Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000578.1 Hibiscus syriacus cultivar Beakdansim tig00001130_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: 149714
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:926 original size:48 final size:49
Alignment explanation
Indices: 868--964 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 49
858 CCCATAGCAT
*
868 TCACCCCTAGTATGAATGCGGGAGATCAACTA-TGCGCCCAATAACTGG
1 TCACCCCTAGTATGAATGCGGGAGATCAACTATTGCACCCAATAACTGG
* *
916 TCACCCCTAGTATGAATGCGGGAGATCAGCTATTGCACCTAATAACTGG
1 TCACCCCTAGTATGAATGCGGGAGATCAACTATTGCACCCAATAACTGG
965 ATATTACCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 31 0.69
49 14 0.31
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (49 bp):
TCACCCCTAGTATGAATGCGGGAGATCAACTATTGCACCCAATAACTGG
Found at i:1931 original size:30 final size:33
Alignment explanation
Indices: 1862--1932 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 33
1852 TAGGGATTAA
* *
1862 AAAATAAATTAAACATGTTAGAAAGACCAAATT
1 AAAATAAATTAAACATATTAGAAAGACCAAATC
* *
1895 AAAATAAATTAAA-A-ATTA-AGAGACTAAATC
1 AAAATAAATTAAACATATTAGAAAGACCAAATC
1925 AAAATAAA
1 AAAATAAA
1933 ATACAAAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.50
31 3 0.09
32 1 0.03
33 13 0.38
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (33 bp):
AAAATAAATTAAACATATTAGAAAGACCAAATC
Found at i:2286 original size:110 final size:110
Alignment explanation
Indices: 2090--2456 Score: 389
Period size: 110 Copynumber: 3.4 Consensus size: 110
2080 GTCACTACAT
* * * ** * ** *
2090 ATGACCAAAATGTAAAAACACGCTGAACTTAGAGTGACTAAATAGAAAATATTCTAATAAACATT
1 ATGACCAAAATGCAAAAACACGCTAAACTTAGAGGGACTAAATAGAAAATAACCCAATAAATGTA
** * * * * *
2155 TAACATACAAGAAAAATGGGTAAATAACAATTTTAGTCCTCAAAG
66 TAACACGCATGAAAAAAGGGTAAATACCAATTTTGGTCCTTAAAG
* * * *
2200 ATGACCAGAATGCAAAAATACGCTAAACTTATAGGGTCTAAATAGAAAATAACCCAATAAATGTA
1 ATGACCAAAATGCAAAAACACGCTAAACTTAGAGGGACTAAATAGAAAATAACCCAATAAATGTA
* * *
2265 TAACACGCATGAAAAAAGGGTAAATACCAATTTCGGTTCTTATATG
66 TAACACGCATGAAAAAAGGGTAAATACCAATTTTGGTCCTTA-AAG
* * * * *
2311 -TGACCAGAATGCAAAAGCGCCCTAAACTTAGAGGGACTAAATAAAAAATAACCCAATAAATGTA
1 ATGACCAAAATGCAAAAACACGCTAAACTTAGAGGGACTAAATAGAAAATAACCCAATAAATGTA
* *
2375 TAACAGGCATG-AAAAAGGGTAAATACCAATTTTGGTCCTTATAG
66 TAACACGCATGAAAAAAGGGTAAATACCAATTTTGGTCCTTAAAG
* * * * *
2419 GTAACCAAAATG-AAAAAAACGCTAAACCTAGGGGGACT
1 ATGACCAAAATGCAAAAACACGCTAAACTTAGAGGGACT
2457 TAAACGTGAT
Statistics
Matches: 212, Mismatches: 43, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
108 21 0.10
109 37 0.17
110 152 0.72
111 2 0.01
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (110 bp):
ATGACCAAAATGCAAAAACACGCTAAACTTAGAGGGACTAAATAGAAAATAACCCAATAAATGTA
TAACACGCATGAAAAAAGGGTAAATACCAATTTTGGTCCTTAAAG
Found at i:3182 original size:23 final size:23
Alignment explanation
Indices: 3150--3215 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
3140 GCTAAGGCTA
* *
3150 GGTTTAGGTTTTGATTTGGGC-CC
1 GGTTTGGGTTTTG-TTTGGACTCC
*
3173 GGTTTGGGTTTTGTTTGGACTCG
1 GGTTTGGGTTTTGTTTGGACTCC
*
3196 GGTTTGGGTTTGGTTTGGAC
1 GGTTTGGGTTTTGTTTGGAC
3216 CCGATTCTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.16
23 32 0.84
ACGTcount: A:0.06, C:0.09, G:0.39, T:0.45
Consensus pattern (23 bp):
GGTTTGGGTTTTGTTTGGACTCC
Found at i:4301 original size:23 final size:23
Alignment explanation
Indices: 4273--4325 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
4263 GAATGAAAAT
4273 AGATGATTGAGATTAACAATAGA
1 AGATGATTGAGATTAACAATAGA
*
4296 AGATGATTGAGATTAACAGTAGA
1 AGATGATTGAGATTAACAATAGA
4319 AGATGAT
1 AGATGAT
4326 AAGATATTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.45, C:0.04, G:0.25, T:0.26
Consensus pattern (23 bp):
AGATGATTGAGATTAACAATAGA
Found at i:5675 original size:29 final size:29
Alignment explanation
Indices: 5634--5690 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
5624 TAAAGTAACT
* *
5634 AAATAATTAAAATAAAATAAATATTAAAC
1 AAATAAATAAAATAAAAGAAATATTAAAC
* *
5663 AAATAAATGAAATAAAAGAAATTTTAAA
1 AAATAAATAAAATAAAAGAAATATTAAA
5691 TTAATTGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (29 bp):
AAATAAATAAAATAAAAGAAATATTAAAC
Found at i:7142 original size:2 final size:2
Alignment explanation
Indices: 7135--7206 Score: 61
Period size: 2 Copynumber: 39.5 Consensus size: 2
7125 ATAAATAATT
7135 TA TA TA TA TA -A TA TA -A TA CTA TA TA -A TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
7173 TA TA TA CA -A TA TA -A TA TA TA -A TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7207 TCTATTATAT
Statistics
Matches: 58, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
1 8 0.14
2 48 0.83
3 2 0.03
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:7148 original size:7 final size:7
Alignment explanation
Indices: 7101--7197 Score: 73
Period size: 7 Copynumber: 14.4 Consensus size: 7
7091 TTAAATAAAA
7101 ATATAAT
1 ATATAAT
*
7108 AAATAAT
1 ATATAAT
*
7115 ATA-CA-
1 ATATAAT
7120 ATATAAT
1 ATATAAT
*
7127 AAATAAT
1 ATATAAT
*
7134 TTAT-AT
1 ATATAAT
7140 ATATAAT
1 ATATAAT
*
7147 ATAATACT
1 AT-ATAAT
7155 ATAT-A-
1 ATATAAT
7160 ATATAAT
1 ATATAAT
7167 ATA-ATAT
1 ATATA-AT
7174 ATATACA-
1 ATATA-AT
7181 ATATAAT
1 ATATAAT
7188 ATATAAT
1 ATATAAT
7195 ATA
1 ATA
7198 CATATATATT
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
5 7 0.10
6 10 0.14
7 45 0.64
8 8 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (7 bp):
ATATAAT
Found at i:7160 original size:10 final size:9
Alignment explanation
Indices: 7120--7206 Score: 67
Period size: 10 Copynumber: 9.4 Consensus size: 9
7110 ATAATATACA
7120 ATATAATA-
1 ATATAATAT
*
7128 A-ATAATTT
1 ATATAATAT
7136 ATAT-ATAT
1 ATATAATAT
7144 AATATAATACT
1 -ATATAATA-T
7155 ATATAATAT
1 ATATAATAT
7164 AATATAATAT
1 -ATATAATAT
7174 ATATACA-AT
1 ATATA-ATAT
7183 ATA-ATATAT
1 ATATA-ATAT
7192 AATATACATAT
1 -ATATA-ATAT
7203 ATAT
1 ATAT
7207 TCTATTATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
7 5 0.08
8 7 0.11
9 19 0.29
10 28 0.43
11 6 0.09
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (9 bp):
ATATAATAT
Found at i:7197 original size:5 final size:5
Alignment explanation
Indices: 7100--7190 Score: 75
Period size: 5 Copynumber: 18.2 Consensus size: 5
7090 GTTAAATAAA
* *
7100 AATAT AATA- AATA- ATATAC AATAT AATA- AATA- ATTTAT ATATAT
1 AATAT AATAT AATAT A-ATAT AATAT AATAT AATAT A-ATAT A-ATAT
*
7144 AATAT AATACT -ATAT AATAT AATAT AATAT ATATAC AATAT AATAT A
1 AATAT AATA-T AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT A
7191 TAATATACAT
Statistics
Matches: 74, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
4 11 0.15
5 51 0.69
6 12 0.16
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:7205 original size:36 final size:36
Alignment explanation
Indices: 7135--7206 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 36
7125 ATAAATAATT
* *
7135 TATATATATAATATAATACTATATAATATAATATAA
1 TATATATACAATATAATACTATATAACATAATATAA
7171 TATATATACAATATAATA-TATAATATACATATATAT
1 TATATATACAATATAATACTAT-ATA-ACATA-ATAT
7207 TCTATTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 3 0.10
36 20 0.65
37 4 0.13
38 4 0.13
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (36 bp):
TATATATACAATATAATACTATATAACATAATATAA
Found at i:7301 original size:37 final size:37
Alignment explanation
Indices: 7249--7382 Score: 168
Period size: 38 Copynumber: 3.6 Consensus size: 37
7239 TTTCAACAAT
7249 TATATATTATATATGCTTTCAAAAACCGTTTTTAAAAAC
1 TATATA-T-TATATGCTTTCAAAAACCGTTTTTAAAAAC
*
7288 TATATATTATATGCTTTCAAAAACCGTCTTTTAAAATC
1 TATATATTATATGCTTTCAAAAACCGT-TTTTAAAAAC
* * *
7326 TATATATTATATGTTTTC-AAAA-C-TATTTAAAAAT
1 TATATATTATATGCTTTCAAAAACCGTTTTTAAAAAC
7360 TATATATTATATG-TTATCAAAAA
1 TATATATTATATGCTT-TCAAAAA
7383 ATATTTCTGA
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
33 2 0.02
34 22 0.25
35 5 0.06
36 1 0.01
37 24 0.28
38 27 0.31
39 6 0.07
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.43
Consensus pattern (37 bp):
TATATATTATATGCTTTCAAAAACCGTTTTTAAAAAC
Found at i:8509 original size:22 final size:22
Alignment explanation
Indices: 8484--8526 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
8474 TATTATATTT
*
8484 TAAATTTA-ATTTGAATAATAAA
1 TAAACTTATATTTGAA-AATAAA
*
8506 TAAACTTATATTTTAAAATAA
1 TAAACTTATATTTGAAAATAA
8527 TTATATGGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAACTTATATTTGAAAATAAA
Found at i:10173 original size:28 final size:28
Alignment explanation
Indices: 10133--10196 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
10123 ATGATTGGAT
10133 TCACAGTTATTACTTATTCTGCAGTCGG
1 TCACAGTTATTACTTATTCTGCAGTCGG
10161 TCACAGTTATTACTTATTCTGCAGTCGG
1 TCACAGTTATTACTTATTCTGCAGTCGG
*
10189 TCTCAGTT
1 TCACAGTT
10197 GCCTTTAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (28 bp):
TCACAGTTATTACTTATTCTGCAGTCGG
Found at i:17548 original size:23 final size:23
Alignment explanation
Indices: 17518--17587 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
17508 CATTTTATAT
17518 GGCACTTCGGTGCAATTCTACGA
1 GGCACTTCGGTGCAATTCTACGA
*
17541 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGA
* * *
17564 GGAACTTCGGTGCATTTATACGA
1 GGCACTTCGGTGCAATTCTACGA
17587 G
1 G
17588 TCGTGGTGAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGA
Found at i:19111 original size:83 final size:83
Alignment explanation
Indices: 19024--19184 Score: 196
Period size: 83 Copynumber: 1.9 Consensus size: 83
19014 CGATATAGAA
* * * *
19024 TTGTACGTTAGCGGCATTTTTCTACAAACGCCGCAATAAGTTTGACCTATAGTGGCAATTTTTCA
1 TTGTACGTTAGCGGCATTCTTATACAAACGCCGCAATAAGTGTAACCTATAGTGGCAATTTTTCA
19089 ACAAACGCCGCAAAATAT
66 ACAAACGCCGCAAAATAT
* * * * * * * ***
19107 TTGTACTTTAGGGGCGTTCTTATACAAACGCCGTAATAGGTGTAATCTATATTGGTGTTTTTTCA
1 TTGTACGTTAGCGGCATTCTTATACAAACGCCGCAATAAGTGTAACCTATAGTGGCAATTTTTCA
19172 ACAAACGCCGCAA
66 ACAAACGCCGCAA
19185 GAGGTGTAAT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
83 64 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (83 bp):
TTGTACGTTAGCGGCATTCTTATACAAACGCCGCAATAAGTGTAACCTATAGTGGCAATTTTTCA
ACAAACGCCGCAAAATAT
Found at i:19199 original size:125 final size:124
Alignment explanation
Indices: 19036--19300 Score: 291
Period size: 125 Copynumber: 2.1 Consensus size: 124
19026 GTACGTTAGC
* * * * *
19036 GGCATTTTTCTACAAACGCCGCAATAAGTTTGACCTATAGTGGCAATTTTTCAACAAACGCCGCA
1 GGCATTTTTCAACAAACGCCGCAAGAAGTGTAACCTATAGTAGCAATTTTTCAACAAACGCCGCA
** ** * *
19101 AAATATTTGTACTTTAGGGGCGTTCTTATACAAA-CGC-CGTAATAGGTGTAATCTATATT
66 AAATATTTAAACTTTAACGGCATTCTTATACAAATCGCAC--AATAGGTGTAATCTATAGT
** * * ** * *
19160 GGTGTTTTTTCAACAAACGCCGCAAGAGGTGTAATCTATAGTAGCGTTTTTTCAACAAATGTCGC
1 GG-CATTTTTCAACAAACGCCGCAAGAAGTGTAACCTATAGTAGCAATTTTTCAACAAACGCCGC
* * *
19225 AACATATTTAAACTTTAACGGCATTTTTATACAAATCTCACAATAGGTGTAATCTATAGT
65 AAAATATTTAAACTTTAACGGCATTCTTATACAAATCGCACAATAGGTGTAATCTATAGT
19285 GGCATTTTTCAACAAA
1 GGCATTTTTCAACAAA
19301 TGTCGCAACA
Statistics
Matches: 114, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
124 14 0.12
125 97 0.85
126 2 0.02
127 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (124 bp):
GGCATTTTTCAACAAACGCCGCAAGAAGTGTAACCTATAGTAGCAATTTTTCAACAAACGCCGCA
AAATATTTAAACTTTAACGGCATTCTTATACAAATCGCACAATAGGTGTAATCTATAGT
Found at i:19226 original size:42 final size:42
Alignment explanation
Indices: 19130--19218 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
19120 GCGTTCTTAT
* * * * *
19130 ACAAACGCCGTAATAGGTGTAATCTATATTGGTGTTTTTTCA
1 ACAAACGCCGCAAGAGGTGTAATCTATAGTAGCGTTTTTTCA
19172 ACAAACGCCGCAAGAGGTGTAATCTATAGTAGCGTTTTTTCA
1 ACAAACGCCGCAAGAGGTGTAATCTATAGTAGCGTTTTTTCA
19214 ACAAA
1 ACAAA
19219 TGTCGCAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (42 bp):
ACAAACGCCGCAAGAGGTGTAATCTATAGTAGCGTTTTTTCA
Found at i:19260 original size:41 final size:41
Alignment explanation
Indices: 19214--19343 Score: 118
Period size: 41 Copynumber: 3.2 Consensus size: 41
19204 CGTTTTTTCA
*
19214 ACAAATGTCGCAACATATTTAAACTTTAACGGCATTTTTAT
1 ACAAATGTCGCAACATATTTAAACTTTAGCGGCATTTTTAT
* * * ** * * * *
19255 ACAAATCTCACAATAGGTGTAATCTATAGTGGCATTTTTCA-
1 ACAAATGTCGCAACATATTTAAACTTTAGCGGCATTTTT-AT
* * *
19296 ACAAATGTCGCAACATATTTATACTTTAGCGGCGTTTATAT
1 ACAAATGTCGCAACATATTTAAACTTTAGCGGCATTTTTAT
*
19337 AAAAATG
1 ACAAATG
19344 CTGCGACAGA
Statistics
Matches: 64, Mismatches: 23, Indels: 4
0.70 0.25 0.04
Matches are distributed among these distances:
40 1 0.02
41 62 0.97
42 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (41 bp):
ACAAATGTCGCAACATATTTAAACTTTAGCGGCATTTTTAT
Found at i:19322 original size:82 final size:83
Alignment explanation
Indices: 19186--19342 Score: 244
Period size: 82 Copynumber: 1.9 Consensus size: 83
19176 ACGCCGCAAG
*
19186 AGGTGTAATCTATAGTAGCGTTTTTTCAACAAATGTCGCAACATATTTAAACTTTAACGGCATTT
1 AGGTGTAATCTATAGTAGCGATTTTTCAACAAATGTCGCAACATATTTAAACTTTAACGGCATTT
* *
19251 TTATACAAATCTCACAAT
66 ATATAAAAATCTCACAAT
* * * *
19269 AGGTGTAATCTATAGTGGC-ATTTTTCAACAAATGTCGCAACATATTTATACTTTAGCGGCGTTT
1 AGGTGTAATCTATAGTAGCGATTTTTCAACAAATGTCGCAACATATTTAAACTTTAACGGCATTT
19333 ATATAAAAAT
66 ATATAAAAAT
19343 GCTGCGACAG
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
82 49 0.73
83 18 0.27
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (83 bp):
AGGTGTAATCTATAGTAGCGATTTTTCAACAAATGTCGCAACATATTTAAACTTTAACGGCATTT
ATATAAAAATCTCACAAT
Found at i:27585 original size:21 final size:21
Alignment explanation
Indices: 27561--27615 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
27551 TCGAAAATGA
*
27561 AGCAAGGGAAGCAGAGAGAGC
1 AGCAAGGGAAGCAGAAAGAGC
* *
27582 AGC-AGCGGAAACATAAAGAGC
1 AGCAAG-GGAAGCAGAAAGAGC
*
27603 AGCAATGGAAGCA
1 AGCAAGGGAAGCA
27616 CATATAGAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.89
22 1 0.04
ACGTcount: A:0.45, C:0.16, G:0.35, T:0.04
Consensus pattern (21 bp):
AGCAAGGGAAGCAGAAAGAGC
Found at i:28107 original size:44 final size:44
Alignment explanation
Indices: 28059--28196 Score: 129
Period size: 44 Copynumber: 3.1 Consensus size: 44
28049 TATATCCCAT
* *
28059 ACCTTTAGC-GACGTTTATATACGACAAACATCGTTATATACAAG
1 ACCTTTAGCAG-CATTTATATACGACAAACATCGCTATATACAAG
* *
28103 ACCTTTAGCAGCATTTATATCCGACAAACGTCGCTATATACAAG
1 ACCTTTAGCAGCATTTATATACGACAAACATCGCTATATACAAG
* * * * * * *
28147 AACTTTTGCGGCATTTGTAT-CTAAAAAACA-CTGCTATATACCAG
1 ACCTTTAGCAGCATTTATATAC-GACAAACATC-GCTATATACAAG
28191 ACCTTT
1 ACCTTT
28197 TGCGACGTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
43 2 0.03
44 75 0.96
45 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.30
Consensus pattern (44 bp):
ACCTTTAGCAGCATTTATATACGACAAACATCGCTATATACAAG
Found at i:28197 original size:44 final size:44
Alignment explanation
Indices: 28135--28219 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
28125 GACAAACGTC
* *
28135 GCTATATACAAGAACTTTTGCGGCATTTGTATCTAAAAAACACT
1 GCTATATACAAGAACTTTTGCGACATTTGTATCCAAAAAACACT
* * *
28179 GCTATATACCAGACCTTTTGCGACGTTTGTATCCAAAAAAC
1 GCTATATACAAGAACTTTTGCGACATTTGTATCCAAAAAAC
28220 GCCGCTAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (44 bp):
GCTATATACAAGAACTTTTGCGACATTTGTATCCAAAAAACACT
Found at i:31215 original size:17 final size:18
Alignment explanation
Indices: 31182--31217 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31172 TTTAGTTTGG
31182 TTCAGTTAAAAATGTTTT
1 TTCAGTTAAAAATGTTTT
*
31200 TTCATTTAAAAA-GTTTT
1 TTCAGTTAAAAATGTTTT
31217 T
1 T
31218 AAAAAGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (18 bp):
TTCAGTTAAAAATGTTTT
Found at i:31962 original size:18 final size:19
Alignment explanation
Indices: 31939--31974 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31929 TTATTGGATA
*
31939 TAAAATATAAAT-TTTAAT
1 TAAAATAAAAATGTTTAAT
31957 TAAAATAAAAATGTTTAA
1 TAAAATAAAAATGTTTAA
31975 CTAATTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
TAAAATAAAAATGTTTAAT
Found at i:32257 original size:31 final size:31
Alignment explanation
Indices: 32189--32257 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
32179 TTAATGGCTG
* *
32189 AGGGACTAAAATCGAATATATCGGTAACGTT
1 AGGGACTAAAATCGAATATATCGATAACATT
* *
32220 AAGGACTAAAATCGAATGA-ATTGATAACATT
1 AGGGACTAAAATCGAAT-ATATCGATAACATT
32251 AGGGACT
1 AGGGACT
32258 GTCGACACCG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.25
Consensus pattern (31 bp):
AGGGACTAAAATCGAATATATCGATAACATT
Found at i:36030 original size:264 final size:261
Alignment explanation
Indices: 35558--36267 Score: 1048
Period size: 264 Copynumber: 2.7 Consensus size: 261
35548 AATATCCTTC
** *
35558 CCGAAGGTCTTATCATCTTGCTCGAAAGACTTATAAATGGTTCGAATGACTTACGCATCATGCTC
1 CCGAAGGTCTTATCATCTTGCTCGAAAGACTTATAAATGGCCCGAATGACTTAAGCATCATGCTC
* * * * *
35623 AAAAGACTTACTGATGGCCCGAATGACGTACTCATCAAGAAACCCTTGAAAATTAAGCTTAGTTT
66 GAAAGACTTACTGATGGCCCGAATGACTTACTCATAAAGAAAACCTTGAAAATAAAGCTTAGTTT
* *
35688 CTT-TAAAATTTCTTTTGAAAATATCATGTTGTTTGGGTAACGTGCCCCTACATCAAGATTCAAC
131 CTTATAAAAATTCTTTTGAAAATATCATGTTGTTTGGGTAACGTGCCCCCACATCAAGATTCAAC
* *
35752 TCCATATGTGATGAATCAAGTACCGAAAATATTGAAAACATCCTGTCTGAAAGTCTTATGGATGG
196 TCCATATGTGATGAATCAAGTAACGAAAATATTGAAAACATCCTGCCTGAAAGTCTTATGGATGG
35817 -
261 A
* * * *
35817 CTCGAAAGTCTTATCATCTTGCTCGAAAGACTTATAAATGGCCCAAAGGACTTAAGCATCATGTT
1 C-CGAAGGTCTTATCATCTTGCTCGAAAGACTTATAAATGGCCCGAATGACTTAAGCATCATGCT
* * * * * * * * *
35882 CGAAAGATTTTATTGATGGTCCGAAGGACTTACTCTTTAAGAAAACCTTAAAAATCAATCTTAGT
65 CGAAAGA-CTTACTGATGGCCCGAATGACTTACTCATAAAGAAAACCTTGAAAATAAAGCTTAG-
35947 TTTCTTATAAAAAATTCTTTTGAAAATATCATGTTGTTTGGGTAACGTGCCCCCACATCAAGATT
128 TTTCTTAT-AAAAATTCTTTTGAAAATATCATGTTGTTTGGGTAACGTGCCCCCACATCAAGATT
* * * * *
36012 CAACTCCATATGTGATGAATCGAGTAATGAAAATGTTGAAAACATCCTGCCTGAAGGTTTTATGG
192 CAACTCCATATGTGATGAATCAAGTAACGAAAATATTGAAAACATCCTGCCTGAAAGTCTTATGG
36077 ATGGA
257 ATGGA
* * *
36082 CAGAAGGTTTTATCATCTTGCTCGAAAGACTTATAAATGGCCTGAATGACTTAAGCATCATGCTC
1 CCGAAGGTCTTATCATCTTGCTCGAAAGACTTATAAATGGCCCGAATGACTTAAGCATCATGCTC
*
36147 GAAAGACTTACTGATGGCCCGAATGCCTTACTCATAAAGAAAACCTTGAAAATAAAGCTTAGTTT
66 GAAAGACTTACTGATGGCCCGAATGACTTACTCATAAAGAAAACCTTGAAAATAAAGCTTAGTTT
*
36212 CTTATAAAAA-TCTTTTGAAAATATCATGTTGTTTGGGTAACGTGCCCCCACGTCAA
131 CTTATAAAAATTCTTTTGAAAATATCATGTTGTTTGGGTAACGTGCCCCCACATCAA
36268 AGTAATGATT
Statistics
Matches: 399, Mismatches: 46, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
259 1 0.00
260 107 0.27
261 50 0.13
262 14 0.04
263 47 0.12
264 179 0.45
265 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (261 bp):
CCGAAGGTCTTATCATCTTGCTCGAAAGACTTATAAATGGCCCGAATGACTTAAGCATCATGCTC
GAAAGACTTACTGATGGCCCGAATGACTTACTCATAAAGAAAACCTTGAAAATAAAGCTTAGTTT
CTTATAAAAATTCTTTTGAAAATATCATGTTGTTTGGGTAACGTGCCCCCACATCAAGATTCAAC
TCCATATGTGATGAATCAAGTAACGAAAATATTGAAAACATCCTGCCTGAAAGTCTTATGGATGG
A
Found at i:36164 original size:42 final size:42
Alignment explanation
Indices: 36095--36176 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
36085 AAGGTTTTAT
* *
36095 CATCTTGCTCGAAAGACTTATAAATGGCCTGAATGACTTAAG
1 CATCATGCTCGAAAGACTTATAAATGGCCCGAATGACTTAAG
* *
36137 CATCATGCTCGAAAGACTTACT-GATGGCCCGAATGCCTTA
1 CATCATGCTCGAAAGACTTA-TAAATGGCCCGAATGACTTA
36177 CTCATAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTATAAATGGCCCGAATGACTTAAG
Found at i:37764 original size:17 final size:17
Alignment explanation
Indices: 37738--37778 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
37728 TGATTTCAAG
*
37738 ACGTCATCTAAAATTTT
1 ACGTCTTCTAAAATTTT
37755 ACGTCTTCTAAAATTTT
1 ACGTCTTCTAAAATTTT
37772 ACGTCTT
1 ACGTCTT
37779 GAACCCTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (17 bp):
ACGTCTTCTAAAATTTT
Found at i:38186 original size:16 final size:16
Alignment explanation
Indices: 38161--38199 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
38151 TTTGATCAGT
38161 TTTC-TTTCTTATTC-C
1 TTTCTTTTCTT-TTCTC
38176 TTTCTTTTCTTTTCTC
1 TTTCTTTTCTTTTCTC
38192 TTTCTTTT
1 TTTCTTTT
38200 TTCCTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTTTTCTTTTCTC
Found at i:38219 original size:50 final size:50
Alignment explanation
Indices: 38165--38267 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 50
38155 ATCAGTTTTC
38165 TTTCT-TATTCCTTTCTTTTCTTTTCTCTTTCTTTT-T-TCCTTTTTCCCTTT
1 TTTCTCTATT-CTTTCTTTT-TTTTCTCTTT-TTTTCTATCCTTTTTCCCTTT
* * * *
38215 TTTCTCTATTTTTTCTTTTTTTTTTCTTTTTTTCTATCTTTTTTTCCTTT
1 TTTCTCTATTCTTTCTTTTTTTTCTCTTTTTTTCTATCCTTTTTCCCTTT
38265 TTT
1 TTT
38268 TGCTATATCT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
48 4 0.09
49 10 0.22
50 28 0.61
51 4 0.09
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (50 bp):
TTTCTCTATTCTTTCTTTTTTTTCTCTTTTTTTCTATCCTTTTTCCCTTT
Found at i:38228 original size:11 final size:10
Alignment explanation
Indices: 38176--38268 Score: 70
Period size: 9 Copynumber: 9.3 Consensus size: 10
38166 TTCTTATTCC
38176 TTTCT-TTTCT
1 TTTCTCTTT-T
38186 TTTCTCTTTCT
1 TTTCTCTTT-T
* *
38197 TTTTTC-CTT
1 TTTCTCTTTT
*
38206 TTTC-CCTTT
1 TTTCTCTTTT
38215 TTTCTCTATTT
1 TTTCTCT-TTT
38226 TTTCT-TTTT
1 TTTCTCTTTT
*
38235 TTTTTCTTTT
1 TTTCTCTTTT
38245 TTTCTATCTTTT
1 TTTC--TCTTTT
38257 TTTC-CTTTT
1 TTTCTCTTTT
38266 TTT
1 TTT
38269 GCTATATCTT
Statistics
Matches: 69, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.01
9 25 0.36
10 15 0.22
11 18 0.26
12 10 0.14
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTCTCTTTT
Found at i:38246 original size:20 final size:21
Alignment explanation
Indices: 38212--38287 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
38202 CCTTTTTCCC
* *
38212 TTTTTTCTCTATTTTTTCT-T
1 TTTTTTTTCTTTTTTTTCTAT
38232 TTTTTTTTC-TTTTTTTCTAT
1 TTTTTTTTCTTTTTTTTCTAT
* *
38252 CTTTTTTTCCTTTTTTTGCTAT
1 -TTTTTTTTCTTTTTTTTCTAT
*
38274 ATCTTTTCTTCTTT
1 -T-TTTTTTTCTTT
38288 CTCTATGTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 8 0.18
20 9 0.20
21 8 0.18
22 11 0.24
23 9 0.20
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.78
Consensus pattern (21 bp):
TTTTTTTTCTTTTTTTTCTAT
Found at i:38260 original size:12 final size:12
Alignment explanation
Indices: 38228--38260 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38218 CTCTATTTTT
*
38228 TCTTTTTTT-TT
1 TCTTTTTTTCTA
38239 TCTTTTTTTCTA
1 TCTTTTTTTCTA
38251 TCTTTTTTTC
1 TCTTTTTTTC
38261 CTTTTTTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (12 bp):
TCTTTTTTTCTA
Found at i:38266 original size:22 final size:21
Alignment explanation
Indices: 38212--38273 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
38202 CCTTTTTCCC
*
38212 TTTTTTCTCTATTTTTTCT-TT
1 TTTTTTC-CTTTTTTTTCTATT
*
38233 TTTTTTTC-TTTTTTTCTATCT
1 TTTTTTCCTTTTTTTTCTAT-T
*
38254 TTTTTTCCTTTTTTTGCTAT
1 TTTTTTCCTTTTTTTTCTAT
38274 ATCTTTTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 8 0.24
20 2 0.06
21 14 0.41
22 10 0.29
ACGTcount: A:0.05, C:0.15, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTTCCTTTTTTTTCTATT
Found at i:38280 original size:22 final size:21
Alignment explanation
Indices: 38213--38280 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
38203 CTTTTTCCCT
*
38213 TTTTTCTCTATTTTTTCT-T-TT
1 TTTTTC-CT-TTTTTTCTATATC
* * *
38234 TTTTTTCTTTTTTTCTATCTT
1 TTTTTCCTTTTTTTCTATATC
38255 TTTTTCCTTTTTTTGCTATATC
1 TTTTTCCTTTTTTT-CTATATC
38277 TTTT
1 TTTT
38281 CTTCTTTCTC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 8 0.20
20 3 0.08
21 20 0.50
22 9 0.22
ACGTcount: A:0.06, C:0.15, G:0.01, T:0.78
Consensus pattern (21 bp):
TTTTTCCTTTTTTTCTATATC
Found at i:40844 original size:17 final size:16
Alignment explanation
Indices: 40813--40846 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
40803 CACGTGAGGA
40813 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
40829 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
40846 T
1 T
40847 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:51047 original size:17 final size:16
Alignment explanation
Indices: 51016--51049 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
51006 CACGTGAGGA
51016 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
51032 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
51049 T
1 T
51050 ACTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:52017 original size:17 final size:18
Alignment explanation
Indices: 51995--52036 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
51985 AACCAAATAA
*
51995 AAATAAAATG-ATAATGC
1 AAATAAAATGAATAAAGC
52012 AAAT-AAATGAATAAAGC
1 AAATAAAATGAATAAAGC
52029 AAATAAAA
1 AAATAAAA
52037 GGAAGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 14 0.64
18 3 0.14
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (18 bp):
AAATAAAATGAATAAAGC
Found at i:52147 original size:18 final size:18
Alignment explanation
Indices: 52091--52162 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 18
52081 TAGATAAATA
52091 AATAAGTAAAATATA-A-
1 AATAAGTAAAATATATAT
* *
52107 AAAAAGTAAAAGTATATGT
1 AATAAGTAAAA-TATATAT
52126 -ATAAGTAAAATA-ATATT
1 AATAAGTAAAATATATA-T
*
52143 AATAAAATAAAATATATAT
1 AAT-AAGTAAAATATATAT
52162 A
1 A
52163 TAATAGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
16 12 0.27
17 7 0.16
18 11 0.25
19 11 0.25
20 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (18 bp):
AATAAGTAAAATATATAT
Found at i:52234 original size:2 final size:2
Alignment explanation
Indices: 52221--52280 Score: 63
Period size: 2 Copynumber: 30.5 Consensus size: 2
52211 AAAATAGGGA
* *
52221 AT AT AA AT AT AT AT AT AT AT AT AT AT A- AT ACT A- AT GAT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT
52262 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
52281 ATTAATAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
1 3 0.06
2 43 0.86
3 4 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:52298 original size:33 final size:32
Alignment explanation
Indices: 52229--52303 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 32
52219 GAATATAAAT
*
52229 ATATATATATATATATATAATACTAATGATAAA
1 ATATATATATATATATATAATA-TAATGAAAAA
*
52262 ATATATATATATATATATAAT-TAAT-AAAAC
1 ATATATATATATATATATAATATAATGAAAAA
*
52292 GTA-ATATATATA
1 ATATATATATATA
52304 ACAAAAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 9 0.23
30 5 0.13
31 4 0.10
33 21 0.54
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (32 bp):
ATATATATATATATATATAATATAATGAAAAA
Found at i:52303 original size:31 final size:32
Alignment explanation
Indices: 52223--52286 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
52213 AATAGGGAAT
52223 ATAAATATATATATATATATATATAATACTAATG
1 ATAAA-ATATATATATATATATATAATA-TAATG
52257 ATAAAATATATATATATATATATAAT-TAAT
1 ATAAAATATATATATATATATATAATATAAT
52287 AAAACGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 4 0.13
33 21 0.70
34 5 0.17
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (32 bp):
ATAAAATATATATATATATATATAATATAATG
Found at i:53565 original size:22 final size:23
Alignment explanation
Indices: 53545--53592 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
53535 ATATGATATG
53545 TATATTAT-A-TAATAA-ACATA
1 TATATTATAAGTAATAACACATA
53565 TATATTATAAGTAATAACACATA
1 TATATTATAAGTAATAACACATA
*
53588 AATAT
1 TATAT
53593 AAATGCCATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 6 0.25
23 9 0.38
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (23 bp):
TATATTATAAGTAATAACACATA
Found at i:54463 original size:22 final size:22
Alignment explanation
Indices: 54438--54538 Score: 59
Period size: 22 Copynumber: 5.2 Consensus size: 22
54428 GGAAACTGTC
54438 TCAAGAGAGACAAGATTTTGTT
1 TCAAGAGAGACAAGATTTTGTT
* *
54460 TCAAG-G-G--AA-A--CTGTC
1 TCAAGAGAGACAAGATTTTGTT
54475 TCAAGAGAGACAAGATTTTGTT
1 TCAAGAGAGACAAGATTTTGTT
* *
54497 TCAA-TG-G--AA-A--TTGTC
1 TCAAGAGAGACAAGATTTTGTT
*
54512 TCAAGAGAAACAAGATTTTGTT
1 TCAAGAGAGACAAGATTTTGTT
54534 TCAAG
1 TCAAG
54539 GGAAACTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 28
0.60 0.10 0.30
Matches are distributed among these distances:
15 16 0.29
16 2 0.04
17 3 0.05
18 4 0.07
19 4 0.07
20 4 0.07
21 2 0.04
22 21 0.38
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.30
Consensus pattern (22 bp):
TCAAGAGAGACAAGATTTTGTT
Found at i:54469 original size:37 final size:37
Alignment explanation
Indices: 54419--54575 Score: 269
Period size: 37 Copynumber: 4.2 Consensus size: 37
54409 TCAGAGGTTG
54419 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
54456 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
* * *
54493 TGTTTCAATGGAAATTGTCTCAAGAGAAACAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
*
54530 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
*
54567 TGTTACAAG
1 TGTTTCAAG
54576 TTGGGTCAAT
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 112 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
Found at i:54827 original size:37 final size:37
Alignment explanation
Indices: 54777--54859 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
54767 TTGAGTTGGA
* * *
54777 TGTTTCAATGGAAACTGTCTCAAGAGAAACAATATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAAACAAGATTT
* *
54814 TGTTTCAAGGGAAACTATCTCAAGAGAGATAAGATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAAACAAGATTT
54851 TGTTTCAAG
1 TGTTTCAAG
54860 TTGGGTCAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAAACAAGATTT
Found at i:55003 original size:284 final size:284
Alignment explanation
Indices: 54493--55061 Score: 1021
Period size: 284 Copynumber: 2.0 Consensus size: 284
54483 GACAAGATTT
*
54493 TGTTTCAATGGAAATTGTCTCAAGAGAAACAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAATGGAAACTGTCTCAAGAGAAACAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
54558 ACAAGATTTTGTTACAAGTTGGGTCAATCTGTTTGTGAAGTTAGAATCGTGTATGGCTCATCCGT
66 ACAAGATTTTGTTACAAGTTGGGTCAATCTGTTTGTGAAGTTAGAATCGTGTATGGCCCATCCGT
* *
54623 CGTGAAGTTAAGCCTTGAAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATGTAAGTTGCGT
131 CGTGAAGTTAAGCCTTGAAATTGGATATCATTCGTCGTGAAGTTGAAATCCAATGTAAGTTGCAT
*
54688 TGTTTCGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTTGTTAA
196 TGTTTCGAGGCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTTGTTAA
54753 CAGACACTCATTCTTTGAGTTGGA
261 CAGACACTCATTCTTTGAGTTGGA
*
54777 TGTTTCAATGGAAACTGTCTCAAGAGAAACAATATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAATGGAAACTGTCTCAAGAGAAACAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* * *
54842 ATAAGATTTTGTTTCAAGTTGGGTCAATCTGTTTGTGAAGTTAGAATCGTGTATGGCCCCTCCGT
66 ACAAGATTTTGTTACAAGTTGGGTCAATCTGTTTGTGAAGTTAGAATCGTGTATGGCCCATCCGT
* *
54907 TGTGAAGTTAAGCCTTGAAATTGGATATCATTCGTCGTGAAGTTGAAATCTAATGTAAGTTGCAT
131 CGTGAAGTTAAGCCTTGAAATTGGATATCATTCGTCGTGAAGTTGAAATCCAATGTAAGTTGCAT
*
54972 TGTTTCGAGGCCAATATTCTTCACTGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTTGTTAA
196 TGTTTCGAGGCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTTGTTAA
*
55037 CAGACACTCCTTCTTTGAGTTGGA
261 CAGACACTCATTCTTTGAGTTGGA
55061 T
1 T
55062 ATCCTTCGTC
Statistics
Matches: 272, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
284 272 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (284 bp):
TGTTTCAATGGAAACTGTCTCAAGAGAAACAAGATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAGATTTTGTTACAAGTTGGGTCAATCTGTTTGTGAAGTTAGAATCGTGTATGGCCCATCCGT
CGTGAAGTTAAGCCTTGAAATTGGATATCATTCGTCGTGAAGTTGAAATCCAATGTAAGTTGCAT
TGTTTCGAGGCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAAACTGGGAAGTTTGTTAA
CAGACACTCATTCTTTGAGTTGGA
Found at i:57030 original size:95 final size:95
Alignment explanation
Indices: 56857--57038 Score: 285
Period size: 95 Copynumber: 1.9 Consensus size: 95
56847 ATATGTAAAT
* * * *
56857 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGTCGGGGCATTTAACCAATTTCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGCCTTAGAGGG
* *
56922 ACAGCTCAGGCTTTATTGTATAGTATAATC
66 ACAACTCAAGCTTTATTGTATAGTATAATC
56952 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTG-CTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGCCT-TAGAGG
*
57016 GATAACTCAAGCTTTATTGTATA
65 GACAACTCAAGCTTTATTGTATA
57039 TAAATAATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 2 0.03
95 77 0.97
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATAGTATAATC
Found at i:61163 original size:12 final size:12
Alignment explanation
Indices: 61136--61193 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 12
61126 AGATAAAAAT
61136 ATAAAAATAGAGA
1 ATAAAAATAGA-A
61149 ATAAAAATAGAA
1 ATAAAAATAGAA
61161 AT-AAAATAGATAA
1 ATAAAAATAG--AA
61174 ATAAATAAGTA-AA
1 ATAAA-AA-TAGAA
61187 ATAAAAA
1 ATAAAAA
61194 AAATAAAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
11 7 0.17
12 5 0.12
13 22 0.55
14 2 0.05
15 2 0.05
16 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (12 bp):
ATAAAAATAGAA
Found at i:61173 original size:21 final size:20
Alignment explanation
Indices: 61126--61174 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
61116 AATAAAAGGA
* *
61126 AGATAAAAATATAAAAATAG
1 AGATAAAAATAGAAAAAAAG
*
61146 AGAATAAAAATAGAAATAAAAT
1 AG-ATAAAAATAGAAA-AAAAG
61168 AGATAAA
1 AGATAAA
61175 TAAATAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 17 0.71
22 5 0.21
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.18
Consensus pattern (20 bp):
AGATAAAAATAGAAAAAAAG
Found at i:61224 original size:36 final size:37
Alignment explanation
Indices: 61148--61255 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 37
61138 AAAAATAGAG
* * * * *
61148 AATAAAAATAGAAATAAAATAGATAAATAAATAAGTAA
1 AATAATAATA-AAATAAAATAAATATATATATAAGAAA
*
61186 AATAA-AA-AAAATAAAAGTATATATATATATAAGAAA
1 AATAATAATAAAATAAAA-TAAATATATATATAAGAAA
*
61222 AATAATAATAATAATAAAATAAAAATATATATAA
1 AATAATAATAA-AATAAAATAAATATATATATAA
61256 TAGAAAATCA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
35 8 0.13
36 21 0.35
37 4 0.07
38 20 0.33
39 7 0.12
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (37 bp):
AATAATAATAAAATAAAATAAATATATATATAAGAAA
Found at i:61261 original size:40 final size:38
Alignment explanation
Indices: 61133--61262 Score: 106
Period size: 40 Copynumber: 3.2 Consensus size: 38
61123 GGAAGATAAA
* *
61133 AATATAAAAATAGAGAATAAAAATAGAAAT-AAAATAGATA-
1 AATAGAAAAATA-A-AAT-AAAATA-AAATAAAAATATATAT
*
61173 AATA-AATAAGTAAAATAAAA-AAAATAAAAGTATATATAT
1 AATAGAA-AAATAAAATAAAATAAAATAAAA--ATATATAT
61212 ATATAAGAAAAATAATAATAATAATAAAATAAAAATATATAT
1 A-AT-AGAAAAATAA-AATAA-AATAAAATAAAAATATATAT
61254 AATAGAAAA
1 AATAGAAAA
61263 TCAAAGGTAA
Statistics
Matches: 76, Mismatches: 3, Indels: 22
0.75 0.03 0.22
Matches are distributed among these distances:
35 4 0.05
36 4 0.05
37 4 0.05
38 9 0.12
39 4 0.05
40 16 0.21
41 8 0.11
42 16 0.21
43 2 0.03
44 9 0.12
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (38 bp):
AATAGAAAAATAAAATAAAATAAAATAAAAATATATAT
Found at i:72772 original size:5 final size:5
Alignment explanation
Indices: 72762--72804 Score: 68
Period size: 5 Copynumber: 8.4 Consensus size: 5
72752 TAATAAATTC
*
72762 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAAAA TAAGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA -AAGAA AA
72805 CTCACGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 31 0.89
6 4 0.11
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:74769 original size:18 final size:18
Alignment explanation
Indices: 74748--74797 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
74738 CACGCATGTA
74748 CGCATGCACACACACATG
1 CGCATGCACACACACATG
** * *
74766 CGCACACACATATACATG
1 CGCATGCACACACACATG
*
74784 TGCATGCACACACA
1 CGCATGCACACACA
74798 TACACGCACT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (18 bp):
CGCATGCACACACACATG
Found at i:77903 original size:63 final size:63
Alignment explanation
Indices: 77781--77913 Score: 164
Period size: 63 Copynumber: 2.1 Consensus size: 63
77771 AGCAATTACC
* * *
77781 AAGTC-AGTTACCAAATACCACCACCGTGCATGAAGAAGATGGTAATGCAGAAGTACATAATG
1 AAGTCGAGTCACCAAATACCACCACCGTGCATGAAAAAGATGGTAATGCAGAAATACATAATG
* * *
77843 AAGTCGAGTCACCAAATATCATCACCGTGCATGAAAAAG-TGAGTAATGCA-ACAATTCATAATG
1 AAGTCGAGTCACCAAATACCACCACCGTGCATGAAAAAGATG-GTAATGCAGA-AATACATAATG
*
77906 AAGACGAG
1 AAGTCGAG
77914 ATGATTAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
62 8 0.13
63 53 0.87
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (63 bp):
AAGTCGAGTCACCAAATACCACCACCGTGCATGAAAAAGATGGTAATGCAGAAATACATAATG
Found at i:79857 original size:18 final size:20
Alignment explanation
Indices: 79818--79860 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
79808 ACTAAATGGT
*
79818 AGTTAGTTTGTTAAACGAGC
1 AGTTAGCTTGTTAAACGAGC
79838 AGTTAGCTTGTT-AA-GAGC
1 AGTTAGCTTGTTAAACGAGC
79856 AGTTA
1 AGTTA
79861 TGTGCTGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 11 0.50
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (20 bp):
AGTTAGCTTGTTAAACGAGC
Found at i:79962 original size:14 final size:14
Alignment explanation
Indices: 79943--79972 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
79933 CATAATTCTT
79943 CACCCATCTTCTAA
1 CACCCATCTTCTAA
79957 CACCCATCTTCTAA
1 CACCCATCTTCTAA
79971 CA
1 CA
79973 TGCTGTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.43, G:0.00, T:0.27
Consensus pattern (14 bp):
CACCCATCTTCTAA
Found at i:87900 original size:60 final size:58
Alignment explanation
Indices: 87789--87920 Score: 135
Period size: 60 Copynumber: 2.2 Consensus size: 58
87779 GTCAAATAAC
* * * * *
87789 CATTTTATAATTTTTAATAATCAGAGACTCAACAAGGCAACGCCTTGTAGTC-GGAGGAA
1 CATTTTGTAACTTTCAATAATCAGAGACTCAACAAAGCAACGCCTTATAGTCAGGA-G-A
* *
87848 CATTTTGTAACTTTCAATAGTCAGGAGACTCAACAAAGCAATGTCC-TATAGTCAGGAGA
1 CATTTTGTAACTTTCAATAATCA-GAGACTCAACAAAGCAACG-CCTTATAGTCAGGAGA
87907 CATTTTTGT-ACTTT
1 CA-TTTTGTAACTTT
87921 ACCCTAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
59 27 0.44
60 30 0.48
61 5 0.08
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (58 bp):
CATTTTGTAACTTTCAATAATCAGAGACTCAACAAAGCAACGCCTTATAGTCAGGAGA
Found at i:88809 original size:38 final size:38
Alignment explanation
Indices: 88765--88839 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
88755 TGTGTGTTTA
* *
88765 GTTCGTTTATGTCCACGAACAAGCTCGTTTATCAACTT
1 GTTCGTTTATGTCAACGAACAAGCTCGTTTATAAACTT
* * *
88803 GTTCGTTTATGTTAATGAACAAGCTTGTTTATAAACT
1 GTTCGTTTATGTCAACGAACAAGCTCGTTTATAAACT
88840 CATTTACTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (38 bp):
GTTCGTTTATGTCAACGAACAAGCTCGTTTATAAACTT
Found at i:89019 original size:22 final size:23
Alignment explanation
Indices: 88994--89051 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
88984 TTAACACTAA
* *
88994 ACGAATATTAAACGTACATG-TC
1 ACGAACATTAAACGAACATGTTC
*
89016 ACGAACGTTAAACGAACATGTTC
1 ACGAACATTAAACGAACATGTTC
*
89039 ACGAACACTAAAC
1 ACGAACATTAAAC
89052 AAACGAACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (23 bp):
ACGAACATTAAACGAACATGTTC
Found at i:89050 original size:23 final size:22
Alignment explanation
Indices: 89002--89051 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
88992 AAACGAATAT
* **
89002 TAAACGTACATGTCACGAACGT
1 TAAACGAACATGTCACGAACAC
89024 TAAACGAACATGTTCACGAACAC
1 TAAACGAACATG-TCACGAACAC
89047 TAAAC
1 TAAAC
89052 AAACGAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (22 bp):
TAAACGAACATGTCACGAACAC
Found at i:89467 original size:41 final size:41
Alignment explanation
Indices: 89422--89651 Score: 197
Period size: 41 Copynumber: 6.0 Consensus size: 41
89412 ATTCGCGTTG
89422 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
89463 CATTTCGCGTTGCGATAGTTGAAAATCGCAATTCGCG--TTGC
1 CATTTCGCGTTGCGATAGTTGAAAATCGC-GTT-GCGATTTTC
* * * * * * *
89504 GA--T--AGTT--GAAAATCGCAATTCGCGTTGC-A-TTT-
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
89536 C-----GCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
89572 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
* *
89613 CATTTCGCGTTGCGATAGTTGAAATTCGCGATGCGATTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTT
89652 GGAAAATCGC
Statistics
Matches: 150, Mismatches: 23, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
31 3 0.02
33 20 0.13
34 3 0.02
35 14 0.09
36 1 0.01
37 3 0.02
39 1 0.01
40 1 0.01
41 98 0.65
42 3 0.02
43 3 0.02
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:89498 original size:28 final size:28
Alignment explanation
Indices: 89466--89531 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
89456 GATTTTCCAT
89466 TTCGCGTTGCGATAGTTGAAAATCGCAA
1 TTCGCGTTGCGATAGTTGAAAATCGCAA
89494 TTCGCGTTGCGATAGTTGAAAATCGCAA
1 TTCGCGTTGCGATAGTTGAAAATCGCAA
89522 TTCGCGTTGC
1 TTCGCGTTGC
89532 ATTTCGCGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (28 bp):
TTCGCGTTGCGATAGTTGAAAATCGCAA
Found at i:89556 original size:68 final size:67
Alignment explanation
Indices: 89425--89559 Score: 209
Period size: 68 Copynumber: 2.0 Consensus size: 67
89415 CGCGTTGCAT
*
89425 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATC
1 TTCGCGTTGCGATAGTTGAAAATCGCATTGCG--TTTCCATTTCGCGTTGCGATAGTTGAAAATC
89490 GCAA
64 GCAA
*
89494 TTCGCGTTGCGATAGTTGAAAATCGCAATTCGCG-TTGCATTTCGCGTTGCGATAGTTGAAAATC
1 TTCGCGTTGCGATAGTTGAAAATCGC-ATT-GCGTTTCCATTTCGCGTTGCGATAGTTGAAAATC
89558 GC
64 GC
89560 GTTGCGATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
68 31 0.50
69 26 0.42
70 2 0.03
71 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (67 bp):
TTCGCGTTGCGATAGTTGAAAATCGCATTGCGTTTCCATTTCGCGTTGCGATAGTTGAAAATCGC
AA
Found at i:89581 original size:20 final size:20
Alignment explanation
Indices: 89556--89628 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
89546 TAGTTGAAAA
89556 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
89576 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
89597 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
89617 TCGCGTTGCGAT
1 TCGCGTTGCGAT
89629 AGTTGAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 4 0.09
20 24 0.55
21 12 0.27
22 4 0.09
ACGTcount: A:0.12, C:0.25, G:0.25, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:89704 original size:20 final size:20
Alignment explanation
Indices: 89679--89730 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
89669 ACTGTAGACT
89679 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
89699 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
89719 ATCACAACGCGA
1 ATCGCAACGCGA
89731 TTTTCAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:89811 original size:20 final size:20
Alignment explanation
Indices: 89788--89893 Score: 63
Period size: 20 Copynumber: 5.2 Consensus size: 20
89778 AGATCGCGTT
*
89788 GCGATTTCAACTATCGCAAC
1 GCGATTGCAACTATCGCAAC
* * *
89808 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTGCAACTATCGCAAC
*
89828 GCGATCTCCAACTATCGCAAC
1 GCGAT-TGCAACTATCGCAAC
* * * *
89849 GCGAAATGGAA-AAACGCAAC
1 GCG-ATTGCAACTATCGCAAC
* *
89869 GCGATTTTCAACTATCGCAAT
1 GCGA-TTGCAACTATCGCAAC
89890 GCGA
1 GCGA
89894 AATGCAACGT
Statistics
Matches: 61, Mismatches: 19, Indels: 11
0.67 0.21 0.12
Matches are distributed among these distances:
19 2 0.03
20 30 0.49
21 28 0.46
22 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (20 bp):
GCGATTGCAACTATCGCAAC
Found at i:89845 original size:41 final size:41
Alignment explanation
Indices: 89795--89897 Score: 170
Period size: 41 Copynumber: 2.5 Consensus size: 41
89785 GTTGCGATTT
*
89795 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
* *
89836 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
*
89877 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
89898 CAACGTGAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (41 bp):
CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
Found at i:89901 original size:21 final size:21
Alignment explanation
Indices: 89795--89901 Score: 92
Period size: 21 Copynumber: 5.2 Consensus size: 21
89785 GTTGCGATTT
89795 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
89816 GAA-AATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
89836 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
89857 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
89877 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
89898 CAAC
1 CAAC
89902 GTGAATTTGC
Statistics
Matches: 61, Mismatches: 23, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
20 29 0.48
21 32 0.52
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:94870 original size:8 final size:8
Alignment explanation
Indices: 94857--94886 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
94847 TTAAGATATC
94857 AATTTTGT
1 AATTTTGT
94865 AATTTTGT
1 AATTTTGT
*
94873 AATTTTAT
1 AATTTTGT
94881 AATTTT
1 AATTTT
94887 TAAATTATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (8 bp):
AATTTTGT
Found at i:95077 original size:53 final size:53
Alignment explanation
Indices: 94993--95095 Score: 145
Period size: 53 Copynumber: 1.9 Consensus size: 53
94983 TATTGTATAT
* * *
94993 CTTGAAATCCTAATTTTTTTATATTTATTGTTTATTTTATTGATGGTGTCCAC
1 CTTGAAATCCTAATTTCTTTATATTTATTGTTCATTTTACTGATGGTGTCCAC
* *
95046 CTTGAAAT-CTGAATTTCTTTATATTTGTTGTTCATTTTACTGGTGGTGTC
1 CTTGAAATCCT-AATTTCTTTATATTTATTGTTCATTTTACTGATGGTGTC
95096 TACATGAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 2 0.05
53 42 0.95
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.53
Consensus pattern (53 bp):
CTTGAAATCCTAATTTCTTTATATTTATTGTTCATTTTACTGATGGTGTCCAC
Found at i:98160 original size:39 final size:33
Alignment explanation
Indices: 98086--98150 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
98076 AAAATCGAAA
98086 ATGAAAAAGCAACAATCGACGGTTTCTATGTCT
1 ATGAAAAAGCAACAATCGACGGTTTCTATGTCT
*
98119 ATGAAAAAGCAACAATCGACGGTTTCGATGTC
1 ATGAAAAAGCAACAATCGACGGTTTCTATGTC
98151 GATGTCTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (33 bp):
ATGAAAAAGCAACAATCGACGGTTTCTATGTCT
Found at i:112027 original size:14 final size:14
Alignment explanation
Indices: 112008--112035 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
111998 AAGTGAAAGA
112008 ATAGTTATATAATT
1 ATAGTTATATAATT
112022 ATAGTTATATAATT
1 ATAGTTATATAATT
112036 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:113317 original size:21 final size:21
Alignment explanation
Indices: 113291--113342 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
113281 TTGTTCAAGA
*
113291 TTAGTTATTTAGTTACAAAGT
1 TTAGTTATTCAGTTACAAAGT
* *
113312 TTAGTTATTCGGTTACTAAGT
1 TTAGTTATTCAGTTACAAAGT
*
113333 TT-GTTGTTCA
1 TTAGTTATTCA
113343 CATATAGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (21 bp):
TTAGTTATTCAGTTACAAAGT
Found at i:114320 original size:27 final size:27
Alignment explanation
Indices: 114289--114353 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
114279 ATTCTTCAAG
*
114289 ATCAAGGTTTTTCGTTAAGACTTCATA
1 ATCAAGGCTTTTCGTTAAGACTTCATA
114316 ATCAAGGCTTTTCGTTAAGACTTCATA
1 ATCAAGGCTTTTCGTTAAGACTTCATA
114343 ATCAAGGCTTT
1 ATCAAGGCTTT
114354 CGCCCTCAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (27 bp):
ATCAAGGCTTTTCGTTAAGACTTCATA
Found at i:117058 original size:21 final size:21
Alignment explanation
Indices: 117012--117053 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
117002 AACTCCCCAA
*
117012 TTTTTAAATAAAAATCATAAT
1 TTTTTAAATAAAAATCAAAAT
117033 TTTTTAAA-AAAAAT-AAAAT
1 TTTTTAAATAAAAATCAAAAT
117052 TT
1 TT
117054 GTTTTGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 6 0.30
21 8 0.40
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTTTAAATAAAAATCAAAAT
Found at i:118664 original size:252 final size:252
Alignment explanation
Indices: 118219--118720 Score: 833
Period size: 252 Copynumber: 2.0 Consensus size: 252
118209 ATAAGAGTTT
118219 TACTTAGTATAGCTCTTAGCAAAGAATTGGTACTTAGACAGATTGATGTAGACAATGCCTTCTTA
1 TACTTAGTATAGCTCTTAGCAAAGAATTGGTACTTAGACAGATTGATGTAGACAATGCCTTCTTA
118284 AATGATGATTTAGTTGAAGAAATTTATATGAAACAACCATATGAATTTGAGAAAGTGGATGAGAA
66 AATGATGATTTAGTTGAAGAAATTTATATGAAACAACCATATGAATTTGAGAAAGTGGATGAGAA
* * *
118349 TGGAAATCAATTGGTTTCCCAGATAAAAAAAATCATTATATGGTTTTAAACAAATTCTTCGTACC
131 TGGAAATCAACTGGTTTCCCAGATAAAAAAAATCATTATATGGTCTTAAACAAACTCTTCGTACC
*
118414 TGGTTCGAGAAGTTTAAATCATTTCTTGTTGAAAATCTTTAGTTCACTGCATCTTGG
196 AGGTTCGAGAAGTTTAAATCATTTCTTGTTGAAAATCTTTAGTTCACTGCATCTTGG
* * * *
118471 TACTTAGTATAGCTCTTAGCAAATAATTGGTACTTAGGCAGATTGATGTAGATAATGCCTTCTTG
1 TACTTAGTATAGCTCTTAGCAAAGAATTGGTACTTAGACAGATTGATGTAGACAATGCCTTCTTA
* * * * *
118536 AATGGTGATTTAGTTGAAGAAGTTTATATGAAACAACCATATGGATTTGAGCAAGTGGATGATAA
66 AATGATGATTTAGTTGAAGAAATTTATATGAAACAACCATATGAATTTGAGAAAGTGGATGAGAA
* * * *
118601 TGGAAATCAACTGGTTTCTCAGTTAAAAAAATTCATTATATGGTCTTAAACAAGCTCTTCGTACC
131 TGGAAATCAACTGGTTTCCCAGATAAAAAAAATCATTATATGGTCTTAAACAAACTCTTCGTACC
* *
118666 AGGTTCGAGAAGTTTAAATTATTTCTTGTTGAAAATTTTTAGTTCACTGCATCTT
196 AGGTTCGAGAAGTTTAAATCATTTCTTGTTGAAAATCTTTAGTTCACTGCATCTT
118721 TGACCGATAC
Statistics
Matches: 231, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
252 231 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.35
Consensus pattern (252 bp):
TACTTAGTATAGCTCTTAGCAAAGAATTGGTACTTAGACAGATTGATGTAGACAATGCCTTCTTA
AATGATGATTTAGTTGAAGAAATTTATATGAAACAACCATATGAATTTGAGAAAGTGGATGAGAA
TGGAAATCAACTGGTTTCCCAGATAAAAAAAATCATTATATGGTCTTAAACAAACTCTTCGTACC
AGGTTCGAGAAGTTTAAATCATTTCTTGTTGAAAATCTTTAGTTCACTGCATCTTGG
Found at i:119293 original size:16 final size:16
Alignment explanation
Indices: 119272--119333 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 16
119262 AATTTTAATT
*
119272 ATTAAAGTAAAACAAA
1 ATTAAAGTAAAAGAAA
*
119288 ATTAAA-T-TAAGAAA
1 ATTAAAGTAAAAGAAA
119302 ATATAAAGTAAAAGAAA
1 AT-TAAAGTAAAAGAAA
*
119319 ACTTTAAATTAAAAG
1 A--TTAAAGTAAAAG
119334 GGTTTAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 7 0.19
15 5 0.14
16 7 0.19
17 7 0.19
18 10 0.27
19 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.08, T:0.24
Consensus pattern (16 bp):
ATTAAAGTAAAAGAAA
Found at i:120344 original size:27 final size:27
Alignment explanation
Indices: 120306--120370 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
120296 TGATCTTGGG
120306 CTGGGTCAGGCCCCCTAACAAGGTTTC
1 CTGGGTCAGGCCCCCTAACAAGGTTTC
*
120333 CTGGGTCAGGCCCCCTAACAAGGTTTG
1 CTGGGTCAGGCCCCCTAACAAGGTTTC
120360 CTGGGTCAGGC
1 CTGGGTCAGGC
120371 TACCGGGTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.22
Consensus pattern (27 bp):
CTGGGTCAGGCCCCCTAACAAGGTTTC
Found at i:120622 original size:38 final size:40
Alignment explanation
Indices: 120580--120661 Score: 114
Period size: 38 Copynumber: 2.1 Consensus size: 40
120570 ATTTAAAAAC
* *
120580 TATATATACGTTTTTGAAATATGTTTTCAAAA-C-TATAT
1 TATATATACGTTTTTCAAAAATGTTTTCAAAACCATATAT
* *
120618 TATATATATGTTTTTCAAAAATGTTTTTAAAACCATATAT
1 TATATATACGTTTTTCAAAAATGTTTTCAAAACCATATAT
120658 TATA
1 TATA
120662 CATTTCGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 28 0.74
39 1 0.03
40 9 0.24
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (40 bp):
TATATATACGTTTTTCAAAAATGTTTTCAAAACCATATAT
Found at i:122548 original size:48 final size:48
Alignment explanation
Indices: 122461--122581 Score: 140
Period size: 48 Copynumber: 2.5 Consensus size: 48
122451 CAATTTAGAT
* * *
122461 CACCCTTTCGAGTTTTCACCCTAAACGTTTTTTTTGCTTCAACTTAGG-G
1 CACCCTTTC-AGTTTTC-CCCTAAGCATTTTTTTGGCTTCAACTTAGGTG
*
122510 CACCCTTTCAGTTTTTCCCTTAAGCATTTTTTTGGCTTCAACTTAGGTG
1 CACCCTTTCAG-TTTTCCCCTAAGCATTTTTTTGGCTTCAACTTAGGTG
*
122559 --CCCTTTTAGGTTTTCCCCTAAGC
1 CACCCTTTCA-GTTTTCCCCTAAGC
122582 GAAATATTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
47 19 0.30
48 29 0.46
49 15 0.24
ACGTcount: A:0.17, C:0.27, G:0.14, T:0.42
Consensus pattern (48 bp):
CACCCTTTCAGTTTTCCCCTAAGCATTTTTTTGGCTTCAACTTAGGTG
Found at i:128575 original size:21 final size:22
Alignment explanation
Indices: 128537--128577 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
128527 TGCCTGAAGT
128537 AAAGAGCCTTCAGTGTTTCCAC
1 AAAGAGCCTTCAGTGTTTCCAC
128559 AAAGAG-CTTCA-TGGTTTCC
1 AAAGAGCCTTCAGT-GTTTCC
128578 TTCTAATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 11 0.61
22 6 0.33
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (22 bp):
AAAGAGCCTTCAGTGTTTCCAC
Found at i:129583 original size:21 final size:19
Alignment explanation
Indices: 129545--129590 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
129535 AATTAATCCT
129545 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
129565 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
129586 A-TAAT
1 ACTAAT
129591 GATTTAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:137809 original size:25 final size:25
Alignment explanation
Indices: 137760--137812 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
137750 TCCTTTTTCT
**
137760 TTATTATTATTAATAATATGTATTA
1 TTATTATTATTAATAATATAAATTA
* *
137785 TTATTATTATTATTATTATAAATTA
1 TTATTATTATTAATAATATAAATTA
137810 TTA
1 TTA
137813 CAAAGCAGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TTATTATTATTAATAATATAAATTA
Found at i:137812 original size:3 final size:3
Alignment explanation
Indices: 137760--137803 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
137750 TCCTTTTTCT
* *
137760 TTA TTA TTA TTA ATA ATA TGTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA T
137804 AAATTATTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:138091 original size:29 final size:29
Alignment explanation
Indices: 138057--138113 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
138047 GTTGCCATGC
* *
138057 CTCGTCGAAGATTCCAGCGGCTGCCACGT
1 CTCGTCAAAGATTCAAGCGGCTGCCACGT
138086 CTCGTCAAAGATTCAAGCGGCTGCCACG
1 CTCGTCAAAGATTCAAGCGGCTGCCACG
138114 ACGCCCTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.19
Consensus pattern (29 bp):
CTCGTCAAAGATTCAAGCGGCTGCCACGT
Found at i:144005 original size:136 final size:136
Alignment explanation
Indices: 143854--144134 Score: 476
Period size: 136 Copynumber: 2.1 Consensus size: 136
143844 AACAGGTTTT
143854 TCAAAAAAAAGAGTCATATATTCAAAGA-ATGACATTGATCGGATATTTGGCAGTTCGGTGTTTG
1 TCAAAAAAAAGAGTCATATATTCAAA-ACATGACATTGATCGGATATTTGGCAGTTCGGTGTTTG
*
143918 CCCCACTGTGATTGTCAAGTCAAAGATATTGTGATGAGTTGAATCC-TTTAATTAGTCCAATGAA
65 CCCCACTGTGATTGTCAAGTCAAAGACATTGTGATGAGTTGAA-CCGTTTAATTAGTCCAATGAA
143982 GGCTAATG
129 GGCTAATG
* *
143990 TCAAAAAAAAGAGTCATATATTCAAAACATGACCTTGATCGGGTATTTGGCAGTTCGGTGTTTGC
1 TCAAAAAAAAGAGTCATATATTCAAAACATGACATTGATCGGATATTTGGCAGTTCGGTGTTTGC
*
144055 TCCACTGTGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCGTTTAATTAGTCCAATGAAGG
66 CCCACTGTGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCGTTTAATTAGTCCAATGAAGG
144120 CTAATG
131 CTAATG
* *
144126 CCAATAAAA
1 TCAAAAAAA
144135 CTGAATTCAA
Statistics
Matches: 137, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
135 3 0.02
136 134 0.98
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (136 bp):
TCAAAAAAAAGAGTCATATATTCAAAACATGACATTGATCGGATATTTGGCAGTTCGGTGTTTGC
CCCACTGTGATTGTCAAGTCAAAGACATTGTGATGAGTTGAACCGTTTAATTAGTCCAATGAAGG
CTAATG
Found at i:146361 original size:75 final size:75
Alignment explanation
Indices: 146161--146369 Score: 319
Period size: 75 Copynumber: 2.8 Consensus size: 75
146151 TTTATATCAA
* * * *
146161 CAAATGTTGAGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATTTTAGAGCATTTTGAACG
1 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGGCGCATTTTGAACG
*
146226 TATGTATTAG
66 TATGCATTAG
* * * *
146236 AAAATGCTGGGGCATGGTGAAAGCCCATTTCAATCAGAAATTGGAATATTGGCGCATTTTTAACG
1 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGGCGCATTTTGAACG
146301 TATGCATTAG
66 TATGCATTAG
* *
146311 CAAATGTTGGGGCATGCTAAAAGCCCATTTCAATCAGAAATTGGAATATTGGCACATTT
1 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGGCGCATTT
146370 GAATGTTCAT
Statistics
Matches: 120, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 120 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (75 bp):
CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGGCGCATTTTGAACG
TATGCATTAG
Found at i:146976 original size:24 final size:25
Alignment explanation
Indices: 146932--146985 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
146922 CTGAGTTTTT
*
146932 ATCTATTTTGTTTCATGTGCGATTC
1 ATCTATTTTGTATCATGTGCGATTC
*
146957 ATCTATTTT-TATCATGTGCGTTTC
1 ATCTATTTTGTATCATGTGCGATTC
146981 ATCTA
1 ATCTA
146986 CAGCAGCAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.52
Consensus pattern (25 bp):
ATCTATTTTGTATCATGTGCGATTC
Found at i:147370 original size:54 final size:54
Alignment explanation
Indices: 147312--147505 Score: 192
Period size: 54 Copynumber: 3.6 Consensus size: 54
147302 GGCACAAGAA
* **
147312 ATGATGAATATGTTGTCAAATATTTTACGAACATTTGTTTAAAAACCATATGAG
1 ATGATGAATATGTTGTCAAATATTTTACGAACATCTGAGTAAAAACCATATGAG
* * ** * * * * ***
147366 ATGATGAATGTGTTATCAAATGCTTTACGAACATCTGGGCAGAAGCCACGGGA-
1 ATGATGAATATGTTGTCAAATATTTTACGAACATCTGAGTAAAAACCATATGAG
* * * *
147419 AAGAATGAATATGTTGTCAAATATTTTACGAGCATCTAAGTAAAATCCATATGAG
1 ATG-ATGAATATGTTGTCAAATATTTTACGAACATCTGAGTAAAAACCATATGAG
* *
147474 ATGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATGATGAATATGTTGTCAAATATTTTACGAAC
147506 CAGTTATTCT
Statistics
Matches: 107, Mismatches: 31, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
53 2 0.02
54 103 0.96
55 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (54 bp):
ATGATGAATATGTTGTCAAATATTTTACGAACATCTGAGTAAAAACCATATGAG
Found at i:147893 original size:22 final size:22
Alignment explanation
Indices: 147865--147943 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
147855 ACATCTACAT
147865 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
147887 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
147909 TCTTCAAAGATAATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
147931 TTTTTAAAGATGA
1 TCTTCAAAGATGA
147944 AAACTTTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:148833 original size:44 final size:44
Alignment explanation
Indices: 148658--149202 Score: 650
Period size: 44 Copynumber: 12.7 Consensus size: 44
148648 GGGAGCTTTT
*
148658 TGATGTTTTCAAA-CCTTGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGTCATCTGTAAGCCCTTCAGTGCA
148701 TGATGTTTTCAAAGCCTTCGGTCA--TGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGTCATCTGTAAGCCCTTCAGTGCA
*
148743 TGATGTTTTTAAAGCCTTCAGGTCA--TGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTC-GGTCATCTGTAAGCCCTTCAGTGCA
* * * *
148786 TGATGTTTTCAAATCCTTCGGTTATCTATAAGCCCTTCAGTGTA
1 TGATGTTTTCAAAGCCTTCGGTCATCTGTAAGCCCTTCAGTGCA
* *
148830 TGATG-TTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGTA
1 TGATGTTTTCAAAGCCTTC-GGTCATCTGTAAGCCCTTCAGTGCA
* *
148874 TG-TATTTTCAAA-CCTTCGGTTAATCTGTAAG-CCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGG-TCATCTGTAAGCCCTTCAGTGCA
* *
148916 TGATGTTTTCAAAGCCTTGGGTCATCTGTAAGCCCTTTAGTGCA
1 TGATGTTTTCAAAGCCTTCGGTCATCTGTAAGCCCTTCAGTGCA
**
148960 TGATGTTTTCAAAGCCTTCGAGTCATCTGTAAAACC-TCAGTGCA
1 TGATGTTTTCAAAGCCTTCG-GTCATCTGTAAGCCCTTCAGTGCA
* * *
149004 TGATGTTTTTAAAGCCTTCGAGTCATTTGTAAGACCTTCAG-GCA
1 TGATGTTTTCAAAGCCTTCG-GTCATCTGTAAGCCCTTCAGTGCA
*
149048 TGATGTTTTGAAAGCCTTCGGGTCATC-GTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTC-GGTCATCTGTAAGCCCTTCAGTGCA
*
149092 TGATGTGTTT--AAGCC-T---T-ATCTG---G-CTTTCAGTGCA
1 TGATGT-TTTCAAAGCCTTCGGTCATCTGTAAGCCCTTCAGTGCA
* * *
149126 TGATGTTTTCAAAACCTTTGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAGCC-TTCGGTCATCTGTAAGCCCTTCAGTGCA
*
149171 TGATGTTTTTAAAGCCTTCGGTCATCTGTAAG
1 TGATGTTTTCAAAGCCTTCGGTCATCTGTAAG
149203 ACCTAAAGTG
Statistics
Matches: 440, Mismatches: 34, Indels: 55
0.83 0.06 0.10
Matches are distributed among these distances:
33 3 0.01
34 16 0.04
35 5 0.01
37 4 0.01
38 2 0.00
40 1 0.00
41 5 0.01
42 55 0.12
43 117 0.27
44 187 0.43
45 45 0.10
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (44 bp):
TGATGTTTTCAAAGCCTTCGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:149169 original size:45 final size:44
Alignment explanation
Indices: 149117--149206 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 44
149107 TTATCTGGCT
*
149117 TTCAGTGCATGATGTTTTCAAAACCTTTGGGTCATCTGTAAGACC
1 TTCAGTGCATGATGTTTTCAAAACC-TTCGGTCATCTGTAAGACC
* *
149162 TTCAGTGCATGATGTTTTTAAAGCCTTCGGTCATCTGTAAGACC
1 TTCAGTGCATGATGTTTTCAAAACCTTCGGTCATCTGTAAGACC
149206 T
1 T
149207 AAAGTGAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 19 0.45
45 23 0.55
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (44 bp):
TTCAGTGCATGATGTTTTCAAAACCTTCGGTCATCTGTAAGACC
Found at i:149175 original size:79 final size:78
Alignment explanation
Indices: 149040--149188 Score: 228
Period size: 78 Copynumber: 1.9 Consensus size: 78
149030 TTGTAAGACC
* * *
149040 TTCAGGCATGATGTTTTGAAAGCCTTCGGGTCATCGTAAGCCCTTCAGTGCATGATGTGTTT-AA
1 TTCAGGCATGATGTTTTCAAAACCTTCGGGTCATCGTAAGACCTTCAGTGCATGATGTGTTTAAA
149104 GCCTTATCTGGCT
66 GCCTTATCTGGCT
* *
149117 TTCAGTGCATGATGTTTTCAAAACCTTTGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTTA
1 TTCAG-GCATGATGTTTTCAAAACCTTCGGGTCATC-GTAAGACCTTCAGTGCATGATGTGTTTA
149182 AAGCCTT
64 AAGCCTT
149189 CGGTCATCTG
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
77 5 0.08
78 27 0.42
79 25 0.39
80 7 0.11
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (78 bp):
TTCAGGCATGATGTTTTCAAAACCTTCGGGTCATCGTAAGACCTTCAGTGCATGATGTGTTTAAA
GCCTTATCTGGCT
Done.