Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_pilon, 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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 37
Found at i:3921429 original size:22 final size:22
Alignment explanation
Indices: 3921402--3921443 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
3921392 CCCATATGAT
3921402 ATACCCAAACATTTAATTTGGG
1 ATACCCAAACATTTAATTTGGG
3921424 ATACCCAAACATTTAATTTG
1 ATACCCAAACATTTAATTTG
3921444 ATAACGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
ATACCCAAACATTTAATTTGGG
Found at i:3921456 original size:21 final size:21
Alignment explanation
Indices: 3921402--3921456 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
3921392 CCCATATGAT
*
3921402 ATACCCAAACATTTAATTTGGG
1 ATACCAAAACATTTAATTT-GG
*
3921424 ATACCCAAACATTTAATTT-G
1 ATACCAAAACATTTAATTTGG
*
3921444 ATAACGAAAACAT
1 AT-ACCAAAACAT
3921457 CAAATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 3 0.10
21 8 0.27
22 19 0.63
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (21 bp):
ATACCAAAACATTTAATTTGG
Found at i:3922195 original size:22 final size:22
Alignment explanation
Indices: 3922168--3922209 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
3922158 CCCATATGAT
3922168 ATACCCAAACATTTAATTTGGG
1 ATACCCAAACATTTAATTTGGG
3922190 ATACCCAAACATTTAATTTG
1 ATACCCAAACATTTAATTTG
3922210 ATAACGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
ATACCCAAACATTTAATTTGGG
Found at i:3922222 original size:21 final size:21
Alignment explanation
Indices: 3922168--3922222 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
3922158 CCCATATGAT
*
3922168 ATACCCAAACATTTAATTTGGG
1 ATACCAAAACATTTAATTT-GG
*
3922190 ATACCCAAACATTTAATTT-G
1 ATACCAAAACATTTAATTTGG
*
3922210 ATAACGAAAACAT
1 AT-ACCAAAACAT
3922223 CAAATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 3 0.10
21 8 0.27
22 19 0.63
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (21 bp):
ATACCAAAACATTTAATTTGG
Found at i:3922988 original size:75 final size:76
Alignment explanation
Indices: 3922899--3923066 Score: 229
Period size: 75 Copynumber: 2.3 Consensus size: 76
3922889 TCCATGTGAG
* ** *
3922899 TTTTTTTTT-TAATTTATTAAAAATTTCTACGAGTTTCATATAACTTTTAACTTCGAAATTTTAA
1 TTTTTTTTTCAAATTTATTAAAAATTTCTAAAAGTTTCATATAACTTTTAACTTCAAAATTTTAA
3922963 AA-ATTTAATA
66 AATATTTAATA
* * *
3922973 TTTTTTTTTCAAATTTATTAAAAATTTGTAAAAGTTTCATATTATTTTTAACTTCAAAATTTTAA
1 TTTTTTTTTCAAATTTATTAAAAATTTCTAAAAGTTTCATATAACTTTTAACTTCAAAATTTTAA
*
3923038 AATTTTTAATA
66 AATATTTAATA
3923049 ---TTTTTTCAAATTTATTAA
1 TTTTTTTTTCAAATTTATTAA
3923067 TTACATTAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
73 18 0.21
74 9 0.11
75 50 0.60
76 7 0.08
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.54
Consensus pattern (76 bp):
TTTTTTTTTCAAATTTATTAAAAATTTCTAAAAGTTTCATATAACTTTTAACTTCAAAATTTTAA
AATATTTAATA
Found at i:3925489 original size:6 final size:6
Alignment explanation
Indices: 3925475--3925519 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
3925465 CTTTATTCGA
* *
3925475 TTTTCC TTTTTC TTTTT- TTTTTC TTTTTC TTCTTC TTCTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTT
3925520 GCTGGATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 5 0.15
6 24 0.71
7 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:3925500 original size:17 final size:19
Alignment explanation
Indices: 3925475--3925519 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
3925465 CTTTATTCGA
*
3925475 TTTTCCTTTTTCTT-TT-T
1 TTTTTCTTTTTCTTCTTCT
3925492 TTTTTCTTTTTCTTCTTCT
1 TTTTTCTTTTTCTTCTTCT
*
3925511 TCTTTCTTT
1 TTTTTCTTT
3925520 GCTGGATGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 13 0.54
18 2 0.08
19 9 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTTCTTCTTCT
Found at i:3926724 original size:1 final size:1
Alignment explanation
Indices: 3926718--3926744 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
3926708 CAGGAAATGG
3926718 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
3926745 AGACTGAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3927919 original size:14 final size:14
Alignment explanation
Indices: 3927886--3927937 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3927876 TATGACATAA
* *
3927886 AAATGCAAAGATGCC
1 AAATGTAAAAATG-C
* *
3927901 AAATGTAGATATGC
1 AAATGTAAAAATGC
*
3927915 AAATGTAAAAATGT
1 AAATGTAAAAATGC
3927929 AAATGTAAA
1 AAATGTAAA
3927938 TACAAACGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
14 21 0.68
15 10 0.32
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (14 bp):
AAATGTAAAAATGC
Found at i:3929405 original size:33 final size:32
Alignment explanation
Indices: 3929363--3929437 Score: 109
Period size: 31 Copynumber: 2.3 Consensus size: 32
3929353 TGAATATAAT
3929363 AAATAAATAAAATAAAAATATATATATATAAAAA
1 AAAT-AATAAAATAAAAATATATATATA-AAAAA
*
3929397 AAATAAT--AATAATAATATATATATAAAAAA
1 AAATAATAAAATAAAAATATATATATAAAAAA
3929427 AAATAATAAAA
1 AAATAATAAAA
3929438 AATTTGAAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
30 12 0.32
31 17 0.45
32 2 0.05
33 3 0.08
34 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (32 bp):
AAATAATAAAATAAAAATATATATATAAAAAA
Found at i:3929424 original size:27 final size:26
Alignment explanation
Indices: 3929355--3929435 Score: 94
Period size: 25 Copynumber: 3.1 Consensus size: 26
3929345 TTAATTCTTG
* * *
3929355 AATATAATAAATAAATAAAATAAAAAT
1 AATAT-ATATATAAAAAAAATAATAAT
3929382 -ATATATATATAAAAAAAATAATAAT
1 AATATATATATAAAAAAAATAATAAT
3929407 AATAATATATATATAAAAAAA-AATAAT
1 AAT-ATATATATA-AAAAAAATAATAAT
3929434 AA
1 AA
3929436 AAAATTTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 18 0.38
26 6 0.12
27 17 0.35
28 7 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (26 bp):
AATATATATATAAAAAAAATAATAAT
Found at i:3930526 original size:10 final size:10
Alignment explanation
Indices: 3930511--3930543 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3930501 AAATTCAGAT
3930511 AATAAATTAA
1 AATAAATTAA
3930521 AATAAATTAA
1 AATAAATTAA
3930531 AA-AAATATAA
1 AATAAAT-TAA
3930541 AAT
1 AAT
3930544 CGGTGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AATAAATTAA
Found at i:3930957 original size:13 final size:13
Alignment explanation
Indices: 3930939--3930963 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3930929 CCGTATTCCG
3930939 CCGCCGGCCACCT
1 CCGCCGGCCACCT
3930952 CCGCCGGCCACC
1 CCGCCGGCCACC
3930964 GTAACGGTGG
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:0.08, C:0.64, G:0.24, T:0.04
Consensus pattern (13 bp):
CCGCCGGCCACCT
Found at i:3931745 original size:3 final size:3
Alignment explanation
Indices: 3931643--3931733 Score: 112
Period size: 3 Copynumber: 29.7 Consensus size: 3
3931633 ATTTATAAAT
*
3931643 ATA ATA ATA TATA ATA ATA ATA TATA ATA TTA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* * *
3931690 ATAA ATA ATT ATA ATT ATA ATA A-A ATA ATA CTA ATA ATA ATA AT
1 AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3931734 TTTTAATAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.03
3 65 0.86
4 9 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:3931745 original size:19 final size:18
Alignment explanation
Indices: 3931637--3931745 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
3931627 GTAATTATTT
*
3931637 ATAAATATAATAATATATA
1 ATAATTATAATAATA-ATA
* *
3931656 ATAATAATATATAATATTA
1 ATAATTATA-ATAATAATA
*
3931675 ATAATAATAATAATAATAA
1 ATAATTATAATAATAAT-A
*
3931694 ATAATTATAATTATAATA
1 ATAATTATAATAATAATA
* *
3931712 A-AATAATACTAATAATA
1 ATAATTATAATAATAATA
*
3931729 ATAATTTTTAATAATAA
1 ATAA-TTATAATAATAA
3931746 ATTTAAATGA
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
17 14 0.19
18 11 0.15
19 43 0.58
20 6 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATTATAATAATAATA
Found at i:3932015 original size:75 final size:75
Alignment explanation
Indices: 3931871--3932053 Score: 293
Period size: 75 Copynumber: 2.5 Consensus size: 75
3931861 GATGGAAATG
* * *
3931871 TTTGAAAACATCATGCACTGAAGGACTTACAG--GACCCGAAGGTTTTGAAAACATCTAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
3931934 CTCGAAGGCT
66 CCCGAAGGCT
3931944 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT-AAGAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAA-AACATCAAAAAGC
3932008 TCCCGAAGGCT
65 TCCCGAAGGCT
3932019 TTTGGAAACATCATGCACTGAAGGACTTAC-GATGA
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA
3932054 AGGAAATAGT
Statistics
Matches: 103, Mismatches: 4, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
73 31 0.30
74 7 0.07
75 65 0.63
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (75 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCT
Found at i:3932443 original size:88 final size:84
Alignment explanation
Indices: 3932285--3932479 Score: 304
Period size: 88 Copynumber: 2.3 Consensus size: 84
3932275 TTTCTTCAGA
3932285 AGTTCTTCTCATTATGAACTTTCCGCTGGGATGAGACCTATTTCCTGTGATAGAGTCATTCAAAA
1 AGTTCTTCTCATTATGAACTTTCCGCTGGGATGAGACCTATTTCCTGTGATAGAGTCATTCAAAA
3932350 AGTTGAATAAGCTCTTGATG
66 AGTTG-ATAAGCTCTTGATG
*
3932370 AG-TCTTCTCATTATGAACTTTCCGCTGGGATGATGATGACCTCCTTT-CTGTGATAGAGTCATT
1 AGTTCTTCTCATTATGAACTTTCCGCT-GG--GATGA-GACCT-ATTTCCTGTGATAGAGTCATT
*
3932433 CAAAAGGTTGATAAGCTCTTGATG
61 CAAAAAGTTGATAAGCTCTTGATG
3932457 AGTTCTTCTCATTATGAACTTTC
1 AGTTCTTCTCATTATGAACTTTC
3932480 TCTTCCTTCT
Statistics
Matches: 102, Mismatches: 2, Indels: 9
0.90 0.02 0.08
Matches are distributed among these distances:
84 24 0.24
85 4 0.04
87 21 0.21
88 50 0.49
89 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37
Consensus pattern (84 bp):
AGTTCTTCTCATTATGAACTTTCCGCTGGGATGAGACCTATTTCCTGTGATAGAGTCATTCAAAA
AGTTGATAAGCTCTTGATG
Found at i:3932699 original size:109 final size:112
Alignment explanation
Indices: 3932506--3932764 Score: 393
Period size: 110 Copynumber: 2.3 Consensus size: 112
3932496 AATATCAAAC
* *
3932506 AAAGGTGAACAAGCTCTTCTCATTATGAA-CTCCTTCTTCCTTCTTCAGATGAGTCTTTTCATTC
1 AAAGTTGAACAAGTTCTTCTCATTATGAACCT-CTTCTTCC-TCTTCAGATGAGTCTTTTCATTC
* * *
3932570 ATGAACTTTCTCTGGCAATGTTGATCCATCAGATGATGAA-TTAAACAA
64 ATGAACCTTCTCTGGCAATGTTGATCCATCAAATAATGAATTTAAACAA
3932618 AAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTT-C-CTTCAGATGAGTTCTTTTCATT-A
1 AAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTCTTCAGATGAG-TCTTTTCATTCA
*
3932680 TGAACCTTCTCTGGTAATGTTGATCCATCAAATAATGAATTTAAACAA
65 TGAACCTTCTCTGGCAATGTTGATCCATCAAATAATGAATTTAAACAA
*
3932728 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
1 AAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCT
3932765 GATATGTTGA
Statistics
Matches: 137, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
109 47 0.34
110 54 0.39
111 1 0.01
112 33 0.24
113 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (112 bp):
AAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCCTCTTCAGATGAGTCTTTTCATTCAT
GAACCTTCTCTGGCAATGTTGATCCATCAAATAATGAATTTAAACAA
Found at i:3932775 original size:72 final size:73
Alignment explanation
Indices: 3932666--3932836 Score: 301
Period size: 72 Copynumber: 2.4 Consensus size: 73
3932656 CCTTCAGATG
* *
3932666 AGTTCTTTTCATTATGAACCTTC-TCTGGTAATGTTGATCCATCAAATAATGAATTTAAACAAAA
1 AGTTCTTCTCATTATGAA-CTTCTTCTGATAATGTTGATCCATCAAATAATGAATTTAAACAAAA
3932730 AGTTGAACA
65 AGTTGAACA
3932739 AGTTCTTCTCATTATGAACTTCTTCTGAT-ATGTTGATCCATCAAATAATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACTTCTTCTGATAATGTTGATCCATCAAATAATGAATTTAAACAAAAA
3932803 GTTGAACA
66 GTTGAACA
3932811 AGTTCTTCTCATTATGAACTTCTTCT
1 AGTTCTTCTCATTATGAACTTCTTCT
3932837 TCTTCAGATG
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
72 73 0.77
73 22 0.23
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACTTCTTCTGATAATGTTGATCCATCAAATAATGAATTTAAACAAAAA
GTTGAACA
Found at i:3932875 original size:181 final size:179
Alignment explanation
Indices: 3932587--3932943 Score: 626
Period size: 181 Copynumber: 2.0 Consensus size: 179
3932577 TTCTCTGGCA
* *
3932587 ATGTTGATCCATCAGATGATGAATTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCT
1 ATGTTGATCCATCAAATAATGAATTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCT
* *
3932652 TCTTCCTTCAGATGAGTTCTTTTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATAATG
66 TCTTCCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAAT--GG
3932717 AATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTGAT
129 AATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTGAT
*
3932768 ATGTTGATCCATCAAATAATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTC
1 ATGTTGATCCATCAAATAATGAA-TTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTC
*
3932833 TTCTT-CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGGA
65 TTCTTCCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGGA
3932897 ATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
130 ATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
3932944 TCCTTCTTCA
Statistics
Matches: 169, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
179 49 0.29
181 75 0.44
182 45 0.27
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (179 bp):
ATGTTGATCCATCAAATAATGAATTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCT
TCTTCCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGGAA
TTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTGAT
Found at i:3933011 original size:291 final size:291
Alignment explanation
Indices: 3932506--3933055 Score: 876
Period size: 291 Copynumber: 1.9 Consensus size: 291
3932496 AATATCAAAC
*
3932506 AAAGGTGAACAAGCTCTTCTCATTATGAACTCCTTCTTCCTTCTTCAGATGAGTCTTTTCATTCA
1 AAAGGTGAACAAGCTCTTCTCATTATGAA--CCTTCTTCCTTCTTCAGATGAGTCTTCTCATTCA
*
3932571 TGAACTTTCTCTGGCAATGTTGATCCATCAGATGATGAATTAAACAAAAAGTTGAACAAGTTCTT
64 TGAACTTTCTCTGGCAATGTTGATCCATCAAATGA-GAATTAAACAAAAAGTTGAACAAGTTCTT
*
3932636 CTCATTATGAACCTCTTCTTCCTTCAGATGAGTTCTTTTCATTATGAACCTTCTCTGGTAATGTT
128 CTCATTATGAACCTCTTCTTCCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTT
* *
3932701 GATCCATCAAATAATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTG
193 GATCCATCAAATAATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTG
3932766 ATATGTTGATCCATCAAATAATGAATTTAAACAA
258 ATATGTTGATCCATCAAATAATGAATTTAAACAA
* *
3932800 AAAGTTGAACAAGTTCTTCTCATTATGAA-CTTCTT-CTTCTTCAGATGAGTTCTTCTCATT-AT
1 AAAGGTGAACAAGCTCTTCTCATTATGAACCTTCTTCCTTCTTCAGATGAG-TCTTCTCATTCAT
*
3932862 GAACTTTCTCTGGTAATGTTGATCCATCAAATG-GAATTTAAACAAAAAGTTGAACAAGTTCTTC
65 GAACTTTCTCTGGCAATGTTGATCCATCAAATGAGAA-TTAAACAAAAAGTTGAACAAGTTCTTC
* *
3932926 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAG-TCTTCTCATTATGAACTTTCTCTGGTAATG
129 TCATTATGAACCTCTTCTT-C--CTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATG
* * *
3932990 TTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
191 TTGATCCATCAAATAATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTC
3933055 T
256 T
3933056 TCCTTCTTCA
Statistics
Matches: 238, Mismatches: 13, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
288 3 0.01
289 45 0.19
290 48 0.20
291 104 0.44
292 11 0.05
294 27 0.11
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (291 bp):
AAAGGTGAACAAGCTCTTCTCATTATGAACCTTCTTCCTTCTTCAGATGAGTCTTCTCATTCATG
AACTTTCTCTGGCAATGTTGATCCATCAAATGAGAATTAAACAAAAAGTTGAACAAGTTCTTCTC
ATTATGAACCTCTTCTTCCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGTAATGTTGAT
CCATCAAATAATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTGATA
TGTTGATCCATCAAATAATGAATTTAAACAA
Found at i:3933057 original size:112 final size:112
Alignment explanation
Indices: 3932739--3933433 Score: 932
Period size: 112 Copynumber: 6.2 Consensus size: 112
3932729 AAGTTGAACA
* * * * *
3932739 AGTTCTTCTCATTATGAACTTCTTCT-GATATGTTGATCCATCAAATAATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAACTTC-TCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAG
3932803 GTTGAACAAGTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * * *
3932847 AGTTCTTCTCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATG--GAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAAC-TTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAG
3932910 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * *
3932958 AG-TCTTCTCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
1 AGTTCTTCTCATTATGAAC-TTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAG
*
3933022 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * * **
3933070 AGTTCTTCTCATTATGAACTT-TCTGGAAAAGATGAT-CACCAAATGATGGA-TCAGGCAAAAGG
1 AGTTCTTCTCATTATGAACTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAGG
3933132 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* * * *
3933179 AGTTCTTCTCATTATGAACCT-TCTGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAG
1 AGTTCTTCTCATTATGAACTTCTCTGGAAATG-ATGATCCATCAAATGATGAATTCAAACAAAAG
*
3933243 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACG
65 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---G
* * * * *
3933294 AGTT-TTCTCATTGTGAACTCTTCCTCTAGAAACGATGATCCATCAATTTGATGAATTCAAGCAA
1 AGTTCTTCTCATTATGAA--CTT-CTCTGGAAATGATGATCCATCAA-ATGATGAATTCAAACAA
3933358 AAGGTTGAACAAGTTC-TCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
62 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
3933408 AGTTCTTCTCATTATGAACCTTCTCT
1 AGTTCTTCTCATTATGAA-CTTCTCT
3933434 AAAATATGAT
Statistics
Matches: 534, Mismatches: 32, Indels: 37
0.89 0.05 0.06
Matches are distributed among these distances:
107 41 0.08
108 22 0.04
109 108 0.20
110 68 0.13
111 37 0.07
112 117 0.22
113 20 0.04
114 20 0.04
115 17 0.03
116 2 0.00
117 45 0.08
118 37 0.07
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (112 bp):
AGTTCTTCTCATTATGAACTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAGG
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:3933219 original size:221 final size:224
Alignment explanation
Indices: 3932739--3933431 Score: 966
Period size: 221 Copynumber: 3.1 Consensus size: 224
3932729 AAGTTGAACA
* * *
3932739 AGTTCTTCTCATTATGAACTTCTTCT-GATATGTTGATCCATCAAATAATGAATTTAAACAAAAA
1 AGTTCTTCTCATTATGAAC-TCTTCTGGAAATGTTGATCCATCAAATGATGAATTTAAACAAAAG
*
3932803 GTTGAACAAGTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGA
65 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * * * *
3932864 ACTTTCTCTGGTAATGTTGATCCATCAAATG--GAATTTAAACAAAAAGTTGAACAAGTTCTTCT
130 AC-TTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCT
3932927 CATTATGAACTTCTTCTTCCTTCTTCAGATG
194 CATTATGAACTTCTTCTTCCTTCTTCAGATG
* * * *
3932958 AG-TCTTCTCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
1 AGTTCTTCTCATTATGAACTCT-TCTGGAAATGTTGATCCATCAAATGATGAATTTAAACAAAAG
3933022 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
65 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * *
3933087 ACTT-TCTGGAAAAGATGAT-CACCAAATGATGGA-TCAGGCAAAAGGTTGAACAAGTTCTTCTC
130 ACTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTC
3933149 ATTATGAACTTCTTCTTCCTTCTTCAGATG
195 ATTATGAACTTCTTCTTCCTTCTTCAGATG
* * *
3933179 AGTTCTTCTCATTATGAAC-CTTCTGGAAAAGAATGATCCATCAAGTGATGAATTTAAACAAAAG
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATG-TTGATCCATCAAATGATGAATTTAAACAAAAG
*
3933243 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTT-TTCTCATTG
65 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTA
* * *
3933307 TGAACTCTTCCTCTAGAAACGATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGT
127 TGAA--CTT-CTCTGGAAAAGATGATCCATCAA-ATGATGAATTCAAGCAAAAGGTTGAACAAGT
3933372 TC-TCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
188 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
3933408 AGTTCTTCTCATTATGAAC-CTTCT
1 AGTTCTTCTCATTATGAACTCTTCT
3933432 CTAAAATATG
Statistics
Matches: 423, Mismatches: 31, Indels: 30
0.87 0.06 0.06
Matches are distributed among these distances:
217 2 0.00
218 19 0.04
219 59 0.14
220 16 0.04
221 145 0.34
222 26 0.06
223 43 0.10
224 5 0.01
225 3 0.01
227 13 0.03
228 5 0.01
229 64 0.15
230 23 0.05
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (224 bp):
AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCATCAAATGATGAATTTAAACAAAAGG
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCA
TTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:3933837 original size:22 final size:22
Alignment explanation
Indices: 3933812--3933866 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3933802 CATAAAGTTT
*
3933812 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
3933834 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
3933856 TCATCTTTGAA
1 TCATCTTTGAA
3933867 GAGTGTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:3936343 original size:52 final size:52
Alignment explanation
Indices: 3936282--3936488 Score: 353
Period size: 52 Copynumber: 4.0 Consensus size: 52
3936272 GTTCCTACCA
* *
3936282 AACCAGATCAAATAACTCAAAGAATACTTCCAGAAGATGCTATGTTATGATC
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATC
* *
3936334 AACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGTTCTG-TCC
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-C
3936386 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATC
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATC
*
3936438 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT
3936489 GCTTTTCCAT
Statistics
Matches: 146, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
51 1 0.01
52 144 0.99
53 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (52 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATC
Found at i:3938567 original size:6 final size:6
Alignment explanation
Indices: 3938553--3938597 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
3938543 CTTTATTCGA
* *
3938553 TTTTCC TTTTTC TTTTT- TTTTTC TTTTTC TTCTTC TTCTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTT
3938598 GCTGGATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 5 0.15
6 24 0.71
7 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:3938578 original size:17 final size:19
Alignment explanation
Indices: 3938553--3938597 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
3938543 CTTTATTCGA
*
3938553 TTTTCCTTTTTCTT-TT-T
1 TTTTTCTTTTTCTTCTTCT
3938570 TTTTTCTTTTTCTTCTTCT
1 TTTTTCTTTTTCTTCTTCT
*
3938589 TCTTTCTTT
1 TTTTTCTTT
3938598 GCTGGATGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 13 0.54
18 2 0.08
19 9 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTTCTTCTTCT
Found at i:3939813 original size:1 final size:1
Alignment explanation
Indices: 3939807--3939839 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
3939797 AGGAAATGGG
3939807 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3939840 AGACTGAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3941094 original size:14 final size:14
Alignment explanation
Indices: 3941061--3941112 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
3941051 TATGACATAA
* *
3941061 AAATGCAAAGATGCC
1 AAATGTAAAAATG-C
* *
3941076 AAATGTAGATATGC
1 AAATGTAAAAATGC
*
3941090 AAATGTAAAAATGT
1 AAATGTAAAAATGC
3941104 AAATGTAAA
1 AAATGTAAA
3941113 TACAAACGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
14 21 0.68
15 10 0.32
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (14 bp):
AAATGTAAAAATGC
Found at i:3942563 original size:13 final size:12
Alignment explanation
Indices: 3942547--3942625 Score: 54
Period size: 13 Copynumber: 6.2 Consensus size: 12
3942537 TTAATTCTTG
3942547 AATATAATAAATA
1 AATATAATAAA-A
*
3942560 AATAAAATAAAA
1 AATATAATAAAA
*
3942572 AATAATAAT-ATA
1 AAT-ATAATAAAA
*
3942584 TATATAA-AAAA
1 AATATAATAAAA
3942595 AATAATAAGTAATAA
1 AAT-ATAA-TAA-AA
3942610 TAATATATATAAAA
1 -AATATA-ATAAAA
3942624 AA
1 AA
3942626 AAATAAGTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
11 8 0.15
12 12 0.23
13 16 0.31
14 4 0.08
15 8 0.15
16 4 0.08
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (12 bp):
AATATAATAAAA
Found at i:3942585 original size:33 final size:34
Alignment explanation
Indices: 3942548--3942643 Score: 117
Period size: 33 Copynumber: 2.8 Consensus size: 34
3942538 TAATTCTTGA
3942548 ATATA-ATAAATAAATAA-AATAAAAAATAATAAT
1 ATATATATAAA-AAATAATAATAAAAAATAATAAT
**
3942581 ATATATATAAAAAA-AATAATAAGTAATAATAAT
1 ATATATATAAAAAATAATAATAAAAAATAATAAT
*
3942614 ATATATAAAAAAAAATAAGTAATAAAAAAT
1 ATATAT-ATAAAAAATAA-TAATAAAAAAT
3942644 TTGAAAGGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
32 2 0.04
33 28 0.53
34 12 0.23
35 2 0.04
36 9 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (34 bp):
ATATATATAAAAAATAATAATAAAAAATAATAAT
Found at i:3942594 original size:23 final size:23
Alignment explanation
Indices: 3942550--3942602 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
3942540 ATTCTTGAAT
3942550 ATAATAAATAAATAAAATAAAAA
1 ATAATAAATAAATAAAATAAAAA
* *
3942573 ATAATAATATATATATAA-AAAAA
1 ATAATAA-ATAAATAAAATAAAAA
3942596 ATAATAA
1 ATAATAA
3942603 GTAATAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (23 bp):
ATAATAAATAAATAAAATAAAAA
Found at i:3942616 original size:29 final size:29
Alignment explanation
Indices: 3942550--3942638 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 29
3942540 ATTCTTGAAT
* * * *
3942550 ATAATAAATAAATAAAATAAAAAATAATA
1 ATAATATATAAAAAAAATAATAAGTAATA
3942579 ATATATATATAAAAAAAATAATAAGTAATA
1 ATA-ATATATAAAAAAAATAATAAGTAATA
3942609 ATAATATATATAAAAAAA-AATAAGTAATA
1 ATAATATATA-AAAAAAATAATAAGTAATA
3942638 A
1 A
3942639 AAAATTTGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
29 22 0.41
30 32 0.59
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (29 bp):
ATAATATATAAAAAAAATAATAAGTAATA
Found at i:3943766 original size:10 final size:10
Alignment explanation
Indices: 3943751--3943783 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3943741 AAATTCAGAT
3943751 AATAAATTAA
1 AATAAATTAA
3943761 AATAAATTAA
1 AATAAATTAA
3943771 AA-AAATATAA
1 AATAAAT-TAA
3943781 AAT
1 AAT
3943784 CGGTGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.19
10 17 0.81
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AATAAATTAA
Found at i:3944204 original size:13 final size:13
Alignment explanation
Indices: 3944186--3944210 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3944176 CCGTATTCCG
3944186 CCGCCGGCCACCT
1 CCGCCGGCCACCT
3944199 CCGCCGGCCACC
1 CCGCCGGCCACC
3944211 GTAACGGTGG
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:0.08, C:0.64, G:0.24, T:0.04
Consensus pattern (13 bp):
CCGCCGGCCACCT
Found at i:3944904 original size:3 final size:3
Alignment explanation
Indices: 3944896--3945017 Score: 163
Period size: 3 Copynumber: 39.7 Consensus size: 3
3944886 TTATTTATTA
*
3944896 AAT AAT AAT AAT ATAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* * *
3944943 AAT AAT AAT AAT AAAT AAT TAT AAT TAT AAT AAT AAT AAT AAT ACT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
3944989 AAT AAT AAT AAT AAT TTT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3945018 ATTTAAATGA
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
3 95 0.91
4 9 0.09
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:3951922 original size:20 final size:23
Alignment explanation
Indices: 3951872--3951933 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 23
3951862 GCATGGGTAG
3951872 TGTATCGATGCACATGTTAATGAA
1 TGTATCGATGCAC-TGTTAATGAA
*
3951896 TGCATCGATGCACTG-T-A-GAA
1 TGTATCGATGCACTGTTAATGAA
3951916 TGTATCGATGCACT-TTAA
1 TGTATCGATGCACTGTTAA
3951934 GGGGAAATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 1 0.03
23 2 0.06
24 12 0.35
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (23 bp):
TGTATCGATGCACTGTTAATGAA
Found at i:3953025 original size:25 final size:26
Alignment explanation
Indices: 3952997--3953045 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
3952987 ATAAGATAAT
* * *
3952997 TATATGCATGCGTA-GATTTGATATA
1 TATATGAATGAGTATGATGTGATATA
3953022 TATATGAATGAGTATGATGTGATA
1 TATATGAATGAGTATGATGTGATA
3953046 GCAATAATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (26 bp):
TATATGAATGAGTATGATGTGATATA
Found at i:3957334 original size:31 final size:31
Alignment explanation
Indices: 3957278--3957353 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
3957268 GTCTTTCGAG
* * *
3957278 ACATATGGATAGTATACATATGTTCTAAGGA
1 ACATATGGACAGTTTACATAGGTTCTAAGGA
* ** *
3957309 ACATATGGACAGTTTACCTAGGTTCTTCGGG
1 ACATATGGACAGTTTACATAGGTTCTAAGGA
*
3957340 ACCTATGGACAGTT
1 ACATATGGACAGTT
3957354 GTCGAGGTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (31 bp):
ACATATGGACAGTTTACATAGGTTCTAAGGA
Found at i:3961173 original size:31 final size:31
Alignment explanation
Indices: 3961072--3961199 Score: 105
Period size: 31 Copynumber: 4.1 Consensus size: 31
3961062 AGAGTCGAGG
*
3961072 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* *** *
3961103 GAATTACCTATG-TCTTTCGAGACATATAGACA
1 G-TTTACCTATGTTCTAAGGA-ACATATGGACA
* * *
3961135 ATATACCTATGTTCTAAGGAATATATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
* ** * *
3961166 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTAAGGAACATATGGACA
3961197 GTT
1 GTT
3961200 GACGAGGTTC
Statistics
Matches: 73, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
31 49 0.67
32 24 0.33
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (31 bp):
GTTTACCTATGTTCTAAGGAACATATGGACA
Found at i:3964353 original size:2 final size:2
Alignment explanation
Indices: 3964346--3964384 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3964336 GACTCGGTAC
3964346 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
3964385 CAAATTTTGT
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:3972968 original size:41 final size:41
Alignment explanation
Indices: 3972911--3972997 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
3972901 GAAATGTCAA
3972911 AGTTTGAATAGGTGTAAATATAAAGCTCTGGTGAGACCTTC
1 AGTTTGAATAGGTGTAAATATAAAGCTCTGGTGAGACCTTC
* * *
3972952 AGTTTGAATAGGTGTAAATATAACGCTCTGGTGAGACTTTT
1 AGTTTGAATAGGTGTAAATATAAAGCTCTGGTGAGACCTTC
3972993 AGTTT
1 AGTTT
3972998 TTTCTTTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (41 bp):
AGTTTGAATAGGTGTAAATATAAAGCTCTGGTGAGACCTTC
Found at i:3975244 original size:24 final size:25
Alignment explanation
Indices: 3975202--3975249 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
3975192 ATAATTTTAA
3975202 AAAATTTATATAAAATTAAAAAAAT
1 AAAATTTATATAAAATTAAAAAAAT
* *
3975227 AAAA-TTATATATATTTAAAAAAA
1 AAAATTTATATAAAATTAAAAAAA
3975250 CAAATAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAATTTATATAAAATTAAAAAAAT
Found at i:3982507 original size:21 final size:21
Alignment explanation
Indices: 3982482--3982537 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
3982472 AAGAAACGAG
3982482 TTTATAAAATTTTATGATAAA
1 TTTATAAAATTTTATGATAAA
*
3982503 TTTATAAAATTTTATTATAAA
1 TTTATAAAATTTTATGATAAA
3982524 TTTATAAAATTTTA
1 TTTATAAAATTTTA
3982538 AGGAAGAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTATAAAATTTTATGATAAA
Found at i:3985545 original size:31 final size:30
Alignment explanation
Indices: 3985458--3985553 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 30
3985448 TAATGAATTT
* *
3985458 TAAACTTTAGATAAAATACTAATTTGA-CCA
1 TAAACTTTAGAT-AAATATTAATTTGACCCC
* * *
3985488 TGAACTTTAGATGAAATATCATTTTGACCCC
1 TAAACTTTAGAT-AAATATTAATTTGACCCC
* *
3985519 TAAATTTTAGATAAAGTATTAATTTGACCTC
1 TAAACTTTAGATAAA-TATTAATTTGACCCC
3985550 TAAA
1 TAAA
3985554 TCCGATCAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
30 25 0.47
31 28 0.53
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (30 bp):
TAAACTTTAGATAAATATTAATTTGACCCC
Found at i:3985554 original size:31 final size:29
Alignment explanation
Indices: 3985458--3985553 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 29
3985448 TAATGAATTT
* *
3985458 TAAACTTTAGATAAAATACTAATTTGACCA
1 TAAACTTTAGAT-AAATATTAATTTGACCC
* * *
3985488 TGAACTTTAGATGAAATATCATTTTGACCCC
1 TAAACTTTAGAT-AAATATTAATTTGA-CCC
*
3985519 TAAATTTTAGATAAAGTATTAATTTGACCTC
1 TAAACTTTAGATAAA-TATTAATTTGACC-C
3985550 TAAA
1 TAAA
3985554 TCCGATCAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
30 27 0.51
31 26 0.49
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (29 bp):
TAAACTTTAGATAAATATTAATTTGACCC
Found at i:3986303 original size:30 final size:29
Alignment explanation
Indices: 3986269--3986350 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 29
3986259 GTTCAATGAT
*
3986269 TAAAATATAATAATTAAA-AATGTAAGTGAC
1 TAAAATGTAATAATTAAATAA--TAAGTGAC
*
3986299 TAAAATGTAACAATTAAATAATAAGTGAC
1 TAAAATGTAATAATTAAATAATAAGTGAC
3986328 TAAAATGTAATAAATT-AATAATA
1 TAAAATGTAAT-AATTAAATAATA
3986351 TAAATGATTG
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
29 25 0.53
30 20 0.43
31 2 0.04
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (29 bp):
TAAAATGTAATAATTAAATAATAAGTGAC
Found at i:3987103 original size:25 final size:25
Alignment explanation
Indices: 3987075--3987124 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3987065 GTTTTTTGTT
3987075 TTCTATAATATTTCAATTTTATAGA
1 TTCTATAATATTTCAATTTTATAGA
* * *
3987100 TTCTATTATTTTTTAATTTTATAGA
1 TTCTATAATATTTCAATTTTATAGA
3987125 GTTTTAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (25 bp):
TTCTATAATATTTCAATTTTATAGA
Found at i:3990299 original size:20 final size:20
Alignment explanation
Indices: 3990274--3990320 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
3990264 TTTCATCCAA
3990274 AAATTTCACAACTTTTCATT
1 AAATTTCACAACTTTTCATT
3990294 AAATTTCACAACTTTTCATT
1 AAATTTCACAACTTTTCATT
3990314 AAATTTC
1 AAATTTC
3990321 CTCATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTTCACAACTTTTCATT
Found at i:3992482 original size:20 final size:20
Alignment explanation
Indices: 3992438--3992475 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3992428 ATTATTTTTG
* *
3992438 ATTTTTTTTAAAAATTATTA
1 ATTTTATTTAAAAATCATTA
3992458 ATTTTATTTAAAAATCAT
1 ATTTTATTTAAAAATCAT
3992476 AACTTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTATTTAAAAATCATTA
Found at i:3992489 original size:20 final size:19
Alignment explanation
Indices: 3992440--3992489 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
3992430 TATTTTTGAT
*
3992440 TTTTTTTAAAAATTATTAA
1 TTTTTTTAAAAATCATTAA
3992459 TTTTATTTAAAAATCA-TAA
1 TTTT-TTTAAAAATCATTAA
3992478 CTTTTTTCTAAA
1 -TTTTTT-TAAA
3992490 GAAAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTTTTAAAAATCATTAA
Found at i:3993817 original size:13 final size:13
Alignment explanation
Indices: 3993799--3993824 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3993789 AAAGATTTTT
3993799 AATATTTTAAAAA
1 AATATTTTAAAAA
3993812 AATATTTTAAAAA
1 AATATTTTAAAAA
3993825 TCTAAAAATA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATTTTAAAAA
Found at i:4006127 original size:2 final size:2
Alignment explanation
Indices: 4006115--4006144 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4006105 TTAAAGATAA
*
4006115 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4006145 TAATAATACA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4006215 original size:17 final size:17
Alignment explanation
Indices: 4006195--4006227 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4006185 TTTAGAATAA
*
4006195 ATATAACTAATAAAAAT
1 ATATAACAAATAAAAAT
4006212 ATATAACAAATAAAAA
1 ATATAACAAATAAAAA
4006228 ATTAAGATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
ATATAACAAATAAAAAT
Found at i:4011834 original size:12 final size:12
Alignment explanation
Indices: 4011817--4011844 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4011807 TGACCGGTCC
4011817 GACCCGACCGTT
1 GACCCGACCGTT
4011829 GACCCGACCGTT
1 GACCCGACCGTT
4011841 GACC
1 GACC
4011845 GTTGACTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.43, G:0.25, T:0.14
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:4019093 original size:17 final size:17
Alignment explanation
Indices: 4019071--4019105 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4019061 CTGACCCGAT
4019071 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
4019088 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
4019105 C
1 C
4019106 GTTGACTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (17 bp):
CCGACCCGACCGTTGAC
Found at i:4027475 original size:16 final size:16
Alignment explanation
Indices: 4027454--4027499 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
4027444 AAACGCTGAC
*
4027454 AGTGACGGCTGTAGAT
1 AGTGACAGCTGTAGAT
4027470 AGTGACAGCTGTAGAT
1 AGTGACAGCTGTAGAT
*
4027486 AGTGACAGTTGTAG
1 AGTGACAGCTGTAG
4027500 CCTCCGACGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.28, C:0.11, G:0.35, T:0.26
Consensus pattern (16 bp):
AGTGACAGCTGTAGAT
Found at i:4031414 original size:297 final size:297
Alignment explanation
Indices: 4030880--4032061 Score: 1767
Period size: 297 Copynumber: 4.0 Consensus size: 297
4030870 AGGCCTTAAA
* * ** * * *
4030880 TGCTTTTTCACCCTCGTTTCCAGCATCCACTGAATAAAGATCAGCTTTGGCATCTTTCATTTTGG
1 TGCTTTTTCTCCCTCATCCCCAGCATCCACTGAATCAAGATCAGCTTTGGCATCTTTCACTTCGG
* * * * * ** *
4030945 CACTCTCTTTCCCCTGATCCCCTGTATCGAAATTAGGTGACTTGTCTTGCGATGCTTCAATCTCA
66 CACTCTCTTTTCCCTGATCCCCTGTATCAAAATCAGTTGACTTGTCATGTAATGCTTCAATTTCA
* *
4031010 TTGACAATCATGCCTGCTGAAGTATCAGCAGAGGACCCAGACATTTTATCTTGAAAATCAGTAGC
131 TTGACAATCATGCCTGCTGAAGTATCAGCAGAGGCCCCAGCCATTTTATCTTGAAAATCAGTAGC
* *
4031075 CACTGCACCCTCCGTTGATTCCTCGCCCTTATCTGCTTGAGGCAGAACTTCCAACTTTGGATCCA
196 CACTGCACCCTCCGTTGATTCCTCACCCTTATCTGCTTGAGGCAAAACTTCCAACTTTGGATCCA
4031140 TTTTAACATCCTCCTCCACCTTAGCAACTTCCGAAGT
261 TTTTAACATCCTCCTCCACCTTAGCAACTTCCGAAGT
* *
4031177 TGCTTTTGCTCCCTCATCCCCAGCATCCACTGAATCAAGATCAGCTTTGGCATCTTTCACTTTGG
1 TGCTTTTTCTCCCTCATCCCCAGCATCCACTGAATCAAGATCAGCTTTGGCATCTTTCACTTCGG
* * * *
4031242 CACTCTCTTTTCTCC-GATTCCCTGTGTCAAAATCAGTTGACTTGTCATGTAATGCTCCAACTTC
66 CACTCTCTTTTC-CCTGATCCCCTGTATCAAAATCAGTTGACTTGTCATGTAATGCTTCAATTTC
* *
4031306 ATTGACAATCATGCCTGCTGAAGTATCAGCAGAGGCCCCAGCCGTTATATCTTGAAAATCAGTAG
130 ATTGACAATCATGCCTGCTGAAGTATCAGCAGAGGCCCCAGCCATTTTATCTTGAAAATCAGTAG
* *
4031371 CCACTGCACCCTCCGTTGATTCCTCACCCTTAACTGCTTGAGGCAAAACTTCCAACTTTAGATCC
195 CCACTGCACCCTCCGTTGATTCCTCACCCTTATCTGCTTGAGGCAAAACTTCCAACTTTGGATCC
* * * * *
4031436 ATTTTATCATCATCCTCCACCTTAGAAACTTCAGGAGT
260 ATTTTAACATCCTCCTCCACCTTAGCAACTTCCGAAGT
*
4031474 TGCTTTTTCTCCCTCATCTCCAGCATCCACTGAATCAAGATCAGCTTTGGCATCTTTCACTTCGG
1 TGCTTTTTCTCCCTCATCCCCAGCATCCACTGAATCAAGATCAGCTTTGGCATCTTTCACTTCGG
*
4031539 CACTCTCTTTTCCCTGATCCCCTGTATCAAAATCAGTTGACTTGACATGTAATGCTTCAATTTCA
66 CACTCTCTTTTCCCTGATCCCCTGTATCAAAATCAGTTGACTTGTCATGTAATGCTTCAATTTCA
**
4031604 TTGACAATCATGCCTGCTGAAGTATCAGCAGAGGCCCTGGCCATTTTATCTTGAAAATCAGTAGC
131 TTGACAATCATGCCTGCTGAAGTATCAGCAGAGGCCCCAGCCATTTTATCTTGAAAATCAGTAGC
* * * *
4031669 CACTACACCCACCGTTGATTCCTCACCCTTATCAGGTTGAGGCAAAACTTCCGAA-TTTGGATCC
196 CACTGCACCCTCCGTTGATTCCTCACCCTTATCTGCTTGAGGCAAAACTTCC-AACTTTGGATCC
*
4031733 ATTTTAACATCCTCCTCCACCTTAGCAACTTCC-ATTGT
260 ATTTTAACATCCTCCTCCACCTTAGCAACTTCCGA-AGT
* * * * *
4031771 TGCTTTTTCTCCCTCGTCCCCAGCATCCACTGAACCAAGACCAGCTTTGGCATTTTTCACTTCAG
1 TGCTTTTTCTCCCTCATCCCCAGCATCCACTGAATCAAGATCAGCTTTGGCATCTTTCACTTCGG
* * * *
4031836 CACTCTGTTTTCCCTGATCCCCTGTATCAAAATTAGCTGATTTGTCATGTAATGCTTCAATTTCA
66 CACTCTCTTTTCCCTGATCCCCTGTATCAAAATCAGTTGACTTGTCATGTAATGCTTCAATTTCA
* *
4031901 TTGCCAATCATGCCTGCTGAAGTATCAGCAGTGGCCCCAGCCATTTTATCTTGAAAATCAGTAGC
131 TTGACAATCATGCCTGCTGAAGTATCAGCAGAGGCCCCAGCCATTTTATCTTGAAAATCAGTAGC
* * * * *
4031966 TACTGCACCCTCTGGTGATTCCTCACCCTTATCTGCTTGAGGTAAAACTTCCAACTTTGGGTCCA
196 CACTGCACCCTCCGTTGATTCCTCACCCTTATCTGCTTGAGGCAAAACTTCCAACTTTGGATCCA
**
4032031 TTTTAACATCCTCCTCCAGTTTAGCAACTTC
261 TTTTAACATCCTCCTCCACCTTAGCAACTTC
4032062 TGGAGTTTCC
Statistics
Matches: 798, Mismatches: 82, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
296 4 0.01
297 790 0.99
298 4 0.01
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (297 bp):
TGCTTTTTCTCCCTCATCCCCAGCATCCACTGAATCAAGATCAGCTTTGGCATCTTTCACTTCGG
CACTCTCTTTTCCCTGATCCCCTGTATCAAAATCAGTTGACTTGTCATGTAATGCTTCAATTTCA
TTGACAATCATGCCTGCTGAAGTATCAGCAGAGGCCCCAGCCATTTTATCTTGAAAATCAGTAGC
CACTGCACCCTCCGTTGATTCCTCACCCTTATCTGCTTGAGGCAAAACTTCCAACTTTGGATCCA
TTTTAACATCCTCCTCCACCTTAGCAACTTCCGAAGT
Found at i:4033909 original size:62 final size:62
Alignment explanation
Indices: 4033813--4033969 Score: 305
Period size: 62 Copynumber: 2.5 Consensus size: 62
4033803 CATTTGGAGG
*
4033813 TGCTGCTTGACCTGGTGTGCTTGGAAGGTATTATTATCTATTGCATTTGGAGTTTGTGGAAC
1 TGCTGCTTGACCTGTTGTGCTTGGAAGGTATTATTATCTATTGCATTTGGAGTTTGTGGAAC
4033875 TGCTGCTTGACCTGTTGTGCTTGGAAGGTATTATTATCTATTGCATTTGGAGTTTGTGGAAC
1 TGCTGCTTGACCTGTTGTGCTTGGAAGGTATTATTATCTATTGCATTTGGAGTTTGTGGAAC
4033937 TGCTGCTTGACCTGTTGTGCTTGGAAGGTATTA
1 TGCTGCTTGACCTGTTGTGCTTGGAAGGTATTA
4033970 GATGGAGCAA
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 94 1.00
ACGTcount: A:0.17, C:0.13, G:0.29, T:0.41
Consensus pattern (62 bp):
TGCTGCTTGACCTGTTGTGCTTGGAAGGTATTATTATCTATTGCATTTGGAGTTTGTGGAAC
Found at i:4034318 original size:29 final size:31
Alignment explanation
Indices: 4034280--4034359 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
4034270 ATTGTAGCGT
*
4034280 TTATACCACTGAACTTTTAATTTT-G-TCAA
1 TTATACCACTGAACCTTTAATTTTCGTTCAA
* *
4034309 TTATAGCACT-AACCTTTGATTTTCGTTTCAA
1 TTATACCACTGAACCTTTAATTTTCG-TTCAA
*
4034340 TTATACCATTGAACCTTTAA
1 TTATACCACTGAACCTTTAA
4034360 ATCATTAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
28 11 0.27
29 10 0.24
31 12 0.29
32 8 0.20
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (31 bp):
TTATACCACTGAACCTTTAATTTTCGTTCAA
Found at i:4034818 original size:42 final size:42
Alignment explanation
Indices: 4034758--4034841 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
4034748 CCCGAAATCT
* * *
4034758 CGTGTTTGTTTCATGTAATTCGTTTTTCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
4034800 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
4034842 GGAAAATGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.18, C:0.17, G:0.18, T:0.48
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
Found at i:4034824 original size:28 final size:28
Alignment explanation
Indices: 4034793--4034883 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 28
4034783 TTCGGAAAAT
4034793 GTTTTCCCGTGTTTGTTTCACGTAATTC
1 GTTTTCCCGTGTTTGTTTCACGTAATTC
* ** * * *
4034821 GTTTTCCGGAAAATAT-TTTC-CGGAAAAT-
1 GTTTTCCCG--TGTTTGTTTCAC-GTAATTC
*
4034849 GTTTTCCCGTGTTTGTTTTACGTAATTC
1 GTTTTCCCGTGTTTGTTTCACGTAATTC
4034877 GTTTTCC
1 GTTTTCC
4034884 GGACCGTAAT
Statistics
Matches: 44, Mismatches: 13, Indels: 12
0.64 0.19 0.17
Matches are distributed among these distances:
26 2 0.05
27 7 0.16
28 25 0.57
29 8 0.18
30 2 0.05
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.47
Consensus pattern (28 bp):
GTTTTCCCGTGTTTGTTTCACGTAATTC
Found at i:4034839 original size:14 final size:14
Alignment explanation
Indices: 4034822--4034855 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
4034812 ACGTAATTCG
4034822 TTTTCCGGAAAATA
1 TTTTCCGGAAAATA
*
4034836 TTTTCCGGAAAATG
1 TTTTCCGGAAAATA
4034850 TTTTCC
1 TTTTCC
4034856 CGTGTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (14 bp):
TTTTCCGGAAAATA
Found at i:4034847 original size:56 final size:56
Alignment explanation
Indices: 4034780--4034886 Score: 196
Period size: 56 Copynumber: 1.9 Consensus size: 56
4034770 ATGTAATTCG
*
4034780 TTTTTCGGAAAATGTTTTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATA
1 TTTTCCGGAAAATGTTTTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATA
*
4034836 TTTTCCGGAAAATGTTTTCCCGTGTTTGTTTTACGTAATTCGTTTTCCGGA
1 TTTTCCGGAAAATGTTTTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGA
4034887 CCGTAATTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.46
Consensus pattern (56 bp):
TTTTCCGGAAAATGTTTTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATA
Found at i:4034852 original size:42 final size:42
Alignment explanation
Indices: 4034764--4034852 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
4034754 ATCTCGTGTT
* * * ****
4034764 TGTTTCATGTAATTCGTTTTTCGGAAAATGTTTTCCCGTGTT
1 TGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCCCGAAAA
*
4034806 TGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCCGGAAAA
1 TGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCCCGAAAA
4034848 TGTTT
1 TGTTT
4034853 TCCCGTGTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (42 bp):
TGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCCCGAAAA
Found at i:4035121 original size:26 final size:24
Alignment explanation
Indices: 4035059--4035121 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
4035049 CATTTTCATC
4035059 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
4035083 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
4035106 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
4035122 ATTTTTAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:4035244 original size:28 final size:29
Alignment explanation
Indices: 4035148--4035251 Score: 99
Period size: 29 Copynumber: 3.5 Consensus size: 29
4035138 TATGATCAAT
* *
4035148 TATATTATAATAATATA-AGATATTATATTTT
1 TATATT-TAATAATATATA-ATAAT-TATTTA
*
4035179 TAT-TTTAATAATATATAATAAATTTTTTA
1 TATATTTAATAATATATAAT-AATTATTTA
4035208 TATATTTAATAATGA-ATAAT-ATTATTTA
1 TATATTTAATAAT-ATATAATAATTATTTA
4035236 TATATTTAAATAATAT
1 TATATTT-AATAATAT
4035252 TTTAGTAAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
28 15 0.24
29 25 0.40
30 19 0.30
31 4 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TATATTTAATAATATATAATAATTATTTA
Found at i:4035420 original size:18 final size:20
Alignment explanation
Indices: 4035393--4035430 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
4035383 TAATAAAATT
4035393 ATAAAAAAA-TA-TTTAATA
1 ATAAAAAAATTATTTTAATA
*
4035411 ATAAATAAATTATTTTAATA
1 ATAAAAAAATTATTTTAATA
4035431 TTTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAAAAATTATTTTAATA
Found at i:4035643 original size:15 final size:15
Alignment explanation
Indices: 4035608--4035687 Score: 99
Period size: 15 Copynumber: 5.4 Consensus size: 15
4035598 TTTCAGAAAT
**
4035608 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
4035623 -TAATTCAAATTCCA
1 GTAATTCAAATTCCA
**
4035637 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
4035652 GTAATTCAAATTTCA
1 GTAATTCAAATTCCA
*
4035667 ATAATTCAAATTCCA
1 GTAATTCAAATTCCA
4035682 GTAATT
1 GTAATT
4035688 TATTTTCCGG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
14 12 0.22
15 42 0.78
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.41
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:4035659 original size:30 final size:30
Alignment explanation
Indices: 4035608--4035687 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
4035598 TTTCAGAAAT
4035608 GTAATTCATTTTCCA-TAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
4035637 GTAATTCATTTTCCAGTAATTCAAATTTCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
* **
4035667 ATAATTCAAATTCCAGTAATT
1 GTAATTCATTTTCCAGTAATT
4035688 TATTTTCCGG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 15 0.33
30 31 0.67
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:4035674 original size:45 final size:44
Alignment explanation
Indices: 4035608--4035695 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 44
4035598 TTTCAGAAAT
* *
4035608 GTAATTCATTTTCCATAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAATTTCAATAATTCAAATTCCAGTAATTCATTTTCCA
*
4035652 GTAATTCAAATTTCAATAATTCAAATTCCAGTAATTTATTTTCC
1 GTAATTC-AATTTCAATAATTCAAATTCCAGTAATTCATTTTCC
4035696 GGAAAACCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 7 0.17
45 33 0.82
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (44 bp):
GTAATTCAATTTCAATAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:4035766 original size:14 final size:14
Alignment explanation
Indices: 4035725--4035766 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
4035715 AACAAACAGA
*
4035725 CTGGAAAATGAATA
1 CTGGAAAATGAATT
**
4035739 CTGGAATTTGAATT
1 CTGGAAAATGAATT
4035753 CTGGAAAATGAATT
1 CTGGAAAATGAATT
4035767 ACATTTATGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.31
Consensus pattern (14 bp):
CTGGAAAATGAATT
Found at i:4035809 original size:14 final size:14
Alignment explanation
Indices: 4035775--4035810 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4035765 TTACATTTAT
*
4035775 GGAAAACGTTTTCC
1 GGAAAATGTTTTCC
4035789 GGAAAATGTTTTCC
1 GGAAAATGTTTTCC
*
4035803 GTAAAATG
1 GGAAAATG
4035811 AATTACATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (14 bp):
GGAAAATGTTTTCC
Found at i:4036151 original size:19 final size:18
Alignment explanation
Indices: 4036127--4036168 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
4036117 GGTCATTTCA
4036127 AATATTAAATACAATAAAT
1 AATATTAAATACAA-AAAT
*
4036146 AATATTAAATACAAATAT
1 AATATTAAATACAAAAAT
4036164 AATAT
1 AATAT
4036169 CTTATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATTAAATACAAAAAT
Found at i:4036232 original size:23 final size:23
Alignment explanation
Indices: 4036201--4036245 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4036191 GATTATTTTA
4036201 TATAATATTAAAAATATAAATAT
1 TATAATATTAAAAATATAAATAT
* * *
4036224 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATAAATA
4036246 AATAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TATAATATTAAAAATATAAATAT
Found at i:4036258 original size:17 final size:16
Alignment explanation
Indices: 4036199--4036249 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
4036189 TTGATTATTT
4036199 TATATAATATTAA-AAA
1 TATA-AATATTAATAAA
* *
4036215 TATAAATATTATATTAT
1 TATAAATATTA-ATAAA
4036232 TATAAATATTAATAAA
1 TATAAATATTAATAAA
4036248 TA
1 TA
4036250 AATAATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.24
16 10 0.34
17 12 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAAATATTAATAAA
Found at i:4036498 original size:42 final size:42
Alignment explanation
Indices: 4036452--4036548 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
4036442 CCACTTAAGT
* **
4036452 GAAACAAACACGGGAAAATATTTTCCGGAAAATAAATTACGC
1 GAAACAAACACGGAAAAATATTTTCCAAAAAATAAATTACGC
* * *
4036494 GAAACAAACACGGAAAAATATTTTCTAAAAAATGAATTACGT
1 GAAACAAACACGGAAAAATATTTTCCAAAAAATAAATTACGC
*
4036536 GAAACAAATACGG
1 GAAACAAACACGG
4036549 TAATTCGGGG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.20
Consensus pattern (42 bp):
GAAACAAACACGGAAAAATATTTTCCAAAAAATAAATTACGC
Found at i:4038410 original size:19 final size:19
Alignment explanation
Indices: 4038386--4038423 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4038376 TTGACATGCA
*
4038386 AATTTTTTTAATTTTTTTC
1 AATTTTTATAATTTTTTTC
*
4038405 AATTTTTATATTTTTTTTC
1 AATTTTTATAATTTTTTTC
4038424 TTTCATTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (19 bp):
AATTTTTATAATTTTTTTC
Found at i:4041703 original size:21 final size:21
Alignment explanation
Indices: 4041673--4041720 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
4041663 TAATTTTCAA
*
4041673 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
4041694 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
4041715 ACATTG
1 ACATTG
4041721 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:4046353 original size:21 final size:21
Alignment explanation
Indices: 4046327--4046371 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
4046317 ATTTTCAAAT
*
4046327 ATTATTGCACCTAATTTTGAC
1 ATTATTACACCTAATTTTGAC
*
4046348 ATTATTACAGCTAATTTTGAC
1 ATTATTACACCTAATTTTGAC
4046369 ATT
1 ATT
4046372 GCAATATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (21 bp):
ATTATTACACCTAATTTTGAC
Found at i:4049027 original size:25 final size:25
Alignment explanation
Indices: 4048977--4049028 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
4048967 ACATTTTTTC
*
4048977 TTAAAAGTTATAAAAAATTATTTAA
1 TTAAAAGTTATAAAAAATTATCTAA
4049002 TTAAAA-TTA-AAAAAATACTATCTAA
1 TTAAAAGTTATAAAAAAT--TATCTAA
4049027 TT
1 TT
4049029 TGATTTGGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 7 0.29
24 3 0.12
25 14 0.58
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
TTAAAAGTTATAAAAAATTATCTAA
Found at i:4049794 original size:20 final size:20
Alignment explanation
Indices: 4049769--4049959 Score: 256
Period size: 20 Copynumber: 9.4 Consensus size: 20
4049759 TTTAGAAGAA
**
4049769 AATCGCAATGCGATTGATTG
1 AATCGCAATGCGATTGAGAG
4049789 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
4049809 AGTCGCAACGCGATTTAGAAGAG
1 AATCGCAATGCGA-TT-G-AGAG
*
4049832 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
4049852 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
4049872 AATCGCAACGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
4049892 AATCGCAATGCGATTGAGAT
1 AATCGCAATGCGATTGAGAG
4049912 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
4049932 AATCGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAG
4049952 AATCGCAA
1 AATCGCAA
4049960 CGTTAAAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
20 131 0.87
21 3 0.02
22 2 0.01
23 15 0.10
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:4049836 original size:63 final size:63
Alignment explanation
Indices: 4049748--4049951 Score: 310
Period size: 63 Copynumber: 3.3 Consensus size: 63
4049738 GCTTCCAAGT
* * *
4049748 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAATGAATCGCAATGCGATTGAGAGAA
*
4049811 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGA-GAATCGCAATGCGATTGAGAGAA
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGA-ATGAATCGCAATGCGATTGAGAGAA
*
4049874 TCGCAACGCGA-CT-G-AGAGAATCGCAATGCGATTGAGAT-AATCGCAATGCGATTGAGAGAA
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGA-ATGAATCGCAATGCGATTGAGAGAA
4049934 TCGCAACGCGATTTAGAA
1 TCGCAACGCGATTTAGAA
4049952 AATCGCAACG
Statistics
Matches: 129, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
60 55 0.43
61 2 0.02
62 2 0.02
63 70 0.54
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (63 bp):
TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAATGAATCGCAATGCGATTGAGAGAA
Found at i:4049960 original size:20 final size:20
Alignment explanation
Indices: 4049644--4049961 Score: 198
Period size: 20 Copynumber: 15.6 Consensus size: 20
4049634 AATGACCAAT
*
4049644 AAAATCGCAACGCGA-T-ATC
1 AAAATCGCAACGCGATTGA-G
*
4049663 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAG
** **
4049683 AAAAATCGCAACGTTA-AAAG
1 -AAAATCGCAACGCGATTGAG
**
4049703 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TGAG
**
4049723 AAAATCGCAACGCGAGCTT-CC
1 AAAATCGCAACGCGA--TTGAG
**
4049744 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA-TT-G-AG
* *
4049767 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTGAG
** *
4049787 TGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTGAG
* *
4049807 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA-TT-G-AG
* * *
4049830 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* *
4049850 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTGAG
* *
4049870 AGAATCGCAACGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* *
4049890 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTGAG
* *
4049910 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTGAG
* *
4049930 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAG
4049950 AAAATCGCAACG
1 AAAATCGCAACG
4049962 TTAAAAAGAA
Statistics
Matches: 246, Mismatches: 37, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
19 27 0.11
20 155 0.63
21 32 0.13
22 4 0.02
23 27 0.11
24 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTGAG
Found at i:4049971 original size:20 final size:20
Alignment explanation
Indices: 4049948--4049991 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
4049938 AACGCGATTT
*
4049948 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
4049968 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
4049988 AGAA
1 AGAA
4049992 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:4050117 original size:5 final size:6
Alignment explanation
Indices: 4050067--4050114 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
4050057 GACACGTATT
4050067 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
4050112 ACC
1 ACC
4050115 CGAGACGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.36
6 27 0.64
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:4050258 original size:26 final size:26
Alignment explanation
Indices: 4050222--4050277 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
4050212 AATAGTATTT
4050222 CCAATACTATGTGGGATTGAGCATTA
1 CCAATACTATGTGGGATTGAGCATTA
4050248 CCAATACTATGTGGGATTGAGCATTA
1 CCAATACTATGTGGGATTGAGCATTA
4050274 CCAA
1 CCAA
4050278 CACTTGTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (26 bp):
CCAATACTATGTGGGATTGAGCATTA
Found at i:4050870 original size:6 final size:6
Alignment explanation
Indices: 4050861--4050986 Score: 207
Period size: 6 Copynumber: 20.8 Consensus size: 6
4050851 GGTGGTGTGG
* *
4050861 GTGGTC GTGGTGG GGGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
1 GTGGTC GTGGT-C GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
* *
4050910 GTGGTC GTGGTA GTGGTA GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
1 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
4050958 GTGGTC GTGGTC GTGGTC GTGGTC GTGGT
1 GTGGTC GTGGTC GTGGTC GTGGTC GTGGT
4050987 AATACGTGTC
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
6 109 0.96
7 4 0.04
ACGTcount: A:0.02, C:0.13, G:0.52, T:0.33
Consensus pattern (6 bp):
GTGGTC
Found at i:4050872 original size:18 final size:17
Alignment explanation
Indices: 4050840--4050985 Score: 89
Period size: 18 Copynumber: 8.3 Consensus size: 17
4050830 GTCGGGTCGG
*
4050840 GGTGGGGTGGTGGTGGT
1 GGTGGGGTGGTCGTGGT
4050857 -GT-GGGTGGTCGTGGT
1 GGTGGGGTGGTCGTGGT
*
4050872 GGGGGGTCGTGGTCGTGGT
1 GGTGGG--GTGGTCGTGGT
* *
4050891 CGTGGTCGTGGTCGTGGT
1 GGTGG-GGTGGTCGTGGT
* * *
4050909 CGTGGTCGTGGTAGTGGT
1 GGTGG-GGTGGTCGTGGT
* *
4050927 AGTGGTCGTGGTCGTGGT
1 GGTGG-GGTGGTCGTGGT
* *
4050945 CGTGGTCGTGGTCGTGGT
1 GGTGG-GGTGGTCGTGGT
* *
4050963 CGTGGTCGTGGTCGTGGT
1 GGTGG-GGTGGTCGTGGT
*
4050981 CGTGG
1 GGTGG
4050986 TAATACGTGT
Statistics
Matches: 115, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.10
16 3 0.03
17 2 0.02
18 84 0.73
19 14 0.12
ACGTcount: A:0.01, C:0.12, G:0.55, T:0.32
Consensus pattern (17 bp):
GGTGGGGTGGTCGTGGT
Found at i:4050884 original size:31 final size:31
Alignment explanation
Indices: 4050818--4050986 Score: 176
Period size: 30 Copynumber: 5.7 Consensus size: 31
4050808 CGTCTGGGTC
*
4050818 GGGTCG-GGTCG-GGTCG-GGTCGGGGTGGG
1 GGGTCGTGGTCGTGGTCGTGGTCGTGGTGGG
*
4050846 GTGGTGGTGGT-GTGG--GTGGTCGTGGTGGG
1 G-GGTCGTGGTCGTGGTCGTGGTCGTGGTGGG
*
4050875 GGGTCGTGGTCGTGGTCGTGGTCGTGGT-CG
1 GGGTCGTGGTCGTGGTCGTGGTCGTGGTGGG
* * * *
4050905 TGGTCGTGGTCGTGGTAGTGGTAGTGGT-CG
1 GGGTCGTGGTCGTGGTCGTGGTCGTGGTGGG
* *
4050935 TGGTCGTGGTCGTGGTCGTGGTCGTGGT-CG
1 GGGTCGTGGTCGTGGTCGTGGTCGTGGTGGG
*
4050965 TGGTCGTGGTCGTGGTCGTGGT
1 GGGTCGTGGTCGTGGTCGTGGT
4050987 AATACGTGTC
Statistics
Matches: 125, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
28 10 0.08
29 21 0.17
30 83 0.66
31 11 0.09
ACGTcount: A:0.01, C:0.12, G:0.56, T:0.30
Consensus pattern (31 bp):
GGGTCGTGGTCGTGGTCGTGGTCGTGGTGGG
Found at i:4051117 original size:20 final size:20
Alignment explanation
Indices: 4051094--4051223 Score: 206
Period size: 20 Copynumber: 6.5 Consensus size: 20
4051084 TTCTTTTTAA
4051094 CATTGCGATTCTCTCAATCG
1 CATTGCGATTCTCTCAATCG
*
4051114 CATTGCGATTCTCTCAGTCG
1 CATTGCGATTCTCTCAATCG
*
4051134 CGTTGCGATTCTCTCAATCG
1 CATTGCGATTCTCTCAATCG
*
4051154 CATTGCGATTCTCTCAGTCG
1 CATTGCGATTCTCTCAATCG
*
4051174 CATTGCGATTCTCTCAGTCG
1 CATTGCGATTCTCTCAATCG
**
4051194 CATTGCGATTCAATCAATCG
1 CATTGCGATTCTCTCAATCG
4051214 CATTGCGATT
1 CATTGCGATT
4051224 TTCTTCTAAA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 102 1.00
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.35
Consensus pattern (20 bp):
CATTGCGATTCTCTCAATCG
Found at i:4051311 original size:20 final size:20
Alignment explanation
Indices: 4051258--4051311 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
4051248 TGGAAGCTCG
* *
4051258 CGTTGCGATTTTCCTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
4051278 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
4051298 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
4051312 AAATCGCGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.20, G:0.19, T:0.50
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:4051321 original size:20 final size:20
Alignment explanation
Indices: 4051298--4051346 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
4051288 TTCTTTTTAA
*
4051298 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTCAATCG
**
4051318 CGTTGCGATTTGAT--ATCG
1 CGTTGCGATTTTCTCAATCG
4051336 CGTTGCGATTT
1 CGTTGCGATTT
4051347 ATTGGTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 15 0.56
20 12 0.44
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.41
Consensus pattern (20 bp):
CGTTGCGATTTTCTCAATCG
Found at i:4051986 original size:18 final size:19
Alignment explanation
Indices: 4051963--4052039 Score: 66
Period size: 21 Copynumber: 3.9 Consensus size: 19
4051953 CGGACGCGGC
4051963 GGCGGCGGTTATGGTGGTGG
1 GGCGGCGGTTATGGTGGT-G
*
4051983 CGGCGGCGGTTATGATGGTAG
1 -GGCGGCGGTTATGGTGGT-G
* *
4052004 CGGAGGCGGTTTTGGTGGT-
1 -GGCGGCGGTTATGGTGGTG
* *
4052023 GGCGGTGGTTACGGTGG
1 GGCGGCGGTTATGGTGG
4052040 ATCTGGTGGA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
18 13 0.28
21 34 0.72
ACGTcount: A:0.08, C:0.12, G:0.55, T:0.26
Consensus pattern (19 bp):
GGCGGCGGTTATGGTGGTG
Found at i:4051986 original size:21 final size:21
Alignment explanation
Indices: 4051960--4052027 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
4051950 ACCCGGACGC
4051960 GGCGGCGGCGGTTATGGTGGT
1 GGCGGCGGCGGTTATGGTGGT
*
4051981 GGCGGCGGCGGTTATGATGGT
1 GGCGGCGGCGGTTATGGTGGT
* * *
4052002 AGCGGAGGCGGTTTTGGTGGT
1 GGCGGCGGCGGTTATGGTGGT
4052023 GGCGG
1 GGCGG
4052028 TGGTTACGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.07, C:0.13, G:0.56, T:0.24
Consensus pattern (21 bp):
GGCGGCGGCGGTTATGGTGGT
Found at i:4056842 original size:17 final size:18
Alignment explanation
Indices: 4056822--4056855 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4056812 CTCAACCTAC
*
4056822 ATTTTATATCA-AACAAA
1 ATTTCATATCACAACAAA
4056839 ATTTCATATCACAACAA
1 ATTTCATATCACAACAA
4056856 TACAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTTCATATCACAACAAA
Found at i:4066853 original size:37 final size:37
Alignment explanation
Indices: 4066783--4067216 Score: 112
Period size: 37 Copynumber: 12.1 Consensus size: 37
4066773 TATAATTATA
*
4066783 ATATATTACAAAAATATTTCTCAAAAAC-T-TATATAAT
1 ATATATTTCAAAAATATTT-TC-AAAACTTATATATAAT
*
4066820 ATATATGTTCAAAAATATTTT-AAAACTTATATATTAT
1 ATATAT-TTCAAAAATATTTTCAAAACTTATATATAAT
* *
4066857 ATATATTTTAAAAAAATGTTTTC-AAA---AT-TAT-AT
1 ATATA-TTT-CAAAAATATTTTCAAAACTTATATATAAT
* ** *
4066890 A-GT-TTTCAAAAA-AAATT-AAAAC-TATATATTAT
1 ATATATTTCAAAAATATTTTCAAAACTTATATATAAT
* *
4066922 ATGT-TTTC-AAAATGA-TTTCAAAAC-TATATATTAT
1 ATATATTTCAAAAAT-ATTTTCAAAACTTATATATAAT
* * * *
4066956 ATATATTTCCAAAATGTTTTGAAAAC-CATATAATATAT
1 ATATATTTCAAAAATATTTTCAAAACTTATAT-ATA-AT
* * *
4066994 ATATAATTTCAAAATGTTTTTTTAAAA---A-ACTAT-AT
1 ATAT-ATTTCAAAA-ATATTTTCAAAACTTATA-TATAAT
* *
4067029 A-ATA--T-ATAAATGTTTTCAAAACTATATAT-TATAT
1 ATATATTTCAAAAATATTTTCAAAACT-TATATATA-AT
* * *
4067063 A-AGT-TTTCAAAATGATTTTTTTAAAAATTATATA-ATAT
1 ATA-TATTTCAAAA--ATATTTTCAAAACTTATATATA-AT
* * ** * *
4067101 ACCATGTTTTTAAAATGTTTTCAAAAC-TATATATTAT
1 A-TATATTTCAAAAATATTTTCAAAACTTATATATAAT
*
4067138 ATATATTTTC-AAAATGTTTTCAAAAAC-TATATA-ATAT
1 ATATA-TTTCAAAAATATTTTC-AAAACTTATATATA-AT
* * *
4067175 ATATATTTTCAAAAAATGTTTTCTAAAAATTATATATTAT
1 ATATA-TTTC-AAAAATATTTTC-AAAACTTATATATAAT
4067215 AT
1 AT
4067217 TTTGTTAGAA
Statistics
Matches: 309, Mismatches: 40, Indels: 93
0.70 0.09 0.21
Matches are distributed among these distances:
28 5 0.02
29 14 0.05
30 8 0.03
31 4 0.01
32 9 0.03
33 14 0.05
34 29 0.09
35 15 0.05
36 32 0.10
37 64 0.21
38 54 0.17
39 35 0.11
40 26 0.08
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (37 bp):
ATATATTTCAAAAATATTTTCAAAACTTATATATAAT
Found at i:4066921 original size:34 final size:35
Alignment explanation
Indices: 4066883--4066958 Score: 111
Period size: 34 Copynumber: 2.2 Consensus size: 35
4066873 TGTTTTCAAA
4066883 ATTATATAGTTTTCAAAAAAAATT-AAAACTATAT
1 ATTATATAGTTTTCAAAAAAAATTCAAAACTATAT
** *
4066917 ATTATAT-GTTTTCAAAATGATTTCAAAACTATAT
1 ATTATATAGTTTTCAAAAAAAATTCAAAACTATAT
4066951 ATTATATA
1 ATTATATA
4066959 TATTTCCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 13 0.35
34 24 0.65
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (35 bp):
ATTATATAGTTTTCAAAAAAAATTCAAAACTATAT
Found at i:4067034 original size:40 final size:36
Alignment explanation
Indices: 4066907--4067216 Score: 185
Period size: 36 Copynumber: 8.5 Consensus size: 36
4066897 AAAAAAAATT
* * * *
4066907 AAAACTATAT-AT-TATATGTTTTCAAAATGATTTC
1 AAAACTATATAATATATATATTTCCAAAATGTTTTA
* *
4066941 AAAACTATATATTATATATATTTCCAAAATGTTTTG
1 AAAACTATATAATATATATATTTCCAAAATGTTTTA
* *
4066977 AAAACCATATAATATATATATAATTTCAAAATGTTTTTTTA
1 AAAACTATATAATATATATAT--TTCCAAAATG---TTTTA
*
4067018 AAAA--ACTAT-ATA-ATATA--T---AAATGTTTTC
1 AAAACTA-TATAATATATATATTTCCAAAATGTTTTA
* *
4067046 AAAACTATATATTATATA-AGTTTTCAAAATGATTTTTTTA
1 AAAACTATATAATATATATA-TTTCCAAAATG----TTTTA
* * * ** *
4067086 AAAATTATATAATATACCATGTTTTTAAAATGTTTTC
1 AAAACTATATAATATA-TATATTTCCAAAATGTTTTA
* *
4067123 AAAACTATATATTATATATATTTTCAAAATGTTTTCA
1 AAAACTATATAATATATATATTTCCAAAATGTTTT-A
*
4067160 AAAACTATATAATATATATATTTTCAAAAAATGTTTTCTA
1 AAAACTATATAATATATATA-TTTC-CAAAATG-TTT-TA
* *
4067200 AAAATTATATATTATAT
1 AAAACTATATAATATAT
4067217 TTTGTTAGAA
Statistics
Matches: 218, Mismatches: 29, Indels: 52
0.73 0.10 0.17
Matches are distributed among these distances:
28 8 0.04
29 3 0.01
30 4 0.02
31 8 0.04
33 1 0.00
34 11 0.05
35 1 0.00
36 58 0.27
37 37 0.17
38 17 0.08
39 10 0.05
40 40 0.18
41 20 0.09
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
AAAACTATATAATATATATATTTCCAAAATGTTTTA
Found at i:4067056 original size:27 final size:25
Alignment explanation
Indices: 4067019--4067074 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 25
4067009 GTTTTTTTAA
4067019 AAAACTATATAATATATAAATGTTTTC
1 AAAACTATATAATATAT-AA-GTTTTC
*
4067046 AAAACTATATATTATATAAGTTTTC
1 AAAACTATATAATATATAAGTTTTC
4067071 AAAA
1 AAAA
4067075 TGATTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 10 0.36
26 2 0.07
27 16 0.57
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (25 bp):
AAAACTATATAATATATAAGTTTTC
Found at i:4067061 original size:25 final size:27
Alignment explanation
Indices: 4067019--4067074 Score: 82
Period size: 25 Copynumber: 2.1 Consensus size: 27
4067009 GTTTTTTTAA
4067019 AAAACTATATAATATATA-AATGTTTTC
1 AAAACTATATAATATATATAA-GTTTTC
4067046 AAAACTATAT-AT-TATATAAGTTTTC
1 AAAACTATATAATATATATAAGTTTTC
4067071 AAAA
1 AAAA
4067075 TGATTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 14 0.50
26 4 0.14
27 10 0.36
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (27 bp):
AAAACTATATAATATATATAAGTTTTC
Found at i:4067082 original size:67 final size:65
Alignment explanation
Indices: 4066967--4067177 Score: 203
Period size: 77 Copynumber: 3.0 Consensus size: 65
4066957 TATATTTCCA
*
4066967 AAATGTTTTGAAAACCATATAATATATATATAA-TTTCAAAATGTTTTTTTAAAAAACTATATAA
1 AAATGTTTTCAAAA-C-TAT-ATAT-TATATAATTTTCAAAATG-TTTTTTAAAAAACTATATAA
4067031 TATAT
61 TATAT
* *
4067036 AAATGTTTTCAAAACTATATATTATATAAGTTTTCAAAATGATTTTTTTAAAAATTATATAATAT
1 AAATGTTTTCAAAACTATATATTATATAA-TTTTCAAAATG-TTTTTTAAAAAACTATATAATAT
4067101 ACCATGTTTTT
64 ---A------T
*
4067112 AAAATGTTTTCAAAACTATATATTATATATATTTTCAAAATG--TTTTCAAAAACTATATAATAT
1 -AAATGTTTTCAAAACTATATATTATATA-ATTTTCAAAATGTTTTTTAAAAAACTATATAATAT
4067175 AT
64 AT
4067177 A
1 A
4067178 TATTTTCAAA
Statistics
Matches: 123, Mismatches: 6, Indels: 31
0.77 0.04 0.19
Matches are distributed among these distances:
64 1 0.01
65 8 0.07
66 4 0.03
67 34 0.28
68 1 0.01
69 13 0.11
70 1 0.01
71 1 0.01
74 19 0.15
76 1 0.01
77 39 0.32
78 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (65 bp):
AAATGTTTTCAAAACTATATATTATATAATTTTCAAAATGTTTTTTAAAAAACTATATAATATAT
Found at i:4067123 original size:77 final size:74
Alignment explanation
Indices: 4067036--4067258 Score: 222
Period size: 77 Copynumber: 2.9 Consensus size: 74
4067026 TATAATATAT
* *
4067036 AAATGTTTTCAAAACTATATATTATATA-AGTTTTCAAAATGATTTTTTTAAAAATTATATAATA
1 AAATGTTTTCAAAACTATATATTATATATA-TTTTCAAAATG---TTTTCAAAAACTATATAATA
* *
4067100 TACCATGTTTT-TA
62 TA-CATATTTTAAA
*
4067113 AAATGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATAATATATA
1 AAATGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATAATATACA
4067178 TATTTTCAAA
66 TATTTT-AAA
* * *
4067188 AAATGTTTTCTAAAAATTATATATTATAT-T-TTGTT-AGAAACGTTTTCAAAAAACTGTAATAA
1 AAATGTTTTC--AAAACTATATATTATATATATT-TTCA-AAATGTTTTC-AAAAACTAT-ATAA
*
4067250 TATATATAT
60 TATACATAT
4067259 ATATATATAG
Statistics
Matches: 129, Mismatches: 8, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
73 6 0.05
74 20 0.16
75 14 0.11
76 12 0.09
77 63 0.49
78 14 0.11
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (74 bp):
AAATGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATAATATACA
TATTTTAAA
Found at i:4073749 original size:22 final size:22
Alignment explanation
Indices: 4073723--4073765 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4073713 AAAAACATTT
*
4073723 TTTAAAGAAATATTTACCAAAC
1 TTTAAAAAAATATTTACCAAAC
*
4073745 TTTAAAAAAATATTTTCCAAA
1 TTTAAAAAAATATTTACCAAA
4073766 GTTGATTGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTAAAAAAATATTTACCAAAC
Found at i:4076980 original size:17 final size:20
Alignment explanation
Indices: 4076958--4077000 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
4076948 AATTCCACGT
4076958 AAATATA-CATT-T-ATAAA
1 AAATATATCATTCTAATAAA
4076975 AAATATATCATTCTAATAAA
1 AAATATATCATTCTAATAAA
*
4076995 AGATAT
1 AAATAT
4077001 TATTTAGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 4 0.18
19 1 0.05
20 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
AAATATATCATTCTAATAAA
Found at i:4089990 original size:21 final size:21
Alignment explanation
Indices: 4089966--4090005 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4089956 TTTTCAAAGG
4089966 CATGCACCGATGCATCAATAT
1 CATGCACCGATGCATCAATAT
*
4089987 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
4090006 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAT
Found at i:4090055 original size:19 final size:19
Alignment explanation
Indices: 4090031--4090069 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
4090021 TCGAATGCAT
4090031 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
4090050 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
4090069 T
1 T
4090070 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:4090093 original size:64 final size:64
Alignment explanation
Indices: 4089987--4090177 Score: 212
Period size: 64 Copynumber: 3.0 Consensus size: 64
4089977 GCATCAATAT
* * * * *
4089987 CATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGCATTCCATGCACCGATGCACTCT
1 CATGCATCGATGCACTC-ATGATTTAATTAAAACATCGAATGCATT-CATGCATCGATGCACTAT
4090051 C
64 C
* *
4090052 CATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTTGATGCATCGATGCACAATC
1 CATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCA-TTCATGCATCGATGCACTATC
* *
4090116 CATGCATCGATGCAC-CAGGCTATTT--TTCAAACATCGAATGCACTTCATGCATCGATGCACTA
1 CATGCATCGATGCACTCATG--ATTTAATTAAAACATCGAATGCA-TTCATGCATCGATGCACTA
4090178 GGAGTCCAAC
Statistics
Matches: 109, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
63 1 0.01
64 86 0.79
65 16 0.15
66 6 0.06
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTCATGCATCGATGCACTATC
Found at i:4095996 original size:24 final size:22
Alignment explanation
Indices: 4095968--4096047 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 22
4095958 CACTTAACAA
4095968 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
4095992 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
*
4096012 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
4096036 TGCATCGATGCA
1 TGCATCGATGCA
4096048 CAAGACCATG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 4 0.08
21 12 0.25
22 2 0.04
23 13 0.27
24 17 0.35
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:4098599 original size:21 final size:21
Alignment explanation
Indices: 4098575--4098614 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4098565 TTTTCAAATG
4098575 CATGCACCGATGCATCAATAT
1 CATGCACCGATGCATCAATAT
*
4098596 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
4098615 GAGTAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAT
Found at i:4098663 original size:19 final size:19
Alignment explanation
Indices: 4098639--4098678 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4098629 ATCGAATGAA
*
4098639 CTCCATGCACCGATGCACT
1 CTCCATACACCGATGCACT
*
4098658 CTCCATACATCGATGCACT
1 CTCCATACACCGATGCACT
4098677 CT
1 CT
4098679 GATTTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.40, G:0.12, T:0.25
Consensus pattern (19 bp):
CTCCATACACCGATGCACT
Found at i:4105930 original size:16 final size:16
Alignment explanation
Indices: 4105909--4105940 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4105899 CCTTTAAAGC
4105909 AAGATGATAAGTCCTT
1 AAGATGATAAGTCCTT
4105925 AAGATGATAAGTCCTT
1 AAGATGATAAGTCCTT
4105941 CGGGCCATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
AAGATGATAAGTCCTT
Found at i:4106137 original size:42 final size:42
Alignment explanation
Indices: 4106078--4106164 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
4106068 TAAGTCCCTC
* *
4106078 GGGCCATCAATAAGTCTTTTGAGCATGATGCTTAAATCCTTA
1 GGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTA
*
4106120 GGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTA
1 GGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTA
4106162 GGG
1 GGG
4106165 TAATTTATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (42 bp):
GGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTA
Found at i:4106326 original size:42 final size:42
Alignment explanation
Indices: 4106217--4106466 Score: 203
Period size: 42 Copynumber: 6.1 Consensus size: 42
4106207 CAGTAAGTGT
* * *
4106217 CATCAGTAAGTCTTTCGAGCATGATAATGAAGTCCTTCAGGC
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGC
4106259 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGC
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGC
* * * *
4106301 CATCAATAAGTCTTTCGAGCATGATGATTAAATTCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGC
* ** * * * * **
4106343 AATTTGTAAG-CCTTC-ACCGAAGA-GTAGTG-AAGCAAAT----C
1 CATCAGTAAGTCTTTCGAGC-ATGATG-A-TGAAATC-CTTCGGGC
* *
4106381 CATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGC
** * *
4106423 CATTTGTAAGTCTTTCGAGCAAGATGAT-AAGTCCTTCGGGC
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGC
4106464 CAT
1 CAT
4106467 TTTAAGCATT
Statistics
Matches: 159, Mismatches: 37, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
38 9 0.06
39 11 0.07
40 6 0.04
41 24 0.15
42 109 0.69
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGC
Found at i:4106375 original size:177 final size:177
Alignment explanation
Indices: 4106069--4106391 Score: 520
Period size: 177 Copynumber: 1.8 Consensus size: 177
4106059 CGCACTTAGT
* * * * *
4106069 AAGTCCCTCGGGCCATCAATAAGTCTTTTGAGCATGATGCTTAAATCCTTAGGGCCATCAGTAAG
1 AAGTCCCTCAGGCCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAATAAG
4106134 TCTTTCGAGCATGATGATTAAATCCTTAGGGTAATTTATAAGCCTTCACAGAAGAGTAGTGAAGC
66 TCTTTCGAGCATGATGATTAAATCCTTAGGGTAATTTATAAGCCTTCACAGAAGAGTAGTGAAGC
*
4106199 AAACCCATCAGTAAGTGTCATCAGTAAGTCTTTCGAGCATGATAATG
131 AAACCCATCAATAAGTGTCATCAGTAAGTCTTTCGAGCATGATAATG
* * *
4106246 AAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGCCATCAATAAG
1 AAGTCCCTCAGGCCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAATAAG
* * * *
4106311 TCTTTCGAGCATGATGATTAAATTCTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGC
66 TCTTTCGAGCATGATGATTAAATCCTTAGGGTAATTTATAAGCCTTCACAGAAGAGTAGTGAAGC
*
4106376 AAATCCATCAATAAGT
131 AAACCCATCAATAAGT
4106392 CTTTCGAGCA
Statistics
Matches: 132, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
177 132 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (177 bp):
AAGTCCCTCAGGCCATCAATAAGTCTTTCGAGCATGATGATGAAATCCTTAGGGCCATCAATAAG
TCTTTCGAGCATGATGATTAAATCCTTAGGGTAATTTATAAGCCTTCACAGAAGAGTAGTGAAGC
AAACCCATCAATAAGTGTCATCAGTAAGTCTTTCGAGCATGATAATG
Found at i:4106965 original size:53 final size:53
Alignment explanation
Indices: 4106845--4107200 Score: 407
Period size: 53 Copynumber: 6.8 Consensus size: 53
4106835 AGAATCACAC
* * * * **
4106845 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAAAGGG--GGGA-TTGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAACGAACCCGTAGG
* * * *
4106895 CAGAAGATT-TTCCGAGTTCTACTCCTTGAAGCAAGAGGAAACGAACACATAGG
1 CAGAAGATTGTT-CGAGTTCTACTCCCTGAAGCAAGAGGGAACGAACCCGTAGG
* *
4106948 TAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAATGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAACGAACCCGTAGG
**
4107001 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAACGAACCCGTAGG
* * * *
4107054 TAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAACGAACCCGTAGG
* * * ***
4107107 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAATAGGGAACGAACCCATTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAACGAACCCGTAGG
* * *
4107160 TAGAAGTTTGTTCGAGTTCCTTAATCCCTGAA-CAAGAGGGA
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGA
4107201 GTGAACCTAT
Statistics
Matches: 264, Mismatches: 35, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
49 2 0.01
50 32 0.12
52 2 0.01
53 207 0.78
54 11 0.04
55 10 0.04
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAACGAACCCGTAGG
Found at i:4107031 original size:106 final size:105
Alignment explanation
Indices: 4106846--4107207 Score: 462
Period size: 106 Copynumber: 3.4 Consensus size: 105
4106836 GAATCACACC
* * * **
4106846 AGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAAAGGG-G-GGA-TTGTAGGCAGAAGATTTTCC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATTTT-C
* * *
4106908 GAGTTCTACTCCTTGAAGCAAGAGGAAACGAACACATAGGT
65 GAGTTCTACTCCCTGAAGCAAGAGGGAACGAACCCATAGGT
*
4106949 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAATGAACCCGTAGGCAGAAGATTGTTC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATT-TTC
** *
4107014 GAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGT
65 GAGTTCTACTCCCTGAAGCAAGAGGGAACGAACCCATAGGT
* * *
4107055 AGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATTC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATT-TTC
* ***
4107120 GAGTTCTACTCCCTGAAGCAATAGGGAACGAACCCATTTTT
65 GAGTTCTACTCCCTGAAGCAAGAGGGAACGAACCCATAGGT
* *
4107161 AGAAGTTTGTTCGAGTTCCTTAATCCCTGAA-CAAGAGGGAGTGAACC
1 AGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGTGAACC
4107208 TATCATTTGA
Statistics
Matches: 225, Mismatches: 28, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
103 36 0.16
105 2 0.01
106 160 0.71
107 18 0.08
108 9 0.04
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (105 bp):
AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATTTTCG
AGTTCTACTCCCTGAAGCAAGAGGGAACGAACCCATAGGT
Found at i:4107131 original size:159 final size:159
Alignment explanation
Indices: 4106845--4107207 Score: 466
Period size: 159 Copynumber: 2.3 Consensus size: 159
4106835 AGAATCACAC
* * * **
4106845 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAAAGGG-G-GGA-TTGTAGGCAGAAGATTTTC
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATTTTC
* * *
4106907 CGAGTTCTACTCCTTGAAGCAAGAGGAAACGAACACATAGGTAGAAGATTGTTCGAGTTCTACTC
66 CGAGTTCTACTCCTTGAAGCAAGAGGAAACGAACACATAAGCAGAAGATTATTCGAGTTCTACTC
* *
4106972 CCTGAAGCAAGAGGGAATGAACCCGTAGG
131 CCTGAAGCAAGAGGGAACGAACCCATAGG
*
4107001 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGTAGAAGATTGTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATT-TT
* * * *
4107066 -CGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTATTCGAGTTCTACT
65 CCGAGTTCTACTCCTTGAAGCAAGAGGAAACGAACACATAAGCAGAAGATTATTCGAGTTCTACT
* ***
4107130 CCCTGAAGCAATAGGGAACGAACCCATTTT
130 CCCTGAAGCAAGAGGGAACGAACCCATAGG
* * *
4107160 TAGAAGTTTGTTCGAGTTCCTTAATCCCTGAA-CAAGAGGGAGTGAACC
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGTGAACC
4107208 TATCATTTGA
Statistics
Matches: 179, Mismatches: 22, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
156 37 0.21
157 1 0.01
158 2 0.01
159 110 0.61
160 19 0.11
161 10 0.06
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (159 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAGAAGATTTTC
CGAGTTCTACTCCTTGAAGCAAGAGGAAACGAACACATAAGCAGAAGATTATTCGAGTTCTACTC
CCTGAAGCAAGAGGGAACGAACCCATAGG
Found at i:4119093 original size:34 final size:34
Alignment explanation
Indices: 4119050--4119115 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
4119040 GTTTGGTTGC
4119050 AATTAATTTTATAGAGATTGAATTCTGAAAAATA
1 AATTAATTTTATAGAGATTGAATTCTGAAAAATA
*
4119084 AATTGATTTTATAGAGATTGAATTCTGAAAAA
1 AATTAATTTTATAGAGATTGAATTCTGAAAAA
4119116 CATTTAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.45, C:0.03, G:0.14, T:0.38
Consensus pattern (34 bp):
AATTAATTTTATAGAGATTGAATTCTGAAAAATA
Found at i:4119269 original size:17 final size:19
Alignment explanation
Indices: 4119247--4119296 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
4119237 CATAAAACTT
4119247 AATATTATTATTT-TTA-A
1 AATATTATTATTTATTATA
4119264 AATATT-TTATTTATTATTA
1 AATATTATTATTTATTA-TA
4119283 AATATTATT-TTTAT
1 AATATTATTATTTAT
4119297 AATTTTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.21
17 9 0.31
19 12 0.41
20 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATATTATTATTTATTATA
Done.