Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 31 of 205
Found at i:9303939 original size:10 final size:11
Alignment explanation
Indices: 9303911--9303948 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9303901 TTTATGATTG
*
9303911 GTTTTTGAAAT
1 GTTTATGAAAT
9303922 GTTTATGAAAT
1 GTTTATGAAAT
9303933 G-TTATGAAAT
1 GTTTATGAAAT
*
9303943 TTTTAT
1 GTTTAT
9303949 ATTTGATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (11 bp):
GTTTATGAAAT
Found at i:9304978 original size:20 final size:20
Alignment explanation
Indices: 9304953--9304994 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
9304943 TAGAGTGCAA
9304953 TGGATATTTAAGGTGGGATT
1 TGGATATTTAAGGTGGGATT
9304973 TGGATATTTAAGGTGGGATT
1 TGGATATTTAAGGTGGGATT
9304993 TG
1 TG
9304995 CCTAGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.36, T:0.40
Consensus pattern (20 bp):
TGGATATTTAAGGTGGGATT
Found at i:9308204 original size:24 final size:25
Alignment explanation
Indices: 9308133--9308308 Score: 106
Period size: 25 Copynumber: 7.1 Consensus size: 25
9308123 AAGCTCTTCC
**
9308133 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATAA
* *
9308158 GAGCCATGTAACGGGAAGATCATAA
1 GAGCCATATAACGGGAAGCTCATAA
* **
9308183 GAGCCCTAT-ACGGGAAGCTCATGC
1 GAGCCATATAACGGGAAGCTCATAA
* * **
9308207 GAGCTA-ATATCGGGAAGCTCCGAA
1 GAGCCATATAACGGGAAGCTCATAA
* ** * *
9308231 GATCCAT-TAATTAGGAAGCTCGTAC
1 GAGCCATATAA-CGGGAAGCTCATAA
** ***
9308256 GAGCCATATGTCGGGAAGCTCCGGA
1 GAGCCATATAACGGGAAGCTCATAA
** *
9308281 GAGCCATATATTGGGACGCTCATAA
1 GAGCCATATAACGGGAAGCTCATAA
9308306 GAG
1 GAG
9308309 TTGTAGTGTA
Statistics
Matches: 108, Mismatches: 39, Indels: 8
0.70 0.25 0.05
Matches are distributed among these distances:
23 2 0.02
24 32 0.30
25 73 0.68
26 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.19
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATAA
Found at i:9308413 original size:25 final size:24
Alignment explanation
Indices: 9308376--9308444 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
9308366 TATGTATCGG
**
9308376 GAAGCTCCGGAGAGCCAAATATCAA
1 GAAGCTCAAGAGAGCC-AATATCAA
* *
9308401 GAAGCTCAAGAGAGTCAATATCGA
1 GAAGCTCAAGAGAGCCAATATCAA
* * *
9308425 CAGGCTCAAGAGAGCTAATA
1 GAAGCTCAAGAGAGCCAATA
9308445 ACGGGATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
24 23 0.64
25 13 0.36
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (24 bp):
GAAGCTCAAGAGAGCCAATATCAA
Found at i:9314608 original size:25 final size:26
Alignment explanation
Indices: 9314563--9314637 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 26
9314553 GAATGCTCAA
* * *
9314563 TCGAGCACATA-AACAGAAAGCTC-TT
1 TCGAGC-CATATAACGGGAAGCTCATG
9314588 TCGAGCCATATAACGGGAAGCTCATG
1 TCGAGCCATATAACGGGAAGCTCATG
*
9314614 T-GAGCCATGTAACGGGAAGCTCAT
1 TCGAGCCATATAACGGGAAGCTCAT
9314638 AAGAGCCCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.09
25 38 0.86
26 2 0.05
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (26 bp):
TCGAGCCATATAACGGGAAGCTCATG
Found at i:9314643 original size:25 final size:25
Alignment explanation
Indices: 9314590--9314741 Score: 87
Period size: 25 Copynumber: 6.1 Consensus size: 25
9314580 AAGCTCTTTC
**
9314590 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATAA
*
9314615 GAGCCATGTAACGGGAAGCTCATAA
1 GAGCCATATAACGGGAAGCTCATAA
* * *
9314640 GAGCCCTAT-TCGAGAAGCTC-TAAA
1 GAGCCATATAACGGGAAGCTCAT-AA
* * ** * **
9314664 GAGTCGT-TAATCAAGAAGCTCGTGC
1 GAGCCATATAA-CGGGAAGCTCATAA
* * *
9314689 GAGCCGTATATCGGGAAGCTC-TGGA
1 GAGCCATATAACGGGAAGCTCAT-AA
* *
9314714 GAGCCATATATCGGGATGCTCATAA
1 GAGCCATATAACGGGAAGCTCATAA
9314739 GAG
1 GAG
9314742 TTGTAGTGTA
Statistics
Matches: 99, Mismatches: 21, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
23 2 0.02
24 17 0.17
25 76 0.77
26 4 0.04
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATAA
Found at i:9314871 original size:24 final size:23
Alignment explanation
Indices: 9314821--9314876 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
9314811 AGCTCCGGAT
*
9314821 AGCCAAATATCAGGAAGCTCAATG
1 AGCC-AATATCAGGAAGCTCAAAG
* *
9314845 AGCCAATATCGGGATGCTCATAAG
1 AGCCAATATCAGGAAGCTCA-AAG
*
9314869 AGCTAATA
1 AGCCAATA
9314877 ATGGGACTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (23 bp):
AGCCAATATCAGGAAGCTCAAAG
Found at i:9315138 original size:21 final size:21
Alignment explanation
Indices: 9315114--9315153 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9315104 AATTTAAGAC
* *
9315114 CAATTTAATACAATTCATACT
1 CAATTCAATACAATACATACT
*
9315135 CAATTCAATCCAATACATA
1 CAATTCAATACAATACATA
9315154 TCTTTTGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (21 bp):
CAATTCAATACAATACATACT
Found at i:9332504 original size:27 final size:27
Alignment explanation
Indices: 9332474--9332529 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
9332464 AAACTAATAT
9332474 AATTGCACATATACTGCACAAGTTTTG
1 AATTGCACATATACTGCACAAGTTTTG
9332501 AATTGCACATATACTGCACAAGTTTTG
1 AATTGCACATATACTGCACAAGTTTTG
9332528 AA
1 AA
9332530 CTTCAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (27 bp):
AATTGCACATATACTGCACAAGTTTTG
Found at i:9336388 original size:68 final size:68
Alignment explanation
Indices: 9336279--9336414 Score: 220
Period size: 68 Copynumber: 2.0 Consensus size: 68
9336269 TGTTTTCACG
* *
9336279 TCAAGCACATTTCTCTTTATGAGATAATCCAAATTTATAAGGAAGTGAC-AGTTATTGATATCGA
1 TCAAGCACATTTCTCTTTATGAGATAATCCAAATTTATAAGGAAGCGACGA-TTATCGATATCGA
9336343 CCCA
65 CCCA
* *
9336347 TCAAGCACATTTCTCTTTATGAGGTAATCCAAATTTATAAGGAAGCGACGATTATCGATGTCGAC
1 TCAAGCACATTTCTCTTTATGAGATAATCCAAATTTATAAGGAAGCGACGATTATCGATATCGAC
9336412 CCA
66 CCA
9336415 AACAAATAGA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 62 0.98
69 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (68 bp):
TCAAGCACATTTCTCTTTATGAGATAATCCAAATTTATAAGGAAGCGACGATTATCGATATCGAC
CCA
Found at i:9338800 original size:40 final size:40
Alignment explanation
Indices: 9338741--9338816 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
9338731 TGTACCTTAA
* *
9338741 TGCCCCTGTAAACAGTTCGGTGTCCCTATTTGCACAACTG
1 TGCCCCTGTAAACACTTCGGTGTCCCTAATTGCACAACTG
9338781 TGCCCCTGTAAACACTTCGGTGTCCCTAATTGCACA
1 TGCCCCTGTAAACACTTCGGTGTCCCTAATTGCACA
9338817 TTTATGCCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (40 bp):
TGCCCCTGTAAACACTTCGGTGTCCCTAATTGCACAACTG
Found at i:9338825 original size:40 final size:40
Alignment explanation
Indices: 9338740--9338827 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
9338730 TTGTACCTTA
* *
9338740 ATGCCCCTGTAAACAGTTCGGTGTCCCTATTTGCACAACT
1 ATGCCCCTGTAAACACTTCGGTGTCCCTAATTGCACAACT
* **
9338780 GTGCCCCTGTAAACACTTCGGTGTCCCTAATTGCACATTT
1 ATGCCCCTGTAAACACTTCGGTGTCCCTAATTGCACAACT
9338820 ATGCCCCT
1 ATGCCCCT
9338828 AAATGCACTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.20, C:0.32, G:0.17, T:0.31
Consensus pattern (40 bp):
ATGCCCCTGTAAACACTTCGGTGTCCCTAATTGCACAACT
Found at i:9338883 original size:20 final size:20
Alignment explanation
Indices: 9338821--9338895 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
9338811 TGCACATTTA
*
9338821 TGCCCCTAAATGCACTCTAG
1 TGCCCCTGAATGCACTCTAG
* *
9338841 TCCCCCTGACA-GCACAT-TCG
1 TGCCCCTGA-ATGCAC-TCTAG
*
9338861 TGCCCTTGAATGCACTCTAG
1 TGCCCCTGAATGCACTCTAG
*
9338881 TGCCCCTGATTGCAC
1 TGCCCCTGAATGCAC
9338896 ACCCGTGCTC
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
19 2 0.05
20 39 0.91
21 2 0.05
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.25
Consensus pattern (20 bp):
TGCCCCTGAATGCACTCTAG
Found at i:9338896 original size:40 final size:40
Alignment explanation
Indices: 9338804--9338896 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
9338794 ACTTCGGTGT
* *
9338804 CCCTAATTGCACATTTATGCCCCTAAATGCACTCTAGTCC
1 CCCTGATTGCACATTCATGCCCCTAAATGCACTCTAGTCC
** * * * *
9338844 CCCTGACAGCACATTCGTGCCCTTGAATGCACTCTAGTGC
1 CCCTGATTGCACATTCATGCCCCTAAATGCACTCTAGTCC
9338884 CCCTGATTGCACA
1 CCCTGATTGCACA
9338897 CCCGTGCTCC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.23, C:0.35, G:0.15, T:0.27
Consensus pattern (40 bp):
CCCTGATTGCACATTCATGCCCCTAAATGCACTCTAGTCC
Found at i:9348592 original size:4 final size:4
Alignment explanation
Indices: 9348583--9348619 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
9348573 CTAAAGGAAA
9348583 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
9348620 CGAGTGTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:9349632 original size:61 final size:59
Alignment explanation
Indices: 9349447--9349640 Score: 153
Period size: 61 Copynumber: 3.2 Consensus size: 59
9349437 GTGGATGTCT
* * *
9349447 TTGTGGCCATCTAACTATATGGACATCTCTATGGCTATCTTCTATATGAGTTTGGACGCCC
1 TTGTGGCCATCTAACTATATGGACA-CTCTATGGCTATCTTGTATA-GTGTTTGGACGCTC
* * * * * * * * * * *
9349508 TTGAGGCTATTTAA-TGTGAGTAGGTTC-CTTTGTGGCTATC-TG-ATATTATGTGGACGCTT
1 TTGTGGCCATCTAACTAT-A-T-GG-ACACTCTATGGCTATCTTGTATAGTGTTTGGACGCTC
9349567 TTGTGGCCATCTAACTATATGGACGACTCTATGGCTATCTTGTATACGTGTTTGGACGCTC
1 TTGTGGCCATCTAACTATATGGAC-ACTCTATGGCTATCTTGTATA-GTGTTTGGACGCTC
*
9349628 TTGTGGCTATCTA
1 TTGTGGCCATCTA
9349641 TGTCAAAGAA
Statistics
Matches: 97, Mismatches: 26, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
56 1 0.01
57 2 0.02
58 12 0.12
59 22 0.23
60 10 0.10
61 35 0.36
62 12 0.12
63 2 0.02
64 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (59 bp):
TTGTGGCCATCTAACTATATGGACACTCTATGGCTATCTTGTATAGTGTTTGGACGCTC
Found at i:9349662 original size:120 final size:119
Alignment explanation
Indices: 9349446--9349668 Score: 281
Period size: 120 Copynumber: 1.9 Consensus size: 119
9349436 AGTGGATGTC
*
9349446 TTTGTGGCCATCTAACTATATGGACATCTCTATGGCTATCTTCTATATGAGTTTGGACGCCCTTG
1 TTTGTGGCCATCTAACTATATGGACATCTCTATGGCTATCTTCTATACGAGTTTGGACGCCCTTG
* * * * *
9349511 AGGCTATTTAATGTGAGTAGGTTCCTTTGTGGCTATCTGATATTATGTGGACGCT
66 AGGCTATCTAATGTAAGAAAG-TACTTTGTGGCTATCTGATATTATGTGGACGCT
* * *
9349566 TTTGTGGCCATCTAACTATATGGACGA-CTCTATGGCTATCTTGTATACGTGTTTGGACGCTCTT
1 TTTGTGGCCATCTAACTATATGGAC-ATCTCTATGGCTATCTTCTATACGAGTTTGGACGCCCTT
* *
9349630 GTGGCTATCT-ATGTCAAAGAAAG-ACTTCTGTGGTTATCT
65 GAGGCTATCTAATGT--AAGAAAGTACTT-TGTGGCTATCT
9349669 ATGTCAAGTG
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
119 7 0.08
120 76 0.86
121 5 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.39
Consensus pattern (119 bp):
TTTGTGGCCATCTAACTATATGGACATCTCTATGGCTATCTTCTATACGAGTTTGGACGCCCTTG
AGGCTATCTAATGTAAGAAAGTACTTTGTGGCTATCTGATATTATGTGGACGCT
Found at i:9360115 original size:26 final size:27
Alignment explanation
Indices: 9360044--9360119 Score: 77
Period size: 26 Copynumber: 2.9 Consensus size: 27
9360034 CTTTGAATGG
* * *
9360044 ATTGCCTTTGTGGCATACTCTGA-ATGG
1 ATTGCCTTTGTGGCGTATTCT-ATATGA
* *
9360071 ATTGCC-TTATGGCGAATTCTATAT-A
1 ATTGCCTTTGTGGCGTATTCTATATGA
9360096 ATTGCCTTTGTGGCGTATTCTATA
1 ATTGCCTTTGTGGCGTATTCTATA
9360120 ATAAGGCCTT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
25 7 0.17
26 27 0.68
27 6 0.15
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (27 bp):
ATTGCCTTTGTGGCGTATTCTATATGA
Found at i:9360128 original size:26 final size:26
Alignment explanation
Indices: 9360080--9360129 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
9360070 GATTGCCTTA
*
9360080 TGGCGAATTCTATATAATTGCCTTTG
1 TGGCGAATTCTATATAATGGCCTTTG
*
9360106 TGGCGTATTCTATAATAA-GGCCTT
1 TGGCGAATTCTAT-ATAATGGCCTT
9360130 ATGGCATATT
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:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (26 bp):
TGGCGAATTCTATATAATGGCCTTTG
Found at i:9360140 original size:25 final size:25
Alignment explanation
Indices: 9360074--9360146 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
9360064 TGAATGGATT
*
9360074 GCCTTATGGCGA-ATTCTATATAATT
1 GCCTTATGGC-ATATTCTATATAATG
* *
9360099 GCCTTTGTGGCGTATTCTATAATAA-G
1 GCC-TTATGGCATATTCTAT-ATAATG
*
9360125 GCCTTATGGCATATTCTGTATA
1 GCCTTATGGCATATTCTATATA
9360147 TCGTTTGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
24 3 0.08
25 16 0.41
26 16 0.41
27 4 0.10
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (25 bp):
GCCTTATGGCATATTCTATATAATG
Found at i:9363298 original size:21 final size:20
Alignment explanation
Indices: 9363263--9363311 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
9363253 TATATGATTT
* *
9363263 ATTACATAATTTTTTTAGAT
1 ATTATATAATTTTTTTAGAA
*
9363283 TTTATATAATTTTTTTTAGAA
1 ATTATATAA-TTTTTTTAGAA
9363304 ATTATATA
1 ATTATATA
9363312 TAAAATTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
ATTATATAATTTTTTTAGAA
Found at i:9363311 original size:23 final size:20
Alignment explanation
Indices: 9363268--9363314 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 20
9363258 GATTTATTAC
*
9363268 ATAATTTTTTTAGATTTTAT
1 ATAATTTTTTTAGATTATAT
9363288 ATAATTTTTTTTAGAAATTATAT
1 ATAA-TTTTTTTAG--ATTATAT
9363311 ATAA
1 ATAA
9363315 AATTTGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 9 0.39
23 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
ATAATTTTTTTAGATTATAT
Found at i:9364069 original size:15 final size:15
Alignment explanation
Indices: 9364051--9364080 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9364041 TTAATGATTA
*
9364051 TCTTTTAAAGATTTT
1 TCTTTTAAAAATTTT
9364066 TCTTTTAAAAATTTT
1 TCTTTTAAAAATTTT
9364081 AAAATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (15 bp):
TCTTTTAAAAATTTT
Found at i:9365467 original size:41 final size:41
Alignment explanation
Indices: 9365410--9365493 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
9365400 AAACTACATA
9365410 CTCATTGTCGTTAAAAAGAGGAAACTTCACTTATTTTGACC
1 CTCATTGTCGTTAAAAAGAGGAAACTTCACTTATTTTGACC
9365451 CTCATTGTCGTTAAAAAGAGGAAACTTCACTTATTTTGACC
1 CTCATTGTCGTTAAAAAGAGGAAACTTCACTTATTTTGACC
9365492 CT
1 CT
9365494 TTCTTTGGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (41 bp):
CTCATTGTCGTTAAAAAGAGGAAACTTCACTTATTTTGACC
Found at i:9366119 original size:36 final size:36
Alignment explanation
Indices: 9366071--9366142 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
9366061 TTCGAGGAGC
*
9366071 TCTTCCGCAATATTATCACGGCAAATAACCCTTGAA
1 TCTTCCGAAATATTATCACGGCAAATAACCCTTGAA
9366107 TCTTCCGAAATATTATCACGGCAAATAACCCTTGAA
1 TCTTCCGAAATATTATCACGGCAAATAACCCTTGAA
9366143 GAAGATGAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (36 bp):
TCTTCCGAAATATTATCACGGCAAATAACCCTTGAA
Found at i:9368148 original size:15 final size:15
Alignment explanation
Indices: 9368123--9368159 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
9368113 TGTTTATATA
9368123 TTTTATTAAATT-AT
1 TTTTATTAAATTAAT
9368137 TTTTAGTTAAATTAAT
1 TTTTA-TTAAATTAAT
9368153 TTTTATT
1 TTTTATT
9368160 TATTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.24
15 9 0.43
16 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTTATTAAATTAAT
Found at i:9368367 original size:10 final size:9
Alignment explanation
Indices: 9368313--9368366 Score: 54
Period size: 10 Copynumber: 5.6 Consensus size: 9
9368303 TTTACATGTT
9368313 ATATTAATAA
1 ATATTAA-AA
9368323 ATATTAAAA
1 ATATTAAAA
*
9368332 ATTAATAAAA
1 A-TATTAAAA
9368342 ATATGTAAAA
1 ATAT-TAAAA
*
9368352 AAATTCAAAA
1 ATATT-AAAA
9368362 ATATT
1 ATATT
9368367 CTATAAAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
9 6 0.16
10 31 0.84
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
ATATTAAAA
Found at i:9380670 original size:18 final size:17
Alignment explanation
Indices: 9380624--9380695 Score: 57
Period size: 17 Copynumber: 4.4 Consensus size: 17
9380614 ATTTAAAAAA
9380624 ATATATTT-ATAATTATTT
1 ATATATTTAAT-ATT-TTT
9380642 -TAT-TTTAATATTTATT
1 ATATATTTAATATTT-TT
9380658 A-ATATTTATATATTTTT
1 ATATATTTA-ATATTTTT
*
9380675 ATATA-TT-ATAATTTT
1 ATATATTTAATATTTTT
9380690 ATATAT
1 ATATAT
9380696 AGTGATCTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
15 13 0.28
16 10 0.22
17 14 0.30
18 9 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATATTTAATATTTTT
Found at i:9380689 original size:15 final size:15
Alignment explanation
Indices: 9380666--9380695 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9380656 TTAATATTTA
*
9380666 TATATTTTTATATAT
1 TATAATTTTATATAT
9380681 TATAATTTTATATAT
1 TATAATTTTATATAT
9380696 AGTGATCTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATAATTTTATATAT
Found at i:9396130 original size:20 final size:18
Alignment explanation
Indices: 9396105--9396160 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
9396095 TCGTAGTGTG
9396105 TTAATAATGTTTTATAATAT
1 TTAATAAT-TTTTATAAT-T
9396125 TTAAT-ATTTTTAT-ATT
1 TTAATAATTTTTATAATT
*
9396141 TTATAAAATTTTTATAATT
1 TTA-ATAATTTTTATAATT
9396160 T
1 T
9396161 GAAGTGATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
18 14 0.44
19 6 0.19
20 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TTAATAATTTTTATAATT
Found at i:9397942 original size:10 final size:10
Alignment explanation
Indices: 9397927--9397956 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
9397917 AAAAATGTAA
9397927 ATTTAAAGGT
1 ATTTAAAGGT
9397937 ATTTAAAGGT
1 ATTTAAAGGT
9397947 ATTTAAAGGT
1 ATTTAAAGGT
9397957 GTAATATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (10 bp):
ATTTAAAGGT
Found at i:9402818 original size:27 final size:27
Alignment explanation
Indices: 9402788--9402864 Score: 145
Period size: 27 Copynumber: 2.9 Consensus size: 27
9402778 GGCCAATCAC
*
9402788 ATTGGCGGCACCAAAGGTGCCAATGTG
1 ATTGGCGGCACCAATGGTGCCAATGTG
9402815 ATTGGCGGCACCAATGGTGCCAATGTG
1 ATTGGCGGCACCAATGGTGCCAATGTG
9402842 ATTGGCGGCACCAATGGTGCCAA
1 ATTGGCGGCACCAATGGTGCCAA
9402865 AGGACTAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.19
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATGTG
Found at i:9403197 original size:19 final size:19
Alignment explanation
Indices: 9403173--9403235 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
9403163 ATTAAAATAG
9403173 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
9403192 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
9403210 TCTT-ATTTAATAACTCTAT
1 T-TTAATTTAATAACTCTAT
9403229 TTTAATT
1 TTTAATT
9403236 AAAAAAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 15 0.41
19 22 0.59
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:9403501 original size:18 final size:19
Alignment explanation
Indices: 9403452--9403510 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
9403442 ATTTTATATT
9403452 TTAAATTAAAATAGATTTA
1 TTAAATTAAAATAGATTTA
* *
9403471 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGATTTA
*
9403489 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGATTTA
9403508 TTA
1 TTA
9403511 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 16 0.47
19 18 0.53
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (19 bp):
TTAAATTAAAATAGATTTA
Found at i:9404201 original size:26 final size:27
Alignment explanation
Indices: 9404149--9404212 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
9404139 TTTTTTTGGT
* *
9404149 ATATTTTGGCAAATAAAAAAAATTTATA
1 ATATTTTGGTAAAT-AAAAAAAGTTATA
9404177 ATATTTTGGTAAAT-AAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
9404203 ATATTTTGGT
1 ATATTTTGGT
9404213 TATTTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 21 0.62
28 13 0.38
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.41
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:9404564 original size:28 final size:28
Alignment explanation
Indices: 9404499--9404564 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
9404489 TTTTTTTGGT
* *
9404499 ATATTTTGGCAAATAAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
9404527 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
9404555 ATATTTTGGT
1 ATATTTTGGT
9404565 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:9411431 original size:22 final size:23
Alignment explanation
Indices: 9411391--9411434 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
9411381 TAAATACATG
9411391 TGTAATAAATATATGTATACATTT
1 TGTAATAAATATA-GTATACATTT
*
9411415 TGTAATTAATATA-TATACAT
1 TGTAATAAATATAGTATACAT
9411435 AATTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (23 bp):
TGTAATAAATATAGTATACATTT
Found at i:9439263 original size:43 final size:43
Alignment explanation
Indices: 9439202--9439348 Score: 174
Period size: 43 Copynumber: 3.5 Consensus size: 43
9439192 CAATGCTAAC
*
9439202 GTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACT
1 GTCCCAGACATGGTCTTACATGTAATCACATATCGATGCCACT
* * * * * *
9439245 GTCCCAAACAAGGTCTTACACG-AATTAAATA-CGATGCCAAT
1 GTCCCAGACATGGTCTTACATGTAATCACATATCGATGCCACT
* *
9439286 GTCCCAGACATGGTCTTACATGTAAACACAAATCGATGCCAAC-
1 GTCCCAGACATGGTCTTACATGTAATCACATATCGATGCC-ACT
*
9439329 GTCCCAGACGTGGTCTTACA
1 GTCCCAGACATGGTCTTACA
9439349 CAAAAACACA
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 28 0.33
42 12 0.14
43 44 0.52
44 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACATGTAATCACATATCGATGCCACT
Found at i:9439356 original size:43 final size:43
Alignment explanation
Indices: 9439194--9439364 Score: 161
Period size: 43 Copynumber: 4.0 Consensus size: 43
9439184 GGCTCGTACA
* * * * *
9439194 ATGCTAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAATCG
* * **
9439237 ATGCC-ACTGTCCCAAACAAGGTCTTACACG--AA-TTAAATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAAACACAAAT-CG
* *
9439278 ATGCCAATGTCCCAGACATGGTCTTACATGTAAACACAAATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAATCG
* ** *
9439321 ATGCCAACGTCCCAGACGTGGTCTTACACAAAAACACACATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAATCG
9439364 A
1 A
9439365 AAATCCTATG
Statistics
Matches: 101, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
40 3 0.03
41 27 0.27
42 3 0.03
43 64 0.63
44 4 0.04
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAATCG
Found at i:9465973 original size:40 final size:40
Alignment explanation
Indices: 9465918--9466037 Score: 154
Period size: 40 Copynumber: 3.0 Consensus size: 40
9465908 GAGGAAGTAC
*
9465918 TGACAGTTTATCTGCAATACTAGTGGCTTGTCCACAATAT
1 TGACAATTTATCTGCAATACTAGTGGCTTGTCCACAATAT
*
9465958 TGACAATTTATCTGCAATACTAGTGGCTAGTCCACAA-AT
1 TGACAATTTATCTGCAATACTAGTGGCTTGTCCACAATAT
* * * * * *
9465997 TGGC-AGTTATCTACAATACTAGTGGTTTGACCATAATAT
1 TGACAATTTATCTGCAATACTAGTGGCTTGTCCACAATAT
9466036 TG
1 TG
9466038 GTAGATTATC
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
38 26 0.37
39 9 0.13
40 35 0.50
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (40 bp):
TGACAATTTATCTGCAATACTAGTGGCTTGTCCACAATAT
Found at i:9466672 original size:22 final size:24
Alignment explanation
Indices: 9466629--9466672 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
9466619 TGATAATATG
9466629 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
*
9466653 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
9466673 TGAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:9469902 original size:12 final size:12
Alignment explanation
Indices: 9469885--9469910 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9469875 TTTAGGAATA
9469885 AGAGCCAAAATT
1 AGAGCCAAAATT
9469897 AGAGCCAAAATT
1 AGAGCCAAAATT
9469909 AG
1 AG
9469911 TTTGGGCTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.15
Consensus pattern (12 bp):
AGAGCCAAAATT
Found at i:9478534 original size:18 final size:18
Alignment explanation
Indices: 9478484--9478543 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
9478474 TTCACAACAT
*
9478484 ATTTCACATTTCATTTTCC
1 ATTTCACATCTCA-TTTCC
*
9478503 A-TCCACTATCTCATTTCC
1 ATTTCAC-ATCTCATTTCC
* *
9478521 ATTTCACATGTCA-TGCC
1 ATTTCACATCTCATTTCC
9478538 ATTTCA
1 ATTTCA
9478544 ATATTAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 9 0.26
18 15 0.44
19 10 0.29
ACGTcount: A:0.23, C:0.30, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTTCACATCTCATTTCC
Found at i:9485533 original size:53 final size:53
Alignment explanation
Indices: 9485453--9485560 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
9485443 GTAGTGTTTG
*
9485453 AGACGTTGACCATTAACTTTAAACGTACCTCCGTAATTATCGTGTAATTCAAC
1 AGACGTTGACCATTAACTTTAAACGTACCTCCGTAATTATCGTATAATTCAAC
*
9485506 AGACGTTGACCATTAACTTTAAACGTACCTCCGTAATTTTCGTATAATTCAAC
1 AGACGTTGACCATTAACTTTAAACGTACCTCCGTAATTATCGTATAATTCAAC
9485559 AG
1 AG
9485561 CTCTGTAAGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.32
Consensus pattern (53 bp):
AGACGTTGACCATTAACTTTAAACGTACCTCCGTAATTATCGTATAATTCAAC
Found at i:9490224 original size:81 final size:81
Alignment explanation
Indices: 9490116--9490396 Score: 316
Period size: 81 Copynumber: 3.5 Consensus size: 81
9490106 ATAACAGTCC
* * * * *
9490116 TTTTACCCTAT-GAGAGTATTTCGATTATTTTACACTTCGAGCGTATTTTGGTCATTTTACCCTT
1 TTTTACCCT-TCGAGGGTATTTCGATTATTTTACCCTTCGAGAGTATTTCGGTCATTTTACCATT
9490180 CGAGGGTATTTTCGTCA
65 CGAGGGTATTTTCGTCA
* *
9490197 TTTTACCCTTTGAGGGTATTTCAATTATTTTACCCTTTC-AGAGTATTTCGGTCATTTTACCATT
1 TTTTACCCTTCGAGGGTATTTCGATTATTTTACCC-TTCGAGAGTATTTCGGTCATTTTACCATT
* **
9490261 CGAGGGAATTTTTTTCA
65 CGAGGGTATTTTCGTCA
* * * ** *
9490278 TGTT-CACCTTCGAGGGTATTTCGGTTATTTTACCCTTCGAGGGTATTTCAATCATTTTACCTTT
1 TTTTAC-CCTTCGAGGGTATTTCGATTATTTTACCCTTCGAGAGTATTTCGGTCATTTTACCATT
* * *
9490342 CGAAGTTATTTTGGTCA
65 CGAGGGTATTTTCGTCA
* * *
9490359 TTTTACCCTTCGAGGGTTTTTCGGTTTTTTTACCCTTC
1 TTTTACCCTTCGAGGGTATTTCGATTATTTTACCCTTC
9490397 AAAGGTATTT
Statistics
Matches: 170, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
80 5 0.03
81 161 0.95
82 4 0.02
ACGTcount: A:0.18, C:0.19, G:0.17, T:0.46
Consensus pattern (81 bp):
TTTTACCCTTCGAGGGTATTTCGATTATTTTACCCTTCGAGAGTATTTCGGTCATTTTACCATTC
GAGGGTATTTTCGTCA
Found at i:9490396 original size:27 final size:27
Alignment explanation
Indices: 9490116--9490407 Score: 259
Period size: 27 Copynumber: 10.8 Consensus size: 27
9490106 ATAACAGTCC
* * *
9490116 TTTTACCCTAT-GAGAGTATTTCGATTA
1 TTTTACCCT-TCGAGGGTATTTCGGTCA
* * *
9490143 TTTTACACTTCGAGCGTATTTTGGTCA
1 TTTTACCCTTCGAGGGTATTTCGGTCA
9490170 TTTTACCCTTCGAGGGTATTTTC-GTCA
1 TTTTACCCTTCGAGGGTA-TTTCGGTCA
* ** *
9490197 TTTTACCCTTTGAGGGTATTTCAATTA
1 TTTTACCCTTCGAGGGTATTTCGGTCA
*
9490224 TTTTACCCTTTC-AGAGTATTTCGGTCA
1 TTTTACCC-TTCGAGGGTATTTCGGTCA
* * ***
9490251 TTTTACCATTCGAGGGAATTTTTTTCA
1 TTTTACCCTTCGAGGGTATTTCGGTCA
* *
9490278 TGTT-CACCTTCGAGGGTATTTCGGTTA
1 TTTTAC-CCTTCGAGGGTATTTCGGTCA
**
9490305 TTTTACCCTTCGAGGGTATTTCAATCA
1 TTTTACCCTTCGAGGGTATTTCGGTCA
* * * *
9490332 TTTTACCTTTCGAAGTTATTTTGGTCA
1 TTTTACCCTTCGAGGGTATTTCGGTCA
* **
9490359 TTTTACCCTTCGAGGGTTTTTCGGTTT
1 TTTTACCCTTCGAGGGTATTTCGGTCA
* *
9490386 TTTTACCCTTCAAAGGTATTTC
1 TTTTACCCTTCGAGGGTATTTC
9490408 AGCTATTTTC
Statistics
Matches: 209, Mismatches: 49, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
26 9 0.04
27 194 0.93
28 6 0.03
ACGTcount: A:0.19, C:0.18, G:0.17, T:0.46
Consensus pattern (27 bp):
TTTTACCCTTCGAGGGTATTTCGGTCA
Found at i:9496597 original size:27 final size:27
Alignment explanation
Indices: 9496167--9496597 Score: 485
Period size: 27 Copynumber: 16.0 Consensus size: 27
9496157 GGTTATAACA
* * *
9496167 GTCATTTTATCCTAT-GGGGGTATTTCA
1 GTCATTTTACCCT-TCGAGGGTATTTCG
*
9496194 GTCATTTTAACCTTC-AGGGGTATTTCG
1 GTCATTTTACCCTTCGA-GGGTATTTCG
*
9496221 ATCA-TTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
9496247 GTCATTTTACCCTTCGAGGGTACTTCA
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * **
9496274 TTCATTTTATCCTTTGAGGGTATTTTA
1 GTCATTTTACCCTTCGAGGGTATTTCG
9496301 GTCATTTTACCCTTCGAGGGTATTT-G
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
9496327 AGTCATTTTACCATTTGAGGGTATTTCG
1 -GTCATTTTACCCTTCGAGGGTATTTCG
** *
9496355 G-CTATTTTACCCTTTAAGGGTATTTTG
1 GTC-ATTTTACCCTTCGAGGGTATTTCG
* ** *
9496382 ATCATTTTACCCTTTAAGGGTATTTCC
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
9496409 GTCATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
9496436 GTCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
9496463 ATCATTTTACCCTTTGAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * * *
9496490 ATTATTTTACCCTTTGAGGGTATTTTG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* *
9496517 GTCATTTTACCTTTCGAGGGTATTTAG
1 GTCATTTTACCCTTCGAGGGTATTTCG
* * *
9496544 GTTATTTTACCCTTTGAGGGTTTTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
*
9496571 GTCATTTTACCCTTCAAGGGTATTTCG
1 GTCATTTTACCCTTCGAGGGTATTTCG
9496598 ATAATTTGCC
Statistics
Matches: 347, Mismatches: 49, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
26 24 0.07
27 321 0.93
28 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTATTTCG
Found at i:9500988 original size:11 final size:11
Alignment explanation
Indices: 9500972--9501008 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
9500962 AAGAGAGAAT
*
9500972 GATGCTTGATG
1 GATGCTTGAGG
9500983 GATGCTTGAGG
1 GATGCTTGAGG
9500994 GATGCTTGAGG
1 GATGCTTGAGG
9501005 GATG
1 GATG
9501009 ATGAATGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.19, C:0.08, G:0.43, T:0.30
Consensus pattern (11 bp):
GATGCTTGAGG
Found at i:9501836 original size:20 final size:20
Alignment explanation
Indices: 9501811--9501851 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
9501801 TTAAGATATA
9501811 GATGAGTTTCCTTCCAAGGT
1 GATGAGTTTCCTTCCAAGGT
*
9501831 GATGAGTTTCCTTTCAAGGT
1 GATGAGTTTCCTTCCAAGGT
9501851 G
1 G
9501852 GTGTAGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (20 bp):
GATGAGTTTCCTTCCAAGGT
Found at i:9502344 original size:21 final size:21
Alignment explanation
Indices: 9502318--9502359 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
9502308 ATCATATAGA
9502318 CGGTTTGGTCATTTCCAAAGG
1 CGGTTTGGTCATTTCCAAAGG
9502339 CGGTTTGGTCATTTCCAAAGG
1 CGGTTTGGTCATTTCCAAAGG
9502360 ACTTCATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (21 bp):
CGGTTTGGTCATTTCCAAAGG
Found at i:9503947 original size:43 final size:42
Alignment explanation
Indices: 9503832--9504044 Score: 153
Period size: 43 Copynumber: 5.0 Consensus size: 42
9503822 CTTTACCATA
* * *
9503832 AAACGCCGCTAAAGAGCTTGACTTTTAACGGCGCTTAAGTCAC
1 AAACGCCGCTAAAGACCTTGACTTTTAGCGGCGCTT-ATTCAC
* * * * * * *
9503875 AAATGCCGCAAAATACATT-AGCCTATAGCGGCGCTTGATTTAC
1 AAACGCCGCTAAAGACCTTGA-CTTTTAGCGGCGCTT-ATTCAC
* * * *
9503918 AAACGCCACTAAAGACCTTGACCTTTAGCGGCACTTCAATCAC
1 AAACGCCGCTAAAGACCTTGACTTTTAGCGGCGCTT-ATTCAC
* * * * *
9503961 AAACGCCGCTAAATACCCTGACTTTTAGCGGTGATT-TTCTTGC
1 AAACGCCGCTAAAGACCTTGACTTTTAGCGGCGCTTATTC--AC
* *
9504004 AAACGCCGCAAAAAGACCTTGACTTTTAGCGACGCTT-TTCA
1 AAACGCCGC-TAAAGACCTTGACTTTTAGCGGCGCTTATTCA
9504045 TAAAAACGCC
Statistics
Matches: 128, Mismatches: 37, Indels: 11
0.73 0.21 0.06
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 100 0.78
44 25 0.20
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCTTGACTTTTAGCGGCGCTTATTCAC
Found at i:9504043 original size:44 final size:43
Alignment explanation
Indices: 9503960--9504043 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
9503950 ACTTCAATCA
* * **
9503960 CAAACGCCGCTAAATACCCTGACTTTTAGCGGTGATTTTCTTG
1 CAAACGCCGCAAAAGACCCTGACTTTTAGCGACGATTTTCTTG
* *
9504003 CAAACGCCGCAAAAAGACCTTGACTTTTAGCGACGCTTTTC
1 CAAACGCCGC-AAAAGACCCTGACTTTTAGCGACGATTTTC
9504044 ATAAAAACGC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 10 0.29
44 24 0.71
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (43 bp):
CAAACGCCGCAAAAGACCCTGACTTTTAGCGACGATTTTCTTG
Found at i:9509966 original size:16 final size:16
Alignment explanation
Indices: 9509941--9510163 Score: 135
Period size: 16 Copynumber: 12.9 Consensus size: 16
9509931 TATATATGAG
*
9509941 TTATGTAAGTTACGTA
1 TTATGTAAGTTATGTA
*
9509957 TTACGTAAGTTATGTA
1 TTATGTAAGTTATGTA
9509973 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
*
9509990 GTTATGTAAGTTAAGTA
1 -TTATGTAAGTTATGTA
* *
9510007 TTATATAAGTTATGCAA
1 TTATGTAAGTTATG-TA
* ** *
9510024 GTCCGACAAGTTAATGTA
1 TTATG-TAAGTT-ATGTA
*
9510042 TAATAT-TAA-TTCATTTA
1 T--TATGTAAGTT-ATGTA
*
9510059 GTTATGTGAGTTATGTAAATA
1 -TTATGTAAGTTATG----TA
*
9510080 TTATGTAACTTATTATGTTA
1 TTATGTAA---GTTATG-TA
9510100 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
9510116 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
*
9510133 GTTATGTAAGTTAAGTA
1 -TTATGTAAGTTATGTA
*
9510150 TTATATAAGTTATG
1 TTATGTAAGTTATG
9510164 CAAGTCCGAC
Statistics
Matches: 160, Mismatches: 28, Indels: 38
0.71 0.12 0.17
Matches are distributed among these distances:
16 72 0.45
17 21 0.13
18 39 0.24
19 3 0.02
20 18 0.11
21 2 0.01
23 5 0.03
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.45
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:9509969 original size:25 final size:25
Alignment explanation
Indices: 9509939--9510311 Score: 117
Period size: 25 Copynumber: 15.5 Consensus size: 25
9509929 AGTATATATG
* *
9509939 AGTTATGTAAGTTACGTATTACGTA
1 AGTTATGTAAGTTAAGTATTATGTA
*
9509964 AGTTATGT-A-TTATGTAAGTTATGTA
1 AGTTATGTAAGTTAAGT-A-TTATGTA
*
9509989 AGTTATGTAAGTTAAGTATTATATA
1 AGTTATGTAAGTTAAGTATTATGTA
* * *
9510014 AGTTATGCAAGTCCGACAAGT-TAATGTA
1 AGTTATGTAAGT----TAAGTATTATGTA
* ** *
9510042 TA-ATAT-TAA-TTCATTTAGTTATGTG
1 -AGTTATGTAAGTT-AAGTA-TTATGTA
9510067 AGTTATGT-A---AA-TATTATGTA
1 AGTTATGTAAGTTAAGTATTATGTA
* *
9510087 ACTTAT-TATG-T---TATTATGTA
1 AGTTATGTAAGTTAAGTATTATGTA
*
9510107 AGTTATGT-A-TTATGTAAGTTATGTA
1 AGTTATGTAAGTTAAGT-A-TTATGTA
*
9510132 AGTTATGTAAGTTAAGTATTATATA
1 AGTTATGTAAGTTAAGTATTATGTA
* * *
9510157 AGTTATGCAAGTCCGACAAGT-TAATGTA
1 AGTTATGTAAGT----TAAGTATTATGTA
* ** *
9510185 TA-ATAT-TAA-TTCATTTAGTTATGTG
1 -AGTTATGTAAGTT-AAGTA-TTATGTA
9510210 AGTTATGT-A---AA-TATTATGTA
1 AGTTATGTAAGTTAAGTATTATGTA
* *
9510230 ACTTAT-TATG-T---TATTATGTA
1 AGTTATGTAAGTTAAGTATTATGTA
*
9510250 AGTTATGTAAGTTAAGTATTAAGTA
1 AGTTATGTAAGTTAAGTATTATGTA
*
9510275 AGTTATGTAAGTTAAGTATTATATA
1 AGTTATGTAAGTTAAGTATTATGTA
*
9510300 AGTTATGCAAGT
1 AGTTATGTAAGT
9510312 CCGACAAGTT
Statistics
Matches: 258, Mismatches: 46, Indels: 88
0.66 0.12 0.22
Matches are distributed among these distances:
19 2 0.01
20 51 0.20
21 8 0.03
22 3 0.01
23 10 0.04
24 5 0.02
25 131 0.51
26 8 0.03
27 14 0.05
28 16 0.06
29 10 0.04
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (25 bp):
AGTTATGTAAGTTAAGTATTATGTA
Found at i:9509987 original size:9 final size:9
Alignment explanation
Indices: 9509939--9510311 Score: 123
Period size: 9 Copynumber: 42.3 Consensus size: 9
9509929 AGTATATATG
9509939 AGTTATGTA
1 AGTTATGTA
*
9509948 AGTTACGT-
1 AGTTATGTA
*
9509956 A-TTACGTA
1 AGTTATGTA
9509964 AGTTATGT-
1 AGTTATGTA
9509972 A-TTATGTA
1 AGTTATGTA
9509980 AGTTATGTA
1 AGTTATGTA
9509989 AGTTATGTA
1 AGTTATGTA
*
9509998 AGTTAAGT-
1 AGTTATGTA
*
9510006 A-TTATATA
1 AGTTATGTA
*
9510014 AGTTATGCA
1 AGTTATGTA
** *
9510023 AG-TCCGACA
1 AGTTATG-TA
9510032 AGTTAATGTA
1 AGTT-ATGTA
*
9510042 TA-ATAT-TA
1 -AGTTATGTA
*
9510050 A-TTCAT-TT
1 AGTT-ATGTA
*
9510058 AGTTATGTG
1 AGTTATGTA
9510067 AGTTATGTAA
1 AGTTATGT-A
*
9510077 ATATTATGTA
1 A-GTTATGTA
*
9510087 ACTTAT-TA
1 AGTTATGTA
*
9510095 TGTTATTATGTA
1 AG---TTATGTA
9510107 AGTTATGT-
1 AGTTATGTA
9510115 A-TTATGTA
1 AGTTATGTA
9510123 AGTTATGTA
1 AGTTATGTA
9510132 AGTTATGTA
1 AGTTATGTA
*
9510141 AGTTAAGT-
1 AGTTATGTA
*
9510149 A-TTATATA
1 AGTTATGTA
*
9510157 AGTTATGCA
1 AGTTATGTA
** *
9510166 AG-TCCGACA
1 AGTTATG-TA
9510175 AGTTAATGTA
1 AGTT-ATGTA
*
9510185 TA-ATAT-TA
1 -AGTTATGTA
*
9510193 A-TTCAT-TT
1 AGTT-ATGTA
*
9510201 AGTTATGTG
1 AGTTATGTA
9510210 AGTTATGTAA
1 AGTTATGT-A
*
9510220 ATATTATGTA
1 A-GTTATGTA
*
9510230 ACTTAT-TA
1 AGTTATGTA
*
9510238 TGTTATTATGTA
1 AG---TTATGTA
9510250 AGTTATGTA
1 AGTTATGTA
*
9510259 AGTTAAGT-
1 AGTTATGTA
*
9510267 A-TTAAGTA
1 AGTTATGTA
9510275 AGTTATGTA
1 AGTTATGTA
*
9510284 AGTTAAGT-
1 AGTTATGTA
*
9510292 A-TTATATA
1 AGTTATGTA
*
9510300 AGTTATGCA
1 AGTTATGTA
9510309 AGT
1 AGT
9510312 CCGACAAGTT
Statistics
Matches: 275, Mismatches: 49, Indels: 80
0.68 0.12 0.20
Matches are distributed among these distances:
7 40 0.15
8 38 0.14
9 155 0.56
10 12 0.04
11 24 0.09
12 6 0.02
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (9 bp):
AGTTATGTA
Found at i:9510092 original size:20 final size:21
Alignment explanation
Indices: 9510060--9510116 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
9510050 ATTCATTTAG
* *
9510060 TTATGTGAGTTATGTA-AATA
1 TTATGTAACTTATGTATAATA
**
9510080 TTATGTAACTTAT-TATGTTA
1 TTATGTAACTTATGTATAATA
*
9510100 TTATGTAAGTTATGTAT
1 TTATGTAACTTATGTAT
9510117 TATGTAAGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.07
20 25 0.83
21 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.51
Consensus pattern (21 bp):
TTATGTAACTTATGTATAATA
Found at i:9510213 original size:143 final size:143
Alignment explanation
Indices: 9509955--9510430 Score: 843
Period size: 143 Copynumber: 3.3 Consensus size: 143
9509945 GTAAGTTACG
* *
9509955 TATTACGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGTAAGTTAAGTATTATATAAGTTAT
1 TATTATGTAAGTTATGTATTATGTAAGTTAAGTAAGTTATGTAAGTTAAGTATTATATAAGTTAT
9510020 GCAAGTCCGACAAGTTAATGTATAATATTAATTCATTTAGTTATGTGAGTTATGTAAATATTATG
66 GCAAGTCCGACAAGTTAATGTATAATATTAATTCATTTAGTTATGTGAGTTATGTAAATATTATG
9510085 TAACTTATTATGT
131 TAACTTATTATGT
*
9510098 TATTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGTAAGTTAAGTATTATATAAGTTAT
1 TATTATGTAAGTTATGTATTATGTAAGTTAAGTAAGTTATGTAAGTTAAGTATTATATAAGTTAT
9510163 GCAAGTCCGACAAGTTAATGTATAATATTAATTCATTTAGTTATGTGAGTTATGTAAATATTATG
66 GCAAGTCCGACAAGTTAATGTATAATATTAATTCATTTAGTTATGTGAGTTATGTAAATATTATG
9510228 TAACTTATTATGT
131 TAACTTATTATGT
*
9510241 TATTATGTAAGTTATGTAAGTTAAGT-A-TTAAGTAAGTTATGTAAGTTAAGTATTATATAAGTT
1 TATTATGTAAGTTATGT-A-TTATGTAAGTTAAGTAAGTTATGTAAGTTAAGTATTATATAAGTT
*
9510304 ATGCAAGTCCGACAAGTTAATGTATAATATGAATTCATTTAGTTATGTGAGTTATGTATAATATT
64 ATGCAAGTCCGACAAGTTAATGTATAATATTAATTCATTTAGTTATGTGAGTTATGTA-AATATT
9510369 ATGTAACTTATTATGT
128 ATGTAACTTATTATGT
*
9510385 TATTATGTAAGTTATGTATTATGTAAGTTAAGT-A-TTATATAAGTTA
1 TATTATGTAAGTTATGTATTATGTAAGTTAAGTAAGTTATGTAAGTTA
9510431 TGGAAGTCCG
Statistics
Matches: 322, Mismatches: 6, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
142 16 0.05
143 254 0.79
144 47 0.15
145 5 0.02
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (143 bp):
TATTATGTAAGTTATGTATTATGTAAGTTAAGTAAGTTATGTAAGTTAAGTATTATATAAGTTAT
GCAAGTCCGACAAGTTAATGTATAATATTAATTCATTTAGTTATGTGAGTTATGTAAATATTATG
TAACTTATTATGT
Found at i:9510228 original size:20 final size:20
Alignment explanation
Indices: 9510203--9510259 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
9510193 ATTCATTTAG
*
9510203 TTATGTGAGTTATGTAAATA
1 TTATGTAAGTTATGTAAATA
* **
9510223 TTATGTAACTTAT-TATGTTA
1 TTATGTAAGTTATGTA-AATA
9510243 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGTAA
9510260 GTTAAGTATT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (20 bp):
TTATGTAAGTTATGTAAATA
Found at i:9510296 original size:16 final size:18
Alignment explanation
Indices: 9510243--9510304 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 18
9510233 TATTATGTTA
*
9510243 TTATGTAAGTTATGTAAG
1 TTATGTAAGTTAAGTAAG
*
9510261 TTAAGT-A-TTAAGTAAG
1 TTATGTAAGTTAAGTAAG
9510277 TTATGTAAGTTAAGT-A-
1 TTATGTAAGTTAAGTAAG
*
9510293 TTATATAAGTTA
1 TTATGTAAGTTA
9510305 TGCAAGTCCG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
16 24 0.63
17 3 0.08
18 11 0.29
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.44
Consensus pattern (18 bp):
TTATGTAAGTTAAGTAAG
Found at i:9510406 original size:16 final size:16
Alignment explanation
Indices: 9510379--9510432 Score: 81
Period size: 16 Copynumber: 3.3 Consensus size: 16
9510369 ATGTAACTTA
9510379 TTATGTTATTATGTAAG
1 TTATG-TATTATGTAAG
9510396 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
* *
9510412 TTAAGTATTATATAAG
1 TTATGTATTATGTAAG
9510428 TTATG
1 TTATG
9510433 GAAGTCCGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 29 0.85
17 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:9510538 original size:126 final size:126
Alignment explanation
Indices: 9510277--9510548 Score: 345
Period size: 126 Copynumber: 2.2 Consensus size: 126
9510267 ATTAAGTAAG
* *
9510277 TTATGTAAGTTAAGTATTATATAAGTTATGCAAGTCCGACAAGTTAATGTATAATATGAATTCAT
1 TTATATAAGTTAAGTATTATATAAGTTATGCAAGTCCGACAAGTTAATGTATAATATAAATTCAT
* * * * * *
9510342 TTAGTTATGTGAGTTATGTATAATATTATGTAACTTATTATGTTATTATGTAAGTTATGTA
66 TTAGTTATGTGAGTTATGCATAATATTATATAACTTATTATATAATTACGTAACTTATGTA
* * *
9510403 TTATGTAAGTTAAGTATTATATAAGTTATGGAAGTCCGACAAGTTAATGTATAATATAAATTGAT
1 TTATATAAGTTAAGTATTATATAAGTTATGCAAGTCCGACAAGTTAATGTATAATATAAATTCAT
* * *
9510468 TTAGTTATGTGAGTTATGCA-AGTTGTTATATAAGTT-TCTATATAAGTTACGTAACTTAT-TA
66 TTAGTTATGTGAGTTATGCATA-ATATTATATAACTTAT-TATATAA-TTACGTAACTTATGTA
*
9510529 TGTA-ATAAGTTATGTATTAT
1 T-TATATAAGTTAAGTATTAT
9510549 NTGTGTACTA
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
125 2 0.02
126 113 0.88
127 13 0.10
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (126 bp):
TTATATAAGTTAAGTATTATATAAGTTATGCAAGTCCGACAAGTTAATGTATAATATAAATTCAT
TTAGTTATGTGAGTTATGCATAATATTATATAACTTATTATATAATTACGTAACTTATGTA
Found at i:9511858 original size:14 final size:14
Alignment explanation
Indices: 9511841--9511867 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9511831 CTATAATTAC
9511841 AAAATTTAAATTTT
1 AAAATTTAAATTTT
9511855 AAAATTTAAATTT
1 AAAATTTAAATTT
9511868 AAAGTTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATTTAAATTTT
Found at i:9512091 original size:22 final size:23
Alignment explanation
Indices: 9512032--9512091 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 23
9512022 ATCCTGTAAT
9512032 ACAAACAGT-TT-CAAACTTATGA
1 ACAAACAGTATTAC-AACTTATGA
* *
9512054 ACAAA-ATTAGTAACAA-TTATGA
1 ACAAACAGTA-TTACAACTTATGA
9512076 ACAAACAGTATTACAA
1 ACAAACAGTATTACAA
9512092 GCCTGCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
21 2 0.07
22 21 0.70
23 6 0.20
24 1 0.03
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (23 bp):
ACAAACAGTATTACAACTTATGA
Found at i:9512579 original size:23 final size:23
Alignment explanation
Indices: 9512553--9512601 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
9512543 TTGAGGGATT
*
9512553 TTTTGGGGAAAATTCGGGGGGAA
1 TTTTGGGGAAAATTCGGGGGAAA
* *
9512576 TTTTGGGGATAATTTGGGGGAAA
1 TTTTGGGGAAAATTCGGGGGAAA
9512599 TTT
1 TTT
9512602 CAGCTAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.02, G:0.39, T:0.35
Consensus pattern (23 bp):
TTTTGGGGAAAATTCGGGGGAAA
Found at i:9512583 original size:11 final size:11
Alignment explanation
Indices: 9512554--9512601 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
9512544 TGAGGGATTT
*
9512554 TTTGGGGAAAA
1 TTTGGGGGAAA
* *
9512565 TTCGGGGGGAA
1 TTTGGGGGAAA
*
9512576 TTTTGGGGATAA
1 TTTGGGGGA-AA
9512588 TTTGGGGGAAA
1 TTTGGGGGAAA
9512599 TTT
1 TTT
9512602 CAGCTAAGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.25, C:0.02, G:0.40, T:0.33
Consensus pattern (11 bp):
TTTGGGGGAAA
Found at i:9512918 original size:16 final size:16
Alignment explanation
Indices: 9512897--9512932 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
9512887 ACATCATTTC
* *
9512897 TTTATTTATTTTATCT
1 TTTATTAATTGTATCT
9512913 TTTATTAATTGTATCT
1 TTTATTAATTGTATCT
9512929 TTTA
1 TTTA
9512933 ATTACTAAGT
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:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTATTAATTGTATCT
Found at i:9513500 original size:8 final size:8
Alignment explanation
Indices: 9513487--9513519 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
9513477 CCTTAATCCC
9513487 AAACCCTA
1 AAACCCTA
9513495 AAACCCTA
1 AAACCCTA
*
9513503 AAA-CCTT
1 AAACCCTA
9513510 AAACCCTA
1 AAACCCTA
9513518 AA
1 AA
9513520 TCACAAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (8 bp):
AAACCCTA
Found at i:9513519 original size:7 final size:7
Alignment explanation
Indices: 9513470--9513728 Score: 92
Period size: 7 Copynumber: 36.9 Consensus size: 7
9513460 AGTCCTTAAC
9513470 CCCTAAA
1 CCCTAAA
* *
9513477 CCTTAAT
1 CCCTAAA
9513484 CCC-AAA
1 CCCTAAA
9513490 CCCTAAAA
1 CCCT-AAA
9513498 CCCTAAAA
1 CCCT-AAA
*
9513506 CCTTAAA
1 CCCTAAA
9513513 CCCTAAA
1 CCCTAAA
*
9513520 TCAC-AAA
1 -CCCTAAA
*
9513527 CCCCAAA
1 CCCTAAA
*
9513534 CCCCAAA
1 CCCTAAA
*
9513541 CCAC-CAA
1 CC-CTAAA
9513548 CCAC-AAA
1 CC-CTAAA
*
9513555 CCCCAAA
1 CCCTAAA
* *
9513562 TCCTTAAC
1 -CCCTAAA
*
9513570 CCCTAAC
1 CCCTAAA
9513577 CCCT-AA
1 CCCTAAA
*
9513583 CCCTAGA
1 CCCTAAA
9513590 CCCT-AA
1 CCCTAAA
*
9513596 -CCTCAAC
1 CCCT-AAA
9513603 CCCTAAA
1 CCCTAAA
* *
9513610 CCTTAAT
1 CCCTAAA
9513617 CCC-AAA
1 CCCTAAA
9513623 CCCTAAAA
1 CCCT-AAA
9513631 CCCTAAAA
1 CCCT-AAA
*
9513639 CCTTAAA
1 CCCTAAA
9513646 CCCTAAA
1 CCCTAAA
*
9513653 TCAC-AAA
1 -CCCTAAA
*
9513660 CCCCAAA
1 CCCTAAA
*
9513667 CCCCAAA
1 CCCTAAA
*
9513674 CCAC-CAA
1 CC-CTAAA
9513681 CCAC-AAA
1 CC-CTAAA
*
9513688 CCCCAAA
1 CCCTAAA
* *
9513695 TCCTTAAC
1 -CCCTAAA
*
9513703 CCCTAAC
1 CCCTAAA
9513710 CCCT-AA
1 CCCTAAA
*
9513716 CCCTAGA
1 CCCTAAA
9513723 CCCTAA
1 CCCTAA
9513729 CCTCAACCCC
Statistics
Matches: 197, Mismatches: 36, Indels: 38
0.73 0.13 0.14
Matches are distributed among these distances:
5 3 0.02
6 27 0.14
7 122 0.62
8 45 0.23
ACGTcount: A:0.41, C:0.45, G:0.01, T:0.14
Consensus pattern (7 bp):
CCCTAAA
Found at i:9513611 original size:133 final size:133
Alignment explanation
Indices: 9513467--9513743 Score: 554
Period size: 133 Copynumber: 2.1 Consensus size: 133
9513457 CTAAGTCCTT
9513467 AACCCCTAAACCTTAATCCCAAACCCTAAAACCCTAAAACCTTAAACCCTAAATCACAAACCCCA
1 AACCCCTAAACCTTAATCCCAAACCCTAAAACCCTAAAACCTTAAACCCTAAATCACAAACCCCA
9513532 AACCCCAAACCACCAACCACAAACCCCAAATCCTTAACCCCTAACCCCTAACCCTAGACCCTAAC
66 AACCCCAAACCACCAACCACAAACCCCAAATCCTTAACCCCTAACCCCTAACCCTAGACCCTAAC
9513597 CTC
131 CTC
9513600 AACCCCTAAACCTTAATCCCAAACCCTAAAACCCTAAAACCTTAAACCCTAAATCACAAACCCCA
1 AACCCCTAAACCTTAATCCCAAACCCTAAAACCCTAAAACCTTAAACCCTAAATCACAAACCCCA
9513665 AACCCCAAACCACCAACCACAAACCCCAAATCCTTAACCCCTAACCCCTAACCCTAGACCCTAAC
66 AACCCCAAACCACCAACCACAAACCCCAAATCCTTAACCCCTAACCCCTAACCCTAGACCCTAAC
9513730 CTC
131 CTC
9513733 AACCCCTAAAC
1 AACCCCTAAAC
9513744 ATAATCATAA
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 144 1.00
ACGTcount: A:0.41, C:0.45, G:0.01, T:0.13
Consensus pattern (133 bp):
AACCCCTAAACCTTAATCCCAAACCCTAAAACCCTAAAACCTTAAACCCTAAATCACAAACCCCA
AACCCCAAACCACCAACCACAAACCCCAAATCCTTAACCCCTAACCCCTAACCCTAGACCCTAAC
CTC
Found at i:9513633 original size:8 final size:8
Alignment explanation
Indices: 9513620--9513652 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
9513610 CCTTAATCCC
9513620 AAACCCTA
1 AAACCCTA
9513628 AAACCCTA
1 AAACCCTA
*
9513636 AAA-CCTT
1 AAACCCTA
9513643 AAACCCTA
1 AAACCCTA
9513651 AA
1 AA
9513653 TCACAAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (8 bp):
AAACCCTA
Found at i:9513648 original size:15 final size:15
Alignment explanation
Indices: 9513603--9513652 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
9513593 TAACCTCAAC
*
9513603 CCCT-AAACCTTAAT
1 CCCTAAAACCTTAAA
* *
9513617 CCC-AAACCCTAAAA
1 CCCTAAAACCTTAAA
9513631 CCCTAAAACCTTAAA
1 CCCTAAAACCTTAAA
9513646 CCCTAAA
1 CCCTAAA
9513653 TCACAAACCC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 13 0.45
15 16 0.55
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (15 bp):
CCCTAAAACCTTAAA
Found at i:9514548 original size:42 final size:42
Alignment explanation
Indices: 9514502--9514636 Score: 125
Period size: 42 Copynumber: 3.2 Consensus size: 42
9514492 TTAAAACCAA
9514502 ACGCCACTAAATACCTTAACATTAGTGGCGATTGACCAAAAC
1 ACGCCACTAAATACCTTAACATTAGTGGCGATTGACCAAAAC
** * * * * * *
9514544 ACGCCACT--ATCACCCCCAACCAATAGCGGCGCTAGGA-TAGAA-
1 ACGCCACTAAAT-A-CCTTAA-CATTAGTGGCGAT-TGACCAAAAC
*
9514586 ACGCCGCTAAATACCTTAACATTAGTGGCGATTGACCAAAAC
1 ACGCCACTAAATACCTTAACATTAGTGGCGATTGACCAAAAC
9514628 ACGCCACTA
1 ACGCCACTA
9514637 TCACCCCTAA
Statistics
Matches: 67, Mismatches: 18, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
40 4 0.06
41 14 0.21
42 31 0.46
43 14 0.21
44 4 0.06
ACGTcount: A:0.36, C:0.30, G:0.16, T:0.18
Consensus pattern (42 bp):
ACGCCACTAAATACCTTAACATTAGTGGCGATTGACCAAAAC
Found at i:9514615 original size:84 final size:84
Alignment explanation
Indices: 9514500--9514659 Score: 302
Period size: 84 Copynumber: 1.9 Consensus size: 84
9514490 ATTTAAAACC
9514500 AAACGCCACTAAATACCTTAACATTAGTGGCGATTGACCAAAACACGCCACTATCACCCCCAACC
1 AAACGCCACTAAATACCTTAACATTAGTGGCGATTGACCAAAACACGCCACTATCACCCCCAACC
9514565 AATAGCGGCGCTAGGATAG
66 AATAGCGGCGCTAGGATAG
* *
9514584 AAACGCCGCTAAATACCTTAACATTAGTGGCGATTGACCAAAACACGCCACTATCACCCCTAACC
1 AAACGCCACTAAATACCTTAACATTAGTGGCGATTGACCAAAACACGCCACTATCACCCCCAACC
9514649 AATAGCGGCGC
66 AATAGCGGCGC
9514660 ATACATAAAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.35, C:0.32, G:0.16, T:0.17
Consensus pattern (84 bp):
AAACGCCACTAAATACCTTAACATTAGTGGCGATTGACCAAAACACGCCACTATCACCCCCAACC
AATAGCGGCGCTAGGATAG
Found at i:9518182 original size:134 final size:133
Alignment explanation
Indices: 9517820--9518186 Score: 421
Period size: 134 Copynumber: 2.7 Consensus size: 133
9517810 TTACAATCAT
* ** *
9517820 AACTTCAGTTCATTGATTTACGATCATGAGCAATTCATTAAGATTTCGTCAATTTACGATCACTA
1 AACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGA-TTCACCAATTTACGATCGCTA
* * *
9517885 CTCCACTTAAATAGTTTGTTGATTTATGATCACAACTGTCATTTTCAAAGCTCACTAATTTACGA
65 CTCTACTTAAATAGTTTGTTGATTTACGATCACAACTGTCATTTTCAAAGCTCACTAATTTAAGA
*
9517950 TCAC
130 CCAC
* * **** * * *
9517954 AACTTCAGTTCATTGATTTATGATCATGAATAATTCATTAAGATTTTGTAGATCTAAGATCGCGA
1 AACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGATTCACCA-ATTTACGATCGCTA
* * ** * * * *
9518019 CTTTACGTAAATAGTTCATTGATTCACGATCACAACTGTTATTTTTAAAGCTCGA-TGATTTAAG
65 CTCTACTTAAATAGTTTGTTGATTTACGATCACAACTGTCATTTTCAAAGCTC-ACTAATTTAAG
9518083 ACCAC
129 ACCAC
* *
9518088 AACTTCAGTTCATTGATTTACGATGATGAACAATTCATTAAGAGTTCACCAATTTACGATTGCTA
1 AACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGA-TTCACCAATTTACGATCGCTA
* * *
9518153 CTCTACTTAAACAGTTTGCTAATTTACGATCACA
65 CTCTACTTAAATAGTTTGTTGATTTACGATCACA
9518187 GTTTCAGTTC
Statistics
Matches: 188, Mismatches: 42, Indels: 6
0.80 0.18 0.03
Matches are distributed among these distances:
133 3 0.02
134 181 0.96
135 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (133 bp):
AACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGATTCACCAATTTACGATCGCTAC
TCTACTTAAATAGTTTGTTGATTTACGATCACAACTGTCATTTTCAAAGCTCACTAATTTAAGAC
CAC
Found at i:9518276 original size:98 final size:98
Alignment explanation
Indices: 9518091--9518284 Score: 253
Period size: 98 Copynumber: 2.0 Consensus size: 98
9518081 AGACCACAAC
* * * *
9518091 TTCAGTTCATTGATTTACGATGATGAACAATTCATTAAGAGTTCACCAATTTACGATTGCTACTC
1 TTCAGTTCATTAATTTACGATCATGAACAATTCATTAAGAGTTCACCAATTTACGATCGCGACTC
* * **
9518156 TACTTAAACAGTTTGCTAATTTACGATCACAGT
66 CACTTAAACAATTCACTAATTTACGATCACAGT
*****
9518189 TTCAGTTCATTAATTTACGATCATGAACAATTCATTAAGAGTTTGTTGATTTACGATCGCGACTC
1 TTCAGTTCATTAATTTACGATCATGAACAATTCATTAAGAGTTCACCAATTTACGATCGCGACTC
* *
9518254 CACTTAAACAATTCATTGATTTACGATCACA
66 CACTTAAACAATTCACTAATTTACGATCACA
9518285 ATTGTAATTT
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
98 81 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (98 bp):
TTCAGTTCATTAATTTACGATCATGAACAATTCATTAAGAGTTCACCAATTTACGATCGCGACTC
CACTTAAACAATTCACTAATTTACGATCACAGT
Found at i:9518282 original size:232 final size:231
Alignment explanation
Indices: 9517939--9518367 Score: 597
Period size: 232 Copynumber: 1.9 Consensus size: 231
9517929 TCAAAGCTCA
* * * *
9517939 CTAATTTACGATCACAACTTCAGTTCATTGATTTATGATCATGAATAATTCATTAAGATTTTGTA
1 CTAATTTACGATCACAACTTCAGTTCATTAATTTACGATCATGAACAATTCATTAAGAGTTTGTA
** * * *
9518004 GATCTAAGATCGCGACTTTACGTAAATAGTTCATTGATTCACGATCACAACTGTTATTTTTAAAG
66 GATCTAAGATCGCGACTCCACGTAAACAATTCATTGATTCACGATCACAACTG-TAATTTTAAAG
*
9518069 CTCGATGATTTAAGACCACAACTTCAGTTCATTGATTTACGATGATGAACAATTCATTAAGAGTT
130 CTCGATGATTTAAGACCACAACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTT
9518134 CACCAATTTACGATTGCTACTCTACTTAAACAGTTTG
195 CACCAATTTACGATTGCTACTCTACTTAAACAGTTTG
** *
9518171 CTAATTTACGATCACAGTTTCAGTTCATTAATTTACGATCATGAACAATTCATTAAGAGTTTGTT
1 CTAATTTACGATCACAACTTCAGTTCATTAATTTACGATCATGAACAATTCATTAAGAGTTTGTA
* * * * *
9518236 GATTTACGATCGCGACTCCACTTAAACAATTCATTGATTTACGATCACAATTGTAATTTTAAAGC
66 GATCTAAGATCGCGACTCCACGTAAACAATTCATTGATTCACGATCACAACTGTAATTTTAAAGC
* * * * * * *** *
9518301 TTGCTGATTTATGATCACAATTTCAGTTTATTGATTTGTTATCATGAACAGTTCATTAAGAGTTC
131 TCGATGATTTAAGACCACAACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTC
9518366 AC
196 AC
9518368 TTATTTATGA
Statistics
Matches: 169, Mismatches: 28, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
231 67 0.40
232 102 0.60
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (231 bp):
CTAATTTACGATCACAACTTCAGTTCATTAATTTACGATCATGAACAATTCATTAAGAGTTTGTA
GATCTAAGATCGCGACTCCACGTAAACAATTCATTGATTCACGATCACAACTGTAATTTTAAAGC
TCGATGATTTAAGACCACAACTTCAGTTCATTGATTTACGATCATGAACAATTCATTAAGAGTTC
ACCAATTTACGATTGCTACTCTACTTAAACAGTTTG
Found at i:9529556 original size:21 final size:21
Alignment explanation
Indices: 9529532--9529684 Score: 134
Period size: 21 Copynumber: 7.4 Consensus size: 21
9529522 AAAGCTAAAT
*
9529532 AGAAGCTCATAAGAGTTAAAC
1 AGAAGCTCATAAGAGTTGAAC
*
9529553 AGAAACTCA-AA-AGTTGAAC
1 AGAAGCTCATAAGAGTTGAAC
* * * *
9529572 AAAAGCTCGTCAGAGCTGAAC
1 AGAAGCTCATAAGAGTTGAAC
*
9529593 AGAATCTCATAAGAGTTGAAC
1 AGAAGCTCATAAGAGTTGAAC
* * *
9529614 ATAAGCTCGTAAGAGCTT-AAT
1 AGAAGCTCATAAGAG-TTGAAC
*
9529635 AGAA-CTCATAAGAGTTGAAT
1 AGAAGCTCATAAGAGTTGAAC
** * *
9529655 AGAAGCTTGTAAGAGCTGAAT
1 AGAAGCTCATAAGAGTTGAAC
9529676 AGAAGCTCA
1 AGAAGCTCA
9529685 AAAAAGCTAA
Statistics
Matches: 104, Mismatches: 23, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
19 15 0.14
20 19 0.18
21 68 0.65
22 2 0.02
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAAGCTCATAAGAGTTGAAC
Found at i:9529661 original size:41 final size:42
Alignment explanation
Indices: 9529532--9529684 Score: 168
Period size: 41 Copynumber: 3.7 Consensus size: 42
9529522 AAAGCTAAAT
* * * *
9529532 AGAAGCTCATAAGAGTTAAACAGAAACTCA-AA-AGTTGAAC
1 AGAAGCTCGTAAGAGCTGAACAGAAGCTCATAAGAGTTGAAC
* * *
9529572 AAAAGCTCGTCAGAGCTGAACAGAATCTCATAAGAGTTGAAC
1 AGAAGCTCGTAAGAGCTGAACAGAAGCTCATAAGAGTTGAAC
* * * *
9529614 ATAAGCTCGTAAGAGCTTAATAGAA-CTCATAAGAGTTGAAT
1 AGAAGCTCGTAAGAGCTGAACAGAAGCTCATAAGAGTTGAAC
* *
9529655 AGAAGCTTGTAAGAGCTGAATAGAAGCTCA
1 AGAAGCTCGTAAGAGCTGAACAGAAGCTCA
9529685 AAAAAGCTAA
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 24 0.25
41 39 0.41
42 33 0.34
ACGTcount: A:0.43, C:0.15, G:0.21, T:0.21
Consensus pattern (42 bp):
AGAAGCTCGTAAGAGCTGAACAGAAGCTCATAAGAGTTGAAC
Found at i:9532232 original size:23 final size:23
Alignment explanation
Indices: 9532184--9532233 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
9532174 GTACAAGTGT
* * *
9532184 GGCCGTGTGGGCCATACAAGCTA
1 GGCCGTGTGCGCCACACAAGCAA
*
9532207 GGCCGTGTGCGCCACACAGGCAA
1 GGCCGTGTGCGCCACACAAGCAA
9532230 GGCC
1 GGCC
9532234 AATCTGGGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.20, C:0.32, G:0.36, T:0.12
Consensus pattern (23 bp):
GGCCGTGTGCGCCACACAAGCAA
Found at i:9538421 original size:4 final size:4
Alignment explanation
Indices: 9538414--9538452 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
9538404 CATACATACA
9538414 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
9538453 CTATATGTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:9542183 original size:17 final size:16
Alignment explanation
Indices: 9542105--9542189 Score: 71
Period size: 17 Copynumber: 5.0 Consensus size: 16
9542095 GACTACGAAG
9542105 CTTTGGTGAGCTCGCA
1 CTTTGGTGAGCTCGCA
*
9542121 CTATTGGAGAGCTCGCA
1 CT-TTGGTGAGCTCGCA
* * *
9542138 GTCTTGATGAGCTCACA
1 CT-TTGGTGAGCTCGCA
*
9542155 GTTTTGGGTGAGCTCGCA
1 -CTTT-GGTGAGCTCGCA
*
9542173 CATTTGGTGAGTTCGCA
1 C-TTTGGTGAGCTCGCA
9542190 ATCCTACGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
16 2 0.04
17 38 0.70
18 14 0.26
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.31
Consensus pattern (16 bp):
CTTTGGTGAGCTCGCA
Found at i:9545237 original size:45 final size:46
Alignment explanation
Indices: 9545173--9545295 Score: 151
Period size: 46 Copynumber: 2.7 Consensus size: 46
9545163 AATCGGACAG
* *
9545173 TGCCAT-GATGTCTTTCAACCATGGTCTTATTTATTCT-ATTCTTGA
1 TGCCATAG-TGTCTTTCAACCATGGTCTTATTTATTCTCAGTCATGA
* * * * *
9545218 TGCCATAGTGTCTTTCAACCATGGTCATATTCATTTTCCGTCATGT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCAGTCATGA
*
9545264 TGCCATAGTGTCTTTCAACTATGGTCTTATTT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTT
9545296 CTTTGATTCG
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
45 32 0.48
46 34 0.52
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.45
Consensus pattern (46 bp):
TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCAGTCATGA
Found at i:9545331 original size:45 final size:45
Alignment explanation
Indices: 9545274--9545470 Score: 129
Period size: 45 Copynumber: 4.5 Consensus size: 45
9545264 TGCCATAGTG
* * * * * * *
9545274 TCTTTCAACTATGGTCTTATTTCTTTGATTCGTAATGTCATAGCA
1 TCTTTCAGCTATGGTCTTACTTCATAGAATCGTAATGACATAACA
* * *
9545319 TCTTTCAGCTATGGCCTTACTTGATAGAATCGTGATGACATAACA
1 TCTTTCAGCTATGGTCTTACTTCATAGAATCGTAATGACATAACA
* * * **
9545364 TCTTTCAGTTATGGTCTTA----ATACAATCGTGATG-CGATAAGG
1 TCTTTCAGCTATGGTCTTACTTCATAGAATCGTAATGAC-ATAACA
* ** * *
9545405 TCTTTCAGCTATGGTCTTAC-TCGACAGAATTTTGATG-CTATAACG
1 TCTTTCAGCTATGGTCTTACTTC-ATAGAATCGTAATGAC-ATAACA
*
9545450 TCTTTCAGCTAAGGTCTTACT
1 TCTTTCAGCTATGGTCTTACT
9545471 CATTTCTAGT
Statistics
Matches: 123, Mismatches: 23, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
40 1 0.01
41 35 0.28
45 87 0.71
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (45 bp):
TCTTTCAGCTATGGTCTTACTTCATAGAATCGTAATGACATAACA
Found at i:9545409 original size:41 final size:41
Alignment explanation
Indices: 9545303--9545423 Score: 118
Period size: 41 Copynumber: 2.9 Consensus size: 41
9545293 TTTCTTTGAT
* * * * *
9545303 TCGTAATGTCATAGCATCTTTCAGCTATGGCCTTACTTGATAGAA
1 TCGTGATGACATAACATCTTTCAGCTATGG---T-CTTAATACAA
*
9545348 TCGTGATGACATAACATCTTTCAGTTATGGTCTTAATACAA
1 TCGTGATGACATAACATCTTTCAGCTATGGTCTTAATACAA
**
9545389 TCGTGATG-CGATAAGGTCTTTCAGCTATGGTCTTA
1 TCGTGATGAC-ATAACATCTTTCAGCTATGGTCTTA
9545424 CTCGACAGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
40 1 0.02
41 38 0.58
42 1 0.02
45 26 0.39
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (41 bp):
TCGTGATGACATAACATCTTTCAGCTATGGTCTTAATACAA
Found at i:9545570 original size:15 final size:17
Alignment explanation
Indices: 9545545--9545579 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
9545535 AACTCGATTC
9545545 ATATATAAACAATT-AA
1 ATATATAAACAATTGAA
9545561 ATAT-TAAACAATTGAA
1 ATATATAAACAATTGAA
9545577 ATA
1 ATA
9545580 ACAACTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (17 bp):
ATATATAAACAATTGAA
Found at i:9547770 original size:20 final size:20
Alignment explanation
Indices: 9547745--9547782 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9547735 TTGTTATTTT
9547745 TTGAAAGTTGAATGACTGAA
1 TTGAAAGTTGAATGACTGAA
*
9547765 TTGAAAGTTGAGTGACTG
1 TTGAAAGTTGAATGACTG
9547783 TTTTGTCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (20 bp):
TTGAAAGTTGAATGACTGAA
Found at i:9551018 original size:24 final size:24
Alignment explanation
Indices: 9550990--9551041 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
9550980 TTTCTAGAAG
* **
9550990 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
9551014 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
9551038 ATTT
1 ATTT
9551042 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:9554556 original size:23 final size:23
Alignment explanation
Indices: 9554529--9554604 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
9554519 AGTGTTATTG
*
9554529 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
9554552 TTCAGTGGTAGTTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
9554575 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
9554598 ATCAGTG
1 ATCAGTG
9554605 TTGTACTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:9558030 original size:24 final size:24
Alignment explanation
Indices: 9557967--9558018 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
9557957 TTTGCAGAAG
* * *
9557967 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
9557991 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
9558015 ATTT
1 ATTT
9558019 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:9558303 original size:36 final size:36
Alignment explanation
Indices: 9558256--9558328 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
9558246 TTTTGAGGGC
*
9558256 ATAATCATAGAGAAAAATTGTGGGGCTTCTCCCTAT
1 ATAATCATAGAGAAAAATTGTCGGGCTTCTCCCTAT
9558292 ATAATCATAGAGAAAAATTGTCGGGCTTCTCCCTAT
1 ATAATCATAGAGAAAAATTGTCGGGCTTCTCCCTAT
9558328 A
1 A
9558329 ATCAGTGTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (36 bp):
ATAATCATAGAGAAAAATTGTCGGGCTTCTCCCTAT
Found at i:9560533 original size:124 final size:125
Alignment explanation
Indices: 9560253--9560556 Score: 391
Period size: 124 Copynumber: 2.5 Consensus size: 125
9560243 TTTGAAGTGT
* * * *
9560253 TTGAAAAACTACGATAGAATCTTTTGGCACAATCATTCAAAAAAT-ACA--GAAAAAAGGGGTAG
1 TTGAAAAACTACGATAGAATCTTTTGGTACAATCATTCAACAAATAAAAGGGAAAAAAGGGGTAA
* * * * *
9560315 TATGTAAGTAAATGACTAAAGTAAATAGTGTAAATTTTGTTTTGGAAGTGCTTGAACAAA
66 AATGTAAGTAAAGGACTAAAGTAAACAGTGTAAATTTTGTTTTGGAAGTACTTGAAAAAA
* ** * *** *
9560375 TTGGAAAACTGTGATAGAATCTTTTGGTATAATCATTCAACAAATAAAAGGGGGGAAATGGGTAA
1 TTGAAAAACTACGATAGAATCTTTTGGTACAATCATTCAACAAATAAAAGGGAAAAAAGGGGTAA
* * *
9560440 AATGTAAGTAAAGGGCTAAAGTAAACCGTGTAAATTTTGTTTT-GAAGTATTTGAAAAAA
66 AATGTAAGTAAAGGACTAAAGTAAACAGTGTAAATTTTGTTTTGGAAGTACTTGAAAAAA
*
9560499 TTGAAAAACTACAATAGAATCTTTTGGTACAATCATTCAACAAATAAAAGGGAAAAAA
1 TTGAAAAACTACGATAGAATCTTTTGGTACAATCATTCAACAAATAAAAGGGAAAAAA
9560557 TTGAGTATGA
Statistics
Matches: 151, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
122 39 0.26
123 2 0.01
124 63 0.42
125 47 0.31
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (125 bp):
TTGAAAAACTACGATAGAATCTTTTGGTACAATCATTCAACAAATAAAAGGGAAAAAAGGGGTAA
AATGTAAGTAAAGGACTAAAGTAAACAGTGTAAATTTTGTTTTGGAAGTACTTGAAAAAA
Found at i:9570894 original size:15 final size:15
Alignment explanation
Indices: 9570874--9570904 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
9570864 TCATAATTGA
9570874 ATCTTCAATACATTC
1 ATCTTCAATACATTC
9570889 ATCTTCAATACATTC
1 ATCTTCAATACATTC
9570904 A
1 A
9570905 AAACATCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (15 bp):
ATCTTCAATACATTC
Found at i:9574181 original size:22 final size:24
Alignment explanation
Indices: 9574156--9574209 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
9574146 TTATAAATTC
9574156 AATTTAA-AATATATAAT-ACAAT
1 AATTTAAGAATATATAATAACAAT
* *
9574178 AATTTCAAGCATATTTAATAACAAT
1 AATTT-AAGAATATATAATAACAAT
9574203 AATTTAA
1 AATTTAA
9574210 TTATAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.19
23 2 0.07
24 10 0.37
25 10 0.37
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (24 bp):
AATTTAAGAATATATAATAACAAT
Found at i:9574938 original size:6 final size:6
Alignment explanation
Indices: 9574921--9574951 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
9574911 TAAAGTTTTT
*
9574921 TTTTAA TCTTAA TTTTAA TTTTAA TTTTAA T
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T
9574952 CCACCACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTTAA
Found at i:9577484 original size:27 final size:23
Alignment explanation
Indices: 9577425--9577472 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
9577415 AAAAATTATA
9577425 TTATCCCAAATAAATAACTAAAG
1 TTATCCCAAATAAATAACTAAAG
9577448 TTATCCCAAATAAATAACTAAAG
1 TTATCCCAAATAAATAACTAAAG
9577471 TT
1 TT
9577473 TACACTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.29
Consensus pattern (23 bp):
TTATCCCAAATAAATAACTAAAG
Found at i:9580671 original size:32 final size:32
Alignment explanation
Indices: 9580630--9580692 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
9580620 ATTCCGAGCA
9580630 AACTAATAAGAAAATAAACACAAATAATAGAT
1 AACTAATAAGAAAATAAACACAAATAATAGAT
*
9580662 AACTAATAAGAAAATAAACACAAGTAATAGA
1 AACTAATAAGAAAATAAACACAAATAATAGA
9580693 GAAGATTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.65, C:0.10, G:0.08, T:0.17
Consensus pattern (32 bp):
AACTAATAAGAAAATAAACACAAATAATAGAT
Found at i:9580839 original size:3 final size:3
Alignment explanation
Indices: 9580826--9580859 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
9580816 ATAAATAAAA
9580826 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9580860 ACTCAATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:9581023 original size:19 final size:20
Alignment explanation
Indices: 9580980--9581025 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
9580970 GAAAAATTAG
*
9580980 TAAAAT-AATAATATAACAA
1 TAAAATAAATAAAATAACAA
*
9580999 -ATAATAAATAAAATAA-AA
1 TAAAATAAATAAAATAACAA
9581017 TAAAATAAA
1 TAAAATAAA
9581026 AGGGGCGGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAAATAAATAAAATAACAA
Found at i:9581272 original size:64 final size:64
Alignment explanation
Indices: 9581190--9581314 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 64
9581180 TGTGTCCAGG
* * * * *
9581190 CCGTGTGTGATTTCCTTCGCTT-TTCTCATGCTCGTGTG-GAATTCCACACGCCCATGTGGCTCG
1 CCGTGTGTGATCTCCTTCGCTTCTTC-CACGCCCATGTGAG-ATCCCACACGCCCATGTGGCTCG
9581253 A
64 A
*
9581254 CCGTGTGTGATCTCCTTCGCTTCTTCCACGCCCATGTGAGATCCCACACGCCCGTGTGGCT
1 CCGTGTGTGATCTCCTTCGCTTCTTCCACGCCCATGTGAGATCCCACACGCCCATGTGGCT
9581315 TTGCCGTGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
64 49 0.92
65 4 0.08
ACGTcount: A:0.12, C:0.34, G:0.23, T:0.31
Consensus pattern (64 bp):
CCGTGTGTGATCTCCTTCGCTTCTTCCACGCCCATGTGAGATCCCACACGCCCATGTGGCTCGA
Found at i:9583864 original size:12 final size:12
Alignment explanation
Indices: 9583844--9583876 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9583834 AAAAAATTAG
9583844 AAAAC-AAAAAT
1 AAAACTAAAAAT
9583855 AAAACTAAAAAT
1 AAAACTAAAAAT
*
9583867 AAAAATAAAA
1 AAAACTAAAA
9583877 TGCAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAACTAAAAAT
Found at i:9586913 original size:86 final size:85
Alignment explanation
Indices: 9586816--9586986 Score: 315
Period size: 86 Copynumber: 2.0 Consensus size: 85
9586806 CTTATAATTT
* *
9586816 GAAGAACACAAAGCAAATAATTAAAGAAAATTATTATTACTAAAAATAAAAAAGGATGAATAGTT
1 GAAGAACACAAAGCAAATAATTAAAAAAAATTATTATTACTAAAAAAAAAAAAGGATGAATAGTT
9586881 AAAAAAAAAAAAAAAAAAGA
66 AAAAAAAAAAAAAAAAAAGA
9586901 NGAAGAACACAAAGCAAATAATTAAAAAAAATTATTATTACTAAAAAAAAAAAAGGATGAATAGT
1 -GAAGAACACAAAGCAAATAATTAAAAAAAATTATTATTACTAAAAAAAAAAAAGGATGAATAGT
9586966 TAAAAAAAAAAAAAAAAAAGA
65 TAAAAAAAAAAAAAAAAAAGA
9586987 CAACTATGGT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (85 bp):
GAAGAACACAAAGCAAATAATTAAAAAAAATTATTATTACTAAAAAAAAAAAAGGATGAATAGTT
AAAAAAAAAAAAAAAAAAGA
Found at i:9586969 original size:43 final size:43
Alignment explanation
Indices: 9586831--9586974 Score: 112
Period size: 43 Copynumber: 3.3 Consensus size: 43
9586821 ACACAAAGCA
* *
9586831 AATAATTAAAGAAAATTATTATTACTAAAAATAAAAAAGGATG
1 AATAATTAAAAAAAATTATTATTACTAAAAAAAAAAAAGGATG
* ** ** ** ** * * * *
9586874 AATAGTTAAAAAAAAAAAAAAAAAAGANGAAGAACACAAAGCA--
1 AATAATTAAAAAAAATTATTATTACTA--AAAAAAAAAAAGGATG
9586917 AATAATTAAAAAAAATTATTATTACTAAAAAAAAAAAAGGATG
1 AATAATTAAAAAAAATTATTATTACTAAAAAAAAAAAAGGATG
*
9586960 AATAGTTAAAAAAAA
1 AATAATTAAAAAAAA
9586975 AAAAAAAAAA
Statistics
Matches: 68, Mismatches: 29, Indels: 8
0.65 0.28 0.08
Matches are distributed among these distances:
41 10 0.15
43 49 0.72
45 9 0.13
ACGTcount: A:0.67, C:0.03, G:0.09, T:0.20
Consensus pattern (43 bp):
AATAATTAAAAAAAATTATTATTACTAAAAAAAAAAAAGGATG
Found at i:9598647 original size:27 final size:27
Alignment explanation
Indices: 9598626--9598715 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
9598616 CTGTCCCAGC
*
9598626 AGACTATCTCGTGTTTAATGTCCCGTT
1 AGACTATCTCATGTTTAATGTCCCGTT
* * *
9598653 GGACTATCCCATGTTTAATGTCTCGTT
1 AGACTATCTCATGTTTAATGTCCCGTT
* *
9598680 AGACTATCTCATGTTTAGTGTCCCGAT
1 AGACTATCTCATGTTTAATGTCCCGTT
*
9598707 AGTCTATCT
1 AGACTATCT
9598716 ATGATGTTGT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (27 bp):
AGACTATCTCATGTTTAATGTCCCGTT
Found at i:9598809 original size:74 final size:74
Alignment explanation
Indices: 9598725--9598960 Score: 321
Period size: 74 Copynumber: 3.2 Consensus size: 74
9598715 TATGATGTTG
*
9598725 TAACATCTTTCAGCTATGGTCTTACACAATATAACCCCATGTTTACTATCTCGACAAACTATCAA
1 TAACATCTTTCAGCTATGGTCTTACACAATATAACCCCATGTTTACTATCTCGACGAACTATCAA
9598790 AGGATGTCA
66 AGGATGTCA
* * * *
9598799 TAACATCTTTCAGCTATGGTCTTACATAATATAA-CCTAGTGTTTACTGTCTCGATGAACTATCA
1 TAACATCTTTCAGCTATGGTCTTACACAATATAACCCCA-TGTTTACTATCTCGACGAACTATCA
9598863 AAGGATGTCA
65 AAGGATGTCA
*** * * * * *
9598873 TAGTGTCTTTCAGCTATGGTCTTACACAAGATAACCCCATGTTTATTATCCCAACGGACTATCAA
1 TAACATCTTTCAGCTATGGTCTTACACAATATAACCCCATGTTTACTATCTCGACGAACTATCAA
9598938 AGGATGTCA
66 AGGATGTCA
**
9598947 TAGTATCTTTCAGC
1 TAACATCTTTCAGC
9598961 CACGGTTTTA
Statistics
Matches: 142, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
73 3 0.02
74 136 0.96
75 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (74 bp):
TAACATCTTTCAGCTATGGTCTTACACAATATAACCCCATGTTTACTATCTCGACGAACTATCAA
AGGATGTCA
Found at i:9599065 original size:45 final size:45
Alignment explanation
Indices: 9599001--9599086 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
9598991 GCACTTTCAT
* * * * *
9599001 ATGATGTCATAGCGTCTTTCAGCTTTGGTCTTACTCATTTTTATC
1 ATGATGCCATAACATCTTTCAGCTATGGTCTTACTAATTTTTATC
9599046 ATGATGCCATAACATCTTTCAGCTATGGTCTTACTAATTTT
1 ATGATGCCATAACATCTTTCAGCTATGGTCTTACTAATTTT
9599087 GCCGTATAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (45 bp):
ATGATGCCATAACATCTTTCAGCTATGGTCTTACTAATTTTTATC
Found at i:9603186 original size:16 final size:18
Alignment explanation
Indices: 9603160--9603192 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9603150 ATAAACATCA
9603160 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
9603177 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
9603193 CCCGATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:9604606 original size:37 final size:36
Alignment explanation
Indices: 9604539--9604658 Score: 157
Period size: 37 Copynumber: 3.5 Consensus size: 36
9604529 CAACTATAAG
*
9604539 TGCCGAATGC--ACATAT-TCACTTATACCCACCTA
1 TGCCGAATGCATACATATATCACTTATATCCACCTA
9604572 TGCCGAATGCATACATATATACACTTATATCCACCTA
1 TGCCGAATGCATACATATAT-CACTTATATCCACCTA
9604609 TGCCGAATGCATAC--ATAT-A--TATATCCACCTA
1 TGCCGAATGCATACATATATCACTTATATCCACCTA
*
9604640 TGCCAAATGCATACATATA
1 TGCCGAATGCATACATATA
9604659 CACATTTAAA
Statistics
Matches: 79, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
31 25 0.32
33 14 0.18
35 10 0.13
36 1 0.01
37 29 0.37
ACGTcount: A:0.35, C:0.28, G:0.09, T:0.28
Consensus pattern (36 bp):
TGCCGAATGCATACATATATCACTTATATCCACCTA
Found at i:9604635 original size:31 final size:31
Alignment explanation
Indices: 9604597--9604658 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
9604587 TATATACACT
*
9604597 TATATCCACCTATGCCGAATGCATACATATA
1 TATATCCACCTATGCCAAATGCATACATATA
9604628 TATATCCACCTATGCCAAATGCATACATATA
1 TATATCCACCTATGCCAAATGCATACATATA
9604659 CACATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (31 bp):
TATATCCACCTATGCCAAATGCATACATATA
Found at i:9604913 original size:41 final size:41
Alignment explanation
Indices: 9604855--9605006 Score: 182
Period size: 41 Copynumber: 3.7 Consensus size: 41
9604845 AGATTCACTA
* * * *
9604855 GCACTTCA-CCTGATAGGCTTATAGTCTAATTCCGTTCACCG
1 GCACTT-AGCCTGCTAGGCGTATAGTCTGATTCAGTTCACCG
* *
9604896 GCACTTAGCCTGCTAGGCCTATAGCCTGATTCAGTTCACCG
1 GCACTTAGCCTGCTAGGCGTATAGTCTGATTCAGTTCACCG
* *
9604937 GCACTTAGCCTGCT-GGACGTATAGTCCGATTCAATTCACCG
1 GCACTTAGCCTGCTAGG-CGTATAGTCTGATTCAGTTCACCG
* *
9604978 ACACTTAGCCTGCTAGACGTATAGTCTGA
1 GCACTTAGCCTGCTAGGCGTATAGTCTGA
9605007 ACAATTTCAC
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
40 3 0.03
41 92 0.96
42 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.28
Consensus pattern (41 bp):
GCACTTAGCCTGCTAGGCGTATAGTCTGATTCAGTTCACCG
Found at i:9618813 original size:62 final size:62
Alignment explanation
Indices: 9618716--9618972 Score: 487
Period size: 62 Copynumber: 4.1 Consensus size: 62
9618706 GAGTAGATAT
* * *
9618716 ATAGGAATCTGCTTTACAAATATACTAATTACAGACATGACTTAAAGGACATGACTCAGCAG
1 ATAGGAATCGGTTTTACAAACATACTAATTACAGACATGACTTAAAGGACATGACTCAGCAG
9618778 ATAGGAATCGGTTTTACAAACATACTAATTACAGACATGACTTAAAGGACATGACTCAGCAG
1 ATAGGAATCGGTTTTACAAACATACTAATTACAGACATGACTTAAAGGACATGACTCAGCAG
9618840 ATAGGAATCGGTTTTACAAACATACTAATTACAGACATGACTTAAAGGACATGACTCAGCAG
1 ATAGGAATCGGTTTTACAAACATACTAATTACAGACATGACTTAAAGGACATGACTCAGCAG
9618902 ATAGGAATCGGTTTTACAAACATACTAATTACAGACATGACTTAAAGGACATGACTCAGCAG
1 ATAGGAATCGGTTTTACAAACATACTAATTACAGACATGACTTAAAGGACATGACTCAGCAG
9618964 ATAGGAATC
1 ATAGGAATC
9618973 TGCTTTTATC
Statistics
Matches: 192, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 192 1.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (62 bp):
ATAGGAATCGGTTTTACAAACATACTAATTACAGACATGACTTAAAGGACATGACTCAGCAG
Found at i:9625788 original size:22 final size:22
Alignment explanation
Indices: 9625763--9625818 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
9625753 GATGAACTTT
9625763 TTAATTTTTTATAATTTTAAAA
1 TTAATTTTTTATAATTTTAAAA
9625785 TTAATTTTTTATAATTTTAAAA
1 TTAATTTTTTATAATTTTAAAA
9625807 TTAATTTTTTAT
1 TTAATTTTTTAT
9625819 TAGATTTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTAATTTTTTATAATTTTAAAA
Found at i:9625791 original size:12 final size:12
Alignment explanation
Indices: 9625774--9625814 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
9625764 TAATTTTTTA
9625774 TAATTTTAAAAT
1 TAATTTTAAAAT
**
9625786 TAATTTT-TTA-
1 TAATTTTAAAAT
9625796 TAATTTTAAAAT
1 TAATTTTAAAAT
9625808 TAATTTT
1 TAATTTT
9625815 TTATTAGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 7 0.30
11 2 0.09
12 14 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TAATTTTAAAAT
Found at i:9627795 original size:129 final size:129
Alignment explanation
Indices: 9627565--9627807 Score: 371
Period size: 129 Copynumber: 1.9 Consensus size: 129
9627555 TCTTGGTTTG
*
9627565 AATTAGTCAGGTACTCGTATTCTCACTGCTGATGCTAGGTTGAATTGGCCCTTAATTGATGTTAA
1 AATTAGTCAGGTACTCGTATTCTCACTGCTGATGCTAGGTTGAATTGACCCTTAATTGATGTTAA
** ** *
9627630 TTGAGATAGTTTTTGGTTTGTTTTCTATTAACAATTTCAATCTTGTGGCCTTCAATTGATGTTA
66 TTGAGATAGTTTTCAGTTTGAATTCTATTAACAATTTCAATCCTGTGGCCTTCAATTGATGTTA
* * * * *
9627694 AATTAGTTATGTACTCGTGTTCTCACTGCTGATGCTAGGTTGGATTGACCTTTAATCT-ATGTTA
1 AATTAGTCAGGTACTCGTATTCTCACTGCTGATGCTAGGTTGAATTGACCCTTAAT-TGATGTTA
9627758 ATTGAGATAGTTTTCAGTTTGAATTCTATTAACAATTTCAATCCTGTGGC
65 ATTGAGATAGTTTTCAGTTTGAATTCTATTAACAATTTCAATCCTGTGGC
9627808 GTTCTTCAGG
Statistics
Matches: 102, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
129 101 0.99
130 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (129 bp):
AATTAGTCAGGTACTCGTATTCTCACTGCTGATGCTAGGTTGAATTGACCCTTAATTGATGTTAA
TTGAGATAGTTTTCAGTTTGAATTCTATTAACAATTTCAATCCTGTGGCCTTCAATTGATGTTA
Found at i:9628746 original size:107 final size:107
Alignment explanation
Indices: 9628584--9628942 Score: 700
Period size: 107 Copynumber: 3.3 Consensus size: 107
9628574 ATGTTTGGAA
*
9628584 TCTATCCTCGTACCCATGTCCAGATAAGTTTTGGACATGAGTACTTCAGGAAAAATGAAGAGTCG
1 TCTATCC-CATACCCATGTCCAGATAAGTTTTGGACATGAGTACTTCAGGAAAAATGAAGAGTCG
9628649 GAGCTATGTACTACTTAGTTGGACTTTAGCATAATAGCACGTG
65 GAGCTATGTACTACTTAGTTGGACTTTAGCATAATAGCACGTG
9628692 TCTATCCCATACCCATGTCCAGATAAGTTTTGGACATGAGTACTTCAGGAAAAATGAAGAGTCGG
1 TCTATCCCATACCCATGTCCAGATAAGTTTTGGACATGAGTACTTCAGGAAAAATGAAGAGTCGG
9628757 AGCTATGTACTACTTAGTTGGACTTTAGCATAATAGCACGTG
66 AGCTATGTACTACTTAGTTGGACTTTAGCATAATAGCACGTG
9628799 TCTATCCCATACCCATGTCCAGATAAGTTTTGGACATGAGTACTTCAGGAAAAATGAAGAGTCGG
1 TCTATCCCATACCCATGTCCAGATAAGTTTTGGACATGAGTACTTCAGGAAAAATGAAGAGTCGG
9628864 AGCTATGTACTACTTAGTTGGACTTTAGCATAATAGCACGTG
66 AGCTATGTACTACTTAGTTGGACTTTAGCATAATAGCACGTG
9628906 TCTATCCCATACCCATGTCCAGATAAGTTTTGGACAT
1 TCTATCCCATACCCATGTCCAGATAAGTTTTGGACAT
9628943 AATCTTATAC
Statistics
Matches: 250, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
107 243 0.97
108 7 0.03
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (107 bp):
TCTATCCCATACCCATGTCCAGATAAGTTTTGGACATGAGTACTTCAGGAAAAATGAAGAGTCGG
AGCTATGTACTACTTAGTTGGACTTTAGCATAATAGCACGTG
Found at i:9638750 original size:6 final size:6
Alignment explanation
Indices: 9638736--9638767 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
9638726 ATTTTCAATA
*
9638736 TCCTCT TCCTTT TCCTTT TCCTTT TCCTTT TC
1 TCCTTT TCCTTT TCCTTT TCCTTT TCCTTT TC
9638768 TGGGTCCGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (6 bp):
TCCTTT
Found at i:9640878 original size:33 final size:33
Alignment explanation
Indices: 9640841--9640908 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
9640831 GTGTCGCTAT
9640841 TTCAGTTAATATAAAGTTAACCACCCTATTAAG
1 TTCAGTTAATATAAAGTTAACCACCCTATTAAG
*
9640874 TTCAGTTAATATAAAGTTAACCACCCTGTTAAG
1 TTCAGTTAATATAAAGTTAACCACCCTATTAAG
9640907 TT
1 TT
9640909 TTAGATTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (33 bp):
TTCAGTTAATATAAAGTTAACCACCCTATTAAG
Found at i:9642594 original size:332 final size:332
Alignment explanation
Indices: 9641988--9642646 Score: 1318
Period size: 332 Copynumber: 2.0 Consensus size: 332
9641978 TCAAGATTTG
9641988 AAAGCTAAAATGCTATAAGATAGTTTAAAAAACGTATACTAGATACTGTAAAGAACGAAGAACGC
1 AAAGCTAAAATGCTATAAGATAGTTTAAAAAACGTATACTAGATACTGTAAAGAACGAAGAACGC
9642053 TGATAATATATGCATGCTTTAAATAAAATGAAAGATCCATAGATAAAGAAACTTAAGGTCTAATA
66 TGATAATATATGCATGCTTTAAATAAAATGAAAGATCCATAGATAAAGAAACTTAAGGTCTAATA
9642118 ACATAAGAGATGTAGCAGGACATAATCATGAGGTCAAGTTCCTCCAAACATTAAAGATAAAAACA
131 ACATAAGAGATGTAGCAGGACATAATCATGAGGTCAAGTTCCTCCAAACATTAAAGATAAAAACA
9642183 GTTGAACTAATAATTATCATAAAATCAAGCTGAAGAAGTAGTACTGGTGGCAGCCATATGCTTTA
196 GTTGAACTAATAATTATCATAAAATCAAGCTGAAGAAGTAGTACTGGTGGCAGCCATATGCTTTA
9642248 TCACAGTCTGCTGAAGCTCTTCTTTCTTTGCTCCCGTCACTTTGTCCACAATCTTCCCTTCCTTG
261 TCACAGTCTGCTGAAGCTCTTCTTTCTTTGCTCCCGTCACTTTGTCCACAATCTTCCCTTCCTTG
9642313 ATACTGT
326 ATACTGT
9642320 AAAGCTAAAATGCTATAAGATAGTTTAAAAAACGTATACTAGATACTGTAAAGAACGAAGAACGC
1 AAAGCTAAAATGCTATAAGATAGTTTAAAAAACGTATACTAGATACTGTAAAGAACGAAGAACGC
9642385 TGATAATATATGCATGCTTTAAATAAAATGAAAGATCCATAGATAAAGAAACTTAAGGTCTAATA
66 TGATAATATATGCATGCTTTAAATAAAATGAAAGATCCATAGATAAAGAAACTTAAGGTCTAATA
9642450 ACATAAGAGATGTAGCAGGACATAATCATGAGGTCAAGTTCCTCCAAACATTAAAGATAAAAACA
131 ACATAAGAGATGTAGCAGGACATAATCATGAGGTCAAGTTCCTCCAAACATTAAAGATAAAAACA
9642515 GTTGAACTAATAATTATCATAAAATCAAGCTGAAGAAGTAGTACTGGTGGCAGCCATATGCTTTA
196 GTTGAACTAATAATTATCATAAAATCAAGCTGAAGAAGTAGTACTGGTGGCAGCCATATGCTTTA
9642580 TCACAGTCTGCTGAAGCTCTTCTTTCTTTGCTCCCGTCACTTTGTCCACAATCTTCCCTTCCTTG
261 TCACAGTCTGCTGAAGCTCTTCTTTCTTTGCTCCCGTCACTTTGTCCACAATCTTCCCTTCCTTG
9642645 AT
326 AT
9642647 GAACATGAAA
Statistics
Matches: 327, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
332 327 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28
Consensus pattern (332 bp):
AAAGCTAAAATGCTATAAGATAGTTTAAAAAACGTATACTAGATACTGTAAAGAACGAAGAACGC
TGATAATATATGCATGCTTTAAATAAAATGAAAGATCCATAGATAAAGAAACTTAAGGTCTAATA
ACATAAGAGATGTAGCAGGACATAATCATGAGGTCAAGTTCCTCCAAACATTAAAGATAAAAACA
GTTGAACTAATAATTATCATAAAATCAAGCTGAAGAAGTAGTACTGGTGGCAGCCATATGCTTTA
TCACAGTCTGCTGAAGCTCTTCTTTCTTTGCTCCCGTCACTTTGTCCACAATCTTCCCTTCCTTG
ATACTGT
Found at i:9644749 original size:28 final size:29
Alignment explanation
Indices: 9644701--9644755 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
9644691 TGAGGATTAT
*
9644701 GGTTTTTAAAAGAATAAATTAAGGTTTAA
1 GGTTTTTAAAAAAATAAATTAAGGTTTAA
9644730 GGTTTTTAAAAAAAT-AATTAAGGTTT
1 GGTTTTTAAAAAAATAAATTAAGGTTT
9644756 GTTTTAGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (29 bp):
GGTTTTTAAAAAAATAAATTAAGGTTTAA
Found at i:9644857 original size:29 final size:29
Alignment explanation
Indices: 9644790--9644877 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
9644780 TGGTAAGTAT
*
9644790 TGTTCTAGAAGAAATAAATTTGACAAGATG
1 TGTTCT-GAAAAAATAAATTTGACAAGATG
* * * **
9644820 GGATATGAAAAAATAAATTTGACGTGATG
1 TGTTCTGAAAAAATAAATTTGACAAGATG
* * *
9644849 TGTTCTGAAAAAATTATTTTGATAAGATG
1 TGTTCTGAAAAAATAAATTTGACAAGATG
9644878 AATTTTATTT
Statistics
Matches: 44, Mismatches: 14, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
29 41 0.93
30 3 0.07
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (29 bp):
TGTTCTGAAAAAATAAATTTGACAAGATG
Found at i:9648389 original size:58 final size:59
Alignment explanation
Indices: 9648269--9648394 Score: 182
Period size: 58 Copynumber: 2.2 Consensus size: 59
9648259 TGTATTGTCT
* * *
9648269 TATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAAAATAATTTCTACAAAAA
1 TATTCAAAACAACTTCTAGTTTATTAAATGAAACAATATAAAAACAATTTCTACAAAAA
* * * *
9648328 TATTCAAAACAACTTCT-GTTTATTAAATGAAACAATATAAAAACAGTTTGTATAAATA
1 TATTCAAAACAACTTCTAGTTTATTAAATGAAACAATATAAAAACAATTTCTACAAAAA
9648386 TATTCAAAA
1 TATTCAAAA
9648395 AAATTAATGC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
58 44 0.73
59 16 0.27
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (59 bp):
TATTCAAAACAACTTCTAGTTTATTAAATGAAACAATATAAAAACAATTTCTACAAAAA
Done.