Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 52 of 204
Found at i:17045993 original size:33 final size:33
Alignment explanation
Indices: 17045917--17046000 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
17045907 TATTTGTTAT
17045917 ATAAATAT-ATATAATATTATAATATTATAATA
1 ATAAATATAATATAATATTATAATATTATAATA
* *
17045949 ATATAAT-TAATATAATACTTAT-TTATTA-AGTAA
1 ATA-AATATAATATAATA-TTATAATATTATAAT-A
17045982 ATAAATATAATAT-ATATTA
1 ATAAATATAATATAATATTA
17046001 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
31 3 0.07
32 12 0.27
33 26 0.58
34 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (33 bp):
ATAAATATAATATAATATTATAATATTATAATA
Found at i:17047930 original size:6 final size:6
Alignment explanation
Indices: 17047921--17047953 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
17047911 GAGAAAGGAG
17047921 AAAGAA AAAGAA AAAGAA AAAGAAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAG-AA AAAGAA AA
17047954 TTGGGGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:17048832 original size:25 final size:25
Alignment explanation
Indices: 17048804--17048884 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
17048794 ACTTTAGCGC
*
17048804 GCTCTCTGATTTTTAGCACT-TCAGT
1 GCTCTCTGATTATTAGCA-TGTCAGT
* * *
17048829 GCTCTTTGATTATTAACATGTTAGT
1 GCTCTCTGATTATTAGCATGTCAGT
* *
17048854 GCTATCTGATTACTAGCATGTCAGT
1 GCTCTCTGATTATTAGCATGTCAGT
17048879 GCTCTC
1 GCTCTC
17048885 CGTTTAGCAC
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
24 1 0.02
25 44 0.98
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCATGTCAGT
Found at i:17050127 original size:5 final size:5
Alignment explanation
Indices: 17050108--17050198 Score: 64
Period size: 5 Copynumber: 18.6 Consensus size: 5
17050098 TTTTTCCGTT
* * ** *
17050108 TCTTC T-TTC -CTTC TCTTC TCTTC TCTTC TTTTT TCCCC TTTTC -CTTC
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC
* * *
17050155 TCTTC TCTTC TCCTC TTTTTC CCTTC TCCTTC TCTTC T-TTC TCT
1 TCTTC TCTTC TCTTC -TCTTC TCTTC T-CTTC TCTTC TCTTC TCT
17050199 ATTCTACTAC
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
4 13 0.20
5 43 0.67
6 8 0.12
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TCTTC
Found at i:17050151 original size:34 final size:32
Alignment explanation
Indices: 17050113--17050198 Score: 129
Period size: 34 Copynumber: 2.7 Consensus size: 32
17050103 CCGTTTCTTC
17050113 TTTCCTTCTCTTCTCTTCTCTTCTTTTTTCCCCT
1 TTTCCTTCTCTTCTCTTCTCTTC-TTTTT-CCCT
*
17050147 TTTCCTTCTCTTCTCTTCTCCTCTTTTTCCCT
1 TTTCCTTCTCTTCTCTTCTCTTCTTTTTCCCT
*
17050179 TCTCCTTCTCTTCT-TTCTCT
1 TTTCCTTCTCTTCTCTTCTCT
17050199 ATTCTACTAC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
31 5 0.10
32 17 0.35
33 5 0.10
34 22 0.45
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (32 bp):
TTTCCTTCTCTTCTCTTCTCTTCTTTTTCCCT
Found at i:17050159 original size:24 final size:26
Alignment explanation
Indices: 17050127--17050192 Score: 82
Period size: 24 Copynumber: 2.6 Consensus size: 26
17050117 CTTCTCTTCT
* *
17050127 CTTCTCTTCTTTTTTCC-CCTTTT-C
1 CTTCTCTTCTCTTCTCCTCCTTTTCC
*
17050151 CTTCTCTTCTCTTCTCCTCTTTTTCC
1 CTTCTCTTCTCTTCTCCTCCTTTTCC
17050177 CTTCTCCTTCTCTTCT
1 CTTCT-CTTCTCTTCT
17050193 TTCTCTATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 15 0.42
25 5 0.14
26 6 0.17
27 10 0.28
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (26 bp):
CTTCTCTTCTCTTCTCCTCCTTTTCC
Found at i:17052519 original size:19 final size:20
Alignment explanation
Indices: 17052486--17052524 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
17052476 ACATGTGTAA
17052486 TAATAACAAATATATGTATT
1 TAATAACAAATATATGTATT
*
17052506 TAATAATAAA-ATATGTATT
1 TAATAACAAATATATGTATT
17052525 GCTTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATAACAAATATATGTATT
Found at i:17056243 original size:16 final size:16
Alignment explanation
Indices: 17056222--17056254 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17056212 TTCGCTGTAT
17056222 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
17056238 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
17056254 T
1 T
17056255 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:17056505 original size:16 final size:16
Alignment explanation
Indices: 17056468--17056508 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
17056458 TTAATCATAT
*
17056468 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
17056484 TT-AAATATATTATAA
1 TTAAAATATATTATAA
17056499 TTAAAATATA
1 TTAAAATATA
17056509 AAATTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.14
15 10 0.45
16 9 0.41
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:17056636 original size:14 final size:15
Alignment explanation
Indices: 17056587--17056638 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
17056577 ATAAAATATA
17056587 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
17056602 TATTAAATATATTAT
1 AATTAAATATATTAT
17056617 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
17056630 AATTTAATA
1 AATTAAATA
17056639 AAATTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:17056764 original size:120 final size:120
Alignment explanation
Indices: 17056471--17056774 Score: 511
Period size: 120 Copynumber: 2.5 Consensus size: 120
17056461 ATCATATTTA
* *
17056471 AACATAATTATTATTAAATATATTATAATTAAAATATAAAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTTTTAATAATTAA
*
17056536 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
17056591 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTTTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTTTTAATAATTAA
*
17056656 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
* * * **
17056711 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTTAAAATAATTA
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTTTTAATAATTA
17056775 TAACTAATAA
Statistics
Matches: 174, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
120 172 0.99
121 2 0.01
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTTTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
Found at i:17056833 original size:26 final size:28
Alignment explanation
Indices: 17056804--17056864 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
17056794 TATGAATTTG
*
17056804 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
17056830 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
17056858 TAAAATT
1 TATAATT
17056865 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:17056862 original size:47 final size:46
Alignment explanation
Indices: 17056811--17056952 Score: 109
Period size: 45 Copynumber: 3.1 Consensus size: 46
17056801 TTGTATAATT
17056811 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
17056858 TAAAAT--TCT-TGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
17056902 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
17056949 TAAA
1 TAAA
17056953 TTTCTTAATA
Statistics
Matches: 70, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.20
46 12 0.17
47 13 0.19
48 9 0.13
49 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:17056874 original size:91 final size:90
Alignment explanation
Indices: 17056779--17056986 Score: 317
Period size: 91 Copynumber: 2.3 Consensus size: 90
17056769 TAATTATAAC
* * * *
17056779 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
17056844 AATATATAATTTCATAAAATTCTTGA
65 AATATATAATTTCATAAAATTCTTAA
17056870 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAA-TTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* *
17056935 GATATATAATTTCATAAATTTCTTAA
65 AATATATAATTTCATAAAATTCTTAA
17056961 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAAT-TTCTTATATGAATTTA
17056987 CTAAAATCAA
Statistics
Matches: 107, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
91 86 0.80
92 21 0.20
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATA
ATATATAATTTCATAAAATTCTTAA
Found at i:17056946 original size:44 final size:43
Alignment explanation
Indices: 17056804--17056946 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
17056794 TATGAATTTG
* *
17056804 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
17056848 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
17056895 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
17056939 TATAATTT
1 TATAATTT
17056947 CATAAATTTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:17060260 original size:6 final size:6
Alignment explanation
Indices: 17060249--17060274 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17060239 TAGTTTGAAC
17060249 ATTTAA ATTTAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA AT
17060275 ATAATTTCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:17060393 original size:17 final size:17
Alignment explanation
Indices: 17060359--17060397 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
17060349 ATGATTAGTT
*
17060359 TAATT-AAGATTGACCA
1 TAATTAAAGATTGAACA
*
17060375 TAATTAAAGGTTGAACA
1 TAATTAAAGATTGAACA
17060392 TAATTA
1 TAATTA
17060398 TTATTATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (17 bp):
TAATTAAAGATTGAACA
Found at i:17060400 original size:20 final size:20
Alignment explanation
Indices: 17060377--17060439 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 20
17060367 ATTGACCATA
17060377 ATTAAAGGTTGAACATAATT
1 ATTAAAGGTTGAACATAATT
* *
17060397 ATTATTA-TTTG-A-ATAATAT
1 ATTA-AAGGTTGAACATAAT-T
17060416 CAATTAAAGGTTGAACATAATT
1 --ATTAAAGGTTGAACATAATT
17060438 AT
1 AT
17060440 ATATTAGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
18 5 0.16
19 2 0.06
20 10 0.31
21 8 0.25
22 2 0.06
23 5 0.16
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (20 bp):
ATTAAAGGTTGAACATAATT
Found at i:17060793 original size:12 final size:12
Alignment explanation
Indices: 17060776--17060800 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17060766 AATATGTTTT
17060776 CATAATTTTAAC
1 CATAATTTTAAC
17060788 CATAATTTTAAC
1 CATAATTTTAAC
17060800 C
1 C
17060801 CAGATAAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (12 bp):
CATAATTTTAAC
Found at i:17066635 original size:30 final size:31
Alignment explanation
Indices: 17066576--17066637 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
17066566 TACAATCATC
*
17066576 GCTCTAACGTTGCTTTTCATTTATTTTGAGA
1 GCTCCAACGTTGCTTTTCATTTATTTTGAGA
*
17066607 GCTCCAACTTTGCTTTTCATTT-TTTTGAGA
1 GCTCCAACGTTGCTTTTCATTTATTTTGAGA
17066637 G
1 G
17066638 AGTGGAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.31
31 20 0.69
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (31 bp):
GCTCCAACGTTGCTTTTCATTTATTTTGAGA
Found at i:17083624 original size:14 final size:14
Alignment explanation
Indices: 17083599--17083632 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
17083589 ATTTTCTTGC
17083599 TTATTT-ATTTTAA
1 TTATTTAATTTTAA
17083612 TTATTTAATTTTAA
1 TTATTTAATTTTAA
17083626 TTATTTA
1 TTATTTA
17083633 TCTCTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTTAATTTTAA
Found at i:17083703 original size:16 final size:16
Alignment explanation
Indices: 17083682--17083714 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17083672 TTCGCTGTAT
17083682 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
17083698 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
17083714 T
1 T
17083715 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:17083965 original size:16 final size:16
Alignment explanation
Indices: 17083928--17083969 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
17083918 TTAATCATAT
*
17083928 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
17083944 TT-AAATATATTATAA
1 TTAAAATATATTATAA
17083959 TTAAAATATAT
1 TTAAAATATAT
17083970 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:17083976 original size:14 final size:15
Alignment explanation
Indices: 17083937--17083978 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
17083927 TTTAAACATA
*
17083937 ATTATTATTAAATAT
1 ATTATAATTAAATAT
17083952 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
17083966 A-TATAATTTAATA
1 ATTATAATTAAATA
17083979 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:17084062 original size:13 final size:12
Alignment explanation
Indices: 17084038--17084078 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
17084028 TATAATACTA
17084038 TAAAATATAATT
1 TAAAATATAATT
17084050 TAAAATAATAATT
1 TAAAAT-ATAATT
*
17084063 ATTAAATATAATT
1 -TAAAATATAATT
17084076 TAA
1 TAA
17084079 TAAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:17084333 original size:16 final size:17
Alignment explanation
Indices: 17084307--17084344 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
17084297 AGTAAATGAT
17084307 ATATAAGATAAATTAAC
1 ATATAAGATAAATTAAC
*
17084324 ATATAA-ATAATTTAAC
1 ATATAAGATAAATTAAC
*
17084340 TTATA
1 ATATA
17084345 TAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (17 bp):
ATATAAGATAAATTAAC
Found at i:17087562 original size:14 final size:14
Alignment explanation
Indices: 17087543--17087570 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17087533 AGCAGAAATC
17087543 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
17087557 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
17087571 GAAATATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:17087568 original size:19 final size:22
Alignment explanation
Indices: 17087546--17087590 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 22
17087536 AGAAATCTGG
17087546 AGAAAAGAAA-ATG-G-AGAAA
1 AGAAAAGAAATATGAGAAGAAA
17087565 AGAAAAGAAATATGAGAAGAAA
1 AGAAAAGAAATATGAGAAGAAA
17087587 AGAA
1 AGAA
17087591 GCGTACCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.43
20 3 0.13
21 1 0.04
22 9 0.39
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (22 bp):
AGAAAAGAAATATGAGAAGAAA
Found at i:17088098 original size:20 final size:20
Alignment explanation
Indices: 17088062--17088099 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17088052 AATAAGTTAT
*
17088062 TAATAATATTATTTAAATTA
1 TAATAATATTATATAAATTA
17088082 TAAT-ATATTAATATAAAT
1 TAATAATATT-ATATAAAT
17088100 ATTAAAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATAATATTATATAAATTA
Found at i:17093432 original size:19 final size:17
Alignment explanation
Indices: 17093408--17093445 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
17093398 AATTAATTAT
17093408 GAAATTAAACATAATATAA
1 GAAATTAAA-ATAATA-AA
17093427 GAAATTAAAATAATAAA
1 GAAATTAAAATAATAAA
17093444 GA
1 GA
17093446 TGATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 6 0.32
19 9 0.47
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (17 bp):
GAAATTAAAATAATAAA
Found at i:17096707 original size:18 final size:19
Alignment explanation
Indices: 17096684--17096732 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
17096674 TTATCACTTT
17096684 TATTTTAATATTA-TATTA
1 TATTTTAATATTATTATTA
*
17096702 TATTTTAA-ATTTATTTTTA
1 TATTTTAATA-TTATTATTA
*
17096721 TATTATAATATT
1 TATTTTAATATT
17096733 CTTTAATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 11 0.42
19 13 0.50
20 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTTAATATTATTATTA
Found at i:17102312 original size:17 final size:16
Alignment explanation
Indices: 17102286--17102326 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
17102276 TAATCTAATT
*
17102286 TATTTGATATATTTAAA
1 TATTTTATATA-TTAAA
17102303 TATTTTATATATTAAA
1 TATTTTATATATTAAA
17102319 TATATTTA
1 TAT-TTTA
17102327 AAAATATCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TATTTTATATATTAAA
Found at i:17102768 original size:17 final size:17
Alignment explanation
Indices: 17102731--17102773 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
17102721 CGTAGCTTTT
* *
17102731 AAAATAAAATAAAATTA
1 AAAATAAAGTAAAACTA
*
17102748 AAAATAAAGTAAAACTG
1 AAAATAAAGTAAAACTA
17102765 AAAA-AAAGT
1 AAAATAAAGT
17102774 GAGAGTGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (17 bp):
AAAATAAAGTAAAACTA
Found at i:17105876 original size:37 final size:36
Alignment explanation
Indices: 17105825--17105918 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 36
17105815 ATTCCAAAAA
*
17105825 TAATATTATTTTAATATTTTATTATTAAATTAA-ATT
1 TAATATTATCTTAATATTTT-TTATTAAATTAATATT
* *
17105861 TAATAATTATCTTAATAGTATTTTATTAATTTAATATT
1 TAAT-ATTATCTTAATA-TTTTTTATTAAATTAATATT
* *
17105899 AAAGTGATCATCTTAATATT
1 TAA-T-ATTATCTTAATATT
17105919 AAATTTAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
36 4 0.09
37 22 0.47
38 9 0.19
39 12 0.26
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (36 bp):
TAATATTATCTTAATATTTTTTATTAAATTAATATT
Found at i:17113460 original size:2 final size:2
Alignment explanation
Indices: 17113453--17113483 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17113443 ATTTATAAAC
17113453 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17113484 ATCGAACCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17114264 original size:4 final size:4
Alignment explanation
Indices: 17114250--17114362 Score: 217
Period size: 4 Copynumber: 28.0 Consensus size: 4
17114240 CTCAACAAAA
17114250 ATAC AATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC -ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
17114299 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
17114347 ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC
17114363 TAATTTAATA
Statistics
Matches: 108, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
4 104 0.96
5 4 0.04
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:17115687 original size:20 final size:20
Alignment explanation
Indices: 17115662--17115703 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
17115652 TTTAGCCATC
17115662 AACCTTTGAATAAAAGCATT
1 AACCTTTGAATAAAAGCATT
17115682 AACCTTTGAATAAAAGCATT
1 AACCTTTGAATAAAAGCATT
17115702 AA
1 AA
17115704 AAGAATTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
AACCTTTGAATAAAAGCATT
Found at i:17116022 original size:30 final size:29
Alignment explanation
Indices: 17115988--17116069 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 29
17115978 AATAAACACA
**
17115988 AAAAATTTAGAAAATTAAAAAAAGTATTTT
1 AAAAATTTTTAAAA-TAAAAAAAGTATTTT
17116018 AAAAATATTTTAAAA-ATAAAAAAGTATTTT
1 AAAAAT-TTTTAAAATA-AAAAAAGTATTTT
17116048 AAAATATTTTTAAAATAAAAAA
1 AAAA-ATTTTTAAAATAAAAAA
17116070 TATATATTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
29 1 0.02
30 36 0.78
31 9 0.20
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTTTTAAAATAAAAAAAGTATTTT
Found at i:17116026 original size:11 final size:11
Alignment explanation
Indices: 17116006--17116064 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
17115996 AGAAAATTAA
17116006 AAAAAGTATTTT
1 AAAAA-TATTTT
17116018 AAAAATATTTT
1 AAAAATATTTT
17116029 AAAAATA----
1 AAAAATATTTT
17116036 AAAAAGTATTTT
1 AAAAA-TATTTT
17116048 -AAAATATTTT
1 AAAAATATTTT
*
17116058 TAAAATA
1 AAAAATA
17116065 AAAAATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
7 5 0.12
8 2 0.05
10 6 0.15
11 23 0.56
12 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:17116038 original size:29 final size:29
Alignment explanation
Indices: 17116005--17116069 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
17115995 TAGAAAATTA
17116005 AAAAAAGTATTTTAAAAATATTTTAAAAAT
1 AAAAAAGTATTTT-AAAATATTTTAAAAAT
*
17116035 AAAAAAGTATTTTAAAATATTTTTAAAAT
1 AAAAAAGTATTTTAAAATATTTTAAAAAT
17116064 AAAAAA
1 AAAAAA
17116070 TATATATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAAAGTATTTTAAAATATTTTAAAAAT
Found at i:17121573 original size:36 final size:36
Alignment explanation
Indices: 17121533--17121604 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
17121523 ATTAGCATAT
17121533 TATTACTCCCCCTTTCTCTAATCATCCCTAATCAAA
1 TATTACTCCCCCTTTCTCTAATCATCCCTAATCAAA
17121569 TATTACTCCCCCTTTCTCTAATCATCCCTAATCAAA
1 TATTACTCCCCCTTTCTCTAATCATCCCTAATCAAA
17121605 ATCCTTCAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.36, G:0.00, T:0.36
Consensus pattern (36 bp):
TATTACTCCCCCTTTCTCTAATCATCCCTAATCAAA
Found at i:17124365 original size:15 final size:15
Alignment explanation
Indices: 17124340--17124393 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
17124330 TAAGGAAAAG
17124340 GAAAGGAAAAAGAATA
1 GAAA-GAAAAAGAATA
* *
17124356 GAAAGAAAAAAAAAA
1 GAAAGAAAAAGAATA
* *
17124371 GAATGAAAAGGAAT-
1 GAAAGAAAAAGAATA
17124385 GAAAGAAAA
1 GAAAGAAAA
17124394 GAAAATAAGG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 8 0.26
15 19 0.61
16 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (15 bp):
GAAAGAAAAAGAATA
Found at i:17131687 original size:19 final size:20
Alignment explanation
Indices: 17131651--17131692 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
17131641 TAAAATACCA
* * *
17131651 AAAAACCCAACGATCAAAGC
1 AAAAACCCAACAAACAAACC
17131671 AAAAACCCAA-AAACAAACC
1 AAAAACCCAACAAACAAACC
17131690 AAA
1 AAA
17131693 TCCGAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.64, C:0.29, G:0.05, T:0.02
Consensus pattern (20 bp):
AAAAACCCAACAAACAAACC
Found at i:17131959 original size:24 final size:23
Alignment explanation
Indices: 17131911--17131964 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
17131901 ACAAATACGT
* *
17131911 TTTCAGATACAGATTCAAATATA
1 TTTCATATACAGAATCAAATATA
* *
17131934 TTCTCATATACAGAATCAACTGTA
1 TT-TCATATACAGAATCAAATATA
17131958 TTTCATA
1 TTTCATA
17131965 ATCAGATACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (23 bp):
TTTCATATACAGAATCAAATATA
Found at i:17138899 original size:26 final size:26
Alignment explanation
Indices: 17138863--17138916 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
17138853 GGTTATCGAG
*
17138863 ATTACGTGTAAGACCATATATTGGAT
1 ATTACGTGTAAGACCATATATGGGAT
*
17138889 ATTACGTGTAAGACCATATCTGGGAT
1 ATTACGTGTAAGACCATATATGGGAT
17138915 AT
1 AT
17138917 GGTATCGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (26 bp):
ATTACGTGTAAGACCATATATGGGAT
Found at i:17138982 original size:43 final size:42
Alignment explanation
Indices: 17138893--17138987 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 42
17138883 TTGGATATTA
* **
17138893 CGTGTAAGACCATATCTGGGATATGGTATCGATATGAGACTT
1 CGTGTAAGACCATATCTGGGACATGACATCGATATGAGACTT
* * *
17138935 CGTGTAAGTCCATGTCTGGGACATTGACATCGATATGTGA-TT
1 CGTGTAAGACCATATCTGGGACA-TGACATCGATATGAGACTT
17138977 CCGTGTAAGAC
1 -CGTGTAAGAC
17138988 TATGGATGGG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
42 22 0.50
43 22 0.50
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGGACATGACATCGATATGAGACTT
Found at i:17139040 original size:43 final size:43
Alignment explanation
Indices: 17138951--17139049 Score: 101
Period size: 43 Copynumber: 2.3 Consensus size: 43
17138941 AGTCCATGTC
* * * * * * *
17138951 TGGGACATTGACATCGATATGTGATTCCGTGTAAGACTATGGA
1 TGGGATATTGGCATCGATACGAGATTACATGTAAGACTATAGA
* * *
17138994 TGGGCTATTGGCATCGATACGAGATTACATGTAGGACTATATA
1 TGGGATATTGGCATCGATACGAGATTACATGTAAGACTATAGA
17139037 TGGGATA-TGGCAT
1 TGGGATATTGGCAT
17139050 TGTTACAGTA
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
42 6 0.13
43 39 0.87
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.30
Consensus pattern (43 bp):
TGGGATATTGGCATCGATACGAGATTACATGTAAGACTATAGA
Found at i:17150032 original size:37 final size:36
Alignment explanation
Indices: 17149991--17150063 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
17149981 CTTGAAATAA
*
17149991 AATATAATT-TAATAAGAATTTAATTTTATATTATTTT
1 AATATAATTCTAA-AAGAATTAAATTTT-TATTATTTT
*
17150028 AATATAATTCTAAATGAATTAAATTTTTATTATTTT
1 AATATAATTCTAAAAGAATTAAATTTTTATTATTTT
17150064 GTAATTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 9 0.27
37 21 0.64
38 3 0.09
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (36 bp):
AATATAATTCTAAAAGAATTAAATTTTTATTATTTT
Found at i:17150648 original size:45 final size:46
Alignment explanation
Indices: 17150584--17150673 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 46
17150574 ATTGGCCACT
* *
17150584 TATAAATAATTAATAATAAATAATATGTAATTTATTTAAA-ATTAG
1 TATAAATAATTAATAATAAATAATATATAATTTAATTAAATATTAG
* *
17150629 TATAAATAATTCATAATAAATATTATATAATTTAATTAAATATTA
1 TATAAATAATTAATAATAAATAATATATAATTTAATTAAATATTA
17150674 AGTAAGCCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 36 0.90
46 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (46 bp):
TATAAATAATTAATAATAAATAATATATAATTTAATTAAATATTAG
Found at i:17153114 original size:38 final size:38
Alignment explanation
Indices: 17153008--17153119 Score: 127
Period size: 38 Copynumber: 2.9 Consensus size: 38
17152998 ACCTAGTGAG
* * *
17153008 TACATGTTAAGCGTGTCAACTGCTAGTGTTAAATTGAA
1 TACATGTTAAGCATGTTAACTGCTAGTGTTGAATTGAA
* * * *
17153046 TACATGATAAGCATGTTGATTGGC-AATGTTGAATTGAA
1 TACATGTTAAGCATGTTAACT-GCTAGTGTTGAATTGAA
* *
17153084 TACATGTTAAGCATGTTTACTACTAGTGTTGAATTG
1 TACATGTTAAGCATGTTAACTGCTAGTGTTGAATTG
17153120 TTCATAGCTT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
37 1 0.02
38 57 0.95
39 2 0.03
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (38 bp):
TACATGTTAAGCATGTTAACTGCTAGTGTTGAATTGAA
Found at i:17157884 original size:85 final size:86
Alignment explanation
Indices: 17157729--17157892 Score: 233
Period size: 85 Copynumber: 1.9 Consensus size: 86
17157719 AAGTAGCGGT
* * * * *
17157729 TCGTCCACAAAACCCAGTGGCAGTTTGTTTAATCTGCAAATATGTTGTGCACTCACAACAAGTGC
1 TCGTCCACAAAACCCAATAGCAGTTTGTTTAACCTGCAAACATGTCGTGCACTCACAACAAGTGC
*
17157794 CAGTAACTGTAAATATGTGGC
66 CAGTAACTGAAAATATGTGGC
17157815 TCGTCCA-AAAACCCAATAGCAGTTTGTTTAACCTG-AAACCATGTCGTGCACTCACAACAAGTG
1 TCGTCCACAAAACCCAATAGCAGTTTGTTTAACCTGCAAA-CATGTCGTGCACTCACAACAAGTG
**
17157878 GTAGTAACTGAAAAT
65 CCAGTAACTGAAAAT
17157893 GATTTTATCT
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
84 3 0.04
85 59 0.86
86 7 0.10
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (86 bp):
TCGTCCACAAAACCCAATAGCAGTTTGTTTAACCTGCAAACATGTCGTGCACTCACAACAAGTGC
CAGTAACTGAAAATATGTGGC
Found at i:17158116 original size:165 final size:165
Alignment explanation
Indices: 17157835--17158160 Score: 535
Period size: 165 Copynumber: 2.0 Consensus size: 165
17157825 ACCCAATAGC
* * * *
17157835 AGTTTGTTTAACCTGAAACCATGTCGTGCACTCACAACAAGTGGTAGTAACTGAAAATGATTTTA
1 AGTTTGGTTAACCTGAAACCATATCGTGCACTCACAACAAGTGGCAGGAACTGAAAATGATTTTA
* *
17157900 TCTAATATACTAGTGGTTTACCTACGTTTTTCTTTACAAAGTGGTAGTTTATCTGCAAACCAGTG
66 TCTAATATACTAGTGGTTTACCCACGTTTTTCTTTACAAAGTGGCAGTTTATCTGCAAACCAGTG
*
17157965 GTGGCTCGTCCACAATCCAGACTGATATGTTAGAT
131 GTGGCTCGTCCACAATCAAGACTGATATGTTAGAT
* * *
17158000 AGTTTGGTTAACCTGAAACCATATTGTGCACTCACAATAAGTGGCAGGAACTGCAAATGATTTTA
1 AGTTTGGTTAACCTGAAACCATATCGTGCACTCACAACAAGTGGCAGGAACTGAAAATGATTTTA
*
17158065 TCTAATATACTAGTGGTTTACCCACGTTTTTCTTTACAAAGTGGCAGTTTATCTGCAAACTAGTG
66 TCTAATATACTAGTGGTTTACCCACGTTTTTCTTTACAAAGTGGCAGTTTATCTGCAAACCAGTG
* *
17158130 GTGGCTCGTCCACAATCAAGAGTGATGTGTT
131 GTGGCTCGTCCACAATCAAGACTGATATGTT
17158161 GCGGAGTTAG
Statistics
Matches: 148, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
165 148 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (165 bp):
AGTTTGGTTAACCTGAAACCATATCGTGCACTCACAACAAGTGGCAGGAACTGAAAATGATTTTA
TCTAATATACTAGTGGTTTACCCACGTTTTTCTTTACAAAGTGGCAGTTTATCTGCAAACCAGTG
GTGGCTCGTCCACAATCAAGACTGATATGTTAGAT
Found at i:17160096 original size:38 final size:38
Alignment explanation
Indices: 17159990--17160101 Score: 127
Period size: 38 Copynumber: 2.9 Consensus size: 38
17159980 ACCTAGTGAG
* * *
17159990 TACATGTTAAGCGTGTCAACTGCTAGTGTTAAATTGAA
1 TACATGTTAAGCATGTTAACTGCTAGTGTTGAATTGAA
* * * *
17160028 TACATGATAAGCATGTTGATTGGC-AATGTTGAATTGAA
1 TACATGTTAAGCATGTTAACT-GCTAGTGTTGAATTGAA
* *
17160066 TACATGTTAAGCATGTTTACTACTAGTGTTGAATTG
1 TACATGTTAAGCATGTTAACTGCTAGTGTTGAATTG
17160102 TTCATAGCTT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
37 1 0.02
38 57 0.95
39 2 0.03
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (38 bp):
TACATGTTAAGCATGTTAACTGCTAGTGTTGAATTGAA
Found at i:17161313 original size:22 final size:22
Alignment explanation
Indices: 17161288--17161330 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17161278 TCTTTAAATC
*
17161288 TCAAA-GAGTAAGTGGATATTTT
1 TCAAATGAGAAAGT-GATATTTT
17161310 TCAAATGAGAAAGTGATATTT
1 TCAAATGAGAAAGTGATATTT
17161331 CCCTAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (22 bp):
TCAAATGAGAAAGTGATATTTT
Found at i:17161868 original size:4 final size:4
Alignment explanation
Indices: 17161859--17161886 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
17161849 TTTTACCTAC
17161859 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
17161887 TGTGAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:17180942 original size:86 final size:84
Alignment explanation
Indices: 17180791--17180955 Score: 240
Period size: 86 Copynumber: 1.9 Consensus size: 84
17180781 CACATGCATA
* * * **
17180791 AGGTTGAGTTCTTACTCTTAATGAATTCATAGCCAGGGTTTGGATGGTCCTGTTGAGACAGACTT
1 AGGTTGAGTTATTACTCTTAATGAATTCATAGCCAGAGTTTGGATGATCCTACTGAGACAGACTT
17180856 GATGAATTCACTGACATGT
66 GATGAATTCACTGACATGT
* * *
17180875 AGGTTGAGTTTATTACTCTTAATGAGTTCATATCTCAGAGTTTGGGTGATCCTACTGAGACAGAC
1 AGGTTGAG-TTATTACTCTTAATGAATTCATAGC-CAGAGTTTGGATGATCCTACTGAGACAGAC
17180940 TTGATGAATTCACTGA
64 TTGATGAATTCACTGA
17180956 ATTTAAATTT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 8 0.11
85 22 0.31
86 41 0.58
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (84 bp):
AGGTTGAGTTATTACTCTTAATGAATTCATAGCCAGAGTTTGGATGATCCTACTGAGACAGACTT
GATGAATTCACTGACATGT
Found at i:17181456 original size:23 final size:23
Alignment explanation
Indices: 17181411--17181456 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
17181401 TATTTTTAGC
*
17181411 AGTTACAAACCATTATTTCCAAT
1 AGTTACAAACCATTATTTACAAT
*
17181434 AGTTACAAACTATT-TCTTACAAT
1 AGTTACAAACCATTAT-TTACAAT
17181457 TACAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (23 bp):
AGTTACAAACCATTATTTACAAT
Found at i:17204495 original size:17 final size:17
Alignment explanation
Indices: 17204473--17204514 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
17204463 TCGGTAATAT
17204473 TATTATTAATCTATTAG
1 TATTATTAATCTATTAG
* *
17204490 TATTATTAATTTATTAT
1 TATTATTAATCTATTAG
17204507 TATTATTA
1 TATTATTA
17204515 TCACCGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTATTAATCTATTAG
Found at i:17204495 original size:20 final size:20
Alignment explanation
Indices: 17204470--17204515 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
17204460 TATTCGGTAA
17204470 TATTATT-ATTAATCTATTAG
1 TATTATTAATTAAT-TATTAG
* *
17204490 TATTATTAATTTATTATTAT
1 TATTATTAATTAATTATTAG
17204510 TATTAT
1 TATTAT
17204516 CACCGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTATTAATTAATTATTAG
Found at i:17211674 original size:131 final size:131
Alignment explanation
Indices: 17211405--17211693 Score: 354
Period size: 131 Copynumber: 2.2 Consensus size: 131
17211395 AAATCACAAG
* * *
17211405 TCCTATGTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAG
1 TCCTATCTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTATCTCCCCAAGCAGTAG
* * *
17211470 CGAAGCAAATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACTA
66 CGAAACAAATCGAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTGAAGCCACTA
*
17211535 G
131 A
* * * *
17211536 TCATATCTCCCTGGTCAGCAGTGG-GATAGGTT-GAAGATTACGGATCTTATCTCCCCCCAGGAG
1 TCCTATCTCCCTGGTCAGCAGTGGAG-TAGGTTGGAA-ATTACAGATCTTATCT-CCCCAAGCAG
* * * *
17211599 TAGGGAAACAGATCTAAG-CGGCAAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTGAAGCTG
63 TAGCGAAACAAATCGAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTGAAGC-C
17211663 A-TAA
127 ACTAA
17211667 TCCTATCTCCCTGAAGT-AGCAGTGGAG
1 TCCTATCTCCCTG--GTCAGCAGTGGAG
17211694 CGGATTAAAA
Statistics
Matches: 135, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
130 4 0.03
131 98 0.73
132 30 0.22
133 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (131 bp):
TCCTATCTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTATCTCCCCAAGCAGTAG
CGAAACAAATCGAAGACGGCAAATCTTATCTTCCCCAGGAGTAGGGAAACAGATTGAAGCCACTA
A
Found at i:17211862 original size:44 final size:44
Alignment explanation
Indices: 17211709--17212135 Score: 186
Period size: 44 Copynumber: 9.8 Consensus size: 44
17211699 TAAAATAAAG
* * * * *
17211709 GATCTTATCTCTCTGA-AGTTACAATAGAGTAGATCGCA-TCA-A
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGTCAGA
* * * ***
17211751 G-TCTTATCTCCCTGAGGTTACAGTGGAGTAGAACGAAGAATTTTA
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG--TCAGA
* * * *
17211796 GATCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAGA
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGTCAGA
* * *
17211840 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-C
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGTCAGA
* * * * ** * * *
17211883 TATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAATAAAA
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGTCAGA
* * * *
17211927 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCA-TCAG-
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGTCAGA
* * * *
17211969 G-TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAG-
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG----TCAGA
* * * *
17212015 G-TCTTATCTCCCTAAGCAGTA-A-TGGAGCAGATCGAGGAT-ACCA
1 GATCTTATCTCCCTGAG-ATTACAGTGGAGCAGATCGAAG-TCA-GA
* * * * *
17212058 -ATCTTATTTCTCTAAGATTACAGCGGAGCAGATAGAAG-CAAGA
1 GATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGTC-AGA
* * * *
17212101 AATCTTATTTCCCTGA-AGTTGCAGTGGAGCGGATC
1 GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATC
17212136 AAAATGATGG
Statistics
Matches: 291, Mismatches: 70, Indels: 46
0.71 0.17 0.11
Matches are distributed among these distances:
41 61 0.21
42 6 0.02
43 51 0.18
44 105 0.36
45 14 0.05
46 52 0.18
47 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
GATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGTCAGA
Found at i:17211910 original size:218 final size:217
Alignment explanation
Indices: 17211665--17212194 Score: 658
Period size: 218 Copynumber: 2.4 Consensus size: 217
17211655 TGAAGCTGAT
*
17211665 AATCCTATCTCCCTG-AAGTAGCAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTT
1 AATCCTATCTCCCTGAAATTA-CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTT
*
17211729 ACAATAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGAACGAAGAATTT
65 ACAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGAACGAAGAATTT
* * * * *
17211794 TAGATCTTATCTCCCTAAG-GTTACAGTGGAGCAGATTGAAGCCA-GAGATCTTATCTCCCTGAG
130 CAGATCTTATCTCCCTAAGAG-TA-A-TGGAGCAGATCGAAGACACCA-ATCTTATCTCCCTAAG
* *
17211857 ATTACAGCGGAGCAGATCGAAG-ACA-C
191 ATTACAGCGGAGCAGATAGAAGCA-AGA
* *
17211883 TATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTA
* * *
17211948 CAGTAGAGTAGATCGCATCAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTTC
66 CAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGAACGAAGAATTTC
* * * * *
17212013 AGGTCTTATCTCCCTAAGCAGTAATGGAGCAGATCGAGGATACCAATCTTATTTCTCTAAGATTA
131 AGATCTTATCTCCCTAAG-AGTAATGGAGCAGATCGAAGACACCAATCTTATCTCCCTAAGATTA
17212078 CAGCGGAGCAGATAGAAGCAAGA
195 CAGCGGAGCAGATAGAAGCAAGA
* * * * * * * * * * *
17212101 AATCTTATTTCCCTGAAGTTGCAGTGGAGCGGATCAAAATGATGGATCTCATCCCTCTAAAGTTG
1 AATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTA
* * *
17212166 CAGTAGAGCAGATCTCATC-AGACTTATCT
66 CAGTAGAGTAGATCGCATCAAGTCTTATCT
17212195 TTAAAAGTTG
Statistics
Matches: 270, Mismatches: 36, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
217 57 0.21
218 206 0.76
219 6 0.02
220 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (217 bp):
AATCCTATCTCCCTGAAATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTA
CAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGAACGAAGAATTTC
AGATCTTATCTCCCTAAGAGTAATGGAGCAGATCGAAGACACCAATCTTATCTCCCTAAGATTAC
AGCGGAGCAGATAGAAGCAAGA
Found at i:17212616 original size:44 final size:43
Alignment explanation
Indices: 17212310--17212631 Score: 208
Period size: 44 Copynumber: 7.5 Consensus size: 43
17212300 AAACCAATCC
* * * *
17212310 TATCTCCCTGGAGGTGCAGTGGAG-TGAATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAA-TAAAATC-CAGATCT
* * * ***
17212354 TATCTCTCTGAAGTTACAGTAGAGCAG-ATCGTATCCAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAATAAAATCCAGATCT
* * * *
17212395 TATCTCCGTGAAGTTGCAGTGGAGCAGACAGAAGAAACCA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-ATAA-AATCCAGATCT
* * ** * *
17212439 TATCTCCCTGAAGGTGTAGTGGAGTGGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAATAAAATC-CAGATCT
* * * ***
17212483 TCTCTCTCTGAAGTTGCAGTAGAGCA-AATCGCATCCAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAATAAAATCCAGATCT
* * * *
17212524 TATCTCTCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-ATAA-AATCCAGATCT
* ** *
17212568 TATCTCCCTGAAGGTGCAGTGGAGTGGATTAAAATCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAATAAAATC-CAGATCT
*
17212612 TATCTCTCTGAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGT
17212632 AAAGTAGATC
Statistics
Matches: 206, Mismatches: 59, Indels: 26
0.71 0.20 0.09
Matches are distributed among these distances:
41 53 0.26
42 13 0.06
43 17 0.08
44 122 0.59
45 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGAATAAAATCCAGATCT
Found at i:17212711 original size:129 final size:129
Alignment explanation
Indices: 17212297--17212687 Score: 622
Period size: 129 Copynumber: 3.0 Consensus size: 129
17212287 GAGAAGCTAC
* *
17212297 AAGAAACCAATCCTATCTCCCTGGAGGTGCAGTGGAGTGAATTAAAACCACAGATCTTATCTCTC
1 AAGAAACCAATCCTATCTCCCTGAAGGTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTC
* * *
17212362 TGAAGTTACAGTAGAGCAGATCGTATCCAGTCTTATCTCCGTGAAGTTGCAGTGGAGCAGACAG
66 TGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAG
* *
17212426 AAGAAACCAATCCTATCTCCCTGAAGGTGTAGTGGAGTGGATTAAAACCACAGATCTTCTCTCTC
1 AAGAAACCAATCCTATCTCCCTGAAGGTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTC
* *
17212491 TGAAGTTGCAGTAGAGCAAATCGCATCCAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACAG
66 TGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAG
*
17212555 AAGAAACCAATCCTATCTCCCTGAAGGTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTC
1 AAGAAACCAATCCTATCTCCCTGAAGGTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTC
* * * * * *
17212620 TGAAGTTGCAGTAAAGTAGATCGCAT-CAGGTCTTATCCCCCTGAAGTTGCAGAGGGGCAGACTG
66 TGAAGTTGCAGTAGAGCAGATCGCATCCA-GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAG
17212684 AAGA
1 AAGA
17212688 TGGCGGATTT
Statistics
Matches: 241, Mismatches: 20, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
128 2 0.01
129 239 0.99
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (129 bp):
AAGAAACCAATCCTATCTCCCTGAAGGTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTC
TGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAG
Found at i:17214120 original size:3 final size:3
Alignment explanation
Indices: 17214114--17214158 Score: 54
Period size: 3 Copynumber: 14.0 Consensus size: 3
17214104 TATTCGGTAA
*
17214114 TAT TAT TAT TAAT CTAT TAC TAT TATT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT T-AT -TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
17214159 CACCGTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 29 0.78
4 7 0.19
5 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:17216295 original size:54 final size:54
Alignment explanation
Indices: 17216205--17216313 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
17216195 TAGATTGATG
* *
17216205 TCAACTAAATTGTGACACCAAACCGGCAAAATACTTGATATTTGTACAGATACA
1 TCAACTAAATTGTGACACCAAACCCGCAAAAGACTTGATATTTGTACAGATACA
* *
17216259 TCAACTAACTTGTGACACCAAACCCGTAAAAGACTTGATATTTGTACAGATACA
1 TCAACTAAATTGTGACACCAAACCCGCAAAAGACTTGATATTTGTACAGATACA
17216313 T
1 T
17216314 AGACCTTGGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (54 bp):
TCAACTAAATTGTGACACCAAACCCGCAAAAGACTTGATATTTGTACAGATACA
Found at i:17219231 original size:21 final size:20
Alignment explanation
Indices: 17219207--17219247 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
17219197 TTAAAATCAG
*
17219207 GTTTGGTTTGAAAAGCTGCTT
1 GTTTGGGTTGAAAAG-TGCTT
17219228 GTTTGGGTTGAAAAGTGCTT
1 GTTTGGGTTGAAAAGTGCTT
17219248 TTGAATCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.20, C:0.07, G:0.32, T:0.41
Consensus pattern (20 bp):
GTTTGGGTTGAAAAGTGCTT
Found at i:17219790 original size:19 final size:18
Alignment explanation
Indices: 17219759--17219811 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
17219749 AATTTTTTTT
*
17219759 ATTTTTTATATATTCTTTAG
1 ATTTTTTA-ATATT-TTTAA
17219779 ATTTTTTAATATTTTTAA
1 ATTTTTTAATATTTTTAA
*
17219797 AATTTTTAA-ATTTTT
1 ATTTTTTAATATTTTT
17219812 TTTAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 6 0.19
18 12 0.39
19 5 0.16
20 8 0.26
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
ATTTTTTAATATTTTTAA
Found at i:17219793 original size:9 final size:9
Alignment explanation
Indices: 17219761--17219811 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
17219751 TTTTTTTTAT
17219761 TTTTTATATA
1 TTTTTA-ATA
17219771 TTCTTTAGAT-
1 TT-TTTA-ATA
17219781 TTTTTAATA
1 TTTTTAATA
*
17219790 TTTTTAAAA
1 TTTTTAATA
17219799 TTTTTAA-A
1 TTTTTAATA
17219807 TTTTT
1 TTTTT
17219812 TTTAAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
8 8 0.22
9 19 0.51
10 4 0.11
11 6 0.16
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTAATA
Found at i:17219812 original size:9 final size:9
Alignment explanation
Indices: 17219748--17219812 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
17219738 ATTATTTTAG
17219748 AAATTTTTT
1 AAATTTTTT
**
17219757 TTATTTTTT
1 AAATTTTTT
*
17219766 ATATATTCTTT
1 A-A-ATTTTTT
*
17219777 AGATTTTTT
1 AAATTTTTT
17219786 -AATATTTTT
1 AAAT-TTTTT
*
17219795 AAAATTTTT
1 AAATTTTTT
17219804 AAATTTTTT
1 AAATTTTTT
17219813 TTAAAAATAT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
8 2 0.05
9 31 0.74
10 2 0.05
11 7 0.17
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (9 bp):
AAATTTTTT
Found at i:17219812 original size:19 final size:20
Alignment explanation
Indices: 17219779--17219818 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
17219769 TATTCTTTAG
*
17219779 ATTTTTTAA-TATTTTTAAA
1 ATTTTTAAATTATTTTTAAA
*
17219798 ATTTTTAAATTTTTTTTAAA
1 ATTTTTAAATTATTTTTAAA
17219818 A
1 A
17219819 ATATAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTAAATTATTTTTAAA
Found at i:17224637 original size:3 final size:3
Alignment explanation
Indices: 17224629--17224675 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
17224619 TTTAGTTTCC
*
17224629 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
17224676 ACCCCTTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:17230624 original size:65 final size:65
Alignment explanation
Indices: 17230517--17230647 Score: 190
Period size: 65 Copynumber: 2.0 Consensus size: 65
17230507 CAATTAATTG
* * *
17230517 AAGGTATTAACTATTCGTGTTAATTTTGAAATCTCAAACTTTTGATATAACAACATTTAAGATAA
1 AAGGTATCAACTATACGAGTTAATTTTGAAATCTCAAACTTTTGATATAACAACATTTAAGATAA
* ** * *
17230582 AAGGTATCAATTATACGAGTTAATTTTGATGTCTCAAGCTTTTGATATAACAATATTTAAGATAA
1 AAGGTATCAACTATACGAGTTAATTTTGAAATCTCAAACTTTTGATATAACAACATTTAAGATAA
17230647 A
1 A
17230648 TTTTTTTATA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (65 bp):
AAGGTATCAACTATACGAGTTAATTTTGAAATCTCAAACTTTTGATATAACAACATTTAAGATAA
Found at i:17230891 original size:22 final size:21
Alignment explanation
Indices: 17230861--17230920 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
17230851 TGGGTTGCAA
*
17230861 GTCTAGAGACATTAGCCTATAT
1 GTCTCGAGACA-TAGCCTATAT
* * *
17230883 GTCTCGAGACATATGTCTGTTT
1 GTCTCGAGACATA-GCCTATAT
17230905 GTCTCGAGACATAGCC
1 GTCTCGAGACATAGCC
17230921 CGCCAATGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (21 bp):
GTCTCGAGACATAGCCTATAT
Found at i:17233061 original size:19 final size:18
Alignment explanation
Indices: 17233041--17233081 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
17233031 ATGTCGTTAT
17233041 TTTCCAAAACATTATTCA
1 TTTCCAAAACATTATTCA
* *
17233059 TTTACAAATCATTATTCAA
1 TTTCCAAAACATTATTC-A
17233078 TTTC
1 TTTC
17233082 AGAACTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTCCAAAACATTATTCA
Found at i:17239034 original size:16 final size:17
Alignment explanation
Indices: 17239007--17239051 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
17238997 TTAATAGTTT
* *
17239007 TTAAAAGGTTAATTTAG
1 TTAAAAGATTAATTAAG
*
17239024 -TAAATGATTAATTAAG
1 TTAAAAGATTAATTAAG
17239040 TTAAAAGATTAA
1 TTAAAAGATTAA
17239052 ATAAAACAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (17 bp):
TTAAAAGATTAATTAAG
Found at i:17242735 original size:7 final size:8
Alignment explanation
Indices: 17242718--17242743 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
17242708 AAATTTTGGG
17242718 AAAAATAA
1 AAAAATAA
17242726 AAAAATAA
1 AAAAATAA
17242734 AAAAATAA
1 AAAAATAA
17242742 AA
1 AA
17242744 TGTATCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:17246393 original size:30 final size:30
Alignment explanation
Indices: 17246359--17246421 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
17246349 ACTTATTTTA
17246359 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
17246389 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
17246419 TTG
1 TTG
17246422 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:17261801 original size:41 final size:41
Alignment explanation
Indices: 17261746--17261947 Score: 237
Period size: 41 Copynumber: 4.9 Consensus size: 41
17261736 TACTGAAGTA
*
17261746 CACCGGCATGAAGCCTGCTAGACAATAAGTCTGAAATAATT
1 CACCGGCATCAAGCCTGCTAGACAATAAGTCTGAAATAATT
* *
17261787 CACCAGCATCAAGCCTGCTAGAC-ATAAAGTCTGAAGTAATT
1 CACCGGCATCAAGCCTGCTAGACAAT-AAGTCTGAAATAATT
17261828 CACCGGCATCAAGCCTGCTAGAC-ATAAAGTCTGAAAATAATT
1 CACCGGCATCAAGCCTGCTAGACAAT-AAGTCTG-AAATAATT
* * * * * *
17261870 CACCGGTATCAAGCTTGCTAGGCATTAAGCCTAAAAATAATT
1 CACCGGCATCAAGCCTGCTAGACAATAAGTCT-GAAATAATT
* * * *
17261912 CACCGGCATCAAGCCTACTAGGCATTAAGCCTGAAA
1 CACCGGCATCAAGCCTGCTAGACAATAAGTCTGAAA
17261948 ATCAATTATA
Statistics
Matches: 142, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
40 2 0.01
41 70 0.49
42 69 0.49
43 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (41 bp):
CACCGGCATCAAGCCTGCTAGACAATAAGTCTGAAATAATT
Found at i:17261882 original size:42 final size:42
Alignment explanation
Indices: 17261746--17261954 Score: 262
Period size: 42 Copynumber: 5.0 Consensus size: 42
17261736 TACTGAAGTA
*
17261746 CACCGGCATGAAGCCTGCTAGACA-ATAAGTCTG-AAATAATT
1 CACCGGCATCAAGCCTGCTAGACATA-AAGTCTGAAAATAATT
* *
17261787 CACCAGCATCAAGCCTGCTAGACATAAAGTCTG-AAGTAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAAATAATT
17261828 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAAATAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAAATAATT
* * * * * *
17261870 CACCGGTATCAAGCTTGCTAGGCATTAAGCCTAAAAATAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAAATAATT
* * * *
17261912 CACCGGCATCAAGCCTACTAGGCATTAAGCCTGAAAATCAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAAAT-AATT
17261955 ATATTCCAAT
Statistics
Matches: 150, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
41 68 0.45
42 78 0.52
43 4 0.03
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22
Consensus pattern (42 bp):
CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAAATAATT
Found at i:17262058 original size:2 final size:2
Alignment explanation
Indices: 17262053--17262099 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
17262043 ATTCAGTCAT
17262053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17262095 TA TA T
1 TA TA T
17262100 TTCTTATACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17269734 original size:103 final size:103
Alignment explanation
Indices: 17269549--17269753 Score: 306
Period size: 103 Copynumber: 2.0 Consensus size: 103
17269539 CCAGTGATTC
* *
17269549 GGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATATGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGAAACCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
* *
17269614 ACCAATCATTCTGGGAATCAGCAGTTAGCAACCCCTTG
66 ACCAATCAGTCTGGGAATCAGCACTTAGCAACCCCTTG
* * *
17269652 GGGGAATCAGCTCTTAGAAACCCCCTTT-ATATTTAAAGATACGGTGGAATCAGCACTTAGCAAC
1 GGGGAATCAGCACTTAGAAA-CCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAAC
*
17269716 CACCAATGAGTC-GAGGAATCAGCACTTAGCAACCCCTT
65 CACCAATCAGTCTG-GGAATCAGCACTTAGCAACCCCTT
17269754 CATATTCAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
102 1 0.01
103 84 0.91
104 7 0.08
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (103 bp):
GGGGAATCAGCACTTAGAAACCCCTTTCACATTCAAAGATACGGTGGAATCAGCACTTAGCAACC
ACCAATCAGTCTGGGAATCAGCACTTAGCAACCCCTTG
Found at i:17270846 original size:11 final size:12
Alignment explanation
Indices: 17270818--17270851 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
17270808 GCCCAAACGT
17270818 CGAAATTTTTGAA
1 CGAAATTTTT-AA
17270831 CGAAATTTTT-A
1 CGAAATTTTTAA
17270842 CGAAATTTTT
1 CGAAATTTTT
17270852 TCCGTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:17273241 original size:42 final size:41
Alignment explanation
Indices: 17273091--17273258 Score: 176
Period size: 42 Copynumber: 4.0 Consensus size: 41
17273081 TACTGAAGTA
* * * *
17273091 CACCGGCATGAAGCCTGCTAGACAATAAGTCT-GAAATAATT
1 CACCGGCATCAAGCCTGCTAG-CATTAAGCCTAAAAATAATT
* * *
17273132 CACCGGCATCAAGCCTGCTAGACATAAAGTCTAAAGATAATT
1 CACCGGCATCAAGCCTGCTAG-CATTAAGCCTAAAAATAATT
* * *
17273174 CACCGACATCAAGCTTGCTAGGCATTAAGCCTAAAAATAGTT
1 CACCGGCATCAAGCCTGCTA-GCATTAAGCCTAAAAATAATT
* *
17273216 CACTGGCATCAAGCCTACTATGCATTAAGCCTAAAAATCAATT
1 CACCGGCATCAAGCCTGCTA-GCATTAAGCCTAAAAAT-AATT
17273259 ATATTCCAAT
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
41 29 0.27
42 74 0.69
43 4 0.04
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (41 bp):
CACCGGCATCAAGCCTGCTAGCATTAAGCCTAAAAATAATT
Found at i:17273362 original size:2 final size:2
Alignment explanation
Indices: 17273357--17273381 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17273347 ATTCAGTCAT
17273357 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17273382 TTCTTATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17274647 original size:13 final size:13
Alignment explanation
Indices: 17274629--17274653 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17274619 TCAAACGATT
17274629 AAATTTTCACACG
1 AAATTTTCACACG
17274642 AAATTTTCACAC
1 AAATTTTCACAC
17274654 ATATAACCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:17278797 original size:19 final size:20
Alignment explanation
Indices: 17278762--17278799 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
17278752 AGAAAAAAAA
17278762 ACAACCTATAACATATATTT
1 ACAACCTATAACATATATTT
17278782 ACAA-CTAT-ACACTATATT
1 ACAACCTATAACA-TATATT
17278800 CTTTAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 10 0.59
20 4 0.24
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (20 bp):
ACAACCTATAACATATATTT
Found at i:17285450 original size:2 final size:2
Alignment explanation
Indices: 17285445--17285472 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17285435 ACAAGAAACC
17285445 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17285473 GCATATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17286742 original size:31 final size:31
Alignment explanation
Indices: 17286703--17286776 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
17286693 CTTAACATAC
**
17286703 CAATGACTTAAATAAAAACTTTTGAATAGTT
1 CAATGACTTAAATAAAAACTTTCAAATAGTT
* *
17286734 CAGTGACTTAAATGAAAACTTTCAAATAGTT
1 CAATGACTTAAATAAAAACTTTCAAATAGTT
17286765 CAATGAC-TAAAT
1 CAATGACTTAAAT
17286777 TGTAACTCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 5 0.13
31 33 0.87
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (31 bp):
CAATGACTTAAATAAAAACTTTCAAATAGTT
Found at i:17290128 original size:27 final size:27
Alignment explanation
Indices: 17290098--17290149 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
17290088 GGACATGGGT
*
17290098 TGTCACACGGTCATGCCACACACAGGA
1 TGTCACACAGTCATGCCACACACAGGA
*
17290125 TGTCACACAGTCGTGCCACACACAG
1 TGTCACACAGTCATGCCACACACAG
17290150 TCGTGTGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.35, G:0.21, T:0.15
Consensus pattern (27 bp):
TGTCACACAGTCATGCCACACACAGGA
Found at i:17298872 original size:20 final size:21
Alignment explanation
Indices: 17298849--17298905 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
17298839 GAAAAAGTAC
* *
17298849 TAAACATAACCTAA-AAACAT
1 TAAAAATAAACTAAGAAACAT
*
17298869 TAAAAATAAACTAAGACACAT
1 TAAAAATAAACTAAGAAACAT
17298890 TAAAAATAAACTAAGA
1 TAAAAATAAACTAAGA
17298906 CTCATTTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 12 0.36
21 21 0.64
ACGTcount: A:0.63, C:0.14, G:0.04, T:0.19
Consensus pattern (21 bp):
TAAAAATAAACTAAGAAACAT
Found at i:17298891 original size:21 final size:21
Alignment explanation
Indices: 17298865--17298911 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
17298855 TAACCTAAAA
17298865 ACATTAAAAATAAACTAAGAC
1 ACATTAAAAATAAACTAAGAC
17298886 ACATTAAAAATAAACTAAGAC
1 ACATTAAAAATAAACTAAGAC
*
17298907 TCATT
1 ACATT
17298912 TTACAACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.57, C:0.15, G:0.04, T:0.23
Consensus pattern (21 bp):
ACATTAAAAATAAACTAAGAC
Found at i:17300973 original size:26 final size:26
Alignment explanation
Indices: 17300942--17300994 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
17300932 ATTAATTTTC
17300942 ATTTAACTATGAAAATTAATGTGTTA
1 ATTTAACTATGAAAATTAATGTGTTA
17300968 ATTTAACTATGAAAATTAATGTGTTA
1 ATTTAACTATGAAAATTAATGTGTTA
17300994 A
1 A
17300995 GTATTATAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (26 bp):
ATTTAACTATGAAAATTAATGTGTTA
Found at i:17301764 original size:91 final size:91
Alignment explanation
Indices: 17301633--17301908 Score: 304
Period size: 91 Copynumber: 3.0 Consensus size: 91
17301623 TTTCAGAGAT
* * * * *
17301633 TTTGGCAGGTTATCGGGGGAGAATATTTAGCCTACA-GGTTTTGTACTATGCGTATCTAGCGTGT
1 TTTGGCATGTTAT-AGGGGAGAATATTTAGCCTA-AGGGTTTTGCACTATGTGCATCTAGCGTGT
* * *
17301697 TATCGGTTGTAATAACTTTTATGAACAA
64 TATCGGTTGAAATAACTCTTATGAGCAA
* * *
17301725 TTTGGCAT-TTATAGGAGGAGAACATTTAGCCTAAGGGTTTTACACTATGTGCATCTAACGTGTT
1 TTTGGCATGTTATAGG-GGAGAATATTTAGCCTAAGGGTTTTGCACTATGTGCATCTAGCGTGTT
* * *
17301789 ATTGATTGAAATAACTCTTATTAGCAA
65 ATCGGTTGAAATAACTCTTATGAGCAA
* * * * * * *
17301816 TTTGGCATGTTATCGGGGAAGAATATTTAACCTACGTGCTTTGCACTATGTGCATCTGGCGTATT
1 TTTGGCATGTTATAGGGG-AGAATATTTAGCCTAAGGGTTTTGCACTATGTGCATCTAGCGTGTT
*
17301881 ATCGGTTGAAATATCTCTTATGAGCAA
65 ATCGGTTGAAATAACTCTTATGAGCAA
17301908 T
1 T
17301909 CTAGCGTGTT
Statistics
Matches: 152, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
90 3 0.02
91 75 0.49
92 74 0.49
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (91 bp):
TTTGGCATGTTATAGGGGAGAATATTTAGCCTAAGGGTTTTGCACTATGTGCATCTAGCGTGTTA
TCGGTTGAAATAACTCTTATGAGCAA
Found at i:17301890 original size:92 final size:90
Alignment explanation
Indices: 17301633--17301923 Score: 314
Period size: 92 Copynumber: 3.2 Consensus size: 90
17301623 TTTCAGAGAT
* * * *
17301633 TTTGGCAGGTTATCGGGGGAGAATATTTAGCCTACAGGTTTTGTACTATGCGTATCTAGCGTGTT
1 TTTGGCATGTTATC-GGGGAGAATATTTAGCCTAC-GGTTTTGCACTATGTGCATCTAGCGTGTT
* * *
17301698 ATCGGTTGTAATAACTTTTATGAACAA
64 ATCGGTTGAAATAACTCTTATGAGCAA
* * * * *
17301725 TTTGGCAT-TTATAGGAGGAGAACATTTAGCCTAAGGGTTTTACACTATGTGCATCTAACGTGTT
1 TTTGGCATGTTATCGG-GGAGAATATTTAGCCT-ACGGTTTTGCACTATGTGCATCTAGCGTGTT
* * *
17301789 ATTGATTGAAATAACTCTTATTAGCAA
64 ATCGGTTGAAATAACTCTTATGAGCAA
* * * *
17301816 TTTGGCATGTTATCGGGGAAGAATATTTAACCTACGTGCTTTGCACTATGTGCATCTGGCGTATT
1 TTTGGCATGTTATCGGGG-AGAATATTTAGCCTACG-GTTTTGCACTATGTGCATCTAGCGTGTT
*
17301881 ATCGGTTGAAATATCTCTTATGAGCAA
64 ATCGGTTGAAATAACTCTTATGAGCAA
* * *
17301908 TCTAGCGTGTTATCGG
1 TTTGGCATGTTATCGG
17301924 TTGGAATAGC
Statistics
Matches: 163, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
90 2 0.01
91 76 0.47
92 85 0.52
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (90 bp):
TTTGGCATGTTATCGGGGAGAATATTTAGCCTACGGTTTTGCACTATGTGCATCTAGCGTGTTAT
CGGTTGAAATAACTCTTATGAGCAA
Found at i:17301937 original size:38 final size:38
Alignment explanation
Indices: 17301869--17301948 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
17301859 CACTATGTGC
* * *
17301869 ATCTGGCGTATTATCGGTTGAAATATCTCTTATGAGCA
1 ATCTAGCGTATTATCGGTTGAAATAGCTCTTATAAGCA
* *
17301907 ATCTAGCGTGTTATCGGTTGGAATAGCTCTTATAAGCA
1 ATCTAGCGTATTATCGGTTGAAATAGCTCTTATAAGCA
17301945 ATCT
1 ATCT
17301949 GGCACGTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (38 bp):
ATCTAGCGTATTATCGGTTGAAATAGCTCTTATAAGCA
Found at i:17301958 original size:38 final size:38
Alignment explanation
Indices: 17301879--17301960 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 38
17301869 ATCTGGCGTA
* * **
17301879 TTATCGGTTGAAATATCTCTTATGAGCAATCTAGCGTG
1 TTATCGGTTGAAATAGCTCTTATAAGCAATCTAGCACG
* *
17301917 TTATCGGTTGGAATAGCTCTTATAAGCAATCTGGCACG
1 TTATCGGTTGAAATAGCTCTTATAAGCAATCTAGCACG
17301955 TTATCG
1 TTATCG
17301961 AATGGATACC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (38 bp):
TTATCGGTTGAAATAGCTCTTATAAGCAATCTAGCACG
Found at i:17303470 original size:5 final size:5
Alignment explanation
Indices: 17303448--17303487 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
17303438 TAGATTTGCG
*
17303448 TTTAT GTTTAT TTCAT TTTAT TTTATT TTTAT TTTAT TTT
1 TTTAT -TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTT
17303488 CTACATAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
5 21 0.68
6 10 0.32
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:17303479 original size:11 final size:11
Alignment explanation
Indices: 17303448--17303487 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
17303438 TAGATTTGCG
*
17303448 TTTATGTTTAT
1 TTTATTTTTAT
*
17303459 TTCA-TTTTAT
1 TTTATTTTTAT
17303469 TTTATTTTTAT
1 TTTATTTTTAT
17303480 TTTATTTT
1 TTTATTTT
17303488 CTACATAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:17303481 original size:16 final size:15
Alignment explanation
Indices: 17303448--17303487 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
17303438 TAGATTTGCG
17303448 TTTATGTTTATTTCAT
1 TTTAT-TTTATTTCAT
*
17303464 TTTATTTTATTTTTAT
1 TTTATTTTA-TTTCAT
17303480 TTTATTTT
1 TTTATTTT
17303488 CTACATAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTATTTTATTTCAT
Found at i:17304442 original size:2 final size:2
Alignment explanation
Indices: 17304435--17304468 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
17304425 ACATACGTAC
17304435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17304469 ATTTTATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17310801 original size:100 final size:99
Alignment explanation
Indices: 17310628--17311543 Score: 991
Period size: 100 Copynumber: 9.2 Consensus size: 99
17310618 CATAGTTTGT
* * * * * * *
17310628 AATTAAAATATTGAAGCCACAATGGCGAATCTTAATCTCCTAGGCGGTGCAATGGAACAGATTGA
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTACT-TCCCAGGCGATGCAGTGGAACAGATTAA
* **
17310693 AGCCACAACGGCGAATCTCACTTCCCCGACATTGC
65 AGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * *
17310728 AATTAAAAGATTGAGGCCACAACGGCGAATCTTACCTTCCCAGGCGATGTAGTGGAACAGATTGA
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTA-CTTCCCAGGCGATGCAGTGGAACAGATTAA
* **
17310793 AGCTACAACGGTGAATCTTGCTTCTTCGACATTGC
65 AGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * *
17310828 AATTAAAAGATTGAAGCCACAATGGCAAATCTTACTTTCCCAGGCGGTGCAGTGGAACAGATTGA
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCGATGCAGTGGAACAGATTAA
* * *
17310893 AGCTACAATGGTGAATCTCGCTTCCCCGACATTGC
65 AGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * *
17310928 AATTAAAA-ATTGAAACCACAACGGCAAATCTTACTTTCCCAGGTGGTGCAGTGGAACAGATTAA
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCGATGCAGTGGAACAGATTAA
* *
17310992 AGCTACAACGACGAATCTCGCTTCCCCGACATTGC
65 AGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * * *
17311027 AATTAAAATATTGAAGCCACAACGACAAATCTTACTTTCCCAGG-TAGTGCAATGGAACAGATTA
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTCCCAGGCGA-TGCAGTGGAACAGATTA
* *
17311091 AAGCTACAATGGTGAATCTTGCTTCCCCGACATTGC
64 AAGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * * *
17311127 AATTGAAAGATTGAAGCCACAACGGCGAATCTTATTTTCCCAAGCGGTGCAGTGGAGCAGATTAA
1 AATTAAAAGATTGAAGCCACAACGGCGAATCTTA-CTTCCCAGGCGATGCAGTGGAACAGATTAA
* * *
17311192 AGCTACGACGGCGAATCTTACTTCCCCGATATTGC
65 AGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * * *
17311227 AATTAAAAATATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGC-AGTACAGTGGAGCAGATTA
1 AATT-AAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGA-TGCAGTGGAACAGATTA
* * **
17311291 AAGCTACGACGGTGAATCTTGCTTCCCCGATTTTGC
64 AAGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * * * * *
17311327 AATTTAAAAGATTGAAGCCGCAATGACGAATCTTACTTCTCTGGC-AGTGCAATGGAGCAGATTA
1 AA-TTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGA-TGCAGTGGAACAGATTA
** * *
17311391 AAGCTAGGACGGCAAATCTTGCTTCCCCGATATTGC
64 AAGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * * * *
17311427 AATTTAAAAGATTGAAACCGCAATGACGAATCTTACTTCCC-GGC-AGTGTAGTGGAACAGATTG
1 AA-TTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGA-TGCAGTGGAACAGATTA
* *
17311490 AAGCTACAACAGCGAAT-TTGTTTCCCCGACATTGC
64 AAGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
*
17311525 AGTTTAAAAAGATTGAAGC
1 A-ATT-AAAAGATTGAAGC
17311544 TATACATTGC
Statistics
Matches: 716, Mismatches: 89, Indels: 23
0.86 0.11 0.03
Matches are distributed among these distances:
98 19 0.03
99 136 0.19
100 531 0.74
101 30 0.04
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (99 bp):
AATTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAA
GCTACAACGGCGAATCTTGCTTCCCCGACATTGC
Found at i:17311197 original size:299 final size:297
Alignment explanation
Indices: 17310628--17311543 Score: 1111
Period size: 299 Copynumber: 3.1 Consensus size: 297
17310618 CATAGTTTGT
* * * * * *
17310628 AATTAAAATATTGAAGCCACAATGGCGAATCTTAATCTCCTAGGCGGTGCAATGGAACAGATTGA
1 AATTAAAATATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGGTGCAGTGGAACAGATTAA
* * * *
17310693 AGCCACAACGGCGAATCTCACTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACGGCGAAT
66 AGCTACAACGGCGAATCTCGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGACGAAT
* * * * **
17310758 CTTACCTTCCCAGGCGATGTAGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCTTCGAC
131 CTTA-CTTCCCAGGAG-TGCAATGGAACAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGAC
*
17310823 ATTGCAATTAAAAGATTGAAGCCACAATGGCAAATCTTACTTTCCCAGGCGGTGCAGTGGAACAG
194 ATTGCAATTAAAAGATTGAAGCCACAATGGCGAATCTTA-TTTCCCAGGCGGTGCAGTGGAACAG
* * *
17310888 ATTGAAGCTACAATGGTGAATCTCGCTTCCCCGACATTGC
258 ATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * *
17310928 AATTAAAA-ATTGAAACCACAACGGCAAATCTTACTTTCCCAGGTGGTGCAGTGGAACAGATTAA
1 AATTAAAATATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGGTGCAGTGGAACAGATTAA
* * *
17310992 AGCTACAACGACGAATCTCGCTTCCCCGACATTGCAATTAAAATATTGAAGCCACAACGACAAAT
66 AGCTACAACGGCGAATCTCGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGACGAAT
*
17311057 CTTACTTTCCCAGGTAGTGCAATGGAACAGATTAAAGCTACAATGGTGAATCTTGCTTCCCCGAC
131 CTTAC-TTCCCAGG-AGTGCAATGGAACAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGAC
* * * *
17311122 ATTGCAATTGAAAGATTGAAGCCACAACGGCGAATCTTATTTTCCCAAGCGGTGCAGTGGAGCAG
194 ATTGCAATTAAAAGATTGAAGCCACAATGGCGAATCTTA-TTTCCCAGGCGGTGCAGTGGAACAG
* * * *
17311187 ATTAAAGCTACGACGGCGAATCTTACTTCCCCGATATTGC
258 ATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* * * * *
17311227 AATTAAAAATATTGAAGCCGCAACGGCGAATCTTAC-TTCCCTGGCAGTACAGTGGAGCAGATTA
1 AATT-AAAATATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGGTGCAGTGGAACAGATTA
* * * ** * *
17311291 AAGCTACGACGGTGAATCTTGCTTCCCCGATTTTGCAATTTAAAAGATTGAAGCCGCAATGACGA
65 AAGCTACAACGGCGAATCTCGCTTCCCCGACATTGCAA-TTAAAAGATTGAAGCCACAACGACGA
* * * ** **
17311356 ATCTTACTTCTCTGGCAGTGCAATGGAGCAGATTAAAGCTAGGACGGCAAATCTTGCTTCCCCGA
129 ATCTTACTTCCCAGG-AGTGCAATGGAACAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGA
* * * * * * *
17311421 TATTGCAATTTAAAAGATTGAAACCGCAATGACGAATCTTACTTCCC-GGCAGTGTAGTGGAACA
193 CATTGCAA-TTAAAAGATTGAAGCCACAATGGCGAATCTTATTTCCCAGGCGGTGCAGTGGAACA
* *
17311485 GATTGAAGCTACAACAGCGAAT-TTGTTTCCCCGACATTGC
257 GATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
* *
17311525 AGTTTAAAAAGATTGAAGC
1 A-ATT-AAAATATTGAAGC
17311544 TATACATTGC
Statistics
Matches: 527, Mismatches: 82, Indels: 15
0.84 0.13 0.02
Matches are distributed among these distances:
298 17 0.03
299 302 0.57
300 129 0.24
301 79 0.15
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (297 bp):
AATTAAAATATTGAAGCCACAACGGCGAATCTTACTTTCCCAGGCGGTGCAGTGGAACAGATTAA
AGCTACAACGGCGAATCTCGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGACGAAT
CTTACTTCCCAGGAGTGCAATGGAACAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACAT
TGCAATTAAAAGATTGAAGCCACAATGGCGAATCTTATTTCCCAGGCGGTGCAGTGGAACAGATT
GAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGC
Found at i:17311290 original size:200 final size:199
Alignment explanation
Indices: 17310628--17311543 Score: 1093
Period size: 200 Copynumber: 4.6 Consensus size: 199
17310618 CATAGTTTGT
* * * *
17310628 AATTAAAATATTGAAGCCACAATGGCGAATCTTAATCTCCTAGGCGGTGCAATGGAACAGATTGA
1 AATTAAAATATTGAAGCCACAATGGCGAATCTTACT-TCCCAGGCAGTGCAGTGGAACAGATTGA
* * ** *
17310693 AGCCACAACGGCGAATCTCACTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACGGCGAAT
65 AGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCGAAT
* * * * **
17310758 CTTACCTTCCCAGGCGATGTAGTGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCTTCGAC
130 CTTACCTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGAC
17310823 ATTGC
195 ATTGC
* * *
17310828 AATTAAAAGATTGAAGCCACAATGGCAAATCTTACTTTCCCAGGCGGTGCAGTGGAACAGATTGA
1 AATTAAAATATTGAAGCCACAATGGCGAATCTTAC-TTCCCAGGCAGTGCAGTGGAACAGATTGA
* * * *
17310893 AGCTACAATGGTGAATCTCGCTTCCCCGACATTGCAATTAAAA-ATTGAAACCACAACGGCAAAT
65 AGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCGAAT
* * * *
17310957 CTTACTTTCCCAGGTGGTGCAGTGGAACAGATTAAAGCTACAACGACGAATCTCGCTTCCCCGAC
130 CTTACCTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGAC
17311022 ATTGC
195 ATTGC
* * * * * *
17311027 AATTAAAATATTGAAGCCACAACGACAAATCTTACTTTCCCAGGTAGTGCAATGGAACAGATTAA
1 AATTAAAATATTGAAGCCACAATGGCGAATCTTAC-TTCCCAGGCAGTGCAGTGGAACAGATTGA
* *
17311092 AGCTACAATGGTGAATCTTGCTTCCCCGACATTGCAATTGAAAGATTGAAGCCACAACGGCGAAT
65 AGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCGAAT
** * * * * *
17311157 CTTATTTTCCCAAGCGGTGCAGTGGAGCAGATTAAAGCTACGACGGCGAATCTTACTTCCCCGAT
130 CTTACCTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGAC
17311222 ATTGC
195 ATTGC
* * * * * *
17311227 AATTAAAAATATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCAGTACAGTGGAGCAGATTAA
1 AATT-AAAATATTGAAGCCACAATGGCGAATCTTACTTCCCAGGCAGTGCAGTGGAACAGATTGA
* ** * * *
17311292 AGCTACGACGGTGAATCTTGCTTCCCCGATTTTGCAATTTAAAAGATTGAAGCCGCAATGACGAA
65 AGCTACAACGGTGAATCTTGCTTCCCCGACATTGCAA-TTAAAAGATTGAAGCCACAACGGCGAA
* * * * * ** *
17311357 TCTTA-CTTCTCTGGCAGTGCAATGGAGCAGATTAAAGCTAGGACGGCAAATCTTGCTTCCCCGA
129 TCTTACCTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGA
*
17311421 TATTGC
194 CATTGC
* * * * *
17311427 AATTTAAAAGATTGAAACCGCAATGACGAATCTTACTTCCC-GGCAGTGTAGTGGAACAGATTGA
1 AA-TTAAAATATTGAAGCCACAATGGCGAATCTTACTTCCCAGGCAGTGCAGTGGAACAGATTGA
* * * *
17311491 AGCTACAACAGCGAAT-TTGTTTCCCCGACATTGCAGTTTAAAAAGATTGAAGC
65 AGCTACAACGGTGAATCTTGCTTCCCCGACATTGCA-ATT-AAAAGATTGAAGC
17311544 TATACATTGC
Statistics
Matches: 627, Mismatches: 82, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
198 18 0.03
199 222 0.35
200 328 0.52
201 59 0.09
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (199 bp):
AATTAAAATATTGAAGCCACAATGGCGAATCTTACTTCCCAGGCAGTGCAGTGGAACAGATTGAA
GCTACAACGGTGAATCTTGCTTCCCCGACATTGCAATTAAAAGATTGAAGCCACAACGGCGAATC
TTACCTTCCCAGGCGGTGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACA
TTGC
Found at i:17311707 original size:44 final size:43
Alignment explanation
Indices: 17311568--17311974 Score: 323
Period size: 44 Copynumber: 9.5 Consensus size: 43
17311558 ATTATATCTT
* * * * *
17311568 TGAAGTTGCAGTAGAGTAGA-TCATATCA-AGTCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACAATCTTATCTCCC
* * *
17311609 TGAAGTTGCAGTGGAGCAGACTGAAGAA--ACTATCCTATCTCCC
1 TGAAGTTGCAGTGGAGCAGA-TTAA-AATCACAATCTTATCTCCC
* *
17311652 TGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTC
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACA-ATCTTATCTCCC
* * * * *
17311696 TAAAGTTGCAGTAGAGTAGA-TCACATC-CAATCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACAATCTTATCTCCC
* *
17311737 TGAAGTTGCAGTGGAGCAGACTGAAGAA--ACTAATCCTATCTCCC
1 TGAAGTTGCAGTGGAGCAGA-TTAA-AATCAC-AATCTTATCTCCC
* * **
17311781 TGAAGTTGCAGTGAAGCGGATTAAAATCACAGATCTTATCTTTC
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACA-ATCTTATCTCCC
* * * *
17311825 TGAAGTTGCAGTAGAGCA-AATCACATC-CAATCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACAATCTTATCTCCC
* * *
17311866 TGAAGTTGCAGTGGAGCAGATTGAAGAAAC-CAATCATATCTTCC
1 TGAAGTTGCAGTGGAGCAGATT-AA-AATCACAATCTTATCTCCC
* * * * * *
17311910 TGAAGTTGCAGTGAAGCGGATTAAAATGATAGGTCTTATCTCTC
1 TGAAGTTGCAGTGGAGCAGATTAAAATCACA-ATCTTATCTCCC
**
17311954 TGAAGTTGCAGAAGAGCAGAT
1 TGAAGTTGCAGTGGAGCAGAT
17311975 CACATCAGAC
Statistics
Matches: 285, Mismatches: 61, Indels: 37
0.74 0.16 0.10
Matches are distributed among these distances:
41 75 0.26
42 14 0.05
43 53 0.19
44 143 0.50
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (43 bp):
TGAAGTTGCAGTGGAGCAGATTAAAATCACAATCTTATCTCCC
Found at i:17311747 original size:85 final size:85
Alignment explanation
Indices: 17311598--17311974 Score: 318
Period size: 85 Copynumber: 4.4 Consensus size: 85
17311588 TCATATCAAG
* * * * *
17311598 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAA-ACTATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TTAA-AATCCAATCTTATCTCCCTGAAGTTGCA
17311662 GTGGAGCGGATTAAAATCACAGA
64 GTGGAGCGGATTAAAATCACA-A
* * * * *
17311685 TCTTATCTCTCTAAAGTTGCAGTAGAGTAGA-TCACATCCAATCTTATCTCCCTGAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAATCCAATCTTATCTCCCTGAAGTTGCAGT
* *
17311749 GGAGCAGACTGAAGAA--ACTAA
66 GGAGCGGA-TTAA-AATCAC-AA
* * **
17311770 TCCTATCTCCCTGAAGTTGCAGT-GAAGCGGATTAAAATCACAGATCTTATCTTTCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTAG-AGCAGATTAAAATC-CA-ATCTTATCTCCCTGAAGTTGC
* * * * *
17311834 AGTAGAGC-AAATCACATC-CAA
63 AGTGGAGCGGATTAAAATCACAA
* * * *
17311855 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAACCAATCATATCTTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT-AA-AATCCAATCTTATCTCCCTGAAGTTGCA
* * * *
17311920 GTGAAGCGGATTAAAATGATAGG
64 GTGGAGCGGATTAAAATCACA-A
* *
17311943 TCTTATCTCTCTGAAGTTGCAGAAGAGCAGAT
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGAT
17311975 CACATCAGAC
Statistics
Matches: 230, Mismatches: 44, Indels: 31
0.75 0.14 0.10
Matches are distributed among these distances:
84 2 0.01
85 116 0.50
86 21 0.09
87 36 0.16
88 55 0.24
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (85 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAATCCAATCTTATCTCCCTGAAGTTGCAGT
GGAGCGGATTAAAATCACAA
Found at i:17311838 original size:129 final size:129
Alignment explanation
Indices: 17311553--17311980 Score: 671
Period size: 129 Copynumber: 3.3 Consensus size: 129
17311543 CTATACATTG
* * * * *
17311553 CAGATATTATATCTTTGAAGTTGCAGTAGAGTAGATCATAT-CAAGTCTTATCTCCCTGAAGTTG
1 CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAA-TCTTATCTCCCTGAAGTTG
*
17311617 CAGTGGAGCAGACTGAAGAAACT-ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCA
65 CAGTGGAGCAGACTGAAGAAACTAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCA
* *
17311681 CAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATCACATCCAATCTTATCTCCCTGAAGTTGC
1 CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGAAGTTGC
17311746 AGTGGAGCAGACTGAAGAAACTAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCA
66 AGTGGAGCAGACTGAAGAAACTAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCA
* *
17311810 CAGATCTTATCTTTCTGAAGTTGCAGTAGAGCAAATCACATCCAATCTTATCTCCCTGAAGTTGC
1 CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGAAGTTGC
* * * * *
17311875 AGTGGAGCAGATTGAAGAAACCAATCATATCTTCCTGAAGTTGCAGTGAAGCGGATTAAAATGA
66 AGTGGAGCAGACTGAAGAAACTAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCA
* * *
17311939 TAGGTCTTATCTCTCTGAAGTTGCAGAAGAGCAGATCACATC
1 CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATC
17311981 AGACTTTATG
Statistics
Matches: 278, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
128 78 0.28
129 200 0.72
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (129 bp):
CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGAAGTTGC
AGTGGAGCAGACTGAAGAAACTAATCCTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAATCA
Found at i:17313959 original size:2 final size:2
Alignment explanation
Indices: 17313952--17313994 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
17313942 AACATACGTG
17313952 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17313993 TA
1 TA
17313995 ATTTTATTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17316802 original size:39 final size:41
Alignment explanation
Indices: 17316726--17316815 Score: 139
Period size: 39 Copynumber: 2.2 Consensus size: 41
17316716 TTAAAAATAT
* *
17316726 TTATATTAAAAAACACTAATGTGAATATAATAAATATTTTA
1 TTATATTAAAAAACACTAATATAAATATAATAAATATTTTA
17316767 TTATATTAAAAAACA-TAA-ATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTAATATAAATATAATAAATATTTTA
*
17316806 TTGTATTAAA
1 TTATATTAAA
17316816 TATAATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 28 0.61
40 3 0.07
41 15 0.33
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (41 bp):
TTATATTAAAAAACACTAATATAAATATAATAAATATTTTA
Found at i:17316907 original size:23 final size:26
Alignment explanation
Indices: 17316888--17316953 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
17316878 TTTTTGAGTA
17316888 ATAAA-AT-TAAATATTATTGAATAT
1 ATAAATATATAAATATTATTGAATAT
* * *
17316912 ATAAATATATAATTATTATTTAACAT
1 ATAAATATATAAATATTATTGAATAT
* *
17316938 ATATATATATATATAT
1 ATAAATATATAAATAT
17316954 ATATATAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 5 0.15
25 2 0.06
26 27 0.79
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
ATAAATATATAAATATTATTGAATAT
Found at i:17316921 original size:2 final size:2
Alignment explanation
Indices: 17316908--17316960 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
17316898 ATATTATTGA
* * *
17316908 AT AT AT AA AT AT AT A- AT -T AT -T AT TT A- AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17316946 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
17316961 ACTAATATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
1 4 0.10
2 38 0.90
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17323431 original size:13 final size:13
Alignment explanation
Indices: 17323413--17323438 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17323403 ATTTCCCTCA
17323413 TTGGGTTAATTCG
1 TTGGGTTAATTCG
17323426 TTGGGTTAATTCG
1 TTGGGTTAATTCG
17323439 AGGGTTTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.31, T:0.46
Consensus pattern (13 bp):
TTGGGTTAATTCG
Found at i:17327968 original size:12 final size:12
Alignment explanation
Indices: 17327960--17327985 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17327950 TTTTCTAGAT
17327960 TTGTTTCTAAAG
1 TTGTTTCTAAAG
17327972 TTGTTTCTAAAG
1 TTGTTTCTAAAG
17327984 TT
1 TT
17327986 AATTCAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (12 bp):
TTGTTTCTAAAG
Found at i:17328209 original size:18 final size:17
Alignment explanation
Indices: 17328186--17328235 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
17328176 ACTAGAAATC
17328186 ATATTTTTATTGTTTTGT
1 ATATTTTTATTGTTTT-T
*
17328204 ATA-TTTTCTT-TTTTT
1 ATATTTTTATTGTTTTT
17328219 ATGATTTTTA-TGTTTTT
1 AT-ATTTTTATTGTTTTT
17328236 TATGATTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.11
16 6 0.22
17 15 0.56
18 3 0.11
ACGTcount: A:0.16, C:0.02, G:0.08, T:0.74
Consensus pattern (17 bp):
ATATTTTTATTGTTTTT
Found at i:17328236 original size:18 final size:18
Alignment explanation
Indices: 17328188--17328242 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
17328178 TAGAAATCAT
*
17328188 ATTTTTATTGTTTTGTAT-
1 ATTTTTA-TGTTTTTTATG
*
17328206 A-TTTTCT-TTTTTTATG
1 ATTTTTATGTTTTTTATG
17328222 ATTTTTATGTTTTTTATG
1 ATTTTTATGTTTTTTATG
17328240 ATT
1 ATT
17328243 AGATGACGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 7 0.23
16 2 0.06
17 9 0.29
18 13 0.42
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.73
Consensus pattern (18 bp):
ATTTTTATGTTTTTTATG
Found at i:17328397 original size:3 final size:3
Alignment explanation
Indices: 17328344--17328378 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17328334 TCTTGATTTA
17328344 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
17328379 ACTTTTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:17335008 original size:3 final size:3
Alignment explanation
Indices: 17334995--17335029 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
17334985 ATCTTGTTGC
* *
17334995 TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT CCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
17335030 CTCCTCAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:17339931 original size:24 final size:26
Alignment explanation
Indices: 17339895--17339949 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
17339885 CATATATCAC
17339895 TAAGCACAAAGTGC-AAAT-A-ACGA
1 TAAGCACAAAGTGCGAAATAATACGA
17339918 TAAGCACCAAAGTGCGAAATAATACGA
1 TAAGCA-CAAAGTGCGAAATAATACGA
17339945 TAAGC
1 TAAGC
17339950 GCGCTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.21
24 8 0.29
25 4 0.14
26 1 0.04
27 9 0.32
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.15
Consensus pattern (26 bp):
TAAGCACAAAGTGCGAAATAATACGA
Found at i:17341131 original size:13 final size:13
Alignment explanation
Indices: 17341109--17341142 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17341099 GTATTCAATT
*
17341109 CAATCCAATTACC
1 CAATCTAATTACC
17341122 CAATCTAATTACC
1 CAATCTAATTACC
*
17341135 CAACCTAA
1 CAATCTAA
17341143 CCCAATCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (13 bp):
CAATCTAATTACC
Found at i:17341270 original size:9 final size:9
Alignment explanation
Indices: 17341250--17341325 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
17341240 TGTATGAATG
*
17341250 AATTAGGTT
1 AATTCGGTT
*
17341259 AATTCGGGT
1 AATTCGGTT
17341268 AATTCGGTT
1 AATTCGGTT
17341277 AATTCGGTT
1 AATTCGGTT
*
17341286 AATTCGGGT
1 AATTCGGTT
17341295 AATTCGGTT
1 AATTCGGTT
**
17341304 AATTTAGTT
1 AATTCGGTT
17341313 AATTCGGTT
1 AATTCGGTT
17341322 AATT
1 AATT
17341326 TTTAACCAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 58 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Done.