Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 54 of 91
Found at i:19197688 original size:2 final size:2
Alignment explanation
Indices: 19197681--19197712 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19197671 TGAAACAAGG
19197681 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
19197713 GTTAGTAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19199908 original size:34 final size:35
Alignment explanation
Indices: 19199835--19199962 Score: 145
Period size: 35 Copynumber: 3.7 Consensus size: 35
19199825 CTGTTGATTT
* *
19199835 TTTTGAGGAAGAACAGG-GCAGCTTTGGCTGTCGAG
1 TTTTGAGGGAGAA-AGGAGCAGCTTTCGCTGTCGAG
* * *
19199870 TTTTGAGGGAGAAAGGAGTAGC-TTCGCTGTTGAT
1 TTTTGAGGGAGAAAGGAGCAGCTTTCGCTGTCGAG
* * *
19199904 TTTTGA-GGAAAAATGGAGCAGCTTTTGCTATCGAG
1 TTTTGAGGGAGAAA-GGAGCAGCTTTCGCTGTCGAG
19199939 TTTTGAGGGAGAAAGGAGCAGCTT
1 TTTTGAGGGAGAAAGGAGCAGCTT
19199963 GGCTTGTCAC
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
33 6 0.08
34 25 0.32
35 40 0.52
36 6 0.08
ACGTcount: A:0.26, C:0.11, G:0.34, T:0.29
Consensus pattern (35 bp):
TTTTGAGGGAGAAAGGAGCAGCTTTCGCTGTCGAG
Found at i:19199925 original size:69 final size:70
Alignment explanation
Indices: 19199803--19199962 Score: 209
Period size: 69 Copynumber: 2.3 Consensus size: 70
19199793 GCTGCCATCT
* * * *
19199803 AGGGAGGAAAAGAGCATCTTGGCTGTTGATTTTTTTGAGGAAGAACAGGGCAGCTTTGGCTGTCG
1 AGGGA-GAAAGGAGCAGCTTCGCTGTTGA-TTTTTTGAGGAAGAACAGGGCAGCTTTGGCTATCG
19199868 AGTTTTG
64 AGTTTTG
* *
19199875 AGGGAGAAAGGAGTAGCTTCGCTGTTGA-TTTTTGAGGAA-AA-ATGGAGCAGCTTTTGCTATCG
1 AGGGAGAAAGGAGCAGCTTCGCTGTTGATTTTTTGAGGAAGAACA-GG-GCAGCTTTGGCTATCG
19199937 AGTTTTG
64 AGTTTTG
19199944 AGGGAGAAAGGAGCAGCTT
1 AGGGAGAAAGGAGCAGCTT
19199963 GGCTTGTCAC
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
67 1 0.01
68 4 0.05
69 50 0.63
71 19 0.24
72 5 0.06
ACGTcount: A:0.26, C:0.11, G:0.34, T:0.29
Consensus pattern (70 bp):
AGGGAGAAAGGAGCAGCTTCGCTGTTGATTTTTTGAGGAAGAACAGGGCAGCTTTGGCTATCGAG
TTTTG
Found at i:19213228 original size:23 final size:22
Alignment explanation
Indices: 19213193--19213259 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
19213183 TTAGATTGGT
19213193 ATCAAAGCCTTTGGTTTTAAAG
1 ATCAAAGCCTTTGGTTTTAAAG
19213215 ATCAAAGGCCTTTGGTTTTAAAG
1 ATCAAA-GCCTTTGGTTTTAAAG
* * * *
19213238 ATTAGAGCTTTTGGGTTTAAAG
1 ATCAAAGCCTTTGGTTTTAAAG
19213260 TTGTTTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 20 0.50
23 20 0.50
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.37
Consensus pattern (22 bp):
ATCAAAGCCTTTGGTTTTAAAG
Found at i:19214935 original size:16 final size:15
Alignment explanation
Indices: 19214914--19214958 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
19214904 ATATAGCATA
19214914 TATTTTTATATATTTT
1 TATTTTTAT-TATTTT
19214930 TATTTTTATT-TTTT
1 TATTTTTATTATTTT
*
19214944 TA-ATTTATTATTTT
1 TATTTTTATTATTTT
19214958 T
1 T
19214959 CAACTAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 6 0.22
14 11 0.41
15 1 0.04
16 9 0.33
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TATTTTTATTATTTT
Found at i:19216554 original size:13 final size:13
Alignment explanation
Indices: 19216533--19216562 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19216523 TAGTACTATT
*
19216533 TTTTTCTTTTTTC
1 TTTTCCTTTTTTC
19216546 TTTTCCTTTTTTC
1 TTTTCCTTTTTTC
19216559 TTTT
1 TTTT
19216563 ATTTTGTTTC
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:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCCTTTTTTC
Found at i:19216567 original size:12 final size:12
Alignment explanation
Indices: 19216534--19216567 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
19216524 AGTACTATTT
19216534 TTTTCTTTTTTC
1 TTTTCTTTTTTC
19216546 TTTTCCTTTTTTC
1 TTTT-CTTTTTTC
*
19216559 TTTTATTTT
1 TTTTCTTTT
19216568 GTTTCTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:19220227 original size:34 final size:34
Alignment explanation
Indices: 19220189--19220253 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
19220179 GGTAAATATG
*
19220189 ACACATGGACTAATGAAATGGTGACACATGGCAA
1 ACACATGGACTAATGAAATAGTGACACATGGCAA
*
19220223 ACACATGGACTAATGGAATAGTGACACATGG
1 ACACATGGACTAATGAAATAGTGACACATGG
19220254 TAAATTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (34 bp):
ACACATGGACTAATGAAATAGTGACACATGGCAA
Found at i:19224135 original size:38 final size:38
Alignment explanation
Indices: 19224059--19224153 Score: 104
Period size: 38 Copynumber: 2.4 Consensus size: 38
19224049 CCCATTTCAT
19224059 GTGCATCCCCCCACATCGTGCACATAGCCGAAGTCATCGA
1 GTGCATCCCCCCACATCGTG-ACATAGCC-AAGTCATCGA
* * *
19224099 GTGCATCCCCCCACATTGTG-CATAGTC-AGTGCCATCGT
1 GTGCATCCCCCCACATCGTGACATAGCCAAGT--CATCGA
*
19224137 GTACATCCCCCCACATC
1 GTGCATCCCCCCACATC
19224154 ATGCACACGG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
36 3 0.06
38 26 0.54
40 19 0.40
ACGTcount: A:0.22, C:0.39, G:0.18, T:0.21
Consensus pattern (38 bp):
GTGCATCCCCCCACATCGTGACATAGCCAAGTCATCGA
Found at i:19225796 original size:25 final size:25
Alignment explanation
Indices: 19225768--19225821 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
19225758 AAAGAGAGAT
*
19225768 TGGGCATAGCTTAATAAGAA-AAGAA
1 TGGGCATAGCCTAATAAGAAGAA-AA
* *
19225793 TGGGCATGGCCTAATAGGAAGAAAA
1 TGGGCATAGCCTAATAAGAAGAAAA
19225818 TGGG
1 TGGG
19225822 AAGAGCCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.41, C:0.09, G:0.31, T:0.19
Consensus pattern (25 bp):
TGGGCATAGCCTAATAAGAAGAAAA
Found at i:19227110 original size:54 final size:54
Alignment explanation
Indices: 19227042--19227146 Score: 183
Period size: 54 Copynumber: 1.9 Consensus size: 54
19227032 CAATGACTCT
* * *
19227042 GGCTATGTGTACGATGTGGGGTGATGCACATGAGCTGGGTGAGATGGGGTGTCC
1 GGCTATGTGCACGATGTAGGGTGATGCACATGAGCTGGGTGAGACGGGGTGTCC
19227096 GGCTATGTGCACGATGTAGGGTGATGCACATGAGCTGGGTGAGACGGGGTG
1 GGCTATGTGCACGATGTAGGGTGATGCACATGAGCTGGGTGAGACGGGGTG
19227147 AGATGGCGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.18, C:0.13, G:0.45, T:0.24
Consensus pattern (54 bp):
GGCTATGTGCACGATGTAGGGTGATGCACATGAGCTGGGTGAGACGGGGTGTCC
Found at i:19238417 original size:18 final size:16
Alignment explanation
Indices: 19238375--19238429 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 16
19238365 GTGGAAAGAG
19238375 GTAATTTCTATTAATTA
1 GTAATTTC-ATTAATTA
*
19238392 GCTTATTTCATTATATATA
1 G-TAATTTCATTA-AT-TA
*
19238411 GTAATTTCATTAATGA
1 GTAATTTCATTAATTA
19238427 GTA
1 GTA
19238430 TTAATAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 4 0.12
17 7 0.22
18 18 0.56
19 3 0.09
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (16 bp):
GTAATTTCATTAATTA
Found at i:19239736 original size:21 final size:22
Alignment explanation
Indices: 19239711--19239751 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
19239701 CCTAGGTGGA
19239711 AAAATTCAAGGAAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
19239732 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
19239752 AAAAAAGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.54, C:0.07, G:0.22, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:19239757 original size:22 final size:21
Alignment explanation
Indices: 19239710--19239757 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
19239700 CCCTAGGTGG
*
19239710 AAAAATTCAAGGAAAAAGTGT
1 AAAAATTCAAGGAAAAAGTGA
*
19239731 GAAAATTCAAGGAAACAAGTGA
1 AAAAATTCAAGGAAA-AAGTGA
19239753 AAAAA
1 AAAAA
19239758 GGTAAGATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.60, C:0.06, G:0.19, T:0.15
Consensus pattern (21 bp):
AAAAATTCAAGGAAAAAGTGA
Found at i:19243910 original size:35 final size:36
Alignment explanation
Indices: 19243856--19243929 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 36
19243846 AGGTAGCGTC
* *
19243856 TTGATAAAGGTTACGCCTGATCTTACAAAAGGCATG
1 TTGATAAAGCTTACGCCTGATCCTACAAAAGGCATG
* *
19243892 TTGA-AAAGCTTATGCCTGATCCTGCAAAAGGCATG
1 TTGATAAAGCTTACGCCTGATCCTACAAAAGGCATG
19243927 TTG
1 TTG
19243930 TGAAGGTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
35 30 0.88
36 4 0.12
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (36 bp):
TTGATAAAGCTTACGCCTGATCCTACAAAAGGCATG
Found at i:19251139 original size:30 final size:32
Alignment explanation
Indices: 19251103--19251166 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
19251093 AAGAAGGGAG
*
19251103 AGAAAATCAA-AGAAAAA-GTGTGAATTTTCA
1 AGAAAATCAAGAGAAAAAGGTATGAATTTTCA
* * *
19251133 AGAAAATTAAGTGAAAAAGGTATGATTTTTCA
1 AGAAAATCAAGAGAAAAAGGTATGAATTTTCA
19251165 AG
1 AG
19251167 CTTAGCTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 9 0.32
31 6 0.21
32 13 0.46
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.27
Consensus pattern (32 bp):
AGAAAATCAAGAGAAAAAGGTATGAATTTTCA
Found at i:19251992 original size:15 final size:17
Alignment explanation
Indices: 19251955--19251995 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
19251945 AAATCCTTAT
19251955 ATTTTATAAGTAAAATG
1 ATTTTATAAGTAAAATG
19251972 -TGTTTA-AA-TAAAATG
1 AT-TTTATAAGTAAAATG
19251987 ATTTTATAA
1 ATTTTATAA
19251996 ATTGTCATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
15 11 0.52
16 6 0.29
17 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (17 bp):
ATTTTATAAGTAAAATG
Found at i:19252017 original size:55 final size:54
Alignment explanation
Indices: 19251951--19252055 Score: 183
Period size: 55 Copynumber: 1.9 Consensus size: 54
19251941 TGGTAAATCC
*
19251951 TTATATTTTATAAGTAAAATGTGTTTAAATAAAATGATTTTATAAATTGTCATCT
1 TTATATTTTATAAGTAAAATGTGTTTAAATAAAACGA-TTTATAAATTGTCATCT
*
19252006 TTATGTTTTATAAGTAAAATGTGTTTAAATAAAACGATTTATAAATTGTC
1 TTATATTTTATAAGTAAAATGTGTTTAAATAAAACGATTTATAAATTGTC
19252056 TTGAAATTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
54 13 0.27
55 35 0.73
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (54 bp):
TTATATTTTATAAGTAAAATGTGTTTAAATAAAACGATTTATAAATTGTCATCT
Found at i:19255187 original size:28 final size:27
Alignment explanation
Indices: 19255151--19255203 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
19255141 ATATCCTGGT
*
19255151 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
19255178 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
19255204 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:19255271 original size:20 final size:20
Alignment explanation
Indices: 19255248--19255293 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
19255238 CTTCTAAACC
19255248 TCAAATCATACT-TCAATAAG
1 TCAAATCATACTCT-AATAAG
*
19255268 TCAAATTATACTCTAATAAG
1 TCAAATCATACTCTAATAAG
19255288 TCAAAT
1 TCAAAT
19255294 GGGGTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (20 bp):
TCAAATCATACTCTAATAAG
Found at i:19256315 original size:34 final size:34
Alignment explanation
Indices: 19256227--19256315 Score: 142
Period size: 34 Copynumber: 2.6 Consensus size: 34
19256217 TTTGACTGCT
* * *
19256227 AAAAATTTGAGCTATTTGCTACCAATTTGTGTAG
1 AAAAATTTGAGCTGTTTGCTGCCAATTTGTGCAG
19256261 AAAAATTTGAGCTGTTTGCTGCCAATTTGTGCAG
1 AAAAATTTGAGCTGTTTGCTGCCAATTTGTGCAG
*
19256295 AAAAATTAGAGCTGTTTGCTG
1 AAAAATTTGAGCTGTTTGCTG
19256316 GTAGTTTGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (34 bp):
AAAAATTTGAGCTGTTTGCTGCCAATTTGTGCAG
Found at i:19256324 original size:34 final size:34
Alignment explanation
Indices: 19256227--19256335 Score: 137
Period size: 34 Copynumber: 3.2 Consensus size: 34
19256217 TTTGACTGCT
* * *
19256227 AAAAATTTGAGCTATTTGCTACCAATTTGTGTAG
1 AAAAATTAGAGCTGTTTGCTGCCAATTTGTGTAG
* *
19256261 AAAAATTTGAGCTGTTTGCTGCCAATTTGTGCAG
1 AAAAATTAGAGCTGTTTGCTGCCAATTTGTGTAG
** *
19256295 AAAAATTAGAGCTGTTTGCTGGTAGTTTGTGTAG
1 AAAAATTAGAGCTGTTTGCTGCCAATTTGTGTAG
*
19256329 GAAAATT
1 AAAAATT
19256336 GGACAGCATT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (34 bp):
AAAAATTAGAGCTGTTTGCTGCCAATTTGTGTAG
Found at i:19256486 original size:6 final size:6
Alignment explanation
Indices: 19256462--19256507 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
19256452 AAGAAACGTG
* *
19256462 GAAAAGA GAAAAA G--AAA GAAGAA GAAAAA GAAAAA GAAATA GAAAA
1 GAAAA-A GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
19256508 TAAATAGGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
4 4 0.12
6 24 0.73
7 5 0.15
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:19256489 original size:16 final size:15
Alignment explanation
Indices: 19256463--19256499 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
19256453 AGAAACGTGG
19256463 AAAAG-AGAAAAAGA
1 AAAAGAAGAAAAAGA
19256477 AAGAAGAAGAAAAAGA
1 AA-AAGAAGAAAAAGA
19256493 AAAAGAA
1 AAAAGAA
19256500 ATAGAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 8 0.38
16 11 0.52
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAAAAGA
Found at i:19256528 original size:25 final size:25
Alignment explanation
Indices: 19256499--19256561 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
19256489 AAGAAAAAGA
19256499 AATAGAAAATAAATAGGCATGACCC
1 AATAGAAAATAAATAGGCATGACCC
* * * *
19256524 AATAGAAAATAAGTGGGCATGGCTC
1 AATAGAAAATAAATAGGCATGACCC
*
19256549 AATAGGAAATAAA
1 AATAGAAAATAAA
19256562 AATAAATGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.51, C:0.11, G:0.21, T:0.17
Consensus pattern (25 bp):
AATAGAAAATAAATAGGCATGACCC
Found at i:19269389 original size:71 final size:71
Alignment explanation
Indices: 19269236--19269389 Score: 222
Period size: 71 Copynumber: 2.2 Consensus size: 71
19269226 TTAATAGAGT
* * *
19269236 TATCAAAACCTAAGCTTCAACGTATCGAGACTTCACCTCCGGCTTCAGTTTCCAAAGAGCAAGTG
1 TATCAAAACCCAAGCTTCAACATATCGAGACTTCACCTCCGGCTTCAGTTTCCAAAGAGCAAGCG
*
19269301 CCTAAG
66 CCGAAG
*
19269307 TATCAAAACCCAAGCTTCAACATATCGAGACTTCACCTCCAGGCTTTAGTTTCCAGAA-AGCAAG
1 TATCAAAACCCAAGCTTCAACATATCGAGACTTCACCTCC-GGCTTCAGTTTCCA-AAGAGCAAG
19269371 CGCCGAAG
64 CGCCGAAG
*
19269379 T-TCAAGACCCA
1 TATCAAAACCCA
19269390 CTATTAAAGT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
71 47 0.63
72 26 0.35
73 2 0.03
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.22
Consensus pattern (71 bp):
TATCAAAACCCAAGCTTCAACATATCGAGACTTCACCTCCGGCTTCAGTTTCCAAAGAGCAAGCG
CCGAAG
Found at i:19270324 original size:61 final size:60
Alignment explanation
Indices: 19270238--19270455 Score: 265
Period size: 61 Copynumber: 3.6 Consensus size: 60
19270228 ATCATCACTG
* * * *
19270238 GCATGTGCACTGCCCACTCAACACATGCACGATTGTAATTATCACGACATGATCATTACCG
1 GCATGTGCACTGCCCACTCCACACATGCACGGTTGTAATTATCATGACA-GATCATTACCA
* * * *
19270299 GCATGTGCACTACCCACTCCGCACATGGACGGTTGTAATTATCATGACAACATCATTACCA
1 GCATGTGCACTGCCCACTCCACACATGCACGGTTGTAATTATCATGAC-AGATCATTACCA
* * * * * *
19270360 GTATGTGCACTGCCTACTCCATACATGGACGGTTATAATTATCATGATAGCATCATTACCA
1 GCATGTGCACTGCCCACTCCACACATGCACGGTTGTAATTATCATGACAG-ATCATTACCA
* *
19270421 GCATGTGCACTGCCCACTCCGCACATGCATGGTTG
1 GCATGTGCACTGCCCACTCCACACATGCACGGTTG
19270456 CATTTGTCAC
Statistics
Matches: 132, Mismatches: 23, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
60 1 0.01
61 130 0.98
62 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (60 bp):
GCATGTGCACTGCCCACTCCACACATGCACGGTTGTAATTATCATGACAGATCATTACCA
Found at i:19288031 original size:20 final size:20
Alignment explanation
Indices: 19288008--19288046 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
19287998 ACTTCTATGG
19288008 ATAAATGAGC-AAATCTATCC
1 ATAAATGA-CTAAATCTATCC
19288028 ATAAATGACTAAATCTATC
1 ATAAATGACTAAATCTATC
19288047 AAGATATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (20 bp):
ATAAATGACTAAATCTATCC
Found at i:19290109 original size:22 final size:23
Alignment explanation
Indices: 19290058--19290100 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
19290048 CTATAAATAT
19290058 CATCTTCCAACAGCTTCTTCTCA
1 CATCTTCCAACAGCTTCTTCTCA
*
19290081 CAT-TTCCAACAGCTTTTTCT
1 CATCTTCCAACAGCTTCTTCT
19290101 TCTTCTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.21, C:0.35, G:0.05, T:0.40
Consensus pattern (23 bp):
CATCTTCCAACAGCTTCTTCTCA
Found at i:19291038 original size:43 final size:41
Alignment explanation
Indices: 19290908--19291040 Score: 185
Period size: 42 Copynumber: 3.1 Consensus size: 41
19290898 TTATGTGATA
* *
19290908 ATGATGACCGAGCTATGTGTGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCG-GTGGGAGTGCACATGAGCTG
*
19290950 ATGATGACCCAGCTATGTGCGGTGTGCAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCGGTG-GGAGTGCACATGAGCTG
* *
19290992 ATGATGACCTAGCTATGTGCGAATGGGAAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCG-GTGGG-AGTGCACATGAGCTG
19291035 ATGATG
1 ATGATG
19291041 GGGGGATGGT
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
41 3 0.04
42 56 0.68
43 23 0.28
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.25
Consensus pattern (41 bp):
ATGATGACCCAGCTATGTGCGGTGGGAGTGCACATGAGCTG
Found at i:19291073 original size:2 final size:2
Alignment explanation
Indices: 19291066--19291120 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
19291056 TGATGATGTG
19291066 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
19291108 TA TA TA TA AA TA T
1 TA TA TA TA TA TA T
19291121 GTGTGTTATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 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):
TA
Found at i:19291368 original size:30 final size:30
Alignment explanation
Indices: 19291332--19291402 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
19291322 TGGTTTGATT
19291332 CTTGCTGCAGCGAGAAAGTTGTCGAAGCTC
1 CTTGCTGCAGCGAGAAAGTTGTCGAAGCTC
* *
19291362 CTTGCTGTAGCGAGAAAGTTGTTGAAGCTC
1 CTTGCTGCAGCGAGAAAGTTGTCGAAGCTC
*
19291392 CTCGCTGCAGC
1 CTTGCTGCAGC
19291403 AAAAAAATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.25
Consensus pattern (30 bp):
CTTGCTGCAGCGAGAAAGTTGTCGAAGCTC
Found at i:19293831 original size:38 final size:38
Alignment explanation
Indices: 19293775--19293852 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 38
19293765 GATCATGATT
* *
19293775 ATATTGAAATGTGTGAGTAAGGAGAGCACATGATAATG
1 ATATGGAAATGTGCGAGTAAGGAGAGCACATGATAATG
* * *
19293813 ATATGGAAATGTGCGAGTAGGGAGGGCACATGATGATG
1 ATATGGAAATGTGCGAGTAAGGAGAGCACATGATAATG
19293851 AT
1 AT
19293853 TTTGCTTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.24
Consensus pattern (38 bp):
ATATGGAAATGTGCGAGTAAGGAGAGCACATGATAATG
Found at i:19304214 original size:44 final size:44
Alignment explanation
Indices: 19304159--19304322 Score: 192
Period size: 38 Copynumber: 4.0 Consensus size: 44
19304149 TCATTGTGTG
* **
19304159 ATGAGATTGAAATGTGTTAGTAGGGAGTA-CACATGATGATGATA
1 ATGATATTGAAATGTGCGAGTAGGGAG-AGCACATGATGATGATA
19304203 ATGATATTGAAATGTGCGAGTAGGGAGAGCAC------ATGATA
1 ATGATATTGAAATGTGCGAGTAGGGAGAGCACATGATGATGATA
19304241 ATGATATTGAAATGTGCGAGTAGGGAGAGCACATGATGATGAT-
1 ATGATATTGAAATGTGCGAGTAGGGAGAGCACATGATGATGATA
*
19304284 ATG-----GAAATGTGCGAGTAGGGAGAGCACATGATAATGATA
1 ATGATATTGAAATGTGCGAGTAGGGAGAGCACATGATGATGATA
19304323 TTGCCTTGTG
Statistics
Matches: 108, Mismatches: 4, Indels: 21
0.81 0.03 0.16
Matches are distributed among these distances:
38 72 0.67
43 4 0.04
44 32 0.30
ACGTcount: A:0.37, C:0.07, G:0.32, T:0.25
Consensus pattern (44 bp):
ATGATATTGAAATGTGCGAGTAGGGAGAGCACATGATGATGATA
Found at i:19304239 original size:38 final size:38
Alignment explanation
Indices: 19304197--19304352 Score: 249
Period size: 38 Copynumber: 4.1 Consensus size: 38
19304187 ACACATGATG
19304197 ATGATAATGATATTGAAATGTGCGAGTAGGGAGAGCAC
1 ATGATAATGATATTGAAATGTGCGAGTAGGGAGAGCAC
19304235 ATGATAATGATATTGAAATGTGCGAGTAGGGAGAGCAC
1 ATGATAATGATATTGAAATGTGCGAGTAGGGAGAGCAC
* *
19304273 ATGATGATGATATGGAAATGTGCGAGTAGGGAGAGCAC
1 ATGATAATGATATTGAAATGTGCGAGTAGGGAGAGCAC
*** * *
19304311 ATGATAATGATATTGCCTTGTGCGTGTAGGGAGTGCAC
1 ATGATAATGATATTGAAATGTGCGAGTAGGGAGAGCAC
19304349 ATGA
1 ATGA
19304353 GCTTAGTTAG
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 109 1.00
ACGTcount: A:0.33, C:0.09, G:0.33, T:0.25
Consensus pattern (38 bp):
ATGATAATGATATTGAAATGTGCGAGTAGGGAGAGCAC
Found at i:19305955 original size:10 final size:10
Alignment explanation
Indices: 19305942--19305977 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
19305932 TACATATCAT
19305942 ATATATTTAG
1 ATATATTTAG
19305952 ATATATTTAG
1 ATATATTTAG
* *
19305962 ATATATATAT
1 ATATATTTAG
19305972 ATATAT
1 ATATAT
19305978 ATATCAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATATATTTAG
Found at i:19308032 original size:2 final size:2
Alignment explanation
Indices: 19308025--19308061 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19308015 GCACTTGTTG
19308025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19308062 ATACTTAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19308214 original size:2 final size:2
Alignment explanation
Indices: 19308207--19308241 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19308197 NNNNNNNNNG
19308207 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19308242 CAAATACTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19319787 original size:38 final size:39
Alignment explanation
Indices: 19319700--19319798 Score: 112
Period size: 38 Copynumber: 2.5 Consensus size: 39
19319690 TCATGTGCAT
* * *
19319700 TCCCCCCACATCGTGCACATAGCTGGAGTCATCGTGTGCA
1 TCCCCCCACATCGTGCACATA-CTGAAGCCATCGTGTACA
* * *
19319740 TCCCTCCACATCGTGCACAT-CT-AATGCCGTCGTGTACG
1 TCCCCCCACATCGTGCACATACTGAA-GCCATCGTGTACA
19319778 TCCCCCCACATCGTGCACATA
1 TCCCCCCACATCGTGCACATA
19319799 GGCAATATCA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 1 0.02
38 30 0.60
40 19 0.38
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.23
Consensus pattern (39 bp):
TCCCCCCACATCGTGCACATACTGAAGCCATCGTGTACA
Found at i:19323208 original size:20 final size:20
Alignment explanation
Indices: 19323167--19323227 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
19323157 ACACGTATAT
19323167 ACCCATCATCATCATCTCACCA
1 ACCCATCATCATCA--TCACCA
19323189 ACCCATCATCATCATCACCA
1 ACCCATCATCATCATCACCA
* *
19323209 GCTCATCATCATCATCACC
1 ACCCATCATCATCATCACC
19323228 GGGTTATGCG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 23 0.62
22 14 0.38
ACGTcount: A:0.31, C:0.44, G:0.02, T:0.23
Consensus pattern (20 bp):
ACCCATCATCATCATCACCA
Found at i:19327559 original size:13 final size:13
Alignment explanation
Indices: 19327522--19327565 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
19327512 CCCTTTCTTC
*
19327522 TTTATTTCTTTTCT
1 TTTATTTC-TCTCT
*
19327536 TTCTCTTTCTCTCT
1 TT-TATTTCTCTCT
19327550 TTTATTTCTCTCT
1 TTTATTTCTCTCT
19327563 TTT
1 TTT
19327566 TCTTACTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 13 0.50
14 8 0.31
15 5 0.19
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATTTCTCTCT
Found at i:19327563 original size:27 final size:27
Alignment explanation
Indices: 19327514--19327575 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
19327504 CTTCCTTCCC
*
19327514 CTTTCT-TCTTTATTTCTTTTCTTTCT
1 CTTTCTCTCTTTATTTCTTCTCTTTCT
*
19327540 CTTTCTCTCTTTTATTTC-TCTCTTTTT
1 CTTTCTCTC-TTTATTTCTTCTCTTTCT
*
19327567 CTTACTCTC
1 CTTTCTCTC
19327576 GGGTGGAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 6 0.19
27 17 0.55
28 8 0.26
ACGTcount: A:0.05, C:0.27, G:0.00, T:0.68
Consensus pattern (27 bp):
CTTTCTCTCTTTATTTCTTCTCTTTCT
Found at i:19327569 original size:19 final size:19
Alignment explanation
Indices: 19327515--19327569 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
19327505 TTCCTTCCCC
* *
19327515 TTTCTTCTTTATTTCTTTTC
1 TTTC-TCTTTCTTTCTTTTA
*
19327535 TTTCTCTTTCTCTCTTTTA
1 TTTCTCTTTCTTTCTTTTA
19327554 TTTCTCTCTT-TTTCTT
1 TTTCTCT-TTCTTTCTT
19327570 ACTCTCGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 24 0.80
20 6 0.20
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTCTCTTTCTTTCTTTTA
Found at i:19332009 original size:26 final size:26
Alignment explanation
Indices: 19331974--19332024 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
19331964 GAAAGCTTAA
*
19331974 TAGTTAGGGTT-TTACCTTCAAAATG
1 TAGTTAGGGTTCTAACCTTCAAAATG
19331999 TAGTTGAGGGTTGCTAACCTTCAAAA
1 TAGTT-AGGGTT-CTAACCTTCAAAA
19332025 AATGTGGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 6 0.27
28 11 0.50
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (26 bp):
TAGTTAGGGTTCTAACCTTCAAAATG
Found at i:19333628 original size:2 final size:2
Alignment explanation
Indices: 19333621--19333647 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19333611 TTATACATAG
19333621 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19333648 CCACATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19334848 original size:35 final size:34
Alignment explanation
Indices: 19334799--19334951 Score: 137
Period size: 35 Copynumber: 4.4 Consensus size: 34
19334789 CTTCTGCCTC
* *
19334799 TTTCAACCTTAAAAATCAATAACCAAAATTGCTCA
1 TTTCAACCTCAAAAATCAATAGCCAAAA-TGCTCA
* * *
19334834 TTTCAGCCTCAAAAATCAACAGCCAAAGCTGCTCA
1 TTTCAACCTCAAAAATCAATAGCCAAA-ATGCTCA
** **
19334869 TTTCCCCCTC-AAAATCGGTAGCCAAACATGCTCA
1 TTTCAACCTCAAAAATCAATAGCCAAA-ATGCTCA
** *
19334903 TTTCAACCTCAAAAATCAGCAGCCAAAGCTGCTCA
1 TTTCAACCTCAAAAATCAATAGCCAAA-ATGCTCA
**
19334938 TTTCCCCCTCAAAA
1 TTTCAACCTCAAAA
19334952 TCGTCAACCA
Statistics
Matches: 96, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
34 27 0.28
35 69 0.72
ACGTcount: A:0.37, C:0.31, G:0.08, T:0.24
Consensus pattern (34 bp):
TTTCAACCTCAAAAATCAATAGCCAAAATGCTCA
Found at i:19334892 original size:34 final size:34
Alignment explanation
Indices: 19334828--19334963 Score: 148
Period size: 35 Copynumber: 3.9 Consensus size: 34
19334818 TAACCAAAAT
** **
19334828 TGCTCATTTCAGCCTCAAAAATCAACAGCCAAAGC
1 TGCTCATTTCCCCCTC-AAAATCGGCAGCCAAAGC
*
19334863 TGCTCATTTCCCCCTCAAAATCGGTAGCCAAA-C
1 TGCTCATTTCCCCCTCAAAATCGGCAGCCAAAGC
** *
19334896 ATGCTCATTTCAACCTCAAAAATCAGCAGCCAAAGC
1 -TGCTCATTTCCCCCTC-AAAATCGGCAGCCAAAGC
* *
19334932 TGCTCATTTCCCCCTCAAAATCGTCAACCAAA
1 TGCTCATTTCCCCCTCAAAATCGGCAGCCAAA
19334964 ACCTCAAAAA
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
33 1 0.01
34 40 0.48
35 42 0.50
36 1 0.01
ACGTcount: A:0.34, C:0.34, G:0.10, T:0.22
Consensus pattern (34 bp):
TGCTCATTTCCCCCTCAAAATCGGCAGCCAAAGC
Found at i:19334963 original size:69 final size:69
Alignment explanation
Indices: 19334818--19334964 Score: 235
Period size: 69 Copynumber: 2.1 Consensus size: 69
19334808 TAAAAATCAA
*
19334818 TAACCAAAATTGCTCATTTCAGCCTCAAAAATCAACAGCCAAAGCTGCTCATTTCCCCCTCAAAA
1 TAACCAAAATTGCTCATTTCAACCTCAAAAATCAACAGCCAAAGCTGCTCATTTCCCCCTCAAAA
19334883 TCGG
66 TCGG
* *
19334887 TAGCCAAACA-TGCTCATTTCAACCTCAAAAATCAGCAGCCAAAGCTGCTCATTTCCCCCTCAAA
1 TAACCAAA-ATTGCTCATTTCAACCTCAAAAATCAACAGCCAAAGCTGCTCATTTCCCCCTCAAA
19334951 ATC-G
65 ATCGG
19334955 TCAACCAAAA
1 T-AACCAAAA
19334965 CCTCAAAAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
68 3 0.04
69 68 0.94
70 1 0.01
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.22
Consensus pattern (69 bp):
TAACCAAAATTGCTCATTTCAACCTCAAAAATCAACAGCCAAAGCTGCTCATTTCCCCCTCAAAA
TCGG
Found at i:19334983 original size:91 final size:92
Alignment explanation
Indices: 19334888--19335107 Score: 277
Period size: 91 Copynumber: 2.4 Consensus size: 92
19334878 CAAAATCGGT
*
19334888 AGCCAAACATGCTCATTTCAACCTCAAAAATCAGCAGCCAAAGCTGCTCATTTCCCCCTCAAAA-
1 AGCCAAACATGCTCATTTCAGCCTCAAAAATCAGCAGCCAAAGCTGCTCATTTCCCCCTCAAAAC
19334952 TCGTCAACCAAAACCTC-AAAAATCAAC
66 TCGT-AACCAAAACCTCAAAAAATCAAC
* * * *
19334979 AGCCAAA-ACTACTCATTTCAGCCTCAAAAATCAGTAGCCAAAGTTGCTCATTTCCCCCTTAAAA
1 AGCCAAACA-TGCTCATTTCAGCCTCAAAAATCAGCAGCCAAAGCTGCTCATTTCCCCCTCAAAA
* * *
19335043 CTTGTAGCCAAAACCTCAAAAAAATCAGC
65 CTCGTAACCAAAACCTC-AAAAAATCAAC
* *
19335072 AACCAAAGC-TGCTCCTTTCAGCCTTCAAAAATCAGC
1 AGCCAAA-CATGCTCATTTCAGCC-TCAAAAATCAGC
19335108 CCTTTCTTTC
Statistics
Matches: 110, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
90 1 0.01
91 68 0.62
92 3 0.03
93 27 0.25
94 11 0.10
ACGTcount: A:0.38, C:0.32, G:0.09, T:0.21
Consensus pattern (92 bp):
AGCCAAACATGCTCATTTCAGCCTCAAAAATCAGCAGCCAAAGCTGCTCATTTCCCCCTCAAAAC
TCGTAACCAAAACCTCAAAAAATCAAC
Found at i:19335324 original size:18 final size:19
Alignment explanation
Indices: 19335297--19335337 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
19335287 TGTTTCTCTC
*
19335297 CTTTTTCTTTCC-TTTGCT
1 CTTTTGCTTTCCTTTTGCT
19335315 CTTTTGCTTTCCTTTTGCT
1 CTTTTGCTTTCCTTTTGCT
19335334 CTTT
1 CTTT
19335338 CTCACAACCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.00, C:0.27, G:0.07, T:0.66
Consensus pattern (19 bp):
CTTTTGCTTTCCTTTTGCT
Found at i:19350299 original size:172 final size:172
Alignment explanation
Indices: 19349779--19351228 Score: 1563
Period size: 172 Copynumber: 8.5 Consensus size: 172
19349769 CCTCAATTGG
* * * *
19349779 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTGAC-TCTCCTTTTTGTTTAAA
1 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTT-TCTTTTCATTTTTGGTTAAA
* * * * * * ** *
19349843 ACATATCATAATTTAATATTTGCAATGGTAAACGTGAAGCGAAAGCTAACCATTGGTAGGAAAAG
65 ACATATCATAATTTCATGTTTGCATTGGGAAACATGAAGCGAAAGCCAACCATTGACAAGAAAAG
* * *
19349908 TTCATTTATAGTCACTTAT-GCCTTCGAAAGCCTAGTTACTTGC
130 TCCATTTATAGTCACTCATAG-CTTCGAAAGCCTAGTTACTCGC
* * *
19349951 TTTAAATAGTTTTATACA-CTTATAAATGATTTTAAATTGAATTTTCTTTTTATTTTTTGTTAAA
1 TTTAAATGGTTTTATA-ATCTTATAAATGATTTTAAATTGAATTTTCTTTTCATTTTTGGTTAAA
* * * * * * * *
19350015 A-AGATCACAATTTCATGTTTTCACTAGAAAATATGAAGCGAAAGCCAACCATTGGCAAGAAAAG
65 ACATATCATAATTTCATGTTTGCATTGGGAAACATGAAGCGAAAGCCAACCATTGACAAGAAAAG
* *
19350079 TCCATTTACAGTCACTCA-AGCCTTCAAAAGCCTAGTTACTCGC
130 TCCATTTATAGTCACTCATAG-CTTCGAAAGCCTAGTTACTCGC
* * * *
19350122 TTTAAATGCTTTTATAATGTTATAAATGATATTCAAA-TGAATTTTCTTTTTATTTTTGGTTAAA
1 TTTAAATGGTTTTATAATCTTATAAATGAT-TTTAAATTGAATTTTCTTTTCATTTTTGGTTAAA
* * * * * *
19350186 ACATATCATAATTTCATGTTT-CGATTGGAAAACGTGAAGTGGAA-CATAACAATTGACAAGAAA
65 ACATATCATAATTTCATGTTTGC-ATTGGGAAACATGAAGCGAAAGC-CAACCATTGACAAGAAA
*
19350249 AGTCCATTTATAGTCACTCATAGCTTCGAAAGCCTAGTTACTCAC
128 AGTCCATTTATAGTCACTCATAGCTTCGAAAGCCTAGTTACTCGC
* * * *
19350294 TTTAAATGATTTTATAATCTTATAAATAATTTTAAGTTGAA--TTCTTTTCTTATTTTTAGTTAA
1 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTTCTTTTC--ATTTTTGGTTAA
**
19350357 AACATATCATAATTT-ATTGTTTGCATTGGGAAACATGAAGCGAAAGCCAACCATTGACGGGAAA
64 AACATATCATAATTTCA-TGTTTGCATTGGGAAACATGAAGCGAAAGCCAACCATTGACAAGAAA
* * * * *
19350421 AGTCCATTTATATTCACTCAT-GCATTTGAAAGGCTAGCTACTCTC
128 AGTCCATTTATAGTCACTCATAGC-TTCGAAAGCCTAGTTACTCGC
* * *
19350466 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTTCTTTTTATTTTAGATTAAAA
1 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTTCTTTTCATTTTTGGTTAAAA
* * * * *
19350531 CATATCATAATTTAATGTTTTCATTAGGAAACGTAAAGCGAAAGCCAACCATTGACAAGAAAAGT
66 CATATCATAATTTCATGTTTGCATTGGGAAACATGAAGCGAAAGCCAACCATTGACAAGAAAAGT
* * * *
19350596 CTATTTACAGTCACTCATAGCTTTGAAAGCCTAGTTACTCGT
131 CCATTTATAGTCACTCATAGCTTCGAAAGCCTAGTTACTCGC
* * * *
19350638 TTTAAATGGTTTTGTAATCATATAAATGATTTTAAATTGAATTTTCTTTTAATTTTTAGTTAAAA
1 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTTCTTTTCATTTTTGGTTAAAA
* * * * *
19350703 CAAATCTTAATTTCATGTTTGCATTGGGAAACATGAAGC-AGAAGCCAACCTTTCACAAGGAAA-
66 CATATCATAATTTCATGTTTGCATTGGGAAACATGAAGCGA-AAGCCAACCATTGACAAGAAAAG
* * ** *
19350766 TCCATTTATAATCATTCAT-GCCTTCGAAAGCCTAAATACTCAC
130 TCCATTTATAGTCACTCATAG-CTTCGAAAGCCTAGTTACTCGC
* * * ***
19350809 TTTTAATGGTTTTATAATCTTATTAATGATTTTAAATTGAATTTTGTTTTCGGCTTTGGTTAAAA
1 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTTCTTTTCATTTTTGGTTAAAA
* * * * * *
19350874 CAAATCATAATTTCATGTTTCCATCGGGAAACATGAAGCGAAAGCTAACAATTGACAAGAAAAAT
66 CATATCATAATTTCATGTTTGCATTGGGAAACATGAAGCGAAAGCCAACCATTGACAAGAAAAGT
* **
19350939 CCATTTATAGTCCCTCATAGCTTTAAAAGCCTAGTTACTCGC
131 CCATTTATAGTCACTCATAGCTTCGAAAGCCTAGTTACTCGC
* * * **
19350981 TTTAAATGGCTTCATAATATTATAAACAATTTTAAATTGAATTTGT-TTTCTCA-TTTTGGTTAA
1 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTT-TCTTT-TCATTTTTGGTTAA
* * * ** ** * *
19351044 AACAGATCATAATTTAATGTTTGCATTGGTAAATGTGATTCGAAAACCACCCATTGACAAGAAAA
64 AACATATCATAATTTCATGTTTGCATTGGGAAACATGAAGCGAAAGCCAACCATTGACAAGAAAA
* * * *
19351109 GTCCATTTATAGTTACTTATTAG-TTTGAAAGCCTAGTTACTCAC
129 GTCCATTTATAGTCACTCA-TAGCTTCGAAAGCCTAGTTACTCGC
* * * **
19351153 TTTAAATGG-TTTGTAGTCTTATAAATGATTTTAAATTGAATTTT-TTCTCATTTTTAATTAAAA
1 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTTCTTTTCATTTTTGGTTAAAA
* *
19351216 TAGATCATAATTT
66 CATATCATAATTT
19351229 TTAAAAAACA
Statistics
Matches: 1076, Mismatches: 173, Indels: 60
0.82 0.13 0.05
Matches are distributed among these distances:
169 3 0.00
170 34 0.03
171 318 0.30
172 699 0.65
173 15 0.01
174 7 0.01
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39
Consensus pattern (172 bp):
TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTTCTTTTCATTTTTGGTTAAAA
CATATCATAATTTCATGTTTGCATTGGGAAACATGAAGCGAAAGCCAACCATTGACAAGAAAAGT
CCATTTATAGTCACTCATAGCTTCGAAAGCCTAGTTACTCGC
Found at i:19350772 original size:515 final size:510
Alignment explanation
Indices: 19349779--19351228 Score: 1706
Period size: 515 Copynumber: 2.8 Consensus size: 510
19349769 CCTCAATTGG
** **
19349779 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTGACTCTCCTTTTTGTTTAAAA
1 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTT-TTTCTTATTTTTG-TTAAAA
* * * * **
19349844 CATATCATAATTTAATATTTGCAATGGTAAACGTGAAGCGAAAGCTAACCATTGGTAGGAAAAGT
64 CATATCATAATTT-ATGTTTGCATTGGGAAACATGAAGCGAAAGCTAACCATTGACAGGAAAAGT
* * * *
19349909 TCATTTATAGTCACTTATGCCTTCGAAAGCCTAGTTACT-TGCTTTAAATAGTTTTATACA-CTT
128 CCATTTATAGTCACTCATG-CTTTGAAAGCCTAGTTACTCT-CTTTAAATGGTTTTATA-ATCTT
* *
19349972 ATAAATGATTTTAAATTGAATTTTCTTTTTATTTTTTGTTAAAA-AGATCACAATTTCATGTTTT
190 ATAAATGATTTTAAATTGAATTTTCTTTTTA--TTTTGTTAAAACAGATCATAATTTAATGTTTT
* * * *
19350036 CACTAGAAAATATGAAGCGAAAGCCAACCATTGGCAAGAAAAGTCCATTTACAGTCACTCA-AGC
253 CATTAGGAAATGTGAAGCGAAAGCCAACCATTGACAAGAAAAGTCCATTTACAGTCACTCATAG-
** * * * *
19350100 CTTCAAAAGCCTAGTTACTCGCTTTAAATGCTTTTATAATGTTATAAATGATATTCAAA-TGAAT
317 CTTTGAAAGCCTAGTTACTCGCTTTAAATGGTTTTGTAATCTTATAAATGAT-TTTAAATTGAAT
* * * * **
19350164 TTTCTTTTTATTTTTGGTTAAAACATATCATAATTTCATGTTTCGATTGGAAAACGTGAAGTGGA
381 TTTCTTTTAATTTTTAGTTAAAACAAATCATAATTTCATGTTTCGATTGGAAAACATGAAGCAGA
* * * **
19350229 ACATAACAATTGACAAGAAAAGTCCATTTATAGTCACTCATAG-CTTCGAAAGCCTAGTTACTCA
446 ACACAACAATTCACAAGAAAAGTCCATTTATAATCACTCAT-GCCTTCGAAAGCCTAAATACTCA
19350293 C
510 C
* * *
19350294 TTTAAATGATTTTATAATCTTATAAATAATTTTAAGTTGAATTCTTTTCTTATTTTTAGTTAAAA
1 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATT-TTTTCTTATTTTT-GTTAAAA
* *
19350359 CATATCATAATTTATTGTTTGCATTGGGAAACATGAAGCGAAAGCCAACCATTGACGGGAAAAGT
64 CATATCATAATTTA-TGTTTGCATTGGGAAACATGAAGCGAAAGCTAACCATTGACAGGAAAAGT
* * *
19350424 CCATTTATATTCACTCATGCATTTGAAAGGCTAGCTACTCTCTTTAAATGGTTTTATAATCTTAT
128 CCATTTATAGTCACTCATGC-TTTGAAAGCCTAGTTACTCTCTTTAAATGGTTTTATAATCTTAT
*
19350489 AAATGATTTTAAATTGAATTTTCTTTTTATTTTAGATTAAAACATATCATAATTTAATGTTTTCA
192 AAATGATTTTAAATTGAATTTTCTTTTTATTTT-G-TTAAAACAGATCATAATTTAATGTTTTCA
* * *
19350554 TTAGGAAACGTAAAGCGAAAGCCAACCATTGACAAGAAAAGTCTATTTACAGTCACTCATAGCTT
255 TTAGGAAATGTGAAGCGAAAGCCAACCATTGACAAGAAAAGTCCATTTACAGTCACTCATAGCTT
* *
19350619 TGAAAGCCTAGTTACTCGTTTTAAATGGTTTTGTAATCATATAAATGATTTTAAATTGAATTTTC
320 TGAAAGCCTAGTTACTCGCTTTAAATGGTTTTGTAATCTTATAAATGATTTTAAATTGAATTTTC
* *
19350684 TTTTAATTTTTAGTTAAAACAAATCTTAATTTCATGTTT-GCATTGGGAAACATGAAGCAGAAGC
385 TTTTAATTTTTAGTTAAAACAAATCATAATTTCATGTTTCG-ATTGGAAAACATGAAGCAGAA-C
** * *
19350748 -CAACCTTTCACAAGGAAA-TCCATTTATAATCATTCATGCCTTCGAAAGCCTAAATACTCAC
448 ACAACAATTCACAAGAAAAGTCCATTTATAATCACTCATGCCTTCGAAAGCCTAAATACTCAC
* * ** *
19350809 TTTTAATGGTTTTATAATCTTATTAATGATTTTAAATTGAATTTTGTT-TTCGGCTTTGGTTAAA
1 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTT-TTCTT--ATTTTTGTTAAA
* * * * * *
19350873 ACAAATCATAATTTCATGTTTCCATCGGGAAACATGAAGCGAAAGCTAACAATTGACAAGAAAAA
63 ACATATCATAATTT-ATGTTTGCATTGGGAAACATGAAGCGAAAGCTAACCATTGACAGGAAAAG
* * * * * *
19350938 TCCATTTATAGTCCCTCATAGCTTTAAAAGCCTAGTTACTCGCTTTAAATGGCTTCATAATATTA
127 TCCATTTATAGTCACTCAT-GCTTTGAAAGCCTAGTTACTCTCTTTAAATGGTTTTATAATCTTA
** * *
19351003 TAAACAATTTTAAATTGAATTTGT-TTTCTCATTTTGGTTAAAACAGATCATAATTTAATGTTTG
191 TAAATGATTTTAAATTGAATTT-TCTTT-TTATTTT-GTTAAAACAGATCATAATTTAATGTTTT
** * * * * *
19351067 CATT-GGTAAATGTGATTCGAAAACCACCCATTGACAAGAAAAGTCCATTTATAGTTACTTATTA
253 CATTAGG-AAATGTGAAGCGAAAGCCAACCATTGACAAGAAAAGTCCATTTACAGTCACTCA-TA
* *
19351131 G-TTTGAAAGCCTAGTTACTCACTTTAAATGG-TTTGTAGTCTTATAAATGATTTTAAATTGAAT
316 GCTTTGAAAGCCTAGTTACTCGCTTTAAATGGTTTTGTAATCTTATAAATGATTTTAAATTGAAT
* * * * *
19351194 TTT-TTCTCATTTTTAATTAAAATAGATCATAATTT
381 TTTCTTTTAATTTTTAGTTAAAACAAATCATAATTT
19351229 TTAAAAAACA
Statistics
Matches: 804, Mismatches: 108, Indels: 48
0.84 0.11 0.05
Matches are distributed among these distances:
513 30 0.04
514 44 0.05
515 517 0.64
516 210 0.26
517 3 0.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39
Consensus pattern (510 bp):
TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTTTTCTTATTTTTGTTAAAACA
TATCATAATTTATGTTTGCATTGGGAAACATGAAGCGAAAGCTAACCATTGACAGGAAAAGTCCA
TTTATAGTCACTCATGCTTTGAAAGCCTAGTTACTCTCTTTAAATGGTTTTATAATCTTATAAAT
GATTTTAAATTGAATTTTCTTTTTATTTTGTTAAAACAGATCATAATTTAATGTTTTCATTAGGA
AATGTGAAGCGAAAGCCAACCATTGACAAGAAAAGTCCATTTACAGTCACTCATAGCTTTGAAAG
CCTAGTTACTCGCTTTAAATGGTTTTGTAATCTTATAAATGATTTTAAATTGAATTTTCTTTTAA
TTTTTAGTTAAAACAAATCATAATTTCATGTTTCGATTGGAAAACATGAAGCAGAACACAACAAT
TCACAAGAAAAGTCCATTTATAATCACTCATGCCTTCGAAAGCCTAAATACTCAC
Found at i:19351100 original size:687 final size:687
Alignment explanation
Indices: 19349779--19351228 Score: 1816
Period size: 687 Copynumber: 2.1 Consensus size: 687
19349769 CCTCAATTGG
* * *
19349779 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTGACTCTCCT-TTTT-GTTTAA
1 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTT-TCT-TCTTATTTTAGATTAA
* * ** *
19349842 AACATATCATAATTTAATATTTGCAATGGTAAACGTGAAGCGAAAGCTAACCATTGGTAGGAAAA
64 AACATATCATAATTTAATATTTGCAATGGTAAACGTAAAGCGAAAGCCAACCATTGACAAGAAAA
* * * *
19349907 GTTCATTTATAGTCACTTATGCCTTCGAAAGCCTAGTTACTTGCTTTAAATAGTTTTATACACTT
129 GTTCATTTACAGTCACTCATGCCTTCGAAAGCCTAGTTACTCGCTTTAAATAGTTTTATACACAT
* * * *
19349972 ATAAATGATTTTAAATTGAATTTTCTTTTTATTTTTTGTTAAAAAGATCACAATTTCATGTTTTC
194 ATAAATGATTTTAAATTGAATTTTCTTTTAATTTTTAGTTAAAAAAATCACAATTTCATGTTTGC
* ** *
19350037 ACTAGAAAATATGAAGCGAAAGCCAACCATTGGCAAGAAAAGTCCATTTACAGTCACTCAAGCCT
259 ACTAGAAAACATGAAGCGAAAGCCAACCATTCACAAGAAAAGTCCATTTACAATCACTCAAGCCT
** * *
19350102 TCAAAAGCCTAGTTACTCGCTTTAAATGCTTTTATAATGTTATAAATGATATTCAAATGAATTTT
324 TCAAAAGCCTAAATACTCACTTTAAATGCTTTTATAATCTTATAAATGATATTCAAATGAATTTT
* ** * * * * * *
19350167 CTTTTTATTTTTGGTTAAAACATATCATAATTTCATGTTTCGATTGGAAAACGTGAAGTGGAACA
389 CTTTTCAGCTTTGGTTAAAACAAATCATAATTTCATGTTTCCATCGGAAAACATGAAGCGAAACA
* *
19350232 TAACAATTGACAAGAAAAGTCCATTTATAGTCACTCATAGCTTCGAAAGCCTAGTTACTCACTTT
454 TAACAATTGACAAGAAAAATCCATTTATAGTCACTCATAGCTTCAAAAGCCTAGTTACTCACTTT
* * * * * * *
19350297 AAATGATTTTATAATCTTATAAATAATTTTAAGTTGAATTCTTTTCTTATTTTTAGTTAAAACAT
519 AAATGACTTCATAATATTATAAACAATTTTAAATTGAATTCTTTTCTCATTTTTAGTTAAAACAG
* * **
19350362 ATCATAATTTATTGTTTGCATTGGGAAACATGAAGCGAAAGCCAACCATTGACGGGAAAAGTCCA
584 ATCATAATTTAATGTTTGCATTGGGAAACATGAAGCGAAAACCAACCATTGACAAGAAAAGTCCA
* *
19350427 TTTATA-TTCACTCATGCA-TTTGAAAGGCTAGCTACTCTC
649 TTTATAGTT-ACTCAT-CAGTTTGAAAGCCTAGCTACTCAC
*
19350466 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTTCTTTTTATTTTAGATTAAAA
1 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTTCTTCTTATTTTAGATTAAAA
* * *
19350531 CATATCATAATTTAATGTTTTCATTAGG-AAACGTAAAGCGAAAGCCAACCATTGACAAGAAAAG
66 CATATCATAATTTAATATTTGCAAT-GGTAAACGTAAAGCGAAAGCCAACCATTGACAAGAAAAG
* * * *
19350595 -TCTATTTACAGTCACTCATAG-CTTTGAAAGCCTAGTTACTCGTTTTAAATGGTTTTGTA-ATC
130 TTC-ATTTACAGTCACTCAT-GCCTTCGAAAGCCTAGTTACTCGCTTTAAATAGTTTTATACA-C
**
19350657 ATATAAATGATTTTAAATTGAATTTTCTTTTAATTTTTAGTTAAAACAAATCTTAATTTCATGTT
192 ATATAAATGATTTTAAATTGAATTTTCTTTTAATTTTTAGTTAAAA-AAATCACAATTTCATGTT
* * * * * * * *
19350722 TGCATTGGGAAACATGAAGC-AGAAGCCAACCTTTCACAAGGAAA-TCCATTTATAATCATTCAT
256 TGCACTAGAAAACATGAAGCGA-AAGCCAACCATTCACAAGAAAAGTCCATTTACAATCACTCAA
* * * * *
19350785 GCCTTCGAAAGCCTAAATACTCACTTTTAATGGTTTTATAATCTTATTAATGAT-TTTAAATTGA
320 GCCTTCAAAAGCCTAAATACTCACTTTAAATGCTTTTATAATCTTATAAATGATATTCAAA-TGA
* * *
19350849 ATTTTGTTTTCGGCTTTGGTTAAAACAAATCATAATTTCATGTTTCCATCGGGAAACATGAAGCG
384 ATTTTCTTTTCAGCTTTGGTTAAAACAAATCATAATTTCATGTTTCCATCGGAAAACATGAAGCG
* *
19350914 AAAGC-TAACAATTGACAAGAAAAATCCATTTATAGTCCCTCATAGCTTTAAAAGCCTAGTTACT
449 AAA-CATAACAATTGACAAGAAAAATCCATTTATAGTCACTCATAGCTTCAAAAGCCTAGTTACT
* * * *
19350978 CGCTTTAAATGGCTTCATAATATTATAAACAATTTTAAATTGAATTTGTTTTCTCA-TTTTGGTT
513 CACTTTAAATGACTTCATAATATTATAAACAATTTTAAATTGAA-TTCTTTTCTCATTTTTAGTT
* ** ** *
19351042 AAAACAGATCATAATTTAATGTTTGCATTGGTAAATGTGATTCGAAAACCACCCATTGACAAGAA
577 AAAACAGATCATAATTTAATGTTTGCATTGGGAAACATGAAGCGAAAACCAACCATTGACAAGAA
* * *
19351107 AAGTCCATTTATAGTTACTTATTAGTTTGAAAGCCTAGTTACTCAC
642 AAGTCCATTTATAGTTACTCATCAGTTTGAAAGCCTAGCTACTCAC
* * *
19351153 TTTAAATGG-TTTGTAGTCTTATAAATGATTTTAAATTGAATTTT-TTCTCATTTTTA-ATTAAA
1 TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTTCTTCTTA-TTTTAGATTAAA
* *
19351215 ATAGATCATAATTT
65 ACATATCATAATTT
19351229 TTAAAAAACA
Statistics
Matches: 654, Mismatches: 95, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
685 24 0.04
686 53 0.08
687 514 0.79
688 63 0.10
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39
Consensus pattern (687 bp):
TTTAAATGGTTTTATAATCTTATAAATGATTTTAAATTGAATTTTCTTCTTATTTTAGATTAAAA
CATATCATAATTTAATATTTGCAATGGTAAACGTAAAGCGAAAGCCAACCATTGACAAGAAAAGT
TCATTTACAGTCACTCATGCCTTCGAAAGCCTAGTTACTCGCTTTAAATAGTTTTATACACATAT
AAATGATTTTAAATTGAATTTTCTTTTAATTTTTAGTTAAAAAAATCACAATTTCATGTTTGCAC
TAGAAAACATGAAGCGAAAGCCAACCATTCACAAGAAAAGTCCATTTACAATCACTCAAGCCTTC
AAAAGCCTAAATACTCACTTTAAATGCTTTTATAATCTTATAAATGATATTCAAATGAATTTTCT
TTTCAGCTTTGGTTAAAACAAATCATAATTTCATGTTTCCATCGGAAAACATGAAGCGAAACATA
ACAATTGACAAGAAAAATCCATTTATAGTCACTCATAGCTTCAAAAGCCTAGTTACTCACTTTAA
ATGACTTCATAATATTATAAACAATTTTAAATTGAATTCTTTTCTCATTTTTAGTTAAAACAGAT
CATAATTTAATGTTTGCATTGGGAAACATGAAGCGAAAACCAACCATTGACAAGAAAAGTCCATT
TATAGTTACTCATCAGTTTGAAAGCCTAGCTACTCAC
Found at i:19360466 original size:43 final size:44
Alignment explanation
Indices: 19360299--19360518 Score: 186
Period size: 42 Copynumber: 5.2 Consensus size: 44
19360289 ACTAGAGCCA
* * * *
19360299 ATCACAA-CAAAATCATGAGAA-ATGGAGACATACTCAATCCAC
1 ATCACAACCAAAATCATGGGAATGTGGAGACTTTCTCAATCCAC
* * * * *
19360341 TTTA-AACCAAAATCAT-GGAAAGTGGAGACCTACTCAATCCAC
1 ATCACAACCAAAATCATGGGAATGTGGAGACTTTCTCAATCCAC
* * * * *
19360383 TTTACCA-C-AAATCATGGGAA-GTGGAGACATACTCAATCCAC
1 ATCACAACCAAAATCATGGGAATGTGGAGACTTTCTCAATCCAC
* * *
19360424 ATGACAA-TAAAATCATGGGAATGTGGAGACTTTCTCACTCCAC
1 ATCACAACCAAAATCATGGGAATGTGGAGACTTTCTCAATCCAC
*** *
19360467 ATCACAACCCCCATCATGGGAATGTGCAGACTTTCTCAATCCAC
1 ATCACAACCAAAATCATGGGAATGTGGAGACTTTCTCAATCCAC
19360511 ATTCACAA
1 A-TCACAA
19360519 TACTCATATG
Statistics
Matches: 149, Mismatches: 21, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
41 36 0.24
42 51 0.34
43 25 0.17
44 31 0.21
45 6 0.04
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (44 bp):
ATCACAACCAAAATCATGGGAATGTGGAGACTTTCTCAATCCAC
Found at i:19363309 original size:42 final size:42
Alignment explanation
Indices: 19363245--19363445 Score: 271
Period size: 42 Copynumber: 4.8 Consensus size: 42
19363235 GTGATAATTA
*
19363245 TGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTATAC
1 TGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGTAC
* * *
19363287 TGACCCAGCCATGGGCGATGTAGGAGTGCACATGAGCTGTGC
1 TGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGTAC
* * *
19363329 TGACTCAGCCATGTGCAGTGTAGGAGTGCACATGAGTTGTGA-
1 TGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGT-AC
* **
19363371 TGACCCAGCCATGTGCGGTGTATGAGTGCACATGAGCTGCGC
1 TGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGTAC
*
19363413 TGACCCAGCTATGTGCGGTGT-GGTAGTGCACAT
1 TGACCCAGCCATGTGCGGTGTAGG-AGTGCACAT
19363446 AAGTTGAGAC
Statistics
Matches: 138, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.01
42 137 0.99
ACGTcount: A:0.21, C:0.22, G:0.33, T:0.23
Consensus pattern (42 bp):
TGACCCAGCCATGTGCGGTGTAGGAGTGCACATGAGCTGTAC
Found at i:19365336 original size:59 final size:58
Alignment explanation
Indices: 19365254--19365427 Score: 208
Period size: 59 Copynumber: 3.0 Consensus size: 58
19365244 ATAAGACAAC
* * *
19365254 TCTTGTCTTTAATTAAGAC-AAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTT
1 TCTTGTC-TAAATTAAGACAAAAAATATTTT-TCTTGTCTAAATTAAGACAAACATGTTT
* * * * *
19365313 TTTTGTCTACATTTAGATAAAAAATATTTTTCTTGTCTTAAATTAAGACAAACATATTT
1 TCTTGTCTAAATTAAGACAAAAAATATTTTTCTTGTC-TAAATTAAGACAAACATGTTT
* * *
19365372 TCTTGTCTAAATTAAGACCAAACAT-GTTTTCTTGTCTAAATTAAGACAAACATGTT
1 TCTTGTCTAAATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTT
19365428 AAGGTTACCA
Statistics
Matches: 97, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
57 19 0.20
58 24 0.25
59 54 0.56
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (58 bp):
TCTTGTCTAAATTAAGACAAAAAATATTTTTCTTGTCTAAATTAAGACAAACATGTTT
Found at i:19365393 original size:29 final size:28
Alignment explanation
Indices: 19365254--19365424 Score: 180
Period size: 29 Copynumber: 5.9 Consensus size: 28
19365244 ATAAGACAAC
* *
19365254 TCTTGTCTTTAATTAAGACAAAAATATTTT
1 TCTTGTC-TAAATTAAGACAAACATA-TTT
* * *
19365284 ATCTTGTCTAAATTGAGACAAATATGTTT
1 -TCTTGTCTAAATTAAGACAAACATATTT
* * * * *
19365313 TTTTGTCTACATTTAGATAAAAAATATTTT
1 TCTTGTCTAAATTAAGA-CAAACATA-TTT
19365343 TCTTGTCTTAAATTAAGACAAACATATTT
1 TCTTGTC-TAAATTAAGACAAACATATTT
*
19365372 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAACATATTT
19365401 TCTTGTCTAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGACAAACAT
19365425 GTTAAGGTTA
Statistics
Matches: 120, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
28 31 0.26
29 45 0.38
30 29 0.24
31 15 0.12
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATATTT
Found at i:19370802 original size:42 final size:42
Alignment explanation
Indices: 19370755--19370838 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
19370745 CATCTCATAT
*
19370755 GCAACGGCTTATGCGCACTTCCACTCGCACATAGCTTGGTCA
1 GCAACGGCTTATGCGCACTTCCACTCGCACATAGCTGGGTCA
* *
19370797 GCAACGGCTTATGTGCACTTCTACTCGCACATAGCTGGGTCA
1 GCAACGGCTTATGCGCACTTCCACTCGCACATAGCTGGGTCA
19370839 ATATCAATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (42 bp):
GCAACGGCTTATGCGCACTTCCACTCGCACATAGCTGGGTCA
Found at i:19378177 original size:38 final size:40
Alignment explanation
Indices: 19378099--19378202 Score: 135
Period size: 38 Copynumber: 2.6 Consensus size: 40
19378089 ACCCGGCTCA
19378099 TGTACA-TCCCCTCACATCGTGCACATAGTCGATGCCATCG
1 TGTACATTCCCC-CACATCGTGCACATAGTCGATGCCATCG
* *
19378139 TGTGCATTCCCCCACATCGTGTACA-A-TC-AGTGCCATCG
1 TGTACATTCCCCCACATCGTGCACATAGTCGA-TGCCATCG
*
19378177 TGTACATCCCCCCACATCGTGCACAT
1 TGTACATTCCCCCACATCGTGCACAT
19378203 GGGCACTATC
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
37 1 0.02
38 32 0.57
39 1 0.02
40 17 0.30
41 5 0.09
ACGTcount: A:0.22, C:0.37, G:0.16, T:0.25
Consensus pattern (40 bp):
TGTACATTCCCCCACATCGTGCACATAGTCGATGCCATCG
Found at i:19378194 original size:19 final size:19
Alignment explanation
Indices: 19378134--19378202 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
19378124 TAGTCGATGC
* *
19378134 CATCGTGTGCATTCCCCCA
1 CATCGTGTACATCCCCCCA
****
19378153 CATCGTGTACAATCAGTGC-
1 CATCGTGTAC-ATCCCCCCA
19378172 CATCGTGTACATCCCCCCA
1 CATCGTGTACATCCCCCCA
*
19378191 CATCGTGCACAT
1 CATCGTGTACAT
19378203 GGGCACTATC
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
18 4 0.11
19 30 0.81
20 3 0.08
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.25
Consensus pattern (19 bp):
CATCGTGTACATCCCCCCA
Found at i:19380330 original size:21 final size:20
Alignment explanation
Indices: 19380306--19380345 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
19380296 AAATTGCAAA
*
19380306 ATGTATTGATACATTAGGTTC
1 ATGTATCGATACATT-GGTTC
19380327 ATGTATCGATACATTGGTT
1 ATGTATCGATACATTGGTT
19380346 TCTAGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTGGTTC
Found at i:19384169 original size:54 final size:54
Alignment explanation
Indices: 19384087--19384192 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
19384077 AATAATCGTT
* * *
19384087 CCATCTCACCCAGCTCATGTGAATCCCACCACATCGTGCATATAGCCGGACATC
1 CCATCTCACCCAACTCATGTGAATCCCACCACATCGTGCACATAACCGGACATC
*
19384141 CCATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAACCGGACA
1 CCATCTCACCCAACTCATGTGAATCCCACCACATCGTGCACATAACCGGACA
19384193 GTATCACCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.27, C:0.41, G:0.13, T:0.19
Consensus pattern (54 bp):
CCATCTCACCCAACTCATGTGAATCCCACCACATCGTGCACATAACCGGACATC
Found at i:19387455 original size:14 final size:15
Alignment explanation
Indices: 19387438--19387466 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19387428 GATTAATATA
19387438 AATTT-TGATCAATT
1 AATTTATGATCAATT
19387452 AATTTATGATCAATT
1 AATTTATGATCAATT
19387467 CCATAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
AATTTATGATCAATT
Found at i:19392378 original size:2 final size:2
Alignment explanation
Indices: 19392332--19392370 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
19392322 CTATTATGTG
*
19392332 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19392371 GAATATATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19392481 original size:42 final size:42
Alignment explanation
Indices: 19392413--19392539 Score: 191
Period size: 42 Copynumber: 3.0 Consensus size: 42
19392403 TTTAATGATA
* * * *
19392413 CTGACCTGGCTATGTGAGAGTAGGAGTACGCATAAGCCGATG
1 CTGACCTGACTATGTGCGAGTGGGAGTGCGCATAAGCCGATG
*
19392455 CTGACCAGACTATGTGCGAGTGGGAGTGCGCATAAGCCGATG
1 CTGACCTGACTATGTGCGAGTGGGAGTGCGCATAAGCCGATG
*
19392497 CTGACCTGACTATGTGCGAGTAGGGAGTGTGCATAAGCCGATG
1 CTGACCTGACTATGTGCGAGT-GGGAGTGCGCATAAGCCGATG
19392540 ATGATGATGA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 57 0.74
43 20 0.26
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.21
Consensus pattern (42 bp):
CTGACCTGACTATGTGCGAGTGGGAGTGCGCATAAGCCGATG
Found at i:19394603 original size:79 final size:80
Alignment explanation
Indices: 19394520--19394735 Score: 251
Period size: 79 Copynumber: 2.7 Consensus size: 80
19394510 CTCAACCCAT
* * * *
19394520 AGTGTATATGACCATCTCAACACATAC-TTTCATGGCATGCATTTCATAATCTCGTAAATCATTC
1 AGTGTACATGA-CATCTCAACACATACATCTCATGGCATGCATTTCATAATCTCATAAATCATCC
19394584 ACATGC-TTAGCCTAG
65 ACATGCTTTAGCCTAG
* * * *
19394599 AGTGTACATGATATGCTCAACACATACAACTCATGGCATGC--TTCATAATCTCATAATTTATCC
1 AGTGTACATGACAT-CTCAACACATACATCTCATGGCATGCATTTCATAATCTCATAAATCATCC
* *
19394662 GCATGCTTTAGCCTAT
65 ACATGCTTTAGCCTAG
* * * *
19394678 AGTGTACATGACATTTTTAACACATACATCTCATGGCATACATCTCATAATCTCATAA
1 AGTGTACATGACA-TCTCAACACATACATCTCATGGCATGCATTTCATAATCTCATAA
19394736 TTGGAACTCA
Statistics
Matches: 115, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
78 25 0.22
79 64 0.56
80 12 0.10
81 14 0.12
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.33
Consensus pattern (80 bp):
AGTGTACATGACATCTCAACACATACATCTCATGGCATGCATTTCATAATCTCATAAATCATCCA
CATGCTTTAGCCTAG
Found at i:19396886 original size:43 final size:43
Alignment explanation
Indices: 19396816--19396934 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
19396806 GTAATTATGT
* *
19396816 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
19396859 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
19396902 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
19396935 GAGCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.22, C:0.21, G:0.38, T:0.19
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:19396944 original size:43 final size:43
Alignment explanation
Indices: 19396826--19396947 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
19396816 TGACTCGGCT
* **
19396826 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
19396869 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
19396912 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
19396948 TGATGATGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:19396958 original size:20 final size:20
Alignment explanation
Indices: 19396933--19396995 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
19396923 GGGAGTGCGC
19396933 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
19396953 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
* *
19396973 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
19396992 ATGA
1 ATGA
19396996 TGGGTATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:19404862 original size:43 final size:43
Alignment explanation
Indices: 19404688--19404849 Score: 245
Period size: 43 Copynumber: 3.8 Consensus size: 43
19404678 GTAATTATGT
* * *
19404688 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
19404731 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGATGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
19404774 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* **
19404817 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCAT
19404850 GAGCTGGTGA
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
43 110 1.00
ACGTcount: A:0.22, C:0.21, G:0.37, T:0.20
Consensus pattern (43 bp):
TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:19404873 original size:20 final size:19
Alignment explanation
Indices: 19404848--19404910 Score: 90
Period size: 20 Copynumber: 3.2 Consensus size: 19
19404838 GGGAGTGCGC
19404848 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGA-GATGATG
19404868 ATGAGCTGGTGACGATGATG
1 ATGAGCTGGTGA-GATGATG
* *
19404888 ATGGGTTGGTGAGATGATG
1 ATGAGCTGGTGAGATGATG
19404907 ATGA
1 ATGA
19404911 TGGATATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 10 0.26
20 29 0.74
ACGTcount: A:0.25, C:0.05, G:0.41, T:0.29
Consensus pattern (19 bp):
ATGAGCTGGTGAGATGATG
Found at i:19407573 original size:2 final size:2
Alignment explanation
Indices: 19407507--19407554 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
19407497 TGATATAGTG
19407507 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19407549 TA TA TA
1 TA TA TA
19407555 AATGCCACGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19417645 original size:34 final size:33
Alignment explanation
Indices: 19417556--19417647 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 33
19417546 CCATTTAAGG
*
19417556 GCTGGTTTGGAGGCTGAAAAGAGCCATTTTTCT
1 GCTGGTTTGGAGGCTGAAAAGTGCCATTTTTCT
* * *
19417589 ACTGGTTTTGAAGGCTGGAAAGTGCCATTTTTCT
1 GCTGG-TTTGGAGGCTGAAAAGTGCCATTTTTCT
**
19417623 GCTGAGTTTGGAGGCCAAAAAGTGC
1 GCTG-GTTTGGAGGCTGAAAAGTGC
19417648 TGAATTTTCT
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
33 4 0.08
34 43 0.90
35 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (33 bp):
GCTGGTTTGGAGGCTGAAAAGTGCCATTTTTCT
Found at i:19417994 original size:18 final size:18
Alignment explanation
Indices: 19417963--19418014 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
19417953 GAATGAAGAG
19417963 AAAGAAAG-AAAGAAAAA
1 AAAGAAAGAAAAGAAAAA
* * *
19417980 AAATAAATAAAAGAAATA
1 AAAGAAAGAAAAGAAAAA
19417998 AAAGAAAGAAAAGAAAA
1 AAAGAAAGAAAAGAAAA
19418015 TAACAAGGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 6 0.21
18 22 0.79
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (18 bp):
AAAGAAAGAAAAGAAAAA
Found at i:19417996 original size:9 final size:9
Alignment explanation
Indices: 19417971--19418013 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
19417961 AGAAAGAAAG
*
19417971 AAAGAAAAA
1 AAAGAAATA
*
19417980 AAATAAATA
1 AAAGAAATA
19417989 AAAGAAATA
1 AAAGAAATA
*
19417998 AAAGAAAGA
1 AAAGAAATA
19418007 AAAGAAA
1 AAAGAAA
19418014 ATAACAAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (9 bp):
AAAGAAATA
Found at i:19418083 original size:25 final size:25
Alignment explanation
Indices: 19418046--19418094 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
19418036 CCCAACAAGC
*
19418046 AAGGAAAATTGGACATGATCCAATA
1 AAGGAAAATTGGACATGACCCAATA
19418071 AAGGAAGAA-TGGACATGACCCAAT
1 AAGGAA-AATTGGACATGACCCAAT
19418095 TAAAAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.16
Consensus pattern (25 bp):
AAGGAAAATTGGACATGACCCAATA
Found at i:19418105 original size:26 final size:25
Alignment explanation
Indices: 19418055--19418105 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
19418045 CAAGGAAAAT
* **
19418055 TGGACATGATCCAATAAAGGAAGAA
1 TGGACATGACCCAATAAAAAAAGAA
19418080 TGGACATGACCCAATTAAAAAAAGAA
1 TGGACATGACCCAA-TAAAAAAAGAA
19418106 ATGGGAGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.51, C:0.14, G:0.20, T:0.16
Consensus pattern (25 bp):
TGGACATGACCCAATAAAAAAAGAA
Found at i:19424224 original size:5 final size:5
Alignment explanation
Indices: 19424214--19424239 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19424204 TATGTGTATA
19424214 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
19424240 TTATAGGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:19424729 original size:34 final size:35
Alignment explanation
Indices: 19424639--19424729 Score: 123
Period size: 34 Copynumber: 2.7 Consensus size: 35
19424629 CCATTTAAGG
19424639 GCTGGTTTTGGAGGCTAAAAAG-AGCCATTTTTCT
1 GCTGGTTTTGGAGGCTAAAAAGTAGCCATTTTTCT
** *
19424673 GCTGGTTTTGGAGGCTGGAAAGTA-CCATTTTTTT
1 GCTGGTTTTGGAGGCTAAAAAGTAGCCATTTTTCT
* *
19424707 GCTGATTTTGGAGGCCAAAAAGT
1 GCTGGTTTTGGAGGCTAAAAAGT
19424730 GCAGAATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
34 48 0.98
35 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.29, T:0.35
Consensus pattern (35 bp):
GCTGGTTTTGGAGGCTAAAAAGTAGCCATTTTTCT
Found at i:19424894 original size:33 final size:35
Alignment explanation
Indices: 19424823--19424895 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
19424813 AAGGAAAGGT
* *
19424823 GCAGCTTAGCTGCTGAAATTTGAAGGAAAAACAAA
1 GCAGCATAACTGCTGAAATTTGAAGGAAAAACAAA
* * *
19424858 GCAGCATAACTGCT-AATTTTGAAGTAAAAA-AGA
1 GCAGCATAACTGCTGAAATTTGAAGGAAAAACAAA
19424891 GCAGC
1 GCAGC
19424896 TTTAGTTGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 7 0.21
34 14 0.42
35 12 0.36
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (35 bp):
GCAGCATAACTGCTGAAATTTGAAGGAAAAACAAA
Found at i:19425067 original size:10 final size:10
Alignment explanation
Indices: 19425054--19425114 Score: 77
Period size: 10 Copynumber: 5.9 Consensus size: 10
19425044 AGAAAGAAAG
19425054 AAAGAAAATA
1 AAAGAAAATA
19425064 AAAGAAAATA
1 AAAGAAAATA
*
19425074 AAAGAAAAGA
1 AAAGAAAATA
**
19425084 AAAGAAAGGA
1 AAAGAAAATA
19425094 AAAGAAAATA
1 AAAGAAAATA
19425104 ACAAGGAAAAT
1 A-AA-GAAAAT
19425115 GGGCATGGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
10 37 0.82
11 2 0.04
12 6 0.13
ACGTcount: A:0.75, C:0.02, G:0.16, T:0.07
Consensus pattern (10 bp):
AAAGAAAATA
Found at i:19425071 original size:5 final size:5
Alignment explanation
Indices: 19425041--19425101 Score: 72
Period size: 5 Copynumber: 12.4 Consensus size: 5
19425031 AGGAAGAAGG
* *
19425041 AAGAGA AAG-A AAG-A AAGAA AATAA AAGAA AATAA AAGAA AAGAA AAGAA
1 AAGA-A AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
*
19425090 AGGAA AAGAA AA
1 AAGAA AAGAA AA
19425102 TAACAAGGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
4 8 0.17
5 37 0.77
6 3 0.06
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (5 bp):
AAGAA
Found at i:19425170 original size:25 final size:25
Alignment explanation
Indices: 19425133--19425181 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
19425123 CCCAACAAGC
*
19425133 AAGGAAAATTGGACATGATCCAATA
1 AAGGAAAATTGGACATGACCCAATA
19425158 AAGGAAGAA-TGGACATGACCCAAT
1 AAGGAA-AATTGGACATGACCCAAT
19425182 TACAAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.16
Consensus pattern (25 bp):
AAGGAAAATTGGACATGACCCAATA
Found at i:19437615 original size:40 final size:40
Alignment explanation
Indices: 19437560--19437638 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
19437550 TTGGCTATTT
**
19437560 TTCACCTTAGTGGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCACCAAGATTGGTGA
*
19437600 TTCACCTTAGTGGGGTTTTCAACCTCACCACGATTGGTG
1 TTCACCTTAGTGGGGTTTTCAACCTCACCAAGATTGGTG
19437639 TCTTTCACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCACCAAGATTGGTGA
Found at i:19443156 original size:19 final size:20
Alignment explanation
Indices: 19443123--19443160 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
19443113 ACCACGATTG
19443123 GTGTCTTTCACAACGCCCAA
1 GTGTCTTTCACAACGCCCAA
19443143 GTGTCTTT-ACAACGCCCA
1 GTGTCTTTCACAACGCCCA
19443161 GGCATCAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (20 bp):
GTGTCTTTCACAACGCCCAA
Found at i:19443584 original size:74 final size:73
Alignment explanation
Indices: 19443494--19443680 Score: 254
Period size: 74 Copynumber: 2.5 Consensus size: 73
19443484 AACAGAGAAG
* * *
19443494 ACTTAGTCGACCAAGAAACATGGTTAGTCGACTAAGAGCTTACTACCAAAAACTT-GGA-CTATA
1 ACTTAATCGACTAAGAAACAT-GTTAGTCGACTAAGAGCTTACTACCAAAAA-TTGGGATC-AAA
*
19443557 AGATAGAAACA
63 ACATAGAAACA
*
19443568 ACTTAATCGACTAAGAAGCATTGTTAGTCGACTAAGAGCTTACTACCAAAAATTGGGATCAAAAC
1 ACTTAATCGACTAAGAAACA-TGTTAGTCGACTAAGAGCTTACTACCAAAAATTGGGATCAAAAC
19443633 ATAGAAACA
65 ATAGAAACA
*
19443642 ACTTAATCGACTAAGAAGA-ATGTTAGTCAACTAAGAGCT
1 ACTTAATCGACTAAGAA-ACATGTTAGTCGACTAAGAGCT
19443681 CTATGTTTGG
Statistics
Matches: 102, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
73 20 0.20
74 80 0.78
75 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (73 bp):
ACTTAATCGACTAAGAAACATGTTAGTCGACTAAGAGCTTACTACCAAAAATTGGGATCAAAACA
TAGAAACA
Found at i:19446864 original size:17 final size:17
Alignment explanation
Indices: 19446842--19446876 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19446832 TTGTATTTTA
19446842 TTTTATATTT-TTATTAT
1 TTTTAT-TTTATTATTAT
19446859 TTTTATTTTATTATTAT
1 TTTTATTTTATTATTAT
19446876 T
1 T
19446877 ATGTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTTTATTATTAT
Found at i:19447155 original size:34 final size:34
Alignment explanation
Indices: 19447047--19447168 Score: 111
Period size: 34 Copynumber: 3.5 Consensus size: 34
19447037 CTTCCTCTCT
* * * * **
19447047 TTTCCTTCCCAAAAATCCAGCAACACAACGCCTCTT
1 TTTCC-TCTCAAAAATCGA-CAGCACAAAGCCTCCA
* *
19447083 TTTCCTCTCAAAAATCGACAGCATAAAGCC-CCTC
1 TTTCCTCTCAAAAATCGACAGCACAAAGCCTCC-A
*
19447117 TTTCCTCTCAAAAATCGACAGCACAAGGCCTCCA
1 TTTCCTCTCAAAAATCGACAGCACAAAGCCTCCA
19447151 TTTCCTCTCTCAAAAATC
1 TTT-C-CTCTCAAAAATC
19447169 AGTTCGTTTC
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
33 1 0.01
34 40 0.56
35 14 0.19
36 17 0.24
ACGTcount: A:0.31, C:0.36, G:0.07, T:0.25
Consensus pattern (34 bp):
TTTCCTCTCAAAAATCGACAGCACAAAGCCTCCA
Found at i:19447973 original size:18 final size:18
Alignment explanation
Indices: 19447932--19447971 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
19447922 ATTAATATTT
*
19447932 AAATATTATTTTATTCATA
1 AAATAATATTTTATTCA-A
19447951 AAATAATATTTTATTTCAA
1 AAATAATATTTTA-TTCAA
19447970 AA
1 AA
19447972 TATTCTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATAATATTTTATTCAA
Found at i:19452190 original size:38 final size:38
Alignment explanation
Indices: 19452139--19452218 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
19452129 CTGACTCAGC
19452139 TCATGTGCACTCCCTACAT-GCACAAGGCAATATCATCA
1 TCATGTGCACTCCCTAC-TCGCACAAGGCAATATCATCA
* **
19452177 TCATGTGCTCTCCCTACTCGCACATTGCAATATCATCA
1 TCATGTGCACTCCCTACTCGCACAAGGCAATATCATCA
19452215 TCAT
1 TCAT
19452219 CATCATGTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 1 0.03
38 37 0.97
ACGTcount: A:0.28, C:0.33, G:0.11, T:0.29
Consensus pattern (38 bp):
TCATGTGCACTCCCTACTCGCACAAGGCAATATCATCA
Found at i:19452234 original size:44 final size:44
Alignment explanation
Indices: 19452170--19452258 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
19452160 ACAAGGCAAT
** **
19452170 ATCATCATCATGTGCTCTCCCTACTCGCACATTGCAATATCATC
1 ATCATCATCATGTGAACTCCCTACTAACACATTGCAATATCATC
* *
19452214 ATCATCATCATGTGAACTCCCTACTAACACATTTCAATCTCATC
1 ATCATCATCATGTGAACTCCCTACTAACACATTGCAATATCATC
19452258 A
1 A
19452259 CACTATGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.29, C:0.33, G:0.07, T:0.31
Consensus pattern (44 bp):
ATCATCATCATGTGAACTCCCTACTAACACATTGCAATATCATC
Found at i:19455187 original size:42 final size:42
Alignment explanation
Indices: 19455100--19455232 Score: 223
Period size: 42 Copynumber: 3.1 Consensus size: 42
19455090 ACCATCCCAC
*
19455100 CATCATCAGCTCATGTGCACTCCCCACTCGCACATAGTTGGGT
1 CATCATCAGCTCATGTGCACT-CCCACACGCACATAGTTGGGT
*
19455143 CATCATCAGCTCATGTGCACT-CCACACCGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCACA-CGCACATAGTTGGGT
19455185 CATCATCAGCTCATGTGCACTCCCACACGCACATAGTTGGGT
1 CATCATCAGCTCATGTGCACTCCCACACGCACATAGTTGGGT
19455227 CATCAT
1 CATCAT
19455233 TATCACATAA
Statistics
Matches: 85, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
41 4 0.05
42 55 0.65
43 26 0.31
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
CATCATCAGCTCATGTGCACTCCCACACGCACATAGTTGGGT
Found at i:19459818 original size:71 final size:71
Alignment explanation
Indices: 19459602--19459860 Score: 260
Period size: 71 Copynumber: 3.7 Consensus size: 71
19459592 CACTAGATTA
* * *** * **
19459602 AAATTGTTTAATTAAG---TTGTGCCTAATTAACT-AAATTATTTAATTAAATCATTACGCCTAA
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATTAAAATTAAACAATTAAATTATTGGGCCTAA
19459663 TTAATT
66 TTAATT
* * *
19459669 AAATTGTTTAAGTAAGTCATTGGACCTAATTAATT-AAATTAAACAATTAAGTTATTGGGCCTAA
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATTAAAATTAAACAATTAAATTATTGGGCCTAA
*
19459733 TTGATT
66 TTAATT
* * * **** * *
19459739 AAATTTGTTTAATTAAGTCGTTGGGCCTAGTTTATTAAAATTGTTTAATTAAATTGTTGGGCTTA
1 AAA-TTGTTTAATTAAGTCATTGGGCCTAATTAATTAAAATTAAACAATTAAATTATTGGGCCTA
19459804 ATTAATT
65 ATTAATT
* *
19459811 AAATTGTTTAATTAAGTTATTGGGCCTAATTGATT-AAATTAAACAATTAA
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATTAAAATTAAACAATTAA
19459861 GTGAATTGGG
Statistics
Matches: 154, Mismatches: 33, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
67 15 0.10
70 54 0.35
71 55 0.36
72 30 0.19
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (71 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATTAAAATTAAACAATTAAATTATTGGGCCTAA
TTAATT
Found at i:19459862 original size:35 final size:35
Alignment explanation
Indices: 19459602--19459850 Score: 252
Period size: 35 Copynumber: 7.1 Consensus size: 35
19459592 CACTAGATTA
* *
19459602 AAATTGTTTAATTAAG---TTGTGCCTAATTAACT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * * **
19459634 AAATTATTTAATTAAATCATTACGCCTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * *
19459669 AAATTGTTTAAGTAAGTCATTGGACCTAATTAATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
**** *
19459704 AAATTAAACAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
** * *
19459739 AAATTTGTTTAATTAAGTCGTTGGGCCTAGTTTATT
1 AAA-TTGTTTAATTAAGTTATTGGGCCTAATTAATT
* * *
19459775 AAAATTGTTTAATTAAATTGTTGGGCTTAATTAATT
1 -AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
*
19459811 AAATTGTTTAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
19459846 AAATT
1 AAATT
19459851 AAACAATTAA
Statistics
Matches: 176, Mismatches: 36, Indels: 7
0.80 0.16 0.03
Matches are distributed among these distances:
32 14 0.08
35 108 0.61
36 51 0.29
37 3 0.02
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTATTGGGCCTAATTAATT
Found at i:19461789 original size:28 final size:29
Alignment explanation
Indices: 19461744--19461807 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
19461734 GTCTATAGGC
*
19461744 AATTTTTCAATTT-TTGGGGCAAAAATAT
1 AATTTTTCAATTTATGGGGGCAAAAATAT
* * *
19461772 AATTTTTCACTTTATGGGGGCAAAAGTGT
1 AATTTTTCAATTTATGGGGGCAAAAATAT
19461801 AATTTTT
1 AATTTTT
19461808 AAAAATTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (29 bp):
AATTTTTCAATTTATGGGGGCAAAAATAT
Found at i:19475627 original size:13 final size:13
Alignment explanation
Indices: 19475609--19475633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19475599 GGAGAAATTG
19475609 TGATTTTATAAAA
1 TGATTTTATAAAA
19475622 TGATTTTATAAA
1 TGATTTTATAAA
19475634 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:19480379 original size:13 final size:13
Alignment explanation
Indices: 19480361--19480385 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19480351 GGAGAAATTG
19480361 TGATTTTATAAAA
1 TGATTTTATAAAA
19480374 TGATTTTATAAA
1 TGATTTTATAAA
19480386 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:19487138 original size:67 final size:68
Alignment explanation
Indices: 19487030--19487204 Score: 189
Period size: 67 Copynumber: 2.6 Consensus size: 68
19487020 TATATATGCC
* * * * * *
19487030 ATGATGCCTTGTATATGATGTAAATTCCATATACCACATGAGATGATGAATAGTAC-A-TGATAA
1 ATGATG-CTAGTATGTGATGTAGATTCCACATACCACATGAGATGATAAAGAGTACTATTGA-AA
19487093 A-TGAT
64 ACT-AT
* *
19487098 ATGATGCTAGTATGTGAGGTAGATTCCACATACCATATGAGATGATAAAGAGTACTTATTGAAAA
1 ATGATGCTAGTATGTGATGTAGATTCCACATACCACATGAGATGATAAAGAGTAC-TATTGAAAA
19487163 CTAT
65 CTAT
*
19487167 A--ATGCTAAGTATGTGATGTAGATTACACATACCACATG
1 ATGATGCT-AGTATGTGATGTAGATTCCACATACCACATG
19487205 TTATGAGTAT
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
67 46 0.51
68 34 0.37
69 7 0.08
70 4 0.04
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (68 bp):
ATGATGCTAGTATGTGATGTAGATTCCACATACCACATGAGATGATAAAGAGTACTATTGAAAAC
TAT
Found at i:19491258 original size:19 final size:19
Alignment explanation
Indices: 19491234--19491271 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19491224 CCTTCATATA
*
19491234 GGGATGTATTGATACATTT
1 GGGATGTATCGATACATTT
19491253 GGGATGTATCGATACATTT
1 GGGATGTATCGATACATTT
19491272 TAAATGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.39
Consensus pattern (19 bp):
GGGATGTATCGATACATTT
Found at i:19492061 original size:20 final size:20
Alignment explanation
Indices: 19492028--19492066 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19492018 CTTCATTCTC
* *
19492028 CAACACGTTCCTCAGATTTT
1 CAACACCTTCCTCAAATTTT
*
19492048 CAACACCTTTCTCAAATTT
1 CAACACCTTCCTCAAATTT
19492067 CTAGCACTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.31, G:0.05, T:0.36
Consensus pattern (20 bp):
CAACACCTTCCTCAAATTTT
Found at i:19503731 original size:55 final size:55
Alignment explanation
Indices: 19503647--19503752 Score: 185
Period size: 55 Copynumber: 1.9 Consensus size: 55
19503637 ATGTATACAA
* *
19503647 CCACCGGTCATTAGCTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCAC
1 CCACCGGTCATCAACTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCAC
*
19503702 CCACCGGTCATCAACTCATGTGCACTCCCACACCGCACATAGCTGGAATCA
1 CCACCGGTCATCAACTCATGTGCACTCCCACACCGCACATAGCTAGAATCA
19503753 CCCATCATCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.27, C:0.39, G:0.15, T:0.19
Consensus pattern (55 bp):
CCACCGGTCATCAACTCATGTGCACTCCCACACCGCACATAGCTAGAATCATCAC
Found at i:19505747 original size:11 final size:11
Alignment explanation
Indices: 19505715--19505748 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
19505705 TTGTTCAACA
19505715 TTTTT-TTTCT
1 TTTTTCTTTCT
*
19505725 GTTTTCTTTCT
1 TTTTTCTTTCT
19505736 TTTTTCTTTCT
1 TTTTTCTTTCT
19505747 TT
1 TT
19505749 CACAATTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:19509274 original size:22 final size:22
Alignment explanation
Indices: 19509242--19509284 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
19509232 TTAAAACAAC
*
19509242 TTTAAACCCAAAAGCTTTGATT
1 TTTAAAACCAAAAGCTTTGATT
19509264 TTTAAAACCAAAAGCTTTGAT
1 TTTAAAACCAAAAGCTTTGAT
19509285 ACCAACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (22 bp):
TTTAAAACCAAAAGCTTTGATT
Found at i:19510510 original size:3 final size:3
Alignment explanation
Indices: 19510502--19510528 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
19510492 TAGCAGCTTG
19510502 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
19510529 CTCTCACGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:19511263 original size:42 final size:42
Alignment explanation
Indices: 19511199--19511322 Score: 176
Period size: 42 Copynumber: 3.0 Consensus size: 42
19511189 GTTGATGTGG
* *
19511199 ACCCAGCTATGTGCAAGTAGGAGTACACATAAGCCGTTGCTA
1 ACCCGGCTATGTGCAAGTAGGAGTGCACATAAGCCGTTGCTA
* *
19511241 ACCCGGCTATGTGCTAGTAGGAGTGCACATAAGCCGTTGCTG
1 ACCCGGCTATGTGCAAGTAGGAGTGCACATAAGCCGTTGCTA
* * **
19511283 ACACGGCTATGTGCAAGTGGGAGTGTGCATAAGCCGTTGC
1 ACCCGGCTATGTGCAAGTAGGAGTGCACATAAGCCGTTGC
19511323 ATATGAGATG
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (42 bp):
ACCCGGCTATGTGCAAGTAGGAGTGCACATAAGCCGTTGCTA
Found at i:19511742 original size:60 final size:61
Alignment explanation
Indices: 19511608--19511779 Score: 181
Period size: 60 Copynumber: 2.9 Consensus size: 61
19511598 ACACTGTAGC
* * * * *
19511608 ATCTCGCTGCAGCGAAATTCATTCTCGCTGCAGCGAGAAACTTTCTGTTTCTGAGTTACAAT
1 ATCTAGCTGCAGCGAAATTCATTCTCGCTGCAGCGAAAAACTTTTTGTTT-TGAGTGACAAA
* * * * *
19511670 TTC-A-CTGTAGCGAAATTTATTCTCACTGCAGCAAAAAACTTTTTGTTTT-A-TGACCAAA
1 ATCTAGCTGCAGCGAAATTCATTCTCGCTGCAGCGAAAAACTTTTTGTTTTGAGTGA-CAAA
** *
19511728 ATCTAGCTGCAGCGAAATTCAACCTCGCTGCAACGAAAAACTTTTTGTTTTG
1 ATCTAGCTGCAGCGAAATTCATTCTCGCTGCAGCGAAAAACTTTTTGTTTTG
19511780 TCTTCTATCT
Statistics
Matches: 88, Mismatches: 18, Indels: 9
0.77 0.16 0.08
Matches are distributed among these distances:
57 2 0.02
58 6 0.07
59 2 0.02
60 76 0.86
62 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (61 bp):
ATCTAGCTGCAGCGAAATTCATTCTCGCTGCAGCGAAAAACTTTTTGTTTTGAGTGACAAA
Found at i:19517277 original size:2 final size:2
Alignment explanation
Indices: 19517270--19517313 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
19517260 TGTTTACTTT
19517270 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19517311 TA T
1 TA T
19517314 TTTTCTTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19521002 original size:42 final size:42
Alignment explanation
Indices: 19520955--19521037 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
19520945 CATCTCATAT
*
19520955 GCAACGGCTTATGCACACTCCCACTTGCACATAGCCGGGTCA
1 GCAACGGCTTATGCACACTCCCACTCGCACATAGCCGGGTCA
** *
19520997 GCAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
1 GCAACGGCTTATGCACACTCCCACTCGCACATAGCCGGGTC
19521038 CACATCAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.22, C:0.35, G:0.23, T:0.20
Consensus pattern (42 bp):
GCAACGGCTTATGCACACTCCCACTCGCACATAGCCGGGTCA
Found at i:19530499 original size:40 final size:40
Alignment explanation
Indices: 19530438--19530516 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
19530428 TTCTCATAGA
19530438 CTTCATTTCATCATTCTTTGCATTATTCTACTTTTATGTT
1 CTTCATTTCATCATTCTTTGCATTATTCTACTTTTATGTT
*
19530478 CTTCATTTCATCATT-TATTGCATTATTCTATTTTTATGT
1 CTTCATTTCATCATTCT-TTGCATTATTCTACTTTTATGT
19530517 GACAGGAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
39 1 0.03
40 36 0.97
ACGTcount: A:0.19, C:0.18, G:0.05, T:0.58
Consensus pattern (40 bp):
CTTCATTTCATCATTCTTTGCATTATTCTACTTTTATGTT
Found at i:19531174 original size:50 final size:50
Alignment explanation
Indices: 19531105--19531204 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 50
19531095 AAACTTAGTA
*
19531105 TTACAATATCCCTCACACTTC-ATCTAATCTTTCCTCTCTTCCTTAACTT
1 TTACAATATCCCTCACACTTCTATCTAATCTTACCTCTCTTCCTTAACTT
*
19531154 NTTACAATATCCCTCACACTTCTATCTAATCTTACCTCTCTTCTTTAACTT
1 -TTACAATATCCCTCACACTTCTATCTAATCTTACCTCTCTTCCTTAACTT
19531205 ATTTCAATGG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 21 0.45
51 26 0.55
ACGTcount: A:0.23, C:0.33, G:0.00, T:0.43
Consensus pattern (50 bp):
TTACAATATCCCTCACACTTCTATCTAATCTTACCTCTCTTCCTTAACTT
Found at i:19532220 original size:20 final size:21
Alignment explanation
Indices: 19532184--19532223 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
19532174 AAAAACTAAT
*
19532184 AAATAACAATCAAATTAAAAG
1 AAATAACAATAAAATTAAAAG
19532205 AAATAAC-ATAAAATTAAAA
1 AAATAACAATAAAATTAAAA
19532224 TAACTCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (21 bp):
AAATAACAATAAAATTAAAAG
Found at i:19532240 original size:15 final size:16
Alignment explanation
Indices: 19532220--19532262 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
19532210 ACATAAAATT
*
19532220 AAAATAACTCACT-TA
1 AAAATAACTAACTATA
*
19532235 AAAATAAACTAATTATA
1 AAAAT-AACTAACTATA
19532252 AAAATAACTAA
1 AAAATAACTAA
19532263 AAATAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAACTAACTATA
Found at i:19543495 original size:25 final size:26
Alignment explanation
Indices: 19543466--19543514 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
19543456 ACAATTATGA
19543466 ACTTCTCA-ACATAAAAGATGTACAC
1 ACTTCTCATACATAAAAGATGTACAC
* *
19543491 ACTTCTCATTCATAAAATATGTAC
1 ACTTCTCATACATAAAAGATGTAC
19543515 CCAATACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (26 bp):
ACTTCTCATACATAAAAGATGTACAC
Found at i:19552147 original size:20 final size:19
Alignment explanation
Indices: 19552113--19552161 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
19552103 ATTTAGTCAT
*
19552113 TTTTAGTTTTTTTATAATTA
1 TTTTAATTTTTTTAT-ATTA
*
19552133 -TTTAATTTTTATTATGTTA
1 TTTTAATTTTT-TTATATTA
19552152 TTTTAATTTT
1 TTTTAATTTT
19552162 ATGTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTTAATTTTTTTATATTA
Found at i:19554092 original size:56 final size:56
Alignment explanation
Indices: 19554031--19554144 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 56
19554021 GATGTAAAGT
* * **
19554031 TTTTACTTGATTCTTGAAAAGGCTAAGATTCTACCTAATCCTTGAAAAGGGTGAGG
1 TTTTACTCGATCCTTGAAAAGGCTAAGATTCTACCTAATCCTTGAAAAGACTGAGG
* * *
19554087 TTTTACTCGATCCTTGAAAAGGCTAAGGTTCTGCCTGATCCTTGAAAAGACTGAGG
1 TTTTACTCGATCCTTGAAAAGGCTAAGATTCTACCTAATCCTTGAAAAGACTGAGG
19554143 TT
1 TT
19554145 ATGTCTATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (56 bp):
TTTTACTCGATCCTTGAAAAGGCTAAGATTCTACCTAATCCTTGAAAAGACTGAGG
Found at i:19554099 original size:28 final size:28
Alignment explanation
Indices: 19554038--19554144 Score: 117
Period size: 28 Copynumber: 3.8 Consensus size: 28
19554028 AGTTTTTACT
* * *
19554038 TGATTCTTGAAAAGGCTAAGATTCTACC
1 TGATCCTTGAAAAGGCTGAGGTTCTACC
* * *
19554066 TAATCCTTGAAAAGGGTGAGGTTTTA-C
1 TGATCCTTGAAAAGGCTGAGGTTCTACC
* *
19554093 TCGATCCTTGAAAAGGCTAAGGTTCTGCC
1 T-GATCCTTGAAAAGGCTGAGGTTCTACC
*
19554122 TGATCCTTGAAAAGACTGAGGTT
1 TGATCCTTGAAAAGGCTGAGGTT
19554145 ATGTCTATTT
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
27 2 0.03
28 60 0.94
29 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (28 bp):
TGATCCTTGAAAAGGCTGAGGTTCTACC
Found at i:19554201 original size:32 final size:34
Alignment explanation
Indices: 19554165--19554228 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
19554155 CTTGAAAGGG
*
19554165 TAGTGTG-GGTTATGCTTGATCC-CATGAAAAAA
1 TAGTGTGAGGTAATGCTTGATCCTCATGAAAAAA
*
19554197 TAGTGTGAGGTAATGCTTGATCCTCTTGAAAA
1 TAGTGTGAGGTAATGCTTGATCCTCATGAAAA
19554229 GGTAATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 7 0.25
33 14 0.50
34 7 0.25
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (34 bp):
TAGTGTGAGGTAATGCTTGATCCTCATGAAAAAA
Found at i:19580375 original size:38 final size:40
Alignment explanation
Indices: 19580333--19580428 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 40
19580323 CCGTGTTCAT
* *
19580333 GATGTGGGGGGATGTACACGAT-G-GCACTGAT-TGTGCAG
1 GATGTGGGGGGATGTACACGATGGTGC-CGGATATGTGCAC
* * * *
19580371 GATGTGGGGAGATGCACATGATGGTGCCGGCTATGTGCAC
1 GATGTGGGGGGATGTACACGATGGTGCCGGATATGTGCAC
19580411 GATGTGGGGGGATGTACA
1 GATGTGGGGGGATGTACA
19580429 TGAGCCGGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
38 19 0.40
39 4 0.09
40 24 0.51
ACGTcount: A:0.21, C:0.14, G:0.43, T:0.23
Consensus pattern (40 bp):
GATGTGGGGGGATGTACACGATGGTGCCGGATATGTGCAC
Found at i:19580880 original size:60 final size:60
Alignment explanation
Indices: 19580781--19580899 Score: 143
Period size: 60 Copynumber: 2.0 Consensus size: 60
19580771 TTCTCGCTAT
**
19580781 AGCGAAAAGGAATCTCGATGCAGTGAAAAACTCTCTGTTTCATCAGTTA-AATTTCGCTGC
1 AGCGAAAAAAAATCTCGATGCAGTGAAAAACTCTCTGTTTC-TCAGTTACAATTTCGCTGC
* * * **
19580841 AGCGAAAAAAAATCTCGCTGCAGTGAGAAAGCT-TTTGTTTCTGGGTTACAATTTCGCTG
1 AGCGAAAAAAAATCTCGATGCAGTGA-AAAACTCTCTGTTTCTCAGTTACAATTTCGCTG
19580900 AATCTCGCTG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 5 0.10
60 40 0.80
61 5 0.10
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (60 bp):
AGCGAAAAAAAATCTCGATGCAGTGAAAAACTCTCTGTTTCTCAGTTACAATTTCGCTGC
Found at i:19581548 original size:63 final size:62
Alignment explanation
Indices: 19581449--19581568 Score: 222
Period size: 63 Copynumber: 1.9 Consensus size: 62
19581439 GGTGTCTCGA
19581449 CATTCAGTAGCTGTACATTCATCCGAGTCCCTCCGCTGGAAGTCGAGTATTATTTTGNCTCAG
1 CATTCAGTAGCTGTACATTCATCCGAGTCCCTCCGCTGGAAGTCGAGTATTATTTTG-CTCAG
*
19581512 CATTCAGTAGCTGTCCATTCATCCGAGTCCCTCCGCTGGAAGTCGAGTATTATTTTG
1 CATTCAGTAGCTGTACATTCATCCGAGTCCCTCCGCTGGAAGTCGAGTATTATTTTG
19581569 TTGTGTATAG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (62 bp):
CATTCAGTAGCTGTACATTCATCCGAGTCCCTCCGCTGGAAGTCGAGTATTATTTTGCTCAG
Done.