Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 108 of 279
Found at i:34325501 original size:13 final size:13
Alignment explanation
Indices: 34325483--34325507 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34325473 GTTAACTTTT
34325483 ATATATTCATTTA
1 ATATATTCATTTA
34325496 ATATATTCATTT
1 ATATATTCATTT
34325508 CACATTTAAA
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATATATTCATTTA
Found at i:34326990 original size:11 final size:11
Alignment explanation
Indices: 34326976--34327015 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
34326966 AATAGTAAAA
34326976 AAAAAAACAAC
1 AAAAAAACAAC
34326987 AAAAAAACAAC
1 AAAAAAACAAC
34326998 AAAAAAAGCAA-
1 AAAAAAA-CAAC
34327009 AAAAAAA
1 AAAAAAA
34327016 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 25 0.89
12 3 0.11
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAC
Found at i:34326990 original size:14 final size:13
Alignment explanation
Indices: 34326972--34327018 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
34326962 GCAAAATAGT
34326972 AAAAAAAAAAACA
1 AAAAAAAAAAACA
*
34326985 ACAAAAAAACAACA
1 A-AAAAAAAAAACA
34326999 AAAAAAGCAAAAA-A
1 AAAAAA--AAAAACA
34327013 AAAAAA
1 AAAAAA
34327019 TTTTTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 6 0.21
14 19 0.66
15 4 0.14
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACA
Found at i:34330923 original size:47 final size:47
Alignment explanation
Indices: 34330854--34330944 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
34330844 ATTGCAATTC
* *
34330854 GATCTTCCTGATTTTCTTCGTTGTCCGATACTAAGTATAGATAGATT
1 GATCTCCCTGATTTTCTTCGTTGTCCAATACTAAGTATAGATAGATT
34330901 GATCTCCCTGATTTTCTTCGTTGTCCAATACTAAGTATAGATAG
1 GATCTCCCTGATTTTCTTCGTTGTCCAATACTAAGTATAGATAG
34330945 TATTCTTAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (47 bp):
GATCTCCCTGATTTTCTTCGTTGTCCAATACTAAGTATAGATAGATT
Found at i:34338341 original size:24 final size:27
Alignment explanation
Indices: 34338312--34338361 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
34338302 TTATATAAGA
34338312 GAAAATACT-A-TACA-TAGTTATACT
1 GAAAATACTAATTACAGTAGTTATACT
*
34338336 GAAAATAGTAATTACAGTAGTTATAC
1 GAAAATACTAATTACAGTAGTTATAC
34338362 AAAATATGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 1 0.05
26 4 0.18
27 9 0.41
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (27 bp):
GAAAATACTAATTACAGTAGTTATACT
Found at i:34342026 original size:351 final size:350
Alignment explanation
Indices: 34341384--34342084 Score: 1294
Period size: 351 Copynumber: 2.0 Consensus size: 350
34341374 CTTCCCAACA
34341384 TCCTTAATTTCTTATAAAAAGATCCAAAATCCACCTAAATTAATTCTAACAAAACCCAATCCCAA
1 TCCTTAATTTCTTATAAAAAGATCCAAAATCCACCTAAATTAATTCTAACAAAACCCAATCCCAA
34341449 AATAAATTTATCCATCACCAACCCAGATCAACGCTCGAACGTTGACTCGAGAATTTGGAACCGTT
66 AATAAATTTATCCATCACCAACCCAGATCAACGCTCGAACGTTGACTCGAGAATTTGGAACCGTT
*
34341514 AAAATTATAATTTTATAAAAGCTCCAATTCACAACAATAAATTATTATTATTATAGTTTTGTAAT
131 AAAATTATAATTTTATAAAAGCTCCAATTCACAACAATAAATTACTATTATTATAGTTTTGTAAT
*
34341579 TTTTAGGTAATTAATACATCAGAAGTCTAATGTTGATTGAAGATGATGATGAGAATGATAGATTG
196 TTTTAGGTAATTAATACATCAGAAGTCCAATGTTGATTGAAGATGATGATGAGAATGATAGATTG
34341644 AAGAAGAATACCCAGATAAAAGATGATGACAAGAATGATAAATTGCAACATAAGATTATAAATAA
261 AAGAAGAATACCCAGATAAAAGATGATGACAAGAATGATAAATTGCAACATAAGATTATAAATAA
*
34341709 AAAAATTAAATAGATTTGTAATATT
326 AAAAATTAAATAGACTTGTAATATT
*
34341734 TCCTTAATTTCTTATAAAAAGATCCAAAATCCACCTAAATTAATTCTAACAAAATCCAATCCCAA
1 TCCTTAATTTCTTATAAAAAGATCCAAAATCCACCTAAATTAATTCTAACAAAACCCAATCCCAA
* * * *
34341799 AATAAATTTATCCATCGCCAATCCAGATCAACGCTCGAACGTTGACTCGAGAATTTGGAGCTGTT
66 AATAAATTTATCCATCACCAACCCAGATCAACGCTCGAACGTTGACTCGAGAATTTGGAACCGTT
*
34341864 ACAAATTATAATTTTATAAAAGCTCCAATTCACAATAATAAATTACTATTATTATAGTTTTGTAA
131 A-AAATTATAATTTTATAAAAGCTCCAATTCACAACAATAAATTACTATTATTATAGTTTTGTAA
34341929 TTTTTAGGTAATTAATACATCAGAAGTCCAATGTTGATTGAAGATGATGATGAGAATGATAGATT
195 TTTTTAGGTAATTAATACATCAGAAGTCCAATGTTGATTGAAGATGATGATGAGAATGATAGATT
* *
34341994 GAAGAAGAATATCCAGATAAAAGATGATGACAAGAATGGTAAATTGCAACATAAGATTATAAATA
260 GAAGAAGAATACCCAGATAAAAGATGATGACAAGAATGATAAATTGCAACATAAGATTATAAATA
34342059 AAAAAATTAAATAGACTTGTAATATT
325 AAAAAATTAAATAGACTTGTAATATT
34342085 ATTAATATTG
Statistics
Matches: 339, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
350 126 0.37
351 213 0.63
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (350 bp):
TCCTTAATTTCTTATAAAAAGATCCAAAATCCACCTAAATTAATTCTAACAAAACCCAATCCCAA
AATAAATTTATCCATCACCAACCCAGATCAACGCTCGAACGTTGACTCGAGAATTTGGAACCGTT
AAAATTATAATTTTATAAAAGCTCCAATTCACAACAATAAATTACTATTATTATAGTTTTGTAAT
TTTTAGGTAATTAATACATCAGAAGTCCAATGTTGATTGAAGATGATGATGAGAATGATAGATTG
AAGAAGAATACCCAGATAAAAGATGATGACAAGAATGATAAATTGCAACATAAGATTATAAATAA
AAAAATTAAATAGACTTGTAATATT
Found at i:34346014 original size:43 final size:43
Alignment explanation
Indices: 34345967--34346089 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 43
34345957 TAACATGTAT
* *
34345967 CGATGCCACTGTCCCACACAGGGTCTTACACG-AAGTCG-ATTAA
1 CGATGCCACTGTCCCACACAAGGTCTTACACGTAA-TCGTAAT-A
* * * *
34346010 CGATGCCAATGTCTCACACATGGTTTTACACGTAATCGTAATA
1 CGATGCCACTGTCCCACACAAGGTCTTACACGTAATCGTAATA
* * *
34346053 CAATGCCACTGTCCCATACAAGGTCTTACATGTAATC
1 CGATGCCACTGTCCCACACAAGGTCTTACACGTAATC
34346090 ACATCTCAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
43 62 0.94
44 4 0.06
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (43 bp):
CGATGCCACTGTCCCACACAAGGTCTTACACGTAATCGTAATA
Found at i:34347434 original size:30 final size:30
Alignment explanation
Indices: 34347376--34347436 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
34347366 TTCCCGAGCC
*
34347376 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATCCAAAAGTT
* * * *
34347406 TAGGGGCAAAATTGTAATTTTCCCAAAGTT
1 TAGGGGCAAAAGTGTAAATATCCAAAAGTT
34347436 T
1 T
34347437 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATCCAAAAGTT
Found at i:34348254 original size:64 final size:64
Alignment explanation
Indices: 34348173--34348356 Score: 187
Period size: 67 Copynumber: 2.8 Consensus size: 64
34348163 AGACATTATG
* *
34348173 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
34348237 ATGTAGCTAGGTCGCATGCGTGGCT-CCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGA
1 ATGTAGCTAGGTCGCATGGGT-GATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
34348301 TAA
62 TAA
* * * *
34348304 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGATACT-ATGTGTACACCATGTAG-ACAAGAGAGC
34348357 CGAACTATAT
Statistics
Matches: 98, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 23 0.23
65 4 0.04
66 18 0.18
67 33 0.34
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:34354151 original size:18 final size:18
Alignment explanation
Indices: 34354128--34354392 Score: 128
Period size: 18 Copynumber: 14.3 Consensus size: 18
34354118 GAATACTTAT
34354128 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
34354146 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
34354164 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
34354182 TTATTCAGTATCGATCAATTGATC-G
1 TTATTCAGTA---A-C-A--G-TCAG
*
34354207 ATTA-TCTAGTAACAGTCAA
1 -TTATTC-AGTAACAGTCAG
* *
34354226 TTATTTAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * * *
34354243 ATATTCAGTAGCAATTAAG
1 TTATTCAGTAAC-AGTCAG
*
34354262 TTATTCAGTAACAGTCAT
1 TTATTCAGTAACAGTCAG
* *
34354280 TTATTCAGTGACAATCAG
1 TTATTCAGTAACAGTCAG
* * *
34354298 TTATTTAGTAA-TGATCAT
1 TTATTCAGTAACAG-TCAG
* * *
34354316 TTATTTAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
34354334 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
*
34354352 TTA-TCTAGTAACAGTCAA
1 TTATTC-AGTAACAGTCAG
* *
34354370 TTATTCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
34354388 TTATT
1 TTATT
34354393 TAGAAATAAT
Statistics
Matches: 186, Mismatches: 41, Indels: 40
0.70 0.15 0.15
Matches are distributed among these distances:
17 15 0.08
18 136 0.73
19 19 0.10
21 2 0.01
22 1 0.01
23 2 0.01
25 3 0.02
26 8 0.04
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:34354168 original size:36 final size:36
Alignment explanation
Indices: 34354128--34354410 Score: 167
Period size: 36 Copynumber: 7.6 Consensus size: 36
34354118 GAATACTTAT
* *
34354128 TTATTCAGTAACAGTCAGTTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * * * *
34354164 TTATTCAATAATAACCAGTTATTCAGTATCGATCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * *
34354200 TTGATCGATTATCTAGTAACAGTCAATTATTTAGTAA-AATCAGA
1 -T--T--A-T-TC-AGTAACAATCAGTTATTCAGTAACAATCA-A
* * * *
34354244 -TATTCAGTAGCAATTAAGTTATTCAGTAACAGTCAT
1 TTATTCAGTAACAA-TCAGTTATTCAGTAACAATCAA
* * ** *
34354280 TTATTCAGTGACAATCAGTTATTTAGTAATGATCAT
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * * * *
34354316 TTATTTAGTAATATTCAGTTATTCAGTAACAGTCTA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * * *
34354352 TTA-TCTAGTAACAGTCAATTATTCGGTAACAGTCAA
1 TTATTC-AGTAACAATCAGTTATTCAGTAACAATCAA
* * *
34354388 TTATTTAGAAATAATCAGTTATT
1 TTATTCAGTAACAATCAGTTATT
34354411 TTATACCTTT
Statistics
Matches: 183, Mismatches: 50, Indels: 28
0.70 0.19 0.11
Matches are distributed among these distances:
35 7 0.04
36 130 0.71
37 18 0.10
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 1 0.01
43 6 0.03
44 17 0.09
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.38
Consensus pattern (36 bp):
TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
Found at i:34354374 original size:72 final size:70
Alignment explanation
Indices: 34354207--34354410 Score: 207
Period size: 72 Copynumber: 2.8 Consensus size: 70
34354197 CAATTGATCG
* *
34354207 ATTATCTAGTAACAGTCAATTATTTAGTAAAATCAGA-TATTCAGTAGCA-ATTAAGTTATTCAG
1 ATTATCTAGTAACAGTCAATTATTTAGTAAAATCA-ATTATTTAGTA--ATATTCAGTTATTCAG
34354270 TAACAGTC
63 TAACAGTC
* * * * *
34354278 ATTTAT-TCAGTGACAATCAGTTATTTAGTAATGATCATTTATTTAGTAATATTCAGTTATTCAG
1 A-TTATCT-AGTAACAGTCAATTATTTAGTAA-AATCAATTATTTAGTAATATTCAGTTATTCAG
34354342 TAACAGTC
63 TAACAGTC
** * * *
34354350 TATTATCTAGTAACAGTCAATTATTCGGTAACAGTCAATTATTTAGAAATAATCAGTTATT
1 -ATTATCTAGTAACAGTCAATTATTTAGTAA-AATCAATTATTTAGTAATATTCAGTTATT
34354411 TTATACCTTT
Statistics
Matches: 108, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
71 3 0.03
72 91 0.84
73 14 0.13
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (70 bp):
ATTATCTAGTAACAGTCAATTATTTAGTAAAATCAATTATTTAGTAATATTCAGTTATTCAGTAA
CAGTC
Found at i:34354645 original size:44 final size:45
Alignment explanation
Indices: 34354577--34354681 Score: 158
Period size: 44 Copynumber: 2.4 Consensus size: 45
34354567 AATCCGGAAT
*
34354577 AGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCGATAAC
1 AGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGATAAC
* * *
34354622 GGTAAC-GTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAC
1 AGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGATAAC
*
34354666 AGTAACGGTAACAGTA
1 AGTAACAGTAACAGTA
34354682 ACAGTAGTCA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 40 0.74
45 14 0.26
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (45 bp):
AGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGATAAC
Found at i:34354676 original size:12 final size:12
Alignment explanation
Indices: 34354659--34354683 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34354649 AGTGCCGAAT
34354659 CGGTAACAGTAA
1 CGGTAACAGTAA
34354671 CGGTAACAGTAA
1 CGGTAACAGTAA
34354683 C
1 C
34354684 AGTAGTCAGC
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:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:34360133 original size:43 final size:43
Alignment explanation
Indices: 34360086--34360209 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
34360076 TAACACATAT
* * * *
34360086 CGATGCCACTTTCCTACACAGGGTCTTACACG-AAGTCCATTA-A
1 CGATGCCACTATCCCACACAAGGTCTTACACGTAA-T-CATAATA
* *
34360129 CGATGCCGA-TGTCCCACACATGGTCTTACACGTAATCATAATA
1 CGATGCC-ACTATCCCACACAAGGTCTTACACGTAATCATAATA
* *
34360172 CAATGCCACTATCCCACACAAGGTCTTACATGTAATCA
1 CGATGCCACTATCCCACACAAGGTCTTACACGTAATCA
34360210 CATCTCAATA
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
42 5 0.07
43 61 0.88
44 3 0.04
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.25
Consensus pattern (43 bp):
CGATGCCACTATCCCACACAAGGTCTTACACGTAATCATAATA
Found at i:34362061 original size:87 final size:86
Alignment explanation
Indices: 34361970--34362464 Score: 319
Period size: 87 Copynumber: 5.6 Consensus size: 86
34361960 GGTTGCCAAA
* *
34361970 TCATCTTGGATTTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCTCTCCGTC
1 TCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTC
* *
34362035 GAATATGGAGACGTCAAATCTG
66 GAA-ATAGAGACGCCAAATCTG
34362057 TCATCTTGGATCTGCTTCAGTA-AAATCATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGT
1 TCATCTTGGATCTGCTTCAGTATAAA-CATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGT
* *
34362121 CGAAATAGAGATGCCAGATCTG
65 CGAAATAGAGACGCCAAATCTG
* * * * * * * *
34362143 TTATCTTGGATCTGCTTTAGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTG-T
1 TCATCTTGGATCTGCTTCAGTAT-A-AACATCTGAAGGTTAGATCTGCTATG---T--ATCTGCT
* * * *
34362207 -TCC-TTGTAAACACAAGAATGCCAAA----
59 CTCCGTCG-AAATA-GAG-ACGCCAAATCTG
* * * * *
34362232 TCATCTTGGATCTACTTCAGTATAAACACCTGAAGGTTAGATCTGCTATGTGTCTACCCTCCGTC
1 TCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTC
* * *
34362297 GAATATGGAGAAGCCAGATCTG
66 GAA-ATAGAGACGCCAAATCTG
* * * * * * * *
34362319 TTATCTTGGATCTACTTTGATGTGAAAAACATCTGGAA-GTCAAATCTGCTATGTCT-TCGATTT
1 TCATCTTGGATCTGC-TTCA-GT-ATAAACATCT-GAAGGTTAGATCTGCTATGTATCT-G--CT
*
34362382 ACTCCTCGTCGAAGATAGAGAAGCCAAATCTTG
59 -CT-C-CGTCGAA-ATAGAGACGCCAAATC-TG
* * * **
34362415 TTATCTTGGATCTGCTTTAGTGTAAACA-CGTGAAGGCCAGATCTGCTATG
1 TCATCTTGGATCTGCTTCAGTATAAACATC-TGAAGGTTAGATCTGCTATG
34362465 CTTTGGTCTG
Statistics
Matches: 319, Mismatches: 56, Indels: 60
0.73 0.13 0.14
Matches are distributed among these distances:
82 2 0.01
83 6 0.02
84 8 0.03
85 3 0.01
86 36 0.11
87 97 0.30
88 25 0.08
89 24 0.08
90 25 0.08
91 11 0.03
92 7 0.02
93 32 0.10
94 3 0.01
95 24 0.08
96 16 0.05
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (86 bp):
TCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTC
GAAATAGAGACGCCAAATCTG
Found at i:34362252 original size:175 final size:177
Alignment explanation
Indices: 34362057--34362381 Score: 505
Period size: 175 Copynumber: 1.8 Consensus size: 177
34362047 GTCAAATCTG
* * * *
34362057 TCATCTTGGATCTGCTTCAGTA-AAATCATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGT
1 TCATCTTGGATCTACTTCAGTATAAA-CACCTGAAGGTTAGATCTGCTATGTATCTACCCTCCGT
* * *
34362121 CGAA-ATAGAGATGCCAGATCTGTTATCTTGGATCTGCTTT-AGTGTG-AGAACATCCGAAAGTC
65 CGAATATAGAGAAGCCAGATCTGTTATCTTGGATCTACTTTGA-TGTGAAAAACATCCGAAAGTC
34362183 AAATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAA
129 AAATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAA
*
34362232 TCATCTTGGATCTACTTCAGTATAAACACCTGAAGGTTAGATCTGCTATGTGTCTACCCTCCGTC
1 TCATCTTGGATCTACTTCAGTATAAACACCTGAAGGTTAGATCTGCTATGTATCTACCCTCCGTC
* * *
34362297 GAATATGGAGAAGCCAGATCTGTTATCTTGGATCTACTTTGATGTGAAAAACATCTGGAAGTCAA
66 GAATATAGAGAAGCCAGATCTGTTATCTTGGATCTACTTTGATGTGAAAAACATCCGAAAGTCAA
34362362 ATCTGCTATGTCTTCGATTT
131 ATCTGCTATGTCTTCGATTT
34362382 ACTCCTCGTC
Statistics
Matches: 135, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
175 59 0.44
176 40 0.30
177 36 0.27
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (177 bp):
TCATCTTGGATCTACTTCAGTATAAACACCTGAAGGTTAGATCTGCTATGTATCTACCCTCCGTC
GAATATAGAGAAGCCAGATCTGTTATCTTGGATCTACTTTGATGTGAAAAACATCCGAAAGTCAA
ATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAA
Found at i:34362461 original size:183 final size:177
Alignment explanation
Indices: 34362031--34362464 Score: 493
Period size: 175 Copynumber: 2.4 Consensus size: 177
34362021 GTCTGCTCTC
* * * * *
34362031 CGTCGAATATGGAGACGTCAAATCTGTCATCTTGGATCTGCTTCAGTAAAATCATCTGAAGGTTA
1 CGTCGAACATAGAGAAGCCAAATCTGT-ATCTTGGATCTGCTTCAGTTAAA-CA-CTGAAGGTTA
* * * *
34362096 GATCTGCTATGTATCTGCTCTCCGTCGAAATAGAGATGCCAGATCTGTTATCTTGGATCTGCTTT
63 GATCTGCTATGTATCTACCCTCCGTCGAAATAGAGAAGCCAGATCTGTTATCTTGGATCTACTTT
* **
34362161 AGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCT
128 AGTGTGAAAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTACTCCT
* * * *
34362211 TGT-AAACACA-AGAATGCCAAATC---ATCTTGGATCTACTTCAGTATAAACACCTGAAGGTTA
1 CGTCGAACATAGAGAA-GCCAAATCTGTATCTTGGATCTGCTTCAGT-TAAACA-CTGAAGGTTA
* *
34362271 GATCTGCTATGTGTCTACCCTCCGTCGAATATGGAGAAGCCAGATCTGTTATCTTGGATCTACTT
63 GATCTGCTATGTATCTACCCTCCGTCGAA-ATAGAGAAGCCAGATCTGTTATCTTGGATCTACTT
* *
34362336 T-GATGTGAAAAACATCTGGAAGTCAAATCTGCTATGTCTTCGATTTACTCCT
127 TAG-TGTG-AAAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTACTCCT
* * **
34362388 CGTCGAAGATAGAGAAGCCAAATCTTGTTATCTTGGATCTGCTTTAGTGTAAACACGTGAAGGCC
1 CGTCGAACATAGAGAAGCCAAATC-TG-TATCTTGGATCTGCTTCAGT-TAAACAC-TGAAGGTT
34362453 AGATCTGCTATG
62 AGATCTGCTATG
34362465 CTTTGGTCTG
Statistics
Matches: 211, Mismatches: 30, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
175 57 0.27
176 40 0.19
177 41 0.19
178 15 0.07
179 14 0.07
180 2 0.01
182 1 0.00
183 41 0.19
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (177 bp):
CGTCGAACATAGAGAAGCCAAATCTGTATCTTGGATCTGCTTCAGTTAAACACTGAAGGTTAGAT
CTGCTATGTATCTACCCTCCGTCGAAATAGAGAAGCCAGATCTGTTATCTTGGATCTACTTTAGT
GTGAAAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTACTCCT
Found at i:34366636 original size:24 final size:24
Alignment explanation
Indices: 34366604--34366651 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
34366594 TTGGTAATAA
34366604 GTGTCCCAATTTTCACCTCTTTCC
1 GTGTCCCAATTTTCACCTCTTTCC
34366628 GTGTCCCAATTTTCACCTCTTTCC
1 GTGTCCCAATTTTCACCTCTTTCC
34366652 CTTCCTCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.38, G:0.08, T:0.42
Consensus pattern (24 bp):
GTGTCCCAATTTTCACCTCTTTCC
Found at i:34373445 original size:21 final size:21
Alignment explanation
Indices: 34373421--34373474 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
34373411 AACTTCTTGA
*
34373421 TGAGTTGGGGTAGTAGGTATC
1 TGAGTTGGGGTAGTAGGTAAC
*
34373442 TGAGTTGGGGCAGTAGGTAAC
1 TGAGTTGGGGTAGTAGGTAAC
34373463 TGAGTTGGGGTA
1 TGAGTTGGGGTA
34373475 CCTTCTTGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.06, G:0.44, T:0.30
Consensus pattern (21 bp):
TGAGTTGGGGTAGTAGGTAAC
Found at i:34374271 original size:16 final size:17
Alignment explanation
Indices: 34374240--34374272 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34374230 TTCATAAGCA
*
34374240 TATATCACTCATTTCAT
1 TATATCAATCATTTCAT
34374257 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
34374273 GCTCCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:34374736 original size:46 final size:46
Alignment explanation
Indices: 34374555--34374736 Score: 229
Period size: 46 Copynumber: 4.0 Consensus size: 46
34374545 TTTGACATAA
* * * * ** * *
34374555 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *** *
34374601 TACCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
34374647 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
34374693 TGCCATGGTATCTATCAACCATGGCCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
34374737 AGAGCACACT
Statistics
Matches: 119, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 119 1.00
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:34377905 original size:43 final size:43
Alignment explanation
Indices: 34377811--34377988 Score: 247
Period size: 43 Copynumber: 4.2 Consensus size: 43
34377801 AAAAAAAAAC
* *
34377811 TCATTGCATGCATATTAAAAAATAGGCAACA-C--ACCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
34377851 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
* * *
34377894 TCATTGCATGCATATTAAAAAATAGTTAACAACTTTCCAATAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
* * *
34377937 TCATTGCATACATATTAAAAGA-AGTCAATAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
*
34377979 TCACTGCATG
1 TCATTGCATG
34377989 TAATCAGCAA
Statistics
Matches: 122, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 30 0.25
41 1 0.01
42 24 0.20
43 67 0.55
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.28
Consensus pattern (43 bp):
TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
Found at i:34377987 original size:85 final size:83
Alignment explanation
Indices: 34377815--34377988 Score: 242
Period size: 85 Copynumber: 2.1 Consensus size: 83
34377805 AAAAACTCAT
*
34377815 TGCATGCATATTAAAAAATAGGCAACACACCAACAATCATTGCATGCATATTAAAAAATAGTCAA
1 TGCATGCATATTAAAAAATAGGCAACACACCAACAATCATTGCATACATATTAAAAAATAGTCAA
*
34377880 CAGCTTTCCAACAATCAT
66 CAGCTTTCCAACAATCAC
** * * *
34377898 TGCATGCATATTAAAAAATAGTTAACAACTTTCCAATAATCATTGCATACATATTAAAAGA-AGT
1 TGCATGCATATTAAAAAATAGGCAAC-AC--ACCAACAATCATTGCATACATATTAAAAAATAGT
*
34377962 CAATAGCTTTCCAACAATCAC
63 CAACAGCTTTCCAACAATCAC
34377983 TGCATG
1 TGCATG
34377989 TAATCAGCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
83 24 0.30
84 2 0.03
85 28 0.35
86 26 0.32
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (83 bp):
TGCATGCATATTAAAAAATAGGCAACACACCAACAATCATTGCATACATATTAAAAAATAGTCAA
CAGCTTTCCAACAATCAC
Found at i:34379362 original size:30 final size:31
Alignment explanation
Indices: 34379338--34379396 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
34379328 GTAAATACTC
*
34379338 AAAATTTGAGAGG-TTAA-AGTGTAAATATGA
1 AAAATTTGA-AGGATCAATAGTGTAAATATGA
34379368 AAAATTTGAAGGATCAATAGTGTAAATAT
1 AAAATTTGAAGGATCAATAGTGTAAATAT
34379397 TTTAAGGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 3 0.12
30 12 0.46
31 11 0.42
ACGTcount: A:0.47, C:0.02, G:0.20, T:0.31
Consensus pattern (31 bp):
AAAATTTGAAGGATCAATAGTGTAAATATGA
Found at i:34379648 original size:11 final size:11
Alignment explanation
Indices: 34379634--34379689 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
34379624 AGATAAATAT
34379634 TATTTTATTAA
1 TATTTTATTAA
*
34379645 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
34379658 TATTTTATTAT
1 TATTTTATTAA
*
34379669 TATTTTATTAT
1 TATTTTATTAA
34379680 TATTTTATTA
1 TATTTTATTA
34379690 GTATATAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
11 27 0.68
12 6 0.15
13 7 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:34381873 original size:46 final size:46
Alignment explanation
Indices: 34381804--34382060 Score: 328
Period size: 46 Copynumber: 5.7 Consensus size: 46
34381794 AGTGTGCTCT
* *
34381804 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
34381850 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
34381896 CTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGC-A-
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
34381940 ---ATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
34381983 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
34382029 ATGACA-GAAAAGGAGTAAGACCATAGTTGAAA
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAA
34382061 AACAATATGG
Statistics
Matches: 192, Mismatches: 13, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
41 37 0.19
42 1 0.01
45 2 0.01
46 152 0.79
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:34382002 original size:87 final size:87
Alignment explanation
Indices: 34381823--34382032 Score: 285
Period size: 87 Copynumber: 2.4 Consensus size: 87
34381813 AATGTGTAAA
**
34381823 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
1 ACCATGGTTGAAAGATACCATGGC-A----ATATGAAATGAATAAGACCATGGTTGAAAGATACC
* * **
34381888 ATGACAACCTGATATGAAATGTGTAAG
61 ATGACAACCTGACATGAAAAGAATAAG
* *
34381915 ACCATAGTTGAAAGATACCATGGCAATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGC
1 ACCATGGTTGAAAGATACCATGGCAATATGAAATGAATAAGACCATGGTTGAAAGATACCATGAC
*
34381980 AACGTGACATGAAAAGAATAAG
66 AACCTGACATGAAAAGAATAAG
*
34382002 ACCATGGTTGAAAGATACCATGGCAACATGA
1 ACCATGGTTGAAAGATACCATGGCAATATGA
34382033 CAGAAAAGGA
Statistics
Matches: 107, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
87 83 0.78
91 1 0.01
92 23 0.21
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.21
Consensus pattern (87 bp):
ACCATGGTTGAAAGATACCATGGCAATATGAAATGAATAAGACCATGGTTGAAAGATACCATGAC
AACCTGACATGAAAAGAATAAG
Found at i:34382047 original size:133 final size:133
Alignment explanation
Indices: 34381807--34382060 Score: 375
Period size: 133 Copynumber: 1.9 Consensus size: 133
34381797 GTGCTCTCTG
** * * **
34381807 ATATGAAATGTGTAAAACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACC
1 ATATGAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACC
* * * *
34381872 ATGGTTGAAAGATACCATGACAACCTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATG
66 ATGGTTGAAAGATACCATGACAACATGACATGAAAGGAGTAAGACCATAGTTGAAAGATACCATG
34381937 GCA
131 GCA
* *
34381940 ATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACC
1 ATATGAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACC
*
34382005 ATGGTTGAAAGATACCATGGCAACATGACA-GAAAAGGAGTAAGACCATAGTTGAAA
66 ATGGTTGAAAGATACCATGACAACATGACATG-AAAGGAGTAAGACCATAGTTGAAA
34382061 AACAATATGG
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
132 1 0.01
133 106 0.99
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (133 bp):
ATATGAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACCTGACATGAAAAGAATAAGACC
ATGGTTGAAAGATACCATGACAACATGACATGAAAGGAGTAAGACCATAGTTGAAAGATACCATG
GCA
Found at i:34383362 original size:15 final size:15
Alignment explanation
Indices: 34383342--34383371 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34383332 ATGCATCACT
34383342 ATCACTACCAGACAC
1 ATCACTACCAGACAC
34383357 ATCACTACCAGACAC
1 ATCACTACCAGACAC
34383372 GTTTTCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.40, G:0.07, T:0.13
Consensus pattern (15 bp):
ATCACTACCAGACAC
Found at i:34383841 original size:48 final size:48
Alignment explanation
Indices: 34383725--34383833 Score: 182
Period size: 48 Copynumber: 2.3 Consensus size: 48
34383715 GCAGATACAA
34383725 ACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCAT
1 ACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCAT
* *
34383773 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCAT
1 ACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCAT
* *
34383821 ATAATGACAGATA
1 ACAATGGCAGATA
34383834 CAAACAATGG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.27
Consensus pattern (48 bp):
ACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCAT
Found at i:34383841 original size:64 final size:64
Alignment explanation
Indices: 34383773--34383905 Score: 230
Period size: 64 Copynumber: 2.1 Consensus size: 64
34383763 TGACATTCAT
*
34383773 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATATAATGACAGATACAA
1 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATACAATGACAGATACAA
* * *
34383837 ACAATGGCATATATACACAATAAAGATCAGTTTGATAATGGCATTCATACAATGGCAGATACAA
1 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATACAATGACAGATACAA
34383901 ACAAT
1 ACAAT
34383906 AAACATCAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (64 bp):
ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATACAATGACAGATACAA
Found at i:34383875 original size:112 final size:110
Alignment explanation
Indices: 34383663--34383913 Score: 351
Period size: 112 Copynumber: 2.3 Consensus size: 110
34383653 TTGGATACAA
* * * *
34383663 ACAATGACAGATATAGACAATAAACATCAGTTTAATAATGTATAATTTAATCGCAGATACAAACA
1 ACAATGGCAGATATAAACAATAAACATCAGTTTAATAATGCATAATATAATCGCAGATACAAACA
34383728 ATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCAT
66 ATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCAT
* * * *
34383773 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATATAAT-GACAGATACAA
1 ACAATGGCAGATATAAACAATAAACATCAGTTTAATAATG-CA-TAATATAATCG-CAGATACAA
* * * *
34383837 ACAATGGCATATATACACAATAAAGATCAGTTTGATAATGGCATTCAT
63 ACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCAT
*
34383885 ACAATGGCAGATACAAACAATAAACATCA
1 ACAATGGCAGATATAAACAATAAACATCA
34383914 AAATCAAAAT
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
110 36 0.29
111 2 0.02
112 86 0.69
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.25
Consensus pattern (110 bp):
ACAATGGCAGATATAAACAATAAACATCAGTTTAATAATGCATAATATAATCGCAGATACAAACA
ATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCAT
Found at i:34383887 original size:34 final size:34
Alignment explanation
Indices: 34383785--34383887 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 34
34383775 AATGGCAGAT
*
34383785 ATACACAATAAAGATCAGTTTGATAATGACATTC
1 ATACACAATAAAGATCAGTTTGATAATGGCATTC
* * * *
34383819 AT--ATAATGACAGATACA----AACAATGGCATAT-
1 ATACACAAT-AAAGAT-CAGTTTGATAATGGCAT-TC
34383849 ATACACAATAAAGATCAGTTTGATAATGGCATTC
1 ATACACAATAAAGATCAGTTTGATAATGGCATTC
34383883 ATACA
1 ATACA
34383888 ATGGCAGATA
Statistics
Matches: 50, Mismatches: 9, Indels: 20
0.63 0.11 0.25
Matches are distributed among these distances:
30 12 0.24
31 6 0.12
32 8 0.16
33 6 0.12
34 18 0.36
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.27
Consensus pattern (34 bp):
ATACACAATAAAGATCAGTTTGATAATGGCATTC
Found at i:34384070 original size:18 final size:18
Alignment explanation
Indices: 34384047--34384129 Score: 63
Period size: 18 Copynumber: 4.9 Consensus size: 18
34384037 AAATAACCCT
34384047 AAATCAAAATCTAAATCG
1 AAATCAAAATCTAAATCG
34384065 AAATCAAAATC-AAAT--
1 AAATCAAAATCTAAATCG
* *
34384080 ---TC-TAATCCTAAATTG
1 AAATCAAAAT-CTAAATCG
* * *
34384095 AGATCAAAATCGAAATTG
1 AAATCAAAATCTAAATCG
34384113 AAATCAAAATCTAAATC
1 AAATCAAAATCTAAATC
34384130 AGAATCAGTG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
11 3 0.06
12 3 0.06
13 4 0.08
17 4 0.08
18 34 0.67
19 3 0.06
ACGTcount: A:0.53, C:0.16, G:0.06, T:0.25
Consensus pattern (18 bp):
AAATCAAAATCTAAATCG
Found at i:34384135 original size:12 final size:12
Alignment explanation
Indices: 34384045--34384084 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
34384035 CGAAATAACC
34384045 CTAAATCAAAAT
1 CTAAATCAAAAT
*
34384057 CTAAATCGAAAT
1 CTAAATCAAAAT
* *
34384069 CAAAATCAAATT
1 CTAAATCAAAAT
34384081 CTAA
1 CTAA
34384085 TCCTAAATTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.25
Consensus pattern (12 bp):
CTAAATCAAAAT
Found at i:34384188 original size:12 final size:12
Alignment explanation
Indices: 34384146--34384194 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
34384136 AGTGAGTGTT
* *
34384146 TCAAAATTGTAA
1 TCAAAATCGAAA
34384158 TCAAAATCGAAA
1 TCAAAATCGAAA
34384170 T-AGAAATCGAAA
1 TCA-AAATCGAAA
*
34384182 TCAAAATCAAAA
1 TCAAAATCGAAA
34384194 T
1 T
34384195 TAAATTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 1 0.03
12 30 0.94
13 1 0.03
ACGTcount: A:0.57, C:0.12, G:0.08, T:0.22
Consensus pattern (12 bp):
TCAAAATCGAAA
Found at i:34384194 original size:18 final size:18
Alignment explanation
Indices: 34384146--34384188 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
34384136 AGTGAGTGTT
* *
34384146 TCAAAATTGTAATCAAAA
1 TCAAAATAGAAATCAAAA
* *
34384164 TCGAAATAGAAATCGAAA
1 TCAAAATAGAAATCAAAA
34384182 TCAAAAT
1 TCAAAAT
34384189 CAAAATTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (18 bp):
TCAAAATAGAAATCAAAA
Found at i:34384762 original size:31 final size:29
Alignment explanation
Indices: 34384723--34384795 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
34384713 GGTAGCTGTT
*
34384723 AGTTAGTGACTGTTTTGTCACTTTTTTATA
1 AGTTAGTGACTGTTTTGTCACTTTTTGA-A
*
34384753 ACGTTAGTGA-TCGTTTTGTTACTTTTTGAA
1 A-GTTAGTGACT-GTTTTGTCACTTTTTGAA
34384783 AGTTAAGTGACTG
1 AGTT-AGTGACTG
34384796 AAATGAAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 3 0.08
30 10 0.27
31 24 0.65
ACGTcount: A:0.22, C:0.10, G:0.21, T:0.48
Consensus pattern (29 bp):
AGTTAGTGACTGTTTTGTCACTTTTTGAA
Found at i:34396676 original size:3 final size:3
Alignment explanation
Indices: 34396668--34396707 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
34396658 TTCCCTACAA
34396668 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
34396708 TTGTTGTCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:34399469 original size:19 final size:20
Alignment explanation
Indices: 34399455--34399492 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
34399445 TGTGAAATTT
*
34399455 AATGCATATG-ATGAAATGC
1 AATGCAGATGCATGAAATGC
34399474 AATGCAGATGCATGAAATG
1 AATGCAGATGCATGAAATG
34399493 AATTCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (20 bp):
AATGCAGATGCATGAAATGC
Found at i:34402168 original size:17 final size:16
Alignment explanation
Indices: 34402146--34402190 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
34402136 ATCATATCTT
34402146 AAAATATAATAGTAA-CA
1 AAAATATAA-A-TAAGCA
34402163 AAAATATAAATAAGCA
1 AAAATATAAATAAGCA
34402179 AGAAATATAAAT
1 A-AAATATAAAT
34402191 CAATAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.12
16 4 0.15
17 19 0.73
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (16 bp):
AAAATATAAATAAGCA
Found at i:34404934 original size:26 final size:26
Alignment explanation
Indices: 34404896--34404953 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
34404886 CATGAAATTC
*
34404896 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACACA
* *
34404922 TTATCATGGAACATTTACCTAACATA
1 TTATCATGAAACATTTACCTAACACA
34404948 TTATCA
1 TTATCA
34404954 ATTTGTACCN
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACACA
Found at i:34407922 original size:39 final size:39
Alignment explanation
Indices: 34407876--34407954 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
34407866 GTCTTATAGT
34407876 TTAAGATCTTATTTTGTATCACTGCTACCAGAAATTTCA
1 TTAAGATCTTATTTTGTATCACTGCTACCAGAAATTTCA
*
34407915 TTAAGATCTTATTTTGTATCATTGCTACCAGAAATTTCA
1 TTAAGATCTTATTTTGTATCACTGCTACCAGAAATTTCA
34407954 T
1 T
34407955 ACTTTTTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.43
Consensus pattern (39 bp):
TTAAGATCTTATTTTGTATCACTGCTACCAGAAATTTCA
Found at i:34426727 original size:106 final size:107
Alignment explanation
Indices: 34426576--34426882 Score: 406
Period size: 106 Copynumber: 2.9 Consensus size: 107
34426566 CATCACAGAC
* * *
34426576 ATTTTGTAACAAGATTATCATATTTAAAATATTTATATTTATATAAAATTTTTA-AAAA-ATTCC
1 ATTTTGTAACAAGATTATCGTATTTAAGATACTTATATTTATATAAAA-TTTTAGAAAACATTCC
* * *
34426639 CTTTATTTTATTTATATATCGATAAATTTTACATTT-AAGTTTT
65 CCTTATTTTATTTATACATCGATAAATTTGACATTTGAA-TTTT
* * *
34426682 ATTTTGTAACAAGATCATCGTATTTAAGATACTTATATTTGTAT-AAATTTTAGAAAACTTTCCC
1 ATTTTGTAACAAGATTATCGTATTTAAGATACTTATATTTATATAAAATTTTAGAAAACATTCCC
* *
34426746 CTTATTTTATTTATACATTGATTAATTTGACATTTGAATTTT
66 CTTATTTTATTTATACATCGATAAATTTGACATTTGAATTTT
* * *
34426788 ATTTTATCACAAGATTATCGTATTTAAGATACTTATATTTATATAAAATTTTAGAAAACCTTCCC
1 ATTTTGTAACAAGATTATCGTATTTAAGATACTTATATTTATATAAAATTTTAGAAAACATTCCC
* * * *
34426853 CTTATTTTATTAATGCATTGACAAATTTGA
66 CTTATTTTATTTATACATCGATAAATTTGA
34426883 AACCATATTT
Statistics
Matches: 177, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
104 5 0.03
105 7 0.04
106 118 0.67
107 47 0.27
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (107 bp):
ATTTTGTAACAAGATTATCGTATTTAAGATACTTATATTTATATAAAATTTTAGAAAACATTCCC
CTTATTTTATTTATACATCGATAAATTTGACATTTGAATTTT
Found at i:34435996 original size:20 final size:20
Alignment explanation
Indices: 34435943--34435998 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
34435933 AAGGTTATAG
34435943 AAAATAATACAAAAA-TTATTA
1 AAAAT-ATA-AAAAATTTATTA
* *
34435964 AAAAGT-TATAAAATTTATTT
1 AAAA-TATAAAAAATTTATTA
34435984 AAAATATAAAAAATT
1 AAAATATAAAAAATT
34435999 GTTATTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 5 0.17
20 19 0.66
21 4 0.14
22 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAATATAAAAAATTTATTA
Found at i:34436390 original size:9 final size:9
Alignment explanation
Indices: 34436378--34436437 Score: 68
Period size: 9 Copynumber: 6.7 Consensus size: 9
34436368 AAAATTAATT
34436378 GAATTAACC
1 GAATTAACC
34436387 GAATT-ACC
1 GAATTAACC
*
34436395 TGAATTACCC
1 -GAATTAACC
* *
34436405 AAATTAATC
1 GAATTAACC
*
34436414 GAATTAACT
1 GAATTAACC
34436423 GAATTAACC
1 GAATTAACC
34436432 GAATTA
1 GAATTA
34436438 TTTGTATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 3 0.07
9 36 0.88
10 2 0.05
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (9 bp):
GAATTAACC
Found at i:34436409 original size:27 final size:27
Alignment explanation
Indices: 34436379--34436437 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
34436369 AAATTAATTG
* *
34436379 AATTAACCGAATTACCTGAATTACCCA
1 AATTAACCGAATTAACTGAATTAACCA
* *
34436406 AATTAATCGAATTAACTGAATTAACCG
1 AATTAACCGAATTAACTGAATTAACCA
34436433 AATTA
1 AATTA
34436438 TTTGTATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (27 bp):
AATTAACCGAATTAACTGAATTAACCA
Found at i:34436468 original size:6 final size:6
Alignment explanation
Indices: 34436457--34436554 Score: 133
Period size: 6 Copynumber: 15.5 Consensus size: 6
34436447 AATTATATGT
*
34436457 TTTTTA TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTTTTA
*
34436507 TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTTTTA GTTTTTA TTT
1 TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTTTTA -TTTTTA TTT
34436555 AGTAAATTAT
Statistics
Matches: 83, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
6 59 0.71
7 22 0.27
8 2 0.02
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:34436494 original size:32 final size:31
Alignment explanation
Indices: 34436457--34436549 Score: 150
Period size: 32 Copynumber: 2.9 Consensus size: 31
34436447 AATTATATGT
34436457 TTTTTATTTTTATTTTTATTTTTAGTTTTAG
1 TTTTTATTTTTATTTTTATTTTTAGTTTTAG
*
34436488 ATTTTTATTTTTATTTTTATTTTTATTTTTAG
1 -TTTTTATTTTTATTTTTATTTTTAGTTTTAG
*
34436520 TTTTAGATTTTTATTTTTATTTTTAGTTTT
1 TTTT-TATTTTTATTTTTATTTTTAGTTTT
34436550 TATTTAGTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 4 0.07
32 53 0.93
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.77
Consensus pattern (31 bp):
TTTTTATTTTTATTTTTATTTTTAGTTTTAG
Found at i:34436500 original size:38 final size:38
Alignment explanation
Indices: 34436457--34436554 Score: 187
Period size: 38 Copynumber: 2.6 Consensus size: 38
34436447 AATTATATGT
34436457 TTTTTATTTTTATTTTTATTTTTAGTTTTAGATTTTTA
1 TTTTTATTTTTATTTTTATTTTTAGTTTTAGATTTTTA
34436495 TTTTTATTTTTATTTTTATTTTTAGTTTTAGATTTTTA
1 TTTTTATTTTTATTTTTATTTTTAGTTTTAGATTTTTA
34436533 TTTTTATTTTTAGTTTTTATTT
1 TTTTTATTTTTA-TTTTTATTT
34436555 AGTAAATTAT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 50 0.85
39 9 0.15
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (38 bp):
TTTTTATTTTTATTTTTATTTTTAGTTTTAGATTTTTA
Found at i:34436595 original size:13 final size:13
Alignment explanation
Indices: 34436579--34436603 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34436569 AATTTTTATG
34436579 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
34436592 ATTGGGTTGGGT
1 ATTGGGTTGGGT
34436604 TGGGTATTTG
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:34436603 original size:18 final size:18
Alignment explanation
Indices: 34436580--34436617 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
34436570 ATTTTTATGA
34436580 TTGGGTTGGGTAATTGGG
1 TTGGGTTGGGTAATTGGG
*
34436598 TTGGGTTGGGTATTTGGG
1 TTGGGTTGGGTAATTGGG
34436616 TT
1 TT
34436618 AATATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.00, G:0.47, T:0.45
Consensus pattern (18 bp):
TTGGGTTGGGTAATTGGG
Found at i:34436730 original size:18 final size:18
Alignment explanation
Indices: 34436707--34436741 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
34436697 TTTTATTAAT
34436707 TTTTTTCGGTTAACCGAA
1 TTTTTTCGGTTAACCGAA
34436725 TTTTTTCGGTTAACCGA
1 TTTTTTCGGTTAACCGA
34436742 CCGGTTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (18 bp):
TTTTTTCGGTTAACCGAA
Found at i:34437432 original size:30 final size:29
Alignment explanation
Indices: 34437395--34437461 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
34437385 ATTTCAAGGC
* *
34437395 CTTAATTAATTGTTAATTTTTAATTAAAAA
1 CTTAATTAAGTG-TAATTTTCAATTAAAAA
* **
34437425 TTTAATTAAGTGTAATTTTCGTTTAAAAA
1 CTTAATTAAGTGTAATTTTCAATTAAAAA
34437454 CTTAATTA
1 CTTAATTA
34437462 TTTTATAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (29 bp):
CTTAATTAAGTGTAATTTTCAATTAAAAA
Found at i:34438024 original size:14 final size:15
Alignment explanation
Indices: 34437986--34438028 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
34437976 TTATAAGTGA
*
34437986 ATAAAAATATTTTAT
1 ATAAAAATATATTAT
34438001 ATTAAAAAATATATT-T
1 A-T-AAAAATATATTAT
34438017 ATAAAAATATAT
1 ATAAAAATATAT
34438029 CAATTAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 2 0.08
16 3 0.12
17 10 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAAAATATATTAT
Found at i:34438442 original size:9 final size:9
Alignment explanation
Indices: 34438430--34438489 Score: 68
Period size: 9 Copynumber: 6.7 Consensus size: 9
34438420 AAAATTAATT
34438430 GAATTAACC
1 GAATTAACC
34438439 GAATT-ACC
1 GAATTAACC
*
34438447 TGAATTACCC
1 -GAATTAACC
* *
34438457 AAATTAATC
1 GAATTAACC
*
34438466 GAATTAACT
1 GAATTAACC
34438475 GAATTAACC
1 GAATTAACC
34438484 GAATTA
1 GAATTA
34438490 TTTGTATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 3 0.07
9 36 0.88
10 2 0.05
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (9 bp):
GAATTAACC
Found at i:34438453 original size:27 final size:27
Alignment explanation
Indices: 34438431--34438489 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
34438421 AAATTAATTG
* *
34438431 AATTAACCGAATTACCTGAATTACCCA
1 AATTAACCGAATTAACTGAATTAACCA
* *
34438458 AATTAATCGAATTAACTGAATTAACCG
1 AATTAACCGAATTAACTGAATTAACCA
34438485 AATTA
1 AATTA
34438490 TTTGTATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (27 bp):
AATTAACCGAATTAACTGAATTAACCA
Found at i:34438524 original size:5 final size:6
Alignment explanation
Indices: 34438509--34438568 Score: 84
Period size: 6 Copynumber: 9.5 Consensus size: 6
34438499 AATTATATGT
*
34438509 TTTTTA TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTTTTA
34438559 GTTTTTA TTT
1 -TTTTTA TTT
34438569 AGTAAATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
6 34 0.69
7 14 0.29
8 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:34438543 original size:20 final size:20
Alignment explanation
Indices: 34438520--34438568 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
34438510 TTTTATTTTT
34438520 ATTTTTATTTTTAGTTTTAG
1 ATTTTTATTTTTAGTTTTAG
*
34438540 ATTTTTATTTTTATTTTTAG
1 ATTTTTATTTTTAGTTTTAG
34438560 -TTTTTATTT
1 ATTTTTATTT
34438569 AGTAAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (20 bp):
ATTTTTATTTTTAGTTTTAG
Found at i:34438543 original size:26 final size:26
Alignment explanation
Indices: 34438514--34438563 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
34438504 TATGTTTTTT
34438514 ATTTTTATTTTTATTTTTAGTTTTAG
1 ATTTTTATTTTTATTTTTAGTTTTAG
34438540 ATTTTTATTTTTATTTTTAGTTTT
1 ATTTTTATTTTTATTTTTAGTTTT
34438564 TATTTAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (26 bp):
ATTTTTATTTTTATTTTTAGTTTTAG
Found at i:34438609 original size:13 final size:13
Alignment explanation
Indices: 34438593--34438617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34438583 AATTTTTATG
34438593 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
34438606 ATTGGGTTGGGT
1 ATTGGGTTGGGT
34438618 TGGGTATTTG
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:34438617 original size:18 final size:18
Alignment explanation
Indices: 34438594--34438631 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
34438584 ATTTTTATGA
34438594 TTGGGTTGGGTAATTGGG
1 TTGGGTTGGGTAATTGGG
*
34438612 TTGGGTTGGGTATTTGGG
1 TTGGGTTGGGTAATTGGG
34438630 TT
1 TT
34438632 AATATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.00, G:0.47, T:0.45
Consensus pattern (18 bp):
TTGGGTTGGGTAATTGGG
Found at i:34438744 original size:18 final size:18
Alignment explanation
Indices: 34438721--34438755 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
34438711 TTTTATTAAT
34438721 TTTTTTCGGTTAACCGAA
1 TTTTTTCGGTTAACCGAA
34438739 TTTTTTCGGTTAACCGA
1 TTTTTTCGGTTAACCGA
34438756 CCGGTTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (18 bp):
TTTTTTCGGTTAACCGAA
Found at i:34439446 original size:30 final size:29
Alignment explanation
Indices: 34439409--34439475 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
34439399 ATTTCAAGGC
* *
34439409 CTTAATTAATTGTTAATTTTTAATTAAAAA
1 CTTAATTAAGTG-TAATTTTCAATTAAAAA
* **
34439439 TTTAATTAAGTGTAATTTTCGTTTAAAAA
1 CTTAATTAAGTGTAATTTTCAATTAAAAA
34439468 CTTAATTA
1 CTTAATTA
34439476 TTTTATAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (29 bp):
CTTAATTAAGTGTAATTTTCAATTAAAAA
Found at i:34440038 original size:14 final size:15
Alignment explanation
Indices: 34440000--34440042 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
34439990 TTATAAGTGA
*
34440000 ATAAAAATATTTTAT
1 ATAAAAATATATTAT
34440015 ATTAAAAAATATATT-T
1 A-T-AAAAATATATTAT
34440031 ATAAAAATATAT
1 ATAAAAATATAT
34440043 CAATTAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 2 0.08
16 3 0.12
17 10 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAAAAATATATTAT
Found at i:34444473 original size:18 final size:17
Alignment explanation
Indices: 34444445--34444479 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
34444435 ATTATTAAGA
*
34444445 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
34444462 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
34444480 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:34444733 original size:16 final size:16
Alignment explanation
Indices: 34444712--34444750 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
34444702 TTGATTTGCT
*
34444712 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
34444728 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
34444744 ATTACAC
1 ATTACAC
34444751 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:34444751 original size:16 final size:16
Alignment explanation
Indices: 34444725--34444781 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
34444715 ACACAGCTTT
* *
34444725 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
34444741 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
34444757 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
34444773 TCCAATACA
1 TCCAATACA
34444782 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:34448850 original size:4 final size:4
Alignment explanation
Indices: 34448841--34448868 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
34448831 AGGTTTGATA
34448841 CGTG CGTG CGTG CGTG CGTG CGTG CGTG
1 CGTG CGTG CGTG CGTG CGTG CGTG CGTG
34448869 AGGAGTGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.50, T:0.25
Consensus pattern (4 bp):
CGTG
Found at i:34449257 original size:19 final size:18
Alignment explanation
Indices: 34449217--34449250 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
34449207 TTTTCATTAC
34449217 AATTTATATATATTAATA
1 AATTTATATATATTAATA
34449235 AATTTAT-TATATTAAT
1 AATTTATATATATTAAT
34449251 CATAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTATATATATTAATA
Found at i:34450172 original size:21 final size:21
Alignment explanation
Indices: 34450142--34450205 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
34450132 TTAAGAATTG
*
34450142 TTTTAGTATTATTTTTATTTA
1 TTTTAATATTATTTTTATTTA
* *
34450163 TTTTAATATTTGTTTTTATGT-
1 TTTTAATA-TTATTTTTATTTA
*
34450184 TTTTAA-A-TATATTTGATTTA
1 TTTTAATATTAT-TTTTATTTA
34450204 TT
1 TT
34450206 ATATTTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 2 0.06
19 6 0.18
20 3 0.09
21 13 0.38
22 10 0.29
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTTAATATTATTTTTATTTA
Found at i:34450228 original size:25 final size:26
Alignment explanation
Indices: 34450168--34450216 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
34450158 ATTTATTTTA
*
34450168 ATATTTG-TTT-TTATGTTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
34450192 ATATTTGATTTATTATATTTTTAAA
1 ATATTTGATTTATTATATTTTTAAA
34450217 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (26 bp):
ATATTTGATTTATTATATTTTTAAAT
Found at i:34450937 original size:28 final size:28
Alignment explanation
Indices: 34450906--34450960 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
34450896 CTCTAACCTA
*
34450906 AAACTCAAAATATTAAAAT-TTAAACTCT
1 AAACCCAAAA-ATTAAAATATTAAACTCT
*
34450934 AAACCCTAAAATTAAAATATTAAACTC
1 AAACCCAAAAATTAAAATATTAAACTC
34450961 CAAGCCCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (28 bp):
AAACCCAAAAATTAAAATATTAAACTCT
Found at i:34450968 original size:28 final size:27
Alignment explanation
Indices: 34450917--34450986 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
34450907 AACTCAAAAT
*
34450917 ATTAAAATTTAAACTCTAAACCCTAAA
1 ATTAAAATTTAAACTCCAAACCCTAAA
*
34450944 ATTAAAATATTAAACTCCAAGCCCTAAA
1 ATTAAAAT-TTAAACTCCAAACCCTAAA
* *
34450972 TCTTAAATTTTAAAC
1 -ATTAAAATTTAAAC
34450987 CTTGAATCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 8 0.22
28 23 0.62
29 6 0.16
ACGTcount: A:0.49, C:0.19, G:0.01, T:0.31
Consensus pattern (27 bp):
ATTAAAATTTAAACTCCAAACCCTAAA
Found at i:34451613 original size:12 final size:12
Alignment explanation
Indices: 34451596--34451622 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
34451586 GAATTTAAAA
34451596 GAAGATAATGTT
1 GAAGATAATGTT
34451608 GAAGATAATGTT
1 GAAGATAATGTT
34451620 GAA
1 GAA
34451623 TTCGAGTGTA
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:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (12 bp):
GAAGATAATGTT
Found at i:34452653 original size:168 final size:168
Alignment explanation
Indices: 34452375--34452710 Score: 672
Period size: 168 Copynumber: 2.0 Consensus size: 168
34452365 GATTCGTAGT
34452375 CCACAAGGGTCAGAGTAGCCGAACCCTGAAACAGGGGAGAATTTTTCTAATAAACTGTACTAATT
1 CCACAAGGGTCAGAGTAGCCGAACCCTGAAACAGGGGAGAATTTTTCTAATAAACTGTACTAATT
34452440 GGCCTGATCAAAAAATTCTAGAAAAAAATTAGTAAGTAGATATATGAATCTAGTTTTAGGAAAAA
66 GGCCTGATCAAAAAATTCTAGAAAAAAATTAGTAAGTAGATATATGAATCTAGTTTTAGGAAAAA
34452505 TTTACAGAATTGGATTTCGAGTTTCGTAACTCGAGATA
131 TTTACAGAATTGGATTTCGAGTTTCGTAACTCGAGATA
34452543 CCACAAGGGTCAGAGTAGCCGAACCCTGAAACAGGGGAGAATTTTTCTAATAAACTGTACTAATT
1 CCACAAGGGTCAGAGTAGCCGAACCCTGAAACAGGGGAGAATTTTTCTAATAAACTGTACTAATT
34452608 GGCCTGATCAAAAAATTCTAGAAAAAAATTAGTAAGTAGATATATGAATCTAGTTTTAGGAAAAA
66 GGCCTGATCAAAAAATTCTAGAAAAAAATTAGTAAGTAGATATATGAATCTAGTTTTAGGAAAAA
34452673 TTTACAGAATTGGATTTCGAGTTTCGTAACTCGAGATA
131 TTTACAGAATTGGATTTCGAGTTTCGTAACTCGAGATA
34452711 TGATTTTTTT
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
168 168 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (168 bp):
CCACAAGGGTCAGAGTAGCCGAACCCTGAAACAGGGGAGAATTTTTCTAATAAACTGTACTAATT
GGCCTGATCAAAAAATTCTAGAAAAAAATTAGTAAGTAGATATATGAATCTAGTTTTAGGAAAAA
TTTACAGAATTGGATTTCGAGTTTCGTAACTCGAGATA
Found at i:34453909 original size:264 final size:264
Alignment explanation
Indices: 34453439--34453967 Score: 941
Period size: 264 Copynumber: 2.0 Consensus size: 264
34453429 TATAGGGCAC
*
34453439 AAGAGCACTATGCTCATCCCACAACAACTTCAATCGATTAAAGTATGCAGCAATCGAATAATCAC
1 AAGAGCACTATGCTCATCCCACAACAACTTCAATCGATTAAAGTATGCAGCAATCGAAGAATCAC
* *
34453504 CCTGACTTGCCGTAGCAATCTCTCTATGCAAGTAAAAAATCCTCGCCCCATCGATTTTATTGAAT
66 CCTGACTTGCCGTAGCAATCTCTCTAAGCAAGTAAAAAATCCTCGCCCCATCGATCTTATTGAAT
* *
34453569 CTCTCCTTCAAGTCTCCCCAAACCAATGCAACGCTAGAAGCAAACACAACACCGGCGGACAAATC
131 CTCTCCTTCAAATCTCCCCAAACCAATGCAACACTAGAAGCAAACACAACACCGGCGGACAAATC
*
34453634 GGGGATCACGGTATTGATGATCCAAGACAAGACTAAAGCATTACAACGATCCCATTGACGACTAA
196 GCGGATCACGGTATTGATGATCCAAGACAAGACTAAAGCATTACAACGATCCCATTGACGACTAA
34453699 TCTG
261 TCTG
*
34453703 AAGAGCACTATGCTTATCCCACAACAACTTCAATCGATTAAAGTATGCAGCAATCGAAGAATCAC
1 AAGAGCACTATGCTCATCCCACAACAACTTCAATCGATTAAAGTATGCAGCAATCGAAGAATCAC
*
34453768 CCTGACTTGCCGTGGCAATCTCTCTAAGCAAGTAAAAAATCCTCGCCCCATCGATCTTATTGAAT
66 CCTGACTTGCCGTAGCAATCTCTCTAAGCAAGTAAAAAATCCTCGCCCCATCGATCTTATTGAAT
* * *
34453833 CTCTCTTTCAAATCTCCCCAAACCAATGCAACACTGGAAGCAAACACAATACCGGCGGACAAATC
131 CTCTCCTTCAAATCTCCCCAAACCAATGCAACACTAGAAGCAAACACAACACCGGCGGACAAATC
* *
34453898 GCGGTTCACGGTATTGATGATCCAAGACAAGACTAAAGCATTACAGCGATCCCATTGACGACTAA
196 GCGGATCACGGTATTGATGATCCAAGACAAGACTAAAGCATTACAACGATCCCATTGACGACTAA
34453963 TCTG
261 TCTG
34453967 A
1 A
34453968 TAATCAAAAT
Statistics
Matches: 252, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
264 252 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (264 bp):
AAGAGCACTATGCTCATCCCACAACAACTTCAATCGATTAAAGTATGCAGCAATCGAAGAATCAC
CCTGACTTGCCGTAGCAATCTCTCTAAGCAAGTAAAAAATCCTCGCCCCATCGATCTTATTGAAT
CTCTCCTTCAAATCTCCCCAAACCAATGCAACACTAGAAGCAAACACAACACCGGCGGACAAATC
GCGGATCACGGTATTGATGATCCAAGACAAGACTAAAGCATTACAACGATCCCATTGACGACTAA
TCTG
Found at i:34454585 original size:11 final size:10
Alignment explanation
Indices: 34454559--34454584 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
34454549 AGCCCCTCTC
34454559 TTTTTTCTTT
1 TTTTTTCTTT
34454569 TTTTTTCTTT
1 TTTTTTCTTT
34454579 TTTTTT
1 TTTTTT
34454585 TTTGCACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:34454859 original size:18 final size:18
Alignment explanation
Indices: 34454805--34454866 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
34454795 AATAATAACT
*
34454805 TTTAGTAAATTTATTAAAT
1 TTTA-TAAATTTATTAAAA
* *
34454824 TTTAATAAA-ATATAAAAA
1 TTT-ATAAATTTATTAAAA
34454842 TTTATAAATTTATTAAAA
1 TTTATAAATTTATTAAAA
*
34454860 ATTATAA
1 TTTATAA
34454867 TTTTTTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
17 5 0.14
18 22 0.63
19 7 0.20
20 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TTTATAAATTTATTAAAA
Found at i:34455134 original size:29 final size:27
Alignment explanation
Indices: 34455101--34455199 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 27
34455091 TTACTTTTTG
34455101 TATAATTTTCTTACAACTTTATAAAATTT
1 TATAATTTT-TTACAA-TTTATAAAATTT
* *
34455130 TATAATTTTTTATATATATCTAT-ATATTT
1 TATAATTTTTTACA-AT-T-TATAAAATTT
34455159 TATAATTTTTTTACAATTTTTATAAAATTT
1 TATAA-TTTTTTACAA--TTTATAAAATTT
*
34455189 TACAATTTTTT
1 TATAATTTTTT
34455200 TATATTTTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
28 5 0.09
29 31 0.53
30 21 0.36
31 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (27 bp):
TATAATTTTTTACAATTTATAAAATTT
Found at i:34455142 original size:58 final size:58
Alignment explanation
Indices: 34455080--34455225 Score: 170
Period size: 58 Copynumber: 2.5 Consensus size: 58
34455070 TTTTACAAAA
* * *
34455080 TTTATATTTTTTTACTTTTTGTATAATTTTCTTACAA-CTTTATAAAATTTTATAATTTT
1 TTTATATTTTTATA-TATTT-TATAATTTTCTTACAATCTTTATAAAATTTTACAATTTT
* * * *
34455139 TTATATATATCTATATATTTTATAATTTTTTTACAATTTTTATAAAATTTTACAATTTT
1 TT-TATATTTTTATATATTTTATAATTTTCTTACAATCTTTATAAAATTTTACAATTTT
*
34455198 TTTATATTTTTATGAT-TTTTATATTTTT
1 TTTATATTTTTAT-ATATTTTATAATTTT
34455226 AATAATTTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
58 35 0.47
59 30 0.41
60 9 0.12
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (58 bp):
TTTATATTTTTATATATTTTATAATTTTCTTACAATCTTTATAAAATTTTACAATTTT
Found at i:34455168 original size:9 final size:9
Alignment explanation
Indices: 34455127--34455306 Score: 75
Period size: 9 Copynumber: 19.4 Consensus size: 9
34455117 CTTTATAAAA
34455127 TTTTATAATT
1 TTTTATAA-T
34455137 TTTTATATAT
1 TTTTATA-AT
* *
34455147 ATCTAT-AT
1 TTTTATAAT
34455155 ATTTTATAATTT
1 -TTTTATAA--T
*
34455167 TTTTACAAT
1 TTTTATAAT
*
34455176 TTTTATAAAA
1 TTTTAT-AAT
*
34455186 TTTTACAAT
1 TTTTATAAT
*
34455195 TTTTTTATAT
1 TTTTATA-AT
*
34455205 TTTTATGAT
1 TTTTATAAT
34455214 TTTTAT-AT
1 TTTTATAAT
34455222 TTTTAATAAT
1 TTTT-ATAAT
34455232 TTTT-TAAT
1 TTTTATAAT
* *
34455240 ATTTA-ATT
1 TTTTATAAT
*
34455248 TTTTATTAAAA
1 TTTTA-T-AAT
*
34455259 TTTAATAAT
1 TTTTATAAT
* **
34455268 ATTTATAGC
1 TTTTATAAT
*
34455277 TTTTATTGA-
1 TTTTA-TAAT
*
34455286 TTTTA-ATT
1 TTTTATAAT
34455294 TTTTATAAT
1 TTTTATAAT
34455303 TTTT
1 TTTT
34455307 TTTCTAATTT
Statistics
Matches: 124, Mismatches: 30, Indels: 33
0.66 0.16 0.18
Matches are distributed among these distances:
8 26 0.21
9 49 0.40
10 35 0.28
11 13 0.10
12 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:34455177 original size:19 final size:19
Alignment explanation
Indices: 34455068--34455197 Score: 59
Period size: 20 Copynumber: 6.7 Consensus size: 19
34455058 TTTCTTTTTC
*
34455068 TTTTTTACAAAATTTAT-AT
1 TTTTTTAC-AATTTTATAAT
**
34455087 TTTTTTACTTTTTGTATAAT
1 TTTTTTACAATTT-TATAAT
* *
34455107 TTTCTTACAACTTTATAA-
1 TTTTTTACAATTTTATAAT
** * *
34455125 AATTTTATAATTTTTTATAT
1 TTTTTTACAATTTTATA-AT
* * * *
34455145 ATATCTATATATTTTATAAT
1 TTTTTTACA-ATTTTATAAT
34455165 TTTTTTACAATTTTTATAA-
1 TTTTTTACAA-TTTTATAAT
**
34455184 AATTTTACAATTTT
1 TTTTTTACAATTTT
34455198 TTTATATTTT
Statistics
Matches: 82, Mismatches: 23, Indels: 13
0.69 0.19 0.11
Matches are distributed among these distances:
18 17 0.21
19 26 0.32
20 32 0.39
21 7 0.09
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (19 bp):
TTTTTTACAATTTTATAAT
Found at i:34455206 original size:29 final size:29
Alignment explanation
Indices: 34455118--34455210 Score: 116
Period size: 29 Copynumber: 3.2 Consensus size: 29
34455108 TTCTTACAAC
*
34455118 TTTATAAAATTTTATAATTTTTTATATATA
1 TTTATAAAATTTTATAATTTTTT-TATATT
* * *
34455148 TCTAT-ATATTTTATAATTTTTTTACAATT
1 TTTATAAAATTTTATAATTTTTTTA-TATT
*
34455177 TTTATAAAATTTTACAATTTTTTTATATT
1 TTTATAAAATTTTATAATTTTTTTATATT
34455206 TTTAT
1 TTTAT
34455211 GATTTTTATA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 2 0.04
29 30 0.57
30 21 0.40
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTATAAAATTTTATAATTTTTTTATATT
Found at i:34455207 original size:8 final size:8
Alignment explanation
Indices: 34455196--34455226 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
34455186 TTTTACAATT
34455196 TTTTTATA
1 TTTTTATA
34455204 TTTTTATGA
1 TTTTTAT-A
34455213 TTTTTATA
1 TTTTTATA
34455221 TTTTTA
1 TTTTTA
34455227 ATAATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (8 bp):
TTTTTATA
Found at i:34455208 original size:19 final size:19
Alignment explanation
Indices: 34455166--34455243 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
34455156 TTTTATAATT
* *
34455166 TTTTTACAATTTTTATAAA
1 TTTTTACAATTTTTTTATA
*
34455185 ATTTTACAATTTTTTTATA
1 TTTTTACAATTTTTTTATA
**
34455204 TTTTTATGA--TTTTTATA
1 TTTTTACAATTTTTTTATA
* *
34455221 TTTTTAATAATTTTTTAATA
1 TTTTT-ACAATTTTTTTATA
34455241 TTT
1 TTT
34455244 AATTTTTTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
17 13 0.27
18 3 0.06
19 22 0.46
20 10 0.21
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (19 bp):
TTTTTACAATTTTTTTATA
Found at i:34455429 original size:90 final size:86
Alignment explanation
Indices: 34455329--34455548 Score: 309
Period size: 90 Copynumber: 2.5 Consensus size: 86
34455319 ACTAAAAGCA
34455329 AGGA-CTTAATTGCTTTTTTTGAAAAAGTTTGAGAGTCTTTTTGATGCATTTTGAAAGTTCAAGT
1 AGGAGCTTAATTGCTTTTTTTGAAAAAGTTTGAGAGTCTTTTTGATGCATTTTGAAAGTTCAAGT
*
34455393 ACCCAATTGAGCGCAAAAAAAAAGT
66 ACCCAAATGAGCG---AAAAAAA-T
* *
34455418 AGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAG-GGCTTTTTTGATGCATTTTGAAAGTTCAAG
1 AGGAGCTTAATTGCTTTTTTTGAAAAAGTTTGAGAGTC-TTTTTGATGCATTTTGAAAGTTCAAG
** *
34455482 TATTCAAATGAGTGAAAAAAAT
65 TACCCAAATGAGCGAAAAAAAT
*
34455504 AGGAGCTTAATTGCTCTTTTTGAAAAAGTTTGAGAGATCTTTTTG
1 AGGAGCTTAATTGCTTTTTTTGAAAAAGTTTGAGAG-TCTTTTTG
34455549 CACCATTAAG
Statistics
Matches: 118, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
86 33 0.28
87 14 0.12
88 1 0.01
89 5 0.04
90 65 0.55
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (86 bp):
AGGAGCTTAATTGCTTTTTTTGAAAAAGTTTGAGAGTCTTTTTGATGCATTTTGAAAGTTCAAGT
ACCCAAATGAGCGAAAAAAAT
Found at i:34457157 original size:18 final size:18
Alignment explanation
Indices: 34457130--34457166 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
34457120 ATAGCAAAAC
* *
34457130 ATGCATAAACAACACTAA
1 ATGCAAAAACAAAACTAA
34457148 ATGCAAAAACAAAACTAA
1 ATGCAAAAACAAAACTAA
34457166 A
1 A
34457167 ACACAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.19, G:0.05, T:0.14
Consensus pattern (18 bp):
ATGCAAAAACAAAACTAA
Found at i:34463632 original size:21 final size:20
Alignment explanation
Indices: 34463581--34463632 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
34463571 GCTACCGTAT
34463581 AATTTATAAATAAAATACAA
1 AATTTATAAATAAAATACAA
* * * *
34463601 AAATT-TAAATATCATTACGA
1 AATTTATAAATA-AAATACAA
34463621 AATTTATAAATA
1 AATTTATAAATA
34463633 CTGCATGTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 6 0.24
20 13 0.52
21 6 0.24
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (20 bp):
AATTTATAAATAAAATACAA
Found at i:34466158 original size:12 final size:12
Alignment explanation
Indices: 34466143--34466172 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
34466133 ACAATAATAC
34466143 TATATATAAATG
1 TATATATAAATG
*
34466155 TATATATATATG
1 TATATATAAATG
34466167 TATATA
1 TATATA
34466173 ATAGAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATATAAATG
Found at i:34466275 original size:19 final size:17
Alignment explanation
Indices: 34466251--34466297 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
34466241 AATTAAAGTA
*
34466251 ATAAAAAATAATACTATAT
1 ATAAAAAAT-ATA-TATAC
*
34466270 ATAAAATATATATATAC
1 ATAAAAAATATATATAC
34466287 AT-AAAAATATA
1 ATAAAAAATATA
34466298 CACTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATATATATAC
Found at i:34466293 original size:18 final size:19
Alignment explanation
Indices: 34466254--34466302 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
34466244 TAAAGTAATA
*
34466254 AAAAATA-ATACTATATAT
1 AAAAATATATACTATACAT
34466272 -AAAATATATA-TATACAT
1 AAAAATATATACTATACAT
*
34466289 AAAAATATACACTA
1 AAAAATATATACTA
34466303 ATATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATATATACTATACAT
Found at i:34469714 original size:87 final size:87
Alignment explanation
Indices: 34469565--34469875 Score: 471
Period size: 87 Copynumber: 3.6 Consensus size: 87
34469555 NNNNNNNNNN
* *
34469565 TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAA
1 TTCGATCTGCTTCACTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTGACCAGCTCCACTGCAA
*
34469630 CCGATGGAGGCAAGGCTTTATT
66 CCGATGGAGGCAAGGCTTTGTT
* * * * * * **
34469652 TTCGATCGGCTCCACTGTTAACGCAGGAAGGTAAGATTTGTTATCTTTAACCAGCTGGACTGCAA
1 TTCGATCTGCTTCACTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTGACCAGCTCCACTGCAA
34469717 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
**
34469739 TTCGATCTGCTTCGGTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTGACCAGCTCCACTGCAA
1 TTCGATCTGCTTCACTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTGACCAGCTCCACTGCAA
*
34469804 CCGATGGAGGCAAAGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
*
34469826 TTCGATCTTCTTCACTGTTAATGCAGGAAGGCAAGATCTGCTT-TCTTTGA
1 TTCGATCTGCTTCACTGTTAATGCAGGAAGGCAAGATCTG-TTATCTTTGA
34469876 TCTATTCTCT
Statistics
Matches: 198, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
87 196 0.99
88 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (87 bp):
TTCGATCTGCTTCACTGTTAATGCAGGAAGGCAAGATCTGTTATCTTTGACCAGCTCCACTGCAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:34470485 original size:108 final size:108
Alignment explanation
Indices: 34470296--34470491 Score: 313
Period size: 108 Copynumber: 1.8 Consensus size: 108
34470286 GAAAAATGCT
34470296 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTATAAACAAACAAAT
1 TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTATAAACAAACAAAT
34470361 CAATCAAGATAGCAAATTTTGCTGAGATACGAGATGTATAAGA
66 CAATCAAGATAGCAAATTTTGCTGAGATACGAGATGTATAAGA
* * * * **
34470404 TGAAAAAGATTATCACAATGGATAAGATGGAAA-TTTGTTGAGAGCAAAGCTCTAAATGAACAAA
1 TGAAAAAGATTATCAAAATGGACAAAAT-GAAATTTTGTTGAGAGCAAAGCTATAAACAAACAAA
*
34470468 TTAATCAAGATAGCAAATTTTGCT
65 TCAATCAAGATAGCAAATTTTGCT
34470492 AGAATACAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
108 76 0.95
109 4 0.05
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (108 bp):
TGAAAAAGATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTATAAACAAACAAAT
CAATCAAGATAGCAAATTTTGCTGAGATACGAGATGTATAAGA
Found at i:34470555 original size:45 final size:43
Alignment explanation
Indices: 34470457--34470557 Score: 112
Period size: 45 Copynumber: 2.3 Consensus size: 43
34470447 GCAAAGCTCT
* * *
34470457 AAATGAACAAATTAATCAAGATAGCAAATTTTGCTAGAATACA
1 AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATACA
* **
34470500 AAATGAGAATAAATTAATCAAGATGGCGTATTTTGTCAAAAATACAA
1 AAAT--GAATAAATTAATCAAGATAGCAAATTTTG-CAAAAATAC-A
34470547 AAATGAATAAA
1 AAATGAATAAA
34470558 ATGGAAATAG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
43 4 0.08
45 32 0.67
46 7 0.15
47 5 0.10
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (43 bp):
AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATACA
Found at i:34470845 original size:13 final size:12
Alignment explanation
Indices: 34470827--34470890 Score: 76
Period size: 13 Copynumber: 5.1 Consensus size: 12
34470817 TGGCCTCTCC
34470827 TTTTTCTTTTTCT
1 TTTTTCTTTTT-T
34470840 TTTTTCTTTTTT
1 TTTTTCTTTTTT
34470852 TCTTTTCTTTTTT
1 T-TTTTCTTTTTT
*
34470865 TGTTTT-TTTGTT
1 T-TTTTCTTTTTT
34470877 TTTTTCGTTTTTT
1 TTTTTC-TTTTTT
34470890 T
1 T
34470891 CAAGTGAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
11 4 0.09
12 8 0.18
13 33 0.73
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:34470850 original size:8 final size:8
Alignment explanation
Indices: 34470833--34470891 Score: 63
Period size: 8 Copynumber: 7.8 Consensus size: 8
34470823 CTCCTTTTTC
34470833 TTTTTC-T
1 TTTTTCTT
34470840 TTTTTCTT
1 TTTTTCTT
34470848 TTTTTC--
1 TTTTTCTT
34470854 -TTTTCTT
1 TTTTTCTT
*
34470861 TTTTTGTT
1 TTTTTCTT
*
34470869 TTTTTGTT
1 TTTTTCTT
34470877 TTTTTCGTT
1 TTTTTC-TT
34470886 TTTTTC
1 TTTTTC
34470892 AAGTGAAGTG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
5 5 0.11
7 6 0.13
8 26 0.58
9 8 0.18
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (8 bp):
TTTTTCTT
Found at i:34470853 original size:21 final size:22
Alignment explanation
Indices: 34470827--34470879 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
34470817 TGGCCTCTCC
34470827 TTTTTCTTTTTC-TTTTTTCTT
1 TTTTTCTTTTTCTTTTTTTCTT
*
34470848 TTTTTC-TTTTCTTTTTTTGTT
1 TTTTTCTTTTTCTTTTTTTCTT
*
34470869 TTTTTGTTTTT
1 TTTTTCTTTTT
34470880 TTCGTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 5 0.18
21 19 0.68
22 4 0.14
ACGTcount: A:0.00, C:0.09, G:0.04, T:0.87
Consensus pattern (22 bp):
TTTTTCTTTTTCTTTTTTTCTT
Found at i:34471319 original size:8 final size:8
Alignment explanation
Indices: 34471302--34471349 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
34471292 GTAGAGGTTT
34471302 TTTTTCTTA
1 TTTTT-TTA
34471311 TTTTTTTA
1 TTTTTTTA
*
34471319 TTCTTTTA
1 TTTTTTTA
*
34471327 TTCTTTTA
1 TTTTTTTA
34471335 TTTTTATT-
1 TTTTT-TTA
34471343 TTTTTTT
1 TTTTTTT
34471350 TGCTTTTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
7 2 0.06
8 27 0.75
9 7 0.19
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTA
Found at i:34471322 original size:14 final size:14
Alignment explanation
Indices: 34471299--34471347 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
34471289 CCGGTAGAGG
34471299 TTTTTT-TTCTTAT
1 TTTTTTATTCTTAT
34471312 TTTTTTATTCTTTTAT
1 TTTTTTATTC--TTAT
* *
34471328 TCTTTTATTTTTAT
1 TTTTTTATTCTTAT
34471342 TTTTTT
1 TTTTTT
34471348 TTTGCTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 6 0.20
14 12 0.40
16 12 0.40
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTATTCTTAT
Found at i:34471330 original size:22 final size:22
Alignment explanation
Indices: 34471300--34471361 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
34471290 CGGTAGAGGT
*
34471300 TTTTTTTCTTATT-TTTTTATTC
1 TTTTATTCTT-TTATTTTTATTC
*
34471322 TTTTATTCTTTTATTTTTATTT
1 TTTTATTCTTTTATTTTTATTC
* *
34471344 TTTTTTTGCTTTTGTTTT
1 TTTTATT-CTTTTATTTT
34471362 CTCGTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.06
22 23 0.68
23 9 0.26
ACGTcount: A:0.08, C:0.06, G:0.03, T:0.82
Consensus pattern (22 bp):
TTTTATTCTTTTATTTTTATTC
Found at i:34471356 original size:9 final size:9
Alignment explanation
Indices: 34471344--34471423 Score: 58
Period size: 8 Copynumber: 8.6 Consensus size: 9
34471334 ATTTTTATTT
34471344 TTTTTTTGC
1 TTTTTTTGC
*
34471353 TTTTGTTTTC
1 TTTT-TTTGC
*
34471363 TCGTTTTTTTAC
1 T---TTTTTTGC
34471375 TTTTTTTGC
1 TTTTTTTGC
34471384 -TTTTTTGC
1 TTTTTTTGC
34471392 -TTTTTTGCTC
1 TTTTTTTG--C
*
34471402 TTTTTTTGT
1 TTTTTTTGC
34471411 TTTTTTTG-
1 TTTTTTTGC
34471419 TTTTT
1 TTTTT
34471424 GCCTCCACTG
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
8 20 0.33
9 19 0.32
10 6 0.10
11 7 0.12
12 5 0.08
13 3 0.05
ACGTcount: A:0.01, C:0.10, G:0.10, T:0.79
Consensus pattern (9 bp):
TTTTTTTGC
Found at i:34471387 original size:17 final size:16
Alignment explanation
Indices: 34471367--34471406 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
34471357 GTTTTCTCGT
34471367 TTTTTTACTTTTTTTGC
1 TTTTTTAC-TTTTTTGC
*
34471384 TTTTTTGCTTTTTTGC
1 TTTTTTACTTTTTTGC
34471400 TCTTTTT
1 T-TTTTT
34471407 TTGTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.03, C:0.12, G:0.07, T:0.78
Consensus pattern (16 bp):
TTTTTTACTTTTTTGC
Found at i:34471413 original size:8 final size:8
Alignment explanation
Indices: 34471335--34471423 Score: 54
Period size: 8 Copynumber: 10.4 Consensus size: 8
34471325 TATTCTTTTA
*
34471335 TTTTTATT
1 TTTTTGTT
34471343 TTTTT-TT
1 TTTTTGTT
34471350 TGCTTTTGTT
1 T--TTTTGTT
* *
34471360 TTCTCGTT
1 TTTTTGTT
*
34471368 TTTTTACTT
1 TTTTT-GTT
*
34471377 TTTTTGCT
1 TTTTTGTT
34471385 TTTTTGCTT
1 TTTTTG-TT
*
34471394 TTTTGCTCTT
1 TTTT--TGTT
34471404 TTTTTGTTT
1 TTTTTG-TT
34471413 TTTTTGTT
1 TTTTTGTT
34471421 TTT
1 TTT
34471424 GCCTCCACTG
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
7 3 0.05
8 26 0.41
9 24 0.38
10 9 0.14
11 1 0.02
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.80
Consensus pattern (8 bp):
TTTTTGTT
Found at i:34472811 original size:62 final size:62
Alignment explanation
Indices: 34472709--34472833 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
34472699 CTAAACTCGA
*
34472709 CGTACTTTTGGATTTTAGGAAATTTACTGTATGCAATGAAACGTAATGTTGATGCATGAATG
1 CGTACTTTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGATGCATGAATG
* * * *
34472771 CGTATTTTTGGATTTTAGGAAATTTATTGCATGCGATGAAATGTAATGTTGATGCATGAATG
1 CGTACTTTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGATGCATGAATG
34472833 C
1 C
34472834 AAAAAANNNN
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (62 bp):
CGTACTTTTGGATTTTAGGAAATTTACTGCATGCAATGAAACGTAATGTTGATGCATGAATG
Found at i:34474551 original size:3 final size:3
Alignment explanation
Indices: 34474538--34474623 Score: 60
Period size: 3 Copynumber: 29.3 Consensus size: 3
34474528 GAGGGCATAT
34474538 ATA AT- ATA ATA ATA AT- ATA A-A A-A ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA
* *
34474582 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
34474624 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 13 0.19
3 46 0.68
4 7 0.10
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:34474564 original size:18 final size:18
Alignment explanation
Indices: 34474543--34474623 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
34474533 CATATATAAT
34474543 ATAATAATAATATAAAAA
1 ATAATAATAATATAAAAA
* *
34474561 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-ATAAAAA
*
34474582 ATAATAATAATATAAATA
1 ATAATAATAATATAAAAA
*
34474600 ATAGTAA-AA-ATAATAAA
1 ATAATAATAATATAA-AAA
34474617 ATAATAA
1 ATAATAA
34474624 AACAAAGCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
16 4 0.08
17 10 0.19
18 18 0.34
19 5 0.09
20 5 0.09
21 11 0.21
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (18 bp):
ATAATAATAATATAAAAA
Found at i:34475172 original size:4 final size:4
Alignment explanation
Indices: 34475163--34475189 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
34475153 GGCCAAGGTT
34475163 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
34475190 TTTTGTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:34481439 original size:15 final size:15
Alignment explanation
Indices: 34481407--34481448 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
34481397 TTCAACAAAT
34481407 AATTAAAAATATTTAAA
1 AATTAAAAA-ATTT-AA
34481424 AATTAAAAAA-TTAA
1 AATTAAAAAATTTAA
34481438 AATTCAAAAAA
1 AATT-AAAAAA
34481449 ATAATTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.25
15 8 0.33
16 1 0.04
17 9 0.38
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
AATTAAAAAATTTAA
Found at i:34481841 original size:32 final size:32
Alignment explanation
Indices: 34481805--34481866 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
34481795 GTTACAAAAT
* * * *
34481805 AGTCACTGAACTATTCGAAATTTTTTATTTTA
1 AGTCACTAAACTATACAAAAGTTTTTATTTTA
34481837 AGTCACTAAACTATACAAAAGTTTTTATTT
1 AGTCACTAAACTATACAAAAGTTTTTATTT
34481867 ATGTCATTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (32 bp):
AGTCACTAAACTATACAAAAGTTTTTATTTTA
Found at i:34486479 original size:36 final size:34
Alignment explanation
Indices: 34486345--34486691 Score: 205
Period size: 35 Copynumber: 9.6 Consensus size: 34
34486335 CCAATCTTTG
* * * *
34486345 AAAAAGGTTGTGATAAACCTGTCTAAGACAACCTT
1 AAAAAGGTTGGGATAGACAT-TCTAAGGCAACCTT
* ** * * * *
34486380 AAAAAGGTCGATATAGTTCTTGTTTAAGGCAACTTTT
1 AAAAAGGTTGGGATAG-ACAT-TCTAAGGCAAC-CTT
*
34486417 AAAAACGGTTGGGATAGAGC-TGTCTAAAGCAACCTT
1 AAAAA-GGTTGGGATAGA-CAT-TCTAAGGCAACCTT
* **
34486453 AAAAAGGTTGGGATCGACATTCTCTAAAACAACCTAT
1 AAAAAGGTTGGGATAGACA-T-TCTAAGGCAACCT-T
*
34486490 AAAAAAATGTTGGGATAGAGC-TGTCTAAGGCAACCTT
1 --AAAAAGGTTGGGATAGA-CAT-TCTAAGGCAACCTT
* *
34486527 AAACAGGTTAGGATAGACCATGTCTAAGGCAACCTTT
1 AAAAAGGTTGGGATAGA-CAT-TCTAAGGCAACC-TT
* *
34486564 AAAAAAGGTTGGAATAGAC-TCGTTTAAGGCAACCTT
1 -AAAAAGGTTGGGATAGACAT--TCTAAGGCAACCTT
* * *
34486600 AAAAAGGTTGGGATAGACCATGTTTAAGGTAACTTTT
1 AAAAAGGTTGGGATAGA-CAT-TCTAAGGCAAC-CTT
* * * *
34486637 AAAAAAGGTTGGGATAGACCTGTTTAAAGCAACTTT
1 -AAAAAGGTTGGGATAGACAT-TCTAAGGCAACCTT
34486673 AAAAAGGTTGGGATAGACA
1 AAAAAGGTTGGGATAGACA
34486692 CGTATAATAT
Statistics
Matches: 255, Mismatches: 39, Indels: 36
0.77 0.12 0.11
Matches are distributed among these distances:
34 1 0.00
35 72 0.28
36 64 0.25
37 50 0.20
38 52 0.20
39 15 0.06
40 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (34 bp):
AAAAAGGTTGGGATAGACATTCTAAGGCAACCTT
Found at i:34486516 original size:74 final size:73
Alignment explanation
Indices: 34486340--34486690 Score: 352
Period size: 73 Copynumber: 4.8 Consensus size: 73
34486330 TAAGACCAAT
* * * * * ** **
34486340 CTTTGAAAAAGGTTGTGATAAACCTGTCT-AAGACAACCTTAAAAAGGTCGATATAGTTC-TTGT
1 CTTTAAAAAAGGTTGGGATAGAGCTGTCTAAAG-CAACCTTAAAAAGGTTGGGATAGACCATT-T
*
34486403 TTAAGGCAAC
64 CTAAGGCAAC
* * *
34486413 TTTTAAAAACGGTTGGGATAGAGCTGTCTAAAGCAACCTTAAAAAGGTTGGGATCGA-CATTCTC
1 CTTTAAAAAAGGTTGGGATAGAGCTGTCTAAAGCAACCTTAAAAAGGTTGGGATAGACCATT-TC
**
34486477 TAAAACAAC
65 TAAGGCAAC
* * * * * *
34486486 CTATAAAAAAATGTTGGGATAGAGCTGTCTAAGGCAACCTTAAACAGGTTAGGATAGACCATGTC
1 CT-TTAAAAAAGGTTGGGATAGAGCTGTCTAAAGCAACCTTAAAAAGGTTGGGATAGACCATTTC
34486551 TAAGGCAAC
65 TAAGGCAAC
* * *
34486560 CTTTAAAAAAGGTTGGAATAGA-CTCGTTTAAGGCAACCTTAAAAAGGTTGGGATAGACCATGTT
1 CTTTAAAAAAGGTTGGGATAGAGCT-GTCTAAAGCAACCTTAAAAAGGTTGGGATAGACCAT-TT
*
34486624 -TAAGGTAAC
64 CTAAGGCAAC
* * * *
34486633 TTTTAAAAAAGGTTGGGATAGACCTGTTTAAAGCAACTTTAAAAAGGTTGGGATAGAC
1 CTTTAAAAAAGGTTGGGATAGAGCTGTCTAAAGCAACCTTAAAAAGGTTGGGATAGAC
34486691 ACGTATAATA
Statistics
Matches: 233, Mismatches: 38, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
72 3 0.01
73 162 0.70
74 65 0.28
75 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (73 bp):
CTTTAAAAAAGGTTGGGATAGAGCTGTCTAAAGCAACCTTAAAAAGGTTGGGATAGACCATTTCT
AAGGCAAC
Found at i:34486640 original size:147 final size:146
Alignment explanation
Indices: 34486345--34486690 Score: 369
Period size: 147 Copynumber: 2.4 Consensus size: 146
34486335 CCAATCTTTG
* * * * ** * *
34486345 AAAAAGGTTGTGATAAACCTGTCT-AAGACAACCTTAAAAAGG-TCGATATAGTTCTTGTTTAAG
1 AAAAAGGTTGGGATAGACCTGTCTAAAG-CAACCTTAAAAAGGTTAG-GATAGACCATGTCTAAG
* * * *
34486408 GCAACTTTTAAAAACGGTTGGGATAGAGCTGTCTAAAGCAACCTTAAAAAGGTTGGGATCGACAT
64 GCAACCTTTAAAAAAGGTTGGAATAGAGCTGTCTAAAGCAACCTTAAAAAGGTTGGGATAGACAT
34486473 TCTCTAAAACAACCTATAA
129 TCTCTAAAACAACCTAT-A
* * * *
34486492 AAAAATGTTGGGATAGAGCTGTCTAAGGCAACCTTAAACAGGTTAGGATAGACCATGTCTAAGGC
1 AAAAAGGTTGGGATAGACCTGTCTAAAGCAACCTTAAAAAGGTTAGGATAGACCATGTCTAAGGC
* *
34486557 AACCTTTAAAAAAGGTTGGAATAGA-CTCGTTTAAGGCAACCTTAAAAAGGTTGGGATAGACCAT
66 AACCTTTAAAAAAGGTTGGAATAGAGCT-GTCTAAAGCAACCTTAAAAAGGTTGGGATAGA-CAT
*** * *
34486621 GT-T-TAAGGTAACTTTTA
129 -TCTCTAAAACAACCTATA
* * *
34486638 AAAAAGGTTGGGATAGACCTGTTTAAAGCAACTTTAAAAAGGTTGGGATAGAC
1 AAAAAGGTTGGGATAGACCTGTCTAAAGCAACCTTAAAAAGGTTAGGATAGAC
34486691 ACGTATAATA
Statistics
Matches: 164, Mismatches: 30, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
146 49 0.30
147 106 0.65
148 8 0.05
149 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (146 bp):
AAAAAGGTTGGGATAGACCTGTCTAAAGCAACCTTAAAAAGGTTAGGATAGACCATGTCTAAGGC
AACCTTTAAAAAAGGTTGGAATAGAGCTGTCTAAAGCAACCTTAAAAAGGTTGGGATAGACATTC
TCTAAAACAACCTATA
Found at i:34486830 original size:6 final size:6
Alignment explanation
Indices: 34486798--34486841 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
34486788 TACAACTAAA
*
34486798 AAAATTT AAAATTT AAAATAC AAAATT AAAATT AAAATT AAAAT
1 AAAA-TT AAAA-TT AAAAT-T AAAATT AAAATT AAAATT AAAAT
34486842 AAAGATTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 18 0.53
7 16 0.47
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:34489682 original size:47 final size:47
Alignment explanation
Indices: 34489608--34489742 Score: 162
Period size: 56 Copynumber: 2.7 Consensus size: 47
34489598 ATCAAATAAA
* *
34489608 TAATGCATACTTTACCCGGGTAAAGTATGCATTATTAGTGAATCTGC
1 TAATACATACTTTATCCGGGTAAAGTATGCATTATTAGTGAATCTGC
34489655 TAATACATACTTTATCCGGGTAAAGTATGCATAGTATGTATTATTAGTGAATCTGC
1 TAATACATACTTTATCCGGGTAAAGTATGC---------ATTATTAGTGAATCTGC
*
34489711 TAATACATATTTTATCCGGGTAAAGTATGCAT
1 TAATACATACTTTATCCGGGTAAAGTATGCAT
34489743 ACATTCTTAA
Statistics
Matches: 76, Mismatches: 3, Indels: 18
0.78 0.03 0.19
Matches are distributed among these distances:
47 30 0.39
56 46 0.61
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (47 bp):
TAATACATACTTTATCCGGGTAAAGTATGCATTATTAGTGAATCTGC
Found at i:34489717 original size:56 final size:56
Alignment explanation
Indices: 34489631--34489743 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
34489621 ACCCGGGTAA
34489631 AGTATGCATTATTAGTGAATCTGCTAATACATACTTTATCCGGGTAAAGTATGCAT
1 AGTATGCATTATTAGTGAATCTGCTAATACATACTTTATCCGGGTAAAGTATGCAT
* *
34489687 AGTATGTATTATTAGTGAATCTGCTAATACATATTTTATCCGGGTAAAGTATGCAT
1 AGTATGCATTATTAGTGAATCTGCTAATACATACTTTATCCGGGTAAAGTATGCAT
34489743 A
1 A
34489744 CATTCTTAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (56 bp):
AGTATGCATTATTAGTGAATCTGCTAATACATACTTTATCCGGGTAAAGTATGCAT
Found at i:34490178 original size:14 final size:15
Alignment explanation
Indices: 34490148--34490193 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
34490138 CAAAACCCTA
* *
34490148 AAACCATAAG-CCTT
1 AAACCACAAGACCAT
34490162 AAACCACAA-ACCAT
1 AAACCACAAGACCAT
*
34490176 AAACCTCAAGACCAT
1 AAACCACAAGACCAT
34490191 AAA
1 AAA
34490194 ATCTTAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 19 0.70
15 8 0.30
ACGTcount: A:0.52, C:0.30, G:0.04, T:0.13
Consensus pattern (15 bp):
AAACCACAAGACCAT
Found at i:34490400 original size:22 final size:22
Alignment explanation
Indices: 34490346--34490389 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
34490336 AGATTAATCG
*
34490346 CAAACCCATAATCACAAAACCC
1 CAAATCCATAATCACAAAACCC
*
34490368 CAAATCCATAATCATAAAACCC
1 CAAATCCATAATCACAAAACCC
34490390 TAACATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (22 bp):
CAAATCCATAATCACAAAACCC
Found at i:34490424 original size:22 final size:24
Alignment explanation
Indices: 34490397--34490448 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
34490387 CCCTAACATC
*
34490397 ATAAACCCCAAACCCGTAAAC-AT
1 ATAAACCCCAAAACCGTAAACTAT
*
34490420 A-AAACCCTAAAACCGTAAACTAT
1 ATAAACCCCAAAACCGTAAACTAT
34490443 ATAAAC
1 ATAAAC
34490449 TATAATCCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 17 0.68
23 4 0.16
24 4 0.16
ACGTcount: A:0.52, C:0.29, G:0.04, T:0.15
Consensus pattern (24 bp):
ATAAACCCCAAAACCGTAAACTAT
Done.