Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 20 of 22
Found at i:8846292 original size:2 final size:2
Alignment explanation
Indices: 8846287--8846319 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
8846277 GAGTTGAGAT
*
8846287 TA TA TA TA AA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8846320 AATGTCGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:8854570 original size:15 final size:17
Alignment explanation
Indices: 8854550--8854593 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
8854540 TTTTTAATAA
8854550 ATTTTTTATATT-AA-T
1 ATTTTTTATATTAAATT
8854565 ATTTTTTATCATTAAATT
1 ATTTTTTAT-ATTAAATT
8854583 ATTTGTTTATA
1 ATTT-TTTATA
8854594 CTCTTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.36
16 3 0.12
17 2 0.08
18 6 0.24
19 5 0.20
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
ATTTTTTATATTAAATT
Found at i:8854628 original size:28 final size:28
Alignment explanation
Indices: 8854597--8854651 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
8854587 GTTTATACTC
*
8854597 TTAAAATTTAAGATTTAGAATATAAAAA
1 TTAAAATTTAAGATTGAGAATATAAAAA
* ** *
8854625 TTAAGATTTTTGATTGATAATATAAAA
1 TTAAAATTTAAGATTGAGAATATAAAA
8854652 CGGCACATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (28 bp):
TTAAAATTTAAGATTGAGAATATAAAAA
Found at i:8855035 original size:22 final size:21
Alignment explanation
Indices: 8854998--8855038 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
8854988 TAAATGAAAT
*
8854998 ATAAATAAATAAATAAAAAGA
1 ATAAAAAAATAAATAAAAAGA
8855019 ATAAAAAAATTAAATAAAAA
1 ATAAAAAAA-TAAATAAAAA
8855039 TATTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (21 bp):
ATAAAAAAATAAATAAAAAGA
Found at i:8855038 original size:13 final size:14
Alignment explanation
Indices: 8854982--8855036 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 14
8854972 TTAATTCGAG
8854982 TAAAATTAAATGAAA
1 TAAAATTAAAT-AAA
8854997 TATAAA-TAAATAAA
1 TA-AAATTAAATAAA
8855011 TAAAA--AGAATAAA
1 TAAAATTA-AATAAA
8855024 -AAAATTAAATAAA
1 TAAAATTAAATAAA
8855037 AATATTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 5 0.14
13 15 0.42
14 6 0.17
15 7 0.19
16 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (14 bp):
TAAAATTAAATAAA
Found at i:8866728 original size:2 final size:2
Alignment explanation
Indices: 8866721--8866748 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8866711 ACATGTTATC
8866721 AT 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 AT
8866749 GTAGGCTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8871786 original size:22 final size:20
Alignment explanation
Indices: 8871756--8871806 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
8871746 GGAGGAGGAA
8871756 AATAAAACCTAGAAATAAAAAT
1 AATAAAACCT--AAATAAAAAT
* *
8871778 AATACAACC-AAATAATAAT
1 AATAAAACCTAAATAAAAAT
8871797 AATAAAACCT
1 AATAAAACCT
8871807 TAATTTAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 17 0.68
22 8 0.32
ACGTcount: A:0.65, C:0.14, G:0.02, T:0.20
Consensus pattern (20 bp):
AATAAAACCTAAATAAAAAT
Found at i:8879903 original size:17 final size:17
Alignment explanation
Indices: 8879878--8879914 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
8879868 TCAATCGTTA
8879878 ATAAATATTAGTGATGT
1 ATAAATATTAGTGATGT
*
8879895 ATAATTATTAGTGATGT
1 ATAAATATTAGTGATGT
8879912 ATA
1 ATA
8879915 GGAAATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (17 bp):
ATAAATATTAGTGATGT
Found at i:8880245 original size:404 final size:406
Alignment explanation
Indices: 8879490--8880288 Score: 1500
Period size: 404 Copynumber: 2.0 Consensus size: 406
8879480 TTATAGAATT
*
8879490 TAATTATTAGTGATGTATAGGAAATATGAATAAAAATATTATTGTAAACATATACGGATTTAGAT
1 TAATTATTAGTGATGTATAGGAAATATGAATAAAAATATTATTGTAAACAGATACGGATTTAGAT
8879555 TTAGATAATTGTATACCCATGAAGAGCATTTTAATAATTTTTTTTGTATAATCAAGTTTTTAAAT
66 TTAGATAATTGTATACCCATGAAGAGCATTTTAATAATTTTTTTTGTATAATCAAGTTTTTAAAT
8879620 GGGTTCAGATATGGGTATGTATTAGGGTTCGAGTGAGAGTAGTAAATTTAAAAAATTTTCAAGTA
131 GGGTTCAGATATGGGTATGTATTAGGGTTCGAGTGAGAGTAGTAAATTTAAAAAATTTTCAAGTA
8879685 ATTTGAGATTCAGGTTCTTTATTTATTAATAGAGTTCGGATTCGGGTATTTCAAAATTAATAAAT
196 ATTTGAGATTCAGGTTCTTTATTTATTAATAGAGTTCGGATTCGGGTATTTCAAAATTAATAAAT
8879750 ATTCTACATGTTGACATCCTTAGCTTGATTGTTGGGTTGCTCAAACTAATATAATTAAAGATTAC
261 ATTCTACATGTTGACATCCTTAGCTTGATTGTTGGGTTGCTCAAACTAATATAATTAAAGATTAC
8879815 CAACATTTAATCATTAAAAAGTTTACTCATTTGAGCAAAGACAAAAATGGTAGTCAATCGTTAAT
326 CAACATTTAATCATTAAAAAGTTTACTCATTTGAGCAAAGACAAAAATGGTAGTCAATCGTTAAT
8879880 AAATATTAGTGATGTA
391 AAATATTAGTGATGTA
8879896 TAATTATTAGTGATGTATAGGAAATATGAATAAAAAATATTATTGTAAACAGATACGGATTTAGA
1 TAATTATTAGTGATGTATAGGAAATATGAAT-AAAAATATTATTGTAAACAGATACGGATTTAGA
*
8879961 TTTAGATAATTGTATACCCATGAAGAGCATTTTAATAATTTTTTTTGTATAATCAGGTTTTTAAA
65 TTTAGATAATTGTATACCCATGAAGAGCATTTTAATAATTTTTTTTGTATAATCAAGTTTTTAAA
8880026 TGGG-TCAGATATGGGTATGTATTAGGGTTCGAGT-AGAGTAGTAAATTTAAAAAA-TTTCAAGT
130 TGGGTTCAGATATGGGTATGTATTAGGGTTCGAGTGAGAGTAGTAAATTTAAAAAATTTTCAAGT
8880088 AATTTGAGATTCAGGTTCTTTATTTATTAATAGAGTTCGGATTCGGGTATTTCAAAATTAATAAA
195 AATTTGAGATTCAGGTTCTTTATTTATTAATAGAGTTCGGATTCGGGTATTTCAAAATTAATAAA
8880153 TATTCTACATGTTGACATCCTTAGCTTGGA-T-TTGGGTTGCTCAAACTAATATAATTAAAGATT
260 TATTCTACATGTTGACATCCTTAGCTT-GATTGTTGGGTTGCTCAAACTAATATAATTAAAGATT
*
8880216 ACCAACATTTAATCATTAAAAAGGTTTACTCATTTGAGCAAAGACGAAAATGGTAGTCAATCGTT
324 ACCAACATTTAATCATTAAAAA-GTTTACTCATTTGAGCAAAGACAAAAATGGTAGTCAATCGTT
*
8880281 AATTAATA
388 AATAAATA
8880289 GTGTAACTAT
Statistics
Matches: 386, Mismatches: 4, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
403 54 0.14
404 149 0.39
405 22 0.06
406 61 0.16
407 100 0.26
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (406 bp):
TAATTATTAGTGATGTATAGGAAATATGAATAAAAATATTATTGTAAACAGATACGGATTTAGAT
TTAGATAATTGTATACCCATGAAGAGCATTTTAATAATTTTTTTTGTATAATCAAGTTTTTAAAT
GGGTTCAGATATGGGTATGTATTAGGGTTCGAGTGAGAGTAGTAAATTTAAAAAATTTTCAAGTA
ATTTGAGATTCAGGTTCTTTATTTATTAATAGAGTTCGGATTCGGGTATTTCAAAATTAATAAAT
ATTCTACATGTTGACATCCTTAGCTTGATTGTTGGGTTGCTCAAACTAATATAATTAAAGATTAC
CAACATTTAATCATTAAAAAGTTTACTCATTTGAGCAAAGACAAAAATGGTAGTCAATCGTTAAT
AAATATTAGTGATGTA
Found at i:8880417 original size:16 final size:17
Alignment explanation
Indices: 8880388--8880421 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
8880378 GTCATTTATC
*
8880388 ATTACATATCATATGAT
1 ATTACATATAATATGAT
8880405 ATTA-ATATAATATGAT
1 ATTACATATAATATGAT
8880421 A
1 A
8880422 ATATCATACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
ATTACATATAATATGAT
Found at i:8883203 original size:93 final size:93
Alignment explanation
Indices: 8883038--8883227 Score: 317
Period size: 93 Copynumber: 2.0 Consensus size: 93
8883028 TTTTGAGTAG
* *
8883038 AATCCCAAACAACTAAGACGTGTTCCTAGAAACCTATGAATAATCAAATTAAATGGAGATTCTTG
1 AATCCCAAACAACTAAGACGTGTTCCTAGAAACCTACGAATAATCAAATTAAACGGAGATTCTTG
* * *
8883103 AATTTTGACACAACTACAGATTCTGCTT
66 AAGTTTGACACAACTACAGACTCTGATT
* *
8883131 AATCCCCAACAACTAAGACGTGTTCCTAGAAACCTACGAATAATCAAATTAAACGGAGATTCTTT
1 AATCCCAAACAACTAAGACGTGTTCCTAGAAACCTACGAATAATCAAATTAAACGGAGATTCTTG
8883196 AAGTTTGACACAACTACAGACTCTGATT
66 AAGTTTGACACAACTACAGACTCTGATT
8883224 AATC
1 AATC
8883228 TCTCAAATTC
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (93 bp):
AATCCCAAACAACTAAGACGTGTTCCTAGAAACCTACGAATAATCAAATTAAACGGAGATTCTTG
AAGTTTGACACAACTACAGACTCTGATT
Found at i:8893237 original size:19 final size:21
Alignment explanation
Indices: 8893215--8893268 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
8893205 GATTAACTTA
8893215 TAAATAAAA-TATTAATA-TT
1 TAAATAAAATTATTAATATTT
8893234 TAAATAATCAATTATTAATATTT
1 TAAATAA--AATTATTAATATTT
8893257 TAAAT-AAATTAT
1 TAAATAAAATTAT
8893269 AAATTATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.23
20 6 0.19
21 2 0.06
22 9 0.29
23 7 0.23
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATAAAATTATTAATATTT
Found at i:8893418 original size:19 final size:19
Alignment explanation
Indices: 8893356--8893420 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 19
8893346 ATAATAGCAT
8893356 TTAAATTATAAATAAAATA
1 TTAAATTATAAATAAAATA
* *
8893375 TTAATATTTTAAAAAATCAATTA
1 TTAA-ATTATAAATAA--AA-TA
*
8893398 TTAACTTATAAATAAAATA
1 TTAAATTATAAATAAAATA
8893417 TTAA
1 TTAA
8893421 TATTTTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
19 10 0.27
20 11 0.30
22 10 0.27
23 6 0.16
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAATTATAAATAAAATA
Found at i:8893440 original size:25 final size:25
Alignment explanation
Indices: 8893412--8893459 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
8893402 CTTATAAATA
8893412 AAATATTAATATTTTATAATATTTT
1 AAATATTAATATTTTATAATATTTT
8893437 AAATATTAATATTTTATAATATT
1 AAATATTAATATTTTATAATATT
8893460 AATAAGTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
AAATATTAATATTTTATAATATTTT
Found at i:8893448 original size:15 final size:16
Alignment explanation
Indices: 8893428--8893463 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
8893418 TAATATTTTA
8893428 TAATATTTTA-AATAT
1 TAATATTTTATAATAT
8893443 TAATATTTTATAATAT
1 TAATATTTTATAATAT
8893459 TAATA
1 TAATA
8893464 AGTAGATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATATTTTATAATAT
Found at i:8896632 original size:18 final size:16
Alignment explanation
Indices: 8896597--8896644 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
8896587 AAGAGTTTTT
8896597 AAATA-TTATGTTTAAAA
1 AAATATTTAT-TTT-AAA
8896614 AAATTATTTGATTTTAAA
1 AAA-TATTT-ATTTTAAA
8896632 AAATATTTATTTT
1 AAATATTTATTTT
8896645 TTTCCCTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.18
17 8 0.29
18 8 0.29
19 5 0.18
20 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (16 bp):
AAATATTTATTTTAAA
Found at i:8900995 original size:65 final size:65
Alignment explanation
Indices: 8900914--8901042 Score: 213
Period size: 65 Copynumber: 2.0 Consensus size: 65
8900904 AACAAAAGTC
*
8900914 ATTTGCATCTTTACGCAATTCCAATAATTCCATGTTTGACAAAAAATGCTAAAGTCAATGTTCTT
1 ATTTGCATCTTTACGCAATTCCAATAATTCCATGTTTGACAAAAAATGCTAAAATCAATGTTCTT
* * * *
8900979 ATTTGCATCTTTACGCAATTCCAATAGTTCTATGTTTGACTAAAAATGCTAAAATGAATGTTCT
1 ATTTGCATCTTTACGCAATTCCAATAATTCCATGTTTGACAAAAAATGCTAAAATCAATGTTCT
8901043 ATGACACTGA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (65 bp):
ATTTGCATCTTTACGCAATTCCAATAATTCCATGTTTGACAAAAAATGCTAAAATCAATGTTCTT
Found at i:8923861 original size:27 final size:26
Alignment explanation
Indices: 8923831--8923884 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
8923821 TTTTAAACAC
* *
8923831 TTAATACTATTTTTTTATATTACAAAT
1 TTAATACTA-ATTTTTATATTAAAAAT
**
8923858 TTAATTTTAATTTTTATATTAAAAAT
1 TTAATACTAATTTTTATATTAAAAAT
8923884 T
1 T
8923885 AAATGATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (26 bp):
TTAATACTAATTTTTATATTAAAAAT
Found at i:8932541 original size:2 final size:2
Alignment explanation
Indices: 8932534--8932570 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
8932524 CTTCCTACCT
*
8932534 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
8932571 AGACCAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8950958 original size:16 final size:17
Alignment explanation
Indices: 8950937--8950968 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
8950927 ATGTATATTT
8950937 TTATTTA-AAATATATA
1 TTATTTAGAAATATATA
8950953 TTATTTAGAAATATAT
1 TTATTTAGAAATATAT
8950969 TGAAAGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTATTTAGAAATATATA
Found at i:8958807 original size:23 final size:23
Alignment explanation
Indices: 8958781--8958826 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
8958771 ATTAGGGAAA
*
8958781 GATGGTGGAGATTAAGGTAATGG
1 GATGCTGGAGATTAAGGTAATGG
8958804 GATGCTGGAGATTAAGGTAATGG
1 GATGCTGGAGATTAAGGTAATGG
8958827 AGGGGAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.02, G:0.41, T:0.26
Consensus pattern (23 bp):
GATGCTGGAGATTAAGGTAATGG
Found at i:8958854 original size:41 final size:41
Alignment explanation
Indices: 8958804--8958887 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
8958794 AAGGTAATGG
*
8958804 GATGCTGGAGATTAAGGTAATGGAGGGGAAAGATGATGAAA
1 GATGCTGGAGATTAAGGTAATGAAGGGGAAAGATGATGAAA
* *
8958845 GATGGTGGAGGTTAAGGTAATGAAGGGGAAAGATGATGAAA
1 GATGCTGGAGATTAAGGTAATGAAGGGGAAAGATGATGAAA
8958886 GA
1 GA
8958888 ATATGGTGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.39, C:0.01, G:0.40, T:0.19
Consensus pattern (41 bp):
GATGCTGGAGATTAAGGTAATGAAGGGGAAAGATGATGAAA
Found at i:8959043 original size:61 final size:61
Alignment explanation
Indices: 8958944--8959135 Score: 359
Period size: 61 Copynumber: 3.2 Consensus size: 61
8958934 AAATTGAATT
*
8958944 ATTT-CGATTTGTGTAGAGGGGTAGTAAGGAGAGAGGACATGATGCAATAAATAAATTAAG
1 ATTTGCGATTTGTGTAGAGGGGTAGCAAGGAGAGAGGACATGATGCAATAAATAAATTAAG
8959004 ATTTGCGATTTGTGTAGAGGGGTAGCAAGGAGAGAGGACATGATGCAATAAATAAATTAAG
1 ATTTGCGATTTGTGTAGAGGGGTAGCAAGGAGAGAGGACATGATGCAATAAATAAATTAAG
8959065 ATTTGCGATTTGTGTAGAGGGGTAGCAAGGAGAGAGGACATGATGCAATAAATAAATTAAG
1 ATTTGCGATTTGTGTAGAGGGGTAGCAAGGAGAGAGGACATGATGCAATAAATAAATTAAG
*
8959126 ATTCGCGATT
1 ATTTGCGATT
8959136 AAGATGTTTT
Statistics
Matches: 129, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
60 4 0.03
61 125 0.97
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.26
Consensus pattern (61 bp):
ATTTGCGATTTGTGTAGAGGGGTAGCAAGGAGAGAGGACATGATGCAATAAATAAATTAAG
Found at i:8959477 original size:2 final size:2
Alignment explanation
Indices: 8959470--8959501 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8959460 TGTTAAGCTC
*
8959470 AT AT AT AT CT 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 AT AT AT
8959502 TAAGTGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8960334 original size:52 final size:52
Alignment explanation
Indices: 8960256--8960455 Score: 231
Period size: 52 Copynumber: 3.8 Consensus size: 52
8960246 ATTCGAGTAG
* * * * *
8960256 AATGTATTGATCGGGTGGCCCAAATAGTTTAAGACTCTGAGCCCCAATATCT
1 AATGTTTTAATCGGGTTGCCCCAATAGTATAAGACTCTGAGCCCCAATATCT
* * *
8960308 AATGTTTTAATCGGGTTGCCCCAATAGTTTAAGACTCTGAG-CCCTATATTT
1 AATGTTTTAATCGGGTTGCCCCAATAGTATAAGACTCTGAGCCCCAATATCT
* ** * * * *
8960359 AAATTTTTTAATCTTGTTGCCCCAATAGTAGAAGACTCTGAGCCCTATTTTCT
1 -AATGTTTTAATCGGGTTGCCCCAATAGTATAAGACTCTGAGCCCCAATATCT
* *
8960412 AATGTTTTAATCGTGTTGCCCCAATAGTACAAGACTCTGAGCCC
1 AATGTTTTAATCGGGTTGCCCCAATAGTATAAGACTCTGAGCCC
8960456 TATTTTCTGC
Statistics
Matches: 127, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
51 8 0.06
52 114 0.90
53 5 0.04
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (52 bp):
AATGTTTTAATCGGGTTGCCCCAATAGTATAAGACTCTGAGCCCCAATATCT
Found at i:8960456 original size:52 final size:52
Alignment explanation
Indices: 8960286--8960463 Score: 250
Period size: 52 Copynumber: 3.4 Consensus size: 52
8960276 CAAATAGTTT
* * * * **
8960286 AAGACTCTGAGCCCCAATATCTAATGTTTTAATCGGGTTGCCCCAATAGTTT
1 AAGACTCTGAGCCCTATTTTCTAATGTTTTAATCGTGTTGCCCCAATAGTAC
* * * *
8960338 AAGACTCTGAGCCCTATATTT-AAATTTTTTAATCTTGTTGCCCCAATAGTAG
1 AAGACTCTGAGCCCTAT-TTTCTAATGTTTTAATCGTGTTGCCCCAATAGTAC
8960390 AAGACTCTGAGCCCTATTTTCTAATGTTTTAATCGTGTTGCCCCAATAGTAC
1 AAGACTCTGAGCCCTATTTTCTAATGTTTTAATCGTGTTGCCCCAATAGTAC
8960442 AAGACTCTGAGCCCTATTTTCT
1 AAGACTCTGAGCCCTATTTTCT
8960464 GCCAAAGGCT
Statistics
Matches: 111, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
51 3 0.03
52 106 0.95
53 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.36
Consensus pattern (52 bp):
AAGACTCTGAGCCCTATTTTCTAATGTTTTAATCGTGTTGCCCCAATAGTAC
Found at i:8965451 original size:2 final size:2
Alignment explanation
Indices: 8965446--8965474 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8965436 TTAAAACATT
8965446 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8965475 GAAACGTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8968136 original size:20 final size:20
Alignment explanation
Indices: 8968111--8968151 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
8968101 GAGCACCTAT
8968111 TGATTTATGGATTTTATGGC
1 TGATTTATGGATTTTATGGC
*
8968131 TGATTTGTGGATTTTATGGC
1 TGATTTATGGATTTTATGGC
8968151 T
1 T
8968152 CAGGGGCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.05, G:0.27, T:0.51
Consensus pattern (20 bp):
TGATTTATGGATTTTATGGC
Found at i:8975327 original size:14 final size:15
Alignment explanation
Indices: 8975310--8975342 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
8975300 TTTTATATAA
8975310 AAAATA-TAAAAAGT
1 AAAATAGTAAAAAGT
8975324 AAAA-AGTAAAAAGT
1 AAAATAGTAAAAAGT
8975338 AAAAT
1 AAAAT
8975343 CATATTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.06
14 16 0.94
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (15 bp):
AAAATAGTAAAAAGT
Found at i:8975334 original size:6 final size:7
Alignment explanation
Indices: 8975316--8975341 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
8975306 ATAAAAAATA
8975316 TAAAAAG
1 TAAAAAG
8975323 TAAAAAG
1 TAAAAAG
8975330 TAAAAAG
1 TAAAAAG
8975337 TAAAA
1 TAAAA
8975342 TCATATTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (7 bp):
TAAAAAG
Found at i:8983624 original size:20 final size:21
Alignment explanation
Indices: 8983599--8983637 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
8983589 TCATCGAGGT
*
8983599 TGAAGAA-GATGTCGTTTTGA
1 TGAAGAAGGATGCCGTTTTGA
8983619 TGAAGAAGGATGCCGTTTT
1 TGAAGAAGGATGCCGTTTT
8983638 TTGTCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.08, G:0.31, T:0.33
Consensus pattern (21 bp):
TGAAGAAGGATGCCGTTTTGA
Found at i:8990512 original size:20 final size:19
Alignment explanation
Indices: 8990476--8990515 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
8990466 TAATGTTTAA
* *
8990476 AAAAATTTGAATTATTTTT
1 AAAAATTTAAATAATTTTT
8990495 AAAAATTTAAATCAATTTTT
1 AAAAATTTAAAT-AATTTTT
8990515 A
1 A
8990516 TTATTCTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
AAAAATTTAAATAATTTTT
Found at i:9004194 original size:5 final size:5
Alignment explanation
Indices: 9004188--9004221 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
9004178 AAAGAAATAT
* *
9004188 GCCAT GCCAT GCCAA GCCAA GCCAA GCCAA GCCA
1 GCCAA GCCAA GCCAA GCCAA GCCAA GCCAA GCCA
9004222 GTGCAGCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.32, C:0.41, G:0.21, T:0.06
Consensus pattern (5 bp):
GCCAA
Found at i:9016136 original size:12 final size:13
Alignment explanation
Indices: 9016106--9016140 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
9016096 TAAAATTGTG
9016106 AAAATCAATAAATC
1 AAAAT-AATAAATC
9016120 AAAATAATAAA-C
1 AAAATAATAAATC
9016132 AAAATAATA
1 AAAATAATA
9016141 CGGATTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.48
13 6 0.29
14 5 0.24
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAATAAATC
Found at i:9021610 original size:24 final size:27
Alignment explanation
Indices: 9021560--9021611 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
9021550 GATAAAAAAT
9021560 TGTTATGTGAGTATATTTTTATCAATA
1 TGTTATGTGAGTATATTTTTATCAATA
*
9021587 TGTTATGT-ATTAT-TTTTTAT-AATA
1 TGTTATGTGAGTATATTTTTATCAATA
9021611 T
1 T
9021612 ATTAATATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 5 0.21
25 7 0.29
26 4 0.17
27 8 0.33
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.58
Consensus pattern (27 bp):
TGTTATGTGAGTATATTTTTATCAATA
Found at i:9025210 original size:12 final size:12
Alignment explanation
Indices: 9025189--9025223 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
9025179 CTGCCACTGA
9025189 AGAA-AAGAAAG
1 AGAAGAAGAAAG
*
9025200 AGAAGAAGAAAA
1 AGAAGAAGAAAG
9025212 AGAAGAAGAAAG
1 AGAAGAAGAAAG
9025224 CTAATCAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
AGAAGAAGAAAG
Found at i:9028824 original size:18 final size:19
Alignment explanation
Indices: 9028788--9028828 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
9028778 GAAATCTGTG
9028788 TGTCTTTCTTCTCTCTCTC
1 TGTCTTTCTTCTCTCTCTC
9028807 TGTCTTTCTAT-T-TCTCTC
1 TGTCTTTCT-TCTCTCTCTC
9028825 TGTC
1 TGTC
9028829 AGATTCAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
19 10 0.48
20 1 0.05
ACGTcount: A:0.02, C:0.32, G:0.07, T:0.59
Consensus pattern (19 bp):
TGTCTTTCTTCTCTCTCTC
Found at i:9034788 original size:2 final size:2
Alignment explanation
Indices: 9034781--9034810 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9034771 TGAATCCGTA
9034781 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9034811 GTCACCTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9043270 original size:12 final size:13
Alignment explanation
Indices: 9043243--9043275 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
9043233 AACCAGGAAA
*
9043243 AAAAAGAAGAAGG
1 AAAAAGAACAAGG
9043256 AAAAAGAACAA-G
1 AAAAAGAACAAGG
9043268 AAAAAGAA
1 AAAAAGAA
9043276 AAATCTCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAGAACAAGG
Found at i:9066902 original size:15 final size:17
Alignment explanation
Indices: 9066879--9066919 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
9066869 TTCTCTTGTT
9066879 CTCTGTTCTTC-A-ACTC
1 CTCT-TTCTTCAATACTC
9066895 CTCTTTCTTCAATACTC
1 CTCTTTCTTCAATACTC
9066912 CT-TTTCTT
1 CTCTTTCTT
9066920 TCTCTGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.12, C:0.34, G:0.02, T:0.51
Consensus pattern (17 bp):
CTCTTTCTTCAATACTC
Found at i:9072129 original size:20 final size:20
Alignment explanation
Indices: 9072106--9072144 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9072096 CCAATCCCTA
9072106 ATTTACTTTACTAATCTTTG
1 ATTTACTTTACTAATCTTTG
* *
9072126 ATTTATTTTATTAATCTTT
1 ATTTACTTTACTAATCTTT
9072145 TTGGGTATAT
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:0.26, C:0.10, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTTACTTTACTAATCTTTG
Found at i:9072784 original size:2 final size:2
Alignment explanation
Indices: 9072777--9072805 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9072767 TTACATCAAT
9072777 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9072806 GTGTATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9086470 original size:21 final size:21
Alignment explanation
Indices: 9086444--9086503 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
9086434 CTACTCAAGA
9086444 AAAATCAATTTCTTTACAAAC
1 AAAATCAATTTCTTTACAAAC
* * *
9086465 AAAATCAAATCCTTTACAAGC
1 AAAATCAATTTCTTTACAAAC
* *
9086486 AGACTCAATTTCTTTACA
1 AAAATCAATTTCTTTACA
9086504 TTCTTTTCAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.03, T:0.32
Consensus pattern (21 bp):
AAAATCAATTTCTTTACAAAC
Found at i:9097820 original size:22 final size:21
Alignment explanation
Indices: 9097789--9097841 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
9097779 TATTATATCA
*
9097789 TATTTATAAAATTATAATAATT
1 TATTTTTAAAATTATAA-AATT
* *
9097811 TATTTTTAAAATTTTTAAATT
1 TATTTTTAAAATTATAAAATT
9097832 TATTTATTAA
1 TATTT-TTAA
9097842 CAAAATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTTAAAATTATAAAATT
Found at i:9098754 original size:26 final size:25
Alignment explanation
Indices: 9098725--9098783 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
9098715 TTTTTTAAAG
*
9098725 TTAATTTCGAGCTTGAATTTCATGTT
1 TTAATTTCAAGCTTGAATTT-ATGTT
* * * *
9098751 TTAATTTAAAGTTTGAATTTTTTTT
1 TTAATTTCAAGCTTGAATTTATGTT
9098776 TTAATTTC
1 TTAATTTC
9098784 CAATAGACGC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.25, C:0.07, G:0.10, T:0.58
Consensus pattern (25 bp):
TTAATTTCAAGCTTGAATTTATGTT
Found at i:9102431 original size:13 final size:13
Alignment explanation
Indices: 9102399--9102440 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
9102389 TTTCAAAATT
9102399 TTTTATTATGTTAAA
1 TTTTA-TAT-TTAAA
*
9102414 TTTTATATTTATA
1 TTTTATATTTAAA
9102427 TTTTAT-TTTAAA
1 TTTTATATTTAAA
9102439 TT
1 TT
9102441 AAATAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.28
13 10 0.40
14 3 0.12
15 5 0.20
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
TTTTATATTTAAA
Found at i:9102451 original size:18 final size:20
Alignment explanation
Indices: 9102430--9102466 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
9102420 ATTTATATTT
9102430 TATTTTAA-ATTAA-ATAAA
1 TATTTTAATATTAATATAAA
9102448 TATTTTAATATTAATATAA
1 TATTTTAATATTAATATAA
9102467 CATTATGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTTTAATATTAATATAAA
Found at i:9102530 original size:18 final size:19
Alignment explanation
Indices: 9102504--9102549 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
9102494 CACATCAATA
*
9102504 TAATAAAATA-TAAAAATT
1 TAATTAAATATTAAAAATT
*
9102522 TAATTAAATATTAAACATT
1 TAATTAAATATTAAAAATT
*
9102541 TATTTAAAT
1 TAATTAAAT
9102550 TTTATTTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATTAAATATTAAAAATT
Found at i:9116769 original size:2 final size:2
Alignment explanation
Indices: 9116762--9116793 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9116752 AAATACACAA
9116762 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9116794 TACCTCCTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9136898 original size:33 final size:33
Alignment explanation
Indices: 9136856--9136919 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
9136846 ATTCTGGCTA
*
9136856 TTTTAGTTTGAATTTCACGTATGATCCAGAATT
1 TTTTAGTTTGAATTTCACGTATGACCCAGAATT
* **
9136889 TTTTTGTTTGAATTTCTGGTATGACCCAGAA
1 TTTTAGTTTGAATTTCACGTATGACCCAGAA
9136920 AAATTCTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.45
Consensus pattern (33 bp):
TTTTAGTTTGAATTTCACGTATGACCCAGAATT
Found at i:9137023 original size:18 final size:17
Alignment explanation
Indices: 9137002--9137049 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
9136992 GGCAGAGGTG
9137002 GTGGTAGAGGTGGATTTC
1 GTGG-AGAGGTGGATTTC
*
9137020 GTGGAGGTGGTGGATTTC
1 GTGGA-GAGGTGGATTTC
9137038 GTGGAAGAGGTG
1 GTGG-AGAGGTG
9137050 CCCCAAGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.17, C:0.04, G:0.50, T:0.29
Consensus pattern (17 bp):
GTGGAGAGGTGGATTTC
Found at i:9151059 original size:3 final size:3
Alignment explanation
Indices: 9151051--9151094 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
9151041 TAAAAGTAGG
* * * *
9151051 ATT ATT ATT ATT GTT GTT GTT GTT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
9151095 GTCCTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:9151479 original size:2 final size:2
Alignment explanation
Indices: 9151472--9151507 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
9151462 TTTCGACAGG
*
9151472 TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9151508 AGGTATTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:9163057 original size:636 final size:638
Alignment explanation
Indices: 9161554--9164021 Score: 3816
Period size: 640 Copynumber: 3.9 Consensus size: 638
9161544 CCACTTCGAG
* * * * * * * *
9161554 GGGAAATTGATCTC-GAAGATGTTTT-TTCCTGCTTCTTGAATAATATTAATTTTATTTACCCTG
1 GGGACATTGATCTCTG-AGTTGTTTTCTT-CTACTTCTTGGATAATATGAATTTCATTTGCCATG
* * * *
9161617 GTAGATTTGGAGAAAAATGTCTCAAATGTAGGACAATCTTCAATAATAAGCTTTTTCAACAAGGG
64 GTAGATTTGGAGAAGAATGCCTCAAATGTAGGACACTCTTCAATAATAAGCTCTTTCAACAAGGG
*
9161682 GAATTCAAAGTGACTTCCATGACAGAATCTCATGAGATTGGGAAGGTCTTCAAACTTCAAAAGTT
129 GAATTCAAAGTGACTTCCATGACAGAATCTCGTGAGATTGGGAAGGTCTTCAAACTTCAAAAGTT
9161747 CTAGTTTAGGGAAAATCCGGTCCATCATATCTTCTTCTATATCCTCCATGAACATTATCTCTTTT
194 CTAGTTTAGGGAAAATCCGGTCCATCATATCTTCTTCTATATCCTCCATGAACATTATCTCTTTT
9161812 AAGCACCCACAACCCTTTATTTCAAAACTTTTGAGATGTGTTAGACTTGTAGCCACAGAATATGA
259 AAGCACCCAC-ACCCTTTATTTCAAAACTTTTGAGATGTGTTAGACTTGTAGCCACAGAATATGA
*
9161877 TAATATGTGCTTTAAGTTGTCACAATACTGAATGGCTTC-ACCTTGTTCAAATTCTGAAGATAGT
323 TAATATGTGCTTTAAGTTGTCACAATACTGAAT-GC-TCAACCATG-TCAAATTCTGAAGATAGT
* *
9161941 CCAGAAGTGGTTGAAAAACTGATTGGGGCCATATCTTCTCAACATTGAGTGAGTACAATTGTAGC
385 -CAGAAATGATTG-AAAACTGATT-GGGCCATATCTTCTCAACATTGAGTGAGTACAATTGTAGC
9162006 TCCTCCAAGCAAGG-AATTTCATTCTACACAAATATAATTCTTATACATTAAAAATTATTAAAAA
447 TCCTCCAAGCAAGGAAATTTCA-TCTACACAAATATAATTCTTATACATTAAAAATTATTAAAAA
9162070 ATATAAAAAAAATTCAAGTTTCAATACAATAATTACATAACATTCATGCTATAT--AAAAAATGA
511 ATATAAAAAAAATTCAAGTTTCAATACAATAATTACATAACATTCATGCTATATAAAAAAAATGA
9162133 TTTGTTATAGCAT-AATACAGTAAGAAAAGGGAGAGTATAGTCACCTTTTCATTGAAGAGATGA
576 TTTGTTATAGCATAAATACAGTAAGAAAA-GGAGAGTATAGTCACCTTTTCATTGAAGAGATGA
9162196 GGGACATTGATCTCTGAGTTGTTTTCTTCTACTTCTTGGATAATATGAATTTCATTTGCCATGGT
1 GGGACATTGATCTCTGAGTTGTTTTCTTCTACTTCTTGGATAATATGAATTTCATTTGCCATGGT
* *
9162261 AGATTTGGAGATGAATGCCTTAAATGTAGGACACTCTTCAATAATAAGCTCTTTCAACAAGGGGA
66 AGATTTGGAGAAGAATGCCTCAAATGTAGGACACTCTTCAATAATAAGCTCTTTCAACAAGGGGA
*
9162326 ATTCAAAGTGACTTCCATGACAGAATCTCGTGAGATT-GGAAGGCCTTCAAACTTCAAAAGTTCT
131 ATTCAAAGTGACTTCCATGACAGAATCTCGTGAGATTGGGAAGGTCTTCAAACTTCAAAAGTTCT
*
9162390 AGTTTAGGGAAAATCTGGTCCATCATATCTTCTTCTATATCCTCCATGAACATTATCTCTTTTAA
196 AGTTTAGGGAAAATCCGGTCCATCATATCTTCTTCTATATCCTCCATGAACATTATCTCTTTTAA
9162455 GCACCCACACCCCTTTATTTCAAAACTTTTGAGATGTGTTAGACTTGTAGCCACAGAATATGATA
261 GCACCCACA-CCCTTTATTTCAAAACTTTTGAGATGTGTTAGACTTGTAGCCACAGAATATGATA
9162520 ATATGTGCTTTAAGTTGTCACAATACTGAATGCTCAACCATGTCAAATTCTGAAGATAGTCAGAA
325 ATATGTGCTTTAAGTTGTCACAATACTGAATGCTCAACCATGTCAAATTCTGAAGATAGTCAGAA
*
9162585 ATGGTTGAAAACTGATTGGGCCATATCTTCTCAACATTGAGTGAGTACAATTGTAGCTCCTCCAA
390 ATGATTGAAAACTGATTGGGCCATATCTTCTCAACATTGAGTGAGTACAATTGTAGCTCCTCCAA
9162650 GCAAGGAAATTTCATCTACACAAATATAATTCTTATACATTAAAAATTATTAAAAAATATAAAAA
455 GCAAGGAAATTTCATCTACACAAATATAATTCTTATACATTAAAAATTATTAAAAAATAT-AAAA
*
9162715 AAAATTCAAGTTTCAATACAATAATTACATAACATTCGTGCTATATAAAAAAAAATGATTTGTTA
519 AAAATTCAAGTTTCAATACAATAATTACATAACATTCATGCTATAT-AAAAAAAATGATTTGTTA
9162780 TAGCATAAATACAGTAAGAAAAGGAGAGTATAGTCACCTTTTCATTGAAGAGATGA
583 TAGCATAAATACAGTAAGAAAAGGAGAGTATAGTCACCTTTTCATTGAAGAGATGA
9162836 GGGACATTGATCTCTGAGTTGTTTTCTTCTACTTCTTGGATAATATGAATTTCATTTGCCATGGT
1 GGGACATTGATCTCTGAGTTGTTTTCTTCTACTTCTTGGATAATATGAATTTCATTTGCCATGGT
* *
9162901 AGATTTGGAGAAGACTGTCTCAAATGTAGGACA-TC-TCAATAATAAGCTCTTTCAACAA-GGGA
66 AGATTTGGAGAAGAATGCCTCAAATGTAGGACACTCTTCAATAATAAGCTCTTTCAACAAGGGGA
* *
9162963 ATTC-AAGTTACTTCCA-GACAGAATCTCGTGAGATTGGGAAGGTCTTCAAGCTTCAAAAGTTCT
131 ATTCAAAGTGACTTCCATGACAGAATCTCGTGAGATTGGGAAGGTCTTCAAACTTCAAAAGTTCT
* *
9163026 AGTTTAGGGAAAATCTGGTCCATCATATCTTCTTCT-TATTCCTCCATGAA-ATTATTATCTCTT
196 AGTTTAGGGAAAATCCGGTCCATCATATCTTCTTCTATA-TCCTCCATGAACATTA-TCTCT-TT
* * *
9163089 TAAGCACTCC-CA-TCATTATTT--AAGCTTTTGAGATGTGTTAGACTTGTAGCCACAGAATATG
258 TAAGCAC-CCACACCCTTTATTTCAAAACTTTTGAGATGTGTTAGACTTGTAGCCACAGAATATG
*
9163150 ATAATATGTGTTTTAAGTTGTCACAAT--T-AATGCTCAA-CATTGTCAAA-TCTTGAAGATAGT
322 ATAATATGTGCTTTAAGTTGTCACAATACTGAATGCTCAACCA-TGTCAAATTC-TGAAGATAGT
* *
9163210 CAGAAGTGATTGAAAACTGATTGGGCCATATCTCCTCAACATTGA-TGAGTACAATTGTAGCTCC
385 CAGAAATGATTGAAAACTGATTGGGCCATATCTTCTCAACATTGAGTGAGTACAATTGTAGCTCC
9163274 TCCAAGCAAGGAAATTTCATCTACACAAATATAATTCTTATACATTAAAAATTA-T-----A-A-
450 TCCAAGCAAGGAAATTTCATCTACACAAATATAATTCTTATACATTAAAAATTATTAAAAAATAT
9163331 AAAAAAAATTCAAGTTTCAATACAATAATTACATAACATTCATGCTATATAAAAAAAATGATTTG
515 AAAAAAAATTCAAGTTTCAATACAATAATTACATAACATTCATGCTATATAAAAAAAATGATTTG
9163396 TTATAGCATAAATACAGTAAGAAAAGGAGAGTATAGTCACCTTTTCATTGAAG-GATGA
580 TTATAGCATAAATACAGTAAGAAAAGGAGAGTATAGTCACCTTTTCATTGAAGAGATGA
9163454 GGGACATTGATCTCTGAGTTGTTTTTCTTCTACTTCTTGGATAATATGAATTTCATTTGCCATGG
1 GGGACATTGATCTCTGAGTTG-TTTTCTTCTACTTCTTGGATAATATGAATTTCATTTGCCATGG
* * * *
9163519 TAGAATTTGGAGATGAATGCCTTAAATGTAGGACACTCTTTAATAATAAGCTTTTTCAACAAGGG
65 TAG-ATTTGGAGAAGAATGCCTCAAATGTAGGACACTCTTCAATAATAAGCTCTTTCAACAAGGG
* * *
9163584 GAATTCAAAGTTACTTCCATGACAGAATCTCGTGAGATTGGGAAGTTCTTGAAACTTCAAAAGTT
129 GAATTCAAAGTGACTTCCATGACAGAATCTCGTGAGATTGGGAAGGTCTTCAAACTTCAAAAGTT
*
9163649 CTAGTTTAGGGAAAAGCCGGTCCATCATATCTTCTTCTATATCCTCCATGAACATTATCTCTTTT
194 CTAGTTTAGGGAAAATCCGGTCCATCATATCTTCTTCTATATCCTCCATGAACATTATCTCTTTT
* * * **
9163714 AAGCACTCACATCCATATATTTCAAGGCTTTTGAGATGTGTTAGACTTGTAGCCACAGAATATGA
259 AAGCACCCACA-CCCTTTATTTCAAAACTTTTGAGATGTGTTAGACTTGTAGCCACAGAATATGA
* ** * * *
9163779 TAATATGTGTTTTAAGTTGTCACAATTTTGAATGCTCAAACTTTTCAAATTCTGAAGATAGTCAG
323 TAATATGTGCTTTAAGTTGTCACAATACTGAATGCTCAACCATGTCAAATTCTGAAGATAGTCAG
* * ** * *
9163844 AAATGATTGAAAACTGATGGGGCCATATCTTCTCAACCTTGAGTGTCTCCAATTGTAGCTTCTCC
388 AAATGATTGAAAACTGATTGGGCCATATCTTCTCAACATTGAGTGAGTACAATTGTAGCTCCTCC
* ** * * * * **
9163909 AAGCAAGGGAACCTCATCTATACAAATGTAATTCTTATACATTAAAAATTATTACAAAACATTTA
453 AAGCAAGGAAATTTCATCTACACAAATATAATTCTTATACATTAAAAATTATTAAAAAATATAAA
* * * * * * *
9163974 AAACATTCAAGTTTCGATATAATAATCACATAACCTTTATGCTTTATA
518 AAAAATTCAAGTTTCAATACAATAATTACATAACATTCATGCTATATA
9164022 TATATAAAAA
Statistics
Matches: 1703, Mismatches: 78, Indels: 92
0.91 0.04 0.05
Matches are distributed among these distances:
618 26 0.02
619 114 0.07
620 76 0.04
621 2 0.00
622 22 0.01
623 10 0.01
624 23 0.01
625 93 0.05
626 11 0.01
628 67 0.04
629 77 0.05
630 69 0.04
631 67 0.04
632 67 0.04
633 66 0.04
635 32 0.02
636 187 0.11
637 85 0.05
638 37 0.02
639 23 0.01
640 200 0.12
641 199 0.12
642 147 0.09
643 3 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (638 bp):
GGGACATTGATCTCTGAGTTGTTTTCTTCTACTTCTTGGATAATATGAATTTCATTTGCCATGGT
AGATTTGGAGAAGAATGCCTCAAATGTAGGACACTCTTCAATAATAAGCTCTTTCAACAAGGGGA
ATTCAAAGTGACTTCCATGACAGAATCTCGTGAGATTGGGAAGGTCTTCAAACTTCAAAAGTTCT
AGTTTAGGGAAAATCCGGTCCATCATATCTTCTTCTATATCCTCCATGAACATTATCTCTTTTAA
GCACCCACACCCTTTATTTCAAAACTTTTGAGATGTGTTAGACTTGTAGCCACAGAATATGATAA
TATGTGCTTTAAGTTGTCACAATACTGAATGCTCAACCATGTCAAATTCTGAAGATAGTCAGAAA
TGATTGAAAACTGATTGGGCCATATCTTCTCAACATTGAGTGAGTACAATTGTAGCTCCTCCAAG
CAAGGAAATTTCATCTACACAAATATAATTCTTATACATTAAAAATTATTAAAAAATATAAAAAA
AATTCAAGTTTCAATACAATAATTACATAACATTCATGCTATATAAAAAAAATGATTTGTTATAG
CATAAATACAGTAAGAAAAGGAGAGTATAGTCACCTTTTCATTGAAGAGATGA
Found at i:9166754 original size:33 final size:33
Alignment explanation
Indices: 9166710--9166773 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
9166700 TTAAAGAGGG
9166710 AAGAAACTTGGAAGTTATTCACAGAAAAGGTTA
1 AAGAAACTTGGAAGTTATTCACAGAAAAGGTTA
* *
9166743 AAGAAAGTTGGAAGTTATTCACAGAAGAGGT
1 AAGAAACTTGGAAGTTATTCACAGAAAAGGT
9166774 AAAAACAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.44, C:0.08, G:0.25, T:0.23
Consensus pattern (33 bp):
AAGAAACTTGGAAGTTATTCACAGAAAAGGTTA
Found at i:9167285 original size:21 final size:22
Alignment explanation
Indices: 9167246--9167288 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
9167236 CAGAGCAAAG
9167246 TGGTGACCGATAATGCAACTTC
1 TGGTGACCGATAATGCAACTTC
9167268 TGGTGA-CGATCAAT-CAACTTC
1 TGGTGACCGAT-AATGCAACTTC
9167289 CTCTGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (22 bp):
TGGTGACCGATAATGCAACTTC
Found at i:9171664 original size:24 final size:24
Alignment explanation
Indices: 9171637--9171688 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
9171627 CTGTAGTGAT
*
9171637 GAGGTGGTTTCCGCCTAGTAATTA
1 GAGGTGGTTTCCACCTAGTAATTA
9171661 GAGGTGGTTTCCACCTAGTAATTA
1 GAGGTGGTTTCCACCTAGTAATTA
9171685 GAGG
1 GAGG
9171689 CTGATCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (24 bp):
GAGGTGGTTTCCACCTAGTAATTA
Found at i:9176418 original size:27 final size:25
Alignment explanation
Indices: 9176366--9176416 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
9176356 GGTGGTGAAG
9176366 ACAGAGAGCAGCATTAACACATTAT
1 ACAGAGAGCAGCATTAACACATTAT
9176391 ACAGAGAGCAGCATTAACACATTAT
1 ACAGAGAGCAGCATTAACACATTAT
9176416 A
1 A
9176417 TATGAAGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (25 bp):
ACAGAGAGCAGCATTAACACATTAT
Found at i:9183240 original size:24 final size:23
Alignment explanation
Indices: 9183190--9183242 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
9183180 AATGGAACAA
9183190 ATAATAT-GGAAAAAATAGAATG
1 ATAATATAGGAAAAAATAGAATG
*
9183212 A-AATATAGGAAAGAAA-AGAATTT
1 ATAATATAGGAAA-AAATAGAA-TG
9183235 ATAATATA
1 ATAATATA
9183243 ATTCTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.19
22 10 0.38
23 5 0.19
24 6 0.23
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (23 bp):
ATAATATAGGAAAAAATAGAATG
Found at i:9184170 original size:30 final size:31
Alignment explanation
Indices: 9184134--9184197 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
9184124 ATGCAAATAT
* *
9184134 TTATAC-TTTTATTTTAAGTTAAATAAACCC
1 TTATACTTTTTATTTTAAGTCAAACAAACCC
* *
9184164 TTATACTTTTTATTTTGAGTCAAACAAACTC
1 TTATACTTTTTATTTTAAGTCAAACAAACCC
9184195 TTA
1 TTA
9184198 AAATTAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (31 bp):
TTATACTTTTTATTTTAAGTCAAACAAACCC
Found at i:9184827 original size:21 final size:21
Alignment explanation
Indices: 9184801--9184852 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
9184791 TACAGAAACA
*
9184801 TGTTACACGCCATGGTTAAGT
1 TGTTACACGCCATGATTAAGT
* *
9184822 TGTTACACGACATGATTAGGT
1 TGTTACACGCCATGATTAAGT
9184843 TGTTACACGC
1 TGTTACACGC
9184853 TATGTACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (21 bp):
TGTTACACGCCATGATTAAGT
Found at i:9184883 original size:66 final size:66
Alignment explanation
Indices: 9184788--9184987 Score: 202
Period size: 66 Copynumber: 3.0 Consensus size: 66
9184778 GTTACACATC
* * **
9184788 ATGTACAGAAACATGTTACACGCCATGGTTAAGTTGTTACACGACATGATTAGGTTGTTACACGC
1 ATGTACAAAAACATGTTACACGTCATGGTTAAGTTGTTACACGACATGATTAAATTGTTACACGC
9184853 T
66 T
* * * * * * * * * * *
9184854 ATGTACAAAAACATATAACACATCATGGTTAGGCTGTTATATGTCATGGTTAAATTGTTATACGT
1 ATGTACAAAAACATGTTACACGTCATGGTTAAGTTGTTACACGACATGATTAAATTGTTACACGC
9184919 T
66 T
* * * *
9184920 ATATACAAAAATATGTTACACGTCATGGTTAAGTTGTTACACGCCATGTATAAAAATATGTTACA
1 ATGTACAAAAACATGTTACACGTCATGGTTAAGTTGTTACACGACATG-AT-TAAAT-TGTTACA
9184985 CGC
63 CGC
9184988 CATGGTTAGG
Statistics
Matches: 102, Mismatches: 29, Indels: 3
0.76 0.22 0.02
Matches are distributed among these distances:
66 89 0.87
67 1 0.01
68 4 0.04
69 8 0.08
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (66 bp):
ATGTACAAAAACATGTTACACGTCATGGTTAAGTTGTTACACGACATGATTAAATTGTTACACGC
T
Found at i:9184957 original size:45 final size:45
Alignment explanation
Indices: 9184896--9185011 Score: 160
Period size: 45 Copynumber: 2.6 Consensus size: 45
9184886 GCTGTTATAT
* * **
9184896 GTCATGGTTAAATTGTTATACGTTATATACAAAAATATGTTACAC
1 GTCATGGTTAAGTTGTTACACGCCATATACAAAAATATGTTACAC
* *
9184941 GTCATGGTTAAGTTGTTACACGCCATGTATAAAAATATGTTACAC
1 GTCATGGTTAAGTTGTTACACGCCATATACAAAAATATGTTACAC
* *
9184986 GCCATGGTTAGGTTGTTACACGCCAT
1 GTCATGGTTAAGTTGTTACACGCCAT
9185012 GTTAAAACAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (45 bp):
GTCATGGTTAAGTTGTTACACGCCATATACAAAAATATGTTACAC
Found at i:9184983 original size:24 final size:24
Alignment explanation
Indices: 9184926--9185079 Score: 94
Period size: 21 Copynumber: 6.5 Consensus size: 24
9184916 CGTTATATAC
*
9184926 AAAAATATGTTACACGTCATGGTT
1 AAAAATATGTTACACGCCATGGTT
*
9184950 --AAGT-TGTTACACGCCAT-GTAT
1 AAAAATATGTTACACGCCATGGT-T
9184971 AAAAATATGTTACACGCCATGGTT
1 AAAAATATGTTACACGCCATGGTT
**
9184995 --AGGT-TGTTACACGCCAT-GTT
1 AAAAATATGTTACACGCCATGGTT
* *
9185015 AAAACAAATATTATTGTTACACGCTAT-GTAC
1 ---A-AAA-A-TA-TGTTACACGCCATGGT-T
*
9185046 AAAAACATGTTACACGCCATGGTT
1 AAAAATATGTTACACGCCATGGTT
9185070 -AAAATATGTT
1 AAAAATATGTT
9185080 GTTATACTGT
Statistics
Matches: 100, Mismatches: 13, Indels: 35
0.68 0.09 0.24
Matches are distributed among these distances:
20 5 0.05
21 26 0.26
22 5 0.05
23 12 0.12
24 26 0.26
25 5 0.05
26 2 0.02
27 3 0.03
28 2 0.02
30 14 0.14
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (24 bp):
AAAAATATGTTACACGCCATGGTT
Found at i:9185137 original size:29 final size:29
Alignment explanation
Indices: 9185094--9185156 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
9185084 TACTGTTGAA
* *
9185094 AAAAAATACTTTTATTACATGTCATATTG
1 AAAAAATACTTTTATTACACGTCATATTC
9185123 AAAAAATA-TTATTATTACACGTCATATTC
1 AAAAAATACTT-TTATTACACGTCATATTC
9185152 AAAAA
1 AAAAA
9185157 CATTTTGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 2 0.06
29 29 0.94
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (29 bp):
AAAAAATACTTTTATTACACGTCATATTC
Found at i:9185167 original size:27 final size:28
Alignment explanation
Indices: 9185094--9185169 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 28
9185084 TACTGTTGAA
* *
9185094 AAAAAATACTTTTATTACATGTCATATTG
1 AAAAAACA-TTTTATTACACGTCATATTG
*
9185123 AAAAAATATTATTATTACACGTCATATT-
1 AAAAAACATT-TTATTACACGTCATATTG
* *
9185151 CAAAAACATTTTGTTACAC
1 AAAAAACATTTTATTACAC
9185170 TTTAACGCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 8 0.19
28 10 0.24
29 24 0.57
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.38
Consensus pattern (28 bp):
AAAAAACATTTTATTACACGTCATATTG
Found at i:9185745 original size:10 final size:10
Alignment explanation
Indices: 9185730--9185755 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
9185720 CTAAGTTATG
9185730 ATTAAAAATA
1 ATTAAAAATA
9185740 ATTAAAAATA
1 ATTAAAAATA
9185750 ATTAAA
1 ATTAAA
9185756 TTTATTTTAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATTAAAAATA
Found at i:9187143 original size:15 final size:16
Alignment explanation
Indices: 9187125--9187162 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
9187115 ATTATATATA
*
9187125 TTATAATTAATAA-TT
1 TTATAAATAATAATTT
*
9187140 TTATAAATGATAATTT
1 TTATAAATAATAATTT
9187156 TTATAAA
1 TTATAAA
9187163 ATAAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTATAAATAATAATTT
Found at i:9187269 original size:27 final size:28
Alignment explanation
Indices: 9187200--9187289 Score: 80
Period size: 27 Copynumber: 3.3 Consensus size: 28
9187190 TTTTAAAAAT
* *
9187200 ATATATATAATAA-TTATATTCTTTATA
1 ATATAAATAATAATTTATATTATTTATA
* *
9187227 ATATAATGTGAT-ATTTATATTATTTA-A
1 ATATAA-ATAATAATTTATATTATTTATA
* *
9187254 ATATAAATAATAATTTA-ATAATTTTTA
1 ATATAAATAATAATTTATATTATTTATA
*
9187281 ATTTAAATA
1 ATATAAATA
9187290 CATTAATAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
26 9 0.18
27 27 0.54
28 14 0.28
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (28 bp):
ATATAAATAATAATTTATATTATTTATA
Found at i:9194681 original size:19 final size:19
Alignment explanation
Indices: 9194657--9194694 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
9194647 CTTGAATATC
*
9194657 TATTATGAGTAAAAACATA
1 TATTATAAGTAAAAACATA
9194676 TATTATAAGTAAAAACATA
1 TATTATAAGTAAAAACATA
9194695 CATTGAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (19 bp):
TATTATAAGTAAAAACATA
Found at i:9209951 original size:12 final size:14
Alignment explanation
Indices: 9209924--9209955 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
9209914 TTTCTTTTCC
9209924 TTTATTCTAGTTTT
1 TTTATTCTAGTTTT
9209938 TTTATT-TA-TTTT
1 TTTATTCTAGTTTT
9209950 TTTATT
1 TTTATT
9209956 GGCTAGTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 2 0.11
14 6 0.33
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (14 bp):
TTTATTCTAGTTTT
Found at i:9211338 original size:17 final size:17
Alignment explanation
Indices: 9211318--9211380 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 17
9211308 GTAGATGAGT
9211318 AAATAAAATAAAAATGA
1 AAATAAAATAAAAATGA
9211335 AAAT-AAATAAATAAT-A
1 AAATAAAATAAA-AATGA
* *
9211351 ATAATAATAT-AAATTGA
1 A-AATAAAATAAAAATGA
9211368 AAA-AAAATAAAAA
1 AAATAAAATAAAAA
9211381 AACTTTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
15 4 0.11
16 16 0.43
17 14 0.38
18 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AAATAAAATAAAAATGA
Found at i:9215648 original size:19 final size:19
Alignment explanation
Indices: 9215624--9215661 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
9215614 CTTGAATATC
*
9215624 TATTATTAGTAAAAACATA
1 TATTATAAGTAAAAACATA
9215643 TATTATAAGTAAAAACATA
1 TATTATAAGTAAAAACATA
9215662 CATTGAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (19 bp):
TATTATAAGTAAAAACATA
Found at i:9224708 original size:15 final size:15
Alignment explanation
Indices: 9224688--9224718 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
9224678 ACAAATAACC
9224688 AATGATGTCAAGTTG
1 AATGATGTCAAGTTG
9224703 AATGATGTCAAGTTG
1 AATGATGTCAAGTTG
9224718 A
1 A
9224719 TAGTGCCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (15 bp):
AATGATGTCAAGTTG
Found at i:9228481 original size:31 final size:32
Alignment explanation
Indices: 9228446--9228505 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
9228436 AATAGAATTA
9228446 GAATTAAAATGT-AAATATCTATTTCTTTAAC
1 GAATTAAAATGTGAAATATCTATTTCTTTAAC
* * * *
9228477 GAATTGAAGTTTGAAATATCTTTTTCTTT
1 GAATTAAAATGTGAAATATCTATTTCTTT
9228506 GCATTGTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 9 0.38
32 15 0.62
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (32 bp):
GAATTAAAATGTGAAATATCTATTTCTTTAAC
Found at i:9260527 original size:2 final size:2
Alignment explanation
Indices: 9260520--9260568 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
9260510 AAACTCTGAA
* *
9260520 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
9260562 TT AT AT A
1 AT AT AT A
9260569 AAAAAGCAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9299927 original size:2 final size:2
Alignment explanation
Indices: 9299920--9299948 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9299910 ACATGATTCA
9299920 TC TC TC TC TC TC TC TC TC TC TC TC T- TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9299949 GATCTGCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9303597 original size:71 final size:71
Alignment explanation
Indices: 9303493--9303636 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 71
9303483 CATTAGGCAT
*
9303493 GTCAGGAATTCCATGGATTATAATGTCTGAGGTTAGTCGGCAACTTCTTTCTTGATTTCTTCATT
1 GTCAGGAATTCCATGGATTATAATGTCTGAGGTTAGTCGACAACTTCTTTCTTGATTTCTTCATT
9303558 CATTTA
66 CATTTA
9303564 GTCAGGAATTCCATGGATTATAATGTCTGAGGTTAGTCGACAACTTCTTTCTTGATTTCTTCATT
1 GTCAGGAATTCCATGGATTATAATGTCTGAGGTTAGTCGACAACTTCTTTCTTGATTTCTTCATT
9303629 CATTTA
66 CATTTA
9303635 GT
1 GT
9303637 GCATAGCTAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (71 bp):
GTCAGGAATTCCATGGATTATAATGTCTGAGGTTAGTCGACAACTTCTTTCTTGATTTCTTCATT
CATTTA
Found at i:9305012 original size:25 final size:25
Alignment explanation
Indices: 9304980--9305044 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
9304970 TCCTCTTTTA
* *
9304980 TTTTTTT-ATATCCAACAGACATAAT
1 TTTTTTTAAT-TCCAACAAAAATAAT
*
9305005 TTTTTTTAATTCCAATAAAAATAAT
1 TTTTTTTAATTCCAACAAAAATAAT
*
9305030 TTTTTTGAATTCCAA
1 TTTTTTTAATTCCAA
9305045 TATAAGATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 33 0.94
26 2 0.06
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.48
Consensus pattern (25 bp):
TTTTTTTAATTCCAACAAAAATAAT
Found at i:9311678 original size:27 final size:28
Alignment explanation
Indices: 9311647--9311719 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
9311637 ATCTATCTAT
* *
9311647 TTTTAGTGAATAAAAG-TATTTATTCAC
1 TTTTAGTGAGTAAAAGATATTTATCCAC
*
9311674 TTTTAGTGGGT-AAAGATATTTATCCAC
1 TTTTAGTGAGTAAAAGATATTTATCCAC
*
9311701 TTTTGGTGAGT-AAAGATAT
1 TTTTAGTGAGTAAAAGATAT
9311720 CTATTTACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.10
27 36 0.90
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (28 bp):
TTTTAGTGAGTAAAAGATATTTATCCAC
Found at i:9311729 original size:27 final size:27
Alignment explanation
Indices: 9311636--9311723 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 27
9311626 ATCTCTTCAT
* * *
9311636 TATCTATCTATTTTTAGTGAATAAA-A
1 TATCTATCCACTTTTAGTGAGTAAAGA
* * *
9311662 GTATTTATTCACTTTTAGTGGGTAAAGA
1 -TATCTATCCACTTTTAGTGAGTAAAGA
* *
9311690 TATTTATCCACTTTTGGTGAGTAAAGA
1 TATCTATCCACTTTTAGTGAGTAAAGA
9311717 TATCTAT
1 TATCTAT
9311724 TTACTTCTGA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
27 49 0.98
28 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (27 bp):
TATCTATCCACTTTTAGTGAGTAAAGA
Found at i:9311782 original size:27 final size:27
Alignment explanation
Indices: 9311752--9311978 Score: 234
Period size: 27 Copynumber: 8.4 Consensus size: 27
9311742 TTTTTTATGA
* * *
9311752 ATAAAAGTATCCATTTATTTTTGGTGG
1 ATAAAAGTATCCATCTACTTCTGGTGG
9311779 AT-AAAGATATCCATCTACCTT-TGGTAGG
1 ATAAAAG-TATCCATCTA-CTTCTGGT-GG
* *
9311807 -TAAAGGTATCCATCCACTTCTGGTGG
1 ATAAAAGTATCCATCTACTTCTGGTGG
*
9311833 ATAAAAGTATCCATCTACTTCTGATGG
1 ATAAAAGTATCCATCTACTTCTGGTGG
*
9311860 ATAAAAGTATCCATCTACTTCTGATGG
1 ATAAAAGTATCCATCTACTTCTGGTGG
9311887 AT-AAAGATATCCATCTACTTCTGGTAGG
1 ATAAAAG-TATCCATCTACTTCTGGT-GG
* *
9311915 -TAAAAATATCCATCCACCTT-TGGTAGG
1 ATAAAAGTATCCATCTA-CTTCTGGT-GG
* * *
9311942 -TAAAGGTATCCATCTACTTCTGTTAG
1 ATAAAAGTATCCATCTACTTCTGGTGG
9311968 ATAAAAGTATC
1 ATAAAAGTATC
9311979 TATCCATTTC
Statistics
Matches: 172, Mismatches: 16, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
26 17 0.10
27 140 0.81
28 15 0.09
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (27 bp):
ATAAAAGTATCCATCTACTTCTGGTGG
Found at i:9311831 original size:54 final size:54
Alignment explanation
Indices: 9311753--9311990 Score: 270
Period size: 54 Copynumber: 4.4 Consensus size: 54
9311743 TTTTTATGAA
** * *
9311753 TAAAAGTATCCATTTATTTTTGGTGGATAAAGATATCCATCTACCTT-TGGTAGG
1 TAAAAGTATCCATCCACTTCTGGTGGATAAAGATATCCATCTA-CTTCTGGTAGG
* *
9311807 TAAAGGTATCCATCCACTTCTGGTGGATAAA-AGTATCCATCTACTTCTGAT-GG
1 TAAAAGTATCCATCCACTTCTGGTGGATAAAGA-TATCCATCTACTTCTGGTAGG
* *
9311860 ATAAAAGTATCCATCTACTTCTGATGGATAAAGATATCCATCTACTTCTGGTAGG
1 -TAAAAGTATCCATCCACTTCTGGTGGATAAAGATATCCATCTACTTCTGGTAGG
* * * *
9311915 TAAAAATATCCATCCACCTT-TGGTAGG-TAAAGGTATCCATCTACTTCTGTTAGA
1 TAAAAGTATCCATCCA-CTTCTGGT-GGATAAAGATATCCATCTACTTCTGGTAGG
* *
9311969 TAAAAGTATCTATCCATTTCTG
1 TAAAAGTATCCATCCACTTCTG
9311991 ATGTATTTTT
Statistics
Matches: 157, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
53 8 0.05
54 141 0.90
55 8 0.05
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (54 bp):
TAAAAGTATCCATCCACTTCTGGTGGATAAAGATATCCATCTACTTCTGGTAGG
Found at i:9311951 original size:108 final size:108
Alignment explanation
Indices: 9311752--9311993 Score: 337
Period size: 108 Copynumber: 2.2 Consensus size: 108
9311742 TTTTTTATGA
* * * **
9311752 ATAAAAGTATCCATTTATTTTTGGTGGATAAAGATATCCATCTACCTTTGGTAGGTAAAGGTATC
1 ATAAAAGTATCCATCTATTTCTGATGGATAAAGATATCCATCTACCTTTGGTAGGTAAAAATATC
*
9311817 CATCCACTTCTGGTGGATAAAAGTATCCATCTACTTCTGATGG
66 CATCCACTTCTGGTGGATAAAAGTATCCATCTACTTCTGATAG
*
9311860 ATAAAAGTATCCATCTACTTCTGATGGATAAAGATATCCATCTA-CTTCTGGTAGGTAAAAATAT
1 ATAAAAGTATCCATCTATTTCTGATGGATAAAGATATCCATCTACCTT-TGGTAGGTAAAAATAT
* *
9311924 CCATCCACCTT-TGGTAGG-TAAAGGTATCCATCTACTTCTGTTAG
65 CCATCCA-CTTCTGGT-GGATAAAAGTATCCATCTACTTCTGATAG
* *
9311968 ATAAAAGTATCTATCCATTTCTGATG
1 ATAAAAGTATCCATCTATTTCTGATG
9311994 TATTTTTAGA
Statistics
Matches: 119, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
107 3 0.03
108 111 0.93
109 5 0.04
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (108 bp):
ATAAAAGTATCCATCTATTTCTGATGGATAAAGATATCCATCTACCTTTGGTAGGTAAAAATATC
CATCCACTTCTGGTGGATAAAAGTATCCATCTACTTCTGATAG
Found at i:9313670 original size:2 final size:2
Alignment explanation
Indices: 9313663--9313718 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
9313653 TTTTACTTAT
* * *
9313663 TA TA TA TA TC TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
9313705 TG TA TG TA T- TA TA T
1 TA TA TA TA TA TA TA T
9313719 TATTATGAGC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:9319750 original size:29 final size:30
Alignment explanation
Indices: 9319656--9319767 Score: 154
Period size: 30 Copynumber: 3.8 Consensus size: 30
9319646 GACAAGCCTG
*
9319656 ATCATGGCAAAGGAAAGGAAGAGCCTGATC
1 ATCATGGCAATGGAAAGGAAGAGCCTGATC
* * *
9319686 ATCATGGCAATAGAAAGGAAGAGTCTGGTC
1 ATCATGGCAATGGAAAGGAAGAGCCTGATC
* *
9319716 GTCATGGCCATGGAAAGG-AGAGCCTGATC
1 ATCATGGCAATGGAAAGGAAGAGCCTGATC
*
9319745 ATCATGGCAATGGAGAGGAAGAG
1 ATCATGGCAATGGAAAGGAAGAG
9319768 TGTTAGAAGT
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
29 24 0.35
30 45 0.65
ACGTcount: A:0.36, C:0.15, G:0.33, T:0.16
Consensus pattern (30 bp):
ATCATGGCAATGGAAAGGAAGAGCCTGATC
Found at i:9332242 original size:21 final size:21
Alignment explanation
Indices: 9332221--9332260 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
9332211 TTGATTCATA
9332221 AAATGTTTTA-TATTTAAAAT
1 AAATGTTTTATTATTTAAAAT
* *
9332241 AAATTTTTTATTTTTTAAAA
1 AAATGTTTTATTATTTAAAA
9332261 AATACAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
AAATGTTTTATTATTTAAAAT
Found at i:9338570 original size:28 final size:29
Alignment explanation
Indices: 9338524--9338579 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
9338514 AAAAAAGCTG
*
9338524 TGGTTTGATTCTCAAACTGAATT-CAAAA
1 TGGTTAGATTCTCAAACTGAATTACAAAA
* *
9338552 TGGTTAGATTCTTACACTGAATTACAAA
1 TGGTTAGATTCTCAAACTGAATTACAAA
9338580 TGCTCAAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (29 bp):
TGGTTAGATTCTCAAACTGAATTACAAAA
Found at i:9350786 original size:2 final size:2
Alignment explanation
Indices: 9350779--9350804 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9350769 ATATGTAACT
9350779 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
9350805 AAGGAGATTC
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:9361091 original size:78 final size:78
Alignment explanation
Indices: 9360962--9361128 Score: 280
Period size: 78 Copynumber: 2.1 Consensus size: 78
9360952 GTGACCGCCG
*
9360962 ATTTCTTGAGCAACTTTTTTATGATCATGGGCTGGATCTGGCTCTACTTTGTCCTGCAAACTTGC
1 ATTTCTTGAGCAACTTTTTTATGATCATGGGCTGGATCTGGCTCTACTTTGTCCTGCAAACCTGC
*
9361027 ATCTTCAAATGGT
66 ATCTGCAAATGGT
* *
9361040 ATTTCTTGGGCAACTTTTTTATGATCATGGGCTGGATCTGGCTCTACTTTGTCCTGCAAGCCTGC
1 ATTTCTTGAGCAACTTTTTTATGATCATGGGCTGGATCTGGCTCTACTTTGTCCTGCAAACCTGC
*
9361105 GTCTGCAAATGGT
66 ATCTGCAAATGGT
*
9361118 GTTTCTTGAGC
1 ATTTCTTGAGC
9361129 TGAAGCCTCA
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 82 1.00
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (78 bp):
ATTTCTTGAGCAACTTTTTTATGATCATGGGCTGGATCTGGCTCTACTTTGTCCTGCAAACCTGC
ATCTGCAAATGGT
Found at i:9372316 original size:25 final size:24
Alignment explanation
Indices: 9372283--9372440 Score: 88
Period size: 26 Copynumber: 6.1 Consensus size: 24
9372273 AATAAAATAT
*
9372283 ATAATATAAAAAATCAAAAATTAAA
1 ATAAAATAAAAAAT-AAAAATTAAA
*
9372308 ATAAAATAAAATATAAAAATTAAA
1 ATAAAATAAAAAATAAAAATTAAA
9372332 ATTTATATAATATAGGTAAAAT--AAATTAAA
1 A--TA-A-AATA-A---AAAATAAAAATTAAA
* *
9372362 ATAAAATATATATAATAAAAATTATA
1 ATAAAATA-A-AAAATAAAAATTAAA
* *
9372388 TTAAAAAATAAAAATAAAATATATAAA
1 ATAAAATA-AAAAATAAAA-AT-TAAA
** *
9372415 ATTTAATAATAAATAAAAA-TAAA
1 ATAAAATAAAAAATAAAAATTAAA
9372438 ATA
1 ATA
9372441 TATGACATTA
Statistics
Matches: 106, Mismatches: 15, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
23 6 0.06
24 16 0.15
25 21 0.20
26 34 0.32
27 9 0.08
28 6 0.06
29 1 0.01
30 9 0.08
32 4 0.04
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (24 bp):
ATAAAATAAAAAATAAAAATTAAA
Found at i:9372323 original size:7 final size:7
Alignment explanation
Indices: 9372274--9372442 Score: 51
Period size: 7 Copynumber: 24.4 Consensus size: 7
9372264 TATAATTAAA
9372274 ATAAAAT
1 ATAAAAT
*
9372281 ATATAAT
1 ATAAAAT
*
9372288 ATAAAAA
1 ATAAAAT
9372295 ATCAAAA-
1 AT-AAAAT
*
9372302 ATTAAA-
1 ATAAAAT
9372308 AT-AAA-
1 ATAAAAT
9372313 ATAAAAT
1 ATAAAAT
9372320 ATAAAA-
1 ATAAAAT
9372326 ATTAAAATTT
1 A-TAAAA--T
*
9372336 ATATAAT
1 ATAAAAT
9372343 ATAGGTAAA-
1 ATA---AAAT
9372352 AT-AAAT
1 ATAAAAT
9372358 -TAAAAT
1 ATAAAAT
9372364 A-AAATAT
1 ATAAA-AT
*
9372371 ATATAAT
1 ATAAAAT
9372378 A-AAAAT
1 ATAAAAT
* *
9372384 -TATATT
1 ATAAAAT
*
9372390 AAAAAAT
1 ATAAAAT
9372397 A-AAAAT
1 ATAAAAT
9372403 A-AAATAT
1 ATAAA-AT
9372410 ATAAAAT
1 ATAAAAT
*
9372417 TTAATAAT
1 ATAA-AAT
9372425 AAATAAAA-
1 --ATAAAAT
9372433 ATAAAAT
1 ATAAAAT
9372440 ATA
1 ATA
9372443 TGACATTAAA
Statistics
Matches: 124, Mismatches: 15, Indels: 46
0.67 0.08 0.25
Matches are distributed among these distances:
5 9 0.07
6 38 0.31
7 51 0.41
8 12 0.10
9 8 0.06
10 6 0.05
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (7 bp):
ATAAAAT
Found at i:9372383 original size:30 final size:28
Alignment explanation
Indices: 9372267--9372381 Score: 60
Period size: 30 Copynumber: 3.9 Consensus size: 28
9372257 ATAATATTAT
*
9372267 AATTAAAATAAAATATATAATATAAAAAATCAAA
1 AATTAAAAT-AAATATATAAGAT--AAAAT---A
*
9372301 AATTAAAATAAA-ATA-AA-ATATAA-A
1 AATTAAAATAAATATATAAGATAAAATA
** *
9372325 AATTAAAATTTATATAATATAGGTAAAATA
1 AATTAAAATAAATAT-ATA-AGATAAAATA
9372355 AATTAAAATAAAATATATATA-ATAAAA
1 AATTAAAAT-AAATATATA-AGATAAAA
9372382 ATTATATTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
24 11 0.17
25 2 0.03
26 1 0.02
27 1 0.02
28 4 0.06
29 9 0.14
30 17 0.26
31 6 0.09
32 3 0.05
33 3 0.05
34 9 0.14
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.30
Consensus pattern (28 bp):
AATTAAAATAAATATATAAGATAAAATA
Found at i:9372402 original size:49 final size:46
Alignment explanation
Indices: 9372287--9372427 Score: 140
Period size: 49 Copynumber: 2.9 Consensus size: 46
9372277 AAATATATAA
* *
9372287 TATAAAAAATCAAAAATTAAAATAAAATAAAATATAAAAATTAAAATT
1 TATAAAAAAT-AAAAA-TAAAATAAAATAAAATATAATAATAAAAATT
* * *
9372335 TATATAATATAGGTAAAATAAATTAAAATAAAATATATATAATAAAAATT
1 TATAAAAAATA---AAAATAAAATAAAATAAAATATA-ATAATAAAAATT
* *
9372385 ATATTAAAAAATAAAAATAAAAT-ATATAAAATTTAATAATAAA
1 -TA-TAAAAAATAAAAATAAAATAAAATAAAATATAATAATAAA
9372428 TAAAAATAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
47 9 0.12
48 18 0.23
49 27 0.35
50 14 0.18
51 2 0.03
52 7 0.09
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (46 bp):
TATAAAAAATAAAAATAAAATAAAATAAAATATAATAATAAAAATT
Found at i:9372406 original size:54 final size:55
Alignment explanation
Indices: 9372300--9372439 Score: 139
Period size: 54 Copynumber: 2.6 Consensus size: 55
9372290 AAAAAATCAA
* * * * **
9372300 AAATTAAAATAAAATAAAAT-ATAAAAATTAAAATTTATATAATATAGGTAAAAT
1 AAATTAAAATAAAATAATATAATAAAAATTAAAATTTAAAAAATAAAAATAAAAT
*
9372354 AAATTAAAATAAAATATATATAATAAAAATT-ATA-TTAAAAAATAAAAATAAAAT
1 AAATTAAAATAAAATA-ATATAATAAAAATTAAAATTTAAAAAATAAAAATAAAAT
* **
9372408 ATA-TAAAATTTAATAATA-AATAAAAA-TAAAAT
1 AAATTAAAATAAAATAATATAATAAAAATTAAAAT
9372440 ATATGACATT
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
50 1 0.01
51 10 0.14
52 3 0.04
53 10 0.14
54 33 0.46
55 5 0.07
56 9 0.13
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (55 bp):
AAATTAAAATAAAATAATATAATAAAAATTAAAATTTAAAAAATAAAAATAAAAT
Found at i:9372432 original size:39 final size:42
Alignment explanation
Indices: 9372262--9372442 Score: 129
Period size: 39 Copynumber: 4.5 Consensus size: 42
9372252 ATTTTATAAT
* * * *
9372262 ATTATAAT-TAAAATAAAATATATAATATA-AAAAATCAAAA
1 ATTATAATAAAAAATAAAATATAAAATATATAAAATTTAAAA
* *
9372302 ATTA-AA-ATAAAATAAAATATAAAA-AT-TAAAATTTATATA
1 ATTATAATAAAAAATAAAATATAAAATATATAAAATTTA-AAA
* * *
9372341 ATATAGGTAA-AATAAATTAAA-ATAAAATATATATAA--TAAAA
1 AT-TA--TAATAAAAAATAAAATATAAAATATATAAAATTTAAAA
* *
9372382 ATTATATTAAAAAATAAAA-ATAAAATATATAAAATTTAATA
1 ATTATAATAAAAAATAAAATATAAAATATATAAAATTTAAAA
9372423 A-TA-AAT-AAAAATAAAATATA
1 ATTATAATAAAAAATAAAATATA
9372443 TGACATTAAA
Statistics
Matches: 113, Mismatches: 15, Indels: 27
0.73 0.10 0.17
Matches are distributed among these distances:
38 20 0.18
39 50 0.44
40 10 0.09
41 9 0.08
42 8 0.07
43 12 0.11
44 4 0.04
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (42 bp):
ATTATAATAAAAAATAAAATATAAAATATATAAAATTTAAAA
Found at i:9372434 original size:32 final size:33
Alignment explanation
Indices: 9372379--9372443 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
9372369 ATATATAATA
*
9372379 AAAATTATATTAAAAAATAAAAATAAAATATAT
1 AAAATTATAATAAAAAATAAAAATAAAATATAT
*
9372412 AAAATT-TAATAATAAATAAAAATAAAATATAT
1 AAAATTATAATAAAAAATAAAAATAAAATATAT
9372444 GACATTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 24 0.80
33 6 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (33 bp):
AAAATTATAATAAAAAATAAAAATAAAATATAT
Found at i:9372495 original size:13 final size:14
Alignment explanation
Indices: 9372364--9372503 Score: 60
Period size: 13 Copynumber: 9.8 Consensus size: 14
9372354 AAATTAAAAT
9372364 AAAATATATATAATA
1 AAAATATA-ATAATA
*
9372379 AAAAT-T-ATATTA
1 AAAATATAATAATA
*
9372391 AAAA-ATAAAAATA
1 AAAATATAATAATA
9372404 AAATATATAAAATTTAATA
1 AAA-ATAT--AA--TAATA
9372423 ATAAATA-AA-AATA
1 A-AAATATAATAATA
* * *
9372436 AAATATATGACATTA
1 AAA-ATATAATAATA
* *
9372451 AAAATATATTAAGA
1 AAAATATAATAATA
**
9372465 GATGATAT-ATATATA
1 -AAAATATAATA-ATA
9372480 AAAAT-TAATAATA
1 AAAATATAATAATA
9372493 AAAATATAATA
1 AAAATATAATA
9372504 TATTAAATTT
Statistics
Matches: 92, Mismatches: 17, Indels: 33
0.65 0.12 0.23
Matches are distributed among these distances:
12 12 0.13
13 24 0.26
14 22 0.24
15 20 0.22
16 2 0.02
17 2 0.02
19 8 0.09
20 2 0.02
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (14 bp):
AAAATATAATAATA
Found at i:9382739 original size:12 final size:13
Alignment explanation
Indices: 9382716--9382750 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
9382706 ATCAACTGAT
9382716 AAATGAAAAAAGAA
1 AAATG-AAAAAGAA
9382730 AAA-GAAAAAGAA
1 AAATGAAAAAGAA
9382742 AAATGAAAA
1 AAATGAAAA
9382751 CAAGAAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 11 0.55
13 6 0.30
14 3 0.15
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (13 bp):
AAATGAAAAAGAA
Found at i:9389059 original size:31 final size:31
Alignment explanation
Indices: 9388988--9389076 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
9388978 TATATATATA
* *
9388988 TATTTTAATTTAATTCTTATATATTCAAAAT
1 TATTTTAATTTAATTTTTATATATTAAAAAT
*** *
9389019 TAAAATAATTTAATCTTTTA-ATTTTAAAAAT
1 TATTTTAATTTAAT-TTTTATATATTAAAAAT
*
9389050 TATTTTAATTTAATTTTTTTAATATTA
1 TATTTTAATTTAATTTTTAT-ATATTA
9389077 TACAATTTAA
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
30 4 0.09
31 31 0.70
32 9 0.20
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (31 bp):
TATTTTAATTTAATTTTTATATATTAAAAAT
Found at i:9407909 original size:12 final size:12
Alignment explanation
Indices: 9407878--9407909 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
9407868 GATTGAAAGA
9407878 TTTTTTTTCTTT
1 TTTTTTTTCTTT
*
9407890 TTCTTTTTCTTT
1 TTTTTTTTCTTT
9407902 TTTTTTTT
1 TTTTTTTT
9407910 TGAATTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:9408293 original size:12 final size:11
Alignment explanation
Indices: 9408276--9408310 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
9408266 AAAAATCGTG
9408276 AAAAATGAACAA
1 AAAAATGAA-AA
9408288 AAAAATGAAAA
1 AAAAATGAAAA
9408299 AAAAA-GAAAA
1 AAAAATGAAAA
9408309 AA
1 AA
9408311 GAGACAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.30
11 7 0.30
12 9 0.39
ACGTcount: A:0.83, C:0.03, G:0.09, T:0.06
Consensus pattern (11 bp):
AAAAATGAAAA
Found at i:9416978 original size:2 final size:2
Alignment explanation
Indices: 9416971--9417002 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
9416961 CATTGGCCAC
*
9416971 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9417003 TTACGAGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9418133 original size:15 final size:16
Alignment explanation
Indices: 9418113--9418155 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
9418103 ACATAAAATT
*
9418113 AAAATAATTCACT-TA
1 AAAATAATTAACTATA
*
9418128 AAAATAAATTAATTATA
1 AAAAT-AATTAACTATA
9418145 AAAATAATTAA
1 AAAATAATTAA
9418156 AAATAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATAATTAACTATA
Found at i:9418153 original size:16 final size:15
Alignment explanation
Indices: 9418113--9418165 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
9418103 ACATAAAATT
*
9418113 AAAATAATTCACTTA
1 AAAATAATTAACTTA
9418128 AAAATAAATTAA-TTA
1 AAAAT-AATTAACTTA
*
9418143 TAAA-AA-TAA-TTA
1 AAAATAATTAACTTA
9418155 AAAATAATTAA
1 AAAATAATTAA
9418166 ATTATAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 9 0.28
13 4 0.12
14 3 0.09
15 11 0.34
16 5 0.16
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATAATTAACTTA
Found at i:9418158 original size:10 final size:10
Alignment explanation
Indices: 9418143--9418180 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
9418133 AAATTAATTA
9418143 TAAAAATAAT
1 TAAAAATAAT
9418153 TAAAAATAAT
1 TAAAAATAAT
*
9418163 TAAATTATAAT
1 TAAA-AATAAT
9418174 TAAAAAT
1 TAAAAAT
9418181 TAAAGACCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
TAAAAATAAT
Found at i:9418178 original size:20 final size:20
Alignment explanation
Indices: 9418109--9418178 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
9418099 ATAAACATAA
* * *
9418109 AATTAAAATAATTCACTTAA
1 AATTAAAATAATTAAATTAT
* * **
9418129 AAATAAATTAATTATAAAAAT
1 AATTAAAATAATTA-AATTAT
9418150 AATTAAAAATAATTAAATTAT
1 AATT-AAAATAATTAAATTAT
9418171 AATTAAAA
1 AATTAAAA
9418179 ATTAAAGACC
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
20 15 0.41
21 13 0.35
22 9 0.24
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
AATTAAAATAATTAAATTAT
Found at i:9418920 original size:63 final size:63
Alignment explanation
Indices: 9418847--9418968 Score: 226
Period size: 63 Copynumber: 1.9 Consensus size: 63
9418837 AATCACAAGC
* *
9418847 GATCTCTCTTAAAACCTAGTCTCCTTTGACAAACTATTGAGACATATAATTATCGTACTTTGT
1 GATCTCTCTTAAAACCTAGTCTCCCTTGACAAACTATTGAGACATATAATCATCGTACTTTGT
9418910 GATCTCTCTTAAAACCTAGTCTCCCTTGACAAACTATTGAGACATATAATCATCGTACT
1 GATCTCTCTTAAAACCTAGTCTCCCTTGACAAACTATTGAGACATATAATCATCGTACT
9418969 ATCTTTTTGC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (63 bp):
GATCTCTCTTAAAACCTAGTCTCCCTTGACAAACTATTGAGACATATAATCATCGTACTTTGT
Found at i:9420288 original size:15 final size:15
Alignment explanation
Indices: 9420268--9420338 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 15
9420258 GATATTACTT
9420268 TTAAATTTAAATAAA
1 TTAAATTTAAATAAA
9420283 TTAAATTTAAATATAA
1 TTAAATTTAAATA-AA
*
9420299 TT-AATCTT---T-AT
1 TTAAAT-TTAAATAAA
*
9420310 TTAAAGTTTAAACAAA
1 TTAAA-TTTAAATAAA
9420326 TTAAATTTAAATA
1 TTAAATTTAAATA
9420339 TAATGAATAG
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
11 3 0.07
12 4 0.09
13 2 0.05
15 23 0.52
16 12 0.27
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (15 bp):
TTAAATTTAAATAAA
Found at i:9420364 original size:43 final size:43
Alignment explanation
Indices: 9420268--9420354 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
9420258 GATATTACTT
* * *** *
9420268 TTAAA-TTTAAATAAATTAAATTTAAATATAATTAATCTTTAT
1 TTAAAGTTTAAACAAATTAAATTTAAATATAATGAATAGATAA
9420310 TTAAAGTTTAAACAAATTAAATTTAAATATAATGAATAGATAA
1 TTAAAGTTTAAACAAATTAAATTTAAATATAATGAATAGATAA
9420353 TT
1 TT
9420355 CTTGTTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
42 5 0.13
43 33 0.87
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (43 bp):
TTAAAGTTTAAACAAATTAAATTTAAATATAATGAATAGATAA
Found at i:9433972 original size:22 final size:24
Alignment explanation
Indices: 9433947--9433992 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
9433937 AAATAAAAAT
9433947 AAAAAGAT-AAAAAAGAG-AAGAG
1 AAAAAGATAAAAAAAGAGTAAGAG
9433969 AAAAAGATAAAAAAAGAGTAAGAG
1 AAAAAGATAAAAAAAGAGTAAGAG
9433993 GCATAGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 8 0.36
23 9 0.41
24 5 0.23
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.07
Consensus pattern (24 bp):
AAAAAGATAAAAAAAGAGTAAGAG
Found at i:9436256 original size:198 final size:199
Alignment explanation
Indices: 9435915--9436312 Score: 735
Period size: 198 Copynumber: 2.0 Consensus size: 199
9435905 CCAACCCATT
9435915 GAAGGTGAGACACTCAGGGACCAGCTTCGATTTTTCCAATCGTTGGACAGTTTGGAGGAGGACAA
1 GAAGGTGAGACACTCAGGGACCAGCTTCGATTTTTCCAATCGTTGGACAGTTT-G-GGAGGACAA
*
9435980 AGCAGCCTTGATGGTGATGCATGTTGTGACTATTTCTAGTACAAGGAATTAAATTAATGCACATT
64 AGCAGCCTTGATGGTGATGCATGTTGTGACTATTTCTAGTACAAGGAATTAAATTAATACACATT
*
9436045 ACTTTTCTCCACTAGGATGCTTTGAGTAACTAGGATGATCCGTTTATGAATTAGTCCTATCTCTT
129 ACTTTTCTCCACTAGGATGCTTTGAGTAACTAGGATGATCCGTTTATGAATTAGTCCTATCTCTG
9436110 TCTATC
194 TCTATC
9436116 GAAGGTGAGACACTCAGGGACCAGCTTCGATTTTTCCAATCGTTGGACAGTTT-GGAGGACAAAG
1 GAAGGTGAGACACTCAGGGACCAGCTTCGATTTTTCCAATCGTTGGACAGTTTGGGAGGACAAAG
9436180 CAGCCTTGATGGTGATGCATGTTGTGACTATTTCTAGTACAAGGAATTAAATTAATACACATTAC
66 CAGCCTTGATGGTGATGCATGTTGTGACTATTTCTAGTACAAGGAATTAAATTAATACACATTAC
* *
9436245 TTTTCTCCACTAGGATGCTTTGAGTGACTAGGATGATCCGTTTATGAATTAGTCTTATCTCTGTC
131 TTTTCTCCACTAGGATGCTTTGAGTAACTAGGATGATCCGTTTATGAATTAGTCCTATCTCTGTC
9436310 TAT
196 TAT
9436313 TCATTGTGGA
Statistics
Matches: 193, Mismatches: 4, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
198 140 0.73
201 53 0.27
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (199 bp):
GAAGGTGAGACACTCAGGGACCAGCTTCGATTTTTCCAATCGTTGGACAGTTTGGGAGGACAAAG
CAGCCTTGATGGTGATGCATGTTGTGACTATTTCTAGTACAAGGAATTAAATTAATACACATTAC
TTTTCTCCACTAGGATGCTTTGAGTAACTAGGATGATCCGTTTATGAATTAGTCCTATCTCTGTC
TATC
Found at i:9439467 original size:20 final size:21
Alignment explanation
Indices: 9439427--9439485 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
9439417 TAAAATATTA
9439427 ATTTT-TTTAATTTTATAGAT
1 ATTTTATTTAATTTTATAGAT
9439447 ATTTTATTTAATTATT-T-GAT
1 ATTTTATTTAATT-TTATAGAT
*
9439467 ATTTATATTTAACTTTATA
1 ATTT-TATTTAATTTTATA
9439486 TGATTTGTGG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 14 0.42
21 17 0.52
22 2 0.06
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (21 bp):
ATTTTATTTAATTTTATAGAT
Found at i:9439991 original size:19 final size:19
Alignment explanation
Indices: 9439969--9440008 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
9439959 AATTTATTTT
9439969 TTAAATAAAAAATTAAATA
1 TTAAATAAAAAATTAAATA
* *
9439988 TTAATTAATAAATTAAATA
1 TTAAATAAAAAATTAAATA
9440007 TT
1 TT
9440009 TGAGTGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAATAAAAAATTAAATA
Found at i:9449277 original size:21 final size:19
Alignment explanation
Indices: 9449234--9449277 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
9449224 CAATTTGATT
*
9449234 AAAATTACAAACCAATTAC
1 AAAATTACAAACCAATCAC
*
9449253 AAAATTATCAAACTTAATCAC
1 AAAATTA-CAAAC-CAATCAC
9449274 AAAA
1 AAAA
9449278 AGGTCAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAATTACAAACCAATCAC
Found at i:9450875 original size:25 final size:24
Alignment explanation
Indices: 9450841--9450898 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
9450831 GACGAATATT
9450841 AATATTTAAT-TTTAAATATTAAAA
1 AATATTTAATATTTAAAT-TTAAAA
9450865 AATATATTAATATTTAAATTT-AAA
1 AATAT-TTAATATTTAAATTTAAAA
9450889 AATAATTTAA
1 AAT-ATTTAA
9450899 AATATCAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
24 15 0.48
25 9 0.29
26 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AATATTTAATATTTAAATTTAAAA
Found at i:9453475 original size:19 final size:18
Alignment explanation
Indices: 9453451--9453486 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9453441 TTTTCATCTT
*
9453451 TTATTTTCTATTATTATTA
1 TTATTTTCAATT-TTATTA
9453470 TTATTTTCAATTTTATT
1 TTATTTTCAATTTTATT
9453487 CTATATAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTTCAATTTTATTA
Found at i:9463334 original size:2 final size:2
Alignment explanation
Indices: 9463327--9463356 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9463317 ATGAGAAAGA
9463327 AT AT 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 AT AT
9463357 GCACGTGGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9483813 original size:13 final size:14
Alignment explanation
Indices: 9483792--9483825 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
9483782 ATTACTATAT
9483792 AATTATACTTAA-AA
1 AATT-TACTTAATAA
9483806 AATTTACTTAATAA
1 AATTTACTTAATAA
9483820 AATTTA
1 AATTTA
9483826 GTCATGATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTACTTAATAA
Found at i:9492210 original size:33 final size:33
Alignment explanation
Indices: 9492161--9492226 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
9492151 TTGCTGACAT
* * * *
9492161 TTATAATTTATGATAATATGATATATTAATATA
1 TTATAATTAATAATAATATAACATATTAATATA
*
9492194 TTATAATTAATAATAATATAACATGTTAATATA
1 TTATAATTAATAATAATATAACATATTAATATA
9492227 AGATTATGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (33 bp):
TTATAATTAATAATAATATAACATATTAATATA
Done.