Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 360 of 433
Found at i:113104230 original size:17 final size:16
Alignment explanation
Indices: 113104208--113104270 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 16
113104198 TTTTTATTTA
113104208 ATATGTATAATAAATAT
1 ATATGTATAAT-AATAT
113104225 ATATGTTATAATAATA-
1 ATATG-TATAATAATAT
*
113104241 AAATGTAT-ATAAT-T
1 ATATGTATAATAATAT
113104255 ATATGTAT-ATAATAT
1 ATATGTATAATAATAT
113104270 A
1 A
113104271 AGTTATGAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 17 0.41
15 5 0.12
16 4 0.10
17 9 0.22
18 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
ATATGTATAATAATAT
Found at i:113104934 original size:43 final size:43
Alignment explanation
Indices: 113104852--113104935 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
113104842 TGTGATTCTG
* *
113104852 ATATGTGTTTACGAGTAAGACCCTGTCTGGGACAGTGGCATCA
1 ATATGTGGTTACGAGTAAGACCCTGTCTGGAACAGTGGCATCA
113104895 ATATGTGGTTAC-ATGTAAGACCAC-GTCTGGAAC-GTTGGCAT
1 ATATGTGGTTACGA-GTAAGACC-CTGTCTGGAACAG-TGGCAT
113104936 TGTACGATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
42 2 0.06
43 33 0.92
44 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (43 bp):
ATATGTGGTTACGAGTAAGACCCTGTCTGGAACAGTGGCATCA
Found at i:113107834 original size:23 final size:23
Alignment explanation
Indices: 113107808--113107855 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
113107798 TGCAGTATAA
*
113107808 ATTCTATTTTTTGAGAAAAGCGT
1 ATTCTATTTTTTAAGAAAAGCGT
113107831 ATTCTATTTTTTAAGAAAAGCGT
1 ATTCTATTTTTTAAGAAAAGCGT
113107854 AT
1 AT
113107856 AGTTTTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (23 bp):
ATTCTATTTTTTAAGAAAAGCGT
Found at i:113108436 original size:31 final size:30
Alignment explanation
Indices: 113108390--113108507 Score: 100
Period size: 31 Copynumber: 3.9 Consensus size: 30
113108380 ATCTCAAAAT
* *
113108390 TATATATAGATTTTAATTTAATATGTAATTA
1 TATATATAAACTTTAATTTAATAT-TAATTA
* *
113108421 TATATATCAACTTTAATTTAGTA-TAATTA
1 TATATATAAACTTTAATTTAATATTAATTA
** *
113108450 TATATATAAAACACTAATATTAAT-TTAAATA
1 TATATAT-AAACTTTAAT-TTAATATTAATTA
*
113108481 TATAT-TTAACTTTAATTTTAAT-TTAAT
1 TATATATAAACTTTAA-TTTAATATTAAT
113108508 CATACATTTA
Statistics
Matches: 70, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
29 28 0.40
30 9 0.13
31 33 0.47
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (30 bp):
TATATATAAACTTTAATTTAATATTAATTA
Found at i:113108664 original size:30 final size:29
Alignment explanation
Indices: 113108624--113108703 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
113108614 GTTAATAATT
113108624 TATA-AAAATTAAATTAAATTAAAATTTTA
1 TATATAAAATTAAATTAAATTAAAA-TTTA
* *
113108653 TATATAAAATTACATAAAATTAAAATTTA
1 TATATAAAATTAAATTAAATTAAAATTTA
*
113108682 TATATAAAGTTAAATTATAATT
1 TATATAAAATTAAATTA-AATT
113108704 CGTATATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 22 0.50
30 22 0.50
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (29 bp):
TATATAAAATTAAATTAAATTAAAATTTA
Found at i:113108686 original size:31 final size:29
Alignment explanation
Indices: 113108624--113108689 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 29
113108614 GTTAATAATT
*
113108624 TATAAAAATTAAATTAAATTAAAATTTTA
1 TATAAAAATTAAATAAAATTAAAATTTTA
*
113108653 TATATAAAATTACATAAAATTAAAATTTATA
1 TATA-AAAATTAAATAAAATTAAAATTT-TA
113108684 TATAAA
1 TATAAA
113108690 GTTAAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 4 0.12
30 23 0.70
31 6 0.18
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
TATAAAAATTAAATAAAATTAAAATTTTA
Found at i:113108696 original size:24 final size:23
Alignment explanation
Indices: 113108633--113108712 Score: 61
Period size: 24 Copynumber: 3.1 Consensus size: 23
113108623 TTATAAAAAT
113108633 TAAATTAAATTAAAATTTTATATA
1 TAAATTAAATTAAAA-TTTATATA
113108657 TAAAATTACATAAAATTAAAATTTATATA
1 T-AAA-T---T-AAATTAAAATTTATATA
* **
113108686 TAAAGTTAAATTATAATTCGTATA
1 TAAA-TTAAATTAAAATTTATATA
113108710 TAA
1 TAA
113108713 TTTTGATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
24 18 0.39
25 4 0.09
26 1 0.02
28 4 0.09
29 10 0.22
30 9 0.20
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (23 bp):
TAAATTAAATTAAAATTTATATA
Found at i:113119193 original size:20 final size:20
Alignment explanation
Indices: 113119170--113119208 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
113119160 AACTATTTAA
**
113119170 ATAATATTATTTGAATAATT
1 ATAATATTAAATGAATAATT
113119190 ATAATATTAAATGAATAAT
1 ATAATATTAAATGAATAAT
113119209 CATGTGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:113130260 original size:48 final size:48
Alignment explanation
Indices: 113130208--113130495 Score: 454
Period size: 48 Copynumber: 6.2 Consensus size: 48
113130198 GGTAAAACTA
*
113130208 AATGGCTAGTGTGAAATATGTATGAGATATGTATACGAGGTAAAGCCG
1 AATGGCTAGTGTGAAATATGTATGAGATATGTATACGTGGTAAAGCCG
*
113130256 AATGGCTA--GTG-----TG-A--A-ATATGTATACGTGGTAAAGCTG
1 AATGGCTAGTGTGAAATATGTATGAGATATGTATACGTGGTAAAGCCG
113130293 AATGGCTAGTGTGAAATATGTATGAGATATGTATACGTGGTAAAGCCG
1 AATGGCTAGTGTGAAATATGTATGAGATATGTATACGTGGTAAAGCCG
113130341 AATGGCTAGTGTGAAATATGTATGAGATATGTATACGTGGTAAAGCCG
1 AATGGCTAGTGTGAAATATGTATGAGATATGTATACGTGGTAAAGCCG
113130389 AATGGCTAGTGTGAAATATGTATGAGATATGTATACGTGGTAAAGCCG
1 AATGGCTAGTGTGAAATATGTATGAGATATGTATACGTGGTAAAGCCG
* * *
113130437 AATGGCTAATGCGAAATATGTATGAGATATGTATATGTGGTAAAGCCG
1 AATGGCTAGTGTGAAATATGTATGAGATATGTATACGTGGTAAAGCCG
113130485 AATGGCTAGTG
1 AATGGCTAGTG
113130496 ATTCGGCTAG
Statistics
Matches: 222, Mismatches: 7, Indels: 22
0.88 0.03 0.09
Matches are distributed among these distances:
37 28 0.13
38 1 0.00
39 3 0.01
40 1 0.00
41 2 0.01
44 2 0.01
45 1 0.00
46 3 0.01
47 1 0.00
48 180 0.81
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (48 bp):
AATGGCTAGTGTGAAATATGTATGAGATATGTATACGTGGTAAAGCCG
Found at i:113130287 original size:37 final size:37
Alignment explanation
Indices: 113130234--113130315 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
113130224 TATGTATGAG
113130234 ATATGTATACGAGGTAAAGCCGAATGGCTAGTGTGAA
1 ATATGTATACGAGGTAAAGCCGAATGGCTAGTGTGAA
* *
113130271 ATATGTATACGTGGTAAAGCTGAATGGCTAGTGTGAA
1 ATATGTATACGAGGTAAAGCCGAATGGCTAGTGTGAA
113130308 ATATGTAT
1 ATATGTAT
113130316 GAGATATGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (37 bp):
ATATGTATACGAGGTAAAGCCGAATGGCTAGTGTGAA
Found at i:113130715 original size:37 final size:37
Alignment explanation
Indices: 113130665--113130767 Score: 188
Period size: 37 Copynumber: 2.8 Consensus size: 37
113130655 GGAAATATAT
113130665 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
113130702 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
113130739 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
113130768 GGACTATTCG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.24
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:113139031 original size:22 final size:23
Alignment explanation
Indices: 113139003--113139045 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
113138993 ACACAAGCAT
*
113139003 AAATGACCA-CATTCCATAACCC
1 AAATGACAATCATTCCATAACCC
*
113139025 AAATGACAATCATTCTATAAC
1 AAATGACAATCATTCCATAAC
113139046 ATTTCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (23 bp):
AAATGACAATCATTCCATAACCC
Found at i:113142438 original size:23 final size:23
Alignment explanation
Indices: 113142387--113142509 Score: 115
Period size: 23 Copynumber: 5.2 Consensus size: 23
113142377 GCCATGATCG
* *
113142387 GTAAGCTCCTCTTGAGCTGATGAATA
1 GTAAGCT-CTATTGAGCTGA--AACA
113142413 GTAAGCTCTATTGAGCTGAAACA
1 GTAAGCTCTATTGAGCTGAAACA
* *
113142436 GTAAACTCTATCGAGCTG-AACA
1 GTAAGCTCTATTGAGCTGAAACA
*
113142458 GTAAGCTC-ATATGAGCTGAAACG
1 GTAAGCTCTAT-TGAGCTGAAACA
* * *
113142481 GTAAGTTCCAATGAGCTGAAAACA
1 GTAAGCTCTATTGAGCTG-AAACA
113142505 GTAAG
1 GTAAG
113142510 ATCATATAAG
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.02
22 17 0.20
23 36 0.43
24 10 0.12
25 11 0.13
26 7 0.08
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (23 bp):
GTAAGCTCTATTGAGCTGAAACA
Found at i:113142497 original size:45 final size:45
Alignment explanation
Indices: 113142407--113142521 Score: 117
Period size: 45 Copynumber: 2.5 Consensus size: 45
113142397 CTTGAGCTGA
* *
113142407 TGAATAGTAAGCTC-TATTGAGCTGAAACAGTAAACTCTATCGAGC
1 TGAACAGTAAGCTCATA-TGAGCTGAAACAGTAAACTCAATCGAGC
* **
113142452 TGAACAGTAAGCTCATATGAGCTGAAACGGTAAGTTCCAAT-GAGC
1 TGAACAGTAAGCTCATATGAGCTGAAACAGTAAACT-CAATCGAGC
* *
113142497 TGAAAACAGTAAGATCATATAAGCT
1 TG--AACAGTAAGCTCATATGAGCT
113142522 AAAATATCGG
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
45 35 0.59
46 5 0.08
47 19 0.32
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (45 bp):
TGAACAGTAAGCTCATATGAGCTGAAACAGTAAACTCAATCGAGC
Found at i:113142508 original size:24 final size:23
Alignment explanation
Indices: 113142412--113142548 Score: 111
Period size: 23 Copynumber: 5.8 Consensus size: 23
113142402 GCTGATGAAT
113142412 AGTAAGCTC-TATTGAGCTGAAAC
1 AGTAAGCTCATA-TGAGCTGAAAC
*
113142435 AGTAAACTC-TATCGAGCTG-AAC
1 AGTAAGCTCATAT-GAGCTGAAAC
113142457 AGTAAGCTCATATGAGCTGAAAC
1 AGTAAGCTCATATGAGCTGAAAC
* *
113142480 GGTAAGTTCCA-ATGAGCTGAAAAC
1 AGTAAGCT-CATATGAGCTG-AAAC
* * *
113142504 AGTAAGATCATATAAGCTAAAATATC
1 AGTAAGCTCATATGAGCT-GAA-A-C
* *
113142530 GGTAAGCTCATACGAGCTG
1 AGTAAGCTCATATGAGCTG
113142549 TGGTGAGTCT
Statistics
Matches: 92, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
22 18 0.20
23 38 0.41
24 20 0.22
25 1 0.01
26 15 0.16
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (23 bp):
AGTAAGCTCATATGAGCTGAAAC
Found at i:113146169 original size:40 final size:34
Alignment explanation
Indices: 113146093--113146158 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
113146083 CCATGCAATT
*
113146093 TCGATTAACTTTAACATGTTTTCACTGAGTGAAA
1 TCGATTAACTTTAACATGTTTTCACTAAGTGAAA
*
113146127 TCGATTAACTTTAACATGTTTTTACTAAGTGA
1 TCGATTAACTTTAACATGTTTTCACTAAGTGA
113146159 GGGTTCAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (34 bp):
TCGATTAACTTTAACATGTTTTCACTAAGTGAAA
Found at i:113146389 original size:20 final size:20
Alignment explanation
Indices: 113146355--113146396 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
113146345 AACTATTTAA
** *
113146355 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
113146375 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
113146395 AT
1 AT
113146397 TTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:113146903 original size:9 final size:9
Alignment explanation
Indices: 113146881--113146920 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
113146871 CTAAAACGTT
113146881 AATTAATT-
1 AATTAATTA
113146889 AATTAATTA
1 AATTAATTA
113146898 AATTAATTA
1 AATTAATTA
**
113146907 CTTTAATTA
1 AATTAATTA
113146916 AATTA
1 AATTA
113146921 TTTTCTCAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (9 bp):
AATTAATTA
Found at i:113149096 original size:2 final size:2
Alignment explanation
Indices: 113149089--113149114 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
113149079 TAAGTTCATA
113149089 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
113149115 TTTAAACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:113161560 original size:39 final size:39
Alignment explanation
Indices: 113161506--113161649 Score: 243
Period size: 39 Copynumber: 3.7 Consensus size: 39
113161496 GAATGTTCGA
113161506 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
113161545 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
113161584 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
113161623 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
113161650 CTTTGTGCGG
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 88 0.91
40 9 0.09
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:113161596 original size:78 final size:79
Alignment explanation
Indices: 113161507--113161689 Score: 278
Period size: 78 Copynumber: 2.3 Consensus size: 79
113161497 AATGTTCGAG
113161507 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
113161571 AATTGTGCGAGTTA
66 AATTGTGCGAGTTA
*
113161585 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
** *
113161650 CTTTGTGCGGGTTA
66 AATTGTGCGAGTTA
** * *
113161664 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
113161690 GTTCGAACGA
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
78 54 0.57
79 32 0.34
80 9 0.09
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTA
Found at i:113163328 original size:34 final size:34
Alignment explanation
Indices: 113163280--113163361 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
113163270 GGATAACCAG
* *** *
113163280 CCAGCACACTAAATGCTCGTATGAGCCAATCTAT
1 CCAGCACACCAAATGCTCGTATGAAAAAATCCAT
113163314 CCAGCACACCAAATGCTCGTATGAAAAAATCCAT
1 CCAGCACACCAAATGCTCGTATGAAAAAATCCAT
*
113163348 CCATCACACCAAAT
1 CCAGCACACCAAAT
113163362 AACACTGTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.20
Consensus pattern (34 bp):
CCAGCACACCAAATGCTCGTATGAAAAAATCCAT
Found at i:113168251 original size:11 final size:12
Alignment explanation
Indices: 113168235--113168263 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
113168225 TTATTAATGG
113168235 TGAATG-ATATT
1 TGAATGAATATT
113168246 TGAATGAATATT
1 TGAATGAATATT
113168258 TGAATG
1 TGAATG
113168264 TTCTTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (12 bp):
TGAATGAATATT
Found at i:113175925 original size:37 final size:37
Alignment explanation
Indices: 113175883--113175961 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
113175873 CAGGGTTTTA
* *
113175883 ACCCGGATAAAATCTCCACACGTGGTCATCGGGTCTT
1 ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
*
113175920 ACCCGGACAGAATCTCCACACGTAGTCATCGGGTCTT
1 ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
113175957 ACCCG
1 ACCCG
113175962 AAATATATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.22
Consensus pattern (37 bp):
ACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTT
Found at i:113176237 original size:48 final size:48
Alignment explanation
Indices: 113176122--113176247 Score: 180
Period size: 48 Copynumber: 2.6 Consensus size: 48
113176112 TATTGCACAA
* * *
113176122 TAGCCATTCGGCTTTACCAAAAATACATCTCTCATACATATTTCATAT
1 TAGCCATTCGGCTTTACCACAAATACATATCTCATACATATCTCATAT
* * *
113176170 TAGCCATTTGGCTTTACCACATATACATATCTCATACATGTCTCATAT
1 TAGCCATTCGGCTTTACCACAAATACATATCTCATACATATCTCATAT
* *
113176218 TAGCCATTCGGCTTTACCACACATATATAT
1 TAGCCATTCGGCTTTACCACAAATACATAT
113176248 ATTTACCTTG
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (48 bp):
TAGCCATTCGGCTTTACCACAAATACATATCTCATACATATCTCATAT
Found at i:113181020 original size:15 final size:16
Alignment explanation
Indices: 113180991--113181020 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
113180981 CAAACATGCT
113180991 TTAACACATTATCAAA
1 TTAACACATTATCAAA
113181007 TTAACACA-TATCAA
1 TTAACACATTATCAA
113181021 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:113182184 original size:25 final size:25
Alignment explanation
Indices: 113182156--113182225 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
113182146 CTGTACATGT
113182156 ATGCTCACATGAGCTGTGAATCAGA
1 ATGCTCACATGAGCTGTGAATCAGA
* * *
113182181 ATGCTCACACGAGCTATGAATTAGA
1 ATGCTCACATGAGCTGTGAATCAGA
* *
113182206 ATGCTCGCATGAACTGTGAA
1 ATGCTCACATGAGCTGTGAA
113182226 AATAGTCCTG
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:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (25 bp):
ATGCTCACATGAGCTGTGAATCAGA
Found at i:113188373 original size:5 final size:6
Alignment explanation
Indices: 113188360--113188419 Score: 75
Period size: 6 Copynumber: 9.5 Consensus size: 6
113188350 ATAATTTAAT
* *
113188360 AAATAA AAATAA AAATCTAA AACTAA AACTAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAATAA AAATAA
113188410 AAATATA AAA
1 AAATA-A AAA
113188420 CATATAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
6 40 0.82
7 4 0.08
8 5 0.10
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:113191584 original size:38 final size:38
Alignment explanation
Indices: 113191541--113191619 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
113191531 ATTTTATACC
113191541 ATTAAACATCAACATCAGTACATGTCACACATGGGTAA
1 ATTAAACATCAACATCAGTACATGTCACACATGGGTAA
*
113191579 ATTAAACATCAACATCAGTGCATGTCACACATGGGTAA
1 ATTAAACATCAACATCAGTACATGTCACACATGGGTAA
113191617 ATT
1 ATT
113191620 TTTAAACATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (38 bp):
ATTAAACATCAACATCAGTACATGTCACACATGGGTAA
Found at i:113192375 original size:19 final size:19
Alignment explanation
Indices: 113192351--113192441 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
113192341 ATAATCTTCA
113192351 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
113192370 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
113192389 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
113192406 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
113192424 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
113192442 AGATATAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:113192422 original size:35 final size:37
Alignment explanation
Indices: 113192351--113192441 Score: 150
Period size: 35 Copynumber: 2.5 Consensus size: 37
113192341 ATAATCTTCA
113192351 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAGATATGATATGCAATCTTAGAT
113192389 ATGATA-CAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
113192424 ATGATATGCAATCTTAGA
1 ATGATA-GCAATCTTAGA
113192442 AGATATAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
35 19 0.37
36 16 0.31
37 10 0.20
38 6 0.12
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:113192752 original size:18 final size:18
Alignment explanation
Indices: 113192726--113192763 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
113192716 TGTTTCCCTG
*
113192726 AATTTTTTTTATATATTTT
1 AATTTTTTTAATA-ATTTT
113192745 AATTTTTTTAATAATTTT
1 AATTTTTTTAATAATTTT
113192763 A
1 A
113192764 GTATCATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
AATTTTTTTAATAATTTT
Found at i:113192840 original size:23 final size:24
Alignment explanation
Indices: 113192813--113192857 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
113192803 AGTATTACTC
* *
113192813 TTATT-AAATTATTTTTTTAAATT
1 TTATTCAAATCATTATTTTAAATT
113192836 TTATTCAAATCATTATTTTAAA
1 TTATTCAAATCATTATTTTAAA
113192858 AAAATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTCAAATCATTATTTTAAATT
Found at i:113197290 original size:55 final size:53
Alignment explanation
Indices: 113197202--113197457 Score: 240
Period size: 55 Copynumber: 4.8 Consensus size: 53
113197192 CATTAGGGTT
* *
113197202 CAAGGATACCGTGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGG
1 CAAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAA-GTTTCTAAGG
* * * * * *
113197257 CAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGG
1 CAAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTT--TCTAAGG
* * * *
113197312 CAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGG
1 C-AAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTC-TAAGG
*
113197365 CAAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC-AA--
1 CAAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAAGTTTCTAAGG
* * *
113197415 -AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 CAAGGATACCATGTAAGACCATGCCAAGACATGG-AATTGGTAAG
113197458 GTACCCGTGT
Statistics
Matches: 170, Mismatches: 24, Indels: 20
0.79 0.11 0.09
Matches are distributed among these distances:
49 40 0.24
52 7 0.04
53 40 0.24
54 12 0.07
55 67 0.39
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (53 bp):
CAAGGATACCATGTAAGACCATGCCAAGACATGGAATTGGTAAGTTTCTAAGG
Found at i:113197409 original size:108 final size:110
Alignment explanation
Indices: 113197213--113197410 Score: 312
Period size: 108 Copynumber: 1.8 Consensus size: 110
113197203 AAGGATACCG
*
113197213 TGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGACCA
1 TGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
*
113197278 TGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCA
66 TGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
* * *
113197323 TGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAGACC
1 TGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGACC
*
113197385 ATGTCAAGACATGGCAATGGTAAGTT
65 ATGTCAAGACATGGCAATGATAAGTT
113197411 TCAAAAGGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 3 0.04
108 48 0.59
109 7 0.09
110 23 0.28
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.23
Consensus pattern (110 bp):
TGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
TGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
Found at i:113199404 original size:12 final size:12
Alignment explanation
Indices: 113199387--113199428 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
113199377 ACATAAATAA
113199387 TCATTCTTAAAT
1 TCATTCTTAAAT
113199399 TCATTCTTAAAT
1 TCATTCTTAAAT
113199411 TCATTCTTAAAT
1 TCATTCTTAAAT
113199423 TCATTC
1 TCATTC
113199429 ATTCTTTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (12 bp):
TCATTCTTAAAT
Found at i:113204100 original size:89 final size:86
Alignment explanation
Indices: 113203971--113204131 Score: 198
Period size: 89 Copynumber: 1.8 Consensus size: 86
113203961 ATTCGACGGA
* **
113203971 GAGCAGATCGAAGACATAGCAGATCTAACATTCGGATGTTTTCACATCGAAGTAGATCCAAGATG
1 GAGCAGATCGAAGACATAGCAGATCTAACATTCCGATG-TTTCAC-T-GAAACAGATCCAAGATG
113204036 ATTTGGCATCATTACGTTGACAAG
63 ATTTGGCATCATTACGTTGACAAG
* ** * * *
113204060 GAGCAGATCGAAGACATAGCAGATTTGGCTTTCACG-TGTTTCGCTGAAACAGATCTAAGATGAT
1 GAGCAGATCGAAGACATAGCAGATCTAACATTC-CGATGTTTCACTGAAACAGATCCAAGATGAT
113204124 TTGGCATC
65 TTGGCATC
113204132 TCTGTACTGT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
86 24 0.39
87 1 0.02
88 5 0.08
89 31 0.50
90 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.27
Consensus pattern (86 bp):
GAGCAGATCGAAGACATAGCAGATCTAACATTCCGATGTTTCACTGAAACAGATCCAAGATGATT
TGGCATCATTACGTTGACAAG
Found at i:113204299 original size:78 final size:78
Alignment explanation
Indices: 113204165--113204458 Score: 412
Period size: 78 Copynumber: 3.8 Consensus size: 78
113204155 GAAGAAATAT
** * *
113204165 ATTTGGCATCTCCATATTCA-ACGGAGAGCAGATCGAAGAAATAGCAGATCTGACCTTCATTGAA
1 ATTTGGCATCTCTGTATT-AGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
113204229 GCAGATCCAAGATG
65 GCAGATCCAAGATG
* * * * *
113204243 ATTTCGCATCTTTGTATTAGACGAGGAGCAGATCGAAGACACAGCAAATCTGACCTTCATTGAAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
*
113204308 TAGATCCAAGATG
66 CAGATCCAAGATG
* * *
113204321 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATATAACAGAT-TGGACCTTCATTGAA
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGAA
113204385 GCAGATCCAAGATG
65 GCAGATCCAAGATG
* * *
113204399 ATTTGGCATCTCTGTATTAGACGGGGAACGGATCGGAGACATAGCAGATCTGACCTTCAT
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
113204459 ATGTTTACAT
Statistics
Matches: 188, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
77 2 0.01
78 185 0.98
79 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (78 bp):
ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAG
CAGATCCAAGATG
Found at i:113204601 original size:46 final size:46
Alignment explanation
Indices: 113204529--113204660 Score: 171
Period size: 45 Copynumber: 2.9 Consensus size: 46
113204519 CAAATCGGAG
* * *
113204529 ATTTGGCATCTCTGTATTAGATGGGGAGAGCAGATTGAAGA-AGCAA
1 ATTTGGCATCTCTGTATTAGA-CGGGAGAGCAGATCGAAGATAACAA
* *
113204575 ATTTGGCGTCTCTGTATTAGACGGG-GAGCAGATCGAAGATAACAG
1 ATTTGGCATCTCTGTATTAGACGGGAGAGCAGATCGAAGATAACAA
* *
113204620 ATTGGGCATCTCTGTATTAGAC-GGAGAGCAGATCAAAGATA
1 ATTTGGCATCTCTGTATTAGACGGGAGAGCAGATCGAAGATA
113204661 GGAGATATCG
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
44 15 0.20
45 41 0.54
46 20 0.26
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.25
Consensus pattern (46 bp):
ATTTGGCATCTCTGTATTAGACGGGAGAGCAGATCGAAGATAACAA
Found at i:113205054 original size:14 final size:15
Alignment explanation
Indices: 113205037--113205092 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
113205027 TCTTAAATAT
113205037 GATATG-CAATCTTA
1 GATATGACAATCTTA
113205051 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
113205068 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
113205086 GATATGA
1 GATATGA
113205093 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:113205087 original size:35 final size:37
Alignment explanation
Indices: 113205016--113205113 Score: 141
Period size: 35 Copynumber: 2.7 Consensus size: 37
113205006 ATAATCTTCA
*
113205016 ATGATATGCAATCTTAAATATGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAGATATGATATGCAATCTTAGAT
113205054 ATGATA-CAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
113205089 ATGATATGCAATCTTAGA-A-GATATG
1 ATGATA-GCAATCTTAGATATGATATG
113205114 ATTTTGTAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 10 0.18
38 6 0.11
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:113205113 original size:17 final size:19
Alignment explanation
Indices: 113205016--113205106 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
113205006 ATAATCTTCA
*
113205016 ATGATATGCAATCTTAAAT
1 ATGATATGCAATCTTAGAT
113205035 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
113205054 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
113205071 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
113205089 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
113205107 AGATATGATT
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 36 0.53
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:113205132 original size:22 final size:22
Alignment explanation
Indices: 113205016--113205129 Score: 96
Period size: 19 Copynumber: 5.8 Consensus size: 22
113205006 ATAATCTTCA
113205016 ATGATATGCAATCTT--AA-AT
1 ATGATATGCAATCTTAGAAGAT
113205035 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
113205054 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
113205071 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
113205089 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
113205111 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
113205130 GATTTAATTT
Statistics
Matches: 85, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
17 16 0.19
18 17 0.20
19 32 0.38
22 8 0.09
23 12 0.14
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:113205422 original size:18 final size:19
Alignment explanation
Indices: 113205399--113205434 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
113205389 TTTCCCTGAT
*
113205399 TTTTTTTATAT-ATTTTAA
1 TTTTTTTAAATAATTTTAA
113205417 TTTTTTTAAATAATTTTA
1 TTTTTTTAAATAATTTTA
113205435 GTATCATATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTTAAATAATTTTAA
Found at i:113217275 original size:18 final size:17
Alignment explanation
Indices: 113217252--113217311 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 17
113217242 CTTAAAAATG
113217252 TTTTAAAAATAAAAAAA
1 TTTTAAAAATAAAAAAA
113217269 TTCTTAAAAAATAAATAAAAA
1 TT-TT-AAAAAT-AA-AAAAA
113217290 TATTTAAAAATATAAAATAA
1 T-TTTAAAAATA-AAAA-AA
113217310 TT
1 TT
113217312 AAAATTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
17 2 0.06
18 2 0.06
19 11 0.31
20 12 0.33
21 8 0.22
22 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
TTTTAAAAATAAAAAAA
Found at i:113217288 original size:23 final size:22
Alignment explanation
Indices: 113217258--113217328 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 22
113217248 AATGTTTTAA
113217258 AAATAAAAAAATTCTTAAAAA-AT
1 AAATAAAAAAA-T-TTAAAAATAT
*
113217281 AAATAAAAATATTTAAAAATAT
1 AAATAAAAAAATTTAAAAATAT
*
113217303 AAAATAATTAAAA-TTAATAAATAT
1 -AAATAA-AAAAATTTAA-AAATAT
113217327 AA
1 AA
113217329 TAGAATATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 7 0.17
22 3 0.07
23 22 0.54
24 9 0.22
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATAAAAAAATTTAAAAATAT
Found at i:113217290 original size:21 final size:20
Alignment explanation
Indices: 113217245--113217306 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 20
113217235 ACATTTTCTT
* *
113217245 AAAAATGTTTTAAAAAT-AA
1 AAAAATATTTAAAAAATAAA
113217264 AAAAAT-TCTTAAAAAATAAA
1 AAAAATAT-TTAAAAAATAAA
113217284 TAAAAATATTTAAAAATATAAA
1 -AAAAATATTTAAAAA-ATAAA
113217306 A
1 A
113217307 TAATTAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
18 1 0.03
19 14 0.38
20 2 0.05
21 14 0.38
22 6 0.16
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAATATTTAAAAAATAAA
Found at i:113217315 original size:16 final size:16
Alignment explanation
Indices: 113217281--113217325 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
113217271 CTTAAAAAAT
*
113217281 AAATAAAAATATTTAA
1 AAATAAAAATAATTAA
113217297 AAATATAAAATAATTAA
1 AAATA-AAAATAATTAA
*
113217314 AATTAATAAATA
1 AAATAA-AAATA
113217326 TAATAGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAAAAATAATTAA
Found at i:113217322 original size:40 final size:40
Alignment explanation
Indices: 113217244--113217325 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 40
113217234 AACATTTTCT
* **
113217244 TAAAAATGTTTTAAAAATAAAAAAATTCTTAAAAAATAAA
1 TAAAAATGATTTAAAAATAAAAAAATAATTAAAAAATAAA
*
113217284 TAAAAAT-ATTTAAAAAT-ATAAAATAATTAAAATTAATAAA
1 TAAAAATGATTTAAAAATAAAAAAATAATTAAAA--AATAAA
113217324 TA
1 TA
113217326 TAATAGAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
38 12 0.33
39 9 0.25
40 15 0.42
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (40 bp):
TAAAAATGATTTAAAAATAAAAAAATAATTAAAAAATAAA
Found at i:113224205 original size:28 final size:28
Alignment explanation
Indices: 113224165--113224222 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
113224155 AAAAGACAAA
113224165 TATAATTAAATGACCATTTTATATAATT
1 TATAATTAAATGACCATTTTATATAATT
113224193 TATAATTAAATGACCATTTTATATAATT
1 TATAATTAAATGACCATTTTATATAATT
113224221 TA
1 TA
113224223 CCCTTACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (28 bp):
TATAATTAAATGACCATTTTATATAATT
Found at i:113224724 original size:92 final size:95
Alignment explanation
Indices: 113224558--113224743 Score: 270
Period size: 92 Copynumber: 2.0 Consensus size: 95
113224548 GTGTAAAAAA
* * * *
113224558 CCCTCAAACTTTTTCAAAAAAAGTAATGAAGCCTCTCCTTTTTTCTTTTTTTGCACTCAATTGAG
1 CCCTCAAACTTCTTCAAAAAAAGCAATGAAGCCTCTACTTATTTCTTTTTTTGCACTCAATTGAG
*
113224623 CACTTGAACTTTCAAAATGCACCAAAAAGG
66 CACTTGAACTTTCAAAATGAACCAAAAAGG
* *
113224653 CCCTCAAACTTCTTC-AAAAAAGCAATTAAGCCTCTACTTATTT-TTTTTTT-CACTCAATTGGG
1 CCCTCAAACTTCTTCAAAAAAAGCAATGAAGCCTCTACTTATTTCTTTTTTTGCACTCAATTGAG
* *
113224715 TACTTGAACTTTCAAAATGAATCAAAAAG
66 CACTTGAACTTTCAAAATGAACCAAAAAG
113224744 ATCCTAAAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
92 37 0.45
93 7 0.09
94 24 0.29
95 14 0.17
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (95 bp):
CCCTCAAACTTCTTCAAAAAAAGCAATGAAGCCTCTACTTATTTCTTTTTTTGCACTCAATTGAG
CACTTGAACTTTCAAAATGAACCAAAAAGG
Found at i:113224761 original size:92 final size:93
Alignment explanation
Indices: 113224569--113224776 Score: 249
Period size: 92 Copynumber: 2.2 Consensus size: 93
113224559 CCTCAAACTT
* * * *
113224569 TTTCAAAAAAAGTAATGAAGCCTCTCCTTTTTTCTTTTTTTGCACTCAATTGAGCACTTGAACTT
1 TTTC-AAAAAAGCAATTAAGCCTCTACTTATTTCTTTTTTTGCACTCAATTGAGCACTTGAACTT
* * * **
113224634 TCAAAATGCACCAAAAAGGCCCTCAAACT
65 TCAAAATGAACCAAAAAGACCCTAAAAAA
* *
113224663 TCTTCAAAAAAGCAATTAAGCCTCTACTTATTT-TTTTTTT-CACTCAATTGGGTACTTGAACTT
1 T-TTCAAAAAAGCAATTAAGCCTCTACTTATTTCTTTTTTTGCACTCAATTGAGCACTTGAACTT
* *
113224726 TCAAAATGAATCAAAAAGATCCTAAAAAAA
65 TCAAAATGAACCAAAAAGACCCT-AAAAAA
*
113224756 TTTCAAAAAATCAATTAAGCC
1 TTTCAAAAAAGCAATTAAGCC
113224777 CTAGTCTTAT
Statistics
Matches: 98, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
92 59 0.60
93 11 0.11
94 25 0.26
95 3 0.03
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (93 bp):
TTTCAAAAAAGCAATTAAGCCTCTACTTATTTCTTTTTTTGCACTCAATTGAGCACTTGAACTTT
CAAAATGAACCAAAAAGACCCTAAAAAA
Found at i:113224865 original size:15 final size:16
Alignment explanation
Indices: 113224845--113224878 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
113224835 ATTAAATTTT
113224845 AATAAAAATATA-AAA
1 AATAAAAATATATAAA
*
113224860 AATAAAAATTTATAAA
1 AATAAAAATATATAAA
113224876 AAT
1 AAT
113224879 CGTATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAAAATATATAAA
Found at i:113224874 original size:10 final size:10
Alignment explanation
Indices: 113224799--113224929 Score: 53
Period size: 10 Copynumber: 13.4 Consensus size: 10
113224789 AAAATTAGAA
*
113224799 AAAAAGTTAT
1 AAAAATTTAT
* *
113224809 AAAAAGTAAT
1 AAAAATTTAT
* *
113224819 -AAATTTTAG
1 AAAAATTTAT
113224828 AAAAA-TTAT
1 AAAAATTTAT
* *
113224837 TAAATTTTAAT
1 AAAAATTT-AT
113224848 AAAAA--TAT
1 AAAAATTTAT
113224856 AAAAA---AT
1 AAAAATTTAT
113224863 AAAAATTTAT
1 AAAAATTTAT
*
113224873 AAAAATCGTAT
1 AAAAAT-TTAT
*
113224884 AAAAATAATTGT
1 AAAAAT--TTAT
*
113224896 AAAATTTTAT
1 AAAAATTTAT
*
113224906 AAAAA-TCAT
1 AAAAATTTAT
*
113224915 AAAAAAATTAT
1 -AAAAATTTAT
113224926 AAAA
1 AAAA
113224930 TGCATCAAAA
Statistics
Matches: 91, Mismatches: 20, Indels: 20
0.69 0.15 0.15
Matches are distributed among these distances:
7 7 0.08
8 7 0.08
9 15 0.16
10 38 0.42
11 17 0.19
12 7 0.08
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:113224905 original size:33 final size:30
Alignment explanation
Indices: 113224828--113224930 Score: 117
Period size: 30 Copynumber: 3.5 Consensus size: 30
113224818 TAAATTTTAG
*
113224828 AAAAATTATTAAATTTTAATAAAAAT-AT-A
1 AAAAATTATAAAATTTT-ATAAAAATCATAA
113224857 AAAAA-TA-AAAA-TTTATAAAAATCGTATAA
1 AAAAATTATAAAATTTTATAAAAATC--ATAA
*
113224886 AAATAATTGTAAAATTTTATAAAAATCATAA
1 AAA-AATTATAAAATTTTATAAAAATCATAA
113224917 AAAAATTATAAAAT
1 AAAAATTATAAAAT
113224931 GCATCAAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
25 8 0.13
26 3 0.05
27 3 0.05
28 4 0.06
29 9 0.14
30 12 0.19
31 8 0.13
32 4 0.06
33 12 0.19
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (30 bp):
AAAAATTATAAAATTTTATAAAAATCATAA
Found at i:113225228 original size:19 final size:19
Alignment explanation
Indices: 113225204--113225283 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
113225194 TTTCTATATA
*
113225204 TTTTATATTTTTTTACGAT
1 TTTTATATTTTTTTACAAT
***
113225223 TTTTATAAAATTTTACAAT
1 TTTTATATTTTTTTACAAT
113225242 TTTT-TATTTTTTTA-ATAT
1 TTTTATATTTTTTTACA-AT
113225260 TTTTATATTTTTTT-CTAAT
1 TTTTATATTTTTTTAC-AAT
113225279 TTTTA
1 TTTTA
113225284 ATAAATTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
17 1 0.02
18 13 0.26
19 35 0.70
20 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (19 bp):
TTTTATATTTTTTTACAAT
Found at i:113225231 original size:46 final size:48
Alignment explanation
Indices: 113225141--113225237 Score: 137
Period size: 46 Copynumber: 2.1 Consensus size: 48
113225131 TTTATGAAAC
*
113225141 TTATATTTCTTTATATTTTGTATAATTTTCTTACGACTTTATAAAATT
1 TTATATTTCTATATATTTTGTATAATTTTCTTACGACTTTATAAAATT
* *
113225189 TTATATTTCTATATA-TTT-TAT-ATTTTTTTACGATTTTTATAAAATT
1 TTATATTTCTATATATTTTGTATAATTTTCTTACGA-CTTTATAAAATT
113225235 TTA
1 TTA
113225238 CAATTTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 11 0.24
46 17 0.38
47 3 0.07
48 14 0.31
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (48 bp):
TTATATTTCTATATATTTTGTATAATTTTCTTACGACTTTATAAAATT
Found at i:113225307 original size:56 final size:57
Alignment explanation
Indices: 113225199--113225309 Score: 131
Period size: 56 Copynumber: 2.0 Consensus size: 57
113225189 TTATATTTCT
* **
113225199 ATATATTTTATATTTTTTTACGATTTTTATAAAATTTTACAATTTTTTATTTTTTTA
1 ATATATTTTATATTTTTTTACAATTTTTATAAAATTTTACAATTTTGAATTTTTTTA
*
113225256 ATAT-TTTTATATTTTTTT-CTAATTTTTA-ATAAATTTT-TAATATTTGAATTTTTT
1 ATATATTTTATATTTTTTTAC-AATTTTTATA-AAATTTTACAAT-TTTGAATTTTTT
113225310 AATTAAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
55 5 0.11
56 38 0.81
57 4 0.09
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.66
Consensus pattern (57 bp):
ATATATTTTATATTTTTTTACAATTTTTATAAAATTTTACAATTTTGAATTTTTTTA
Found at i:113225561 original size:91 final size:90
Alignment explanation
Indices: 113225388--113225595 Score: 239
Period size: 90 Copynumber: 2.3 Consensus size: 90
113225378 ATAAAAGCAA
* * * * *
113225388 GGGCTTAATTACTTTTTTTGAAAAAAGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTA
1 GGGCTTAATTACTTTTTTTGAAAAAAGTTTGAGGGCCTTTTTAATACATTTTAAAAGCTCAAGTA
* **
113225453 TCCAATTGAGGGTAAAAAAAAAGTAG
66 CCCAA-TGAAAGTAAAAAAAAAGTAG
*
113225479 GGGCTTAATTACTTTTTTTGAAAAGA-TTTGAGGGCCTTTTTAATACATTTTAAAAGCTCAAGTA
1 GGGCTTAATTACTTTTTTTGAAAAAAGTTTGAGGGCCTTTTTAATACATTTTAAAAGCTCAAGTA
113225543 CCCAA-GAAAGTACAAAAAAAA--A-
66 CCCAATGAAAGTA-AAAAAAAAGTAG
* *
113225565 -GACTTAATTGCCTTTTTTTGTAAAAAAGTTT
1 GGGCTTAATT-ACTTTTTTTG-AAAAAAGTTT
113225596 AAAAGCTTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
85 8 0.08
86 9 0.09
87 6 0.06
88 8 0.08
89 8 0.08
90 37 0.37
91 25 0.25
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (90 bp):
GGGCTTAATTACTTTTTTTGAAAAAAGTTTGAGGGCCTTTTTAATACATTTTAAAAGCTCAAGTA
CCCAATGAAAGTAAAAAAAAAGTAG
Found at i:113233792 original size:22 final size:24
Alignment explanation
Indices: 113233749--113233792 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
113233739 TGATAATATG
113233749 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
*
113233773 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
113233793 TGAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:113240608 original size:17 final size:19
Alignment explanation
Indices: 113240566--113240609 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
113240556 ATGAAATTTT
*
113240566 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
113240585 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
113240603 AA-TATTA
1 AATTATTA
113240610 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:113242913 original size:28 final size:27
Alignment explanation
Indices: 113242822--113242934 Score: 77
Period size: 28 Copynumber: 3.9 Consensus size: 27
113242812 ACTTGTAATA
*
113242822 GGGCTACGGCCCAGATTGATACTGATAT
1 GGGCTA-GGCCCAGATTAATACTGATAT
** *
113242850 GGGCTAGGCCCAGTATACTCTGTTACTG-TAAG
1 GGGCTAGGCCCAG---A-T-TAATACTGAT-AT
113242882 GGGCTATGGCCCAGATTAATACTGATAT
1 GGGCTA-GGCCCAGATTAATACTGATAT
* *
113242910 GGGCTAAGGCCTAG-TTAACACTGAT
1 GGGCT-AGGCCCAGATTAATACTGAT
113242935 TTCTAAATAG
Statistics
Matches: 69, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
27 17 0.25
28 24 0.35
29 3 0.04
30 2 0.03
31 2 0.03
32 14 0.20
33 7 0.10
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (27 bp):
GGGCTAGGCCCAGATTAATACTGATAT
Found at i:113244318 original size:29 final size:31
Alignment explanation
Indices: 113244277--113244341 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 31
113244267 GCCTAATGTG
* *
113244277 CAATCATATACAC-AAACTTTAATTTT-GTT
1 CAATTATATACACAAAACTTTAATTTTAATT
113244306 CAATTATATACACAAAACTTTAATTTTAATT
1 CAATTATATACACAAAACTTTAATTTTAATT
113244337 CAATT
1 CAATT
113244342 TGCCCGTACC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 12 0.38
30 13 0.41
31 7 0.22
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.42
Consensus pattern (31 bp):
CAATTATATACACAAAACTTTAATTTTAATT
Found at i:113254510 original size:26 final size:26
Alignment explanation
Indices: 113254471--113254578 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
113254461 TGGTACAAAT
113254471 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
113254497 TTATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
113254523 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
113254549 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
113254575 TGAT
1 TGAT
113254579 GGCCATTTCA
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:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:113256114 original size:26 final size:26
Alignment explanation
Indices: 113256062--113256114 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
113256052 TTTACAGTTT
*
113256062 TACCCCTAGGAGATAAATTATCGAAA
1 TACCCCTAGGAGATAAATTACCGAAA
* *
113256088 TACCCCTAGG-GTTAAATTGACCTAAA
1 TACCCCTAGGAGATAAATT-ACCGAAA
113256114 T
1 T
113256115 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGAGATAAATTACCGAAA
Found at i:113260319 original size:26 final size:26
Alignment explanation
Indices: 113260290--113260365 Score: 143
Period size: 26 Copynumber: 2.9 Consensus size: 26
113260280 TTGATTAAAA
*
113260290 GGTTAGGTAAATGTTCCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATG
113260316 GGTTAGGTAAATGTTTCATGATAATG
1 GGTTAGGTAAATGTTTCATGATAATG
113260342 GGTTAGGTAAATGTTTCATGATAA
1 GGTTAGGTAAATGTTTCATGATAA
113260366 GAATTTCATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (26 bp):
GGTTAGGTAAATGTTTCATGATAATG
Found at i:113261890 original size:20 final size:20
Alignment explanation
Indices: 113261865--113261906 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
113261855 CATGTTTGAC
*
113261865 TGTTGTTTTTA-CTGCATGCA
1 TGTTGTTATTATCTG-ATGCA
113261885 TGTTGTTATTATCTGATGCA
1 TGTTGTTATTATCTGATGCA
113261905 TG
1 TG
113261907 GGACTGGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.17, C:0.12, G:0.21, T:0.50
Consensus pattern (20 bp):
TGTTGTTATTATCTGATGCA
Found at i:113264148 original size:40 final size:40
Alignment explanation
Indices: 113264040--113264249 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
113264030 CGGGATTTAA
* * * * *
113264040 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
113264080 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
113264120 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
113264160 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
113264200 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
113264240 CCGGATATAT
1 CCGGATATAT
113264250 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:113272283 original size:40 final size:40
Alignment explanation
Indices: 113272175--113272384 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
113272165 CGGGATTTAA
* * * * *
113272175 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
113272215 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
113272255 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
113272295 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
113272335 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
113272375 CCGGATATAT
1 CCGGATATAT
113272385 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:113274894 original size:33 final size:33
Alignment explanation
Indices: 113274857--113274926 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
113274847 ATAATAAATT
* *
113274857 ATATTTAAATAATTTAATATAATTATACATGAA
1 ATATTTAAATAATTTAATATAATAATACATAAA
*
113274890 ATATTTAAATAATTTAATTTAATAATACATAAA
1 ATATTTAAATAATTTAATATAATAATACATAAA
113274923 ATAT
1 ATAT
113274927 AAATTAATCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (33 bp):
ATATTTAAATAATTTAATATAATAATACATAAA
Found at i:113276484 original size:17 final size:18
Alignment explanation
Indices: 113276464--113276497 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
113276454 AAAGGTTTTA
*
113276464 TTAA-TATAAACAATAAC
1 TTAATTATAAAAAATAAC
113276481 TTAATTATAAAAAATAA
1 TTAATTATAAAAAATAA
113276498 AATATTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (18 bp):
TTAATTATAAAAAATAAC
Found at i:113276926 original size:26 final size:24
Alignment explanation
Indices: 113276886--113276945 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
113276876 TTATTTCATT
* * *
113276886 AAATAAAAAAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
113276910 TAAATCAAATATATTTAAAAACATAA
1 -AAAT-AAATATATTTAAAAACATAA
113276936 AAATAAATAT
1 AAATAAATAT
113276946 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:113276957 original size:22 final size:22
Alignment explanation
Indices: 113276916--113276974 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
113276906 ATAATAAATC
* *
113276916 AAATATAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
113276936 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
113276958 AAAT-AATACTAAAACAA
1 AAATAAATATTAAAACAA
113276975 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 18 0.53
22 9 0.26
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:113277051 original size:15 final size:16
Alignment explanation
Indices: 113277021--113277053 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
113277011 AAATAGTTAT
113277021 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
113277038 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
113277053 A
1 A
113277054 AAAATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:113284160 original size:20 final size:20
Alignment explanation
Indices: 113284135--113284175 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
113284125 GATCAAATTA
113284135 TGATTTTGATCTCTAATGTT
1 TGATTTTGATCTCTAATGTT
113284155 TGATTTTGATCTCTAATGTT
1 TGATTTTGATCTCTAATGTT
113284175 T
1 T
113284176 AAATTCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.56
Consensus pattern (20 bp):
TGATTTTGATCTCTAATGTT
Found at i:113286188 original size:13 final size:13
Alignment explanation
Indices: 113286170--113286198 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
113286160 ATCTTGCTTA
113286170 GTCCTAAACTTGT
1 GTCCTAAACTTGT
113286183 GTCCTAAACTTGT
1 GTCCTAAACTTGT
113286196 GTC
1 GTC
113286199 GTGCTGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (13 bp):
GTCCTAAACTTGT
Found at i:113287122 original size:16 final size:17
Alignment explanation
Indices: 113287097--113287133 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
113287087 AACTCGTTAG
*
113287097 AAAAAGAAAAG-GAAAA
1 AAAAAAAAAAGAGAAAA
113287113 AAAAAAAAAAGAGAAAA
1 AAAAAAAAAAGAGAAAA
113287130 AAAA
1 AAAA
113287134 GAAGCTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAGAAAA
Found at i:113291488 original size:32 final size:32
Alignment explanation
Indices: 113291452--113291514 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
113291442 CCTAATTTGG
*
113291452 GTTGCCAACACTTTTATAAATAAGACATTAGA
1 GTTGCCAACACTTCTATAAATAAGACATTAGA
113291484 GTTGCCAACACTTCTATAAATAAGACATTAG
1 GTTGCCAACACTTCTATAAATAAGACATTAG
113291515 GGGTTTGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (32 bp):
GTTGCCAACACTTCTATAAATAAGACATTAGA
Found at i:113300766 original size:40 final size:40
Alignment explanation
Indices: 113300672--113300816 Score: 202
Period size: 40 Copynumber: 3.6 Consensus size: 40
113300662 TACTCGAATG
*
113300672 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
113300713 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
113300753 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
*
113300793 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
113300817 CTTGTGCGAG
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 63 0.68
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:113306649 original size:29 final size:28
Alignment explanation
Indices: 113306615--113306718 Score: 109
Period size: 29 Copynumber: 3.6 Consensus size: 28
113306605 TACTCGATCA
* *
113306615 CGCACACTTAGTGCCATGTGATTTAAGCC
1 CGCACACTTAGTGCCATAT-ATTTAAGCT
* * * *
113306644 CGCACACATAGTGCCGTACAATTTGAGCT
1 CGCACACTTAGTGCCATA-TATTTAAGCT
*
113306673 CGCACACTTAGTGCCATATATTTCCAGCT
1 CGCACACTTAGTGCCATATATTT-AAGCT
*
113306702 TGCACACTTAGTGCCAT
1 CGCACACTTAGTGCCAT
113306719 TCTCGTCACC
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
28 4 0.06
29 58 0.94
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTTAAGCT
Found at i:113320793 original size:27 final size:27
Alignment explanation
Indices: 113320740--113320797 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
113320730 AAATATAAAT
* *
113320740 ATTA-TAAAATAATTATTTTGTACTTAA
1 ATTATTAAAATAATTAATTTGTAATT-A
*
113320767 ATTATTAACATAATTAATTT-TAATTA
1 ATTATTAAAATAATTAATTTGTAATTA
113320793 ATTAT
1 ATTAT
113320798 AATAAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.22
27 8 0.30
28 13 0.48
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (27 bp):
ATTATTAAAATAATTAATTTGTAATTA
Found at i:113320805 original size:20 final size:20
Alignment explanation
Indices: 113320776--113320815 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
113320766 AATTATTAAC
*
113320776 ATAATTAATTTTAATTAATT
1 ATAATAAATTTTAATTAATT
*
113320796 ATAATAAATTTTGATTAATT
1 ATAATAAATTTTAATTAATT
113320816 CTGATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
ATAATAAATTTTAATTAATT
Found at i:113320822 original size:10 final size:10
Alignment explanation
Indices: 113320777--113320815 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
113320767 ATTATTAACA
113320777 TAATTAATTT
1 TAATTAATTT
*
113320787 TAATTAATTA
1 TAATTAATTT
*
113320797 TAATAAATTT
1 TAATTAATTT
*
113320807 TGATTAATT
1 TAATTAATT
113320816 CTGATTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (10 bp):
TAATTAATTT
Found at i:113323673 original size:27 final size:27
Alignment explanation
Indices: 113323635--113323895 Score: 292
Period size: 27 Copynumber: 9.7 Consensus size: 27
113323625 GGCATTTGGT
*
113323635 TAGCCTCTATGGCGAACTCTGAAAGAA
1 TAGCCTTTATGGCGAACTCTGAAAGAA
* *
113323662 TAGCCTTTATGGCAAACTTTGAAAGAA
1 TAGCCTTTATGGCGAACTCTGAAAGAA
*
113323689 TATCCTTTATGGCGAACTCTGAAAGAA
1 TAGCCTTTATGGCGAACTCTGAAAGAA
*
113323716 TAG-CTTCTGTGGC-AAGCTCTGAAAGAA
1 TAGCCTT-TATGGCGAA-CTCTGAAAGAA
* * * *
113323743 TAGGCTTTGTGGCGAAATTTGAAAGAA
1 TAGCCTTTATGGCGAACTCTGAAAGAA
* * *
113323770 TATCCTTTATGGTGAACTCTAAAAGAA
1 TAGCCTTTATGGCGAACTCTGAAAGAA
* * * *
113323797 TATCCTCTGTGGCGAACACTGAAAGAA
1 TAGCCTTTATGGCGAACTCTGAAAGAA
* * * * *
113323824 TAACCTCTGTGGCGAAATCTAAAAGAA
1 TAGCCTTTATGGCGAACTCTGAAAGAA
*
113323851 TATCCTTTATGGCGAACTCTGAAAGAA
1 TAGCCTTTATGGCGAACTCTGAAAGAA
113323878 TAGCCTTTATGGCGAACT
1 TAGCCTTTATGGCGAACT
113323896 GTAACATCCC
Statistics
Matches: 198, Mismatches: 32, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
26 5 0.03
27 188 0.95
28 5 0.03
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (27 bp):
TAGCCTTTATGGCGAACTCTGAAAGAA
Found at i:113323787 original size:81 final size:81
Alignment explanation
Indices: 113323635--113323895 Score: 364
Period size: 81 Copynumber: 3.2 Consensus size: 81
113323625 GGCATTTGGT
* *
113323635 TAGCCTCTATGGCGAACTCTGAAAGAATAGCCTTTATGGC-AAACTTTGAAAGAATATCCTTTAT
1 TAGCCTCTGTGGCGAACTCTGAAAGAATAGCCTTTGTGGCGAAA-TTTGAAAGAATATCCTTTAT
113323699 GGCGAACTCTGAAAGAA
65 GGCGAACTCTGAAAGAA
* *
113323716 TAGCTTCTGTGGC-AAGCTCTGAAAGAATAGGCTTTGTGGCGAAATTTGAAAGAATATCCTTTAT
1 TAGCCTCTGTGGCGAA-CTCTGAAAGAATAGCCTTTGTGGCGAAATTTGAAAGAATATCCTTTAT
* *
113323780 GGTGAACTCTAAAAGAA
65 GGCGAACTCTGAAAGAA
* * * * * *
113323797 TATCCTCTGTGGCGAACACTGAAAGAATAACCTCTGTGGCGAAATCTAAAAGAATATCCTTTATG
1 TAGCCTCTGTGGCGAACTCTGAAAGAATAGCCTTTGTGGCGAAATTTGAAAGAATATCCTTTATG
113323862 GCGAACTCTGAAAGAA
66 GCGAACTCTGAAAGAA
* *
113323878 TAGCCTTTATGGCGAACT
1 TAGCCTCTGTGGCGAACT
113323896 GTAACATCCC
Statistics
Matches: 157, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
80 2 0.01
81 150 0.96
82 5 0.03
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (81 bp):
TAGCCTCTGTGGCGAACTCTGAAAGAATAGCCTTTGTGGCGAAATTTGAAAGAATATCCTTTATG
GCGAACTCTGAAAGAA
Found at i:113326432 original size:80 final size:80
Alignment explanation
Indices: 113326292--113326498 Score: 222
Period size: 80 Copynumber: 2.6 Consensus size: 80
113326282 CGGAATACAA
* * *
113326292 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCTGGATAGATCGACTTGCACAAATG
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGATCGACTAGCACAAATG
113326357 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAGC
* * * *
113326372 CCGGATTTAACAACTTGCACGGATGCCTTCGGGTCTTAGCCCGGAT-GTAGTC-ACTAGCACAAT
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAG-A-TCGACTAGCACAAA
* *
113326435 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAGC
* ** ** * *
113326452 TCGGATATAATTAC-TAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACAT-GCACGAATGCCTTCGGGTCTTAGCCCGGATA
113326499 TCATTCAATT
Statistics
Matches: 105, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
79 2 0.02
80 101 0.96
81 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (80 bp):
CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGATCGACTAGCACAAATG
CCTTCGGGTATTAGC
Found at i:113326457 original size:40 final size:40
Alignment explanation
Indices: 113326292--113326499 Score: 170
Period size: 40 Copynumber: 5.2 Consensus size: 40
113326282 CGGAATACAA
* * *
113326292 CCGGATATAACCAC-ATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTA-GCACAAATGCCTTCGGGTCTTAAC
* * * * *
113326332 CTGGATA-GATCGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
* * ** *
113326372 CCGGATTTAA-CAACTTGCACGGATGCCTTCGGGTCTTAGC
1 CCGGATATAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
* * *
113326412 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * * * *
113326452 TCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAAC
113326492 CCGGATAT
1 CCGGATAT
113326500 CATTCAATTG
Statistics
Matches: 134, Mismatches: 30, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
39 2 0.01
40 130 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:113326686 original size:125 final size:125
Alignment explanation
Indices: 113326464--113326806 Score: 602
Period size: 125 Copynumber: 2.8 Consensus size: 125
113326454 GGATATAATT
* *
113326464 ACTAGCATAAAT-GTCTTCGGGACTTAGCCCGGATATCATTCAATTGCTCATGCACACATATACA
1 ACTAGCAT-AATCGCCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATATACA
* *
113326528 TCAATAATCATTACACATCCATATTTCCTTTTCGTTACTGAGGCTCAAACACAAACATATC
65 TCAATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
113326589 ACTAGCATAATCGCCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATATACAT
1 ACTAGCATAATCGCCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATATACAT
* *
113326654 CAATGATCATTACACATCCATGTTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
66 CAATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
113326714 ACTAGCATAATCGCCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATA-A-AT
1 ACTAGCATAATCGCCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATATACAT
113326777 CAATAATCATTACACATCCATATTTCATTT
66 CAATAATCATTACACATCCATATTTCATTT
113326807 CACATAATTC
Statistics
Matches: 209, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
123 30 0.14
124 4 0.02
125 175 0.84
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (125 bp):
ACTAGCATAATCGCCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATATACAT
CAATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
Found at i:113334497 original size:40 final size:40
Alignment explanation
Indices: 113334452--113334659 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 40
113334442 CGGAATACAA
*
113334452 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* * * * *
113334492 CCGGATAGATCGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* *
113334532 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
* ** * * *
113334572 CCGGATGTAGTCACTAGCAC-AATTGCCTTTGGGTCTTAAC
1 CCGGATATAACCACTTGCACGAA-TGCCTTCGGGTCTTAGC
** * ** * *
113334612 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
*
113334652 TCGGATAT
1 CCGGATAT
113334660 CATTCAATTG
Statistics
Matches: 138, Mismatches: 28, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
39 2 0.01
40 134 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAACCACTTGCACGAATGCCTTCGGGTCTTAGC
Found at i:113334592 original size:80 final size:80
Alignment explanation
Indices: 113334452--113334621 Score: 236
Period size: 80 Copynumber: 2.1 Consensus size: 80
113334442 CGGAATACAA
* *
113334452 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGATCGACTTGCACAAATG
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGATCGACTAGCACAAATG
*
113334517 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
* * *
113334532 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTAGTC-ACTAGCACAAT
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAG-A-TCGACTAGCACAAA
* *
113334595 TGCCTTTGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
113334612 CCGGATATAA
1 CCGGATATAA
113334622 TTACTAGCAT
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
79 1 0.01
80 76 0.96
81 2 0.03
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (80 bp):
CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGATCGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:113334846 original size:125 final size:125
Alignment explanation
Indices: 113334624--113334966 Score: 602
Period size: 125 Copynumber: 2.8 Consensus size: 125
113334614 GGATATAATT
* * *
113334624 ACTAGCATAAAT-GTCTTCGGGACTTAGCTCGGATATCATTCAATTGCTCATGCACACATATACA
1 ACTAGCAT-AATCGCCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATATACA
*
113334688 TCAATAATCATTACACATCCATATTTCATTTTCGTTACTGAGGCTCAAACACAAACATATC
65 TCAATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
113334749 ACTAGCATAATCGCCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATATACAT
1 ACTAGCATAATCGCCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATATACAT
* *
113334814 CAATGATCATTACACATCCATGTTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
66 CAATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
113334874 ACTAGCATAATCGCCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATA-A-AT
1 ACTAGCATAATCGCCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATATACAT
113334937 CAATAATCATTACACATCCATATTTCATTT
66 CAATAATCATTACACATCCATATTTCATTT
113334967 CACATAATTC
Statistics
Matches: 209, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
123 30 0.14
124 4 0.02
125 175 0.84
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (125 bp):
ACTAGCATAATCGCCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATATACAT
CAATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
Found at i:113338699 original size:27 final size:27
Alignment explanation
Indices: 113338661--113339017 Score: 345
Period size: 27 Copynumber: 13.2 Consensus size: 27
113338651 CAAATCCCTT
*
113338661 AACTCTGAAAGAATAACCTTTGTGGTG
1 AACTCTGAAAGAATAGCCTTTGTGGTG
* * * *
113338688 AACTCTGAAAGAATAACCTCTATGCTG
1 AACTCTGAAAGAATAGCCTTTGTGGTG
* * * * *
113338715 AACTCTGAACGAATATCCTCTATGATG
1 AACTCTGAAAGAATAGCCTTTGTGGTG
* * * * * **
113338742 AACTTTGAAAGAATATCCTCTATAGCA
1 AACTCTGAAAGAATAGCCTTTGTGGTG
*
113338769 AACTCTGAAAGAATAGCCTTTGTGGCG
1 AACTCTGAAAGAATAGCCTTTGTGGTG
* * *
113338796 AACACTGAAAGAATATCCTTTGTGGCG
1 AACTCTGAAAGAATAGCCTTTGTGGTG
* *
113338823 AACTCTGAAAGAATATCCTTTGTGGCG
1 AACTCTGAAAGAATAGCCTTTGTGGTG
*
113338850 AACTCTGAAAGAATAGCCTTTGTGGCG
1 AACTCTGAAAGAATAGCCTTTGTGGTG
**
113338877 AACTCTGAAAGAATAGCCTTCATGGTG
1 AACTCTGAAAGAATAGCCTTTGTGGTG
* * *
113338904 AATTCTAAAAGAATAGCCTTTGTGGTA
1 AACTCTGAAAGAATAGCCTTTGTGGTG
* * * *
113338931 AATTCTGAAAAAATAGCCTCTATGGTG
1 AACTCTGAAAGAATAGCCTTTGTGGTG
* ** * ***
113338958 AACTCTAAAAGAATAGTTTTTATGACA
1 AACTCTGAAAGAATAGCCTTTGTGGTG
*
113338985 AACTCTGAAAGAATAACCTTTGTGGTG
1 AACTCTGAAAGAATAGCCTTTGTGGTG
113339012 AACTCT
1 AACTCT
113339018 AAATGGACTA
Statistics
Matches: 278, Mismatches: 52, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 278 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (27 bp):
AACTCTGAAAGAATAGCCTTTGTGGTG
Found at i:113341949 original size:19 final size:19
Alignment explanation
Indices: 113341908--113341952 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
113341898 TAAACTTTTT
*
113341908 TAATTATAATTAAGTTAGT
1 TAATTATAATTAAGTTAGC
*
113341927 TAATTATATTTAA-TTAGAC
1 TAATTATAATTAAGTTAG-C
113341946 TAATTAT
1 TAATTAT
113341953 TGATTAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (19 bp):
TAATTATAATTAAGTTAGC
Found at i:113342907 original size:22 final size:22
Alignment explanation
Indices: 113342882--113342932 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
113342872 CATTTCTTTT
**
113342882 CTCTCT-TATTAACACTTTAGTG
1 CTCTCTGT-TTAACACTACAGTG
*
113342904 CTCTCTGTTTAGCACTACAGTG
1 CTCTCTGTTTAACACTACAGTG
113342926 CTCTCTG
1 CTCTCTG
113342933 ATGTGGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.18, C:0.27, G:0.14, T:0.41
Consensus pattern (22 bp):
CTCTCTGTTTAACACTACAGTG
Found at i:113351710 original size:6 final size:6
Alignment explanation
Indices: 113351699--113351751 Score: 70
Period size: 6 Copynumber: 8.3 Consensus size: 6
113351689 TGCCAACCGA
*
113351699 CCCCTT CCCCTT CCCCTTT CCCCTT CCCCTT CCCCCTT CCCCCTT CCCTTT
1 CCCCTT CCCCTT CCCC-TT CCCCTT CCCCTT -CCCCTT -CCCCTT CCCCTT
113351750 CC
1 CC
113351752 TTTCTCTTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
6 25 0.57
7 19 0.43
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CCCCTT
Found at i:113351721 original size:13 final size:13
Alignment explanation
Indices: 113351699--113351751 Score: 72
Period size: 13 Copynumber: 4.2 Consensus size: 13
113351689 TGCCAACCGA
113351699 CCCC-TTCCCCTT
1 CCCCTTTCCCCTT
113351711 CCCCTTTCCCCTT
1 CCCCTTTCCCCTT
*
113351724 CCCCTTCCCCCTT
1 CCCCTTTCCCCTT
* *
113351737 CCCCCTTCCCTTT
1 CCCCTTTCCCCTT
113351750 CC
1 CC
113351752 TTTCTCTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
12 4 0.11
13 32 0.89
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (13 bp):
CCCCTTTCCCCTT
Found at i:113351723 original size:19 final size:19
Alignment explanation
Indices: 113351699--113351751 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
113351689 TGCCAACCGA
*
113351699 CCCCTTCCCCTTCCCCTTT
1 CCCCTTCCCCTTCCCCTTC
113351718 CCCCTTCCCCTTCCCCCTTC
1 CCCCTTCCCCTT-CCCCTTC
*
113351738 CCCCTTCCCTTTCC
1 CCCCTTCCCCTTCC
113351752 TTTCTCTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (19 bp):
CCCCTTCCCCTTCCCCTTC
Found at i:113351762 original size:24 final size:24
Alignment explanation
Indices: 113351735--113351810 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
113351725 CCCTTCCCCC
113351735 TTCCCCCTTCCCTTTCCTTTCTCT
1 TTCCCCCTTCCCTTTCCTTTCTCT
** *
113351759 TTCCTTCTT-CCTCATCCTTTCTTCT
1 TTCCCCCTTCCCT-TTCCTTTC-TCT
* *
113351784 TT-TCCCTTCCCTTTCTTTTCTCCT
1 TTCCCCCTTCCCTTTCCTTTCT-CT
113351808 TTC
1 TTC
113351811 ACCTTCTTCC
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
23 4 0.10
24 27 0.69
25 8 0.21
ACGTcount: A:0.01, C:0.43, G:0.00, T:0.55
Consensus pattern (24 bp):
TTCCCCCTTCCCTTTCCTTTCTCT
Found at i:113353829 original size:47 final size:46
Alignment explanation
Indices: 113353729--113353946 Score: 225
Period size: 47 Copynumber: 4.7 Consensus size: 46
113353719 TATACGTGTT
* *
113353729 GATGCATGTCCC-GAACATGTCTTACACTAGCAC-GACTC-TTA-GCA
1 GATGCATGTCCCAG-ACATGTCTTACACTGGCACTCA-TCATTAGGCA
* *
113353773 GATGCATGTCCCAGACACGTCTTACACTGGCTA-TCATCATTGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGC-ACTCATCATT-AGGCA
* *
113353820 GATGCATGTCCCAGACATGTCTTACACTGGCACTCATC-TCTACGCG
1 GATGCATGTCCCAGACATGTCTTACACTGGCACTCATCAT-TAGGCA
* * *
113353866 GATGCCATGTCCCAGACATGGTCTTACACTAGCACTCAT-AATATGGAA
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCATCATTA-GGCA
*
113353914 GATGCATGTCCCAGACATGTGTTACACTGGCAC
1 GATGCATGTCCCAGACATGTCTTACACTGGCAC
113353947 ACAAGAAATC
Statistics
Matches: 148, Mismatches: 14, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
44 29 0.20
45 5 0.03
46 23 0.16
47 68 0.46
48 23 0.16
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCACTCATCATTAGGCA
Found at i:113353838 original size:91 final size:94
Alignment explanation
Indices: 113353676--113353949 Score: 267
Period size: 94 Copynumber: 2.9 Consensus size: 94
113353666 GGGATAAGTT
* * * * ** * **
113353676 GCAGATGCCATGTCCCAGACATGGTCCTATACTAGCTCTTGTATATACGTGTTGATGCATGTCCC
1 GCAGATGCCATGTCCCAGACATCGTCTTACACTAGCACTCATA-ATATG-GAAGATGCATGTCCC
*
113353741 -GAACATGTCTTACACTAGCACGAC-TCT-TA-
64 AG-ACATGTCTTACACTGGCAC-ACATCTCTAC
* * **
113353770 GCAGATG-CATGTCCCAGACA-CGTCTTACACTGGCTA-TCATCAT-TGAGGCCGATGCATGTCC
1 GCAGATGCCATGTCCCAGACATCGTCTTACACTAGC-ACTCATAATAT--GGAAGATGCATGTCC
*
113353831 CAGACATGTCTTACACTGGCACTCATCTCTAC
63 CAGACATGTCTTACACTGGCACACATCTCTAC
* *
113353863 GCGGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATAATATGGAAGATGCATGTCCCAG
1 GCAGATGCCATGTCCCAGACATCGTCTTACACTAGCACTCATAATATGGAAGATGCATGTCCCAG
*
113353928 ACATGTGTTACACTGGCACACA
66 ACATGTCTTACACTGGCACACA
113353950 AGAAATCCGA
Statistics
Matches: 148, Mismatches: 21, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
90 1 0.01
91 36 0.24
92 16 0.11
93 19 0.13
94 57 0.39
95 18 0.12
96 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (94 bp):
GCAGATGCCATGTCCCAGACATCGTCTTACACTAGCACTCATAATATGGAAGATGCATGTCCCAG
ACATGTCTTACACTGGCACACATCTCTAC
Found at i:113361268 original size:47 final size:45
Alignment explanation
Indices: 113361207--113361383 Score: 203
Period size: 47 Copynumber: 3.8 Consensus size: 45
113361197 ACGACTCTTA
* * *
113361207 GCCGATGCAGGTCCCAGACACGTCTTACACTGGCTATCGTCAT-CGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC-A-C-TCATATGAG
* *
113361254 GCCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATATTTAA
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATA-TGAG
* *
113361300 GCCGATGTCATGTCCTAGACATGGTCTTACACTGGCACTCATAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCAT-ATGAG
* *
113361348 GCTGATGCATGTCCCAGACATGTGTTACACTGGCAC
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCAC
113361384 ATAAGAAATC
Statistics
Matches: 113, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
44 4 0.04
45 1 0.01
46 23 0.20
47 58 0.51
48 26 0.23
49 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCACTCATATGAG
Found at i:113361359 original size:94 final size:91
Alignment explanation
Indices: 113361165--113361383 Score: 239
Period size: 94 Copynumber: 2.4 Consensus size: 91
113361155 ATATACGTGT
** *
113361165 TGATGCATGTCCC-GAACATGTCTTACACTACCACGACTCTTAGCCGATGCAGGTCCCAGACACG
1 TGATGCATGTCCCAG-ACATGTCTTACACTGGCACCACTCTTAGCCGATGCAGGTCCCAGACACG
* *
113361229 TCTTACACTGGCTATCGTCATCGAGGC
65 TCTTACACTGGCTATCATAATCGAGGC
* * * *
113361256 CGATGCATGTCCCAGACATGTCTTACACTGGCACTCA-TATTTAAGCCGATGTCATGTCCTAGAC
1 TGATGCATGTCCCAGACATGTCTTACACTGGCAC-CACT-CTT-AGCCGATG-CAGGTCCCAGAC
* *
113361320 ATGGTCTTACACTGGC-ACTCATAAT-GTGGC
62 A-CGTCTTACACTGGCTA-TCATAATCGAGGC
*
113361350 TGATGCATGTCCCAGACATGTGTTACACTGGCAC
1 TGATGCATGTCCCAGACATGTCTTACACTGGCAC
113361384 ATAAGAAATC
Statistics
Matches: 108, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
91 30 0.28
92 4 0.04
93 8 0.07
94 48 0.44
95 18 0.17
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (91 bp):
TGATGCATGTCCCAGACATGTCTTACACTGGCACCACTCTTAGCCGATGCAGGTCCCAGACACGT
CTTACACTGGCTATCATAATCGAGGC
Found at i:113368610 original size:18 final size:18
Alignment explanation
Indices: 113368587--113368624 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
113368577 GTATATCAGA
*
113368587 CTGGATTTAGGACTAGAT
1 CTGGATTCAGGACTAGAT
*
113368605 CTGGATTCAGGACTGGAT
1 CTGGATTCAGGACTAGAT
113368623 CT
1 CT
113368625 AAGAAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (18 bp):
CTGGATTCAGGACTAGAT
Found at i:113370290 original size:10 final size:8
Alignment explanation
Indices: 113370256--113370289 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
113370246 AAAAATGTTG
113370256 TATTT-TA
1 TATTTATA
113370263 TATTTATA
1 TATTTATA
113370271 TATTTATA
1 TATTTATA
*
113370279 TATTTAAA
1 TATTTATA
113370287 TAT
1 TAT
113370290 AAATTTAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTTATA
Found at i:113382699 original size:17 final size:16
Alignment explanation
Indices: 113382648--113382700 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
113382638 TTAAATTTAA
*
113382648 AAAATTATTAAAATCAT
1 AAAATTA-TAAAATTAT
113382665 AAAAATTATAAAAATTAT
1 -AAAATTAT-AAAATTAT
113382683 AAAATTATAAAACTTAT
1 AAAATTATAAAA-TTAT
113382700 A
1 A
113382701 TTAAAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 4 0.12
17 14 0.44
18 14 0.44
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATTATAAAATTAT
Found at i:113382700 original size:9 final size:9
Alignment explanation
Indices: 113382647--113382700 Score: 74
Period size: 9 Copynumber: 6.1 Consensus size: 9
113382637 TTTAAATTTA
113382647 AAAAATTAT
1 AAAAATTAT
* *
113382656 TAAAATCAT
1 AAAAATTAT
113382665 AAAAATTAT
1 AAAAATTAT
113382674 AAAAATTAT
1 AAAAATTAT
113382683 -AAAATTAT
1 AAAAATTAT
*
113382691 AAAACTTAT
1 AAAAATTAT
113382700 A
1 A
113382701 TTAAAAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
8 8 0.21
9 31 0.79
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:113382834 original size:10 final size:10
Alignment explanation
Indices: 113382814--113382867 Score: 58
Period size: 9 Copynumber: 5.3 Consensus size: 10
113382804 AAATTTATAA
113382814 TTTTA-AATT
1 TTTTATAATT
113382823 TTTTATAATTTT
1 TTTTATAA--TT
113382835 TTTTATAAATT
1 TTTTAT-AATT
113382846 TTTTATAA-T
1 TTTTATAATT
*
113382855 TTTTATGATT
1 TTTTATAATT
113382865 TTT
1 TTT
113382868 AAATAATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
9 13 0.33
10 8 0.21
11 8 0.21
12 8 0.21
13 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTTATAATT
Found at i:113382837 original size:11 final size:11
Alignment explanation
Indices: 113382821--113382858 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
113382811 TAATTTTAAA
113382821 TTTTTTATAATT
1 TTTTTTATAA-T
*
113382833 TTTTTTATAAA
1 TTTTTTATAAT
113382844 TTTTTTATAAT
1 TTTTTTATAAT
113382855 TTTT
1 TTTT
113382859 ATGATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTTATAAT
Found at i:113382845 original size:13 final size:12
Alignment explanation
Indices: 113382821--113382858 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
113382811 TAATTTTAAA
113382821 TTTTTTATAATT
1 TTTTTTATAATT
*
113382833 TTTTTTATAA-A
1 TTTTTTATAATT
113382844 TTTTTTATAATT
1 TTTTTTATAATT
113382856 TTT
1 TTT
113382859 ATGATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTATAATT
Found at i:113400236 original size:18 final size:19
Alignment explanation
Indices: 113400207--113400242 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
113400197 GTGAAAAAAT
*
113400207 TGAAATTTAGGGATTTAAG
1 TGAAATTTAGGGAATTAAG
113400226 TGAAA-TTAGGGAATTAA
1 TGAAATTTAGGGAATTAA
113400243 TTTAGTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (19 bp):
TGAAATTTAGGGAATTAAG
Found at i:113410701 original size:44 final size:45
Alignment explanation
Indices: 113410586--113411131 Score: 264
Period size: 44 Copynumber: 11.9 Consensus size: 45
113410576 CATTATGGCG
* * * *
113410586 AATCTTATCTCCCTGAAGTTTCAGTGCAACAGATTAAAGCTACAAATTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC--C--A--GCA
* *
113410637 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTAAAGCCA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAGCA
* * * **
113410681 GATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAGCA
* * * * *
113410726 AATCTTATCTCTCTGAAGTTGCAATAGAGCAGATTAAAGCTA-TA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAGCA
* * * * * ** *
113410770 AACCTTATCACTCTGAAGTTGCAGTAGAGCAGGTTGAAA-TTA-CG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCCAGCA
* * * * * * * * ** **
113410814 AGTCTTATTTCTCTGAAGTTGTAATAGAGCAGACTGAAGATAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAGCA
* ** *
113410859 AATCTTATTTCCCTGAAGTTGCAGTGGAATAGATTAAAGCTACAAATTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC--C--A--GCA
* * * * *
113410910 AGTCTTATCTCCCTGAAGTTACGGTAGAGCAGATTAAAGCTA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAGCA
* * *** **
113410954 AACCTTATCTCCCTGAAGTTGCAATGGAGCA-AGTTAAAAATAAATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TT-AAAGCCAGCA
* ** * *
113411000 AATCTTATCTCCTTGAAGTTGCAGCAGAGCAGATTGAAGACAGGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-G---CA
* *
113411049 AATCTTATC-CCTCAGAAGTTGCAGTGGAGTAGATTAAAGCCA-CA
1 AATCTTATCTCC-CTGAAGTTGCAGTGGAGCAGATTAAAGCCAGCA
* * * * *
113411093 AGTAC-AATCTCCCTGAAGTTGCAATAGAGCAGTTTAAAG
1 AAT-CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
113411132 TGACAAATCC
Statistics
Matches: 379, Mismatches: 95, Indels: 49
0.72 0.18 0.09
Matches are distributed among these distances:
43 3 0.01
44 158 0.42
45 81 0.21
46 29 0.08
47 3 0.01
48 2 0.01
49 35 0.09
51 68 0.18
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Consensus pattern (45 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAGCA
Found at i:113410762 original size:89 final size:88
Alignment explanation
Indices: 113410633--113411266 Score: 382
Period size: 89 Copynumber: 7.0 Consensus size: 88
113410623 AGCTACAAAT
* * * * * *
113410633 TACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTAAAGCCACAGATCTTATCTCCCTGAA
1 TACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAA
*
113410698 GTTGCAGTGGAGTAGATTGAAGA
66 GTTGCAGTGGAGTAGATTGAAAA
* * * * *
113410721 TAGCAAATCTTATCTCTCTGAAGTTGCAATAGAGCAGATTAAAGCTATAAACCTTATCACTCTGA
1 TA-CAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATTAAAGCTACAAATCTTATCTCCCTGA
* * * *
113410786 AGTTGCAGTAGAGCAGGTTGAAAT
65 AGTTGCAGTGGAGTAGATTGAAAA
* * * * * * * * ** *
113410810 TACGAGTCTTATTTCTCTGAAGTTGTAATAGAGCAGACTGAAGATAGTGAATCTTATTTCCCTGA
1 TACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATTAAAGCTA-CAAATCTTATCTCCCTGA
*
113410875 AGTTGCAGTGGAATAGATTAAAGCTACAAA
65 AGTTGCAGTGGAGTAGATT---G--A-AAA
* * ** *
113410905 TTACAAGTCTTATCTCCCTGAAGTTACGGTAGAGCAGATTAAAGCTACAAACCTTATCTCCCTGA
1 -TACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATTAAAGCTACAAATCTTATCTCCCTGA
* * *
113410970 AGTTGCAATGGAGCA-AGTTAAAAA
65 AGTTGCAGTGGAGTAGA-TTGAAAA
* * **
113410994 TAAATAAATCTTATCTCCTTGAAGTTGCAGCAGAGCAGATTGAAGACAGGCTACAAATCTTATC-
1 T--ACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATT--A-A-A-GCTACAAATCTTATCT
* *
113411058 CCTCAGAAGTTGCAGTGGAGTAGATT-AAAGC
59 CC-CTGAAGTTGCAGTGGAGTAGATTGAAA-A
* * * * * **
113411089 CACAAGTAC-AATCTCCCTGAAGTTGCAATAGAGCAGTTTAAAG-TGACAAATCCTATAC-CTTT
1 TACAAAT-CTTATCTCCCTGAAGTTGCAATAGAGCAGATTAAAGCT-ACAAATCTTAT-CTCCCT
* * * *
113411151 GGAGTTACAGTGG-GTTGGATTAAATCAAA
63 GAAGTTGCAGTGGAG-TAGATT-GA--AAA
* * * * *** * * * * *
113411180 TCACAAATCTCATCTCCCTCAAATTACAGCGGAGCAGATTGAAGCTACGAGTCTTATCTCTCTAA
1 T-ACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATTAAAGCTACAAATCTTATCTCCCTGA
*
113411245 AGTTGCAGTGGAGTGGATTGAA
65 AGTTGCAGTGGAGTAGATTGAA
113411267 GCAACAAGAT
Statistics
Matches: 416, Mismatches: 97, Indels: 65
0.72 0.17 0.11
Matches are distributed among these distances:
87 2 0.00
88 67 0.16
89 107 0.26
90 35 0.08
91 4 0.01
92 61 0.15
93 32 0.08
94 9 0.02
95 62 0.15
96 37 0.09
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (88 bp):
TACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAA
GTTGCAGTGGAGTAGATTGAAAA
Found at i:113415801 original size:48 final size:48
Alignment explanation
Indices: 113415738--113415896 Score: 158
Period size: 48 Copynumber: 3.3 Consensus size: 48
113415728 TATTGCATCA
** * *
113415738 GCATCGATAAAAGATCCCGTATAAGACCACGTTTGGGACATGGCATTG
1 GCATCGATATGAGATCCCGTATAAGACCATGTCTGGGACATGGCATTG
* * * * * *
113415786 TCATC-AGTATGAGATCCCATCTAAGACCATATCTGGGATATGACATTG
1 GCATCGA-TATGAGATCCCGTATAAGACCATGTCTGGGACATGGCATTG
* * * *
113415834 GCATCGATATGAGGTCCCGTATAAGACGATGTCTGGGACATAGCATCG
1 GCATCGATATGAGATCCCGTATAAGACCATGTCTGGGACATGGCATTG
* *
113415882 GCACCGTTATGAGAT
1 GCATCGATATGAGAT
113415897 TTCATGTAAG
Statistics
Matches: 86, Mismatches: 23, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
47 1 0.01
48 84 0.98
49 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.25
Consensus pattern (48 bp):
GCATCGATATGAGATCCCGTATAAGACCATGTCTGGGACATGGCATTG
Found at i:113415893 original size:96 final size:95
Alignment explanation
Indices: 113415684--113415918 Score: 231
Period size: 96 Copynumber: 2.5 Consensus size: 95
113415674 TAAGAATATG
** * *
113415684 GCATCGGCATCAAAATGAAATCCCATATAAGACCATATTTGAGGTATTGCATCAGCATCGATAAA
1 GCATCGGCATCAGTATGAGATCCCATATAAGACCATATCTG-GGTATTGCATCAGCATCGATAAA
* *
113415749 AGATCCCGTATAAGACCACGTTTGGGACATG
65 AGATCCCGTATAAGACCACGTCTGGGACATA
* * * ** *
113415780 GCATTGTCATCAGTATGAGATCCCATCTAAGACCATATCTGGG-ATATGACATTGGCATCGATAT
1 GCATCGGCATCAGTATGAGATCCCATATAAGACCATATCTGGGTAT-TG-CATCAGCATCGATAA
* * * *
113415844 GAGGTCCCGTATAAGACGATGTCTGGGACATA
64 AAGATCCCGTATAAGACCACGTCTGGGACATA
* ** * *
113415876 GCATCGGCA-CCGTTATGAGATTTCATGTAAGACCATAGCTGGG
1 GCATCGGCATCAG-TATGAGATCCCATATAAGACCATATCTGGG
113415919 CTATAGGCTT
Statistics
Matches: 113, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
94 2 0.02
95 6 0.05
96 105 0.93
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (95 bp):
GCATCGGCATCAGTATGAGATCCCATATAAGACCATATCTGGGTATTGCATCAGCATCGATAAAA
GATCCCGTATAAGACCACGTCTGGGACATA
Found at i:113417227 original size:27 final size:26
Alignment explanation
Indices: 113417157--113417292 Score: 136
Period size: 27 Copynumber: 5.2 Consensus size: 26
113417147 GACGAAGTCT
*
113417157 CCAGATACAGATATTGCGGCAGAGCCA
1 CCAGAT-CAGATATTGTGGCAGAGCCA
*
113417184 CCA-A-AAGATATATGTGGCAGAGCCA
1 CCAGATCAGATAT-TGTGGCAGAGCCA
*
113417209 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGATCAGAT-ATTGTGGCAGAGCCA
*
113417236 TCAGGA-CAGATATATGTGGCAGAGCCA
1 CCA-GATCAGATAT-TGTGGCAGAGCCA
* *
113417263 CCA-ATCAAATAATTGTGGCATAGCCA
1 CCAGATCAGAT-ATTGTGGCAGAGCCA
113417289 CCAG
1 CCAG
113417293 GAAGCTTCCT
Statistics
Matches: 91, Mismatches: 9, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
24 6 0.07
25 16 0.18
26 23 0.25
27 42 0.46
28 4 0.04
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (26 bp):
CCAGATCAGATATTGTGGCAGAGCCA
Found at i:113417294 original size:53 final size:54
Alignment explanation
Indices: 113417189--113417294 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 54
113417179 AGCCACCAAA
* *
113417189 AGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCATCAGGAC
1 AGATATATGTGGCAGAGCCACCAGATCAAATAATTGTGGCATAGCCACCAGGAC
113417243 AGATATATGTGGCAGAGCCACCA-ATCAAATAATTGTGGCATAGCCACCAGGA
1 AGATATATGTGGCAGAGCCACCAGATCAAATAATTGTGGCATAGCCACCAGGA
113417295 AGCTTCCTCC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 27 0.54
54 23 0.46
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.20
Consensus pattern (54 bp):
AGATATATGTGGCAGAGCCACCAGATCAAATAATTGTGGCATAGCCACCAGGAC
Found at i:113418920 original size:26 final size:26
Alignment explanation
Indices: 113418890--113418971 Score: 164
Period size: 26 Copynumber: 3.2 Consensus size: 26
113418880 TGAAATTCCC
113418890 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
113418916 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
113418942 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
113418968 ATCA
1 ATCA
113418972 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:113421699 original size:6 final size:5
Alignment explanation
Indices: 113421644--113421714 Score: 106
Period size: 5 Copynumber: 13.6 Consensus size: 5
113421634 ATTGAGTCCA
*
113421644 TTTAT TTTAT TTTGT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTATT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T
113421695 TTTATT TTTATT TTTAT TTT
1 TTTA-T TTTA-T TTTAT TTT
113421715 CCTAGACCTC
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
5 46 0.73
6 17 0.27
ACGTcount: A:0.17, C:0.00, G:0.01, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:113423807 original size:44 final size:42
Alignment explanation
Indices: 113423737--113423895 Score: 128
Period size: 44 Copynumber: 3.7 Consensus size: 42
113423727 TATGTTTTAT
* *
113423737 CGTGTAAGACCACGTCCGAGACGTTGGCATCGACTTATGAATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-TT-TGAATTA
* *
113423781 CGTGTAAGACCACGTCTGGGATGTTGGCATCGTATTT-AATTT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCG-ATTTGAATTA
* * ** *
113423823 CTTGTAAGACC-CTGTCTGGGATAG-TGTTATTGATATTTG-ATTA
1 CGTGTAAGACCAC-GTCTGGGA-CGTTGGCATCG--ATTTGAATTA
* *
113423866 CATGTAAGACCACGTTTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
113423896 TGTACGAGCT
Statistics
Matches: 93, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
41 1 0.01
42 28 0.30
43 31 0.33
44 32 0.34
45 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATTTGAATTA
Found at i:113423886 original size:43 final size:42
Alignment explanation
Indices: 113423739--113423895 Score: 131
Period size: 43 Copynumber: 3.7 Consensus size: 42
113423729 TGTTTTATCG
* * * *
113423739 TGTAAGACCACGTCCGAGACGTTGGCATCG-ACTTATGAATTACG
1 TGTAAGACCACGTCTGGGATGTTGGCATCGTA-TT-T-AATTACA
* *
113423783 TGTAAGACCACGTCTGGGATGTTGGCATCGTATTTAATTTCT
1 TGTAAGACCACGTCTGGGATGTTGGCATCGTATTTAATTACA
** * *
113423825 TGTAAGACC-CTGTCTGGGATAG-TGTTATTGATATTTGATTACA
1 TGTAAGACCAC-GTCTGGGAT-GTTGGCATCG-TATTTAATTACA
* *
113423868 TGTAAGACCACGTTTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGATGTTGGCAT
113423896 TGTACGAGCT
Statistics
Matches: 92, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 29 0.32
43 31 0.34
44 30 0.33
45 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGATGTTGGCATCGTATTTAATTACA
Done.