Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 68 of 205
Found at i:20366207 original size:8 final size:8
Alignment explanation
Indices: 20366194--20366225 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
20366184 TAAAGGAAAG
20366194 TTTAAAAT
1 TTTAAAAT
20366202 TTTAAAAT
1 TTTAAAAT
20366210 TTTAAAAT
1 TTTAAAAT
20366218 TTTAAAAT
1 TTTAAAAT
20366226 AAAGTTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTTAAAAT
Found at i:20366803 original size:10 final size:10
Alignment explanation
Indices: 20366788--20366851 Score: 58
Period size: 10 Copynumber: 6.1 Consensus size: 10
20366778 CCATTGTATA
20366788 ATTTTTATTT
1 ATTTTTATTT
20366798 ATTTTTATTT
1 ATTTTTATTT
* *
20366808 CGTCTTTATTT
1 -ATTTTTATTT
20366819 ATTTTTATGTCT
1 ATTTTTAT-T-T
*
20366831 ATTTATATTT
1 ATTTTTATTT
20366841 ATGTTTT-TTT
1 AT-TTTTATTT
20366851 A
1 A
20366852 CACATTCTCC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
10 23 0.52
11 13 0.30
12 8 0.18
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.72
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:20366851 original size:16 final size:16
Alignment explanation
Indices: 20366814--20366844 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20366804 ATTTCGTCTT
*
20366814 TATTTATTTTTATGTC
1 TATTTATATTTATGTC
20366830 TATTTATATTTATGT
1 TATTTATATTTATGT
20366845 TTTTTTACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (16 bp):
TATTTATATTTATGTC
Found at i:20371475 original size:30 final size:31
Alignment explanation
Indices: 20371395--20371476 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
20371385 AGGGATTTAT
* *
20371395 TGAGAATTTTCAAAAATTTTGGTAGGCCTAA
1 TGAGAACTTTAAAAAATTTTGGTAGGCCTAA
* * *
20371426 TTAGAACTTTAACAAATTTTGG-AGGCTTAA
1 TGAGAACTTTAAAAAATTTTGGTAGGCCTAA
*
20371456 TGAG-AGTTCTAAAAAATTTTG
1 TGAGAACTT-TAAAAAATTTTG
20371477 AAATGCTTCA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 3 0.07
30 21 0.50
31 18 0.43
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.37
Consensus pattern (31 bp):
TGAGAACTTTAAAAAATTTTGGTAGGCCTAA
Found at i:20371877 original size:22 final size:21
Alignment explanation
Indices: 20371852--20371901 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
20371842 TTTTTTTTTC
* *
20371852 ATTTTAATAGATTATATTTATAA
1 ATTTTAAAAGATTA-AATTA-AA
*
20371875 TTTTTAAAAGATTAAATTAAA
1 ATTTTAAAAGATTAAATTAAA
20371896 ATTTTA
1 ATTTTA
20371902 TATAAAAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 7 0.30
22 4 0.17
23 12 0.52
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (21 bp):
ATTTTAAAAGATTAAATTAAA
Found at i:20372403 original size:45 final size:44
Alignment explanation
Indices: 20372314--20372406 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
20372304 ATTACAACAT
*
20372314 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
*
20372358 CATTCCATTCAACCAAACA-ATTGAATTACTATTAC-GCCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAG-CTCTATTC
20372403 CATT
1 CATT
20372407 ACAACTCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 1 0.02
44 23 0.52
45 20 0.45
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.32
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:20372424 original size:21 final size:21
Alignment explanation
Indices: 20372399--20372443 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
20372389 TTACGCCTCT
20372399 ATTCCATTACAACTCTATTCC
1 ATTCCATTACAACTCTATTCC
*
20372420 ATTCCATTACACCTCTATTCC
1 ATTCCATTACAACTCTATTCC
20372441 ATT
1 ATT
20372444 ACAGCGAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTCCATTACAACTCTATTCC
Found at i:20372439 original size:16 final size:16
Alignment explanation
Indices: 20372388--20372446 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
20372378 TTGAATTACT
*
20372388 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
20372404 ATTACAACTCTATTCCATTCC
1 ATTAC-AC-C---TCTATTCC
20372425 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
20372441 ATTACA
1 ATTACA
20372447 GCGAATCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
16 18 0.51
17 1 0.03
18 1 0.03
19 1 0.03
20 2 0.06
21 12 0.34
ACGTcount: A:0.27, C:0.34, G:0.02, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:20372578 original size:18 final size:17
Alignment explanation
Indices: 20372543--20372575 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20372533 TCTAAGAGAT
20372543 GAATTTTTGTAGGGAAG
1 GAATTTTTGTAGGGAAG
*
20372560 GAATTTTTGTGGGGAA
1 GAATTTTTGTAGGGAA
20372576 AGGGTATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.36, T:0.36
Consensus pattern (17 bp):
GAATTTTTGTAGGGAAG
Found at i:20380126 original size:51 final size:51
Alignment explanation
Indices: 20380006--20380338 Score: 318
Period size: 51 Copynumber: 6.6 Consensus size: 51
20379996 AGTTGCTAGG
* * *
20380006 TCACGTGTGTAGTACTATGTTCAGGCTACTACGTGTACCCGA-ATG-ATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GAATAGA
** * *** * ** *
20380056 TTGCATGTGTAGTACTATGTGCAGGCTACTATACGTACCGAATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGAATAGA
* * * *
20380107 TCACGTGTGTAGTACTATGTACAGGCTACTACGTGTATCGGAT-GAAAATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGAATA-GA
* * *
20380158 TCACGTATGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATAG-
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-AGAATAGA
* * *
20380209 TCACTTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAAATG-ATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GAATAGA
* * * * ** *
20380259 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTTGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGAATAGA
20380310 TCACGTGTGTAGTACTATGTGCAGGCTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTAC
20380339 CATGTGAACC
Statistics
Matches: 229, Mismatches: 45, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
49 5 0.02
50 73 0.32
51 147 0.64
52 1 0.00
53 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (51 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGAATAGA
Found at i:20380284 original size:152 final size:152
Alignment explanation
Indices: 20380004--20380338 Score: 383
Period size: 152 Copynumber: 2.2 Consensus size: 152
20379994 GAAGTTGCTA
* **
20380004 GGTCACGTGTGTAGTACTATGTTCAGGCTACTACGTGTACCCGAATGATAGGTTGCATGTGTAGT
1 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCCGAATGATAGGTCACATGTGTAGT
* * * *
20380069 ACTATGTGCAGGCTACTATACGTACCGAATAGCTTCGATCACGTGTGTAGTACTATGTACAGGCT
66 ACTATGTGCAGGCTACTACACGTACCGAATAGCATAGATCACATGTGTAGTACTATGTACAGGCT
* *
20380134 ACTACGTGTATCGGAT-GAAAAT
131 ACTACGCGTACCGGATAG-AAAT
* * * *
20380156 GGTCACGTATGTAGTACTATGTGCAGGCTACTACGTGTA-TCGGATGAAAATA-GTCACTTGTGT
1 GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCCGAATG---ATAGGTCACATGTGT
** * * *
20380219 AGTACTATGTGCAGGCTACTACGTGTACCGAA-ATG-ATAGGTCGCATGTGTAGTACTATGTGCA
63 AGTACTATGTGCAGGCTACTACACGTACCGAATA-GCATAGATCACATGTGTAGTACTATGTACA
* ***
20380282 GGCTACTATGCGTACCGGATAGCTTT
127 GGCTACTACGCGTACCGGATAGAAAT
*
20380308 GATCACGTGTGTAGTACTATGTGCAGGCTAC
1 GGTCACGTGTGTAGTACTATGTGCAGGCTAC
20380339 CATGTGAACC
Statistics
Matches: 154, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
151 5 0.03
152 107 0.69
153 39 0.25
154 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (152 bp):
GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCCGAATGATAGGTCACATGTGTAGT
ACTATGTGCAGGCTACTACACGTACCGAATAGCATAGATCACATGTGTAGTACTATGTACAGGCT
ACTACGCGTACCGGATAGAAAT
Found at i:20391919 original size:26 final size:26
Alignment explanation
Indices: 20391890--20391942 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
20391880 AAAATTGAAT
20391890 AATGGATTGGAAAAGAGTGTACATTC
1 AATGGATTGGAAAAGAGTGTACATTC
*
20391916 AATGGATTGGAAAAGAGTGTACCTTC
1 AATGGATTGGAAAAGAGTGTACATTC
20391942 A
1 A
20391943 TTGATCTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.26
Consensus pattern (26 bp):
AATGGATTGGAAAAGAGTGTACATTC
Found at i:20394219 original size:20 final size:18
Alignment explanation
Indices: 20394181--20394215 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20394171 TTAAAATACT
20394181 TTTTTAAAAAAAATTTTA
1 TTTTTAAAAAAAATTTTA
*
20394199 TTTTTAAAATAAATTTT
1 TTTTTAAAAAAAATTTT
20394216 TTATGTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTTAAAAAAAATTTTA
Found at i:20397346 original size:11 final size:11
Alignment explanation
Indices: 20397330--20397354 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20397320 AAAGAGGTAG
20397330 AGAATTACCAA
1 AGAATTACCAA
20397341 AGAATTACCAA
1 AGAATTACCAA
20397352 AGA
1 AGA
20397355 GGCGGAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (11 bp):
AGAATTACCAA
Found at i:20400568 original size:21 final size:21
Alignment explanation
Indices: 20400539--20400597 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
20400529 TTTGATTAAC
*
20400539 ATAATAAAT-TTATAATTAGTT
1 ATAAAAAATATTATAATTA-TT
*
20400560 ATAAAAAATATTTTAATTATT
1 ATAAAAAATATTATAATTATT
* *
20400581 ATTAAATATAATTATAA
1 ATAAAAAAT-ATTATAA
20400598 ATTACATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATAAAAAATATTATAATTATT
Found at i:20400689 original size:16 final size:17
Alignment explanation
Indices: 20400665--20400700 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
20400655 ACCTACAATT
*
20400665 ATAATTATAAATT-AGA
1 ATAAATATAAATTAAGA
20400681 ATAAATATAAATTAAGA
1 ATAAATATAAATTAAGA
20400698 ATA
1 ATA
20400701 GCAATAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
ATAAATATAAATTAAGA
Found at i:20400913 original size:31 final size:30
Alignment explanation
Indices: 20400878--20400941 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
20400868 TATAATTTGA
***
20400878 TCATTGAACTATTTGTAAGTTTTTATTTAAG
1 TCATTGAACTATTAAAAAGTTTTTA-TTAAG
*
20400909 TCATTGATCTATTAAAAAGTTTTTATTAAG
1 TCATTGAACTATTAAAAAGTTTTTATTAAG
20400939 TCA
1 TCA
20400942 CTAAGTTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (30 bp):
TCATTGAACTATTAAAAAGTTTTTATTAAG
Found at i:20409922 original size:51 final size:51
Alignment explanation
Indices: 20409867--20409983 Score: 216
Period size: 51 Copynumber: 2.3 Consensus size: 51
20409857 CAGATCACAT
20409867 TTATCACTTGTCACTTGTCACTGATCAGATAAATGTAGCGAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAATGTAGCGAAAGCTACCAC
* *
20409918 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAATGTAGCGAAAGCTACCAC
20409969 TTATCACTTGTCACT
1 TTATCACTTGTCACT
20409984 GATCAAAAGT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 64 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAATGTAGCGAAAGCTACCAC
Found at i:20418578 original size:21 final size:21
Alignment explanation
Indices: 20418548--20418609 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
20418538 GCTTCAGTTT
20418548 AACCCTTATGAGTTTTTGTTC
1 AACCCTTATGAGTTTTTGTTC
* * * *
20418569 AGCTCTTATGAGCTTTCGTTC
1 AACCCTTATGAGTTTTTGTTC
* *
20418590 AACCCTTATGGGTTTCTGTT
1 AACCCTTATGAGTTTTTGTT
20418610 TAGCACTTCA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (21 bp):
AACCCTTATGAGTTTTTGTTC
Found at i:20418594 original size:42 final size:42
Alignment explanation
Indices: 20418499--20418609 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 42
20418489 TAACTCATAT
* * *
20418499 TTCAGTTTAACCC-TATTGGGTTTCT-TTTAGCTCTTTCGAGC
1 TTCAGTTCAACCCTTA-TGAGTTTCTGTTCAGCTCTTTCGAGC
* *
20418540 TTCAGTTTAACCCTTATGAGTTTTTGTTCAGCTCTTAT-GAGC
1 TTCAGTTCAACCCTTATGAGTTTCTGTTCAGCTCTT-TCGAGC
*
20418582 TTTC-GTTCAACCCTTATGGGTTTCTGTT
1 -TTCAGTTCAACCCTTATGAGTTTCTGTT
20418610 TAGCACTTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
41 20 0.33
42 36 0.60
43 4 0.07
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (42 bp):
TTCAGTTCAACCCTTATGAGTTTCTGTTCAGCTCTTTCGAGC
Found at i:20429170 original size:18 final size:18
Alignment explanation
Indices: 20429147--20429185 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
20429137 CCACATCAAT
* *
20429147 AAATATTTAAAAATTAAA
1 AAATATTAAAAAAATAAA
20429165 AAATATTAAAAAAATAAA
1 AAATATTAAAAAAATAAA
20429183 AAA
1 AAA
20429186 AAAATCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATATTAAAAAAATAAA
Found at i:20431864 original size:36 final size:35
Alignment explanation
Indices: 20431817--20431938 Score: 147
Period size: 36 Copynumber: 3.4 Consensus size: 35
20431807 GAAAATCCCA
*
20431817 CCAAAACACACCAGATGCTCATAAGAGCTAGTCCAT
1 CCAAAACACACCA-ATGCTCATAAGAGCTAATCCAT
*
20431853 CCAAAGCACACCAAATGCTCATAAGAGCTAATCCAT
1 CCAAAACACACC-AATGCTCATAAGAGCTAATCCAT
* * *
20431889 TCAAAACACACCAATAGCTC-TGAAGAGCTAATCTAA
1 CCAAAACACACCAAT-GCTCAT-AAGAGCTAATCCAT
*
20431925 CCGAAACACACCAA
1 CCAAAACACACCAA
20431939 AACAAAGAGT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 4 0.05
36 70 0.93
37 1 0.01
ACGTcount: A:0.43, C:0.30, G:0.11, T:0.16
Consensus pattern (35 bp):
CCAAAACACACCAATGCTCATAAGAGCTAATCCAT
Found at i:20433188 original size:13 final size:13
Alignment explanation
Indices: 20433172--20433198 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20433162 ATATTTTAAA
20433172 AATAATATTTACG
1 AATAATATTTACG
20433185 AATAATATTTACG
1 AATAATATTTACG
20433198 A
1 A
20433199 GTTGACAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
AATAATATTTACG
Found at i:20436243 original size:20 final size:20
Alignment explanation
Indices: 20436215--20436255 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20436205 ACTCTGTTGC
*
20436215 TTGAGTTTGCCGCTGGAATT
1 TTGACTTTGCCGCTGGAATT
* *
20436235 TTGACTTTGCTGCTTGAATT
1 TTGACTTTGCCGCTGGAATT
20436255 T
1 T
20436256 ACTGCTTGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.46
Consensus pattern (20 bp):
TTGACTTTGCCGCTGGAATT
Found at i:20437203 original size:20 final size:20
Alignment explanation
Indices: 20437178--20437220 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
20437168 AAATAAAAGT
*
20437178 ATGGTGATTAAACAGGTGGC
1 ATGGTGATTAAACAGGCGGC
20437198 ATGGTGATTAAACAGGCGGC
1 ATGGTGATTAAACAGGCGGC
20437218 ATG
1 ATG
20437221 TATTAAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.12, G:0.35, T:0.23
Consensus pattern (20 bp):
ATGGTGATTAAACAGGCGGC
Found at i:20441917 original size:236 final size:236
Alignment explanation
Indices: 20441499--20441973 Score: 833
Period size: 236 Copynumber: 2.0 Consensus size: 236
20441489 TTATTGGGGG
* * * *
20441499 AAAACATACGGACTGTTGGCTTTGAATTAAGTAGGAGCATTTCCTCTGAGAAAGTAATTTAAGAA
1 AAAACATACGGACTGTTGGCCTTGAATTAAGTAGAAGCATTGCCTCCGAGAAAGTAATTTAAGAA
* * *
20441564 AGTGCTTAAAAATTATATCCAACCTTATAAAAAGTATAATGATTAATTGAGGATGAGCGCTATCG
66 AGTGCTCAAAAATTATATCCAACCTTATAAAAAGTAGAAGGATTAATTGAGGATGAGCGCTATCG
* *
20441629 TGCATTAAGCAAAATTCCTGACTATCCAATGCAAATGCTTATTTTCTTCAGTCTACCTTCTTCAG
131 TGCATTAAGCAAAATTCCTGACCATCCAATGCAAATGCTTATTTTCTTCAGTCTACCTTCTTCAA
20441694 TGCGATTGGAATGGGTTAGAAGATTTCTTTCTGACCATTAA
196 TGCGATTGGAATGGGTTAGAAGATTTCTTTCTGACCATTAA
*
20441735 AAAATATACGGACTGTTGGCCTTGAATTAAGTAGAAGCATTGCCTCCGAGAAAGTAATTTAAGAA
1 AAAACATACGGACTGTTGGCCTTGAATTAAGTAGAAGCATTGCCTCCGAGAAAGTAATTTAAGAA
*
20441800 AGTGCTCAAAAATTATATCCGACCTTATAAAAAGTAGAAGGATTAATTGAGGATGAGCGCTATCG
66 AGTGCTCAAAAATTATATCCAACCTTATAAAAAGTAGAAGGATTAATTGAGGATGAGCGCTATCG
* *
20441865 TGCGTTGAGCAAAATTCCTGACCATCCAATGCAAATGCTTATTTTCTTCAGTCTACCTTCTTCAA
131 TGCATTAAGCAAAATTCCTGACCATCCAATGCAAATGCTTATTTTCTTCAGTCTACCTTCTTCAA
20441930 TGCGATTGGAATGGGTTAGAAGATTTCTTTCTGACCATTAA
196 TGCGATTGGAATGGGTTAGAAGATTTCTTTCTGACCATTAA
20441971 AAA
1 AAA
20441974 TCATGGTTGT
Statistics
Matches: 226, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
236 226 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (236 bp):
AAAACATACGGACTGTTGGCCTTGAATTAAGTAGAAGCATTGCCTCCGAGAAAGTAATTTAAGAA
AGTGCTCAAAAATTATATCCAACCTTATAAAAAGTAGAAGGATTAATTGAGGATGAGCGCTATCG
TGCATTAAGCAAAATTCCTGACCATCCAATGCAAATGCTTATTTTCTTCAGTCTACCTTCTTCAA
TGCGATTGGAATGGGTTAGAAGATTTCTTTCTGACCATTAA
Found at i:20442406 original size:61 final size:59
Alignment explanation
Indices: 20442258--20442411 Score: 170
Period size: 61 Copynumber: 2.6 Consensus size: 59
20442248 TATAATATTA
* * * *
20442258 TATATTATGATTTTTATT-AATTCATATTTTAATAATAATTATATTAAGAATGTTATTAAAT
1 TATA-TATTATTTTTATTAAATT-ATA-TTTAATAAAAATTATATTAAGAATATGATTAAAT
* *
20442319 TATATATTA-TTTTATTAAATTGTATTTAATAAAAATTATGTTAA-AATATGATTAAAT
1 TATATATTATTTTTATTAAATTATATTTAATAAAAATTATATTAAGAATATGATTAAAT
*
20442376 TATTTATTTTTATTTTTATTAAATTATATTTAATAA
1 TA--TA-TATTATTTTTATTAAATTATATTTAATAA
20442412 TAATCTTATT
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
57 13 0.16
58 18 0.22
59 11 0.14
60 12 0.15
61 26 0.32
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (59 bp):
TATATATTATTTTTATTAAATTATATTTAATAAAAATTATATTAAGAATATGATTAAAT
Found at i:20442618 original size:16 final size:16
Alignment explanation
Indices: 20442599--20442647 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
20442589 AATTACTAAA
*
20442599 TACAACTCTAATCCAT
1 TACAACTCTATTCCAT
*
20442615 TACATCTCTATTCCAT
1 TACAACTCTATTCCAT
*
20442631 TACAACCCTATTCCAT
1 TACAACTCTATTCCAT
20442647 T
1 T
20442648 CACCCTAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.37
Consensus pattern (16 bp):
TACAACTCTATTCCAT
Found at i:20445102 original size:6 final size:6
Alignment explanation
Indices: 20445091--20445124 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
20445081 TTTTGAGCCT
*
20445091 TATATC TATATC TATATC TATATC TATATA TATA
1 TATATC TATATC TATATC TATATC TATATC TATA
20445125 ATATTATTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:20450770 original size:49 final size:49
Alignment explanation
Indices: 20450698--20451079 Score: 392
Period size: 49 Copynumber: 7.8 Consensus size: 49
20450688 GAACTTGTAC
* * ** * *
20450698 ATTCTACCAT-CCTGGTTGGCCCGACAACGATTGCCTTCACTATCTGTAT
1 ATTCTACCATCCCAGG-TGGCCCGACAACGATAGTTTTCACTATTTGCAT
* *
20450747 ATTCTACCATCCCAGGTGACCCGACAACGATAGCTTTCACTATTTGCAT
1 ATTCTACCATCCCAGGTGGCCCGACAACGATAGTTTTCACTATTTGCAT
* *
20450796 ATTCTACCATCCC-GAGTGACCCGACAACGATGGTTTTCACTATTTGCAT
1 ATTCTACCATCCCAG-GTGGCCCGACAACGATAGTTTTCACTATTTGCAT
* ** ** *
20450845 ATTCTACCATCTCAGGTGGCTTGATTACGATAGTTTTCACTATTTACAT
1 ATTCTACCATCCCAGGTGGCCCGACAACGATAGTTTTCACTATTTGCAT
*** * *
20450894 ATTCTACCATCTTGGGTGGCCCGACAACGATGGTTTTCGCTATTTGCAT
1 ATTCTACCATCCCAGGTGGCCCGACAACGATAGTTTTCACTATTTGCAT
* * * * *
20450943 ATTCTACCATCCCAGGTGGCTCGATAACGATAGTTTTTAGTATTTACAT
1 ATTCTACCATCCCAGGTGGCCCGACAACGATAGTTTTCACTATTTGCAT
*** * * *
20450992 ATTCTACCATCTTGGGTGGCCCGACAACAATAGCTTTCACTATTTACAT
1 ATTCTACCATCCCAGGTGGCCCGACAACGATAGTTTTCACTATTTGCAT
* ** *
20451041 ATTCTACCAT-CCTGAGTGGCCTAACAACGATGGTTTTCA
1 ATTCTACCATCCCAG-GTGGCCCGACAACGATAGTTTTCA
20451080 ATCACTATAT
Statistics
Matches: 277, Mismatches: 52, Indels: 8
0.82 0.15 0.02
Matches are distributed among these distances:
48 2 0.01
49 270 0.97
50 5 0.02
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (49 bp):
ATTCTACCATCCCAGGTGGCCCGACAACGATAGTTTTCACTATTTGCAT
Found at i:20450972 original size:147 final size:147
Alignment explanation
Indices: 20450698--20451079 Score: 444
Period size: 147 Copynumber: 2.6 Consensus size: 147
20450688 GAACTTGTAC
* * * * * ** **
20450698 ATTCTACCATC-CTGGTTGGCCCGACAACGATTGCCTTCACTATCTGTATATTCTACCATCCCAG
1 ATTCTACCATCTCAGG-TGGCCCGACAACAATAGCTTTCACTATTTACATATTCTACCATCCTGG
* * *
20450762 GTGACCCGACAACGATAGCTTTCACTATTTGCATATTCTACCATCCCGAGTGACCCGACAACGAT
65 GTGGCCCGACAACGATGGTTTTCACTATTTGCATATTCTACCATCCCGAGTGACCCGACAACGAT
* *
20450827 GGTTTTCACTATTTGCAT
130 AGTTTTCACTATTTACAT
** ** * * *
20450845 ATTCTACCATCTCAGGTGGCTTGATTACGATAGTTTTCACTATTTACATATTCTACCATCTTGGG
1 ATTCTACCATCTCAGGTGGCCCGACAACAATAGCTTTCACTATTTACATATTCTACCATCCTGGG
* * * *
20450910 TGGCCCGACAACGATGGTTTTCGCTATTTGCATATTCTACCATCCC-AGGTGGCTCGATAACGAT
66 TGGCCCGACAACGATGGTTTTCACTATTTGCATATTCTACCATCCCGA-GTGACCCGACAACGAT
* *
20450974 AGTTTTTAGTATTTACAT
130 AGTTTTCACTATTTACAT
** *
20450992 ATTCTACCATCTTGGGTGGCCCGACAACAATAGCTTTCACTATTTACATATTCTACCATCCTGAG
1 ATTCTACCATCTCAGGTGGCCCGACAACAATAGCTTTCACTATTTACATATTCTACCATCCTGGG
**
20451057 TGGCCTAACAACGATGGTTTTCA
66 TGGCCCGACAACGATGGTTTTCA
20451080 ATCACTATAT
Statistics
Matches: 195, Mismatches: 38, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
146 1 0.01
147 191 0.98
148 3 0.02
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (147 bp):
ATTCTACCATCTCAGGTGGCCCGACAACAATAGCTTTCACTATTTACATATTCTACCATCCTGGG
TGGCCCGACAACGATGGTTTTCACTATTTGCATATTCTACCATCCCGAGTGACCCGACAACGATA
GTTTTCACTATTTACAT
Found at i:20451060 original size:98 final size:98
Alignment explanation
Indices: 20450698--20451052 Score: 476
Period size: 98 Copynumber: 3.6 Consensus size: 98
20450688 GAACTTGTAC
* * * * *
20450698 ATTCTACCATCCTGGTTGGCCCGACAACGATTGCCTTCACTATCTGTATATTCTACCATCCCAGG
1 ATTCTACCATCCTGGGTGGCCCGACAACGATGGCTTTCACTATTTGCATATTCTACCATCCCAGG
* * * * *
20450763 TGACCCGACAACGATAGCTTTCACTATTTGCAT
66 TGGCTCGATAACGATAGTTTTCACTATTTACAT
* * * * *
20450796 ATTCTACCATCCCGAGTGACCCGACAACGATGGTTTTCACTATTTGCATATTCTACCATCTCAGG
1 ATTCTACCATCCTGGGTGGCCCGACAACGATGGCTTTCACTATTTGCATATTCTACCATCCCAGG
* *
20450861 TGGCTTGATTACGATAGTTTTCACTATTTACAT
66 TGGCTCGATAACGATAGTTTTCACTATTTACAT
* * *
20450894 ATTCTACCATCTTGGGTGGCCCGACAACGATGGTTTTCGCTATTTGCATATTCTACCATCCCAGG
1 ATTCTACCATCCTGGGTGGCCCGACAACGATGGCTTTCACTATTTGCATATTCTACCATCCCAGG
* *
20450959 TGGCTCGATAACGATAGTTTTTAGTATTTACAT
66 TGGCTCGATAACGATAGTTTTCACTATTTACAT
* * * *
20450992 ATTCTACCATCTTGGGTGGCCCGACAACAATAGCTTTCACTATTTACATATTCTACCATCC
1 ATTCTACCATCCTGGGTGGCCCGACAACGATGGCTTTCACTATTTGCATATTCTACCATCC
20451053 TGAGTGGCCT
Statistics
Matches: 225, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
98 225 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (98 bp):
ATTCTACCATCCTGGGTGGCCCGACAACGATGGCTTTCACTATTTGCATATTCTACCATCCCAGG
TGGCTCGATAACGATAGTTTTCACTATTTACAT
Found at i:20453098 original size:21 final size:21
Alignment explanation
Indices: 20453072--20453114 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
20453062 GTGTGGAAAG
20453072 AACATCCCGAATCTAGAATTC
1 AACATCCCGAATCTAGAATTC
20453093 AACATCCCGAATCTAGAATTC
1 AACATCCCGAATCTAGAATTC
20453114 A
1 A
20453115 TTCAGATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.23
Consensus pattern (21 bp):
AACATCCCGAATCTAGAATTC
Found at i:20458038 original size:19 final size:20
Alignment explanation
Indices: 20458008--20458045 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
20457998 GACAATCTCT
20458008 CATAATTTTTAGTATTTTCC
1 CATAATTTTTAGTATTTTCC
20458028 CATAA-TTTTAGTATTTTC
1 CATAATTTTTAGTATTTTC
20458046 TCGTAAGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.55
Consensus pattern (20 bp):
CATAATTTTTAGTATTTTCC
Found at i:20458259 original size:20 final size:20
Alignment explanation
Indices: 20458236--20458310 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
20458226 CCTCTTATAA
20458236 TTTTTGGTACTCCATCATGT
1 TTTTTGGTACTCCATCATGT
*
20458256 TTTTTGGTACTCACATCATAT
1 TTTTTGGTACTC-CATCATGT
* *
20458277 TTTTTGGTATTTCC-TCGTGT
1 TTTTTGGTA-CTCCATCATGT
*
20458297 TTTTTAGTACTCCA
1 TTTTTGGTACTCCA
20458311 AAAATTATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
19 3 0.07
20 24 0.52
21 17 0.37
22 2 0.04
ACGTcount: A:0.16, C:0.19, G:0.13, T:0.52
Consensus pattern (20 bp):
TTTTTGGTACTCCATCATGT
Found at i:20458272 original size:21 final size:20
Alignment explanation
Indices: 20458236--20458285 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 20
20458226 CCTCTTATAA
*
20458236 TTTTTGGTACTCCATCATGT
1 TTTTTGGTACTCCATCATAT
20458256 TTTTTGGTACTCACATCATAT
1 TTTTTGGTACTC-CATCATAT
20458277 TTTTTGGTA
1 TTTTTGGTA
20458286 TTTCCTCGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.52
Consensus pattern (20 bp):
TTTTTGGTACTCCATCATAT
Found at i:20463033 original size:16 final size:17
Alignment explanation
Indices: 20463014--20463046 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20463004 CTTATAATTT
20463014 TTTTCAT-TTATTTAAA
1 TTTTCATATTATTTAAA
*
20463030 TTTTCATATTTTTTAAA
1 TTTTCATATTATTTAAA
20463047 AATTATCATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTCATATTATTTAAA
Found at i:20464799 original size:30 final size:28
Alignment explanation
Indices: 20464725--20464884 Score: 142
Period size: 29 Copynumber: 5.5 Consensus size: 28
20464715 ACAAAAAATA
*
20464725 AAAATTACATTTTGACCCCTAAACTTCTT
1 AAAATTACATTTTGACCCCTAAA-TTTTT
* ** *
20464754 GAAATCGC-GTTTGACCCCTAAATTTTCCT
1 AAAATTACATTTTGACCCCTAAATTTT--T
* *
20464783 AAAATTATATTTTGACCCCCAAACTTTTT
1 AAAATTACATTTTGACCCCTAAA-TTTTT
* *
20464812 GAAATTACATTTTGACCCATTAAATTTTT
1 AAAATTACATTTTGACCC-CTAAATTTTT
* *
20464841 GAAATTACATTTTGACTCCTAAATTTTCT
1 AAAATTACATTTTGACCCCTAAATTTT-T
*
20464870 AAAAATTATATTTTG
1 -AAAATTACATTTTG
20464885 GCCACACAAG
Statistics
Matches: 105, Mismatches: 19, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
27 3 0.03
28 21 0.20
29 50 0.48
30 27 0.26
31 4 0.04
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (28 bp):
AAAATTACATTTTGACCCCTAAATTTTT
Found at i:20464852 original size:14 final size:14
Alignment explanation
Indices: 20464807--20464853 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
20464797 ACCCCCAAAC
20464807 TTTTTGAAATTACA
1 TTTTTGAAATTACA
* *
20464821 -TTTTGACCCATTAAA
1 TTTTTGA--AATTACA
20464836 TTTTTGAAATTACA
1 TTTTTGAAATTACA
20464850 TTTT
1 TTTT
20464854 GACTCCTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
13 6 0.23
14 9 0.35
15 5 0.19
16 6 0.23
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (14 bp):
TTTTTGAAATTACA
Found at i:20464864 original size:28 final size:28
Alignment explanation
Indices: 20464726--20464867 Score: 151
Period size: 29 Copynumber: 4.9 Consensus size: 28
20464716 CAAAAAATAA
*
20464726 AAATTACATTTTGACCCCTAAACTTCTTG
1 AAATTACATTTTGACCCCTAAA-TTTTTG
** * *
20464755 AAATCGC-GTTTGACCCCTAAATTTTCCTA
1 AAATTACATTTTGACCCCTAAATTTT--TG
* *
20464784 AAATTATATTTTGACCCCCAAACTTTTTG
1 AAATTACATTTTGACCCCTAAA-TTTTTG
*
20464813 AAATTACATTTTGACCCATTAAATTTTTG
1 AAATTACATTTTGACCC-CTAAATTTTTG
*
20464842 AAATTACATTTTGACTCCTAAATTTT
1 AAATTACATTTTGACCCCTAAATTTT
20464868 CTAAAAATTA
Statistics
Matches: 92, Mismatches: 16, Indels: 11
0.77 0.13 0.09
Matches are distributed among these distances:
27 3 0.03
28 21 0.23
29 49 0.53
30 15 0.16
31 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (28 bp):
AAATTACATTTTGACCCCTAAATTTTTG
Found at i:20465255 original size:3 final size:3
Alignment explanation
Indices: 20465247--20465290 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
20465237 GGTTTTGAGA
* *
20465247 AAG AAG AAGG AAG AAG AAG AAA AAT AAG AAG AAG AAG AA- AAG AA
1 AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
20465291 AAAAAAGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:20465296 original size:9 final size:9
Alignment explanation
Indices: 20465284--20465322 Score: 51
Period size: 10 Copynumber: 4.0 Consensus size: 9
20465274 GAAGAAGAAG
20465284 AAAAGAAAA
1 AAAAGAAAA
20465293 AAAAGAAAGAA
1 AAAAG-AA-AA
20465304 AAAAGAGAAA
1 AAAAGA-AAA
20465314 AAAAGAAAA
1 AAAAGAAAA
20465323 TAAATTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.30
10 11 0.41
11 8 0.30
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:20465298 original size:14 final size:14
Alignment explanation
Indices: 20465281--20465314 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
20465271 TAAGAAGAAG
20465281 AAGAAAAGAAAAAA
1 AAGAAAAGAAAAAA
20465295 AAG-AAAGAAAAAA
1 AAGAAAAGAAAAAA
*
20465308 GAGAAAA
1 AAGAAAA
20465315 AAAGAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAAAAA
Found at i:20465303 original size:13 final size:13
Alignment explanation
Indices: 20465285--20465322 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
20465275 AAGAAGAAGA
20465285 AAAGAAAAAAAAG
1 AAAGAAAAAAAAG
*
20465298 AAAGAAAAAAGAG
1 AAAGAAAAAAAAG
20465311 AAA-AAAAGAAAA
1 AAAGAAAA-AAAA
20465323 TAAATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAG
Found at i:20465321 original size:21 final size:22
Alignment explanation
Indices: 20465250--20465321 Score: 78
Period size: 21 Copynumber: 3.3 Consensus size: 22
20465240 TTTGAGAAAG
* *
20465250 AAGAAGGAAGAAGAAGA-AAAAT
1 AAGAAAGAAGAA-AAGAGAAAAA
20465272 AAGAAGAAGAAGAAAAGA-AAAAA
1 AAG-A-AAGAAGAAAAGAGAAAAA
20465295 AAGAAAGAA-AAAAGAGAAAAA
1 AAGAAAGAAGAAAAGAGAAAAA
20465316 AAGAAA
1 AAGAAA
20465322 ATAAATTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.13
21 16 0.36
22 4 0.09
23 12 0.27
24 7 0.16
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.01
Consensus pattern (22 bp):
AAGAAAGAAGAAAAGAGAAAAA
Found at i:20465579 original size:21 final size:21
Alignment explanation
Indices: 20465546--20465640 Score: 81
Period size: 21 Copynumber: 4.6 Consensus size: 21
20465536 AGTCCAGAAT
* *
20465546 AAAGGAAGGAAAAAAAGGAAA
1 AAAGAAAGAAAAAAAAGGAAA
20465567 AAAGAAAGAAAAAAAA-GAAA
1 AAAGAAAGAAAAAAAAGGAAA
* * *
20465587 AAAAAAAGAGAAAAAGAGTAATGA
1 AAAGAAAGA-AAAAAAAGGAA--A
*
20465611 AAA-AAAG-AAAAAAAGAAAA
1 AAAGAAAGAAAAAAAAGGAAA
20465630 AAAGAAA-AAAA
1 AAAGAAAGAAAA
20465641 GGAAAAAGGG
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.07
20 18 0.30
21 29 0.48
22 2 0.03
23 4 0.07
24 4 0.07
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAGAAAGAAAAAAAAGGAAA
Found at i:20465580 original size:13 final size:13
Alignment explanation
Indices: 20465564--20465645 Score: 63
Period size: 13 Copynumber: 6.8 Consensus size: 13
20465554 GAAAAAAAGG
20465564 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
20465577 AAAAAAG-AA-AA
1 AAAAAAGAAAGAA
20465588 AAAAAAG--AG-A
1 AAAAAAGAAAGAA
* *
20465598 AAAAGAGTAATG-A
1 AAAAAAG-AAAGAA
20465611 AAAAAAGAAA-AA
1 AAAAAAGAAAGAA
20465623 AAGAAAA-AAAGAA
1 AA-AAAAGAAAGAA
*
20465636 AAAAAGGAAA
1 AAAAAAGAAA
20465646 AAGGGTTGTG
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
10 8 0.14
11 9 0.16
12 13 0.23
13 26 0.46
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAGAA
Found at i:20465590 original size:8 final size:8
Alignment explanation
Indices: 20465554--20465647 Score: 95
Period size: 8 Copynumber: 11.8 Consensus size: 8
20465544 ATAAAGGAAG
20465554 GAAAAAAA
1 GAAAAAAA
*
20465562 GGAAAAAA
1 GAAAAAAA
20465570 GAAAGAAAA
1 GAAA-AAAA
20465579 -AAAAGAAA
1 GAAAA-AAA
20465587 -AAAAAAA
1 GAAAAAAA
*
20465594 GAGAAAAA
1 GAAAAAAA
** *
20465602 G-AGTAAT
1 GAAAAAAA
20465609 GAAAAAAA
1 GAAAAAAA
20465617 GAAAAAAA
1 GAAAAAAA
20465625 GAAAAAAA
1 GAAAAAAA
20465633 GAAAAAAA
1 GAAAAAAA
20465641 GGAAAAA
1 -GAAAAA
20465648 GGGTTGTGTA
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
7 7 0.10
8 54 0.76
9 10 0.14
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (8 bp):
GAAAAAAA
Found at i:20465614 original size:34 final size:32
Alignment explanation
Indices: 20465555--20465624 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 32
20465545 TAAAGGAAGG
20465555 AAAAAAAGGAAAAAAGAAAGAAAAAAAAGAAA
1 AAAAAAAGGAAAAAAGAAAGAAAAAAAAGAAA
*
20465587 AAAAAAAGAGAAAAAGAGTAATG-AAAAAAAGAAA
1 AAAAAAAG-GAAAAA-AG-AAAGAAAAAAAAGAAA
20465621 AAAA
1 AAAA
20465625 GAAAAAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
32 8 0.24
33 6 0.18
34 17 0.50
35 3 0.09
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (32 bp):
AAAAAAAGGAAAAAAGAAAGAAAAAAAAGAAA
Found at i:20478173 original size:160 final size:158
Alignment explanation
Indices: 20477915--20478692 Score: 984
Period size: 160 Copynumber: 4.9 Consensus size: 158
20477905 CAAGAAATAT
* * *
20477915 TTTTTAATTTCTGTTTTTTT-CAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAATTTCT-TTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
* *
20477979 ACATACCGAGGTATTTTTTTAAA-TTCTGTTTTTCAAAAATCAACTCATATTGAGAGAGGCGAGT
65 ACATACCGAGGTATTTTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
* * *
20478043 TGAGCCTCGGGCACATGCTGAGGAATTT-
130 TGAGCCTCGGACACATGCCGAGGTATTTC
*
20478071 TTTTTAATTTCTATTTTTTTTAAAAAAAACTCTACTCATATTGCGAGAGGTGAGTTGAGCCTC-G
1 TTTTTAATTTC--TTTTTTTT-AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
* * *
20478135 GACATATACCGAGGTATTTTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTC
62 GTCACATACCGAGGTATTTTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTG
* * *
20478200 ACTTGAGCCTCGAACACATGCCGATGTATTTC
127 AGTTGAGCCTCGGACACATGCCGAGGTATTTC
* * * *
20478232 TTTTAAATTTC-TGTTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGATGAGCCTCAGGTCA
1 TTTTTAATTTCTTTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCA
* * *
20478295 CATGCTGAGGTATTTTTTTAAATTTCTATTTTTTTGCAAAAATCAACTCATATTGCGAGAGGTGA
66 CATACCGAGGTATTTTTTTAAATTTC--TGTTTTT-CAAAAATCAACTCATATTGCGAGAGGTGA
20478360 GTTGAGCCTCGGACACATGCCGAGGTATTTC
128 GTTGAGCCTCGGACACATGCCGAGGTATTTC
**
20478391 TTTTTAATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
1 TTTTTAATTTCT-TTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTC
** *
20478456 ACACGCTGAGGTATTTTTTTTAAATTTCTGTTTTTTTCAAAAAATCAACTCATATTGCGAGAGGT
65 ACATACCGAGGTA-TTTTTTTAAATTTCTG--TTTTTC-AAAAATCAACTCATATTGCGAGAGGT
* * *
20478521 GAGTTGAGCCTCAGGTCACACGCTGAGGTATTT-
126 GAGTTGAGCCTC-GGACACATGCCGAGGTATTTC
* *
20478554 TTTTTAAATTTCTGTTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
1 TTTTT-AATTTCT-TTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
* * *
20478619 CACACGA-CGAGGTA-TTTTTT-AATTTTTGTTTTTTTTC-TAAATCAACTCATATTGCGAGAGG
64 CACA-TACCGAGGTATTTTTTTAAATTTCTG---TTTTTCAAAAATCAACTCATATTGCGAGAGG
20478680 TGAGTTGAGCCTC
125 TGAGTTGAGCCTC
20478693 AAGTCGCAAG
Statistics
Matches: 552, Mismatches: 48, Indels: 40
0.86 0.08 0.06
Matches are distributed among these distances:
155 31 0.06
156 43 0.08
157 7 0.01
158 13 0.02
159 95 0.17
160 128 0.23
161 22 0.04
162 69 0.12
163 62 0.11
164 82 0.15
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (158 bp):
TTTTTAATTTCTTTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCA
CATACCGAGGTATTTTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTT
GAGCCTCGGACACATGCCGAGGTATTTC
Found at i:20478518 original size:82 final size:80
Alignment explanation
Indices: 20477914--20478692 Score: 991
Period size: 82 Copynumber: 9.8 Consensus size: 80
20477904 TCAAGAAATA
*
20477914 TTTTTT-AATTTCTGTTTTTTTCAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTTAAATTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGT
* *
20477978 CACATACCGAGGTA-T
65 CACATGCTGAGGTATT
* * *
20477993 TTTTTTAAA-TTCTG--TTTTTCAAAAATCAACTCATATTGAGAGAGGCGAGTTGAGCCTCGGGC
1 TTTTTTAAATTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTC
*
20478055 ACATGCTGAGGAATT
66 ACATGCTGAGGTATT
* * *
20478070 TTTTTT-AATTTCTATTTTTTTTAAAAAAAACTCTACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TTTTTTAAATTTCT-GTTTTTTT--CAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* * * *
20478134 GGACATATACCGAGGTA-T
62 GGTCACATGCTGAGGTATT
* * **
20478152 TTTTTTAAATTTCTG--TTTTTCAAAAATCAACTCATATTGCGAGAGGTCACTTGAGCCTCGAAC
1 TTTTTTAAATTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTC
* *
20478215 ACATGCCGATGTATT
66 ACATGCTGAGGTATT
* *
20478230 TCTTTTAAATTTCTG--TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGATGAGCCTCAGGT
1 TTTTTTAAATTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGT
20478293 CACATGCTGAGGTA-T
65 CACATGCTGAGGTATT
* *
20478308 TTTTTTAAATTTCTATTTTTTTGCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGA
1 TTTTTTAAATTTCTGTTTTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGT
*
20478373 CACATGCCGAGGTATT
65 CACATGCTGAGGTATT
***
20478389 TCTTTTT-AATTTCTGTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
1 T-TTTTTAAATTTCTGTTTTT-TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G
*
20478453 GTCACACGCTGAGGTATT
63 GTCACATGCTGAGGTATT
20478471 TTTTTTAAATTTCTGTTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1 TTTTTTAAATTTCTGTTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG
*
20478536 TCACACGCTGAGGTATT
64 TCACATGCTGAGGTATT
20478553 TTTTTTAAATTTCTGTTTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TTTTTTAAATTTCTGTTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG
*
20478618 TCACACGAC-GAGGTA--
64 TCACATG-CTGAGGTATT
* *
20478633 TTTTTT-AATTTTTGTTTTTTTTC-TAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TTTTTTAAATTTCTG-TTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
20478693 AAGTCGCAAG
Statistics
Matches: 625, Mismatches: 52, Indels: 47
0.86 0.07 0.06
Matches are distributed among these distances:
76 15 0.02
77 95 0.15
78 111 0.18
79 31 0.05
80 46 0.07
81 95 0.15
82 182 0.29
83 50 0.08
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (80 bp):
TTTTTTAAATTTCTGTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTC
ACATGCTGAGGTATT
Found at i:20481738 original size:59 final size:58
Alignment explanation
Indices: 20481667--20481805 Score: 179
Period size: 59 Copynumber: 2.4 Consensus size: 58
20481657 AAAAATTCAA
* * * * *
20481667 AAAATTATATTTTGACCCCTAAACTTCTTGAAATCATATTTTGACCCCTAAATTTTTC
1 AAAATTAAATTTTGACCCCTAAAATTCTTGAAATCACATTTTGACCCATAAAATTTTC
* * *
20481725 TAAAATTAAATTTTGACCCCTAAAATTTTTGAAATTACATTTTGATCCATAAAATTTTC
1 -AAAATTAAATTTTGACCCCTAAAATTCTTGAAATCACATTTTGACCCATAAAATTTTC
* *
20481784 AAAATTACATTTTGACTCCTAA
1 AAAATTAAATTTTGACCCCTAA
20481806 GTTTTCTCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
58 20 0.29
59 50 0.71
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (58 bp):
AAAATTAAATTTTGACCCCTAAAATTCTTGAAATCACATTTTGACCCATAAAATTTTC
Found at i:20481740 original size:30 final size:30
Alignment explanation
Indices: 20481667--20481832 Score: 160
Period size: 29 Copynumber: 5.6 Consensus size: 30
20481657 AAAAATTCAA
* *
20481667 AAAATTATATTTTGACCCCTAAACTTCT-T
1 AAAATTATATTTTGACCCCTAAAATTTTCT
* * *
20481696 GAAATCATATTTTGACCCCTAAATTTTTCT
1 AAAATTATATTTTGACCCCTAAAATTTTCT
*
20481726 AAAATTAAATTTTGACCCCTAAAATTTT-T
1 AAAATTATATTTTGACCCCTAAAATTTTCT
* * * *
20481755 GAAATTACATTTTGATCCATAAAATTTTC-
1 AAAATTATATTTTGACCCCTAAAATTTTCT
* * *
20481784 AAAATTACATTTTGACTCCT-AAGTTTTCT
1 AAAATTATATTTTGACCCCTAAAATTTTCT
* *
20481813 CAAAAGTATATTTTGGCCCC
1 -AAAATTATATTTTGACCCC
20481833 AGAAGTTTTG
Statistics
Matches: 112, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
28 7 0.06
29 65 0.58
30 40 0.36
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCTAAAATTTTCT
Found at i:20482485 original size:28 final size:28
Alignment explanation
Indices: 20482453--20482507 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
20482443 CCAGGCCCAA
*
20482453 CAGCAGGCCAGCAGGCCCATCCCAGCAT
1 CAGCAGGCCACCAGGCCCATCCCAGCAT
* * *
20482481 CAGCAGGCCCCCAGGCCCGTTCCAGCA
1 CAGCAGGCCACCAGGCCCATCCCAGCA
20482508 GCAGGCCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.22, C:0.45, G:0.25, T:0.07
Consensus pattern (28 bp):
CAGCAGGCCACCAGGCCCATCCCAGCAT
Found at i:20482570 original size:7 final size:7
Alignment explanation
Indices: 20482553--20482608 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
20482543 AAAGGAAGGA
20482553 AAAAAAGG
1 AAAAAA-G
20482561 AAAAAAG
1 AAAAAAG
20482568 AAAGAAA-
1 AAA-AAAG
20482575 AAAAGAA-
1 AAAA-AAG
20482582 AAAAAAG
1 AAAAAAG
*
20482589 AGAAAAG
1 AAAAAAG
*
20482596 AGAAAAG
1 AAAAAAG
20482603 AAAAAA
1 AAAAAA
20482609 AAAGCAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
6 3 0.07
7 31 0.72
8 9 0.21
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:20482587 original size:23 final size:23
Alignment explanation
Indices: 20482561--20482611 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
20482551 GAAAAAAAGG
20482561 AAAAAAG-AAAGAAAAAAAGAAAA
1 AAAAAAGAAAAG-AAAAAAGAAAA
* *
20482584 AAAAGAGAAAAGAGAAAAGAAAA
1 AAAAAAGAAAAGAAAAAAGAAAA
20482607 AAAAA
1 AAAAA
20482612 GCAAAAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAAAGAAAAAAGAAAA
Found at i:20482594 original size:30 final size:30
Alignment explanation
Indices: 20482552--20482609 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
20482542 TAAAGGAAGG
20482552 AAAAAAAGGAAAAAAG-AAAGAAAAAAAGA
1 AAAAAAAGGAAAAAAGAAAAGAAAAAAAGA
*
20482581 AAAAAAAGAGAAAAGAGAAAAGAAAAAAA
1 AAAAAAAG-GAAAAAAGAAAAGAAAAAAA
20482610 AAGCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 8 0.31
30 7 0.27
31 11 0.42
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (30 bp):
AAAAAAAGGAAAAAAGAAAAGAAAAAAAGA
Found at i:20483544 original size:20 final size:20
Alignment explanation
Indices: 20483519--20483643 Score: 81
Period size: 20 Copynumber: 6.5 Consensus size: 20
20483509 CGTTCGAAAC
*
20483519 AATACAAAAAATTATGATAG
1 AATACAAAAAATTATGAGAG
20483539 AATACAAATAAA-TATGAGA-
1 AATACAAA-AAATTATGAGAG
*
20483558 AAGTACAAAAAA-TATAAG-G
1 AA-TACAAAAAATTATGAGAG
*
20483577 AAGTAC-CAAAATTATGAGA-
1 AA-TACAAAAAATTATGAGAG
* * *
20483596 AAGTACCAAAACTTA-GA-TG
1 AA-TACAAAAAATTATGAGAG
*
20483615 --TATAAAAAATTATGAGAG
1 AATACAAAAAATTATGAGAG
20483633 AATACAAAAAA
1 AATACAAAAAA
20483644 AAAAATGAGG
Statistics
Matches: 82, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
16 9 0.11
17 2 0.02
18 5 0.06
19 29 0.35
20 34 0.41
21 3 0.04
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.21
Consensus pattern (20 bp):
AATACAAAAAATTATGAGAG
Found at i:20483572 original size:19 final size:19
Alignment explanation
Indices: 20483521--20483643 Score: 85
Period size: 19 Copynumber: 6.5 Consensus size: 19
20483511 TTCGAAACAA
*
20483521 TACAAAAAATTATGATAGAA-
1 TACAAAAAA-TATGAGA-AAG
20483541 TACAAATAAATATGAGAAAG
1 TACAAA-AAATATGAGAAAG
* *
20483561 TACAAAAAATATAAGGAAG
1 TACAAAAAATATGAGAAAG
* *
20483580 TACCAAAATTATGAGAAAG
1 TACAAAAAATATGAGAAAG
* * *
20483599 TACCAAAACT-T-AG-ATG
1 TACAAAAAATATGAGAAAG
*
20483615 TATAAAAAATTATGAGAGAA-
1 TACAAAAAA-TATGAGA-AAG
20483635 TACAAAAAA
1 TACAAAAAA
20483644 AAAAATGAGG
Statistics
Matches: 82, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
16 8 0.10
17 3 0.04
18 2 0.02
19 39 0.48
20 26 0.32
21 4 0.05
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.21
Consensus pattern (19 bp):
TACAAAAAATATGAGAAAG
Found at i:20483671 original size:20 final size:18
Alignment explanation
Indices: 20483519--20483713 Score: 81
Period size: 19 Copynumber: 10.1 Consensus size: 18
20483509 CGTTCGAAAC
*
20483519 AATACAAAAAATTATGATAG
1 AATAC-AAAAATTATGA-GG
* *
20483539 AATACAAATAAATATGAGA
1 AATACAAA-AATTATGAGG
* *
20483558 AAGTACAAAAAATATAAGG
1 AA-TACAAAAATTATGAGG
* *
20483577 AAGTACCAAAATTATGAGA
1 AA-TACAAAAATTATGAGG
* *
20483596 AAGTACCAAAACTTA-GATG
1 AA-TA-CAAAAATTATGAGG
*
20483615 TATA-AAAAATTATGAGAG
1 AATACAAAAATTATGAG-G
**
20483633 AATACAAAAAAAAAAATGAGG
1 AATAC---AAAAATTATGAGG
20483654 AAGTAGCAAAAATTATGATCGG
1 AA-TA-CAAAAATTATGA--GG
*
20483676 -ATACCAAAAGTTATGAGG
1 AATA-CAAAAATTATGAGG
* *
20483694 GATAGCAAAAAATATGAGG
1 AATA-CAAAAATTATGAGG
20483713 A
1 A
20483714 TGTAAATGTA
Statistics
Matches: 134, Mismatches: 27, Indels: 29
0.71 0.14 0.15
Matches are distributed among these distances:
16 7 0.05
17 2 0.01
18 8 0.06
19 51 0.38
20 47 0.35
21 4 0.03
22 14 0.10
23 1 0.01
ACGTcount: A:0.56, C:0.07, G:0.17, T:0.20
Consensus pattern (18 bp):
AATACAAAAATTATGAGG
Found at i:20483711 original size:19 final size:19
Alignment explanation
Indices: 20483641--20483712 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 19
20483631 AGAATACAAA
* *
20483641 AAAAAAAATGAGGAAGTAGC
1 AAAAAATATGAGGGA-TAGC
* * *
20483661 AAAAATTATGATCGGATACC
1 AAAAAATATGA-GGGATAGC
**
20483681 AAAAGTTATGAGGGATAGC
1 AAAAAATATGAGGGATAGC
20483700 AAAAAATATGAGG
1 AAAAAATATGAGG
20483713 ATGTAAATGT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
19 17 0.41
20 22 0.54
21 2 0.05
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (19 bp):
AAAAAATATGAGGGATAGC
Found at i:20483747 original size:20 final size:22
Alignment explanation
Indices: 20483717--20483762 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
20483707 ATGAGGATGT
20483717 AAATGTATGA-GG-ATACATAAA
1 AAATGTATGAGGGAATAC-TAAA
20483738 AAAT-TATGAGGGAATACTAAA
1 AAATGTATGAGGGAATACTAAA
20483759 AAAT
1 AAAT
20483763 ATTAAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.22
21 14 0.61
22 4 0.17
ACGTcount: A:0.54, C:0.04, G:0.17, T:0.24
Consensus pattern (22 bp):
AAATGTATGAGGGAATACTAAA
Found at i:20483901 original size:19 final size:16
Alignment explanation
Indices: 20483857--20483889 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
20483847 AAGTACAAAA
20483857 AAAAATATGAGGATGT
1 AAAAATATGAGGATGT
*
20483873 AAAAATATGATGATGT
1 AAAAATATGAGGATGT
20483889 A
1 A
20483890 CCAAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (16 bp):
AAAAATATGAGGATGT
Found at i:20483915 original size:20 final size:20
Alignment explanation
Indices: 20483892--20484116 Score: 90
Period size: 20 Copynumber: 10.9 Consensus size: 20
20483882 ATGATGTACC
20483892 AAAAATATGAGAGAATACAAAAA
1 AAAAATATGAGAGAATAC---AA
* * * *
20483915 AAAAAAAGGAGTGAATAC-T
1 AAAAATATGAGAGAATACAA
*
20483934 AAAAATATGA-AGAAGTACTA
1 AAAAATATGAGAGAA-TACAA
* *
20483954 AATATTATGAGAGAATATC-A
1 AAAAATATGAGAGAATA-CAA
* ** *
20483974 TAAAACCTGAG-GAAGTAC-C
1 AAAAATATGAGAGAA-TACAA
20483993 AAAAA-ATGAGA-AAGTACAA
1 AAAAATATGAGAGAA-TACAA
*
20484012 AAAATTATGAGAGAATACAACCA
1 AAAAATATGAGAGAATAC-A--A
20484035 AAAAATTATGAGAGAATACACA
1 AAAAA-TATGAGAGAATACA-A
*
20484057 AAAAATAT-ATGAAAATGTACAA
1 AAAAATATGA-GAGAA--TACAA
* **
20484079 AAAATTATGAG-GAAGTGTAA
1 AAAAATATGAGAGAA-TACAA
*
20484099 AAAATTATGAGAGAATAC
1 AAAAATATGAGAGAATAC
20484117 CAAATAACAT
Statistics
Matches: 156, Mismatches: 28, Indels: 39
0.70 0.13 0.17
Matches are distributed among these distances:
18 13 0.08
19 23 0.15
20 45 0.29
21 20 0.13
22 16 0.10
23 26 0.17
24 13 0.08
ACGTcount: A:0.58, C:0.07, G:0.16, T:0.19
Consensus pattern (20 bp):
AAAAATATGAGAGAATACAA
Found at i:20483919 original size:58 final size:57
Alignment explanation
Indices: 20483798--20483970 Score: 141
Period size: 58 Copynumber: 2.9 Consensus size: 57
20483788 AGAATTCCAT
* * * * * *
20483798 AAAACATGAGGAAGTATAAAACAATGAGGATGTACCAATAAATTTGGGA-AAGTACAAAAA
1 AAAAAATGAGGATGTA-AAAA-TATGAAGATGTACCAA-AAATATGAGAGAA-TACAAAAA
* *
20483858 AAAATATGAGGATGTAAAAATATGATGATGTACCAAAAATATGAGAGAATACAAAAAA
1 AAAAAATGAGGATGTAAAAATATGAAGATGTACCAAAAATATGAGAGAATAC-AAAAA
* * * * *
20483916 AAAAAAGGAGTGAATACTAAAAATATGAAGAAGTACTAAATATTATGAGAGAATA
1 AAAAAATGAG-G-AT-GTAAAAATATGAAGATGTACCAAA-AATATGAGAGAATA
20483971 TCATAAAACC
Statistics
Matches: 94, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
57 11 0.12
58 29 0.31
59 5 0.05
60 16 0.17
61 20 0.21
62 13 0.14
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.20
Consensus pattern (57 bp):
AAAAAATGAGGATGTAAAAATATGAAGATGTACCAAAAATATGAGAGAATACAAAAA
Found at i:20484014 original size:17 final size:18
Alignment explanation
Indices: 20483981--20484016 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20483971 TCATAAAACC
*
20483981 TGAGGAAGTACCAAAAAA
1 TGAGAAAGTACCAAAAAA
20483999 TGAGAAAGTA-CAAAAAA
1 TGAGAAAGTACCAAAAAA
20484016 T
1 T
20484017 TATGAGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.58, C:0.08, G:0.19, T:0.14
Consensus pattern (18 bp):
TGAGAAAGTACCAAAAAA
Found at i:20484041 original size:24 final size:22
Alignment explanation
Indices: 20484008--20484120 Score: 112
Period size: 24 Copynumber: 5.2 Consensus size: 22
20483998 ATGAGAAAGT
20484008 ACAAAAAATTATGAGAGAATAC
1 ACAAAAAATTATGAGAGAATAC
20484030 AACCAAAAAATTATGAGAGAATAC
1 -A-CAAAAAATTATGAGAGAATAC
**
20484054 ACAAAAAATATATGA-A-AATGT
1 ACAAAAAAT-TATGAGAGAATAC
20484075 ACAAAAAATTATGAG-GAAGT--
1 ACAAAAAATTATGAGAGAA-TAC
**
20484095 GTAAAAAATTATGAGAGAATAC
1 ACAAAAAATTATGAGAGAATAC
20484117 -CAAA
1 ACAAA
20484121 TAACATAAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
20 19 0.25
21 20 0.26
22 10 0.13
23 7 0.09
24 21 0.27
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.19
Consensus pattern (22 bp):
ACAAAAAATTATGAGAGAATAC
Found at i:20484101 original size:21 final size:21
Alignment explanation
Indices: 20483981--20484114 Score: 93
Period size: 20 Copynumber: 6.4 Consensus size: 21
20483971 TCATAAAACC
*
20483981 TGAGGAA-GTACCAAAAA--A
1 TGAGGAATGTACAAAAAATTA
*
20483999 TGA-GAAAGTACAAAAAATTA
1 TGAGGAATGTACAAAAAATTA
**
20484019 TGAGAGAATACAACCAAAAAATTA
1 TGAG-GAAT-GTA-CAAAAAATTA
**
20484043 TGAGAGAATACACAAAAAATATA
1 TGAG-GAATGTACAAAAAAT-TA
*
20484066 TGA-AAATGTACAAAAAATTA
1 TGAGGAATGTACAAAAAATTA
20484086 TGAGGAAGTGT--AAAAAATTA
1 TGAGGAA-TGTACAAAAAATTA
20484106 TGAGAGAAT
1 TGAG-GAAT
20484115 ACCAAATAAC
Statistics
Matches: 95, Mismatches: 10, Indels: 20
0.76 0.08 0.16
Matches are distributed among these distances:
17 3 0.03
18 12 0.13
20 23 0.24
21 17 0.18
22 14 0.15
23 7 0.07
24 19 0.20
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.19
Consensus pattern (21 bp):
TGAGGAATGTACAAAAAATTA
Found at i:20494705 original size:21 final size:21
Alignment explanation
Indices: 20494679--20494734 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
20494669 CACCATTGTT
**
20494679 TCTAATCTCAGTGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
20494700 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
*
20494721 ACTAATCTCACCGC
1 TCTAATCTCACCGC
20494735 CACCGCTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.32, G:0.11, T:0.29
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAGTA
Found at i:20497194 original size:48 final size:48
Alignment explanation
Indices: 20497123--20497280 Score: 203
Period size: 49 Copynumber: 3.2 Consensus size: 48
20497113 GAACTTGTAC
*
20497123 ATTCTACCATCCTGGTTGGCCCGACAACGATTGCTTTCACTA-CTGCAT
1 ATTCTACCATCCTGG-TGGCCCGACAACGATTGCTTTCACTATTTGCAT
* *
20497171 ATTCTACCATCCCAGGTGGCCCGACAACGATAGCTTTCACTATTTGCAT
1 ATTCTACCAT-CCTGGTGGCCCGACAACGATTGCTTTCACTATTTGCAT
* * * *
20497220 ATTCTACCATCCTGAATGGCTCGACAATGA-TGATTTCCACTATTTGCAT
1 ATTCTACCATCCTG-GTGGCCCGACAACGATTGCTTT-CACTATTTGCAT
20497269 ATTCTACCATCC
1 ATTCTACCATCC
20497281 CGAGTGACCC
Statistics
Matches: 97, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
48 42 0.43
49 55 0.57
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.32
Consensus pattern (48 bp):
ATTCTACCATCCTGGTGGCCCGACAACGATTGCTTTCACTATTTGCAT
Found at i:20499432 original size:41 final size:41
Alignment explanation
Indices: 20499382--20499499 Score: 139
Period size: 41 Copynumber: 2.9 Consensus size: 41
20499372 GTGAAATTAT
* *
20499382 TCAGACTATACGTCTAGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGACTATACGCCTAGCAGGCTAAGTGCCGGTGAACGGAA
* *
20499423 TCAGGCTATAGGCCTAGCAGGCTAAGTGCCGGTGAACGGAA
1 TCAGACTATACGCCTAGCAGGCTAAGTGCCGGTGAACGGAA
* * * * *
20499464 TTAAACTATAAGCCTATCAGG-TGAAGTGCCAGTGAA
1 TCAGACTATACGCCTAGCAGGCT-AAGTGCCGGTGAA
20499500 TCTGTTTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
40 1 0.02
41 65 0.98
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (41 bp):
TCAGACTATACGCCTAGCAGGCTAAGTGCCGGTGAACGGAA
Found at i:20500470 original size:49 final size:49
Alignment explanation
Indices: 20500398--20500612 Score: 268
Period size: 49 Copynumber: 4.4 Consensus size: 49
20500388 CGGTGTTACA
* * * *
20500398 CCGACAACGATGTTTTTCACTATTTGCATATTTTACCATCTTGGGTGGC
1 CCGACAACGATGGTTTTCACTATTTACATATTCTACCATCCTGGGTGGC
* **
20500447 CCGACAACGATGGTTTTCACTATTTGCATATTCTACCATCCCAGGTGGC
1 CCGACAACGATGGTTTTCACTATTTACATATTCTACCATCCTGGGTGGC
* * * * *
20500496 TCGATAACGATAGTTTTCAGTATTTACATATTCTACCATCTTGGGTGGC
1 CCGACAACGATGGTTTTCACTATTTACATATTCTACCATCCTGGGTGGC
* * * *
20500545 ACGACAACAATGGCTTTCACTATTTACATATTCTACCATCCTGAGTGGC
1 CCGACAACGATGGTTTTCACTATTTACATATTCTACCATCCTGGGTGGC
**
20500594 CTAACAACGATGGTTTTCA
1 CCGACAACGATGGTTTTCA
20500613 ATCACTATAT
Statistics
Matches: 140, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 140 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (49 bp):
CCGACAACGATGGTTTTCACTATTTACATATTCTACCATCCTGGGTGGC
Found at i:20501282 original size:85 final size:85
Alignment explanation
Indices: 20501139--20501312 Score: 321
Period size: 85 Copynumber: 2.0 Consensus size: 85
20501129 GGGATACTAT
*
20501139 ACTTTTCATTTGCAACATAATCTCATGAAAATTTTAAATTTATTCAATTTAGTCCTTAATGTTAC
1 ACTTTTCATCTGCAACATAATCTCATGAAAATTTTAAATTTATTCAATTTAGTCCTTAATGTTAC
*
20501204 AAAATTATCTAACAAGTTTA
66 AAAATTATCTAACAAGCTTA
*
20501224 ACTTTTCATCTGCAACATAATCTCATGAAAATTTTCAATTTATTCAATTTAGTCCTTAATGTTAC
1 ACTTTTCATCTGCAACATAATCTCATGAAAATTTTAAATTTATTCAATTTAGTCCTTAATGTTAC
20501289 AAAATTATCTAACAAGCTTA
66 AAAATTATCTAACAAGCTTA
20501309 ACTT
1 ACTT
20501313 AGTTTCCAAT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (85 bp):
ACTTTTCATCTGCAACATAATCTCATGAAAATTTTAAATTTATTCAATTTAGTCCTTAATGTTAC
AAAATTATCTAACAAGCTTA
Found at i:20504546 original size:12 final size:12
Alignment explanation
Indices: 20504518--20504561 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
20504508 ATGTTATTTT
*
20504518 ATAATAAAA-AC
1 ATAATAAAAGAA
20504529 ATAATAAAAGAA
1 ATAATAAAAGAA
**
20504541 ATAATAAAAGTT
1 ATAATAAAAGAA
20504553 ATAATAAAA
1 ATAATAAAA
20504562 AAAAGAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (12 bp):
ATAATAAAAGAA
Found at i:20512796 original size:15 final size:17
Alignment explanation
Indices: 20512756--20512797 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
20512746 AAAAATGTTT
*
20512756 TGAGACTCACATGGCCG
1 TGAGACTCACACGGCCG
*
20512773 TGTGACTCACACGG-C-
1 TGAGACTCACACGGCCG
20512788 TGAGACTCAC
1 TGAGACTCAC
20512798 GCCCGTGTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 9 0.41
16 1 0.05
17 12 0.55
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.19
Consensus pattern (17 bp):
TGAGACTCACACGGCCG
Found at i:20516255 original size:27 final size:27
Alignment explanation
Indices: 20516214--20516302 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 27
20516204 TTGTTACAAC
* **
20516214 TATTCTTTTAGAGTTCGCCATGAAGGT
1 TATTCTTTTATAGTTCGCCACAAAGGT
* *
20516241 TATTCTTTTTTAGTTCGCCACAAAGGC
1 TATTCTTTTATAGTTCGCCACAAAGGT
* *
20516268 TATTCTTTCATAGTTCGCAACAAAGGT
1 TATTCTTTTATAGTTCGCCACAAAGGT
20516295 TATTCTTT
1 TATTCTTT
20516303 CATGTCATGT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.43
Consensus pattern (27 bp):
TATTCTTTTATAGTTCGCCACAAAGGT
Found at i:20517051 original size:49 final size:50
Alignment explanation
Indices: 20516974--20517074 Score: 168
Period size: 49 Copynumber: 2.0 Consensus size: 50
20516964 CAATAACAAC
* *
20516974 CACTGATTTGCATATTCTACCATCCTGGGTGGCCTGACAATGATGGTTTT
1 CACTGATTTGCATATTCTACCATCCTGGGTGGCCTGACAACGATGATTTT
*
20517024 CACT-ATTTGCATATTCTACCATTCTGGGTGGCCTGACAACGATGATTTT
1 CACTGATTTGCATATTCTACCATCCTGGGTGGCCTGACAACGATGATTTT
20517073 CA
1 CA
20517075 ATCACTATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 44 0.92
50 4 0.08
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.36
Consensus pattern (50 bp):
CACTGATTTGCATATTCTACCATCCTGGGTGGCCTGACAACGATGATTTT
Found at i:20530401 original size:16 final size:17
Alignment explanation
Indices: 20530380--20530413 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
20530370 CTAACTTTAT
20530380 GAAAAAAAA-TATTGTA
1 GAAAAAAAATTATTGTA
20530396 GAAAAAAAATTATTGTA
1 GAAAAAAAATTATTGTA
20530413 G
1 G
20530414 CCATTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (17 bp):
GAAAAAAAATTATTGTA
Found at i:20530403 original size:17 final size:17
Alignment explanation
Indices: 20530381--20530413 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20530371 TAACTTTATG
20530381 AAAAAAAATATTGTAGA
1 AAAAAAAATATTGTAGA
*
20530398 AAAAAAATTATTGTAG
1 AAAAAAAATATTGTAG
20530414 CCATTCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (17 bp):
AAAAAAAATATTGTAGA
Found at i:20530615 original size:23 final size:22
Alignment explanation
Indices: 20530570--20530615 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
20530560 ACTTATTAAA
*
20530570 ATTTTTAAAAATTAAAAGTATT
1 ATTTTTAAAAATTAAAAATATT
20530592 ATTTTTAAAAATTAAAAATCATT
1 ATTTTTAAAAATTAAAAAT-ATT
20530615 A
1 A
20530616 AAATTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
ATTTTTAAAAATTAAAAATATT
Found at i:20533782 original size:20 final size:19
Alignment explanation
Indices: 20533757--20533804 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
20533747 AGGATAAATT
20533757 AAAAAAAATGA-AGAAATACC
1 AAAAAAAATGAGAG-AATA-C
*
20533777 AAAAAAATTGAGAGAATAC
1 AAAAAAAATGAGAGAATAC
20533796 AAAAAAAAT
1 AAAAAAAAT
20533805 AAAAGAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 14 0.56
21 2 0.08
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.12
Consensus pattern (19 bp):
AAAAAAAATGAGAGAATAC
Found at i:20534460 original size:39 final size:37
Alignment explanation
Indices: 20534417--20534528 Score: 111
Period size: 36 Copynumber: 3.0 Consensus size: 37
20534407 ATTTATAAGA
*
20534417 AAGTACCAAAATTTATGAGCGAATACAAAAACGATGAGG
1 AAGTACCAAAAATTATGAG-GAATACAAAAA-GATGAGG
* ** * *
20534456 AAGTACCAAAAGTTATGAGG-ATGTAAATATATGAGG
1 AAGTACCAAAAATTATGAGGAATACAAAAAGATGAGG
* *
20534492 ATGCACCAAAAATTATGAGGGAATACAAAAA-ATGAGG
1 AAGTACCAAAAATTATGA-GGAATACAAAAAGATGAGG
20534529 GGATACTAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
36 21 0.35
37 14 0.23
38 7 0.12
39 18 0.30
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.20
Consensus pattern (37 bp):
AAGTACCAAAAATTATGAGGAATACAAAAAGATGAGG
Found at i:20534466 original size:19 final size:21
Alignment explanation
Indices: 20534417--20534466 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 21
20534407 ATTTATAAGA
**
20534417 AAGTACCAAAATTTATGAGCG
1 AAGTACCAAAATCGATGAGCG
*
20534438 AA-TA-CAAAAACGATGAG-G
1 AAGTACCAAAATCGATGAGCG
20534456 AAGTACCAAAA
1 AAGTACCAAAA
20534467 GTTATGAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
18 3 0.12
19 12 0.50
20 7 0.29
21 2 0.08
ACGTcount: A:0.52, C:0.14, G:0.18, T:0.16
Consensus pattern (21 bp):
AAGTACCAAAATCGATGAGCG
Found at i:20534473 original size:20 final size:20
Alignment explanation
Indices: 20534397--20534476 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
20534387 AAATACAAGT
* * * *
20534397 AAGTACCCAAATTTATAAGA
1 AAGTACCAAAAGTTATGAGG
*
20534417 AAGTACCAAAATTTATGAGCG
1 AAGTACCAAAAGTTATGAG-G
*
20534438 AA-TACAAAAACG--ATGAGG
1 AAGTACCAAAA-GTTATGAGG
20534456 AAGTACCAAAAGTTATGAGG
1 AAGTACCAAAAGTTATGAGG
20534476 A
1 A
20534477 TGTAAATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
18 4 0.08
19 12 0.24
20 31 0.63
21 2 0.04
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.20
Consensus pattern (20 bp):
AAGTACCAAAAGTTATGAGG
Found at i:20534522 original size:20 final size:18
Alignment explanation
Indices: 20534498--20534540 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
20534488 GAGGATGCAC
20534498 CAAAAATTATGAGGGAATA
1 CAAAAA-TATGAGGGAATA
*
20534517 CAAAAA-ATGAGGGGATA
1 CAAAAATATGAGGGAATA
20534534 CTAAAAA
1 C-AAAAA
20534541 ATATTAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 11 0.50
18 5 0.23
19 6 0.27
ACGTcount: A:0.56, C:0.07, G:0.21, T:0.16
Consensus pattern (18 bp):
CAAAAATATGAGGGAATA
Found at i:20534528 original size:17 final size:18
Alignment explanation
Indices: 20534506--20534542 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
20534496 ACCAAAAATT
20534506 ATGAGGGAATAC-AAAAA
1 ATGAGGGAATACTAAAAA
*
20534523 ATGAGGGGATACTAAAAA
1 ATGAGGGAATACTAAAAA
20534541 AT
1 AT
20534543 ATTAGAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.54, C:0.05, G:0.24, T:0.16
Consensus pattern (18 bp):
ATGAGGGAATACTAAAAA
Found at i:20534575 original size:20 final size:20
Alignment explanation
Indices: 20534496--20534581 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 20
20534486 ATGAGGATGC
*
20534496 ACCAAAAATTATGAGGGAAT
1 ACCAAAAATTATGAGAGAAT
* *
20534516 A-CAAAAA--ATGAGGGGAT
1 ACCAAAAATTATGAGAGAAT
* * *
20534533 ACTAAAAAATATTAGA-AAGT
1 ACCAAAAATTATGAGAGAA-T
20534553 ACCAAAAATTATGAGAGAAT
1 ACCAAAAATTATGAGAGAAT
20534573 ACCATAAAA
1 ACCA-AAAA
20534582 CTTGAGGAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
17 10 0.19
18 5 0.10
19 7 0.13
20 24 0.46
21 6 0.12
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.19
Consensus pattern (20 bp):
ACCAAAAATTATGAGAGAAT
Found at i:20534674 original size:152 final size:151
Alignment explanation
Indices: 20534471--20534758 Score: 395
Period size: 152 Copynumber: 1.9 Consensus size: 151
20534461 CCAAAAGTTA
* * * * *
20534471 TGAGGATGTAAATATATGAGGATGCACCAAAAATTATGAGGGAATACAAAAA-ATGAGGGGATAC
1 TGAGGACGTAAAAATATGAGGATGCACCAAAAATTATGAGAGAATAAAAAAACACGAGGGGATA-
* *
20534535 TAAAAAATATTA-GAAAGTACCAAAAATTATGAGAGAATACCATAAAACTTGAGGAAGTA-TAAA
65 TAAAAAATATGATG-AAGTACCAAAAATTATGAGAGAATACCATAAAACTTGAGGAAGTACCAAA
20534598 AAAATGAGGATGTACCGATAATT
129 AAAATGAGGATGTACCGATAATT
* *
20534621 TGAGGACGTAAAAATATGATGATGTACCAAAAA-TATGAGAGAATGCCAAAAAAACACGAGGGGA
1 TGAGGACGTAAAAATATGAGGATGCACCAAAAATTATGAGAGAAT---AAAAAAACACGAGGGGA
* * *
20534685 TATTAAAAATATGATGAAGTACTAAATATTATGAGAGAATACCATAAAACTTGAGGAAGTACCAA
63 TATAAAAAATATGATGAAGTACCAAAAATTATGAGAGAATACCATAAAACTTGAGGAAGTACCAA
20534750 AAAAATGAG
128 AAAAATGAG
20534759 AAAGTACAAA
Statistics
Matches: 120, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
149 10 0.08
150 29 0.24
152 59 0.49
153 22 0.18
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.21
Consensus pattern (151 bp):
TGAGGACGTAAAAATATGAGGATGCACCAAAAATTATGAGAGAATAAAAAAACACGAGGGGATAT
AAAAAATATGATGAAGTACCAAAAATTATGAGAGAATACCATAAAACTTGAGGAAGTACCAAAAA
AATGAGGATGTACCGATAATT
Found at i:20534768 original size:18 final size:19
Alignment explanation
Indices: 20534736--20534771 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20534726 CCATAAAACT
*
20534736 TGAGGAAGTACCAAAAAAA
1 TGAGAAAGTACCAAAAAAA
20534755 TGAGAAAGTA-CAAAAAA
1 TGAGAAAGTACCAAAAAA
20534772 TTATGAGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.61, C:0.08, G:0.19, T:0.11
Consensus pattern (19 bp):
TGAGAAAGTACCAAAAAAA
Found at i:20534777 original size:20 final size:20
Alignment explanation
Indices: 20534689--20534779 Score: 66
Period size: 20 Copynumber: 4.6 Consensus size: 20
20534679 AGGGGATATT
*
20534689 AAAAATATGATG-AAGTACTA
1 AAAAATATGA-GAAAGTACCA
* *
20534709 AATATTATGAGAGAA-TACCA
1 AAAAATATGAGA-AAGTACCA
* *
20534729 TAAAACT-TGAGGAAGTACCA
1 -AAAAATATGAGAAAGTACCA
20534749 AAAAA-ATGAGAAAGTA-CA
1 AAAAATATGAGAAAGTACCA
20534767 AAAAATTATGAGA
1 AAAAA-TATGAGA
20534780 GTGTAACACT
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
18 7 0.12
19 16 0.29
20 27 0.48
21 6 0.11
ACGTcount: A:0.55, C:0.08, G:0.16, T:0.21
Consensus pattern (20 bp):
AAAAATATGAGAAAGTACCA
Found at i:20535485 original size:34 final size:34
Alignment explanation
Indices: 20535447--20535511 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
20535437 CACATGTCAA
20535447 ATCAAAATGTCATATTTCCAGAAACATATACTGG
1 ATCAAAATGTCATATTTCCAGAAACATATACTGG
*
20535481 ATCAAAATGTCATATTTTCAGAAACATATAC
1 ATCAAAATGTCATATTTCCAGAAACATATAC
20535512 CATAGCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (34 bp):
ATCAAAATGTCATATTTCCAGAAACATATACTGG
Found at i:20535521 original size:34 final size:34
Alignment explanation
Indices: 20535449--20535528 Score: 115
Period size: 34 Copynumber: 2.4 Consensus size: 34
20535439 CATGTCAAAT
** *
20535449 CAAAATGTCATATTTCCAGAAACATATACTGGAT
1 CAAAATGTCATATTTCCAGAAACATATACCAGAG
* *
20535483 CAAAATGTCATATTTTCAGAAACATATACCATAG
1 CAAAATGTCATATTTCCAGAAACATATACCAGAG
20535517 CAAAATGTCATA
1 CAAAATGTCATA
20535529 ACATATCAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (34 bp):
CAAAATGTCATATTTCCAGAAACATATACCAGAG
Found at i:20536712 original size:19 final size:18
Alignment explanation
Indices: 20536688--20536795 Score: 82
Period size: 19 Copynumber: 5.9 Consensus size: 18
20536678 TTTTTTTATA
20536688 TTTTTAATTTTAAAATACT
1 TTTTTAATTTTAAAATA-T
20536707 TTTTTAATTTTAAAATAT
1 TTTTTAATTTTAAAATAT
* **
20536725 TTTTAAAATACCTTTTTAAT-T
1 TTTT-TAAT---TTTAAAATAT
20536746 TTTTTAATTTTAAAATA-
1 TTTTTAATTTTAAAATAT
**
20536763 TTTTTAA-AAT-AAAT-T
1 TTTTTAATTTTAAAATAT
20536778 TTTTTAATTTTTAAAATA
1 TTTTTAA-TTTTAAAATA
20536796 AATTTTTGGT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
15 11 0.16
16 1 0.01
17 14 0.20
18 9 0.13
19 20 0.29
20 3 0.04
21 5 0.07
22 6 0.09
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTAATTTTAAAATAT
Found at i:20536780 original size:39 final size:40
Alignment explanation
Indices: 20536706--20536789 Score: 134
Period size: 39 Copynumber: 2.1 Consensus size: 40
20536696 TTTAAAATAC
**
20536706 TTTTTTAATTTTAAAATATTTTTAAAAT-ACCTTTTTAAT
1 TTTTTTAATTTTAAAATATTTTTAAAATAAATTTTTTAAT
20536745 TTTTTTAATTTTAAAATATTTTTAAAATAAATTTTTTTAAT
1 TTTTTTAATTTTAAAATATTTTTAAAATAAA-TTTTTTAAT
20536786 TTTT
1 TTTT
20536790 AAAATAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 28 0.68
40 1 0.02
41 12 0.29
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (40 bp):
TTTTTTAATTTTAAAATATTTTTAAAATAAATTTTTTAAT
Found at i:20536809 original size:22 final size:21
Alignment explanation
Indices: 20536761--20536809 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 21
20536751 AATTTTAAAA
*
20536761 TATTTTTAAAATAAATTTTTT
1 TATTTTTAAAATAAATTTTTG
20536782 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
20536805 TATTT
1 TATTT
20536810 ATTTAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:20537465 original size:15 final size:15
Alignment explanation
Indices: 20537447--20537481 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
20537437 TGGTTTAAAT
20537447 TTATATATTATCATC
1 TTATATATTATCATC
*
20537462 TTATATATTATTATC
1 TTATATATTATCATC
20537477 -TATAT
1 TTATAT
20537482 TAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATATTATCATC
Found at i:20538273 original size:107 final size:107
Alignment explanation
Indices: 20538146--20538458 Score: 545
Period size: 107 Copynumber: 2.9 Consensus size: 107
20538136 AGGAAAATTT
* ** * * * **
20538146 TTTCAAAACGAGGCAATGTTTTGTTTTTAGAAAATCGAGAAAATGTGCCCTAACGTGTTGGGTTT
1 TTTCAAAAAGAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTACTGGGTTT
20538211 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTCAATAA
66 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTCAATAA
20538253 TTTCAAAAAGAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTACTGGGTTT
1 TTTCAAAAAGAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTACTGGGTTT
20538318 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTCAATAA
66 CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTCAATAA
20538360 TTTCAAAAAGAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTACTGGGTTT
1 TTTCAAAAAGAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTACTGGGTTT
*
20538425 CGATTTCTCGTTCGACTAAATAGCCAAATATCCT
66 CGATTTCTCGTTCGACCAAATAGCCAAATATCCT
20538459 CTTAAAACTT
Statistics
Matches: 197, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 197 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (107 bp):
TTTCAAAAAGAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTACTGGGTTT
CGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTCAATAA
Found at i:20539773 original size:76 final size:76
Alignment explanation
Indices: 20539647--20539796 Score: 291
Period size: 76 Copynumber: 2.0 Consensus size: 76
20539637 TATAAATTCG
20539647 ATATTATTTTGACTTAATTTAAGCATTATAAAAAGGGAGATAACCTAGCATAAGTCTTTCTCCAA
1 ATATTATTTTGACTTAATTTAAGCATTATAAAAAGGGAGATAACCTAGCATAAGTCTTTCTCCAA
*
20539712 ATTAAGTTTCA
66 AGTAAGTTTCA
20539723 ATATTATTTTGACTTAATTTAAGCATTATAAAAAGGGAGATAACCTAGCATAAGTCTTTCTCCAA
1 ATATTATTTTGACTTAATTTAAGCATTATAAAAAGGGAGATAACCTAGCATAAGTCTTTCTCCAA
20539788 AGTAAGTTT
66 AGTAAGTTT
20539797 ATATAAGTTC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (76 bp):
ATATTATTTTGACTTAATTTAAGCATTATAAAAAGGGAGATAACCTAGCATAAGTCTTTCTCCAA
AGTAAGTTTCA
Found at i:20566785 original size:12 final size:12
Alignment explanation
Indices: 20566768--20566797 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
20566758 GAGGATGACC
20566768 AAAAGAAGAAAA
1 AAAAGAAGAAAA
20566780 AAAAGAAGAAAA
1 AAAAGAAGAAAA
20566792 ACAAAG
1 A-AAAG
20566798 CTGTTACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAAA
Found at i:20579432 original size:33 final size:33
Alignment explanation
Indices: 20579395--20579459 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
20579385 CCTTCCCTTT
*
20579395 TCCATA-AGGTAGAAAGCTGGTTTTTGTCATTTC
1 TCCATAGA-GTAGAAAGCTGGGTTTTGTCATTTC
*
20579428 TCCATAGAGTAGAAAGTTGGGTTTTGTCATTT
1 TCCATAGAGTAGAAAGCTGGGTTTTGTCATTT
20579460 TAGATTACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (33 bp):
TCCATAGAGTAGAAAGCTGGGTTTTGTCATTTC
Found at i:20582765 original size:17 final size:17
Alignment explanation
Indices: 20582743--20582776 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20582733 ATCAAACTCA
20582743 TCTGTCATAATTCTAAG
1 TCTGTCATAATTCTAAG
20582760 TCTGTCATAATTCTAAG
1 TCTGTCATAATTCTAAG
20582777 GCAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (17 bp):
TCTGTCATAATTCTAAG
Found at i:20590445 original size:11 final size:10
Alignment explanation
Indices: 20590431--20590504 Score: 52
Period size: 11 Copynumber: 7.5 Consensus size: 10
20590421 TATCTTGAAT
20590431 TTTTTAGATAA
1 TTTTTA-ATAA
20590442 TTTTTAAT-A
1 TTTTTAATAA
20590451 TTTTT--T-A
1 TTTTTAATAA
20590458 TTTTTATATAA
1 TTTTTA-ATAA
*
20590469 TCTTT-ATAA
1 TTTTTAATAA
20590478 TATTTTACA-AA
1 T-TTTTA-ATAA
20590489 TTTTTAATAA
1 TTTTTAATAA
20590499 TATTTT
1 T-TTTT
20590505 TTTAAAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
7 7 0.13
9 12 0.23
10 14 0.27
11 18 0.35
12 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:20590484 original size:27 final size:26
Alignment explanation
Indices: 20590431--20590483 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
20590421 TATCTTGAAT
20590431 TTTTTAGATAATTTTTAATATTTTTTA
1 TTTTTAGATAATTTTTAATA-TTTTTA
*
20590458 TTTTTATATAATCTTTATAATATTTT
1 TTTTTAGATAAT-TTT-TAATATTTT
20590484 ACAAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 11 0.48
28 7 0.30
29 5 0.22
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTTTAGATAATTTTTAATATTTTTA
Found at i:20592852 original size:72 final size:72
Alignment explanation
Indices: 20592735--20592871 Score: 215
Period size: 72 Copynumber: 1.9 Consensus size: 72
20592725 GGCTCACGGG
*
20592735 TCAACGAGTCTAATGCCTCTATCTAAATTGATACCTAAATCAATTCTCGATCCAA-TCAATTTAA
1 TCAACGAGTCTAATGCCTCTATCTAAATTGATACCTAAACCAATTCTCGATCCAACT-AATTTAA
20592799 CTAGCAGA
65 CTAGCAGA
* *
20592807 TCAACGAGTCTAATATCC-CTCTCTAAATTGATACCTAAACCAATTCTCGATCCAACTAATTTAA
1 TCAACGAGTCTAAT-GCCTCTATCTAAATTGATACCTAAACCAATTCTCGATCCAACTAATTTAA
20592871 C
65 C
20592872 AATTCGAACA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
72 57 0.95
73 3 0.05
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.31
Consensus pattern (72 bp):
TCAACGAGTCTAATGCCTCTATCTAAATTGATACCTAAACCAATTCTCGATCCAACTAATTTAAC
TAGCAGA
Found at i:20601752 original size:35 final size:35
Alignment explanation
Indices: 20601617--20601783 Score: 212
Period size: 34 Copynumber: 4.8 Consensus size: 35
20601607 CTTTGTTGGT
*
20601617 GTGTTTCGGGTGGATTAGCTCTTATGAGCACACTGGT
1 GTGTTTCGGGTGGATTAGCTCTTATGAG--CACTGGC
* *
20601654 GTGTTTCGAG-GGATTAGTTCTTATGAGCACTGGC
1 GTGTTTCGGGTGGATTAGCTCTTATGAGCACTGGC
** * *
20601688 GTGTTTCAAG-GGTTTAGTTCTTATGAGCACTGGC
1 GTGTTTCGGGTGGATTAGCTCTTATGAGCACTGGC
20601722 GTGTTTCGGGTGGATTAGCTCTTATGAGCACTGGC
1 GTGTTTCGGGTGGATTAGCTCTTATGAGCACTGGC
* * *
20601757 GTATATCAGGTGGATTAGCTCTTATGA
1 GTGTTTCGGGTGGATTAGCTCTTATGA
20601784 ACATCGGCGT
Statistics
Matches: 117, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
34 46 0.39
35 46 0.39
36 16 0.14
37 9 0.08
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (35 bp):
GTGTTTCGGGTGGATTAGCTCTTATGAGCACTGGC
Found at i:20619271 original size:24 final size:24
Alignment explanation
Indices: 20619244--20619295 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
20619234 AATCAAAGTC
* *
20619244 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
20619268 AAATATATTGTACTCATAAATACT
1 AAATATATTATACTAATAAATACT
20619292 AAAT
1 AAAT
20619296 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:20624291 original size:19 final size:19
Alignment explanation
Indices: 20624250--20624292 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
20624240 AATCCAAAAC
* * **
20624250 CAAAACAGTCCCAAAATGT
1 CAAAACAATCCAAAAATAA
20624269 CAAAACAATCCAAAAATAA
1 CAAAACAATCCAAAAATAA
20624288 CAAAA
1 CAAAA
20624293 TGTGATAACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.23, G:0.05, T:0.12
Consensus pattern (19 bp):
CAAAACAATCCAAAAATAA
Found at i:20624478 original size:41 final size:41
Alignment explanation
Indices: 20624421--20624502 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
20624411 GTGAGTTTCG
*
20624421 AAACTCAGTGTGTAACATATCATATTATCAACAGAAGAAAA
1 AAACTCAGTGTGTAACACATCATATTATCAACAGAAGAAAA
20624462 AAACTCAGTGTGTAACACATCATATTATCAACAGAAGAAAA
1 AAACTCAGTGTGTAACACATCATATTATCAACAGAAGAAAA
20624503 TCAGATATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (41 bp):
AAACTCAGTGTGTAACACATCATATTATCAACAGAAGAAAA
Found at i:20625273 original size:26 final size:25
Alignment explanation
Indices: 20625227--20625275 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
20625217 TAATGGGTTG
* **
20625227 AAAATATAGAGATAATTCTATTTCT
1 AAAATATAGAGACAAACCTATTTCT
20625252 AAAATTATAGAGACAAACCTATTT
1 AAAA-TATAGAGACAAACCTATTT
20625276 ATAGCATGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (25 bp):
AAAATATAGAGACAAACCTATTTCT
Found at i:20626099 original size:24 final size:23
Alignment explanation
Indices: 20626059--20626117 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
20626049 AACATTATTC
* *
20626059 CTGAACATGTTTAATTATATGTTCA
1 CTGAACATGTTCAATTA-A-GTTAA
*
20626084 -TGAACATGTTCGATTAAGTTAA
1 CTGAACATGTTCAATTAAGTTAA
20626106 CTGAACATGTTC
1 CTGAACATGTTC
20626118 TTGAACATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 4 0.13
23 12 0.40
24 14 0.47
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (23 bp):
CTGAACATGTTCAATTAAGTTAA
Found at i:20626942 original size:20 final size:21
Alignment explanation
Indices: 20626917--20626958 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
20626907 AAGGTTTTTA
20626917 TTTTATTAGAG-TTAGGGTTT
1 TTTTATTAGAGTTTAGGGTTT
*
20626937 TTTTATTAGGGTTTAGGGTTT
1 TTTTATTAGAGTTTAGGGTTT
20626958 T
1 T
20626959 ATAAAAGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.17, C:0.00, G:0.26, T:0.57
Consensus pattern (21 bp):
TTTTATTAGAGTTTAGGGTTT
Found at i:20630028 original size:23 final size:22
Alignment explanation
Indices: 20629987--20630085 Score: 90
Period size: 23 Copynumber: 4.3 Consensus size: 22
20629977 ATATGTAGCT
* * *
20629987 GCTACCATTGATATATAGCCATA
1 GCTACCACTGAAATGTAGCCA-A
*
20630010 GCTACCACTGAAATGTAGCTGAA
1 GCTACCACTGAAATGTAGC-CAA
*
20630033 GCTACCACTGAAATGTAGCTGAA
1 GCTACCACTGAAATGTAGC-CAA
* *
20630056 GCTATCGCTGAAATGTAGCCGAA
1 GCTACCACTGAAATGTAGCC-AA
*
20630079 ACTACCA
1 GCTACCA
20630086 TTGGTCAATA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
23 63 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (22 bp):
GCTACCACTGAAATGTAGCCAA
Found at i:20631506 original size:45 final size:45
Alignment explanation
Indices: 20631437--20631522 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
20631427 AGATACTCGA
* *
20631437 TGGATTCAGCACATAGCAACCACCTTAGTAATCAATGATGTCTAG
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCTAG
*
20631482 TGGAATCAGCACGTAGCAACCACCTTACTAATCAATGATGT
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
20631523 TTGGTTCACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (45 bp):
TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCTAG
Found at i:20631656 original size:50 final size:49
Alignment explanation
Indices: 20631530--20631717 Score: 182
Period size: 50 Copynumber: 3.8 Consensus size: 49
20631520 TGTTTGGTTC
* **
20631530 ACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATCCGAT
1 ACATAGTAGCCTGCACATAGTACTACACATGTGACCAGAACCATCCGAT
* * * * *
20631579 ACATGTAGTAGCCTGCACATAGAACTACACACGTGATCAGAACTATCCGGT
1 ACA--TAGTAGCCTGCACATAGTACTACACATGTGACCAGAACCATCCGAT
* * * *
20631630 CGCATAGTAGCCTGCACATAGTACTACACATGTGACC--TATCATTCTGAT
1 -ACATAGTAGCCTGCACATAGTACTACACATGTGACCAGAACCA-TCCGAT
* *
20631679 ACACGTAGTAGCCTGCACATAGTACTGCACACGTGACCA
1 ACA--TAGTAGCCTGCACATAGTACTACACATGTGACCA
20631718 TCACTTTCAC
Statistics
Matches: 112, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
48 4 0.04
49 7 0.06
50 61 0.54
51 38 0.34
52 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (49 bp):
ACATAGTAGCCTGCACATAGTACTACACATGTGACCAGAACCATCCGAT
Found at i:20631752 original size:101 final size:100
Alignment explanation
Indices: 20631528--20631717 Score: 283
Period size: 100 Copynumber: 1.9 Consensus size: 100
20631518 GATGTTTGGT
*
20631528 TCACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATCCGATACATGTAGTAGCCT
1 TCACATAGTAGCCTACACATAGTACTACACATGTGACCA-TACCATCCGATACACGTAGTAGCCT
*
20631593 GCACATAGAACTACACACGTGATCAGAACTATCCGG
65 GCACATAGAACTACACACGTGACCAGAACTATCCGG
* * * *
20631629 TCGCATAGTAGCCTGCACATAGTACTACACATGTGACC-TATCATTCTGATACACGTAGTAGCCT
1 TCACATAGTAGCCTACACATAGTACTACACATGTGACCATACCA-TCCGATACACGTAGTAGCCT
* *
20631693 GCACATAGTACTGCACACGTGACCA
65 GCACATAGAACTACACACGTGACCA
20631718 TCACTTTCAC
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
99 4 0.05
100 40 0.50
101 36 0.45
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (100 bp):
TCACATAGTAGCCTACACATAGTACTACACATGTGACCATACCATCCGATACACGTAGTAGCCTG
CACATAGAACTACACACGTGACCAGAACTATCCGG
Found at i:20635424 original size:45 final size:46
Alignment explanation
Indices: 20635330--20635425 Score: 106
Period size: 45 Copynumber: 2.1 Consensus size: 46
20635320 TGATGATGAC
* * *
20635330 TTTTACTACAATGACTTATCATCCAAGTTGCCTGATTTTGATGGCT
1 TTTTACTACAATAACTTATCATCCAAGTTGCCTAAATTTGATGGCT
** * *
20635376 TTTTACTACAATAAC-TATCATCCCGGTTGACC-AAATTTGGTGGTT
1 TTTTACTACAATAACTTATCATCCAAGTTG-CCTAAATTTGATGGCT
20635421 TTTTA
1 TTTTA
20635426 ACCTACCATC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
45 26 0.62
46 16 0.38
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (46 bp):
TTTTACTACAATAACTTATCATCCAAGTTGCCTAAATTTGATGGCT
Found at i:20639396 original size:22 final size:22
Alignment explanation
Indices: 20639371--20639413 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
20639361 CAAATAAACT
*
20639371 CCAAACAATAGCATCA-GAATAG
1 CCAAAC-ACAGCATCACGAATAG
*
20639393 CCAATCACAGCATCACGAATA
1 CCAAACACAGCATCACGAATA
20639414 TTTAACATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.47, C:0.28, G:0.12, T:0.14
Consensus pattern (22 bp):
CCAAACACAGCATCACGAATAG
Found at i:20646728 original size:18 final size:19
Alignment explanation
Indices: 20646705--20646767 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 19
20646695 TATTAATAAC
20646705 ATAAATATAATAATAAAA-
1 ATAAATATAATAATAAAAT
*
20646723 ATAAATAATTTATAATAAAAT
1 ATAAAT-A-TAATAATAAAAT
20646744 ATAAA-A-AATACATAAAAT
1 ATAAATATAATA-ATAAAAT
20646762 AATAAA
1 -ATAAA
20646768 CGATATAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 3 0.08
18 13 0.34
19 7 0.18
20 10 0.26
21 5 0.13
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAAATATAATAATAAAAT
Found at i:20647336 original size:21 final size:21
Alignment explanation
Indices: 20647313--20647399 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 21
20647303 TATTTTAATA
20647313 TTTTAAAAATTCAAAAAATTAT
1 TTTTAAAAATT-AAAAAATTAT
20647335 TTTTAAAAATTAAAAATCATTAAATT
1 TTTTAAAAATTAAAAA--ATT--A-T
*
20647361 TATTTAAAAATTATAAAA-TAT
1 T-TTTAAAAATTAAAAAATTAT
*
20647382 ATTTTAAATATTAAAAAA
1 -TTTTAAAAATTAAAAAA
20647400 GTAATTAAAC
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
21 20 0.36
22 13 0.24
23 3 0.05
24 1 0.02
25 2 0.04
26 2 0.04
27 14 0.25
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTTAAAAATTAAAAAATTAT
Found at i:20647347 original size:29 final size:28
Alignment explanation
Indices: 20647315--20647379 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
20647305 TTTTAATATT
*
20647315 TTAAAAATTCAAAAAATTATTTTTAAAAA
1 TTAAAAATTCAAAAAATT-TATTTAAAAA
**
20647344 TTAAAAA-TCATTAAATTTATTTAAAAA
1 TTAAAAATTCAAAAAATTTATTTAAAAA
20647371 TTATAAAAT
1 TTA-AAAAT
20647380 ATATTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 12 0.39
28 12 0.39
29 7 0.23
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (28 bp):
TTAAAAATTCAAAAAATTTATTTAAAAA
Done.