Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 3 of 27
Found at i:292324 original size:35 final size:33
Alignment explanation
Indices: 292269--292333 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 33
292259 TTTTTATATT
* *
292269 AATATTTATTTATTTTATAATTATTTAAATAAA
1 AATATTTATTTATTTAATAATAATTTAAATAAA
*
292302 AATATTTTTATTATTTAAATAATAATTTAAAT
1 AATATTTAT-TTATTT-AATAATAATTTAAAT
292334 TAAATTAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 8 0.30
34 6 0.22
35 13 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
AATATTTATTTATTTAATAATAATTTAAATAAA
Found at i:297714 original size:32 final size:29
Alignment explanation
Indices: 297641--297715 Score: 71
Period size: 32 Copynumber: 2.4 Consensus size: 29
297631 TAATACATAA
* *
297641 ATATATT-AAAATTTATATAAAATATATT
1 ATATATTCAAAATTTATATAAAAAATATG
297669 ATTATCATGTCAAAATTTATATAATATTAAATATG
1 A-TAT-AT-TCAAAATTTATATAA-A--AAATATG
297704 ATATATTCAAAA
1 ATATATTCAAAA
297716 AAAATAACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
28 1 0.03
29 3 0.08
30 2 0.05
31 1 0.03
32 19 0.50
33 3 0.08
34 3 0.08
35 6 0.16
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (29 bp):
ATATATTCAAAATTTATATAAAAAATATG
Found at i:299306 original size:28 final size:28
Alignment explanation
Indices: 299244--299340 Score: 81
Period size: 27 Copynumber: 3.4 Consensus size: 28
299234 TTAAAAATAA
*
299244 AAATTAAATTATTTAAATATTATTTAA-TTA
1 AAATTAAATTATTT--ATA-TATTTAATTTT
* *
299274 AAAATAAACTTATTTTTATATTTAATTTT
1 AAATTAAA-TTATTTATATATTTAATTTT
* *
299303 AAATTTAATTATTTATAT-TTTAACTTT
1 AAATTAAATTATTTATATATTTAATTTT
* *
299330 AATTTGAATTA
1 AAATTAAATTA
299341 AGATTATCTG
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
27 17 0.30
28 16 0.29
29 10 0.18
30 7 0.12
31 6 0.11
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (28 bp):
AAATTAAATTATTTATATATTTAATTTT
Found at i:299324 original size:21 final size:20
Alignment explanation
Indices: 299292--299333 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
299282 CTTATTTTTA
299292 TATTTAATTTTAAATTTAAT
1 TATTTAATTTTAAATTTAAT
*
299312 TATTTATATTTTAACTTTAAT
1 TATTTA-ATTTTAAATTTAAT
299333 T
1 T
299334 TGAATTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTAATTTTAAATTTAAT
Found at i:299961 original size:15 final size:15
Alignment explanation
Indices: 299941--299974 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
299931 ACATTTATAA
*
299941 TATAATATTATAAAT
1 TATAATAATATAAAT
299956 TATAATAATATAAAT
1 TATAATAATATAAAT
299971 TATA
1 TATA
299975 TTAAAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATAATAATATAAAT
Found at i:301696 original size:15 final size:15
Alignment explanation
Indices: 301673--301740 Score: 54
Period size: 15 Copynumber: 4.6 Consensus size: 15
301663 TTTTTTGGCG
301673 AGATG-TTTTAGTCA
1 AGATGTTTTTAGTCA
**
301687 AGATGTTTTTAGGGGA
1 AGATGTTTTTA-GTCA
301703 A-ATGTTTTCTAG-CA
1 AGATGTTTT-TAGTCA
*
301717 AGATGTTTTTTGTCGA
1 AGATGTTTTTAGTC-A
301733 A-ATGTTTT
1 AGATGTTTT
301741 CAACGAGATG
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
14 9 0.20
15 28 0.64
16 7 0.16
ACGTcount: A:0.25, C:0.06, G:0.24, T:0.46
Consensus pattern (15 bp):
AGATGTTTTTAGTCA
Found at i:301719 original size:30 final size:30
Alignment explanation
Indices: 301659--301741 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
301649 TTTTTAAGAG
* *
301659 AGAT-TTTTTTGGCGAGATG-TTT-TAGTCA
1 AGATGTTTTTAGGCGAAATGTTTTCTAG-CA
*
301687 AGATGTTTTTAGGGGAAATGTTTTCTAGCA
1 AGATGTTTTTAGGCGAAATGTTTTCTAGCA
* *
301717 AGATGTTTTTTGTCGAAATGTTTTC
1 AGATGTTTTTAGGCGAAATGTTTTC
301742 AACGAGATGT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.09
29 12 0.26
30 27 0.59
31 3 0.07
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (30 bp):
AGATGTTTTTAGGCGAAATGTTTTCTAGCA
Found at i:302105 original size:77 final size:77
Alignment explanation
Indices: 301977--302183 Score: 197
Period size: 77 Copynumber: 2.7 Consensus size: 77
301967 TTTAAGAAAC
* ** * *
301977 ATCTCAACATATATTCAAA-AGTCATCTAGCTC-AAAGGGTTTCT-AGGACATCATCTAGCCAAC
1 ATCTCAACATATATTCAAACA-TCATCTA-ATCAAAATAGATTCTAAGG-CATCATCTAGACAAC
*
302039 ACGTCTTCAAGAATT
63 ACGCCTTCAAGAATT
* * * * * * *
302054 ATCTCAACATATATTTAAACATCATTTAGA-CAAAATAGTTTTTAAGGCATCATTTAGACAATAT
1 ATCTCAACATATATTCAAACATCATCTA-ATCAAAATAGATTCTAAGGCATCATCTAGACAACAC
302118 GCCTTCAAGAATT
65 GCCTTCAAGAATT
* * * *
302131 ATCTTAATATATATTCAAGCATTATCTAATCAAAATAGATTCTAAGGCATCAT
1 ATCTCAACATATATTCAAACATCATCTAATCAAAATAGATTCTAAGGCATCAT
302184 GTAACTAACA
Statistics
Matches: 107, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
76 2 0.02
77 101 0.94
78 4 0.04
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (77 bp):
ATCTCAACATATATTCAAACATCATCTAATCAAAATAGATTCTAAGGCATCATCTAGACAACACG
CCTTCAAGAATT
Found at i:302491 original size:80 final size:78
Alignment explanation
Indices: 302370--302585 Score: 227
Period size: 80 Copynumber: 2.7 Consensus size: 78
302360 ATCACTGGCG
* * *
302370 ACAAAGGCTTAAGAATTCAAATATTATTATCTCACCAACGACAAAAGCTTGAGAAA-TCAAAGAT
1 ACAAAGGCTTAA-AATTCAAA-ATTATTATCTTACTAACGACAAAAGCTTGA-AAATTCAAAAAT
*
302434 TATTATTAATGTCGGCA
63 TATTATT-ATGTCGACA
* * * **
302451 ACAAAGGCTTGAAAGTTCAAAATTATTATCTTGCTTACGACAATGGCTTGAAAATTCAAAAATTA
1 ACAAAGGCTT-AAAATTCAAAATTATTATCTTACTAACGACAAAAGCTTGAAAATTCAAAAATTA
* *
302516 TTATTTTGTCGACG
65 TTATTATGTCGACA
* *
302530 ACAAAAGCTTTAAAATTCAAAATTATTATCTCACTACTGACGACAAAAGCTTGAAA
1 ACAAAGGC-TTAAAATTCAAAATTATTATCT---TACTAACGACAAAAGCTTGAAA
302586 TTATTAGCTT
Statistics
Matches: 112, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
79 35 0.31
80 40 0.36
81 17 0.15
82 20 0.18
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.30
Consensus pattern (78 bp):
ACAAAGGCTTAAAATTCAAAATTATTATCTTACTAACGACAAAAGCTTGAAAATTCAAAAATTAT
TATTATGTCGACA
Found at i:302503 original size:39 final size:39
Alignment explanation
Indices: 302368--302560 Score: 169
Period size: 40 Copynumber: 4.8 Consensus size: 39
302358 ATATCACTGG
*** *
302368 CGACAAAGGCTT-AAGAATTCAAATATTATTATCTCACCAA
1 CGACAAAGGCTTGAA-AATTCAAA-ATTATTATCTTGTCGA
* *
302408 CGACAAAAGCTTGAGAAA-TCAAAGATTATTAT-TAATGTCGG
1 CGACAAAGGCTTGA-AAATTCAAA-ATTATTATCT--TGTCGA
* * *
302449 CAACAAAGGCTTGAAAGTTCAAAATTATTATCTTG-CTTA
1 CGACAAAGGCTTGAAAATTCAAAATTATTATCTTGTC-GA
* *
302488 CGACAATGGCTTGAAAATTCAAAAATTATTATTTTGTCGA
1 CGACAAAGGCTTGAAAATTC-AAAATTATTATCTTGTCGA
* *
302528 CGACAAAAGCTTTAAAATTCAAAATTATTATCT
1 CGACAAAGGCTTGAAAATTCAAAATTATTATCT
302561 CACTACTGAC
Statistics
Matches: 123, Mismatches: 21, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
38 1 0.01
39 32 0.26
40 66 0.54
41 23 0.19
42 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (39 bp):
CGACAAAGGCTTGAAAATTCAAAATTATTATCTTGTCGA
Found at i:304625 original size:27 final size:27
Alignment explanation
Indices: 304595--304648 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
304585 TCGGCAAAGG
304595 AGTATTTATTTATTTTTTACTTCTCTT
1 AGTATTTATTTATTTTTTACTTCTCTT
304622 AGTATTTATTTATTTTTTACTTCTCTT
1 AGTATTTATTTATTTTTTACTTCTCTT
304649 CATTCTTTTT
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:0.19, C:0.11, G:0.04, T:0.67
Consensus pattern (27 bp):
AGTATTTATTTATTTTTTACTTCTCTT
Found at i:306991 original size:12 final size:12
Alignment explanation
Indices: 306974--307012 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
306964 TTTCAATACT
306974 TATATTTAGATA
1 TATATTTAGATA
306986 TATA-TTA-A-A
1 TATATTTAGATA
306995 TATATTTAGATA
1 TATATTTAGATA
307007 TATATT
1 TATATT
307013 AAATACGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
9 5 0.21
10 4 0.17
11 4 0.17
12 11 0.46
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (12 bp):
TATATTTAGATA
Found at i:306998 original size:21 final size:21
Alignment explanation
Indices: 306974--307017 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
306964 TTTCAATACT
306974 TATATTTAGATATATATTAAA
1 TATATTTAGATATATATTAAA
306995 TATATTTAGATATATATTAAA
1 TATATTTAGATATATATTAAA
307016 TA
1 TA
307018 CGAATGTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
TATATTTAGATATATATTAAA
Found at i:307007 original size:10 final size:10
Alignment explanation
Indices: 306974--307009 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
306964 TTTCAATACT
306974 TATATTTAGA
1 TATATTTAGA
*
306984 TATATATTAAA
1 TATAT-TTAGA
306995 TATATTTAGA
1 TATATTTAGA
307005 TATAT
1 TATAT
307010 ATTAAATACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
TATATTTAGA
Found at i:313608 original size:29 final size:30
Alignment explanation
Indices: 313556--313618 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 30
313546 TAATGAAAGA
313556 AATATTTTAATTTTGTATTATT-AAATT-T
1 AATATTTTAATTTTGTATTATTAAAATTAT
313584 AATATTTTAATTTTTGTATGT-TTAAAATTAT
1 AATATTTTAA-TTTTGTAT-TATTAAAATTAT
313615 AATA
1 AATA
313619 AATAGAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
28 10 0.32
29 10 0.32
30 6 0.19
31 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (30 bp):
AATATTTTAATTTTGTATTATTAAAATTAT
Found at i:314288 original size:17 final size:17
Alignment explanation
Indices: 314266--314304 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
314256 GATATTATTG
**
314266 ATAAATTTTTAAAAATT
1 ATAAATTTAAAAAAATT
314283 ATAAATTTAAAAAAATT
1 ATAAATTTAAAAAAATT
314300 -TAAAT
1 ATAAAT
314305 ATATGATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAAATTTAAAAAAATT
Found at i:314585 original size:14 final size:13
Alignment explanation
Indices: 314566--314599 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
314556 TATTAATATA
314566 AAAATAATATTTT
1 AAAATAATATTTT
*
314579 AATAATATTATTTT
1 AA-AATAATATTTT
314593 AAAATAA
1 AAAATAA
314600 ATTACCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATAATATTTT
Found at i:314629 original size:2 final size:2
Alignment explanation
Indices: 314622--314674 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
314612 CTTAAACTCA
314622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
314664 AT AT AT AT AT A
1 AT AT AT AT AT A
314675 AAATTCAAGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:316943 original size:2 final size:2
Alignment explanation
Indices: 316936--316993 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
316926 TTAGTAGAAG
316936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
316978 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
316994 GGAGACAACA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:323901 original size:79 final size:80
Alignment explanation
Indices: 323760--323922 Score: 256
Period size: 79 Copynumber: 2.0 Consensus size: 80
323750 TGTTGAAATA
* * * *
323760 TCAACAACTACTTTAAGGTTCTAGAATTTTCTCATCAAATCTTTGTTTTTAGTTCTAAAAGTGTC
1 TCAACAACTACTCTAAGATTCTAGAATTTTCTCATCAAATCCTTGTTTTTAATTCTAAAAGTGTC
323825 TATCTAGAATACTCT
66 TATCTAGAATACTCT
* *
323840 TCAA-AACTACTCTAATATTCTAGAATTTTCTCATCAAATCCTTGTTTTTAATTCTAGAAGTGTC
1 TCAACAACTACTCTAAGATTCTAGAATTTTCTCATCAAATCCTTGTTTTTAATTCTAAAAGTGTC
*
323904 TATTTAGAATACTCT
66 TATCTAGAATACTCT
323919 TCAA
1 TCAA
323923 TCTCTTACTT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
79 72 0.95
80 4 0.05
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (80 bp):
TCAACAACTACTCTAAGATTCTAGAATTTTCTCATCAAATCCTTGTTTTTAATTCTAAAAGTGTC
TATCTAGAATACTCT
Found at i:329283 original size:45 final size:45
Alignment explanation
Indices: 329202--329293 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 45
329192 TGCTATTTAT
* *
329202 TTCTGTTATGTTTAGGTCTAGAATCCGACCTCATAGTTTAGGATA
1 TTCTGTTATGTTTAGGTCTAGAAGCCGAACTCATAGTTTAGGATA
* * * *
329247 TTCTTTTATGTTTTGGTCTAG-AGCCTGAACTTATAGTTTAGTATA
1 TTCTGTTATGTTTAGGTCTAGAAGCC-GAACTCATAGTTTAGGATA
329292 TT
1 TT
329294 GCTTAAGCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
44 3 0.08
45 37 0.93
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (45 bp):
TTCTGTTATGTTTAGGTCTAGAAGCCGAACTCATAGTTTAGGATA
Found at i:330568 original size:4 final size:4
Alignment explanation
Indices: 330559--330593 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
330549 TATCAAAGGA
*
330559 AAAT AAAT AAAT AAAT AAAT AAAC AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
330594 AGCCTCCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:331041 original size:21 final size:23
Alignment explanation
Indices: 331004--331051 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
330994 AATTAAAGAT
331004 ATTTTTTTAATCAT-A-ATTTAA
1 ATTTTTTTAATCATAATATTTAA
*
331025 ATTTTTTTATAT-TTAATATTTAA
1 ATTTTTTTA-ATCATAATATTTAA
331048 ATTT
1 ATTT
331052 AAAATAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 10 0.43
22 3 0.13
23 10 0.43
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTTTTTAATCATAATATTTAA
Found at i:335906 original size:20 final size:19
Alignment explanation
Indices: 335883--335935 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
335873 TATTTCAAGC
*
335883 ATGTATCGATACATTCACTT
1 ATGTATCGATACA-TCACCT
** *
335903 ATGTATTAATATATCACCT
1 ATGTATCGATACATCACCT
335922 ATTGTATCGATACA
1 A-TGTATCGATACA
335936 AATTATAAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACATCACCT
Found at i:336770 original size:24 final size:25
Alignment explanation
Indices: 336718--336770 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
336708 ATATCCTTAC
* *
336718 ATTTATATATTTTAATATAAATTTT
1 ATTTATATATTTTAATATAAATATA
336743 ATTTA-ATATTTTAATA-AAATAATA
1 ATTTATATATTTTAATATAAAT-ATA
336767 ATTT
1 ATTT
336771 TATCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.16
24 16 0.64
25 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTTATATATTTTAATATAAATATA
Found at i:338044 original size:2 final size:2
Alignment explanation
Indices: 338037--338064 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
338027 AGAAAGATGC
338037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
338065 GCTTCCACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:338431 original size:6 final size:7
Alignment explanation
Indices: 338401--338438 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
338391 CAAAATTTTA
338401 TAAATTT
1 TAAATTT
338408 TAAATTT
1 TAAATTT
*
338415 TAAAGTT
1 TAAATTT
338422 TAAA-TT
1 TAAATTT
338428 TAAA-TT
1 TAAATTT
338434 TAAAT
1 TAAAT
338439 GTTATGCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (7 bp):
TAAATTT
Found at i:338866 original size:5 final size:5
Alignment explanation
Indices: 338852--338966 Score: 69
Period size: 5 Copynumber: 22.6 Consensus size: 5
338842 CGCATACGAA
* * *
338852 AATAT TATAT AATAT AAAAT AATATT AATAT AATAT GATAT AA-ATT ATATAT
1 AATAT AATAT AATAT AATAT AATA-T AATAT AATAT AATAT AATA-T A-ATAT
** * *
338904 AATAT TTTA- AATAT AATTAT ATTAT CAA-AT AATAT AAATAT GATAT
1 AATAT AATAT AATAT AA-TAT AATAT -AATAT AATAT -AATAT AATAT
338950 AA-AT AA-ATT AATAT AAT
1 AATAT AATA-T AATAT AAT
338967 TATTAATTTG
Statistics
Matches: 85, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
4 10 0.12
5 55 0.65
6 19 0.22
7 1 0.01
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:338881 original size:26 final size:27
Alignment explanation
Indices: 338854--338919 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 27
338844 CATACGAAAA
338854 TATTATATAATATAAAATAATAT-TAA
1 TATTATATAATATAAAATAATATATAA
* * *
338880 TATAATATGATAT-AAATTATATATAA
1 TATTATATAATATAAAATAATATATAA
*
338906 TATTTTA-AATATAA
1 TATTATATAATATAA
338920 TTATATTATC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 12 0.38
26 20 0.62
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TATTATATAATATAAAATAATATATAA
Found at i:338882 original size:16 final size:17
Alignment explanation
Indices: 338850--338944 Score: 55
Period size: 16 Copynumber: 6.0 Consensus size: 17
338840 TCCGCATACG
*
338850 AAAATATTATATAATAT
1 AAAATAATATATAATAT
338867 AAAATAATAT-TAATAT
1 AAAATAATATATAATAT
* *
338883 AATATGATATA-AAT-T
1 AAAATAATATATAATAT
*
338898 ATATATAATAT-T--T-T
1 A-AAATAATATATAATAT
*
338912 AAATATAAT-TATATTAT
1 AAA-ATAATATATAATAT
*
338929 CAAATAATATA-AATAT
1 AAAATAATATATAATAT
338945 GATATAAATA
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
13 2 0.03
14 9 0.15
15 2 0.03
16 35 0.56
17 14 0.23
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (17 bp):
AAAATAATATATAATAT
Found at i:338884 original size:21 final size:20
Alignment explanation
Indices: 338852--338966 Score: 87
Period size: 21 Copynumber: 5.7 Consensus size: 20
338842 CGCATACGAA
338852 AATATT-ATATAATATAAAAT
1 AATATTAATATAATAT-AAAT
*
338872 AATATTAATATAATATGATAT
1 AATATTAATATAATAT-AAAT
**
338893 AA-ATTATATATAATAT-TTT
1 AATATTA-ATATAATATAAAT
*
338912 AA-ATATAATTATATTATCAAAT
1 AATAT-TAA-TATAATAT-AAAT
* *
338934 AATATAAATATGATATAAAT
1 AATATTAATATAATATAAAT
338954 AA-ATTAATATAAT
1 AATATTAATATAAT
338967 TATTAATTTG
Statistics
Matches: 77, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
19 16 0.21
20 25 0.32
21 29 0.38
22 5 0.06
23 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (20 bp):
AATATTAATATAATATAAAT
Found at i:338914 original size:19 final size:20
Alignment explanation
Indices: 338875--338944 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 20
338865 ATAAAATAAT
*
338875 ATTA-ATATAATATGATATAA
1 ATTATATATAATATTAT-TAA
338895 ATTATATATAATATT-TTAA
1 ATTATATATAATATTATTAA
* *
338914 A-TATA-ATTATATTATCAA
1 ATTATATATAATATTATTAA
*
338932 ATAATATA-AATAT
1 ATTATATATAATAT
338945 GATATAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 7 0.17
18 8 0.20
19 11 0.27
20 6 0.15
21 9 0.22
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (20 bp):
ATTATATATAATATTATTAA
Found at i:339366 original size:22 final size:21
Alignment explanation
Indices: 339341--339409 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 21
339331 ATTAATTATG
339341 TATATTTTAATTTTTTTGAATT
1 TATATTTTAATTTTTTT-AATT
**
339363 TATATTATTAATTTATTTTTAACA
1 TATATT-TTAA-TT-TTTTTAATT
339387 TATAATTTTAATATTTTTTAATT
1 TAT-ATTTTAAT-TTTTTTAATT
339410 ATTTATTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
22 6 0.16
23 12 0.32
24 12 0.32
25 8 0.21
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (21 bp):
TATATTTTAATTTTTTTAATT
Found at i:339390 original size:24 final size:22
Alignment explanation
Indices: 339341--339407 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 22
339331 ATTAATTATG
* **
339341 TATATTTTAATTTTTTTGAATT
1 TATATTTTAATTTTTTTTAACA
339363 TATATTATTAATTTATTTTTAACA
1 TATATT-TTAATTT-TTTTTAACA
*
339387 TATAATTTTAATATTTTTTAA
1 TAT-ATTTTAATTTTTTTTAA
339408 TTATTTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
22 6 0.16
23 14 0.37
24 15 0.39
25 3 0.08
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (22 bp):
TATATTTTAATTTTTTTTAACA
Found at i:339824 original size:22 final size:22
Alignment explanation
Indices: 339799--339840 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
339789 AAATTATATT
339799 ATTAAATT-TTTATTATTAATAA
1 ATTAAATTATTTA-TATTAATAA
339821 ATTAAATTATTTATATTAAT
1 ATTAAATTATTTATATTAAT
339841 TTTATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTAAATTATTTATATTAATAA
Found at i:340085 original size:19 final size:19
Alignment explanation
Indices: 340003--340085 Score: 51
Period size: 19 Copynumber: 4.2 Consensus size: 19
339993 GATTTAATTT
340003 ATTAATAATAAAATTTTAATA
1 ATTAATAAT-AAA-TTTAATA
* *
340024 ATTTAATTAAAAAAATTAA-A
1 A-TTAA-TAATAAATTTAATA
* * * * *
340044 ATTTTATAACATATATAAAA
1 A-TTAATAATAAATTTAATA
340064 ATTAATAATAAATTTAATA
1 ATTAATAATAAATTTAATA
340083 ATT
1 ATT
340086 TAAAATATAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
19 24 0.51
20 8 0.17
21 5 0.11
22 7 0.15
23 3 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTAATAATAAATTTAATA
Found at i:340497 original size:14 final size:13
Alignment explanation
Indices: 340468--340512 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
340458 ATTGTTAATC
340468 AAAATTATAAATTT
1 AAAATTA-AAATTT
*
340482 AAGATTAAAATATT
1 AAAATTAAAAT-TT
*
340496 AAAATTAAATTTT
1 AAAATTAAAATTT
340509 AAAA
1 AAAA
340513 ATTGATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:343017 original size:36 final size:35
Alignment explanation
Indices: 342976--343048 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
342966 AAATATTTTT
342976 AATTAAAAATATTAATTAATACA-TATAATAT-ATAAA
1 AATTAAAAATA-T-ATTAATA-ATTATAATATAATAAA
* *
343012 AATTAAAACTATATTTATAATTATAATATAATAAA
1 AATTAAAAATATATTAATAATTATAATATAATAAA
343047 AA
1 AA
343049 AAATATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
33 1 0.03
34 14 0.42
35 8 0.24
36 10 0.30
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (35 bp):
AATTAAAAATATATTAATAATTATAATATAATAAA
Found at i:343223 original size:23 final size:21
Alignment explanation
Indices: 343170--343226 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 21
343160 ACGTTTTAAA
343170 TTATTAAATTTAAAATTAATTT
1 TTATTAAA-TTAAAATTAATTT
343192 TTATATAAATTAAAATTTTTAA-TT
1 TTAT-TAAATTAAAA---TTAATTT
343216 TTATTAAATTA
1 TTATTAAATTA
343227 TATTTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 10 0.32
23 11 0.35
24 6 0.19
25 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATTAAATTAAAATTAATTT
Found at i:343254 original size:16 final size:15
Alignment explanation
Indices: 343213--343256 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
343203 AAAATTTTTA
*
343213 ATTTTATTAAATTAT
1 ATTTTAATAAATTAT
*
343228 ATTTTAA-AAATTTT
1 ATTTTAATAAATTAT
343242 ATTATTAATAAATTA
1 ATT-TTAATAAATTA
343257 AATTAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.38
15 10 0.42
16 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTAATAAATTAT
Found at i:349471 original size:45 final size:45
Alignment explanation
Indices: 349401--349489 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
349391 TTTTTGAAAG
* *
349401 TTAATAGAGGTAATCTCAGTGTTTTAAAAAGAAATTAATTATCAC
1 TTAATAGAGGAAATCTCAGTATTTTAAAAAGAAATTAATTATCAC
**
349446 TTAATAGAGGAAATCTTGGTATTTTAAAAAGAAATTAATTATCA
1 TTAATAGAGGAAATCTCAGTATTTTAAAAAGAAATTAATTATCA
349490 ATTATTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (45 bp):
TTAATAGAGGAAATCTCAGTATTTTAAAAAGAAATTAATTATCAC
Found at i:351024 original size:3 final size:3
Alignment explanation
Indices: 351018--351049 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
351008 TTATTATTAT
*
351018 TAG TAG TAG TGG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
351050 TTACTAGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:351057 original size:12 final size:12
Alignment explanation
Indices: 351030--351091 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
351020 GTAGTAGTGG
* *
351030 TAGTAGTAGTAG
1 TAGTAGTATTAC
351042 TAGTAGTATTAC
1 TAGTAGTATTAC
* *
351054 TAGTATTATTAT
1 TAGTAGTATTAC
351066 TAGT-GTTATTAC
1 TAGTAG-TATTAC
* *
351078 TATTACTATTAC
1 TAGTAGTATTAC
351090 TA
1 TA
351092 TTACTATTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (12 bp):
TAGTAGTATTAC
Found at i:351081 original size:6 final size:6
Alignment explanation
Indices: 351072--351100 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
351062 TTATTAGTGT
351072 TATTAC TATTAC TATTAC TATTAC TATTA
1 TATTAC TATTAC TATTAC TATTAC TATTA
351101 TCGTGCAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (6 bp):
TATTAC
Found at i:357951 original size:18 final size:18
Alignment explanation
Indices: 357928--358008 Score: 69
Period size: 18 Copynumber: 4.6 Consensus size: 18
357918 TTTTTTATAA
357928 TTATATAATATATTAATT
1 TTATATAATATATTAATT
* *
357946 TTATAT-ATGAGA-TCATT
1 TTATATAAT-ATATTAATT
* * *
357963 TT-TATCATAAATTAACT
1 TTATATAATATATTAATT
**
357980 TTCGATAATATATTAATT
1 TTATATAATATATTAATT
357998 TTATATAATAT
1 TTATATAATAT
358009 TATGTTATAA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
16 5 0.10
17 15 0.31
18 28 0.58
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.51
Consensus pattern (18 bp):
TTATATAATATATTAATT
Found at i:358057 original size:7 final size:7
Alignment explanation
Indices: 358045--358090 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
358035 TAAGTTATTT
358045 AAAATTA
1 AAAATTA
358052 AAAATTA
1 AAAATTA
358059 AGAAA--A
1 A-AAATTA
358065 AAATATTA
1 AAA-ATTA
358073 AATAATTA
1 AA-AATTA
358081 AAAATTA
1 AAAATTA
358088 AAA
1 AAA
358091 TTTTTAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 2 0.06
6 3 0.09
7 16 0.47
8 12 0.35
9 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (7 bp):
AAAATTA
Found at i:358393 original size:33 final size:32
Alignment explanation
Indices: 358356--358426 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 32
358346 AATACGATAC
* *
358356 ATATTTAAATATATTATATTA-ATTTTATTAATT
1 ATATTTAAATATATCATATTATA-TTTATT-ATA
*
358389 ATATTTAAATATGTCATATTATATTTATTATA
1 ATATTTAAATATATCATATTATATTTATTATA
358421 ATATTT
1 ATATTT
358427 TTATATGGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 8 0.24
33 25 0.74
34 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (32 bp):
ATATTTAAATATATCATATTATATTTATTATA
Found at i:358424 original size:12 final size:12
Alignment explanation
Indices: 358409--358459 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
358399 ATGTCATATT
358409 ATATTTATTATA
1 ATATTTATTATA
358421 ATATTT-TTAT-
1 ATATTTATTATA
* **
358431 ATGGTAAATTATA
1 AT-ATTTATTATA
358444 ATATTTATTATA
1 ATATTTATTATA
358456 ATAT
1 ATAT
358460 AATAGTAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
10 2 0.07
11 5 0.17
12 21 0.70
13 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
ATATTTATTATA
Found at i:358433 original size:32 final size:34
Alignment explanation
Indices: 358371--358459 Score: 85
Period size: 35 Copynumber: 2.6 Consensus size: 34
358361 TAAATATATT
* *
358371 ATATTA-ATTTTATTAATTATATTTAAATAT-GT-C
1 ATATTATA-TTTATT-ATAATATTTAAATATGGTAA
**
358404 ATATTATATTTATTATAATATTTTTATATGGTAA
1 ATATTATATTTATTATAATATTTAAATATGGTAA
*
358438 ATTATAATATTTATTATAATAT
1 A-TATTATATTTATTATAATAT
358460 AATAGTAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
32 12 0.26
33 14 0.30
34 2 0.04
35 19 0.40
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (34 bp):
ATATTATATTTATTATAATATTTAAATATGGTAA
Found at i:359908 original size:73 final size:74
Alignment explanation
Indices: 359790--359951 Score: 247
Period size: 74 Copynumber: 2.2 Consensus size: 74
359780 ATATTGTCTA
*
359790 ATCATG-TTGTGTTCAAGATTATTAAATCTAATTGATACTATTC-AAATAACTTCAAATTTTGAA
1 ATCATGTTTGTGTTCAAGATTATTAAATCTAATTGATACTATTCAAAAAAACTTCAAATTTTGAA
*
359853 TCATGTGTC
66 TCATGTATC
* * *
359862 ATCATGTTTGTGTTCGAGATTATTAAATCTAATTGATATTATTCAAAAAAACTTCAAATTTTGAG
1 ATCATGTTTGTGTTCAAGATTATTAAATCTAATTGATACTATTCAAAAAAACTTCAAATTTTGAA
359927 TCATGTATC
66 TCATGTATC
* *
359936 GTCATGTTTGTATTCA
1 ATCATGTTTGTGTTCA
359952 TGACATGTTA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
72 6 0.08
73 35 0.44
74 39 0.49
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (74 bp):
ATCATGTTTGTGTTCAAGATTATTAAATCTAATTGATACTATTCAAAAAAACTTCAAATTTTGAA
TCATGTATC
Found at i:360048 original size:29 final size:27
Alignment explanation
Indices: 359985--360056 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
359975 AAAATTTAGC
* *
359985 ATATTATTTATTTATGTTGTTTTCATT
1 ATATTTTTTATTTATGTTGTTTTAATT
*
360012 TTATTTTTTATATTATGTAATGTTTTAATT
1 ATATTTTTTAT-TTATGT--TGTTTTAATT
*
360042 AT-TTTTTTATGTATG
1 ATATTTTTTATTTATG
360057 CATCACGTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
27 9 0.24
28 10 0.27
29 8 0.22
30 10 0.27
ACGTcount: A:0.24, C:0.01, G:0.08, T:0.67
Consensus pattern (27 bp):
ATATTTTTTATTTATGTTGTTTTAATT
Found at i:360448 original size:16 final size:16
Alignment explanation
Indices: 360427--360457 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
360417 ACCCTTTAAA
*
360427 AATTATATTATAAAAT
1 AATTATAATATAAAAT
360443 AATTATAATATAAAA
1 AATTATAATATAAAA
360458 CTATATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTATAATATAAAAT
Found at i:363603 original size:17 final size:19
Alignment explanation
Indices: 363566--363601 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
363556 TATAATTTTT
363566 TAAATATATTTATATCAAA
1 TAAATATATTTATATCAAA
*
363585 TAAATATTTTTAT-TCAA
1 TAAATATATTTATATCAA
363602 TATTTATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAATATATTTATATCAAA
Found at i:363832 original size:3 final size:3
Alignment explanation
Indices: 363824--363856 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
363814 GTTCTTGAAC
363824 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
363857 GGTAGAGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:364186 original size:17 final size:17
Alignment explanation
Indices: 364139--364186 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
364129 TGGATTTTAA
* *
364139 TTTAATTAATTTATTTTT
1 TTTAA-TAATTAAATTTT
* *
364157 TTTAAGAAATAAATTTT
1 TTTAATAATTAAATTTT
364174 TTTAATAATTAAA
1 TTTAATAATTAAA
364187 GTTATCTGAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAATAATTAAATTTT
Found at i:365367 original size:2 final size:2
Alignment explanation
Indices: 365318--365359 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
365308 TTTAAAAGAT
*
365318 TA TA TA T- TA TA T- TCA TA TA TA AA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
365359 T
1 T
365360 CGTATATACG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 32 0.91
3 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:365656 original size:17 final size:17
Alignment explanation
Indices: 365613--365668 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
365603 TTCCTTTTTT
365613 TATAATTATTATATATTAA
1 TATAA-TATTATATA-TAA
365632 -AT-ATATTATA-ATAGA
1 TATAATATTATATATA-A
365647 TATAATATTATATATAA
1 TATAATATTATATATAA
365664 TATAA
1 TATAA
365669 AAATATACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.06
15 2 0.06
16 9 0.27
17 15 0.45
18 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TATAATATTATATATAA
Found at i:366022 original size:5 final size:5
Alignment explanation
Indices: 366007--366235 Score: 89
Period size: 5 Copynumber: 44.2 Consensus size: 5
365997 TTTTAATCAT
*
366007 TTATGA TTATA TTATA TGTTATA TATATA TTATA TTATA -TATTA TACATA
1 TTAT-A TTATA TTATA --TTATA T-TATA TTATA TTATA TTA-TA T-TATA
** * * *
366057 TTATA TTATATA TTATA TATATA ACATA TAATA ATATA -TATA ATATAA
1 TTATA -T-TATA TTATA T-TATA TTATA TTATA TTATA TTATA TTAT-A
** * * * * * *
366105 CAATA TATATA ATATAA TAATA TAATA TCATA TATATA ATATA ATATA
1 TTATA T-TATA TTAT-A TTATA TTATA TTATA T-TATA TTATA TTATA
* * *
366153 TAATA ATATA TAATA TTATA TTATA -T-TA TTATA TTATA --ATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
366199 -TATCA -TACTA TTATA TTATTA TTAT- TTATA TATATA T
1 TTAT-A TTA-TA TTATA TTA-TA TTATA TTATA T-TATA T
366236 CTCTTATATA
Statistics
Matches: 174, Mismatches: 25, Indels: 48
0.70 0.10 0.19
Matches are distributed among these distances:
3 5 0.03
4 15 0.09
5 101 0.58
6 43 0.25
7 10 0.06
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (5 bp):
TTATA
Found at i:366033 original size:2 final size:2
Alignment explanation
Indices: 366014--366556 Score: 166
Period size: 2 Copynumber: 301.5 Consensus size: 2
366004 CATTTATGAT
*
366014 TA TA T- TA TA TG T- TA TA TA TA TA T- TA TA T- TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
366051 TA CA TA T- TA TA T- TA TA TA T- TA TA TA TA TA -A CA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
366088 TA -A TA TA TA TA -A TA TA -A CA -A TA TA TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
366124 -A TA TA -A TA TCA TA TA TA TA -A TA TA -A TA TA TA -A TA -A TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
366161 TA TA -A TA T- TA TA T- TA TA T- TA T- TA TA T- TA TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
366195 TA TA TA TCA TA CTA T- TA TA T- TA T- TA T- TA TT TA TA TA TA TA
1 TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
366235 TC TC T- TA TA TA TC TT TC TC T- TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
366274 -A TA T- TA TA T- TT TA TA GTA T- TA TA -A TC T- TA -A TA -A TC
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
366309 TA GTA TA TA -A TA TA TA T- TA -A TC TA AA TA T- TA TT TT TCA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
* * * * *
366349 TA AA T- TA TT TA T- TA TA TA TA TG TA T- TA TC TA TT TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
366386 TA -A TA TA TA -A CA TC TA -A TA TA TA TA -A TC TCA TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA -TA
* * *
366426 TA TA TA -A TA CTA TA TA TA -A TC TA TA GTA TA -A TA TC TA TA TT
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
** * *
366467 TA TA T- TA TA CG TGA TA TA T- TA TA TA TC TC TA T- TA TA T- TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
366506 TT TA TA T- TA -A TA TA TA -A TA TA TA TA TA TA TA -A AA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
366543 TC TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA T
366557 TAATAATTAT
Statistics
Matches: 407, Mismatches: 52, Indels: 164
0.65 0.08 0.26
Matches are distributed among these distances:
1 71 0.17
2 317 0.78
3 19 0.05
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:366042 original size:23 final size:22
Alignment explanation
Indices: 366012--366296 Score: 129
Period size: 23 Copynumber: 13.3 Consensus size: 22
366002 ATCATTTATG
366012 ATTATATTATATGTTATATATAT
1 ATTATATTATAT-TTATATATAT
* *
366035 ATTATATTATATAT-TATACAT
1 ATTATATTATATTTATATATAT
366056 ATTATATTATATATTATATATAT
1 ATTATATTATAT-TTATATATAT
** * *
366079 AACATATAATA-ATATATATAAT
1 ATTATATTATATTTATATAT-AT
* * * *
366101 ATAACAATATATATA-ATATA-
1 ATTATATTATATTTATATATAT
* * *
366121 ATAATATAATA-TCATATATAT
1 ATTATATTATATTTATATATAT
* * *
366142 AATATAATATA-TAATA-ATAT
1 ATTATATTATATTTATATATAT
*
366162 ATAATATTATA-TTATATTATTAT
1 ATTATATTATATTTATA-TA-TAT
366185 ATTATA--ATATTATATATCATACT
1 ATTATATTATATT-TATAT-ATA-T
366208 ATTATATTAT-TATTAT-T-TAT
1 ATTATATTATAT-TTATATATAT
* *
366228 A-TATA-TATCTCTTATATATCT
1 ATTATATTATAT-TTATATATAT
* * *
366249 -TTCTCTTAATATATATATATAT
1 ATTATATT-ATATTTATATATAT
* *
366271 ATAATATTATATTT-TATA-GT
1 ATTATATTATATTTATATATAT
366291 ATTATA
1 ATTATA
366297 ATCTTAATAA
Statistics
Matches: 198, Mismatches: 41, Indels: 49
0.69 0.14 0.17
Matches are distributed among these distances:
18 3 0.02
19 10 0.05
20 38 0.19
21 50 0.25
22 33 0.17
23 57 0.29
24 4 0.02
25 3 0.02
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (22 bp):
ATTATATTATATTTATATATAT
Found at i:366062 original size:44 final size:44
Alignment explanation
Indices: 366015--366556 Score: 212
Period size: 44 Copynumber: 12.4 Consensus size: 44
366005 ATTTATGATT
* * *
366015 ATATTATATGTTATATATATATTATATTATATAT-TATACATATT
1 ATATTATATATAATATATATATTATATTATATATATATA-ATATA
* ** *
366059 ATATTATATATTATATATATAACATATAATAATATATATAATATA
1 ATATTATATATAATATATATATTATATTAT-ATATATATAATATA
* * * *
366104 ACAATATATATAATATA-ATAATATAATATCATATATATAATATA
1 ATATTATATATAATATATATATTATATTAT-ATATATATAATATA
*
366148 ATA-TATA-ATAATATATAATATTATATTATAT-TATTATATTATA
1 ATATTATATATAATATAT-ATATTATATTATATATA-TATAATATA
* *
366191 ATATTATATATCATACTATTATATTATTATTATTTATATAT-ATAT-
1 ATATTATATATAATA-TA-TATATTA-TATTATATATATATAATATA
* * * * * *
366236 CTCTTATATAT-CT-T-TCTCTTAATATATATATATATATAATATT
1 ATATTATATATAATATATATATT-ATAT-TATATATATATAATATA
* * * * *
366279 ATATTTTATAGTATTATA-ATCTTA-ATAATCTAGTATATAATAT-
1 ATATTATATA-TAATATATATATTATATTATATA-TATATAATATA
* * *
366322 ATATTA-ATCTAA-ATAT-TATT-T-TTCATATA-A-ATTATTTA
1 ATATTATATATAATATATATATTATATT-ATATATATATAATATA
* * * * *
366360 TTATATATATGTATTATCTAT-TTA-ATTA-ATATATA-ACATCTA
1 ATAT-TATATATAATATATATATTATATTATATATATATA-ATATA
* *
366402 ATA-TATATA-ATCTCATATATACTATA-TATA-ATACTAT-ATATA
1 ATATTATATATA-AT-ATATATATTATATTATATATA-TATAATATA
* * *
366444 AT-CTATAGTATAATATCTATATTTATATTATACGTGATATATTATAT-
1 ATATTATA-TATAATATATATA-TTATATTATA--T-ATATATAATATA
* * * *
366491 ATCTCTAT-TATATTATTTATATTAATATATAATATATATATATATAAA
1 ATAT-TATATATAATATATATATT-ATAT-T-ATATATATATA-ATATA
* *
366539 ATAATCTATATAATATAT
1 ATATTATATATAATATAT
366557 TAATAATTAT
Statistics
Matches: 375, Mismatches: 65, Indels: 112
0.68 0.12 0.20
Matches are distributed among these distances:
37 5 0.01
38 4 0.01
39 4 0.01
40 30 0.08
41 25 0.07
42 50 0.13
43 44 0.12
44 84 0.22
45 38 0.10
46 28 0.07
47 37 0.10
48 20 0.05
49 6 0.02
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (44 bp):
ATATTATATATAATATATATATTATATTATATATATATAATATA
Found at i:366093 original size:17 final size:16
Alignment explanation
Indices: 366073--366178 Score: 99
Period size: 17 Copynumber: 6.4 Consensus size: 16
366063 TATATATTAT
366073 ATATATAACATATAATA
1 ATATATAA-ATATAATA
*
366090 ATATATATAATATAACA
1 ATATATA-AATATAATA
366107 ATATATATAATATAATA
1 ATATATA-AATATAATA
*
366124 ATATAATATCATATATATA
1 ATAT-ATA-AATATA-ATA
*
366143 ATATA-ATATATAATA
1 ATATATAAATATAATA
*
366158 ATATAT-AATATTATA
1 ATATATAAATATAATA
*
366173 TTATAT
1 ATATAT
366179 TATTATATTA
Statistics
Matches: 78, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
15 20 0.26
16 5 0.06
17 35 0.45
18 11 0.14
19 7 0.09
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATAAATATAATA
Found at i:366120 original size:34 final size:35
Alignment explanation
Indices: 366027--366201 Score: 128
Period size: 35 Copynumber: 5.0 Consensus size: 35
366017 ATTATATGTT
* * *
366027 ATATATATATTATAT-TATATATTATACATAT-TATA
1 ATATATACAATATATATA-ATATAATA-ATATATATA
* **
366062 TTATATATTATATATATAACATATAATAATATATATA
1 ATATATACAATATATAT-A-ATATAATAATATATATA
*
366099 ATATA-ACAATATATATAATATAATAATATAATATC
1 ATATATACAATATATATAATATAATAATAT-ATATA
*
366134 ATATATATAATATA-AT-ATATAATAATATATAATA
1 ATATATACAATATATATAATATAATAATATAT-ATA
* * * * *
366168 TTATATTATATTAT-TATATTATAATATTATATAT
1 ATATA-TACAATATATATAATATAATAATATATAT
366202 CATACTATTA
Statistics
Matches: 116, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
33 2 0.02
34 30 0.26
35 35 0.30
36 33 0.28
37 16 0.14
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (35 bp):
ATATATACAATATATATAATATAATAATATATATA
Found at i:366427 original size:21 final size:23
Alignment explanation
Indices: 366403--366465 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 23
366393 TAACATCTAA
366403 TATATATAATCTCATATAT-A-C
1 TATATATAATCTCATATATAATC
366424 TATATATAATACT-ATATATAATC
1 TATATATAAT-CTCATATATAATC
*
366447 TATAGTATAATATC-TATAT
1 TATA-TATAATCTCATATAT
366466 TTATATTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 16 0.44
22 3 0.08
23 11 0.31
24 6 0.17
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (23 bp):
TATATATAATCTCATATATAATC
Found at i:367853 original size:30 final size:30
Alignment explanation
Indices: 367813--367869 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
367803 AAGCATTTCT
*
367813 TATACAATTCAATACATCTATAAATTATAA
1 TATACAATTCAATACATATATAAATTATAA
* * *
367843 TATACGATTCATTACATATATGAATTA
1 TATACAATTCAATACATATATAAATTA
367870 CACATATTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.39
Consensus pattern (30 bp):
TATACAATTCAATACATATATAAATTATAA
Found at i:370109 original size:22 final size:22
Alignment explanation
Indices: 370083--370135 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
370073 ATGTAATATT
*
370083 TAATATATATACGT-ATTTATAA
1 TAATATATATACGTAAATT-TAA
*
370105 TAATAT-TAT-CTTAAATTTAA
1 TAATATATATACGTAAATTTAA
370125 TAATATATATA
1 TAATATATATA
370136 AAAAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 11 0.42
21 9 0.35
22 6 0.23
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (22 bp):
TAATATATATACGTAAATTTAA
Found at i:371497 original size:21 final size:22
Alignment explanation
Indices: 371447--371498 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
371437 TAATTATGTA
*
371447 ATTTATTATTATGATTAAATTT
1 ATTTATTATTATAATTAAATTT
* *
371469 AATT-TTATTATAATTAAGTTT
1 ATTTATTATTATAATTAAATTT
371490 -TTTATTATT
1 ATTTATTATT
371499 GCTGATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 20 0.80
22 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTTATTATTATAATTAAATTT
Found at i:372043 original size:21 final size:22
Alignment explanation
Indices: 371991--372045 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
371981 ATTAGTTATG
* *
371991 TAATGTGTTGTTATGATTAAATT
1 TAAT-TGTTATTATAATTAAATT
372014 TAATT-TTATTATAATTAAATT
1 TAATTGTTATTATAATTAAATT
*
372035 T-TTTGTTATTA
1 TAATTGTTATTA
372046 CTGACTAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 2 0.07
21 21 0.75
22 1 0.04
23 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (22 bp):
TAATTGTTATTATAATTAAATT
Found at i:372403 original size:538 final size:536
Alignment explanation
Indices: 371296--372613 Score: 1658
Period size: 540 Copynumber: 2.4 Consensus size: 536
371286 TCGGAGCTTG
* *
371296 AAACTCTTTCATTCATATAAA-AAAAAATTTACAATTTATATTTATGTTATTGTTAAAAAAATTT
1 AAACTCTTTCATTCATATAAAGAAAAAATTTAAAATTTATATTTATGTTGTTG-TAAAAAAATTT
* * * * * *
371360 TATTTAAGTTATAT-AAAGTTTTAAAGTTAAGTTTTATTTTTATTTTTATAAGTATTGTTATAAT
65 TGTTCAAGTTATATAAAAATTTTGAAGATAAGTTTTATTTTTATTTCTATAAGTATTGTTATAAT
*
371424 CTTAAAATATAATTAATTATGTAATTTATTATTATGATTAAATTTAATTTTATTATAATTAAGTT
130 CTTAAAATATAATTAATTATGTAATTTATTATTATGATTAAATTTAATTTTATTATAATTAAATT
* * *
371489 TTTTATTATTGCTGATTAA-AGTATAATTAATTTTATTTTTGGACGTGAGTTTTTAAAATTTTTT
195 TTTTATTATTGCTGACTAAGA-TATAATTAGTTTTA-TTTTGGACATGAG--TTT---ATTTTTT
* ** *
371553 TTTGTTTTTTTAAATTTATGAAGTTGAGAACTCGTCAATTACTAAATTTTTTTCTTGACTTTTTT
253 TTGGTTTTTTTAAA-TTATGAAGTTGAGAACTCACCAATTACTAAATTTTTTTCGTGACTTTTTT
* *
371618 CATAGTTTTTTTTTAAAAAATAATGAAGTTGAGAACTCGCCACTTTCCCAACATAGAAATTTTTT
317 CATAGTTTTTTTTT--AAAATAATGAAGTTGAGAACTCGCCACCTTCCCAACATAGAAATTCTTT
* * *
371683 TATATAAAAGTTTTTTATTTGTTAGCCCTTGAAGAGCCATTGACAAGGTCATGTCTACCAATTTT
380 TATATAAAAGTTTTTTATTTGTTAGCCCTTGAAGAGCAATAGACAAGGTCATGCCTACCAATTTT
* * *
371748 GTTGATAAGGATCACAGGTTTTGAGCCTATGACCTTTATTATTAAAGAGAAGCGGGAGATGAAAG
445 ATTGATAAGGATCACAGGTTCTGAGCCCATGACCTTTATTATTAAAGAGAAGCGGGAGATGAAAG
* *
371813 GGTTTTAAGCTCTATAAATAGAGCTCA
510 GGTTTCAAACTCTATAAATAGAGCTCA
*
371840 AAACTCTTTCATTCATATGAAAGAAAAAAGTTTAAAATTTATATTTGTGTTGTTGT-AAAAAATT
1 AAACTCTTTCATTCATAT-AAAGAAAAAA-TTTAAAATTTATATTTATGTTGTTGTAAAAAAATT
* * * *
371904 TTGTTCAGGTTATATAAAAATTTTGAAGATACGTTTTATTTTTATTTCTACAAATATTGTTATAA
64 TTGTTCAAGTTATATAAAAATTTTGAAGATAAGTTTTATTTTTATTTCTATAAGTATTGTTATAA
* * * * * *
371969 TTTTGAAATATAATTAGTTATGTAATGTGTTGTTATGATTAAATTTAATTTTATTATAATTAAAT
129 TCTTAAAATATAATTAATTATGTAATTTATTATTATGATTAAATTTAATTTTATTATAATTAAAT
* *
372034 TTTTTGTTATTACTGACTAAGATATAATTAGTTTTATTTTGGACATGAG-TT-TTTTTTTTGGTT
194 TTTTTATTATTGCTGACTAAGATATAATTAGTTTTATTTTGGACATGAGTTTATTTTTTTTGGTT
*
372097 TTTTTAAGA-TATGAGGTT-AGGAACTCACCAATTGA-TAAATATTTTTTCGTGACTTTTCTTTC
259 TTTTTAA-ATTATGAAGTTGA-GAACTCACCAATT-ACTAAAT-TTTTTTCGTGAC-TTT-TTTC
* * * * *
372159 GTAGTTTTTTTTT-AAGTAATGAAGTTGGGAACTCGTCACCTTCCCAATATA-AAATTCTTTTAT
318 ATAGTTTTTTTTTAAAATAATGAAGTTGAGAACTCGCCACCTTCCCAACATAGAAATTCTTTTAT
* * * ** * * *
372222 GTATAAATTTTTTTGTTTGTTAGCTTTTGGAGAGACAATAG-CAAGGTCGTGCCCTGCCAATTTT
383 ATA-AAAGTTTTTTATTTGTTAGCCCTTGAAGAG-CAATAGACAAGGTCATG-CCTACCAATTTT
* * * * *
372286 ATTGATAAAGG-TCACGGGTTCTGAGCCCATGATCTTTATTATTAAA-AGGGAGTGGGAGATGGA
445 ATTGAT-AAGGATCACAGGTTCTGAGCCCATGACCTTTATTATTAAAGA-GAAGCGGGAGATGAA
*
372349 AGGGTTTCAAACTCTATGAATAGAGCTCA
508 AGGGTTTCAAACTCTATAAATAGAGCTCA
* *
372378 AAACTCTTTCATTTATATAAAAGAAAAAAATTTAAAATTTATATTTATGTTGTTGTAAAAAAAAA
1 AAACTCTTTCATTCATAT-AAAG-AAAAAATTTAAAATTTATATTTATGTTGTTGT-AAAAAAAT
* * * *
372443 TTTGTTCACGTTATATAAAAATTTTGAAGGTATA-TTTTATTTTTATTTCTATAAGTATTATTTT
63 TTTGTTCAAGTTATATAAAAATTTTGAAGATA-AGTTTTATTTTTATTTCTATAAGTATTGTTAT
* *
372507 AATCTTAAAATATAATTAATTTTGTAATTTATTATTATGATTAAATTTAATTTTATTGTAATTAA
127 AATCTTAAAATATAATTAATTATGTAATTTATTATTATGATTAAATTTAATTTTATTATAATTAA
**
372572 ATTTTTTATTATTGCTGACTAAGGCATAATTAGTTTTATTTT
192 ATTTTTTATTATTGCTGACTAAGATATAATTAGTTTTATTTT
372614 TGAACTTGAT
Statistics
Matches: 672, Mismatches: 82, Indels: 44
0.84 0.10 0.06
Matches are distributed among these distances:
536 14 0.02
537 92 0.14
538 164 0.24
539 14 0.02
540 173 0.26
542 2 0.00
544 18 0.03
545 35 0.05
546 137 0.20
547 23 0.03
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (536 bp):
AAACTCTTTCATTCATATAAAGAAAAAATTTAAAATTTATATTTATGTTGTTGTAAAAAAATTTT
GTTCAAGTTATATAAAAATTTTGAAGATAAGTTTTATTTTTATTTCTATAAGTATTGTTATAATC
TTAAAATATAATTAATTATGTAATTTATTATTATGATTAAATTTAATTTTATTATAATTAAATTT
TTTATTATTGCTGACTAAGATATAATTAGTTTTATTTTGGACATGAGTTTATTTTTTTTGGTTTT
TTTAAATTATGAAGTTGAGAACTCACCAATTACTAAATTTTTTTCGTGACTTTTTTCATAGTTTT
TTTTTAAAATAATGAAGTTGAGAACTCGCCACCTTCCCAACATAGAAATTCTTTTATATAAAAGT
TTTTTATTTGTTAGCCCTTGAAGAGCAATAGACAAGGTCATGCCTACCAATTTTATTGATAAGGA
TCACAGGTTCTGAGCCCATGACCTTTATTATTAAAGAGAAGCGGGAGATGAAAGGGTTTCAAACT
CTATAAATAGAGCTCA
Found at i:372583 original size:21 final size:22
Alignment explanation
Indices: 372533--372585 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
372523 TAATTTTGTA
* *
372533 ATTTATTATTATGATTAAATTT
1 ATTTATTATTGTAATTAAATTT
*
372555 AATT-TTATTGTAATTAAATTT
1 ATTTATTATTGTAATTAAATTT
372576 -TTTATTATTG
1 ATTTATTATTG
372586 CTGACTAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 21 0.81
22 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (22 bp):
ATTTATTATTGTAATTAAATTT
Found at i:372629 original size:538 final size:532
Alignment explanation
Indices: 371296--372629 Score: 1605
Period size: 538 Copynumber: 2.5 Consensus size: 532
371286 TCGGAGCTTG
* *
371296 AAACTCTTTCATTCATAT-AA-AAAAAAATTTACAATTTATATTTATGTTATTGTTAAAAAAATT
1 AAACTCTTTCATTCATATAAAGAAAAAAATTTAAAATTTATATTTATGTTGTTG-TAAAAAAATT
* * * * * *
371359 TTATTTAAGTTATAT-AAAGTTTTAAAGTTAAGTTTTATTTTTATTTTTATAAGTATTGTTATAA
65 TTGTTCAAGTTATATAAAAATTTTGAAGATAA-TTTTATTTTTATTTCTATAAGTATTGTTATAA
*
371423 TCTTAAAATATAATTAATTATGTAATTTATTATTATGATTAAATTTAATTTTATTATAATTAAGT
129 TCTTAAAATATAATTAATTATGTAATTTATTATTATGATTAAATTTAATTTTATTATAATTAAAT
* * * * *
371488 TTTTTATTATTGCTGATTAAAGTATAATTAATTTTATTTTTGGACGTGAGTTTTTAAAATTTTTT
194 TTTTTATTATTGCTGACTAAGGTATAATTAGTTTTATTTTT-GA----A---CTT--GATTTTTT
* ** *
371553 TTTGTTTTTTTAAATTTATGAAGTTGAGAACTCGTCAATTACTAAATTTTTTTCTTGACTTTTTT
249 TTGGTTTTTTTAAA-TTATGAAGTTGAGAACTCACCAATTACTAAATTTTTTTCGTGACTTTTTT
* *
371618 CATAGTTTTTTTTTAAAAAATAATGAAGTTGAGAACTCGCCACTTTCCCAACATAGAAATTTTTT
313 CATAGTTTTTTTTT--AAAATAATGAAGTTGAGAACTCGCCACCTTCCCAACATAGAAATTCTTT
* * *
371683 TATATAAAAGTTTTTTATTTGTTAGCCCTTGAAGAGCCATTGACAAGGTCATGTCTACCAATTTT
376 TATATAAAAGTTTTTTATTTGTTAGCCCTTGAAGAGCAATAGACAAGGTCATGCCTACCAATTTT
* * *
371748 GTTGATAAGGATCACAGGTTTTGAGCCTATGACCTTTATTATTAAAGAGAAGCGGGAGATGAAAG
441 ATTGATAAGGATCACAGGTTCTGAGCCCATGACCTTTATTATTAAAGAGAAGCGGGAGATGAAAG
* *
371813 GGTTTTAAGCTCTATAAATAGAGCTCA
506 GGTTTCAAACTCTATAAATAGAGCTCA
* *
371840 AAACTCTTTCATTCATATGAAAGAAAAAAGTTTAAAATTTATATTTGTGTTGTTGT-AAAAAATT
1 AAACTCTTTCATTCATAT-AAAGAAAAAAATTTAAAATTTATATTTATGTTGTTGTAAAAAAATT
* * * *
371904 TTGTTCAGGTTATATAAAAATTTTGAAGATACGTTTTATTTTTATTTCTACAAATATTGTTATAA
65 TTGTTCAAGTTATATAAAAATTTTGAAGATA-ATTTTATTTTTATTTCTATAAGTATTGTTATAA
* * * * * *
371969 TTTTGAAATATAATTAGTTATGTAATGTGTTGTTATGATTAAATTTAATTTTATTATAATTAAAT
129 TCTTAAAATATAATTAATTATGTAATTTATTATTATGATTAAATTTAATTTTATTATAATTAAAT
* * * * *
372034 TTTTTGTTATTACTGACTAAGATATAATTAGTTTTA-TTTTGGACATGAGTTTTTTTTTTGGTTT
194 TTTTTATTATTGCTGACTAAGGTATAATTAGTTTTATTTTTGAACTTGA---TTTTTTTTGGTTT
* *
372098 TTTTAAGA-TATGAGGTT-AGGAACTCACCAATTGA-TAAATATTTTTTCGTGACTTTTCTTTCG
256 TTTTAA-ATTATGAAGTTGA-GAACTCACCAATT-ACTAAAT-TTTTTTCGTGAC-TTT-TTTCA
* * * * *
372160 TAGTTTTTTTTT-AAGTAATGAAGTTGGGAACTCGTCACCTTCCCAATATA-AAATTCTTTTATG
315 TAGTTTTTTTTTAAAATAATGAAGTTGAGAACTCGCCACCTTCCCAACATAGAAATTCTTTTATA
* * ** * * *
372223 TATAAATTTTTTTGTTTGTTAGCTTTTGGAGAGACAATAG-CAAGGTCGTGCCCTGCCAATTTTA
380 TA-AAAGTTTTTTATTTGTTAGCCCTTGAAGAG-CAATAGACAAGGTCATG-CCTACCAATTTTA
* * * * *
372287 TTGATAAAGG-TCACGGGTTCTGAGCCCATGATCTTTATTATTAAA-AGGGAGTGGGAGATGGAA
442 TTGAT-AAGGATCACAGGTTCTGAGCCCATGACCTTTATTATTAAAGA-GAAGCGGGAGATGAAA
*
372350 GGGTTTCAAACTCTATGAATAGAGCTCA
505 GGGTTTCAAACTCTATAAATAGAGCTCA
* *
372378 AAACTCTTTCATTTATATAAAAGAAAAAAATTTAAAATTTATATTTATGTTGTTGTAAAAAAAAA
1 AAACTCTTTCATTCATAT-AAAGAAAAAAATTTAAAATTTATATTTATGTTGTTGT-AAAAAAAT
* * * *
372443 TTTGTTCACGTTATATAAAAATTTTGAAGGTATATTTTATTTTTATTTCTATAAGTATTATTTTA
64 TTTGTTCAAGTTATATAAAAATTTTGAAGATA-ATTTTATTTTTATTTCTATAAGTATTGTTATA
* *
372508 ATCTTAAAATATAATTAATTTTGTAATTTATTATTATGATTAAATTTAATTTTATTGTAATTAAA
128 ATCTTAAAATATAATTAATTATGTAATTTATTATTATGATTAAATTTAATTTTATTATAATTAAA
*
372573 TTTTTTATTATTGCTGACTAAGGCATAATTAGTTTTATTTTTGAACTTGATTTTTTT
193 TTTTTTATTATTGCTGACTAAGGTATAATTAGTTTTATTTTTGAACTTGATTTTTTT
372630 ATTTATTTTT
Statistics
Matches: 676, Mismatches: 92, Indels: 50
0.83 0.11 0.06
Matches are distributed among these distances:
535 1 0.00
536 14 0.02
537 93 0.14
538 177 0.26
539 8 0.01
540 170 0.25
541 10 0.01
544 19 0.03
545 24 0.04
546 132 0.20
547 28 0.04
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (532 bp):
AAACTCTTTCATTCATATAAAGAAAAAAATTTAAAATTTATATTTATGTTGTTGTAAAAAAATTT
TGTTCAAGTTATATAAAAATTTTGAAGATAATTTTATTTTTATTTCTATAAGTATTGTTATAATC
TTAAAATATAATTAATTATGTAATTTATTATTATGATTAAATTTAATTTTATTATAATTAAATTT
TTTATTATTGCTGACTAAGGTATAATTAGTTTTATTTTTGAACTTGATTTTTTTTGGTTTTTTTA
AATTATGAAGTTGAGAACTCACCAATTACTAAATTTTTTTCGTGACTTTTTTCATAGTTTTTTTT
TAAAATAATGAAGTTGAGAACTCGCCACCTTCCCAACATAGAAATTCTTTTATATAAAAGTTTTT
TATTTGTTAGCCCTTGAAGAGCAATAGACAAGGTCATGCCTACCAATTTTATTGATAAGGATCAC
AGGTTCTGAGCCCATGACCTTTATTATTAAAGAGAAGCGGGAGATGAAAGGGTTTCAAACTCTAT
AAATAGAGCTCA
Found at i:373213 original size:12 final size:12
Alignment explanation
Indices: 373196--373234 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
373186 TTGAAAAATG
373196 TATTTTTTTTGT
1 TATTTTTTTTGT
373208 TATTTTTTTTGT
1 TATTTTTTTTGT
373220 T-TTTTTTATTGT
1 TATTTTTT-TTGT
373232 TAT
1 TAT
373235 GATTAGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.24
12 18 0.72
13 1 0.04
ACGTcount: A:0.10, C:0.00, G:0.08, T:0.82
Consensus pattern (12 bp):
TATTTTTTTTGT
Found at i:373331 original size:40 final size:40
Alignment explanation
Indices: 373242--373348 Score: 162
Period size: 41 Copynumber: 2.6 Consensus size: 40
373232 TATGATTAGC
*
373242 TTTGAAATTTATTATTATGATTAAATAAAAAATATAAATA
1 TTTGTAATTTATTATTATGATTAAATAAAAAATATAAATA
* *
373282 GTTTTTAATTTATTATTATGATTAAATAAAAAATAATTAAT-
1 -TTTGTAATTTATTATTATGATTAAATAAAAAAT-ATAAATA
373323 TTTGTAATTTATTATTATGATTAAAT
1 TTTGTAATTTATTATTATGATTAAAT
373349 TTAATTTTGG
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
40 25 0.41
41 31 0.51
42 5 0.08
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (40 bp):
TTTGTAATTTATTATTATGATTAAATAAAAAATATAAATA
Found at i:375426 original size:15 final size:16
Alignment explanation
Indices: 375387--375429 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
375377 AGATGAATTC
375387 ACTCAGGAAGAA-GCT
1 ACTCAGGAAGAAGGCT
*
375402 ACTCAAGAAGAAGGC-
1 ACTCAGGAAGAAGGCT
*
375417 ATTCAGGAAGAAG
1 ACTCAGGAAGAAG
375430 CATCGACGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 22 0.92
16 2 0.08
ACGTcount: A:0.44, C:0.16, G:0.28, T:0.12
Consensus pattern (16 bp):
ACTCAGGAAGAAGGCT
Found at i:375857 original size:88 final size:86
Alignment explanation
Indices: 375732--376519 Score: 597
Period size: 88 Copynumber: 8.9 Consensus size: 86
375722 ATAAAATTAA
* *
375732 TCTTGAAACTCGAAAGATGTGACAGATACATGAGGTATCAGATTTTTTCTGACATGATAGAAATT
1 TCTTGAAACTCGAAAGATGTGACA-ATGCATGAGGTATCAGATTTTTT-TGACATGATAGAAAAT
* *
375797 ATTTGACTAATACTTAATAAATT
64 ATTTGACTAATGCCTAATAAATT
* * * * * * * *
375820 TTTTGAAACCCGAAAGACGTAACGAATGCATGGGGTATCAAATTTCTTCTGACATTATAGAAAAT
1 TCTTGAAACTCGAAAGATGTGAC-AATGCATGAGGTATCAGATTT-TTTTGACATGATAGAAAAT
375885 ATTTGACTAATGCCTAATAAAGTT
64 ATTTGACTAATGCCTAATAAA-TT
* * ** * * * * *
375909 AATCTTAAAACTTGAAAGATACGATATATGCACGAGGTATCAAATTCCTTTTGACATGATAAAAA
1 --TCTTGAAACTCGAAAGATGTGACA-ATGCATGAGGTATCAGATT-TTTTTGACATGATAGAAA
* *
375974 ATATTTAACTAATTCCTAATAAATT
62 ATATTTGACTAATGCCTAATAAATT
* * * * * *
375999 TTTTAAAACTTGAAAGATGTGACAAATACATGGGGTATCAGATTCATTTTGACATGATAGAAAAT
1 TCTTGAAACTCGAAAGATGTGAC-AATGCATGAGGTATCAGATT-TTTTTGACATGATAGAAAAT
*
376064 ATTTGATTAATGCCTAATGAAATT
64 ATTTGACTAATGCCTAAT-AAATT
* * * *
376088 AATCTT-AGAACCCGAAAAATGTGACAAATACATGAGGTATCAGATTCTTTTTGACATGATAAAA
1 --TCTTGA-AACTCGAAAGATGTGAC-AATGCATGAGGTATCAGATT-TTTTTGACATGATAGAA
376152 AAT-TTTGACTAATGCCTAATAAATT
61 AATATTTGACTAATGCCTAATAAATT
* * * * * *
376177 TCTTGAAACCCAAAAGATATGACAGATGTATG-GAGTATCAGATTTATTCTT-ACAT-ACAAAAA
1 TCTTGAAACTCGAAAGATGTGACA-ATGCATGAG-GTATCAGATTT-TT-TTGACATGATAGAAA
* *
376239 ATATTTGACTAATGTCTCATAAATT
62 ATATTTGACTAATGCCTAATAAATT
* * * * ** * *
376264 TCTTGAAACTCAAAAAATGTGATAGATGCATTG-GGTATCAAATTCCTACTCGA-ATGACAGAAA
1 TCTTGAAACTCGAAAGATGTGACA-ATGCA-TGAGGTATCAGATT--TTTTTGACATGATAGAAA
* * *
376327 ATATTTAAGTAATGCTTAATAAAATTAAT
62 ATATTTGACTAATGCCTAAT-AAA-T--T
* ** * * *
376356 TTTTG-AACTCGAAAGATGTGACAAATGCATGAGGTATCAGATTTCTTTAAATATGACAAAAAAT
1 TCTTGAAACTCGAAAGATGTGAC-AATGCATGAGGTATCAGATTT-TTTTGACATGATAGAAAAT
**
376420 ATTTGACTAATATCTAATAAATT
64 ATTTGACTAATGCCTAATAAATT
* * * * *
376443 T-TATGGAAC-CTGAAAAATGTGACAGATGCATGAGGTATCAGATTCCTTTTAACATGACAGAAA
1 TCT-TGAAACTC-GAAAGATGTGACA-ATGCATGAGGTATCAGATT-TTTTTGACATGATAGAAA
376506 ATATTTGACTAATG
62 ATATTTGACTAATG
376520 ACACGATAAA
Statistics
Matches: 570, Mismatches: 94, Indels: 72
0.77 0.13 0.10
Matches are distributed among these distances:
86 12 0.02
87 102 0.18
88 225 0.39
89 22 0.04
90 28 0.05
91 175 0.31
92 6 0.01
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (86 bp):
TCTTGAAACTCGAAAGATGTGACAATGCATGAGGTATCAGATTTTTTTGACATGATAGAAAATAT
TTGACTAATGCCTAATAAATT
Found at i:376033 original size:179 final size:178
Alignment explanation
Indices: 375719--376519 Score: 719
Period size: 179 Copynumber: 4.5 Consensus size: 178
375709 ATAATATGTT
* * * *
375719 CTAATAAAATTAATCTTGAAACTCGAAAGATGTGACAGATACATGAGGTATCAGATT-TTTTCTG
1 CTAAT-AAATTAATCTTAAAACTCGAAAAATGTGACAGATACATGAGGTATCAAATTCCTTT-TG
* * * * * * * *
375783 ACATGATAGAAATTATTTGACTAATACTTAATAAATTTTTTGAAACCCGAAAGACGTAACGAATG
64 ACATGATAAAAAATATTTAACTAATGCCTAATAAATTTTTTGAAACCCGAAAGATGTGACAAATG
*
375848 CATGGGGTATCAAATTTCTTCTGACATTATAGAAAATATTTGACTAATGC
129 CATGGGGTATCAGATTTCTTCTGACATTATAGAAAATATTTGACTAATGC
* * ** * * * *
375898 CTAATAAAGTTAATCTTAAAACTTGAAAGATACGATATATGCACGAGGTATCAAATTCCTTTTGA
1 CTAATAAA-TTAATCTTAAAACTCGAAAAATGTGACAGATACATGAGGTATCAAATTCCTTTTGA
* * ** *
375963 CATGATAAAAAATATTTAACTAATTCCTAATAAATTTTTTAAAACTTGAAAGATGTGACAAATAC
65 CATGATAAAAAATATTTAACTAATGCCTAATAAATTTTTTGAAACCCGAAAGATGTGACAAATGC
* * *
376028 ATGGGGTATCAGA-TTCATTTTGACATGATAGAAAATATTTGATTAATGC
130 ATGGGGTATCAGATTTC-TTCTGACATTATAGAAAATATTTGACTAATGC
* * * * *
376077 CTAATGAAATTAATCTTAGAACCCGAAAAATGTGACAAATACATGAGGTATCAGATTCTTTTTGA
1 CTAAT-AAATTAATCTTAAAACTCGAAAAATGTGACAGATACATGAGGTATCAAATTCCTTTTGA
* * * * * *
376142 CATGATAAAAAAT-TTTGACTAATGCCTAATAAATTTCTTGAAACCCAAAAGATATGACAGATGT
65 CATGATAAAAAATATTTAACTAATGCCTAATAAATTTTTTGAAACCCGAAAGATGTGACAAATGC
* * * * * *
376206 ATGGAGTATCAGATTTATTCTTACA-TACAAAAAATATTTGACTAATGT
130 ATGGGGTATCAGATTTCTTCTGACATTATAGAAAATATTTGACTAATGC
* * * * * * *
376254 CTCATAAATT--TCTTGAAACTCAAAAAATGTGATAGATGCATTG-GGTATCAAATTCCTACTCG
1 CTAATAAATTAATCTTAAAACTCGAAAAATGTGACAGATACA-TGAGGTATCAAATTCCT-TTTG
* * * * *
376316 A-ATGACAGAAAATATTTAAGTAATGCTTAATAAAATTAATTTTTG-AACTCGAAAGATGTGACA
64 ACATGATAAAAAATATTTAACTAATGCCTAAT-AAA-T--TTTTTGAAACCCGAAAGATGTGACA
* * * * **
376379 AATGCATGAGGTATCAGATTTCTT-T-AAATATGACAAAAAATATTTGACTAATAT
125 AATGCATGGGGTATCAGATTTCTTCTGACAT-T-ATAGAAAATATTTGACTAATGC
* * ** * * * *
376433 CTAATAAATT-TTATGGAACCT-GAAAAATGTGACAGATGCATGAGGTATCAGATTCCTTTTAAC
1 CTAATAAATTAATCTTAAAACTCGAAAAATGTGACAGATACATGAGGTATCAAATTCCTTTTGAC
* * *
376496 ATGACAGAAAATATTTGACTAATG
66 ATGATAAAAAATATTTAACTAATG
376520 ACACGATAAA
Statistics
Matches: 506, Mismatches: 98, Indels: 36
0.79 0.15 0.06
Matches are distributed among these distances:
174 45 0.09
175 19 0.04
176 10 0.02
177 24 0.05
178 103 0.20
179 292 0.58
180 13 0.03
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (178 bp):
CTAATAAATTAATCTTAAAACTCGAAAAATGTGACAGATACATGAGGTATCAAATTCCTTTTGAC
ATGATAAAAAATATTTAACTAATGCCTAATAAATTTTTTGAAACCCGAAAGATGTGACAAATGCA
TGGGGTATCAGATTTCTTCTGACATTATAGAAAATATTTGACTAATGC
Found at i:378751 original size:79 final size:79
Alignment explanation
Indices: 378594--378815 Score: 225
Period size: 79 Copynumber: 2.8 Consensus size: 79
378584 TGAGAAATTT
* * * * * * *
378594 AATATTTTGGAGATAATAA-CGGGGTTGGAGCATCCCCTTAAAAATAATGGGGTTAGAGTATCCC
1 AATATTTAGGAAATAA-AACCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTAGAGTATCCC
** *
378658 CGGTTGTGAAAAATC
65 CAATTATGAAAAATC
* ** *
378673 GATGA-TTAGGAAATAAAATTGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCC
1 AAT-ATTTAGGAAATAAAACCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTAGAGTATCCC
*
378737 CAATTATGAGAAATC
65 CAATTATGAAAAATC
* * * *
378752 AATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTC-GAAGGTAACGGGGTTAGAGTATCCC
1 AATATTTAGGAAATAAAACCGGGATTGGAGTATCCCCTCAGAA-ATAACGGGGTTAGAGTATCCC
378816 GATGAAATAA
Statistics
Matches: 117, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
78 6 0.05
79 110 0.94
80 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (79 bp):
AATATTTAGGAAATAAAACCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTAGAGTATCCCC
AATTATGAAAAATC
Found at i:378837 original size:27 final size:29
Alignment explanation
Indices: 378774--378846 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
378764 ATAAAGCCGG
* * *
378774 GGTTGGAGTATCCC-CTCGAAGGTAACGG
1 GGTTGGAGTATCCCGATCGAAGATAACGA
*
378802 GGTTAGAGTATCCCGAT-GAA-ATAACGA
1 GGTTGGAGTATCCCGATCGAAGATAACGA
378829 GGTTGGAGTATCCTCGAT
1 GGTTGGAGTATCC-CGAT
378847 TGTAAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 17 0.45
28 20 0.53
29 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.25
Consensus pattern (29 bp):
GGTTGGAGTATCCCGATCGAAGATAACGA
Found at i:378899 original size:52 final size:52
Alignment explanation
Indices: 378830--379162 Score: 179
Period size: 52 Copynumber: 6.3 Consensus size: 52
378820 AAATAACGAG
*
378830 GTTGGAGTATCCTCGATTGTAA-AAAATTGGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAAGAAAATTGGTGTTTTTGGAAATAAAA-CGGA
* * * *
378882 GTTGGAGTATCCCCGATT-AAAGGAAAATTAGTG-TTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTAA-GAAAATTGGTGTTTTTGGAAATAAAA-CGGA
* * * *** * * *
378934 GTTGGAGTATCCCTGATTATGAG-AAATCAAT-ATTTTGAAAATAAAGCCAGG-
1 GTTGGAGTATCCCCGATTGTAAGAAAATTGGTGTTTTTGGAAATAAA-AC-GGA
* *** * ***
378985 GTTGGAGTATCCCCTCGGA-GGTAACG-GGGTTGGAGTATCCCCGATGAAAT--AAC-GA
1 GTTGGAGTAT-CCC-C-GATTGTAA-GAAAATTGGTGT-T-TTTG--GAAATAAAACGGA
* *
379040 GGTTGGAGTATCCTCGATTGTGA-AAAATTGGTGTTTTTGGAAATAAAATCGGA
1 -GTTGGAGTATCCCCGATTGTAAGAAAATTGGTGTTTTTGGAAATAAAA-CGGA
** * *
379093 GTTGGAGTATCCCCGATTAAAAGAAAATTGGTG-TTTTGAAAATAAAACTGGG
1 GTTGGAGTATCCCCGATTGTAAGAAAATTGGTGTTTTTGGAAATAAAAC-GGA
379145 GTTGGAGTATCCCCGATT
1 GTTGGAGTATCCCCGATT
379163 ATGAACAATT
Statistics
Matches: 209, Mismatches: 47, Indels: 50
0.68 0.15 0.16
Matches are distributed among these distances:
49 5 0.02
51 34 0.16
52 109 0.52
53 32 0.15
54 9 0.04
55 2 0.01
56 12 0.06
57 2 0.01
59 4 0.02
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTAAGAAAATTGGTGTTTTTGGAAATAAAACGGA
Found at i:379037 original size:28 final size:28
Alignment explanation
Indices: 378983--379057 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
378973 AATAAAGCCA
*** **
378983 GGGTTGGAGTATCCCCTCGGAGGTAACG
1 GGGTTGGAGTATCCCCGATGAAATAACG
379011 GGGTTGGAGTATCCCCGATGAAATAACG
1 GGGTTGGAGTATCCCCGATGAAATAACG
* *
379039 AGGTTGGAGTATCCTCGAT
1 GGGTTGGAGTATCCCCGAT
379058 TGTGAAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGAAATAACG
Found at i:379121 original size:211 final size:210
Alignment explanation
Indices: 378720--379166 Score: 779
Period size: 211 Copynumber: 2.1 Consensus size: 210
378710 TCAGAAATAA
* * *
378720 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGAAAATAAAGCCAGGGTTGGAGTAT
378785 CCCCTCGAAGGTAACGGGGTTAGAGTATCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
66 CCCCTCGAAGGTAACGGGGTTAGAGTATCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
*
378850 AAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
131 AAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAAGAAAATTAGTG
378915 TTTT-AGAAATAAAAC
196 TTTTGA-AAATAAAAC
*
378930 CGGGGTTGGAGTATCCCTGATTATGAGAAATCAATATTTTGAAAATAAAGCCAGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGAAAATAAAGCCAGGGTTGGAGTAT
* *
378995 CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
66 CCCCTCGAAGGTAACGGGGTTAGAGTAT-CCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
* *
379060 TGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAAGAAAATTGGT
130 TAAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAAGAAAATTAGT
379125 GTTTTGAAAATAAAAC
195 GTTTTGAAAATAAAAC
*
379141 TGGGGTTGGAGTATCCCCGATTATGA
1 CGGGGTTGGAGTATCCCCGATTATGA
379167 ACAATTGAGA
Statistics
Matches: 224, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
210 87 0.39
211 136 0.61
212 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (210 bp):
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGAAAATAAAGCCAGGGTTGGAGTAT
CCCCTCGAAGGTAACGGGGTTAGAGTATCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
AAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAAGAAAATTAGTG
TTTTGAAAATAAAAC
Found at i:381570 original size:21 final size:21
Alignment explanation
Indices: 381546--381587 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
381536 ATATCGATAC
381546 AATGTATCGACACATTTCCTT
1 AATGTATCGACACATTTCCTT
*
381567 AATGTATCGATACATTTCCTT
1 AATGTATCGACACATTTCCTT
381588 GGTAGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (21 bp):
AATGTATCGACACATTTCCTT
Found at i:381622 original size:13 final size:13
Alignment explanation
Indices: 381604--381655 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
381594 AGCTTCGTAG
381604 CGATACATTGTAT
1 CGATACATTGTAT
381617 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
381636 CGATACATTGTAT
1 CGATACATTGTAT
381649 CGATACA
1 CGATACA
381656 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:381636 original size:19 final size:18
Alignment explanation
Indices: 381612--381674 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
381602 AGCGATACAT
381612 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
381631 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
381644 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
381663 TGTATCGATACA
1 TGTATCGATACA
381675 TTTACGGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:381645 original size:32 final size:32
Alignment explanation
Indices: 381604--381676 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
381594 AGCTTCGTAG
381604 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
381636 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
381668 CGATACATT
1 CGATACATT
381677 TACGGTTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:384405 original size:10 final size:10
Alignment explanation
Indices: 384390--384446 Score: 50
Period size: 10 Copynumber: 5.7 Consensus size: 10
384380 TTCGGAACCT
384390 TAAAAAAATA
1 TAAAAAAATA
384400 TAAAAAAATTA
1 TAAAAAAA-TA
384411 TAAAAAAA-A
1 TAAAAAAATA
384420 CT--AAAAATA
1 -TAAAAAAATA
384429 -AAAAAAACTA
1 TAAAAAAA-TA
384439 TGAAAAAA
1 T-AAAAAA
384447 CTCAAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
8 5 0.13
9 7 0.18
10 11 0.28
11 10 0.26
12 6 0.15
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.18
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:384433 original size:28 final size:29
Alignment explanation
Indices: 384393--384454 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
384383 GGAACCTTAA
*
384393 AAAAATATAAAAAAATTATAAAAAAAACT-
1 AAAAATATAAAAAAACTAT-AAAAAAACTC
*
384422 AAAAATA-AAAAAAACTATGAAAAAACTC
1 AAAAATATAAAAAAACTATAAAAAAACTC
384450 AAAAA
1 AAAAA
384455 ATTGATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 8 0.27
28 15 0.50
29 7 0.23
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (29 bp):
AAAAATATAAAAAAACTATAAAAAAACTC
Found at i:384446 original size:21 final size:19
Alignment explanation
Indices: 384391--384493 Score: 70
Period size: 21 Copynumber: 5.3 Consensus size: 19
384381 TCGGAACCTT
*
384391 AAAAAAATATAAAAAAATTA
1 AAAAAAATATGAAAAAA-TA
384411 TAAAAAAA-ACT--AAAAATA
1 -AAAAAAATA-TGAAAAAATA
*
384429 AAAAAAACTATGAAAAAACTC
1 AAAAAAA-TATGAAAAAA-TA
* **
384450 AAAAAATTGATGAAAAAAGG
1 AAAAAAAT-ATGAAAAAATA
384470 AAAAAAA-ATGCAAAAAATA
1 AAAAAAATATG-AAAAAATA
384489 AAAAA
1 AAAAA
384494 GCTATTGAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
17 7 0.10
18 6 0.09
19 17 0.25
20 13 0.19
21 24 0.36
ACGTcount: A:0.75, C:0.05, G:0.06, T:0.15
Consensus pattern (19 bp):
AAAAAAATATGAAAAAATA
Found at i:384598 original size:11 final size:11
Alignment explanation
Indices: 384582--384607 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
384572 CTTATTTTTT
384582 AAATTAATTTA
1 AAATTAATTTA
384593 AAATTAATTTA
1 AAATTAATTTA
384604 AAAT
1 AAAT
384608 AAAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTAATTTA
Found at i:384845 original size:3 final size:3
Alignment explanation
Indices: 384837--384880 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
384827 ATTACTTACT
384837 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
384881 TACAATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:384911 original size:2 final size:2
Alignment explanation
Indices: 384904--384928 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
384894 CTTCAAATGA
384904 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 A
384929 AAAACCAGGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:386037 original size:26 final size:26
Alignment explanation
Indices: 386008--386057 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
385998 CTTCAAGTTT
* *
386008 TATTTAT-TTTTTCAATTTAATCTTCA
1 TATTTATAGTTTT-AATATAATCTTCA
386034 TATTTATAGTTTTAATATAATCTT
1 TATTTATAGTTTTAATATAATCTT
386058 AACACAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTTATAGTTTTAATATAATCTTCA
Found at i:386326 original size:17 final size:19
Alignment explanation
Indices: 386291--386336 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
386281 AAACTTTATC
386291 ATTTTTTTTGGCACAATTAA
1 ATTTTTTTTGG-ACAATTAA
386311 ATTTTTTTTGG-C-ATTAA
1 ATTTTTTTTGGACAATTAA
*
386328 GTTTTTTTT
1 ATTTTTTTT
386337 CCTATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 13 0.52
18 1 0.04
20 11 0.44
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.61
Consensus pattern (19 bp):
ATTTTTTTTGGACAATTAA
Found at i:386629 original size:105 final size:106
Alignment explanation
Indices: 386421--386634 Score: 288
Period size: 105 Copynumber: 2.0 Consensus size: 106
386411 TTATAAATTC
* * * * ** *
386421 TAATAATGTTTTAGTATTTAACTTAACCAACTATCTATCAAATATTTATTCCATTAATTATTTTA
1 TAATAATGTTTTAATATTTAACTTAACCAACCATCTATCAAACATTTAGTCCATTAACCAATTTA
* * *
386486 ATTTAATTAGTTTTTAGCGTTTAACATTTTGGTATTAAAAT
66 ATTTAATCACTTTTTAGCGTTTAACATTTTAGTATTAAAAT
*
386527 TAATAACT-TTTTAATATTTAACTTAACCTACCATCTATCAAACATTTAGT-CATTAACCAATTT
1 TAATAA-TGTTTTAATATTTAACTTAACCAACCATCTATCAAACATTTAGTCCATTAACCAATTT
* *
386590 AATTTAATCACTTTTTAGTGTTTAACATTTTAGTCTTAAAAT
65 AATTTAATCACTTTTTAGCGTTTAACATTTTAGTATTAAAAT
386632 TAA
1 TAA
386635 GAAGTAAGAA
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
105 50 0.53
106 43 0.46
107 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (106 bp):
TAATAATGTTTTAATATTTAACTTAACCAACCATCTATCAAACATTTAGTCCATTAACCAATTTA
ATTTAATCACTTTTTAGCGTTTAACATTTTAGTATTAAAAT
Found at i:389925 original size:16 final size:16
Alignment explanation
Indices: 389904--389954 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
389894 ATTATTATTC
389904 AATATAAATATAATTT
1 AATATAAATATAATTT
* *
389920 AATATAATTTTTATTATTT
1 AATATAA---ATATAATTT
389939 AATATAAATATAATTT
1 AATATAAATATAATTT
389955 TATTAATTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
16 14 0.50
19 14 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATATAAATATAATTT
Found at i:389943 original size:35 final size:35
Alignment explanation
Indices: 389895--389973 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
389885 CTTATTGTTA
*
389895 TTATTATTCAATATAAATATAATTTAATATAATT-T
1 TTATTATTTAATATAAATATAATTTAAT-TAATTCT
*
389930 TTATTATTTAATATAAATATAATTTTATTAATTCT
1 TTATTATTTAATATAAATATAATTTAATTAATTCT
*
389965 TAATTATTT
1 TTATTATTT
389974 GTTATATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
34 5 0.12
35 35 0.88
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (35 bp):
TTATTATTTAATATAAATATAATTTAATTAATTCT
Found at i:394455 original size:21 final size:23
Alignment explanation
Indices: 394396--394469 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 23
394386 AAATTATTAA
*
394396 AATATTAAAAAAATATTTTATATT
1 AATATTAAAATAAT-TTTTATATT
* *
394420 AATATTTATAT-ATTTTTA-ATT
1 AATATTAAAATAATTTTTATATT
*
394441 AA-ATTAAAATAATTTTTTTATT
1 AATATTAAAATAATTTTTATATT
394463 -ATATTAA
1 AATATTAA
394470 TAGTGACCCA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 6 0.15
21 12 0.29
22 13 0.32
23 2 0.05
24 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATATTAAAATAATTTTTATATT
Found at i:395136 original size:22 final size:21
Alignment explanation
Indices: 395110--395158 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 21
395100 TGTACGAACG
395110 TATTAAAATATACATAAAAAAT
1 TATTAAAATATACA-AAAAAAT
*
395132 TATT--AATATATAAAAAAAT
1 TATTAAAATATACAAAAAAAT
395151 TATATAAA
1 TAT-TAAA
395159 TAAAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 10 0.43
20 8 0.35
22 5 0.22
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TATTAAAATATACAAAAAAAT
Found at i:395141 original size:20 final size:19
Alignment explanation
Indices: 395116--395153 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
395106 AACGTATTAA
395116 AATATACATAAAAAATTATT
1 AATATACA-AAAAAATTATT
*
395136 AATATATAAAAAAATTAT
1 AATATACAAAAAAATTAT
395154 ATAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
AATATACAAAAAAATTATT
Found at i:395161 original size:17 final size:19
Alignment explanation
Indices: 395125--395164 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
395115 AAATATACAT
*
395125 AAAAAATTATTAATATATA
1 AAAAAATTATTAATAAATA
395144 AAAAAATTA-T-ATAAATA
1 AAAAAATTATTAATAAATA
395161 AAAA
1 AAAA
395165 TTTATTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 1 0.05
19 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAAATTATTAATAAATA
Found at i:395386 original size:14 final size:13
Alignment explanation
Indices: 395360--395394 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
395350 ATAACTTTTA
395360 ATAATAGTTGTAG
1 ATAATAGTTGTAG
395373 ATAATAGATTGTAG
1 ATAATAG-TTGTAG
395387 AT-ATAGTT
1 ATAATAGTT
395395 TCAATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.10
13 11 0.52
14 8 0.38
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (13 bp):
ATAATAGTTGTAG
Found at i:398054 original size:20 final size:20
Alignment explanation
Indices: 398029--398069 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
398019 TAAAACTCAG
398029 AATGTATAGATACAATGATA
1 AATGTATAGATACAATGATA
* *
398049 AATGTATCGATACAATTATA
1 AATGTATAGATACAATGATA
398069 A
1 A
398070 GAATGTATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (20 bp):
AATGTATAGATACAATGATA
Found at i:398107 original size:20 final size:20
Alignment explanation
Indices: 398074--398127 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
398064 TTATAAGAAT
* *
398074 GTATCAATATATTTACTTAC
1 GTATCGATACATTTACTTAC
398094 GTATCGATACATTTACTTAC
1 GTATCGATACATTTACTTAC
*
398114 GTATTGATACATTT
1 GTATCGATACATTT
398128 CCTTGATAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.44
Consensus pattern (20 bp):
GTATCGATACATTTACTTAC
Found at i:399859 original size:16 final size:16
Alignment explanation
Indices: 399840--399873 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
399830 AAATATTAAA
399840 ATAA-TTAAATTTATTT
1 ATAAGTTAAATTT-TTT
399856 ATAAGTTAAATTTTTT
1 ATAAGTTAAATTTTTT
399872 AT
1 AT
399874 CAATAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
ATAAGTTAAATTTTTT
Found at i:400388 original size:22 final size:24
Alignment explanation
Indices: 400358--400402 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
400348 TACTATTTTA
400358 ATTTCTTAATAATAAAT-ATTATT
1 ATTTCTTAATAATAAATGATTATT
*
400381 ATTT-TTAATAGTAAATGATTAT
1 ATTTCTTAATAATAAATGATTAT
400403 ATGAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (24 bp):
ATTTCTTAATAATAAATGATTATT
Found at i:401991 original size:1 final size:1
Alignment explanation
Indices: 401987--402022 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
401977 AAAAAAAAAA
*
401987 GGGGGGGGGGGGGGGCGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
402023 CTTAGTTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:405573 original size:16 final size:16
Alignment explanation
Indices: 405562--405653 Score: 62
Period size: 16 Copynumber: 5.8 Consensus size: 16
405552 AGGTTTGGGT
405562 TTATTCAAGTTTAAGC
1 TTATTCAAGTTTAAGC
* *
405578 TTATTCGAA-TTTAGGT
1 TTATTC-AAGTTTAAGC
* *
405594 TTTTTCAAGTTTGAGC
1 TTATTCAAGTTTAAGC
* *
405610 CTATTCAAGTTCAAGCC
1 TTATTCAAGTTTAAG-C
**
405627 TT-TTCGGGTTTAAGC
1 TTATTCAAGTTTAAGC
* *
405642 TTTTTCAGGTTT
1 TTATTCAAGTTT
405654 GAACCTTTTC
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
15 5 0.09
16 48 0.84
17 4 0.07
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (16 bp):
TTATTCAAGTTTAAGC
Found at i:405646 original size:48 final size:48
Alignment explanation
Indices: 405563--405672 Score: 123
Period size: 48 Copynumber: 2.3 Consensus size: 48
405553 GGTTTGGGTT
* * * *
405563 TATTCAAGTTTAAGCTTATTCGAATTTAGGTTTTTTCAAGTTTGAGCC
1 TATTCAAGTTCAAGCTTATTCGAATTTAAGCTTTTTCAAGTTTGAACC
** *
405611 TATTCAAGTTCAAGCCTT-TTCGGGTTTAAGCTTTTTCAGGTTTGAACC
1 TATTCAAGTTCAAG-CTTATTCGAATTTAAGCTTTTTCAAGTTTGAACC
* *
405659 TTTTCGAGTTCAAG
1 TATTCAAGTTCAAG
405673 TTTTTTTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 49 0.94
49 3 0.06
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (48 bp):
TATTCAAGTTCAAGCTTATTCGAATTTAAGCTTTTTCAAGTTTGAACC
Found at i:405662 original size:16 final size:16
Alignment explanation
Indices: 405595--405663 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 16
405585 AATTTAGGTT
* *
405595 TTTTCAAGTTTGAGCC
1 TTTTCAGGTTTAAGCC
* * *
405611 TATTCAAGTTCAAGCC
1 TTTTCAGGTTTAAGCC
* *
405627 TTTTCGGGTTTAAGCT
1 TTTTCAGGTTTAAGCC
405643 TTTTCAGGTTTGAA-CC
1 TTTTCAGGTTT-AAGCC
405659 TTTTC
1 TTTTC
405664 GAGTTCAAGT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
16 40 0.95
17 2 0.05
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (16 bp):
TTTTCAGGTTTAAGCC
Found at i:406846 original size:22 final size:22
Alignment explanation
Indices: 406793--406836 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
406783 TAAAGCTCAT
*
406793 GATATAATTTATTTTTTGATAA
1 GATATAATTTACTTTTTGATAA
406815 GATATAATTTACTTTTTGATAA
1 GATATAATTTACTTTTTGATAA
406837 ATTATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.52
Consensus pattern (22 bp):
GATATAATTTACTTTTTGATAA
Found at i:407987 original size:38 final size:38
Alignment explanation
Indices: 407902--407987 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 38
407892 TATTAGTTTC
*
407902 AAAATAATTTTAAATATTATTTTCATGTATAATTTATT
1 AAAACAATTTTAAATATTATTTTCATGTATAATTTATT
* *
407940 -AAACTAATTTTAGATATTATTTTTAT-TAATATATTT-TT
1 AAAAC-AATTTTAAATATTATTTTCATGT-ATA-ATTTATT
407978 AAAACAATTT
1 AAAACAATTT
407988 ATTTTATTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
37 4 0.10
38 29 0.71
39 8 0.20
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.52
Consensus pattern (38 bp):
AAAACAATTTTAAATATTATTTTCATGTATAATTTATT
Found at i:410395 original size:23 final size:21
Alignment explanation
Indices: 410362--410459 Score: 88
Period size: 23 Copynumber: 4.2 Consensus size: 21
410352 AATACATGAG
410362 AAATTATTTTATTTATCGTAAATA
1 AAATT-TTTTATTTAT--TAAATA
*
410386 AAATTTTTTAATTTTATAAAATA
1 AAATTTTTT-A-TTTATTAAATA
*
410409 AAATTTTTTATTTTTATAAAATA
1 AAATTTTTTA--TTTATTAAATA
*
410432 AAATTTTTTATTTTTATAAAATA
1 AAATTTTTTA--TTTATTAAATA
410455 AAATT
1 AAATT
410460 AACAAAATGA
Statistics
Matches: 70, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
22 1 0.01
23 58 0.83
24 6 0.09
25 5 0.07
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (21 bp):
AAATTTTTTATTTATTAAATA
Found at i:410418 original size:46 final size:47
Alignment explanation
Indices: 410362--410460 Score: 148
Period size: 46 Copynumber: 2.1 Consensus size: 47
410352 AATACATGAG
*
410362 AAATTATTTTATTTATCGT-AAATAAAATTTTTTAATTTTATAAAATA
1 AAATTATTTTATTT-TCATAAAATAAAATTTTTTAATTTTATAAAATA
* *
410409 AAATT-TTTTATTTTTATAAAATAAAATTTTTTATTTTTATAAAATA
1 AAATTATTTTATTTTCATAAAATAAAATTTTTTAATTTTATAAAATA
410455 AAATTA
1 AAATTA
410461 ACAAAATGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
45 2 0.04
46 40 0.85
47 5 0.11
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (47 bp):
AAATTATTTTATTTTCATAAAATAAAATTTTTTAATTTTATAAAATA
Found at i:410696 original size:2 final size:2
Alignment explanation
Indices: 410689--410722 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
410679 ACTTTTACTC
410689 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
410723 ATAAAATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:413936 original size:21 final size:22
Alignment explanation
Indices: 413911--413951 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
413901 TTTATGCTCT
*
413911 AAATTTAA-TAAAAATTACTAA
1 AAATTAAATTAAAAATTACTAA
413932 AAATTAAATTAAAAATTACT
1 AAATTAAATTAAAAATTACT
413952 TGTTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (22 bp):
AAATTAAATTAAAAATTACTAA
Found at i:416119 original size:20 final size:19
Alignment explanation
Indices: 416090--416127 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
416080 ATGTAAAAAT
416090 GGGGGAGGGGAGGAGAGGGG
1 GGGGGAGGGGAGG-GAGGGG
*
416110 GGGGGGGGGGAGGGAGGG
1 GGGGGAGGGGAGGGAGGG
416128 TTAAGAGCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.16, C:0.00, G:0.84, T:0.00
Consensus pattern (19 bp):
GGGGGAGGGGAGGGAGGGG
Found at i:417584 original size:4 final size:4
Alignment explanation
Indices: 417575--417600 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
417565 TTCGGCTTCC
417575 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
417601 ATTAACATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:426173 original size:22 final size:22
Alignment explanation
Indices: 426148--426202 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
426138 TCATGAACAC
426148 GCTTGTTTATGGCTCATTTAAA
1 GCTTGTTTATGGCTCATTTAAA
* *
426170 GCTTGTTTAATAGTTCATTTAAA
1 GCTTGTTT-ATGGCTCATTTAAA
426193 -CTTGTTTATG
1 GCTTGTTTATG
426203 TTAGATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 15 0.52
23 12 0.41
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.49
Consensus pattern (22 bp):
GCTTGTTTATGGCTCATTTAAA
Found at i:428712 original size:16 final size:16
Alignment explanation
Indices: 428693--428723 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
428683 TATTTATAAA
428693 TTAAATTAAATTTAAT
1 TTAAATTAAATTTAAT
*
428709 TTAAATTGAATTTAA
1 TTAAATTAAATTTAA
428724 ATATGATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TTAAATTAAATTTAAT
Found at i:429605 original size:16 final size:17
Alignment explanation
Indices: 429584--429652 Score: 56
Period size: 16 Copynumber: 4.3 Consensus size: 17
429574 TCTAAATTTA
429584 AAAATAATTTGAATCT-
1 AAAATAATTTGAATCTC
*
429600 AAAATAATTCGAAT-TC
1 AAAATAATTTGAATCTC
* * *
429616 AAAATGATCT-AAACTC
1 AAAATAATTTGAATCTC
* *
429632 GAAATAACTTGAATCT-
1 AAAATAATTTGAATCTC
429648 AAAAT
1 AAAAT
429653 GATGTAATCC
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
15 3 0.08
16 32 0.82
17 4 0.10
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (17 bp):
AAAATAATTTGAATCTC
Done.