Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 100 of 226
Found at i:34417030 original size:50 final size:50
Alignment explanation
Indices: 34416909--34417200 Score: 363
Period size: 50 Copynumber: 5.7 Consensus size: 50
34416899 CATTTGGGTA
* *
34416909 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATC
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C
*
34416963 ATGAGAGGTCACC-TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
1 A--AGAGGTC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAC
*
34417015 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCA-TGCGCACCGGGAC
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTG-GCACCGAGAC
* * *
34417065 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAC
* * * *
34417115 GAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAC
* * * *
34417165 GAGAGGTCCCCTATATGACCATGTCTGGGACATGGC
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
34417201 TTTAGCATGT
Statistics
Matches: 216, Mismatches: 16, Indels: 16
0.87 0.06 0.06
Matches are distributed among these distances:
49 3 0.01
50 164 0.76
51 2 0.01
52 2 0.01
53 3 0.01
54 1 0.00
55 2 0.01
56 37 0.17
57 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAC
Found at i:34417186 original size:150 final size:154
Alignment explanation
Indices: 34416909--34417200 Score: 423
Period size: 150 Copynumber: 1.9 Consensus size: 154
34416899 CATTTGGGTA
34416909 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCA
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CCTT-AGATCATGAGAGGTCA
* *
34416974 CCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACAAGAGGTCCCATGTAAGACCATGT
64 CCTGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGACAAGAGGTCCCATATAAGACCATGT
34417039 CTGGGACATGGCATGCGCACCGGGAC
129 CTGGGACATGGCATGCGCACCGGGAC
* * *
34417065 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-T-GA-GATGAGAGGTC-CC
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCTTAGATCATGAGAGGTCACC
* * ** * *
34417125 ATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATATGACCATGTC
66 -TGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGACAAGAGGTCCCATATAAGACCATGTC
34417190 TGGGACATGGC
130 TGGGACATGGC
34417201 TTTAGCATGT
Statistics
Matches: 124, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
149 2 0.02
150 77 0.62
151 2 0.02
153 1 0.01
154 1 0.01
156 41 0.33
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (154 bp):
AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCTTAGATCATGAGAGGTCACC
TGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGACAAGAGGTCCCATATAAGACCATGTCT
GGGACATGGCATGCGCACCGGGAC
Found at i:34418944 original size:36 final size:35
Alignment explanation
Indices: 34418897--34418967 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
34418887 CATCTCCGGA
34418897 GCTTGGCAAATAAGGAAAGTGATCTTCTAAAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTT-TAAAGATAT
* * *
34418933 GCTTGGCAAATATGGAAGGTGATCTTTAGAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTTAAAGATAT
34418968 ATGATCCTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 8 0.25
36 24 0.75
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (35 bp):
GCTTGGCAAATAAGGAAAGTGATCTTTAAAGATAT
Found at i:34425169 original size:16 final size:16
Alignment explanation
Indices: 34425148--34425184 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
34425138 AGGGATATAG
34425148 TAAAATATTAAAAAAA
1 TAAAATATTAAAAAAA
**
34425164 TAAAATATTTTAAAAA
1 TAAAATATTAAAAAAA
34425180 TAAAA
1 TAAAA
34425185 GAACATATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAATATTAAAAAAA
Found at i:34425572 original size:22 final size:22
Alignment explanation
Indices: 34425537--34425587 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
34425527 GCATAATAAA
34425537 ATTAAAA-TGTATAAAAGAAAT
1 ATTAAAATTGTATAAAAGAAAT
34425558 ATTAAAATTGTATAAAAGAAAT
1 ATTAAAATTGTATAAAAGAAAT
34425580 ATTAAAAT
1 ATTAAAAT
34425588 GAAGCTTCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (22 bp):
ATTAAAATTGTATAAAAGAAAT
Found at i:34425861 original size:31 final size:28
Alignment explanation
Indices: 34425821--34425933 Score: 82
Period size: 30 Copynumber: 3.8 Consensus size: 28
34425811 ATAAATATCA
*
34425821 AATTTATACATGAACTTTGGTCTAAGGTGC
1 AATTTATACATGAACTTTGAT-T-AGGTGC
** *
34425851 AATTTGATACAAAAACTTTGATTTGGTGC
1 AATTT-ATACATGAACTTTGATTAGGTGC
** *
34425880 AATTATATACATGAAACTTAAATTAGGTTC
1 AATT-TATACATG-AACTTTGATTAGGTGC
* *
34425910 ATATGTATATATGGAACTTTGATT
1 A-ATTTATACAT-GAACTTTGATT
34425934 TTAATTCAAT
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
29 14 0.22
30 34 0.53
31 16 0.25
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (28 bp):
AATTTATACATGAACTTTGATTAGGTGC
Found at i:34431500 original size:38 final size:38
Alignment explanation
Indices: 34431423--34431514 Score: 116
Period size: 38 Copynumber: 2.4 Consensus size: 38
34431413 ACCACTTTGA
*
34431423 CCACCCTACACACCACATATGAGCTATATCAAGCCCAT
1 CCACCCTACACACCACATATGAGCCATATCAAGCCCAT
* * *
34431461 CCACCCTGCACACCACATATG-GACCATGAT-AGGCTCAT
1 CCACCCTACACACCACATATGAG-CCAT-ATCAAGCCCAT
34431499 CCACCCTACACACCAC
1 CCACCCTACACACCAC
34431515 GTAACATGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
37 1 0.02
38 44 0.94
39 2 0.04
ACGTcount: A:0.32, C:0.42, G:0.10, T:0.16
Consensus pattern (38 bp):
CCACCCTACACACCACATATGAGCCATATCAAGCCCAT
Found at i:34433342 original size:38 final size:37
Alignment explanation
Indices: 34433270--34433351 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
34433260 AATTAATTAA
34433270 TTTTTAAAAATTTAAAAATATTTTTTAGTGTTTATAC
1 TTTTTAAAAATTTAAAAATATTTTTTAGTGTTTATAC
* * *
34433307 TTTTTAAATAATTT-AATATTTTTTTTA-TGTTTTTA-
1 TTTTTAAA-AATTTAAAAATATTTTTTAGTGTTTATAC
*
34433342 TATTTAAAAA
1 TTTTTAAAAA
34433352 ACTAATTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
34 2 0.05
35 7 0.17
36 7 0.17
37 19 0.47
38 5 0.12
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.59
Consensus pattern (37 bp):
TTTTTAAAAATTTAAAAATATTTTTTAGTGTTTATAC
Found at i:34433418 original size:14 final size:14
Alignment explanation
Indices: 34433399--34433426 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
34433389 CACGTCAGCA
34433399 AAATTAACCAATGT
1 AAATTAACCAATGT
34433413 AAATTAACCAATGT
1 AAATTAACCAATGT
34433427 TAACATTTCT
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:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
AAATTAACCAATGT
Found at i:34439405 original size:19 final size:17
Alignment explanation
Indices: 34439370--34439409 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 17
34439360 TATTTAGGTA
34439370 AAAATTTGGAGAATTTC
1 AAAATTTGGAGAATTTC
34439387 AAAATTTGTGAGTAATTTC
1 AAAATTTG-GAG-AATTTC
34439406 AAAA
1 AAAA
34439410 GGGATTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.38
18 3 0.14
19 10 0.48
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (17 bp):
AAAATTTGGAGAATTTC
Found at i:34443339 original size:63 final size:61
Alignment explanation
Indices: 34443186--34443402 Score: 192
Period size: 61 Copynumber: 3.5 Consensus size: 61
34443176 GATGCATGTT
* * * * * *
34443186 CAAGCCGTGTAACTAACTGTTTTAGAATTAAAGGCACATGGGTTAGAGAC-TCGGGCGTGTGTC
1 CAAGCCGTGTAACTCACTGTTTT-GAATTAGAGACACA-CGGTCAAAGACAT-GGGCGTGTGTC
* * *
34443249 CAAGGCGTCTAA--CACTGTTTTTGAATTAGAGACGCACGAGTCAAAGACATGGGCGTGTGTC
1 CAAGCCGTGTAACTCACTG-TTTTGAATTAGAGACACACG-GTCAAAGACATGGGCGTGTGTC
* * *
34443310 CAAGCCGTGTAACTCACTGTTTTGGAATTAGAGGCACACGGGCTAAAGACACT-AGC-TGTGTC
1 CAAGCCGTGTAACTCACTGTTTT-GAATTAGAGACACACGGTC-AAAGACA-TGGGCGTGTGTC
* *
34443372 CAAGCTGTGTAACTCACTAATTTTGAATTAG
1 CAAGCCGTGTAACTCACT-GTTTTGAATTAG
34443403 GGACGCTCGG
Statistics
Matches: 128, Mismatches: 17, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
60 1 0.01
61 43 0.34
62 41 0.32
63 42 0.33
64 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (61 bp):
CAAGCCGTGTAACTCACTGTTTTGAATTAGAGACACACGGTCAAAGACATGGGCGTGTGTC
Found at i:34444058 original size:6 final size:6
Alignment explanation
Indices: 34444047--34444076 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
34444037 TATCTAGTAT
*
34444047 TTTCTG TTTCTG TTTCTG TTTCTG TATCTG
1 TTTCTG TTTCTG TTTCTG TTTCTG TTTCTG
34444077 ATTCCGAGAG
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:0.03, C:0.17, G:0.17, T:0.63
Consensus pattern (6 bp):
TTTCTG
Found at i:34449079 original size:43 final size:43
Alignment explanation
Indices: 34449032--34449154 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 43
34449022 TGATAACATG
* * *
34449032 TAAGACCATGTTTGGAACATTGGCATTG-TATTGTGATTACGTA
1 TAAGACCATGTCTGGAACATTGGCATCGTTA-TATGATTACGTA
* *
34449075 TAAGACCATGTCTGGGACATTGGCATCGTTATATGATTTCGTA
1 TAAGACCATGTCTGGAACATTGGCATCGTTATATGATTACGTA
* * * *
34449118 TAAGACCCTGTCTAGG-ACAATGGCATCGATATGTGAT
1 TAAGACCATGTCT-GGAACATTGGCATCGTTATATGAT
34449155 AACATGTAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 65 0.94
44 4 0.06
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (43 bp):
TAAGACCATGTCTGGAACATTGGCATCGTTATATGATTACGTA
Found at i:34449165 original size:43 final size:42
Alignment explanation
Indices: 34449021--34449165 Score: 130
Period size: 43 Copynumber: 3.4 Consensus size: 42
34449011 TTACTGAGAG
* * *
34449021 GTGATAACATGTAAGACCATGT-TTGGAACATTGGCATTGTATT
1 GTGATAACATATAAGACCATGTCTAGG-ACATTGGCATCGTA-T
* * *
34449064 GTGATTACGTATAAGACCATGTCTGGGACATTGGCATCGTTAT
1 GTGATAACATATAAGACCATGTCTAGGACATTGGCATCG-TAT
* ** * * *
34449107 ATGATTTCGTATAAGACCCTGTCTAGGACAATGGCATCGATAT
1 GTGATAACATATAAGACCATGTCTAGGACATTGGCATCG-TAT
*
34449150 GTGATAACATGTAAGA
1 GTGATAACATATAAGA
34449166 TCGTATCTGG
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
43 79 0.94
44 5 0.06
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.32
Consensus pattern (42 bp):
GTGATAACATATAAGACCATGTCTAGGACATTGGCATCGTAT
Found at i:34452623 original size:16 final size:16
Alignment explanation
Indices: 34452604--34452639 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
34452594 TACGTTTTTC
* *
34452604 CTTTTTCTTTTTTCTT
1 CTTTTCCTTTCTTCTT
34452620 CTTTTCCTTTCTTCTT
1 CTTTTCCTTTCTTCTT
34452636 CTTT
1 CTTT
34452640 CTTCAATACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
CTTTTCCTTTCTTCTT
Found at i:34453418 original size:26 final size:26
Alignment explanation
Indices: 34453365--34453420 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
34453355 AATTTTAAAA
** * *
34453365 TATTTTTAAAATACTTTTTTATTTTT
1 TATTTTTAAAATAAATTTTTAGTGTT
*
34453391 TATTTTTAAAATAAATTTTTGGTGTT
1 TATTTTTAAAATAAATTTTTAGTGTT
34453417 TATT
1 TATT
34453421 AAAAAAATAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (26 bp):
TATTTTTAAAATAAATTTTTAGTGTT
Found at i:34453653 original size:63 final size:62
Alignment explanation
Indices: 34453507--34453773 Score: 218
Period size: 63 Copynumber: 4.5 Consensus size: 62
34453497 TCACGTGTCT
* * * ** * * *
34453507 AGCCATGTAACTTATTGTTTTAAAATTAGAGGCACACGAGCTAAAGACACAGTGTGTGTTCA
1 AGCCATGTAACTCACTATTTTGGAATTAGAGGCACACGGGCTAAAGACACAGGGTGTGTCCA
* * *
34453569 AGCCGTGTAACTCACTGTTTTGGAATTAGAGGCACACGGGCTAGAGACAC-GGGCATGTGTCCA
1 AGCCATGTAACTCACTATTTTGGAATTAGAGGCACACGGGCTAAAGACACAGGG--TGTGTCCA
*
34453632 GGCCATGTAACTCACTATTTTGGAATTAGAGGCACACGGG-T-----------GTGTGTCCA
1 AGCCATGTAACTCACTATTTTGGAATTAGAGGCACACGGGCTAAAGACACAGGGTGTGTCCA
* * * * ** ** *
34453682 GGCCATGTAACTCACTGTTTTTGAATTAGAGGAACACTTGCTAAAGACACAAGCATGTGTCAA
1 AGCCATGTAACTCACTATTTTGGAATTAGAGGCACACGGGCTAAAGACAC-AGGGTGTGTCCA
*
34453745 AGCCGTGTAACTCACTATTTTGGAATTAG
1 AGCCATGTAACTCACTATTTTGGAATTAG
34453774 GGACGCACAA
Statistics
Matches: 167, Mismatches: 23, Indels: 29
0.76 0.11 0.13
Matches are distributed among these distances:
50 43 0.26
51 1 0.01
52 1 0.01
61 2 0.01
62 44 0.26
63 76 0.46
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (62 bp):
AGCCATGTAACTCACTATTTTGGAATTAGAGGCACACGGGCTAAAGACACAGGGTGTGTCCA
Found at i:34453683 original size:50 final size:50
Alignment explanation
Indices: 34453615--34453718 Score: 163
Period size: 50 Copynumber: 2.1 Consensus size: 50
34453605 CGGGCTAGAG
*
34453615 ACACGGGCATGTGTCCAGGCCATGTAACTCACTATTTTGGAATTAGAGGC
1 ACACGGGCATGTGTCCAGGCCATGTAACTCACTATTTTGGAATTAGAGGA
** * *
34453665 ACACGGGTGTGTGTCCAGGCCATGTAACTCACTGTTTTTGAATTAGAGGA
1 ACACGGGCATGTGTCCAGGCCATGTAACTCACTATTTTGGAATTAGAGGA
34453715 ACAC
1 ACAC
34453719 TTGCTAAAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (50 bp):
ACACGGGCATGTGTCCAGGCCATGTAACTCACTATTTTGGAATTAGAGGA
Found at i:34453756 original size:113 final size:113
Alignment explanation
Indices: 34453558--34453773 Score: 315
Period size: 113 Copynumber: 1.9 Consensus size: 113
34453548 TAAAGACACA
* * * * **
34453558 GTGTGTGTTCAAGCCGTGTAACTCACTGTTTTGGAATTAGAGGCACACGGGCTAGAGACACGGGC
1 GTGTGTGTCCAAGCCATGTAACTCACTGTTTTGGAATTAGAGGAACACGGGCTAAAGACACAAGC
* *
34453623 ATGTGTCCAGGCCATGTAACTCACTATTTTGGAATTAGAGGCACACGG
66 ATGTGTCAAAGCCATGTAACTCACTATTTTGGAATTAGAGGCACACGG
* * **
34453671 GTGTGTGTCCAGGCCATGTAACTCACTGTTTTTGAATTAGAGGAACACTTGCTAAAGACACAAGC
1 GTGTGTGTCCAAGCCATGTAACTCACTGTTTTGGAATTAGAGGAACACGGGCTAAAGACACAAGC
*
34453736 ATGTGTCAAAGCCGTGTAACTCACTATTTTGGAATTAG
66 ATGTGTCAAAGCCATGTAACTCACTATTTTGGAATTAG
34453774 GGACGCACAA
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
113 90 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (113 bp):
GTGTGTGTCCAAGCCATGTAACTCACTGTTTTGGAATTAGAGGAACACGGGCTAAAGACACAAGC
ATGTGTCAAAGCCATGTAACTCACTATTTTGGAATTAGAGGCACACGG
Found at i:34453791 original size:63 final size:63
Alignment explanation
Indices: 34453687--34453828 Score: 171
Period size: 63 Copynumber: 2.3 Consensus size: 63
34453677 GTCCAGGCCA
* ** *
34453687 TGTAACTCACTGTTTTTGAATTAGAGGAACACTTGCTAAAGACACAAGCATGTGTCAAAG-CCG
1 TGTAACTCACTGTTTTGGAATTAGAGGAACACAAGCCAAAGACACAAGCATGTGT-AAAGACCG
* * * *
34453750 TGTAACTCACTATTTTGGAATTAG-GGACGCACAAGCCAAAGACACAAGCGTGTGTATAGACCG
1 TGTAACTCACTGTTTTGGAATTAGAGGA-ACACAAGCCAAAGACACAAGCATGTGTAAAGACCG
*
34453813 TGTGACTCACTGTTTT
1 TGTAACTCACTGTTTT
34453829 AAGCCGTACA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
62 6 0.09
63 61 0.91
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (63 bp):
TGTAACTCACTGTTTTGGAATTAGAGGAACACAAGCCAAAGACACAAGCATGTGTAAAGACCG
Found at i:34453823 original size:176 final size:175
Alignment explanation
Indices: 34453508--34453828 Score: 385
Period size: 176 Copynumber: 1.8 Consensus size: 175
34453498 CACGTGTCTA
* * * **
34453508 GCCATGTAACTTATTGTTTTAAAATTAGAGGCACACGAGCTAAAGACACAGTGTGTGTTCAAGCC
1 GCCATGTAACTCACTGTTTTAAAATTAGAGGAACACGAGCTAAAGACACAGCATGTGTTCAAGCC
* ** * * ** * *
34453573 GTGTAACTCACTGTTTTGGAATTAGAGGCACACGGGCTAGAGACACGGGCATGTGTCCAGGCCAT
66 GTGTAACTCACTATTTTGGAATTAGAGGCACACAAGCCAAAGACACAAGCATGTGTACAGACCAT
34453638 GTAACTCACTATTTTGGAATTAGAGGCACACGGGTGTGTGTCCAG
131 GTAACTCACTATTTTGGAATTAGAGGCACACGGGTGTGTGTCCAG
** **
34453683 GCCATGTAACTCACTGTTTTTGAATTAGAGGAACACTTGCTAAAGACACAAGCATGTG-TCAAAG
1 GCCATGTAACTCACTGTTTTAAAATTAGAGGAACACGAGCTAAAGACAC-AGCATGTGTTC-AAG
* * *
34453747 CCGTGTAACTCACTATTTTGGAATTAG-GGACGCACAAGCCAAAGACACAAGCGTGTGTATAGAC
64 CCGTGTAACTCACTATTTTGGAATTAGAGG-CACACAAGCCAAAGACACAAGCATGTGTACAGAC
* * *
34453811 CGTGTGACTCACTGTTTT
128 CATGTAACTCACTATTTT
34453829 AAGCCGTACA
Statistics
Matches: 119, Mismatches: 24, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
175 46 0.39
176 73 0.61
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (175 bp):
GCCATGTAACTCACTGTTTTAAAATTAGAGGAACACGAGCTAAAGACACAGCATGTGTTCAAGCC
GTGTAACTCACTATTTTGGAATTAGAGGCACACAAGCCAAAGACACAAGCATGTGTACAGACCAT
GTAACTCACTATTTTGGAATTAGAGGCACACGGGTGTGTGTCCAG
Found at i:34458679 original size:33 final size:32
Alignment explanation
Indices: 34458642--34458703 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
34458632 ATTTTTATTT
34458642 AATTTTTAAAAAATAAAAAATTCTAGAAAAATG
1 AATTTTTAAAAAA-AAAAAATTCTAGAAAAATG
* *
34458675 AATTTTTAAAAAAATAAAATTTTAGAAAA
1 AATTTTTAAAAAAAAAAAATTCTAGAAAA
34458704 CTGTAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (32 bp):
AATTTTTAAAAAAAAAAAATTCTAGAAAAATG
Found at i:34458689 original size:16 final size:17
Alignment explanation
Indices: 34458645--34458703 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 17
34458635 TTTATTTAAT
*
34458645 TTTTA-AAAAATAAAAAA
1 TTTTAGAAAAA-ATAAAA
* * *
34458662 TTCTAG-AAAAATGAAT
1 TTTTAGAAAAAATAAAA
34458678 TTTTA-AAAAAATAAAA
1 TTTTAGAAAAAATAAAA
34458694 TTTTAGAAAA
1 TTTTAGAAAA
34458704 CTGTAAATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
16 20 0.62
17 12 0.38
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (17 bp):
TTTTAGAAAAAATAAAA
Found at i:34461255 original size:38 final size:38
Alignment explanation
Indices: 34461189--34461370 Score: 276
Period size: 38 Copynumber: 4.8 Consensus size: 38
34461179 AATATACATA
**
34461189 CACAAAGCCTGCTAGGCAC-GAGCCCGAATATCATTGG
1 CACAAAGCCTGCTAGGCACGGAGCCCGAATATCACCGG
* *
34461226 CACAAAGCCTACTAGACACGGAGCCCGAATATCACCGG
1 CACAAAGCCTGCTAGGCACGGAGCCCGAATATCACCGG
*
34461264 CACAAAGTCTGCTAGGCACGGAGCCCGAATATCACCGG
1 CACAAAGCCTGCTAGGCACGGAGCCCGAATATCACCGG
** *
34461302 CACAAAGCCTGCTAGGCGTGGAGCCCGAATATCACCAG
1 CACAAAGCCTGCTAGGCACGGAGCCCGAATATCACCGG
*
34461340 CACAAAGCCTGCTAGGCATGGAGCCCGAATA
1 CACAAAGCCTGCTAGGCACGGAGCCCGAATA
34461371 ACGTTACATT
Statistics
Matches: 132, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
37 17 0.13
38 115 0.87
ACGTcount: A:0.31, C:0.31, G:0.25, T:0.13
Consensus pattern (38 bp):
CACAAAGCCTGCTAGGCACGGAGCCCGAATATCACCGG
Found at i:34463442 original size:2 final size:2
Alignment explanation
Indices: 34463402--34463431 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34463392 GATTGAATTG
34463402 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
34463432 TATGAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34466538 original size:22 final size:21
Alignment explanation
Indices: 34466494--34466538 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
34466484 CCCTTTAAAT
* *
34466494 CAAAACAAACCAACCTTGGAG
1 CAAAACAAACCAACCATGAAG
*
34466515 CAAAACAAAAGCAACCATGAAG
1 CAAAAC-AAACCAACCATGAAG
34466537 CA
1 CA
34466539 CAAAAACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.53, C:0.27, G:0.13, T:0.07
Consensus pattern (21 bp):
CAAAACAAACCAACCATGAAG
Found at i:34475093 original size:24 final size:24
Alignment explanation
Indices: 34475064--34475136 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
34475054 AACGACTCGT
*
34475064 CTGGAAGAAACAGTCATGTCAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
*
34475088 CTGGAAGAAGCAGTCATGTAAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
* *
34475112 CTGGAAGAAGCAGCCATGGCAGCA
1 CTGGAAGAAGCAGTCATGTCAGCA
34475136 C
1 C
34475137 AATTACACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.36, C:0.22, G:0.29, T:0.14
Consensus pattern (24 bp):
CTGGAAGAAGCAGTCATGTCAGCA
Found at i:34479137 original size:70 final size:70
Alignment explanation
Indices: 34479024--34479165 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
34479014 CGTTAAACAT
34479024 GTTCACATATATGTATATACATACTCATTCTTTCATAATATTTATACTACCATATTTAAGCATAT
1 GTTCACATATATGTATATACATACTCATTCTTTCATAATATTTATACTACCATATTTAAGCATAT
34479089 GTCAA
66 GTCAA
34479094 GTTCACATATATGTATATACATACTCATTCTTTCATAATATTTATACTACCATATTTAAGCATAT
1 GTTCACATATATGTATATACATACTCATTCTTTCATAATATTTATACTACCATATTTAAGCATAT
34479159 GTCAA
66 GTCAA
34479164 GT
1 GT
34479166 CATTTGATTA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (70 bp):
GTTCACATATATGTATATACATACTCATTCTTTCATAATATTTATACTACCATATTTAAGCATAT
GTCAA
Found at i:34495432 original size:26 final size:26
Alignment explanation
Indices: 34495376--34495434 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
34495366 TCCCATTATG
34495376 TGGCTCTTCATGAGCTACCCAATTAA
1 TGGCTCTTCATGAGCTACCCAATTAA
* * * **
34495402 AGGCTCTTTATGAGCTTCCTGATTAA
1 TGGCTCTTCATGAGCTACCCAATTAA
34495428 TGGCTCT
1 TGGCTCT
34495435 CGAGAGCTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.36
Consensus pattern (26 bp):
TGGCTCTTCATGAGCTACCCAATTAA
Found at i:34495910 original size:27 final size:27
Alignment explanation
Indices: 34495879--34495938 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
34495869 GTGGAAATTG
34495879 AATATTATGAGCTCATATATGTTCCTT
1 AATATTATGAGCTCATATATGTTCCTT
34495906 AATATTATGAGCTCATATATGTTCCTT
1 AATATTATGAGCTCATATATGTTCCTT
*
34495933 GATATT
1 AATATT
34495939 CATGTGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (27 bp):
AATATTATGAGCTCATATATGTTCCTT
Found at i:34496565 original size:14 final size:16
Alignment explanation
Indices: 34496538--34496569 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
34496528 TTCAATATTT
34496538 TATAATATATAAATTA
1 TATAATATATAAATTA
34496554 TATAA-ATA-AAATTA
1 TATAATATATAAATTA
34496568 TA
1 TA
34496570 AAACATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAATATATAAATTA
Found at i:34501821 original size:47 final size:47
Alignment explanation
Indices: 34501748--34501840 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 47
34501738 AAACAAGTTA
*
34501748 CATTATAGAGATTTACAATCTAATGAACAACTTACGAATATGAGTAG
1 CATTACAGAGATTTACAATCTAATGAACAACTTACGAATATGAGTAG
* *
34501795 CATTACAGAGATTTACAATCTGATGAACGACTTACGAATATGAGTA
1 CATTACAGAGATTTACAATCTAATGAACAACTTACGAATATGAGTA
34501841 CATCGATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (47 bp):
CATTACAGAGATTTACAATCTAATGAACAACTTACGAATATGAGTAG
Found at i:34506396 original size:23 final size:23
Alignment explanation
Indices: 34506370--34506413 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
34506360 TAAATATTAT
34506370 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
** *
34506393 TTTATTTTTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
34506414 AAATGGTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:34514395 original size:22 final size:19
Alignment explanation
Indices: 34514370--34514411 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
34514360 TGATAATCAT
34514370 TAATATATAATTATATCTATTA
1 TAATATAT-ATTA-AT-TATTA
34514392 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
34514411 T
1 T
34514412 CAACTTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:34516025 original size:25 final size:27
Alignment explanation
Indices: 34515975--34516033 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
34515965 AAATATATAT
* *
34515975 TATA-ATATTATATCTTAATTATTAAG
1 TATATATATTATATATTAATTAATAAG
34516001 TATATATATTATATATT-A-TAATAAG
1 TATATATATTATATATTAATTAATAAG
*
34516026 TAAATATA
1 TATATATA
34516034 ATAAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 13 0.45
26 5 0.17
27 11 0.38
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (27 bp):
TATATATATTATATATTAATTAATAAG
Found at i:34516107 original size:15 final size:16
Alignment explanation
Indices: 34516040--34516121 Score: 58
Period size: 16 Copynumber: 4.8 Consensus size: 16
34516030 TATAATAAAT
* *
34516040 AAAAGAAACAAAAAGA
1 AAAAGAAAGAAAGAGA
* *
34516056 AATAGAAAGAAATAGGA
1 AAAAGAAAGAAAGA-GA
*
34516073 TAGAAATGAAACAAAGAGA
1 -A-AAA-GAAAGAAAGAGA
34516092 AAAAGAAAGAAA-AGA
1 AAAAGAAAGAAAGAGA
34516107 AAAAGGAAAAGAAAG
1 AAAA-G-AAAGAAAG
34516122 GAAGGAGGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
15 7 0.13
16 19 0.37
17 12 0.23
18 2 0.04
19 4 0.08
20 8 0.15
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.05
Consensus pattern (16 bp):
AAAAGAAAGAAAGAGA
Found at i:34517114 original size:40 final size:40
Alignment explanation
Indices: 34516990--34517129 Score: 151
Period size: 40 Copynumber: 3.5 Consensus size: 40
34516980 GACTTCGAGT
* * *
34516990 CGATGAGACACTAGGTGACAAATTATTACTTCGGATATATT
1 CGATGAGACACTGGGTGCCAAATTATTACTTCGGAT-TATC
* * * *
34517031 CGATGAGGCACTGGGTGCC-GA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGCCAAATTATTACTTCGGATTATC
* *
34517068 CGATGAGACATTGGGTGCCAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGCCAAATTATTACTTCGGATTATC
* *
34517108 CAATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTGGGTGCCAAA
34517130 CTGGTGTGTT
Statistics
Matches: 80, Mismatches: 16, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
37 19 0.24
38 11 0.14
39 2 0.03
40 32 0.40
41 16 0.20
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (40 bp):
CGATGAGACACTGGGTGCCAAATTATTACTTCGGATTATC
Found at i:34526697 original size:15 final size:16
Alignment explanation
Indices: 34526670--34526704 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
34526660 ATTGTGTATC
34526670 ATATTATTTAATATAA
1 ATATTATTTAATATAA
34526686 ATATTA-TTAATATAA
1 ATATTATTTAATATAA
34526701 ATAT
1 ATAT
34526705 AATCTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTATTTAATATAA
Found at i:34527260 original size:25 final size:26
Alignment explanation
Indices: 34527223--34527272 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
34527213 TCACAAACAA
34527223 TAAATCAAACAAACAAACAAAATTTT
1 TAAATCAAACAAACAAACAAAATTTT
* *
34527249 TAAAT-AAACAAACCAACTAAATTT
1 TAAATCAAACAAACAAACAAAATTT
34527273 AAATATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (26 bp):
TAAATCAAACAAACAAACAAAATTTT
Found at i:34529635 original size:241 final size:241
Alignment explanation
Indices: 34529210--34529696 Score: 911
Period size: 241 Copynumber: 2.0 Consensus size: 241
34529200 GGGTTTTAGT
*
34529210 ATCGATTTTAATTATGCACTTTTGTGTGCTACCAAGAGAGGATTGAGAGGAAATTGGTGCTCCTC
1 ATCGATTTTAATTATGCACTTTTGTCTGCTACCAAGAGAGGATTGAGAGGAAATTGGTGCTCCTC
*
34529275 CAACCATTTAAACTGCAGGTTGTTGTTGTTCACTGTTGCATAAGTATTTTAACATTTTTGGAAGC
66 CAACCATTTAAACGGCAGGTTGTTGTTGTTCACTGTTGCATAAGTATTTTAACATTTTTGGAAGC
* *
34529340 CGAATATGGGCATTTTTGTGGCATATTTAATTTAGTTTCCGTACAATTATTACTGATTTGAGCAT
131 CGAATATGGGCATTTTTGTGGCATATTTAATTTAGTTTCCGTACAATCATTACTGATTTGAACAT
34529405 GTTAAATGACGATTTTAGGTTCTGGGAGTTTCGTGGTGGCATTTAC
196 GTTAAATGACGATTTTAGGTTCTGGGAGTTTCGTGGTGGCATTTAC
* * *
34529451 ATCGATTTTAGTTATGCACTTTTGTCTGCTGCCAGGAGAGGATTGAGAGGAAATTGGTGCTCCTC
1 ATCGATTTTAATTATGCACTTTTGTCTGCTACCAAGAGAGGATTGAGAGGAAATTGGTGCTCCTC
34529516 CAACCATTTAAACGGCAGGTTGTTGTTGTTCACTGTTGCATAAGTATTTTAACATTTTTGGAAGC
66 CAACCATTTAAACGGCAGGTTGTTGTTGTTCACTGTTGCATAAGTATTTTAACATTTTTGGAAGC
34529581 CGAATATGGGCATTTTTGTGGCATATTTAATTTAGTTTCCGTACAATCATTACTGATTTGAACAT
131 CGAATATGGGCATTTTTGTGGCATATTTAATTTAGTTTCCGTACAATCATTACTGATTTGAACAT
34529646 GTTAAATGACGATTTTAGGTTCTGGGAGTTTCGTGGTGGCATTTAC
196 GTTAAATGACGATTTTAGGTTCTGGGAGTTTCGTGGTGGCATTTAC
34529692 ATCGA
1 ATCGA
34529697 AATTGGATCA
Statistics
Matches: 239, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
241 239 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (241 bp):
ATCGATTTTAATTATGCACTTTTGTCTGCTACCAAGAGAGGATTGAGAGGAAATTGGTGCTCCTC
CAACCATTTAAACGGCAGGTTGTTGTTGTTCACTGTTGCATAAGTATTTTAACATTTTTGGAAGC
CGAATATGGGCATTTTTGTGGCATATTTAATTTAGTTTCCGTACAATCATTACTGATTTGAACAT
GTTAAATGACGATTTTAGGTTCTGGGAGTTTCGTGGTGGCATTTAC
Found at i:34531168 original size:18 final size:18
Alignment explanation
Indices: 34531145--34531182 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
34531135 TGAACCTTTA
*
34531145 ATAATTTTAAAATTTTTT
1 ATAATTTTAAAATTATTT
*
34531163 ATAATTTTTAAATTATTT
1 ATAATTTTAAAATTATTT
34531181 AT
1 AT
34531183 TGGCATGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATAATTTTAAAATTATTT
Found at i:34532371 original size:14 final size:14
Alignment explanation
Indices: 34532352--34532391 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
34532342 TTGATTGCCA
34532352 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
34532366 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
34532380 GGAAAATGTTTT
1 GTAAAATGTTTT
34532392 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:34532400 original size:20 final size:20
Alignment explanation
Indices: 34532375--34532414 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34532365 CGTAAAATGA
*
34532375 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
34532395 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
34532415 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:34532404 original size:34 final size:35
Alignment explanation
Indices: 34532360--34532426 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
34532350 CAGTAAAATG
*
34532360 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
34532394 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
34532427 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:34532430 original size:14 final size:15
Alignment explanation
Indices: 34532354--34532430 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
34532344 GATTGCCAGT
* *
34532354 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
34532368 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
34532382 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
34532402 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
34532417 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
34532431 TGTTTGATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:34532904 original size:26 final size:26
Alignment explanation
Indices: 34532871--34532928 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
34532861 ATATCAAAAT
*
34532871 TTATAGAGACCAATTTAAAATCTTGA
1 TTATAGAGACCAATTTAAAATCTAGA
*
34532897 TTATAGAGACCAATTTAATATCTAGA
1 TTATAGAGACCAATTTAAAATCTAGA
34532923 TTATAG
1 TTATAG
34532929 TTTGAGGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.36
Consensus pattern (26 bp):
TTATAGAGACCAATTTAAAATCTAGA
Found at i:34534967 original size:12 final size:11
Alignment explanation
Indices: 34534953--34534994 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 11
34534943 CCAGATCAAG
34534953 GGAGAACGAAA
1 GGAGAACGAAA
34534964 GG-G-A-GAAA
1 GGAGAACGAAA
34534972 GGAGAACGAAA
1 GGAGAACGAAA
34534983 GGGAGAACGAAA
1 -GGAGAACGAAA
34534995 CCAGATCGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.22
9 2 0.07
10 2 0.07
11 6 0.22
12 11 0.41
ACGTcount: A:0.52, C:0.07, G:0.40, T:0.00
Consensus pattern (11 bp):
GGAGAACGAAA
Found at i:34534977 original size:19 final size:19
Alignment explanation
Indices: 34534953--34534989 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
34534943 CCAGATCAAG
34534953 GGAGAACGAAAGGGAGAAA
1 GGAGAACGAAAGGGAGAAA
34534972 GGAGAACGAAAGGGAGAA
1 GGAGAACGAAAGGGAGAA
34534990 CGAAACCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.43, T:0.00
Consensus pattern (19 bp):
GGAGAACGAAAGGGAGAAA
Found at i:34543075 original size:22 final size:22
Alignment explanation
Indices: 34543047--34543108 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
34543037 TTTATTGTTC
34543047 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
34543069 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
34543091 AGCCATGAGAGCTTAGTA
1 AAACATGAGAGCTTAGTA
34543109 TCTGTTGGGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:34548980 original size:18 final size:17
Alignment explanation
Indices: 34548957--34548990 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34548947 CGCCGCACGT
34548957 CCCACGTCGCAGCAACCG
1 CCCACGT-GCAGCAACCG
*
34548975 CCCACGTTCAGCAACC
1 CCCACGTGCAGCAACC
34548991 CCGCACGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.50, G:0.18, T:0.09
Consensus pattern (17 bp):
CCCACGTGCAGCAACCG
Found at i:34548988 original size:17 final size:17
Alignment explanation
Indices: 34548966--34548999 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
34548956 TCCCACGTCG
34548966 CAGCAACCGCC-CACGTT
1 CAGCAACC-CCGCACGTT
34548983 CAGCAACCCCGCACGTT
1 CAGCAACCCCGCACGTT
34549000 GTGCACATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.24, C:0.47, G:0.18, T:0.12
Consensus pattern (17 bp):
CAGCAACCCCGCACGTT
Found at i:34549834 original size:18 final size:16
Alignment explanation
Indices: 34549813--34549858 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 16
34549803 GATTGTATCC
34549813 TTATTATTATATTATTTA
1 TTATT-TTATATTA-TTA
34549831 TTATTTTTATCATTATTA
1 TTA-TTTTAT-ATTATTA
34549849 TTATTTTATA
1 TTATTTTATA
34549859 CATATACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.04
17 6 0.23
18 13 0.50
19 6 0.23
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTTATATTATTA
Found at i:34549911 original size:25 final size:25
Alignment explanation
Indices: 34549874--34549922 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
34549864 ACACACGCAT
*
34549874 TTTTTTAATAATATATATGCATATA
1 TTTTTTAATAATACATATGCATATA
*
34549899 TTTTTT-ATAAATACATGTGCATAT
1 TTTTTTAAT-AATACATATGCATAT
34549923 TTTATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (25 bp):
TTTTTTAATAATACATATGCATATA
Found at i:34549947 original size:11 final size:12
Alignment explanation
Indices: 34549919--34549952 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
34549909 ATACATGTGC
34549919 ATATTTTATATAT
1 ATATTTTAT-TAT
34549932 ATATTTTATTAT
1 ATATTTTATTAT
34549944 -TATTTTATT
1 ATATTTTATT
34549953 CTCATAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 3 0.14
13 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTTTATTAT
Found at i:34549998 original size:18 final size:17
Alignment explanation
Indices: 34549961--34549999 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
34549951 TTCTCATAGT
* *
34549961 TTTTATATACATTTATA
1 TTTTATATACATATACA
34549978 TTTTATAATACATATACA
1 TTTTAT-ATACATATACA
34549996 TTTT
1 TTTT
34550000 CCTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTATATACATATACA
Found at i:34560234 original size:20 final size:20
Alignment explanation
Indices: 34560211--34560249 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
34560201 TGAAATAATC
*
34560211 AAAAATG-AATAAAATTTTA
1 AAAAATGAAACAAAATTTTA
34560230 AAAAATGAAACAAAATTTTA
1 AAAAATGAAACAAAATTTTA
34560250 TAAATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAAATGAAACAAAATTTTA
Found at i:34562448 original size:44 final size:42
Alignment explanation
Indices: 34562376--34562769 Score: 195
Period size: 44 Copynumber: 8.8 Consensus size: 42
34562366 ATCTGATGCG
* * * *
34562376 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TTTACTTTA
* * * *
34562420 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-TTA-CTTTA
* * *
34562464 ATCTGCTCC-GTAGTAATCTCAGGGAGATAAGATTTCTGGCTTCA
1 ATCTGCTCCACT-GTAATCTCAGGGAGATAAGATTT-T-ACTTTA
** *
34562508 ATCTGATGCGATCTACACTACTGTAA-CTTCAGAAAGATAAGATCTTTTATTTTA
1 ATC---T--G--CT-C-C-ACTGTAATC-TCAGGGAGATAAGA--TTTTACTTTA
* * * * *
34562562 ATCCGCTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-TTA-CTTTA
* ** * * *
34562606 ATCTACTCCGTTGTAATCTCAGGGAGATAAGATTTGA-TGTG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTTACTTTA
* * * *
34562647 ATCTACTCCACTGTAA-CTTCAGAGAGATAAGATCCCTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TTTACTTTA
* * *
34562691 ATCTGCTCCACTGTAATCTCGGGGAGATAGGATTACTAGCTTTA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-TTA-CTTTA
* *
34562735 ATCTACTCCACTGTAATCTCAAGGAGATAAGATTT
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTT
34562770 CTGACTTCAG
Statistics
Matches: 265, Mismatches: 55, Indels: 61
0.70 0.14 0.16
Matches are distributed among these distances:
40 1 0.00
41 29 0.11
42 3 0.01
43 10 0.04
44 180 0.68
45 4 0.02
46 1 0.00
47 3 0.01
49 2 0.01
51 2 0.01
52 1 0.00
53 2 0.01
54 22 0.08
55 2 0.01
56 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (42 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTTACTTTA
Found at i:34562533 original size:142 final size:141
Alignment explanation
Indices: 34562227--34562778 Score: 772
Period size: 142 Copynumber: 4.0 Consensus size: 141
34562217 GAGATAAGAC
* * * *
34562227 CTGATGCGATCTACTCAACTGTAACTTCAGAAAGATAAGATTCTTTACTTTAATTCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
34562292 TAATCTCAGAGAGATAGGATTACT-GCTTCAATCTGCTCCGCTGTAATCTCAAGGAGGTAAGATT
66 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCG-TGTAATCTCAAGGAGATAAGATT
34562356 TCTGGCTTCAAT
130 TCTGGCTTCAAT
*
34562368 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * *
34562433 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGTAGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGT-GTAATCTCAAGGAGATAAGATT
34562498 TCTGGCTTCAAT
130 TCTGGCTTCAAT
* *
34562510 CTGATGCGATCTACACTACTGTAACTTCAGAAAGATAAGATCTTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTATTTTAATCCGCTCCACTG
*
34562575 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGTTGTAATCTCAGGGAGATAAGA-T
66 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCG-TGTAATCTCAAGGAGATAAGATT
34562639 T-T-G-----A-
130 TCTGGCTTCAAT
* * * *
34562643 -TG-T--GATCTACTCCACTGTAACTTCAGAGAGATAAGATCCCTTATTTTAATCTGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * * *
34562704 TAATCTCGGGGAGATAGGATTACTAGCTTTAATCTACTCCACTGTAATCTCAAGGAGATAAGATT
66 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCC-GTGTAATCTCAAGGAGATAAGATT
*
34562769 TCTGACTTCA
130 TCTGGCTTCA
34562779 GTTTGTTCCA
Statistics
Matches: 374, Mismatches: 25, Indels: 28
0.88 0.06 0.07
Matches are distributed among these distances:
129 109 0.29
130 2 0.01
131 2 0.01
132 2 0.01
134 1 0.00
139 1 0.00
140 1 0.00
141 86 0.23
142 169 0.45
143 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (141 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGTGTAATCTCAAGGAGATAAGATTT
CTGGCTTCAAT
Found at i:34562741 original size:129 final size:129
Alignment explanation
Indices: 34562511--34562769 Score: 401
Period size: 129 Copynumber: 2.0 Consensus size: 129
34562501 GGCTTCAATC
* **
34562511 TGATGCGATCTACACTACTGTAACTTCAGAAAGATAAGATCTTTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACACCACTGTAACTTCAGAAAGATAAGATCCCTTATTTTAATCCGCTCCACTGT
** *
34562576 AATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGTTGTAATCTCAGGGAGATAAGATT
66 AATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCACTGTAATCTCAAGGAGATAAGATT
* * * *
34562640 TGATGTGATCTACTCCACTGTAACTTCAGAGAGATAAGATCCCTTATTTTAATCTGCTCCACTGT
1 TGATGCGATCTACACCACTGTAACTTCAGAAAGATAAGATCCCTTATTTTAATCCGCTCCACTGT
* * *
34562705 AATCTCGGGGAGATAGGATTACTAGCTTTAATCTACTCCACTGTAATCTCAAGGAGATAAGATT
66 AATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCACTGTAATCTCAAGGAGATAAGATT
34562769 T
1 T
34562770 CTGACTTCAG
Statistics
Matches: 117, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
129 117 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (129 bp):
TGATGCGATCTACACCACTGTAACTTCAGAAAGATAAGATCCCTTATTTTAATCCGCTCCACTGT
AATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCACTGTAATCTCAAGGAGATAAGATT
Found at i:34577819 original size:22 final size:19
Alignment explanation
Indices: 34577781--34577821 Score: 55
Period size: 22 Copynumber: 2.0 Consensus size: 19
34577771 AAATTATTGG
34577781 AAAGATGACTGAGAATTAC
1 AAAGATGACTGAGAATTAC
34577800 AAAGACTGACATGAGAAATTAC
1 AAAGA-TGAC-TGAG-AATTAC
34577822 CATTCTCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 4 0.21
21 4 0.21
22 6 0.32
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (19 bp):
AAAGATGACTGAGAATTAC
Found at i:34579727 original size:50 final size:50
Alignment explanation
Indices: 34579659--34579776 Score: 157
Period size: 50 Copynumber: 2.4 Consensus size: 50
34579649 AATACACCAG
* * * * *
34579659 TCTTATCGCCTTGACGTTGCAATGGAATAGATTGAAGCCACAGCGGCGAA
1 TCTTATCTCCCTGGCGTTGCAATGGAATAGATTGAAGCCACAACGGCAAA
* *
34579709 TCTTA-CTTCCCTGGCGTTGCAGTGGAGTAGATTGAAGCCACAACGGCAAA
1 TCTTATC-TCCCTGGCGTTGCAATGGAATAGATTGAAGCCACAACGGCAAA
34579759 TCTTATCTCCCTGGCGTT
1 TCTTATCTCCCTGGCGTT
34579777 AAGACTTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
49 1 0.02
50 57 0.97
51 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.27
Consensus pattern (50 bp):
TCTTATCTCCCTGGCGTTGCAATGGAATAGATTGAAGCCACAACGGCAAA
Found at i:34579976 original size:100 final size:100
Alignment explanation
Indices: 34579855--34580161 Score: 427
Period size: 100 Copynumber: 3.1 Consensus size: 100
34579845 CAGTGGAACG
* * * * *
34579855 GATTGAAGCCACAACGGTGAATCTTGCTTCCCTGGTGGTGTAGTGGAACAGATTAAAGTTACGAC
1 GATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGAC
34579920 GGTGAATCTGATTTCCCCGACATTGCAATTAAAAA
66 GGTGAATCTGATTTCCCCGACATTGCAATTAAAAA
* * * ** *
34579955 TATTGAAGCCACAACGGTGAATCTTACTTCTCTGACGGTGTAGTGGAATAGATTGAAGCTGTGGC
1 GATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGAC
* *
34580020 GGCGGATCTGATTTCCCCGACATTGCAATTAAAAA
66 GGTGAATCTGATTTCCCCGACATTGCAATTAAAAA
* *
34580055 GATTGAAGCCACAACTGTGAATCTTACTTTCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGAC
1 GATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGAC
* * * *
34580120 GGTGAATATTG-TTTCCTCGACATTGCAGTTAAACA
66 GGTGAAT-CTGATTTCCCCGACATTGCAATTAAAAA
34580155 GATTGAA
1 GATTGAA
34580162 AATGGCGAAT
Statistics
Matches: 179, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
100 177 0.99
101 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (100 bp):
GATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGAC
GGTGAATCTGATTTCCCCGACATTGCAATTAAAAA
Found at i:34580125 original size:50 final size:50
Alignment explanation
Indices: 34579846--34580126 Score: 145
Period size: 50 Copynumber: 5.6 Consensus size: 50
34579836 TTGGCATTAC
** * * **
34579846 AGTGGAACGGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGGTGGTGT
1 AGTGGAAAAGATTGAAGCCACAACGGTGAATCTTACTTTCCTGACGGTGT
* * ** * * * ** *
34579896 AGTGGAACAGATTAAAGTTACGACGGTGAATCTGA-TTTCCCCGACATTGC
1 AGTGGAAAAGATTGAAGCCACAACGGTGAATCTTACTTT-CCTGACGGTGT
* ** *
34579946 AATTAAAAATATTGAAGCCACAACGGTGAATCTTAC-TTCTCTGACGGTGT
1 AGTGGAAAAGATTGAAGCCACAACGGTGAATCTTACTTTC-CTGACGGTGT
* ***** * * * * ** *
34579996 AGTGGAATAGATTGAAGCTGTGGCGGCGGATCTGA-TTTCCCCGACATTGC
1 AGTGGAAAAGATTGAAGCCACAACGGTGAATCTTACTTT-CCTGACGGTGT
* ** * *
34580046 AATTAAAAAGATTGAAGCCACAACTGTGAATCTTACTTTCCTGGCGGTGT
1 AGTGGAAAAGATTGAAGCCACAACGGTGAATCTTACTTTCCTGACGGTGT
* * *
34580096 AGTGGAATAGATTGAAGCTACGACGGTGAAT
1 AGTGGAAAAGATTGAAGCCACAACGGTGAAT
34580127 ATTGTTTCCT
Statistics
Matches: 155, Mismatches: 70, Indels: 12
0.65 0.30 0.05
Matches are distributed among these distances:
49 3 0.02
50 148 0.95
51 4 0.03
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (50 bp):
AGTGGAAAAGATTGAAGCCACAACGGTGAATCTTACTTTCCTGACGGTGT
Found at i:34581738 original size:3 final size:3
Alignment explanation
Indices: 34581730--34581780 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
34581720 GATTGTATCC
* *
34581730 TTA TTA TTA -TA TTA TTTA TTA TTT TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
34581775 TT- TTA T
1 TTA TTA T
34581781 ACATATACAC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:34581823 original size:25 final size:25
Alignment explanation
Indices: 34581797--34581844 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
34581787 ACACACGCAT
*
34581797 TTTTTTAT-AATATATATGCATATA
1 TTTTTTATAAATACATATGCATATA
*
34581821 TTTTTTATAAATACATGTGCATAT
1 TTTTTTATAAATACATATGCATAT
34581845 TATATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (25 bp):
TTTTTTATAAATACATATGCATATA
Found at i:34581923 original size:18 final size:17
Alignment explanation
Indices: 34581886--34581924 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
34581876 TTCTCATAGT
* *
34581886 TTTTATATACATTTATA
1 TTTTATATACATATACA
34581903 TTTTATAATACATATACA
1 TTTTAT-ATACATATACA
34581921 TTTT
1 TTTT
34581925 CCTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTATATACATATACA
Found at i:34582132 original size:13 final size:14
Alignment explanation
Indices: 34582114--34582142 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
34582104 TCTCAAGATT
34582114 TACTTATATAT-TA
1 TACTTATATATATA
34582127 TACTTATATATATA
1 TACTTATATATATA
34582141 TA
1 TA
34582143 TTGCAAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TACTTATATATATA
Found at i:34583788 original size:7 final size:7
Alignment explanation
Indices: 34583776--34583802 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
34583766 AAATTATCAT
34583776 TTTAAAC
1 TTTAAAC
34583783 TTTAAAC
1 TTTAAAC
34583790 TTTAAAC
1 TTTAAAC
34583797 TTTAAA
1 TTTAAA
34583803 TTTCCTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
TTTAAAC
Found at i:34584875 original size:29 final size:30
Alignment explanation
Indices: 34584812--34584889 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 30
34584802 GTTTTTGTAC
*
34584812 TCTTTATAAATTTA-GAATTTAGTCTCAGTA
1 TCTTT-TATATTTAGGAATTTAGTCTCAGTA
* *
34584842 -CTTTTATTTTTAGGAATTTAGTGCTTA-TA
1 TCTTTTATATTTAGGAATTTAGT-CTCAGTA
* *
34584871 TTTTTTATATTTCGGAATT
1 TCTTTTATATTTAGGAATT
34584890 CAGATCCAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 6 0.15
29 15 0.38
30 18 0.46
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.54
Consensus pattern (30 bp):
TCTTTTATATTTAGGAATTTAGTCTCAGTA
Found at i:34585736 original size:2 final size:2
Alignment explanation
Indices: 34585729--34585761 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34585719 TTCTTTTCTT
34585729 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34585762 GAAATGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34588261 original size:16 final size:16
Alignment explanation
Indices: 34588240--34588272 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
34588230 TACTTAGTTC
34588240 ATAATGATGCTTCTAA
1 ATAATGATGCTTCTAA
34588256 ATAATGATGCTTCTAA
1 ATAATGATGCTTCTAA
34588272 A
1 A
34588273 ATTGGTATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (16 bp):
ATAATGATGCTTCTAA
Found at i:34593648 original size:27 final size:26
Alignment explanation
Indices: 34593605--34593701 Score: 70
Period size: 27 Copynumber: 3.6 Consensus size: 26
34593595 GTGTTTTAAT
* *
34593605 AAAAAAA-TATAACTACTTAATTAGGA
1 AAAAAAACT-TAAATACTTAAATAGGA
* *
34593631 CAAAAAAACTTAAATACTAAAATATTGA
1 -AAAAAAACTTAAATACTTAAATA-GGA
*** *
34593659 AGTCAAACTAAAATACTTAAATAGGA
1 AAAAAAACTTAAATACTTAAATAGGA
34593685 TAAAAAGAACTTAAATA
1 -AAAAA-AACTTAAATA
34593702 TCATTTTTTT
Statistics
Matches: 52, Mismatches: 14, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
26 2 0.04
27 38 0.73
28 12 0.23
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.25
Consensus pattern (26 bp):
AAAAAAACTTAAATACTTAAATAGGA
Found at i:34599338 original size:16 final size:16
Alignment explanation
Indices: 34599317--34599368 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
34599307 TTTGGTTCGC
34599317 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
34599333 TGTATTGAATTAGAGG
1 TGTATTGGATTAGAGG
* * *
34599349 TATAATGGATTAGAGA
1 TGTATTGGATTAGAGG
34599365 TGTA
1 TGTA
34599369 ATAACAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:34599831 original size:57 final size:60
Alignment explanation
Indices: 34599733--34599880 Score: 205
Period size: 57 Copynumber: 2.5 Consensus size: 60
34599723 ACCCTAATTC
* * * *
34599733 GGATTACCCATCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATC-A-A
1 GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA
34599791 -GATCACCCGTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGCTATATCAGGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGGGAGGGCTATATC--GATA
34599852 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACCCGTCCGGGCTAGATCCTTTTT
34599881 ACCGTCAATT
Statistics
Matches: 79, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
56 6 0.08
57 44 0.56
60 1 0.01
61 1 0.01
62 21 0.27
63 6 0.08
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (60 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA
Found at i:34602363 original size:23 final size:23
Alignment explanation
Indices: 34602333--34602393 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
34602323 TGGACAAATG
34602333 AAGGCCATGTTCCTGTTTTTATT
1 AAGGCCATGTTCCTGTTTTTATT
34602356 AAGGCCATGTTCCTGTTTTTATT
1 AAGGCCATGTTCCTGTTTTTATT
** *
34602379 GTGGCTATGTTCCTG
1 AAGGCCATGTTCCTG
34602394 AGTTGAACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (23 bp):
AAGGCCATGTTCCTGTTTTTATT
Found at i:34604086 original size:2 final size:2
Alignment explanation
Indices: 34604079--34604107 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34604069 TGTTTTAACA
34604079 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 A
34604108 AATTTTGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34604153 original size:14 final size:14
Alignment explanation
Indices: 34604125--34604160 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
34604115 ATTAATTTGG
34604125 TTAACC-AACCAAA
1 TTAACCGAACCAAA
*
34604138 TTAACCGAACCGAA
1 TTAACCGAACCAAA
34604152 TTAACCGAA
1 TTAACCGAA
34604161 AAAAATTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.47, C:0.28, G:0.08, T:0.17
Consensus pattern (14 bp):
TTAACCGAACCAAA
Found at i:34604752 original size:2 final size:2
Alignment explanation
Indices: 34604740--34604903 Score: 220
Period size: 2 Copynumber: 84.0 Consensus size: 2
34604730 GATAGCATTC
34604740 AT AT GAT 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
34604783 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
34604825 AT AT AT AT AT AT -T AT AT AT ACT AT -T AT -T AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
34604864 ACT AT AT AGT AT AT -T AT -T AT -T AT AT AT -T AT ACT AT -T AT
1 A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
34604902 AT
1 AT
34604904 TATTATTATT
Statistics
Matches: 148, Mismatches: 0, Indels: 28
0.84 0.00 0.16
Matches are distributed among these distances:
1 9 0.06
2 129 0.87
3 10 0.07
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:34604854 original size:3 final size:3
Alignment explanation
Indices: 34604846--34605240 Score: 523
Period size: 3 Copynumber: 132.7 Consensus size: 3
34604836 TTATATATAC
* *
34604846 TAT TAT TA- TAT TA- TAT ATAC TAT ATAG TA- TAT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT -TAT TAT TAT TAT TAT TAT -TAT
*
34604891 TA- TAC TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34604936 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
34604984 TAT TAT TAA TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34605032 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
34605080 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAA TAC TAG TAT TAG TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** *
34605128 TAT TCG TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *** *
34605176 TAT TAG TCT TAT GAG GGG TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34605224 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
34605241 GTGTCGGGGG
Statistics
Matches: 352, Mismatches: 31, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
2 12 0.03
3 333 0.95
4 7 0.02
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:34629746 original size:2 final size:2
Alignment explanation
Indices: 34629721--34629771 Score: 70
Period size: 2 Copynumber: 26.0 Consensus size: 2
34629711 TTAAAACATT
*
34629721 TA TA GTA TA TA TG TA TA T- TA -A 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 TA TA TA TA
34629762 TA TA TA TA TA
1 TA TA TA TA TA
34629772 GGCGCACACA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:34631344 original size:18 final size:18
Alignment explanation
Indices: 34631317--34631370 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
34631307 ATAAAATTCA
* *
34631317 ATAAAATTTATT-AAATT
1 ATAAATTTTATTAAAAAT
*
34631334 ATTAAATTTTAATAAAAAT
1 A-TAAATTTTATTAAAAAT
*
34631353 ATAAATTTTATTTAAAAT
1 ATAAATTTTATTAAAAAT
34631371 TAGAAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 1 0.03
18 24 0.80
19 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAAATTTTATTAAAAAT
Found at i:34631399 original size:20 final size:19
Alignment explanation
Indices: 34631376--34631438 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
34631366 AAAATTAGAA
*
34631376 AAAAATTTATAAAAATCGTT
1 AAAAATTTAAAAAAATCG-T
* *
34631396 AAAAATATAAAAAAATTGT
1 AAAAATTTAAAAAAATCGT
* * *
34631415 AAAATTTTACAAAAATCAT
1 AAAAATTTAAAAAAATCGT
34631434 AAAAA
1 AAAAA
34631439 AATGCTCTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAAATTTAAAAAAATCGT
Found at i:34631722 original size:29 final size:28
Alignment explanation
Indices: 34631642--34631744 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 28
34631632 CTTTATATTT
* *
34631642 TTTTATAATTTTCTTACGACTTTATAAAA
1 TTTTATAATTTTTTTATGA-TTTATAAAA
* * *
34631671 TTTTGTAATTTTTTTCTAT-ATTTCTACATA
1 TTTTATAA-TTTTTT-TATGATTTATA-AAA
34631701 TTTTATAATTTTTTTATGATTTTTTATAAAA
1 TTTTATAATTTTTTTATGA---TTTATAAAA
*
34631732 TTTTACAATTTTT
1 TTTTATAATTTTT
34631745 CTATAAATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
28 3 0.05
29 19 0.33
30 15 0.26
31 16 0.28
32 5 0.09
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTTATAATTTTTTTATGATTTATAAAA
Found at i:34631769 original size:20 final size:21
Alignment explanation
Indices: 34631701--34631778 Score: 79
Period size: 22 Copynumber: 3.7 Consensus size: 21
34631691 TTTCTACATA
*
34631701 TTTTATAATTTTTTTA-TGATT
1 TTTTATAAATTTTTTACT-ATT
* *
34631722 TTTTATAAA-ATTTTACAATT
1 TTTTATAAATTTTTTACTATT
34631742 TTTCTATAAATTTTTTACTATT
1 TTT-TATAAATTTTTTACTATT
*
34631764 TTTATATATATTTTT
1 TTT-TATAAATTTTT
34631779 AGTTTTTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 11 0.23
21 14 0.30
22 22 0.47
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (21 bp):
TTTTATAAATTTTTTACTATT
Found at i:34631779 original size:21 final size:21
Alignment explanation
Indices: 34631678--34631779 Score: 68
Period size: 20 Copynumber: 4.9 Consensus size: 21
34631668 AAATTTTGTA
* * *
34631678 ATTTTTTTCTATATTTCTAC-
1 ATTTTTATATATATTTTTACT
*
34631698 ATATTTTATA-ATTTTTTTA-T
1 AT-TTTTATATATATTTTTACT
* * *
34631718 GATTTTT-TATAAAATTTTACA
1 -ATTTTTATATATATTTTTACT
* *
34631739 ATTTTTCTATAAATTTTTTACT
1 ATTTTTATATATA-TTTTTACT
34631761 ATTTTTATATATATTTTTA
1 ATTTTTATATATATTTTTA
34631780 GTTTTTAATA
Statistics
Matches: 63, Mismatches: 12, Indels: 13
0.72 0.14 0.15
Matches are distributed among these distances:
19 2 0.03
20 25 0.40
21 19 0.30
22 17 0.27
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (21 bp):
ATTTTTATATATATTTTTACT
Found at i:34631785 original size:20 final size:19
Alignment explanation
Indices: 34631701--34631785 Score: 55
Period size: 21 Copynumber: 4.2 Consensus size: 19
34631691 TTTCTACATA
*
34631701 TTTTATAATTTTTTTATGATT
1 TTTTATAATATTTTTA-G-TT
* * *
34631722 TTTTATAAAATTTTACAATT
1 TTTTATAATATTTT-TAGTT
*
34631742 TTTCTATAA-ATTTTTTACTAT
1 TTT-TATAATA-TTTTTAGT-T
34631763 TTTTATATATATTTTTAGTT
1 TTTTATA-ATATTTTTAGTT
34631783 TTT
1 TTT
34631786 AATATTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
20 16 0.31
21 33 0.65
22 2 0.04
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTATAATATTTTTAGTT
Found at i:34631785 original size:61 final size:61
Alignment explanation
Indices: 34631662--34631779 Score: 139
Period size: 61 Copynumber: 1.9 Consensus size: 61
34631652 TTCTTACGAC
** * * * *
34631662 TTTATAAAATTTTGTAATTTTTTTCTATATTTCTACATATTTTATAATTTTTTTATGATTT
1 TTTATAAAATTTTACAATTTTTCTATAAATTTCTACATATTTTATAATATTTTTATGATTT
*
34631723 TTTATAAAATTTTACAATTTTTCTATAAATTTTTTAC-TATTTTTATATATATTTTTA
1 TTTATAAAATTTTACAATTTTTCTATAAA-TTTCTACATA-TTTTATA-ATATTTTTA
34631780 GTTTTTAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
61 26 0.55
62 13 0.28
63 8 0.17
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (61 bp):
TTTATAAAATTTTACAATTTTTCTATAAATTTCTACATATTTTATAATATTTTTATGATTT
Found at i:34631785 original size:71 final size:73
Alignment explanation
Indices: 34631677--34631815 Score: 176
Period size: 71 Copynumber: 1.9 Consensus size: 73
34631667 AAAATTTTGT
* * * * *
34631677 AATTTTTTTCTATATTTCTACATATTTTATAATTTTTTTATGATTTTTTA-TAAAATTTTACAAT
1 AATTTTTTACTATATTTATACATATTTTATAAGTTTTTAAT-ATTTTTTATTAAAATTTAACAAT
34631741 TTTTCTATA
65 TTTTCTATA
* * *
34631750 AATTTTTTACTATTTTTATATATATTTT-T-AGTTTTTAATATTTTTTATTAAAATTTAATAATT
1 AATTTTTTACTATATTTATACATATTTTATAAGTTTTTAATATTTTTTATTAAAATTTAACAATT
34631813 TTT
66 TTT
34631816 ACAATTTATA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
70 8 0.14
71 24 0.42
72 1 0.02
73 24 0.42
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (73 bp):
AATTTTTTACTATATTTATACATATTTTATAAGTTTTTAATATTTTTTATTAAAATTTAACAATT
TTTCTATA
Found at i:34631790 original size:18 final size:18
Alignment explanation
Indices: 34631762--34631796 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
34631752 TTTTTTACTA
34631762 TTTTTATATATATTTTTAG
1 TTTTTATATAT-TTTTTAG
34631781 TTTTTA-ATATTTTTTA
1 TTTTTATATATTTTTTA
34631797 TTAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTTATATATTTTTTAG
Found at i:34635198 original size:730 final size:729
Alignment explanation
Indices: 34633798--34635242 Score: 2872
Period size: 730 Copynumber: 2.0 Consensus size: 729
34633788 GTGAATGGTG
34633798 AATAAAAATTCACTATGTTTCTAACAGAAGAGAGAAAGACTTAATGTTACACGAAAATGTTAAGA
1 AATAAAAATTCACTATGTTTCTAACAGAAGAGAGAAAGACTTAATGTTACACGAAAATGTTAAGA
34633863 GGAAAGTCTCTTATCTCTATGTCTAATCTATCAAGACAAACTTTTTGAAACATCCCAAGAGTGAA
66 GGAAAGTCTCTTATCTCTATGTCTAATCTATCAAGACAAACTTTTTGAAACATCCCAAGAGTGAA
34633928 GGCAACCCAAGAACTTTACCATATTCTAAGGTTATTTTCACTTCTTCCATTTCAGTGAAGCAGTA
131 GGCAACCCAAGAACTTTACCATATTCTAAGGTTATTTTCACTTCTTCCATTTCAGTGAAGCAGTA
34633993 TTATGTAAAACATTTCCCCGAAACTTTTGTTGAAATGCAAAACGTTAATGGTTAAATATAACTCA
196 TTATGTAAAACATTTCCCCGAAACTTTTGTTGAAATGCAAAACGTTAATGGTTAAATATAACTCA
34634058 AAAAAGAATAAGGACCAAATTGATTAAAAAATATAAACATTGAGAGCTAAATTTATCATTATATC
261 AAAAAGAATAAGGACCAAATTGATTAAAAAATATAAACATTGAGAGCTAAATTTATCATTATATC
34634123 TTGAATAATGAATATTGTGTATGAATGTTAATTTTTTTACTATTATTTTTTAGTGTTGACATATT
326 TTGAATAATGAATATTGTGTATGAATGTTAATTTTTTTACTATTATTTTTTAGTGTTGACATATT
34634188 ATTGTATTAGTAATGGTGTTAATATATTTTAATTAAAGTTAAAATATGTCATAAATAGATGTAGT
391 ATTGTATTAGTAATGGTGTTAATATATTTTAATTAAAGTTAAAATATGTCATAAATAGATGTAGT
*
34634253 TTTTATAAATTTAGAATTTAGTTACTGTACTTTAATTTATAAGAATTTAGTTTGTTTGTTTTTTA
456 TTTTATAAATTTAGAATTTAGTTACTGTACTTTAATTTATAAGAATTTAATTTGTTTGTTTTTTA
34634318 AAATTTAAAATTTAAGTCAAATAATTATTAAATTATTTTATTATTTTATTTTTAGGAATAAATTG
521 AAATTTAAAATTTAAGTCAAATAATTATTAAATTATTTTATTATTTTATTTTTAGGAATAAATTG
34634383 TTTTTATTTTTATATGCTATGCCATTTATATAAAATAAAATTAAATATTTAATGCTTTATGGTTA
586 TTTTTATTTTTATATGCTATGCCATTTATATAAAATAAAATTAAATATTTAATGCTTTATGGTTA
34634448 AAATTTTAACAAAAGAAAAACATATAAAAATATAATTAATAATTAATACAATTTTACAAAAGAAA
651 AAATTTTAACAAAAGAAAAACATATAAAAATATAATTAATAATTAATACAATTTTACAAAA-AAA
34634513 AACATATAAAAATAT
715 AACATATAAAAATAT
34634528 AATAAAAATTCACTATGTTTCTAACAGAAGAGAGAAAGACTTAATGTTACACGAAAATGTTAAGA
1 AATAAAAATTCACTATGTTTCTAACAGAAGAGAGAAAGACTTAATGTTACACGAAAATGTTAAGA
34634593 GGAAAGTCTCTTATCTCTATGTCTAATCTATCAAGACAAACTTTTTGAAACATCCCAAGAGTGAA
66 GGAAAGTCTCTTATCTCTATGTCTAATCTATCAAGACAAACTTTTTGAAACATCCCAAGAGTGAA
34634658 GGCAACCCAAGAACTTTACCATATTCTAAGGTTATTTTCACTTCTTCCATTTCAGTGAAGCAGTA
131 GGCAACCCAAGAACTTTACCATATTCTAAGGTTATTTTCACTTCTTCCATTTCAGTGAAGCAGTA
34634723 TTATGTAAAACATTTCCCCGAAACTTTTGTTGAAATGCAAAACGTTAATGGTTAAATATAACTCA
196 TTATGTAAAACATTTCCCCGAAACTTTTGTTGAAATGCAAAACGTTAATGGTTAAATATAACTCA
34634788 AAAAAGAATAAGGACCAAATTGATTAAAAAATATAAACATTGAGAGCTAAATTTATCATTATATC
261 AAAAAGAATAAGGACCAAATTGATTAAAAAATATAAACATTGAGAGCTAAATTTATCATTATATC
34634853 TTGAATAATGAATATTGTGTATGAATGTTAATTTTTTTACTATTATTTTTTAGTGTTGACATATT
326 TTGAATAATGAATATTGTGTATGAATGTTAATTTTTTTACTATTATTTTTTAGTGTTGACATATT
34634918 ATTGTATTAGTAATGGTGTTAATATATTTTAATTAAAGTTAAAATATGTCATAAATAGATGTAGT
391 ATTGTATTAGTAATGGTGTTAATATATTTTAATTAAAGTTAAAATATGTCATAAATAGATGTAGT
34634983 TTTTATAAATTTAGAATTTAGTTACTGTACTTTAATTTATAAGAATTTAATTTGTTTGTTTTTTA
456 TTTTATAAATTTAGAATTTAGTTACTGTACTTTAATTTATAAGAATTTAATTTGTTTGTTTTTTA
34635048 AAATTTAAAATTTAAGTCAAATAATTATTAAATTATTTTATTATTTTATTTTTAGGAATAAATTG
521 AAATTTAAAATTTAAGTCAAATAATTATTAAATTATTTTATTATTTTATTTTTAGGAATAAATTG
34635113 TTTTTATTTTTATATGCTATGCCATTTATATAAAATAAAATTAAATATTTAATGCTTTATGGTTA
586 TTTTTATTTTTATATGCTATGCCATTTATATAAAATAAAATTAAATATTTAATGCTTTATGGTTA
34635178 AAATTTTAACAAAAGAAAAACATATAAAAATATAATTAATAATTAATACAATTTTACAAAAAAAA
651 AAATTTTAACAAAAGAAAAACATATAAAAATATAATTAATAATTAATACAATTTTACAAAAAAAA
34635243 TTAAAATTTA
Statistics
Matches: 714, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
729 4 0.01
730 710 0.99
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (729 bp):
AATAAAAATTCACTATGTTTCTAACAGAAGAGAGAAAGACTTAATGTTACACGAAAATGTTAAGA
GGAAAGTCTCTTATCTCTATGTCTAATCTATCAAGACAAACTTTTTGAAACATCCCAAGAGTGAA
GGCAACCCAAGAACTTTACCATATTCTAAGGTTATTTTCACTTCTTCCATTTCAGTGAAGCAGTA
TTATGTAAAACATTTCCCCGAAACTTTTGTTGAAATGCAAAACGTTAATGGTTAAATATAACTCA
AAAAAGAATAAGGACCAAATTGATTAAAAAATATAAACATTGAGAGCTAAATTTATCATTATATC
TTGAATAATGAATATTGTGTATGAATGTTAATTTTTTTACTATTATTTTTTAGTGTTGACATATT
ATTGTATTAGTAATGGTGTTAATATATTTTAATTAAAGTTAAAATATGTCATAAATAGATGTAGT
TTTTATAAATTTAGAATTTAGTTACTGTACTTTAATTTATAAGAATTTAATTTGTTTGTTTTTTA
AAATTTAAAATTTAAGTCAAATAATTATTAAATTATTTTATTATTTTATTTTTAGGAATAAATTG
TTTTTATTTTTATATGCTATGCCATTTATATAAAATAAAATTAAATATTTAATGCTTTATGGTTA
AAATTTTAACAAAAGAAAAACATATAAAAATATAATTAATAATTAATACAATTTTACAAAAAAAA
ACATATAAAAATAT
Found at i:34636571 original size:17 final size:17
Alignment explanation
Indices: 34636545--34636577 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
34636535 AAAATTATAA
*
34636545 ATAAAGTATTAAAAAAT
1 ATAAAATATTAAAAAAT
34636562 ATAAAATATTAAAAAA
1 ATAAAATATTAAAAAA
34636578 GTAATCAATC
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:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
ATAAAATATTAAAAAAT
Found at i:34639418 original size:14 final size:14
Alignment explanation
Indices: 34639401--34639431 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
34639391 TTAAATTATG
*
34639401 AAAATAAAATCTCT
1 AAAACAAAATCTCT
34639415 AAAACAAAATCTCT
1 AAAACAAAATCTCT
34639429 AAA
1 AAA
34639432 CTAAGTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAACAAAATCTCT
Found at i:34640574 original size:16 final size:16
Alignment explanation
Indices: 34640537--34640576 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
34640527 TTAATAAAAT
* *
34640537 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
34640553 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
34640569 TAAAATTA
1 TAAAATTA
34640577 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:34640646 original size:66 final size:59
Alignment explanation
Indices: 34640579--34640698 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
34640569 TAAAATTATC
* * *
34640579 AAATTAT-TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
*
34640637 AATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
34640696 AAA
1 AAA
34640699 CAAACTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 6 0.11
59 50 0.89
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
Found at i:34640796 original size:23 final size:24
Alignment explanation
Indices: 34640762--34640809 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
34640752 GTAAATAAAC
*
34640762 TTAAAACAAAAAACTAT-TATATT
1 TTAAAACAAAAAAATATATATATT
34640785 TTAAAA-ATAAAAAATATATATATT
1 TTAAAACA-AAAAAATATATATATT
34640809 T
1 T
34640810 AATATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 14 0.64
24 7 0.32
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAAAACAAAAAAATATATATATT
Found at i:34640811 original size:23 final size:24
Alignment explanation
Indices: 34640764--34640809 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
34640754 AAATAAACTT
34640764 AAAACAAAAAACTATTATATTTTA
1 AAAACAAAAAACTATTATATTTTA
*
34640788 AAAATAAAAAA-TATATATATTT
1 AAAACAAAAAACTAT-TATATTT
34640810 AATATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAACAAAAAACTATTATATTTTA
Found at i:34657406 original size:14 final size:17
Alignment explanation
Indices: 34657387--34657424 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
34657377 ATTTATTTCT
34657387 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
34657401 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
34657418 TAATATA
1 TAATATA
34657425 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:34657432 original size:12 final size:11
Alignment explanation
Indices: 34657404--34657447 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
34657394 ATATTTATAA
34657404 TATAATTAATT
1 TATAATTAATT
*
34657415 TAATAATATACTT
1 T-ATAAT-TAATT
34657428 TATAATTAATT
1 TATAATTAATT
34657439 TATATATTA
1 TATA-ATTA
34657448 TATAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.32
12 14 0.50
13 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TATAATTAATT
Found at i:34657451 original size:20 final size:23
Alignment explanation
Indices: 34657399--34657461 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
34657389 ATATAATATT
34657399 TATA-ATATAATTAATTTAATAA
1 TATATATATAATTAATTTAATAA
* *
34657421 TATACTTTATAATTAATTTATATAT
1 TATA-TATATAATTAATTTA-ATAA
* *
34657446 TATATAAATAAATAAT
1 TATATATATAATTAAT
34657462 ATAAATATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 4 0.12
24 22 0.67
25 7 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATATATAATTAATTTAATAA
Found at i:34657463 original size:20 final size:20
Alignment explanation
Indices: 34657416--34657464 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
34657406 TAATTAATTT
*
34657416 AATAATATACTTTATAATTA
1 AATAATATACTTTATAAATA
* *
34657436 ATTTATATA-TTATATAAATA
1 AATAATATACTT-TATAAATA
34657456 AATAATATA
1 AATAATATA
34657465 AATATCTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATATACTTTATAAATA
Found at i:34664705 original size:157 final size:157
Alignment explanation
Indices: 34664403--34664696 Score: 342
Period size: 157 Copynumber: 1.9 Consensus size: 157
34664393 CCAAAAAAGG
* * * * * * * * *
34664403 AAAATGGGTGTTGTGATTAGGGATTAATACGATGGCTTGAAATCTAGCATAAGTTGTGGATTCTT
1 AAAATGGGTATTGTGATTAGGAATTAATACGATGACTGGAAATCCAACATAAGTTGCGGATCCTC
* ** *
34664468 TGAAGCTAGTGTTAGTAGCATCGTACTAAGCTAGTGTTAGCAACCCTGATCTGAAGCTAGTGCTA
66 TGAAGCTAGTGTTAGTAGAATCAAACTAAACTAGTGTTAGCAACCCTGATCTGAAGCTAGTGCTA
** *
34664533 GTAGCTCAAATATGTCGACTTGTATAA
131 ACAGCCCAAATATGTCGACTTGTATAA
* * *
34664560 AAAATGGGTATTGTGATT-GAGAATTAATTCGATGACTGGAGATCCAACATATGTTGCGGATCCT
1 AAAATGGGTATTGTGATTAG-GAATTAATACGATGACTGGAAATCCAACATAAGTTGCGGATCCT
* *
34664624 CTGAAGCTAGTGTTCGTA-AATTCAAACTAAACTAGTGTTAGCAA-CCTGGATTTGAAGCTAGTG
65 CTGAAGCTAGTGTTAGTAGAA-TCAAACTAAACTAGTGTTAGCAACCCT-GATCTGAAGCTAGTG
*
34664687 TTAACAGCCC
128 CTAACAGCCC
34664697 GATAATGTCA
Statistics
Matches: 112, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
156 5 0.04
157 107 0.96
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (157 bp):
AAAATGGGTATTGTGATTAGGAATTAATACGATGACTGGAAATCCAACATAAGTTGCGGATCCTC
TGAAGCTAGTGTTAGTAGAATCAAACTAAACTAGTGTTAGCAACCCTGATCTGAAGCTAGTGCTA
ACAGCCCAAATATGTCGACTTGTATAA
Found at i:34666470 original size:27 final size:26
Alignment explanation
Indices: 34666415--34666468 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
34666405 GGTCCAGCAA
*
34666415 TTATTATTTTAAAAAATTTCAATTTT
1 TTATAATTTTAAAAAATTTCAATTTT
* *
34666441 TTATAATTTTTAAAAATTTTAATTTT
1 TTATAATTTTAAAAAATTTCAATTTT
34666467 TT
1 TT
34666469 TAAAAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATAATTTTAAAAAATTTCAATTTT
Found at i:34666480 original size:17 final size:18
Alignment explanation
Indices: 34666447--34666480 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34666437 TTTTTTATAA
*
34666447 TTTTTAAAAATTTTAATT
1 TTTTTAAAAATTATAATT
34666465 TTTTTAAAAA-TATAAT
1 TTTTTAAAAATTATAAT
34666481 CTTTGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTTAAAAATTATAATT
Found at i:34685093 original size:13 final size:15
Alignment explanation
Indices: 34685074--34685106 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
34685064 GACTAAAATT
34685074 CTAAAAATA-AAAAA
1 CTAAAAATATAAAAA
34685088 -TAAAAATATAAAAA
1 CTAAAAATATAAAAA
34685102 CTAAA
1 CTAAA
34685107 TTCTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.47
14 5 0.29
15 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
CTAAAAATATAAAAA
Found at i:34685635 original size:15 final size:15
Alignment explanation
Indices: 34685578--34685636 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
34685568 TATACTTCAT
*
34685578 TTTTCTTTTTATTTTA
1 TTTT-TTTTTCTTTTA
*
34685594 TTTTTTATTTTCTTTCA
1 -TTTTT-TTTTCTTTTA
**
34685611 TTTTCGTTTCTTTTA
1 TTTTTTTTTCTTTTA
34685626 TTTTTTTTTCT
1 TTTTTTTTTCT
34685637 GGGTCTTCTT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
15 17 0.50
16 5 0.15
17 12 0.35
ACGTcount: A:0.08, C:0.10, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTTTTTCTTTTA
Found at i:34690752 original size:17 final size:19
Alignment explanation
Indices: 34690718--34690758 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
34690708 TAAAATATTG
34690718 AAAAATTATAAGAATTAAA
1 AAAAATTATAAGAATTAAA
*
34690737 AAAAATT-TAA-ATTTAAA
1 AAAAATTATAAGAATTAAA
34690754 AAAAA
1 AAAAA
34690759 AAACTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.52
18 3 0.14
19 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAATTATAAGAATTAAA
Found at i:34691117 original size:21 final size:21
Alignment explanation
Indices: 34691091--34691148 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
34691081 CCTTAAAACG
34691091 AGATGTCTCGATACATCCCTT
1 AGATGTCTCGATACATCCCTT
* * *
34691112 AGATGT-TCAATATATCCTTT
1 AGATGTCTCGATACATCCCTT
*
34691132 AGTTGTGC-CGATACATC
1 AGATGT-CTCGATACATC
34691149 TTTAAATGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (21 bp):
AGATGTCTCGATACATCCCTT
Found at i:34692347 original size:46 final size:46
Alignment explanation
Indices: 34692280--34692374 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
34692270 AAGAAAACCC
*
34692280 TTTGTGGGATCAATGCTTGTGATATTATGTATAGTTTTTATGCATG
1 TTTGTGGGATCAATGCTTGTGATATTAGGTATAGTTTTTATGCATG
34692326 TTTGTGGGATCAATGCTTGTGATATTAGGTATAGTTTTTATGCATG
1 TTTGTGGGATCAATGCTTGTGATATTAGGTATAGTTTTTATGCATG
34692372 TTT
1 TTT
34692375 ATTATATCTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.48
Consensus pattern (46 bp):
TTTGTGGGATCAATGCTTGTGATATTAGGTATAGTTTTTATGCATG
Found at i:34695435 original size:2 final size:2
Alignment explanation
Indices: 34695428--34695459 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34695418 AAGTCATTAC
34695428 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
34695460 CACATATCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34698857 original size:13 final size:13
Alignment explanation
Indices: 34698839--34698863 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34698829 TTAAACGGTA
34698839 AAATTTTCACACG
1 AAATTTTCACACG
34698852 AAATTTTCACAC
1 AAATTTTCACAC
34698864 ATAAATTAAC
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:34704549 original size:20 final size:21
Alignment explanation
Indices: 34704524--34704564 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34704514 ATTGTGAGAG
34704524 TTAAAA-ATAAAACGAAATAA
1 TTAAAACATAAAACGAAATAA
* *
34704544 TTAAAACATGAAACGAGATAA
1 TTAAAACATAAAACGAAATAA
34704565 AATTAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (21 bp):
TTAAAACATAAAACGAAATAA
Found at i:34706821 original size:224 final size:225
Alignment explanation
Indices: 34706431--34706870 Score: 846
Period size: 224 Copynumber: 2.0 Consensus size: 225
34706421 TAATTAGATC
* *
34706431 ATTCAACAAAACAAGAAATTTGAATCCTATGTTTTTCGGATTTGGGTGAGTTTGTGTTCAGTTTT
1 ATTCAACAAAACAAGAAATTTGAATCCTATGTTATTCGGATTTGGGTGAGTTTGAGTTCAGTTTT
*
34706496 TCATGTATTTGGTGGGTTCTTGGGGTCCTATCCCTATATATATGTCGAAATGTGTTGTATACAGG
66 TCATGTATTTGGTGGGTTCTTGGGGTCCTATCCCTATATATATGTCGAAATGTGTTGAATACAGG
34706561 TATTTCAGTCAGAATGAACAGTTGAAGCAGCACAGTCTGAATTTTCTAGTAGTTTTAGCACCA-C
131 TATTTCAGTCAGAATGAACAGTTGAAGCAGCACAGTCTGAATTTTCTAGTAGTTTTAGCACCATC
34706625 CATATTGGTAATAATAATGAATCCTATGTT
196 CATATTGGTAATAATAATGAATCCTATGTT
34706655 ATTCAACAAAACAAGAAATTTGAATCCTATGTTATTCGGATTTGGGTGAGTTTGAGTTCAGTTTT
1 ATTCAACAAAACAAGAAATTTGAATCCTATGTTATTCGGATTTGGGTGAGTTTGAGTTCAGTTTT
34706720 TCATGTATTTGGTGGGTTCTTGGGGTCCTATCCCTATATATATGTCGAAATGTGTTGAATACAGG
66 TCATGTATTTGGTGGGTTCTTGGGGTCCTATCCCTATATATATGTCGAAATGTGTTGAATACAGG
34706785 TATTTCAGTCAGAATGAACAGTTGAAGCAGCACAGTCTGAATTTTCTAGTAGTTTTAGCACCATC
131 TATTTCAGTCAGAATGAACAGTTGAAGCAGCACAGTCTGAATTTTCTAGTAGTTTTAGCACCATC
34706850 CATATTGGTAATAATAATGAA
196 CATATTGGTAATAATAATGAA
34706871 ACTACGATGC
Statistics
Matches: 212, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
224 190 0.90
225 22 0.10
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.37
Consensus pattern (225 bp):
ATTCAACAAAACAAGAAATTTGAATCCTATGTTATTCGGATTTGGGTGAGTTTGAGTTCAGTTTT
TCATGTATTTGGTGGGTTCTTGGGGTCCTATCCCTATATATATGTCGAAATGTGTTGAATACAGG
TATTTCAGTCAGAATGAACAGTTGAAGCAGCACAGTCTGAATTTTCTAGTAGTTTTAGCACCATC
CATATTGGTAATAATAATGAATCCTATGTT
Found at i:34710212 original size:26 final size:24
Alignment explanation
Indices: 34710175--34710228 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
34710165 GAAAATAAAC
34710175 AAATTTGAATTTCAAAGCAAATTTGT
1 AAATTTGAATTTCAAAG--AATTTGT
* *
34710201 AAATTT-ATATTTTATAGAATTTGT
1 AAATTTGA-ATTTCAAAGAATTTGT
34710225 AAAT
1 AAAT
34710229 ATCCAACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 11 0.44
25 1 0.04
26 13 0.52
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (24 bp):
AAATTTGAATTTCAAAGAATTTGT
Found at i:34713740 original size:2 final size:2
Alignment explanation
Indices: 34713733--34713768 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
34713723 AGTATAGCCT
*
34713733 TA TA TA TA TA TA TA TA TG 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 TA
34713769 AAGGTTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34715411 original size:41 final size:41
Alignment explanation
Indices: 34715349--34715468 Score: 145
Period size: 41 Copynumber: 2.9 Consensus size: 41
34715339 CCGGATTTAT
* * * *
34715349 TGCCAGTGAAATAATTCAGACTTTAGGTCTAGCAGGCTTGA
1 TGCCAGTGAAATTATTCAGACTATAAGTCTAGCAGGCTTAA
* * *
34715390 TGCCGGTGAAATTATTCAGACTATACGTCTAGCAAGCTTAA
1 TGCCAGTGAAATTATTCAGACTATAAGTCTAGCAGGCTTAA
34715431 TGCCAGTGATACA-T-TTCAGACTATAAGTCTAGCAGGCT
1 TGCCAGTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCT
34715469 AAAAGACGGT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 65 0.96
42 2 0.03
43 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (41 bp):
TGCCAGTGAAATTATTCAGACTATAAGTCTAGCAGGCTTAA
Found at i:34721643 original size:2 final size:2
Alignment explanation
Indices: 34721636--34721660 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34721626 CTAGAGTTAA
34721636 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
34721661 TTATTATTAT
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:34725036 original size:16 final size:15
Alignment explanation
Indices: 34725011--34725041 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
34725001 ACTTTATTTT
34725011 TAAAATATTTTTTAA
1 TAAAATATTTTTTAA
34725026 TAAATATATTTTTTAA
1 TAAA-ATATTTTTTAA
34725042 AATTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAAATATTTTTTAA
Found at i:34727010 original size:75 final size:76
Alignment explanation
Indices: 34726927--34727077 Score: 250
Period size: 76 Copynumber: 2.0 Consensus size: 76
34726917 ATCATTGAAG
* * *
34726927 CAAT-AAAAAAAACATGCAAGGTTTCGTGATTTCATCCCAATAAGTTTCACCCAAAACATTGCCC
1 CAATAAAAAAAAACATGCAAGATTTCATGATTTCATCCAAATAAGTTTCACCCAAAACATTGCCC
34726991 ATATCAAAAGA
66 ATATCAAAAGA
* *
34727002 CAATAAAAAAAAACATGCAAGATTTCATGATTTCATCTAAATAAGTTTCATCCAAAACATTGCCC
1 CAATAAAAAAAAACATGCAAGATTTCATGATTTCATCCAAATAAGTTTCACCCAAAACATTGCCC
34727067 ATATCAAAAGA
66 ATATCAAAAGA
34727078 GGGATATGCA
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
75 4 0.06
76 66 0.94
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.25
Consensus pattern (76 bp):
CAATAAAAAAAAACATGCAAGATTTCATGATTTCATCCAAATAAGTTTCACCCAAAACATTGCCC
ATATCAAAAGA
Found at i:34736507 original size:25 final size:26
Alignment explanation
Indices: 34736457--34736509 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
34736447 TTTAAAATAC
*
34736457 TTTTAAAATATATATTTTTATTTTTA
1 TTTTAAAATATATATTTTTATGTTTA
34736483 TTTTAAAATA-AT-TTTTTAATGTTTA
1 TTTTAAAATATATATTTTT-ATGTTTA
34736508 TT
1 TT
34736510 AAAAAATGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 5 0.20
25 10 0.40
26 10 0.40
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTTAAAATATATATTTTTATGTTTA
Found at i:34736515 original size:25 final size:26
Alignment explanation
Indices: 34736461--34736516 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
34736451 AAATACTTTT
* **
34736461 AAAATATATATTTTTATTTTTATTTT
1 AAAATATATATTTTTATGTTTATTAA
34736487 AAAATA-AT-TTTTTAATGTTTATTAA
1 AAAATATATATTTTT-ATGTTTATTAA
34736512 AAAAT
1 AAAAT
34736517 GGGCCGGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 5 0.19
25 15 0.58
26 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
AAAATATATATTTTTATGTTTATTAA
Done.