Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, whole genome shotgun sequence
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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 11 of 109
Found at i:1913141 original size:12 final size:12
Alignment explanation
Indices: 1913124--1913157 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1913114 TTATTTAATT
1913124 AAAAAACAAAAA
1 AAAAAACAAAAA
*
1913136 AAAAAAGAAAAA
1 AAAAAACAAAAA
*
1913148 AAAAACCAAA
1 AAAAAACAAA
1913158 TGGAGTGTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAA
Found at i:1922027 original size:4 final size:4
Alignment explanation
Indices: 1922018--1922042 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1922008 ACAGTGCAAG
1922018 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
1922043 CAATATCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:1926592 original size:5 final size:5
Alignment explanation
Indices: 1926584--1926629 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
1926574 TTCGATAATT
* *
1926584 ATATA ATAT- ATATG AT-TA TATATA ATATA ATATA ATTTA ATATA AT
1 ATATA ATATA ATATA ATATA -ATATA ATATA ATATA ATATA ATATA AT
1926630 TATATTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
4 5 0.14
5 28 0.80
6 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (5 bp):
ATATA
Found at i:1928185 original size:51 final size:48
Alignment explanation
Indices: 1928093--1928187 Score: 129
Period size: 51 Copynumber: 1.9 Consensus size: 48
1928083 AAGGAGACAT
*
1928093 AAATGAGATGAAGAATGATGAAGCAAAGGAAGGAGATGTTGAGGTTAC
1 AAATGAGATGAAGAATGATGAAGCAAAGCAAGGAGATGTTGAGGTTAC
*
1928141 AAATGAGATGAAGAATGATAATGAAGCAGA-CAATGGAGATGTTGAGG
1 AAATGAGATGAAGAATG---ATGAAGCAAAGCAA-GGAGATGTTGAGG
1928188 ATGAAACAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
48 17 0.41
50 2 0.05
51 22 0.54
ACGTcount: A:0.44, C:0.04, G:0.33, T:0.19
Consensus pattern (48 bp):
AAATGAGATGAAGAATGATGAAGCAAAGCAAGGAGATGTTGAGGTTAC
Found at i:1928334 original size:48 final size:48
Alignment explanation
Indices: 1928241--1928400 Score: 180
Period size: 48 Copynumber: 3.3 Consensus size: 48
1928231 TGAAGTAGAG
* *
1928241 AAAGGAGATGTTAAGGCTACAATAAATGAGAT-AACGATTGGTGAAGCAGAA-
1 AAAGGAGATGTTAAGGCT---ATAAATGAGATGAA-GAATGATGAAGCA-AAC
* *
1928292 AAAGGAGACGTTAAGGGTATAAATGAGATGAAGAATGATGAAGCAAAC
1 AAAGGAGATGTTAAGGCTATAAATGAGATGAAGAATGATGAAGCAAAC
* * * * *
1928340 AAAGGAGATGTTACGGCTATAACTGAGATAAAAAATGATGAAGCAAAG
1 AAAGGAGATGTTAAGGCTATAAATGAGATGAAGAATGATGAAGCAAAC
1928388 AAAGGAGATGTTA
1 AAAGGAGATGTTA
1928401 TTATAAATGA
Statistics
Matches: 96, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
47 2 0.02
48 76 0.79
49 2 0.02
51 16 0.17
ACGTcount: A:0.47, C:0.07, G:0.28, T:0.19
Consensus pattern (48 bp):
AAAGGAGATGTTAAGGCTATAAATGAGATGAAGAATGATGAAGCAAAC
Found at i:1935972 original size:20 final size:19
Alignment explanation
Indices: 1935949--1935988 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1935939 ATAATAATTG
*
1935949 TATATCAAAATCTACTTAAA
1 TATATCAAAATATA-TTAAA
*
1935969 TATATTAAAATATATTAAA
1 TATATCAAAATATATTAAA
1935988 T
1 T
1935989 TAATATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATCAAAATATATTAAA
Found at i:1937268 original size:29 final size:29
Alignment explanation
Indices: 1937235--1937291 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1937225 TTCAACACCT
*
1937235 AAAACATTGA-TAAGATTTCACAAGTTTCA
1 AAAACATTGACT-AGATCTCACAAGTTTCA
*
1937264 AAAACATTGACTAGATCTCATAAGTTTC
1 AAAACATTGACTAGATCTCACAAGTTTC
1937292 TATTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (29 bp):
AAAACATTGACTAGATCTCACAAGTTTCA
Found at i:1938695 original size:29 final size:30
Alignment explanation
Indices: 1938663--1938744 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 30
1938653 AATATAATAT
1938663 TTTATTAAATAAATATAT-TAAATAA-TAAA
1 TTTATTAAATAAATATATATAAA-AATTAAA
1938692 TTTATT-AATATAATATATATAAAAATTAAA
1 TTTATTAAATA-AATATATATAAAAATTAAA
* *
1938722 TTAAATAAATAATAATATATATA
1 TTTATTAAAT-A-AATATATATA
1938745 TTCTTATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
28 4 0.09
29 15 0.33
30 12 0.26
31 3 0.07
32 12 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
TTTATTAAATAAATATATATAAAAATTAAA
Found at i:1938740 original size:30 final size:31
Alignment explanation
Indices: 1938674--1938742 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
1938664 TTATTAAATA
* *
1938674 AATATATTAAATAATAAATTTATTAATATAAT
1 AATATA-TAAATAATAAATTAAATAATATAAT
1938706 -ATATATAAA-AATTAAATTAAATAA-ATAAT
1 AATATATAAATAA-TAAATTAAATAATATAAT
1938735 AATATATA
1 AATATATA
1938743 TATTCTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 7 0.21
30 21 0.64
31 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
AATATATAAATAATAAATTAAATAATATAAT
Found at i:1939791 original size:17 final size:17
Alignment explanation
Indices: 1939770--1939821 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
1939760 ACTTATCTAA
1939770 TAAAAAAATAATTAAA-
1 TAAAAAAATAATTAAAT
* *
1939786 TAAAAAAAT-TTTAAAAA
1 TAAAAAAATAATT-AAAT
1939803 TAAAAAAATAATATAAAT
1 TAAAAAAATAAT-TAAAT
1939821 T
1 T
1939822 TTAAAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 2 0.07
16 12 0.41
17 9 0.31
18 5 0.17
19 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAAAATAATTAAAT
Found at i:1939811 original size:25 final size:26
Alignment explanation
Indices: 1939773--1939827 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
1939763 TATCTAATAA
**
1939773 AAAAATAATTAAATAA-AAAAATTTT
1 AAAAATAAAAAAATAATAAAAATTTT
*
1939798 AAAAATAAAAAAATAATATAAATTTT
1 AAAAATAAAAAAATAATAAAAATTTT
1939824 AAAA
1 AAAA
1939828 GAAAGTTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAAATAAAAAAATAATAAAAATTTT
Found at i:1940834 original size:6 final size:6
Alignment explanation
Indices: 1940823--1940847 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1940813 ATTATAAAAT
1940823 ATTATA ATTATA ATTATA ATTATA A
1 ATTATA ATTATA ATTATA ATTATA A
1940848 AAATTCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTATA
Found at i:1960506 original size:3 final size:3
Alignment explanation
Indices: 1960500--1960529 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1960490 ATGATGATAG
*
1960500 TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1960530 AAACTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1962322 original size:75 final size:75
Alignment explanation
Indices: 1962199--1962347 Score: 271
Period size: 75 Copynumber: 2.0 Consensus size: 75
1962189 TGGGTCAAGA
*
1962199 TAAATTTTTTTCATTCTAACTTCGACCCAACTCTCTATTAATTCAATACAACTCCAACTCATATC
1 TAAATTTTTTTCATTCTAACTTCGACCCAACTCTCTAATAATTCAATACAACTCCAACTCATATC
1962264 GGATATCAAT
66 GGATATCAAT
**
1962274 TAAATTTTTTTCATTCTAACTTCGACCCAACTCTCTAATAATTCAATACAACTCTGACTCATATC
1 TAAATTTTTTTCATTCTAACTTCGACCCAACTCTCTAATAATTCAATACAACTCCAACTCATATC
1962339 GGATATCAA
66 GGATATCAA
1962348 GTTATTATTT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (75 bp):
TAAATTTTTTTCATTCTAACTTCGACCCAACTCTCTAATAATTCAATACAACTCCAACTCATATC
GGATATCAAT
Found at i:1962489 original size:11 final size:11
Alignment explanation
Indices: 1962470--1962500 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1962460 TTATTTGGTA
1962470 ATATAAATTAT
1 ATATAAATTAT
*
1962481 ATTTAAATTAT
1 ATATAAATTAT
1962492 ATATAAATT
1 ATATAAATT
1962501 TAGTATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATATAAATTAT
Found at i:1962543 original size:16 final size:16
Alignment explanation
Indices: 1962522--1962582 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
1962512 TTTAAATTAG
*
1962522 TTAT-TAAATAATAACA
1 TTATATAAAT-ATAAAA
*
1962538 TTAT-T-AATATAATA
1 TTATATAAATATAAAA
1962552 -TATATAAATATAAAA
1 TTATATAAATATAAAA
1962567 TTATATAAATAATAAA
1 TTATATAAAT-ATAAA
1962583 GAATATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
13 3 0.08
14 6 0.15
15 11 0.28
16 14 0.36
17 5 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
TTATATAAATATAAAA
Found at i:1962856 original size:20 final size:20
Alignment explanation
Indices: 1962818--1962867 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1962808 TAAAAAAATG
*
1962818 AAAAAGACAAAAATAAAAA-A
1 AAAAAGA-AAAAACAAAAACA
*
1962838 TAAAAGAAAAAACACAAAACA
1 AAAAAGAAAAAACA-AAAACA
1962859 AAAAAGAAA
1 AAAAAGAAA
1962868 CTAAATGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 6 0.24
20 10 0.40
21 9 0.36
ACGTcount: A:0.82, C:0.08, G:0.06, T:0.04
Consensus pattern (20 bp):
AAAAAGAAAAAACAAAAACA
Found at i:1963802 original size:15 final size:17
Alignment explanation
Indices: 1963782--1963814 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1963772 TCTAAACAAA
1963782 TTTTTT-ATTTT-ACTT
1 TTTTTTAATTTTAACTT
1963797 TTTTTTAATTTTAACTT
1 TTTTTTAATTTTAACTT
1963814 T
1 T
1963815 CATCCCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTAATTTTAACTT
Found at i:1964293 original size:19 final size:17
Alignment explanation
Indices: 1964258--1964308 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 17
1964248 TTATATATTT
1964258 AAATATTTTTATTTAAA
1 AAATATTTTTATTTAAA
1964275 AAATATTTTATATTTTAAA
1 AAATATTTT-TA-TTTAAA
1964294 AAATAATATTTTATT
1 AAAT-AT-TTTTATT
1964309 AATTTCAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.30
18 2 0.07
19 12 0.40
20 4 0.13
21 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATATTTTTATTTAAA
Found at i:1964431 original size:26 final size:27
Alignment explanation
Indices: 1964372--1964433 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
1964362 AAAAAATTTT
* *
1964372 TGAATCAAATCAAATTTAAATTTAATA
1 TGAATAAAATCAAATTTAAATTTAAGA
*
1964399 -GATATAAAATCATA-TTAAATTTAAGA
1 TGA-ATAAAATCAAATTTAAATTTAAGA
1964425 TGAATAAAA
1 TGAATAAAA
1964434 ATTTATTTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (27 bp):
TGAATAAAATCAAATTTAAATTTAAGA
Found at i:1965118 original size:2 final size:2
Alignment explanation
Indices: 1965111--1965148 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1965101 CTGTCACATG
* *
1965111 TA TA TA TA TA TA TA TA TA TA TG TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1965149 AAGAGAGGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1969098 original size:70 final size:70
Alignment explanation
Indices: 1968985--1969125 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
1968975 TAGAGCTGAA
1968985 ACAGAAACTTCATTAAAAACACAGTCTTTAGATAAACTATGGTTCACTAAAACTGTAAGGCTTAA
1 ACAGAAACTTCATTAAAAACACAGTCTTTAGATAAACTATGGTTCACTAAAACTGTAAGGCTTAA
1969050 AGCAT
66 AGCAT
1969055 ACAGAAACTTCATTAAAAACACAGTCTTTAGATAAACTATGGTTCACTAAAACTGTAAGGCTTAA
1 ACAGAAACTTCATTAAAAACACAGTCTTTAGATAAACTATGGTTCACTAAAACTGTAAGGCTTAA
1969120 AGCAT
66 AGCAT
1969125 A
1 A
1969126 GTTTAGCCAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (70 bp):
ACAGAAACTTCATTAAAAACACAGTCTTTAGATAAACTATGGTTCACTAAAACTGTAAGGCTTAA
AGCAT
Found at i:1969106 original size:34 final size:34
Alignment explanation
Indices: 1968993--1969106 Score: 81
Period size: 34 Copynumber: 3.3 Consensus size: 34
1968983 AAACAGAAAC
*
1968993 TTCATTAAAAACACAGTCTTTAGATAAACTATGG
1 TTCACTAAAAACACAGTCTTTAGATAAACTATGG
* * * * ***
1969027 TTCACT-AAAACTGTA-AGGCTTAAAGCATACA-GAAAC
1 TTCACTAAAAAC---ACAGTCTT-TAG-ATAAACTATGG
*
1969063 TTCATTAAAAACACAGTCTTTAGATAAACTATGG
1 TTCACTAAAAACACAGTCTTTAGATAAACTATGG
1969097 TTCACTAAAA
1 TTCACTAAAA
1969107 CTGTAAGGCT
Statistics
Matches: 55, Mismatches: 17, Indels: 16
0.62 0.19 0.18
Matches are distributed among these distances:
33 9 0.16
34 18 0.33
35 10 0.18
36 9 0.16
37 9 0.16
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (34 bp):
TTCACTAAAAACACAGTCTTTAGATAAACTATGG
Found at i:1971552 original size:15 final size:15
Alignment explanation
Indices: 1971534--1971603 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
1971524 CTAAAATTTC
1971534 TTTCATCAAAAGTTA
1 TTTCATCAAAAGTTA
*
1971549 TTTCA-CTAAGAGTTA
1 TTTCATC-AAAAGTTA
* * *
1971564 TTTTAT-AAAAGATG
1 TTTCATCAAAAGTTA
* *
1971578 CTTCATCAAATGTTA
1 TTTCATCAAAAGTTA
*
1971593 TTTCATTAAAA
1 TTTCATCAAAA
1971604 AAAAGTGAAA
Statistics
Matches: 39, Mismatches: 13, Indels: 6
0.67 0.22 0.10
Matches are distributed among these distances:
14 10 0.26
15 29 0.74
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (15 bp):
TTTCATCAAAAGTTA
Found at i:1982862 original size:27 final size:27
Alignment explanation
Indices: 1982812--1982865 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1982802 TGTTTTATAG
**
1982812 ACCAGCTTGCAATGAGTTCAGCAACTT
1 ACCAGCTTGCAATGAGAGCAGCAACTT
*
1982839 ACCAGCTTGCAATGAGAGCTGCAACTT
1 ACCAGCTTGCAATGAGAGCAGCAACTT
1982866 TTAAAATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (27 bp):
ACCAGCTTGCAATGAGAGCAGCAACTT
Found at i:1983800 original size:17 final size:16
Alignment explanation
Indices: 1983741--1983801 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
1983731 CATTTTTTTG
1983741 AAACATAAAAATAAAA
1 AAACATAAAAATAAAA
* *
1983757 AATAGATAAAAACAAAA
1 AA-ACATAAAAATAAAA
* *
1983774 AAACTTTAAAAATGACAA
1 AAAC-ATAAAAAT-AAAA
1983792 AAACATAAAA
1 AAACATAAAA
1983802 GTTAGATTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
16 3 0.09
17 25 0.71
18 7 0.20
ACGTcount: A:0.74, C:0.08, G:0.03, T:0.15
Consensus pattern (16 bp):
AAACATAAAAATAAAA
Found at i:1984039 original size:19 final size:20
Alignment explanation
Indices: 1984017--1984055 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1984007 GGCCTAAAAG
1984017 TATTTTATTT-TTTATTTTT
1 TATTTTATTTATTTATTTTT
*
1984036 TATTTTCTTTATTTATTTTT
1 TATTTTATTTATTTATTTTT
1984056 ATTGCTTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (20 bp):
TATTTTATTTATTTATTTTT
Found at i:1985777 original size:3 final size:3
Alignment explanation
Indices: 1985769--1985810 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1985759 ATTAATACAT
*
1985769 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1985811 TCACATTGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1985987 original size:25 final size:24
Alignment explanation
Indices: 1985958--1986012 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1985948 TTTTTGATAA
1985958 AATTACAATTACAAAT-TATAATTAT
1 AATTACAATTACAAATATAT-A-TAT
* *
1985983 AATTAAGAATTACATATATATATAT
1 AATT-ACAATTACAAATATATATAT
1986008 AATTA
1 AATTA
1986013 TTAAATAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.04
25 11 0.42
26 11 0.42
27 3 0.12
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (24 bp):
AATTACAATTACAAATATATATAT
Found at i:1987927 original size:31 final size:31
Alignment explanation
Indices: 1987881--1987974 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 31
1987871 CTATTTAATG
*
1987881 AAATATGATAT-AATATTTATTATTTAATATT
1 AAATATAATATAAATATTTATT-TTTAATATT
*
1987912 AAATATAAT-TAAATATTATATGTTTAATATT
1 AAATATAATATAAATATT-TATTTTTAATATT
*
1987943 ---TATAATGATAAATATTTA-TTTTAATGTT
1 AAATATAAT-ATAAATATTTATTTTTAATATT
1987971 AAAT
1 AAAT
1987975 CTTAAATAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
28 14 0.27
29 2 0.04
30 9 0.17
31 24 0.46
32 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (31 bp):
AAATATAATATAAATATTTATTTTTAATATT
Found at i:1988498 original size:25 final size:25
Alignment explanation
Indices: 1988456--1988504 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1988446 AAAAAAATTT
* * *
1988456 TATTTTATTATCCCTATATTTATAA
1 TATTTTATTATACATATATATATAA
*
1988481 TATTTTATTATATATATATATATA
1 TATTTTATTATACATATATATATA
1988505 TTTAGATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTTTATTATACATATATATATAA
Found at i:1989539 original size:61 final size:61
Alignment explanation
Indices: 1989413--1989548 Score: 150
Period size: 61 Copynumber: 2.2 Consensus size: 61
1989403 ACAAAAATGT
* * * *
1989413 ATTTTCATAATTATGGTAAAAGGGTATTATAATAATTTTGATAAATTAAAATACGAGAGGT
1 ATTTTTATAATTATGGTAAAAGGGTATTATAATAATTTTGACAAATTAAAATAAGAGAGGC
* ** * **
1989474 ATTTTTATAATTATGGTAAGAGGGGTATTATTGTAATTTTGGCAAA-TAATGGTAAGA-AGGC
1 ATTTTTATAATTATGGTAA-AAGGGTATTATAATAATTTTGACAAATTAA-AATAAGAGAGGC
1989535 ATTTTTATAATTAT
1 ATTTTTATAATTAT
1989549 AGTTGTAGGA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
61 38 0.60
62 25 0.40
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.40
Consensus pattern (61 bp):
ATTTTTATAATTATGGTAAAAGGGTATTATAATAATTTTGACAAATTAAAATAAGAGAGGC
Found at i:1989565 original size:61 final size:61
Alignment explanation
Indices: 1989474--1989594 Score: 149
Period size: 61 Copynumber: 2.0 Consensus size: 61
1989464 TACGAGAGGT
* * *
1989474 ATTTTTATAATTATGGTAAGAGGGGTATTAT-TGTAATTTTGGCA-AATAATGGTAAGAAGGC
1 ATTTTTATAATTATAGTAAGAGGAGCATTATAT-TAATTTTGG-ATAATAATGGTAAGAAGGC
* *
1989535 ATTTTTATAATTATAGT-TGTAGGAGCATTATATTAATTTTGGATAATTATGGTAAGAAGG
1 ATTTTTATAATTATAGTAAG-AGGAGCATTATATTAATTTTGGATAATAATGGTAAGAAGG
1989595 GTATTTTAGC
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
60 2 0.04
61 49 0.94
62 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.40
Consensus pattern (61 bp):
ATTTTTATAATTATAGTAAGAGGAGCATTATATTAATTTTGGATAATAATGGTAAGAAGGC
Found at i:1989986 original size:115 final size:112
Alignment explanation
Indices: 1989783--1989988 Score: 252
Period size: 115 Copynumber: 1.8 Consensus size: 112
1989773 GTAATTATGG
* * * * * *
1989783 AGCAATTAAAATGATATTTTTCGTAATTATGCTTAGAGGGTATTATAATAATTTTAGTTAATTAT
1 AGCAATTAAAATGATATTTTTCGTAATTATGATCAAAGGGTATTACAATAATTTTAGTCAACTAT
1989848 AATAGAATGGGTATTTTAATAATTATGGCAGAAGAGGCATTATATAA
66 AATAGAATGGGTATTTTAATAATTATGGCAGAAGAGGCATTATATAA
* * * *
1989895 AGCAATTAAAATGACATTTTTTTTTGTAATTATGATCAAAGGGTGTTACAGTAATTTTAGTCAAC
1 AGCAATTAAAATG--A-TATTTTTCGTAATTATGATCAAAGGGTATTACAATAATTTTAGTCAAC
* **
1989960 TATAATATAA-GGGATATTTTTGTAATTAT
63 TATAATAGAATGGG-TATTTTAATAATTAT
1989989 AGTTAAATGA
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
112 13 0.17
114 4 0.05
115 60 0.78
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (112 bp):
AGCAATTAAAATGATATTTTTCGTAATTATGATCAAAGGGTATTACAATAATTTTAGTCAACTAT
AATAGAATGGGTATTTTAATAATTATGGCAGAAGAGGCATTATATAA
Found at i:1991433 original size:62 final size:59
Alignment explanation
Indices: 1991354--1991495 Score: 153
Period size: 62 Copynumber: 2.4 Consensus size: 59
1991344 AAGTAATCAA
* * **
1991354 AAGAATATTTTGC-TAATTATGTTTTGAA-GTCATTATAGTAAATTCGGCCTAATTATAATAT
1 AAGAGTATTTT-CATAATTATG-TTTAAAGGTCATTATAGTAAATTCAACC--ATTATAATAT
* *
1991415 AAGGGTTATTTTCATAATTATGTTTAAAGGTCATTATAGTAATTTCAACCATTATAATAT
1 AAGAG-TATTTTCATAATTATGTTTAAAGGTCATTATAGTAAATTCAACCATTATAATAT
* *
1991475 GAGAGTATTTTTATAATTATG
1 AAGAGTATTTTCATAATTATG
1991496 GTAGGAGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
59 15 0.22
60 13 0.19
61 9 0.13
62 32 0.46
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (59 bp):
AAGAGTATTTTCATAATTATGTTTAAAGGTCATTATAGTAAATTCAACCATTATAATAT
Found at i:1993979 original size:11 final size:11
Alignment explanation
Indices: 1993963--1993994 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1993953 TGAAATAAAC
1993963 CCAAATTTATA
1 CCAAATTTATA
1993974 CCAAATTTATA
1 CCAAATTTATA
1993985 CCAAATTTAT
1 CCAAATTTAT
1993995 GCTTCAACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
CCAAATTTATA
Found at i:1994320 original size:14 final size:14
Alignment explanation
Indices: 1994298--1994327 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1994288 CTTGTTAATT
*
1994298 ATATTTTTAATTAA
1 ATATATTTAATTAA
1994312 ATATATTTAATTAA
1 ATATATTTAATTAA
1994326 AT
1 AT
1994328 TTTTCCTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATATTTAATTAA
Found at i:1999063 original size:19 final size:17
Alignment explanation
Indices: 1999034--1999077 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
1999024 CCTTTAAAAA
1999034 TAAATATTAATAAATTTATT
1 TAAA-ATTAATAAA-TTA-T
*
1999054 TAAAATTAATTAATTAT
1 TAAAATTAATAAATTAT
1999071 TAAAATT
1 TAAAATT
1999078 TTGCTCTCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
18 3 0.13
19 8 0.35
20 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAATTAATAAATTAT
Found at i:2000956 original size:52 final size:51
Alignment explanation
Indices: 2000899--2001055 Score: 181
Period size: 52 Copynumber: 3.0 Consensus size: 51
2000889 TATAATCATA
*
2000899 CAAACTTG-CTCATTAAGAATCTCTCTCCTTTTAGAATTCTTCTCCTATAAGT
1 CAAACTTGCCT-ATTAAGAATCTCT-TCCTTTTAGAATTCTTCTCCTACAAGT
* * *
2000951 CAAACTTGCCTATTAAGAATCTCTTTCCTTTTAAAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCTC-TTCCTTTTAGAATTCTTCTCCTACAAGT
* * ** **
2001003 TATACTTGCCTATTAAGAATCATCTTTATTTTAGAATTCTTCTTTTACAAGT
1 CAAACTTGCCTATTAAGAATC-TCTTCCTTTTAGAATTCTTCTCCTACAAGT
2001055 C
1 C
2001056 TTCTTGTCTA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
52 85 0.94
53 5 0.06
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCTCTTCCTTTTAGAATTCTTCTCCTACAAGT
Found at i:2001393 original size:25 final size:25
Alignment explanation
Indices: 2001359--2001406 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2001349 CTCAAATCAT
2001359 GTTCTTCCCACATCTAGAACCTTCA
1 GTTCTTCCCACATCTAGAACCTTCA
* *
2001384 GTTCTTCCCACGTCTTGAACCTT
1 GTTCTTCCCACATCTAGAACCTT
2001407 TGACTTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.19, C:0.35, G:0.10, T:0.35
Consensus pattern (25 bp):
GTTCTTCCCACATCTAGAACCTTCA
Found at i:2009495 original size:7 final size:7
Alignment explanation
Indices: 2009426--2009477 Score: 63
Period size: 7 Copynumber: 7.7 Consensus size: 7
2009416 GTATAATATG
2009426 TTATAGA
1 TTATAGA
*
2009433 ATATAGA
1 TTATAGA
2009440 -TATAGA
1 TTATAGA
*
2009446 -TATAAA
1 TTATAGA
2009452 TTATAGA
1 TTATAGA
2009459 TTATAGA
1 TTATAGA
*
2009466 TTATCGA
1 TTATAGA
2009473 TTATA
1 TTATA
2009478 AAATTAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
6 11 0.28
7 28 0.72
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (7 bp):
TTATAGA
Found at i:2012405 original size:13 final size:15
Alignment explanation
Indices: 2012376--2012409 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
2012366 AATAATTTTT
2012376 TTATTTTACACAAAA
1 TTATTTTACACAAAA
2012391 TTATTTTA-A-AAAA
1 TTATTTTACACAAAA
2012404 TTATTT
1 TTATTT
2012410 ATGTAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 1 0.05
15 8 0.42
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATTTTACACAAAA
Found at i:2015830 original size:2 final size:2
Alignment explanation
Indices: 2015823--2015861 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2015813 CCATTCCACA
2015823 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2015862 GTTGGACTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2020672 original size:11 final size:11
Alignment explanation
Indices: 2020637--2020681 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
2020627 TATAACTTTG
2020637 AATTTTTTATTAA
1 AATTTTTT-TT-A
* *
2020650 AAATTTTATTA
1 AATTTTTTTTA
2020661 AATTTTTTTTA
1 AATTTTTTTTA
2020672 AATTTTTTTT
1 AATTTTTTTT
2020682 TTTTATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 20 0.71
12 2 0.07
13 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
AATTTTTTTTA
Found at i:2020682 original size:12 final size:12
Alignment explanation
Indices: 2020637--2020679 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
2020627 TATAACTTTG
2020637 AATTTTTTATTA
1 AATTTTTTATTA
**
2020649 AAAATTTTATTA
1 AATTTTTTATTA
2020661 AATTTTTT-TTA
1 AATTTTTTATTA
2020672 AATTTTTT
1 AATTTTTT
2020680 TTTTTTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 11 0.41
12 16 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
AATTTTTTATTA
Found at i:2029755 original size:7 final size:7
Alignment explanation
Indices: 2029719--2029766 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
2029709 TAATATGTTA
*
2029719 ATAGAAT
1 ATAGATT
2029726 ATAGA-T
1 ATAGATT
*
2029732 ATAGATA
1 ATAGATT
*
2029739 ATAAATT
1 ATAGATT
2029746 ATAGATT
1 ATAGATT
2029753 ATAGATT
1 ATAGATT
*
2029760 ATCGATT
1 ATAGATT
2029767 TATTAAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
6 6 0.17
7 29 0.83
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (7 bp):
ATAGATT
Found at i:2032580 original size:22 final size:21
Alignment explanation
Indices: 2032555--2032599 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2032545 TCAAATATCA
2032555 AATTAAAAAATTTAAAAATTTT
1 AATTAAAAAA-TTAAAAATTTT
**
2032577 AATTATCAAATTAAAAATTTT
1 AATTAAAAAATTAAAAATTTT
2032598 AA
1 AA
2032600 ATTTAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTAAAAAATTAAAAATTTT
Found at i:2032716 original size:13 final size:15
Alignment explanation
Indices: 2032687--2032720 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
2032677 GAATAATTTT
2032687 TTATTTTACACAAAA
1 TTATTTTACACAAAA
2032702 TTATTTTA-A-AAAA
1 TTATTTTACACAAAA
2032715 TTATTT
1 TTATTT
2032721 ATGTAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 1 0.05
15 8 0.42
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATTTTACACAAAA
Found at i:2036146 original size:2 final size:2
Alignment explanation
Indices: 2036139--2036175 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2036129 CCATTCCACA
2036139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2036176 GTTGGACTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2040287 original size:11 final size:11
Alignment explanation
Indices: 2040252--2040296 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
2040242 TATAACTTTG
2040252 AATTTTTTATTAA
1 AATTTTTT-TT-A
* *
2040265 AAATTTTATTA
1 AATTTTTTTTA
2040276 AATTTTTTTTA
1 AATTTTTTTTA
2040287 AATTTTTTTT
1 AATTTTTTTT
2040297 TTTTATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 20 0.71
12 2 0.07
13 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
AATTTTTTTTA
Found at i:2040297 original size:12 final size:12
Alignment explanation
Indices: 2040252--2040294 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
2040242 TATAACTTTG
2040252 AATTTTTTATTA
1 AATTTTTTATTA
**
2040264 AAAATTTTATTA
1 AATTTTTTATTA
2040276 AATTTTTT-TTA
1 AATTTTTTATTA
2040287 AATTTTTT
1 AATTTTTT
2040295 TTTTTTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
11 11 0.41
12 16 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
AATTTTTTATTA
Found at i:2043286 original size:28 final size:29
Alignment explanation
Indices: 2043224--2043279 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
2043214 AAGTAGTGAC
2043224 TTATTTGAATACAAAATAAAAGATAAAAAA
1 TTATTTGAATA-AAAATAAAAGATAAAAAA
* *
2043254 TTATTTGAAT-ATAATAAAATATAAAA
1 TTATTTGAATAAAAATAAAAGATAAAA
2043280 TTTTATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.58
30 10 0.42
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (29 bp):
TTATTTGAATAAAAATAAAAGATAAAAAA
Found at i:2044478 original size:1 final size:1
Alignment explanation
Indices: 2044474--2044549 Score: 53
Period size: 1 Copynumber: 76.0 Consensus size: 1
2044464 CAGATAGAAG
* * * * * * * * * *
2044474 AAAAAGAAAAAAATAATAAATAAAACAAAAATAAAAAAATAAAAACAAAAAAAAAGAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
2044539 CAAAAAAAAAA
1 AAAAAAAAAAA
2044550 CAATTCAGCT
Statistics
Matches: 53, Mismatches: 22, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.86, C:0.04, G:0.03, T:0.08
Consensus pattern (1 bp):
A
Found at i:2044506 original size:15 final size:13
Alignment explanation
Indices: 2044480--2044546 Score: 71
Period size: 14 Copynumber: 4.8 Consensus size: 13
2044470 GAAGAAAAAG
*
2044480 AAAAAAATAATAA
1 AAAAAAAAAATAA
2044493 ATAAAACAAAAATAA
1 A-AAAA-AAAAATAA
*
2044508 AAAAATAAAAACAA
1 AAAAA-AAAAATAA
2044522 AAAAAAAGAAATAA
1 AAAAAAA-AAATAA
2044536 AAACAAAAAAA
1 AAA-AAAAAAA
2044547 AAACAATTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
13 3 0.07
14 31 0.67
15 12 0.26
ACGTcount: A:0.85, C:0.04, G:0.01, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAATAA
Found at i:2044507 original size:11 final size:10
Alignment explanation
Indices: 2044480--2044548 Score: 68
Period size: 10 Copynumber: 6.7 Consensus size: 10
2044470 GAAGAAAAAG
*
2044480 AAAAAAATAA
1 AAAAAAACAA
2044490 TAAATAAAACAA
1 -AAA-AAAACAA
2044502 AAATAAAA-AA
1 AAA-AAAACAA
*
2044512 ATAAAAACAA
1 AAAAAAACAA
*
2044522 AAAAAAAGAA
1 AAAAAAACAA
*
2044532 ATAAAAACAA
1 AAAAAAACAA
2044542 AAAAAAA
1 AAAAAAA
2044549 ACAATTCAGC
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
9 4 0.08
10 28 0.57
11 11 0.22
12 6 0.12
ACGTcount: A:0.86, C:0.04, G:0.01, T:0.09
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:2044513 original size:19 final size:19
Alignment explanation
Indices: 2044474--2044549 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 19
2044464 CAGATAGAAG
*
2044474 AAAAAGAAAAAAATAATAAAT
1 AAAAACAAAAAAA-AA-AAAT
2044495 -AAAACAAAAATAAAAAAAT
1 AAAAACAAAAA-AAAAAAAT
2044514 AAAAACAAAAAAAAAGAAAT
1 AAAAACAAAAAAAAA-AAAT
2044534 AAAAACAAAAAAAAAA
1 AAAAACAAAAAAAAAA
2044550 CAATTCAGCT
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
19 9 0.18
20 40 0.78
21 2 0.04
ACGTcount: A:0.86, C:0.04, G:0.03, T:0.08
Consensus pattern (19 bp):
AAAAACAAAAAAAAAAAAT
Found at i:2048215 original size:12 final size:12
Alignment explanation
Indices: 2048198--2048237 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
2048188 ACGTTCTATT
2048198 ATATATTTAATG
1 ATATATTTAATG
2048210 ATATATTTAATG
1 ATATATTTAATG
*
2048222 ATATCTTTAATG
1 ATATATTTAATG
2048234 ATAT
1 ATAT
2048238 TAATACAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (12 bp):
ATATATTTAATG
Found at i:2049017 original size:2 final size:2
Alignment explanation
Indices: 2049010--2049040 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2049000 AATAATTGTT
2049010 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2049041 TGTTCATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2049620 original size:31 final size:31
Alignment explanation
Indices: 2049585--2049661 Score: 77
Period size: 33 Copynumber: 2.4 Consensus size: 31
2049575 CGCCTTGATA
2049585 TTATATT-TATTATTAA-AATATTAAAAATATT
1 TTATATTATATT-TTAAGAATATTAAAAAT-TT
* *
2049616 TTATATTAATATTTTAAGAATTTTAAATATTT
1 TTATATT-ATATTTTAAGAATATTAAAAATTT
*
2049648 TTATAATTAAATTT
1 TTAT-ATTATATTT
2049662 AAATAAAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 7 0.18
32 15 0.38
33 17 0.44
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (31 bp):
TTATATTATATTTTAAGAATATTAAAAATTT
Found at i:2050437 original size:40 final size:40
Alignment explanation
Indices: 2050382--2050463 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
2050372 AATGTGGAGA
* *
2050382 TTTTTTTTTATTTGTTTGGTTGTGAAATCTTGTTCTTAGG
1 TTTTTTTTTATTTGTTTGGTCGTGAAATCCTGTTCTTAGG
2050422 TTTTTTTTTATTTGTTTGGTCGTGAAATCCTGTTCTTAGG
1 TTTTTTTTTATTTGTTTGGTCGTGAAATCCTGTTCTTAGG
2050462 TT
1 TT
2050464 GGTTGCCTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.12, C:0.07, G:0.20, T:0.61
Consensus pattern (40 bp):
TTTTTTTTTATTTGTTTGGTCGTGAAATCCTGTTCTTAGG
Found at i:2050633 original size:21 final size:21
Alignment explanation
Indices: 2050585--2050635 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2050575 AGTAATAATA
*
2050585 ATGAGATTAGTTATTAAGACG
1 ATGAGATTAGATATTAAGACG
* * **
2050606 ATAAGATTAGATATTATGTTG
1 ATGAGATTAGATATTAAGACG
2050627 ATGAGATTA
1 ATGAGATTA
2050636 AAATCAATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (21 bp):
ATGAGATTAGATATTAAGACG
Found at i:2050783 original size:18 final size:18
Alignment explanation
Indices: 2050762--2050796 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2050752 TGACATTTAT
*
2050762 AAAATTAATAAATTATTA
1 AAAATTAATAAAATATTA
*
2050780 AAAATTATTAAAATATT
1 AAAATTAATAAAATATT
2050797 TATGTCAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTAATAAAATATTA
Found at i:2050912 original size:22 final size:25
Alignment explanation
Indices: 2050861--2050914 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 25
2050851 ATAACTTAAC
*
2050861 AAATAATATTAAATATGTAAAATATA
1 AAATAATATTAAATA-GTAAAAGATA
2050887 AAATAAT-TTAAATA-T-AAAGATA
1 AAATAATATTAAATAGTAAAAGATA
2050909 AAATAA
1 AAATAA
2050915 AAATAGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 12 0.44
23 1 0.04
25 7 0.26
26 7 0.26
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (25 bp):
AAATAATATTAAATAGTAAAAGATA
Found at i:2052416 original size:90 final size:88
Alignment explanation
Indices: 2052259--2052516 Score: 415
Period size: 90 Copynumber: 3.0 Consensus size: 88
2052249 TCAATTCCCA
2052259 AAACACACCAATTCAGTTCTTGATAGATAGA-A-AGGTAGGTAGGTAGATTCATGCATACATATA
1 AAACACACCAATTCAGTTCTTGATAGATAGATAGAGGTAGGTAGGTAGATTCATGCATACATATA
2052322 GAAACAGTAAGCAATCCAAGATG
66 GAAACAGTAAGCAATCCAAGATG
2052345 AAACACACCAATTCAGTTCTTGATAGATAGATAGGTAGGTAGGTAGGTAGATTCATGCATACATA
1 AAACACACCAATTCAGTTCTTGATAGATAGATA-G-AGGTAGGTAGGTAGATTCATGCATACATA
*
2052410 TAGAAACAGTAAGCAATCCAAGATA
64 TAGAAACAGTAAGCAATCCAAGATG
*
2052435 AAACACACCAATTCAGTTCTTGATAGATAGATAGA--TA---A-GTAGATTCATGCATACATAAA
1 AAACACACCAATTCAGTTCTTGATAGATAGATAGAGGTAGGTAGGTAGATTCATGCATACATATA
*
2052494 GAAACAGTAGGCAATCCAAGATG
66 GAAACAGTAAGCAATCCAAGATG
2052517 CTTGCTCTTC
Statistics
Matches: 164, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
82 41 0.25
83 1 0.01
86 33 0.20
87 1 0.01
88 1 0.01
89 1 0.01
90 86 0.52
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (88 bp):
AAACACACCAATTCAGTTCTTGATAGATAGATAGAGGTAGGTAGGTAGATTCATGCATACATATA
GAAACAGTAAGCAATCCAAGATG
Found at i:2053202 original size:29 final size:29
Alignment explanation
Indices: 2053160--2053218 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2053150 CCTTAAAAAA
*
2053160 TTTGCTAAGAGAGTTCATACTGCACAGCT
1 TTTGCTAAGAGAGTTCATACTACACAGCT
*
2053189 TTTGCTAAGAGAGTTCATATTACACAGCT
1 TTTGCTAAGAGAGTTCATACTACACAGCT
2053218 T
1 T
2053219 GCTTGTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (29 bp):
TTTGCTAAGAGAGTTCATACTACACAGCT
Found at i:2054889 original size:16 final size:18
Alignment explanation
Indices: 2054865--2054906 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
2054855 AGTTTCATTT
*
2054865 ATTACTATTAAA-AT-TA
1 ATTAATATTAAATATATA
2054881 ATTAATATTAAATATAATA
1 ATTAATATTAAATAT-ATA
2054900 ATTAATA
1 ATTAATA
2054907 AAAATAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 11 0.50
17 2 0.09
19 9 0.41
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAATATTAAATATATA
Found at i:2060469 original size:30 final size:28
Alignment explanation
Indices: 2060435--2060511 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
2060425 TAAAGTAATG
2060435 ACTTATTTGAATACAAAATAAAAGATAAAA
1 ACTTATTTGAAT--AAAATAAAAGATAAAA
* *
2060465 ACTTATTTGAATATAATAAAATATAAAA
1 ACTTATTTGAATAAAATAAAAGATAAAA
* *
2060493 ATTTA-TTCAA-AAAATAAAA
1 ACTTATTTGAATAAAATAAAA
2060512 TAGTTTGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.19
27 4 0.10
28 18 0.43
30 12 0.29
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (28 bp):
ACTTATTTGAATAAAATAAAAGATAAAA
Found at i:2060483 original size:28 final size:29
Alignment explanation
Indices: 2060435--2060499 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 29
2060425 TAAAGTAATG
2060435 ACTTATTTGAATACAAAATAAAAGATAAAA
1 ACTTATTTGAATA-AAAATAAAAGATAAAA
* *
2060465 ACTTATTTGAAT-ATAATAAAATATAAAA
1 ACTTATTTGAATAAAAATAAAAGATAAAA
*
2060493 ATTTATT
1 ACTTATT
2060500 CAAAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 20 0.62
30 12 0.38
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (29 bp):
ACTTATTTGAATAAAAATAAAAGATAAAA
Found at i:2061733 original size:10 final size:10
Alignment explanation
Indices: 2061718--2061757 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
2061708 AATAAAACAA
2061718 AAATAAAATG
1 AAATAAAATG
*
2061728 AAATAAAGATAA
1 AAATAAA-AT-G
2061740 AAATAAAATG
1 AAATAAAATG
2061750 AAATAAAA
1 AAATAAAA
2061758 ACAAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 15 0.58
11 4 0.15
12 7 0.27
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (10 bp):
AAATAAAATG
Found at i:2061755 original size:16 final size:16
Alignment explanation
Indices: 2061700--2061768 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
2061690 AAAAAGAAAA
*
2061700 AAATAATAAATAAAA-C
1 AAATAA-AAATAAAATG
* * *
2061716 AAAAATAAAATGAAATA
1 AAATA-AAAATAAAATG
2061733 AAGATAAAAATAAAATG
1 AA-ATAAAAATAAAATG
* *
2061750 AAATAAAAACAAAAAG
1 AAATAAAAATAAAATG
2061766 AAA
1 AAA
2061769 CAATTCTGCT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
16 26 0.62
17 14 0.33
18 2 0.05
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (16 bp):
AAATAAAAATAAAATG
Found at i:2061763 original size:22 final size:22
Alignment explanation
Indices: 2061690--2061764 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
2061680 ATAGAAGAAG
*
2061690 AAAAAGAAAAA-AATAAT-AAAT
1 AAAAACAAAAATAA-AATGAAAT
2061711 -AAAACAAAAATAAAATGAAAT
1 AAAAACAAAAATAAAATGAAAT
* *
2061732 AAAGATAAAAATAAAATGAAAT
1 AAAAACAAAAATAAAATGAAAT
2061754 AAAAACAAAAA
1 AAAAACAAAAA
2061765 GAAACAATTC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.26
21 6 0.13
22 28 0.61
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (22 bp):
AAAAACAAAAATAAAATGAAAT
Found at i:2066231 original size:2 final size:2
Alignment explanation
Indices: 2066224--2066256 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2066214 AATAATTGTT
2066224 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2066257 TGTTCATATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2066826 original size:31 final size:31
Alignment explanation
Indices: 2066791--2066867 Score: 77
Period size: 33 Copynumber: 2.4 Consensus size: 31
2066781 CGCCCTGATA
2066791 TTATATT-TATTATTAA-AATATTAAAAATATT
1 TTATATTATATT-TTAAGAATATTAAAAAT-TT
* *
2066822 TTATATTAGTATTTTAAGAATTTTAAATATTT
1 TTATATTA-TATTTTAAGAATATTAAAAATTT
*
2066854 TTATAATTAAATTT
1 TTAT-ATTATATTT
2066868 AAATAAAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 7 0.18
32 14 0.36
33 18 0.46
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (31 bp):
TTATATTATATTTTAAGAATATTAAAAATTT
Found at i:2067922 original size:18 final size:18
Alignment explanation
Indices: 2067901--2067935 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2067891 TGACATTTAT
*
2067901 AAAATTAATAAATTATTA
1 AAAATTAATAAAATATTA
*
2067919 AAAATTATTAAAATATT
1 AAAATTAATAAAATATT
2067936 TATGTCAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTAATAAAATATTA
Found at i:2068044 original size:17 final size:17
Alignment explanation
Indices: 2068022--2068068 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2068012 ATATGTAAAT
2068022 TTTAAAATATAAAATAA
1 TTTAAAATATAAAATAA
2068039 TTT-AAATATAAATATAA
1 TTTAAAATATAAA-ATAA
**
2068056 AATAAAA-ATAAAA
1 TTTAAAATATAAAA
2068069 AACAGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 10 0.38
17 13 0.50
18 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTTAAAATATAAAATAA
Found at i:2068045 original size:16 final size:16
Alignment explanation
Indices: 2068000--2068055 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
2067990 ATAACTTAAC
*
2068000 AAATAATATTAAATATGT
1 AAATAAT-TTAAATAT-A
2068018 AAAT--TTTAAAATATA
1 AAATAATTT-AAATATA
2068033 AAATAATTTAAATATA
1 AAATAATTTAAATATA
2068049 AATATAA
1 AA-ATAA
2068056 AATAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
15 6 0.18
16 16 0.48
17 7 0.21
18 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAATAATTTAAATATA
Found at i:2068060 original size:11 final size:11
Alignment explanation
Indices: 2068026--2068068 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
2068016 GTAAATTTTA
2068026 AAATATAAAAT
1 AAATATAAAAT
*
2068037 -AATTTAAATAT
1 AAATATAAA-AT
2068048 AAATATAAAAT
1 AAATATAAAAT
*
2068059 AAAAATAAAA
1 AAATATAAAA
2068069 AACAGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 7 0.26
11 13 0.48
12 7 0.26
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:2069790 original size:90 final size:88
Alignment explanation
Indices: 2069632--2069889 Score: 397
Period size: 90 Copynumber: 3.0 Consensus size: 88
2069622 TCAATTCCCA
2069632 AAACACACCAATTCAGTTCTTGATAGATAGA-A-AGGTAGGTAGGTAGATTCATGCATACATATA
1 AAACACACCAATTCAGTTCTTGATAGATAGATAGAGGTAGGTAGGTAGATTCATGCATACATATA
2069695 GAAACAGTAAGCAATCCAAGATG
66 GAAACAGTAAGCAATCCAAGATG
*
2069718 AAACACACCAATTCAGTTCTTGATAGATAGATAGGTAGGTAGGTAGGTAGACTCATGCATACATA
1 AAACACACCAATTCAGTTCTTGATAGATAGATA-G-AGGTAGGTAGGTAGATTCATGCATACATA
*
2069783 TAGAAACAGTAAGCAATCCAAGATA
64 TAGAAACAGTAAGCAATCCAAGATG
* *
2069808 AAACACACCAATTCAGTTCTCGATAGATAGATAGA--TA---A-GTAGATTCATGCATACATAAA
1 AAACACACCAATTCAGTTCTTGATAGATAGATAGAGGTAGGTAGGTAGATTCATGCATACATATA
*
2069867 GAAACAGTAGGCAATCCAAGATG
66 GAAACAGTAAGCAATCCAAGATG
2069890 CTTGCTCTTC
Statistics
Matches: 161, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
82 40 0.25
83 1 0.01
86 33 0.20
87 1 0.01
88 1 0.01
89 1 0.01
90 84 0.52
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (88 bp):
AAACACACCAATTCAGTTCTTGATAGATAGATAGAGGTAGGTAGGTAGATTCATGCATACATATA
GAAACAGTAAGCAATCCAAGATG
Found at i:2070567 original size:29 final size:29
Alignment explanation
Indices: 2070525--2070583 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
2070515 CCTTAAAAAA
2070525 TTTGCTAAGAGAGTTCATACTACACAGCT
1 TTTGCTAAGAGAGTTCATACTACACAGCT
*
2070554 TTTGCTAAGAGAGTTCATATTACACAGCT
1 TTTGCTAAGAGAGTTCATACTACACAGCT
2070583 T
1 T
2070584 GCTCGTTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (29 bp):
TTTGCTAAGAGAGTTCATACTACACAGCT
Found at i:2075876 original size:22 final size:22
Alignment explanation
Indices: 2075851--2075910 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
2075841 TCTGTAAGAT
*
2075851 CTCCGAGCATGATTTCTAAAAC
1 CTCCGAGCATAATTTCTAAAAC
* *
2075873 CTCCGGGCATAATCTT-TAAGAC
1 CTCCGAGCATAAT-TTCTAAAAC
*
2075895 CTCTGAGCATAATTTC
1 CTCCGAGCATAATTTC
2075911 AATTCACGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (22 bp):
CTCCGAGCATAATTTCTAAAAC
Found at i:2076249 original size:22 final size:22
Alignment explanation
Indices: 2076212--2076274 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
2076202 GTCGATTCTG
* * * *
2076212 TAAGACCTACAGACATGATTTT
1 TAAGACCTCCAAACATAATCTT
*
2076234 TAATACCTCCAAACATAATCTT
1 TAAGACCTCCAAACATAATCTT
**
2076256 TAAGACCTCCGGACATAAT
1 TAAGACCTCCAAACATAAT
2076275 TTCGACTTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (22 bp):
TAAGACCTCCAAACATAATCTT
Found at i:2076252 original size:110 final size:110
Alignment explanation
Indices: 2076043--2076252 Score: 271
Period size: 110 Copynumber: 1.9 Consensus size: 110
2076033 TTTGACTTGC
* *
2076043 GATGTTGTCCCAATCAATTCTTTATTTTTTGACTTATGGTGTTATCTCAGTCGATTTTGTAAGAC
1 GATGTTGTCCCAATCAATTCTTTATTTTTTGACTTACGGTGTTATCTCAGTCGATTCTGTAAGAC
* * ****
2076108 CTCCGAGCATGATTTCTAAGACTTCCGGGTATAATTTCGATTCGT
66 CTCAGAGCATGATTTCTAAGACCTCCAAACATAATTTCGATTCGT
* * *
2076153 GATGTTGTCCTAATCAATTCTTTATTTTTTGACTTGCGGTGTTAT-TCTTGTCGATTCTGTAAGA
1 GATGTTGTCCCAATCAATTCTTTATTTTTTGACTTACGGTGTTATCTC-AGTCGATTCTGTAAGA
* *
2076217 CCTACAGA-CATGATTTTTAATACCTCCAAACATAAT
65 CCT-CAGAGCATGATTTCTAAGACCTCCAAACATAAT
2076253 CTTTAAGACC
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
109 2 0.02
110 80 0.94
111 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (110 bp):
GATGTTGTCCCAATCAATTCTTTATTTTTTGACTTACGGTGTTATCTCAGTCGATTCTGTAAGAC
CTCAGAGCATGATTTCTAAGACCTCCAAACATAATTTCGATTCGT
Found at i:2076329 original size:36 final size:36
Alignment explanation
Indices: 2076289--2076525 Score: 127
Period size: 36 Copynumber: 6.5 Consensus size: 36
2076279 ACTTATGATA
* *
2076289 TTGTCCCAGTTGATTTCATAATTTTGACTTGCAATG
1 TTGTCCCAATCGATTTCATAATTTTGACTTGCAATG
* * * ** * * *
2076325 TTGTCCTAGTCGTTTTTTTTACTTTTCAACTTGCGATG
1 TTGTCCCAATCG-ATTTCATAATTTT-GACTTGCAATG
* * * **
2076363 TTGTTCCAATCGATTTCATAATTTCGACTTACGGTG
1 TTGTCCCAATCGATTTCATAATTTTGACTTGCAATG
*
2076399 TTGTCCTAATCGATTTCATAATTTTGACTTG-AGATG
1 TTGTCCCAATCGATTTCATAATTTTGACTTGCA-ATG
* * ** * **
2076435 TTGTTCCGATC-ATTTTTTTTACTTTTTGACTTGCGGTG
1 TTGTCCCAATCGA--TTTCATA-ATTTTGACTTGCAATG
* * * * * * *
2076473 TTATTCCGATCGATTCCATAATTTCGACTTACAGTG
1 TTGTCCCAATCGATTTCATAATTTTGACTTGCAATG
*
2076509 TTGTCCCAATCGTTTTC
1 TTGTCCCAATCGATTTC
2076526 TTTACTATTA
Statistics
Matches: 147, Mismatches: 46, Indels: 16
0.70 0.22 0.08
Matches are distributed among these distances:
35 1 0.01
36 79 0.54
37 26 0.18
38 40 0.27
39 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.46
Consensus pattern (36 bp):
TTGTCCCAATCGATTTCATAATTTTGACTTGCAATG
Found at i:2076423 original size:110 final size:110
Alignment explanation
Indices: 2076269--2076525 Score: 338
Period size: 110 Copynumber: 2.3 Consensus size: 110
2076259 GACCTCCGGA
* * * * * *
2076269 CATAATTTCGACTTATGATATTGTCCCAGTTGATTTCATAATTTTGACTTGCA-ATGTTG-TCCT
1 CATAATTTCGACTTACGGTGTTGTCCCAATCGATTTCATAATTTTGACTTG-AGATGTTGTTCCG
* * *
2076332 AGTCGTTTTTTTTACTTTTCAACTTGCGATGTTGTTCCAATCGATTT
65 A-TCATTTTTTTTACTTTTCAACTTGCGATGTTATTCCAATCGATTC
*
2076379 CATAATTTCGACTTACGGTGTTGTCCTAATCGATTTCATAATTTTGACTTGAGATGTTGTTCCGA
1 CATAATTTCGACTTACGGTGTTGTCCCAATCGATTTCATAATTTTGACTTGAGATGTTGTTCCGA
** * *
2076444 TCATTTTTTTTACTTTTTGACTTGCGGTGTTATTCCGATCGATTC
66 TCATTTTTTTTACTTTTCAACTTGCGATGTTATTCCAATCGATTC
* *
2076489 CATAATTTCGACTTACAGTGTTGTCCCAATCGTTTTC
1 CATAATTTCGACTTACGGTGTTGTCCCAATCGATTTC
2076526 TTTACTATTA
Statistics
Matches: 128, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
109 1 0.01
110 123 0.96
111 4 0.03
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (110 bp):
CATAATTTCGACTTACGGTGTTGTCCCAATCGATTTCATAATTTTGACTTGAGATGTTGTTCCGA
TCATTTTTTTTACTTTTCAACTTGCGATGTTATTCCAATCGATTC
Found at i:2076472 original size:74 final size:74
Alignment explanation
Indices: 2076388--2076562 Score: 183
Period size: 74 Copynumber: 2.4 Consensus size: 74
2076378 TCATAATTTC
* * * * * * *
2076388 GACTTACGGTGTTGTCCTAATCGATTTCATAATTTTGACTT-GAGATGTTGTTCCGATCATTTTT
1 GACTTGCGGTGTTGTCCTAATCGATTCCATAATTTCGACTTACAG-TGTTGTCCCAATCATTTTC
* *
2076452 TTTACTTTTT
65 TTTACTATTA
* * *
2076462 GACTTGCGGTGTTATTCC-GATCGATTCCATAATTTCGACTTACAGTGTTGTCCCAATCGTTTTC
1 GACTTGCGGTGTT-GTCCTAATCGATTCCATAATTTCGACTTACAGTGTTGTCCCAATCATTTTC
2076526 TTTACTATTA
65 TTTACTATTA
* * *
2076536 AACTTGTGGTGTTGTCCTAATTGATTC
1 GACTTGCGGTGTTGTCCTAATCGATTC
2076563 TTTATTTCTC
Statistics
Matches: 81, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
73 3 0.04
74 73 0.90
75 5 0.06
ACGTcount: A:0.19, C:0.18, G:0.17, T:0.46
Consensus pattern (74 bp):
GACTTGCGGTGTTGTCCTAATCGATTCCATAATTTCGACTTACAGTGTTGTCCCAATCATTTTCT
TTACTATTA
Found at i:2077188 original size:29 final size:29
Alignment explanation
Indices: 2077125--2077241 Score: 94
Period size: 29 Copynumber: 4.0 Consensus size: 29
2077115 TTTCGAACAC
* *
2077125 TCCAAATCCTAAAACAAAACTCC-AAACCT
1 TCCAAACCCTAAAACAAAAC-CCTAAAACT
* *
2077154 TTCAAACCCTAAAACAAAACCCTAAATCT
1 TCCAAACCCTAAAACAAAACCCTAAAACT
** * * * *
2077183 TCCAAATTCTGAAACCAAACCTTAAAACC
1 TCCAAACCCTAAAACAAAACCCTAAAACT
* *
2077212 T-CAAACCCTAATATCGAAACCCTAAAACT
1 TCCAAACCCTAA-AACAAAACCCTAAAACT
2077241 T
1 T
2077242 TAAATCCTAA
Statistics
Matches: 68, Mismatches: 18, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
28 9 0.13
29 59 0.87
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.21
Consensus pattern (29 bp):
TCCAAACCCTAAAACAAAACCCTAAAACT
Found at i:2077232 original size:58 final size:57
Alignment explanation
Indices: 2077155--2077295 Score: 149
Period size: 58 Copynumber: 2.4 Consensus size: 57
2077145 TCCAAACCTT
* * * *
2077155 TCAAACCCTAAAACAAAACCCTAAATCTTCCAAATTCTGAAA-CCAAACCTTAAAACC
1 TCAAACCCTAAATCAAAACCCTAAAACTT-CAAATCCTAAAATCCAAACCTTAAAACC
* * **
2077212 TCAAACCCTAATATCGAAACCCTAAAACTTTAAATCCTAAAATTGAAACCTTAAAACC
1 TCAAACCCTAA-ATCAAAACCCTAAAACTTCAAATCCTAAAATCCAAACCTTAAAACC
* * *
2077270 TTAAATCCTAAAATCAAAACCATAAA
1 TCAAACCCT-AAATCAAAACCCTAAA
2077296 CCCTAAACCC
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
57 20 0.29
58 47 0.68
59 2 0.03
ACGTcount: A:0.49, C:0.27, G:0.02, T:0.22
Consensus pattern (57 bp):
TCAAACCCTAAATCAAAACCCTAAAACTTCAAATCCTAAAATCCAAACCTTAAAACC
Found at i:2077250 original size:29 final size:29
Alignment explanation
Indices: 2077199--2077309 Score: 125
Period size: 29 Copynumber: 3.9 Consensus size: 29
2077189 TTCTGAAACC
* * *
2077199 AAACCTTAAAACCTCAAACCCTAATATCG
1 AAACCTTAAAACCTTAAATCCTAAAATCG
* * *
2077228 AAACCCTAAAACTTTAAATCCTAAAATTG
1 AAACCTTAAAACCTTAAATCCTAAAATCG
*
2077257 AAACCTTAAAACCTTAAATCCTAAAATCA
1 AAACCTTAAAACCTTAAATCCTAAAATCG
* * *
2077286 AAACCAT-AAACCCTAAACCCTAAA
1 AAACCTTAAAACCTTAAATCCTAAA
2077310 TCTTAAACCT
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
28 15 0.22
29 54 0.78
ACGTcount: A:0.50, C:0.27, G:0.02, T:0.22
Consensus pattern (29 bp):
AAACCTTAAAACCTTAAATCCTAAAATCG
Found at i:2077252 original size:15 final size:15
Alignment explanation
Indices: 2077232--2077282 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
2077222 ATATCGAAAC
2077232 CCTAAAACTTTAAAT
1 CCTAAAACTTTAAAT
*
2077247 CCTAAAA-TTGAAA-
1 CCTAAAACTTTAAAT
*
2077260 CCTTAAAACCTTAAAT
1 CC-TAAAACTTTAAAT
2077276 CCTAAAA
1 CCTAAAA
2077283 TCAAAACCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 2 0.07
14 10 0.33
15 16 0.53
16 2 0.07
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (15 bp):
CCTAAAACTTTAAAT
Found at i:2077260 original size:21 final size:21
Alignment explanation
Indices: 2077236--2077275 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2077226 CGAAACCCTA
* *
2077236 AAACTTTAAATCCTAAAATTG
1 AAACCTTAAAACCTAAAATTG
*
2077257 AAACCTTAAAACCTTAAAT
1 AAACCTTAAAACCTAAAAT
2077276 CCTAAAATCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30
Consensus pattern (21 bp):
AAACCTTAAAACCTAAAATTG
Found at i:2077288 original size:21 final size:20
Alignment explanation
Indices: 2077264--2077324 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
2077254 TTGAAACCTT
2077264 AAAACCTTAAATCCTAAAATC
1 AAAACCTTAAA-CCTAAAATC
* **
2077285 AAAACCATAAACCCTAAACCC
1 AAAACCTTAAA-CCTAAAATC
* *
2077306 TAAATCTTAAACCTAAAAT
1 AAAACCTTAAACCTAAAAT
2077325 GAAACCATTA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
20 6 0.19
21 25 0.81
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAACCTTAAACCTAAAATC
Found at i:2077342 original size:42 final size:42
Alignment explanation
Indices: 2077260--2077367 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
2077250 AAAATTGAAA
* *
2077260 CCTTAAAACCTTAAATCCTAAAATCAAAACCATAAACCCTAAAC
1 CCTT-AAATCTTAAACCCTAAAATCAAAACCATAAACCCT-AAC
*
2077304 CC-TAAATCTTAAA-CCTAAAAT-GAAACCATTAAAGCCCTAAC
1 CCTTAAATCTTAAACCCTAAAATCAAAACCA-TAAA-CCCTAAC
*
2077345 CCTTAAAT-TGAAACCCTAAAATC
1 CCTTAAATCTTAAACCCTAAAATC
2077368 TTTGTCGTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
40 6 0.11
41 21 0.38
42 26 0.46
43 1 0.02
44 2 0.04
ACGTcount: A:0.47, C:0.28, G:0.03, T:0.22
Consensus pattern (42 bp):
CCTTAAATCTTAAACCCTAAAATCAAAACCATAAACCCTAAC
Found at i:2079104 original size:26 final size:24
Alignment explanation
Indices: 2079050--2079108 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
2079040 TAAAAAAATC
* * *
2079050 TTTTTTTGTGTTTTTTTGGTTTGT
1 TTTTTTTGTGTGTTTTTGATGTGT
*
2079074 CTTTTTTGTGTGTTTTTGCATGTG-
1 TTTTTTTGTGTGTTTTTG-ATGTGT
*
2079098 TATTTTTGTGT
1 TTTTTTTGTGT
2079109 TGGGTTTCTC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.03, C:0.03, G:0.22, T:0.71
Consensus pattern (24 bp):
TTTTTTTGTGTGTTTTTGATGTGT
Found at i:2079445 original size:10 final size:9
Alignment explanation
Indices: 2079430--2079470 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
2079420 AATCAGATAT
2079430 AGAAAAAAG
1 AGAAAAAAG
2079439 CAGAAAAAAG
1 -AGAAAAAAG
*
2079449 A-AAAAAAA
1 AGAAAAAAG
2079457 AGAAAAAAG
1 AGAAAAAAG
2079466 A-AAAA
1 AGAAAA
2079471 TATATAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 11 0.39
9 8 0.29
10 9 0.32
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:2079452 original size:17 final size:17
Alignment explanation
Indices: 2079430--2079470 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2079420 AATCAGATAT
**
2079430 AGAAAAAAGCAGAAAAA
1 AGAAAAAAAAAGAAAAA
2079447 AGAAAAAAAAAGAAAAA
1 AGAAAAAAAAAGAAAAA
2079464 AGAAAAA
1 AGAAAAA
2079471 TATATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAGAAAAA
Found at i:2079482 original size:3 final size:3
Alignment explanation
Indices: 2079469--2079511 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
2079459 AAAAAAGAAA
2079469 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2079512 TTTAAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2079684 original size:22 final size:22
Alignment explanation
Indices: 2079651--2079706 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
2079641 CTGAAATCCA
* *
2079651 AAAATCTCAAATCTCAAATC-TT
1 AAAATCTAAAATC-CAAAACTTT
2079673 -AAATCCTAAAATCCAAAACTTT
1 AAAAT-CTAAAATCCAAAACTTT
2079695 AAAATCTAAAAT
1 AAAATCTAAAAT
2079707 TCTAAAAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 9 0.31
22 16 0.55
23 4 0.14
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATCTAAAATCCAAAACTTT
Found at i:2079712 original size:15 final size:15
Alignment explanation
Indices: 2079651--2079713 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
2079641 CTGAAATCCA
*
2079651 AAAATCTCAAA-TCT
1 AAAATCTAAAATTCT
* * *
2079665 CAAATCTTAAATCCT
1 AAAATCTAAAATTCT
*
2079680 AAAATCCAAAACTT-T
1 AAAATCTAAAA-TTCT
2079695 AAAATCTAAAATTCT
1 AAAATCTAAAATTCT
2079710 AAAA
1 AAAA
2079714 ACCCTAAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
14 11 0.29
15 26 0.68
16 1 0.03
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATCTAAAATTCT
Found at i:2081141 original size:22 final size:21
Alignment explanation
Indices: 2081104--2081161 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
2081094 AAAGGAAAAA
2081104 AAATAAAACAAAAATAAAATG
1 AAATAAAACAAAAATAAAATG
*
2081125 AAATAAAGATAAAAATAAAATG
1 AAATAAA-ACAAAAATAAAATG
*
2081147 AAGTAAAAACAAAAA
1 AAAT-AAAACAAAAA
2081162 GAAACAATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.22
22 22 0.69
23 3 0.09
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (21 bp):
AAATAAAACAAAAATAAAATG
Found at i:2091427 original size:79 final size:79
Alignment explanation
Indices: 2091296--2091454 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
2091286 AACAACATAG
2091296 ACGTTGATCCATTTACCATACCAGAATTTTATCCTTGCTCCATCCATGCATAGAGAAGAAAACTA
1 ACGTTGATCCATTTACCATACCAGAATTTTATCCTTGCTCCATCCATGCATAGAGAAGAAAACTA
2091361 GAAATAATAAGATT
66 GAAATAATAAGATT
*
2091375 ACGTTGATCCATTTACCATACCAGAATTTTATCCTTGCTCCGTCCATGCATAGAGAAGAAAACTA
1 ACGTTGATCCATTTACCATACCAGAATTTTATCCTTGCTCCATCCATGCATAGAGAAGAAAACTA
2091440 GAAATAATAAGATT
66 GAAATAATAAGATT
2091454 A
1 A
2091455 GAATTTCTTT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (79 bp):
ACGTTGATCCATTTACCATACCAGAATTTTATCCTTGCTCCATCCATGCATAGAGAAGAAAACTA
GAAATAATAAGATT
Found at i:2105009 original size:31 final size:32
Alignment explanation
Indices: 2104974--2105043 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
2104964 ATTTCCAGAA
*
2104974 TCCGGCGAA-AATTCCGGCGAA-ATTTGAATTT
1 TCCGGCGAACAATTCCGGCGAACA-TTGAAGTT
*
2105005 TCCGGC-AACAATTCCGGTGAACATTGAAGTT
1 TCCGGCGAACAATTCCGGCGAACATTGAAGTT
2105036 TCCGGCGA
1 TCCGGCGA
2105044 CCAGTCCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 30 0.88
32 2 0.06
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (32 bp):
TCCGGCGAACAATTCCGGCGAACATTGAAGTT
Found at i:2105121 original size:19 final size:20
Alignment explanation
Indices: 2105096--2105141 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2105086 TCCGGCCAAC
2105096 ATCCGGCG-AAATCTCCAGA
1 ATCCGGCGAAAATCTCCAGA
* *
2105115 TTCCGGCGAAAATTTCCAGA
1 ATCCGGCGAAAATCTCCAGA
2105135 ATCCGGC
1 ATCCGGC
2105142 ACCGGTGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (20 bp):
ATCCGGCGAAAATCTCCAGA
Found at i:2105743 original size:59 final size:58
Alignment explanation
Indices: 2105593--2105868 Score: 385
Period size: 59 Copynumber: 4.7 Consensus size: 58
2105583 AAAAAATTCC
* *
2105593 AAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCA
* *
2105651 AAAAAAATATTTTCGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATTTTCA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTCA
*
2105710 AAAAAAATATTTTCGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCA
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTCA
*** *
2105769 AAAAAAGGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTC-
1 AAAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTCA
* *
2105829 CAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
2105869 TCCTACAAAA
Statistics
Matches: 197, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
58 50 0.25
59 98 0.50
60 42 0.21
61 4 0.02
62 3 0.02
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.33
Consensus pattern (58 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCA
Found at i:2105851 original size:119 final size:115
Alignment explanation
Indices: 2105589--2105868 Score: 384
Period size: 119 Copynumber: 2.4 Consensus size: 115
2105579 AAATAAAAAA
2105589 TTCCAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAA
1 TTCC-AAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAA
* *
2105654 AAAATATTTTCGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATT
64 AAAAGATTTTCGAGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATT
* * *
2105706 TTCAAAAAAAATATTTTCGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAA
1 TTC-CAAAAAATATTTT-TGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAA
* * *
2105771 AAAAGGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT-TGAAAATCGAAA-T
64 AAAA--GATTTTCGAGGAAAAGTTGAAAGTATCAATTTTCCTCAG-AAAT--AAATT
2105826 TTCCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTT
1 TTCCAAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTT
2105869 TCCTACAAAA
Statistics
Matches: 145, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
117 64 0.44
118 4 0.03
119 70 0.48
120 4 0.03
121 3 0.02
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.34
Consensus pattern (115 bp):
TTCCAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAA
AAGATTTTCGAGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAATAAATT
Found at i:2106759 original size:15 final size:15
Alignment explanation
Indices: 2106739--2106767 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2106729 ATAGGGAAGG
2106739 AAAAAAAATTTTGAA
1 AAAAAAAATTTTGAA
2106754 AAAAAAAATTTTGA
1 AAAAAAAATTTTGA
2106768 GCAAACTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (15 bp):
AAAAAAAATTTTGAA
Found at i:2106959 original size:22 final size:22
Alignment explanation
Indices: 2106934--2106978 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2106924 AACAAAAGTC
* *
2106934 AAAAAATCGAAATTG-TGAAGAA
1 AAAAAAGCAAAATTGATG-AGAA
2106956 AAAAAAGCAAAATTGATGAGAA
1 AAAAAAGCAAAATTGATGAGAA
2106978 A
1 A
2106979 TGAGCAGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.62, C:0.04, G:0.18, T:0.16
Consensus pattern (22 bp):
AAAAAAGCAAAATTGATGAGAA
Found at i:2107232 original size:35 final size:35
Alignment explanation
Indices: 2107193--2107259 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
2107183 GTATTTTTGA
*
2107193 AAAAGACATTTGCATTTCATGTGCATCATTTTAAG
1 AAAAGACATTTGCATTTCATGTACATCATTTTAAG
* *
2107228 AAAAGACATTTGCATTTTATTTACATCATTTT
1 AAAAGACATTTGCATTTCATGTACATCATTTT
2107260 TATCATTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (35 bp):
AAAAGACATTTGCATTTCATGTACATCATTTTAAG
Found at i:2107261 original size:36 final size:35
Alignment explanation
Indices: 2107185--2107261 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
2107175 TAGGAATGGT
* *
2107185 ATTTTTGAAAAAGACATTTGCATTTCATGTGCATC
1 ATTTTTAAAAAAGACATTTGCATTTCATGTACATC
* *
2107220 A-TTTTAAGAAAAGACATTTGCATTTTATTTACATC
1 ATTTTTAA-AAAAGACATTTGCATTTCATGTACATC
2107255 ATTTTTA
1 ATTTTTA
2107262 TCATTTTGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 5 0.14
35 26 0.72
36 5 0.14
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (35 bp):
ATTTTTAAAAAAGACATTTGCATTTCATGTACATC
Found at i:2107977 original size:137 final size:136
Alignment explanation
Indices: 2107546--2108086 Score: 572
Period size: 137 Copynumber: 4.0 Consensus size: 136
2107536 GTGACATTTG
* * * * * * *
2107546 AGTATTAAAATATGAATTTTATTTTCTTGATGGTGATATTCAAGACATTTTAAAAAACACTTGGT
1 AGTATTAAAGTATGAATTTTATTTTCTTGATGGTGATATCCAAGACATTATCAAAATCACTCGAT
* * * ** * * * *
2107611 GGTGAAATTCGAATTTATGGTTTGAATTTGTATTCTTTCTCTATATTTGCATTTTCTTTATAGTG
66 GGTGATATCCGAGTTTAAAGTTTGAATTTGCATTCTTTCTCTACATTTGCATTTTCTTAATGGTG
2107676 ATATCC
131 ATATCC
** * * *
2107682 AAGTATTAAAGTATGAA-TTT-TTTTAAT-AT--TGATATTCAATACATTTTCAAAATCACTCGA
1 -AGTATTAAAGTATGAATTTTATTTTCTTGATGGTGATATCCAAGACATTATCAAAATCACTCGA
* ** * ***
2107742 TGGTGATATCCTAGTTTAAAGTTTGAATTTGTTTTTTTTTCTCTACATTTGCATTTTCTGGGTGG
65 TGGTGATATCCGAGTTTAAAGTTTGAATTTG-CATTCTTTCTCTACATTTGCATTTTCTTAATGG
*
2107807 TGATATCTA
129 TGATATC-C
* * * * * * * *
2107816 AGTATTAAAGTAGGAATTTCATTTTCTTGGTGGTGATAGCCAATACATTATCGAAATCATTCAAT
1 AGTATTAAAGTATGAATTTTATTTTCTTGATGGTGATATCCAAGACATTATCAAAATCACTCGAT
* * * *
2107881 GGTGGTATTCGAGTTTAAAGTTTAAATTTGCATTCTTTCTCTATATTTGCATTTTCTTAATGGTG
66 GGTGATATCCGAGTTTAAAGTTTGAATTTGCATTCTTTCTCTACATTTGCATTTTCTTAATGGTG
2107946 ATATCC
131 ATATCC
*
2107952 GGTTATTAAAGTATGAATTTTATTTTCTT-AGTGGTGATATCCAAGACATTATCAAAATCACTCG
1 AG-TATTAAAGTATGAATTTTATTTTCTTGA-TGGTGATATCCAAGACATTATCAAAATCACTCG
* * * * *
2108016 GTGGTGATATCCAAGTTTAAAGTTTGAATTTGCATTCTTTCTCTACATTTACATTTTCTCAATGA
64 ATGGTGATATCCGAGTTTAAAGTTTGAATTTGCATTCTTTCTCTACATTTGCATTTTCTTAATGG
2108081 TGATAT
129 TGATAT
2108087 TCGAGTTTCC
Statistics
Matches: 332, Mismatches: 63, Indels: 18
0.80 0.15 0.04
Matches are distributed among these distances:
132 51 0.15
133 48 0.14
134 4 0.01
135 10 0.03
136 5 0.02
137 162 0.49
138 52 0.16
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (136 bp):
AGTATTAAAGTATGAATTTTATTTTCTTGATGGTGATATCCAAGACATTATCAAAATCACTCGAT
GGTGATATCCGAGTTTAAAGTTTGAATTTGCATTCTTTCTCTACATTTGCATTTTCTTAATGGTG
ATATCC
Found at i:2108371 original size:99 final size:99
Alignment explanation
Indices: 2108070--2108429 Score: 339
Period size: 99 Copynumber: 3.6 Consensus size: 99
2108060 ACATTTACAT
* ** * * *
2108070 TTTCTCAATGATGATATTCGAGTTTCCTTCGGTGACGATATCCGAAGTTATTTACATCTTT-TCG
1 TTTCTCAATGATGATATTTGAGTTTCCTTCGGTGGTGATATCTGAAGTCATTTGCAT-TTTCTCG
* *
2108134 ATGGTGATATCTGAGTATTAAAGCTTGAATTGTAT
65 GTGGTGATATCTGAGTATTAAAGCTTGAATTGTAA
* * * * * * * * *
2108169 TTTTTCGATAATGATA-TTCAGGTTTCCTTCAGTGGTGACATCTGAAGTCATTTGTATATTCTCA
1 TTTCTCAATGATGATATTTGA-GTTTCCTTCGGTGGTGATATCTGAAGTCATTTGCATTTTCTCG
* * * *
2108233 GTGGTGATATCTAAGTGTTAAAGCTTGAATTGCAT
65 GTGGTGATATCTGAGTATTAAAGCTTGAATTGTAA
* * * * *
2108268 TTTCTTAATGGTGATATTTGAGTTTCCGTCGGTGGTGATATATGAAATCATTTGCATTTTCTCGG
1 TTTCTCAATGATGATATTTGAGTTTCCTTCGGTGGTGATATCTGAAGTCATTTGCATTTTCTCGG
* * *
2108333 TGGTGATATTTGAGTATTAAAGCTTGAAATATAA
66 TGGTGATATCTGAGTATTAAAGCTTGAATTGTAA
* * * * * * *
2108367 TTTCTCGAT-AGGGATATTTGAGTTTTCTTGGGGTGGAGATATCCGAAGTCATTTGTATTTTCT
1 TTTCTCAATGA-TGATATTTGAGTTTCCTT-CGGTGGTGATATCTGAAGTCATTTGCATTTTCT
2108430 TGATGGCGAT
Statistics
Matches: 204, Mismatches: 52, Indels: 9
0.77 0.20 0.03
Matches are distributed among these distances:
98 4 0.02
99 170 0.83
100 30 0.15
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.42
Consensus pattern (99 bp):
TTTCTCAATGATGATATTTGAGTTTCCTTCGGTGGTGATATCTGAAGTCATTTGCATTTTCTCGG
TGGTGATATCTGAGTATTAAAGCTTGAATTGTAA
Found at i:2108595 original size:49 final size:50
Alignment explanation
Indices: 2108490--2108616 Score: 195
Period size: 49 Copynumber: 2.6 Consensus size: 50
2108480 GATGGTTCAA
* * *
2108490 TTTAAAGTTGTTGAGCCTTTACTTAGAGAAACTTTTTTCAAGATGAAATT
1 TTTAAAGTTGTTGAGCCTCTACTTAGAAAAACTTTTTTCAAGATGAAAAT
*
2108540 TTTAAAGTTGTTAAGCCTCTACTTA-AAAAAGC-TTTTTCAAGATGAAAAT
1 TTTAAAGTTGTTGAGCCTCTACTTAGAAAAA-CTTTTTTCAAGATGAAAAT
2108589 TTTAAAGTTGTTGAGCCTCTACTTAGAA
1 TTTAAAGTTGTTGAGCCTCTACTTAGAA
2108617 GAGCCCTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
49 44 0.63
50 26 0.37
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (50 bp):
TTTAAAGTTGTTGAGCCTCTACTTAGAAAAACTTTTTTCAAGATGAAAAT
Found at i:2108822 original size:3 final size:3
Alignment explanation
Indices: 2108814--2108859 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
2108804 GACACTCATT
*
2108814 TTA TTA TTA TTT TTA TT- TT- TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2108859 T
1 T
2108860 GCTTTATCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:2108836 original size:19 final size:19
Alignment explanation
Indices: 2108812--2108849 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2108802 TAGACACTCA
*
2108812 TTTTATTATTATTTTTATT
1 TTTTATTATTATTATTATT
2108831 TTTTATTATTATTATTATT
1 TTTTATTATTATTATTATT
2108850 ATTATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTATTATTATTATTATT
Found at i:2109743 original size:21 final size:21
Alignment explanation
Indices: 2109695--2109754 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
2109685 TGGCTCAAGG
*
2109695 AAATTTTTTTTTTATT-TTTT
1 AAATTTTATTTTTATTATTTT
*
2109715 -AATATTATTTTTATTATTTT
1 AAATTTTATTTTTATTATTTT
* *
2109735 AAATTTTATTATTAGTATTT
1 AAATTTTATTTTTATTATTT
2109755 ATACATGTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 13 0.39
20 4 0.12
21 16 0.48
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
AAATTTTATTTTTATTATTTT
Found at i:2113544 original size:33 final size:31
Alignment explanation
Indices: 2113501--2113573 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
2113491 AACGCCAGAA
*
2113501 ATTTAATATTATAAATAAAAATGATAATTTATAT
1 ATTT-ATATTAT-AA-AAAAATAATAATTTATAT
* *
2113535 ATTTATATTATAAAATATTAATAATTTATAT
1 ATTTATATTATAAAAAAATAATAATTTATAT
2113566 ATTTATAT
1 ATTTATAT
2113574 GATATTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.64
32 2 0.06
33 7 0.19
34 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTATATTATAAAAAAATAATAATTTATAT
Found at i:2113713 original size:22 final size:22
Alignment explanation
Indices: 2113672--2113714 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2113662 ATTTAAATTG
*
2113672 TATTATTTTTTATTTTTATTTT
1 TATTATTTTTTATTTATATTTT
2113694 TATTA-TTTTTATGTTATATTT
1 TATTATTTTTTAT-TTATATTT
2113715 AAAATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (22 bp):
TATTATTTTTTATTTATATTTT
Found at i:2114486 original size:15 final size:15
Alignment explanation
Indices: 2114468--2114507 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
2114458 TTAATAATTT
2114468 TTTTTAAAATATTAA
1 TTTTTAAAATATTAA
* *
2114483 TTTTTTATATATTAA
1 TTTTTAAAATATTAA
2114498 TTTTTAAAAT
1 TTTTTAAAAT
2114508 TAATATTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTAAAATATTAA
Found at i:2114555 original size:24 final size:23
Alignment explanation
Indices: 2114511--2114581 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 23
2114501 TTAAAATTAA
*
2114511 TATTTATTTATTAATAAAATATAAT
1 TATTTATTTACTAAT--AATATAAT
2114536 TATTTAATTTACTAATAATAT-AT
1 TATTT-ATTTACTAATAATATAAT
*
2114559 TAAATTTATATACTAATAATATA
1 T--ATTTATTTACTAATAATATA
2114582 TTAAATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
23 3 0.08
24 19 0.47
25 9 0.22
26 9 0.22
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTTATTTACTAATAATATAAT
Found at i:2114561 original size:19 final size:22
Alignment explanation
Indices: 2114545--2114590 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
2114535 TTATTTAATT
2114545 TACTAATAATATATTAAATTTATA
1 TACTAATAATATATT-AA-TTATA
*
2114569 TACTAATAATATATTAAATATA
1 TACTAATAATATATTAATTATA
2114591 ATTTCTGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 2 0.10
24 15 0.71
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
TACTAATAATATATTAATTATA
Found at i:2115148 original size:2 final size:2
Alignment explanation
Indices: 2115141--2115170 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2115131 AAAACAATGC
*
2115141 CT CT CT CT CT CT CT CT CT CT AT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2115171 TAAGAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.