Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008913.1 Hibiscus syriacus cultivar Beakdansim tig00112216_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 629305
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:414666 original size:30 final size:30
Alignment explanation
Indices: 414632--414712 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
414622 AGCCAGGCTA
414632 AACTCACGATATAATGCACTCAAAATAAAT
1 AACTCACGATATAATGCACTCAAAATAAAT
*
414662 AACTCACGATATAATGCACTCAAAATTAAT
1 AACTCACGATATAATGCACTCAAAATAAAT
* *
414692 AATTCACGATCTAATGCACTC
1 AACTCACGATATAATGCACTC
414713 CTTATATTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.26
Consensus pattern (30 bp):
AACTCACGATATAATGCACTCAAAATAAAT
Found at i:414682 original size:16 final size:16
Alignment explanation
Indices: 414633--414683 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
414623 GCCAGGCTAA
414633 ACTCACGATATAATGC
1 ACTCACGATATAATGC
** *
414649 ACTCAAAATA-AAT-A
1 ACTCACGATATAATGC
414663 ACTCACGATATAATGC
1 ACTCACGATATAATGC
414679 ACTCA
1 ACTCA
414684 AAATTAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 8 0.30
15 6 0.22
16 13 0.48
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.24
Consensus pattern (16 bp):
ACTCACGATATAATGC
Found at i:414878 original size:33 final size:33
Alignment explanation
Indices: 414841--414917 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
414831 CTGCATGGCA
414841 CATGCACGTCCCCAACACCCCAAAACAGGTCGC
1 CATGCACGTCCCCAACACCCCAAAACAGGTCGC
* * *
414874 CATGCACGTCCCCAGCACCCCAACACAGTTCGC
1 CATGCACGTCCCCAACACCCCAAAACAGGTCGC
414907 CATGCA-GTCCC
1 CATGCACGTCCC
414918 AGTGACCTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 5 0.12
33 36 0.88
ACGTcount: A:0.26, C:0.47, G:0.16, T:0.12
Consensus pattern (33 bp):
CATGCACGTCCCCAACACCCCAAAACAGGTCGC
Found at i:415029 original size:32 final size:31
Alignment explanation
Indices: 414947--415033 Score: 122
Period size: 30 Copynumber: 2.8 Consensus size: 31
414937 ATGCACTCCC
* *
414947 AGCGACCTTGTAGGGGTGTT-GGGAGTGCTT
1 AGCGACCTTGTAGGGGTGTTGGGGAATGCAT
414977 AGCGACCTTGTAGGGGTGTTGGGGAATGCAT
1 AGCGACCTTGTAGGGGTGTTGGGGAATGCAT
* *
415008 GGCGACCTGTGTTGGGGTGTTGGGGA
1 AGCGACCT-TGTAGGGGTGTTGGGGA
415034 CGTGCATGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.39
31 15 0.29
32 16 0.31
ACGTcount: A:0.14, C:0.13, G:0.46, T:0.28
Consensus pattern (31 bp):
AGCGACCTTGTAGGGGTGTTGGGGAATGCAT
Found at i:416648 original size:2 final size:2
Alignment explanation
Indices: 416641--416680 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
416631 TATTTTTATT
416641 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
416681 ATTTTTGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:416728 original size:37 final size:37
Alignment explanation
Indices: 416683--417072 Score: 300
Period size: 37 Copynumber: 10.6 Consensus size: 37
416673 ATAATATAAT
416683 TTTTGAAAATTTATATAATATATGGTTTTTAAAAACA
1 TTTTGAAAATTTATATAATATATGGTTTTTAAAAACA
* * *
416720 TTTCGAAAACTTATATAATATATAGTTTTTTAAAAAACA
1 TTTTGAAAATTTATATAATATAT-GGTTTTT-AAAAACA
** *
416759 TTTTGAAAATAAATATAATATGTGGTTTTTAAAAAACA
1 TTTTGAAAATTTATATAATATATGGTTTTT-AAAAACA
* * * * * * * *
416797 TTTTGCAAATATATAT-ATATAT-ATATATATATATA
1 TTTTGAAAATTTATATAATATATGGTTTTTAAAAACA
* * * * *
416832 -TAT-ATATATATATATATTATATAGTTTTT-AAAACA
1 TTTTGA-AAATTTATATAATATATGGTTTTTAAAAACA
* *
416867 TTTTGAAAACTTATATAATATATGGTTTTT-AAAATA
1 TTTTGAAAATTTATATAATATATGGTTTTTAAAAACA
* *
416903 TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
1 TTTTGAAAATTTATATAATATATGGTTTTTAAAAACA
* * *
416940 ATTTGAAAACTTATATAAT-TATAGTTTTT-AAAACA
1 TTTTGAAAATTTATATAATATATGGTTTTTAAAAACA
* * * **
416975 TTTTGAAAAATTATGTATAATATATAG-TTTTGAAAATG
1 TTTTG-AAAATT-TATATAATATATGGTTTTTAAAAACA
*
417013 TTTT-AAAATATATATATAATATATGGTTTTGAAAATA-A
1 TTTTGAAAAT-T-TATATAATATATGGTTTTTAAAA-ACA
* *
417051 TTTTTG-AAATATATATTATATA
1 -TTTTGAAAATTTATATAATATA
417073 GTTTTAAAAC
Statistics
Matches: 282, Mismatches: 54, Indels: 34
0.76 0.15 0.09
Matches are distributed among these distances:
34 11 0.04
35 22 0.08
36 79 0.28
37 83 0.29
38 53 0.19
39 34 0.12
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTGAAAATTTATATAATATATGGTTTTTAAAAACA
Found at i:416810 original size:2 final size:2
Alignment explanation
Indices: 416805--416854 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
416795 CATTTTGCAA
416805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
416847 AT -T AT AT A
1 AT AT AT AT A
416855 GTTTTTAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:416887 original size:108 final size:107
Alignment explanation
Indices: 416731--416926 Score: 281
Period size: 108 Copynumber: 1.8 Consensus size: 107
416721 TTCGAAAACT
*
416731 TATATAATATATAGTTTTTTAAAAAACATTTTGAAAATAAATATAATATGTGGTTTTTAAAAAAC
1 TATATAATATATAGTTTTTT-AAAAACATTTTGAAAATAAATATAATATATGGTTTTT--AAAAC
*
416796 ATTTTGCAAATATATATATATATATATATATATATATATATATATA
63 ATTTTGAAAATATATATA-ATATATATATATATATATATATATATA
* * *
416842 TATATATTATATAG-TTTTT-AAAACATTTTGAAAACT-TATATAATATATGGTTTTTAAAATAT
1 TATATAATATATAGTTTTTTAAAAACATTTTGAAAA-TAAATATAATATATGGTTTTTAAAACAT
416904 TTTGAAAATATATATAATATATA
65 TTTGAAAATATATATAATATATA
416927 GTTTTTAAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
105 7 0.09
106 21 0.27
108 32 0.41
109 1 0.01
110 5 0.06
111 13 0.16
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (107 bp):
TATATAATATATAGTTTTTTAAAAACATTTTGAAAATAAATATAATATATGGTTTTTAAAACATT
TTGAAAATATATATAATATATATATATATATATATATATATA
Found at i:416915 original size:72 final size:73
Alignment explanation
Indices: 416683--417122 Score: 368
Period size: 72 Copynumber: 6.0 Consensus size: 73
416673 ATAATATAAT
* * * *
416683 TTTTGAAAATTTATATAATATATGGTTTTTAAAAACATTTCGAAAACTTATATAATATATAGTTT
1 TTTTGAAAATATATATAATATATAGTTTTTAAAAACATTTTGAAAACTTATATAATATAT-GGTT
*
416748 TTTAAAAAACA
65 TTT--AAAATA
* * * * * *
416759 TTTTGAAAATAAATATAATATGTGGTTTTTAAAAAACATTTTGCAAA--TATAT-ATATAT-ATA
1 TTTTGAAAATATATATAATATATAGTTTTT-AAAAACATTTTGAAAACTTATATAATATATGGTT
* *
416820 TATATATATA
65 TTTA-AAATA
* * *
416830 TATAT-ATATATATATATATTATATAGTTTTT-AAAACATTTTGAAAACTTATATAATATATGGT
1 T-TTTGA-AAATATATATAATATATAGTTTTTAAAAACATTTTGAAAACTTATATAATATATGGT
416893 TTTTAAAATA
64 TTTTAAAATA
* *
416903 TTTTGAAAATATATATAATATATAGTTTTTAAAAACAATTTGAAAACTTATATAAT-TATAGTTT
1 TTTTGAAAATATATATAATATATAGTTTTTAAAAACATTTTGAAAACTTATATAATATATGGTTT
*
416967 TTAAAACA
66 TTAAAATA
* * ** *
416975 TTTTGAAAAATTATGTATAATATATAG-TTTTGAAAATGTTTT-AAAATATATATATAATATATG
1 TTTTG-AAAA-TATATATAATATATAGTTTTTAAAAACATTTTGAAAA-CT-TATATAATATATG
*
417038 GTTTTGAAAATAA
62 GTTTTTAAAAT-A
* ** * *
417051 TTTTTG-AAATATATAT--TATATAGTTTTAAAACAATTTTTTTTAAAA--TATATATTATATGG
1 -TTTTGAAAATATATATAATATATAGTTTTTAAA-AA-CATTTTGAAAACTTATATAATATATGG
*
417111 TTTTGAAAATA
63 TTTTTAAAATA
417122 T
1 T
417123 ATATATTATA
Statistics
Matches: 302, Mismatches: 41, Indels: 48
0.77 0.10 0.12
Matches are distributed among these distances:
70 16 0.05
71 6 0.02
72 106 0.35
73 57 0.19
74 41 0.14
75 25 0.08
76 32 0.11
77 19 0.06
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (73 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAAACATTTTGAAAACTTATATAATATATGGTTT
TTAAAATA
Found at i:417000 original size:183 final size:182
Alignment explanation
Indices: 416641--417000 Score: 481
Period size: 183 Copynumber: 2.0 Consensus size: 182
416631 TATTTTTATT
* * *
416641 TATATATATATATATATATATATATATATAGTATAATATAATTTTTGAAAATTTATATAATATAT
1 TATATATATATATATATATATATATATATAGTATAATAAAAATTTTGAAAACTTATATAATATAT
*
416706 GGTTTTTAAAAACATTTCGAAAACTTATATAATATATAGTTTTTTAAAAAACATTTTGAAAATAA
66 GGTTTTTAAAAACATTTCGAAAACTTATATAATATATAGTTTTTTAAAAAACAATTTGAAAATAA
* * *
416771 ATATAATATGTGGTTTTTAAAAAACATTTTGCAAATATATATATATATATATA
131 ATATAATATATAGTTTTT-AAAAACATTTTGAAAATATATATATATATATATA
**
416824 TATATATATATATATATATATATATTATATAGT-TTTTAAAACATTTTGAAAACTTATATAATAT
1 TATATATATATATATATATATATA-TATATAGTATAATAAAA-ATTTTGAAAACTTATATAATAT
* *
416888 ATGGTTTTT-AAAATATTTTGAAAA-TATATATAATATATAG-TTTTT-AAAAACAATTTGAAAA
64 ATGGTTTTTAAAAACATTTCGAAAACT-TATATAATATATAGTTTTTTAAAAAACAATTTGAAAA
* *
416949 CT-TATATAAT-TATAGTTTTT-AAAACATTTTGAAAA-AT-TATGTATA-ATATA
128 -TAAATATAATATATAGTTTTTAAAAACATTTTGAAAATATATATATATATATATA
416999 TA
1 TA
417001 GTTTTGAAAA
Statistics
Matches: 160, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
175 7 0.04
176 7 0.04
177 2 0.01
178 14 0.09
180 8 0.05
181 22 0.14
182 7 0.04
183 56 0.35
184 37 0.23
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (182 bp):
TATATATATATATATATATATATATATATAGTATAATAAAAATTTTGAAAACTTATATAATATAT
GGTTTTTAAAAACATTTCGAAAACTTATATAATATATAGTTTTTTAAAAAACAATTTGAAAATAA
ATATAATATATAGTTTTTAAAAACATTTTGAAAATATATATATATATATATA
Found at i:417145 original size:23 final size:23
Alignment explanation
Indices: 417087--417145 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
417077 TAAAACAATT
*
417087 TTTTTTAAAATATATATTATATGG
1 TTTTTT-ATATATATATTATATGG
**
417111 TTTTGAAAATATATATATTATATGG
1 TTTT--TTATATATATATTATATGG
417136 TTTTTTATAT
1 TTTTTTATAT
417146 TAATATATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
23 4 0.14
24 4 0.14
25 20 0.71
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (23 bp):
TTTTTTATATATATATTATATGG
Found at i:418562 original size:30 final size:29
Alignment explanation
Indices: 418482--418562 Score: 74
Period size: 30 Copynumber: 2.7 Consensus size: 29
418472 AATGACTGTG
* *
418482 GTCCTTTATATTTCTATTTTTGATATTTTA
1 GTCCTTTA-ATTTTTATTTTTGATATTTGA
* * *
418512 GTCCTTTAACCTTTTGTTTTTGCTATTTG-
1 GTCCTTTAA-TTTTTATTTTTGATATTTGA
418541 GATCCTTTACATTTTTATTTTT
1 G-TCCTTTA-ATTTTTATTTTT
418563 TTATTTATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
29 2 0.05
30 38 0.93
31 1 0.02
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.62
Consensus pattern (29 bp):
GTCCTTTAATTTTTATTTTTGATATTTGA
Found at i:419627 original size:32 final size:32
Alignment explanation
Indices: 419583--419653 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
419573 CCATTCACCA
*
419583 AATAATACATATATATAACATATA-ATAATAGT
1 AATAATACATATATAT-ACATATATATAATAAT
* *
419615 AATAATATATATATATATATATATATAATAAT
1 AATAATACATATATATACATATATATAATAAT
419647 AATAATA
1 AATAATA
419654 AGGGTAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 6 0.17
32 29 0.83
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (32 bp):
AATAATACATATATATACATATATATAATAAT
Found at i:419654 original size:12 final size:13
Alignment explanation
Indices: 419584--419654 Score: 58
Period size: 13 Copynumber: 5.3 Consensus size: 13
419574 CATTCACCAA
419584 ATAATACAT-ATAT
1 ATAATA-ATAATAT
*
419597 ATAACATATAATA-
1 ATAATA-ATAATAT
*
419610 ATAGTAATAATAT
1 ATAATAATAATAT
419623 ATATATATATATATAT
1 ATA-ATA-ATA-ATAT
419639 ATAATAATAATA-
1 ATAATAATAATAT
419651 ATAA
1 ATAA
419655 GGGTAAAAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
12 10 0.21
13 17 0.35
14 8 0.17
15 6 0.12
16 7 0.15
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (13 bp):
ATAATAATAATAT
Found at i:419702 original size:20 final size:21
Alignment explanation
Indices: 419664--419718 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
419654 AGGGTAAAAG
419664 AATAAATAAAAATATATAGTA
1 AATAAATAAAAATATATAGTA
419685 AATAAA-AATAAA-ATATAGTA
1 AATAAATAA-AAATATATAGTA
*
419705 CGATATAATAAAAA
1 -AATA-AATAAAAA
419719 ACAAAAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 10 0.34
21 12 0.41
22 5 0.17
23 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (21 bp):
AATAAATAAAAATATATAGTA
Found at i:419719 original size:22 final size:19
Alignment explanation
Indices: 419668--419719 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 19
419658 TAAAAGAATA
419668 AATAAAAATATATAGTAAAT
1 AATAAAAA-ATATAGTAAAT
*
419688 AAAAATAAAATATAGTACGATAT
1 AATAA-AAAATATAGTA--A-AT
419711 AATAAAAAA
1 AATAAAAAA
419720 CAAAAATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 12 0.46
21 3 0.12
22 5 0.19
23 6 0.23
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (19 bp):
AATAAAAAATATAGTAAAT
Found at i:419831 original size:2 final size:2
Alignment explanation
Indices: 419824--419896 Score: 53
Period size: 2 Copynumber: 37.5 Consensus size: 2
419814 ACTACAACAA
* * * *
419824 AT AT AT AT AT AT AT AT AT AC AT AT AT A- AA AT GAT A- AG GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
* * *
419865 AA AA AT AT AC AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
419897 AAATATTTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
1 3 0.05
2 52 0.91
3 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.38
Consensus pattern (2 bp):
AT
Found at i:419852 original size:45 final size:45
Alignment explanation
Indices: 419791--419900 Score: 111
Period size: 45 Copynumber: 2.5 Consensus size: 45
419781 AATAACTAAA
* *
419791 ATATATA-AAATA-AT-AAACGTATAA-CTACAACAAATATATATAT
1 ATATATATAAATATATAAAATG-ATAAGCTACAA-AAATATACATAT
* * *
419834 ATATATATACATATATAAAATGATAAGGTATAAAAATATACATAT
1 ATATATATAAATATATAAAATGATAAGCTACAAAAATATACATAT
*
419879 ATATATATATATAATATAAAAT
1 ATATATATAAAT-ATATAAAAT
419901 ATTTAAATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
43 7 0.12
44 4 0.07
45 28 0.50
46 17 0.30
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (45 bp):
ATATATATAAATATATAAAATGATAAGCTACAAAAATATACATAT
Found at i:421689 original size:106 final size:105
Alignment explanation
Indices: 421558--421904 Score: 511
Period size: 106 Copynumber: 3.3 Consensus size: 105
421548 GTATTGTTCC
* * *
421558 GAGTCCAATATCC-TCTGTCGGGAAGTTGAAATTGGTTCTGGAA-TTGGGAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTC-GTCGTGAAGTTGAAATTGGCTCT-GAAGTTGGGAAATTATTTGTTGAC
* *
421621 AGTCAGTCTCCCCTTCGCAGTGAAGTTGAGCTTGTGTTGTCTT
64 AGTCAG-CACCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTT
* *
421664 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
*
421729 TCAGCACCTCCTTCGCCGTGAAGTTGAGCTTGTGCTGTCTT
66 TCAGCACC-CCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTT
* *
421770 GAGTCCAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTAAAGTTGGGAAATTATTTGTTGATA
1 GAGTCCAATATCCTTCGTC-GTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACA
*
421834 GTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTT
65 GTCAG-CACCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTT
*
421876 GAGTCCAATATCCTTCATCGTGAAGTTGA
1 GAGTCCAATATCCTTCGTCGTGAAGTTGA
421905 GCCTTGACTT
Statistics
Matches: 220, Mismatches: 15, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
105 6 0.03
106 208 0.95
107 6 0.03
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.35
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAGTTGGGAAATTATTTGTTGACAG
TCAGCACCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTT
Found at i:430041 original size:19 final size:19
Alignment explanation
Indices: 429997--430041 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
429987 AAAAACATGG
429997 AAAATATAAAATAAAAAAC
1 AAAATATAAAATAAAAAAC
* * **
430016 AACATATAATATAAAATGC
1 AAAATATAAAATAAAAAAC
430035 AAAATAT
1 AAAATAT
430042 GCAATGTATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAATATAAAATAAAAAAC
Found at i:433397 original size:2 final size:2
Alignment explanation
Indices: 433390--433442 Score: 76
Period size: 2 Copynumber: 27.5 Consensus size: 2
433380 CAAATAATAC
433390 AT AT AT AT A- AT AGT A- AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
433430 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
433443 ATAATAATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.06
2 42 0.89
3 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:433452 original size:6 final size:7
Alignment explanation
Indices: 433383--433451 Score: 65
Period size: 6 Copynumber: 9.9 Consensus size: 7
433373 CCATCACCAA
*
433383 ATAATAC
1 ATAATAT
433390 AT-ATAT
1 ATAATAT
433396 ATAATAGT
1 ATAATA-T
433404 AATAATAT
1 -ATAATAT
433412 AT-ATAT
1 ATAATAT
433418 AT-ATAT
1 ATAATAT
433424 ATATATAT
1 ATA-ATAT
433432 ATATATAT
1 ATA-ATAT
433440 ATAATA-
1 ATAATAT
433446 ATAATA
1 ATAATA
433452 AGGGTAAAAG
Statistics
Matches: 56, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
6 23 0.41
7 10 0.18
8 17 0.30
9 6 0.11
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (7 bp):
ATAATAT
Found at i:433500 original size:20 final size:21
Alignment explanation
Indices: 433462--433516 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
433452 AGGGTAAAAG
433462 AATAAATAAAAATATATAGTA
1 AATAAATAAAAATATATAGTA
433483 AATAAA-AATAAA-ATATAGTA
1 AATAAATAA-AAATATATAGTA
*
433503 CGATATAATAAAAA
1 -AATA-AATAAAAA
433517 ATAAAAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 10 0.34
21 12 0.41
22 5 0.17
23 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (21 bp):
AATAAATAAAAATATATAGTA
Found at i:446124 original size:29 final size:29
Alignment explanation
Indices: 446089--446175 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
446079 AAACTAAATT
*
446089 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
* * *
446118 GATGTCATTGCTTACCTCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
*
446147 GATGTCATTGCTTACATCAATTTAGTTAA
1 GATGTCATTGCTTACATC-ATTTAATTAA
446176 GTGAGAGTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 42 0.84
30 8 0.16
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:447481 original size:15 final size:15
Alignment explanation
Indices: 447458--447487 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
447448 ACGAGGCTGG
447458 AATTACAACAACAAC
1 AATTACAACAACAAC
*
447473 AATTCCAACAACAAC
1 AATTACAACAACAAC
447488 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:450876 original size:29 final size:29
Alignment explanation
Indices: 450841--450922 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
450831 AAACTAAATT
* *
450841 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
450870 GATGTCATTGCTTACCTCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
450899 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
450923 GTTAGGTGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 42 0.89
30 5 0.11
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:454266 original size:20 final size:21
Alignment explanation
Indices: 454241--454333 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
454231 TTTTCCCAAT
*
454241 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
454261 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
454282 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
454302 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
454323 TCGCAATGCGA
1 TCGCAATGCGA
454334 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:454298 original size:41 final size:41
Alignment explanation
Indices: 454241--454333 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
454231 TTTTCCCAAT
454241 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
454282 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
454323 TCGCAATGCGA
1 TCGCAATGCGA
454334 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:454346 original size:41 final size:41
Alignment explanation
Indices: 454260--454394 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
454250 GAATAAGTAA
* *
454260 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
454301 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
454342 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
454383 TTCGCAACGCGA
1 ATCGCAACGCGA
454395 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:454347 original size:20 final size:20
Alignment explanation
Indices: 454322--454416 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
454312 AATTGGGAAA
*
454322 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
454342 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
454363 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
454383 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
454403 TTCGCAACGCGATA
1 ATCGCAACGCGATA
454417 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:454632 original size:22 final size:22
Alignment explanation
Indices: 454604--454647 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
454594 CACTCTCTCA
454604 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
454626 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
454648 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:454936 original size:20 final size:20
Alignment explanation
Indices: 454911--454948 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
454901 TGATTCTCTC
454911 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
454931 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
454949 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:457401 original size:20 final size:19
Alignment explanation
Indices: 457370--457430 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
457360 TCTTTTGGTT
457370 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
457389 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
457410 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
457429 GA
1 GA
457431 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:457452 original size:33 final size:33
Alignment explanation
Indices: 457395--457480 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
457385 ACGAGATAAT
*
457395 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
457429 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
*
457462 GACAATCGCAACGCGAAAT
1 GAGAATCGCAACGCGAAAT
457481 AAAAATCGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:457487 original size:19 final size:20
Alignment explanation
Indices: 457465--457508 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
457455 GCGACCAGAC
457465 AATCGCAA-CGCGAAATAAA
1 AATCGCAACCGCGAAATAAA
457484 AATCGCAACCGCGAAATAAA
1 AATCGCAACCGCGAAATAAA
457504 AATCG
1 AATCG
457509 AATGAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AATCGCAACCGCGAAATAAA
Found at i:457529 original size:30 final size:32
Alignment explanation
Indices: 457482--457543 Score: 101
Period size: 30 Copynumber: 2.0 Consensus size: 32
457472 ACGCGAAATA
457482 AAAATCGCAACCGCGAAATAAAAATCG-AATG
1 AAAATCGCAACCGCGAAATAAAAATCGCAATG
*
457513 AAAATCGCAA-CGCGAAATGAAAATCGCAATG
1 AAAATCGCAACCGCGAAATAAAAATCGCAATG
457544 CGATTTTGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.50, C:0.19, G:0.18, T:0.13
Consensus pattern (32 bp):
AAAATCGCAACCGCGAAATAAAAATCGCAATG
Found at i:457533 original size:19 final size:19
Alignment explanation
Indices: 457370--457546 Score: 93
Period size: 19 Copynumber: 10.1 Consensus size: 19
457360 TCTTTTGGTT
*
457370 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
457389 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
457409 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
457427 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
457443 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
457461 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
457476 GAAATAAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
457496 GAAAT--AAA----AA-TC
1 GAAATGAAAATCGCAACGC
457508 G-AATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
457526 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
457545 GA
1 GA
457547 TTTTGGTTTC
Statistics
Matches: 121, Mismatches: 16, Indels: 42
0.68 0.09 0.23
Matches are distributed among these distances:
11 3 0.02
12 2 0.02
13 3 0.02
14 21 0.17
15 3 0.02
16 2 0.02
17 3 0.02
18 9 0.07
19 38 0.31
20 35 0.29
21 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:458148 original size:20 final size:20
Alignment explanation
Indices: 458123--458174 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
458113 CGCTATGTAA
*
458123 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
458143 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
458163 ATCTCGTTGCGA
1 ATCGCGTTGCGA
458175 TTTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:458235 original size:41 final size:41
Alignment explanation
Indices: 458205--458297 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
458195 ATAGTCAGTA
* *
458205 TCGAATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGAATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
458246 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGAATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
*
458287 TCGCATTGCGA
1 TCGAATTGCGA
458298 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGAATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:458236 original size:21 final size:21
Alignment explanation
Indices: 458210--458280 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
458200 CAGTATCGAA
458210 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** *
458231 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCCAATTCGCG
458251 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
458272 TTGCGATTT
1 TTGCGATTT
458281 ACTTATTCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:458249 original size:20 final size:20
Alignment explanation
Indices: 458224--458297 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
458214 GATTTTCCCA
*
458224 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
458244 ATTCGCATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
458265 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
458285 ATTCGCATTGCGA
1 ATTCGCATTGCGA
458298 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:458688 original size:2 final size:2
Alignment explanation
Indices: 458681--458733 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
458671 AATATTTTTA
458681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
458723 AT AT AT AT AT A
1 AT AT AT AT AT A
458734 GTTTTGAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:458764 original size:36 final size:36
Alignment explanation
Indices: 458722--459033 Score: 288
Period size: 36 Copynumber: 8.6 Consensus size: 36
458712 TATATATATA
*
458722 TATATATATATAGTTTTGAAAACATGTTTGAAAACATT
1 TATATATATATAGTTTTTAAAACAT-TTTGAAAACA-T
458760 TATATATTATATAGTTTTTAAAACATTTTG-AAA-AT
1 TATATA-TATATAGTTTTTAAAACATTTTGAAAACAT
*
458795 TAATATAATATATAGTTTTTAAAACATTTTTGAAAATA-
1 T-ATAT-ATATATAGTTTTTAAAACA-TTTTGAAAACAT
* *
458833 TACATATTATATAGTTTTTAAAACATTTTGAAAATA-
1 TATATA-TATATAGTTTTTAAAACATTTTGAAAACAT
* *
458869 AATATAATATATAGTTTTTAAAACATTTTTAAAA-AT
1 TATAT-ATATATAGTTTTTAAAACATTTTGAAAACAT
* * *
458905 ATATATATTATATAATTTTTAAAATATTTCG-AAA-A-
1 -TATATA-TATATAGTTTTTAAAACATTTTGAAAACAT
* *
458940 TATATATAT-T--TTTTAAAAAACATTTCGAAAACAT
1 TATATATATATAGTTTT-TAAAACATTTTGAAAACAT
* *
458974 ATATATATTATATAGTTTTGAAATCATTTTGAAAAC-T
1 -TATATA-TATATAGTTTTTAAAACATTTTGAAAACAT
*
459011 TATATAATATATAGTTTTAAAAA
1 TATAT-ATATATAGTTTTTAAAA
459034 AACATTTTTG
Statistics
Matches: 236, Mismatches: 17, Indels: 44
0.79 0.06 0.15
Matches are distributed among these distances:
30 4 0.02
31 10 0.04
32 4 0.02
33 4 0.02
34 6 0.03
35 9 0.04
36 91 0.39
37 57 0.24
38 28 0.12
39 23 0.10
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (36 bp):
TATATATATATAGTTTTTAAAACATTTTGAAAACAT
Found at i:458855 original size:73 final size:73
Alignment explanation
Indices: 458720--459044 Score: 387
Period size: 73 Copynumber: 4.4 Consensus size: 73
458710 TATATATATA
* * *
458720 TATATATATATATAGTTTTGAAAACATGTTTGAAAACATTTATATATTATATAGTTTTTAAAACA
1 TATATA-ATATATAGTTTTAAAAACATTTTTG-AAACATATATATATTATATAGTTTTTAAAACA
458785 TTTTGAAAAT
64 TTTTGAAAAT
* *
458795 TAATATAATATATAGTTTTTAAAACATTTTTGAAA-ATATACATATTATATAGTTTTTAAAACAT
1 T-ATATAATATATAGTTTTAAAAACATTTTTGAAACATATATATATTATATAGTTTTTAAAACAT
458859 TTTGAAAAT
65 TTTGAAAAT
* * * * *
458868 AAATATAATATATAGTTTTTAAAACATTTTT-AAAAATATATATATTATATAATTTTTAAAATAT
1 -TATATAATATATAGTTTTAAAAACATTTTTGAAACATATATATATTATATAGTTTTTAAAACAT
*
458932 TTCGAAAA-
65 TTTGAAAAT
* * *
458940 TATAT-ATAT-T--TTTTAAAAAACA-TTTCGAAAACATATATATATTATATAGTTTTGAAATCA
1 TATATAATATATAGTTTT-AAAAACATTTTTG-AAACATATATATATTATATAGTTTTTAAAACA
459000 TTTTGAAAACT
64 TTTTGAAAA-T
459011 TATATAATATATAGTTTTAAAAAAACATTTTTGA
1 TATATAATATATAGTTTT--AAAAACATTTTTGA
459045 TTAGTGTTGA
Statistics
Matches: 217, Mismatches: 19, Indels: 27
0.83 0.07 0.10
Matches are distributed among these distances:
67 7 0.03
68 6 0.03
69 36 0.17
70 4 0.02
71 9 0.04
72 7 0.03
73 99 0.46
74 3 0.01
75 28 0.13
76 14 0.06
77 4 0.02
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (73 bp):
TATATAATATATAGTTTTAAAAACATTTTTGAAACATATATATATTATATAGTTTTTAAAACATT
TTGAAAAT
Found at i:458952 original size:29 final size:30
Alignment explanation
Indices: 458913--458979 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
458903 ATATATATAT
* * *
458913 TATATAATTTTT-AAAATATTTCGAAAATA
1 TATATATTTTTTAAAAACATTTCGAAAACA
458942 TATATATTTTTTAAAAAACATTTCGAAAACA
1 TATATATTTTTT-AAAAACATTTCGAAAACA
458973 TATATAT
1 TATATAT
458980 ATTATATAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 11 0.33
31 22 0.67
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (30 bp):
TATATATTTTTTAAAAACATTTCGAAAACA
Found at i:459040 original size:38 final size:39
Alignment explanation
Indices: 458941--459041 Score: 118
Period size: 38 Copynumber: 2.6 Consensus size: 39
458931 TTTCGAAAAT
* *
458941 ATATATATTTTTTAAAAAACATTTCGAAAACATATATATA
1 ATATATA-GTTTTAAAAAACATTTTGAAAACATATATATA
* * *
458981 TTATATAGTTTT-GAAATCATTTTGAAAAC-T-TATATA
1 ATATATAGTTTTAAAAAACATTTTGAAAACATATATATA
459017 ATATATAGTTTTAAAAAAACATTTT
1 ATATATAGTTTT-AAAAAACATTTT
459042 TGATTAGTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
36 17 0.33
37 1 0.02
38 23 0.45
39 4 0.08
40 6 0.12
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.44
Consensus pattern (39 bp):
ATATATAGTTTTAAAAAACATTTTGAAAACATATATATA
Found at i:459646 original size:3 final size:3
Alignment explanation
Indices: 459638--459681 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
459628 GTTTATTTAA
*
459638 TAT TAT TAT TAT GAT TAT TAT TAT T-T TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
459682 TGTATTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:459670 original size:14 final size:14
Alignment explanation
Indices: 459633--459681 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
459623 ATTGGGTTTA
*
459633 TTTAATATTATTAT
1 TTTATTATTATTAT
*
459647 TATGATTATTATTAT
1 T-TTATTATTATTAT
459662 TTTATTATTATTAT
1 TTTATTATTATTAT
459676 TTTATT
1 TTTATT
459682 TGTATTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTATTATTATTAT
Found at i:459687 original size:14 final size:13
Alignment explanation
Indices: 459630--459696 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 13
459620 TTTATTGGGT
* *
459630 TTATTTAATATTA
1 TTATTTTATTTTA
*
459643 TTATTATGATTATTA
1 TTATT-TTATT-TTA
459658 TTATTTTATTATTA
1 TTATTTTATT-TTA
459672 TTATTTTATTTGTA
1 TTATTTTATTT-TA
459686 TT-TATTTATTT
1 TTAT-TTTATTT
459697 ATTTATTCCC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
13 7 0.15
14 32 0.68
15 8 0.17
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:459910 original size:13 final size:13
Alignment explanation
Indices: 459892--459921 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
459882 AATCGAATGC
459892 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
459905 TTTTAATTTTTAA
1 TTTTAAATTTTAA
459918 TTTT
1 TTTT
459922 TTTCAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:461752 original size:17 final size:16
Alignment explanation
Indices: 461732--461768 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
461722 TCAATTCGTA
*
461732 TTTAATTTTTATTATTT
1 TTTAATTTTT-TAATTT
461749 TTTAATTTTTTAATTT
1 TTTAATTTTTTAATTT
461765 TTTA
1 TTTA
461769 TTACGTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTAATTTTTTAATTT
Found at i:461756 original size:8 final size:8
Alignment explanation
Indices: 461732--461768 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
461722 TCAATTCGTA
461732 TTTAATTT
1 TTTAATTT
*
461740 TTATTATTT
1 TT-TAATTT
461749 TTTAATTT
1 TTTAATTT
461757 TTTAATTT
1 TTTAATTT
461765 TTTA
1 TTTA
461769 TTACGTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTAATTT
Found at i:461790 original size:2 final size:2
Alignment explanation
Indices: 461783--461835 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
461773 GTTTTATTAT
*
461783 TA TA TA TA T- TA T- TA T- TA T- TA TA TG 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
461821 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
461836 TATTCTATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
1 4 0.09
2 41 0.91
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (2 bp):
TA
Found at i:461792 original size:12 final size:12
Alignment explanation
Indices: 461777--461873 Score: 70
Period size: 10 Copynumber: 8.6 Consensus size: 12
461767 TATTACGTTT
461777 TATTATTATATA
1 TATTATTATATA
461789 TATTATTAT-TA
1 TATTATTATATA
461800 T-TATATGTATATA
1 TAT-TAT-TATATA
461813 TA-TA-TATATA
1 TATTATTATATA
461823 TA-TA-TATATA
1 TATTATTATATA
*
461833 TATTATTCTATA
1 TATTATTATATA
*
461845 T-TTGATTAGTGTA
1 TATT-ATTA-TATA
461858 TA-TA-TATATA
1 TATTATTATATA
461868 T-TTATT
1 TATTATT
461874 TATTTTTCCC
Statistics
Matches: 70, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
10 25 0.36
11 13 0.19
12 24 0.34
13 8 0.11
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (12 bp):
TATTATTATATA
Found at i:462622 original size:37 final size:38
Alignment explanation
Indices: 462573--462945 Score: 301
Period size: 36 Copynumber: 10.1 Consensus size: 38
462563 CCTATTTTTT
* *
462573 TATATATTATATAG-TTTGAAAACATTTTTAAAAAATA
1 TATATAATATATAGTTTTTAAAACATTTTTAAAAAATA
* * * *
462610 TATATAATATATAGTTTTGAAAACATGTTTGAAAACATT
1 TATATAATATATAGTTTTTAAAACAT-TTTTAAAAAATA
* * *
462649 TATATATTATATAGTTTTTAAAACA-TTTTGAAAATTA
1 TATATAATATATAGTTTTTAAAACATTTTTAAAAAATA
* *
462686 -ATATAATATATAGTTTTTAAATCATTTTT-GAAAATA
1 TATATAATATATAGTTTTTAAAACATTTTTAAAAAATA
* * *
462722 TATATATTATATAGTTTTTAAATCA-TTTT-GAAAATA
1 TATATAATATATAGTTTTTAAAACATTTTTAAAAAATA
* * *
462758 AATATAATATATAGTTTTTTTAAA-TTTTTTAAAAATATA
1 TATATAATATATAG-TTTTTAAAACATTTTTAAAAA-ATA
* *
462797 TATATATTATATAGTTTTTAAAACA--TTTAGAAAATA
1 TATATAATATATAGTTTTTAAAACATTTTTAAAAAATA
* ** * *
462833 TATAT-A-GT-T--TTTAAAAAACATTTTGAAAACATA
1 TATATAATATATAGTTTTTAAAACATTTTTAAAAAATA
* * * * *
462866 TATATATTATATAGTTTTGAAATCA-TTTTGAAAACT-
1 TATATAATATATAGTTTTTAAAACATTTTTAAAAAATA
* * *
462902 TATATAATATATAGTTTTAAAAAAACATTTTTGAAAACTA
1 TATATAATATATAGTTTT--TAAAACATTTTTAAAAAATA
462942 TATA
1 TATA
462946 ATTTTGAAAA
Statistics
Matches: 270, Mismatches: 46, Indels: 37
0.76 0.13 0.10
Matches are distributed among these distances:
31 9 0.03
33 14 0.05
34 1 0.00
35 1 0.00
36 76 0.28
37 72 0.27
38 35 0.13
39 58 0.21
40 4 0.01
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (38 bp):
TATATAATATATAGTTTTTAAAACATTTTTAAAAAATA
Found at i:462700 original size:75 final size:75
Alignment explanation
Indices: 462571--462939 Score: 404
Period size: 73 Copynumber: 5.0 Consensus size: 75
462561 GTCCTATTTT
* * * *
462571 TTTATATATTATATAG-TTTGAAAACATTTTTAAAAAATATATATAATATATAGTTTTGAAAACA
1 TTTATATATTATATAGTTTTTAAAACA-TTTTGAAAATTA-ATATAATATATAGTTTTAAAAACA
*
462635 TGTTTGAAAACA
64 TTTTTGAAAACA
* *
462647 TTTATATATTATATAGTTTTTAAAACATTTTGAAAATTAATATAATATATAGTTTTTAAATCATT
1 TTTATATATTATATAGTTTTTAAAACATTTTGAAAATTAATATAATATATAGTTTTAAAAACATT
462712 TTTG-AAA-A
66 TTTGAAAACA
* * * ***
462720 TATATATATTATATAGTTTTTAAATCATTTTGAAAATAAATATAATATATAGTTTTTTTAA-ATT
1 TTTATATATTATATAGTTTTTAAAACATTTTGAAAATTAATATAATATATAGTTTTAAAAACATT
*
462784 TTTTAAAA-A
66 TTTGAAAACA
* *
462793 TATATATATATTATATAGTTTTTAAAACATTTAGAAAA-T-ATAT-ATAGT-T--TTTAAAAAAC
1 T-T-TATATATTATATAGTTTTTAAAACATTTTGAAAATTAATATAATA-TATAGTTTTAAAAAC
462852 A-TTTTGAAAACA
63 ATTTTTGAAAACA
* * *
462864 TATATATATTATATAGTTTTGAAATCATTTTGAAAACTT-ATATAATATATAGTTTTAAAAAAAC
1 TTTATATATTATATAGTTTTTAAAACATTTTGAAAA-TTAATATAATATATAGTTTT--AAAAAC
462928 ATTTTTGAAAAC
63 ATTTTTGAAAAC
462940 TATATAATTT
Statistics
Matches: 250, Mismatches: 27, Indels: 31
0.81 0.09 0.10
Matches are distributed among these distances:
69 31 0.12
70 13 0.05
71 9 0.04
72 14 0.06
73 66 0.26
74 6 0.02
75 59 0.24
76 33 0.13
77 19 0.08
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (75 bp):
TTTATATATTATATAGTTTTTAAAACATTTTGAAAATTAATATAATATATAGTTTTAAAAACATT
TTTGAAAACA
Found at i:462836 original size:29 final size:30
Alignment explanation
Indices: 462804--462869 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
462794 ATATATATAT
*
462804 TATATAGTTTTT-AAAACATTTAGAAAATA
1 TATATAGTTTTTAAAAACATTTAGAAAACA
*
462833 TATATAGTTTTTAAAAAACATTTTGAAAACA
1 TATATAGTTTTT-AAAAACATTTAGAAAACA
462864 TATATA
1 TATATA
462870 TATTATATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 12 0.36
31 21 0.64
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (30 bp):
TATATAGTTTTTAAAAACATTTAGAAAACA
Found at i:462931 original size:38 final size:37
Alignment explanation
Indices: 462832--462947 Score: 146
Period size: 38 Copynumber: 3.1 Consensus size: 37
462822 TTTAGAAAAT
462832 ATATATAGTTTTTAAAAAACATTTTGAAAACATATATATA
1 ATATATAG-TTTTAAAAAACATTTTGAAAAC-T-TATATA
* * *
462872 TTATATAGTTTT-GAAATCATTTTGAAAACTTATATA
1 ATATATAGTTTTAAAAAACATTTTGAAAACTTATATA
462908 ATATATAGTTTTAAAAAAACATTTTTGAAAAC-TATATA
1 ATATATAGTTTT-AAAAAACA-TTTTGAAAACTTATATA
462946 AT
1 AT
462948 TTTGAAAACA
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
36 17 0.25
37 1 0.01
38 28 0.42
39 14 0.21
40 7 0.10
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (37 bp):
ATATATAGTTTTAAAAAACATTTTGAAAACTTATATA
Found at i:462982 original size:38 final size:38
Alignment explanation
Indices: 462940--463040 Score: 109
Period size: 36 Copynumber: 2.7 Consensus size: 38
462930 TTTTGAAAAC
*
462940 TATATAATTTTGAAAACATTTTTTTAAAAA-ATGTATAA
1 TATATAATTTTGAAAA-ATTTTTTTAAAAATATATATAA
* **
462978 TATATAATTTT--AAAATATTTTTAAAAATATATATTG
1 TATATAATTTTGAAAAATTTTTTTAAAAATATATATAA
*
463014 TATATATTTTTGGAAAATATTTTTTTA
1 TATATAATTTT-GAAAA-ATTTTTTTA
463041 TATGTTATTG
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
35 12 0.23
36 18 0.35
38 11 0.21
39 3 0.06
40 8 0.15
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (38 bp):
TATATAATTTTGAAAAATTTTTTTAAAAATATATATAA
Found at i:462999 original size:36 final size:38
Alignment explanation
Indices: 462940--463038 Score: 114
Period size: 38 Copynumber: 2.6 Consensus size: 38
462930 TTTTGAAAAC
* *
462940 TATATAATTTTGAAAACATTTTTTTAAAAA-ATGTATAA
1 TATATAATTTTGAAAATA-TTTTTTAAAAATATATATAA
**
462978 TATATAATTTT-AAAATA-TTTTTAAAAATATATATTG
1 TATATAATTTTGAAAATATTTTTTAAAAATATATATAA
*
463014 TATATATTTTTGGAAAATATTTTTT
1 TATATAATTTT-GAAAATATTTTTT
463039 TATATGTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
35 10 0.19
36 15 0.29
37 5 0.10
38 17 0.33
39 5 0.10
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (38 bp):
TATATAATTTTGAAAATATTTTTTAAAAATATATATAA
Found at i:463079 original size:3 final size:3
Alignment explanation
Indices: 463071--463100 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
463061 AATTATTTAC
463071 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
463101 ATTTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:464280 original size:2 final size:2
Alignment explanation
Indices: 464275--464326 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
464265 TTTATCATTC
464275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
464317 AT AT AT -T AT A
1 AT AT AT AT AT A
464327 ATCGTTTACT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:464402 original size:11 final size:11
Alignment explanation
Indices: 464360--464479 Score: 50
Period size: 12 Copynumber: 10.4 Consensus size: 11
464350 TTGTTTTCCC
464360 TTTTATTTTA-
1 TTTTATTTTAT
*
464370 TTTGATCTTATAT
1 TTTTAT-TT-TAT
464383 TTTTATTTTTAT
1 TTTTA-TTTTAT
* **
464395 TTTCTTTTTTGG
1 TTT-TATTTTAT
*
464407 GTTTATTTAATAT
1 TTTTATTT--TAT
*
464420 TATTATTATTAT
1 TTTTATT-TTAT
*
464432 TATTATTTTAT
1 TTTTATTTTAT
*
464443 TATTA--TTA-
1 TTTTATTTTAT
464451 TTTTATTTGTATT
1 TTTTATTT-TA-T
464464 TATTTATTTTAT
1 T-TTTATTTTAT
464476 TTTT
1 TTTT
464480 TCCCCTTTGA
Statistics
Matches: 84, Mismatches: 12, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
8 4 0.05
9 3 0.04
10 6 0.07
11 20 0.24
12 26 0.31
13 16 0.19
14 9 0.11
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:464425 original size:3 final size:3
Alignment explanation
Indices: 464417--464457 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
464407 GTTTATTTAA
464417 TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
464458 TGTATTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:464463 original size:14 final size:14
Alignment explanation
Indices: 464417--464457 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
464407 GTTTATTTAA
464417 TATTATTATTATTAT
1 TATTATT-TTATTAT
464432 TATTATTTTATTAT
1 TATTATTTTATTAT
464446 TATTATTTTATT
1 TATTATTTTATT
464458 TGTATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:464467 original size:10 final size:9
Alignment explanation
Indices: 464408--464521 Score: 56
Period size: 9 Copynumber: 11.9 Consensus size: 9
464398 CTTTTTTGGG
*
464408 TTTATTTAA
1 TTTATTTTA
464417 TATTATTATTA
1 T-TTATT-TTA
464428 -TTATTATTA
1 TTTATT-TTA
464437 TTTTATTATTA
1 -TTTATT-TTA
464448 -TTATTTTA
1 TTTATTTTA
*
464456 TTTGTATTTA
1 TTTAT-TTTA
464466 TTTATTTTA
1 TTTATTTTA
**
464475 TTT-TTTCCCC
1 TTTATTT--TA
464485 TTTGATTTTA
1 TTT-ATTTTA
*
464495 TTTA-TCTA
1 TTTATTTTA
464503 TTTATTCTTA
1 TTTATT-TTA
464513 TTTTATTTT
1 -TTTATTTT
464522 TTTCCTTATA
Statistics
Matches: 83, Mismatches: 9, Indels: 25
0.71 0.08 0.21
Matches are distributed among these distances:
8 13 0.16
9 27 0.33
10 23 0.28
11 17 0.20
12 3 0.04
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (9 bp):
TTTATTTTA
Found at i:471022 original size:13 final size:12
Alignment explanation
Indices: 471004--471051 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
470994 AGGTAGGTTC
471004 TAGGTAGCTAGT
1 TAGGTAGCTAGT
* *
471016 ATAGGTAGTTAGC
1 -TAGGTAGCTAGT
*
471029 TAGGTAGGTAGCT
1 TAGGTAGCTAG-T
471042 TAGGTAGCTA
1 TAGGTAGCTA
471052 ACTAGGTATC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.27, C:0.08, G:0.33, T:0.31
Consensus pattern (12 bp):
TAGGTAGCTAGT
Found at i:471045 original size:25 final size:25
Alignment explanation
Indices: 471003--471059 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
470993 TAGGTAGGTT
* *
471003 CTAGGTAGCTAGTATAGGTAGTTAG
1 CTAGGTAGCTAGTATAGGTAGCTAA
*
471028 CTAGGTAGGTAGCT-TAGGTAGCTAA
1 CTAGGTAGCTAG-TATAGGTAGCTAA
471053 CTAGGTA
1 CTAGGTA
471060 TCTACTGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.28, C:0.11, G:0.32, T:0.30
Consensus pattern (25 bp):
CTAGGTAGCTAGTATAGGTAGCTAA
Found at i:471409 original size:30 final size:30
Alignment explanation
Indices: 471375--471463 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
471365 TGAACTAAAT
* *
471375 ATGAGCTA-AACTAAGATGTATATACATATG
1 ATGAGCTAGAA-TAAGATGCATAAACATATG
* *
471405 ATGAGGTAGGATAAGATGCATAAACATATG
1 ATGAGCTAGAATAAGATGCATAAACATATG
* * *
471435 ATAAGCTAG-ATATGAATGCATAATCATAT
1 ATGAGCTAGAATAAG-ATGCATAAACATAT
471464 AATAAGTATA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 4 0.08
30 44 0.90
31 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (30 bp):
ATGAGCTAGAATAAGATGCATAAACATATG
Found at i:478923 original size:13 final size:13
Alignment explanation
Indices: 478905--478930 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
478895 GGGACCGTTT
478905 TCTGCATTCCAGG
1 TCTGCATTCCAGG
478918 TCTGCATTCCAGG
1 TCTGCATTCCAGG
478931 CTTTTTTGTT
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:0.31, G:0.23, T:0.31
Consensus pattern (13 bp):
TCTGCATTCCAGG
Found at i:486341 original size:90 final size:90
Alignment explanation
Indices: 486188--486364 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 90
486178 CTAACTCACC
* * * *
486188 CTTTTATAGCCAAGTTATCCTAATCATATTAGGGTTTTTATTATTTTAAATTAATTAAATCTATA
1 CTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATCAAATCTATA
* *
486253 TTTAATTAATTAGAATTTAATAATT
66 TTTAATTAATTAAAATTAAATAATT
*
486278 CTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATCAAATCTATA
1 CTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATCAAATCTATA
486343 TTTAATTAATTAAAATTAAATA
66 TTTAATTAATTAAAATTAAATA
486365 TTCGGGATTA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (90 bp):
CTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATCAAATCTATA
TTTAATTAATTAAAATTAAATAATT
Found at i:490092 original size:20 final size:20
Alignment explanation
Indices: 490067--490105 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
490057 TTTGTCCTAG
*
490067 TTCATCCAGTATCGATACTA
1 TTCATCCAATATCGATACTA
490087 TTCATCCAATATCGATACT
1 TTCATCCAATATCGATACT
490106 CAGACCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.36
Consensus pattern (20 bp):
TTCATCCAATATCGATACTA
Found at i:498000 original size:312 final size:313
Alignment explanation
Indices: 497396--498022 Score: 1238
Period size: 312 Copynumber: 2.0 Consensus size: 313
497386 GAAATTCAGC
*
497396 ATGAAACAAACGACCTTAGTGATTAAGAGATTGTTGTTATCCTTGAGGTCCCGAGTTCAAGCACG
1 ATGAAACAAACGACATTAGTGATTAAGAGATTGTTGTTATCCTTGAGGTCCCGAGTTCAAGCACG
497461 TATGTAAGTGTATGAGCGTTCATTGTCAAATAGTTAAAAGTCTTTATACATATATTACCTTGTAT
66 TATGTAAGTGTATGAGCGTTCATTGTCAAATAGTTAAAAGTCTTTATACATATATTACCTTGTAT
497526 TCACCCTAAATTAAAAAAAAAACCTCAAAACTCAAAAGACAACTTCTAATTTGTCTACTATTTAA
131 TCACCCTAAATTAAAAAAAAAACCTCAAAACTCAAAAGACAACTTCTAATTTGTCTACTATTTAA
497591 ACTTACAATGATTTAAATTGTGATTAGTCAAAAAATTTGAGAACACAGACTTATCATTCTTCAGT
196 ACTTACAATGATTTAAATTGTGATTAGTCAAAAAATTTGAGAACACAGACTTATCATTCTTCAGT
497656 TCAACACTACTTGATTAAATATTTAATAAATTTTATATTTTTTAAATTTAAAT
261 TCAACACTACTTGATTAAATATTTAATAAATTTTATATTTTTTAAATTTAAAT
497709 ATGAAACAAACGACATTAGTGATTAAGAGATTGTTGTTATCCTTGAGGTCCCGAGTTCAAGCACG
1 ATGAAACAAACGACATTAGTGATTAAGAGATTGTTGTTATCCTTGAGGTCCCGAGTTCAAGCACG
497774 TATGTAAGTGTATGAGCGTTCATTGTCAAATAGTTAAAAGTCTTTATACATATATTACCTTGTAT
66 TATGTAAGTGTATGAGCGTTCATTGTCAAATAGTTAAAAGTCTTTATACATATATTACCTTGTAT
497839 TCACCCTAAATT-AAAAAAAAACCTCAAAACTCAAAAGACAACTTCTAATTTGTCTACTATTTAA
131 TCACCCTAAATTAAAAAAAAAACCTCAAAACTCAAAAGACAACTTCTAATTTGTCTACTATTTAA
497903 ACTTACAATGATTTAAATTGTGATTAGTCAAAAAATTTGAGAACACAGACTTATCATTCTTCAGT
196 ACTTACAATGATTTAAATTGTGATTAGTCAAAAAATTTGAGAACACAGACTTATCATTCTTCAGT
497968 TCAACACTACTTGATTAAATATTTAATAAATTTTATATTTTTTAAATTTAAAT
261 TCAACACTACTTGATTAAATATTTAATAAATTTTATATTTTTTAAATTTAAAT
498021 AT
1 AT
498023 TTATTTTTAC
Statistics
Matches: 313, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
312 172 0.55
313 141 0.45
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (313 bp):
ATGAAACAAACGACATTAGTGATTAAGAGATTGTTGTTATCCTTGAGGTCCCGAGTTCAAGCACG
TATGTAAGTGTATGAGCGTTCATTGTCAAATAGTTAAAAGTCTTTATACATATATTACCTTGTAT
TCACCCTAAATTAAAAAAAAAACCTCAAAACTCAAAAGACAACTTCTAATTTGTCTACTATTTAA
ACTTACAATGATTTAAATTGTGATTAGTCAAAAAATTTGAGAACACAGACTTATCATTCTTCAGT
TCAACACTACTTGATTAAATATTTAATAAATTTTATATTTTTTAAATTTAAAT
Found at i:498978 original size:2 final size:2
Alignment explanation
Indices: 498971--499000 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
498961 CCGCCCCGAT
498971 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
499001 TTTGTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:499045 original size:33 final size:34
Alignment explanation
Indices: 498987--499070 Score: 152
Period size: 33 Copynumber: 2.5 Consensus size: 34
498977 TATATATATA
*
498987 TATATATATAATATTTTGTATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
499021 TATATATATAATATTTTATA-TTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
499054 TATATATATAATATTTT
1 TATATATATAATATTTT
499071 CGGGTTCGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 30 0.61
34 19 0.39
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:499057 original size:42 final size:42
Alignment explanation
Indices: 498979--499058 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
498969 ATTATATATA
*
498979 TATATATATATATATATAATATTTTGTATTTTTTATATTAAT
1 TATATATATATATATATAATATTTTGTATTTATTATATTAAT
* *
499021 TATATATATA-ATATTTTATATTTT-TATATTAATTATAT
1 TATATATATATATATATAATATTTTGTAT-TT-ATTATAT
499059 ATATAATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 3 0.09
41 14 0.42
42 16 0.48
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (42 bp):
TATATATATATATATATAATATTTTGTATTTATTATATTAAT
Found at i:501755 original size:18 final size:18
Alignment explanation
Indices: 501732--501769 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
501722 GTCAATGCCG
*
501732 AAAACAAGAAAATAAAGC
1 AAAACAAGAAAAGAAAGC
*
501750 AAAACAAGAAGAGAAAGC
1 AAAACAAGAAAAGAAAGC
501768 AA
1 AA
501770 CACCTTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.71, C:0.11, G:0.16, T:0.03
Consensus pattern (18 bp):
AAAACAAGAAAAGAAAGC
Found at i:508918 original size:61 final size:61
Alignment explanation
Indices: 508833--508985 Score: 218
Period size: 61 Copynumber: 2.5 Consensus size: 61
508823 ACCTAAGGGA
*
508833 ACATCTTAGGGCCTG-AGAGCCTACCCAAGAAAGTTCGGGCCCACGGGGCCTACCTAAAAAC
1 ACATCTTAGGG-CTGCAGGGCCTACCCAAGAAAGTTCGGGCCCACGGGGCCTACCTAAAAAC
* * * *
508894 ACATCTTAGGGCTGCAGGGCCTACCTAAAAAAGTTCGGGGCCACGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCTGCAGGGCCTACCCAAGAAAGTTCGGGCCCACGGGGCCTACCTAAAAAC
* * *
508955 ATATCTTAGGGCCGCAGGGCCTACCCGAGAA
1 ACATCTTAGGGCTGCAGGGCCTACCCAAGAA
508986 TGATCTCAGG
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 3 0.04
61 78 0.96
ACGTcount: A:0.28, C:0.29, G:0.27, T:0.16
Consensus pattern (61 bp):
ACATCTTAGGGCTGCAGGGCCTACCCAAGAAAGTTCGGGCCCACGGGGCCTACCTAAAAAC
Found at i:508919 original size:32 final size:31
Alignment explanation
Indices: 508878--509013 Score: 114
Period size: 32 Copynumber: 4.4 Consensus size: 31
508868 CGGGCCCACG
*
508878 GGGCCTACCTAAAAACACATCTTAGGGCTGCA
1 GGGCCTACCTAAAAACA-ATCTTAGGGCCGCA
* ** * *
508910 GGGCCTACCTAAAAA-AGT-TCGGGGCCACG
1 GGGCCTACCTAAAAACAATCTTAGGGCCGCA
*
508939 GGGCCTACCTAAGAACATATCTTAGGGCCGCA
1 GGGCCTACCTAAAAACA-ATCTTAGGGCCGCA
** * ** *
508971 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAAAACAATCTTAGGGCCGCA
*
509002 GAGCCTACCTAA
1 GGGCCTACCTAA
509014 GAGTCACATT
Statistics
Matches: 81, Mismatches: 20, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
29 20 0.25
30 2 0.02
31 24 0.30
32 35 0.43
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAAAACAATCTTAGGGCCGCA
Found at i:508944 original size:29 final size:29
Alignment explanation
Indices: 508851--508950 Score: 92
Period size: 29 Copynumber: 3.3 Consensus size: 29
508841 GGGCCTGAGA
* * *
508851 GCCTACCCAAGAAAGTTCGGGCCCACGGG
1 GCCTACCTAAAAAAGTTCGGGGCCACGGG
* ** ** *
508880 GCCTACCTAAAAACACATCTTAGGGCTGCAGG
1 GCCTACCTAAAAA-A-GT-TCGGGGCCACGGG
508912 GCCTACCTAAAAAAGTTCGGGGCCACGGG
1 GCCTACCTAAAAAAGTTCGGGGCCACGGG
508941 GCCTACCTAA
1 GCCTACCTAA
508951 GAACATATCT
Statistics
Matches: 53, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
29 29 0.55
30 2 0.04
31 2 0.04
32 20 0.38
ACGTcount: A:0.28, C:0.31, G:0.26, T:0.15
Consensus pattern (29 bp):
GCCTACCTAAAAAAGTTCGGGGCCACGGG
Found at i:514215 original size:61 final size:61
Alignment explanation
Indices: 514070--514200 Score: 187
Period size: 61 Copynumber: 2.1 Consensus size: 61
514060 CTAAGGGTAT
*
514070 ATCTTAGGGCCTG-AGAGCCTATCCAAGAAAGTTTAGGGCCACGGGGCTCACCTAAGAACAC
1 ATCTTAGGGCC-GCAGAGCCTACCCAAGAAAGTTTAGGGCCACGGGGCTCACCTAAGAACAC
* *
514131 ATCTTAGGGCCGCAGAACCTACCCAAGAAAGTTT-GGGTCCATGGGGC-CTACCTAAGAACAC
1 ATCTTAGGGCCGCAGAGCCTACCCAAGAAAGTTTAGGG-CCACGGGGCTC-ACCTAAGAACAC
514192 ATCTTAGGG
1 ATCTTAGGG
514201 TGGTAGGGCC
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
60 5 0.08
61 59 0.92
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (61 bp):
ATCTTAGGGCCGCAGAGCCTACCCAAGAAAGTTTAGGGCCACGGGGCTCACCTAAGAACAC
Found at i:517341 original size:23 final size:24
Alignment explanation
Indices: 517285--517341 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 24
517275 CAGGATGTAA
517285 ATACTTATATAATTTATATATATAT
1 ATAC-TATATAATTTATATATATAT
*
517310 ATACT-TATAGTTTATATATATAT
1 ATACTATATAATTTATATATATAT
517333 ATA-TATATA
1 ATACTATATA
517342 TATATAGTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 1 0.03
23 24 0.80
24 1 0.03
25 4 0.13
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
ATACTATATAATTTATATATATAT
Found at i:517361 original size:7 final size:7
Alignment explanation
Indices: 517351--517599 Score: 83
Period size: 7 Copynumber: 34.9 Consensus size: 7
517341 ATATATAGTC
517351 TATAAAG
1 TATAAAG
517358 TATATAAG
1 TATA-AAG
517366 TATTAAAG
1 TA-TAAAG
* *
517374 TATACAC
1 TATAAAG
*
517381 TATAAAA
1 TATAAAG
*
517388 TATAAAAC
1 TAT-AAAG
517396 TATACAA-
1 TATA-AAG
517403 TAT-AAG
1 TATAAAG
517409 TATTAAA-
1 TA-TAAAG
*
517416 TATAAAA
1 TATAAAG
517423 TATTAAAG
1 TA-TAAAG
*
517431 TATATA-
1 TATAAAG
* *
517437 TACATA-
1 TATAAAG
*
517443 TATAAAA
1 TATAAAG
517450 TATAAAG
1 TATAAAG
* *
517457 TGTATA-
1 TATAAAG
*
517463 TATATA-
1 TATAAAG
*
517469 TATAAAC
1 TATAAAG
517476 TATATATAG
1 TATA-A-AG
517485 TCTATAAAG
1 --TATAAAG
*
517494 TATATAG
1 TATAAAG
517501 TATAAAG
1 TATAAAG
517508 TATTAAA-
1 TA-TAAAG
*
517515 TAAAAAG
1 TATAAAG
*
517522 TATAAAAC
1 TAT-AAAG
517530 TATATAA-
1 TATA-AAG
517537 TAT-AAG
1 TATAAAG
517543 TATTAAAG
1 TA-TAAAG
517551 TATTAAAG
1 TA-TAAAG
*
517559 TATAAAAC
1 TAT-AAAG
517567 TATAGAA-
1 TATA-AAG
517574 -ATAAA-
1 TATAAAG
517579 TATTAAAG
1 TA-TAAAG
*
517587 TATATAG
1 TATAAAG
517594 TATAAA
1 TATAAA
517600 ACTATATATT
Statistics
Matches: 191, Mismatches: 24, Indels: 54
0.71 0.09 0.20
Matches are distributed among these distances:
5 6 0.03
6 34 0.18
7 79 0.41
8 62 0.32
9 5 0.03
10 1 0.01
11 4 0.02
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (7 bp):
TATAAAG
Found at i:517363 original size:2 final size:2
Alignment explanation
Indices: 517290--517347 Score: 66
Period size: 2 Copynumber: 29.0 Consensus size: 2
517280 TGTAAATACT
* *
517290 TA TA TA -A TT TA TA TA TA TA TA TA CT- TA TA GTT 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
517332 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
517348 GTCTATAAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
1 2 0.04
2 44 0.92
3 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:517366 original size:8 final size:9
Alignment explanation
Indices: 517340--517592 Score: 61
Period size: 8 Copynumber: 30.7 Consensus size: 9
517330 TATATATATA
*
517340 TATATATAG
1 TATATAAAG
*
517349 TCTATAAAG
1 TATATAAAG
517358 TATAT-AAG
1 TATATAAAG
517366 TAT-TAAAG
1 TATATAAAG
* *
517374 --TATACAC
1 TATATAAAG
517381 TATA-AAA-
1 TATATAAAG
*
517388 TATA-AAAC
1 TATATAAAG
517396 TATACAATATAAG
1 TAT---ATA-AAG
517409 TAT-TAAA-
1 TATATAAAG
517416 TATA-AAA-
1 TATATAAAG
517423 TAT-TAAAG
1 TATATAAAG
517431 TATATATACA-
1 TATATA-A-AG
517441 TATATAAA-
1 TATATAAAG
517449 -ATATAAAGTG
1 TATATAAA--G
*
517459 TATATATA-
1 TATATAAAG
*
517467 TATATAAAC
1 TATATAAAG
*
517476 TATATATAG
1 TATATAAAG
*
517485 TCTATAAAG
1 TATATAAAG
517494 TATAT--AG
1 TATATAAAG
517501 --TATAAAG
1 TATATAAAG
517508 TAT-TAAA-
1 TATATAAAG
517515 TA-A-AAAG
1 TATATAAAG
*
517522 TATA-AAAC
1 TATATAAAG
517530 TATAT--A-
1 TATATAAAG
517536 -ATAT-AAG
1 TATATAAAG
517543 TAT-TAAAG
1 TATATAAAG
517551 TAT-TAAAG
1 TATATAAAG
*
517559 TATA-AAAC
1 TATATAAAG
*
517567 TATAGAAA-
1 TATATAAAG
517575 TAAATATTAAAG
1 T--ATA-TAAAG
517587 TATATA
1 TATATA
517593 GTATAAAACT
Statistics
Matches: 188, Mismatches: 17, Indels: 78
0.66 0.06 0.28
Matches are distributed among these distances:
5 7 0.04
6 5 0.03
7 40 0.21
8 63 0.34
9 42 0.22
10 13 0.07
11 11 0.06
12 2 0.01
13 5 0.03
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (9 bp):
TATATAAAG
Found at i:517480 original size:28 final size:27
Alignment explanation
Indices: 517415--518105 Score: 182
Period size: 26 Copynumber: 25.6 Consensus size: 27
517405 TAAGTATTAA
*
517415 ATATA-AAATAT-TAAAGTATATATAC
1 ATATATAAATATATAAAGTATATATAT
*
517440 ATATATAAA-ATATAAAGTGTATATAT
1 ATATATAAATATATAAAGTATATATAT
* *
517466 ATATATAAACTATATATAGTCTATAAAGTAT
1 ATATATAAA-TATATAAAG--TATATA-TAT
* *
517497 ATAGTATAAAGTAT-TAAA-TAAAAAGTAT
1 ATA-TATAAA-TATATAAAGTATATA-TAT
* *
517525 A-AAACTATATA-ATATAAGTAT-TA-A-
1 ATATA-TAAATATATA-AAGTATATATAT
* * *
517549 AGTAT-TAAAGTATA-AAACTATAGAAAT
1 A-TATATAAA-TATATAAAGTATATATAT
* *
517576 AAATATTAAAGTATAT--AGTATA-AAACT
1 ATATA-TAAA-TATATAAAGTATATATA-T
** *
517603 ATATATTCATATATATA-TATATATAT
1 ATATATAAATATATAAAGTATATATAT
* *
517629 ATATATATATATATATA-TATATATAT
1 ATATATAAATATATAAAGTATATATAT
* *
517655 ATATATATATATATATA-TATATAT-T
1 ATATATAAATATATAAAGTATATATAT
* * * * *
517680 ATAAAGACAAAAGGATAAAAGTATACAATAT
1 ATATATA-AATA-TAT-AAAGTATA-TATAT
* * *
517711 AAAGTATAAAGTATATAAACTATATAGTGT
1 ATA-TATAAA-TATATAAAGTATATA-TAT
** *
517741 ATATATATTTATAAAAAGTATA-A-AT
1 ATATATAAATATATAAAGTATATATAT
*
517766 ATATA-AACTAT-TAAA-T-TATATAT
1 ATATATAAATATATAAAGTATATATAT
*
517789 ATATAT--ATATATATA-TATATATAT
1 ATATATAAATATATAAAGTATATATAT
* *
517813 ATATATATATATATATA-TATATATAT
1 ATATATAAATATATAAAGTATATATAT
*
517839 A-ATATAAA-CTAT-AAGTATATATAT
1 ATATATAAATATATAAAGTATATATAT
* * * *
517863 AAACTAT-ATTTTATAAAGTA-ATACTTT
1 ATA-TATAAATATATAAAGTATATA-TAT
* * * * * *
517890 TTATTTAATACTTTATAGACTATAGTTTAT
1 ATATATAA-A-TATATAAAGTATA-TATAT
** **
517920 ATATATACTTATAGTTTA-TATATATAT
1 ATATATAAATATA-TAAAGTATATATAT
* * * *
517947 ATATATGTAGTCTATAAAGTATAT-TAA
1 ATATAT-AAATATATAAAGTATATATAT
* *
517974 AGTATATAAGTAT-TAAAGTATACACTAT
1 A-TATATAAATATATAAAGTATATA-TAT
* *
518002 AAAATATAAA-ACTATATAAGTATTAAATAT
1 -ATATATAAATA-TATA-AAGTA-TATATAT
*
518032 AAAATATAAA-ATATTAAAGTATATATTAT
1 -ATATATAAATATA-TAAAGTATATA-TAT
* * *
518061 AAAGTATAAATATATAAACTATTAAAGTAT
1 ATA-TATAAATATATAAAGTA-TATA-TAT
*
518091 ATATATGAATATATA
1 ATATATAAATATATA
518106 TAAAAGTAAT
Statistics
Matches: 505, Mismatches: 92, Indels: 134
0.69 0.13 0.18
Matches are distributed among these distances:
21 2 0.00
22 5 0.01
23 15 0.03
24 39 0.08
25 37 0.07
26 133 0.26
27 53 0.10
28 76 0.15
29 56 0.11
30 57 0.11
31 20 0.04
32 12 0.02
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.40
Consensus pattern (27 bp):
ATATATAAATATATAAAGTATATATAT
Found at i:517596 original size:43 final size:43
Alignment explanation
Indices: 517505--517605 Score: 100
Period size: 43 Copynumber: 2.3 Consensus size: 43
517495 ATATAGTATA
* *
517505 AAGTATTAAATA-AAAAGTATAAAACTATATAATATAAGTATTA
1 AAGTATTAAATATAAAACTATAAAACTAAATAATATAAGTA-TA
*
517548 AAGTATTAAAGTATAAAACTATAGAAA-TAAATATTA-AAGTATA
1 AAGTATTAAA-TATAAAACTATA-AAACTAAATAATATAAGTATA
* *
517591 TAGTATAAAACTATA
1 AAGTATTAAA-TATA
517606 TATTCATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
43 24 0.49
44 7 0.14
45 15 0.31
46 3 0.06
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (43 bp):
AAGTATTAAATATAAAACTATAAAACTAAATAATATAAGTATA
Found at i:517603 original size:35 final size:36
Alignment explanation
Indices: 517501--517605 Score: 142
Period size: 35 Copynumber: 2.9 Consensus size: 36
517491 AAGTATATAG
* *
517501 TATAAAGTATTAAA-TAAAAAGTATAAAACTATATAA
1 TATAAA-TATTAAAGTATAAAGTATAAAACTATAGAA
*
517537 TATAAGTATTAAAGTATTAAAGTATAAAACTATAGAA
1 TATAAATATTAAAGTA-TAAAGTATAAAACTATAGAA
*
517574 -ATAAATATTAAAGTATATAGTATAAAACTATA
1 TATAAATATTAAAGTATAAAGTATAAAACTATA
517606 TATTCATATA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
35 23 0.37
36 21 0.34
37 18 0.29
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (36 bp):
TATAAATATTAAAGTATAAAGTATAAAACTATAGAA
Found at i:517607 original size:2 final size:2
Alignment explanation
Indices: 517602--517863 Score: 200
Period size: 2 Copynumber: 130.0 Consensus size: 2
517592 AGTATAAAAC
517602 TA TA TA T- TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
517644 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
517685 GA CA -A AA GGA TA -A AA GTA TA CA -A TA TA AA GTA TA AA GTA TA
1 TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA -TA TA
* * * * * *
517726 TA AA CTA TA TA GTG TA TA TA TA TT TA TA AA AA GTA TA AA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
517769 TA AA CTA T- TA AA T- 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
*
517810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA AA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
517852 -A GTA TA TA TA TA
1 TA -TA TA TA TA TA
517864 AACTATATTT
Statistics
Matches: 213, Mismatches: 27, Indels: 40
0.76 0.10 0.14
Matches are distributed among these distances:
1 9 0.04
2 193 0.91
3 11 0.05
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (2 bp):
TA
Found at i:517957 original size:23 final size:23
Alignment explanation
Indices: 517917--517962 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
517907 GACTATAGTT
*
517917 TATATATATACTTATAGTTTATA
1 TATATATATACTTATAGTCTATA
*
517940 TATATATATA-TATGTAGTCTATA
1 TATATATATACT-TATAGTCTATA
517963 AAGTATATTA
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:0.04, G:0.07, T:0.50
Consensus pattern (23 bp):
TATATATATACTTATAGTCTATA
Found at i:518004 original size:14 final size:14
Alignment explanation
Indices: 517971--518078 Score: 90
Period size: 14 Copynumber: 7.3 Consensus size: 14
517961 TAAAGTATAT
*
517971 TAAAGTATATAAGTA
1 TAAAGTATA-AAATA
* *
517986 TTAAAGTATACACTA
1 -TAAAGTATAAAATA
*
518001 TAAAATATAAAACTA
1 TAAAGTATAAAA-TA
*
518016 TATAAGTATTAAATA
1 TA-AAGTATAAAATA
*
518031 TAAAATATAAAATA
1 TAAAGTATAAAATA
* *
518045 TTAAAGTATATATTA
1 -TAAAGTATAAAATA
518060 TAAAGTATAAATATA
1 TAAAGTATAAA-ATA
518075 TAAA
1 TAAA
518079 CTATTAAAGT
Statistics
Matches: 74, Mismatches: 14, Indels: 9
0.76 0.14 0.09
Matches are distributed among these distances:
14 29 0.39
15 28 0.38
16 17 0.23
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (14 bp):
TAAAGTATAAAATA
Found at i:518009 original size:7 final size:7
Alignment explanation
Indices: 517999--518078 Score: 70
Period size: 7 Copynumber: 10.9 Consensus size: 7
517989 AAGTATACAC
517999 TATAAAA
1 TATAAAA
518006 TATAAAA
1 TATAAAA
*
518013 CTATATAAG
1 -TATA-AAA
*
518022 TATTAAA
1 TATAAAA
518029 TATAAAA
1 TATAAAA
518036 TATAAAA
1 TATAAAA
*
518043 TATTAAAG
1 TA-TAAAA
* *
518051 TATATAT
1 TATAAAA
*
518058 TATAAAG
1 TATAAAA
518065 TATAAATA
1 TATAAA-A
518073 TATAAA
1 TATAAA
518079 CTATTAAAGT
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
7 38 0.64
8 19 0.32
9 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (7 bp):
TATAAAA
Found at i:518055 original size:37 final size:38
Alignment explanation
Indices: 517967--518093 Score: 170
Period size: 37 Copynumber: 3.4 Consensus size: 38
517957 TCTATAAAGT
* *
517967 ATATTAAAGTATATAAGTATTAAAGTATACACTATAAA
1 ATATTAAAGTATATAAGTATTAAAGTATAAAATATAAA
* *
518005 ATATAAAACTATATAAGTATTAAA-TATAAAATATAAA
1 ATATTAAAGTATATAAGTATTAAAGTATAAAATATAAA
*
518042 ATATTAAAGTATAT-ATTA-TAAAGTATAAATATATAAA
1 ATATTAAAGTATATAAGTATTAAAGTATAAA-ATATAAA
*
518079 CTATTAAAGTATATA
1 ATATTAAAGTATATA
518094 TATGAATATA
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
35 4 0.05
36 9 0.12
37 43 0.55
38 22 0.28
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (38 bp):
ATATTAAAGTATATAAGTATTAAAGTATAAAATATAAA
Found at i:518300 original size:31 final size:31
Alignment explanation
Indices: 518254--518314 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
518244 TATGAGTTGC
* *
518254 TAGTATAGCTTTCGAAACTCACTGCTTGTGA
1 TAGTATAGCTGTCGAAACTCACTACTTGTGA
* *
518285 TAGTATTGCTGTCGAAATTCACTACTTGTG
1 TAGTATAGCTGTCGAAACTCACTACTTGTG
518315 CTTAGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.38
Consensus pattern (31 bp):
TAGTATAGCTGTCGAAACTCACTACTTGTGA
Found at i:518916 original size:55 final size:55
Alignment explanation
Indices: 518859--519183 Score: 460
Period size: 55 Copynumber: 5.9 Consensus size: 55
518849 TGACGAGCCT
*** *
518859 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATATGTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCC
* * *
518914 GCTCCCTATTCATTCAGGGAGTATCAG-ACTCGAACAATCTTCA-ATAAATGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCATA-AAACGGGTCC
*
518969 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
* *
519024 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
* *
519079 GCTCTCTATTCCTTCCGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
* *
519134 GCTCCCTATTCCATCAGAGAGTATAGAACTCGAACAATCTTCATCAAACG
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACG
519184 TGTTTGCTTC
Statistics
Matches: 249, Mismatches: 15, Indels: 12
0.90 0.05 0.04
Matches are distributed among these distances:
54 3 0.01
55 243 0.98
56 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
Found at i:519293 original size:37 final size:37
Alignment explanation
Indices: 519187--519296 Score: 150
Period size: 37 Copynumber: 3.0 Consensus size: 37
519177 TCAAACGTGT
* * * *
519187 TTGCTTCACTATTCTTCCATGAAGGCTTATAG-ATGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTA-AGTTTGAA
519224 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTGAA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTGAA
* *
519261 TTGCTTCACAACTCTTTCGTGAAGGCTTAAGTTTGA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTGA
519297 CTTGTTTCGA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 2 0.03
37 64 0.97
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTGAA
Found at i:520538 original size:24 final size:24
Alignment explanation
Indices: 520506--520558 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
520496 GCCCTTTGCG
*
520506 GGTTTTCAACTTGAGACCTCCTTT
1 GGTTTTCAACTTAAGACCTCCTTT
520530 GGTTTTCAACTTAAGACCTCCTTT
1 GGTTTTCAACTTAAGACCTCCTTT
520554 GGTTT
1 GGTTT
520559 CAAGACGCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (24 bp):
GGTTTTCAACTTAAGACCTCCTTT
Found at i:520619 original size:5 final size:6
Alignment explanation
Indices: 520600--520748 Score: 85
Period size: 6 Copynumber: 24.0 Consensus size: 6
520590 CCCCCTTTTA
* **
520600 TTTCTT TTTCTT TTTCTTT TTTCAT CAT-TT TTTCTTT TTTCATTT TTTCATT
1 TTTCTT TTTCTT TTTC-TT TTTCTT TTTCTT TTTC-TT TTTC--TT TTTC-TT
* *
520652 TTT-TC TTT-TT TTTCTT TTTCTT TTCTTTT TTTCTT TTTC-T TTTC-T
1 TTTCTT TTTCTT TTTCTT TTTCTT TT-TCTT TTTCTT TTTCTT TTTCTT
** *
520697 TTTCTT CAT-TT TTTCTTT TTCTCTT TTTCCTTT TTTCATT TTTCCT TTTCTT
1 TTTCTT TTTCTT TTTC-TT TT-TCTT TTT-C-TT TTTC-TT TTTCTT TTTCTT
520749 CCTTTTTTCC
Statistics
Matches: 113, Mismatches: 18, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
5 23 0.20
6 38 0.34
7 38 0.34
8 14 0.12
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:520636 original size:24 final size:24
Alignment explanation
Indices: 520604--520745 Score: 112
Period size: 25 Copynumber: 5.7 Consensus size: 24
520594 CTTTTATTTC
520604 TTTTTCTTTTTCTTTTTTCATCAT
1 TTTTTCTTTTTCTTTTTTCATCAT
*
520628 TTTTTCTTTTTTCATTTTTTCAT-TT
1 TTTTTC-TTTTTC-TTTTTTCATCAT
* ** *
520653 TTTCTTTTTTTTCTTTTTCTTTTCTT
1 TTT-TTCTTTTTCTTTTT-TCATCAT
*
520679 TTTTTCTTTTTCTTTTCTTTTCTTCAT
1 TTTTTCTTTTTC--TT-TTTTCATCAT
520706 TTTTTCTTTTTCTCTTTTTC--C-T
1 TTTTTCTTTTTCT-TTTTTCATCAT
*
520728 TTTTTCATTTTTCCTTTT
1 TTTTTC-TTTTTCTTTTT
520746 CTTCCTTTTT
Statistics
Matches: 100, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
22 11 0.11
23 7 0.07
24 11 0.11
25 32 0.32
26 17 0.17
27 19 0.19
28 3 0.03
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTTCTTTTTCTTTTTTCATCAT
Found at i:520638 original size:8 final size:8
Alignment explanation
Indices: 520610--520757 Score: 101
Period size: 8 Copynumber: 18.8 Consensus size: 8
520600 TTTCTTTTTC
520610 TTTTTCTT
1 TTTTTCTT
*
520618 TTTTCATCAT
1 TTTT--TCTT
520628 TTTTTC-T
1 TTTTTCTT
*
520635 TTTTTCAT
1 TTTTTCTT
*
520643 TTTTTCAT
1 TTTTTCTT
520651 TTTTTCTT
1 TTTTTCTT
*
520659 TTTTT-TC
1 TTTTTCTT
520666 TTTTTCTT
1 TTTTTCTT
520674 TTCTTT-TT
1 TT-TTTCTT
520682 TTCTTT-TT
1 TT-TTTCTT
*
520690 CTTTTCTT
1 TTTTTCTT
* *
520698 TTCTTCAT
1 TTTTTCTT
520706 TTTTTC--
1 TTTTTCTT
*
520712 TTTTTCTC
1 TTTTTCTT
*
520720 TTTTTCCT
1 TTTTTCTT
*
520728 TTTTTCAT
1 TTTTTCTT
*
520736 TTTTCCTT
1 TTTTTCTT
* *
520744 TTCTTCCT
1 TTTTTCTT
520752 TTTTTC
1 TTTTTC
520758 CATCATTTTC
Statistics
Matches: 114, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
6 6 0.05
7 16 0.14
8 82 0.72
9 3 0.03
10 7 0.06
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTCTT
Found at i:520644 original size:15 final size:15
Alignment explanation
Indices: 520610--520757 Score: 115
Period size: 15 Copynumber: 9.4 Consensus size: 15
520600 TTTCTTTTTC
520610 TTTTTCTTTTTTCATCAT
1 TTTTTC-TTTTT--TCAT
520628 TTTTTCTTTTTTCAT
1 TTTTTCTTTTTTCAT
520643 TTTTTCATTTTTTC-T
1 TTTTTC-TTTTTTCAT
*
520658 TTTTTTTCTTTTTC-T
1 TTTTTCT-TTTTTCAT
**
520673 TTTCTT-TTTTTCTTTT
1 TTT-TTCTTTTT-TCAT
520689 TCTTTTCTTTTCTTCAT
1 T-TTTTCTTTT-TTCAT
520706 TTTTTCTTTTTCTC-T
1 TTTTTCTTTTT-TCAT
*
520721 TTTTCCTTTTTTCAT
1 TTTTTCTTTTTTCAT
* *
520736 TTTTCCTTTTCTTCCT
1 TTTTTCTTTT-TTCAT
520752 TTTTTC
1 TTTTTC
520758 CATCATTTTC
Statistics
Matches: 112, Mismatches: 7, Indels: 24
0.78 0.05 0.17
Matches are distributed among these distances:
14 7 0.06
15 51 0.46
16 33 0.29
17 14 0.12
18 7 0.06
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTTTTCAT
Found at i:520666 original size:62 final size:63
Alignment explanation
Indices: 520594--520724 Score: 180
Period size: 62 Copynumber: 2.1 Consensus size: 63
520584 CTTGAACCCC
*
520594 CTTTTATTTCTTTTTCTTTT-TCTTTTTTCATCATT-TTTTCTTTT-TTCATTTTTTCATTTTT-
1 CTTTTTTTTCTTTTTCTTTTCT-TTTTTTC-TCATTCTTTTCTTTTCTTCATTTTTTC-TTTTTC
520655 T
63 T
**
520656 CTTTTTTTTCTTTTTCTTTTCTTTTTTTCTTTTTCTTTTCTTTTCTTCATTTTTTCTTTTTCT
1 CTTTTTTTTCTTTTTCTTTTCTTTTTTTCTCATTCTTTTCTTTTCTTCATTTTTTCTTTTTCT
520719 CTTTTT
1 CTTTTT
520725 CCTTTTTTCA
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
61 3 0.05
62 40 0.65
63 19 0.31
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (63 bp):
CTTTTTTTTCTTTTTCTTTTCTTTTTTTCTCATTCTTTTCTTTTCTTCATTTTTTCTTTTTCT
Found at i:520681 original size:35 final size:35
Alignment explanation
Indices: 520636--520748 Score: 119
Period size: 35 Copynumber: 3.2 Consensus size: 35
520626 ATTTTTTCTT
520636 TTTTCATTTTTTCAT-TTTTTCTTTTTTTTCTTTTTC
1 TTTTC-TTTTTTC-TCTTTTTCTTTTTTTTCTTTTTC
*
520672 TTTTCTTTTTT-TCTTTTTCTTTTCTTTTCTTCATT-
1 TTTTCTTTTTTCTCTTTTTCTTTT-TTTTCTT-TTTC
*
520707 TTTTC-TTTTTCTCTTTTTC-CTTTTTTCATTTTTCC
1 TTTTCTTTTTTCTCTTTTTCTTTTTTTTC-TTTTT-C
520742 TTTTCTT
1 TTTTCTT
520749 CCTTTTTTCC
Statistics
Matches: 66, Mismatches: 3, Indels: 16
0.78 0.04 0.19
Matches are distributed among these distances:
33 8 0.12
34 19 0.29
35 31 0.47
36 8 0.12
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (35 bp):
TTTTCTTTTTTCTCTTTTTCTTTTTTTTCTTTTTC
Found at i:520756 original size:24 final size:22
Alignment explanation
Indices: 520628--520757 Score: 105
Period size: 22 Copynumber: 6.0 Consensus size: 22
520618 TTTTCATCAT
*
520628 TTTTTCT-TTTTTCATTTTTTC
1 TTTTTCTCTTTTTCCTTTTTTC
**
520649 ATTTTT-TCTTTTTTTTCTTTTTC
1 -TTTTTCTCTTTTTCCT-TTTTTC
*
520672 -TTTTCT-TTTTTTC-TTTTTC
1 TTTTTCTCTTTTTCCTTTTTTC
*
520691 -TTTTCT-TTTCTTCATTTTTTC
1 TTTTTCTCTTT-TTCCTTTTTTC
520712 TTTTTCTCTTTTTCCTTTTTTC
1 TTTTTCTCTTTTTCCTTTTTTC
520734 ATTTTTC-CTTTTCTTCCTTTTTTC
1 -TTTTTCTC-TTT-TTCCTTTTTTC
520758 CATCATTTTC
Statistics
Matches: 92, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
19 15 0.16
20 2 0.02
21 17 0.18
22 29 0.32
23 18 0.20
24 11 0.12
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTCTCTTTTTCCTTTTTTC
Found at i:520757 original size:62 final size:61
Alignment explanation
Indices: 520602--520757 Score: 174
Period size: 62 Copynumber: 2.5 Consensus size: 61
520592 CCCTTTTATT
* **
520602 TCTTTTTCTTTTTCTTTTTTCATCATTTTTTCTTTTTTCATTTTTTCATTTTTTCTTTTTTT
1 TCTTTTTCTTTTTC-TTTTTCTTCATTTTTTCTTTTTTCATTTTTTCATTTTTTCTTTTTCC
* *
520664 TCTTTTTCTTTTCTTTTTTTCTT-TTTCTTTTCTTTTCTTCATTTTTTC-TTTTTCTCTTTTTCC
1 TCTTTTTCTTTT-TCTTTTTCTTCATT-TTTTCTTTT-TTCATTTTTTCATTTTT-TCTTTTTCC
* *
520727 T-TTTTTCATTTTTCCTTTTCTTCCTTTTTTC
1 TCTTTTTC-TTTTTCTTTTTCTTCATTTTTTC
520758 CATCATTTTC
Statistics
Matches: 80, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
61 2 0.03
62 52 0.65
63 26 0.32
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.78
Consensus pattern (61 bp):
TCTTTTTCTTTTTCTTTTTCTTCATTTTTTCTTTTTTCATTTTTTCATTTTTTCTTTTTCC
Found at i:529396 original size:48 final size:48
Alignment explanation
Indices: 529272--529425 Score: 217
Period size: 48 Copynumber: 3.2 Consensus size: 48
529262 CCATGCTTTG
* * *
529272 TTATTC-ACAAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGC--
1 TTATTCGA-AAAAATAAA-CCTAACCGCATGATATCTAGTTTGCATGCAT
*
529319 TTATTC-AAAAAATAAATCTAACCGCATGATATCTAGTTTGCATGCAT
1 TTATTCGAAAAAATAAACCTAACCGCATGATATCTAGTTTGCATGCAT
*
529366 TTATTCGAAAAAATAGACCTAACCGCATGATATCTAGTTTGCATGCAT
1 TTATTCGAAAAAATAAACCTAACCGCATGATATCTAGTTTGCATGCAT
529414 TTATTCGAAAAA
1 TTATTCGAAAAA
529426 CAAAAATAAA
Statistics
Matches: 98, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
45 26 0.27
46 8 0.08
47 13 0.13
48 51 0.52
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (48 bp):
TTATTCGAAAAAATAAACCTAACCGCATGATATCTAGTTTGCATGCAT
Found at i:532612 original size:19 final size:19
Alignment explanation
Indices: 532576--532631 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
532566 TAAATTCGTG
532576 TTGCGAATTCGAAAATTCAA
1 TTGCGAATTCG-AAATTCAA
*
532596 TTGCGAATTCGAAATTCAG
1 TTGCGAATTCGAAATTCAA
*
532615 TTGCGAATTTGAAATTC
1 TTGCGAATTCGAAATTC
532632 CGCGTTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 23 0.68
20 11 0.32
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (19 bp):
TTGCGAATTCGAAATTCAA
Found at i:532645 original size:21 final size:19
Alignment explanation
Indices: 532575--532647 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
532565 TTAAATTCGT
*
532575 GTTGCGAATTCGAAAATTCA
1 GTTGCGAATTTG-AAATTCA
* *
532595 ATTGCGAATTCGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
532614 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-C-A
532635 GTTGCGAATTTGA
1 GTTGCGAATTTGA
532648 CTTTTGTGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
19 22 0.47
20 12 0.26
21 13 0.28
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:532664 original size:20 final size:20
Alignment explanation
Indices: 532635--532679 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
532625 GAAATTCCGC
* *
532635 GTTGCGAATTTGACTTTTGT
1 GTTGCAAATTTGACTTCTGT
532655 GTTGCAAATTTGACTTCTGT
1 GTTGCAAATTTGACTTCTGT
532675 GTTGC
1 GTTGC
532680 GATTTACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.13, G:0.24, T:0.47
Consensus pattern (20 bp):
GTTGCAAATTTGACTTCTGT
Found at i:532696 original size:60 final size:58
Alignment explanation
Indices: 532626--532801 Score: 167
Period size: 60 Copynumber: 2.9 Consensus size: 58
532616 TGCGAATTTG
* *
532626 AAATTCCGCGTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTTCTGTGTTGCGATTTAC
1 AAATT-CGCGTTGCG-ATTT-ACTTTTGTGTTGCAAATTTGACATATGTGTTGCGATTTAC
* *** * *
532687 AAATTCGCGTTGCGATTTACAGATTCACGTTGCGAATTTGACATATTTGTTGCGATTTAC
1 AAATTCGCGTTGCGATTTAC--TTTTGTGTTGCAAATTTGACATATGTGTTGCGATTTAC
* *
532747 AAATTCGTGTTGCGATTTACTTATTCGTGTTGC-GATTT-ACATATTCGTGTTGCGA
1 AAATTCGCGTTGCGATTTACTT-TT-GTGTTGCAAATTTGACATA-T-GTGTTGCGA
532802 AATTGGAAAC
Statistics
Matches: 94, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
58 8 0.09
59 10 0.11
60 71 0.76
61 5 0.05
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (58 bp):
AAATTCGCGTTGCGATTTACTTTTGTGTTGCAAATTTGACATATGTGTTGCGATTTAC
Found at i:532698 original size:20 final size:20
Alignment explanation
Indices: 532673--532801 Score: 163
Period size: 20 Copynumber: 6.5 Consensus size: 20
532663 TTTGACTTCT
*
532673 GTGTTGCGATTTACAAATTC
1 GTGTTGCGATTTACATATTC
* *
532693 GCGTTGCGATTTACAGATTC
1 GTGTTGCGATTTACATATTC
**
532713 ACGTTGCGAATTTGACATATT-
1 GTGTTGCG-ATTT-ACATATTC
*
532734 -TGTTGCGATTTACAAATTC
1 GTGTTGCGATTTACATATTC
*
532753 GTGTTGCGATTTACTTATTC
1 GTGTTGCGATTTACATATTC
532773 GTGTTGCGATTTACATATTC
1 GTGTTGCGATTTACATATTC
532793 GTGTTGCGA
1 GTGTTGCGA
532802 AATTGGAAAC
Statistics
Matches: 96, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
18 6 0.06
19 4 0.04
20 76 0.79
21 4 0.04
22 6 0.06
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (20 bp):
GTGTTGCGATTTACATATTC
Found at i:533814 original size:27 final size:27
Alignment explanation
Indices: 533777--533848 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 27
533767 TGTTTAAAGA
* *
533777 AATTTTGCTTTTAAGTTGTTATCTATAT
1 AATTTT-CTTTCAAGTTGTTATCTAGAT
*
533805 ACTTTTCTTTCAAGTTGTTATCTAGAT
1 AATTTTCTTTCAAGTTGTTATCTAGAT
533832 AATTTTCTTTCAAGTTG
1 AATTTTCTTTCAAGTTG
533849 ATACCTGCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 35 0.88
28 5 0.12
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.54
Consensus pattern (27 bp):
AATTTTCTTTCAAGTTGTTATCTAGAT
Found at i:541517 original size:36 final size:35
Alignment explanation
Indices: 541465--541678 Score: 155
Period size: 36 Copynumber: 6.0 Consensus size: 35
541455 AAGTCTCTGT
** *
541465 AGGTTCAGTTCTGATCAAGCTAGTAATTCCTTATAA
1 AGGTTCAGCACTGATCAAGCT-GTAATTCCTTATAC
* * * *
541501 AGGTTCAACACCGATC-AGCTGGTAATTCCATATTGC
1 AGGTTCAGCACTGATCAAGCT-GTAATTCCTTA-TAC
** * * *
541537 AGGTTCAGTTCTGATCAAGTTGGTAATTCTTTATAT
1 AGGTTCAGCACTGATCAAGCT-GTAATTCCTTATAC
* * * *
541573 AGGTTGAGCACCGAT-AAGCTGATAATTCCATATTGC
1 AGGTTCAGCACTGATCAAGCTG-TAATTCCTTA-TAC
** *
541609 AGGTTCAGTTCTGATCAAGCTGATAATTCCTTATAT
1 AGGTTCAGCACTGATCAAGCTG-TAATTCCTTATAC
*
541645 AGGTTCAACACTGATCAA-CTAGTAATTCCTTATA
1 AGGTTCAGCACTGATCAAGCT-GTAATTCCTTATA
541679 GACCTAAGGC
Statistics
Matches: 136, Mismatches: 36, Indels: 13
0.74 0.19 0.07
Matches are distributed among these distances:
34 1 0.01
35 40 0.29
36 66 0.49
37 29 0.21
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (35 bp):
AGGTTCAGCACTGATCAAGCTGTAATTCCTTATAC
Found at i:541564 original size:72 final size:72
Alignment explanation
Indices: 541465--541673 Score: 310
Period size: 72 Copynumber: 2.9 Consensus size: 72
541455 AAGTCTCTGT
* *
541465 AGGTTCAGTTCTGATCAAGCTAGTAATTCCTTATAAAGGTTCAACACCGATCAGCTGGTAATTCC
1 AGGTTCAGTTCTGATCAAGCTGGTAATTCCTTATATAGGTTCAACACCGATCAGCTGGTAATTCC
541530 ATATTGC
66 ATATTGC
* * * * * *
541537 AGGTTCAGTTCTGATCAAGTTGGTAATTCTTTATATAGGTTGAGCACCGATAAGCTGATAATTCC
1 AGGTTCAGTTCTGATCAAGCTGGTAATTCCTTATATAGGTTCAACACCGATCAGCTGGTAATTCC
541602 ATATTGC
66 ATATTGC
* * * *
541609 AGGTTCAGTTCTGATCAAGCTGATAATTCCTTATATAGGTTCAACACTGATCAACTAGTAATTCC
1 AGGTTCAGTTCTGATCAAGCTGGTAATTCCTTATATAGGTTCAACACCGATCAGCTGGTAATTCC
541674 TTATAGACCT
Statistics
Matches: 119, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 119 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (72 bp):
AGGTTCAGTTCTGATCAAGCTGGTAATTCCTTATATAGGTTCAACACCGATCAGCTGGTAATTCC
ATATTGC
Found at i:542798 original size:3 final size:3
Alignment explanation
Indices: 542790--542841 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
542780 TGAATTAGTG
542790 ATA ATA ATA ATA ATAA ATA A-A A-A ATA A-A ATA A-A ATA ATA AT-
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
542831 ATA AT- ATA ATA
1 ATA ATA ATA ATA
542842 TTTTCAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
2 12 0.28
3 28 0.65
4 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:542809 original size:16 final size:16
Alignment explanation
Indices: 542790--542841 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
542780 TGAATTAGTG
542790 ATAATAATAATAATAA
1 ATAATAATAATAATAA
*
542806 ATAAAAAATAA-AATAAA
1 AT-AATAATAATAAT-AA
542823 ATAATAAT-ATAATATA
1 ATAATAATAATAATA-A
542839 ATA
1 ATA
542842 TTTTCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 2 0.07
16 17 0.57
17 11 0.37
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAATAATAATAATAA
Found at i:542828 original size:13 final size:13
Alignment explanation
Indices: 542792--542841 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
542782 AATTAGTGAT
542792 AATAATAATAAT-A
1 AATAA-AATAATAA
542805 AATAAAA-AATAA
1 AATAAAATAATAA
542817 AATAAAATAATAA
1 AATAAAATAATAA
* *
542830 TATAATATAATA
1 AATAAAATAATA
542842 TTTTCAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 3 0.09
12 10 0.30
13 20 0.61
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAAAATAATAA
Found at i:542850 original size:27 final size:27
Alignment explanation
Indices: 542820--542894 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
542810 AAAATAAAAT
542820 AAAATAATAATATAATATAATATTTTC
1 AAAATAATAATATAATATAATATTTTC
* * *
542847 AAAATTAT-ATATTAAAATACTATTTTC
1 AAAATAATAATA-TAATATAATATTTTC
* *
542874 AGAACTATATAATATATTATA
1 A-AAATA-ATAATATAATATA
542895 TACTATTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
26 3 0.08
27 21 0.57
28 3 0.08
29 7 0.19
30 3 0.08
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.41
Consensus pattern (27 bp):
AAAATAATAATATAATATAATATTTTC
Found at i:550776 original size:24 final size:24
Alignment explanation
Indices: 550749--550802 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
550739 TCAGATTTTG
*
550749 AAAAACGATTTTTAAAAATGTTAT
1 AAAAACGAATTTTAAAAATGTTAT
*
550773 AAAAACGAATTTTAAAAGTGTTAT
1 AAAAACGAATTTTAAAAATGTTAT
550797 ATAAAA
1 A-AAAA
550803 GTGCAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (24 bp):
AAAAACGAATTTTAAAAATGTTAT
Found at i:552673 original size:18 final size:18
Alignment explanation
Indices: 552650--552690 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
552640 ACCGGTCACG
552650 ACCCGACCCGACCCGTTA
1 ACCCGACCCGACCCGTTA
*
552668 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTA
552686 ACCCG
1 ACCCG
552691 TTGACAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.51, G:0.20, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTA
Done.