Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold138
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: 1735418
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 2489 characters in sequence are not A, C, G, or T
File 3 of 11
Found at i:383018 original size:22 final size:19
Alignment explanation
Indices: 382988--383036 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
382978 CTAATGGCAT
382988 TCATATTCATAGCATTCATTCA
1 TCATATTCATA--A-TCATTCA
*
383010 TCATTTTCATAATCATTCA
1 TCATATTCATAATCATTCA
383029 TCAGTATT
1 TCA-TATT
383037 TACTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 4 0.17
22 10 0.42
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (19 bp):
TCATATTCATAATCATTCA
Found at i:391314 original size:42 final size:42
Alignment explanation
Indices: 391258--392431 Score: 865
Period size: 42 Copynumber: 27.9 Consensus size: 42
391248 ATCTTTTCTG
* * * *
391258 TTTT-CCCTTAGTCTGCCTATCGGTTTTGACCTTGGAGACTT
1 TTTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * *
391299 TTTTACTCTCAGTCTGCCCGTCGGCTTTGACCTTGGAGAC-T
1 TTTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * * *
391340 TTTCATCCCTTATTCTGCCTGTCAGCTTTGACCCTGGGGACTT
1 TTTTA-CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
** * *
391383 TTCAACCCTCAGTCTGCTTGTCGGTTTTGACCCTGGAGACTT
1 TTTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * *
391425 TTCTT-CCCTAAGTCTGCTTGTCGACTTTGACCCTGAAGAC-T
1 TT-TTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * *
391466 TTTCATCCCTTAGTCTGCCTGTCGACTTTGACCCCGGAGACTT
1 TTTTA-CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* *
391509 TTCTT-CCCTCAGTCTGCCTATCGGCTTTGACTCTGGAGACTT
1 TT-TTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * * * *
391551 TTCTT-CCCTTAGTCTACCTGTCGGCTTCGTCCTTGAAGACTT
1 TT-TTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * *
391593 TCTTT-CCCTTAGTCTGCCTATCGGCTTTGACCCTAGAGACTT
1 T-TTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * * *
391635 TTTTACCATCAATCTGCCTGTCGGCTTTGACCTTAGAGA-AT
1 TTTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * * * * *
391676 TTTCATCCTTAGTTTGCCTATTGGCTTTGACCTTGGAGACTT
1 TTTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * ** *
391718 TTTAACCCTAAGTCTGCTTGTCAACTTTGACCCTAGAGACTT
1 TTTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * ** *
391760 TCCTTT-CTCTCAGTCTACCTGTTGGCTTTGACCCTACAGACTA
1 T--TTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * *** * * * * * *
391803 TCTCATTTTAAGTCTGCTTGTTGGCTTCGTCCCTGGAAACTT
1 TTTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * *
391845 TTCTACCCTTAGTCTGCCTGTCGG-TTTAACCCTGGAAACTT
1 TTTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* *
391886 TCTTACCCTTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTT
1 TTTTACCC-TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
*
391929 TCCTT-CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
1 T-TTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * * *
391971 TCCTT-CCCTCAATCTGCCTATCAGCTTTGACCTTGGAGACTT
1 T-TTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * *
392013 TTCTACCCTTAGTCTGCCTGTCAG-TTTAACCCTGGAGACTT
1 TTTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* *
392054 TTTTACCCTTCAGTCTGCTTATCGGCTTTGACCCTGGAGACTT
1 TTTTACCC-TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * * *
392097 TCCTT-CCCTTAGTCTGCTTGTCGGCTTCGTCCCTGGAGACTT
1 T-TTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * *
392139 TCCTT-CCCTCAGTCTGCCTGTCGACTTTGACCTTGGAGAC-T
1 T-TTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * * * *
392180 TTTCATCTCTCAGTCTACCTGTCGGCTTTAACCCTAGACAC-T
1 TTTTA-CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * *
392222 TTTCATCCCTTAATCTGCCTGTCGGCTTTGATCCTGGAGACTT
1 TTTTA-CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * ** * *
392265 TCTTT-CCTTAAGTCTGTTTGTCGGCTTTGACCTTGAAGACTT
1 T-TTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
** * * * ** *
392307 TCCTAGTCCTAAGTCTGCTTGTCGGCTTTGATTCAGGAGACTT
1 TTTTA-CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
** * * *
392350 TCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTCGAGA-TT
1 TTTTA-CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
* * * * *
392392 TTCTTTCCCTAAGTATGCCTGTTGGCTTTGACCCAGGAGA
1 TT-TTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGA
392432 ATATTTTCTT
Statistics
Matches: 901, Mismatches: 204, Indels: 55
0.78 0.18 0.05
Matches are distributed among these distances:
40 2 0.00
41 93 0.10
42 658 0.73
43 138 0.15
44 10 0.01
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.38
Consensus pattern (42 bp):
TTTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT
Found at i:391495 original size:126 final size:126
Alignment explanation
Indices: 391262--392431 Score: 1002
Period size: 126 Copynumber: 9.3 Consensus size: 126
391252 TTTCTGTTTT
* * * * * *
391262 CCCTTAGTCTGCCTATCGGTTTTGACCTTGGAGACTTTT-TTACTCTCAGTCTGCCCGTCGGCTT
1 CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT-CCCTCAGTCTGCCTGTCGGCTT
* * * *
391326 TGACCTTGGAGACTTTTCATCCCTTATTCTGCCTGTC-AGCTTTGACCCTGGGGACTTTTCAA
65 TGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGA-CTTTGACCCTGGAGACTTTTCTA
* * * * *
391388 CCCTCAGTCTGCTTGTCGGTTTTGACCCTGGAGACTTTTCTTCCCTAAGTCTGCTTGTCGACTTT
1 CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTCAGTCTGCCTGTCGGCTTT
* * *
391453 GACCCTGAAGACTTTTCATCCCTTAGTCTGCCTGTCGACTTTGACCCCGGAGACTTTTCTT
66 GACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTTCTA
* * * * *
391514 CCCTCAGTCTGCCTATCGGCTTTGACTCTGGAGACTTTTCTTCCCTTAGTCTACCTGTCGGCTTC
1 CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTCAGTCTGCCTGTCGGCTTT
* * * * * * * *
391579 GTCCTTGAAGAC-TTTCTTTCCCTTAGTCTGCCTATCGGCTTTGACCCTAGAGACTTTTTTA
66 GACCCTGGAGACTTTTC-ATCCCTTAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTTCTA
* * * * * * * * * *
391640 CCATCAATCTGCCTGTCGGCTTTGACCTTAGAGAATTTTCAT-CCTTAGTTTGCCTATTGGCTTT
1 CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTCAGTCTGCCTGTCGGCTTT
* * * * * * * * *
391704 GACCTTGGAGACTTTTTAACCCTAAGTCTGCTTGTCAACTTTGACCCTAGAGACTTTCCTTT
66 GACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTTC-TA
* * * ** * * * * *
391766 CTCTCAGTCTACCTGTTGGCTTTGACCCTACAGACTATCTCATT--TTAAGTCTGCTTGTTGGCT
1 CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACT-TTTC-TTCCCTCAGTCTGCCTGTCGGCT
* * * * * *
391829 TCGTCCCTGGAAACTTTTC-TACCCTTAGTCTGCCTGTCG-GTTTAACCCTGGAAAC-TTTCTTA
64 TTGACCCTGGAGACTTTTCAT-CCCTTAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTTC-TA
* *
391891 CCCTTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTTCCCTCAGTCTGCCTGTCGGCTT
1 CCC-TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTCAGTCTGCCTGTCGGCTT
* * * * * *
391956 TGACCCTGGAGACTTTCCTTCCCTCAATCTGCCTATC-AGCTTTGACCTTGGAGACTTTTCTA
65 TGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGA-CTTTGACCCTGGAGACTTTTCTA
* * * * *
392018 CCCTTAGTCTGCCTGTCAG-TTTAACCCTGGAGACTTTT-TTACCCTTCAGTCTGCTTATCGGCT
1 CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTT-CCC-TCAGTCTGCCTGTCGGCT
* * * * * * * *
392081 TTGACCCTGGAGACTTTCCTTCCCTTAGTCTGCTTGTCGGCTTCGTCCCTGGAGACTTTCCTT
64 TTGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTTCTA
* * * * *
392144 CCCTCAGTCTGCCTGTCGACTTTGACCTTGGAGACTTTTCATCTCTCAGTCTACCTGTCGGCTTT
1 CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTCAGTCTGCCTGTCGGCTTT
* * * * * * *
392209 AACCCTAGACACTTTTCATCCCTTAATCTGCCTGTCGGCTTTGATCCTGGAGAC-TTTCTTT
66 GACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTTC-TA
* * ** * * * * *
392270 CCTTAAGTCTGTTTGTCGGCTTTGACCTTGAAGACTTTCCTAGT-CCTAAGTCTGCTTGTCGGCT
1 CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCT--TCCCTCAGTCTGCCTGTCGGCT
** * * * * * *
392334 TTGATTCAGGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTCGAGA-TTTTCTTT
64 TTGACCCTGGAGACTTTTC-ATCCCTTAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTTC-TA
* * * *
392398 CCCTAAGTATGCCTGTTGGCTTTGACCCAGGAGA
1 CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGA
392432 ATATTTTCTT
Statistics
Matches: 839, Mismatches: 180, Indels: 48
0.79 0.17 0.04
Matches are distributed among these distances:
124 4 0.00
125 95 0.11
126 554 0.66
127 114 0.14
128 72 0.09
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.38
Consensus pattern (126 bp):
CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTCAGTCTGCCTGTCGGCTTT
GACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTCGACTTTGACCCTGGAGACTTTTCTA
Found at i:391552 original size:168 final size:169
Alignment explanation
Indices: 391259--392431 Score: 1032
Period size: 168 Copynumber: 7.0 Consensus size: 169
391249 TCTTTTCTGT
* * * * * ** * *
391259 TTTCCCTTAGTCTGCCTATCGGTTTTGACCTTGGAGACTTT-TTTACTCTCAGTCTGCCCGTCGG
1 TTTCCCTAAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTCCAT-CCCTCAGTCTGCCTGTCGG
* * * *
391323 CTTTGACCTTGGAGACTTTTCATCCCTTATTCTGCCTGTCAGCTTTGACCCTGGGGACTTTTCAA
65 CTTTGACCTTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAA
* * *
391388 CCCTCAGTCTGCTTGTCGGTTTTGACCCTGGAGACTTTTC
130 CCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC
* * * * *
391428 -TTCCCTAAGTCTGCTTGTCGACTTTGACCCTGAAGACTTTTCATCCCTTAGTCTGCCTGTCGAC
1 TTTCCCTAAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTCCATCCCTCAGTCTGCCTGTCGGC
** * * * **
391492 TTTGACCCCGGAGACTTTTCTTCCCTCAGTCTGCCTATCGGCTTTGACTCTGGAGACTTTTCTTC
66 TTTGACCTTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAAC
* * * * * *
391557 CCTTAGTCTACCTGTCGGCTTCGTCCTTGAAGACTTT-C
131 CCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC
* * ** * *
391595 TTTCCCTTAGTCTGCCTATCGGCTTTGACCCT-AGAGACTTT-TTTACCATCAATCTGCCTGTCG
1 TTTCCCTAAGTCTGCCTGTCGGCTTTGACCCTGA-AGACTTTCCAT-CCCTCAGTCTGCCTGTCG
* * * * * * * *
391658 GCTTTGACCTTAGAGAATTTTCAT-CCTTAGTTTGCCTATTGGCTTTGACCTTGGAGACTTTTTA
64 GCTTTGACCTTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCA
* * ** *
391722 ACCCTAAGTCTGCTTGTCAACTTTGACCCTAGAGACTTTCC
129 ACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC
* * * * * ** * * *
391763 TTTCTCTCAGTCTACCTGTTGGCTTTGACCCT-ACAGACTATCTCAT-TTTAAGTCTGCTTGTTG
1 TTTCCCTAAGTCTGCCTGTCGGCTTTGACCCTGA-AGACTTTC-CATCCCTCAGTCTGCCTGTCG
* * * * * * *
391826 GCTTCGTCCCTGGAAACTTTTCTACCCTTAGTCTGCCTGTCGG-TTTAACCCTGGAAAC-TTTCT
64 GCTTTGACCTTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-
* *
391889 TACCCTTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCC
128 AACCC-TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC
* * * * * *
391932 -TTCCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTCCCTCAATCTGCCTATCAGC
1 TTTCCCTAAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTCCATCCCTCAGTCTGCCTGTCGGC
* * * **
391996 TTTGACCTTGGAGACTTTTCTACCCTTAGTCTGCCTGTCAG-TTTAACCCTGGAGACTTTTTTAC
66 TTTGACCTTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAAC
* *
392060 CCTTCAGTCTGCTTATCGGCTTTGACCCTGGAGACTTTCC
131 CC-TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC
* * * * * * *
392100 -TTCCCTTAGTCTGCTTGTCGGCTTCGTCCCTGGAGACTTTCCTTCCCTCAGTCTGCCTGTCGAC
1 TTTCCCTAAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTCCATCCCTCAGTCTGCCTGTCGGC
* * * * * * * *
392164 TTTGACCTTGGAGACTTTTCATCTCTCAGTCTACCTGTCGGCTTTAACCCTAGACACTTTTCATC
66 TTTGACCTTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAAC
* * *
392229 CCTTAATCTGCCTGTCGGCTTTGATCCTGGAGACTTT-C
131 CCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC
* ** * * *
392267 TTTCCTTAAGTCTGTTTGTCGGCTTTGACCTTGAAGACTTTCCTAGT-CCTAAGTCTGCTTGTCG
1 TTTCCCTAAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTCC-A-TCCCTCAGTCTGCCTGTCG
* * *
392331 GCTTTGA--TTCAGGAGACTTTCCTATCCCTTAGTCTGCCTGTCGGCTTTGACCTTCGAGA-TTT
64 GCTTTGACCTT--GGAGACTTTTCT-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT
** * * * *
392393 TCTTTCCCTAAGTATGCCTGTTGGCTTTGACCCAGGAGA
126 TC-AACCCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGA
392432 ATATTTTCTT
Statistics
Matches: 808, Mismatches: 175, Indels: 41
0.79 0.17 0.04
Matches are distributed among these distances:
167 72 0.09
168 569 0.70
169 108 0.13
170 59 0.07
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.38
Consensus pattern (169 bp):
TTTCCCTAAGTCTGCCTGTCGGCTTTGACCCTGAAGACTTTCCATCCCTCAGTCTGCCTGTCGGC
TTTGACCTTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCAAC
CCTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC
Found at i:392902 original size:21 final size:21
Alignment explanation
Indices: 392869--392926 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
392859 TAAAAAAATT
392869 ATTAAACATAAAAAATGAATAA
1 ATTAAA-ATAAAAAATGAATAA
* **
392891 ATTAAAATAAAAATTTTATAA
1 ATTAAAATAAAAAATGAATAA
*
392912 AATAATAATAAAAAA
1 ATTAA-AATAAAAAA
392927 AATGAAATGC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (21 bp):
ATTAAAATAAAAAATGAATAA
Found at i:393035 original size:25 final size:25
Alignment explanation
Indices: 393007--393123 Score: 113
Period size: 25 Copynumber: 4.8 Consensus size: 25
392997 TCATGCATGC
*
393007 ATTTTTATTTCATGCATTTCACATA
1 ATTTTCATTTCATGCATTTCACATA
393032 ATTTTCATTTCATGCATTT--CATA
1 ATTTTCATTTCATGCATTTCACATA
* * * *
393055 A---ACATTTCAAGC--TTCGTGCATGC
1 ATTTTCATTTCATGCATTTC--ACAT-A
393078 ATTTTCATTTCATGCATTTCACATA
1 ATTTTCATTTCATGCATTTCACATA
393103 ATTTTCATTTCATGCATTTCA
1 ATTTTCATTTCATGCATTTCA
393124 TTTCATGCAT
Statistics
Matches: 74, Mismatches: 8, Indels: 20
0.73 0.08 0.20
Matches are distributed among these distances:
18 2 0.03
20 9 0.12
22 3 0.04
23 6 0.08
25 39 0.53
26 12 0.16
28 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (25 bp):
ATTTTCATTTCATGCATTTCACATA
Found at i:393124 original size:14 final size:14
Alignment explanation
Indices: 393073--393142 Score: 69
Period size: 14 Copynumber: 5.2 Consensus size: 14
393063 AAGCTTCGTG
393073 CATGCATTTTCATTT
1 CATGCA-TTTCATTT
393088 CATGCATTTCA---
1 CATGCATTTCATTT
*
393099 CAT-AATTTTCATTT
1 CATGCA-TTTCATTT
393113 CATGCATTTCATTT
1 CATGCATTTCATTT
*
393127 CATGCA-TGCATTT
1 CATGCATTTCATTT
393140 CAT
1 CAT
393143 AAACATTTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
10 1 0.02
11 8 0.17
13 9 0.19
14 22 0.47
15 7 0.15
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.47
Consensus pattern (14 bp):
CATGCATTTCATTT
Found at i:393212 original size:89 final size:88
Alignment explanation
Indices: 393042--393222 Score: 208
Period size: 89 Copynumber: 2.0 Consensus size: 88
393032 ATTTTCATTT
* * * *
393042 CATGCATTTCATAAACATTTCAAGCTTCGTGCATGCATTTTCATTTCATGCATTTCACATAATTT
1 CATGCATTTCATAAACATTTCAAGCTTCATGCAAGAATTTTCATTTCATGCA-TTCACATAATCT
* *
393107 TCATTTCATGCATTTCATTTCATG
65 TCATTGCATGCATTTCATTCCATG
* *
393131 CATGCATTTCATAAACATTTCATGCTTCATGCAAGAAAATTTTCATTTCATGCA-T-ACATGCA-
1 CATGCATTTCATAAACATTTCAAGCTTCATGCAAG--AATTTTCATTTCATGCATTCACAT-AAT
393193 CTTCATTGCATTTGC-TTTCATTCCATG
63 CTTCATTGCA--TGCATTTCATTCCATG
393220 CAT
1 CAT
393223 TCATATGCAA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
88 12 0.15
89 48 0.61
90 3 0.04
91 16 0.20
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.41
Consensus pattern (88 bp):
CATGCATTTCATAAACATTTCAAGCTTCATGCAAGAATTTTCATTTCATGCATTCACATAATCTT
CATTGCATGCATTTCATTCCATG
Found at i:393839 original size:31 final size:30
Alignment explanation
Indices: 393800--393865 Score: 105
Period size: 31 Copynumber: 2.2 Consensus size: 30
393790 TAGCAACTTC
* *
393800 CAGTAGCTCCCACGACAGCCTTCAGCAGCT
1 CAGTAGCTCCCACGACAGCCTCCAACAGCT
393830 CTAGTAGCTCCCACGACAGCCTCCAACAGCT
1 C-AGTAGCTCCCACGACAGCCTCCAACAGCT
393861 CAGTA
1 CAGTA
393866 ACCACGAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.26, C:0.39, G:0.18, T:0.17
Consensus pattern (30 bp):
CAGTAGCTCCCACGACAGCCTCCAACAGCT
Found at i:393911 original size:22 final size:22
Alignment explanation
Indices: 393883--393931 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
393873 GCAGCCCCCT
* *
393883 ACAGCTCCTATAGTAACTTCCA
1 ACAGCTCCCACAGTAACTTCCA
393905 ACAGCTCCCACAGTAACTTCCA
1 ACAGCTCCCACAGTAACTTCCA
*
393927 GCAGC
1 ACAGC
393932 GACGGCGGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.37, G:0.12, T:0.20
Consensus pattern (22 bp):
ACAGCTCCCACAGTAACTTCCA
Found at i:405401 original size:12 final size:12
Alignment explanation
Indices: 405386--405436 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
405376 AAAAAAAATT
405386 AAAAAAAA-AAA
1 AAAAAAAACAAA
*
405397 CAAAAAAACGAAGA
1 AAAAAAAAC-AA-A
* *
405411 AAAAATAACCAA
1 AAAAAAAACAAA
405423 AAAAAAAACAAA
1 AAAAAAAACAAA
405435 AA
1 AA
405437 GAGGTCCAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
11 7 0.23
12 13 0.42
13 3 0.10
14 8 0.26
ACGTcount: A:0.84, C:0.10, G:0.04, T:0.02
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:406677 original size:28 final size:28
Alignment explanation
Indices: 406643--407358 Score: 803
Period size: 28 Copynumber: 25.1 Consensus size: 28
406633 CGTTCATCTC
* *
406643 TTCAAAGCCCATAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
406671 TTCAAAGCCCATAAGTCAGTGGCAACCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
406699 TTCAAAGCCCACAAGTCGGTAGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-A-TCCT
*
406729 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
406757 TTCATAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
406785 TTCAAAGCCCACAAGTCAGTGGCA-CATT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
* *
406813 TTCAAAGCCCACAAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-A-TCCT
* *
406843 TTCAAAGACCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
406871 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
406899 TTCAAAGCCCACAATTCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* * *
406927 TTCAAAGCCCATAAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-A-TCCT
* *
406957 TTCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
406985 TTTAAAGCCCACAAATCAGTAGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
407013 TTCAAAGCCCACAAATTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
407041 TTTAAAGCCCACAAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-A-TCCT
407071 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
407099 TTCAAAGCCCACAAGTCAGTGGCA-CTCT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
* * *
407127 TTCAAAGCCCACAAGTTAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
407155 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
407183 TTCAAAGCCCACAAGTCAATGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* * * *
407212 TTCAAAGCCCGCAAGTCTGTGTCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
407240 TTCAAAGCCCACAAGTTAATGGCA-CTCT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
*
407268 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
407296 TTCAAAGCCCACACGAGTCGGTGGTAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGG-CA-TCCT
*
407328 TTCAAAGCCCATACAAGTTAGTGGCA-CCT
1 TTCAAAGCCC--ACAAGTCAGTGGCATCCT
407357 TT
1 TT
407359 TTTAAAAAAA
Statistics
Matches: 587, Mismatches: 78, Indels: 45
0.83 0.11 0.06
Matches are distributed among these distances:
27 5 0.01
28 423 0.72
29 36 0.06
30 97 0.17
31 4 0.01
32 19 0.03
34 3 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:406788 original size:86 final size:85
Alignment explanation
Indices: 406643--407355 Score: 862
Period size: 86 Copynumber: 8.3 Consensus size: 85
406633 CGTTCATCTC
* * * * *
406643 TTCAAAGCCCATAAGTTAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCAACCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
* *
406708 CACAAGTCGGTAGCAACTCTT
66 CACAAGTCAGTGGC-ACTCTT
*
406729 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCATAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
*
406794 CACAAGTCAGTGGCAC-ATT
66 CACAAGTCAGTGGCACTCTT
* * * *
406813 TTCAAAGCCCACAAGTCGGTGGCAACTCTTTTCAAAGACCACAAGTTAGTGGCATCCTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGC-AC-CCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG
*
406878 CCCACAAGTCAGTGGCAC-CCT
64 CCCACAAGTCAGTGGCACTCTT
* * * * *
406899 TTCAAAGCCCACAATTCAGTGGCACCTTTTCAAAGCCCATAAGTCGGTGGCAACTCTTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGC-A-TCCTTTCAAAG
* *
406964 CCCACAAGTCAATGGCACCCTT
64 CCCACAAGTCAGTGGCACTCTT
* * * * * * *
406986 TT-AAAGCCCACAAATCAGTAGCATCCTTTCAAAGCCCACAAATTAGTGGCACCCTTTTAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
*
407050 CACAAGTCGGTGGCAACTCTT
66 CACAAGTCAGTGGC-ACTCTT
*
407071 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CTCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGC
* * *
407135 CCACAAGTTAATGGCAC-CCT
65 CCACAAGTCAGTGGCACTCTT
* *
407155 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGC
* * *
407220 CCGCAAGTCTGTGTCA-TCTT
65 CCACAAGTCAGTGGCACTCTT
* * * *
407240 TTCAAAGCCCACAAGTTAATGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
* *
407305 CACACGAGTCGGTGGTAACTCTT
66 CACA--AGTCAGTGG-CACTCTT
*
407328 TTCAAAGCCCATACAAGTTAGTGGCACC
1 TTCAAAGCCC--ACAAGTCAGTGGCACC
407356 TTTTTTAAAA
Statistics
Matches: 541, Mismatches: 69, Indels: 30
0.85 0.11 0.05
Matches are distributed among these distances:
84 134 0.25
85 88 0.16
86 286 0.53
87 5 0.01
88 14 0.03
90 14 0.03
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (85 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
CACAAGTCAGTGGCACTCTT
Found at i:406848 original size:114 final size:114
Alignment explanation
Indices: 406643--407358 Score: 928
Period size: 114 Copynumber: 6.3 Consensus size: 114
406633 CGTTCATCTC
* * *
406643 TTCAAAGCCCATAAGTTAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCAACC-TTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC-ACCTTTTCAAAGC
*
406707 CCACAAGTCGGTAGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
65 CCACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
* *
406757 TTCATAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACATTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
* * *
406822 CACAAGTCGGTGGCAACTCTTTTCAAAGACCACAAGTTAGTGGCATCCT
66 CACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
* *
406871 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAATTCAGTGGCACCTTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
* *
406936 CATAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAATGGCACCCT
66 CACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * * *
406985 TTTAAAGCCCACAAATCAGTAGCATCCTTTCAAAGCCCACAAATTAGTGGCACCCTTTT-AAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGC
*
407049 CCACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
65 CCACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
407099 TTCAAAGCCCACAAGTCAGTGGCA-CTCTTTCAAAGCCCACAAGTTAATGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGC
* * * *
407163 CCACAAGTCAGTGGC-AC-CCTTTCAAAGCCCACAAGTCAATGGCACTCTT
65 CCACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * * * * *
407212 TTCAAAGCCCGCAAGTCTGTGTCATCTTTTCAAAGCCCACAAGTTAATGGCA-CTCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCT-TTTCAAAGC
* * * * *
407276 CCACAAGTCAGTGGC-AC-CCTTTCAAAGCCCACACGAGTCGGTGGTAACTCTT
65 CCACAAGTCGGTGGCAACTCTTTTCAAAGCCCACA--AGTCAGTGG-CAC-CCT
*
407328 TTCAAAGCCCATACAAGTTAGTGGCA-CCTTT
1 TTCAAAGCCC--ACAAGTCAGTGGCATCCTTT
407359 TTTAAAAAAA
Statistics
Matches: 539, Mismatches: 51, Indels: 21
0.88 0.08 0.03
Matches are distributed among these distances:
112 26 0.05
113 100 0.19
114 370 0.69
115 13 0.02
116 16 0.03
117 4 0.01
118 10 0.02
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (114 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCC
CACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:406899 original size:142 final size:141
Alignment explanation
Indices: 406643--407354 Score: 892
Period size: 142 Copynumber: 5.0 Consensus size: 141
406633 CGTTCATCTC
* * * *
406643 TTCAAAGCCCATAAGTTAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCAAC-CTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGC-ACTCTTTCAAAGC
* * * *
406707 CCACAAGTCGGTAGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCATAGCCCACAAG
65 CCACAAGTCAGTGGC-A-TCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
406772 TCAGTGGCA-TCCT
128 TCAGTGGCACTCCT
*
406785 TTCAAAGCCCACAAGTCAGTGGCA-CATTTTCAAAGCCCACAAGTCGGTGGCAACTCTTTTCAAA
1 TTCAAAGCCCACAAGTCAGTGGCATC-TTTTCAAAGCCCACAAGTCAGTGGC-ACTC-TTTCAAA
* * *
406849 GACCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAT
63 GCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG
*
406914 TCAGTGGCAC-CTT
128 TCAGTGGCACTCCT
* * * * *
406927 TTCAAAGCCCATAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCAATGGCACCCTTTTAAAG
1 TTCAAAGCCCACAAGTCAGTGGC-A-TCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAG
* * * * *
406992 CCCACAAATCAGTAGCATCCTTTCAAAGCCCACAAATTAGTGGCACCCTTTTAAAGCCCACAAGT
64 CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT
* *
407057 CGGTGGCAACTCTT
129 CAGTGGC-ACTCCT
*
407071 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCC
* * *
407136 CACAAGTTAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
66 CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
* *
407201 ATGGCACTCTT
131 GTGGCACTCCT
* * * * *
407212 TTCAAAGCCCGCAAGTCTGTGTCATCTTTTCAAAGCCCACAAGTTAATGGCACTCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCC
* * * *
407277 CACAAGTCAGTGGCACCCTTTCAAAGCCCACACGAGTCGGTGGTAACTCTTTTCAAAGCCCATAC
66 CACAAGTCAGTGGCATCCTTTCAAAGCCCACA--AGTCAGTGG-CAC-CCTTTCAAAGCCC--AC
*
407342 AAGTTAGTGGCAC
125 AAGTCAGTGGCAC
407355 CTTTTTTAAA
Statistics
Matches: 498, Mismatches: 57, Indels: 25
0.86 0.10 0.04
Matches are distributed among these distances:
141 96 0.19
142 290 0.58
143 17 0.03
144 69 0.14
145 13 0.03
147 13 0.03
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (141 bp):
TTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGCC
CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCA
GTGGCACTCCT
Found at i:413644 original size:6 final size:6
Alignment explanation
Indices: 413633--413681 Score: 89
Period size: 6 Copynumber: 8.0 Consensus size: 6
413623 TAAAAAAAAT
413633 TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TTGGAGA
1 TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA -TGGAGA
413682 GGGGAGAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 36 0.86
7 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.49, T:0.18
Consensus pattern (6 bp):
TGGAGA
Found at i:416094 original size:12 final size:13
Alignment explanation
Indices: 416043--416113 Score: 51
Period size: 13 Copynumber: 5.6 Consensus size: 13
416033 AAAACGAAAA
416043 TAAATT-TTTAAT
1 TAAATTATTTAAT
* *
416055 TCAATTGATTCAAT
1 TAAATT-ATTTAAT
416069 TAAAATT-TTT-AT
1 T-AAATTATTTAAT
416081 T-AATTATTTAAT
1 TAAATTATTTAAT
* *
416093 TAAATTAATTATT
1 TAAATTATTTAAT
*
416106 TAATTTAT
1 TAAATTAT
416114 AATATAAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
10 4 0.09
11 3 0.07
12 11 0.24
13 17 0.38
14 6 0.13
15 4 0.09
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (13 bp):
TAAATTATTTAAT
Found at i:418015 original size:18 final size:19
Alignment explanation
Indices: 417994--418030 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
417984 ACAATGCATT
*
417994 TAATAAACATAA-ATATTA
1 TAATAAACACAACATATTA
418012 TAATAAACACAACATATTA
1 TAATAAACACAACATATTA
418031 CGTTTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (19 bp):
TAATAAACACAACATATTA
Found at i:420897 original size:3 final size:3
Alignment explanation
Indices: 420889--420920 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
420879 TTGGGCCAAT
420889 ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA A
420921 CAAAAAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:421051 original size:22 final size:23
Alignment explanation
Indices: 420984--421051 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 23
420974 GTATTCAAAC
* *
420984 AAATATAAATT-AATTTATTATT
1 AAATAAAAATTAAATTAATTATT
*
421006 AAATAAAAATTAAATTAAAT-TT
1 AAATAAAAATTAAATTAATTATT
* * *
421028 AAATCAAATTTATA-TAATTATT
1 AAATAAAAATTAAATTAATTATT
421050 AA
1 AA
421052 TTTTTATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 4 0.11
22 27 0.73
23 6 0.16
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATAAAAATTAAATTAATTATT
Found at i:422173 original size:9 final size:9
Alignment explanation
Indices: 422159--422189 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
422149 CCATTTTTTT
422159 AAAAAAA-A
1 AAAAAAAGA
422167 AAAAAAAGA
1 AAAAAAAGA
422176 AAAAAAAGA
1 AAAAAAAGA
422185 AAAAA
1 AAAAA
422190 CTTAATTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:425830 original size:14 final size:15
Alignment explanation
Indices: 425794--425830 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
425784 TCTTTACTGT
425794 TTGATTATCTTATTGA
1 TTGATT-TCTTATTGA
425810 TTG-TTTCTTATTG-
1 TTGATTTCTTATTGA
425823 TTGATTTC
1 TTGATTTC
425831 GGCTGTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.15
14 12 0.60
15 2 0.10
16 3 0.15
ACGTcount: A:0.16, C:0.08, G:0.14, T:0.62
Consensus pattern (15 bp):
TTGATTTCTTATTGA
Found at i:432135 original size:2 final size:2
Alignment explanation
Indices: 432128--432152 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
432118 CTATCTTTAG
432128 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
432153 CCCCCCATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:433075 original size:17 final size:17
Alignment explanation
Indices: 433055--433104 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
433045 TTTATCAATT
433055 ATTTATTTAAAATTAAA
1 ATTTATTTAAAATTAAA
*
433072 ATTT-TTTAATATTTAAA
1 ATTTATTTAA-AATTAAA
*
433089 A-TTATTT-TAATTAAA
1 ATTTATTTAAAATTAAA
433104 A
1 A
433105 CTAATCGATC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 7 0.25
16 7 0.25
17 14 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTATTTAAAATTAAA
Found at i:438037 original size:24 final size:24
Alignment explanation
Indices: 438004--438058 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
437994 AATATTTGCC
*
438004 AAAAAAATTATT-TTA--AAAATT
1 AAAAAAATTATTATTATTAAAATA
*
438025 AAAAAAATTATTATTATTATAATA
1 AAAAAAATTATTATTATTAAAATA
438049 AAAAAAATTA
1 AAAAAAATTA
438059 AAAATATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 12 0.41
22 3 0.10
24 14 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAAAAATTATTATTATTAAAATA
Found at i:438742 original size:23 final size:23
Alignment explanation
Indices: 438699--438742 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
438689 TTTAAAGTTG
*
438699 TTTTATTTTAAAATATGATTTAT
1 TTTTATTTTAAAATATAATTTAT
438722 TTTTATTTATAAAAT-TAATTT
1 TTTTATTT-TAAAATATAATTT
438743 GATTAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTATTTTAAAATATAATTTAT
Found at i:445304 original size:15 final size:15
Alignment explanation
Indices: 445284--445314 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
445274 AGTGCAACAA
445284 ATCAATACTATTTGC
1 ATCAATACTATTTGC
445299 ATCAATACTATTTGC
1 ATCAATACTATTTGC
445314 A
1 A
445315 GCAAATATCA
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:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (15 bp):
ATCAATACTATTTGC
Found at i:445758 original size:92 final size:92
Alignment explanation
Indices: 445652--445848 Score: 236
Period size: 92 Copynumber: 2.1 Consensus size: 92
445642 CCTTCAACTG
* * *
445652 TGACATTTATAATCAATCAACTTTTCTGTT-TTTCTACCAAAAAGAATAT-AATTTTCAAATATA
1 TGACATTTACAATCAATCAACTTTTCT-TTCTTTCTACCAAAAAGAAT-TCAATTCTCAAATACA
*
445715 ATCCATACATTAGTCTAATCCTTGCAGTA
64 ATCCATACATTAGTCTAATCATTGCAGTA
* * * * *
445744 TGACATTTACAATCAATTAACTTTTCTTTCTTTCTATCAAAAGGAATTCGATTCTCAGATACAAT
1 TGACATTTACAATCAATCAACTTTTCTTTCTTTCTACCAAAAAGAATTCAATTCTCAAATACAAT
* * * * *
445809 TCATGCATTAGTGTAATCATTGTAGTC
66 CCATACATTAGTCTAATCATTGCAGTA
445836 TGACATTTACAAT
1 TGACATTTACAAT
445849 TCATGCATTT
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
91 3 0.03
92 86 0.97
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.40
Consensus pattern (92 bp):
TGACATTTACAATCAATCAACTTTTCTTTCTTTCTACCAAAAAGAATTCAATTCTCAAATACAAT
CCATACATTAGTCTAATCATTGCAGTA
Found at i:446240 original size:165 final size:163
Alignment explanation
Indices: 445916--446359 Score: 466
Period size: 165 Copynumber: 2.7 Consensus size: 163
445906 ATCTGTGTAT
* * * * * ** * *
445916 CATGCATTAGTATTATCAACTTCTTTCATATCA-AAATGAATCTAATTATTATCAATAATTTATG
1 CATGCATTAGTTTTATCAACTTCTTTTACATCAGAAA-AAATCTGATT-CCATTAAGAATTTATG
* * * * * *
445980 CATTAATCACATTTATTTTAAAACAGAAT-TCATGCATTAGTCCCATCTTTTGAATTTCAATCCA
64 CATT-ATCATATTTA-TTCAAAACAGAATCT-ATGCATTAGTTCCATCTTTCGAACTCCAATCCA
* * **
446044 TGCATTAGTCTATTATTTATAGTTTAACATTTATAATC
126 TCCATTAGTCTATTATTTACAGTCCAACATTTATAATC
* * *
446082 TATGCATTAGTTTTATCAACTT-TTTTGACATCAGAAAGAATCTGATTCCCATTAGGAATTTATG
1 CATGCATTAGTTTTATCAACTTCTTTT-ACATCAGAAAAAATCTGATT-CCATTAAGAATTTATG
*
446146 CATTATCATATTTATTCAAAACCAGAATCTATGCATTAGTTCCATCTTTCGAACTCCAATCTATC
64 CATTATCATATTTATTCAAAA-CAGAATCTATGCATTAGTTCCATCTTTCGAACTCCAATCCATC
* *
446211 CATTTGTCTATT-TATTGCAGTCCAACATTTATAATC
128 CATTAGTCTATTAT-TTACAGTCCAACATTTATAATC
* * * *
446247 CATGCATTAGTTTTATTAACTTCTTTTATATTAGAAAAAATCTGATTCCATTAAGAATCTATGCA
1 CATGCATTAGTTTTATCAACTTCTTTTACATCAGAAAAAATCTGATTCCATTAAGAATTTATGCA
* *
446312 TTTATCATATTTATTCAAAAATAAAATCTATGCATTAG-TCTCATCTTT
66 -TTATCATATTTATTC-AAAACAGAATCTATGCATTAGTTC-CATCTTT
446360 TAAATTTTAA
Statistics
Matches: 236, Mismatches: 33, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
164 25 0.11
165 150 0.64
166 58 0.25
167 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.42
Consensus pattern (163 bp):
CATGCATTAGTTTTATCAACTTCTTTTACATCAGAAAAAATCTGATTCCATTAAGAATTTATGCA
TTATCATATTTATTCAAAACAGAATCTATGCATTAGTTCCATCTTTCGAACTCCAATCCATCCAT
TAGTCTATTATTTACAGTCCAACATTTATAATC
Found at i:446468 original size:39 final size:38
Alignment explanation
Indices: 446344--446471 Score: 115
Period size: 39 Copynumber: 3.4 Consensus size: 38
446334 AAAATCTATG
* *
446344 CATTAGTC-TCATCTTTTAAATTTTAATAAAAAATTTATA
1 CATTAGTCAT-ATC-TTTAAAATTTAATAAAAAATTCATA
* * * * *
446383 TATTAGTCATATCTTTTATATTTCAAT-AAATATACAT-
1 CATTAGTCATATCTTTAAAATTT-AATAAAAAATTCATA
446420 CATTA---ATATCTTTCAAAATTTAATAAAAAATTCATA
1 CATTAGTCATATCTTT-AAAATTTAATAAAAAATTCATA
446456 CATTAGTCATATCTTT
1 CATTAGTCATATCTTT
446472 TAGATATCAA
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
34 11 0.16
35 13 0.19
36 5 0.07
37 4 0.06
38 14 0.20
39 21 0.30
40 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (38 bp):
CATTAGTCATATCTTTAAAATTTAATAAAAAATTCATA
Found at i:447254 original size:2 final size:2
Alignment explanation
Indices: 447204--447236 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
447194 CAACAATTAA
*
447204 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
447237 AGAATTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:447354 original size:18 final size:18
Alignment explanation
Indices: 447331--447379 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
447321 ACGCATAAGA
447331 TAATTAAATATTATATTT
1 TAATTAAATATTATATTT
* *
447349 TAATTATATTTTATATTT
1 TAATTAAATATTATATTT
* *
447367 AAATTAAAAATTA
1 TAATTAAATATTA
447380 AAAATTTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAAATATTATATTT
Found at i:448062 original size:23 final size:23
Alignment explanation
Indices: 448008--448062 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
447998 TTTTAATTTG
**
448008 AATTAATTATACTAAGAAATATT
1 AATTAATTATACTAAGAAATAAA
* *
448031 AAGTAATTATACTAATAAATAAA
1 AATTAATTATACTAAGAAATAAA
*
448054 AATTGATTA
1 AATTAATTA
448063 ATTTAAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (23 bp):
AATTAATTATACTAAGAAATAAA
Found at i:448167 original size:33 final size:34
Alignment explanation
Indices: 448130--448199 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
448120 GTTAAATATC
448130 ATTTTTAAATTTATATTAAA-TATATGCTTATTA
1 ATTTTTAAATTTATATTAAATTATATGCTTATTA
* * * *
448163 ATTTTTGATTTTTTATTAAATTTATATTCTTATTA
1 ATTTTTAAATTTATATTAAA-TTATATGCTTATTA
448198 AT
1 AT
448200 ATATAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 17 0.55
35 14 0.45
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (34 bp):
ATTTTTAAATTTATATTAAATTATATGCTTATTA
Found at i:448224 original size:25 final size:26
Alignment explanation
Indices: 448187--448238 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
448177 ATTAAATTTA
*
448187 TATTCTTATTAATATATAA-TATTAT
1 TATTCTTAATAATATATAATTATTAT
* * *
448212 TATTGTTAATAATTTTTAATTATTAT
1 TATTCTTAATAATATATAATTATTAT
448238 T
1 T
448239 TTTAAAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTCTTAATAATATATAATTATTAT
Found at i:450260 original size:21 final size:21
Alignment explanation
Indices: 450220--450260 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
450210 TTAAGTATAA
*
450220 ATATTTTTCAAGCTATAAATC
1 ATATTTTTCAAGCTAAAAATC
450241 ATATGTTTTCAAG-TAAAAAT
1 ATAT-TTTTCAAGCTAAAAAT
450261 AATCTAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (21 bp):
ATATTTTTCAAGCTAAAAATC
Found at i:453306 original size:19 final size:18
Alignment explanation
Indices: 453247--453344 Score: 72
Period size: 19 Copynumber: 5.8 Consensus size: 18
453237 ATTTCAATGA
453247 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
*
453266 TATTATATCGATAC--AA-
1 T-TTGTATCGATACATAAG
453282 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
453298 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
453314 --TGTATTGATACATAAG
1 TTTGTATCGATACATAAG
453330 TTTTGTATCGATACA
1 -TTTGTATCGATACA
453345 ATATAAGCTA
Statistics
Matches: 62, Mismatches: 4, Indels: 26
0.67 0.04 0.28
Matches are distributed among these distances:
13 20 0.32
15 4 0.06
17 4 0.06
19 23 0.37
20 11 0.18
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:453312 original size:32 final size:32
Alignment explanation
Indices: 453249--453346 Score: 151
Period size: 32 Copynumber: 3.0 Consensus size: 32
453239 TTCAATGATT
*
453249 TGTATCGATACATAAAGTATTATATCGATACAA
1 TGTATCGATACAT-AAGTATTGTATCGATACAA
*
453282 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
* *
453314 TGTATTGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
453346 T
1 T
453347 ATAAGCTACT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 48 0.79
33 13 0.21
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:453462 original size:52 final size:52
Alignment explanation
Indices: 453421--453536 Score: 205
Period size: 52 Copynumber: 2.2 Consensus size: 52
453411 CACTGATCTT
* * *
453421 TGTATCGATACATGTAGGCAAGTTTGCCTAGATGTATCGATACACTGTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTGTAAAA
453473 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTGTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTGTAAAA
453525 TGTATCGATACA
1 TGTATCGATACA
453537 CTGTAAAATG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTGTAAAA
Found at i:453529 original size:20 final size:20
Alignment explanation
Indices: 453504--453560 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
453494 ATTTGCCCAG
453504 ATGTATCGATACACTGTAAA
1 ATGTATCGATACACTGTAAA
453524 ATGTATCGATACACTGTAAA
1 ATGTATCGATACACTGTAAA
*
453544 ATGTATGGATACA-TGTA
1 ATGTATCGATACACTGTA
453561 GGCAAATTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 4 0.11
20 32 0.89
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACACTGTAAA
Found at i:453531 original size:72 final size:72
Alignment explanation
Indices: 453452--453612 Score: 279
Period size: 72 Copynumber: 2.2 Consensus size: 72
453442 GTTTGCCTAG
453452 ATGTATCGATACACTGTAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACA
1 ATGTATCGATACACTGTAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACA
*
453517 CTGTAAA
66 CTATAAA
* *
453524 ATGTATCGATACACTGTAAAATGTATGGATACATGTAGGCAAATTTGCCCAGATGTATCGATACA
1 ATGTATCGATACACTGTAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACA
*
453589 CTATGAA
66 CTATAAA
453596 ATGTATCGATACA-TGTA
1 ATGTATCGATACACTGTA
453613 GGCAAATTTT
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 4 0.05
72 81 0.95
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (72 bp):
ATGTATCGATACACTGTAAAATGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACA
CTATAAA
Found at i:467460 original size:21 final size:21
Alignment explanation
Indices: 467436--467583 Score: 162
Period size: 21 Copynumber: 7.0 Consensus size: 21
467426 AGGCGTCTTC
467436 CAAAAAAAAAAACAAACAAAA
1 CAAAAAAAAAAACAAACAAAA
* *
467457 CAAAAAAAGAAGAGAAA-AAAA
1 CAAAAAAA-AAAACAAACAAAA
*
467478 C-GAAAAAAAAACAAACAAAA
1 CAAAAAAAAAAACAAACAAAA
*
467498 CAAAAGAAAAAAAACAAAAAAAAA
1 C-AAA-AAAAAAAAC-AAACAAAA
*
467522 CAACAAAAAAAACAAA-AAAA
1 CAAAAAAAAAAACAAACAAAA
467542 CAAAAAAAAACAACAAAC-AAA
1 CAAAAAAAAA-AACAAACAAAA
467563 CAAAAAAAAACAAC-AACAAAA
1 CAAAAAAAAA-AACAAACAAAA
467584 AGGGTCCAGA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.06
20 26 0.24
21 42 0.39
22 16 0.15
23 11 0.10
24 8 0.07
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAAAACAAACAAAA
Found at i:467476 original size:33 final size:33
Alignment explanation
Indices: 467437--467572 Score: 122
Period size: 34 Copynumber: 4.1 Consensus size: 33
467427 GGCGTCTTCC
*
467437 AAAAAAAAAAACAAACAAAACAAA-AAAAGAAGA
1 AAAAAAAAAAAAAAACAAAACAAACAAAAGAA-A
467470 GAAAAAAACGAAAAAAAA-ACAAACAAAACAAAAGAAA
1 -AAAAAAA--AAAAAAAACA-AAAC-AAACAAAAGAAA
* * *
467507 AAAAACAAAAAAAAAC--AACAAAAAAAACAAA
1 AAAAAAAAAAAAAAACAAAACAAACAAAAGAAA
467538 AAAACAAAAAAAAACAAC-AAACAAACAAAA-AAA
1 AAAA-AAAAAAAAA-AACAAAACAAACAAAAGAAA
467571 AA
1 AA
467573 CAACAACAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 19
0.78 0.05 0.17
Matches are distributed among these distances:
31 14 0.16
32 11 0.13
33 8 0.09
34 25 0.29
35 1 0.01
36 17 0.20
37 4 0.05
38 7 0.08
ACGTcount: A:0.85, C:0.12, G:0.04, T:0.00
Consensus pattern (33 bp):
AAAAAAAAAAAAAAACAAAACAAACAAAAGAAA
Found at i:467494 original size:41 final size:38
Alignment explanation
Indices: 467439--467575 Score: 150
Period size: 41 Copynumber: 3.3 Consensus size: 38
467429 CGTCTTCCAA
*
467439 AAAAAAAAACAAACAAAACAAAAAAAGAAGAGAAAAAAAC
1 AAAAAAAAACAAACAAAACAAAAAAA-AACA-AAAAAAAC
467479 GAAAAAAAAACAAACAAAACAAAAGAAAAAAAACAAAAAAAAAC
1 -AAAAAAAAACAAACAAAAC---A-AAAAAAAAC-AAAAAAAAC
467523 AACAAAAAAAACAAA-AAAACAAAAAAAAACAACAAACAAAC
1 -A-AAAAAAAACAAACAAAACAAAAAAAAACAA-AAA-AAAC
467564 AAAAAAAAACAA
1 AAAAAAAAACAA
467576 CAACAAAAAG
Statistics
Matches: 86, Mismatches: 2, Indels: 18
0.81 0.02 0.17
Matches are distributed among these distances:
39 13 0.15
40 13 0.15
41 24 0.28
44 17 0.20
45 19 0.22
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (38 bp):
AAAAAAAAACAAACAAAACAAAAAAAAACAAAAAAAAC
Found at i:467584 original size:1 final size:1
Alignment explanation
Indices: 467437--467572 Score: 83
Period size: 1 Copynumber: 136.0 Consensus size: 1
467427 GGCGTCTTCC
* * * * * * ** * * *
467437 AAAAAAAAAAACAAACAAAACAAAAAAAGAAGAGAAAAAAACGAAAAAAAAACAAACAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * * *
467502 AGAAAAAAAACAAAAAAAAACAACAAAAAAAACAAAAAAACAAAAAAAAACAACAAACAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
467567 AAAAAA
1 AAAAAA
467573 CAACAACAAA
Statistics
Matches: 94, Mismatches: 41, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 94 1.00
ACGTcount: A:0.85, C:0.12, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:469187 original size:86 final size:87
Alignment explanation
Indices: 469021--469204 Score: 219
Period size: 86 Copynumber: 2.1 Consensus size: 87
469011 CCTCACCCTT
* * * *
469021 CAAAAGCCCACAAGTCAATGGCATCTTTTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCCAAA
1 CAAAAGCCCACAAGTCAATGGCAAC-TCTTCAAAGCCAACAAATCAGTGGCACCCTTTTCCAAAA
* *
469086 GTCCACAAGTCAGTGGCAATCTC
65 GCCCACAAGTCAGTGGCAACCTC
* * * * * *
469109 CCAAAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCAACAAGTTAGTGGCA-CTTTTTTCAAAA
1 CAAAAGCCCACAAGTCAATGGCAACTCTTC-AAAGCCAACAAATCAGTGGCACCCTTTTCCAAAA
*
469172 GCCCACAAGTCAGTGGCAACCTT
65 GCCCACAAGTCAGTGGCAACCTC
469195 CAAAAGCCCA
1 CAAAAGCCCA
469205 TACAAGTTGG
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
86 41 0.51
87 18 0.22
88 22 0.27
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.20
Consensus pattern (87 bp):
CAAAAGCCCACAAGTCAATGGCAACTCTTCAAAGCCAACAAATCAGTGGCACCCTTTTCCAAAAG
CCCACAAGTCAGTGGCAACCTC
Found at i:469211 original size:30 final size:28
Alignment explanation
Indices: 469017--469204 Score: 173
Period size: 28 Copynumber: 6.5 Consensus size: 28
469007 TATTCCTCAC
* *
469017 CCTTCAAAAGCCCACAAGTCAATGGCAT
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* * *
469045 CTTTTTC-AAAGCCCACAAATCAGTGGCAC
1 C--CTTCAAAAGCCCACAAGTCAGTGGCAA
* *
469074 CCTTTTCCCAAAGTCCACAAGTCAGTGGCAA
1 CC--TT-CAAAAGCCCACAAGTCAGTGGCAA
* * *
469105 TCTCCCAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* *
469133 CCTTCAAAAGCCAACAAGTTAGTGGC-A
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
469160 CTTTTTTCAAAAGCCCACAAGTCAGTGGCAA
1 C---CTTCAAAAGCCCACAAGTCAGTGGCAA
469191 CCTTCAAAAGCCCA
1 CCTTCAAAAGCCCA
469205 TACAAGTTGG
Statistics
Matches: 130, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
27 2 0.02
28 57 0.44
29 23 0.18
30 26 0.20
31 22 0.17
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.20
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:469218 original size:30 final size:29
Alignment explanation
Indices: 469090--469219 Score: 124
Period size: 28 Copynumber: 4.5 Consensus size: 29
469080 CCCAAAGTCC
* * * *
469090 ACAAGTCAGTGGCAATCTCCCAAAGCCC-
1 ACAAGTTAGTGGCAACCTTCAAAAGCCCA
*
469118 ACAAGTCAGTGGCAACCTTCAAAAG-CCA
1 ACAAGTTAGTGGCAACCTTCAAAAGCCCA
*
469146 ACAAGTTAGTGGC-ACTTTTTTCAAAAGCCC-
1 ACAAGTTAGTGGCAAC---CTTCAAAAGCCCA
*
469176 ACAAGTCAGTGGCAACCTTCAAAAGCCCA
1 ACAAGTTAGTGGCAACCTTCAAAAGCCCA
*
469205 TACAAGTTGGTGGCA
1 -ACAAGTTAGTGGCA
469220 TCTTCTTCTA
Statistics
Matches: 85, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
27 4 0.05
28 45 0.53
30 32 0.38
31 4 0.05
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (29 bp):
ACAAGTTAGTGGCAACCTTCAAAAGCCCA
Found at i:469296 original size:49 final size:49
Alignment explanation
Indices: 469223--469593 Score: 374
Period size: 49 Copynumber: 7.8 Consensus size: 49
469213 GGTGGCATCT
*
469223 TCTTCTAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCA
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCA
* * * * *
469273 TCTTTAAGTCCAATGTCGTTGGCCTTGAACCAACACATTGGCA----C-
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCA
* *
469317 -CTTTAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCA
* * * *
469365 TCTTTAAGTCCAATGTCGCTGGCCTTGAACCAACACATT-G-A----CA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCA
* * * *
469408 GCTTTAAGTCCAATATCGCTGGCCTTAAATCAACATATTGGCACTGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCA
* * * * *
469457 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCA
** * *
469506 TCTTTAAGTCCGGTATCGTTGG-CTTGAATTAGCATATTGGCACCGTCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCA
* * *
469554 TCTTTAAGAT-CAATGTCGCTGGCCATGAAGCAGCATATTG
1 TCTTTAAG-TCCAATATCGCTGGCCTTGAATCAGCATATTG
469594 TCATTCTTCG
Statistics
Matches: 260, Mismatches: 47, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
43 72 0.28
44 1 0.00
45 2 0.01
47 2 0.01
48 39 0.15
49 140 0.54
50 4 0.02
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (49 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCA
Found at i:469388 original size:92 final size:92
Alignment explanation
Indices: 469228--469582 Score: 480
Period size: 92 Copynumber: 3.8 Consensus size: 92
469218 CATCTTCTTC
*
469228 TAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATGTCGTT
1 TAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATGTCGCT
469293 GGCCTTGAACCAACACATTGGCACCTT
66 GGCCTTGAACCAACACATTGGCACCTT
*
469320 TAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTGTCATCTTTAAGTCCAATGTCGCT
1 TAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATGTCGCT
* *
469385 GGCCTTGAACCAACACATTGACAGCTT
66 GGCCTTGAACCAACACATTGGCACCTT
* * * * *
469412 TAAGTCCAATATCGCTGGCCTTAAATCAACATATTGGCACTGTCATCTTTAAGACCAATGTCGCT
1 TAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATGTCGCT
* *
469477 GGCCTTGAATCAGCACATTGGCATCTTCATCTT
66 GGCCTTGAACCAACACATTGGCA----C--CTT
* ** * *
469510 TAAGTCCGGTATCGTTGG-CTTGAATTAGCATATTGGCACCGTCATCTTTAAGAT-CAATGTCGC
1 TAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAG-TCCAATGTCGC
*
469573 TGGCCATGAA
65 TGGCCTTGAA
469583 GCAGCATATT
Statistics
Matches: 235, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
92 169 0.72
97 48 0.20
98 18 0.08
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (92 bp):
TAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATGTCGCT
GGCCTTGAACCAACACATTGGCACCTT
Found at i:470305 original size:13 final size:13
Alignment explanation
Indices: 470287--470311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
470277 CATAAAGTGT
470287 TGTATCGATACAA
1 TGTATCGATACAA
470300 TGTATCGATACA
1 TGTATCGATACA
470312 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:470327 original size:32 final size:33
Alignment explanation
Indices: 470267--470332 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
470257 TTCAACGATT
470267 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
470300 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
470332 T
1 T
470333 ATAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:470391 original size:13 final size:13
Alignment explanation
Indices: 470373--470397 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
470363 ATTACTCAAA
470373 TGTATCGATACAT
1 TGTATCGATACAT
470386 TGTATCGATACA
1 TGTATCGATACA
470398 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:470447 original size:52 final size:52
Alignment explanation
Indices: 470406--470690 Score: 489
Period size: 52 Copynumber: 5.5 Consensus size: 52
470396 CACTGATCTT
*
470406 TGTATCGATACATGCAGGCAAGTTTGCCCAGATGTATCGATACACTGTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTGTAAAA
*
470458 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTGTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTGTAAAA
*
470510 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTGTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTGTAAAA
* *
470562 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATATACTGTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTGTAAAA
* * * *
470614 TGTATCGATATATGCAGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTGTAAAA
470666 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
470691 TCATATTTCG
Statistics
Matches: 221, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 221 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTGTAAAA
Found at i:477445 original size:20 final size:21
Alignment explanation
Indices: 477415--477455 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
477405 GCTTTGTATC
*
477415 GATACATTGTATTGATACATG
1 GATACATTGTATCGATACATG
477436 GATA-ATTGTATCGATACATG
1 GATACATTGTATCGATACATG
477456 AAACTGGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (21 bp):
GATACATTGTATCGATACATG
Found at i:483802 original size:21 final size:22
Alignment explanation
Indices: 483776--483825 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
483766 ATAAAATCTT
* *
483776 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTAATTTTTCA
483797 CTTCAAAATACTTAATTTTTCA
1 CTTCAAAATACTTAATTTTTCA
483819 --TCAAAAT
1 CTTCAAAAT
483826 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTAATTTTTCA
Found at i:485976 original size:13 final size:13
Alignment explanation
Indices: 485958--485983 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
485948 ACATTATGCT
485958 TTGTATCGATACA
1 TTGTATCGATACA
485971 TTGTATCGATACA
1 TTGTATCGATACA
485984 GAGACAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:486069 original size:13 final size:13
Alignment explanation
Indices: 486051--486080 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
486041 AATACATGGC
*
486051 ACATTGTATCGAT
1 ACATTGCATCGAT
486064 ACATTGCATCGAT
1 ACATTGCATCGAT
486077 ACAT
1 ACAT
486081 GATGAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (13 bp):
ACATTGCATCGAT
Found at i:489672 original size:21 final size:23
Alignment explanation
Indices: 489626--489673 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
489616 AGAGTTAAGT
*
489626 ATAA-ATGTTTTTCAAGCTATAA
1 ATAATATGTTTTTCAAGCTAAAA
489648 ATAATATG-TTTTCAAG-TAAAA
1 ATAATATGTTTTTCAAGCTAAAA
489669 ATAAT
1 ATAAT
489674 CAAAGTATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 12 0.50
23 3 0.12
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (23 bp):
ATAATATGTTTTTCAAGCTAAAA
Found at i:489811 original size:19 final size:19
Alignment explanation
Indices: 489768--489826 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
489758 CACACCCAGA
* *
489768 TGTATTGATACATATTGCTT
1 TGTATTGATACATGTT-CAT
*
489788 TGTATTAATACATGTTCAT
1 TGTATTGATACATGTTCAT
*
489807 TGTATCGATACATGTTCAT
1 TGTATTGATACATGTTCAT
489826 T
1 T
489827 ATATCGATAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (19 bp):
TGTATTGATACATGTTCAT
Found at i:489831 original size:19 final size:19
Alignment explanation
Indices: 489795--489835 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
489785 CTTTGTATTA
*
489795 ATACATGTTCATTGTATCG
1 ATACATGTTCATTATATCG
489814 ATACATGTTCATTATATCG
1 ATACATGTTCATTATATCG
489833 ATA
1 ATA
489836 GACACTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (19 bp):
ATACATGTTCATTATATCG
Found at i:489924 original size:20 final size:20
Alignment explanation
Indices: 489897--489951 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
489887 GTATTGATAC
*
489897 AATGTATCGATACATGAAGG
1 AATGTATCGATACATGAAGA
* **
489917 ATTGTATCGATACATGGTGA
1 AATGTATCGATACATGAAGA
489937 AATGTATCGATACAT
1 AATGTATCGATACAT
489952 TGAACCTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATGAAGA
Found at i:490224 original size:34 final size:34
Alignment explanation
Indices: 490190--490255 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
490180 TATATCTCAA
490190 AAAGCT-TTTGTATT-CTTTGT-CGTTATTCTTTC
1 AAAGCTATTTGTATTCCTTTGTGC-TTATTCTTTC
490222 AAAGCTCATTTGTATTCCTTTGTGCTTATTCTTT
1 AAAGCT-ATTTGTATTCCTTTGTGCTTATTCTTT
490256 TCACAAACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 6 0.20
34 8 0.27
35 15 0.50
36 1 0.03
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.55
Consensus pattern (34 bp):
AAAGCTATTTGTATTCCTTTGTGCTTATTCTTTC
Found at i:495395 original size:16 final size:17
Alignment explanation
Indices: 495374--495407 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
495364 TTTAAAATTG
495374 AATTTGA-TAGTTTTTA
1 AATTTGAGTAGTTTTTA
*
495390 AATTTGAGTTGTTTTTA
1 AATTTGAGTAGTTTTTA
495407 A
1 A
495408 GAAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (17 bp):
AATTTGAGTAGTTTTTA
Found at i:498373 original size:30 final size:30
Alignment explanation
Indices: 498339--498423 Score: 73
Period size: 30 Copynumber: 2.8 Consensus size: 30
498329 CTTTAAAAAA
498339 TAAATTTTATTGCTACAAAATTAAGTATAT
1 TAAATTTTATTGCTACAAAATTAAGTATAT
** * * * *
498369 TAAATATAAAAT-ATATAAAATTAAGTGTAT
1 TAAAT-TTTATTGCTACAAAATTAAGTATAT
* * *
498399 TCATTTTTATCGCTACAAAATTAAG
1 TAAATTTTATTGCTACAAAATTAAG
498424 GGTATCAAAT
Statistics
Matches: 39, Mismatches: 14, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
29 2 0.05
30 34 0.87
31 3 0.08
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (30 bp):
TAAATTTTATTGCTACAAAATTAAGTATAT
Found at i:498644 original size:31 final size:33
Alignment explanation
Indices: 498609--498678 Score: 108
Period size: 31 Copynumber: 2.2 Consensus size: 33
498599 AAATAATGGT
*
498609 AAATATAATTTTTAAAAA-TA-ATAGACAAATA
1 AAATATAATTTTTAAAAATTACATAGAAAAATA
*
498640 AAATATAATTTTTAAAAATTACATATAAAAATA
1 AAATATAATTTTTAAAAATTACATAGAAAAATA
498673 AAATAT
1 AAATAT
498679 TAGTAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 18 0.51
32 2 0.06
33 15 0.43
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (33 bp):
AAATATAATTTTTAAAAATTACATAGAAAAATA
Found at i:498703 original size:59 final size:61
Alignment explanation
Indices: 498640--498753 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 61
498630 TAGACAAATA
* * *
498640 AAATATAATTTTTAAAAATTACATAT-AAAAATAAAATATTAGT-AAATATTATGAATAAT
1 AAATATAACTTTTAAAAATTACAAATAAAAAATAAAATATTAATAAAATATTATGAATAAT
* * *
498699 AAATATAACTTTTAAAAATTATAAATAAAAAATACAATCTTAATAAAATATTATG
1 AAATATAACTTTTAAAAATTACAAATAAAAAATAAAATATTAATAAAATATTATG
498754 GATTACAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 23 0.49
60 14 0.30
61 10 0.21
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.36
Consensus pattern (61 bp):
AAATATAACTTTTAAAAATTACAAATAAAAAATAAAATATTAATAAAATATTATGAATAAT
Found at i:498771 original size:59 final size:59
Alignment explanation
Indices: 498640--498771 Score: 133
Period size: 59 Copynumber: 2.2 Consensus size: 59
498630 TAGACAAATA
* * * * *
498640 AAATATAATTTTTAAAAATTACATATAAAAATAAAATATTAGTAAATATTATGAATAAT
1 AAATAGAACTTTTAAAAATTACAAATAAAAATAAAATATTAATAAATATTATGAATAAC
* * * * * *
498699 AAATATAACTTTTAAAAATTATAAATAAAAAATACAATCTTAATAAAATATTATGGATTAC
1 AAATAGAACTTTTAAAAATTACAAAT-AAAAATAAAATATTAAT-AAATATTATGAATAAC
498760 AAAT-GAA-TTTTA
1 AAATAGAACTTTTA
498772 GTTTAAAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
59 28 0.46
60 16 0.26
61 17 0.28
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (59 bp):
AAATAGAACTTTTAAAAATTACAAATAAAAATAAAATATTAATAAATATTATGAATAAC
Found at i:499051 original size:11 final size:11
Alignment explanation
Indices: 499037--499078 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
499027 AATTTTTTTT
499037 AAATTAATAAA
1 AAATTAATAAA
*
499048 AAATTAAT--T
1 AAATTAATAAA
499057 AAATTAATAAA
1 AAATTAATAAA
499068 AAATTAATAAA
1 AAATTAATAAA
499079 TAACTTGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 8 0.30
11 19 0.70
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAATTAATAAA
Found at i:499060 original size:20 final size:20
Alignment explanation
Indices: 499035--499079 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
499025 TGAATTTTTT
499035 TTAAATTAATAAAAAATTAA
1 TTAAATTAATAAAAAATTAA
499055 TTAAATTAATAAAAAATTAA
1 TTAAATTAATAAAAAATTAA
499075 -TAAAT
1 TTAAAT
499080 AACTTGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TTAAATTAATAAAAAATTAA
Found at i:504830 original size:100 final size:100
Alignment explanation
Indices: 504657--504856 Score: 391
Period size: 100 Copynumber: 2.0 Consensus size: 100
504647 TATGTTTAAA
504657 CCAATGATTCTAGATGATTAGTCATGCACTAATCCACACATAAAATTTCAAATCTCATAAAATGC
1 CCAATGATTCTAGATGATTAGTCATGCACTAATCCACACATAAAATTTCAAATCTCATAAAATGC
504722 CATTTAATAATGCTTGACACTATAACTAGCCAAGT
66 CATTTAATAATGCTTGACACTATAACTAGCCAAGT
*
504757 CCAATGATTCTAGATGATTAGTCATGCACTAATCCACACATAGAATTTCAAATCTCATAAAATGC
1 CCAATGATTCTAGATGATTAGTCATGCACTAATCCACACATAAAATTTCAAATCTCATAAAATGC
504822 CATTTAATAATGCTTGACACTATAACTAGCCAAGT
66 CATTTAATAATGCTTGACACTATAACTAGCCAAGT
504857 GACTTGTATC
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 99 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (100 bp):
CCAATGATTCTAGATGATTAGTCATGCACTAATCCACACATAAAATTTCAAATCTCATAAAATGC
CATTTAATAATGCTTGACACTATAACTAGCCAAGT
Found at i:507200 original size:16 final size:15
Alignment explanation
Indices: 507148--507201 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
507138 AGGGTGAAAA
*
507148 GAAAAATAGAAAGAT
1 GAAAAATTGAAAGAT
* * *
507163 GGAAACTTGAAAGAG
1 GAAAAATTGAAAGAT
507178 GAGAAAATTGAAAAGAT
1 GA-AAAATTG-AAAGAT
507195 GAAAAAT
1 GAAAAAT
507202 AGATTTTTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 12 0.40
16 11 0.37
17 7 0.23
ACGTcount: A:0.59, C:0.02, G:0.24, T:0.15
Consensus pattern (15 bp):
GAAAAATTGAAAGAT
Found at i:508545 original size:16 final size:17
Alignment explanation
Indices: 508518--508561 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
508508 TAAAAATAAT
**
508518 TAAAATATAATATTATA
1 TAAAATATAATAAAATA
508535 TAAAA-ATAATAAAATA
1 TAAAATATAATAAAATA
508551 TAAAATA-AATA
1 TAAAATATAATA
508562 CATAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATATAATAAAATA
Found at i:508560 original size:19 final size:22
Alignment explanation
Indices: 508538--508578 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
508528 TATTATATAA
508538 AAATA-ATAAA-ATAT-AAAAT
1 AAATACATAAATATATCAAAAT
508557 AAATACATAAATATATCAAAAT
1 AAATACATAAATATATCAAAAT
508579 TTATATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 5 0.26
21 4 0.21
22 5 0.26
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATACATAAATATATCAAAAT
Found at i:509860 original size:22 final size:23
Alignment explanation
Indices: 509835--509880 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
509825 TAAATATTTT
*
509835 TGTATTTATGTTTAATTAT-TAA
1 TGTAATTATGTTTAATTATATAA
* *
509857 TGTAATTATTTTTTATTATATAA
1 TGTAATTATGTTTAATTATATAA
509880 T
1 T
509881 AAATATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (23 bp):
TGTAATTATGTTTAATTATATAA
Found at i:510598 original size:17 final size:17
Alignment explanation
Indices: 510573--510606 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
510563 ATTTTATGTC
*
510573 AAATTTAAATATATATT
1 AAATATAAATATATATT
*
510590 AAATATAAATATTTATT
1 AAATATAAATATATATT
510607 TAAAAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATATAAATATATATT
Found at i:511534 original size:24 final size:27
Alignment explanation
Indices: 511475--511538 Score: 71
Period size: 30 Copynumber: 2.4 Consensus size: 27
511465 TCTCTATAGT
*
511475 AATTTATATATTTATATTATGTGTATA
1 AATTTTTATATTTATATTATGTGTATA
511502 ATATTTTTTTATATTTA-ATTATGT-T-TA
1 A-A--TTTTTATATTTATATTATGTGTATA
511529 AATTTTTATA
1 AATTTTTATA
511539 AATTTTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
24 8 0.24
26 1 0.03
27 4 0.12
28 2 0.06
29 7 0.21
30 11 0.33
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (27 bp):
AATTTTTATATTTATATTATGTGTATA
Found at i:511546 original size:36 final size:37
Alignment explanation
Indices: 511498--511579 Score: 114
Period size: 36 Copynumber: 2.2 Consensus size: 37
511488 ATATTATGTG
* *
511498 TATAATATTTTTTTATATTTAATTATGTTT-AAATTTT
1 TATAA-ATTTTTTTATAATTAATTATATTTAAAATTTT
*
511535 TATAAATTTTTTTATAATTAATTGTATTTAAAATTTT
1 TATAAATTTTTTTATAATTAATTATATTTAAAATTTT
511572 TA-AAATTT
1 TATAAATTT
511580 ATATAAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
36 27 0.66
37 14 0.34
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (37 bp):
TATAAATTTTTTTATAATTAATTATATTTAAAATTTT
Found at i:511618 original size:28 final size:27
Alignment explanation
Indices: 511578--511645 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 27
511568 TTTTTAAAAT
* * *
511578 TTATATAAAATTTGATA-TATTTGTGTA
1 TTATATCATATTT-ATATTATTTGTATA
*
511605 TTATTATCATATTTATATTATTTTTATA
1 TTA-TATCATATTTATATTATTTGTATA
*
511633 TTATATTATATTT
1 TTATATCATATTT
511646 TGGTTTGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 15 0.44
28 19 0.56
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (27 bp):
TTATATCATATTTATATTATTTGTATA
Found at i:512229 original size:7 final size:7
Alignment explanation
Indices: 512217--512280 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
512207 ACTTTTTAAA
512217 AATTTTT
1 AATTTTT
512224 AA-TTTT
1 AATTTTT
512230 AATTTTT
1 AATTTTT
* *
512237 AAATTCT
1 AATTTTT
512244 AATTTTTAT
1 AA-TTTT-T
512253 AATTTTT
1 AATTTTT
*
512260 ATAATTTT
1 A-ATTTTT
512268 AACTTTTT
1 AA-TTTTT
512276 -ATTTT
1 AATTTT
512281 AATGATGAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
6 10 0.22
7 17 0.37
8 16 0.35
9 3 0.07
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (7 bp):
AATTTTT
Found at i:512241 original size:14 final size:14
Alignment explanation
Indices: 512217--512258 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
512207 ACTTTTTAAA
512217 AATTTTT-AATTTT
1 AATTTTTAAATTTT
*
512230 AATTTTTAAATTCT
1 AATTTTTAAATTTT
512244 AATTTTTATAATTTT
1 AATTTTTA-AATTTT
512259 TATAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 7 0.28
14 13 0.52
15 5 0.20
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
AATTTTTAAATTTT
Found at i:512257 original size:9 final size:9
Alignment explanation
Indices: 512243--512267 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
512233 TTTTAAATTC
512243 TAATTTTTA
1 TAATTTTTA
512252 TAATTTTTA
1 TAATTTTTA
512261 TAATTTT
1 TAATTTT
512268 AACTTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TAATTTTTA
Found at i:512588 original size:20 final size:19
Alignment explanation
Indices: 512546--512598 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
512536 CAATCCAACA
*
512546 ATTTAGAAATATTAACTTAAT
1 ATTTA-AAAT-TTAAATTAAT
*
512567 ATTTATAAATTTAAATTGAT
1 ATTTA-AAATTTAAATTAAT
512587 ATTTAAAATTTA
1 ATTTAAAATTTA
512599 CACAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.24
20 13 0.45
21 9 0.31
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (19 bp):
ATTTAAAATTTAAATTAAT
Found at i:518055 original size:19 final size:20
Alignment explanation
Indices: 518031--518068 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
518021 ATTTATGCAT
*
518031 TTGAATGTA-TTTTGAATGA
1 TTGAATGGATTTTTGAATGA
518050 TTGAATGGATTTTTGAATG
1 TTGAATGGATTTTTGAATG
518069 GAATTGGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (20 bp):
TTGAATGGATTTTTGAATGA
Found at i:522626 original size:2 final size:2
Alignment explanation
Indices: 522619--522644 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
522609 ACAGTGTTTA
522619 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
522645 GAGAAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:523433 original size:19 final size:18
Alignment explanation
Indices: 523409--523444 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
523399 AAAAAAATTT
*
523409 TAAAATTATTATTTAATAA
1 TAAAATTAATA-TTAATAA
523428 TAAAATTAATATTAATA
1 TAAAATTAATATTAATA
523445 TTTATATTTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATTAATATTAATAA
Found at i:523478 original size:42 final size:40
Alignment explanation
Indices: 523423--523506 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 40
523413 ATTATTATTT
* * *
523423 AATAATAAAATTAATATTAATAT-TTATATTTAATTATATA
1 AATAATAAAATTAATATAAAAATAATAT-TTTAATTATATA
523463 AATATATAAATATTAATATAAAAATAATATTTTAATTATATA
1 AATA-ATAAA-ATTAATATAAAAATAATATTTTAATTATATA
523505 AA
1 AA
523507 ATAAATTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 4 0.11
41 5 0.13
42 26 0.68
43 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (40 bp):
AATAATAAAATTAATATAAAAATAATATTTTAATTATATA
Found at i:523527 original size:20 final size:20
Alignment explanation
Indices: 523468--523531 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
523458 ATATAAATAT
*
523468 ATAAATATTAAT-AT-AAAA
1 ATAAATTTTAATGATAAAAA
* *
523486 ATAATATTTTAATTATATAAA
1 ATAA-ATTTTAATGATAAAAA
523507 ATAAA-TTTAATCGATAAAAA
1 ATAAATTTTAAT-GATAAAAA
523527 ATAAA
1 ATAAA
523532 ATATTCGGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
18 4 0.11
19 13 0.34
20 14 0.37
21 7 0.18
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
ATAAATTTTAATGATAAAAA
Found at i:531380 original size:2 final size:2
Alignment explanation
Indices: 531373--531409 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
531363 AGGGAGGGAA
531373 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
531410 CACTGTGCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:537552 original size:25 final size:24
Alignment explanation
Indices: 537507--537553 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
537497 TTGCCGAGGC
*
537507 TTTTAAAATTTTTAATTAATTATT
1 TTTTAAAATTTTTAATCAATTATT
537531 TTTTAAAAATTTTTTAA-CAATTA
1 TTTT-AAAA-TTTTTAATCAATTA
537554 AATTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 4 0.20
25 9 0.45
26 7 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTAAAATTTTTAATCAATTATT
Found at i:537602 original size:17 final size:17
Alignment explanation
Indices: 537559--537598 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
537549 AATTAAATTT
537559 TATTAAATTATAATTAA
1 TATTAAATTATAATTAA
*
537576 TTTTAAATTATAA-TAA
1 TATTAAATTATAATTAA
537592 TATTAAA
1 TATTAAA
537599 ATTAACATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTAAATTATAATTAA
Found at i:538090 original size:14 final size:15
Alignment explanation
Indices: 538073--538103 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
538063 AAATAATACT
538073 AACATAAAAATA-AA
1 AACATAAAAATATAA
538087 AACATAAAAATATAA
1 AACATAAAAATATAA
538102 AA
1 AA
538104 TTTTCTCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (15 bp):
AACATAAAAATATAA
Found at i:538752 original size:11 final size:11
Alignment explanation
Indices: 538736--538776 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
538726 ATATTTATGT
538736 TAATAAAAAAA
1 TAATAAAAAAA
538747 TAATAAAAATAA
1 TAATAAAAA-AA
* *
538759 AAATAAAAATA
1 TAATAAAAAAA
538770 TAATAAA
1 TAATAAA
538777 TTATTAACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
TAATAAAAAAA
Found at i:538759 original size:6 final size:6
Alignment explanation
Indices: 538737--538769 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
538727 TATTTATGTT
*
538737 AATAAA AA-AAT AATAAA AATAAA AATAAA AATA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATA
538770 TAATAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:538883 original size:14 final size:14
Alignment explanation
Indices: 538824--538890 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
538814 TTAATATGTC
*
538824 AAATATTAATATTT
1 AAATATTTATATTT
*
538838 AAA-ATAATATATTT
1 AAATAT-TTATATTT
*
538852 -AATATATATA-TT
1 AAATATTTATATTT
*
538864 --ATATTTATGTTT
1 AAATATTTATATTT
538876 AAATATTTATATTT
1 AAATATTTATATTT
538890 A
1 A
538891 TATCTAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
11 7 0.16
12 4 0.09
13 9 0.21
14 23 0.53
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (14 bp):
AAATATTTATATTT
Found at i:540179 original size:49 final size:49
Alignment explanation
Indices: 540102--540206 Score: 192
Period size: 49 Copynumber: 2.1 Consensus size: 49
540092 AGTTGATGTG
*
540102 AGAATGACTTAGATAGCACTTTTAGATTTTGAAAGTAAGAAAGTGTAAAA
1 AGAA-GACTTAGATAGCACTTTTAGATTTTAAAAGTAAGAAAGTGTAAAA
540152 AGAAGACTTAGATAGCACTTTTAGATTTTAAAAGTAAGAAAGTGTAAAA
1 AGAAGACTTAGATAGCACTTTTAGATTTTAAAAGTAAGAAAGTGTAAAA
540201 AGAAGA
1 AGAAGA
540207 AGAAAGAGGT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 50 0.93
50 4 0.07
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.28
Consensus pattern (49 bp):
AGAAGACTTAGATAGCACTTTTAGATTTTAAAAGTAAGAAAGTGTAAAA
Found at i:542993 original size:26 final size:27
Alignment explanation
Indices: 542964--543014 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
542954 AGTGAGGATA
542964 AAGTAGCTACG-CTTTGTGATACTAGT
1 AAGTAGCTACGCCTTTGTGATACTAGT
*
542990 AAGTAGCTATGCCTTTGTGATACTA
1 AAGTAGCTACGCCTTTGTGATACTA
543015 CTTTATACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (27 bp):
AAGTAGCTACGCCTTTGTGATACTAGT
Found at i:553822 original size:21 final size:21
Alignment explanation
Indices: 553796--553835 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
553786 AAAAATTCCA
553796 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
553817 AATGTATCGATACATTTGT
1 AATGTATCGATACATTTGT
553836 GGGTCCCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:553895 original size:19 final size:19
Alignment explanation
Indices: 553871--553938 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
553861 AATTCAACAA
553871 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
553890 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
553905 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
553922 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
553939 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:553910 original size:13 final size:13
Alignment explanation
Indices: 553892--553916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
553882 ACATAAGTTT
553892 TGTATCGATACAA
1 TGTATCGATACAA
553905 TGTATCGATACA
1 TGTATCGATACA
553917 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:553914 original size:32 final size:32
Alignment explanation
Indices: 553873--553935 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
553863 TTCAACAATT
*
553873 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
553905 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
553936 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:553997 original size:13 final size:13
Alignment explanation
Indices: 553979--554005 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
553969 ATTTTTCTGT
553979 GTATCGATACATG
1 GTATCGATACATG
553992 GTATCGATACATG
1 GTATCGATACATG
554005 G
1 G
554006 ATCTTTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (13 bp):
GTATCGATACATG
Found at i:554001 original size:33 final size:33
Alignment explanation
Indices: 553959--554023 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
553949 CCAAGGAAAT
***
553959 GTATCGATACATTTTTCTGTGTATCGATACATG
1 GTATCGATACATGGATCTGTGTATCGATACATG
*
553992 GTATCGATACATGGATCTTTGTATCGATACAT
1 GTATCGATACATGGATCTGTGTATCGATACAT
554024 TTGAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.40
Consensus pattern (33 bp):
GTATCGATACATGGATCTGTGTATCGATACATG
Found at i:556427 original size:51 final size:53
Alignment explanation
Indices: 556363--556704 Score: 212
Period size: 52 Copynumber: 6.5 Consensus size: 53
556353 AGTTTATCAA
* * * *
556363 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
556414 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * *
556468 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * *
556526 TAT-TTC-CGA--GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAAT
* * * * *
556575 TTTTTCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCTAATT
1 TTCTTCACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-T
* *
556628 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
556680 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
556705 CTCGTTATTT
Statistics
Matches: 226, Mismatches: 37, Indels: 55
0.71 0.12 0.17
Matches are distributed among these distances:
48 1 0.00
49 5 0.02
50 6 0.03
51 36 0.16
52 80 0.35
53 32 0.14
54 35 0.15
55 20 0.09
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:556547 original size:28 final size:27
Alignment explanation
Indices: 556480--556548 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
556470 CTTCACAATC
**
556480 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
556507 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
556535 GGGGATACTCCAAC
1 GGGGATACTCCAAC
556549 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:556720 original size:28 final size:28
Alignment explanation
Indices: 556688--556763 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 28
556678 ATTTTTCACA
* *
556688 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTACTTC
*
556716 ATCGA-GACACTCCAACCCCGTTACTTC
1 ATCGAGGATACTCCAACCCCGTTACTTC
556743 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
556764 GCTTTATTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 3 0.07
27 19 0.46
28 19 0.46
ACGTcount: A:0.25, C:0.36, G:0.17, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTACTTC
Found at i:556747 original size:211 final size:212
Alignment explanation
Indices: 556368--556770 Score: 625
Period size: 211 Copynumber: 1.9 Consensus size: 212
556358 ATCAATTCTC
*
556368 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATA
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATA
* *
556433 CTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCG
66 CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
* * * * *
556498 TTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCCGGTTTTATCGC
131 TTAATCATCGGAGACACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATCGC
556563 TAAAACACTAATTTTTT
196 TAAAACACTAATTTTTT
* * *
556580 CACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCTAATTTTCCTTTAATCGGGGA
1 CACAATCGGGGATACTCCAACTCC-GATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGA
* *
556644 TACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCT
64 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
*
556707 CGTTATTTCATC-GAGACACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTAT
129 CGTTA-ATCATCGGAGACACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTAT
556771 TCCCAAAATA
Statistics
Matches: 174, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
211 78 0.45
212 61 0.35
213 35 0.20
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (212 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
TTAATCATCGGAGACACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATCGC
TAAAACACTAATTTTTT
Found at i:556777 original size:107 final size:106
Alignment explanation
Indices: 556426--556820 Score: 333
Period size: 107 Copynumber: 3.7 Consensus size: 106
556416 TTCTATAATC
* *
556426 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTA-TTCCCAAAAACACCAATTT-TTCACAATCGGGGATACTCC
* * *
556491 AACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTCCGA
64 AACCCCGTTATTTCATC-GAGAAACTCCAACCCCGTTA-TTCCGA
* * * *
556535 GGGGATACTCCAACTCCGGTTTTA-TCGCTAAAACACTAATTTTTTCACAATCGGGGATACTCCA
1 GGGGATACTCCAACTCCGATTTTATTCCCAAAAACACCAA-TTTTTCACAATCGGGGATACTCCA
** * * ** * *
556599 ATCCTGGTTTTATTT--TC-A-AAACGCTAATTTTCCTTTAAT-C--
65 A-CCCCG--TTATTTCATCGAGAAACTCCAA--CCCCGTTATTCCGA
* * *
556639 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTCCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* *
556704 CCTCGTTATTTCATCGAGACACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTTCATCGAGAAACTCCAACCCCGTTA-TTCCGA
* ** * *** * * *
556746 GGGGATACTCCAACCCCGGCTTTATTCCC-AAAATATTGATTTCTCATAATGGGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTCCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
556810 CCCCGTTATTT
66 CCCCGTTATTT
556821 TCGAAGGGAT
Statistics
Matches: 226, Mismatches: 44, Indels: 35
0.74 0.14 0.11
Matches are distributed among these distances:
101 6 0.03
103 11 0.05
104 49 0.22
105 17 0.08
106 45 0.20
107 59 0.26
108 11 0.05
109 24 0.11
110 3 0.01
111 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (106 bp):
GGGGATACTCCAACTCCGATTTTATTCCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
CCCCGTTATTTCATCGAGAAACTCCAACCCCGTTATTCCGA
Found at i:563652 original size:17 final size:17
Alignment explanation
Indices: 563630--563663 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
563620 CAGAGGTAAG
*
563630 AAGGAAGGCAAAGTCAA
1 AAGGAAGCCAAAGTCAA
*
563647 AAGGAAGCCACAGTCAA
1 AAGGAAGCCAAAGTCAA
563664 GAATCGATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.18, G:0.26, T:0.06
Consensus pattern (17 bp):
AAGGAAGCCAAAGTCAA
Found at i:569344 original size:14 final size:13
Alignment explanation
Indices: 569324--569362 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
569314 ACCTTCTCTT
569324 CAAAAAAAAAAAG
1 CAAAAAAAAAAAG
569337 CAAAAAAAAAAAG
1 CAAAAAAAAAAAG
*
569350 GAAAAAAACAAAA
1 CAAAAAAA-AAAA
569363 AAAACAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAAG
Found at i:569371 original size:14 final size:14
Alignment explanation
Indices: 569324--569381 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
569314 ACCTTCTCTT
*
569324 CAAAA-AAAAAAAG
1 CAAAACAAAAAAAA
*
569337 CAAAAAAAAAAAGGAA
1 CAAAACAAAAAA--AA
*
569353 AAAAACAAAAAAAA
1 CAAAACAAAAAAAA
569367 CAAAACAAAGAAAAA
1 CAAAACAAA-AAAAA
569382 GAGAGAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
13 5 0.14
14 16 0.43
15 5 0.14
16 11 0.30
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (14 bp):
CAAAACAAAAAAAA
Found at i:570449 original size:55 final size:55
Alignment explanation
Indices: 570364--571426 Score: 1669
Period size: 55 Copynumber: 19.3 Consensus size: 55
570354 TCCGCTTTTT
570364 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
570419 AGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
570474 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
570529 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
570584 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
570639 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
**
570694 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
570749 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
570804 AGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
570859 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
570914 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
570969 AGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACCCAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
571024 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
571079 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
571134 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
571189 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
571244 AATCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
571299 ATTCCCCAAAGAGCAGGACA-CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
571354 AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
571409 ACTGCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
571427 TACAGTTTAT
Statistics
Matches: 942, Mismatches: 48, Indels: 36
0.92 0.05 0.04
Matches are distributed among these distances:
54 23 0.02
55 895 0.95
56 24 0.03
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:570536 original size:29 final size:29
Alignment explanation
Indices: 570504--570591 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
570494 CCTCTTAAAG
570504 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
** * *
570533 CCCA-A-AGAG-CAG-GACACCTCTTAAAG--
1 CCCACACA-AGTTGGTGGCACCT-TT-CAGTC
570559 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
570588 CCCA
1 CCCA
570592 AAGAGCAGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 18
0.62 0.12 0.26
Matches are distributed among these distances:
26 10 0.24
27 9 0.21
28 9 0.21
29 14 0.33
ACGTcount: A:0.26, C:0.35, G:0.19, T:0.19
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAGTC
Found at i:570921 original size:29 final size:29
Alignment explanation
Indices: 570889--570976 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
570879 CCTCTTAAAG
570889 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
** * *
570918 CCCA-A-AGAG-CAG-GACACCTCTTAAAG--
1 CCCACACA-AGTTGGTGGCACCT-TT-CAGTC
570944 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
570973 CCCA
1 CCCA
570977 AAGAGCAGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 18
0.62 0.12 0.26
Matches are distributed among these distances:
26 10 0.24
27 9 0.21
28 9 0.21
29 14 0.33
ACGTcount: A:0.26, C:0.35, G:0.19, T:0.19
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAGTC
Found at i:571086 original size:29 final size:29
Alignment explanation
Indices: 571054--571141 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
571044 CCTCTTAAAG
571054 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
** * *
571083 CCCA-A-AGAG-CAG-GACACCTCTTAAAG--
1 CCCACACA-AGTTGGTGGCACCT-TT-CAGTC
571109 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
571138 CCCA
1 CCCA
571142 AAGAGCAGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 18
0.62 0.12 0.26
Matches are distributed among these distances:
26 10 0.24
27 9 0.21
28 9 0.21
29 14 0.33
ACGTcount: A:0.26, C:0.35, G:0.19, T:0.19
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAGTC
Found at i:572054 original size:21 final size:21
Alignment explanation
Indices: 572028--572084 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
572018 AAAAATTCCA
572028 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
572049 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
572070 AATGTATCGATACAT
1 AATGTATCGATACAT
572085 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:572164 original size:19 final size:19
Alignment explanation
Indices: 572140--572207 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
572130 AATTCAACAA
572140 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
572159 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
572174 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
572191 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
572208 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:572179 original size:13 final size:13
Alignment explanation
Indices: 572161--572185 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
572151 ACATAAGTTT
572161 TGTATCGATACAA
1 TGTATCGATACAA
572174 TGTATCGATACA
1 TGTATCGATACA
572186 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:572183 original size:32 final size:32
Alignment explanation
Indices: 572142--572204 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
572132 TTCAACAATT
*
572142 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
572174 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
572205 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:572266 original size:13 final size:13
Alignment explanation
Indices: 572248--572274 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
572238 ATTTTTCTGT
572248 GTATCGATACATG
1 GTATCGATACATG
572261 GTATCGATACATG
1 GTATCGATACATG
572274 G
1 G
572275 ATCTTTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (13 bp):
GTATCGATACATG
Done.