Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 6 of 427
Found at i:1778105 original size:17 final size:19
Alignment explanation
Indices: 1778083--1778120 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1778073 AAAAATATAG
1778083 ATATAT-ATAAT-TAAAAA
1 ATATATAATAATATAAAAA
*
1778100 ATATATAATATTATAAAAA
1 ATATATAATAATATAAAAA
1778119 AT
1 AT
1778121 TTTAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATATAATAATATAAAAA
Found at i:1778129 original size:17 final size:19
Alignment explanation
Indices: 1778094--1778132 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1778084 TATATATAAT
1778094 TAAAAAATATATAATATTA
1 TAAAAAATATATAATATTA
*
1778113 TAAAAAAT-TTTAA-ATTA
1 TAAAAAATATATAATATTA
1778130 TAA
1 TAA
1778133 TATTACAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAATATATAATATTA
Found at i:1783566 original size:19 final size:19
Alignment explanation
Indices: 1783519--1783558 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1783509 TATTTTGTTA
1783519 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
1783538 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
1783557 TT
1 TT
1783559 ACTTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTTTTATTTCATCTT
Found at i:1788663 original size:19 final size:19
Alignment explanation
Indices: 1788616--1788655 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1788606 TATTTTGTTA
1788616 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
1788635 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
1788654 TT
1 TT
1788656 ACTTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTTTTATTTCATCTT
Found at i:1804301 original size:30 final size:31
Alignment explanation
Indices: 1804267--1804338 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
1804257 AGGTGGCAAC
* *
1804267 TGCAGCAGCATGCATGTAACCATGCA-ACCA
1 TGCAGCAGCATGCAAGTAACCAAGCAGACCA
* *
1804297 TGCAGCAGCATGCAAGTGACCAAGCAGTCCA
1 TGCAGCAGCATGCAAGTAACCAAGCAGACCA
1804328 -GCAGCAGCATG
1 TGCAGCAGCATG
1804339 GAAATGTCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 34 0.92
31 3 0.08
ACGTcount: A:0.32, C:0.29, G:0.25, T:0.14
Consensus pattern (31 bp):
TGCAGCAGCATGCAAGTAACCAAGCAGACCA
Found at i:1807253 original size:10 final size:10
Alignment explanation
Indices: 1807240--1807299 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
1807230 TTTTATTTAG
1807240 ATTTAT-TTT
1 ATTTATCTTT
1807249 CATTTATCTTT
1 -ATTTATCTTT
1807260 ATTTATCTTT
1 ATTTATCTTT
*
1807270 AATTATCTTT
1 ATTTATCTTT
1807280 ATTTAT-TTGT
1 ATTTATCTT-T
1807290 ATTTATCTTT
1 ATTTATCTTT
1807300 TAGAATATCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:1824498 original size:26 final size:26
Alignment explanation
Indices: 1824469--1824534 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
1824459 CTAGTTTGGT
1824469 AATACTTTTGAAAAGTATTTTTGAGA
1 AATACTTTTGAAAAGTATTTTTGAGA
* *
1824495 AATA-TTGTAGAAAAGTGTTTTTGAGA
1 AATACTT-TTGAAAAGTATTTTTGAGA
*
1824521 AATACTTTTAAAAA
1 AATACTTTTGAAAA
1824535 ATTTGGTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 2 0.06
26 30 0.88
27 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (26 bp):
AATACTTTTGAAAAGTATTTTTGAGA
Found at i:1826423 original size:31 final size:29
Alignment explanation
Indices: 1826357--1826433 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 29
1826347 CAAAATTATA
* *
1826357 ATGAACTTTGATTTATTGTGCAATTTAATAC
1 ATGAACTTTGA-TT-TGGTGCAATTCAATAC
*
1826388 ATGAACTTTGATTTGGTGCAATTACACATAT
1 ATGAACTTTGATTTGGTGCAATT-CA-ATAC
*
1826419 ATGAAACTTTAATTT
1 ATG-AACTTTGATTT
1826434 TGATTCAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 9 0.23
30 3 0.08
31 17 0.44
32 10 0.26
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (29 bp):
ATGAACTTTGATTTGGTGCAATTCAATAC
Found at i:1826951 original size:19 final size:19
Alignment explanation
Indices: 1826906--1826953 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1826896 AAACTTAATT
*
1826906 AAAATATTTTAAAATTTAC
1 AAAATAATTTAAAATTTAC
*
1826925 AAACTAATTTAAAATTTA-
1 AAAATAATTTAAAATTTAC
1826943 AATAATAATTT
1 AA-AATAATTT
1826954 GAGAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 2 0.08
19 23 0.92
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATAATTTAAAATTTAC
Found at i:1828514 original size:12 final size:12
Alignment explanation
Indices: 1828497--1828522 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1828487 CTACAAGGTG
1828497 TACATACATATA
1 TACATACATATA
1828509 TACATACATATA
1 TACATACATATA
1828521 TA
1 TA
1828523 TAGGTGATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (12 bp):
TACATACATATA
Found at i:1830167 original size:30 final size:30
Alignment explanation
Indices: 1830114--1830170 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1830104 AGCCCACTTC
*
1830114 CACACGGGTAATCCACACACCCGTGTGAGA
1 CACACGGGTAAGCCACACACCCGTGTGAGA
* * *
1830144 CACACGGGTAGGCCATACGCCCGTGTG
1 CACACGGGTAAGCCACACACCCGTGTG
1830171 TCATGGCCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.25, C:0.33, G:0.28, T:0.14
Consensus pattern (30 bp):
CACACGGGTAAGCCACACACCCGTGTGAGA
Found at i:1831379 original size:20 final size:21
Alignment explanation
Indices: 1831333--1831373 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1831323 TTAGCCATTT
1831333 TTATTTTTATTGCAATTTATTC
1 TTATTTTTATT-CAATTTATTC
*
1831355 TTATTTTTATT-ATTTTATT
1 TTATTTTTATTCAATTTATT
1831374 ACTATTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (21 bp):
TTATTTTTATTCAATTTATTC
Found at i:1835668 original size:93 final size:93
Alignment explanation
Indices: 1835509--1835680 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
1835499 CACCCATAAG
* * *
1835509 CGAACTCAGACTCAACCCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACCCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1835574 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* * *
1835602 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACCCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1835667 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
1835681 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCAGACTCAACCCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:1835677 original size:46 final size:46
Alignment explanation
Indices: 1835502--1835677 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
1835492 TGTAACCCAC
* * * * * *
1835502 CCATAAGCGAACTCAGACTCAACCCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
1835548 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
1835598 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
1835641 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
1835678 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 60 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:1835696 original size:46 final size:44
Alignment explanation
Indices: 1835553--1835696 Score: 141
Period size: 46 Copynumber: 3.1 Consensus size: 44
1835543 CGCATCCATA
1835553 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * *
1835600 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
1835646 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
1835692 AGTGA
1 AGTGA
1835697 CATGTCACTT
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
44 9 0.11
45 1 0.01
46 33 0.41
47 31 0.39
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:1836131 original size:29 final size:30
Alignment explanation
Indices: 1836099--1836157 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1836089 ATTTAATACG
* * *
1836099 AACTTTGGCA-AATTATATTTTTGCCCCTA
1 AACTTTGACATAATTACACTTTTGCCCCTA
*
1836128 AACTTTTACATAATTACACTTTTGCCCCTA
1 AACTTTGACATAATTACACTTTTGCCCCTA
1836158 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.41
Consensus pattern (30 bp):
AACTTTGACATAATTACACTTTTGCCCCTA
Found at i:1837487 original size:24 final size:24
Alignment explanation
Indices: 1837437--1837495 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
1837427 TTTCATTTAA
**
1837437 TTTTTATTTTTATTTTTATTTGTC
1 TTTTTATTTTTAGGTTTATTTGTC
*
1837461 TTTTTCTTTTTAGGTTTATTT-TGC
1 TTTTTATTTTTAGGTTTATTTGT-C
1837485 TTTTATATTTT
1 TTTT-TATTTT
1837496 GAACTATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 1 0.03
24 23 0.79
25 5 0.17
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (24 bp):
TTTTTATTTTTAGGTTTATTTGTC
Found at i:1841572 original size:47 final size:47
Alignment explanation
Indices: 1841480--1841573 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
1841470 TTTGAACACT
*
1841480 TGATGCAATCTCACTTTTGTACAATTAAGTAAATTCTCTCCCAACTC
1 TGATGCAATCTCACTTTTGTACAATTAAGTAAATTCTCTACCAACTC
* * *
1841527 TGATGCAATTTCACTTTTGTACAATTAAGTAAGTTCTCTATCAACTC
1 TGATGCAATCTCACTTTTGTACAATTAAGTAAATTCTCTACCAACTC
1841574 ATTTTAGCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (47 bp):
TGATGCAATCTCACTTTTGTACAATTAAGTAAATTCTCTACCAACTC
Found at i:1847754 original size:29 final size:29
Alignment explanation
Indices: 1847723--1847779 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
1847713 GAATTGGATC
*
1847723 AAATTAAAATTTCATGTATAAAATTACACA
1 AAATCAAAA-TTCATGTATAAAATTACACA
1847753 AAATCAAAATTCATGTATAAAATTACA
1 AAATCAAAATTCATGTATAAAATTACA
1847780 TATCAGGCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.32
Consensus pattern (29 bp):
AAATCAAAATTCATGTATAAAATTACACA
Found at i:1848116 original size:30 final size:31
Alignment explanation
Indices: 1848076--1848135 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
1848066 AAAGACTTAA
*
1848076 TTAAAATATTT-T-AAAATTTAAATAATAAT
1 TTAAAATATTTATAAAAATATAAATAATAAT
1848105 TTAAGAATATTTAATAAAAATATAAATAATA
1 TTAA-AATATTT-ATAAAAATATAAATAATA
1848136 CTATATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 4 0.15
30 7 0.27
32 1 0.04
33 14 0.54
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (31 bp):
TTAAAATATTTATAAAAATATAAATAATAAT
Found at i:1853862 original size:28 final size:28
Alignment explanation
Indices: 1853822--1853877 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1853812 TAGTATATTA
1853822 TTTCAATTTTGATGAGAATTGTACTCTC
1 TTTCAATTTTGATGAGAATTGTACTCTC
1853850 TTTCAATTTTGATGAGAATTGTACTCTC
1 TTTCAATTTTGATGAGAATTGTACTCTC
1853878 GCTTAACGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (28 bp):
TTTCAATTTTGATGAGAATTGTACTCTC
Found at i:1862780 original size:29 final size:30
Alignment explanation
Indices: 1862746--1862812 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
1862736 AATTAAAATT
*
1862746 AATTTTTAAGAA-TT-TTTATACTTTTTTAA
1 AATTTTTAAGAAGTTGTATATA-TTTTTTAA
* *
1862775 AATTTTTAATAAGTTGTATATATTTTTTTA
1 AATTTTTAAGAAGTTGTATATATTTTTTAA
1862805 AATTTTTA
1 AATTTTTA
1862813 TATTTAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 11 0.33
30 17 0.52
31 5 0.15
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (30 bp):
AATTTTTAAGAAGTTGTATATATTTTTTAA
Found at i:1871911 original size:13 final size:13
Alignment explanation
Indices: 1871893--1871919 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1871883 CCTTACCACC
1871893 ATTAATAAAAAAT
1 ATTAATAAAAAAT
1871906 ATTAATAAAAAAT
1 ATTAATAAAAAAT
1871919 A
1 A
1871920 AATCATTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATTAATAAAAAAT
Found at i:1873586 original size:12 final size:12
Alignment explanation
Indices: 1873554--1873587 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
1873544 CTACACGCCA
1873554 CATTCTATCTTTC
1 CATT-TATCTTTC
1873567 CA-TTATCTTTC
1 CATTTATCTTTC
1873578 CATTTATCTT
1 CATTTATCTT
1873588 CTTTATTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 10 0.50
12 8 0.40
13 2 0.10
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (12 bp):
CATTTATCTTTC
Found at i:1874482 original size:78 final size:78
Alignment explanation
Indices: 1874398--1874632 Score: 443
Period size: 78 Copynumber: 3.0 Consensus size: 78
1874388 ATTAAGTAAC
*
1874398 ATATAAAATTAACATAATATAAAATATTACAAACTAAAAAAAAGGGTCGGGACAAACTTAGGTTT
1 ATATAAAATTAACATAATATAAAATATTACAAACTAAAAAAATGGGTCGGGACAAACTTAGGTTT
1874463 TGAATGTTCAAGT
66 TGAATGTTCAAGT
*
1874476 ATATAAAATTAACATAATATAAAATATTATAAACTAAAAAAATGGGTCGGGACAAACTTAGGTTT
1 ATATAAAATTAACATAATATAAAATATTACAAACTAAAAAAATGGGTCGGGACAAACTTAGGTTT
1874541 TGAATGTTCAAGT
66 TGAATGTTCAAGT
*
1874554 ATATAAAATCAACATAATATAAAATATTACAAACTAAAAAAATGGGTCGGGACAAACTTAGGTTT
1 ATATAAAATTAACATAATATAAAATATTACAAACTAAAAAAATGGGTCGGGACAAACTTAGGTTT
1874619 TGAATGTTCAAGT
66 TGAATGTTCAAGT
1874632 A
1 A
1874633 CTAACTGAAC
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 153 1.00
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (78 bp):
ATATAAAATTAACATAATATAAAATATTACAAACTAAAAAAATGGGTCGGGACAAACTTAGGTTT
TGAATGTTCAAGT
Found at i:1876237 original size:21 final size:21
Alignment explanation
Indices: 1876213--1876277 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
1876203 TGCATGCTCT
1876213 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
** * *
1876234 GAAGC-CCGAAG-GCT-ATCT
1 GAAGCACATAAGTGCTAAACG
1876252 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
1876273 GAAGC
1 GAAGC
1876278 CCGAAGGCTA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 7 0.21
19 7 0.21
20 7 0.21
21 12 0.36
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACG
Found at i:1876264 original size:39 final size:39
Alignment explanation
Indices: 1876210--1876295 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
1876200 TATTGCATGC
1876210 TCTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTA
1 TCTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTA
1876249 TCTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTA
1 TCTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTA
*
1876288 ACTGAAGC
1 TCTGAAGC
1876296 TCACCAGAGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.36, C:0.23, G:0.26, T:0.15
Consensus pattern (39 bp):
TCTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTA
Found at i:1878537 original size:13 final size:13
Alignment explanation
Indices: 1878521--1878549 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1878511 TCTCAGAAGT
1878521 ATTTTTCAAAAGC
1 ATTTTTCAAAAGC
1878534 ATTTTTCAAAAGC
1 ATTTTTCAAAAGC
1878547 ATT
1 ATT
1878550 GCTAAACTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (13 bp):
ATTTTTCAAAAGC
Found at i:1879981 original size:19 final size:19
Alignment explanation
Indices: 1879937--1879983 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1879927 GACTTAATTC
*
1879937 AAATATTTTAAAATTTACA
1 AAATAATTTAAAATTTACA
*
1879956 AACTAATTTAAAATTTA-A
1 AAATAATTTAAAATTTACA
1879974 ATAATAATTT
1 A-AATAATTT
1879984 GAGAATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATAATTTAAAATTTACA
Found at i:1880458 original size:35 final size:35
Alignment explanation
Indices: 1880419--1880524 Score: 91
Period size: 35 Copynumber: 3.2 Consensus size: 35
1880409 GTACTAAATC
1880419 ATTTTATTGATACAATATTAATTAAAATATTTTAA
1 ATTTTATTGATACAATATTAATTAAAATATTTTAA
* * *
1880454 ATTTTA-T-AAACCA-A-T--TTAAAAT-TTAAATAA
1 ATTTTATTGATACAATATTAATTAAAATATT--TTAA
* *
1880484 ATCTTATTGATATAATATTAATTAAAATATTTTAA
1 ATTTTATTGATACAATATTAATTAAAATATTTTAA
*
1880519 AATTTA
1 ATTTTA
1880525 AATAGTATTC
Statistics
Matches: 52, Mismatches: 10, Indels: 18
0.65 0.12 0.22
Matches are distributed among these distances:
28 2 0.04
29 7 0.13
30 8 0.15
31 2 0.04
32 4 0.08
33 5 0.10
34 2 0.04
35 13 0.25
36 7 0.13
37 2 0.04
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (35 bp):
ATTTTATTGATACAATATTAATTAAAATATTTTAA
Found at i:1881099 original size:28 final size:28
Alignment explanation
Indices: 1881055--1881114 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1881045 ATATTTATAT
*
1881055 TATATTGTTTTAATATTTAATAATTTTA
1 TATATTGTTTTAATATTGAATAATTTTA
* **
1881083 TATATT-TTTTATTTATTGAATTTTTTTA
1 TATATTGTTTTA-ATATTGAATAATTTTA
1881111 TATA
1 TATA
1881115 GTGATCTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (28 bp):
TATATTGTTTTAATATTGAATAATTTTA
Found at i:1887804 original size:1 final size:1
Alignment explanation
Indices: 1887798--1887822 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1887788 AGTATAAAGG
1887798 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1887823 ATACTTCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1889565 original size:2 final size:2
Alignment explanation
Indices: 1889560--1889586 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1889550 TTCAAATATA
1889560 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1889587 ATATACATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1901016 original size:20 final size:21
Alignment explanation
Indices: 1900968--1901016 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1900958 TTAATAGTTT
*
1900968 ACATAGAAAATAATAATTCATA
1 ACAT-GAAAATAATAATCCATA
*
1900990 A-AAGAAAATAATAATCCA-A
1 ACATGAAAATAATAATCCATA
1901009 ACATGAAA
1 ACATGAAA
1901017 CACACATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.09
20 19 0.83
21 1 0.04
22 1 0.04
ACGTcount: A:0.63, C:0.10, G:0.06, T:0.20
Consensus pattern (21 bp):
ACATGAAAATAATAATCCATA
Found at i:1911038 original size:5 final size:5
Alignment explanation
Indices: 1911028--1911059 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1911018 AATAATTAAG
1911028 TATAT TATAT TATAT TATAT TATA- TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TAT
1911060 TATATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:1911060 original size:12 final size:11
Alignment explanation
Indices: 1911005--1911067 Score: 62
Period size: 12 Copynumber: 5.7 Consensus size: 11
1910995 GATTAAAAAA
1911005 TATATATATAT
1 TATATATATAT
1911016 T-TA-ATA-AT
1 TATATATATAT
1911024 TAAGTATATTATAT
1 T-A-TATA-TATAT
1911038 TATAT-TATAT
1 TATATATATAT
1911048 TATATATATTAT
1 TATATATA-TAT
1911060 TATATATA
1 TATATATA
1911068 AAAGAAACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
8 3 0.07
9 3 0.07
10 12 0.27
11 5 0.11
12 15 0.34
13 3 0.07
14 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (11 bp):
TATATATATAT
Found at i:1911063 original size:10 final size:9
Alignment explanation
Indices: 1911004--1911066 Score: 52
Period size: 8 Copynumber: 7.7 Consensus size: 9
1910994 TGATTAAAAA
1911004 ATATA-TAT
1 ATATATTAT
1911012 ATAT-TTA-
1 ATATATTAT
1911019 ATA-ATTA-
1 ATATATTAT
1911026 AGTATATTAT
1 A-TATATTAT
1911036 AT-TA-TAT
1 ATATATTAT
1911043 -TATATTAT
1 ATATATTAT
1911051 ATATATTATT
1 ATATATTA-T
1911061 ATATAT
1 ATATAT
1911067 AAAAGAAACA
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
6 1 0.02
7 12 0.26
8 13 0.28
9 12 0.26
10 8 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATTAT
Found at i:1911134 original size:31 final size:30
Alignment explanation
Indices: 1911099--1911159 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
1911089 GAAACAGAAT
*
1911099 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
1911130 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
1911160 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:1912733 original size:39 final size:39
Alignment explanation
Indices: 1912626--1912760 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
1912616 GACCTCGAGT
* * *
1912626 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
1912667 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
1912705 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
1912744 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
1912761 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:1916042 original size:21 final size:21
Alignment explanation
Indices: 1915997--1916051 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1915987 ATGCTAATTT
* *
1915997 TTTTAGAAATTTTATGAACTA
1 TTTTATAATTTTTATGAACTA
1916018 -TTTATAATTTTTATTGAA-TA
1 TTTTATAATTTTTA-TGAACTA
*
1916038 TTTTATGATTTTTA
1 TTTTATAATTTTTA
1916052 AATTATTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (21 bp):
TTTTATAATTTTTATGAACTA
Found at i:1916905 original size:25 final size:25
Alignment explanation
Indices: 1916877--1916926 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1916867 GTTTAAGAAT
1916877 TCACAATTTTAGTTTAATGTCTATC
1 TCACAATTTTAGTTTAATGTCTATC
1916902 TCACAATTTTAGTTTAATGTCTATC
1 TCACAATTTTAGTTTAATGTCTATC
1916927 GAGATTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (25 bp):
TCACAATTTTAGTTTAATGTCTATC
Found at i:1917160 original size:25 final size:25
Alignment explanation
Indices: 1917115--1917162 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1917105 TAAGCTATTA
**
1917115 AATAATAAAATTACATTTTAATTTT
1 AATAATAAAATTACAACTTAATTTT
1917140 AATAA-AAAATATACAACTTAATT
1 AATAATAAAAT-TACAACTTAATT
1917163 CTAACACTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (25 bp):
AATAATAAAATTACAACTTAATTTT
Found at i:1920957 original size:15 final size:16
Alignment explanation
Indices: 1920936--1920976 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1920926 TAATCCTCTA
1920936 AAAATTATAAAGATA-T
1 AAAATTATAAA-ATAGT
1920952 -AAATTATTAAAATAGT
1 AAAATTA-TAAAATAGT
1920968 AAAATTATA
1 AAAATTATA
1920977 TTTTACTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (16 bp):
AAAATTATAAAATAGT
Found at i:1924010 original size:15 final size:15
Alignment explanation
Indices: 1923993--1924040 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
1923983 TTTTAATTAG
*
1923993 TTTTTAAATAATATG
1 TTTTTAAATAATATA
1924008 TTTTT---TAAT-TA
1 TTTTTAAATAATATA
*
1924019 TTTTTAAATAACATA
1 TTTTTAAATAATATA
1924034 TTTTTAA
1 TTTTTAA
1924041 TTACTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
11 6 0.22
12 4 0.15
14 3 0.11
15 14 0.52
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTTTAAATAATATA
Found at i:1924011 original size:26 final size:26
Alignment explanation
Indices: 1923980--1924043 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
1923970 TATGCATTTA
*
1923980 ATTTTTTAATTAGTTTTTAAATAATAT
1 ATTTTTTAATTA-TTTTTAAATAACAT
*
1924007 GTTTTTTAATTATTTTTAAATAACAT
1 ATTTTTTAATTATTTTTAAATAACAT
1924033 A-TTTTTAATTA
1 ATTTTTTAATTA
1924044 CTATAATTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 10 0.29
26 13 0.38
27 11 0.32
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (26 bp):
ATTTTTTAATTATTTTTAAATAACAT
Found at i:1928120 original size:23 final size:23
Alignment explanation
Indices: 1928093--1928138 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1928083 AAATTATATA
1928093 TAGTCTAATACGTTTCATTGTAG
1 TAGTCTAATACGTTTCATTGTAG
1928116 TAGTCTAATACGTTTCATTGTAG
1 TAGTCTAATACGTTTCATTGTAG
1928139 AAGGTTGCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (23 bp):
TAGTCTAATACGTTTCATTGTAG
Found at i:1931801 original size:79 final size:81
Alignment explanation
Indices: 1931700--1931884 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
1931690 ACGACTCGCT
** * *
1931700 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
1931763 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* **
1931780 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
1931844 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
1931860 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1931885 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:1931884 original size:40 final size:39
Alignment explanation
Indices: 1931693--1931884 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
1931683 GGATATAACG
* ** * *
1931693 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
1931733 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
1931773 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
1931812 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
1931852 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
1931885 CATCATTCGA
Statistics
Matches: 121, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 79 0.65
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:1939820 original size:79 final size:81
Alignment explanation
Indices: 1939719--1939903 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
1939709 ACGACTCGCT
** * *
1939719 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
1939782 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* **
1939799 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
1939863 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
1939879 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1939904 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:1939903 original size:40 final size:39
Alignment explanation
Indices: 1939712--1939903 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
1939702 GGATATAACG
* ** * *
1939712 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
1939752 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
1939792 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
1939831 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
1939871 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
1939904 CATCATTCGA
Statistics
Matches: 121, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 79 0.65
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:1942889 original size:25 final size:26
Alignment explanation
Indices: 1942861--1942910 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
1942851 AAAATAAAAT
1942861 AAAATCTAATCTAAAAA-GAAAAGAG
1 AAAATCTAATCTAAAAATGAAAAGAG
1942886 AAAATCTAATCTAAAAATGAAAAGA
1 AAAATCTAATCTAAAAATGAAAAGA
1942911 AAGGACATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (26 bp):
AAAATCTAATCTAAAAATGAAAAGAG
Found at i:1947239 original size:16 final size:16
Alignment explanation
Indices: 1947199--1947236 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1947189 TGAAAAAGCA
*
1947199 AAAAATTAAATTTTAG
1 AAAATTTAAATTTTAG
*
1947215 AGAATTTAAATTTTA-
1 AAAATTTAAATTTTAG
1947230 AAAATTT
1 AAAATTT
1947237 TAAGAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (16 bp):
AAAATTTAAATTTTAG
Found at i:1957503 original size:14 final size:14
Alignment explanation
Indices: 1957480--1957509 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1957470 TTTTGACTCG
1957480 AATTTAATAAATTT
1 AATTTAATAAATTT
*
1957494 AATTTGATAAATTT
1 AATTTAATAAATTT
1957508 AA
1 AA
1957510 ATCTAAATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
AATTTAATAAATTT
Found at i:1958065 original size:60 final size:61
Alignment explanation
Indices: 1957963--1958084 Score: 237
Period size: 60 Copynumber: 2.0 Consensus size: 61
1957953 TCTCTAATTT
1957963 TTGTTGGGTTGAGTAGTAAAGAGCTTATGCTCCTTAAATAAAGTTTCAAGTTCAAGTATTA
1 TTGTTGGGTTGAGTAGTAAAGAGCTTATGCTCCTTAAATAAAGTTTCAAGTTCAAGTATTA
1958024 TTGTTGGGTTGAGTAGTAAAG-GCTTATGCTCCTTAAATAAAGTTTCAAGTTCAAGTATTA
1 TTGTTGGGTTGAGTAGTAAAGAGCTTATGCTCCTTAAATAAAGTTTCAAGTTCAAGTATTA
1958084 T
1 T
1958085 GAATAGAGAA
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 40 0.66
61 21 0.34
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (61 bp):
TTGTTGGGTTGAGTAGTAAAGAGCTTATGCTCCTTAAATAAAGTTTCAAGTTCAAGTATTA
Found at i:1958101 original size:60 final size:61
Alignment explanation
Indices: 1957976--1958101 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 61
1957966 TTGGGTTGAG
* * ** *
1957976 TAGTAAAGAGCTTATGCTCCTTAAATAAAGTTTCAAGTTCAAGTATTATTGTTGGGTTGAG
1 TAGTAAAGAGCTTATGCTCCTTAAATAAAGTTTCAAGTTCAAGTATTATTGTAGAGTAAAA
1958037 TAGTAAAG-GCTTATGCTCCTTAAATAAAGTTTCAAGTTCAAGTATTA-TGAATAGAG-AAAA
1 TAGTAAAGAGCTTATGCTCCTTAAATAAAGTTTCAAGTTCAAGTATTATTG--TAGAGTAAAA
1958097 TAGTA
1 TAGTA
1958102 TTGAAAGAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
59 2 0.03
60 45 0.78
61 11 0.19
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (61 bp):
TAGTAAAGAGCTTATGCTCCTTAAATAAAGTTTCAAGTTCAAGTATTATTGTAGAGTAAAA
Found at i:1963767 original size:47 final size:47
Alignment explanation
Indices: 1963713--1963906 Score: 255
Period size: 47 Copynumber: 4.1 Consensus size: 47
1963703 TTAGGATTTT
** * * *
1963713 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCCAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1963760 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
1963807 ATGCGATAAATGCGAGA-ATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGA-ACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
1963854 ATGTGATGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1963901 ATGTGA
1 ATGTGA
1963907 AATATGTATG
Statistics
Matches: 128, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
46 1 0.01
47 126 0.98
48 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:1963858 original size:24 final size:24
Alignment explanation
Indices: 1963786--1963858 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
1963776 CATGCATATA
1963786 TGTGATAAGGCCGAATGGCCAA--
1 TGTGATAAGGCCGAATGGCCAATG
* * *
1963808 TGCGATAAATGCGAGAAT-G-CATATG
1 TGTGAT-AAGGC-CGAATGGCCA-ATG
1963833 TGTGATAAGGCCGAATGGCCAATG
1 TGTGATAAGGCCGAATGGCCAATG
1963857 TG
1 TG
1963859 ATGAATATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
22 7 0.18
23 10 0.26
24 14 0.37
25 7 0.18
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.22
Consensus pattern (24 bp):
TGTGATAAGGCCGAATGGCCAATG
Found at i:1963859 original size:22 final size:22
Alignment explanation
Indices: 1963785--1963860 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
1963775 ACATGCATAT
1963785 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * *
1963807 ATGCGATAAATGCGAGAAT-G-CA
1 ATGTGAT-AAGGC-CGAATGGCCA
1963829 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCCGAATGGCCA
1963854 ATGTGAT
1 ATGTGAT
1963861 GAATATGAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 14 0.34
23 10 0.24
24 10 0.24
25 7 0.17
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.22
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:1964163 original size:37 final size:37
Alignment explanation
Indices: 1964113--1964184 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
1964103 GGAAATATAT
*
1964113 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
**
1964150 TCCGGGTAAGACCCGATAACTTTGTGTGGAGATTT
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTT
1964185 CGTCTGAGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
Found at i:1971995 original size:31 final size:31
Alignment explanation
Indices: 1971957--1972019 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1971947 AGGAACAAAG
* * *
1971957 TTCATTTCCTTTCTGGGACTTGATTTTATCT
1 TTCATTTCCTTTCTAGGACTCGATTCTATCT
1971988 TTCATTTCCTTTCTAGGACTCGATTCTATCT
1 TTCATTTCCTTTCTAGGACTCGATTCTATCT
1972019 T
1 T
1972020 CAATCAGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.14, C:0.22, G:0.11, T:0.52
Consensus pattern (31 bp):
TTCATTTCCTTTCTAGGACTCGATTCTATCT
Found at i:1974919 original size:43 final size:43
Alignment explanation
Indices: 1974871--1974956 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
1974861 TGCTTTTTCT
*
1974871 TTGTTACTTGAAGAATTTCTTTTTCCAATTTATGTTATTCGAA
1 TTGTTACTTGAAGAATTTCTTTTTCCAATTTATATTATTCGAA
1974914 TTGTTACTTGAAGAATTTCTTTTTCCAATTTATATTATTCGAA
1 TTGTTACTTGAAGAATTTCTTTTTCCAATTTATATTATTCGAA
1974957 ATTAGACATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (43 bp):
TTGTTACTTGAAGAATTTCTTTTTCCAATTTATATTATTCGAA
Found at i:1979782 original size:27 final size:21
Alignment explanation
Indices: 1979764--1979818 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
1979754 TGGCTGAGAG
1979764 ACACTGCCATGTGACTGTGGT
1 ACACTGCCATGTGACTGTGGT
1979785 ACACTGCCATGTGACTGTGGT
1 ACACTGCCATGTGACTGTGGT
*
1979806 ACACTGCCGTGTG
1 ACACTGCCATGTG
1979819 GGCTGACCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.18, C:0.25, G:0.29, T:0.27
Consensus pattern (21 bp):
ACACTGCCATGTGACTGTGGT
Found at i:1981718 original size:25 final size:24
Alignment explanation
Indices: 1981659--1981718 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
1981649 AGGAAATAAC
* * *
1981659 AAAAATAAAATTTACTCTAAAAAG
1 AAAAAAAAAATCTAATCTAAAAAG
**
1981683 AAAAGGGAAAATCTAATCTAAAAATG
1 AAAA-AAAAAATCTAATCTAAAAA-G
1981709 AAAAAAAAAA
1 AAAAAAAAAA
1981719 CTCAACCCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 4 0.14
25 19 0.68
26 5 0.18
ACGTcount: A:0.67, C:0.07, G:0.08, T:0.18
Consensus pattern (24 bp):
AAAAAAAAAATCTAATCTAAAAAG
Found at i:1985193 original size:131 final size:130
Alignment explanation
Indices: 1984960--1985206 Score: 386
Period size: 131 Copynumber: 1.9 Consensus size: 130
1984950 TCGTGATACT
* * * *
1984960 CAGGCTTGAGTGTCACAGTACCCACAAAAGTCTTGAGATTAGGAATTTGGGGTGTCGGTATCACG
1 CAGGCTTGAGTGTCACAATACCCACAAAAGTCTTGAGATTAGGAATTTAGGGTGTCAGTATCACA
* ** *
1985025 ATAACCATTACTAGGTATCCCTGTATCATTGTAGTTGGCTTGAATTCTCTTTTATAACCATTACC
66 ATAACCATTACTAGGCATCCCCATATCATTGTAGTTGGCCTGAATTCTCTTTTATAACCATTACC
* * *
1985090 CAGGCTTGGGTTTCACAATACCCACAAAAGTCTTGAGATTGGGAATCTTAGGGTGTCAGTATCAC
1 CAGGCTTGAGTGTCACAATACCCACAAAAGTCTTGAGATTAGGAAT-TTAGGGTGTCAGTATCAC
1985155 AATAACCATTACTAGGCATCCCCATATCATTGTAGTTGGCCTGAATTCTCTT
65 AATAACCATTACTAGGCATCCCCATATCATTGTAGTTGGCCTGAATTCTCTT
1985207 CATTTCAACA
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
130 42 0.40
131 63 0.60
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (130 bp):
CAGGCTTGAGTGTCACAATACCCACAAAAGTCTTGAGATTAGGAATTTAGGGTGTCAGTATCACA
ATAACCATTACTAGGCATCCCCATATCATTGTAGTTGGCCTGAATTCTCTTTTATAACCATTACC
Found at i:1988598 original size:45 final size:46
Alignment explanation
Indices: 1988482--1988609 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
1988472 TGGTTGAGCA
*
1988482 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1988528 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
1988574 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1988610 GCGGGTTACA
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
45 34 0.43
46 45 0.57
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:1993956 original size:46 final size:46
Alignment explanation
Indices: 1993906--1994030 Score: 196
Period size: 46 Copynumber: 2.7 Consensus size: 46
1993896 TGAGCATCCG
* *
1993906 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
1 AACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTCCA
**
1993952 AACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTCTG
1 AACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTCCA
* *
1993998 AGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1994031 GCGGGTTACA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.33
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTCCA
Found at i:1998847 original size:52 final size:52
Alignment explanation
Indices: 1998773--1998931 Score: 201
Period size: 52 Copynumber: 3.0 Consensus size: 52
1998763 CCATGGCAAC
*
1998773 ATGTGATATGTGCTTCCGTATAAGACCATAGTAGGGCTATGGCATCGGTGTG
1 ATGTGATATGTGCTTCCGTATAAGACCATAATAGGGCTATGGCATCGGTGTG
* * * * *
1998825 ATGTGATAAGTGCTCCCATATAAGACCATAACAGGGCTATGGCATCGGTGAG
1 ATGTGATATGTGCTTCCGTATAAGACCATAATAGGGCTATGGCATCGGTGTG
* * * * * *
1998877 ATGTGATTATGTACTTCTGTGTAAGACCATATTAGGGATATGGCATCAGTGTG
1 ATGTGA-TATGTGCTTCCGTATAAGACCATAATAGGGCTATGGCATCGGTGTG
1998930 AT
1 AT
1998932 ATGTGATCCG
Statistics
Matches: 89, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
52 52 0.58
53 37 0.42
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (52 bp):
ATGTGATATGTGCTTCCGTATAAGACCATAATAGGGCTATGGCATCGGTGTG
Found at i:2000671 original size:16 final size:17
Alignment explanation
Indices: 2000650--2000706 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 17
2000640 TATGAATTTC
2000650 TAAGCTCAAGCTTG-AT
1 TAAGCTCAAGCTTGTAT
2000666 TAAGCT--AGCTTGTAT
1 TAAGCTCAAGCTTGTAT
*
2000681 TCAAGCTCACATCTTGTAT
1 T-AAGCTCA-AGCTTGTAT
2000700 TCAAGCT
1 T-AAGCT
2000707 TGGATCTAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
14 6 0.17
15 3 0.09
16 11 0.31
19 15 0.43
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (17 bp):
TAAGCTCAAGCTTGTAT
Found at i:2001613 original size:16 final size:16
Alignment explanation
Indices: 2001594--2001627 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2001584 GATCACAAAT
2001594 AAAAACAAAATTACAC
1 AAAAACAAAATTACAC
**
2001610 AAAAATTAAATTACAC
1 AAAAACAAAATTACAC
2001626 AA
1 AA
2001628 TATGTAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAACAAAATTACAC
Found at i:2007093 original size:4 final size:4
Alignment explanation
Indices: 2007084--2007117 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
2007074 CACTATGAGG
2007084 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
2007118 CTGCTTCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2007391 original size:21 final size:20
Alignment explanation
Indices: 2007349--2007397 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
2007339 ATCTCACTTG
2007349 TAATTTTTTTAAAATACCAAA
1 TAATTTTTTTAAAATA-CAAA
2007370 TAATATTTTTTAAATATA-AAA
1 TAAT-TTTTTTAAA-ATACAAA
2007391 T-ATTTTT
1 TAATTTTT
2007398 AGAATGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.15
20 2 0.08
21 8 0.31
22 9 0.35
23 3 0.12
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATTTTTTTAAAATACAAA
Found at i:2009367 original size:31 final size:31
Alignment explanation
Indices: 2009332--2009390 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2009322 AACAGACCTA
*
2009332 TAACTTAAATAAAAACTTTCAAATAATTCAG
1 TAACTAAAATAAAAACTTTCAAATAATTCAG
* *
2009363 TAACTAAAATGAAAACTTTTAAATAATT
1 TAACTAAAATAAAAACTTTCAAATAATT
2009391 TAATGAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (31 bp):
TAACTAAAATAAAAACTTTCAAATAATTCAG
Found at i:2011174 original size:4 final size:4
Alignment explanation
Indices: 2011167--2011191 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2011157 ATGAAGCATG
2011167 CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA C
2011192 GACATTTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:2011454 original size:16 final size:16
Alignment explanation
Indices: 2011432--2011503 Score: 92
Period size: 16 Copynumber: 4.5 Consensus size: 16
2011422 CGTTTGGTTG
2011432 GCTGTAATGGAATA-A
1 GCTGTAATGGAATAGA
* *
2011447 GACTGTAATTGAATAAA
1 G-CTGTAATGGAATAGA
* *
2011464 GTTGTAATAGAATAGA
1 GCTGTAATGGAATAGA
2011480 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
2011496 GCTGTAAT
1 GCTGTAAT
2011504 AAGTAATTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
15 1 0.02
16 46 0.94
17 2 0.04
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:2011541 original size:46 final size:44
Alignment explanation
Indices: 2011485--2011578 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
2011475 ATAGAGCTGT
* *
2011485 AATGGAATAGAGCTGTAATAAGTAATTCAACTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAT-AGT-ATTCAACTGTTTGGTTAAATGG
***
2011531 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTAAATGG
1 AATGGAATAGAACTGTAATAGTATTCAACTGTTTGGTTAAATGG
2011575 AATG
1 AATG
2011579 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 22 0.51
45 3 0.07
46 18 0.42
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCAACTGTTTGGTTAAATGG
Found at i:2018509 original size:25 final size:25
Alignment explanation
Indices: 2018481--2018528 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2018471 ATTATTTAAC
* *
2018481 AATTA-AAACATATTTATTTAAATTT
1 AATTATAAA-ATATATATTAAAATTT
2018506 AATTATAAAATATATATTAAAAT
1 AATTATAAAATATATATTAAAAT
2018529 AAATAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTATAAAATATATATTAAAATTT
Found at i:2021393 original size:23 final size:23
Alignment explanation
Indices: 2021366--2021411 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2021356 TCCTAAGATC
2021366 ACCTCCACAACTTCCTCAATGTG
1 ACCTCCACAACTTCCTCAATGTG
2021389 ACCTCCACAACTTCCTCAATGTG
1 ACCTCCACAACTTCCTCAATGTG
2021412 GAAGTTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.39, G:0.09, T:0.26
Consensus pattern (23 bp):
ACCTCCACAACTTCCTCAATGTG
Found at i:2026907 original size:18 final size:18
Alignment explanation
Indices: 2026884--2027030 Score: 222
Period size: 18 Copynumber: 8.2 Consensus size: 18
2026874 TACGACCGTT
*
2026884 TACGGTACTATTCACATA
1 TACGGTACTATTCACGTA
2026902 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
2026920 TACGGTACTATTTACGTA
1 TACGGTACTATTCACGTA
* *
2026938 TACGGTACTATTTACATA
1 TACGGTACTATTCACGTA
2026956 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
2026974 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
2026992 TACAGCACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
2027010 TACGATACTGTTCACGTA
1 TACGGTACTATTCACGTA
2027028 TAC
1 TAC
2027031 AGTAGTTGGG
Statistics
Matches: 118, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 118 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:2031699 original size:75 final size:73
Alignment explanation
Indices: 2031611--2031782 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 73
2031601 GGTTTTCCTC
*** * * **
2031611 ATTGAAATACCATACCTACATTTTTTAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
2031675 TCAGTATGG
65 TCAGTATGG
*
2031684 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
2031749 CTCAGTATGG
64 CTCAGTATGG
2031759 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
2031783 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 57 0.65
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:2031780 original size:35 final size:35
Alignment explanation
Indices: 2031616--2031782 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
2031606 TCCTCATTGA
*** *
2031616 AATACCATACCTACATTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
2031651 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
2031691 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
2031726 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
2031761 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
2031783 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
35 88 0.75
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:2039179 original size:35 final size:35
Alignment explanation
Indices: 2039112--2039279 Score: 185
Period size: 35 Copynumber: 4.6 Consensus size: 35
2039102 TCCTCATTGA
*** *
2039112 AATACCATACCTACATTTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACA-TTTCACAACTCAGTAT-GGAT
* **
2039148 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
2039188 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
2039223 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
2039258 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
2039280 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 9, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
35 74 0.63
36 14 0.12
39 3 0.03
40 27 0.23
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:2039238 original size:75 final size:73
Alignment explanation
Indices: 2039107--2039279 Score: 210
Period size: 75 Copynumber: 2.4 Consensus size: 73
2039097 GGTTTTCCTC
*** * * **
2039107 ATTGAAATACCATACCTACATTTTTTTAACTCGGTATGGGAAATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACA-TTTCACAACTCAGTATGGGAAATACCATACCTACATTTCACAAC
2039172 TCAGTATGG
65 TCAGTATGG
*
2039181 ATTTGATAATACCATACCTACATTTCACAGCTCAGTAT-GGATAATACCATACCTACATTTCACA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGGA-AATACCATACCTACATTTCACA
2039245 ACTCAGTATGG
63 ACTCAGTATGG
2039256 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
2039280 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 2 0.02
74 4 0.05
75 46 0.52
76 15 0.17
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGGAAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:2047177 original size:51 final size:53
Alignment explanation
Indices: 2047114--2047214 Score: 134
Period size: 55 Copynumber: 1.9 Consensus size: 53
2047104 CATTGAAATT
* *
2047114 AAATCCACTTAAA-TG-TGCTTTGGTTATTTTTAGATAATCATTAAATTTGTG
1 AAATCCAATTAAACTGTTGCTTTAGTTATTTTTAGATAATCATTAAATTTGTG
**
2047165 AAATCCAATTAAATCTGTTTTTTTTAGTTATTTTTAGATAATCATTAAAT
1 AAATCCAATTAAA-CTG-TTGCTTTAGTTATTTTTAGATAATCATTAAAT
2047215 AATAAATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 12 0.29
53 2 0.05
55 28 0.67
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.48
Consensus pattern (53 bp):
AAATCCAATTAAACTGTTGCTTTAGTTATTTTTAGATAATCATTAAATTTGTG
Found at i:2051097 original size:23 final size:23
Alignment explanation
Indices: 2051032--2051098 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
2051022 TTTACACCTT
*
2051032 ATAATTTAATTATAATTTT-TTC
1 ATAAATTAATTATAATTTTATTC
* *
2051054 ATAAATTAAAATATAAATTTATT-
1 ATAAATT-AATTATAATTTTATTC
*
2051077 ATATATTAATTTATAATTTTAT
1 ATAAATTAA-TTATAATTTTAT
2051099 ATTTTTAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
22 8 0.22
23 26 0.72
24 2 0.06
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (23 bp):
ATAAATTAATTATAATTTTATTC
Found at i:2051343 original size:19 final size:19
Alignment explanation
Indices: 2051319--2051357 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2051309 TGGCCCTTGT
2051319 CTACTCTCCTGGATTCGTC
1 CTACTCTCCTGGATTCGTC
*
2051338 CTACTCTCTTGGATTCGTC
1 CTACTCTCCTGGATTCGTC
2051357 C
1 C
2051358 GACGGTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.10, C:0.36, G:0.15, T:0.38
Consensus pattern (19 bp):
CTACTCTCCTGGATTCGTC
Found at i:2051366 original size:19 final size:19
Alignment explanation
Indices: 2051328--2051375 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2051318 TCTACTCTCC
* *
2051328 TGGATTCGTCCTACTCTCT
1 TGGATTCGTCCGACGCTCT
*
2051347 TGGATTCGTCCGACGGTCT
1 TGGATTCGTCCGACGCTCT
*
2051366 TAGATTCGTC
1 TGGATTCGTC
2051376 TTTATCCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.38
Consensus pattern (19 bp):
TGGATTCGTCCGACGCTCT
Found at i:2059076 original size:31 final size:32
Alignment explanation
Indices: 2059012--2059080 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
2059002 TTAACAATCA
2059012 AGTGACTTAAATAAAAAATTTTTAAATAGTTT
1 AGTGACTTAAATAAAAAATTTTTAAATAGTTT
* * * *
2059044 AGTGATTTAAAT-AAAAGTTTTTTAATATTTT
1 AGTGACTTAAATAAAAAATTTTTAAATAGTTT
2059075 AGTGAC
1 AGTGAC
2059081 CAATTTGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 21 0.66
32 11 0.34
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.43
Consensus pattern (32 bp):
AGTGACTTAAATAAAAAATTTTTAAATAGTTT
Found at i:2060773 original size:36 final size:36
Alignment explanation
Indices: 2060726--2060834 Score: 218
Period size: 36 Copynumber: 3.0 Consensus size: 36
2060716 TTAATTGGGC
2060726 TAAATTAATATTTTCACTATTAGTTTTTGAAAGGAG
1 TAAATTAATATTTTCACTATTAGTTTTTGAAAGGAG
2060762 TAAATTAATATTTTCACTATTAGTTTTTGAAAGGAG
1 TAAATTAATATTTTCACTATTAGTTTTTGAAAGGAG
2060798 TAAATTAATATTTTCACTATTAGTTTTTGAAAGGAG
1 TAAATTAATATTTTCACTATTAGTTTTTGAAAGGAG
2060834 T
1 T
2060835 CTTTTGGGTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 73 1.00
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.45
Consensus pattern (36 bp):
TAAATTAATATTTTCACTATTAGTTTTTGAAAGGAG
Found at i:2065969 original size:187 final size:187
Alignment explanation
Indices: 2065651--2066007 Score: 633
Period size: 187 Copynumber: 1.9 Consensus size: 187
2065641 CTTATTACAT
* * *
2065651 TGATTTAAGTTTTGCAAATCCTTCTTACTCTATATTATGTGATGCATTTAGTTCTATTAACCATG
1 TGATTTAAGTTTTGCAAATCCTTCCTACTCTATATTACGTGATGCATGTAGTTCTATTAACCATG
**
2065716 TCTCATGCTAAACCGATCCATTTTTATTTGTTATATCTATTTGTACTATGAATTTGATCCGTTAT
66 TCTCATGCTAAACCGATCCATTTTTATTTGTTATATCTATTTGTACTACAAATTTGATCCGTTAT
*
2065781 ATTTGGCATTTATCATGGTAATGGAATTGTTCTACAATATATTCTCCTCGGAGGATG
131 ATCTGGCATTTATCATGGTAATGGAATTGTTCTACAATATATTCTCCTCGGAGGATG
2065838 TGATTTAAGTTTTGCAAATCCTTCCTACTCTATATTACGTGATGCATGTAGTTCTATTAACCATG
1 TGATTTAAGTTTTGCAAATCCTTCCTACTCTATATTACGTGATGCATGTAGTTCTATTAACCATG
* *
2065903 TCTCATGCTAAACCGATCCATTTTTCTTTGTTATATCTATTTGTACTACAAATTTGATCTGTTAT
66 TCTCATGCTAAACCGATCCATTTTTATTTGTTATATCTATTTGTACTACAAATTTGATCCGTTAT
*
2065968 ATCTGGCATTTATCATGGTAATGGAATTGTTTTACAATAT
131 ATCTGGCATTTATCATGGTAATGGAATTGTTCTACAATAT
2066008 GTGTCCGACA
Statistics
Matches: 161, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
187 161 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (187 bp):
TGATTTAAGTTTTGCAAATCCTTCCTACTCTATATTACGTGATGCATGTAGTTCTATTAACCATG
TCTCATGCTAAACCGATCCATTTTTATTTGTTATATCTATTTGTACTACAAATTTGATCCGTTAT
ATCTGGCATTTATCATGGTAATGGAATTGTTCTACAATATATTCTCCTCGGAGGATG
Found at i:2066506 original size:230 final size:230
Alignment explanation
Indices: 2066103--2066528 Score: 667
Period size: 230 Copynumber: 1.9 Consensus size: 230
2066093 ACACTGGACA
2066103 ACATGCCAATGTCCAAATATACATCGGACATGAGTGTTGGAATTGAGTACTTAAAAGAAAAATGA
1 ACATGCCAATGTCCAAATATACATCGGACATGAGTGTTGGAATTGAGTACTTAAAAGAAAAATGA
* * * * *
2066168 AGAGTCGGTGCAACATAGGTCTTACACGAAGGAAACTTGATTTATGTCTTATATGTAGTCATGTT
66 AGAGCCAGAGCAACATAGGTCTTACACAAAGGAAACTTGATTTATGTCTTATATCTAGTCATGTT
* * * *
2066233 CTTGGTATTCTTAACTTTTTGTTTTAATGGGAATTTTTTATATCTCCGGTGACTTTTGCCTTGTT
131 CTCGGCATTCTTAACTTTATGTTTTAATGGGAATTTTTTATATCTCCGGTGACTTTCGCCTTGTT
2066298 GGTCCCTTGCAAACCGATGTCTAGATATACACTGT
196 GGTCCCTTGCAAACCGATGTCTAGATATACACTGT
* * *
2066333 ACATGCCAATGTCCAAATATACGTCGGACATGAGTGTTGGAATTGGGTGCTTAAAAGAAAAATGA
1 ACATGCCAATGTCCAAATATACATCGGACATGAGTGTTGGAATTGAGTACTTAAAAGAAAAATGA
* *
2066398 AGAGCCAGAGTAACATAGGTCTTACACAAAGGAAACTTGATTTATGTCTTATATCTAGTCGTGTT
66 AGAGCCAGAGCAACATAGGTCTTACACAAAGGAAACTTGATTTATGTCTTATATCTAGTCATGTT
* * *
2066463 CTCGGCCTTCTTAAC-TTATGTTTTAAT-GGAATTTTTGTTATATCTCTGGTGACTTTCGGCTTG
131 CTCGGCATTCTTAACTTTATGTTTTAATGGGAA-TTTT-TTATATCTCCGGTGACTTTCGCCTTG
2066526 TTG
194 TTG
2066529 TGGTCTCCTC
Statistics
Matches: 177, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
228 4 0.02
229 15 0.08
230 158 0.89
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (230 bp):
ACATGCCAATGTCCAAATATACATCGGACATGAGTGTTGGAATTGAGTACTTAAAAGAAAAATGA
AGAGCCAGAGCAACATAGGTCTTACACAAAGGAAACTTGATTTATGTCTTATATCTAGTCATGTT
CTCGGCATTCTTAACTTTATGTTTTAATGGGAATTTTTTATATCTCCGGTGACTTTCGCCTTGTT
GGTCCCTTGCAAACCGATGTCTAGATATACACTGT
Found at i:2071918 original size:22 final size:21
Alignment explanation
Indices: 2071883--2071941 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
2071873 ATATAATTTT
*
2071883 AATATATGAATAAATTATAT-TA
1 AATAT-TGAATAAA-AATATGTA
2071905 AATATTGAACTAAAAATATGTA
1 AATATTGAA-TAAAAATATGTA
* *
2071927 AATATTAAAAAAAAA
1 AATATTGAATAAAAA
2071942 CTAAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 13 0.41
22 19 0.59
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (21 bp):
AATATTGAATAAAAATATGTA
Found at i:2071940 original size:21 final size:21
Alignment explanation
Indices: 2071899--2071941 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2071889 TGAATAAATT
**
2071899 ATATTAAATATTGAACTAAAA
1 ATATTAAATATTGAAAAAAAA
2071920 ATATGTAAATATT-AAAAAAAA
1 ATAT-TAAATATTGAAAAAAAA
2071941 A
1 A
2071942 CTAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (21 bp):
ATATTAAATATTGAAAAAAAA
Found at i:2072655 original size:17 final size:16
Alignment explanation
Indices: 2072630--2072660 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2072620 TAATTCTTTT
*
2072630 TTTTTAAATTTAAATA
1 TTTTTAAAATTAAATA
2072646 TTTTTAAAATTAAAT
1 TTTTTAAAATTAAAT
2072661 TACGTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTTAAAATTAAATA
Found at i:2075237 original size:28 final size:28
Alignment explanation
Indices: 2075184--2075238 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
2075174 GATGACACGA
*
2075184 ATTTTTATTATAAAAATTTATCCAAACT
1 ATTTTTATTATAAAAAGTTATCCAAACT
* *
2075212 ATTTTTGTTGTAATAAAGTTAT-CAAAC
1 ATTTTTATTATAA-AAAGTTATCCAAAC
2075239 AAAATTAGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.45
Consensus pattern (28 bp):
ATTTTTATTATAAAAAGTTATCCAAACT
Found at i:2091032 original size:2 final size:2
Alignment explanation
Indices: 2091022--2091060 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2091012 TACTAAAAAA
* * *
2091022 AT AT TT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2091061 CCGGGTCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2091397 original size:14 final size:15
Alignment explanation
Indices: 2091380--2091418 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
2091370 GAGAAAGGAG
2091380 AAGAAAAAAAGAA-A
1 AAGAAAAAAAGAACA
*
2091394 AAGAAAGAAAGAACA
1 AAGAAAAAAAGAACA
2091409 AA-AAAAAAAG
1 AAGAAAAAAAG
2091419 GTAATGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAGAACA
Found at i:2091414 original size:28 final size:31
Alignment explanation
Indices: 2091356--2091418 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 31
2091346 GGTGTGTAGG
* * *
2091356 AAAGAAAAGAGAGAGAGAAAGGAGAAGAAAA
1 AAAGAAAAGAGAGAGAGAAAGAACAAAAAAA
2091387 AAAGAAAA-AGA-A-AGAAAGAACAAAAAAA
1 AAAGAAAAGAGAGAGAGAAAGAACAAAAAAA
2091415 AAAG
1 AAAG
2091419 GTAATGTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.59
29 1 0.03
30 3 0.10
31 8 0.28
ACGTcount: A:0.75, C:0.02, G:0.24, T:0.00
Consensus pattern (31 bp):
AAAGAAAAGAGAGAGAGAAAGAACAAAAAAA
Found at i:2091957 original size:104 final size:100
Alignment explanation
Indices: 2091719--2092045 Score: 326
Period size: 102 Copynumber: 3.2 Consensus size: 100
2091709 TAAATTGTTA
* * *** *
2091719 TGTTTTGTGAGTTTTTAGTAATGTAAATTTTTAAAAAAAAAAAAATTATAGTTATTTTGTTAGTA
1 TGTTTTGTGATTTTTTAGTAATGT-AATTTTTTAAAAATTTATAATTAT--TTATTTTGTTAGTA
*
2091784 GTTTATGATTAGGTTATAAATTGTTAGTG--T-TTT-G
63 ATTTATGATTAGGTTATAAATTGTTAGTGTTTATTTAG
*
2091818 TGTTTTGTTATTTTTTAGTAATGTAATTTCGTTTTTAAAAATGTTATAAGTTATTTATTTTGTTA
1 TGTTTTGTGATTTTTTAGTAATGTAA--T--TTTTTAAAAAT-TTATAA-TTATTTATTTTGTTA
2091883 GTAATTTATGGGATTAGGTTATAAATTGTTAGTGTTTAGTTTAG
60 GTAATTTAT--GATTAGGTTATAAATTGTTAGTGTTTA-TTTAG
* * **
2091927 GGTTTTGTGATTTTTTAGTAATATAATTTTTTTAAATAATTT-T-A-TAGCTATTTTGTTAGTAA
1 TGTTTTGTGATTTTTTAGTAATGTAA-TTTTTTAAA-AATTTATAATTATTTATTTTGTTAGTAA
* *
2091989 TTTAAGATTAAGTTATATAAATTGTTAGTGTTTAATTTAG
64 TTTATGATT-AGGT-TATAAATTGTTAGTGTTT-ATTTAG
2092029 TGTTTTGTGATTTTTTA
1 TGTTTTGTGATTTTTTA
2092046 ATGTAAATTT
Statistics
Matches: 195, Mismatches: 16, Indels: 31
0.81 0.07 0.13
Matches are distributed among these distances:
98 2 0.01
99 22 0.11
100 5 0.03
101 3 0.02
102 87 0.45
103 4 0.02
104 28 0.14
105 1 0.01
106 11 0.06
107 3 0.02
108 5 0.03
109 24 0.12
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (100 bp):
TGTTTTGTGATTTTTTAGTAATGTAATTTTTTAAAAATTTATAATTATTTATTTTGTTAGTAATT
TATGATTAGGTTATAAATTGTTAGTGTTTATTTAG
Found at i:2094114 original size:33 final size:32
Alignment explanation
Indices: 2094077--2094170 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 32
2094067 TCCAGGCTCA
*
2094077 TATCCACCTCAGCACTCCACTCATCTCGACTCG
1 TATCCACCTC-GTACTCCACTCATCTCGACTCG
* * *
2094110 TATCCACCATCGTACTCCACT-ACTCCCGGCTTG
1 TATCCACC-TCGTACTCCACTCA-TCTCGACTCG
* *
2094143 TATCCACCGCCGTACTCCACTCCTCTCG
1 TATCCACC-TCGTACTCCACTCATCTCG
2094171 GCTTAGGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
32 1 0.02
33 47 0.94
34 2 0.04
ACGTcount: A:0.18, C:0.46, G:0.11, T:0.26
Consensus pattern (32 bp):
TATCCACCTCGTACTCCACTCATCTCGACTCG
Found at i:2094173 original size:33 final size:33
Alignment explanation
Indices: 2094090--2094174 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 33
2094080 CCACCTCAGC
* * * *
2094090 ACTCCACTCATCTCGACTCGTATCCACCATCGT
1 ACTCCACTCCTCTCGGCTTGTATCCACCACCGT
* * *
2094123 ACTCCACTACTCCCGGCTTGTATCCACCGCCGT
1 ACTCCACTCCTCTCGGCTTGTATCCACCACCGT
2094156 ACTCCACTCCTCTCGGCTT
1 ACTCCACTCCTCTCGGCTT
2094175 AGGTTTATCG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.16, C:0.45, G:0.12, T:0.27
Consensus pattern (33 bp):
ACTCCACTCCTCTCGGCTTGTATCCACCACCGT
Found at i:2098512 original size:20 final size:20
Alignment explanation
Indices: 2098489--2098527 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2098479 TCAAATTCGA
2098489 GGTTTAAGTTTAAGATTCAT
1 GGTTTAAGTTTAAGATTCAT
*
2098509 GGTTTAGGTTTAAGATTCA
1 GGTTTAAGTTTAAGATTCA
2098528 AAGTTTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (20 bp):
GGTTTAAGTTTAAGATTCAT
Found at i:2098533 original size:20 final size:20
Alignment explanation
Indices: 2098490--2098536 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2098480 CAAATTCGAG
**
2098490 GTTTAAGTTTAAGATTCATG
1 GTTTAAGTTTAAGATTCAAA
*
2098510 GTTTAGGTTTAAGATTCAAA
1 GTTTAAGTTTAAGATTCAAA
2098530 GTTTAAG
1 GTTTAAG
2098537 ACTCAGGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (20 bp):
GTTTAAGTTTAAGATTCAAA
Found at i:2102025 original size:31 final size:31
Alignment explanation
Indices: 2101990--2102049 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2101980 TTATAAAATG
* * *
2101990 GTTATTGAATTGTTCTAAAATTTTTATTTAA
1 GTTATTGAACTATTCGAAAATTTTTATTTAA
*
2102021 GTTATTGAACTATTCGAAAGTTTTTATTT
1 GTTATTGAACTATTCGAAAATTTTTATTT
2102050 GATTCAGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (31 bp):
GTTATTGAACTATTCGAAAATTTTTATTTAA
Found at i:2105207 original size:16 final size:17
Alignment explanation
Indices: 2105186--2105218 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2105176 AATGTCTCAT
*
2105186 ATTATTTTTTTA-ATTA
1 ATTATTATTTTATATTA
2105202 ATTATTATTTTATATTA
1 ATTATTATTTTATATTA
2105219 TCTATGGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATTATTTTATATTA
Found at i:2106345 original size:15 final size:15
Alignment explanation
Indices: 2106321--2106351 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2106311 AAAAGTTTAA
2106321 AAAAAAAATATTTTG
1 AAAAAAAATATTTTG
*
2106336 AAAAACAATATTTTG
1 AAAAAAAATATTTTG
2106351 A
1 A
2106352 GCCCCTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (15 bp):
AAAAAAAATATTTTG
Found at i:2109947 original size:19 final size:19
Alignment explanation
Indices: 2109923--2109986 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
2109913 AACTCATACC
*
2109923 ATTTATACATTCTATCAAT
1 ATTTATACATTCTATAAAT
* * * *
2109942 ATTTATGCAAAATATATAAAC
1 ATTTAT--ACATTCTATAAAT
*
2109963 ATTTATACATTCTATTAAT
1 ATTTATACATTCTATAAAT
2109982 ATTTA
1 ATTTA
2109987 CGCAAAATAT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
19 19 0.58
21 14 0.42
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (19 bp):
ATTTATACATTCTATAAAT
Found at i:2109970 original size:40 final size:40
Alignment explanation
Indices: 2109922--2110005 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 40
2109912 CAACTCATAC
*
2109922 CATTTATACATTCTATCAATATTTATGCAAAATATATAAA
1 CATTTATACATTCTATCAATATTTACGCAAAATATATAAA
* *
2109962 CATTTATACATTCTATTAATATTTACGCAAAATATGTAAA
1 CATTTATACATTCTATCAATATTTACGCAAAATATATAAA
2110002 CATT
1 CATT
2110006 CTCTCATACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (40 bp):
CATTTATACATTCTATCAATATTTACGCAAAATATATAAA
Found at i:2112018 original size:29 final size:29
Alignment explanation
Indices: 2111963--2112018 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
2111953 TATATTAGAA
* * *
2111963 TTATATTGTATAAAAATTATAATATAAAT
1 TTATATTGTATAAAAATAAAAAAATAAAT
* *
2111992 TTATATTGTTTTAAAATAAAAAAATAA
1 TTATATTGTATAAAAATAAAAAAATAA
2112019 CAGAAAACAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (29 bp):
TTATATTGTATAAAAATAAAAAAATAAAT
Found at i:2115644 original size:18 final size:18
Alignment explanation
Indices: 2115621--2115663 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2115611 GAATAGGTCT
2115621 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
2115639 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
2115657 TTAATTA
1 TTAATTA
2115664 TACATTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:2117703 original size:27 final size:27
Alignment explanation
Indices: 2117665--2117730 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
2117655 TTTTTTTGGG
2117665 GGGTTAGG-TTTTTC-TTTTTTTTTTT
1 GGGTTAGGTTTTTTCTTTTTTTTTTTT
2117690 GGGTTAGGTTTTTTCTTTTTTTTTTTT
1 GGGTTAGGTTTTTTCTTTTTTTTTTTT
*
2117717 TGGTTAGGTTTTTT
1 GGGTTAGGTTTTTT
2117731 TTTGGGGGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 8 0.21
26 6 0.16
27 24 0.63
ACGTcount: A:0.05, C:0.03, G:0.21, T:0.71
Consensus pattern (27 bp):
GGGTTAGGTTTTTTCTTTTTTTTTTTT
Found at i:2118604 original size:31 final size:29
Alignment explanation
Indices: 2118552--2118613 Score: 97
Period size: 31 Copynumber: 2.1 Consensus size: 29
2118542 TTTTGAAAAA
2118552 CAGAAATTAAAAACTCAACTCAACTCTCG
1 CAGAAATTAAAAACTCAACTCAACTCTCG
*
2118581 CAGAAATTAAAAAGCTTCAACTCACCTCTCG
1 CAGAAATTAAAAA-C-TCAACTCAACTCTCG
2118612 CA
1 CA
2118614 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 13 0.43
30 1 0.03
31 16 0.53
ACGTcount: A:0.42, C:0.29, G:0.08, T:0.21
Consensus pattern (29 bp):
CAGAAATTAAAAACTCAACTCAACTCTCG
Found at i:2118726 original size:13 final size:13
Alignment explanation
Indices: 2118708--2118741 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2118698 TGAGTTGATT
2118708 TTTGAAAACAGAA
1 TTTGAAAACAGAA
*
2118721 TTTGAAAACAGAT
1 TTTGAAAACAGAA
2118734 TTTGAAAA
1 TTTGAAAA
2118742 TACCTCGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (13 bp):
TTTGAAAACAGAA
Found at i:2118823 original size:165 final size:165
Alignment explanation
Indices: 2118597--2119964 Score: 1361
Period size: 165 Copynumber: 8.2 Consensus size: 165
2118587 TTAAAAAGCT
*
2118597 TCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAAAAAAAAGAAATTGAAAATA-CTC
1 TCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTTG----AAAAACAGAAATTGAAAATACCTC
* * * *
2118661 AGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGA-TTTTTGAAA-ACAGAATTT
61 AG-GCGTGATCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGACAGAAATT
** * * *
2118724 GAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGC
125 GAAAACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGC
* * * *
2118765 TCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCTCAGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTG--AAAATACCTCAG-
* * *
2118830 GTGTGATCTGAA-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT-------TGAAA--G-
63 GCGTGATC-CAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGACAGAAATTGA
* * * *
2118884 --ACAGAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGC
127 AAACAGAAATTGAAAATACCTCGGCGTGTGA-CCTGAGGC
* *
2118921 TCAACTCACCTCTCGCAATATAAGTTGA-TTTTTTG-AAAACAGAAATTGAAAATACCTCA-ACG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGGCG
** ** *
2118983 TG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAA-ACAGAAATTGAAAA
66 TGATC-CAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGACAGAAATTGAAAA
* *
2119045 -ATGGAAATTGAAAATACCTCGACGTGTGATCTGAGGC
130 CA--GAAATTGAAAATACCTCGGCGTGTGACCTGAGGC
* *
2119082 TCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAATATAAATTGAAGTAAAAAAAATAC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATT---G-----AAAATAC
* *
2119145 CTCAGTGTGTGATCTGAA-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAG
58 CTCAG-GCGTGATC-CAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAGACAG
* **
2119209 AAATTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGATATGAGGC
120 AAATTG-AAAACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGC
* * *
2119256 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATAGCTCAGCGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAG-GC
* * *
2119321 GTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTTTTGAAAGGCAGAAATTG
65 GTGATCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTGAAAGACAGAAATTG
*
2119386 AAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGC
126 -AAAACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGC
* * * * * *
2119427 TCAACTCGCCGCTCGCAATACGAGTTGACTTTTTTG-ACAACAGAAATTGAAATTACCTCA-GCG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGGCG
* *
2119490 TG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGGCAGAAATTGAA
66 TGATCC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTGAAAGACAGAAATTGAA
*
2119554 AACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGC
128 AACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGC
* * * * *
2119592 TCAACTCGCCACTCGCAATACGAGTTGATTTTTTTG-ACAACAGAAATTGAAATTACCTCA-GCG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGGCG
*
2119655 TG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAA
66 TGATCC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAGACAGAAATTG-AA
*
2119719 AACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGC
128 AACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGC
* * *
2119757 TCAACTCGCCTCTCGCAATACGAGTTGATTCTTTCAAAAACATAATAATGAAAACAGAAATTGAA
1 TCAACTCACCTCTCGCAATATGAGTTGATT-TTT--------T--TGA--AAAACAGAAATTGAA
* * * *
2119822 AATACCTC-GGCGTGA-CCTAAGGCTCAACTCACCTCTCGCAATATGAGCTGATTCTTTCAAAAA
53 AATACCTCAGGCGTGATCC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGA
* * *
2119885 CATAATAATGAAGACAGAAATTGAAAATACCTCGGC--GTGACCTGAGGC
117 CAGAA-ATTGAAAACAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGC
*
2119933 TCAACTCACCTCTCGCAATATGAGCTGATTTT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTT
2119965 GAAAAAGTAG
Statistics
Matches: 1042, Mismatches: 95, Indels: 119
0.83 0.08 0.09
Matches are distributed among these distances:
149 8 0.01
150 31 0.03
152 11 0.01
154 11 0.01
155 11 0.01
156 51 0.05
157 3 0.00
159 2 0.00
160 8 0.01
161 66 0.06
163 12 0.01
164 22 0.02
165 215 0.21
166 65 0.06
167 20 0.02
168 107 0.10
169 11 0.01
170 19 0.02
171 123 0.12
172 4 0.00
173 9 0.01
174 71 0.07
175 6 0.01
176 56 0.05
178 37 0.04
179 63 0.06
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (165 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGGCG
TGATCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAGACAGAAATTGAAAAC
AGAAATTGAAAATACCTCGGCGTGTGACCTGAGGC
Found at i:2118929 original size:77 final size:75
Alignment explanation
Indices: 2118721--2119044 Score: 329
Period size: 79 Copynumber: 4.3 Consensus size: 75
2118711 GAAAACAGAA
** * * * *
2118721 TTTGAAAACAGATTTTGAAAATACCTC-GACATGTGA-CCCGAGGCTCAACTCACATCTCGCAAT
1 TTTGAAAACAGAAATTGAAAATACCTCAGGC--GTGATCTCAAGGCTCAACTCACCTCTCGCAAT
*
2118784 GTGAGTTGATTTT
64 ATGAGTTGA-TTT
* * * *
2118797 TTTGAAAAATATAAATTGAAAAAATACCTCAGTGTGTGATCTGAA-GCTCAACTCACCTCTCGCA
1 TTTG-AAAACAGAAATTG--AAAATACCTCAG-GCGTGATCTCAAGGCTCAACTCACCTCTCGCA
2118861 ATATGAGTTGATTTT
62 ATATGAGTTGA-TTT
* *
2118876 TTTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGC-CAAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAA-ACAGAAATTGAAAATACCTCAG-GCGTGATCTCAAGGCTCAACTCACCTCTCGCAAT
*
2118940 ATAAGTTGATTT
64 ATGAGTTGATTT
* ** **
2118952 TTTGAAAACAGAAATTGAAAATACCTCA-ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATAT
1 TTTGAAAACAGAAATTGAAAATACCTCAGGCGTGATCTCAAGGCTCAACTCACCTCTCGCAATAT
*
2119015 GAGTTGA-AT
66 GAGTTGATTT
2119024 TTTGAAAACAGAAATTGAAAA
1 TTTGAAAACAGAAATTGAAAA
2119045 ATGGAAATTG
Statistics
Matches: 211, Mismatches: 28, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
72 23 0.11
73 33 0.16
75 20 0.09
76 16 0.08
77 55 0.26
78 3 0.01
79 58 0.27
80 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (75 bp):
TTTGAAAACAGAAATTGAAAATACCTCAGGCGTGATCTCAAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTT
Found at i:2119177 original size:83 final size:85
Alignment explanation
Indices: 2118957--2119979 Score: 716
Period size: 88 Copynumber: 12.0 Consensus size: 85
2118947 GATTTTTTGA
* * * **
2118957 AAACAGAAATTGAAAATACCTCAACGTGT-CT-TGAGGCTCAACTCATTTCTCGCAATATGAGTT
1 AAACGGAAA-TGAAAATACCTC-GCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
2119020 GAATTTTG-AAAACAGAAATTG
64 GATTTTTGAAAAACAGAAATTG
*
2119041 AAAAATGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 --AAACGGAAA-TGAAAATACCTCG-CGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAG
* *
2119106 TTGATTTTTGAAAAATATAAATTG
62 TTGATTTTTGAAAAACAGAAATTG
* * * *
2119130 -AA-GTAAA-AAAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAACGGAAATGAAAATACCTC-GCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
2119192 ATTTTTTTGAAAGACAGAAATTG
65 A--TTTTTGAAAAACAGAAATTG
*
2119215 AAAAACGGAAATTGAAAATACCTCGGCGTGTGATATGAGGCTCAACTCACCTCTCGCAATATGAG
1 --AAACGGAAA-TGAAAATACCTC-GCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAG
*** *
2119280 TTGATTTTT-TTGAA-AG--A--C
62 TTGATTTTTGAAAAACAGAAATTG
* * * * ** *
2119298 AAA---AATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTCG
1 AAACGGAAATGAAAATACCTC-GCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
**
2119360 ATTTTTTTTTTGAAAGGCAGAAATTG
65 A-----TTTTTGAAAAACAGAAATTG
* * * *
2119386 AAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATACGAG
1 --AAACGGAAA-TGAAAATACCTC-GCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAG
*
2119451 TTGACTTTTTTG-ACAACAGAAATT-
62 TTGA--TTTTTGAAAAACAGAAATTG
*
2119475 -----GAAAT-----TACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAACGGAAATGAAAATACCTC-GCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
**
2119528 ATTTTTTTTGAAAGGCAGAAATTG
65 A---TTTTTGAAAAACAGAAATTG
* * * *
2119552 AAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGT
1 -AAACGGAAA-TGAAAATACCTC-GCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGT
*
2119617 TGATTTTTTTG-ACAACAGAAATT-
63 TGA--TTTTTGAAAAACAGAAATTG
*
2119640 -----GAAAT-----TACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAACGGAAATGAAAATACCTC-GCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
2119693 ATTTTTTTGAAAGACAGAAATTG
65 A--TTTTTGAAAAACAGAAATTG
* * *
2119716 AAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAG
1 --AAACGGAAA-TGAAAATACCTC-GCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAG
* * *
2119781 TTGATTCTTTCAAAAACATAATAATG
62 TTGATT-TTTGAAAAACAGAA-ATTG
* * * * *
2119807 AAAACAGAAATTGAAAATACCTCG-GCGTGACCTAAGGCTCAACTCACCTCTCGCAATATGAGCT
1 -AAACGGAAA-TGAAAATACCTCGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* * *
2119871 GATTCTTTCAAAAACATAATAATG
64 GATT-TTTGAAAAACAGAA-ATTG
* * * *
2119895 AAGACAGAAATTGAAAATACCTCG-GCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGCT
1 AA-ACGGAAA-TGAAAATACCTCGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
2119959 GA-TTTTGAAAAAGTAGAAATT
64 GATTTTTGAAAAA-CAGAAATT
2119980 AAAAGGTTCA
Statistics
Matches: 773, Mismatches: 96, Indels: 136
0.77 0.10 0.14
Matches are distributed among these distances:
74 74 0.10
75 17 0.02
76 33 0.04
77 49 0.06
78 2 0.00
81 5 0.01
82 13 0.02
83 59 0.08
84 5 0.01
85 22 0.03
86 38 0.05
87 9 0.01
88 161 0.21
89 56 0.07
90 53 0.07
91 128 0.17
93 2 0.00
94 47 0.06
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (85 bp):
AAACGGAAATGAAAATACCTCGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTGAAAAACAGAAATTG
Found at i:2119217 original size:14 final size:14
Alignment explanation
Indices: 2119198--2119232 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2119188 GTTGATTTTT
*
2119198 TTGAAAGACAGAAA
1 TTGAAAAACAGAAA
*
2119212 TTGAAAAACGGAAA
1 TTGAAAAACAGAAA
2119226 TTGAAAA
1 TTGAAAA
2119233 TACCTCGGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:2119259 original size:91 final size:89
Alignment explanation
Indices: 2118956--2119309 Score: 438
Period size: 91 Copynumber: 4.0 Consensus size: 89
2118946 TGATTTTTTG
* * **
2118956 AAAACAGAAATTGAAAATACCTCAACGTGT-CT-TGAGGCTCAACTCATTTCTCGCAATATGAGT
1 AAAACGGAAATTGAAAATACCTCAACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGT
*
2119019 TGAATTTTGAAA-ACAGAAATTGA
66 TGATTTTTGAAAGACAGAAATTGA
* *
2119042 AAAATGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAACGGAAATTGAAAATACCTCAACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * *
2119107 TGATTTTTGAAAAATATAAATTG-
66 TGATTTTTGAAAGACAGAAATTGA
* * ** *
2119130 --AA-GTAAA--AAAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGT
1 AAAACGGAAATTGAAAATACCTCAACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGT
2119190 TGATTTTTTTGAAAGACAGAAATTGA
66 TGA--TTTTTGAAAGACAGAAATTGA
** *
2119216 AAAACGGAAATTGAAAATACCTCGGCGTGTGATATGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAACGGAAATTGAAAATACCTCAACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGT
*
2119281 TGATTTTTTTGAAAGACAAAAATTGA
66 TGA--TTTTTGAAAGACAGAAATTGA
2119307 AAA
1 AAA
2119310 TAGCTCAGCG
Statistics
Matches: 232, Mismatches: 25, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
83 51 0.22
85 21 0.09
86 29 0.12
87 1 0.00
88 42 0.18
89 12 0.05
91 76 0.33
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (89 bp):
AAAACGGAAATTGAAAATACCTCAACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTGAAAGACAGAAATTGA
Found at i:2119518 original size:74 final size:76
Alignment explanation
Indices: 2119393--2119719 Score: 238
Period size: 74 Copynumber: 4.1 Consensus size: 76
2119383 TTGAAAAACG
* *
2119393 GAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATACGAGTTGA-CT
1 GAAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATCT
2119457 TTTTTGACAA-CA
65 TTTTTGA-AAGCA
* * * *
2119469 GAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATCTT
2119533 TTTTGAAAGGCA
66 TTTTGAAA-GCA
* ** * **** * * *
2119545 GAAATTGAAAACGGAAAT-TGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCA
1 GAAATTGAAAA--TACCTCAGCGTGTACCT----GAG-G--CTCA-ACTC-AC-CG---CTCGCA
2119609 ATACGAGTTGAT-TTTTTTGACAA-CA
51 ATACGAGTTGATCTTTTTTGA-AAGCA
* * *
2119634 GAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TT
1 GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATCTT
2119697 TTTTGAAAGACA
66 TTTTGAAAG-CA
2119709 GAAATTGAAAA
1 GAAATTGAAAA
2119720 ACGGAAATTG
Statistics
Matches: 193, Mismatches: 35, Indels: 47
0.70 0.13 0.17
Matches are distributed among these distances:
73 2 0.01
74 60 0.31
75 20 0.10
76 34 0.18
77 3 0.02
78 7 0.04
79 3 0.02
80 3 0.02
82 3 0.02
83 3 0.02
85 3 0.02
86 3 0.02
87 7 0.04
88 3 0.02
89 12 0.06
90 8 0.04
91 19 0.10
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (76 bp):
GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATCTT
TTTTGAAAGCA
Found at i:2119636 original size:89 final size:88
Alignment explanation
Indices: 2119460--2119643 Score: 255
Period size: 89 Copynumber: 2.1 Consensus size: 88
2119450 GTTGACTTTT
* * * *
2119460 TTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCACTCGCAATACGAG
2119525 TTGATTTTTTTTGAAAGGCAGAAA
66 TTGATTTTTTTTGAAA-GCAGAAA
* * *
2119549 TTGAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCACTCGCAATACG
2119614 AGTTGA-TTTTTTTGACAA-CAGAAA
64 AGTTGATTTTTTTTGA-AAGCAGAAA
2119638 TTGAAA
1 TTGAAA
2119644 TTACCTCAGC
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
89 41 0.48
90 9 0.11
91 35 0.41
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (88 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCACTCGCAATACGAG
TTGATTTTTTTTGAAAGCAGAAA
Found at i:2119718 original size:14 final size:14
Alignment explanation
Indices: 2119699--2119733 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2119689 GTTGATTTTT
*
2119699 TTGAAAGACAGAAA
1 TTGAAAAACAGAAA
*
2119713 TTGAAAAACGGAAA
1 TTGAAAAACAGAAA
2119727 TTGAAAA
1 TTGAAAA
2119734 TACCTCGGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Done.