Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 98 of 160
Found at i:18490250 original size:50 final size:51
Alignment explanation
Indices: 18490135--18490233 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 51
18490125 TTACCAATAA
* *
18490135 TATATAAAATTTATATATTAATAATACATCTAATATCTAATTTATTGATAG
1 TATATATAATTTATATATTAATAATACATCTAATATCTAATTTATGGATAG
18490186 TATATATAATTTATATA-TAATAATACAT-TAAATATCTAATTTATGGAT
1 TATATATAATTTATATATTAATAATACATCT-AATATCTAATTTATGGAT
18490234 GGTGTATAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
49 1 0.02
50 28 0.62
51 16 0.36
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (51 bp):
TATATATAATTTATATATTAATAATACATCTAATATCTAATTTATGGATAG
Found at i:18490370 original size:49 final size:52
Alignment explanation
Indices: 18490254--18490378 Score: 184
Period size: 53 Copynumber: 2.4 Consensus size: 52
18490244 TATTATACAC
* *
18490254 TAATCATATGTCAAATATAAACTATTAAATAAATTATTATATGTTTATTTCAT
1 TAATAATATATCAAATATAAACTATTAAATAAA-TATTATATGTTTATTTCAT
* *
18490307 TAATAGTATATCAAATATAAACTCTTAAAT-AA-ATTATATGTTTATTTCAT
1 TAATAATATATCAAATATAAACTATTAAATAAATATTATATGTTTATTTCAT
18490357 T-ATAATATATCAAATATAAACT
1 TAATAATATATCAAATATAAACT
18490379 TATAGTTTAC
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
49 20 0.30
50 19 0.28
52 2 0.03
53 26 0.39
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (52 bp):
TAATAATATATCAAATATAAACTATTAAATAAATATTATATGTTTATTTCAT
Found at i:18490848 original size:37 final size:35
Alignment explanation
Indices: 18490801--18490873 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 35
18490791 ATATTTTTAG
*
18490801 ACATTATAAAATTTATTCTTGA-AAATATATAATTAAA
1 ACATTATAAAA-ATATT-TTGAGAAA-ATATAATTAAA
* *
18490838 ACATTCTAAAAATATTTTTAGAAAATATAATTAAA
1 ACATTATAAAAATATTTTGAGAAAATATAATTAAA
18490873 A
1 A
18490874 TAAAAGTACC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 15 0.47
36 7 0.22
37 10 0.31
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (35 bp):
ACATTATAAAAATATTTTGAGAAAATATAATTAAA
Found at i:18495490 original size:26 final size:26
Alignment explanation
Indices: 18495460--18495518 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
18495450 TTATGTTTTA
18495460 AATTTAATTTGATAGCTATGTAAATC
1 AATTTAATTTGATAGCTATGTAAATC
18495486 AATTTAATTTGATAGCTATGTAAATC
1 AATTTAATTTGATAGCTATGTAAATC
18495512 AATTTAA
1 AATTTAA
18495519 GTCAAGGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (26 bp):
AATTTAATTTGATAGCTATGTAAATC
Found at i:18503415 original size:21 final size:20
Alignment explanation
Indices: 18503389--18503427 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
18503379 TGTATTAAGA
18503389 ATTTTTAATTTATAGGTTTTG
1 ATTTTTAATTT-TAGGTTTTG
*
18503410 ATTTTTGATTTTA-GTTTT
1 ATTTTTAATTTTAGGTTTT
18503428 TACTTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.67
Consensus pattern (20 bp):
ATTTTTAATTTTAGGTTTTG
Found at i:18503725 original size:14 final size:14
Alignment explanation
Indices: 18503708--18503740 Score: 57
Period size: 14 Copynumber: 2.3 Consensus size: 14
18503698 TTTTTTTTAA
18503708 TTTTTGTAGATTTTT
1 TTTTTGTAG-TTTTT
18503723 TTTTTGTAGTTTTT
1 TTTTTGTAGTTTTT
18503737 TTTT
1 TTTT
18503741 CTTGTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.09, C:0.00, G:0.12, T:0.79
Consensus pattern (14 bp):
TTTTTGTAGTTTTT
Found at i:18503737 original size:16 final size:15
Alignment explanation
Indices: 18503708--18503752 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
18503698 TTTTTTTTAA
18503708 TTTTTGTAGATTTTT
1 TTTTTGTAGATTTTT
*
18503723 TTTTTGTAGTTTTTT
1 TTTTTGTAGATTTTT
18503738 TTTCTTGT-GATTTTT
1 TTT-TTGTAGATTTTT
18503753 ATATGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.09, C:0.02, G:0.13, T:0.76
Consensus pattern (15 bp):
TTTTTGTAGATTTTT
Found at i:18503923 original size:19 final size:19
Alignment explanation
Indices: 18503896--18503938 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
18503886 GGCTTTGAGA
*
18503896 GTGACTTGTTGTGTTCATG
1 GTGATTTGTTGTGTTCATG
18503915 GTGATTTGTTGTGTTCATG
1 GTGATTTGTTGTGTTCATG
18503934 GTGAT
1 GTGAT
18503939 GGTGGTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.12, C:0.07, G:0.33, T:0.49
Consensus pattern (19 bp):
GTGATTTGTTGTGTTCATG
Found at i:18504554 original size:23 final size:21
Alignment explanation
Indices: 18504524--18504590 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 21
18504514 TTTTTTGCAT
18504524 TTTTATATTTATTAAAATTACA
1 TTTTATATTTATTAAAATTA-A
*
18504546 GTTTTATATTTTTGTGCAAAATTAA
1 -TTTTATATTTAT-T--AAAATTAA
* *
18504571 TTATGTATTTATTAAAATTA
1 TTTTATATTTATTAAAATTA
18504591 GAATTTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 7 0.19
23 12 0.32
24 10 0.27
25 1 0.03
26 7 0.19
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTTATATTTATTAAAATTAA
Found at i:18509950 original size:138 final size:138
Alignment explanation
Indices: 18509702--18509996 Score: 581
Period size: 138 Copynumber: 2.1 Consensus size: 138
18509692 ATACAAAAAT
*
18509702 TATCATGTAAATATATTATAAATCATACCAAATATCATGTAATAATATCATGCCTAGATCATGCT
1 TATCATGCAAATATATTATAAATCATACCAAATATCATGTAATAATATCATGCCTAGATCATGCT
18509767 AAAACATTCATGCAAGAATGTCATGCAAATATATTAATTATCATACAATAATAACAATCATGTAA
66 AAAACATTCATGCAAGAATGTCATGCAAATATATTAATTATCATACAATAATAACAATCATGTAA
18509832 ATATATAA
131 ATATATAA
18509840 TATCATGCAAATATATTATAAATCATACCAAATATCATGTAATAATATCATGCCTAGATCATGCT
1 TATCATGCAAATATATTATAAATCATACCAAATATCATGTAATAATATCATGCCTAGATCATGCT
18509905 AAAACATTCATGCAAGAATGTCATGCAAATATATTAATTATCATACAATAATAACAATCATGTAA
66 AAAACATTCATGCAAGAATGTCATGCAAATATATTAATTATCATACAATAATAACAATCATGTAA
18509970 ATATATAA
131 ATATATAA
18509978 TATCATGCAAATATATTAT
1 TATCATGCAAATATATTAT
18509997 CATGCAATAA
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 156 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (138 bp):
TATCATGCAAATATATTATAAATCATACCAAATATCATGTAATAATATCATGCCTAGATCATGCT
AAAACATTCATGCAAGAATGTCATGCAAATATATTAATTATCATACAATAATAACAATCATGTAA
ATATATAA
Found at i:18509997 original size:16 final size:17
Alignment explanation
Indices: 18509961--18510003 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
18509951 AATAATAACA
*
18509961 ATCATGTAAATATATAAT
1 ATCATGCAAATATAT-AT
18509979 ATCATGCAAATATAT-T
1 ATCATGCAAATATATAT
18509995 ATCATGCAA
1 ATCATGCAA
18510004 TAATAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 10 0.42
18 14 0.58
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (17 bp):
ATCATGCAAATATATAT
Found at i:18510008 original size:18 final size:17
Alignment explanation
Indices: 18509925--18510008 Score: 55
Period size: 16 Copynumber: 4.7 Consensus size: 17
18509915 TGCAAGAATG
18509925 TCATGCAAATATATTAATTA
1 TCATGCAAA-ATA-T-ATTA
* **
18509945 TCATACAATAATA-ACAA
1 TCATGCAA-AATATATTA
* *
18509962 TCATGTAAATATATAATA
1 TCATGCAAA-ATATATTA
18509980 TCATGC-AAATATATTA
1 TCATGCAAAATATATTA
18509996 TCATGCAATAATA
1 TCATGCAA-AATA
18510009 ATAAATAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
16 14 0.28
17 14 0.28
18 11 0.22
20 10 0.20
21 1 0.02
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.35
Consensus pattern (17 bp):
TCATGCAAAATATATTA
Found at i:18510113 original size:32 final size:30
Alignment explanation
Indices: 18510070--18510268 Score: 107
Period size: 32 Copynumber: 6.7 Consensus size: 30
18510060 AATAAATTAA
18510070 TAAATTAATAATCATGCAAATAAACATGCAAT
1 TAAA-TAATAATCATGCAAATAAACAT-CAAT
*
18510102 TAAATATATAATCATACAAAT-AA-A--AA-
1 TAAATA-ATAATCATGCAAATAAACATCAAT
* * * * *
18510128 T-ATTAATAGTCATGCAAACACACAAATAAAT
1 TAAATAATAATCATGCAAATA-A-ACATCAAT
* * * *
18510159 TAATTAATAATTATGCAATTAGACATACAAT
1 TAAATAATAATCATGCAAATAAACAT-CAAT
* *
18510190 TAAATATTTAATCATGTAAAT--A-AT-AA-
1 TAAATA-ATAATCATGCAAATAAACATCAAT
*
18510216 T-ATTAATAATCATGCAAATAAACATGCAAT
1 TAAATAATAATCATGCAAATAAACAT-CAAT
*
18510246 TAAATATATAATCTTGCAAATAA
1 TAAATA-ATAATCATGCAAATAA
18510269 GGTTAAGGCT
Statistics
Matches: 126, Mismatches: 22, Indels: 38
0.68 0.12 0.20
Matches are distributed among these distances:
24 23 0.18
25 6 0.05
26 4 0.03
27 7 0.06
28 1 0.01
29 4 0.03
30 8 0.06
31 16 0.13
32 57 0.45
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (30 bp):
TAAATAATAATCATGCAAATAAACATCAAT
Found at i:18510190 original size:88 final size:91
Alignment explanation
Indices: 18510027--18510233 Score: 269
Period size: 88 Copynumber: 2.3 Consensus size: 91
18510017 ATAACTAGGT
* *
18510027 AAATAAATAA-ATTAATAATCATACAATCACACAAATAAATTAATAAATTAATAATCATGCAAAT
1 AAATAAA-AATATTAATAATCATGCAAACACACAAATAAATT-ATAAATTAATAATCATGCAAAT
*
18510091 AAACATGCAATTAAATATATAATCATAC
64 AAACATACAATTAAATATATAATCATAC
* * * *
18510119 AAATAAAAATATTAATAGTCATGCAAACACACAAATAAA-T-T-AATTAATAATTATGCAATTAG
1 AAATAAAAATATTAATAATCATGCAAACACACAAATAAATTATAAATTAATAATCATGCAAATAA
* **
18510181 ACATACAATTAAATATTTAATCATGT
66 ACATACAATTAAATATATAATCATAC
*
18510207 AAATAATAATATTAATAATCATGCAAA
1 AAATAAAAATATTAATAATCATGCAAA
18510234 TAAACATGCA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
88 65 0.64
89 1 0.01
91 3 0.03
92 33 0.32
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.30
Consensus pattern (91 bp):
AAATAAAAATATTAATAATCATGCAAACACACAAATAAATTATAAATTAATAATCATGCAAATAA
ACATACAATTAAATATATAATCATAC
Found at i:18510211 original size:56 final size:57
Alignment explanation
Indices: 18510150--18510268 Score: 152
Period size: 56 Copynumber: 2.1 Consensus size: 57
18510140 TGCAAACACA
* * * * *
18510150 CAAATAAATTA-ATTAATAATTATGCAATTAGACATACAATTAAATATTTAATCATG
1 CAAATAAATAATATTAATAATCATGCAAATAAACATACAATTAAATATATAATCATG
* * *
18510206 TAAAT-AATAATATTAATAATCATGCAAATAAACATGCAATTAAATATATAATCTTG
1 CAAATAAATAATATTAATAATCATGCAAATAAACATACAATTAAATATATAATCATG
18510262 CAAATAA
1 CAAATAA
18510269 GGTTAAGGCT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
55 4 0.08
56 47 0.90
57 1 0.02
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (57 bp):
CAAATAAATAATATTAATAATCATGCAAATAAACATACAATTAAATATATAATCATG
Found at i:18510257 original size:88 final size:88
Alignment explanation
Indices: 18510027--18510268 Score: 256
Period size: 88 Copynumber: 2.7 Consensus size: 88
18510017 ATAACTAGGT
* *
18510027 AAATAAATAA-ATTAATAATCATACAATCACACAAATAAATTAATAAATTAATAATCATGCAAAT
1 AAATAAA-AATATTAATAATCATGCAAACACACAAATAAA-T--TAAA-TAATAATCATGCAAAT
*
18510091 AAACATGCAATTAAATATATAATCATAC
61 AAACATACAATTAAATATATAATCATAC
* * * * *
18510119 AAATAAAAATATTAATAGTCATGCAAACACACAAATAAATTAATTAATAATTATGCAATTAGACA
1 AAATAAAAATATTAATAATCATGCAAACACACAAATAAATTAAATAATAATCATGCAAATAAACA
* **
18510184 TACAATTAAATATTTAATCATGT
66 TACAATTAAATATATAATCATAC
* * * * *
18510207 AAATAATAATATTAATAATCATGCAAATA-A-ACATGCAATTAAATATATAATCTTGCAAATAA
1 AAATAAAAATATTAATAATCATGCAAACACACAAAT-AAATTAAATA-ATAATCATGCAAATAA
18510269 GGTTAAGGCT
Statistics
Matches: 126, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
86 3 0.02
87 9 0.07
88 75 0.60
89 3 0.02
91 3 0.02
92 33 0.26
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (88 bp):
AAATAAAAATATTAATAATCATGCAAACACACAAATAAATTAAATAATAATCATGCAAATAAACA
TACAATTAAATATATAATCATAC
Found at i:18515698 original size:17 final size:17
Alignment explanation
Indices: 18515676--18515714 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
18515666 ATACATATCC
18515676 TATTAATACA-ATGTACA
1 TATTAATA-ATATGTACA
*
18515693 TATTAATAATATGTGCA
1 TATTAATAATATGTACA
18515710 TATTA
1 TATTA
18515715 TTAGCTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (17 bp):
TATTAATAATATGTACA
Found at i:18515899 original size:22 final size:22
Alignment explanation
Indices: 18515871--18515950 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
18515861 TCTCAGCAAG
* *
18515871 TGTACATATAATTATAGGAATA
1 TGTACATATAATTATAAGAACA
* *
18515893 TGTACATATATTTATAATAACA
1 TGTACATATAATTATAAGAACA
* ***
18515915 TGTACATAGAATTATAATTTCA
1 TGTACATATAATTATAAGAACA
18515937 TGTACATATAATTA
1 TGTACATATAATTA
18515951 ACTTACATAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (22 bp):
TGTACATATAATTATAAGAACA
Found at i:18526749 original size:25 final size:24
Alignment explanation
Indices: 18526705--18526751 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
18526695 AAAAAAAAGT
*
18526705 AAAAAAAAGATTAATTTTTTTTAA
1 AAAAAAAAGATTAATGTTTTTTAA
18526729 AAAAGAAAAGA-TATATGTTTTTT
1 AAAA-AAAAGATTA-ATGTTTTTT
18526752 TATTTGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (24 bp):
AAAAAAAAGATTAATGTTTTTTAA
Found at i:18537619 original size:239 final size:241
Alignment explanation
Indices: 18537170--18537623 Score: 653
Period size: 239 Copynumber: 1.9 Consensus size: 241
18537160 TTATCCAAGT
18537170 CTTAACCATATTTATGATTTACCAAAATATTTGATATTGAAAATTAATCTTAAAATTACTTCAAT
1 CTTAACCATATTTATGATTTACCAAAATATTTGATATTGAAAATTAATCTTAAAATTACTTCAAT
* ** *
18537235 AGTTTGGTAGCAATTTAAGATAATTCTCTCTTCTCAGAAGTATTCATAGAAACTAGTGCCCCACC
66 AGTTTGGTAACAATTTAAGATAATTCTCTCACCTCAGAAGTATTCATAGAAACTAATGCCCCACC
* ** * * * *
18537300 ATGAAGATGCTTCATTGTCGGATTCATTTAAATTTTAGTTAAAGACATAATTAATAAAATATTTC
131 ATGAAGAAGCTTCATCATCAGATTCATTTAAATTTTAATTAAAGAAATAATCAATAAAATATTTC
*
18537365 AATAGTTTGGTAAGATTTACATTGATGCAGATCTTCCAGTAGTTTC
196 AATAGTTTAGTAAGATTTACATTGATGCAGATCTTCCAGTAGTTTC
*
18537411 CTTAACCATATTTATGA-TTATCAAAATATTTGATATTGAAAATTAATCTTAAAATTA-TTCCAA
1 CTTAACCATATTTATGATTTACCAAAATATTTGATATTGAAAATTAATCTTAAAATTACTT-CAA
* * * * * * * * *
18537474 TAGTTTGGTAACAATTTGATATAATTGTCTCACCTTAGGAGT-TTCATGGAGACTAATGTCCCAT
65 TAGTTTGGTAACAATTTAAGATAATTCTCTCACCTCAGAAGTATTCATAGAAACTAATGCCCCAC
* * *
18537538 CTTGAAGAAGCTTCATCATCAGATTTATTTAAATTTTAATTAAAGAAATAATCAATAAAATCTTT
130 CATGAAGAAGCTTCATCATCAGATTCATTTAAATTTTAATTAAAGAAATAATCAATAAAATATTT
18537603 CAATAGTTTAGTAAGATTTAC
195 CAATAGTTTAGTAAGATTTAC
18537624 TTTAGTATAG
Statistics
Matches: 187, Mismatches: 25, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
239 94 0.50
240 76 0.41
241 17 0.09
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.39
Consensus pattern (241 bp):
CTTAACCATATTTATGATTTACCAAAATATTTGATATTGAAAATTAATCTTAAAATTACTTCAAT
AGTTTGGTAACAATTTAAGATAATTCTCTCACCTCAGAAGTATTCATAGAAACTAATGCCCCACC
ATGAAGAAGCTTCATCATCAGATTCATTTAAATTTTAATTAAAGAAATAATCAATAAAATATTTC
AATAGTTTAGTAAGATTTACATTGATGCAGATCTTCCAGTAGTTTC
Found at i:18541897 original size:3 final size:3
Alignment explanation
Indices: 18541886--18541926 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
18541876 TTTCACTAAA
18541886 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
18541927 CTACTACTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:18541931 original size:3 final size:3
Alignment explanation
Indices: 18541925--18541958 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
18541915 TTATTATTAT
*
18541925 TAC TAC TAC TAC TAC TAC TAC TAT TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
18541959 GATTTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (3 bp):
TAC
Found at i:18542112 original size:18 final size:17
Alignment explanation
Indices: 18542091--18542124 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18542081 AACATGTATT
*
18542091 TTTTATTTTTTATTAGTA
1 TTTTATCTTTT-TTAGTA
18542109 TTTTATCTTTTTTAGT
1 TTTTATCTTTTTTAGT
18542125 TTATTTTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTATCTTTTTTAGTA
Found at i:18542282 original size:4 final size:4
Alignment explanation
Indices: 18542275--18542407 Score: 70
Period size: 4 Copynumber: 33.2 Consensus size: 4
18542265 AATAAAATAA
* * * * * * * *
18542275 ATAT ATAT ATAC ATAC ATAT ATAT GTAT ATAT ATAT GTAT GTGT GTGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * *
18542323 ATCT ATAT ATAT ATGT ATAT ATGT ATGT ATAC ATAT ATAT GTAT GTA-
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * *
18542370 AGTAT GTAC ATAT ATAT ATAT ATAC ATAC CTAT ATAT A
1 A-TAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
18542408 CATACATGGA
Statistics
Matches: 102, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
4 102 1.00
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:18542329 original size:26 final size:26
Alignment explanation
Indices: 18542300--18542390 Score: 85
Period size: 26 Copynumber: 3.4 Consensus size: 26
18542290 CATATATATG
18542300 TATATATATATGTATGTGTGTGTATC
1 TATATATATATGTATGTGTGTGTATC
* * * * *
18542326 TATATATATATGTATATATGTATGTA
1 TATATATATATGTATGTGTGTGTATC
* *
18542352 TACATATATATGTATGTAAGTATGTA-C
1 TATATATATATGTATGT--GTGTGTATC
18542379 ATATATATATAT
1 -TATATATATAT
18542391 ATACATACCT
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
26 36 0.73
28 13 0.27
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.47
Consensus pattern (26 bp):
TATATATATATGTATGTGTGTGTATC
Found at i:18542405 original size:14 final size:14
Alignment explanation
Indices: 18542386--18542412 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18542376 TACATATATA
18542386 TATATATACATACC
1 TATATATACATACC
18542400 TATATATACATAC
1 TATATATACATAC
18542413 ATGGATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (14 bp):
TATATATACATACC
Found at i:18542547 original size:39 final size:39
Alignment explanation
Indices: 18542446--18542550 Score: 102
Period size: 39 Copynumber: 2.6 Consensus size: 39
18542436 ATTTTTGCAG
*
18542446 ACCAAACCAAAGAAAATGTCATGAAGCCTTAAGCTTCCGCCA
1 ACCAAACCCAA-AAAA--TCATGAAGCCTTAAGCTTCCGCCA
* * *
18542488 ACCAAACCCAAAAAACCATGAAGCTTTAAGCTTCTGCCA
1 ACCAAACCCAAAAAATCATGAAGCCTTAAGCTTCCGCCA
* *** *
18542527 ATCAAATTGAGAAAATCATGAAGC
1 ACCAAACCCAAAAAATCATGAAGC
18542551 ACAATTTGGA
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
39 39 0.74
41 4 0.08
42 10 0.19
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.18
Consensus pattern (39 bp):
ACCAAACCCAAAAAATCATGAAGCCTTAAGCTTCCGCCA
Found at i:18543881 original size:3 final size:3
Alignment explanation
Indices: 18543875--18543910 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
18543865 TTTTTTTATT
*
18543875 TCA TCA T-A TCA TTA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
18543911 TATTATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:18543892 original size:6 final size:6
Alignment explanation
Indices: 18543877--18543937 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
18543867 TTTTTATTTC
* * * * *
18543877 ATCA-T ATCATT ATCATC ATCATC ATCATC ATCATT ATTATT ATTATT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
* *
18543924 ATTATT ATTATT AT
1 ATCATT ATCATT AT
18543938 TATTTTGTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 4 0.08
6 48 0.92
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (6 bp):
ATCATT
Found at i:18543915 original size:3 final size:3
Alignment explanation
Indices: 18543909--18543941 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
18543899 CATCATCATC
18543909 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18543942 TTGTGTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:18546803 original size:13 final size:13
Alignment explanation
Indices: 18546785--18546819 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
18546775 TTTAGGTAAG
18546785 TGTAAGGTAACCT
1 TGTAAGGTAACCT
18546798 TGTAAGGTAACCT
1 TGTAAGGTAACCT
18546811 TGTAAGGTA
1 TGTAAGGTA
18546820 TCTATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (13 bp):
TGTAAGGTAACCT
Found at i:18555648 original size:28 final size:28
Alignment explanation
Indices: 18555617--18555682 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
18555607 TCCCCTTAAC
*
18555617 TTTTATTTTTGTATGAAATCTCCAATTA
1 TTTTGTTTTTGTATGAAATCTCCAATTA
*
18555645 TTTTGTTCTTGTATGAAATCTCCAATTA
1 TTTTGTTTTTGTATGAAATCTCCAATTA
18555673 TTTTGTTTTT
1 TTTTGTTTTT
18555683 ACAGAGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.58
Consensus pattern (28 bp):
TTTTGTTTTTGTATGAAATCTCCAATTA
Found at i:18556985 original size:18 final size:18
Alignment explanation
Indices: 18556962--18556999 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
18556952 TGCTAATACC
18556962 TTTATATCCATAAGCTAA
1 TTTATATCCATAAGCTAA
18556980 TTTATATCCATAAGCTAA
1 TTTATATCCATAAGCTAA
18556998 TT
1 TT
18557000 ACCCTATGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (18 bp):
TTTATATCCATAAGCTAA
Found at i:18558151 original size:31 final size:31
Alignment explanation
Indices: 18558116--18558208 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 31
18558106 GTGTTGATAG
*
18558116 GATTTATATTGAGGTGAATTTGTGTCGAGGT
1 GATTTACATTGAGGTGAATTTGTGTCGAGGT
** * *
18558147 GATTTACATTGAAATGAATTTGTG-CCAGAAT
1 GATTTACATTGAGGTGAATTTGTGTCGAG-GT
* *
18558178 GGTTTACACTGAGGTGAATTTGTGTCGAGGT
1 GATTTACATTGAGGTGAATTTGTGTCGAGGT
18558209 AAATTTGGTG
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
30 3 0.06
31 43 0.88
32 3 0.06
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.38
Consensus pattern (31 bp):
GATTTACATTGAGGTGAATTTGTGTCGAGGT
Found at i:18560564 original size:17 final size:17
Alignment explanation
Indices: 18560542--18560576 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
18560532 ATAGCTAAGG
18560542 TTCTTATTGACAATGGC
1 TTCTTATTGACAATGGC
18560559 TTCTTATTGACAATGGC
1 TTCTTATTGACAATGGC
18560576 T
1 T
18560577 CTTCAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (17 bp):
TTCTTATTGACAATGGC
Found at i:18566267 original size:51 final size:50
Alignment explanation
Indices: 18566129--18566388 Score: 191
Period size: 51 Copynumber: 4.9 Consensus size: 50
18566119 AAAAAAAAGA
*
18566129 TTTTTAAAGTTTCAAAGCCTCTGTTTAGGGGGAGCCATTTTCAAACAAATT
1 TTTTTAAAGTGTCAAAGCCTCTGTTTA-GGGGAGCCATTTTCAAACAAATT
* * **** *
18566180 TTTTGTAAAGTGTCAAAACCTTTGTTTGAGGGGAGCCATTTTCATTTGAGTT
1 TTTT-TAAAGTGTCAAAGCCTCTGTTT-AGGGGAGCCATTTTCAAACAAATT
* * *
18566232 TTTTTAAAGTGTGAAAGCCTCTATTTAGGGAGAGCCATTTTCAAACAAGTTTTTTTTT
1 TTTTTAAAGTGTCAAAGCCTCTGTTTAGGG-GAGCCATTTTCAAACAA-------ATT
* * * ** *
18566290 TTTTTTAAGTGTCAAAGCCTCTATTTAAAGGGAGCCATTTTCAAGTAAGTT
1 TTTTTAAAGTGTCAAAGCCTCTGTTT-AGGGGAGCCATTTTCAAACAAATT
* * *
18566341 TTTTTAAAGTTTCAAAG-CTCT-TAATGAGGGGAAGCCATTTTTAAACAA
1 TTTTTAAAGTGTCAAAGCCTCTGT--TTAGGGG-AGCCATTTTCAAACAA
18566389 GAACTTTTAA
Statistics
Matches: 165, Mismatches: 30, Indels: 28
0.74 0.13 0.13
Matches are distributed among these distances:
49 1 0.01
50 12 0.07
51 66 0.40
52 41 0.25
53 1 0.01
58 41 0.25
59 3 0.02
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (50 bp):
TTTTTAAAGTGTCAAAGCCTCTGTTTAGGGGAGCCATTTTCAAACAAATT
Found at i:18566315 original size:58 final size:58
Alignment explanation
Indices: 18566230--18566345 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
18566220 TTCATTTGAG
* *
18566230 TTTTTTTAAAGTGTGAAAGCCTCTATTT-AGGGAGAGCCATTTTCAAACAAGTTTTTTT
1 TTTTTTTAAAGTGTCAAAGCCTCTATTTAAAGG-GAGCCATTTTCAAACAAGTTTTTTT
* **
18566288 TTTTTTTTAAGTGTCAAAGCCTCTATTTAAAGGGAGCCATTTTCAAGTAAGTTTTTTT
1 TTTTTTTAAAGTGTCAAAGCCTCTATTTAAAGGGAGCCATTTTCAAACAAGTTTTTTT
18566346 AAAGTTTCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
58 49 0.94
59 3 0.06
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (58 bp):
TTTTTTTAAAGTGTCAAAGCCTCTATTTAAAGGGAGCCATTTTCAAACAAGTTTTTTT
Found at i:18566350 original size:109 final size:109
Alignment explanation
Indices: 18566178--18566389 Score: 257
Period size: 109 Copynumber: 1.9 Consensus size: 109
18566168 TTCAAACAAA
* * * * ** *
18566178 TTTTTTGTAAAGTGTCAAAACCTTTGTTTGAGGGGAGCCATTTTCATTTGAGTTTTTTTAAAGTG
1 TTTTTTGTAAAGTGTCAAAACCTCTATTTAAAGGGAGCCATTTTCAAGTAAGTTTTTTTAAAGTG
* * *
18566243 TGAAAGC-CTCTATTTA-GGGAGAGCCATTTTCAAACAAGTTTTTT
66 TCAAAGCTCT-TAATGAGGGGA-AGCCATTTTCAAACAAGTTTTTT
* * * *
18566287 TTTTTTTTTAAGTGTCAAAGCCTCTATTTAAAGGGAGCCATTTTCAAGTAAGTTTTTTTAAAGTT
1 TTTTTTGTAAAGTGTCAAAACCTCTATTTAAAGGGAGCCATTTTCAAGTAAGTTTTTTTAAAGTG
*
18566352 TCAAAGCTCTTAATGAGGGGAAGCCATTTTTAAACAAG
66 TCAAAGCTCTTAATGAGGGGAAGCCATTTTCAAACAAG
18566390 AACTTTTAAT
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
109 80 0.93
110 6 0.07
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (109 bp):
TTTTTTGTAAAGTGTCAAAACCTCTATTTAAAGGGAGCCATTTTCAAGTAAGTTTTTTTAAAGTG
TCAAAGCTCTTAATGAGGGGAAGCCATTTTCAAACAAGTTTTTT
Found at i:18566735 original size:22 final size:24
Alignment explanation
Indices: 18566687--18566755 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 24
18566677 CCCACAAGTT
*
18566687 GGCCCATTT-AGAGACCCA-AACAAA
1 GGCCCATTTAAGAG-CTCATAA-AAA
*
18566711 GG-CCATTTGA-AGCTCATAAAAA
1 GGCCCATTTAAGAGCTCATAAAAA
*
18566733 GGCCCTTTTAAGAGCTCATAAAA
1 GGCCCATTTAAGAGCTCATAAAA
18566756 TGCATCAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 8 0.21
23 16 0.42
24 14 0.37
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (24 bp):
GGCCCATTTAAGAGCTCATAAAAA
Found at i:18568379 original size:279 final size:279
Alignment explanation
Indices: 18567873--18568721 Score: 1306
Period size: 280 Copynumber: 3.0 Consensus size: 279
18567863 TGTACCTTTC
* * * *
18567873 TTTATAAACTGCCATGCACAAAGATTATGTCCCTCTTCCCAGTTTTGCTAAAATTTTTTATGTTT
1 TTTATAAACTGCCATGCACACAGATTACGTCCTTCTTCCCAGTTTTGCTAAAATTTTTTGTGTTT
*
18567938 TCATCTTTGCTGATATGGTTTCATCTAAAAGGTGGAAGCTTCTTTTTTAGCATCTAGGAACTTCC
66 TCATCTTTGCTGATATGGTTTCGTCTAAAAGGTGGAAGCTT-TTTTTTAGCATCTAGGAACTTCC
*
18568003 AATAAATAGAGGGAAATGAAGGTTTTGAAGTCTAAGGGGTTGTCTTGGTTATGCTTTTCTTTTGG
130 AATAAACAGAGGGAAATGAAGGTTTTGAAGTCTAAGGGGTTGTCTTGGTTATGCTTTTCTTTTGG
* *
18568068 CTGTCCATAGGGCTTCAAGATTGCATCTTTGTTCTATGTCTATTGGCATTTTCTGGACAAAGTGT
195 CTGTCCATAGGGCTTCAAGATTGCAGCTTTGTTCTATGTCTATTGGAATTTTCTGGACAAAGTGT
18568133 CTTCGCAAGCTTACTGTTTT
260 CTTCGCAAGCTTACTGTTTT
* *
18568153 TTTATAAACTGCCATGCACACAGTTTACGTCCTTCTTCCCAGTTTTGCTAAAATTTTTTGTGCTT
1 TTTATAAACTGCCATGCACACAGATTACGTCCTTCTTCCCAGTTTTGCTAAAATTTTTTGTGTTT
18568218 TCATCTTTGCTGATATGGTTTCGTCTAAAAGGTGGAAGCTTTTTTTTAGCATCTAGGAACTTCCA
66 TCATCTTTGCTGATATGGTTTCGTCTAAAAGGTGGAAGCTTTTTTTTAGCATCTAGGAACTTCCA
* * * * *
18568283 AAAAACAAAGGCAAATGAAGGTTTTGAAGTCTAGGGGGTTGTCTTGGTTACGCTTTTCTTTTGGC
131 ATAAACAGAGGGAAATGAAGGTTTTGAAGTCTAAGGGGTTGTCTTGGTTATGCTTTTCTTTTGGC
* *
18568348 TGTCCATAGGGCTTCAAGATTGCAGCTTTGTTCCATGTCTATTGGTATTTTCTGGACAAAGTGTC
196 TGTCCATAGGGCTTCAAGATTGCAGCTTTGTTCTATGTCTATTGGAATTTTCTGGACAAAGTGTC
* *
18568413 TTCACAAGCTTAATGTTTT
261 TTCGCAAGCTTACTGTTTT
* *
18568432 TTTATAAACTGCCATGCACACAAATTACGTCCTTCTTCCCAGTTTTGCTAAAACTTTTGTGTGTT
1 TTTATAAACTGCCATGCACACAGATTACGTCCTTCTTCCCAGTTTTGCTAAAA-TTTTTTGTGTT
* * * *
18568497 TTCATCTTTGCTGATATGGTTTCGTTTAAAAGGTGGAATCTTTTTTTCAGCATCAAGGAACTTCC
65 TTCATCTTTGCTGATATGGTTTCGTCTAAAAGGTGGAAGCTTTTTTTTAGCATCTAGGAACTTCC
* * ** *
18568562 AATAAACAGAGGGAATTGAAGGTTTTGGAGTCTAAGGTTTTGTCTCGGTTATGCTTTTCTTTTGG
130 AATAAACAGAGGGAAATGAAGGTTTTGAAGTCTAAGGGGTTGTCTTGGTTATGCTTTTCTTTTGG
* * * * *
18568627 CTATCCATAGGGCTTCAAGATTGCAGCTTCGTT-TCATGTCGGAGT-GAATTTTCTGGACAAAAT
195 CTGTCCATAGGGCTTCAAGATTGCAGCTTTGTTCT-ATGTC-TATTGGAATTTTCTGGACAAAGT
* * *
18568690 GTCTTTGCTAGCTTACTGTTTC
258 GTCTTCGCAAGCTTACTGTTTT
18568712 TTTATAAACT
1 TTTATAAACT
18568722 ACCAAGCATA
Statistics
Matches: 518, Mismatches: 48, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
279 213 0.41
280 303 0.58
281 2 0.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (279 bp):
TTTATAAACTGCCATGCACACAGATTACGTCCTTCTTCCCAGTTTTGCTAAAATTTTTTGTGTTT
TCATCTTTGCTGATATGGTTTCGTCTAAAAGGTGGAAGCTTTTTTTTAGCATCTAGGAACTTCCA
ATAAACAGAGGGAAATGAAGGTTTTGAAGTCTAAGGGGTTGTCTTGGTTATGCTTTTCTTTTGGC
TGTCCATAGGGCTTCAAGATTGCAGCTTTGTTCTATGTCTATTGGAATTTTCTGGACAAAGTGTC
TTCGCAAGCTTACTGTTTT
Found at i:18571833 original size:15 final size:14
Alignment explanation
Indices: 18571815--18571844 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18571805 CTTGAAGTAG
18571815 AAAAAGAAAAATTGA
1 AAAAAG-AAAATTGA
18571830 AAAAAGAAAATTGA
1 AAAAAGAAAATTGA
18571844 A
1 A
18571845 GACTCTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (14 bp):
AAAAAGAAAATTGA
Found at i:18576806 original size:149 final size:150
Alignment explanation
Indices: 18576536--18576835 Score: 557
Period size: 149 Copynumber: 2.0 Consensus size: 150
18576526 TTTAGACTCA
* *
18576536 TATTCAGTGAGCTTTTTACTTAAGTAATAAATGACTTGCTTTTCCTTGCTCATTTCATCTTGTTG
1 TATTCAATGAACTTTTTACTTAAGTAATAAATGACTTGCTTTTCCTTGCTCATTTCATCTTGTTG
*
18576601 CCTTAACACACATCCCATAGAATGGTTATATACTATGAGATATGGAATCAATGGTTTCCC-CTCA
66 CCTTAACACACATCCCATAGAATGGTTATATACTATGAGATATGGAATCAATGGTTTCCCTCTAA
18576665 ACAGGTGGTACCAACACTGG
131 ACAGGTGGTACCAACACTGG
18576685 TATTCAATGAACTTTTTACTTAAGTAATAAATGACTTGCTTTTCCTTGCTCATTTCATCTTGTTG
1 TATTCAATGAACTTTTTACTTAAGTAATAAATGACTTGCTTTTCCTTGCTCATTTCATCTTGTTG
18576750 CCTTAACACACATCCCATAGAATGGTTATATACTATGAGATATGGAATCAATGGTTTCCCTCTAA
66 CCTTAACACACATCCCATAGAATGGTTATATACTATGAGATATGGAATCAATGGTTTCCCTCTAA
*
18576815 ACAGGTGGTACCAACATTGG
131 ACAGGTGGTACCAACACTGG
18576835 T
1 T
18576836 GGATTTGCTA
Statistics
Matches: 146, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
149 123 0.84
150 23 0.16
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Consensus pattern (150 bp):
TATTCAATGAACTTTTTACTTAAGTAATAAATGACTTGCTTTTCCTTGCTCATTTCATCTTGTTG
CCTTAACACACATCCCATAGAATGGTTATATACTATGAGATATGGAATCAATGGTTTCCCTCTAA
ACAGGTGGTACCAACACTGG
Found at i:18587818 original size:7 final size:8
Alignment explanation
Indices: 18587791--18587819 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
18587781 TCTTTTTTTC
18587791 CTTTCTAG
1 CTTTCTAG
18587799 CTTTCTAG
1 CTTTCTAG
18587807 CTTTCT-G
1 CTTTCTAG
18587814 CTTTCT
1 CTTTCT
18587820 TCCTTGACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.07, C:0.28, G:0.10, T:0.55
Consensus pattern (8 bp):
CTTTCTAG
Found at i:18596375 original size:50 final size:50
Alignment explanation
Indices: 18596300--18596633 Score: 289
Period size: 50 Copynumber: 6.4 Consensus size: 50
18596290 GAGAAAAGAA
*
18596300 AAACAAGATTTTTAAAGTTACAAAGCCTCTTTTTAGGGGGAGCCATTTTC
1 AAACAAGATTTTTAAAGTTTCAAAGCCTCTTTTTAGGGGGAGCCATTTTC
* *
18596350 AAACAAGATTTTTAAAGTTTCAAAGCCTCTGTTTAGGGGGAGCCACTTTC
1 AAACAAGATTTTTAAAGTTTCAAAGCCTCTTTTTAGGGGGAGCCATTTTC
** * *
18596400 AAGTAAGATTTTTAAAAGTATCAAAGCCT-TTATTTAGGGGGAACCATTTTC
1 AAACAAGATTTTT-AAAGTTTCAAAGCCTCTT-TTTAGGGGGAGCCATTTTC
* * *
18596451 AAACAAAATTTTTAAAGTTTCAAAGCCT-TTGTTAAGGGGGAGCCATTTCC
1 AAACAAGATTTTTAAAGTTTCAAAGCCTCTT-TTTAGGGGGAGCCATTTTC
* * ** *
18596501 AAGCAAGTTTTTTTTTTTTTTTAAA-TGGCAAAGCCTCTGTTTAGGGGGAGCCATTTTC
1 AAACAAG---------ATTTTTAAAGTTTCAAAGCCTCTTTTTAGGGGGAGCCATTTTC
* * * * * *
18596559 AAGCAAGTTTTTTCTAAAGTGTT-AAAGCCCCTATTTAGGGGAAGCCATTTTT
1 AAACAAG-ATTTT-TAAAGT-TTCAAAGCCTCTTTTTAGGGGGAGCCATTTTC
* *
18596611 AAACAAGAACTTTTAAAGCTTCA
1 AAACAAG-ATTTTTAAAGTTTCA
18596634 CATCAGATAA
Statistics
Matches: 232, Mismatches: 36, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
50 104 0.45
51 51 0.22
52 35 0.15
58 33 0.14
59 9 0.04
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Consensus pattern (50 bp):
AAACAAGATTTTTAAAGTTTCAAAGCCTCTTTTTAGGGGGAGCCATTTTC
Found at i:18596489 original size:101 final size:100
Alignment explanation
Indices: 18596303--18596513 Score: 311
Period size: 101 Copynumber: 2.1 Consensus size: 100
18596293 AAAAGAAAAA
* *
18596303 CAAGATTTTTAAAGTTACAAAGCCTCTTTTTAGGGGGAGCCATTTTCAAACAAGATTTTTAAAGT
1 CAAGATTTTTAAAGTTACAAAGCCTCTTTTTAGGGGGAACCATTTTCAAACAAAATTTTTAAAGT
*
18596368 TTCAAAGCCTCTGTTTAGGGGGAGCCACTTT-CAAG
66 TTCAAAGCCTCTGTTAAGGGGGAGCCA-TTTCCAAG
*
18596403 TAAGATTTTTAAAAG-TATCAAAGCCT-TTATTTAGGGGGAACCATTTTCAAACAAAATTTTTAA
1 CAAGATTTTT-AAAGTTA-CAAAGCCTCTT-TTTAGGGGGAACCATTTTCAAACAAAATTTTTAA
*
18596466 AGTTTCAAAGCCTTTGTTAAGGGGGAGCCATTTCCAAG
63 AGTTTCAAAGCCTCTGTTAAGGGGGAGCCATTTCCAAG
*
18596504 CAAGTTTTTT
1 CAAGATTTTT
18596514 TTTTTTTTTA
Statistics
Matches: 100, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
100 16 0.16
101 84 0.84
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (100 bp):
CAAGATTTTTAAAGTTACAAAGCCTCTTTTTAGGGGGAACCATTTTCAAACAAAATTTTTAAAGT
TTCAAAGCCTCTGTTAAGGGGGAGCCATTTCCAAG
Found at i:18599421 original size:9 final size:9
Alignment explanation
Indices: 18599413--18599453 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
18599403 TCTTTTTAAT
*
18599413 AATAATAAT
1 AATAATAAC
*
18599422 AATAACAAC
1 AATAATAAC
*
18599431 AACAATAAC
1 AATAATAAC
18599440 AATAATAAC
1 AATAATAAC
18599449 AATAA
1 AATAA
18599454 AAGGGAAACG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (9 bp):
AATAATAAC
Found at i:18603496 original size:85 final size:85
Alignment explanation
Indices: 18603390--18603546 Score: 217
Period size: 85 Copynumber: 1.8 Consensus size: 85
18603380 CCAATATGAA
* * * * * * *
18603390 CTCTTTTGGCTAAGTTGAGTCTAAGC-TCTTTGGTCGAGTTGTTTTGTCGAGTTAGGCCTTTATG
1 CTCTTTTGGCCAAGCTAAGTCTAAGCAT-TTTAGTCGAGCTGTTTTGTCAAGTTAGGCCTTCATG
18603454 AAGGCATTTTGTATATCTAAG
65 AAGGCATTTTGTATATCTAAG
* *
18603475 CTCTTTTGGCCAAGCTAAGTCTGAGCATTTTAGTTGAGCTGTTTTGTCAAGTTAGGCCTTCATGA
1 CTCTTTTGGCCAAGCTAAGTCTAAGCATTTTAGTCGAGCTGTTTTGTCAAGTTAGGCCTTCATGA
18603540 AGGCATT
66 AGGCATT
18603547 ATTTGGATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 61 0.98
86 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (85 bp):
CTCTTTTGGCCAAGCTAAGTCTAAGCATTTTAGTCGAGCTGTTTTGTCAAGTTAGGCCTTCATGA
AGGCATTTTGTATATCTAAG
Found at i:18603577 original size:85 final size:85
Alignment explanation
Indices: 18603429--18603585 Score: 192
Period size: 85 Copynumber: 1.8 Consensus size: 85
18603419 TTGGTCGAGT
* * * * *
18603429 TGTTTTGTCGAGTTAGGCCTTTATGAAGGCATTTTGTATATCTAAGCTCTTTTGGCCAAGCTAAG
1 TGTTTTGTCAAGTTAGGCCTTCATGAAGGCATTTTGGATATCTAAGCTCTTTTAGCCAAGCTAAA
18603494 TCTGAGCATTTTAGTTGAGC
66 TCTGAGCATTTTAGTTGAGC
* * * **
18603514 TGTTTTGTCAAGTTAGGCCTTCATGAAGGCATTATTTGGAT-T-TGAGCTTTTTTAGTCGCGCTA
1 TGTTTTGTCAAGTTAGGCCTTCATGAAGGCA-T-TTTGGATATCTAAGCTCTTTTAGCCAAGCTA
18603577 AATCTGAGC
64 AATCTGAGC
18603586 TCCTTTACTT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
85 52 0.87
86 2 0.03
87 6 0.10
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (85 bp):
TGTTTTGTCAAGTTAGGCCTTCATGAAGGCATTTTGGATATCTAAGCTCTTTTAGCCAAGCTAAA
TCTGAGCATTTTAGTTGAGC
Found at i:18605896 original size:13 final size:13
Alignment explanation
Indices: 18605878--18605902 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18605868 GATAAGTTCA
18605878 AAAATAAAATAAT
1 AAAATAAAATAAT
18605891 AAAATAAAATAA
1 AAAATAAAATAA
18605903 AAATCGAAGA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:18606270 original size:42 final size:41
Alignment explanation
Indices: 18606211--18606296 Score: 109
Period size: 42 Copynumber: 2.1 Consensus size: 41
18606201 AAATAGCAAA
** *
18606211 GCTCCTCTAAACAGAGGCTTAACGACTTTAGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACAACTTT-GGAAAGTAAATT
* * *
18606253 GCTCCTCTAAATAGAGGCACCACAACTTTTGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACAACTTTGGAAAGTAAATT
18606294 GCT
1 GCT
18606297 ACTTGACAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
41 14 0.37
42 24 0.63
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACAACAACTTTGGAAAGTAAATT
Found at i:18606818 original size:21 final size:21
Alignment explanation
Indices: 18606792--18607066 Score: 83
Period size: 21 Copynumber: 12.3 Consensus size: 21
18606782 CTTTCACACC
*
18606792 TTAAAAGATTCTTATTTGAAA
1 TTAAAAGATTCTCATTTGAAA
*
18606813 TTAAAAAATTCTCATTT-AAGA
1 TTAAAAGATTCTCATTTGAA-A
*
18606834 TTCAAAGATTCTCATTTGAAAA
1 TTAAAAGATTCTCATTTG-AAA
* *
18606856 TGTCTTAAAGATTCCCATTT-AAGA
1 --T-TAAAAGATTCTCATTTGAA-A
* * * *
18606880 CTCAAAGATTTTCATTTCAAAA
1 TTAAAAGATTCTCATTT-GAAA
* *
18606902 TGTCTTAAAGATTCTTATTT-AAGA
1 --T-TAAAAGATTCTCATTTGAA-A
* *
18606926 CTCAAAGATTCTCATTTGGAAA
1 TTAAAAGATTCTCATTT-GAAA
* *
18606948 TGTCTTAAAGATTTTCATTT-AAGA
1 --T-TAAAAGATTCTCATTTGAA-A
* * *
18606972 CTCAAAGATTTTCATTTAAGTTTAAAA
1 TTAAAAGATTCTCATTT--G----AAA
* * *
18606999 CTCAAAGATTCTCATTTGACA
1 TTAAAAGATTCTCATTTGAAA
* * *
18607020 GTCAAAGATTTTCATTTGAAA
1 TTAAAAGATTCTCATTTGAAA
* *
18607041 TTCAAATATTCTCATTTG-AA
1 TTAAAAGATTCTCATTTGAAA
18607061 TTAAAA
1 TTAAAA
18607067 TTTTCATCAA
Statistics
Matches: 197, Mismatches: 31, Indels: 53
0.70 0.11 0.19
Matches are distributed among these distances:
20 9 0.05
21 108 0.55
22 3 0.02
23 12 0.06
24 4 0.02
25 42 0.21
27 17 0.09
28 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (21 bp):
TTAAAAGATTCTCATTTGAAA
Found at i:18606874 original size:25 final size:23
Alignment explanation
Indices: 18606820--18606990 Score: 117
Period size: 21 Copynumber: 7.5 Consensus size: 23
18606810 AAATTAAAAA
18606820 ATTCTCATTTAAGAT-TC--AAAG
1 ATTCTCATTTAA-ATGTCTTAAAG
18606841 ATTCTCATTTGAAAATGTCTTAAAG
1 ATTCTCATTT--AAATGTCTTAAAG
* * *
18606866 ATTCCCATTT-AA-GACTCAAAG
1 ATTCTCATTTAAATGTCTTAAAG
*
18606887 ATTTTCATTTCAAAATGTCTTAAAG
1 ATTCTCATTT--AAATGTCTTAAAG
* * *
18606912 ATTCTTATTT-AA-GACTCAAAG
1 ATTCTCATTTAAATGTCTTAAAG
18606933 ATTCTCATTTGGAAATGTCTTAAAG
1 ATTCTCATTT--AAATGTCTTAAAG
* * *
18606958 ATTTTCATTT-AA-GACTCAAAG
1 ATTCTCATTTAAATGTCTTAAAG
*
18606979 ATTTTCATTTAA
1 ATTCTCATTTAA
18606991 GTTTAAAACT
Statistics
Matches: 119, Mismatches: 17, Indels: 27
0.73 0.10 0.17
Matches are distributed among these distances:
21 58 0.49
22 9 0.08
23 4 0.03
24 4 0.03
25 44 0.37
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (23 bp):
ATTCTCATTTAAATGTCTTAAAG
Found at i:18606887 original size:46 final size:46
Alignment explanation
Indices: 18606820--18606988 Score: 266
Period size: 46 Copynumber: 3.7 Consensus size: 46
18606810 AAATTAAAAA
*
18606820 ATTCTCATTTAAGATTCAAAGATTCTCATTTGAAAATGTCTTAAAG
1 ATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTTAAAG
* * *
18606866 ATTCCCATTTAAGACTCAAAGATTTTCATTTCAAAATGTCTTAAAG
1 ATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTTAAAG
* *
18606912 ATTCTTATTTAAGACTCAAAGATTCTCATTTGGAAATGTCTTAAAG
1 ATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTTAAAG
* *
18606958 ATTTTCATTTAAGACTCAAAGATTTTCATTT
1 ATTCTCATTTAAGACTCAAAGATTCTCATTT
18606989 AAGTTTAAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 111 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (46 bp):
ATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTTAAAG
Found at i:18606977 original size:92 final size:92
Alignment explanation
Indices: 18606820--18606988 Score: 293
Period size: 92 Copynumber: 1.8 Consensus size: 92
18606810 AAATTAAAAA
*
18606820 ATTCTCATTTAAGATTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTCCCATTTAAGACTCAA
1 ATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTCCCATTTAAGACTCAA
18606885 AGATTTTCATTTCAAAATGTCTTAAAG
66 AGATTTTCATTTCAAAATGTCTTAAAG
* * **
18606912 ATTCTTATTTAAGACTCAAAGATTCTCATTTGGAAATGTCTTAAAGATTTTCATTTAAGACTCAA
1 ATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTCCCATTTAAGACTCAA
18606977 AGATTTTCATTT
66 AGATTTTCATTT
18606989 AAGTTTAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 72 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (92 bp):
ATTCTCATTTAAGACTCAAAGATTCTCATTTGAAAATGTCTTAAAGATTCCCATTTAAGACTCAA
AGATTTTCATTTCAAAATGTCTTAAAG
Found at i:18607563 original size:63 final size:63
Alignment explanation
Indices: 18607459--18607634 Score: 237
Period size: 63 Copynumber: 2.8 Consensus size: 63
18607449 GCTTCTCAAT
* ** * * * *
18607459 ACAAATTTTATCCTCCATCACTTGATCATCATTCATAGGCTTTTCAGCACTAGCAATTTTAGA
1 ACAAATTTCATCCTCTGTCACTTGGTCATCGTTCATGGGCTTTTCAGCACTAGCAATTTCAGA
* * * *
18607522 ATAAATTTCCTCCTCTGTCACTTGGTCATCGTTCATGGGCTTCTCAGCACTAGCCATTTCAGA
1 ACAAATTTCATCCTCTGTCACTTGGTCATCGTTCATGGGCTTTTCAGCACTAGCAATTTCAGA
18607585 ACAAATTTCATCCTCTGTCACTTGGTCATCGTTCATGGGCTTCTT-AGCAC
1 ACAAATTTCATCCTCTGTCACTTGGTCATCGTTCATGGGCTT-TTCAGCAC
18607635 CAATTTTGTC
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 97 0.99
64 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.36
Consensus pattern (63 bp):
ACAAATTTCATCCTCTGTCACTTGGTCATCGTTCATGGGCTTTTCAGCACTAGCAATTTCAGA
Found at i:18608401 original size:19 final size:17
Alignment explanation
Indices: 18608366--18608431 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
18608356 TGAGTCCTCA
* *
18608366 TTTTCTTTCCTTTCCAT
1 TTTTTTTTCTTTTCCAT
*
18608383 TTTTCTTTTTTTCTTCCA-
1 TTTT-TTTTCTT-TTCCAT
18608401 TTTTTTTTCTTTTCCAT
1 TTTTTTTTCTTTTCCAT
18608418 TTTTTTTTCATTTT
1 TTTTTTTTC-TTTT
18608432 TTTTTTCTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
16 5 0.12
17 19 0.46
18 12 0.29
19 5 0.12
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTTTCTTTTCCAT
Found at i:18608421 original size:16 final size:16
Alignment explanation
Indices: 18608364--18608424 Score: 68
Period size: 16 Copynumber: 3.6 Consensus size: 16
18608354 TTTGAGTCCT
* *
18608364 CATTTTCTTTCCTTTC
1 CATTTTTTTTCTTTTC
*
18608380 CATTTTTCTTTTTTTCTTC
1 CA-TTTT-TTTTCTT-TTC
18608399 CATTTTTTTTCTTTTC
1 CATTTTTTTTCTTTTC
18608415 CATTTTTTTT
1 CATTTTTTTT
18608425 TCATTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
16 15 0.39
17 10 0.26
18 8 0.21
19 5 0.13
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (16 bp):
CATTTTTTTTCTTTTC
Found at i:18608436 original size:11 final size:12
Alignment explanation
Indices: 18608404--18608436 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
18608394 TCTTCCATTT
18608404 TTTTTCTTTTCCA
1 TTTTT-TTTTCCA
18608417 TTTTTTTTT-CA
1 TTTTTTTTTCCA
18608428 TTTTTTTTT
1 TTTTTTTTT
18608437 TCTTTCCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 4 0.20
13 5 0.25
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTCCA
Found at i:18614992 original size:22 final size:22
Alignment explanation
Indices: 18614967--18615012 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
18614957 TTTAATAATA
18614967 AAAAAGCTAAAATAAAATAAAT
1 AAAAAGCTAAAATAAAATAAAT
* *
18614989 AAAATGCTTAAATAAAATAAAT
1 AAAAAGCTAAAATAAAATAAAT
18615011 AA
1 AA
18615013 GAAAATACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAAAGCTAAAATAAAATAAAT
Found at i:18618123 original size:57 final size:57
Alignment explanation
Indices: 18618056--18618164 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
18618046 AGTTCTTGAA
*
18618056 AATTAAAT-AAATTTCTATAATATTTGCATAACAACATCACTACAATTTAGTTAATTT
1 AATTAAATAAAAATT-TATAATATTTGCATAACAACATCACTACAATTTAGTTAATTT
* *
18618113 AATTAAATAAAAATTTATGATATTTGCATAACAACATCACTATAATTTAGTT
1 AATTAAATAAAAATTTATAATATTTGCATAACAACATCACTACAATTTAGTT
18618165 GTTTGTAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
57 43 0.90
58 5 0.10
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (57 bp):
AATTAAATAAAAATTTATAATATTTGCATAACAACATCACTACAATTTAGTTAATTT
Found at i:18626223 original size:26 final size:24
Alignment explanation
Indices: 18626171--18626230 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 24
18626161 GTTGGATCTT
*
18626171 TTTATTTCTTTTGAAACCAAATCAA
1 TTTATTT-TTTTGAAAACAAATCAA
18626196 TTATATATTTTTTGAAAACAAAGT-AA
1 TT-TAT-TTTTTTGAAAACAAA-TCAA
18626222 TTTATTTTT
1 TTTATTTTT
18626231 GGATCAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 4 0.13
25 5 0.16
26 19 0.61
27 3 0.10
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (24 bp):
TTTATTTTTTTGAAAACAAATCAA
Found at i:18626667 original size:13 final size:13
Alignment explanation
Indices: 18626651--18626691 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
18626641 AGGTTTAGCA
18626651 TTTGGTTTTAGGG
1 TTTGGTTTTAGGG
18626664 TTTGGTTTT-GGG
1 TTTGGTTTTAGGG
*
18626676 TTTTGGGTTTAGGG
1 -TTTGGTTTTAGGG
18626690 TT
1 TT
18626692 AGGGTTTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 3 0.12
13 19 0.76
14 3 0.12
ACGTcount: A:0.05, C:0.00, G:0.39, T:0.56
Consensus pattern (13 bp):
TTTGGTTTTAGGG
Found at i:18626717 original size:32 final size:32
Alignment explanation
Indices: 18626658--18626718 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
18626648 GCATTTGGTT
** * **
18626658 TTAGGGTTTGGTTTTGGGTTTTGGGTTTAGGG
1 TTAGGGTTTGGTTTAAGGTGTAAGGTTTAGGG
18626690 TTAGGGTTTGGTTTAAGGTGTAAGGTTTA
1 TTAGGGTTTGGTTTAAGGTGTAAGGTTTA
18626719 AGATATGATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (32 bp):
TTAGGGTTTGGTTTAAGGTGTAAGGTTTAGGG
Found at i:18626732 original size:38 final size:38
Alignment explanation
Indices: 18626690--18626774 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 38
18626680 GGGTTTAGGG
* *
18626690 TTAGGGTTTGGTTTAAGGTGTAAGGTTTA-AGA-TATGAT
1 TTAGGGTTTGGCTT-AGGT-TAAGGTTTAGAGATTAAGAT
* *
18626728 TTAGGGTTTGGCTTAGGTTTAGGTTTAGAGATTAAGGT
1 TTAGGGTTTGGCTTAGGTTAAGGTTTAGAGATTAAGAT
18626766 TTAGGGTTT
1 TTAGGGTTT
18626775 AAGATTTAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 8 0.20
37 7 0.17
38 26 0.63
ACGTcount: A:0.22, C:0.01, G:0.33, T:0.44
Consensus pattern (38 bp):
TTAGGGTTTGGCTTAGGTTAAGGTTTAGAGATTAAGAT
Found at i:18626767 original size:20 final size:20
Alignment explanation
Indices: 18626702--18626780 Score: 67
Period size: 19 Copynumber: 4.1 Consensus size: 20
18626692 AGGGTTTGGT
* *
18626702 TTAAGGTGTAAGGTTTAAGA
1 TTAAGGTTTAGGGTTTAAGA
* * * *
18626722 -TATGATTTAGGGTTT-GGC
1 TTAAGGTTTAGGGTTTAAGA
18626740 TT-AGGTTTA-GGTTTAGAGA
1 TTAAGGTTTAGGGTTTA-AGA
18626759 TTAAGGTTTAGGGTTTAAGA
1 TTAAGGTTTAGGGTTTAAGA
18626779 TT
1 TT
18626781 TAGGATTTGC
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
17 5 0.11
18 6 0.14
19 15 0.34
20 12 0.27
21 6 0.14
ACGTcount: A:0.27, C:0.01, G:0.30, T:0.42
Consensus pattern (20 bp):
TTAAGGTTTAGGGTTTAAGA
Found at i:18627740 original size:10 final size:11
Alignment explanation
Indices: 18627720--18627751 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
18627710 GTTTTCTCAT
18627720 AAAAACAAAAA
1 AAAAACAAAAA
18627731 AAAAACAAAAA
1 AAAAACAAAAA
18627742 AAAAATCAAA
1 AAAAA-CAAA
18627752 GGGAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:18631905 original size:3 final size:3
Alignment explanation
Indices: 18631897--18632021 Score: 168
Period size: 3 Copynumber: 42.3 Consensus size: 3
18631887 TATAGTACGC
*
18631897 TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18631945 TAT TA- TAGT TAT TAT TAT TAT TAT TAT TAT TA- TAGT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
* * *
18631990 TAT T-T CAT TA- TAT TAT TAA TAA TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18632022 TTTTTTTTAT
Statistics
Matches: 110, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
2 7 0.06
3 99 0.90
4 4 0.04
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:18632532 original size:19 final size:19
Alignment explanation
Indices: 18632508--18632545 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18632498 TGGGTTTGAG
*
18632508 ATGAATTTTCCAGTTGAAT
1 ATGAATTTTCCAATTGAAT
*
18632527 ATGAATTTTTCAATTGAAT
1 ATGAATTTTCCAATTGAAT
18632546 TTTCTGGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (19 bp):
ATGAATTTTCCAATTGAAT
Found at i:18632910 original size:13 final size:12
Alignment explanation
Indices: 18632894--18632984 Score: 60
Period size: 12 Copynumber: 7.2 Consensus size: 12
18632884 TTCTTTTCCA
*
18632894 TTTTCATTTTAT
1 TTTTTATTTTAT
*
18632906 TTTTTGATTTCAT
1 TTTTT-ATTTTAT
18632919 TTTTT-TATTTAT
1 TTTTTAT-TTTAT
*
18632931 TTTATTATCTTAAT
1 TTT-TTAT-TTTAT
18632945 TATTTTATTTTAT
1 T-TTTTATTTTAT
*
18632958 TTTATT-TTTAAT
1 TTT-TTATTTTAT
* *
18632970 TTTTAATTTAAT
1 TTTTTATTTTAT
18632982 TTT
1 TTT
18632985 ACTATTTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
11 2 0.03
12 30 0.47
13 20 0.31
14 10 0.16
15 2 0.03
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:18632923 original size:26 final size:27
Alignment explanation
Indices: 18632893--18632985 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 27
18632883 TTTCTTTTCC
*
18632893 ATTTTCATTTTATTTT-TTGAT-TTCATT
1 ATTTT-ATTTTATTTTATT-ATCTTAATT
*
18632920 TTTTTA-TTTATTTTATTATCTTAATT
1 ATTTTATTTTATTTTATTATCTTAATT
18632946 ATTTTATTTTATTTTATT-T-TTAATT
1 ATTTTATTTTATTTTATTATCTTAATT
* *
18632971 -TTTAATTTAATTTTA
1 ATTTTATTTTATTTTA
18632986 CTATTTTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
24 13 0.22
25 16 0.28
26 14 0.24
27 15 0.26
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (27 bp):
ATTTTATTTTATTTTATTATCTTAATT
Found at i:18632932 original size:12 final size:12
Alignment explanation
Indices: 18632901--18632984 Score: 62
Period size: 13 Copynumber: 6.7 Consensus size: 12
18632891 CCATTTTCAT
*
18632901 TTTATTTTTTGA
1 TTTATTTTTTTA
18632913 TTTCATTTTTTTA
1 TTT-ATTTTTTTA
*
18632926 TTTATTTTATTA
1 TTTATTTTTTTA
*
18632938 TCTTAATTATTTTA
1 T-TT-ATTTTTTTA
*
18632952 TTTTATTTTATT-
1 -TTTATTTTTTTA
* *
18632964 TTTAATTTTTAA
1 TTTATTTTTTTA
18632976 TTTAATTTT
1 TTT-ATTTT
18632985 ACTATTTTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
11 8 0.14
12 15 0.27
13 23 0.41
14 9 0.16
15 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.74
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:18632935 original size:9 final size:9
Alignment explanation
Indices: 18632901--18632964 Score: 62
Period size: 8 Copynumber: 7.3 Consensus size: 9
18632891 CCATTTTCAT
18632901 TTTATTTT-
1 TTTATTTTA
* *
18632909 TTGATTTCA
1 TTTATTTTA
18632918 TTT-TTTTA
1 TTTATTTTA
18632926 TTTATTTTA
1 TTTATTTTA
*
18632935 -TTATCTTA
1 TTTATTTTA
*
18632943 ATTATTTTA
1 TTTATTTTA
18632952 TTTTATTTTA
1 -TTTATTTTA
18632962 TTT
1 TTT
18632965 TTAATTTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
8 20 0.44
9 17 0.38
10 8 0.18
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTATTTTA
Found at i:18636686 original size:196 final size:196
Alignment explanation
Indices: 18636347--18636733 Score: 729
Period size: 196 Copynumber: 2.0 Consensus size: 196
18636337 CTCTTAGGCC
*
18636347 TTCAATTCATCCAACCACCTCGACAAGTGGTGCGTAAGAATCACATAATAGGGAAAAGCCTACAT
1 TTCAATTCATCCAACCACCTCGACAAGTGGTGCGCAAGAATCACATAATAGGGAAAAGCCTACAT
18636412 TTGACCCTATTCTCATGAGTTATACTAAACTATATCAAAAGCTTTACAAGAACCATTTGATTGCT
66 TTGACCCTATTCTCATGAGTTATACTAAACTATATCAAAAGCTTTACAAGAACCATTTGATTGCT
*
18636477 CTGTTTTCTATAAACAACTTGAGCTTTTCTATACCAAATGGTATGATTCCATTTCTCACTGAGCT
131 CTGTTTCCTATAAACAACTTGAGCTTTTCTATACCAAATGGTATGATTCCATTTCTCACTGAGCT
18636542 T
196 T
* *
18636543 TTCAATTCATCCCACCACCTCGACAAGTGGTGTGCAAGAATCACATAATAGGGAAAAGCCTACAT
1 TTCAATTCATCCAACCACCTCGACAAGTGGTGCGCAAGAATCACATAATAGGGAAAAGCCTACAT
*
18636608 TTGACCCTATTCTCATGAGTTATATTAAACTATATCAAAAGCTTTACAAGAACCATTTGATTGCT
66 TTGACCCTATTCTCATGAGTTATACTAAACTATATCAAAAGCTTTACAAGAACCATTTGATTGCT
18636673 CTGTTTCCTATAAACAACTTGAGCTTTTCTATACCAAATGGTATGATTCCATTTCTCACTG
131 CTGTTTCCTATAAACAACTTGAGCTTTTCTATACCAAATGGTATGATTCCATTTCTCACTG
18636734 TGACTATCAT
Statistics
Matches: 186, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
196 186 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (196 bp):
TTCAATTCATCCAACCACCTCGACAAGTGGTGCGCAAGAATCACATAATAGGGAAAAGCCTACAT
TTGACCCTATTCTCATGAGTTATACTAAACTATATCAAAAGCTTTACAAGAACCATTTGATTGCT
CTGTTTCCTATAAACAACTTGAGCTTTTCTATACCAAATGGTATGATTCCATTTCTCACTGAGCT
T
Found at i:18637540 original size:15 final size:15
Alignment explanation
Indices: 18637522--18637559 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
18637512 AAAATGATGG
18637522 AAAAAAAAGAAAACA
1 AAAAAAAAGAAAACA
18637537 AAAAAAAAGAAAACA
1 AAAAAAAAGAAAACA
18637552 AAAGAAAA
1 AAA-AAAA
18637560 TAAAGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAACA
Found at i:18639637 original size:3 final size:3
Alignment explanation
Indices: 18639629--18639743 Score: 91
Period size: 3 Copynumber: 39.3 Consensus size: 3
18639619 TATAGTATGC
* *
18639629 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT GATT TAT TA- TAG TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
*
18639672 TAG TAT TA- TAT TAT TA- TAGT TAT TA- TAT TAT GTCAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT -T-AT TAT TAT TAT
* * *
18639716 TAT TAA TAT TAA TAT TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18639744 TATTTCTTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
2 14 0.15
3 70 0.76
4 6 0.07
5 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:18639711 original size:13 final size:14
Alignment explanation
Indices: 18639683--18639715 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
18639673 AGTATTATAT
*
18639683 TATTATAGTTATTA
1 TATTATAGTCATTA
18639697 TATTAT-GTCATTA
1 TATTATAGTCATTA
18639710 TATTAT
1 TATTAT
18639716 TATTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (14 bp):
TATTATAGTCATTA
Found at i:18640394 original size:51 final size:50
Alignment explanation
Indices: 18640313--18640418 Score: 117
Period size: 51 Copynumber: 2.1 Consensus size: 50
18640303 TTGGGCAACC
* *
18640313 TTTCCAGAAACCAGTGGGTTTTCCAATTTTTAGTTGAA-TTTCCCGATAACG
1 TTTCTAGAAACCAGTGGATTTTCCAATTTTTAGTTGAAGTTT-CCGATAA-G
* * * *
18640364 TTTCTAGAAACCAGTGGAATTTT-TAGTTTTTGGTTGAAGTTTTCGATAAG
1 TTTCTAGAAACCAGTGG-ATTTTCCAATTTTTAGTTGAAGTTTCCGATAAG
18640414 TTTCT
1 TTTCT
18640419 TGAAGAATTC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
50 6 0.13
51 34 0.72
52 7 0.15
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (50 bp):
TTTCTAGAAACCAGTGGATTTTCCAATTTTTAGTTGAAGTTTCCGATAAG
Found at i:18640606 original size:6 final size:6
Alignment explanation
Indices: 18640597--18640671 Score: 55
Period size: 6 Copynumber: 12.3 Consensus size: 6
18640587 TCCATTTTCA
* * * *
18640597 TTTTATT TTTTAC TTTTAT TTTTAT TTATT-T TATTAT CTTAAT TTTT-T
1 TTTTA-T TTTTAT TTTTAT TTTTAT TT-TTAT TTTTAT TTTTAT TTTTAT
* *
18640645 ATTTAA TTTTAT TTTTAGT TTTTAT TT
1 TTTTAT TTTTAT TTTTA-T TTTTAT TT
18640672 AATTTTACTT
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
5 6 0.12
6 33 0.63
7 13 0.25
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:18640628 original size:23 final size:23
Alignment explanation
Indices: 18640604--18640683 Score: 92
Period size: 23 Copynumber: 3.4 Consensus size: 23
18640594 TCATTTTATT
18640604 TTTTACTTTTA-TTTTTATTT-A
1 TTTTACTTTTAGTTTTTATTTAA
* *
18640625 TTTTATTATCTTAATTTTTTATTTAA
1 TTTTACT-T-TT-AGTTTTTATTTAA
*
18640651 TTTTATTTTTAGTTTTTATTTAA
1 TTTTACTTTTAGTTTTTATTTAA
18640674 TTTTACTTTT
1 TTTTACTTTT
18640684 TTATTTAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
21 6 0.12
22 1 0.02
23 23 0.45
24 3 0.06
25 10 0.20
26 8 0.16
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (23 bp):
TTTTACTTTTAGTTTTTATTTAA
Found at i:18640658 original size:41 final size:41
Alignment explanation
Indices: 18640596--18640691 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
18640586 TTCCATTTTC
* * *
18640596 ATTTTATTTTTTACTTTTATTTTTA-TTTATT-TTATTATCTTA
1 ATTTT-TTATTTAATTTTATTTTTAGTTT-TTATT-TAATCTTA
*
18640638 ATTTTTTATTTAATTTTATTTTTAGTTTTTATTTAATTTTA
1 ATTTTTTATTTAATTTTATTTTTAGTTTTTATTTAATCTTA
*
18640679 CTTTTTTATTTAA
1 ATTTTTTATTTAA
18640692 AAAAAGAGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
41 37 0.79
42 10 0.21
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (41 bp):
ATTTTTTATTTAATTTTATTTTTAGTTTTTATTTAATCTTA
Found at i:18640660 original size:17 final size:17
Alignment explanation
Indices: 18640621--18640691 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 17
18640611 TTTATTTTTA
18640621 TTTATTTTATTATCTTAAT
1 TTTATTTT-TTAT-TTAAT
* *
18640640 TTT-TTATTTAATTTTATT
1 TTTATT-TTTTA-TTTAAT
*
18640658 TTTAGTTTTTATTTAAT
1 TTTATTTTTTATTTAAT
18640675 TTTACTTTTTTATTTAA
1 TTTA-TTTTTTATTTAA
18640692 AAAAAGAGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
17 9 0.21
18 26 0.62
19 7 0.17
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (17 bp):
TTTATTTTTTATTTAAT
Found at i:18645431 original size:32 final size:31
Alignment explanation
Indices: 18645395--18645482 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 31
18645385 TAATAAGACC
*
18645395 CTTGAAGAATGTAAGAACAAGTCTTAACGACT
1 CTTGAAGAAT-TAAGAACAAGTCTCAACGACT
* * *
18645427 CTTGAAGGATTCAAGAACAAATCTCAATGACT
1 CTTGAAGAATT-AAGAACAAGTCTCAACGACT
*
18645459 CTTG-AGACATTTAAGAAGAAGTCT
1 CTTGAAGA-A-TTAAGAACAAGTCT
18645483 ACTTGACCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
31 3 0.07
32 41 0.89
33 2 0.04
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (31 bp):
CTTGAAGAATTAAGAACAAGTCTCAACGACT
Found at i:18648552 original size:63 final size:63
Alignment explanation
Indices: 18648447--18648566 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 63
18648437 GAAACTAATC
18648447 TGCAAGTAAATTATGAATAAAAAAATGCTAAGCCTACAACACCATCACCAGTGAATATTGATT
1 TGCAAGTAAATTATGAATAAAAAAATGCTAAGCCTACAACACCATCACCAGTGAATATTGATT
* * * * ** *
18648510 TGCAAGTAAATTTTGAATTAGAAAATGTTGTGCCTATC-ACACCATCACCATTGAATA
1 TGCAAGTAAATTATGAATAAAAAAATGCTAAGCCTA-CAACACCATCACCAGTGAATA
18648567 CTCTATCTGA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
63 48 0.98
64 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (63 bp):
TGCAAGTAAATTATGAATAAAAAAATGCTAAGCCTACAACACCATCACCAGTGAATATTGATT
Found at i:18648642 original size:76 final size:76
Alignment explanation
Indices: 18648516--18648745 Score: 363
Period size: 76 Copynumber: 3.0 Consensus size: 76
18648506 GATTTGCAAG
*
18648516 TAAATTTTGAATTAGAAAATGTTGTGCCTATCACACCATCACCATTGAATACTCTATCTGACGAT
1 TAAATTCTGAATTAGAAAATGTTGTGCCTATCACACCATCACCATTGAATACTCTATCTGACGAT
18648581 CTAGACATGCC
66 CTAGACATGCC
* * * * *
18648592 TAAATTCTGAATCAAAAAATGTTATGCCTATCACACCATCACCATTGAATACTTTATCTAACGAT
1 TAAATTCTGAATTAGAAAATGTTGTGCCTATCACACCATCACCATTGAATACTCTATCTGACGAT
18648657 CTAGACATGCC
66 CTAGACATGCC
* * *
18648668 TAAATTCTAAATTAGAAAATGTTGTGCCTATCACACCATCACCATTGAATACTCCA-CTTGATGA
1 TAAATTCTGAATTAGAAAATGTTGTGCCTATCACACCATCACCATTGAATACTCTATC-TGACGA
18648732 TCTAGACATGCC
65 TCTAGACATGCC
18648744 TA
1 TA
18648746 TAACATTTAG
Statistics
Matches: 139, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
75 1 0.01
76 138 0.99
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (76 bp):
TAAATTCTGAATTAGAAAATGTTGTGCCTATCACACCATCACCATTGAATACTCTATCTGACGAT
CTAGACATGCC
Found at i:18652209 original size:22 final size:22
Alignment explanation
Indices: 18652183--18652231 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
18652173 CAACAAGGAT
18652183 ATCATGCAAATAA-AGAAAAAAA
1 ATCATGC-AATAATAGAAAAAAA
* *
18652205 ATCATGCAATAATAGTAAATAA
1 ATCATGCAATAATAGAAAAAAA
18652227 ATCAT
1 ATCAT
18652232 AATTATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.22
Consensus pattern (22 bp):
ATCATGCAATAATAGAAAAAAA
Found at i:18653355 original size:43 final size:46
Alignment explanation
Indices: 18653299--18653417 Score: 129
Period size: 46 Copynumber: 2.7 Consensus size: 46
18653289 CCCCTCAATA
* * * * *
18653299 AAGGTTTTGAAACTTTTGAAAAATAAACT-ATT-TCCCTC-CAGT-G
1 AAGGCTTTAAAACTTTTGAAAAATAAAATGATTCCCCCCCTCA-TCG
* *
18653342 AAGGCTTTAAAACTTTGGAAAAATAAAATGCTTCCCCCCCTCATCG
1 AAGGCTTTAAAACTTTTGAAAAATAAAATGATTCCCCCCCTCATCG
*
18653388 AAGACTTTAAAACTTTTGAAAAATAAAATG
1 AAGGCTTTAAAACTTTTGAAAAATAAAATG
18653418 CTCCCATTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
43 25 0.40
44 2 0.03
45 5 0.08
46 31 0.49
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (46 bp):
AAGGCTTTAAAACTTTTGAAAAATAAAATGATTCCCCCCCTCATCG
Found at i:18660193 original size:17 final size:18
Alignment explanation
Indices: 18660167--18660205 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
18660157 TCAATCATAC
18660167 AAAAAGAT-AATCAAAAAT
1 AAAAAGATAAAT-AAAAAT
18660185 AAAAA-ATAAATAAAAAT
1 AAAAAGATAAATAAAAAT
18660202 AAAA
1 AAAA
18660206 GAAATACCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAAAGATAAATAAAAAT
Found at i:18661291 original size:12 final size:12
Alignment explanation
Indices: 18661274--18661316 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
18661264 AACTCTTTTG
18661274 ACTAAACAAAAA
1 ACTAAACAAAAA
18661286 ACTAAA-ATAAAA
1 ACTAAACA-AAAA
*
18661298 AGTAAATCAAAAA
1 ACTAAA-CAAAAA
18661311 ACTAAA
1 ACTAAA
18661317 AGGAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 1 0.04
12 15 0.58
13 9 0.35
14 1 0.04
ACGTcount: A:0.72, C:0.12, G:0.02, T:0.14
Consensus pattern (12 bp):
ACTAAACAAAAA
Found at i:18661323 original size:25 final size:24
Alignment explanation
Indices: 18661276--18661324 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
18661266 CTCTTTTGAC
*
18661276 TAAACAAAAAACTAAAATAAAAAG
1 TAAACAAAAAACTAAAAGAAAAAG
18661300 TAAATCAAAAAACTAAAAGGAAAAA
1 TAAA-CAAAAAACTAAAA-GAAAAA
18661325 TACAAATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.18
25 13 0.59
26 5 0.23
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.12
Consensus pattern (24 bp):
TAAACAAAAAACTAAAAGAAAAAG
Found at i:18663256 original size:8 final size:8
Alignment explanation
Indices: 18663243--18663267 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
18663233 CTTTGCACTT
18663243 TTATTTTC
1 TTATTTTC
18663251 TTATTTTC
1 TTATTTTC
18663259 TTATTTTC
1 TTATTTTC
18663267 T
1 T
18663268 AAATAAGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTTTC
Found at i:18676215 original size:21 final size:21
Alignment explanation
Indices: 18676191--18676230 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18676181 GATTTTTTGG
*
18676191 TATTTTATTTATTTATTTAGC
1 TATTATATTTATTTATTTAGC
*
18676212 TATTATATTTATTTTTTTA
1 TATTATATTTATTTATTTA
18676231 TTTTGTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (21 bp):
TATTATATTTATTTATTTAGC
Found at i:18684435 original size:32 final size:32
Alignment explanation
Indices: 18684394--18684457 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
18684384 AAAAAGAGGA
18684394 AAATGGGAAACCGTGGTATTATAATATCTTGT
1 AAATGGGAAACCGTGGTATTATAATATCTTGT
18684426 AAATGGGAAACCGTGGTATTATAATATCTTGT
1 AAATGGGAAACCGTGGTATTATAATATCTTGT
18684458 CATACATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (32 bp):
AAATGGGAAACCGTGGTATTATAATATCTTGT
Found at i:18686816 original size:43 final size:43
Alignment explanation
Indices: 18686748--18687098 Score: 262
Period size: 43 Copynumber: 8.1 Consensus size: 43
18686738 CATGATTGTT
* * *
18686748 GAGGAACTGTATTTATTTTTCAAAGTCATTAAGCCTCTATTTA
1 GAGGAGCTTTATTTATTTTTCAAAGTCATTGAGCCTCTATTTA
* * ** * * *
18686791 TAGGAGCTTTATTTATTTTTTAAAGTTGTTGAGCTTCTGTGTA
1 GAGGAGCTTTATTTATTTTTCAAAGTCATTGAGCCTCTATTTA
* * *
18686834 GA-GAGAC-TTATTTATTTTTCAAAGTCCTTGAGCCTCTACTCA
1 GAGGAG-CTTTATTTATTTTTCAAAGTCATTGAGCCTCTATTTA
* * * * *
18686876 AAGGAGCTTTATTTATCTTTGAAAGTCATTGAGCCTTTGTTTA
1 GAGGAGCTTTATTTATTTTTCAAAGTCATTGAGCCTCTATTTA
* * ** * * **
18686919 GAGGAGCCTTATTTAATTTTTCAAAAATTGTTGAATCC-GTGCTTA
1 GAGGAGCTTTATTT-ATTTTTC-AAAGTCATTG-AGCCTCTATTTA
* * * * ** *
18686964 GAAGAACTTTATTAATTTTTCAAAAATTGTTGAGCCTCTATTAA
1 GAGGAGCTTTATTTATTTTTC-AAAGTCATTGAGCCTCTATTTA
* *
18687008 GAGGAGTTTTATTTATTTTTCAAAGTC-GTGAGCCTCTATTTA
1 GAGGAGCTTTATTTATTTTTCAAAGTCATTGAGCCTCTATTTA
* * *
18687050 GAGGAGCTTTATTTGTTTCTCAAAAGT-TTTGGAGCCTCTATTTA
1 GAGGAGCTTTATTTATTTTTC-AAAGTCATT-GAGCCTCTATTTA
18687094 GAGGA
1 GAGGA
18687099 ATTTTTATAT
Statistics
Matches: 240, Mismatches: 58, Indels: 19
0.76 0.18 0.06
Matches are distributed among these distances:
42 63 0.26
43 91 0.38
44 61 0.25
45 22 0.09
46 3 0.01
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (43 bp):
GAGGAGCTTTATTTATTTTTCAAAGTCATTGAGCCTCTATTTA
Found at i:18686901 original size:85 final size:86
Alignment explanation
Indices: 18686748--18686943 Score: 245
Period size: 85 Copynumber: 2.3 Consensus size: 86
18686738 CATGATTGTT
* * * * *
18686748 GAGGA-ACTGTATTTATTTTTCAAAGTCATTAAGCCTCTATTTATAGGAGCTTTATTTATTTTTT
1 GAGGAGACT-TATTTATTTTTCAAAGTCATTAAGCCTCTACTCAAAGGAGCTTTATTTATCTTTG
**
18686812 AAAGTTGTTGAG-CTTCTGTGTA
65 AAAGTCATTGAGCCTT-TGTGTA
* *
18686834 GA-GAGACTTATTTATTTTTCAAAGTCCTTGAGCCTCTACTCAAAGGAGCTTTATTTATCTTTGA
1 GAGGAGACTTATTTATTTTTCAAAGTCATTAAGCCTCTACTCAAAGGAGCTTTATTTATCTTTGA
*
18686898 AAGTCATTGAGCCTTTGTTTA
66 AAGTCATTGAGCCTTTGTGTA
*
18686919 GAGGAGCCTTATTTAATTTTTCAAA
1 GAGGAGACTTATTT-ATTTTTCAAA
18686944 AATTGTTGAA
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
85 67 0.71
86 18 0.19
87 10 0.11
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (86 bp):
GAGGAGACTTATTTATTTTTCAAAGTCATTAAGCCTCTACTCAAAGGAGCTTTATTTATCTTTGA
AAGTCATTGAGCCTTTGTGTA
Found at i:18687121 original size:44 final size:42
Alignment explanation
Indices: 18686993--18687122 Score: 113
Period size: 44 Copynumber: 3.0 Consensus size: 42
18686983 TCAAAAATTG
* * * * *
18686993 TTGAGCCTCTATTAAGAGGAGTTTTATTTATT-TTTCAAAGTC
1 TTGAGCCTCTATTTAGAGGAATTTT-TATATTGTTTAAAAGTT
* **
18687035 GTGAGCCTCTATTTAGAGG-AGCTTTAT-TTGTTTCTCAAAAGTT
1 TTGAGCCTCTATTTAGAGGAATTTTTATATTG-TT-T-AAAAGTT
18687078 TTGGAGCCTCTATTTAGAGGAATTTTTATATTGTTTAAGAAGTT
1 TT-GAGCCTCTATTTAGAGGAATTTTTATATTGTTTAA-AAGTT
18687122 T
1 T
18687123 GAATGTGCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
39 2 0.03
40 2 0.03
41 4 0.06
42 18 0.26
43 8 0.12
44 24 0.35
45 8 0.12
46 3 0.04
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (42 bp):
TTGAGCCTCTATTTAGAGGAATTTTTATATTGTTTAAAAGTT
Found at i:18688364 original size:7 final size:7
Alignment explanation
Indices: 18688354--18688378 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18688344 TTCAATTTAA
18688354 AAAAATT
1 AAAAATT
18688361 AAAAATT
1 AAAAATT
18688368 AAAAATT
1 AAAAATT
18688375 AAAA
1 AAAA
18688379 TTTGAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:18688828 original size:46 final size:49
Alignment explanation
Indices: 18688714--18688828 Score: 139
Period size: 46 Copynumber: 2.4 Consensus size: 49
18688704 TTTTCTTTCC
* *
18688714 AAAAATTTCAAAAAAAAAAAGAGAGAATTTCTAAATAGACCCAAAGGGTG
1 AAAAATTT-AGAAATAAAAAGAGAGAATTTCTAAATAGACCCAAAGGGTG
* * *
18688764 AAAAATTTAG-AATCAAAAAGA-A-AA-TTCTTAATCGACCCAAATGGTG
1 AAAAATTTAGAAAT-AAAAAGAGAGAATTTCTAAATAGACCCAAAGGGTG
18688810 AAAAATTTAGAAATAAAAA
1 AAAAATTTAGAAATAAAAA
18688829 TAAATAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
46 34 0.59
47 5 0.09
48 3 0.05
49 8 0.14
50 8 0.14
ACGTcount: A:0.57, C:0.10, G:0.13, T:0.21
Consensus pattern (49 bp):
AAAAATTTAGAAATAAAAAGAGAGAATTTCTAAATAGACCCAAAGGGTG
Found at i:18690900 original size:16 final size:17
Alignment explanation
Indices: 18690879--18690918 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
18690869 TAACAACCTA
18690879 CCATTTATAATAA-TTT
1 CCATTTATAATAACTTT
* *
18690895 CCATTTTTAGTAACTTT
1 CCATTTATAATAACTTT
18690912 CCATTTA
1 CCATTTA
18690919 GGATTTTGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.30, C:0.17, G:0.03, T:0.50
Consensus pattern (17 bp):
CCATTTATAATAACTTT
Found at i:18692541 original size:21 final size:21
Alignment explanation
Indices: 18692500--18692538 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
18692490 TTATTATTAT
*
18692500 TATTATTATAATATAAAAATA
1 TATTAATATAATATAAAAATA
18692521 TATTAATA-AATATAAAAA
1 TATTAATATAATATAAAAA
18692539 ATAAACAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TATTAATATAATATAAAAATA
Found at i:18699904 original size:19 final size:19
Alignment explanation
Indices: 18699880--18699920 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
18699870 GGCCATTAAT
*
18699880 AAAAAA-AAGAAACTAAAGC
1 AAAAAATAA-AAAATAAAGC
18699899 AAAAAATAAAAAATAAAGC
1 AAAAAATAAAAAATAAAGC
18699918 AAA
1 AAA
18699921 TTGGATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.78, C:0.07, G:0.07, T:0.07
Consensus pattern (19 bp):
AAAAAATAAAAAATAAAGC
Found at i:18700695 original size:2 final size:2
Alignment explanation
Indices: 18700688--18700716 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18700678 TATGATTTTC
18700688 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
18700717 CCAAATATAA
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:18702692 original size:141 final size:142
Alignment explanation
Indices: 18702506--18702989 Score: 540
Period size: 141 Copynumber: 3.4 Consensus size: 142
18702496 GACCTTTCGG
* * * *
18702506 GCTCGAATTTTCATG-AACTTTTCAGATCAT-GATTTCATAATATTTCATGTTTTTTTATACATT
1 GCTCGAATTTTCATGAAACTTTTCAGATC-TCAATTTCATAATATTTCATGATTTTTGATGCATT
*
18702569 TGAAATCACAATATTACCCTAAAAAGTGTGAAATTACTAAAATACCCCTATAAAGTATTTTCATA
65 TGAAATCACAATAGTACCCTAAAAAGTGTGAAATTACTAAAATACCCCTATAAAGTATTTTCATA
18702634 ATTTG-TTCTTAA
130 ATTTGCTTCTTAA
* * * *
18702646 GCTCGAATTTTTATGAAACTTTTCACATCTCAATTTCATAATATTTCATAATTTTTGGTGCATTT
1 GCTCGAATTTTCATGAAACTTTTCAGATCTCAATTTCATAATATTTCATGATTTTTGATGCATTT
* * * *
18702711 GAAATCA-TATCAGTATCTTGAAAAA-TGTGAAATTA-TCAAAATATCCCTATAAAGGTATTTTC
66 GAAATCACAAT-AGTACCCT-AAAAAGTGTGAAATTACT-AAAATACCCCTATAAA-GTATTTTC
**
18702773 ATAATTTGGCCTTCTCCA
127 ATAATTT-G-CTTCTTAA
** *
18702791 GCTTTAATTTTTATGAAAC-TTTCTAGATCTCAATTTCATAATATTTCATGATTTTTGATGCATT
1 GCTCGAATTTTCATGAAACTTTTC-AGATCTCAATTTCATAATATTTCATGATTTTTGATGCATT
* * * * * *
18702855 TG-AATCACAACAGTACCCTAAAAAGTATGAAATTACCAAAATACCCTTATAAGGGTA-ATTCAT
65 TGAAATCACAATAGTACCCTAAAAAGTGTGAAATTACTAAAATACCCCTATAA-AGTATTTTCAT
18702918 AATTTGACCTT-TCTAA
129 AATTTG--CTTCT-TAA
* *
18702934 GCTTGAATTTTCATGAAACCTTTCAGATCTCAA-TTCTATAATATTTCATGATTTTT
1 GCTCGAATTTTCATGAAACTTTTCAGATCTCAATTTC-ATAATATTTCATGATTTTT
18702990 AGTGTTTTAA
Statistics
Matches: 292, Mismatches: 34, Indels: 33
0.81 0.09 0.09
Matches are distributed among these distances:
140 18 0.06
141 77 0.26
142 25 0.09
143 66 0.23
144 44 0.15
145 62 0.21
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.41
Consensus pattern (142 bp):
GCTCGAATTTTCATGAAACTTTTCAGATCTCAATTTCATAATATTTCATGATTTTTGATGCATTT
GAAATCACAATAGTACCCTAAAAAGTGTGAAATTACTAAAATACCCCTATAAAGTATTTTCATAA
TTTGCTTCTTAA
Found at i:18702963 original size:143 final size:144
Alignment explanation
Indices: 18702446--18702989 Score: 574
Period size: 143 Copynumber: 3.8 Consensus size: 144
18702436 TATTGCATTA
* * * * ** **
18702446 AAAAAATATAAAATAACCAAAATACCCTTACAAGGGTATTTTTGTAATTTGACCTT-TCGGGCTC
1 AAAAAGTATGAAATTACCAAAATACCCTTATAAGGGTATTTTCATAATTTGACCTTCT-AAGCTC
* * * * *
18702510 GAATTTTCATG-AACTTTTCAGATCAT-GATTTCATAATATTTCATGTTTTTTTATACATTTGAA
65 GAATTTTCATGAAACCTTTCAGATC-TCAATTTCATAATATTTCATGATTTTTGATGCATTTGAA
* *
18702573 ATCACAATATTACCCT
129 ATCACAACAGTACCCT
* * * *
18702589 AAAAAGTGTGAAATTACTAAAATACCCCTATAA-AGTATTTTCATAATTTG---TTCTTAAGCTC
1 AAAAAGTATGAAATTACCAAAATACCCTTATAAGGGTATTTTCATAATTTGACCTTC-TAAGCTC
* * * * *
18702650 GAATTTTTATGAAACTTTTCACATCTCAATTTCATAATATTTCATAATTTTTGGTGCATTTGAAA
65 GAATTTTCATGAAACCTTTCAGATCTCAATTTCATAATATTTCATGATTTTTGATGCATTTGAAA
* * * *
18702715 TCATATCAGTATCTT
130 TCACAACAGTACCCT
* * * * *
18702730 GAAAAA-TGTGAAATTATCAAAATATCCC-TATAAAGGTATTTTCATAATTTGGCCTTCTCCAGC
1 -AAAAAGTATGAAATTACCAAAATA-CCCTTATAAGGGTATTTTCATAATTTGACCTTCT-AAGC
** *
18702793 TTTAATTTTTATGAAA-CTTTCTAGATCTCAATTTCATAATATTTCATGATTTTTGATGCATTTG
63 TCGAATTTTCATGAAACCTTTC-AGATCTCAATTTCATAATATTTCATGATTTTTGATGCATTTG
18702857 -AATCACAACAGTACCCT
127 AAATCACAACAGTACCCT
* *
18702874 AAAAAGTATGAAATTACCAAAATACCCTTATAAGGGTA-ATTCATAATTTGACCTTTCTAAGCTT
1 AAAAAGTATGAAATTACCAAAATACCCTTATAAGGGTATTTTCATAATTTGACC-TTCTAAGCTC
18702938 GAATTTTCATGAAACCTTTCAGATCTCAA-TTCTATAATATTTCATGATTTTT
65 GAATTTTCATGAAACCTTTCAGATCTCAATTTC-ATAATATTTCATGATTTTT
18702990 AGTGTTTTAA
Statistics
Matches: 336, Mismatches: 48, Indels: 34
0.80 0.11 0.08
Matches are distributed among these distances:
139 2 0.01
140 15 0.04
141 75 0.22
142 41 0.12
143 92 0.27
144 52 0.15
145 59 0.18
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (144 bp):
AAAAAGTATGAAATTACCAAAATACCCTTATAAGGGTATTTTCATAATTTGACCTTCTAAGCTCG
AATTTTCATGAAACCTTTCAGATCTCAATTTCATAATATTTCATGATTTTTGATGCATTTGAAAT
CACAACAGTACCCT
Found at i:18703423 original size:21 final size:21
Alignment explanation
Indices: 18703382--18703436 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
18703372 GAAGAGAAAA
*
18703382 AAAAAAGAAAAAGAGATTGCC
1 AAAAAAGAAAAAGAGACTGCC
*
18703403 AAAAAAGAATAAGA-AGCTGCC
1 AAAAAAGAAAAAGAGA-CTGCC
*
18703424 AGCAAAAGAAAAA
1 A-AAAAAGAAAAA
18703437 AAAAAGAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.04
21 18 0.64
22 9 0.32
ACGTcount: A:0.64, C:0.11, G:0.18, T:0.07
Consensus pattern (21 bp):
AAAAAAGAAAAAGAGACTGCC
Found at i:18712866 original size:44 final size:44
Alignment explanation
Indices: 18712807--18712912 Score: 113
Period size: 44 Copynumber: 2.4 Consensus size: 44
18712797 CAAGCCTAAT
* * *
18712807 TTAGCTAGTACATAAGCCCAAATTAGCTGGCACATAAGTCCAGA
1 TTAGCTAGCACATAAGCCCAAATTAGATGGCACATAAGCCCAGA
* * * * **
18712851 TTAGCTAGCATATAAGCTCGATTTAGATGGCATGTAAGCCCAGA
1 TTAGCTAGCACATAAGCCCAAATTAGATGGCACATAAGCCCAGA
* *
18712895 TTAGTTGGCACATAAGCC
1 TTAGCTAGCACATAAGCC
18712913 TAGATTAATT
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (44 bp):
TTAGCTAGCACATAAGCCCAAATTAGATGGCACATAAGCCCAGA
Found at i:18712917 original size:22 final size:22
Alignment explanation
Indices: 18712807--18712919 Score: 102
Period size: 22 Copynumber: 5.1 Consensus size: 22
18712797 CAAGCCTAAT
* * *
18712807 TTAGCTAGTACATAAGCCCAAA
1 TTAGCTGGCACATAAGCCCAGA
*
18712829 TTAGCTGGCACATAAGTCCAGA
1 TTAGCTGGCACATAAGCCCAGA
* * *
18712851 TTAGCTAGCATATAAGCTC-GA
1 TTAGCTGGCACATAAGCCCAGA
* **
18712872 TTTAGATGGCATGTAAGCCCAGA
1 -TTAGCTGGCACATAAGCCCAGA
* *
18712895 TTAGTTGGCACATAAGCCTAGA
1 TTAGCTGGCACATAAGCCCAGA
18712917 TTA
1 TTA
18712920 ATTAAAAAAG
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
21 2 0.03
22 69 0.95
23 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (22 bp):
TTAGCTGGCACATAAGCCCAGA
Found at i:18713236 original size:34 final size:34
Alignment explanation
Indices: 18713086--18713744 Score: 161
Period size: 34 Copynumber: 19.4 Consensus size: 34
18713076 AGCCTACACA
* *
18713086 AAAATTT-AA-CCTAGTTTATCTAGCCCATAATG
1 AAAATTTAAAGCCTAGTTTATCTAGCCCTTGATG
* * * *
18713118 AAAGAATTT--AGCC-AATTTATTTGGCACC-TGATA
1 -AA-AATTTAAAGCCTAGTTTATCTAGC-CCTTGATG
* * ** *
18713151 AAAATTT-AAGCCTAATTTATCTGGCCCTCAAAG
1 AAAATTTAAAGCCTAGTTTATCTAGCCCTTGATG
18713184 AAAGATTTTAAA-CC-AGTTTATCTAGCCCTTGATG
1 AAA-A-TTTAAAGCCTAGTTTATCTAGCCCTTGATG
* * * *
18713218 AAAATTTAAAGCCTAGTTTACCTGGCTCCTAG-TA
1 AAAATTTAAAGCCTAGTTTATCTAGC-CCTTGATG
* * *
18713252 AAAATTT-AAGCCTAGTTTACCTA-CCATCTAATG
1 AAAATTTAAAGCCTAGTTTATCTAGCCCT-TGATG
* * ** * ** *
18713285 AAGATTTTAAAGCCCAACTTAGCTAGCTCCCAG-TA
1 AA-AATTTAAAGCCTAGTTTATCTAGC-CCTTGATG
* * * *
18713320 AAAATTT-AAGCCCAGTTTATTTGGCCCATGATG
1 AAAATTTAAAGCCTAGTTTATCTAGCCCTTGATG
* * * *
18713353 AAAA-TTAAAGCCCAGTTTAT-TTGAACCTTTATG
1 AAAATTTAAAGCCTAGTTTATCTAG-CCCTTGATG
* * * * * *
18713386 AAAACTTT-AAGCCCAATTTACCTTGCACTTAAT-
1 AAAA-TTTAAAGCCTAGTTTATCTAGCCCTTGATG
* * *
18713419 AAAGATTTTAAAGCCCAGTTTATCTGGCCCTTGATA
1 AAA-A-TTTAAAGCCTAGTTTATCTAGCCCTTGATG
* ** *
18713455 AAAATTTTAAGCCTAGTTTGCCTAGCACC-CGAT-
1 AAAATTTAAAGCCTAGTTTATCTAGC-CCTTGATG
* ** * * *
18713488 AAAGATTTTAAAGCCCAACTTAGCTGGCTCCTAG-T-
1 AAA-A-TTTAAAGCCTAGTTTATCTAGC-CCTTGATG
* * * * * * *
18713523 AAAATTTGAAGCCCAATTTTTTTTGCCTTTGATG
1 AAAATTTAAAGCCTAGTTTATCTAGCCCTTGATG
* * *
18713557 AAAACTTT-AAGCCTAGTTTA-CTTGGCACTTGATA
1 AAAA-TTTAAAGCCTAGTTTATC-TAGCCCTTGATG
* * *
18713591 AAAATTTCAAAGCCTAATTTATCT-GACCCCTAATG
1 AAAATTT-AAAGCCTAGTTTATCTAG-CCCTTGATG
* * * **
18713626 AAAATTTTAATCCTAGTTTACCTAGCACC-CAATG
1 AAAATTTAAAGCCTAGTTTATCTAGC-CCTTGATG
* * * * * *
18713660 AAGATTTTAAAGCCCAGTTTATTTGACCCCCT-AAG
1 AA-AATTTAAAGCCTAGTTTATCT-AGCCCTTGATG
*
18713695 AAAAATTTTAA-CCTCAGTTTATCTAG-CCTCTGATG
1 -AAAATTTAAAGCCT-AGTTTATCTAGCCCT-TGATG
*
18713730 AAAATTTTAAGCCTA
1 AAAATTTAAAGCCTA
18713745 ATTGACCTAG
Statistics
Matches: 462, Mismatches: 115, Indels: 97
0.69 0.17 0.14
Matches are distributed among these distances:
31 7 0.02
32 25 0.05
33 120 0.26
34 156 0.34
35 141 0.31
36 12 0.03
37 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (34 bp):
AAAATTTAAAGCCTAGTTTATCTAGCCCTTGATG
Found at i:18713526 original size:69 final size:68
Alignment explanation
Indices: 18713239--18713537 Score: 218
Period size: 69 Copynumber: 4.4 Consensus size: 68
18713229 CCTAGTTTAC
* * * *
18713239 CTGGCTCCTAGTAAAAATTTAAGCCTAGTTTACCTACCATCTAATGAAGATTTTAAAGCCCAACT
1 CTGGCTCCTAGTAAAAATTTAAGCCCAGTTTACCTAGCACCTAATAAAGATTTTAAAGCCCAACT
18713304 TAG
66 TAG
* * ** * * *
18713307 CTAGCTCCCAGTAAAAATTTAAGCCCAGTTTATTTGGC-CCATGATGAAA-A--TTAAAGCCCAG
1 CTGGCTCCTAGTAAAAATTTAAGCCCAGTTTACCTAGCACC-TAAT-AAAGATTTTAAAGCCCAA
* *
18713368 TTTAT
64 CTTAG
* * * * * * *
18713373 TTGAAC-CTTTA-TGAAAACTTTAAGCCCAATTTACCTTGCACTTAATAAAGATTTTAAAGCCCA
1 CTG-GCTC-CTAGT-AAAAATTTAAGCCCAGTTTACCTAGCACCTAATAAAGATTTTAAAGCCCA
** *
18713436 GTTTAT
63 ACTTAG
* * * **
18713442 CTGGC-CCTTGATAAAAATTTTAAGCCTAGTTTGCCTAGCACCCGATAAAGATTTTAAAGCCCAA
1 CTGGCTCCTAG-TAAAAA-TTTAAGCCCAGTTTACCTAGCACCTAATAAAGATTTTAAAGCCCAA
18713506 CTTAG
64 CTTAG
18713511 CTGGCTCCTAGT-AAAATTTGAAGCCCA
1 CTGGCTCCTAGTAAAAATTT-AAGCCCA
18713538 ATTTTTTTTG
Statistics
Matches: 175, Mismatches: 42, Indels: 28
0.71 0.17 0.11
Matches are distributed among these distances:
66 19 0.11
67 32 0.18
68 52 0.30
69 68 0.39
70 4 0.02
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (68 bp):
CTGGCTCCTAGTAAAAATTTAAGCCCAGTTTACCTAGCACCTAATAAAGATTTTAAAGCCCAACT
TAG
Found at i:18713731 original size:70 final size:69
Alignment explanation
Indices: 18713554--18713747 Score: 171
Period size: 69 Copynumber: 2.8 Consensus size: 69
18713544 TTTGCCTTTG
* * * * *** * * *
18713554 ATGAAAACTTTAAGCCTAGTTTACTTGGCACTTGATAAAAATTTCAAAGCCTAATTTATCTGACC
1 ATGAAAATTTTAATCCTAGTTTACCTAGCACCCAATGAAAATTTTAAAGCCCAATTTATCTGACC
18713619 CCTA
66 CCTA
* * *
18713623 ATGAAAATTTTAATCCTAGTTTACCTAGCACCCAATGAAGATTTTAAAGCCCAGTTTATTTGACC
1 ATGAAAATTTTAATCCTAGTTTACCTAGCACCCAATGAAAATTTTAAAGCCCAATTTATCTGA-C
18713688 CCCTA
65 CCCTA
* ** *
18713693 A-GAAAAATTTTAA-CCTCAGTTTATCTAGC-CTCTGATGAAAATTTT-AAGCCTAATT
1 ATG-AAAATTTTAATCCT-AGTTTACCTAGCAC-CCAATGAAAATTTTAAAGCCCAATT
18713748 GACCTAGCAC
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
69 63 0.62
70 39 0.38
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (69 bp):
ATGAAAATTTTAATCCTAGTTTACCTAGCACCCAATGAAAATTTTAAAGCCCAATTTATCTGACC
CCTA
Found at i:18713852 original size:34 final size:34
Alignment explanation
Indices: 18713814--18713886 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
18713804 TTAAGCTCAA
* *
18713814 TTTACCTGACACTTGATAAAGATTTTAAACGCAG
1 TTTACCTGACACTTAATAAAAATTTTAAACGCAG
* *
18713848 TTTACCTGATACTTAATAAAAATTTTAAACTCAG
1 TTTACCTGACACTTAATAAAAATTTTAAACGCAG
18713882 TTTAC
1 TTTAC
18713887 TTAATAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (34 bp):
TTTACCTGACACTTAATAAAAATTTTAAACGCAG
Found at i:18713873 original size:136 final size:135
Alignment explanation
Indices: 18713730--18714045 Score: 334
Period size: 136 Copynumber: 2.3 Consensus size: 135
18713720 GCCTCTGATG
* * * *
18713730 AAAATTTTAAGCCTAATTGACCTAGCACCTGATAAAGATTTTAAATACCAGCTTAGCTGGCTCCT
1 AAAATTTTAAGCCTAGTTTACCTAGCACTTGATGAAGATTTTAAA-ACCAGCTTAGCTGGCTCCT
* * * * *
18713795 AATGAAAATTTAAGCTCAATTTACCTGACACTTGATAAAGATTTTAAA-CGC-AGTTTACCT-GA
65 AATAAAAATTTAAGCCCAATTTACCTGACACCTGATAAAGATTTTAAAGCCCTA-TTTAACTGGA
18713857 TACTTAAT
129 T-CTTAAT
* * ** * * *
18713865 AAAAATTTTAA-ACTCAGTTTACTTAATAATTGATGAAGATTTTGAAACCCAGCTTAGCTGGTTC
1 -AAAATTTTAAGCCT-AGTTTACCTAGCACTTGATGAAGATTTT-AAAACCAGCTTAGCTGGCTC
* * * * *
18713929 TTAGTAAAAATTTAAGCCCAATTTACTTGGCACCTGATGAAGATTTTAAAGCCCTATTTAACTGG
63 CTAATAAAAATTTAAGCCCAATTTACCTGACACCTGATAAAGATTTTAAAGCCCTATTTAACTGG
* *
18713994 CTCTTAGT
128 ATCTTAAT
*
18714002 AAAACTTTAAGCCTAGTTTACCTAGCACTTGATGAAGATTTTAA
1 AAAATTTTAAGCCTAGTTTACCTAGCACTTGATGAAGATTTTAA
18714046 GCCCAGTTTA
Statistics
Matches: 145, Mismatches: 29, Indels: 13
0.78 0.16 0.07
Matches are distributed among these distances:
135 4 0.03
136 120 0.83
137 18 0.12
138 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (135 bp):
AAAATTTTAAGCCTAGTTTACCTAGCACTTGATGAAGATTTTAAAACCAGCTTAGCTGGCTCCTA
ATAAAAATTTAAGCCCAATTTACCTGACACCTGATAAAGATTTTAAAGCCCTATTTAACTGGATC
TTAAT
Found at i:18713907 original size:34 final size:34
Alignment explanation
Indices: 18713826--18713912 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 34
18713816 TACCTGACAC
* *
18713826 TTGATAAAGATTTTAAACGCAGTTTACCTGATAC
1 TTGATAAAGATTTTAAACGCAGTTTACCTAATAA
* * * *
18713860 TTAATAAAAATTTTAAACTCAGTTTACTTAATAA
1 TTGATAAAGATTTTAAACGCAGTTTACCTAATAA
*
18713894 TTGATGAAGATTTTGAAAC
1 TTGATAAAGATTTT-AAAC
18713913 CCAGCTTAGC
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
34 39 0.91
35 4 0.09
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.38
Consensus pattern (34 bp):
TTGATAAAGATTTTAAACGCAGTTTACCTAATAA
Found at i:18713999 original size:68 final size:68
Alignment explanation
Indices: 18713200--18714051 Score: 278
Period size: 68 Copynumber: 12.5 Consensus size: 68
18713190 TTTAAACCAG
* * * * * *
18713200 TTTATCTAGC-CCTTGATGAA-AATTTAAAGCCTAGTTTACCTGGCTCCTAGTAAAAATTTAAGC
1 TTTACCTAGCACC-TGATGAAGATTTTAAAGCCCAGCTTAACTGGCTCTTAGTAAAAATTTAAGC
* *
18713263 CTAG
65 CCAA
* * * * * * **
18713267 TTTACCTACCATCTAATGAAGATTTTAAAGCCCAACTTAGCTAGCTCCCAGTAAAAATTTAAGCC
1 TTTACCTAGCACCTGATGAAGATTTTAAAGCCCAGCTTAACTGGCTCTTAGTAAAAATTTAAGCC
*
18713332 CAG
66 CAA
** * * * ** * *
18713335 TTTATTTGGC-CCATGATGAA-A-ATTAAAGCCCAGTTTATTTGAAC-CTTTA-TGAAAACTTTA
1 TTTACCTAGCACC-TGATGAAGATTTTAAAGCCCAGCTTAACTG-GCTC-TTAGT-AAAAATTTA
18713395 AGCCCAA
62 AGCCCAA
* * * * * * *
18713402 TTTACCTTGCACTTAATAAAGATTTTAAAGCCCAGTTTATCTGGCCCTT-GATAAAAATTTTAAG
1 TTTACCTAGCACCTGATGAAGATTTTAAAGCCCAGCTTAACTGGCTCTTAG-TAAAAA-TTTAAG
* *
18713466 CCTAG
64 CCCAA
* * * * * *
18713471 TTTGCCTAGCACCCGATAAAGATTTTAAAGCCCAACTTAGCTGGCTCCTAGT-AAAATTTGAAGC
1 TTTACCTAGCACCTGATGAAGATTTTAAAGCCCAGCTTAACTGGCTCTTAGTAAAAATTT-AAGC
18713535 CCAA
65 CCAA
*** * * * * * * *
18713539 TTTTTTTTGC-CTTTGATGAAAACTTT-AAGCCTAG-TTTACTTGGCACTT-GATAAAAATTTCA
1 TTTACCTAGCAC-CTGATGAAGATTTTAAAGCCCAGCTTAAC-TGGCTCTTAG-TAAAAATTT--
*
18713600 AAGCCTAA
61 AAGCCCAA
* * * * * * * * * * ** * * *
18713608 TTTATCT-GACCCCTAATGAAAATTTT-AATCCTAGTTTACCTAGCACCCAATGAAGATTTTAAA
1 TTTACCTAG-CACCTGATGAAGATTTTAAAGCCCAGCTTAACTGGCTCTTAGT-AAAAATTT-AA
*
18713671 GCCCAG
63 GCCCAA
** * * * * * * * * *
18713677 TTTATTTGACCCCCT-AAGAAAAATTTT-AA-CCTCAGTTTATCTAGCCTCTGA-TGAAAATTTT
1 TTTACCT-AGCACCTGATG-AAGATTTTAAAGCC-CAGCTTAACT-GGCTCTTAGT-AAAAATTT
*
18713738 AAGCCTAA
61 AAGCCCAA
* * ** * * * * *
18713746 TTGACCTAGCACCTGATAAAGATTTTAAATACCAGCTTAGCTGGCTCCTAATGAAAATTTAAGCT
1 TTTACCTAGCACCTGATGAAGATTTTAAAGCCCAGCTTAACTGGCTCTTAGTAAAAATTTAAGCC
18713811 CAA
66 CAA
* * * * * * *
18713814 TTTACCT-GACACTTGATAAAGATTTTAAA-CGCAGTTTACCT-GATACTTAATAAAAATTTTAA
1 TTTACCTAG-CACCTGATGAAGATTTTAAAGCCCAGCTTAACTGGCT-CTTAGTAAAAA-TTTAA
* * *
18713876 ACTCAG
63 GCCCAA
* ** ** * *
18713882 TTTACTTAATAATTGATGAAGATTTTGAAA-CCCAGCTTAGCTGGTTCTTAGTAAAAATTTAAGC
1 TTTACCTAGCACCTGATGAAGATTTT-AAAGCCCAGCTTAACTGGCTCTTAGTAAAAATTTAAGC
18713946 CCAA
65 CCAA
* * * *
18713950 TTTACTTGGCACCTGATGAAGATTTTAAAGCCCTA-TTTAACTGGCTCTTAGTAAAACTTTAAGC
1 TTTACCTAGCACCTGATGAAGATTTTAAAGCCC-AGCTTAACTGGCTCTTAGTAAAAATTTAAGC
* *
18714014 CTAG
65 CCAA
*
18714018 TTTACCTAGCACTTGATGAAGATTTT-AAGCCCAG
1 TTTACCTAGCACCTGATGAAGATTTTAAAGCCCAG
18714052 TTTATTAATT
Statistics
Matches: 587, Mismatches: 155, Indels: 86
0.71 0.19 0.10
Matches are distributed among these distances:
66 23 0.04
67 88 0.15
68 259 0.44
69 168 0.29
70 46 0.08
71 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (68 bp):
TTTACCTAGCACCTGATGAAGATTTTAAAGCCCAGCTTAACTGGCTCTTAGTAAAAATTTAAGCC
CAA
Found at i:18714932 original size:126 final size:126
Alignment explanation
Indices: 18714721--18715072 Score: 402
Period size: 127 Copynumber: 2.8 Consensus size: 126
18714711 TTTAGAAGAA
* * * *
18714721 AAAACATTTTGAACTTTTAAAGTTTTAATGCCTCTGATTGAAAGAGCATTCAAAGATTTTGATAT
1 AAAACATTTTAAATTTTTAAAGTTTTAATGCCTCTAATTG-AAGAGCATTCAAAGATTTTGAGA-
* * * * ***
18714786 TTTGTAAGATCTCCGGGCATAATCTCTAAAACCTACAGACATAATTTTCAAGACCTCT-AGGT
64 TTTGTAAAACCTCCGAGCATAATCTCTAAAACCTACAGACACAATTTTCAAGACCTCTCAAAC
* * *
18714848 AAAACATTTT-AATTTTTAAAGTTTTAATGCCTCTAATTTCGAGGAGCATTCAAAGATTGTAAGA
1 AAAACATTTTAAATTTTTAAAGTTTTAATGCCTCTAA-TT-GAAGAGCATTCAAAGATTTTGAGA
* * * * * * * * *
18714912 TTTCTAATACCTCCAAGCATAATCTCTAAGACCTTCATATACAATTTTCAAGACTTTTCAAAC
64 TTTGTAAAACCTCCGAGCATAATCTCTAAAACCTACAGACACAATTTTCAAGACCTCTCAAAC
* * *
18714975 AAAACATTTTAAATTTTTAAAGTTTCAATGCCTCTTATTAGATGAGCATTCAAAGATTTTGAGAT
1 AAAACATTTTAAATTTTTAAAGTTTTAATGCCTCTAATT-GAAGAGCATTCAAAGATTTTGAGAT
*
18715040 TTGTAAAACCTCCGAGCATAATCTCCAAAACCT
65 TTGTAAAACCTCCGAGCATAATCTCTAAAACCT
18715073 CCAAGCAAAA
Statistics
Matches: 189, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
126 70 0.37
127 94 0.50
128 25 0.13
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (126 bp):
AAAACATTTTAAATTTTTAAAGTTTTAATGCCTCTAATTGAAGAGCATTCAAAGATTTTGAGATT
TGTAAAACCTCCGAGCATAATCTCTAAAACCTACAGACACAATTTTCAAGACCTCTCAAAC
Found at i:18715211 original size:37 final size:36
Alignment explanation
Indices: 18715151--18715289 Score: 136
Period size: 37 Copynumber: 3.6 Consensus size: 36
18715141 ATTTGGGAAC
*
18715151 CCTTTATTTGAGGGGAGCCATTTTTAAAGTTTCAAAG
1 CCTTTGTTT-AGGGGAGCCATTTTTAAAGTTTCAAAG
*
18715188 CCTTTGTTTAGGGGAAGCTATTTTCATTCAAAGTTTCAAAG
1 CCTTTGTTTAGGGG-AGCCA-TTT--TT-AAAGTTTCAAAG
* *
18715229 -CTTCTGTTTGGGGGAAGCCATTTTTAAAGTTTCAAAA
1 CCTT-TGTTTAGGGG-AGCCATTTTTAAAGTTTCAAAG
* *
18715266 CCTTTGATTAGAGGGAGCAATTTT
1 CCTTTGTTTAG-GGGAGCCATTTT
18715290 CAAACAAGAT
Statistics
Matches: 86, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
36 5 0.06
37 36 0.42
38 11 0.13
40 8 0.09
41 26 0.30
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (36 bp):
CCTTTGTTTAGGGGAGCCATTTTTAAAGTTTCAAAG
Found at i:18715226 original size:41 final size:40
Alignment explanation
Indices: 18715174--18715291 Score: 129
Period size: 41 Copynumber: 3.0 Consensus size: 40
18715164 GGAGCCATTT
*
18715174 TTAAAGTTTCAAAGCCTTTGTTTAGGGGAAGCTATTTTCA
1 TTAAAGTTTCAAAGCCTTTGTTTAGGGGAAGCAATTTTCA
* *
18715214 TTCAAAGTTTCAAAG-CTTCTGTTTGGGGGAAGCCA-TTT--
1 TT-AAAGTTTCAAAGCCTT-TGTTTAGGGGAAGCAATTTTCA
* *
18715252 TTAAAGTTTCAAAACCTTTGATTAGAGGG-AGCAATTTTCA
1 TTAAAGTTTCAAAGCCTTTGTTTAG-GGGAAGCAATTTTCA
18715292 AACAAGATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
37 20 0.31
38 11 0.17
40 8 0.12
41 26 0.40
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (40 bp):
TTAAAGTTTCAAAGCCTTTGTTTAGGGGAAGCAATTTTCA
Found at i:18716796 original size:19 final size:19
Alignment explanation
Indices: 18716774--18716811 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18716764 AGCTACTAGC
*
18716774 AAAAGAAAAAAAAAGGAGA
1 AAAAGAAAAAAAAAAGAGA
18716793 AAAAGAAAAAAAAAAGAGA
1 AAAAGAAAAAAAAAAGAGA
18716812 GGCAAGCTAA
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:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAAAAAGAGA
Found at i:18716824 original size:70 final size:69
Alignment explanation
Indices: 18716721--18716857 Score: 213
Period size: 70 Copynumber: 2.0 Consensus size: 69
18716711 TAGGAGAAGA
*
18716721 AGAAAAAAAAAGAAAAAGAGAGGCAAGACAAAAAAGAAGAAGAAGCTACTAGCAAAAGAAAAAAA
1 AGAAAAAAAAAAAAAAAGAGAGGCAAGACAAAAAAGAAGAAGAAGCTACTAGCAAAAGAAAAAAA
18716786 AAGG
66 AAGG
* * *
18716790 AGAAAAAGAAAAAAAAAAGAGAGGCAAG-CTAAAAAGGAAGAAGAAGCTATTAGTAAAAGAAAAA
1 AGAAAAA-AAAAAAAAAAGAGAGGCAAGAC-AAAAAAGAAGAAGAAGCTACTAGCAAAAGAAAAA
18716854 AAAA
64 AAAA
18716858 AGGGAACAGG
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
69 8 0.13
70 54 0.87
ACGTcount: A:0.68, C:0.06, G:0.21, T:0.05
Consensus pattern (69 bp):
AGAAAAAAAAAAAAAAAGAGAGGCAAGACAAAAAAGAAGAAGAAGCTACTAGCAAAAGAAAAAAA
AAGG
Found at i:18722871 original size:20 final size:19
Alignment explanation
Indices: 18722839--18722886 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
18722829 CGACTCAAAA
18722839 TTAATA-AAA-TATTATTT
1 TTAATATAAATTATTATTT
18722856 TTAAATATAAATTATTATTT
1 TT-AATATAAATTATTATTT
18722876 TTAATATAAAT
1 TTAATATAAAT
18722887 ATAAAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.07
18 4 0.14
19 12 0.43
20 10 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAATATAAATTATTATTT
Found at i:18722876 original size:19 final size:20
Alignment explanation
Indices: 18722842--18722886 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
18722832 CTCAAAATTA
*
18722842 ATAAAATATTATTTTTAAAT
1 ATAAATTATTATTTTTAAAT
18722862 ATAAATTATTATTTTT-AAT
1 ATAAATTATTATTTTTAAAT
18722881 ATAAAT
1 ATAAAT
18722887 ATAAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAAATTATTATTTTTAAAT
Done.