Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 84 of 316
Found at i:25381226 original size:46 final size:46
Alignment explanation
Indices: 25381178--25381403 Score: 308
Period size: 46 Copynumber: 4.9 Consensus size: 46
25381168 TCTCTAATAT
* * * *
25381178 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATAT
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
* *
25381224 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACGG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
* * *
25381270 GAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGCGTGACAG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
* *
25381316 GAAATGAATAAGACCATGGTTGAAAGATACCATGACAACATGACAG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
* * * * *
25381362 AAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
25381404 TCAAAGATAA
Statistics
Matches: 161, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 161 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (46 bp):
GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
Found at i:25385667 original size:6 final size:6
Alignment explanation
Indices: 25385653--25385683 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
25385643 ACAAATCTGG
*
25385653 AACAAT AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT A
25385684 TGGCACACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:25385994 original size:22 final size:22
Alignment explanation
Indices: 25385949--25385994 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
25385939 TCCCTCTTTC
*
25385949 TTTCTTTTATTTCTTTATTCTA
1 TTTCTTTTATTTCTTTAATCTA
25385971 TTTCTTTTATTTACTTTAAT-TA
1 TTTCTTTTATTT-CTTTAATCTA
25385993 TT
1 TT
25385995 AAATTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTCTTTTATTTCTTTAATCTA
Found at i:25386007 original size:3 final size:3
Alignment explanation
Indices: 25385997--25386041 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
25385987 TAATTATTAA
*
25385997 ATT A-T ATT ATT ATT A-T ATT -TT AGTA ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
25386040 AT
1 AT
25386042 AATATTTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
2 6 0.17
3 28 0.78
4 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:25386047 original size:32 final size:32
Alignment explanation
Indices: 25385987--25386050 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
25385977 TTATTTACTT
*
25385987 TAATTATTAAATTATATTATTATTATATTTTAG
1 TAATTATT-AATTATATTATTATAATATTTTAG
25386020 TAATTATT-ATTATTATTATTATAATATTTTA
1 TAATTATTAATTA-TATTATTATAATATTTTA
25386051 CTTAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 4 0.14
32 17 0.59
33 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (32 bp):
TAATTATTAATTATATTATTATAATATTTTAG
Found at i:25390803 original size:26 final size:26
Alignment explanation
Indices: 25390767--25390816 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
25390757 AAAAAAGACG
*
25390767 GAATAGTTTTCGAGTATTATTACACA
1 GAATAGTTTTCGAGCATTATTACACA
25390793 GAATAGTTTTCGAGCATTATTACA
1 GAATAGTTTTCGAGCATTATTACA
25390817 AACCTTTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (26 bp):
GAATAGTTTTCGAGCATTATTACACA
Found at i:25393456 original size:24 final size:23
Alignment explanation
Indices: 25393407--25393454 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
25393397 CAGGAAGGTC
25393407 TTCCTGCATTGTGGGTTTTTTAT
1 TTCCTGCATTGTGGGTTTTTTAT
25393430 TTCCTGCATTGTGGGTTTTTTAT
1 TTCCTGCATTGTGGGTTTTTTAT
25393453 TT
1 TT
25393455 TCATTATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.08, C:0.12, G:0.21, T:0.58
Consensus pattern (23 bp):
TTCCTGCATTGTGGGTTTTTTAT
Found at i:25400113 original size:14 final size:14
Alignment explanation
Indices: 25400094--25400120 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25400084 AAGATATTCT
25400094 TTTTCTAAATAAAA
1 TTTTCTAAATAAAA
25400108 TTTTCTAAATAAA
1 TTTTCTAAATAAA
25400121 GTTGAACCAA
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:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTTCTAAATAAAA
Found at i:25423050 original size:173 final size:173
Alignment explanation
Indices: 25422761--25423107 Score: 694
Period size: 173 Copynumber: 2.0 Consensus size: 173
25422751 TCCAGAGTAA
25422761 TACTTTTTTATAGTATTGAATCGTTTTTGGAGCTTGAGTTCAATTTTCCATTCCATCCTATCTAT
1 TACTTTTTTATAGTATTGAATCGTTTTTGGAGCTTGAGTTCAATTTTCCATTCCATCCTATCTAT
25422826 AAACTATTTACCTTATTTCTTTGTTAAATCGAACCTACGAAAATCATACCTAGCTTATCATTCGA
66 AAACTATTTACCTTATTTCTTTGTTAAATCGAACCTACGAAAATCATACCTAGCTTATCATTCGA
25422891 ACCACTTTGTCAACTTTCGCTCATACTTAACTTAATACGTCAT
131 ACCACTTTGTCAACTTTCGCTCATACTTAACTTAATACGTCAT
25422934 TACTTTTTTATAGTATTGAATCGTTTTTGGAGCTTGAGTTCAATTTTCCATTCCATCCTATCTAT
1 TACTTTTTTATAGTATTGAATCGTTTTTGGAGCTTGAGTTCAATTTTCCATTCCATCCTATCTAT
25422999 AAACTATTTACCTTATTTCTTTGTTAAATCGAACCTACGAAAATCATACCTAGCTTATCATTCGA
66 AAACTATTTACCTTATTTCTTTGTTAAATCGAACCTACGAAAATCATACCTAGCTTATCATTCGA
25423064 ACCACTTTGTCAACTTTCGCTCATACTTAACTTAATACGTCAT
131 ACCACTTTGTCAACTTTCGCTCATACTTAACTTAATACGTCAT
25423107 T
1 T
25423108 TTTAAGCCGA
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
173 174 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (173 bp):
TACTTTTTTATAGTATTGAATCGTTTTTGGAGCTTGAGTTCAATTTTCCATTCCATCCTATCTAT
AAACTATTTACCTTATTTCTTTGTTAAATCGAACCTACGAAAATCATACCTAGCTTATCATTCGA
ACCACTTTGTCAACTTTCGCTCATACTTAACTTAATACGTCAT
Found at i:25426822 original size:11 final size:12
Alignment explanation
Indices: 25426806--25426834 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
25426796 CGAAATAATA
25426806 TTTTTTTGAATT
1 TTTTTTTGAATT
25426818 TTTTTTTGAATT
1 TTTTTTTGAATT
25426830 TTTTT
1 TTTTT
25426835 CACAAACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:25432396 original size:40 final size:40
Alignment explanation
Indices: 25432339--25432516 Score: 218
Period size: 40 Copynumber: 4.5 Consensus size: 40
25432329 CGGATGATAA
* * * *
25432339 CCGGGCTAGGTCCCGAAGGCCTTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
25432379 CCGGGCTAAGTCACGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
25432419 CTGGGCTAGGTCCCAAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
25432459 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
25432499 CC-GGCAAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
25432517 TACTTGGTTT
Statistics
Matches: 121, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
39 16 0.13
40 104 0.86
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:25433895 original size:38 final size:38
Alignment explanation
Indices: 25433853--25433938 Score: 145
Period size: 38 Copynumber: 2.3 Consensus size: 38
25433843 TACCAATTTT
* *
25433853 ACTGCTTCTGCCCTACTGAGTACATGTTAAGCCTGTCC
1 ACTGCTTCTGCCCTACTGAGTACATGTGAAGCATGTCC
*
25433891 ACTGCTTCTGCCCTACTGAGTACATGTGAAGCATGTCT
1 ACTGCTTCTGCCCTACTGAGTACATGTGAAGCATGTCC
25433929 ACTGCTTCTG
1 ACTGCTTCTG
25433939 TTGAACTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.33
Consensus pattern (38 bp):
ACTGCTTCTGCCCTACTGAGTACATGTGAAGCATGTCC
Found at i:25433947 original size:38 final size:38
Alignment explanation
Indices: 25433852--25433967 Score: 133
Period size: 38 Copynumber: 3.1 Consensus size: 38
25433842 TTACCAATTT
* * *
25433852 TACTGCTTCTGCCCTACTGAGTACATGTTAAGCCTGTC
1 TACTGCTTCTGCCCAACTGAGTACATGTCAAGCATGTC
* * *
25433890 CACTGCTTCTGCCCTACTGAGTACATGTGAAGCATGTC
1 TACTGCTTCTGCCCAACTGAGTACATGTCAAGCATGTC
*** * *
25433928 TACTGCTTCTGTTGAACTGAATATATGTCAAGCATGTC
1 TACTGCTTCTGCCCAACTGAGTACATGTCAAGCATGTC
25433966 TA
1 TA
25433968 TTATTTCTGC
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 67 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (38 bp):
TACTGCTTCTGCCCAACTGAGTACATGTCAAGCATGTC
Found at i:25435353 original size:43 final size:42
Alignment explanation
Indices: 25435297--25435471 Score: 156
Period size: 43 Copynumber: 4.1 Consensus size: 42
25435287 ACATAGGATT
25435297 TTGATTTGTGATTTCGTGTAAGACCACATCTGGGACATTGGCA
1 TTGATTT-TGATTTCGTGTAAGACCACATCTGGGACATTGGCA
* ** *
25435340 TTGATTTGAGATTTACGTGTAAGACCATGTCTGGGACATCGGCA
1 TTGATTT-TGATTT-CGTGTAAGACCACATCTGGGACATTGGCA
* * * *
25435384 -TCATATTTGATTTCGTGTAAGACC-CTATTTAGGACAGTGGCA
1 TTGAT-TTTGATTTCGTGTAAGACCAC-ATCTGGGACATTGGCA
* * * ** *
25435426 TCGATATTTGATTACATGTAAGACCATGTCTGGGACGTTGGCA
1 TTGAT-TTTGATTTCGTGTAAGACCACATCTGGGACATTGGCA
25435469 TTG
1 TTG
25435472 TACGAGCTCT
Statistics
Matches: 104, Mismatches: 23, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
42 22 0.21
43 54 0.52
44 28 0.27
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (42 bp):
TTGATTTTGATTTCGTGTAAGACCACATCTGGGACATTGGCA
Found at i:25435394 original size:50 final size:44
Alignment explanation
Indices: 25435296--25435407 Score: 133
Period size: 44 Copynumber: 2.6 Consensus size: 44
25435286 GACATAGGAT
* *
25435296 TTTGATTTGTGATTTCGTGTAAGACCACATCTGGGACATTGGCA
1 TTTGATTTGAGATTTCGTGTAAGACCACATCTGGGACATCGGCA
**
25435340 -TTGATTTGAGATTTACGTGTAAGACCATGTCTGGGACATCGGCA
1 TTTGATTTGAGATTT-CGTGTAAGACCACATCTGGGACATCGGCA
*
25435384 TCAT-ATTT--GATTTCGTGTAAGACC
1 T-TTGATTTGAGATTTCGTGTAAGACC
25435408 CTATTTAGGA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
42 11 0.18
43 18 0.30
44 26 0.43
45 4 0.07
46 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (44 bp):
TTTGATTTGAGATTTCGTGTAAGACCACATCTGGGACATCGGCA
Found at i:25438971 original size:13 final size:13
Alignment explanation
Indices: 25438953--25438979 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25438943 GCTCGGGAAG
25438953 GACACGCCCGTGT
1 GACACGCCCGTGT
25438966 GACACGCCCGTGT
1 GACACGCCCGTGT
25438979 G
1 G
25438980 CGATTACTTC
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:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:25450209 original size:42 final size:42
Alignment explanation
Indices: 25450162--25450325 Score: 161
Period size: 42 Copynumber: 3.9 Consensus size: 42
25450152 ATTGGCATCA
* *
25450162 ATATGAG-TTATCATGTAAGACCATATCTGGGATATGGCGTTG
1 ATATGAGATT-TCATGTAAGACCATATCTGGGACATGGCGTCG
* **
25450204 ATATGAGATTTCGTGTAAGACCACGTCTGGGACATGGCGTCG
1 ATATGAGATTTCATGTAAGACCATATCTGGGACATGGCGTCG
* * * * * *
25450246 AAATGAGAATTT-GTATAAGACCATATCTGGGATATGACATCG
1 ATATGAG-ATTTCATGTAAGACCATATCTGGGACATGGCGTCG
* ** *
25450288 ATGTGAGATCCCATGTAAGACCATGTCTGGGACATGGC
1 ATATGAGATTTCATGTAAGACCATATCTGGGACATGGC
25450326 ATTGGCATCT
Statistics
Matches: 98, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
41 2 0.02
42 90 0.92
43 6 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (42 bp):
ATATGAGATTTCATGTAAGACCATATCTGGGACATGGCGTCG
Found at i:25452294 original size:6 final size:5
Alignment explanation
Indices: 25452276--25452332 Score: 51
Period size: 6 Copynumber: 10.0 Consensus size: 5
25452266 GAAGTATAAG
25452276 AAAAT AACAAT AAACAT AAAAAT ACAAAT ACAAAT AAAAAT AAAAAT AAAAT
1 AAAAT AA-AAT AAA-AT -AAAAT A-AAAT A-AAAT -AAAAT -AAAAT AAAAT
25452328 AAAAT
1 AAAAT
25452333 GAATGGACTT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
5 14 0.30
6 29 0.62
7 4 0.09
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:25452299 original size:12 final size:11
Alignment explanation
Indices: 25452276--25452331 Score: 67
Period size: 12 Copynumber: 4.8 Consensus size: 11
25452266 GAAGTATAAG
*
25452276 AAAATAACAAT
1 AAAATAAAAAT
25452287 AAACATAAAAAT
1 AAA-ATAAAAAT
*
25452299 ACAAATACAAAT
1 A-AAATAAAAAT
25452311 AAAAATAAAAAT
1 -AAAATAAAAAT
25452323 AAAATAAAA
1 AAAATAAAA
25452332 TGAATGGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
11 12 0.31
12 24 0.62
13 3 0.08
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:25452299 original size:18 final size:17
Alignment explanation
Indices: 25452276--25452331 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
25452266 GAAGTATAAG
25452276 AAAATAACAATAAACATA
1 AAAATAACAATAAA-ATA
25452294 AAAAT-ACAAATACAAATA
1 AAAATAAC-AATA-AAATA
*
25452312 AAAATAAAAATAAAATA
1 AAAATAACAATAAAATA
25452329 AAA
1 AAA
25452332 TGAATGGACT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
17 10 0.29
18 21 0.62
19 3 0.09
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAATAACAATAAAATA
Found at i:25453986 original size:18 final size:18
Alignment explanation
Indices: 25453965--25454001 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25453955 GCTAAAATTG
25453965 AAATAAA-ATAACAAATAA
1 AAATAAATA-AACAAATAA
25453983 AAATAAATAAACAAATAA
1 AAATAAATAAACAAATAA
25454001 A
1 A
25454002 TAAATATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.16
Consensus pattern (18 bp):
AAATAAATAAACAAATAA
Found at i:25464445 original size:90 final size:90
Alignment explanation
Indices: 25464314--25464492 Score: 261
Period size: 90 Copynumber: 2.0 Consensus size: 90
25464304 AATTTTCGGC
* *
25464314 AATCCAGTTGTCACACCCTAGAATATATATAGTTAAAAAATAAGATTAAACAAGAAATAAGCTAC
1 AATCCAGTTGTCACACCCGAGAATAAATATAGTTAAAAAATAAGATTAAACAAGAAATAAGCTAC
25464379 AGGCTCAATGGTTAAATGATAGTAG
66 AGGCTCAATGGTTAAATGATAGTAG
* * * *
25464404 AATCCAGTTGTCACACCTCGA-AATAAATATGGTTAAGAAATAAGATTAAAGAAGAAATGAGCTA
1 AATCCAGTTGTCACACC-CGAGAATAAATATAGTTAAAAAATAAGATTAAACAAGAAATAAGCTA
* * *
25464468 TATGCTCAATGGTTAAGTGATAGTA
65 CAGGCTCAATGGTTAAATGATAGTA
25464493 CATCCATTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 77 0.97
91 2 0.03
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.26
Consensus pattern (90 bp):
AATCCAGTTGTCACACCCGAGAATAAATATAGTTAAAAAATAAGATTAAACAAGAAATAAGCTAC
AGGCTCAATGGTTAAATGATAGTAG
Found at i:25467816 original size:64 final size:63
Alignment explanation
Indices: 25467709--25467837 Score: 213
Period size: 64 Copynumber: 2.0 Consensus size: 63
25467699 GGGATCGGCT
* *
25467709 TGGATAGCTTTTTTTTATAAAAATATTTAGACTTATTATTTGAAATTTCTAATATTTGGAAAC
1 TGGATAGCTTTTTTTTATAAAAATATTTAGACTTATTAGTTGAAATTTCTAATATTTAGAAAC
* *
25467772 TGGATAGCTTTTTCTTTATAAAAATATTTAGACTTGTTAGTTGAAATTTCTATTATTTAGAAAC
1 TGGATAGCTTTTT-TTTATAAAAATATTTAGACTTATTAGTTGAAATTTCTAATATTTAGAAAC
25467836 TG
1 TG
25467838 TATTGTTCTA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
63 13 0.21
64 48 0.79
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (63 bp):
TGGATAGCTTTTTTTTATAAAAATATTTAGACTTATTAGTTGAAATTTCTAATATTTAGAAAC
Found at i:25469046 original size:16 final size:16
Alignment explanation
Indices: 25469021--25469052 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25469011 TCAAGTGAGA
25469021 TAATTAATTGATGTAT
1 TAATTAATTGATGTAT
*
25469037 TAATTCATTGATGTAT
1 TAATTAATTGATGTAT
25469053 ATATATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.50
Consensus pattern (16 bp):
TAATTAATTGATGTAT
Found at i:25482409 original size:56 final size:55
Alignment explanation
Indices: 25482323--25482499 Score: 257
Period size: 56 Copynumber: 3.2 Consensus size: 55
25482313 ACCATGGCAT
25482323 CGATATATGTGTG-AGTAAGACCACATTTAATACATTGGCATCGATATGTGATTC
1 CGATATATGTGTGCAGTAAGACCACATTTAATACATTGGCATCGATATGTGATTC
*
25482377 CAATATATGTGTGCAAGTAAGACCACATTTAATACATTGGCATCGATATGTGATTC
1 CGATATATGTGTGC-AGTAAGACCACATTTAATACATTGGCATCGATATGTGATTC
* * * * * * *
25482433 CGATATTTATGTGCGAGTAAGACCACGTTTAATACGTTGGCATCAATATGTGGTTT
1 CGATATATGTGTGC-AGTAAGACCACATTTAATACATTGGCATCGATATGTGATTC
25482489 CGATATATGTG
1 CGATATATGTG
25482500 ATTACATGTA
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
54 12 0.11
56 97 0.89
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (55 bp):
CGATATATGTGTGCAGTAAGACCACATTTAATACATTGGCATCGATATGTGATTC
Found at i:25488699 original size:12 final size:13
Alignment explanation
Indices: 25488677--25488706 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
25488667 ATTTTATGTT
25488677 TTTTTCTTTTTTA
1 TTTTTCTTTTTTA
25488690 TTTTTC-TTTTTA
1 TTTTTCTTTTTTA
25488702 TTTTT
1 TTTTT
25488707 TAGCAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTCTTTTTTA
Found at i:25509934 original size:18 final size:19
Alignment explanation
Indices: 25509893--25509935 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
25509883 CCGTGCATCA
*
25509893 TGCCCGTGTGGGCCCACAC
1 TGCCCATGTGGGCCCACAC
*
25509912 -ACCCATGT-GGCCCACAC
1 TGCCCATGTGGGCCCACAC
25509929 TGCCCAT
1 TGCCCAT
25509936 CTTGGTCTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.16, C:0.44, G:0.23, T:0.16
Consensus pattern (19 bp):
TGCCCATGTGGGCCCACAC
Found at i:25518875 original size:20 final size:20
Alignment explanation
Indices: 25518846--25518883 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25518836 GCTCCATAGA
* *
25518846 CAAGGGACACGGGTGTGTCC
1 CAAGGCACACGGGCGTGTCC
25518866 CAAGGCACACGGGCGTGT
1 CAAGGCACACGGGCGTGT
25518884 GCAATCCACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.39, T:0.13
Consensus pattern (20 bp):
CAAGGCACACGGGCGTGTCC
Found at i:25521043 original size:27 final size:27
Alignment explanation
Indices: 25520984--25521107 Score: 194
Period size: 27 Copynumber: 4.6 Consensus size: 27
25520974 TAAATTGTAC
*
25520984 AGCACTAAGTGTGCGAGTTGGACTATGT
1 AGCACTAAGTGTGCGAATT-GACTATGT
25521012 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
25521039 TGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
25521066 AGCACTAAGTGTGCGAGTTGACTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
25521093 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
25521108 GACTTAATAT
Statistics
Matches: 90, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
27 72 0.80
28 18 0.20
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:25526660 original size:13 final size:13
Alignment explanation
Indices: 25526642--25526667 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25526632 ATAGCTGGTG
25526642 GTATCGCACGGCC
1 GTATCGCACGGCC
25526655 GTATCGCACGGCC
1 GTATCGCACGGCC
25526668 ATGTAGCCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GTATCGCACGGCC
Found at i:25531668 original size:20 final size:20
Alignment explanation
Indices: 25531643--25531682 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
25531633 ATTGGGCCTT
25531643 GCCCATATT-AACACAGTTGG
1 GCCCAT-TTCAACACAGTTGG
*
25531663 GCCCATTTCAATACAGTTGG
1 GCCCATTTCAACACAGTTGG
25531683 CTCCGTCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (20 bp):
GCCCATTTCAACACAGTTGG
Found at i:25534011 original size:19 final size:18
Alignment explanation
Indices: 25533974--25534017 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
25533964 ATACATACAG
25533974 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
25533991 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
25534010 TACTAATT
1 TAATAATT
25534018 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:25534866 original size:21 final size:21
Alignment explanation
Indices: 25534827--25534866 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25534817 GTTTGGTTGT
*
25534827 CTACACACTCATGTAGAGGCC
1 CTACACACCCATGTAGAGGCC
* *
25534848 CTACACACCCGTGTGGAGG
1 CTACACACCCATGTAGAGG
25534867 GGACAGACGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.17
Consensus pattern (21 bp):
CTACACACCCATGTAGAGGCC
Found at i:25541426 original size:13 final size:13
Alignment explanation
Indices: 25541408--25541433 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25541398 TCTCAATTCG
25541408 GTGGAAAATGAGC
1 GTGGAAAATGAGC
25541421 GTGGAAAATGAGC
1 GTGGAAAATGAGC
25541434 ACCAGGGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.38, T:0.15
Consensus pattern (13 bp):
GTGGAAAATGAGC
Found at i:25547632 original size:25 final size:25
Alignment explanation
Indices: 25547604--25547652 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
25547594 CCAGTAGGAG
*
25547604 TGTAACTCTTCCATTGATCAACCAA
1 TGTAACTCTTCCACTGATCAACCAA
25547629 TGTAACTCTTCCACTGATCAACCA
1 TGTAACTCTTCCACTGATCAACCA
25547653 CCGATAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (25 bp):
TGTAACTCTTCCACTGATCAACCAA
Found at i:25548026 original size:13 final size:13
Alignment explanation
Indices: 25548010--25548034 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25548000 TTTTTCAAGA
25548010 AAATTCTTTAATC
1 AAATTCTTTAATC
25548023 AAATTCTTTAAT
1 AAATTCTTTAAT
25548035 TGAATAATTC
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:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATTCTTTAATC
Found at i:25564636 original size:47 final size:47
Alignment explanation
Indices: 25564583--25564767 Score: 280
Period size: 47 Copynumber: 3.9 Consensus size: 47
25564573 GATAATTGTG
**
25564583 ATGTGAATGTGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
*
25564630 ATGTGAACATGCATATATGTGATAAGGCCAAATGGCCAATGTGATGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
* * *
25564677 ATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCATTGTGATGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
* * * *
25564724 ATATGAACATGCATATATGTGGTAAAGCCGAATGGCTAATGTGA
1 ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGA
25564768 AATATATGTA
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 124 1.00
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.27
Consensus pattern (47 bp):
ATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGA
Found at i:25564674 original size:22 final size:22
Alignment explanation
Indices: 25564599--25564674 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
25564589 ATGTGCATAT
*
25564599 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCAAATGGCCA
* ** *
25564621 ATGTGATGAATGTGAACAT-GCATA
1 ATGTGAT-AAGGCCAA-ATGGC-CA
25564645 TATGTGATAAGGCCAAATGGCCA
1 -ATGTGATAAGGCCAAATGGCCA
25564668 ATGTGAT
1 ATGTGAT
25564675 GAATGTGAGC
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 14 0.35
23 9 0.22
24 10 0.25
25 7 0.17
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCAAATGGCCA
Found at i:25565022 original size:37 final size:37
Alignment explanation
Indices: 25564972--25565084 Score: 199
Period size: 37 Copynumber: 3.1 Consensus size: 37
25564962 GGAAATATAT
*
25564972 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
25565009 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
25565046 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
25565083 TC
1 TC
25565085 TGAGCTAAAG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:25577439 original size:72 final size:72
Alignment explanation
Indices: 25577329--25577530 Score: 248
Period size: 72 Copynumber: 2.8 Consensus size: 72
25577319 CCACATATTT
* * * * *
25577329 TGTAATGCCCG-T-ATTTGAGCTACTCAAGGGTTTGTACACAAAGTCAGCACCTGGACCCTAAAG
1 TGTAATGCCCGCTCA-TTGAGCTACTCACGGGTTTATACACAAAGTCAGTACCCGGACCCCAAAG
*
25577392 CATTACCA
65 CATTAACA
* *
25577400 TGTAATGCCCGCTCATTGAGCTATTCACGAGTTTATACACAAAGTCAGTACCCGGACCCCAAAGC
1 TGTAATGCCCGCTCATTGAGCTACTCACGGGTTTATACACAAAGTCAGTACCCGGACCCCAAAGC
25577465 ATTAACA
66 ATTAACA
* *** *
25577472 TG-ACATGCTCGCTCAGCAAGTTACTCACGGGTTTATACACAAAGTCAGTACCCGGACCC
1 TGTA-ATGCCCGCTCATTGAGCTACTCACGGGTTTATACACAAAGTCAGTACCCGGACCC
25577531 ACATTACATA
Statistics
Matches: 113, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
71 12 0.11
72 100 0.88
73 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (72 bp):
TGTAATGCCCGCTCATTGAGCTACTCACGGGTTTATACACAAAGTCAGTACCCGGACCCCAAAGC
ATTAACA
Found at i:25583960 original size:46 final size:46
Alignment explanation
Indices: 25583888--25584063 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
25583878 TGGTTGAGCA
*
25583888 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
25583934 TCCGAACTCGTTGAGTTGAGTTCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
25583981 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
25584027 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
25584064 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
45 7 0.06
46 58 0.54
47 28 0.26
48 3 0.03
50 6 0.06
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:25584044 original size:93 final size:93
Alignment explanation
Indices: 25583885--25584056 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
25583875 AGATGGTTGA
* * *
25583885 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCCAACTCGTTGAGT
*
25583950 TGAGTTCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
25583978 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACG-CCCAAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCCAA-CTCGTTGAG
25584042 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
25584057 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 4 0.05
93 70 0.95
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGTCCCAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:25587614 original size:7 final size:7
Alignment explanation
Indices: 25587596--25587625 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
25587586 TTTGTGGTTG
25587596 TGGACTTT
1 TGGAC-TT
25587604 TGGACTT
1 TGGACTT
25587611 TGGACTT
1 TGGACTT
25587618 TGGACTT
1 TGGACTT
25587625 T
1 T
25587626 ACCTCTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.13, C:0.13, G:0.27, T:0.47
Consensus pattern (7 bp):
TGGACTT
Found at i:25603323 original size:36 final size:36
Alignment explanation
Indices: 25603256--25603329 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
25603246 GGAGGAGCAC
*
25603256 ATCAGTCAGAATAGATCCAAAATACAGCTGAACTGA
1 ATCAGTCAGAATAGATCCAAAAGACAGCTGAACTGA
**
25603292 ATCAGTCAGAATAGATCTGAAAGACTA-CTGAACTGA
1 ATCAGTCAGAATAGATCCAAAAGAC-AGCTGAACTGA
25603328 AT
1 AT
25603330 AGAGTTTACT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 33 0.97
37 1 0.03
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.22
Consensus pattern (36 bp):
ATCAGTCAGAATAGATCCAAAAGACAGCTGAACTGA
Found at i:25604268 original size:16 final size:16
Alignment explanation
Indices: 25604247--25604283 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
25604237 TATAATAAAA
*
25604247 AAATTAAATTAATGCT
1 AAATTAAATTAACGCT
25604263 AAATTAAATTAACGCT
1 AAATTAAATTAACGCT
25604279 AAATT
1 AAATT
25604284 TGAACCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (16 bp):
AAATTAAATTAACGCT
Found at i:25612163 original size:20 final size:20
Alignment explanation
Indices: 25612138--25612182 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
25612128 AGGATCAAAA
*
25612138 ATGAAAAGTT-GAAAATTTT
1 ATGAAAAATTCGAAAATTTT
*
25612157 GATGAAAAATTCTAAAATTTT
1 -ATGAAAAATTCGAAAATTTT
25612178 ATGAA
1 ATGAA
25612183 TACATGTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCGAAAATTTT
Found at i:25614316 original size:66 final size:66
Alignment explanation
Indices: 25614206--25614338 Score: 205
Period size: 66 Copynumber: 2.0 Consensus size: 66
25614196 TTTTGAATGT
* *
25614206 TTTGGTAATGCTTCGAAACCCTGTTTCAGCGACGGATACGAGTTAAGGATGTTATATTTAGTGGT
1 TTTGGTAATGCTTCGAAACCCTATTTCAGCGACGGATACAAGTTAAGGATGTTATATTTAGTGGT
25614271 A
66 A
* * *
25614272 TTTGGTAATGC-TCTGAAACCCTATTTTAGTGACGGATACAAGTTAAGGGTGTTATATTTAGTGG
1 TTTGGTAATGCTTC-GAAACCCTATTTCAGCGACGGATACAAGTTAAGGATGTTATATTTAGTGG
25614336 TA
65 TA
25614338 T
1 T
25614339 CAGAGCTATT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 2 0.03
66 59 0.97
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (66 bp):
TTTGGTAATGCTTCGAAACCCTATTTCAGCGACGGATACAAGTTAAGGATGTTATATTTAGTGGT
A
Found at i:25620308 original size:13 final size:13
Alignment explanation
Indices: 25620290--25620314 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25620280 CTAATATTTT
25620290 TCAAATTCTTTAA
1 TCAAATTCTTTAA
25620303 TCAAATTCTTTA
1 TCAAATTCTTTA
25620315 GTTGAATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TCAAATTCTTTAA
Found at i:25621534 original size:4 final size:4
Alignment explanation
Indices: 25621533--25621627 Score: 118
Period size: 4 Copynumber: 23.8 Consensus size: 4
25621523 TAGTGTGTGT
* * * *
25621533 GTGC GTGC GTGC GTGT GTGC GTGC GTGC GTGT GTGC ATGC GTGC GAGC
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC
** * *
25621581 AAGC GTGC GTGC GTGC GTGC TTGC GTGC GTGC GTGC ATGC GTGC GTG
1 GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTGC GTG
25621628 TGTGTGTGTG
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 77 1.00
ACGTcount: A:0.05, C:0.22, G:0.46, T:0.26
Consensus pattern (4 bp):
GTGC
Found at i:25621550 original size:16 final size:16
Alignment explanation
Indices: 25621529--25621644 Score: 128
Period size: 16 Copynumber: 7.4 Consensus size: 16
25621519 AATATAGTGT
25621529 GTGTGTGCGTGCGTGC
1 GTGTGTGCGTGCGTGC
25621545 GTGTGTGCGTGCGTGC
1 GTGTGTGCGTGCGTGC
*
25621561 GTGTGTGCATGCGTGC
1 GTGTGTGCGTGCGTGC
* ***
25621577 GAGCAAGCGTGCGTGC
1 GTGTGTGCGTGCGTGC
* *
25621593 GTGCGTGCTTGCGTGC
1 GTGTGTGCGTGCGTGC
* *
25621609 GTGCGTGCATGCGTGC
1 GTGTGTGCGTGCGTGC
*
25621625 GTGTGT--GTGTGTGC
1 GTGTGTGCGTGCGTGC
25621639 GTGTGT
1 GTGTGT
25621645 ATTCTTGGCC
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
14 12 0.14
16 74 0.86
ACGTcount: A:0.04, C:0.19, G:0.47, T:0.30
Consensus pattern (16 bp):
GTGTGTGCGTGCGTGC
Found at i:25622513 original size:12 final size:12
Alignment explanation
Indices: 25622496--25622520 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25622486 ATCCCTTCTC
25622496 TTTATTTATATA
1 TTTATTTATATA
25622508 TTTATTTATATA
1 TTTATTTATATA
25622520 T
1 T
25622521 AATTGGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTATATA
Found at i:25626380 original size:13 final size:13
Alignment explanation
Indices: 25626364--25626395 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
25626354 ATTAAAAATC
*
25626364 ATAAACAAAAGTT
1 ATAAAAAAAAGTT
25626377 ATAAAAAAAAGTT
1 ATAAAAAAAAGTT
25626390 ATAAAA
1 ATAAAA
25626396 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (13 bp):
ATAAAAAAAAGTT
Found at i:25626551 original size:23 final size:25
Alignment explanation
Indices: 25626509--25626554 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
25626499 ATCGAAATTA
25626509 TTCTTTTCTAATAAAAAATTATAAC
1 TTCTTTTCTAATAAAAAATTATAAC
25626534 TTCTTTT-TAA-AAAAAATTATA
1 TTCTTTTCTAATAAAAAATTATA
25626555 GTTTTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 11 0.52
24 3 0.14
25 7 0.33
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (25 bp):
TTCTTTTCTAATAAAAAATTATAAC
Found at i:25629488 original size:15 final size:15
Alignment explanation
Indices: 25629468--25629496 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25629458 AGCAATTCAG
25629468 GTATGGATCATTGGT
1 GTATGGATCATTGGT
25629483 GTATGGATCATTGG
1 GTATGGATCATTGG
25629497 AAAGTAGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.34, T:0.38
Consensus pattern (15 bp):
GTATGGATCATTGGT
Found at i:25630685 original size:44 final size:43
Alignment explanation
Indices: 25630289--25630732 Score: 239
Period size: 43 Copynumber: 10.3 Consensus size: 43
25630279 TTTGAACGGA
* * * *
25630289 AAACGCCGCTAAAAGTAGATACCTTTAGCGACGCTTT-ACCAT
1 AAACGCCGCTAAAAGTACAGACCTTTAGCGACGCTTTCTCCAC
* * * * **
25630331 AAACGCCGCTAAGAGTATAGACCTTTAGCGGCGCTTAGC-AAAC
1 AAACGCCGCTAAAAGTACAGACCTTTAGCGACGCTT-TCTCCAC
* * * * **
25630374 AAACGCCACTAAAAGCACATACCTTTAGCGGCGCTTTGC-AAAC
1 AAACGCCGCTAAAAGTACAGACCTTTAGCGACGCTTT-CTCCAC
* * ** * *
25630417 AAACGTCG-TTAAAGCTGTAGACCTTTAGCGGCGTTTTAC-CCAC
1 AAACGCCGCTAAAAG-TACAGACCTTTAGCGACGCTTT-CTCCAC
* * * ***
25630460 AAACGCCACTAAAGGTATAGACCTTTAGC-A-GCGTTTC-CGGGG
1 AAACGCCGCTAAAAGTACAGACCTTTAGCGACGC-TTTCTC-CAC
* * * *
25630502 AAAGCGCCGCTAAAAGTGCAGACCTTTAGCGACGTTTGTTTGCA-
1 AAA-CGCCGCTAAAAGTACAGACCTTTAGCGACGCTT-TCTCCAC
*
25630546 AAGCGCCGCTAAAAGTACAGACCTTTAGCGGA-GCTTT-TGCC-C
1 AAACGCCGCTAAAAGTACAGACCTTTAGC-GACGCTTTCT-CCAC
* ** * * * * *
25630588 GAAAAGGCCGCTAAATTTACAGACCTATAGCGGCGCTTACACCAA
1 --AAACGCCGCTAAAAGTACAGACCTTTAGCGACGCTTTCTCCAC
*
25630633 AAACGCCGCCAAAAGTACAGACCTTTTAGCGACGCTTTCTCCAC
1 AAACGCCGCTAAAAGTACAGACC-TTTAGCGACGCTTTCTCCAC
* * * * *
25630677 AAATGCCGCCAAAAGTAGAGTCCTTTAGCGGCGCTTTC-CCTAC
1 AAACGCCGCTAAAAGTACAGACCTTTAGCGACGCTTTCTCC-AC
*
25630720 AAACGCCACTAAA
1 AAACGCCGCTAAA
25630733 TTTACAGATT
Statistics
Matches: 307, Mismatches: 73, Indels: 43
0.73 0.17 0.10
Matches are distributed among these distances:
41 4 0.01
42 47 0.15
43 178 0.58
44 76 0.25
45 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAAGTACAGACCTTTAGCGACGCTTTCTCCAC
Found at i:25630685 original size:87 final size:86
Alignment explanation
Indices: 25630549--25630712 Score: 190
Period size: 87 Copynumber: 1.9 Consensus size: 86
25630539 GTTTGCAAAG
* * **
25630549 CGCCGCTAAAAGTACAGACCTTTAGCGGAGCTTTTGCCCGAAAAGGCCGCTAAATTTACAGACCT
1 CGCCGCCAAAAGTACAGACCTTTAGCGGAGCTTTTGCCC-AAAAGGCCGCCAAAAGTACAGACCT
25630614 ATAGCGGCGCTTACACCAAAAA
65 ATAGCGGCGCTTACACCAAAAA
* * *
25630636 CGCCGCCAAAAGTACAGACCTTTTAGC-GACGC-TTT-CTCCACAAATGCCGCCAAAAGTAGAGT
1 CGCCGCCAAAAGTACAGACC-TTTAGCGGA-GCTTTTGC-CCA-AAAGGCCGCCAAAAGTACAGA
*
25630698 CCTTTAGCGGCGCTT
62 CCTATAGCGGCGCTT
25630713 TCCCTACAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
86 2 0.03
87 55 0.85
88 8 0.12
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (86 bp):
CGCCGCCAAAAGTACAGACCTTTAGCGGAGCTTTTGCCCAAAAGGCCGCCAAAAGTACAGACCTA
TAGCGGCGCTTACACCAAAAA
Found at i:25636690 original size:9 final size:9
Alignment explanation
Indices: 25636676--25636808 Score: 76
Period size: 9 Copynumber: 14.6 Consensus size: 9
25636666 ATGTATTAGT
25636676 TAAGTTATG
1 TAAGTTATG
25636685 TAAGTTATG
1 TAAGTTATG
*
25636694 TGAGTTATG
1 TAAGTTATG
*
25636703 TAAGTTGTTATA
1 TAA---GTTATG
*
25636715 TACGTTATG
1 TAAGTTATG
* *
25636724 TGAGTTATA
1 TAAGTTATG
*
25636733 TAAATTATG
1 TAAGTTATG
25636742 T-A---ATG
1 TAAGTTATG
25636747 TAAGTTATG
1 TAAGTTATG
*
25636756 TAGGTTGTTATG
1 TA---AGTTATG
*
25636768 TAAATTATG
1 TAAGTTATG
*
25636777 TAAGTTACG
1 TAAGTTATG
*
25636786 TGAGTTATG
1 TAAGTTATG
* *
25636795 TAACTTATT
1 TAAGTTATG
25636804 TAAGT
1 TAAGT
25636809 AATGATCAAT
Statistics
Matches: 92, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
5 4 0.04
6 1 0.01
8 1 0.01
9 71 0.77
12 15 0.16
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:25638515 original size:46 final size:46
Alignment explanation
Indices: 25638465--25638640 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
25638455 TGGTTGAGCA
* *
25638465 TCCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
25638511 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* **
25638556 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
25638604 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
25638641 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 60 0.58
47 28 0.27
48 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:25638621 original size:93 final size:93
Alignment explanation
Indices: 25638462--25638632 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
25638452 GGATGGTTGA
* * ***
25638462 GCATCCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCGAACACCCGAACTCGTTGAGT
*
25638527 TGAGTCTGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
25638555 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCGAACACCCGAACTCGTTGAGT
25638620 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
25638633 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACCTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:25641583 original size:15 final size:15
Alignment explanation
Indices: 25641565--25641633 Score: 68
Period size: 15 Copynumber: 4.6 Consensus size: 15
25641555 ATCTTGGGTT
*
25641565 TCTTTATCCTGGATC
1 TCTTTATTCTGGATC
*
25641580 TCTTTATTCTGGATT
1 TCTTTATTCTGGATC
* *
25641595 TCTTTATTCTGGGTT
1 TCTTTATTCTGGATC
* *
25641610 TCTCTATAT-TGGATT
1 TCTTTAT-TCTGGATC
25641625 TCTTTATTC
1 TCTTTATTC
25641634 GGTTTTCTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
14 1 0.02
15 44 0.96
16 1 0.02
ACGTcount: A:0.13, C:0.17, G:0.13, T:0.57
Consensus pattern (15 bp):
TCTTTATTCTGGATC
Found at i:25641632 original size:30 final size:29
Alignment explanation
Indices: 25641558--25641641 Score: 89
Period size: 30 Copynumber: 2.9 Consensus size: 29
25641548 GTATTGTATC
* * * *
25641558 TTGGGTTTCTTTATCCTGGATCTCTTTAT
1 TTGGATTTCTTTATTCTGGATTTCTCTAT
*
25641587 TCTGGATTTCTTTATTCTGGGTTTCTCTAT
1 T-TGGATTTCTTTATTCTGGATTTCTCTAT
*
25641617 ATTGGATTTCTTTATTC-GGTTTTCT
1 -TTGGATTTCTTTATTCTGGATTTCT
25641642 TGTTATCTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 8 0.17
30 38 0.81
31 1 0.02
ACGTcount: A:0.11, C:0.15, G:0.17, T:0.57
Consensus pattern (29 bp):
TTGGATTTCTTTATTCTGGATTTCTCTAT
Found at i:25644080 original size:46 final size:46
Alignment explanation
Indices: 25644030--25644205 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
25644020 TGGTTGAGCA
*
25644030 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
25644076 TCCGAACTCATTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
25644121 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
25644169 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
25644206 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 16, Indels: 18
0.76 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.58
47 28 0.27
48 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:25644186 original size:93 final size:93
Alignment explanation
Indices: 25644027--25644197 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
25644017 GGATGGTTGA
* * * *
25644027 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
25644092 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
25644120 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
25644185 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
25644198 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:25647105 original size:25 final size:26
Alignment explanation
Indices: 25647050--25647105 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
25647040 TTATAATTAA
* * *
25647050 ATTAATATAATATATAAAAATTTAGG
1 ATTAATATAAGATAAAAAAATTTACG
*
25647076 A-TAATATTAGATAAAAAAATTT-CG
1 ATTAATATAAGATAAAAAAATTTACG
25647100 ATTAAT
1 ATTAAT
25647106 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 2 0.08
25 22 0.88
26 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (26 bp):
ATTAATATAAGATAAAAAAATTTACG
Found at i:25649628 original size:47 final size:47
Alignment explanation
Indices: 25649571--25649874 Score: 403
Period size: 47 Copynumber: 6.4 Consensus size: 47
25649561 ATTGATGTAC
* * * *
25649571 AAGTATATATATGTGATAGGGTCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * * *
25649618 AAGTATATATATATGTGATAGGGCCGAGTGGCCAACGTGATGAATGTGA
1 AAG--TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * * * *
25649667 AAGTGTATATATGTGATTCA-GTCGAGTGACCAACGTGATGAATGTGA
1 AAGTGTATATATGTGA-TAAGGCCGAATGGCCAATGTGATGAATGTGA
25649714 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
25649761 AAGTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
25649808 AAGTGTATATATGTGATAAAGCCGAATGGCCAATGTGATGGATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
25649855 AAGTGTATAGATGTGATAAG
1 AAGTGTATATATGTGATAAG
25649875 TCCCGAAGGG
Statistics
Matches: 231, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
46 2 0.01
47 183 0.79
48 1 0.00
49 45 0.19
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.28
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:25653061 original size:7 final size:7
Alignment explanation
Indices: 25653049--25653098 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
25653039 ACAAAATCAT
25653049 ACCCTAA
1 ACCCTAA
25653056 ACCCTAA
1 ACCCTAA
* *
25653063 ATCTTAA
1 ACCCTAA
25653070 ACCCTAA
1 ACCCTAA
*
25653077 ACTCTAA
1 ACCCTAA
*
25653084 ACCATAA
1 ACCCTAA
25653091 ATCCCTAA
1 A-CCCTAA
25653099 CCTTATAAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
7 29 0.85
8 5 0.15
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (7 bp):
ACCCTAA
Found at i:25653072 original size:14 final size:15
Alignment explanation
Indices: 25653052--25653098 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
25653042 AAATCATACC
25653052 CTAAACCCTAAATCT
1 CTAAACCCTAAATCT
25653067 -TAAACCCTAAA-CT
1 CTAAACCCTAAATCT
* *
25653080 CTAAACCATAAATCC
1 CTAAACCCTAAATCT
25653095 CTAA
1 CTAA
25653099 CCTTATAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 2 0.07
14 21 0.75
15 5 0.18
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (15 bp):
CTAAACCCTAAATCT
Found at i:25653074 original size:21 final size:21
Alignment explanation
Indices: 25653049--25653121 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
25653039 ACAAAATCAT
*
25653049 ACCCTAAACCCTAAATCTTAA
1 ACCCTAAACCCTAAAACTTAA
* * *
25653070 ACCCTAAACTCTAAACCATAA
1 ACCCTAAACCCTAAAACTTAA
*
25653091 ATCCCT-AACCTTATAAACATTAA
1 A-CCCTAAACCCTA-AAAC-TTAA
25653114 ACCCTAAA
1 ACCCTAAA
25653122 TTCTAGATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
21 24 0.59
22 11 0.27
23 6 0.15
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (21 bp):
ACCCTAAACCCTAAAACTTAA
Found at i:25653600 original size:21 final size:19
Alignment explanation
Indices: 25653564--25653602 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
25653554 CATGCATAAA
*
25653564 CCCTTAACTTATCCCCTAT
1 CCCTTAACTTAACCCCTAT
25653583 CCCTTAAACCTTAACCCCTA
1 CCCTT-AA-CTTAACCCCTA
25653603 ACCACTAACC
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:0.26, C:0.44, G:0.00, T:0.31
Consensus pattern (19 bp):
CCCTTAACTTAACCCCTAT
Found at i:25654391 original size:15 final size:16
Alignment explanation
Indices: 25654371--25654421 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
25654361 AAATCACAAA
25654371 CACTAAACCCCT-AAC
1 CACTAAACCCCTAAAC
*
25654386 CACT-AACCCTTAAAC
1 CACTAAACCCCTAAAC
*
25654401 CCCTAAA-CCCTAAAC
1 CACTAAACCCCTAAAC
25654416 CA-TAAA
1 CACTAAA
25654422 AACATAAACC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 10 0.33
15 18 0.60
16 2 0.07
ACGTcount: A:0.43, C:0.41, G:0.00, T:0.16
Consensus pattern (16 bp):
CACTAAACCCCTAAAC
Found at i:25654411 original size:7 final size:7
Alignment explanation
Indices: 25654368--25654512 Score: 53
Period size: 7 Copynumber: 19.7 Consensus size: 7
25654358 TATAAATCAC
*
25654368 AAACACT
1 AAACCCT
25654375 AAACCCCT
1 AAA-CCCT
25654383 -AACCACT
1 AAACC-CT
25654390 -AACCCTT
1 AAACCC-T
25654397 AAACCCCT
1 AAA-CCCT
25654405 AAACCCT
1 AAACCCT
*
25654412 AAACCAT
1 AAACCCT
* *
25654419 AAAAACAT
1 -AAACCCT
*
25654427 AAACCAT
1 AAACCCT
*
25654434 GAACCCTT
1 AAACCC-T
25654442 AAA-CCT
1 AAACCCT
*
25654448 AAACCAT
1 AAACCCT
25654455 AAACCCTT
1 AAACCC-T
25654463 AATACCGCT
1 AA-ACC-CT
**
25654472 AAACATT
1 AAACCCT
* *
25654479 AAGATCAT
1 AA-ACCCT
*
25654487 AAACACT
1 AAACCCT
*
25654494 AAACACT
1 AAACCCT
*
25654501 AAACACT
1 AAACCCT
25654508 AAACC
1 AAACC
25654513 TCAAACCCAA
Statistics
Matches: 108, Mismatches: 18, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
6 7 0.06
7 64 0.59
8 27 0.25
9 9 0.08
10 1 0.01
ACGTcount: A:0.48, C:0.32, G:0.02, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:25654444 original size:15 final size:15
Alignment explanation
Indices: 25654390--25654452 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
25654380 CCTAACCACT
*
25654390 AACCCTTAAACCCCTA
1 AACCCTTAAA-CCATA
25654406 AACCC-TAAACCATA
1 AACCCTTAAACCATA
** * *
25654420 AAAACATAAACCATG
1 AACCCTTAAACCATA
25654435 AACCCTTAAACC-TA
1 AACCCTTAAACCATA
25654449 AACC
1 AACC
25654453 ATAAACCCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
14 12 0.32
15 21 0.55
16 5 0.13
ACGTcount: A:0.48, C:0.35, G:0.02, T:0.16
Consensus pattern (15 bp):
AACCCTTAAACCATA
Found at i:25654450 original size:21 final size:21
Alignment explanation
Indices: 25654421--25654464 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
25654411 TAAACCATAA
*
25654421 AAACATAAACCATGAACCCTT
1 AAACATAAACCATAAACCCTT
*
25654442 AAACCTAAACCATAAACCCTT
1 AAACATAAACCATAAACCCTT
25654463 AA
1 AA
25654465 TACCGCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.18
Consensus pattern (21 bp):
AAACATAAACCATAAACCCTT
Found at i:25654595 original size:35 final size:35
Alignment explanation
Indices: 25654530--25654603 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
25654520 CAAAATAACA
** *
25654530 AAACCCTAAACCATAAAATTAACATTTTAAATCTT
1 AAACCCTAAACCATAAAATTAACACCTTAAATATT
**
25654565 AAACCCTAAACCATAGACCTTAA-ACCTTAAATATT
1 AAACCCTAAACCATA-AAATTAACACCTTAAATATT
25654600 AAAC
1 AAAC
25654604 TGTAAACCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
35 28 0.85
36 5 0.15
ACGTcount: A:0.49, C:0.23, G:0.01, T:0.27
Consensus pattern (35 bp):
AAACCCTAAACCATAAAATTAACACCTTAAATATT
Found at i:25654943 original size:122 final size:121
Alignment explanation
Indices: 25654664--25655393 Score: 849
Period size: 122 Copynumber: 6.0 Consensus size: 121
25654654 AATTCAAAAA
* * * * *
25654664 AGACATTTAGCGGCGTTTCTCCAAAAACGCTGCTAATTCTCAGACTTTTGGCGGCGTTTTTCCAA
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTCAGACTTTTGGCGGCG-TTTTCCAA
* * * *
25654729 AAACGTCGCGAATACTCAGACTTTTGGCGGCGTTTTCCCAAAAACGCCGCTAATACTC
65 AAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTT-CCAAAAACGCCGCTAATGCTC
* *
25654787 AGACTTTTGGCGGCGTTTTCCCAAAAACGCCGCTAATGCTCAGTA-TTTTGGGGGCGTTTTCCGA
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTCAG-ACTTTTGGCGGCGTTTTCC-A
* * * *
25654851 AAAACGCCGCTAATTCTCAGACTTTTAGCGGCGCTTTCCAAAAACGCCGCAAATGCTC
64 AAAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTCCAAAAACGCCGCTAATGCTC
* * * * *
25654909 AGACTTTTTGCGGCGTTTTTTCAACAACGCCGCTAATTCTCAGACTTTTAGCGGCGTTTTTCCAA
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTCAGACTTTTGGCGGCG-TTTTCCAA
* *
25654974 CAACGCCGCTAATGCTCAGACTTTTAGCGGCGCTTTTCCAAAAA-GCCGCTAATGCTC
65 AAACGCCGCTAATGCTCAGACTTTTGGCGGCG-TTTTCCAAAAACGCCGCTAATGCTC
* ** **
25655031 AGACTTTTAGCGGCGCGTTTCCAAAAACGCCGCTAATGCTCAGACTTTTGGCGGCGTGTTTATAA
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTCAGACTTTTGGCGGCGT-TTTCCAA
** *
25655096 AAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTGGTAAAAAACGCCGCTAACGCTC
65 AAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTT--CCAAAAACGCCGCTAATGCTC
* * * * *
25655155 AGACTTTTGGCGGCGTTTTGGT-AAAAAACGCCGCTAACGCTCAGACCTTTGGCTGCGTTTTTCT
1 AGACTTTTGGCGGCGTTTT--TCCAAAAACGCCGCTAATGCTCAGACTTTTGGCGGCG-TTTTCC
* * *
25655219 AAAAACGCCGCTAACGCTCAGACTTTTGGCGGCGTTTTTCTAAAAATGCCGCTAATGCTC
63 AAAAACGCCGCTAATGCTCAGACTTTTGGCGGCG-TTTTCCAAAAACGCCGCTAATGCTC
** * * * * **
25655279 AGACTTTTGGCGGCGTTTTTGGAAAAATGCCGCGAATTCTCAGAC--TTGGCAGCGTTTCTTGAA
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTT-TCCAA
* * *
25655342 AAACGCCGCTAATTCTCGGACTTTTGGCGGCGTTTTTCCGAAAACGCCGCTA
65 AAACGCCGCTAATGCTCAGACTTTTGGCGGCG-TTTTCCAAAAACGCCGCTA
25655394 TTTCTCGACT
Statistics
Matches: 526, Mismatches: 66, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
120 3 0.01
121 63 0.12
122 201 0.38
123 120 0.23
124 65 0.12
125 68 0.13
126 6 0.01
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (121 bp):
AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTCCAAA
AACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTCCAAAAACGCCGCTAATGCTC
Found at i:25655400 original size:41 final size:41
Alignment explanation
Indices: 25654664--25655393 Score: 884
Period size: 41 Copynumber: 17.9 Consensus size: 41
25654654 AATTCAAAAA
* * * * *
25654664 AGACATTTAGCGGCGTTTCTCCAAAAACGCTGCTAATTCTC
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
* * *
25654705 AGACTTTTGGCGGCGTTTTTCCAAAAACGTCGCGAATACTC
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
* *
25654746 AGACTTTTGGCGGCGTTTTCCCAAAAACGCCGCTAATACTC
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
*
25654787 AGACTTTTGGCGGCGTTTTCCCAAAAACGCCGCTAATGCTC
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
* *
25654828 AGTA-TTTTGGGGGCG-TTTTCCGAAAAACGCCGCTAATTCTC
1 AG-ACTTTTGGCGGCGTTTTTCC-AAAAACGCCGCTAATGCTC
* * *
25654869 AGACTTTTAGCGGCG-CTTTCCAAAAACGCCGCAAATGCTC
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
* * * *
25654909 AGACTTTTTGCGGCGTTTTTTCAACAACGCCGCTAATTCTC
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
* *
25654950 AGACTTTTAGCGGCGTTTTTCCAACAACGCCGCTAATGCTC
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
* *
25654991 AGACTTTTAGCGGCGCTTTTCCAAAAA-GCCGCTAATGCTC
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
* **
25655031 AGACTTTTAGCGGCGCGTTTCCAAAAACGCCGCTAATGCTC
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
* **
25655072 AGACTTTTGGCGGCGTGTTTATAAAAACGCCGCTAATGCTC
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
* *
25655113 AGACTTTTGGCGGCGTTTTGGT-AAAAAACGCCGCTAACGCTC
1 AGACTTTTGGCGGCGTTTT--TCCAAAAACGCCGCTAATGCTC
* *
25655155 AGACTTTTGGCGGCGTTTTGGT-AAAAAACGCCGCTAACGCTC
1 AGACTTTTGGCGGCGTTTT--TCCAAAAACGCCGCTAATGCTC
* * * *
25655197 AGACCTTTGGCTGCGTTTTTCTAAAAACGCCGCTAACGCTC
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
* *
25655238 AGACTTTTGGCGGCGTTTTTCTAAAAATGCCGCTAATGCTC
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
** * * *
25655279 AGACTTTTGGCGGCGTTTTTGGAAAAATGCCGCGAATTCTC
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
* * *
25655320 AGAC--TTGGCAGCGTTTCTT-GAAAAACGCCGCTAATTCTC
1 AGACTTTTGGCGGCGTTT-TTCCAAAAACGCCGCTAATGCTC
* *
25655359 GGACTTTTGGCGGCGTTTTTCCGAAAACGCCGCTA
1 AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTA
25655394 TTTCTCGACT
Statistics
Matches: 621, Mismatches: 56, Indels: 24
0.89 0.08 0.03
Matches are distributed among these distances:
39 32 0.05
40 81 0.13
41 429 0.69
42 78 0.13
43 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (41 bp):
AGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCTAATGCTC
Found at i:25663058 original size:2 final size:2
Alignment explanation
Indices: 25663051--25663081 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
25663041 TAAAGAAGAA
*
25663051 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
25663082 TGAAATCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25663064 original size:12 final size:12
Alignment explanation
Indices: 25663047--25663081 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
25663037 GAGATAAAGA
25663047 AGAAAGAGAGAG
1 AGAAAGAGAGAG
25663059 AGAAAGAGAGAG
1 AGAAAGAGAGAG
*
25663071 AGAGAGAGAGA
1 AGAAAGAGAGA
25663082 TGAAATCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (12 bp):
AGAAAGAGAGAG
Found at i:25668105 original size:27 final size:26
Alignment explanation
Indices: 25668063--25668123 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
25668053 ACCTATTTTA
*
25668063 AATTTATATATTGCTTCATTTTAAATC
1 AATTTATATATAGCTT-ATTTTAAATC
*
25668090 AATTTTTATATAGCTTATTTTAAACTC
1 AATTTATATATAGCTTATTTTAAA-TC
*
25668117 CATTTAT
1 AATTTAT
25668124 TTATTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.33, C:0.11, G:0.03, T:0.52
Consensus pattern (26 bp):
AATTTATATATAGCTTATTTTAAATC
Found at i:25668126 original size:29 final size:29
Alignment explanation
Indices: 25668064--25668127 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
25668054 CCTATTTTAA
25668064 ATTTATATATTGCTTCATTTTAAATCAATT
1 ATTTATATA-TGCTTCATTTTAAATCAATT
*
25668094 -TTTATATA-GCTT-ATTTTAAACTCCATTT
1 ATTTATATATGCTTCATTTTAAA-T-CAATT
25668122 ATTTAT
1 ATTTAT
25668128 TTAAAAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 8 0.27
27 5 0.17
28 4 0.13
29 13 0.43
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTATATATGCTTCATTTTAAATCAATT
Found at i:25669606 original size:46 final size:46
Alignment explanation
Indices: 25669539--25669669 Score: 199
Period size: 46 Copynumber: 2.8 Consensus size: 46
25669529 GATATTTGGG
* *
25669539 CATCCAAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
*
25669585 CATCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
** * *
25669631 CGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
25669670 GCGGGTTACA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:25674758 original size:14 final size:14
Alignment explanation
Indices: 25674739--25674776 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
25674729 GTTTGCCAGT
25674739 AAAATATTTTCTGG
1 AAAATATTTTCTGG
*
25674753 AAAATAATTTCTGG
1 AAAATATTTTCTGG
25674767 AAAATGATTT
1 AAAAT-ATTT
25674777 ACTTTTCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.86
15 3 0.14
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (14 bp):
AAAATATTTTCTGG
Found at i:25674815 original size:19 final size:20
Alignment explanation
Indices: 25674760--25674823 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
25674750 TGGAAAATAA
*
25674760 TTTCTGGAAAATGATTTACT
1 TTTCTAGAAAATGATTTACT
* *
25674780 TTTCTAGAAAATAATTTAAT
1 TTTCTAGAAAATGATTTACT
*
25674800 TTTTTAG-AAATGATTTACT
1 TTTCTAGAAAATGATTTACT
25674819 TTTCT
1 TTTCT
25674824 GGTGTTTGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 14 0.38
20 23 0.62
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (20 bp):
TTTCTAGAAAATGATTTACT
Found at i:25674927 original size:18 final size:19
Alignment explanation
Indices: 25674900--25674945 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
25674890 GAAAATCTGT
*
25674900 TTTTACATATATTAATAAA
1 TTTTATATATATTAATAAA
*
25674919 TTTATATATATATTACTAAA
1 TTT-TATATATATTAATAAA
25674939 -TTTATAT
1 TTTTATAT
25674946 TTTAAACTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 5 0.21
20 14 0.58
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTATATATATTAATAAA
Found at i:25674931 original size:20 final size:20
Alignment explanation
Indices: 25674906--25674945 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
25674896 CTGTTTTTAC
25674906 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
*
25674926 ATATATTACTAAATTTATAT
1 ATATATTAATAAATTTATAT
25674946 TTTAAACTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:25681931 original size:39 final size:39
Alignment explanation
Indices: 25681888--25681966 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
25681878 AATGGATCAA
* *
25681888 ACATGTTGATATCATCCAATTAAAATAGACAGCTTTCAT
1 ACATGTTGATATCATCCAACTAAAATAAACAGCTTTCAT
*
25681927 ACATGTTGATATCATCCAACTAAAATAAACGGCTTTCAT
1 ACATGTTGATATCATCCAACTAAAATAAACAGCTTTCAT
25681966 A
1 A
25681967 GATTAATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (39 bp):
ACATGTTGATATCATCCAACTAAAATAAACAGCTTTCAT
Found at i:25683328 original size:24 final size:23
Alignment explanation
Indices: 25683300--25683351 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
25683290 CCTTAGAAAG
*
25683300 AGAGATTTGCCTTTGCCTGAGAA
1 AGAGATTTGCCTTTGCCTAAGAA
*
25683323 ATGAGATTTGCCTTTGGCTAAGAA
1 A-GAGATTTGCCTTTGCCTAAGAA
25683347 AGAGA
1 AGAGA
25683352 GAAAAAGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (23 bp):
AGAGATTTGCCTTTGCCTAAGAA
Found at i:25697635 original size:19 final size:18
Alignment explanation
Indices: 25697609--25697662 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
25697599 TTTTGGTACA
25697609 ATAATTTTTATATTTTTT
1 ATAATTTTTATATTTTTT
25697627 ATGAA-TTTTATATTTCTTT
1 AT-AATTTTTATATTT-TTT
*
25697646 ATATTTTTTATAATTTT
1 ATAATTTTTAT-ATTTT
25697663 CTTACTACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 13 0.42
19 14 0.45
20 4 0.13
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
ATAATTTTTATATTTTTT
Found at i:25697646 original size:10 final size:9
Alignment explanation
Indices: 25697613--25697662 Score: 57
Period size: 9 Copynumber: 5.3 Consensus size: 9
25697603 GGTACAATAA
25697613 TTTTTATAT
1 TTTTTATAT
25697622 TTTTTATGA-
1 TTTTTAT-AT
*
25697631 ATTTTATAT
1 TTTTTATAT
25697640 TTCTTTATAT
1 TT-TTTATAT
25697650 TTTTTATAAT
1 TTTTTAT-AT
25697660 TTT
1 TTT
25697663 CTTACTACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 1 0.03
9 19 0.54
10 15 0.43
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (9 bp):
TTTTTATAT
Found at i:25697673 original size:28 final size:27
Alignment explanation
Indices: 25697615--25697691 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 27
25697605 TACAATAATT
* *
25697615 TTTATATTTTTTATGAATTTTATATTTC
1 TTTATATTTTTTAT-AATTTTATACTAC
*
25697643 TTTATATTTTTTATAATTTTCTTACTAC
1 TTTATATTTTTTATAATTTT-ATACTAC
**
25697671 TTTATAAAATTTTATAATTTT
1 TTTAT-ATTTTTTATAATTTT
25697692 TTTCTATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 6 0.14
28 23 0.55
29 13 0.31
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (27 bp):
TTTATATTTTTTATAATTTTATACTAC
Found at i:25697754 original size:12 final size:13
Alignment explanation
Indices: 25697728--25697755 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
25697718 TGTTTTACTA
25697728 TTTTTATCAATTT
1 TTTTTATCAATTT
25697741 TTTTTATCAATTT
1 TTTTTATCAATTT
25697754 TT
1 TT
25697756 AATAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTATCAATTT
Found at i:25697782 original size:9 final size:9
Alignment explanation
Indices: 25697741--25697835 Score: 64
Period size: 10 Copynumber: 9.8 Consensus size: 9
25697731 TTATCAATTT
25697741 TTTTTATCAA
1 TTTTTAT-AA
25697751 TTTTTAATAA
1 TTTTT-ATAA
* * *
25697761 ATTTAAAATA
1 TTTTTATA-A
25697771 TTTTTATAA
1 TTTTTATAA
25697780 TTTTTATTAAA
1 TTTTTA-T-AA
*
25697791 ATTTTATAA
1 TTTTTATAA
25697800 TTTTTATAA
1 TTTTTATAA
* *
25697809 ATTTTATTTA
1 TTTTTA-TAA
*
25697819 TTTTTATTTA
1 TTTTTA-TAA
25697829 TTTTTAT
1 TTTTTAT
25697836 CTTTTTGCCA
Statistics
Matches: 69, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
9 25 0.36
10 35 0.51
11 9 0.13
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:25697783 original size:29 final size:29
Alignment explanation
Indices: 25697741--25697814 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
25697731 TTATCAATTT
25697741 TTTTTATCAATTTTTAAT-AAATTTAAAATA
1 TTTTTAT-AATTTTTAATAAAATTTAAAA-A
* * *
25697771 TTTTTATAATTTTTATTAAAATTTTATAA
1 TTTTTATAATTTTTAATAAAATTTAAAAA
*
25697800 TTTTTATAAATTTTA
1 TTTTTATAATTTTTA
25697815 TTTATTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 24 0.62
30 15 0.38
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTTATAATTTTTAATAAAATTTAAAAA
Found at i:25697831 original size:29 final size:29
Alignment explanation
Indices: 25697769--25697835 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
25697759 AAATTTAAAA
*
25697769 TATTTTTATAATTTTTATTAAAATTTTAT
1 TATTTTTATAAATTTTATTAAAATTTTAT
* * *
25697798 AATTTTTATAAATTTTATT-TATTTTTATT
1 TATTTTTATAAATTTTATTAAAATTTTA-T
25697827 TATTTTTAT
1 TATTTTTAT
25697836 CTTTTTGCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (29 bp):
TATTTTTATAAATTTTATTAAAATTTTAT
Found at i:25698438 original size:83 final size:83
Alignment explanation
Indices: 25698297--25698500 Score: 238
Period size: 83 Copynumber: 2.5 Consensus size: 83
25698287 TGAAAATGAA
* *** * *
25698297 AAAAAATAGGGGCTTAATTGCTTTTTTTTTTAAATTTGAGGACTTTTTTATACATTTTGACAGCT
1 AAAAAATAGGGGCTTAATTACTTTTTTTGAAAAATTTGAGAACTTTTTTATACATTTTGAAAGCT
25698362 CAAATACACAATTGAGTG
66 CAAATACACAATTGAGTG
*
25698380 AAAAAA-A-GGGCTTAATTACTTTTTTTGAAAAAGTTTGAGAACTTTTTTGTTACATTTTGAAAG
1 AAAAAATAGGGGCTTAATTACTTTTTTTGAAAAA-TTTGAGAACTTTTTT-ATACATTTTGAAAG
* * * *
25698443 TTTAAGTACCCAATTGAGTG
64 CTCAAATACACAATTGAGTG
* *
25698463 AAAAAATAGGGGCTTAA--A-TTTTTTTTAAAGATTTGAGA
1 AAAAAATAGGGGCTTAATTACTTTTTTTGAAAAATTTGAGA
25698501 TCATTTTACA
Statistics
Matches: 104, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
81 28 0.27
82 26 0.25
83 41 0.39
84 1 0.01
85 8 0.08
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (83 bp):
AAAAAATAGGGGCTTAATTACTTTTTTTGAAAAATTTGAGAACTTTTTTATACATTTTGAAAGCT
CAAATACACAATTGAGTG
Found at i:25700500 original size:25 final size:25
Alignment explanation
Indices: 25700464--25700512 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
25700454 CCAACGATAT
*
25700464 CCAACAGTTTTAAGTATTCACATTG
1 CCAACAGTTTTAAGTAATCACATTG
*
25700489 CCAACA-TATTTAATTAATCACATT
1 CCAACAGT-TTTAAGTAATCACATT
25700513 TTATTACGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (25 bp):
CCAACAGTTTTAAGTAATCACATTG
Found at i:25715296 original size:39 final size:40
Alignment explanation
Indices: 25715234--25715311 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 40
25715224 GGTACTTTAT
* *
25715234 GGTGTGTAGGGTTGGATGGGTCGATTATAT-CCCATATAC
1 GGTGTGTAGGGATGGATGCGTCGATTATATCCCCATATAC
* *
25715273 GGTGTGTAGGGATGGGTGCGTCGATTTTATCCCCATATA
1 GGTGTGTAGGGATGGATGCGTCGATTATATCCCCATATA
25715312 GTGTGTTGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 26 0.76
40 8 0.24
ACGTcount: A:0.19, C:0.14, G:0.33, T:0.33
Consensus pattern (40 bp):
GGTGTGTAGGGATGGATGCGTCGATTATATCCCCATATAC
Found at i:25717656 original size:41 final size:41
Alignment explanation
Indices: 25717611--25717699 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
25717601 TGTAAATTAG
* *
25717611 TAGCGGGGTTCATGAGAAAAATGCCACAAAAGGTCAAGTAT
1 TAGCGGCGTTCATGAGAAAAATGCCACAAAAGGTCAAGCAT
* *
25717652 TAGCGGCGTTTATGAGAAAAATGCCGCAAAAGGTCAAGCAT
1 TAGCGGCGTTCATGAGAAAAATGCCACAAAAGGTCAAGCAT
25717693 TAGCGGC
1 TAGCGGC
25717700 ACCAGGAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (41 bp):
TAGCGGCGTTCATGAGAAAAATGCCACAAAAGGTCAAGCAT
Found at i:25717720 original size:40 final size:41
Alignment explanation
Indices: 25717624--25717721 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
25717614 CGGGGTTCAT
* * *** *
25717624 GAGAAAAATGCCACAAAAGGTCAAGTATTAGCGGCGTTTAT
1 GAGAAAAATGCCGCAAAAGGTCAAGCATTAGCGGCGACCAG
25717665 GAGAAAAATGCCGCAAAAGGTCAAGCATTAGCGGC-ACCAG
1 GAGAAAAATGCCGCAAAAGGTCAAGCATTAGCGGCGACCAG
*
25717705 GAGAAAAACGCCGCAAA
1 GAGAAAAATGCCGCAAA
25717722 GTATAATCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 17 0.34
41 33 0.66
ACGTcount: A:0.42, C:0.19, G:0.26, T:0.13
Consensus pattern (41 bp):
GAGAAAAATGCCGCAAAAGGTCAAGCATTAGCGGCGACCAG
Found at i:25719373 original size:40 final size:40
Alignment explanation
Indices: 25719322--25719511 Score: 260
Period size: 40 Copynumber: 4.8 Consensus size: 40
25719312 GAATATAGCT
* * *
25719322 ACTCGCTCAAATGCCTTAGGGACTTAGCCCTG-ATATAGT-
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTC
* *
25719361 AGTTCGCACAAATGCCTTCGGGACTTAGCCCGG-ATATAGTA
1 A-CTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTC
*
25719402 ACTCGCACAAATGCCTTCGGGACTTAGCCCAGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
*
25719442 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
*
25719482 ACTAGCACAAATGCCTTCGGGACTTAGCCC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCC
25719512 CGTTATCATC
Statistics
Matches: 139, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 1 0.01
40 135 0.97
41 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
Found at i:25719450 original size:80 final size:79
Alignment explanation
Indices: 25719296--25719511 Score: 269
Period size: 80 Copynumber: 2.7 Consensus size: 79
25719286 AAACCAAGTA
* * * * * *
25719296 CCTTCGGGATTTA-ACCGAATATAGCTACTCGCTCAAATGCCTTAGGGACTTAGCCCTGATATAG
1 CCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCAGATATAG
* *
25719360 TAGTTCGCACAAATG
65 TAGCTAGCACAAATG
25719375 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCAGA-ATTA
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCAGATA-TA
25719439 GTCA-CTAGCACAAATG
64 GT-AGCTAGCACAAATG
*
25719455 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCCGGATA-TAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCC
25719512 CGTTATCATC
Statistics
Matches: 122, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
79 15 0.12
80 106 0.87
81 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCAGATATAGT
AGCTAGCACAAATG
Found at i:25727406 original size:40 final size:39
Alignment explanation
Indices: 25727329--25727582 Score: 313
Period size: 40 Copynumber: 6.4 Consensus size: 39
25727319 AAACCAAGTA
* * *
25727329 CCTTCGGGATTTA-ACC-GAATATAGCTACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGAAT-TAG-TACTCGCACAAATG
* *
25727368 CCTTCGGGACTTAGCCCTG-ATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAAT-TAGTA-CTCGCACAAATG
25727408 CCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAAT-TAGT-ACTCGCACAAATG
25727448 -CTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAATTAGT-ACTCGCACAAATG
*
25727487 CCTT-GGGACTTAGCCCGGAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGAATTAGT-ACTCGCACAAATG
*
25727526 CCTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGAATTAGT-ACTCGCACAAATG
*
25727566 CCTTCAGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
25727583 CGTTATCATC
Statistics
Matches: 199, Mismatches: 8, Indels: 15
0.90 0.04 0.07
Matches are distributed among these distances:
39 86 0.43
40 111 0.56
41 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGAATTAGTACTCGCACAAATG
Found at i:25727461 original size:79 final size:78
Alignment explanation
Indices: 25727329--25727582 Score: 329
Period size: 79 Copynumber: 3.2 Consensus size: 78
25727319 AAACCAAGTA
* * * *
25727329 CCTTCGGGATTTA-ACCGAATATAGCTACTCGCTCAAATGCCTTCGGGACTTAGCCCTG-ATATA
1 CCTTCGGGACTTAGCCCGAATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TA
*
25727392 GTAGTTCGCACAAATG
64 GTA-CTCGCACAAATG
25727408 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG-CTTCGGGACTTAGCCCGGAATTAG
1 CCTTCGGGACTTAGCCCGAATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAG
25727472 TAACTCGCACAAATG
65 T-ACTCGCACAAATG
*
25727487 CCTT-GGGACTTAGCCCGGAAT-TAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
1 CCTTCGGGACTTAGCCC-GAATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
*
25727550 GTCACTAGCACAAATG
64 GT-ACTCGCACAAATG
*
25727566 CCTTCAGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
25727583 CGTTATCATC
Statistics
Matches: 158, Mismatches: 10, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
78 28 0.18
79 94 0.59
80 36 0.23
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (78 bp):
CCTTCGGGACTTAGCCCGAATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
ACTCGCACAAATG
Found at i:25727463 original size:39 final size:40
Alignment explanation
Indices: 25727355--25727582 Score: 329
Period size: 40 Copynumber: 5.8 Consensus size: 40
25727345 GAATATAGCT
* *
25727355 ACTCGCTCAAATGCCTTCGGGACTTAGCCCTG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
**
25727395 GTTCGCACAAATGCCTTCGGGACTTAGCCC-GAATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
25727435 ACTCGCACAAATG-CTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
25727474 ACTCGCACAAATGCCTT-GGGACTTAGCCCGGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
25727513 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
25727553 ACTAGCACAAATGCCTTCAGGACTTAGCCC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCC
25727583 CGTTATCATC
Statistics
Matches: 176, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
39 72 0.41
40 104 0.59
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:25731741 original size:35 final size:35
Alignment explanation
Indices: 25731673--25731738 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
25731663 TAATTGTGTT
25731673 ATTAATTTATTATTTTAAATTTTAAATTTAAATTC
1 ATTAATTTATTATTTTAAATTTTAAATTTAAATTC
*
25731708 ATTAATTT-TTATATTT-AGTTTTAAATTTAAA
1 ATTAATTTATTAT-TTTAAATTTTAAATTTAAA
25731739 ATTTTCATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 18 0.62
35 11 0.38
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (35 bp):
ATTAATTTATTATTTTAAATTTTAAATTTAAATTC
Found at i:25732215 original size:35 final size:35
Alignment explanation
Indices: 25732170--25732236 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
25732160 AAATTTAAAG
*
25732170 ATGATAATCATAACTTACATAAACGTTTAAAGTTT
1 ATGATAATCATAACTTACATAAACATTTAAAGTTT
* *
25732205 ATGATTATCATAACTTATATAAACATTTAAAG
1 ATGATAATCATAACTTACATAAACATTTAAAG
25732237 AATAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.37
Consensus pattern (35 bp):
ATGATAATCATAACTTACATAAACATTTAAAGTTT
Found at i:25732430 original size:36 final size:37
Alignment explanation
Indices: 25732380--25732483 Score: 102
Period size: 43 Copynumber: 2.7 Consensus size: 37
25732370 AGAACATGAC
**
25732380 CTTTAGTGGTGTTTTTGGGAAAAGC-AAGGTCACGTT
1 CTTTAGTGACGTTTTTGGGAAAAGCAAAGGTCACGTT
*
25732416 CTTTAGTGACGTTTTTGGGGAAAGCACCGCTAAAGGTCATGTT
1 CTTTAGTGACGTTTTT-GGGAAA--A--GC-AAAGGTCACGTT
* *
25732459 CTTTAGCGACGTTTGTGGGAAAAGC
1 CTTTAGTGACGTTTTTGGGAAAAGC
25732484 GTTGCTAAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 14 0.25
37 6 0.11
38 2 0.04
39 1 0.02
40 1 0.02
41 2 0.04
42 6 0.11
43 24 0.43
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (37 bp):
CTTTAGTGACGTTTTTGGGAAAAGCAAAGGTCACGTT
Found at i:25732470 original size:43 final size:43
Alignment explanation
Indices: 25732405--25732503 Score: 135
Period size: 43 Copynumber: 2.3 Consensus size: 43
25732395 TGGGAAAAGC
* * * *
25732405 AAGGTCACGTTCTTTAGTGACGTTTTTGGGGAAAGCACCGCTA
1 AAGGTCATGTTCTTTAGCGACGTTTGTGGGAAAAGCACCGCTA
***
25732448 AAGGTCATGTTCTTTAGCGACGTTTGTGGGAAAAGCGTTGCTA
1 AAGGTCATGTTCTTTAGCGACGTTTGTGGGAAAAGCACCGCTA
25732491 AAGGTCATGTTCT
1 AAGGTCATGTTCT
25732504 ATAGTAGCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.32
Consensus pattern (43 bp):
AAGGTCATGTTCTTTAGCGACGTTTGTGGGAAAAGCACCGCTA
Found at i:25732533 original size:43 final size:45
Alignment explanation
Indices: 25732444--25732550 Score: 125
Period size: 43 Copynumber: 2.5 Consensus size: 45
25732434 GGAAAGCACC
*
25732444 GCTAAAGGTCATGTTCT-T--TAGCGACGTTTGTGGGAAAAGCGTT
1 GCTAAAGGTCATGTTCTATAGTAGCGACGTTTGTGAGAAAAGCG-T
** *
25732487 GCTAAAGGTCATGTTCTATAGTAGC-ATTTTTGTGAGAAATGC-T
1 GCTAAAGGTCATGTTCTATAGTAGCGACGTTTGTGAGAAAAGCGT
*
25732530 GCTAAAGGTCATGTTTTATAG
1 GCTAAAGGTCATGTTCTATAG
25732551 CAGCCTATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
43 38 0.68
44 1 0.02
45 13 0.23
46 4 0.07
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.36
Consensus pattern (45 bp):
GCTAAAGGTCATGTTCTATAGTAGCGACGTTTGTGAGAAAAGCGT
Found at i:25733224 original size:13 final size:11
Alignment explanation
Indices: 25733204--25733240 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
25733194 ATTCCATATG
25733204 AATTCACAATT
1 AATTCACAATT
25733215 AATTTTCACAATT
1 AA--TTCACAATT
25733228 AATTCACAATT
1 AATTCACAATT
25733239 AA
1 AA
25733241 ATATATGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 13 0.54
13 11 0.46
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (11 bp):
AATTCACAATT
Found at i:25738500 original size:11 final size:11
Alignment explanation
Indices: 25738484--25738508 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25738474 GCACTACTGA
25738484 TTTATTTTTAT
1 TTTATTTTTAT
25738495 TTTATTTTTAT
1 TTTATTTTTAT
25738506 TTT
1 TTT
25738509 TTTACAGTTT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:25741239 original size:11 final size:11
Alignment explanation
Indices: 25741222--25741251 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
25741212 TAATGTCTTA
25741222 AGATAATCTAC
1 AGATAATCTAC
*
25741233 GGATAATCTAC
1 AGATAATCTAC
25741244 AGATAATC
1 AGATAATC
25741252 ATGCAATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (11 bp):
AGATAATCTAC
Found at i:25744935 original size:81 final size:81
Alignment explanation
Indices: 25744838--25744999 Score: 324
Period size: 81 Copynumber: 2.0 Consensus size: 81
25744828 CATATCAAAT
25744838 CAATAATGTGGTATCGACATGTATAACTAAAGCAAGTTCTAGAATAACAAATCAAGTTGACATAC
1 CAATAATGTGGTATCGACATGTATAACTAAAGCAAGTTCTAGAATAACAAATCAAGTTGACATAC
25744903 TCACAACCAAAGATAA
66 TCACAACCAAAGATAA
25744919 CAATAATGTGGTATCGACATGTATAACTAAAGCAAGTTCTAGAATAACAAATCAAGTTGACATAC
1 CAATAATGTGGTATCGACATGTATAACTAAAGCAAGTTCTAGAATAACAAATCAAGTTGACATAC
25744984 TCACAACCAAAGATAA
66 TCACAACCAAAGATAA
25745000 AATGAGCAGG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (81 bp):
CAATAATGTGGTATCGACATGTATAACTAAAGCAAGTTCTAGAATAACAAATCAAGTTGACATAC
TCACAACCAAAGATAA
Found at i:25749392 original size:3 final size:3
Alignment explanation
Indices: 25749384--25749477 Score: 54
Period size: 3 Copynumber: 31.7 Consensus size: 3
25749374 AATTGCAGTG
* * * *
25749384 ATA ATA ATA ATT ATA ATA CA-A AGA ATA A-A CACA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* * *
25749429 GTA ATA ATA AAA ATA ACA A-A ATA ATA ATA ATTA ACTA A-A ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA A-TA ATA ATA ATA
25749473 ATA AT
1 ATA AT
25749478 TTAAAACTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
2 8 0.11
3 57 0.78
4 8 0.11
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:25749487 original size:21 final size:19
Alignment explanation
Indices: 25749431--25749478 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
25749421 TAATAGTAGT
*
25749431 AATAATAA-AAATAAC-AA
1 AATAATAATAATTAACTAA
25749448 AATAATAATAATTAACTAA
1 AATAATAATAATTAACTAA
25749467 AATAA-AATAATT
1 AATAATAATAATT
25749479 TAAAACTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 8 0.29
18 13 0.46
19 7 0.25
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (19 bp):
AATAATAATAATTAACTAA
Found at i:25749558 original size:18 final size:18
Alignment explanation
Indices: 25749524--25749565 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
25749514 GTAAGTAGAG
25749524 TAATAATAACAATAAAAA
1 TAATAATAACAATAAAAA
*
25749542 TAATACTAA-AATGAAAAA
1 TAATAATAACAAT-AAAAA
*
25749560 AAATAA
1 TAATAA
25749566 AAGTATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (18 bp):
TAATAATAACAATAAAAA
Found at i:25752645 original size:28 final size:28
Alignment explanation
Indices: 25752603--25752681 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
25752593 GAATCATTCG
*
25752603 ATATTTCACACACTAAGTGCCATTCTCA
1 ATATCTCACACACTAAGTGCCATTCTCA
* * *
25752631 ATATCTCGCATACTAAGTGTCATTCTCA
1 ATATCTCACACACTAAGTGCCATTCTCA
* *
25752659 ATATTTCACACACTACGTGCCAT
1 ATATCTCACACACTAAGTGCCAT
25752682 ATTTGATATC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (28 bp):
ATATCTCACACACTAAGTGCCATTCTCA
Found at i:25756462 original size:20 final size:20
Alignment explanation
Indices: 25756437--25756474 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25756427 GAATGTAAAA
*
25756437 ATTAAATTAAAAACAAAATT
1 ATTAAAATAAAAACAAAATT
*
25756457 ATTAAAATAAAAATAAAA
1 ATTAAAATAAAAACAAAA
25756475 ATGATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
ATTAAAATAAAAACAAAATT
Found at i:25756475 original size:21 final size:20
Alignment explanation
Indices: 25756437--25756484 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
25756427 GAATGTAAAA
* * *
25756437 ATTAAATTAAAAACAAAATT
1 ATTAAAATAAAAAAAAAATG
25756457 ATTAAAATAAAAATAAAAATG
1 ATTAAAATAAAAA-AAAAATG
25756478 A-TAAAAT
1 ATTAAAAT
25756485 TAACAGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
ATTAAAATAAAAAAAAAATG
Found at i:25758556 original size:23 final size:23
Alignment explanation
Indices: 25758526--25758573 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
25758516 ACTTTTGTGA
25758526 AAGGATTTTCATGGAAACACCTC
1 AAGGATTTTCATGGAAACACCTC
25758549 AAGGATTTTCATGGAAACACCTC
1 AAGGATTTTCATGGAAACACCTC
25758572 AA
1 AA
25758574 ATGAACTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (23 bp):
AAGGATTTTCATGGAAACACCTC
Done.