Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 166 of 259
Found at i:53985106 original size:22 final size:22
Alignment explanation
Indices: 53985057--53985106 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
53985047 AAAATAGTAG
*
53985057 AAAAAATAGCGAGAAAATAACA
1 AAAAAATAGCGAGAAAACAACA
* *
53985079 AGAAAATAGC-AGTAAAACAATA
1 AAAAAATAGCGAG-AAAACAACA
53985101 AAAAAA
1 AAAAAA
53985107 AAGACAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.70, C:0.08, G:0.12, T:0.10
Consensus pattern (22 bp):
AAAAAATAGCGAGAAAACAACA
Found at i:53992050 original size:14 final size:15
Alignment explanation
Indices: 53992031--53992070 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
53992021 CGAAATTTTT
53992031 ATAAAAAAAAT-AAA
1 ATAAAAAAAATAAAA
*
53992045 ATAAAATAAATAAAA
1 ATAAAAAAAATAAAA
53992060 ATAAATAAAAA
1 ATAAA-AAAAA
53992071 AATTTAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 8 0.36
16 4 0.18
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
ATAAAAAAAATAAAA
Found at i:53992059 original size:19 final size:19
Alignment explanation
Indices: 53992031--53992073 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
53992021 CGAAATTTTT
53992031 ATAAA-AAAAATAAAATAAA
1 ATAAATAAAAAT-AAATAAA
53992050 ATAAATAAAAATAAATAAA
1 ATAAATAAAAATAAATAAA
53992069 A-AAAT
1 ATAAAT
53992074 TTAGAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.17
19 13 0.57
20 6 0.26
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (19 bp):
ATAAATAAAAATAAATAAA
Found at i:53992070 original size:10 final size:9
Alignment explanation
Indices: 53992031--53992070 Score: 53
Period size: 10 Copynumber: 4.1 Consensus size: 9
53992021 CGAAATTTTT
53992031 ATAAAAAAA
1 ATAAAAAAA
53992040 ATAAAATAAA
1 ATAAAA-AAA
53992050 ATAAATAAAA
1 ATAAA-AAAA
53992060 ATAAATAAAA
1 ATAAA-AAAA
53992070 A
1 A
53992071 AATTTAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 6 0.21
10 22 0.76
11 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:53992868 original size:143 final size:143
Alignment explanation
Indices: 53992611--53992870 Score: 321
Period size: 143 Copynumber: 1.8 Consensus size: 143
53992601 AGTTGCAAAC
* *
53992611 TTAGTCCTTATACTCTAATTTGGTTAATTTAATCCATGTACTCTTTTGAATTTTGAAATTTTAAT
1 TTAGTCCTTATACTCTAATTTGATCAATTTAATCCATGTACTCTTTTGAATTTTGAAATTTTAAT
* ** * * * * * * **
53992676 TATGACTTAAATGTTTATAGTTTAATTTGTTAGGTCAAAATTTGTTATTAGTTCATGTACTATGC
66 TATAACCCAAATGGTAACAATTAAATCTGTTAGGTCAAAATTTACTATTAGTTCATGTACTATGC
53992741 ATACATAGCATAA
131 ATACATAGCATAA
* *
53992754 TTAGTCTTTATACTCTAATTTGATCAATTTTAGTCCATGTA-T-TTTTCGAATTTTGAAATTTTA
1 TTAGTCCTTATACTCTAATTTGATCAA-TTTAATCCATGTACTCTTTT-GAATTTTGAAATTTTA
53992817 ATCT-TAACCCAAATGGTAACAATTAAATCTGTTAGGTC-AAATTCTACTATTAGT
64 AT-TATAACCCAAATGGTAACAATTAAATCTGTTAGGTCAAAATT-TACTATTAGT
53992871 CATTATATTA
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
142 9 0.09
143 76 0.78
144 13 0.13
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (143 bp):
TTAGTCCTTATACTCTAATTTGATCAATTTAATCCATGTACTCTTTTGAATTTTGAAATTTTAAT
TATAACCCAAATGGTAACAATTAAATCTGTTAGGTCAAAATTTACTATTAGTTCATGTACTATGC
ATACATAGCATAA
Found at i:53993490 original size:26 final size:27
Alignment explanation
Indices: 53993442--53993494 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
53993432 TTATATTAAT
53993442 TTTTTTTATTTTTTTAAATAAAATATTA
1 TTTTTTTATTTTTTT-AATAAAATATTA
53993470 TTTTTTTATTTTTATT-A-AAAATATT
1 TTTTTTTATTTTT-TTAATAAAATATT
53993495 TAAATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 8 0.33
27 1 0.04
28 13 0.54
29 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTTTTTATTTTTTTAATAAAATATTA
Found at i:53994346 original size:27 final size:27
Alignment explanation
Indices: 53994316--53994385 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
53994306 CCTACCATTT
* *
53994316 GCGCCTCTGAGATAGGCACGATTAGTC
1 GCGCCTCTGAGATAGGCACAACTAGTC
* *
53994343 GCGCCTCTGAGAAAGGCTCAACTAGTC
1 GCGCCTCTGAGATAGGCACAACTAGTC
*
53994370 GCGCCTCTGACATAGG
1 GCGCCTCTGAGATAGG
53994386 TGCAACCTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.20
Consensus pattern (27 bp):
GCGCCTCTGAGATAGGCACAACTAGTC
Found at i:53998015 original size:146 final size:147
Alignment explanation
Indices: 53997767--53998035 Score: 362
Period size: 146 Copynumber: 1.8 Consensus size: 147
53997757 CTGAATTCGT
*
53997767 AAGGGATGAAAGAACGCTCAGAGTCTCAAATCATGACATGAATGAAAGCAGAACATCGGAAGGCC
1 AAGGGATGAAAGAAC-CTCAGAGTCTCAAATCATGACATGAATGAAAGCAGAACATCGGAAGACC
* * * *
53997832 TCATAGCACAATAGGACTATACTGAATGCACAGCTTCCAGGTTTCAACATAGTTATGCACATTAG
65 TCATAGCACAATAGGACTATACCGAATACACAGCTTCCAGATTTCAACATAATTATGCACATTAG
53997897 CATCGGACACCGACAGAC
130 CATCGGACACCGACAGAC
* * * *
53997915 AAGGGATGTAAGAA-CTCTGAGTCTCAAATTATGACATGAATGAGAGCAGAACATCGGAAGACCT
1 AAGGGATGAAAGAACCTCAGAGTCTCAAATCATGACATGAATGAAAGCAGAACATCGGAAGACCT
** ** * * *
53997979 TGTAGCACGGTAGGATTATACCGAATATAC-GCCTTCCAGATTTCGACATAATTATGC
66 CATAGCACAATAGGACTATACCGAATACACAG-CTTCCAGATTTCAACATAATTATGC
53998036 CTTGAGCTAG
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
145 1 0.01
146 90 0.87
148 13 0.12
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (147 bp):
AAGGGATGAAAGAACCTCAGAGTCTCAAATCATGACATGAATGAAAGCAGAACATCGGAAGACCT
CATAGCACAATAGGACTATACCGAATACACAGCTTCCAGATTTCAACATAATTATGCACATTAGC
ATCGGACACCGACAGAC
Found at i:54002213 original size:17 final size:17
Alignment explanation
Indices: 54002172--54002213 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
54002162 ATAAAATTAT
*
54002172 TGATAAATTAAATATTA
1 TGATAAATTAAATATCA
* *
54002189 TAAAAAATTAAATATCA
1 TGATAAATTAAATATCA
54002206 TGATAAAT
1 TGATAAAT
54002214 GATATTTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (17 bp):
TGATAAATTAAATATCA
Found at i:54012834 original size:13 final size:13
Alignment explanation
Indices: 54012816--54012840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54012806 AAAAAATATT
54012816 AATTAATTAATTA
1 AATTAATTAATTA
54012829 AATTAATTAATT
1 AATTAATTAATT
54012841 TTAGTTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTAATTAATTA
Found at i:54013254 original size:14 final size:14
Alignment explanation
Indices: 54013211--54013282 Score: 65
Period size: 14 Copynumber: 4.9 Consensus size: 14
54013201 TGTGAAAATG
*
54013211 ATTAAAATAATATG
1 ATTAAAATAATATT
*
54013225 AATAAAATAATTTATT
1 ATTAAAATAA--TATT
54013241 ATTAAAATAATATT
1 ATTAAAATAATATT
*
54013255 AGTTCAAAATTA-ATT
1 A-TT-AAAATAATATT
*
54013270 ATTGAAATAATAT
1 ATTAAAATAATAT
54013283 GATGTGGGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
13 5 0.11
14 18 0.38
15 6 0.13
16 18 0.38
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (14 bp):
ATTAAAATAATATT
Found at i:54028168 original size:64 final size:64
Alignment explanation
Indices: 54027983--54028482 Score: 424
Period size: 64 Copynumber: 7.8 Consensus size: 64
54027973 AGTTTCAGGC
* * * * * ** *
54027983 TTTCAGCTAAAAGATAAAGCGATATAGCGTC-AAACTGAGTGAAAAAAACATAATGAAATTAAG
1 TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAAGATTTTCAG
* * * * * *** *
54028046 TTTCAGCTAGAAGATAGAGCTGAATAGCATCAAAACCAAGTG--AAAAACATAAAAATTTTCAG
1 TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAAGATTTTCAG
* * * *
54028108 TTTCAGATAAAACATAAA-CTAAATAGCGTAAAAAATGAGTGAAAAAAAACATAATGATTTTCAG
1 TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGTG-AAAAAAACATAAAGATTTTCAG
* * * *
54028172 TTTCAGCTAAAAGGTAAAGCTTAATAGCGTCAAAATTGAGTG-AAAAAACA-AAACGGTTTTCAG
1 TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAA-GATTTTCAG
* * * * * ** * *
54028235 TTTCAGCTAAAAAGATAAAGCTAAATAGAGTCAAATTTTAGTTAAAAGTACATTAAGATTTACAG
1 TTTCAGAT-AAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAAGATTTTCAG
** *
54028300 TTTCAGATTTTCAGCTCAAAGATAAAGCTAAATAGCGTCAAAATTTTGTGGAAAAAA-ATAAAGA
1 TTTCAGA---T-A----AAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAAGA
54028364 TTTTCAG
58 TTTTCAG
* * * * *
54028371 -TACAGATAAAAGATAAAG-AAAATAGCATCAAAATTGAGTGAAAAAGACGTAAAGATTTTCAG
1 TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAAGATTTTCAG
* * *
54028433 TTTCAGTTAAAAGATAAAGATAAATAACGTCAAAATTGAGTGGAAAAAAA
1 TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGT-GAAAAAAA
54028483 TAATAAAATA
Statistics
Matches: 348, Mismatches: 69, Indels: 38
0.76 0.15 0.08
Matches are distributed among these distances:
61 40 0.11
62 54 0.16
63 65 0.19
64 87 0.25
65 46 0.13
66 3 0.01
67 1 0.00
68 2 0.01
70 5 0.01
71 12 0.03
72 33 0.09
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.25
Consensus pattern (64 bp):
TTTCAGATAAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGAAAAAAACATAAAGATTTTCAG
Found at i:54028368 original size:136 final size:131
Alignment explanation
Indices: 54028044--54028485 Score: 344
Period size: 136 Copynumber: 3.4 Consensus size: 131
54028034 AATGAAATTA
* * * *** * *
54028044 AGTTTCAGCTAGAAGATAGAGCTGAATAGCATCAAAACCAAGT-GAAAAACATAAA-AATTTTCA
1 AGTTTCAGCTA-AAGATAAAGCTAAATAGCGTCAAAATTGAGTGGAAAAAAATAAACGATTTTCA
* * ** * * * * *
54028107 GTTTCAGATAAAACATAAACTAAATAGCGTAAAAAATGAGTGAAAAAAAACATAATGA--T----
65 G-TACAGATAAAAGATAAAGAAAATAGCATCAAAATTGAGTG-AAAAAGACATAAAGATTTACAG
54028166 TTTC
128 TTTC
* * *
54028170 AGTTTCAGCTAAAAGGTAAAGCTTAATAGCGTCAAAATTGAGT-GAAAAAACA-AAACGGTTTTC
1 AGTTTCAGCT-AAAGATAAAGCTAAATAGCGTCAAAATTGAGTGGAAAAAA-ATAAACGATTTTC
* * * * * * *
54028233 AGTTTCAGCTAAAAAGATAAAGCTAAATAG-AGTCAAATTTTAGT-TAAAAGTACATTAAGATTT
64 AG-TACAGAT-AAAAGATAAAG-AAAATAGCA-TCAAAATTGAGTGAAAAAG-ACATAAAGATTT
54028296 ACAGTTTC
124 ACAGTTTC
**
54028304 AGATTTTCAGCTCAAAGATAAAGCTAAATAGCGTCAAAATTTTGTGGAAAAAAATAAA-GATTTT
1 AG--TTTCAGCT-AAAGATAAAGCTAAATAGCGTCAAAATTGAGTGGAAAAAAATAAACGATTTT
* *
54028368 CAGTACAGATAAAAGATAAAGAAAATAGCATCAAAATTGAGTGAAAAAGACGTAAAGATTTTCAG
63 CAGTACAGATAAAAGATAAAGAAAATAGCATCAAAATTGAGTGAAAAAGACATAAAGATTTACAG
54028433 TTTC
128 TTTC
* *
54028437 AG-TT-A---AAAGATAAAGATAAATAACGTCAAAATTGAGTGGAAAAAAATAA
1 AGTTTCAGCTAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGGAAAAAAATAA
54028486 TAAAATAAAA
Statistics
Matches: 256, Mismatches: 41, Indels: 39
0.76 0.12 0.12
Matches are distributed among these distances:
125 40 0.16
126 43 0.17
127 20 0.08
128 16 0.06
129 16 0.06
130 3 0.01
133 35 0.14
134 23 0.09
135 5 0.02
136 45 0.18
137 10 0.04
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (131 bp):
AGTTTCAGCTAAAGATAAAGCTAAATAGCGTCAAAATTGAGTGGAAAAAAATAAACGATTTTCAG
TACAGATAAAAGATAAAGAAAATAGCATCAAAATTGAGTGAAAAAGACATAAAGATTTACAGTTT
C
Found at i:54030224 original size:91 final size:91
Alignment explanation
Indices: 54030085--54030357 Score: 305
Period size: 91 Copynumber: 3.0 Consensus size: 91
54030075 ATACGTCAAT
*
54030085 TTGCTCATAAGAGCTTTCCAACCGATAACATGTCAGATGCACATAGTGCAAAGCCCATAGACTAA
1 TTGCTCATAAGAGCTTTCCAACCGATAACATGCCAGATGCACATAGTGCAAAGCCCATAGACTAA
* *
54030150 ATAATCTCTCTCAATAACACGCC-GAA
66 ATAATCTCCCCCAATAACACGCCAG-A
* * * * * ** *
54030176 TTGCTTATAAGAGCTTTCCAACTGATAGCATGCCATACGCACATAGTGCAAAGCCCATAGGTTGA
1 TTGCTCATAAGAGCTTTCCAACCGATAACATGCCAGATGCACATAGTGCAAAGCCCATAGACTAA
* **
54030241 ATATTCTCCCCCAATAACACTTCAGA
66 ATAATCTCCCCCAATAACACGCCAGA
* * * *** ** *
54030267 TTGCTCATAAGAGCTTTCCAACCAATAACACGCTAGATGCACATAGTGCAAAGCTTGTAGGTTGA
1 TTGCTCATAAGAGCTTTCCAACCGATAACATGCCAGATGCACATAGTGCAAAGCCCATAGACTAA
* *
54030332 ATATTCTCCCCCGATAACACGCCAGA
66 ATAATCTCCCCCAATAACACGCCAGA
54030358 ATCTCTGAAA
Statistics
Matches: 153, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
91 152 0.99
92 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (91 bp):
TTGCTCATAAGAGCTTTCCAACCGATAACATGCCAGATGCACATAGTGCAAAGCCCATAGACTAA
ATAATCTCCCCCAATAACACGCCAGA
Found at i:54033263 original size:24 final size:25
Alignment explanation
Indices: 54033235--54033282 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
54033225 GATAAATGAA
54033235 ATACATGTGTAATAAATAT-TGTAC
1 ATACATGTGTAATAAATATATGTAC
* *
54033259 ATACATTTGTAATACATATATGTA
1 ATACATGTGTAATAAATATATGTA
54033283 TTTACTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (25 bp):
ATACATGTGTAATAAATATATGTAC
Found at i:54034796 original size:18 final size:18
Alignment explanation
Indices: 54034739--54034798 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
54034729 GATTGTTTGC
* *
54034739 TACTGAATAATTGACTGT
1 TACTGAATAAATGACTAT
* *
54034757 TACGGAATAAACGACTGA-
1 TACTGAATAAATGACT-AT
54034775 TACTGAATAAATGACTAT
1 TACTGAATAAATGACTAT
54034793 TACTGA
1 TACTGA
54034799 TTAACCAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 1 0.03
18 33 0.97
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (18 bp):
TACTGAATAAATGACTAT
Found at i:54043014 original size:25 final size:25
Alignment explanation
Indices: 54042986--54043077 Score: 95
Period size: 25 Copynumber: 3.8 Consensus size: 25
54042976 AATATACATT
*
54042986 TTATGCATCACATCTTCAACATGTA
1 TTATTCATCACATCTTCAACATGTA
* *
54043011 TTATTCATCCATATCAAT-ATACAT-T-
1 TTATTCAT-CACATC-TTCA-ACATGTA
54043036 TTATTCATCACATCTTCAACATGTA
1 TTATTCATCACATCTTCAACATGTA
54043061 TTATTCATC-CAT-TTCAA
1 TTATTCATCACATCTTCAA
54043078 AGCATTTATA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
23 10 0.18
24 10 0.18
25 24 0.43
26 7 0.12
27 5 0.09
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (25 bp):
TTATTCATCACATCTTCAACATGTA
Found at i:54043025 original size:50 final size:50
Alignment explanation
Indices: 54042970--54043077 Score: 198
Period size: 50 Copynumber: 2.2 Consensus size: 50
54042960 ATATTAGGAA
54042970 CATATCAATATACATTTTATGCATCACATCTTCAACATGTATTATTCATC
1 CATATCAATATACATTTTATGCATCACATCTTCAACATGTATTATTCATC
*
54043020 CATATCAATATACATTTTATTCATCACATCTTCAACATGTATTATTCATC
1 CATATCAATATACATTTTATGCATCACATCTTCAACATGTATTATTCATC
*
54043070 CATTTCAA
1 CATATCAA
54043078 AGCATTTATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.41
Consensus pattern (50 bp):
CATATCAATATACATTTTATGCATCACATCTTCAACATGTATTATTCATC
Found at i:54057143 original size:293 final size:293
Alignment explanation
Indices: 54056611--54057196 Score: 1127
Period size: 293 Copynumber: 2.0 Consensus size: 293
54056601 TTAATATCTT
*
54056611 CAAATGGTTCAAATGGTAGTATAGGGCTTTCAACCTGATAAGGTAACTTTAGGGATCCTTAGCCA
1 CAAATGGTTCAAATGGTAGTACAGGGCTTTCAACCTGATAAGGTAACTTTAGGGATCCTTAGCCA
54056676 AGCAGTTTCAAATGGTTCGATAAAGAGATTTCCCAAAGTCGCTAAAGTTCTAGATTGGGTGATAA
66 AGCAGTTTCAAATGGTTCGATAAAGAGATTTCCCAAAGTCGCTAAAGTTCTAGATTGGGTGATAA
*
54056741 GTAATGACTTTTAGAAAGAAAAAGATCAAAAGACAATAGTTGGCTGATTTATTTAGTTTTTGAAG
131 GTAATGACTTTTAGAAAGAAAAAGATCAAAAGACAATAGCTGGCTGATTTATTTAGTTTTTGAAG
*
54056806 TTTCTTTTCATATGATTGCTTGAAGCAAATTATGGCTTGCTTGGTCTTTTCTAAGAACATTTATG
196 TTTCTTTTCATATGATTGCTTGAAGCAAATTATGGCTCGCTTGGTCTTTTCTAAGAACATTTATG
54056871 AAGATTCAAGCCTGAATCAGGTATGAAAAGTTC
261 AAGATTCAAGCCTGAATCAGGTATGAAAAGTTC
54056904 CAAATGGTTCAAATGGTAGTACAGGGCTTTCAACCTGATAAGGTAACTTTAGGGATCCTTAGCCA
1 CAAATGGTTCAAATGGTAGTACAGGGCTTTCAACCTGATAAGGTAACTTTAGGGATCCTTAGCCA
*
54056969 AGCAGTTTCAAATGGTTCGATAAAGAGATTTCCTAAAGTCGCTAAAGTTCTAGATTGGGTGATAA
66 AGCAGTTTCAAATGGTTCGATAAAGAGATTTCCCAAAGTCGCTAAAGTTCTAGATTGGGTGATAA
54057034 GTAATGACTTTTAGAAAGAAAAAGATCAAAAGACAATAGCTGGCTGATTTATTTAGTTTTTGAAG
131 GTAATGACTTTTAGAAAGAAAAAGATCAAAAGACAATAGCTGGCTGATTTATTTAGTTTTTGAAG
*
54057099 TTTCTTTTCATATGATTGCTTGGAGCAAATTATGGCTCGCTTGGTCTTTTCTAAGAACATTTATG
196 TTTCTTTTCATATGATTGCTTGAAGCAAATTATGGCTCGCTTGGTCTTTTCTAAGAACATTTATG
54057164 AAGATTCAAGCCTGAATCAGGTATGAAAAGTTC
261 AAGATTCAAGCCTGAATCAGGTATGAAAAGTTC
54057197 TTAATCAATG
Statistics
Matches: 288, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
293 288 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (293 bp):
CAAATGGTTCAAATGGTAGTACAGGGCTTTCAACCTGATAAGGTAACTTTAGGGATCCTTAGCCA
AGCAGTTTCAAATGGTTCGATAAAGAGATTTCCCAAAGTCGCTAAAGTTCTAGATTGGGTGATAA
GTAATGACTTTTAGAAAGAAAAAGATCAAAAGACAATAGCTGGCTGATTTATTTAGTTTTTGAAG
TTTCTTTTCATATGATTGCTTGAAGCAAATTATGGCTCGCTTGGTCTTTTCTAAGAACATTTATG
AAGATTCAAGCCTGAATCAGGTATGAAAAGTTC
Found at i:54058279 original size:18 final size:17
Alignment explanation
Indices: 54058244--54058285 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
54058234 ATTTTTATGC
54058244 AAATAAATAAAAACAAT
1 AAATAAATAAAAACAAT
* *
54058261 AAATAACATAAATATAAT
1 AAATAA-ATAAAAACAAT
54058279 AAA-AAAT
1 AAATAAAT
54058286 TTATGAGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 8 0.36
18 12 0.55
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAAATAAAAACAAT
Found at i:54058689 original size:21 final size:20
Alignment explanation
Indices: 54058665--54058719 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
54058655 TTTTAAAATT
54058665 ATACATAATATAATAAATAAG
1 ATACATAA-ATAATAAATAAG
*
54058686 ATACAATAAA-ATATAAATAAT
1 ATAC-ATAAATA-ATAAATAAG
54058707 ATA-ATAAATAATA
1 ATACATAAATAATA
54058720 CAAATAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 8 0.27
20 2 0.07
21 16 0.53
22 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
ATACATAAATAATAAATAAG
Found at i:54058706 original size:33 final size:32
Alignment explanation
Indices: 54058658--54058730 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 32
54058648 TACAAATTTT
*
54058658 TAAAATTATACATAATATAATAAATAAGATAC-AA
1 TAAAA-TATAAATAATATAATAAAT-A-ATACAAA
54058692 TAAAATATAAATAATATAATAAATAATACAAA
1 TAAAATATAAATAATATAATAAATAATACAAA
54058724 TAAAATA
1 TAAAATA
54058731 AATATTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 4 0.11
32 10 0.27
33 18 0.49
34 5 0.14
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (32 bp):
TAAAATATAAATAATATAATAAATAATACAAA
Found at i:54058715 original size:12 final size:11
Alignment explanation
Indices: 54058664--54058719 Score: 51
Period size: 12 Copynumber: 5.0 Consensus size: 11
54058654 TTTTTAAAAT
*
54058664 TATACATAATA
1 TATAAATAATA
*
54058675 TAATAAATAAGA
1 T-ATAAATAATA
* *
54058687 TA-CAATAAAA
1 TATAAATAATA
54058697 TATAAATAATA
1 TATAAATAATA
54058708 TAATAAATAATA
1 T-ATAAATAATA
54058720 CAAATAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
10 8 0.22
11 9 0.25
12 19 0.53
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (11 bp):
TATAAATAATA
Found at i:54058777 original size:30 final size:28
Alignment explanation
Indices: 54058743--54058809 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 28
54058733 TATTTTTTAC
* *
54058743 ATATAAATAAGGTTTAAAGTAAAATAAATA
1 ATATAAA-AAGATTTAAAAT-AAATAAATA
* *
54058773 ATATACAAAATATTTAAAATAAATAAATT
1 ATATA-AAAAGATTTAAAATAAATAAATA
54058802 ATATAAAA
1 ATATAAAA
54058810 TATATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 3 0.09
29 13 0.41
30 14 0.44
31 2 0.06
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (28 bp):
ATATAAAAAGATTTAAAATAAATAAATA
Found at i:54058790 original size:25 final size:27
Alignment explanation
Indices: 54058762--54058812 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
54058752 AGGTTTAAAG
54058762 TAAAATAAAT-AA-TATACAAAATATT
1 TAAAATAAATAAATTATACAAAATATT
*
54058787 TAAAATAAATAAATTATATAAAATAT
1 TAAAATAAATAAATTATACAAAATAT
54058813 ATATAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.43
26 2 0.09
27 11 0.48
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
TAAAATAAATAAATTATACAAAATATT
Found at i:54058791 original size:9 final size:9
Alignment explanation
Indices: 54058772--54058815 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
54058762 TAAAATAAAT
*
54058772 AATATACAA
1 AATATATAA
*
54058781 AATATTTAA
1 AATATATAA
*
54058790 AATAAATAA
1 AATATATAA
*
54058799 ATTATATAA
1 AATATATAA
54058808 AATATATA
1 AATATATA
54058816 TAAAAAGGAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (9 bp):
AATATATAA
Found at i:54058805 original size:29 final size:30
Alignment explanation
Indices: 54058755--54058820 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
54058745 ATAAATAAGG
*
54058755 TTTAAAGTAAAATAAATAATATACAAA-ATA
1 TTTAAAATAAAATAAATAATATA-AAATATA
*
54058785 TTTAAAAT-AAATAAATTATATAAAATATA
1 TTTAAAATAAAATAAATAATATAAAATATA
*
54058814 TATAAAA
1 TTTAAAA
54058821 AGGATTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 3 0.09
29 22 0.69
30 7 0.22
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (30 bp):
TTTAAAATAAAATAAATAATATAAAATATA
Found at i:54063184 original size:26 final size:26
Alignment explanation
Indices: 54063153--54063260 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
54063143 TGAAATGCCC
*
54063153 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
54063179 ATCATGGAGCATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
54063205 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
54063231 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
54063257 ATCA
1 ATCA
54063261 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:54064446 original size:19 final size:19
Alignment explanation
Indices: 54064422--54064459 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
54064412 CATCCAAACA
54064422 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
*
54064441 CCAGAAAAGTAAATTATTT
1 CCAGAAAAGTAAATCATTT
54064460 TTCGGAAATC
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:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:54069123 original size:8 final size:8
Alignment explanation
Indices: 54069106--54069164 Score: 64
Period size: 8 Copynumber: 7.4 Consensus size: 8
54069096 GATTCGAGTA
*
54069106 ATATATAT
1 ATATACAT
54069114 ATATACAT
1 ATATACAT
54069122 ATATACAT
1 ATATACAT
54069130 ATATACAT
1 ATATACAT
* *
54069138 ATACATAT
1 ATATACAT
* **
54069146 ACATATGT
1 ATATACAT
54069154 ATATACAT
1 ATATACAT
54069162 ATA
1 ATA
54069165 CACACATGCA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 42 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (8 bp):
ATATACAT
Found at i:54069165 original size:6 final size:6
Alignment explanation
Indices: 54069108--54069166 Score: 59
Period size: 6 Copynumber: 10.2 Consensus size: 6
54069098 TTCGAGTAAT
* * * **
54069108 ATATAT ATATAC ATAT-- ATACAT ATATAC ATATAC ATATAC ATATGT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
54069154 ATATAC ATATAC A
1 ATATAC ATATAC A
54069167 CACATGCATG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
4 3 0.07
6 40 0.93
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (6 bp):
ATATAC
Found at i:54071045 original size:2 final size:2
Alignment explanation
Indices: 54071038--54071067 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54071028 TGCTTTTTAA
54071038 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
54071068 TTTGTTGCTA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:54073363 original size:10 final size:10
Alignment explanation
Indices: 54073346--54073381 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
54073336 TTTTTTGAAC
54073346 ATTAAAATAA
1 ATTAAAATAA
*
54073356 AATAAAATAA
1 ATTAAAATAA
*
54073366 ATTAAATTAA
1 ATTAAAATAA
54073376 ATTAAA
1 ATTAAA
54073382 GTTAGAACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATTAAAATAA
Found at i:54077560 original size:12 final size:12
Alignment explanation
Indices: 54077543--54077567 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54077533 TGCGCCTACG
54077543 CGCCGTCTCGAA
1 CGCCGTCTCGAA
54077555 CGCCGTCTCGAA
1 CGCCGTCTCGAA
54077567 C
1 C
54077568 TCAAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.44, G:0.24, T:0.16
Consensus pattern (12 bp):
CGCCGTCTCGAA
Found at i:54078594 original size:87 final size:88
Alignment explanation
Indices: 54078492--54079098 Score: 402
Period size: 87 Copynumber: 7.0 Consensus size: 88
54078482 GTTTTTTGAC
* *
54078492 AACACAA-AGATGCCAAATCATCTTAGATCTGCTTCAGCGT-AAACA-CGTGAAAGCCAAATCTG
1 AACACAAGA-ATGCCAAATCATCTTGGATCTGCTTCAGTGTAAAACATC-TGAAAGCCAAATCTG
* *
54078554 CTGTGTCTTTGATTTGCTCCTTGTG
64 CTATGTCTTCGATTTGCTCCTTGTG
* * ** *
54078579 AACACAAGAATGCCAAATCCTCTTGGATCTGCTTCA--GTAAAATCATCTGAAGGTTAGATCTGC
1 AACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTGTAAAA-CATCTGAAAGCCAAATCTGC
* *
54078642 TATG---T--ATCTGCT-CTCCGTCG
65 TATGTCTTCGATTTGCTCCT-TGT-G
** * * ** * *
54078662 AA-A-TGGAGATGCCAGATCTGTTATCTTGGATCTACTTTGGTGTAAGAACATCCGAAAGTCAAA
1 AACACAAGA-ATGCCAAATC----ATCTTGGATCTGCTTCAGTGTAA-AACATCTGAAAGCCAAA
*
54078725 TCTGCTATGTCTTCGATTTGTTCCTTGT-
60 TCTGCTATGTCTTCGATTTGCTCCTTGTG
* * *
54078753 AAGCACAAGAACGCCAAATCATCTTGGATCTGCTTCAGTAT-AAACATCTGAAAGCCAAATCTGT
1 AA-CACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTGTAAAACATCTGAAAGCCAAATCTGC
*
54078817 TGTGTCTTCGATTTGCTCCTTGTG
65 TATGTCTTCGATTTGCTCCTTGTG
* * * ** *
54078841 AACACAAGGATGCCAAATCATCTTGGATTTGCTTCA--GTAAAATCATCTGAAGGTTAGATCTGC
1 AACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTGTAAAA-CATCTGAAAGCCAAATCTGC
*
54078904 TATG---T--ATCTGCT-CTCTGTCG
65 TATGTCTTCGATTTGCTCCT-TGT-G
** * ** * * *
54078924 AA-A-TGGAGATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAAA
1 AACACAAGA-ATGCCAAATC----ATCTTGGATCTGCTTCAGTGT-AAAACATCTGAAAGCCAAA
* * *
54078987 TCTGCTATGTCTTCGATTTGTTCCCTGTA
60 TCTGCTATGTCTTCGATTTGCTCCTTGTG
* * * *
54079016 AACACAAGAATGCCAACTCATCTTGGATCTGCTTCAGTAT-AAACATCTGAAAGCCAAATTTGTT
1 AACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTGTAAAACATCTGAAAGCCAAATCTGCT
* * *
54079080 GTTTCTTCGATTTTCTCCT
66 ATGTCTTCGATTTGCTCCT
54079099 CGTCGAAGAT
Statistics
Matches: 396, Mismatches: 80, Indels: 88
0.70 0.14 0.16
Matches are distributed among these distances:
81 7 0.02
82 37 0.09
83 6 0.02
84 2 0.01
85 3 0.01
86 33 0.08
87 171 0.43
88 51 0.13
89 40 0.10
91 4 0.01
92 2 0.01
93 33 0.08
94 7 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (88 bp):
AACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTGTAAAACATCTGAAAGCCAAATCTGCT
ATGTCTTCGATTTGCTCCTTGTG
Found at i:54078937 original size:262 final size:262
Alignment explanation
Indices: 54078503--54079098 Score: 1014
Period size: 262 Copynumber: 2.3 Consensus size: 262
54078493 ACACAAAGAT
* ** * *
54078503 GCCAAATCATCTTAGATCTGCTTCAGCGTAAACA-CGTGAAAGCCAAATCTGCTGTGTCTTTGAT
1 GCCAAATCATCTTGGATCTGCTTCAGTATAAACATC-TGAAAGCCAAATCTGTTGTGTCTTCGAT
*
54078567 TTGCTCCTTGTGAACACAAGAATGCCAAATCCTCTTGGATCTGCTTCAGTAAAATCATCTGAAGG
65 TTGCTCCTTGTGAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAATCATCTGAAGG
54078632 TTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGATCTGTTATCTTGGATCTAC
130 TTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGATCTGTTATCTTGGATCTAC
* *
54078697 TTTGGTGTAAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAG
195 TTTGGTGTAAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCCTGTAAACACAAG
54078762 AAC
260 AAC
54078765 GCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCCAAATCTGTTGTGTCTTCGATT
1 GCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCCAAATCTGTTGTGTCTTCGATT
* *
54078830 TGCTCCTTGTGAACACAAGGATGCCAAATCATCTTGGATTTGCTTCAGTAAAATCATCTGAAGGT
66 TGCTCCTTGTGAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAATCATCTGAAGGT
* *
54078895 TAGATCTGCTATGTATCTGCTCTCTGTCGAAATGGAGATGCCAGATCTGTTATCTTGGATCTGCT
131 TAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGATCTGTTATCTTGGATCTACT
*
54078960 TTGGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCCTGTAAACACAAGA
196 TTGGTGTAAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCCTGTAAACACAAGA
*
54079025 AT
261 AC
* * *
54079027 GCCAACTCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCCAAATTTGTTGTTTCTTCGATT
1 GCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCCAAATCTGTTGTGTCTTCGATT
*
54079092 TTCTCCT
66 TGCTCCT
54079099 CGTCGAAGAT
Statistics
Matches: 315, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
262 314 1.00
263 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (262 bp):
GCCAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCCAAATCTGTTGTGTCTTCGATT
TGCTCCTTGTGAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTAAAATCATCTGAAGGT
TAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAGATGCCAGATCTGTTATCTTGGATCTACT
TTGGTGTAAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCCTGTAAACACAAGA
AC
Found at i:54081691 original size:4 final size:4
Alignment explanation
Indices: 54081676--54081705 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
54081666 GCTTGGGCCT
54081676 TAAA TCAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA T-AAA TAAA TAAA TAAA TAAA TAAA T
54081706 GTTTATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:54082990 original size:19 final size:19
Alignment explanation
Indices: 54082966--54083010 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
54082956 TATAGTCCTT
*
54082966 TTAAATATTTTTTTATCTA
1 TTAAATATTTTTATATCTA
*
54082985 TTAAATA-CTTTATATCTA
1 TTAAATATTTTTATATCTA
54083003 -TAAATATT
1 TTAAATATT
54083011 AATTATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 6 0.27
18 9 0.41
19 7 0.32
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAAATATTTTTATATCTA
Found at i:54083044 original size:13 final size:13
Alignment explanation
Indices: 54083026--54083064 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
54083016 TAAAAAATAG
54083026 TATATATTATTTT
1 TATATATTATTTT
*
54083039 TATATATTATTTA
1 TATATATTATTTT
54083052 T-TATATTATTTT
1 TATATATTATTTT
54083064 T
1 T
54083065 TACTTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATATATTATTTT
Found at i:54083058 original size:12 final size:12
Alignment explanation
Indices: 54083028--54083093 Score: 57
Period size: 13 Copynumber: 5.5 Consensus size: 12
54083018 AAAAATAGTA
*
54083028 TATATTATTTTT
1 TATATTATTTAT
54083040 ATATATTATTTAT
1 -TATATTATTTAT
54083053 TATATTATTT-T
1 TATATTATTTAT
**
54083064 T-TACTTATAAAT
1 TATA-TTATTTAT
54083076 TATATTTATTTA-
1 TATA-TTATTTAT
54083088 TATATT
1 TATATT
54083094 TCATATATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
10 2 0.05
11 8 0.18
12 16 0.36
13 18 0.41
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATTATTTAT
Found at i:54083084 original size:43 final size:43
Alignment explanation
Indices: 54083026--54083107 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
54083016 TAAAAAATAG
* *
54083026 TATATATTATTTTTATATAT-TATTT-ATTATATTATTTTTTACT
1 TATAAATTATATTTATATATATATTTCA-TATA-TATTTTTTACT
*
54083069 TATAAATTATATTTATTTATATATTTCATATATATTTTT
1 TATAAATTATATTTATATATATATTTCATATATATTTTT
54083108 AAAAAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
43 24 0.71
44 9 0.26
45 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (43 bp):
TATAAATTATATTTATATATATATTTCATATATATTTTTTACT
Found at i:54083435 original size:35 final size:35
Alignment explanation
Indices: 54083389--54083459 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
54083379 TTTTTTCTTT
*
54083389 TTATTCTGTCACGGTTGGAGTCGTGGGCACGACGC
1 TTATTCTGTCACGGCTGGAGTCGTGGGCACGACGC
54083424 TTATTCTGTCACGGCTGGAGTCGTGGGCACGACGC
1 TTATTCTGTCACGGCTGGAGTCGTGGGCACGACGC
54083459 T
1 T
54083460 GGGCACGACG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.14, C:0.24, G:0.34, T:0.28
Consensus pattern (35 bp):
TTATTCTGTCACGGCTGGAGTCGTGGGCACGACGC
Found at i:54084903 original size:22 final size:22
Alignment explanation
Indices: 54084877--54084918 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
54084867 TTTTAATACG
**
54084877 TATTAAATTTTTTATATATTGT
1 TATTAAATCATTTATATATTGT
*
54084899 TATTATATCATTTATATATT
1 TATTAAATCATTTATATATT
54084919 AAATGCTAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TATTAAATCATTTATATATTGT
Found at i:54095012 original size:12 final size:14
Alignment explanation
Indices: 54094986--54095024 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
54094976 TGAAAAACTT
54094986 AAATATATATAATG
1 AAATATATATAATG
54095000 AAATATA-AT-ATG
1 AAATATATATAATG
*
54095012 AAATATGTATAAT
1 AAATATATATAAT
54095025 AATAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 9 0.41
13 4 0.18
14 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (14 bp):
AAATATATATAATG
Found at i:54095130 original size:23 final size:20
Alignment explanation
Indices: 54095066--54095129 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 20
54095056 TACATATAAA
*
54095066 AATATAAT-AAAATA-A-GT
1 AATATAATAAAAATATATAT
54095083 AATATAATAAAAATATATA-
1 AATATAATAAAAATATATAT
*
54095102 ACATATAAT-AAAATTTATAT
1 A-ATATAATAAAAATATATAT
54095122 -ATATAATA
1 AATATAATA
54095130 TTACAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 8 0.21
18 13 0.33
19 11 0.28
20 7 0.18
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
AATATAATAAAAATATATAT
Found at i:54099944 original size:13 final size:13
Alignment explanation
Indices: 54099926--54099955 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
54099916 ATCAAATCAG
54099926 TCAAACCGATAAA
1 TCAAACCGATAAA
54099939 TCAAACCGATAAA
1 TCAAACCGATAAA
54099952 TCAA
1 TCAA
54099956 TGACCTGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.23, G:0.07, T:0.17
Consensus pattern (13 bp):
TCAAACCGATAAA
Found at i:54114221 original size:23 final size:23
Alignment explanation
Indices: 54114195--54114240 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
54114185 ACACATAGCC
54114195 TGCTATTCAATAGACATCTTATG
1 TGCTATTCAATAGACATCTTATG
54114218 TGCTATTCAATAGACATCTTATG
1 TGCTATTCAATAGACATCTTATG
54114241 ATCACGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (23 bp):
TGCTATTCAATAGACATCTTATG
Found at i:54116075 original size:12 final size:14
Alignment explanation
Indices: 54116049--54116080 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
54116039 AATTATTTTT
54116049 ATTTTTTTAATTTA
1 ATTTTTTTAATTTA
54116063 ATTTTTTT-A-TTA
1 ATTTTTTTAATTTA
54116075 ATTTTT
1 ATTTTT
54116081 AAAGGGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.50
13 1 0.06
14 8 0.44
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
ATTTTTTTAATTTA
Found at i:54117353 original size:16 final size:16
Alignment explanation
Indices: 54117332--54117362 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54117322 CATTTTATTT
*
54117332 ATATTAGGATAATTAA
1 ATATTAAGATAATTAA
54117348 ATATTAAGATAATTA
1 ATATTAAGATAATTA
54117363 TTATGATTAT
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:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (16 bp):
ATATTAAGATAATTAA
Found at i:54123329 original size:9 final size:9
Alignment explanation
Indices: 54123317--54123382 Score: 71
Period size: 9 Copynumber: 7.3 Consensus size: 9
54123307 AAAAGTATAA
54123317 AATTAACCG
1 AATTAACCG
**
54123326 AATTAATTG
1 AATTAACCG
54123335 AATTAACCG
1 AATTAACCG
*
54123344 AATTACCCG
1 AATTAACCG
54123353 AATT-ACTCG
1 AATTAAC-CG
*
54123362 AATTAACAG
1 AATTAACCG
*
54123371 AATTAACTG
1 AATTAACCG
54123380 AAT
1 AAT
54123383 CATTTGTATA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
8 1 0.02
9 44 0.94
10 2 0.04
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:54123347 original size:27 final size:27
Alignment explanation
Indices: 54123317--54123382 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
54123307 AAAAGTATAA
* *
54123317 AATTAACCGAATTAATTGAATTAACCG
1 AATTAACCGAATTAATCGAATTAACAG
* *
54123344 AATTACCCGAATTACTCGAATTAACAG
1 AATTAACCGAATTAATCGAATTAACAG
*
54123371 AATTAACTGAAT
1 AATTAACCGAAT
54123383 CATTTGTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (27 bp):
AATTAACCGAATTAATCGAATTAACAG
Found at i:54123704 original size:18 final size:18
Alignment explanation
Indices: 54123654--54123706 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
54123644 CTGAACCCTG
*
54123654 ACCGAATTAATTCGGTTA
1 ACCGAATTTATTCGGTTA
* *
54123672 ACAGAATTTAGTCGGTTA
1 ACCGAATTTATTCGGTTA
*
54123690 ACCGAATTTTTTCGGTT
1 ACCGAATTTATTCGGTT
54123707 TTACCTGAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (18 bp):
ACCGAATTTATTCGGTTA
Found at i:54131249 original size:33 final size:33
Alignment explanation
Indices: 54131212--54131455 Score: 136
Period size: 33 Copynumber: 7.3 Consensus size: 33
54131202 TGGCCCTGCC
*
54131212 ATGGTCTTACATTAGTAGTGCCATAGCCCAGTT
1 ATGGTCTTACATTAATAGTGCCATAGCCCAGTT
* * * * *
54131245 ATGGTCTTATCGTCAA-AATACCATAGCCCAGCT
1 ATGGTCTTA-CATTAATAGTGCCATAGCCCAGTT
* * * * ***
54131278 ATGGTCTTACATATAATTACTACCATGGTCCAACC
1 ATGGTCTTACAT-TAA-TAGTGCCATAGCCCAGTT
* *
54131313 ATGGTCTTACGTTCAA-AGTGCCATAACCCAGTT
1 ATGGTCTTACATT-AATAGTGCCATAGCCCAGTT
* * *
54131346 ATAGTCTT--ATCAATAGAATGCCATAACCCAGTT
1 ATGGTCTTACATTAATAG--TGCCATAGCCCAGTT
* * * * ***
54131379 ATGGTCTTACATATAAACACTGCCATGGTCCAACC
1 ATGGTCTTACAT-T-AATAGTGCCATAGCCCAGTT
* * *
54131414 ATGGTCTTACGTTCATAGTGCCATAACCCAGTT
1 ATGGTCTTACATTAATAGTGCCATAGCCCAGTT
54131447 ATGGTCTTA
1 ATGGTCTTA
54131456 TCCGTCAATT
Statistics
Matches: 154, Mismatches: 45, Indels: 24
0.69 0.20 0.11
Matches are distributed among these distances:
30 2 0.01
31 3 0.02
32 2 0.01
33 92 0.60
34 5 0.03
35 47 0.31
37 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (33 bp):
ATGGTCTTACATTAATAGTGCCATAGCCCAGTT
Found at i:54131343 original size:101 final size:101
Alignment explanation
Indices: 54131210--54131463 Score: 359
Period size: 101 Copynumber: 2.5 Consensus size: 101
54131200 TATGGCCCTG
* * *
54131210 CCATGGTCTTACATT-AGTAGTGCCATAGCCCAGTTATGGTCTTATCGTCAAAATACCATAGCCC
1 CCATGGTCTTACGTTCA-TAGTGCCATAACCCAGTTATGGTCTTATCGTCAAAATACCATAACCC
**
54131274 AGCTATGGTCTTACATATAATTACTACCATGGTCCAA
65 AGCTATGGTCTTACATATAAACACTACCATGGTCCAA
* * * * *
54131311 CCATGGTCTTACGTTCAAAGTGCCATAACCCAGTTATAGTCTTATCAAT-AGAATGCCATAACCC
1 CCATGGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC-GTCAAAATACCATAACCC
* *
54131375 AGTTATGGTCTTACATATAAACACTGCCATGGTCCAA
65 AGCTATGGTCTTACATATAAACACTACCATGGTCCAA
54131412 CCATGGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCCGTCAA
1 CCATGGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTAT-CGTCAA
54131464 TTCATCTTTT
Statistics
Matches: 133, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
101 129 0.97
102 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (101 bp):
CCATGGTCTTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCGTCAAAATACCATAACCCA
GCTATGGTCTTACATATAAACACTACCATGGTCCAA
Found at i:54132637 original size:14 final size:15
Alignment explanation
Indices: 54132606--54132640 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
54132596 TTTATTTCTA
54132606 TTAAAAATATAGAAT
1 TTAAAAATATAGAAT
*
54132621 TTAAATATATA-AAT
1 TTAAAAATATAGAAT
54132635 TTAAAA
1 TTAAAA
54132641 CCCTAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
TTAAAAATATAGAAT
Found at i:54136296 original size:19 final size:19
Alignment explanation
Indices: 54136258--54136297 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54136248 AAAATATCAT
*
54136258 ATTAATTTAAATTGATTTG
1 ATTAATTTAAATTGACTTG
* *
54136277 ATTAATTTAATTTTACTTG
1 ATTAATTTAAATTGACTTG
54136296 AT
1 AT
54136298 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (19 bp):
ATTAATTTAAATTGACTTG
Found at i:54144223 original size:29 final size:29
Alignment explanation
Indices: 54144191--54144268 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
54144181 AATACTGATA
*
54144191 TCATGGCCCGAAGCTAAATTAGCCAATAT
1 TCATGGCCCGAAGCCAAATTAGCCAATAT
* * * *
54144220 TCATGGCCTGAAGCCAAATCAGTCGATAT
1 TCATGGCCCGAAGCCAAATTAGCCAATAT
*
54144249 TCATGGCTCGAAGCCAAATT
1 TCATGGCCCGAAGCCAAATT
54144269 GGTATAACTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (29 bp):
TCATGGCCCGAAGCCAAATTAGCCAATAT
Found at i:54149052 original size:26 final size:26
Alignment explanation
Indices: 54149023--54149098 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 26
54149013 TCTTATCCCT
*
54149023 ATTTTACCCTTAATAAAATTTTGACG
1 ATTTTACCCTTGATAAAATTTTGACG
*
54149049 ATTTTA-CCTCTGATAAAATTTTAACG
1 ATTTTACCCT-TGATAAAATTTTGACG
*
54149075 ATTTTACCCTTGGTAAAATTTTGA
1 ATTTTACCCTTGATAAAATTTTGA
54149099 GAAAATATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.07
26 38 0.86
27 3 0.07
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.43
Consensus pattern (26 bp):
ATTTTACCCTTGATAAAATTTTGACG
Found at i:54149258 original size:12 final size:12
Alignment explanation
Indices: 54149241--54149265 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54149231 TGCAAATGAA
54149241 TCATTTCCATTT
1 TCATTTCCATTT
54149253 TCATTTCCATTT
1 TCATTTCCATTT
54149265 T
1 T
54149266 GAAAACTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:54152640 original size:31 final size:33
Alignment explanation
Indices: 54152583--54152649 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 33
54152573 GGAAACACCC
*
54152583 AAAAATTGAATATAGTTTAGTCACCAAAAAAGA
1 AAAAATTGAATATAGTTGAGTCACCAAAAAAGA
* *
54152616 AAAAATTG-A-ATAGTTGAGTGACCAAAAATGA
1 AAAAATTGAATATAGTTGAGTCACCAAAAAAGA
54152647 AAA
1 AAA
54152650 TTACTAATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 22 0.71
32 1 0.03
33 8 0.26
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.22
Consensus pattern (33 bp):
AAAAATTGAATATAGTTGAGTCACCAAAAAAGA
Found at i:54153239 original size:12 final size:12
Alignment explanation
Indices: 54153222--54153261 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
54153212 TTAAAAGATA
54153222 TTTTTA-AAATAT
1 TTTTTATAAAT-T
54153234 TTTTTATAAATT
1 TTTTTATAAATT
54153246 TTTTTATAAATT
1 TTTTTATAAATT
54153258 TTTT
1 TTTT
54153262 GAATTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTATAAATT
Found at i:54154849 original size:6 final size:6
Alignment explanation
Indices: 54154838--54154865 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
54154828 CCGAAAAGAG
54154838 TGAAAA TGAAAA TGAAAA TGAAAA TGAA
1 TGAAAA TGAAAA TGAAAA TGAAAA TGAA
54154866 GAGGAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (6 bp):
TGAAAA
Found at i:54176951 original size:21 final size:21
Alignment explanation
Indices: 54176926--54176977 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
54176916 TGTTTTGAGG
54176926 TAAAAAAATATTTAGAATAA-T
1 TAAAAAAATATTTA-AATAATT
*
54176947 TAAAAATATTATTTAAATAATT
1 TAAAAA-AATATTTAAATAATT
*
54176969 TGAAAAAAT
1 TAAAAAAAT
54176978 TATCCAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
TAAAAAAATATTTAAATAATT
Found at i:54176979 original size:22 final size:21
Alignment explanation
Indices: 54176926--54176980 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
54176916 TGTTTTGAGG
*
54176926 TAAAAAAATATTTAGAATAAT
1 TAAAAAATTATTTAGAATAAT
54176947 TAAAAATATTATTTA-AATAATT
1 TAAAAA-ATTATTTAGAATAA-T
54176969 TGAAAAAATTAT
1 T-AAAAAATTAT
54176981 CCAAATTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.37
22 14 0.47
23 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
TAAAAAATTATTTAGAATAAT
Found at i:54181917 original size:17 final size:18
Alignment explanation
Indices: 54181885--54181919 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
54181875 GGAATTTGGG
*
54181885 GAGTTTTGTCTTTTTATT
1 GAGTTTTCTCTTTTTATT
54181903 GAGTTTTCT-TTTTTATT
1 GAGTTTTCTCTTTTTATT
54181920 ATCCTATGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.06, G:0.14, T:0.69
Consensus pattern (18 bp):
GAGTTTTCTCTTTTTATT
Found at i:54185549 original size:12 final size:12
Alignment explanation
Indices: 54185532--54185558 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
54185522 CATTCTGTAA
54185532 CAACTCAATTTT
1 CAACTCAATTTT
54185544 CAACTCAATTTT
1 CAACTCAATTTT
54185556 CAA
1 CAA
54185559 TGGTGTCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (12 bp):
CAACTCAATTTT
Found at i:54189783 original size:22 final size:21
Alignment explanation
Indices: 54189758--54189816 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 21
54189748 CGACTCGTAT
54189758 GAGCTTACTGTTCAGCTCAATA
1 GAGCTTACT-TTCAGCTCAATA
* *
54189780 GAGCTTACCATTTTAGCTCATTA
1 GAGCTTA-C-TTTCAGCTCAATA
54189803 GAGCTTACTATTCA
1 GAGCTTACT-TTCA
54189817 TCAGCTTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 1 0.03
22 11 0.35
23 18 0.58
24 1 0.03
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (21 bp):
GAGCTTACTTTCAGCTCAATA
Found at i:54196585 original size:25 final size:24
Alignment explanation
Indices: 54196557--54196775 Score: 86
Period size: 25 Copynumber: 8.7 Consensus size: 24
54196547 CTATTATTTA
*
54196557 GCTCTCATGAGCATCCCGTTAGATG
1 GCTCTCATGAGCTTCCCGTTA-ATG
* * *
54196582 GCTCTGACGAGCTTCTCGATTAATG
1 GCTCTCATGAGCTTCCCG-TTAATG
* * *
54196607 GCTCTCTTGAGCTTCCCGTTTACG
1 GCTCTCATGAGCTTCCCGTTAATG
* * * *
54196631 GCT-TATATGAGCTTTCTGATAATTG
1 GCTCT-CATGAGCTTCCCGTTAA-TG
* * * * *
54196656 GATCTCCA-AAGCTTCCCAATAAAAG
1 GCTCT-CATGAGCTTCCC-GTTAATG
* *
54196681 GCTCTCACATGAGCTTCCCGATAAAAG
1 GCTCT--CATGAGCTTCCCG-TTAATG
54196708 GCTCTCACATGAGCTTCCCGATTAATG
1 GCTCT--CATGAGCTTCCCG-TTAATG
* * * *
54196735 GCTCTC-TGAAGCTACTCGATATTG
1 GCTCTCATG-AGCTTCCCGTTAATG
54196759 GCT-TGCATGAGCTTCCC
1 GCTCT-CATGAGCTTCCC
54196776 TATATTTCGC
Statistics
Matches: 144, Mismatches: 39, Indels: 23
0.70 0.19 0.11
Matches are distributed among these distances:
23 2 0.01
24 34 0.24
25 55 0.38
26 9 0.06
27 44 0.31
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (24 bp):
GCTCTCATGAGCTTCCCGTTAATG
Found at i:54196611 original size:50 final size:50
Alignment explanation
Indices: 54196531--54196626 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
54196521 CTTGATAATA
* *
54196531 GGCTCTCACGAGCTTCCTATTATTTAGCTCTCATGAGCATCCCGTTAGAT
1 GGCTCTCACGAGCTTCCGATTATATAGCTCTCATGAGCATCCCGTTAGAT
* * * *
54196581 GGCTCTGACGAGCTTCTCGATTA-ATGGCTCTCTTGAGCTTCCCGTT
1 GGCTCTCACGAGCTTC-CGATTATATAGCTCTCATGAGCATCCCGTT
54196627 TACGGCTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 34 0.87
51 5 0.13
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (50 bp):
GGCTCTCACGAGCTTCCGATTATATAGCTCTCATGAGCATCCCGTTAGAT
Found at i:54196699 original size:27 final size:27
Alignment explanation
Indices: 54196665--54196740 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
54196655 GGATCTCCAA
*
54196665 AGCTTCCCAATAAAAGGCTCTCACATG
1 AGCTTCCCGATAAAAGGCTCTCACATG
54196692 AGCTTCCCGATAAAAGGCTCTCACATG
1 AGCTTCCCGATAAAAGGCTCTCACATG
* *
54196719 AGCTTCCCGATTAATGGCTCTC
1 AGCTTCCCGATAAAAGGCTCTC
54196741 TGAAGCTACT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (27 bp):
AGCTTCCCGATAAAAGGCTCTCACATG
Found at i:54198818 original size:22 final size:23
Alignment explanation
Indices: 54198793--54198838 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
54198783 CAACCAAATC
54198793 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
54198815 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
54198838 A
1 A
54198839 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:54198844 original size:23 final size:23
Alignment explanation
Indices: 54198800--54198844 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54198790 ATCAATTCAA
*
54198800 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
54198823 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
54198845 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:54207142 original size:49 final size:50
Alignment explanation
Indices: 54207036--54207131 Score: 124
Period size: 49 Copynumber: 1.9 Consensus size: 50
54207026 TCCTGATATT
* * *
54207036 TAGCTCCCATGAGCATCCCGTTATATGGCTCTCACGAGCTTCTCAATTAA
1 TAGCTCTCTTGAGCATCCCGTTATATGGCTCTCACGAGCTTCCCAATTAA
* *
54207086 TAGCTCTCTTGAGCTTCCCGTT-TATGGCTCGT-ATGAGCTTCCCAAT
1 TAGCTCTCTTGAGCATCCCGTTATATGGCTC-TCACGAGCTTCCCAAT
54207132 AATTGGCTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
49 20 0.50
50 20 0.50
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (50 bp):
TAGCTCTCTTGAGCATCCCGTTATATGGCTCTCACGAGCTTCCCAATTAA
Found at i:54207142 original size:74 final size:74
Alignment explanation
Indices: 54207061--54207213 Score: 197
Period size: 74 Copynumber: 2.1 Consensus size: 74
54207051 TCCCGTTATA
* * *
54207061 TGGCTCTCACG-AGCTT-CTCAATTAATAGCTCTCTT-GAGCTTCCCG-TTTATGGCTCGTATGA
1 TGGCTCTC-CGAAGCTTCCT-AATTAATAGCTC-CTTAGAGCTACCCGATAT-TGGCTCGCATGA
54207122 GCTTCCCAATAAT
62 GCTTCCCAATAAT
*
54207135 TGGCTCTCCGAAGCTTCCTGATTAATAGCTCCTTAGAGCTACCCGATATTGGCTCGCATGAGCTT
1 TGGCTCTCCGAAGCTTCCTAATTAATAGCTCCTTAGAGCTACCCGATATTGGCTCGCATGAGCTT
*
54207200 CCCAATATT
66 CCCAATAAT
54207209 TGGCT
1 TGGCT
54207214 TGCAAGAGCT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
73 5 0.07
74 61 0.87
75 4 0.06
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.33
Consensus pattern (74 bp):
TGGCTCTCCGAAGCTTCCTAATTAATAGCTCCTTAGAGCTACCCGATATTGGCTCGCATGAGCTT
CCCAATAAT
Found at i:54207222 original size:25 final size:24
Alignment explanation
Indices: 54207169--54207251 Score: 76
Period size: 25 Copynumber: 3.4 Consensus size: 24
54207159 ATAGCTCCTT
* * *
54207169 AGAGCTACCCGATATTGGCTCGCA
1 AGAGCTTCCCAATATTGGCTTGCA
*
54207193 TGAGCTTCCCAATATTTGGCTTGCA
1 AGAGCTTCCCAATA-TTGGCTTGCA
* * *
54207218 AGAGCTTCCCATTACATGGCTTACA
1 AGAGCTTCCCAATA-TTGGCTTGCA
*
54207243 TGAGCTTCC
1 AGAGCTTCC
54207252 TGTTACATGG
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 11 0.23
25 37 0.77
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (24 bp):
AGAGCTTCCCAATATTGGCTTGCA
Found at i:54207248 original size:74 final size:74
Alignment explanation
Indices: 54207110--54207248 Score: 158
Period size: 74 Copynumber: 1.9 Consensus size: 74
54207100 TTCCCGTTTA
* * * * *
54207110 TGGCTCGTATGAGCTTCCCAATAATTGGCTCTCCGAAGCTTCCTGATTAATAGCTCCTTAGAGCT
1 TGGCTCGCATGAGCTTCCCAATAATTGGCTCTCCAAAGCTTCCTCATTAATAGCTACATAGAGCT
54207175 ACCCGATAT
66 ACCCGATAT
* * *
54207184 TGGCTCGCATGAGCTTCCCAATATTTGGCT-TGCAAGAGCTTCC-CATTACATGGCTTACAT-GA
1 TGGCTCGCATGAGCTTCCCAATAATTGGCTCTCCAA-AGCTTCCTCATTA-ATAGC-TACATAGA
54207246 GCT
63 GCT
54207249 TCCTGTTACA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
73 7 0.13
74 44 0.81
75 3 0.06
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (74 bp):
TGGCTCGCATGAGCTTCCCAATAATTGGCTCTCCAAAGCTTCCTCATTAATAGCTACATAGAGCT
ACCCGATAT
Found at i:54207257 original size:25 final size:25
Alignment explanation
Indices: 54207194--54207263 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
54207184 TGGCTCGCAT
* ** *
54207194 GAGCTTCCCAATATTTGGCTTGCAA
1 GAGCTTCCCATTACATGGCTTACAA
*
54207219 GAGCTTCCCATTACATGGCTTACAT
1 GAGCTTCCCATTACATGGCTTACAA
**
54207244 GAGCTTCCTGTTACATGGCT
1 GAGCTTCCCATTACATGGCT
54207264 CGAAACAGCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (25 bp):
GAGCTTCCCATTACATGGCTTACAA
Found at i:54208530 original size:20 final size:19
Alignment explanation
Indices: 54208507--54208560 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
54208497 TAGACTATGA
54208507 ACCACTTCATTTACATACTT
1 ACCA-TTCATTTACATACTT
*
54208527 ACCATTCCATTTACTTACTT
1 ACCATT-CATTTACATACTT
*
54208547 TCCATTCTATTTAC
1 ACCATTC-ATTTAC
54208561 TTAGCATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (19 bp):
ACCATTCATTTACATACTT
Found at i:54208561 original size:20 final size:20
Alignment explanation
Indices: 54208514--54208563 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
54208504 TGAACCACTT
*
54208514 CATTTACATACTTACCATTC
1 CATTTACTTACTTACCATTC
*
54208534 CATTTACTTACTTTCCATTC
1 CATTTACTTACTTACCATTC
*
54208554 TATTTACTTA
1 CATTTACTTA
54208564 GCATAAGCTT
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:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (20 bp):
CATTTACTTACTTACCATTC
Found at i:54215099 original size:7 final size:7
Alignment explanation
Indices: 54215087--54215125 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
54215077 TTTCTCATAT
54215087 AAAATGA
1 AAAATGA
54215094 AAAATGA
1 AAAATGA
54215101 AAAATGA
1 AAAATGA
54215108 AAAATGA
1 AAAATGA
54215115 AAAATGA
1 AAAATGA
54215122 AAAA
1 AAAA
54215126 GAATTAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAATGA
Found at i:54221935 original size:31 final size:31
Alignment explanation
Indices: 54221900--54221961 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
54221890 CATGAAATAA
54221900 GTATGGATGTTTGCTAATTACTCGGTAAGTT
1 GTATGGATGTTTGCTAATTACTCGGTAAGTT
54221931 GTATGGATGTTTGCTAATTACTCGGTAAGTT
1 GTATGGATGTTTGCTAATTACTCGGTAAGTT
54221962 TACTTTCCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.42
Consensus pattern (31 bp):
GTATGGATGTTTGCTAATTACTCGGTAAGTT
Found at i:54223130 original size:21 final size:22
Alignment explanation
Indices: 54223097--54223137 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
54223087 ACAATTTATG
*
54223097 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
54223118 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
54223138 CAATACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:54226077 original size:383 final size:382
Alignment explanation
Indices: 54225230--54226381 Score: 2196
Period size: 383 Copynumber: 3.0 Consensus size: 382
54225220 AATCATTAGT
* *
54225230 TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTACTGGTTGTTTATGATGAATTAA
1 TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTGCTGGGTGTTTATGATGAATTAA
*
54225295 CATGGAATTGAAGCTTTAACTTAGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
66 CATGGAATTGAAGCTTTAACTTTGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
* *
54225360 TTTCAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTTTAAATATCGAAG
131 TTTCAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTCTAAATATCAAAG
54225425 GCTGTATAGTAGCCTAAAATAATTAGAGAAATTTTTAATTGAGAAAATATAGCTCAATTGGTGGA
196 GCTGTATAGTAGCCTAAAATAATTAGAGAAATTTTTAATTGAGAAAATATAGCTCAATTGGTGGA
*
54225490 AAATTGATATGGGACTAAATTGTTAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAATT
261 AAATTGATATGGGACTAAATTGTAAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAATT
*
54225555 AAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATGAATAA
326 GAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATGAATAA
54225612 TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTGCTGGGTGTTTATGATGAATTAA
1 TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTGCTGGGTGTTTATGATGAATTAA
54225677 CATGGAATTGAAGCTTTAACTTTGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
66 CATGGAATTGAAGCTTTAACTTTGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
54225742 TTTCAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTCTAAATATCAAAG
131 TTTCAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTCTAAATATCAAAG
54225807 GCTGTATAGTAGCCTAAAATAATTAGAGAAATTTTTAATTGAGAAAATATAGCTCAATTGGTAGG
196 GCTGTATAGTAGCCTAAAATAATTAGAGAAATTTTTAATTGAGAAAATATAGCTCAATTGGT-GG
54225872 AAAATTGATATGGGACTAAATTGTAAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAAT
260 AAAATTGATATGGGACTAAATTGTAAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAAT
54225937 TGAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATGAATAA
325 TGAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATGAATAA
54225995 TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTGCTGGGTGTTTATGATGAATTAA
1 TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTGCTGGGTGTTTATGATGAATTAA
54226060 CATGGAATTGAAGCTTTAACTTTGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
66 CATGGAATTGAAGCTTTAACTTTGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
*
54226125 TTTTAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTCTAAATATCAAAG
131 TTTCAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTCTAAATATCAAAG
*
54226190 GCTGTATAGTAGCCTAAAATAATTAGGGAAATTTTTAATTGAGAAAATATAGCTCAATTGGTGGG
196 GCTGTATAGTAGCCTAAAATAATTAGAGAAATTTTTAATTGAGAAAATATAGCTCAATTGGT-GG
54226255 AAAATTGATATGGGACTAAATTGTAAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAAT
260 AAAATTGATATGGGACTAAATTGTAAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAAT
*
54226320 TGAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATAAATAA
325 TGAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATGAATAA
54226378 TTTT
1 TTTT
54226382 ATATTATAGA
Statistics
Matches: 758, Mismatches: 11, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
382 252 0.33
383 506 0.67
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (382 bp):
TTTTGATTTCATGGGTGATTTTGAAAGTTACCATTGATGAGTGCTGGGTGTTTATGATGAATTAA
CATGGAATTGAAGCTTTAACTTTGTTATGTGATGATTTCATCAAGTGATTTTAATAGAAAATGAT
TTTCAAAACTAAATTGTGAAAATCTTAAGAATTAGGGTTTGGTACTGAAATTCTAAATATCAAAG
GCTGTATAGTAGCCTAAAATAATTAGAGAAATTTTTAATTGAGAAAATATAGCTCAATTGGTGGA
AAATTGATATGGGACTAAATTGTAAAAACTGTAAAAGTTAGGGTAAATGTGTAAATTTAAAAATT
GAAGGGCATAAATTGTGAAGTGAATTAGAATTGAATTAGATGCTGATGAATGAATAA
Found at i:54226868 original size:33 final size:33
Alignment explanation
Indices: 54226795--54226872 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
54226785 ATATATATAT
* *
54226795 GTGTAAGACCATAGCTGGGCTATGGCATCATGA
1 GTGTAAGACCATAACTGGGCTATGGCATCACGA
* *
54226828 -TGATAAGACCATAACTGGGTTGTGGCA-CTACGA
1 GTG-TAAGACCATAACTGGGCTATGGCATC-ACGA
54226861 GTGTAAGACCAT
1 GTGTAAGACCAT
54226873 GGCAATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
32 3 0.08
33 33 0.87
34 2 0.05
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (33 bp):
GTGTAAGACCATAACTGGGCTATGGCATCACGA
Found at i:54232987 original size:25 final size:25
Alignment explanation
Indices: 54232958--54233005 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
54232948 TTATAACATG
* *
54232958 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
54232983 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
54233006 GTTTATGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:54233089 original size:11 final size:11
Alignment explanation
Indices: 54233053--54233108 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
54233043 CATGGTATGT
54233053 ATGATATGCAC
1 ATGATATGCAC
* *
54233064 ATGACATG--T
1 ATGATATGCAC
54233073 ATGATATGCAC
1 ATGATATGCAC
*
54233084 ATGATATG--T
1 ATGATATGCAC
54233093 ATGATATGCAC
1 ATGATATGCAC
54233104 ATGAT
1 ATGAT
54233109 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:54233108 original size:20 final size:20
Alignment explanation
Indices: 54233042--54233108 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
54233032 ATTTTGATAA
*
54233042 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
54233062 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
54233082 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
54233102 ACATGAT
1 ACATGAT
54233109 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:54233192 original size:23 final size:23
Alignment explanation
Indices: 54233159--54233276 Score: 175
Period size: 23 Copynumber: 5.1 Consensus size: 23
54233149 AGGAAGTGAA
* *
54233159 AAAGGGATTATGCCCCAATTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
54233182 AAAGGGCTTATGTCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
54233205 AAAGGGCTTATACCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
54233228 AAAGGGCTTATG-CCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
54233250 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
54233274 AAA
1 AAA
54233277 AGAGGCTAGG
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
22 10 0.12
23 66 0.77
24 10 0.12
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:54233529 original size:31 final size:31
Alignment explanation
Indices: 54233491--54233554 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
54233481 CGTTTACAGT
54233491 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
54233522 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
54233553 AA
1 AA
54233555 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:54240204 original size:25 final size:25
Alignment explanation
Indices: 54240175--54240222 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
54240165 TTATAACATG
* *
54240175 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
54240200 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
54240223 GTTTATGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:54240306 original size:11 final size:11
Alignment explanation
Indices: 54240270--54240325 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
54240260 CATGGTATGT
54240270 ATGATATGCAC
1 ATGATATGCAC
* *
54240281 ATGACATG--T
1 ATGATATGCAC
54240290 ATGATATGCAC
1 ATGATATGCAC
*
54240301 ATGATATG--T
1 ATGATATGCAC
54240310 ATGATATGCAC
1 ATGATATGCAC
54240321 ATGAT
1 ATGAT
54240326 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:54240325 original size:20 final size:20
Alignment explanation
Indices: 54240259--54240325 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
54240249 ATTTTGATAA
*
54240259 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
54240279 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
54240299 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
54240319 ACATGAT
1 ACATGAT
54240326 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:54240406 original size:23 final size:22
Alignment explanation
Indices: 54240376--54240470 Score: 145
Period size: 23 Copynumber: 4.1 Consensus size: 22
54240366 AGGAAGTGAA
54240376 AAAGGGCTTATGTCCCAGTTATT
1 AAAGGGCTTATG-CCCAGTTATT
54240399 AAAGGGCTTATGCCCGAGTTATT
1 AAAGGGCTTATGCCC-AGTTATT
54240422 AAAGGGCTTATGCCCAGTTATT
1 AAAGGGCTTATGCCCAGTTATT
*
54240444 AAAAGGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATG-CCCAGTTATT
54240468 AAA
1 AAA
54240471 ATAGGCTAGG
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
22 10 0.15
23 48 0.71
24 10 0.15
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (22 bp):
AAAGGGCTTATGCCCAGTTATT
Found at i:54240720 original size:31 final size:31
Alignment explanation
Indices: 54240685--54240748 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
54240675 CGTTTATAGT
54240685 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
54240716 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
54240747 AA
1 AA
54240749 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:54243354 original size:21 final size:24
Alignment explanation
Indices: 54243311--54243359 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 24
54243301 GTTTGAAGCA
54243311 CTTCATAAAATTAAAAGTTATAAAC
1 CTTCATAAAATT-AAAGTTATAAAC
54243336 CTTCATAAAA-T-AAG-TATAAAC
1 CTTCATAAAATTAAAGTTATAAAC
54243357 CTT
1 CTT
54243360 TACTAATGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
24 1 0.04
25 10 0.42
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (24 bp):
CTTCATAAAATTAAAGTTATAAAC
Found at i:54247989 original size:37 final size:37
Alignment explanation
Indices: 54247939--54248012 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
54247929 ATAACGGAAC
54247939 ACAAAGTATTCTGAAGGTCAAACCAAAAAGAGTTCGG
1 ACAAAGTATTCTGAAGGTCAAACCAAAAAGAGTTCGG
54247976 ACAAAGTATTCTGAAGGTCAAACCAAAAAGAGTTCGG
1 ACAAAGTATTCTGAAGGTCAAACCAAAAAGAGTTCGG
54248013 CTGATAAGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (37 bp):
ACAAAGTATTCTGAAGGTCAAACCAAAAAGAGTTCGG
Found at i:54250305 original size:38 final size:37
Alignment explanation
Indices: 54250249--54250327 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 37
54250239 TAACCCGGAT
54250249 ATTTTTCCAGCACTTAGCCTGCGGACTTTAAGTCCAG
1 ATTTTTCCAGCACTTAGCCTGCGGACTTTAAGTCCAG
*
54250286 ATTTATTCCAGCA-TATAGCCTGCGGACTTTAAGTCCGG
1 ATTT-TTCCAGCACT-TAGCCTGCGGACTTTAAGTCCAG
54250324 ATTT
1 ATTT
54250328 CTTCTTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
37 5 0.13
38 34 0.87
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (37 bp):
ATTTTTCCAGCACTTAGCCTGCGGACTTTAAGTCCAG
Found at i:54254867 original size:44 final size:45
Alignment explanation
Indices: 54254772--54254905 Score: 162
Period size: 46 Copynumber: 3.0 Consensus size: 45
54254762 ACAGGACAGA
* *
54254772 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
54254818 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
54254862 ACAGGAATAATTCATGTAAGTCCATGTCAAAGATATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
54254906 CAGGATATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 36 0.48
45 1 0.01
46 38 0.51
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:54256847 original size:79 final size:79
Alignment explanation
Indices: 54256728--54256886 Score: 210
Period size: 79 Copynumber: 2.0 Consensus size: 79
54256718 TTATGCATGC
* * * * *
54256728 AAAACATGAAAGATAGAAACACAAAGGGCATAATACTGAAATGTGAAATTAACTTTATCTATTTA
1 AAAACATGAAAGACACAAACACAAAAGACATAATACTGAAATGTAAAATTAACTTTATCTATTTA
54256793 TTCATAGTTCAAAT
66 TTCATAGTTCAAAT
* * * * * *
54256807 AAAACATGAAAGACACAAATATAAAAGACATAATAGTGAAATGTAAAATTAAGTTTGTTTATTTA
1 AAAACATGAAAGACACAAACACAAAAGACATAATACTGAAATGTAAAATTAACTTTATCTATTTA
*
54256872 TTCATTGTTCAAAT
66 TTCATAGTTCAAAT
54256886 A
1 A
54256887 CATAAAAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (79 bp):
AAAACATGAAAGACACAAACACAAAAGACATAATACTGAAATGTAAAATTAACTTTATCTATTTA
TTCATAGTTCAAAT
Found at i:54260783 original size:52 final size:52
Alignment explanation
Indices: 54260697--54260804 Score: 191
Period size: 52 Copynumber: 2.1 Consensus size: 52
54260687 ATAGAAGTTC
*
54260697 ACTTCCTC-ATTTGATATTGATTTGAATAAGGTGTTTCAACTTTAGTGCATT
1 ACTTCATCTATTTGATATTGATTTGAATAAGGTGTTTCAACTTTAGTGCATT
*
54260748 TCTTCATCTATTTGATATTGATTTGAATAAGGTGTTTCAACTTTAGTGCATT
1 ACTTCATCTATTTGATATTGATTTGAATAAGGTGTTTCAACTTTAGTGCATT
54260800 ACTTC
1 ACTTC
54260805 TACTAGATGT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 6 0.11
52 47 0.89
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (52 bp):
ACTTCATCTATTTGATATTGATTTGAATAAGGTGTTTCAACTTTAGTGCATT
Found at i:54262037 original size:20 final size:20
Alignment explanation
Indices: 54262014--54262051 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54262004 TTATTTTTTT
54262014 AATT-TATTGATGCTTTTTAG
1 AATTATATTGAT-CTTTTTAG
*
54262034 AATTATATTTATCTTTTT
1 AATTATATTGATCTTTTT
54262052 TTTTCTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (20 bp):
AATTATATTGATCTTTTTAG
Found at i:54262576 original size:36 final size:36
Alignment explanation
Indices: 54262536--54262608 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
54262526 AATAGTTTTC
*
54262536 TATATTATAGGAAGTAGATGGCGAG-TAGGAGTAGTT
1 TATATTATAGGAAGTAGAGGGCG-GTTAGGAGTAGTT
* *
54262572 TATATTTTAGGAAGTAGAGGGTGGTTAGGAGTAGTT
1 TATATTATAGGAAGTAGAGGGCGGTTAGGAGTAGTT
54262608 T
1 T
54262609 TCCTATTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 1 0.03
36 32 0.97
ACGTcount: A:0.30, C:0.01, G:0.34, T:0.34
Consensus pattern (36 bp):
TATATTATAGGAAGTAGAGGGCGGTTAGGAGTAGTT
Found at i:54270605 original size:7 final size:7
Alignment explanation
Indices: 54270595--54270619 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54270585 TGGGGCTTAG
54270595 GTGGGTA
1 GTGGGTA
54270602 GTGGGTA
1 GTGGGTA
54270609 GTGGGTA
1 GTGGGTA
54270616 GTGG
1 GTGG
54270620 ACAGTGGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.60, T:0.28
Consensus pattern (7 bp):
GTGGGTA
Found at i:54270625 original size:14 final size:14
Alignment explanation
Indices: 54270595--54270628 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54270585 TGGGGCTTAG
**
54270595 GTGGGTAGTGGGTA
1 GTGGGTAGTGGACA
54270609 GTGGGTAGTGGACA
1 GTGGGTAGTGGACA
54270623 GTGGGT
1 GTGGGT
54270629 TAATTGTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.03, G:0.56, T:0.26
Consensus pattern (14 bp):
GTGGGTAGTGGACA
Found at i:54276844 original size:15 final size:15
Alignment explanation
Indices: 54276807--54276845 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
54276797 AACATTAAAA
54276807 ATATATATAATATAC
1 ATATATATAATATAC
* * *
54276822 ACAAATATAATATAT
1 ATATATATAATATAC
54276837 ATATATATA
1 ATATATATA
54276846 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATATATAATATAC
Found at i:54279046 original size:54 final size:55
Alignment explanation
Indices: 54278946--54279051 Score: 135
Period size: 54 Copynumber: 1.9 Consensus size: 55
54278936 GTCCTGAGGC
* * *
54278946 TCAACTCACCTTTCGCAATATGAGTTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGTTGATTTTGAAAAAGCAGAAATTGAAAAGGT
* * *
54279000 TCAACCCACCTCTCGCAATATGAGTTGGTTCTTGAACAA-CATAAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGTTGATT-TTGAAAAAGCAGAAATTGAAAA
54279052 TAGAAATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
54 33 0.75
55 11 0.25
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (55 bp):
TCAACCCACCTCTCGCAATATGAGTTGATTTTGAAAAAGCAGAAATTGAAAAGGT
Found at i:54279060 original size:13 final size:13
Alignment explanation
Indices: 54279042--54279066 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54279032 TGAACAACAT
54279042 AAATTGAAAATAG
1 AAATTGAAAATAG
54279055 AAATTGAAAATA
1 AAATTGAAAATA
54279067 CCTCAGCGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
AAATTGAAAATAG
Found at i:54279185 original size:87 final size:86
Alignment explanation
Indices: 54279000--54279196 Score: 236
Period size: 87 Copynumber: 2.3 Consensus size: 86
54278990 ATTAAAAGGT
* * * *
54279000 TCAACCCACCTCTCGCAATATGAGTTGGTTCTTGAACAACATAAATTGAAAATAGAAATTGAAAA
1 TCAACTCACCTCTCGCAATATGAGCTGATTCTTGAACAACATAAATTGAAAACAGAAATTGAAAA
* * *
54279065 TACCTCAGCGTGACCTGAGGC
66 GACCTCAACGTGACCCGAGGC
* * *
54279086 TCAACTCACCTCTCGCAATATGAGCTGATTTTTGAA-AA-GTAGGAATTGAAAAGCATAAATTGA
1 TCAACTCACCTCTCGCAATATGAGCTGATTCTTGAACAACATA--AATTGAAAA-CAGAAATTGA
*
54279149 AAAGACCTCAACGTGCCCCGAGGC
63 AAAGACCTCAACGTGACCCGAGGC
**
54279173 TTGACTCACCTCTCGCAATATGAG
1 TCAACTCACCTCTCGCAATATGAG
54279197 TATTTTCTAA
Statistics
Matches: 95, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
84 2 0.02
85 2 0.02
86 41 0.43
87 50 0.53
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (86 bp):
TCAACTCACCTCTCGCAATATGAGCTGATTCTTGAACAACATAAATTGAAAACAGAAATTGAAAA
GACCTCAACGTGACCCGAGGC
Found at i:54279250 original size:69 final size:70
Alignment explanation
Indices: 54279139--54279447 Score: 307
Period size: 73 Copynumber: 4.3 Consensus size: 70
54279129 AATTGAAAAG
* * * * * *
54279139 CATAAATTGAAAAGACCTCAACGTGCCCCGAGGCTTGACTCACCTCTCGCAATATGAGT-ATTTT
1 CATAAACTAAAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTCGCAATATGAGTAATTTT
54279203 CT-AAA
66 -TGAAA
* * *
54279208 CATAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCGACTCACCCCTCGCAATATGAGCTGATTT
1 CATAAACTAAAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTCGCAATATGAG-TAATTT
54279273 TTGAAA
65 TTGAAA
* * * * *
54279279 CAAAAGGAATTAAAATACCTCAGCGTGACCTGAGGCTTGACTCACCTCTCGCAATATGAGTCAAT
1 CATAA--ACTAAAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTCGCAATATGAGT-AAT
54279344 TTTTGAAA
63 TTTTGAAA
* * ** * *
54279352 CATAAACTAAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCATTTCTCACAATATGAGTTGAT
1 CATAAACTAAAAATACCTCAGC--GTGACCCGAGGCTCGACTCACCTCTCGCAATATGAG-T-AA
54279417 TTTTTGAAAA
62 TTTTTG-AAA
* * *
54279427 CATGAATTAAAGATACCTCAG
1 CATAAACTAAAAATACCTCAG
54279448 AGTACCCAAA
Statistics
Matches: 203, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
69 52 0.26
70 2 0.01
71 27 0.13
72 1 0.00
73 92 0.45
74 8 0.04
75 21 0.10
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (70 bp):
CATAAACTAAAAATACCTCAGCGTGACCCGAGGCTCGACTCACCTCTCGCAATATGAGTAATTTT
TGAAA
Found at i:54284259 original size:21 final size:21
Alignment explanation
Indices: 54284233--54284272 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
54284223 AAAAAGCTCA
54284233 AAAATACGAGATTGACCGATC
1 AAAATACGAGATTGACCGATC
*
54284254 AAAATACGAGCTTGACCGA
1 AAAATACGAGATTGACCGA
54284273 GAGGGTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.17
Consensus pattern (21 bp):
AAAATACGAGATTGACCGATC
Found at i:54284309 original size:7 final size:7
Alignment explanation
Indices: 54284297--54284376 Score: 81
Period size: 7 Copynumber: 11.1 Consensus size: 7
54284287 TCGAGCCTTC
54284297 CTTTTTT
1 CTTTTTT
54284304 CTTTTTT
1 CTTTTTT
*
54284311 C-TTTTC
1 CTTTTTT
54284317 CTTTTTCCCT
1 CTTTTT---T
*
54284327 TTTTTTT
1 CTTTTTT
*
54284334 CTCTTTT
1 CTTTTTT
54284341 CTTTTTT
1 CTTTTTT
54284348 CTTTTTT
1 CTTTTTT
*
54284355 CTGTTTT
1 CTTTTTT
*
54284362 CTGTTTT
1 CTTTTTT
54284369 CTTTTTT
1 CTTTTTT
54284376 C
1 C
54284377 CTTCTTTTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
6 5 0.08
7 51 0.84
10 5 0.08
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (7 bp):
CTTTTTT
Found at i:54284321 original size:12 final size:12
Alignment explanation
Indices: 54284300--54284390 Score: 69
Period size: 14 Copynumber: 7.2 Consensus size: 12
54284290 AGCCTTCCTT
54284300 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
54284312 TTTTCCTTTTTCCC
1 TTTT-CTTTTT-TC
*
54284326 TTTT-TTTTCTC
1 TTTTCTTTTTTC
54284337 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
54284349 TTTTTTCTGTTTTCTG
1 --TTTTCT-TTTT-TC
54284365 TTTTCTTTTTTC
1 TTTTCTTTTTTC
* *
54284377 -CTTCTTTTTCC
1 TTTTCTTTTTTC
54284388 TTT
1 TTT
54284391 GGCCTGCTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
11 14 0.23
12 16 0.26
13 10 0.16
14 17 0.27
15 4 0.06
16 1 0.02
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:54284383 original size:44 final size:43
Alignment explanation
Indices: 54284297--54284384 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 43
54284287 TCGAGCCTTC
*
54284297 CTTTTTTCTTTTTTCTTTTCCTTTTTCCCTTTTTTTTCTCTTTT
1 CTTTTTTCTTTTTTCTTTTCCTTTTT-CCTTTTTTCTCTCTTTT
*
54284341 CTTTTTTCTTTTTTCTGTTTTCTGTTTT-CTTTTTTC-CTTCTTTT
1 CTTTTTTCTTTTTTCT-TTTCCT-TTTTCCTTTTTTCTC-TCTTTT
54284385 TCCTTTGGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
43 1 0.03
44 29 0.74
45 5 0.13
46 4 0.10
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.77
Consensus pattern (43 bp):
CTTTTTTCTTTTTTCTTTTCCTTTTTCCTTTTTTCTCTCTTTT
Found at i:54284610 original size:25 final size:25
Alignment explanation
Indices: 54284581--54284637 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
54284571 GCTGTTTTGA
*
54284581 TTTTTTTGTATTG-CT-TTTTCTTTT
1 TTTTTTTGT-TTGCCTAATTTCTTTT
54284605 TCTTTTTT-TTTGCCTAATTTCTTTT
1 T-TTTTTTGTTTGCCTAATTTCTTTT
54284630 TTTTTTTG
1 TTTTTTTG
54284638 GGTTTTTGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 3 0.11
24 10 0.36
25 15 0.54
ACGTcount: A:0.05, C:0.11, G:0.07, T:0.77
Consensus pattern (25 bp):
TTTTTTTGTTTGCCTAATTTCTTTT
Found at i:54284678 original size:18 final size:18
Alignment explanation
Indices: 54284657--54284700 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
54284647 GTTTGGGTTG
54284657 CGGGTCGGGTCACCGGAT
1 CGGGTCGGGTCACCGGAT
** *
54284675 CGGGTCATGTCGCCGGAT
1 CGGGTCGGGTCACCGGAT
54284693 CGGGTCGG
1 CGGGTCGG
54284701 TTTGACCCGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.09, C:0.27, G:0.45, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCACCGGAT
Found at i:54284755 original size:6 final size:6
Alignment explanation
Indices: 54284745--54284825 Score: 74
Period size: 6 Copynumber: 13.3 Consensus size: 6
54284735 TTTTTTTATT
* **
54284745 TTTTTCC TTTTTC -TTTTC TTTTTC TTTTTC TTTTTTC TTCTTC TCCTTC
1 TTTTT-C TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC
* * * *
54284794 TTCTTC TTTTTC TTCTTC TTCTTC TTCTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT
54284826 CTTCACGAGC
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
5 5 0.07
6 51 0.76
7 11 0.16
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:54284787 original size:3 final size:3
Alignment explanation
Indices: 54284755--54284829 Score: 93
Period size: 3 Copynumber: 26.0 Consensus size: 3
54284745 TTTTTCCTTT
* * *
54284755 TTC TT- TTC TTT TTC TTT TTC TT- TT- TTC TTC TTC TCC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
54284800 TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
54284830 ACGAGCCCTA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 6 0.10
3 56 0.90
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:54284886 original size:18 final size:18
Alignment explanation
Indices: 54284846--54284889 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
54284836 CCTAGCCGCC
54284846 GCGCCG-CGCCGTCGCTT
1 GCGCCGTCGCCGTCGCTT
*
54284863 GTGCCGTCGCCGTCGTCTT
1 GCGCCGTCGCCGTCG-CTT
54284882 -CGCCGTCG
1 GCGCCGTCG
54284890 AGCCGCTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 15 0.65
19 3 0.13
ACGTcount: A:0.00, C:0.43, G:0.34, T:0.23
Consensus pattern (18 bp):
GCGCCGTCGCCGTCGCTT
Found at i:54284940 original size:20 final size:20
Alignment explanation
Indices: 54284907--54284964 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
54284897 GTCGGAGGCT
54284907 CTCTTC-TTCTTCTCCTTTCTC
1 CTCTTCTTTC-TCTCCTTT-TC
54284928 CTC-TCTTTCTCTCCTTTTC
1 CTCTTCTTTCTCTCCTTTTC
*
54284947 CTCTTCTTTTTCT-CTTTT
1 CTCTTCTTTCTCTCCTTTT
54284965 TTGCAAGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 10 0.29
20 18 0.53
21 6 0.18
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTCTTTCTCTCCTTTTC
Found at i:54285247 original size:30 final size:30
Alignment explanation
Indices: 54285207--54285308 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
54285197 ATTTAGGATT
*
54285207 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
54285237 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* *
54285267 AAAATGGAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
54285297 AAAATGCAATTT
1 AAAATGAAATTT
54285309 TTATTTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 59 0.97
ACGTcount: A:0.43, C:0.04, G:0.24, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Done.