Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 137 of 218
Found at i:41790905 original size:20 final size:18
Alignment explanation
Indices: 41790850--41790907 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 18
41790840 CTGACTTGTT
41790850 TTGAAAATAGTTTAACTTTGA
1 TTGAAAAT--TTTAAC-TTGA
41790871 TTGAAAATTTCTAACTTGA
1 TTGAAAATTT-TAACTTGA
41790890 TTGAAACCATTTTAACTT
1 TTGAAA--ATTTTAACTT
41790908 AATTTAAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
19 12 0.35
20 10 0.29
21 12 0.35
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (18 bp):
TTGAAAATTTTAACTTGA
Found at i:41791039 original size:22 final size:25
Alignment explanation
Indices: 41791014--41791061 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 25
41791004 TTTGTTCAAC
41791014 TTTAATTT-TTAT-TCAAAA-ATAT
1 TTTAATTTGTTATATCAAAACATAT
41791036 TTTAATTTGTTATATCAAAACATAT
1 TTTAATTTGTTATATCAAAACATAT
41791061 T
1 T
41791062 ATCAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.35
23 4 0.17
24 6 0.26
25 5 0.22
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTAATTTGTTATATCAAAACATAT
Found at i:41792661 original size:13 final size:13
Alignment explanation
Indices: 41792643--41792667 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41792633 AATCTAATTT
41792643 AAATTTTTTTATC
1 AAATTTTTTTATC
41792656 AAATTTTTTTAT
1 AAATTTTTTTAT
41792668 AATTATCAAA
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:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
AAATTTTTTTATC
Found at i:41796445 original size:12 final size:12
Alignment explanation
Indices: 41796408--41796432 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41796398 TTTGTATATA
41796408 TTTTAGAATTTT
1 TTTTAGAATTTT
41796420 TTTTAGAATTTT
1 TTTTAGAATTTT
41796432 T
1 T
41796433 ATAATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTTAGAATTTT
Found at i:41796961 original size:19 final size:19
Alignment explanation
Indices: 41796934--41796971 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41796924 TCCATATCAT
*
41796934 CATTAAACATGCCATTTAA
1 CATTAAACATGCCACTTAA
*
41796953 CATTCAACATGCCACTTAA
1 CATTAAACATGCCACTTAA
41796972 TCACCACTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.29
Consensus pattern (19 bp):
CATTAAACATGCCACTTAA
Found at i:41802568 original size:25 final size:27
Alignment explanation
Indices: 41802535--41802587 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
41802525 ACAGTCATAC
*
41802535 ATAACATAA-AGC-ATACAATCATTTT
1 ATAACATAAGAGCAAAACAATCATTTT
*
41802560 ATAACATAAGGGCAAAACAATCATTTT
1 ATAACATAAGAGCAAAACAATCATTTT
41802587 A
1 A
41802588 CCATGTAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.38
26 2 0.08
27 13 0.54
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (27 bp):
ATAACATAAGAGCAAAACAATCATTTT
Found at i:41809997 original size:27 final size:27
Alignment explanation
Indices: 41809955--41810026 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
41809945 ATAATATAAA
*
41809955 GCATACAA-TCATTTTATAACATAAGG
1 GCATAAAAGTCATTTTATAACATAAGG
* * *
41809981 GCATAATAGTCATTTTACT-ACGTGAGG
1 GCATAAAAGTCATTTTA-TAACATAAGG
41810008 GCATAAAAGTCATTTTATA
1 GCATAAAAGTCATTTTATA
41810027 TCAGTTTGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
26 7 0.18
27 30 0.79
28 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (27 bp):
GCATAAAAGTCATTTTATAACATAAGG
Found at i:41813858 original size:16 final size:16
Alignment explanation
Indices: 41813837--41813894 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 16
41813827 ATTAAGATCT
41813837 TTACTTTCTTCTTTAC
1 TTACTTTCTTCTTTAC
41813853 TTACTTTCTTACTCGTTTAC
1 TTACTTTC-T--TC-TTTAC
* *
41813873 TTACTTGCTTGCTTAAC
1 TTACTTTCTT-CTTTAC
41813890 TTACT
1 TTACT
41813895 CCTTCGTTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 8 0.23
17 11 0.31
18 1 0.03
19 3 0.09
20 12 0.34
ACGTcount: A:0.16, C:0.24, G:0.05, T:0.55
Consensus pattern (16 bp):
TTACTTTCTTCTTTAC
Found at i:41814348 original size:56 final size:51
Alignment explanation
Indices: 41814073--41814369 Score: 255
Period size: 50 Copynumber: 5.8 Consensus size: 51
41814063 GAATATAACA
* * * * ** * * *
41814073 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGAGATGTTTCTTGT-AT-
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCATG
* * * * * ** * *
41814122 TGCCAATGCCATATCCCAGATATGGTCTTGCATGAGAGTTCTCATAT-AGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCATG
* * * **
41814172 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCT--TGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAT-G
*
41814222 TGCCAACGCCATGTCCCAGACATCGTCTTACATGGGACCTCTCATCTCA-G
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCATG
*
41814272 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC-ATG
* *
41814327 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
41814370 TTACCCAAAT
Statistics
Matches: 203, Mismatches: 35, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
49 37 0.18
50 120 0.59
53 5 0.02
54 1 0.00
55 1 0.00
56 39 0.19
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (51 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCATG
Found at i:41815070 original size:24 final size:24
Alignment explanation
Indices: 41815042--41815089 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
41815032 AAATTATTGC
*
41815042 TAGAACAAGCTAAATGAAGTTACT
1 TAGAACAAGCTAAATCAAGTTACT
41815066 TAGAACAAGCTAAATCAAGTTACT
1 TAGAACAAGCTAAATCAAGTTACT
41815090 GGGACTCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (24 bp):
TAGAACAAGCTAAATCAAGTTACT
Found at i:41819442 original size:19 final size:21
Alignment explanation
Indices: 41819395--41819444 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
41819385 ATCAACCATT
41819395 CATAT-ATATATTCAATATCA
1 CATATCATATATTCAATATCA
* *
41819415 TATAGCATA-ATTC-ATATCA
1 CATATCATATATTCAATATCA
41819434 CATATCATATA
1 CATATCATATA
41819445 CCAATAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
19 13 0.54
20 8 0.33
21 3 0.12
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (21 bp):
CATATCATATATTCAATATCA
Found at i:41822439 original size:44 final size:45
Alignment explanation
Indices: 41822350--41822479 Score: 192
Period size: 45 Copynumber: 2.9 Consensus size: 45
41822340 TGTTATCATA
41822350 AACATGATTAAAACGAGTAAGACCATAGCTGAAAGACGCTATGGC
1 AACATGATTAAAACGAGTAAGACCATAGCTGAAAGACGCTATGGC
*
41822395 AACATGATTAAAACGAGTAAGACCA-AGCTGAAAGATGCTATGGC
1 AACATGATTAAAACGAGTAAGACCATAGCTGAAAGACGCTATGGC
* * * *
41822439 ATCATGA-CAAAAGTGAGTAAGACCATGGCTGAAAGACGCTA
1 AACATGATTAAAA-CGAGTAAGACCATAGCTGAAAGACGCTA
41822480 CAATATCCTT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
43 4 0.05
44 35 0.45
45 38 0.49
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (45 bp):
AACATGATTAAAACGAGTAAGACCATAGCTGAAAGACGCTATGGC
Found at i:41824282 original size:15 final size:15
Alignment explanation
Indices: 41824262--41824290 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41824252 TATAGGGTAC
41824262 AATTGTGAAAATAAT
1 AATTGTGAAAATAAT
41824277 AATTGTGAAAATAA
1 AATTGTGAAAATAA
41824291 ATATGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (15 bp):
AATTGTGAAAATAAT
Found at i:41827781 original size:20 final size:18
Alignment explanation
Indices: 41827734--41827782 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
41827724 GTGACCCCTA
41827734 TTTTCAAAATTTTTAGAT
1 TTTTCAAAATTTTTAGAT
**
41827752 TTTTCTAAAACTTTTTATTT
1 TTTTC-AAAA-TTTTTAGAT
41827772 TGTTTCAAAAT
1 T-TTTCAAAAT
41827783 AGTCCCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 12 0.46
21 4 0.15
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (18 bp):
TTTTCAAAATTTTTAGAT
Found at i:41829749 original size:29 final size:29
Alignment explanation
Indices: 41829668--41829750 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 29
41829658 TGCTAATTAT
* *
41829668 TGTTCTGGAAAAATAATTTTGACAAGATG
1 TGTTCTGAAAAAATAATTTTGACGAGATG
* * * *
41829697 GGTTTTGAAAAAATAAATTTGACGTGATG
1 TGTTCTGAAAAAATAATTTTGACGAGATG
*
41829726 TGTTCTGAAAAAATTATTTTGACGA
1 TGTTCTGAAAAAATAATTTTGACGA
41829751 TATGGATTTT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.36
Consensus pattern (29 bp):
TGTTCTGAAAAAATAATTTTGACGAGATG
Found at i:41833318 original size:59 final size:59
Alignment explanation
Indices: 41833187--41833365 Score: 227
Period size: 59 Copynumber: 3.1 Consensus size: 59
41833177 GTCCACATCG
* * * ** ** *
41833187 AAAGAACTTCTAATTTATTAAATGAAACAATAT-TATTTGGTTTGTACAAAAATATTCA
1 AAAGAACTTATATTTTATTAAATGAAACAATATAAAAATAATTTATACAAAAATATTCA
* * *
41833245 AAAGAACTTCTATTTTATTAAATGAAATAATATAAAAATAAATTT-TACAAAAATATTGA
1 AAAGAACTTATATTTTATTAAATGAAACAATATAAAAAT-AATTTATACAAAAATATTCA
*
41833304 AAAGAACTTATATTTTATTAAATGAAACAATATAAAAATAATTTAAACAAAAATATTCA
1 AAAGAACTTATATTTTATTAAATGAAACAATATAAAAATAATTTATACAAAAATATTCA
41833363 AAA
1 AAA
41833366 ATAAATCAAT
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
58 36 0.34
59 67 0.63
60 3 0.03
ACGTcount: A:0.53, C:0.07, G:0.06, T:0.35
Consensus pattern (59 bp):
AAAGAACTTATATTTTATTAAATGAAACAATATAAAAATAATTTATACAAAAATATTCA
Found at i:41833734 original size:18 final size:18
Alignment explanation
Indices: 41833711--41833752 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
41833701 GAAGTGAAAA
*
41833711 AGGATACATATAAGGGTT
1 AGGATAAATATAAGGGTT
41833729 AGGATAAATATAAGGGTT
1 AGGATAAATATAAGGGTT
41833747 AGGATA
1 AGGATA
41833753 TGCACTTGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.29, T:0.26
Consensus pattern (18 bp):
AGGATAAATATAAGGGTT
Found at i:41837678 original size:21 final size:22
Alignment explanation
Indices: 41837642--41837693 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
41837632 ACATTATATT
41837642 ATTATATATTGCTATAAATTTA
1 ATTATATATTGCTATAAATTTA
*
41837664 ATTAT-TATTGTTATAAA-TTA
1 ATTATATATTGCTATAAATTTA
41837684 CATTATATAT
1 -ATTATATAT
41837694 AAAAATAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 16 0.59
22 8 0.30
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (22 bp):
ATTATATATTGCTATAAATTTA
Found at i:41839896 original size:19 final size:19
Alignment explanation
Indices: 41839874--41839911 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
41839864 AAATTCAAAT
*
41839874 AAGTATAAAAGTTATTAAA
1 AAGTATAAAAATTATTAAA
41839893 AAGTATAAAAATTATTAAA
1 AAGTATAAAAATTATTAAA
41839912 GATATTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (19 bp):
AAGTATAAAAATTATTAAA
Found at i:41846283 original size:41 final size:39
Alignment explanation
Indices: 41846221--41846297 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 39
41846211 TTTTTAAATA
* *
41846221 AATATTTTTTATTCAACAATTTCATAATTCACATATTTAGT
1 AATATTTTATATCCAACAATTTC-TAATTCACA-ATTTAGT
*
41846262 AATATTTTATACTCCAA-AATTTCTTATTCACAATTT
1 AATATTTTATA-TCCAACAATTTCTAATTCACAATTT
41846298 CCAATTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 4 0.12
40 8 0.25
41 16 0.50
42 4 0.12
ACGTcount: A:0.36, C:0.14, G:0.01, T:0.48
Consensus pattern (39 bp):
AATATTTTATATCCAACAATTTCTAATTCACAATTTAGT
Found at i:41855236 original size:21 final size:21
Alignment explanation
Indices: 41855212--41855255 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
41855202 TTAATTACAA
*
41855212 CCAATCTTAGAAACTCAACAC
1 CCAATCTCAGAAACTCAACAC
41855233 CCAATCTCAGAAACTCAACAC
1 CCAATCTCAGAAACTCAACAC
41855254 CC
1 CC
41855256 GTCGCATCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.39, G:0.05, T:0.16
Consensus pattern (21 bp):
CCAATCTCAGAAACTCAACAC
Found at i:41856816 original size:17 final size:17
Alignment explanation
Indices: 41856791--41856824 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41856781 ATGTTTGATG
*
41856791 GAGTTGTCAGAACACTT
1 GAGTCGTCAGAACACTT
41856808 GAGTCGTCAGAACACTT
1 GAGTCGTCAGAACACTT
41856825 AGTGGCGTAT
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:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (17 bp):
GAGTCGTCAGAACACTT
Found at i:41860141 original size:5 final size:5
Alignment explanation
Indices: 41860133--41860167 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
41860123 AAATTAAATT
41860133 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
41860168 AGATAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:41862793 original size:16 final size:15
Alignment explanation
Indices: 41862767--41862796 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41862757 TTTGCTCAAA
41862767 TTACTGGCACGAAGC
1 TTACTGGCACGAAGC
41862782 TTACTAGGCACGAAG
1 TTACT-GGCACGAAG
41862797 GCCCGAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (15 bp):
TTACTGGCACGAAGC
Found at i:41862855 original size:40 final size:40
Alignment explanation
Indices: 41862810--41863207 Score: 609
Period size: 40 Copynumber: 9.9 Consensus size: 40
41862800 CGAATACACG
* * * * *
41862810 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
* * * *** * *
41862850 ACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
*
41862890 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
*
41862930 TCACTAGCATGAATGCTCTTTGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
*
41862970 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
41863010 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
* *
41863050 TCACTAGCATGAATGCTCTTCGGGACTTAACCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
41863090 TCACTAGCATGAATGCTCTTCAGG-ACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTC-GGAACTTAGCCCGGATACA
41863130 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
*
41863170 TCACTAGCATGAATGCTCTTCGGAACTTAGTCCGGATA
1 TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATA
41863208 TGGTCACTTA
Statistics
Matches: 333, Mismatches: 23, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
39 2 0.01
40 329 0.99
41 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGAACTTAGCCCGGATACA
Found at i:41865640 original size:49 final size:49
Alignment explanation
Indices: 41865574--41866011 Score: 600
Period size: 49 Copynumber: 9.4 Consensus size: 49
41865564 GCCACTTATC
41865574 ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC-T
1 ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
* *
41865622 CATACATGCA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATC-C--
1 -ATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
41865669 ---TAT--A---TCACATTCATCACATTGGCCATTCGGCCTTATCAC--
1 ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
* *
41865708 --ACAT-CAC-ATCACATTCATCACATTGGCCATTCGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
41865753 ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--
1 ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
* *
41865800 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
* *
41865849 ATATATACACTTTCACATTCATCACATCGG-CATTAGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
*
41865897 ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACAT
1 ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
*
41865946 ATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCAC--
1 ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
41865993 ATATATACACTTTCACATT
1 ATATATACACTTTCACATT
41866012 TATTCAAATA
Statistics
Matches: 365, Mismatches: 9, Indels: 32
0.90 0.02 0.08
Matches are distributed among these distances:
38 33 0.09
39 1 0.00
40 2 0.01
41 2 0.01
43 37 0.10
47 67 0.18
48 52 0.14
49 171 0.47
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (49 bp):
ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
Found at i:41865752 original size:22 final size:22
Alignment explanation
Indices: 41865681--41865752 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
41865671 TATCACATTC
41865681 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
41865703 ATCACACAT--CACA-TC-ACATT
1 ATCACA-TTGGC-CATTCGGCCTT
41865723 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
41865746 ATCACAT
1 ATCACAT
41865753 ATATATACAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
20 4 0.11
21 11 0.30
22 18 0.49
23 4 0.11
ACGTcount: A:0.26, C:0.33, G:0.11, T:0.29
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:41865777 original size:130 final size:137
Alignment explanation
Indices: 41865578--41866011 Score: 519
Period size: 144 Copynumber: 3.1 Consensus size: 137
41865568 CTTATCATAT
* * *
41865578 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC-TCATACATGCA-TGTTCACAT
1 ATACACTATCACATTCATCACATTGGCCATTCGGCCTTATCACAT-ATATATACACT-TTCACAT
* *
41865641 TCATCACATTGGCCATTCGGCCTTATC-C-TAT-A-TCACATTCATCACATTGGCCATTCGGCCT
64 TCATCACATTGGCCATTCGGCCTTATCACATATAATTCACATTCATCACATCGGCCATTAGGCCT
41865702 TATCAC-AC
129 TATCACAAC
41865710 AT-CAC-ATCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTC
1 ATACACTATCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTC
41865773 ATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGG
66 ATCACATTGGCCATTCGGCCTTATCAC--ATATA-A--TTCACATTCATCACATCGGCCATTAGG
*
41865838 CCTTATCACATATAT
126 CCTTATCAC--A-AC
* * *
41865853 ATACACTTTCACATTCATCACATCGG-CATTAGGCCTTATCACATATATATACACTTTCACATTC
1 ATACACTATCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTC
* *
41865917 ATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTA
66 ATCACATTGGCCATTCGGCCTTATCAC----ATATA-A--TTCACATTCATCACATCGGCCATTA
*
41865982 GGCCTTATCACATAT
124 GGCCTTATCACA-AC
*
41865997 ATACACTTTCACATT
1 ATACACTATCACATT
41866012 TATTCAAATA
Statistics
Matches: 272, Mismatches: 11, Indels: 26
0.88 0.04 0.08
Matches are distributed among these distances:
130 76 0.28
131 6 0.02
132 2 0.01
134 3 0.01
136 1 0.00
139 33 0.12
143 3 0.01
144 85 0.31
145 17 0.06
146 46 0.17
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (137 bp):
ATACACTATCACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTC
ATCACATTGGCCATTCGGCCTTATCACATATAATTCACATTCATCACATCGGCCATTAGGCCTTA
TCACAAC
Found at i:41865919 original size:144 final size:144
Alignment explanation
Indices: 41865673--41866011 Score: 546
Period size: 144 Copynumber: 2.4 Consensus size: 144
41865663 TTATCCTATA
* * * *
41865673 TCACATTCATCACATTGGCCATTCGGCCTTATCAC--ACAT-CAC-ATCACATTCATCACATTGG
1 TCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
* *
41865734 CCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCA
66 CCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCA
41865799 C-ATATATACACTT
131 CAATATATACACTT
*
41865812 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATC
1 TCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATC
41865877 GG-CATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTAT
64 GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTAT
41865941 CACATATATATACACTT
129 CACA-ATATATACACTT
41865958 TCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATT
1 TCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATT
41866012 TATTCAAATA
Statistics
Matches: 184, Mismatches: 8, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
139 33 0.18
143 3 0.02
144 85 0.46
145 17 0.09
146 46 0.25
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (144 bp):
TCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
CCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCA
CAATATATACACTT
Found at i:41867533 original size:56 final size:56
Alignment explanation
Indices: 41867466--41867585 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
41867456 TATTAGTTTA
41867466 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
41867522 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
41867578 TTGCCCAT
1 TTGCCCAT
41867586 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:41871550 original size:17 final size:17
Alignment explanation
Indices: 41871525--41871580 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
41871515 TTTTCTAGGG
*
41871525 CTTAGTGTTTATGTTTT
1 CTTAATGTTTATGTTTT
*
41871542 CTTAATGTTTATGCTTT
1 CTTAATGTTTATGTTTT
***
41871559 -TT-CCCTTTATGTTTT
1 CTTAATGTTTATGTTTT
41871574 CTTAATG
1 CTTAATG
41871581 CCTATTGCGA
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
15 9 0.32
16 4 0.14
17 15 0.54
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.61
Consensus pattern (17 bp):
CTTAATGTTTATGTTTT
Found at i:41874498 original size:4 final size:4
Alignment explanation
Indices: 41874483--41874514 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
41874473 TCAACTTACA
*
41874483 AATT AGTT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT
41874515 GAACTTCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:41877382 original size:47 final size:47
Alignment explanation
Indices: 41877329--41877547 Score: 393
Period size: 47 Copynumber: 4.7 Consensus size: 47
41877319 ACATCACCTC
* *
41877329 TCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACATTT
1 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
41877376 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
1 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
41877423 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
1 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
* *
41877470 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTT
1 TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
*
41877517 TCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATTCATCACATCGGCTATTAGGCCTTA
41877548 CTATCATTTC
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 168 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.32
Consensus pattern (47 bp):
TCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACACTT
Found at i:41883514 original size:17 final size:17
Alignment explanation
Indices: 41883492--41883524 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41883482 TTTTGAATTA
41883492 GTGAATTCTGTGATTTT
1 GTGAATTCTGTGATTTT
*
41883509 GTGAATTTTGTGATTT
1 GTGAATTCTGTGATTT
41883525 AAAAAGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.03, G:0.24, T:0.55
Consensus pattern (17 bp):
GTGAATTCTGTGATTTT
Found at i:41884756 original size:46 final size:46
Alignment explanation
Indices: 41884702--41884887 Score: 318
Period size: 46 Copynumber: 4.0 Consensus size: 46
41884692 CCATGGAAAA
** *
41884702 TTGTGAAAAGTAGGTATGGTGTTTCAGGGAAGAAAGCCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
*
41884748 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
41884794 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
* *
41884840 TTGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATATTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
41884886 TT
1 TT
41884888 ATAGCATTGT
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 135 1.00
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.29
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
Found at i:41885846 original size:23 final size:25
Alignment explanation
Indices: 41885811--41885856 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
41885801 GTGGAAATTG
*
41885811 AATTAGAAGCTGAGTGAG-ATATGA
1 AATTAGAAGCTGAATGAGTATATGA
*
41885835 AATTA-AATCTGAATGAGTATAT
1 AATTAGAAGCTGAATGAGTATAT
41885857 TTTCACATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.30
Consensus pattern (25 bp):
AATTAGAAGCTGAATGAGTATATGA
Found at i:41889199 original size:14 final size:12
Alignment explanation
Indices: 41889169--41889194 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41889159 TATTATTATT
41889169 TAACATTAAAAA
1 TAACATTAAAAA
41889181 TAACATTAAAAA
1 TAACATTAAAAA
41889193 TA
1 TA
41889195 TAACAAAACA
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:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (12 bp):
TAACATTAAAAA
Found at i:41891406 original size:58 final size:60
Alignment explanation
Indices: 41891344--41891460 Score: 166
Period size: 61 Copynumber: 2.0 Consensus size: 60
41891334 AATCACTTTA
* *
41891344 ATATTAAATTAATATAATACTTA-T-CAAGATAAATATTAGATTAAATTTAACATTAAAT
1 ATATTAAATTAATAGAATACTTACTACAAGATAAATATTAAATTAAATTTAACATTAAAT
* * *
41891402 ATATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTTAATTTAATATTAA
1 ATATTAAATTAATAGAATACTTA-CTACAAGATAAATATTAAATTAAATTTAACATTAA
41891461 GATAATCACT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
58 21 0.41
60 1 0.02
61 29 0.57
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.41
Consensus pattern (60 bp):
ATATTAAATTAATAGAATACTTACTACAAGATAAATATTAAATTAAATTTAACATTAAAT
Found at i:41900235 original size:40 final size:41
Alignment explanation
Indices: 41900154--41900235 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 41
41900144 TATGGAATAT
* * * * *
41900154 TGAATATTGTTTTTGAGTACTGAATTGAATTGTGAAGTTAC
1 TGAATATTGTTTATGAGTACTGAATTGAACTCTAAAATTAC
* *
41900195 TGAATATTG-TTATGTGTACTGCATTGAACTCTAAAATTAC
1 TGAATATTGTTTATGAGTACTGAATTGAACTCTAAAATTAC
41900235 T
1 T
41900236 AAAGTAATGA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 25 0.74
41 9 0.26
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (41 bp):
TGAATATTGTTTATGAGTACTGAATTGAACTCTAAAATTAC
Found at i:41904279 original size:16 final size:16
Alignment explanation
Indices: 41904260--41904294 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
41904250 AGACATTGAA
41904260 GCAGATGTTGATCAAG
1 GCAGATGTTGATCAAG
*
41904276 GCAGATGTTGATCGAG
1 GCAGATGTTGATCAAG
41904292 GCA
1 GCA
41904295 CCTATTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (16 bp):
GCAGATGTTGATCAAG
Found at i:41915534 original size:18 final size:18
Alignment explanation
Indices: 41915493--41915527 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41915483 GGCTAATACA
*
41915493 AATGGTTATGTAATATGG
1 AATGGTTATGAAATATGG
41915511 AATGGTTATGAAATATG
1 AATGGTTATGAAATATG
41915528 AATTGGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (18 bp):
AATGGTTATGAAATATGG
Found at i:41921198 original size:79 final size:82
Alignment explanation
Indices: 41921087--41921271 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
41921077 GCTACTCGTT
* * *
41921087 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
41921150 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
41921167 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
41921230 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
41921247 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41921272 CATCATTCAA
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:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:41921271 original size:40 final size:40
Alignment explanation
Indices: 41921068--41921271 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
41921058 CGGAATTTAA
** *
41921068 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
41921108 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
41921148 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41921187 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
41921227 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
41921267 CCGGA
1 CCGGA
41921272 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:41924328 original size:63 final size:63
Alignment explanation
Indices: 41924220--41924362 Score: 173
Period size: 63 Copynumber: 2.3 Consensus size: 63
41924210 AATATCTCTC
* * * * *
41924220 ACACAGCCTGGACACATGCCCGTGTCTCTAGCCCATGTGATTCTAATTCACAAACAGTTAGTT
1 ACACGGCCTGGACACATGCCCGTGTCTCTAGCACATGTGACTCTAATTCAAAAACAGTGAGTT
* * * * *
41924283 ACATGGCCTGGACACATGCTCGTGT-TCCTAGCACGTGTGGCTCTAATTTAAAAACAGTGAGTT
1 ACACGGCCTGGACACATGCCCGTGTCT-CTAGCACATGTGACTCTAATTCAAAAACAGTGAGTT
41924346 ACACGGCC-GGACACATG
1 ACACGGCCTGGACACATG
41924363 GGCTACCACA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
62 10 0.15
63 58 0.85
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (63 bp):
ACACGGCCTGGACACATGCCCGTGTCTCTAGCACATGTGACTCTAATTCAAAAACAGTGAGTT
Found at i:41932116 original size:37 final size:37
Alignment explanation
Indices: 41932057--41932134 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
41932047 GGTGTTAGAA
*
41932057 TAATTTAATTTCTATAGAATTAGATTATTAATT-TTGT
1 TAATTTAATTTCCATAGAATTAGATTATT-ATTGTTGT
**
41932094 TAATTTAATTTCCATATCATTAGATTATTATTGTTGT
1 TAATTTAATTTCCATAGAATTAGATTATTATTGTTGT
41932131 TAAT
1 TAAT
41932135 GATATTATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 3 0.08
37 34 0.92
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (37 bp):
TAATTTAATTTCCATAGAATTAGATTATTATTGTTGT
Found at i:41942762 original size:21 final size:21
Alignment explanation
Indices: 41942723--41942763 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41942713 AACTTGGTTA
*
41942723 TATTACCAAAGACCAAGATTG
1 TATTACCAAAGAACAAGATTG
*
41942744 TATTACCAAAGAACGAGATT
1 TATTACCAAAGAACAAGATT
41942764 TTGGGAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (21 bp):
TATTACCAAAGAACAAGATTG
Found at i:41943100 original size:62 final size:61
Alignment explanation
Indices: 41943004--41943127 Score: 194
Period size: 62 Copynumber: 2.0 Consensus size: 61
41942994 ACACTATAAA
* * *
41943004 TTCAATTAGATTTTTTTTGGTAAATTTATCAACTGAATTATGTTTTATTGACAATTTTAAC
1 TTCAATTAGATTTTTTTTGGTAAATTTATCAACTGAATTATGTTTCATTAACAATGTTAAC
* *
41943065 TTCAATTTGATTTGTTTTTGGTAAATTTATCAACTGAGTTATGTTTCATTAACAATGTTAAC
1 TTCAATTAGATTT-TTTTTGGTAAATTTATCAACTGAATTATGTTTCATTAACAATGTTAAC
41943127 T
1 T
41943128 CTTTTTTCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
61 12 0.21
62 45 0.79
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (61 bp):
TTCAATTAGATTTTTTTTGGTAAATTTATCAACTGAATTATGTTTCATTAACAATGTTAAC
Found at i:41943957 original size:17 final size:17
Alignment explanation
Indices: 41943935--41943974 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
41943925 AAAAATATTG
*
41943935 ATTTTATT-TTTTATACA
1 ATTTTATTATTTT-TAAA
41943952 ATTTTATTATTTTTAAA
1 ATTTTATTATTTTTAAA
41943969 ATTTTA
1 ATTTTA
41943975 AATAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTATTATTTTTAAA
Found at i:41945436 original size:86 final size:81
Alignment explanation
Indices: 41945334--41945520 Score: 207
Period size: 79 Copynumber: 2.3 Consensus size: 81
41945324 TTAAGTTTAT
41945334 GTTTATTTGAATAAATTTGTGCGTGTTTACTGCAAGTTTTGCCGCGAATATACTATCAAATTTGA
1 GTTTATTTGAATAAATTTGTGCGTG-----TGCAAGTTTTGCCGCGAATATACTATCAAATTTGA
41945399 ATGGTTAAGTTTAAAGTCTAC
61 ATGGTTAAGTTTAAAGTCTAC
* * * * * *
41945420 GTTTATTTGAATAAATTTGT--GTGTGCAAGTTTTGCTGTGAGTATGCTATCATATTTGAATTGT
1 GTTTATTTGAATAAATTTGTGCGTGTGCAAGTTTTGCCGCGAATATACTATCAAATTTGAATGGT
* * *
41945483 TAATTTTAAAGTTTAT
66 TAAGTTTAAAGTCTAC
* * *
41945499 ATTTATCTAAATAAATTTGTGC
1 GTTTATTTGAATAAATTTGTGC
41945521 ACTTTTGTAC
Statistics
Matches: 87, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
79 64 0.74
84 3 0.03
86 20 0.23
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.45
Consensus pattern (81 bp):
GTTTATTTGAATAAATTTGTGCGTGTGCAAGTTTTGCCGCGAATATACTATCAAATTTGAATGGT
TAAGTTTAAAGTCTAC
Found at i:41946023 original size:16 final size:17
Alignment explanation
Indices: 41945993--41946025 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41945983 TGTATTTTTC
41945993 TTTTTAAAATATTTATT
1 TTTTTAAAATATTTATT
*
41946010 TTTTTAATAT-TTTATT
1 TTTTTAAAATATTTATT
41946026 ATATTTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTAAAATATTTATT
Found at i:41946731 original size:13 final size:13
Alignment explanation
Indices: 41946715--41946739 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41946705 AATTGTAAAA
41946715 AAATAATTATTAT
1 AAATAATTATTAT
41946728 AAATAATTATTA
1 AAATAATTATTA
41946740 AATATTGTTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATTATTAT
Found at i:41946799 original size:20 final size:19
Alignment explanation
Indices: 41946723--41946805 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 19
41946713 AAAAATAATT
*
41946723 ATTATAAATAATTATTAAA
1 ATTATAAAAAATTATTAAA
*
41946742 TATTGTTAAAAATATT-TTAAA
1 -ATT-ATAAAAA-ATTATTAAA
* *
41946763 ATTGTAAAGAAGTTATTAAA
1 ATTATAAA-AAATTATTAAA
*
41946783 ATTATAAAAAATATATTTAA
1 ATTATAAAAAAT-TATTAAA
41946803 ATT
1 ATT
41946806 CTTTAAAAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
19 9 0.18
20 29 0.57
21 10 0.20
22 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTATAAAAAATTATTAAA
Found at i:41947088 original size:10 final size:11
Alignment explanation
Indices: 41947073--41947097 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41947063 TAAAGAATTC
41947073 TTTTTTACATT
1 TTTTTTACATT
41947084 TTTTTTACATT
1 TTTTTTACATT
41947095 TTT
1 TTT
41947098 AATGATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTACATT
Found at i:41947137 original size:21 final size:20
Alignment explanation
Indices: 41947087--41947295 Score: 88
Period size: 20 Copynumber: 10.8 Consensus size: 20
41947077 TTACATTTTT
*
41947087 TTTAC-ATTTTTAATGATTA
1 TTTACAATTTTTAATAATTA
*
41947106 TTTACACTTTTTAATAATTA
1 TTTACAATTTTTAATAATTA
* *
41947126 TTTGCAAATTTTTAGTAATT-
1 TTTAC-AATTTTTAATAATTA
* * ***
41947146 TTCAAAAAAATTAAT-ATT-
1 TTTACAATTTTTAATAATTA
*
41947164 TTAATA-AATTTTAAATAATGT-
1 TT--TACAATTTTTAATAAT-TA
*
41947185 TTTATAATTTTATAATAACTT-
1 TTTACAATTTT-TAATAA-TTA
* *
41947206 GTTACAA-TTTTAA-AATATT
1 TTTACAATTTTTAATAAT-TA
* *
41947225 TTTAACAATATTTAATAGTTA
1 TTT-ACAATTTTTAATAATTA
*
41947246 TTTACAATATTTAAT--TT-
1 TTTACAATTTTTAATAATTA
*
41947263 TTTACAATTTTT-AT--TTT
1 TTTACAATTTTTAATAATTA
41947280 TTTACAATTTTTAATA
1 TTTACAATTTTTAATA
41947296 TTTTTAATAA
Statistics
Matches: 148, Mismatches: 25, Indels: 34
0.71 0.12 0.16
Matches are distributed among these distances:
16 4 0.03
17 24 0.16
18 12 0.08
19 24 0.16
20 46 0.31
21 35 0.24
22 3 0.02
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTACAATTTTTAATAATTA
Found at i:41947268 original size:17 final size:18
Alignment explanation
Indices: 41947219--41947345 Score: 113
Period size: 18 Copynumber: 7.0 Consensus size: 18
41947209 ACAATTTTAA
41947219 AATATTTTTAACAATATTT
1 AATATTTTT-ACAATATTT
41947238 AATAGTTATTTACAATATTT
1 AATA-TT-TTTACAATATTT
41947258 AAT-TTTTTACAAT-TTT
1 AATATTTTTACAATATTT
* * *
41947274 TATTTTTTTACAATTTTT
1 AATATTTTTACAATATTT
41947292 AATATTTTT--AATAATTT
1 AATATTTTTACAAT-ATTT
*
41947309 AAATGTTTTTACAAT-TCTT
1 -AATATTTTTACAATAT-TT
41947328 ATATATTTTTA-AATATTT
1 A-ATATTTTTACAATATTT
41947346 TTTTACTATT
Statistics
Matches: 91, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
16 8 0.09
17 21 0.23
18 27 0.30
19 15 0.16
20 17 0.19
21 3 0.03
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (18 bp):
AATATTTTTACAATATTT
Found at i:41947299 original size:20 final size:20
Alignment explanation
Indices: 41947074--41947337 Score: 83
Period size: 20 Copynumber: 13.7 Consensus size: 20
41947064 AAAGAATTCT
41947074 TTTTTACAT-TTTTTTTAC-A
1 TTTTTA-ATATTTTTTTACAA
* *
41947093 TTTTTAATGA-TTATTTACAC
1 TTTTTAAT-ATTTTTTTACAA
* * *
41947113 TTTTTAATAATTATTTGCAAA
1 TTTTTAATATTTTTTTAC-AA
* * * *
41947134 TTTTTAGTA-ATTTTCAAAA
1 TTTTTAATATTTTTTTACAA
*** **
41947153 AAATTAATATTTTAATA-AA
1 TTTTTAATATTTTTTTACAA
* * * *
41947172 TTTTAAATAATGTTTTATAA
1 TTTTTAATATTTTTTTACAA
** *
41947192 TTTTATAATAACTTGTTACAA
1 TTTT-TAATATTTTTTTACAA
* *
41947213 -TTTTAAAATATTTTTAACAA
1 TTTTTAATAT-TTTTTTACAA
* * *
41947233 TATTTAATAGTTATTTACAA
1 TTTTTAATATTTTTTTACAA
*
41947253 TATTT-A-A-TTTTTTACAA
1 TTTTTAATATTTTTTTACAA
41947270 -TTTT--TATTTTTTTACAA
1 TTTTTAATATTTTTTTACAA
* *
41947287 TTTTTAATA-TTTTTAATAA
1 TTTTTAATATTTTTTTACAA
*
41947306 --TTTAA-ATGTTTTTACAA
1 TTTTTAATATTTTTTTACAA
*
41947323 TTCTTATATATTTTT
1 TTTTTA-ATATTTTT
41947338 AAATATTTTT
Statistics
Matches: 175, Mismatches: 50, Indels: 38
0.67 0.19 0.14
Matches are distributed among these distances:
16 5 0.03
17 31 0.18
18 7 0.04
19 48 0.27
20 53 0.30
21 31 0.18
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTAATATTTTTTTACAA
Found at i:41947303 original size:9 final size:9
Alignment explanation
Indices: 41947219--41947366 Score: 67
Period size: 9 Copynumber: 16.0 Consensus size: 9
41947209 ACAATTTTAA
41947219 AATATTTTT
1 AATATTTTT
* *
41947228 AACAATATTT
1 AA-TATTTTT
41947238 AATAGTTATTT
1 AATA-TT-TTT
*
41947249 ACA-ATATTT
1 A-ATATTTTT
41947258 AAT-TTTTT
1 AATATTTTT
41947266 ACA-ATTTTT
1 A-ATATTTTT
*
41947275 -ATTTTTTT
1 AATATTTTT
41947283 ACA-ATTTTT
1 A-ATATTTTT
41947292 AATATTTTT
1 AATATTTTT
* *
41947301 AATAATTTA
1 AATATTTTT
*
41947310 AATGTTTTT
1 AATATTTTT
*
41947319 ACA-ATTCTT
1 A-ATATTTTT
41947328 ATATATTTTT
1 A-ATATTTTT
41947338 AAATATTTTTTT
1 -AATA--TTTTT
*
41947350 ACTATTTTT
1 AATATTTTT
41947359 AAT-TTTTT
1 AATATTTTT
41947367 TTACAAATTT
Statistics
Matches: 104, Mismatches: 19, Indels: 33
0.67 0.12 0.21
Matches are distributed among these distances:
7 1 0.01
8 17 0.16
9 52 0.50
10 19 0.18
11 9 0.09
12 6 0.06
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (9 bp):
AATATTTTT
Found at i:41947366 original size:17 final size:17
Alignment explanation
Indices: 41947207--41947366 Score: 98
Period size: 17 Copynumber: 9.1 Consensus size: 17
41947197 TAATAACTTG
*
41947207 TTACAATTTTAAAATATTT
1 TTACAATTTT-TAAT-TTT
*
41947226 TTAACAATATTTAATAGTTAT
1 TT-ACAATTTTTAAT--TT-T
*
41947247 TTACAATATTTAATTTT
1 TTACAATTTTTAATTTT
*
41947264 TTACAATTTTTATTTTT
1 TTACAATTTTTAATTTT
41947281 TTACAATTTTTAATATTT
1 TTACAATTTTTAAT-TTT
* *
41947299 TTA-ATAATTTAAATGTTT
1 TTACA-ATTTTTAAT-TTT
*
41947317 TTACAATTCTTATATATTT
1 TTACAATTTTTA-AT-TTT
*
41947336 TTA-AA----TATTTTT
1 TTACAATTTTTAATTTT
*
41947348 TTACTATTTTTAATTTT
1 TTACAATTTTTAATTTT
41947365 TT
1 TT
41947367 TTACAAATTT
Statistics
Matches: 113, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
12 6 0.05
13 2 0.02
14 2 0.02
17 38 0.34
18 27 0.24
19 14 0.12
20 21 0.19
21 3 0.03
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (17 bp):
TTACAATTTTTAATTTT
Found at i:41947376 original size:20 final size:21
Alignment explanation
Indices: 41947332--41947378 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
41947322 ATTCTTATAT
*
41947332 ATTTTTAAATATTTTTTTACT
1 ATTTTTAAATATTTTTTTACA
41947353 ATTTTT-AAT-TTTTTTTACAA
1 ATTTTTAAATATTTTTTTAC-A
41947373 ATTTTT
1 ATTTTT
41947379 GGTCTAGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 9 0.38
20 9 0.38
21 6 0.25
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTTTAAATATTTTTTTACA
Found at i:41949449 original size:51 final size:51
Alignment explanation
Indices: 41949373--41949500 Score: 193
Period size: 51 Copynumber: 2.5 Consensus size: 51
41949363 GAAGACGATT
* *
41949373 TATGGCATAAGACCATAGATAAAAGAAGCTACGGTAGTCTAGTATAAGGTA
1 TATGGCATAAGACCATAGATGAAAGAAGCTACGGTAGTCTAGTATAAGGCA
* * * *
41949424 TATGGCATAAAACCATAGATGAAAGAGGCTATGGTAGTCTGGTATAAGGCA
1 TATGGCATAAGACCATAGATGAAAGAAGCTACGGTAGTCTAGTATAAGGCA
*
41949475 TATGGCATAAGACCATGGATGAAAGA
1 TATGGCATAAGACCATAGATGAAAGA
41949501 TGTCATGGTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.23
Consensus pattern (51 bp):
TATGGCATAAGACCATAGATGAAAGAAGCTACGGTAGTCTAGTATAAGGCA
Found at i:41950974 original size:27 final size:28
Alignment explanation
Indices: 41950944--41951037 Score: 124
Period size: 27 Copynumber: 3.5 Consensus size: 28
41950934 AACACGTTAG
*
41950944 GAAAGAAAAACCTTTGTGGC-AAATCAT
1 GAAAGAAAAGCCTTTGTGGCGAAATCAT
*
41950971 GAAAGAAAAGCCTTTGTGACGAAA-CAT
1 GAAAGAAAAGCCTTTGTGGCGAAATCAT
*
41950998 GAAAGGAAAGCCTTTGTGGCGAAATACA-
1 GAAAGAAAAGCCTTTGTGGCGAAAT-CAT
41951026 -AAAGAAAAGCCT
1 GAAAGAAAAGCCT
41951038 GTGTAGTGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
27 54 0.92
28 3 0.05
29 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (28 bp):
GAAAGAAAAGCCTTTGTGGCGAAATCAT
Found at i:41957231 original size:12 final size:13
Alignment explanation
Indices: 41957214--41957246 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
41957204 CTAATTTTTG
41957214 TTTATTTATT-TA
1 TTTATTTATTATA
*
41957226 TTTATTTATTATT
1 TTTATTTATTATA
41957239 TTTATTTA
1 TTTATTTA
41957247 ATCTTTGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTATTATA
Found at i:41957516 original size:19 final size:17
Alignment explanation
Indices: 41957477--41957510 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41957467 AACTCTTGAG
*
41957477 AAATGATATTTTCATTA
1 AAATAATATTTTCATTA
41957494 AAATAATATTTTCATTA
1 AAATAATATTTTCATTA
41957511 TAAAATTCTT
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:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
AAATAATATTTTCATTA
Found at i:41960015 original size:45 final size:45
Alignment explanation
Indices: 41959958--41960125 Score: 219
Period size: 45 Copynumber: 3.7 Consensus size: 45
41959948 ATGTTATCAT
*
41959958 CAACATGACAAAAACGAATAAGACCATAGCTGAAAGACGTTATGG
1 CAACATGACAAAAACGAATAAGACCATAGCTGAAAGACGCTATGG
* *
41960003 CAACATGACAAAAACGAATAAGACCATAGCTAAAAGACGCTGTGG
1 CAACATGACAAAAACGAATAAGACCATAGCTGAAAGACGCTATGG
* * **
41960048 CAACATGACAGAAATGAATAAGACCATATTTGAAAGACGCTATGG
1 CAACATGACAAAAACGAATAAGACCATAGCTGAAAGACGCTATGG
** * * * *
41960093 CAATTTGTCAGAAACGAGTAAGACCATGGCTGA
1 CAACATGACAAAAACGAATAAGACCATAGCTGA
41960126 TAAACAGGAT
Statistics
Matches: 106, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 106 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (45 bp):
CAACATGACAAAAACGAATAAGACCATAGCTGAAAGACGCTATGG
Found at i:41960258 original size:66 final size:66
Alignment explanation
Indices: 41960181--41960313 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
41960171 AAGACACTAT
* *
41960181 GGCATCCTTTGATAGTTTTTTATCAGGTACTATGTACCGGTGAAGGAGTTCACACCGATGGCTCG
1 GGCATCCTTTGATAGTTATTTATCAGGTACTATGTACCGATGAAGGAGTTCACACCGATGGCTCG
41960246 A
66 A
*
41960247 GGCATCCTTTGATAGTTATTTATCAGGTACTATGTACCGATGAAGGAGTTCATACCGATGGCTCG
1 GGCATCCTTTGATAGTTATTTATCAGGTACTATGTACCGATGAAGGAGTTCACACCGATGGCTCG
41960312 A
66 A
41960313 G
1 G
41960314 ATAGTACATG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (66 bp):
GGCATCCTTTGATAGTTATTTATCAGGTACTATGTACCGATGAAGGAGTTCACACCGATGGCTCG
A
Found at i:41961314 original size:14 final size:14
Alignment explanation
Indices: 41961295--41961321 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41961285 AAGTTGATTA
41961295 TGAATTGTGGTATT
1 TGAATTGTGGTATT
41961309 TGAATTGTGGTAT
1 TGAATTGTGGTAT
41961322 GTTTTGGCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (14 bp):
TGAATTGTGGTATT
Found at i:41961826 original size:13 final size:13
Alignment explanation
Indices: 41961808--41961865 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
41961798 TAATGTTTGA
41961808 ATATTTATTTATG
1 ATATTTATTTATG
**
41961821 ATATTTAAAT-TG
1 ATATTTATTTATG
*
41961833 AT-TTT-TTGTTTG
1 ATATTTATT-TATG
41961845 AATATTTATTTATG
1 -ATATTTATTTATG
41961859 ATATTTA
1 ATATTTA
41961866 AATTTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
11 4 0.11
12 6 0.17
13 17 0.49
14 6 0.17
15 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (13 bp):
ATATTTATTTATG
Found at i:41961843 original size:38 final size:38
Alignment explanation
Indices: 41961801--41961877 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
41961791 CTATGAATAA
41961801 TGTTTGAATATTTATTTATGATATTTAAATTGATTTTT
1 TGTTTGAATATTTATTTATGATATTTAAATTGATTTTT
*
41961839 TGTTTGAATATTTATTTATGATATTTAAATTTATTTTT
1 TGTTTGAATATTTATTTATGATATTTAAATTGATTTTT
41961877 T
1 T
41961878 AACTATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (38 bp):
TGTTTGAATATTTATTTATGATATTTAAATTGATTTTT
Found at i:41961870 original size:19 final size:19
Alignment explanation
Indices: 41961810--41961874 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
41961800 ATGTTTGAAT
41961810 ATTTATTTATGATATTTAA
1 ATTTATTTATGATATTTAA
* * *
41961829 ATTGATTTTTTG-T-TTGAA
1 ATTTA-TTTATGATATTTAA
41961847 TATTTATTTATGATATTTAA
1 -ATTTATTTATGATATTTAA
41961867 ATTTATTT
1 ATTTATTT
41961875 TTTAACTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
18 9 0.25
19 18 0.50
20 9 0.25
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (19 bp):
ATTTATTTATGATATTTAA
Found at i:41966724 original size:29 final size:32
Alignment explanation
Indices: 41966668--41966726 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
41966658 AGTACAAATC
* *
41966668 TAAAATAATAATAATTACTAATTAAATTAATA
1 TAAAATAACAATAATTACAAATTAAATTAATA
41966700 TAAAATAACAATAA-TA-AAATT-AATTAA
1 TAAAATAACAATAATTACAAATTAAATTAA
41966727 CTAAAACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 4 0.16
31 2 0.08
32 13 0.52
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (32 bp):
TAAAATAACAATAATTACAAATTAAATTAATA
Found at i:41968799 original size:4 final size:4
Alignment explanation
Indices: 41968790--41968814 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
41968780 ATTAAAAGAG
41968790 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
41968815 AAGCTTCTAT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:41988858 original size:11 final size:12
Alignment explanation
Indices: 41988842--41988874 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41988832 CTTAGACACG
41988842 ATAAAAAAAA-T
1 ATAAAAAAAATT
41988853 ATAAAAGAAAATT
1 ATAAAA-AAAATT
41988866 ATAAAAAAA
1 ATAAAAAAA
41988875 GTGAAATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.30
12 7 0.35
13 7 0.35
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (12 bp):
ATAAAAAAAATT
Found at i:41992640 original size:25 final size:25
Alignment explanation
Indices: 41992611--41992662 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
41992601 AGCTACTCAT
41992611 AGTCCCACCCCAATCCTTAAATAGG
1 AGTCCCACCCCAATCCTTAAATAGG
41992636 AGTCCCACCCCAATCCTTAAATAGG
1 AGTCCCACCCCAATCCTTAAATAGG
41992661 AG
1 AG
41992663 GATAACGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.35, G:0.13, T:0.19
Consensus pattern (25 bp):
AGTCCCACCCCAATCCTTAAATAGG
Found at i:41993279 original size:19 final size:18
Alignment explanation
Indices: 41993237--41993279 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
41993227 CCAAACACTA
41993237 AAAAAATAAATCATTTTT
1 AAAAAATAAATCATTTTT
* *
41993255 AGAAAAGTAAATTATTTTCT
1 A-AAAAATAAATCATTTT-T
41993275 AAAAA
1 AAAAA
41993280 TCATTTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 18 0.86
20 2 0.10
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (18 bp):
AAAAAATAAATCATTTTT
Found at i:41993498 original size:21 final size:21
Alignment explanation
Indices: 41993472--41993527 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
41993462 AACAGCGGTG
*
41993472 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
41993493 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
*
41993514 GCGATGAGATTAGA
1 GCGGTGAGATTAGA
41993528 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:42002294 original size:253 final size:252
Alignment explanation
Indices: 42001845--42002597 Score: 1407
Period size: 253 Copynumber: 3.0 Consensus size: 252
42001835 ATGGTACAAA
*
42001845 TGACTTGTCTGAAATTATGAACTATCAACCTGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
1 TGACTTGTCTGAAATTATGAACTATCTACCTGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
* *
42001910 GTGCAACCACTATTTCATGAAAAAAGCATGCATCGTCCAAAAGATCTTCAAGAATTGAGGACTTG
66 GTGCAACCACTATTTCAGGAAAAAAGCATGCATCGTCCAAAAGTTCTTCAAGAATTGAGGACTTG
42001975 ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGAGAAATGGCAGGTATTTTGCGTGA
131 ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGAGAAATGGCAGGTATTTTGCGTGA
42002040 TAGTTTAGCATCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
196 TAGTTTAGCATCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
42002097 TGACTTGTCTGAAATTATGAACTATCTACCTGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
1 TGACTTGTCTGAAATTATGAACTATCTACCTGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
*
42002162 GTGCAACCACTATTTCAGGAAAAAAGCATGCATTTGTCCAAAAGTTCTTCAAGAATTGAGGACTT
66 GTGCAACCACTATTTCAGGAAAAAAGCATGCA-TCGTCCAAAAGTTCTTCAAGAATTGAGGACTT
*
42002227 GATGAAAGTTATTAATAGAGAAAAGAGCGATCCAACAGCAGGAGAAATGGCAGGTATTTTGCGTG
130 GATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGAGAAATGGCAGGTATTTTGCGTG
42002292 ATAGTTTAGCATCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
195 ATAGTTTAGCATCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
42002350 TGACTTGTCTGAAATTATGAACTATCTACCTGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
1 TGACTTGTCTGAAATTATGAACTATCTACCTGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
* *
42002415 GTGCAACCATTATTTCAGGAAAAAAGCATGCATCGTCCAAAAGTTTTTCAAGAATTGAGGACTTG
66 GTGCAACCACTATTTCAGGAAAAAAGCATGCATCGTCCAAAAGTTCTTCAAGAATTGAGGACTTG
*
42002480 ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGAGAAATGGCAGGTATTTTGCATGA
131 ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGAGAAATGGCAGGTATTTTGCGTGA
* *
42002545 TACTTTAGCACCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAA
196 TAGTTTAGCATCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAA
42002598 CCAAATCTCA
Statistics
Matches: 488, Mismatches: 12, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
252 240 0.49
253 248 0.51
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (252 bp):
TGACTTGTCTGAAATTATGAACTATCTACCTGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
GTGCAACCACTATTTCAGGAAAAAAGCATGCATCGTCCAAAAGTTCTTCAAGAATTGAGGACTTG
ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGAGAAATGGCAGGTATTTTGCGTGA
TAGTTTAGCATCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
Found at i:42003606 original size:13 final size:13
Alignment explanation
Indices: 42003588--42003651 Score: 92
Period size: 13 Copynumber: 4.9 Consensus size: 13
42003578 AGTTCTTCAT
42003588 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
42003601 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
42003614 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* *
42003627 TGCTTTTCAAAAG
1 TGCTTTTGAGAAG
*
42003640 TGTTTTTGAGAA
1 TGCTTTTGAGAA
42003652 ATTTGAGTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:42003617 original size:26 final size:26
Alignment explanation
Indices: 42003588--42003651 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
42003578 AGTTCTTCAT
*
42003588 TGCTTTTGAGAAGTGCTTTTCAGAAG
1 TGCTTTTGAGAAGTGCTTTTCAAAAG
42003614 TGCTTTTGAGAAGTGCTTTTCAAAAG
1 TGCTTTTGAGAAGTGCTTTTCAAAAG
*
42003640 TGTTTTTGAGAA
1 TGCTTTTGAGAA
42003652 ATTTGAGTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (26 bp):
TGCTTTTGAGAAGTGCTTTTCAAAAG
Found at i:42003865 original size:24 final size:23
Alignment explanation
Indices: 42003837--42003890 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
42003827 AATATATAAT
*
42003837 ATTAATTTTAAATATTTCTAAATA
1 ATTAATTTTAAATATTTATAAA-A
* *
42003861 ATTAATATTAATTATTTATAAAA
1 ATTAATTTTAAATATTTATAAAA
*
42003884 TTTAATT
1 ATTAATT
42003891 AGAATATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTAATTTTAAATATTTATAAAA
Found at i:42008698 original size:15 final size:15
Alignment explanation
Indices: 42008651--42008690 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
42008641 TATAAGCAAC
42008651 AAAACATAGTAATTA
1 AAAACATAGTAATTA
* *
42008666 AAAAAATAATTAATTA
1 AAAACAT-AGTAATTA
42008682 AAAACATAG
1 AAAACATAG
42008691 CTATTAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (15 bp):
AAAACATAGTAATTA
Found at i:42008908 original size:19 final size:20
Alignment explanation
Indices: 42008884--42008921 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
42008874 TGAGCTGGTT
42008884 GGAGCTGAAA-TGAGCTAAG
1 GGAGCTGAAATTGAGCTAAG
42008903 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAATTGAGCTAA
42008922 AATGTGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAG
Found at i:42014603 original size:131 final size:130
Alignment explanation
Indices: 42014307--42014603 Score: 314
Period size: 131 Copynumber: 2.3 Consensus size: 130
42014297 CATATATCGC
** * * *
42014307 TAAAATGTGTAACGACCAAACAAGTTGTTGCTAAATGTTAAAATATTTGCAACAATCTTAAATTG
1 TAAAATGTACAACGACAAAACAAGTTGTTGTTAAATGTTAAAATATTAGCAACAATCTTAAATTG
** * * * **
42014372 TCGTTATGTAATTTAATTTTATGCTTATTCATTGCAACGACAAATCGTGTTGTTGTGAATTTGTA
66 TCGTTACATAATTTAATTTTATACTTATTAATAGCAACGACAAATC-TGTCATTGTGAATTTGTA
42014437 A
130 A
* * * *
42014438 TAAAATGTATAACGACAAAACAAGGTGTTATTAAATGTTAAAATATTAGCAGCAA-CTTTGAAA-
1 TAAAATGTACAACGACAAAACAAGTTGTTGTTAAATGTTAAAATATTAGCAACAATC-TT-AAAT
* * *
42014501 TGTTGTTACATAATTTAATTTTCTACTTATTAATAGCAATGACACAAAT-TGTCATTGTGAATTA
64 TGTCGTTACATAATTTAATTTTATACTTATTAATAGCAACG--ACAAATCTGTCATTGTGAATT-
42014565 T-TAA
126 TGTAA
* **
42014569 TAAAATTTACAACGACAAAATTAGTTGTTGTTAAA
1 TAAAATGTACAACGACAAAACAAGTTGTTGTTAAA
42014604 CCTTTAAATA
Statistics
Matches: 138, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
130 1 0.01
131 127 0.92
132 4 0.03
133 6 0.04
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.37
Consensus pattern (130 bp):
TAAAATGTACAACGACAAAACAAGTTGTTGTTAAATGTTAAAATATTAGCAACAATCTTAAATTG
TCGTTACATAATTTAATTTTATACTTATTAATAGCAACGACAAATCTGTCATTGTGAATTTGTAA
Found at i:42016130 original size:24 final size:24
Alignment explanation
Indices: 42016096--42016148 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
42016086 TTTCTAGAAG
* **
42016096 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
42016120 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
42016144 ATTTA
1 ATTTA
42016149 ACTTTGATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:42016158 original size:24 final size:24
Alignment explanation
Indices: 42016113--42016158 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
42016103 ATTTATGAGT
*
42016113 ATAATATATTTAGCATTTATTAAC
1 ATAATATATTTAACATTTATTAAC
42016137 ATAATATATTTAAC-TTTGATTA
1 ATAATATATTTAACATTT-ATTA
42016159 GAATTAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (24 bp):
ATAATATATTTAACATTTATTAAC
Found at i:42020448 original size:24 final size:24
Alignment explanation
Indices: 42020385--42020436 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
42020375 TTTCTAGAAG
* * *
42020385 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
42020409 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
42020433 ATTT
1 ATTT
42020437 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:42022399 original size:2 final size:2
Alignment explanation
Indices: 42022392--42022423 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42022382 TCCTATTCCT
42022392 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42022424 ATGAAAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:42026600 original size:24 final size:24
Alignment explanation
Indices: 42026568--42026617 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
42026558 TTTAAGACTT
42026568 AGGTAGTTTTAATATGTTGAATTG
1 AGGTAGTTTTAATATGTTGAATTG
42026592 AGGTAGTTTTAATATGTTGAATTG
1 AGGTAGTTTTAATATGTTGAATTG
42026616 AG
1 AG
42026618 CGTGCAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (24 bp):
AGGTAGTTTTAATATGTTGAATTG
Found at i:42035787 original size:45 final size:45
Alignment explanation
Indices: 42035723--42035858 Score: 184
Period size: 45 Copynumber: 3.0 Consensus size: 45
42035713 GTTTGCAAAC
* *
42035723 AAGCTGCTAGTACGGTGTGGATAAACCACTCATCGGTGCAGATAA
1 AAGCTACTAGTACGTTGTGGATAAACCACTCATCGGTGCAGATAA
* * * *
42035768 AAGCTACTAGTACATTGTGGATAAACTAGTCATTGGTGCAGATAA
1 AAGCTACTAGTACGTTGTGGATAAACCACTCATCGGTGCAGATAA
* *
42035813 AAGCTACTAGTATGTTGTGGATGAACCACTCATCGGT-CGAGATAA
1 AAGCTACTAGTACGTTGTGGATAAACCACTCATCGGTGC-AGATAA
42035858 A
1 A
42035859 TCACTCATTG
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
44 1 0.01
45 77 0.99
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (45 bp):
AAGCTACTAGTACGTTGTGGATAAACCACTCATCGGTGCAGATAA
Found at i:42041539 original size:22 final size:22
Alignment explanation
Indices: 42041512--42041567 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
42041502 TACTTAGGTG
*
42041512 TAAATTAAAATTCATGGGTGTA
1 TAAATTAAAATTCAAGGGTGTA
*
42041534 TAAATT-AAATATCAAGGGTTTA
1 TAAATTAAAAT-TCAAGGGTGTA
42041556 TAAATTAAAATT
1 TAAATTAAAATT
42041568 GTAGAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 4 0.13
22 22 0.73
23 4 0.13
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (22 bp):
TAAATTAAAATTCAAGGGTGTA
Found at i:42042928 original size:18 final size:18
Alignment explanation
Indices: 42042905--42042947 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
42042895 ATAACATTGA
**
42042905 ATTTTGAAATTTTTTTAT
1 ATTTTGAAATCATTTTAT
42042923 ATTTTGAAATCATTTTAT
1 ATTTTGAAATCATTTTAT
42042941 ATTTTGA
1 ATTTTGA
42042948 TCTTTTTGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.60
Consensus pattern (18 bp):
ATTTTGAAATCATTTTAT
Found at i:42043257 original size:14 final size:14
Alignment explanation
Indices: 42043238--42043283 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
42043228 TCAATGTCTC
42043238 AAAATTAAAATATA
1 AAAATTAAAATATA
42043252 AAAATTAAAAT-TA
1 AAAATTAAAATATA
* *
42043265 AAATTTCAAAAAATA
1 AAAATT-AAAATATA
42043280 AAAA
1 AAAA
42043284 AAATTTAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 7 0.26
14 15 0.56
15 5 0.19
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATTAAAATATA
Found at i:42048533 original size:23 final size:23
Alignment explanation
Indices: 42048502--42048552 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
42048492 ACCTACTTTC
* *
42048502 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
42048525 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
42048548 TTACA
1 TTACA
42048553 ATATAGATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:42056109 original size:21 final size:20
Alignment explanation
Indices: 42056083--42056156 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
42056073 AAACATTCGT
42056083 TAAAAAAAATAAATATGTACA
1 TAAAAAAAATAAATAT-TACA
* *
42056104 TAAAAACAACAAATA-TACA
1 TAAAAAAAATAAATATTACA
*
42056123 TATATATAAAA-AAATAATTACA
1 TA-A-AAAAAATAAAT-ATTACA
*
42056145 TTAAAAAAATAA
1 TAAAAAAAATAA
42056157 TTACATTATG
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
19 6 0.14
20 10 0.24
21 21 0.50
22 5 0.12
ACGTcount: A:0.68, C:0.07, G:0.01, T:0.24
Consensus pattern (20 bp):
TAAAAAAAATAAATATTACA
Found at i:42056171 original size:17 final size:17
Alignment explanation
Indices: 42056129--42056164 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
42056119 TACATATATA
42056129 TAAAAAAATAATTACAT
1 TAAAAAAATAATTACAT
42056146 TAAAAAAATAATTACAT
1 TAAAAAAATAATTACAT
42056163 TA
1 TA
42056165 TGGAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAAATAATTACAT
Found at i:42058042 original size:217 final size:217
Alignment explanation
Indices: 42057667--42058239 Score: 984
Period size: 217 Copynumber: 2.6 Consensus size: 217
42057657 ATTTTAGAAA
42057667 GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTG
1 GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTG
* * *
42057732 CTCTCTGCAACTTCATAGAGATAAGATCCAAGATTTTAATCCGCTCCACTGCAACTTCAGGAATA
66 CTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGA
*
42057797 TAGGATTATCGACTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTT
131 TAGGATTATCGACTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTC
*
42057862 TGCCTCATTGCAACTTCAAGAG
196 TGCCTCACTGCAACTTCAAGAG
*
42057884 GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTAGATGCGATCTG
1 GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTG
* *
42057949 CTCTCTGTAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGA
66 CTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGA
* *
42058014 TAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATTTTCAGTC
131 TAGGATTATCGACTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTC
*
42058079 TGCCTCACTGCAACTTCAGGAG
196 TGCCTCACTGCAACTTCAAGAG
* * *
42058101 GATAAGACTTGCTTACTTAGTCTGCTCCACTACAACTTTAGGGAGATCAGACTAGATGCGATCTG
1 GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTG
* ** *
42058166 CTCTCTACAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTGTACTGTAACTTCAGGAAGA
66 CTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGA
42058231 TAGGATTAT
131 TAGGATTAT
42058240 TGGCCACCTA
Statistics
Matches: 335, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
217 335 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (217 bp):
GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTG
CTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGAAGA
TAGGATTATCGACTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTC
TGCCTCACTGCAACTTCAAGAG
Found at i:42058093 original size:45 final size:43
Alignment explanation
Indices: 42057666--42058153 Score: 195
Period size: 44 Copynumber: 11.2 Consensus size: 43
42057656 GATTTTAGAA
*
42057666 AGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGG
1 AGATAAGACTTGCTTA-TTAGTCTGCTCCACTGCAACTTTAGGG
* ** * * **
42057710 AGATAAGACTAG---ATGCGATCTGCT-CTCTGCAACTTCATAG
1 AGATAAGACTTGCTTATTAG-TCTGCTCCACTGCAACTTTAGGG
** * * * * *
42057750 AGATAAGATCCAAGATT-TTAATCCGCTCCACTGCAACTTCAGGA
1 AGATAAGA--CTTGCTTATTAGTCTGCTCCACTGCAACTTTAGGG
* * * *
42057794 ATATAGGATTATCGAC-T-TTAATCTGCTCCACTGCAACTTTAGGG
1 AGATAAGACT-T-G-CTTATTAGTCTGCTCCACTGCAACTTTAGGG
* * * * * * *
42057838 AGATAAGATTTGCCATCTTCAGTTTGC-CTCATTGCAACTTCA-AG
1 AGATAAGACTTG-CTTATT-AGTCTGCTC-CACTGCAACTTTAGGG
* *
42057882 AGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAAGG
1 A-GATAAGACTTGCTTA-TTAGTCTGCTCCACTGCAACTTTAGGG
* ** * * * *
42057927 AGATAAGACTAG---ATGCGATCTGCT-CTCTGTAACTTCAGAG
1 AGATAAGACTTGCTTATTAG-TCTGCTCCACTGCAACTTTAGGG
** * * * *
42057967 AGATAAGATCCAAGGTT-TTAATCCGCTCCACTGCAACTTCAGGG
1 AGATAAGA--CTTGCTTATTAGTCTGCTCCACTGCAACTTTAGGG
* * *
42058011 AGATAGGATTATCGGC-T-TTAATCTGCTCCACTGCAACTTTAGGG
1 AGATAAGACT-T--GCTTATTAGTCTGCTCCACTGCAACTTTAGGG
* *
42058055 AGATAAGATTTGCCATT-TTCAGTCTGC-CTCACTGCAACTTCA-GG
1 AGATAAGACTTG-C-TTATT-AGTCTGCTC-CACTGCAACTTTAGGG
*
42058099 AGGATAAGACTTGCTTACTTAGTCTGCTCCACTACAACTTTAGGG
1 A-GATAAGACTTGCTTA-TTAGTCTGCTCCACTGCAACTTTAGGG
*
42058144 AGATCAGACT
1 AGATAAGACT
42058154 AGATGCGATC
Statistics
Matches: 339, Mismatches: 67, Indels: 76
0.70 0.14 0.16
Matches are distributed among these distances:
40 45 0.13
41 15 0.04
42 9 0.03
43 15 0.04
44 189 0.56
45 66 0.19
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (43 bp):
AGATAAGACTTGCTTATTAGTCTGCTCCACTGCAACTTTAGGG
Found at i:42070693 original size:21 final size:19
Alignment explanation
Indices: 42070667--42070722 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
42070657 AAACATTCGT
42070667 TAAAAAAAATAAATATGTACA
1 TAAAAAAAATAAATA--TACA
*
42070688 TAAAAAAAACAAATATACA
1 TAAAAAAAATAAATATACA
*
42070707 TATAAATAAATAAATA
1 TA-AAAAAAATAAATA
42070723 AATAATTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.19
20 11 0.35
21 14 0.45
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (19 bp):
TAAAAAAAATAAATATACA
Found at i:42070741 original size:16 final size:16
Alignment explanation
Indices: 42070717--42070774 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
42070707 TATAAATAAA
42070717 TAAATAAATAATTACAT
1 TAAA-AAATAATTACAT
42070734 TAAAAAATAATTACAT
1 TAAAAAATAATTACAT
* * *
42070750 TATGGAAATTAATTAAAT
1 TA--AAAAATAATTACAT
42070768 TAAAAAA
1 TAAAAAA
42070775 AACTAAATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
16 17 0.50
17 4 0.12
18 13 0.38
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
TAAAAAATAATTACAT
Found at i:42072854 original size:146 final size:146
Alignment explanation
Indices: 42072590--42072882 Score: 541
Period size: 146 Copynumber: 2.0 Consensus size: 146
42072580 AAAACCATGA
*
42072590 CATAGTGGAACGCAGTCTAATCGCAGCTTAGATTAACTAAATACTTTCAGCAAGATTCAAAGTTC
1 CATAGTGAAACGCAGTCTAATCGCAGCTTAGATTAACTAAATACTTTCAGCAAGATTCAAAGTTC
* *
42072655 TATAGTTAGATTAAAAATATTATCTGAGTGTTTATCCTTTTGTTATTAAATTTTATATTTTCAAT
66 TATAGTTAGATTAAAAACATTATCTGAGTGTATATCCTTTTGTTATTAAATTTTATATTTTCAAT
42072720 TATTAAACCCTCAAAT
131 TATTAAACCCTCAAAT
*
42072736 CATAGTGAAACGCAGTCTAATCGCAGCTTAGATTAACTAAATACTTTCGGCAAGATTCAAAGTTC
1 CATAGTGAAACGCAGTCTAATCGCAGCTTAGATTAACTAAATACTTTCAGCAAGATTCAAAGTTC
*
42072801 TATAGTTAGATTAAAAACATTATCTGAGTGTATATCCTTTTGTTATTAAATTTTATTTTTTCAAT
66 TATAGTTAGATTAAAAACATTATCTGAGTGTATATCCTTTTGTTATTAAATTTTATATTTTCAAT
42072866 TATTAAACCCTCAAAT
131 TATTAAACCCTCAAAT
42072882 C
1 C
42072883 TTAGGTATCT
Statistics
Matches: 142, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
146 142 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (146 bp):
CATAGTGAAACGCAGTCTAATCGCAGCTTAGATTAACTAAATACTTTCAGCAAGATTCAAAGTTC
TATAGTTAGATTAAAAACATTATCTGAGTGTATATCCTTTTGTTATTAAATTTTATATTTTCAAT
TATTAAACCCTCAAAT
Found at i:42076755 original size:16 final size:17
Alignment explanation
Indices: 42076724--42076757 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
42076714 GGGAATGGCG
42076724 TTGTTTGATGTTTATTT
1 TTGTTTGATGTTTATTT
*
42076741 TTGTTT-ATTTTTATTT
1 TTGTTTGATGTTTATTT
42076757 T
1 T
42076758 ATAATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (17 bp):
TTGTTTGATGTTTATTT
Found at i:42078361 original size:29 final size:31
Alignment explanation
Indices: 42078326--42078383 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
42078316 TTCGAGCTTG
42078326 GGGACAAAAT-GTAATTAT-ACAAAAGTTTA
1 GGGACAAAATCGTAATTATGACAAAAGTTTA
* *
42078355 GGGACAAAATCGTGATTTTGACAAAAGTT
1 GGGACAAAATCGTAATTATGACAAAAGTT
42078384 GAGTCAAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 6 0.24
31 9 0.36
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (31 bp):
GGGACAAAATCGTAATTATGACAAAAGTTTA
Found at i:42079027 original size:102 final size:102
Alignment explanation
Indices: 42078851--42079194 Score: 419
Period size: 102 Copynumber: 3.4 Consensus size: 102
42078841 TATCGATGAA
* * * * *
42078851 CACGTGTGTAGTATTGTGTAAAGGCTACTACGTGTATCTATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* *
42078916 TAAGTGAAGGCTACAATGTGTACC-AAGAAGCTTTGGT
66 TAATTGAAGGCTACTATGTGTACCGAA-AAGCTTTGGT
* * *
42078953 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAGTGATGGTCACATTTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
42079018 TAATTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAATTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
* * * *** * *
42079055 TACGTGTGTAGTACTATGTGAAGGCTACTAGGTGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* * *
42079119 T-ATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGAT
66 TAAT-TGAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
* *
42079155 CATGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
42079195 ATGATAAAAG
Statistics
Matches: 211, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
100 40 0.19
101 39 0.18
102 130 0.62
103 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAATTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
Found at i:42079121 original size:50 final size:49
Alignment explanation
Indices: 42078851--42079188 Score: 322
Period size: 51 Copynumber: 6.7 Consensus size: 49
42078841 TATCGATGAA
* * * * * *
42078851 CACGTGTGTAGTATTGTGTAAAGGCTACTACGTGTATCTATAAA-TGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGA-AAACT--TGGT
* * * * *
42078902 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACC-AAGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAA-AA-C-TTGGT
* * * *
42078953 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAGTGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAAAACT--TGGT
* * * *
42079004 CACATTTGTAGTACTAAT-TGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
1 CACGTGTGTAGTACT-ATGTGAAGGCTACTACGTGAACCGAAAA-C-TTGGT
* * *
42079055 TACGTGTGTAGTACTATGTGAAGGCTACTAGGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-AAAACTTGGT
*
42079105 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-AAAACTTGGT
*
42079155 CATGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
42079189 TATCGAATGA
Statistics
Matches: 241, Mismatches: 34, Indels: 25
0.80 0.11 0.08
Matches are distributed among these distances:
49 2 0.01
50 90 0.37
51 141 0.59
52 6 0.02
53 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (49 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAAAACTTGGT
Found at i:42083046 original size:50 final size:50
Alignment explanation
Indices: 42082969--42083076 Score: 189
Period size: 50 Copynumber: 2.2 Consensus size: 50
42082959 GTAGTATTAT
*
42082969 GTGAACCGTAAAACTTGATCACATGTGTAGTACTATGTGAAGGCTACTAC
1 GTGAATCGTAAAACTTGATCACATGTGTAGTACTATGTGAAGGCTACTAC
*
42083019 GTGAATCGTAAAACTTGATCACGTGTGTAGTACTATGTGAAGGCTACTAC
1 GTGAATCGTAAAACTTGATCACATGTGTAGTACTATGTGAAGGCTACTAC
*
42083069 GTGTATCG
1 GTGAATCG
42083077 AATGATAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (50 bp):
GTGAATCGTAAAACTTGATCACATGTGTAGTACTATGTGAAGGCTACTAC
Found at i:42101414 original size:68 final size:68
Alignment explanation
Indices: 42101260--42101416 Score: 181
Period size: 68 Copynumber: 2.3 Consensus size: 68
42101250 GGATTATTGC
* * * * * *
42101260 AACATGTGAAGTCTGCCAGGATAGTAAACATGACACTATATTATATAAAATCATAACTGGGATAT
1 AACATTTGAAGTCTACTAGGACAGTAAACATGACACCATATTATATAAAACCATAACTGGGATAT
*
42101325 GGA
66 GAA
* * * * * *
42101328 AACATTTGAAGTCTACTAGGACAGTAAATATGACACCATATTGTGTAAGACCATAGCTGGGCTAT
1 AACATTTGAAGTCTACTAGGACAGTAAACATGACACCATATTATATAAAACCATAACTGGGATAT
42101393 GAA
66 GAA
42101396 AACATTTGAAGT-TCACTAGGA
1 AACATTTGAAGTCT-ACTAGGA
42101417 TTGCGATCTA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
67 1 0.01
68 74 0.99
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (68 bp):
AACATTTGAAGTCTACTAGGACAGTAAACATGACACCATATTATATAAAACCATAACTGGGATAT
GAA
Found at i:42112953 original size:17 final size:17
Alignment explanation
Indices: 42112931--42112963 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42112921 ATGAATGAAA
42112931 AAATGCTAG-GGCAATTG
1 AAATGCT-GTGGCAATTG
42112948 AAATGCTGTGGCAATT
1 AAATGCTGTGGCAATT
42112964 CTCAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (17 bp):
AAATGCTGTGGCAATTG
Found at i:42116977 original size:51 final size:51
Alignment explanation
Indices: 42116814--42117002 Score: 150
Period size: 51 Copynumber: 3.7 Consensus size: 51
42116804 GAAGTTGCTA
* * * * *
42116814 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTATATTGGAATG-ATA-
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTATCGG-ATGAAAAT
* * * * * * ***
42116864 GGTCGCATGTGTAGTACTATGTTCAAGCTACTATGCGTACCGAAT-AGCTT
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATGAAAAT
* * *
42116914 CGATCACGTGTGTAGTACTATGTGCAGGCTACTATTTGTATCGGATGAAAAT
1 -GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATGAAAAT
* * * *
42116966 GGTCACATGTGTAGTACTACGTGTAGACTACCATGTG
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
42117003 AACCGGGTAT
Statistics
Matches: 103, Mismatches: 32, Indels: 7
0.73 0.23 0.05
Matches are distributed among these distances:
49 2 0.02
50 33 0.32
51 66 0.64
52 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATGAAAAT
Found at i:42121094 original size:21 final size:23
Alignment explanation
Indices: 42121068--42121124 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 23
42121058 ACTCAGGAAC
42121068 AAAAGTATT-A-GAGATATTCTT
1 AAAAGTATTAATGAGATATTCTT
42121089 AAAAGTATTTAGAATTGAGATATTCTT
1 AAAAGTA-TT--AA-TGAGATATTCTT
42121116 AAAAGTATT
1 AAAAGTATT
42121125 TAGAATTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 7 0.23
22 2 0.07
25 1 0.03
26 2 0.07
27 18 0.60
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.39
Consensus pattern (23 bp):
AAAAGTATTAATGAGATATTCTT
Found at i:42121116 original size:27 final size:27
Alignment explanation
Indices: 42121078--42121134 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
42121068 AAAAGTATTA
42121078 GAGATATTCTTAAAAGTATTTAGAATT
1 GAGATATTCTTAAAAGTATTTAGAATT
42121105 GAGATATTCTTAAAAGTATTTAGAATT
1 GAGATATTCTTAAAAGTATTTAGAATT
42121132 GAG
1 GAG
42121135 TCATCTCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.39
Consensus pattern (27 bp):
GAGATATTCTTAAAAGTATTTAGAATT
Found at i:42138129 original size:19 final size:20
Alignment explanation
Indices: 42138092--42138129 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42138082 TATGTGTTTT
42138092 GTTCAAATGTAACTTTGTTA
1 GTTCAAATGTAACTTTGTTA
*
42138112 GTTCAATTGTAA-TTTGTT
1 GTTCAAATGTAACTTTGTT
42138130 CAGCAAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (20 bp):
GTTCAAATGTAACTTTGTTA
Found at i:42139777 original size:21 final size:22
Alignment explanation
Indices: 42139739--42139782 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
42139729 TAATATGTTT
42139739 TAAATAGACATAACTATTAAAG
1 TAAATAGACATAACTATTAAAG
* * *
42139761 TAAA-AGATATAATTATTCAAG
1 TAAATAGACATAACTATTAAAG
42139782 T
1 T
42139783 GACATCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (22 bp):
TAAATAGACATAACTATTAAAG
Found at i:42142541 original size:14 final size:14
Alignment explanation
Indices: 42142522--42142549 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42142512 TTAATTTATT
42142522 AATGAATTATTAAA
1 AATGAATTATTAAA
42142536 AATGAATTATTAAA
1 AATGAATTATTAAA
42142550 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:42148287 original size:6 final size:6
Alignment explanation
Indices: 42148276--42148384 Score: 76
Period size: 6 Copynumber: 17.7 Consensus size: 6
42148266 ACATTGTAAT
* ** *
42148276 GAAAAA GAAAAA GAAAACA -AAAAC GAAAAA GAAAAA GAAATT GGAAAA
1 GAAAAA GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
** ** * * *
42148324 GAAAAA GAAATC GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A
42148375 GAAAAA GAAA
1 GAAAAA GAAA
42148385 TTGAGATTGA
Statistics
Matches: 76, Mismatches: 22, Indels: 10
0.70 0.20 0.09
Matches are distributed among these distances:
6 64 0.84
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.03, G:0.19, T:0.06
Consensus pattern (6 bp):
GAAAAA
Found at i:42148378 original size:27 final size:29
Alignment explanation
Indices: 42148348--42148410 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
42148338 AAAAGTGAGA
42148348 GAAAAAGAAAATGA-A-GA-AAAGAAAATT
1 GAAAAAGAAAATGAGATGAGAAA-AAAATT
*
42148375 GAAAAAGAAATTGAGATTGAGAAAAAAATT
1 GAAAAAGAAAATGAGA-TGAGAAAAAAATT
42148405 GAAAAA
1 GAAAAA
42148411 AAAGATGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 13 0.42
28 1 0.03
30 14 0.45
31 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (29 bp):
GAAAAAGAAAATGAGATGAGAAAAAAATT
Found at i:42148393 original size:18 final size:18
Alignment explanation
Indices: 42148372--42148406 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42148362 AGAAAAGAAA
42148372 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
42148390 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
42148407 AAAAAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:42161908 original size:4 final size:4
Alignment explanation
Indices: 42161899--42161925 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
42161889 GAAACCCATA
42161899 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
42161926 ACTAAGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:42163988 original size:20 final size:20
Alignment explanation
Indices: 42163950--42163988 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42163940 AATAAATAAA
* **
42163950 TTATTACTATTCATTTAATT
1 TTATAACTATTCAAATAATT
42163970 TTATAACTATTCAAATAAT
1 TTATAACTATTCAAATAAT
42163989 ATTGTTTGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATAACTATTCAAATAATT
Found at i:42168137 original size:10 final size:10
Alignment explanation
Indices: 42168108--42168144 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
42168098 TAGGTTCGTA
*
42168108 AAAAAATTTG
1 AAAAAATTTC
42168118 AAACAAATTTC
1 AAA-AAATTTC
42168129 AAAAAATTTC
1 AAAAAATTTC
42168139 AAAAAA
1 AAAAAA
42168145 AAAGAGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.65, C:0.08, G:0.03, T:0.24
Consensus pattern (10 bp):
AAAAAATTTC
Found at i:42168145 original size:11 final size:11
Alignment explanation
Indices: 42168107--42168145 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
42168097 GTAGGTTCGT
*
42168107 AAAAAAATTTG
1 AAAAAAATTTC
*
42168118 AAACAAATTTC
1 AAAAAAATTTC
42168129 -AAAAAATTTC
1 AAAAAAATTTC
42168139 AAAAAAA
1 AAAAAAA
42168146 AAGAGAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.23
Consensus pattern (11 bp):
AAAAAAATTTC
Found at i:42184291 original size:24 final size:25
Alignment explanation
Indices: 42184239--42184291 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
42184229 CTTTCTAGAA
*
42184239 GATTTAGTATTTATTAGTATAATAT
1 GATTTAGCATTTATTAGTATAATAT
*
42184264 -ATTTAGCATTTATTAGTATAGT-T
1 GATTTAGCATTTATTAGTATAATAT
42184287 GATTT
1 GATTT
42184292 GACTCACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (25 bp):
GATTTAGCATTTATTAGTATAATAT
Done.