Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 133 of 136
Found at i:45973496 original size:22 final size:23
Alignment explanation
Indices: 45973471--45973517 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
45973461 TTTAAGTTGA
45973471 TAAA-TTTATCTT-TTTATCTTTT
1 TAAATTTTATCTTATTTAT-TTTT
*
45973493 TAAATTTTATTTTATTTATTTTT
1 TAAATTTTATCTTATTTATTTTT
45973516 TA
1 TA
45973518 CTTTGCACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 13 0.59
24 5 0.23
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (23 bp):
TAAATTTTATCTTATTTATTTTT
Found at i:45978216 original size:101 final size:98
Alignment explanation
Indices: 45978034--45978221 Score: 234
Period size: 101 Copynumber: 1.9 Consensus size: 98
45978024 ACAAAAGTTA
* * * * *
45978034 ATAAACATATTTAATAATATTGATTAAAAAATTGTCGAATTTTGACTTTCTTTTTAAAACAAACC
1 ATAAACATATTTAATAATAGTGATTAAAAAACTGTCAAAATTTGACTTTCTTTTCAAAACAAACC
45978099 CACTAAACATTTTTCATCTGCACAACTAAATTG
66 CACTAAACATTTTTCATCTGCACAACTAAATTG
* * *
45978132 ATAAATATATTTAATAATAGTGATTAAAAAACAACTGTTAAAATTTGACTTTCTTTTCAAAGCAA
1 ATAAACATATTTAATAATAGTGATT--AAAA-AACTGTCAAAATTTGACTTTCTTTTCAAAACAA
* * *
45978197 GCTCTC-AAATCATTTTTCATCTGCA
63 ACCCACTAAA-CATTTTTCATCTGCA
45978222 TCAAACAAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
98 23 0.31
100 7 0.09
101 45 0.60
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (98 bp):
ATAAACATATTTAATAATAGTGATTAAAAAACTGTCAAAATTTGACTTTCTTTTCAAAACAAACC
CACTAAACATTTTTCATCTGCACAACTAAATTG
Found at i:45981875 original size:2 final size:2
Alignment explanation
Indices: 45981868--45981904 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
45981858 ATACTTGAAC
45981868 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
45981905 NNNNNNNNNN
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:45987407 original size:57 final size:56
Alignment explanation
Indices: 45987336--45987466 Score: 154
Period size: 57 Copynumber: 2.3 Consensus size: 56
45987326 ATTAGAGCCT
** * * * *
45987336 AAATTTTTTTTCAAGTTCGATATTGAGCTTGACAATTGTTCTCATATTAAGACTTG
1 AAATTTTTTTTCAAGTTAAATACTGAACTTGACAATTGTACCCATATTAAGACTTG
* ** *
45987392 AAATTTTTTATTCAAGTTAAATCCTGAACTTGACAATTGTACCCATATTGGGGCTTG
1 AAATTTTTT-TTCAAGTTAAATACTGAACTTGACAATTGTACCCATATTAAGACTTG
*
45987449 AATTTTTTTTTCAAGTTA
1 AAATTTTTTTTCAAGTTA
45987467 GTCCTTGAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
56 18 0.29
57 45 0.71
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (56 bp):
AAATTTTTTTTCAAGTTAAATACTGAACTTGACAATTGTACCCATATTAAGACTTG
Found at i:45993059 original size:18 final size:17
Alignment explanation
Indices: 45993038--45993074 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
45993028 TTATTTAAAT
45993038 TTAATAATAAAATTTATA
1 TTAAT-ATAAAATTTATA
*
45993056 TTAATATGAAATTTATA
1 TTAATATAAAATTTATA
45993073 TT
1 TT
45993075 TTAAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TTAATATAAAATTTATA
Found at i:46002901 original size:36 final size:37
Alignment explanation
Indices: 46002847--46002919 Score: 139
Period size: 36 Copynumber: 2.0 Consensus size: 37
46002837 GCTCGACACA
46002847 TACACCAAAAAAAAAAAAAAAAGTCTAAATTTATTGT
1 TACACCAAAAAAAAAAAAAAAAGTCTAAATTTATTGT
46002884 TACACC-AAAAAAAAAAAAAAAGTCTAAATTTATTGT
1 TACACCAAAAAAAAAAAAAAAAGTCTAAATTTATTGT
46002920 CAGTGGTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 30 0.83
37 6 0.17
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (37 bp):
TACACCAAAAAAAAAAAAAAAAGTCTAAATTTATTGT
Found at i:46008747 original size:16 final size:17
Alignment explanation
Indices: 46008717--46008749 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
46008707 TTGTTTATTA
*
46008717 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
46008734 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
46008750 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:46008958 original size:21 final size:21
Alignment explanation
Indices: 46008934--46008975 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
46008924 GCTTATGCCG
46008934 CCTCAAATTTGGCAATTGGCA
1 CCTCAAATTTGGCAATTGGCA
46008955 CCTCAAATTTGGCAATTGGCA
1 CCTCAAATTTGGCAATTGGCA
46008976 TAATTCGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (21 bp):
CCTCAAATTTGGCAATTGGCA
Found at i:46010726 original size:20 final size:20
Alignment explanation
Indices: 46010697--46010740 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
46010687 TTAAATAAAT
**
46010697 AATTAAAAATCCATAAAAA-
1 AATTAAAAATAAATAAAAAC
46010716 AATTAAAAAATAAATAAAAAC
1 AATT-AAAAATAAATAAAAAC
46010737 AATT
1 AATT
46010741 TATTAAATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 13 0.62
21 4 0.19
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (20 bp):
AATTAAAAATAAATAAAAAC
Found at i:46010734 original size:19 final size:18
Alignment explanation
Indices: 46010688--46010735 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
46010678 CAATAATAAT
*
46010688 TAAATAAATAATTAAAAA
1 TAAATAAAAAATTAAAAA
**
46010706 TCCATAAAAAAATTAAAAAA
1 TAAAT-AAAAAATT-AAAAA
46010726 TAAATAAAAA
1 TAAATAAAAA
46010736 CAATTTATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
18 3 0.13
19 12 0.52
20 8 0.35
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAATAAAAAATTAAAAA
Found at i:46013960 original size:21 final size:21
Alignment explanation
Indices: 46013934--46013979 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
46013924 TTGATCACAT
*
46013934 GCAATGATACTGACAATAATG
1 GCAATGATACAGACAATAATG
**
46013955 GCAATGATACAGACGTTAATG
1 GCAATGATACAGACAATAATG
46013976 GCAA
1 GCAA
46013980 ATCTGATTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (21 bp):
GCAATGATACAGACAATAATG
Found at i:46019279 original size:105 final size:104
Alignment explanation
Indices: 46018717--46019279 Score: 606
Period size: 105 Copynumber: 5.4 Consensus size: 104
46018707 AAGAGTGTTG
* *** * * ** *
46018717 TATGTGACAACATCAAATTCAATACCTTGTTTTCTCATCATGCCAACAATAACTTCAGCTTTAGA
1 TATGTGACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGCCAACAATATCTTCAGCTTTAGA
* * * *
46018782 AACCAACCTTTCTTGCAAAGCGCATTGATCAATGTATTA
66 AACCATCCCTTCTTGCAAAGCGCATCGATCAATGTACTA
* * * * * *
46018821 TACGTGACAACATCAGGCTCGATGCCTTGCTTTCTCATCGTGTCAACAATAACTTCAGCTTTAGA
1 TATGTGACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGCCAACAATATCTTCAGCTTTAGA
* * **
46018886 AACCAT-CCTGTCCTTGCAAAGCACATCAATCAATGTGTTA
66 AACCATCCCT-T-CTTGCAAAGCGCATCGATCAATGTACTA
* * * * *
46018926 TACGTGACAACATTAGGCTCAATGCCTTGCTTTGTCATTCTGCCAACAATACCTTCGGCTTTAGA
1 TATGTGACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGCCAACAATATCTTCAGCTTTAGA
* * * *
46018991 AACCATTCCCTTCTTGCAGAGAGCATCGATGAATATACTA
66 AACCA-TCCCTTCTTGCAAAGCGCATCGATCAATGTACTA
* * * * *
46019031 CATGTGACAACATCAAGCTTAATGCCTTGCTTTGTCATTGTGCCAACAATATCTTCAGCTTTAGA
1 TATGTGACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGCCAACAATATCTTCAGCTTTAGA
** * *
46019096 AACCATTCCCTTCTTGCAAAGCGGGTCAATCAATATACTA
66 AACCA-TCCCTTCTTGCAAAGCGCATCGATCAATGTACTA
* ** **
46019136 TATGTGACAACATTAGGCTCAATGCCTTGCTTTTTCATTGTGCCAAGGATATCTTTGGCTTTAGA
1 TATGTGACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGCCAACAATATCTTCAGCTTTAGA
* * *
46019201 AACCACTCCCTTCTTGCAAAGGGCATCGATCAATGTAGTG
66 AACCA-TCCCTTCTTGCAAAGCGCATCGATCAATGTACTA
** *
46019241 TATGTGATGACATTAGGCTTAATGCCTTGCTTTCTCATT
1 TATGTGACAACATTAGGCTCAATGCCTTGCTTTCTCATT
46019280 TTGAAGAAGA
Statistics
Matches: 389, Mismatches: 66, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
103 2 0.01
104 62 0.16
105 320 0.82
106 2 0.01
107 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (104 bp):
TATGTGACAACATTAGGCTCAATGCCTTGCTTTCTCATTGTGCCAACAATATCTTCAGCTTTAGA
AACCATCCCTTCTTGCAAAGCGCATCGATCAATGTACTA
Found at i:46024411 original size:169 final size:168
Alignment explanation
Indices: 46024211--46024548 Score: 658
Period size: 169 Copynumber: 2.0 Consensus size: 168
46024201 TCCCAAACTT
46024211 AAAAAAAAAAAAAAAAAAAAACCAAGCCATAAAAGCTCATTTCTCAACCTATGAACATCTAAATT
1 AAAAAAAAAAAAAAAAAAAAACCAAGCCATAAAAGCTCATTTCTCAACCTATGAACATCTAAATT
46024276 ACGATAAAAAAATGCAATCATTCCCATGCAAAACCTTGATAAATCAAGTAAAAGATTAAAAACAT
66 ACGATAAAAAAATGCAATCATTCCCATGCAAAACCTTGATAAATCAAGTAAAAGATTAAAAACAT
46024341 TACCTGAGAAATGATGATGGGGTTGAATGTGAAAGAAA
131 TACCTGAGAAATGATGATGGGGTTGAATGTGAAAGAAA
*
46024379 AAAAAAAAAAAAAAAAAAAAACCCCAGCCATAAAAGCTCATTTCTCAACCTATGAACATCTAAAT
1 AAAAAAAAAAAAAAAAAAAAA-CCAAGCCATAAAAGCTCATTTCTCAACCTATGAACATCTAAAT
46024444 TACGATAAAAAAATGCAATCATTCCCATGCAAAACCTTGATAAATCAAGTAAAAGATTAAAAACA
65 TACGATAAAAAAATGCAATCATTCCCATGCAAAACCTTGATAAATCAAGTAAAAGATTAAAAACA
46024509 TTACCTGAGAAATGATGATGGGGTTGAATGTGAAAGAAA
130 TTACCTGAGAAATGATGATGGGGTTGAATGTGAAAGAAA
46024548 A
1 A
46024549 TGGTTTGTTG
Statistics
Matches: 168, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
168 21 0.12
169 147 0.88
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.21
Consensus pattern (168 bp):
AAAAAAAAAAAAAAAAAAAAACCAAGCCATAAAAGCTCATTTCTCAACCTATGAACATCTAAATT
ACGATAAAAAAATGCAATCATTCCCATGCAAAACCTTGATAAATCAAGTAAAAGATTAAAAACAT
TACCTGAGAAATGATGATGGGGTTGAATGTGAAAGAAA
Found at i:46033514 original size:12 final size:12
Alignment explanation
Indices: 46033497--46033522 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
46033487 CTCCTCAAGA
46033497 ATATAATTAAGG
1 ATATAATTAAGG
46033509 ATATAATTAAGG
1 ATATAATTAAGG
46033521 AT
1 AT
46033523 TAAATATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (12 bp):
ATATAATTAAGG
Found at i:46033593 original size:29 final size:31
Alignment explanation
Indices: 46033537--46033611 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
46033527 TATTTGATTC
*
46033537 ATATATAAACT-TTAATTTAACGTGTAATT-T
1 ATATATAAA-TATTAATTTAACATGTAATTAT
46033567 AATATATAAATATTAATTTAA-AT-TAATTAT
1 -ATATATAAATATTAATTTAACATGTAATTAT
*
46033597 ATATATAAAAATTAA
1 ATATATAAATATTAA
46033612 ATTGTGGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
29 19 0.47
30 3 0.08
31 18 0.45
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (31 bp):
ATATATAAATATTAATTTAACATGTAATTAT
Found at i:46033603 original size:31 final size:31
Alignment explanation
Indices: 46033537--46033611 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
46033527 TATTTGATTC
*
46033537 ATATATAAACT-TTAATTTAACGTGTAATTTA
1 ATATATAAA-TATTAATTTAACATGTAATTTA
46033568 ATATATAAATATTAATTTAA-AT-TAA-TTA
1 ATATATAAATATTAATTTAACATGTAATTTA
*
46033596 TATATATAAAAATTAA
1 -ATATATAAATATTAA
46033612 ATTGTGGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 3 0.08
29 17 0.43
30 2 0.05
31 18 0.45
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (31 bp):
ATATATAAATATTAATTTAACATGTAATTTA
Found at i:46037005 original size:23 final size:24
Alignment explanation
Indices: 46036961--46037005 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
46036951 TAAGCTTTAG
*
46036961 ATTTATATGTTGACATATAATTGT
1 ATTTATATGTTGACATAAAATTGT
46036985 ATTTATTATG-TG-CATAAAATT
1 ATTTA-TATGTTGACATAAAATT
46037006 TTGAATGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 7 0.37
25 4 0.21
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (24 bp):
ATTTATATGTTGACATAAAATTGT
Found at i:46048718 original size:17 final size:17
Alignment explanation
Indices: 46048698--46048730 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
46048688 TATATGTGTA
46048698 AATGTATTATACTTATG
1 AATGTATTATACTTATG
*
46048715 AATGTATTGTACTTAT
1 AATGTATTATACTTAT
46048731 AATAGTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (17 bp):
AATGTATTATACTTATG
Found at i:46049946 original size:132 final size:133
Alignment explanation
Indices: 46049766--46050030 Score: 523
Period size: 132 Copynumber: 2.0 Consensus size: 133
46049756 TAACTATAAA
46049766 AAAATTATTTAATTTTTATAAAAAATTTTATTTAAAATTATGGAATTTATAGGTTTAGTGTCCAT
1 AAAATTATTTAATTTTTATAAAAAATTTTATTTAAAATTATGGAATTTATAGGTTTAGTGTCCAT
46049831 TGGTCAATCCTTGAATATTGAGTTTATCCTTTATATGATTATCTCTTTTTACACGCATCCCACAC
66 TGGTCAATCCTTGAATATTGAGTTTATCCTTTATATGATTATCTCTTTTTACACGCATCCCACAC
46049896 GAG
131 GAG
46049899 AAAATTATTT-ATTTTTATAAAAAATTTTATTTAAAATTATGGAATTTATAGGTTTAGTGTCCAT
1 AAAATTATTTAATTTTTATAAAAAATTTTATTTAAAATTATGGAATTTATAGGTTTAGTGTCCAT
46049963 TGGTCAATCCTTGAATATTGAGTTTATCCTTTATATGATTATCTCTTTTTACACGCATCCCACAC
66 TGGTCAATCCTTGAATATTGAGTTTATCCTTTATATGATTATCTCTTTTTACACGCATCCCACAC
46050028 GAG
131 GAG
46050031 TTGGGTAGGC
Statistics
Matches: 132, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
132 122 0.92
133 10 0.08
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (133 bp):
AAAATTATTTAATTTTTATAAAAAATTTTATTTAAAATTATGGAATTTATAGGTTTAGTGTCCAT
TGGTCAATCCTTGAATATTGAGTTTATCCTTTATATGATTATCTCTTTTTACACGCATCCCACAC
GAG
Found at i:46051753 original size:3 final size:3
Alignment explanation
Indices: 46051747--46051797 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
46051737 ATACTACTAC
*
46051747 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46051795 TAA
1 TAA
46051798 AAAATTAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:46052563 original size:11 final size:11
Alignment explanation
Indices: 46052547--46052612 Score: 63
Period size: 11 Copynumber: 6.4 Consensus size: 11
46052537 ACCACTTTAA
46052547 TTTTAAAATAT
1 TTTTAAAATAT
46052558 TTTTAAAATACT
1 TTTTAAAATA-T
*
46052570 TTTT--ATTAT
1 TTTTAAAATAT
46052579 TTTT--AA-A-
1 TTTTAAAATAT
46052586 TTTTAAAATAT
1 TTTTAAAATAT
46052597 TTTTAAAATACT
1 TTTTAAAATA-T
46052609 TTTT
1 TTTT
46052613 TTAATTTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
7 4 0.09
8 1 0.02
9 8 0.17
10 4 0.09
11 20 0.43
12 10 0.21
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:46052580 original size:21 final size:21
Alignment explanation
Indices: 46052555--46052627 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
46052545 AATTTTAAAA
46052555 TATTTTTAAAATACTTTTTAT
1 TATTTTTAAAATACTTTTTAT
** *
46052576 TATTTTT-AAAT--TTTAAAA
1 TATTTTTAAAATACTTTTTAT
46052594 TATTTTTAAAATACTTTTT-T
1 TATTTTTAAAATACTTTTTAT
46052614 TAATTTTTAAAATA
1 T-ATTTTTAAAATA
46052628 AACTTTTGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 11 0.26
19 4 0.10
20 5 0.12
21 22 0.52
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTTAAAATACTTTTTAT
Found at i:46052595 original size:39 final size:39
Alignment explanation
Indices: 46052545--46052624 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
46052535 GCACCACTTT
46052545 AATTTTAAAATATTTTTAAAATACTTTTTATT-ATTTTTA
1 AATTTTAAAATATTTTTAAAATACTTTTT-TTAATTTTTA
46052584 AATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTA
1 AATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTA
46052623 AA
1 AA
46052625 ATAAACTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 2 0.05
39 38 0.95
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (39 bp):
AATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTA
Found at i:46052634 original size:21 final size:21
Alignment explanation
Indices: 46052595--46052634 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
46052585 ATTTTAAAAT
***
46052595 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAACTTTTTA
46052616 ATTTTTAAAATAAACTTTT
1 ATTTTTAAAATAAACTTTT
46052635 GGTATTTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTAAAATAAACTTTTTA
Found at i:46055111 original size:105 final size:105
Alignment explanation
Indices: 46054947--46055166 Score: 244
Period size: 105 Copynumber: 2.1 Consensus size: 105
46054937 ATTTAATGTA
* * ** *
46054947 TTGCTTTCTCATTGTGTCAACAATATCTTCAACTTAAGAAATCAACATTTTCTTACAAAGCGCAT
1 TTGCTTTCTCATTGTGCCAACAATATCTTCAACTTAAGAAACCAACATTAACTTACAAAGAGCAT
* *
46055012 CAATCAATATACTATATGTGACAATATTAGGCACGATGCC
66 CAATCAATATACTATACGTGACAACATTAGGCACGATGCC
* * * * * * *
46055052 TTGCTTTGTCATTGTGCCAACGATATCTTCAGCTTTAGAAACCATC-TCTAACTTGCAAAGAGTA
1 TTGCTTTCTCATTGTGCCAACAATATCTTCAACTTAAGAAACCAACAT-TAACTTACAAAGAGCA
* * ***
46055116 TCGATGAATATACTATACGTGACAACATTAGGCTTAATGCC
65 TCAATCAATATACTATACGTGACAACATTAGGCACGATGCC
*
46055157 TTGTTTTCTC
1 TTGCTTTCTC
46055167 TTATCTGTTT
Statistics
Matches: 93, Mismatches: 21, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
104 1 0.01
105 92 0.99
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.35
Consensus pattern (105 bp):
TTGCTTTCTCATTGTGCCAACAATATCTTCAACTTAAGAAACCAACATTAACTTACAAAGAGCAT
CAATCAATATACTATACGTGACAACATTAGGCACGATGCC
Found at i:46057077 original size:94 final size:95
Alignment explanation
Indices: 46056969--46057157 Score: 371
Period size: 94 Copynumber: 2.0 Consensus size: 95
46056959 TATCATTTAG
46056969 AAATAATAAAAAATATAAAATAATTTTATAATAATATTTATCAATCTTATAATTAAGTTTACTTT
1 AAATAATAAAAAATATAAAATAATTTTATAATAATATTTATCAATCTTATAATTAAGTTTACTTT
46057034 TTTTATATTTTAAATAAAAAAATAAATCGT
66 TTTTATATTTTAAATAAAAAAATAAATCGT
46057064 AAATAAT-AAAAATATAAAATAATTTTATAATAATATTTATCAATCTTATAATTAAGTTTACTTT
1 AAATAATAAAAAATATAAAATAATTTTATAATAATATTTATCAATCTTATAATTAAGTTTACTTT
46057128 TTTTATATTTTAAATAAAAAAATAAATCGT
66 TTTTATATTTTAAATAAAAAAATAAATCGT
46057158 TTAAATAAAT
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 87 0.93
95 7 0.07
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (95 bp):
AAATAATAAAAAATATAAAATAATTTTATAATAATATTTATCAATCTTATAATTAAGTTTACTTT
TTTTATATTTTAAATAAAAAAATAAATCGT
Found at i:46059106 original size:14 final size:14
Alignment explanation
Indices: 46059087--46059114 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46059077 GCGTGTAACT
46059087 TTTGTTGATGTACA
1 TTTGTTGATGTACA
46059101 TTTGTTGATGTACA
1 TTTGTTGATGTACA
46059115 GAGACAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (14 bp):
TTTGTTGATGTACA
Found at i:46062377 original size:30 final size:31
Alignment explanation
Indices: 46062313--46062379 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
46062303 TTAATAAATA
*
46062313 AAAAAT-ATATAAATGTATTAGATATTAAAT
1 AAAAATAATATAAATGTATTAGATATTAAAG
** *
46062343 AAAAATAATATAAATGTA-TATTTATTTAAG
1 AAAAATAATATAAATGTATTAGATATTAAAG
46062373 AAAAATA
1 AAAAATA
46062380 TAGGTGGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 21 0.66
31 11 0.34
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (31 bp):
AAAAATAATATAAATGTATTAGATATTAAAG
Found at i:46062430 original size:106 final size:107
Alignment explanation
Indices: 46062301--46062526 Score: 427
Period size: 106 Copynumber: 2.1 Consensus size: 107
46062291 TATGTATAAC
46062301 TTTTAATAAATAAAAAATATATAAATGTATTAGATATTAAATAAAAATAATATAAATGTATATTT
1 TTTTAATAAATAAAAAATATATAAATGTATTAGATATTAAATAAAAATAATATAAATGTATATTT
46062366 ATTTAAGAAAAATATAGGTGGCTTAAAAGGGGCTTGACTTAA
66 ATTTAAGAAAAATATAGGTGGCTTAAAAGGGGCTTGACTTAA
46062408 TTTTAATAAA-AAAAAATATATAAATGTATTAGATATTAAATAAAAATAATATAAATGTATATTT
1 TTTTAATAAATAAAAAATATATAAATGTATTAGATATTAAATAAAAATAATATAAATGTATATTT
46062472 ATTTAAGAAAAATATAGGTGGCTTAAAAGGGGCTTGACTTAA
66 ATTTAAGAAAAATATAGGTGGCTTAAAAGGGGCTTGACTTAA
*
46062514 TTATTTATAAATA
1 TT-TTAATAAATA
46062527 TGAGTGGGCT
Statistics
Matches: 116, Mismatches: 1, Indels: 3
0.97 0.01 0.03
Matches are distributed among these distances:
106 98 0.84
107 17 0.15
108 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.36
Consensus pattern (107 bp):
TTTTAATAAATAAAAAATATATAAATGTATTAGATATTAAATAAAAATAATATAAATGTATATTT
ATTTAAGAAAAATATAGGTGGCTTAAAAGGGGCTTGACTTAA
Found at i:46062483 original size:30 final size:31
Alignment explanation
Indices: 46062414--46062485 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
46062404 TTAATTTTAA
*
46062414 TAAAAAAAAAT-ATATAAATGTATTAGATAT
1 TAAAGAAAAATAATATAAATGTATTAGATAT
* **
46062444 TAAATAAAAATAATATAAATGTA-TATTTAT
1 TAAAGAAAAATAATATAAATGTATTAGATAT
*
46062474 TTAAGAAAAATA
1 TAAAGAAAAATA
46062486 TAGGTGGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 25 0.69
31 11 0.31
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.35
Consensus pattern (31 bp):
TAAAGAAAAATAATATAAATGTATTAGATAT
Found at i:46063315 original size:18 final size:18
Alignment explanation
Indices: 46063289--46063337 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
46063279 TAATTTTTTT
*
46063289 ATATTTTGGGCTTACATA
1 ATATATTGGGCTTACATA
* * *
46063307 ATATATTGGACCTATATA
1 ATATATTGGGCTTACATA
46063325 ATATATTGGGCTT
1 ATATATTGGGCTT
46063338 GTAATACTTT
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:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (18 bp):
ATATATTGGGCTTACATA
Found at i:46063641 original size:17 final size:17
Alignment explanation
Indices: 46063619--46063665 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
46063609 AACATGTCAA
** *
46063619 AATAATCATCATTTAGG
1 AATAATCATCATCCAAG
*
46063636 AATAATTATCATCCAAG
1 AATAATCATCATCCAAG
46063653 AATAATCATCATC
1 AATAATCATCATC
46063666 TTATGTTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (17 bp):
AATAATCATCATCCAAG
Found at i:46069433 original size:27 final size:27
Alignment explanation
Indices: 46069402--46069455 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
46069392 AGAATAGGAA
46069402 AGATATATAATATATTCCTAAATATAT
1 AGATATATAATATATTCCTAAATATAT
46069429 AGATATATAATATATTCCTAAATATAT
1 AGATATATAATATATTCCTAAATATAT
46069456 GCCTAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (27 bp):
AGATATATAATATATTCCTAAATATAT
Found at i:46069467 original size:27 final size:27
Alignment explanation
Indices: 46069410--46069468 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
46069400 AAAGATATAT
* *
46069410 AATATATTCCTAAATATATAGATATAT
1 AATATATTCCTAAATATATAGATAAAA
*
46069437 AATATATTCCTAAATATAT-GCCTAAAA
1 AATATATTCCTAAATATATAG-ATAAAA
46069464 AATAT
1 AATAT
46069469 CCCACAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.37
Consensus pattern (27 bp):
AATATATTCCTAAATATATAGATAAAA
Found at i:46070513 original size:24 final size:24
Alignment explanation
Indices: 46070464--46070514 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
46070454 GCTAAAATCG
**
46070464 ATTTAAATAATAAAATATTTTTAA
1 ATTTAAATAATAAAATATTTAAAA
* *
46070488 ATTTAATTATTAAAATATTTAAAA
1 ATTTAAATAATAAAATATTTAAAA
46070512 ATT
1 ATT
46070515 AATATAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTTAAATAATAAAATATTTAAAA
Found at i:46080120 original size:80 final size:81
Alignment explanation
Indices: 46079963--46080125 Score: 233
Period size: 80 Copynumber: 2.0 Consensus size: 81
46079953 CAAGAGCTTC
* * *
46079963 AAAATTTTGCAAGTACAAGTTAAATCATCGCTTAAAAGACTTAAATATTCAATTTAATAATTCAG
1 AAAATTTTGCAAGTACAAGTCAAATCACCGCTTAAAAGACTTAAATAGTCAATTTAATAATTCAG
46080028 TATCTTTTCCAAATTT
66 TATCTTTTCCAAATTT
* * *
46080044 AAAATTTTGCAAGTACAAGTCAAATCACCG-TCT-AAAGACTTCAATAGTCAATTTAATATTTTA
1 AAAATTTTGCAAGTACAAGTCAAATCACCGCT-TAAAAGACTTAAATAGTCAATTTAATAATTCA
46080107 GTAT-TTTTCCCAAATTT
65 GTATCTTTT-CCAAATTT
46080124 AA
1 AA
46080126 TACATGAGTT
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
79 4 0.05
80 41 0.55
81 29 0.39
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (81 bp):
AAAATTTTGCAAGTACAAGTCAAATCACCGCTTAAAAGACTTAAATAGTCAATTTAATAATTCAG
TATCTTTTCCAAATTT
Found at i:46081618 original size:31 final size:31
Alignment explanation
Indices: 46081583--46081647 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
46081573 TATAAGATGA
* * * * *
46081583 TCACTGAATTATTTAAAAGTTTTCATTTAAG
1 TCACTAAACTATTCAAAAGTTGTCACTTAAG
46081614 TCACTAAACTATTCAAAAGTTGTCACTTAAG
1 TCACTAAACTATTCAAAAGTTGTCACTTAAG
46081645 TCA
1 TCA
46081648 TTGGATTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAGTTGTCACTTAAG
Found at i:46107697 original size:18 final size:18
Alignment explanation
Indices: 46107674--46107710 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
46107664 GCCGTTTCAC
*
46107674 CATCATAATCTTCTTCTT
1 CATCATAATCTTCATCTT
*
46107692 CATCATCATCTTCATCTT
1 CATCATAATCTTCATCTT
46107710 C
1 C
46107711 GTTGTTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.32, G:0.00, T:0.46
Consensus pattern (18 bp):
CATCATAATCTTCATCTT
Found at i:46117596 original size:14 final size:15
Alignment explanation
Indices: 46117579--46117609 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
46117569 TTAGTTTATT
46117579 ATATTTTTAAA-AAA
1 ATATTTTTAAATAAA
46117593 ATATTTTTAAATAAA
1 ATATTTTTAAATAAA
46117608 AT
1 AT
46117610 TAATCTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATTTTTAAATAAA
Found at i:46118311 original size:14 final size:15
Alignment explanation
Indices: 46118280--46118327 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
46118270 TCAAACCGAA
*
46118280 TTTTATTTTTAATAAT
1 TTTTAATTTT-ATAAT
46118296 TTTTAATTTT-TAA-
1 TTTTAATTTTATAAT
*
46118309 TTTTATTTTTATAAT
1 TTTTAATTTTATAAT
46118324 TTTT
1 TTTT
46118328 TAATAATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 9 0.32
14 6 0.21
15 4 0.14
16 9 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTAATTTTATAAT
Found at i:46118340 original size:29 final size:29
Alignment explanation
Indices: 46118278--46118340 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
46118268 AATCAAACCG
**
46118278 AATTTTATTTTTAATAATTTTTAATTTTT
1 AATTTTATTTTTAATAATTTTTAATAATT
46118307 AATTTTATTTTT-ATAATTTTTTAATAATT
1 AATTTTATTTTTAATAA-TTTTTAATAATT
*
46118336 CATTT
1 AATTT
46118341 GATCGATCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (29 bp):
AATTTTATTTTTAATAATTTTTAATAATT
Found at i:46121383 original size:195 final size:198
Alignment explanation
Indices: 46121031--46121430 Score: 560
Period size: 195 Copynumber: 2.0 Consensus size: 198
46121021 AGCTAAAAAC
***
46121031 AATCAAAGTCCCACCTGCATCTTTAAACTCCAAATGGGGAAATTTTTTAAAAAATACCTTTACTT
1 AATCAAAGTCCCACCTGCATCTTTAAACTCCAAATGGGGAAAAAATTTAAAAAATACCTTTACTT
* *
46121096 ATACTTAAGAACTAGGAACTCAAAATTCAATAATCAACATATACAATAAATTAATGAAGAAAGGA
66 ATACTTAAGAACTACGAACTCAAAATT--AT-ATCAACATATACAATAAATTAATAAAGAAAGGA
46121161 AGAAAAACCCAGAAATTCAATCACAAAAAA-AGAGCTAAAAAAGCATCAAAACTAAAATAATAAT
128 AGAAAAACCCAGAAATTCAATCACAAAAAAGAGAGCTAAAAAAGCATCAAAA-T-AAA-AATAAT
46121225 AACTGGATT
190 AACTGGATT
* * * *
46121234 AATCAAAGTTCCACCTGCATCTTTAAACTCCAAATGGGGAAAAAATTT-AAAGATCCCTTTATTT
1 AATCAAAGTCCCACCTGCATCTTTAAACTCCAAATGGGGAAAAAATTTAAAAAATACCTTTACTT
* * * * * *
46121298 CTACTTAATAACTACGAATTCAAAA-T-T-T-AACATATACAATAATTTGATAAAGAAATGAAGA
66 ATACTTAAGAACTACGAACTCAAAATTATATCAACATATACAATAAATTAATAAAGAAAGGAAGA
*
46121359 AAAACCCAGAAATTCAATCACAAAAAAGAGAGCTAAAAAAGCATCAAAATTAAAATAATAACTGG
131 AAAACCCAGAAATTCAATCACAAAAAAGAGAGCTAAAAAAGCATCAAAATAAAAATAATAACTGG
46121424 ATT
196 ATT
46121427 AATC
1 AATC
46121431 GAAGATTAAA
Statistics
Matches: 180, Mismatches: 16, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
193 19 0.11
194 2 0.01
195 57 0.32
196 22 0.12
198 1 0.01
201 1 0.01
202 34 0.19
203 44 0.24
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.25
Consensus pattern (198 bp):
AATCAAAGTCCCACCTGCATCTTTAAACTCCAAATGGGGAAAAAATTTAAAAAATACCTTTACTT
ATACTTAAGAACTACGAACTCAAAATTATATCAACATATACAATAAATTAATAAAGAAAGGAAGA
AAAACCCAGAAATTCAATCACAAAAAAGAGAGCTAAAAAAGCATCAAAATAAAAATAATAACTGG
ATT
Found at i:46122051 original size:11 final size:11
Alignment explanation
Indices: 46122025--46122056 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
46122015 TTTTATCATT
46122025 TAATT-TTAAA
1 TAATTATTAAA
46122035 -AATTATTAAA
1 TAATTATTAAA
46122045 TAATTATTAAA
1 TAATTATTAAA
46122056 T
1 T
46122057 TATTTAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 4 0.20
10 5 0.25
11 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAATTATTAAA
Found at i:46122064 original size:16 final size:17
Alignment explanation
Indices: 46122022--46122077 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
46122012 TATTTTTATC
46122022 ATTTAATT-TTAAAAATT
1 ATTTAATTATT-AAAATT
46122039 ATTAAATAATTATT-AAATT
1 ATT---TAATTATTAAAATT
*
46122058 ATTTAATTGTTAAAATT
1 ATTTAATTATTAAAATT
46122075 ATT
1 ATT
46122078 ATTGTATAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
16 7 0.21
17 11 0.33
19 8 0.24
20 5 0.15
21 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTAATTATTAAAATT
Found at i:46126304 original size:2 final size:2
Alignment explanation
Indices: 46126297--46126332 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
46126287 AGTTTTCCTC
46126297 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
46126333 TTATTAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:46127939 original size:37 final size:38
Alignment explanation
Indices: 46127837--46127951 Score: 107
Period size: 36 Copynumber: 3.1 Consensus size: 38
46127827 ATTTCATGTA
**
46127837 TTATTATTTATTGTATGCTATTTTTAAACATATATTTCAT
1 TTATTATTTATTGTATATTATTTTTAAACA-ATATTT-AT
* * * *
46127877 ATATTA-TTA-T-TA-ATCAATTTCAAACAATATTT-T
1 TTATTATTTATTGTATATTATTTTTAAACAATATTTAT
46127910 TTATTATTTATTGTATATTATTTTTAAAC-ATATTTAT
1 TTATTATTTATTGTATATTATTTTTAAACAATATTTAT
46127947 ATTAT
1 -TTAT
46127952 AAATACGTTG
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
33 6 0.10
34 3 0.05
35 7 0.12
36 17 0.29
37 13 0.22
38 5 0.08
39 3 0.05
40 5 0.08
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.57
Consensus pattern (38 bp):
TTATTATTTATTGTATATTATTTTTAAACAATATTTAT
Found at i:46128586 original size:22 final size:22
Alignment explanation
Indices: 46128561--46128625 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
46128551 AATGCTTGTT
46128561 TAAAGGATGATAATATGTTGAA
1 TAAAGGATGATAATATGTTGAA
* **
46128583 TAAA--A--ACAA-ATGCTTGTT
1 TAAAGGATGATAATATG-TTGAA
46128601 TAAAGGATGATAATATGTTGAA
1 TAAAGGATGATAATATGTTGAA
46128623 TAA
1 TAA
46128626 TATGAATACA
Statistics
Matches: 31, Mismatches: 6, Indels: 12
0.63 0.12 0.24
Matches are distributed among these distances:
17 3 0.10
18 10 0.32
20 2 0.06
22 13 0.42
23 3 0.10
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.32
Consensus pattern (22 bp):
TAAAGGATGATAATATGTTGAA
Found at i:46128598 original size:40 final size:40
Alignment explanation
Indices: 46128543--46128625 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
46128533 CTTTTATGAG
46128543 TAAAAACAAATGCTTGTTTAAAGGATGATAATATGTTGAA
1 TAAAAACAAATGCTTGTTTAAAGGATGATAATATGTTGAA
46128583 TAAAAACAAATGCTTGTTTAAAGGATGATAATATGTTGAA
1 TAAAAACAAATGCTTGTTTAAAGGATGATAATATGTTGAA
46128623 TAA
1 TAA
46128626 TATGAATACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.33
Consensus pattern (40 bp):
TAAAAACAAATGCTTGTTTAAAGGATGATAATATGTTGAA
Found at i:46129408 original size:31 final size:31
Alignment explanation
Indices: 46129366--46129428 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
46129356 ATGAGTCAAG
*
46129366 TAAAAGAAATGTTGCCAAACTTGCTCACTCA
1 TAAAAGAAATGTTGCCAAACTTGCTCAATCA
* * *
46129397 TAAAAGGAATGTTGCTAAACTTGGTCAATCA
1 TAAAAGAAATGTTGCCAAACTTGCTCAATCA
46129428 T
1 T
46129429 TTCTAAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (31 bp):
TAAAAGAAATGTTGCCAAACTTGCTCAATCA
Found at i:46132988 original size:110 final size:110
Alignment explanation
Indices: 46132791--46133004 Score: 374
Period size: 110 Copynumber: 1.9 Consensus size: 110
46132781 TATGCTTGAA
*
46132791 CCACTAGTACTGACCACATCAGGAAAATGATTTTGCCAGTTGAGTGGAACGGGGAAAATTTGTCA
1 CCACTAGTACTGACCACATCAGGAAAATGATTTTGCCAGTTGAGTGGAACAGGGAAAATTTGTCA
*
46132856 TCTAAGATTTAACAGAGCACTCTTCCTCCCCTTCCCCTTCCCCTT
66 TCTAAGATTTAACACAGCACTCTTCCTCCCCTTCCCCTTCCCCTT
*
46132901 CCACTAGTACTGACCGCATCAGGAAAATGATTTTGCCAGTTGAGTGGAACAGGGAAAATTTGTCA
1 CCACTAGTACTGACCACATCAGGAAAATGATTTTGCCAGTTGAGTGGAACAGGGAAAATTTGTCA
* * *
46132966 TCTAAGATTTAATACAGTACTCTTCCTCCCCTTTCCCTT
66 TCTAAGATTTAACACAGCACTCTTCCTCCCCTTCCCCTT
46133005 TCACTTCCTG
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 98 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (110 bp):
CCACTAGTACTGACCACATCAGGAAAATGATTTTGCCAGTTGAGTGGAACAGGGAAAATTTGTCA
TCTAAGATTTAACACAGCACTCTTCCTCCCCTTCCCCTTCCCCTT
Found at i:46142862 original size:9 final size:9
Alignment explanation
Indices: 46142844--46142874 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
46142834 TTTGGTTAAA
*
46142844 AATTAACCG
1 AATTACCCG
46142853 AATTACCCG
1 AATTACCCG
46142862 AATTACCCG
1 AATTACCCG
46142871 AATT
1 AATT
46142875 GAATCACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.39, C:0.26, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTACCCG
Found at i:46142961 original size:37 final size:37
Alignment explanation
Indices: 46142873--46142947 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
46142863 ATTACCCGAA
* * *
46142873 TTGAATCACTACATAATTAAAAATATTACGTAAGTCT
1 TTGAATTACTACATAATTAAAAACATTACATAAGTCT
*
46142910 TTGAATTACTACATAATTAAAAACATTACATAATTCT
1 TTGAATTACTACATAATTAAAAACATTACATAAGTCT
46142947 T
1 T
46142948 GAAATTAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.37
Consensus pattern (37 bp):
TTGAATTACTACATAATTAAAAACATTACATAAGTCT
Found at i:46143121 original size:38 final size:39
Alignment explanation
Indices: 46143077--46143154 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
46143067 ACTTAAGAGT
*
46143077 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
46143115 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
46143154 T
1 T
46143155 TGGGTTGGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 27 0.71
39 11 0.29
ACGTcount: A:0.18, C:0.03, G:0.28, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:46143153 original size:13 final size:13
Alignment explanation
Indices: 46143135--46143159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46143125 TTTTAGTTTT
46143135 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
46143148 ATTGGGTTGGGT
1 ATTGGGTTGGGT
46143160 TGGATAATTT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:46148121 original size:24 final size:23
Alignment explanation
Indices: 46148083--46148129 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
46148073 TCACCCAATT
* *
46148083 ATAAATATATATAAAATGTATAAA
1 ATAAATAAATAT-AAATGGATAAA
*
46148107 ATAAATAAATTTAAATGGATAAA
1 ATAAATAAATATAAATGGATAAA
46148130 TCTCTTTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (23 bp):
ATAAATAAATATAAATGGATAAA
Found at i:46148937 original size:24 final size:23
Alignment explanation
Indices: 46148893--46148945 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
46148883 AATATCTAAC
* *
46148893 AAATTTAAAAAATGTTTAATTTT
1 AAATTTAAAAAATATTCAATTTT
*
46148916 AAATTTCAATAAATATTCAA--TT
1 AAATTT-AAAAAATATTCAATTTT
46148938 AAATTTAA
1 AAATTTAA
46148946 TTTAAACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 2 0.08
22 8 0.31
23 6 0.23
24 10 0.38
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
AAATTTAAAAAATATTCAATTTT
Found at i:46160852 original size:30 final size:31
Alignment explanation
Indices: 46160812--46160874 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 31
46160802 TTTTAAAATA
46160812 AAAATAAATAAAAATTTTAACGAAAAAGACT
1 AAAATAAATAAAAATTTTAACGAAAAAGACT
46160843 AAAA-AAATAAAAATTTTAACGAAAAAGACT
1 AAAATAAATAAAAATTTTAACGAAAAAGACT
46160873 AA
1 AA
46160875 TTTATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (31 bp):
AAAATAAATAAAAATTTTAACGAAAAAGACT
Found at i:46161135 original size:42 final size:42
Alignment explanation
Indices: 46161075--46161347 Score: 189
Period size: 42 Copynumber: 6.4 Consensus size: 42
46161065 TTTCCGCGAA
* *
46161075 ATCGCGTCCACGTAAGCGCAATGTCAGGGTAAATGTCAGGAC
1 ATCGCGTCCACGTCAGCGCGATGTCAGGGTAAATGTCAGGAC
*
46161117 ATCGCGTCCACGTCAGCGCGATGTCAGGGTACATGTCAGGAC
1 ATCGCGTCCACGTCAGCGCGATGTCAGGGTAAATGTCAGGAC
* * * * ** ** * * *
46161159 ATCGCGTCCATGTCAGAGTGAT-T-TGCTTACGTGGACA-CAA
1 ATCGCGTCCACGTCAGCGCGATGTCAGGGTAAAT-GTCAGGAC
* * * * * *
46161199 ATCGCG-CCTACG--AGGACGCGTATTTACCGAATGGTCAATTTTCCGCGAA
1 ATCGCGTCC-ACGTCA-G-CGCG-ATGT--C--AGGGT-AAATGTCAG-GAC
* *
46161248 ATCGCGTCCACGTAAGCGCAATGTCAGGGTAAATGTCAGGAC
1 ATCGCGTCCACGTCAGCGCGATGTCAGGGTAAATGTCAGGAC
*
46161290 ATCGCGTCCACGTCAGCGCGATGTCAGGGTACATGTCAGGAC
1 ATCGCGTCCACGTCAGCGCGATGTCAGGGTAAATGTCAGGAC
*
46161332 ATCGCGTCCATGTCAG
1 ATCGCGTCCACGTCAG
46161348 AGTGATTTGC
Statistics
Matches: 177, Mismatches: 37, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 3 0.02
40 16 0.09
41 6 0.03
42 115 0.65
43 6 0.03
44 4 0.02
46 1 0.01
47 2 0.01
48 5 0.03
49 14 0.08
50 3 0.02
51 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.22
Consensus pattern (42 bp):
ATCGCGTCCACGTCAGCGCGATGTCAGGGTAAATGTCAGGAC
Found at i:46161172 original size:19 final size:19
Alignment explanation
Indices: 46161107--46161174 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
46161097 GTCAGGGTAA
46161107 ATGTCAGGACATCGCGTCC
1 ATGTCAGGACATCGCGTCC
* * *
46161126 ACGTCAGCG-CGATGTCAGGGTAC
1 ATGTCAG-GAC-A--TC-GCGTCC
46161149 ATGTCAGGACATCGCGTCC
1 ATGTCAGGACATCGCGTCC
46161168 ATGTCAG
1 ATGTCAG
46161175 AGTGATTTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 18 0.49
20 4 0.11
22 4 0.11
23 11 0.30
ACGTcount: A:0.22, C:0.28, G:0.29, T:0.21
Consensus pattern (19 bp):
ATGTCAGGACATCGCGTCC
Found at i:46161343 original size:173 final size:174
Alignment explanation
Indices: 46161045--46161395 Score: 688
Period size: 173 Copynumber: 2.0 Consensus size: 174
46161035 GTTTTTTAAT
46161045 TATTTACCGGAATGGTCAATTTTCCGCGAAATCGCGTCCACGTAAGCGCAATGTCAGGGTAAATG
1 TATTTACCGGAATGGTCAATTTTCCGCGAAATCGCGTCCACGTAAGCGCAATGTCAGGGTAAATG
46161110 TCAGGACATCGCGTCCACGTCAGCGCGATGTCAGGGTACATGTCAGGACATCGCGTCCATGTCAG
66 TCAGGACATCGCGTCCACGTCAGCGCGATGTCAGGGTACATGTCAGGACATCGCGTCCATGTCAG
46161175 AGTGATTTGCTTACGTGGACACAAATCGCGCCTACGAGGACGCG
131 AGTGATTTGCTTACGTGGACACAAATCGCGCCTACGAGGACGCG
46161219 TATTTACC-GAATGGTCAATTTTCCGCGAAATCGCGTCCACGTAAGCGCAATGTCAGGGTAAATG
1 TATTTACCGGAATGGTCAATTTTCCGCGAAATCGCGTCCACGTAAGCGCAATGTCAGGGTAAATG
46161283 TCAGGACATCGCGTCCACGTCAGCGCGATGTCAGGGTACATGTCAGGACATCGCGTCCATGTCAG
66 TCAGGACATCGCGTCCACGTCAGCGCGATGTCAGGGTACATGTCAGGACATCGCGTCCATGTCAG
46161348 AGTGATTTGCTTACGTGGACACAAATCGCGCCTACGAGGACGCG
131 AGTGATTTGCTTACGTGGACACAAATCGCGCCTACGAGGACGCG
46161392 -ATTT
1 TATTT
46161396 GCTGACGTGG
Statistics
Matches: 177, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
172 4 0.02
173 165 0.93
174 8 0.05
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (174 bp):
TATTTACCGGAATGGTCAATTTTCCGCGAAATCGCGTCCACGTAAGCGCAATGTCAGGGTAAATG
TCAGGACATCGCGTCCACGTCAGCGCGATGTCAGGGTACATGTCAGGACATCGCGTCCATGTCAG
AGTGATTTGCTTACGTGGACACAAATCGCGCCTACGAGGACGCG
Found at i:46161345 original size:19 final size:19
Alignment explanation
Indices: 46161280--46161347 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
46161270 GTCAGGGTAA
46161280 ATGTCAGGACATCGCGTCC
1 ATGTCAGGACATCGCGTCC
* * *
46161299 ACGTCAGCG-CGATGTCAGGGTAC
1 ATGTCAG-GAC-A--TC-GCGTCC
46161322 ATGTCAGGACATCGCGTCC
1 ATGTCAGGACATCGCGTCC
46161341 ATGTCAG
1 ATGTCAG
46161348 AGTGATTTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 18 0.49
20 4 0.11
22 4 0.11
23 11 0.30
ACGTcount: A:0.22, C:0.28, G:0.29, T:0.21
Consensus pattern (19 bp):
ATGTCAGGACATCGCGTCC
Found at i:46174366 original size:292 final size:281
Alignment explanation
Indices: 46173769--46174895 Score: 1353
Period size: 272 Copynumber: 4.0 Consensus size: 281
46173759 AAATCCCAAA
* * * *
46173769 AGTATAATTGGTGCATAACAATATAGATTAGCAGTCAGGTTAGCAATTTAAACCCTAATAAGAAA
1 AGTATAACTGGTGCATAACAAAATAAATTAGCAGTCAGGTTAGCAATTTAAACCCTAA-AAAAAA
* * * * * * *
46173834 ACTCATAAAGGTCAATTCTTTTTTTCACAATCTTCGATCCTTCATTCAAACAAATCTCCCAAACC
65 AATCATAAAGGT-AAATCCTTTTTTCACATTCTTCGATCCCTCATTCAAACCAATCTCCTAAACC
* *
46173899 CCAAAACTAAT-AAATCACCATTAAAAAAGTAC--AAAAAAAAACAATTACTTTGAACTTA--AA
129 CC-AAACTAATAAAAAC-CCATTAAACAAGTACAAAAAAAAAAACAATTACTTTGAACTTATTAA
* * *
46173959 CACA-TAAAAAAAAATCAAATTAGAACCATTAAAAGAACAAACTTTAAAGCAAAATACCTTGAGG
192 AACACTAAAAAAAAATCAAATTAGAACCATTAAAAGAACAAACATTAAAGCAAAATACCTCGAGG
* * * *
46174023 GTCTGATTGGAGTAGTAGATGGAGA
257 GTCTGATTGGAGGAGTGGATGAAGG
* * * *
46174048 AGTGTAACTGGTGCATAGCAAAATAAATTAACAGTCAGGTTAACAATTTAAACCCTAGCAAAAAA
1 AGTATAACTGGTGCATAACAAAATAAATTAGCAGTCAGGTTAGCAATTTAAACCCT---AAAAAA
* *
46174113 ATAAATCGTATAGGTAAATCCTTTTTTCACATTCTTCGATCCCTCATTCAACGCAACCAATCTCC
63 A-AAATCATAAAGGTAAATCCTTTTTTCACATTCTTCGATCCCTCATTC-A---AACCAATCTCC
*
46174178 TAAAGCCCAAACTAAT-AAAACCCATTAAACAAGTACAAAAAAAAAAACAATTACTTTGAACTTA
123 TAAACCCCAAACTAATAAAAACCCATTAAACAAGTACAAAAAAAAAAACAATTACTTTGAACTT-
*
46174242 AAAGTTAAAACACTGAAAAAAAATCAAATTAGAACCATTAAAAGAACAAACAGTT-AAGCAAAAT
187 --A-TTAAAACACTAAAAAAAAATCAAATTAGAACCATTAAAAGAACAAACA-TTAAAGCAAAAT
46174306 ACCTCGAGGGTCTGATTGGAGGAGTGGATGAAGG
248 ACCTCGAGGGTCTGATTGGAGGAGTGGATGAAGG
46174340 AGTATAACTGGTGCATAACAAAATAAATTAGCAGTCAGGTTAGCAATTTAAACCCT---------
1 AGTATAACTGGTGCATAACAAAATAAATTAGCAGTCAGGTTAGCAATTTAAACCCTAAAAAAAAA
*
46174396 A--AT-AA--T---T-CTTTTATTCACATTCTTCGATCCCTCATTCAAACCAATCTCCTACACCC
66 ATCATAAAGGTAAATCCTTTT-TTCACATTCTTCGATCCCTCATTCAAACCAATCTCCTAAACCC
46174452 CAAACTAATAAAAACCCATTAAACAAGTACAAAAAAAAAAAAAAACAATTACTTTGAACTTAAAA
130 CAAACTAATAAAAACCCATTAAACAAGTAC----AAAAAAAAAAACAATTACTTTGAACTT---A
* *
46174517 GTTAAAACACTAAAAAAAAATCAAATTAGAATCATTAAAAGAACAAACATTGAAGCAAAATACCT
188 -TTAAAACACTAAAAAAAAATCAAATTAGAACCATTAAAAGAACAAACATTAAAGCAAAATACCT
* *
46174582 GGAGGGCCTGATTGGAGGAGTGGATGAAGG
252 CGAGGGTCTGATTGGAGGAGTGGATGAAGG
* *
46174612 AGTATAACTGGTGCATAACAAAATAAACTAGCAGTCAGGTTAGCAATTTAAACCCTAATAAAAAA
1 AGTATAACTGGTGCATAACAAAATAAATTAGCAGTCAGGTTAGCAATTTAAACCCTAAAAAAAAA
* * **
46174677 ACCATAAAAGTCGATCCTTTTTTTTCACATTCTTCGATCCCTCATTCAATACAACCAATCTCCTA
66 ATCATAAAGGTAAATCC--TTTTTTCACATTCTTCGATCCCTCATTC---A-AACCAATCTCCTA
* *
46174742 AACCCCAAACTAATAAAAACCCATTAAAGAAGTACAAAAAAAAAAAC-ATTACTTCGAAC---TT
125 AACCCCAAACTAATAAAAACCCATTAAACAAGTACAAAAAAAAAAACAATTACTTTGAACTTATT
* * *
46174803 -AAACACTGAAAAAAAATCAAATTAGAACCGTTAAAAGAACAAGCATTAAAGCAAAATACCTCGA
190 AAAACACTAAAAAAAAATCAAATTAGAACCATTAAAAGAACAAACATTAAAGCAAAATACCTCGA
46174867 GGGTCTGATTGGAGGAGTGGATGAAGG
255 GGGTCTGATTGGAGGAGTGGATGAAGG
46174894 AG
1 AG
46174896 GAGGAGGGCG
Statistics
Matches: 748, Mismatches: 51, Indels: 95
0.84 0.06 0.11
Matches are distributed among these distances:
267 25 0.03
268 20 0.03
270 6 0.01
271 27 0.04
272 174 0.23
274 1 0.00
276 1 0.00
277 1 0.00
279 50 0.07
281 35 0.05
282 99 0.13
283 18 0.02
284 14 0.02
285 41 0.05
286 1 0.00
288 1 0.00
289 1 0.00
290 12 0.02
291 41 0.05
292 131 0.18
293 2 0.00
294 1 0.00
295 46 0.06
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (281 bp):
AGTATAACTGGTGCATAACAAAATAAATTAGCAGTCAGGTTAGCAATTTAAACCCTAAAAAAAAA
ATCATAAAGGTAAATCCTTTTTTCACATTCTTCGATCCCTCATTCAAACCAATCTCCTAAACCCC
AAACTAATAAAAACCCATTAAACAAGTACAAAAAAAAAAACAATTACTTTGAACTTATTAAAACA
CTAAAAAAAAATCAAATTAGAACCATTAAAAGAACAAACATTAAAGCAAAATACCTCGAGGGTCT
GATTGGAGGAGTGGATGAAGG
Found at i:46178167 original size:31 final size:32
Alignment explanation
Indices: 46178120--46178179 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
46178110 CAAATTTAGC
*
46178120 AAGTAATAAATATTTAAA-TAAAATTTTAAAA
1 AAGTAAAAAATATTTAAATTAAAATTTTAAAA
* *
46178151 AAGTAAAAAATGTTTAAATTATAATTTTA
1 AAGTAAAAAATATTTAAATTAAAATTTTA
46178180 GTATTCGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (32 bp):
AAGTAAAAAATATTTAAATTAAAATTTTAAAA
Found at i:46179946 original size:26 final size:27
Alignment explanation
Indices: 46179911--46179967 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
46179901 AATTTTAAAA
* * *
46179911 TATTTTTAAAAT-ACTTTTTATTTTTT
1 TATTTTTAAAATAAATTTTTAGTGTTT
46179937 TATTTTTAAAATAAATTTTTAGTGTTT
1 TATTTTTAAAATAAATTTTTAGTGTTT
46179964 TATT
1 TATT
46179968 AAAAAATAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (27 bp):
TATTTTTAAAATAAATTTTTAGTGTTT
Found at i:46180755 original size:24 final size:23
Alignment explanation
Indices: 46180722--46180766 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
46180712 ATGTTTGGTT
*
46180722 AAAATTGGGTTAATTTTTTTTTG
1 AAAATTGGGTTAAATTTTTTTTG
46180745 AAAATATGGGTTAAATTTTTTT
1 AAAAT-TGGGTTAAATTTTTTT
46180767 GGAATATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (23 bp):
AAAATTGGGTTAAATTTTTTTTG
Found at i:46180772 original size:22 final size:24
Alignment explanation
Indices: 46180722--46180777 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
46180712 ATGTTTGGTT
*
46180722 AAAAT-TGGGTTAATTTTTTTTTG
1 AAAATATGGGTTAATATTTTTTTG
46180745 AAAATATGGGTTAA-ATTTTTTTG
1 AAAATATGGGTTAATATTTTTTTG
*
46180768 -GAATATGGGT
1 AAAATATGGGT
46180778 GGGTTTGAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 9 0.30
23 13 0.43
24 8 0.27
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (24 bp):
AAAATATGGGTTAATATTTTTTTG
Found at i:46181563 original size:11 final size:11
Alignment explanation
Indices: 46181547--46181573 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
46181537 ACGTTTAATG
46181547 TAAAATAAACA
1 TAAAATAAACA
46181558 TAAAATAAACA
1 TAAAATAAACA
46181569 TAAAA
1 TAAAA
46181574 ATCAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (11 bp):
TAAAATAAACA
Found at i:46186323 original size:16 final size:16
Alignment explanation
Indices: 46186302--46186335 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
46186292 ATATATATTC
*
46186302 TTTTGAGATTAAGAGA
1 TTTTGAGATTAAAAGA
*
46186318 TTTTGATATTAAAAGA
1 TTTTGAGATTAAAAGA
46186334 TT
1 TT
46186336 GTCCTTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (16 bp):
TTTTGAGATTAAAAGA
Found at i:46188987 original size:29 final size:30
Alignment explanation
Indices: 46188928--46188988 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
46188918 TAAAATTAAA
***
46188928 AACTTTTGGATAGTTAAGTGACCATTTTGT
1 AACTTTTGGATAGTTAAGTGACCAAAATGT
* *
46188958 AACTTTTTGA-AGTTGAGTGACCAAAATGT
1 AACTTTTGGATAGTTAAGTGACCAAAATGT
46188987 AA
1 AA
46188989 ATTTACTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (30 bp):
AACTTTTGGATAGTTAAGTGACCAAAATGT
Found at i:46194516 original size:19 final size:19
Alignment explanation
Indices: 46194474--46194532 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
46194464 ATTTTTTAAA
* *
46194474 ATTTAAAAAATTCAAAAACAT
1 ATTTTAAAAATT-AAAAA-TT
46194495 ATTTTAAAAATTAAAAATT
1 ATTTTAAAAATTAAAAATT
*
46194514 ATTAT-AAAATTATAAAATT
1 ATTTTAAAAATTA-AAAATT
46194533 TATAAAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.21
19 11 0.32
20 5 0.15
21 11 0.32
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTTTAAAAATTAAAAATT
Found at i:46194537 original size:17 final size:17
Alignment explanation
Indices: 46194495--46194539 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
46194485 TCAAAAACAT
46194495 ATTTTA-AAAATTAAAA
1 ATTTTATAAAATTAAAA
46194511 ATTATTATAAAATTATAAA
1 ATT-TTATAAAATTA-AAA
46194530 A-TTTATAAAA
1 ATTTTATAAAA
46194540 GAAAATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.12
17 11 0.42
18 8 0.31
19 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTTATAAAATTAAAA
Found at i:46200394 original size:18 final size:18
Alignment explanation
Indices: 46200364--46200405 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
46200354 GTTAAATGGT
46200364 AAAT-ATTTATTTTATAAA
1 AAATAATTTATTTTA-AAA
46200382 AAATAATTT-TTTTAAAA
1 AAATAATTTATTTTAAAA
*
46200399 AATTAAT
1 AAATAAT
46200406 AATATCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 9 0.41
19 4 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AAATAATTTATTTTAAAA
Found at i:46204856 original size:26 final size:26
Alignment explanation
Indices: 46204825--46204876 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
46204815 TCGAAAGAAG
*
46204825 AGTCGATTCCAAGAAAACATTGAAAA
1 AGTCGATTCCAAGAAAACATCGAAAA
46204851 AGTCGATTCCAAGAAAACATCGAAAA
1 AGTCGATTCCAAGAAAACATCGAAAA
46204877 CCCAAGTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.17
Consensus pattern (26 bp):
AGTCGATTCCAAGAAAACATCGAAAA
Found at i:46216777 original size:142 final size:135
Alignment explanation
Indices: 46216544--46216986 Score: 421
Period size: 142 Copynumber: 3.2 Consensus size: 135
46216534 TTGGGGTGAT
* ** * * *
46216544 TAATGTCTATGTTACAAGACTCTGGTTTGTTTTTCTTTCAAAAAAG--T-CGTCATAGCTGAACC
1 TAATGTCGATGTTACTCGACTCGGGTTTGTTTTTCTTTCAAAAAAGTATATGTCATAGCCGAACC
* * * * *
46216606 TCATAGTTTAGGGAATAGGGTGCTACACTTGTAAACCTATGGAATTGGTGATTGATTACAGTTTG
66 TCATAGTTTTGGGACTA-GGTGTTACACTTGTAAACCTACGGAATTGATGATTGATTACAG-TTG
46216671 AGTAATCAA
129 -G-AATCAA
* *
46216680 T-ATTTGCGATTGATTACTCGATTCGGGTTTGTTTTTCTTTCAAAAAAGTTATATGTCATAGCCG
1 TAATGT-CGA-TG-TTACTCGACTCGGGTTTGTTTTTCTTTCAAAAAAG-TATATGTCATAGCCG
* *
46216744 AACCTCATAGTTTTCGGACTAGAGTGTTACACTTGTGAACCTACGGAATTGATGATTGATTACCA
62 AACCTCATAGTTTTGGGACTAG-GTGTTACACTTGTAAACCTACGGAATTGATGATTGATTA-CA
* * *
46216809 GTTGGGATGAT
125 GTTGGAATCAA
* * * * * *
46216820 TAATGTCTATGTTACTTGACTCGGGTTTGTTTTTCTTT-GAAAAGGATACATGTCATAGCGGAAC
1 TAATGTCGATGTTACTCGACTCGGGTTTGTTTTTCTTTCAAAAAAG-TATATGTCATAGCCGAAC
* * * *
46216884 CTCGTAGTTTTGGGACTAGG-GTTACACTTGTAAAACTACAGAATTGATGATTGATTACCAATTG
65 CTCATAGTTTTGGGACTAGGTGTTACACTTGTAAACCTACGGAATTGATGATTGATTA-CAGTTG
* * *
46216948 GAGTGAT
129 GAATCAA
* * *
46216955 TAATGTCTATGCTACTCAGACTCGGATTTGTT
1 TAATGTCGATGTTACTC-GACTCGGGTTTGTT
46216987 CTGTCTCTAC
Statistics
Matches: 258, Mismatches: 38, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
135 63 0.24
136 17 0.07
137 40 0.16
138 56 0.22
139 2 0.01
140 6 0.02
141 6 0.02
142 65 0.25
143 3 0.01
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.37
Consensus pattern (135 bp):
TAATGTCGATGTTACTCGACTCGGGTTTGTTTTTCTTTCAAAAAAGTATATGTCATAGCCGAACC
TCATAGTTTTGGGACTAGGTGTTACACTTGTAAACCTACGGAATTGATGATTGATTACAGTTGGA
ATCAA
Found at i:46216943 original size:135 final size:133
Alignment explanation
Indices: 46216520--46216986 Score: 476
Period size: 135 Copynumber: 3.4 Consensus size: 133
46216510 TTAATATTTG
* * * *
46216520 TGATTGATTACC-GATTGGGGTGATTAATGTCTATGTTACAAGACTCTGGTTTGTTTTTCTTTCA
1 TGATTGATTACCAG-TTGGAGTGATTAATGTCTATGTTACTAGACTCGGGTTTGTTTTTCTTTAA
* * * * *
46216584 AAA-A-AGTCGTCATAGCTGAACCTCATAGTTTAGGGAATAGGGTGCTACACTTGTAAACCTATG
65 AAAGATAAT-GTCATAGCCGAACCTCATAGTTTTGGGACTAGGGT--TACACTTGTAAACCTACG
*
46216647 GAATTGG
127 GAATTGA
* * * * * * *
46216654 TGATTGATTA-CAGTTTGAGTAATCAATATTTGCGATTGATTACTCGATTCGGGTTTGTTTTTCT
1 TGATTGATTACCAGTTGGAGTGAT-TA-ATGT-CTA-TG-TTACTAGACTCGGGTTTGTTTTTCT
* * *
46216718 TTCAAAAAAGTTATATGTCATAGCCGAACCTCATAGTTTTCGGACTAGAGTGTTACACTTGTGAA
61 TT--AAAAAGATA-ATGTCATAGCCGAACCTCATAGTTTTGGGACTAG-G-GTTACACTTGTAAA
46216783 CCTACGGAATTGA
121 CCTACGGAATTGA
*
46216796 TGATTGATTACCAGTTGG-GATGATTAATGTCTATGTTACTTGACTCGGGTTTGTTTTTCTTTGA
1 TGATTGATTACCAGTTGGAG-TGATTAATGTCTATGTTACTAGACTCGGGTTTGTTTTTCTTT-A
* * * * *
46216860 AAAGGATACATGTCATAGCGGAACCTCGTAGTTTTGGGACTAGGGTTACACTTGTAAAACTACAG
64 AAAAGATA-ATGTCATAGCCGAACCTCATAGTTTTGGGACTAGGGTTACACTTGTAAACCTACGG
46216925 AATTGA
128 AATTGA
* * *
46216931 TGATTGATTACCAATTGGAGTGATTAATGTCTATGCTACTCAGACTCGGATTTGTT
1 TGATTGATTACCAGTTGGAGTGATTAATGTCTATGTTACT-AGACTCGGGTTTGTT
46216987 CTGTCTCTAC
Statistics
Matches: 275, Mismatches: 41, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
133 8 0.03
134 12 0.04
135 63 0.23
136 17 0.06
137 40 0.15
138 48 0.17
139 2 0.01
140 6 0.02
141 3 0.01
142 63 0.23
143 11 0.04
144 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (133 bp):
TGATTGATTACCAGTTGGAGTGATTAATGTCTATGTTACTAGACTCGGGTTTGTTTTTCTTTAAA
AAGATAATGTCATAGCCGAACCTCATAGTTTTGGGACTAGGGTTACACTTGTAAACCTACGGAAT
TGA
Found at i:46217547 original size:95 final size:95
Alignment explanation
Indices: 46217386--46217575 Score: 371
Period size: 95 Copynumber: 2.0 Consensus size: 95
46217376 ACTGAAAACC
*
46217386 GAAAACCGAAGGAAACCGAAATGTTTGATTCGGTTTCAGTTCGGTTTTCATATTTCAGTATATGA
1 GAAAACCGAAGGAAACCGAAATGTTTGATTCAGTTTCAGTTCGGTTTTCATATTTCAGTATATGA
46217451 TTTGCAACAGTAGCTAATACATGTTTCTCT
66 TTTGCAACAGTAGCTAATACATGTTTCTCT
46217481 GAAAACCGAAGGAAACCGAAATGTTTGATTCAGTTTCAGTTCGGTTTTCATATTTCAGTATATGA
1 GAAAACCGAAGGAAACCGAAATGTTTGATTCAGTTTCAGTTCGGTTTTCATATTTCAGTATATGA
46217546 TTTGCAACAGTAGCTAATACATGTTTCTCT
66 TTTGCAACAGTAGCTAATACATGTTTCTCT
46217576 CTATTACCAC
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (95 bp):
GAAAACCGAAGGAAACCGAAATGTTTGATTCAGTTTCAGTTCGGTTTTCATATTTCAGTATATGA
TTTGCAACAGTAGCTAATACATGTTTCTCT
Found at i:46219936 original size:21 final size:21
Alignment explanation
Indices: 46219910--46219962 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
46219900 TTTGGGAACA
46219910 TCACAAGCTGGAGCAGCTTGT
1 TCACAAGCTGGAGCAGCTTGT
46219931 TCACAAGCTGGAGCAGCTTGT
1 TCACAAGCTGGAGCAGCTTGT
*
46219952 TCACGAGCTGG
1 TCACAAGCTGG
46219963 TGTGCAGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (21 bp):
TCACAAGCTGGAGCAGCTTGT
Found at i:46232964 original size:19 final size:19
Alignment explanation
Indices: 46232940--46232977 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
46232930 GGAGGAGAAA
46232940 AGTAAGAACAGCTTCATTT
1 AGTAAGAACAGCTTCATTT
46232959 AGTAAGAACAGCTTCATTT
1 AGTAAGAACAGCTTCATTT
46232978 GGCGAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
AGTAAGAACAGCTTCATTT
Found at i:46235835 original size:52 final size:52
Alignment explanation
Indices: 46235757--46235856 Score: 200
Period size: 52 Copynumber: 1.9 Consensus size: 52
46235747 CCAGTTAAGC
46235757 ATATTGATACGGAGAAATGCATGTAAAGGCTTCATCATATGGACTATGGACT
1 ATATTGATACGGAGAAATGCATGTAAAGGCTTCATCATATGGACTATGGACT
46235809 ATATTGATACGGAGAAATGCATGTAAAGGCTTCATCATATGGACTATG
1 ATATTGATACGGAGAAATGCATGTAAAGGCTTCATCATATGGACTATG
46235857 TTACCCGAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (52 bp):
ATATTGATACGGAGAAATGCATGTAAAGGCTTCATCATATGGACTATGGACT
Found at i:46237680 original size:102 final size:103
Alignment explanation
Indices: 46237528--46237738 Score: 406
Period size: 102 Copynumber: 2.1 Consensus size: 103
46237518 AACTTTTAAA
*
46237528 TAATTCAATAATCATTTTATAATTTTTTAAAATTAAAAAATTAAATCATAAATTTATTAATAATT
1 TAATTGAATAATCATTTTATAATTTTTTAAAATTAAAAAATTAAATCATAAATTTATTAATAATT
46237593 TCCCGACCTATGTAATTTATCCTTAAAATTATTTTATG
66 TCCCGACCTATGTAATTTATCCTTAAAATTATTTTATG
46237631 TAATTGAATAATCA-TTTATAATTTTTTAAAATTAAAAAATTAAATCATAAATTTATTAATAATT
1 TAATTGAATAATCATTTTATAATTTTTTAAAATTAAAAAATTAAATCATAAATTTATTAATAATT
46237695 TCCCGACCTATGTAATTTATCCTTAAAATTATTTTATG
66 TCCCGACCTATGTAATTTATCCTTAAAATTATTTTATG
46237733 TAATTG
1 TAATTG
46237739 CATTAAATAA
Statistics
Matches: 107, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
102 94 0.88
103 13 0.12
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (103 bp):
TAATTGAATAATCATTTTATAATTTTTTAAAATTAAAAAATTAAATCATAAATTTATTAATAATT
TCCCGACCTATGTAATTTATCCTTAAAATTATTTTATG
Found at i:46237762 original size:102 final size:102
Alignment explanation
Indices: 46237544--46237762 Score: 343
Period size: 102 Copynumber: 2.1 Consensus size: 102
46237534 AATAATCATT
**
46237544 TTATAATTTTTTAAAATTAAAAAATTAAATCATAAATTTATTAATAATTTCCCGACCTATGTAAT
1 TTATAATTAATTAAAATTAAAAAATTAAATCATAAATTTATTAATAATTTCCCGACCTATGTAAT
* *
46237609 TTATCCTTAAAATTATTTTATGTAATTGAATAATCAT
66 TTATCCTTAAAATTATTTTATGTAATTGAATAATAAA
**
46237646 TTATAATTTTTTAAAATTAAAAAATTAAATCATAAATTTATTAATAATTTCCCGACCTATGTAAT
1 TTATAATTAATTAAAATTAAAAAATTAAATCATAAATTTATTAATAATTTCCCGACCTATGTAAT
*
46237711 TTATCCTTAAAATTATTTTATGTAATTGCATTAAATAAA
66 TTATCCTTAAAATTATTTTATGTAATTG-AAT-AATAAA
46237750 TT-T-ATTAATTAAA
1 TTATAATTAATTAAA
46237763 TAATGAAAAT
Statistics
Matches: 110, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
102 101 0.92
103 3 0.03
104 6 0.05
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (102 bp):
TTATAATTAATTAAAATTAAAAAATTAAATCATAAATTTATTAATAATTTCCCGACCTATGTAAT
TTATCCTTAAAATTATTTTATGTAATTGAATAATAAA
Found at i:46242899 original size:18 final size:18
Alignment explanation
Indices: 46242878--46242921 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
46242868 AAAATACCTC
46242878 TTTTT-TAATTTATAACTA
1 TTTTTATAATTTA-AACTA
*
46242896 TTTTTATATTTTAAACTA
1 TTTTTATAATTTAAACTA
*
46242914 ATTTTATA
1 TTTTTATA
46242922 GGATTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTATAATTTAAACTA
Found at i:46269230 original size:33 final size:34
Alignment explanation
Indices: 46269171--46269243 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 34
46269161 ATAAATTTAA
*
46269171 ATAAATGAATATATCATTTTATTTTTTATGCTGG
1 ATAAGTGAATATATCATTTTATTTTTTATGCTGG
46269205 ATAAGTGAATATATCA-TTTATTTTTTATGCTGG
1 ATAAGTGAATATATCATTTTATTTTTTATGCTGG
46269238 ATAAGT
1 ATAAGT
46269244 ATAATTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 23 0.61
34 15 0.39
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (34 bp):
ATAAGTGAATATATCATTTTATTTTTTATGCTGG
Found at i:46281704 original size:54 final size:54
Alignment explanation
Indices: 46281622--46281779 Score: 235
Period size: 54 Copynumber: 2.9 Consensus size: 54
46281612 AAATTTAACC
* * *
46281622 CACATCTCGAAAGATAAACACCTTAATTACCAAGCTATCACGGGTTTACAAACT
1 CACATCTAGAAAGATAAACACCTTAATTACCAGGCTATCACGGGTTCACAAACT
** * *
46281676 CACATCTAGAAAGATAAACACCTTAATTATGAGGCTATCACGGATTCATAAACT
1 CACATCTAGAAAGATAAACACCTTAATTACCAGGCTATCACGGGTTCACAAACT
* *
46281730 CACGTCTGGAAAGATAAACACCTTAATTACCAGGCTATCACGGGTTCACA
1 CACATCTAGAAAGATAAACACCTTAATTACCAGGCTATCACGGGTTCACA
46281780 CATTATTTTC
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 91 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (54 bp):
CACATCTAGAAAGATAAACACCTTAATTACCAGGCTATCACGGGTTCACAAACT
Found at i:46284960 original size:23 final size:25
Alignment explanation
Indices: 46284927--46284977 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
46284917 TCTTTTAAAC
46284927 TTTTATGAA-TTTTAAGAA-TATATA
1 TTTTATGAATTTTTAAGAATTA-ATA
46284951 TTTTA-GAATTTTTAAGAATTAATA
1 TTTTATGAATTTTTAAGAATTAATA
46284975 TTT
1 TTT
46284978 CTAAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 3 0.12
24 20 0.80
25 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (25 bp):
TTTTATGAATTTTTAAGAATTAATA
Found at i:46287740 original size:42 final size:42
Alignment explanation
Indices: 46287679--46287760 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
46287669 TTAAAAAAAT
** *
46287679 GACCAATTTGTTCTATAATCTAACGTATAGGGACTAATTTAG
1 GACCAATTTACTCTATAATCTAACGTATAGGGACCAATTTAG
*
46287721 GACCAATTTACTCTTTAATCTAACGTATAGGGACCAATTT
1 GACCAATTTACTCTATAATCTAACGTATAGGGACCAATTT
46287761 GTCATTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (42 bp):
GACCAATTTACTCTATAATCTAACGTATAGGGACCAATTTAG
Found at i:46298019 original size:179 final size:180
Alignment explanation
Indices: 46297813--46298172 Score: 713
Period size: 179 Copynumber: 2.0 Consensus size: 180
46297803 TAATTTTAGT
46297813 TATTATATCTAATTTTATTTTTTTCAAAAAAAATAATTTTATATTTAAGTAATATTATCTACTTT
1 TATTATATCTAATTTTATTTTTTTCAAAAAAAATAATTTTATATTTAAGTAATATTATCTACTTT
46297878 ACCTTCAAAGATTTATCCAAAGTTTTAAAGTATATAGTTAATTATTTTTAATTATTTAGTTAAAT
66 ACCTTCAAAGATTTATCCAAAGTTTTAAAGTATATAGTTAATTATTTTTAATTATTTAGTTAAAT
46297943 TTCTAATCTATTGGTTCAAATCTCTATCACAAAACATATTAGAATTTATC
131 TTCTAATCTATTGGTTCAAATCTCTATCACAAAACATATTAGAATTTATC
46297993 TATTATATCT-ATTTTATTTTTTTCAAAAAAAATAATTTTATATTTAAGTAATATTATCTACTTT
1 TATTATATCTAATTTTATTTTTTTCAAAAAAAATAATTTTATATTTAAGTAATATTATCTACTTT
46298057 ACCTTCAAAGATTTATCCAAAGTTTTAAAGTATATAGTTAATTATTTTTAATTATTTAGTTAAAT
66 ACCTTCAAAGATTTATCCAAAGTTTTAAAGTATATAGTTAATTATTTTTAATTATTTAGTTAAAT
46298122 TTCTAATCTATTGGTTCAAATCTCTATCACAAAACATATTAGAATTTATC
131 TTCTAATCTATTGGTTCAAATCTCTATCACAAAACATATTAGAATTTATC
46298172 T
1 T
46298173 TCCCTTTTGA
Statistics
Matches: 180, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
179 170 0.94
180 10 0.06
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (180 bp):
TATTATATCTAATTTTATTTTTTTCAAAAAAAATAATTTTATATTTAAGTAATATTATCTACTTT
ACCTTCAAAGATTTATCCAAAGTTTTAAAGTATATAGTTAATTATTTTTAATTATTTAGTTAAAT
TTCTAATCTATTGGTTCAAATCTCTATCACAAAACATATTAGAATTTATC
Found at i:46304340 original size:107 final size:107
Alignment explanation
Indices: 46304145--46304347 Score: 262
Period size: 107 Copynumber: 1.9 Consensus size: 107
46304135 TTTTAAATTA
* ** * * **
46304145 ATCCGATATCTTTATATGAAACAAATTTGGCATGCAAACTCTATATGAGTATCATATAAAATATG
1 ATCCAATATCTTTATATGAAACAAATTTAACATACAAACTCTATATGAATAAAATATAAAATATG
** *
46304210 ACGGTTAAATCATTATGACATTAATGGTAAATTTTCGAATCG
66 ACGGTTAAATCATTAAAACATTAATGATAAATTTTCGAATCG
* * * *
46304252 ATCCAATATCTTTATATGAAACAAATTTAACGTACATACTTTATATGAATAAAATATGAAATATG
1 ATCCAATATCTTTATATGAAACAAATTTAACATACAAACTCTATATGAATAAAATATAAAATATG
* *
46304317 ACGGTTAAATTATTAAAATATTAATGATAAA
66 ACGGTTAAATCATTAAAACATTAATGATAAA
46304348 AAAAATAAGA
Statistics
Matches: 80, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
107 80 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (107 bp):
ATCCAATATCTTTATATGAAACAAATTTAACATACAAACTCTATATGAATAAAATATAAAATATG
ACGGTTAAATCATTAAAACATTAATGATAAATTTTCGAATCG
Found at i:46305135 original size:24 final size:24
Alignment explanation
Indices: 46305108--46305187 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
46305098 CCAAATTTTC
* *
46305108 CACCACCACTAGCTCTTCCACCTG
1 CACCACCTCTAGCTCCTCCACCTG
* * *
46305132 CACCTCCTCCAGCTCCTCCACCTA
1 CACCACCTCTAGCTCCTCCACCTG
* * * *
46305156 CGCCTCCTCTAGCACCACCACCTG
1 CACCACCTCTAGCTCCTCCACCTG
46305180 CACCACCT
1 CACCACCT
46305188 TTGACTCCTC
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.19, C:0.55, G:0.07, T:0.19
Consensus pattern (24 bp):
CACCACCTCTAGCTCCTCCACCTG
Found at i:46305232 original size:18 final size:18
Alignment explanation
Indices: 46305209--46305321 Score: 73
Period size: 18 Copynumber: 6.3 Consensus size: 18
46305199 TTGGACACCT
* **
46305209 GCACCAGCTCCACCTTTA
1 GCACCAGCACCACCACTA
*
46305227 GCACCACCACCACCACTA
1 GCACCAGCACCACCACTA
* **
46305245 GCACCAGCACCAGCACCC
1 GCACCAGCACCACCACTA
* * * * *
46305263 CCACTAGCTCCACCTCCA
1 GCACCAGCACCACCACTA
* * *
46305281 GCACTAGCACTAGCACTA
1 GCACCAGCACCACCACTA
* *
46305299 GCACCAGCACCAGCACCA
1 GCACCAGCACCACCACTA
46305317 GCACC
1 GCACC
46305322 CCCACTAGCT
Statistics
Matches: 72, Mismatches: 23, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 72 1.00
ACGTcount: A:0.28, C:0.50, G:0.12, T:0.10
Consensus pattern (18 bp):
GCACCAGCACCACCACTA
Found at i:46305249 original size:12 final size:12
Alignment explanation
Indices: 46305234--46305350 Score: 90
Period size: 12 Copynumber: 9.8 Consensus size: 12
46305224 TTAGCACCAC
46305234 CACCACCACTAG
1 CACCACCACTAG
* *
46305246 CACCAGCACCAG
1 CACCACCACTAG
*
46305258 CACCCCCACTAG
1 CACCACCACTAG
* * *
46305270 CTCCACCTCCAG
1 CACCACCACTAG
* *
46305282 CACTAGCACTAG
1 CACCACCACTAG
* * *
46305294 CACTAGCACCAG
1 CACCACCACTAG
* *
46305306 CACCAGCACCAG
1 CACCACCACTAG
*
46305318 CACCCCCACTAG
1 CACCACCACTAG
* *
46305330 CTCCACCGCTAG
1 CACCACCACTAG
46305342 CACCACCAC
1 CACCACCAC
46305351 CACCACCTAA
Statistics
Matches: 81, Mismatches: 24, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 81 1.00
ACGTcount: A:0.28, C:0.51, G:0.12, T:0.09
Consensus pattern (12 bp):
CACCACCACTAG
Found at i:46305253 original size:24 final size:24
Alignment explanation
Indices: 46305228--46305357 Score: 116
Period size: 24 Copynumber: 5.4 Consensus size: 24
46305218 CCACCTTTAG
* *
46305228 CACCACCACCACCACTAGCACCAG
1 CACCAGCACCACCACTAGCACCAC
* *
46305252 CACCAGCACCCCCACTAGCTCCAC
1 CACCAGCACCACCACTAGCACCAC
* * * * *
46305276 CTCCAGCACTAGCACTAGCACTAG
1 CACCAGCACCACCACTAGCACCAC
* * *
46305300 CACCAGCACCAGCACCAGCACCCC
1 CACCAGCACCACCACTAGCACCAC
* * *
46305324 CACTAGCTCCACCGCTAGCACCAC
1 CACCAGCACCACCACTAGCACCAC
*
46305348 CACCACCACC
1 CACCAGCACC
46305358 TAATCCACCC
Statistics
Matches: 80, Mismatches: 26, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 80 1.00
ACGTcount: A:0.28, C:0.53, G:0.11, T:0.08
Consensus pattern (24 bp):
CACCAGCACCACCACTAGCACCAC
Found at i:46305255 original size:42 final size:42
Alignment explanation
Indices: 46305204--46305350 Score: 132
Period size: 42 Copynumber: 3.5 Consensus size: 42
46305194 CCTCCTTGGA
* * **
46305204 CACCTGCACCAGCTCCACCTTTAGCACCACCACCACCACTAG
1 CACCAGCACCAGCACCACCACTAGCACCACCACCACCACTAG
* * * *
46305246 CACCAGCACCAGCACCCCCACTAGCTCCACCTCCAGCACTAG
1 CACCAGCACCAGCACCACCACTAGCACCACCACCACCACTAG
* * * * * *
46305288 CACTAGCACTAGCACCAGCACCAGCACCAGCACCCCCACTAG
1 CACCAGCACCAGCACCACCACTAGCACCACCACCACCACTAG
* * * *
46305330 CTCCACCGCTAGCACCACCAC
1 CACCAGCACCAGCACCACCAC
46305351 CACCACCTAA
Statistics
Matches: 82, Mismatches: 23, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.27, C:0.51, G:0.12, T:0.10
Consensus pattern (42 bp):
CACCAGCACCAGCACCACCACTAGCACCACCACCACCACTAG
Found at i:46305282 original size:30 final size:30
Alignment explanation
Indices: 46305246--46305356 Score: 123
Period size: 30 Copynumber: 3.7 Consensus size: 30
46305236 CCACCACTAG
*
46305246 CACCAGCACCAGCACCCCCACTAGCTCCAC
1 CACCAGCACCAGCACCACCACTAGCTCCAC
* * * * * *
46305276 CTCCAGCACTAGCACTAGCACTAGCACCAG
1 CACCAGCACCAGCACCACCACTAGCTCCAC
*
46305306 CACCAGCACCAGCACCCCCACTAGCTCCAC
1 CACCAGCACCAGCACCACCACTAGCTCCAC
* * *
46305336 CGCTAGCACCACCACCACCAC
1 CACCAGCACCAGCACCACCAC
46305357 CTAATCCACC
Statistics
Matches: 63, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.28, C:0.52, G:0.12, T:0.08
Consensus pattern (30 bp):
CACCAGCACCAGCACCACCACTAGCTCCAC
Found at i:46305289 original size:6 final size:6
Alignment explanation
Indices: 46305278--46305321 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
46305268 AGCTCCACCT
* * *
46305278 CCAGCA CTAGCA CTAGCA CTAGCA CCAGCA CCAGCA CCAGCA CC
1 CCAGCA CCAGCA CCAGCA CCAGCA CCAGCA CCAGCA CCAGCA CC
46305322 CCCACTAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.32, C:0.45, G:0.16, T:0.07
Consensus pattern (6 bp):
CCAGCA
Found at i:46308372 original size:5 final size:5
Alignment explanation
Indices: 46308364--46308409 Score: 65
Period size: 5 Copynumber: 9.2 Consensus size: 5
46308354 TATTTAATTT
* * *
46308364 ATATA ATATA ATACA ATACA ATACA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
46308410 AACATCTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (5 bp):
ATATA
Found at i:46308798 original size:29 final size:29
Alignment explanation
Indices: 46308764--46308857 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
46308754 TTTGGCTGTC
46308764 CAACTATGAAAAGTTACAAACTAGTCACT
1 CAACTATGAAAAGTTACAAACTAGTCACT
* * *
46308793 CAACTATTAGTAAAA---A-AAATTTGACCACT
1 CAACTA-T-G-AAAAGTTACAAACTAG-TCACT
* *
46308822 CAACTATGAAAAGTTACAAGCTGGTCACT
1 CAACTATGAAAAGTTACAAACTAGTCACT
46308851 CAACTAT
1 CAACTAT
46308858 TAGTAAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
26 4 0.08
27 1 0.02
28 6 0.12
29 29 0.58
30 5 0.10
31 1 0.02
32 4 0.08
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.26
Consensus pattern (29 bp):
CAACTATGAAAAGTTACAAACTAGTCACT
Found at i:46308835 original size:58 final size:59
Alignment explanation
Indices: 46308763--46308917 Score: 240
Period size: 58 Copynumber: 2.6 Consensus size: 59
46308753 TTTTGGCTGT
*
46308763 CCAACTATGAAAAGTTACAAACTAGTCACTCAACTATTAGTAAAAAAAA-TTTGACCAC
1 CCAACTATGAAAAGTTACAAACTGGTCACTCAACTATTAGTAAAAAAAATTTTGACCAC
* * *
46308821 TCAACTATGAAAAGTTACAAGCTGGTCACTCAACTATTAGTAAAAAAAATTTTGATCAC
1 CCAACTATGAAAAGTTACAAACTGGTCACTCAACTATTAGTAAAAAAAATTTTGACCAC
* * *
46308880 CCAACTATGAAAAATTACAAAATGGTCACCCAACTATT
1 CCAACTATGAAAAGTTACAAACTGGTCACTCAACTATT
46308918 CAATTTTGTC
Statistics
Matches: 87, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
58 46 0.53
59 41 0.47
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.26
Consensus pattern (59 bp):
CCAACTATGAAAAGTTACAAACTGGTCACTCAACTATTAGTAAAAAAAATTTTGACCAC
Found at i:46309188 original size:17 final size:17
Alignment explanation
Indices: 46309163--46309200 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
46309153 TCTCTTTTTC
*
46309163 TTTTTCTTT-TTTTTCAG
1 TTTTACTTTATTTTT-AG
46309180 TTTTACTTTATTTTTAG
1 TTTTACTTTATTTTTAG
46309197 TTTT
1 TTTT
46309201 TACTATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTACTTTATTTTTAG
Found at i:46309201 original size:18 final size:18
Alignment explanation
Indices: 46309163--46309204 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
46309153 TCTCTTTTTC
46309163 TTTTT-CTTTTTTTTCAG
1 TTTTTACTTTTTTTTCAG
46309180 -TTTTACTTTATTTTT-AG
1 TTTTTACTTT-TTTTTCAG
46309197 TTTTTACT
1 TTTTTACT
46309205 ATTAAAAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 6 0.27
18 12 0.55
ACGTcount: A:0.12, C:0.10, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTTTACTTTTTTTTCAG
Found at i:46310052 original size:3 final size:3
Alignment explanation
Indices: 46310037--46310152 Score: 83
Period size: 3 Copynumber: 35.7 Consensus size: 3
46310027 TCCAATTCCT
* *
46310037 CCA CCA GCA CCA CCA CCGAA TCCA CCA CCA CCA CCA CCA CCA -AA CCCA
1 CCA CCA CCA CCA CCA CC--A -CCA CCA CCA CCA CCA CCA CCA CCA -CCA
*
46310085 CCA CCA CCA CCA CCA CCGAA TCCA CCA CCA CCA CCGAA TCCA CCA CCT
1 CCA CCA CCA CCA CCA CC--A -CCA CCA CCA CCA CC--A -CCA CCA CCA
*
46310133 CCA CCT CCA CC- CGCA CCA CC
1 CCA CCA CCA CCA C-CA CCA CC
46310153 TCCAATTCCT
Statistics
Matches: 92, Mismatches: 8, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
2 2 0.02
3 76 0.83
4 5 0.05
5 3 0.03
6 6 0.07
ACGTcount: A:0.31, C:0.60, G:0.04, T:0.04
Consensus pattern (3 bp):
CCA
Found at i:46310067 original size:18 final size:18
Alignment explanation
Indices: 46310044--46310137 Score: 112
Period size: 18 Copynumber: 5.6 Consensus size: 18
46310034 CCTCCACCAG
46310044 CACCACCACCGAATCCAC
1 CACCACCACCGAATCCAC
46310062 CACCACCACC--A-CCAC
1 CACCACCACCGAATCCAC
*
46310077 CA-AACCCACC--A-CCAC
1 CACCA-CCACCGAATCCAC
46310092 CACCACCACCGAATCCAC
1 CACCACCACCGAATCCAC
46310110 CACCACCACCGAATCCAC
1 CACCACCACCGAATCCAC
*
46310128 CACCTCCACC
1 CACCACCACC
46310138 TCCACCCGCA
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.01
15 23 0.34
16 2 0.03
17 1 0.01
18 41 0.60
ACGTcount: A:0.33, C:0.60, G:0.03, T:0.04
Consensus pattern (18 bp):
CACCACCACCGAATCCAC
Found at i:46310143 original size:24 final size:24
Alignment explanation
Indices: 46310037--46310119 Score: 139
Period size: 24 Copynumber: 3.5 Consensus size: 24
46310027 TCCAATTCCT
*
46310037 CCACCAGCACCACCACCGAATCCA
1 CCACCACCACCACCACCGAATCCA
* *
46310061 CCACCACCACCACCACCAAACCCA
1 CCACCACCACCACCACCGAATCCA
46310085 CCACCACCACCACCACCGAATCCA
1 CCACCACCACCACCACCGAATCCA
46310109 CCACCACCACC
1 CCACCACCACC
46310120 GAATCCACCA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.34, C:0.60, G:0.04, T:0.02
Consensus pattern (24 bp):
CCACCACCACCACCACCGAATCCA
Found at i:46310179 original size:42 final size:42
Alignment explanation
Indices: 46310123--46310240 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
46310113 CACCACCGAA
* * * * **
46310123 TCCACCACCTCCACCTCCACCCGCACCACCTCCAATTCCTCC
1 TCCAACACCACCACCTGCACCCGCACCACCACCAAGCCCTCC
* *
46310165 TCCAACTCCACCACCTGCACCAC-CCCCACCACCAAGCCCTCC
1 TCCAACACCACCACCTGCACC-CGCACCACCACCAAGCCCTCC
* * *
46310207 TCCAACACCGCCACCTGCTCCAGCACCACCACCA
1 TCCAACACCACCACCTGCACCCGCACCACCACCA
46310241 GCTCCAGCAC
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 60 0.98
43 1 0.02
ACGTcount: A:0.23, C:0.60, G:0.05, T:0.12
Consensus pattern (42 bp):
TCCAACACCACCACCTGCACCCGCACCACCACCAAGCCCTCC
Found at i:46310227 original size:18 final size:18
Alignment explanation
Indices: 46310206--46310264 Score: 91
Period size: 18 Copynumber: 3.3 Consensus size: 18
46310196 CCAAGCCCTC
* * *
46310206 CTCCAACACCGCCACCTG
1 CTCCAGCACCACCACCAG
46310224 CTCCAGCACCACCACCAG
1 CTCCAGCACCACCACCAG
46310242 CTCCAGCACCACCACCAG
1 CTCCAGCACCACCACCAG
46310260 CTCCA
1 CTCCA
46310265 CCTCCTAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.25, C:0.56, G:0.10, T:0.08
Consensus pattern (18 bp):
CTCCAGCACCACCACCAG
Found at i:46310269 original size:24 final size:24
Alignment explanation
Indices: 46310242--46310484 Score: 147
Period size: 24 Copynumber: 9.7 Consensus size: 24
46310232 CCACCACCAG
46310242 CTCCAGCACCACCACCAGCTCCACCTC
1 CTCCAGCACCACCACCAGCT---CCTC
* *
46310269 CTAAACCGGCACCACCGCCAAGC-CCTC
1 CT---CCAGCACCACCACC-AGCTCCTC
* *
46310296 CTCCAGCACCCCCACCGGCTCCTC
1 CTCCAGCACCACCACCAGCTCCTC
*
46310320 CTCCTA-AACCACCACCAAGC-CCTC
1 CTCC-AGCACCACCACC-AGCTCCTC
* *
46310344 CTCCAGCACCCCCACCGGCTCCTC
1 CTCCAGCACCACCACCAGCTCCTC
*
46310368 CTCCTA-AACCACCACCAAGC-CCTC
1 CTCC-AGCACCACCACC-AGCTCCTC
46310392 CTCCAGCACCACCACCAGCTCCACCTC
1 CTCCAGCACCACCACCAGCT---CCTC
** * * *
46310419 CTACCCCCCCCGCCACCGAAC-CCTC
1 CT-CCAGCACCACCACC-AGCTCCTC
* * *
46310444 CTCCTGCACCCCCACCAGCTCCAC
1 CTCCAGCACCACCACCAGCTCCTC
*
46310468 CTCTAGCACCACCACCA
1 CTCCAGCACCACCACCA
46310485 CCTCTAATCC
Statistics
Matches: 167, Mismatches: 30, Indels: 41
0.70 0.13 0.17
Matches are distributed among these distances:
23 11 0.07
24 103 0.62
25 12 0.07
27 14 0.08
28 10 0.06
29 2 0.01
30 12 0.07
31 3 0.02
ACGTcount: A:0.21, C:0.59, G:0.09, T:0.11
Consensus pattern (24 bp):
CTCCAGCACCACCACCAGCTCCTC
Found at i:46310281 original size:48 final size:48
Alignment explanation
Indices: 46310242--46310421 Score: 198
Period size: 48 Copynumber: 3.6 Consensus size: 48
46310232 CCACCACCAG
* *
46310242 CTCCAGCACCACCACCAGCTCCACCTCCTAAACCGGCACCACCGCCAAGCCCTC
1 CTCCAGCACCACCACCAGCTCCACCTCCTAAA-C--CACCA---CCAACCCCAC
* * * * *
46310296 CTCCAGCACCCCCACCGGCTCCTCCTCCTAAACCACCACCAAGCCCTC
1 CTCCAGCACCACCACCAGCTCCACCTCCTAAACCACCACCAACCCCAC
* * * * *
46310344 CTCCAGCACCCCCACCGGCTCCTCCTCCTAAACCACCACCAAGCCCTC
1 CTCCAGCACCACCACCAGCTCCACCTCCTAAACCACCACCAACCCCAC
46310392 CTCCAGCACCACCACCAGCTCCACCTCCTA
1 CTCCAGCACCACCACCAGCTCCACCTCCTA
46310422 CCCCCCCCGC
Statistics
Matches: 120, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
48 85 0.71
51 5 0.04
53 1 0.01
54 29 0.24
ACGTcount: A:0.22, C:0.57, G:0.09, T:0.12
Consensus pattern (48 bp):
CTCCAGCACCACCACCAGCTCCACCTCCTAAACCACCACCAACCCCAC
Found at i:46312526 original size:9 final size:9
Alignment explanation
Indices: 46312491--46312594 Score: 50
Period size: 9 Copynumber: 11.2 Consensus size: 9
46312481 TCCTCCAATT
46312491 CCTCCACCA
1 CCTCCACCA
* *
46312500 GCACCACCA
1 CCTCCACCA
46312509 CCGAATCCACCA
1 CC---TCCACCA
46312521 CCTCCACCTA
1 CCTCCACC-A
* *
46312531 -CACCTCCA
1 CCTCCACCA
46312539 CC-CGCACCA
1 CCTC-CACCA
***
46312548 CCTCCAATT
1 CCTCCACCA
*
46312557 CCTCCTCCA
1 CCTCCACCA
*
46312566 ACTCCACCA
1 CCTCCACCA
*
46312575 CCTGCACCA
1 CCTCCACCA
*
46312584 CCCCCACCA
1 CCTCCACCA
46312593 CC
1 CC
46312595 AAGCCCTCCT
Statistics
Matches: 68, Mismatches: 20, Indels: 14
0.67 0.20 0.14
Matches are distributed among these distances:
8 2 0.03
9 56 0.82
10 2 0.03
12 8 0.12
ACGTcount: A:0.24, C:0.61, G:0.04, T:0.12
Consensus pattern (9 bp):
CCTCCACCA
Found at i:46312618 original size:42 final size:42
Alignment explanation
Indices: 46312543--46312637 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 42
46312533 CCTCCACCCG
* ** *
46312543 CACCACCTCCAATTCCTCCTCCAACTCCACCACCTGCACCAC
1 CACCACCACCAAGCCCTCCTCCAACACCACCACCTGCACCAC
* * * * *
46312585 CCCCACCACCAAGCCCTCCTCCAAGACCGCCACCTGCTCCAG
1 CACCACCACCAAGCCCTCCTCCAACACCACCACCTGCACCAC
46312627 CACCACCACCA
1 CACCACCACCA
46312638 GCTCCACCTC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.58, G:0.06, T:0.12
Consensus pattern (42 bp):
CACCACCACCAAGCCCTCCTCCAACACCACCACCTGCACCAC
Found at i:46312678 original size:30 final size:30
Alignment explanation
Indices: 46312644--46312732 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 30
46312634 ACCAGCTCCA
46312644 CCTCCTAAACCGGCACCCCCGCCAAGCCCT
1 CCTCCTAAACCGGCACCCCCGCCAAGCCCT
* * * *
46312674 CCTCC---A---GCACCACCACC-CGCTCCA
1 CCTCCTAAACCGGCACCCCCGCCAAGC-CCT
46312698 CCTCCTAAACCGGCACCCCCGCCAAGCCCT
1 CCTCCTAAACCGGCACCCCCGCCAAGCCCT
46312728 CCTCC
1 CCTCC
46312733 AGCACCACCA
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
23 2 0.05
24 16 0.37
27 2 0.05
30 21 0.49
31 2 0.05
ACGTcount: A:0.19, C:0.60, G:0.11, T:0.10
Consensus pattern (30 bp):
CCTCCTAAACCGGCACCCCCGCCAAGCCCT
Found at i:46312680 original size:54 final size:53
Alignment explanation
Indices: 46312621--46312841 Score: 257
Period size: 54 Copynumber: 4.3 Consensus size: 53
46312611 CCGCCACCTG
*
46312621 CTCCAGCACCACCACCAGCTCCACCTCCTAAACCGGCACCCCCGCCAAGCCCTC
1 CTCCAGCACCACCACCAGCTCCACCTCCTAAACC-GCACCCCCACCAAGCCCTC
* *
46312675 CTCCAGCACCACCACCCGCTCCACCTCCTAAACCGGCACCCCCGCCAAGCCCTC
1 CTCCAGCACCACCACCAGCTCCACCTCCTAAACC-GCACCCCCACCAAGCCCTC
* * * *
46312729 CTCCAGCACCACCACCTA-ATCCACC-CC--CACCG--CCGCCACCGAGCCCTC
1 CTCCAGCACCACCACC-AGCTCCACCTCCTAAACCGCACCCCCACCAAGCCCTC
* *
46312777 CTCCTGCACCCCCACCAGCTCCACCTCCTAAA-C-CA---CCACCAAGCCCTC
1 CTCCAGCACCACCACCAGCTCCACCTCCTAAACCGCACCCCCACCAAGCCCTC
46312825 CTCCAGCACCACCACCA
1 CTCCAGCACCACCACCA
46312842 AAACCACCAC
Statistics
Matches: 146, Mismatches: 14, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
47 1 0.01
48 60 0.41
49 2 0.01
50 2 0.01
51 4 0.03
53 2 0.01
54 75 0.51
ACGTcount: A:0.22, C:0.59, G:0.10, T:0.10
Consensus pattern (53 bp):
CTCCAGCACCACCACCAGCTCCACCTCCTAAACCGCACCCCCACCAAGCCCTC
Found at i:46312683 original size:24 final size:24
Alignment explanation
Indices: 46312656--46312842 Score: 96
Period size: 24 Copynumber: 7.5 Consensus size: 24
46312646 TCCTAAACCG
*
46312656 GCACCCCCGCCAAGCCCTCCTCCA
1 GCACCCCCACCAAGCCCTCCTCCA
* * *
46312680 GCACCACCACC-CGCTCCACCTCCTAAACCG
1 GCACCCCCACCAAG---C-CCTCCT---CCA
*
46312710 GCACCCCCGCCAAGCCCTCCTCCA
1 GCACCCCCACCAAGCCCTCCTCCA
* *
46312734 GCACCACCACCTAATCCAC-CC-CCA
1 GCACCCCCACC-AAGCC-CTCCTCCA
* * * * *
46312758 CCGCCGCCACCGAGCCCTCCTCCT
1 GCACCCCCACCAAGCCCTCCTCCA
*
46312782 GCACCCCCACC-AGCTCCACCTCCTA
1 GCACCCCCACCAAGC-CCTCCTCC-A
* *
46312807 -AACCACCACCAAGCCCTCCTCCA
1 GCACCCCCACCAAGCCCTCCTCCA
*
46312830 GCACCACCACCAA
1 GCACCCCCACCAA
46312843 AACCACCACC
Statistics
Matches: 121, Mismatches: 26, Indels: 32
0.68 0.15 0.18
Matches are distributed among these distances:
22 1 0.01
23 10 0.08
24 74 0.61
25 9 0.07
26 2 0.02
27 12 0.10
28 1 0.01
30 11 0.09
31 1 0.01
ACGTcount: A:0.22, C:0.59, G:0.10, T:0.09
Consensus pattern (24 bp):
GCACCCCCACCAAGCCCTCCTCCA
Found at i:46312800 original size:48 final size:47
Alignment explanation
Indices: 46312665--46312856 Score: 152
Period size: 48 Copynumber: 3.9 Consensus size: 47
46312655 GGCACCCCCG
** * *
46312665 CCAAGCCCTCCTCCAGCACCACCACCCGCTCCACCTCCTAAACCGGCACCCCCG
1 CCAAGCCCTCCTCCAGCACCACCA-CCAATCCACCTCCCAAA-C--CA---CCA
** *
46312719 CCAAGCCCTCCTCCAGCACCACCACCTAATCCACC-CCCACCGCCGCCA
1 CCAAGCCCTCCTCCAGCACCACCACC-AATCCACCTCCCA-AACCACCA
* * * * *
46312767 CCGAGCCCTCCTCCTGCACCCCCACCAGCTCCACCTCCTAAACCACCA
1 CCAAGCCCTCCTCCAGCACCACCACCA-ATCCACCTCCCAAACCACCA
* *
46312815 CCAAGCCCTCCTCCAGCACCACCACCAAAACCACCACCCAAA
1 CCAAGCCCTCCTCCAGCACCACCACC-AATCCACCTCCCAAA
46312857 TTCTCCTTCT
Statistics
Matches: 111, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
47 1 0.01
48 69 0.62
49 4 0.04
51 1 0.01
53 6 0.05
54 30 0.27
ACGTcount: A:0.24, C:0.58, G:0.08, T:0.09
Consensus pattern (47 bp):
CCAAGCCCTCCTCCAGCACCACCACCAATCCACCTCCCAAACCACCA
Found at i:46324203 original size:6 final size:6
Alignment explanation
Indices: 46324197--46324226 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
46324187 AATTTTTTAA
*
46324197 TTATAA TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT
46324227 AAAAAAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TTATAT
Found at i:46326102 original size:20 final size:20
Alignment explanation
Indices: 46326077--46326114 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46326067 TATTAGGGAC
46326077 ATTAAATTATTT-TAATATAA
1 ATTAAATT-TTTATAATATAA
46326097 ATTAAATTTTTATAATAT
1 ATTAAATTTTTATAATAT
46326115 TTTTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTAAATTTTTATAATATAA
Found at i:46326265 original size:15 final size:16
Alignment explanation
Indices: 46326237--46326272 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
46326227 CACGATTAAG
46326237 AAATAAACAATAATAA
1 AAATAAACAATAATAA
46326253 AAATAAA-AATAATAA
1 AAATAAACAATAATAA
46326268 AAATA
1 AAATA
46326273 TATTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATAAACAATAATAA
Found at i:46326979 original size:1 final size:1
Alignment explanation
Indices: 46326975--46327003 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
46326965 AGAAAAAGTG
46326975 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
46327004 GCGTTGGTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:46335032 original size:16 final size:18
Alignment explanation
Indices: 46335000--46335032 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46334990 ATTAATAAAA
46335000 TAAATTTAGTGTTAATTG
1 TAAATTTAGTGTTAATTG
46335018 TAAATTT-GT-TTAATT
1 TAAATTTAGTGTTAATT
46335033 TTACGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (18 bp):
TAAATTTAGTGTTAATTG
Found at i:46351377 original size:77 final size:78
Alignment explanation
Indices: 46351279--46351433 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 78
46351269 TTTTAATAAC
46351279 GTATATTATATTATATTATAAAACTGCATATTATATTTTAAAGTTTTATGAATTATACTTTTTGA
1 GTATATTATATTATATTATAAAACTGCATATTATATTTTAAAGTTTTATGAATTATACTTTTTGA
46351344 AATTAAGAATTAA
66 AATTAAGAATTAA
46351357 GTATATTATA-TATATTATAAAACTGCATATTATATTTTAAAGTTTTATGAATTATACTTTTTGA
1 GTATATTATATTATATTATAAAACTGCATATTATATTTTAAAGTTTTATGAATTATACTTTTTGA
46351421 AATTAAGAATTAA
66 AATTAAGAATTAA
46351434 AATTAATATT
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 67 0.87
78 10 0.13
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (78 bp):
GTATATTATATTATATTATAAAACTGCATATTATATTTTAAAGTTTTATGAATTATACTTTTTGA
AATTAAGAATTAA
Found at i:46353709 original size:43 final size:43
Alignment explanation
Indices: 46353660--46353741 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
46353650 AAGAAGTTGG
46353660 TTGCAGGGATGTTATGGCAGAGAGAGATAAGAGTAAGAAGATT
1 TTGCAGGGATGTTATGGCAGAGAGAGATAAGAGTAAGAAGATT
*
46353703 TTGCAGGGATGTTATGGCGGAGAGAGATAAGAGTAAGAA
1 TTGCAGGGATGTTATGGCAGAGAGAGATAAGAGTAAGAA
46353742 AGAAAAGTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.37, T:0.22
Consensus pattern (43 bp):
TTGCAGGGATGTTATGGCAGAGAGAGATAAGAGTAAGAAGATT
Done.