Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 141 of 235
Found at i:47404086 original size:48 final size:48
Alignment explanation
Indices: 47404027--47404455 Score: 653
Period size: 48 Copynumber: 8.9 Consensus size: 48
47404017 TATACACACG
* * *
47404027 TCTCCTACATATTTCACACTAGCCCTTTGGCTTTACCACATATACGTA
1 TCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACGTA
*
47404075 TCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACATA
1 TCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACGTA
* * * *
47404123 TCTCATATATATTTCACATTAGCCATTCGGCTTTATCACATATACATA
1 TCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACGTA
* *
47404171 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACATA
1 TCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACGTA
* * *
47404219 TCTCATACATATTTCACACTAGCCCTTTGGCTTTACCACAGATACGTA
1 TCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACGTA
* * *
47404267 TCTCATACATATTTCACACTAGCCCTTTGGCTTTACCACAGATACGTA
1 TCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACGTA
* * *
47404315 TCTCATACATATTTCACACTAGCCCTTTGGCTTTACCACAGATACGTA
1 TCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACGTA
*
47404363 TCTCATACATATTTCACA-TGAGCCATTCGGCTTTACCACATATACCTA
1 TCTCATACATATTTCACACT-AGCCATTCGGCTTTACCACATATACGTA
*
47404411 TCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATAC
1 TCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATAC
47404456 ATATATTTAT
Statistics
Matches: 361, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 1 0.00
48 359 0.99
49 1 0.00
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.35
Consensus pattern (48 bp):
TCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACGTA
Found at i:47409760 original size:13 final size:13
Alignment explanation
Indices: 47409742--47409784 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
47409732 AAGATTTTTC
47409742 CTAAATATTATTA
1 CTAAATATTATTA
47409755 CTAAATA--ATT-
1 CTAAATATTATTA
*
47409765 CTAAATATTATCA
1 CTAAATATTATTA
47409778 CTAAATA
1 CTAAATA
47409785 ATTCTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
12 2 0.08
13 14 0.54
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
CTAAATATTATTA
Found at i:47409772 original size:23 final size:23
Alignment explanation
Indices: 47409742--47409793 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
47409732 AAGATTTTTC
*
47409742 CTAAATATTATTACTAAATAATT
1 CTAAATATTATCACTAAATAATT
47409765 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
47409788 CTAAAT
1 CTAAAT
47409794 TTAAAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:47409806 original size:23 final size:23
Alignment explanation
Indices: 47409742--47409806 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
47409732 AAGATTTTTC
** *
47409742 CTAAATATTATTACTAAATAATT
1 CTAAATATTAAAAATAAATAATT
** *
47409765 CTAAATATTATCACTAAATAATT
1 CTAAATATTAAAAATAAATAATT
47409788 CTAAAT-TTAAAAATCAAAT
1 CTAAATATTAAAAAT-AAAT
47409807 TTAAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.14
23 32 0.86
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (23 bp):
CTAAATATTAAAAATAAATAATT
Found at i:47410525 original size:22 final size:22
Alignment explanation
Indices: 47410483--47410525 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
47410473 TTAATGAAAT
* *
47410483 ATTATAAAAATTAAATGGATTC
1 ATTAAAAAAATTAAATAGATTC
*
47410505 ATTAAAAAAATTAATTAGATT
1 ATTAAAAAAATTAAATAGATT
47410526 TTTTTTAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (22 bp):
ATTAAAAAAATTAAATAGATTC
Found at i:47410834 original size:30 final size:30
Alignment explanation
Indices: 47410775--47410834 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
47410765 TATATATTAT
*
47410775 ATTAAAAGGTCTAAGATCTTAACTGATGTG
1 ATTAAAAGGTCTAAGATCTTAACTAATGTG
* *
47410805 ATTATAAGGTCTAAGATCTTAATTAATGTG
1 ATTAAAAGGTCTAAGATCTTAACTAATGTG
47410835 GACGCCTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (30 bp):
ATTAAAAGGTCTAAGATCTTAACTAATGTG
Found at i:47416258 original size:56 final size:56
Alignment explanation
Indices: 47416210--47416345 Score: 254
Period size: 56 Copynumber: 2.4 Consensus size: 56
47416200 TCTTACTGAT
* *
47416210 ACACATATATCGAAATCACATATCGATGCCAGCGTATTAAACGTGGTCTAACTCGC
1 ACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGC
47416266 ACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGC
1 ACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGC
47416322 ACACATATATCGAAATCACATATC
1 ACACATATATCGAAATCACATATC
47416346 ACAAGTCGAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
56 78 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (56 bp):
ACACATATATCGAAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGC
Found at i:47417690 original size:15 final size:15
Alignment explanation
Indices: 47417665--47417718 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
47417655 ACAAAAATTT
47417665 CACATATATAAATTCA
1 CACATA-ATAAATTCA
*
47417681 CACATAATAAA--AA
1 CACATAATAAATTCA
* *
47417694 AAGAT-ATAAATTCA
1 CACATAATAAATTCA
47417708 CACATAATAAA
1 CACATAATAAA
47417719 CACAAAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
12 5 0.17
13 4 0.14
14 4 0.14
15 10 0.34
16 6 0.21
ACGTcount: A:0.59, C:0.15, G:0.02, T:0.24
Consensus pattern (15 bp):
CACATAATAAATTCA
Found at i:47418752 original size:21 final size:21
Alignment explanation
Indices: 47418726--47418769 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
47418716 ATATCGGTAA
47418726 TAGAATATCAAAGAGAATTTG
1 TAGAATATCAAAGAGAATTTG
*
47418747 TAGAATATGAAAGAGAATTTG
1 TAGAATATCAAAGAGAATTTG
47418768 TA
1 TA
47418770 TGACTCAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.30
Consensus pattern (21 bp):
TAGAATATCAAAGAGAATTTG
Found at i:47421454 original size:241 final size:241
Alignment explanation
Indices: 47421031--47421515 Score: 934
Period size: 241 Copynumber: 2.0 Consensus size: 241
47421021 GCATGAAAAG
47421031 AATTATCCGACGCATGACTTAGAGTTGGCTGCAATTGTGTTCGCATTGAAAATTTGGCGACATTA
1 AATTATCCGACGCATGACTTAGAGTTGGCTGCAATTGTGTTCGCATTGAAAATTTGGCGACATTA
*
47421096 CTTATACGGTGAGAATTGCCACATTTATACAGATAAAAAAAGCTTAAAATATCTGATGTCACAAA
66 CTTACACGGTGAGAATTGCCACATTTATACAGATAAAAAAAGCTTAAAATATCTGATGTCACAAA
47421161 AAGATTTGAATCTGCGACAACGAAGATTGCTTGAGTTATTGAAAGATTATGAATTTGTGATTGAT
131 AAGATTTGAATCTGCGACAACGAAGATTGCTTGAGTTATTGAAAGATTATGAATTTGTGATTGAT
*
47421226 TATCACTCGGGAAAAGCTAATGTTGTTGCTGATGCCCTGAGCCAAA
196 TATCACTCAGGAAAAGCTAATGTTGTTGCTGATGCCCTGAGCCAAA
*
47421272 AATTATCCGACGCATGACTTAGAGTTGGCTGCAATTGTGTTTGCATTGAAAATTTGGCGACATTA
1 AATTATCCGACGCATGACTTAGAGTTGGCTGCAATTGTGTTCGCATTGAAAATTTGGCGACATTA
47421337 CTTACACGGTGAGAATTGCCACATTTATACAGATAAAAAAAGCTTAAAATATCTGATGTCACAAA
66 CTTACACGGTGAGAATTGCCACATTTATACAGATAAAAAAAGCTTAAAATATCTGATGTCACAAA
*
47421402 AAGATTTGAATTTGCGACAACGAAGATTGCTTGAGTTATTGAAAGATTATGAATTTGTGATTGAT
131 AAGATTTGAATCTGCGACAACGAAGATTGCTTGAGTTATTGAAAGATTATGAATTTGTGATTGAT
47421467 TATCACTCAGGAAAAGCTAATGTTGTTGCTGATGCCCTGAGCCAAA
196 TATCACTCAGGAAAAGCTAATGTTGTTGCTGATGCCCTGAGCCAAA
47421513 AAT
1 AAT
47421516 CTTTGTTTGC
Statistics
Matches: 240, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
241 240 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (241 bp):
AATTATCCGACGCATGACTTAGAGTTGGCTGCAATTGTGTTCGCATTGAAAATTTGGCGACATTA
CTTACACGGTGAGAATTGCCACATTTATACAGATAAAAAAAGCTTAAAATATCTGATGTCACAAA
AAGATTTGAATCTGCGACAACGAAGATTGCTTGAGTTATTGAAAGATTATGAATTTGTGATTGAT
TATCACTCAGGAAAAGCTAATGTTGTTGCTGATGCCCTGAGCCAAA
Found at i:47427616 original size:15 final size:15
Alignment explanation
Indices: 47427592--47427622 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
47427582 TAATGTCTTG
47427592 CAACTAGGATAAAAA
1 CAACTAGGATAAAAA
*
47427607 CAACTGGGATAAAAA
1 CAACTAGGATAAAAA
47427622 C
1 C
47427623 TTCTGTGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.13
Consensus pattern (15 bp):
CAACTAGGATAAAAA
Found at i:47427897 original size:36 final size:36
Alignment explanation
Indices: 47427828--47427900 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
47427818 CACTTTCCAT
** *
47427828 TTTGCCTCATTGGCAACACTTTCAAATCTTGTTGGG
1 TTTGCCTCATTAACAACACTTTCAAATCATGTTGGG
47427864 TTTGCCTCATTAACAACACTTTCAAAAT-ATGTTGGG
1 TTTGCCTCATTAACAACACTTTC-AAATCATGTTGGG
47427900 T
1 T
47427901 CACAATATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 29 0.88
37 4 0.12
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (36 bp):
TTTGCCTCATTAACAACACTTTCAAATCATGTTGGG
Found at i:47429130 original size:74 final size:74
Alignment explanation
Indices: 47429009--47429304 Score: 583
Period size: 74 Copynumber: 4.0 Consensus size: 74
47428999 TTATGAATCT
47429009 ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
1 ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
47429074 TAACTTGTA
66 TAACTTGTA
47429083 ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
1 ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
47429148 TAACTTGTA
66 TAACTTGTA
47429157 ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
1 ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
47429222 TAACTTGTA
66 TAACTTGTA
47429231 ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
1 ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
*
47429296 TGACTTGTA
66 TAACTTGTA
47429305 CACTTTAATT
Statistics
Matches: 221, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 221 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (74 bp):
ATTCACTTGTGACATTCATAGTGTGGCATACCATAATCTTGAGTGGATGGTGGACTATGTATGCG
TAACTTGTA
Found at i:47431568 original size:28 final size:27
Alignment explanation
Indices: 47431534--47431597 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
47431524 GTATTGTGAT
* *
47431534 TGTACTGTTTTGGGCATAGGCCCATAC
1 TGTACTGTTTAGGGCATAGGCCCAGAC
** *
47431561 TGTTACTGCATAGGGCTTAGGCCCAGAC
1 TG-TACTGTTTAGGGCATAGGCCCAGAC
47431589 TGTACTGTT
1 TGTACTGTT
47431598 AATGAATAGG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.33
Consensus pattern (27 bp):
TGTACTGTTTAGGGCATAGGCCCAGAC
Found at i:47431607 original size:33 final size:33
Alignment explanation
Indices: 47431558--47431620 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
47431548 CATAGGCCCA
* * * *
47431558 TACTGTTACTGCATAGGGCTTAGGCCCAGACTG
1 TACTGTTAATGAATAGGGCTCAAGCCCAGACTG
47431591 TACTGTTAATGAATAGGGCTCAAGCCCAGA
1 TACTGTTAATGAATAGGGCTCAAGCCCAGA
47431621 ACGTTACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (33 bp):
TACTGTTAATGAATAGGGCTCAAGCCCAGACTG
Found at i:47432797 original size:12 final size:12
Alignment explanation
Indices: 47432780--47432805 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
47432770 AGAGTTTAAC
47432780 TATGATTAAACT
1 TATGATTAAACT
47432792 TATGATTAAACT
1 TATGATTAAACT
47432804 TA
1 TA
47432806 ATCACTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
TATGATTAAACT
Found at i:47432937 original size:68 final size:67
Alignment explanation
Indices: 47432860--47432986 Score: 177
Period size: 68 Copynumber: 1.9 Consensus size: 67
47432850 TTAGATTAAA
*
47432860 TTTAATATTAAATCTTATTAAAATA-ATGT-AGATAAACATTAAATTAAATTTAATATTAAGATA
1 TTTAATATT-AAT-TTAATAAAATACAT-TAAGATAAACATTAAATTAAATTTAATATTAAGATA
47432923 TTCAC
63 TTCAC
**
47432928 TTTAATATTAATTTAATAAAATACTATTAAGATAAGTATTAAATTAAATTTAATATTAA
1 TTTAATATTAATTTAATAAAATAC-ATTAAGATAAACATTAAATTAAATTTAATATTAA
47432987 ACTATTAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
66 10 0.19
67 4 0.08
68 39 0.74
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (67 bp):
TTTAATATTAATTTAATAAAATACATTAAGATAAACATTAAATTAAATTTAATATTAAGATATTC
AC
Found at i:47435217 original size:48 final size:48
Alignment explanation
Indices: 47435162--47435259 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
47435152 ATTTCTCCAT
47435162 TTAAGAGAAAATCATTTTTAATGAATTCTTTTTCTCTATTTCTATTCA
1 TTAAGAGAAAATCATTTTTAATGAATTCTTTTTCTCTATTTCTATTCA
47435210 TTAAGAGAAAATCATTTTTAATGAATTCTTTTTCTCTATTTCTATTCA
1 TTAAGAGAAAATCATTTTTAATGAATTCTTTTTCTCTATTTCTATTCA
47435258 TT
1 TT
47435260 TCATTCATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (48 bp):
TTAAGAGAAAATCATTTTTAATGAATTCTTTTTCTCTATTTCTATTCA
Found at i:47437922 original size:40 final size:40
Alignment explanation
Indices: 47437783--47437968 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
47437773 ACTGGAATTC
* * * *
47437783 TCACACATTAAGTGCCAAAACATAGCTGAAGCTATTT-TAA
1 TCACACACTAAGTGCC-ATATATAGCTGAAGCTATTTCGAA
* * * * **
47437823 TCTCGCACACTAAGTGCC-TTTCATAGCCGAAGCTATCTTAGTC
1 --TCACACACTAAGTGCCATAT-ATAGCTGAAGCTAT-TTCGAA
*
47437866 TCACACACTAAGTGCCACATATAGCTGAAGCTATTTCGAA
1 TCACACACTAAGTGCCATATATAGCTGAAGCTATTTCGAA
* *
47437906 TCGCACACTAAGTGCCATATATAGCTGAAGCTATTTCAAA
1 TCACACACTAAGTGCCATATATAGCTGAAGCTATTTCGAA
*
47437946 TCACACATTAAGTGCCATATATA
1 TCACACACTAAGTGCCATATATA
47437969 TATCCAAATC
Statistics
Matches: 119, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
40 61 0.51
41 41 0.34
42 17 0.14
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (40 bp):
TCACACACTAAGTGCCATATATAGCTGAAGCTATTTCGAA
Found at i:47437930 original size:81 final size:82
Alignment explanation
Indices: 47437781--47437939 Score: 216
Period size: 81 Copynumber: 1.9 Consensus size: 82
47437771 ATACTGGAAT
* * *
47437781 TCTCACACATTAAGTGCCAAAACATAGCTGAAGCTATTTTAATCTCGCACACTAAGTGCCTTTCA
1 TCTCACACACTAAGTGCCAAAACATAGCTGAAGCTATTTGAA-CTCGCACACTAAGTGCCTATCA
47437846 TAGCCGAAGCTATCTTAG
65 TAGCCGAAGCTATCTTAG
* *
47437864 TCTCACACACTAAGTGCC-ACATATAGCTGAAGCTATTTCGAA-TCGCACACTAAGTGCCATAT-
1 TCTCACACACTAAGTGCCAAAACATAGCTGAAGCTATTT-GAACTCGCACACTAAGTGCC-TATC
*
47437926 ATAGCTGAAGCTAT
64 ATAGCCGAAGCTAT
47437940 TTCAAATCAC
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
81 29 0.43
82 20 0.29
83 19 0.28
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (82 bp):
TCTCACACACTAAGTGCCAAAACATAGCTGAAGCTATTTGAACTCGCACACTAAGTGCCTATCAT
AGCCGAAGCTATCTTAG
Found at i:47439195 original size:35 final size:35
Alignment explanation
Indices: 47439149--47439215 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
47439139 AAAATCTTAC
* *
47439149 TAGTGAATAGGTTAGGGTATTGTTTTCTCATACCT
1 TAGTGAATAGGTTAGGGTACTATTTTCTCATACCT
47439184 TAGTGAATAGGTTAGGGTACTATTTTCTCATA
1 TAGTGAATAGGTTAGGGTACTATTTTCTCATA
47439216 GCATTCTCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.42
Consensus pattern (35 bp):
TAGTGAATAGGTTAGGGTACTATTTTCTCATACCT
Found at i:47443416 original size:49 final size:49
Alignment explanation
Indices: 47443339--47443436 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
47443329 CCCAGGTGAC
*
47443339 TCTTTCCCTCGACACCACCGATATTAATGTATTCAACCACTGATACACG
1 TCTTTCCCTCGACACCACCGATACTAATGTATTCAACCACTGATACACG
* *
47443388 TCTTTCCCTCGATACCACCGATACTAATGTATTCCACCACTGATACACG
1 TCTTTCCCTCGACACCACCGATACTAATGTATTCAACCACTGATACACG
47443437 GTATCTCTCG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.28, C:0.34, G:0.10, T:0.29
Consensus pattern (49 bp):
TCTTTCCCTCGACACCACCGATACTAATGTATTCAACCACTGATACACG
Found at i:47444451 original size:12 final size:12
Alignment explanation
Indices: 47444434--47444459 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
47444424 CACACGCCAA
47444434 TGTGCTAGGCCG
1 TGTGCTAGGCCG
47444446 TGTGCTAGGCCG
1 TGTGCTAGGCCG
47444458 TG
1 TG
47444460 CCAAACCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.23, G:0.42, T:0.27
Consensus pattern (12 bp):
TGTGCTAGGCCG
Found at i:47444610 original size:32 final size:32
Alignment explanation
Indices: 47444563--47444635 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
47444553 ACACCAGAGG
47444563 ACACACGGCCATGCAACATGACCGTGTGTCAC
1 ACACACGGCCATGCAACATGACCGTGTGTCAC
* *
47444595 ACACATGGCCGTGCAACATGACCGTGTGTCAC
1 ACACACGGCCATGCAACATGACCGTGTGTCAC
47444627 ACACACGGC
1 ACACACGGC
47444636 TGAGACACAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.27, C:0.34, G:0.23, T:0.15
Consensus pattern (32 bp):
ACACACGGCCATGCAACATGACCGTGTGTCAC
Found at i:47444652 original size:32 final size:32
Alignment explanation
Indices: 47444563--47444653 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 32
47444553 ACACCAGAGG
*
47444563 ACACACGGCC-ATGCAACATGACCGTGTGTCAC
1 ACACACGGCCGA-GCAACACGACCGTGTGTCAC
* * *
47444595 ACACATGGCCGTGCAACATGACCGTGTGTCAC
1 ACACACGGCCGAGCAACACGACCGTGTGTCAC
* *
47444627 ACACACGGCTGAG-ACACACGCCCGTGT
1 ACACACGGCCGAGCA-ACACGACCGTGT
47444654 CTCTGCCCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 1 0.02
32 49 0.98
ACGTcount: A:0.26, C:0.34, G:0.24, T:0.15
Consensus pattern (32 bp):
ACACACGGCCGAGCAACACGACCGTGTGTCAC
Found at i:47445610 original size:40 final size:40
Alignment explanation
Indices: 47445507--47445650 Score: 173
Period size: 40 Copynumber: 3.6 Consensus size: 40
47445497 ACTCGAATTC
* *
47445507 TCGCACACTAAGTGCC-TTTCATAGCCGAAGCTATCTCAGTA
1 TCGCACACTAAGTGCCATAT-ATAGCCGAAGCTATCTCA-AA
* * * * *
47445548 TCGTACAATAAGTGCCACATATAGCCGTAGCTATTTCAAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCAAA
* **
47445588 TTGCACACTAAGTGCCATATATAGCCGAAGCTATCTCGGA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCAAA
47445628 TCGCACACTAAGTGCCATATATA
1 TCGCACACTAAGTGCCATATATA
47445651 TATATCCAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
40 55 0.64
41 30 0.35
42 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCAAA
Found at i:47446997 original size:90 final size:90
Alignment explanation
Indices: 47446844--47447071 Score: 307
Period size: 90 Copynumber: 2.5 Consensus size: 90
47446834 TTTTATTTTT
* **
47446844 GGTTTTGATTTTTATTTCCAGAAGCGAGTTTTTTAAATTAGAATAAAATCTGTTTCGATATTTAT
1 GGTTTTGATTTTTATTTCCAAAAATGAG-TTTTTAAATTAGAATAAAATCTGTTTCGATATTTAT
* * *
47446909 TCCC-GCTGTTTAATGGATTTTATTCC
65 TCCCATC-GCTCAATGGATTTTATTCC
47446935 GGTTTTGATTTTTATTTCCAAAAATGAGTTTTTAAATTAGAATAAAATCTGTTTCAGA-ATTTAT
1 GGTTTTGATTTTTATTTCCAAAAATGAGTTTTTAAATTAGAATAAAATCTGTTTC-GATATTTAT
*
47446999 TCCCATCGCTCAATGGATTTTTTTCC
65 TCCCATCGCTCAATGGATTTTATTCC
** * * *
47447025 AATTTTTATTTTTATTTCCAAAAATAAGTTTTTAAATTTGAATAAAA
1 GGTTTTGATTTTTATTTCCAAAAATGAGTTTTTAAATTAGAATAAAA
47447072 AATTTTTCGC
Statistics
Matches: 123, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
90 95 0.77
91 28 0.23
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (90 bp):
GGTTTTGATTTTTATTTCCAAAAATGAGTTTTTAAATTAGAATAAAATCTGTTTCGATATTTATT
CCCATCGCTCAATGGATTTTATTCC
Found at i:47455063 original size:28 final size:27
Alignment explanation
Indices: 47455000--47455151 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
47454990 ATATTAAGTC
* * *
47455000 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
47455027 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
47455055 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
47455082 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
47455110 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
*
47455137 TGCACACTTAGTGCT
1 CGCACACTTAGTGCT
47455152 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 65 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:47455084 original size:55 final size:55
Alignment explanation
Indices: 47455000--47455151 Score: 250
Period size: 55 Copynumber: 2.8 Consensus size: 55
47454990 ATATTAAGTC
* * *
47455000 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
47455055 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
47455110 CGCACACTTAGTGCTACATAGTCAATTTGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
47455152 GCACAATTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:47458909 original size:21 final size:21
Alignment explanation
Indices: 47458883--47458923 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
47458873 TGGTAAGGAT
*
47458883 AATGTAGTGGCTGACGCACTG
1 AATGTAGTGGCTAACGCACTG
47458904 AATGTAGTGGCTAACGCACT
1 AATGTAGTGGCTAACGCACT
47458924 TAGCCGTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (21 bp):
AATGTAGTGGCTAACGCACTG
Found at i:47464074 original size:18 final size:18
Alignment explanation
Indices: 47464051--47464098 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
47464041 GTAATAAGTG
47464051 ACGTTTTGAAAGTAAATA
1 ACGTTTTGAAAGTAAATA
47464069 ACGTTTTGAAAGTAAATA
1 ACGTTTTGAAAGTAAATA
*
47464087 ACATTTTGAAAG
1 ACGTTTTGAAAG
47464099 AGAATAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (18 bp):
ACGTTTTGAAAGTAAATA
Found at i:47464094 original size:36 final size:36
Alignment explanation
Indices: 47464054--47464133 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 36
47464044 ATAAGTGACG
47464054 TTTTGAAAGTA-AATAACGTTT-TGA-AAGTAAATAACA
1 TTTTGAAAG-AGAATAAC-TTTGTGATAA-TAAATAACA
* *
47464090 TTTTGAAAGAGAATAACTTTGTGATAATGAATTACA
1 TTTTGAAAGAGAATAACTTTGTGATAATAAATAACA
47464126 TTTTGAAA
1 TTTTGAAA
47464134 ACGAATGACA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
35 4 0.10
36 33 0.85
37 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (36 bp):
TTTTGAAAGAGAATAACTTTGTGATAATAAATAACA
Found at i:47464104 original size:18 final size:18
Alignment explanation
Indices: 47464054--47464133 Score: 85
Period size: 18 Copynumber: 4.4 Consensus size: 18
47464044 ATAAGTGACG
*
47464054 TTTTGAAAGTAAATAACG
1 TTTTGAAAGTAAATAACA
47464072 TTTTGAAAGTAAATAACA
1 TTTTGAAAGTAAATAACA
47464090 TTTTGAAAG-AGAATAAC-
1 TTTTGAAAGTA-AATAACA
* *
47464107 TTTGTGATAA-TGAATTACA
1 TTT-TGA-AAGTAAATAACA
47464126 TTTTGAAA
1 TTTTGAAA
47464134 ACGAATGACA
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
17 6 0.11
18 43 0.80
19 5 0.09
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (18 bp):
TTTTGAAAGTAAATAACA
Found at i:47467024 original size:20 final size:19
Alignment explanation
Indices: 47466996--47467065 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 19
47466986 AAAAGTTAAA
*
47466996 AAAAATCAAAATAATTTTC
1 AAAATTCAAAATAATTTTC
*
47467015 AAATATTCAAAATAATTTTT
1 AAA-ATTCAAAATAATTTTC
*
47467035 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TC
47467054 AAAATTCTAAAA
1 AAAATTC-AAAA
47467066 ATTATATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.09
19 20 0.44
20 21 0.47
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTC
Found at i:47467043 original size:19 final size:19
Alignment explanation
Indices: 47466996--47467080 Score: 82
Period size: 19 Copynumber: 4.2 Consensus size: 19
47466986 AAAAGTTAAA
* *
47466996 AAAAATCAAAATAATTTTC
1 AAAATTCAAAATAATTTTT
47467015 AAATATTCAAAATAATTTTT
1 AAA-ATTCAAAATAATTTTT
*
47467035 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TT
47467054 AAAATTCTAAAAATTATATTTTT
1 AAAATTC--AAAA-TA-ATTTTT
47467077 AAAA
1 AAAA
47467081 AATTATAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.07
19 20 0.36
20 17 0.31
21 4 0.07
22 1 0.02
23 5 0.09
24 4 0.07
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:47467073 original size:24 final size:25
Alignment explanation
Indices: 47467045--47467093 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
47467035 AAAATTCAAA
*
47467045 ATATTTAT-AAAAATTCTAAAAATT
1 ATATTTATAAAAAATTATAAAAATT
*
47467069 ATATTTTTAAAAAATTATAAAAATT
1 ATATTTATAAAAAATTATAAAAATT
47467094 TTGAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATTTATAAAAAATTATAAAAATT
Found at i:47477972 original size:55 final size:55
Alignment explanation
Indices: 47477885--47478020 Score: 141
Period size: 55 Copynumber: 2.5 Consensus size: 55
47477875 TGCGACATGG
* * ** ** *
47477885 CCGTGGACGAACCTGCCAAAACAACACAGGCGTGCGACACGCCCGTGCCTTA-AAA
1 CCGTGGTCGAACCTGTCAAATTAACATGGGCGTGAGACACGCCCGTGCC-TAGAAA
* * *
47477940 CCGTGG-CTGAACCTGTCAAATTAACATGGGCGTGAGACACGCCCGTGTCTAGCAC
1 CCGTGGTC-GAACCTGTCAAATTAACATGGGCGTGAGACACGCCCGTGCCTAGAAA
*
47477995 CCGTGGTCGAACCTGTGAAATTAACA
1 CCGTGGTCGAACCTGTCAAATTAACA
47478021 CGGGTGTGGG
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
54 3 0.04
55 64 0.94
56 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (55 bp):
CCGTGGTCGAACCTGTCAAATTAACATGGGCGTGAGACACGCCCGTGCCTAGAAA
Found at i:47484592 original size:13 final size:13
Alignment explanation
Indices: 47484574--47484599 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47484564 TTCAAACTAC
47484574 TTTTTATTTTTTA
1 TTTTTATTTTTTA
47484587 TTTTTATTTTTTA
1 TTTTTATTTTTTA
47484600 GAAGATTTAA
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:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:47487266 original size:45 final size:45
Alignment explanation
Indices: 47487197--47487288 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 45
47487187 AATGCAACCC
47487197 TAGAGTGTTAATTAGAGAAAAGTCTC-AGTTACTCAATCTAGGGAT
1 TAGAGTGTTAATTAGAGAAAAGTCTCGA-TTACTCAATCTAGGGAT
* *
47487242 TAGATTGTTAATTAGAGAAAAGTCTCGATTATTCAATCTAGGGAT
1 TAGAGTGTTAATTAGAGAAAAGTCTCGATTACTCAATCTAGGGAT
47487287 TA
1 TA
47487289 AACGTTATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 43 0.98
46 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.34
Consensus pattern (45 bp):
TAGAGTGTTAATTAGAGAAAAGTCTCGATTACTCAATCTAGGGAT
Found at i:47488959 original size:31 final size:31
Alignment explanation
Indices: 47488913--47488981 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
47488903 TACTAGGCTG
*
47488913 AAGCC-TTTCATAATTCATAACACTGGGCCA
1 AAGCCTTTTCAAAATTCATAACACTGGGCCA
** **
47488943 AAGCCTTTTCAAAATTCATATTACTGGGCTG
1 AAGCCTTTTCAAAATTCATAACACTGGGCCA
47488974 AAGCCTTT
1 AAGCCTTT
47488982 ACTGTAAGCG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (31 bp):
AAGCCTTTTCAAAATTCATAACACTGGGCCA
Found at i:47489303 original size:11 final size:10
Alignment explanation
Indices: 47489287--47489323 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
47489277 CATCTCGTAA
47489287 CATATCATGT
1 CATATCATGT
47489297 GCATATCATGT
1 -CATATCATGT
47489308 CATATCATGT
1 CATATCATGT
47489318 -ATATCA
1 CATATCA
47489324 AAATCTCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.23
10 10 0.38
11 10 0.38
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (10 bp):
CATATCATGT
Found at i:47489311 original size:21 final size:21
Alignment explanation
Indices: 47489267--47489317 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
47489257 TTTAATGAGT
* *
47489267 ATATCATGTGCATCTCGTAAC
1 ATATCATGTGCATATCATAAC
**
47489288 ATATCATGTGCATATCATGTC
1 ATATCATGTGCATATCATAAC
47489309 ATATCATGT
1 ATATCATGT
47489318 ATATCAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (21 bp):
ATATCATGTGCATATCATAAC
Found at i:47504242 original size:39 final size:39
Alignment explanation
Indices: 47504131--47504260 Score: 170
Period size: 40 Copynumber: 3.3 Consensus size: 39
47504121 GGACTAAGAT
* * *
47504131 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGG-CATTGTGCGAGTTACTAAATCCGGGTTATGTC
**
47504171 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATT-GTGCGAGTTACTAAATCCGGGTTATGTC
* * *
47504211 CCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTATGTC
47504250 CCGAAGGCATT
1 CCGAAGGCATT
47504261 TGAACGAGGA
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 37 0.47
40 42 0.53
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTATGTC
Found at i:47504280 original size:79 final size:79
Alignment explanation
Indices: 47504131--47504295 Score: 179
Period size: 79 Copynumber: 2.1 Consensus size: 79
47504121 GGACTAAGAT
* * * ** ** *
47504131 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
**
47504196 AATCCGGGTTATGTC
66 AATCC-GGTTAAATC
* * * *
47504211 CCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
47504275 CATCCGGTTAAATC
66 AATCCGGTTAAATC
47504289 CCGAAGG
1 CCGAAGG
47504296 TACGTGATTT
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
78 14 0.20
79 49 0.70
80 7 0.10
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGTTAAATC
Found at i:47507557 original size:47 final size:47
Alignment explanation
Indices: 47507503--47507838 Score: 465
Period size: 47 Copynumber: 7.1 Consensus size: 47
47507493 TTAGGATTTT
** * * *
47507503 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
47507550 ATGTGATGAATGTGAACCTGTATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATG--CATATAT--GTGATAAGGCCGAATGGCCA
* * *
47507601 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
47507648 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
47507695 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
47507742 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
47507789 ATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
47507836 ATG
1 ATG
47507839 CGAAATGTGT
Statistics
Matches: 266, Mismatches: 19, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
47 218 0.82
49 11 0.04
51 37 0.14
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:47507994 original size:46 final size:46
Alignment explanation
Indices: 47507812--47507993 Score: 265
Period size: 46 Copynumber: 4.0 Consensus size: 46
47507802 GAACATGTAT
* * *
47507812 ATATGTGGTAAGGCCGAATGGCTAATGCGAAATGTGTATAAGATAG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATAG
* *
47507858 ATATGAGGTAAAGTCGAATGGCTAATGCGAAACGTGTATGAGATAG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATAG
*
47507904 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATAG
* * * * *
47507950 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGAT
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGAT
47507994 GTGTATATAT
Statistics
Matches: 123, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 123 1.00
ACGTcount: A:0.36, C:0.08, G:0.30, T:0.26
Consensus pattern (46 bp):
ATATGAGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATAG
Found at i:47514253 original size:37 final size:37
Alignment explanation
Indices: 47514203--47514281 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
47514193 TTATTACGAA
* *
47514203 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
47514240 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
47514277 GTCTT
1 GTCTT
47514282 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:47514526 original size:49 final size:47
Alignment explanation
Indices: 47514400--47514943 Score: 890
Period size: 47 Copynumber: 11.4 Consensus size: 47
47514390 CCCTTCGGGA
* * * * * * *
47514400 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
47514447 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
47514494 CTTATCACATATATATGCACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATA--CACTTTCACATTCATCACATCGGCCATTAGGC
47514543 CTTATCACATATATATGCACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATA--CACTTTCACATTCATCACATCGGCCATTAGGC
47514592 CTTATCACATATATATGCACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATA--CACTTTCACATTCATCACATCGGCCATTAGGC
*
47514641 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
47514688 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
47514735 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
47514782 CTTATCACATATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
47514831 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
47514878 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
47514925 CTTATCACATATATACACT
1 CTTATCACATATATACACT
47514944 GTCTTGGCTG
Statistics
Matches: 474, Mismatches: 19, Indels: 8
0.95 0.04 0.02
Matches are distributed among these distances:
47 283 0.60
49 191 0.40
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:47514799 original size:143 final size:143
Alignment explanation
Indices: 47514400--47514939 Score: 895
Period size: 143 Copynumber: 3.8 Consensus size: 143
47514390 CCCTTCGGGA
* * * * * * * * *
47514400 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
47514465 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATGCACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
47514530 TCGGCCATTAGGC
131 TCGGCCATTAGGC
47514543 CTTATCACATATATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATA--CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA-
47514608 GCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCAT
63 -CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCAT
*
47514671 CACATCGGCTATTAGGC
127 CACATCGGCCATTAGGC
*
47514688 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
47514753 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
*
47514818 TCAGCCATTAGGC
131 TCGGCCATTAGGC
*
47514831 CTTATCACATATATACACTTTCACATTCATCACATCGGCGATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
47514896 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
47514940 CACTGTCTTG
Statistics
Matches: 374, Mismatches: 17, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
141 40 0.11
143 203 0.54
145 91 0.24
147 40 0.11
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.32
Consensus pattern (143 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:47550976 original size:28 final size:28
Alignment explanation
Indices: 47550906--47550976 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
47550896 GCAATCAAAT
* * *
47550906 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
47550934 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
47550962 ATGTCACTTAGTGTG
1 ATGGCACTTAGTGTG
47550977 AAAAATATCG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:47550984 original size:28 final size:28
Alignment explanation
Indices: 47550923--47550984 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
47550913 TCAGTGTACG
**
47550923 AAATATTGAGAATGGCACTTAGTGTGCG
1 AAATATTGAGAATGGCACTTAGTGTGAA
* *
47550951 AGATATTGAGAATGTCACTTAGTGTGAA
1 AAATATTGAGAATGGCACTTAGTGTGAA
47550979 AAATAT
1 AAATAT
47550985 CGAATGATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (28 bp):
AAATATTGAGAATGGCACTTAGTGTGAA
Found at i:47556308 original size:69 final size:69
Alignment explanation
Indices: 47556229--47556365 Score: 265
Period size: 69 Copynumber: 2.0 Consensus size: 69
47556219 TTAAAATTCC
*
47556229 CGAGGTCTCGATACCTCGTTTTCAATTCTAATTATTTTAATATATATATTTTGTACATTTCACTA
1 CGAGGGCTCGATACCTCGTTTTCAATTCTAATTATTTTAATATATATATTTTGTACATTTCACTA
47556294 TTTT
66 TTTT
47556298 CGAGGGCTCGATACCTCGTTTTCAATTCTAATTATTTTAATATATATATTTTGTACATTTCACTA
1 CGAGGGCTCGATACCTCGTTTTCAATTCTAATTATTTTAATATATATATTTTGTACATTTCACTA
47556363 TTT
66 TTT
47556366 CAAAATTTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.48
Consensus pattern (69 bp):
CGAGGGCTCGATACCTCGTTTTCAATTCTAATTATTTTAATATATATATTTTGTACATTTCACTA
TTTT
Found at i:47558926 original size:23 final size:23
Alignment explanation
Indices: 47558900--47558962 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
47558890 AAATGTCCAA
*
47558900 CCAAAACACACTAGTATAATCCT
1 CCAAAACACACCAGTATAATCCT
47558923 CCAAAACACACCAGTATAATCCT
1 CCAAAACACACCAGTATAATCCT
47558946 CCAAAACACACCAGTAT
1 CCAAAACACACCAGTAT
47558963 CATATAATCC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.44, C:0.33, G:0.05, T:0.17
Consensus pattern (23 bp):
CCAAAACACACCAGTATAATCCT
Found at i:47558969 original size:28 final size:26
Alignment explanation
Indices: 47558914--47559017 Score: 124
Period size: 28 Copynumber: 3.9 Consensus size: 26
47558904 AACACACTAG
47558914 TATAATCCTCCAAAACACACCAG---
1 TATAATCCTCCAAAACACACCAGATA
47558937 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAG-AT-A
* *
47558965 TATAATCCTCCCAAACACACCAAAATAA
1 TATAATCCTCCAAAACACACC-AGAT-A
47558993 TATAATCCATCCAAAACACACCAGA
1 TATAATCC-TCCAAAACACACCAGA
47559018 ATAGCACAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
23 23 0.33
28 33 0.48
29 13 0.19
ACGTcount: A:0.46, C:0.33, G:0.03, T:0.18
Consensus pattern (26 bp):
TATAATCCTCCAAAACACACCAGATA
Found at i:47558992 original size:23 final size:23
Alignment explanation
Indices: 47558880--47558993 Score: 95
Period size: 23 Copynumber: 4.7 Consensus size: 23
47558870 GATTCCATCC
* *
47558880 AAACACACCAAAAT-GTCCAACCA
1 AAACACACCAAAATAATCC-TCCA
* **
47558903 AAACACACTAGTATAATCCTCCA
1 AAACACACCAAAATAATCCTCCA
**
47558926 AAACACACCAGTATAATCCTCCA
1 AAACACACCAAAATAATCCTCCA
*
47558949 AAACACACCAGTATCATATAATCCTCCC
1 AAACACACCA--A--A-ATAATCCTCCA
47558977 AAACACACCAAAATAAT
1 AAACACACCAAAATAAT
47558994 ATAATCCATC
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
23 51 0.67
24 4 0.05
26 1 0.01
28 20 0.26
ACGTcount: A:0.47, C:0.32, G:0.04, T:0.17
Consensus pattern (23 bp):
AAACACACCAAAATAATCCTCCA
Found at i:47570313 original size:40 final size:40
Alignment explanation
Indices: 47570269--47570365 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
47570259 CAACTATTTG
* * * *
47570269 TGGCACGTAGTGTGTGATTCGACATAGCTTTGGCTATATA
1 TGGCACTTAGTGTGCGATTCGACATAGCTTCGACTATATA
* * *
47570309 TGGCACTTAGTGTGCGATTTGAGATAGCTTCGACTATGTA
1 TGGCACTTAGTGTGCGATTCGACATAGCTTCGACTATATA
47570349 TGGCACTTAGTGTGCGA
1 TGGCACTTAGTGTGCGA
47570366 GATATCGAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATTCGACATAGCTTCGACTATATA
Found at i:47570412 original size:28 final size:28
Alignment explanation
Indices: 47570346--47570416 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
47570336 CTTCGACTAT
47570346 GTATGGCACTTAGTGTGCGAGATATCGA
1 GTATGGCACTTAGTGTGCGAGATATCGA
* * *
47570374 GTGTGGTACTTAGTGTGCGTGATATCGA
1 GTATGGCACTTAGTGTGCGAGATATCGA
*
47570402 GTATGACACTTAGTG
1 GTATGGCACTTAGTG
47570417 CGAGGCATTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.23, C:0.13, G:0.32, T:0.32
Consensus pattern (28 bp):
GTATGGCACTTAGTGTGCGAGATATCGA
Found at i:47573155 original size:28 final size:27
Alignment explanation
Indices: 47573123--47573482 Score: 214
Period size: 27 Copynumber: 13.3 Consensus size: 27
47573113 TTTAGTTTAC
47573123 AAAATTACTAAAATACCCTCGATTTTGT
1 AAAATTACTAAAATACCCTCGA-TTTGT
*
47573151 AAAATTACTAAAATACCC-CTGGTTTGT
1 AAAATTACTAAAATACCCTC-GATTTGT
*
47573178 AAAATTACTAAAATACCCCCTGATTTGT
1 AAAATTACTAAAATACCCTC-GATTTGT
*
47573206 AAAATTACTAAAATACCCTCGACTTGT
1 AAAATTACTAAAATACCCTCGATTTGT
* * *
47573233 AAAATTACCAAAGTACCCTCGATTTAT
1 AAAATTACTAAAATACCCTCGATTTGT
* **** * * **
47573260 AGAATTACTGTTTTACTCTTGATTTAC
1 AAAATTACTAAAATACCCTCGATTTGT
* **** **
47573287 AGAATTACTGTTTTACCCTCGATTTAC
1 AAAATTACTAAAATACCCTCGATTTGT
**
47573314 AAAATTATCGT--TTTACCCTCGA-TTGT
1 AAAATTA-C-TAAAATACCCTCGATTTGT
* * * **
47573340 GAAATTACTGAAATACCC-CTATAGGGT
1 AAAATTACTAAAATACCCTCGAT-TTGT
* * *
47573367 AGAATTACCAAAATACCC-CTAGTTTGT
1 AAAATTACTAAAATACCCTCGA-TTTGT
* *
47573394 AAAATTACCAAAATACCACT-GGTTTGT
1 AAAATTACTAAAATACC-CTCGATTTGT
* ** *
47573421 GAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACTAAAATACCCTCGATTTGT
* **
47573448 AAAATTACCAAAATACCC-CTGATTTAC
1 AAAATTACTAAAATACCCTC-GATTTGT
47573475 AAAATTAC
1 AAAATTAC
47573483 AGAAAAACCC
Statistics
Matches: 273, Mismatches: 46, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.00
25 3 0.01
26 16 0.06
27 203 0.74
28 49 0.18
29 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (27 bp):
AAAATTACTAAAATACCCTCGATTTGT
Found at i:47573191 original size:55 final size:55
Alignment explanation
Indices: 47573123--47573257 Score: 193
Period size: 55 Copynumber: 2.5 Consensus size: 55
47573113 TTTAGTTTAC
**
47573123 AAAATTACTAAAATACCCTCGATTTTGTAAAATTACTAAAATACCC-CTGGTTTGT
1 AAAATTACTAAAATACCCTCGATTTTGTAAAATTACTAAAATACCCTC-GACTTGT
*
47573178 AAAATTACTAAAATACCCCCTGA-TTTGTAAAATTACTAAAATACCCTCGACTTGT
1 AAAATTACTAAAATACCCTC-GATTTTGTAAAATTACTAAAATACCCTCGACTTGT
* *
47573233 AAAATTACCAAAGTACCCTCGATTT
1 AAAATTACTAAAATACCCTCGATTT
47573258 ATAGAATTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
54 2 0.03
55 66 0.93
56 3 0.04
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (55 bp):
AAAATTACTAAAATACCCTCGATTTTGTAAAATTACTAAAATACCCTCGACTTGT
Found at i:47573480 original size:54 final size:55
Alignment explanation
Indices: 47573369--47573549 Score: 165
Period size: 54 Copynumber: 3.3 Consensus size: 55
47573359 TATAGGGTAG
* * * ***
47573369 AATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGA
1 AATTACCGAAATACCCTCTAATTTGTAAAATTACCAAAATACCACTGATTTACAA
*
47573423 AATTACCGAAATACCCTC-AATTTGTAAAATTACCAAAATACCCCTGATTTACAA
1 AATTACCGAAATACCCTCTAATTTGTAAAATTACCAAAATACCACTGATTTACAA
* * * * * *
47573477 AATTACAGAAAAACCCT-TGACTTTCTAAAAATTA-TAGAAATACCA-TTAGTTTACAA
1 AATTACCGAAATACCCTCT-AATTTGT-AAAATTACCA-AAATACCACTGA-TTTACAA
*
47573533 AATTACTGAAATACCCT
1 AATTACCGAAATACCCT
47573550 TGGTTTGTAG
Statistics
Matches: 105, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
54 60 0.57
55 9 0.09
56 36 0.34
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (55 bp):
AATTACCGAAATACCCTCTAATTTGTAAAATTACCAAAATACCACTGATTTACAA
Found at i:47573555 original size:27 final size:27
Alignment explanation
Indices: 47573448--47573555 Score: 85
Period size: 27 Copynumber: 3.9 Consensus size: 27
47573438 CTCAATTTGT
** * *
47573448 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
* * *
47573475 AAAATTACAGAAAAACCCTTGACTTT-C
1 AAAATTACTGAAATACCCTTG-GTTTAC
* *
47573502 TAAAAATTA-TAGAAATACCATTAGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
47573531 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
47573556 GTAGATTTAC
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
27 39 0.62
28 7 0.11
29 17 0.27
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.31
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:47573639 original size:27 final size:27
Alignment explanation
Indices: 47573596--47573669 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
47573586 AAATGACTAC
*
47573596 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
47573623 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
47573650 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
47573670 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:47573673 original size:27 final size:27
Alignment explanation
Indices: 47573609--47573673 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
47573599 ACCCCTAATA
*
47573609 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
47573636 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
47573663 GGTAAAATGAC
1 GGTAAAATGAC
47573674 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:47574326 original size:25 final size:25
Alignment explanation
Indices: 47574297--47574344 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
47574287 TTATAATGTG
47574297 AAAATGACTGTTTTGCCCCTAGGTA
1 AAAATGACTGTTTTGCCCCTAGGTA
*
47574322 AAAATGACTGTTTTGCCCTTAGG
1 AAAATGACTGTTTTGCCCCTAGG
47574345 GTTTAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (25 bp):
AAAATGACTGTTTTGCCCCTAGGTA
Found at i:47574405 original size:20 final size:20
Alignment explanation
Indices: 47574380--47574446 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
47574370 GGTATGATAA
47574380 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
*
47574400 ACATGATATGCATGATATGC
1 ACATGATATGTATGATATGC
*
47574420 ACATGATATGTATGAAATGC
1 ACATGATATGTATGATATGC
47574440 ACATGAT
1 ACATGAT
47574447 GAATTCATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:47574407 original size:11 final size:11
Alignment explanation
Indices: 47574391--47574446 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
47574381 CATGATTGAT
47574391 ATGATATGCAC
1 ATGATATGCAC
47574402 ATGATATG--C
1 ATGATATGCAC
47574411 ATGATATGCAC
1 ATGATATGCAC
*
47574422 ATGATATG--T
1 ATGATATGCAC
*
47574431 ATGAAATGCAC
1 ATGATATGCAC
47574442 ATGAT
1 ATGAT
47574447 GAATTCATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 16 0.43
11 21 0.57
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:47574574 original size:52 final size:51
Alignment explanation
Indices: 47574496--47574618 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
47574486 GAGGAAGTGC
*
47574496 AAAAGGGCTTATGCCCTAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
*
47574548 AAAAGGCCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
47574599 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
47574619 ATTAAAGAGG
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
50 10 0.15
51 24 0.35
52 34 0.50
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:47574593 original size:25 final size:26
Alignment explanation
Indices: 47574496--47574618 Score: 178
Period size: 26 Copynumber: 4.8 Consensus size: 26
47574486 GAGGAAGTGC
* **
47574496 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
47574522 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* **
47574548 AAAAGGCCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
47574574 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
47574599 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
47574619 ATTAAAGAGG
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
25 33 0.38
26 55 0.62
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:47574822 original size:42 final size:42
Alignment explanation
Indices: 47574763--47574854 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
47574753 TAGTCTCCCC
*
47574763 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
*
47574805 AAATGGGCTTGCATACATTCATTGATATTTCATGTGTTATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
47574847 AAATGGGC
1 AAATGGGC
47574855 CTATGGGCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
Found at i:47574913 original size:31 final size:31
Alignment explanation
Indices: 47574878--47574956 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
47574868 CGTTTACAAT
47574878 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
47574909 AAAGGCTTCAGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
47574940 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
47574957 AACCGTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:47581415 original size:39 final size:40
Alignment explanation
Indices: 47581359--47581465 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 40
47581349 TGATGAAAAA
* * * *
47581359 TCGGCTATTTGTGGCACTTAGTGTGTGA-TCGACATAGCT
1 TCGGCTATATATGGCACTTAGTGTGCGATTCGACATAACT
* * *
47581398 TTGGCTATATATGGCACTTAGTGTGCGATTTGAGATAACT
1 TCGGCTATATATGGCACTTAGTGTGCGATTCGACATAACT
*
47581438 TCGGCTATGTATGGCACTTAGTGTGCGA
1 TCGGCTATATATGGCACTTAGTGTGCGA
47581466 GATATCGAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
39 24 0.41
40 34 0.59
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.36
Consensus pattern (40 bp):
TCGGCTATATATGGCACTTAGTGTGCGATTCGACATAACT
Found at i:47581533 original size:28 final size:28
Alignment explanation
Indices: 47581446--47581522 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 28
47581436 CTTCGGCTAT
47581446 GTATGGCACTTAGTGTGCGAGATATCGA
1 GTATGGCACTTAGTGTGCGAGATATCGA
* * *
47581474 ATGTGGCACTTAGTGTGTGAGATATCGA
1 GTATGGCACTTAGTGTGCGAGATATCGA
*
47581502 GTATGGCACTTAGTTTGCGAG
1 GTATGGCACTTAGTGTGCGAG
47581523 GCATTGAGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.23, C:0.13, G:0.32, T:0.31
Consensus pattern (28 bp):
GTATGGCACTTAGTGTGCGAGATATCGA
Found at i:47584965 original size:53 final size:47
Alignment explanation
Indices: 47584856--47584949 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
47584846 CACCAAGTGC
* *
47584856 CTTCGGGATTATTACAGCCAGTTAAAATACCGGAATGGAAATGGGAA
1 CTTCAGGATTATTACAGCCAGTTAAAATACCGAAATGGAAATGGGAA
* *
47584903 CTTCAGGATTATTATAGCCAGTTACAATACCGAAATTGG-AATGGGAA
1 CTTCAGGATTATTACAGCCAGTTAAAATACCGAAA-TGGAAATGGGAA
47584950 AGAGTTACCA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 39 0.93
48 3 0.07
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (47 bp):
CTTCAGGATTATTACAGCCAGTTAAAATACCGAAATGGAAATGGGAA
Found at i:47586523 original size:24 final size:25
Alignment explanation
Indices: 47586481--47586537 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
47586471 CAAGCTTTCT
47586481 TGGTTCTTTGTGAGATTCCCAA-TA
1 TGGTTCTTTGTGAGATTCCCAATTA
*
47586505 TGGTTCTTTGTGA-ACTTCCTAATTA
1 TGGTTCTTTGTGAGA-TTCCCAATTA
*
47586530 TGGCTCTT
1 TGGTTCTT
47586538 ATGAGCTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 1 0.03
24 19 0.66
25 9 0.31
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.46
Consensus pattern (25 bp):
TGGTTCTTTGTGAGATTCCCAATTA
Found at i:47594757 original size:23 final size:23
Alignment explanation
Indices: 47594731--47594780 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
47594721 ACCCCATGCA
47594731 ATGCAACATA-ATATCATACATGG-
1 ATGCAACATACATAT-A-ACATGGC
47594754 ATGCAACATACATATAACATGGC
1 ATGCAACATACATATAACATGGC
47594777 ATGC
1 ATGC
47594781 TCAAATACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.24
23 15 0.60
24 4 0.16
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (23 bp):
ATGCAACATACATATAACATGGC
Found at i:47594846 original size:27 final size:27
Alignment explanation
Indices: 47594816--47594920 Score: 88
Period size: 27 Copynumber: 3.9 Consensus size: 27
47594806 AAAAAATCTA
*
47594816 TCATTTTACCATATCGGGGTATTACAG
1 TCATTTTACCATATCGGGGTATTTCAG
*
47594843 TCATTTTACCCA-A-CAAGGGTATTTCAG
1 TCATTTTA-CCATATC-GGGGTATTTCAG
* ** * *
47594870 TCATTCTACTTTATTGGGGTATTTCGG
1 TCATTTTACCATATCGGGGTATTTCAG
* **
47594897 TCATTTTACCCTATAAGGGTATTT
1 TCATTTTACCATATCGGGGTATTT
47594921 TGGTTATTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
26 2 0.03
27 56 0.92
28 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (27 bp):
TCATTTTACCATATCGGGGTATTTCAG
Found at i:47594939 original size:27 final size:27
Alignment explanation
Indices: 47594832--47594943 Score: 82
Period size: 27 Copynumber: 4.1 Consensus size: 27
47594822 TACCATATCG
* * * * *
47594832 GGGTATTACAGTCATTTTACCCAACAA
1 GGGTATTTCGGTCATTTTACACTATAA
* * ** **
47594859 GGGTATTTCAGTCATTCTACTTTATTG
1 GGGTATTTCGGTCATTTTACACTATAA
*
47594886 GGGTATTTCGGTCATTTTACCCTATAA
1 GGGTATTTCGGTCATTTTACACTATAA
* *
47594913 GGGTATTTTGGTTATTTTATCAC-ATAA
1 GGGTATTTCGGTCATTTTA-CACTATAA
47594940 GGGT
1 GGGT
47594944 TTAGGTACGC
Statistics
Matches: 67, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
27 65 0.97
28 2 0.03
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (27 bp):
GGGTATTTCGGTCATTTTACACTATAA
Found at i:47602892 original size:27 final size:27
Alignment explanation
Indices: 47602854--47602908 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
47602844 ATGATTATAA
*
47602854 CCTAGCAGTACACTGTTGGTATTCTAT
1 CCTAGCAATACACTGTTGGTATTCTAT
47602881 CCTAGCAATACACTGTTGGTATTCTAT
1 CCTAGCAATACACTGTTGGTATTCTAT
47602908 C
1 C
47602909 TCAAAACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (27 bp):
CCTAGCAATACACTGTTGGTATTCTAT
Found at i:47608850 original size:31 final size:32
Alignment explanation
Indices: 47608793--47608854 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
47608783 ACGAAGTCAC
* *
47608793 CAGATATAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATAGATATTGTGGCAAAGCCACCAGAA
*
47608825 CAGATATATATA-TGTGGCAAAGCCACCAGA
1 CAGATATAGATATTGTGGCAAAGCCACCAGA
47608855 TTGTAGCGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (32 bp):
CAGATATAGATATTGTGGCAAAGCCACCAGAA
Found at i:47616291 original size:71 final size:67
Alignment explanation
Indices: 47616212--47616353 Score: 203
Period size: 67 Copynumber: 2.1 Consensus size: 67
47616202 TCACCAGTTA
* * *
47616212 CAGATATTCTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCAGCGA
1 CAGATATTCTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCGA
47616277 GGCTAC
62 GGCTAC
* *
47616283 CAGATATTCTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCT
1 CAGATATTCTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
47616348 AC
66 AC
47616350 CAGA
1 CAGA
47616354 ACACTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
67 41 0.62
71 25 0.38
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (67 bp):
CAGATATTCTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
AC
Found at i:47626179 original size:40 final size:40
Alignment explanation
Indices: 47626135--47626211 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
47626125 TAGTGCCTCA
* *
47626135 TGTAGTCGAAGCTA-TTCCAACTCGCACACTTAGTGTCATT
1 TGTAGCCGAAGCTATTTCAAAC-CGCACACTTAGTGTCATT
47626175 TGTAGCCGAAGCTATTTCAAACCGCACACTTAGTGTC
1 TGTAGCCGAAGCTATTTCAAACCGCACACTTAGTGTC
47626212 GAACTTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 28 0.82
41 6 0.18
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (40 bp):
TGTAGCCGAAGCTATTTCAAACCGCACACTTAGTGTCATT
Found at i:47628670 original size:42 final size:42
Alignment explanation
Indices: 47628539--47628691 Score: 137
Period size: 42 Copynumber: 3.7 Consensus size: 42
47628529 AATAAGATGA
* * ** *
47628539 CAATGCCATGTCCCAGATGTGGTTTTACATGGGATCTCACAT
1 CAATGCCATATCCCAGATGTGGTCTTACATGAAATCTCATAT
** * * * *
47628581 CGGTGCCA-ATCCCAGATATGGTCTTATACGAAATCTCATTT
1 CAATGCCATATCCCAGATGTGGTCTTACATGAAATCTCATAT
** * * *
47628622 TGATGCCATGTCCCAGACGTAGTCTTACATGAAATCTCATAT
1 CAATGCCATATCCCAGATGTGGTCTTACATGAAATCTCATAT
* *
47628664 CAATGCCATATCCCATATATGGTCTTAC
1 CAATGCCATATCCCAGATGTGGTCTTAC
47628692 TTGATAACAC
Statistics
Matches: 83, Mismatches: 27, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
41 30 0.36
42 53 0.64
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (42 bp):
CAATGCCATATCCCAGATGTGGTCTTACATGAAATCTCATAT
Found at i:47637289 original size:58 final size:58
Alignment explanation
Indices: 47637219--47637334 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
47637209 TTTCACGTTC
* *
47637219 TTCCTTTCCCAAATAGATGATCTATTGAGTAACCCTATAAAACAATTAATAAATCATA
1 TTCCTTTCCCAAATAGATGATCCATTAAGTAACCCTATAAAACAATTAATAAATCATA
47637277 TTCCTTTCCCAAATAGATGATCCATTAAGTAACCCTATAAAACAATTAATAAATCATA
1 TTCCTTTCCCAAATAGATGATCCATTAAGTAACCCTATAAAACAATTAATAAATCATA
47637335 CCTCCACTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (58 bp):
TTCCTTTCCCAAATAGATGATCCATTAAGTAACCCTATAAAACAATTAATAAATCATA
Found at i:47654033 original size:14 final size:14
Alignment explanation
Indices: 47654014--47654042 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
47654004 TTAGACTTAG
47654014 TATTGTAAAAAGTA
1 TATTGTAAAAAGTA
47654028 TATTGTAAAAAGTA
1 TATTGTAAAAAGTA
47654042 T
1 T
47654043 TTTCATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (14 bp):
TATTGTAAAAAGTA
Found at i:47656561 original size:26 final size:26
Alignment explanation
Indices: 47656514--47656563 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
47656504 TTTATACTGA
**
47656514 TTACTGGCAGCTTTGCTGCGATACCG
1 TTACTGGCAGCTTTGCCACGATACCG
47656540 TTACTGGCAGCTTTGCCACGATAC
1 TTACTGGCAGCTTTGCCACGATAC
47656564 TGATTAGTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.28, G:0.24, T:0.30
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCCACGATACCG
Found at i:47659228 original size:40 final size:40
Alignment explanation
Indices: 47659182--47659365 Score: 219
Period size: 40 Copynumber: 4.6 Consensus size: 40
47659172 CTCGCACAAG
* * *
47659182 GCCTTCGGGTCTTAGCTCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * * *
47659222 GCCTTCGGGACTTAGCCTGGATATAGTCGCTATCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
*
47659262 GCCTTCGGGTCTTAGCCCTGATATAG-CAACTCA-CACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACT-AGCACAAAT
* * * *
47659302 GCCTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
*
47659342 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
47659366 CATTCGAATA
Statistics
Matches: 121, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.02
40 117 0.97
41 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:47668118 original size:40 final size:40
Alignment explanation
Indices: 47668088--47668216 Score: 195
Period size: 40 Copynumber: 3.2 Consensus size: 40
47668078 GGACTAAGAT
* * *
47668088 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
*
47668128 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
* * *
47668168 CCGAAGGCATTCATGCGAGATGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
47668208 CCGAAGGCA
1 CCGAAGGCA
47668217 CTTGAACGAG
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
Found at i:47668238 original size:80 final size:79
Alignment explanation
Indices: 47668101--47668253 Score: 175
Period size: 80 Copynumber: 1.9 Consensus size: 79
47668091 AAGGCCTTTG
** * * *
47668101 TGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAG
1 TGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCC-GGTTAAA
47668166 TCCCGAAGGCATTCA
65 TCCCGAAGGCATTCA
** * *
47668181 TGCGAGATGTTAAATCCGGGTTATGTCCCGAAGGCACTT-GAACGAG-GAGCTATATCCGGTTAA
1 TGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCA-TTCGAACGAGTGA-CTAAATCCGGTTAA
*
47668244 ATTCCGAAGG
64 ATCCCGAAGG
47668254 TACGTGATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
79 15 0.25
80 44 0.72
81 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (79 bp):
TGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGTTAAAT
CCCGAAGGCATTCA
Found at i:47674258 original size:100 final size:100
Alignment explanation
Indices: 47674085--47674284 Score: 382
Period size: 100 Copynumber: 2.0 Consensus size: 100
47674075 ACGTCTTTCA
*
47674085 TGTTTCGATGCTTCGATGCTATCGATCTGATCCATCGCACATAATTAGCCCATCAGAGGTTGAAA
1 TGTTTCGATGCTTCGACGCTATCGATCTGATCCATCGCACATAATTAGCCCATCAGAGGTTGAAA
47674150 TTCAAGTCGACATGAGCTATGAAGAAGAACCGATG
66 TTCAAGTCGACATGAGCTATGAAGAAGAACCGATG
*
47674185 TGTTTCGATGCTTCGACGCTATCGATCTGATCCATCGCAGATAATTAGCCCATCAGAGGTTGAAA
1 TGTTTCGATGCTTCGACGCTATCGATCTGATCCATCGCACATAATTAGCCCATCAGAGGTTGAAA
47674250 TTCAAGTCGACATGAGCTATGAAGAAGAACCGATG
66 TTCAAGTCGACATGAGCTATGAAGAAGAACCGATG
47674285 CGTATCCTAG
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (100 bp):
TGTTTCGATGCTTCGACGCTATCGATCTGATCCATCGCACATAATTAGCCCATCAGAGGTTGAAA
TTCAAGTCGACATGAGCTATGAAGAAGAACCGATG
Found at i:47674525 original size:53 final size:53
Alignment explanation
Indices: 47674462--47674568 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
47674452 CTTAAGTGGG
*
47674462 GGAGAGTTGTGACAGCCCAAAATTGACCCTAGTCGGGAAGTGGTTTCGGGACC
1 GGAGAGTTGTGACAGCCCAAAATTGACCCTAGTCGGGAAGTAGTTTCGGGACC
* *
47674515 GGAGAGTTGTGACAGCCCAAAGTTGCCCCTAGTCGGGAAGTAGTTTCGGGACC
1 GGAGAGTTGTGACAGCCCAAAATTGACCCTAGTCGGGAAGTAGTTTCGGGACC
47674568 G
1 G
47674569 CTAAACCGAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (53 bp):
GGAGAGTTGTGACAGCCCAAAATTGACCCTAGTCGGGAAGTAGTTTCGGGACC
Found at i:47676187 original size:80 final size:79
Alignment explanation
Indices: 47676103--47676274 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
47676093 GGACTAAGAT
*
47676103 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
47676167 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
47676183 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
47676248 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
47676262 CCGAAGGCATTTG
1 CCGAAGGCATTTG
47676275 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:47676254 original size:39 final size:39
Alignment explanation
Indices: 47676050--47676272 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
47676040 TTGAATGCTG
* * * * *
47676050 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
47676090 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
47676129 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
47676170 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
47676210 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
47676249 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
47676273 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:47676292 original size:79 final size:80
Alignment explanation
Indices: 47676130--47676307 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
47676120 AGATACAAAT
* * * *
47676130 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
47676195 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
47676210 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
47676274 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
47676289 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
47676308 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:47677406 original size:57 final size:57
Alignment explanation
Indices: 47677318--47677431 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 57
47677308 GCATCAGTAT
*
47677318 TGAAGCTCTGTGCAGAGAGATATCCAAGTCGTAATGGAAAAAGGTCAGTGTAGTCGA
1 TGAAGCTCCGTGCAGAGAGATATCCAAGTCGTAATGGAAAAAGGTCAGTGTAGTCGA
* **
47677375 TGAAGCTCCGTGCAGGGAGATATCCAAGTCGTAATGGGCAAAGGTCAGTGTAGTCGA
1 TGAAGCTCCGTGCAGAGAGATATCCAAGTCGTAATGGAAAAAGGTCAGTGTAGTCGA
47677432 CCCCTGCAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.31, C:0.16, G:0.32, T:0.22
Consensus pattern (57 bp):
TGAAGCTCCGTGCAGAGAGATATCCAAGTCGTAATGGAAAAAGGTCAGTGTAGTCGA
Found at i:47684163 original size:80 final size:79
Alignment explanation
Indices: 47684079--47684250 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
47684069 GGACTAAGAT
*
47684079 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
47684143 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
47684159 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
47684224 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
47684238 CCGAAGGCATTTG
1 CCGAAGGCATTTG
47684251 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:47684230 original size:39 final size:39
Alignment explanation
Indices: 47684026--47684248 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
47684016 TTGAATGCTG
* * * * *
47684026 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
47684066 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
47684105 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
47684146 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
47684186 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
47684225 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
47684249 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:47684268 original size:79 final size:80
Alignment explanation
Indices: 47684106--47684283 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
47684096 AGATACAAAT
* * * *
47684106 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
47684171 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
47684186 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
47684250 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
47684265 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
47684284 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:47697818 original size:51 final size:51
Alignment explanation
Indices: 47697671--47697807 Score: 166
Period size: 51 Copynumber: 2.7 Consensus size: 51
47697661 CTACCATCAA
* * * *
47697671 ATCTTTAAGAATATAATATCATATCTTCTAAGATTCCATATCTTAGATAAG
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
* * ** * * * *
47697722 ATATGTAATCTTATAAAATAATATCTTATAAGATTCCATATCATATCTAAG
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
47697773 ATCTCTAAGATTATAATATCATATCTTCTAAGATT
1 ATCTCTAAGATTATAATATCATATCTTCTAAGATT
47697808 AGTTACCATA
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (51 bp):
ATCTCTAAGATTATAATATCATATCTTCTAAGATTCCATATCATATATAAG
Found at i:47699590 original size:18 final size:17
Alignment explanation
Indices: 47699563--47699596 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
47699553 TGAGATGACA
47699563 AGATGAGAAATGGAAATG
1 AGATGAGAAAT-GAAATG
*
47699581 AGATGGGAAATGAAAT
1 AGATGAGAAATGAAAT
47699597 ATGAAATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (17 bp):
AGATGAGAAATGAAATG
Found at i:47701940 original size:34 final size:32
Alignment explanation
Indices: 47701881--47701960 Score: 90
Period size: 34 Copynumber: 2.5 Consensus size: 32
47701871 GATTGCATGC
**
47701881 CTGAACTGATACTGTAATGGGCTAAGGCCCACA
1 CTGAACTGATACTGTAATGCACTAAGGCCCA-A
* *
47701914 CTGATACTGATACTGTAGTGCACTAAGGTCCAA
1 CTGA-ACTGATACTGTAATGCACTAAGGCCCAA
*
47701947 CTGAATTGA-ACTGT
1 CTGAACTGATACTGT
47701961 TATTGATCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 5 0.12
32 4 0.10
33 9 0.22
34 23 0.56
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (32 bp):
CTGAACTGATACTGTAATGCACTAAGGCCCAA
Found at i:47735202 original size:18 final size:20
Alignment explanation
Indices: 47735179--47735218 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
47735169 TTTTTAAAAC
47735179 AATATTGAT-A-AATTTAAA
1 AATATTGATAATAATTTAAA
*
47735197 AATATTTATAATAATTTAAA
1 AATATTGATAATAATTTAAA
47735217 AA
1 AA
47735219 ATAATGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
AATATTGATAATAATTTAAA
Found at i:47735219 original size:21 final size:19
Alignment explanation
Indices: 47735171--47735221 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
47735161 ATTATATATT
47735171 TTTAAAACAATATTGATAAA
1 TTTAAAA-AATATTGATAAA
*
47735191 TTT-AAAAATATTTATAATAA
1 TTTAAAAAATATTGAT-A-AA
47735211 TTTAAAAAATA
1 TTTAAAAAATA
47735222 ATGTATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 8 0.30
19 4 0.15
20 8 0.30
21 7 0.26
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
TTTAAAAAATATTGATAAA
Found at i:47738852 original size:36 final size:36
Alignment explanation
Indices: 47738806--47738889 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
47738796 ATTTCCATTA
* *
47738806 TTTTTGCTCTTCCTTGACTTCCTCTTTCTTCTCCTCG
1 TTTTT-CTCTTCCTTCACTTCCTCTTTCTTCTCCTCC
* ** * *
47738843 TTTTTCTCTTCTTTCTTTTCCTCTTTCTTTTCTTCC
1 TTTTTCTCTTCCTTCACTTCCTCTTTCTTCTCCTCC
47738879 TTTTTCTCTTC
1 TTTTTCTCTTC
47738890 TTTTGCAGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 35 0.88
37 5 0.12
ACGTcount: A:0.01, C:0.32, G:0.04, T:0.63
Consensus pattern (36 bp):
TTTTTCTCTTCCTTCACTTCCTCTTTCTTCTCCTCC
Found at i:47738861 original size:15 final size:16
Alignment explanation
Indices: 47738851--47738893 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
47738841 CGTTTTTCTC
47738851 TTCTTTCTTTTCCTCT
1 TTCTTTCTTTTCCTCT
* *
47738867 TTCTTT-TCTTCCTTT
1 TTCTTTCTTTTCCTCT
47738882 TTCTCTTCTTTT
1 TTCT-TTCTTTT
47738894 GCAGGTCCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 11 0.50
16 8 0.36
17 3 0.14
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (16 bp):
TTCTTTCTTTTCCTCT
Found at i:47738869 original size:21 final size:21
Alignment explanation
Indices: 47738845--47738888 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
47738835 TCTCCTCGTT
*
47738845 TTTCTCTTCTTTCTTTTCCTC
1 TTTCTCTTCTTCCTTTTCCTC
* *
47738866 TTTCTTTTCTTCCTTTTTCTC
1 TTTCTCTTCTTCCTTTTCCTC
47738887 TT
1 TT
47738889 CTTTTGCAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCTCTTCTTCCTTTTCCTC
Found at i:47738888 original size:12 final size:12
Alignment explanation
Indices: 47738828--47738892 Score: 62
Period size: 12 Copynumber: 5.4 Consensus size: 12
47738818 CTTGACTTCC
*
47738828 TCTTTCTTCTCC
1 TCTTTCTTCTCT
47738840 TCGTTT-TTCTCT
1 TC-TTTCTTCTCT
* *
47738852 TCTTTCTTTTCC
1 TCTTTCTTCTCT
*
47738864 TCTTTCTTTTCT
1 TCTTTCTTCTCT
47738876 TCCTTT-TTCTCT
1 T-CTTTCTTCTCT
47738888 TCTTT
1 TCTTT
47738893 TGCAGGTCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
11 7 0.16
12 31 0.69
13 7 0.16
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.68
Consensus pattern (12 bp):
TCTTTCTTCTCT
Found at i:47738890 original size:36 final size:36
Alignment explanation
Indices: 47738824--47738892 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
47738814 CTTCCTTGAC
*
47738824 TTCCTCTTTCTTCTCCTCGTTTTTCTCTTCTTTCTT
1 TTCCTCTTTCTTCTCCTCCTTTTTCTCTTCTTTCTT
* *
47738860 TTCCTCTTTCTTTTCTTCCTTTTTCTCTTCTTT
1 TTCCTCTTTCTTCTCCTCCTTTTTCTCTTCTTT
47738893 TGCAGGTCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.67
Consensus pattern (36 bp):
TTCCTCTTTCTTCTCCTCCTTTTTCTCTTCTTTCTT
Found at i:47739954 original size:28 final size:27
Alignment explanation
Indices: 47739897--47739954 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
47739887 TAGAAGAAGA
**
47739897 AAAAAAATGCATAAAAACAATTTGTAC
1 AAAAAAATGCATAAAAACAATTTCCAC
* * *
47739924 AAAAAAATGCTTAAAATCAATATTCCCC
1 AAAAAAATGCATAAAAACAAT-TTCCAC
47739952 AAA
1 AAA
47739955 TTTTCTTGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.57, C:0.16, G:0.05, T:0.22
Consensus pattern (27 bp):
AAAAAAATGCATAAAAACAATTTCCAC
Found at i:47750854 original size:3 final size:3
Alignment explanation
Indices: 47750842--47750870 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
47750832 TATGTATGTT
47750842 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
47750871 GTGCCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:47754588 original size:18 final size:18
Alignment explanation
Indices: 47754565--47754600 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
47754555 AAAAACAAAA
47754565 ATTAATGATGTTCAAACT
1 ATTAATGATGTTCAAACT
*
47754583 ATTAATGATGTTTAAACT
1 ATTAATGATGTTCAAACT
47754601 TAAGTAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (18 bp):
ATTAATGATGTTCAAACT
Found at i:47756500 original size:27 final size:27
Alignment explanation
Indices: 47756470--47756540 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
47756460 TGGCAAGCTA
*
47756470 GTGTTCGCCAGTGGGCCTAGCAAATTG
1 GTGTTCGCCAGTAGGCCTAGCAAATTG
* *
47756497 GTGTTCGCTAGTAGGCCTAGCGAATTG
1 GTGTTCGCCAGTAGGCCTAGCAAATTG
*
47756524 GTGTTCG-CAATAGGCCT
1 GTGTTCGCCAGTAGGCCT
47756541 GACGAGCTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 8 0.21
27 31 0.79
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.28
Consensus pattern (27 bp):
GTGTTCGCCAGTAGGCCTAGCAAATTG
Found at i:47756553 original size:26 final size:27
Alignment explanation
Indices: 47756524--47756581 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
47756514 TAGCGAATTG
*
47756524 GTGTTCG-CAATAGGCCTGACGAGCTA
1 GTGTTCGCCAATAGGCCAGACGAGCTA
*
47756550 GTGTTCGCCAATAGGCCAGGCGAGCTA
1 GTGTTCGCCAATAGGCCAGACGAGCTA
47756577 GTGTT
1 GTGTT
47756582 TACCAGTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.21, C:0.22, G:0.33, T:0.24
Consensus pattern (27 bp):
GTGTTCGCCAATAGGCCAGACGAGCTA
Found at i:47756591 original size:27 final size:27
Alignment explanation
Indices: 47756531--47756591 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
47756521 TTGGTGTTCG
* *
47756531 CAATAGGCCTGACGAGCTAGTGTTCGC
1 CAATAGGCCAGACGAGCTAGTGTTCAC
* *
47756558 CAATAGGCCAGGCGAGCTAGTGTTTAC
1 CAATAGGCCAGACGAGCTAGTGTTCAC
*
47756585 CAGTAGG
1 CAATAGG
47756592 TTTGGCGAGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (27 bp):
CAATAGGCCAGACGAGCTAGTGTTCAC
Found at i:47766047 original size:16 final size:15
Alignment explanation
Indices: 47766024--47766053 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
47766014 GCTAAAGCAA
47766024 TTAAATTTTAATGTC
1 TTAAATTTTAATGTC
47766039 TTAACATTTTAATGT
1 TTAA-ATTTTAATGT
47766054 GATGATTGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
TTAAATTTTAATGTC
Found at i:47772537 original size:21 final size:19
Alignment explanation
Indices: 47772513--47772551 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
47772503 ACTTCTTTTT
47772513 CAGCAACAACTTTCTCTTCTG
1 CAGCAACAA-TTTC-CTTCTG
*
47772534 CAGCAGCAATTTCCTTCT
1 CAGCAACAATTTCCTTCT
47772552 CAACAGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 8 0.47
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.33
Consensus pattern (19 bp):
CAGCAACAATTTCCTTCTG
Found at i:47778103 original size:4 final size:4
Alignment explanation
Indices: 47778094--47778120 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
47778084 AAACTAAGTA
47778094 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
47778121 AATAAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:47779526 original size:23 final size:22
Alignment explanation
Indices: 47779474--47779526 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
47779464 TCCACGTCTT
*
47779474 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
47779496 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
47779519 TTTCTTTT
1 TTTCTTTT
47779527 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:47781913 original size:4 final size:4
Alignment explanation
Indices: 47781904--47781931 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
47781894 TTAAACTAAG
47781904 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
47781932 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:47782217 original size:7 final size:7
Alignment explanation
Indices: 47782196--47782260 Score: 60
Period size: 7 Copynumber: 9.3 Consensus size: 7
47782186 GGGTTGTGAT
*
47782196 TTAAGGT
1 TTAAGGG
*
47782203 TTATGGG
1 TTAAGGG
47782210 TTAAGGG
1 TTAAGGG
*
47782217 TTAGGGG
1 TTAAGGG
47782224 TTAAGGG
1 TTAAGGG
47782231 TT-AGAGG
1 TTAAG-GG
*
47782238 TTAAGAG
1 TTAAGGG
*
47782245 TTAAGGA
1 TTAAGGG
*
47782252 TTTAGGG
1 TTAAGGG
47782259 TT
1 TT
47782261 TATAGATTCG
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
6 2 0.04
7 42 0.91
8 2 0.04
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.35
Consensus pattern (7 bp):
TTAAGGG
Found at i:47782863 original size:17 final size:17
Alignment explanation
Indices: 47782842--47782875 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
47782832 ATACTAGATT
47782842 TAAAAAAAT-TAATAAA
1 TAAAAAAATATAATAAA
47782858 TAAAAAAATATAATAAA
1 TAAAAAAATATAATAAA
47782875 T
1 T
47782876 TGATACGGAT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAAAATATAATAAA
Done.