTTTC-TTT
4079546 TTTTCTTT
1 TTTTCTTT
4079554 CTTCTTCTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
8 28 0.65
9 15 0.35
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTCTTT
Found at i:4079514 original size:10 final size:10
Alignment explanation
Indices: 4079486--4079553 Score: 66
Period size: 10 Copynumber: 6.7 Consensus size: 10
4079476 CTGTGATGTA
4079486 TTTCTTTTTCT
1 TTTCTTTTT-T
*
4079497 TTTATTTTTT
1 TTTCTTTTTT
*
4079507 TAT-TTTTTT
1 TTTCTTTTTT
* *
4079516 CTTCTTTTTC
1 TTTCTTTTTT
*
4079526 TTTCTTTCTT
1 TTTCTTTTTT
4079536 TTTCTCTTTTT
1 TTTCT-TTTTT
4079547 TTTCTTT
1 TTTCTTT
4079554 CTTCTTCTTC
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
9 7 0.15
10 22 0.48
11 17 0.37
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:4079537 original size:25 final size:25
Alignment explanation
Indices: 4079493--4079556 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
4079483 GTATTTCTTT
*
4079493 TTCTTTTAT-TTT-TTTATTTTTTTC
1 TTCTTTT-TCTTTCTTTATTTTTCTC
*
4079517 TTCTTTTTCTTTCTTTCTTTTTCTC
1 TTCTTTTTCTTTCTTTATTTTTCTC
*
4079542 TTTTTTTTCTTTCTT
1 TTCTTTTTCTTTCTT
4079557 CTTCTTCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.03
24 10 0.29
25 24 0.69
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (25 bp):
TTCTTTTTCTTTCTTTATTTTTCTC
Found at i:4079550 original size:21 final size:21
Alignment explanation
Indices: 4079486--4079561 Score: 84
Period size: 21 Copynumber: 3.5 Consensus size: 21
4079476 CTGTGATGTA
4079486 TTTCTTTTTCT-TTTATTTTT-
1 TTTCTTTTTCTCTTT-TTTTTC
*
4079506 TTATTTTTTTCTTCTTTTTCTTTC
1 TT-TCTTTTTC-TCTTTTT-TTTC
4079530 TTTCTTTTTCTCTTTTTTTTC
1 TTTCTTTTTCTCTTTTTTTTC
*
4079551 TTTCTTCTTCT
1 TTTCTTTTTCT
4079562 TCCTTCCCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.04
21 21 0.44
22 10 0.21
23 13 0.27
24 2 0.04
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTCTTTTTCTCTTTTTTTTC
Found at i:4079862 original size:23 final size:23
Alignment explanation
Indices: 4079818--4079862 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4079808 GCCCTTTGGC
* *
4079818 TTGCTGCTTTTTGTTTGATTTTT
1 TTGCTGCTTTTTCTTAGATTTTT
4079841 TTGCTGCTGTTTTCTTAG-TTTT
1 TTGCTGCT-TTTTCTTAGATTTT
4079863 CTTTCTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.04, C:0.11, G:0.18, T:0.67
Consensus pattern (23 bp):
TTGCTGCTTTTTCTTAGATTTTT
Found at i:4080226 original size:29 final size:29
Alignment explanation
Indices: 4080126--4080280 Score: 129
Period size: 30 Copynumber: 5.2 Consensus size: 29
4080116 AAATATGGGC
* *
4080126 CAAAATGT-AATTTCTTGAGAGTTTAGGGGT
1 CAAAATGTAAATTT-TAGAAAGTTT-GGGGT
* * **
4080156 CAAAGTG-CAATTTTGAGAAAGTCTAAGGGT
1 CAAAATGTAAATTTT-AGAAAGT-TTGGGGT
* *
4080186 CGAAATGT-AATTTTAGAAATTTTGGGGT
1 CAAAATGTAAATTTTAGAAAGTTTGGGGT
4080214 CAAAATGTAAATTTTAGAAAAGTTTGGGGT
1 CAAAATGTAAATTTTAG-AAAGTTTGGGGT
*
4080244 CAAAATGTAAATTTT-GAAAAGTATAGGGGT
1 CAAAATGTAAATTTTAG-AAAGT-TTGGGGT
*
4080274 AAAAATG
1 CAAAATG
4080281 CAAAAAAAAA
Statistics
Matches: 104, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
28 12 0.12
29 22 0.21
30 69 0.66
31 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (29 bp):
CAAAATGTAAATTTTAGAAAGTTTGGGGT
Found at i:4080242 original size:30 final size:30
Alignment explanation
Indices: 4080182--4080280 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 30
4080172 GAAAGTCTAA
* *
4080182 GGGTCGAAATGT-AATTTTAG-AAATTTTG
1 GGGTCAAAATGTAAATTTTAGAAAAGTTTG
4080210 GGGTCAAAATGTAAATTTTAGAAAAGTTTG
1 GGGTCAAAATGTAAATTTTAGAAAAGTTTG
*
4080240 GGGTCAAAATGTAAATTTT-GAAAAGTATAG
1 GGGTCAAAATGTAAATTTTAGAAAAGT-TTG
*
4080270 GGGTAAAAATG
1 GGGTCAAAATG
4080281 CAAAAAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
28 11 0.17
29 15 0.23
30 38 0.59
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGTCAAAATGTAAATTTTAGAAAAGTTTG
Found at i:4080878 original size:79 final size:75
Alignment explanation
Indices: 4080479--4081594 Score: 1109
Period size: 74 Copynumber: 14.6 Consensus size: 75
4080469 CTCGGCGTGC
* * * ** * *
4080479 GACCCGAGACTCAACTCACCTCTTGGATTATGAGTTGA-TCTTCGAAAAAC--AAATATCAAAAA
1 GACCCGAGGCTCAACTCACCTC-TGTATTATGAGTTGATTTTTTAAAAAACATAAATTTAAAAAA
4080541 TACCTC-GACATGT
65 TACCTCAG-C--GT
* * ** * * *
4080554 GCCCCGAGGCTCAACTCACCTCTCGCAAAATGAGTTGA-TTTTTGAAAAACATGAA-TTGAAAAA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTAAAAAACATAAATTTAAAAAA
*
4080617 TACCTCGGCGT
65 TACCTCAGCGT
* * * *
4080628 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTTAAAAGA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTAAAAAACATAAATTT-AAA-A
* * *
4080692 AACACCTCGGCAT
63 AATACCTCAGCGT
** * * * *
4080705 GGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAATTTAAAAGA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTAAAAAACATAAATTT-AAA-A
* *
4080770 AATACCTCGGCAT
63 AATACCTCAGCGT
** * * * *
4080783 GGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAAATTTAAAAG
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTTTTAAAAAACATAAATTT-AAA-
* *
4080848 AAATACCTCGGCAT
62 AAATACCTCAGCGT
** * * * *
4080862 GGTCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAAAAACAGAAATTT
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTTTT-----AAAAAACATAAATTT
4080927 AAAAGAAATACCTCAGCGT
59 -AAA-AAATACCTCAGCGT
* * * **
4080946 GACCTGAGGCACAACTCACCTCTCATATTATGAGTTGA-TTTAAAAAAATACATAAA-TT-AAAA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTAAAAA-ACATAAATTTAAAAA
4081008 ATACCTCAGCGT
64 ATACCTCAGCGT
** *
4081020 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA-TTTAAAAAAAAGACTGAAA-TT-AAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTAAAAAACA-T-AAATTTAAAAA
4081082 ATACCTCAGCGT
64 ATACCTCAGCGT
* *
4081094 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTTAAAAAAAGAAGAAATTTAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA--TTTTTT-AAAAAA-CATAAATTTAAA
4081159 AAATACCTCAGCGT
62 AAATACCTCAGCGT
**
4081173 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAATACATAAA-TT-AAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTAAAAA-ACATAAATTTAAAAAA
4081236 TACCTCAGCGT
65 TACCTCAGCGT
***
4081247 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAGACATAAA-TT-AAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTAAAAA-ACATAAATTTAAAAAA
4081310 TACCTCAGCGT
65 TACCTCAGCGT
* ** **
4081321 GACCCGATGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAGACCGAAA-TT-AAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTAAAAA-ACATAAATTTAAAAAA
4081384 TACCTCAGCGT
65 TACCTCAGCGT
* *
4081395 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGCTTTTTTAAAAAAAGCAGAAATTTAAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTT-AAAAAA-CATAAATTTAAAAA
4081460 ATACCTCAGCGT
64 ATACCTCAGCGT
* *
4081472 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAATAGAAATTAAATTAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTT-AAAAAACATAAA-T---TTAA
4081537 AAAATACCTCAGCGT
61 AAAATACCTCAGCGT
4081552 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTT
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTT
4081595 TGAAAAAAAA
Statistics
Matches: 943, Mismatches: 65, Indels: 61
0.88 0.06 0.06
Matches are distributed among these distances:
72 2 0.00
73 24 0.03
74 345 0.37
75 57 0.06
76 31 0.03
77 133 0.14
78 89 0.09
79 137 0.15
80 62 0.07
82 3 0.00
84 60 0.06
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (75 bp):
GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTAAAAAACATAAATTTAAAAAAT
ACCTCAGCGT
Found at i:4081217 original size:227 final size:227
Alignment explanation
Indices: 4080479--4081619 Score: 1208
Period size: 227 Copynumber: 4.9 Consensus size: 227
4080469 CTCGGCGTGC
* * * ** *
4080479 GACCCGAGACTCAACTCACCTCTTGGATTATGAGTTGATCTT-CGAAAAACA-AATATCAAAAAT
1 GACCCGAGGCTCAACTCACCTC-TGTATTATGAGTTGATTTTAAAAAAAACATAA-ATTAAAAAT
* * ** *** *
4080542 ACCTC-GACATGTGCCCCGAGGCTCAACTCACCTCTCGCAAAATGAGTTGATTTTTGAAAAACA-
64 ACCTCAG-C--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAAGAC
* * * * *
4080605 TGAATTGAAAAATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---T
125 TAAATTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTT
* * * *
4080667 TTTT---GAAAAACAGAAATTTAAAAGAAACACCTCGGCAT
189 TTTTAAAAAAAAACAGAAATTT-AAA-AAATACCTCAGCGT
** * * * ***
4080705 GGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAATTTAAAAGA
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTAAAAAAAACATAAA-TT--AA-A
* * ** * * * ****
4080770 AATACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA-A
61 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTAAAAAAAAGA
* * ** * * *
4080834 CATAAATTTAAAAGAAATACCTCGGCATGGTCCGAGGCTTAACTCACCTCTCGCAATATGAGTTG
124 C-TAAA-TT-AAA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTG
*
4080899 ATTTTTTTGAAAAAAAAAACAGAAATTTAAAAGAAATACCTCAGCGT
184 ATTTTTTT-TAAAAAAAAACAGAAATTT-AAA-AAATACCTCAGCGT
* * *
4080946 GACCTGAGGCACAACTCACCTCTCATATTATGAGTTGA-TTTAAAAAAATACATAAATTAAAAAT
1 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTAAAAAAA-ACATAAATTAAAAAT
4081010 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAGACTGAA
64 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAGACT-AA
4081075 ATT-AAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTT
128 ATTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTT
*
4081139 AAAAAAAGA-AGAAATTTAAAAAATACCTCAGCGT
193 AAAAAAAAACAGAAATTTAAAAAATACCTCAGCGT
4081173 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAATACATAAATTAAAAATA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAA-ACATAAATTAAAAATA
4081238 CCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAGACATAAA
65 CCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAGAC-TAAA
*
4081303 TT-AAAAATACCTCAGCGTGACCCGATGCTCAACTCACCTCTGTATTATGAGTTGA----TTTTA
129 TTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTTA
* *
4081363 AAAAAAGACCGAAA-TT-AAAAATACCTCAGCGT
194 AAAAAAAACAGAAATTTAAAAAATACCTCAGCGT
* * *
4081395 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGCTTTTTTAAAAAAAGCAGAAATTTAAAAA
1 GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTG--ATTTTAAAAAAAACATAAA-TT-AAAA
4081460 ATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAATAG
62 ATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA---TTT-AAAAAA-A-
* *
4081525 AAATTAAATTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGAT
121 AGACTAAATTAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGAT
* *
4081590 TTTTTTGAAAAAAAAACAGAATTTTAAAAA
186 TTTTTTTAAAAAAAAACAGAAATTTAAAAA
4081620 TATTTCTTGA
Statistics
Matches: 798, Mismatches: 73, Indels: 77
0.84 0.08 0.08
Matches are distributed among these distances:
222 52 0.07
223 20 0.03
224 17 0.02
225 54 0.07
226 46 0.06
227 188 0.24
228 10 0.01
229 50 0.06
230 26 0.03
231 86 0.11
232 35 0.04
233 4 0.01
234 48 0.06
235 25 0.03
236 19 0.02
237 40 0.05
238 2 0.00
240 9 0.01
241 67 0.08
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (227 bp):
GACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAAAAACATAAATTAAAAATAC
CTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTAAAAAAAAGACTAAATT
AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTTTAAA
AAAAAACAGAAATTTAAAAAATACCTCAGCGT
Found at i:4081321 original size:301 final size:303
Alignment explanation
Indices: 4080556--4081591 Score: 1267
Period size: 301 Copynumber: 3.4 Consensus size: 303
4080546 CGACATGTGC
* * *
4080556 CCCGAGGCTCAACTCACCTCTCGCAAAATGAGTTGATTTTTG---AAAAACATGAATTGAAAAAT
1 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAACATAAATTAAAAAAT
* * * *** *
4080618 ACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-ACAGAA
66 ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTAAAAAAAGACATAA
* * * ** * * *
4080682 ATTTAAAAGAAACACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
131 A-TT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTT
*** * * ** * *
4080747 TTGAAAA-ACAT-AAATTTAAAAGAAATACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCA
191 AAAAAAAGAC-TGAAA-TT--AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTA
* * * * * *
4080810 ATATGAGTTGATTTTTTT-GAAAAA-CATAAATTTAAAAGAAATACCTCGGCATGG
250 TTATGAGTTGATTTTTTTAAAAAAAGCAGAAATTT-AAA-AAATACCTCAGCGTGA
* * *
4080864 TCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAAAAACAGAAATTTAA
1 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG--AAAAAAAACATAAA-TT-A
* * *
4080929 AAGAAATACCTCAGCGTGACCTGAGGCACAACTCACCTCTCATATTATGAGTTGATTTAAAAAAA
60 AA-AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTAAAAAAA
*
4080994 TACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATT
124 GACATAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATT
*
4081059 TAAAAAAAAGACTGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTAT
189 TTAAAAAAAGACTGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTAT
*
4081124 GAGTTGATTTTTTTTAAAAAAAGAAGAAATTTAAAAAATACCTCAGCGTGA
254 GAGTTGA-TTTTTTTAAAAAAAGCAGAAATTTAAAAAATACCTCAGCGTGA
* *
4081175 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTT-AAAAAAATACATAAATT-AAAAA
1 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAA-ACATAAATTAAAAAA
4081236 TACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTAAAAAAAAGACAT
65 TACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTT-AAAAAAAGACAT
*
4081300 AAATTAAAAATACCTCAGCGTGACCCGATGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAA
129 AAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAA
*
4081365 AAAAGACCGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
194 AAAAGACTGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTT
*
4081430 G-CTTTTTTAAAAAAAGCAGAAATTTAAAAAATACCTCAGCGTGA
259 GATTTTTTTAAAAAAAGCAGAAATTTAAAAAATACCTCAGCGTGA
* * *
4081474 CCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAAATAGAAATTAAATTAAA
1 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAA-A-ACA-TAAATTAAA
4081538 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTT
62 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTT
4081592 TTTTGAAAAA
Statistics
Matches: 647, Mismatches: 57, Indels: 51
0.86 0.08 0.07
Matches are distributed among these distances:
299 76 0.12
300 16 0.02
301 178 0.28
302 8 0.01
303 3 0.00
304 15 0.02
305 62 0.10
307 4 0.01
308 33 0.05
310 30 0.05
311 71 0.11
312 10 0.02
313 7 0.01
314 22 0.03
315 45 0.07
316 4 0.01
317 2 0.00
318 55 0.09
319 6 0.01
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (303 bp):
CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAAACATAAATTAAAAAAT
ACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTAAAAAAAGACATAA
ATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTAAAAA
AAGACTGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGA
TTTTTTTAAAAAAAGCAGAAATTTAAAAAATACCTCAGCGTGA
Found at i:4088115 original size:18 final size:18
Alignment explanation
Indices: 4088094--4088334 Score: 131
Period size: 18 Copynumber: 13.6 Consensus size: 18
4088084 AAATATGAGA
*
4088094 ATTTTTAAAAACACGAAG
1 ATTTTTGAAAACACGAAG
*** *
4088112 ATTTTTG-AAACATTTAT
1 ATTTTTGAAAACACGAAG
* *
4088129 TTTTTTGAAAACACGAAAA
1 ATTTTTGAAAACACG-AAG
*
4088148 AATTTT-AAAACACG-AG
1 ATTTTTGAAAACACGAAG
* * *
4088164 AATTTT-AGAGACACGAAA
1 ATTTTTGA-AAACACGAAG
* * * *
4088182 ATTCTTAAAAATACGAAA
1 ATTTTTGAAAACACGAAG
4088200 ATTTTTGAAAACACGGAA-
1 ATTTTTGAAAACAC-GAAG
*
4088218 ATTTTT-AAAACACG-GG
1 ATTTTTGAAAACACGAAG
* *
4088234 AATTTTTGAAAACATGAAA
1 -ATTTTTGAAAACACGAAG
* * * *
4088253 AATTTCG-AGACACCGGA-
1 ATTTTTGAAAACA-CGAAG
* *
4088270 ATTTTTGAAAATACGAGG
1 ATTTTTGAAAACACGAAG
*
4088288 ATTCTTGAAAACACGAAG
1 ATTTTTGAAAACACGAAG
* *
4088306 ATTTTTTAAAACACGAAA
1 ATTTTTGAAAACACGAAG
4088324 ATTTTTGAAAA
1 ATTTTTGAAAA
4088335 TACGGAAATT
Statistics
Matches: 166, Mismatches: 44, Indels: 26
0.70 0.19 0.11
Matches are distributed among these distances:
16 9 0.05
17 42 0.25
18 106 0.64
19 9 0.05
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (18 bp):
ATTTTTGAAAACACGAAG
Found at i:4088178 original size:35 final size:34
Alignment explanation
Indices: 4088130--4088328 Score: 125
Period size: 35 Copynumber: 5.6 Consensus size: 34
4088120 AACATTTATT
*
4088130 TTTTTGAAAACACGAAAAAATTTTAAAACACGAGAA
1 TTTTAGAAAACACG--AAAATTTTAAAACACGAGAA
* * *
4088166 TTTTAG-AGACACGAAAATTCTTAAAAATACGAAAA
1 TTTTAGAAAACACGAAAATT-TT-AAAACACGAGAA
* * *
4088201 TTTTTGAAAACACGGAAATTTTTAAAACACGGGAA
1 TTTTAGAAAACAC-GAAAATTTTAAAACACGAGAA
* * ** *
4088236 TTTTTGAAAACATGAAAAATTTCGAGACACCG-GAA
1 TTTTAGAAAACACG-AAAATTTTAAAACA-CGAGAA
* * **
4088271 TTTTTGAAAATACGAGGATTCTTGAAAACACGA-AGA
1 TTTTAGAAAACACGAAAATT-TT-AAAACACGAGA-A
**
4088307 TTTTTTAAAACACGAAAATTTT
1 TTTTAGAAAACACGAAAATTTT
4088329 TGAAAATACG
Statistics
Matches: 127, Mismatches: 26, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
33 6 0.05
34 7 0.06
35 73 0.57
36 35 0.28
37 6 0.05
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.29
Consensus pattern (34 bp):
TTTTAGAAAACACGAAAATTTTAAAACACGAGAA
Found at i:4088231 original size:53 final size:54
Alignment explanation
Indices: 4088133--4088344 Score: 175
Period size: 53 Copynumber: 4.0 Consensus size: 54
4088123 ATTTATTTTT
* *
4088133 TTGAAAACACGAAAAAATTTT-AAAACAC-GAGAATTTTAG-AGACACGAAAATTC
1 TTGAAAACACG-AAAAATTTTGAAAACACGGA-AATTTTTGAAAACACGAAAATTC
* * * ** *
4088186 TTAAAAATACGAAAATTTTTGAAAACACGGAAATTTTT-AAAACACGGGAATTT
1 TTGAAAACACGAAAAATTTTGAAAACACGGAAATTTTTGAAAACACGAAAATTC
* * * * **
4088239 TTGAAAACATGAAAAATTTCG-AGACACCGG-AATTTTTGAAAATACGAGGATTC
1 TTGAAAACACGAAAAATTTTGAAAACA-CGGAAATTTTTGAAAACACGAAAATTC
* * * * * *
4088292 TTGAAAACACGAAGATTTTTTAAAACACGAAAATTTTTGAAAATACGGAAATT
1 TTGAAAACACGAAAAATTTTGAAAACACGGAAATTTTTGAAAACACGAAAATT
4088345 TGAAATACGG
Statistics
Matches: 124, Mismatches: 28, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
52 19 0.15
53 80 0.65
54 25 0.20
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (54 bp):
TTGAAAACACGAAAAATTTTGAAAACACGGAAATTTTTGAAAACACGAAAATTC
Found at i:4088343 original size:18 final size:18
Alignment explanation
Indices: 4088130--4088345 Score: 142
Period size: 18 Copynumber: 12.2 Consensus size: 18
4088120 AACATTTATT
*
4088130 TTTTTGAAAACACGAAAAA
1 TTTTTGAAAACACG-GAAA
*
4088149 ATTTT-AAAACAC-GAGAA
1 TTTTTGAAAACACGGA-AA
* * *
4088166 TTTTAG-AGACACGAAAA
1 TTTTTGAAAACACGGAAA
* * * *
4088183 TTCTTAAAAATACGAAAA
1 TTTTTGAAAACACGGAAA
4088201 TTTTTGAAAACACGGAAA
1 TTTTTGAAAACACGGAAA
*
4088219 TTTTT-AAAACACGGGAA
1 TTTTTGAAAACACGGAAA
* *
4088236 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGGAAA
* * *
4088254 ATTTCG-AGACACCGG-AA
1 TTTTTGAAAACA-CGGAAA
* *
4088271 TTTTTGAAAATAC-GAGGA
1 TTTTTGAAAACACGGA-AA
*
4088289 TTCTTGAAAACAC-GAAGA
1 TTTTTGAAAACACGGAA-A
* *
4088307 TTTTTTAAAACACGAAAA
1 TTTTTGAAAACACGGAAA
*
4088325 TTTTTGAAAATACGGAAA
1 TTTTTGAAAACACGGAAA
4088343 TTT
1 TTT
4088346 GAAATACGGA
Statistics
Matches: 148, Mismatches: 38, Indels: 23
0.71 0.18 0.11
Matches are distributed among these distances:
16 2 0.01
17 42 0.28
18 98 0.66
19 6 0.04
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (18 bp):
TTTTTGAAAACACGGAAA
Found at i:4088352 original size:15 final size:16
Alignment explanation
Indices: 4088327--4088359 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
4088317 CACGAAAATT
4088327 TTTGAAAATACGGAAA
1 TTTGAAAATACGGAAA
4088343 TTTG-AAATACGGAAA
1 TTTGAAAATACGGAAA
4088358 TT
1 TT
4088360 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (16 bp):
TTTGAAAATACGGAAA
Found at i:4088363 original size:18 final size:19
Alignment explanation
Indices: 4088189--4088363 Score: 53
Period size: 18 Copynumber: 9.9 Consensus size: 19
4088179 AAAATTCTTA
*
4088189 AAAATACGAAAATT-TTTG
1 AAAATACGGAAATTATTTG
*
4088207 AAAACACGGAAATT-TTT-
1 AAAATACGGAAATTATTTG
* *
4088224 AAAACACGGGAATT-TTTG
1 AAAATACGGAAATTATTTG
* * *
4088242 AAAACA-TGAAA-AATTTCG
1 AAAATACGGAAATTATTT-G
* *
4088260 AGACA-CCGG-AATT-TTTG
1 A-AAATACGGAAATTATTTG
* *
4088277 AAAATAC-GAGGATT-CTTG
1 AAAATACGGA-AATTATTTG
* *
4088295 AAAACAC-GAAGATT-TTTT
1 AAAATACGGAA-ATTATTTG
* *
4088313 AAAACACGAAAATT-TTTG
1 AAAATACGGAAATTATTTG
4088331 AAAATACGG-AA--ATTTG
1 AAAATACGGAAATTATTTG
4088347 -AAATACGGAAATTATTT
1 AAAATACGGAAATTATTT
4088364 TTAAAAAACA
Statistics
Matches: 120, Mismatches: 22, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
15 8 0.07
16 9 0.08
17 27 0.22
18 71 0.59
19 5 0.04
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.29
Consensus pattern (19 bp):
AAAATACGGAAATTATTTG
Found at i:4089130 original size:20 final size:21
Alignment explanation
Indices: 4089105--4089144 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
4089095 TGGGCCTGGC
*
4089105 CTGCTGCTGTTT-TTTTTTTG
1 CTGCTGCTATTTCTTTTTTTG
4089125 CTGCTGCTATTTCTTTTTTT
1 CTGCTGCTATTTCTTTTTTT
4089145 TTCTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.15, T:0.65
Consensus pattern (21 bp):
CTGCTGCTATTTCTTTTTTTG
Found at i:4089270 original size:10 final size:10
Alignment explanation
Indices: 4089242--4089333 Score: 69
Period size: 10 Copynumber: 8.7 Consensus size: 10
4089232 CTGTGATGTA
*
4089242 TTTCTTTTTC
1 TTTCTTTTTT
*
4089252 TTT-TATTTT
1 TTTCTTTTTT
*
4089261 TTTATTTTTT
1 TTTCTTTTTT
* *
4089271 CTTCTTTTTC
1 TTTCTTTTTT
4089281 TTTCTTTCTTTT
1 TTTC-TT-TTTT
*
4089293 TCTTCTTTTTC
1 T-TTCTTTTTT
4089304 TTTCTTTCTTT
1 TTTCTTT-TTT
4089315 TTCTCTTTTTT
1 TT-TCTTTTTT
4089326 CTTTCTTT
1 -TTTCTTT
4089334 CTTCTTCTTC
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
9 7 0.11
10 24 0.37
11 18 0.28
12 13 0.20
13 3 0.05
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:4089286 original size:4 final size:4
Alignment explanation
Indices: 4089277--4089336 Score: 65
Period size: 4 Copynumber: 15.5 Consensus size: 4
4089267 TTTTCTTCTT
*
4089277 TTTC TTTC TTTC -TT- TTTC TTCTT TTTC TTTC TTTC TTT- TTCTC TTT-
1 TTTC TTTC TTTC TTTC TTTC TT-TC TTTC TTTC TTTC TTTC TT-TC TTTC
4089323 TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TT
4089337 CTTCTTCCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
3 9 0.19
4 34 0.71
5 5 0.10
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:4089291 original size:14 final size:14
Alignment explanation
Indices: 4089242--4089329 Score: 80
Period size: 13 Copynumber: 6.5 Consensus size: 14
4089232 CTGTGATGTA
4089242 TTTCTTTTTCTTT-
1 TTTCTTTTTCTTTC
*
4089255 TATT-TTTTTATTT-
1 T-TTCTTTTTCTTTC
*
4089268 TTTCTTCTT-TTTC
1 TTTCTTTTTCTTTC
4089281 TTTCTTTCTT-TTTC
1 TTTCTTT-TTCTTTC
4089295 -TTCTTTTTCTTTC
1 TTTCTTTTTCTTTC
*
4089308 TTTCTTTTTCTCTTT
1 TTTCTTTTTCT-TTC
4089323 TTTCTTT
1 TTTCTTT
4089330 CTTTCTTCTT
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
12 7 0.11
13 30 0.47
14 18 0.28
15 9 0.14
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTCTTTTTCTTTC
Found at i:4089302 original size:33 final size:33
Alignment explanation
Indices: 4089248--4089342 Score: 90
Period size: 33 Copynumber: 2.9 Consensus size: 33
4089238 TGTATTTCTT
* *
4089248 TTTCTTT-TATTTTTTTATTTTTTCTTCTTTTTC
1 TTTCTTTCT-TTTTCTTCTTTTTTCTTCTTTTTC
*
4089281 TTTCTTTCTTTTTCTTC-TTTTTCTT-TCTTTC
1 TTTCTTTCTTTTTCTTCTTTTTTCTTCTTTTTC
*
4089312 TTT-TTCTCTTTTTTCTTTCTTTCTTCTTCTT
1 TTTCTT-TC-TTTTTC-TTCTTTTTTCTTCTT
4089343 CCTTCCCTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
30 2 0.04
31 10 0.20
32 14 0.27
33 16 0.31
34 8 0.16
35 1 0.02
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (33 bp):
TTTCTTTCTTTTTCTTCTTTTTTCTTCTTTTTC
Found at i:4089334 original size:23 final size:23
Alignment explanation
Indices: 4089242--4089343 Score: 133
Period size: 23 Copynumber: 4.6 Consensus size: 23
4089232 CTGTGATGTA
4089242 TTTCTTTTTCTT-TTATTT-TTT-
1 TTTCTTTTTCTTCTT-TTTCTTTC
*
4089263 TAT-TTTTTCTTCTTTTTCTTTC
1 TTTCTTTTTCTTCTTTTTCTTTC
4089285 TTTCTTTTTCTTCTTTTTCTTTC
1 TTTCTTTTTCTTCTTTTTCTTTC
4089308 TTTCTTTTTC-TCTTTTTTCTTTC
1 TTTCTTTTTCTTC-TTTTTCTTTC
*
4089331 TTTCTTCTTCTTC
1 TTTCTTTTTCTTC
4089344 CTTCCCTTCG
Statistics
Matches: 72, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
20 11 0.15
21 7 0.10
22 4 0.06
23 48 0.67
24 2 0.03
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTCTTTTTCTTCTTTTTCTTTC
Found at i:4089341 original size:29 final size:27
Alignment explanation
Indices: 4089243--4089342 Score: 62
Period size: 29 Copynumber: 3.6 Consensus size: 27
4089233 TGTGATGTAT
* * *
4089243 TTCTTTTTC-TTTTATTTTTTTATTTT
1 TTCTTCTTCTTTTTCTTTTTTTCTTTT
* *
4089269 TTCTTCTTTTTCTTTCTTTCTTTTTCTTCT
1 TTCTTCTTCTT-TTTC-TT-TTTTTCTTTT
* *
4089299 TT-TTCTT-TCTTTCTTTTTCTCTTTT
1 TTCTTCTTCTTTTTCTTTTTTTCTTTT
*
4089324 TTCTTTCTTTCTTCTTCTT
1 TTC-TTC-TTCTTTTTCTT
4089343 CCTTCCCTTC
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
25 10 0.18
26 9 0.16
27 8 0.14
28 6 0.11
29 13 0.23
30 10 0.18
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (27 bp):
TTCTTCTTCTTTTTCTTTTTTTCTTTT
Found at i:4089642 original size:22 final size:22
Alignment explanation
Indices: 4089599--4089642 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4089589 GCCCTTTGGC
*
4089599 TTGCTGCTTTTTGTTTGATTTT
1 TTGCTGCTTTTTGTTAGATTTT
4089621 TTGCTGCTGTTTTGTTAG-TTTT
1 TTGCTGCT-TTTTGTTAGATTTT
4089643 CTTTCTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.05, C:0.09, G:0.20, T:0.66
Consensus pattern (22 bp):
TTGCTGCTTTTTGTTAGATTTT
Found at i:4090008 original size:30 final size:30
Alignment explanation
Indices: 4089974--4090061 Score: 115
Period size: 30 Copynumber: 2.9 Consensus size: 30
4089964 GTCGAAATAT
** *
4089974 AATTTTAGAAATTTTTGGGGTTAAAATGTA
1 AATTTTAGAAAAGTTTGGGGTCAAAATGTA
4090004 AATTTTAGAAAAGTTTGGGGTCAAAATGTA
1 AATTTTAGAAAAGTTTGGGGTCAAAATGTA
* *
4090034 AATTTT-GAAAAGTATAGGGGTAAAAATG
1 AATTTTAGAAAAGT-TTGGGGTCAAAATG
4090062 CAAAAAAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
29 7 0.13
30 45 0.87
ACGTcount: A:0.41, C:0.01, G:0.23, T:0.35
Consensus pattern (30 bp):
AATTTTAGAAAAGTTTGGGGTCAAAATGTA
Found at i:4090650 original size:79 final size:78
Alignment explanation
Indices: 4090237--4090991 Score: 647
Period size: 77 Copynumber: 9.7 Consensus size: 78
4090227 AGAAATCGAG
* * * * * * * *
4090237 AATAGCTCGGCGTGCGACCCGAGACTCAATTCACCTCTTGGATTATGAGTTGA-TCTTCGAAAAA
1 AATACCTCGGCGTG-G-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAA
* *
4090301 C--AAATAT-CAA-A
64 CATAAATTTAAAAGA
* * *
4090312 AATACCTCGACATGTGCCCCGAGGCTCAACTCACCTCTCGCAAAATGAGTTGA-TTTTTGAAAAA
1 AATACCTCGGC--GTGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAA
* *
4090376 CATGAA-TT-GAA-A
64 CATAAATTTAAAAGA
*
4090388 AATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACA
1 AATACCTCGGCGTGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA
*
4090452 GAAATTTAAAAGA
66 TAAATTTAAAAGA
* * * *
4090465 AACACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAACA
1 AATACCTCGGCGTGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA
4090529 TAAATTTAAAAGA
66 TAAATTTAAAAGA
* * *
4090542 AATACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAC
1 AATACCTCGGCGTGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAAC
4090607 ATAAATTTAAAAGA
65 ATAAATTTAAAAGA
* * *
4090621 AATACCTCGGCATGGTCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAA
1 AATACCTCGGCGTGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-----A
*
4090686 AAAACAGAAATTTAAAAGA
60 AAAACATAAATTTAAAAGA
* * * * * ** * ***
4090705 AATACCTCAGCGTGACCTGAGGCACAATTCACCTCTCATATTATGAGTTGA-TTTAAAAAAATAC
1 AATACCTCGGCGTGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA-AC
4090769 ATAAA-TT--AA-A
65 ATAAATTTAAAAGA
* * * * *
4090779 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAGAAAA
1 AATACCTCGGCGTGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT---TGAAAA
*
4090843 AGACTGAAA-TT--AA-A
63 ACA-T-AAATTTAAAAGA
* * * *
4090857 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAAAC
1 AATACCTCGGCGTGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAAAC
* * *
4090921 AGAAATTAAATTAAAA
65 ATAAATTTAA--AAGA
** * * * *
4090937 AATACCTCAACGTGACTCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTT
1 AATACCTCGGCGTGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
4090992 AAAAAAAAAA
Statistics
Matches: 593, Mismatches: 58, Indels: 53
0.84 0.08 0.08
Matches are distributed among these distances:
73 13 0.02
74 93 0.16
75 55 0.09
76 24 0.04
77 132 0.22
78 82 0.14
79 78 0.13
80 54 0.09
82 3 0.01
84 59 0.10
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (78 bp):
AATACCTCGGCGTGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA
TAAATTTAAAAGA
Found at i:4090650 original size:156 final size:151
Alignment explanation
Indices: 4090252--4090991 Score: 590
Period size: 158 Copynumber: 4.8 Consensus size: 151
4090242 CTCGGCGTGC
* * * * * * * * * *
4090252 GACCCGAGACTCAATTCACCTCTTGGATTATGAGTTGATCTTCGAAAAAC--AAATAT-CAA-AA
1 GACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
* * *
4090313 ATACCTCGACATGTGCCCCGAGGCTCAACTCACCTCTCGCAAAATGAGTTGA-TTTTTGAAAAAC
66 ATACCTCGGCATG-G-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAAC
* * *
4090377 ATGAATTGAAAAATACCTCGGCGT
128 ATAAATTAAAAAATACCTCGGCAT
*
4090401 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
1 GACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
* *
4090466 ACACCTCGGCATGGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACATA
66 ATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACATA
4090531 AATTTAAAAGAAATACCTCGGCAT
131 AA-TT-AAA-AAATACCTCGGCAT
** *
4090555 GGTCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACATAAATTTAAAAG
1 GACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTTAAAAG
*
4090620 AAATACCTCGGCATGGTCCGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAA
64 AAATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-----
* * *
4090685 AAAAACAGAAATTTAAAAGAAATACCTCAGCGT
123 -AAAACATAAA-TT-AAA-AAATACCTCGGCAT
** * * ** * *** *
4090718 GACCTGAGGCACAATTCACCTCTCATATTATGAGTTGATTTAAAAAAATACATAAA-TT--AA-A
1 GACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-ACAGAAATTTAAAAGA
* * ** * * *
4090779 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTAAAAGAAAA
65 AATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT---TG-AAA
* * *
4090843 AGACTGAAATT-AAAAATACCTCAGCGT
126 ACA-T-AAATTAAAAAATACCTCGGCAT
* * * *
4090870 GACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAAACAGAAATTAAATTA
1 GACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-AAAAACAGAAATTTAA--A
* ** * * * *
4090934 AAAAATACCTCAACGT-GACTCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTT
62 AGAAATACCTCGGCATGGTC-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
4090992 AAAAAAAAAA
Statistics
Matches: 498, Mismatches: 61, Indels: 55
0.81 0.10 0.09
Matches are distributed among these distances:
149 43 0.09
151 60 0.12
152 54 0.11
153 22 0.04
154 54 0.11
155 2 0.00
156 81 0.16
157 22 0.04
158 83 0.17
159 3 0.01
161 9 0.02
162 7 0.01
163 58 0.12
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (151 bp):
GACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
ATACCTCGGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACATA
AATTAAAAAATACCTCGGCAT
Found at i:4091954 original size:20 final size:21
Alignment explanation
Indices: 4091929--4091968 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
4091919 TGGGCCTGGC
*
4091929 CTGCTGCTGTTT-TTTTTTTG
1 CTGCTGCTATTTCTTTTTTTG
4091949 CTGCTGCTATTTCTTTTTTT
1 CTGCTGCTATTTCTTTTTTT
4091969 TCTTTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.15, T:0.65
Consensus pattern (21 bp):
CTGCTGCTATTTCTTTTTTTG
Found at i:4092099 original size:4 final size:4
Alignment explanation
Indices: 4092092--4092140 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
4092082 TTTTTATTTT
*
4092092 TTTC TTTC TCTTT TTTC TTTC TTT- TTT- TTCTC TTT- TTTC TTTC TTTC
1 TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TT-TC TTTC TTTC TTTC TTTC
4092139 TT
1 TT
4092141 CTTCTTCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 8 0.21
4 26 0.67
5 5 0.13
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:4092107 original size:13 final size:13
Alignment explanation
Indices: 4092089--4092135 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
4092079 TTTTTTTTAT
4092089 TTTTTTCTTTCTC
1 TTTTTTCTTTCTC
4092102 TTTTTTC-TT-TC
1 TTTTTTCTTTCTC
4092113 -TTTTT-TTTCTC
1 TTTTTTCTTTCTC
4092124 TTTTTTCTTTCT
1 TTTTTTCTTTCT
4092136 TTCTTCTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 7 0.23
11 4 0.13
12 7 0.23
13 12 0.40
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTCTTTCTC
Found at i:4092109 original size:35 final size:35
Alignment explanation
Indices: 4092068--4092135 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
4092058 GATGTATTTC
4092068 TTTTTCTTTTATTTTTTTTAT-TTTTTTCTTTCTCT
1 TTTTTC-TTTATTTTTTTTATCTTTTTTCTTTCTCT
* *
4092103 TTTTTCTTTCTTTTTTTTCTCTTTTTTCTTTCT
1 TTTTTCTTTATTTTTTTTATCTTTTTTCTTTCT
4092136 TTCTTCTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (35 bp):
TTTTTCTTTATTTTTTTTATCTTTTTTCTTTCTCT
Found at i:4092116 original size:22 final size:22
Alignment explanation
Indices: 4092081--4092137 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
4092071 TTCTTTTATT
*
4092081 TTTTTTATTT-TTTTCTTTCTC
1 TTTTTTCTTTCTTTTCTTTCTC
*
4092102 TTTTTTCTTTCTTTTTTTTCTC
1 TTTTTTCTTTCTTTTCTTTCTC
4092124 TTTTTTCTTTCTTT
1 TTTTTTCTTTCTTT
4092138 CTTCTTCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
21 9 0.27
22 24 0.73
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTTCTTTCTTTTCTTTCTC
Found at i:4092136 original size:11 final size:11
Alignment explanation
Indices: 4092064--4092143 Score: 69
Period size: 11 Copynumber: 7.2 Consensus size: 11
4092054 CTGTGATGTA
4092064 TTTC-TTTTTC
1 TTTCTTTTTTC
4092074 TTT-TATTTTT-
1 TTTCT-TTTTTC
*
4092084 TTTATTTTTTTC
1 TTT-CTTTTTTC
4092096 TTTCTCTTTTTTC
1 -TT-TCTTTTTTC
4092109 TTTCTTTTTT-
1 TTTCTTTTTTC
4092119 TTCTCTTTTTTC
1 TT-TCTTTTTTC
*
4092131 TTTCTTTCTTC
1 TTTCTTTTTTC
4092142 TT
1 TT
4092144 CTTCCTTCCC
Statistics
Matches: 59, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
10 8 0.14
11 36 0.61
12 5 0.08
13 9 0.15
14 1 0.02
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:4092286 original size:20 final size:20
Alignment explanation
Indices: 4092239--4092279 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4092229 TTCTTTCTTC
* *
4092239 TTCTCTTTCTTCTTGGCTGT
1 TTCTTTTTCTTCTTGGCTAT
*
4092259 TTCTTTTTCTTCTTGGTTAT
1 TTCTTTTTCTTCTTGGCTAT
4092279 T
1 T
4092280 GTTTTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.02, C:0.20, G:0.12, T:0.66
Consensus pattern (20 bp):
TTCTTTTTCTTCTTGGCTAT
Found at i:4092447 original size:22 final size:22
Alignment explanation
Indices: 4092404--4092447 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4092394 GCCCTTTGGC
* *
4092404 TTGCTGCTTTTTGTTTGATTTT
1 TTGCTGCTTTTTCTTAGATTTT
4092426 TTGCTGCTGTTTTCTTAG-TTTT
1 TTGCTGCT-TTTTCTTAGATTTT
4092448 CTTTCTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.05, C:0.11, G:0.18, T:0.66
Consensus pattern (22 bp):
TTGCTGCTTTTTCTTAGATTTT
Found at i:4092798 original size:59 final size:58
Alignment explanation
Indices: 4092680--4092865 Score: 137
Period size: 60 Copynumber: 3.1 Consensus size: 58
4092670 GCTTCTGAGG
* * * *
4092680 CAAAAGTGT-AATTTTAGCAAAA-ATATGGGCCAAAATGTAATTTCTTGAGAGTTTAGGGGT
1 CAAAA-TGTAAATTTTAG-AAAAGTTAAGGGTCAAAATGTAA-TT-TTGAAAGTTTAGGGGT
* * * *
4092740 CAAAGTG-CAATTTT-GAGAAAGTCTAAGGGTCAAAATGTAATTTTAGAAATTTTTGGGGT
1 CAAAATGTAAATTTTAGA-AAAGT-TAAGGGTCAAAATGTAATTTT-GAAAGTTTAGGGGT
* ** **
4092799 TAAAATGTAAATTTTAGAAAAGTTTGGGGTCAAAATGTAAATTTTGAAAAGTACAGGGGT
1 CAAAATGTAAATTTTAGAAAAGTTAAGGGTCAAAATGT-AATTTTG-AAAGTTTAGGGGT
*
4092859 AAAAATG
1 CAAAATG
4092866 CAAAAAAAAT
Statistics
Matches: 100, Mismatches: 17, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
57 1 0.01
58 6 0.06
59 40 0.40
60 51 0.51
61 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (58 bp):
CAAAATGTAAATTTTAGAAAAGTTAAGGGTCAAAATGTAATTTTGAAAGTTTAGGGGT
Found at i:4092812 original size:30 final size:30
Alignment explanation
Indices: 4092766--4092850 Score: 129
Period size: 30 Copynumber: 2.9 Consensus size: 30
4092756 GAAAGTCTAA
**
4092766 GGGTCAAAATGT-AATTTTAGAAATTTTTG
1 GGGTCAAAATGTAAATTTTAGAAAAGTTTG
*
4092795 GGGTTAAAATGTAAATTTTAGAAAAGTTTG
1 GGGTCAAAATGTAAATTTTAGAAAAGTTTG
4092825 GGGTCAAAATGTAAATTTT-GAAAAGT
1 GGGTCAAAATGTAAATTTTAGAAAAGT
4092851 ACAGGGGTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 18 0.35
30 33 0.65
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (30 bp):
GGGTCAAAATGTAAATTTTAGAAAAGTTTG
Found at i:4092858 original size:30 final size:30
Alignment explanation
Indices: 4092734--4092865 Score: 103
Period size: 30 Copynumber: 4.4 Consensus size: 30
4092724 TTGAGAGTTT
* *
4092734 AGGGGTCAAAGTG-CAATTTTGAGAAAGTC
1 AGGGGTCAAAATGTAAATTTTGAGAAAGTC
* * *
4092763 TAAGGGTCAAAATGT-AATTTT-AGAAATTTT
1 -AGGGGTCAAAATGTAAATTTTGAGAAA-GTC
* * *
4092793 TGGGGTTAAAATGTAAATTTT-AGAAAAGTT
1 AGGGGTCAAAATGTAAATTTTGAG-AAAGTC
*
4092823 TGGGGTCAAAATGTAAATTTTGA-AAAGTAC
1 AGGGGTCAAAATGTAAATTTTGAGAAAGT-C
*
4092853 AGGGGTAAAAATG
1 AGGGGTCAAAATG
4092866 CAAAAAAAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
29 21 0.25
30 59 0.70
31 4 0.05
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (30 bp):
AGGGGTCAAAATGTAAATTTTGAGAAAGTC
Found at i:4093198 original size:26 final size:24
Alignment explanation
Indices: 4093169--4093249 Score: 69
Period size: 26 Copynumber: 3.3 Consensus size: 24
4093159 ATTATAGAAT
*
4093169 AATATAATAAAATAATTTAAGTTTG
1 AATATAATAAAATAATTTAA-ATTG
*
4093194 AAATATAA-AAATTAAATTTAAATTG
1 -AATATAATAAAAT-AATTTAAATTG
* *
4093219 AATAT-ATAACATAATTTATAACT-
1 AATATAATAAAATAATTTA-AATTG
4093242 AATATAAT
1 AATATAAT
4093250 GAGAAGCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
23 12 0.26
24 13 0.28
25 7 0.15
26 14 0.30
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (24 bp):
AATATAATAAAATAATTTAAATTG
Found at i:4093204 original size:24 final size:23
Alignment explanation
Indices: 4093169--4093236 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 23
4093159 ATTATAGAAT
*
4093169 AATATAATAAAATAATTTAAGTTTG
1 AATAT-ATAAAATAATTTAA-ATTG
4093194 AA-ATATAAAAATTAAATTTAAATTG
1 AATATAT-AAAA-T-AATTTAAATTG
*
4093219 AATATATAACATAATTTA
1 AATATATAAAATAATTTA
4093237 TAACTAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
23 8 0.22
24 7 0.19
25 11 0.30
26 11 0.30
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (23 bp):
AATATATAAAATAATTTAAATTG
Found at i:4095139 original size:10 final size:10
Alignment explanation
Indices: 4095120--4095149 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
4095110 ACGAAACAAC
4095120 TTTA-AAAAT
1 TTTATAAAAT
4095129 TTTATAAAAT
1 TTTATAAAAT
4095139 TTTATAAAAT
1 TTTATAAAAT
4095149 T
1 T
4095150 AGTAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTTATAAAAT
Found at i:4095205 original size:21 final size:20
Alignment explanation
Indices: 4095181--4095219 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
4095171 TTTAAACTTT
4095181 ATTTAAAAATATATAAAAATA
1 ATTTAAAAATAT-TAAAAATA
4095202 ATTTAAAAATATTAAAAA
1 ATTTAAAAATATTAAAAA
4095220 GTTGTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTTAAAAATATTAAAAATA
Found at i:4095216 original size:9 final size:9
Alignment explanation
Indices: 4095183--4095300 Score: 55
Period size: 9 Copynumber: 12.6 Consensus size: 9
4095173 TAAACTTTAT
4095183 TTAAAAATA
1 TTAAAAATA
4095192 TATAAAAATAA
1 T-TAAAAAT-A
4095203 TTTAAAAATA
1 -TTAAAAATA
4095213 TTAAAAAGT-
1 TTAAAAA-TA
* *
4095222 TGTAAAAGTTC
1 T-TAAAA-ATA
*
4095233 TTAAAAATG
1 TTAAAAATA
*
4095242 GTAAAAAGTA
1 TTAAAAA-TA
4095252 -TAAAAAT-
1 TTAAAAATA
*
4095259 TGTAAAAAAA
1 T-TAAAAATA
* *
4095269 TTTAAAATG
1 TTAAAAATA
*
4095278 TAAAAAATA
1 TTAAAAATA
4095287 TTAAATAAT-
1 TTAAA-AATA
4095296 TTAAA
1 TTAAA
4095301 TTTTTTTTGA
Statistics
Matches: 84, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
8 1 0.01
9 48 0.57
10 25 0.30
11 9 0.11
12 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.32
Consensus pattern (9 bp):
TTAAAAATA
Found at i:4095300 original size:19 final size:18
Alignment explanation
Indices: 4095181--4095300 Score: 75
Period size: 18 Copynumber: 6.4 Consensus size: 18
4095171 TTTAAACTTT
4095181 ATTT-AAAAATATATAAAA
1 ATTTAAAAAATAT-TAAAA
*
4095199 ATAATTTAAAAATATTAAAA
1 AT--TTAAAAAATATTAAAA
** *
4095219 AGTTGTAAAAGTTCTTAAAA
1 A-TT-TAAAAAATATTAAAA
* *
4095239 ATGGTAAAAAGTA-TAAAA
1 AT-TTAAAAAATATTAAAA
*
4095257 ATTGTAAAAAA-ATTTAAA
1 ATT-TAAAAAATATTAAAA
*
4095275 ATGTAAAAAATATTAAATA
1 ATTTAAAAAATATTAAA-A
4095294 ATTTAAA
1 ATTTAAA
4095301 TTTTTTTTGA
Statistics
Matches: 78, Mismatches: 14, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
17 8 0.10
18 26 0.33
19 15 0.19
20 20 0.26
21 9 0.12
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.33
Consensus pattern (18 bp):
ATTTAAAAAATATTAAAA
Found at i:4108208 original size:31 final size:29
Alignment explanation
Indices: 4108155--4108216 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
4108145 TTATAACTTG
*
4108155 TTGTTAATATTTTAATATATAAAATATAAA
1 TTGTAAATATTTTAATATAT-AAATATAAA
*
4108185 TTGTAAATATTTTTAAT-TAATAAATATTAA
1 TTGTAAATA-TTTTAATAT-ATAAATATAAA
4108215 TT
1 TT
4108217 ATTTATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (29 bp):
TTGTAAATATTTTAATATATAAATATAAA
Found at i:4109884 original size:6 final size:6
Alignment explanation
Indices: 4109875--4109912 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
4109865 TATATATATA
4109875 GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GT
1 GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GTAGTG GT
4109913 TCATAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.50, T:0.34
Consensus pattern (6 bp):
GTAGTG
Found at i:4110431 original size:21 final size:22
Alignment explanation
Indices: 4110391--4110432 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4110381 AAATTAATCA
*
4110391 TGAAAACTCATTTATCCATAAT
1 TGAAAACTCATTTATACATAAT
4110413 TGAAAACTCA-TTATACATAA
1 TGAAAACTCATTTATACATAA
4110433 ATGTCTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (22 bp):
TGAAAACTCATTTATACATAAT
Found at i:4111952 original size:20 final size:20
Alignment explanation
Indices: 4111927--4111981 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
4111917 TAAAATATAA
4111927 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAATTTTTATAAATT
*
4111947 ATTTTGAATTTTTAAAAATT
1 ATTTTGAATTTTTATAAATT
*
4111967 ATTTTAAATTTTTAT
1 ATTTTGAATTTTTAT
4111982 TTAGAGAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTTTGAATTTTTATAAATT
Found at i:4111957 original size:19 final size:19
Alignment explanation
Indices: 4111922--4111981 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
4111912 TTTTTTAAAA
*
4111922 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
4111940 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
* *
4111959 TAAAAATTATTTTAAATTTT
1 TATAAA-TATTTTGAATTTT
4111979 TAT
1 TAT
4111982 TTAGAGAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.19
19 15 0.42
20 14 0.39
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:4113643 original size:18 final size:18
Alignment explanation
Indices: 4113620--4113655 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4113610 AGATTTATCA
4113620 TTTTAGCACGTTAAACTT
1 TTTTAGCACGTTAAACTT
*
4113638 TTTTAGCACGTTGAACTT
1 TTTTAGCACGTTAAACTT
4113656 ACTAAGCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (18 bp):
TTTTAGCACGTTAAACTT
Found at i:4114453 original size:20 final size:20
Alignment explanation
Indices: 4114404--4114454 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
4114394 GTGACCCCTG
* *
4114404 TTTTA-CAAATTTTGCATAT
1 TTTTACCAAATTTTCCAAAT
*
4114423 TTTTACTAAATTTTCCAAAT
1 TTTTACCAAATTTTCCAAAT
*
4114443 TTTTCCCAAATT
1 TTTTACCAAATT
4114455 GATTCTAGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTTACCAAATTTTCCAAAT
Found at i:4114967 original size:43 final size:43
Alignment explanation
Indices: 4114912--4115223 Score: 357
Period size: 43 Copynumber: 7.3 Consensus size: 43
4114902 TTTTATAAAT
* * * * *
4114912 AAACGCCACTAAAGACCATGACATTTAGCGGCACTTTTTCAAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
*
4114955 AAACGCCGCTAAAGACCAT-AGCCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTAAAGACCATGA-CCTTTAGCGGCGCTTTTCCCAC
*
4114998 AAACGCCACTAAAGACCATGACCTTTAG-GGCGC-TTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
4115039 AAACGCCGCTAAAGACCATGACTTTTAGCGGCGCTTTTTCTAT
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* *
4115082 AAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
4115125 AAACGCCGCTAAAGA-TATTGAGCTTTAGCGGCGCTTTTTCCCGC
1 AAACGCCGCTAAAGACCA-TGACCTTTAGCGGCGC-TTTTCCCAC
* ** *
4115169 AAACGCCGCTATAGA--ATAGACCTTTAGCGATGCTTTTCACAC
1 AAACGCCGCTAAAGACCAT-GACCTTTAGCGGCGCTTTTCCCAC
*
4115211 AAAAGCCGCTAAA
1 AAACGCCGCTAAA
4115224 AATATATCTT
Statistics
Matches: 232, Mismatches: 30, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
41 34 0.15
42 30 0.13
43 145 0.62
44 23 0.10
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:4115138 original size:127 final size:129
Alignment explanation
Indices: 4114912--4115179 Score: 382
Period size: 127 Copynumber: 2.1 Consensus size: 129
4114902 TTTTATAAAT
* *
4114912 AAACGCCACTAAAGACCATGACATTTAGCGGCACTTTTTCAACAAACGCCGCTAAAGACCATAGC
1 AAACGCCGCTAAAGACCATGACATTTAGCGGCACTTTTTCAACAAACACCGCTAAAGACCATAGC
4114977 CTTTAGCGGCACTTTTCCCACAAACGCCACTAAAGACCA-TGACCTTTAG-GGCGC-TTTCCCAC
66 CTTTAGCGGCACTTTTCCCACAAACGCCACTAAAGA-CATTGACCTTTAGCGGCGCTTTTCCCAC
* * * *
4115039 AAACGCCGCTAAAGACCATGACTTTTAGCGGCGCTTTTTCTATAAACACCGCTAAAGACCA-AGA
1 AAACGCCGCTAAAGACCATGACATTTAGCGGCACTTTTTCAACAAACACCGCTAAAGACCATAG-
* * * * *
4115103 CCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATATTGAGCTTTAGCGGCGCTTTTTCCCG
65 CCTTTAGCGGCACTTTTCCCACAAACGCCACTAAAGACATTGACCTTTAGCGGCGC-TTTTCCCA
4115168 C
129 C
4115169 AAACGCCGCTA
1 AAACGCCGCTA
4115180 TAGAATAGAC
Statistics
Matches: 125, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
126 3 0.02
127 99 0.79
128 5 0.04
130 18 0.14
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (129 bp):
AAACGCCGCTAAAGACCATGACATTTAGCGGCACTTTTTCAACAAACACCGCTAAAGACCATAGC
CTTTAGCGGCACTTTTCCCACAAACGCCACTAAAGACATTGACCTTTAGCGGCGCTTTTCCCAC
Found at i:4120131 original size:7 final size:7
Alignment explanation
Indices: 4120100--4120144 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
4120090 TCTTAACCTT
4120100 TAACCCC
1 TAACCCC
*
4120107 TAATCCC
1 TAACCCC
*
4120114 TAATCCC
1 TAACCCC
4120121 TAACCCC
1 TAACCCC
**
4120128 TAACTAC
1 TAACCCC
4120135 TAACCCC
1 TAACCCC
4120142 TAA
1 TAA
4120145 ATCTTATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.22
Consensus pattern (7 bp):
TAACCCC
Found at i:4120202 original size:7 final size:7
Alignment explanation
Indices: 4120190--4120240 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
4120180 AATCTAGACA
4120190 CTAAACC
1 CTAAACC
4120197 CTAAACC
1 CTAAACC
4120204 CTAAACC
1 CTAAACC
4120211 CT-AACC
1 CTAAACC
*
4120217 C-AAATCT
1 CTAAA-CC
*
4120224 CTAACCC
1 CTAAACC
*
4120231 CTAACCC
1 CTAAACC
4120238 CTA
1 CTA
4120241 CACATTGTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
6 7 0.18
7 29 0.76
8 2 0.05
ACGTcount: A:0.37, C:0.45, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:4120464 original size:14 final size:14
Alignment explanation
Indices: 4120442--4120478 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4120432 AATCTAAATT
4120442 AACCATATACCCTA
1 AACCATATACCCTA
*
4120456 AATCATATACCCTA
1 AACCATATACCCTA
4120470 AACCATATA
1 AACCATATA
4120479 TATTAAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (14 bp):
AACCATATACCCTA
Found at i:4120905 original size:41 final size:41
Alignment explanation
Indices: 4120845--4121126 Score: 424
Period size: 41 Copynumber: 6.9 Consensus size: 41
4120835 CAAAAACGGA
* *
4120845 CATTAGCGGCGCTTTTTCAAAAACACCGCTAAAGGCCCGAG
1 CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAG
* *
4120886 CATTAGCAGCGCTTCTTCAAAAAAGCCGCTAAAGGCCCGAG
1 CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAG
* *
4120927 CATTAGCGGCGCTTCCTCAAAAACGCCGCTAAAGGACCGAG
1 CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAG
*
4120968 CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAA
1 CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAG
4121009 CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAG
1 CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAG
* * * *
4121050 CATTAGCGACGCTTCTT-AAAAA-ACCGTTAAAAGCCCGAG
1 CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAG
* * *
4121089 CATTAGCGACACTTCTTGAAAAACGCCGCTAAAGGCCC
1 CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
4121127 TAAAAACTCA
Statistics
Matches: 219, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 30 0.14
40 10 0.05
41 179 0.82
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (41 bp):
CATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAG
Found at i:4121212 original size:39 final size:39
Alignment explanation
Indices: 4121162--4121295 Score: 164
Period size: 40 Copynumber: 3.4 Consensus size: 39
4121152 GGGCTTAGGC
** *
4121162 TTTTTA-CGGCGTTTGTCAAAAAATGTCGCTAATGCTT-A
1 TTTTTAGCGGCGTTT-TCAAAAAGCGCCGCTAATGCTTGA
4121200 TTTTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTT-CAAAAAGCGCCGCTAATGCTTGA
** *
4121240 CCTTTAGCGGCGTTTTTATAAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTCA-AAAAGCGCCGCTAATGCTTGA
*
4121280 TTTTTAGTGGCGTTTT
1 TTTTTAGCGGCGTTTT
4121296 TTGTCCAAAC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
38 7 0.08
39 27 0.33
40 49 0.59
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTCAAAAAGCGCCGCTAATGCTTGA
Found at i:4121309 original size:41 final size:40
Alignment explanation
Indices: 4121188--4121313 Score: 136
Period size: 40 Copynumber: 3.1 Consensus size: 40
4121178 CAAAAAATGT
4121188 CGCTAATGCTT-ATTTTTAGCGGCG--TTTTCCAAAAAGCGC
1 CGCTAATGCTTGATTTTTAGCGGCGTTTTTTCC--AAAGCGC
** *
4121227 CGCTAATGCTTGACCTTTAGCGGCGTTTTTAT-AAAAGCGC
1 CGCTAATGCTTGATTTTTAGCGGCGTTTTT-TCCAAAGCGC
*
4121267 CGCTAATGCTTGATTTTTAGTGGCGTTTTTTGTCCAAA-CGC
1 CGCTAATGCTTGATTTTTAGCGGCG-TTTTT-TCCAAAGCGC
4121308 CGCTAA
1 CGCTAA
4121314 AAGCCTGTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
39 11 0.15
40 40 0.55
41 15 0.21
42 6 0.08
43 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (40 bp):
CGCTAATGCTTGATTTTTAGCGGCGTTTTTTCCAAAGCGC
Found at i:4125332 original size:30 final size:30
Alignment explanation
Indices: 4125296--4125356 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
4125286 CTTGCGAGCT
*
4125296 TCCCGTTAATAGCTATT-TGAAGCATCTCGA
1 TCCCGTTAATAGCTATTATG-AGCATCCCGA
4125326 TCCCGTTAATAGCTATTATGAGCATCCCGA
1 TCCCGTTAATAGCTATTATGAGCATCCCGA
4125356 T
1 T
4125357 ATATGGCTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (30 bp):
TCCCGTTAATAGCTATTATGAGCATCCCGA
Done.