Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 67 of 438
Found at i:17486890 original size:64 final size:64
Alignment explanation
Indices: 17486809--17486992 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
17486799 AGACATTATG
* *
17486809 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
17486873 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
17486938 AA
63 AA
* * * *
17486940 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
17486993 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:17491406 original size:29 final size:30
Alignment explanation
Indices: 17491361--17491428 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
17491351 TGGCCCAAGA
* * *
17491361 GTAAATACTCAAAATTTGAGGGATTAA-AGT
1 GTAAATA-TAAAAATTTGAAGGACTAATAGT
17491391 GTAAATATAAAAATTTGAAGGACTAATAGT
1 GTAAATATAAAAATTTGAAGGACTAATAGT
*
17491421 GCAAATAT
1 GTAAATAT
17491429 TTCAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (30 bp):
GTAAATATAAAAATTTGAAGGACTAATAGT
Found at i:17491689 original size:29 final size:31
Alignment explanation
Indices: 17491641--17491704 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
17491631 TTTATATTTA
*
17491641 TTTAATTAGATAATTATTATT-TATTTAATAT
1 TTTAATAAGATAATTATTATTAT-TTTAATAT
*
17491672 TTTAATAAGAT-ATT-TTATTATTTTATTAT
1 TTTAATAAGATAATTATTATTATTTTAATAT
17491701 TTTA
1 TTTA
17491705 TTTAGTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTAATAAGATAATTATTATTATTTTAATAT
Found at i:17491693 original size:8 final size:8
Alignment explanation
Indices: 17491682--17491706 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
17491672 TTTAATAAGA
17491682 TATTTTAT
1 TATTTTAT
17491690 TATTTTAT
1 TATTTTAT
17491698 TATTTTAT
1 TATTTTAT
17491706 T
1 T
17491707 TAGTCTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:17501121 original size:83 final size:83
Alignment explanation
Indices: 17501021--17501193 Score: 310
Period size: 83 Copynumber: 2.1 Consensus size: 83
17501011 TTGAACTTTT
*
17501021 TAAACAACTACATATTAACTTACCTTTTGTTGAAGCTATATCGTAGATGCCTGCATACGCAAAAT
1 TAAACAACTACATATTAACTTACCTTTTGTTGAAGCTATATCGCAGATGCCTGCATACGCAAAAT
*
17501086 TTTTAAAGGATCTCCTAA
66 TTTTAAAGGAGCTCCTAA
*
17501104 TAAACAACTACATATTAACTTACCTTTTGTTGAAGCTATATCGCGGATGCCTGCATACGCAAAAT
1 TAAACAACTACATATTAACTTACCTTTTGTTGAAGCTATATCGCAGATGCCTGCATACGCAAAAT
17501169 TTTTAAAGGAGCTCCTAA
66 TTTTAAAGGAGCTCCTAA
*
17501187 CAAACAA
1 TAAACAA
17501194 AATGAAGTTT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (83 bp):
TAAACAACTACATATTAACTTACCTTTTGTTGAAGCTATATCGCAGATGCCTGCATACGCAAAAT
TTTTAAAGGAGCTCCTAA
Found at i:17503969 original size:40 final size:40
Alignment explanation
Indices: 17503875--17504019 Score: 168
Period size: 40 Copynumber: 3.6 Consensus size: 40
17503865 TACTCGAATG
* *
17503875 ATATCCGGGGTAAG-TCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCT-AGCGACT
* *
17503916 ACATCCGGACTAAGATCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
* * * *
17503956 ATATCTGGGCTAAG-TCCTGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGATCC-GAAGGCATTTGTGCTAGCGACT
*
17503996 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
17504020 CTTGTGCGAG
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
39 3 0.03
40 56 0.63
41 29 0.33
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGCGACT
Found at i:17505560 original size:49 final size:49
Alignment explanation
Indices: 17505498--17505785 Score: 460
Period size: 49 Copynumber: 6.0 Consensus size: 49
17505488 ATGTAGGAGA
17505498 TGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAG
1 TGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAG
*
17505547 TGTATATACATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAG
1 TGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAG
* * *
17505596 AG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAATG
1 TGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAG
*
17505643 TGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATATGAAAG
1 TGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAG
* * *
17505692 AG--TATATATGTGATAAGG-CTAATGGCCGATGTGATGAATGTGAAGG
1 TGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAG
*
17505738 TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 TGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
17505786 CATATGTGTG
Statistics
Matches: 219, Mismatches: 15, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
46 26 0.12
47 59 0.27
48 16 0.07
49 118 0.54
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (49 bp):
TGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAG
Found at i:17505656 original size:96 final size:96
Alignment explanation
Indices: 17505502--17505785 Score: 507
Period size: 96 Copynumber: 3.0 Consensus size: 96
17505492 AGGAGATGTA
* *
17505502 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATACATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
17505567 CCTAATGGCCAATGTGATGAATGTGAAAGAG
66 CCTAATGGCCAATGTGATGAATGTGAAAGAG
*
17505598 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAATGTGTATATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
*
17505663 CCTAATGGCCAATGTGATGAATATGAAAGAG
66 CCTAATGGCCAATGTGATGAATGTGAAAGAG
*
17505694 TATATATGTGATAAGG-CTAATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
*
17505758 CCTAATGGCCGATGTGATGAATGTGAAA
66 CCTAATGGCCAATGTGATGAATGTGAAA
17505786 CATATGTGTG
Statistics
Matches: 181, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
95 73 0.40
96 108 0.60
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (96 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
CCTAATGGCCAATGTGATGAATGTGAAAGAG
Found at i:17505833 original size:48 final size:48
Alignment explanation
Indices: 17505777--17505976 Score: 355
Period size: 48 Copynumber: 4.2 Consensus size: 48
17505767 CGATGTGATG
*
17505777 AATGTGAAACATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
* *
17505825 AATGTGAAATATATGTGTGATGTGTATATGTGGTAAAGCCGAAGGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
17505873 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
* *
17505921 AATGTGAAATATATGTGTGATGTGTATGTGTGGTAAAGCCGAATGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
17505969 AATGTGAA
1 AATGTGAA
17505977 TGTTGTAACA
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 145 1.00
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.32
Consensus pattern (48 bp):
AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
Found at i:17506070 original size:37 final size:37
Alignment explanation
Indices: 17506016--17506106 Score: 164
Period size: 37 Copynumber: 2.4 Consensus size: 37
17506006 AACTTGGAAA
*
17506016 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGTAAGACCCGATGACTACGTGTGGAGAT
17506054 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
17506091 TATGTCCGGGTAAGAC
1 TATGTCCGGGTAAGAC
17506107 TTCGTAATAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 48 0.92
38 4 0.08
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (37 bp):
TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
Found at i:17520871 original size:20 final size:20
Alignment explanation
Indices: 17520846--17520885 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
17520836 AGTAAATAAG
*
17520846 AAAAGAAATATGATTTTAAC
1 AAAAGAAATATAATTTTAAC
17520866 AAAAGAAATATAATTTTAAC
1 AAAAGAAATATAATTTTAAC
17520886 TCAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (20 bp):
AAAAGAAATATAATTTTAAC
Found at i:17521112 original size:21 final size:21
Alignment explanation
Indices: 17521087--17521133 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
17521077 TCAAGATATA
17521087 AAAATATATATAATTATTTT-T
1 AAAATA-ATATAATTATTTTAT
**
17521108 AAAATAATATTTTTATTTTAT
1 AAAATAATATAATTATTTTAT
17521129 AAAAT
1 AAAAT
17521134 GAATGAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAATAATATAATTATTTTAT
Found at i:17531386 original size:21 final size:19
Alignment explanation
Indices: 17531342--17531392 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
17531332 TGGACACAAG
17531342 GACACACCCGTGTGCCCTT
1 GACACACCCGTGTGCCCTT
17531361 GACACACCCGTGTGCCCTT
1 GACACACCCGTGTGCCCTT
17531380 GACACACCCGTGT
1 GACACACCCGTGT
17531393 CTTTAGGCCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.18, C:0.41, G:0.22, T:0.20
Consensus pattern (19 bp):
GACACACCCGTGTGCCCTT
Found at i:17532820 original size:48 final size:48
Alignment explanation
Indices: 17532747--17532922 Score: 262
Period size: 48 Copynumber: 3.7 Consensus size: 48
17532737 TCATGTCAGT
* *
17532747 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAT
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAC
* * *
17532795 GCCGATGCCATTTCCCAGACATGGTCTTACACTAGCTTACATATCAAC
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAC
* * *
17532843 GTCGATGCCATGTTCCAGACATGGTTTTACACTGGCTCACATATCAAC
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAC
* *
17532891 ATCGATGCTATGTCCCAGACATGGTCTTACAC
1 GTCGATGCCATGTCCCAGACATGGTCTTACAC
17532923 GGAATCTCAT
Statistics
Matches: 113, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 113 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (48 bp):
GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATCAAC
Found at i:17534668 original size:15 final size:15
Alignment explanation
Indices: 17534648--17534677 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17534638 TTCACTATTA
*
17534648 TGTCTTTTGTATTTT
1 TGTCTTTTATATTTT
17534663 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
17534678 CCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (15 bp):
TGTCTTTTATATTTT
Found at i:17534770 original size:17 final size:17
Alignment explanation
Indices: 17534750--17534794 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
17534740 AGAAAAGTGG
* *
17534750 CATTGTAAGAACGTTTA
1 CATTGCAAGAACATTTA
*
17534767 CATTGCGAGAACATTTA
1 CATTGCAAGAACATTTA
*
17534784 CATTGCGAGAA
1 CATTGCAAGAA
17534795 AGATGACTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (17 bp):
CATTGCAAGAACATTTA
Found at i:17536315 original size:19 final size:19
Alignment explanation
Indices: 17536291--17536383 Score: 70
Period size: 19 Copynumber: 4.9 Consensus size: 19
17536281 TATTTCAAAA
17536291 TAATATTATTTTAATATTT
1 TAATATTATTTTAATATTT
*
17536310 TAATATTA-ATTAA-A-TT
1 TAATATTATTTTAATATTT
*
17536326 TAATACTTATCTTAATATTAT
1 TAATA-TTATTTTAATATT-T
* *
17536347 T-TTATTAATTTAATA-TT
1 TAATATTATTTTAATATTT
*
17536364 AAAGTGATTATTTTAATATT
1 TAA-T-ATTATTTTAATATT
17536384 AAATTTAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
16 7 0.12
17 5 0.09
18 9 0.16
19 19 0.33
20 14 0.25
21 3 0.05
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TAATATTATTTTAATATTT
Found at i:17536353 original size:36 final size:36
Alignment explanation
Indices: 17536291--17536383 Score: 91
Period size: 36 Copynumber: 2.5 Consensus size: 36
17536281 TATTTCAAAA
*
17536291 TAATATTATTTTAATATTTTAATATTAATTAAAT-T
1 TAATATTATCTTAATATTTTAATATTAATTAAATAT
* *
17536326 TAATACTTATCTTAATATTATT-TTATTAATTTAATAT
1 TAATA-TTATCTTAATATT-TTAATATTAATTAAATAT
*
17536363 TAAAGTGATTATTTTAATATT
1 T-AA-T-ATTATCTTAATATT
17536384 AAATTTAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
35 5 0.10
36 23 0.48
37 4 0.08
38 2 0.04
39 13 0.27
40 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (36 bp):
TAATATTATCTTAATATTTTAATATTAATTAAATAT
Found at i:17536660 original size:26 final size:25
Alignment explanation
Indices: 17536614--17536664 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
17536604 AGTTGTAGAG
17536614 AGAAAATTCTCTGAAGAAATTATTTT
1 AGAAAATTCTCTGAAGAAATT-TTTT
17536640 AGAAAATT-TCT-AGAGATAATTTTTT
1 AGAAAATTCTCTGA-AGA-AATTTTTT
17536665 GATTTATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 1 0.04
25 10 0.43
26 12 0.52
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (25 bp):
AGAAAATTCTCTGAAGAAATTTTTT
Found at i:17538293 original size:12 final size:12
Alignment explanation
Indices: 17538276--17538310 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
17538266 CACTTAATTG
17538276 TAAAATTATTCA
1 TAAAATTATTCA
*
17538288 TAAAATTATTCG
1 TAAAATTATTCA
17538300 TAAAATTATTC
1 TAAAATTATTC
17538311 TTTACAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (12 bp):
TAAAATTATTCA
Found at i:17540735 original size:16 final size:18
Alignment explanation
Indices: 17540708--17540743 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
17540698 TAGAATTGGG
17540708 TTGAGAAAATT-ATTTAT
1 TTGAGAAAATTAATTTAT
17540725 TTGAG-AAATTAATTTAT
1 TTGAGAAAATTAATTTAT
17540742 TT
1 TT
17540744 AAATTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAT
Found at i:17542495 original size:27 final size:27
Alignment explanation
Indices: 17542465--17542616 Score: 153
Period size: 27 Copynumber: 5.5 Consensus size: 27
17542455 TAGTGAATCT
17542465 GCACACTTAGTGCTATAAAATCAGCTC
1 GCACACTTAGTGCTATAAAATCAGCTC
* * **
17542492 GCACACATAGTGCTATATAATCAAATTC
1 GCACACTTAGTGCTATAAAATC-AGCTC
17542520 G-ACACTTAGTGCTATAAAATCAGCTC
1 GCACACTTAGTGCTATAAAATCAGCTC
* * *
17542546 GCACACATAGTGCTATATAATTTGAGCTC
1 GCACACTTAGTGCTATA-AA-ATCAGCTC
* ** *
17542575 GCACACTTAGTGCCATATATTTCCAGCTT
1 GCACACTTAGTGCTATA-AAAT-CAGCTC
17542604 GCACACTTAGTGC
1 GCACACTTAGTGC
17542617 CATTCTCGTC
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.04
27 52 0.50
28 8 0.08
29 40 0.38
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (27 bp):
GCACACTTAGTGCTATAAAATCAGCTC
Found at i:17542617 original size:29 final size:29
Alignment explanation
Indices: 17542465--17542619 Score: 128
Period size: 29 Copynumber: 5.6 Consensus size: 29
17542455 TAGTGAATCT
**
17542465 GCACACTTAGTG-C-TATAAAATCAGCTC
1 GCACACTTAGTGCCATATAATTTCAGCTC
* * **
17542492 GCACACATAGTGCTATATAA--TCAAATTC
1 GCACACTTAGTGCCATATAATTTC-AGCTC
**
17542520 G-ACACTTAGTG-C-TATAAAATCAGCTC
1 GCACACTTAGTGCCATATAATTTCAGCTC
* * *
17542546 GCACACATAGTGCTATATAATTTGAGCTC
1 GCACACTTAGTGCCATATAATTTCAGCTC
*
17542575 GCACACTTAGTGCCATAT-ATTTCCAGCTT
1 GCACACTTAGTGCCATATAATTT-CAGCTC
17542604 GCACACTTAGTGCCAT
1 GCACACTTAGTGCCAT
17542620 TCTCGTCACC
Statistics
Matches: 102, Mismatches: 17, Indels: 16
0.76 0.13 0.12
Matches are distributed among these distances:
25 5 0.05
26 4 0.04
27 33 0.32
28 8 0.08
29 52 0.51
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29
Consensus pattern (29 bp):
GCACACTTAGTGCCATATAATTTCAGCTC
Found at i:17543262 original size:2 final size:2
Alignment explanation
Indices: 17543250--17543283 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
17543240 TGATGGTCGA
*
17543250 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17543284 CAACTATGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17550361 original size:27 final size:27
Alignment explanation
Indices: 17550331--17550484 Score: 164
Period size: 27 Copynumber: 5.5 Consensus size: 27
17550321 ATAGTGAATC
17550331 CGCACACTTAGTGCTATAAAATCAGCT
1 CGCACACTTAGTGCTATAAAATCAGCT
* * **
17550358 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATAAAATC-AGCT
17550386 CGCACACTTAGTGCTATAAAATCAGCT
1 CGCACACTTAGTGCTATAAAATCAGCT
* * *
17550413 CGCACACATAGTGCTATATAATTTGAGCT
1 CGCACACTTAGTGCTATA-AA-ATCAGCT
* **
17550442 CGCACACTTAGTGCCATATATTTCCAGCT
1 CGCACACTTAGTGCTATA-AAAT-CAGCT
*
17550471 TGCACACTTAGTGC
1 CGCACACTTAGTGC
17550485 CATTCTCGTC
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
27 40 0.37
28 27 0.25
29 40 0.37
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATAAAATCAGCT
Found at i:17550378 original size:29 final size:28
Alignment explanation
Indices: 17550331--17550484 Score: 145
Period size: 29 Copynumber: 5.5 Consensus size: 28
17550321 ATAGTGAATC
17550331 CGCACACTTAGTGC-TATAAAATCAGCT
1 CGCACACTTAGTGCATATAAAATCAGCT
* * **
17550358 CGCACACATAGTGC-TATATAATCAAATT
1 CGCACACTTAGTGCATATAAAATC-AGCT
17550386 CGCACACTTAGTGC-TATAAAATCAGCT
1 CGCACACTTAGTGCATATAAAATCAGCT
* ** *
17550413 CGCACACATAGTGCTATATAATTTGAGCT
1 CGCACACTTAGTGC-ATATAAAATCAGCT
**
17550442 CGCACACTTAGTGCCATAT-ATTTCCAGCT
1 CGCACACTTAGTG-CATATAAAAT-CAGCT
*
17550471 TGCACACTTAGTGC
1 CGCACACTTAGTGC
17550485 CATTCTCGTC
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
27 36 0.34
28 28 0.26
29 42 0.39
30 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCATATAAAATCAGCT
Found at i:17550402 original size:55 final size:55
Alignment explanation
Indices: 17550331--17550434 Score: 208
Period size: 55 Copynumber: 1.9 Consensus size: 55
17550321 ATAGTGAATC
17550331 CGCACACTTAGTGCTATAAAATCAGCTCGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATAAAATCAGCTCGCACACATAGTGCTATATAATCAAATT
17550386 CGCACACTTAGTGCTATAAAATCAGCTCGCACACATAGTGCTATATAAT
1 CGCACACTTAGTGCTATAAAATCAGCTCGCACACATAGTGCTATATAAT
17550435 TTGAGCTCGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTATAAAATCAGCTCGCACACATAGTGCTATATAATCAAATT
Found at i:17556719 original size:27 final size:27
Alignment explanation
Indices: 17556681--17556735 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
17556671 TTATTAGGTG
17556681 TGATTGGATCATCTCGAAATTTAATCA
1 TGATTGGATCATCTCGAAATTTAATCA
17556708 TGATTGGATCATCTCGAAATTTAATCA
1 TGATTGGATCATCTCGAAATTTAATCA
17556735 T
1 T
17556736 TTTAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (27 bp):
TGATTGGATCATCTCGAAATTTAATCA
Found at i:17562915 original size:24 final size:24
Alignment explanation
Indices: 17562830--17562980 Score: 87
Period size: 24 Copynumber: 6.2 Consensus size: 24
17562820 CATAATGTAG
*
17562830 TTTAAACTATTTTATATATTATTTAT
1 TTTAAA-TATTTT-TATATTGTTTAT
**
17562856 TTTAAA-CCTTTTATATTAG-TTAT
1 TTTAAATATTTTTATATT-GTTTAT
*** *
17562879 TTTAAACCGTTTTACATTGTTTAT
1 TTTAAATATTTTTATATTGTTTAT
* *
17562903 TTTAAATATTTTT-TGTTATTT-T
1 TTTAAATATTTTTATATTGTTTAT
* * * *
17562925 TTTAACTATTTTATATATTATTCAC
1 TTTAAATATTTT-TATATTGTTTAT
*
17562950 TTTAAAT-TTTTTATATAATATTTAT
1 TTTAAATATTTTTATAT--TGTTTAT
17562975 TTTAAA
1 TTTAAA
17562981 CTGTTTTTTA
Statistics
Matches: 99, Mismatches: 18, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
22 12 0.12
23 28 0.28
24 36 0.36
25 17 0.17
26 6 0.06
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (24 bp):
TTTAAATATTTTTATATTGTTTAT
Found at i:17562987 original size:28 final size:28
Alignment explanation
Indices: 17562956--17563021 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
17562946 TCACTTTAAA
*
17562956 TTTTTTATATA-ATATTTATTTTAAACTG
1 TTTTTTATATACAT-GTTATTTTAAACTG
* *
17562984 TTTTTTA-ATACATGTTATTTTGAATTG
1 TTTTTTATATACATGTTATTTTAAACTG
*
17563011 TTTTATATATA
1 TTTTTTATATA
17563022 TTAATTACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 20 0.62
28 12 0.38
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (28 bp):
TTTTTTATATACATGTTATTTTAAACTG
Found at i:17563226 original size:48 final size:48
Alignment explanation
Indices: 17563137--17563231 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
17563127 TTTTATATGG
* *
17563137 ATTATTTATTTTCAAATTTCTATTTATTGTTTATCTTAAACTCTTTATAC
1 ATTATTTATTTT-AAATTTCTATATATTATTTATCTTAAACT-TTTATAC
* * *
17563187 ATTATTTATTTT-ATTTTTTATATATTATTTATGTTAAACTTTTAT
1 ATTATTTATTTTAAATTTCTATATATTATTTATCTTAAACTTTTAT
17563232 TTTATTTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
47 5 0.12
48 23 0.57
50 12 0.30
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.62
Consensus pattern (48 bp):
ATTATTTATTTTAAATTTCTATATATTATTTATCTTAAACTTTTATAC
Found at i:17563231 original size:36 final size:36
Alignment explanation
Indices: 17563191--17563260 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
17563181 TTATACATTA
*
17563191 TTTATTTTATTTTTTATATATTATTTATGTTAAACT
1 TTTATTTTATTTTATATATATTATTTATGTTAAACT
* *
17563227 TTTATTTTATTTTATGTATATTATTTATTTTAAA
1 TTTATTTTATTTTATATATATTATTTATGTTAAA
17563261 TTTCTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (36 bp):
TTTATTTTATTTTATATATATTATTTATGTTAAACT
Found at i:17563237 original size:25 final size:23
Alignment explanation
Indices: 17563127--17563238 Score: 77
Period size: 25 Copynumber: 4.7 Consensus size: 23
17563117 TAAACTTCCT
17563127 TTTTATATGGATTATTTATTTTCAAA-
1 TTTTATAT--ATTATTTA-TTT-AAAC
* *
17563153 TTTCTATTTATTGTTTATCTTAAAC
1 TTT-TATATATTATTTAT-TTAAAC
* * **
17563178 TCTTTATACATTATTTATTTTATT
1 T-TTTATATATTATTTATTTAAAC
17563202 TTTTATATATTATTTATGTTAAAC
1 TTTTATATATTATTTAT-TTAAAC
17563226 TTTTAT-T-TTATTT
1 TTTTATATATTATTT
17563239 TATGTATATT
Statistics
Matches: 69, Mismatches: 12, Indels: 14
0.73 0.13 0.15
Matches are distributed among these distances:
22 6 0.09
23 16 0.23
24 17 0.25
25 21 0.30
26 5 0.07
27 4 0.06
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTTATATATTATTTATTTAAAC
Found at i:17563292 original size:25 final size:26
Alignment explanation
Indices: 17563245--17563295 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
17563235 ATTTTATGTA
17563245 TATTATTTATTTTAAATTTCTTTTTACG
1 TATTATTTATTTTAAA--TCTTTTTACG
*
17563273 TATTATTTATTTTAGA-CTTTTTA
1 TATTATTTATTTTAAATCTTTTTA
17563296 TTTTAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
28 15 0.68
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (26 bp):
TATTATTTATTTTAAATCTTTTTACG
Found at i:17563342 original size:25 final size:24
Alignment explanation
Indices: 17563292--17563351 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
17563282 TTTTAGACTT
*
17563292 TTTATTTTAAATTGTTTTGTATTA
1 TTTATTTTAAATTGCTTTGTATTA
*
17563316 TTTACTTTAAATTGCTTT-TATGGTA
1 TTTATTTTAAATTGCTTTGTAT--TA
17563341 TTTATTTTAAA
1 TTTATTTTAAA
17563352 CCTTTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.10
24 16 0.52
25 12 0.39
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (24 bp):
TTTATTTTAAATTGCTTTGTATTA
Found at i:17563780 original size:20 final size:20
Alignment explanation
Indices: 17563755--17563794 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
17563745 CGCGTTTTGG
17563755 AACATCGAGGAATTGTGCAC
1 AACATCGAGGAATTGTGCAC
17563775 AACATCGAGGAATTGTGCAC
1 AACATCGAGGAATTGTGCAC
17563795 TAACTTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (20 bp):
AACATCGAGGAATTGTGCAC
Found at i:17565435 original size:25 final size:25
Alignment explanation
Indices: 17565395--17565464 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
17565385 CTCTTTCTAT
*
17565395 TTGCA-TTCATCCCATGCATTTGCA
1 TTGCATTTCATCACATGCATTTGCA
*
17565419 TTGTATTTCATCACATGCATTTGCA
1 TTGCATTTCATCACATGCATTTGCA
17565444 TTGCATTTCATCACATGCATT
1 TTGCATTTCATCACATGCATT
17565465 AGATTTTCAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 4 0.10
25 38 0.90
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.41
Consensus pattern (25 bp):
TTGCATTTCATCACATGCATTTGCA
Found at i:17567256 original size:32 final size:32
Alignment explanation
Indices: 17567212--17567276 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
17567202 TGCCTAAGCT
17567212 ACTAAGACATGAGGATGCTATGGGGTGTTCGA
1 ACTAAGACATGAGGATGCTATGGGGTGTTCGA
*
17567244 ACTAAGATATGAGGATGCTATGGGGTGTTCGA
1 ACTAAGACATGAGGATGCTATGGGGTGTTCGA
17567276 A
1 A
17567277 AAGCACAGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (32 bp):
ACTAAGACATGAGGATGCTATGGGGTGTTCGA
Found at i:17569613 original size:45 final size:44
Alignment explanation
Indices: 17569564--17569771 Score: 140
Period size: 44 Copynumber: 4.8 Consensus size: 44
17569554 AAGATTGCAG
*
17569564 ATCTTGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGA
1 ATCTTGTCTCCCTAAAGTAGCAGTGGAACAGATCGAAGACAGC-A
* * ** ** * *
17569609 ATCTTGTCTCCCT-AACTAGTAGTGGAGTAGATTTAAGCCATC-
1 ATCTTGTCTCCCTAAAGTAGCAGTGGAACAGATCGAAGACAGCA
* * * * ** * *
17569651 ATCCTATCTCCCT-AAGCAGTAGTGGAGTAG-GCTGAAGATTA-CA
1 ATCTTGTCTCCCTAAAGTAGCAGTGGAACAGATC-GAAGA-CAGCA
*
17569694 GATCTTGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGA
1 -ATCTTGTCTCCCTAAAGTAGCAGTGGAACAGATCGAAGACAGC-A
* * *
17569740 ATCTTGTCTCCCT-AACTAGTAGTGGAGCAGAT
1 ATCTTGTCTCCCTAAAGTAGCAGTGGAACAGAT
17569772 TTAAGCCATC
Statistics
Matches: 124, Mismatches: 31, Indels: 17
0.72 0.18 0.10
Matches are distributed among these distances:
42 30 0.24
43 1 0.01
44 47 0.38
45 44 0.35
46 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (44 bp):
ATCTTGTCTCCCTAAAGTAGCAGTGGAACAGATCGAAGACAGCA
Found at i:17569672 original size:42 final size:43
Alignment explanation
Indices: 17569438--17570334 Score: 134
Period size: 42 Copynumber: 20.6 Consensus size: 43
17569428 TCATAGATCT
* * * *** * *
17569438 TATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGTGAATCT
1 TATCTCCCTAAGCAGTAGTGGAGTAGATTGAAG-CCATCAATCC
* * * * * * *
17569482 TGTCTTCCTAACCAGTAGTAGAGTAGATTTAAGCTA-CCATCC
1 TATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGCCATCAATCC
* * ** *
17569524 TACCTCCCTAAGCAGTAGTAGAGTAGGCTGAAG--ATTGCAGATCT
1 TATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGCCA-T-CA-ATCC
* ** * ** * * * *
17569568 TGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCT
1 TATCTCCCT-AAGCAGTAGTGGAGTAGATTGAAGCCATC-AATCC
* *
17569613 TGTCTCCCTAA-CTAGTAGTGGAGTAGATTTAAGCCATC-ATCC
1 TATCTCCCTAAGC-AGTAGTGGAGTAGATTGAAGCCATCAATCC
** *
17569655 TATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAG--ATTACAGATCT
1 TATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGCCA-T-CA-ATCC
* ** * ** * * * *
17569699 TGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCT
1 TATCTCCCT-AAGCAGTAGTGGAGTAGATTGAAGCCATC-AATCC
* * *
17569744 TGTCTCCCTAA-CTAGTAGTGGAGCAGATTTAAGCCATC-ATCC
1 TATCTCCCTAAGC-AGTAGTGGAGTAGATTGAAGCCATCAATCC
* * * * *
17569786 TATCTCCCTAAGCAATAGTGGAGTA-AGCTGAAG--ATTGTAGGTCT
1 TATCTCCCTAAGCAGTAGTGGAGTAGA-TTGAAGCCA-T-CA-ATCC
* * ** * * **** *
17569830 TGTCTTCCTGAAGTTGTAGTGGAGAAGATCGAAGCTGGAAATCT
1 TATCTCCCT-AAGCAGTAGTGGAGTAGATTGAAGCCATCAATCC
* * * * * *
17569874 TGTCTCCCTAACCAATAGTGGAGCAGATTTAAGCCA-CCATCC
1 TATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGCCATCAATCC
** *
17569916 TATCTCCCTAAGCAGTAGTGGAGTAGGCTAAAG--ATTACAGAT-C
1 TATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGCCA-T-CA-ATCC
* ** * ** * * * *
17569959 TCGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGGCAGCGAATCT
1 T-ATCTCCCT-AAGCAGTAGTGGAGTAGATTGAAGCCATC-AATCC
* * * * *
17570005 TGTCTCCCTAACCAGTAGTGGAGTAGATTTAATCCA-CCATCC
1 TATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGCCATCAATCC
* ** * *
17570047 TATCTCCCTAAGCAGTAATGGAGTAGGCTAAAG--ATTGCAGATCT
1 TATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGCCA-T-CA-ATCC
* ** * ** * *** * *
17570091 TGTCTCCCTTAAGTTGCAG-GAGAACAGATCGAAGATGGTGAATCT
1 TATCTCCC-TAAGCAGTAGTG-GAGTAGATTGAAG-CCATCAATCC
* * * * *
17570136 TGTCTCCCTAACCAGTAGTGGAGCAGATTTAAGCCA-CCATCC
1 TATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGCCATCAATCC
* ** *
17570178 TATCTTCCTAAGCAGTAGTGGAGTAGGCTGAA--TATTGCAAAT-C
1 TATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGCCA-T-C-AATCC
* ** * * * ** * **
17570221 TCGTCTCCCTAGAGGTGCAGTGGAATAGATCGAAGACGGTGAATTT
1 T-ATCTCCCTA-AGCAGTAGTGGAGTAGATTGAAG-CCATCAATCC
** * *
17570267 TATCTCCCTAAGCAGTAGTGGAACAGATTTAAGCCA-CCATCC
1 TATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGCCATCAATCC
17570309 TATCTCCCTAAGCAGTAGTGGAGTAG
1 TATCTCCCTAAGCAGTAGTGGAGTAG
17570335 GCTGAAGATT
Statistics
Matches: 588, Mismatches: 206, Indels: 120
0.64 0.23 0.13
Matches are distributed among these distances:
40 6 0.01
41 3 0.01
42 199 0.34
43 30 0.05
44 184 0.31
45 154 0.26
46 7 0.01
47 5 0.01
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (43 bp):
TATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGCCATCAATCC
Found at i:17570201 original size:392 final size:392
Alignment explanation
Indices: 17569440--17570402 Score: 1389
Period size: 392 Copynumber: 2.5 Consensus size: 392
17569430 ATAGATCTTA
* * * * *
17569440 TCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGTGAATCTTGTCTTCCTAACCAGTAGTAGAG
1 TCTCCCTAAGTTGTAGTGGAGAAGATCGAAGCTGGTGAATCTTGTCTCCCTAACCAGTAGTGGAG
* * * *
17569505 TAGATTTAAGCTACCATCCTACCTCCCTAAGCAGTAGTAGAGTAGGCTGAAGATTGCAGATCTTG
66 CAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATCTTG
* *
17569570 TCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACTAGTAGTGGA
131 TCTCCCTAAAGTTGCAGTGGAACAGATCGAAGGCAGCGAATCTTGTCTCCCTAACCAGTAGTGGA
* * *
17569635 GTAGATTTAAGCCATCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTACAGATCTT
196 GTAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAATGGAGTAGGCTAAAGATTACAGATCTT
*
17569700 GTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACTAGTAGTGG
261 GTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACCAGTAGTGG
* * **
17569765 AGCAGATTTAAGCCATCATCCTATCTCCCTAAGCAATAGTGGAGTAAGCTGAAGATTGTAGGTCT
326 AGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAATAGTGGAGTAAGCTGAAGATTGCAAATCT
*
17569830 TG
391 CG
* * *
17569832 TCTTCCTGAAGTTGTAGTGGAGAAGATCGAAGCTGG-AAATCTTGTCTCCCTAACCAATAGTGGA
1 TCTCCCT-AAGTTGTAGTGGAGAAGATCGAAGCTGGTGAATCTTGTCTCCCTAACCAGTAGTGGA
* * *
17569896 GCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGATTACAGATCTC
65 GCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATCTT
17569961 GTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGGCAGCGAATCTTGTCTCCCTAACCAGTAGTGG
130 GTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGGCAGCGAATCTTGTCTCCCTAACCAGTAGTGG
* *
17570026 AGTAGATTTAATCCACCATCCTATCTCCCTAAGCAGTAATGGAGTAGGCTAAAGATTGCAGATCT
195 AGTAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAATGGAGTAGGCTAAAGATTACAGATCT
* ** *
17570091 TGTCTCCCTTAAGTTGCAG-GAGAACAGATCGAAGATGGTGAATCTTGTCTCCCTAACCAGTAGT
260 TGTCTCCCTAAAGTTGCAGTG-GAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACCAGTAGT
* * * *
17570155 GGAGCAGATTTAAGCCACCATCCTATCTTCCTAAGCAGTAGTGGAGTAGGCTGAATATTGCAAAT
324 GGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAATAGTGGAGTAAGCTGAAGATTGCAAAT
17570220 CTCG
389 CTCG
* * * * *
17570224 TCTCCCTAGAGGTGCAGTGGA-ATAGATCGAAGAC-GGTGAATTTTATCTCCCTAAGCAGTAGTG
1 TCTCCCTA-AGTTGTAGTGGAGA-AGATCGAAG-CTGGTGAATCTTGTCTCCCTAACCAGTAGTG
* *
17570287 GAACAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGTAGATC
63 GAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATC
* * * * * *
17570352 TTGTCTCTCTGAAGTTGCAGTAGAGA-AGATC-AAAGCCGCAAATCTTGTCTC
128 TTGTCTCCCTAAAGTTGCAGTGGA-ACAGATCGAAGGCAGCGAATCTTGTCTC
17570403 TTTGAAATTG
Statistics
Matches: 509, Mismatches: 55, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
391 3 0.01
392 372 0.73
393 133 0.26
394 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (392 bp):
TCTCCCTAAGTTGTAGTGGAGAAGATCGAAGCTGGTGAATCTTGTCTCCCTAACCAGTAGTGGAG
CAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATCTTG
TCTCCCTAAAGTTGCAGTGGAACAGATCGAAGGCAGCGAATCTTGTCTCCCTAACCAGTAGTGGA
GTAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAATGGAGTAGGCTAAAGATTACAGATCTT
GTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACCAGTAGTGG
AGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAATAGTGGAGTAAGCTGAAGATTGCAAATCT
CG
Found at i:17570426 original size:131 final size:131
Alignment explanation
Indices: 17569432--17570402 Score: 1317
Period size: 131 Copynumber: 7.4 Consensus size: 131
17569422 GTGAATTCAT
* * * * ** * *
17569432 AGATCTTATCTCCCT-AAGTAGTAGTGGAGCAGATCGAAGATGGTGAATCTTGTCTTCCTAACCA
1 AGATCTTGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACCA
* * * * *
17569496 GTAGTAGAGTAGATTTAAGCTACCATCCTACCTCCCTAAGCAGTAGTAGAGTAGGCTGAAGATTG
66 GTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTG
17569561 C
131 C
*
17569562 AGATCTTGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACTA
1 AGATCTTGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACCA
* * *
17569627 GTAGTGGAGTAGATTTAAGCCATCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTA
66 GTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTG
17569692 C
131 C
*
17569693 AGATCTTGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACTA
1 AGATCTTGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACCA
* * *
17569758 GTAGTGGAGCAGATTTAAGCCATCATCCTATCTCCCTAAGCAATAGTGGAGTAAGCTGAAGATTG
66 GTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTG
*
17569823 T
131 C
* * * * *
17569824 AGGTCTTGTCTTCCTGAAGTTGTAGTGGAGA-AGATCGAAG-CTG-GAAATCTTGTCTCCCTAAC
1 AGATCTTGTCTCCCTAAAGTTGCAGTGGA-ACAGATCGAAGACAGCG-AATCTTGTCTCCCTAAC
* *
17569886 CAATAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTAAAGAT
64 CAGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGAT
*
17569951 TAC
129 TGC
* *
17569954 AGATCTCGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGGCAGCGAATCTTGTCTCCCTAACCA
1 AGATCTTGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACCA
* * * *
17570019 GTAGTGGAGTAGATTTAATCCACCATCCTATCTCCCTAAGCAGTAATGGAGTAGGCTAAAGATTG
66 GTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTG
17570084 C
131 C
* ** *
17570085 AGATCTTGTCTCCCTTAAGTTGCAG-GAGAACAGATCGAAGATGGTGAATCTTGTCTCCCTAACC
1 AGATCTTGTCTCCCTAAAGTTGCAGTG-GAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACC
* *
17570149 AGTAGTGGAGCAGATTTAAGCCACCATCCTATCTTCCTAAGCAGTAGTGGAGTAGGCTGAATATT
65 AGTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATT
17570214 GC
130 GC
* * * * * * * * * *
17570216 AAATCTCGTCTCCCTAGAGGTGCAGTGGAATAGATCGAAGACGGTGAATTTTATCTCCCTAAGCA
1 AGATCTTGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACCA
*
17570281 GTAGTGGAACAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTG
66 GTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTG
*
17570346 T
131 C
* * * * * *
17570347 AGATCTTGTCTCTCTGAAGTTGCAGTAGAGA-AGATCAAAG-CCGCAAATCTTGTCTC
1 AGATCTTGTCTCCCTAAAGTTGCAGTGGA-ACAGATCGAAGACAGCGAATCTTGTCTC
17570403 TTTGAAATTG
Statistics
Matches: 749, Mismatches: 83, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
129 2 0.00
130 138 0.18
131 605 0.81
132 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (131 bp):
AGATCTTGTCTCCCTAAAGTTGCAGTGGAACAGATCGAAGACAGCGAATCTTGTCTCCCTAACCA
GTAGTGGAGCAGATTTAAGCCACCATCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTG
C
Found at i:17570454 original size:88 final size:88
Alignment explanation
Indices: 17570347--17570552 Score: 204
Period size: 88 Copynumber: 2.3 Consensus size: 88
17570337 TGAAGATTGT
* * * * **
17570347 AGATCTTGTCTCTCTGAAGTTGCAGTAGAGAAGATCAAAGCCGCAAATCTTGT-CTCTTTGAAAT
1 AGATCTTATCTCCCTGAAGTTGCAGTAGAGAAGATCAAAGCCACAAATCTTATAC-CCCTGAAAT
*
17570411 TGC-AGTGGAGCAGATTGAAG-TTA
65 TGCAAG-AGAGCAGATTGAAGTTTA
* * * * * *
17570434 CGAATCTTATCTCCCTGAAGTTGCGGT-GAAGCAGATTAAAGCCACAAGTCTTATACCCCTGAAG
1 AG-ATCTTATCTCCCTGAAGTTGCAGTAG-AGAAGATCAAAGCCACAAATCTTATACCCCTGAAA
17570498 TTGCAAGAGAGCAGATTGAAGTTTA
64 TTGCAAGAGAGCAGATTGAAGTTTA
* * *
17570523 AGACCTTATCTCCTTAAAGTTGCAGTAGAG
1 AGATCTTATCTCCCTGAAGTTGCAGTAGAG
17570553 CAGACTGAAG
Statistics
Matches: 95, Mismatches: 18, Indels: 11
0.77 0.15 0.09
Matches are distributed among these distances:
87 2 0.02
88 85 0.89
89 8 0.08
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (88 bp):
AGATCTTATCTCCCTGAAGTTGCAGTAGAGAAGATCAAAGCCACAAATCTTATACCCCTGAAATT
GCAAGAGAGCAGATTGAAGTTTA
Found at i:17570486 original size:44 final size:43
Alignment explanation
Indices: 17570349--17570502 Score: 123
Period size: 44 Copynumber: 3.5 Consensus size: 43
17570339 AAGATTGTAG
* * * * *
17570349 ATCTTGTCTCTCTGAAGTTGCAGT-AGAGAAGATCAAAGCCGCAA
1 ATCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTAAAGCCAC-A
* ** * * * **
17570393 ATCTTGTCTCTTTGAAATTGCAGTGGAGCAGATTGAAGTTACGA
1 ATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCAC-A
*
17570437 ATCTTATCTCCCTGAAGTTGCGGTGAAGCAGATTAAAGCCACA
1 ATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCACA
17570480 AGTCTTATAC-CCCTGAAGTTGCA
1 A-TCTTAT-CTCCCTGAAGTTGCA
17570503 AGAGAGCAGA
Statistics
Matches: 87, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
43 2 0.02
44 84 0.97
45 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCACA
Found at i:17572057 original size:51 final size:51
Alignment explanation
Indices: 17572002--17572143 Score: 139
Period size: 51 Copynumber: 2.8 Consensus size: 51
17571992 CCTGTTTCAT
* *
17572002 TACATACTATTTTAAATTATTTTACATATTATTTATTTTAAGTTT-TTTATA
1 TACATACTATTTTAAA-TATTTTACATATTATTTATTTTAAGTTTATGTACA
* * *
17572053 TACATTATTTATTTTAAA-CTTTTACATATTATATATTTTAAGTTTATGTACA
1 TACA-TA-CTATTTTAAATATTTTACATATTATTTATTTTAAGTTTATGTACA
* * * *
17572105 TA-AT-GTAGTTTAAACTATTTTATATATTAGTTATTTTAA
1 TACATACTATTTTAAA-TATTTTACATATTATTTATTTTAA
17572144 ACCGTTTTAC
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
48 8 0.11
50 20 0.27
51 30 0.40
52 8 0.11
53 9 0.12
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.56
Consensus pattern (51 bp):
TACATACTATTTTAAATATTTTACATATTATTTATTTTAAGTTTATGTACA
Found at i:17572089 original size:24 final size:25
Alignment explanation
Indices: 17572021--17572094 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 25
17572011 TTTTAAATTA
**
17572021 TTTTACATATTATTTATTTTAAGTT
1 TTTTACATATTATTTATTTTAAGAC
*
17572046 TTTTATATACATTATTTATTTTAA-AC
1 TTTTACAT--ATTATTTATTTTAAGAC
*
17572072 TTTTACATATTATATATTTTAAG
1 TTTTACATATTATTTATTTTAAG
17572095 TTTATGTACA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
24 13 0.32
25 7 0.17
26 7 0.17
27 14 0.34
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (25 bp):
TTTTACATATTATTTATTTTAAGAC
Found at i:17572175 original size:24 final size:24
Alignment explanation
Indices: 17572113--17572175 Score: 56
Period size: 24 Copynumber: 2.5 Consensus size: 24
17572103 CATAATGTAG
*
17572113 TTTAAACTATTTTATATATTAGTTAT
1 TTTAAA-TATTTT-TACATTAGTTAT
***
17572139 TTTAAACCGTTTTACATT-GTTTAT
1 TTTAAATATTTTTACATTAG-TTAT
17572163 TTTAAATATTTTT
1 TTTAAATATTTTT
17572176 TTGTTATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
23 1 0.03
24 19 0.66
25 3 0.10
26 6 0.21
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.59
Consensus pattern (24 bp):
TTTAAATATTTTTACATTAGTTAT
Found at i:17572221 original size:24 final size:24
Alignment explanation
Indices: 17572194--17572240 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
17572184 TTTTTAACTA
*
17572194 TTTTATATATTATTCACTTTAAAT
1 TTTTATATAATATTCACTTTAAAT
* *
17572218 TTTTATATAATATTTATTTTAAA
1 TTTTATATAATATTCACTTTAAA
17572241 CTGTTTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTATATAATATTCACTTTAAAT
Found at i:17572497 original size:35 final size:35
Alignment explanation
Indices: 17572455--17572522 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
17572445 TTATACATTA
*
17572455 TTTATTTTATTTTTATATATTATTTATGTTAAACT
1 TTTATTTTATTTATATATATTATTTATGTTAAACT
* *
17572490 TTTATTTTATTTATGTATATTATTTATTTTAAA
1 TTTATTTTATTTATATATATTATTTATGTTAAA
17572523 TTTCTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.66
Consensus pattern (35 bp):
TTTATTTTATTTATATATATTATTTATGTTAAACT
Found at i:17572538 original size:28 final size:30
Alignment explanation
Indices: 17572506--17572565 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 30
17572496 TTATTTATGT
17572506 ATATTATTTATTTTA-AATTTCT-TTTTAA
1 ATATTATTTATTTTAGAATTTCTATTTTAA
*
17572534 ATATTATTTATTTTAGAATTTTTATTTTAA
1 ATATTATTTATTTTAGAATTTCTATTTTAA
17572564 AT
1 AT
17572566 TGTTTGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 15 0.52
29 6 0.21
30 8 0.28
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (30 bp):
ATATTATTTATTTTAGAATTTCTATTTTAA
Found at i:17572589 original size:65 final size:63
Alignment explanation
Indices: 17572464--17572594 Score: 163
Period size: 65 Copynumber: 2.0 Consensus size: 63
17572454 ATTTATTTTA
* * * *
17572464 TTTTTATATATTATTTATGTTAAACTTTTATTTTATTTATGTATATTATTTATTTTAAATTTC
1 TTTTTAAATATTATTTATGTTAAACTTTTATTTTAATTATGTATATTATTTACTTTAAATTAC
* * * * *
17572527 TTTTTAAATATTATTTATTTTAGAATTTTTATTTTAAATTGTTTGTATTATTTACTTTAAATTAC
1 TTTTTAAATATTATTTATGTTA-AACTTTTATTTT-AATTATGTATATTATTTACTTTAAATTAC
17572592 TTT
1 TTT
17572595 ATGGTATTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 20 0.35
64 11 0.19
65 26 0.46
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (63 bp):
TTTTTAAATATTATTTATGTTAAACTTTTATTTTAATTATGTATATTATTTACTTTAAATTAC
Found at i:17572609 original size:24 final size:23
Alignment explanation
Indices: 17572554--17572611 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
17572544 TTTTAGAATT
**
17572554 TTTATTTTAAATTGTTTGTATTA
1 TTTATTTTAAATTACTTGTATTA
*
17572577 TTTACTTTAAATTACTT-TATGGTA
1 TTTATTTTAAATTACTTGTAT--TA
17572601 TTTATTTTAAA
1 TTTATTTTAAA
17572612 CCTTTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 3 0.10
23 14 0.48
24 12 0.41
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.60
Consensus pattern (23 bp):
TTTATTTTAAATTACTTGTATTA
Found at i:17572864 original size:8 final size:8
Alignment explanation
Indices: 17572851--17572875 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
17572841 ATTTATATTT
17572851 TCGTATCA
1 TCGTATCA
17572859 TCGTATCA
1 TCGTATCA
17572867 TCGTATCA
1 TCGTATCA
17572875 T
1 T
17572876 AAATTTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (8 bp):
TCGTATCA
Found at i:17575204 original size:21 final size:21
Alignment explanation
Indices: 17575174--17575214 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17575164 CGTTACTTTG
*
17575174 GTTTAATGATTTTGA-AAATC
1 GTTTAATGATATTGAGAAATC
17575194 GTTTATATGATATTGAGAAAT
1 GTTTA-ATGATATTGAGAAAT
17575215 GGTATAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (21 bp):
GTTTAATGATATTGAGAAATC
Found at i:17577559 original size:5 final size:5
Alignment explanation
Indices: 17577549--17577580 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
17577539 AATTGTGTTC
17577549 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
17577581 TTCACAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:17577563 original size:9 final size:9
Alignment explanation
Indices: 17577549--17577579 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
17577539 AATTGTGTTC
17577549 TTTATTTTA
1 TTTATTTTA
17577558 TTTATTTTA
1 TTTATTTTA
17577567 TTTTATTTTA
1 -TTTATTTTA
17577577 TTT
1 TTT
17577580 TTTCACAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:17582007 original size:5 final size:5
Alignment explanation
Indices: 17581997--17582028 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
17581987 TTGTGTGTTC
17581997 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
17582029 TTCACAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:17582011 original size:9 final size:9
Alignment explanation
Indices: 17581997--17582027 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
17581987 TTGTGTGTTC
17581997 TTTATTTTA
1 TTTATTTTA
17582006 TTTATTTTA
1 TTTATTTTA
17582015 TTTTATTTTA
1 -TTTATTTTA
17582025 TTT
1 TTT
17582028 TTTCACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:17584459 original size:19 final size:19
Alignment explanation
Indices: 17584435--17584483 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
17584425 TTTTTGGGCT
17584435 TAATGGGCCAAAAACGGGA
1 TAATGGGCCAAAAACGGGA
17584454 TAATGGGCCAAAAACGGGA
1 TAATGGGCCAAAAACGGGA
17584473 TAATGGGCCAA
1 TAATGGGCCAA
17584484 CGGGCCCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.31, T:0.12
Consensus pattern (19 bp):
TAATGGGCCAAAAACGGGA
Found at i:17584764 original size:27 final size:27
Alignment explanation
Indices: 17584726--17584854 Score: 90
Period size: 27 Copynumber: 4.8 Consensus size: 27
17584716 AAGCGTCCTG
*
17584726 GTGGCTATGCCACAATTATCTGATCTA
1 GTGGCTCTGCCACAATTATCTGATCTA
17584753 GTGGCTCTGCCAC-ATATATCTG-TCCTTA
1 GTGGCTCTGCCACAAT-TATCTGAT-C-TA
* * * *
17584781 -TGGTTATGCCAC-ATATATCTGTTCTG
1 GTGGCTCTGCCACAAT-TATCTGATCTA
*
17584807 GTGGCTCTGCCACAA-TATCTGTATCTG
1 GTGGCTCTGCCACAATTATCTG-ATCTA
* * *
17584834 GTGACTCCGTCACAA-TATCTG
1 GTGGCTCTGCCACAATTATCTG
17584855 GTAGCCTCGC
Statistics
Matches: 85, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
26 10 0.12
27 71 0.84
28 4 0.05
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (27 bp):
GTGGCTCTGCCACAATTATCTGATCTA
Found at i:17591020 original size:46 final size:46
Alignment explanation
Indices: 17590970--17591142 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
17590960 TGGTTGAGCA
*
17590970 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
17591016 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
17591063 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
17591109 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
17591143 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:17591126 original size:93 final size:93
Alignment explanation
Indices: 17590967--17591137 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
17590957 GGATGGTTGA
* *
17590967 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
17591032 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
17591060 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
17591125 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
17591138 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:17598592 original size:46 final size:46
Alignment explanation
Indices: 17598542--17598714 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
17598532 TGGTTGAGCA
*
17598542 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
17598588 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
17598635 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
17598681 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
17598715 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:17598698 original size:93 final size:93
Alignment explanation
Indices: 17598539--17598709 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
17598529 GGATGGTTGA
* *
17598539 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
17598604 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
17598632 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
17598697 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
17598710 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:17609699 original size:24 final size:24
Alignment explanation
Indices: 17609672--17609734 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
17609662 ACCTAGAAAG
* * *
17609672 CAATAGAAACACAAACCCATATAT
1 CAATAGAAACGCAAACCCACAAAT
* * *
17609696 CAATAAAAATGCAAACTCACAAAT
1 CAATAGAAACGCAAACCCACAAAT
17609720 CAATAGAAACGCAAA
1 CAATAGAAACGCAAA
17609735 ATCACAAACC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.57, C:0.22, G:0.06, T:0.14
Consensus pattern (24 bp):
CAATAGAAACGCAAACCCACAAAT
Found at i:17609739 original size:24 final size:24
Alignment explanation
Indices: 17609694--17609742 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
17609684 AAACCCATAT
* *
17609694 ATCAATAAAAATGCAAACTCACAA
1 ATCAATAAAAACGCAAAATCACAA
*
17609718 ATCAATAGAAACGCAAAATCACAA
1 ATCAATAAAAACGCAAAATCACAA
17609742 A
1 A
17609743 CCTTGAAGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.59, C:0.20, G:0.06, T:0.14
Consensus pattern (24 bp):
ATCAATAAAAACGCAAAATCACAA
Found at i:17610748 original size:19 final size:19
Alignment explanation
Indices: 17610711--17610748 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
17610701 TTATATAGAT
*
17610711 ATTTATAAATTAATTTATA
1 ATTTATAAATTAATATATA
17610730 ATTTAT-AATTAAATATATA
1 ATTTATAAATT-AATATATA
17610749 TTAATATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTATAAATTAATATATA
Found at i:17612390 original size:24 final size:26
Alignment explanation
Indices: 17612345--17612395 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
17612335 AACAATTTAT
17612345 TTATATAGATAAAATGAAAATTATATAA
1 TTATATAGATAAAAT--AAATTATATAA
17612373 TTATATA-ATAAAAT-AATTATATA
1 TTATATAGATAAAATAAATTATATA
17612396 TATATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.39
27 7 0.30
28 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (26 bp):
TTATATAGATAAAATAAATTATATAA
Found at i:17612407 original size:16 final size:15
Alignment explanation
Indices: 17612366--17612408 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
17612356 AAATGAAAAT
17612366 TATATAATTATATAA
1 TATATAATTATATAA
*
17612381 TAAAATAATTATATATA
1 T-ATATAATTATATA-A
*
17612398 TATATTATTAT
1 TATATAATTAT
17612409 GTTAAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 1 0.04
16 20 0.87
17 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATAATTATATAA
Found at i:17612572 original size:19 final size:17
Alignment explanation
Indices: 17612531--17612574 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
17612521 TTTTAATATT
17612531 ATAAAAATAATTATTTC
1 ATAAAAATAATTATTTC
* *
17612548 AAAAAAATAAATATTTTTC
1 ATAAAAAT-AAT-TATTTC
17612567 ATAAAAAT
1 ATAAAAAT
17612575 TATATATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 7 0.32
18 3 0.14
19 12 0.55
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAAAATAATTATTTC
Found at i:17612579 original size:18 final size:19
Alignment explanation
Indices: 17612531--17612579 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
17612521 TTTTAATATT
17612531 ATAAAAA-TA-ATTATTTC
1 ATAAAAATTATATTATTTC
* *
17612548 AAAAAAATAAATATT-TTTC
1 ATAAAAAT-TATATTATTTC
17612567 ATAAAAATTATAT
1 ATAAAAATTATAT
17612580 ATAAAGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
17 6 0.24
18 4 0.16
19 12 0.48
20 3 0.12
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAAAAATTATATTATTTC
Found at i:17612658 original size:56 final size:54
Alignment explanation
Indices: 17612589--17612711 Score: 185
Period size: 54 Copynumber: 2.2 Consensus size: 54
17612579 TATAAAGAAA
17612589 AATATATCAAAAAAATTAATTGATGT-TTTTAAAAAATAAAATATATTTAATATAAT
1 AATATAT-AAAAAAATTAATTGATGTATTTT-AAAAAT-AAATATATTTAATATAAT
* *
17612645 AATATATAGAAAAATTAGTTGATGTATTTTAAAAATAAATATATTTAATATAAT
1 AATATATAAAAAAATTAATTGATGTATTTTAAAAATAAATATATTTAATATAAT
*
17612699 CATATATAAAAAA
1 AATATATAAAAAA
17612712 TTATTTCATT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
54 29 0.47
55 22 0.35
56 11 0.18
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (54 bp):
AATATATAAAAAAATTAATTGATGTATTTTAAAAATAAATATATTTAATATAAT
Found at i:17616969 original size:140 final size:140
Alignment explanation
Indices: 17616717--17616995 Score: 540
Period size: 140 Copynumber: 2.0 Consensus size: 140
17616707 TTTCATAGAT
17616717 TGTCTATTTGTTCCCCAAGATCAGTAGTTCTTAACGTATTTCAACTTCAATTTTAGGCTTCTCCC
1 TGTCTATTTGTTCCCCAAGATCAGTAGTTCTTAACGTATTTCAACTTCAATTTTAGGCTTCTCCC
*
17616782 ATTTTAAAGTTTTCCTGATATAACTGTCATTTAGATTTGGTGTTTCCATTAGAGTAACTAAAACA
66 ATTTTAAAGTTTTCCTGATATAACTGTCATTTAGATTTGGTGTTTCCATTAAAGTAACTAAAACA
17616847 TAGTTATTGG
131 TAGTTATTGG
17616857 TGTCTATTTGTTCCCCAAGATCAGTAGTTCTTAACGTATTTCAACTTCAATTTTAGGCTTCTCCC
1 TGTCTATTTGTTCCCCAAGATCAGTAGTTCTTAACGTATTTCAACTTCAATTTTAGGCTTCTCCC
*
17616922 ATTTTAAAGTTTTCCTGATATAGCTGTCATTTAGATTTGGTGTTTCCATTAAAGTAACTAAAACA
66 ATTTTAAAGTTTTCCTGATATAACTGTCATTTAGATTTGGTGTTTCCATTAAAGTAACTAAAACA
17616987 TAGTTATTG
131 TAGTTATTG
17616996 TTGGTCAAAA
Statistics
Matches: 137, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (140 bp):
TGTCTATTTGTTCCCCAAGATCAGTAGTTCTTAACGTATTTCAACTTCAATTTTAGGCTTCTCCC
ATTTTAAAGTTTTCCTGATATAACTGTCATTTAGATTTGGTGTTTCCATTAAAGTAACTAAAACA
TAGTTATTGG
Found at i:17622891 original size:2 final size:2
Alignment explanation
Indices: 17622884--17622919 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17622874 AAATAGTTTA
17622884 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17622920 TAAGAGAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17628315 original size:24 final size:24
Alignment explanation
Indices: 17628269--17628324 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
17628259 AGGTCATATC
*
17628269 TTTAAAAATAATATATTTTAAATAA
1 TTTAAAAATAATATATTTAAAAT-A
*
17628294 TTTAAAAATTATA-ATTTAAAATA
1 TTTAAAAATAATATATTTAAAATA
17628317 TTGTAAAA
1 TT-TAAAA
17628325 CAACTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 3 0.11
24 13 0.46
25 12 0.43
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TTTAAAAATAATATATTTAAAATA
Found at i:17628424 original size:21 final size:20
Alignment explanation
Indices: 17628400--17628461 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
17628390 ATTTAAATGT
17628400 TTTATATTATTAAAAAATATA
1 TTTA-ATTATTAAAAAATATA
17628421 TTTAA-TATTTAAAAAATAATA
1 TTTAATTA-TTAAAAAAT-ATA
17628442 TTTAAAATT-TTAAAAAATAT
1 TTT--AATTATTAAAAAATAT
17628462 TAAAAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
19 2 0.06
20 10 0.28
21 12 0.33
22 9 0.25
23 2 0.06
24 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAATTATTAAAAAATATA
Found at i:17628428 original size:22 final size:21
Alignment explanation
Indices: 17628403--17628461 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 21
17628393 TAAATGTTTT
17628403 ATATTATTAAAAAATATATTTA
1 ATATT-TTAAAAAATATATTTA
17628425 ATA-TTTAAAAAATAATATTTA
1 ATATTTTAAAAAAT-ATATTTA
*
17628446 AAATTTTAAAAAATAT
1 ATATTTTAAAAAATAT
17628462 TAAAAAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 9 0.26
21 12 0.35
22 13 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATTTTAAAAAATATATTTA
Found at i:17628457 original size:23 final size:20
Alignment explanation
Indices: 17628409--17628531 Score: 92
Period size: 20 Copynumber: 6.7 Consensus size: 20
17628399 TTTTATATTA
*
17628409 TTAAAAAATATATTTAATAT
1 TTAAAAAATATATTTAAAAT
17628429 TTAAAAAATAATATTTAAAAT
1 TTAAAAAAT-ATATTTAAAAT
*
17628450 TTTAAAAA-ATA-TT-AAA-
1 TTAAAAAATATATTTAAAAT
*
17628466 --AAATAATA-ATTTAAAAT
1 TTAAAAAATATATTTAAAAT
17628483 TTAGAAAAATA-ATTT--AA-
1 TTA-AAAAATATATTTAAAAT
*
17628500 --AAAATATATATTTAAAAT
1 TTAAAAAATATATTTAAAAT
17628518 TTAAAAATATATAT
1 TTAAAAA-ATATAT
17628532 ATTATAAAAC
Statistics
Matches: 81, Mismatches: 7, Indels: 29
0.69 0.06 0.25
Matches are distributed among these distances:
14 11 0.14
15 8 0.10
16 3 0.04
17 5 0.06
18 4 0.05
19 4 0.05
20 23 0.28
21 23 0.28
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (20 bp):
TTAAAAAATATATTTAAAAT
Found at i:17628459 original size:113 final size:113
Alignment explanation
Indices: 17628226--17628475 Score: 278
Period size: 113 Copynumber: 2.2 Consensus size: 113
17628216 AATTATATTA
*
17628226 TTAAAATATTATAAAACAAATAATAAATTTGAAAGGTCATATCTTTAAAAATAATATATTTTAAA
1 TTAAAATATTAT-AAACTAATAATAAATTTGAAAGGTCATATCTTTAAAAATAATATATTTTAAA
* ** *
17628291 TAATTTAAAAATTATAATTTAAAATATTGTAAAACAACTTAAATAATAT
65 TAATTTAAAAAATATAATTTAAAATATTAAAAAACAAATTAAATAATAT
*
17628340 TTAAAATATTATAAACTAATAATAAATTTGAAAGGTCATATCTTTAAAATATTTAA-ATGTTTTA
1 TTAAAATATTATAAACTAATAATAAATTTGAAAGGTCATATCTTTAAAA-A--TAATATATTTTA
* * * * *
17628404 TATTA-TTAAAAAATAT-ATTTAATAT-TTAAAAAATAATATTTAA-AAT-T
63 AATAATTTAAAAAATATAATTTAAAATATTAAAAAACAA-ATTAAATAATAT
* *
17628451 TTAAAAAATATTAAAAAATAATAAT
1 TT--AAAATATTATAAACTAATAAT
17628476 TTAAAATTTA
Statistics
Matches: 117, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
111 3 0.03
112 11 0.09
113 67 0.57
114 23 0.20
115 10 0.09
116 3 0.03
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (113 bp):
TTAAAATATTATAAACTAATAATAAATTTGAAAGGTCATATCTTTAAAAATAATATATTTTAAAT
AATTTAAAAAATATAATTTAAAATATTAAAAAACAAATTAAATAATAT
Found at i:17628468 original size:33 final size:32
Alignment explanation
Indices: 17628424--17628529 Score: 151
Period size: 35 Copynumber: 3.2 Consensus size: 32
17628414 AAATATATTT
17628424 AATATTTAAAAAATAATATTTAAAATTTTAAAA
1 AATATTTAAAAAATAATATTTAAAA-TTTAAAA
17628457 AATA-TTAAAAAATAATAATTTAAAATTTAGAAA
1 AATATTTAAAAAATAAT-ATTTAAAATTTA-AAA
17628490 AATAATTTAAAAAATATATATTTAAAATTTAAAA
1 AAT-ATTTAAAAAATA-ATATTTAAAATTTAAAA
17628524 ATATAT
1 A-ATAT
17628530 ATATTATAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 11
0.86 0.00 0.14
Matches are distributed among these distances:
32 16 0.24
33 18 0.27
34 7 0.10
35 24 0.36
36 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (32 bp):
AATATTTAAAAAATAATATTTAAAATTTAAAA
Found at i:17628532 original size:23 final size:23
Alignment explanation
Indices: 17628411--17628540 Score: 89
Period size: 22 Copynumber: 5.8 Consensus size: 23
17628401 TTATATTATT
*
17628411 AAAAA-ATATATT-TAATATTTA
1 AAAAATATATATTATAAAATTTA
17628432 AAAAATA-ATATT-TAAAATTTTA
1 AAAAATATATATTATAAAA-TTTA
* **
17628454 AAAAATATTAAAAAATAATAATTT-
1 AAAAATA-TATATTATAA-AATTTA
** *
17628478 -AAAAT-T-TAGAAAAATAATTTA
1 AAAAATATATATTATAA-AATTTA
17628499 AAAAATATATATT-TAAAATTTA
1 AAAAATATATATTATAAAATTTA
17628521 AAAATATATATATTATAAAA
1 AAAA-ATATATATTATAAAA
17628541 CATTTCAAAT
Statistics
Matches: 87, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
20 11 0.13
21 15 0.17
22 27 0.31
23 17 0.20
24 9 0.10
25 6 0.07
26 2 0.02
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.38
Consensus pattern (23 bp):
AAAAATATATATTATAAAATTTA
Found at i:17628603 original size:14 final size:14
Alignment explanation
Indices: 17628578--17628629 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
17628568 TAAATTAATC
17628578 ATAAAAAAATAAA-
1 ATAAAAAAATAAAG
17628591 ATAAAATAAATAAAG
1 ATAAAA-AAATAAAG
* *
17628606 ATAAAAGACA-AAAC
1 ATAAAA-AAATAAAG
17628620 ATAAAAAAAT
1 ATAAAAAAAT
17628630 TAAAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 8 0.25
14 16 0.50
15 8 0.25
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (14 bp):
ATAAAAAAATAAAG
Found at i:17628658 original size:30 final size:29
Alignment explanation
Indices: 17628622--17628678 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
17628612 GACAAAACAT
*
17628622 AAAAAAATTAAAAAAAAAGAAACGAAAGTA
1 AAAAAAAGTAAAAAAAAAGAAA-GAAAGTA
*
17628652 AAAAAAAGTAAATAAAAAGAAAGAAAG
1 AAAAAAAGTAAAAAAAAAGAAAGAAAG
17628679 AAAGTAACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (29 bp):
AAAAAAAGTAAAAAAAAAGAAAGAAAGTA
Found at i:17637407 original size:34 final size:34
Alignment explanation
Indices: 17637364--17637484 Score: 127
Period size: 34 Copynumber: 3.6 Consensus size: 34
17637354 GTTCTAATCT
*
17637364 AATATGACATTCTGATATGATATATGTTTCTGAA
1 AATATGACATTCTAATATGATATATGTTTCTGAA
* * * *
17637398 AATATGACATTCTGATCTGGTATATGTTTCTGGA
1 AATATGACATTCTAATATGATATATGTTTCTGAA
* * * * *
17637432 AATATCACATTCTAATTTAATATATATTTCT-AGT
1 AATATGACATTCTAATATGATATATGTTTCTGA-A
*
17637466 AATGTGACATTCTAATATG
1 AATATGACATTCTAATATG
17637485 GTATTTGTAT
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
34 71 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (34 bp):
AATATGACATTCTAATATGATATATGTTTCTGAA
Found at i:17640349 original size:57 final size:57
Alignment explanation
Indices: 17640216--17640358 Score: 164
Period size: 57 Copynumber: 2.5 Consensus size: 57
17640206 CTCGTTATGG
* * * * *
17640216 AAAGGATTTAGCCCGGACAGGTAATCCCAATATAATCCTTCTCGAGTATATGTTACA
1 AAAGGATTTAGCCCGGACTGGTAATCCTAATATAAGCCTTCTCGAGCATACGTTACA
* * *
17640273 ATTAGGATTTAGCCGGGACTGGTAATCCTAAT-TGAGCTCTTCT-GAGCATACGTTACA
1 A-AAGGATTTAGCCCGGACTGGTAATCCTAATATAAGC-CTTCTCGAGCATACGTTACA
*
17640330 TAAAGGATTTAGCCTGGACTGGTAATCCT
1 -AAAGGATTTAGCCCGGACTGGTAATCCT
17640359 GTAATACGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
57 41 0.56
58 32 0.44
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (57 bp):
AAAGGATTTAGCCCGGACTGGTAATCCTAATATAAGCCTTCTCGAGCATACGTTACA
Found at i:17646948 original size:20 final size:21
Alignment explanation
Indices: 17646899--17646949 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
17646889 TTATACAATC
*
17646899 TTATGATTTTTAATTAAATTT
1 TTATGTTTTTTAATTAAATTT
* * *
17646920 TAATATTTTTTAA-TAATTTT
1 TTATGTTTTTTAATTAAATTT
17646940 TTATGTTTTT
1 TTATGTTTTT
17646950 CTATAATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (21 bp):
TTATGTTTTTTAATTAAATTT
Found at i:17651282 original size:9 final size:9
Alignment explanation
Indices: 17651268--17651294 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
17651258 ACTATATTTG
17651268 ACAAATTAA
1 ACAAATTAA
17651277 ACAAATTAA
1 ACAAATTAA
17651286 ACAAATTAA
1 ACAAATTAA
17651295 CAATTAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (9 bp):
ACAAATTAA
Found at i:17653255 original size:12 final size:12
Alignment explanation
Indices: 17653238--17653267 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
17653228 TATAAAACTT
17653238 ATTTTATTATTA
1 ATTTTATTATTA
17653250 ATTTTATTATTA
1 ATTTTATTATTA
*
17653262 TTTTTA
1 ATTTTA
17653268 AGACATTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTTATTATTA
Found at i:17653283 original size:30 final size:30
Alignment explanation
Indices: 17653247--17653308 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
17653237 TATTTTATTA
17653247 TTAATTTTATTATTATTTTTA-AGACATTTG
1 TTAATTTTATTATTA-TTTTAGAGACATTTG
*
17653277 TTAATTTTGTTATTATTTTAGAGACATTTG
1 TTAATTTTATTATTATTTTAGAGACATTTG
17653307 TT
1 TT
17653309 TGGTAAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.60
Consensus pattern (30 bp):
TTAATTTTATTATTATTTTAGAGACATTTG
Found at i:17653410 original size:18 final size:18
Alignment explanation
Indices: 17653389--17653428 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
17653379 AAAATATTTA
*
17653389 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
17653407 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
17653425 TTTT
1 TTTT
17653429 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:17653460 original size:12 final size:12
Alignment explanation
Indices: 17653430--17653462 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
17653420 TATATTTTTT
17653430 AAAATT-ATATA
1 AAAATTAATATA
17653441 AAAA-TAATATA
1 AAAATTAATATA
17653452 AAAATTAATAT
1 AAAATTAATAT
17653463 GGGCGGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:17657097 original size:23 final size:23
Alignment explanation
Indices: 17657057--17657107 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
17657047 AATTATTTTA
*
17657057 TTAAATTTAAATTCATTACAATG
1 TTAAATTCAAATTCATTACAATG
* * * *
17657080 TTAAATTCAAGTTTATTACCATT
1 TTAAATTCAAATTCATTACAATG
17657103 TTAAA
1 TTAAA
17657108 ATATCATTCG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (23 bp):
TTAAATTCAAATTCATTACAATG
Found at i:17658272 original size:5 final size:5
Alignment explanation
Indices: 17658262--17658328 Score: 63
Period size: 5 Copynumber: 14.4 Consensus size: 5
17658252 ATAAGAGAGG
* * *
17658262 GAGAA GAGAA GA-AA -AAAA GAAAA GAGAA GA-AA GA-AA GAAAA GAGAA
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA
*
17658308 AAGAA GAGAA GAGAA GA-AA GA
1 GAGAA GAGAA GAGAA GAGAA GA
17658329 AAAGTTTTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
3 1 0.02
4 16 0.29
5 38 0.69
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:17658288 original size:18 final size:18
Alignment explanation
Indices: 17658265--17658332 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
17658255 AGAGAGGGAG
17658265 AAGAGAAGAAAAAAAGAA
1 AAGAGAAGAAAAAAAGAA
*
17658283 AAGAGAAGAAAGAAAG-A
1 AAGAGAAGAAAAAAAGAA
* *
17658300 AA-AG-AGAAAAGAAGAG
1 AAGAGAAGAAAAAAAGAA
17658316 AAGAGAAGAAAGAAAAG
1 AAGAGAAGAAA-AAAAG
17658333 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
15 8 0.20
16 4 0.10
17 5 0.12
18 20 0.49
19 4 0.10
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AAGAGAAGAAAAAAAGAA
Found at i:17662468 original size:19 final size:20
Alignment explanation
Indices: 17662444--17662493 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
17662434 TTAATAGTAA
*
17662444 ATACATGTGTA-AAAATAAT
1 ATACATATGTATAAAATAAT
*
17662463 ATACATATGTATAAATTAAT
1 ATACATATGTATAAAATAAT
*
17662483 A-AAATATGTAT
1 ATACATATGTAT
17662494 TACTTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (20 bp):
ATACATATGTATAAAATAAT
Found at i:17663375 original size:16 final size:15
Alignment explanation
Indices: 17663351--17663380 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17663341 TGAATATGTC
17663351 ATGAATGATTAATTT
1 ATGAATGATTAATTT
17663366 ATGAATTGATTAATT
1 ATGAA-TGATTAATT
17663381 GAATGGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
ATGAATGATTAATTT
Found at i:17664271 original size:29 final size:29
Alignment explanation
Indices: 17664236--17664297 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
17664226 GAGCAGGCAG
* *
17664236 TGTGCCTCACACGGCCTTAGACACGCCCA
1 TGTGCCTCACACGGCCCTAAACACGCCCA
*
17664265 TGTGCCTCACACGGCCCTAAACACGCCCG
1 TGTGCCTCACACGGCCCTAAACACGCCCA
17664294 TGTG
1 TGTG
17664298 TCTAAGCCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.19, C:0.40, G:0.23, T:0.18
Consensus pattern (29 bp):
TGTGCCTCACACGGCCCTAAACACGCCCA
Found at i:17669384 original size:24 final size:25
Alignment explanation
Indices: 17669338--17669384 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
17669328 CGCTCTCTTC
*
17669338 TTTTTCTTCTTCTCTTCTTCAAAGA
1 TTTTTCTTCTTCTCTTCTGCAAAGA
17669363 TTTTT-TTC-TCTCTTCTGGCAAA
1 TTTTTCTTCTTCTCTTCT-GCAAA
17669385 AAATGGGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 7 0.35
25 5 0.25
ACGTcount: A:0.15, C:0.23, G:0.06, T:0.55
Consensus pattern (25 bp):
TTTTTCTTCTTCTCTTCTGCAAAGA
Found at i:17671798 original size:49 final size:49
Alignment explanation
Indices: 17671737--17672024 Score: 458
Period size: 49 Copynumber: 6.0 Consensus size: 49
17671727 TGTAGGAGGT
*
17671737 GTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGC
1 GTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
*
17671786 GTATATACATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
1 GTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
* * *
17671835 G--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGT
1 GTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
*
17671882 GTATATATATGTGATAAGGCCTAATGGCCAATGTGATAAATGTGAAAGA
1 GTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
* * *
17671931 G--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGT
1 GTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
*
17671978 GTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
17672025 CATATGTGTG
Statistics
Matches: 220, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
47 86 0.39
49 134 0.61
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (49 bp):
GTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGA
Found at i:17671903 original size:96 final size:96
Alignment explanation
Indices: 17671740--17672024 Score: 516
Period size: 96 Copynumber: 3.0 Consensus size: 96
17671730 AGGAGGTGTA
* * * *
17671740 TATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGCGTATATACATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGG
17671805 CCTAATGGCCAATGTGATGAATGTGAAAGAG
66 CCTAATGGCCAATGTGATGAATGTGAAAGAG
17671836 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGG
*
17671901 CCTAATGGCCAATGTGATAAATGTGAAAGAG
66 CCTAATGGCCAATGTGATGAATGTGAAAGAG
17671932 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGG
*
17671997 CCTAATGGCCGATGTGATGAATGTGAAA
66 CCTAATGGCCAATGTGATGAATGTGAAA
17672025 CATATGTGTG
Statistics
Matches: 182, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 182 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.29
Consensus pattern (96 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGG
CCTAATGGCCAATGTGATGAATGTGAAAGAG
Found at i:17671996 original size:145 final size:144
Alignment explanation
Indices: 17671733--17672023 Score: 503
Period size: 145 Copynumber: 2.0 Consensus size: 144
17671723 AATATGTAGG
* *
17671733 AGGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGCGTATATACATGT
1 AGGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATAAATGTGAAAGAGTATATA-ATGT
17671798 GATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAGTATATATGTGATAAGGCCTAATGGCCG
65 GATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAGTATATATGTGATAAGGCCTAATGGCCG
17671863 ATGTGATGAATGTGA
130 ATGTGATGAATGTGA
17671878 AGGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATAAATGTGAAAGAGTATAT-ATGTG
1 AGGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATAAATGTGAAAGAGTATATAATGTG
* * *
17671942 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTGTATATATATGTGATAAGGCCTAATGGCC
66 ATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAG--TATATATGTGATAAGGCCTAATGGCC
17672007 GATGTGATGAATGTGA
129 GATGTGATGAATGTGA
17672023 A
1 A
17672024 ACATATGTGT
Statistics
Matches: 139, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
143 39 0.28
145 100 0.72
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (144 bp):
AGGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATAAATGTGAAAGAGTATATAATGTG
ATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGAGTATATATGTGATAAGGCCTAATGGCCGA
TGTGATGAATGTGA
Found at i:17672072 original size:48 final size:48
Alignment explanation
Indices: 17672016--17672215 Score: 337
Period size: 48 Copynumber: 4.2 Consensus size: 48
17672006 CGATGTGATG
* * *
17672016 AATGTGAAACATATGTGTGATATGTATATGTGGTAAAGCAGAATAGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
* *
17672064 AATGTGAAATATATGTGTGATGTGTATATGTGGTAAAGCCGAAGGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
17672112 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
* *
17672160 AATGTGAAATATATGTGTGATGTGTATGTGTGGTAAAGCCGAATGGCT
1 AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
17672208 AATGTGAA
1 AATGTGAA
17672216 TGTTGTAACA
Statistics
Matches: 143, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 143 1.00
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (48 bp):
AATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCT
Found at i:17672306 original size:37 final size:37
Alignment explanation
Indices: 17672255--17672382 Score: 220
Period size: 37 Copynumber: 3.4 Consensus size: 37
17672245 AACTTGGAAA
*
17672255 TATGTTCCGGGTGAGACCCGATGACTACGTGTGGAGAT
1 TATG-TCCGGGTAAGACCCGATGACTACGTGTGGAGAT
* *
17672293 TATGTCCGGGTGAGACCCGATGATTACGTGTGGAGAT
1 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
17672330 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
1 TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
17672367 TATGTCCGGGTAAGAC
1 TATGTCCGGGTAAGAC
17672383 TTCGTAATAA
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
37 83 0.95
38 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.26
Consensus pattern (37 bp):
TATGTCCGGGTAAGACCCGATGACTACGTGTGGAGAT
Found at i:17674265 original size:14 final size:14
Alignment explanation
Indices: 17674229--17674267 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
17674219 TTGTTTCACT
*
17674229 GAAAATGACTTCCG
1 GAAAATGATTTCCG
* *
17674243 AAAAATGATTTCTG
1 GAAAATGATTTCCG
17674257 GAAAATGATTT
1 GAAAATGATTT
17674268 ACTTTTCTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (14 bp):
GAAAATGATTTCCG
Found at i:17674844 original size:16 final size:16
Alignment explanation
Indices: 17674813--17674849 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
17674803 ATGTGAATAA
17674813 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
17674829 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
17674845 TATTA
1 TATTA
17674850 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:17675206 original size:10 final size:10
Alignment explanation
Indices: 17675183--17675216 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
17675173 AACTATTTTC
17675183 TATAAAATAAA
1 TATAAAA-AAA
*
17675194 TATATAAAAA
1 TATAAAAAAA
17675204 TATAAAAAAA
1 TATAAAAAAA
17675214 TAT
1 TAT
17675217 TTTTCGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
TATAAAAAAA
Found at i:17677931 original size:30 final size:29
Alignment explanation
Indices: 17677886--17677942 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
17677876 CAACATTATA
*
17677886 TGAATTAATTAAATTTTAATATTTAAAAT
1 TGAAGTAATTAAATTTTAATATTTAAAAT
* *
17677915 TGAAGTAATATAAATTTTACTTTTTAAA
1 TGAAGTAAT-TAAATTTTAATATTTAAA
17677943 GATAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (29 bp):
TGAAGTAATTAAATTTTAATATTTAAAAT
Found at i:17679920 original size:46 final size:44
Alignment explanation
Indices: 17679816--17679923 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
17679806 TGTCTTTGAC
** * * *
17679816 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
17679860 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
17679906 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
17679924 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:17684559 original size:6 final size:6
Alignment explanation
Indices: 17684548--17684573 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17684538 TGGAGAAAAA
17684548 ATATGT ATATGT ATATGT ATATGT AT
1 ATATGT ATATGT ATATGT ATATGT AT
17684574 GTATATACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:17686700 original size:15 final size:16
Alignment explanation
Indices: 17686680--17686709 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17686670 GAGTAATTTT
17686680 AAATATT-GTATTAAA
1 AAATATTAGTATTAAA
17686695 AAATATTAGTATTAA
1 AAATATTAGTATTAA
17686710 TCTTGACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
AAATATTAGTATTAAA
Found at i:17687913 original size:8 final size:8
Alignment explanation
Indices: 17687902--17687926 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
17687892 TTTAATAAGA
17687902 TATTTTAT
1 TATTTTAT
17687910 TATTTTAT
1 TATTTTAT
17687918 TATTTTAT
1 TATTTTAT
17687926 T
1 T
17687927 TAGTCTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:17695672 original size:24 final size:24
Alignment explanation
Indices: 17695645--17695693 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
17695635 ACAATTAATC
* *
17695645 CGAGTTACTTAACAATAATTCTAA
1 CGAGTAACTTAACAACAATTCTAA
17695669 CGAGTAACTTAACAACAATTCTAA
1 CGAGTAACTTAACAACAATTCTAA
17695693 C
1 C
17695694 ATGATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (24 bp):
CGAGTAACTTAACAACAATTCTAA
Found at i:17698130 original size:69 final size:67
Alignment explanation
Indices: 17698003--17698168 Score: 179
Period size: 69 Copynumber: 2.4 Consensus size: 67
17697993 GAGGTTTAGG
* * * * * *
17698003 GAGTAAGACCATAGCTAGGCTATGGAAACCAATAGAGTCTGACGAGACAGTAAACATGAGGATTA
1 GAGTAAGACTATAGCTCGGCTATGGAAACTAATAGAGTCCGACAAAACAGTAAACATGA-GATT-
*
17698068 CGAG
64 CGAC
* * * * * * *
17698072 GTGTAAGACTATAGCTCGACTATGGTAACTAATAGAGTCCGCCAAAACATTAAGCATGAGATTTG
1 GAGTAAGACTATAGCTCGGCTATGGAAACTAATAGAGTCCGACAAAACAGTAAACATGAGATTCG
17698137 AC
66 AC
*
17698139 GAGTAAGACTATAGTTCGGCTATGGAAACT
1 GAGTAAGACTATAGCTCGGCTATGGAAACT
17698169 TGTGAAGTCT
Statistics
Matches: 79, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
67 28 0.35
68 4 0.05
69 47 0.59
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (67 bp):
GAGTAAGACTATAGCTCGGCTATGGAAACTAATAGAGTCCGACAAAACAGTAAACATGAGATTCG
AC
Found at i:17700619 original size:24 final size:26
Alignment explanation
Indices: 17700592--17700652 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
17700582 ACATATTTTC
17700592 TCAAAATTTTA-CAAAGGCAAAA-TG
1 TCAAAATTTTACCAAAGGCAAAATTG
* * *
17700616 TCAAAATGTTACCAAGGGTAAAATTG
1 TCAAAATTTTACCAAAGGCAAAATTG
17700642 TCAAAATTTTA
1 TCAAAATTTTA
17700653 TTGAGGGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 10 0.32
25 9 0.29
26 12 0.39
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (26 bp):
TCAAAATTTTACCAAAGGCAAAATTG
Found at i:17700647 original size:26 final size:24
Alignment explanation
Indices: 17700592--17700648 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
17700582 ACATATTTTC
*
17700592 TCAAAATTTTACAAAGGCAAAATG
1 TCAAAATGTTACAAAGGCAAAATG
* *
17700616 TCAAAATGTTACCAAGGGTAAAATTG
1 TCAAAATGTTA-CAAAGGCAAAA-TG
17700642 TCAAAAT
1 TCAAAAT
17700649 TTTATTGAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 10 0.36
25 9 0.32
26 9 0.32
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.26
Consensus pattern (24 bp):
TCAAAATGTTACAAAGGCAAAATG
Found at i:17702961 original size:37 final size:37
Alignment explanation
Indices: 17702920--17702992 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
17702910 ACTTAATACA
17702920 TAACCTACATAGCCAAAGTACATATAACCCTAATGAG
1 TAACCTACATAGCCAAAGTACATATAACCCTAATGAG
17702957 TAACCTACATAGCCAAAGTACATATAACCCTAATGA
1 TAACCTACATAGCCAAAGTACATATAACCCTAATGA
17702993 CTGAATATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.22
Consensus pattern (37 bp):
TAACCTACATAGCCAAAGTACATATAACCCTAATGAG
Found at i:17715354 original size:20 final size:21
Alignment explanation
Indices: 17715329--17715367 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
17715319 ACGTCCACGT
17715329 ATATATAAAATT-TTAAAAAA
1 ATATATAAAATTATTAAAAAA
17715349 ATATATAAAATTATTAAAA
1 ATATATAAAATTATTAAAA
17715368 TTTTCATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATATAAAATTATTAAAAAA
Found at i:17717468 original size:10 final size:10
Alignment explanation
Indices: 17717453--17717488 Score: 72
Period size: 10 Copynumber: 3.6 Consensus size: 10
17717443 TTATTTGTAA
17717453 AAAAAAAAAG
1 AAAAAAAAAG
17717463 AAAAAAAAAG
1 AAAAAAAAAG
17717473 AAAAAAAAAG
1 AAAAAAAAAG
17717483 AAAAAA
1 AAAAAA
17717489 GGGCAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:17719620 original size:14 final size:14
Alignment explanation
Indices: 17719593--17719633 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
17719583 ATAATTATAT
*
17719593 ATTTATATATTAAA
1 ATTTATATTTTAAA
17719607 ATTT-TA-TTTATAA
1 ATTTATATTTTA-AA
17719620 ATTTATATTTTAAA
1 ATTTATATTTTAAA
17719634 TATAAAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
12 3 0.13
13 8 0.35
14 8 0.35
15 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTATATTTTAAA
Found at i:17719820 original size:45 final size:40
Alignment explanation
Indices: 17719794--17719887 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 40
17719784 TATTGTTAAC
* *
17719794 ATTATTAATTTATTCAACTACTATTGCAATTAATATAATAA
1 ATTATCAATTTATTCAA-TACTATTGCAAGTAATATAATAA
*
17719835 ATTATCAATTTATTCAATACTATT--AA-TAATCTAAT--
1 ATTATCAATTTATTCAATACTATTGCAAGTAATATAATAA
*
17719870 ATTATAAATTTATTCAAT
1 ATTATCAATTTATTCAAT
17719888 TAGCATTATA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
35 17 0.34
37 8 0.16
38 2 0.04
40 7 0.14
41 16 0.32
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.46
Consensus pattern (40 bp):
ATTATCAATTTATTCAATACTATTGCAAGTAATATAATAA
Done.