Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 109 of 198
Found at i:34911170 original size:13 final size:13
Alignment explanation
Indices: 34911152--34911180 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
34911142 GCCATGCAAG
34911152 AGAACTATCTCTA
1 AGAACTATCTCTA
34911165 AGAACTATCTCTA
1 AGAACTATCTCTA
34911178 AGA
1 AGA
34911181 TATAAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (13 bp):
AGAACTATCTCTA
Found at i:34919708 original size:11 final size:11
Alignment explanation
Indices: 34919679--34919717 Score: 62
Period size: 12 Copynumber: 3.5 Consensus size: 11
34919669 TTTTACTCCC
34919679 TATAATAAAAT
1 TATAATAAAAT
34919690 TATAAATAAAAT
1 TAT-AATAAAAT
34919702 TATAAT-AAAT
1 TATAATAAAAT
34919712 TATAAT
1 TATAAT
34919718 TTAGTTCCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.37
11 6 0.22
12 11 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAATAAAAT
Found at i:34921457 original size:23 final size:24
Alignment explanation
Indices: 34921431--34921477 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
34921421 TATATACCTT
34921431 AATTTGAA-TAAAAAAATATTTAA
1 AATTTGAATTAAAAAAATATTTAA
* * *
34921454 AATTTTAATTAAACAATTATTTAA
1 AATTTGAATTAAAAAAATATTTAA
34921478 TACAAATTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
AATTTGAATTAAAAAAATATTTAA
Found at i:34926209 original size:13 final size:13
Alignment explanation
Indices: 34926191--34926217 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34926181 CATGGCTAGG
34926191 TTTCTTCTTTTTT
1 TTTCTTCTTTTTT
34926204 TTTCTTCTTTTTT
1 TTTCTTCTTTTTT
34926217 T
1 T
34926218 GATGGAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTCTTCTTTTTT
Found at i:34929296 original size:24 final size:24
Alignment explanation
Indices: 34929252--34929312 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
34929242 AACACCATGT
* *
34929252 GAACCCTTATCACTAGACATGTGC
1 GAACCCCTATCACTAGACATGTAC
*
34929276 GAACCCCTATCA-TCAGTCATGTAC
1 GAACCCCTATCACT-AGACATGTAC
*
34929300 AAACCCCTATCAC
1 GAACCCCTATCAC
34929313 ATGGTACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.31, C:0.34, G:0.11, T:0.23
Consensus pattern (24 bp):
GAACCCCTATCACTAGACATGTAC
Found at i:34929397 original size:32 final size:32
Alignment explanation
Indices: 34929361--34929484 Score: 167
Period size: 32 Copynumber: 3.9 Consensus size: 32
34929351 CTATATGCTA
*
34929361 TGTGACTGTATGTGATGTGTGAACCTATGTTG
1 TGTGACTGTATGTGATGTGCGAACCTATGTTG
* * *
34929393 TGTGACTGCACGTGATGTGCGAACCTATGTTA
1 TGTGACTGTATGTGATGTGCGAACCTATGTTG
* *
34929425 TTTGACTGTATGTGATGTACGAACCTATGTTG
1 TGTGACTGTATGTGATGTGCGAACCTATGTTG
* * *
34929457 TGTGATTGTGTGTGATGTGCAAACCTAT
1 TGTGACTGTATGTGATGTGCGAACCTAT
34929485 TATACGTATG
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 78 1.00
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.38
Consensus pattern (32 bp):
TGTGACTGTATGTGATGTGCGAACCTATGTTG
Found at i:34929549 original size:23 final size:23
Alignment explanation
Indices: 34929495--34929568 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
34929485 TATACGTATG
*
34929495 GCGAACCTATGCTTAAGTGATAT
1 GCGAACCTATGCTAAAGTGATAT
* *
34929518 GCAAACCTACGCTAAAGTGATAT
1 GCGAACCTATGCTAAAGTGATAT
* * **
34929541 GCGAGCCTATACTAATTTGATAT
1 GCGAACCTATGCTAAAGTGATAT
34929564 GCGAA
1 GCGAA
34929569 TTGTGATTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (23 bp):
GCGAACCTATGCTAAAGTGATAT
Found at i:34934886 original size:43 final size:43
Alignment explanation
Indices: 34934758--34934887 Score: 131
Period size: 43 Copynumber: 3.0 Consensus size: 43
34934748 CACAGGACCT
** *
34934758 TCGATATGTGTTTTTATGTAAGACCACATCTGGGACGTCGGCA
1 TCGATATGTGTTTACATGTAAGACCACATCTGGGACGTTGGCA
* * * *
34934801 TCGACT-TTTGTTTACGTGTAAGACC-CTGTTTGGGACAG-TGGCA
1 TCGA-TATGTGTTTACATGTAAGACCAC-ATCTGGGAC-GTTGGCA
* *
34934844 TCGATATGTGATTACATGTAAGACCACATCTAGGACGTTGGCA
1 TCGATATGTGTTTACATGTAAGACCACATCTGGGACGTTGGCA
34934887 T
1 T
34934888 TGTAAGTGTT
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
42 3 0.04
43 62 0.91
44 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
TCGATATGTGTTTACATGTAAGACCACATCTGGGACGTTGGCA
Found at i:34940463 original size:43 final size:41
Alignment explanation
Indices: 34940395--34940554 Score: 117
Period size: 43 Copynumber: 3.8 Consensus size: 41
34940385 GAAACACATA
* *
34940395 TATCACATA-CAATGCCATATCCCAGATATGGTCTTACATG
1 TATCACATATCGATGCCATATCCCAGATATGGTCTTACACG
* * * *
34940435 TTATCACATATCGATGTCACTATCCCAGACAAGGTCTTATACG
1 -TATCACATATCGATGCCA-TATCCCAGATATGGTCTTACACG
* * * *
34940478 AAAC-CATATACGATGCCAATGTCCCAGATATGGTCTTACACA
1 TATCACATAT-CGATGCC-ATATCCCAGATATGGTCTTACACG
** * * *
34940520 TAATCTTATATTGATGCCAATGTCCCAGACATGGT
1 T-ATCACATATCGATGCC-ATATCCCAGATATGGT
34940555 TATACAAAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
41 14 0.15
42 32 0.34
43 44 0.47
44 4 0.04
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.29
Consensus pattern (41 bp):
TATCACATATCGATGCCATATCCCAGATATGGTCTTACACG
Found at i:34940505 original size:42 final size:43
Alignment explanation
Indices: 34940442--34940550 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 43
34940432 ATGTTATCAC
* * * *
34940442 ATATCGATGTCACTATCCCAGACAAGGTCTTATACGA-AACCAT
1 ATATCGATGCCAATGTCCCAGACAAGGTCTTACAC-ATAACCAT
* * * *
34940485 ATA-CGATGCCAATGTCCCAGATATGGTCTTACACATAATCTT
1 ATATCGATGCCAATGTCCCAGACAAGGTCTTACACATAACCAT
*
34940527 ATATTGATGCCAATGTCCCAGACA
1 ATATCGATGCCAATGTCCCAGACA
34940551 TGGTTATACA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 1 0.02
42 32 0.59
43 21 0.39
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (43 bp):
ATATCGATGCCAATGTCCCAGACAAGGTCTTACACATAACCAT
Found at i:34945610 original size:54 final size:53
Alignment explanation
Indices: 34945552--34945680 Score: 134
Period size: 54 Copynumber: 2.4 Consensus size: 53
34945542 CTTATTATTT
* * *
34945552 CAAGTCAGTGAGTTACACAGTCTAGCACACGGCCTGCGACATGAGTGTGTGTC
1 CAAGTCAGTGAGTTACACAGTCTAGCACACGGCCTGCGACACGACTGTGTGAC
* * * * *
34945605 ACAAGTCAGAGAGTTACAC-GATTTGGCACAGGGCCTGTGACACGACTGTGTGAC
1 -CAAGTCAGTGAGTTACACAG-TCTAGCACACGGCCTGCGACACGACTGTGTGAC
* *
34945659 CTAACTCAATGAGTTACACAGT
1 C-AAGTCAGTGAGTTACACAGT
34945681 TTAAGACACG
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
53 2 0.03
54 58 0.95
55 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.22
Consensus pattern (53 bp):
CAAGTCAGTGAGTTACACAGTCTAGCACACGGCCTGCGACACGACTGTGTGAC
Found at i:34958734 original size:21 final size:21
Alignment explanation
Indices: 34958705--34958756 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
34958695 GAATTTATTT
*
34958705 AATATTAAATAATTTAATTAA
1 AATAATAAATAATTTAATTAA
34958726 AATAATAAATAATTTAATTAA
1 AATAATAAATAATTTAATTAA
34958747 AATAATAAAT
1 AATAATAAAT
34958757 TGCATTAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATAATAAATAATTTAATTAA
Found at i:34958753 original size:17 final size:20
Alignment explanation
Indices: 34958696--34958756 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
34958686 TTATTATTAG
* *
34958696 AATTT-ATTTAATATTAAAT
1 AATTTAATTAAATAATAAAT
34958715 AATTTAATTAAAATAATAAAT
1 AATTTAATT-AAATAATAAAT
34958736 AATTTAATTAAAATAATAAAT
1 AATTTAATT-AAATAATAAAT
34958757 TGCATTAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.13
20 3 0.08
21 30 0.79
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTTAATTAAATAATAAAT
Found at i:34965340 original size:19 final size:20
Alignment explanation
Indices: 34965297--34965341 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
34965287 TGCAAGTGGG
34965297 TTATTTTCATATACATTTGT
1 TTATTTTCATATACATTTGT
*
34965317 TTATTTTTATAT-CAATTT-T
1 TTATTTTCATATAC-ATTTGT
34965336 TTATTT
1 TTATTT
34965342 GTATTTCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATTTTCATATACATTTGT
Found at i:34969541 original size:12 final size:12
Alignment explanation
Indices: 34969524--34969552 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
34969514 AAAGGAAAGT
34969524 AACTACGTAAGC
1 AACTACGTAAGC
34969536 AACTACGTAAGC
1 AACTACGTAAGC
34969548 AACTA
1 AACTA
34969553 ATGCTTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.17
Consensus pattern (12 bp):
AACTACGTAAGC
Found at i:34972274 original size:2 final size:2
Alignment explanation
Indices: 34972267--34972304 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
34972257 AAATTAGTTA
*
34972267 TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
34972305 AAGGGTTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:34988332 original size:10 final size:10
Alignment explanation
Indices: 34988289--34988335 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
34988279 AAATCTGTCG
34988289 AAAA-TAATT
1 AAAATTAATT
*
34988298 AAAATTAATC
1 AAAATTAATT
34988308 AAAATTTAATAT
1 AAAA-TTAAT-T
*
34988320 AAAATGAATT
1 AAAATTAATT
34988330 AAAATT
1 AAAATT
34988336 CAACATGTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
9 4 0.13
10 14 0.45
11 9 0.29
12 4 0.13
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (10 bp):
AAAATTAATT
Found at i:34988333 original size:22 final size:21
Alignment explanation
Indices: 34988293--34988335 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
34988283 CTGTCGAAAA
*
34988293 TAATTAAAATTAATCAAAATT
1 TAATTAAAATGAATCAAAATT
*
34988314 TAATATAAAATGAATTAAAATT
1 TAAT-TAAAATGAATCAAAATT
34988336 CAACATGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
TAATTAAAATGAATCAAAATT
Found at i:34988721 original size:27 final size:26
Alignment explanation
Indices: 34988671--34988732 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
34988661 TGAGCTAGGG
34988671 GTTCGCCAGTCTGTTTGAAAAACTGAA
1 GTTCGCCAGTCTGTTTGAAAAACT-AA
* *** *
34988698 GTTCGCCAGTTTGTTTGGTGAACTAG
1 GTTCGCCAGTCTGTTTGAAAAACTAA
34988724 GTTCGCCAG
1 GTTCGCCAG
34988733 GTAAGTTGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 10 0.33
27 20 0.67
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.32
Consensus pattern (26 bp):
GTTCGCCAGTCTGTTTGAAAAACTAA
Found at i:34990220 original size:12 final size:12
Alignment explanation
Indices: 34990203--34990229 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
34990193 TAGACTCAAT
34990203 AATATTTAATTA
1 AATATTTAATTA
34990215 AATATTTAATTA
1 AATATTTAATTA
34990227 AAT
1 AAT
34990230 TTATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATATTTAATTA
Found at i:34990976 original size:13 final size:11
Alignment explanation
Indices: 34990944--34990986 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
34990934 CCATTTTCTG
*
34990944 AATAAAATAAT
1 AATAAAATATT
34990955 AAT-AAATATCT
1 AATAAAATAT-T
34990966 AAGTAAAATATT
1 AA-TAAAATATT
34990978 AATAAAATA
1 AATAAAATA
34990987 ATATTGAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:34993907 original size:29 final size:28
Alignment explanation
Indices: 34993869--34993992 Score: 106
Period size: 29 Copynumber: 4.2 Consensus size: 28
34993859 TAAAGGACAA
*
34993869 CCTTTATGGCACAACTCTGGACAGGAAAG
1 CCTTTGTGGCA-AACTCTGGACAGGAAAG
* * * *
34993898 CCTTTGTGGCAAGTACTGAATGTAAATGACAA-
1 CCTTTGTGGCAA--ACT--CTGGACAGGA-AAG
* *
34993930 CCTTTGTGGCATAACTCTAGATAGGAAAG
1 CCTTTGTGGCA-AACTCTGGACAGGAAAG
34993959 CCTTTGTGGCAAAACTCTGGACAGGAAAG
1 CCTTTGTGGC-AAACTCTGGACAGGAAAG
34993988 CCTTT
1 CCTTT
34993993 CTGGTGAGTA
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
28 3 0.04
29 45 0.60
30 4 0.05
31 3 0.04
32 17 0.23
33 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (28 bp):
CCTTTGTGGCAAACTCTGGACAGGAAAG
Found at i:35004694 original size:19 final size:20
Alignment explanation
Indices: 35004666--35004715 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
35004656 TATGGGATTT
35004666 CACTTCGGTGCCTCTG-TTA
1 CACTTCGGTGCCTCTGTTTA
* *
35004685 CACTTTGGTGTCTCTGTTTA
1 CACTTCGGTGCCTCTGTTTA
35004705 CACTTCGGTGC
1 CACTTCGGTGC
35004716 TTCTAATTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.10, C:0.28, G:0.22, T:0.40
Consensus pattern (20 bp):
CACTTCGGTGCCTCTGTTTA
Found at i:35008036 original size:38 final size:39
Alignment explanation
Indices: 35007955--35008036 Score: 89
Period size: 36 Copynumber: 2.2 Consensus size: 39
35007945 ATGCTCCACT
**
35007955 TTTATTTTTCTTGAACTTTGAGCACTCCTTTATTTGCTC
1 TTTATTTTTCTTGAACTTTGAGCAAACCTTTATTTGCTC
* * *
35007994 -TTATTTTTC-TGCA-TTTGAGCAAACTTTTCTTTGCTTC
1 TTTATTTTTCTTGAACTTTGAGCAAACCTTTATTTGC-TC
35008031 TTTATT
1 TTTATT
35008037 CATTTTTCTC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
36 17 0.47
37 5 0.14
38 14 0.39
ACGTcount: A:0.16, C:0.18, G:0.10, T:0.56
Consensus pattern (39 bp):
TTTATTTTTCTTGAACTTTGAGCAAACCTTTATTTGCTC
Found at i:35010934 original size:37 final size:35
Alignment explanation
Indices: 35010887--35010966 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 35
35010877 AACTAACATT
* * * *
35010887 AAAATTAAAAATTAAATTAAAATTAAAGACAAAGATA
1 AAAATGAAAAATAAAAATAAAACT-AAGA-AAAGATA
*
35010924 AAAATGAAAAATAAAAATAAAACTAAGAAAAGATT
1 AAAATGAAAAATAAAAATAAAACTAAGAAAAGATA
35010959 AAAATGAA
1 AAAATGAA
35010967 TTAGAAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
35 14 0.37
36 4 0.11
37 20 0.53
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (35 bp):
AAAATGAAAAATAAAAATAAAACTAAGAAAAGATA
Found at i:35017869 original size:27 final size:26
Alignment explanation
Indices: 35017813--35018092 Score: 328
Period size: 27 Copynumber: 10.4 Consensus size: 26
35017803 CCCCAAAATA
35017813 GGTAAAATGACCGAAATA-CCCCATAG
1 GGTAAAATGA-CGAAATACCCCCATAG
*
35017839 GGTAAAATGATCAAAATACCCCCATAG
1 GGTAAAATGA-CGAAATACCCCCATAG
*
35017866 GGTAAAATGACTGAAATACCCTCATAG
1 GGTAAAATGAC-GAAATACCCCCATAG
*
35017893 GGTAAAATGACAAAAATACCCCCATAG
1 GGTAAAATGAC-GAAATACCCCCATAG
35017920 GGTAAAATGATCGAAATACCCCCATAG
1 GGTAAAATGA-CGAAATACCCCCATAG
*
35017947 GGTAAAATGATCGAAATACCCCCATAA
1 GGTAAAATGA-CGAAATACCCCCATAG
* ** *
35017974 GATAGTATGATTGAAATACCCCCATAG
1 GGTAAAATGA-CGAAATACCCCCATAG
* *
35018001 GGTAAAATGACTAAAATACCCCCATAA
1 GGTAAAATGAC-GAAATACCCCCATAG
* *
35018028 GGTAGAATGACCGAAATACCCCTATAG
1 GGTAAAATGA-CGAAATACCCCCATAG
* * *
35018055 GTTAAAATGACGAAAATACACCCATAA
1 GGTAAAATGACG-AAATACCCCCATAG
35018082 GGTAAAATGAC
1 GGTAAAATGAC
35018093 TGTTATACCC
Statistics
Matches: 218, Mismatches: 30, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
26 19 0.09
27 197 0.90
28 2 0.01
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.19
Consensus pattern (26 bp):
GGTAAAATGACGAAATACCCCCATAG
Found at i:35018119 original size:54 final size:53
Alignment explanation
Indices: 35017812--35018107 Score: 366
Period size: 54 Copynumber: 5.5 Consensus size: 53
35017802 ACCCCAAAAT
*
35017812 AGGTAAAATGACCGAAATACCCCATAGGGTAAAATGATC-AAAATACCCCCATA
1 AGGTAAAATGACTGAAATACCCCATAGGGTAAAATGA-CGAAAATACCCCCATA
* *
35017865 GGGTAAAATGACTGAAATACCCTCATAGGGTAAAATGACAAAAATACCCCCATA
1 AGGTAAAATGACTGAAATACCC-CATAGGGTAAAATGACGAAAATACCCCCATA
*
35017919 GGGTAAAATGA-TCGAAATACCCCCATAGGGTAAAATGATCG-AAATACCCCCATA
1 AGGTAAAATGACT-GAAATA-CCCCATAGGGTAAAATGA-CGAAAATACCCCCATA
* ** * *
35017973 AGATAGTATGATTGAAATACCCCCATAGGGTAAAATGACTAAAATACCCCCATA
1 AGGTAAAATGACTGAAATA-CCCCATAGGGTAAAATGACGAAAATACCCCCATA
* * * *
35018027 AGGTAGAATGACCGAAATACCCCTATAGGTTAAAATGACGAAAATACACCCATA
1 AGGTAAAATGACTGAAATACCCC-ATAGGGTAAAATGACGAAAATACCCCCATA
**
35018081 AGGTAAAATGACTGTTATACCCC-TAGG
1 AGGTAAAATGACTGAAATACCCCATAGG
35018108 AGATGAAATG
Statistics
Matches: 216, Mismatches: 19, Indels: 17
0.86 0.08 0.07
Matches are distributed among these distances:
52 4 0.02
53 27 0.12
54 180 0.83
55 5 0.02
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.20
Consensus pattern (53 bp):
AGGTAAAATGACTGAAATACCCCATAGGGTAAAATGACGAAAATACCCCCATA
Found at i:35033368 original size:7 final size:6
Alignment explanation
Indices: 35033352--35033427 Score: 64
Period size: 6 Copynumber: 12.3 Consensus size: 6
35033342 ATTTTCCTGC
* *
35033352 AAAAAT AAAAAT GAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT AATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT AAAAAT
* * * *
35033402 AATAAT AATAAT AATAAT AATAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
35033428 TAGGAAAATT
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
5 5 0.08
6 47 0.73
7 7 0.11
8 5 0.08
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (6 bp):
AAAAAT
Found at i:35033398 original size:3 final size:3
Alignment explanation
Indices: 35033367--35033429 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
35033357 TAAAAATGAA
* *
35033367 AAT AA- AAT AA- AAT AGT AAA AAT AAAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
35033411 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
35033430 GGAAAATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
2 4 0.08
3 46 0.87
4 3 0.06
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:35047287 original size:21 final size:21
Alignment explanation
Indices: 35047248--35047287 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35047238 TATCAGAATT
*
35047248 ATATTAATATTTTTCAAAAAA
1 ATATTAATATTTTTAAAAAAA
35047269 ATATTAAT-TTTATTAAAAA
1 ATATTAATATTT-TTAAAAA
35047288 TTAACCTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATTAATATTTTTAAAAAAA
Found at i:35060708 original size:50 final size:50
Alignment explanation
Indices: 35060627--35060773 Score: 163
Period size: 50 Copynumber: 2.9 Consensus size: 50
35060617 CATTGAGATT
* ** *
35060627 ATGAGAGGTCCCATGTAAGACTGTGCCTGGGACATGGCGTTGGCACCAAG
1 ATGAAAGGTCCCATGTAAGACCATGCTTGGGACATGGCGTTGGCACCAAG
* *
35060677 ATGAAAGGTCCCATGTAAGACCATGTTTGGGACATGGAGTTGGCACCAAG
1 ATGAAAGGTCCCATGTAAGACCATGCTTGGGACATGGCGTTGGCACCAAG
* ** * *
35060727 ATGAGAA-ATCCCGCGTAAGACCATGCCTT-GGACATGGCATGGGCACC
1 ATGA-AAGGTCCCATGTAAGACCATG-CTTGGGACATGGCGTTGGCACC
35060774 TATATAAGAA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
50 78 0.95
51 4 0.05
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20
Consensus pattern (50 bp):
ATGAAAGGTCCCATGTAAGACCATGCTTGGGACATGGCGTTGGCACCAAG
Found at i:35067465 original size:50 final size:50
Alignment explanation
Indices: 35067354--35067700 Score: 311
Period size: 50 Copynumber: 6.8 Consensus size: 50
35067344 ATTTGGGTAA
* * * *
35067354 AGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C---CA-A-TATG
* * *
35067410 AGAGGTCCCATGAAAGACCATGTTTGGGACATGGCGTTGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAATATG
* * *
35067460 AGAGGTCCCATGTAAAACAATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAATATG
* *
35067510 AGATGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAATATG
** * * * * * *
35067560 AGAGGTCCCCCGTAAGACCATGCCTTGGACATGGCATGGGCACCTATATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAATATG
** * * * * **
35067610 AGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACA-A-G
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCA-ATATG
* ** * * *
35067659 AAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
35067701 TGTTATATTC
Statistics
Matches: 241, Mismatches: 49, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
49 33 0.14
50 168 0.70
51 2 0.01
55 1 0.00
56 37 0.15
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAATATG
Found at i:35067594 original size:150 final size:150
Alignment explanation
Indices: 35067358--35067700 Score: 352
Period size: 150 Copynumber: 2.3 Consensus size: 150
35067348 GGGTAAAGAG
* * *
35067358 ATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATGA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-T-AG--TATGAGAGGTCCCACGA
* * * * ** *
35067423 AAGACCATGTTTGGGACATGGCGTTGGCACCGATATGAGAGGTCCCATGTAAAACAATGTCTGGG
62 AAGACCATGCTTGGGACATGGCATGGGCACCGATATAAGAACTCCCATGTAAAACAATATCTGGG
* * *
35067488 ACATGGCGTTGGCA-CCAAGATGAGAT
127 ACATGGCATTGGCAGACAAGA--A-AC
* * * *
35067514 GTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCA-AG-ATGAGAGGTCCCCCGTAAGA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGTATGAGAGGTCCCACGAAAGA
* * * * *
35067577 CCATGCCTT-GGACATGGCATGGGCACCTATATAAGAACTCTCATGTAAGACCATATCTGGGATA
66 CCATG-CTTGGGACATGGCATGGGCACCGATATAAGAACTCCCATGTAAAACAATATCTGGGACA
35067641 TGGCATTGGCAGTACAAGAAAC
130 TGGCATTGGCAG-ACAAGAAAC
* * *
35067663 ATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
35067701 TGTTATATTC
Statistics
Matches: 158, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
149 35 0.22
150 77 0.49
151 2 0.01
152 5 0.03
153 2 0.01
156 37 0.23
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (150 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGTATGAGAGGTCCCACGAAAGA
CCATGCTTGGGACATGGCATGGGCACCGATATAAGAACTCCCATGTAAAACAATATCTGGGACAT
GGCATTGGCAGACAAGAAAC
Found at i:35070420 original size:16 final size:16
Alignment explanation
Indices: 35070395--35070425 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35070385 ATAAGAATTT
35070395 TTTATAGTTTTTTAAG
1 TTTATAGTTTTTTAAG
*
35070411 TTTATTGTTTTTTAA
1 TTTATAGTTTTTTAA
35070426 AAAATAATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (16 bp):
TTTATAGTTTTTTAAG
Found at i:35081249 original size:7 final size:7
Alignment explanation
Indices: 35081237--35081291 Score: 58
Period size: 7 Copynumber: 7.4 Consensus size: 7
35081227 CCTCTTCTTT
35081237 TTTGTTC
1 TTTGTTC
35081244 TTTGTTC
1 TTTGTTC
35081251 TTTGTTC
1 TTTGTTC
35081258 TTT-TTCCC
1 TTTGTT--C
*
35081266 GTTATCTTC
1 -TT-TGTTC
35081275 TTTGTTC
1 TTTGTTC
35081282 TTTGTTC
1 TTTGTTC
35081289 TTT
1 TTT
35081292 TTCCTTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
6 2 0.05
7 31 0.74
8 3 0.07
9 3 0.07
10 1 0.02
11 2 0.05
ACGTcount: A:0.02, C:0.18, G:0.11, T:0.69
Consensus pattern (7 bp):
TTTGTTC
Found at i:35083094 original size:3 final size:3
Alignment explanation
Indices: 35083086--35083140 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
35083076 GAAAAGTGTG
35083086 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35083134 TTA TTA T
1 TTA TTA T
35083141 GTGAAGATAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:35086733 original size:25 final size:27
Alignment explanation
Indices: 35086683--35086741 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
35086673 AAATATATAT
* *
35086683 TATA-ATATTATATCTTAATTATTAAG
1 TATATATATTATATATTAATTAATAAG
35086709 TATATATATTATATATT-A-TAATAAG
1 TATATATATTATATATTAATTAATAAG
*
35086734 TAAATATA
1 TATATATA
35086742 ATAAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 13 0.45
26 5 0.17
27 11 0.38
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (27 bp):
TATATATATTATATATTAATTAATAAG
Found at i:35086774 original size:21 final size:20
Alignment explanation
Indices: 35086744--35086787 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
35086734 TAAATATAAT
35086744 AAATAAAAGAAACAAAAAAG
1 AAATAAAAGAAACAAAAAAG
*
35086764 AAATAGAAAGAAACAAAATAG
1 AAATA-AAAGAAACAAAAAAG
35086785 AAA
1 AAA
35086788 CGAAACAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.77, C:0.05, G:0.11, T:0.07
Consensus pattern (20 bp):
AAATAAAAGAAACAAAAAAG
Found at i:35086784 original size:15 final size:16
Alignment explanation
Indices: 35086764--35086794 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
35086754 AACAAAAAAG
35086764 AAATAGAAA-GAAACA
1 AAATAGAAACGAAACA
35086779 AAATAGAAACGAAACA
1 AAATAGAAACGAAACA
35086795 GGGAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.71, C:0.10, G:0.13, T:0.06
Consensus pattern (16 bp):
AAATAGAAACGAAACA
Found at i:35102254 original size:25 final size:24
Alignment explanation
Indices: 35102218--35102267 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
35102208 ATATTAATTG
*
35102218 TTTTATTAATTTATATATTTTAAAA
1 TTTTATTAATTTATA-ATTTCAAAA
*
35102243 TTTTA-TATATTTTTAATTTCAAAA
1 TTTTATTA-ATTTATAATTTCAAAA
35102267 T
1 T
35102268 AATAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTATTAATTTATAATTTCAAAA
Found at i:35102260 original size:16 final size:16
Alignment explanation
Indices: 35102223--35102261 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
35102213 AATTGTTTTA
35102223 TTAA-TTTATATATTT
1 TTAATTTTATATATTT
*
35102238 TAAAATTTTATATATTT
1 T-TAATTTTATATATTT
35102255 TTAATTT
1 TTAATTT
35102262 CAAAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 7 0.35
17 12 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAATTTTATATATTT
Found at i:35102432 original size:22 final size:20
Alignment explanation
Indices: 35102402--35102441 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
35102392 TTATACTTTT
35102402 TATTAATTTATATATTTTTACA
1 TATTAATTT-T-TATTTTTACA
*
35102424 TATTTATTTTTATTTTTA
1 TATTAATTTTTATTTTTA
35102442 TTTATACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 1 0.06
22 8 0.47
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTAATTTTTATTTTTACA
Found at i:35105195 original size:40 final size:40
Alignment explanation
Indices: 35105135--35105281 Score: 194
Period size: 39 Copynumber: 3.7 Consensus size: 40
35105125 AATATTTTTA
* **
35105135 TTTTTT-A-TTTTTTAACTTTAAAATGCTTTTAAAATACT
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
*
35105173 TTTTTTAATTTTTTTAATTTT-AAATTTTTTTAAAATACT
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
35105212 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC-
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
35105251 TTTTTTAATTTTTATTTTAATTTTTAAAATA
1 TTTTTTAA--TTT-TTTTAA-TTTTAAAATA
35105282 AATTTTTGGT
Statistics
Matches: 98, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
38 6 0.06
39 46 0.47
40 27 0.28
41 3 0.03
42 6 0.06
43 10 0.10
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (40 bp):
TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:35105198 original size:16 final size:16
Alignment explanation
Indices: 35105174--35105205 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35105164 TAAAATACTT
*
35105174 TTTTTAATTTTTTTAA
1 TTTTAAATTTTTTTAA
35105190 TTTTAAATTTTTTTAA
1 TTTTAAATTTTTTTAA
35105206 AATACTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTAAATTTTTTTAA
Found at i:35105232 original size:8 final size:9
Alignment explanation
Indices: 35105172--35105232 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 9
35105162 TTTAAAATAC
35105172 TTTTTTTAA
1 TTTTTTTAA
35105181 TTTTTTTAA
1 TTTTTTTAA
*
35105190 --TTTTAAA
1 TTTTTTTAA
35105197 TTTTTTTAAAATA
1 TTTTTTT---A-A
35105210 CTTTTTTTAA
1 -TTTTTTTAA
35105220 TTTTTTTAA
1 TTTTTTTAA
35105229 TTTT
1 TTTT
35105233 AAAATATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
7 6 0.14
9 26 0.60
10 1 0.02
11 1 0.02
12 1 0.02
13 1 0.02
14 7 0.16
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:35105297 original size:32 final size:32
Alignment explanation
Indices: 35105238--35105299 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
35105228 ATTTTAAAAT
** *
35105238 ATTTTTAAAATACTTTTTTAATTTTTATTTTA
1 ATTTTTAAAATAAATTTTTAATATTTATTTTA
**
35105270 ATTTTTAAAATAAATTTTTGGTATTTATTT
1 ATTTTTAAAATAAATTTTTAATATTTATTT
35105300 AAAAAACGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (32 bp):
ATTTTTAAAATAAATTTTTAATATTTATTTTA
Found at i:35111784 original size:19 final size:19
Alignment explanation
Indices: 35111760--35111818 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 19
35111750 AGGTTACTTG
35111760 AATTTGATATATATTTTTT
1 AATTTGATATATATTTTTT
35111779 AATTTGATATTTAAGTATTTTTT
1 AATTTGATA--T-A-TATTTTTT
35111802 -ATTTGATATATACTTTT
1 AATTTGATATATA-TTTT
35111819 CTTGATATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
18 2 0.06
19 14 0.40
20 1 0.03
21 1 0.03
22 9 0.26
23 8 0.23
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.61
Consensus pattern (19 bp):
AATTTGATATATATTTTTT
Found at i:35119568 original size:21 final size:21
Alignment explanation
Indices: 35119515--35119569 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
35119505 ACCATTGTTT
* *
35119515 CTAATCTCACCACTAAAGTAT
1 CTAATCTCACCGCTAAAGTAA
* *
35119536 CCAATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTAAAGTAA
35119557 CTAATCTCACCGC
1 CTAATCTCACCGC
35119570 CACTGCTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.36, G:0.07, T:0.24
Consensus pattern (21 bp):
CTAATCTCACCGCTAAAGTAA
Found at i:35127304 original size:3 final size:3
Alignment explanation
Indices: 35127296--35127356 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
35127286 TGTTTAATTA
* * *
35127296 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ACT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35127344 ATT AATT ATT ATT
1 ATT -ATT ATT ATT
35127357 TGCTTTATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:35132860 original size:23 final size:23
Alignment explanation
Indices: 35132834--35132877 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
35132824 GTAATTATAA
35132834 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
35132857 ATACATTTGTAATTAATATAT
1 ATACATGTGTAATAAATATAT
35132878 ATACATACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:35134292 original size:23 final size:23
Alignment explanation
Indices: 35134265--35134313 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
35134255 ACCGATCCGA
35134265 CACTTTATGTATCGTATATCAAG
1 CACTTTATGTATCGTATATCAAG
* * *
35134288 CACTTTATGTGTCGTATTTCAGG
1 CACTTTATGTATCGTATATCAAG
35134311 CAC
1 CAC
35134314 CTCGTGTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (23 bp):
CACTTTATGTATCGTATATCAAG
Found at i:35142635 original size:34 final size:35
Alignment explanation
Indices: 35142576--35142642 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
35142566 TGATAATACT
* * *
35142576 GACAATAAATGTGCCCAGCATTGGTCGGTAAAACC
1 GACAATAAATGAGCCCAACACTGGTCGGTAAAACC
35142611 GACAAT-AATGAGCCCAACACTGGTCGGTAAAA
1 GACAATAAATGAGCCCAACACTGGTCGGTAAAA
35142643 TCGTCAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 23 0.79
35 6 0.21
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.18
Consensus pattern (35 bp):
GACAATAAATGAGCCCAACACTGGTCGGTAAAACC
Found at i:35145678 original size:20 final size:20
Alignment explanation
Indices: 35145631--35145684 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
35145621 TTTATGCTAG
* * *
35145631 GTAAATGAAATGGAAAGCAA
1 GTAAATGGAATGGTAAGAAA
35145651 GTAAATGGAATGGTAAGAAA
1 GTAAATGGAATGGTAAGAAA
*
35145671 GTAAATGGATTGGT
1 GTAAATGGAATGGT
35145685 TCGTAGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.22
Consensus pattern (20 bp):
GTAAATGGAATGGTAAGAAA
Found at i:35147267 original size:38 final size:38
Alignment explanation
Indices: 35147218--35147293 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
35147208 ATTATTTTTG
*
35147218 TTGTATCCACCAAGAAACTTATTGCCCAAAGCGCAGTT
1 TTGTATCCACCAAGAAACTGATTGCCCAAAGCGCAGTT
35147256 TTGTATCCACCAAGAAACTGATTGCCCAAAGCGCAGTT
1 TTGTATCCACCAAGAAACTGATTGCCCAAAGCGCAGTT
35147294 GCCTATATGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (38 bp):
TTGTATCCACCAAGAAACTGATTGCCCAAAGCGCAGTT
Found at i:35151959 original size:68 final size:68
Alignment explanation
Indices: 35151850--35151983 Score: 250
Period size: 68 Copynumber: 2.0 Consensus size: 68
35151840 AATCCTGTAG
*
35151850 AAAGGTTCAGATGTACTATTAGTAATGTTAAGTATGATTTCTCTTTGGAACTCACTAAGTTTGTA
1 AAAGGTTCAGATGTACTATCAGTAATGTTAAGTATGATTTCTCTTTGGAACTCACTAAGTTTGTA
35151915 TGA
66 TGA
*
35151918 AAAGGTTCAGATGTACTATCAGTAATGTTATGTATGATTTCTCTTTGGAACTCACTAAGTTTGTA
1 AAAGGTTCAGATGTACTATCAGTAATGTTAAGTATGATTTCTCTTTGGAACTCACTAAGTTTGTA
35151983 T
66 T
35151984 AAACTTACTC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (68 bp):
AAAGGTTCAGATGTACTATCAGTAATGTTAAGTATGATTTCTCTTTGGAACTCACTAAGTTTGTA
TGA
Found at i:35154035 original size:10 final size:10
Alignment explanation
Indices: 35154020--35154061 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
35154010 TGTATATATA
35154020 TTTTATAATT
1 TTTTATAATT
35154030 TTTTATAATT
1 TTTTATAATT
**
35154040 TTTT-TGAAAA
1 TTTTAT-AATT
35154050 TTTTATAATT
1 TTTTATAATT
35154060 TT
1 TT
35154062 GCATATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 1 0.04
10 24 0.92
11 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:35155967 original size:7 final size:7
Alignment explanation
Indices: 35155957--35155989 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
35155947 TCAAAATTTA
*
35155957 AAATTAG
1 AAATTGG
35155964 AAATTGG
1 AAATTGG
35155971 AAATTGG
1 AAATTGG
35155978 AAATTGG
1 AAATTGG
35155985 AAATT
1 AAATT
35155990 TAAATTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.30
Consensus pattern (7 bp):
AAATTGG
Found at i:35155967 original size:14 final size:14
Alignment explanation
Indices: 35155938--35155989 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
35155928 AATATTGAGG
35155938 ATTGAAAATTCA-AA
1 ATTGAAAATT-AGAA
*
35155952 ATTTAAAATTAGAA
1 ATTGAAAATTAGAA
* *
35155966 ATTGGAAATTGGAA
1 ATTGAAAATTAGAA
*
35155980 ATTGGAAATT
1 ATTGAAAATT
35155990 TAAATTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 1 0.03
14 32 0.97
ACGTcount: A:0.50, C:0.02, G:0.15, T:0.33
Consensus pattern (14 bp):
ATTGAAAATTAGAA
Found at i:35155974 original size:21 final size:21
Alignment explanation
Indices: 35155950--35155989 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35155940 TGAAAATTCA
*
35155950 AAATTTAAAATTAGAAATTGG
1 AAATTGAAAATTAGAAATTGG
* *
35155971 AAATTGGAAATTGGAAATT
1 AAATTGAAAATTAGAAATT
35155990 TAAATTTGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (21 bp):
AAATTGAAAATTAGAAATTGG
Found at i:35156004 original size:21 final size:20
Alignment explanation
Indices: 35155971--35156025 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
35155961 TAGAAATTGG
* * *
35155971 AAATTGGAAATTGGAAATTT
1 AAATTTGAAATTGAAAATAT
35155991 AAATTTGAATATTGAAAATAT
1 AAATTTGAA-ATTGAAAATAT
35156012 AAATTTGGAAATTG
1 AAATTT-GAAATTG
35156026 TGGAAAGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.27
21 19 0.63
22 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.36
Consensus pattern (20 bp):
AAATTTGAAATTGAAAATAT
Found at i:35156871 original size:24 final size:22
Alignment explanation
Indices: 35156806--35156864 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
35156796 TGTTGATAGT
*
35156806 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
35156828 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
35156850 ACGTACTAAGCTCTC
1 ACGTACTAAGCTCTC
35156865 TCTTGTTCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:35165357 original size:45 final size:46
Alignment explanation
Indices: 35165258--35166024 Score: 238
Period size: 45 Copynumber: 17.7 Consensus size: 46
35165248 GGCTTTAAGT
* * * *
35165258 TGCTCCACTGCAACTTCAGG-GAAATAAAATTTGC-CATCTTCAG-TC
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTA-CTT-AGATC
35165303 TGC-CTCACTGCAACTTCAGGAG-GATAAGACTTGCTTTACTTAGA-C
1 TGCTC-CACTGCAACTTCAGGAGAGATAAGACTTGC-TTACTTAGATC
* * **
35165348 TGCTCCACTGCAACTTTAGG-GAGATAAGACTAG---A-TGCGATC
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAGATC
* * * * *
35165389 TGCT-CTCTACAACTTCA-GAGAGATAAGATTTGAGGTT--TTA-ACC
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTT--GCTTACTTAGATC
* * * **
35165432 CGCT-CACTGCAACTTCA-GCGAGATAGGA-TTG-TCGGCTTTA-ATC
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCT-TAC-TTAGATC
* *
35165475 TGCTCCACTGCAACTTCAGG-GAGATAAGATTTGC-CATCTTCAG-TC
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTA-CTT-AGATC
* * *
35165520 TGC-CTCGCTGCAACTTCAGGAG-GATAGGACTTGCTTAATTAG-TC
1 TGCTC-CACTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAGATC
* **
35165564 TGCTCCACTGCAACTTCAGG-GAGATAAGACTAG---A-TGCGATC
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAGATC
* * * *
35165605 TGCT-CTCTGCAACTTTA-GAGAGATAAGATCTAAGGTT--TTA-ATC
1 TGCTCCACTGCAACTTCAGGAGAGATAAGA-CT-TGCTTACTTAGATC
** * * ** *
35165648 CAC-CCACTGCAACTTCA-GCGAGATAGGA-TTG-TCGGCTTTA-CTC
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCT-TAC-TTAGATC
* * *
35165691 TACTCCACTGCAACTTCAGG-GAGATAAGATTTGC-CATCTTCAG-TC
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTA-CTT-AGATC
* * * *
35165736 TGC-CTCGCTGCAACTTCAGAAG-GATAAGACTTGCTCAGTTAG-TC
1 TGCTC-CACTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAGATC
* * **
35165780 TGCTCTACTGCAACTTCA-G-G-GATAAGACTAG---A-TGCGATC
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAGATC
* * *
35165819 TGCT-CTCTGCAACTTCA-GAGAGATAAGATCTAAGGTT--TTA-ATC
1 TGCTCCACTGCAACTTCAGGAGAGATAAGA-CT-TGCTTACTTAGATC
* * * **
35165862 CGC-CCACTGCAACTTCA-GTGAGATAGGA-TTG-TCGGCTTTA-ATC
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCT-TAC-TTAGATC
* * * *
35165905 TGCTCCATTGTAACTTCAGG-GAGATAAGATTTGC-CATCTTCAG-TC
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTA-CTT-AGATC
* *
35165950 TGC-CTCGCTGCAACTTCAGGAG-GATAAGACTTGCTTATTTAG-TC
1 TGCTC-CACTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAGATC
*
35165994 TGCTCCACTGCAACTTCAAG-GAGATAAGACT
1 TGCTCCACTGCAACTTCAGGAGAGATAAGACT
35166025 CGATTTGTTA
Statistics
Matches: 555, Mismatches: 89, Indels: 157
0.69 0.11 0.20
Matches are distributed among these distances:
38 14 0.03
39 13 0.02
40 55 0.10
41 19 0.03
42 18 0.03
43 100 0.18
44 154 0.28
45 169 0.30
46 12 0.02
47 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (46 bp):
TGCTCCACTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAGATC
Found at i:35165449 original size:43 final size:45
Alignment explanation
Indices: 35165398--35165507 Score: 136
Period size: 43 Copynumber: 2.5 Consensus size: 45
35165388 CTGCTCTCTA
*
35165398 CAACTTCAGAGAGATAAGATTTG-AGGTTTTAACCCGCT-CACTG
1 CAACTTCAGAGAGATAAGATTTGTAGGCTTTAACCCGCTCCACTG
* * * * *
35165441 CAACTTCAGCGAGATAGGA-TTGTCGGCTTTAATCTGCTCCACTG
1 CAACTTCAGAGAGATAAGATTTGTAGGCTTTAACCCGCTCCACTG
*
35165485 CAACTTCAGGGAGATAAGATTTG
1 CAACTTCAGAGAGATAAGATTTG
35165508 CCATCTTCAG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 3 0.05
43 28 0.50
44 22 0.39
45 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (45 bp):
CAACTTCAGAGAGATAAGATTTGTAGGCTTTAACCCGCTCCACTG
Found at i:35165492 original size:44 final size:45
Alignment explanation
Indices: 35165210--35166024 Score: 320
Period size: 44 Copynumber: 18.8 Consensus size: 45
35165200 TTGGTACTTC
* * * * **
35165210 AATCTACTCCTCTACAACTTCAGGGAGATAGGA-TTACCGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCGGCTTT
* * * * ** *
35165254 AAGT-TGCTCCACTGCAACTTCAGGGAAATAAAATTTGCCATCTTC
1 AA-TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCGGCTTT
* ***
35165299 AGTCTGC-CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTTAC-TT
1 AATCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTG-TCGGCTTT
* *
35165344 AGA-CTGCTCCACTGCAACTTTAGGGAGATAAGACTAGAT--GC---
1 A-ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TCGGCTTT
* * * * * * *
35165385 GATCTGCT-CTCTACAACTTCAGAGAGATAAGATTTG-AGGTTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCGGCTTT
* * * *
35165428 AACCCGCT-CACTGCAACTTCAGCGAGATAGGA-TTGTCGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCGGCTTT
* * ** *
35165471 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCGGCTTT
* * * ****
35165516 AGTCTGC-CTCGCTGCAACTTCA-GGAGGATAGGACTTG-CTTAATT
1 AATCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGTCGGCTTT
* *
35165560 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGAT--GC---
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TCGGCTTT
* * * * ** *
35165601 GATCTGCT-CTCTGCAACTTTAGAGAGATAAGA-TCT-AAGGTTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGTCGGCTTT
** * *
35165644 AATCCAC-CCACTGCAACTTCAGCGAGATAGGA-TTGTCGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCGGCTTT
* * * * ** *
35165687 ACTCTACTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCGGCTTT
* * * *
35165732 AGTCTGC-CTCGCTGCAACTTCA-GAAGGATAAGACTTGCTCAG--TT
1 AATCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTG-TCGGCTTT
* * *
35165776 AGTCTGCTCTACTGCAACTTCA-GG-GATAAGACTAGAT--GC---
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TCGGCTTT
* * * ** *
35165815 GATCTGCT-CTCTGCAACTTCAGAGAGATAAGA-TCT-AAGGTTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGTCGGCTTT
* * *
35165858 AATCCGC-CCACTGCAACTTCAGTGAGATAGGA-TTGTCGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCGGCTTT
* * * * ** *
35165901 AATCTGCTCCATTGTAACTTCAGGGAGATAAGATTTGCCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCGGCTTT
* * ***
35165946 AGTCTGC-CTCGCTGCAACTTCA-GGAGGATAAGACTTG-CTTATTT
1 AATCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGTCGGCTTT
* *
35165990 AGTCTGCTCCACTGCAACTTCAAGGAGATAAGACT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
35166025 CGATTTGTTA
Statistics
Matches: 581, Mismatches: 135, Indels: 110
0.70 0.16 0.13
Matches are distributed among these distances:
38 11 0.02
39 9 0.02
40 55 0.09
41 11 0.02
42 16 0.03
43 110 0.19
44 190 0.33
45 172 0.30
46 7 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTCGGCTTT
Found at i:35165566 original size:89 final size:89
Alignment explanation
Indices: 35165473--35166022 Score: 296
Period size: 89 Copynumber: 6.3 Consensus size: 89
35165463 TCGGCTTTAA
*
35165473 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCGCTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCA
*
35165538 GGAGGATAGGACTTGCTTAATTAG
66 GGAGGATAAGACTTGCTTAATTAG
* * * * *
35165562 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG--A--TGC-GATCTG-CTCTCTGCAACTTT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAG-TCTGCCTCACTGCAACTTC
* * *
35165621 A-GAGAGATAAGATCTAAGGTT--TTAA
65 AGGAG-GATAAGA-CT-TGCTTAATTAG
** * * * ** * * *
35165646 TCCAC-CCACTGCAACTTCAGCGAGATAGGA-TTGTCGGCTTTACTCT-ACTCCACTGCAACTTC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCT-CACTGCAACTTC
* * *
35165708 AGG-GAGATAAGATTTGC-CATCTTCAG
65 AGGAG-GATAAGACTTGCTTA-ATT-AG
* * * *
35165734 TCTGC-CTCGCTGCAACTTCA-GAAGGATAAGACTTGCTCA-GTT-AGTCTG-CTCTACTGCAAC
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGATTTGC-CATCTTCAGTCTGCCTC-ACTGCAAC
* **
35165794 TTCA-G-GGATAAGACTAG----ATGCG
62 TTCAGGAGGATAAGACTTGCTTAATTAG
* * * **** * * *
35165816 ATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTAAGGT-TTTAATCCGCC-CACTGCAACTTC
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC
* **** *
35165878 AGTGA-GATAGGA-TTGTCGGCTTTAA
65 AG-GAGGATAAGACTTG-CTTAATTAG
* * *
35165903 TCTGCTCCATTGTAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCGCTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCA
*
35165968 GGAGGATAAGACTTGCTTATTTAG
66 GGAGGATAAGACTTGCTTAATTAG
*
35165992 TCTGCTCCACTGCAACTTCAAGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
35166023 CTCGATTTGT
Statistics
Matches: 342, Mismatches: 78, Indels: 82
0.68 0.16 0.16
Matches are distributed among these distances:
81 14 0.04
82 30 0.09
83 41 0.12
84 26 0.08
85 9 0.03
86 16 0.05
87 56 0.16
88 20 0.06
89 121 0.35
90 8 0.02
91 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (89 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCA
GGAGGATAAGACTTGCTTAATTAG
Found at i:35165922 original size:214 final size:216
Alignment explanation
Indices: 35165224--35166024 Score: 1311
Period size: 216 Copynumber: 3.7 Consensus size: 216
35165214 TACTCCTCTA
* ** * *
35165224 CAACTTCAGGGAGATAGGATTACCGGCTTTAAGT-TGCTCCACTGCAACTTCAGGGAAATAAAAT
1 CAACTTCAGCGAGATAGGATTGTCGGCTTTAA-TCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * *
35165288 TTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTTACTTAGACTGCTC
65 TTGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGC-TTAATTAGTCTGCTC
* *
35165353 CACTGCAACTTTAGGGAGATAAGACTAGATGCGATCTGCTCTCTACAACTTCAGAGAGATAAGAT
129 CACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGAT
* * * *
35165418 TTGAGGTTTTAACCCGCTCACTG
194 CTAAGGTTTTAATCCGCCCACTG
35165441 CAACTTCAGCGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
1 CAACTTCAGCGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
*
35165506 TGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAGGACTTGCTTAATTAGTCTGCTCCA
66 TGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCA
*
35165571 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTTAGAGAGATAAGATCT
131 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
*
35165636 AAGGTTTTAATCCACCCACTG
196 AAGGTTTTAATCCGCCCACTG
* *
35165657 CAACTTCAGCGAGATAGGATTGTCGGCTTTACTCTACTCCACTGCAACTTCAGGGAGATAAGATT
1 CAACTTCAGCGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
* * * *
35165722 TGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGAAGGATAAGACTTGCTCAGTTAGTCTGCTCTA
66 TGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCA
35165787 CTGCAACTTCA-GG-GATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
131 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
35165850 AAGGTTTTAATCCGCCCACTG
196 AAGGTTTTAATCCGCCCACTG
* * *
35165871 CAACTTCAGTGAGATAGGATTGTCGGCTTTAATCTGCTCCATTGTAACTTCAGGGAGATAAGATT
1 CAACTTCAGCGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
*
35165936 TGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGTCTGCTCCA
66 TGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCA
*
35166001 CTGCAACTTCAAGGAGATAAGACT
131 CTGCAACTTCAGGGAGATAAGACT
35166025 CGATTTGTTA
Statistics
Matches: 546, Mismatches: 35, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
214 201 0.37
215 4 0.01
216 237 0.43
217 104 0.19
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (216 bp):
CAACTTCAGCGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
TGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCA
CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
AAGGTTTTAATCCGCCCACTG
Found at i:35180284 original size:10 final size:10
Alignment explanation
Indices: 35180207--35180289 Score: 51
Period size: 10 Copynumber: 7.9 Consensus size: 10
35180197 TCTTTAAATG
35180207 ATTACTAAAAA
1 ATTA-TAAAAA
*
35180218 ATTACAAAACA
1 ATTATAAAA-A
35180229 ATTATAAAAA
1 ATTATAAAAA
*
35180239 A-TATCAGGAAA
1 ATTAT-A-AAAA
* * *
35180250 ACTATTAATA
1 ATTATAAAAA
*
35180260 ATTATAAGAA
1 ATTATAAAAA
*
35180270 GTTATAAAAA
1 ATTATAAAAA
35180280 ATTATTAAAA
1 ATTA-TAAAA
35180290 TTCTATAAAT
Statistics
Matches: 54, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
9 3 0.06
10 26 0.48
11 22 0.41
12 3 0.06
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.29
Consensus pattern (10 bp):
ATTATAAAAA
Found at i:35180668 original size:10 final size:10
Alignment explanation
Indices: 35180653--35180696 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
35180643 TCTAGTGTAG
*
35180653 TTTTTAACAA
1 TTTTTAATAA
*
35180663 TTTTTAAATAT
1 TTTTT-AATAA
*
35180674 TTTTTATTAA
1 TTTTTAATAA
35180684 TTTTTAATAA
1 TTTTTAATAA
35180694 TTT
1 TTT
35180697 AAAAATTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:35180805 original size:19 final size:21
Alignment explanation
Indices: 35180781--35180819 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
35180771 AATATTTACA
35180781 TTAATAAAA-T-AAATTATTG
1 TTAATAAAATTGAAATTATTG
35180800 TTAATAAAATTGAAATTATT
1 TTAATAAAATTGAAATTATT
35180820 TGTTCTCCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TTAATAAAATTGAAATTATTG
Found at i:35183190 original size:10 final size:11
Alignment explanation
Indices: 35183134--35183193 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
35183124 CTTAATCACT
*
35183134 TTAATATTAAA
1 TTAATATTATA
*
35183145 TTAATATAATA
1 TTAATATTATA
* *
35183156 TTTATTTTGTATA
1 -TTAATAT-TATA
*
35183169 TAAATATTATA
1 TTAATATTATA
35183180 TTAAT-TTATA
1 TTAATATTATA
35183190 TTAA
1 TTAA
35183194 GATAAGTATT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
10 9 0.24
11 17 0.45
12 9 0.24
13 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
TTAATATTATA
Found at i:35193613 original size:10 final size:9
Alignment explanation
Indices: 35193590--35193632 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
35193580 TTTTGGGGTT
35193590 TTAAAAAAA
1 TTAAAAAAA
35193599 TT--AAAAA
1 TTAAAAAAA
*
35193606 TTAATAAAA
1 TTAAAAAAA
35193615 TTAAAACAAA
1 TTAAAA-AAA
35193625 TTAAAAAA
1 TTAAAAAA
35193633 TAACTAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
7 7 0.24
9 13 0.45
10 9 0.31
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:35193614 original size:16 final size:16
Alignment explanation
Indices: 35193590--35193620 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35193580 TTTTGGGGTT
35193590 TTAAAAAAATTAAAAA
1 TTAAAAAAATTAAAAA
*
35193606 TTAATAAAATTAAAA
1 TTAAAAAAATTAAAA
35193621 CAAATTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TTAAAAAAATTAAAAA
Found at i:35194637 original size:12 final size:12
Alignment explanation
Indices: 35194620--35194645 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35194610 ACATAATTTA
35194620 AAATCATTTTTG
1 AAATCATTTTTG
35194632 AAATCATTTTTG
1 AAATCATTTTTG
35194644 AA
1 AA
35194646 GTGGTTTGGA
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:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
AAATCATTTTTG
Found at i:35198011 original size:18 final size:18
Alignment explanation
Indices: 35197980--35198017 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
35197970 TATATTATAA
35197980 TATTAATTAATAAAATAT
1 TATTAATTAATAAAATAT
* *
35197998 TATTACTTATTAAAATAT
1 TATTAATTAATAAAATAT
35198016 TA
1 TA
35198018 ATAAAAATAT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAATTAATAAAATAT
Found at i:35205926 original size:76 final size:76
Alignment explanation
Indices: 35205800--35205956 Score: 314
Period size: 76 Copynumber: 2.1 Consensus size: 76
35205790 AAGTGCTTTG
35205800 ACAACTCTATCAAAGATATTAACTTTAATTGTTCCAACACCTACGATTTTTACACGAAGGATTAT
1 ACAACTCTATCAAAGATATTAACTTTAATTGTTCCAACACCTACGATTTTTACACGAAGGATTAT
35205865 TTCCCATCAAA
66 TTCCCATCAAA
35205876 ACAACTCTATCAAAGATATTAACTTTAATTGTTCCAACACCTACGATTTTTACACGAAGGATTAT
1 ACAACTCTATCAAAGATATTAACTTTAATTGTTCCAACACCTACGATTTTTACACGAAGGATTAT
35205941 TTCCCATCAAA
66 TTCCCATCAAA
35205952 ACAAC
1 ACAAC
35205957 ACTTTCAGAC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 81 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.32
Consensus pattern (76 bp):
ACAACTCTATCAAAGATATTAACTTTAATTGTTCCAACACCTACGATTTTTACACGAAGGATTAT
TTCCCATCAAA
Found at i:35211360 original size:12 final size:12
Alignment explanation
Indices: 35211343--35211367 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35211333 GGTGTTCATT
35211343 CGGTTAACCGAC
1 CGGTTAACCGAC
35211355 CGGTTAACCGAC
1 CGGTTAACCGAC
35211367 C
1 C
35211368 CGAAATTACT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:35211540 original size:9 final size:9
Alignment explanation
Indices: 35211526--35211593 Score: 84
Period size: 9 Copynumber: 7.4 Consensus size: 9
35211516 TTTAGTTAAA
35211526 AATTACCCG
1 AATTACCCG
35211535 AATTACCCG
1 AATTACCCG
*
35211544 AATTAACCG
1 AATTACCCG
*
35211553 AATTAACCG
1 AATTACCCG
35211562 AATTA-CCG
1 AATTACCCG
*
35211570 AAAAATACCCG
1 --AATTACCCG
35211581 AATTACCCG
1 AATTACCCG
35211590 AATT
1 AATT
35211594 TTTTTATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
8 3 0.06
9 43 0.81
10 4 0.08
11 3 0.06
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:35211751 original size:13 final size:13
Alignment explanation
Indices: 35211733--35211762 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
35211723 TTTTAGTTTT
35211733 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
35211746 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
35211759 ATTG
1 ATTG
35211763 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:35229475 original size:45 final size:45
Alignment explanation
Indices: 35229415--35229506 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
35229405 TTTCAAACCG
* * *
35229415 AATAACCCGCAAATGGAATTTGCCTCTAATTATGGATACATAGCA
1 AATAACCCACAAATGGAAATTGCCTCTAACTATGGATACATAGCA
* * * *
35229460 AATAACCTACAAATGGAAATTGCCTCTACCTGTGGGTACATAGCA
1 AATAACCCACAAATGGAAATTGCCTCTAACTATGGATACATAGCA
35229505 AA
1 AA
35229507 ATTCTATTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (45 bp):
AATAACCCACAAATGGAAATTGCCTCTAACTATGGATACATAGCA
Found at i:35233836 original size:31 final size:30
Alignment explanation
Indices: 35233797--35233856 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
35233787 TAAAATTACA
*
35233797 ATTTAGTCATTGAACTATTCGAAAGTTTTC
1 ATTTAGTCATTGAACTATTCAAAAGTTTTC
*
35233827 ATTTAAGTCATTGAACTATTCAAAATTTTT
1 ATTT-AGTCATTGAACTATTCAAAAGTTTT
35233857 TTAATTGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (30 bp):
ATTTAGTCATTGAACTATTCAAAAGTTTTC
Found at i:35239509 original size:26 final size:29
Alignment explanation
Indices: 35239466--35239530 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 29
35239456 CTTTTATATA
**
35239466 AATTTTATAATTAATTATAA-TT-T-CTT
1 AATTTTATAACCAATTATAACTTATACTT
* *
35239492 AATTTTATAACCATTTATAACTTATATTT
1 AATTTTATAACCAATTATAACTTATACTT
35239521 AATTTTATAA
1 AATTTTATAA
35239531 ATACTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 17 0.53
27 2 0.06
28 1 0.03
29 12 0.38
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (29 bp):
AATTTTATAACCAATTATAACTTATACTT
Found at i:35240915 original size:3 final size:3
Alignment explanation
Indices: 35240907--35240967 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
35240897 AATTCAAAAG
35240907 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35240955 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
35240968 AAGAAACCAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35248411 original size:18 final size:18
Alignment explanation
Indices: 35248378--35248415 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
35248368 TCTTTTAATG
35248378 TTTATTTTATTATTATTA
1 TTTATTTTATTATTATTA
35248396 TTTATATTTATT-TTATTA
1 TTTAT-TTTATTATTATTA
35248414 TT
1 TT
35248416 CATGTTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTATTATTATTA
Found at i:35250033 original size:21 final size:20
Alignment explanation
Indices: 35250009--35250052 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
35249999 AAAATATTAA
* *
35250009 AAATACTTTTTATAATATTTT
1 AAATAATTTTAATAAT-TTTT
*
35250030 AAATAATTTTAATGATTTTT
1 AAATAATTTTAATAATTTTT
35250050 AAA
1 AAA
35250053 AATAAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
AAATAATTTTAATAATTTTT
Found at i:35250108 original size:7 final size:8
Alignment explanation
Indices: 35250073--35250114 Score: 75
Period size: 8 Copynumber: 5.2 Consensus size: 8
35250063 TGAATTTTTG
35250073 AATTTTAA
1 AATTTTAA
35250081 AATTTTAA
1 AATTTTAA
35250089 AATTTTAA
1 AATTTTAA
35250097 AATTTTAA
1 AATTTTAA
*
35250105 ATTTTTAA
1 AATTTTAA
35250113 AA
1 AA
35250115 ACTAATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AATTTTAA
Found at i:35250114 original size:24 final size:24
Alignment explanation
Indices: 35250055--35250114 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
35250045 TTTTTAAAAA
* **
35250055 TAAATTTTT-GAATTTTTGAATTT
1 TAAATTTTTAAAATTTTAAAATTT
*
35250078 TAAAATTTTAAAATTTTAAAATTT
1 TAAATTTTTAAAATTTTAAAATTT
35250102 TAAATTTTTAAAA
1 TAAATTTTTAAAA
35250115 ACTAATTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 8 0.26
24 23 0.74
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (24 bp):
TAAATTTTTAAAATTTTAAAATTT
Found at i:35250834 original size:20 final size:19
Alignment explanation
Indices: 35250802--35250844 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
35250792 AAAAAATAAT
*
35250802 TTTTAATTCTTTTATTCTC
1 TTTTAATTATTTTATTCTC
*
35250821 TTTTACATTATTTTTTTCTC
1 TTTTA-ATTATTTTATTCTC
35250841 TTTT
1 TTTT
35250845 TCCCCTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTAATTATTTTATTCTC
Found at i:35252903 original size:3 final size:3
Alignment explanation
Indices: 35252889--35252950 Score: 97
Period size: 3 Copynumber: 20.0 Consensus size: 3
35252879 ATACTTCAAG
35252889 ATA ATGA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
35252935 ATA ACA ATAA ATA ATA
1 ATA ATA AT-A ATA ATA
35252951 TGAAGATTTG
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:35254307 original size:16 final size:16
Alignment explanation
Indices: 35254286--35254319 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
35254276 TCAATCTTTC
35254286 TTCTCTTTCTCCTATT
1 TTCTCTTTCTCCTATT
* *
35254302 TTCTCTTTGTGCTATT
1 TTCTCTTTCTCCTATT
35254318 TT
1 TT
35254320 GTTATTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.24, G:0.06, T:0.65
Consensus pattern (16 bp):
TTCTCTTTCTCCTATT
Found at i:35254573 original size:14 final size:15
Alignment explanation
Indices: 35254551--35254579 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
35254541 TTTTGGGCTG
35254551 GTAATTTGGGTTATT
1 GTAATTTGGGTTATT
35254566 GTAA-TTGGGTTATT
1 GTAATTTGGGTTATT
35254580 TTTGGACTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (15 bp):
GTAATTTGGGTTATT
Found at i:35255915 original size:35 final size:35
Alignment explanation
Indices: 35255867--35255942 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
35255857 GATTATAAGA
* * *
35255867 AAAAATACTCAAATAAAATATCACTAAGTTTATAT
1 AAAATTACCCAAATAAAATATCACTAAATTTATAT
35255902 AAAATTACCCAAATAAAATATCACTAAATTTATAT
1 AAAATTACCCAAATAAAATATCACTAAATTTATAT
*
35255937 AGAATT
1 AAAATT
35255943 TTTCTTTAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.32
Consensus pattern (35 bp):
AAAATTACCCAAATAAAATATCACTAAATTTATAT
Found at i:35257114 original size:18 final size:19
Alignment explanation
Indices: 35257093--35257129 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
35257083 TTATTAAAAA
35257093 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
35257111 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
35257130 GAAAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:35257135 original size:18 final size:18
Alignment explanation
Indices: 35257094--35257136 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
35257084 TATTAAAAAT
*
35257094 ATAAATTTTAGAATTTTT
1 ATAAATTTTAGAATTTTG
35257112 ATAAATATTTAGAATTTTG
1 ATAAAT-TTTAGAATTTTG
35257131 A-AAATT
1 ATAAATT
35257137 AATTTGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 10 0.43
19 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (18 bp):
ATAAATTTTAGAATTTTG
Found at i:35260378 original size:6 final size:7
Alignment explanation
Indices: 35260351--35260376 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
35260341 TGTGTTATAA
35260351 AAAAAAT
1 AAAAAAT
35260358 AAAAAAT
1 AAAAAAT
35260365 AAAAAAT
1 AAAAAAT
35260372 AAAAA
1 AAAAA
35260377 TAGAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:35261504 original size:32 final size:32
Alignment explanation
Indices: 35261458--35261539 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 32
35261448 TGTCAATCAT
*
35261458 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAACTTAAAACATAATAAA
* * * *
35261490 TTCAATATCTAACAAATTTAAGACATAATAAT
1 TTCAATATCCAACAAACTTAAAACATAATAAA
* *
35261522 TTCAAAACCCAACAAACT
1 TTCAATATCCAACAAACT
35261540 AATTTCAATA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.51, C:0.20, G:0.02, T:0.27
Consensus pattern (32 bp):
TTCAATATCCAACAAACTTAAAACATAATAAA
Found at i:35265019 original size:4 final size:4
Alignment explanation
Indices: 35265012--35265112 Score: 202
Period size: 4 Copynumber: 25.2 Consensus size: 4
35265002 TTATTACTGA
35265012 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
35265060 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
35265108 ACAT A
1 ACAT A
35265113 TAAACAAAAT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 97 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:35266100 original size:17 final size:18
Alignment explanation
Indices: 35266078--35266111 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35266068 AACATCACAT
35266078 ATAAATTCATTT-ATAAC
1 ATAAATTCATTTCATAAC
*
35266095 ATAAATTGATTTCATAA
1 ATAAATTCATTTCATAA
35266112 GATGCATCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (18 bp):
ATAAATTCATTTCATAAC
Found at i:35283600 original size:28 final size:28
Alignment explanation
Indices: 35283513--35283601 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 28
35283503 TATACAGTGT
* * *
35283513 CAGT-ACAGTGTGGGCCTTCGCCCATTA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
* ** * *
35283540 CAGTATCAGCGTGGACCTTAGCCTAATA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
*
35283568 CAGTAACAATGTGGGCCTTAGCCCAGTA
1 CAGTAACAATGTGGGCCTTAGCCCAATA
*
35283596 TAGTAA
1 CAGTAA
35283602 ATAGTACAAT
Statistics
Matches: 48, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
27 4 0.08
28 44 0.92
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.25
Consensus pattern (28 bp):
CAGTAACAATGTGGGCCTTAGCCCAATA
Found at i:35283736 original size:26 final size:26
Alignment explanation
Indices: 35283706--35283785 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 26
35283696 GTCAACACAC
35283706 CAATATCGCAGCAAAGCTGCCAGTAA
1 CAATATCGCAGCAAAGCTGCCAGTAA
* *
35283732 TAATAAT-GCAGCAGAGCTGCCAGTAA
1 CAAT-ATCGCAGCAAAGCTGCCAGTAA
* * *
35283758 CAGTAGCACAGCAAAGCTGCCAGTAA
1 CAATATCGCAGCAAAGCTGCCAGTAA
35283784 CA
1 CA
35283786 GTATTTGTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
25 1 0.02
26 42 0.93
27 2 0.04
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15
Consensus pattern (26 bp):
CAATATCGCAGCAAAGCTGCCAGTAA
Found at i:35283998 original size:27 final size:26
Alignment explanation
Indices: 35283979--35284098 Score: 78
Period size: 27 Copynumber: 4.5 Consensus size: 26
35283969 TTTGCCTTAT
35283979 GGGGGTATTTCGGGCATTTTACCCTTC
1 GGGGGTATTTCGGGCATTTTA-CCTTC
* *
35284006 GGGGGTATTTTGGTCATTTTACCTTTC
1 GGGGGTATTTCGGGCATTTTACC-TTC
*** **** *
35284033 AAAGGTATTTCAATAATTTTACCCTTT
1 GGGGGTATTTCGGGCATTTTA-CCTTC
* ** *
35284060 GAGGGTATTTCGGTAATTTTACCTTAT
1 GGGGGTATTTCGGGCATTTTACCTT-C
35284087 GGGGGTATTTCG
1 GGGGGTATTTCG
35284099 ATAATTTTAC
Statistics
Matches: 75, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
26 6 0.08
27 67 0.89
28 2 0.03
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.42
Consensus pattern (26 bp):
GGGGGTATTTCGGGCATTTTACCTTC
Found at i:35284103 original size:27 final size:27
Alignment explanation
Indices: 35283994--35284241 Score: 238
Period size: 27 Copynumber: 9.2 Consensus size: 27
35283984 TATTTCGGGC
* * * * *
35283994 ATTTTACCCTTCGGGGGTATTTTGGTC
1 ATTTTACCCTTTGAGGGTATTTCGATA
* * *
35284021 ATTTTA-CCTTTCAAAGGTATTTCAATA
1 ATTTTACCCTTT-GAGGGTATTTCGATA
*
35284048 ATTTTACCCTTTGAGGGTATTTCGGTA
1 ATTTTACCCTTTGAGGGTATTTCGATA
*
35284075 ATTTTA-CCTTATGGGGGTATTTCGATA
1 ATTTTACCCTT-TGAGGGTATTTCGATA
*
35284102 ATTTTACCCTTTGAAGGTATTTCGATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
*
35284129 ATTTTACCCTTTGAGGGTATTT-TAGTA
1 ATTTTACCCTTTGAGGGTATTTCGA-TA
* *
35284156 ATTTTACCC-TTCAGTGGTATTTCGGTA
1 ATTTTACCCTTTGAG-GGTATTTCGATA
* * *
35284183 ATTTTATCCTTTGAGGGTATTTTGGTA
1 ATTTTACCCTTTGAGGGTATTTCGATA
*
35284210 ATTTTACCCTATATGA--GTATTTTGATA
1 ATTTTACCCT-T-TGAGGGTATTTCGATA
35284237 ATTTT
1 ATTTT
35284242 TCAGCCCAAG
Statistics
Matches: 185, Mismatches: 26, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
26 13 0.07
27 155 0.84
28 14 0.08
29 3 0.02
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (27 bp):
ATTTTACCCTTTGAGGGTATTTCGATA
Found at i:35284230 original size:81 final size:78
Alignment explanation
Indices: 35283994--35284241 Score: 268
Period size: 81 Copynumber: 3.1 Consensus size: 78
35283984 TATTTCGGGC
* * * * *
35283994 ATTTTACCCTTCGGGGGTATTTTGGTCATTTTACCTTTCAAAGGTATTTCAATAATTTTACCCTT
1 ATTTTACCCTTCAGGGGTATTTCGGTAATTTTACCTTT-GAAGGTATTTCGATAATTTTACCCTT
*
35284059 TGAGGGTATTTCGGTA
65 TGA-GGTATTT-TGTA
*
35284075 ATTTTA-CCTT-ATGGGGGTATTTCGATAATTTTACCCTTTGAAGGTATTTCGATAATTTTACCC
1 ATTTTACCCTTCA--GGGGTATTTCGGTAATTTTA-CCTTTGAAGGTATTTCGATAATTTTACCC
35284138 TTTGAGGGTATTTTAGTA
63 TTTGA-GGTATTTT-GTA
* * * *
35284156 ATTTTACCCTTCAGTGGTATTTCGGTAATTTTATCCTTTGAGGGTATTTTGGTAATTTTACCCTA
1 ATTTTACCCTTCAGGGGTATTTCGGTAATTTTA-CCTTTGAAGGTATTTCGATAATTTTACCCT-
35284221 TATGA-GTATTTTGATA
64 T-TGAGGTATTTTG-TA
35284237 ATTTT
1 ATTTT
35284242 TCAGCCCAAG
Statistics
Matches: 145, Mismatches: 13, Indels: 18
0.82 0.07 0.10
Matches are distributed among these distances:
80 5 0.03
81 126 0.87
82 10 0.07
83 4 0.03
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (78 bp):
ATTTTACCCTTCAGGGGTATTTCGGTAATTTTACCTTTGAAGGTATTTCGATAATTTTACCCTTT
GAGGTATTTTGTA
Found at i:35292720 original size:28 final size:28
Alignment explanation
Indices: 35292673--35292772 Score: 123
Period size: 28 Copynumber: 3.6 Consensus size: 28
35292663 GAGCCCTATA
*
35292673 CAATATCAGT-ACAATGTGGGCCTTAGCC
1 CAATA-CAGTAACAACGTGGGCCTTAGCC
* * *
35292701 CATTACAGTAATAGCGTGGGCCTTAGCC
1 CAATACAGTAACAACGTGGGCCTTAGCC
* *
35292729 AAATACAGTAACAATGTGGGCCTTAGCC
1 CAATACAGTAACAACGTGGGCCTTAGCC
35292757 CAATACAGTAA-AACGT
1 CAATACAGTAACAACGT
35292773 ACAATGCAGT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
27 8 0.13
28 52 0.87
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (28 bp):
CAATACAGTAACAACGTGGGCCTTAGCC
Found at i:35293146 original size:27 final size:27
Alignment explanation
Indices: 35293102--35293563 Score: 445
Period size: 27 Copynumber: 17.2 Consensus size: 27
35293092 TATATCATTC
* *
35293102 ATTTTACCCTAT-GGGGGTATTTCGGTC
1 ATTTTACCCT-TCGAGGGTATTTCGGTA
** *
35293129 ATTTTACCCTTCGAGGGTATTTTAGTT
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
35293156 ATTTTACCCTTTGAGGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* **
35293183 ATTTTACCCTTCGGGGGTATTTTAGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* * ***
35293210 ATTTTACCCTTCAAGGATATTTTAATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* * *
35293237 ATTTTACCATATTG-GGGTATTTCAGTA
1 ATTTTACCCT-TCGAGGGTATTTCGGTA
* *
35293264 ATTTTACCCTTCAAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
35293291 ATTTTACCCTTCGAGGGTATTTTGGTG
1 ATTTTACCCTTCGAGGGTATTTCGGTA
*
35293318 ATTTTACCCTTCGAGGGT-TTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* * * *
35293344 ATTTTACTCTTCAAGGTTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
*
35293371 ATTTTACCCTT--ATGGGTATTTTGGTA
1 ATTTTACCCTTCGA-GGGTATTTCGGTA
* *
35293397 ATTTTA-CCTTATGGGGGTATTTCGGTA
1 ATTTTACCCTT-CGAGGGTATTTCGGTA
* *
35293424 ATTTTACCCTAT-AAGGGTATTTCAGTA
1 ATTTTACCCT-TCGAGGGTATTTCGGTA
* **
35293451 ATTTTACCCTTTGAGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
35293478 ATTTTTCCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
35293505 ATTTTACCCTTCAAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGGTA
* *
35293532 ATTTTACCCTAT-GGGGGTATTTTGGTA
1 ATTTTACCCT-TCGAGGGTATTTCGGTA
35293559 ATTTT
1 ATTTT
35293564 CTGGCCCAAG
Statistics
Matches: 368, Mismatches: 55, Indels: 24
0.82 0.12 0.05
Matches are distributed among these distances:
25 5 0.01
26 41 0.11
27 316 0.86
28 5 0.01
29 1 0.00
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.45
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGGTA
Found at i:35305229 original size:12 final size:11
Alignment explanation
Indices: 35305196--35305229 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
35305186 ATTCATATAC
35305196 CAAAAAAAAAA
1 CAAAAAAAAAA
35305207 -AAAAAAAAAA
1 CAAAAAAAAAA
35305217 CAAAGAAAAAAA
1 CAAA-AAAAAAA
35305229 C
1 C
35305230 GGAGATCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 3 0.14
12 8 0.38
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:35307453 original size:22 final size:21
Alignment explanation
Indices: 35307401--35307455 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
35307391 CTCTCTCCAA
*
35307401 GGTTAGGGCTTTTTATTTTTAT
1 GGTTAGGG-TTTTTATTTTTAG
35307423 GGTTAAGGG-TTTTATTTTATTAG
1 GGTT-AGGGTTTTTA-TTT-TTAG
35307446 GGTTAGGGTT
1 GGTTAGGGTT
35307456 AGGATTTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 5 0.18
22 11 0.39
23 12 0.43
ACGTcount: A:0.16, C:0.02, G:0.29, T:0.53
Consensus pattern (21 bp):
GGTTAGGGTTTTTATTTTTAG
Found at i:35312328 original size:18 final size:18
Alignment explanation
Indices: 35312305--35312341 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
35312295 AAGTTACATA
*
35312305 GGTACGGACACGGGCTGG
1 GGTACGGAAACGGGCTGG
35312323 GGTACGGAAACGGGCTGG
1 GGTACGGAAACGGGCTGG
35312341 G
1 G
35312342 ACATGACCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.19, G:0.51, T:0.11
Consensus pattern (18 bp):
GGTACGGAAACGGGCTGG
Found at i:35313191 original size:17 final size:18
Alignment explanation
Indices: 35313171--35313208 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
35313161 TTTTATATAA
*
35313171 TTATTAAGTA-TTTTAAG
1 TTATTAAGGAGTTTTAAG
*
35313188 TTATTTAGGAGTTTTAAG
1 TTATTAAGGAGTTTTAAG
35313206 TTA
1 TTA
35313209 ACAAAAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (18 bp):
TTATTAAGGAGTTTTAAG
Found at i:35314793 original size:28 final size:29
Alignment explanation
Indices: 35314762--35314856 Score: 111
Period size: 29 Copynumber: 3.3 Consensus size: 29
35314752 AATAGAGTTT
* * *
35314762 GCCATAATG-CATTCATTTAACTAAGATA
1 GCCATAAAGACATCCATTTAACAAAGATA
* *
35314790 GCCACAAAGACATCCTTTTAACAAAGATA
1 GCCATAAAGACATCCATTTAACAAAGATA
* * *
35314819 GCCATAAAGATATCCTTTTAACAGAGATA
1 GCCATAAAGACATCCATTTAACAAAGATA
35314848 GCCATAAAG
1 GCCATAAAG
35314857 GCTTCTTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
28 7 0.12
29 51 0.88
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (29 bp):
GCCATAAAGACATCCATTTAACAAAGATA
Found at i:35314879 original size:28 final size:28
Alignment explanation
Indices: 35314777--35314926 Score: 126
Period size: 29 Copynumber: 5.2 Consensus size: 28
35314767 AATGCATTCA
* *
35314777 TTTAACTA-AGATAGCCACAAAGACATCCT
1 TTTAAC-AGAGATAGCCACAAAGGC-TTCT
* * *
35314806 TTTAACAAAGATAGCCATAAA-GATATCCT
1 TTTAACAGAGATAGCCACAAAGGCT-T-CT
*
35314835 TTTAACAGAGATAGCCATAAAGGCTTCT
1 TTTAACAGAGATAGCCACAAAGGCTTCT
* *
35314863 TTTAACAGATACT-GCCACAAAGGCTTCC
1 TTTAACAGAGA-TAGCCACAAAGGCTTCT
** *
35314891 TTTAGTAGAGATAGCCACAAAGGCTCCCT
1 TTTAACAGAGATAGCCACAAAGGCT-TCT
35314920 TTTAACA
1 TTTAACA
35314927 TAACCAGCTA
Statistics
Matches: 98, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
27 2 0.02
28 46 0.47
29 48 0.49
30 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (28 bp):
TTTAACAGAGATAGCCACAAAGGCTTCT
Found at i:35317903 original size:21 final size:20
Alignment explanation
Indices: 35317864--35317903 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
35317854 ACTGTTGATT
*
35317864 TTCAAAAGAAAATAGAGGAA
1 TTCAAAAGAAAACAGAGGAA
*
35317884 TTCAAATAGAGAACAGAGGA
1 TTCAAA-AGAAAACAGAGGA
35317904 TTTTTAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.55, C:0.07, G:0.23, T:0.15
Consensus pattern (20 bp):
TTCAAAAGAAAACAGAGGAA
Found at i:35320117 original size:112 final size:114
Alignment explanation
Indices: 35319904--35320137 Score: 339
Period size: 112 Copynumber: 2.1 Consensus size: 114
35319894 AGAATTAAAC
* *
35319904 AAAA-AAATTAAGAATGTGTTGGGCTGAGTAACTGCGGTGGGGTGCTTGGGTTGTCATTCCACTT
1 AAAATAAATTAAGAATATGTTGGGCTGAGTAACTGCGGTGGGGTGCTTGGGTTGTCACTCCACTT
*
35319968 CGCGTCAAAAGGGCCAAAACATTCTTAAACAAAAAAAAAAAATATAAT-
66 CGCGTCAAAAGGGCCAAAACATTCTTAAACAAAAAAAAAAAATAAAATA
* * * *
35320016 ATAATAAATTAAGAGTATGTTGGGCTGAGTAACTGGGGTGGGGTG-TTTGGTTGTCACTCCACTT
1 AAAATAAATTAAGAATATGTTGGGCTGAGTAACTGCGGTGGGGTGCTTGGGTTGTCACTCCACTT
* * * **
35320080 CGCGTCAAAAGGGCCAATACATTTTTAAGCATTAAAAAAAAATAAAATA
66 CGCGTCAAAAGGGCCAAAACATTCTTAAACAAAAAAAAAAAATAAAATA
35320129 AAAATAAAT
1 AAAATAAAT
35320138 AAGTAAAACG
Statistics
Matches: 107, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
112 62 0.58
113 45 0.42
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (114 bp):
AAAATAAATTAAGAATATGTTGGGCTGAGTAACTGCGGTGGGGTGCTTGGGTTGTCACTCCACTT
CGCGTCAAAAGGGCCAAAACATTCTTAAACAAAAAAAAAAAATAAAATA
Found at i:35327195 original size:18 final size:18
Alignment explanation
Indices: 35327172--35327207 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35327162 TCCCTCTCCC
35327172 TTCTCTTTTTTTCTATAT
1 TTCTCTTTTTTTCTATAT
*
35327190 TTCTCTTTTTTTGTATAT
1 TTCTCTTTTTTTCTATAT
35327208 AAAAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.14, G:0.03, T:0.72
Consensus pattern (18 bp):
TTCTCTTTTTTTCTATAT
Found at i:35330424 original size:30 final size:30
Alignment explanation
Indices: 35330390--35330469 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 30
35330380 AGCTTCGGGT
*
35330390 ATCAAATTATAAAAAGGGATGGTAACAACC
1 ATCAAATTATGAAAAGGGATGGTAACAACC
** * *
35330420 ATCAAACAATGAAAAGGGATGGTGACGACC
1 ATCAAATTATGAAAAGGGATGGTAACAACC
*
35330450 ATTAAATTATGAAAAGGGAT
1 ATCAAATTATGAAAAGGGAT
35330470 TGCTTCGACT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.20
Consensus pattern (30 bp):
ATCAAATTATGAAAAGGGATGGTAACAACC
Found at i:35349199 original size:14 final size:14
Alignment explanation
Indices: 35349180--35349219 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
35349170 TTGATTGGCA
35349180 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
35349194 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
35349208 GGAAAATGTTTT
1 GTAAAATGTTTT
35349220 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:35349228 original size:20 final size:20
Alignment explanation
Indices: 35349203--35349242 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35349193 CGTAAAATGA
*
35349203 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
35349223 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
35349243 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:35349232 original size:34 final size:35
Alignment explanation
Indices: 35349188--35349254 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
35349178 CAGTAAAATG
*
35349188 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
35349222 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
35349255 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:35349258 original size:14 final size:15
Alignment explanation
Indices: 35349182--35349258 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
35349172 GATTGGCAGT
* *
35349182 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
35349196 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
35349210 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
35349230 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
35349245 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
35349259 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:35349319 original size:32 final size:32
Alignment explanation
Indices: 35349235--35349320 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 32
35349225 TCTGTAAAAT
* * *
35349235 GATTTACTGGAAAATATTTTCTGGTGTTTGATT
1 GATTTCCT-GAAAATATTTTCTGCTGTTTGATA
* *
35349268 GA-ATCTGTGTAAAATATTTTCTGCTGTTTGATA
1 GATTTC-CTG-AAAATATTTTCTGCTGTTTGATA
35349301 GATTTCCTGAAAATATTTTC
1 GATTTCCTGAAAATATTTTC
35349321 CGGAAAAGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
32 13 0.30
33 28 0.65
34 2 0.05
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (32 bp):
GATTTCCTGAAAATATTTTCTGCTGTTTGATA
Found at i:35349366 original size:20 final size:20
Alignment explanation
Indices: 35349341--35349379 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
35349331 GTTTTTACAT
35349341 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
35349361 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
35349380 TTTTAAATTA
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Done.