Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007744.1 Hibiscus syriacus cultivar Beakdansim tig00110007_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: 4276731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 16
Found at i:2969052 original size:22 final size:22
Alignment explanation
Indices: 2969004--2969052 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2968994 TGAGTCAACT
* *
2969004 CGTTGACTTTGACCGATCTGTC
1 CGTTGACTTTGACCGATCAGAC
* * *
2969026 TGTTGACTTTGACTGGTCAGAC
1 CGTTGACTTTGACCGATCAGAC
2969048 CGTTG
1 CGTTG
2969053 TGTGTTGACT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.37
Consensus pattern (22 bp):
CGTTGACTTTGACCGATCAGAC
Found at i:2971157 original size:59 final size:59
Alignment explanation
Indices: 2971070--2971184 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
2971060 GGATGGTTGT
* *
2971070 TTAGAGCCATATTACCGAGTTTGACTTTTCATTGCGACTAGGAGAGTTCGATAGGATAC
1 TTAGAGCCATATTACCGAGTTTGACTTTTCATTACGACTAGAAGAGTTCGATAGGATAC
** * * *
2971129 TTAGAGCCATATTATTGAGTTTGCCTTTTTATTACGACTAGAAGGGTTCGATAGGA
1 TTAGAGCCATATTACCGAGTTTGACTTTTCATTACGACTAGAAGAGTTCGATAGGA
2971185 CCCTTATCCA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (59 bp):
TTAGAGCCATATTACCGAGTTTGACTTTTCATTACGACTAGAAGAGTTCGATAGGATAC
Found at i:2974377 original size:22 final size:22
Alignment explanation
Indices: 2974349--2974400 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2974339 AGGCAACTCA
*
2974349 TTGACTTTAACCGAT-ATATCTG
1 TTGACTTTAACCGATCAGATC-G
* *
2974371 TTGACTTTGACCGGTCAGATCG
1 TTGACTTTAACCGATCAGATCG
2974393 TTGACTTT
1 TTGACTTT
2974401 GATCGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (22 bp):
TTGACTTTAACCGATCAGATCG
Found at i:2986398 original size:13 final size:13
Alignment explanation
Indices: 2986380--2986412 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
2986370 GACTACAATA
2986380 AGGCATAATAGTG
1 AGGCATAATAGTG
2986393 AGGCATAATAGTG
1 AGGCATAATAGTG
2986406 AGGCATA
1 AGGCATA
2986413 CCAGGTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.21
Consensus pattern (13 bp):
AGGCATAATAGTG
Found at i:2987382 original size:22 final size:22
Alignment explanation
Indices: 2987354--2987408 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
2987344 ATACTGAAAG
2987354 GGAGTATCGATACCATAGTATA
1 GGAGTATCGATACCATAGTATA
2987376 GGAGTATCGATACCATAGTATA
1 GGAGTATCGATACCATAGTATA
2987398 GGAGTATCGAT
1 GGAGTATCGAT
2987409 GCTGAGAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (22 bp):
GGAGTATCGATACCATAGTATA
Found at i:2987910 original size:46 final size:46
Alignment explanation
Indices: 2987839--2988021 Score: 280
Period size: 46 Copynumber: 4.0 Consensus size: 46
2987829 TTAATGTATA
2987839 CATTAAGGCATGAAAGGAT-TCCATAACTAAAATGCATGAAAGGATG
1 CATTAAGGCATGAAAGGATGT-CATAACTAAAATGCATGAAAGGATG
* * *
2987885 CATTAAGGCATGAAAGGATGTCATAATTGAAATTCATGAAAGGATG
1 CATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAAGGATG
* *
2987931 CATTAAGGCATGAATGGATGCCATAACTAAAATGCATGAAAGGATG
1 CATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAAGGATG
*
2987977 CATTAAGGCATGAAAGGATG-CTATAACTAAAATACATGAAAGGAT
1 CATTAAGGCATGAAAGGATGTC-ATAACTAAAATGCATGAAAGGAT
2988022 CCCATAACTA
Statistics
Matches: 125, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
45 1 0.01
46 123 0.98
47 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.23
Consensus pattern (46 bp):
CATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAAGGATG
Found at i:2988016 original size:72 final size:72
Alignment explanation
Indices: 2987939--2988095 Score: 269
Period size: 72 Copynumber: 2.2 Consensus size: 72
2987929 TGCATTAAGG
* * *
2987939 CATGAATGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCTATAAC
1 CATGAAAGGATGCCATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAC
2988004 TAAAATA
66 TAAAATA
*
2988011 CATGAAAGGATCCCATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAC
1 CATGAAAGGATGCCATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAC
*
2988076 TAAAATG
66 TAAAATA
2988083 CATGAAAGGATGC
1 CATGAAAGGATGC
2988096 ATTAAGGCAT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 79 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (72 bp):
CATGAAAGGATGCCATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAC
TAAAATA
Found at i:2988028 original size:118 final size:118
Alignment explanation
Indices: 2987893--2988112 Score: 377
Period size: 118 Copynumber: 1.9 Consensus size: 118
2987883 TGCATTAAGG
** * * * * *
2987893 CATGAAAGGATGTCATAATTGAAATTCATGAAAGGATGCATTAAGGCATGAATGGATGCCATAAC
1 CATGAAAGGATCCCATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAC
2987958 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCTATAACTAAAATA
66 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCTATAACTAAAATA
2988011 CATGAAAGGATCCCATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAC
1 CATGAAAGGATCCCATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAC
2988076 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGA
66 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGA
2988113 GCCCATAACT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 95 1.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.21
Consensus pattern (118 bp):
CATGAAAGGATCCCATAACTAAAATGCATGAAAGGATACATTAAGGCATGAAAGGATGCCATAAC
TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCTATAACTAAAATA
Found at i:2988060 original size:92 final size:89
Alignment explanation
Indices: 2987839--2988069 Score: 218
Period size: 92 Copynumber: 2.5 Consensus size: 89
2987829 TTAATGTATA
** *
2987839 CATTAAGGCATGAAAGGATTCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
1 CATTAAGGCATGAAAGGATGACAT-A-T-AAAGGCATGAAAGGATGCATTAAGGCATGAAAGGAT
* * * *
2987904 GTCATAATTGAAATTCATGAAAGGATG
63 GTCATAACTAAAATACATGAAAGGATC
* * *
2987931 CATTAAGGCATGAATGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAT
1 CATTAAGGCATGAAAGGATGACAT-A-T-AAAGGCATGAAAGGATGCATTAAGGCATGAAAGGAT
2987996 G-CTATAACTAAAATACATGAAAGGATCC
63 GTC-ATAACTAAAATACATGAAAGGAT-C
*
2988024 CATAACTAAAATGCATGAAAGGAT-ACAT-T-AAGGCATGAAAGGATGC
1 CAT---T--AAGGCATGAAAGGATGACATATAAAGGCATGAAAGGATGC
2988070 CATAACTAAA
Statistics
Matches: 122, Mismatches: 10, Indels: 14
0.84 0.07 0.10
Matches are distributed among these distances:
91 1 0.01
92 100 0.82
93 3 0.02
94 1 0.01
96 1 0.01
97 3 0.02
98 13 0.11
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (89 bp):
CATTAAGGCATGAAAGGATGACATATAAAGGCATGAAAGGATGCATTAAGGCATGAAAGGATGTC
ATAACTAAAATACATGAAAGGATC
Found at i:2988061 original size:46 final size:46
Alignment explanation
Indices: 2988011--2988127 Score: 198
Period size: 46 Copynumber: 2.5 Consensus size: 46
2988001 AACTAAAATA
2988011 CATGAAAGGATCCCATAACTAAAATGCATGAAAGGATACATTAAGG
1 CATGAAAGGATCCCATAACTAAAATGCATGAAAGGATACATTAAGG
* *
2988057 CATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGG
1 CATGAAAGGATCCCATAACTAAAATGCATGAAAGGATACATTAAGG
* *
2988103 CATGAAAGGAGCCCATAACTGAAAT
1 CATGAAAGGATCCCATAACTAAAAT
2988128 TAACGAATAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.19
Consensus pattern (46 bp):
CATGAAAGGATCCCATAACTAAAATGCATGAAAGGATACATTAAGG
Found at i:2993195 original size:5 final size:5
Alignment explanation
Indices: 2993185--2993234 Score: 68
Period size: 5 Copynumber: 10.2 Consensus size: 5
2993175 TACTCAAAAG
*
2993185 AAGAA AAGAA AA-AT AAGAA AAGAA AAGAA AAGAAA AAGAA AAG-A AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAG-AA AAGAA AAGAA AAGAA
2993234 A
1 A
2993235 TGTTGAAGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 7 0.17
5 28 0.70
6 5 0.12
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (5 bp):
AAGAA
Found at i:2993202 original size:14 final size:14
Alignment explanation
Indices: 2993180--2993234 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
2993170 GCAAGTACTC
*
2993180 AAAAGAAGAAAAGA
1 AAAAAAAGAAAAGA
*
2993194 AAAATAAGAAAAGA
1 AAAAAAAGAAAAGA
2993208 AAAGAAAAGAAAAAGA
1 AAA-AAAAG-AAAAGA
*
2993224 AAAGAAAGAAA
1 AAAAAAAGAAA
2993235 TGTTGAAGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 19 0.53
15 8 0.22
16 9 0.25
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAAAAAGAAAAGA
Found at i:2993204 original size:9 final size:10
Alignment explanation
Indices: 2993185--2993234 Score: 68
Period size: 9 Copynumber: 5.1 Consensus size: 10
2993175 TACTCAAAAG
2993185 AAGAAAAGAA
1 AAGAAAAGAA
*
2993195 AA-ATAAGAA
1 AAGAAAAGAA
2993204 AAGAAAAGAA
1 AAGAAAAGAA
2993214 AAGAAAAAGAA
1 AAG-AAAAGAA
2993225 AAG-AAAGAA
1 AAGAAAAGAA
2993234 A
1 A
2993235 TGTTGAAGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
9 15 0.42
10 11 0.31
11 10 0.28
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (10 bp):
AAGAAAAGAA
Found at i:2994106 original size:24 final size:21
Alignment explanation
Indices: 2994072--2994114 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2994062 CCCACAAGAC
*
2994072 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AGTTCAAAGG
2994094 ATGTACCTCTTGAAGTTCAAA
1 ATGT-CCT-TTGAAGTTCAAA
2994115 AGAATATGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAGTTCAAAGG
Found at i:2999677 original size:45 final size:47
Alignment explanation
Indices: 2999613--2999725 Score: 133
Period size: 45 Copynumber: 2.4 Consensus size: 47
2999603 TGTCAAAATA
**
2999613 AAAGGATGCCATATTTAAAATGCATGAAA-GAATG-AAT-AAGGCATG
1 AAAGGATGCCATAACTAAAATGCATGAAATG-ATGTAATAAAGGCATG
* *
2999658 AAAGGATGCCATAACTAAAATGCGTGAAATGATGTATTAAAGGCATG
1 AAAGGATGCCATAACTAAAATGCATGAAATGATGTAATAAAGGCATG
* * *
2999705 AATGGAGGCCATAACTGAAAT
1 AAAGGATGCCATAACTAAAAT
2999726 TAACGAATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
45 29 0.50
46 3 0.05
47 26 0.45
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (47 bp):
AAAGGATGCCATAACTAAAATGCATGAAATGATGTAATAAAGGCATG
Found at i:3007036 original size:20 final size:21
Alignment explanation
Indices: 3007011--3007092 Score: 84
Period size: 20 Copynumber: 4.0 Consensus size: 21
3007001 AGTACTTACT
3007011 TTATT-ATGCCTCACTAAGTG
1 TTATTAATGCCTCACTAAGTG
3007031 TTATTAAATGCCTCAC-AA-TG
1 TTATT-AATGCCTCACTAAGTG
* * *
3007051 TTATTAAATGCCTTACTTACT-
1 TTATT-AATGCCTCACTAAGTG
3007072 TTATT-ATGCCTCACTAAGTG
1 TTATTAATGCCTCACTAAGTG
3007092 T
1 T
3007093 ATAGTTATCG
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
19 11 0.21
20 23 0.44
21 8 0.15
22 10 0.19
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (21 bp):
TTATTAATGCCTCACTAAGTG
Found at i:3010548 original size:10 final size:10
Alignment explanation
Indices: 3010533--3010562 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
3010523 TGAATTCTAA
3010533 TTTCAAATTC
1 TTTCAAATTC
3010543 TTTCAAATTC
1 TTTCAAATTC
3010553 TTTCAAATTC
1 TTTCAAATTC
3010563 GTCATGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (10 bp):
TTTCAAATTC
Found at i:3017372 original size:56 final size:56
Alignment explanation
Indices: 3017299--3017457 Score: 158
Period size: 56 Copynumber: 2.8 Consensus size: 56
3017289 TAGAGGTGGA
* * * *
3017299 GCATTTAGTACACCTGACGTTACTTATGTGACGGTTGTGCCACTAGT-AGTTCCATG
1 GCATTTAGCACATCTGACGTTACTTATGTGACGGTGGTGCCACTA-TAAGTTACATG
* * * * *
3017355 GCATTTAGCACATCTGACGTCACTTATATGATGGTGGTGCTATTATAAGTTACATG
1 GCATTTAGCACATCTGACGTTACTTATGTGACGGTGGTGCCACTATAAGTTACATG
* * ** ** *
3017411 GTACTTAGCATGTCTGATATTACTTATGTGACGGTGGTGCCAATATA
1 GCATTTAGCACATCTGACGTTACTTATGTGACGGTGGTGCCACTATA
3017458 CATTCGAAAT
Statistics
Matches: 82, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
55 1 0.01
56 81 0.99
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (56 bp):
GCATTTAGCACATCTGACGTTACTTATGTGACGGTGGTGCCACTATAAGTTACATG
Found at i:3020372 original size:16 final size:17
Alignment explanation
Indices: 3020336--3020376 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
3020326 TTTGCTGTTT
**
3020336 AAAAAAAACAAAAAGGG
1 AAAAAAAACAAAAAGAC
3020353 AAAAAAAACAAAAA-AC
1 AAAAAAAACAAAAAGAC
3020369 AAAAAAAA
1 AAAAAAAA
3020377 GCCAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.00
Consensus pattern (17 bp):
AAAAAAAACAAAAAGAC
Found at i:3034686 original size:56 final size:56
Alignment explanation
Indices: 3034600--3034712 Score: 163
Period size: 56 Copynumber: 2.0 Consensus size: 56
3034590 GAGGTGGAGC
* * * *
3034600 ATTTAGCACGTCTGACGTTACTTATGTGACGGTCGTGCTACTAGCAATTACATGGT
1 ATTTAACACGTCTGACATCACTTATCTGACGGTCGTGCTACTAGCAATTACATGGT
* * *
3034656 ATTTAACACGTCTGACATCACTTATCTGACGGTGGTGCTACTATCAGTTACATGGT
1 ATTTAACACGTCTGACATCACTTATCTGACGGTCGTGCTACTAGCAATTACATGGT
3034712 A
1 A
3034713 CTTAGCATGG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (56 bp):
ATTTAACACGTCTGACATCACTTATCTGACGGTCGTGCTACTAGCAATTACATGGT
Found at i:3034735 original size:56 final size:56
Alignment explanation
Indices: 3034614--3034747 Score: 151
Period size: 56 Copynumber: 2.4 Consensus size: 56
3034604 AGCACGTCTG
* * * *
3034614 ACGTTACTTATGTGACGGTCGTGCTACTAGCAATTACATGGTATTTAACACGTCTG
1 ACGTTACTTATGTGACGGTGGTGCTACTAGCAATTACATGGTACTTAACACGGCTA
* * * * * * *
3034670 ACATCACTTATCTGACGGTGGTGCTACTATCAGTTACATGGTACTTAGCATGGCTA
1 ACGTTACTTATGTGACGGTGGTGCTACTAGCAATTACATGGTACTTAACACGGCTA
* *
3034726 ATGTTACTTATGTGATGGTGGT
1 ACGTTACTTATGTGACGGTGGT
3034748 TCTAATGTAC
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (56 bp):
ACGTTACTTATGTGACGGTGGTGCTACTAGCAATTACATGGTACTTAACACGGCTA
Found at i:3043404 original size:47 final size:45
Alignment explanation
Indices: 3043334--3043458 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
3043324 TATAAAATCT
*
3043334 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
3043379 CTTACCATTTAAATTCCATAAGCTCGTAAGTTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
3043426 CTTGCCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
3043459 GCACACTTAC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 20 0.28
44 3 0.04
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:3049767 original size:211 final size:210
Alignment explanation
Indices: 3049405--3049826 Score: 819
Period size: 211 Copynumber: 2.0 Consensus size: 210
3049395 TTTTTATTTC
3049405 ATTCCATTTTAATCCCTTCATTCTGTTTAATTACATTTAATTTTTTGGGTAATTTCTATTCCTTT
1 ATTCCATTTTAATCCCTTCATTCTGTTTAATTACATTTAATTTTTTGGGTAATTTCTATTCCTTT
3049470 CAATCTAGTTAAAATCTTAATTTAGATTGAATCCATAGGTTTCGATTTCATTTAAATTAATCATA
66 CAATCTAGTTAAAATCTTAATTTAGATTGAATCCATAGGTTTCGATTTCATTTAAATTAATCATA
3049535 CTAGAGTAATTAGACCTAATATCAAAGAAAAAAAACTAGATGTTTTGTTTTTTGCCTTCACAATG
131 CTAGAGTAATTAGACCTAATATCAAAGAAAAAAAACTAGATGTTTTGTTTTTTGCCTTCACAATG
3049600 AAAG-AGAAAGATAA
196 AAAGAAGAAAGATAA
3049614 ATTCCATTTTAATCCCTTCATTCTGTTTAATTACATTTAATTTTTTGGGTAATTTCTATTCCTTT
1 ATTCCATTTTAATCCCTTCATTCTGTTTAATTACATTTAATTTTTTGGGTAATTTCTATTCCTTT
3049679 CAATCTAGTCATAAAATCTTAATTTAGATTGAATCCATAGGTTTCGATTTCATTTAAATTAATCA
66 CAATCTAGT--TAAAATCTTAATTTAGATTGAATCCATAGGTTTCGATTTCATTTAAATTAATCA
3049744 TACTAGAGTAATTAGACCTAATATCAAAGAAAAAAAACTAGATGTTTTGTTTTTTGCCTTCACAA
129 TACTAGAGTAATTAGACCTAATATCAAAGAAAAAAAACTAGATGTTTTGTTTTTTGCCTTCACAA
3049809 TGAAAGAAGAAAGATAA
194 TGAAAGAAGAAAGATAA
3049826 A
1 A
3049827 GTTGGGATAA
Statistics
Matches: 210, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
209 74 0.35
211 125 0.60
212 11 0.05
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (210 bp):
ATTCCATTTTAATCCCTTCATTCTGTTTAATTACATTTAATTTTTTGGGTAATTTCTATTCCTTT
CAATCTAGTTAAAATCTTAATTTAGATTGAATCCATAGGTTTCGATTTCATTTAAATTAATCATA
CTAGAGTAATTAGACCTAATATCAAAGAAAAAAAACTAGATGTTTTGTTTTTTGCCTTCACAATG
AAAGAAGAAAGATAA
Found at i:3050170 original size:3 final size:3
Alignment explanation
Indices: 3050162--3050205 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3050152 ATGTCTTTTT
3050162 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3050206 TAAAGTATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3050876 original size:21 final size:21
Alignment explanation
Indices: 3050827--3050876 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3050817 TTCGTTGATA
3050827 TATTGTTTAATTTTTAGCAATT
1 TATT-TTTAATTTTTAGCAATT
* * * *
3050849 TAATTTTCATTTTTAGTATTT
1 TATTTTTAATTTTTAGCAATT
3050870 TATTTTT
1 TATTTTT
3050877 TTTGTGTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.66
Consensus pattern (21 bp):
TATTTTTAATTTTTAGCAATT
Found at i:3050982 original size:2 final size:2
Alignment explanation
Indices: 3050975--3051009 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3050965 ATTCCATTTA
3050975 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 A
3051010 AATTGATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3055337 original size:17 final size:16
Alignment explanation
Indices: 3055315--3055358 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
3055305 AAATTAGAGT
3055315 ACAAAAAGAAAGAAAAA
1 ACAAAAAGAAAG-AAAA
*
3055332 ACAAAAAG-AAGAAAT
1 ACAAAAAGAAAGAAAA
*
3055347 TCAAAAAGAAAG
1 ACAAAAAGAAAG
3055359 CAAAGCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.42
16 6 0.25
17 8 0.33
ACGTcount: A:0.75, C:0.07, G:0.14, T:0.05
Consensus pattern (16 bp):
ACAAAAAGAAAGAAAA
Found at i:3083652 original size:24 final size:24
Alignment explanation
Indices: 3083592--3083657 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
3083582 TCAATGATCG
*
3083592 TAACTTTTGGCACTTCAAGTGACA
1 TAACTTTTGGAACTTCAAGTGACA
* * * *
3083616 CATCTTTTTGAACTTCAAGTGGCA
1 TAACTTTTGGAACTTCAAGTGACA
* *
3083640 TAACTATTGGAACGTCAA
1 TAACTTTTGGAACTTCAA
3083658 AGGACATGTC
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (24 bp):
TAACTTTTGGAACTTCAAGTGACA
Found at i:3096400 original size:18 final size:19
Alignment explanation
Indices: 3096362--3096400 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3096352 TTGAATCGGC
*
3096362 TATAGGAAAATGGTTAGGG
1 TATAGGAAAATGGATAGGG
*
3096381 TATA-GAAAATGGATATGG
1 TATAGGAAAATGGATAGGG
3096399 TA
1 TA
3096401 AAGGTACGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (19 bp):
TATAGGAAAATGGATAGGG
Found at i:3096479 original size:14 final size:15
Alignment explanation
Indices: 3096450--3096482 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3096440 ATAGGGAAAT
*
3096450 ATGAAAGTAAAGAAA
1 ATGAAAGTAAAAAAA
3096465 ATGAAA-TAAAAAAA
1 ATGAAAGTAAAAAAA
3096479 ATGA
1 ATGA
3096483 TGAAGATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (15 bp):
ATGAAAGTAAAAAAA
Found at i:3096700 original size:16 final size:18
Alignment explanation
Indices: 3096681--3096717 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 18
3096671 TAGGAGTCTT
3096681 TTCTTCTCTTTTGTTTTTC
1 TTCTTCT-TTTTGTTTTTC
3096700 TTCTTTCTTTTTGTTTTT
1 TTC-TTCTTTTTGTTTTT
3096718 GTTGCAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (18 bp):
TTCTTCTTTTTGTTTTTC
Found at i:3096898 original size:17 final size:17
Alignment explanation
Indices: 3096871--3096904 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3096861 TAAGTAATCT
3096871 GAAAAATTAAAA-GAAA
1 GAAAAATTAAAATGAAA
3096887 GAAAATATTAAAATGAAA
1 GAAAA-ATTAAAATGAAA
3096905 ATATGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 7 0.44
18 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (17 bp):
GAAAAATTAAAATGAAA
Found at i:3139154 original size:14 final size:13
Alignment explanation
Indices: 3139135--3139172 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
3139125 TATCCCTTTA
3139135 ATTTCTTATCATTT
1 ATTTCTT-TCATTT
3139149 ATTTCTTTCATTT
1 ATTTCTTTCATTT
*
3139162 -TTTATTTCATT
1 ATTTCTTTCATT
3139173 AATCCATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.43
13 6 0.26
14 7 0.30
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTCTTTCATTT
Found at i:3149369 original size:28 final size:29
Alignment explanation
Indices: 3149310--3149388 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 29
3149300 AGACTTGTTG
* * *
3149310 TTGAGTTCTTTAACTTTTCTTTCTTCTTT
1 TTGAGTGCTTGAATTTTTCTTTCTTCTTT
*
3149339 TTGAGTGCTTGAATTTTTTTTTCTTC-TT
1 TTGAGTGCTTGAATTTTTCTTTCTTCTTT
*
3149367 TTGAGTGCTTGCATTTTTCTTT
1 TTGAGTGCTTGAATTTTTCTTT
3149389 ACTGAATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 22 0.50
29 22 0.50
ACGTcount: A:0.10, C:0.14, G:0.13, T:0.63
Consensus pattern (29 bp):
TTGAGTGCTTGAATTTTTCTTTCTTCTTT
Found at i:3153636 original size:29 final size:27
Alignment explanation
Indices: 3153590--3153654 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 27
3153580 AGATTTGTTG
* *
3153590 TTGATTGCTTCAACTTTTCTTTCTTCTTT
1 TTGAGTGCTTGAA-TTTTCTTTCTTC-TT
3153619 TTGAGTGCTTGAA-TTT-TTTCTTCTT
1 TTGAGTGCTTGAATTTTCTTTCTTCTT
3153644 TTGAGTGCTTG
1 TTGAGTGCTTG
3153655 CACTTTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 13 0.38
26 7 0.21
27 3 0.09
29 11 0.32
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.58
Consensus pattern (27 bp):
TTGAGTGCTTGAATTTTCTTTCTTCTT
Found at i:3153651 original size:25 final size:26
Alignment explanation
Indices: 3153609--3153665 Score: 89
Period size: 25 Copynumber: 2.2 Consensus size: 26
3153599 TCAACTTTTC
*
3153609 TTTCTTCTTTTTGAGTGCTTGAATTT
1 TTTCTTCTTTTTGAGTGCTTGAACTT
*
3153635 TTTCTTC-TTTTGAGTGCTTGCACTT
1 TTTCTTCTTTTTGAGTGCTTGAACTT
3153660 TTTCTT
1 TTTCTT
3153666 TACTGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.09, C:0.16, G:0.14, T:0.61
Consensus pattern (26 bp):
TTTCTTCTTTTTGAGTGCTTGAACTT
Found at i:3156431 original size:32 final size:33
Alignment explanation
Indices: 3156381--3156445 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 33
3156371 AAGATAAGAA
* *
3156381 ATAAATAGGATTAATAATGGAAT-AAGAAATGG
1 ATAAATAAGATTAATAATGAAATAAAGAAATGG
3156413 ATAAATAAGA-TAATTAATGAAATGAAAGAAATG
1 ATAAATAAGATTAA-TAATGAAAT-AAAGAAATG
3156446 ATTAGAGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 3 0.11
32 17 0.61
34 8 0.29
ACGTcount: A:0.57, C:0.00, G:0.18, T:0.25
Consensus pattern (33 bp):
ATAAATAAGATTAATAATGAAATAAAGAAATGG
Found at i:3157796 original size:239 final size:239
Alignment explanation
Indices: 3157368--3157801 Score: 807
Period size: 239 Copynumber: 1.8 Consensus size: 239
3157358 TCGTGAAAAG
* * *
3157368 GTAAAGAAAATTGCAAGCATTCAAAAGAAGAAAACAAATGAAAGAAAAGTGAAGCACTTAATAAA
1 GTAAAGAAAATTGCAAGCATTCAAAAGAAGAAAACAAAGGAAAGAAAAGTGAAGCACTCAACAAA
3157433 AGGTCTCATCACCAAGCCAGTCAAGTAAGCCTTTAAATTGATTGTGGTGATAGAAGGGTTGTGTA
66 AGGTCTCATCACCAAGCCAGTCAAGTAAGCCTTTAAATTGATTGTGGTGATAGAAGGGTTGTGTA
3157498 GTGACTTCTGTAAGTAACCCTTTTATTCTCTTCTTTCTTATTTCCTAGCCACCCTTTTCATTATA
131 GTGACTTCTGTAAGTAACCCTTTTATTCTCTTCTTTCTTATTTCCTAGCCACCCTTTTCATTATA
3157563 AAAAATAAAAAATAAGAAGTGCAAGTGAAAGAAATAAAAAATTA
196 AAAAATAAAAAATAAGAAGTGCAAGTGAAAGAAATAAAAAATTA
*
3157607 GTAAAGAAAATTGCAAGCATTCAAAAGAAGAAAACAAAGGAAAGAAAAGTGAAGCACTCAACAAC
1 GTAAAGAAAATTGCAAGCATTCAAAAGAAGAAAACAAAGGAAAGAAAAGTGAAGCACTCAACAAA
3157672 AGGTCTCATCACCAAGCCAGTCAAGTAAGCCTTTAAATTGATTGTGGTGATAGAAGGGTTGTGTA
66 AGGTCTCATCACCAAGCCAGTCAAGTAAGCCTTTAAATTGATTGTGGTGATAGAAGGGTTGTGTA
*
3157737 GTGACTTCTGTAAGTAACCCTTTTATTCTCTTCTTTCTTATTT-CTAAGCCACTCTTTTCATTAT
131 GTGACTTCTGTAAGTAACCCTTTTATTCTCTTCTTTCTTATTTCCT-AGCCACCCTTTTCATTAT
3157801 A
195 A
3157802 TTTTGCTTTC
Statistics
Matches: 189, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
238 2 0.01
239 187 0.99
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (239 bp):
GTAAAGAAAATTGCAAGCATTCAAAAGAAGAAAACAAAGGAAAGAAAAGTGAAGCACTCAACAAA
AGGTCTCATCACCAAGCCAGTCAAGTAAGCCTTTAAATTGATTGTGGTGATAGAAGGGTTGTGTA
GTGACTTCTGTAAGTAACCCTTTTATTCTCTTCTTTCTTATTTCCTAGCCACCCTTTTCATTATA
AAAAATAAAAAATAAGAAGTGCAAGTGAAAGAAATAAAAAATTA
Found at i:3159440 original size:22 final size:22
Alignment explanation
Indices: 3159415--3159470 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
3159405 GGACGGTAAT
* *
3159415 ATGAACAAACATGGGTGGCAAA
1 ATGAACCAACACGGGTGGCAAA
3159437 ATGAACCAACACGGGTGGCAAA
1 ATGAACCAACACGGGTGGCAAA
3159459 ATGAACCAACAC
1 ATGAACCAACAC
3159471 TTACCTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (22 bp):
ATGAACCAACACGGGTGGCAAA
Found at i:3160280 original size:18 final size:18
Alignment explanation
Indices: 3160257--3160291 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3160247 CAACAAACGA
3160257 AAAAGA-AAGAAGAAAAAT
1 AAAAGAGAA-AAGAAAAAT
3160275 AAAAGAGAAAAGAAAAA
1 AAAAGAGAAAAGAAAAA
3160292 GACTCCTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (18 bp):
AAAAGAGAAAAGAAAAAT
Found at i:3165964 original size:22 final size:20
Alignment explanation
Indices: 3165930--3165969 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
3165920 ATAGCAGCAT
3165930 GCTTATTCATTCATTTGATA
1 GCTTATTCATTCATTTGATA
3165950 GCTTATGTGCATTCATTTGA
1 GCTTAT-T-CATTCATTTGA
3165970 GCTCTTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (20 bp):
GCTTATTCATTCATTTGATA
Found at i:3169914 original size:17 final size:17
Alignment explanation
Indices: 3169777--3169916 Score: 122
Period size: 17 Copynumber: 8.1 Consensus size: 17
3169767 TTCAACTAAG
* *
3169777 TAGTTCACTCATTAAAC
1 TAGTTCATTAATTAAAC
*
3169794 TAGTTCATTCATTAAAC
1 TAGTTCATTAATTAAAC
* *
3169811 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
3169828 TAGTTCATTCAAGATT--AC
1 TAGTTCATT--A-ATTAAAC
* * *
3169846 AAGTTCATTAAATAAAGT
1 TAGTTCATTAATTAAA-C
3169864 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
3169881 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
**
3169898 TAGTTCATTTTTTAAAC
1 TAGTTCATTAATTAAAC
3169915 TA
1 TA
3169917 TCTCTTAATT
Statistics
Matches: 102, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
15 2 0.02
16 1 0.01
17 73 0.72
18 24 0.24
20 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.39
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:3174135 original size:17 final size:17
Alignment explanation
Indices: 3173998--3174137 Score: 147
Period size: 17 Copynumber: 8.1 Consensus size: 17
3173988 TTCAACTAAG
*
3173998 TAGTTCACTCATTAAAC
1 TAGTTCATTCATTAAAC
3174015 TAGTTCATTCATTAAAC
1 TAGTTCATTCATTAAAC
*
3174032 TAGTTCATTCATCAAAC
1 TAGTTCATTCATTAAAC
** *
3174049 TAGTTCATTCAAGATTAC
1 TAGTTCATTCATTA-AAC
* * * *
3174067 AAGTTCATTAAATAAAGT
1 TAGTTCATTCATTAAA-C
*
3174085 TAGTTCATTAATTAAAC
1 TAGTTCATTCATTAAAC
*
3174102 TAGTTCATTCATCAAAC
1 TAGTTCATTCATTAAAC
3174119 TAGTTCATT-ATTTAAAC
1 TAGTTCATTCA-TTAAAC
3174136 TA
1 TA
3174138 TCTCTTAATT
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
16 1 0.01
17 76 0.73
18 27 0.26
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (17 bp):
TAGTTCATTCATTAAAC
Found at i:3179435 original size:78 final size:78
Alignment explanation
Indices: 3179306--3179470 Score: 321
Period size: 78 Copynumber: 2.1 Consensus size: 78
3179296 AATGTCAAAG
3179306 GACATGTCTTATAGGTCATTAAGGGTCATGAATATTGGTTCTTCAAAAGACATATTTCTTGAATC
1 GACATGTCTTATAGGTCATTAAGGGTCATGAATATTGGTTCTTCAAAAGACATATTTCTTGAATC
*
3179371 TTCTACTTGAAAA
66 TTCAACTTGAAAA
3179384 GACATGTCTTATAGGTCATTAAGGGTCATGAATATTGGTTCTTCAAAAGACATATTTCTTGAATC
1 GACATGTCTTATAGGTCATTAAGGGTCATGAATATTGGTTCTTCAAAAGACATATTTCTTGAATC
3179449 TTCAACTTGAAAA
66 TTCAACTTGAAAA
3179462 GACATGTCT
1 GACATGTCT
3179471 CTTGGAATAT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 86 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (78 bp):
GACATGTCTTATAGGTCATTAAGGGTCATGAATATTGGTTCTTCAAAAGACATATTTCTTGAATC
TTCAACTTGAAAA
Found at i:3183088 original size:35 final size:35
Alignment explanation
Indices: 3183015--3183089 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
3183005 CGTCACGTCC
** **
3183015 AGTAAGGCCCTGAGCACACAGCCGAGGATTCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
3183050 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
3183085 AGTAA
1 AGTAA
3183090 TCTTCCTCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.32, C:0.28, G:0.28, T:0.12
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:3183194 original size:24 final size:24
Alignment explanation
Indices: 3183167--3183248 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
3183157 CATAATTCAA
*
3183167 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
3183191 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
3183215 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
3183238 TTCAGGTATCA
1 GTCAAGTATCA
3183249 TAACAAAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 20 0.40
24 30 0.60
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:3185576 original size:15 final size:16
Alignment explanation
Indices: 3185546--3185579 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
3185536 GGTCAACAGT
3185546 GGTCAACATCGGTCAAC
1 GGTCAACA-CGGTCAAC
3185563 GGTCAACA-GGTCAAC
1 GGTCAACACGGTCAAC
3185578 GG
1 GG
3185580 GTCGAGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.15
Consensus pattern (16 bp):
GGTCAACACGGTCAAC
Found at i:3198146 original size:24 final size:24
Alignment explanation
Indices: 3198100--3198147 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3198090 CAATGTGCTG
*
3198100 AAACAAAAGAAAAAGGAAGAAGAA
1 AAACAAAAGAAAAAGGAAAAAGAA
*
3198124 AAACAAAAGAGAAAA-TAAAAAGAA
1 AAACAAAAGA-AAAAGGAAAAAGAA
3198148 TCCTGCATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (24 bp):
AAACAAAAGAAAAAGGAAAAAGAA
Found at i:3214914 original size:14 final size:14
Alignment explanation
Indices: 3214895--3214922 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3214885 TAAGATACTA
3214895 TTTCCATAACCATC
1 TTTCCATAACCATC
3214909 TTTCCATAACCATC
1 TTTCCATAACCATC
3214923 AATCCTTAAC
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:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTCCATAACCATC
Found at i:3214932 original size:14 final size:14
Alignment explanation
Indices: 3214897--3214935 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3214887 AGATACTATT
**
3214897 TCCATAACCATCTT
1 TCCATAACCATCAA
3214911 TCCATAACCATCAA
1 TCCATAACCATCAA
*
3214925 TCCTTAACCAT
1 TCCATAACCAT
3214936 AGTCCATCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (14 bp):
TCCATAACCATCAA
Found at i:3221570 original size:27 final size:26
Alignment explanation
Indices: 3221523--3221582 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
3221513 TTTCCTTGGC
3221523 TTTC-TTTCTCTTTTTGAATTTTTCT
1 TTTCTTTTCTCTTTTTGAATTTTTCT
3221548 TTTCTTTTCTTCTTTTATG-ATTTTTCT
1 TTTCTTTTC-TCTTTT-TGAATTTTTCT
*
3221575 TTTTTTTT
1 TTTCTTTT
3221583 TGTATTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 4 0.13
26 4 0.13
27 21 0.68
28 2 0.06
ACGTcount: A:0.07, C:0.13, G:0.03, T:0.77
Consensus pattern (26 bp):
TTTCTTTTCTCTTTTTGAATTTTTCT
Found at i:3221575 original size:22 final size:20
Alignment explanation
Indices: 3221547--3221601 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 20
3221537 TGAATTTTTC
3221547 TTTTCTTTTCTTCTTTTATGAT
1 TTTTCTTTTCTT-TTTTAT-AT
*
3221569 TTTTCTTTT-TTTTTTGTAT
1 TTTTCTTTTCTTTTTTATAT
3221588 TTTTCTTTCTCTTT
1 TTTTCTTT-TCTTT
3221602 GCACTCTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.33
20 6 0.20
21 5 0.17
22 9 0.30
ACGTcount: A:0.05, C:0.13, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTTATAT
Found at i:3223671 original size:24 final size:24
Alignment explanation
Indices: 3223644--3223711 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
3223634 CCTCAATGCT
*
3223644 CACAACTTTTGGCACTTCAAGTGA
1 CACAACTTTTGGAACTTCAAGTGA
* * *
3223668 CACATCTTTTTGAACTTCAAGTGG
1 CACAACTTTTGGAACTTCAAGTGA
* * *
3223692 CATAACTGTTGGAACGTCAA
1 CACAACTTTTGGAACTTCAA
3223712 AGGACATGTC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (24 bp):
CACAACTTTTGGAACTTCAAGTGA
Found at i:3224947 original size:12 final size:13
Alignment explanation
Indices: 3224930--3224958 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3224920 GTGCTTCAAC
3224930 TTTTCTTTCTT-T
1 TTTTCTTTCTTCT
3224942 TTTTCTTTCTTCT
1 TTTTCTTTCTTCT
3224955 TTTT
1 TTTT
3224959 GAGTGCTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTTCTTCT
Found at i:3224991 original size:26 final size:27
Alignment explanation
Indices: 3224943--3224993 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
3224933 TCTTTCTTTT
*
3224943 TTTCTTTCTTCTTTTTGAGTGCTTGAA
1 TTTCTTTATTCTTTTTGAGTGCTTGAA
3224970 TTTCTTTATTC-TTTTGAGTGCTTG
1 TTTCTTTATTCTTTTTGAGTGCTTG
3224994 CACTTTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.10, C:0.14, G:0.16, T:0.61
Consensus pattern (27 bp):
TTTCTTTATTCTTTTTGAGTGCTTGAA
Found at i:3225038 original size:12 final size:12
Alignment explanation
Indices: 3225021--3225046 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3225011 ATTTTGATTT
3225021 CTTTCACTTGCA
1 CTTTCACTTGCA
3225033 CTTTCACTTGCA
1 CTTTCACTTGCA
3225045 CT
1 CT
3225047 ATTTTTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.35, G:0.08, T:0.42
Consensus pattern (12 bp):
CTTTCACTTGCA
Found at i:3229392 original size:16 final size:15
Alignment explanation
Indices: 3229371--3229404 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3229361 AAATTTTGTG
3229371 TTTTTTGGTTTTGTTT
1 TTTTTTGGTTTT-TTT
*
3229387 TTTTTTTGTTTTTTT
1 TTTTTTGGTTTTTTT
3229402 TTT
1 TTT
3229405 CAAGAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (15 bp):
TTTTTTGGTTTTTTT
Found at i:3229398 original size:10 final size:11
Alignment explanation
Indices: 3229364--3229404 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
3229354 TCTTATGAAA
*
3229364 TTTTGTGTTTT
1 TTTTTTGTTTT
3229375 TTGGTTTTGTTTT
1 TT--TTTTGTTTT
3229388 TTTTTTGTTTT
1 TTTTTTGTTTT
3229399 TTTTTT
1 TTTTTT
3229405 CAAGAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:3229603 original size:213 final size:217
Alignment explanation
Indices: 3229185--3229618 Score: 799
Period size: 213 Copynumber: 2.0 Consensus size: 217
3229175 TCCTGTAGAA
*
3229185 TTTTCAAGAAATTTGACAAGATCCTAGACCAAATATGCTGATGAAACTTGAAGAATGTATTTGAA
1 TTTTCAAGAAATTTGACAAGATCCTAGACCAAATATGATGATGAAACTTGAAGAATGTATTTGAA
3229250 GGCTCTAATGAACTCCGATGTGGGTGAATTTTGGACTGGAGATTTATATTATGATGAATATGATA
66 GGCTCTAATGAACTCCGATGTGGGTGAATTTTGGACTGGAGATTTATATTATGATGAATATGATA
3229315 TCTGGAGAAAATAAGCCCTAAATACCTTCAATTGCAATTTCTTATGAAATTTTGTGTTTTTTGGT
131 TCTGGAGAAAATAAGCCCTAAATACCTTCAATTGCAATTTCTTATGAAATTTTGTGTTTTTTGGT
3229380 TTTGTTTTTTTTTTGT-TTTTT
196 TTTGTTTTTTTTTTGTGTTTTT
3229401 TTTTCAAGAAA-TTGACAAGATCCTAGACCAAA-ATGATGATG-AACTTGAAGAATGTATTTGAA
1 TTTTCAAGAAATTTGACAAGATCCTAGACCAAATATGATGATGAAACTTGAAGAATGTATTTGAA
3229463 GGCTCTAATGAACTCCGATGTGGGTGAATTTTGGACTGGAGATTTATATTATGATGAATATGATA
66 GGCTCTAATGAACTCCGATGTGGGTGAATTTTGGACTGGAGATTTATATTATGATGAATATGATA
3229528 TCTGGAGAAAATAAGCCCTAAATACCTTCAATTGCAATTTCTTATTGAAATTTTTGTGTTTTTTG
131 TCTGGAGAAAATAAGCCCTAAATACCTTCAATTGCAATTTCTTA-TGAAA-TTTTGTGTTTTTTG
3229593 G-TTT-TTTTTTTTTTGTGTTTTT
194 GTTTTGTTTTTTTTTTGTGTTTTT
3229615 TTTT
1 TTTT
3229619 TTTTGAAAAA
Statistics
Matches: 214, Mismatches: 1, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
213 142 0.66
214 25 0.12
215 36 0.17
216 11 0.05
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.42
Consensus pattern (217 bp):
TTTTCAAGAAATTTGACAAGATCCTAGACCAAATATGATGATGAAACTTGAAGAATGTATTTGAA
GGCTCTAATGAACTCCGATGTGGGTGAATTTTGGACTGGAGATTTATATTATGATGAATATGATA
TCTGGAGAAAATAAGCCCTAAATACCTTCAATTGCAATTTCTTATGAAATTTTGTGTTTTTTGGT
TTTGTTTTTTTTTTGTGTTTTT
Found at i:3229605 original size:16 final size:16
Alignment explanation
Indices: 3229586--3229623 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3229576 AATTTTTGTG
3229586 TTTTTTG-GTTTTTTT
1 TTTTTTGTGTTTTTTT
3229601 TTTTTTGTGTTTTTTT
1 TTTTTTGTGTTTTTTT
3229617 TTTTTTG
1 TTTTTTG
3229624 AAAAAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (16 bp):
TTTTTTGTGTTTTTTT
Found at i:3229607 original size:24 final size:22
Alignment explanation
Indices: 3229578--3229622 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
3229568 CTTATTGAAA
3229578 TTTTTGTGTTTTTTGGTTTTTTTT
1 TTTTTGTGTTTTTT--TTTTTTTT
3229602 TTTTTGTGTTTTTTTTTTTTT
1 TTTTTGTGTTTTTTTTTTTTT
3229623 GAAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.33
24 14 0.67
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (22 bp):
TTTTTGTGTTTTTTTTTTTTTT
Found at i:3230249 original size:15 final size:17
Alignment explanation
Indices: 3230224--3230257 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3230214 TAATGGTCCT
3230224 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
3230240 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
3230256 AA
1 AA
3230258 CATGTCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:3231594 original size:49 final size:49
Alignment explanation
Indices: 3231538--3231638 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
3231528 TTCATGAATG
3231538 TAATTAATCATGCTTAAATGAATGCATGACTATTATAACATACTTAACA
1 TAATTAATCATGCTTAAATGAATGCATGACTATTATAACATACTTAACA
3231587 TAATTAATCATGCTTAAATGAATGCATGACTATTATAACATACTTAACA
1 TAATTAATCATGCTTAAATGAATGCATGACTATTATAACATACTTAACA
3231636 TAA
1 TAA
3231639 CATTGTGCAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.35
Consensus pattern (49 bp):
TAATTAATCATGCTTAAATGAATGCATGACTATTATAACATACTTAACA
Found at i:3233975 original size:5 final size:5
Alignment explanation
Indices: 3233944--3233968 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3233934 AGTGCTTTAA
3233944 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
3233969 TTCTTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:3234001 original size:25 final size:24
Alignment explanation
Indices: 3233965--3234022 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
3233955 TTTTCTTTTC
3233965 TTTTTTC-TTTTTGAGTGCTTGAA
1 TTTTTTCTTTTTTGAGTGCTTGAA
*
3233988 TTTTTTCTTCTTTTGAGTGCTTGCA
1 TTTTTTCTT-TTTTGAGTGCTTGAA
*
3234013 CTTTTTCTTT
1 TTTTTTCTTT
3234023 GCTGAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 7 0.23
24 2 0.06
25 22 0.71
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.64
Consensus pattern (24 bp):
TTTTTTCTTTTTTGAGTGCTTGAA
Found at i:3238476 original size:18 final size:16
Alignment explanation
Indices: 3238433--3238464 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3238423 ATAACATATC
3238433 TATCCATTTCCTTTCT
1 TATCCATTTCCTTTCT
3238449 TAT-CATTTCCTTTCT
1 TATCCATTTCCTTTCT
3238464 T
1 T
3238465 CTTCCATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.81
16 3 0.19
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.59
Consensus pattern (16 bp):
TATCCATTTCCTTTCT
Found at i:3238713 original size:6 final size:6
Alignment explanation
Indices: 3238672--3238715 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
3238662 AAAAGCAACA
*
3238672 AAAAGAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAAAG A
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
3238716 CTCCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3242550 original size:32 final size:33
Alignment explanation
Indices: 3242509--3242575 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
3242499 TTTATAACAT
*
3242509 TTCTATCCAT-TTCC-TTTCTTATCATTTCCTTTC
1 TTCTATCCATATTCCATTT-TAATCATTT-CTTTC
3242542 TTCT-TCCATATTCCATTTTAATCATTTCTTTC
1 TTCTATCCATATTCCATTTTAATCATTTCTTTC
3242574 TT
1 TT
3242576 TTAATTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 12 0.39
33 16 0.52
34 3 0.10
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58
Consensus pattern (33 bp):
TTCTATCCATATTCCATTTTAATCATTTCTTTC
Found at i:3242555 original size:18 final size:17
Alignment explanation
Indices: 3242509--3242555 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
3242499 TTTATAACAT
3242509 TTCTATCCATTTCCTTTC
1 TTCT-TCCATTTCCTTTC
*
3242527 TT-AT-CATTTCCTTTC
1 TTCTTCCATTTCCTTTC
3242542 TTCTTCCATATTCC
1 TTCTTCCAT-TTCC
3242556 ATTTTAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 13 0.54
16 2 0.08
17 3 0.12
18 6 0.25
ACGTcount: A:0.13, C:0.32, G:0.00, T:0.55
Consensus pattern (17 bp):
TTCTTCCATTTCCTTTC
Found at i:3246172 original size:10 final size:10
Alignment explanation
Indices: 3246157--3246191 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
3246147 GCTTCATATC
3246157 ATTTCTTTCA
1 ATTTCTTTCA
3246167 ATTTCTTTC-
1 ATTTCTTTCA
3246176 ATTTCTTATCA
1 ATTTCTT-TCA
3246187 ATTTC
1 ATTTC
3246192 CAATTAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.30
10 11 0.48
11 5 0.22
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTCTTTCA
Found at i:3248883 original size:14 final size:14
Alignment explanation
Indices: 3248864--3248928 Score: 114
Period size: 14 Copynumber: 4.7 Consensus size: 14
3248854 TAAGATACTA
3248864 TTTCCATCACCATC
1 TTTCCATCACCATC
3248878 TTTCCATCACCATC
1 TTTCCATCACCATC
*
3248892 TTTCCATCACCATA
1 TTTCCATCACCATC
3248906 TTTCCATCACCATC
1 TTTCCATCACCATC
3248920 TTT-CATCAC
1 TTTCCATCAC
3248929 TTTCACGCCA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
13 6 0.12
14 43 0.88
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:3255467 original size:13 final size:13
Alignment explanation
Indices: 3255449--3255531 Score: 51
Period size: 14 Copynumber: 6.0 Consensus size: 13
3255439 CTTGGCTTGC
3255449 TTTCTTTTTTACT
1 TTTCTTTTTTACT
*
3255462 TTTCTTCTTTTTCT
1 TTTCTT-TTTTACT
*
3255476 TTTCATTTTTTTCT
1 TTTC-TTTTTTACT
* *
3255490 GATTTTTTTCTTTATT
1 --TTTCTTT-TTTACT
* *
3255506 TTTGTCTTTTA-T
1 TTTCTTTTTTACT
3255518 TTTCTTTTTATACT
1 TTTCTTTTT-TACT
3255532 ACAATTTTGT
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
12 8 0.15
13 12 0.22
14 23 0.42
15 5 0.09
16 7 0.13
ACGTcount: A:0.08, C:0.13, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTCTTTTTTACT
Found at i:3255506 original size:12 final size:13
Alignment explanation
Indices: 3255453--3255520 Score: 61
Period size: 14 Copynumber: 5.3 Consensus size: 13
3255443 GCTTGCTTTC
* *
3255453 TTTTTTACTTTTC
1 TTTTTTTCTTTTA
3255466 TTCTTTTTCTTTTCA
1 TT-TTTTTCTTTT-A
*
3255481 TTTTTTTC--TGA
1 TTTTTTTCTTTTA
3255492 TTTTTTTC-TTTA
1 TTTTTTTCTTTTA
*
3255504 TTTTTGTCTTTTA
1 TTTTTTTCTTTTA
3255517 TTTT
1 TTTT
3255521 CTTTTTATAC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
11 9 0.20
12 10 0.22
13 10 0.22
14 15 0.33
15 2 0.04
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTTTTTCTTTTA
Found at i:3261966 original size:20 final size:20
Alignment explanation
Indices: 3261941--3262109 Score: 79
Period size: 20 Copynumber: 8.3 Consensus size: 20
3261931 TTTTTGAAAT
3261941 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
* ** *
3261961 TCGCAAGGATAATATGTACA
1 TCGCAACGCGAATATGTAAA
* * * **
3261981 TCGCAATGCGATTTTCCAAA
1 TCGCAACGCGAATATGTAAA
* * **
3262001 TTCGCAACGCGATTTTCCAAA
1 -TCGCAACGCGAATATGTAAA
** * *
3262022 TTCATAATGCGAATAGGTAAA
1 -TCGCAACGCGAATATGTAAA
**
3262043 TCGCAACGATAATATGTAAA
1 TCGCAACGCGAATATGTAAA
* *
3262063 TCGCAACGCG-ATTTTTCAAAA
1 TCGCAACGCGAATATGT--AAA
* * *
3262084 TTGCAAAGCAAATATGTAAA
1 TCGCAACGCGAATATGTAAA
3262104 TCGCAA
1 TCGCAA
3262110 TGAGAATATT
Statistics
Matches: 108, Mismatches: 37, Indels: 8
0.71 0.24 0.05
Matches are distributed among these distances:
19 4 0.04
20 58 0.54
21 42 0.39
22 4 0.04
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:3262000 original size:82 final size:82
Alignment explanation
Indices: 3261912--3262082 Score: 243
Period size: 82 Copynumber: 2.1 Consensus size: 82
3261902 GCAACACAGG
* ** * * *
3261912 TTCCAAATTCGCAACTCGATTTTTGAAATTCGCAACGCGAATATGTAAATCGCAAGGATAATATG
1 TTCCAAATTCGCAACGCGATTTTCCAAATTCACAACGCGAATAGGTAAATCGCAACGATAATATG
* *
3261977 TACATCGCAATGCGATT
66 TAAATCGCAACGCGATT
* *
3261994 TTCCAAATTCGCAACGCGATTTTCCAAATTCATAATGCGAATAGGTAAATCGCAACGATAATATG
1 TTCCAAATTCGCAACGCGATTTTCCAAATTCACAACGCGAATAGGTAAATCGCAACGATAATATG
3262059 TAAATCGCAACGCGATT
66 TAAATCGCAACGCGATT
*
3262076 TTTCAAA
1 TTCCAAA
3262083 ATTGCAAAGC
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (82 bp):
TTCCAAATTCGCAACGCGATTTTCCAAATTCACAACGCGAATAGGTAAATCGCAACGATAATATG
TAAATCGCAACGCGATT
Found at i:3262067 original size:61 final size:61
Alignment explanation
Indices: 3262002--3262118 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 61
3261992 TTTTCCAAAT
* * *
3262002 TCGCAACGCGA-TTTTCCAAATT-CATAATGCGAATAGGTAAATCGCAACGATAATATGTAAA
1 TCGCAACGCGATTTTTCAAAATTGCA-AA-GCAAATAGGTAAATCGCAACGAGAATATGTAAA
* *
3262063 TCGCAACGCGATTTTTCAAAATTGCAAAGCAAATATGTAAATCGCAATGAGAATAT
1 TCGCAACGCGATTTTTCAAAATTGCAAAGCAAATAGGTAAATCGCAACGAGAATAT
3262119 TATTTTCGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
61 35 0.71
62 12 0.24
63 2 0.04
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.26
Consensus pattern (61 bp):
TCGCAACGCGATTTTTCAAAATTGCAAAGCAAATAGGTAAATCGCAACGAGAATATGTAAA
Found at i:3262666 original size:20 final size:20
Alignment explanation
Indices: 3262619--3262680 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
3262609 AAACTTAAAT
*
3262619 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
3262639 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
3262659 TCGCAACGTTGCGAAAATGAAA
1 TCGCAAC---GCGAAAATGAAA
3262681 TTGCGTTGCG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
20 26 0.68
23 12 0.32
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:3264493 original size:21 final size:21
Alignment explanation
Indices: 3264457--3264508 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
3264447 GACAATGGTG
* * * *
3264457 CTTTACGTGGTGAGGTATCTA
1 CTTTACGTGATAAGGTAGCCA
3264478 CTTTACGTGATAAGGTAGCCA
1 CTTTACGTGATAAGGTAGCCA
*
3264499 CTCTACGTGA
1 CTTTACGTGA
3264509 GATTGTTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (21 bp):
CTTTACGTGATAAGGTAGCCA
Found at i:3264861 original size:21 final size:20
Alignment explanation
Indices: 3264837--3264907 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
3264827 CCTATCATCC
3264837 TTCAAGAGGCACCTCCCACCG
1 TTCAAGAGGC-CCTCCCACCG
* * ** *
3264858 TTCAAGATGTCTCTGTCATCG
1 TTCAAGA-GGCCCTCCCACCG
*
3264879 TTCAAGAGGTCCCTTCCACCG
1 TTCAAGAGG-CCCTCCCACCG
3264900 TTCAAGAG
1 TTCAAGAG
3264908 CCCGATTCAC
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
20 1 0.03
21 35 0.92
22 2 0.05
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (20 bp):
TTCAAGAGGCCCTCCCACCG
Found at i:3264862 original size:42 final size:42
Alignment explanation
Indices: 3264816--3264907 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
3264806 TCTCCTATCA
3264816 TTCAAGAGGCCCCTATCATCCTTCAAGAGG-CACCTCCCACCG
1 TTCAAGAGGCCCCTATCATCCTTCAAGAGGTC-CCTCCCACCG
* * * * * *
3264858 TTCAAGATGTCTCTGTCATCGTTCAAGAGGTCCCTTCCACCG
1 TTCAAGAGGCCCCTATCATCCTTCAAGAGGTCCCTCCCACCG
3264900 TTCAAGAG
1 TTCAAGAG
3264908 CCCGATTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATCCTTCAAGAGGTCCCTCCCACCG
Found at i:3265184 original size:18 final size:18
Alignment explanation
Indices: 3265161--3265196 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3265151 AAGTCGGTTG
*
3265161 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
3265179 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
3265197 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:3268488 original size:20 final size:20
Alignment explanation
Indices: 3268444--3268526 Score: 91
Period size: 20 Copynumber: 4.2 Consensus size: 20
3268434 CAAAACATTT
* *
3268444 GTGTTGCGAAAATAAAA-GC
1 GTGTTGCGAAATTAAAATTC
3268463 -TGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
*
3268482 GTGTTGCG-AATTCAAAAATC
1 GTGTTGCGAAATT-AAAATTC
* *
3268502 GAGTTGCGAAATCAAAATTC
1 GTGTTGCGAAATTAAAATTC
3268522 GTGTT
1 GTGTT
3268527 CCGATTTAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
18 15 0.28
19 5 0.09
20 30 0.57
21 3 0.06
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:3268610 original size:20 final size:20
Alignment explanation
Indices: 3268578--3268733 Score: 134
Period size: 20 Copynumber: 7.8 Consensus size: 20
3268568 TGAAAAATAA
*
3268578 ATTCACGTTGCGATTTACAT
1 ATTCGCGTTGCGATTTACAT
** * *
3268598 ATTATCATTGCGATTTACCT
1 ATTCGCGTTGCGATTTACAT
* *
3268618 ATTCGCATTGCGATTTTCACT
1 ATTCGCGTTGCGATTTACA-T
3268639 -TTCGCGTTGCGATTTACAT
1 ATTCGCGTTGCGATTTACAT
***
3268658 ATTATTGTTGCGATTTACAT
1 ATTCGCGTTGCGATTTACAT
**
3268678 AGCCGCGTTGCGATTTACAT
1 ATTCGCGTTGCGATTTACAT
*** * *
3268698 ATTATTGTTGCAATTTACCT
1 ATTCGCGTTGCGATTTACAT
*
3268718 ATTCGCATTGCGATTT
1 ATTCGCGTTGCGATTT
3268734 TGGAACATGT
Statistics
Matches: 104, Mismatches: 30, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
19 1 0.01
20 102 0.98
21 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACAT
Found at i:3268669 original size:40 final size:41
Alignment explanation
Indices: 3268584--3268733 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 41
3268574 ATAAATTCAC
** * * ***
3268584 GTTGCGATTTACA-TATTATCATTGCGATTTACCTATTCGC
1 GTTGCGATTTACACTATTCGCGTTGCGATTTACATATTATT
* *
3268624 ATTGCGATTTTCACT-TTCGCGTTGCGATTTACATATTATT
1 GTTGCGATTTACACTATTCGCGTTGCGATTTACATATTATT
**
3268664 GTTGCGATTTACA-TAGCCGCGTTGCGATTTACATATTATT
1 GTTGCGATTTACACTATTCGCGTTGCGATTTACATATTATT
* *
3268704 GTTGCAATTTAC-CTATTCGCATTGCGATTT
1 GTTGCGATTTACACTATTCGCGTTGCGATTT
3268734 TGGAACATGT
Statistics
Matches: 90, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 1 0.01
40 88 0.98
41 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (41 bp):
GTTGCGATTTACACTATTCGCGTTGCGATTTACATATTATT
Found at i:3268708 original size:60 final size:60
Alignment explanation
Indices: 3268583--3268733 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 60
3268573 AATAAATTCA
* ** * *
3268583 CGTTGCGATTTACATATTATCATTGCGATTTACCTATTCGCATTGCGATTTTCACTTTCG
1 CGTTGCGATTTACATATTATCATTGCGATTTACATAGCCGCATTGCGATTTACACTTTAG
** * *
3268643 CGTTGCGATTTACATATTATTGTTGCGATTTACATAGCCGCGTTGCGATTTACA-TATTAT
1 CGTTGCGATTTACATATTATCATTGCGATTTACATAGCCGCATTGCGATTTACACT-TTAG
* * * **
3268703 TGTTGCAATTTACCTATTCGCATTGCGATTT
1 CGTTGCGATTTACATATTATCATTGCGATTT
3268734 TGGAACATGT
Statistics
Matches: 74, Mismatches: 16, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
59 1 0.01
60 73 0.99
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (60 bp):
CGTTGCGATTTACATATTATCATTGCGATTTACATAGCCGCATTGCGATTTACACTTTAG
Found at i:3269430 original size:24 final size:24
Alignment explanation
Indices: 3269395--3269447 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3269385 TGACCCGACT
* *
3269395 CCTGATCAGCACCTTTCTGAGACA
1 CCTGATCAGCACCATTCTAAGACA
* *
3269419 CCTGATCTGCACCATTCTAAGACC
1 CCTGATCAGCACCATTCTAAGACA
3269443 CCTGA
1 CCTGA
3269448 ATATCAACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.36, G:0.15, T:0.25
Consensus pattern (24 bp):
CCTGATCAGCACCATTCTAAGACA
Found at i:3274172 original size:27 final size:27
Alignment explanation
Indices: 3274142--3274203 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
3274132 ATGGCTACGT
3274142 TTGTGCAACTCCCTCCATCAATAATCA
1 TTGTGCAACTCCCTCCATCAATAATCA
3274169 TTGTGCAACTCCCTCCATCAATAATCA
1 TTGTGCAACTCCCTCCATCAATAATCA
3274196 TTGTGCAA
1 TTGTGCAA
3274204 ACATTTTCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31
Consensus pattern (27 bp):
TTGTGCAACTCCCTCCATCAATAATCA
Found at i:3275918 original size:22 final size:23
Alignment explanation
Indices: 3275877--3275922 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
3275867 CTTTTTTTTC
3275877 CTTTTGAGTGCTTAAAAATTTCTT
1 CTTTTGAGTGCTT-AAAATTTCTT
*
3275901 CTTTTGAGTGCTT-TAATTTCTT
1 CTTTTGAGTGCTTAAAATTTCTT
3275923 TTCTGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
24 13 0.62
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.54
Consensus pattern (23 bp):
CTTTTGAGTGCTTAAAATTTCTT
Found at i:3275926 original size:24 final size:25
Alignment explanation
Indices: 3275872--3275926 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
3275862 CTTTTCTTTT
3275872 TTTTCCTTTTGAGTGCTTAAAAATTTC
1 TTTT-CTTTTGAGTGCTT-AAAATTTC
*
3275899 --TTCTTTTGAGTGCTT-TAATTTC
1 TTTTCTTTTGAGTGCTTAAAATTTC
3275921 TTTTCT
1 TTTTCT
3275927 GATTTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
22 6 0.24
24 17 0.68
25 2 0.08
ACGTcount: A:0.16, C:0.15, G:0.11, T:0.58
Consensus pattern (25 bp):
TTTTCTTTTGAGTGCTTAAAATTTC
Found at i:3280068 original size:38 final size:38
Alignment explanation
Indices: 3279972--3280182 Score: 271
Period size: 38 Copynumber: 5.5 Consensus size: 38
3279962 ATATCAAACA
* *
3279972 ATTTATTTTCTTTTACAAAACAGGAA-ATTAAATCCAACG
1 ATTTATTTCCTTTTACAAAATAGGAAGA-TAAAT-CAACG
* *
3280011 ATTTATTCCCTTTTACAAAATAGGAAGATAAATCAAAG
1 ATTTATTTCCTTTTACAAAATAGGAAGATAAATCAACG
* *
3280049 ATTTATTTCCTTCTGCAAAATAGGAAGATAAATCAACG
1 ATTTATTTCCTTTTACAAAATAGGAAGATAAATCAACG
* *
3280087 ATTTATTTCCTTCTGCAAAATAGGAAGATAAATCAACG
1 ATTTATTTCCTTTTACAAAATAGGAAGATAAATCAACG
* * * *
3280125 ATTTATTTCCTTTTACAAAATAGGAAAACAAATTATACA
1 ATTTATTTCCTTTTACAAAATAGGAAGATAAATCA-ACG
*
3280164 ATTTATTTCCTTTCACAAA
1 ATTTATTTCCTTTTACAAA
3280183 TCATAATCAT
Statistics
Matches: 155, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
38 106 0.68
39 48 0.31
40 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (38 bp):
ATTTATTTCCTTTTACAAAATAGGAAGATAAATCAACG
Found at i:3280450 original size:57 final size:59
Alignment explanation
Indices: 3280290--3280490 Score: 175
Period size: 58 Copynumber: 3.5 Consensus size: 59
3280280 AATAGGATCC
* * * * *
3280290 TTCAAGATTCAT-AA-GAAACTAAATTTAACAATGTATTTACTTTTACAAA-ATAGAATCA
1 TTCAAGATTC-TCAAGGAAA-TAAATTCAACTATATATTTACTCTTACAAAGTTAGAATCA
*
3280348 TTTAAGATTCTCAAGGAAATAAATTCAACTATATATTT-CTCTTACAAAGTTAGAATCA
1 TTCAAGATTCTCAAGGAAATAAATTCAACTATATATTTACTCTTACAAAGTTAGAATCA
* * * * *
3280406 TTCAATATTCTCACGGAAAT-AATT-TAGTAATTTATTTAC-CTTACAAAGTTAGAATCAA
1 TTCAAGATTCTCAAGGAAATAAATTCAACT-ATATATTTACTCTTACAAAGTTAGAATC-A
** **
3280464 CGCAAGATTCT-ATTGAAATAAATTCAA
1 TTCAAGATTCTCAAGGAAATAAATTCAA
3280491 TGATTTATTT
Statistics
Matches: 117, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
56 2 0.02
57 44 0.38
58 66 0.56
59 5 0.04
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.35
Consensus pattern (59 bp):
TTCAAGATTCTCAAGGAAATAAATTCAACTATATATTTACTCTTACAAAGTTAGAATCA
Found at i:3280686 original size:45 final size:44
Alignment explanation
Indices: 3280637--3280776 Score: 163
Period size: 45 Copynumber: 3.1 Consensus size: 44
3280627 TCAGCAATCG
* *
3280637 AAAGGAACTAATTATTTGATTTTGATTTTTGCAACCCAATAATCA
1 AAAGGAACTAATCATTTGATTTT-ATTTTTGCAACCCAATAATAA
* * *
3280682 AAAGGAACTAATCCTTTGATTTTAATTTTTCCAACTCAATAATAAAA
1 AAAGGAACTAATCATTTGATTTT-ATTTTTGCAACCCAATAAT--AA
* * *
3280729 AAAAGAATTAATCATTTGATTTTACTTTTGACAACCCAATAATAA
1 AAAGGAACTAATCATTTGATTTTATTTTTG-CAACCCAATAATAA
3280774 AAA
1 AAA
3280777 ATCATTGGAT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
45 43 0.54
46 5 0.06
47 32 0.40
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.36
Consensus pattern (44 bp):
AAAGGAACTAATCATTTGATTTTATTTTTGCAACCCAATAATAA
Found at i:3280750 original size:47 final size:47
Alignment explanation
Indices: 3280641--3280777 Score: 161
Period size: 47 Copynumber: 3.0 Consensus size: 47
3280631 CAATCGAAAG
* * * * *
3280641 GAACTAATTATTTGATTTTGATTTTTGCAACCCAATAAT--CAAAAG
1 GAACTAATCATTTGATTTTAATTTTTACAACCCAATAATAAAAAAAA
* * *
3280686 GAACTAATCCTTTGATTTTAATTTTTCCAACTCAATAATAAAAAAAA
1 GAACTAATCATTTGATTTTAATTTTTACAACCCAATAATAAAAAAAA
* * *
3280733 GAATTAATCATTTGATTTTACTTTTGACAACCCAATAATAAAAAA
1 GAACTAATCATTTGATTTTAATTTTTACAACCCAATAATAAAAAA
3280778 TCATTGGATT
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
45 34 0.44
47 43 0.56
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.36
Consensus pattern (47 bp):
GAACTAATCATTTGATTTTAATTTTTACAACCCAATAATAAAAAAAA
Found at i:3281099 original size:41 final size:41
Alignment explanation
Indices: 3281054--3281135 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
3281044 ATCTTACCAT
*
3281054 AATGATATTTCCC-AATAATATCATAAGAATCACATTTATTC
1 AATGATA-TTCCCTAATAATATCATAAGAATCACATTAATTC
3281095 AATGATATTCCCTAATAATATCATAAGAATCACATTAATTC
1 AATGATATTCCCTAATAATATCATAAGAATCACATTAATTC
3281136 TTTATTTGCA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 5 0.13
41 34 0.87
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.35
Consensus pattern (41 bp):
AATGATATTCCCTAATAATATCATAAGAATCACATTAATTC
Found at i:3281933 original size:122 final size:122
Alignment explanation
Indices: 3281716--3281960 Score: 463
Period size: 122 Copynumber: 2.0 Consensus size: 122
3281706 ATACAACAAC
3281716 AATACGATCAACGCAAAGTAGCTTAACTTGCGAGATCACAAACTTTTATCTTGCTAGAGACTATC
1 AATACGATCAACGCAAAGTAGCTTAACTTGCGAGATCACAAACTTTTATCTTGCTAGAGACTATC
*
3281781 ACCGAAAACAAAAGGAGAATAAAAGAATTTATGAGTTGTGTAAAACCTAGAAGGTTT
66 ACCGAAAACAAAAGGAGAAGAAAAGAATTTATGAGTTGTGTAAAACCTAGAAGGTTT
*
3281838 AATACGATCAACGCAAAGTAGCTTAACTTGCGTGATCACAAACTTTTATCTTGCTAGAGACTATC
1 AATACGATCAACGCAAAGTAGCTTAACTTGCGAGATCACAAACTTTTATCTTGCTAGAGACTATC
*
3281903 ACCGAAAACAAAAGGAGAAGAAAATAATTTATGAGTTGTGTAAAACCTAGAAGGTTT
66 ACCGAAAACAAAAGGAGAAGAAAAGAATTTATGAGTTGTGTAAAACCTAGAAGGTTT
3281960 A
1 A
3281961 CACAATATTT
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 120 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.26
Consensus pattern (122 bp):
AATACGATCAACGCAAAGTAGCTTAACTTGCGAGATCACAAACTTTTATCTTGCTAGAGACTATC
ACCGAAAACAAAAGGAGAAGAAAAGAATTTATGAGTTGTGTAAAACCTAGAAGGTTT
Found at i:3284261 original size:16 final size:17
Alignment explanation
Indices: 3284240--3284273 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3284230 TGGTATCTAT
*
3284240 ACTTTAATTCC-ATGAC
1 ACTTTAATACCTATGAC
3284256 ACTTTAATACCTATGAC
1 ACTTTAATACCTATGAC
3284273 A
1 A
3284274 TATGTACCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (17 bp):
ACTTTAATACCTATGAC
Found at i:3286945 original size:13 final size:13
Alignment explanation
Indices: 3286927--3286960 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3286917 TAAGATTTTC
*
3286927 TTTGAAAATCATT
1 TTTGAAAATCAAT
3286940 TTTG-AAATCAAT
1 TTTGAAAATCAAT
3286952 TTTGAAAAT
1 TTTGAAAAT
3286961 TACTCCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:3291302 original size:3 final size:3
Alignment explanation
Indices: 3291294--3291358 Score: 87
Period size: 3 Copynumber: 22.0 Consensus size: 3
3291284 TTTGATTTAT
* * * *
3291294 TTA TTA TTA TT- TTA CTA TAA TTA TTA TTA TTA TAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3291341 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
3291359 AATATATTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3296793 original size:15 final size:15
Alignment explanation
Indices: 3296773--3296804 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3296763 ATCAATACCT
3296773 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
3296788 TTTTGCATACATTCA
1 TTTTGCATACATGCA
3296803 TT
1 TT
3296805 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:3304146 original size:9 final size:9
Alignment explanation
Indices: 3304132--3304194 Score: 67
Period size: 10 Copynumber: 6.9 Consensus size: 9
3304122 ATTATGCTTG
3304132 AAGAAAAAA
1 AAGAAAAAA
3304141 AAGAAAAAAA
1 AAG-AAAAAA
*
3304151 AAGAGAGAAA
1 AAGA-AAAAA
3304161 AAG--AAAA
1 AAGAAAAAA
3304168 AAGAAAAAA
1 AAGAAAAAA
*
3304177 GAGAAAAAA
1 AAGAAAAAA
3304186 GAAGAAAAA
1 -AAGAAAAA
3304195 GGGGGGTCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
7 6 0.13
9 16 0.36
10 23 0.51
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:3305630 original size:83 final size:83
Alignment explanation
Indices: 3305342--3305818 Score: 688
Period size: 83 Copynumber: 5.6 Consensus size: 83
3305332 AACAAATGAC
* * * * * *
3305342 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGAACTGATTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
3305407 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
*
3305425 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-----A-A
* **
3305490 GAACCAGTTATTGAATTTGAAAGATAA
58 -AACCAGTTATTGAATTTGGAAGAGGA
3305517 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
3305582 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
* *
3305600 ATGTGCT-AGTAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 ATGTGCTCA-TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
* * **
3305664 CATTGAATTTGAAAGATAA
65 TATTGAATTTGGAAGAGGA
*
3305683 ATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
3305748 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
3305766 ATGTGCT-AGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 ATGTGCTCA-TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
3305819 ATATGAAACC
Statistics
Matches: 355, Mismatches: 27, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
82 2 0.01
83 273 0.77
84 2 0.01
85 2 0.01
90 2 0.01
91 1 0.00
92 73 0.21
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (83 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
ATTGAATTTGGAAGAGGA
Found at i:3305745 original size:166 final size:170
Alignment explanation
Indices: 3305342--3305870 Score: 780
Period size: 166 Copynumber: 3.1 Consensus size: 170
3305332 AACAAATGAC
* * * * * *
3305342 ATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGAACTGATTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
3305407 ATTGAATTTGGAAGAGGAATGTGCTCA-TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
66 ATTGAATTTGGAAGAGGAATGTGCT-AGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
3305471 TGTTTTGGTATGAACCACAGAACCAGTTATTGAATTTGAAAGATAA
130 TGGTTTGG-AT--A--ACAGAACCAATCATTGAATTTGAAAGATAA
3305517 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
*
3305582 ATTGAATTTGGAAGAGGAATGTGCTAGTAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCT
66 ATTGAATTTGGAAGAGGAATGTGCTAGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
3305647 GGTTTGG-T-A-A-AACCAATCATTGAATTTGAAAGATAA
131 GGTTTGGATAACAGAACCAATCATTGAATTTGAAAGATAA
*
3305683 ATGTGCTCATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
3305748 ATTGAATTTGGAAGAGGAATGTGCTAGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
66 ATTGAATTTGGAAGAGGAATGTGCTAGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
* * *
3305813 GGTTTGATATGAAACCACAGAACCAATCATTAAATTTGAAAGATGA
131 GGTTTG----GATA--ACAGAACCAATCATTGAATTTGAAAGATAA
*
3305859 ATTTGCTCATAG
1 ATGTGCTCATAG
3305871 TAGAAATAAG
Statistics
Matches: 327, Mismatches: 16, Indels: 21
0.90 0.04 0.06
Matches are distributed among these distances:
166 158 0.48
167 1 0.00
168 1 0.00
170 1 0.00
173 1 0.00
174 2 0.01
175 128 0.39
176 35 0.11
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (170 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGTT
ATTGAATTTGGAAGAGGAATGTGCTAGTAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
GGTTTGGATAACAGAACCAATCATTGAATTTGAAAGATAA
Found at i:3306372 original size:52 final size:52
Alignment explanation
Indices: 3306310--3306410 Score: 202
Period size: 52 Copynumber: 1.9 Consensus size: 52
3306300 TATCGATATC
3306310 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
3306362 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCA
1 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCA
3306411 AAATTAACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (52 bp):
TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
Found at i:3307393 original size:20 final size:20
Alignment explanation
Indices: 3307330--3307393 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
3307320 CCAGGTAGAG
*
3307330 TTCATAATGAGAAGAACTCA
1 TTCATAATGAGAAGAACTAA
* * *
3307350 TCTGAAAAAG-GAAGAA-TAA
1 T-TCATAATGAGAAGAACTAA
*
3307369 GTTCATAATGAGAAGAACTTA
1 -TTCATAATGAGAAGAACTAA
3307390 TTCA
1 TTCA
3307394 ACTTTTTGCT
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
19 7 0.22
20 18 0.56
21 7 0.22
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (20 bp):
TTCATAATGAGAAGAACTAA
Found at i:3307412 original size:113 final size:113
Alignment explanation
Indices: 3306748--3307766 Score: 1137
Period size: 113 Copynumber: 8.9 Consensus size: 113
3306738 TTCCAGAGAA
* * * *
3306748 AGTTCATAATGAAAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * *
3306813 AACCTTTTGTTTGAATTCATCATGT-GATGGATTAAAATTTCCA-GTAG
66 AACTTTTTGCTCGAATTCATCAT-TCGATGGATCAATATTTCCAGGTAG
* * *
3306860 AGTTCATAATGAGAAGAACTCATTACTTGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAACTCA-T-C-TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * * * *
3306925 TTCAACCTTGTGCTCAAATCCATCACTT-GATGGATCAGCT-TTTCCA-GAAG
63 TTCAACTTTTTGCTCGAATTCATCA-TTCGATGGATCA-ATATTTCCAGGTAG
* *
3306975 AAGTTCATAATAAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTT
1 -AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* * * * ** *
3307040 GTTCAACCTTTTGCTCAAATCCATCACTT-GATGGACCAGCATTTCCAGAG-AA
62 GTTCAACTTTTTGCTCGAATTCATCA-TTCGATGGATCAATATTTCCAG-GTAG
* ** *
3307092 AGTTCATAATGAGAAGAACTTATCAT-TTGAA-GAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AGTTCATAATGAGAAGAACTCATC-TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * ** *
3307155 CAACTTTTTGCTCG-ACTCTATCGTAGAAAGAGATAGATCAACATCAATATTTCCA-GAAGG
65 CAACTTTTTGCTCGAATTC-ATC--------A-TTCGAT--GGATCAATATTTCCAGGTA-G
* * * *
3307215 AGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAAAATAAATTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
3307280 AA-TCTTTTGCTCGAATTCATCATTCGATGGATCAGTATTGCCAGGTAG
66 AACT-TTTTGCTCGAATTCATCATTCGATGGATCAATATTTCCAGGTAG
* * *
3307328 AGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAATAAGTTCATAATGAGAAGAACTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
3307393 AACTTTTTGCTCGAATTCATCATTCGATGGATCAGTATTGCCAGGTAG
66 AACTTTTTGCTCGAATTCATCATTCGATGGATCAATATTTCCAGGTAG
* * *
3307441 AGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAATAAGTTCATAATGAGAAGAACTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * *
3307506 AACTTTTTGCTCGAATTCATCATTCGATGGATCAACACTACCAGGTAG
66 AACTTTTTGCTCGAATTCATCATTCGATGGATCAATATTTCCAGGTAG
* * *
3307554 AGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAAAAGAAGTTCATAATGAGAAGAACTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
3307619 AACTTTTTGCTCGAATTCATCATTCGATGGATCAACATTGCCAGGTAG
66 AACTTTTTGCTCGAATTCATCATTCGATGGATCAATATTTCCAGGTAG
*
3307667 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
3307732 AA-TCTTTTGATCGAATTCATCACTCGATGGATCAA
66 AACT-TTTTGCTCGAATTCATCATTCGATGGATCAA
3307767 ACATTTTTAG
Statistics
Matches: 802, Mismatches: 71, Indels: 67
0.85 0.08 0.07
Matches are distributed among these distances:
111 2 0.00
112 69 0.09
113 440 0.55
114 6 0.01
115 76 0.09
116 111 0.14
117 2 0.00
118 3 0.00
119 3 0.00
120 2 0.00
121 4 0.00
122 2 0.00
123 36 0.04
124 43 0.05
125 3 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTTGCTCGAATTCATCATTCGATGGATCAATATTTCCAGGTAG
Found at i:3307506 original size:20 final size:20
Alignment explanation
Indices: 3307443--3307506 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
3307433 CCAGGTAGAG
*
3307443 TTCATAATGAGAAGAACTCA
1 TTCATAATGAGAAGAACTAA
* * *
3307463 TCTGAAAAAG-GAAGAA-TAA
1 T-TCATAATGAGAAGAACTAA
*
3307482 GTTCATAATGAGAAGAACTTA
1 -TTCATAATGAGAAGAACTAA
3307503 TTCA
1 TTCA
3307507 ACTTTTTGCT
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
19 7 0.22
20 18 0.56
21 7 0.22
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (20 bp):
TTCATAATGAGAAGAACTAA
Found at i:3308059 original size:3 final size:3
Alignment explanation
Indices: 3308051--3308116 Score: 96
Period size: 3 Copynumber: 22.0 Consensus size: 3
3308041 TTTGATTTAT
* * * *
3308051 TTA TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3308099 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
3308117 AATATATTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:3308124 original size:15 final size:16
Alignment explanation
Indices: 3308058--3308125 Score: 79
Period size: 15 Copynumber: 4.3 Consensus size: 16
3308048 TATTTATTAT
*
3308058 TATTATTACTATAAT-
1 TATTATTATTATAATA
3308073 TATTATTATTATAA-A
1 TATTATTATTATAATA
*
3308088 TATTATTATTATTAT-
1 TATTATTATTATAATA
3308103 TATTATTATTATTAAATA
1 TATTATTATTA-T-AATA
3308121 TATTA
1 TATTA
3308126 AATATATAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
15 37 0.82
16 1 0.02
17 2 0.04
18 5 0.11
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATTATTATAATA
Found at i:3313971 original size:23 final size:23
Alignment explanation
Indices: 3313939--3313985 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
3313929 TACCATGTAG
* *
3313939 AAACATAGTTTTCTGACTTTGGT
1 AAACAGAGTTTTCTGACTATGGT
3313962 AAACAGAGTTTTCTGACTATGGT
1 AAACAGAGTTTTCTGACTATGGT
3313985 A
1 A
3313986 GCAAAGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (23 bp):
AAACAGAGTTTTCTGACTATGGT
Found at i:3313996 original size:23 final size:23
Alignment explanation
Indices: 3313939--3313995 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
3313929 TACCATGTAG
* *
3313939 AAACATAGTTTTCTGACTTTGGT
1 AAACAAAGTTTTCTGACTATGGT
*
3313962 AAACAGAGTTTTCTGACTATGGT
1 AAACAAAGTTTTCTGACTATGGT
*
3313985 -AGCAAAGTTTT
1 AAACAAAGTTTT
3313996 TGATTCTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 9 0.30
23 21 0.70
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (23 bp):
AAACAAAGTTTTCTGACTATGGT
Found at i:3315318 original size:38 final size:36
Alignment explanation
Indices: 3315276--3315346 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 36
3315266 AACCCGAGTT
*
3315276 GACCC-AAAAATTATACATCCTCCACTCGAACCCGATCC
1 GACCCGAAAAA-TATACACCCTCCAC-CG-ACCCGATCC
3315314 GACCCGAAAAATATACACCCTCCACCGACCCGA
1 GACCCGAAAAATATACACCCTCCACCGACCCGA
3315347 CTTTTTGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 6 0.19
37 2 0.06
38 18 0.58
39 5 0.16
ACGTcount: A:0.35, C:0.41, G:0.10, T:0.14
Consensus pattern (36 bp):
GACCCGAAAAATATACACCCTCCACCGACCCGATCC
Found at i:3316567 original size:101 final size:104
Alignment explanation
Indices: 3316422--3316656 Score: 327
Period size: 101 Copynumber: 2.3 Consensus size: 104
3316412 CAACTTTGGC
3316422 ATCATTTCACTCAAAAAGAAAGTTTCATATCACTTGAGATTGTTTTTCTTAAAAC-AATTTCTAT
1 ATCATTTCACTCAAAAAGAAAGTTTCATATCACTTGAGATTGTTTTTCTTAAAACAAATTT-TAT
* * *
3316486 CTCACTTGAGACGGTTTTCCCTTGAAACACAAATTTTAAA
65 CTCACTTAAGACGATTTTCCCTTGAAACACAAACTTTAAA
* * *
3316526 ATCATTTCACT-AGAAA-AAA-TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTATC
1 ATCATTTCACTCAAAAAGAAAGTTTCATATCACTTGAGATTGTTTTTCTTAAAACAAATTTTATC
* * *
3316588 TCACTTAAGACGATTTTCCCTTGAAACATAAACTTTGAC
66 TCACTTAAGACGATTTTCCCTTGAAACACAAACTTTAAA
* *
3316627 ATCATTTTACTCAAAAAGAAAATTT-ATATC
1 ATCATTTCACTCAAAAAGAAAGTTTCATATC
3316657 TTTTATCTTT
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
101 78 0.68
102 12 0.10
103 11 0.10
104 14 0.12
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.38
Consensus pattern (104 bp):
ATCATTTCACTCAAAAAGAAAGTTTCATATCACTTGAGATTGTTTTTCTTAAAACAAATTTTATC
TCACTTAAGACGATTTTCCCTTGAAACACAAACTTTAAA
Found at i:3317522 original size:18 final size:19
Alignment explanation
Indices: 3317497--3317580 Score: 68
Period size: 19 Copynumber: 4.5 Consensus size: 19
3317487 GAAAGTTAGT
3317497 TTTATATTAATTATAATT-
1 TTTATATTAATTATAATTC
* **
3317515 TGTATATTATAAATT-TGGTT-
1 T-T-TA-TATTAATTATAATTC
**
3317535 TTTATATTAATTCCAATTC
1 TTTATATTAATTATAATTC
3317554 TTTATATTAATTATAATTC
1 TTTATATTAATTATAATTC
3317573 -TTATATTA
1 TTTATATTA
3317581 TAAAGTTTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
17 7 0.13
18 13 0.25
19 19 0.37
20 6 0.12
21 7 0.13
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.57
Consensus pattern (19 bp):
TTTATATTAATTATAATTC
Found at i:3318371 original size:20 final size:20
Alignment explanation
Indices: 3318295--3318362 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
3318285 AACCCTTACA
*
3318295 AATATCAAGCAGAATCAAAC
1 AATATCAAACAGAATCAAAC
* **
3318315 AATAACAAACAGAAGAAAAC
1 AATATCAAACAGAATCAAAC
* * *
3318335 AATATAAAATAGAATCAAGC
1 AATATCAAACAGAATCAAAC
3318355 AATATCAA
1 AATATCAA
3318363 GTAGAATCAT
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.62, C:0.15, G:0.09, T:0.15
Consensus pattern (20 bp):
AATATCAAACAGAATCAAAC
Found at i:3318571 original size:4 final size:4
Alignment explanation
Indices: 3318562--3318587 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3318552 CAAAAGTTAA
3318562 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
3318588 GAAATTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3319078 original size:7 final size:7
Alignment explanation
Indices: 3319068--3319093 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3319058 AATAAAAAAA
3319068 TTAAATT
1 TTAAATT
3319075 TTAAATT
1 TTAAATT
3319082 TTAAATT
1 TTAAATT
3319089 TTAAA
1 TTAAA
3319094 ACTACTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TTAAATT
Found at i:3320732 original size:69 final size:69
Alignment explanation
Indices: 3320650--3320819 Score: 286
Period size: 69 Copynumber: 2.5 Consensus size: 69
3320640 AAATAAAAAA
* * *
3320650 AATATCAGTAACCATATTGAAATCATAAATATAAAACAAACAAGAAAAGGAAAAGGGTTCCTCTT
1 AATATCAATAACCATACTCAAATCATAAATATAAAACAAACAAGAAAAGGAAAAGGGTTCCTCTT
3320715 TCAT
66 TCAT
* * *
3320719 AATATCAATAACCATACTCAAATCATAAATATAAAACAAATAAGAAAAGTAAAATGGTTCCTCTT
1 AATATCAATAACCATACTCAAATCATAAATATAAAACAAACAAGAAAAGGAAAAGGGTTCCTCTT
3320784 TCAT
66 TCAT
3320788 AATATCAATAACCATACTCAAATCATAAATAT
1 AATATCAATAACCATACTCAAATCATAAATAT
3320820 CAGTAACCAC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 95 1.00
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (69 bp):
AATATCAATAACCATACTCAAATCATAAATATAAAACAAACAAGAAAAGGAAAAGGGTTCCTCTT
TCAT
Found at i:3320861 original size:21 final size:21
Alignment explanation
Indices: 3320805--3320861 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 21
3320795 ATAACCATAC
3320805 TCAAA-TCATAAATATCAGTAA
1 TCAAACTCA-AAATATCAGTAA
* *
3320826 CCACACACACAAAATATCAGTAA
1 TCA-A-ACTCAAAATATCAGTAA
3320849 TCAAACTCAAAAT
1 TCAAACTCAAAAT
3320862 CTCAAATCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 10 0.34
22 2 0.07
23 15 0.52
24 2 0.07
ACGTcount: A:0.53, C:0.23, G:0.04, T:0.21
Consensus pattern (21 bp):
TCAAACTCAAAATATCAGTAA
Found at i:3320905 original size:25 final size:25
Alignment explanation
Indices: 3320876--3320970 Score: 86
Period size: 24 Copynumber: 3.8 Consensus size: 25
3320866 AATCATAAAT
3320876 ATCAGTAACCATACACACAAAATAA-
1 ATCAGTAACCATACACA-AAAATAAC
* * *
3320901 ATCAGTGACCATACTCAAATCATAAAC
1 ATCAGTAACCATACACAAA-AAT-AAC
*
3320928 ATCAGTAACCATACACAAAAA-AAT
1 ATCAGTAACCATACACAAAAATAAC
* * *
3320952 ACCAATAACCATACTCAAA
1 ATCAGTAACCATACACAAA
3320971 TCATAAATAT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
24 20 0.35
25 17 0.30
26 3 0.05
27 17 0.30
ACGTcount: A:0.53, C:0.25, G:0.04, T:0.18
Consensus pattern (25 bp):
ATCAGTAACCATACACAAAAATAAC
Found at i:3321002 original size:51 final size:52
Alignment explanation
Indices: 3320788--3320991 Score: 243
Period size: 51 Copynumber: 3.8 Consensus size: 52
3320778 CCTCTTTCAT
*
3320788 AATATCAATAACCATACTCAAATCATAAATATCAGTAACCACACACACAAAA
1 AATATCAATAACCATACTCAAATCATAAATATCAGTAACCATACACACAAAA
* *
3320840 TATCAGT-AATCAAACTCAAAATCTCAAATCATAAATATCAGTAACCATACACACAAAA
1 AAT-A-TCAAT--AAC-C-ATA-CTCAAATCATAAATATCAGTAACCATACACACAAAA
* * *
3320898 TAA-ATCAGTGACCATACTCAAATCATAAACATCAGTAACCATACACA-AAAA
1 -AATATCAATAACCATACTCAAATCATAAATATCAGTAACCATACACACAAAA
* *
3320949 AATACCAATAACCATACTCAAATCATAAATATCAGAAACCATA
1 AATATCAATAACCATACTCAAATCATAAATATCAGTAACCATA
3320992 GATAAAAAAA
Statistics
Matches: 129, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
50 2 0.02
51 39 0.30
52 32 0.25
53 6 0.05
54 2 0.02
55 5 0.04
56 2 0.02
57 5 0.04
58 35 0.27
59 1 0.01
ACGTcount: A:0.52, C:0.24, G:0.03, T:0.21
Consensus pattern (52 bp):
AATATCAATAACCATACTCAAATCATAAATATCAGTAACCATACACACAAAA
Done.