Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, whole genome shotgun sequence
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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 71 of 100
Found at i:12633112 original size:15 final size:14
Alignment explanation
Indices: 12633092--12633135 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
12633082 TTACTGAAAT
*
12633092 ATTTTATTTTTATTC
1 ATTTTATTTTT-TTA
*
12633107 ATTTTAATTTTTTA
1 ATTTTATTTTTTTA
*
12633121 AATTTATTTTTTTA
1 ATTTTATTTTTTTA
12633135 A
1 A
12633136 AATGGACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTATTTTTTTA
Found at i:12633811 original size:24 final size:23
Alignment explanation
Indices: 12633766--12633815 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
12633756 AAGAAGATGT
**
12633766 AAAATTATAGTTAAAATGTTAATA
1 AAAATTATAAATAAAATGTTAA-A
* *
12633790 AAAATTATAAATAAATTTTTAAA
1 AAAATTATAAATAAAATGTTAAA
12633813 AAA
1 AAA
12633816 TAGAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
AAAATTATAAATAAAATGTTAAA
Found at i:12635759 original size:27 final size:24
Alignment explanation
Indices: 12635705--12635759 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
12635695 TATTTAATTT
* *
12635705 TTAAATAATTTTTAAAATACTAAT
1 TTAAATAATTTTTAAAATAATAAA
*
12635729 TTAAATAATATTTTTTAAATAAATAAA
1 TTAAAT-A-ATTTTTAAAAT-AATAAA
12635756 TTAA
1 TTAA
12635760 TTACATCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 6 0.24
25 1 0.04
26 10 0.40
27 8 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TTAAATAATTTTTAAAATAATAAA
Found at i:12636611 original size:58 final size:59
Alignment explanation
Indices: 12636478--12636623 Score: 161
Period size: 60 Copynumber: 2.5 Consensus size: 59
12636468 GCATTTATAT
* *
12636478 AAGGAAAATTGATACTTTCAACTTTTCCTAAAAAGAAACCTTTTTTAGGAAATTATTTGA
1 AAGGAAAATTGATACTTTCAATTTTTCCTAAAAAGAAA-CTTTTTTAGAAAATTATTTGA
** ** * **
12636538 AAAAAAAATTGATACTTTCAATTTTTCCTCGAAA-ATA-TTTTTTAGAAAACTTATTTTC
1 AAGGAAAATTGATACTTTCAATTTTTCCTAAAAAGAAACTTTTTTAGAAAA-TTATTTGA
*
12636596 AAGGAAAACTGATACTTTCAACTTTTTC
1 AAGGAAAATTGATACTTTCAA-TTTTTC
12636624 TCAACAATAT
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
57 11 0.15
58 24 0.33
59 8 0.11
60 29 0.40
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (59 bp):
AAGGAAAATTGATACTTTCAATTTTTCCTAAAAAGAAACTTTTTTAGAAAATTATTTGA
Found at i:12636633 original size:58 final size:56
Alignment explanation
Indices: 12636478--12636647 Score: 155
Period size: 58 Copynumber: 2.9 Consensus size: 56
12636468 GCATTTATAT
* * * *
12636478 AAGGAAAATTGATACTTTCAACTTTTCCTAAAAAGAAACCTTTTTTAGGAAATTATTTGA
1 AAGGAAAATTGATACTTTCAACTTTTTCT-CAAA-ATA--TTTTTTAGAAAATTATTTGA
** **
12636538 AAAAAAAATTGATACTTTCAA-TTTTTCCTCGAAAATATTTTTTAGAAAACTTATTTTC
1 AAGGAAAATTGATACTTTCAACTTTTT-CTC-AAAATATTTTTTAGAAAA-TTATTTGA
*
12636596 AAGGAAAACTGATACTTTCAACTTTTTCTCAACAATATTATTCTT-GAAAATT
1 AAGGAAAATTGATACTTTCAACTTTTTCTCAA-AATATT-TT-TTAGAAAATT
12636648 TTATTTTATA
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
57 13 0.14
58 35 0.38
59 18 0.20
60 26 0.28
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (56 bp):
AAGGAAAATTGATACTTTCAACTTTTTCTCAAAATATTTTTTAGAAAATTATTTGA
Found at i:12636745 original size:10 final size:9
Alignment explanation
Indices: 12636721--12636772 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
12636711 ACAAACACAT
12636721 AAATAAAAA
1 AAATAAAAA
12636730 AAATAAAAA
1 AAATAAAAA
* *
12636739 ACTATAAACA
1 A-AATAAAAA
12636749 AAATAAACAAA
1 AAAT-AA-AAA
12636760 AAATACAAAA
1 AAATA-AAAA
12636770 AAA
1 AAA
12636773 AATCGAAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
9 12 0.34
10 16 0.46
11 7 0.20
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.12
Consensus pattern (9 bp):
AAATAAAAA
Found at i:12636745 original size:23 final size:22
Alignment explanation
Indices: 12636701--12636774 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
12636691 AAAATATTCC
* *
12636701 AAAAATATAAACAAACACATAAATA
1 AAAAAAATAAA-AAAC-TATAAA-A
12636726 AAAAAAATAAAAAACTATAAACA
1 AAAAAAATAAAAAACTATAAA-A
* * *
12636749 AAATAAACAAAAAA-TACAAAA
1 AAAAAAATAAAAAACTATAAAA
12636770 AAAAA
1 AAAAA
12636775 TCGAAACAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 5 0.12
22 5 0.12
23 18 0.43
24 4 0.10
25 10 0.24
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.12
Consensus pattern (22 bp):
AAAAAAATAAAAAACTATAAAA
Found at i:12641075 original size:9 final size:9
Alignment explanation
Indices: 12641031--12641083 Score: 52
Period size: 9 Copynumber: 5.3 Consensus size: 9
12641021 ACAATGGATG
12641031 AAAAATAAGA
1 AAAAATAA-A
12641041 AAAAATAAA
1 AAAAATAAA
*
12641050 AGAAGATGATGAA
1 A-AA-A--ATAAA
12641063 AAAAATAAA
1 AAAAATAAA
12641072 AAAAATAAA
1 AAAAATAAA
12641081 AAA
1 AAA
12641084 TAGAGGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 18 0.49
10 10 0.27
11 2 0.05
12 2 0.05
13 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.11
Consensus pattern (9 bp):
AAAAATAAA
Found at i:12641093 original size:17 final size:15
Alignment explanation
Indices: 12641060--12641136 Score: 59
Period size: 17 Copynumber: 4.9 Consensus size: 15
12641050 AGAAGATGAT
*
12641060 GAAAAAAATAAAA-A
1 GAAAAAAAAAAAAGA
* *
12641074 -AAATAAAAAATAGA
1 GAAAAAAAAAAAAGA
12641088 GGAAAAAAAAAGAAAGAA
1 -GAAAAAAAAA-AAAG-A
12641106 GAAAAAAGAAAAAATGA
1 GAAAAAA-AAAAAA-GA
12641123 GAAAATAAAAAAAA
1 GAAAA-AAAAAAAA
12641137 AGATTCAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
13 9 0.18
14 1 0.02
16 8 0.16
17 25 0.50
18 7 0.14
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (15 bp):
GAAAAAAAAAAAAGA
Found at i:12641097 original size:32 final size:32
Alignment explanation
Indices: 12641031--12641139 Score: 89
Period size: 32 Copynumber: 3.3 Consensus size: 32
12641021 ACAATGGATG
* * **
12641031 AAAAATAAGAAAAAATAAAAGAAGATGATGAA
1 AAAAATAAGAAAAAATAAAAAAAGAGGAAAAA
12641063 AAAAATAA-AAAAAATAAAAAATAGAGGAAAAA
1 AAAAATAAGAAAAAATAAAAAA-AGAGGAAAAA
*
12641095 AAAAGA-AAGAAGAAAAAAGAAAAAATGA-GAAAATA
1 AAAA-ATAAGAA-AAAATA-AAAAAA-GAGGAAAA-A
*
12641130 AAAAAAAAGA
1 AAAAATAAGA
12641140 TTCAAAATGA
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
31 12 0.19
32 21 0.33
33 3 0.05
34 12 0.19
35 16 0.25
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (32 bp):
AAAAATAAGAAAAAATAAAAAAAGAGGAAAAA
Found at i:12641113 original size:10 final size:9
Alignment explanation
Indices: 12641061--12641137 Score: 50
Period size: 9 Copynumber: 8.4 Consensus size: 9
12641051 GAAGATGATG
*
12641061 AAAAAAATA
1 AAAAAAAGA
*
12641070 AAAAAAATA
1 AAAAAAAGA
*
12641079 AAAAATAGA
1 AAAAAAAGA
**
12641088 GGAAAAA-A
1 AAAAAAAGA
*
12641096 AAAGAAAGA
1 AAAAAAAGA
12641105 AGAAAAAAGA
1 A-AAAAAAGA
*
12641115 AAAAATGAGA
1 AAAAA-AAGA
12641125 AAATAAAA-A
1 AAA-AAAAGA
12641134 AAAA
1 AAAA
12641138 GATTCAAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
8 6 0.11
9 30 0.57
10 15 0.28
11 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:12641152 original size:35 final size:36
Alignment explanation
Indices: 12641061--12641139 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 36
12641051 GAAGATGATG
* *
12641061 AAAAAAATAAAAAAAAT-AAAAAATAGAGGAAAAAA
1 AAAAAAAGAAGAAAAATGAAAAAATAGAGGAAAAAA
* *
12641096 AAAGAAAGAAGAAAAAAGAAAAAAT-GA-GAAAATAA
1 AAAAAAAGAAGAAAAATGAAAAAATAGAGGAAAA-AA
12641131 AAAAAAAGA
1 AAAAAAAGA
12641140 TTCAAAATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
34 5 0.14
35 25 0.68
36 7 0.19
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (36 bp):
AAAAAAAGAAGAAAAATGAAAAAATAGAGGAAAAAA
Found at i:12641308 original size:23 final size:21
Alignment explanation
Indices: 12641266--12641308 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
12641256 GCCAAGCTCA
* *
12641266 GAATGACTTTAACAGTAAATG
1 GAATGACTTTAAAAGAAAATG
12641287 GAATGACTTTTTAAAAGAAAAT
1 GAATGAC--TTTAAAAGAAAAT
12641309 CCTAGATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (21 bp):
GAATGACTTTAAAAGAAAATG
Found at i:12641898 original size:63 final size:63
Alignment explanation
Indices: 12641829--12642013 Score: 316
Period size: 63 Copynumber: 2.9 Consensus size: 63
12641819 ACTAGTGCTT
* * *
12641829 AGAAGCTTATGAATGATGACCAAGTGATAGATGATGAAATTTATCTTGAAATGGCTAGTATTG
1 AGAAGCTTATGAACGATGACCAAGTGACAGATGATGAAATTTATTTTGAAATGGCTAGTATTG
12641892 AGAAGCTTATGAACGATGACCAAGTGACAGATGATGAAATTTATTTTGAAATGGCTAGTATTG
1 AGAAGCTTATGAACGATGACCAAGTGACAGATGATGAAATTTATTTTGAAATGGCTAGTATTG
* * *
12641955 AGAAGCTTATGAACGATGACCAAGTAACAGAAGATGAAATTTATTTTGAAATGGTTAGT
1 AGAAGCTTATGAACGATGACCAAGTGACAGATGATGAAATTTATTTTGAAATGGCTAGT
12642014 GCTGATAAAC
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 116 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (63 bp):
AGAAGCTTATGAACGATGACCAAGTGACAGATGATGAAATTTATTTTGAAATGGCTAGTATTG
Found at i:12642438 original size:21 final size:21
Alignment explanation
Indices: 12642414--12642466 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
12642404 GAACCTTTTG
*
12642414 ATGAAAATTTTTGAATTTCAA
1 ATGAAAATCTTTGAATTTCAA
*
12642435 ATGAGAATCTTTGAATTTCAA
1 ATGAAAATCTTTGAATTTCAA
12642456 A-GAAAAATCTT
1 ATG-AAAATCTT
12642467 AAAGTTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (21 bp):
ATGAAAATCTTTGAATTTCAA
Found at i:12643126 original size:41 final size:41
Alignment explanation
Indices: 12643060--12643282 Score: 139
Period size: 43 Copynumber: 5.3 Consensus size: 41
12643050 GATTGTTAAT
* *
12643060 GAGCCATTTATTTT-TAAAAAGTTATGTTGCCTCTGTTTAGAA
1 GAGCAATTTATTTTCT--AAAGTTATGGTGCCTCTGTTTAGAA
* * *
12643102 GAGCAATTTATTTTCTAAAGTTATGGCGCCTCTATTTAGAG
1 GAGCAATTTATTTTCTAAAGTTATGGTGCCTCTGTTTAGAA
* * * * * *
12643143 GAGCAATTTAATTTCCAAAATTGTGGTGCCTTTGTTTAGAT
1 GAGCAATTTATTTTCTAAAGTTATGGTGCCTCTGTTTAGAA
*** * * * *
12643184 GAGTTTTGTTTATTTT-TCAAAGTCATTGAGCCTCTGTTTAGAG
1 GAG--CAATTTATTTTCT-AAAGTTATGGTGCCTCTGTTTAGAA
* * * * *
12643227 GAGCTTTATTTATTTT-TCAAAGTCATTGTGCCTATGTTTAGAG
1 GAGC--AATTTATTTTCT-AAAGTTATGGTGCCTCTGTTTAGAA
12643270 GAGC-ATTTATTTT
1 GAGCAATTTATTTT
12643283 TCAAAGTCGT
Statistics
Matches: 146, Mismatches: 29, Indels: 14
0.77 0.15 0.07
Matches are distributed among these distances:
40 9 0.06
41 57 0.39
42 13 0.09
43 67 0.46
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (41 bp):
GAGCAATTTATTTTCTAAAGTTATGGTGCCTCTGTTTAGAA
Found at i:12643239 original size:43 final size:43
Alignment explanation
Indices: 12643170--12643462 Score: 326
Period size: 43 Copynumber: 6.9 Consensus size: 43
12643160 AAATTGTGGT
* * * *
12643170 GCCTTTGTTTAGATGAGTTTTGTTTATTTTTCAAAGTCATTGA
1 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGA
*
12643213 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGT
1 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGA
* *
12643256 GCCTATGTTTAGAGGAGC---ATTTATTTTTCAAAGTCGTTGA
1 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGA
* * * *
12643296 GCCTCTGTCTAGAGGAGCTTTGTTTATTTTTTAAAATCATTGA
1 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGA
* * *
12643339 GCCTCTATTTAGAAGAGCTTTATTTATTTTTGCAAAGTCATTAA
1 GCCTCTGTTTAGAGGAGCTTTATTTATTTTT-CAAAGTCATTGA
* * * * **
12643383 GCCTCTATTTAGAGAAGCTTTGTTTATTTTTCTGAAGTGGTTGA
1 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTC-AAAGTCATTGA
* *
12643427 GCCTCTGTTTAGAGAAGC--AATTTATTTTTTCAAAGT
1 GCCTCTGTTTAGAGGAGCTTTATTTA-TTTTTCAAAGT
12643463 TGTTGAGTTT
Statistics
Matches: 212, Mismatches: 32, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
40 36 0.17
42 8 0.04
43 107 0.50
44 61 0.29
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.45
Consensus pattern (43 bp):
GCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGA
Found at i:12643296 original size:83 final size:84
Alignment explanation
Indices: 12643192--12643462 Score: 337
Period size: 83 Copynumber: 3.2 Consensus size: 84
12643182 ATGAGTTTTG
* *
12643192 TTTATTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGTG
1 TTTATTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCATTGAG
*
12643257 CCTATGTTTAGAGGAGC-A
66 CCTCTGTTTAGAGGAGCTA
* * * *
12643275 TTTATTTTTCAAAGTCGTTGAGCCTCTGTCTAGAGGAGCTTTGTTTATTTTTTAAAATCATTGAG
1 TTTATTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCATTGAG
* *
12643340 CCTCTATTTAGAAGAGCTTTA
66 CCTCTGTTTAGAGGAGC--TA
* * * * **
12643361 TTTATTTTTGCAAAGTCATTAAGCCTCTATTTAGAGAAGCTTTGTTTATTTTTCTGAAGTGGTTG
1 TTTATTTTT-CAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTC-AAAGTCATTG
* *
12643426 AGCCTCTGTTTAGAGAAGCAA
64 AGCCTCTGTTTAGAGGAGCTA
12643447 TTTATTTTTTCAAAGT
1 TTTA-TTTTTCAAAGT
12643463 TGTTGAGTTT
Statistics
Matches: 159, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
83 73 0.46
86 21 0.13
87 43 0.27
88 22 0.14
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (84 bp):
TTTATTTTTCAAAGTCATTGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCATTGAG
CCTCTGTTTAGAGGAGCTA
Found at i:12643325 original size:126 final size:127
Alignment explanation
Indices: 12643088--12643440 Score: 390
Period size: 126 Copynumber: 2.8 Consensus size: 127
12643078 AAGTTATGTT
* * * * *
12643088 GCCTCTGTTTAGAAGAGC--AATTTA-TTTTCTAAAGTTATGGCGCCTCTATTTAGAGGAGCAAT
1 GCCTCTGTTTAGAAGAGCTTTATTTATTTTTC-AAAGTCATTGAGCCTCTATTTAGAGGAGCTAT
* * * * * * * * * *
12643150 TTAATTTCCAAAATTGTGGTGCCTTTGTTTAGATGAGTTTTGTTTATTTTTCAAAGTCATTGA
65 TTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAATCATTGA
* * * *
12643213 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGTGCCTATGTTTAGAGGAGC-ATT
1 GCCTCTGTTTAGAAGAGCTTTATTTATTTTTCAAAGTCATTGAGCCTCTATTTAGAGGAGCTATT
* *
12643277 TATTTTTCAAAGTCGTTGAGCCTCTGTCTAGAGGAGCTTTGTTTATTTTTTAAAATCATTGA
66 TATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAATCATTGA
* * *
12643339 GCCTCTATTTAGAAGAGCTTTATTTATTTTTGCAAAGTCATTAAGCCTCTATTTAGAGAAGCTTT
1 GCCTCTGTTTAGAAGAGCTTTATTTATTTTT-CAAAGTCATTGAGCCTCTATTTAGAGGAGC--T
* * *
12643404 GTTTATTTTTCTGAAGTGGTTGAGCCTCTGTTTAGAG
63 ATTTATTTTTC-AAAGTCGTTGAGCCTCTGTTTAGAG
12643441 AAGCAATTTA
Statistics
Matches: 190, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
125 17 0.09
126 82 0.43
127 54 0.28
128 5 0.03
130 10 0.05
131 22 0.12
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (127 bp):
GCCTCTGTTTAGAAGAGCTTTATTTATTTTTCAAAGTCATTGAGCCTCTATTTAGAGGAGCTATT
TATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAATCATTGA
Found at i:12656868 original size:21 final size:22
Alignment explanation
Indices: 12656832--12656874 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
12656822 TTTAGCTTTT
*
12656832 GTATTGAACAATACGAGCATCA
1 GTATTAAACAATACGAGCATCA
12656854 GTATTAAAC-ATACGAGCATCA
1 GTATTAAACAATACGAGCATCA
12656875 CCTTTTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (22 bp):
GTATTAAACAATACGAGCATCA
Found at i:12659649 original size:14 final size:14
Alignment explanation
Indices: 12659630--12659661 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
12659620 TTTCCTTTTC
12659630 AAATATATTTTATA
1 AAATATATTTTATA
*
12659644 AAATATGTTTTATA
1 AAATATATTTTATA
12659658 AAAT
1 AAAT
12659662 GAAAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
AAATATATTTTATA
Found at i:12659882 original size:32 final size:31
Alignment explanation
Indices: 12659788--12659896 Score: 91
Period size: 31 Copynumber: 3.5 Consensus size: 31
12659778 ATAAATCTAT
*
12659788 TTTTTAAAA-TACTAT-GAAAATTTTTACATAA
1 TTTTTAAAACTA-TATAG-AAATTTTTACTTAA
* *
12659819 TATTTTAAAACTATATAG-AGTTTTTATTTAA
1 T-TTTTAAAACTATATAGAAATTTTTACTTAA
*
12659850 TTTCTTAAAGC-ATTATAGAAATTTTTACTTAA
1 TTT-TTAAAACTA-TATAGAAATTTTTACTTAA
* *
12659882 TTTTTTAAATTATAT
1 TTTTTAAAACTATAT
12659897 CTACTTTAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
30 3 0.05
31 30 0.48
32 26 0.42
33 3 0.05
ACGTcount: A:0.39, C:0.06, G:0.05, T:0.50
Consensus pattern (31 bp):
TTTTTAAAACTATATAGAAATTTTTACTTAA
Found at i:12659925 original size:13 final size:15
Alignment explanation
Indices: 12659885--12659925 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
12659875 TACTTAATTT
12659885 TTTAAATTATATCTAC
1 TTTAAATTATA-CTAC
12659901 TTTAAATATATA-TA-
1 TTTAAAT-TATACTAC
12659915 TTTAAATTATA
1 TTTAAATTATA
12659926 GACATTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.17
14 7 0.29
15 2 0.08
16 7 0.29
17 4 0.17
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTAAATTATACTAC
Found at i:12659925 original size:15 final size:16
Alignment explanation
Indices: 12659885--12659925 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
12659875 TACTTAATTT
*
12659885 TTTAAATTATATCTAC
1 TTTAAATTATATATAC
12659901 TTTAAA-TATATATA-
1 TTTAAATTATATATAC
12659915 TTTAAATTATA
1 TTTAAATTATA
12659926 GACATTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 6 0.26
15 11 0.48
16 6 0.26
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAAATTATATATAC
Found at i:12660626 original size:16 final size:17
Alignment explanation
Indices: 12660590--12660626 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
12660580 TATTAAACTT
*
12660590 AATTTTTATTTTTATAT
1 AATTTTTATTTTTATAA
12660607 AATTTTTATTTTT-TAA
1 AATTTTTATTTTTATAA
12660623 AATT
1 AATT
12660627 GCATATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
AATTTTTATTTTTATAA
Found at i:12662677 original size:52 final size:52
Alignment explanation
Indices: 12662590--12662746 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
12662580 TGGACAAGAA
* * *
12662590 GACTTGCAAAAGAATAATTCTAAGA-GAAATAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAA-GGGATTCTTAATAGGTAAGTTT
* * *
12662642 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAATTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
* * * *
12662694 GACTTACAGGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
12662746 G
1 G
12662747 TATGGTTATA
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
52 87 0.96
53 4 0.04
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.27
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
Found at i:12667288 original size:17 final size:16
Alignment explanation
Indices: 12667247--12667290 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
12667237 TTTTAAGATC
12667247 TTAAGG-TTTTAGGGT
1 TTAAGGTTTTTAGGGT
*
12667262 TTTAGAGTTTTTAGGGT
1 TTAAG-GTTTTTAGGGT
12667279 TTCAAGGTTTTT
1 TT-AAGGTTTTT
12667291 TCCTCTTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 4 0.17
16 1 0.04
17 17 0.71
18 2 0.08
ACGTcount: A:0.18, C:0.02, G:0.27, T:0.52
Consensus pattern (16 bp):
TTAAGGTTTTTAGGGT
Found at i:12668328 original size:17 final size:16
Alignment explanation
Indices: 12668306--12668347 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
12668296 AAACTACTTT
12668306 TCTCTTTCTTTTTCTTC
1 TCTCTTTC-TTTTCTTC
12668323 TCTCTTATCTTTTCTTC
1 TCTCTT-TCTTTTCTTC
*
12668340 TTTCTTTC
1 TCTCTTTC
12668348 CATTCGCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (16 bp):
TCTCTTTCTTTTCTTC
Found at i:12668465 original size:22 final size:22
Alignment explanation
Indices: 12668440--12668486 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
12668430 CTCTTCCATC
12668440 TCTCTCTTATTT-TTATTCTTCT
1 TCTCTCTTATTTGTT-TTCTTCT
* *
12668462 TCTCTTTTCTTTGTTTTCTTCT
1 TCTCTCTTATTTGTTTTCTTCT
12668484 TCT
1 TCT
12668487 TCCTCCTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.04, C:0.23, G:0.02, T:0.70
Consensus pattern (22 bp):
TCTCTCTTATTTGTTTTCTTCT
Found at i:12679688 original size:18 final size:18
Alignment explanation
Indices: 12679655--12679689 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12679645 TTATTTTATT
*
12679655 AATATTTATGTATGTTAA
1 AATATTTATATATGTTAA
*
12679673 AATATTTATATTTGTTA
1 AATATTTATATATGTTA
12679690 GACTAATTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (18 bp):
AATATTTATATATGTTAA
Found at i:12683963 original size:4 final size:4
Alignment explanation
Indices: 12683954--12683980 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
12683944 AAATTGGTAT
12683954 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
12683981 TCCATATTTC
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:12684349 original size:3 final size:3
Alignment explanation
Indices: 12684341--12684424 Score: 152
Period size: 3 Copynumber: 28.3 Consensus size: 3
12684331 ACAAAAATTG
12684341 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
12684389 ATA ATA ATA ATA ATA ATA ATA ATA AT- AGA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12684425 AAAAGGATTT
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 1 0.01
3 77 0.99
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:12684544 original size:14 final size:14
Alignment explanation
Indices: 12684525--12684563 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
12684515 AATTATTAAA
*
12684525 TAATTAATAATTAC
1 TAATTAATAAATAC
12684539 TAATTAATAAATAC
1 TAATTAATAAATAC
12684553 TAA-TAATAAAT
1 TAATTAATAAAT
12684564 TTTTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATTAATAAATAC
Found at i:12684851 original size:16 final size:16
Alignment explanation
Indices: 12684760--12685370 Score: 173
Period size: 16 Copynumber: 39.2 Consensus size: 16
12684750 TCCAAATCCA
*
12684760 AAACCTTAAAACCTTTC
1 AAACCCTAAAACC-TTC
*
12684777 AAACCCT-AAACCATC
1 AAACCCTAAAACCTTC
*
12684792 GAAACACT-AAACCTTC
1 -AAACCCTAAAACCTTC
** *
12684808 GAAACTTTAAAACTCTTG
1 -AAACCCTAAAAC-CTTC
12684826 AAACCCTAAAATCCTTC
1 AAACCCTAAAA-CCTTC
*
12684843 AAA-CCTAAAACCCTTG
1 AAACCCTAAAA-CCTTC
*
12684859 AAACCTTAAAA-C-TC
1 AAACCCTAAAACCTTC
12684873 AAACCCTAAAACCTTTC
1 AAACCCTAAAACC-TTC
*
12684890 AAACCCTAAACCCTTC
1 AAACCCTAAAACCTTC
12684906 AAACCCTAAAA-C--C
1 AAACCCTAAAACCTTC
* *
12684919 AAACCTTAAAACCTTT
1 AAACCCTAAAACCTTC
* * * *
12684935 AAATGCTTAAAAGAC--A
1 AAA-CCCTAAAA-CCTTC
*
12684951 AAACCCTAAAA-CAT-
1 AAACCCTAAAACCTTC
* * * *
12684965 AAAACCGAAAACCATG
1 AAACCCTAAAACCTTC
* * * * *
12684981 TATCCCCAAAACTTTA
1 AAACCCTAAAACCTTC
**
12684997 AAACTTTAAAACC-TC
1 AAACCCTAAAACCTTC
*
12685012 GAACCCTTAAAACCTT-
1 AAACCC-TAAAACCTTC
*
12685028 ------TAAAACCCT-
1 AAACCCTAAAACCTTC
* *
12685037 GAACCCTTAAAACCTTTA
1 AAACCC-TAAAACC-TTC
12685055 AAACCCT-AAACC-TC
1 AAACCCTAAAACCTTC
*
12685069 AAAACTCC-AAAA-CTTT
1 -AAAC-CCTAAAACCTTC
*
12685085 AGACCCTAAAACCTTC
1 AAACCCTAAAACCTTC
* *
12685101 AAACCCTAAAACTTTA
1 AAACCCTAAAACCTTC
** *
12685117 AAAGAACTAAAACCTTTA
1 AAA-CCCTAAAACC-TTC
* *
12685135 AAACCCTAAAATC-TA
1 AAACCCTAAAACCTTC
*
12685150 AAACCCT-AAACC-CC
1 AAACCCTAAAACCTTC
* * *
12685164 AAAATCC-AAAAACTTT
1 -AAACCCTAAAACCTTC
* *
12685180 AAACTCT-AAACCTCC
1 AAACCCTAAAACCTTC
*
12685195 AAACCCTAAAACTCTCC
1 AAACCCTAAAAC-CTTC
** ** *
12685212 AAAACCAAAAAAATTTA
1 -AAACCCTAAAACCTTC
* * *
12685229 AAACCTTAAAA-TTTA
1 AAACCCTAAAACCTTC
*
12685244 AAACCCTAAAACCCTCC
1 AAACCCTAAAA-CCTTC
*
12685261 AAA-CCT-AAACCCTC
1 AAACCCTAAAACCTTC
12685275 TAAACCCT-AAACCTTTC
1 -AAACCCTAAAACC-TTC
* *
12685292 CAACCCTAAAACCTCC
1 AAACCCTAAAACCTTC
* *
12685308 AAACCTTAAAACCTTA
1 AAACCCTAAAACCTTC
*
12685324 AAACCCTAAAA--TCC
1 AAACCCTAAAACCTTC
* * *
12685338 AAAACCTAAAAACTTA
1 AAACCCTAAAACCTTC
12685354 AAACCC-AAAA-CTTC
1 AAACCCTAAAACCTTC
12685368 AAA
1 AAA
12685371 ACTTTAAAGC
Statistics
Matches: 442, Mismatches: 101, Indels: 105
0.68 0.16 0.16
Matches are distributed among these distances:
9 8 0.02
13 12 0.03
14 48 0.11
15 87 0.20
16 177 0.40
17 85 0.19
18 25 0.06
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.21
Consensus pattern (16 bp):
AAACCCTAAAACCTTC
Found at i:12684870 original size:8 final size:8
Alignment explanation
Indices: 12684809--12685386 Score: 107
Period size: 8 Copynumber: 73.2 Consensus size: 8
12684799 TAAACCTTCG
*
12684809 AAACTTTA
1 AAACCTTA
*
12684817 AAACTCTTG
1 AAAC-CTTA
*
12684826 AAACCCTA
1 AAACCTTA
*
12684834 AAATCCTTC
1 AAA-CCTTA
12684843 AAACC-TA
1 AAACCTTA
*
12684850 AAACCCTTG
1 AAA-CCTTA
12684859 AAACCTTA
1 AAACCTTA
*
12684867 AAA-C-TC
1 AAACCTTA
*
12684873 AAACCCTA
1 AAACCTTA
*
12684881 AAACCTTTC
1 AAACC-TTA
*
12684890 AAACCCTA
1 AAACCTTA
* *
12684898 AACCCTTC
1 AAACCTTA
*
12684906 AAACCCTA
1 AAACCTTA
12684914 AAACC---
1 AAACCTTA
12684919 AAACCTTA
1 AAACCTTA
12684927 AAACCTTTA
1 AAACC-TTA
**
12684936 AATGCTTA
1 AAACCTTA
*
12684944 AAAGAC--A
1 AAA-CCTTA
*
12684951 AAACCCTA
1 AAACCTTA
*
12684959 AAA-CATA
1 AAACCTTA
*
12684966 AAACC-GA
1 AAACCTTA
* *
12684973 AAACCATG
1 AAACCTTA
* * **
12684981 TATCCCCA
1 AAACCTTA
*
12684989 AAACTTTA
1 AAACCTTA
*
12684997 AAACTTTA
1 AAACCTTA
**
12685005 AAACCTCG
1 AAACCTTA
*
12685013 AACCCTTA
1 AAACCTTA
12685021 AAACCTTTA
1 AAACC-TTA
* *
12685030 AAACCCTG
1 AAACCTTA
*
12685038 AACCCTTA
1 AAACCTTA
12685046 AAACCTTTA
1 AAACC-TTA
*
12685055 AAACCCT-
1 AAACCTTA
*
12685062 AAACCTCA
1 AAACCTTA
*
12685070 AAA-CTCCA
1 AAACCT-TA
*
12685078 AAA-CTTT
1 AAACCTTA
* *
12685085 AGACCCTA
1 AAACCTTA
*
12685093 AAACCTTC
1 AAACCTTA
*
12685101 AAACCCTA
1 AAACCTTA
*
12685109 AAACTTTAA
1 AAACCTT-A
*
12685118 AAGAAC-TA
1 AA-ACCTTA
12685126 AAACCTTTA
1 AAACC-TTA
*
12685135 AAACCCTA
1 AAACCTTA
*
12685143 AAATC-TA
1 AAACCTTA
*
12685150 AAACCCT-
1 AAACCTTA
**
12685157 AAACCCCA
1 AAACCTTA
12685165 AAATCC--A
1 AAA-CCTTA
* *
12685172 AAAACTTT
1 AAACCTTA
12685180 AAA-CTCT-
1 AAACCT-TA
**
12685187 AAACCTCC
1 AAACCTTA
*
12685195 AAACCCTA
1 AAACCTTA
*
12685203 AAACTCTCCA
1 AAAC-CT-TA
**
12685213 AAACCAAA
1 AAACCTTA
**
12685221 AAAATTTA
1 AAACCTTA
12685229 AAACCTTA
1 AAACCTTA
*
12685237 AAA-TTTA
1 AAACCTTA
*
12685244 AAACCCTA
1 AAACCTTA
**
12685252 AAACCCTCC
1 AAA-CCTTA
12685261 AAACC-TA
1 AAACCTTA
*
12685268 AACCCTCT-
1 AAACCT-TA
*
12685276 AAACCCT-
1 AAACCTTA
*
12685283 AAACCTTTC
1 AAACC-TTA
* *
12685292 CAACCCTA
1 AAACCTTA
**
12685300 AAACCTCC
1 AAACCTTA
12685308 AAACCTTA
1 AAACCTTA
12685316 AAACCTTA
1 AAACCTTA
*
12685324 AAACCCTA
1 AAACCTTA
12685332 AAATCC--A
1 AAA-CCTTA
12685339 AAACC-TA
1 AAACCTTA
*
12685346 AAAACTTA
1 AAACCTTA
*
12685354 AAACC-CA
1 AAACCTTA
12685361 AAA-CTTCA
1 AAACCTT-A
*
12685369 AAACTTTA
1 AAACCTTA
*
12685377 AAGCCTTA
1 AAACCTTA
12685385 AA
1 AA
12685387 TTCAAAGCCC
Statistics
Matches: 403, Mismatches: 120, Indels: 94
0.65 0.19 0.15
Matches are distributed among these distances:
5 5 0.01
6 9 0.02
7 83 0.21
8 226 0.56
9 74 0.18
10 6 0.01
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (8 bp):
AAACCTTA
Found at i:12684913 original size:33 final size:32
Alignment explanation
Indices: 12684768--12684918 Score: 123
Period size: 33 Copynumber: 4.7 Consensus size: 32
12684758 CAAAACCTTA
* *
12684768 AAACCTTTCAAACCCT-AAACC-ATCGAAACACT
1 AAACC-TTCAAACCCTAAAACCTTTC-AAACCCT
** *
12684800 AAACCTTCGAAACTTTAAAA-CTCTTGAAACCCT
1 AAACCTTC-AAACCCTAAAACCT-TTCAAACCCT
* * *
12684833 AAAATCCTTCAAA-CCTAAAACCCTTGAAACCTT
1 -AAA-CCTTCAAACCCTAAAACCTTTCAAACCCT
*
12684866 AAAAC-TCAAACCCTAAAACCTTTCAAACCCT
1 AAACCTTCAAACCCTAAAACCTTTCAAACCCT
12684897 AAACCCTTCAAACCCTAAAACC
1 AAA-CCTTCAAACCCTAAAACC
12684919 AAACCTTAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
30 5 0.05
31 24 0.25
32 15 0.16
33 38 0.40
34 8 0.08
35 5 0.05
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.21
Consensus pattern (32 bp):
AAACCTTCAAACCCTAAAACCTTTCAAACCCT
Found at i:12685031 original size:25 final size:25
Alignment explanation
Indices: 12684994--12685066 Score: 114
Period size: 25 Copynumber: 3.0 Consensus size: 25
12684984 CCCCAAAACT
12684994 TTAAAA-CTTTAAAA-CCTCGAACCC
1 TTAAAACCTTTAAAACCCT-GAACCC
12685018 TTAAAACCTTTAAAACCCTGAACCC
1 TTAAAACCTTTAAAACCCTGAACCC
*
12685043 TTAAAACCTTTAAAACCCTAAACC
1 TTAAAACCTTTAAAACCCTGAACC
12685067 TCAAAACTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
24 6 0.13
25 37 0.80
26 3 0.07
ACGTcount: A:0.42, C:0.30, G:0.03, T:0.25
Consensus pattern (25 bp):
TTAAAACCTTTAAAACCCTGAACCC
Found at i:12685097 original size:31 final size:30
Alignment explanation
Indices: 12685038--12685207 Score: 89
Period size: 30 Copynumber: 5.4 Consensus size: 30
12685028 TAAAACCCTG
*
12685038 AACCCTTAAAACCTTTAAAACCCTAAACC-TCAA
1 AACCC-TAAAA-CTTT-AGACCCTAAACCTTC-A
12685071 AACTCC-AAAACTTTAGACCCTAAAACCTTCA
1 AAC-CCTAAAACTTTAGACCCT-AAACCTTCA
* *
12685102 AACCCTAAAACTTTAAAAGA-ACTAAAACCTTTAA
1 AACCCTAAAACTTT---AGACCCT-AAACC-TTCA
* * *
12685136 AACCCTAAAA-TCTAAAACCCTAAACC-CCAA
1 AACCCTAAAACT-TTAGACCCTAAACCTTC-A
* * * * *
12685166 AATCCAAAAACTTTAAACTCTAAACCTCCA
1 AACCCTAAAACTTTAGACCCTAAACCTTCA
12685196 AACCCTAAAACT
1 AACCCTAAAACT
12685208 CTCCAAAACC
Statistics
Matches: 110, Mismatches: 14, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
30 40 0.36
31 31 0.28
32 8 0.07
33 12 0.11
34 19 0.17
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.21
Consensus pattern (30 bp):
AACCCTAAAACTTTAGACCCTAAACCTTCA
Found at i:12685152 original size:33 final size:33
Alignment explanation
Indices: 12685090--12685152 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
12685080 ACTTTAGACC
* *
12685090 CTAAAACCTTCAAACCCTAAAACTTTAAAAGAA
1 CTAAAACCTTAAAACCCTAAAACTCTAAAAGAA
12685123 CTAAAACCTTTAAAACCCTAAAA-TCTAAAA
1 CTAAAACC-TTAAAACCCTAAAACTCTAAAA
12685153 CCCTAAACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 14 0.52
34 13 0.48
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.22
Consensus pattern (33 bp):
CTAAAACCTTAAAACCCTAAAACTCTAAAAGAA
Found at i:12685348 original size:30 final size:31
Alignment explanation
Indices: 12685089--12685386 Score: 121
Period size: 30 Copynumber: 9.5 Consensus size: 31
12685079 AACTTTAGAC
* **
12685089 CCTAAAACCTTCAAACCCTAAAACTTTAAAAGA
1 CCTAAAACCTTAAAACCCTAAAAC-TCCAAA-A
* *
12685122 ACTAAAACCTTTAAAACCCTAAAA-TCTAAAA
1 CCTAAAACC-TTAAAACCCTAAAACTCCAAAA
** * * **
12685153 CCCT-AAACCCCAAAATCCAAAAACT-TTAAA
1 -CCTAAAACCTTAAAACCCTAAAACTCCAAAA
**
12685183 CTCT-AAACCTCCAAACCCTAAAACTCTCCAAAA
1 C-CTAAAACCTTAAAACCCTAAAA--CTCCAAAA
* ** * **
12685216 CCAAAAAAATTTAAAACCTTAAAA-TTTAAAA
1 CC-TAAAACCTTAAAACCCTAAAACTCCAAAA
** * * *
12685247 CCCTAAAACCCTCCAAA-CCTAAACCCTCTAAAC
1 -CCTAAAA-CCTTAAAACCCTAAA-ACTCCAAAA
**
12685280 CCT-AAACCTTTCCAACCCTAAAACCTCC-AAA
1 CCTAAAACC-TTAAAACCCTAAAA-CTCCAAAA
12685311 CCTTAAAACCTTAAAACCCTAAAA-TCCAAAA
1 CC-TAAAACCTTAAAACCCTAAAACTCCAAAA
* *
12685342 CCTAAAAACTTAAAACCC-AAAACTTCAAAA
1 CCTAAAACCTTAAAACCCTAAAACTCCAAAA
* *
12685372 CTTTAAAGCCTTAAA
1 C-CTAAAACCTTAAA
12685387 TTCAAAGCCC
Statistics
Matches: 199, Mismatches: 45, Indels: 44
0.69 0.16 0.15
Matches are distributed among these distances:
29 5 0.03
30 58 0.29
31 47 0.24
32 40 0.20
33 22 0.11
34 27 0.14
ACGTcount: A:0.49, C:0.31, G:0.01, T:0.20
Consensus pattern (31 bp):
CCTAAAACCTTAAAACCCTAAAACTCCAAAA
Found at i:12685355 original size:22 final size:22
Alignment explanation
Indices: 12685315--12685374 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
12685305 TCCAAACCTT
* * *
12685315 AAAACCTTAAAACCCTAAAATCC
1 AAAACC-TAAAAACTTAAAACCC
12685338 AAAACCTAAAAACTTAAAACCC
1 AAAACCTAAAAACTTAAAACCC
* *
12685360 AAAACTTCAAAACTT
1 AAAACCTAAAAACTT
12685375 TAAAGCCTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (22 bp):
AAAACCTAAAAACTTAAAACCC
Found at i:12685356 original size:15 final size:15
Alignment explanation
Indices: 12685308--12685372 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 15
12685298 TAAAACCTCC
*
12685308 AAACCTTAAAACCTTA
1 AAACC-TAAAAACTTA
* *
12685324 AAACCCTAAAATC-CA
1 AAA-CCTAAAAACTTA
12685339 AAACCTAAAAACTTA
1 AAACCTAAAAACTTA
*
12685354 AAACC-CAAAACTTCA
1 AAACCTAAAAACTT-A
12685369 AAAC
1 AAAC
12685373 TTTAAAGCCT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
14 15 0.37
15 15 0.37
16 9 0.22
17 2 0.05
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (15 bp):
AAACCTAAAAACTTA
Found at i:12685400 original size:22 final size:23
Alignment explanation
Indices: 12685375--12685433 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 23
12685365 TTCAAAACTT
* *
12685375 TAAAGCCTTAAATTCAAAG-CCC
1 TAAAGCCTTAAAATCAAAGACCA
* *
12685397 TAAA-CCCTAAAATCATAGACCA
1 TAAAGCCTTAAAATCAAAGACCA
12685419 TCAAAGCCTTAAAAT
1 T-AAAGCCTTAAAAT
12685434 TTTAAAACCC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 11 0.38
22 7 0.24
23 3 0.10
24 8 0.28
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.22
Consensus pattern (23 bp):
TAAAGCCTTAAAATCAAAGACCA
Found at i:12685449 original size:16 final size:16
Alignment explanation
Indices: 12685428--12685476 Score: 66
Period size: 15 Copynumber: 3.2 Consensus size: 16
12685418 ATCAAAGCCT
12685428 TAAAATTTTAAAACCC
1 TAAAATTTTAAAACCC
*
12685444 TAAAA-TTGAAAA-CC
1 TAAAATTTTAAAACCC
*
12685458 TAAAATCTTAAAACCC
1 TAAAATTTTAAAACCC
12685474 TAA
1 TAA
12685477 TCTTGAAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 7 0.25
15 11 0.39
16 10 0.36
ACGTcount: A:0.53, C:0.18, G:0.02, T:0.27
Consensus pattern (16 bp):
TAAAATTTTAAAACCC
Found at i:12685462 original size:30 final size:30
Alignment explanation
Indices: 12685425--12685493 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
12685415 ACCATCAAAG
*
12685425 CCTTAAAATTTTAAAACCCTAAAATTGAAAA
1 CCTTAAAATCTTAAAACCCTAAAATTG-AAA
**
12685456 CC-TAAAATCTTAAAACCCTAATCTTGAAA
1 CCTTAAAATCTTAAAACCCTAAAATTGAAA
12685485 CCTTAAAAT
1 CCTTAAAAT
12685494 GAGATCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 5 0.15
30 27 0.79
31 2 0.06
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.29
Consensus pattern (30 bp):
CCTTAAAATCTTAAAACCCTAAAATTGAAA
Found at i:12686344 original size:57 final size:57
Alignment explanation
Indices: 12686047--12686492 Score: 663
Period size: 57 Copynumber: 7.7 Consensus size: 57
12686037 TTTTTTTTAG
12686047 GGAAAATTGATACTTTCAACTTTTCCC-AAAAAT-TTTTTT-GAAATTTATTTC-AA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTCTAA
*
12686100 GGAAAATTGATACTTTCAACTTTTCCCCAAAAACCCCT-TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAA----TATTTTTTGGAAATTTATTTCTAA
12686160 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTA-TTCTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGGAAATTTATTTC-TAA
12686218 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA---TTTTTTGGAAATTTATTTCTAA
*
12686278 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTAGAAATTTA-TTCTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTC-TAA
* * *
12686335 GGAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA--TTTTTTGGAAATTTATTTCTAA
*
12686394 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTCTAA
*
12686451 GAAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTT
12686493 TTAGAATTTT
Statistics
Matches: 364, Mismatches: 11, Indels: 31
0.90 0.03 0.08
Matches are distributed among these distances:
53 27 0.07
54 5 0.01
56 4 0.01
57 108 0.30
58 65 0.18
59 61 0.17
60 91 0.25
61 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTCTAA
Found at i:12686353 original size:117 final size:116
Alignment explanation
Indices: 12686047--12686494 Score: 724
Period size: 116 Copynumber: 3.9 Consensus size: 116
12686037 TTTTTTTTAG
*
12686047 GGAAAATTGATACTTTCAACTTTTCCC-AAAAAT-TTTTTT-GAAATTTATTTCAAGGAAAATTG
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTTAAGGAAAATTG
* ****
12686109 ATACTTTCAACTTTTCCCCAAAAACCCCTTTTTTTGGAAATTTATTTCTAA
66 ATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTATTTCTAA
12686160 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTCTTAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGGAAATTTATT-TTAAGGAAAAT
12686225 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTATTTCTAA
64 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTATTTCTAA
*
12686278 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTAGAAATTTATTCTTAAGGAAAATT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATT-TTAAGGAAAATT
* *
12686343 GATACTTTCAACTTTTTCCTAAAAATATTTTTTTTT-GAAATTTATTTCTGA
65 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTATTTCTAA
* *
12686394 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGAAAAATT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTT-TAAGGAAAATT
*
12686459 GATACTTTCAACTTTTCCCTAAAAATATATTTTTTT
65 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTTT
12686495 AGAATTTTTT
Statistics
Matches: 315, Mismatches: 14, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
113 27 0.09
114 6 0.02
115 1 0.00
116 114 0.36
117 74 0.23
118 93 0.30
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.44
Consensus pattern (116 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTTAAGGAAAATTG
ATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTATTTCTAA
Found at i:12686368 original size:27 final size:27
Alignment explanation
Indices: 12686280--12686368 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
12686270 ATTTCTAAGG
*
12686280 AAAATTGATACTTTCAACTTTTCCCTA
1 AAAATTGATACTTTCAACTTTTTCCTA
** * * *
12686307 AAAA-T-ATTTTTTAGAAATTTATTCTTAA
1 AAAATTGATACTTT-CAACTTT-TTCCT-A
12686335 GGAAAATTGATACTTTCAACTTTTTCCTA
1 --AAAATTGATACTTTCAACTTTTTCCTA
12686364 AAAAT
1 AAAAT
12686369 ATTTTTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 14
0.64 0.16 0.20
Matches are distributed among these distances:
25 5 0.11
26 6 0.14
27 12 0.27
28 1 0.02
29 1 0.02
30 8 0.18
31 6 0.14
32 5 0.11
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTTCCTA
Found at i:12686604 original size:8 final size:7
Alignment explanation
Indices: 12686574--12686634 Score: 56
Period size: 7 Copynumber: 8.4 Consensus size: 7
12686564 CTAATCTAAT
12686574 AAATAAA
1 AAATAAA
12686581 AAATAAA
1 AAATAAA
12686588 AAAT--A
1 AAATAAA
12686593 AAATAAA
1 AAATAAA
12686600 CAAATAAA
1 -AAATAAA
12686608 CAAATAAACAA
1 -AAAT--A-AA
12686619 AAATAAA
1 AAATAAA
12686626 AAA-AAA
1 AAATAAA
12686632 AAA
1 AAA
12686635 CCTGGAGCGG
Statistics
Matches: 48, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
5 5 0.10
6 6 0.12
7 17 0.35
8 13 0.27
10 5 0.10
11 2 0.04
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (7 bp):
AAATAAA
Found at i:12686614 original size:16 final size:15
Alignment explanation
Indices: 12686574--12686619 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 15
12686564 CTAATCTAAT
12686574 AAATAAAAAATAAA-
1 AAATAAAAAATAAAC
12686588 AAAT--AAAATAAAC
1 AAATAAAAAATAAAC
12686601 AAATAAACAAATAAAC
1 AAATAAA-AAATAAAC
12686617 AAA
1 AAA
12686620 AATAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 8 0.29
13 4 0.14
14 4 0.14
15 1 0.04
16 11 0.39
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (15 bp):
AAATAAAAAATAAAC
Found at i:12686965 original size:18 final size:18
Alignment explanation
Indices: 12686942--12686984 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
12686932 GAACACCGGT
*
12686942 GCCGGATTTGGAAAATTC
1 GCCGGATCTGGAAAATTC
*
12686960 GCCGGAATCTGGAAATTTC
1 GCCGG-ATCTGGAAAATTC
12686979 GCCGGA
1 GCCGGA
12686985 AGTTGGCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (18 bp):
GCCGGATCTGGAAAATTC
Found at i:12687164 original size:25 final size:25
Alignment explanation
Indices: 12687118--12687165 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
12687108 AATCTGGAAA
*
12687118 TTTCCCAGAAATTTCCAGAAAAATT
1 TTTCCCAGAAATTTCCAAAAAAATT
*
12687143 TTTCGCCA-AAATTTCTAAAAAAA
1 TTTC-CCAGAAATTTCCAAAAAAA
12687166 ATTCTCCTCA
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:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (25 bp):
TTTCCCAGAAATTTCCAAAAAAATT
Found at i:12687923 original size:1 final size:1
Alignment explanation
Indices: 12687919--12688006 Score: 95
Period size: 1 Copynumber: 88.0 Consensus size: 1
12687909 TTTTTAAAAA
* * * * * * * *
12687919 TTTTTGTTTTTTTGTTTTTTGTTTTTGTTTTTTGTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
12687984 TGTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTT
12688007 GCCGAAGTTC
Statistics
Matches: 69, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (1 bp):
T
Found at i:12687932 original size:8 final size:8
Alignment explanation
Indices: 12687919--12688007 Score: 127
Period size: 8 Copynumber: 11.8 Consensus size: 8
12687909 TTTTTAAAAA
12687919 TTTTTGTT
1 TTTTTGTT
12687927 TTTTTG-T
1 TTTTTGTT
12687934 TTTTTG--
1 TTTTTGTT
12687940 TTTTTG-T
1 TTTTTGTT
12687947 TTTTTGTT
1 TTTTTGTT
12687955 TTTTTGTTT
1 TTTTTG-TT
12687964 TTTTTGTT
1 TTTTTGTT
12687972 TTTTTGTT
1 TTTTTGTT
12687980 TTTTTGTT
1 TTTTTGTT
12687988 TTTTT-TT
1 TTTTTGTT
12687995 TTTTT-TT
1 TTTTTGTT
12688002 TTTTTG
1 TTTTTG
12688008 CCGAAGTTCC
Statistics
Matches: 77, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.08
7 27 0.35
8 36 0.47
9 8 0.10
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTTGTT
Found at i:12687972 original size:45 final size:46
Alignment explanation
Indices: 12687919--12688005 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
12687909 TTTTTAAAAA
12687919 TTTTTGTTTTTTTG-TTTTTTGTTTTTGTTTTTTGTTTTTTTGTTT
1 TTTTTGTTTTTTTGTTTTTTTGTTTTTGTTTTTTGTTTTTTTGTTT
* *
12687964 TTTTTGTTTTTTTGTTTTTTTGTTTTTTTTTTTTTTTTTTTT
1 TTTTTGTTTTTTTGTTTTTTTGTTTTTGTTTTTTGTTTTTTT
12688006 TGCCGAAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 14 0.36
46 25 0.64
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (46 bp):
TTTTTGTTTTTTTGTTTTTTTGTTTTTGTTTTTTGTTTTTTTGTTT
Found at i:12688076 original size:42 final size:42
Alignment explanation
Indices: 12688015--12688507 Score: 722
Period size: 41 Copynumber: 11.9 Consensus size: 42
12688005 TTGCCGAAGT
* *
12688015 TCCTCTAAACAGAGACACCACGACTTTGGAAAAATAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
*
12688057 TCCTCTCAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
* *
12688099 TCCTCTAAACAGAGGTATCACGACTTT-GAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
12688140 TCCTCTAAACAGAGGCA--ACGAAC-TTGGAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAATTGC
*
12688180 TCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
* * * * *
12688222 TCCTCTCAACAGAGGTATCACGACTTTGAAAAAATAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
12688264 TCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
* * *
12688305 TCCTCTCAACAGAGGTACCACGACTTTGGAAAAATAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
*
12688347 TCCTCTAAACAGAGGCA--ACGGAACTTT-GAAAAATAAATTGC
1 TCCTCTAAACAGAGGCACCAC-G-ACTTTGGAAAAGTAAATTGC
12688388 TCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
12688429 TCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
*
12688470 TCCTCTAAACAGAGGCA--ACGAACTTTGAAAAAGTAAAT
1 TCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAAT
12688508 ACTCCTAGAC
Statistics
Matches: 414, Mismatches: 24, Indels: 27
0.89 0.05 0.06
Matches are distributed among these distances:
39 8 0.02
40 40 0.10
41 185 0.45
42 179 0.43
43 2 0.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (42 bp):
TCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
Found at i:12688288 original size:165 final size:164
Alignment explanation
Indices: 12688015--12688507 Score: 760
Period size: 165 Copynumber: 3.0 Consensus size: 164
12688005 TTGCCGAAGT
*
12688015 TCCTCTAAACAGAGACACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACGA
1 TCCTCTAAACAGAG-GACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACGA
* * *
12688080 CTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGTATCACGACTTTGAAAAGTAAATTGCTCCTC
65 CTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTC
12688145 TAAACAGAGGCAACGAAC-TTGGAAAAGTAAATTGC
129 TAAACAGAGGCAACGAACTTTGGAAAAGTAAATTGC
* * *
12688180 TCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATTGCTCCTCTCAACAGAGGTATCACGA
1 TCCTCTAAACAGAGG-ACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACGA
*
12688245 CTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTC
65 CTTTG-AAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTC
* * *
12688310 TCAACAGAGGTACCACG-ACTTTGGAAAAATAAATTGC
129 TAAACAGAGG--CAACGAACTTTGGAAAAGTAAATTGC
* *
12688347 TCCTCTAAACAGAGG-CAACGGAACTTT-GAAAAATAAATTGCTCCTCTAAACAGAGGCACCACG
1 TCCTCTAAACAGAGGACCAC-G-ACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACG
12688410 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTC
64 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTC
*
12688475 TAAACAGAGGCAACGAACTTTGAAAAAGTAAAT
129 TAAACAGAGGCAACGAACTTTGGAAAAGTAAAT
12688508 ACTCCTAGAC
Statistics
Matches: 299, Mismatches: 21, Indels: 17
0.89 0.06 0.05
Matches are distributed among these distances:
163 4 0.01
164 16 0.05
165 198 0.66
166 41 0.14
167 40 0.13
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (164 bp):
TCCTCTAAACAGAGGACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACGAC
TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTA
AACAGAGGCAACGAACTTTGGAAAAGTAAATTGC
Found at i:12689668 original size:9 final size:8
Alignment explanation
Indices: 12689537--12689665 Score: 174
Period size: 8 Copynumber: 15.8 Consensus size: 8
12689527 ACTTTTTCTT
12689537 TTTTTTCA
1 TTTTTTCA
12689545 TTTTTTC-
1 TTTTTTCA
12689552 TTTTTTCA
1 TTTTTTCA
12689560 -TTTTTCA
1 TTTTTTCA
12689567 TTTTTTCA
1 TTTTTTCA
12689575 TTTTTTCA
1 TTTTTTCA
12689583 TTTTTTCA
1 TTTTTTCA
12689591 TTTTTTCA
1 TTTTTTCA
12689599 TTTTTTTTCCA
1 --TTTTTT-CA
12689610 TTTTTTCA
1 TTTTTTCA
12689618 TTTTTTTTCCA
1 --TTTTTT-CA
12689629 TTTTTTCA
1 TTTTTTCA
12689637 -TTTTTCA
1 TTTTTTCA
*
12689644 TTTTTCCA
1 TTTTTTCA
12689652 TTTTTTCA
1 TTTTTTCA
12689660 TTTTTT
1 TTTTTT
12689666 TCAAGCATAG
Statistics
Matches: 110, Mismatches: 2, Indels: 18
0.85 0.02 0.14
Matches are distributed among these distances:
7 21 0.19
8 61 0.55
9 12 0.11
10 12 0.11
11 4 0.04
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTTCA
Found at i:12692394 original size:30 final size:31
Alignment explanation
Indices: 12692334--12692394 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
12692324 AATAATATCA
* * *
12692334 AGATAATTCAAAAAAAATCAGATAAAATAAC
1 AGATAATTAAAAAAAAATAACATAAAATAAC
*
12692365 AGATAA-TAAAAAAAAATAACATAAGATAAC
1 AGATAATTAAAAAAAAATAACATAAAATAAC
12692395 CCAAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.67, C:0.08, G:0.07, T:0.18
Consensus pattern (31 bp):
AGATAATTAAAAAAAAATAACATAAAATAAC
Found at i:12692754 original size:1 final size:1
Alignment explanation
Indices: 12692745--12692813 Score: 75
Period size: 1 Copynumber: 69.0 Consensus size: 1
12692735 TTTTTTAAAA
* * * * * * *
12692745 TTTTGTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTGTTTTTTTTTTGTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12692810 TTTT
1 TTTT
12692814 GCCGAAGTTC
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (1 bp):
T
Found at i:12692769 original size:16 final size:16
Alignment explanation
Indices: 12692750--12692814 Score: 85
Period size: 17 Copynumber: 3.9 Consensus size: 16
12692740 TAAAATTTTG
12692750 TTTTTGTTTTTTTGTT
1 TTTTTGTTTTTTTGTT
12692766 TTTTTGTTTTTTTTGTTT
1 TTTTTG-TTTTTTTG-TT
*
12692784 TTTTTTTGTTTTTTGTT
1 TTTTTGT-TTTTTTGTT
*
12692801 TTTTTTTTTTTTTG
1 TTTTTGTTTTTTTG
12692815 CCGAAGTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
16 13 0.29
17 18 0.40
18 14 0.31
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (16 bp):
TTTTTGTTTTTTTGTT
Found at i:12692790 original size:36 final size:34
Alignment explanation
Indices: 12692745--12692814 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 34
12692735 TTTTTTAAAA
12692745 TTTTGTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTG
1 TTTTGTTTTTG-TTTTTTGTTTTTTT-TTTTTTTTG
*
12692781 TTTTTTTTTTGTTTTTTGTTTTTTTTTTTTTTTG
1 TTTTGTTTTTGTTTTTTGTTTTTTTTTTTTTTTG
12692815 CCGAAGTTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 9 0.27
35 14 0.42
36 10 0.30
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (34 bp):
TTTTGTTTTTGTTTTTTGTTTTTTTTTTTTTTTG
Found at i:12692907 original size:41 final size:41
Alignment explanation
Indices: 12692822--12693269 Score: 703
Period size: 41 Copynumber: 10.9 Consensus size: 41
12692812 TTGCCGAAGT
*
12692822 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGC
*
12692864 TCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
12692905 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
* * *
12692946 TCCTCTCAACAGAGGTA-CACGACTTGGAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
12692986 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGC
*
12693028 TCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
12693069 TCCTCTAAACAGAGGCACCCACGACTTTGGAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCA-CCACGACTTT-GAAAAGTAAATTGC
* *
12693112 TCCTCTCAACAGAGGCA--ACGGACTTTGAAAAATAAATTGC
1 TCCTCTAAACAGAGGCACCAC-GACTTTGAAAAGTAAATTGC
12693152 TCCTCTAAACAGAGGCA-CACGACTTTGAAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
*
12693192 TCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGC
1 TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
12693233 TCCTCTAAACAGAGGCA--ACGAACTTTGGAAAA-TAAAT
1 TCCTCTAAACAGAGGCACCACG-ACTTT-GAAAAGTAAAT
12693270 ACTCCTAGAC
Statistics
Matches: 380, Mismatches: 17, Indels: 20
0.91 0.04 0.05
Matches are distributed among these distances:
39 3 0.01
40 114 0.30
41 157 0.41
42 77 0.20
43 29 0.08
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (41 bp):
TCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGC
Found at i:12693176 original size:206 final size:203
Alignment explanation
Indices: 12692822--12693269 Score: 749
Period size: 206 Copynumber: 2.2 Consensus size: 203
12692812 TTGCCGAAGT
*
12692822 TCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACGA
1 TCCTCTAAACAGAGGCACCACGACTTTGG-AAAATAAATTGCTCCTCTAAACAGAGGCACCACGA
*
12692887 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCT
65 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-CACGACTTTGAAAAATAAATTGCTCCTCT
* *
12692952 CAACAGAGGTACACGACTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAA
129 AAACAGAGGCACACGACTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG-A
12693017 AAGTAAATTGC
193 AAGTAAATTGC
*
12693028 TCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCCACGA
1 TCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCA-CCACGA
*
12693093 CTTTGGAAAAGTAAATTGCTCCTCTCAACAGAGGCA-ACGGACTTTGAAAAATAAATTGCTCCTC
65 CTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCACAC-GACTTTGAAAAATAAATTGCTCCTC
*
12693157 TAAACAGAGGCACACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGA
128 TAAACAGAGGCACACGACTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGA
12693222 AAGTAAATTGC
193 AAGTAAATTGC
12693233 TCCTCTAAACAGAGGCA--ACGAACTTTGGAAAATAAAT
1 TCCTCTAAACAGAGGCACCACG-ACTTTGGAAAATAAAT
12693270 ACTCCTAGAC
Statistics
Matches: 230, Mismatches: 8, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
203 3 0.01
204 15 0.07
205 58 0.25
206 124 0.54
207 30 0.13
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (203 bp):
TCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATTGCTCCTCTAAACAGAGGCACCACGAC
TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACACGACTTTGAAAAATAAATTGCTCCTCTAA
ACAGAGGCACACGACTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAG
TAAATTGC
Found at i:12694319 original size:6 final size:6
Alignment explanation
Indices: 12694301--12694380 Score: 53
Period size: 6 Copynumber: 13.2 Consensus size: 6
12694291 TTTTTTTTCA
* *
12694301 TCATTT TCTTTT TCATTTTT TCATTTT TCATTTT TCATTT T--TTT CCATTTTT
1 TCATTT TCATTT TCA--TTT TCA-TTT TCA-TTT TCATTT TCATTT TCA--TTT
12694353 TCA-TT T--TTT TCATTT TCATTT TCATTT T
1 TCATTT TCATTT TCATTT TCATTT TCATTT T
12694381 TTCCATTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
4 6 0.10
5 3 0.05
6 27 0.44
7 14 0.23
8 11 0.18
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.72
Consensus pattern (6 bp):
TCATTT
Found at i:12694322 original size:8 final size:8
Alignment explanation
Indices: 12694309--12694400 Score: 90
Period size: 8 Copynumber: 11.9 Consensus size: 8
12694299 CATCATTTTC
12694309 TTTTTCAT
1 TTTTTCAT
12694317 TTTTTCA-
1 TTTTTCAT
12694324 TTTTTCA-
1 TTTTTCAT
12694331 TTTTTCATT
1 TTTTTCA-T
12694340 TTTTTCCAT
1 TTTTT-CAT
12694349 TTTTTCATT
1 TTTTTCA-T
12694358 TTTTTCA-
1 TTTTTCAT
12694365 -TTTTCA-
1 TTTTTCAT
12694371 -TTTTCAT
1 TTTTTCAT
12694378 TTTTTCCA-
1 TTTTT-CAT
*
12694386 TTTTTCTT
1 TTTTTCAT
12694394 TTTTTCA
1 TTTTTCA
12694401 AGCATAGTAT
Statistics
Matches: 74, Mismatches: 2, Indels: 16
0.80 0.02 0.17
Matches are distributed among these distances:
6 12 0.16
7 15 0.20
8 24 0.32
9 21 0.28
10 2 0.03
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTCAT
Found at i:12694363 original size:55 final size:54
Alignment explanation
Indices: 12694293--12694399 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 54
12694283 TTGTTCACTT
*
12694293 TTTTTTCATCATTTTCTTTTTCATTTTTTCA-TTTTT-CATTTTTCATTTTTTTCCA
1 TTTTTTCATCATTTTCATTTTCA--TTTTCATTTTTTCCATTTTTC-TTTTTTTCCA
**
12694348 TTTTTTCATTTTTTTCATTTTCATTTTCATTTTTTCCATTTTTCTTTTTTTC
1 TTTTTTCATCATTTTCATTTTCATTTTCATTTTTTCCATTTTTCTTTTTTTC
12694400 AAGCATAGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
53 6 0.13
54 13 0.28
55 28 0.60
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (54 bp):
TTTTTTCATCATTTTCATTTTCATTTTCATTTTTTCCATTTTTCTTTTTTTCCA
Found at i:12694395 original size:15 final size:15
Alignment explanation
Indices: 12694294--12694400 Score: 98
Period size: 15 Copynumber: 7.0 Consensus size: 15
12694284 TGTTCACTTT
*
12694294 TTTTTCATCATTTTC-
1 TTTTTCAT-TTTTTCA
12694309 TTTTTCATTTTTTCA
1 TTTTTCATTTTTTCA
12694324 TTTTTCA-TTTTTCA
1 TTTTTCATTTTTTCA
12694338 TTTTTTTCCATTTTTTCA
1 --TTTTT-CATTTTTTCA
12694356 TTTTT--TTCATTTTCA
1 TTTTTCATT--TTTTCA
12694371 -TTTTCATTTTTTCCA
1 TTTTTCATTTTTT-CA
*
12694386 TTTTTCTTTTTTTCA
1 TTTTTCATTTTTTCA
12694401 AGCATAGTAT
Statistics
Matches: 79, Mismatches: 2, Indels: 22
0.77 0.02 0.21
Matches are distributed among these distances:
13 2 0.03
14 20 0.25
15 25 0.32
16 23 0.29
17 2 0.03
18 7 0.09
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTCATTTTTTCA
Found at i:12694398 original size:9 final size:9
Alignment explanation
Indices: 12694309--12694390 Score: 77
Period size: 9 Copynumber: 9.3 Consensus size: 9
12694299 CATCATTTTC
12694309 TTTTTCA-T
1 TTTTTCATT
12694317 TTTTTCA--
1 TTTTTCATT
12694324 TTTTTCA--
1 TTTTTCATT
12694331 TTTTTCATT
1 TTTTTCATT
12694340 TTTTTCCA-T
1 TTTTT-CATT
12694349 TTTTTCATT
1 TTTTTCATT
12694358 TTTTTCATTT
1 TTTTTCA-TT
12694368 TCATTTTCATT
1 T--TTTTCATT
*
12694379 TTTTCCATT
1 TTTTTCATT
12694388 TTT
1 TTT
12694391 CTTTTTTTCA
Statistics
Matches: 66, Mismatches: 1, Indels: 13
0.82 0.01 0.16
Matches are distributed among these distances:
7 14 0.21
8 9 0.14
9 29 0.44
10 5 0.08
11 3 0.05
12 6 0.09
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTCATT
Found at i:12701637 original size:15 final size:16
Alignment explanation
Indices: 12701617--12701648 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12701607 TTGTAAGCGT
12701617 AATGAATGAG-AATGC
1 AATGAATGAGAAATGC
12701632 AATGAATGAGAAATGC
1 AATGAATGAGAAATGC
12701648 A
1 A
12701649 TGTATGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (16 bp):
AATGAATGAGAAATGC
Found at i:12704901 original size:59 final size:59
Alignment explanation
Indices: 12704827--12705402 Score: 796
Period size: 59 Copynumber: 9.7 Consensus size: 59
12704817 TTTTTTTTAG
12704827 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTCTATTTTC-AA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAA-TT-TATTTTCTAA
* ** *
12704886 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTA-TTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTTGGAAATTTATTTTCTAA
*
12704945 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTTTC-AA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAA-TTT-ATTTTCTAA
12705005 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGGAAATTTATTTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTTGGAAATTTA-TTTTC---TAA
* *
12705070 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTCT-TAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTCTAA
* *
12705128 GAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTA-TTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGGAAATTTATTTTCTAA
* * *
12705187 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTAGAAATTTATTCT-TAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTCTAA
* * * *
12705244 GGAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTTTTTGAAATTTA-TTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGGAAATTTATTTTCTAA
12705303 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTA-TTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTCTAA
*
12705360 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTTT
12705403 TAGAATTTTT
Statistics
Matches: 470, Mismatches: 26, Indels: 42
0.87 0.05 0.08
Matches are distributed among these distances:
57 105 0.22
58 57 0.12
59 179 0.38
60 41 0.09
61 22 0.05
62 14 0.03
63 16 0.03
65 36 0.08
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTCTAA
Found at i:12705277 original size:27 final size:27
Alignment explanation
Indices: 12705189--12705277 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
12705179 ATTTCTAAGG
*
12705189 AAAATTGATACTTTCAACTTTTCCCTA
1 AAAATTGATACTTTCAACTTTTTCCTA
** * * *
12705216 AAAA-T-ATTTTTTAGAAATTTATTCTTAA
1 AAAATTGATACTTT-CAACTTT-TTCCT-A
12705244 GGAAAATTGATACTTTCAACTTTTTCCTA
1 --AAAATTGATACTTTCAACTTTTTCCTA
12705273 AAAAT
1 AAAAT
12705278 ATTTTTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 14
0.64 0.16 0.20
Matches are distributed among these distances:
25 5 0.11
26 6 0.14
27 12 0.27
28 1 0.02
29 1 0.02
30 8 0.18
31 6 0.14
32 5 0.11
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (27 bp):
AAAATTGATACTTTCAACTTTTTCCTA
Found at i:12705279 original size:116 final size:115
Alignment explanation
Indices: 12704827--12705403 Score: 859
Period size: 116 Copynumber: 4.9 Consensus size: 115
12704817 TTTTTTTTAG
12704827 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTCTATTTTCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAA-TT-TATTTT-AAGGAAAA
*** *
12704892 TTGATACTTTCAACTTTT-CCTCAAAAACCCTTTTTTTGAAAATTTATTTCTAA
63 TTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTTGGAAATTTATTTCTAA
*
12704945 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTTTCAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAA-TTT-ATTTT-AAGGAAA
*
12705010 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGGAAATTTATTTTTCTTTTAA
62 ATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTGGAAATTTA--TTTC---TAA
* *
12705070 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTCTTAAGAAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTATT-TTAAGGAAAAT
12705135 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTAA
64 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTAA
* *
12705187 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTAGAAATTTATTCTTAAGGAAAATT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATT-TTAAGGAAAATT
* * *
12705252 GATACTTTCAACTTTTTCCTAAAAATATTTTTTTTTGAAATTTATTTCTGA
65 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTAA
12705303 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGGAAAATT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTT-TAAGGAAAATT
12705368 GATACTTTCAACTTTTCCCTAAAAATATATTTTTTT
65 GATACTTTCAACTTTTCCCTAAAAATAT-TTTTTTT
12705404 AGAATTTTTT
Statistics
Matches: 429, Mismatches: 18, Indels: 25
0.91 0.04 0.05
Matches are distributed among these distances:
115 1 0.00
116 164 0.38
117 45 0.10
118 36 0.08
119 50 0.12
120 21 0.05
122 21 0.05
123 38 0.09
124 5 0.01
125 48 0.11
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (115 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTTAAGGAAAATTG
ATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTAA
Found at i:12705501 original size:13 final size:13
Alignment explanation
Indices: 12705483--12705529 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
12705473 CTAATCTAAT
12705483 AAATAAAAATAAA
1 AAATAAAAATAAA
12705496 AAAT-AAAATAAA
1 AAATAAAAATAAA
* *
12705508 CAAATAAACA-AAG
1 -AAATAAAAATAAA
12705521 AAATAAAAA
1 AAATAAAAA
12705530 AAGAAGATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 16 0.55
13 10 0.34
14 3 0.10
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:12705532 original size:12 final size:12
Alignment explanation
Indices: 12705483--12705539 Score: 60
Period size: 13 Copynumber: 4.5 Consensus size: 12
12705473 CTAATCTAAT
*
12705483 AAATAAAAATAAA
1 AAATAAAAA-AAG
*
12705496 AAATAAAATAAAC
1 AAATAAAA-AAAG
*
12705509 AAATAAACAAAG
1 AAATAAAAAAAG
12705521 AAATAAAAAAAG
1 AAATAAAAAAAG
12705533 AAGATAA
1 AA-ATAA
12705540 TAATAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
12 16 0.42
13 21 0.55
14 1 0.03
ACGTcount: A:0.79, C:0.04, G:0.05, T:0.12
Consensus pattern (12 bp):
AAATAAAAAAAG
Found at i:12712815 original size:32 final size:32
Alignment explanation
Indices: 12712779--12712840 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
12712769 TATCTGGTAA
* *
12712779 CAATGAAGTTTTAAGCATAGATTATCTGACGC
1 CAATGAAGTCTTAAGCATAGATTAGCTGACGC
* * *
12712811 CAATGGAGTCTTAAGCTTAGTTTAGCTGAC
1 CAATGAAGTCTTAAGCATAGATTAGCTGAC
12712841 ACGTAAGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (32 bp):
CAATGAAGTCTTAAGCATAGATTAGCTGACGC
Found at i:12713174 original size:33 final size:33
Alignment explanation
Indices: 12713135--12713340 Score: 124
Period size: 33 Copynumber: 6.4 Consensus size: 33
12713125 CCATGAAAAG
12713135 ATTTTAAGCCCAGCTTAGTTGACACCCAATAAA
1 ATTTTAAGCCCAGCTTAGTTGACACCCAATAAA
* ** * *
12713168 ATTTTAAACCCAATTTACTTGATACCCAATGAAA
1 ATTTTAAGCCCAGCTTAGTTGACACCCAAT-AAA
* ** * *
12713202 GA-TTTAAGCCCAGATTA-TCTGGTACCCAATGAG
1 -ATTTTAAGCCCAGCTTAGT-TGACACCCAATAAA
* * *
12713235 ATTTTAAGCCTAGCTTAGTTGGCA--C-A-CAA
1 ATTTTAAGCCCAGCTTAGTTGACACCCAATAAA
* * *
12713264 A-TTTAAGCCCAGATTAGCTAACACCCAATGAAA
1 ATTTTAAGCCCAGCTTAGTTGACACCCAAT-AAA
* * * *
12713297 A-TTTAAGCTCAACTTAGCT-AGCACCCAATTAA
1 ATTTTAAGCCCAGCTTAGTTGA-CACCCAATAAA
12713329 ATTTTAAGCCCA
1 ATTTTAAGCCCA
12713341 ATTTACCTAG
Statistics
Matches: 134, Mismatches: 27, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
28 17 0.13
29 2 0.01
30 2 0.01
31 2 0.01
32 5 0.04
33 79 0.59
34 26 0.19
35 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (33 bp):
ATTTTAAGCCCAGCTTAGTTGACACCCAATAAA
Found at i:12713446 original size:28 final size:28
Alignment explanation
Indices: 12713397--12713454 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
12713387 ACCCAATGAG
* *
12713397 ATTTTAAACCTAGCTTAGCTAGCACCTA
1 ATTTTAAACCCAGATTAGCTAGCACCTA
* * *
12713425 ATTTTAAGCCCAGATTATCTAGCATCTA
1 ATTTTAAACCCAGATTAGCTAGCACCTA
12713453 AT
1 AT
12713455 AAAAATTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.34
Consensus pattern (28 bp):
ATTTTAAACCCAGATTAGCTAGCACCTA
Found at i:12713486 original size:162 final size:161
Alignment explanation
Indices: 12713137--12713495 Score: 447
Period size: 162 Copynumber: 2.2 Consensus size: 161
12713127 ATGAAAAGAT
* *
12713137 TTTAAGCCCAGCTTAGTTGACACCCAATAAAATTTTAAACCCAATTTACTTGATACCCAATGAAA
1 TTTAAGCTCAGCTTAGTTGACACCCAATAAAATTTTAAACCCAATTTACTAGATACCCAATGAAA
* * * *
12713202 GATTTAAGCCCAGATTATCTGGTACCCAATGAGATTTTAAGCCTAGCTTAGTTGGCACACAAATT
66 GATTTAAGCCCAGATTATCTGGCACCCAATGAGATTTTAAACCTAGCTTAGCTAGCACACAAATT
*
12713267 TAAGCCCAGATTAGCTAACACCCAATGAAAA
131 TAAGCCCAGATTAGCTAACACCCAATAAAAA
* * * * * *
12713298 TTTAAGCTCAACTTAGCT-AGCACCCAATTAAATTTTAAGCCCAATTTACCTAG-TGCCTAA-GT
1 TTTAAGCTCAGCTTAGTTGA-CACCCAATAAAATTTTAAACCCAATTTA-CTAGATACCCAATG-
* *
12713360 AAAGGTTTAAGCCCAGATTTATTTGGCACCCAATGAGATTTTAAACCTAGCTTAGCTAGCAC-CT
63 AAAGATTTAAGCCCAGA-TTATCTGGCACCCAATGAGATTTTAAACCTAGCTTAGCTAGCACAC-
* * * * *
12713424 AATTTTAAGCCCAGATTATCTAGCATCTAATAAAAA
126 AAATTTAAGCCCAGATTAGCTAACACCCAATAAAAA
12713460 TTTAAGCTCAGCTTAGTTGACACCCAAGTGAAAATT
1 TTTAAGCTCAGCTTAGTTGACACCCAA-T-AAAATT
12713496 AAGCCTAATT
Statistics
Matches: 167, Mismatches: 23, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
160 2 0.01
161 63 0.38
162 95 0.57
163 2 0.01
164 5 0.03
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (161 bp):
TTTAAGCTCAGCTTAGTTGACACCCAATAAAATTTTAAACCCAATTTACTAGATACCCAATGAAA
GATTTAAGCCCAGATTATCTGGCACCCAATGAGATTTTAAACCTAGCTTAGCTAGCACACAAATT
TAAGCCCAGATTAGCTAACACCCAATAAAAA
Found at i:12713875 original size:14 final size:13
Alignment explanation
Indices: 12713852--12713915 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 13
12713842 CCCAAACCAT
*
12713852 AAAACTAAAAAAGC
1 AAAAC-AAAAAAAC
*
12713866 AAAACAAAAAAAAA
1 AAAAC-AAAAAAAC
*
12713880 AAAACCAAAAACAC
1 AAAA-CAAAAAAAC
*
12713894 CAAA-AAAAAAAC
1 AAAACAAAAAAAC
12713906 AAAA-AAAAAA
1 AAAACAAAAAA
12713916 CCTTTTGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 16 0.39
14 24 0.59
15 1 0.02
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.02
Consensus pattern (13 bp):
AAAACAAAAAAAC
Found at i:12715976 original size:20 final size:20
Alignment explanation
Indices: 12715907--12715980 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
12715897 ATATAAAAAG
* *
12715907 AAAATTTTTAAAAATTC-AA
1 AAAATTATTAAAACTTCTAA
* * *
12715926 AAAATT-CTAAAATTTTTAA
1 AAAATTATTAAAACTTCTAA
*
12715945 AAACTTCA-TAAAACTTCTAA
1 AAAATT-ATTAAAACTTCTAA
12715965 AAAATTATTAAAACTT
1 AAAATTATTAAAACTT
12715981 TTTCTACAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.16
19 14 0.32
20 23 0.52
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTATTAAAACTTCTAA
Found at i:12716235 original size:30 final size:31
Alignment explanation
Indices: 12716159--12716235 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
12716149 AATATTTTGG
* * *
12716159 AAAATTAAATAATTTAAAATTTTTGAAGCATT
1 AAAAATAAA-AATTTAAAATTTTTGAAGAATA
** *
12716191 CTAAA-AAAATTTTAAAATTTTTGAA-AATA
1 AAAAATAAAAATTTAAAATTTTTGAAGAATA
12716220 AAAAATAAAAATTTAA
1 AAAAATAAAAATTTAA
12716236 TATTCAAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
29 5 0.14
30 25 0.71
31 3 0.09
32 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (31 bp):
AAAAATAAAAATTTAAAATTTTTGAAGAATA
Found at i:12716454 original size:29 final size:28
Alignment explanation
Indices: 12716418--12716478 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
12716408 AATTTTCATA
**
12716418 TTTTTTAAGTTTTTGAAATTTTTTGAAT
1 TTTTTTAAAATTTTGAAATTTTTTGAAT
**
12716446 TTTTATTAAAATTTTGAGGTTTTTTGAAT
1 TTTT-TTAAAATTTTGAAATTTTTTGAAT
12716475 TTTT
1 TTTT
12716479 CATTTTTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (28 bp):
TTTTTTAAAATTTTGAAATTTTTTGAAT
Found at i:12716562 original size:83 final size:82
Alignment explanation
Indices: 12716391--12716562 Score: 231
Period size: 83 Copynumber: 2.1 Consensus size: 82
12716381 ATTTAAAGAA
* * * *
12716391 AATTTT-ATTTTTATTAGAATTTTCATATTTTTTAAGTTTTTGAAATTTTTTGAATTTTTATTAA
1 AATTTTCATTTTTATTAAAATTTCCATATTCTTGAAGTTTTTGAAATTTTTTGAATTTTTATTAA
12716455 AATTTTGAGGTTTTTTG
66 AATTTTGAGGTTTTTTG
* *
12716472 AATTTTTCATTTTTCTTAAAATTTCCA-ATTCTTGAATTTTTTGAAATTTTTTGAATTTTTAATT
1 AA-TTTTCATTTTTATTAAAATTTCCATATTCTTGAAGTTTTTGAAATTTTTTGAATTTTT-ATT
* *
12716536 AAAATTTTGAGATTTTTTTT
64 AAAATTTTGAG-GTTTTTTG
12716556 AATTTTC
1 AATTTTC
12716563 TAAAGTTTTG
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
81 2 0.03
82 34 0.43
83 35 0.44
84 8 0.10
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.60
Consensus pattern (82 bp):
AATTTTCATTTTTATTAAAATTTCCATATTCTTGAAGTTTTTGAAATTTTTTGAATTTTTATTAA
AATTTTGAGGTTTTTTG
Found at i:12716602 original size:20 final size:20
Alignment explanation
Indices: 12716579--12716617 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12716569 TTTGTAAAAT
12716579 TTTTA-AAAATTTTAAGAATG
1 TTTTAGAAAATTTT-AGAATG
*
12716599 TTTTAGAATATTTTAGAAT
1 TTTTAGAAAATTTTAGAAT
12716618 ATTCTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (20 bp):
TTTTAGAAAATTTTAGAATG
Found at i:12716614 original size:10 final size:10
Alignment explanation
Indices: 12716587--12716620 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
12716577 ATTTTTAAAA
12716587 ATTTTAAGAAT
1 ATTTT-AGAAT
*
12716598 GTTTTAGAAT
1 ATTTTAGAAT
12716608 ATTTTAGAAT
1 ATTTTAGAAT
12716618 ATT
1 ATT
12716621 CTTTTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (10 bp):
ATTTTAGAAT
Found at i:12717139 original size:16 final size:17
Alignment explanation
Indices: 12717118--12717149 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12717108 AATATTAAAT
12717118 TAAAATTTATA-TATAA
1 TAAAATTTATAGTATAA
12717134 TAAAATTTATAGTATA
1 TAAAATTTATAGTATA
12717150 TATTTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAAATTTATAGTATAA
Found at i:12723332 original size:19 final size:20
Alignment explanation
Indices: 12723295--12723333 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12723285 CAATTTTTTA
*
12723295 AAAAATATATATTAAAATAT
1 AAAAATAAATATTAAAATAT
*
12723315 AAAAATAAAT-TTATAATAT
1 AAAAATAAATATTAAAATAT
12723334 TTTCTAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATAAATATTAAAATAT
Found at i:12732602 original size:159 final size:158
Alignment explanation
Indices: 12732008--12733248 Score: 749
Period size: 161 Copynumber: 7.9 Consensus size: 158
12731998 AAATACCTAC
* ** * * * *
12732008 TTAGGAC-TTTTGTGTTGTTAAAAGATAAAAATACAAGTTTGTAGTTATTGTTCTATTTTAACAG
1 TTAGGACTTTTTGTGTCGTTAAAAGGCAAAAATACAAATTTGCAGTTATTATTCTATTTTAATAG
* * * * * * * *
12732072 TTTAGATAGCATCAATGCAT-AGTATTAAA-TCTATCCAAATGATTGAGCTTGATTTTCATAATT
66 TTTGGATAGCTTAAATACATGA-TATTAAACT-TGTCCAAATGATTGAACTTG-TTTCCACAATT
* * * * *
12732135 GATATGTGTAAAAAGTTGCAGTCTATATCAAT
128 GATATGTGTGAAAAGTTAC-GTTTATGTCTAT
* * * * * * *
12732167 TTAGGACTTTTTTGTGCCATTAAAAGGCAAAAA-AGCAAATTTACAATTATTATTTTGTTTTAAC
1 TTAGGAC-TTTTTGTGTCGTTAAAAGGCAAAAATA-CAAATTTGCAGTTATTATTCTATTTTAAT
* * * * * ** * *
12732231 AATTTGGATAGTTTTAATACATGACATTAAACTTGTTCAAATGATTGATGTTCTTTTTCACAATT
64 AGTTTGGATAGCTTAAATACATGATATTAAACTTGTCCAAATGATTGAACTT-GTTTCCACAATT
*
12732296 GATATATGTGAAAA-TAGTACCGTTTATGTC-AGT
128 GATATGTGTGAAAAGT--TA-CGTTTATGTCTA-T
* * * * * * * *
12732329 ATAAGACATTTTATGAT-GTTAAAGGGAAAAAATATAATTTTGCAGTTATGT-TTCTATTTTAAT
1 TTAGGACTTTTTGTG-TCGTTAAAAGGCAAAAATACAAATTTGCAGTTAT-TATTCTATTTTAAT
** * * *
12732392 AGTTCAGATAGCTTAAATACATAATATTAAATTTGTCCAAATGATTTAACTTAGTTTCCACAATT
64 AGTTTGGATAGCTTAAATACATGATATTAAACTTGTCCAAATGATTGAACTT-GTTTCCACAATT
*
12732457 AATATGTGTGAAAAGTTACTGTTTATGTCTAT
128 GATATGTGTGAAAAGTTAC-GTTTATGTCTAT
* * **
12732489 TTAGGATTTTTTGTGTCGTTAAAAGGCAAAAATGCAAATTTGCAACTATTATTCTATTTTAATAG
1 TTAGGACTTTTTGTGTCGTTAAAAGGCAAAAATACAAATTTGCAGTTATTATTCTATTTTAATAG
* * *
12732554 TTTGGATAGC-TAAATACATGGTATCAAACTTGTCCAAATGATTGAACTTGGTTTCCATAATTGA
66 TTTGGATAGCTTAAATACATGATATTAAACTTGTCCAAATGATTGAACTT-GTTTCCACAATTGA
*
12732618 TATGTGTGAAAAGTTGACATTTATGTCTAT
130 TATGTGTGAAAAGTT-ACGTTTATGTCTAT
* * ** *
12732648 TTAGGACTTTTT-TATCGTTAAAAGGCAAAAATACAAAGTTATAGTTATTGTTCTATTTTAATAG
1 TTAGGACTTTTTGTGTCGTTAAAAGGCAAAAATACAAATTTGCAGTTATTATTCTATTTTAATAG
* * ** * * *
12732712 TTTGGATAGCTTCAATACATGATATTAAACTTGTCTAAATGATTGATGTTCCTTTCCGCAGTTGA
66 TTTGGATAGCTTAAATACATGATATTAAACTTGTCCAAATGATTGAACTT-GTTTCCACAATTGA
* *
12732777 TATGTGTGAAAAAGTTGTCATTTA-GTCTAT
130 TATGTGTG-AAAAGTT-ACGTTTATGTCTAT
* * * * * ** * *
12732807 TTAGGACATTTTGTGCCATT-AAAGGGAGAAATGTAATTTTGCAGTTA-TATT-T-TTTTAACAG
1 TTAGGACTTTTTGTGTCGTTAAAAGGCAAAAATACAAATTTGCAGTTATTATTCTATTTTAATAG
* * * **
12732868 TTTAGATAGCTTAGATAAATGATATTAAAC---T-----TG---G----T-TTT-CATTATTGAT
66 TTTGGATAGCTTAAATACATGATATTAAACTTGTCCAAATGATTGAACTTGTTTCCACAATTGAT
* **
12732916 ATGTATGAAAAGTTGTTGTTTATGTCTAT
131 ATGTGTGAAAAGTT-ACGTTTATGTCTAT
* * * * * ***
12732945 TTAGGA-TTTTTTTATACCATTAAAAGGTAGAAAA-ACACATTTTTTTGTTATTATTCTATTTTA
1 TTAGGACTTTTTGTGT--CGTTAAAAGGCA-AAAATACA-AATTTGCAGTTATTATTCTATTTTA
* * * * * * *** * *
12733008 ACAGTTTGGATAACTTTAATACTTAATAATAAACTTGTTTGAATGATTGGTA-TTCTTTTCCACA
62 ATAGTTTGGATAGCTTAAATACATGATATTAAACTTGTCCAAATGATT-GAACTT-GTTTCCACA
* * * * *
12733072 ATTGATATATATAAAAAAGTTACCGTTTATATCTGT
125 ATTGATATGTGT-GAAAAGTTA-CGTTTATGTCTAT
* * * * * ** *
12733108 TTAGGACATTTTGTGCCGTT-AAAGGACAAAATTATAATTTTATAGTTA-TATTTATATTTTAAT
1 TTAGGACTTTTTGTGTCGTTAAAAGG-CAAAAATACAAATTTGCAGTTATTA-TTCTATTTTAAT
* * ** * * * **
12733171 AGTTAT-GATAGCTTAAATATATAATATTAAACTTGTCTTACTGATTGAATTTGTTTTCATGATT
64 AGTT-TGGATAGCTTAAATACATGATATTAAACTTGTCCAAATGATTGAACTTGTTTCCACAATT
12733235 GATATGTGTGAAAA
128 GATATGTGTGAAAA
12733249 TGTTGTCGTT
Statistics
Matches: 839, Mismatches: 186, Indels: 114
0.74 0.16 0.10
Matches are distributed among these distances:
137 18 0.02
138 24 0.03
139 7 0.01
140 7 0.01
141 13 0.02
142 4 0.00
143 1 0.00
144 31 0.04
145 1 0.00
147 1 0.00
148 2 0.00
152 2 0.00
153 1 0.00
156 35 0.04
157 1 0.00
158 57 0.07
159 185 0.22
160 110 0.13
161 271 0.32
162 39 0.05
163 24 0.03
164 5 0.01
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (158 bp):
TTAGGACTTTTTGTGTCGTTAAAAGGCAAAAATACAAATTTGCAGTTATTATTCTATTTTAATAG
TTTGGATAGCTTAAATACATGATATTAAACTTGTCCAAATGATTGAACTTGTTTCCACAATTGAT
ATGTGTGAAAAGTTACGTTTATGTCTAT
Found at i:12732807 original size:318 final size:315
Alignment explanation
Indices: 12732008--12732829 Score: 811
Period size: 318 Copynumber: 2.6 Consensus size: 315
12731998 AAATACCTAC
*
12732008 TTAGGACTTTTGTGT-TGTTAAAA-GATAAAAATAC-AAGTTTGTAGTTATTGTTCTATTTTAAC
1 TTAGGACTTTT-T-TATGTTAAAAGGA-AAAAATACAAAG-TTGTAGTTATTGTTCTATTTTAAT
* * * * * *
12732070 AGTTTAGATAGCATCAATGCATAGTATTAAATCTATCCAAATGATTGAGCTTGATTTTCATAATT
62 AGTTTAGATAGCTTCAATACATA-TATTAAAT-TGTCCAAATGATTGAG-TTAATTTCCACAATT
*
12732135 GATATGTGT-AAAAAGTTGCAGTCTATA-TCAATTTAGGACTTTTTTGTGCCATTAAAAGGCAAA
124 GATATGTGTGAAAAAGTTGCA-T-T-TAGTCTATTTAGGA-TTTTTTGTGCCATTAAAAGGCAAA
* * * * * *
12732198 AAAGCAAATTTACAATTATTATTTTGTTTTAACAATTTGGATAGTTTTAATACATGACATTAAAC
185 AAAGCAAATTTACAACTATTATTCTATTTTAACAATTTGGATAGTCTAAATACATGACATCAAAC
* ** * * *
12732263 TTGTTCAAATGATTGATGTTCTTTTTCACAATTGATATATGTGAAAATAGTACCGTTTATGTCAG
250 TTGTCCAAATGATTGAACTTCGTTTCCACAATTGATATATGTGAAAATAGTACCATTTATGTCAG
12732328 T
315 T
* * * * * ** *
12732329 ATAAGACATTTTATGATGTTAAAGGGAAAAAATATAATTTTGCAGTTA-TGTTTCTATTTTAATA
1 TTAGGAC-TTTT-TTATGTTAAAAGGAAAAAATACAAAGTTGTAGTTATTG-TTCTATTTTAATA
* * * * * *
12732393 GTTCAGATAGCTTAAATACATAATATTAAATTTGTCCAAATGATTTAACTTAGTTTCCACAATTA
63 GTTTAGATAGCTTCAATACAT-ATATTAAA-TTGTCCAAATGA-TTGAGTTAATTTCCACAATTG
* * * * *
12732458 ATATGTGTG-AAAAGTTACTGTTTATGTCTATTTAGGATTTTTTGTGTCGTTAAAAGGCAAAAAT
125 ATATGTGTGAAAAAGTTGC-ATTTA-GTCTATTTAGGATTTTTTGTGCCATTAAAAGGCAAAAAA
* * * **
12732522 GCAAATTTGCAACTATTATTCTATTTTAATAGTTTGGATAG-CTAAATACATGGTATCAAACTTG
188 GCAAATTTACAACTATTATTCTATTTTAACAATTTGGATAGTCTAAATACATGACATCAAACTTG
* * * *
12732586 TCCAAATGATTGAACTTGGTTTCCATAATTGATATGTGTGAAAAGTTG-A-CATTTATGTCTA-T
253 TCCAAATGATTGAACTTCGTTTCCACAATTGATATATGTGAAAA-TAGTACCATTTATGTC-AGT
* *
12732648 TTAGGACTTTTTTATCGTTAAAAGGCAAAAATACAAAGTTATAGTTATTGTTCTATTTTAATAGT
1 TTAGGACTTTTTTAT-GTTAAAAGGAAAAAATACAAAGTTGTAGTTATTGTTCTATTTTAATAGT
* * ** * *
12732713 TTGGATAGCTTCAATACATGATATTAAACTTGTCTAAATGATTGATGTTCCTTTCCGCAGTTGAT
65 TTAGATAGCTTCAATACAT-ATATTAAA-TTGTCCAAATGATTGA-GTTAATTTCCACAATTGAT
**
12732778 ATGTGTGAAAAAGTTGTCATTTAGTCTATTTAGGACATTTTGTGCCATTAAA
127 ATGTGTGAAAAAGTTG-CATTTAGTCTATTTAGGATTTTTTGTGCCATTAAA
12732830 GGGAGAAATG
Statistics
Matches: 404, Mismatches: 78, Indels: 41
0.77 0.15 0.08
Matches are distributed among these distances:
317 6 0.01
318 123 0.30
319 28 0.07
320 59 0.15
321 69 0.17
322 111 0.27
323 8 0.02
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (315 bp):
TTAGGACTTTTTTATGTTAAAAGGAAAAAATACAAAGTTGTAGTTATTGTTCTATTTTAATAGTT
TAGATAGCTTCAATACATATATTAAATTGTCCAAATGATTGAGTTAATTTCCACAATTGATATGT
GTGAAAAAGTTGCATTTAGTCTATTTAGGATTTTTTGTGCCATTAAAAGGCAAAAAAGCAAATTT
ACAACTATTATTCTATTTTAACAATTTGGATAGTCTAAATACATGACATCAAACTTGTCCAAATG
ATTGAACTTCGTTTCCACAATTGATATATGTGAAAATAGTACCATTTATGTCAGT
Found at i:12733172 original size:20 final size:20
Alignment explanation
Indices: 12733139--12733176 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12733129 AAGGACAAAA
12733139 TTATAATTTTATAGTTATAT
1 TTATAATTTTATAGTTATAT
12733159 TTAT-ATTTTAATAGTTAT
1 TTATAATTTT-ATAGTTAT
12733177 GATAGCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTATAATTTTATAGTTATAT
Found at i:12734353 original size:20 final size:20
Alignment explanation
Indices: 12734328--12734367 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12734318 TATAGACACC
12734328 CAATTGGGTCC-GGCCCAAAT
1 CAATTGGG-CCTGGCCCAAAT
12734348 CAATTGGGCCTGGCCCAAAT
1 CAATTGGGCCTGGCCCAAAT
12734368 GGGTAAGCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (20 bp):
CAATTGGGCCTGGCCCAAAT
Found at i:12734458 original size:16 final size:19
Alignment explanation
Indices: 12734437--12734485 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 19
12734427 TTTTATGTAT
12734437 TGTATTATTTATT-AT-TA
1 TGTATTATTTATTAATATA
*
12734454 T-TATTATGTATTAATATA
1 TGTATTATTTATTAATATA
12734472 TGTATATATTTATT
1 TGTAT-TATTTATT
12734486 TATTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 10 0.38
17 3 0.12
18 3 0.12
19 3 0.12
20 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
TGTATTATTTATTAATATA
Found at i:12734559 original size:63 final size:64
Alignment explanation
Indices: 12734446--12734627 Score: 153
Period size: 65 Copynumber: 2.8 Consensus size: 64
12734436 TTGTATTATT
* * *
12734446 TATTATTATTA-TTATGTATTAATATATGTATATATTTATTTATTTATTTTT-TGTTAAT-ATTT
1 TATT-TTATTATTTATGTA-T-ATATATATATAT-TTTTTTTATCTATTTTTATGTTAATCATTT
12734508 ATGTG
62 -T-TG
* *
12734513 TATTTTATTATTTATGTATATATATATATATTTTTTTTATCT-TTTTTATTTTATTCATTTTTG
1 TATTTTATTATTTATGTATATATATATATATTTTTTTTATCTATTTTTATGTTAATCATTTTTG
* *
12734576 TATTTTTACTTATCTAAT-TATATATCTGATATA-TTTTTTTAT-TATTATTTAT
1 TA-TTTTA-TTAT-TTATGTATATATAT-ATATATTTTTTTTATCTATT-TTTAT
12734628 CCTATAATAT
Statistics
Matches: 99, Mismatches: 7, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
63 9 0.09
64 21 0.21
65 38 0.38
66 20 0.20
67 11 0.11
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.65
Consensus pattern (64 bp):
TATTTTATTATTTATGTATATATATATATATTTTTTTTATCTATTTTTATGTTAATCATTTTTG
Found at i:12734573 original size:55 final size:60
Alignment explanation
Indices: 12734442--12734573 Score: 134
Period size: 63 Copynumber: 2.2 Consensus size: 60
12734432 TGTATTGTAT
* *
12734442 TATTTATTATTATTATTATGTATTAATATATGTATATATTTATTTATTTATTTTTTGTTAA
1 TATTTATTATT-TTATTATGTATTAATATATATATATATTTATTTATTTATCTTTTGTTAA
*
12734503 TATTTATGTGTATTTTATTATTTATGT-ATATATATATATA-TT-TTT-TTTATCTTTT-TT-A
1 TATTTA--T-TATTTTATTATGTAT-TAATATATATATATATTTATTTATTTATCTTTTGTTAA
12734561 T-TTTATTCATTTT
1 TATTTATT-ATTTT
12734574 TGTATTTTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
54 1 0.02
55 6 0.10
57 4 0.06
58 2 0.03
59 2 0.03
60 9 0.14
61 9 0.14
62 2 0.03
63 23 0.37
64 5 0.08
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (60 bp):
TATTTATTATTTTATTATGTATTAATATATATATATATTTATTTATTTATCTTTTGTTAA
Found at i:12735531 original size:8 final size:7
Alignment explanation
Indices: 12735474--12735609 Score: 57
Period size: 7 Copynumber: 18.6 Consensus size: 7
12735464 CCGCTCCAGG
12735474 TTTTTT-
1 TTTTTTA
*
12735480 TTTTTTT
1 TTTTTTA
12735487 TTTTTTGAA
1 TTTTTT--A
*
12735496 TTTTTGAA
1 TTTTT-TA
12735504 TTTTTT-
1 TTTTTTA
*
12735510 TTTATTTC
1 TTT-TTTA
12735518 TTTGTTTA
1 TTT-TTTA
12735526 TTTGTTTA
1 TTT-TTTA
12735534 --TTTTA
1 TTTTTTA
12735539 TTTTTTA
1 TTTTTTA
12735546 TTTTTTA
1 TTTTTTA
*
12735553 TTTATTAGA
1 TTT-TT-TA
12735562 TTAGTTTTA
1 TT--TTTTA
* **
12735571 TGTAATA
1 TTTTTTA
*
12735578 TTCTTT-
1 TTTTTTA
*
12735584 TTATTTA
1 TTTTTTA
12735591 TTTTTTA
1 TTTTTTA
12735598 TTATTTTA
1 TT-TTTTA
12735606 TTTT
1 TTTT
12735610 CTTTAAATAA
Statistics
Matches: 100, Mismatches: 16, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
5 4 0.04
6 15 0.15
7 39 0.39
8 29 0.29
9 10 0.10
10 2 0.02
11 1 0.01
ACGTcount: A:0.17, C:0.01, G:0.05, T:0.76
Consensus pattern (7 bp):
TTTTTTA
Found at i:12735533 original size:20 final size:19
Alignment explanation
Indices: 12735507--12735555 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
12735497 TTTTGAATTT
12735507 TTTTTTATTTCT-TTGTTTA
1 TTTTTTATTT-TATTGTTTA
*
12735526 TTTGTTTATTTTATTTTTTA
1 TTT-TTTATTTTATTGTTTA
12735546 TTTTTTATTT
1 TTTTTTATTT
12735556 ATTAGATTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (19 bp):
TTTTTTATTTTATTGTTTA
Found at i:12735545 original size:12 final size:12
Alignment explanation
Indices: 12735504--12735558 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
12735494 AATTTTTGAA
12735504 TTTTT-TTTTAT
1 TTTTTATTTTAT
*
12735515 TTCTTT-GTTTAT
1 TT-TTTATTTTAT
12735527 TTGTTTATTTTAT
1 TT-TTTATTTTAT
12735540 TTTTTATTTT-T
1 TTTTTATTTTAT
*
12735551 TATTTATT
1 TTTTTATT
12735559 AGATTAGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.26
12 21 0.55
13 7 0.18
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.82
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:12735570 original size:32 final size:32
Alignment explanation
Indices: 12735507--12735571 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
12735497 TTTTGAATTT
* * *
12735507 TTTTTTATTTCTTTGTTTATTTGTTTATTTTA
1 TTTTTTATTTCTTTATTTATTAGATTATTTTA
12735539 TTTTTTATTT-TTTATTTATTAGATTAGTTTTA
1 TTTTTTATTTCTTTATTTATTAGATTA-TTTTA
12735571 T
1 T
12735572 GTAATATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (32 bp):
TTTTTTATTTCTTTATTTATTAGATTATTTTA
Found at i:12735601 original size:10 final size:11
Alignment explanation
Indices: 12735503--12735604 Score: 57
Period size: 11 Copynumber: 8.5 Consensus size: 11
12735493 GAATTTTTGA
12735503 ATTTTTT-TTT
1 ATTTTTTATTT
*
12735513 ATTTCTTTGTTT
1 ATTT-TTTATTT
12735525 ATTTGTTTATTTT
1 ATTT-TTTA-TTT
12735538 ATTTTTTATTT
1 ATTTTTTATTT
*
12735549 -TTTATTTATTAG
1 ATTT-TTTATT-T
12735561 ATTAGTTTTATGTAAT
1 ATT--TTTTAT-T--T
12735577 ATTCTTTTTATTT
1 A-T-TTTTTATTT
12735590 ATTTTTTA-TT
1 ATTTTTTATTT
12735600 ATTTT
1 ATTTT
12735605 ATTTTCTTTA
Statistics
Matches: 76, Mismatches: 4, Indels: 24
0.73 0.04 0.23
Matches are distributed among these distances:
10 14 0.18
11 18 0.24
12 15 0.20
13 11 0.14
14 5 0.07
15 3 0.04
16 8 0.11
17 1 0.01
18 1 0.01
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.75
Consensus pattern (11 bp):
ATTTTTTATTT
Found at i:12735691 original size:60 final size:57
Alignment explanation
Indices: 12735624--12736223 Score: 599
Period size: 60 Copynumber: 9.9 Consensus size: 57
12735614 AAATAAAAAT
12735624 AAAAAAAATTCTAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA
1 AAAAAAAATT-TAAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---A
** * *
12735686 GAAAAATAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCA
1 -AAAAA-AAATTTAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA
* * *
12735745 GAAAAAAATTTCAAAAAAATTATTTTTAGGGGAAAGTTGAAAGTATCAATTTTCCTTA
1 AAAAAAAATTT-AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA
* * ** * *
12735803 AGAATAAATTTTCAAAATATATTTTTAGGGAAAAATTGAAAGTATCAATTTTCCTTA
1 AAAAAAAATTTAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA
* * *
12735860 GAAATAAATTTCCAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTA
1 AAAAAAAATTT----AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA
* *
12735921 GAAATAAATTTCCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA
1 AAAAAAAATTT---AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---A
*
12735984 GAAAAATAAATTTCCAAAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTG
1 -AAAAA-AAATTT------AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-
12736049 A
57 A
* *
12736050 AAATCAAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTA
1 AAA-AAAAATTT-AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA
* * *** *
12736109 GAAATAAATTTTCAAAAAAAGGGTTTTT-GAGGAAAAGTTGAAATTATCAATTTTCCTTGA
1 -AAAAAAAATTT-AAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTT-A
** ** *
12736169 AAATCGAAATTTCCAAACAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAA-AAAAATTTAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
12736224 CTCCTTTCTA
Statistics
Matches: 464, Mismatches: 53, Indels: 44
0.83 0.09 0.08
Matches are distributed among these distances:
57 55 0.12
58 53 0.11
59 85 0.18
60 101 0.22
61 52 0.11
62 36 0.08
63 12 0.03
64 8 0.02
65 15 0.03
66 2 0.00
68 45 0.10
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (57 bp):
AAAAAAAATTTAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA
Found at i:12736122 original size:59 final size:59
Alignment explanation
Indices: 12735636--12736223 Score: 685
Period size: 59 Copynumber: 9.7 Consensus size: 59
12735626 AAAAAATTCT
*
12735636 AAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAA-TTTC
1 AAAAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTTC
* * *
12735700 -CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAA-AAAATTTC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
*
12735757 AAAAAAATTATTTTTAGGGG-AAAGTTGAAAGTATCAATTTTCCTTA-AGAATAAATTTTC
1 AAAAAAAATATTTTT-GGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AATAAATTTTC
* * * *
12735816 --AAAATATATTTTTAGGGAAAAATTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
*
12735873 AAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 --AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
* *
12735934 AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 -AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTTC
*
12735999 AAAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCAAAATTTC
1 ----AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT-AAATTTTC
12736063 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
*** * *
12736122 AAAAAAAGGGTTTTTGAGGAAAAGTTGAAATTATCAATTTTCCTT-GAAAATCGAAA-TTTC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTTC
* * *
12736182 -CAAACAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
12736224 CTCCTTTCTA
Statistics
Matches: 467, Mismatches: 33, Indels: 53
0.84 0.06 0.10
Matches are distributed among these distances:
56 6 0.01
57 54 0.12
58 41 0.09
59 98 0.21
60 98 0.21
61 58 0.12
62 36 0.08
63 12 0.03
64 7 0.01
65 12 0.03
68 45 0.10
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (59 bp):
AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
Found at i:12736255 original size:119 final size:116
Alignment explanation
Indices: 12736013--12736223 Score: 334
Period size: 119 Copynumber: 1.8 Consensus size: 116
12736003 AAAAAAAATA
*
12736013 TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCAAAAAAAATATTTTT
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCAAAAAAAATATTTTT
*
12736078 GGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAAAAGGG
66 AGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTT---AAAAAGGG
* * * *
12736132 TTTTTGAGGAAAAGTTGAAATTATCAATTTTCCTTGAAAATCGAAATTTC-CAAACAATATTTTT
1 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCAAAAAAAATATTTTT
12736196 AGGGAAAAGTTGAAAGTATCAATTTTCC
66 AGGGAAAAGTTGAAAGTATCAATTTTCC
12736224 CTCCTTTCTA
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
118 39 0.45
119 47 0.55
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (116 bp):
TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTCAAAAAAAATATTTTT
AGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTAAAAAGGG
Found at i:12737049 original size:22 final size:22
Alignment explanation
Indices: 12737001--12737049 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
12736991 TTTCTTCAAA
*
12737001 TCTC-CTTTTTTTGTCTCTCTT
1 TCTCTCTTTTTTTGTCTCTATT
12737022 TC-CTCTTTTTTT-TCCTCTATT
1 TCTCTCTTTTTTTGT-CTCTATT
12737043 TCTCTCT
1 TCTCTCT
12737050 CTAAAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 18 0.75
22 4 0.17
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (22 bp):
TCTCTCTTTTTTTGTCTCTATT
Found at i:12737474 original size:15 final size:14
Alignment explanation
Indices: 12737447--12737484 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
12737437 AACCTACCAG
12737447 ATTTTCTTTTTTTC
1 ATTTTCTTTTTTTC
*
12737461 ATTTTCTATTTTTTT
1 ATTTTCT-TTTTTTC
12737476 ATTTT-TTTT
1 ATTTTCTTTT
12737485 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 8 0.36
15 11 0.50
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.82
Consensus pattern (14 bp):
ATTTTCTTTTTTTC
Found at i:12737480 original size:24 final size:24
Alignment explanation
Indices: 12737448--12737494 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
12737438 ACCTACCAGA
*
12737448 TTTTCTTTTTTTCATTTTCTATTT
1 TTTTATTTTTTTCATTTTCTATTT
* *
12737472 TTTTATTTTTTTTATTTTTTATT
1 TTTTATTTTTTTCATTTTCTATT
12737495 AACAAAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTATTTTTTTCATTTTCTATTT
Found at i:12737723 original size:17 final size:17
Alignment explanation
Indices: 12737671--12737724 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
12737661 TGTTTCAATA
*
12737671 TACACGCATTATACATT
1 TACATGCATTATACATT
* *
12737688 TACTAAATACATGATACATT
1 TAC---ATGCATTATACATT
12737708 TACATGCATTATACATT
1 TACATGCATTATACATT
12737725 ACTTTCTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
17 15 0.52
20 14 0.48
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.37
Consensus pattern (17 bp):
TACATGCATTATACATT
Found at i:12742011 original size:18 final size:17
Alignment explanation
Indices: 12741988--12742021 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12741978 GGAAAATTAA
12741988 TGTTTTAAAAAGAAATTG
1 TGTTTTAAAAA-AAATTG
*
12742006 TGTTTTGAAAAAAATT
1 TGTTTTAAAAAAAATT
12742022 AAATATCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (17 bp):
TGTTTTAAAAAAAATTG
Found at i:12742700 original size:31 final size:31
Alignment explanation
Indices: 12742664--12742743 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
12742654 AAATTTTACC
* * *
12742664 ATTTAATTAAGTTATAGTTTATTAGTTAATT
1 ATTTAATGAAGTAATAGTTAATTAGTTAATT
* *
12742695 ATTTAATGATGTAATAGTTAATTATTTAATT
1 ATTTAATGAAGTAATAGTTAATTAGTTAATT
*
12742726 AATTATATGAATGTAATA
1 ATTTA-ATGAA-GTAATA
12742744 CTTTATTATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 30 0.75
32 4 0.10
33 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (31 bp):
ATTTAATGAAGTAATAGTTAATTAGTTAATT
Found at i:12753031 original size:5 final size:5
Alignment explanation
Indices: 12753021--12753055 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
12753011 GATTCCCTCT
* *
12753021 TTTCC TTTCC TTTCT TTTCC TTTCC TTTCT TTTCC
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC
12753056 CTCCACTTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (5 bp):
TTTCC
Found at i:12753038 original size:15 final size:15
Alignment explanation
Indices: 12753018--12753055 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
12753008 AAGGATTCCC
12753018 TCTTTTCCTTTCCTT
1 TCTTTTCCTTTCCTT
12753033 TCTTTTCCTTTCCTT
1 TCTTTTCCTTTCCTT
12753048 TCTTTTCC
1 TCTTTTCC
12753056 CTCCACTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
TCTTTTCCTTTCCTT
Found at i:12761988 original size:16 final size:16
Alignment explanation
Indices: 12761967--12762006 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
12761957 ATTACTCACA
12761967 TTATTTTATTATCTTT-
1 TTATTTT-TTATCTTTC
*
12761983 TTATTTTTTATTTTTC
1 TTATTTTTTATCTTTC
12761999 TTATTTTT
1 TTATTTTT
12762007 AAATTTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (16 bp):
TTATTTTTTATCTTTC
Found at i:12764218 original size:15 final size:16
Alignment explanation
Indices: 12764188--12764221 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
12764178 TTCTCTTAAA
*
12764188 ATTATAATTATTTTAT
1 ATTATAAATATTTTAT
12764204 ATTATAAAT-TTTTAT
1 ATTATAAATATTTTAT
12764219 ATT
1 ATT
12764222 TTCAAACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATAAATATTTTAT
Found at i:12767175 original size:52 final size:52
Alignment explanation
Indices: 12767037--12767176 Score: 156
Period size: 52 Copynumber: 2.7 Consensus size: 52
12767027 GTCCATCAAG
* * * * *
12767037 AATCTCTTTTCTCTTAAAATTCTTCTCCTGTAAGTCAAACTTACTTATTAAT
1 AATCTATTTTCTCTTAAAATTCTTCTCTTGCAAGTCAAACTTACATATTAAA
* * * *
12767089 AATAC-ATTTACTCTTATAATTATTCTCTTACAAGTCAAACTTACATATTAAA
1 AAT-CTATTTTCTCTTAAAATTCTTCTCTTGCAAGTCAAACTTACATATTAAA
* * *
12767141 AATCTATTTTCTCTTAGAATTCTTATTTTGCAAGTC
1 AATCTATTTTCTCTTAAAATTCTTCTCTTGCAAGTC
12767177 TTCTTATCCA
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
51 1 0.01
52 69 0.97
53 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (52 bp):
AATCTATTTTCTCTTAAAATTCTTCTCTTGCAAGTCAAACTTACATATTAAA
Found at i:12767217 original size:11 final size:11
Alignment explanation
Indices: 12767197--12767232 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
12767187 TTAAGTAATA
12767197 TCTAACAAATC
1 TCTAACAAATC
*
12767208 TCTAATAAATC
1 TCTAACAAATC
*
12767219 TCAAACAAATC
1 TCTAACAAATC
12767230 TCT
1 TCT
12767233 TATGTGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (11 bp):
TCTAACAAATC
Found at i:12770765 original size:16 final size:16
Alignment explanation
Indices: 12770744--12770789 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
12770734 TTAGGGTTTT
*
12770744 GATTTTAGAGTTTGAA
1 GATTTTAGGGTTTGAA
12770760 GATTTTAGGGTTTGAA
1 GATTTTAGGGTTTGAA
12770776 GATTTTAGGGTTTG
1 GATTTTAGGGTTTG
12770790 GGTTTTGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (16 bp):
GATTTTAGGGTTTGAA
Found at i:12770842 original size:16 final size:16
Alignment explanation
Indices: 12770821--12770998 Score: 109
Period size: 16 Copynumber: 11.2 Consensus size: 16
12770811 ATTTTAAGGG
12770821 TTTGGATTTTAGGGAT
1 TTTGGATTTTAGGGAT
*
12770837 TTTGGA-TTTAGGGGGT
1 TTTGGATTTTA-GGGAT
* * *
12770853 TTAGG-TTTAAGAG-T
1 TTTGGATTTTAGGGAT
*** *
12770867 TTAAAAGTTT-GGGAT
1 TTTGGATTTTAGGGAT
12770882 TTTGGATTTT-GGGAGGT
1 TTTGGATTTTAGGGA--T
12770899 TTTGGATTTTA-GGAGT
1 TTTGGATTTTAGGGA-T
**
12770915 TTTGGATTTTAGGGGG
1 TTTGGATTTTAGGGAT
* *
12770931 TTTGAATTTAAGGGAT
1 TTTGGATTTTAGGGAT
*
12770947 TTTGGATTTTTAGGG-G
1 TTTGGA-TTTTAGGGAT
* *
12770963 TTTGGATTTAAAGGAT
1 TTTGGATTTTAGGGAT
*
12770979 TTTGGATTTTTAGGGGT
1 TTTGGA-TTTTAGGGAT
12770996 TTT
1 TTT
12770999 AAAAACTTAG
Statistics
Matches: 123, Mismatches: 28, Indels: 21
0.72 0.16 0.12
Matches are distributed among these distances:
14 6 0.05
15 25 0.20
16 59 0.48
17 33 0.27
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (16 bp):
TTTGGATTTTAGGGAT
Found at i:12770903 original size:17 final size:17
Alignment explanation
Indices: 12770881--12770933 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
12770871 AAGTTTGGGA
12770881 TTTTGGATTTTGGGAGG
1 TTTTGGATTTTGGGAGG
*
12770898 TTTTGGATTTTAGGA-G
1 TTTTGGATTTTGGGAGG
12770914 TTTTGGATTTTAGGG-GG
1 TTTTGGATTTT-GGGAGG
12770931 TTT
1 TTT
12770934 GAATTTAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 12 0.38
17 20 0.62
ACGTcount: A:0.13, C:0.00, G:0.36, T:0.51
Consensus pattern (17 bp):
TTTTGGATTTTGGGAGG
Found at i:12770955 original size:32 final size:33
Alignment explanation
Indices: 12770877--12770994 Score: 147
Period size: 32 Copynumber: 3.6 Consensus size: 33
12770867 TTAAAAGTTT
*
12770877 GGGATTTTGGA-TTTT-GGGAGGTTTTGGATTTTA
1 GGGATTTTGGATTTTTAGGG-GG-TTTGGATTTAA
*
12770910 -GGAGTTTTGGA-TTTTAGGGGGTTTGAATTTAA
1 GGGA-TTTTGGATTTTTAGGGGGTTTGGATTTAA
12770942 GGGATTTTGGATTTTTA-GGGGTTTGGATTTAA
1 GGGATTTTGGATTTTTAGGGGGTTTGGATTTAA
*
12770974 AGGATTTTGGATTTTTAGGGG
1 GGGATTTTGGATTTTTAGGGG
12770995 TTTTAAAAAC
Statistics
Matches: 76, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
32 49 0.64
33 24 0.32
34 3 0.04
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.46
Consensus pattern (33 bp):
GGGATTTTGGATTTTTAGGGGGTTTGGATTTAA
Found at i:12772392 original size:14 final size:14
Alignment explanation
Indices: 12772373--12772408 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12772363 TACTTTTCTA
*
12772373 TTTTTTTGTT-TTG
1 TTTTTTTATTATTG
12772386 TTTTTTTATTATTG
1 TTTTTTTATTATTG
12772400 TTTTTTTAT
1 TTTTTTTAT
12772409 ATATATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.83
Consensus pattern (14 bp):
TTTTTTTATTATTG
Done.