Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 177 of 182
Found at i:53873518 original size:16 final size:17
Alignment explanation
Indices: 53873485--53873519 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
53873475 TAAACACCCA
53873485 TTTTCTATTCTTTCATT
1 TTTTCTATTCTTTCATT
*
53873502 TTTTTTATTCTTT-ATT
1 TTTTCTATTCTTTCATT
53873518 TT
1 TT
53873520 GTATATTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTCTATTCTTTCATT
Found at i:53877901 original size:15 final size:15
Alignment explanation
Indices: 53877862--53877914 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 15
53877852 GAACATTTGG
53877862 AATTTAATTAGATAAAA
1 AATTT-ATTA-ATAAAA
53877879 AACTTTTATTAATAAAA
1 AA--TTTATTAATAAAA
*
53877896 AATTTATTTATAAATA
1 AATTTATTAATAAA-A
53877912 AAT
1 AAT
53877915 CATTGCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.34
16 4 0.12
17 10 0.31
18 4 0.12
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTTATTAATAAAA
Found at i:53877988 original size:22 final size:20
Alignment explanation
Indices: 53877945--53877983 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
53877935 TAATTTAAAA
53877945 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
53877965 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
53877984 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:53878124 original size:34 final size:35
Alignment explanation
Indices: 53878070--53878136 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
53878060 CAAACACTAG
*
53878070 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
53878105 AAAACATTTTCTAG-AAATCATTTTACAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
53878137 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 18 0.60
35 12 0.40
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:53878128 original size:14 final size:14
Alignment explanation
Indices: 53878105--53878144 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
53878095 ACAGAAAAGT
53878105 AAAACATTTT-CTAG
1 AAAACATTTTAC-AG
*
53878119 AAATCATTTTACAG
1 AAAACATTTTACAG
53878133 AAAACATTTTAC
1 AAAACATTTTAC
53878145 TGCCAATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 22 0.96
15 1 0.04
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:53883532 original size:29 final size:30
Alignment explanation
Indices: 53883473--53883530 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
53883463 TCAGAGCCTT
* *
53883473 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATATAATTATGAAAAAGTTTA
* *
53883503 GGGGCAAAATTATAATTTTGAAAAAGTT
1 GGGGCAAAAATATAATTATGAAAAAGTT
53883531 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATATAATTATGAAAAAGTTTA
Found at i:53883976 original size:50 final size:50
Alignment explanation
Indices: 53883869--53884118 Score: 286
Period size: 50 Copynumber: 4.9 Consensus size: 50
53883859 ATTTGGGTAA
* *
53883869 AGAGATCCCATGTAAGACCATGCCTGGGACATGGCATTGGCATCCTTGAGATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT-C--GAG---ACG
*
53883925 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGACG
* * *
53883975 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGACG
* * * * *
53884025 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCA-TGGCCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG-CATCGAGACG
** * *
53884075 AGAACATCCTATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
53884119 GTTATGATCA
Statistics
Matches: 173, Mismatches: 18, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
49 3 0.02
50 93 0.54
51 30 0.17
52 3 0.02
53 3 0.02
55 1 0.01
56 40 0.23
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGACG
Found at i:53885196 original size:547 final size:547
Alignment explanation
Indices: 53884162--53885255 Score: 2188
Period size: 547 Copynumber: 2.0 Consensus size: 547
53884152 ATTCCAATGT
53884162 CGCTCAACGGGCTAGTAAACGAATCATATATATGAAAGTTCAGTTAAAAGCAAAAAAGGCAAGCT
1 CGCTCAACGGGCTAGTAAACGAATCATATATATGAAAGTTCAGTTAAAAGCAAAAAAGGCAAGCT
53884227 TAGGTGAGTTATAAGAGTTAAGAATTTATTAAATTAACAATTGATATTCAACGATGTAGCAAGAG
66 TAGGTGAGTTATAAGAGTTAAGAATTTATTAAATTAACAATTGATATTCAACGATGTAGCAAGAG
53884292 AAGAGTAAGTTATGCACACAAGTATACTAAGTAAACAAACAAGAGAACTAGAATGAGATTAACTA
131 AAGAGTAAGTTATGCACACAAGTATACTAAGTAAACAAACAAGAGAACTAGAATGAGATTAACTA
53884357 AAGAGTAAAGTAGAGATATAGACACTTGAGTTTAATTATTTGTGTTTAATGTTGTTATTTATTTG
196 AAGAGTAAAGTAGAGATATAGACACTTGAGTTTAATTATTTGTGTTTAATGTTGTTATTTATTTG
53884422 CTAGTAAACTTACTAAGCGTTATGTTTACTTCTTTTATTTCTCTTTCTCTTATAGTATTGCAAAG
261 CTAGTAAACTTACTAAGCGTTATGTTTACTTCTTTTATTTCTCTTTCTCTTATAGTATTGCAAAG
53884487 CTACTTCAATGATCCTAAAGAAGTCGAAGATCGTCCGTACTATCAACCACAACTGCTTGGTATTT
326 CTACTTCAATGATCCTAAAGAAGTCGAAGATCGTCCGTACTATCAACCACAACTGCTTGGTATTT
53884552 TATGATGAAACACGTTTGAGTTATGGCATGTATAGGGATTTAGTTATTTTGCATGTTTGCAATTA
391 TATGATGAAACACGTTTGAGTTATGGCATGTATAGGGATTTAGTTATTTTGCATGTTTGCAATTA
53884617 TGATTTTGCTAAAGAATGATGTGTAAGTATTTGATGGTGAATGGTTATTAAAATGGTTAAGTATG
456 TGATTTTGCTAAAGAATGATGTGTAAGTATTTGATGGTGAATGGTTATTAAAATGGTTAAGTATG
53884682 AAGGTGTTTGTTGTTATAAGAGTCTAG
521 AAGGTGTTTGTTGTTATAAGAGTCTAG
53884709 CGCTCAACGGGCTAGTAAACGAATCATATATATGAAAGTTCAGTTAAAAGCAAAAAAGGCAAGCT
1 CGCTCAACGGGCTAGTAAACGAATCATATATATGAAAGTTCAGTTAAAAGCAAAAAAGGCAAGCT
53884774 TAGGTGAGTTATAAGAGTTAAGAATTTATTAAATTAACAATTGATATTCAACGATGTAGCAAGAG
66 TAGGTGAGTTATAAGAGTTAAGAATTTATTAAATTAACAATTGATATTCAACGATGTAGCAAGAG
53884839 AAGAGTAAGTTATGCACACAAGTATACTAAGTAAACAAACAAGAGAACTAGAATGAGATTAACTA
131 AAGAGTAAGTTATGCACACAAGTATACTAAGTAAACAAACAAGAGAACTAGAATGAGATTAACTA
53884904 AAGAGTAAAGTAGAGATATAGACACTTGAGTTTAATTATTTGTGTTTAATGTTGTTATTTATTTG
196 AAGAGTAAAGTAGAGATATAGACACTTGAGTTTAATTATTTGTGTTTAATGTTGTTATTTATTTG
53884969 CTAGTAAACTTACTAAGCGTTATGTTTACTTCTTTTATTTCTCTTTCTCTTATAGTATTGCAAAG
261 CTAGTAAACTTACTAAGCGTTATGTTTACTTCTTTTATTTCTCTTTCTCTTATAGTATTGCAAAG
53885034 CTACTTCAATGATCCTAAAGAAGTCGAAGATCGTCCGTACTATCAACCACAACTGCTTGGTATTT
326 CTACTTCAATGATCCTAAAGAAGTCGAAGATCGTCCGTACTATCAACCACAACTGCTTGGTATTT
53885099 TATGATGAAACACGTTTGAGTTATGGCATGTATAGGGATTTAGTTATTTTGCATGTTTGCAATTA
391 TATGATGAAACACGTTTGAGTTATGGCATGTATAGGGATTTAGTTATTTTGCATGTTTGCAATTA
53885164 TGATTTTGCTAAAGAATGATGTGTAAGTATTTGATGGTGAATGGTTATTAAAATGGTTAAGTATG
456 TGATTTTGCTAAAGAATGATGTGTAAGTATTTGATGGTGAATGGTTATTAAAATGGTTAAGTATG
53885229 AAGGTGTTTGTTGTTATAAGAGTCTAG
521 AAGGTGTTTGTTGTTATAAGAGTCTAG
53885256 GTGATAAGTT
Statistics
Matches: 547, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
547 547 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (547 bp):
CGCTCAACGGGCTAGTAAACGAATCATATATATGAAAGTTCAGTTAAAAGCAAAAAAGGCAAGCT
TAGGTGAGTTATAAGAGTTAAGAATTTATTAAATTAACAATTGATATTCAACGATGTAGCAAGAG
AAGAGTAAGTTATGCACACAAGTATACTAAGTAAACAAACAAGAGAACTAGAATGAGATTAACTA
AAGAGTAAAGTAGAGATATAGACACTTGAGTTTAATTATTTGTGTTTAATGTTGTTATTTATTTG
CTAGTAAACTTACTAAGCGTTATGTTTACTTCTTTTATTTCTCTTTCTCTTATAGTATTGCAAAG
CTACTTCAATGATCCTAAAGAAGTCGAAGATCGTCCGTACTATCAACCACAACTGCTTGGTATTT
TATGATGAAACACGTTTGAGTTATGGCATGTATAGGGATTTAGTTATTTTGCATGTTTGCAATTA
TGATTTTGCTAAAGAATGATGTGTAAGTATTTGATGGTGAATGGTTATTAAAATGGTTAAGTATG
AAGGTGTTTGTTGTTATAAGAGTCTAG
Found at i:53887121 original size:14 final size:14
Alignment explanation
Indices: 53887102--53887185 Score: 54
Period size: 13 Copynumber: 6.1 Consensus size: 14
53887092 ATAAATATTT
53887102 TTATATTAAAAATA
1 TTATATTAAAAATA
**
53887116 TTATA-TAGAACTTAA
1 TTATATTA-AAAAT-A
53887131 TT-T-TTAAAAATA
1 TTATATTAAAAATA
*
53887143 TTATA-TAAAACTTA
1 TTATATTAAAA-ATA
53887157 TTGA-ATTAAAAATA
1 TT-ATATTAAAAATA
*
53887171 TT-TATTGAAAATA
1 TTATATTAAAAATA
53887184 TT
1 TT
53887186 TTAAAATATA
Statistics
Matches: 54, Mismatches: 7, Indels: 19
0.68 0.09 0.24
Matches are distributed among these distances:
12 3 0.06
13 22 0.41
14 20 0.37
15 9 0.17
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (14 bp):
TTATATTAAAAATA
Found at i:53887167 original size:27 final size:27
Alignment explanation
Indices: 53887105--53887172 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
53887095 AATATTTTTA
*
53887105 TATTAAAAATATTATATAGAACTTAAT
1 TATTAAAAATATTATATAAAACTTAAT
*
53887132 TTTTAAAAATATTATATAAAACTT-AT
1 TATTAAAAATATTATATAAAACTTAAT
53887158 TGAATTAAAAATATT
1 T--ATTAAAAATATT
53887173 TATTGAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.08
27 22 0.61
28 11 0.31
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (27 bp):
TATTAAAAATATTATATAAAACTTAAT
Found at i:53891781 original size:14 final size:14
Alignment explanation
Indices: 53891762--53891845 Score: 54
Period size: 13 Copynumber: 6.1 Consensus size: 14
53891752 ATAAATATTT
53891762 TTATATTAAAAATA
1 TTATATTAAAAATA
**
53891776 TTATA-TAGAACTTAA
1 TTATATTA-AAAAT-A
53891791 TT-T-TTAAAAATA
1 TTATATTAAAAATA
*
53891803 TTATA-TAAAACTTA
1 TTATATTAAAA-ATA
53891817 TTGA-ATTAAAAATA
1 TT-ATATTAAAAATA
*
53891831 TT-TATTGAAAATA
1 TTATATTAAAAATA
53891844 TT
1 TT
53891846 TTAAAATATA
Statistics
Matches: 54, Mismatches: 7, Indels: 19
0.68 0.09 0.24
Matches are distributed among these distances:
12 3 0.06
13 22 0.41
14 20 0.37
15 9 0.17
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (14 bp):
TTATATTAAAAATA
Found at i:53891827 original size:27 final size:27
Alignment explanation
Indices: 53891765--53891832 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
53891755 AATATTTTTA
*
53891765 TATTAAAAATATTATATAGAACTTAAT
1 TATTAAAAATATTATATAAAACTTAAT
*
53891792 TTTTAAAAATATTATATAAAACTT-AT
1 TATTAAAAATATTATATAAAACTTAAT
53891818 TGAATTAAAAATATT
1 T--ATTAAAAATATT
53891833 TATTGAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.08
27 22 0.61
28 11 0.31
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (27 bp):
TATTAAAAATATTATATAAAACTTAAT
Found at i:53894431 original size:20 final size:21
Alignment explanation
Indices: 53894406--53894455 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
53894396 TTTAAAAATA
53894406 TTTTAAAATAATTTTTTT-AT
1 TTTTAAAATAATTTTTTTAAT
*
53894426 TTTTAAAATACTTTTTTTAAT
1 TTTTAAAATAATTTTTTTAAT
53894447 TTTCTAAAA
1 TTT-TAAAA
53894456 AAAAATTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 17 0.63
21 5 0.19
22 5 0.19
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTAAAATAATTTTTTTAAT
Found at i:53894443 original size:21 final size:20
Alignment explanation
Indices: 53894406--53894455 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
53894396 TTTAAAAATA
*
53894406 TTTTAAAATAATTTTTTTAT
1 TTTTAAAATAATTTTTTAAT
*
53894426 TTTTAAAATACTTTTTTTAAT
1 TTTTAAAATA-ATTTTTTAAT
53894447 TTTCTAAAA
1 TTT-TAAAA
53894456 AAAAATTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 10 0.38
21 11 0.42
22 5 0.19
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTAAAATAATTTTTTAAT
Found at i:53897101 original size:18 final size:18
Alignment explanation
Indices: 53897067--53897112 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
53897057 ATTGTTTAGC
*
53897067 AATA-TTTTTATCTTAAA
1 AATACTTTTTATCCTAAA
*
53897084 AATACTTTTTGTCCTAAA
1 AATACTTTTTATCCTAAA
*
53897102 AAAACTTTTTA
1 AATACTTTTTA
53897113 GAAGTAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (18 bp):
AATACTTTTTATCCTAAA
Found at i:53901463 original size:29 final size:29
Alignment explanation
Indices: 53901426--53901483 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
53901416 ATAATTTCTC
*
53901426 AATAAAATT-TTAATTATTTTTAAAATATT
1 AATAAAATTGTTAATGA-TTTTAAAATATT
* *
53901455 AATACAATTGTTAATGATTTTAATATATT
1 AATAAAATTGTTAATGATTTTAAAATATT
53901484 TTTTAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (29 bp):
AATAAAATTGTTAATGATTTTAAAATATT
Found at i:53903085 original size:36 final size:36
Alignment explanation
Indices: 53903045--53903117 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
53903035 AATTCCATGT
53903045 ATATACTATCAATCAATATGAAAACATTATATAATC
1 ATATACTATCAATCAATATGAAAACATTATATAATC
53903081 ATATACTATCAATCAATATGAAAACATTATATAATC
1 ATATACTATCAATCAATATGAAAACATTATATAATC
53903117 A
1 A
53903118 ATCTCATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.33
Consensus pattern (36 bp):
ATATACTATCAATCAATATGAAAACATTATATAATC
Found at i:53905869 original size:15 final size:15
Alignment explanation
Indices: 53905845--53905876 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53905835 AATAAATATT
*
53905845 AAAAATTTATTTTAA
1 AAAAAATTATTTTAA
53905860 AAAAAATTATTTTAA
1 AAAAAATTATTTTAA
53905875 AA
1 AA
53905877 GTATTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAAATTATTTTAA
Found at i:53905870 original size:26 final size:25
Alignment explanation
Indices: 53905829--53905887 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
53905819 CATGGCCCAT
* *
53905829 TTTTAAAATAAATA-TTAAAAATTTA
1 TTTTAAAAAAAATATTTAAAAA-GTA
*
53905854 TTTTAAAAAAAATTATTTTAAAAGTA
1 TTTTAAAAAAAA-TATTTAAAAAGTA
53905880 TTTTAAAA
1 TTTTAAAA
53905888 TTAAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 11 0.38
26 12 0.41
27 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTTAAAAAAAATATTTAAAAAGTA
Found at i:53908379 original size:36 final size:36
Alignment explanation
Indices: 53908320--53908389 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
53908310 CTGTTAACTA
* *
53908320 CACTGCTTCTTTGGTTACCTATGGTGAACCCACTTT
1 CACTGCTTCTATGGTAACCTATGGTGAACCCACTTT
* *
53908356 CACTGCTTCTATGGTAACTTATGGTGAATCCACT
1 CACTGCTTCTATGGTAACCTATGGTGAACCCACT
53908390 GCATCTATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (36 bp):
CACTGCTTCTATGGTAACCTATGGTGAACCCACTTT
Found at i:53917736 original size:19 final size:19
Alignment explanation
Indices: 53917709--53917785 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 19
53917699 AAGAAAAATT
53917709 AATA-AAAATTATAAAAAA
1 AATATAAAATTATAAAAAA
* * *
53917727 AATATTAAATTGT-AATAA
1 AATATAAAATTATAAAAAA
*
53917745 AATATAAAATT-TATAAAAT
1 AATATAAAATTATA-AAAAA
** *
53917764 CGTAAAAAATTATAAAAAA
1 AATATAAAATTATAAAAAA
53917783 AAT
1 AAT
53917786 TGTAAAATTT
Statistics
Matches: 43, Mismatches: 12, Indels: 7
0.69 0.19 0.11
Matches are distributed among these distances:
17 1 0.02
18 18 0.42
19 22 0.51
20 2 0.05
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (19 bp):
AATATAAAATTATAAAAAA
Found at i:53917762 original size:16 final size:18
Alignment explanation
Indices: 53917725--53917763 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
53917715 AATTATAAAA
*
53917725 AAAATATTAAATTGTAAT
1 AAAATATAAAATTGTAAT
53917743 AAAATATAAAATT-T-AT
1 AAAATATAAAATTGTAAT
53917759 AAAAT
1 AAAAT
53917764 CGTAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AAAATATAAAATTGTAAT
Found at i:53917790 original size:22 final size:22
Alignment explanation
Indices: 53917759--53917802 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
53917749 TAAAATTTAT
53917759 AAAATCGTAAAAAATTATAAAA
1 AAAATCGTAAAAAATTATAAAA
* **
53917781 AAAATTGTAAAATTTTATAAAA
1 AAAATCGTAAAAAATTATAAAA
53917803 GTTATAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (22 bp):
AAAATCGTAAAAAATTATAAAA
Found at i:53918089 original size:17 final size:19
Alignment explanation
Indices: 53918058--53918093 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
53918048 CTAAAGAGTC
53918058 TTTTTTATGTATTTTATAA
1 TTTTTTATGTATTTTATAA
53918077 TTTTTTAT-T-TTTTATAA
1 TTTTTTATGTATTTTATAA
53918094 AAATTTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTTTTATGTATTTTATAA
Found at i:53918164 original size:28 final size:27
Alignment explanation
Indices: 53918068--53918172 Score: 88
Period size: 28 Copynumber: 3.8 Consensus size: 27
53918058 TTTTTTATGT
* * * *
53918068 ATTTTATAATTTTTTATTTTTTATAAAA
1 ATTTAATAATTTTATA-ATTTTATTAAA
* * *
53918096 ATTT-ACAATTTT-TATATTTTCTTACTA
1 ATTTAATAATTTTATA-ATTTTATTA-AA
53918123 ATTTAATAATTTTAATAATTTTATTAAA
1 ATTTAATAATTTT-ATAATTTTATTAAA
53918151 ATTTAATAATTTTATAACTTTT
1 ATTTAATAATTTTATAA-TTTT
53918173 TTTATTTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
26 9 0.14
27 16 0.25
28 29 0.45
29 8 0.12
30 2 0.03
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTTAATAATTTTATAATTTTATTAAA
Found at i:53930643 original size:24 final size:24
Alignment explanation
Indices: 53930598--53930650 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
53930588 TAATCAAAGT
* *
53930598 TAAATATATTATGCTAAAAAATGC
1 TAAATATATTATACTAAAAAATAC
* *
53930622 TAAATATATTATACTCATAAATAC
1 TAAATATATTATACTAAAAAATAC
53930646 TAAAT
1 TAAAT
53930651 CTTCAATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (24 bp):
TAAATATATTATACTAAAAAATAC
Found at i:53934731 original size:20 final size:20
Alignment explanation
Indices: 53934685--53934735 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
53934675 TTGATTCCGA
53934685 TTTTTTTCTGTTCTTGTTAT
1 TTTTTTTCTGTTCTTGTTAT
* * *
53934705 TTATTTTCTTTTCTT-TTCT
1 TTTTTTTCTGTTCTTGTTAT
*
53934724 TTTTTTTTTGTT
1 TTTTTTTCTGTT
53934736 GTTTGTTTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.04, C:0.10, G:0.06, T:0.80
Consensus pattern (20 bp):
TTTTTTTCTGTTCTTGTTAT
Found at i:53946839 original size:3 final size:3
Alignment explanation
Indices: 53946827--53946856 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
53946817 TTCCTAAACC
53946827 ATA ATAA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT
53946857 TTGGGGACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53947523 original size:3 final size:3
Alignment explanation
Indices: 53947511--53947540 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
53947501 TTCCTAAACC
53947511 ATA ATAA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT
53947541 TTGGGGACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53947918 original size:684 final size:684
Alignment explanation
Indices: 53946611--53947978 Score: 2736
Period size: 684 Copynumber: 2.0 Consensus size: 684
53946601 GTGACGTGTT
53946611 GGTAAAATTCCGCTAACCGGAATTAATTTTTAAAAACATGTTGGGCTGAGTAACCGGGGTTGGGT
1 GGTAAAATTCCGCTAACCGGAATTAATTTTTAAAAACATGTTGGGCTGAGTAACCGGGGTTGGGT
53946676 GCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTTGATGTGTTCTTAAAAAGAATTATAATAAAT
66 GCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTTGATGTGTTCTTAAAAAGAATTATAATAAAT
53946741 TAGGAGTCTGCTGGGCTGAGTAATCAGGGTGGGGTGCTTAGCTGCCATCTCTCTTCGCGTCAAAA
131 TAGGAGTCTGCTGGGCTGAGTAATCAGGGTGGGGTGCTTAGCTGCCATCTCTCTTCGCGTCAAAA
53946806 GGTTCAGTATATTCCTAAACCATAATAAATAATAATAATAATAATAATAATTTGGGGACTAAAGG
196 GGTTCAGTATATTCCTAAACCATAATAAATAATAATAATAATAATAATAATTTGGGGACTAAAGG
53946871 AGGAAACAAATAGGGTGTCTTGGTAAGTTTGGTAATTTACCTAATTTTCATTAAATAATTCAAGT
261 AGGAAACAAATAGGGTGTCTTGGTAAGTTTGGTAATTTACCTAATTTTCATTAAATAATTCAAGT
53946936 CGATTCTAATTTTTGCGTGTATTAATTGGAAAATTTTTTCTGTTTTACCTAAAGTAAGCTTAGGG
326 CGATTCTAATTTTTGCGTGTATTAATTGGAAAATTTTTTCTGTTTTACCTAAAGTAAGCTTAGGG
53947001 TTCTCTTTATTTTTTATATGCATTTTTGACTGATTTTTATAAAACTTTGGAGTTGTATTTCTTTT
391 TTCTCTTTATTTTTTATATGCATTTTTGACTGATTTTTATAAAACTTTGGAGTTGTATTTCTTTT
53947066 ATGGCAAAATCTAACTTTCACAGTAGATAGGAACCATACTTGAGGGTAAGCATGGGCTAAGTATG
456 ATGGCAAAATCTAACTTTCACAGTAGATAGGAACCATACTTGAGGGTAAGCATGGGCTAAGTATG
53947131 GGGGATTTGATAACACTCTAGAATAACGTATTTTTATGTATTAATTATGTATTTATTCTGAGTAT
521 GGGGATTTGATAACACTCTAGAATAACGTATTTTTATGTATTAATTATGTATTTATTCTGAGTAT
53947196 GATCTTGCTAATTTGAGCTATTTATTATCTTTTATCTCATAGATACTAAATTTGAGGCAAAAGTG
586 GATCTTGCTAATTTGAGCTATTTATTATCTTTTATCTCATAGATACTAAATTTGAGGCAAAAGTG
53947261 AAATTAAGGGCCAAAAGCGTGAATTTAGAGATAA
651 AAATTAAGGGCCAAAAGCGTGAATTTAGAGATAA
53947295 GGTAAAATTCCGCTAACCGGAATTAATTTTTAAAAACATGTTGGGCTGAGTAACCGGGGTTGGGT
1 GGTAAAATTCCGCTAACCGGAATTAATTTTTAAAAACATGTTGGGCTGAGTAACCGGGGTTGGGT
53947360 GCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTTGATGTGTTCTTAAAAAGAATTATAATAAAT
66 GCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTTGATGTGTTCTTAAAAAGAATTATAATAAAT
53947425 TAGGAGTCTGCTGGGCTGAGTAATCAGGGTGGGGTGCTTAGCTGCCATCTCTCTTCGCGTCAAAA
131 TAGGAGTCTGCTGGGCTGAGTAATCAGGGTGGGGTGCTTAGCTGCCATCTCTCTTCGCGTCAAAA
53947490 GGTTCAGTATATTCCTAAACCATAATAAATAATAATAATAATAATAATAATTTGGGGACTAAAGG
196 GGTTCAGTATATTCCTAAACCATAATAAATAATAATAATAATAATAATAATTTGGGGACTAAAGG
53947555 AGGAAACAAATAGGGTGTCTTGGTAAGTTTGGTAATTTACCTAATTTTCATTAAATAATTCAAGT
261 AGGAAACAAATAGGGTGTCTTGGTAAGTTTGGTAATTTACCTAATTTTCATTAAATAATTCAAGT
53947620 CGATTCTAATTTTTGCGTGTATTAATTGGAAAATTTTTTCTGTTTTACCTAAAGTAAGCTTAGGG
326 CGATTCTAATTTTTGCGTGTATTAATTGGAAAATTTTTTCTGTTTTACCTAAAGTAAGCTTAGGG
53947685 TTCTCTTTATTTTTTATATGCATTTTTGACTGATTTTTATAAAACTTTGGAGTTGTATTTCTTTT
391 TTCTCTTTATTTTTTATATGCATTTTTGACTGATTTTTATAAAACTTTGGAGTTGTATTTCTTTT
53947750 ATGGCAAAATCTAACTTTCACAGTAGATAGGAACCATACTTGAGGGTAAGCATGGGCTAAGTATG
456 ATGGCAAAATCTAACTTTCACAGTAGATAGGAACCATACTTGAGGGTAAGCATGGGCTAAGTATG
53947815 GGGGATTTGATAACACTCTAGAATAACGTATTTTTATGTATTAATTATGTATTTATTCTGAGTAT
521 GGGGATTTGATAACACTCTAGAATAACGTATTTTTATGTATTAATTATGTATTTATTCTGAGTAT
53947880 GATCTTGCTAATTTGAGCTATTTATTATCTTTTATCTCATAGATACTAAATTTGAGGCAAAAGTG
586 GATCTTGCTAATTTGAGCTATTTATTATCTTTTATCTCATAGATACTAAATTTGAGGCAAAAGTG
53947945 AAATTAAGGGCCAAAAGCGTGAATTTAGAGATAA
651 AAATTAAGGGCCAAAAGCGTGAATTTAGAGATAA
53947979 AATGGGCCAA
Statistics
Matches: 684, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
684 684 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (684 bp):
GGTAAAATTCCGCTAACCGGAATTAATTTTTAAAAACATGTTGGGCTGAGTAACCGGGGTTGGGT
GCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTTGATGTGTTCTTAAAAAGAATTATAATAAAT
TAGGAGTCTGCTGGGCTGAGTAATCAGGGTGGGGTGCTTAGCTGCCATCTCTCTTCGCGTCAAAA
GGTTCAGTATATTCCTAAACCATAATAAATAATAATAATAATAATAATAATTTGGGGACTAAAGG
AGGAAACAAATAGGGTGTCTTGGTAAGTTTGGTAATTTACCTAATTTTCATTAAATAATTCAAGT
CGATTCTAATTTTTGCGTGTATTAATTGGAAAATTTTTTCTGTTTTACCTAAAGTAAGCTTAGGG
TTCTCTTTATTTTTTATATGCATTTTTGACTGATTTTTATAAAACTTTGGAGTTGTATTTCTTTT
ATGGCAAAATCTAACTTTCACAGTAGATAGGAACCATACTTGAGGGTAAGCATGGGCTAAGTATG
GGGGATTTGATAACACTCTAGAATAACGTATTTTTATGTATTAATTATGTATTTATTCTGAGTAT
GATCTTGCTAATTTGAGCTATTTATTATCTTTTATCTCATAGATACTAAATTTGAGGCAAAAGTG
AAATTAAGGGCCAAAAGCGTGAATTTAGAGATAA
Found at i:53949470 original size:21 final size:21
Alignment explanation
Indices: 53949446--53949486 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53949436 AAGCCCGAAG
*
53949446 GCTAAACAGAAGCACATAAGT
1 GCTAAACAGAAACACATAAGT
*
53949467 GCTAAACAGAAACCCATAAG
1 GCTAAACAGAAACACATAAG
53949487 GGTTGAACGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (21 bp):
GCTAAACAGAAACACATAAGT
Found at i:53949500 original size:21 final size:21
Alignment explanation
Indices: 53949476--53949532 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
53949466 TGCTAAACAG
53949476 AAACCCATAAGGGTTGAACGA
1 AAACCCATAAGGGTTGAACGA
* * *
53949497 AAACTCATAAGAGCTGAACGA
1 AAACCCATAAGGGTTGAACGA
*
53949518 AAACCCATAACGGTT
1 AAACCCATAAGGGTT
53949533 AAACAGAAGC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (21 bp):
AAACCCATAAGGGTTGAACGA
Found at i:53949595 original size:42 final size:42
Alignment explanation
Indices: 53949448--53949586 Score: 129
Period size: 42 Copynumber: 3.3 Consensus size: 42
53949438 GCCCGAAGGC
* * * * * *
53949448 TAAACAGAAGCACATAAGTGCTAAACAGAAACCCATAAGGGT
1 TAAACAGAAGCTCAAAAGAGCTGAACGGAAACCCATAACGGT
* * * *
53949490 TGAAC-GAAAACTCATAAGAGCTGAACGAAAACCCATAACGGT
1 TAAACAG-AAGCTCAAAAGAGCTGAACGGAAACCCATAACGGT
* *
53949532 TAAACAGAAGCTCAAAAGAGCTGAACGGAAACTCAT-ATGAGT
1 TAAACAGAAGCTCAAAAGAGCTGAACGGAAACCCATAACG-GT
*
53949574 TAAACTGAAGCTC
1 TAAACAGAAGCTC
53949587 GTGAGAGCTA
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 3 0.04
42 75 0.95
43 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.16
Consensus pattern (42 bp):
TAAACAGAAGCTCAAAAGAGCTGAACGGAAACCCATAACGGT
Found at i:53951612 original size:19 final size:19
Alignment explanation
Indices: 53951590--53951648 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
53951580 AAAGAAAGAT
53951590 AAATTAATAAAAATTATAA
1 AAATTAATAAAAATTATAA
**
53951609 AAATCGTAA-AAAAATTGCAA
1 AAAT--TAATAAAAATTATAA
* *
53951629 AATTTTATAAAAATTATAA
1 AAATTAATAAAAATTATAA
53951648 A
1 A
53951649 TTATATAGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
18 2 0.06
19 14 0.45
20 12 0.39
21 3 0.10
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (19 bp):
AAATTAATAAAAATTATAA
Found at i:53951700 original size:21 final size:20
Alignment explanation
Indices: 53951666--53951719 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
53951656 GAAATACAGA
*
53951666 AAAAAATTAT--AAAATTGT
1 AAAAAATTATAAAAAAATGT
53951684 AAGAAAATTATAAAAAAATGT
1 AA-AAAATTATAAAAAAATGT
53951705 AAAGAAA-TATAAAAA
1 AAA-AAATTATAAAAA
53951720 TAGTAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 2 0.06
19 8 0.26
20 9 0.29
21 12 0.39
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (20 bp):
AAAAAATTATAAAAAAATGT
Found at i:53951980 original size:19 final size:18
Alignment explanation
Indices: 53951958--53952035 Score: 52
Period size: 19 Copynumber: 4.1 Consensus size: 18
53951948 TTATAAAAAA
*
53951958 TTACAATTTTTATATTTT
1 TTACAATTTTTATAATTT
53951976 CTTACTAA-TTTTATAATTT
1 -TTAC-AATTTTTATAATTT
**
53951995 TTA-ATATTTTTATTAAAAT
1 TTACA-ATTTTTA-TAATTT
*
53952014 TTAGTAATTTTTATAACTTT
1 TTA-CAATTTTTATAA-TTT
53952034 TT
1 TT
53952036 TTTATTTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
16 1 0.02
17 1 0.02
18 8 0.17
19 24 0.51
20 12 0.26
21 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (18 bp):
TTACAATTTTTATAATTT
Found at i:53952014 original size:29 final size:29
Alignment explanation
Indices: 53951925--53952026 Score: 84
Period size: 28 Copynumber: 3.5 Consensus size: 29
53951915 TTTTTGATGT
** *
53951925 ATTTTATAATTTTTTTTATTTTTTTATAAA
1 ATTTTATAATTTTTAATATTTTTAT-TAAA
** * * *
53951955 AAATTACAATTTTT-ATA-TTTTCTTACTA
1 ATTTTATAATTTTTAATATTTTTATTA-AA
53951983 ATTTTATAATTTTTAATATTTTTATTAAA
1 ATTTTATAATTTTTAATATTTTTATTAAA
53952012 A-TTTAGTAATTTTTA
1 ATTTTA-TAATTTTTA
53952027 TAACTTTTTT
Statistics
Matches: 57, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
27 2 0.04
28 21 0.37
29 16 0.28
30 18 0.32
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (29 bp):
ATTTTATAATTTTTAATATTTTTATTAAA
Found at i:53955395 original size:18 final size:18
Alignment explanation
Indices: 53955374--53955408 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53955364 GGAATTTAAT
53955374 CTTTTTGTTAAACTTGTA
1 CTTTTTGTTAAACTTGTA
* *
53955392 CTTTTTTTTTAACTTGT
1 CTTTTTGTTAAACTTGT
53955409 TGCTGTGACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (18 bp):
CTTTTTGTTAAACTTGTA
Found at i:53962912 original size:17 final size:18
Alignment explanation
Indices: 53962886--53962922 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
53962876 AATTTGGGGC
*
53962886 TTAAAGTTTT-ATAAATA
1 TTAAAATTTTCATAAATA
53962903 TTAAAATTTTCATAAATA
1 TTAAAATTTTCATAAATA
53962921 TT
1 TT
53962923 TTACTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
TTAAAATTTTCATAAATA
Found at i:53963408 original size:31 final size:33
Alignment explanation
Indices: 53963343--53963410 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 33
53963333 ATCTGAAAAC
*
53963343 TATACATAAACTTTGAATTCGTGTGTAATATTA
1 TATACATAAACTTTGAATTCGTGCGTAATATTA
* * *
53963376 TATACATAAATTTTG-ATT-TTGCGTAATTTTA
1 TATACATAAACTTTGAATTCGTGCGTAATATTA
53963407 TATA
1 TATA
53963411 TTATATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 14 0.45
32 3 0.10
33 14 0.45
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (33 bp):
TATACATAAACTTTGAATTCGTGCGTAATATTA
Found at i:53965597 original size:19 final size:19
Alignment explanation
Indices: 53965558--53965616 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
53965548 TGTAAAAAAA
53965558 TATAAA-ATTTTGAATTCTTT
1 TATAAATATTTTGAA-T-TTT
53965578 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
*
53965597 T-GAAATATTTTGTAATTTT
1 TATAAATATTTTG-AATTTT
53965616 T
1 T
53965617 GTTGAGAGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 10 0.28
19 11 0.31
20 7 0.19
21 8 0.22
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.58
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:53965602 original size:18 final size:19
Alignment explanation
Indices: 53965581--53965617 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
53965571 ATTCTTTTAT
53965581 AAATATTTTG-AATTTTTG
1 AAATATTTTGTAATTTTTG
53965599 AAATATTTTGTAATTTTTG
1 AAATATTTTGTAATTTTTG
53965618 TTGAGAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (19 bp):
AAATATTTTGTAATTTTTG
Found at i:53971213 original size:4 final size:4
Alignment explanation
Indices: 53971204--53971260 Score: 96
Period size: 4 Copynumber: 14.2 Consensus size: 4
53971194 AACAATGTTG
*
53971204 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGCA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
53971252 TGTA CGTA T
1 TGTA TGTA T
53971261 TTTCGAGACG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.47
Consensus pattern (4 bp):
TGTA
Found at i:53971666 original size:24 final size:24
Alignment explanation
Indices: 53971616--53971667 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
53971606 TAACTTATAT
* ** *
53971616 AAAAAGTATTATTAAATCTATTCA
1 AAAAAATATTATTAAATAAATTAA
53971640 AAAAAATATTATTAAATAAATTAA
1 AAAAAATATTATTAAATAAATTAA
53971664 AAAA
1 AAAA
53971668 TAAATTAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (24 bp):
AAAAAATATTATTAAATAAATTAA
Found at i:53971674 original size:24 final size:24
Alignment explanation
Indices: 53971623--53971674 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
53971613 TATAAAAAGT
** *
53971623 ATTATTAAATCTATTCAAAAAAAT
1 ATTATTAAATAAATTCAAAAAAAA
53971647 ATTATTAAATAAATT-AAAAAATAA
1 ATTATTAAATAAATTCAAAAAA-AA
53971671 ATTA
1 ATTA
53971675 AGAGTATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
ATTATTAAATAAATTCAAAAAAAA
Found at i:53975177 original size:17 final size:17
Alignment explanation
Indices: 53975155--53975188 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
53975145 CCAATCGCTC
53975155 ATCTAAACCCCACCCTT
1 ATCTAAACCCCACCCTT
53975172 ATCTAAACCCCACCCTT
1 ATCTAAACCCCACCCTT
53975189 TGTCCTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.47, G:0.00, T:0.24
Consensus pattern (17 bp):
ATCTAAACCCCACCCTT
Found at i:53976537 original size:40 final size:40
Alignment explanation
Indices: 53976493--53976576 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
53976483 AAACGCCGGT
* * *
53976493 AAAAATCGGGCATTAGTGGCG-TTTGTGAGAAAACGCCACA
1 AAAAATAGGCCATTAGCGGCGCTTT-TGAGAAAACGCCACA
* **
53976533 AAAAATAGGCCTTTAGCGGCGCTTTTGCTAAAACGCCACA
1 AAAAATAGGCCATTAGCGGCGCTTTTGAGAAAACGCCACA
53976573 AAAA
1 AAAA
53976577 CTCCAAACTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
40 34 0.92
41 3 0.08
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (40 bp):
AAAAATAGGCCATTAGCGGCGCTTTTGAGAAAACGCCACA
Found at i:53976686 original size:40 final size:40
Alignment explanation
Indices: 53976639--53976774 Score: 132
Period size: 40 Copynumber: 3.3 Consensus size: 40
53976629 TTTAAACAAA
*
53976639 CGCCGCTAATGTTATGGTTTTTAGTGGCGTTTTTTCTGAA-
1 CGCCGCTAATGTTAAGGTTTTTAGTGGCGTTTTTT-TGAAG
* * * ** **
53976679 CGCCGCTAATTTTAGGGCTTTTAGCAGCGTTTTCGAT-AATG
1 CGCCGCTAATGTTAAGGTTTTTAGTGGCGTTTT-TTTGAA-G
*
53976720 CGCCGCTAAAGTTAAGGTTTTTAGTGGCGTTTTTTTGTAAAG
1 CGCCGCTAATGTTAAGGTTTTTAGTGGCGTTTTTTTG--AAG
53976762 CGCCGCTAATGTT
1 CGCCGCTAATGTT
53976775 GGAGTTTTAG
Statistics
Matches: 74, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
39 2 0.03
40 30 0.41
41 27 0.36
42 13 0.18
43 2 0.03
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (40 bp):
CGCCGCTAATGTTAAGGTTTTTAGTGGCGTTTTTTTGAAG
Found at i:53976728 original size:81 final size:81
Alignment explanation
Indices: 53976639--53976793 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 81
53976629 TTTAAACAAA
* * *
53976639 CGCCGCTAATGTTATGGTTTTTAGTGGCGTTTTTTCTG-AA-CGCCGCTAATTTTAGG-GCTTTT
1 CGCCGCTAAAGTTAAGGTTTTTAGTGGCGTTTTTT-TGAAAGCGCCGCTAATGTT-GGAG-TTTT
53976701 AGCAGCGTTTTCGATAATG
63 AGCAGCGTTTTCGATAATG
53976720 CGCCGCTAAAGTTAAGGTTTTTAGTGGCGTTTTTTTGTAAAGCGCCGCTAATGTTGGAGTTTTAG
1 CGCCGCTAAAGTTAAGGTTTTTAGTGGCGTTTTTTTG-AAAGCGCCGCTAATGTTGGAGTTTTAG
*
53976785 CGGCGTTTT
65 CAGCGTTTT
53976794 GATGGAAACG
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
80 2 0.03
81 33 0.50
82 18 0.27
83 13 0.20
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.40
Consensus pattern (81 bp):
CGCCGCTAAAGTTAAGGTTTTTAGTGGCGTTTTTTTGAAAGCGCCGCTAATGTTGGAGTTTTAGC
AGCGTTTTCGATAATG
Found at i:53977330 original size:43 final size:43
Alignment explanation
Indices: 53977279--53977365 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
53977269 AATTTTTAAC
*
53977279 TATTAATTATTGTTTAATCGATTTAAACTATATTTTATGATTA
1 TATTAATTATTGTTTAATCGATGTAAACTATATTTTATGATTA
*
53977322 TATTAATTATTGTTTAATCTATGTAAACTATATTTTATGATTA
1 TATTAATTATTGTTTAATCGATGTAAACTATATTTTATGATTA
53977365 T
1 T
53977366 TAAAGATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (43 bp):
TATTAATTATTGTTTAATCGATGTAAACTATATTTTATGATTA
Found at i:53977450 original size:14 final size:14
Alignment explanation
Indices: 53977415--53977456 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
53977405 TAAGGGGTAT
*
53977415 GGATTAGGGTTT-G
1 GGATTAAGGTTTAG
53977428 GGATTAAGGTTTAG
1 GGATTAAGGTTTAG
* *
53977442 GGGTTAAGGGTTAG
1 GGATTAAGGTTTAG
53977456 G
1 G
53977457 AATTTAGGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.33
Consensus pattern (14 bp):
GGATTAAGGTTTAG
Found at i:53977508 original size:15 final size:15
Alignment explanation
Indices: 53977478--53977542 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 15
53977468 TAGATGTTAA
*
53977478 GGGTTAGTGATTTAGG
1 GGGTTAG-GGTTTAGG
53977494 GGGTTAGGGTTTAGG
1 GGGTTAGGGTTTAGG
53977509 GGGATTTAAGGG-TTA-G
1 GGG--TT-AGGGTTTAGG
53977525 GGGTTAGGGATTTAGG
1 GGGTTAGGG-TTTAGG
53977541 GG
1 GG
53977543 TTAAGGTGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 4 0.10
14 2 0.05
15 13 0.31
16 14 0.33
17 5 0.12
18 4 0.10
ACGTcount: A:0.18, C:0.00, G:0.49, T:0.32
Consensus pattern (15 bp):
GGGTTAGGGTTTAGG
Found at i:53977509 original size:29 final size:28
Alignment explanation
Indices: 53977442--53977509 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
53977432 TAAGGTTTAG
53977442 GGGTTAAGGGTTAGGAATTTAGGGCTTA
1 GGGTTAAGGGTTAGGAATTTAGGGCTTA
* *
53977470 GATGTTAAGGGTTAGTG-ATTTAGGGGGTTA
1 G-GGTTAAGGGTTAG-GAATTTA-GGGCTTA
*
53977500 GGGTTTAGGG
1 GGGTTAAGGG
53977510 GGATTTAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 1 0.03
29 24 0.73
30 8 0.24
ACGTcount: A:0.22, C:0.01, G:0.43, T:0.34
Consensus pattern (28 bp):
GGGTTAAGGGTTAGGAATTTAGGGCTTA
Found at i:53977523 original size:24 final size:22
Alignment explanation
Indices: 53977473--53977545 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
53977463 GGGCTTAGAT
* * *
53977473 GTTAAGGGTTAGTGATTTAGGGG
1 GTTAGGGGTTAGGGATTTA-AGG
*
53977496 GTTAGGGTTTAGGGGGATTTAAGG
1 GTTAGGGGTTA--GGGATTTAAGG
*
53977520 GTTAGGGGTTAGGGATTTAGGG
1 GTTAGGGGTTAGGGATTTAAGG
53977542 GTTA
1 GTTA
53977546 AGGTGCCAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
22 14 0.33
23 9 0.21
24 12 0.29
25 7 0.17
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (22 bp):
GTTAGGGGTTAGGGATTTAAGG
Found at i:53977543 original size:15 final size:15
Alignment explanation
Indices: 53977449--53977545 Score: 69
Period size: 15 Copynumber: 6.4 Consensus size: 15
53977439 TAGGGGTTAA
*
53977449 GGGTTAGGAATTTAG
1 GGGTTAGGGATTTAG
* *
53977464 GGCTTA--GATGTTAA
1 GGGTTAGGGAT-TTAG
*
53977478 GGGTTAGTGATTTAGG
1 GGGTTAGGGATTTA-G
53977494 GGGTTAGGG-TTTAGG
1 GGGTTAGGGATTTA-G
53977509 GGGATTTAAGGG--TTAG
1 GGG--TT-AGGGATTTAG
53977525 GGGTTAGGGATTTAG
1 GGGTTAGGGATTTAG
53977540 GGGTTA
1 GGGTTA
53977546 AGGTGCCAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
13 6 0.09
14 10 0.15
15 27 0.40
16 15 0.22
17 5 0.07
18 4 0.06
ACGTcount: A:0.22, C:0.01, G:0.43, T:0.34
Consensus pattern (15 bp):
GGGTTAGGGATTTAG
Found at i:53979621 original size:26 final size:26
Alignment explanation
Indices: 53979592--53979649 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
53979582 CTCGTTGCAT
*
53979592 AATAATTCTCACTCTATAGCTTATCA
1 AATAATTCTCACTCTATAGCTTATAA
*
53979618 AATAATTCTTACTCTATAGCTTATAA
1 AATAATTCTCACTCTATAGCTTATAA
53979644 AATAAT
1 AATAAT
53979650 ATAAATCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (26 bp):
AATAATTCTCACTCTATAGCTTATAA
Found at i:53980137 original size:16 final size:16
Alignment explanation
Indices: 53980116--53980146 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
53980106 CCAATGCAAA
53980116 TAGTATTATTTAATAC
1 TAGTATTATTTAATAC
53980132 TAGTATTATTTAATA
1 TAGTATTATTTAATA
53980147 TGGTTCCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (16 bp):
TAGTATTATTTAATAC
Found at i:53980464 original size:29 final size:31
Alignment explanation
Indices: 53980423--53980559 Score: 124
Period size: 30 Copynumber: 4.6 Consensus size: 31
53980413 TTATTTTTTG
* **
53980423 CATTTTAACCCCTGTACTTT-TCAAAATTTA
1 CATTTTGACCCCTAAACTTTATCAAAATTTA
53980453 CATTTTGA-CCCTAAACTTT-TCTAAAATTTA
1 CATTTTGACCCCTAAACTTTATC-AAAATTTA
* *
53980483 CATTTTTACCCCAAAACTTTAT-AAAA-TTA
1 CATTTTGACCCCTAAACTTTATCAAAATTTA
* * * *
53980512 CATTTCGACCCTTATACTTTCTCAAAATTT-
1 CATTTTGACCCCTAAACTTTATCAAAATTTA
* *
53980542 CACTTTAACCCCTAAACT
1 CATTTTGACCCCTAAACT
53980560 CTCAAGAAAT
Statistics
Matches: 86, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
29 30 0.35
30 43 0.50
31 12 0.14
32 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (31 bp):
CATTTTGACCCCTAAACTTTATCAAAATTTA
Found at i:53980494 original size:60 final size:59
Alignment explanation
Indices: 53980423--53980559 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 59
53980413 TTATTTTTTG
** *
53980423 CATTTTAACCCCTGTACTTT-TCAAAATTTACATTTTGACCC-TAAACTTT-TCTAAAATTT
1 CATTTTAACCCCTAAACTTTAT-AAAA-TTACATTTCGACCCTTAAACTTTCTC-AAAATTT
* * *
53980482 ACATTTTTACCCCAAAACTTTATAAAATTACATTTCGACCCTTATACTTTCTCAAAATTT
1 -CATTTTAACCCCTAAACTTTATAAAATTACATTTCGACCCTTAAACTTTCTCAAAATTT
*
53980542 CACTTTAACCCCTAAACT
1 CATTTTAACCCCTAAACT
53980560 CTCAAGAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 28 0.43
60 34 0.52
61 3 0.05
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (59 bp):
CATTTTAACCCCTAAACTTTATAAAATTACATTTCGACCCTTAAACTTTCTCAAAATTT
Found at i:53980553 original size:59 final size:60
Alignment explanation
Indices: 53980445--53980559 Score: 146
Period size: 59 Copynumber: 1.9 Consensus size: 60
53980435 TGTACTTTTC
* * *
53980445 AAAATTTACATTTTGACCCTAAACTTTTCTAAAATTTACATTTTTACCCCAAAACTTTAT
1 AAAATTTACATTTCGACCCTAAACTTTTCTAAAATTTACACTTTAACCCCAAAACTTTAT
* *
53980505 AAAA-TTACATTTCGACCCTTATAC-TTTCTCAAAATTT-CACTTTAACCCCTAAACT
1 AAAATTTACATTTCGACCC-TAAACTTTTCT-AAAATTTACACTTTAACCCCAAAACT
53980560 CTCAAGAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
59 33 0.69
60 15 0.31
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (60 bp):
AAAATTTACATTTCGACCCTAAACTTTTCTAAAATTTACACTTTAACCCCAAAACTTTAT
Found at i:53980572 original size:60 final size:59
Alignment explanation
Indices: 53980445--53980574 Score: 140
Period size: 59 Copynumber: 2.2 Consensus size: 59
53980435 TGTACTTTTC
* * * *
53980445 AAAATTTACATTTTGACCCTAAACTTTTCTAAAATTTACATTTTTACCCCAAAACTTTAT
1 AAAA-TTACATTTCGACCCTAAACTTTTCTAAAATTTACACTTTAACCCCAAAACTTCAT
* *
53980505 AAAATTACATTTCGACCCTTATAC-TTTCTCAAAATTT-CACTTTAACCCCTAAACTCTCA-
1 AAAATTACATTTCGACCC-TAAACTTTTCT-AAAATTTACACTTTAACCCCAAAACT-TCAT
53980564 AGAAATTACAT
1 A-AAATTACAT
53980575 CTTGGCCCGT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
59 34 0.57
60 26 0.43
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (59 bp):
AAAATTACATTTCGACCCTAAACTTTTCTAAAATTTACACTTTAACCCCAAAACTTCAT
Found at i:53980864 original size:22 final size:22
Alignment explanation
Indices: 53980839--53980882 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
53980829 AGAACGAAAG
* *
53980839 AAAA-CAAAGAAAACAGCAGCAA
1 AAAATCAAACAAAAAAG-AGCAA
53980861 AAAATCAAACAAAAAAGAGCAA
1 AAAATCAAACAAAAAAGAGCAA
53980883 CGAAAGGGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.70, C:0.16, G:0.11, T:0.02
Consensus pattern (22 bp):
AAAATCAAACAAAAAAGAGCAA
Found at i:53981038 original size:14 final size:13
Alignment explanation
Indices: 53981020--53981051 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
53981010 AAAGAAGAAA
53981020 CAAAAACAGCAAC
1 CAAAAACAGCAAC
*
53981033 CAAAAATAGCAAC
1 CAAAAACAGCAAC
53981046 CAAAAA
1 CAAAAA
53981052 GGAAGAAGAG
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:0.66, C:0.25, G:0.06, T:0.03
Consensus pattern (13 bp):
CAAAAACAGCAAC
Found at i:53981188 original size:10 final size:10
Alignment explanation
Indices: 53981167--53981220 Score: 56
Period size: 10 Copynumber: 5.1 Consensus size: 10
53981157 AGCCCCGAAG
53981167 AGGAAGGAAAA
1 AGGAA-GAAAA
53981178 AGGAAGAAAA
1 AGGAAGAAAA
*
53981188 AAGAAGAAAA
1 AGGAAGAAAA
53981198 A-GAGAGAAGAA
1 AGGA-AGAA-AA
53981209 AGGAAGGAAAA
1 AGGAA-GAAAA
53981220 A
1 A
53981221 AAAAAAGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 2 0.05
10 19 0.50
11 12 0.32
12 5 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
AGGAAGAAAA
Found at i:53981205 original size:20 final size:22
Alignment explanation
Indices: 53981169--53981220 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
53981159 CCCCGAAGAG
53981169 GAAGGAAAAAGGAAGAA-AAAA
1 GAAGGAAAAAGGAAGAAGAAAA
*
53981190 GAA-GAAAAA-GAGAGAAGAAAG
1 GAAGGAAAAAGGA-AGAAGAAAA
53981211 GAAGGAAAAA
1 GAAGGAAAAA
53981221 AAAAAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 10 0.37
21 9 0.33
22 6 0.22
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (22 bp):
GAAGGAAAAAGGAAGAAGAAAA
Found at i:53981350 original size:17 final size:17
Alignment explanation
Indices: 53981313--53981378 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 17
53981303 AGCAGCCCCA
53981313 AAAAAAAACAAAAC-GCCC
1 AAAAAAAACAAAACAG--C
53981331 AAAAAAAACAAAACAGC
1 AAAAAAAACAAAACAGC
* *
53981348 AAAAAAAACCAGAATAGC
1 AAAAAAAA-CAAAACAGC
53981366 AAAAAAGAACAAA
1 AAAAAA-AACAAA
53981379 GCAGGCCCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 9 0.21
18 30 0.71
19 3 0.07
ACGTcount: A:0.73, C:0.18, G:0.08, T:0.02
Consensus pattern (17 bp):
AAAAAAAACAAAACAGC
Found at i:53982071 original size:17 final size:16
Alignment explanation
Indices: 53982051--53982094 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
53982041 AAGAGTTTTC
53982051 GTGTTTCACAAATGTTA
1 GTGTTTCA-AAATGTTA
* * *
53982068 GTGTTTTAAAATTTTT
1 GTGTTTCAAAATGTTA
53982084 GTGTTTCAAAA
1 GTGTTTCAAAA
53982095 ATTTTCATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.48
Consensus pattern (16 bp):
GTGTTTCAAAATGTTA
Found at i:53982106 original size:33 final size:34
Alignment explanation
Indices: 53982036--53982199 Score: 89
Period size: 42 Copynumber: 4.6 Consensus size: 34
53982026 ACTTTTAACA
* *
53982036 TTTTCAAGAGTTTTCGTGTTTCACAAATGTTAGTG
1 TTTTCAA-AATTTTCGTGTTTCAAAAATGTTAGTG
* *
53982071 TTTT-AAAATTTTTGTGTTTCAAAAATTTTCA-TG
1 TTTTCAAAATTTTCGTGTTTCAAAAATGTT-AGTG
** ** * *
53982104 TTTTCAAAAATTCCCGTGTTAAAAAAATTTTCGTG
1 TTTTC-AAAATTTTCGTGTTTCAAAAATGTTAGTG
* * *
53982139 TTTTCGTGTCATAAAAATTCTCGTGTTTCAAAAATTTTCGTG
1 --TT--T-TC---AAAATTTTCGTGTTTCAAAAATGTTAGTG
*
53982181 TTTTCAAAATTTTCATGTT
1 TTTTCAAAATTTTCGTGTT
53982200 ATCGTGTTTT
Statistics
Matches: 103, Mismatches: 15, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
33 25 0.24
34 15 0.15
35 26 0.25
37 4 0.04
38 1 0.01
39 1 0.01
40 4 0.04
42 27 0.26
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.48
Consensus pattern (34 bp):
TTTTCAAAATTTTCGTGTTTCAAAAATGTTAGTG
Found at i:53982110 original size:18 final size:18
Alignment explanation
Indices: 53982036--53982657 Score: 263
Period size: 17 Copynumber: 32.7 Consensus size: 18
53982026 ACTTTTAACA
* *
53982036 TTTTCAAGAGTTTTCGTG
1 TTTTCAAAAATTTTCGTG
* * *
53982054 -TTTCACAAATGTTAGTG
1 TTTTCAAAAATTTTCGTG
*
53982071 TTTT--AAAATTTTTGTG
1 TTTTCAAAAATTTTCGTG
*
53982087 -TTTCAAAAATTTTCATG
1 TTTTCAAAAATTTTCGTG
**
53982104 TTTTCAAAAATTCCCGTG
1 TTTTCAAAAATTTTCGTG
**
53982122 -TTAAAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
53982139 TTTTCGTGTCATAAAAATTCTCGTG
1 --TT--T-TC--AAAAATTTTCGTG
53982164 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
53982181 TTTTCAAAATTTTCATGTTATCGTG
1 TTTTCAAAA-----AT-TT-TCGTG
*
53982206 TTTTCAAAAAATTCTCGTG
1 TTTTC-AAAAATTTTCGTG
*
53982225 TTTTAAAAAAATTTTGCGTG
1 TTTT-CAAAAATTTT-CGTG
53982245 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
53982262 TTTTC-AAAATTTTCATGTTTTTG
1 TTTTCAAAAATTTTC--G----TG
*
53982285 TGCTTTCAAAAAAAAAATTCTCGTG
1 T--TTTC-----AAAAATTTTCGTG
* ***
53982310 TTTTTAAAAAAAATCGTG
1 TTTTCAAAAATTTTCGTG
** *
53982328 TTTT-AAAAAAATTCATG
1 TTTTCAAAAATTTTCGTG
*
53982345 TTTTC-GAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
53982362 TTTT-AAAATTTTTCGTG
1 TTTTCAAAAATTTTCGTG
** *
53982379 TCAT-AAAAATTCTCGTG
1 TTTTCAAAAATTTTCGTG
53982396 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
53982413 TTTTCAAAATTTTCATGTTTTCGTG
1 TTTTCAAAA-----A--TTTTCGTG
53982438 TTTTCAAAAAAAATTCTT-GTG
1 TTTTC---AAAAATT-TTCGTG
* *
53982459 TTTGTAAAAAAATTTCGTG
1 TTT-TCAAAAATTTTCGTG
* ** * *
53982478 TTTTAAAAAAAATACATG
1 TTTTCAAAAATTTTCGTG
*
53982496 TTTTC-GAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
53982513 TTTTCAAAATTTTTCGTG
1 TTTTCAAAAATTTTCGTG
** *
53982531 TCAT-AAAAATTCTCGTG
1 TTTTCAAAAATTTTCGTG
53982548 -TTTCAAAAATTTTCGTG
1 TTTTCAAAAATTTTCGTG
*
53982565 TTTTCAAAATTTTCATGTTTTCGGG
1 TTTTCAAAA-----A--TTTTCGTG
*
53982590 TTTTCAAAAAATTCTCGTG
1 TTTTC-AAAAATTTTCGTG
*
53982609 TTTTAAAAAAATTTTCGTG
1 TTTT-CAAAAATTTTCGTG
*
53982628 -TTTCAAAAAATCTTCGTG
1 TTTTC-AAAAATTTTCGTG
53982646 TTTTCAAAAATT
1 TTTTCAAAAATT
53982658 ATTATTTTGT
Statistics
Matches: 462, Mismatches: 73, Indels: 138
0.69 0.11 0.21
Matches are distributed among these distances:
15 3 0.01
16 11 0.02
17 157 0.34
18 119 0.26
19 61 0.13
20 7 0.02
21 11 0.02
22 5 0.01
23 11 0.02
24 2 0.00
25 54 0.12
26 8 0.02
28 4 0.01
29 1 0.00
31 8 0.02
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (18 bp):
TTTTCAAAAATTTTCGTG
Found at i:53982147 original size:25 final size:25
Alignment explanation
Indices: 53982118--53982166 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
53982108 CAAAAATTCC
* *
53982118 CGTGTTAAAAAAATTTTCGTGTTTT
1 CGTGTCAAAAAAATTCTCGTGTTTT
*
53982143 CGTGTCATAAAAATTCTCGTGTTT
1 CGTGTCAAAAAAATTCTCGTGTTT
53982167 CAAAAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (25 bp):
CGTGTCAAAAAAATTCTCGTGTTTT
Found at i:53982416 original size:151 final size:151
Alignment explanation
Indices: 53982231--53982637 Score: 653
Period size: 152 Copynumber: 2.7 Consensus size: 151
53982221 CGTGTTTTAA
* * *
53982231 AAAAATTTTGCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTTGTGCTTTCAAAA
1 AAAAATTCT-CGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTC--AA
* *
53982296 AAAAAATTCTCGTGTTTTTAAAAAAA-ATCGTGTTTTAAAAAAATTCATGTTTTCGAAATTTTCG
63 AAAAAATTCTCGTGTTTTTAAAAAAATTTCGTGTTTTAAAAAAATACATGTTTTCGAAATTTTCG
53982360 TGTTTT-AAAATTTTTCGTGTCAT
128 TGTTTTCAAAATTTTTCGTGTCAT
53982383 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTCAAAAA
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTCAAAAA
* *
53982448 AAATTCTTGTGTTTGTAAAAAAATTTCGTGTTTTAAAAAAAATACATGTTTTCGAAATTTTCGTG
66 AAATTCTCGTGTTTTTAAAAAAATTTCGTGTTTT-AAAAAAATACATGTTTTCGAAATTTTCGTG
53982513 TTTTCAAAATTTTTCGTGTCAT
130 TTTTCAAAATTTTTCGTGTCAT
*
53982535 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGGGTTTTC--AAA
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTCAAAAA
*
53982598 AAATTCTCGTG-TTTTAAAAAAATTTTCGTGTTTCAAAAAA
66 AAATTCTCGTGTTTTTAAAAAAA-TTTCGTGTTTTAAAAAA
53982638 TCTTCGTGTT
Statistics
Matches: 240, Mismatches: 11, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
149 42 0.17
150 32 0.13
151 82 0.34
152 84 0.35
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (151 bp):
AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTCAAAAA
AAATTCTCGTGTTTTTAAAAAAATTTCGTGTTTTAAAAAAATACATGTTTTCGAAATTTTCGTGT
TTTCAAAATTTTTCGTGTCAT
Found at i:53982461 original size:21 final size:19
Alignment explanation
Indices: 53982431--53982490 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
53982421 ATTTTCATGT
53982431 TTTCGTGTTTTCAAAAAAAA
1 TTTCGTGTTTT-AAAAAAAA
*
53982451 TTCTTGTGTTTGT-AAAAAAA
1 TT-TCGTGTTT-TAAAAAAAA
53982471 TTTCGTGTTTTAAAAAAAA
1 TTTCGTGTTTTAAAAAAAA
53982490 T
1 T
53982491 ACATGTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 15 0.43
20 11 0.31
21 7 0.20
22 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (19 bp):
TTTCGTGTTTTAAAAAAAA
Found at i:53982469 original size:20 final size:18
Alignment explanation
Indices: 53982431--53982655 Score: 100
Period size: 18 Copynumber: 11.9 Consensus size: 18
53982421 ATTTTCATGT
53982431 TTTCGTGTTTTCAAAAAAAA
1 TTTCGTGTTTT--AAAAAAA
*
53982451 TTCTTGTGTTTGTAAAAAAA
1 TT-TCGTGTTT-TAAAAAAA
53982471 TTTCGTGTTTTAAAAAAA
1 TTTCGTGTTTTAAAAAAA
* * * ** *
53982489 ATACATGTTTT-CGAAAT
1 TTTCGTGTTTTAAAAAAA
* **
53982506 TTTCGTGTTTTCAAAATT
1 TTTCGTGTTTTAAAAAAA
* *
53982524 TTTCGTG--TCATAAAAA
1 TTTCGTGTTTTAAAAAAA
* *
53982540 TTCTCGTG-TTTCAAAAAT
1 TT-TCGTGTTTTAAAAAAA
**
53982558 TTTCGTGTTTTCAAAATTTTCATGT
1 TTTCGTGTTTT-AAAA-----A-AA
* *
53982583 TTTCGGGTTTTCAAAAAA
1 TTTCGTGTTTTAAAAAAA
53982601 TTCTCGTGTTTTAAAAAAA
1 TT-TCGTGTTTTAAAAAAA
*
53982620 TTTTCGTG-TTTCAAAAAA
1 -TTTCGTGTTTTAAAAAAA
53982638 TCTTCGTGTTTTCAAAAA
1 T-TTCGTGTTTT-AAAAA
53982656 TTATTATTTT
Statistics
Matches: 154, Mismatches: 33, Indels: 36
0.69 0.15 0.16
Matches are distributed among these distances:
16 6 0.04
17 22 0.14
18 53 0.34
19 33 0.21
20 17 0.11
21 7 0.05
22 1 0.01
24 4 0.03
25 11 0.07
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTCGTGTTTTAAAAAAA
Found at i:53983964 original size:42 final size:42
Alignment explanation
Indices: 53983905--53983986 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
53983895 ACTTACAGAA
*
53983905 AAAAAAAGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGT
1 AAAAAAAGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGT
* *
53983947 AAAAAACGTCGCTAAAGAACATGTTCTTTAGCGGCGCTTA
1 AAAAAAAGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA
53983987 TTTCACAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (42 bp):
AAAAAAAGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGT
Found at i:53984441 original size:12 final size:12
Alignment explanation
Indices: 53984424--53984450 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53984414 TTTTGAACCT
53984424 CTGCTTCTCTCG
1 CTGCTTCTCTCG
53984436 CTGCTTCTCTCG
1 CTGCTTCTCTCG
53984448 CTG
1 CTG
53984451 TAGCCTCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.19, T:0.41
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:53988177 original size:9 final size:9
Alignment explanation
Indices: 53988163--53988193 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
53988153 GTTAAACGAA
53988163 TCGAGTTAT
1 TCGAGTTAT
*
53988172 TCGAGTTAA
1 TCGAGTTAT
53988181 TCGAGTTAT
1 TCGAGTTAT
53988190 TCGA
1 TCGA
53988194 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:53988366 original size:29 final size:30
Alignment explanation
Indices: 53988326--53988382 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
53988316 CTTTTTTACT
* *
53988326 TTTCCCTCAAAACTTTTCCTCCT-TCCCAC
1 TTTCCCCCAAAACTTTTACTCCTCTCCCAC
53988355 TTTCCCCCAAAACTTTTACTCCTCTCCC
1 TTTCCCCCAAAACTTTTACTCCTCTCCC
53988383 CTCCTAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.18, C:0.46, G:0.00, T:0.37
Consensus pattern (30 bp):
TTTCCCCCAAAACTTTTACTCCTCTCCCAC
Found at i:53989235 original size:40 final size:39
Alignment explanation
Indices: 53989158--53989235 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
53989148 AAACACAAAA
* * * *
53989158 TAACATTTTTGCGGCATTTTAAGAGAAGCGCCGCTAAAG
1 TAACATTTTTGCGGCATTTTAACAAAAACGCCACTAAAG
53989197 TAACATCTTTTGCGGCATTTTAACAAAAACGCCACTAAA
1 TAACAT-TTTTGCGGCATTTTAACAAAAACGCCACTAAA
53989236 TACATAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 6 0.18
40 28 0.82
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (39 bp):
TAACATTTTTGCGGCATTTTAACAAAAACGCCACTAAAG
Found at i:53989277 original size:115 final size:115
Alignment explanation
Indices: 53989075--53989386 Score: 511
Period size: 115 Copynumber: 2.7 Consensus size: 115
53989065 CTCACCCCTA
*
53989075 GCTAAAGTAACATCTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAAGGGTCAC
1 GCTAAAGTAACATCTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCAC
53989140 GTTTTGGTAAACACAAAATAACATTTTTGCGGCATTTTAAGAGAAGCGCC
66 GTTTTGGTAAACACAAAATAACATTTTTGCGGCATTTTAAGAGAAGCGCC
*
53989190 GCTAAAGTAACATCTTTTGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCAC
1 GCTAAAGTAACATCTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCAC
**
53989255 GTTTTGGTAAACACAAAATAACATTTTTGCGGTGTTTTAAGAGAAGCGCC
66 GTTTTGGTAAACACAAAATAACATTTTTGCGGCATTTTAAGAGAAGCGCC
* * * **
53989305 GCTAAAGCAAGATCTTTTGCGGCGTTTTAACAAAAACGCCACTAAAAACAT--AAAAACGGTTTC
1 GCTAAAGTAACATCTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCAC
* *
53989368 GTTTCGGTCAACACAAAAT
66 GTTTTGGTAAACACAAAAT
53989387 CCAACAAAAC
Statistics
Matches: 185, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
113 27 0.15
115 158 0.85
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (115 bp):
GCTAAAGTAACATCTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCAC
GTTTTGGTAAACACAAAATAACATTTTTGCGGCATTTTAAGAGAAGCGCC
Found at i:53989678 original size:115 final size:112
Alignment explanation
Indices: 53989425--53989880 Score: 435
Period size: 115 Copynumber: 4.0 Consensus size: 112
53989415 ACCCATTGAA
* * * *
53989425 ATTTTGCGGCGTTTTCAACGCAGCGCCGCTAAAGGCTGACATTTTTCGGCATTTTACAAAAAACG
1 ATTTTGCGGCGTTTTTAAC-TAGCGCCGCTAAAGGCTGACCTTTTGCGGCATTTTAC-AAAAACG
* * ** * * * *
53989490 CCACTAATAAATCCTACACCACGGAAGCGTTTTATTAAAACAGAATCAC
64 CCAGTAAGAAATCCTACAAAACGCAAGCTTTTTATTGAAACAAAATCAC
* *
53989539 ATTTTGCTGCGTTTTTAATCTAGCGCCGCTAAAGGCTGACCTTTTGCGGCATTTTGGCAAAAACG
1 ATTTTGCGGCGTTTTTAA-CTAGCGCCGCTAAAGGCTGACCTTTTGCGGCATTTT-ACAAAAACG
* *
53989604 CCAGTAAGAAATCCCACAAAACGACAAGATTTTTATTGAAACAAAATCAC
64 CCAGTAAGAAATCCTACAAAACG-CAAGCTTTTTATTGAAACAAAATCAC
* * * *
53989654 ATTTTGCGGCGTTTTTGACATAGCGCCGCTAAAGGATGATCTTTTGCGGCGTTTTACCAAAAACG
1 ATTTTGCGGCGTTTTTAAC-TAGCGCCGCTAAAGGCTGACCTTTTGCGGCATTTTA-CAAAAACG
* * *
53989719 CCAGTAAGAAATCTTACAGAACGGCAACCTTTTTATTGAAACAAAATCAC
64 CCAGTAAGAAATCCTACAAAAC-GCAAGCTTTTTATTGAAACAAAATCAC
* * * ** * ** * * * *
53989769 ATTTTACGGCGTTTTCAGCTTAGCGCCGGGAAAGCCCAAACTTTTACGGCGTTTTACCCAAAACG
1 ATTTTGCGGCGTTTTTAAC-TAGCGCCGCTAAAGGCTGACCTTTTGCGGCATTTTA-CAAAAACG
* * * * * * *
53989834 CCACTAATATATCCTATAGAACGCCACCGTTTTTATTGAAACAAAAT
64 CCAGTAAGAAATCCTACAAAACGCAAGC-TTTTTATTGAAACAAAAT
53989881 TCCTTTAAAT
Statistics
Matches: 288, Mismatches: 47, Indels: 13
0.83 0.14 0.04
Matches are distributed among these distances:
114 79 0.27
115 208 0.72
116 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (112 bp):
ATTTTGCGGCGTTTTTAACTAGCGCCGCTAAAGGCTGACCTTTTGCGGCATTTTACAAAAACGCC
AGTAAGAAATCCTACAAAACGCAAGCTTTTTATTGAAACAAAATCAC
Found at i:53989869 original size:230 final size:229
Alignment explanation
Indices: 53989425--53989880 Score: 495
Period size: 230 Copynumber: 2.0 Consensus size: 229
53989415 ACCCATTGAA
* * *
53989425 ATTTTGCGGCGTTTTCAACGCAGCGCCGCTAAAGGCTGACATTTTTCGGCATTTTACAAAAAACG
1 ATTTTGCGGCGTTTTCAACACAGCGCCGCTAAAGGATGACATTTTGCGGCATTTTACAAAAAACG
* * * * * * *
53989490 CCACTAATAAATCCTACACCACGGAAGCGTTTTATTAAAACAGAATCACATTTTGCTGCGTTTTT
66 CCACTAAGAAATCCTACACAACGGAACCGTTTTATTAAAACAAAATCACATTTTACGGCGTTTTC
* * ** * * ** *
53989555 AATCTAGCGCCGCTAAAGGCTGACCTTTTGCGGCATTTTGGCAAAAACGCCAGTAAGAAATCCCA
131 AATCTAGCGCCGCGAAAGCCCAAACTTTTACGGCATTTTACCAAAAACGCCACTAAGAAATCCCA
53989620 CAAAACGACAAGATTTTTATTGAAACAAAATCAC
196 CAAAACGACAAGATTTTTATTGAAACAAAATCAC
** * * *
53989654 ATTTTGCGGCGTTTTTGACATAGCGCCGCTAAAGGATGATC-TTTTGCGGCGTTTTACCAAAAAC
1 ATTTTGCGGCGTTTTCAACACAGCGCCGCTAAAGGATGA-CATTTTGCGGCATTTTACAAAAAAC
* * * * *
53989718 GCCAGTAAGAAATCTTACAGAACGGCAACCTTTTTATTGAAACAAAATCACATTTTACGGCGTTT
65 GCCACTAAGAAATCCTACACAACGG-AACCGTTTTATTAAAACAAAATCACATTTTACGGCGTTT
* * * * * *
53989783 TC-AGCTTAGCGCCGGGAAAGCCCAAACTTTTACGGCGTTTTACCCAAAACGCCACTAATATATC
129 TCAATC-TAGCGCCGCGAAAGCCCAAACTTTTACGGCATTTTACCAAAAACGCCACTAAGAAATC
* * * * *
53989847 CTATAGAACGCCACCG-TTTTTATTGAAACAAAAT
193 CCACAAAACGACA-AGATTTTTATTGAAACAAAAT
53989881 TCCTTTAAAT
Statistics
Matches: 183, Mismatches: 40, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
229 76 0.42
230 106 0.58
231 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (229 bp):
ATTTTGCGGCGTTTTCAACACAGCGCCGCTAAAGGATGACATTTTGCGGCATTTTACAAAAAACG
CCACTAAGAAATCCTACACAACGGAACCGTTTTATTAAAACAAAATCACATTTTACGGCGTTTTC
AATCTAGCGCCGCGAAAGCCCAAACTTTTACGGCATTTTACCAAAAACGCCACTAAGAAATCCCA
CAAAACGACAAGATTTTTATTGAAACAAAATCAC
Found at i:53990431 original size:21 final size:21
Alignment explanation
Indices: 53990401--53990451 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
53990391 CCTAGCCTAG
*
53990401 ACCCTAAACCCCAACTCATAA
1 ACCCTAAACCCCAACCCATAA
* *
53990422 ACCTTAAACCCCAACCCGTAA
1 ACCCTAAACCCCAACCCATAA
53990443 ACCCTAAAC
1 ACCCTAAAC
53990452 TGTAAACCAT
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:0.41, C:0.43, G:0.02, T:0.14
Consensus pattern (21 bp):
ACCCTAAACCCCAACCCATAA
Found at i:53990495 original size:16 final size:15
Alignment explanation
Indices: 53990454--53990496 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
53990444 CCCTAAACTG
53990454 TAAACCATAA-TCAC
1 TAAACCATAATTCAC
53990468 TAAAGCCATAATTCAC
1 TAAA-CCATAATTCAC
*
53990484 ATAAACCTTAATT
1 -TAAACCATAATT
53990497 AAACCCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 4 0.16
15 6 0.24
16 11 0.44
17 4 0.16
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (15 bp):
TAAACCATAATTCAC
Found at i:53990780 original size:9 final size:10
Alignment explanation
Indices: 53990754--53990783 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
53990744 TTTTTAATAA
*
53990754 ATATTTTTAT
1 ATATTTTTAC
53990764 ATATTTTTAC
1 ATATTTTTAC
53990774 ATATTTTTAC
1 ATATTTTTAC
53990784 TTTCAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (10 bp):
ATATTTTTAC
Found at i:53991167 original size:113 final size:113
Alignment explanation
Indices: 53990957--53991279 Score: 486
Period size: 113 Copynumber: 2.8 Consensus size: 113
53990947 GTTTTTTGCG
** **
53990957 GCGCTTTTACAAAAACGCCACCAAAGCCTCCCAAACTAAGAAAAACGACGTCGTTAGGCTTAGGT
1 GCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAG-AAAACGACGTCGTTAGGCTTAGGT
** * *
53991022 TTTTTGCGGCTATTTTTAAAAAACGCCGCTAAAACCCTGAGCATTAGCA
65 TTTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCTGAGAATTACCA
* * * *
53991071 GCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAATGATGTCGTTGGGCTTAGGTC
1 GCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAACGACGTCGTTAGGCTTAGGTT
* *
53991136 TTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAGCCCTGAGAATTACCT
66 TTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCTGAGAATTACCA
*
53991184 GCGC-TTCTCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAACGACGTCGTTTGGCTTAGGT
1 GCGCTTTC-CCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAACGACGTCGTTAGGCTTAGGT
53991248 TTTTTGCGGCGCTTTTTAAAAAACGCCGCTAA
65 TTTTTGCGGCGCTTTTTAAAAAACGCCGCTAA
53991280 TGCTCATTGT
Statistics
Matches: 190, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
112 3 0.02
113 151 0.79
114 36 0.19
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (113 bp):
GCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAACGACGTCGTTAGGCTTAGGTT
TTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCTGAGAATTACCA
Found at i:53993122 original size:21 final size:21
Alignment explanation
Indices: 53993096--53993163 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
53993086 CAACAACTTA
* *
53993096 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
** *
53993117 AAGCAGAGGCTACAGCAAGAG
1 AAGCAGAGGCCGCAGCGAGAG
*
53993138 AAGCAGAGGCCGCAGTGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
53993159 AAGCA
1 AAGCA
53993164 ACGAGAGAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.37, C:0.19, G:0.41, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:53993766 original size:42 final size:43
Alignment explanation
Indices: 53993629--53993816 Score: 267
Period size: 43 Copynumber: 4.4 Consensus size: 43
53993619 GTGAAATAAA
* *
53993629 CGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTCCTCCCAAG
1 CGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTCTTCCTAAG
*
53993672 CACCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTTCCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTTCCTAAG
*
53993715 CGCCGCTAAAGAATATGATCTTTAGCGGCGTTTT-TTCCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTTCCTAAG
* *
53993757 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTAT-TTTCTTAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-TCTTCCTAAG
53993800 CGCCGCTAAAGAACATG
1 CGCCGCTAAAGAACATG
53993817 CTAAAGAACA
Statistics
Matches: 134, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
42 41 0.31
43 92 0.69
44 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (43 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTTCCTAAG
Found at i:53993802 original size:85 final size:86
Alignment explanation
Indices: 53993649--53993812 Score: 260
Period size: 85 Copynumber: 1.9 Consensus size: 86
53993639 GAACACTACT
53993649 TTTAGCGGCGTTTTCCTCCCAAGCACCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTTCCTAA
1 TTTAGCGGCGTTTTCCTCCCAAGCACCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTTCCTAA
53993714 GCGCCGCTAAAGAATATGATC
66 GCGCCGCTAAAGAATATGATC
* * * * *
53993735 TTTAGCGGCGTTTT-TTCCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTAT-TTTCTT
1 TTTAGCGGCGTTTTCCTCCCAAGCACCGCTAAAGAACATGATCTTTAGCGGCGTTT-TCTTCCTA
53993798 AGCGCCGCTAAAGAA
65 AGCGCCGCTAAAGAA
53993813 CATGCTAAAG
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
85 57 0.79
86 15 0.21
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (86 bp):
TTTAGCGGCGTTTTCCTCCCAAGCACCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTTCCTAA
GCGCCGCTAAAGAATATGATC
Found at i:53993821 original size:12 final size:12
Alignment explanation
Indices: 53993804--53993828 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53993794 TCTTAGCGCC
53993804 GCTAAAGAACAT
1 GCTAAAGAACAT
53993816 GCTAAAGAACAT
1 GCTAAAGAACAT
53993828 G
1 G
53993829 TTCTTTAGCG
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:0.48, C:0.16, G:0.20, T:0.16
Consensus pattern (12 bp):
GCTAAAGAACAT
Found at i:53993826 original size:55 final size:56
Alignment explanation
Indices: 53993761--53993866 Score: 171
Period size: 55 Copynumber: 1.9 Consensus size: 56
53993751 CCTAAGCGCC
*
53993761 GCTAAAGAACATGATCTTTAGCGGCGTTTATTTTCT-T-AGCGCCGCTAAAGAACAT
1 GCTAAAGAACATGATCTTTAGCGGCGTTT-TTTTCTGTAAGCGCCGCAAAAGAACAT
*
53993816 GCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTGTAAGCGCCGCAAAAG
1 GCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTGTAAGCGCCGCAAAAG
53993867 TTAGCGATGT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
54 6 0.13
55 29 0.62
56 12 0.26
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (56 bp):
GCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTGTAAGCGCCGCAAAAGAACAT
Found at i:53998490 original size:20 final size:20
Alignment explanation
Indices: 53998453--53998496 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
53998443 AAAATTACAA
* *
53998453 TTTTTATACTTTTTAAATTAT
1 TTTTTATAC-TTTAAAAATAT
53998474 TTTTTAT-CTTTAAAAATAT
1 TTTTTATACTTTAAAAATAT
53998493 TTTT
1 TTTT
53998497 AAAATTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 1 0.05
21 7 0.33
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTATACTTTAAAAATAT
Found at i:54001509 original size:21 final size:21
Alignment explanation
Indices: 54001488--54001526 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
54001478 TTACAATACA
54001488 AATAGATTAAC-AATTGAAAC
1 AATAGATTAACTAATTGAAAC
* *
54001508 AATATATTTACTAATTGAA
1 AATAGATTAACTAATTGAA
54001527 CTTAAATCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (21 bp):
AATAGATTAACTAATTGAAAC
Found at i:54003112 original size:31 final size:32
Alignment explanation
Indices: 54003068--54003142 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 32
54003058 TCGAGCGGGA
* *
54003068 TGGGTTAAGTTTTGA-TCTGGGTCACTTCA-GTT
1 TGGGTCAA-TTTTGACTCCGGGTCA-TTCAGGTT
54003100 TGGGTCAATTTTGACTCCGGGTCATTCAGGTT
1 TGGGTCAATTTTGACTCCGGGTCATTCAGGTT
54003132 TGGGTCAATTT
1 TGGGTCAATTT
54003143 CAAGTTCAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
31 10 0.26
32 29 0.74
ACGTcount: A:0.16, C:0.15, G:0.28, T:0.41
Consensus pattern (32 bp):
TGGGTCAATTTTGACTCCGGGTCATTCAGGTT
Found at i:54012406 original size:16 final size:16
Alignment explanation
Indices: 54012378--54012419 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
54012368 AAGAATAATT
*
54012378 ATTT-AAATGATTCAA
1 ATTTAAAATAATTCAA
54012393 ATTTAAAATAATTCAA
1 ATTTAAAATAATTCAA
*
54012409 AATTAAAATAA
1 ATTTAAAATAA
54012420 CTCATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (16 bp):
ATTTAAAATAATTCAA
Found at i:54012432 original size:18 final size:16
Alignment explanation
Indices: 54012389--54012423 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54012379 TTTAAATGAT
* *
54012389 TCAAATTTAAAATAAT
1 TCAAAATTAAAATAAC
54012405 TCAAAATTAAAATAAC
1 TCAAAATTAAAATAAC
54012421 TCA
1 TCA
54012424 TAAAATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (16 bp):
TCAAAATTAAAATAAC
Found at i:54019479 original size:16 final size:16
Alignment explanation
Indices: 54019442--54019481 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 16
54019432 AATATTAAAC
*
54019442 AATTTATTAAAATAAT
1 AATTTATTATAATAAT
54019458 AA---ATTATAATAAT
1 AATTTATTATAATAAT
54019471 AATTTATTATA
1 AATTTATTATA
54019482 TGACTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 6
0.74 0.04 0.22
Matches are distributed among these distances:
13 12 0.60
16 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTATTATAATAAT
Found at i:54019961 original size:22 final size:23
Alignment explanation
Indices: 54019930--54020008 Score: 117
Period size: 23 Copynumber: 3.5 Consensus size: 23
54019920 GACCCACCCG
54019930 TATTATTTTTTAAAATATATTTA
1 TATTATTTTTTAAAATATATTTA
54019953 TATTATTTTTTAAAATATATTTA
1 TATTATTTTTTAAAATATATTTA
**
54019976 TATTA-TTTTTAATTTATATTTA
1 TATTATTTTTTAAAATATATTTA
*
54019998 T-TAATTTTTTA
1 TATTATTTTTTA
54020009 TTTTTATTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
21 2 0.04
22 22 0.42
23 28 0.54
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTATTTTTTAAAATATATTTA
Found at i:54020004 original size:21 final size:21
Alignment explanation
Indices: 54019930--54020006 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 21
54019920 GACCCACCCG
*
54019930 TATTATTTTTTAAAATATATTT
1 TATTAATTTTTAAAATATA-TT
*
54019952 ATATTATTTTTTAAAATATATT
1 -TATTAATTTTTAAAATATATT
* **
54019974 TATATTATTTTTAATTTATATT
1 TAT-TAATTTTTAAAATATATT
54019996 TATTAATTTTT
1 TATTAATTTTT
54020007 TATTTTTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 10 0.21
22 19 0.40
23 19 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTAATTTTTAAAATATATT
Found at i:54020011 original size:21 final size:22
Alignment explanation
Indices: 54019945--54020035 Score: 80
Period size: 21 Copynumber: 4.2 Consensus size: 22
54019935 TTTTTTAAAA
* **
54019945 TATATTTATATTATTTTTTAAAA
1 TATATTTATATAATTTTTT-ATT
* *
54019968 TATATTTATATTATTTTTAATT
1 TATATTTATATAATTTTTTATT
54019990 TATATTTAT-TAATTTTTTATT
1 TATATTTATATAATTTTTTATT
* **
54020011 TTTATTTAT-TAAACTTTT-TT
1 TATATTTATATAATTTTTTATT
54020031 TATAT
1 TATAT
54020036 ATTCATCCTG
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.10
21 25 0.42
22 10 0.17
23 18 0.31
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (22 bp):
TATATTTATATAATTTTTTATT
Found at i:54020028 original size:22 final size:22
Alignment explanation
Indices: 54019936--54020029 Score: 66
Period size: 23 Copynumber: 4.2 Consensus size: 22
54019926 CCCGTATTAT
** * *
54019936 TTTTTAAAATATATTTATATTAT
1 TTTTTAATTTATATTTAT-TAAC
** *
54019959 TTTTTAAAATATATTTATATTA-
1 TTTTTAATTTATATTTAT-TAAC
54019981 TTTTTAATTTATATTTATTAA-
1 TTTTTAATTTATATTTATTAAC
* *
54020002 TTTTTTATTTTTATTTATTAAAC
1 TTTTTAATTTATATTTATT-AAC
54020025 TTTTT
1 TTTTT
54020030 TTATATATTC
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
21 19 0.30
22 18 0.28
23 27 0.42
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTTAATTTATATTTATTAAC
Found at i:54020735 original size:10 final size:10
Alignment explanation
Indices: 54020714--54020781 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 10
54020704 TAAGTAATAA
*
54020714 AAAGAAATAG
1 AAAGAAAAAG
54020724 AAA-AAGAAAG
1 AAAGAA-AAAG
54020734 AAAGATAGAAACG
1 AAAGA-A-AAA-G
*
54020747 AAACGAAACAG
1 AAA-GAAAAAG
54020758 AAAGAAAAAAG
1 AAAG-AAAAAG
54020769 AAAGAAAAAG
1 AAAGAAAAAG
54020779 AAA
1 AAA
54020782 AGGGAGAAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
9 2 0.04
10 19 0.39
11 14 0.29
12 7 0.14
13 5 0.10
14 2 0.04
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.03
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:54020770 original size:11 final size:11
Alignment explanation
Indices: 54020712--54020781 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 11
54020702 AATAAGTAAT
*
54020712 AAAAAGAAATA
1 AAAAAGAAAGA
54020723 GAAAAAGAAAGA
1 -AAAAAGAAAGA
*
54020735 AAGATAGAAACGAA
1 AA-AAAGAAA-G-A
54020749 ACGAAACAGAAAGA
1 A--AAA-AGAAAGA
54020763 AAAAAGAAAG-
1 AAAAAGAAAGA
54020773 AAAAAGAAA
1 AAAAAGAAA
54020782 AGGGAGAAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
10 9 0.18
11 8 0.16
12 19 0.39
13 1 0.02
14 4 0.08
15 2 0.04
16 6 0.12
ACGTcount: A:0.74, C:0.04, G:0.19, T:0.03
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:54021677 original size:41 final size:40
Alignment explanation
Indices: 54021617--54021710 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
54021607 CAACTTCGAG
* * * *
54021617 TCGATGAGACACTGGGTGTCAATTTACTACTTTGGATTAAT
1 TCGATGAGGCACTGAGTGTCAATTTACTACTTCGAATT-AT
*
54021658 TCGATGAGGCACTGAGTGTCAATTTATTACTTCGAATTAT
1 TCGATGAGGCACTGAGTGTCAATTTACTACTTCGAATTAT
*
54021698 CCGATGAGGCACT
1 TCGATGAGGCACT
54021711 AGATGCCAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 14 0.30
41 33 0.70
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (40 bp):
TCGATGAGGCACTGAGTGTCAATTTACTACTTCGAATTAT
Found at i:54027523 original size:38 final size:36
Alignment explanation
Indices: 54027448--54027524 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 36
54027438 AGACATAATA
* *
54027448 TTTTTTTTAAAACCAAAATTTATGAAACACGAGATT
1 TTTTTTTTAAAACCAAAATTTATAAAACACGAAATT
* *
54027484 TTTTTTTTGAAAACGAAAATTT-TCAAAACCCCGAAATT
1 TTTTTTTT-AAAACCAAAATTTAT-AAAA-CACGAAATT
54027522 TTT
1 TTT
54027525 GAAAACAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
36 9 0.26
37 15 0.44
38 10 0.29
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (36 bp):
TTTTTTTTAAAACCAAAATTTATAAAACACGAAATT
Found at i:54027572 original size:17 final size:17
Alignment explanation
Indices: 54027488--54027583 Score: 72
Period size: 17 Copynumber: 5.6 Consensus size: 17
54027478 GAGATTTTTT
54027488 TTTTG-AAA-ACGAAAA
1 TTTTGAAAACACGAAAA
* * *
54027503 TTTTCAAAACCCCGAAAT
1 TTTTGAAAA-CACGAAAA
* * *
54027521 TTTTGAAAACAAGAGGAT
1 TTTTGAAAACACGA-AAA
*
54027539 TTTTG-AAATACGAAAAA
1 TTTTGAAAACACG-AAAA
54027556 TTTTGAAAACACGAAAA
1 TTTTGAAAACACGAAAA
*
54027573 TTTCGAAAACA
1 TTTTGAAAACA
54027584 TGTATTTTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
15 4 0.06
16 3 0.05
17 28 0.45
18 27 0.44
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (17 bp):
TTTTGAAAACACGAAAA
Found at i:54027611 original size:17 final size:18
Alignment explanation
Indices: 54027578--54027616 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
54027568 GAAAATTTCG
*
54027578 AAAACATGTATTTTTTTT
1 AAAACATGTAATTTTTTT
54027596 AAAACATG-AATTTTTTT
1 AAAACATGTAATTTTTTT
54027613 AAAA
1 AAAA
54027617 AAACACGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
AAAACATGTAATTTTTTT
Found at i:54027665 original size:17 final size:16
Alignment explanation
Indices: 54027643--54027693 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 16
54027633 TTGAAAACAC
54027643 GAAAACATGAAAATTTT
1 GAAAACA-GAAAATTTT
54027660 GAAAACACGAAAATTTTT
1 GAAAACA-GAAAA-TTTT
54027678 GAAACACA-AAAATTTT
1 GAAA-ACAGAAAATTTT
54027694 TAGAAGACAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 4 0.13
17 16 0.52
18 8 0.26
19 3 0.10
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (16 bp):
GAAAACAGAAAATTTT
Found at i:54027679 original size:18 final size:18
Alignment explanation
Indices: 54027487--54027719 Score: 93
Period size: 18 Copynumber: 12.6 Consensus size: 18
54027477 CGAGATTTTT
54027487 TTTTTG-AAA-ACGAAAA
1 TTTTTGAAAACACGAAAA
* *
54027503 -TTTTCAAAACCCCG-AAA
1 TTTTTGAAAA-CACGAAAA
* **
54027520 TTTTTGAAAACAAGAGGA
1 TTTTTGAAAACACGAAAA
*
54027538 TTTTTG-AAATACGAAAA
1 TTTTTGAAAACACGAAAA
*
54027555 ATTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * * **
54027573 -TTTCGAAAACATGTATT
1 TTTTTGAAAACACGAAAA
* * **
54027590 TTTTTTAAAACATGAATT
1 TTTTTGAAAACACGAAAA
* *
54027608 TTTTTAAAAAAACACGAGAATT
1 TTTTT--GAAAACACGA-AA-A
54027630 TTTTTGAAAACACGAAAACA
1 TTTTTGAAAACACG-AAA-A
54027650 TGAAAATTTTGAAAACACGAAAA
1 T-----TTTTGAAAACACGAAAA
*
54027673 TTTTTG-AAACACAAAAA
1 TTTTTGAAAACACGAAAA
* *
54027690 TTTTTAGAAGACACTAAAAA
1 TTTTT-GAAAACAC-GAAAA
*
54027710 TTTTGGAAAA
1 TTTTTGAAAA
54027720 TGGATTTTTT
Statistics
Matches: 166, Mismatches: 31, Indels: 37
0.71 0.13 0.16
Matches are distributed among these distances:
15 4 0.02
16 3 0.02
17 44 0.27
18 52 0.31
19 9 0.05
20 28 0.17
21 2 0.01
22 6 0.04
23 2 0.01
24 3 0.02
25 13 0.08
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:54027694 original size:17 final size:17
Alignment explanation
Indices: 54027652--54027718 Score: 73
Period size: 17 Copynumber: 3.8 Consensus size: 17
54027642 CGAAAACATG
*
54027652 AAAA-TTTTGAAAACACG
1 AAAATTTTTG-AAACACA
54027669 AAAATTTTTGAAACACA
1 AAAATTTTTGAAACACA
54027686 AAAATTTTTAGAAGACACTA
1 AAAATTTTT-GAA-ACAC-A
*
54027706 AAAATTTTGGAAA
1 AAAATTTTTGAAA
54027719 ATGGATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
17 19 0.43
18 9 0.20
19 7 0.16
20 9 0.20
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.28
Consensus pattern (17 bp):
AAAATTTTTGAAACACA
Found at i:54027929 original size:20 final size:19
Alignment explanation
Indices: 54027891--54027937 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
54027881 AATATATATT
54027891 TTTTTGAAACACGAGAAAAA
1 TTTTTGAAACACG-GAAAAA
*
54027911 TTTTTGAAGGCAC-GAAAAA
1 TTTTTGAA-ACACGGAAAAA
54027930 -TTTTGAAA
1 TTTTTGAAA
54027938 AATAGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 8 0.33
21 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (19 bp):
TTTTTGAAACACGGAAAAA
Found at i:54028311 original size:8 final size:8
Alignment explanation
Indices: 54028298--54028393 Score: 99
Period size: 8 Copynumber: 12.0 Consensus size: 8
54028288 TTGAAACTCT
54028298 TTTTTTTC
1 TTTTTTTC
54028306 TTTTTTTC
1 TTTTTTTC
54028314 TTCTTTTTTCC
1 -T-TTTTTT-C
*
54028325 TTTTTTCC
1 TTTTTTTC
54028333 TTTTTTTC
1 TTTTTTTC
*
54028341 -TCTTTTC
1 TTTTTTTC
54028348 TTTTTTTC
1 TTTTTTTC
*
54028356 -TTCTTTC
1 TTTTTTTC
54028363 TTTTTTTC
1 TTTTTTTC
54028371 -TTTTTTC
1 TTTTTTTC
* *
54028378 TTTCTCTC
1 TTTTTTTC
54028386 TTTTTTTC
1 TTTTTTTC
54028394 CTGGCCTGCT
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
7 19 0.26
8 39 0.54
9 6 0.08
10 7 0.10
11 1 0.01
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTTC
Found at i:54028350 original size:15 final size:15
Alignment explanation
Indices: 54028295--54028391 Score: 108
Period size: 15 Copynumber: 6.5 Consensus size: 15
54028285 GAATTGAAAC
*
54028295 TCTTTTTT-TTCTTT
1 TCTTTTTTCTTTTTT
*
54028309 T-TTTCTTCTTTTTT
1 TCTTTTTTCTTTTTT
*
54028323 CCTTTTTTCCTTTTTT
1 TCTTTTTT-CTTTTTT
*
54028339 TCTCTTTTCTTTTTT
1 TCTTTTTTCTTTTTT
*
54028354 TCTTCTTTCTTTTTT
1 TCTTTTTTCTTTTTT
* *
54028369 TCTTTTTTCTTTCTC
1 TCTTTTTTCTTTTTT
54028384 TCTTTTTT
1 TCTTTTTT
54028392 TCCTGGCCTG
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
13 5 0.07
14 6 0.09
15 45 0.65
16 13 0.19
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TCTTTTTTCTTTTTT
Found at i:54028382 original size:23 final size:22
Alignment explanation
Indices: 54028295--54028393 Score: 96
Period size: 23 Copynumber: 4.5 Consensus size: 22
54028285 GAATTGAAAC
*
54028295 TCTTTTTTT-TCTTTTTTTC-T
1 TCTTTTTTTCTTTTTTTTTCTT
* *
54028315 TCTTTTTTCCTTTTTTCCTTTTTT
1 TCTTTTTTTCTTTTTT--TTTCTT
*
54028339 TC-TCTTTTCTTTTTTTCTTCTT
1 TCTTTTTTTCTTTTTTT-TTCTT
*
54028361 TCTTTTTTTCTTTTTTCTTTCTC
1 TCTTTTTTTCTTTTTT-TTTCTT
54028384 TCTTTTTTTC
1 TCTTTTTTTC
54028394 CTGGCCTGCT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
20 8 0.12
21 6 0.09
22 6 0.09
23 40 0.62
24 4 0.06
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (22 bp):
TCTTTTTTTCTTTTTTTTTCTT
Found at i:54028524 original size:15 final size:16
Alignment explanation
Indices: 54028506--54028546 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
54028496 GCTGTTTTTT
54028506 CTTTTTTTTTTGGGC-
1 CTTTTTTTTTTGGGCG
*
54028521 CTTTTCTTTTTGGGCTG
1 CTTTTTTTTTTGGGC-G
54028538 CTTTTTTTT
1 CTTTTTTTT
54028547 GCTTTGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
17 8 0.36
ACGTcount: A:0.00, C:0.15, G:0.17, T:0.68
Consensus pattern (16 bp):
CTTTTTTTTTTGGGCG
Found at i:54029093 original size:29 final size:29
Alignment explanation
Indices: 54029060--54029176 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
54029050 TGTAATTTTT
*
54029060 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
54029089 TGAAAGTTTAGGGGTCT-AAGTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
54029119 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
54029148 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
54029177 TTATTTTTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.30
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:54029115 original size:30 final size:30
Alignment explanation
Indices: 54029075--54029176 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
54029065 ATTTAGGATT
*
54029075 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
54029105 TAAGTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
54029135 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
54029165 AAAATGCAATTT
1 AAAATGAAATTT
54029177 TTATTTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:54029633 original size:54 final size:55
Alignment explanation
Indices: 54029447--54029664 Score: 324
Period size: 54 Copynumber: 4.1 Consensus size: 55
54029437 CACGTGAGCC
* *
54029447 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
*
54029502 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAA
* *
54029553 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
54029607 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
54029662 AAG
1 AAG
54029665 TAGAAATTGA
Statistics
Matches: 150, Mismatches: 6, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
50 14 0.09
51 34 0.23
52 1 0.01
54 52 0.35
55 37 0.25
56 6 0.04
57 6 0.04
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:54029662 original size:14 final size:14
Alignment explanation
Indices: 54029643--54029677 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
54029633 GAGTTGATTT
54029643 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
54029657 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
54029671 TTGAAAA
1 TTGAAAA
54029678 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:54029910 original size:85 final size:87
Alignment explanation
Indices: 54029766--54030013 Score: 299
Period size: 85 Copynumber: 2.8 Consensus size: 87
54029756 AAAAAAAATT
* * * *
54029766 AAAAACATAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
54029831 TTGATTTGAAAAG-TAGAATT-AG
65 TTGATTTGAAAAGATAG-ATTGAA
* * * *
54029853 TAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
54029916 TTGATTTTTGAAAAGCATAGATTGAA
65 TTGA--TTTGAAAAG-ATAGATTGAA
*
54029942 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
54030006 GTTGATTT
64 GTTGATTT
54030014 TTGAAAAACA
Statistics
Matches: 137, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 31 0.23
88 3 0.02
89 31 0.23
91 33 0.24
93 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTGAAAAGATAGATTGAA
Found at i:54029959 original size:15 final size:16
Alignment explanation
Indices: 54029926--54029959 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54029916 TTGATTTTTG
* *
54029926 AAAAGCATAGATTGAA
1 AAAAACATAAATTGAA
54029942 AAAAACATAAATTGAA
1 AAAAACATAAATTGAA
54029958 AA
1 AA
54029960 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAACATAAATTGAA
Done.