Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 137 of 410
Found at i:41488237 original size:17 final size:17
Alignment explanation
Indices: 41488191--41488238 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
41488181 ACTTGAACTC
*
41488191 TTGAAACTTTTTTAAAAT
1 TTGAAA-TTATTTAAAAT
*
41488209 TTG-AATTCTTTAAAAT
1 TTGAAATTATTTAAAAT
41488225 TTGAAATTATTTAA
1 TTGAAATTATTTAA
41488239 TATATAGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 13 0.48
17 11 0.41
18 3 0.11
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (17 bp):
TTGAAATTATTTAAAAT
Found at i:41488354 original size:7 final size:7
Alignment explanation
Indices: 41488338--41488548 Score: 54
Period size: 7 Copynumber: 29.1 Consensus size: 7
41488328 TACACTAATT
*
41488338 ACCCTAA
1 ACCCTTA
41488345 ACCCTTA
1 ACCCTTA
*
41488352 ACCCCTA
1 ACCCTTA
*
41488359 ATCCTCTA
1 ACCCT-TA
* *
41488367 ACCCATG
1 ACCCTTA
*
41488374 TCCCTTTA
1 ACCC-TTA
41488382 A-CCTTAAA
1 ACCCTT--A
*
41488390 ACCCCTA
1 ACCCTTA
*
41488397 ACCCCTA
1 ACCCTTA
*
41488404 ACCCCTA
1 ACCCTTA
41488411 ACCAC-TA
1 ACC-CTTA
*
41488418 AACCTTAA
1 ACCCTT-A
*
41488426 ACCC-CA
1 ACCCTTA
41488432 ACCCTTA
1 ACCCTTA
*
41488439 ACCACATA
1 ACC-CTTA
*
41488447 ACCCTAAA
1 ACCCT-TA
*
41488455 ACCCATA
1 ACCCTTA
41488462 ACCCTTA
1 ACCCTTA
*
41488469 TCCCTTTA
1 ACCC-TTA
*
41488477 ACCCTAAA
1 ACCCT-TA
*
41488485 ACCCATA
1 ACCCTTA
* *
41488492 TCTCTTA
1 ACCCTTA
41488499 ATCCC-TA
1 A-CCCTTA
*
41488506 ACCCCTA
1 ACCCTTA
* *
41488513 ACCATTG
1 ACCCTTA
*
41488520 ATCCTTA
1 ACCCTTA
*
41488527 AACCTTA
1 ACCCTTA
*
41488534 GACCC-CA
1 -ACCCTTA
41488541 ACCCTTA
1 ACCCTTA
41488548 A
1 A
41488549 ATCATGAACC
Statistics
Matches: 145, Mismatches: 42, Indels: 34
0.66 0.19 0.15
Matches are distributed among these distances:
6 15 0.10
7 87 0.60
8 40 0.28
9 3 0.02
ACGTcount: A:0.34, C:0.42, G:0.01, T:0.23
Consensus pattern (7 bp):
ACCCTTA
Found at i:41488359 original size:15 final size:14
Alignment explanation
Indices: 41488339--41488515 Score: 70
Period size: 15 Copynumber: 12.1 Consensus size: 14
41488329 ACACTAATTA
41488339 CCCTAAACCCTTAAC
1 CCCT-AACCCTTAAC
*
41488354 CCCTAATCCTCTAAC
1 CCCTAACCCT-TAAC
* **
41488369 CCATGTCCCTTTAA-
1 CCCTAACCC-TTAAC
* *
41488383 CCTTAAAACCCCTAAC
1 CCCT--AACCCTTAAC
*
41488399 CCCTAACCCCTAAC
1 CCCTAACCCTTAAC
* *
41488413 CACTAAACCTTAAAC
1 CCCTAACCCTT-AAC
41488428 CCC-AACCCTTAAC
1 CCCTAACCCTTAAC
* *
41488441 CACATAACCCTAAAAC
1 C-CCTAACCCT-TAAC
* *
41488457 CCATAACCCTTATC
1 CCCTAACCCTTAAC
* *
41488471 CCTTTAACCCTAAAAC
1 CC-CTAACCCT-TAAC
* * * *
41488487 CCATATCTCTTAAT
1 CCCTAACCCTTAAC
*
41488501 CCCTAACCCCTAAC
1 CCCTAACCCTTAAC
41488515 C
1 C
41488516 ATTGATCCTT
Statistics
Matches: 119, Mismatches: 32, Indels: 23
0.68 0.18 0.13
Matches are distributed among these distances:
13 4 0.03
14 49 0.41
15 51 0.43
16 15 0.13
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.23
Consensus pattern (14 bp):
CCCTAACCCTTAAC
Found at i:41488442 original size:28 final size:29
Alignment explanation
Indices: 41488396--41488468 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
41488386 TAAAACCCCT
* *
41488396 AACCCCTAACCCCTAACCAC-TAAACCTTA
1 AACCCC-AACCCTTAACCACATAAACCTAA
*
41488425 AACCCCAACCCTTAACCACATAACCCTAA
1 AACCCCAACCCTTAACCACATAAACCTAA
*
41488454 AACCCATAACCCTTA
1 AACCC-CAACCCTTA
41488469 TCCCTTTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 12 0.32
29 18 0.47
30 8 0.21
ACGTcount: A:0.40, C:0.44, G:0.00, T:0.16
Consensus pattern (29 bp):
AACCCCAACCCTTAACCACATAAACCTAA
Found at i:41488467 original size:30 final size:29
Alignment explanation
Indices: 41488396--41488509 Score: 99
Period size: 30 Copynumber: 3.9 Consensus size: 29
41488386 TAAAACCCCT
* * * *
41488396 AACCCCTAACCCCTAACCACTAAACCTTA
1 AACCCATAACCCTTAACCACTAACCCTAA
*
41488425 AACCC-CAACCCTTAACCACATAACCCTAA
1 AACCCATAACCCTTAACCAC-TAACCCTAA
*
41488454 AACCCATAACCCTTATCC-CTTTAACCCTAA
1 AACCCATAACCCTTAACCAC--TAACCCTAA
* *
41488484 AACCCATATCTCTTAATCC-CTAACCC
1 AACCCATAACCCTTAA-CCACTAACCC
41488510 CTAACCATTG
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
28 12 0.17
29 24 0.34
30 32 0.45
31 3 0.04
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (29 bp):
AACCCATAACCCTTAACCACTAACCCTAA
Found at i:41488493 original size:23 final size:23
Alignment explanation
Indices: 41488461--41488506 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41488451 TAAAACCCAT
*
41488461 AACCCTTATCCCTTTAA-CCCTAA
1 AACCCATATCCC-TTAATCCCTAA
*
41488484 AACCCATATCTCTTAATCCCTAA
1 AACCCATATCCCTTAATCCCTAA
41488507 CCCCTAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (23 bp):
AACCCATATCCCTTAATCCCTAA
Found at i:41488634 original size:14 final size:14
Alignment explanation
Indices: 41488605--41488648 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
41488595 TTAAAATATT
41488605 AACTCATAAACTATA
1 AACTC-TAAACTATA
*
41488620 AACTCTAAACCATA
1 AACTCTAAACTATA
*
41488634 AACCCTAAACTATA
1 AACTCTAAACTATA
41488648 A
1 A
41488649 TGATAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (14 bp):
AACTCTAAACTATA
Found at i:41488828 original size:7 final size:7
Alignment explanation
Indices: 41488816--41488937 Score: 86
Period size: 7 Copynumber: 17.0 Consensus size: 7
41488806 ACACTAATTC
41488816 CCCTAAA
1 CCCTAAA
41488823 CCCTAAA
1 CCCTAAA
41488830 CCCTAAA
1 CCCTAAA
**
41488837 CCCTTACC
1 CCC-TAAA
*
41488845 CCCTTAA
1 CCCTAAA
41488852 CCCTTAAA
1 CCC-TAAA
*
41488860 CCCCTAAC
1 -CCCTAAA
41488868 CCCTAAA
1 CCCTAAA
*
41488875 CCTTAAA
1 CCCTAAA
41488882 CCC--AA
1 CCCTAAA
41488887 CCCTTAAA
1 CCC-TAAA
*
41488895 CCATAAA
1 CCCTAAA
* *
41488902 CCATAAT
1 CCCTAAA
41488909 CCCTAAA
1 CCCTAAA
*
41488916 CCCATAAT
1 CCC-TAAA
*
41488924 CCATAAA
1 CCCTAAA
*
41488931 CCTTAAA
1 CCCTAAA
41488938 ATAGTAACTC
Statistics
Matches: 90, Mismatches: 18, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
5 5 0.06
7 62 0.69
8 20 0.22
9 3 0.03
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (7 bp):
CCCTAAA
Found at i:41488848 original size:22 final size:22
Alignment explanation
Indices: 41488815--41488918 Score: 97
Period size: 22 Copynumber: 4.8 Consensus size: 22
41488805 CACACTAATT
*
41488815 CCCCTAAACCCTAAACCCTAAA
1 CCCCTAACCCCTAAACCCTAAA
* * *
41488837 CCCTTACCCCCTTAACCCTTAAA
1 CCCCTAACCCCTAAACCC-TAAA
*
41488860 CCCCTAACCCCTAAACCTTAAA
1 CCCCTAACCCCTAAACCCTAAA
* *
41488882 -CCC-AACCCTTAAACCATAAA
1 CCCCTAACCCCTAAACCCTAAA
* *
41488902 -CCATAATCCCTAAACCC
1 CCCCTAACCCCTAAACCC
41488919 ATAATCCATA
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
20 17 0.26
21 13 0.20
22 18 0.27
23 18 0.27
ACGTcount: A:0.37, C:0.45, G:0.00, T:0.18
Consensus pattern (22 bp):
CCCCTAACCCCTAAACCCTAAA
Found at i:41488867 original size:15 final size:16
Alignment explanation
Indices: 41488815--41488876 Score: 69
Period size: 15 Copynumber: 4.1 Consensus size: 16
41488805 CACACTAATT
41488815 CCCCTAAACCC-TAAA
1 CCCCTAAACCCTTAAA
*
41488830 -CCCTAAACCCTT-AC
1 CCCCTAAACCCTTAAA
*
41488844 CCCCTTAACCCTTAAA
1 CCCCTAAACCCTTAAA
*
41488860 CCCCT-AACCCCTAAA
1 CCCCTAAACCCTTAAA
41488875 CC
1 CC
41488877 TTAAACCCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
14 11 0.28
15 23 0.57
16 6 0.15
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (16 bp):
CCCCTAAACCCTTAAA
Found at i:41488920 original size:22 final size:22
Alignment explanation
Indices: 41488823--41488929 Score: 78
Period size: 22 Copynumber: 5.0 Consensus size: 22
41488813 TTCCCCTAAA
* *
41488823 CCCTAAACCC-TAAACCCTTACC
1 CCCTAAACCCATAAA-CCATAAC
* * *
41488845 CCCTTAACCCTTAAACCCCTAAC
1 CCCTAAACCCATAAA-CCATAAC
* *
41488868 CCCTAAA-CCTTAAACC-CAAC
1 CCCTAAACCCATAAACCATAAC
* *
41488888 CCTTAAA-CCATAAACCATAAT
1 CCCTAAACCCATAAACCATAAC
*
41488909 CCCTAAACCCATAATCCATAA
1 CCCTAAACCCATAAACCATAA
41488930 ACCTTAAAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
20 17 0.24
21 10 0.14
22 28 0.39
23 16 0.23
ACGTcount: A:0.38, C:0.42, G:0.00, T:0.20
Consensus pattern (22 bp):
CCCTAAACCCATAAACCATAAC
Found at i:41488959 original size:7 final size:7
Alignment explanation
Indices: 41488891--41488988 Score: 58
Period size: 7 Copynumber: 13.4 Consensus size: 7
41488881 ACCCAACCCT
41488891 TAAACCA
1 TAAACCA
41488898 TAAACCA
1 TAAACCA
* *
41488905 TAATCCC
1 TAAACCA
41488912 TAAACCCA
1 TAAA-CCA
*
41488920 TAATCCA
1 TAAACCA
*
41488927 TAAACCT
1 TAAACCA
41488934 TAAA--A
1 TAAACCA
41488939 TAGTAACTCA
1 TA--AAC-CA
41488949 TAAACCA
1 TAAACCA
*
41488956 TAAACGA
1 TAAACCA
41488963 TCTAAACCA
1 --TAAACCA
41488972 TAAATCC-
1 TAAA-CCA
*
41488979 TAAGCCA
1 TAAACCA
41488986 TAA
1 TAA
41488989 TGATAATTAA
Statistics
Matches: 70, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
5 2 0.03
6 2 0.03
7 47 0.67
8 10 0.14
9 6 0.09
10 3 0.04
ACGTcount: A:0.49, C:0.27, G:0.03, T:0.21
Consensus pattern (7 bp):
TAAACCA
Found at i:41489447 original size:40 final size:39
Alignment explanation
Indices: 41489403--41489570 Score: 135
Period size: 40 Copynumber: 4.2 Consensus size: 39
41489393 GAATTTTTTT
41489403 GCGGCGTTTTTAAAAACGCGCCTCTAATGCTCGATCTATA
1 GCGGCGTTTTTAAAAA-GCGCCTCTAATGCTCGATCTATA
* **
41489443 GCGGCGTTTTTCAAAAAGAGCAGCTAATAG-TCGATCTATA
1 GCGGCGTTTTT-AAAAAGCGCCTCTAAT-GCTCGATCTATA
* * * * *
41489483 GTGGCATTTTTAGAAAAGC-ACTGCTAATACTCAATCTATA
1 GCGGCGTTTTTA-AAAAGCGCCT-CTAATGCTCGATCTATA
* * * *
41489523 GCGGCGTTTTTTAGTAAA-CGCCGCTAATGCTCAATATATA
1 GCGGCG-TTTTTA-AAAAGCGCCTCTAATGCTCGATCTATA
*
41489563 ACGGCGTT
1 GCGGCGTT
41489571 CTTTGTCCAA
Statistics
Matches: 102, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
39 3 0.03
40 82 0.80
41 17 0.17
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (39 bp):
GCGGCGTTTTTAAAAAGCGCCTCTAATGCTCGATCTATA
Found at i:41490305 original size:13 final size:13
Alignment explanation
Indices: 41490287--41490311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41490277 AGGCCATGTG
41490287 AGGGACACGGGCC
1 AGGGACACGGGCC
41490300 AGGGACACGGGC
1 AGGGACACGGGC
41490312 GTGTGCTTGG
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:0.24, C:0.28, G:0.48, T:0.00
Consensus pattern (13 bp):
AGGGACACGGGCC
Found at i:41498201 original size:28 final size:29
Alignment explanation
Indices: 41498169--41498223 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
41498159 AACGGGCAAT
*
41498169 GACACGGGCGTGT-CTAGGCCATGTGAGG
1 GACACGGGCATGTGCTAGGCCATGTGAGG
* *
41498197 GACACGGGCATGTGCTCGGCCTTGTGA
1 GACACGGGCATGTGCTAGGCCATGTGA
41498224 AAACCCCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (29 bp):
GACACGGGCATGTGCTAGGCCATGTGAGG
Found at i:41500054 original size:55 final size:54
Alignment explanation
Indices: 41499946--41500153 Score: 253
Period size: 55 Copynumber: 3.8 Consensus size: 54
41499936 ATTAGGGTTT
* * *
41499946 AAGGATACCATGTAAGACCATGCCAAGGCATGACAATTGGTAAGGTT-TCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-GTTCTATAAGGC
* *
41500001 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-CTATAAGGC
* *
41500056 AAAGG-T-CCTATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATACC-ATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGC
* * *
41500109 AAGGATACCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT
41500154 TCAAAAGGAT
Statistics
Matches: 133, Mismatches: 14, Indels: 14
0.83 0.09 0.09
Matches are distributed among these distances:
52 4 0.03
53 42 0.32
54 12 0.09
55 71 0.53
56 4 0.03
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTATAAGGC
Found at i:41500152 original size:108 final size:110
Alignment explanation
Indices: 41499955--41500153 Score: 323
Period size: 108 Copynumber: 1.8 Consensus size: 110
41499945 TAAGGATACC
41499955 ATGTAAGACCATGCCAAGGCATGACAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGACC
1 ATGTAAGACCATGCCAAGGCATGACAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGACC
*
41500020 ATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCT
66 ATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCT
* *
41500065 ATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAGAC
1 ATGTAAGACCATGCCAAGGCATGACAATTGGTAAGGTTTC-TAAGGCAAGGATACCATGTAAGAC
* *
41500127 CATGTCGAGACATGGCAATGGTAAGTT
65 CATGTCAAGACATGGCAATGATAAGTT
41500154 TCAAAAGGAT
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 3 0.04
108 49 0.59
109 7 0.08
110 24 0.29
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (110 bp):
ATGTAAGACCATGCCAAGGCATGACAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGACC
ATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCT
Found at i:41503215 original size:50 final size:50
Alignment explanation
Indices: 41503090--41503475 Score: 373
Period size: 50 Copynumber: 7.7 Consensus size: 50
41503080 CTGGTACGCA
* * * *
41503090 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AACAAT-TCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGA-TACACG
* * * *
41503139 TAGTAACTTG-ACTTAGTATTAGACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
* * *** * * * *
41503188 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTGTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CCATCTGATACACG
* * * * *
41503239 TAGTAGCCTACACTTAGTACTACACATGCGACCTAACTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
*
41503289 TAGTAGCCTGCACTTAGTACTAGACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
* * * *** * * ***
41503339 TAGTAGCCTGCACTTAGTACTACACATGTGATCAAAGTTGTCGGGTACGTA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CCATCTGATACACG
* * * *
41503390 TAGTAGCCTACACTTAGTACTACACATGCGACCTAACCATCTGTTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
*
41503440 TAGTAGCCTACACTTAGTACTACACACGTGACCTAA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
41503476 AATCATTTTA
Statistics
Matches: 269, Mismatches: 63, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
48 18 0.07
49 27 0.10
50 148 0.55
51 76 0.28
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
Found at i:41503349 original size:151 final size:151
Alignment explanation
Indices: 41503082--41503475 Score: 641
Period size: 151 Copynumber: 2.6 Consensus size: 151
41503072 GAAGCTATCT
* * *
41503082 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACAAT-TCAGTACACGTAGTAA
1 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAACAATCT-GGTACACGTAGTAG
* *
41503145 CTTG-ACTTAGTATTAGACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACT
65 CCTGCACTTAGTACTAGACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACT
*
41503209 ACACACGTGATCGAAGTTGTCG
130 ACACACGTGATCAAAGTTGTCG
*
41503231 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAACTATCTGGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTAGC
41503296 CTGCACTTAGTACTAGACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
66 CTGCACTTAGTACTAGACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
*
41503361 CACATGTGATCAAAGTTGTCG
131 CACACGTGATCAAAGTTGTCG
* * *
41503382 GGTACGTATAGTAGCCTACACTTAGTACTACACATGCGACCTAACCATCTGTTACACGTAGTAGC
1 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTAGC
* *
41503447 CTACACTTAGTACTACACACGTGACCTAA
66 CTGCACTTAGTACTAGACACGTGACCTAA
41503476 AATCATTTTA
Statistics
Matches: 229, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
149 40 0.17
150 20 0.09
151 169 0.74
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAACAATCTGGTACACGTAGTAGC
CTGCACTTAGTACTAGACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
CACACGTGATCAAAGTTGTCG
Found at i:41503386 original size:101 final size:100
Alignment explanation
Indices: 41503076--41503472 Score: 368
Period size: 101 Copynumber: 4.0 Consensus size: 100
41503066 GTAACCGAAG
* * * * * * *
41503076 CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACAAT-TCAGTACACG
1 CTATCGGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGA-TACACG
* ** * * * *
41503139 TAGTA-ACTTGACTTAGTATTAGACACGTGACCTAA
65 TAGTAGCCTACACTTAGTACTACACATGTGACCAAA
* * * * * *** * * * *
41503174 CCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTGTCGGGTACGCA
1 CTATCGGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CCATCTGATACACG
* *
41503239 TAGTAGCCTACACTTAGTACTACACATGCGACCTAA
65 TAGTAGCCTACACTTAGTACTACACATGTGACCAAA
* *
41503275 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTAGACACGTGACCTAACCATCTGATACACGT
1 CTATCGGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGT
* *
41503340 AGTAGCCTGCACTTAGTACTACACATGTGATCAAA
66 AGTAGCCTACACTTAGTACTACACATGTGACCAAA
* * *** * * * *
41503375 GTTGTCGGGTACGTATAGTAGCCTACACTTAGTACTACACATGCGACCTAACCATCTGTTACACG
1 -CTATCGGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
*
41503440 TAGTAGCCTACACTTAGTACTACACACGTGACC
65 TAGTAGCCTACACTTAGTACTACACATGTGACC
41503473 TAAAATCATT
Statistics
Matches: 242, Mismatches: 52, Indels: 7
0.80 0.17 0.02
Matches are distributed among these distances:
98 40 0.17
99 2 0.01
100 49 0.20
101 151 0.62
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (100 bp):
CTATCGGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGT
AGTAGCCTACACTTAGTACTACACATGTGACCAAA
Found at i:41503515 original size:52 final size:50
Alignment explanation
Indices: 41503078--41503517 Score: 305
Period size: 50 Copynumber: 8.8 Consensus size: 50
41503068 AACCGAAGCT
* * * *
41503078 ATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACA
1 ATCTGTTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACA
* * * ** * * * *
41503127 ATTCAG-TACACGTAGTA-ACTTGACTTAGTATTAGACACGTGACCTAACC
1 A-TCTGTTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACA
* * * * * * **
41503176 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTT
1 ATCTGTTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAA-CA
* * * * * *
41503227 GTCGGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCTAACT
1 ATCTGTTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACA
* * * * * *
41503277 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTAGACACGTGACCTAACC
1 ATCTGTTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACA
* * * * * * * **
41503327 ATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGTGATCAAAGTT
1 ATCTGTTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAA-CA
* * * ** * *
41503378 GTCGGGTACGTATAGTAGCCTACACTTAGTACTACACATGCGACCTAACC
1 ATCTGTTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACA
* *
41503428 ATCTGTTACACGTAGTAGCCTACACTTAGTACTACACACGTGACCTAA-A
1 ATCTGTTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACA
* *
41503477 ATCATTTTAAGCACATAGTAGCCTGCA-TATAGTACTACACA
1 ATC-TGTT-A-CACATAGTAGCCTACACT-TAGTACTACACA
41503518 TGTGTTCTCG
Statistics
Matches: 309, Mismatches: 72, Indels: 17
0.78 0.18 0.04
Matches are distributed among these distances:
48 23 0.07
49 28 0.09
50 154 0.50
51 78 0.25
52 26 0.08
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (50 bp):
ATCTGTTACACATAGTAGCCTACACTTAGTACTACACACGCGACCTAACA
Found at i:41512364 original size:93 final size:93
Alignment explanation
Indices: 41512253--41512424 Score: 254
Period size: 93 Copynumber: 1.8 Consensus size: 93
41512243 GGATGGTTGA
* * ** * ** *
41512253 GCATCCGAACCCGTTGAGTTGAGTTCGAGTTCACTTACGGATGGGAATGTTCGAACTCGTTGTGT
1 GCATCCGAACACGTTGAGTTGAGTCCGAGTTCACTTACGGATGCAAACGCCCGAACTCGTTGAGT
41512318 TGAGTCTGAGTTCATGAGATGTAACTAG
66 TGAGTCTGAGTTCATGAGATGTAACTAG
* *
41512346 GCATCCGAACACGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACACGTTGAGTTGAGTCCGAGTTCACTTACGGATGCAAACGCCCGAACTCGTTGAGT
41512411 TGAGTCTGAGTTCA
66 TGAGTCTGAGTTCA
41512425 CTTAGGGGAG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACACGTTGAGTTGAGTCCGAGTTCACTTACGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCTGAGTTCATGAGATGTAACTAG
Found at i:41517283 original size:29 final size:29
Alignment explanation
Indices: 41517248--41517321 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
41517238 GTTGTGAGAT
* *
41517248 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
41517277 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
41517306 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41517322 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:41523422 original size:28 final size:28
Alignment explanation
Indices: 41523390--41523458 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
41523380 GCGTAGATCA
41523390 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
41523418 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
41523446 CGATA-TACCCCTA
1 CGAAATTACCCCTA
41523459 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:41529756 original size:20 final size:20
Alignment explanation
Indices: 41529731--41529768 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41529721 GTTTATTCGC
*
41529731 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
41529751 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
41529769 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:41531433 original size:28 final size:28
Alignment explanation
Indices: 41531391--41531464 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
41531381 AATTACGTAG
*
41531391 AATTACC-GAATTACCCCTAAAGAGCAA
1 AATTACCAAAATTACCCCTAAAGAGCAA
*
41531418 AATTACCAAAATTACCCCTAAGGAGCAA
1 AATTACCAAAATTACCCCTAAAGAGCAA
*
41531446 AATTACCAATA-TACCCCTA
1 AATTACCAAAATTACCCCTA
41531465 GGGTTTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 15 0.35
28 28 0.65
ACGTcount: A:0.45, C:0.27, G:0.08, T:0.20
Consensus pattern (28 bp):
AATTACCAAAATTACCCCTAAAGAGCAA
Found at i:41533740 original size:40 final size:39
Alignment explanation
Indices: 41533653--41533802 Score: 130
Period size: 40 Copynumber: 3.8 Consensus size: 39
41533643 AAATTGATGA
* * * **
41533653 TATCCGGGCTAAGCCCCGAAGACAATTATGCTG-GAAAT-
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTCATC
* *
41533691 TATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TAT--CCGGGCTAAGACCCGAAGGCAATTGTGCGAGT--CAT-C
41533734 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTCATC
*
41533772 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
41533803 AAATCGTGAT
Statistics
Matches: 91, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
38 5 0.05
39 30 0.33
40 53 0.58
41 1 0.01
42 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (39 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATC
Found at i:41533787 original size:39 final size:38
Alignment explanation
Indices: 41533696--41533802 Score: 128
Period size: 39 Copynumber: 2.7 Consensus size: 38
41533686 GAAATTATAA
* *
41533696 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACAT
1 CCGGGCTAAGACCCGAAGGC-ATTGTGCGAGT-GCTACAT
41533736 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGT-C-ATCTAT
1 CCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGCTA-C-AT
41533775 CCGGGCTAAGACCCGAAGGCATTTGTGC
1 CCGGGCTAAGACCCGAAGGCA-TTGTGC
41533803 AAATCGTGAT
Statistics
Matches: 61, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
37 1 0.02
38 2 0.03
39 30 0.49
40 28 0.46
ACGTcount: A:0.23, C:0.26, G:0.30, T:0.21
Consensus pattern (38 bp):
CCGGGCTAAGACCCGAAGGCATTGTGCGAGTGCTACAT
Found at i:41533817 original size:79 final size:79
Alignment explanation
Indices: 41533696--41533879 Score: 181
Period size: 79 Copynumber: 2.3 Consensus size: 79
41533686 GAAATTATAA
* * * *
41533696 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCATTCG
41533761 TGCGAGTCATCTAT
66 TGCGAGTCATCTAT
* * * * * * *
41533775 CCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGCCTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGCATTC
* * * *
41533839 GTGCGGGTTACCATAA
65 GTGCGAGTCATC-TAT
* * *
41533855 CCGGGCTATGTCCCGAAGGCGATTG
1 CCGGGCTAAGACCCGAAGGCAATTG
41533880 ATCGAGTAGC
Statistics
Matches: 84, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
78 1 0.01
79 60 0.71
80 23 0.27
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.22
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCATTCG
TGCGAGTCATCTAT
Found at i:41539273 original size:29 final size:29
Alignment explanation
Indices: 41539238--41539311 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
41539228 GTTGTGAGAT
* *
41539238 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
41539267 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
41539296 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41539312 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:41557364 original size:16 final size:17
Alignment explanation
Indices: 41557328--41557364 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
41557318 CCACGTCAAA
41557328 TCAAATCTTAAATTAAC
1 TCAAATCTTAAATTAAC
41557345 TCAAA-CTTGAAATT-AC
1 TCAAATCTT-AAATTAAC
41557361 TCAA
1 TCAA
41557365 TTCTAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (17 bp):
TCAAATCTTAAATTAAC
Found at i:41575052 original size:46 final size:46
Alignment explanation
Indices: 41575000--41575175 Score: 160
Period size: 46 Copynumber: 3.8 Consensus size: 46
41574990 TATTTGGGCA
*
41575000 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCTAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCTAACG
* * * * * *
41575046 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCTA-ACG
* * * *
41575093 TCTGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCTAACG
* * * *
41575139 -CCTGAGCTCATTGAGTTGAGTCTGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41575176 GCGAGTTACA
Statistics
Matches: 102, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
45 2 0.02
46 64 0.63
47 35 0.34
48 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCTAACG
Found at i:41575155 original size:93 final size:93
Alignment explanation
Indices: 41574996--41575168 Score: 258
Period size: 93 Copynumber: 1.9 Consensus size: 93
41574986 CAGATATTTG
* * *
41574996 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCTAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
41575061 TTGAGTCCGAGTTCGTGAAATGTAACTA
66 TTGAGTCCGAGTTCGTGAAATGTAACTA
* * * *
41575089 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATG-CCTGAGCTCATTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCATTGA
*
41575153 GTTGAGTCTGAGTTCG
65 GTTGAGTCCGAGTTCG
41575169 CTTATGGGCG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
92 2 0.03
93 69 0.97
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAG
TTGAGTCCGAGTTCGTGAAATGTAACTA
Found at i:41579715 original size:49 final size:48
Alignment explanation
Indices: 41579657--41579924 Score: 196
Period size: 49 Copynumber: 5.6 Consensus size: 48
41579647 TATGTGTGCT
41579657 AGTGTAAGACCTGTCTGGGACATGGCATCGGCATCAATAGATGAGAGGC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGCATCAATA-ATGAGAGGC
* * * *
41579706 GGTGTAAGACCTGTCTGGGACACGGCATCGACCTCAGGAT-ATGCA-A-GC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGCATCA--ATAATG-AGAGGC
* * * * **
41579754 TAGTGTAAGACCTGTTTGGGACATGGCATCGGC-T---TAAGGTGTGTT
1 -AGTGTAAGACCTGTCTGGGACATGGCATCGGCATCAATAATGAGAGGC
* *
41579799 AGTGTAAGACCTGTCTGGGACATGGCATCGACA-CAGATAAGTGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGCATCA-ATAA-TGAGAGGC
* ** * * * * *
41579848 AGTGTAAAACCTAACTGGGACATGGGATCGGCCTCGATGTATGTA-AGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGCATCAAT-AATG-AGAGGC
41579897 AGTGTAAGACC-GATCTGGGACATGGCAT
1 AGTGTAAGACCTG-TCTGGGACATGGCAT
41579925 TGACTTAGAT
Statistics
Matches: 169, Mismatches: 33, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
43 1 0.01
44 32 0.19
48 6 0.04
49 124 0.73
50 4 0.02
51 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGGCATCAATAATGAGAGGC
Found at i:41579852 original size:93 final size:95
Alignment explanation
Indices: 41579657--41579976 Score: 269
Period size: 98 Copynumber: 3.3 Consensus size: 95
41579647 TATGTGTGCT
* * * * *
41579657 AGTGTAAGACCTGTCTGGGACATGGCATCGGCATCAATAG-ATGAGAGGCGGTGTAAGACCTGTC
1 AGTGTAAGACCTGTTTGGGACATGGCATCGGC-TCGA-AGTATG-TAGTCAGTGTAAGACCTGTC
* *
41579721 TGGGACACGGCATCGACCTCAGGATA-TGCA-AGCT
63 TGGGACATGGCATCGA-CTCA-GATAGTG-AGAGCC
* * *
41579755 AGTGTAAGACCTGTTTGGGACATGGCATCGGCT-TAAG-GTGT-GTTAGTGTAAGACCTGTCTGG
1 AGTGTAAGACCTGTTTGGGACATGGCATCGGCTCGAAGTATGTAGTCAGTGTAAGACCTGTCTGG
*
41579817 GACATGGCATCGACACAGATAAGTGAGAGCC
66 GACATGGCATCGACTCAGAT-AGTGAGAGCC
* *** * *
41579848 AGTGTAAAACCTAACTGGGACATGGGATCGGCCTCGATGTATGTAAGTCAGTGTAAGACC-GATC
1 AGTGTAAGACCTGTTTGGGACATGGCATCGG-CTCGAAGTATGT-AGTCAGTGTAAGACCTG-TC
* *
41579912 TGGGACATGGCATTGACTTAGAT-GTGAGAGCC
63 TGGGACATGGCATCGACTCAGATAGTGAGAGCC
* * * * *
41579944 AGTATAAGAACATGTTTGGAACATAGCACCGGC
1 AGTGTAAG-ACCTGTTTGGGACATGGCATCGGC
41579977 ATTGTACCCT
Statistics
Matches: 180, Mismatches: 32, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
91 3 0.02
92 5 0.03
93 61 0.34
94 2 0.01
95 6 0.03
96 20 0.11
97 17 0.09
98 66 0.37
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.23
Consensus pattern (95 bp):
AGTGTAAGACCTGTTTGGGACATGGCATCGGCTCGAAGTATGTAGTCAGTGTAAGACCTGTCTGG
GACATGGCATCGACTCAGATAGTGAGAGCC
Found at i:41579906 original size:142 final size:142
Alignment explanation
Indices: 41579650--41579924 Score: 353
Period size: 142 Copynumber: 1.9 Consensus size: 142
41579640 TGGGTGATAT
* * * *
41579650 GTGTGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCATCAATAGATGAGAGGCGGTGTAAGA
1 GTGTGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACATCAATAGATGAGAGCCAGTGTAAAA
** *
41579715 CCTGTCTGGGACACGGCATCGACCTCAGGATATGCAAGCTAGTGTAAGACCTG-TTTGGGACATG
66 CCTAACTGGGACACGGCATCGACCTCAGGATATGCAAGCTAGTGTAAGACC-GATCTGGGACATG
41579779 GCATCGGCTTAAG
130 GCATCGGCTTAAG
*
41579792 GTGTGTTAGTGTAAGACCTGTCTGGGACATGGCATCGACA-CAGATA-AGTGAGAGCCAGTGTAA
1 GTGTGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACATCA-ATAGA-TGAGAGCCAGTGTAA
* * * * *
41579855 AACCTAACTGGGACATGGGATCGGCCTCGATG-TATGTAAG-TCAGTGTAAGACCGATCTGGGAC
64 AACCTAACTGGGACACGGCATCGACCTC-AGGATATGCAAGCT-AGTGTAAGACCGATCTGGGAC
41579918 ATGGCAT
127 ATGGCAT
41579925 TGACTTAGAT
Statistics
Matches: 115, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
141 5 0.04
142 108 0.94
143 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (142 bp):
GTGTGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACATCAATAGATGAGAGCCAGTGTAAAA
CCTAACTGGGACACGGCATCGACCTCAGGATATGCAAGCTAGTGTAAGACCGATCTGGGACATGG
CATCGGCTTAAG
Found at i:41580140 original size:22 final size:23
Alignment explanation
Indices: 41580114--41580168 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 23
41580104 GAAATTGATG
41580114 ATGAACATGA-GTAAGAATTGTT
1 ATGAACATGACGTAAGAATTGTT
*
41580136 ATGAACATTTACTGTAAGAATTGTT
1 ATGAACA-TGAC-GTAAGAATTGTT
41580161 ATGAACAT
1 ATGAACAT
41580169 TTATTGTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 7 0.24
23 2 0.07
24 1 0.03
25 19 0.66
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (23 bp):
ATGAACATGACGTAAGAATTGTT
Found at i:41580152 original size:25 final size:25
Alignment explanation
Indices: 41580124--41580171 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
41580114 ATGAACATGA
41580124 GTAAGAATTGTTATGAACATTTACT
1 GTAAGAATTGTTATGAACATTTACT
41580149 GTAAGAATTGTTATGAACATTTA
1 GTAAGAATTGTTATGAACATTTA
41580172 TTGTTTGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (25 bp):
GTAAGAATTGTTATGAACATTTACT
Found at i:41587638 original size:93 final size:95
Alignment explanation
Indices: 41587523--41587772 Score: 267
Period size: 93 Copynumber: 2.6 Consensus size: 95
41587513 AGATGAGAGC
* * * *
41587523 TAGTGTAAGACCTATCTAGGACACGGCATCTACCTCAAGATATGCA-AGCTAGTGTAAGACCTAT
1 TAGTGTAAGACCTGTCTGGGACATGGCATCCA-CTC-AGATATG-AGAGCTAGTGTAAGACCTAT
* * * *
41587587 CTGGGACATGGCATTGG-CTTGA-G-GTGT-GT
63 CTAGGACATGGCATCGGCCTCGATGTATGTAGT
* * * *
41587616 TAGTGTAAGACCTGTCTGGGACATGGCATCGACACAGATAAGTGAGAGCCAGTGTAAGACCTGTC
1 TAGTGTAAGACCTGTCTGGGACATGGCATCCACTCAGAT-A-TGAGAGCTAGTGTAAGACCTATC
41587681 TAGGACATGGCATCGGCCTCGATGTATGTAAGT
64 TAGGACATGGCATCGGCCTCGATGTATGT-AGT
* * * *
41587714 CAGTGTAAGACCTGTCTGGGGCATGGCATCCACTTAGATGTGAGAGCTAGTGTAAGACC
1 TAGTGTAAGACCTGTCTGGGACATGGCATCCACTCAGATATGAGAGCTAGTGTAAGACC
41587773 ATGTTTGGAA
Statistics
Matches: 131, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
91 4 0.03
92 4 0.03
93 61 0.47
94 4 0.03
95 1 0.01
96 21 0.16
98 36 0.27
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.25
Consensus pattern (95 bp):
TAGTGTAAGACCTGTCTGGGACATGGCATCCACTCAGATATGAGAGCTAGTGTAAGACCTATCTA
GGACATGGCATCGGCCTCGATGTATGTAGT
Found at i:41587680 original size:49 final size:48
Alignment explanation
Indices: 41587473--41587788 Score: 242
Period size: 49 Copynumber: 6.6 Consensus size: 48
41587463 TGATGTGTGT
41587473 GCTAGTGTAAGACCTGTC-GGGACATGGCATCGACACAGATAGATGAGA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGACACAGATAG-TGAGA
* * * * *
41587521 GCTAGTGTAAGACCTATCTAGGACACGGCATCTACCTCAAGATA-TGCA-A
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGA-CAC-AGATAGTG-AGA
* * * ** * *
41587570 GCTAGTGTAAGACCTATCTGGGACATGGCATTGGC-TTG--AG-GTGT
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGACACAGATAGTGAGA
*
41587614 GTTAGTGTAAGACCTGTCTGGGACATGGCATCGACACAGATAAGTGAGA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGACACAGAT-AGTGAGA
* * * *
41587663 GCCAGTGTAAGACCTGTCTAGGACATGGCATCGGC-CTCGAT-GT-ATGTAA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGACAC-AGATAGTGA-G--A
* * **
41587712 G-TCAGTGTAAGACCTGTCTGGGGCATGGCATCCACTTAGAT-GTGAGA
1 GCT-AGTGTAAGACCTGTCTGGGACATGGCATCGACACAGATAGTGAGA
* *
41587759 GCTAGTGTAAGACCATGTTTGGAACATGGC
1 GCTAGTGTAAGACC-TGTCTGGGACATGGC
41587789 GTTAGCATCG
Statistics
Matches: 211, Mismatches: 37, Indels: 40
0.73 0.13 0.14
Matches are distributed among these distances:
44 33 0.16
45 1 0.00
46 2 0.01
47 16 0.08
48 34 0.16
49 116 0.55
50 4 0.02
51 5 0.02
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACCTGTCTGGGACATGGCATCGACACAGATAGTGAGA
Found at i:41587724 original size:142 final size:141
Alignment explanation
Indices: 41587469--41587742 Score: 401
Period size: 142 Copynumber: 1.9 Consensus size: 141
41587459 TGGGTGATGT
*
41587469 GTGTGCTAGTGTAAGACCTGTCGGGACATGGCATCGACACAGATAGATGAGAGCTAGTGTAAGAC
1 GTGTGCTAGTGTAAGACCTGTCGGGACATGGCATCGACACAGATAGATGAGAGCCAGTGTAAGAC
*
41587534 CTATCTAGGACACGGCATCTACCTCAAGATATGCAAGCTAGTGTAAGACCTATCTGGGACATGGC
66 CTATCTAGGACACGGCATCGACCTCAAGATATGCAAGCTAGTGTAAGACCTATCTGGGACATGGC
41587599 ATTGGCTTGAG
131 ATTGGCTTGAG
*
41587610 GTGTGTTAGTGTAAGACCTGTCTGGGACATGGCATCGACACAGATA-AGTGAGAGCCAGTGTAAG
1 GTGTGCTAGTGTAAGACCTGTC-GGGACATGGCATCGACACAGATAGA-TGAGAGCCAGTGTAAG
* * * * * * *
41587674 ACCTGTCTAGGACATGGCATCGGCCTCGATG-TATGTAAG-TCAGTGTAAGACCTGTCTGGGGCA
64 ACCTATCTAGGACACGGCATCGACCTC-AAGATATGCAAGCT-AGTGTAAGACCTATCTGGGACA
41587737 TGGCAT
127 TGGCAT
41587743 CCACTTAGAT
Statistics
Matches: 119, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
141 23 0.19
142 94 0.79
143 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (141 bp):
GTGTGCTAGTGTAAGACCTGTCGGGACATGGCATCGACACAGATAGATGAGAGCCAGTGTAAGAC
CTATCTAGGACACGGCATCGACCTCAAGATATGCAAGCTAGTGTAAGACCTATCTGGGACATGGC
ATTGGCTTGAG
Found at i:41592671 original size:17 final size:17
Alignment explanation
Indices: 41592649--41592682 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41592639 TCCATAGAAT
*
41592649 TTTTTTTCTTTTTTTTG
1 TTTTTTTCTATTTTTTG
41592666 TTTTTTTCTATTTTTTG
1 TTTTTTTCTATTTTTTG
41592683 ACTTTTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.06, G:0.06, T:0.85
Consensus pattern (17 bp):
TTTTTTTCTATTTTTTG
Found at i:41592688 original size:17 final size:17
Alignment explanation
Indices: 41592651--41592689 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
41592641 CATAGAATTT
* **
41592651 TTTTTCTTTTTTTTGTT
1 TTTTTCTATTTTTTGAC
41592668 TTTTTCTATTTTTTGAC
1 TTTTTCTATTTTTTGAC
41592685 TTTTT
1 TTTTT
41592690 GATCAGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.82
Consensus pattern (17 bp):
TTTTTCTATTTTTTGAC
Found at i:41594977 original size:40 final size:40
Alignment explanation
Indices: 41594842--41595030 Score: 229
Period size: 40 Copynumber: 4.8 Consensus size: 40
41594832 CGAATGGTGT
* * * * * *
41594842 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACCAAAA
* *
41594883 CCGGGTCAA-TTCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
41594922 -CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* * *
41594961 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* * *
41595001 CCGGGCTAATTCCCGAAGGCAATTGTGCGA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGA
41595031 ATCACTATAA
Statistics
Matches: 129, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
38 7 0.05
39 37 0.29
40 78 0.60
41 7 0.05
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
Found at i:41595043 original size:80 final size:79
Alignment explanation
Indices: 41594841--41595072 Score: 245
Period size: 79 Copynumber: 2.9 Consensus size: 79
41594831 TCGAATGGTG
* * * *
41594841 TCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAA-TTCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAA-TCACTAAA-CCGGGTCAAGTCCCGAAGGCATT
*
41594905 TGTGCGAGTTACCAAA
64 CGTGCGAGTTACCAAA
* * * * * *
41594921 -ACGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAACCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATCA-CTAAACCGGGTCAAGTCCCGAAGGCATTC
*
41594985 GTGCGAGTTACTAAA
65 GTGCGAGTTACCAAA
* * * *
41595000 TCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAACCGGG-CAATGTCCCGAAGACAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATCACTA-AACCGGGTCAA-GTCCCGAAGGCATT
*
41595064 CGAGCGAGT
64 CGTGCGAGT
41595073 CGCTATATCC
Statistics
Matches: 125, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
78 10 0.08
79 60 0.48
80 55 0.44
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAATCACTAAACCGGGTCAAGTCCCGAAGGCATTCG
TGCGAGTTACCAAA
Found at i:41595045 original size:40 final size:39
Alignment explanation
Indices: 41594842--41595072 Score: 200
Period size: 40 Copynumber: 5.8 Consensus size: 39
41594832 CGAATGGTGT
** * *
41594842 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAA
1 CCGGGCTAAGTCCCGAAGGCAATTGTGC-GAGTTACTAAA
* * *
41594882 TCCGGG-TCAA-TTCCGAAGGCATTTGTGCGAGTTACCAAA
1 -CCGGGCT-AAGTCCCGAAGGCAATTGTGCGAGTTACTAAA
* * * *
41594921 ACGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA-CTAAA
*
41594961 CCGGGTTAAGTCCCGAAGGC-ATTCGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCAATT-GTGCGAGTTACTAAA
* * *
41595000 TCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 -CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTA-AA
* * *
41595041 CCGGGC-AATGTCCCGAAGACAATCGAGCGAGT
1 CCGGGCTAA-GTCCCGAAGGCAATTGTGCGAGT
41595073 CGCTATATCC
Statistics
Matches: 161, Mismatches: 20, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
38 6 0.04
39 40 0.25
40 103 0.64
41 12 0.07
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTAAA
Found at i:41603052 original size:40 final size:40
Alignment explanation
Indices: 41602955--41603143 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
41602945 CGAATGGTGT
* * * * * *
41602955 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACCAAAA
* * *
41602996 CCGGGTCAATTACCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
*
41603036 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* * * *
41603076 CTGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* * *
41603116 CCGGGCTAATTCCCGAAGGCAATTGTGC
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC
41603144 AAATCACTAT
Statistics
Matches: 127, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 104 0.82
41 23 0.18
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
Found at i:41603160 original size:40 final size:39
Alignment explanation
Indices: 41602955--41603187 Score: 168
Period size: 40 Copynumber: 5.8 Consensus size: 39
41602945 CGAATGGTGT
** * *
41602955 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAA
1 CCGGGCTAAGTCCCGAAGGCAATTGTGC-GAGTTACTAAA
* * * *
41602995 TCCGGG-TCAATTACCGAAGGCATTTGTGCGAGTTACCAAAA
1 -CCGGGCT-AAGTCCCGAAGGCAATTGTGCGAGTTA-CTAAA
* *
41603036 CCGGGTTAAGTCCCGAAGGC-ATTCGTGCGAGTTACCAAAA
1 CCGGGCTAAGTCCCGAAGGCAATT-GTGCGAGTTA-CTAAA
* *
41603076 CTGGGTTAAGTCCCGAAGGC-ATTCGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCAATT-GTGCGAGTTACTAAA
* * * *
41603115 TCCGGGCTAATTCCCGAAGGCAATTGTGCAAATCACTATAA
1 -CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTA-AA
* * * *
41603156 CCGGGC-AATGTCCCAAAGACAATCGAGCGAGT
1 CCGGGCTAA-GTCCCGAAGGCAATTGTGCGAGT
41603188 CGCTATATCC
Statistics
Matches: 160, Mismatches: 24, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
39 8 0.05
40 119 0.74
41 33 0.21
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTAAA
Found at i:41603169 original size:80 final size:79
Alignment explanation
Indices: 41602954--41603187 Score: 222
Period size: 80 Copynumber: 2.9 Consensus size: 79
41602944 TCGAATGGTG
* * *
41602954 TCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAAT-TACCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-ATTGTGC-AAGTCACTAAA-CCGGGTCAATGTCCCGAAGGCAT
*
41603018 TTGTGCGAGTTACCAAA
63 TCGTGCGAGTTACCAAA
* * * * * * *
41603035 ACCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACCAAAACTGGGTTAA-GTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT-GTGCAAGTCA-CTAAACCGGGTCAATGTCCCGAAGGCATT
*
41603099 CGTGCGAGTTACTAAA
64 CGTGCGAGTTACCAAA
* * * * *
41603115 TCCGGGCTAATTCCCGAAGGCAATTGTGCAAATCACTATAACCGGG-CAATGTCCCAAAGACAAT
1 TCCGGGCTAAGTCCCGAAGGC-ATTGTGCAAGTCACTA-AACCGGGTCAATGTCCCGAAGGCATT
*
41603179 CGAGCGAGT
64 CGTGCGAGT
41603188 CGCTATATCC
Statistics
Matches: 123, Mismatches: 24, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
79 4 0.03
80 89 0.72
81 30 0.24
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCAAGTCACTAAACCGGGTCAATGTCCCGAAGGCATTCG
TGCGAGTTACCAAA
Found at i:41606062 original size:14 final size:14
Alignment explanation
Indices: 41606043--41606071 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41606033 TACAATATAT
41606043 ATAAGAATTATACG
1 ATAAGAATTATACG
41606057 ATAAGAATTATACG
1 ATAAGAATTATACG
41606071 A
1 A
41606072 ATCCATCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:41606696 original size:43 final size:43
Alignment explanation
Indices: 41606605--41606733 Score: 213
Period size: 44 Copynumber: 3.0 Consensus size: 43
41606595 CCAAAAAAGT
* *
41606605 TTTCTTTCTCTTTCCTAAGATTTCTATTATTTTTTGGGGAAGGC
1 TTTCTTTCTCTTTCCTAGGATTTCCATTA-TTTTTGGGGAAGGC
41606649 TTTCTTTCTCTTTCCTAGGATTTCCATTATTTTTGGGGAAGGC
1 TTTCTTTCTCTTTCCTAGGATTTCCATTATTTTTGGGGAAGGC
*
41606692 TTTCTTTCTCTTTCCTAGGGTTTCCATGTATTTTTGGGGAAG
1 TTTCTTTCTCTTTCCTAGGATTTCCAT-TATTTTTGGGGAAG
41606734 AAGATGATAA
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
43 40 0.49
44 41 0.51
ACGTcount: A:0.14, C:0.17, G:0.19, T:0.50
Consensus pattern (43 bp):
TTTCTTTCTCTTTCCTAGGATTTCCATTATTTTTGGGGAAGGC
Found at i:41614200 original size:56 final size:56
Alignment explanation
Indices: 41614124--41614364 Score: 297
Period size: 56 Copynumber: 4.3 Consensus size: 56
41614114 ATTTATATTA
* * *
41614124 GGCATCGACATGTGATTCCGATATATGTGTGCGAGTAAGATCACGTTTTATACGTC
1 GGCATCGATATGTGATTCCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTT
* ** * *
41614180 GACATCGATATGTGATTCCGATATATGTGCACGAGTAAGACCACGTTTTCTACATT
1 GGCATCGATATGTGATTCCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTT
* * *
41614236 GGCATCGATATGTGATTCCAATATATGAGTGCGAGTAAAACCACGTTTTATACGTT
1 GGCATCGATATGTGATTCCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTT
* * * * * *
41614292 GGCATCGATATGTGACTCCGATATATATGTGCGAGTATGACC-CTGTCTGAGACAG-T
1 GGCATCGATATGTGATTCCGATATATGTGTGCGAGTAAGACCAC-GTTTTATAC-GTT
41614348 GGCATCGATATGTGATT
1 GGCATCGATATGTGATT
41614365 ACATGTAAGA
Statistics
Matches: 157, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
55 1 0.01
56 155 0.99
57 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (56 bp):
GGCATCGATATGTGATTCCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTT
Found at i:41622818 original size:37 final size:37
Alignment explanation
Indices: 41622768--41622991 Score: 385
Period size: 37 Copynumber: 6.1 Consensus size: 37
41622758 CTTTAGCTCA
* * *
41622768 GACAAAATCTCCACACGAAGTTATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
* *
41622805 GACAAAATCTCCACACATAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
41622842 GACATAATCTTCACACGTAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
41622879 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
41622916 GACATAATCTCCACACGTAGTCATCGGGTCTTACTCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
41622953 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
41622990 GA
1 GA
41622992 ATATATTTCC
Statistics
Matches: 178, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 178 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
Found at i:41624507 original size:40 final size:40
Alignment explanation
Indices: 41624462--41624629 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
41624452 CGGAATATAA
41624462 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
41624502 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
41624542 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
41624582 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
41624622 CCGGATAT
1 CCGGATAT
41624630 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41626432 original size:48 final size:51
Alignment explanation
Indices: 41626378--41626512 Score: 186
Period size: 48 Copynumber: 2.7 Consensus size: 51
41626368 GCACATCGCC
**
41626378 TACATATTTCACACTATTCATTCGGCTTTACCACATATACATAT-C-T-CA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCCATACA
* *
41626426 TACATATTTCACACTAGCCATTCAGCTTTACCACATATACATATCCCATATA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATAT-CCATACA
* *
41626478 TATATATTTCACATTAGCCATTCGGCTTTACCACA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACA
41626513 CATATGCATG
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
48 41 0.54
50 1 0.01
51 1 0.01
52 33 0.43
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (51 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCCATACA
Found at i:41626516 original size:48 final size:48
Alignment explanation
Indices: 41626381--41626517 Score: 141
Period size: 52 Copynumber: 2.8 Consensus size: 48
41626371 CATCGCCTAC
** * * * *
41626381 ATATTTCACACTATTCATTCGGCTTTACCACATATA-CATATCTCATAC
1 ATATTTCACACTAGCCATTCGGCTTTACCACACATATCACATAT-ATAT
* *
41626429 ATATTTCACACTAGCCATTCAGCTTTACCACATATACATATCCCATATATAT
1 ATATTTCACACTAGCCATTCGGCTTTACCAC----ACATATCACATATATAT
*
41626481 ATATTTCACATTAGCCATTCGGCTTTACCACACATAT
1 ATATTTCACACTAGCCATTCGGCTTTACCACACATAT
41626518 GCATGTTCAT
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
48 34 0.46
52 36 0.49
53 4 0.05
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (48 bp):
ATATTTCACACTAGCCATTCGGCTTTACCACACATATCACATATATAT
Found at i:41626538 original size:47 final size:47
Alignment explanation
Indices: 41626486--41626733 Score: 325
Period size: 47 Copynumber: 5.1 Consensus size: 47
41626476 TATATATATT
* * * *
41626486 TCACATTAGCCATTCGGCTTTACCACACATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
*
41626533 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
* *
41626580 TCACATTGGCCATTCAGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
* *
41626627 TCACATTGGCCATTGGCCATTCGGCCTTATCACATATATGCATGTTCACGTTCA
1 T--CA-----CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
* **
41626681 TCACATTGGCCATTCGGCCTTATCACATATATGCACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
41626728 TCACAT
1 TCACAT
41626734 AAAATCCTAA
Statistics
Matches: 181, Mismatches: 13, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
47 136 0.75
49 2 0.01
52 2 0.01
54 41 0.23
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
Found at i:41626654 original size:54 final size:54
Alignment explanation
Indices: 41626583--41626699 Score: 189
Period size: 54 Copynumber: 2.1 Consensus size: 54
41626573 ATATTCATCA
41626583 CATTGGCCATTCAGCCTTATCACACATATGCATGCTCACATTCATCACATTGGC
1 CATTGGCCATTCAGCCTTATCACACATATGCATGCTCACATTCATCACATTGGC
* * * *
41626637 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACGTTCATCACATTGGC
1 CATTGGCCATTCAGCCTTATCACACATATGCATGCTCACATTCATCACATTGGC
41626691 CATTCGGCC
1 CATT-GGCC
41626700 TTATCACATA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 54 0.93
55 4 0.07
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (54 bp):
CATTGGCCATTCAGCCTTATCACACATATGCATGCTCACATTCATCACATTGGC
Found at i:41626681 original size:101 final size:101
Alignment explanation
Indices: 41626536--41626733 Score: 324
Period size: 101 Copynumber: 2.0 Consensus size: 101
41626526 ATATTCATCA
*
41626536 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCATATTCATCACATTGGCCATTCAGCCTT
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTGGCCATTCAGCCTT
**
41626601 ATCACACATATGCATGCTCACATTCATCACATTGGC
66 ATCACACATATGCACACTCACATTCATCACATTGGC
* * *
41626637 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACGTTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTGGCCATTCAGCCTT
* *
41626702 ATCACATATATGCACATTCACATTCATCACAT
66 ATCACACATATGCACACTCACATTCATCACAT
41626734 AAAATCCTAA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 89 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (101 bp):
CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTGGCCATTCAGCCTT
ATCACACATATGCACACTCACATTCATCACATTGGC
Found at i:41626708 original size:22 final size:22
Alignment explanation
Indices: 41626637--41626708 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
41626627 TCACATTGGC
41626637 CATTGGCCATTCGGCCTTATCA
1 CATTGGCCATTCGGCCTTATCA
* * *
41626659 CATATATG-CATGTTC-ACGTTCATCA
1 CAT-T-GGCCA--TTCGGCCTT-ATCA
41626684 CATTGGCCATTCGGCCTTATCA
1 CATTGGCCATTCGGCCTTATCA
41626706 CAT
1 CAT
41626709 ATATGCACAT
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.33
Consensus pattern (22 bp):
CATTGGCCATTCGGCCTTATCA
Found at i:41626730 original size:25 final size:25
Alignment explanation
Indices: 41626655--41626734 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
41626645 ATTCGGCCTT
** *
41626655 ATCACATATATGCATGTTCACGTTC
1 ATCACATATATGCACATTCACATTC
* * *
41626680 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATGCACATTC-ACATTC
41626702 ATCACATATATGCACATTCACATTC
1 ATCACATATATGCACATTCACATTC
41626727 ATCACATA
1 ATCACATA
41626735 AAATCCTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
22 10 0.24
23 6 0.14
24 6 0.14
25 20 0.48
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.33
Consensus pattern (25 bp):
ATCACATATATGCACATTCACATTC
Found at i:41630124 original size:10 final size:10
Alignment explanation
Indices: 41630109--41630141 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
41630099 GTTAAGTGAA
41630109 TTGGGAGTGC
1 TTGGGAGTGC
41630119 TTGGGAGTGC
1 TTGGGAGTGC
41630129 TTGGGAGTGC
1 TTGGGAGTGC
41630139 TTG
1 TTG
41630142 AGAAGTCCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.48, T:0.33
Consensus pattern (10 bp):
TTGGGAGTGC
Found at i:41630153 original size:20 final size:20
Alignment explanation
Indices: 41630110--41630153 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
41630100 TTAAGTGAAT
* *
41630110 TGGGAGTGCTTGGGAGTGCT
1 TGGGAGTGCTTGGAAGTGCC
41630130 TGGGAGTGCTTGAGAAGT-CC
1 TGGGAGTGCTTG-GAAGTGCC
41630150 TGGG
1 TGGG
41630154 TTCAAGCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.14, C:0.11, G:0.48, T:0.27
Consensus pattern (20 bp):
TGGGAGTGCTTGGAAGTGCC
Found at i:41632167 original size:27 final size:26
Alignment explanation
Indices: 41632104--41632341 Score: 197
Period size: 27 Copynumber: 8.9 Consensus size: 26
41632094 AGACCTCGAA
*
41632104 TTGTAAAATTACCAAAATACCCCATT
1 TTGTAAAATTACCAAAATACCCCAGT
* * *
41632130 TTGAAAAATTATCAAAATACCCCTGGT
1 TTGTAAAATTACCAAAATACCCC-AGT
*
41632157 TTGTACAATTACCAAAATACACCCAGT
1 TTGTAAAATTACCAAAATAC-CCCAGT
** *
41632184 TTGTAAAATTACTGAAATACCCCCAAT
1 TTGTAAAATTACCAAAATA-CCCCAGT
*** * *
41632211 TTGTAAAATTATTGAAATACCCCGGA
1 TTGTAAAATTACCAAAATACCCCAGT
*** *
41632237 TTGTAAAATTATTGAAGTACTCCCAGT
1 TTGTAAAATTACCAAAATAC-CCCAGT
* *
41632264 TTGTAAAATTACCAAAATACCCTTAGA
1 TTGTAAAATTACCAAAATACCC-CAGT
* * *
41632291 TTGTAAAATTACCGAATTACCCCCATTT
1 TTGTAAAATTACCAAAATA-CCCCA-GT
**
41632319 TTGTAAAATTACTGAAATACCCC
1 TTGTAAAATTACCAAAATACCCC
41632342 CGATTTGTGA
Statistics
Matches: 173, Mismatches: 32, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
26 46 0.27
27 103 0.60
28 24 0.14
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (26 bp):
TTGTAAAATTACCAAAATACCCCAGT
Found at i:41632241 original size:80 final size:81
Alignment explanation
Indices: 41632104--41632285 Score: 233
Period size: 80 Copynumber: 2.3 Consensus size: 81
41632094 AGACCTCGAA
* * *
41632104 TTGTAAAATTACCAAAATA-CCCCATTTTGAAAAATTATCAAAATACCCCTGGTTTGTACAATTA
1 TTGTAAAATTACCAAAATACCCCCAATTTGAAAAATTATCAAAATACCCCTGGATTGTAAAATTA
41632168 CCAAAATACACCCAGT
66 CCAAAATACACCCAGT
** * **
41632184 TTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTATTGAAATACCCC-GGATTGTAAAATTA
1 TTGTAAAATTACCAAAATACCCCCAATTTGAAAAATTATCAAAATACCCCTGGATTGTAAAATTA
*** * *
41632248 TTGAAGTACTCCCAGT
66 CCAAAATACACCCAGT
41632264 TTGTAAAATTACCAAAATACCC
1 TTGTAAAATTACCAAAATACCC
41632286 TTAGATTGTA
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 60 0.70
81 26 0.30
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.30
Consensus pattern (81 bp):
TTGTAAAATTACCAAAATACCCCCAATTTGAAAAATTATCAAAATACCCCTGGATTGTAAAATTA
CCAAAATACACCCAGT
Found at i:41632267 original size:53 final size:53
Alignment explanation
Indices: 41632104--41632367 Score: 224
Period size: 54 Copynumber: 4.9 Consensus size: 53
41632094 AGACCTCGAA
** ** * * ***
41632104 TTGTAAAATTACCAAAATACCCCATTTTGAAAAATTA-TCAAAATACCCCTGGT
1 TTGTAAAATTACTGAAATACCCCAGATTGTAAAATTACT-GAAATACCCCCAAT
* ** *
41632157 TTGTACAATTACCAAAATACACCCAGTTTGTAAAATTACTGAAATACCCCCAAT
1 TTGTAAAATTACTGAAATAC-CCCAGATTGTAAAATTACTGAAATACCCCCAAT
* * * * * *
41632211 TTGTAAAATTATTGAAATACCCCGGATTGTAAAATTATTGAAGTACTCCCAGT
1 TTGTAAAATTACTGAAATACCCCAGATTGTAAAATTACTGAAATACCCCCAAT
** * * * *
41632264 TTGTAAAATTACCAAAATACCCTTAGATTGTAAAATTACCGAATTACCCCCATTT
1 TTGTAAAATTACTGAAATACCC-CAGATTGTAAAATTACTGAAATACCCCCA-AT
* * *
41632319 TTGTAAAATTACTGAAATACCCCCGATTTGTGAAACTACTGAAATACCC
1 TTGTAAAATTACTGAAATACCCCAGA-TTGTAAAATTACTGAAATACCC
41632368 TTATAGTGTA
Statistics
Matches: 171, Mismatches: 35, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
53 65 0.38
54 66 0.39
55 40 0.23
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.31
Consensus pattern (53 bp):
TTGTAAAATTACTGAAATACCCCAGATTGTAAAATTACTGAAATACCCCCAAT
Found at i:41632312 original size:80 final size:79
Alignment explanation
Indices: 41632104--41632313 Score: 224
Period size: 80 Copynumber: 2.6 Consensus size: 79
41632094 AGACCTCGAA
* * * * *
41632104 TTGTAAAATTACCAAAATACCCCATTTTGAAAAATTATCAAAATACCCCTGGTTTGTACAATTAC
1 TTGTAAAATTACCAAAATACCCCA-ATTGTAAAATTATCGAAATACCCCTGGATTGTAAAATTAC
41632169 CAAAATACACCCAGT
65 CAAAATACACCCAGT
** *
41632184 TTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTATTGAAATACCCC-GGATTGTAAAATTA
1 TTGTAAAATTACCAAAATA-CCCCAA-TTGTAAAATTATCGAAATACCCCTGGATTGTAAAATTA
*** * *
41632248 TTGAAGTACTCCCAGT
64 CCAAAATACACCCAGT
* * *
41632264 TTGTAAAATTACCAAAATACCCTTAGATTGTAAAATTACCGAATTACCCC
1 TTGTAAAATTACCAAAATACCC-CA-ATTGTAAAATTATCGAAATACCCC
41632314 CATTTTTGTA
Statistics
Matches: 107, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
79 3 0.03
80 78 0.73
81 26 0.24
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (79 bp):
TTGTAAAATTACCAAAATACCCCAATTGTAAAATTATCGAAATACCCCTGGATTGTAAAATTACC
AAAATACACCCAGT
Found at i:41632365 original size:82 final size:80
Alignment explanation
Indices: 41632157--41632421 Score: 198
Period size: 80 Copynumber: 3.3 Consensus size: 80
41632147 TACCCCTGGT
* ** * * ** ** *
41632157 TTGTACAATTACCAAAATACACCCAGTTTGTAAAATTACTGAAATACCCCCA-ATTTGTAAAATT
1 TTGTAAAATTACTGAAATACCCCCAGTTTGTAAAACTACCAAAATACCCTTAGA-GTGTAAAATT
** * *
41632221 ATTGAAATACCC-CGGA
65 ACCG-AATACCCTTGTA
* * * * *
41632237 TTGTAAAATTATTGAAGTACTCCCAGTTTGTAAAATTACCAAAATACCCTTAGATTGTAAAATTA
1 TTGTAAAATTACTGAAATACCCCCAGTTTGTAAAACTACCAAAATACCCTTAGAGTGTAAAATTA
41632302 CCGAATTACCCCCATT-T-
66 CCGAA-TA--CCC-TTGTA
* ** * *
41632319 TTGTAAAATTACTGAAATACCCCC-GATTTGTGAAACTACTGAAATACCCTTATAGTGTACAATT
1 TTGTAAAATTACTGAAATACCCCCAG-TTTGTAAAACTACCAAAATACCCTTAGAGTGTAAAATT
*
41632383 ACCGTATACCCTTGTA
65 ACCGAATACCCTTGTA
*
41632399 GTGTAAAATTACTGAAATACCCC
1 TTGTAAAATTACTGAAATACCCC
41632422 TGTAGGGCAA
Statistics
Matches: 150, Mismatches: 26, Indels: 18
0.77 0.13 0.09
Matches are distributed among these distances:
78 2 0.01
79 6 0.04
80 78 0.52
81 4 0.03
82 60 0.40
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (80 bp):
TTGTAAAATTACTGAAATACCCCCAGTTTGTAAAACTACCAAAATACCCTTAGAGTGTAAAATTA
CCGAATACCCTTGTA
Found at i:41632426 original size:27 final size:27
Alignment explanation
Indices: 41632103--41632425 Score: 184
Period size: 27 Copynumber: 12.0 Consensus size: 27
41632093 AAGACCTCGA
**
41632103 ATTGTAAAATTACCAAAATACCCCAT-T
1 ATTGTAAAATTACTGAAATACCCC-TGT
* *
41632130 -TTGAAAAATTA-TCAAAATACCCCTGGT
1 ATTGTAAAATTACT-GAAATACCCCT-GT
* ** *
41632157 -TTGTACAATTACCAAAATACACCCAGT
1 ATTGTAAAATTACTGAAATAC-CCCTGT
**
41632184 -TTGTAAAATTACTGAAATACCCC-CA
1 ATTGTAAAATTACTGAAATACCCCTGT
* *
41632209 ATTTGTAAAATTATTGAAATACCCC-GG
1 A-TTGTAAAATTACTGAAATACCCCTGT
* * *
41632236 ATTGTAAAATTATTGAAGTACTCCCAGT
1 ATTGTAAAATTACTGAAATAC-CCCTGT
** *
41632264 -TTGTAAAATTACCAAAATACCCTTAG-
1 ATTGTAAAATTACTGAAATACCCCT-GT
* *
41632290 ATTGTAAAATTACCGAATTACCCCCAT-T
1 ATTGTAAAATTACTGAAATA-CCCC-TGT
* *
41632318 TTTGTAAAATTACTGAAATACCCCCG-
1 ATTGTAAAATTACTGAAATACCCCTGT
* * * *
41632344 ATTTGTGAAACTACTGAAATACCCTTAT
1 A-TTGTAAAATTACTGAAATACCCCTGT
* * * * *
41632372 AGTGTACAATTACCG-TATACCCTTGT
1 ATTGTAAAATTACTGAAATACCCCTGT
*
41632398 AGTGTAAAATTACTGAAATACCCCTGT
1 ATTGTAAAATTACTGAAATACCCCTGT
41632425 A
1 A
41632426 GGGCAAAATG
Statistics
Matches: 232, Mismatches: 46, Indels: 36
0.74 0.15 0.11
Matches are distributed among these distances:
25 1 0.00
26 66 0.28
27 139 0.60
28 25 0.11
29 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (27 bp):
ATTGTAAAATTACTGAAATACCCCTGT
Found at i:41632433 original size:27 final size:27
Alignment explanation
Indices: 41632388--41632439 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
41632378 CAATTACCGT
* * * *
41632388 ATACCCTTGTAGTGTAAAATTACTGAA
1 ATACCCCTGTAGGGCAAAATGACTGAA
41632415 ATACCCCTGTAGGGCAAAATGACTG
1 ATACCCCTGTAGGGCAAAATGACTG
41632440 TTTTGCCATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (27 bp):
ATACCCCTGTAGGGCAAAATGACTGAA
Found at i:41632805 original size:22 final size:23
Alignment explanation
Indices: 41632780--41632841 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 23
41632770 GTAATCTGAT
41632780 TATGGCTCTGTGCCAATC-TAAA
1 TATGGCTCTGTGCCAATCTTAAA
*
41632802 TATGGCTCTGTGCC-ATCTTAAT
1 TATGGCTCTGTGCCAATCTTAAA
*
41632824 TATGGCTTTGTGCCAATC
1 TATGGCTCTGTGCCAATC
41632842 GTATTTACCT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 3 0.08
22 30 0.83
23 3 0.08
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (23 bp):
TATGGCTCTGTGCCAATCTTAAA
Found at i:41633028 original size:22 final size:22
Alignment explanation
Indices: 41632981--41633043 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
41632971 TAGCCTTGTG
* *
41632981 CCATCCTGATTATGGCTCTGTG
1 CCATCCTGATTATGGCTCTATA
*
41633003 CCATCCTGATTATGG-TTTATAA
1 CCATCCTGATTATGGCTCTAT-A
* *
41633025 CCATTCTGTTTATGGCTCT
1 CCATCCTGATTATGGCTCT
41633044 TGGCTATTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.09
22 28 0.85
23 2 0.06
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (22 bp):
CCATCCTGATTATGGCTCTATA
Found at i:41637086 original size:26 final size:27
Alignment explanation
Indices: 41636964--41637170 Score: 240
Period size: 27 Copynumber: 7.8 Consensus size: 27
41636954 AGACCCCGGA
41636964 TTGTAAAATTACCGAAATACCCCCAAT
1 TTGTAAAATTACCGAAATACCCCCAAT
* * *
41636991 TTGTAAAATTACTGAAATACCCTCAGT
1 TTGTAAAATTACCGAAATACCCCCAAT
* * **
41637018 TTGTAAAATTATCAAAATACCCCCGGT
1 TTGTAAAATTACCGAAATACCCCCAAT
* ***
41637045 TTGTAACATTACCGAAATACCTTAAAT
1 TTGTAAAATTACCGAAATACCCCCAAT
* *
41637072 TT-TAAAATTATCGAAATACCCCCAGT
1 TTGTAAAATTACCGAAATACCCCCAAT
* **
41637098 TTGTAAAATTACCAAAATA-CCCTGAT
1 TTGTAAAATTACCGAAATACCCCCAAT
41637124 TTGTAAAATTACCGAAATA-CCCCAAT
1 TTGTAAAATTACCGAAATACCCCCAAT
*
41637150 TTGTAAAATTACTGAAATACC
1 TTGTAAAATTACCGAAATACC
41637171 ATTGAAGTGT
Statistics
Matches: 147, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
26 65 0.44
27 82 0.56
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
TTGTAAAATTACCGAAATACCCCCAAT
Found at i:41637100 original size:53 final size:53
Alignment explanation
Indices: 41636964--41637170 Score: 265
Period size: 53 Copynumber: 3.9 Consensus size: 53
41636954 AGACCCCGGA
* *
41636964 TTGTAAAATTACCGAAATACCCCCAATTTGTAAAATTACTGAAATACCCTCAGT
1 TTGTAAAATTACCGAAATACCCCCAATTTGTAAAATTACCGAAATACCCT-AAT
* * ** * *
41637018 TTGTAAAATTATCAAAATACCCCCGGTTTGTAACATTACCGAAATACCTTAAAT
1 TTGTAAAATTACCGAAATACCCCCAATTTGTAAAATTACCGAAATACCCT-AAT
* * * *
41637072 TT-TAAAATTATCGAAATACCCCCAGTTTGTAAAATTACCAAAATACCCTGAT
1 TTGTAAAATTACCGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTAAT
*
41637124 TTGTAAAATTACCGAAATA-CCCCAATTTGTAAAATTACTGAAATACC
1 TTGTAAAATTACCGAAATACCCCCAATTTGTAAAATTACCGAAATACC
41637171 ATTGAAGTGT
Statistics
Matches: 133, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
52 29 0.22
53 57 0.43
54 47 0.35
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (53 bp):
TTGTAAAATTACCGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTAAT
Found at i:41637187 original size:53 final size:53
Alignment explanation
Indices: 41636965--41637198 Score: 247
Period size: 53 Copynumber: 4.4 Consensus size: 53
41636955 GACCCCGGAT
* *
41636965 TGTAAAATTACCGAAATACCCCCAATTTGTAAAATTACTGAAATACCCT-CAG
1 TGTAAAATTACCGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTGAAG
* * ** * * * *
41637017 TTTGTAAAATTATCAAAATACCCCCGGTTTGTAACATTACCGAAATACCTTAAAT
1 --TGTAAAATTACCGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTGAAG
* * * * **
41637072 TTTAAAATTATCGAAATACCCCCAGTTTGTAAAATTACCAAAATACCCTGATT
1 TGTAAAATTACCGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTGAAG
* *
41637125 TGTAAAATTACCGAAATA-CCCCAATTTGTAAAATTACTGAAATACCATTGAAG
1 TGTAAAATTACCGAAATACCCCCAATTTGTAAAATTACCGAAATACC-CTGAAG
* *
41637178 TGTACAATTACCAAAATACCC
1 TGTAAAATTACCGAAATACCC
41637199 TTGTGGTGTA
Statistics
Matches: 150, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
52 25 0.17
53 80 0.53
54 44 0.29
55 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (53 bp):
TGTAAAATTACCGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTGAAG
Found at i:41637225 original size:27 final size:26
Alignment explanation
Indices: 41636964--41637229 Score: 205
Period size: 27 Copynumber: 10.0 Consensus size: 26
41636954 AGACCCCGGA
**
41636964 TTGTAAAATTACCGAAATACCCCCAAT
1 TTGTAAAATTACCGAAATA-CCCCTGT
* *
41636991 TTGTAAAATTACTGAAATACCCTCAGT
1 TTGTAAAATTACCGAAATACCC-CTGT
* * *
41637018 TTGTAAAATTATCAAAATACCCCCGGT
1 TTGTAAAATTACCGAAATA-CCCCTGT
* * *
41637045 TTGTAACATTACCGAAATA-CCTTAAAT
1 TTGTAAAATTACCGAAATACCCCT--GT
* *
41637072 TT-TAAAATTATCGAAATACCCCCAGT
1 TTGTAAAATTACCGAAATA-CCCCTGT
*
41637098 TTGTAAAATTACCAAAATA-CCCTGAT
1 TTGTAAAATTACCGAAATACCCCTG-T
**
41637124 TTGTAAAATTACCGAAATACCCCAAT
1 TTGTAAAATTACCGAAATACCCCTGT
* ** *
41637150 TTGTAAAATTACTGAAATACCATTGAA
1 TTGTAAAATTACCGAAATACCCCTG-T
* * * *
41637177 GTGTACAATTACCAAAATACCCTTGT
1 TTGTAAAATTACCGAAATACCCCTGT
* *
41637203 GGTGTAAAATTATCGAAATACCCCTGT
1 -TTGTAAAATTACCGAAATACCCCTGT
41637230 AAGGAAAAAT
Statistics
Matches: 189, Mismatches: 39, Indels: 22
0.76 0.16 0.09
Matches are distributed among these distances:
25 6 0.03
26 60 0.32
27 118 0.62
28 5 0.03
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.30
Consensus pattern (26 bp):
TTGTAAAATTACCGAAATACCCCTGT
Found at i:41637799 original size:22 final size:22
Alignment explanation
Indices: 41637771--41637831 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
41637761 GATAGCCTTG
41637771 TGCCATCCTGATTATGGCTCTA
1 TGCCATCCTGATTATGGCTCTA
*
41637793 TGCCATCCTGATTATGGCTCTG
1 TGCCATCCTGATTATGGCTCTA
* * *
41637815 TGCTATCTTCATTATGG
1 TGCCATCCTGATTATGG
41637832 TTTATAACCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (22 bp):
TGCCATCCTGATTATGGCTCTA
Found at i:41638916 original size:23 final size:24
Alignment explanation
Indices: 41638886--41638931 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
41638876 ATAACTTTTA
*
41638886 ATCAGGAA-GCTCACGAAGAGCCT
1 ATCAGGAATGCTCACAAAGAGCCT
41638909 ATCAGGAATGCTCACAAAGAGCC
1 ATCAGGAATGCTCACAAAGAGCC
41638932 ATGTAACAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.37, C:0.26, G:0.24, T:0.13
Consensus pattern (24 bp):
ATCAGGAATGCTCACAAAGAGCCT
Found at i:41639982 original size:28 final size:28
Alignment explanation
Indices: 41639938--41639999 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
41639928 CGGGACAAAA
41639938 TTAC-TTACCCAATTAAGCCAAGAAAGC
1 TTACTTTACCCAATTAAGCCAAGAAAGC
*
41639965 TTGCTTTACCCAATTAAGCCAAGAAAGC
1 TTACTTTACCCAATTAAGCCAAGAAAGC
41639993 TTACTTT
1 TTACTTT
41640000 CTCTTTCCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 3 0.09
28 29 0.91
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.29
Consensus pattern (28 bp):
TTACTTTACCCAATTAAGCCAAGAAAGC
Found at i:41652473 original size:40 final size:40
Alignment explanation
Indices: 41652414--41652518 Score: 149
Period size: 40 Copynumber: 2.6 Consensus size: 40
41652404 CATTTGAATG
* * *
41652414 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTCATGCGAGTTG-TT
* *
41652454 ATGTCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCATGCGAGTTGTT
41652494 ATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
41652519 ATGTGCAAGT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 56 0.97
41 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCATGCGAGTTGTT
Found at i:41652550 original size:39 final size:39
Alignment explanation
Indices: 41652457--41652564 Score: 135
Period size: 39 Copynumber: 2.7 Consensus size: 39
41652447 AGTGATTATG
* * *** *
41652457 TCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATA
1 TCCGGGCTAAGACCCGAAGGCAAT-GTGCAAGTTACCAAA
41652497 TCCGGGCTAAGACCCGAAGGCAATGTGCAAGTTACCAAA
1 TCCGGGCTAAGACCCGAAGGCAATGTGCAAGTTACCAAA
*
41652536 TCCGGGTTAAGACCCGAAGGCAATTGTGC
1 TCCGGGCTAAGACCCGAAGGCAA-TGTGC
41652565 TTGTGGTTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 32 0.53
40 28 0.47
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (39 bp):
TCCGGGCTAAGACCCGAAGGCAATGTGCAAGTTACCAAA
Found at i:41660569 original size:40 final size:40
Alignment explanation
Indices: 41660404--41660570 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
41660394 CATTTGAATG
* * *
41660404 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * *
41660444 ATGTCCGGGCTAAGACCCTAAGGC-ATTCGTGCGAGTTG-TT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATT
* * * **
41660484 ATATCC-GGCTAAGACCCGAAGGCAATGGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
* * * *
41660523 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
*
41660563 GTATCCGG
1 ATATCCGG
41660571 TTAAATCCCG
Statistics
Matches: 98, Mismatches: 24, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
38 1 0.01
39 29 0.30
40 66 0.67
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATT
Found at i:41673201 original size:42 final size:43
Alignment explanation
Indices: 41673105--41673251 Score: 235
Period size: 43 Copynumber: 3.4 Consensus size: 43
41673095 AAAAACACTC
*
41673105 CTAAAGAACATGACCTTTAGCGGTGCTTTTCCCACAAACGCCG
1 CTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
41673148 CTAAAGAACATGACCTTTAGCGGCGCTTTT-CCACAAACGCCG
1 CTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
**
41673190 CTAAA-ATACATGACCTTTAGCGGCGCTTTTCCCACAAGTGCCG
1 CTAAAGA-ACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
*
41673233 CTAAAGAACATAACCTTTA
1 CTAAAGAACATGACCTTTA
41673252 AAAAATATAT
Statistics
Matches: 97, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
41 1 0.01
42 40 0.41
43 55 0.57
44 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (43 bp):
CTAAAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCG
Found at i:41673284 original size:20 final size:20
Alignment explanation
Indices: 41673257--41673302 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
41673247 CTTTAAAAAA
*
41673257 TATATTTTAATTATATAATAT
1 TATATTTTAATGATA-AATAT
*
41673278 T-TATTTTTATGATAAATAT
1 TATATTTTAATGATAAATAT
41673297 TATATT
1 TATATT
41673303 ATGTTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 6 0.27
20 15 0.68
21 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TATATTTTAATGATAAATAT
Found at i:41677426 original size:40 final size:41
Alignment explanation
Indices: 41677371--41677454 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 41
41677361 AATAATGGTC
*
41677371 TTTTGCGGCGTTTTTA-CCAAAAACGCCACTATAGCTCAACT
1 TTTTGCGGCGTTTTTACCCAAAAACACCACTATAGCTCAA-T
* *
41677412 TTTTGTGGCG-TTTTACCCAAAAACACCACTATTGCTCAAT
1 TTTTGCGGCGTTTTTACCCAAAAACACCACTATAGCTCAAT
41677452 TTT
1 TTT
41677455 ATTTTTTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 9 0.23
41 30 0.77
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (41 bp):
TTTTGCGGCGTTTTTACCCAAAAACACCACTATAGCTCAAT
Found at i:41678322 original size:21 final size:21
Alignment explanation
Indices: 41678296--41678342 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
41678286 TCCAAACACC
*
41678296 AAACCCCAAATCCTAGACCAT
1 AAACCCCAAATCCTAGACAAT
* *
41678317 AAACCCTAAATCTTAGACAAT
1 AAACCCCAAATCCTAGACAAT
41678338 AAACC
1 AAACC
41678343 TACACCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.32, G:0.04, T:0.17
Consensus pattern (21 bp):
AAACCCCAAATCCTAGACAAT
Found at i:41678757 original size:7 final size:7
Alignment explanation
Indices: 41678738--41678770 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
41678728 ATAAAACATA
41678738 AACCC-T
1 AACCCAT
41678744 AAGCCCAT
1 AA-CCCAT
41678752 AACCCAT
1 AACCCAT
41678759 AACCCAT
1 AACCCAT
41678766 AACCC
1 AACCC
41678771 CTAAACCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 2 0.08
7 20 0.80
8 3 0.12
ACGTcount: A:0.39, C:0.45, G:0.03, T:0.12
Consensus pattern (7 bp):
AACCCAT
Found at i:41678821 original size:28 final size:27
Alignment explanation
Indices: 41678790--41678888 Score: 84
Period size: 28 Copynumber: 3.8 Consensus size: 27
41678780 AAGCCCCAAC
41678790 CCTTAAACCATAAACTATAATCCATAAA
1 CCTTAAACCATAAACTATAATCC-TAAA
* *
41678818 CCTTAAA--AT--AGTAT-CTCCTAAA
1 CCTTAAACCATAAACTATAATCCTAAA
* *
41678840 GCTTAAACCCTAAACTATATATCCTAAA
1 CCTTAAACCATAAACTATA-ATCCTAAA
*
41678868 -CTATAAACCCTAAACTATAAT
1 CCT-TAAACCATAAACTATAAT
41678889 GATAATTAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
22 10 0.17
23 3 0.05
24 5 0.09
26 6 0.10
27 4 0.07
28 30 0.52
ACGTcount: A:0.45, C:0.24, G:0.02, T:0.28
Consensus pattern (27 bp):
CCTTAAACCATAAACTATAATCCTAAA
Found at i:41678853 original size:14 final size:14
Alignment explanation
Indices: 41678834--41678887 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
41678824 AATAGTATCT
41678834 CCTAAAGCT-TAAAC
1 CCTAAA-CTATAAAC
* *
41678848 CCTAAACTATATAT
1 CCTAAACTATAAAC
41678862 CCTAAACTATAAAC
1 CCTAAACTATAAAC
41678876 CCTAAACTATAA
1 CCTAAACTATAA
41678888 TGATAATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 2 0.06
14 33 0.94
ACGTcount: A:0.46, C:0.26, G:0.02, T:0.26
Consensus pattern (14 bp):
CCTAAACTATAAAC
Found at i:41679093 original size:29 final size:29
Alignment explanation
Indices: 41679060--41679118 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
41679050 ATTAAAAATA
41679060 AATTGTATTTTAATTAATATAAATAAACC
1 AATTGTATTTTAATTAATATAAATAAACC
41679089 AATTGTATTTTAATTAATATAAATAAACC
1 AATTGTATTTTAATTAATATAAATAAACC
41679118 A
1 A
41679119 GTTAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (29 bp):
AATTGTATTTTAATTAATATAAATAAACC
Found at i:41679256 original size:41 final size:40
Alignment explanation
Indices: 41679182--41679303 Score: 172
Period size: 40 Copynumber: 3.0 Consensus size: 40
41679172 GACGCTAAAA
41679182 CTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATG
1 CTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATG
* * * *
41679222 GTCGACCTATAGTGGCGTTTTTTAAAAAAGCGCCGCTAATG
1 CTCGATCTATAGCGGCG-TTTTTCAAAAAGCGCCGCTAATG
* * *
41679263 CTCAATCTATAACGGTGTTTTTCAAAAAGCGCCGCTAATG
1 CTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATG
41679303 C
1 C
41679304 CACCAAAGCT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
40 37 0.53
41 33 0.47
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (40 bp):
CTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATG
Found at i:41679380 original size:40 final size:40
Alignment explanation
Indices: 41679336--41679445 Score: 103
Period size: 40 Copynumber: 2.8 Consensus size: 40
41679326 TTAATTTTTT
* * * *
41679336 GCGGCATTCTTAAAAAAGCGTCGCTAATGGTCGACCTATA
1 GCGGCATTCTTAAAAAAGCGCCACTAATGCTCAACCTATA
* * * *
41679376 GCGGCGTTTTTTAAAAAGCGCCACTAATGCTCAATCTATA
1 GCGGCATTCTTAAAAAAGCGCCACTAATGCTCAACCTATA
* * * * *
41679416 GCGGCGTTTTTGAAAATGCGCCTCTAATGC
1 GCGGCATTCTTAAAAAAGCGCCACTAATGC
41679446 CACTATAGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (40 bp):
GCGGCATTCTTAAAAAAGCGCCACTAATGCTCAACCTATA
Found at i:41679535 original size:40 final size:40
Alignment explanation
Indices: 41679491--41679571 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
41679481 TATTTTTTGT
* *
41679491 GGCGTTTTTCAAAAAGCGCCGCTAATGCTTGATCTATAGC
1 GGCGTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGC
41679531 GGCGTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGC
1 GGCGTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGC
41679571 G
1 G
41679572 AAGTTTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.28
Consensus pattern (40 bp):
GGCGTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGC
Found at i:41687121 original size:70 final size:70
Alignment explanation
Indices: 41687047--41687276 Score: 169
Period size: 70 Copynumber: 3.2 Consensus size: 70
41687037 TTTATGGTAG
41687047 AAAATG-AAAGGTTGTTGATAGATGAACAACTTTTACAAAGTGATTTTTGATGAAAACAGATTTA
1 AAAATGTAAA-GTTGTTGATAGATGAACAACTTTTACAAAGTGATTTTTGATGAAAACAGATTTA
41687111 GGGACT
65 GGGACT
* * *
41687117 AAAATGTAAAGTTG-TGAAATTTGATGAA-AAATTTT-----G-AATTTTT-ATGAATACATGTG
1 AAAATGTAAAGTTGTTG--A-TAGATGAACAACTTTTACAAAGTGATTTTTGATGAA-A-A----
* * *
41687173 CTGTAAGTTTTTATGGTA-G
57 C----AG-ATTTA-GGGACT
41687192 AAAATG-AAAGGTTGTTGATAGATGAACAACTTTTACAAAGTGATTTTTGATGAAAACAGATTTA
1 AAAATGTAAA-GTTGTTGATAGATGAACAACTTTTACAAAGTGATTTTTGATGAAAACAGATTTA
41687256 GGGACT
65 GGGACT
41687262 AAAATGTAAAGTTGT
1 AAAATGTAAAGTTGT
41687277 GAAATTTGAT
Statistics
Matches: 120, Mismatches: 12, Indels: 56
0.64 0.06 0.30
Matches are distributed among these distances:
64 5 0.04
65 7 0.06
66 2 0.02
69 5 0.04
70 26 0.22
71 15 0.12
72 7 0.06
73 7 0.06
74 12 0.10
75 15 0.12
76 5 0.04
79 2 0.02
80 7 0.06
81 5 0.04
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (70 bp):
AAAATGTAAAGTTGTTGATAGATGAACAACTTTTACAAAGTGATTTTTGATGAAAACAGATTTAG
GGACT
Found at i:41687300 original size:145 final size:145
Alignment explanation
Indices: 41687037--41687329 Score: 568
Period size: 145 Copynumber: 2.0 Consensus size: 145
41687027 AAATTAGAAA
41687037 TTTATGGTAGAAAATGAAAGGTTGTTGATAGATGAACAACTTTTACAAAGTGATTTTTGATGAAA
1 TTTATGGTAGAAAATGAAAGGTTGTTGATAGATGAACAACTTTTACAAAGTGATTTTTGATGAAA
41687102 ACAGATTTAGGGACTAAAATGTAAAGTTGTGAAATTTGATGAAAAATTTTGAATTTTTATGAATA
66 ACAGATTTAGGGACTAAAATGTAAAGTTGTGAAATTTGATGAAAAATTTTGAATTTTTATGAATA
*
41687167 CATGTGCTGTAAGTT
131 CATGTGCTGTAAATT
41687182 TTTATGGTAGAAAATGAAAGGTTGTTGATAGATGAACAACTTTTACAAAGTGATTTTTGATGAAA
1 TTTATGGTAGAAAATGAAAGGTTGTTGATAGATGAACAACTTTTACAAAGTGATTTTTGATGAAA
41687247 ACAGATTTAGGGACTAAAATGTAAAGTTGTGAAATTTGATGAAAAATTTTGAATTTTTATGAATA
66 ACAGATTTAGGGACTAAAATGTAAAGTTGTGAAATTTGATGAAAAATTTTGAATTTTTATGAATA
*
41687312 CATTTGCTGTAAATT
131 CATGTGCTGTAAATT
41687327 TTT
1 TTT
41687330 GTAATGGGAT
Statistics
Matches: 146, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 146 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (145 bp):
TTTATGGTAGAAAATGAAAGGTTGTTGATAGATGAACAACTTTTACAAAGTGATTTTTGATGAAA
ACAGATTTAGGGACTAAAATGTAAAGTTGTGAAATTTGATGAAAAATTTTGAATTTTTATGAATA
CATGTGCTGTAAATT
Found at i:41690113 original size:13 final size:13
Alignment explanation
Indices: 41690095--41690120 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41690085 AATTCAGAAA
41690095 GAAATATGTTAGT
1 GAAATATGTTAGT
41690108 GAAATATGTTAGT
1 GAAATATGTTAGT
41690121 CAGAGATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
GAAATATGTTAGT
Found at i:41694065 original size:33 final size:34
Alignment explanation
Indices: 41694022--41694094 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 34
41694012 CATAGGCCCA
* * * *
41694022 TACTATTATTGCATAGGGCTTAGACCCAGACTG-
1 TACTGTTATTGAATAGGGCTCAGACCCAGACCGT
*
41694055 TACTGTTATTGAATAGGGCTCAGGCCCAGACCGT
1 TACTGTTATTGAATAGGGCTCAGACCCAGACCGT
41694089 TACTGT
1 TACTGT
41694095 ATGCACTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (34 bp):
TACTGTTATTGAATAGGGCTCAGACCCAGACCGT
Found at i:41700647 original size:40 final size:40
Alignment explanation
Indices: 41700588--41700729 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
41700578 AAATTGAATG
* * *
41700588 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
41700628 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
41700668 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
41700708 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
41700730 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:41700753 original size:40 final size:40
Alignment explanation
Indices: 41700626--41700755 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
41700616 ATGCTGGAAA
* * *
41700626 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * **
41700666 CTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* *
41700706 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
41700746 TTATATCCGG
1 TTATATCCGG
41700756 TTATATTCCG
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
39 1 0.01
40 74 0.99
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:41708758 original size:40 final size:39
Alignment explanation
Indices: 41708590--41708760 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
41708580 AGAAATTGAA
* *
41708590 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
41708630 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
41708670 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
41708710 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
41708750 TGATATCCGGG
1 TGATATCCGGG
41708761 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:41714647 original size:39 final size:39
Alignment explanation
Indices: 41714529--41714711 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
41714519 TCGTTCAAAC
* * ** * **
41714529 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
41714569 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
*
41714609 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
41714648 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
41714687 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
41714712 CTCGAACATT
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:41721060 original size:13 final size:13
Alignment explanation
Indices: 41721042--41721066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41721032 TCTGAGTTAG
41721042 AAAAATATTTTTT
1 AAAAATATTTTTT
41721055 AAAAATATTTTT
1 AAAAATATTTTT
41721067 GGTGTTTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAAATATTTTTT
Found at i:41722260 original size:43 final size:43
Alignment explanation
Indices: 41722190--41722308 Score: 161
Period size: 43 Copynumber: 2.8 Consensus size: 43
41722180 AGGATTTACA
* *
41722190 ATATGTGATTGCGTGTAAGACCATGTCTGGGACA-TCGGCATCG
1 ATATGTGATTACGTGTAAGACCATGTCTAGGACAGT-GGCATCG
*
41722233 TATATGTGATT-CGTGTAAGACCCTGTCTAGGACAGTGGCATCG
1 -ATATGTGATTACGTGTAAGACCATGTCTAGGACAGTGGCATCG
* *
41722276 ATATGTGATTACATGTAAGACCACGTCTAGGAC
1 ATATGTGATTACGTGTAAGACCATGTCTAGGAC
41722309 GTTGGCACTG
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
42 10 0.15
43 47 0.69
44 11 0.16
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (43 bp):
ATATGTGATTACGTGTAAGACCATGTCTAGGACAGTGGCATCG
Found at i:41727278 original size:29 final size:29
Alignment explanation
Indices: 41727245--41727318 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
41727235 GTGACGAGAT
41727245 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
41727274 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
41727303 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41727319 AGCTCGAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:41727334 original size:29 final size:28
Alignment explanation
Indices: 41727302--41727376 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
41727292 CTGGAAATAT
* *
41727302 ATGGCACTAAGTGTGCGAGCTCGAAGGGC
1 ATGGCACTAAGTGTGCGAGCT-AAAGCGC
** * *
41727331 ATGGCACTGTGTGTGCGGGCTAAATCGC
1 ATGGCACTAAGTGTGCGAGCTAAAGCGC
41727359 ATGGCACTAAGTGTGCGA
1 ATGGCACTAAGTGTGCGA
41727377 AATCGAGTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 19 0.51
29 18 0.49
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (28 bp):
ATGGCACTAAGTGTGCGAGCTAAAGCGC
Found at i:41727345 original size:58 final size:57
Alignment explanation
Indices: 41727245--41727376 Score: 131
Period size: 58 Copynumber: 2.3 Consensus size: 57
41727235 GTGACGAGAT
* * * * * *
41727245 TGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAAAT-ATA
1 TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCT--AAATCACA
* * ** * *
41727303 TGGCACTAAGTGTGCGAGCTCGAAGGGCATGGCACTGTGTGTGCGGGCTAAATCGCA
1 TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCTAAATCACA
41727360 TGGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
41727377 AATCGAGTAT
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
56 4 0.07
57 18 0.30
58 39 0.64
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.24
Consensus pattern (57 bp):
TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCTAAATCACA
Found at i:41735151 original size:29 final size:29
Alignment explanation
Indices: 41735118--41735191 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
41735108 GTGACGAGAT
41735118 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
41735147 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
41735176 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41735192 AGCTCGAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:41735207 original size:29 final size:28
Alignment explanation
Indices: 41735175--41735249 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
41735165 CTGGAAATAT
* *
41735175 ATGGCACTAAGTGTGCGAGCTCGAAGGGC
1 ATGGCACTAAGTGTGCGAGCT-AAAGCGC
** * *
41735204 ATGGCACTGTGTGTGCGGGCTAAATCGC
1 ATGGCACTAAGTGTGCGAGCTAAAGCGC
41735232 ATGGCACTAAGTGTGCGA
1 ATGGCACTAAGTGTGCGA
41735250 AATCGAGTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 19 0.51
29 18 0.49
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (28 bp):
ATGGCACTAAGTGTGCGAGCTAAAGCGC
Found at i:41735218 original size:58 final size:57
Alignment explanation
Indices: 41735118--41735249 Score: 131
Period size: 58 Copynumber: 2.3 Consensus size: 57
41735108 GTGACGAGAT
* * * * * *
41735118 TGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAAAT-ATA
1 TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCT--AAATCACA
* * ** * *
41735176 TGGCACTAAGTGTGCGAGCTCGAAGGGCATGGCACTGTGTGTGCGGGCTAAATCGCA
1 TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCTAAATCACA
41735233 TGGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
41735250 AATCGAGTAT
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
56 4 0.07
57 18 0.30
58 39 0.64
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.24
Consensus pattern (57 bp):
TGGCACTAAGTGTGCGAGCTCGAAAGACATGGCACTAAGTGTGCAGGCTAAATCACA
Found at i:41737057 original size:47 final size:47
Alignment explanation
Indices: 41736988--41737381 Score: 646
Period size: 47 Copynumber: 8.4 Consensus size: 47
41736978 CCCTTCGGGA
* * *
41736988 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTAGGC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
* *
41737035 CTTATCACATATACACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
* *
41737082 CTTATCACATATATACACTTTCACATTCGTCACATTGGCCATTCA-GC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATT-AGGC
* * *
41737129 CTTATCACATATATACACTTTCACGTTCATCACATCGGCCATTAGGC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
**
41737176 CTTATCACATATACACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
*
41737223 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
41737270 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
*
41737317 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
41737364 CTTATCACATATACACAC
1 CTTATCACATATACACAC
41737382 CTTGTACATC
Statistics
Matches: 325, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
46 1 0.00
47 324 1.00
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTAGGC
Found at i:41737160 original size:25 final size:25
Alignment explanation
Indices: 41737038--41737163 Score: 70
Period size: 25 Copynumber: 5.3 Consensus size: 25
41737028 ATTAGGCCTT
*
41737038 ATCACATATACACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
*** * *
41737063 ATCACAT-TGGCCAC--TCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
41737085 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
* ** * *
41737110 GTCACAT-T-GGC-CATTCAGCCTT-
1 ATCACATATATACACTTTCA-CATTC
*
41737132 ATCACATATATACACTTTCACGTTC
1 ATCACATATATACACTTTCACATTC
41737157 ATCACAT
1 ATCACAT
41737164 CGGCCATTAG
Statistics
Matches: 71, Mismatches: 20, Indels: 20
0.64 0.18 0.18
Matches are distributed among these distances:
22 20 0.28
23 12 0.17
24 12 0.17
25 27 0.38
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:41737279 original size:22 final size:22
Alignment explanation
Indices: 41737251--41737373 Score: 65
Period size: 22 Copynumber: 5.3 Consensus size: 22
41737241 TTTCACATTC
41737251 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
41737273 ATCACATAT-ACACACTTTC-ACATT
1 ATCACAT-TGGC-CA--TTCGGCCTT
*
41737297 CATCACATTGGCCATTAGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * *
41737320 ATCACATAT-ACACACTTTC-ACATT
1 ATCACAT-TGGC-CA--TTCGGCCTT
41737344 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
41737367 ATCACAT
1 ATCACAT
41737374 ATACACACCT
Statistics
Matches: 73, Mismatches: 14, Indels: 28
0.63 0.12 0.24
Matches are distributed among these distances:
22 28 0.38
23 12 0.16
24 12 0.16
25 21 0.29
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:41741139 original size:18 final size:18
Alignment explanation
Indices: 41741103--41741177 Score: 73
Period size: 18 Copynumber: 4.2 Consensus size: 18
41741093 TTCAATCTTC
* *
41741103 TTTTCTTGTTCAAATTCT
1 TTTTCTTTTTCATATTCT
*
41741121 TTTTCTTTTTCATAGTCT
1 TTTTCTTTTTCATATTCT
*
41741139 TTCTCTTTTTC-T-TTCT
1 TTTTCTTTTTCATATTCT
* *
41741155 TTTTCTTCTTTCACACTCT
1 TTTTCTT-TTTCATATTCT
41741174 TTTT
1 TTTT
41741178 TCGATTTTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
16 9 0.20
17 5 0.11
18 25 0.54
19 7 0.15
ACGTcount: A:0.09, C:0.21, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTCTTTTTCATATTCT
Found at i:41746939 original size:23 final size:23
Alignment explanation
Indices: 41746909--41746958 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
41746899 ATAGAAGTGG
41746909 ACAAGGACAGCAATCCAACTTCT
1 ACAAGGACAGCAATCCAACTTCT
* *
41746932 ACAAGGACTGCAGTCCAACTTCT
1 ACAAGGACAGCAATCCAACTTCT
41746955 ACAA
1 ACAA
41746959 TCCTTTGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.18
Consensus pattern (23 bp):
ACAAGGACAGCAATCCAACTTCT
Found at i:41751637 original size:42 final size:42
Alignment explanation
Indices: 41751526--41751652 Score: 132
Period size: 42 Copynumber: 3.0 Consensus size: 42
41751516 CACACAGTAC
* *
41751526 CATACCAATGCCATATCCCAGATATGGTCTTACAT-GTAA-TTT
1 CATAACAATGCCATATCCCAGATATGGTCTTAC-TCG-AAGTCT
** * *
41751568 TGTAACAATACCAATATCCCAGCTATGGTCTTACTCGAAGTCT
1 CATAACAATGCC-ATATCCCAGATATGGTCTTACTCGAAGTCT
* * *
41751611 CATATCAATGCCATATCCCAGATATGGTCTTACACGTAGTCT
1 CATAACAATGCCATATCCCAGATATGGTCTTACTCGAAGTCT
41751653 TAGTAACCCT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 38 0.55
43 31 0.45
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.31
Consensus pattern (42 bp):
CATAACAATGCCATATCCCAGATATGGTCTTACTCGAAGTCT
Found at i:41753774 original size:13 final size:13
Alignment explanation
Indices: 41753756--41753799 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
41753746 TTGGCCCATT
41753756 ACAGTAACAGTAA
1 ACAGTAACAGTAA
*
41753769 ACAGT-ACAGTAT
1 ACAGTAACAGTAA
*
41753781 GCAGTAACAGTAA
1 ACAGTAACAGTAA
41753794 ACAGTA
1 ACAGTA
41753800 TGCAAGTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (13 bp):
ACAGTAACAGTAA
Found at i:41753778 original size:18 final size:18
Alignment explanation
Indices: 41753755--41753792 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41753745 CTTGGCCCAT
41753755 TACAGTA-ACAGTAAACAG
1 TACAGTATACAGT-AACAG
*
41753773 TACAGTATGCAGTAACAG
1 TACAGTATACAGTAACAG
41753791 TA
1 TA
41753793 AACAGTATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (18 bp):
TACAGTATACAGTAACAG
Found at i:41753965 original size:24 final size:24
Alignment explanation
Indices: 41753933--41753985 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
41753923 TATTTACAGC
41753933 AGAGCTGCCAATAATAATAGGCTT
1 AGAGCTGCCAATAATAATAGGCTT
*
41753957 AGAGCTGCCAGTAATAATAGGCTT
1 AGAGCTGCCAATAATAATAGGCTT
41753981 AGAGC
1 AGAGC
41753986 CACCAGTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (24 bp):
AGAGCTGCCAATAATAATAGGCTT
Found at i:41753991 original size:24 final size:24
Alignment explanation
Indices: 41753944--41753992 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
41753934 GAGCTGCCAA
**
41753944 TAATAATAGGCTTAGAGCTGCCAG
1 TAATAATAGGCTTAGAGCCACCAG
41753968 TAATAATAGGCTTAGAGCCACCAG
1 TAATAATAGGCTTAGAGCCACCAG
41753992 T
1 T
41753993 GATTTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (24 bp):
TAATAATAGGCTTAGAGCCACCAG
Found at i:41755184 original size:27 final size:28
Alignment explanation
Indices: 41755168--41755418 Score: 322
Period size: 27 Copynumber: 9.3 Consensus size: 28
41755158 CGACTTGTAA
41755168 AATTACCATTTTACCCTCGA-TTTACAG
1 AATTACCATTTTACCCTCGAGTTTACAG
41755195 AATTACCATTTTACCCTC-AGTTTACAG
1 AATTACCATTTTACCCTCGAGTTTACAG
** *
41755222 AATTACTGTTTTACCCTCGA-TTTATAG
1 AATTACCATTTTACCCTCGAGTTTACAG
*
41755249 AATTACCGTTTTACCCTC-AGTTTACAG
1 AATTACCATTTTACCCTCGAGTTTACAG
* *
41755276 AATTACTATTTTATCCTCGA-TTTACAG
1 AATTACCATTTTACCCTCGAGTTTACAG
41755303 AATTACCATTTTACCCTC-AGTTTACAG
1 AATTACCATTTTACCCTCGAGTTTACAG
* *
41755330 AATTACTATTTTACCCTCGA-TTTATAG
1 AATTACCATTTTACCCTCGAGTTTACAG
*
41755357 AATTACCGTTTTACCCTC-AGTTTACAG
1 AATTACCATTTTACCCTCGAGTTTACAG
* * * *
41755384 AATTACCGTTTTACCTTC-AATTTATAG
1 AATTACCATTTTACCCTCGAGTTTACAG
41755411 AATTACCA
1 AATTACCA
41755419 AAATACCCTT
Statistics
Matches: 198, Mismatches: 19, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
26 4 0.02
27 191 0.96
28 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (28 bp):
AATTACCATTTTACCCTCGAGTTTACAG
Done.