Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 197 of 313
Found at i:60417710 original size:19 final size:19
Alignment explanation
Indices: 60417697--60417740 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
60417687 TTTTTATGTG
*
60417697 TTTTTTTAGATTTTATATA
1 TTTTTTCAGATTTTATATA
*
60417716 TTTTTTCAGAATTTATAATA
1 TTTTTTCAGATTTTAT-ATA
60417736 TTTTT
1 TTTTT
60417741 ATGTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTTTCAGATTTTATATA
Found at i:60417720 original size:20 final size:20
Alignment explanation
Indices: 60417678--60417740 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 20
60417668 GTTAATTTTA
* * *
60417678 TTTTTATATTTTTTATGTGTT
1 TTTTTAGATTTTATATAT-TT
60417699 TTTTTAGATTTTATATA-TT
1 TTTTTAGATTTTATATATTT
* *
60417718 TTTTCAGAATTTATAATATTT
1 TTTTTAGATTTTAT-ATATTT
60417739 TT
1 TT
60417741 ATGTTTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 14 0.40
20 3 0.09
21 18 0.51
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (20 bp):
TTTTTAGATTTTATATATTT
Found at i:60418763 original size:14 final size:13
Alignment explanation
Indices: 60418723--60418775 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
60418713 TCAAAATGAA
60418723 TAATTAATTTAATT
1 TAATT-ATTTAATT
60418737 TAATT-TTTGAATT
1 TAATTATTT-AATT
60418750 TCAATTATTTAATT
1 T-AATTATTTAATT
*
60418764 GTAATTAATTAA
1 -TAATTATTTAA
60418776 ATAAAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 3 0.09
13 5 0.15
14 22 0.65
15 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (13 bp):
TAATTATTTAATT
Found at i:60420203 original size:20 final size:20
Alignment explanation
Indices: 60420178--60420231 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
60420168 ATTACTCTAC
* *
60420178 TATTATAGTATATGATATAG
1 TATTATAGTATATGAAATAA
60420198 TATTATA-TATAATGAAATAA
1 TATTATAGTAT-ATGAAATAA
*
60420218 TATGTTTAGTATAT
1 TAT-TATAGTATAT
60420232 TAAAATGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 3 0.11
20 17 0.61
21 5 0.18
22 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (20 bp):
TATTATAGTATATGAAATAA
Found at i:60420920 original size:5 final size:5
Alignment explanation
Indices: 60420552--60420905 Score: 708
Period size: 5 Copynumber: 70.8 Consensus size: 5
60420542 TTCAATTGCC
60420552 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
60420602 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
60420652 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
60420702 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
60420752 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
60420802 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
60420852 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
60420902 AATA
1 AATA
60420906 ATGAACAATA
Statistics
Matches: 349, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 349 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:60426520 original size:18 final size:18
Alignment explanation
Indices: 60426497--60426534 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
60426487 ATACTTAATC
*
60426497 ATGCAAATTAACATGAAT
1 ATGCAAATAAACATGAAT
*
60426515 ATGCAAATAAACATGTAT
1 ATGCAAATAAACATGAAT
60426533 AT
1 AT
60426535 TGATCTCGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (18 bp):
ATGCAAATAAACATGAAT
Found at i:60428421 original size:30 final size:31
Alignment explanation
Indices: 60428385--60428469 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 31
60428375 GAGTGAATAA
* *
60428385 GTTGCTCACACAAGCTAACATTATAT-CAGG
1 GTTGCTCACACAAGCTGACATTATATAAAGG
* * *
60428415 GTTGCTCACATAAGTTGACATTATGTAAAGG
1 GTTGCTCACACAAGCTGACATTATATAAAGG
*
60428446 TTTG-TCACACAAGCTGAC-TTATAT
1 GTTGCTCACACAAGCTGACATTATAT
60428470 TAGGTTACCC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 5 0.11
30 34 0.76
31 6 0.13
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (31 bp):
GTTGCTCACACAAGCTGACATTATATAAAGG
Found at i:60432035 original size:19 final size:19
Alignment explanation
Indices: 60431988--60432035 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
60431978 ATTTTGGGCA
60431988 TTTGGTTTTGGATCGTGTT
1 TTTGGTTTTGGATCGTGTT
** *
60432007 TTTGAATTTGGTTC-TGTT
1 TTTGGTTTTGGATCGTGTT
60432025 TTTGGGTTTTG
1 TTT-GGTTTTG
60432036 ATTTGTTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.06, C:0.04, G:0.29, T:0.60
Consensus pattern (19 bp):
TTTGGTTTTGGATCGTGTT
Found at i:60434173 original size:47 final size:47
Alignment explanation
Indices: 60434082--60434494 Score: 727
Period size: 47 Copynumber: 8.7 Consensus size: 47
60434072 TTAGGATTCT
*
60434082 ATGTGATGAATGTGAAAGTGTATATATATGTTATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
60434131 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
60434178 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
60434225 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
60434272 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
60434319 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
60434366 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
60434413 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
60434460 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
60434495 TCCCGAAGGG
Statistics
Matches: 353, Mismatches: 11, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
47 333 0.94
49 20 0.06
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:60434687 original size:37 final size:37
Alignment explanation
Indices: 60434613--60434691 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
60434603 CCGAGCTCTA
* * **
60434613 AAGACCCGATGACTACGTGTGGGAATTTTGTTTGGGT
1 AAGACCCGATAACTACGTGTGGGAATTATGTCCGGGT
*
60434650 AAGACCCGATAACTTCGTGT-GGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGGA-ATTATGTCCGGGT
60434687 AAGAC
1 AAGAC
60434692 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
36 3 0.08
37 33 0.92
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.28
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGGAATTATGTCCGGGT
Found at i:60436687 original size:42 final size:43
Alignment explanation
Indices: 60436544--60436685 Score: 259
Period size: 43 Copynumber: 3.3 Consensus size: 43
60436534 TTGGTTTTCA
*
60436544 GCACTAAGTGTGCGAGCAATAAGTGTTCAAGGTTGTGAGATTG
1 GCACTAAGTGTGCGAGCAATAAGTGTTCACGGTTGTGAGATTG
60436587 GCACTAAGTGTGCGAGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGAGCAATAAGTGTTCACGGTTGTGAGATTG
*
60436630 GCACTAAGTGTGCG-GGAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGAGCAATAAGTGTTCACGGTTGTGAGATTG
60436672 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
60436686 GGTTGTGAGA
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
42 41 0.42
43 56 0.58
ACGTcount: A:0.25, C:0.13, G:0.34, T:0.27
Consensus pattern (43 bp):
GCACTAAGTGTGCGAGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:60436692 original size:27 final size:27
Alignment explanation
Indices: 60436659--60436714 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
60436649 AAGTGTTCAC
60436659 GGTTGTGAGATTGGCACTAAGTGTGCG
1 GGTTGTGAGATTGGCACTAAGTGTGCG
60436686 GGTTGTGAGATTGGCACTAAGTGTGCG
1 GGTTGTGAGATTGGCACTAAGTGTGCG
60436713 GG
1 GG
60436715 CAATAAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.11, G:0.43, T:0.29
Consensus pattern (27 bp):
GGTTGTGAGATTGGCACTAAGTGTGCG
Found at i:60436732 original size:70 final size:69
Alignment explanation
Indices: 60436617--60436784 Score: 275
Period size: 70 Copynumber: 2.4 Consensus size: 69
60436607 AAGTGTTCAC
60436617 GGTTGTGAGATTGGCACTAAGTGTGCGGGAATAAGTGTTCACGGTTGTGAGATTGGCACTAAGTG
1 GGTTGTGAGATTGGCACTAAGTGTGCGGGAATAAGTGTTCACGGTTGTGAGATTGGCACTAAGTG
60436682 TGCG
66 TGCG
60436686 GGTTGTGAGATTGGCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTGGCACTAAGT
1 GGTTGTGAGATTGGCACTAAGTGTGCGGG-AATAAGTGTTCACGGTTGTGAGATTGGCACTAAGT
60436751 GTGCG
65 GTGCG
* *
60436756 GGCT-TGAAATGCATGGCACTAAGTGTGCG
1 GGTTGTGAGAT---TGGCACTAAGTGTGCG
60436785 AGTTTAAAGT
Statistics
Matches: 93, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
69 34 0.37
70 43 0.46
72 16 0.17
ACGTcount: A:0.22, C:0.13, G:0.37, T:0.28
Consensus pattern (69 bp):
GGTTGTGAGATTGGCACTAAGTGTGCGGGAATAAGTGTTCACGGTTGTGAGATTGGCACTAAGTG
TGCG
Found at i:60436775 original size:29 final size:29
Alignment explanation
Indices: 60436740--60436813 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
60436730 GTTGTGAGAT
* *
60436740 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
60436769 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
60436798 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
60436814 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:60437346 original size:39 final size:39
Alignment explanation
Indices: 60437206--60437362 Score: 131
Period size: 40 Copynumber: 4.0 Consensus size: 39
60437196 TGCAAGTTGA
* *
60437206 TATATCCGGGCTAAGACCCGAAG-GCATTGGTGC-GAGTT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG-GTT
* * * * *
60437244 ACTAAATCCGGGCTAAATTCCGAAGAGCATTCGTACTAG-T
1 --TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTT
* * *
60437284 GAGGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTGGTT
1 TA--TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTT
* * *
60437325 TATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGT
60437363 GACATGTATT
Statistics
Matches: 93, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
39 31 0.33
40 50 0.54
41 11 0.12
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTT
Found at i:60439685 original size:96 final size:94
Alignment explanation
Indices: 60439575--60439879 Score: 484
Period size: 96 Copynumber: 3.2 Consensus size: 94
60439565 CAGCCAAGAC
60439575 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGAT
*
60439640 AAGGCTTAATGGCCGATGTGATGAATGTGAA
64 AAGGCCTAATGGCCGATGTGATGAATGTGAA
60439671 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
60439736 GGCCTAATGGCCGATGTGATGAATGTGAA
66 GGCCTAATGGCCGATGTGATGAATGTGAA
* *
60439765 AGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAC
1 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
* * * * * *
60439830 AGGGCCGAGTGGCCAACGTGATGGATGTGAA
64 AAGGCCTAATGGCCGATGTGATGAATGTGAA
*
60439861 AGTGTATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
60439880 TCCCGAAGGG
Statistics
Matches: 196, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
94 59 0.30
96 137 0.70
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (94 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
GGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:60439697 original size:47 final size:47
Alignment explanation
Indices: 60439575--60439879 Score: 484
Period size: 47 Copynumber: 6.4 Consensus size: 47
60439565 CAGCCAAGAC
60439575 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
60439622 AGTGTATATATATGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
60439671 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
60439718 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
60439765 AGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
60439814 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
60439861 AGTGTATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
60439880 TCCCGAAGGG
Statistics
Matches: 242, Mismatches: 12, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
47 150 0.62
49 92 0.38
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:60439735 original size:143 final size:143
Alignment explanation
Indices: 60439575--60439879 Score: 520
Period size: 143 Copynumber: 2.1 Consensus size: 143
60439565 CAGCCAAGAC
60439575 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
* * * * *
60439640 AAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATG
66 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAACG
60439705 TGATGAATGTGAA
131 TGATGAATGTGAA
60439718 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
* * *
60439783 AGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACG
66 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAACG
*
60439848 TGATGGATGTGAA
131 TGATGAATGTGAA
*
60439861 AGTGTATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
60439880 TCCCGAAGGG
Statistics
Matches: 152, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
143 152 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (143 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAACG
TGATGAATGTGAA
Found at i:60440054 original size:37 final size:37
Alignment explanation
Indices: 60439998--60440075 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
60439988 CTGAGCTCTA
* *
60439998 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
* *
60440035 AAGACTCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
60440072 AAGA
1 AAGA
60440076 TTTCGTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 35 0.97
38 1 0.03
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:60443047 original size:28 final size:28
Alignment explanation
Indices: 60442963--60443047 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 28
60442953 CCTTCAACGG
* * *
60442963 TTGTCTTATGT-GAAGGTCTACTAAGGG
1 TTGTCTTATGTGGAAAGTCAACTAAGGA
* * * * *
60442990 CTATCTTATGCGGAAAGTCCA-TCAATGA
1 TTGTCTTATGTGGAAAGTCAACT-AAGGA
60443018 TTGTCTTATGTGGAAAGTCAACTAAGGA
1 TTGTCTTATGTGGAAAGTCAACTAAGGA
60443046 TT
1 TT
60443048 ATCATATGCG
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
27 9 0.21
28 33 0.77
29 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (28 bp):
TTGTCTTATGTGGAAAGTCAACTAAGGA
Found at i:60443098 original size:28 final size:28
Alignment explanation
Indices: 60442990--60443116 Score: 87
Period size: 28 Copynumber: 4.5 Consensus size: 28
60442980 CTACTAAGGG
* *
60442990 CTATCTTATGCGGAAAGTCCATCAATG-A
1 CTATCTTATGTGGAAAGTCCACCAA-GAA
* * * * *
60443018 TTGTCTTATGTGGAAAGTCAACTAAGGA
1 CTATCTTATGTGGAAAGTCCACCAAGAA
* * * * * *
60443046 TTATCATATGCGGGAACTCCGCCAAGAA
1 CTATCTTATGTGGAAAGTCCACCAAGAA
60443074 CTATCTTATGTGGAAAGTCCACCAA-AGA
1 CTATCTTATGTGGAAAGTCCACCAAGA-A
* *
60443102 CTATCTCATATGGAA
1 CTATCTTATGTGGAA
60443117 TGCTTGCCAA
Statistics
Matches: 74, Mismatches: 23, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
27 2 0.03
28 72 0.97
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (28 bp):
CTATCTTATGTGGAAAGTCCACCAAGAA
Found at i:60446351 original size:28 final size:28
Alignment explanation
Indices: 60446320--60446376 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
60446310 ACGACAACGA
*
60446320 CTACTACACGGGCGCATAGACACTCGTG
1 CTACTACACGGGCGCAAAGACACTCGTG
*
60446348 CTACTACATGGGCGCAAAGACACTCGTG
1 CTACTACACGGGCGCAAAGACACTCGTG
60446376 C
1 C
60446377 AGGGAAGTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.32, G:0.25, T:0.18
Consensus pattern (28 bp):
CTACTACACGGGCGCAAAGACACTCGTG
Found at i:60447112 original size:27 final size:26
Alignment explanation
Indices: 60447081--60447149 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
60447071 CCCACAATTT
* * *
60447081 GTAAAATAACTGTAATGCCCTTGTAGG
1 GTAAAATGACTGTAATGCCCCTATA-G
* *
60447108 GTAAAATGACCGTGATGCCCCTATAG
1 GTAAAATGACTGTAATGCCCCTATAG
60447134 GTAAAATGACTGTAAT
1 GTAAAATGACTGTAAT
60447150 ACCTTTGTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
26 15 0.43
27 20 0.57
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (26 bp):
GTAAAATGACTGTAATGCCCCTATAG
Found at i:60447171 original size:53 final size:53
Alignment explanation
Indices: 60447081--60447197 Score: 123
Period size: 53 Copynumber: 2.2 Consensus size: 53
60447071 CCCACAATTT
* * * *
60447081 GTAAAATAACTGTAATGCCCTTGTAGGGTAAAATGACCG-TGATGCCCCTATA-G
1 GTAAAATGACTGTAATACCCTTGTAGGGTAAAATGACCGAT-ATACCCC-AAAGG
* * *
60447134 GTAAAATGACTGTAATACCTTTGTTA-GGTGAATTGACCGATATACCCCAAAGG
1 GTAAAATGACTGTAATACCCTTG-TAGGGTAAAATGACCGATATACCCCAAAGG
60447187 GTAAAATGACT
1 GTAAAATGACT
60447198 ATTTTGCCCC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
52 2 0.04
53 49 0.91
54 3 0.06
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (53 bp):
GTAAAATGACTGTAATACCCTTGTAGGGTAAAATGACCGATATACCCCAAAGG
Found at i:60447274 original size:24 final size:24
Alignment explanation
Indices: 60447218--60447276 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
60447208 TCGATTTTAA
60447218 ATGACTGATTTGTCTGTGATTGGT
1 ATGACTGATTTGTCTGTGATTGGT
* *
60447242 ATAAATGATTTGTCTGTGAATT-GT
1 ATGACTGATTTGTCTGTG-ATTGGT
60447266 ATGACTGATTT
1 ATGACTGATTT
60447277 TGAGCATGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.46
Consensus pattern (24 bp):
ATGACTGATTTGTCTGTGATTGGT
Found at i:60447422 original size:26 final size:26
Alignment explanation
Indices: 60447392--60447447 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
60447382 TGGCCACACA
*
60447392 TACTATTACTGGCAGCTTTGTTGTGG
1 TACTATTACTGGCAGCTTTGCTGTGG
*
60447418 TACTATTACTTGCAGCTTTGCTGTGG
1 TACTATTACTGGCAGCTTTGCTGTGG
60447444 TACT
1 TACT
60447448 GTTGCTAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGTGG
Found at i:60447458 original size:26 final size:26
Alignment explanation
Indices: 60447392--60447458 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
60447382 TGGCCACACA
* *
60447392 TACTATTACTGGCAGCTTTGTTGTGG
1 TACTATTACTAGCAGCTTTGCTGTGG
*
60447418 TACTATTACTTGCAGCTTTGCTGTGG
1 TACTATTACTAGCAGCTTTGCTGTGG
* *
60447444 TACTGTTGCTAGCAG
1 TACTATTACTAGCAG
60447459 GTTTACTGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.40
Consensus pattern (26 bp):
TACTATTACTAGCAGCTTTGCTGTGG
Found at i:60447522 original size:32 final size:32
Alignment explanation
Indices: 60447472--60447565 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 32
60447462 TACTGCGATG
* *
60447472 CTACTAATGGCT-TGGTGCCAATCATATTACCG
1 CTACTGATGGCTGT-GTGCCAATCATATTACCA
* * * **
60447504 TTACTGTTGGCTGTGTGCCGATCATATTAATA
1 CTACTGATGGCTGTGTGCCAATCATATTACCA
*
60447536 CTACTGATGGCTTTGTGCCAATCATATTAC
1 CTACTGATGGCTGTGTGCCAATCATATTAC
60447566 TATACTTGTG
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
32 48 0.98
33 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.36
Consensus pattern (32 bp):
CTACTGATGGCTGTGTGCCAATCATATTACCA
Found at i:60455116 original size:23 final size:23
Alignment explanation
Indices: 60455090--60455138 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
60455080 TAGCGGCTTA
60455090 ATTATATACATAAAATTTTAATT
1 ATTATATACATAAAATTTTAATT
60455113 ATTATATACATAAAATTTTAATT
1 ATTATATACATAAAATTTTAATT
60455136 ATT
1 ATT
60455139 GTTGATATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTATATACATAAAATTTTAATT
Found at i:60460214 original size:18 final size:18
Alignment explanation
Indices: 60460186--60460221 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
60460176 TTTTAGCTTC
60460186 TCCCTAAAAGTTCTTTTTT
1 TCCCTAAAAGTT-TTTTTT
60460205 TCCC-AAAAGTTTTTTTT
1 TCCCTAAAAGTTTTTTTT
60460222 AGAAGCAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (18 bp):
TCCCTAAAAGTTTTTTTT
Found at i:60466108 original size:27 final size:26
Alignment explanation
Indices: 60466074--60466407 Score: 380
Period size: 27 Copynumber: 12.4 Consensus size: 26
60466064 CCCTAAAATA
** *
60466074 GGTAAAATGATTGAAATATCTCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
*
60466101 GATAAAATGACCGAAATACTCCCATAG
1 GGTAAAATGACCGAAATAC-CCCATAG
*
60466128 GATAAAATGACCGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCC-ATAG
* *
60466155 GATAGAATGACCGAAATAACCCCATAG
1 GGTAAAATGACCGAAAT-ACCCCATAG
* *
60466182 GGTAGAATGATCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
* **
60466209 GGTAGAATGATAGAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
*
60466236 GGTAAAATAACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATA-CCCCATAG
** *
60466263 GGTAAAATGATAGAAATACCCCGTAG
1 GGTAAAATGACCGAAATACCCCATAG
* *
60466289 GGTAAAATGACCAAAATACCCTCACAG
1 GGTAAAATGACCGAAATACCC-CATAG
*
60466316 GGTAAAATGACCGAAATACCTTCATAG
1 GGTAAAATGACCGAAATACC-CCATAG
*
60466343 GGTAAAATGACCGAAATACCCCCATAA
1 GGTAAAATGACCGAAATA-CCCCATAG
*
60466370 GGTAAAATGACCAAAATACCCTCATAG
1 GGTAAAATGACCGAAATACCC-CATAG
60466397 GGTAAAATGAC
1 GGTAAAATGAC
60466408 TATTATACCC
Statistics
Matches: 271, Mismatches: 28, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
26 33 0.12
27 231 0.85
28 7 0.03
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.19
Consensus pattern (26 bp):
GGTAAAATGACCGAAATACCCCATAG
Found at i:60469605 original size:4 final size:4
Alignment explanation
Indices: 60469567--60469647 Score: 51
Period size: 4 Copynumber: 20.2 Consensus size: 4
60469557 TCCTAATTGG
* * * * *
60469567 TTTA TTGA TTTA TTTTG TTTG TTTA -TT- TTTC TTTA TTTA TTTCT TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA
* *
60469615 GTTA TTTA TTTA TTT- TTTA TCTA TTTAA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA T
60469648 ATGGTTTATA
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
3 7 0.12
4 43 0.72
5 10 0.17
ACGTcount: A:0.19, C:0.04, G:0.05, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:60476374 original size:20 final size:20
Alignment explanation
Indices: 60476349--60476392 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
60476339 AAAAGGTAAT
*
60476349 GATACTAAGC-CTACAGTACC
1 GATACTAACCTCTA-AGTACC
*
60476369 GATACTTACCTCTAAGTACC
1 GATACTAACCTCTAAGTACC
60476389 GATA
1 GATA
60476393 ACGATACCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (20 bp):
GATACTAACCTCTAAGTACC
Found at i:60478682 original size:43 final size:43
Alignment explanation
Indices: 60478634--60478803 Score: 124
Period size: 43 Copynumber: 3.7 Consensus size: 43
60478624 TTCTGTAAAA
*
60478634 AAACACCGCTAAAGAACATGATTTTTAGCGACGCTTTACCCAC
1 AAACACCGCTAAAGAACATGATCTTTAGCGACGCTTTACCCAC
* *** * ** *
60478677 AAACACTGCTAAAGGTTATGATCTTTAGGGGAACTTTTATCACAAACGCCGC
1 AAACACCGCTAAAGAACATGATCTTTA-GCG-ACGCTT-T-----AC-CCAC
* *
60478729 TAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
1 --AAACACCGCTAAAGAACATGATCTTTAGCGACGCTTTACCCAC
* *
60478774 AAATACCGCTAAAGAACATGACCTTTAGCG
1 AAACACCGCTAAAGAACATGATCTTTAGCG
60478804 GCACTTTTAT
Statistics
Matches: 94, Mismatches: 22, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
43 49 0.52
44 2 0.02
45 7 0.07
46 3 0.03
51 3 0.03
52 6 0.06
53 2 0.02
54 22 0.23
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (43 bp):
AAACACCGCTAAAGAACATGATCTTTAGCGACGCTTTACCCAC
Found at i:60478800 original size:97 final size:97
Alignment explanation
Indices: 60478633--60478818 Score: 273
Period size: 97 Copynumber: 1.9 Consensus size: 97
60478623 TTTCTGTAAA
* * ***
60478633 AAAACACCGCTAAAGAACATGATTTTTAGCGACGCTTTACCCACAAACACTGCTAAAGGTTATGA
1 AAAACACCGCTAAAGAACATGATCTTTAGCGACGCTTTACCCACAAACACCGCTAAAGAACATGA
* *
60478698 TCTTTAGGGGAACTTTTATCACAAACGCCGCT
66 CCTTTAGCGGAACTTTTATCACAAACGCCGCT
* * *
60478730 AAAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAATACCGCTAAAGAACATGA
1 AAAACACCGCTAAAGAACATGATCTTTAGCGACGCTTTACCCACAAACACCGCTAAAGAACATGA
*
60478795 CCTTTAGCGGCACTTTTATCACAA
66 CCTTTAGCGGAACTTTTATCACAA
60478819 CCATCGCTAA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 78 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (97 bp):
AAAACACCGCTAAAGAACATGATCTTTAGCGACGCTTTACCCACAAACACCGCTAAAGAACATGA
CCTTTAGCGGAACTTTTATCACAAACGCCGCT
Found at i:60482557 original size:46 final size:46
Alignment explanation
Indices: 60482490--60482586 Score: 176
Period size: 46 Copynumber: 2.1 Consensus size: 46
60482480 TTGACAACTC
*
60482490 TACTTCTGACTTCACCAATGCTAAACCCTAATCTGGAAACACCCAA
1 TACTTCTGACTTCACCAATGCTAAACCCTAATCTAGAAACACCCAA
*
60482536 TACTTCTGACTTCGCCAATGCTAAACCCTAATCTAGAAACACCCAA
1 TACTTCTGACTTCACCAATGCTAAACCCTAATCTAGAAACACCCAA
60482582 TACTT
1 TACTT
60482587 TAATGCCAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.34, C:0.32, G:0.08, T:0.26
Consensus pattern (46 bp):
TACTTCTGACTTCACCAATGCTAAACCCTAATCTAGAAACACCCAA
Found at i:60483624 original size:18 final size:19
Alignment explanation
Indices: 60483601--60483636 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
60483591 TTATCTCTTA
60483601 CATAATTTAAAT-TATAAT
1 CATAATTTAAATATATAAT
*
60483619 CATAATTTTAATATATAA
1 CATAATTTAAATATATAA
60483637 AATAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
CATAATTTAAATATATAAT
Found at i:60483806 original size:15 final size:15
Alignment explanation
Indices: 60483781--60483818 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
60483771 AACCCTCAAA
60483781 CCATAAA-CCATAAT
1 CCATAAACCCATAAT
*
60483795 CCCTAAACCCATAAT
1 CCATAAACCCATAAT
60483810 CCATAAACC
1 CCATAAACC
60483819 TTAAGATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.45, C:0.37, G:0.00, T:0.18
Consensus pattern (15 bp):
CCATAAACCCATAAT
Found at i:60483806 original size:22 final size:22
Alignment explanation
Indices: 60483773--60483815 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
60483763 GTACCCCTAA
60483773 CCCTCAAACCATAAACCATAAT
1 CCCTCAAACCATAAACCATAAT
*
60483795 CCCT-AAACCCATAATCCATAA
1 CCCTCAAA-CCATAAACCATAA
60483816 ACCTTAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (22 bp):
CCCTCAAACCATAAACCATAAT
Found at i:60483990 original size:7 final size:7
Alignment explanation
Indices: 60483980--60484076 Score: 52
Period size: 7 Copynumber: 13.3 Consensus size: 7
60483970 TCTCCTATCT
60483980 CCTAAAC
1 CCTAAAC
*
60483987 CCTAAAT
1 CCTAAAC
*
60483994 CATAAAC
1 CCTAAAC
*
60484001 CCTTAAC
1 CCTAAAC
60484008 CCTTAAATAAC
1 CC-T--A-AAC
*
60484019 CCTAACC
1 CCTAAAC
60484026 CCTAAAC
1 CCTAAAC
**
60484033 TTTAAAC
1 CCTAAAC
*
60484040 CC-CAAC
1 CCTAAAC
60484046 CCTTAAAC
1 CC-TAAAC
*
60484054 CATAAAC
1 CCTAAAC
* *
60484061 CATAATC
1 CCTAAAC
60484068 CCTAAAC
1 CCTAAAC
60484075 CC
1 CC
60484077 ATGATCCATA
Statistics
Matches: 66, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
6 5 0.08
7 49 0.74
8 6 0.09
10 1 0.02
11 5 0.08
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (7 bp):
CCTAAAC
Found at i:60484026 original size:17 final size:18
Alignment explanation
Indices: 60483998--60484031 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
60483988 CTAAATCATA
*
60483998 AACCCTTAACCCTTAAAT
1 AACCCTTAACCCCTAAAT
60484016 AACCC-TAACCCCTAAA
1 AACCCTTAACCCCTAAA
60484032 CTTTAAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (18 bp):
AACCCTTAACCCCTAAAT
Found at i:60484059 original size:21 final size:21
Alignment explanation
Indices: 60483984--60484075 Score: 70
Period size: 21 Copynumber: 4.6 Consensus size: 21
60483974 CTATCTCCTA
*
60483984 AACCC-TAAATCATAAACCCTT
1 AACCCTTAAACCATAAACCC-T
60484005 AACCCTT-AA--AT-AACCCT
1 AACCCTTAAACCATAAACCCT
* ** *
60484022 AACCCCTAAACTTTAAACCCC
1 AACCCTTAAACCATAAACCCT
*
60484043 AACCCTTAAACCATAAACCAT
1 AACCCTTAAACCATAAACCCT
60484064 AATCCC-TAAACC
1 AA-CCCTTAAACC
60484076 CATGATCCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
17 7 0.12
18 7 0.12
19 2 0.04
20 1 0.02
21 36 0.63
22 4 0.07
ACGTcount: A:0.42, C:0.37, G:0.00, T:0.21
Consensus pattern (21 bp):
AACCCTTAAACCATAAACCCT
Found at i:60484078 original size:15 final size:15
Alignment explanation
Indices: 60484043--60484090 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
60484033 TTTAAACCCC
* *
60484043 AACCCTTAAACCATA
1 AACCCATAATCCATA
*
60484058 AA-CCATAATCCCTA
1 AACCCATAATCCATA
*
60484072 AACCCATGATCCATA
1 AACCCATAATCCATA
60484087 AACC
1 AACC
60484091 TTAAGATAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:60484130 original size:272 final size:272
Alignment explanation
Indices: 60483765--60484484 Score: 1413
Period size: 272 Copynumber: 2.6 Consensus size: 272
60483755 ACCCTTTAGT
* *
60483765 ACCCCTAACCCTCAAACCATAAACCATAATCCCTAAACCCATAATCCATAAACCTTAAGATAGTA
1 ACCCC-AACCCTTAAACCATAAACCATAATCCCTAAACCCATGATCCATAAACCTTAAGATAGTA
60483830 ACTCCTAAACCTTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAATTAATACTATC
65 ACTCCTAAACCTTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAATTAATACTATC
60483895 TCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAATACTAATTAATCTAAACCC
130 TCTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAATACTAATTAATCTAAACCC
60483960 TAAACCCCTATCTCCTATCTCCTAAACCCTAAATCATAAACCCTTAACCCTTAAATAACCCTAAC
195 TAAACCCCTATCTCCTATCTCCTAAACCCTAAATCATAAACCCTTAACCCTTAAATAACCCTAAC
60484025 CCCTAAACTTTAA
260 CCCTAAACTTTAA
60484038 ACCCCAACCCTTAAACCATAAACCATAATCCCTAAACCCATGATCCATAAACCTTAAGATAGTAA
1 ACCCCAACCCTTAAACCATAAACCATAATCCCTAAACCCATGATCCATAAACCTTAAGATAGTAA
60484103 CTCCTAAACCTTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAATTAATACTATCT
66 CTCCTAAACCTTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAATTAATACTATCT
60484168 CTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAATACTAATTAATCTAAACCCT
131 CTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAATACTAATTAATCTAAACCCT
60484233 AAACCCCTATCTCCTATCTCCTAAACCCTAAATCATAAACCCTTAACCCTTAAATAACCCTAACC
196 AAACCCCTATCTCCTATCTCCTAAACCCTAAATCATAAACCCTTAACCCTTAAATAACCCTAACC
60484298 CCTAAACTTTAA
261 CCTAAACTTTAA
60484310 ACCCCAACCCTTAAACCATAAACCATAATCCCTAAACCCATGATCCATAAACCTTAAGATAGTAA
1 ACCCCAACCCTTAAACCATAAACCATAATCCCTAAACCCATGATCCATAAACCTTAAGATAGTAA
60484375 CTCCTAAACCTTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAATTAATACTATCT
66 CTCCTAAACCTTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAATTAATACTATCT
60484440 CTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAA
131 CTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAA
60484485 CAATCAATAA
Statistics
Matches: 445, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
272 440 0.99
273 5 0.01
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.30
Consensus pattern (272 bp):
ACCCCAACCCTTAAACCATAAACCATAATCCCTAAACCCATGATCCATAAACCTTAAGATAGTAA
CTCCTAAACCTTAAACCCTAAACTATAATGATAATTAATTCAATATTTTAAAATTAATACTATCT
CTTTTACGATTATATAAGAAATTATTTAATATATAAATTAAAAAATACTAATTAATCTAAACCCT
AAACCCCTATCTCCTATCTCCTAAACCCTAAATCATAAACCCTTAACCCTTAAATAACCCTAACC
CCTAAACTTTAA
Found at i:60484262 original size:7 final size:7
Alignment explanation
Indices: 60484252--60484348 Score: 52
Period size: 7 Copynumber: 13.3 Consensus size: 7
60484242 TCTCCTATCT
60484252 CCTAAAC
1 CCTAAAC
*
60484259 CCTAAAT
1 CCTAAAC
*
60484266 CATAAAC
1 CCTAAAC
*
60484273 CCTTAAC
1 CCTAAAC
60484280 CCTTAAATAAC
1 CC-T--A-AAC
*
60484291 CCTAACC
1 CCTAAAC
60484298 CCTAAAC
1 CCTAAAC
**
60484305 TTTAAAC
1 CCTAAAC
*
60484312 CC-CAAC
1 CCTAAAC
60484318 CCTTAAAC
1 CC-TAAAC
*
60484326 CATAAAC
1 CCTAAAC
* *
60484333 CATAATC
1 CCTAAAC
60484340 CCTAAAC
1 CCTAAAC
60484347 CC
1 CC
60484349 ATGATCCATA
Statistics
Matches: 66, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
6 5 0.08
7 49 0.74
8 6 0.09
10 1 0.02
11 5 0.08
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (7 bp):
CCTAAAC
Found at i:60484298 original size:17 final size:18
Alignment explanation
Indices: 60484270--60484303 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
60484260 CTAAATCATA
*
60484270 AACCCTTAACCCTTAAAT
1 AACCCTTAACCCCTAAAT
60484288 AACCC-TAACCCCTAAA
1 AACCCTTAACCCCTAAA
60484304 CTTTAAACCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (18 bp):
AACCCTTAACCCCTAAAT
Found at i:60484331 original size:21 final size:21
Alignment explanation
Indices: 60484256--60484347 Score: 70
Period size: 21 Copynumber: 4.6 Consensus size: 21
60484246 CTATCTCCTA
*
60484256 AACCC-TAAATCATAAACCCTT
1 AACCCTTAAACCATAAACCC-T
60484277 AACCCTT-AA--AT-AACCCT
1 AACCCTTAAACCATAAACCCT
* ** *
60484294 AACCCCTAAACTTTAAACCCC
1 AACCCTTAAACCATAAACCCT
*
60484315 AACCCTTAAACCATAAACCAT
1 AACCCTTAAACCATAAACCCT
60484336 AATCCC-TAAACC
1 AA-CCCTTAAACC
60484348 CATGATCCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
17 7 0.12
18 7 0.12
19 2 0.04
20 1 0.02
21 36 0.63
22 4 0.07
ACGTcount: A:0.42, C:0.37, G:0.00, T:0.21
Consensus pattern (21 bp):
AACCCTTAAACCATAAACCCT
Found at i:60484350 original size:15 final size:15
Alignment explanation
Indices: 60484315--60484362 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
60484305 TTTAAACCCC
* *
60484315 AACCCTTAAACCATA
1 AACCCATAATCCATA
*
60484330 AA-CCATAATCCCTA
1 AACCCATAATCCATA
*
60484344 AACCCATGATCCATA
1 AACCCATAATCCATA
60484359 AACC
1 AACC
60484363 TTAAGATAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:60484881 original size:40 final size:41
Alignment explanation
Indices: 60484705--60484900 Score: 232
Period size: 41 Copynumber: 4.8 Consensus size: 41
60484695 AATGTTTTTT
* * * *
60484705 GCGGCGCTTTTTTTAAAAATGCCGCTAAATCCCCGAGCATTA
1 GCGGCGC-TTTTTCAAAAACGCCGCTAAAGCCCCAAGCATTA
* * *
60484747 GCGGCGCTTTTTCAAAAACGCCGTTAAAGCACCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCAAGCATTA
* * * *
60484788 GCGGCGCTTTTTTAGAAACGCCGCTAAAGCACCAATCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCAAGCATTA
* * *
60484829 GCGGCACATTTTCAAAAACGTCGCT-AAGCCCCAAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCAAGCATTA
* *
60484869 GCTGTGCTTTTTCAAAAACGCCGCTAAAGCCC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCC
60484901 AGAAAGGTCG
Statistics
Matches: 131, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
40 33 0.25
41 91 0.69
42 7 0.05
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCCAAGCATTA
Found at i:60485012 original size:40 final size:38
Alignment explanation
Indices: 60484923--60485057 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 38
60484913 TGGGTTTAGG
* *
60484923 TCTTTTGCGGCGTTTCTTGGAAAAACGCCGCTAATGCTCA
1 TCTTTAGCGGCGTTTC-T-GAAAAGCGCCGCTAATGCTCA
*
60484963 T-TTTCAGCGGCGTGTTCTGAAAAGCGCCGCAAATGCTCAA
1 TCTTT-AGCGGCGT-TTCTGAAAAGCGCCGCTAATGCTC-A
* *
60485003 TCTTTAGCGGCGTTT-TCCATAAAGCGCTGCTAATGCTCTA
1 TCTTTAGCGGCGTTTCT-GA-AAAGCGCCGCTAATGCTC-A
*
60485043 TTTTTAGCGGCGTTT
1 TCTTTAGCGGCGTTT
60485058 TTTGTCCAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
38 1 0.01
39 24 0.30
40 50 0.62
41 6 0.07
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (38 bp):
TCTTTAGCGGCGTTTCTGAAAAGCGCCGCTAATGCTCA
Found at i:60485058 original size:40 final size:39
Alignment explanation
Indices: 60484943--60485058 Score: 135
Period size: 40 Copynumber: 2.9 Consensus size: 39
60484933 CGTTTCTTGG
* * * *
60484943 AAAAACGCCGCTAATGCTCATTTTCAGCGGCGTGTTCTG
1 AAAAGCGCCGCTAATGCTCATTTTTAGCGGCGTTTTCTC
* *
60484982 AAAAGCGCCGCAAATGCTCAATCTTTAGCGGCGTTTTC-C
1 AAAAGCGCCGCTAATGCTC-ATTTTTAGCGGCGTTTTCTC
*
60485021 ATAAAGCGCTGCTAATGCTCTATTTTTAGCGGCGTTTT
1 A-AAAGCGCCGCTAATGCTC-ATTTTTAGCGGCGTTTT
60485059 TTGTCCAAAC
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
39 18 0.28
40 47 0.72
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (39 bp):
AAAAGCGCCGCTAATGCTCATTTTTAGCGGCGTTTTCTC
Found at i:60488368 original size:16 final size:16
Alignment explanation
Indices: 60488347--60488377 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60488337 AAAAATTCAG
60488347 AAAAAATTAATAAAAT
1 AAAAAATTAATAAAAT
*
60488363 AAAAAATTATTAAAA
1 AAAAAATTAATAAAA
60488378 ACATAAAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAAATTAATAAAAT
Found at i:60503487 original size:27 final size:27
Alignment explanation
Indices: 60503457--60503634 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
60503447 ATATTGAGTC
* * * *
60503457 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
60503484 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
60503511 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
60503539 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
60503566 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
60503593 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
60503620 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
60503635 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:60503596 original size:82 final size:81
Alignment explanation
Indices: 60503478--60503633 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
60503468 TGCTATATAA
* *
60503478 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
60503543 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
60503560 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
60503624 CACTTAGTGC
65 CACTTAGTGC
60503634 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:60507688 original size:32 final size:32
Alignment explanation
Indices: 60507648--60507708 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
60507638 AAGAAAATTA
*
60507648 TTAATTAAAAATTGATAAAGATTAATTAATGG
1 TTAATTAAAAATTAATAAAGATTAATTAATGG
*
60507680 TTAATTAAAAGTTAATAAAGATTAATTAA
1 TTAATTAAAAATTAATAAAGATTAATTAA
60507709 CTTATAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (32 bp):
TTAATTAAAAATTAATAAAGATTAATTAATGG
Found at i:60518461 original size:9 final size:9
Alignment explanation
Indices: 60518445--60518478 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
60518435 TTTAATTAGA
60518445 AATTAATTT
1 AATTAATTT
*
60518454 AGTTAATTT
1 AATTAATTT
*
60518463 AATTAATTA
1 AATTAATTT
60518472 AATTAAT
1 AATTAAT
60518479 AGAATAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (9 bp):
AATTAATTT
Found at i:60519078 original size:18 final size:18
Alignment explanation
Indices: 60519057--60519091 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
60519047 TATATTCAAA
*
60519057 ATTTTATTAATTTTTATG
1 ATTTTATTAATATTTATG
*
60519075 ATTTTTTTAATATTTAT
1 ATTTTATTAATATTTAT
60519092 TTAATTATTG
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:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
ATTTTATTAATATTTATG
Found at i:60524625 original size:24 final size:24
Alignment explanation
Indices: 60524562--60524613 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
60524552 TTCCTAGAAG
* *
60524562 ATTTAGCATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
60524586 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
60524610 ATTT
1 ATTT
60524614 GACTTTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:60525527 original size:59 final size:59
Alignment explanation
Indices: 60525457--60525586 Score: 242
Period size: 59 Copynumber: 2.2 Consensus size: 59
60525447 AAAAAGTTAT
60525457 TTTTTTTATAAATAAGTTATGATAACAAAAAATATAACATTATTTTATGAATAAGTATA
1 TTTTTTTATAAATAAGTTATGATAACAAAAAATATAACATTATTTTATGAATAAGTATA
*
60525516 TTTTTTTATAAATAAGTTATGATAACAAAAAATATAACATTATTTTCTGAATAAGTATA
1 TTTTTTTATAAATAAGTTATGATAACAAAAAATATAACATTATTTTATGAATAAGTATA
60525575 TTATTTTTATAA
1 TT-TTTTTATAA
60525587 TATATAATGT
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
59 60 0.87
60 9 0.13
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (59 bp):
TTTTTTTATAAATAAGTTATGATAACAAAAAATATAACATTATTTTATGAATAAGTATA
Found at i:60527049 original size:44 final size:44
Alignment explanation
Indices: 60526970--60527075 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
60526960 ATATTGAGTA
* * * **
60526970 ACATTTCATAGCATATCATGTATCATGTCGGAACATATCA-TACC
1 ACATATCATAGCATATCATATATCATATCAAAACATAT-ATTACC
* * *
60527014 ACATGTCATAGCATATCATATTTCATATCAAAACATATATTATC
1 ACATATCATAGCATATCATATATCATATCAAAACATATATTACC
*
60527058 ACATATCATAACATATCA
1 ACATATCATAGCATATCA
60527076 AATCCTACCC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 1 0.02
44 51 0.98
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.33
Consensus pattern (44 bp):
ACATATCATAGCATATCATATATCATATCAAAACATATATTACC
Found at i:60527050 original size:22 final size:23
Alignment explanation
Indices: 60527001--60527075 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 23
60526991 ATCATGTCGG
* * *
60527001 AACATATCA-TACCACATGTCAT
1 AACATATCATTATCACATATCAA
* **
60527023 AGCATATCA-TATTTCATATCAA
1 AACATATCATTATCACATATCAA
*
60527045 AACATAT-ATTATCACATATCAT
1 AACATATCATTATCACATATCAA
60527067 AACATATCA
1 AACATATCA
60527076 AATCCTACCC
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
21 1 0.02
22 39 0.95
23 1 0.02
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (23 bp):
AACATATCATTATCACATATCAA
Found at i:60527608 original size:12 final size:12
Alignment explanation
Indices: 60527591--60527623 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
60527581 CTGTGTGGTG
*
60527591 CACACGATCTAC
1 CACACGACCTAC
60527603 CACACGACCTAC
1 CACACGACCTAC
60527615 CACACGACC
1 CACACGACC
60527624 GTGTGGCGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.33, C:0.48, G:0.09, T:0.09
Consensus pattern (12 bp):
CACACGACCTAC
Found at i:60537395 original size:19 final size:18
Alignment explanation
Indices: 60537361--60537396 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
60537351 GTAAATATTT
*
60537361 TTATCATTTCACTTTTAG
1 TTATCATTTAACTTTTAG
60537379 TTATCATTTTAACTTTTA
1 TTATCA-TTTAACTTTTA
60537397 TCATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (18 bp):
TTATCATTTAACTTTTAG
Found at i:60537723 original size:42 final size:43
Alignment explanation
Indices: 60537578--60537885 Score: 306
Period size: 42 Copynumber: 7.2 Consensus size: 43
60537568 TCTGCCAAAA
* * * * *
60537578 TTAGCGGCGTTTTT-TAAAAAAGCTCCACTAAAGGTC-GTTGTCA
1 TTAGCGGCGTTTTTGT-GAAAAGCGCCGCTAAAGGTCAG-GGTCT
* * *
60537621 TTAGCGGCGTTTGTG-GAAAAAATCGCCGTTAAAGGTCAGGGTCT
1 TTAGCGGCGTTTTTGTG--AAAAGCGCCGCTAAAGGTCAGGGTCT
* *** *
60537665 TTAGCGGCATTTTTGTGAAAAGCGCCGCTAAAGGTCCTTGTCA
1 TTAGCGGCGTTTTTGTGAAAAGCGCCGCTAAAGGTCAGGGTCT
*
60537708 TT-GCGGCGTTTTTGTGAAAAGCGCCGCTAAAGGTCAGAGTCT
1 TTAGCGGCGTTTTTGTGAAAAGCGCCGCTAAAGGTCAGGGTCT
* * * *
60537750 TTAGCGGCGATTGTAG-GAAAAGTGCCGCTAAAGATCAGGGTCT
1 TTAGCGGCG-TTTTTGTGAAAAGCGCCGCTAAAGGTCAGGGTCT
* * *
60537793 TTAGCGGCGTTTTTG-GGAATGCGCCGCTAAAGATCAGGGTCT
1 TTAGCGGCGTTTTTGTGAAAAGCGCCGCTAAAGGTCAGGGTCT
* * *
60537835 TTAGCTGCGTTTTTGT-AAAAGCGCCGGTAAAGGTCATGGTCT
1 TTAGCGGCGTTTTTGTGAAAAGCGCCGCTAAAGGTCAGGGTCT
60537877 TTAGCGGCG
1 TTAGCGGCG
60537886 CATTCCCAAA
Statistics
Matches: 219, Mismatches: 38, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
42 108 0.49
43 74 0.34
44 35 0.16
45 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (43 bp):
TTAGCGGCGTTTTTGTGAAAAGCGCCGCTAAAGGTCAGGGTCT
Found at i:60537770 original size:85 final size:85
Alignment explanation
Indices: 60537578--60537885 Score: 325
Period size: 85 Copynumber: 3.6 Consensus size: 85
60537568 TCTGCCAAAA
* ** * * * *
60537578 TTAGCGGCGTTTTTTAAAAAAGCTCCACTAAAGGTCGTTGTCATTAGCGGCGTTTGTGGAAAAAA
1 TTAGCGGCGATTTTTGGAAAAGCGCCGCTAAAGGTCATTGTCATTAGCGGCGTTTTTGG--AAAA
* *
60537643 TCGCCGTTAAAGGTCAGGGTCT
64 GCGCCGCTAAAGGTCAGGGTCT
*
60537665 TTAGCGGC-ATTTTTGTGAAAAGCGCCGCTAAAGGTCCTTGTCATT-GCGGCGTTTTTGTGAAAA
1 TTAGCGGCGATTTTTG-GAAAAGCGCCGCTAAAGGTCATTGTCATTAGCGGCGTTTTTG-GAAAA
*
60537728 GCGCCGCTAAAGGTCAGAGTCT
64 GCGCCGCTAAAGGTCAGGGTCT
* * * * ** * * *
60537750 TTAGCGGCGATTGTAGGAAAAGTGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTTGGGAATGC
1 TTAGCGGCGATTTTTGGAAAAGCGCCGCTAAAGGTCATTGTCATTAGCGGCGTTTTTGGAAAAGC
*
60537815 GCCGCTAAAGATCAGGGTCT
66 GCCGCTAAAGGTCAGGGTCT
* * * * *
60537835 TTAGCTGCG-TTTTTGTAAAAGCGCCGGTAAAGGTCATGGTCTTTAGCGGCG
1 TTAGCGGCGATTTTTGGAAAAGCGCCGCTAAAGGTCATTGTCATTAGCGGCG
60537886 CATTCCCAAA
Statistics
Matches: 187, Mismatches: 30, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
84 35 0.19
85 85 0.45
86 33 0.18
87 34 0.18
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (85 bp):
TTAGCGGCGATTTTTGGAAAAGCGCCGCTAAAGGTCATTGTCATTAGCGGCGTTTTTGGAAAAGC
GCCGCTAAAGGTCAGGGTCT
Found at i:60547366 original size:18 final size:17
Alignment explanation
Indices: 60547339--60547373 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
60547329 AGAAAATTGG
60547339 TTATTGAGTTGGATAAA
1 TTATTGAGTTGGATAAA
*
60547356 TTATATGAGTTGGTTAAA
1 TTAT-TGAGTTGGATAAA
60547374 AATTCAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (17 bp):
TTATTGAGTTGGATAAA
Found at i:60547974 original size:10 final size:10
Alignment explanation
Indices: 60547944--60547974 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
60547934 ATCACAAGTC
60547944 TTGTGATATA
1 TTGTGATATA
*
60547954 GTGTGATATA
1 TTGTGATATA
60547964 TTGTGATATA
1 TTGTGATATA
60547974 T
1 T
60547975 ATATATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (10 bp):
TTGTGATATA
Found at i:60551803 original size:15 final size:15
Alignment explanation
Indices: 60551783--60551813 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
60551773 GACGGTTCCG
60551783 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
60551798 TGTGCTCTGATTCAT
1 TGTGCTCTGATTCAT
60551813 T
1 T
60551814 ACTGATACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
TGTGCTCTGATTCAT
Found at i:60558737 original size:125 final size:126
Alignment explanation
Indices: 60558509--60558929 Score: 621
Period size: 126 Copynumber: 3.3 Consensus size: 126
60558499 ATTTAAAGAC
* * *
60558509 GCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCTTGAGAAAATAATTTCGAGTAGACGTTTCT
1 GCTCCCACGTAGACGCGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGACGTTTCT
** *
60558574 GAGCAAACAGTGTCAAAAACGCTTTAAATAGGATGCTTTGTCAGCAGAAGTACTGAAAAAA
66 GAGCAAACAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAGAAGTACTGAAAAAA
* * * *
60558635 GCTCTCACGTAGACGCGTTTTTGCTACAGTAGCTCCT-AAAAAATAATTTCGAGTAGACGTTTTT
1 GCTCCCACGTAGACGCGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGACGTTTCT
* * *
60558699 GAGTAAACAGTGTCAAGAACGCTTTAAGCAATATGCTTTGTCAGCAGAAGTACTGAAAAAA
66 GAGCAAACAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAGAAGTACTGAAAAAA
* * *
60558760 GCTTCCACATGGACGCGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGACGTTTCT
1 GCTCCCACGTAGACGCGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGACGTTTCT
* * * *
60558825 GAGCAAACAATGTCAAAAACGCTTTAAGCAAGATGCTTTGTTAGAAGAAGTACTGAAAGAA
66 GAGCAAACAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAGAAGTACTGAAAAAA
* *
60558886 GCTCCCACGTAGACACGCTTTTGCTACAGTAACTAC-TGAAAAAA
1 GCTCCCACGTAGACGCGCTTTTGCTACAGTAGCT-CTTGAAAAAA
60558930 GCTCTCACGT
Statistics
Matches: 261, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
125 111 0.43
126 149 0.57
127 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (126 bp):
GCTCCCACGTAGACGCGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTCGAGTAGACGTTTCT
GAGCAAACAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAGAAGTACTGAAAAAA
Found at i:60558925 original size:44 final size:44
Alignment explanation
Indices: 60558875--60558959 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
60558865 TTAGAAGAAG
*
60558875 TACTGAAAGAAGCTCCCACGTAGACACGCTTTTGCTACAGTAAC
1 TACTGAAAAAAGCTCCCACGTAGACACGCTTTTGCTACAGTAAC
* * *
60558919 TACTGAAAAAAGCTCTCACGTGGACGCGCTTTTGCTACAGT
1 TACTGAAAAAAGCTCCCACGTAGACACGCTTTTGCTACAGT
60558960 GGCGCATGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (44 bp):
TACTGAAAAAAGCTCCCACGTAGACACGCTTTTGCTACAGTAAC
Found at i:60564294 original size:18 final size:18
Alignment explanation
Indices: 60564235--60564296 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
60564225 AACAAATAAT
60564235 AAATT-AATAATTATTT-A
1 AAATTAAATAA-TATTTAA
* *
60564252 AAATTACATAA-A-TAAA
1 AAATTAAATAATATTTAA
60564268 AAATCTTAAATAATATTTAA
1 AAA--TTAAATAATATTTAA
60564288 AAATTAAAT
1 AAATTAAAT
60564297 TTAACACTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
15 1 0.03
16 5 0.14
17 5 0.14
18 17 0.49
19 1 0.03
20 6 0.17
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTAAATAATATTTAA
Found at i:60564484 original size:11 final size:11
Alignment explanation
Indices: 60564470--60564581 Score: 110
Period size: 11 Copynumber: 10.6 Consensus size: 11
60564460 AAATAGGGAT
*
60564470 TTGAGAGGAAT
1 TTGAGAGGAAA
*
60564481 TTGAGAGAAAA
1 TTGAGAGGAAA
*
60564492 TTGAGAGCAAA
1 TTGAGAGGAAA
**
60564503 TTGAGATTAAA
1 TTGAGAGGAAA
*
60564514 -T-AG-GG-AT
1 TTGAGAGGAAA
60564521 TTGAGA-GAAA
1 TTGAGAGGAAA
60564531 TTTGAGAGGAAA
1 -TTGAGAGGAAA
*
60564543 TTGAGAGCAAA
1 TTGAGAGGAAA
60564554 TTGAGAGGAAA
1 TTGAGAGGAAA
60564565 TTGAGAGGAAA
1 TTGAGAGGAAA
60564576 TT-AGAG
1 TTGAGAG
60564582 AAAGGATTTA
Statistics
Matches: 84, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 5 0.06
10 6 0.07
11 67 0.80
12 4 0.05
ACGTcount: A:0.44, C:0.02, G:0.31, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:60564518 original size:51 final size:51
Alignment explanation
Indices: 60564458--60564559 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
60564448 TAAAGCTCCT
*
60564458 TTAAATAGGGATTTGAGAGGAATTTGAGAGAAAATTGAGAGCAAATTGAGA
1 TTAAATAGGGATTTGAGAGAAATTTGAGAGAAAATTGAGAGCAAATTGAGA
*
60564509 TTAAATAGGGATTTGAGAGAAATTTGAGAGGAAATTGAGAGCAAATTGAGA
1 TTAAATAGGGATTTGAGAGAAATTTGAGAGAAAATTGAGAGCAAATTGAGA
60564560 GGAAATTGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.43, C:0.02, G:0.29, T:0.25
Consensus pattern (51 bp):
TTAAATAGGGATTTGAGAGAAATTTGAGAGAAAATTGAGAGCAAATTGAGA
Found at i:60570474 original size:9 final size:9
Alignment explanation
Indices: 60570462--60570508 Score: 53
Period size: 8 Copynumber: 5.2 Consensus size: 9
60570452 TGTATTAAAT
60570462 TTATTTTTA
1 TTATTTTTA
60570471 TTA-TTTTA
1 TTATTTTTA
60570479 TTA-TTTTA
1 TTATTTTTA
60570487 GTTATTTTTA
1 -TTATTTTTA
*
60570497 TTTTATTTTA
1 TTAT-TTTTA
60570507 TT
1 TT
60570509 TTATTGTTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
8 13 0.38
9 9 0.26
10 12 0.35
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (9 bp):
TTATTTTTA
Found at i:60570491 original size:26 final size:25
Alignment explanation
Indices: 60570462--60570511 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
60570452 TGTATTAAAT
60570462 TTATTTTTATTATT-TTATTATTTTAG
1 TTATTTTTATT-TTATT-TTATTTTAG
60570488 TTATTTTTATTTTATTTTATTTTA
1 TTATTTTTATTTTATTTTATTTTA
60570512 TTGTTAGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (25 bp):
TTATTTTTATTTTATTTTATTTTAG
Found at i:60570502 original size:5 final size:5
Alignment explanation
Indices: 60570461--60570513 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
60570451 GTGTATTAAA
* *
60570461 TTTAT TTT-T ATTAT TTTA- -TTAT TTTA- GTTATT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT
60570508 TTTAT T
1 TTTAT T
60570514 GTTAGCTACC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
3 3 0.08
4 6 0.15
5 27 0.69
6 3 0.08
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:60572152 original size:9 final size:9
Alignment explanation
Indices: 60572135--60572171 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
60572125 TGAGTTTTTG
60572135 AATTCGAAT
1 AATTCGAAT
*
60572144 AACTCGAAT
1 AATTCGAAT
60572153 AATTCGAAT
1 AATTCGAAT
60572162 AATTCGAAT
1 AATTCGAAT
60572171 A
1 A
60572172 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:60574651 original size:13 final size:14
Alignment explanation
Indices: 60574623--60574658 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
60574613 CAAAGTGAGT
60574623 AGAAAAATAAAAAA
1 AGAAAAATAAAAAA
*
60574637 AGAAAAA-AAAGAA
1 AGAAAAATAAAAAA
60574650 AGAAAAATA
1 AGAAAAATA
60574659 CTCATTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (14 bp):
AGAAAAATAAAAAA
Found at i:60579100 original size:29 final size:29
Alignment explanation
Indices: 60578968--60579104 Score: 122
Period size: 29 Copynumber: 4.8 Consensus size: 29
60578958 CAAAGTCATT
60578968 CTTTG-AGAGGTTTGCCACAAAGGC-TAC
1 CTTTGTAGAGGTTTGCCACAAAGGCTTAC
* *
60578995 CTTT-TAATAGGTTTGCCACAAATGCTTAC
1 CTTTGT-AGAGGTTTGCCACAAAGGCTTAC
* * * * *
60579024 CTTTCTAGAGTTTTACCACAAGGGTTGTA-
1 CTTTGTAGAGGTTTGCCACAAAGGCT-TAC
* *
60579053 C-TTGAACAGGTTTGCCACAAAGGCTTAC
1 CTTTGTAGAGGTTTGCCACAAAGGCTTAC
* *
60579081 CTTTGTAGAGTTTTTCCACAAAGG
1 CTTTGTAGAGGTTTGCCACAAAGG
60579105 TGCCCTGAAA
Statistics
Matches: 84, Mismatches: 19, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
27 6 0.07
28 35 0.42
29 40 0.48
30 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (29 bp):
CTTTGTAGAGGTTTGCCACAAAGGCTTAC
Found at i:60579370 original size:53 final size:53
Alignment explanation
Indices: 60579255--60579405 Score: 155
Period size: 53 Copynumber: 2.9 Consensus size: 53
60579245 CTTAAAATTT
* ** * * * * *
60579255 TCCATATGATTCTATAACCTACTAGTTACAGTCTTACATGAAATGATTTTTTT
1 TCCATATGATACTATAACCTACTAGTTATGGTCTTACACGATATGAATTCTTC
*
60579308 TCCACATGATACTATAACCTACTAGTTATGGTCTTACACGATATGACATTCTTC
1 TCCATATGATACTATAACCTACTAGTTATGGTCTTACACGATATGA-ATTCTTC
* * *
60579362 T-CATATGATAC-ATAA-CTCACCAATTATGGTCTTACACAATATGA
1 TCCATATGATACTATAACCT-ACTAGTTATGGTCTTACACGATATGA
60579406 TTTTATTCAG
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
51 2 0.02
52 27 0.33
53 49 0.59
54 5 0.06
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (53 bp):
TCCATATGATACTATAACCTACTAGTTATGGTCTTACACGATATGAATTCTTC
Found at i:60583379 original size:16 final size:17
Alignment explanation
Indices: 60583333--60583379 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
60583323 ATCATATCAC
60583333 ATATTCACATGTATC-ATT
1 ATATTCACA--TATCAATT
60583351 ATATTCACA-ATCAATT
1 ATATTCACATATCAATT
60583367 ATATTCA-ATATCA
1 ATATTCACATATCA
60583380 CCATCCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.15
16 14 0.52
18 9 0.33
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATTCACATATCAATT
Found at i:60583974 original size:21 final size:20
Alignment explanation
Indices: 60583921--60583975 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 20
60583911 TTAATCATAG
60583921 TTAATTAGTTTAATTATAAT
1 TTAATTAGTTTAATTATAAT
* *
60583941 TTATTTTA-CTTAATTACTAA-
1 TTA-ATTAGTTTAATTA-TAAT
60583961 TTAATTAAGTTTAAT
1 TTAATT-AGTTTAAT
60583976 GACATCTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
19 2 0.07
20 14 0.52
21 11 0.41
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (20 bp):
TTAATTAGTTTAATTATAAT
Found at i:60587323 original size:23 final size:22
Alignment explanation
Indices: 60587280--60587337 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
60587270 AAAGGGTATC
* *
60587280 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
60587301 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
60587324 TGCATATCATATCT
1 TACAAATCATATCT
60587338 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:60588036 original size:131 final size:132
Alignment explanation
Indices: 60587817--60588119 Score: 410
Period size: 131 Copynumber: 2.3 Consensus size: 132
60587807 AAGGCTGGTG
* * * *
60587817 GCTTAAATCTGCTTCCCTACTACCTCGAGAAGATAAGACTTGCCATCTTTGATTTGCTCCACTAC
1 GCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTTGCCATCTTCGATCTGCTCCACTAC
* *
60587882 TACTTAGAGAGACAAGATATACAATCTTTAATCTACTCCACTACTGCTCAGGGAGATAGGAATGA
66 TACTTAGAGAGACAAGATATACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAGGAATGA
60587947 TA
131 TA
* * * *
60587949 GCTTAAATATGCTT-CCTACTATCTCGGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTAT
1 GCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTTGCCATCTTCGATCTGCTCCACTAC
* * * * * * ** *
60588013 TGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCTATTACTGCTCAGGGAGATAGGTCTGG
66 TACTTAGAGAGACAAGATATACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAGGAATGA
*
60588078 TG
131 TA
*
60588080 GCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATT
1 GCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATT
60588120 CACTGTCTTT
Statistics
Matches: 147, Mismatches: 23, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
131 111 0.76
132 36 0.24
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (132 bp):
GCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTTGCCATCTTCGATCTGCTCCACTAC
TACTTAGAGAGACAAGATATACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAGGAATGA
TA
Found at i:60588279 original size:44 final size:44
Alignment explanation
Indices: 60588172--60588564 Score: 158
Period size: 44 Copynumber: 8.8 Consensus size: 44
60588162 GATTTACTAT
* * * *
60588172 CTTCAGTCTACTCCACAGCAACTTCAGGGAGATAAGA--CTTCA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTCA
* * **
60588214 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATAGGATTATTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTCA
*
60588258 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TTC-
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTCA
* * * * ** * *
60588300 CAT-GATCTACTCTACTGCAACTTCAAAGAGAAAAGATCTGTGATTTATA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-T-A-TT-CA
* ** * * * * * * **
60588349 GCTTTAATCTATTCCGCTACAGCTTCAGGAAAATGAGATT-CGCTA
1 -CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTC-A
* * * * ** *
60588394 TCTTCAGTTTGCTCCACTGGAACTTCAGGGAGATAAGACTGGTCT
1 -CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTCA
* * ** *
60588439 CTTCAGT-TCGCTCCACTGTAACTTCAAAGAGATAGGATTATT-A
1 CTTCAATCT-GCTCCACTGCAACTTCAGGGAGATAAGATTATTCA
* * * *
60588482 GCTTTAATCTACTCCGCTGCAACTTCAGGGAGATAAGATT-TGCCA
1 -CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT-TCA
* * * *
60588527 TCTTCAGTCTGC-CCTACTACAACTTTAGGGGGATAAGA
1 -CTTCAATCTGCTCC-ACTGCAACTTCAGGGAGATAAGA
60588565 CTTGCTTTCT
Statistics
Matches: 253, Mismatches: 78, Indels: 37
0.69 0.21 0.10
Matches are distributed among these distances:
41 27 0.11
42 34 0.13
43 5 0.02
44 103 0.41
45 56 0.22
46 1 0.00
47 2 0.01
48 1 0.00
49 1 0.00
50 2 0.01
51 21 0.08
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATTCA
Found at i:60588654 original size:44 final size:44
Alignment explanation
Indices: 60588585--60589070 Score: 451
Period size: 44 Copynumber: 11.0 Consensus size: 44
60588575 GCAATAAGAC
*
60588585 TTGTAACTTTAATC-GCTCCACTGCAACTTCAAGGAGATAGGAT
1 TTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT
* * * *
60588628 TTGTAAATTTAATCCGCTCCACTGCAACTTTAGAGAGATAGGAT
1 TTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT
** * * * * *
60588672 TAT-TGGCTTTAATCTGCTCCATTACAACTTTAGGGAGTTAAGAT
1 T-TGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT
* * ** * * * * *
60588716 TTGCCATCTTTTGTTTGCTTCACTGCAACTTTAGGGAGATAAGAC
1 TTG-TAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT
* *
60588761 TTGTAACTTTAAT-TCGCTCGATTGCAACTTCAGGGAGATAGGAT
1 TTGTAACTTTAATCT-GCTCCACTGCAACTTCAGGGAGATAGGAT
* * *
60588805 TTGTAACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGAAT
1 TTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT
** ** * *
60588849 TACTGGCTTTAATCTGCTCCACTTCAACTTCAGGGAGATAAGAT
1 TTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT
* * * * * * * *
60588893 TTGTCATCTTCAGTCTGCTCCATTGTAACTTCAGGTAGATAAGAC
1 TTGT-AACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT
*
60588938 TTGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT
1 TTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT
* * *
60588982 TAT-TAGCTTTAATCTGCTCCATTGTAACTTCAGGGAGATAGGAT
1 T-TGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT
** * *
60589026 TAT-TGGCTTTAATCTGCTCCACTGCAACTTCATGGAGATAAGAT
1 T-TGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT
60589070 T
1 T
60589071 CACCATCTTC
Statistics
Matches: 359, Mismatches: 76, Indels: 15
0.80 0.17 0.03
Matches are distributed among these distances:
43 15 0.04
44 274 0.76
45 70 0.19
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (44 bp):
TTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGAT
Found at i:60588841 original size:133 final size:131
Alignment explanation
Indices: 60588591--60589070 Score: 455
Period size: 133 Copynumber: 3.6 Consensus size: 131
60588581 AGACTTGTAA
* * * *
60588591 CTTTAATC-GCTCCACTGCAACTTCAAGGAGATAGGATTTGTAAATTTAATCCGCTCCACTGCAA
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-AATTTAATTCGCTCCATTGCAA
* * ** * * * * * *
60588655 CTTTAGAGAGATAGGATTAT-TGGCTTTAATCTGCTCCATTACAACTTTAGGGAGTTAAGATTTG
65 CTTCAGGGAGATAGGATT-TGTAACTTTAATCCGCTCCACTACAACTTCAGGGAGAT-AGAATTA
*
60588719 CCAT
128 CCAG
** * * * * *
60588723 CTTTTGTTTGCTTCACTGCAACTTTAGGGAGATAAGACTTGTAACTTTAATTCGCTCGATTGCAA
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAA-TTTAATTCGCTCCATTGCAA
*
60588788 CTTCAGGGAGATAGGATTTGTAACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGAATTACT
65 CTTCAGGGAGATAGGATTTGTAACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGAATTACC
*
60588853 GG
130 AG
* * * * *
60588855 CTTTAATCTGCTCCACTTCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCTGCTCCATTGTA
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAAT-TTAATTC-GCTCCATTGCA
* * * * * *
60588920 ACTTCAGGTAGATAAGACTTGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAT
64 ACTTCAGGGAGATAGGATTTGTAACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGAATTAC
*
60588985 TAG
129 CAG
* * * ** *
60588988 CTTTAATCTGCTCCATTGTAACTTCAGGGAGATAGGATTAT-TGGCTTTAA-TCTGCTCCACTGC
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGT-AATTTAATTC-GCTCCATTGC
* *
60589051 AACTTCATGGAGATAAGATT
63 AACTTCAGGGAGATAGGATT
60589071 CACCATCTTC
Statistics
Matches: 286, Mismatches: 55, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
131 1 0.00
132 83 0.29
133 200 0.70
134 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (131 bp):
CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAATTTAATTCGCTCCATTGCAAC
TTCAGGGAGATAGGATTTGTAACTTTAATCCGCTCCACTACAACTTCAGGGAGATAGAATTACCA
G
Found at i:60588893 original size:177 final size:177
Alignment explanation
Indices: 60588578--60589080 Score: 706
Period size: 177 Copynumber: 2.8 Consensus size: 177
60588568 GCTTTCTGCA
* *
60588578 ATAAGACTTGTAACTTTAA-TCGCTCCACTGCAACTTCAAGGAGATAGGATTTGTAAATTTAATC
1 ATAAGACTTGTAACTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTAACTTTAATC
* * *
60588642 CGCTCCACTGCAACTTTAGAGAGATAGGATTATTGGCTTTAATCTGCTCCA-TTACAACTTTAGG
66 CGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTT-CAACTTCAGG
* ** * * *
60588706 GAGTTAAGATTTGCCATCTTTTGTTTGCTTCACTGCAACTTTAGGGAG
130 GAGATAAGATTTGCCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
* *
60588754 ATAAGACTTGTAACTTTAATTCGCTCGATTGCAACTTCAGGGAGATAGGATTTGTAACTTTAATC
1 ATAAGACTTGTAACTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTAACTTTAATC
* * *
60588819 CGCTCCACTACAACTTCAGGGAGATAGAATTACTGGCTTTAATCTGCTCCACTTCAACTTCAGGG
66 CGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTTCAACTTCAGGG
* * * *
60588884 AGATAAGATTTGTCATCTTCAGTCTGCTCCATTGTAACTTCAGGTAG
131 AGATAAGATTTGCCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
* *
60588931 ATAAGACTTGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAT-TAGCTTTAAT
1 ATAAGACTTGTAACTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATT-TGTAACTTTAAT
* * * * *
60588995 CTGCTCCATTGTAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTCATG
65 CCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTTCAACTTCAGG
**
60589060 GAGATAAGATTCACCATCTTC
130 GAGATAAGATTTGCCATCTTC
60589081 TTCAATATAT
Statistics
Matches: 289, Mismatches: 35, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
176 19 0.07
177 267 0.92
178 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (177 bp):
ATAAGACTTGTAACTTTAATTCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTAACTTTAATC
CGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTTCAACTTCAGGG
AGATAAGATTTGCCATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
Found at i:60605649 original size:14 final size:12
Alignment explanation
Indices: 60605612--60605641 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
60605602 AAATTTTATA
60605612 TTTAAAATATTT
1 TTTAAAATATTT
*
60605624 TTTTAAATATTT
1 TTTAAAATATTT
60605636 TTTAAA
1 TTTAAA
60605642 TAATATTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTAAAATATTT
Found at i:60609670 original size:12 final size:12
Alignment explanation
Indices: 60609653--60609680 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
60609643 GAATGTTTCT
60609653 AATGTTACAAGC
1 AATGTTACAAGC
60609665 AATGTTACAAGC
1 AATGTTACAAGC
60609677 AATG
1 AATG
60609681 AGTGGCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (12 bp):
AATGTTACAAGC
Found at i:60612311 original size:61 final size:61
Alignment explanation
Indices: 60612206--60612373 Score: 185
Period size: 61 Copynumber: 2.8 Consensus size: 61
60612196 ATTTTTGAAG
* * * * * *
60612206 GGAAAGCCTTTGTGGTGAGTACTGGTTATAAATGACAGCTTTTGTGGCATAACTTTAGACA
1 GGAAAGCCTTTGTGGTGAGTACTGGATATAAAGGATAGCCTTTGTGGCACAACTCTAGACA
* * *
60612267 GGAAAGCCTTTATGGTGAGTATTGGATATAAAGGATAGCCTTTGTGACACAACTCTAGACA
1 GGAAAGCCTTTGTGGTGAGTACTGGATATAAAGGATAGCCTTTGTGGCACAACTCTAGACA
** * * * * *
60612328 ACAAAACCTTTGTGGGGAGCACTAGATATAAAGGAT-GGCTTTGTGG
1 GGAAAGCCTTTGTGGTGAGTACTGGATATAAAGGATAGCCTTTGTGG
60612374 AAAAACTCAG
Statistics
Matches: 88, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 8 0.09
61 80 0.91
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (61 bp):
GGAAAGCCTTTGTGGTGAGTACTGGATATAAAGGATAGCCTTTGTGGCACAACTCTAGACA
Found at i:60612728 original size:16 final size:16
Alignment explanation
Indices: 60612707--60612737 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60612697 TTTCACTTTA
*
60612707 TGTCTTTTGTATTTTT
1 TGTCTTTTATATTTTT
60612723 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
60612738 GTATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTT
Found at i:60622425 original size:30 final size:31
Alignment explanation
Indices: 60622391--60622448 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
60622381 GTAAATACTC
* **
60622391 AAAATTTGAGGGGTTAA-AGTGCAAATAAGA
1 AAAATTTGAAGGACTAATAGTGCAAATAAGA
60622421 AAAATTTGAAGGACTAATAGTGCAAATA
1 AAAATTTGAAGGACTAATAGTGCAAATA
60622449 TTTTAAGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.48, C:0.05, G:0.22, T:0.24
Consensus pattern (31 bp):
AAAATTTGAAGGACTAATAGTGCAAATAAGA
Found at i:60631165 original size:25 final size:25
Alignment explanation
Indices: 60631105--60631165 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
60631095 CTACTAAATT
*
60631105 TTAATTTAATTATCTAATTTTTAAA
1 TTAATTAAATTATCTAATTTTTAAA
* * *
60631130 TTTATTGAATTAT-TAATATTTTATA
1 TTAATTAAATTATCTAAT-TTTTAAA
60631155 TTAATTAAATT
1 TTAATTAAATT
60631166 TTTGAGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATCTAATTTTTAAA
Found at i:60637159 original size:17 final size:17
Alignment explanation
Indices: 60637137--60637191 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
60637127 ACGAAACAAA
60637137 TTGATAGGAAGAATCAC
1 TTGATAGGAAGAATCAC
**
60637154 TTGATA-TNA-AA-CAC
1 TTGATAGGAAGAATCAC
*
60637168 ATTGATCGGAAGAATCAC
1 -TTGATAGGAAGAATCAC
60637186 TTGATA
1 TTGATA
60637192 TGAGAGGCAG
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 3 0.11
15 7 0.25
16 2 0.07
17 13 0.46
18 3 0.11
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.27
Consensus pattern (17 bp):
TTGATAGGAAGAATCAC
Found at i:60637166 original size:32 final size:31
Alignment explanation
Indices: 60637130--60637192 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
60637120 CAAGAGGACG
60637130 AAACAAATTGATAGGAAGAATCACTTGATAT
1 AAACAAATTGATAGGAAGAATCACTTGATAT
* *
60637161 NAAACACATTGATCGGAAGAATCACTTGATAT
1 -AAACAAATTGATAGGAAGAATCACTTGATAT
60637193 GAGAGGCAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.25
Consensus pattern (31 bp):
AAACAAATTGATAGGAAGAATCACTTGATAT
Found at i:60637475 original size:14 final size:14
Alignment explanation
Indices: 60637453--60637487 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
60637443 CACATTTTAC
* *
60637453 TATTATGTCTCTTT
1 TATTTTGTCTCTTA
60637467 TATTTTGTCTCTTA
1 TATTTTGTCTCTTA
60637481 TATTTTG
1 TATTTTG
60637488 CATACATAGC
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:0.14, C:0.11, G:0.09, T:0.66
Consensus pattern (14 bp):
TATTTTGTCTCTTA
Found at i:60644080 original size:19 final size:19
Alignment explanation
Indices: 60644056--60644093 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
60644046 GACTTTTGCT
60644056 GATTATGGTTTGTTAGAAG
1 GATTATGGTTTGTTAGAAG
60644075 GATTATGGTTTGTTAGAAG
1 GATTATGGTTTGTTAGAAG
60644094 ACATTCATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
GATTATGGTTTGTTAGAAG
Found at i:60645774 original size:26 final size:26
Alignment explanation
Indices: 60645738--60645791 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
60645728 ATGTTTGAAG
60645738 CTACATCGATTAGTTGGATATTCTAA
1 CTACATCGATTAGTTGGATATTCTAA
60645764 CTACATCGATTAGTTGGATATTCTAA
1 CTACATCGATTAGTTGGATATTCTAA
60645790 CT
1 CT
60645792 TTTGTACCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (26 bp):
CTACATCGATTAGTTGGATATTCTAA
Found at i:60649735 original size:47 final size:47
Alignment explanation
Indices: 60649678--60649934 Score: 365
Period size: 47 Copynumber: 5.4 Consensus size: 47
60649668 ATTGATGTAC
* * *
60649678 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
60649725 AAGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
60649774 ACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
60649821 ACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
60649868 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGG
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
60649915 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
60649935 TCCCGAAGGG
Statistics
Matches: 192, Mismatches: 14, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
46 1 0.01
47 150 0.78
49 40 0.21
50 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.27
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:60649812 original size:22 final size:22
Alignment explanation
Indices: 60649785--60649906 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
60649775 CATGTGTATG
60649785 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
60649807 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
60649832 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
60649854 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
60649879 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
60649901 TGTGAT
1 TGTGAT
60649907 GGATGTGGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 21 0.30
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:60653535 original size:57 final size:57
Alignment explanation
Indices: 60653468--60653576 Score: 182
Period size: 57 Copynumber: 1.9 Consensus size: 57
60653458 CATTTTGACA
**
60653468 AACATAAATATGTGCATTAAGAGACATTATCACAGCAACTATAAATTACATTTGGCC
1 AACATAAATATGCACATTAAGAGACATTATCACAGCAACTATAAATTACATTTGGCC
* *
60653525 AACATAAATATGCACATTAAGAGACATTTTGACAGCAACTATAAATTACATT
1 AACATAAATATGCACATTAAGAGACATTATCACAGCAACTATAAATTACATT
60653577 AAGGCCGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (57 bp):
AACATAAATATGCACATTAAGAGACATTATCACAGCAACTATAAATTACATTTGGCC
Found at i:60653588 original size:57 final size:57
Alignment explanation
Indices: 60653468--60653590 Score: 176
Period size: 57 Copynumber: 2.2 Consensus size: 57
60653458 CATTTTGACA
** *
60653468 AACATAAATATGTGCATTAAGAGACATTATCACAGCAACTATAAATTACATTTGGCC
1 AACATAAATATGCACATTAAGAGACATTATCACAGCAACTATAAATTACATTAGGCC
* *
60653525 AACATAAATATGCACATTAAGAGACATTTTGACAGCAACTATAAATTACATTAAGGCC
1 AACATAAATATGCACATTAAGAGACATTATCACAGCAACTATAAATTACATT-AGGCC
*
60653583 -GCATAAAT
1 AACATAAAT
60653591 GTAGAAATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 55 0.93
58 4 0.07
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (57 bp):
AACATAAATATGCACATTAAGAGACATTATCACAGCAACTATAAATTACATTAGGCC
Found at i:60662044 original size:5 final size:5
Alignment explanation
Indices: 60662034--60662063 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
60662024 TCCAAAACTC
60662034 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
60662064 TTTAATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:60665569 original size:16 final size:18
Alignment explanation
Indices: 60665533--60665569 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
60665523 TAATATTAAA
*
60665533 TAATAAAATATTATTATT
1 TAATAAAATATTATCATT
60665551 TAATAAAA-A-TATCATT
1 TAATAAAATATTATCATT
60665567 TAA
1 TAA
60665570 AAGCATCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 1 0.06
18 8 0.44
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAAATATTATCATT
Found at i:60665858 original size:22 final size:22
Alignment explanation
Indices: 60665833--60665875 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
60665823 TTATTTAAGG
60665833 TCTTCTACCATAAATATTCTTC
1 TCTTCTACCATAAATATTCTTC
60665855 TCTTCTACCATAAATATTCTT
1 TCTTCTACCATAAATATTCTT
60665876 TTTTTTAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.47
Consensus pattern (22 bp):
TCTTCTACCATAAATATTCTTC
Found at i:60667730 original size:16 final size:16
Alignment explanation
Indices: 60667711--60667743 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
60667701 AAAGAAGGGA
60667711 CGAATCAAATTATCAT
1 CGAATCAAATTATCAT
60667727 CGAATCAAATTATCAT
1 CGAATCAAATTATCAT
60667743 C
1 C
60667744 CCATTGTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (16 bp):
CGAATCAAATTATCAT
Found at i:60671017 original size:22 final size:22
Alignment explanation
Indices: 60670991--60671035 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
60670981 ATTATATGTA
60670991 TTAATTCATAATATAA-TTAATT
1 TTAATTCAT-ATATAATTTAATT
* *
60671013 TTAATTTATATCTAATTTAATT
1 TTAATTCATATATAATTTAATT
60671035 T
1 T
60671036 GGGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTCATATATAATTTAATT
Found at i:60674031 original size:39 final size:37
Alignment explanation
Indices: 60673961--60674033 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 37
60673951 AATAGATTAA
60673961 TATTAAATTAAATTAAATACTTATCTTAATATTATTT
1 TATTAAATTAAATTAAATACTTATCTTAATATTATTT
*
60673998 TATTAATTTAATATTAAAGTGA-TTATCTTAATATTA
1 TATTAAATTAA-ATTAAA-T-ACTTATCTTAATATTA
60674034 AATTAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 10 0.31
38 6 0.19
39 15 0.47
40 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (37 bp):
TATTAAATTAAATTAAATACTTATCTTAATATTATTT
Found at i:60674097 original size:61 final size:59
Alignment explanation
Indices: 60674025--60674140 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 59
60674015 AGTGATTATC
* * * *
60674025 TTAATATTAAATTAAATTTAATGGTTATCCTATG-TATAATATTGTATTATTTTAATAAGAT
1 TTAATATTAAATTAAATCTAATAGTTAT-CT-TGATA-AATATTATATTAGTTTAATAAGAT
* *
60674086 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAGTTTAATA
1 TTAATATTAAATTAAATCTAATAGTTATCTTGATAAATATTATATTAGTTTAATA
60674141 TTAAAGTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 20 0.42
60 4 0.08
61 24 0.50
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTAAATCTAATAGTTATCTTGATAAATATTATATTAGTTTAATAAGAT
Found at i:60679544 original size:12 final size:12
Alignment explanation
Indices: 60679527--60679553 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
60679517 AAAGAAAGAT
60679527 AAATAAAAAATA
1 AAATAAAAAATA
60679539 AAATAAAAAATA
1 AAATAAAAAATA
60679551 AAA
1 AAA
60679554 AAGAAACTAA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:60679735 original size:5 final size:5
Alignment explanation
Indices: 60679727--60679785 Score: 61
Period size: 5 Copynumber: 12.0 Consensus size: 5
60679717 AAAAAATTAG
* *
60679727 TAAAA TAAAA -ATAAA TAATA TAACAA -ATAA T-AAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TA-AAA TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA TAAAA
60679776 TAAAA TAAAA
1 TAAAA TAAAA
60679786 GGGGGTGGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
4 6 0.13
5 37 0.82
6 2 0.04
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:60679743 original size:34 final size:33
Alignment explanation
Indices: 60679641--60679785 Score: 86
Period size: 34 Copynumber: 4.3 Consensus size: 33
60679631 AAACACTTAA
* * *
60679641 AAAAATAGAAATAACAAAAAAAATTAAAATAAATT
1 AAAAATAAAAATAATAAATAAAA-TAAAATAAA-T
* * *
60679676 TAAAATATAAGT-ATAAGTATAAGAAT-AAA-AAAT
1 AAAAATAAAAATAATAA--ATAA-AATAAAATAAAT
* *
60679709 AAAAAATAAAAA-AATTAGTAAAATAAAAATAAAT
1 -AAAAATAAAAATAATAAATAAAAT-AAAATAAAT
*
60679743 -AATATAACAAATAATAAATAAAATAAAATAAA-
1 AAAAATAA-AAATAATAAATAAAATAAAATAAAT
60679775 ATAAAATAAAA
1 A-AAAATAAAA
60679786 GGGGGTGGCC
Statistics
Matches: 84, Mismatches: 14, Indels: 26
0.68 0.11 0.21
Matches are distributed among these distances:
31 3 0.04
32 9 0.11
33 17 0.20
34 37 0.44
35 12 0.14
36 4 0.05
37 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.22
Consensus pattern (33 bp):
AAAAATAAAAATAATAAATAAAATAAAATAAAT
Found at i:60679781 original size:15 final size:14
Alignment explanation
Indices: 60679694--60679785 Score: 71
Period size: 15 Copynumber: 6.1 Consensus size: 14
60679684 AAGTATAAGT
60679694 ATAAGAATAAAAAATA
1 ATAA-AATAAAAAA-A
60679710 A-AAAATAAAAAAA
1 ATAAAATAAAAAAA
60679723 TTAGTAAAATAAAAATAA
1 --A-TAAAATAAAAA-AA
* *
60679741 ATAATATAACAAATA
1 ATAAAATAA-AAAAA
60679756 AT-AAATAAAATAAA
1 ATAAAATAAAA-AAA
60679770 ATAAAATAAAATAAA
1 ATAAAATAAAA-AAA
60679785 A
1 A
60679786 GGGGGTGGCC
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
13 3 0.05
14 18 0.28
15 26 0.41
16 5 0.08
17 10 0.16
18 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.02, T:0.21
Consensus pattern (14 bp):
ATAAAATAAAAAAA
Found at i:60680196 original size:104 final size:102
Alignment explanation
Indices: 60680037--60680232 Score: 270
Period size: 104 Copynumber: 1.9 Consensus size: 102
60680027 ACTCTTTGAC
* * *
60680037 TTTGAAAAATTAGCTCCAGGTTTCACACGGCCTAGGACACGCCCGCGTGTCCAGGCCGTATGGGT
1 TTTGAAAAATTAGCTCCAAGTTTCACACGGCCAAGGACACACCCGCGTGTCCAGGCCGTATGGGT
* *
60680102 CACATGGCCATGTCGCCAGGCCGTGTAATCGTTGAATT
66 CACACGACCATGT-GCCAGGCCGTGTAATCGTTGAATT
* * *
60680140 TTTGAAAATTTAAG-TCCAAGTATTCACACGGCCAAGGACACACCTC-TGTGTCCAGGCCGTGTG
1 TTTGAAAAATT-AGCTCCAAGT-TTCACACGGCCAAGGACACACC-CGCGTGTCCAGGCCGTATG
60680203 GGTCACACGACCATGTGCCAGGCCGTGTAA
63 GGTCACACGACCATGTGCCAGGCCGTGTAA
60680233 CTAACTGTCG
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
103 30 0.37
104 51 0.62
105 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.23
Consensus pattern (102 bp):
TTTGAAAAATTAGCTCCAAGTTTCACACGGCCAAGGACACACCCGCGTGTCCAGGCCGTATGGGT
CACACGACCATGTGCCAGGCCGTGTAATCGTTGAATT
Found at i:60683180 original size:6 final size:6
Alignment explanation
Indices: 60683153--60683214 Score: 72
Period size: 6 Copynumber: 10.2 Consensus size: 6
60683143 TACTAGAAGC
* *
60683153 AAATAA AAGA-AA AATTATA AAACAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AA-ATAA AAATA-A AAATAA AAATAA AAATAA AAATAA AAATAA
*
60683202 AAATAA GAATAA A
1 AAATAA AAATAA A
60683215 TGGCTAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
6 42 0.89
7 5 0.11
ACGTcount: A:0.79, C:0.02, G:0.03, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:60686788 original size:16 final size:16
Alignment explanation
Indices: 60686767--60686797 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60686757 TTCATTATTA
*
60686767 TGTCTTTTGTATTTTT
1 TGTCTTTTATATTTTT
60686783 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
60686798 GCACGAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTT
Found at i:60706022 original size:20 final size:20
Alignment explanation
Indices: 60705979--60706019 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
60705969 TGATCAGTTT
60705979 AATTAAAAAAATCATTAAAA
1 AATTAAAAAAATCATTAAAA
*
60705999 AATTATAAAAAT-ATTAAAA
1 AATTAAAAAAATCATTAAAA
60706018 AA
1 AA
60706020 ATTGATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AATTAAAAAAATCATTAAAA
Found at i:60706492 original size:14 final size:14
Alignment explanation
Indices: 60706473--60706504 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
60706463 ATAAATGAGT
60706473 TCGAATCGTCAAAA
1 TCGAATCGTCAAAA
60706487 TCGAATCGTCAAAA
1 TCGAATCGTCAAAA
60706501 TCGA
1 TCGA
60706505 CTAACTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (14 bp):
TCGAATCGTCAAAA
Found at i:60710096 original size:44 final size:44
Alignment explanation
Indices: 60710042--60710130 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
60710032 TACCGATGGG
*
60710042 TGGTTTAACTAGCCTCCAAGTCTCATTCTTTTGAAACGATTTCA
1 TGGTTGAACTAGCCTCCAAGTCTCATTCTTTTGAAACGATTTCA
* *
60710086 TGGTTGAACTAGCCTCCAAGTCTCGTTCTTTTGAAGCGATTTCA
1 TGGTTGAACTAGCCTCCAAGTCTCATTCTTTTGAAACGATTTCA
60710130 T
1 T
60710131 CTCTTCTTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.38
Consensus pattern (44 bp):
TGGTTGAACTAGCCTCCAAGTCTCATTCTTTTGAAACGATTTCA
Done.