Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 189 of 226
Found at i:60114067 original size:88 final size:87
Alignment explanation
Indices: 60113919--60114087 Score: 232
Period size: 88 Copynumber: 1.9 Consensus size: 87
60113909 GTATCGACGC
** * *
60113919 CCATCGAATATGAAAAGGGATGGTGGTGATCATCGAGTATGAAAAGAGATGGTAGCGACCATCGA
1 CCATCGAATATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGAGATGGTAGCGACCATCGA
*
60113984 ATATGAAAAGGGATGGCTTTGA
66 ATATAAAAAGGGATGGCTTTGA
* * *
60114006 CCATCGAATATGAAAAAGGGTTGGTGACGACCATCGAATATGAAAAGGGATGGCT-TCGACCATC
1 CCATCGAATATG-AAAAGGGATGGTGACGACCATCGAATATGAAAAGAGATGG-TAGCGACCATC
*
60114070 GAATATAAAAATGGATGG
64 GAATATAAAAAGGGATGG
60114088 TTCTGACAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
87 12 0.17
88 58 0.82
89 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.21
Consensus pattern (87 bp):
CCATCGAATATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGAGATGGTAGCGACCATCGA
ATATAAAAAGGGATGGCTTTGA
Found at i:60128273 original size:15 final size:15
Alignment explanation
Indices: 60128253--60128283 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
60128243 AAAATAACAT
60128253 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
60128268 AACTCTTGACCTTTC
1 AACTCTTGACCTTTC
60128283 A
1 A
60128284 CTTACATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGACCTTTC
Found at i:60129942 original size:30 final size:30
Alignment explanation
Indices: 60129906--60129965 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
60129896 CAATATGTAC
60129906 CTCATTTGTTGAATCATACAAATCTTGCAA
1 CTCATTTGTTGAATCATACAAATCTTGCAA
60129936 CTCATTTGTTGAATCATACAAATCTTGCAA
1 CTCATTTGTTGAATCATACAAATCTTGCAA
60129966 ACTTCGCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (30 bp):
CTCATTTGTTGAATCATACAAATCTTGCAA
Found at i:60131693 original size:15 final size:15
Alignment explanation
Indices: 60131675--60131704 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
60131665 TCCCTTCTTG
*
60131675 ACCACGACCTTTTCC
1 ACCACGACCATTTCC
60131690 ACCACGACCATTTCC
1 ACCACGACCATTTCC
60131705 TCGATCTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.47, G:0.07, T:0.23
Consensus pattern (15 bp):
ACCACGACCATTTCC
Found at i:60133114 original size:12 final size:12
Alignment explanation
Indices: 60133099--60133131 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
60133089 CAAAGTTCAA
60133099 AACTCACAACAC
1 AACTCACAACAC
60133111 AACTCACAACAC
1 AACTCACAACAC
60133123 AACTCACAA
1 AACTCACAA
60133132 GCAAACGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.52, C:0.39, G:0.00, T:0.09
Consensus pattern (12 bp):
AACTCACAACAC
Found at i:60147099 original size:23 final size:23
Alignment explanation
Indices: 60147072--60147124 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
60147062 GTACTCAGTA
* *
60147072 AGGGTTTGCATTACAATTACTAT
1 AGGGTTCGCATAACAATTACTAT
* *
60147095 GGGGTTCGCATAACAATTCCTAT
1 AGGGTTCGCATAACAATTACTAT
60147118 AGGGTTC
1 AGGGTTC
60147125 ACATGATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (23 bp):
AGGGTTCGCATAACAATTACTAT
Found at i:60154241 original size:25 final size:25
Alignment explanation
Indices: 60154213--60154285 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 25
60154203 GTCATTAGGG
*
60154213 TTACTGATTCTCAGCTCATATGAGC
1 TTACTGATTCTCAGCTCGTATGAGC
*
60154238 TTACCGATT-TACAGCTCGTGA-GAGC
1 TTACTGATTCT-CAGCTCGT-ATGAGC
*
60154263 ATACTGATTCAT-AGCTCGTATGA
1 TTACTGATTC-TCAGCTCGTATGA
60154286 CCATGCATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
24 2 0.05
25 35 0.90
26 1 0.03
27 1 0.03
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (25 bp):
TTACTGATTCTCAGCTCGTATGAGC
Found at i:60160139 original size:22 final size:21
Alignment explanation
Indices: 60160093--60160159 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
60160083 GGATCACTGA
* *
60160093 TTTTATTTATTTTCTTTCTCT
1 TTTTATTTATTTTATTTTTCT
60160114 TTTTATTTATTTTTATTTTTGC-
1 TTTTATTTA-TTTTATTTTT-CT
* * *
60160136 TTTTAGTTGTTTTATTTTTAT
1 TTTTATTTATTTTATTTTTCT
60160157 TTT
1 TTT
60160160 CTTAGACTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 22 0.58
22 15 0.39
23 1 0.03
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.78
Consensus pattern (21 bp):
TTTTATTTATTTTATTTTTCT
Found at i:60160887 original size:46 final size:46
Alignment explanation
Indices: 60160812--60161155 Score: 256
Period size: 46 Copynumber: 7.5 Consensus size: 46
60160802 AATGGAAAGT
*
60160812 AGCACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGC
1 AGCACTTAAACACTTCAATTTACAGCATTTAAACACTTCAATTTGC
* * * * * *
60160858 AGCACTTTAACA-TATCAATTAACAACATTTATACACATCAA-TTAC
1 AGCACTTAAACACT-TCAATTTACAGCATTTAAACACTTCAATTTGC
* * **
60160903 AGCGAC-AAAACA-TCTCAATTTCCAGCAACTAAACACTTCAATTTGC
1 AGC-ACTTAAACACT-TCAATTTACAGCATTTAAACACTTCAATTTGC
* * *
60160949 AGCACTTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTAC
1 AGCACTTAAACACTTCAATTTACAGCATTTAAACACTTCAATTTGC
* * * * **
60160995 AACATTTAAACACTTCAATTTGCAGCATTTAAACA-TATAAATTAAC
1 AGCACTTAAACACTTCAATTTACAGCATTTAAACACT-TCAATTTGC
* * * * ** *
60161041 AACATTTATACACCTCAA-TTACAG-AGATAAA-ACATCTCAATTTCC
1 AGCACTTAAACACTTCAATTTACAGCATTTAAACAC-T-TCAATTTGC
* * * *
60161086 AGCAAC-TAAATACTTCAATTTGCAGCACTTAAACACTTCAATTTAC
1 AGC-ACTTAAACACTTCAATTTACAGCATTTAAACACTTCAATTTGC
* * *
60161132 AACATTTAAACACTTAAATTTACA
1 AGCACTTAAACACTTCAATTTACA
60161156 AATCCACCAT
Statistics
Matches: 236, Mismatches: 49, Indels: 26
0.76 0.16 0.08
Matches are distributed among these distances:
43 1 0.00
44 5 0.02
45 59 0.25
46 162 0.69
47 7 0.03
48 2 0.01
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (46 bp):
AGCACTTAAACACTTCAATTTACAGCATTTAAACACTTCAATTTGC
Found at i:60160990 original size:91 final size:91
Alignment explanation
Indices: 60160826--60160991 Score: 226
Period size: 91 Copynumber: 1.8 Consensus size: 91
60160816 CTTTAACACT
** * * *
60160826 TCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACATATCAATTAACAACATTTATA
1 TCAATTTACAGCAACTAAACACTTCAATTTGCAGCACTTAAACATATCAATTAACAACACTTAAA
60160891 CACATCAATTACAGCGACAAAACATC
66 CACATCAATTACAGCGACAAAACATC
* ** *
60160917 TCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACT-TCAATTTGCAGCACTTAA
1 TCAATTTACAGCAACTAAACACTTCAATTTGCAGCACTTAAACA-TATCAATTAACAACACTTAA
*
60160981 ACACTTCAATT
65 ACACATCAATT
60160992 TACAACATTT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
91 63 0.98
92 1 0.02
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.30
Consensus pattern (91 bp):
TCAATTTACAGCAACTAAACACTTCAATTTGCAGCACTTAAACATATCAATTAACAACACTTAAA
CACATCAATTACAGCGACAAAACATC
Found at i:60161076 original size:160 final size:160
Alignment explanation
Indices: 60160812--60161156 Score: 575
Period size: 160 Copynumber: 2.2 Consensus size: 160
60160802 AATGGAAAGT
* * *
60160812 AGCACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACATATCAAT
1 AGCACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACTTTAACATATAAAT
*
60160877 TAACAACATTTATACACATCAATTACAGCGACAAAACATCTCAATTTCCAGCAACTAAACACTTC
66 TAACAACATTTATACACATCAATTACAGAGACAAAACATCTCAATTTCCAGCAACTAAACACTTC
*
60160942 AATTTGCAGCACTTAAACACTTCAATTTGC
131 AATTTGCAGCACTTAAACACTTCAATTTAC
60160972 AGCACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTGCAGCA-TTTAAACATATAAA
1 AGCACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACTTT-AACATATAAA
* * *
60161036 TTAACAACATTTATACACCTCAATTACAGAGATAAAACATCTCAATTTCCAGCAACTAAATACTT
65 TTAACAACATTTATACACATCAATTACAGAGACAAAACATCTCAATTTCCAGCAACTAAACACTT
60161101 CAATTTGCAGCACTTAAACACTTCAATTTAC
130 CAATTTGCAGCACTTAAACACTTCAATTTAC
* * *
60161132 AACATTTAAACACTTAAATTTACAA
1 AGCACTTAAACACTTCAATTTACAA
60161157 ATCCACCATC
Statistics
Matches: 173, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
159 3 0.02
160 170 0.98
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.30
Consensus pattern (160 bp):
AGCACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACTTTAACATATAAAT
TAACAACATTTATACACATCAATTACAGAGACAAAACATCTCAATTTCCAGCAACTAAACACTTC
AATTTGCAGCACTTAAACACTTCAATTTAC
Found at i:60161156 original size:23 final size:23
Alignment explanation
Indices: 60160820--60161156 Score: 224
Period size: 23 Copynumber: 14.7 Consensus size: 23
60160810 GTAGCACTTT
*
60160820 AACACTTCAATTTACAGCATTTA
1 AACACTTCAATTTACAACATTTA
* *
60160843 AACACTTCAATTTGCAGCACTTT-
1 AACACTTCAATTTACAACA-TTTA
*
60160866 AACA-TATCAATTAACAACATTTA
1 AACACT-TCAATTTACAACATTTA
* * * **
60160889 TACACATCAA-TTACAGCGA-CAA
1 AACACTTCAATTTACAAC-ATTTA
* * **
60160911 AACA-TCTCAATTTCCAGCAACTA
1 AACACT-TCAATTTACAACATTTA
* * *
60160934 AACACTTCAATTTGCAGCACTTA
1 AACACTTCAATTTACAACATTTA
* * *
60160957 AACACTTCAATTTGCAGCACTTA
1 AACACTTCAATTTACAACATTTA
60160980 AACACTTCAATTTACAACATTTA
1 AACACTTCAATTTACAACATTTA
* *
60161003 AACACTTCAATTTGCAGCATTTA
1 AACACTTCAATTTACAACATTTA
* *
60161026 AACA-TATAAATTAACAACATTTA
1 AACACT-TCAATTTACAACATTTA
* * * *
60161049 TACACCTCAA-TTACAGAGA-TAA
1 AACACTTCAATTTACA-ACATTTA
* * **
60161071 AACA-TCTCAATTTCCAGCAACTA
1 AACACT-TCAATTTACAACATTTA
* * * *
60161094 AATACTTCAATTTGCAGCACTTA
1 AACACTTCAATTTACAACATTTA
60161117 AACACTTCAATTTACAACATTTA
1 AACACTTCAATTTACAACATTTA
*
60161140 AACACTTAAATTTACAA
1 AACACTTCAATTTACAA
60161157 ATCCACCATC
Statistics
Matches: 250, Mismatches: 48, Indels: 32
0.76 0.15 0.10
Matches are distributed among these distances:
22 33 0.13
23 212 0.85
24 5 0.02
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (23 bp):
AACACTTCAATTTACAACATTTA
Found at i:60165287 original size:89 final size:90
Alignment explanation
Indices: 60165190--60165366 Score: 266
Period size: 89 Copynumber: 2.0 Consensus size: 90
60165180 TTAACCCCAA
* *
60165190 ACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCCTAAC
1 ACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAAC
* * *
60165255 CCGACCCCAAATCCCT-AACCCTTT
66 ACGACACCAAATCCATAAACCCTTT
* * *
60165279 ACCCCTAAACATTATTTAATATATAAATTAAAACACATTAATTAATCTAAACCCTAAACCTTAAC
1 ACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAAC
*
60165344 ATGACACCAAATCCATAAACCCT
66 ACGACACCAAATCCATAAACCCT
60165367 AAATCCCAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
89 72 0.92
90 6 0.08
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.27
Consensus pattern (90 bp):
ACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCTAAC
ACGACACCAAATCCATAAACCCTTT
Found at i:60165917 original size:41 final size:41
Alignment explanation
Indices: 60165872--60166071 Score: 231
Period size: 41 Copynumber: 4.9 Consensus size: 41
60165862 AAATGTTTTT
60165872 GCGGCGCTTTTTTAAAAACGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGCCCCGAGCATTA
**
60165913 GCGGCGC-TTCCTAGAAAACGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTTA-AAAACGCCGCTAAAGCCCCGAGCATTA
* * * *
60165954 GTGGCGCTTCTTGAAAAACGCCACTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * ** *
60165995 GCAGCGCTTTTTCAAAAACGCCGCCAAAGATCTGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGCCCCGAGCATTA
* * * *
60166036 GCGGTGCTTTTATAAAAAATGCTGCTAAAGCCCCGA
1 GCGGCGCTTTT-TTAAAAACGCCGCTAAAGCCCCGA
60166072 AAGGTAGAAA
Statistics
Matches: 130, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
40 4 0.03
41 107 0.82
42 19 0.15
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTTTTTAAAAACGCCGCTAAAGCCCCGAGCATTA
Found at i:60172412 original size:42 final size:41
Alignment explanation
Indices: 60172345--60172568 Score: 132
Period size: 42 Copynumber: 5.3 Consensus size: 41
60172335 ATGCAATCAC
* ***
60172345 GTAAGTGCATCATTGGATGTGCTGAAGAAAATATACTGGCAA
1 GTAAGTGCATCATCGGATAAACTGAA-AAAATATACTGGCAA
* *
60172387 GTATGTGCATCATCGGATAAACTGAAATAACTATACTGGCATA
1 GTAAGTGCATCATCGGATAAACTGAAA-AAATATACTGGCA-A
* * * * ** *
60172430 -TAAGTGCACCATCGAATAAATTGAATCAAATATACTATCAC
1 GTAAGTGCATCATCGGATAAACTGAA-AAAATATACTGGCAA
** ** **
60172471 GTAAGTGCATCATTAGATAAACCAAAAAAATATACAAGCACA
1 GTAAGTGCATCATCGGATAAACTGAAAAAATATACTGGCA-A
* * * *
60172513 -TAAGTGCAT-ATTTGGATCAA-TCGAAGCAAAATATCCTGGCAC
1 GTAAGTGCATCA-TCGGATAAACT-GAA--AAAATATACTGGCAA
60172555 GTAAGTGCATCATC
1 GTAAGTGCATCATC
60172569 AACTACACCA
Statistics
Matches: 136, Mismatches: 35, Indels: 21
0.71 0.18 0.11
Matches are distributed among these distances:
40 1 0.01
41 30 0.22
42 82 0.60
43 22 0.16
44 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (41 bp):
GTAAGTGCATCATCGGATAAACTGAAAAAATATACTGGCAA
Found at i:60174877 original size:17 final size:18
Alignment explanation
Indices: 60174855--60174888 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
60174845 AATGATTTTT
*
60174855 TATATTTTAT-AAATTAA
1 TATATTTAATGAAATTAA
60174872 TATATTTAATGAAATTA
1 TATATTTAATGAAATTA
60174889 TTAATTTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TATATTTAATGAAATTAA
Found at i:60184493 original size:23 final size:20
Alignment explanation
Indices: 60184458--60184499 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 20
60184448 TAAAATGTTT
60184458 TATATAAATTTAATTATAAAG
1 TATATAAATTTAA-TATAAAG
60184479 TATATAAAATATTAATATAAA
1 TATAT-AAAT-TTAATATAAA
60184500 ATAATTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TATATAAATTTAATATAAAG
Found at i:60189895 original size:20 final size:20
Alignment explanation
Indices: 60189862--60189916 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
60189852 AAAAATATTG
60189862 AAATT-ATATATTAAAATTT
1 AAATTAATATATTAAAATTT
* * *
60189881 ATATTAATATTTTAAATTTT
1 AAATTAATATATTAAAATTT
*
60189901 AAATTTATATATTAAA
1 AAATTAATATATTAAA
60189917 CTTGTATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATTAATATATTAAAATTT
Found at i:60189915 original size:13 final size:13
Alignment explanation
Indices: 60189856--60189916 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 13
60189846 TAGTTAAAAA
60189856 ATATTGAAA-TTAT
1 ATATT-AAATTTAT
*
60189869 ATATTAAAATT-T
1 ATATTAAATTTAT
*
60189881 ATATTAATATTTTAA
1 ATATTAA-A-TTTAT
*
60189896 ATTTTAAATTTAT
1 ATATTAAATTTAT
60189909 ATATTAAA
1 ATATTAAA
60189917 CTTGTATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
12 11 0.28
13 19 0.49
14 3 0.08
15 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
ATATTAAATTTAT
Found at i:60201737 original size:27 final size:27
Alignment explanation
Indices: 60201705--60201771 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
60201695 AAAGGTTGTT
60201705 AAATGACCGTAATACCCCTATAAGGTA
1 AAATGACCGTAATACCCCTATAAGGTA
*
60201732 AAATGACCGAAATACCCCTATAAGGTA
1 AAATGACCGTAATACCCCTATAAGGTA
*
60201759 AAATGATCGTAAT
1 AAATGACCGTAAT
60201772 GCCCTTGAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.22
Consensus pattern (27 bp):
AAATGACCGTAATACCCCTATAAGGTA
Found at i:60203893 original size:16 final size:17
Alignment explanation
Indices: 60203862--60203894 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
60203852 TAAATTTTAT
*
60203862 TGAAAATATACCAAAAA
1 TGAAAACATACCAAAAA
60203879 TGAAAACAT-CCAAAAA
1 TGAAAACATACCAAAAA
60203895 CTCGATATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.64, C:0.15, G:0.06, T:0.15
Consensus pattern (17 bp):
TGAAAACATACCAAAAA
Found at i:60210075 original size:40 final size:40
Alignment explanation
Indices: 60210029--60210104 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
60210019 TTATGAAAGA
*
60210029 AAAATAATAAAAGAAAAGGGTTTATTACAAATAAAATAAT
1 AAAATAATAAAAGAAAAAGGTTTATTACAAATAAAATAAT
60210069 AAAATAATAAAAGAAAAAGGTTTATTACAAATAAAA
1 AAAATAATAAAAGAAAAAGGTTTATTACAAATAAAA
60210105 GGGTTTATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.24
Consensus pattern (40 bp):
AAAATAATAAAAGAAAAAGGTTTATTACAAATAAAATAAT
Found at i:60210109 original size:19 final size:19
Alignment explanation
Indices: 60210082--60210119 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
60210072 ATAATAAAAG
60210082 AAAAAGGTTTATTACAAAT
1 AAAAAGGTTTATTACAAAT
*
60210101 AAAAGGGTTTATTACAAAT
1 AAAAAGGTTTATTACAAAT
60210120 CTAATCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (19 bp):
AAAAAGGTTTATTACAAAT
Found at i:60215224 original size:23 final size:23
Alignment explanation
Indices: 60215030--60215224 Score: 103
Period size: 23 Copynumber: 8.5 Consensus size: 23
60215020 TTAAGCACCG
* * * *
60215030 AAATTGAAGTGCTTAAATGCTAT
1 AAATTGAGGTGTTTAAGTGCTGT
* * *
60215053 AAATTGAAGTGTTTAACTACTGT
1 AAATTGAGGTGTTTAAGTGCTGT
* *
60215076 AAATTGAAGTGTTT-AGTTGCTGG
1 AAATTGAGGTGTTTAAG-TGCTGT
* * * *
60215099 AAATTAAGATGTTTTA-TCGCAGT
1 AAATTGAGGTGTTTAAGT-GCTGT
* *
60215122 -AATTGAGGTGTATAAGTGTTGT
1 AAATTGAGGTGTTTAAGTGCTGT
* *
60215144 TAATTG-GGAT-TTTAAAGTGTTGT
1 AAATTGAGG-TGTTT-AAGTGCTGT
* ** *
60215167 AAGTTGAGGTGTTTAAAAGTTGT
1 AAATTGAGGTGTTTAAGTGCTGT
* * *
60215190 AAATTAAAGTGTTTAAGTGCTGC
1 AAATTGAGGTGTTTAAGTGCTGT
60215213 AAATTGAGGTGT
1 AAATTGAGGTGT
60215225 ACAAATGAGT
Statistics
Matches: 131, Mismatches: 32, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
22 20 0.15
23 105 0.80
24 6 0.05
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.39
Consensus pattern (23 bp):
AAATTGAGGTGTTTAAGTGCTGT
Found at i:60216532 original size:22 final size:23
Alignment explanation
Indices: 60216506--60216809 Score: 165
Period size: 22 Copynumber: 13.0 Consensus size: 23
60216496 ATTTTCACAC
*
60216506 CAAAATTTGGACAGCATATATA-
1 CAAAATTTGGACAGCATATACAT
60216528 CAAAATTTGGACTA-CATTTATACAT
1 CAAAATTTGGAC-AGCA--TATACAT
*
60216553 CAAAATTT-GACAGCATATGCAT
1 CAAAATTTGGACAGCATATACAT
*
60216575 -ATATAA-TTGGACTGCATTTATACAT
1 CA-A-AATTTGGACAGCA--TATACAT
*
60216600 CAAAAATT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* * *
60216622 -AAATAATTGGACTGCATTTGTACAT
1 CAAA-ATTTGGACAGCA--TATACAT
60216647 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* *
60216669 -ATATAA-TTGGACTGCATTTGTACAT
1 CA-A-AATTTGGACAGCA--TATACAT
60216694 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* *
60216716 -ATATAA-TTGGACTGCATTTATACAC
1 CA-A-AATTTGGACAGCA--TATACAT
*
60216741 CAAAATTT-GATAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* *
60216763 -ATATAA-TTGGACTGCATTTGTACAT
1 CA-A-AATTTGGACAGCA--TATACAT
60216788 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
60216810 TCATTTACTC
Statistics
Matches: 220, Mismatches: 24, Indels: 76
0.69 0.08 0.24
Matches are distributed among these distances:
21 7 0.03
22 67 0.30
23 39 0.18
24 47 0.21
25 53 0.24
26 7 0.03
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (23 bp):
CAAAATTTGGACAGCATATACAT
Found at i:60216806 original size:47 final size:47
Alignment explanation
Indices: 60216506--60216809 Score: 477
Period size: 47 Copynumber: 6.5 Consensus size: 47
60216496 ATTTTCACAC
* * *
60216506 CAAAATTTGGACAGCATAT--ATACAAAATTTGGACTACATTTATACAT
1 CAAAATTT-GACAGCATATACATATATAA-TTGGACTGCATTTATACAT
*
60216553 CAAAATTTGACAGCATATGCATATATAATTGGACTGCATTTATACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* * *
60216600 CAAAAATTGACAGCATATACATAAATAATTGGACTGCATTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
*
60216647 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
*
60216694 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAC
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* *
60216741 CAAAATTTGATAGCATATACATATATAATTGGACTGCATTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
60216788 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
60216810 TCATTTACTC
Statistics
Matches: 240, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
46 10 0.04
47 224 0.93
48 6 0.03
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (47 bp):
CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
Found at i:60223499 original size:22 final size:23
Alignment explanation
Indices: 60223473--60223776 Score: 127
Period size: 22 Copynumber: 13.0 Consensus size: 23
60223463 ATTTTCACAC
*
60223473 CAAAATTTGGACAGCATATATA-
1 CAAAATTTGGACAGCATATACAT
**
60223495 CAAAATTTGGATTGCATTTATACAT
1 CAAAATTTGGACAGCA--TATACAT
*
60223520 CAAAATTT-GACAGCATATGCAT
1 CAAAATTTGGACAGCATATACAT
*
60223542 -ATATAA-TTGGACTGCATTTATACAT
1 CA-A-AATTTGGACAGCA--TATACAT
* *
60223567 CAAAAATT-GACCGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* * * *
60223589 -AAATAATTGAACTGCATTTGTACAT
1 CAAA-ATTTGGACAGCA--TATACAT
*
60223614 CAAACTTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* * *
60223636 -ATATAA-TTGGACTGCATTTGTAAAT
1 CA-A-AATTTGGACAGCA--TATACAT
60223661 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
**
60223683 -ATATAA-TTGGATTGCATTTATACAT
1 CA-A-AATTTGGACAGCA--TATACAT
*
60223708 CAAAATTT-GATAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
* *
60223730 -ATATAA-TTGGACTGCATTTGTACAT
1 CA-A-AATTTGGACAGCA--TATACAT
60223755 CAAAATTT-GACAGCATATACAT
1 CAAAATTTGGACAGCATATACAT
60223777 TCATTTACTC
Statistics
Matches: 214, Mismatches: 32, Indels: 72
0.67 0.10 0.23
Matches are distributed among these distances:
21 7 0.03
22 67 0.31
23 34 0.16
24 47 0.22
25 52 0.24
26 7 0.03
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (23 bp):
CAAAATTTGGACAGCATATACAT
Found at i:60223773 original size:47 final size:47
Alignment explanation
Indices: 60223473--60223776 Score: 441
Period size: 47 Copynumber: 6.5 Consensus size: 47
60223463 ATTTTCACAC
* * *
60223473 CAAAATTTGGACAGCATAT--ATACAAAATTTGGATTGCATTTATACAT
1 CAAAATTT-GACAGCATATACATATATAA-TTGGACTGCATTTATACAT
*
60223520 CAAAATTTGACAGCATATGCATATATAATTGGACTGCATTTATACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* * * * *
60223567 CAAAAATTGACCGCATATACATAAATAATTGAACTGCATTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* * *
60223614 CAAACTTTGACAGCATATACATATATAATTGGACTGCATTTGTAAAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
*
60223661 CAAAATTTGACAGCATATACATATATAATTGGATTGCATTTATACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* *
60223708 CAAAATTTGATAGCATATACATATATAATTGGACTGCATTTGTACAT
1 CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
60223755 CAAAATTTGACAGCATATACAT
1 CAAAATTTGACAGCATATACAT
60223777 TCATTTACTC
Statistics
Matches: 232, Mismatches: 23, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
46 10 0.04
47 216 0.93
48 6 0.03
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (47 bp):
CAAAATTTGACAGCATATACATATATAATTGGACTGCATTTATACAT
Found at i:60224046 original size:14 final size:15
Alignment explanation
Indices: 60224022--60224056 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
60224012 TATATACATT
60224022 ACCATATAAATACTA
1 ACCATATAAATACTA
60224037 ACCATA-AAATACTA
1 ACCATATAAATACTA
60224051 ATCCAT
1 A-CCAT
60224057 GATGAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:60224792 original size:43 final size:43
Alignment explanation
Indices: 60224745--60224827 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 43
60224735 AATCACATAC
60224745 CGATG-CCACTGTCCCAGACAG-GGTCTTACACGAAAACACAAGT
1 CGATGTCCAC-GTCCCAGAC-GTGGTCTTACACGAAAACACAAGT
**
60224788 CGATGTTGACGTCCCAGACGTGGTCTTACACGAAAACACA
1 CGATGTCCACGTCCCAGACGTGGTCTTACACGAAAACACA
60224828 TATCGGAGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
42 1 0.03
43 33 0.92
44 2 0.06
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (43 bp):
CGATGTCCACGTCCCAGACGTGGTCTTACACGAAAACACAAGT
Found at i:60228923 original size:66 final size:65
Alignment explanation
Indices: 60228797--60228935 Score: 154
Period size: 66 Copynumber: 2.1 Consensus size: 65
60228787 CACCCTTTTA
* * * *
60228797 AGAATTGGAGCTAATGATATGTACTCAACCTATCCAGAATTAGAGTATTACTCTTGACCCCTTTG
1 AGAATTGGAGCCAATGATATGTACTCAACCCATCCAGAATTAGAGTATCACTCTTGACCCCTTCG
* * * * * * *
60228862 GGAATTGGAGCCAATGTTTTGTACTCGACCCCTCTAGGAATTAGAGTATCATTCTCT-ACCCCTT
1 AGAATTGGAGCCAATGATATGTACTCAACCCATCCA-GAATTAGAGTATCACTCT-TGACCCCTT
60228926 CG
64 CG
60228928 AGAATTGG
1 AGAATTGG
60228936 GGAACTCAGG
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
65 28 0.47
66 31 0.52
67 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (65 bp):
AGAATTGGAGCCAATGATATGTACTCAACCCATCCAGAATTAGAGTATCACTCTTGACCCCTTCG
Found at i:60229614 original size:75 final size:75
Alignment explanation
Indices: 60229531--60229740 Score: 284
Period size: 75 Copynumber: 2.8 Consensus size: 75
60229521 TTGATCTACC
** *
60229531 ATACTTAAATTATAAATTTATTTATTAAATCTAGATTATTAAATTATAAGTTGAGCTTTACGT-A
1 ATACTTAAATTATAAATTTAACTATTAAATCTA-AATATTAAATTATAAGTTGAGCTTTACGTCA
60229595 GACAT-TTTTAA
65 -ACATCTTTTAA
60229606 ATACTTAAATTATAAATTTAACTATTAACTAT-TAAATATTAAATTATAAGTTGAGCTTTACGTC
1 ATACTTAAATTATAAATTTAACTATTAA--ATCTAAATATTAAATTATAAGTTGAGCTTTACGTC
*
60229670 AACATCTTTTTA
64 AACATCTTTTAA
* * *
60229682 ATATTTAAATTATAAA-TTAACTATTAAACCTAAAATATTAAATTTTAAGTTGAGCTTTA
1 ATACTTAAATTATAAATTTAACTATTAAATCT-AAATATTAAATTATAAGTTGAGCTTTA
60229741 TATTAATATT
Statistics
Matches: 122, Mismatches: 7, Indels: 12
0.87 0.05 0.09
Matches are distributed among these distances:
73 1 0.01
74 1 0.01
75 95 0.78
76 23 0.19
77 2 0.02
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (75 bp):
ATACTTAAATTATAAATTTAACTATTAAATCTAAATATTAAATTATAAGTTGAGCTTTACGTCAA
CATCTTTTAA
Found at i:60229793 original size:75 final size:73
Alignment explanation
Indices: 60229535--60229796 Score: 239
Period size: 75 Copynumber: 3.5 Consensus size: 73
60229525 TCTACCATAC
** * *
60229535 TTAAATTATAAATTTATTTATTAAATCTAGATTATTAAATTATAAGTTGAGCTTTACGT-AGACA
1 TTAAATTATAAA-TTAACTATTAAAT-TA-AATATTAAATTATAAGTTGAGCTTTACATCA-ACA
* *
60229599 T-TTTTAAATAC
62 TCTTTTTAATAT
*
60229610 TTAAATTATAAATTTAACTATTAACTATTAAATATTAAATTATAAGTTGAGCTTTACGTCAACAT
1 TTAAATTATAAA-TTAACTATTAA--ATTAAATATTAAATTATAAGTTGAGCTTTACATCAACAT
60229675 CTTTTTAATAT
63 CTTTTTAATAT
* * * * *
60229686 TTAAATTATAAATTAACTATTAAACCTAAAATATTAAATTTTAAGTTGAGCTTTATATTAATATT
1 TTAAATTATAAATTAACTATTAAA--TTAAATATTAAATTATAAGTTGAGCTTTACATCAACA-T
60229751 CTTTTAGCTAACTA-
63 CTTTT---TAA-TAT
60229765 TT-AATTATAAATTAA-T-TTATAATTAAATATTA
1 TTAAATTATAAATTAACTATTA-AATTAAATATTA
60229797 TTATTTAATC
Statistics
Matches: 163, Mismatches: 12, Indels: 24
0.82 0.06 0.12
Matches are distributed among these distances:
73 1 0.01
75 105 0.64
76 32 0.20
77 5 0.03
78 13 0.08
79 5 0.03
80 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (73 bp):
TTAAATTATAAATTAACTATTAAATTAAATATTAAATTATAAGTTGAGCTTTACATCAACATCTT
TTTAATAT
Found at i:60232373 original size:23 final size:23
Alignment explanation
Indices: 60232347--60232397 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
60232337 ATTGATATTC
*
60232347 TGATCTGTATCGTTCTAGG-TATA
1 TGATCTGTATCATTCT-GGTTATA
* *
60232370 TGATTTGTTTCATTCTGGTTATA
1 TGATCTGTATCATTCTGGTTATA
60232393 TGATC
1 TGATC
60232398 ACTATTAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.49
Consensus pattern (23 bp):
TGATCTGTATCATTCTGGTTATA
Found at i:60238594 original size:23 final size:23
Alignment explanation
Indices: 60238568--60238617 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
60238558 GTTGATATTC
60238568 TGATCTGTTGTGTTCTAGG-TATA
1 TGATCTGTTGTGTTCT-GGTTATA
*
60238591 TGATCTGTTTTGTTCTGGTTATA
1 TGATCTGTTGTGTTCTGGTTATA
60238614 TGAT
1 TGAT
60238618 TGCTATTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.52
Consensus pattern (23 bp):
TGATCTGTTGTGTTCTGGTTATA
Found at i:60261037 original size:27 final size:27
Alignment explanation
Indices: 60261005--60261082 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
60260995 AAATACACCC
60261005 ATAGGGTAATATTATCGAAATACCCTCG
1 ATAGGGTAA-ATTATCGAAATACCCTCG
** *
60261033 A-AGGGTAAAATTATTAAAATA-CCTCT
1 ATAGGGT-AAATTATCGAAATACCCTCG
* *
60261059 ATAGGGGAAATTACCGAAATACCC
1 ATAGGGTAAATTATCGAAATACCC
60261083 CTAAAGGGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
26 16 0.40
27 21 0.52
28 3 0.08
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (27 bp):
ATAGGGTAAATTATCGAAATACCCTCG
Found at i:60261094 original size:53 final size:53
Alignment explanation
Indices: 60260986--60261160 Score: 183
Period size: 54 Copynumber: 3.3 Consensus size: 53
60260976 AATGGGTCAC
* * *
60260986 AAATTACCAAAATACAC-CCATAGGGTAATATTATCGAAATA-CCCTCGAAGGGTA
1 AAATGACCAAAATAC-CTCTATAGGGTAA-ATTACCGAAATACCCCT-GAAGGGTA
* ** * *
60261040 AAATTATTAAAATACCTCTATAGGGGAAATTACCGAAATACCCCTAAAGGGTA
1 AAATGACCAAAATACCTCTATAGGGTAAATTACCGAAATACCCCTGAAGGGTA
* * * * *
60261093 AAATGACCAAAATATCTCTAAATGGTATAATAACCAAAATACCCCTGAAGGGTA
1 AAATGACCAAAATACCTCTATAGGGTA-AATTACCGAAATACCCCTGAAGGGTA
60261147 AAATGACCAAAATA
1 AAATGACCAAAATA
60261161 TCCCCCGAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
53 39 0.38
54 63 0.62
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (53 bp):
AAATGACCAAAATACCTCTATAGGGTAAATTACCGAAATACCCCTGAAGGGTA
Found at i:60261105 original size:27 final size:27
Alignment explanation
Indices: 60261033--60261208 Score: 158
Period size: 27 Copynumber: 6.5 Consensus size: 27
60261023 AATACCCTCG
* ** *
60261033 AAGGGTAAAATTATTAAAATACCTCTA
1 AAGGGTAAAATGACCAAAATACCCCTA
* * * *
60261060 TAGGG-GAAATTACCGAAATACCCCTA
1 AAGGGTAAAATGACCAAAATACCCCTA
* *
60261086 AAGGGTAAAATGACCAAAATATCTCTA
1 AAGGGTAAAATGACCAAAATACCCCTA
* * * *
60261113 AATGGTATAATAACCAAAATACCCCTG
1 AAGGGTAAAATGACCAAAATACCCCTA
*
60261140 AAGGGTAAAATGACCAAAATATCCCCCGA
1 AAGGGTAAAATGACCAAAATA--CCCCTA
*
60261169 AA-GGTAAAATGACCAAAATACCCCCA
1 AAGGGTAAAATGACCAAAATACCCCTA
* *
60261195 CAGGGTAAACTGAC
1 AAGGGTAAAATGAC
60261209 TGATATACCC
Statistics
Matches: 119, Mismatches: 26, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
26 26 0.22
27 69 0.58
28 18 0.15
29 6 0.05
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.19
Consensus pattern (27 bp):
AAGGGTAAAATGACCAAAATACCCCTA
Found at i:60261420 original size:26 final size:26
Alignment explanation
Indices: 60261384--60261460 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 26
60261374 TTGCCACAAA
*
60261384 TACTATTACTGGCAGCTTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCGC
* * * *
60261410 TACTGTTACTGGCAGCTCTGTTGCAC
1 TACTATTACTGGCAGCTTTGCTGCGC
* *
60261436 TATTATTACTGGCAACTTTGCTGCG
1 TACTATTACTGGCAGCTTTGCTGCG
60261461 ATATTTGTGT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGCGC
Found at i:60261608 original size:28 final size:28
Alignment explanation
Indices: 60261565--60261692 Score: 161
Period size: 28 Copynumber: 4.5 Consensus size: 28
60261555 ACTGCATTGT
*
60261565 ACTGTTTACTATATTGGGCTAAGGCCCAC
1 ACTG-TTACTGTATTGGGCTAAGGCCCAC
*
60261594 -CTTGTTACTGTATTGGGCTAAGACCCAC
1 AC-TGTTACTGTATTGGGCTAAGGCCCAC
* *
60261622 GCTGTTACTGTATTAGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
* *
60261650 ACTATTACTGTAATGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
60261678 ACTG-TACTGATATTG
1 ACTGTTACTG-TATTG
60261693 TATAGGGCTT
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.06
28 78 0.91
29 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAGGCCCAC
Found at i:60263444 original size:26 final size:26
Alignment explanation
Indices: 60263377--60263446 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
60263367 CTTTTTTAAC
* ** *
60263377 AGAGATAACCACAAAAACATCTTTTT
1 AGAGATAGCCACAAAGGCATCCTTTT
60263403 AGAGATAGCCACAAAGGCATCCTTTT
1 AGAGATAGCCACAAAGGCATCCTTTT
60263429 AGAGATAGCCACAAAGGC
1 AGAGATAGCCACAAAGGC
60263447 TTACTTATAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (26 bp):
AGAGATAGCCACAAAGGCATCCTTTT
Found at i:60268555 original size:17 final size:17
Alignment explanation
Indices: 60268533--60268565 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
60268523 ATTTAACTAG
60268533 CAATTAAATTAATTCAA
1 CAATTAAATTAATTCAA
*
60268550 CAATTAATTTAATTCA
1 CAATTAAATTAATTCA
60268566 CGTGACAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (17 bp):
CAATTAAATTAATTCAA
Found at i:60274232 original size:33 final size:33
Alignment explanation
Indices: 60274190--60274253 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
60274180 TTTTCACCCA
60274190 AGCTAGTTGTCCTAATAGGACCAAACAAGTCAC
1 AGCTAGTTGTCCTAATAGGACCAAACAAGTCAC
60274223 AGCTAGTTGTCCTAATAGGACCAAACAAGTC
1 AGCTAGTTGTCCTAATAGGACCAAACAAGTC
60274254 TACGTGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (33 bp):
AGCTAGTTGTCCTAATAGGACCAAACAAGTCAC
Found at i:60278545 original size:14 final size:14
Alignment explanation
Indices: 60278526--60278553 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
60278516 TAAAGTTATA
60278526 TTTAATAATTCATT
1 TTTAATAATTCATT
60278540 TTTAATAATTCATT
1 TTTAATAATTCATT
60278554 AATAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:60283057 original size:13 final size:13
Alignment explanation
Indices: 60283039--60283064 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60283029 TGGTGATGTA
60283039 GTCCAACTTTTGT
1 GTCCAACTTTTGT
60283052 GTCCAACTTTTGT
1 GTCCAACTTTTGT
60283065 TCATTAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
GTCCAACTTTTGT
Found at i:60288907 original size:20 final size:18
Alignment explanation
Indices: 60288882--60288920 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
60288872 ATCCATGGTA
60288882 AGTAATTCTTACATGTTTTT
1 AGTAATT-TT-CATGTTTTT
*
60288902 AGTAATTTTGATGTTTTT
1 AGTAATTTTCATGTTTTT
60288920 A
1 A
60288921 AGATTGTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.56
Consensus pattern (18 bp):
AGTAATTTTCATGTTTTT
Found at i:60295654 original size:26 final size:26
Alignment explanation
Indices: 60295625--60295691 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
60295615 CATTTAGACC
*
60295625 CACAGCTCGTGTGAGTAGG-CTTATTT
1 CACAGCTCGTGTGAG-AGGACCTATTT
*
60295651 CACAGCTCGTGTGAGCGGACCTATTT
1 CACAGCTCGTGTGAGAGGACCTATTT
*
60295677 CACAACTCGTGTGAG
1 CACAGCTCGTGTGAG
60295692 CAATGATGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 2 0.05
26 35 0.95
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (26 bp):
CACAGCTCGTGTGAGAGGACCTATTT
Found at i:60298130 original size:27 final size:27
Alignment explanation
Indices: 60298112--60298391 Score: 380
Period size: 27 Copynumber: 10.4 Consensus size: 27
60298102 GGTATAACAA
*
60298112 TCATTTTACCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
*
60298139 TCATTTTACCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
*
60298166 TCATTTTACACTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
60298193 TCATTTTACCCTATAGGCGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
60298220 TCATTTTACCCTATAGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
60298247 TCATTTGACCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
60298274 TTATTTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
60298301 TCATTTTACCCAATGAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
*
60298328 TCATTTTACCCTATGAGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * **
60298355 TCATTTTATCCTATGAGGGTATTTTAG
1 TCATTTTACCCTATGGGGGTATTTCGG
60298382 TCATTTTACC
1 TCATTTTACC
60298392 TATTTTAGGG
Statistics
Matches: 225, Mismatches: 28, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 225 1.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGG
Found at i:60299475 original size:17 final size:17
Alignment explanation
Indices: 60299453--60299485 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
60299443 CACAAAACCG
*
60299453 AAATGAAGAGTATACCA
1 AAATGAACAGTATACCA
60299470 AAATGAACAGTATACC
1 AAATGAACAGTATACC
60299486 CCTCTGGCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.18
Consensus pattern (17 bp):
AAATGAACAGTATACCA
Found at i:60303270 original size:18 final size:18
Alignment explanation
Indices: 60303247--60303284 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
60303237 CAACTTAGTT
60303247 TAGTATTTTGTCAAAATG
1 TAGTATTTTGTCAAAATG
60303265 TAGTATTTTGTCAAAATG
1 TAGTATTTTGTCAAAATG
60303283 TA
1 TA
60303285 CCATAACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (18 bp):
TAGTATTTTGTCAAAATG
Found at i:60304698 original size:4 final size:4
Alignment explanation
Indices: 60304689--60304722 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
60304679 GTGTCCCAAT
* *
60304689 TTCA TTCA TTCA TTCA TTCA CTCA TTCA CTCA TT
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TT
60304723 TGTTTATTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (4 bp):
TTCA
Found at i:60313579 original size:13 final size:13
Alignment explanation
Indices: 60313561--60313586 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60313551 CATTACTACT
60313561 AATATTATTATTA
1 AATATTATTATTA
60313574 AATATTATTATTA
1 AATATTATTATTA
60313587 TCTCTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTATTATTA
Found at i:60314867 original size:15 final size:15
Alignment explanation
Indices: 60314847--60314876 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
60314837 TGAGAAGGAC
60314847 AAGAAAGAAGATGCT
1 AAGAAAGAAGATGCT
*
60314862 AAGAAAGAATATGCT
1 AAGAAAGAAGATGCT
60314877 CGAAACATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.07, G:0.23, T:0.17
Consensus pattern (15 bp):
AAGAAAGAAGATGCT
Found at i:60318527 original size:50 final size:50
Alignment explanation
Indices: 60318409--60318707 Score: 400
Period size: 50 Copynumber: 5.8 Consensus size: 50
60318399 GATAATAACA
* * ** * * *
60318409 TGCCAAAGCCATGTTCCAGACATGGTCTTACATGGGATGTTTTCATATCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
60318460 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
60318510 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
60318560 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
60318610 TGCCAATTCCATGTCCCAGACATAGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* *
60318665 ATGCCAATGCCATGTCCCAGACATGGTCTTCCATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
60318708 TTACCTAAAT
Statistics
Matches: 221, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
50 144 0.65
51 32 0.14
53 5 0.02
55 2 0.01
56 38 0.17
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:60327677 original size:21 final size:22
Alignment explanation
Indices: 60327634--60327683 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
60327624 TTTGATCTTT
*
60327634 AAGAAAAGTTGTGATATTTTAA
1 AAGAAAACTTGTGATATTTTAA
60327656 AAGAAAACTT-TGAT-TTTCTAA
1 AAGAAAACTTGTGATATTT-TAA
*
60327677 AAAAAAA
1 AAGAAAA
60327684 AAAGGGATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 13 0.52
22 9 0.36
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.32
Consensus pattern (22 bp):
AAGAAAACTTGTGATATTTTAA
Found at i:60355018 original size:62 final size:62
Alignment explanation
Indices: 60354887--60355021 Score: 207
Period size: 62 Copynumber: 2.2 Consensus size: 62
60354877 CACGAATTGT
* * ** *
60354887 TGTAACTTTTTTATGCTATAGAATTTAACATATAGATTATGGCATATAAGCTAATGACATTA
1 TGTAACTTTTTTATGCTATAAAATTTAACATATAGATTATAGCATATAAGCTAACAACATCA
**
60354949 TCCAACTTTTTTATGCTATAAAATTTAACATATAGATTATAGCATATAAGCTAACAACATCA
1 TGTAACTTTTTTATGCTATAAAATTTAACATATAGATTATAGCATATAAGCTAACAACATCA
60355011 TGTAACTTTTT
1 TGTAACTTTTT
60355022 GTTAATGTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.40
Consensus pattern (62 bp):
TGTAACTTTTTTATGCTATAAAATTTAACATATAGATTATAGCATATAAGCTAACAACATCA
Found at i:60355324 original size:59 final size:57
Alignment explanation
Indices: 60355206--60355371 Score: 185
Period size: 59 Copynumber: 2.9 Consensus size: 57
60355196 TTTTTCTAAT
* * *
60355206 ATTATATATTA-TTTTTATTAATTCATATTTTAATAATAATCATATTAAGAATGTTATTAA
1 ATTATATATTATTTTTTA-AAATT-ATA-TTTAATAATAATCATATTAA-AATATGATTAA
**
60355266 ATTATATATTATTTTTTAAAAATTATATTTAATAATAATTGTATTAAATATATGATTAA
1 ATTATATATTATTTTTT-AAAATTATATTTAATAATAATCATATTAAA-ATATGATTAA
* * *
60355325 ATTATTTATT-TTTATT-AAATTATATTTAATAATAATCCTATTAAAAT
1 ATTATATATTATTTTTTAAAATTATATTTAATAATAATCATATTAAAAT
60355372 TTAATAACAA
Statistics
Matches: 94, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
55 2 0.02
56 27 0.29
58 6 0.06
59 35 0.37
60 14 0.15
61 9 0.10
62 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (57 bp):
ATTATATATTATTTTTTAAAATTATATTTAATAATAATCATATTAAAATATGATTAA
Found at i:60355569 original size:16 final size:16
Alignment explanation
Indices: 60355545--60355575 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60355535 TGATTGTTGT
*
60355545 TCTATTCCATTACAGC
1 TCTACTCCATTACAGC
60355561 TCTACTCCATTACAG
1 TCTACTCCATTACAG
60355576 TGAACCAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.35
Consensus pattern (16 bp):
TCTACTCCATTACAGC
Found at i:60356164 original size:4 final size:4
Alignment explanation
Indices: 60356155--60356190 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
60356145 GAACCCCTGA
60356155 AGGT AGGT AGGT AGGT AGGT AGGT AGGT AGGT AGGT
1 AGGT AGGT AGGT AGGT AGGT AGGT AGGT AGGT AGGT
60356191 GTAATCCGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
AGGT
Found at i:60357108 original size:24 final size:24
Alignment explanation
Indices: 60357081--60357128 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
60357071 TTTTATTTTT
* *
60357081 TAAAAAATATA-AAATTGTAAAAAA
1 TAAAAAACATATAAACT-TAAAAAA
60357105 TAAAAAACATATAAACTTAAAAAA
1 TAAAAAACATATAAACTTAAAAAA
60357129 ATTTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (24 bp):
TAAAAAACATATAAACTTAAAAAA
Found at i:60357855 original size:37 final size:37
Alignment explanation
Indices: 60357805--60357879 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
60357795 GCTTATTTGA
60357805 GTCTGATTTCACAACCTAAATTCCATGAGAAGAAACG
1 GTCTGATTTCACAACCTAAATTCCATGAGAAGAAACG
60357842 GTCTGATTTCACAACCTAAATTCCATGAGAAGAAACG
1 GTCTGATTTCACAACCTAAATTCCATGAGAAGAAACG
60357879 G
1 G
60357880 AAACCCTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.24
Consensus pattern (37 bp):
GTCTGATTTCACAACCTAAATTCCATGAGAAGAAACG
Found at i:60360358 original size:17 final size:17
Alignment explanation
Indices: 60360336--60360369 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
60360326 CAACAGCGGT
*
60360336 TGAAATAGGTGGGCAGG
1 TGAAATAAGTGGGCAGG
60360353 TGAAATAAGTGGGCAGG
1 TGAAATAAGTGGGCAGG
60360370 AAAGCGTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.44, T:0.18
Consensus pattern (17 bp):
TGAAATAAGTGGGCAGG
Found at i:60361883 original size:31 final size:31
Alignment explanation
Indices: 60361848--60361921 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
60361838 TTAACGGTAT
* *
60361848 AGTGACTAAAATTGATTACTTATCTAACGAG
1 AGTGACTAAAATTGATAACTTATCTAACAAG
* * *
60361879 AGTGATTAAAATTGATAACTTATTTAATAAG
1 AGTGACTAAAATTGATAACTTATCTAACAAG
60361910 AGTGACTAAAAT
1 AGTGACTAAAAT
60361922 AACAAAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (31 bp):
AGTGACTAAAATTGATAACTTATCTAACAAG
Found at i:60370776 original size:20 final size:21
Alignment explanation
Indices: 60370751--60370803 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
60370741 TGTACTTATA
*
60370751 TCTCGAGAC-A-AATGCATTTG
1 TCTCGAGACTAGAA-GCAATTG
60370771 TCTCGAGACTTAGAAGCAATTG
1 TCTCGAGAC-TAGAAGCAATTG
60370793 TCTCGAGACTA
1 TCTCGAGACTA
60370804 ACTAGATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.31
21 2 0.07
22 16 0.55
23 2 0.07
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (21 bp):
TCTCGAGACTAGAAGCAATTG
Found at i:60374538 original size:23 final size:23
Alignment explanation
Indices: 60374485--60374534 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
60374475 TTTTTTAAAA
60374485 TTTTTAAAAAATAATTTAATGAT
1 TTTTTAAAAAATAATTTAATGAT
* *
60374508 TTTTTAAAAAATATTTTTAT-AT
1 TTTTTAAAAAATAATTTAATGAT
60374530 TTTTT
1 TTTTT
60374535 TAAATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTTTAAAAAATAATTTAATGAT
Found at i:60374556 original size:19 final size:18
Alignment explanation
Indices: 60374520--60374558 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
60374510 TTTAAAAAAT
* *
60374520 ATTTTTATATTTTTTTAA
1 ATTTTTAAATTTTATTAA
60374538 ATTTTTAAATTTTAATTAA
1 ATTTTTAAATTTT-ATTAA
60374557 AT
1 AT
60374559 GTTTGATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTAAATTTTATTAA
Found at i:60376430 original size:7 final size:7
Alignment explanation
Indices: 60376418--60376460 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
60376408 AATAAATATT
60376418 TTTTTAA
1 TTTTTAA
60376425 TTTTTAA
1 TTTTTAA
60376432 TTTTTAA
1 TTTTTAA
60376439 TTTTTAA
1 TTTTTAA
**
60376446 TTCAT-A
1 TTTTTAA
60376452 TTTTTAA
1 TTTTTAA
60376459 TT
1 TT
60376461 AATAACTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 4 0.13
7 27 0.87
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTTAA
Found at i:60376711 original size:18 final size:18
Alignment explanation
Indices: 60376690--60376724 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
60376680 TAATATTATA
60376690 AAATAAAATAATTATTTC
1 AAATAAAATAATTATTTC
* *
60376708 AAATATAATTATTATTT
1 AAATAAAATAATTATTT
60376725 TTATATGTAA
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:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATAAAATAATTATTTC
Found at i:60378868 original size:20 final size:20
Alignment explanation
Indices: 60378843--60378892 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
60378833 AAGGAGCCAA
*
60378843 TAAATCAATTTGATTAAAAT
1 TAAATCAAATTGATTAAAAT
60378863 TAAATCAAATTGATTAAAAT
1 TAAATCAAATTGATTAAAAT
* *
60378883 CAAATAAAAT
1 TAAATCAAAT
60378893 AAGATAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (20 bp):
TAAATCAAATTGATTAAAAT
Found at i:60382311 original size:59 final size:59
Alignment explanation
Indices: 60382192--60382303 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 59
60382182 TTCTGAAACA
* * * *
60382192 AAATCAAAATAAATTTTGTTAAATGACAGGACTAAATCCCGAAACTAAATTATATAATT
1 AAATCAAAATAAAATCTATTAAATGACAGGAATAAATCCCGAAACTAAATTATATAATT
*
60382251 AAATCAAAATAAAATCTATTAAATGACGGGAATAAATCCCGAAAC-AGAATTAT
1 AAATCAAAATAAAATCTATTAAATGACAGGAATAAATCCCGAAACTA-AATTAT
60382304 TTGATTAAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 1 0.02
59 46 0.98
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (59 bp):
AAATCAAAATAAAATCTATTAAATGACAGGAATAAATCCCGAAACTAAATTATATAATT
Found at i:60382436 original size:83 final size:83
Alignment explanation
Indices: 60382258--60382467 Score: 221
Period size: 83 Copynumber: 2.6 Consensus size: 83
60382248 ATTAAATCAA
* * * * * **
60382258 AATAAAATC-TATTAAATGACGGGAATAAATCCCGAAACAGAATTATTTGATTAAGTATTTCTTT
1 AATAAAATCTTGTTAAACGGCGAGAATAAATCCCGAAACAGAATTATTTAATTAAGTATTAATTT
* *
60382322 GGAAACAAAACAATATCG
66 GAAAACAAAACAAAATCG
* * * *
60382340 AATAAAATCTTGTTAAACGGCTAGAATAAATCCCGAAATAGATTTTATTTAATTTAATTA-TAAT
1 AATAAAATCTTGTTAAACGGCGAGAATAAATCCCGAAACAGA-ATTATTTAA-TTAAGTATTAAT
*
60382404 TTGAAAACAAAATAAAATCG
64 TTGAAAACAAAACAAAATCG
* * *
60382424 AAT-AAATTTTGTTAAACGGCGGGAATAAATCCCAAAACA-AATTA
1 AATAAAATCTTGTTAAACGGCGAGAATAAATCCCGAAACAGAATTA
60382468 GTCATTCAAT
Statistics
Matches: 105, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
81 3 0.03
82 10 0.10
83 57 0.54
84 29 0.28
85 6 0.06
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (83 bp):
AATAAAATCTTGTTAAACGGCGAGAATAAATCCCGAAACAGAATTATTTAATTAAGTATTAATTT
GAAAACAAAACAAAATCG
Found at i:60390160 original size:43 final size:43
Alignment explanation
Indices: 60390096--60390244 Score: 165
Period size: 43 Copynumber: 3.4 Consensus size: 43
60390086 AAAATAAGCT
* *
60390096 TTTAGCGACG-TTTTACCCACAAACGACGCTAAAGAACATGACC
1 TTTAGCGACGCTTTTA-TCACAAACGCCGCTAAAGAACATGACC
* * * * *
60390139 TTTAGCGGCGCTTTTATCACAAATGCCACTAAAGAGCATCACC
1 TTTAGCGACGCTTTTATCACAAACGCCGCTAAAGAACATGACC
* * * *
60390182 TTTAACGACGCTTTTTTTCACAAACGCCGCTAAAAAACATGATC
1 TTTAGCGACGC-TTTTATCACAAACGCCGCTAAAGAACATGACC
*
60390226 TTTAGCGGCGCTTTTATCA
1 TTTAGCGACGCTTTTATCA
60390245 AAAATTCTGC
Statistics
Matches: 85, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
43 46 0.54
44 39 0.46
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
TTTAGCGACGCTTTTATCACAAACGCCGCTAAAGAACATGACC
Found at i:60392866 original size:9 final size:9
Alignment explanation
Indices: 60392852--60393134 Score: 135
Period size: 9 Copynumber: 30.0 Consensus size: 9
60392842 TAAGTATAAT
60392852 TAAGTTATG
1 TAAGTTATG
60392861 TAAGTTATG
1 TAAGTTATG
* * *
60392870 ATATGATATA
1 -TAAGTTATG
*
60392880 T-ATTTATG
1 TAAGTTATG
60392888 T-A-TTATG
1 TAAGTTATG
*
60392895 TGAGTTATG
1 TAAGTTATG
60392904 TAAGTTATG
1 TAAGTTATG
* *
60392913 ATAGGATATATA
1 -TAAG-T-TATG
60392925 TAAGTTAT-
1 TAAGTTATG
60392933 TAAGTTATG
1 TAAGTTATG
60392942 TAAGTTATG
1 TAAGTTATG
60392951 TAAGTTATG
1 TAAGTTATG
*
60392960 TATGTTATG
1 TAAGTTATG
*
60392969 TGAGTTATG
1 TAAGTTATG
* *
60392978 CAAGTTAAG
1 TAAGTTATG
* *
60392987 ATATGATATATA
1 -TAAG-T-TATG
60392999 TAAGTTAT-
1 TAAGTTATG
*
60393007 TAAGTTAAG
1 TAAGTTATG
* * *
60393016 ATCCAAATTTTTTT
1 -T---AA-GTTATG
* * *
60393030 TAAATTCTT
1 TAAGTTATG
60393039 TAAAGTTATG
1 T-AAGTTATG
*
60393049 TAAATTATG
1 TAAGTTATG
60393058 TAAGTTATG
1 TAAGTTATG
*
60393067 TAAGTTTTG
1 TAAGTTATG
* *
60393076 ATATGATATATATT
1 -TA--A-GT-TATG
60393090 TAAGTTATG
1 TAAGTTATG
*
60393099 TAAATTATG
1 TAAGTTATG
*
60393108 CAAGTTATG
1 TAAGTTATG
60393117 TAAGTTATG
1 TAAGTTATG
60393126 TAAGTTATG
1 TAAGTTATG
60393135 ATATATATTT
Statistics
Matches: 208, Mismatches: 44, Indels: 44
0.70 0.15 0.15
Matches are distributed among these distances:
7 6 0.03
8 21 0.10
9 131 0.63
10 25 0.12
11 9 0.04
12 6 0.03
13 6 0.03
14 4 0.02
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:60392903 original size:43 final size:45
Alignment explanation
Indices: 60392852--60392963 Score: 151
Period size: 43 Copynumber: 2.5 Consensus size: 45
60392842 TAAGTATAAT
60392852 TAAGTTATGTAAGTTATGATATGATATATAT-TTATGT-A-TTATG
1 TAAGTTATGTAAGTTATGATATGATATATATATTAT-TAAGTTATG
* *
60392895 TGAGTTATGTAAGTTATGATAGGATATATATAAGTTATTAAGTTATG
1 TAAGTTATGTAAGTTATGATATGATATATAT-A-TTATTAAGTTATG
60392942 TAAGTTATGTAAGTTATG-TATG
1 TAAGTTATGTAAGTTATGATATG
60392964 TTATGTGAGT
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
43 29 0.48
45 1 0.02
46 8 0.13
47 22 0.37
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.46
Consensus pattern (45 bp):
TAAGTTATGTAAGTTATGATATGATATATATATTATTAAGTTATG
Found at i:60392983 original size:74 final size:72
Alignment explanation
Indices: 60392852--60393013 Score: 218
Period size: 74 Copynumber: 2.2 Consensus size: 72
60392842 TAAGTATAAT
* * * *
60392852 TAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTGAGTTATGTAAGTTATGATAG
1 TAAGTTAT-TAAGTTATGATAAGATATATAGTTATGTATTATGTGAGTTATGCAAGTTAAGATAG
60392917 GATATATA
65 GATATATA
* *
60392925 TAAGTTATTAAGTTATG-TAAGTTATGTAAGTTATGTATGTTATGTGAGTTATGCAAGTTAAGAT
1 TAAGTTATTAAGTTATGATAAGATATAT-AGTTATGTA--TTATGTGAGTTATGCAAGTTAAGAT
*
60392989 ATGATATATA
63 AGGATATATA
60392999 TAAGTTATTAAGTTA
1 TAAGTTATTAAGTTA
60393014 AGATCCAAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
71 7 0.09
72 17 0.22
73 8 0.10
74 47 0.59
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.44
Consensus pattern (72 bp):
TAAGTTATTAAGTTATGATAAGATATATAGTTATGTATTATGTGAGTTATGCAAGTTAAGATAGG
ATATATA
Found at i:60400199 original size:14 final size:14
Alignment explanation
Indices: 60400180--60400210 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
60400170 AATTTATATG
60400180 TTTATAAATCCATT
1 TTTATAAATCCATT
60400194 TTTATAAATCCATT
1 TTTATAAATCCATT
60400208 TTT
1 TTT
60400211 TTCCCAAAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTATAAATCCATT
Found at i:60401024 original size:23 final size:22
Alignment explanation
Indices: 60400993--60401038 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
60400983 TTCAAACAAT
*
60400993 AAACACTAAGCCCTAAGCCCCTA
1 AAACACTAAACCCT-AGCCCCTA
* *
60401016 AAACCCTAAATCCTAGCCCCTA
1 AAACACTAAACCCTAGCCCCTA
60401038 A
1 A
60401039 CCCAAAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.39, C:0.39, G:0.07, T:0.15
Consensus pattern (22 bp):
AAACACTAAACCCTAGCCCCTA
Found at i:60401067 original size:14 final size:14
Alignment explanation
Indices: 60401050--60401185 Score: 93
Period size: 14 Copynumber: 9.8 Consensus size: 14
60401040 CCAAAAACTT
*
60401050 TAAACTCTAAACCA
1 TAAACCCTAAACCA
*
60401064 TAAAACCCTAAGCTC-
1 T-AAACCCTAAAC-CA
60401079 T-AACCCATAAACC-
1 TAAACCC-TAAACCA
*
60401092 TACACCCTAAACCA
1 TAAACCCTAAACCA
*
60401106 TAAACACTAAACTC-
1 TAAACCCTAAAC-CA
* * *
60401120 TTAATCCTAAATCA
1 TAAACCCTAAACCA
* *
60401134 TAAATCCTAAACCT
1 TAAACCCTAAACCA
*
60401148 TAAACCCTAAACTA
1 TAAACCCTAAACCA
* *
60401162 TAAA-CCTACACCC
1 TAAACCCTAAACCA
60401175 TAAACCCTAAA
1 TAAACCCTAAA
60401186 TATATTAGAA
Statistics
Matches: 94, Mismatches: 20, Indels: 16
0.72 0.15 0.12
Matches are distributed among these distances:
13 24 0.26
14 58 0.62
15 11 0.12
16 1 0.01
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:60401068 original size:22 final size:22
Alignment explanation
Indices: 60401035--60401120 Score: 72
Period size: 22 Copynumber: 4.1 Consensus size: 22
60401025 ATCCTAGCCC
**
60401035 CTAACCCA-AAAACTTTAAACT
1 CTAACCCATAAAACCCTAAACT
* *
60401056 CTAAACCATAAAACCCTAAGCT
1 CTAACCCATAAAACCCTAAACT
* *
60401078 CTAACCCAT-AAA-CCTACACC
1 CTAACCCATAAAACCCTAAACT
* *
60401098 CTAAACCAT-AAACACTAAACT
1 CTAACCCATAAAACCCTAAACT
60401119 CT
1 CT
60401121 TAATCCTAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
20 16 0.31
21 17 0.33
22 18 0.35
ACGTcount: A:0.45, C:0.34, G:0.01, T:0.20
Consensus pattern (22 bp):
CTAACCCATAAAACCCTAAACT
Found at i:60401090 original size:21 final size:21
Alignment explanation
Indices: 60401035--60401184 Score: 83
Period size: 21 Copynumber: 7.2 Consensus size: 21
60401025 ATCCTAGCCC
* **
60401035 CTAACCCAAAAACTTTAAACT
1 CTAACCCATAAACCCTAAACT
* *
60401056 CTAAACCATAAAACCCTAAGCT
1 CTAACCCAT-AAACCCTAAACT
* *
60401078 CTAACCCATAAA-CCTACACC
1 CTAACCCATAAACCCTAAACT
* *
60401098 CTAAACCATAAACACTAAACT
1 CTAACCCATAAACCCTAAACT
* * *
60401119 CTTAATCC-TAAATCATAAA-T
1 C-TAACCCATAAACCCTAAACT
* *
60401139 CCTAAACCTTAAACCCTAAACT
1 -CTAACCCATAAACCCTAAACT
* * * *
60401161 ATAAACC-TACACCCTAAACC
1 CTAACCCATAAACCCTAAACT
60401181 CTAA
1 CTAA
60401185 ATATATTAGA
Statistics
Matches: 99, Mismatches: 24, Indels: 13
0.73 0.18 0.10
Matches are distributed among these distances:
20 36 0.36
21 40 0.40
22 23 0.23
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (21 bp):
CTAACCCATAAACCCTAAACT
Found at i:60401129 original size:28 final size:27
Alignment explanation
Indices: 60401050--60401185 Score: 107
Period size: 27 Copynumber: 4.9 Consensus size: 27
60401040 CCAAAAACTT
* *
60401050 TAAACTCTAAACCATAAAACCCTAAGCTC-
1 TAAAC-CTAAACC-TTAAACCCTAAAC-CA
* *
60401079 TAACCCATAAACC-TACACCCTAAACCA
1 TAAACC-TAAACCTTAAACCCTAAACCA
* *
60401106 TAAACACTAAACTCTT-AATCCTAAATCA
1 TAAAC-CTAAAC-CTTAAACCCTAAACCA
*
60401134 TAAATCCTAAACCTTAAACCCTAAACTA
1 TAAA-CCTAAACCTTAAACCCTAAACCA
* *
60401162 TAAACCTACACCCTAAACCCTAAA
1 TAAACCTAAACCTTAAACCCTAAA
60401186 TATATTAGAA
Statistics
Matches: 87, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.01
27 39 0.45
28 35 0.40
29 12 0.14
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (27 bp):
TAAACCTAAACCTTAAACCCTAAACCA
Found at i:60401176 original size:20 final size:21
Alignment explanation
Indices: 60401141--60401179 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
60401131 TCATAAATCC
60401141 TAAACCTTAAACCCTAAACTA
1 TAAACCTTAAACCCTAAACTA
*
60401162 TAAACC-TACACCCTAAAC
1 TAAACCTTAAACCCTAAAC
60401180 CCTAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (21 bp):
TAAACCTTAAACCCTAAACTA
Found at i:60401654 original size:40 final size:40
Alignment explanation
Indices: 60401554--60401655 Score: 98
Period size: 40 Copynumber: 2.5 Consensus size: 40
60401544 GCGTTGTTTT
* * * * * *
60401554 CTCAACTTTTTACGGTGTTTTGCTATAAGCGCCGCTAATG
1 CTCAACCTATTACGGTGTTTTTCAACAAGCGCAGCTAATG
* * *
60401594 CTCGACCTA-TAGCGGCGTTTTTCAACAAGCGCAGCTAATT
1 CTCAACCTATTA-CGGTGTTTTTCAACAAGCGCAGCTAATG
*
60401634 CTCAATCTATTACGGTGTTTTT
1 CTCAACCTATTACGGTGTTTTT
60401656 TAAAAAAGCA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
39 2 0.04
40 44 0.92
41 2 0.04
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.36
Consensus pattern (40 bp):
CTCAACCTATTACGGTGTTTTTCAACAAGCGCAGCTAATG
Found at i:60401985 original size:40 final size:40
Alignment explanation
Indices: 60401884--60401987 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 40
60401874 TTTTGCGGCA
* **
60401884 TTTTCCAAAAAG-AGCCGCTAATGCTCGATCTATAGTGGCG
1 TTTTTCAAAAAGCA-CCGCTAATGCTCGATCTATAGCAGCG
** * * *
60401924 TTTTTCAAATGGCGCCTCTAATGCTCGATCTATTGCAGCG
1 TTTTTCAAAAAGCACCGCTAATGCTCGATCTATAGCAGCG
*
60401964 TTTTTTAAAAAGCACCGCTAATGC
1 TTTTTCAAAAAGCACCGCTAATGC
60401988 CACTAAAGCT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (40 bp):
TTTTTCAAAAAGCACCGCTAATGCTCGATCTATAGCAGCG
Found at i:60402100 original size:154 final size:154
Alignment explanation
Indices: 60401512--60402140 Score: 674
Period size: 154 Copynumber: 4.1 Consensus size: 154
60401502 GATAAAAATG
* * * * *
60401512 CCGCTAATGCCACTAAAGCTCAACACCAAACGGCGTTGTTTT-CTCAAC-TTTTTACGGTGTTTT
1 CCGCTAATGCCACTAAAGCTCAACAACAAACGACGTCGTTTTGCTCAACTTTTTTGCGGCGTTTT
* * * * *
60401575 GCT-ATAAGCGCCGCTAATGCTCGACCTATAGCGGCGTTTTTCAACAAGCGCAGCTAATTCTCAA
66 -CTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAA-AAGCGCCGCTAATGCTCGA
* * *
60401639 TCTATTACGGTGTTTTTTAAAAAAGCA
129 TCTATTGCAGCGTTTTTT-AAAAAGCA
* * ** *
60401666 TCGCTAATGCAACTAAAGCAAAAAAAAACAAACGACGTCGTTTTGCTCAACTTTTTTGCGGCGTT
1 CCGCTAATGCCACTAAAGC--TCAACAACAAACGACGTCGTTTTGCTCAACTTTTTTGCGGCGTT
* * * * * * * *
60401731 TCCAAAAAAGCGCAGCTAATGCTCAATCTATAGCGGTGTTTTTCGACAACCGCCGCTAATTCTCG
64 TTCTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTC-AAAAGCGCCGCTAATGCTCG
* ** *
60401796 ATTTATTGTGGCGTTTTTTAAAAAGCG
128 ATCTATTGCAGCGTTTTTTAAAAAGCA
* * *
60401823 CCGCTAATG-CATTAAAGCTCAACAACAAACGGCGTCGTTTTGCTCAACTTTTTTTGCGGCATTT
1 CCGCTAATGCCACTAAAGCTCAACAACAAACGACGTCGTTTTGCTCAAC-TTTTTTGCGGCGTTT
* * * * *
60401887 TCCAAAAAGAGCCGCTAATGCTCGATCTATAGTGGCGTTTTTCAAATGGCGCCTCTAATGCTCGA
65 TCTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAA-AGCGCCGCTAATGCTCGA
60401952 TCTATTGCAGCGTTTTTTAAAAAGCA
129 TCTATTGCAGCGTTTTTTAAAAAGCA
* * **
60401978 CCGCTAATGCCACTAAAGCTCAACAACAAACGATGT-GTTTTGCTAAACTTTTTTGCGTTGTTTT
1 CCGCTAATGCCACTAAAGCTCAACAACAAACGACGTCGTTTTGCTCAACTTTTTTGCGGCGTTTT
* * * * * *
60402042 CTGAAAAGCGCCGCTAATGCTCTATCTATAACGGTGTTTTTTGAAAAGCGCCGCTAATGCTTGAT
66 CTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG-TTTTTCAAAAGCGCCGCTAATGCTCGAT
* * *
60402107 CTATAGCATCGTTTTTCAAAAAGCA
130 CTATTGCAGCGTTTTTTAAAAAGCA
*
60402132 CCGTTAATG
1 CCGCTAATG
60402141 TTTGATCTAT
Statistics
Matches: 393, Mismatches: 72, Indels: 20
0.81 0.15 0.04
Matches are distributed among these distances:
154 133 0.34
155 114 0.29
156 47 0.12
157 22 0.06
158 76 0.19
159 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (154 bp):
CCGCTAATGCCACTAAAGCTCAACAACAAACGACGTCGTTTTGCTCAACTTTTTTGCGGCGTTTT
CTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAGCGCCGCTAATGCTCGATC
TATTGCAGCGTTTTTTAAAAAGCA
Found at i:60402196 original size:40 final size:40
Alignment explanation
Indices: 60402045--60402201 Score: 179
Period size: 40 Copynumber: 3.9 Consensus size: 40
60402035 TTGTTTTCTG
* * * **
60402045 AAAAGCGCCGCTAATGCTCTATCTATAACGGTGTTTTTTG
1 AAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCA
* **
60402085 AAAAGCGCCGCTAATGCTTGATCTATAGCATCGTTTTTCA
1 AAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCA
* * * *
60402125 AAAAGCACCGTTAATGTTTGATCTATAGCGGCGTTTTTCA
1 AAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCA
* * *
60402165 AAAAGCGCCGCTAATGCTCGACCTTTTGCGGCGTTTT
1 AAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTT
60402202 CATAGTAGCA
Statistics
Matches: 97, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 97 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (40 bp):
AAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCA
Found at i:60402220 original size:80 final size:80
Alignment explanation
Indices: 60402065--60402221 Score: 172
Period size: 80 Copynumber: 2.0 Consensus size: 80
60402055 CTAATGCTCT
* ** * * *
60402065 ATCTATAACGGTGTTTTTTGAAAAGCGCCGCTAATGCTTGATCTATAGCATCGTTTTTCAAAAAG
1 ATCTATAACGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCAGCGTTTTTCAAAAAG
**
60402130 CACCGTTAATGTTTG
66 CACCACTAATGTTTG
* * * * **
60402145 ATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGACCTTTTGCGGCG-TTTTCATAGTA
1 ATCTATAACGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCAGCGTTTTTCA-AAAA
60402209 GCACCACTAATGT
65 GCACCACTAATGT
60402222 ACAACTTTTG
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
79 6 0.10
80 56 0.90
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (80 bp):
ATCTATAACGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCAGCGTTTTTCAAAAAG
CACCACTAATGTTTG
Found at i:60403193 original size:21 final size:21
Alignment explanation
Indices: 60403154--60403193 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
60403144 TTTATTTAAA
* *
60403154 AATATAAATGATATAGAATAT
1 AATATAAATAAAATAGAATAT
*
60403175 AATATAAATAAAATGGAAT
1 AATATAAATAAAATAGAAT
60403194 TACTGATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (21 bp):
AATATAAATAAAATAGAATAT
Found at i:60403341 original size:23 final size:19
Alignment explanation
Indices: 60403294--60403352 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
60403284 ATATCTATGG
60403294 ATTAATAATACTCTATATA
1 ATTAATAATACTCTATATA
60403313 ATTAATAATACTCTATATA
1 ATTAATAATACTCTATATA
* *
60403332 GATAAATAATAATCTATATA
1 -ATTAATAATACTCTATATA
60403352 A
1 A
60403353 CATAATCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (19 bp):
ATTAATAATACTCTATATA
Found at i:60403359 original size:14 final size:14
Alignment explanation
Indices: 60403340--60403368 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
60403330 TAGATAAATA
60403340 ATAATCTATATAAC
1 ATAATCTATATAAC
60403354 ATAATCTATATAAC
1 ATAATCTATATAAC
60403368 A
1 A
60403369 AAGTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATCTATATAAC
Found at i:60404536 original size:4 final size:4
Alignment explanation
Indices: 60404529--60404572 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
60404519 TAATATTAGA
* *
60404529 ATTT ATTT ATTT ATTTT ATTA ATTT ATTT ATAT ATTTT ATTT AT
1 ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT A-TTT ATTT AT
60404573 AATATATTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
4 27 0.79
5 7 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:60404548 original size:13 final size:13
Alignment explanation
Indices: 60404529--60404633 Score: 52
Period size: 13 Copynumber: 7.6 Consensus size: 13
60404519 TAATATTAGA
60404529 ATTTATTTA-TTT
1 ATTTATTTATTTT
*
60404541 ATTT-TATTAATTT
1 ATTTAT-TTATTTT
*
60404554 ATTTATATATTTT
1 ATTTATTTATTTT
* *
60404567 ATTTATAATATATT
1 ATTTAT-TTATTTT
**
60404581 AGAATATTATATTTAT
1 A-TTTATT-TATTT-T
*
60404597 ATTATATTTATATT
1 ATT-TATTTATTTT
*
60404611 ATTTATCTATTTCT
1 ATTTATTTATTT-T
60404625 ATTTCATTT
1 ATTT-ATTT
60404634 GTTTCTATTC
Statistics
Matches: 70, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
11 1 0.01
12 7 0.10
13 25 0.36
14 17 0.24
15 14 0.20
16 6 0.09
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:60404553 original size:21 final size:21
Alignment explanation
Indices: 60404528--60404569 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
60404518 TTAATATTAG
*
60404528 AATTTATTTATTTATTTTATT
1 AATTTATTTATATATTTTATT
60404549 AATTTATTTATATATTTTATT
1 AATTTATTTATATATTTTATT
60404570 TATAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
AATTTATTTATATATTTTATT
Found at i:60404580 original size:24 final size:24
Alignment explanation
Indices: 60404479--60404614 Score: 79
Period size: 24 Copynumber: 5.7 Consensus size: 24
60404469 TAATTCTATT
*
60404479 ATATATTTATCA-ATTCTA-TTAT-
1 ATATATTTAT-ATATTTTATTTATA
* *
60404501 ATATATTCTAATATATATTAATATTAGA
1 ATATATT-T-ATATAT-TTTAT-TTATA
* *
60404529 ATTTATTTATTTATTTTA--T-TA
1 ATATATTTATATATTTTATTTATA
*
60404550 ATTTATTTATATATTTTATTTATA
1 ATATATTTATATATTTTATTTATA
* *
60404574 ATATA-TTAGAATATTATATTTATA
1 ATATATTTA-TATATTTTATTTATA
*
60404598 TTATATTTATATTATTT
1 ATATATTTATA-TATTT
60404615 ATCTATTTCT
Statistics
Matches: 87, Mismatches: 14, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
21 18 0.21
22 8 0.09
23 6 0.07
24 28 0.32
25 12 0.14
26 5 0.06
27 4 0.05
28 6 0.07
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (24 bp):
ATATATTTATATATTTTATTTATA
Found at i:60413837 original size:19 final size:19
Alignment explanation
Indices: 60413799--60413838 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
60413789 TCATACATGA
*
60413799 AATTAAAAAAATAACTCTT
1 AATTAAAAAAATAACACTT
60413818 AATTAAAAAAAATAA-ACTT
1 AATT-AAAAAAATAACACTT
60413837 AA
1 AA
60413839 CTATCAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (19 bp):
AATTAAAAAAATAACACTT
Found at i:60416618 original size:18 final size:18
Alignment explanation
Indices: 60416581--60416618 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
60416571 AAAAAATCAC
*
60416581 ATTTTTTACATTTAATAT
1 ATTTTTTACATTTAAAAT
60416599 ATTTTTTA-ATTTCAAAAT
1 ATTTTTTACATTT-AAAAT
60416617 AT
1 AT
60416619 ATAGTGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTTTACATTTAAAAT
Found at i:60428941 original size:2 final size:2
Alignment explanation
Indices: 60428934--60428963 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60428924 TCTTGTATTG
60428934 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
60428964 GGTGTTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60436509 original size:504 final size:504
Alignment explanation
Indices: 60435562--60436576 Score: 2021
Period size: 504 Copynumber: 2.0 Consensus size: 504
60435552 ACCGCCTTTT
60435562 ACCTCATCAACTTAGGCATTTAATTTCATTTACCTAAAATCTGACCCCACCTTATCTAGTTATGA
1 ACCTCATCAACTTAGGCATTTAATTTCATTTACCTAAAATCTGACCCCACCTTATCTAGTTATGA
60435627 TTTCAATTTATCCCCTGTTTTTCATGACTTTCTACCAGCTTCCAGCCTTAATAAATGGCTCCATC
66 TTTCAATTTATCCCCTGTTTTTCATGACTTTCTACCAGCTTCCAGCCTTAATAAATGGCTCCATC
60435692 ACAGAAAAAGCATTCTTTCAGATCCAAGCAATCTGAGGCACCATTATATACTTTGTAGACTTCGA
131 ACAGAAAAAGCATTCTTTCAGATCCAAGCAATCTGAGGCACCATTATATACTTTGTAGACTTCGA
60435757 AAGCAGATTTTTATCATTTGCCAATTGAAAACCAAAGAGTGCGGGTAACAACAGGGTGCTCAACT
196 AAGCAGATTTTTATCATTTGCCAATTGAAAACCAAAGAGTGCGGGTAACAACAGGGTGCTCAACT
60435822 TAAGCATTCACAATGGCATTAGCATTTCTAGTTCTATTTACTCATATCGCCAACCAAAAGCAATT
261 TAAGCATTCACAATGGCATTAGCATTTCTAGTTCTATTTACTCATATCGCCAACCAAAAGCAATT
60435887 TGAGTAGAATAACAAAAGATTGCTAACAAAAGATGATGACAGGCAAGTAGGAAAGCACTATACTC
326 TGAGTAGAATAACAAAAGATTGCTAACAAAAGATGATGACAGGCAAGTAGGAAAGCACTATACTC
60435952 GCTTCAGAAGGAAAAATGAAATGGAGATGAACAAATATGTGACCATATAAGGAAATTGATGTGAG
391 GCTTCAGAAGGAAAAATGAAATGGAGATGAACAAATATGTGACCATATAAGGAAATTGATGTGAG
60436017 AAAACCCAGCTAAAGGGAATAATAGCTTAAAGAGATTCCAAACCAATAC
456 AAAACCCAGCTAAAGGGAATAATAGCTTAAAGAGATTCCAAACCAATAC
60436066 ACCTCATCAACTTAGGCATTTAATTTCATTTACCTAAAATCTGACCCCACCTTATCTAGTTATGA
1 ACCTCATCAACTTAGGCATTTAATTTCATTTACCTAAAATCTGACCCCACCTTATCTAGTTATGA
60436131 TTTCAATTTATCCCCTGTTTTTCATGACTTTCTACCAGCTTCCAGCCTTAATAAATGGCTCCATC
66 TTTCAATTTATCCCCTGTTTTTCATGACTTTCTACCAGCTTCCAGCCTTAATAAATGGCTCCATC
60436196 ACAGAAAAAGCATTCTTTCAGATCCAAGCAATCTGAGGCACCATTATATACTTTGTAGACTTCGA
131 ACAGAAAAAGCATTCTTTCAGATCCAAGCAATCTGAGGCACCATTATATACTTTGTAGACTTCGA
60436261 AAGCAGATTTTTATCATTTGCCAATTGAAAACCAAAGAGTGCGGGTAACAACAGGGTGCTCAACT
196 AAGCAGATTTTTATCATTTGCCAATTGAAAACCAAAGAGTGCGGGTAACAACAGGGTGCTCAACT
60436326 TAAGCATTCACAATGGCATTAGCATTTCTAGTTCTATTTACTCATATCGCCAACCAAAAGCAATT
261 TAAGCATTCACAATGGCATTAGCATTTCTAGTTCTATTTACTCATATCGCCAACCAAAAGCAATT
60436391 TGAGTAGAATAACAAAAGATTGCTAACAAAAGATGATGACAGGCAAGTAGGAAAGCACTATACTC
326 TGAGTAGAATAACAAAAGATTGCTAACAAAAGATGATGACAGGCAAGTAGGAAAGCACTATACTC
60436456 GCTTCAGAAGGAAAAATGAAATGGAGATGAACAAATATGTGACCATATAAGGAAATTGATGTGAG
391 GCTTCAGAAGGAAAAATGAAATGGAGATGAACAAATATGTGACCATATAAGGAAATTGATGTGAG
60436521 AAAACCCAGCTAAAGGGAATAATAGCTTAAAGAGATTCCAAACCAATAC
456 AAAACCCAGCTAAAGGGAATAATAGCTTAAAGAGATTCCAAACCAATAC
*
60436570 ACTTCAT
1 ACCTCAT
60436577 TAGATATAGG
Statistics
Matches: 510, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
504 510 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (504 bp):
ACCTCATCAACTTAGGCATTTAATTTCATTTACCTAAAATCTGACCCCACCTTATCTAGTTATGA
TTTCAATTTATCCCCTGTTTTTCATGACTTTCTACCAGCTTCCAGCCTTAATAAATGGCTCCATC
ACAGAAAAAGCATTCTTTCAGATCCAAGCAATCTGAGGCACCATTATATACTTTGTAGACTTCGA
AAGCAGATTTTTATCATTTGCCAATTGAAAACCAAAGAGTGCGGGTAACAACAGGGTGCTCAACT
TAAGCATTCACAATGGCATTAGCATTTCTAGTTCTATTTACTCATATCGCCAACCAAAAGCAATT
TGAGTAGAATAACAAAAGATTGCTAACAAAAGATGATGACAGGCAAGTAGGAAAGCACTATACTC
GCTTCAGAAGGAAAAATGAAATGGAGATGAACAAATATGTGACCATATAAGGAAATTGATGTGAG
AAAACCCAGCTAAAGGGAATAATAGCTTAAAGAGATTCCAAACCAATAC
Found at i:60437461 original size:319 final size:319
Alignment explanation
Indices: 60436882--60437524 Score: 1277
Period size: 319 Copynumber: 2.0 Consensus size: 319
60436872 ATAATATAAA
60436882 AATTGAACTCAAAAGAACTCTGCGAAACATTTTAACAAACCTACATCGAGACGCACATTGATGAC
1 AATTGAACTCAAAAGAACTCTGCGAAACATTTTAACAAACCTACATCGAGACGCACATTGATGAC
60436947 AGCAAAACTAAAAAAAATATCCATTAATCCCAATTTACACTTACAATCCAAATTATCTTTCCTTT
66 AGCAAAACTAAAAAAAATATCCATTAATCCCAATTTACACTTACAATCCAAATTATCTTTCCTTT
60437012 TTTTTCCCCACAGTATAGAACTTGCAATTTATTTTCCTGTACAATTCAATTTCAAGAAGAAAGGA
131 TTTTTCCCCACAGTATAGAACTTGCAATTTATTTTCCTGTACAATTCAATTTCAAGAAGAAAGGA
60437077 AGAGCTTTAACGAATAAGGCACAGCTAAAACTGAGTTCACCTCAAGAATATTAGCGCAGACAGTA
196 AGAGCTTTAACGAATAAGGCACAGCTAAAACTGAGTTCACCTCAAGAATATTAGCGCAGACAGTA
60437142 GCAGCAATGGCCTTGGCGGCATGAACATTCTCGCCAGCGATTATTGTCAAGTTAGTAAT
261 GCAGCAATGGCCTTGGCGGCATGAACATTCTCGCCAGCGATTATTGTCAAGTTAGTAAT
*
60437201 AATTGAACTCAAAAGAACTCTGCGAAACATTTTAACAAACCTATATCGAGACGCACATTGATGAC
1 AATTGAACTCAAAAGAACTCTGCGAAACATTTTAACAAACCTACATCGAGACGCACATTGATGAC
60437266 AGCAAAACTAAAAAAAATATCCATTAATCCCAATTTACACTTACAATCCAAATTATCTTTCCTTT
66 AGCAAAACTAAAAAAAATATCCATTAATCCCAATTTACACTTACAATCCAAATTATCTTTCCTTT
60437331 TTTTTCCCCACAGTATAGAACTTGCAATTTATTTTCCTGTACAATTCAATTTCAAGAAGAAAGGA
131 TTTTTCCCCACAGTATAGAACTTGCAATTTATTTTCCTGTACAATTCAATTTCAAGAAGAAAGGA
60437396 AGAGCTTTAACGAATAAGGCACAGCTAAAACTGAGTTCACCTCAAGAATATTAGCGCAGACAGTA
196 AGAGCTTTAACGAATAAGGCACAGCTAAAACTGAGTTCACCTCAAGAATATTAGCGCAGACAGTA
60437461 GCAGCAATGGCCTTGGCGGCATGAACATTCTCGCCAGCGATTATTGTCAAGTTAGTAAT
261 GCAGCAATGGCCTTGGCGGCATGAACATTCTCGCCAGCGATTATTGTCAAGTTAGTAAT
60437520 AATTG
1 AATTG
60437525 GTTTCGAGTT
Statistics
Matches: 323, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
319 323 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (319 bp):
AATTGAACTCAAAAGAACTCTGCGAAACATTTTAACAAACCTACATCGAGACGCACATTGATGAC
AGCAAAACTAAAAAAAATATCCATTAATCCCAATTTACACTTACAATCCAAATTATCTTTCCTTT
TTTTTCCCCACAGTATAGAACTTGCAATTTATTTTCCTGTACAATTCAATTTCAAGAAGAAAGGA
AGAGCTTTAACGAATAAGGCACAGCTAAAACTGAGTTCACCTCAAGAATATTAGCGCAGACAGTA
GCAGCAATGGCCTTGGCGGCATGAACATTCTCGCCAGCGATTATTGTCAAGTTAGTAAT
Found at i:60437681 original size:14 final size:15
Alignment explanation
Indices: 60437651--60437683 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
60437641 CCACGGATCA
*
60437651 AATCATTGGTGCCGG
1 AATCATTGGTACCGG
60437666 AATCATTGG-ACCGG
1 AATCATTGGTACCGG
60437680 AATC
1 AATC
60437684 TCAAACCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (15 bp):
AATCATTGGTACCGG
Found at i:60440159 original size:19 final size:19
Alignment explanation
Indices: 60440132--60440187 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
60440122 CCAGGGCTCG
60440132 TGGCACACGAAGTGCAT-A
1 TGGCACACGAAGTGCATCA
*
60440150 CTGGCGCACGAAGTGCATCA
1 -TGGCACACGAAGTGCATCA
*
60440170 TGGCACACGAGGTGCATC
1 TGGCACACGAAGTGCATC
60440188 GTAGCGTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 32 0.97
20 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (19 bp):
TGGCACACGAAGTGCATCA
Found at i:60445342 original size:40 final size:40
Alignment explanation
Indices: 60445267--60445724 Score: 479
Period size: 40 Copynumber: 11.5 Consensus size: 40
60445257 AATTATTGAA
* * **
60445267 TGATTGTACATACGTGCCCCT-TTTGTACTTTGGTACCAT
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* *
60445306 TGATTGCACATATGTGCCCC-ATTTTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTA-TTTGTACTTCGGTACCCC
* * * *
60445346 TAAATGCACATACGTGCCCCTGTTTGTACTTAGGTACCCC
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * *
60445386 TGATTGCACATACGTGCCCCTGTTTGTACTTCAGTACCCT
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * * * *
60445426 TGATTACACATATGTGCTCTTATTTGTACTTCGGCACCCC
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * * *
60445466 TGATTGCACATACATGCTCTTATTTGTACTTCGGCACCCC
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* *
60445506 TGATTGCACATACGTGCTCCTATTTGTACTTCGGCACCCC
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * * **
60445546 TGATTGCACATACGTGCTCCTATTTGTACTTCGGCATCTT
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* *
60445586 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * * * * *
60445626 TAAATGCACATACGTGCTCATGTTTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * ** **
60445666 TAAATGCACATACGTGCCATTGCTTGTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * *
60445706 TGGTTGCACTTTCGTGCCC
1 TGATTGCACATACGTGCCC
60445725 TGGTTATACT
Statistics
Matches: 364, Mismatches: 52, Indels: 5
0.86 0.12 0.01
Matches are distributed among these distances:
39 18 0.05
40 346 0.95
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
Found at i:60445385 original size:20 final size:20
Alignment explanation
Indices: 60445356--60445416 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
60445346 TAAATGCACA
*
60445356 TACGTGCCCCTGTTTGTACT
1 TACGTACCCCTGTTTGTACT
* * * *
60445376 TAGGTACCCCTGATTGCACA
1 TACGTACCCCTGTTTGTACT
*
60445396 TACGTGCCCCTGTTTGTACT
1 TACGTACCCCTGTTTGTACT
60445416 T
1 T
60445417 CAGTACCCTT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.15, C:0.30, G:0.20, T:0.36
Consensus pattern (20 bp):
TACGTACCCCTGTTTGTACT
Found at i:60456916 original size:24 final size:26
Alignment explanation
Indices: 60456863--60456910 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
60456853 TTAGTAATGA
60456863 ATTTGAAAAATATAAAATGTTTTTAG
1 ATTTGAAAAATATAAAATGTTTTTAG
*
60456889 ATTTGACAAAT-T-AAATGTTTTT
1 ATTTGAAAAATATAAAATGTTTTT
60456911 GTATTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 1 0.05
26 10 0.48
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (26 bp):
ATTTGAAAAATATAAAATGTTTTTAG
Found at i:60457843 original size:16 final size:15
Alignment explanation
Indices: 60457822--60457870 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
60457812 CTAGATACAA
60457822 AAAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAA-G
60457838 AAAAAAAAAAGAAAAG
1 AAAAAAAAAA-AAAAG
*
60457854 -AAAAGAAAAAAAAG
1 AAAAAAAAAAAAAAG
60457868 AAA
1 AAA
60457871 CCTCTTCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 5 0.17
15 10 0.33
16 11 0.37
17 4 0.13
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:60457846 original size:21 final size:21
Alignment explanation
Indices: 60457820--60457866 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
60457810 ATCTAGATAC
*
60457820 AAAAAAAA-AAAAAAAAGGAA
1 AAAAAAAAGAAAAAAAAAGAA
*
60457840 AAAAAAAAGAAAAGAAAAGAA
1 AAAAAAAAGAAAAAAAAAGAA
60457861 AAAAAA
1 AAAAAA
60457867 GAAACCTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (21 bp):
AAAAAAAAGAAAAAAAAAGAA
Found at i:60457867 original size:19 final size:18
Alignment explanation
Indices: 60457820--60457870 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 18
60457810 ATCTAGATAC
60457820 AAAAAAAAAAAA-AAAAG
1 AAAAAAAAAAAAGAAAAG
*
60457837 -GAAAAAAAAAAGAAAAG
1 AAAAAAAAAAAAGAAAAG
60457854 AAAAGAAAAAAAAGAAA
1 AAAA-AAAAAAAAGAAA
60457871 CCTCTTCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 10 0.34
17 5 0.17
18 2 0.07
19 12 0.41
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAGAAAAG
Found at i:60461355 original size:57 final size:57
Alignment explanation
Indices: 60461286--60461399 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
60461276 TCATTTGGGA
*
60461286 ATCAGGGTAAAAAGTTAGCCTTGCCAAATCTAGGGTTCTGTTATCTAAGAACACTGG
1 ATCAGGGTAAAAAGTTAGCCTTGCCAAATCTAGGATTCTGTTATCTAAGAACACTGG
60461343 ATCAGGGTAAAAAGTTAGCCTTGCCAAATCTAGGATTCTGTTATCTAAGAACACTGG
1 ATCAGGGTAAAAAGTTAGCCTTGCCAAATCTAGGATTCTGTTATCTAAGAACACTGG
60461400 CCATATTTAG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (57 bp):
ATCAGGGTAAAAAGTTAGCCTTGCCAAATCTAGGATTCTGTTATCTAAGAACACTGG
Found at i:60462935 original size:31 final size:31
Alignment explanation
Indices: 60462887--60462969 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
60462877 GAAAGCTTTT
* *
60462887 TATGGGAGTTCTCTGTGATAAATAAGCTCCC
1 TATGCGAGCTCTCTGTGATAAATAAGCTCCC
* *
60462918 TATGCGAGCTCTTTGTGATAAATAAGCTCTC
1 TATGCGAGCTCTCTGTGATAAATAAGCTCCC
* *
60462949 TATGTGAGCTCTCTATGATAA
1 TATGCGAGCTCTCTGTGATAA
60462970 GTCTCTGTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (31 bp):
TATGCGAGCTCTCTGTGATAAATAAGCTCCC
Found at i:60462974 original size:13 final size:14
Alignment explanation
Indices: 60462939--60462975 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
60462929 TTTGTGATAA
60462939 ATAAGCTCTCTATG
1 ATAAGCTCTCTATG
*
60462953 -TGAGCTCTCTATG
1 ATAAGCTCTCTATG
60462966 ATAAG-TCTCT
1 ATAAGCTCTCT
60462976 GTGCGTGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 17 0.85
14 3 0.15
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (14 bp):
ATAAGCTCTCTATG
Found at i:60463328 original size:49 final size:49
Alignment explanation
Indices: 60463252--60463385 Score: 160
Period size: 49 Copynumber: 2.7 Consensus size: 49
60463242 AGGGTGGGCT
* * * * * *
60463252 TGAACATATCTTATGCTCCTCAACCATTCTGATAAGTGTGTTAGGTGTG
1 TGAACATATTTTATGTTCTTCAGCCATTCTGATAAGTGTGTTAAGTGCG
*
60463301 TGAACATATTTTATGTTCTTCAGCCATTCTCATAAGTGTGTTAAGTGCG
1 TGAACATATTTTATGTTCTTCAGCCATTCTGATAAGTGTGTTAAGTGCG
* * * * *
60463350 AGAACATATTTTATGTTTTTTAGCCGTTTTGATAAG
1 TGAACATATTTTATGTTCTTCAGCCATTCTGATAAG
60463386 ATAAGCATGT
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 72 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (49 bp):
TGAACATATTTTATGTTCTTCAGCCATTCTGATAAGTGTGTTAAGTGCG
Found at i:60479229 original size:23 final size:23
Alignment explanation
Indices: 60479203--60479324 Score: 174
Period size: 23 Copynumber: 5.3 Consensus size: 23
60479193 ATAAGTGCCA
60479203 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
60479226 CACTTATACGTAGCC-ATAGGTAC
1 CACTGATATGTAGCCGA-AGCTAC
*
60479249 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
60479272 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
60479295 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
60479318 CACTGAT
1 CACTGAT
60479325 CAATAACATT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
22 1 0.01
23 83 0.98
24 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:60479270 original size:46 final size:46
Alignment explanation
Indices: 60479203--60479324 Score: 199
Period size: 46 Copynumber: 2.7 Consensus size: 46
60479193 ATAAGTGCCA
* * *
60479203 CACTGATATGTAGCCGAAGCTACCACTTATACGTAGCCATAGGTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCATAGCTAC
* *
60479249 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCATAGCTAC
60479295 CACTGAAATGTAGCCGAAGCTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
60479325 CAATAACATT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCATAGCTAC
Found at i:60486638 original size:21 final size:20
Alignment explanation
Indices: 60486568--60486640 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 20
60486558 CATGAGGACA
*
60486568 TTGTTGTTAAGAAG-G-AAG
1 TTGTTGCTAAGAAGAGAAAG
* *
60486586 TTGCTGCTACAGAAAAGAAAG
1 TTGTTGCTA-AGAAGAGAAAG
60486607 TTGTTGC--AGAAGAGAAAG
1 TTGTTGCTAAGAAGAGAAAG
60486625 TTGTTGCTGAAGAAGA
1 TTGTTGCT-AAGAAGA
60486641 AGAAGATGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
18 24 0.55
19 4 0.09
20 1 0.02
21 15 0.34
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.26
Consensus pattern (20 bp):
TTGTTGCTAAGAAGAGAAAG
Found at i:60487122 original size:17 final size:17
Alignment explanation
Indices: 60487100--60487133 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
60487090 GATAAATATA
60487100 TATTGTCATTACATTTT
1 TATTGTCATTACATTTT
60487117 TATTGTCATTACATTTT
1 TATTGTCATTACATTTT
60487134 CATGTTAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.59
Consensus pattern (17 bp):
TATTGTCATTACATTTT
Found at i:60489926 original size:31 final size:31
Alignment explanation
Indices: 60489881--60489940 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
60489871 TTTCAAGCAA
* * *
60489881 GCTCCTTATGCGAGCTTTCTGTGATAAGTAT
1 GCTCCCTATACGAGCTCTCTGTGATAAGTAT
60489912 GCTCCCTATACGAGCTCTCTGTGATAAGT
1 GCTCCCTATACGAGCTCTCTGTGATAAGT
60489941 CTCTGTGCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (31 bp):
GCTCCCTATACGAGCTCTCTGTGATAAGTAT
Found at i:60491097 original size:13 final size:13
Alignment explanation
Indices: 60491079--60491156 Score: 78
Period size: 13 Copynumber: 6.5 Consensus size: 13
60491069 AATTTTAAAT
60491079 TATTTAGTAATAA
1 TATTTAGTAATAA
60491092 TATTTAG-AAT--
1 TATTTAGTAATAA
*
60491102 TATTTAGTGATAA
1 TATTTAGTAATAA
*
60491115 TATTTAGTGATAA
1 TATTTAGTAATAA
60491128 TATTTAG-AAT--
1 TATTTAGTAATAA
* *
60491138 TATTTAATGATAA
1 TATTTAGTAATAA
60491151 TATTTA
1 TATTTA
60491157 AGAAAAATCT
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
10 13 0.24
11 4 0.07
12 5 0.09
13 33 0.60
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (13 bp):
TATTTAGTAATAA
Found at i:60491120 original size:23 final size:23
Alignment explanation
Indices: 60491072--60491121 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
60491062 ATTTTTAAAT
60491072 TTTA-AATTATTTAGTAATAATA
1 TTTAGAATTATTTAGTAATAATA
*
60491094 TTTAGAATTATTTAGTGATAATA
1 TTTAGAATTATTTAGTAATAATA
60491117 TTTAG
1 TTTAG
60491122 TGATAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (23 bp):
TTTAGAATTATTTAGTAATAATA
Found at i:60491128 original size:36 final size:36
Alignment explanation
Indices: 60491079--60491156 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
60491069 AATTTTAAAT
*
60491079 TATTTAGTAATAATATTTAGAATTATTTAGTGATAA
1 TATTTAGTAATAATATTTAGAATTATTTAATGATAA
*
60491115 TATTTAGTGATAATATTTAGAATTATTTAATGATAA
1 TATTTAGTAATAATATTTAGAATTATTTAATGATAA
60491151 TATTTA
1 TATTTA
60491157 AGAAAAATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (36 bp):
TATTTAGTAATAATATTTAGAATTATTTAATGATAA
Found at i:60494162 original size:20 final size:20
Alignment explanation
Indices: 60494137--60494176 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
60494127 TAACGGTTGA
60494137 TATCAAGAT-TTTGGCAAGAT
1 TATCAA-ATATTTGGCAAGAT
60494157 TATCAAATATTTGGCAAGAT
1 TATCAAATATTTGGCAAGAT
60494177 CCAAAAAAAA
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:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (20 bp):
TATCAAATATTTGGCAAGAT
Done.