Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold23
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: 3125668
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 362582 characters in sequence are not A, C, G, or T
File 4 of 18
Found at i:474767 original size:51 final size:50
Alignment explanation
Indices: 474641--475279 Score: 357
Period size: 49 Copynumber: 13.5 Consensus size: 50
474631 GACGTCTTCT
* * *
474641 TCTAAGTCCAATGTC-CTTGGCCTTGAATCAACACATTGGCACC-TTCATC
1 TCTAAGTCCAATATCGC-TGGCCTTGAATCAGCATATTGGCACCTTTCATC
*
474690 TCTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACCATC
1 TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT--CATC
* *
474742 T-TGAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-GTC
1 TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCATC
* * * * * *
474789 TCTAAGACTAATGTCGCTAGCCTTGAATTAGCACATTGG-------CA--
1 TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCATC
*
474830 -C-AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTC-T-
1 TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-TCATC
* * * * *
474877 T-TAAGACCAATGTCGCTAGCCTTGAATTAGCACATTGG-------CA--
1 TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCATC
*
474917 -C-AA-CCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCA--
1 TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-TCATC
* * *
474963 T-TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG-------CA--
1 TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCATC
* *
475003 --TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTTTGTCATC
1 TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-TCATC
* ** * * * * *
475053 TTTAAGTCCAACGTCACTGGCCTTGAATTAGTACATTGGCACC-TTCATT
1 TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCATC
* * * * *
475102 TTTAAGTCCAATATCGCTGGCCTTCAATCAGCATACTGGCGCATTCGTCATC
1 TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--TCATC
* * * * * * *
475154 TTTAAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCATC-TTCAGC
1 TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCATC
* * * * * *
475203 TTTAAGTCCGATATCGTTGACCTTGAATTAGCATATTGGCATCTTTAACAT-
1 TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT--CATC
* * *
475254 TCCTAAGCCCAATGTCGTTGGCCTTG
1 T-CTAAGTCCAATATCGCTGGCCTTG
475280 TCTCAGCACA
Statistics
Matches: 460, Mismatches: 80, Indels: 97
0.72 0.13 0.15
Matches are distributed among these distances:
38 28 0.06
39 65 0.14
40 4 0.01
46 2 0.00
47 6 0.01
48 93 0.20
49 113 0.25
50 9 0.02
51 41 0.09
52 99 0.22
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (50 bp):
TCTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCATC
Found at i:474894 original size:87 final size:87
Alignment explanation
Indices: 474748--475194 Score: 545
Period size: 87 Copynumber: 4.9 Consensus size: 87
474738 CATCTTGAGT
* *
474748 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACTAATGTCGCTAGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTAGCCTT
474813 GAATTAGCACATTGGCACAAGC
66 GAATTAGCACATTGGCACAAGC
474835 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTAGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTAGCCTT
474900 GAATTAGCACATTGGCACAA-C
66 GAATTAGCACATTGGCACAAGC
* *
474921 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCATTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTAGCCTT
* * *
474986 GAATCAGCACATTGGCATAAGT
66 GAATTAGCACATTGGCACAAGC
* * * * * *
475008 CCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAACGTCACTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTG---TCTTTAAGACCAATGTCGCTAG
* *
475073 CCTTGAATTAGTACATTGGCACCTTCATTTTTAAGT
62 CCTTGAATTAGCACATTGGCA----C------AAGC
* * * *
475109 CCAATATCGCTGGCCTTCAATCAGCATACTGGCGCATTCGTCATCTTTAAGACCAATGTCGCTAG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-G---TCTTTAAGACCAATGTCGCTAG
*
475174 CCTTGAATCAGCACATTGGCA
62 CCTTGAATTAGCACATTGGCA
475195 TCTTCAGCTT
Statistics
Matches: 318, Mismatches: 26, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
86 82 0.26
87 117 0.37
88 3 0.01
91 37 0.12
100 2 0.01
101 77 0.24
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (87 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTAGCCTT
GAATTAGCACATTGGCACAAGC
Found at i:475037 original size:173 final size:178
Alignment explanation
Indices: 474748--475195 Score: 566
Period size: 173 Copynumber: 2.5 Consensus size: 178
474738 CATCTTGAGT
*
474748 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTC-TCTAAGACTAATGTCGCTAGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCAT-TAAGACCAATGTCGCTAGCCT
* *
474812 TGAATTAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTG-T
65 TGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGAT
* *
474875 CTTTAAGACCAATGTCGCTAGCCTTGAATTAGCACATTGGCA-C-AA-C
130 CTTTAAGACCAACGTCACTAGCCTTGAATTAGCACATTGGCACCTAAGC
*
474921 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCATTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCATTAAGACCAATGTCGCTAGCCTT
* * *
474986 GAATCAGCACATTGGCATAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTTTGTCA
66 GAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTG--A
* * * *
475051 TCTTTAAGTCCAACGTCACTGGCCTTGAATTAGTACATTGGCACCTTCATTTTTAAGT
129 TCTTTAAGACCAACGTCACTAGCCTTGAATTAGCACATTGGCA-C--C-----TAAGC
* * * *
475109 CCAATATCGCTGGCCTTCAATCAGCATACTGGCGCATTCGTCATCTTTAAGACCAATGTCGCTAG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCA---TTAAGACCAATGTCGCTAG
475174 CCTTGAATCAGCACATTGGCAT
62 CCTTGAATCAGCACATTGGCAT
475196 CTTCAGCTTT
Statistics
Matches: 237, Mismatches: 18, Indels: 21
0.86 0.07 0.08
Matches are distributed among these distances:
173 114 0.48
174 4 0.02
177 38 0.16
181 1 0.00
187 2 0.01
188 34 0.14
189 4 0.02
192 40 0.17
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (178 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCATTAAGACCAATGTCGCTAGCCTT
GAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGATC
TTTAAGACCAACGTCACTAGCCTTGAATTAGCACATTGGCACCTAAGC
Found at i:475178 original size:101 final size:101
Alignment explanation
Indices: 475003--475242 Score: 327
Period size: 101 Copynumber: 2.4 Consensus size: 101
474993 CACATTGGCA
* * *
475003 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAACGTC
1 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCATTCGTCATCTTTAAGACCAACGTC
* * * **
475068 ACTGGCCTTGAATTAGTACATTGGCACCTTCATTTT
66 ACTAGCCTTGAATCAGCACATTGGCACCTTCAGCTT
* * * *
475104 TAAGTCCAATATCGCTGGCCTTCAATCAGCATACTGGCGCATTCGTCATCTTTAAGACCAATGTC
1 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCATTCGTCATCTTTAAGACCAACGTC
* *
475169 GCTAGCCTTGAATCAGCACATTGGCATCTTCAGCTT
66 ACTAGCCTTGAATCAGCACATTGGCACCTTCAGCTT
* * *
475205 TAAGTCCGATATCGTTGACCTTGAATTAGCATATTGGC
1 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGC
475243 ATCTTTAACA
Statistics
Matches: 119, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
101 119 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (101 bp):
TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCATTCGTCATCTTTAAGACCAACGTC
ACTAGCCTTGAATCAGCACATTGGCACCTTCAGCTT
Found at i:475244 original size:49 final size:49
Alignment explanation
Indices: 475003--475371 Score: 240
Period size: 52 Copynumber: 7.3 Consensus size: 49
474993 CACATTGGCA
* *
475003 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTTTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATT-G-GCATCT-TCATCTT
** * * * * *
475055 TAAGTCCAACGTCACTGGCCTTGAATTAGTACATTGGCACCTTCATTTT
1 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCATCTTCATCTT
* * * *
475104 TAAGTCCAATATCGCTGGCCTTCAATCAGCATACTGGCGCATTCGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATTAGCATA-TTG-GCA-TCTTCATCTT
* * * * * *
475156 TAAGACCAATGTCGCTAGCCTTGAATCAGCACATTGGCATCTTCAGCTT
1 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCATCTTCATCTT
* * * * *
475205 TAAGTCCGATATCGTTGACCTTGAATTAGCATATTGGCATCTTTAACATT
1 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCATCTTCATC-TT
* * * ** * * * *
475255 CCTAAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTAGCA--TTCTTCTT
1 --TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCATCTTCATCTT
* * * * *
475304 CAAGTCTAATGTCGCTGGCCATGAATTAGCACT-TTGTCATTCTTCGCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATTAGCA-TATTGGCA-TCTT--CATCTT
* *
475356 TGAGCCCAATATCGCT
1 TAAGTCCAATATCGCT
475372 AGCCGCATAT
Statistics
Matches: 238, Mismatches: 67, Indels: 24
0.72 0.20 0.07
Matches are distributed among these distances:
47 27 0.11
49 79 0.33
50 15 0.06
51 6 0.03
52 111 0.47
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (49 bp):
TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCATCTTCATCTT
Found at i:475266 original size:101 final size:100
Alignment explanation
Indices: 475003--475334 Score: 296
Period size: 101 Copynumber: 3.3 Consensus size: 100
474993 CACATTGGCA
** * * * *
475003 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAACGTC
1 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCATCTTTATCAT-TCTAAGACCAATGTC
* * * * **
475068 ACTGGCCTTGAATTAGTACATTGGCACCTTCATTTT
65 GCTGGCCTTGAATCAGCACATTGGCATCTTCAGCTT
* * * * *
475104 TAAGTCCAATATCGCTGGCCTTCAATCAGCATACTGGCGCATTCGTCATC-TT-TAAGACCAATG
1 TAAGTCCAATATCGCTGGCCTTGAATTAGCATA-TTG-GCA-TCTTTATCATTCTAAGACCAATG
*
475167 TCGCTAGCCTTGAATCAGCACATTGGCATCTTCAGCTT
63 TCGCTGGCCTTGAATCAGCACATTGGCATCTTCAGCTT
* * * * *
475205 TAAGTCCGATATCGTTGACCTTGAATTAGCATATTGGCATCTTTAACATTCCTAAGCCCAATGTC
1 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCATCTTTATCATT-CTAAGACCAATGTC
* ** *
475270 GTTGGCCTTGTCTCAGCACATTAGCATTCTT---CTT
65 GCTGGCCTTGAATCAGCACATTGGCA-TCTTCAGCTT
* * * *
475304 CAAGTCTAATGTCGCTGGCCATGAATTAGCA
1 TAAGTCCAATATCGCTGGCCTTGAATTAGCA
475335 CTTTGTCATT
Statistics
Matches: 185, Mismatches: 39, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
98 5 0.03
99 32 0.17
100 2 0.01
101 132 0.71
102 7 0.04
103 3 0.02
104 4 0.02
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (100 bp):
TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCATCTTTATCATTCTAAGACCAATGTCG
CTGGCCTTGAATCAGCACATTGGCATCTTCAGCTT
Found at i:479736 original size:13 final size:13
Alignment explanation
Indices: 479718--479742 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
479708 CAAAGATCAG
479718 TGTATCGATACAA
1 TGTATCGATACAA
479731 TGTATCGATACA
1 TGTATCGATACA
479743 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:479805 original size:13 final size:13
Alignment explanation
Indices: 479787--479870 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
479777 GGCTTCGTAG
479787 CGATACATTGTAT
1 CGATACATTGTAT
479800 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
479819 CGATACATTGTAT
1 CGATACATTGTAT
479832 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
479851 CGATACATTGTAT
1 CGATACATTGTAT
479864 CGATACA
1 CGATACA
479871 AATCGTTGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:479819 original size:19 final size:18
Alignment explanation
Indices: 479795--479857 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
479785 AGCGATACAT
479795 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
479814 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
479827 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
479846 TGTATCGATACA
1 TGTATCGATACA
479858 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:479828 original size:32 final size:32
Alignment explanation
Indices: 479787--479872 Score: 163
Period size: 32 Copynumber: 2.7 Consensus size: 32
479777 GGCTTCGTAG
479787 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
479819 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
479851 CGATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
479873 TCGTTGAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:481278 original size:102 final size:102
Alignment explanation
Indices: 481146--481810 Score: 727
Period size: 102 Copynumber: 6.6 Consensus size: 102
481136 CTTAGGAATG
* * *
481146 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAAGATGACAAAG
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGATGACAAAG
* *
481211 GCGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
66 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * *
481248 TTAAAGATGAAGTTGCCAATGTGCTAATTCAAGGCCAGCGATATTGGACTTAAAAGATGACAAAG
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGATGACAAAG
* * *
481313 GTGCCAATATACTGATTCAAGGCCAGCGATATTAGAC
66 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
481350 TTAAAGGTGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGA-TT------T---A
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGATGACA
* *
481405 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
63 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
** *
481445 TTAAAGACAAAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAG-TGACAAAG
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGATGACAAAG
* *
481509 GCGCCAATATGCTGATTCAAGGCCAGCGACCCAGCGACATTGGTC
66 GTGCCAATATGCTGATTC-A----AG-G--CCAGCGACATTGGAC
** *
481554 TTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAGGTGACAAAG
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGATGACAAAG
* * *
481618 GTGCCAATATGCTGATTCAAGGCAAACGATATT-GATC
66 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGA-C
* * *
481655 TTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTT-AAAGATG---AA
1 -TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGATGACAAA
* * * *
481716 GATGCCAATATGTTGATTCAAGGCCAGTGACATT-AATC
65 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGA-C
** * * * *
481754 TTAAAGACAAAGGTGCCAATATGCTAATTCAACGTCAGCGATATTGGACTTAGAAGA
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGA
481811 AGACGCCACC
Statistics
Matches: 487, Mismatches: 52, Indels: 51
0.83 0.09 0.09
Matches are distributed among these distances:
92 37 0.08
93 2 0.00
95 42 0.09
98 45 0.09
99 37 0.08
100 1 0.00
101 29 0.06
102 156 0.32
103 1 0.00
104 4 0.01
105 35 0.07
106 2 0.00
107 1 0.00
108 5 0.01
109 90 0.18
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (102 bp):
TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGATGACAAAG
GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
Found at i:481383 original size:52 final size:52
Alignment explanation
Indices: 481155--481810 Score: 679
Period size: 49 Copynumber: 12.9 Consensus size: 52
481145 GTTAAAGATG
* * *
481155 AAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAAGATGACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAGATGACA
*
481208 AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACA
* * *
481257 AAGTTGCCAATGTGCTAATTCAAGGCCAGCGATATTGGACTTAAAAGATGACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAGATGACA
* * *
481310 AAGGTGCCAATATACTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACA
*
481362 AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGA-TT-----T---A
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACA
* * *
481405 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACA
*
481454 AAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-AGTGACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-TGACA
* * *
481506 AAGGCGCCAATATGCTGATTCAAGGCCAGCGACCCAGCGACATTGGTCTT-AA-A-GACA
1 AAGGTGCCAATATGCTGATTC-A----AG-G--CCAGCGATATTGGACTTAAAGATGACA
*
481563 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACA
* *
481615 AAGGTGCCAATATGCTGATTCAAGGCAAACGATATT-GATCTTTAAAGATG---
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA-C-TTAAAGATGACA
* * *
481665 AAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATG---
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACA
* * * * *
481714 AAGATGCCAATATGTTGATTCAAGGCCAGTGACATT-AATCTT-AA-A-GACA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA-CTTAAAGATGACA
* * *
481763 AAGGTGCCAATATGCTAATTCAACGTCAGCGATATTGGACTTAGAAGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
481811 AGACGCCACC
Statistics
Matches: 514, Mismatches: 53, Indels: 73
0.80 0.08 0.11
Matches are distributed among these distances:
43 36 0.07
44 2 0.00
46 2 0.00
47 1 0.00
48 3 0.01
49 167 0.32
50 47 0.09
51 9 0.02
52 117 0.23
53 84 0.16
56 1 0.00
57 26 0.05
58 1 0.00
59 3 0.01
60 15 0.03
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (52 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACA
Found at i:481422 original size:43 final size:43
Alignment explanation
Indices: 481361--481498 Score: 161
Period size: 43 Copynumber: 3.1 Consensus size: 43
481351 TAAAGGTGAC
*
481361 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGATTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGATTT
* *
481404 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGG-TCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAT-TT
* *
481447 AAAGACAAAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ------AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGATTT
481496 AAA
1 AAA
481499 AGTGACAAAG
Statistics
Matches: 80, Mismatches: 7, Indels: 16
0.78 0.07 0.16
Matches are distributed among these distances:
42 1 0.01
43 41 0.51
49 38 0.47
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGATTT
Found at i:481583 original size:57 final size:59
Alignment explanation
Indices: 481479--481640 Score: 182
Period size: 52 Copynumber: 2.9 Consensus size: 59
481469 TGATTCAAGG
*
481479 CCAGCGATATTGGACTTAAAAGTGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGAC
1 CCAGCGACATTGGACTTAAAAG-GACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGAC
* *
481539 CCAGCGACATTGGTCTT-AAA-GACAAAGGTGCCAATATGCTGATTC-A----AG-G--
1 CCAGCGACATTGGACTTAAAAGGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGAC
* * *
481588 CCAGCGATATTGGACTTAAAGGTGACAAAGGTGCCAATATGCTGATTCAAGGC
1 CCAGCGACATTGGACTTAAAAG-GACAAAGGCGCCAATATGCTGATTCAAGGC
481641 AAACGATATT
Statistics
Matches: 89, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
49 15 0.17
50 2 0.02
51 1 0.01
52 27 0.30
53 1 0.01
56 1 0.01
57 24 0.27
59 3 0.03
60 15 0.17
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (59 bp):
CCAGCGACATTGGACTTAAAAGGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGAC
Found at i:481624 original size:109 final size:106
Alignment explanation
Indices: 481404--481805 Score: 462
Period size: 109 Copynumber: 3.9 Consensus size: 106
481394 TATTGGATTT
* * *
481404 AAAGGTGCCAATGTGCTGATTC-A---AGG-CCAGCGACATTGGTCTTAAAGACAAAGGTGCTAA
1 AAAGGTGCCAATATGCTGATTCAAGGCAGGACCAGCGACATTGATCTTAAAGACAAAGGTGCCAA
*
481464 TATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGAC
66 TATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAC
* *
481505 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGACCCAGCGACATTGGTCTTAAAGACAAAGGTGC
1 AAAGGTGCCAATATGCTGATTCAAGG-CAG-GA-CCAGCGACATTGATCTTAAAGACAAAGGTGC
481570 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAC
63 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAC
* **
481614 AAAGGTGCCAATATGCTGATTCAAGGCA--A--A-CGATATTGATCTTTAAAGATGAAGGTGCCA
1 AAAGGTGCCAATATGCTGATTCAAGGCAGGACCAGCGACATTGATC-TTAAAGACAAAGGTGCCA
* * * *
481674 ATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATG--
65 ATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAC
* * * *
481714 -AAGATGCCAATATGTTGATTC-A---AGG-CCAGTGACATTAATCTTAAAGACAAAGGTGCCAA
1 AAAGGTGCCAATATGCTGATTCAAGGCAGGACCAGCGACATTGATCTTAAAGACAAAGGTGCCAA
* * *
481773 TATGCTAATTCAACGTCAGCGATATTGGACTTA
66 TATGCTGATTCAAGGCCAGCGATATTGGACTTA
481806 GAAGAAGACG
Statistics
Matches: 261, Mismatches: 26, Indels: 31
0.82 0.08 0.10
Matches are distributed among these distances:
95 1 0.00
98 46 0.18
99 27 0.10
101 29 0.11
102 54 0.21
105 1 0.00
106 2 0.01
107 1 0.00
108 2 0.01
109 98 0.38
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (106 bp):
AAAGGTGCCAATATGCTGATTCAAGGCAGGACCAGCGACATTGATCTTAAAGACAAAGGTGCCAA
TATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAC
Found at i:481919 original size:34 final size:34
Alignment explanation
Indices: 481864--481977 Score: 133
Period size: 34 Copynumber: 3.4 Consensus size: 34
481854 TGGGCTTTTG
* * * *
481864 AAAAGGGTGCCACTGACTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGA
* *
481898 AAAATAGTGCCATGGAGTTGTGGGCTTACAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTA-AAAAGA
*
481933 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAA-A
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGA
481966 GAAAAG-GTGCCA
1 -AAAAGAGTGCCA
481978 ATATGCTGAC
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
33 7 0.10
34 32 0.46
35 30 0.43
ACGTcount: A:0.38, C:0.13, G:0.30, T:0.19
Consensus pattern (34 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGA
Found at i:482060 original size:32 final size:32
Alignment explanation
Indices: 482012--482077 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
482002 ATTGGGCTTG
*
482012 AAGGTGCCACGAAGTTG-TGGACTTAAAAAGAA
1 AAGGCGCCACGAAGTTGTTGG-CTTAAAAAGAA
*
482044 AAGGCGCCACGGAGTTGTTGGCTTAAAAAGAA
1 AAGGCGCCACGAAGTTGTTGGCTTAAAAAGAA
482076 AA
1 AA
482078 AGATGCTGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 28 0.90
33 3 0.10
ACGTcount: A:0.39, C:0.14, G:0.29, T:0.18
Consensus pattern (32 bp):
AAGGCGCCACGAAGTTGTTGGCTTAAAAAGAA
Found at i:482100 original size:33 final size:32
Alignment explanation
Indices: 482017--482100 Score: 78
Period size: 32 Copynumber: 2.6 Consensus size: 32
482007 GCTTGAAGGT
* * * *
482017 GCCACGAAGTTGTGGACTTAAAAAGAAAAGGC
1 GCCACGGACTTGTGGGCTTAAAAAGAAAAGAC
* * *
482049 GCCACGGAGTTGTTGGCTTAAAAAGAAAAAGAT
1 GCCACGGACTTGTGGGCTTAAAAAG-AAAAGAC
**
482082 GCTGCGGACTTGTGGGCTT
1 GCCACGGACTTGTGGGCTT
482101 TTGAAGGTTG
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 22 0.52
33 20 0.48
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.21
Consensus pattern (32 bp):
GCCACGGACTTGTGGGCTTAAAAAGAAAAGAC
Found at i:482151 original size:29 final size:29
Alignment explanation
Indices: 482088--482161 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
482078 AGATGCTGCG
*
482088 GACTTGTGGGCTTTTG--AAGGTTGCCACT
1 GACTTGTGGGC-TTTGAAAAGGGTGCCACT
* *
482116 GATTTGTGGGCTTTGAAAAGGGTGCCATT
1 GACTTGTGGGCTTTGAAAAGGGTGCCACT
482145 GACTTGTGGGCTTTGAA
1 GACTTGTGGGCTTTGAA
482162 GGTTGCCACA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 4 0.10
28 10 0.25
29 26 0.65
ACGTcount: A:0.18, C:0.14, G:0.34, T:0.35
Consensus pattern (29 bp):
GACTTGTGGGCTTTGAAAAGGGTGCCACT
Found at i:484607 original size:13 final size:13
Alignment explanation
Indices: 484589--484645 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
484579 CATAAAGTGT
484589 TGTATCGATACAA
1 TGTATCGATACAA
484602 TGTATCGATACATAA
1 TGTATCGATAC--AA
484617 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
484634 TGTATCGATACA
1 TGTATCGATACA
484646 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:484624 original size:32 final size:32
Alignment explanation
Indices: 484569--484666 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
484559 TTCAACGATT
484569 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
484602 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
484634 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
484666 T
1 T
484667 ATAAGCTACT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 51 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:484626 original size:19 final size:18
Alignment explanation
Indices: 484567--484664 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
484557 ATTTCAACGA
484567 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
484586 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
484602 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
484618 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
484634 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
484650 TTTTGTATCGATACA
1 -TTTGTATCGATACA
484665 ATATAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:484770 original size:52 final size:52
Alignment explanation
Indices: 484727--484855 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
484717 CACTGATCTT
*
484727 TGTATCGACACATGCAGGCAAATTTCCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTCCCCAGATGTATCGATACACTATAAAA
* *
484779 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTCCCCAGATGTATCGATACACTATAAAA
484831 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
484856 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTCCCCAGATGTATCGATACACTATAAAA
Found at i:492064 original size:27 final size:24
Alignment explanation
Indices: 492027--492088 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
492017 GTTCTTTTCC
*
492027 AAAAAAAGAA-ACAA-AAAAAAAGGA
1 AAAAAAAGAAGA-AACAAAAAAA-CA
*
492051 AAAAAAAGAAGAAACAAACAAACA
1 AAAAAAAGAAGAAACAAAAAAACA
492075 AAAAAAAGAAGAAA
1 AAAAAAAGAAGAAA
492089 GGAAAAACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 27 0.79
25 7 0.21
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.00
Consensus pattern (24 bp):
AAAAAAAGAAGAAACAAAAAAACA
Found at i:493148 original size:30 final size:31
Alignment explanation
Indices: 493046--493197 Score: 204
Period size: 31 Copynumber: 4.9 Consensus size: 31
493036 TTCAAATACC
*
493046 TTCTT-AAAGTCCACGACTCAGTGGCAATCTC
1 TTCTTCAAAGTCCACGACTCAGTGGC-ATCTT
493077 TTC-TCAAAGTCCACGACTCAGTGGCATCCTT
1 TTCTTCAAAGTCCACGACTCAGTGGCAT-CTT
493108 TTCTTCAAAGTCCACGACTCAGTGGCAT-TT
1 TTCTTCAAAGTCCACGACTCAGTGGCATCTT
* *
493138 TGTC-TCAAAGTCCACGACTCAATGGCATTTT
1 T-TCTTCAAAGTCCACGACTCAGTGGCATCTT
* *
493169 TTCTTTAAAGTCCACCACTCAGTGGCATC
1 TTCTTCAAAGTCCACGACTCAGTGGCATC
493198 CTCTGTTCAA
Statistics
Matches: 109, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
30 31 0.28
31 54 0.50
32 24 0.22
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (31 bp):
TTCTTCAAAGTCCACGACTCAGTGGCATCTT
Found at i:493312 original size:32 final size:33
Alignment explanation
Indices: 493206--493441 Score: 394
Period size: 32 Copynumber: 7.3 Consensus size: 33
493196 TCCTCTGTTC
493206 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
* *
493239 AAGCCCACACAAGTTGGTGGCAACCTTTCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
493272 AAGCCCACACAAGTCGGTGGCAACCCTTCTC-A
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
493304 AAGCCCACACAAGTCGGTGGCAACCCTTCTC-A
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
*
493336 AAGCCCACACAAGTCAGTGGCAACCC-TCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
*
493368 AAGCCCACACAAGTTGGTGGCAACCC-TCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
493400 AAGCCCACACAAGTCGGTGGCAACCC-T-TCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
493431 AAGCCCACACA
1 AAGCCCACACA
493442 GCCCTTCTCT
Statistics
Matches: 194, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
31 19 0.10
32 115 0.59
33 60 0.31
ACGTcount: A:0.29, C:0.36, G:0.18, T:0.17
Consensus pattern (33 bp):
AAGCCCACACAAGTCGGTGGCAACCCTTCTCTA
Found at i:493371 original size:64 final size:63
Alignment explanation
Indices: 493206--493649 Score: 594
Period size: 64 Copynumber: 7.1 Consensus size: 63
493196 TCCTCTGTTC
* *
493206 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCTTTCTCT
1 AAGCCCACACAAGTCGGTGGCAACCC-T-TCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTC-
493271 A
63 A
493272 AAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAACCCTTCTCA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCT-AAAGCCCACACAAGTCGGTGGCAACCCTTCTCA
* *
493336 AAGCCCACACAAGTCAGTGGCAACCCTCTCTAAAGCCCACACAAGTTGGTGGCAACCC-TCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCT-TCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTC-A
*
493400 AAGCCCACACAAGTCGGTGGCAACCCTTCTAAAGCCCACAC-A-------G---CCCTTCTCT
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCA
* *
493452 AAGCCCACATAAGTTGGTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCA
1 AAGCCCACACAAGTCGGTGGCAACCCTTC-TAAAGCCCACACAAGTCGGTGGCAACCCTTCTCA
493516 AAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAACCC-TCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCT-AAAGCCCACACAAGTCGGTGGCAACCCTTCTC-A
* * *
493580 AAGCCCATACAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT--
1 AAGCCCACACAAGTCGGTGGCAACC-CT-TCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCA
493643 AAGCCCA
1 AAGCCCA
493650 ATATCGCTGG
Statistics
Matches: 343, Mismatches: 14, Indels: 45
0.85 0.03 0.11
Matches are distributed among these distances:
52 30 0.09
53 16 0.05
54 1 0.00
55 1 0.00
61 1 0.00
62 1 0.00
63 30 0.09
64 169 0.49
65 62 0.18
66 32 0.09
ACGTcount: A:0.28, C:0.36, G:0.18, T:0.18
Consensus pattern (63 bp):
AAGCCCACACAAGTCGGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCA
Found at i:493488 original size:32 final size:32
Alignment explanation
Indices: 493443--493649 Score: 296
Period size: 32 Copynumber: 6.5 Consensus size: 32
493433 GCCCACACAG
* *
493443 CCCTTCTCT-AAGCCCACATAAGTTGGTGGCAA
1 CCCTTCT-TAAAGCCCACACAAGTCGGTGGCAA
493475 CCCTTCTTAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTCTTAAAGCCCACACAAGTCGGTGGCAA
*
493507 CCCTTCTCAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTCTTAAAGCCCACACAAGTCGGTGGCAA
*
493539 CCCTTCTCAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTCTTAAAGCCCACACAAGTCGGTGGCAA
* *
493571 CCC-TCTCTAAAGCCCATACAAGTTGGTGGCAA
1 CCCTTCT-TAAAGCCCACACAAGTCGGTGGCAA
*
493603 CCATTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTCT-TAAAGCCCACACAAGTCGGTGGCAA
493636 CCCTTC-T-AAGCCCA
1 CCCTTCTTAAAGCCCA
493650 ATATCGCTGG
Statistics
Matches: 162, Mismatches: 10, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
30 7 0.04
31 5 0.03
32 118 0.73
33 32 0.20
ACGTcount: A:0.28, C:0.35, G:0.18, T:0.19
Consensus pattern (32 bp):
CCCTTCTTAAAGCCCACACAAGTCGGTGGCAA
Found at i:493563 original size:148 final size:149
Alignment explanation
Indices: 493295--493586 Score: 491
Period size: 148 Copynumber: 2.0 Consensus size: 149
493285 TCGGTGGCAA
493295 CCCTTCTCAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCAGTGGCAAC
1 CCCTTCTCAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCAGTGGCAAC
*
493360 CCTCTCTAAAGCCCACACAAGTTGGTGGCAACCCTCTCTAAAGCCCACACAAGTCGGTGGCAACC
66 CCTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTCTCTAAAGCCCACACAAGTCGGTGGCAACC
493425 CT-TCTAAAGCCCACACAG
131 CTCTCTAAAGCCCACACAG
* * * * *
493443 CCCTTCTCTAAGCCCACATAAGTTGGTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTGGCAAC
1 CCCTTCTCAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCAGTGGCAAC
493508 CCT-TCTCAAAGCCCACACAAGTCGGTGGCAACCCT-TCTCAAAGCCCACACAAGTCGGTGGCAA
66 CCTCTCT-AAAGCCCACACAAGTCGGTGGCAACCCTCTCT-AAAGCCCACACAAGTCGGTGGCAA
493571 CCCTCTCTAAAGCCCA
129 CCCTCTCTAAAGCCCA
493587 TACAAGTTGG
Statistics
Matches: 135, Mismatches: 6, Indels: 5
0.92 0.04 0.03
Matches are distributed among these distances:
147 6 0.04
148 118 0.87
149 11 0.08
ACGTcount: A:0.28, C:0.37, G:0.17, T:0.17
Consensus pattern (149 bp):
CCCTTCTCAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCAGTGGCAAC
CCTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTCTCTAAAGCCCACACAAGTCGGTGGCAACC
CTCTCTAAAGCCCACACAG
Found at i:493574 original size:180 final size:183
Alignment explanation
Indices: 493265--493623 Score: 609
Period size: 180 Copynumber: 2.0 Consensus size: 183
493255 GTGGCAACCT
493265 TTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAACCC
1 TTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAACCC
*
493330 TTCTCAAAGCCCACACAAGTCAGTGGCAACCCTCTCTAAAGCCCACACAAGTTGGTGGCAACCCT
66 TTCTCAAAGCCCACACAAGTCAGTGGCAACCCTCTCTAAAGCCCACACAAGTCGGTGGCAACCCT
493395 CTCTAAAGCCCACACAAGTCGGTGGCAACC-CT-TCTAAAGCCCACACAGCCC
131 CTCTAAAGCCCACACAAGTCGGTGGCAACCACTCTCTAAAGCCCACACAGCCC
* * *
493446 TTCTCT-AAGCCCACATAAGTTGGTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTGGCAACCC
1 TTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAACCC
*
493510 TTCTCAAAGCCCACACAAGTCGGTGGCAACCCT-TCTCAAAGCCCACACAAGTCGGTGGCAACCC
66 TTCTCAAAGCCCACACAAGTCAGTGGCAACCCTCTCT-AAAGCCCACACAAGTCGGTGGCAACCC
* * *
493574 TCTCTAAAGCCCATACAAGTTGGTGGCAACCATTCTCTAAAGCCCACACA
130 TCTCTAAAGCCCACACAAGTCGGTGGCAACCACTCTCTAAAGCCCACACA
493624 AGTCGGTGGC
Statistics
Matches: 167, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
179 3 0.02
180 142 0.85
181 7 0.04
182 15 0.09
ACGTcount: A:0.29, C:0.36, G:0.17, T:0.18
Consensus pattern (183 bp):
TTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCCCACACAAGTCGGTGGCAACCC
TTCTCAAAGCCCACACAAGTCAGTGGCAACCCTCTCTAAAGCCCACACAAGTCGGTGGCAACCCT
CTCTAAAGCCCACACAAGTCGGTGGCAACCACTCTCTAAAGCCCACACAGCCC
Found at i:493708 original size:49 final size:49
Alignment explanation
Indices: 493642--493987 Score: 434
Period size: 49 Copynumber: 7.1 Consensus size: 49
493632 GCAACCCTTC
* *
493642 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
493691 TAAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCACCTTCATTTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
493740 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
493789 TAAGTGCAATGTAGCTGGGCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
493832 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTT
* *
493884 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGTCTCTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-AC-CT-TCATCTT
* * * *
493936 TAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCCTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
493985 TAA
1 TAA
493988 CATTCCTAAG
Statistics
Matches: 256, Mismatches: 30, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
43 37 0.14
45 1 0.00
49 130 0.51
50 2 0.01
51 1 0.00
52 83 0.32
53 1 0.00
54 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (49 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:493849 original size:43 final size:43
Alignment explanation
Indices: 493786--493875 Score: 135
Period size: 43 Copynumber: 2.1 Consensus size: 43
493776 GCACCTTCAT
* * *
493786 CTTTAAGTGCAATGTAGCTGGGCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
493829 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
493872 CTTT
1 CTTT
493876 GTCATCTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:493907 original size:52 final size:52
Alignment explanation
Indices: 493829--493987 Score: 234
Period size: 52 Copynumber: 3.1 Consensus size: 52
493819 ACATTGGCAC
*
493829 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCTGTCAT
* **
493881 CTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGTCTCTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCTGTCAT
* * *
493933 CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACC-C--TCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCTGTCAT
493982 CTTTAA
1 CTTTAA
493988 CATTCCTAAG
Statistics
Matches: 97, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
49 10 0.10
51 1 0.01
52 86 0.89
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (52 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCTGTCAT
Found at i:494810 original size:14 final size:15
Alignment explanation
Indices: 494781--494810 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
494771 ACGATTTGTA
494781 TCGATACATAAAGTG
1 TCGATACATAAAGTG
494796 TCGATACAT-AAGTG
1 TCGATACATAAAGTG
494810 T
1 T
494811 TGTATCGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (15 bp):
TCGATACATAAAGTG
Found at i:494820 original size:19 final size:18
Alignment explanation
Indices: 494776--494886 Score: 86
Period size: 19 Copynumber: 6.7 Consensus size: 18
494766 TTTCAACGAT
*
494776 TTGTATCGATACATAAAG
1 TTGTATCGATACATAATG
494794 -TG--TCGATACATAAGTG
1 TTGTATCGATACATAA-TG
494810 TTGTATCGATAC--AA--
1 TTGTATCGATACATAATG
494824 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAA-TG
494842 TTGTATCGATAC--AA--
1 TTGTATCGATACATAATG
494856 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAA-TG
*
494874 TTGTATCAATACA
1 TTGTATCGATACA
494887 ATATAAGCTA
Statistics
Matches: 75, Mismatches: 2, Indels: 31
0.69 0.02 0.29
Matches are distributed among these distances:
13 22 0.29
15 15 0.20
16 1 0.01
17 8 0.11
19 29 0.39
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (18 bp):
TTGTATCGATACATAATG
Found at i:494829 original size:13 final size:13
Alignment explanation
Indices: 494811--494867 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
494801 ACATAAGTGT
494811 TGTATCGATACAA
1 TGTATCGATACAA
494824 TGTATCGATACATAA
1 TGTATCGATAC--AA
494839 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
494856 TGTATCGATACA
1 TGTATCGATACA
494868 TAAGTGTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:494837 original size:32 final size:32
Alignment explanation
Indices: 494776--494888 Score: 181
Period size: 32 Copynumber: 3.5 Consensus size: 32
494766 TTTCAACGAT
* *
494776 TTGTATCGATACATAAAGTGTCGATACATAAGTG
1 TTGTATCGATAC--AATGTATCGATACATAAGTG
494810 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
494842 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
494874 TTGTATCAATACAAT
1 TTGTATCGATACAAT
494889 ATAAGCTACT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
32 64 0.84
34 12 0.16
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:494947 original size:13 final size:13
Alignment explanation
Indices: 494929--494953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
494919 ATTACTCAAA
494929 TGTATCGATACAT
1 TGTATCGATACAT
494942 TGTATCGATACA
1 TGTATCGATACA
494954 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:495007 original size:52 final size:52
Alignment explanation
Indices: 494962--495090 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
494952 CACTAATCTT
*
494962 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
495014 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
495066 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
495091 TCATATTTCG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:495790 original size:52 final size:52
Alignment explanation
Indices: 495642--495770 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
495632 CGAAATATGA
495642 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
495694 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
495746 AAATTTGCCTACATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
495771 AAGATTAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:496709 original size:49 final size:48
Alignment explanation
Indices: 496576--497562 Score: 1014
Period size: 49 Copynumber: 20.8 Consensus size: 48
496566 GAGAAGAATT
* * * ** *
496576 CCAATGTGCTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGATGTAGGCG
1 CCAATATGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGAT-A---AGGTG
* *
496629 CCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-AAGGTG
* * *
496678 TCAATGTGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-AAGGTG
* *
496727 CCAGTATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-AAGGTG
* **
496776 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT----AAGGTG
* * *
496828 CCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-AAGGTG
*
496877 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-AAGGTG
* *
496926 CCAATATGCTGTTTCAAGGCCAGCGACATTGGACTTAAAGACAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-TAAGGTG
*
496975 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTG
* * *
497018 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATTAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTG
* * * *
497066 CCAATATGTTGATTCAAGGCCAACAATATTGGACTT----A-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTG
* * * * *
497109 CCAATGTGCTAATTCAAGGGCAGCGACATTGGTCTTAAAAGACAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AAAGA-TAAGGTG
*
497159 CCAATATGCTGATTCAAGGCCAGCGATATTGGA-TT---GA-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTG
* * *
497202 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTG
* * **
497250 CCAATATGCTGATTTAAGGCTAGCGATTTTGGAC-T-----TAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTG
* * * *
497292 CCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTG
* * *
497340 CCAATATGCTAATTCAAGGCTAGCGATATTGGACTT--A-A-AA-GTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTG
* *
497383 CCACTATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGGCA-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAA-G-ATAAGGTG
*
497432 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTG
* * *
497475 CCAATGTGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGGCA-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAA-G-ATAAGGTG
* * * *
497524 CCAATATACTAATTCAAGGCCAGCGATATTGGGCTTAAA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAA
497563 AGAAGATGTC
Statistics
Matches: 786, Mismatches: 109, Indels: 82
0.80 0.11 0.08
Matches are distributed among these distances:
42 33 0.04
43 182 0.23
44 4 0.01
45 5 0.01
46 1 0.00
47 4 0.01
48 108 0.14
49 335 0.43
50 34 0.04
52 55 0.07
53 25 0.03
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (48 bp):
CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTG
Found at i:496917 original size:199 final size:189
Alignment explanation
Indices: 496619--497562 Score: 1100
Period size: 199 Copynumber: 5.0 Consensus size: 189
496609 TTTTAAAGAT
* * * * * *
496619 GATGTAGGCGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGGTGTCAATG
1 GATG-AGGCACCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATA
* * * *
496684 TGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATAAAGGTGCCAGTATGCTGATTCAAGGCCA
65 TGCTGATTCAAGGCCAGCGATATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAAGGCCA
* * ** * *
496749 GCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAA
124 GCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
496814 A
189 A
* * * *
496815 GATGACAAAGGCACCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTACCA
1 GATG----AGGCACCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCA
* * * *
496880 ATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGCCAATATGCTGTTTCAAGG
62 ATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAAGG
*
496945 CCAGCGACATTGGACTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
121 CCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
497010 TAAA
186 TAAA
* * *
497014 G--G-TG--CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT-TAGGTGCCAATAT
1 GATGAGGCACCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATAT
* * * * *
497073 GTTGATTCAAGGCCAACAATATTGGACTTAAAGGTGCCAATGTGCTAATTCAAGGGCAGCGACAT
66 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACAT
497138 TGGTCTTAAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA-TTGAAA
131 TGGTCTT-AAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAA
* *
497198 G--G-TG--CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATG-AGGTGCCAATAT
1 GATGAGGCACCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATAT
* * * *
497257 GCTGATTTAAGGCTAGCGATTTTGGACTT-AAGGTGCCAATGTGCTGATTCAAGGCCAACGACAT
66 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACAT
** * *
497321 TGGTCTTAAAGA-TGAGGTGCCAATATGCTAATTCAAGGCTAGCGATATTGGACTTAAA
131 TGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
* * ***
497379 -A-G-TG--CCACTATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGGCAAAGGTGCCAATAT
1 GATGAGGCACCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATAT
*
497439 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGTCAGCGACAT
66 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACAT
* * * *
497504 TGGTCTTAAAGGCAAAGGTGCCAATATACTAATTCAAGGCCAGCGATATTGGGCTTAAA
131 TGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
497563 AGAAGATGTC
Statistics
Matches: 677, Mismatches: 60, Indels: 34
0.88 0.08 0.04
Matches are distributed among these distances:
181 80 0.12
182 45 0.07
183 124 0.18
184 171 0.25
188 1 0.00
189 33 0.05
190 38 0.06
192 1 0.00
196 4 0.01
197 1 0.00
199 179 0.26
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (189 bp):
GATGAGGCACCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATAT
GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACAT
TGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
Found at i:497449 original size:92 final size:92
Alignment explanation
Indices: 496828--497562 Score: 991
Period size: 92 Copynumber: 8.0 Consensus size: 92
496818 GACAAAGGCA
* * * * *** * *
496828 CCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTACCAATGTGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGGCAAAGGTGCCAATATGCTGATTCA
*
496893 AGGCCAGCGACATTGGACTTAAAGATAAAGGTG
66 AGGCCAGCGATATTGGAC-T-----TAAAGGTG
* * * *
496926 CCAATATGCTGTTTCAAGGCCAGCGACATTGGACTTAAAGACAAAGGTGCCAATATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGGCAAAGGTGCCAATATGCTGATTCA
496991 AGGCCAGCGATATTGGACTTAAAGGTG
66 AGGCCAGCGATATTGGACTTAAAGGTG
* *
497018 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAA-G-ATTAGGTGCCAATATGTTGATTC
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGGCA-AAGGTGCCAATATGCTGATTC
* *
497081 AAGGCCAACAATATTGGACTTAAAGGTG
65 AAGGCCAGCGATATTGGACTTAAAGGTG
* * *
497109 CCAATGTGCTAATTCAAGGGCAGCGACATTGGTCTTAAAAGACAAAGGTGCCAATATGCTGATTC
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AAAGGCAAAGGTGCCAATATGCTGATTC
497174 AAGGCCAGCGATATTGGA-TTGAAAGGTG
65 AAGGCCAGCGATATTGGACTT-AAAGGTG
* *
497202 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAA-G-ATGAGGTGCCAATATGCTGATTT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGGCA-AAGGTGCCAATATGCTGATTC
* *
497265 AAGGCTAGCGATTTTGGACTT-AAGGTG
65 AAGGCCAGCGATATTGGACTTAAAGGTG
* * *
497292 CCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAA-G-ATGAGGTGCCAATATGCTAATTC
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGGCA-AAGGTGCCAATATGCTGATTC
* *
497355 AAGGCTAGCGATATTGGACTTAAAAGTG
65 AAGGCCAGCGATATTGGACTTAAAGGTG
* *
497383 CCACTATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGGCAAAGGTGCCAATATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGGCAAAGGTGCCAATATGCTGATTCA
497448 AGGCCAGCGATATTGGACTTAAAGGTG
66 AGGCCAGCGATATTGGACTTAAAGGTG
* * *
497475 CCAATGTGCTGATTCAAGGTCAGCGACATTGGTCTTAAAGGCAAAGGTGCCAATATACTAATTCA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGGCAAAGGTGCCAATATGCTGATTCA
*
497540 AGGCCAGCGATATTGGGCTTAAA
66 AGGCCAGCGATATTGGACTTAAA
497563 AGAAGATGTC
Statistics
Matches: 579, Mismatches: 48, Indels: 26
0.89 0.07 0.04
Matches are distributed among these distances:
90 88 0.15
91 155 0.27
92 182 0.31
93 77 0.13
94 1 0.00
97 1 0.00
98 75 0.13
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGGCAAAGGTGCCAATATGCTGATTCA
AGGCCAGCGATATTGGACTTAAAGGTG
Found at i:497732 original size:67 final size:67
Alignment explanation
Indices: 497594--498028 Score: 497
Period size: 67 Copynumber: 6.5 Consensus size: 67
497584 TCGGCTTTTG
* * * * * * * *
497594 AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGAGAAAGATGCCACGGAGTTGTGGACTTAAAA
1 AAGG-TGCCACGGAGTTGTGGAC-TTT-AAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
497659 AGGAAAA
63 A-G-AAA
* * * * *
497666 AAGATGTCACGAAGTTGTGGAC-TTAAAAAG-AAAAGGTGCCACGAAGTGGTGGGCTTTGAAAAG
1 AAGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAG
497729 AAA
65 AAA
*
497732 AAGGTGCCACGGAGTTGTAGG-CTTTAAAAAG-AAAAGGTGCCACGGAGTGGTGGGCTTTGAAAA
1 AAGGTGCCACGGAGTTGT-GGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA
497795 GAAA
64 GAAA
* * *
497799 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TTAAAAGG
1 AAGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGA
497863 AA
66 AA
* *
497865 AAGGTGCCACGGAGTGGTGGACTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAATAG
1 AAGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA-AG
497930 -AA
65 AAA
* * * * *
497932 AAGGTGCCACGGAGTGGTGGGCTTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGAC-TTAAAAGG
1 AAGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGA
497996 AA
66 AA
* * *
497998 AAGGTGCCACGGAGTGGTGGGCTTTGAAAAG
1 AAGGTGCCACGGAGTTGTGGACTTTAAAAAG
498029 CATGTGAGAA
Statistics
Matches: 326, Mismatches: 29, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
65 2 0.01
66 117 0.36
67 156 0.48
68 33 0.10
69 2 0.01
71 13 0.04
72 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (67 bp):
AAGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGA
AA
Found at i:497738 original size:34 final size:34
Alignment explanation
Indices: 497594--498028 Score: 510
Period size: 34 Copynumber: 12.9 Consensus size: 34
497584 TCGGCTTTTG
* * * *
497594 AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGAGA
1 AAGG-TGCCACGGAGTTGTGGGC-TTT-AAAAAGAAA
* *
497631 AAGATGCCACGGAGTTGTGGAC-TTAAAAAGGAAAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAA-G-AAA
* * * *
497666 AAGATGTCACGAAGTTGTGGAC-TTAAAAAG-AA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* * *
497698 AAGGTGCCACGAAGTGGTGGGCTTTGAAAAGAAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
*
497732 AAGGTGCCACGGAGTTGTAGGCTTTAAAAAG-AA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* *
497765 AAGGTGCCACGGAGTGGTGGGCTTTGAAAAGAAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
497799 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* *
497833 AAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* * *
497865 AAGGTGCCACGGAGTGGTGGACTTTGAAAAGAAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
*
497899 AAGGTGCCACGGAGTTGTGGGCTTTAAATAG-AA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
*
497932 AAGGTGCCACGGAGTGGTGGGCTTTAAAAAGAAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* * *
497966 AAGGTGCCATGGAGTTGTGGAC-TT-AAAAGGAA
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* *
497998 AAGGTGCCACGGAGTGGTGGGCTTTGAAAAG
1 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
498029 CATGTGAGAA
Statistics
Matches: 349, Mismatches: 39, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
32 74 0.21
33 80 0.23
34 148 0.42
35 29 0.08
36 15 0.04
37 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (34 bp):
AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
Found at i:497816 original size:133 final size:132
Alignment explanation
Indices: 497611--498028 Score: 545
Period size: 133 Copynumber: 3.1 Consensus size: 132
497601 CCACTGACTT
* * * * * *
497611 GTGGGCTTTTGAAAAGGAGAAAGATGCCACGGAGTTGTGGACTTAAAAAGGAAAAAAGATGTCAC
1 GTGGGC-TTT-AAAAAGA-AAAGGTGCCACGGAGTTGTGGGCTTTAAAA-G-AAAAAGGTGCCAC
* * * * * *
497676 GAAGTTGTGGAC-TTAAAAAG-AAAAGGTGCCACGAAGTGGTGGGCTTTGAAAAGAAAAAGGTGC
61 GGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGAAAAGGTGC
*
497739 CACGGAGTT
124 CACGGAGTG
* *
497748 GTAGGCTTTAAAAAGAAAAGGTGCCACGGAGTGGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAG
1 GTGGGCTTTAAAAAGAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAG
497813 TTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGGA
65 TTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGGA
497878 GTG
130 GTG
* *
497881 GTGGACTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAATAG-AAAAGGTGCCACGGA
1 GTGGGCTTTAAAAAG-AAAAGGTGCCACGGAGTTGTGGGCTTTAAA-AGAAAAAGGTGCCACGGA
* *
497945 GTGGTGGGCTTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGG
64 GTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGG
498010 AGTG
129 AGTG
*
498014 GTGGGCTTTGAAAAG
1 GTGGGCTTTAAAAAG
498029 CATGTGAGAA
Statistics
Matches: 254, Mismatches: 22, Indels: 14
0.88 0.08 0.05
Matches are distributed among these distances:
133 154 0.61
134 61 0.24
135 31 0.12
136 3 0.01
137 5 0.02
ACGTcount: A:0.35, C:0.11, G:0.34, T:0.20
Consensus pattern (132 bp):
GTGGGCTTTAAAAAGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGT
TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGGAG
TG
Found at i:497896 original size:167 final size:166
Alignment explanation
Indices: 497611--498017 Score: 627
Period size: 167 Copynumber: 2.4 Consensus size: 166
497601 CCACTGACTT
* * * *
497611 GTGGGCTTTTGAAAAGGAGAAAGATGCCACGGAGTTGTGGACTTAAAAAGGAAAAAAGATGTCAC
1 GTGGGC-TTTGAAAA-GAAAAAGGTGCCACGGAGTTGTGGACTTAAAAA-G-AAAAAGGTGCCAC
* *
497676 GAAGTTGTGGACTTAAAAAGAAAAGGTGCCACGAAGTGGTGGGCTTTGAAAAGAAAAAGGTGCCA
62 GGAGTTGTGGACTTAAAAAGAAAAGGTGCCACGAAGTGGTGGACTTTGAAAAGAAAAAGGTGCCA
497741 CGGAGTTGTAGGCTTTAAAAAGAAAAGGTGCCACGGAGTG
127 CGGAGTTGTAGGCTTTAAAAAGAAAAGGTGCCACGGAGTG
*
497781 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGA
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TTAAAAAGAAAAAGGTGCCACGGA
* *
497846 GTTGTGGACTTAAAAGGAAAAGGTGCCACGGAGTGGTGGACTTTGAAAAGAAAAAGGTGCCACGG
65 GTTGTGGACTTAAAAAGAAAAGGTGCCACGAAGTGGTGGACTTTGAAAAGAAAAAGGTGCCACGG
* *
497911 AGTTGTGGGCTTTAAATAGAAAAGGTGCCACGGAGTG
130 AGTTGTAGGCTTTAAAAAGAAAAGGTGCCACGGAGTG
* * *
497948 GTGGGCTTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGACTT-AAAAGGAAAAGGTGCCACGGAG
1 GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAAGAAAAAGGTGCCACGGAG
*
498012 TGGTGG
66 TTGTGG
498018 GCTTTGAAAA
Statistics
Matches: 220, Mismatches: 16, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
165 26 0.12
166 2 0.01
167 147 0.67
168 24 0.11
169 15 0.07
170 6 0.03
ACGTcount: A:0.35, C:0.11, G:0.34, T:0.20
Consensus pattern (166 bp):
GTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAAGAAAAAGGTGCCACGGAG
TTGTGGACTTAAAAAGAAAAGGTGCCACGAAGTGGTGGACTTTGAAAAGAAAAAGGTGCCACGGA
GTTGTAGGCTTTAAAAAGAAAAGGTGCCACGGAGTG
Found at i:502281 original size:52 final size:52
Alignment explanation
Indices: 502203--502331 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
502193 CGAAATATGA
* *
502203 AAATTTGCCTGCATGTATCGATACATTTCATTGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATCTGGGC
*
502255 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATCTGGGC
*
502307 AAATTTTCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
502332 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATCTGGGC
Found at i:502342 original size:52 final size:51
Alignment explanation
Indices: 502203--502351 Score: 176
Period size: 52 Copynumber: 2.9 Consensus size: 51
502193 CGAAATATGA
* *
502203 AAATTTGCCTGCATGTATCGATACATTTCAT-TGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--ACATCAGTGTATCGATACATCTGGGC
* * *
502255 AAATTTGCCTGTATGTATCGATACATTTCAT-AGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--ACATCAGTGTATCGATACATCTGGGC
* *
502307 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATAC-AACATCAGTGTATCGATACA
502352 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.97
53 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACAACATCAGTGTATCGATACATCTGGGC
Found at i:503153 original size:20 final size:20
Alignment explanation
Indices: 503128--503166 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
503118 ACTACCAAGG
503128 CAATGTATCGATACATTATT
1 CAATGTATCGATACATTATT
503148 CAATGTATCGATACATTAT
1 CAATGTATCGATACATTAT
503167 ATCGATACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (20 bp):
CAATGTATCGATACATTATT
Found at i:503171 original size:13 final size:13
Alignment explanation
Indices: 503153--503178 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
503143 TTATTCAATG
503153 TATCGATACATTA
1 TATCGATACATTA
503166 TATCGATACATTA
1 TATCGATACATTA
503179 ATCTTTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:503175 original size:33 final size:33
Alignment explanation
Indices: 503133--503196 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
503123 CAAGGCAATG
*
503133 TATCGATACATTATTCAATGTATCGATACATTA
1 TATCGATACATTAATCAATGTATCGATACATTA
**
503166 TATCGATACATTAATCTTTGTATCGATACAT
1 TATCGATACATTAATCAATGTATCGATACAT
503197 CTGGGAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (33 bp):
TATCGATACATTAATCAATGTATCGATACATTA
Found at i:508721 original size:20 final size:20
Alignment explanation
Indices: 508698--508765 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
508688 CATGTGTCAG
508698 TACATTGAATAATGTATCGA
1 TACATTGAATAATGTATCGA
*
508718 TACAAT-AGATAATGTATCGA
1 TACATTGA-ATAATGTATCGA
** *
508738 TACAATTGTAAGCATGTATTGA
1 TAC-ATTG-AATAATGTATCGA
508760 TACATT
1 TACATT
508766 TACTTATGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.03
20 20 0.51
21 5 0.13
22 12 0.31
23 1 0.03
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (20 bp):
TACATTGAATAATGTATCGA
Found at i:508861 original size:20 final size:21
Alignment explanation
Indices: 508838--508884 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
508828 GGCATGTACT
*
508838 GATACATTCACTG-ATGTATC
1 GATACATTCACTGTATATATC
* * *
508858 GATATATTTACTGTTTATATC
1 GATACATTCACTGTATATATC
508879 GATACA
1 GATACA
508885 AATTGTAGAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (21 bp):
GATACATTCACTGTATATATC
Found at i:517829 original size:21 final size:21
Alignment explanation
Indices: 517803--517843 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
517793 GAATTCTTTG
517803 TTTTTT-GAGATGAAAAAGTGC
1 TTTTTTGGAG-TGAAAAAGTGC
*
517824 TTTTTTGGAGTTAAAAAGTG
1 TTTTTTGGAGTGAAAAAGTG
517844 TTGGAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.41
Consensus pattern (21 bp):
TTTTTTGGAGTGAAAAAGTGC
Found at i:518465 original size:20 final size:20
Alignment explanation
Indices: 518440--518477 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
518430 CATTTAAGAC
*
518440 ATGTATCGATACATTCACTT
1 ATGTATCAATACATTCACTT
518460 ATGTATCAATACATTCAC
1 ATGTATCAATACATTCAC
518478 CAATTTTATC
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:0.21, G:0.08, T:0.37
Consensus pattern (20 bp):
ATGTATCAATACATTCACTT
Found at i:519086 original size:31 final size:31
Alignment explanation
Indices: 519048--519745 Score: 570
Period size: 31 Copynumber: 22.7 Consensus size: 31
519038 TCATACTTAA
*
519048 GTGCCACCAACTTGTGTGGGCTTTGACTAGG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
*
519079 GTGCCACCAACTCGTGTAGGCTTTGACTAGG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
** * *
519110 GCACCACCAACTCGTGTGGGCTTAGACTCA-A
1 GTGCCACCAACTCGTGTGGGCTTTGACT-AGG
* * **
519141 GTGTCGCCAACT-GTACGGGCTTTGACTAGG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
* * * *
519171 GTGCCACTAACTCGTGTGGGCTTAGACCCA-A
1 GTGCCACCAACTCGTGTGGGCTTTGA-CTAGG
* * *
519202 GTGTCACCAACTTGTGTGAGCTTTGACTAGG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
* * * *
519233 GTGCTACCAACTCGTGTTGGCTTAGACTTGG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
* ** * *
519264 GT---ACC-GCTTATATGGGCTTTGACTAAG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
* * * *
519291 GTACCACCAACTCATGTGGGCTTAGACTCGG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
* *
519322 GTGTCGCCAACTCGTGTGGGCTTTGACTAGG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
* * * * *
519353 ATGCCACCAACTCGTGTGGGCCTAGACTCGA
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
*** * *
519384 GTGTTGCCAACTCGTGCGGGTTTTGACTAGG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
* * * *
519415 ATGCCACCAACTCATGTGGGCTTGGACTTGG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
* * * *
519446 GTGTCACCAACTCGCGTAGGCTTTGACTAAG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
* * *
519477 GTGCCACCAACTCATGTGTGCTTTGACTCGG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
* **
519508 GTGCCGCCAACTCGTGCAGGCTTTGACTAGG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
** *
519539 GTGCCACCAACTTTTGTGGGCTTTGACTCGG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
* * *
519570 GTGCCGCCAACTCGTGTAGGCTTTGACTAAG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
* * * * *
519601 ATGCCACCAACTTGTGTGAGCTTTAACTCA-A
1 GTGCCACCAACTCGTGTGGGCTTTGACT-AGG
*
519632 GTGCCACCAACACGTGCT-GGCTTTGACTAGG
1 GTGCCACCAACTCGTG-TGGGCTTTGACTAGG
* *
519663 GTGCCACCAACTTGTGTGGGCTTTGACTCA-A
1 GTGCCACCAACTCGTGTGGGCTTTGACT-AGG
* * * * **
519694 GTGCCGCCAATTTGTGTAGGCTTTGAAAAGG
1 GTGCCACCAACTCGTGTGGGCTTTGACTAGG
* * *
519725 TTGCCACCGACTTGTGTGGGC
1 GTGCCACCAACTCGTGTGGGC
519746 CTTAAAGAAT
Statistics
Matches: 509, Mismatches: 143, Indels: 30
0.75 0.21 0.04
Matches are distributed among these distances:
27 16 0.03
28 3 0.01
29 1 0.00
30 29 0.06
31 454 0.89
32 6 0.01
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (31 bp):
GTGCCACCAACTCGTGTGGGCTTTGACTAGG
Found at i:519456 original size:124 final size:124
Alignment explanation
Indices: 519048--519745 Score: 710
Period size: 124 Copynumber: 5.7 Consensus size: 124
519038 TCATACTTAA
* * * ***
519048 GTGCCACCAACTTGTGTGGGCTTTGACTAGGGTGCCACCAACTCGTGTAGGCTTTGACTAGGGCA
1 GTGCCACCAACTCGTGTGGGCTTTGACTCGGGTGTCACCAACTCGTGTAGGCTTTGACTAGGATG
* * *
519113 CCACCAACTCGTGTGGGCTTAGACTCAAGTGTCGCCAACT-GTACGGGCTTTGACTAGG
66 CCACCAACTCGTGTGGGCTTAGACTCGAGTGCCGCCAACTCGTGCGGGCTTTGACTAGG
* * * ** * *
519171 GTGCCACTAACTCGTGTGGGCTTAGACCCAAGTGTCACCAACTTGTGT-GAGCTTTGACTAGGGT
1 GTGCCACCAACTCGTGTGGGCTTTGACTCGGGTGTCACCAACTCGTGTAG-GCTTTGACTAGGAT
* * * * * ** * *
519235 GCTACCAACTCGTGTTGGCTTAGACTTGGGTACCGCTTA-T-AT--GGGCTTTGACTAAG
65 GCCACCAACTCGTGTGGGCTTAGACTCGAGTGCCGCCAACTCGTGCGGGCTTTGACTAGG
* * * * *
519291 GTACCACCAACTCATGTGGGCTTAGACTCGGGTGTCGCCAACTCGTGTGGGCTTTGACTAGGATG
1 GTGCCACCAACTCGTGTGGGCTTTGACTCGGGTGTCACCAACTCGTGTAGGCTTTGACTAGGATG
* ** *
519356 CCACCAACTCGTGTGGGCCTAGACTCGAGTGTTGCCAACTCGTGCGGGTTTTGACTAGG
66 CCACCAACTCGTGTGGGCTTAGACTCGAGTGCCGCCAACTCGTGCGGGCTTTGACTAGG
* * * * *
519415 ATGCCACCAACTCATGTGGGCTTGGACTTGGGTGTCACCAACTCGCGTAGGCTTTGACTAAGG-T
1 GTGCCACCAACTCGTGTGGGCTTTGACTCGGGTGTCACCAACTCGTGTAGGCTTTGACT-AGGAT
* * * * *
519479 GCCACCAACTCATGTGTGCTTTGACTCGGGTGCCGCCAACTCGTGCAGGCTTTGACTAGG
65 GCCACCAACTCGTGTGGGCTTAGACTCGAGTGCCGCCAACTCGTGCGGGCTTTGACTAGG
** * * *
519539 GTGCCACCAACTTTTGTGGGCTTTGACTCGGGTGCCGCCAACTCGTGTAGGCTTTGACTAAGATG
1 GTGCCACCAACTCGTGTGGGCTTTGACTCGGGTGTCACCAACTCGTGTAGGCTTTGACTAGGATG
* * * * * *
519604 CCACCAACTTGTGTGAGCTTTA-ACTCAAGTGCCACCAACACGTGCTGGCTTTGACTAGG
66 CCACCAACTCGTGTGGGC-TTAGACTCGAGTGCCGCCAACTCGTGCGGGCTTTGACTAGG
* ** * * * * ** *
519663 GTGCCACCAACTTGTGTGGGCTTTGACTCAAGTGCCGCCAATTTGTGTAGGCTTTGAAAAGGTTG
1 GTGCCACCAACTCGTGTGGGCTTTGACTCGGGTGTCACCAACTCGTGTAGGCTTTGACTAGGATG
* *
519728 CCACCGACTTGTGTGGGC
66 CCACCAACTCGTGTGGGC
519746 CTTAAAGAAT
Statistics
Matches: 477, Mismatches: 89, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
120 95 0.20
121 2 0.00
122 4 0.01
123 83 0.17
124 288 0.60
125 5 0.01
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (124 bp):
GTGCCACCAACTCGTGTGGGCTTTGACTCGGGTGTCACCAACTCGTGTAGGCTTTGACTAGGATG
CCACCAACTCGTGTGGGCTTAGACTCGAGTGCCGCCAACTCGTGCGGGCTTTGACTAGG
Found at i:520006 original size:27 final size:26
Alignment explanation
Indices: 519969--520021 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
519959 CTTTAAAAGA
519969 AAAATGTGCCACGGAA-TTATGGACTT
1 AAAATGTGCCAC-GAAGTTATGGACTT
519995 AAAATGGTGCCACGAAGTTATGGACTT
1 AAAAT-GTGCCACGAAGTTATGGACTT
520022 TGAAAGCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (26 bp):
AAAATGTGCCACGAAGTTATGGACTT
Found at i:521000 original size:20 final size:20
Alignment explanation
Indices: 520975--521026 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
520965 GTCAACCGTA
*
520975 ATGTATCGATATAGATACCT
1 ATGTATCGATACAGATACCT
520995 ATGTATCGATACAGATACCT
1 ATGTATCGATACAGATACCT
*
521015 ATGTATCAATAC
1 ATGTATCGATAC
521027 TTGGAAGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAGATACCT
Found at i:523310 original size:21 final size:22
Alignment explanation
Indices: 523272--523313 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
523262 TGATTTTGAC
* *
523272 GAAAAATGAAGTATTTTGAAGT
1 GAAAAATGAAGAAATTTGAAGT
523294 GAAAAAT-AAGAAATTTGAAG
1 GAAAAATGAAGAAATTTGAAG
523314 AAGTTTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.26
Consensus pattern (22 bp):
GAAAAATGAAGAAATTTGAAGT
Found at i:523420 original size:13 final size:13
Alignment explanation
Indices: 523398--523433 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
523388 TAACCCTTGT
523398 ATCGATACAATGC
1 ATCGATACAATGC
* *
523411 ATCTATACAATGT
1 ATCGATACAATGC
523424 ATCGATACAA
1 ATCGATACAA
523434 AGAATATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (13 bp):
ATCGATACAATGC
Found at i:524457 original size:19 final size:18
Alignment explanation
Indices: 524432--524496 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
524422 ATTTCAGCGA
524432 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
524450 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
524466 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
524482 TTTTGTATCAATACA
1 -TTTGTATCGATACA
524497 ATGTATCGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:524470 original size:32 final size:32
Alignment explanation
Indices: 524434--524504 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
524424 TTCAGCGATT
*
524434 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCAATACAA
*
524466 TGTATCGATACATAAGTTTTGTATCAATACAA
1 TGTATCGATACATAAGTGTTGTATCAATACAA
524498 TGTATCG
1 TGTATCG
524505 CTAGGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCAATACAA
Found at i:524471 original size:13 final size:13
Alignment explanation
Indices: 524453--524477 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
524443 ACATAAGTGT
524453 TGTATCGATACAA
1 TGTATCGATACAA
524466 TGTATCGATACA
1 TGTATCGATACA
524478 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:524566 original size:13 final size:13
Alignment explanation
Indices: 524548--524573 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
524538 CATTTTTTTG
524548 TGTATCGATACAT
1 TGTATCGATACAT
524561 TGTATCGATACAT
1 TGTATCGATACAT
524574 CTATTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:527070 original size:27 final size:26
Alignment explanation
Indices: 527032--527106 Score: 123
Period size: 27 Copynumber: 2.8 Consensus size: 26
527022 CATCAATTTT
527032 TCATCGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTT-A
527059 TCATCGGGGATACTCCAACCCCGTTA
1 TCATCGGGGATACTCCAACCCCGTTA
* *
527085 TAATCGGAGATACTCCAACCCC
1 TCATCGGGGATACTCCAACCCC
527107 CAGCTTTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 21 0.46
27 25 0.54
ACGTcount: A:0.27, C:0.35, G:0.17, T:0.21
Consensus pattern (26 bp):
TCATCGGGGATACTCCAACCCCGTTA
Found at i:527160 original size:105 final size:101
Alignment explanation
Indices: 526982--527184 Score: 259
Period size: 105 Copynumber: 2.0 Consensus size: 101
526972 ACTAATTTTC
* * * *
526982 TATAATCAGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTC
1 TATAATCAGGGATACTCCAACCCCCACTTTATTTCTAAAACATCAATTTTTAATCGGGGATACTC
527047 CAACCCCGTTAATCAT-C-GGGGATACTCCAACCCCGT
66 CAACCCCGTT-ATC-TCCAGGGGATACTCCAACCCCGT
* *
527083 TATAATC-GGAGATACTCCAACCCCCAGCTTTATTTCTAAAATATTAATTTCTCATAATCGGGGA
1 TATAATCAGG-GATACTCCAACCCCCA-CTTTATTTCTAAAACATCAATTT-T--TAATCGGGGA
527147 TACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACC
61 TACTCCAACCCCGTTATCTCC-AGGGGATACTCCAACC
527185 TCGGTTTTAT
Statistics
Matches: 88, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
100 2 0.02
101 21 0.24
102 20 0.23
103 2 0.02
104 4 0.05
105 24 0.27
106 15 0.17
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (101 bp):
TATAATCAGGGATACTCCAACCCCCACTTTATTTCTAAAACATCAATTTTTAATCGGGGATACTC
CAACCCCGTTATCTCCAGGGGATACTCCAACCCCGT
Found at i:527245 original size:51 final size:52
Alignment explanation
Indices: 527170--527339 Score: 182
Period size: 52 Copynumber: 3.3 Consensus size: 52
527160 TTATCTCCGA
* * * *
527170 GGGGATACTCCAACCTCGGTTTTATTTCCAAATCATCGATTTTCC-ACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTACAATC
* * * * **
527221 GGGGGTACTCTAACCCCGGCTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTACAATC
* * * *
527273 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-ACAATT
1 GGGGATACTCCAACCCCGGTTTTATTTCC-AAAACACCAATTTTCCTACAATC
*
527325 GAGGATACTCCAACC
1 GGGGATACTCCAACC
527340 TCGTTATTTC
Statistics
Matches: 95, Mismatches: 22, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
51 37 0.39
52 43 0.45
53 15 0.16
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTACAATC
Found at i:527530 original size:78 final size:79
Alignment explanation
Indices: 527352--527555 Score: 223
Period size: 78 Copynumber: 2.6 Consensus size: 79
527342 GTTATTTCAT
** * *
527352 CGGGGATACTCCAACCCCGTTACCTCCGATGGGATACTCCAACCCCGGCTTTATTCTTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGATTTATTCTTAAAATAT
* *
527417 TGATTTCTCATAAT
66 TGATTTCTCACAAC
* * * * * **
527431 TGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAATCTC-GATTT-TTTTTCTAATCA
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGATTTATTCTTAAAAT-A
527494 TTGATTTCTCACAAC
65 TTGATTTCTCACAAC
* * * * *
527509 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGGACACTGCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG
527556 TTATTATCTC
Statistics
Matches: 101, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
77 7 0.07
78 55 0.54
79 39 0.39
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGATTTATTCTTAAAATAT
TGATTTCTCACAAC
Found at i:533948 original size:55 final size:55
Alignment explanation
Indices: 533691--535112 Score: 1461
Period size: 55 Copynumber: 24.9 Consensus size: 55
533681 CCTTTTTTCT
* * *
533691 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-GAGTCCTCAAAAAGCAGGACACCTTTTCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGG--A-C---GCC
* * *
533751 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTCAAAAAGCAGGATGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCC
*
533805 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGATGCCTTCTCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTCAAAGAGCAGGA------CGCC
* *
533866 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAATCCTCAAAGAGCAGGATGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCC-AGTCCTCAAAGAGCAGGACGCC
533921 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTCAAAGAGCAGGACG------CC
* *
533982 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAATCCTCAAAGAGCAGGATGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCC-AGTCCTCAAAGAGCAGGACGCC
* * *
534037 TTTTAAAGCCCACACAAGTTGTTGGCA-CTTCTCAGTCCTTAAAGAGCAGGATGCCTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTC-CAGTCCTCAAAGAGCAGGACG-C--C
* *
534095 TTTTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAATCCTCAAAGAGCAGGATGCC
1 ---TTTTAAAGCCCACACAAGTTGGTGGCACCTTCC-AGTCCTCAAAGAGCAGGACGCC
*
534153 TTTTAAAGCCCACACAAGTTGGTGGTA-CTTCCCAGTCCTCAAAGAGCAGGACGCCTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTCAAAGAGCAGGACG-C--C
534211 TCCCTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCCTTC
1 T---TTTAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTCAAAGAGCAGGACG-C--C
*
534272 TCCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC
1 T--T-TTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCC
** *
534330 TTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACG-C----C
*
534390 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCGGGACGCCTTTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACG-C----C
* *
534449 TTTTAAAGCCCACAC-AGTTGGTGGCACCTT-TAGTCCTCAAAGAGCGGGACGCCTTTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACG-C----C
*
534507 TTTTAAAGCCCAC-CTAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGATGCTTTTTC
1 TTTTAAAGCCCACAC-AAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGC-----C
** * *
534566 TTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCCCAAAGAGCAGGACCCC
1 TTTT-AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCC
** ** * * *
534622 TTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAATTCTCAAAGAGCAGGACACC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCC
* ** *
534677 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCC
* * * * *
534732 TCTTAAAGCCCACATAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCC
* ** * *
534787 TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAAGACACC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCC
* * * * * *
534842 TCTTAAAGCCCACACAAGTTGGCGGCACCTTTCAGTCCCCAAAGAGCAGGGCACC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCC
** ** * *
534897 TTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACACC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCC
* * ** *
534952 TTTCAAAACCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCC
* * *
535007 TCTTAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCC
* * * ** *
535062 TTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGTAGGA
1 TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGA
535113 TACACTTTAT
Statistics
Matches: 1211, Mismatches: 106, Indels: 95
0.86 0.08 0.07
Matches are distributed among these distances:
53 3 0.00
54 29 0.02
55 634 0.52
56 13 0.01
57 1 0.00
58 63 0.05
59 83 0.07
60 113 0.09
61 269 0.22
62 3 0.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (55 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCC
Found at i:533949 original size:116 final size:115
Alignment explanation
Indices: 533691--535112 Score: 1516
Period size: 116 Copynumber: 12.4 Consensus size: 115
533681 CCTTTTTTCT
* * * *
533691 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-GAGTCCTCAAAAAGCAGGACACCTTTTCCTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGA-GCCTTCTCCTTTT
* *
533755 AAAGCCCACACAAGTTGGTGGCACCTT--TAGTCCTCAAAAAGCAGGATGCC
64 AAAGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCC
533805 TTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACTT-CCAGTCCTCAAAGAGCAGGA-GCCTTCTCCTTTT
* *
533870 AAAGCCCACACAAGTTGGTGGCA-CTTCCTAATCCTCAAAGAGCAGGATGCC
64 AAAGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCC
533921 TTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACTT-CCAGTCCTCAAAGAGCAGGA-GCCTTCTCCTTTT
* *
533986 AAAGCCCACACAAGTTGGTGGCA-CTTCCTAATCCTCAAAGAGCAGGATGCC
64 AAAGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCC
* * **
534037 TTTTAAAGCCCACACAAGTTGTTGGCACTTCTCAGTCCTTAAAGAGCAGGATGCCTTCTTTTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACTTC-CAGTCCTCAAAGAGCAGGA-GCCTTCTCCTTTT
* *
534102 AAAGCCCACACAAGTTGGTGGCA-CTTCCTAATCCTCAAAGAGCAGGATGCC
64 AAAGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCC
* *
534153 TTTTAAAGCCCACACAAGTTGGTGGTACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCCTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCACTT-CCAGTCCTCAAAGAGCAGGA-GCCTTCTCCTTTT
*
534218 AAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCCTTC
64 AAAGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACG-C--C
* *
534272 TCCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA-----CGCCTT
1 T--T-TTAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGAGCCTTCTCCTT
* *
534332 TTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTC
62 TTAAAGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACG-C----C
* *
534390 TTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCGGGACGCCTT-TTCTTTT
1 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGA-GCCTTCTCCTTTT
*
534453 AAAGCCCACAC-AGTTGGTGGCACCTT--TAGTCCTCAAAGAGCGGGACGCCTTTTC
64 AAAGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACG-C----C
* *
534507 TTTTAAAGCCCAC-CTAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGATG-CTTTTTCTTT
1 TTTTAAAGCCCACAC-AAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGA-GCCTTCTCCTTT
* * *
534569 TCAAAGCCCACACAAGTTGGTGGCACCTT-TTAGTCCCCAAAGAGCAGGACCCC
63 T-AAAGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCC
** * * * * *
534622 TTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAATTCTCAAAGAGCAGGA-----CACCTTTCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGAGCCTTCTCCTTTTA
** *
534682 AAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGACACC
65 AAGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCC
* * * * * *
534732 TCTTAAAGCCCACATAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGA-----CACCTTTCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGAGCCTTCTCCTTTTA
** * *
534792 AAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAAGACACC
65 AAGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCC
* * * * * **
534842 TCTTAAAGCCCACACAAGTTGGCGGCACCTTTCAGTCCCCAAAGAGCAGG-G----CACCTTTCG
1 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGAGCCTTCTCCTTTTA
** * *
534902 AAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGTAGGACACC
65 AAGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCC
* * *
534952 TTTCAAAACCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA-CAC--CT-C--TT
1 TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAGGAGC-CTTCTCCTTTT
* *
535011 AAAGCCTACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCC
64 AAAGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCC
* * ** *
535062 TTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGTAGGA
1 TTTTAAAGCCCACACAAGTTGGTGGCAC-TTCCAGTCCTCAAAGAGCAGGA
535113 TACACTTTAT
Statistics
Matches: 1178, Mismatches: 94, Indels: 76
0.87 0.07 0.06
Matches are distributed among these distances:
110 379 0.32
111 4 0.00
112 1 0.00
113 4 0.00
114 48 0.04
115 107 0.09
116 424 0.36
117 84 0.07
118 26 0.02
119 36 0.03
120 18 0.02
121 1 0.00
122 43 0.04
123 3 0.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (115 bp):
TTTTAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCTCAAAGAGCAGGAGCCTTCTCCTTTTAA
AGCCCACACAAGTTGGTGGCACCTTCCTAGTCCTCAAAGAGCAGGACGCC
Found at i:535900 original size:19 final size:19
Alignment explanation
Indices: 535876--535926 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
535866 TTTCAGCGAT
535876 TTGTATCGATACATAAATG
1 TTGTATCGATACATAAATG
* *
535895 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAATG
535914 TTGTATCGATACA
1 TTGTATCGATACA
535927 ATGTATCGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATAAATG
Found at i:535996 original size:13 final size:13
Alignment explanation
Indices: 535978--536003 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
535968 CATTTTTCTG
535978 TGTATCGATACAT
1 TGTATCGATACAT
535991 TGTATCGATACAT
1 TGTATCGATACAT
536004 CTATTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:536021 original size:34 final size:33
Alignment explanation
Indices: 535958--536024 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
535948 GCCAAGGAAA
*
535958 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
535991 TGTATCGATACATCTATTCTTTGTATCGATACAT
1 TGTATCGATACAT-TATTCTGTGTATCGATACAT
536025 CTAGGAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:538460 original size:51 final size:50
Alignment explanation
Indices: 538371--538485 Score: 123
Period size: 51 Copynumber: 2.3 Consensus size: 50
538361 AATTCTCCGC
*
538371 AATCGGGGATA-TCCCAACTCCGATTTCATTTTCCAAACA-CTAATTTTCTAT
1 AATCGGGGATACT-CCAACTCCGATTTCATTTTCAAAACATC-AATTTT-TAT
* * *
538422 AATCGGGGATACTCCAACTTCGATTTTA-TTTCTAAAACATCAATTTTTCT
1 AATCGGGGATACTCCAACTCCGATTTCATTTTC-AAAACATCAATTTTTAT
538472 --TCGGGGATACTCCA
1 AATCGGGGATACTCCA
538486 TCCCCGTTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
48 14 0.25
50 6 0.11
51 35 0.61
52 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (50 bp):
AATCGGGGATACTCCAACTCCGATTTCATTTTCAAAACATCAATTTTTAT
Found at i:538501 original size:26 final size:26
Alignment explanation
Indices: 538472--538541 Score: 131
Period size: 26 Copynumber: 2.7 Consensus size: 26
538462 CAATTTTTCT
*
538472 TCGGGGATACTCCATCCCCGTTATAA
1 TCGGGGATACTCCAACCCCGTTATAA
538498 TCGGGGATACTCCAACCCCGTTATAA
1 TCGGGGATACTCCAACCCCGTTATAA
538524 TCGGGGATACTCCAACCC
1 TCGGGGATACTCCAACCC
538542 TCGGCTTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (26 bp):
TCGGGGATACTCCAACCCCGTTATAA
Found at i:538672 original size:51 final size:52
Alignment explanation
Indices: 538610--538775 Score: 176
Period size: 52 Copynumber: 3.2 Consensus size: 52
538600 CTCCGAGGGT
* * *
538610 ATACTCCAACCCCGGTTTTATTTCCAAATCATCGATTTTCC-ACAATCG-GAG
1 ATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTACAATCGAG-G
* * * * **
538661 ATACTCTAACCCCTGCTTTATTTTCAAAACACCAATTTTCCTTTAATCGAGG
1 ATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTACAATCGAGG
* * * *
538713 ATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-ACAATTGAGG
1 ATACTCCAACCCCGGTTTTATTTCC-AAAACACCAATTTTCCTACAATCGAGG
538765 ATACTCCAACC
1 ATACTCCAACC
538776 TCGTTATTTC
Statistics
Matches: 92, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 34 0.37
52 42 0.46
53 16 0.17
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (52 bp):
ATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCTACAATCGAGG
Found at i:538966 original size:78 final size:78
Alignment explanation
Indices: 538788--539009 Score: 207
Period size: 78 Copynumber: 2.8 Consensus size: 78
538778 GTTATTTCAT
** * *
538788 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCC-GATTTATTCCCAAAATAT
* * **
538853 TGATTTCTCATAGT
65 CGATTTCTCACAAC
* * * * ** *
538867 TGGGGATACTCCAACCTCGTTATTTCTGAGGGGATACTCCAATCCCGATTTTTTTTC-TAATCAT
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTATTCCCAAAAT-AT
538931 CGATTTCTCACAAC
65 CGATTTCTCACAAC
* * * *
538945 CGGGGATACTCCAGCCCCGTTATTT-TCAAGGGGACACTCCAACCCCGTTATTA-TCTCCAAAAT
1 CGGGGATACTCCAACCCCGTTATTTCT-GAGGGGATACTCCAACCCCGAT-TTATTC-CCAAAAT
539008 AT
63 AT
539010 TAAATTTCTC
Statistics
Matches: 112, Mismatches: 26, Indels: 10
0.76 0.18 0.07
Matches are distributed among these distances:
77 4 0.04
78 60 0.54
79 45 0.40
80 3 0.03
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGATTTATTCCCAAAATATC
GATTTCTCACAAC
Found at i:543742 original size:3 final size:3
Alignment explanation
Indices: 543734--543758 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
543724 TCCGAGTCAC
543734 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
543759 GTCTTTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:545869 original size:61 final size:59
Alignment explanation
Indices: 545754--545907 Score: 173
Period size: 61 Copynumber: 2.5 Consensus size: 59
545744 TTGAAAAGAA
* * * * *
545754 AAAAGAGGGCCATGAGTTATGGACTTAAAAAGGGTGCTACGGAGTTATGGACTTAAAAAG
1 AAAA-AGGGCCAAGAGTTATGGACTTAAAAAGAGTGCCACGAAGTTATGAACTTAAAAAG
* *
545814 AAAAAGGGCCACAGAGTTGTGGACTTTAAAAAGAGTGCCACGAAGTTGTGAACTTAAAAAG
1 AAAAAGGGCCA-AGAGTTATGGAC-TTAAAAAGAGTGCCACGAAGTTATGAACTTAAAAAG
* *
545875 AAAAAAAGGACCATTGAGTTATGGACTTAAAAA
1 --AAAAAGGGCCA-AGAGTTATGGACTTAAAAA
545908 AGGGTACCAT
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
59 7 0.09
60 14 0.18
61 31 0.39
62 7 0.09
63 20 0.25
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (59 bp):
AAAAAGGGCCAAGAGTTATGGACTTAAAAAGAGTGCCACGAAGTTATGAACTTAAAAAG
Found at i:545871 original size:28 final size:28
Alignment explanation
Indices: 545753--545875 Score: 99
Period size: 28 Copynumber: 4.2 Consensus size: 28
545743 CTTGAAAAGA
*
545753 AAAAAGAGGGCCATG-AGTTATGGACTT
1 AAAAAGAGGGCCACGAAGTTATGGACTT
* *
545780 AAAAAG-GGTGCTACGGAGTTATGGACTT
1 AAAAAGAGG-GCCACGAAGTTATGGACTT
*
545808 AAAAAGAAAAAGGGCCAC-AGAGTTGTGGACTTT
1 AAAAAG----AGGGCCACGA-AGTTATGGAC-TT
* * *
545841 AAAAAGAGTGCCACGAAGTTGTGAACTT
1 AAAAAGAGGGCCACGAAGTTATGGACTT
545869 AAAAAGA
1 AAAAAGA
545876 AAAAAAGGAC
Statistics
Matches: 79, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
26 2 0.03
27 10 0.13
28 27 0.34
29 16 0.20
30 1 0.01
32 13 0.16
33 10 0.13
ACGTcount: A:0.41, C:0.11, G:0.28, T:0.20
Consensus pattern (28 bp):
AAAAAGAGGGCCACGAAGTTATGGACTT
Found at i:545908 original size:63 final size:61
Alignment explanation
Indices: 545741--545936 Score: 218
Period size: 63 Copynumber: 3.2 Consensus size: 61
545731 GATCCTAACA
* * * *
545741 GACTTGAAAAGAAAAAAGAGGGCCATGAGTTATGGACTTAAAAAGGGTGCTACGGAGTTATG
1 GACTTAAAAAGAAAAAA-AGGGCCATGAGTTATGGACTTAAAAAGGGTGCCACGAAGTTGTG
* * *
545803 GACTTAAAAAG--AAAAAGGGCCACAGAGTTGTGGACTTTAAAAAGAGTGCCACGAAGTTGTG
1 GACTTAAAAAGAAAAAAAGGGCCA-TGAGTTATGGAC-TTAAAAAGGGTGCCACGAAGTTGTG
* * * *
545864 AACTTAAAAAGAAAAAAAGGACCATTGAGTTATGGACTTAAAAAAGGGTACCA-TAGAGTTGTG
1 GACTTAAAAAGAAAAAAAGGGCCA-TGAGTTATGGACTT-AAAAAGGGTGCCACGA-AGTTGTG
545927 GACTTAAAAA
1 GACTTAAAAA
545937 AAAGCAAGGT
Statistics
Matches: 112, Mismatches: 16, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
59 7 0.06
60 14 0.12
61 31 0.28
62 13 0.12
63 47 0.42
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (61 bp):
GACTTAAAAAGAAAAAAAGGGCCATGAGTTATGGACTTAAAAAGGGTGCCACGAAGTTGTG
Found at i:546029 original size:34 final size:28
Alignment explanation
Indices: 545885--546012 Score: 122
Period size: 28 Copynumber: 4.7 Consensus size: 28
545875 AAAAAAAGGA
* * *
545885 CCATTGAGTTATGGACTTAAAAAAGGGTA
1 CCATGGAGTTGTGGACTT-AAAAAGGGTG
* ***
545914 CCATAGAGTTGTGGACTTAAAAA-AAAG
1 CCATGGAGTTGTGGACTTAAAAAGGGTG
* *
545941 -CA---AGGTGTGGACTTAAAAATGGTG
1 CCATGGAGTTGTGGACTTAAAAAGGGTG
*
545965 CCATGGAGTTATGGACTTAAAAAGGGTG
1 CCATGGAGTTGTGGACTTAAAAAGGGTG
545993 CCATGGAGTTGTGGACTTAA
1 CCATGGAGTTGTGGACTTAA
546013 CAAAAAGCAA
Statistics
Matches: 80, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
23 16 0.20
24 1 0.01
25 2 0.03
26 2 0.03
28 43 0.54
29 16 0.20
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (28 bp):
CCATGGAGTTGTGGACTTAAAAAGGGTG
Found at i:546062 original size:27 final size:28
Alignment explanation
Indices: 546014--546068 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
546004 TGGACTTAAC
* * *
546014 AAAAAGCAAGGTGCCACGAAGTTGTGGA
1 AAAAAACAAGGTGCCACAAAGTTCTGGA
546042 AAAAAACAAGGTG-CACAAAGTTCTGGA
1 AAAAAACAAGGTGCCACAAAGTTCTGGA
546069 CTTAAAGGCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.44, C:0.15, G:0.27, T:0.15
Consensus pattern (28 bp):
AAAAAACAAGGTGCCACAAAGTTCTGGA
Found at i:546156 original size:30 final size:30
Alignment explanation
Indices: 546117--546181 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
546107 AAAAAGAAAG
*
546117 AAGACAAGATGCCATTGAGTCGTGGACTTT
1 AAGAAAAGATGCCATTGAGTCGTGGACTTT
546147 AAGAAAAGATGCCATTGAGTCGTGGACTTT
1 AAGAAAAGATGCCATTGAGTCGTGGACTTT
546177 AAGAA
1 AAGAA
546182 GGGTATCACT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (30 bp):
AAGAAAAGATGCCATTGAGTCGTGGACTTT
Found at i:554749 original size:20 final size:21
Alignment explanation
Indices: 554724--554774 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
554714 TTGAGACATA
*
554724 TATCGATACATTCACTTA-TG
1 TATCGATACATTCACTAATTG
*
554744 TATCGATATATTCACTAATTG
1 TATCGATACATTCACTAATTG
*
554765 TATTGATACA
1 TATCGATACA
554775 AATTGTAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (21 bp):
TATCGATACATTCACTAATTG
Found at i:556409 original size:19 final size:19
Alignment explanation
Indices: 556382--556433 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
556372 TGTATCGATA
* *
556382 CATTATATCGATACATGCT
1 CATTGTATCGATACATACT
556401 CATTGTATCGATACATACT
1 CATTGTATCGATACATACT
*
556420 CAATTGGATCGATA
1 C-ATTGTATCGATA
556434 TATGAAACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:559694 original size:20 final size:20
Alignment explanation
Indices: 559665--559717 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
559655 ATTTACCTGC
*
559665 ATGTACCGATACACTGAGTA
1 ATGTATCGATACACTGAGTA
559685 ATGTATCGATACACTGAGTA
1 ATGTATCGATACACTGAGTA
559705 ATGTATCGATACA
1 ATGTATCGATACA
559718 TCTAGGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (20 bp):
ATGTATCGATACACTGAGTA
Found at i:559814 original size:19 final size:19
Alignment explanation
Indices: 559790--559872 Score: 115
Period size: 19 Copynumber: 4.7 Consensus size: 19
559780 CGTTTGAGTA
*
559790 ATGTATCGATACAAAACTT
1 ATGTATCGATACAACACTT
559809 ATGTATCGAT---ACA--T
1 ATGTATCGATACAACACTT
559823 -TGTATCGATACAACACTT
1 ATGTATCGATACAACACTT
559841 ATGTATCGATACAACACTT
1 ATGTATCGATACAACACTT
559860 ATGTATCGATACA
1 ATGTATCGATACA
559873 GTTACGATTT
Statistics
Matches: 57, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
16 5 0.09
18 1 0.02
19 41 0.72
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAACACTT
Found at i:559828 original size:13 final size:13
Alignment explanation
Indices: 559810--559834 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
559800 ACAAAACTTA
559810 TGTATCGATACAT
1 TGTATCGATACAT
559823 TGTATCGATACA
1 TGTATCGATACA
559835 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:559832 original size:32 final size:32
Alignment explanation
Indices: 559791--559853 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
559781 GTTTGAGTAA
559791 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
559823 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
559854 ACACTTATGT
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:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:563855 original size:33 final size:32
Alignment explanation
Indices: 563810--563874 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
563800 ACATATCCAG
* * *
563810 ATGTATCGATACATTATGCTTTGTATCGATACA
1 ATGTATCAATACATGAT-CATTGTATCGATACA
*
563843 ATGTATCAATACATGCTCATTGTATCGATACA
1 ATGTATCAATACATGATCATTGTATCGATACA
563875 TACTCAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (32 bp):
ATGTATCAATACATGATCATTGTATCGATACA
Found at i:563868 original size:19 final size:20
Alignment explanation
Indices: 563844--563896 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
563834 ATCGATACAA
*
563844 TGTATCAATACATGCTC-AT
1 TGTATCGATACATGCTCAAT
*
563863 TGTATCGATACATACTCAAT
1 TGTATCGATACATGCTCAAT
563883 TGTATCGATACATG
1 TGTATCGATACATG
563897 AAACTAGCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGCTCAAT
Found at i:563982 original size:33 final size:32
Alignment explanation
Indices: 563927--563990 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
563917 AAGTGAAATG
*
563927 TATCGATACATGGGATAATGTATCGATACATTT
1 TATCGATACATGGGAT-ATGTATCGAGACATTT
563960 TATCGATACATGAAGGAT-TGTATCGAGACAT
1 TATCGATACATG--GGATATGTATCGAGACAT
563991 CATGCCTAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 24 0.86
35 4 0.14
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (32 bp):
TATCGATACATGGGATATGTATCGAGACATTT
Found at i:564411 original size:23 final size:23
Alignment explanation
Indices: 564385--564434 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
564375 GTATTCAACC
*
564385 TTGGGTTATAATTTCTCAAGAAT
1 TTGGGGTATAATTTCTCAAGAAT
564408 TTGGGGTATAATTTCTCAAGAAT
1 TTGGGGTATAATTTCTCAAGAAT
564431 TTGG
1 TTGG
564435 AAATATTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (23 bp):
TTGGGGTATAATTTCTCAAGAAT
Found at i:570168 original size:20 final size:19
Alignment explanation
Indices: 570143--570216 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
570133 TTTTAACTAG
570143 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAA-A
* *
570163 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGA-AA
*
570183 ATGTATTGATACATTGGAAA
1 ATGTATCGATACATT-GAAA
*
570203 ATGTATTGATACAT
1 ATGTATCGATACAT
570217 CTAGGTAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 45 0.96
21 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACATTGAAA
Found at i:571318 original size:28 final size:29
Alignment explanation
Indices: 571272--571839 Score: 550
Period size: 28 Copynumber: 19.9 Consensus size: 29
571262 TTAAAAGGGT
* *
571272 TGCCACTAACTT-GTGGGCTTTAAAAGGA
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
* * *
571300 TGCCACTGA-TTAGTAGGCTTCGAAAGGG
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
* * * *
571328 TACCACTAACTT-GTGGGCTTCGAAAAGGG
1 TGCCACTGACTTAGTGGGCTTTG-AAAGGA
* *
571357 TG-CAGCTGACTT-GTGGACTTTGAGAGGA
1 TGCCA-CTGACTTAGTGGGCTTTGAAAGGA
*
571385 TGCCACTGACAT-GTGGGCTTTGAAAGGA
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
* *
571413 TGCCACTGACTTA-TGAGCTTTAAAAGGA
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
571441 TGCCACTGACTT-GTGGGCTTTGAGAAGGA
1 TGCCACTGACTTAGTGGGCTTTGA-AAGGA
*
571470 TGCCACTAACTTA-TGGGCTTTGAAA-GA
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
* * *
571497 TGCCACTGATTTA-TGGGCTTTGAGATGA
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
* *
571525 TACCACTGACTT-GTGGGCTTTCAAAGGA
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
* * *
571553 TGCCACTGGCAT-GTGGGCATTGAAAGGA
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
* * * *
571581 TGCCACTTACAT-GTGGGCTTCGAAAGGG
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
*
571609 TGCCACTAACTTA-TGGGCTTTTGAAAGGATTGAAAGGA
1 TGCCACTGACTTAGTGGGC---T-------TTGAAAGGA
*
571647 TGCCACTGACTT-GTGGGCTTTGAAAGGG
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
* *
571675 TGCCACTGACAT-GTGGGCTTTAAAAGGA
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
*
571703 TGCCACTGACTT-GTAGGCTTTGAAAGGA
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
571731 TGCCACTGACTTA-TGGGCTTTGAAAGGA
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
* *
571759 TGCCACTAACTT-GTGGGTTTTGAAAGGA
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
571787 TGCCACTGACTTA-TGGGCTTTGAAAGGA
1 TGCCACTGACTTAGTGGGCTTTGAAAGGA
*
571815 TGCCACTAACTT-GTGGGCTTTGAAA
1 TGCCACTGACTTAGTGGGCTTTGAAA
571840 AAGGTCGTAT
Statistics
Matches: 454, Mismatches: 59, Indels: 54
0.80 0.10 0.10
Matches are distributed among these distances:
27 26 0.06
28 352 0.78
29 51 0.11
31 1 0.00
35 1 0.00
38 23 0.05
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (29 bp):
TGCCACTGACTTAGTGGGCTTTGAAAGGA
Found at i:571499 original size:84 final size:84
Alignment explanation
Indices: 571260--571839 Score: 617
Period size: 84 Copynumber: 6.8 Consensus size: 84
571250 CTTTTATGGA
* * * * *
571260 CTTTAAAAGGGTTGCCACTAACTTGTGGGCTTTAAAAGGATGCCACTGA-TTAGTAGGCTTCGAA
1 CTTTAAAA-GGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTT-GTGGGCTTTGAA
* * *
571324 AGGGTACCACTAACTTGTGGG
64 AGGATGCCACTGACTTGTGGG
* * * * *
571345 CTTCGAAAAGGGTG-CAGCTGACTTGTGGACTTTGAGAGGATGCCACTGACATGTGGGCTTTGAA
1 CTT-TAAAAGGATGCCA-CTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
* *
571409 AGGATGCCACTGACTTATGAG
64 AGGATGCCACTGACTTGTGGG
* *
571430 CTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATGCCACTAACTTATGGGCTTTGAAA
1 CTTTAAAAGGATGCCACTGACTTGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTGAAA
* *
571495 -GATGCCACTGATTTATGGG
65 GGATGCCACTGACTTGTGGG
* * * * * * * *
571514 CTTTGAGATGATACCACTGACTTGTGGGCTTTCAAAGGATGCCACTGGCATGTGGGCATTGAAAG
1 CTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAG
* *
571579 GATGCCACTTACATGTGGG
66 GATGCCACTGACTTGTGGG
** * * *
571598 CTTCGAAAGGGTGCCACTAACTTATGGGCTTTTGAAAGGATTGAAAGGATGCCACTGACTTGTGG
1 CTTTAAAAGGATGCCACTGACTTGTGGGC---T-------TTGAAAGGATGCCACTGACTTGTGG
* *
571663 GCTTTGAAAGGGTGCCACTGACATGTGGG
56 GCTTTGAAAGGATGCCACTGACTTGTGGG
* *
571692 CTTTAAAAGGATGCCACTGACTTGTAGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAG
1 CTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAG
*
571757 GATGCCACTAACTTGTGGG
66 GATGCCACTGACTTGTGGG
* * * *
571776 TTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAA
1 CTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAA
571840 AAGGTCGTAT
Statistics
Matches: 413, Mismatches: 66, Indels: 33
0.81 0.13 0.06
Matches are distributed among these distances:
83 25 0.06
84 218 0.53
85 92 0.22
86 5 0.01
87 1 0.00
91 1 0.00
94 71 0.17
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (84 bp):
CTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAG
GATGCCACTGACTTGTGGG
Found at i:571653 original size:38 final size:37
Alignment explanation
Indices: 571602--571673 Score: 108
Period size: 38 Copynumber: 1.9 Consensus size: 37
571592 TGTGGGCTTC
*
571602 GAAAGGGTGCCACTAACTTATGGGCTTTTGAAAGGATT
1 GAAAGGATGCCACTAACTTATGGGC-TTTGAAAGGATT
* *
571640 GAAAGGATGCCACTGACTTGTGGGCTTTGAAAGG
1 GAAAGGATGCCACTAACTTATGGGCTTTGAAAGG
571674 GTGCCACTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 9 0.29
38 22 0.71
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (37 bp):
GAAAGGATGCCACTAACTTATGGGCTTTGAAAGGATT
Found at i:571766 original size:150 final size:148
Alignment explanation
Indices: 571489--571840 Score: 432
Period size: 150 Copynumber: 2.4 Consensus size: 148
571479 CTTATGGGCT
* * * * *
571489 TTGAAAGATGCCACTGATTTATGGGCTTTGAGATGATACCACTGACTTGTGGGCTTTCAAAGGAT
1 TTGAAAGATGCCACTGACTTATGGGCTTTGAAAGGATACCACTGACATGTGGGCTTTAAAAGGAT
* * * * *
571554 GCCACTGGCATGTGGGCATTGAAAGGATGCCACTTACATGTGGGCTTCGAAAGGGTGCCACTAAC
66 GCCACTGACATGTAGGCATTGAAAGGATGCCACTGACATATGGGCTTCGAAAGGATGCCACTAAC
571619 TTATGGGCTTTTGAAAGGA
131 TTATGGG-TTTTGAAAGGA
* * *
571638 TTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACATGTGGGCTTTAAAAGGA
1 TTGAAA-GATGCCACTGACTTATGGGCTTTGAAAGGATACCACTGACATGTGGGCTTTAAAAGGA
* * * *
571703 TGCCACTGACTTGTAGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAGGATGCCACTAA
65 TGCCACTGACATGTAGGCATTGAAAGGATGCCACTGACATATGGGCTTCGAAAGGATGCCACTAA
*
571768 CTTGTGGGTTTTG-AA--A
130 CTTATGGGTTTTGAAAGGA
* * *
571784 --G---GATGCCACTGACTTATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAA
1 TTGAAAGATGCCACTGACTTATGGGCTTTGAAAGGATACCACTGACATGTGGGCTTT-AAAA
571841 AGGTCGTATT
Statistics
Matches: 179, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
140 47 0.26
141 4 0.02
144 1 0.01
146 1 0.01
148 2 0.01
149 11 0.06
150 113 0.63
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (148 bp):
TTGAAAGATGCCACTGACTTATGGGCTTTGAAAGGATACCACTGACATGTGGGCTTTAAAAGGAT
GCCACTGACATGTAGGCATTGAAAGGATGCCACTGACATATGGGCTTCGAAAGGATGCCACTAAC
TTATGGGTTTTGAAAGGA
Found at i:578546 original size:34 final size:35
Alignment explanation
Indices: 578508--578574 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
578498 CCTTACAACA
578508 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
578542 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
578575 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:579050 original size:13 final size:13
Alignment explanation
Indices: 579032--579057 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
579022 CAATTTTTTG
579032 TGTATCGATACAT
1 TGTATCGATACAT
579045 TGTATCGATACAT
1 TGTATCGATACAT
579058 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:579122 original size:21 final size:21
Alignment explanation
Indices: 579096--579171 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
579086 CTGCCAAGAA
579096 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
579117 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
579137 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
579158 ATGTATCGATACAT
1 ATGTATCGATACAT
579172 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:579141 original size:20 final size:20
Alignment explanation
Indices: 579116--579189 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
579106 ACATCTTTTT
579116 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
579136 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
579157 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
579177 CATGTATCGATAC
1 CATGTATCGATAC
579190 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:579153 original size:41 final size:41
Alignment explanation
Indices: 579096--579189 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
579086 CTGCCAAGAA
579096 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
579137 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
579178 ATGTATCGATAC
1 ATGTATCGATAC
579190 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:580848 original size:13 final size:13
Alignment explanation
Indices: 580830--580854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
580820 ACTGAAGCAA
580830 TGTATCGATACAT
1 TGTATCGATACAT
580843 TGTATCGATACA
1 TGTATCGATACA
580855 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:581454 original size:23 final size:24
Alignment explanation
Indices: 581409--581455 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
581399 CAAAGAATTG
*
581409 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
581433 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
581456 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:584047 original size:34 final size:35
Alignment explanation
Indices: 584009--584075 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
583999 CCTTACAACA
584009 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
584043 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
584076 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:584551 original size:13 final size:13
Alignment explanation
Indices: 584533--584558 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
584523 CAATTTTTTG
584533 TGTATCGATACAT
1 TGTATCGATACAT
584546 TGTATCGATACAT
1 TGTATCGATACAT
584559 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:584623 original size:21 final size:21
Alignment explanation
Indices: 584597--584672 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
584587 CTGCCAAGAA
584597 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
584618 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
584638 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
584659 ATGTATCGATACAT
1 ATGTATCGATACAT
584673 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:584642 original size:20 final size:20
Alignment explanation
Indices: 584617--584690 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
584607 ACATCTTTTT
584617 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
584637 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
584658 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
584678 CATGTATCGATAC
1 CATGTATCGATAC
584691 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:584654 original size:41 final size:41
Alignment explanation
Indices: 584597--584690 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
584587 CTGCCAAGAA
584597 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
584638 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
584679 ATGTATCGATAC
1 ATGTATCGATAC
584691 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:585535 original size:15 final size:15
Alignment explanation
Indices: 585494--585540 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
585484 CAGTCTATTA
585494 ATGATTTTGTGGTGG
1 ATGATTTTGTGGTGG
* * **
585509 GTAATTAGGTGGTGG
1 ATGATTTTGTGGTGG
585524 ATGATTTTGTGGTGG
1 ATGATTTTGTGGTGG
585539 AT
1 AT
585541 TTGGCGGAAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.40, T:0.43
Consensus pattern (15 bp):
ATGATTTTGTGGTGG
Found at i:590188 original size:25 final size:26
Alignment explanation
Indices: 590151--590208 Score: 109
Period size: 25 Copynumber: 2.3 Consensus size: 26
590141 CATCCATATC
590151 ATAAAAGAAAGAAATTAGTAAATAAG
1 ATAAAAGAAAGAAATTAGTAAATAAG
590177 ATAAAA-AAAGAAATTAGTAAATAAG
1 ATAAAAGAAAGAAATTAGTAAATAAG
590202 ATAAAAG
1 ATAAAAG
590209 GGAATCATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 25 0.81
26 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (26 bp):
ATAAAAGAAAGAAATTAGTAAATAAG
Found at i:592753 original size:22 final size:22
Alignment explanation
Indices: 592727--592769 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
592717 CTGTTCACGT
592727 ATCACTATTCATATATCGATAA
1 ATCACTATTCATATATCGATAA
*
592749 ATCACTATTCATGTATCGATA
1 ATCACTATTCATATATCGATA
592770 CAGTGTATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (22 bp):
ATCACTATTCATATATCGATAA
Found at i:593621 original size:51 final size:51
Alignment explanation
Indices: 593545--593642 Score: 187
Period size: 51 Copynumber: 1.9 Consensus size: 51
593535 GCTAACAAAA
*
593545 AATGTATCGATACATCTGGGTAAAAAGACAGAATGTGTCGATACATTGAAG
1 AATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAG
593596 AATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATT
1 AATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATT
593643 CATACATGTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (51 bp):
AATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAG
Found at i:593712 original size:70 final size:71
Alignment explanation
Indices: 593585--593731 Score: 215
Period size: 70 Copynumber: 2.1 Consensus size: 71
593575 GAATGTGTCG
* * * * *
593585 ATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTCATACAT
1 ATACATTGAAAAATGTATCAATACATCTAGGTAAAAAGACAGAATGTATCGATACATTCAAAAAT
593650 GTATTC
66 GTATTC
* *
593656 ATACATTGAAAAATTTATCAATACATCTAGGT-AAAAGACAGAATGTATCGATACATTGAAAAAT
1 ATACATTGAAAAATGTATCAATACATCTAGGTAAAAAGACAGAATGTATCGATACATTCAAAAAT
*
593720 GTATTG
66 GTATTC
593726 ATACAT
1 ATACAT
593732 CTTGGTAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
70 40 0.59
71 28 0.41
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (71 bp):
ATACATTGAAAAATGTATCAATACATCTAGGTAAAAAGACAGAATGTATCGATACATTCAAAAAT
GTATTC
Found at i:594740 original size:31 final size:31
Alignment explanation
Indices: 594658--594781 Score: 187
Period size: 31 Copynumber: 4.0 Consensus size: 31
594648 CCAATGACAT
* * *
594658 TGGG-TTTATAAGGGTTGCCACCAACTTGCG
1 TGGGCTTTAGAAGGGTTGCCACTAACTTGTG
* *
594688 TGGGCTTTACAAAAGGTTGCCACTAACTTGTG
1 TGGGCTTTA-GAAGGGTTGCCACTAACTTGTG
594720 TGGGCTTTAGAAGGGTTGCCACTAACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACTAACTTGTG
594751 TGGGCTTTAGAAGGGTTGCCACTAACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACTAACTTGTG
594782 GGCTTCGAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.05
31 55 0.64
32 27 0.31
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACTAACTTGTG
Found at i:598666 original size:20 final size:20
Alignment explanation
Indices: 598641--598713 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
598631 CAACTTTTTT
598641 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
598661 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
598682 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
598702 ATGTATCGATAC
1 ATGTATCGATAC
598714 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Done.