Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 29
Found at i:5676640 original size:226 final size:226
Alignment explanation
Indices: 5676209--5676678 Score: 673
Period size: 237 Copynumber: 2.1 Consensus size: 226
5676199 AGTGTGATAT
* *
5676209 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAATACCCTACCCGAAAATATATATAATTTTACC
1 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAATACCCGACCCGAAAAAATATATAATTTTACC
* *
5676274 TTATATATTTAGAAATAATTACAATAATACCCTTCTATATATAATTTTTTTTCCAATTAAATCAC
66 TTATATATTTAGAAATAATTACAATAATACCCATCTACATATAATTTTTTTTCCAATTAAATCAC
* *
5676339 TATTTTTATTGAATAAAAATATTTTTTTAATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTC
131 TATTTTTATTGAATAAAAATATATTTTTAATTATTTCAGGT---GT--GG-CGGATTTCTAATTC
*
5676404 ATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGG
190 ATATATTCGGGTCAGGTCGGGTGAAACTTTATTTTGG
* *
5676441 TCGGGTCGGGTCGGGTTTGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAAATATATAATT
1 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTG-AAAATACCCGACCCG----AAAAAATATATAATT
* *
5676506 TTACCTTATATATTTAGGAATAATTATAATAATACCCATCTACATATATATTTTTTTTCCAATTA
61 TTACCTTATATATTTAGAAATAATTACAATAATACCCATCTACATATA-ATTTTTTTTCCAATTA
* *
5676571 AGTCACTGTTTTTATTGAATAAAAATA-ATTTTT-ATTATTTCAGGT-T-G-GG-TTTCTAATTC
125 AATCACTATTTTTATTGAATAAAAATATATTTTTAATTATTTCAGGTGTGGCGGATTTCTAATTC
5676630 ATATATTCGGGTCAGGTCGGGTGAAACTTTATTTTGG
190 ATATATTCGGGTCAGGTCGGGTGAAACTTTATTTTGG
5676667 TCGGGTCGGGTC
1 TCGGGTCGGGTC
5676679 TCGGATGGAG
Statistics
Matches: 219, Mismatches: 13, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
226 58 0.26
227 2 0.01
229 1 0.00
232 29 0.13
233 14 0.06
236 11 0.05
237 63 0.29
238 41 0.19
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (226 bp):
TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAATACCCGACCCGAAAAAATATATAATTTTACC
TTATATATTTAGAAATAATTACAATAATACCCATCTACATATAATTTTTTTTCCAATTAAATCAC
TATTTTTATTGAATAAAAATATATTTTTAATTATTTCAGGTGTGGCGGATTTCTAATTCATATAT
TCGGGTCAGGTCGGGTGAAACTTTATTTTGG
Found at i:5678474 original size:64 final size:63
Alignment explanation
Indices: 5678351--5678491 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
5678341 TCTTTAACAT
* * *
5678351 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAAGA
* * * * * *
5678414 GATGTATCGATGCACT-CCTTATGCATCGATGCACTAATTGCATTCGATG-TTTCTTCTTTAAAG
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATTACATTCGATGTTTTCAT-TTTAAAG
5678477 A
63 A
5678478 GTGCATCGATGCAC
1 GTGCATCGATGCAC
5678492 ATTGAATATG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 20 0.31
64 45 0.69
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAAGA
Found at i:5679383 original size:18 final size:17
Alignment explanation
Indices: 5679342--5679392 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
5679332 TATAAAATTG
*
5679342 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
* *
5679359 TATTCCAATTACTTCACA
1 GATTCCAATT-CCTCACA
5679377 GATTCCAATTCTCTCA
1 GATTCCAATTC-CTCA
5679393 AAAACATTAC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:5681726 original size:8 final size:8
Alignment explanation
Indices: 5681712--5681753 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
5681702 ATTAATAAAT
5681712 AATTTTTA
1 AATTTTTA
*
5681720 GATTTTTA
1 AATTTTTA
5681728 AATTTTT-
1 AATTTTTA
5681735 AATATTTTA
1 AAT-TTTTA
5681744 AATTTTTA
1 AATTTTTA
5681752 AA
1 AA
5681754 ATTAATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 3 0.10
8 24 0.80
9 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (8 bp):
AATTTTTA
Found at i:5681733 original size:16 final size:16
Alignment explanation
Indices: 5681712--5681752 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
5681702 ATTAATAAAT
5681712 AATTTTTAGAT-TTTTA
1 AATTTTTA-ATATTTTA
5681728 AATTTTTAATATTTTA
1 AATTTTTAATATTTTA
5681744 AATTTTTAA
1 AATTTTTAA
5681753 AATTAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
AATTTTTAATATTTTA
Found at i:5681999 original size:26 final size:26
Alignment explanation
Indices: 5681951--5682000 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
5681941 TTCTGCCCCC
* *
5681951 TAAAATTCTATAAGTTAGTCTCATCT
1 TAAAATTCTAGAAGTTAGCCTCATCT
* *
5681977 TAAAATTTTAGAAGTTCGCCTCAT
1 TAAAATTCTAGAAGTTAGCCTCAT
5682001 AGTATAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (26 bp):
TAAAATTCTAGAAGTTAGCCTCATCT
Found at i:5682499 original size:8 final size:9
Alignment explanation
Indices: 5682446--5682499 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 9
5682436 TGACTATCAA
5682446 TATTTT-TT
1 TATTTTCTT
5682454 TATTTTCTAT
1 TATTTTCT-T
5682464 TATTTTC-T
1 TATTTTCTT
*
5682472 TATATTCTT
1 TATTTTCTT
5682481 TGATTTATCTT
1 T-ATTT-TCTT
5682492 T-TTTTCTT
1 TATTTTCTT
5682500 AGTTTTTCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 17 0.44
9 6 0.15
10 11 0.28
11 5 0.13
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (9 bp):
TATTTTCTT
Found at i:5683002 original size:22 final size:23
Alignment explanation
Indices: 5682966--5683011 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
5682956 TTTTATTTCA
*
5682966 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTATATATTATTATTAT
5682989 TTTGTTTTA-ATATTATTATTAT
1 TTTGTTTTATATATTATTATTAT
5683011 T
1 T
5683012 ATTAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTGTTTTATATATTATTATTAT
Found at i:5684667 original size:20 final size:19
Alignment explanation
Indices: 5684642--5684683 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5684632 CTATTTTATA
5684642 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
5684662 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
5684681 AAT
1 AAT
5684684 ATCGAGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:5684679 original size:119 final size:117
Alignment explanation
Indices: 5684537--5684774 Score: 282
Period size: 120 Copynumber: 2.0 Consensus size: 117
5684527 TATTTTAATC
* * * *
5684537 TTGTTTTAATATTTATTTATTTTTCAATAT-TAAGAAAGGA-CAGTCTTAAAACAACTGGATGTC
1 TTGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
* * *
5684600 CATTTTCTAATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAA
66 C-TTTTATAATATTTCTAAATAAATAAATATCCTA-TTTATAAA-TATATATAAA
* * * ** *
5684655 TTGTTTTAATTATTTATTTATTTTTTAATATCGAGGAAAAGAGCTGTCTTAAGGCACCTAGAAGT
1 TTGTTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT
* **
5684720 CCTTTTATGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAA
65 CCTTTTATAATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAA
5684773 TT
1 TT
5684775 AATATATATT
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 20 0.20
119 28 0.28
120 35 0.35
121 18 0.18
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (117 bp):
TTGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
CTTTTATAATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAA
Found at i:5685300 original size:23 final size:23
Alignment explanation
Indices: 5685274--5685323 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
5685264 TCTTTCAAAT
5685274 TTTTTATTACTTATTACTTATTA
1 TTTTTATTACTTATTACTTATTA
* *
5685297 TTTTTATTACTTATTATTTTTTA
1 TTTTTATTACTTATTACTTATTA
5685320 TTTT
1 TTTT
5685324 ATTTAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTTTATTACTTATTACTTATTA
Found at i:5685305 original size:16 final size:16
Alignment explanation
Indices: 5685284--5685317 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5685274 TTTTTATTAC
5685284 TTATTACTTATTATTT
1 TTATTACTTATTATTT
5685300 TTATTACTTATTATTT
1 TTATTACTTATTATTT
5685316 TT
1 TT
5685318 TATTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTACTTATTATTT
Found at i:5686973 original size:14 final size:14
Alignment explanation
Indices: 5686953--5686988 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5686943 ATTTTAAATA
5686953 ATTTACATTTACAT
1 ATTTACATTTACAT
* *
5686967 TTTTACATTTGCAT
1 ATTTACATTTACAT
5686981 ATTTACAT
1 ATTTACAT
5686989 CTGGCATCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.53
Consensus pattern (14 bp):
ATTTACATTTACAT
Found at i:5690569 original size:26 final size:26
Alignment explanation
Indices: 5690539--5690591 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
5690529 TCTTATACTC
*
5690539 ATCCAGCAAAGAAATAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAA
5690565 ATCCAGCAAAGAAAGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAA
5690591 A
1 A
5690592 AAGAAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.70, C:0.11, G:0.13, T:0.06
Consensus pattern (26 bp):
ATCCAGCAAAGAAAGAAAAAAGAAAA
Found at i:5690594 original size:34 final size:33
Alignment explanation
Indices: 5690554--5690663 Score: 98
Period size: 36 Copynumber: 3.2 Consensus size: 33
5690544 GCAAAGAAAT
5690554 AAAAAAGAAAAATCCA-GCAAAGAAAGAAAAA-AGA
1 AAAAAAGAAAAAT-CATG-AAA-AAAGAAAAAGAGA
*
5690588 AAAAAAGAAAAATGATGAAAAAAGAAAAATGAGA
1 AAAAAAGAAAAATCATGAAAAAAGAAAAA-GAGA
** * *
5690622 AAAAAAGGAAAAAAAGATGAAAAAGGAAAATTGAGA
1 AAAAAA-G-AAAAATCATGAAAAAAGAAAA-AGAGA
5690658 AAAAAA
1 AAAAAA
5690664 AAAGAAAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
32 9 0.14
33 4 0.06
34 23 0.35
35 1 0.02
36 29 0.44
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (33 bp):
AAAAAAGAAAAATCATGAAAAAAGAAAAAGAGA
Found at i:5690609 original size:18 final size:17
Alignment explanation
Indices: 5690554--5690663 Score: 93
Period size: 17 Copynumber: 6.4 Consensus size: 17
5690544 GCAAAGAAAT
*
5690554 AAAAAAGAAAAATCCAGCA
1 AAAAAAGAAAAAT-GAG-A
*
5690573 AAGAAAGAAAAA--AGA
1 AAAAAAGAAAAATGAGA
5690588 AAAAAAGAAAAATGATG-
1 AAAAAAGAAAAATGA-GA
5690605 AAAAAAGAAAAATGAGA
1 AAAAAAGAAAAATGAGA
*
5690622 AAAAAAGGAAAAA-AAGA
1 AAAAAA-GAAAAATGAGA
* *
5690639 TGAAAAAGGAAAATTGAGA
1 --AAAAAAGAAAAATGAGA
5690658 AAAAAA
1 AAAAAA
5690664 AAAGAAAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
15 12 0.16
16 3 0.04
17 30 0.39
18 12 0.16
19 19 0.25
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (17 bp):
AAAAAAGAAAAATGAGA
Found at i:5690627 original size:36 final size:36
Alignment explanation
Indices: 5690587--5690672 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
5690577 AAGAAAAAAG
5690587 AAAAAAAGAAAAATGATGAAAAAAGAAAAATGAGAAA
1 AAAAAAAGAAAAA-GATGAAAAAAGAAAAATGAGAAA
* * *
5690624 AAAAGGAA-AAAAAGATGAAAAAGGAAAATTGAGAAA
1 AAAA-AAAGAAAAAGATGAAAAAAGAAAAATGAGAAA
5690660 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
5690673 AAGGGGGGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
35 2 0.05
36 30 0.70
37 9 0.21
38 2 0.05
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (36 bp):
AAAAAAAGAAAAAGATGAAAAAAGAAAAATGAGAAA
Found at i:5690632 original size:25 final size:24
Alignment explanation
Indices: 5690554--5690635 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 24
5690544 GCAAAGAAAT
* *
5690554 AAAAAAGAAAAATCCAGCAAAGAAAG
1 AAAAAAGAAAAAT-AAG-AAAAAAAG
*
5690580 AAAAAAGAAAAA-AAGAAAAATGATG
1 AAAAAAGAAAAATAAGAAAAA--AAG
*
5690605 AAAAAAGAAAAATGAGAAAAAAAGG
1 AAAAAAGAAAAATAAGAAAAAAA-G
5690630 AAAAAA
1 AAAAAA
5690636 AGATGAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
23 4 0.09
24 3 0.06
25 21 0.45
26 19 0.40
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.05
Consensus pattern (24 bp):
AAAAAAGAAAAATAAGAAAAAAAG
Found at i:5694102 original size:74 final size:74
Alignment explanation
Indices: 5693964--5694135 Score: 213
Period size: 74 Copynumber: 2.3 Consensus size: 74
5693954 ATTAATAAGA
* *
5693964 AGCAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGAAATGTTGAAATATTTTGAA
1 AGCAAATGTTGGGGCATGCTG-AAACCCTTTTCAATCAGAATCAGAAATGTTGAAACATCTTGAA
*
5694029 TA-TT-TATC
65 CACTTGTATC
* * * **
5694037 AGCAAAATATTGGGGCATGCTGAAAGCCTATTTCAATCAGAATCAGAACTGTTGATGCATCTTGA
1 AGC-AAATGTTGGGGCATGCTGAAACCCT-TTTCAATCAGAATCAGAAATGTTGAAACATCTTGA
*
5694102 ACACTTGTATT
64 ACACTTGTATC
*
5694113 AGCCAATGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
5694136 GGCCCACAAC
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
73 9 0.11
74 49 0.58
75 20 0.24
76 6 0.07
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (74 bp):
AGCAAATGTTGGGGCATGCTGAAACCCTTTTCAATCAGAATCAGAAATGTTGAAACATCTTGAAC
ACTTGTATC
Found at i:5695098 original size:54 final size:54
Alignment explanation
Indices: 5695016--5695169 Score: 254
Period size: 54 Copynumber: 2.9 Consensus size: 54
5695006 AAATCTTGGC
*
5695016 AGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAAA
1 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAAA
**
5695070 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAGC
1 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAAA
* * *
5695124 AGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGAAC
1 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
5695170 CTACTATTCT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 94 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (54 bp):
AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAAA
Found at i:5695561 original size:22 final size:22
Alignment explanation
Indices: 5695533--5695614 Score: 101
Period size: 22 Copynumber: 3.7 Consensus size: 22
5695523 TCTACATCTA
* *
5695533 CACTCTTCAAAGATGATAGATT
1 CACTCTTCAAAGATGACAAATT
5695555 CACTCTTCAAAGATGACAAATT
1 CACTCTTCAAAGATGACAAATT
* * *
5695577 CTCTTTTCAAATATGACAAATT
1 CACTCTTCAAAGATGACAAATT
* *
5695599 CTCTTTTCAAAGATGA
1 CACTCTTCAAAGATGA
5695615 AAGCTTTATC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.34
Consensus pattern (22 bp):
CACTCTTCAAAGATGACAAATT
Found at i:5696212 original size:113 final size:113
Alignment explanation
Indices: 5696014--5697139 Score: 1691
Period size: 113 Copynumber: 10.0 Consensus size: 113
5696004 TTAGAAAAGT
* * **
5696014 TCAAATTCATCATTCGATGGATCAGCATTGCCAG-GTCGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTCGATGGATCAGCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
* * *
5696078 AAGAATGAAGAAGAACTTCATAATGAGAAGAGCTTGTTCAACCTTTTAC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * ** *
5696127 TCAAATCCATCATTAGATGGATCAGCATTACCAG-GTCGAGTTCATAATGAGAAGAATTCATCTG
1 TCAAATCCATCATTCGATGGATCAGCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
*
5696191 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* **
5696240 TCAAATCCATCATTCGATGGATCAGCATTACCAG-GTCGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTCGATGGATCAGCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
5696304 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * *
5696353 TCAAATTCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
5696418 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * ** *
5696466 TCGAATTCATCACTT-GATGGATCAAAATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTG
1 TCAAATCCATCA-TTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
5696530 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
*
5696579 TCAAATCCATCACTCGATGGATCAG-ATTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTCGATGGATCAGCA-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* *
5696643 AAGAATGAAGAAGAAGTTCATAATGAGAAGAGATTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * * **
5696692 TCGAATCCATCATTCGATGGATCAACATTACCAG-GTCGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTCGATGGATCAGCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
*
5696756 AAAAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * *
5696805 TCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
5696870 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * ** *
5696918 TCGAATTCATCACTT-GATGGATCAAAATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTG
1 TCAAATCCATCA-TTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* *
5696982 AAGAA-G--GAAGAAGTTCATAATGAGAAGAGCATGTTCAACATTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
5697028 TCAAATCCATCAATT-GATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATC-ATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
**
5697092 AAG-AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
5697140 ATGACTCTAT
Statistics
Matches: 938, Mismatches: 63, Indels: 25
0.91 0.06 0.02
Matches are distributed among these distances:
109 1 0.00
110 99 0.11
111 1 0.00
112 40 0.04
113 792 0.84
114 5 0.01
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (113 bp):
TCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
Found at i:5696219 original size:24 final size:23
Alignment explanation
Indices: 5696176--5696220 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
5696166 GTTCATAATG
*
5696176 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
5696199 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
5696221 AACTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:5697390 original size:113 final size:112
Alignment explanation
Indices: 5697188--5697542 Score: 456
Period size: 113 Copynumber: 3.2 Consensus size: 112
5697178 TTTCCAGAGA
5697188 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAACATT
1 AAGTTCATAATGAGAAGAACTTGTTCAAC-TTTTGCTTGAATTCATCATTCGATGGATCAACATT
*
5697253 ACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
65 ACCAGGGCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * * *
5697301 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTTATCATTAGATGGACCAGCATT
1 AAGTTCATAATGAGAAGAACTTGTTCAACTTTT-GCTTGAATTCATCATTCGATGGATCAACATT
* * *
5697366 GCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAG
65 ACCAGGGCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* ** * * *
5697414 AAATTCATAATGAGAAGAACTTG--------TTGCTCAAATTCATCACTCGATGGATCAACTTTT
1 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
** * ** *
5697471 CCAAAGAGAGTTCATAATGAGAAGATTTCATCTGAGGAAGGAAGAAG
66 CCAGGGCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
5697518 AAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTTGTT
5697543 AGCTTTTTGC
Statistics
Matches: 212, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
104 84 0.40
105 2 0.01
112 4 0.02
113 122 0.58
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (112 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCATTCGATGGATCAACATTA
CCAGGGCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
Found at i:5697460 original size:104 final size:104
Alignment explanation
Indices: 5697352--5697542 Score: 265
Period size: 104 Copynumber: 1.8 Consensus size: 104
5697342 TTTATCATTA
* ** *
5697352 GATGGACCAGCATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAA
1 GATGGACCAACATTGCCAAAGAGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAA
5697417 TTCATAATGAGAAGAACTTGTTGCTCAAATTCATCACTC
66 TTCATAATGAGAAGAACTTGTTGCTCAAATTCATCACTC
* * * * ** * * *
5697456 GATGGATCAACTTTTCCAAAGAGAGTTCATAATGAGAAGATTTCATCTGAGGAAGGAAGAAGAAG
1 GATGGACCAACATTGCCAAAGAGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAA
5697521 TTCATAATGAGAAGAACTTGTT
66 TTCATAATGAGAAGAACTTGTT
5697543 AGCTTTTTGC
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
104 74 1.00
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (104 bp):
GATGGACCAACATTGCCAAAGAGAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAA
TTCATAATGAGAAGAACTTGTTGCTCAAATTCATCACTC
Found at i:5697802 original size:19 final size:20
Alignment explanation
Indices: 5697775--5697852 Score: 79
Period size: 19 Copynumber: 4.0 Consensus size: 20
5697765 ATTTGTTTTA
* *
5697775 TTTATTATTATTATT-TTGT
1 TTTAATATTATTATTATTAT
5697794 TTTAATATTATTATTATTAT
1 TTTAATATTATTATTATTAT
* *
5697814 ATT-ATATTATTATTATTAA
1 TTTAATATTATTATTATTAT
* *
5697833 ATAAATAATTATTATTATTA
1 TTTAAT-ATTATTATTATTA
5697853 CAAACAAGCC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 31 0.61
20 7 0.14
21 13 0.25
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (20 bp):
TTTAATATTATTATTATTAT
Found at i:5697802 original size:22 final size:22
Alignment explanation
Indices: 5697766--5697831 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
5697756 TTTTATTTCA
5697766 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTA-TTATTATTATTAT
*
5697789 TTTGTTTTAATATTATTATTAT
1 TTTGTTTTATTATTATTATTAT
* * *
5697811 TATATTATATTATTATTATTA
1 TTTGTTTTATTATTATTATTA
5697832 AATAAATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
22 29 0.76
23 9 0.24
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (22 bp):
TTTGTTTTATTATTATTATTAT
Found at i:5697852 original size:3 final size:3
Alignment explanation
Indices: 5697776--5697831 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
5697766 TTTGTTTTAT
* *
5697776 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5697820 TTA TTA TTA TTA
1 TTA TTA TTA TTA
5697832 AATAAATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 8 0.17
3 39 0.83
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5698766 original size:14 final size:14
Alignment explanation
Indices: 5698747--5698778 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
5698737 CGTTCGTGAA
5698747 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
5698761 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
5698775 CGTT
1 CGTT
5698779 TATGTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:5698795 original size:24 final size:24
Alignment explanation
Indices: 5698748--5698798 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5698738 GTTCGTGAAC
*
5698748 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
* * *
5698772 GTTCGTTTATGTTCTTTCATTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
5698796 GTT
1 GTT
5698799 TAACCCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.57
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTCAGTTAT
Found at i:5699797 original size:10 final size:10
Alignment explanation
Indices: 5699779--5699853 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
5699769 GGGTCTCCAA
*
5699779 CGTTGATGTT
1 CGTTTATGTT
5699789 CGTTTATGTT
1 CGTTTATGTT
5699799 CGTGTTTAT-TT
1 C--GTTTATGTT
* *
5699810 ATGTTCATGTT
1 -CGTTTATGTT
5699821 CGTTTATGTT
1 CGTTTATGTT
5699831 CG----TGTT
1 CGTTTATGTT
5699837 CGTTTATGTT
1 CGTTTATGTT
*
5699847 TGTTTAT
1 CGTTTAT
5699854 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 35 0.69
11 4 0.08
12 6 0.12
ACGTcount: A:0.11, C:0.09, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:5699810 original size:16 final size:16
Alignment explanation
Indices: 5699785--5699846 Score: 79
Period size: 16 Copynumber: 3.9 Consensus size: 16
5699775 CCAACGTTGA
*
5699785 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
* *
5699801 TGTTTATTTATGTTCA
1 TGTTCATTTATGTTCG
*
5699817 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
*
5699833 TGTTCGTTTATGTT
1 TGTTCATTTATGTT
5699847 TGTTTATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:5699825 original size:32 final size:32
Alignment explanation
Indices: 5699784--5699846 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
5699774 TCCAACGTTG
*
5699784 ATGTTCGTTTATGTTCGTGTTTATTTATGTTC
1 ATGTTCGTTTATGTTCGTGTTCATTTATGTTC
*
5699816 ATGTTCGTTTATGTTCGTGTTCGTTTATGTT
1 ATGTTCGTTTATGTTCGTGTTCATTTATGTT
5699847 TGTTTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.11, C:0.10, G:0.21, T:0.59
Consensus pattern (32 bp):
ATGTTCGTTTATGTTCGTGTTCATTTATGTTC
Found at i:5699940 original size:16 final size:16
Alignment explanation
Indices: 5699919--5699951 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5699909 AAACAAATTT
5699919 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
5699935 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
5699951 T
1 T
5699952 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:5701275 original size:33 final size:33
Alignment explanation
Indices: 5701223--5701296 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
5701213 CAAACCCATC
* *
5701223 AAAATATAATCACAAATCTCCAACATGAACAAT
1 AAAACATAACCACAAATCTCCAACATGAACAAT
* *
5701256 AAAACATAACCACAAATCTCTAACATGAACAGT
1 AAAACATAACCACAAATCTCCAACATGAACAAT
5701289 AAAACATA
1 AAAACATA
5701297 CGTCAAAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.55, C:0.22, G:0.04, T:0.19
Consensus pattern (33 bp):
AAAACATAACCACAAATCTCCAACATGAACAAT
Found at i:5701323 original size:32 final size:32
Alignment explanation
Indices: 5701287--5701373 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
5701277 AACATGAACA
5701287 GTAAAACATACGTCAAAACATAACCATGAATG
1 GTAAAACATACGTCAAAACATAACCATGAATG
*
5701319 GTAAAACATACGTCTAAACATAACCATGAATG
1 GTAAAACATACGTCAAAACATAACCATGAATG
* * *
5701351 GTAAAACATGCATCAGAACATAA
1 GTAAAACATACGTCAAAACATAA
5701374 TTAAGAATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (32 bp):
GTAAAACATACGTCAAAACATAACCATGAATG
Found at i:5716890 original size:21 final size:21
Alignment explanation
Indices: 5716866--5716920 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
5716856 ATTTACGGTG
* *
5716866 TTGATGTAATTATTCATGGCA
1 TTGACGTAATGATTCATGGCA
*
5716887 TTGACGTGATGATTCATGGCA
1 TTGACGTAATGATTCATGGCA
*
5716908 TTGACGTGATGAT
1 TTGACGTAATGAT
5716921 CTATAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.38
Consensus pattern (21 bp):
TTGACGTAATGATTCATGGCA
Found at i:5716896 original size:26 final size:21
Alignment explanation
Indices: 5716877--5716920 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5716867 TGATGTAATT
5716877 ATTCATGGCATTGACGTGATG
1 ATTCATGGCATTGACGTGATG
5716898 ATTCATGGCATTGACGTGATG
1 ATTCATGGCATTGACGTGATG
5716919 AT
1 AT
5716921 CTATAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (21 bp):
ATTCATGGCATTGACGTGATG
Found at i:5717145 original size:14 final size:13
Alignment explanation
Indices: 5717119--5717153 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
5717109 TATTTTAAAT
*
5717119 AAAATAAATATAA
1 AAAATAAAAATAA
5717132 AAAACTAAAAATAA
1 AAAA-TAAAAATAA
5717146 AAAATAAA
1 AAAATAAA
5717154 TCAATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:5717650 original size:2 final size:2
Alignment explanation
Indices: 5717639--5717670 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5717629 GTCATTTCTG
5717639 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5717671 TAATTTCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5722341 original size:20 final size:21
Alignment explanation
Indices: 5722299--5722347 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
5722289 TTATTTTCAT
* *
5722299 TTTTTA-ATTTTGAAACATCA
1 TTTTTATATTTTGAAAAATAA
5722319 TTTTTATATTTT-AAAAATAA
1 TTTTTATATTTTGAAAAATAA
5722339 TTTCTTATA
1 TTT-TTATA
5722348 ATCCGAAGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTTTATATTTTGAAAAATAA
Found at i:5738939 original size:25 final size:25
Alignment explanation
Indices: 5738911--5738964 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
5738901 CAACTAAATC
* *
5738911 CTAAACCTTAAATTACAATCAAACT
1 CTAAAACTTAAATCACAATCAAACT
* *
5738936 CTAAAACTTATATCACAGTCAAACT
1 CTAAAACTTAAATCACAATCAAACT
5738961 CTAA
1 CTAA
5738965 TCGCAATAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (25 bp):
CTAAAACTTAAATCACAATCAAACT
Found at i:5745387 original size:18 final size:19
Alignment explanation
Indices: 5745366--5745405 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5745356 ATAAAATCCC
*
5745366 AAAATTT-TTAAAAATGTT
1 AAAATTTATGAAAAATGTT
*
5745384 AAAATTTATGAGAAATGTT
1 AAAATTTATGAAAAATGTT
5745403 AAA
1 AAA
5745406 TTATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
AAAATTTATGAAAAATGTT
Found at i:5745448 original size:12 final size:12
Alignment explanation
Indices: 5745417--5745451 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5745407 TATAAAAAAA
5745417 ATATAAAATT-T
1 ATATAAAATTAT
5745428 ATATAAAATTAT
1 ATATAAAATTAT
*
5745440 ATTTAAAATTAT
1 ATATAAAATTAT
5745452 TTAGATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
ATATAAAATTAT
Found at i:5749220 original size:20 final size:20
Alignment explanation
Indices: 5749192--5749240 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
5749182 TTTTTGAAAA
*
5749192 TTATAAAATAATTATTAAAT
1 TTATTAAATAATTATTAAAT
*
5749212 TTATTAAATTATTATTAAAT
1 TTATTAAATAATTATTAAAT
5749232 TATATTAAA
1 T-TATTAAA
5749241 AAAATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATAATTATTAAAT
Found at i:5749226 original size:11 final size:11
Alignment explanation
Indices: 5749191--5749240 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
5749181 ATTTTTGAAA
* *
5749191 ATTATAAAATA
1 ATTATTAAATT
5749202 ATTATTAAA-T
1 ATTATTAAATT
5749212 -TTATTAAATT
1 ATTATTAAATT
5749222 ATTATTAAATT
1 ATTATTAAATT
5749233 A-TATTAAA
1 ATTATTAAA
5749241 AAAATTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 8 0.23
10 8 0.23
11 19 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:5752537 original size:115 final size:116
Alignment explanation
Indices: 5752331--5752589 Score: 387
Period size: 115 Copynumber: 2.2 Consensus size: 116
5752321 ATCGGAAAAA
* * *
5752331 ATATCAAAATTAACTGAATCAGTTCAAATTCCTTTTGATTCCTCGTTCGTTTCTTCAGATTTCAC
1 ATATCAAAATTAACTGAATCAGCTCAAATTCCTTTTGATTCCTCGTTCATTTCTTCAGATTCCAC
* * *
5752396 GTTCATAGTTACTTACATGACCTCATTAAACTTAAA-TTCGAACTGATATT
66 ATTCATAGTCACTTACATGACATCATTAAACTTAAATTTCGAACTGATATT
*
5752446 ATATCAAAATTTACTGAATCAGCTCAAATTCCTTTTGA-TCCATCGTTCATTTCTTCAGATTCCA
1 ATATCAAAATTAACTGAATCAGCTCAAATTCCTTTTGATTCC-TCGTTCATTTCTTCAGATTCCA
* *
5752510 CATTCATAGTCACTTATATGACATCATTAAACTTAAATTTCGAACTGATGTT
65 CATTCATAGTCACTTACATGACATCATTAAACTTAAATTTCGAACTGATATT
* * *
5752562 AGATCAAAATTAACTGAACCATCTCAAA
1 ATATCAAAATTAACTGAATCAGCTCAAA
5752590 ATCTCAAAGC
Statistics
Matches: 129, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
114 3 0.02
115 89 0.69
116 37 0.29
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.37
Consensus pattern (116 bp):
ATATCAAAATTAACTGAATCAGCTCAAATTCCTTTTGATTCCTCGTTCATTTCTTCAGATTCCAC
ATTCATAGTCACTTACATGACATCATTAAACTTAAATTTCGAACTGATATT
Found at i:5767933 original size:20 final size:20
Alignment explanation
Indices: 5767910--5767961 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
5767900 AACGCGATCC
5767910 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
5767930 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
5767950 CCAAAATCGCAA
1 CCAGAATCGCAA
5767962 CGCGATTCTT
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:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:5768042 original size:20 final size:20
Alignment explanation
Indices: 5768017--5768210 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
5768007 GATTTTCCAT
* *
5768017 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
5768037 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
5768057 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
5768077 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
5768097 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
5768117 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
5768137 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
5768157 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
5768178 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
5768198 AATCGCAACGCGA
1 AATCGCAACGCGA
5768211 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:5768062 original size:40 final size:39
Alignment explanation
Indices: 5768013--5768210 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
5768003 TTGCGATTTT
* ** *
5768013 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
5768051 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
5768092 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
5768132 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
5768171 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
5768211 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:5768100 original size:60 final size:60
Alignment explanation
Indices: 5768017--5768209 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
5768007 GATTTTCCAT
* ** * *
5768017 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
5768077 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
5768137 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
5768198 AATCGCAACGCG
1 AATCGCAACGCG
5768210 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:5768630 original size:33 final size:33
Alignment explanation
Indices: 5768591--5768661 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
5768581 TTCACTTAGA
*
5768591 TTTCATTTCGCATTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCATTACGATTCTCTCGTTGCGAT
* * *
5768624 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCATTACGATTCTCTCGTTGCGAT
5768657 TTTCA
1 TTTCA
5768662 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCATTACGATTCTCTCGTTGCGAT
Found at i:5768801 original size:14 final size:14
Alignment explanation
Indices: 5768782--5768836 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
5768772 AGAATGACTG
5768782 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
5768796 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
5768815 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
5768829 TCGCAACG
1 TCGCAACG
5768837 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:5768818 original size:19 final size:19
Alignment explanation
Indices: 5768794--5768858 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
5768784 GCAACGAGAG
5768794 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
5768813 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
5768827 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
5768846 AATCGCAATGCGA
1 AATCGCAACGCGA
5768859 TTTTCATTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:5768819 original size:33 final size:33
Alignment explanation
Indices: 5768782--5768853 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
5768772 AGAATGACTG
5768782 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
5768815 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
5768848 TCGCAA
1 TCGCAA
5768854 TGCGATTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
Found at i:5768876 original size:19 final size:18
Alignment explanation
Indices: 5768854--5768965 Score: 77
Period size: 14 Copynumber: 6.7 Consensus size: 18
5768844 AAAATCGCAA
5768854 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCA-TTCGCGT
*
5768873 TGCGA--TTC--TCTCGT
1 TGCGATTTTCATTCGCGT
5768887 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCA-TTCGCGT
*
5768906 TGCGA--TTC--TCTCGT
1 TGCGATTTTCATTCGCGT
*
5768920 TGCGATTGTCATCTCGCGT
1 TGCGATTTTCAT-TCGCGT
*
5768939 TGCGA--TTC--TCTCGT
1 TGCGATTTTCATTCGCGT
5768953 TGCGATTTTCATT
1 TGCGATTTTCATT
5768966 TCAACCAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 29
0.67 0.06 0.27
Matches are distributed among these distances:
14 30 0.42
16 8 0.11
17 8 0.11
18 1 0.01
19 25 0.35
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (18 bp):
TGCGATTTTCATTCGCGT
Found at i:5768889 original size:14 final size:14
Alignment explanation
Indices: 5768870--5768959 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
5768860 TTTCATTTCG
5768870 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
5768884 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
5768903 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
5768917 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
5768934 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
5768950 CGTTGCGATT
1 CGTTGCGATT
5768960 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:5768896 original size:33 final size:33
Alignment explanation
Indices: 5768854--5768967 Score: 210
Period size: 33 Copynumber: 3.5 Consensus size: 33
5768844 AAAATCGCAA
5768854 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5768887 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
* *
5768920 TGCGATTGTCATCTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
5768953 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
5768968 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:5769524 original size:14 final size:14
Alignment explanation
Indices: 5769505--5769540 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5769495 ATTGTTTAAT
5769505 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
5769519 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
5769533 TGATTTGT
1 TGATTTGT
5769541 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5769663 original size:19 final size:19
Alignment explanation
Indices: 5769647--5769748 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
5769637 AAAAATGACT
5769647 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5769666 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
5769685 ATAGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
5769699 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
5769718 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
5769738 ATCGCAATGCG
1 ATCGCAATGCG
5769749 TTTATAATTT
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 19 0.26
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5769797 original size:33 final size:36
Alignment explanation
Indices: 5769755--5770069 Score: 300
Period size: 33 Copynumber: 9.1 Consensus size: 36
5769745 TGCGTTTATA
*
5769755 ATTTCGCATTGCGA-TT-ATCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
5769788 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
5769824 -TTTCG--TTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
5769857 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
5769892 ATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
5769925 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
5769963 ATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
5769996 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTC
*
5770032 -TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TTTCATTT-CG-ATTGCGATTTTC
5770068 AT
1 AT
5770070 GTTGGGATTT
Statistics
Matches: 250, Mismatches: 8, Indels: 44
0.83 0.03 0.15
Matches are distributed among these distances:
33 136 0.54
34 10 0.04
35 27 0.11
36 33 0.13
37 1 0.00
38 43 0.17
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (36 bp):
ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTC
Found at i:5769801 original size:19 final size:19
Alignment explanation
Indices: 5769777--5770097 Score: 369
Period size: 19 Copynumber: 18.4 Consensus size: 19
5769767 GATTATCTCG
5769777 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5769796 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5769815 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
5769829 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5769848 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
5769862 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5769881 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5769900 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
5769914 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5769933 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5769952 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5769971 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5769985 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
5770004 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5770023 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
5770037 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
5770057 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
5770071 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
5770090 TTGCGATT
1 TTGCGATT
5770098 GTATTTTCCG
Statistics
Matches: 261, Mismatches: 10, Indels: 62
0.78 0.03 0.19
Matches are distributed among these distances:
14 41 0.16
16 39 0.15
17 35 0.13
18 3 0.01
19 131 0.50
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5769817 original size:52 final size:52
Alignment explanation
Indices: 5769755--5770069 Score: 412
Period size: 52 Copynumber: 6.0 Consensus size: 52
5769745 TGCGTTTATA
*
5769755 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
5769807 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
5769857 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * * *
5769913 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
5769963 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
5770015 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
5770068 AT
1 AT
5770070 GTTGGGATTT
Statistics
Matches: 233, Mismatches: 14, Indels: 31
0.84 0.05 0.11
Matches are distributed among these distances:
47 6 0.03
49 8 0.03
50 17 0.07
51 5 0.02
52 165 0.71
53 17 0.07
54 2 0.01
55 1 0.00
56 4 0.02
57 4 0.02
58 1 0.00
59 3 0.01
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:5769834 original size:14 final size:14
Alignment explanation
Indices: 5769815--5769869 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
5769805 TCATTTCGCA
5769815 TTGCGATTCTTTCG
1 TTGCGATTCTTTCG
5769829 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
5769846 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
5769862 TTGCGATT
1 TTGCGATT
5769870 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 14 0.39
16 8 0.22
17 8 0.22
19 6 0.17
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:5771965 original size:24 final size:24
Alignment explanation
Indices: 5771931--5771977 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5771921 CTGAAACATC
5771931 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
5771955 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
5771978 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:5772688 original size:20 final size:20
Alignment explanation
Indices: 5772660--5772929 Score: 357
Period size: 20 Copynumber: 13.5 Consensus size: 20
5772650 AAATTTCAGT
* * * *
5772660 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
5772680 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
5772700 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
5772720 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
5772740 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5772760 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
5772780 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
5772800 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5772820 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5772840 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
5772860 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
5772880 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5772900 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
5772920 ATTGCGATTT
1 GTTGCGATTT
5772930 TTATTTCGCG
Statistics
Matches: 225, Mismatches: 19, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
19 5 0.02
20 216 0.96
21 4 0.02
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:5776590 original size:9 final size:9
Alignment explanation
Indices: 5776546--5776634 Score: 70
Period size: 9 Copynumber: 9.3 Consensus size: 9
5776536 CAGCTGGAAA
5776546 ACCGGTTTG
1 ACCGGTTTG
*
5776555 ACCAGTTTTG
1 ACC-GGTTTG
5776565 AACCGGTTTTG
1 -ACCGG-TTTG
*
5776576 ATCGGTTTG
1 ACCGGTTTG
*
5776585 ACCGGTTCG
1 ACCGGTTTG
* *
5776594 AACTGGTCTG
1 -ACCGGTTTG
*
5776604 ACCGGTATG
1 ACCGGTTTG
5776613 AACCGGTTTG
1 -ACCGGTTTG
*
5776623 ACCGGTATG
1 ACCGGTTTG
5776632 ACC
1 ACC
5776635 CGACCCGACC
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
9 32 0.51
10 24 0.38
11 7 0.11
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:5776605 original size:19 final size:19
Alignment explanation
Indices: 5776578--5776632 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
5776568 CGGTTTTGAT
*
5776578 CGGTTTGACCGGT-TCGAAC
1 CGGTCTGACCGGTAT-GAAC
*
5776597 TGGTCTGACCGGTATGAAC
1 CGGTCTGACCGGTATGAAC
*
5776616 CGGTTTGACCGGTATGA
1 CGGTCTGACCGGTATGA
5776633 CCCGACCCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 30 0.97
20 1 0.03
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.27
Consensus pattern (19 bp):
CGGTCTGACCGGTATGAAC
Found at i:5776648 original size:14 final size:14
Alignment explanation
Indices: 5776631--5776659 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5776621 TGACCGGTAT
5776631 GACCCGACCCGACC
1 GACCCGACCCGACC
5776645 GACCCGACCCGACC
1 GACCCGACCCGACC
5776659 G
1 G
5776660 TTGACCCGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.55, G:0.24, T:0.00
Consensus pattern (14 bp):
GACCCGACCCGACC
Found at i:5776667 original size:12 final size:12
Alignment explanation
Indices: 5776650--5776676 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5776640 CGACCGACCC
5776650 GACCCGACCGTT
1 GACCCGACCGTT
5776662 GACCCGACCGTT
1 GACCCGACCGTT
5776674 GAC
1 GAC
5776677 TGTTGACCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.41, G:0.26, T:0.15
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:5778689 original size:3 final size:3
Alignment explanation
Indices: 5778681--5778711 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5778671 AAAGTCTAAT
5778681 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5778712 TAAATTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5784853 original size:20 final size:20
Alignment explanation
Indices: 5784830--5784870 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5784820 TTTTCGAGCT
5784830 GCTCACGAACTTCTCGAGTC
1 GCTCACGAACTTCTCGAGTC
*
5784850 GCTCACGAGCTTCTCGAGTC
1 GCTCACGAACTTCTCGAGTC
5784870 G
1 G
5784871 AATAACAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.34, G:0.24, T:0.24
Consensus pattern (20 bp):
GCTCACGAACTTCTCGAGTC
Found at i:5785764 original size:23 final size:23
Alignment explanation
Indices: 5785730--5785779 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5785720 CCAAACGGGG
*
5785730 GAATGTGAATTTTATT-CTCATGA
1 GAATGTGAATTTCATTCCT-ATGA
*
5785753 GAATGTGGATTTCATTCCTATGA
1 GAATGTGAATTTCATTCCTATGA
5785776 GAAT
1 GAAT
5785780 CTCACATTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (23 bp):
GAATGTGAATTTCATTCCTATGA
Found at i:5794303 original size:74 final size:74
Alignment explanation
Indices: 5794182--5794321 Score: 280
Period size: 74 Copynumber: 1.9 Consensus size: 74
5794172 TACATCTTGT
5794182 AGATGTAATTGATCGAATACAAGATCTCTAGAAAGAACAATATTCCCTTTAACTATTGAGGTCGT
1 AGATGTAATTGATCGAATACAAGATCTCTAGAAAGAACAATATTCCCTTTAACTATTGAGGTCGT
5794247 TCGAATCCA
66 TCGAATCCA
5794256 AGATGTAATTGATCGAATACAAGATCTCTAGAAAGAACAATATTCCCTTTAACTATTGAGGTCGT
1 AGATGTAATTGATCGAATACAAGATCTCTAGAAAGAACAATATTCCCTTTAACTATTGAGGTCGT
5794321 T
66 T
5794322 TGATGGATTC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (74 bp):
AGATGTAATTGATCGAATACAAGATCTCTAGAAAGAACAATATTCCCTTTAACTATTGAGGTCGT
TCGAATCCA
Found at i:5796449 original size:2 final size:2
Alignment explanation
Indices: 5796442--5796487 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
5796432 GACCCAATAA
5796442 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5796484 AT AT
1 AT AT
5796488 TACTTTCATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5800642 original size:18 final size:18
Alignment explanation
Indices: 5800619--5800664 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
5800609 ACCAATCACA
5800619 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
5800637 ACCCGACCCAACCCGTTT
1 ACCCGACCCGACCCGTTG
*
5800655 ACCTGACCCG
1 ACCCGACCCG
5800665 TTGGCCCGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.50, G:0.17, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:5800676 original size:18 final size:18
Alignment explanation
Indices: 5800655--5800690 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5800645 CAACCCGTTT
*
5800655 ACCTGACCCGTTGGCCCG
1 ACCTGACCCGTTGACCCG
5800673 ACCTGACCCGTTGACCCG
1 ACCTGACCCGTTGACCCG
5800691 TTGACCGTCG
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:0.14, C:0.44, G:0.25, T:0.17
Consensus pattern (18 bp):
ACCTGACCCGTTGACCCG
Found at i:5801965 original size:18 final size:18
Alignment explanation
Indices: 5801939--5801974 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5801929 TCGAAAGGAC
*
5801939 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
5801957 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
5801975 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:5805770 original size:31 final size:31
Alignment explanation
Indices: 5805735--5805793 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5805725 CAACCCGACC
*
5805735 CGACCCGACCCGTTTAC-CTGACCCGTTGGCT
1 CGACCCGACCCGTTGACTC-GACCCGTTGGCT
5805766 CGACCCGACCCGTTGACTCGACCCGTTG
1 CGACCCGACCCGTTGACTCGACCCGTTG
5805794 ACCATTGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.14, C:0.42, G:0.24, T:0.20
Consensus pattern (31 bp):
CGACCCGACCCGTTGACTCGACCCGTTGGCT
Found at i:5805775 original size:18 final size:18
Alignment explanation
Indices: 5805754--5805790 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5805744 CCGTTTACCT
*
5805754 GACCCGTTGGCTCGACCC
1 GACCCGTTGACTCGACCC
5805772 GACCCGTTGACTCGACCC
1 GACCCGTTGACTCGACCC
5805790 G
1 G
5805791 TTGACCATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.14, C:0.43, G:0.27, T:0.16
Consensus pattern (18 bp):
GACCCGTTGACTCGACCC
Found at i:5805805 original size:15 final size:14
Alignment explanation
Indices: 5805767--5805811 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
5805757 CCGTTGGCTC
5805767 GACC-CGACCCGTT
1 GACCTCGACCCGTT
5805780 GA-CTCGACCCGTT
1 GACCTCGACCCGTT
*
5805793 GACCATTGACCCGTT
1 GACC-TCGACCCGTT
5805808 GACC
1 GACC
5805812 GTCGTTGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 1 0.04
13 13 0.46
14 1 0.04
15 13 0.46
ACGTcount: A:0.18, C:0.40, G:0.22, T:0.20
Consensus pattern (14 bp):
GACCTCGACCCGTT
Found at i:5807078 original size:18 final size:18
Alignment explanation
Indices: 5807052--5807086 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5807042 TCGAAAGGAC
*
5807052 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
5807070 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
5807087 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:5809778 original size:31 final size:30
Alignment explanation
Indices: 5809743--5809843 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 30
5809733 GTTTGAGTAC
*
5809743 TTTGTAGAAGTTTGATAAAATTAATGATTAT
1 TTTGTA-AAATTTGATAAAATTAATGATTAT
* * *
5809774 TTTGTAAAATTTTAATAAAATTTGATGACTAT
1 TTTGTAAAA-TTTGATAAAA-TTAATGATTAT
* * * *
5809806 TTTATAACAATTCGATAAATTTAATTATTAT
1 TTTGTAA-AATTTGATAAAATTAATGATTAT
5809837 TTTGTAA
1 TTTGTAA
5809844 TTTTCGAAAG
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
30 2 0.04
31 29 0.53
32 22 0.40
33 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.48
Consensus pattern (30 bp):
TTTGTAAAATTTGATAAAATTAATGATTAT
Found at i:5811452 original size:29 final size:30
Alignment explanation
Indices: 5811410--5811478 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
5811400 GGGATCTTTT
5811410 TGCTCCAAAATGAAACGTT-GGGGCCAAAA
1 TGCTCCAAAATGAAACGTTGGGGGCCAAAA
5811439 TGCTCCAAAATGAAACGTTGGGGGCCAAAA
1 TGCTCCAAAATGAAACGTTGGGGGCCAAAA
5811469 TGCTCCAAAA
1 TGCTCCAAAA
5811479 AAAGAATATG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
29 19 0.49
30 20 0.51
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (30 bp):
TGCTCCAAAATGAAACGTTGGGGGCCAAAA
Found at i:5822962 original size:2 final size:2
Alignment explanation
Indices: 5822955--5822980 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5822945 AGACACATAC
5822955 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5822981 TAACAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5823320 original size:15 final size:16
Alignment explanation
Indices: 5823300--5823340 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
5823290 GTTTACTTCA
*
5823300 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
5823315 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
5823331 GAATGATTCA
1 GAATGATTCA
5823341 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:5831488 original size:19 final size:19
Alignment explanation
Indices: 5831404--5831489 Score: 59
Period size: 19 Copynumber: 4.4 Consensus size: 19
5831394 AATTAAAGAC
*
5831404 TAATTTAAAATAAGAATTA
1 TAATTTAAAATAAAAATTA
* *
5831423 TGATTTAAGGAT-AAAATTA
1 TAATTTAA-AATAAAAATTA
***
5831442 TAATATTTAAAAGTTTGGAATT-
1 T-A-ATTTAAAA--TAAAAATTA
5831464 TAATTTAAAATAAAAATTA
1 TAATTTAAAATAAAAATTA
5831483 TAATTTA
1 TAATTTA
5831490 TAGACATGTA
Statistics
Matches: 50, Mismatches: 10, Indels: 14
0.68 0.14 0.19
Matches are distributed among these distances:
18 5 0.10
19 21 0.42
20 11 0.22
21 7 0.14
22 2 0.04
23 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (19 bp):
TAATTTAAAATAAAAATTA
Found at i:5851496 original size:13 final size:13
Alignment explanation
Indices: 5851478--5851503 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5851468 AAATAAATAA
5851478 AAATAAAAAAATC
1 AAATAAAAAAATC
5851491 AAATAAAAAAATC
1 AAATAAAAAAATC
5851504 GATACTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATAAAAAAATC
Found at i:5852800 original size:34 final size:37
Alignment explanation
Indices: 5852751--5852836 Score: 133
Period size: 36 Copynumber: 2.4 Consensus size: 37
5852741 TTTTCACAAC
5852751 TATATATTATATGTTTTCAAAA-T-TATTTTAAAAAT
1 TATATATTATATGTTTTCAAAATTGTATTTTAAAAAT
* *
5852786 TATATACTA-ATGTTTTCAAAATTGTTTTTTAAAAAT
1 TATATATTATATGTTTTCAAAATTGTATTTTAAAAAT
5852822 TATATATTATATGTT
1 TATATATTATATGTT
5852837 ATTTTTGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
34 12 0.27
35 9 0.20
36 19 0.42
37 5 0.11
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (37 bp):
TATATATTATATGTTTTCAAAATTGTATTTTAAAAAT
Found at i:5853279 original size:20 final size:18
Alignment explanation
Indices: 5853238--5853282 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
5853228 GATTTTATAT
5853238 TAATTT-TAAAAATATTA
1 TAATTTATAAAAATATTA
*
5853255 AAATTTATAAAATACTATTA
1 TAATTTATAAAA-A-TATTA
5853275 TAATTTAT
1 TAATTTAT
5853283 GAATATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 5 0.22
19 1 0.04
20 12 0.52
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATTTATAAAAATATTA
Found at i:5853305 original size:27 final size:27
Alignment explanation
Indices: 5853248--5853326 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
5853238 TAATTTTAAA
* * *
5853248 AATATTA-AAATTTATAAAATACTATTAT
1 AATATTATAAATATAAAAAATA-TAAT-T
*
5853276 AAT-TTATGAATATTAAAAAATATAATT
1 AATATTATAAATA-TAAAAAATATAATT
5853303 AATATTATAAATATAAAAAATATA
1 AATATTATAAATATAAAAAATATA
5853327 TCAATAACAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 18 0.42
28 17 0.40
29 8 0.19
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (27 bp):
AATATTATAAATATAAAAAATATAATT
Found at i:5853327 original size:29 final size:29
Alignment explanation
Indices: 5853248--5853345 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 29
5853238 TAATTTTAAA
* * *
5853248 AATATTA-AAATTTATAAAATACTATTA-T
1 AATATTATAAATATAAAAAATA-TATAATT
*
5853276 AAT-TTATGAATATTAAAAAA--TATAATT
1 AATATTATAAATA-TAAAAAATATATAATT
*
5853303 AATATTATAAATATAAAAAATATATCAATAAC
1 AATATTATAAATATAAAAAATATAT-AAT--T
5853335 AATATTATAAA
1 AATATTATAAA
5853346 CAAAAATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
26 4 0.07
27 14 0.25
28 14 0.25
29 9 0.16
30 3 0.05
32 11 0.20
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (29 bp):
AATATTATAAATATAAAAAATATATAATT
Found at i:5853933 original size:31 final size:31
Alignment explanation
Indices: 5853832--5853934 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 31
5853822 AAAATTTAAT
* * * *
5853832 GGTCAAATTGATATTTCATATGAAGTTTAGA
1 GGTCAAATTAATATTTCATCTAAAGTTCAGA
*
5853863 GGTCAAAATT-ATATTTCATCTAAA-TATCA-T
1 GGTC-AAATTAATATTTCATCTAAAGT-TCAGA
* * *
5853893 GTTCAAATTAATATTTTATCTAAAGTTCAGG
1 GGTCAAATTAATATTTCATCTAAAGTTCAGA
5853924 GGTCAAATTAA
1 GGTCAAATTAA
5853935 AAACCAACAT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
29 5 0.08
30 20 0.34
31 29 0.49
32 5 0.08
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (31 bp):
GGTCAAATTAATATTTCATCTAAAGTTCAGA
Found at i:5855227 original size:17 final size:19
Alignment explanation
Indices: 5855192--5855230 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5855182 TTACTTTTTA
*
5855192 TTTTCTTATATTTTAATTT
1 TTTTCTTATATTATAATTT
5855211 TTTTCTTATA-TAT-ATTT
1 TTTTCTTATATTATAATTT
5855228 TTT
1 TTT
5855231 CTCCAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 10 0.53
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTCTTATATTATAATTT
Found at i:5855876 original size:23 final size:23
Alignment explanation
Indices: 5855818--5855880 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
5855808 TTGAACTATA
* *
5855818 AATGAACGATAAACGAATACGTT
1 AATGAACAATAAACTAATACGTT
* * *
5855841 CATGAACATTAAACTAATATGTT
1 AATGAACAATAAACTAATACGTT
*
5855864 AATGAATAATAAA-TAAT
1 AATGAACAATAAACTAAT
5855881 CTAACACAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 4 0.12
23 28 0.88
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.29
Consensus pattern (23 bp):
AATGAACAATAAACTAATACGTT
Found at i:5859617 original size:58 final size:58
Alignment explanation
Indices: 5859527--5859641 Score: 221
Period size: 58 Copynumber: 2.0 Consensus size: 58
5859517 CGATTCATAT
*
5859527 TTAATTTCATTACTTAAGCTTTTAGGACTTGAATGTCTATGCATGTAAAGTTCTCCCC
1 TTAATTTCATTACTTAAGCTTTTAGCACTTGAATGTCTATGCATGTAAAGTTCTCCCC
5859585 TTAATTTCATTACTTAAGCTTTTAGCACTTGAATGTCTATGCATGTAAAGTTCTCCC
1 TTAATTTCATTACTTAAGCTTTTAGCACTTGAATGTCTATGCATGTAAAGTTCTCCC
5859642 TTTATGTACT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (58 bp):
TTAATTTCATTACTTAAGCTTTTAGCACTTGAATGTCTATGCATGTAAAGTTCTCCCC
Found at i:5865744 original size:29 final size:29
Alignment explanation
Indices: 5865689--5865754 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
5865679 CATTTTACAC
* * *
5865689 AAATAGCACCCTTTTTAAAATATTTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
* *
5865718 AAATAGCACCCATTTCGAATTAATTACCA
1 AAATAGCACCCATTTCAAAATAATTACCA
*
5865747 TAATAGCA
1 AAATAGCA
5865755 GAAAACCGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAAATAATTACCA
Found at i:5865823 original size:17 final size:16
Alignment explanation
Indices: 5865801--5865842 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
5865791 CGGTCAACTA
*
5865801 TCGGGTCGGTCAACGGG
1 TCGGGTCGGTAAAC-GG
5865818 TCGGGTCGGGTAAACGG
1 TCGGGTC-GGTAAACGG
5865835 TCGGGTCG
1 TCGGGTCG
5865843 TGACCGGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 16 0.70
18 6 0.26
ACGTcount: A:0.12, C:0.21, G:0.48, T:0.19
Consensus pattern (16 bp):
TCGGGTCGGTAAACGG
Found at i:5873098 original size:29 final size:29
Alignment explanation
Indices: 5873059--5873132 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
5873049 TTTAAAATAT
* * **
5873059 TTACCAAAATAGCACCCATTTCGAATTAA
1 TTACCAGAATAGCACCAAAATCGAATTAA
* * *
5873088 TTATCAGAATAGCAGCAAAATCGAATTAT
1 TTACCAGAATAGCACCAAAATCGAATTAA
5873117 TTACCAGAATAGCACC
1 TTACCAGAATAGCACC
5873133 GGTCAACGGT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.26
Consensus pattern (29 bp):
TTACCAGAATAGCACCAAAATCGAATTAA
Found at i:5873173 original size:13 final size:13
Alignment explanation
Indices: 5873152--5873186 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
5873142 TCAACGATCA
5873152 GGTCGGGTCAACG
1 GGTCGGGTCAACG
*
5873165 GGTCAGGTCAACG
1 GGTCGGGTCAACG
5873178 GGTCGGGTC
1 GGTCGGGTC
5873187 GGGTAAAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (13 bp):
GGTCGGGTCAACG
Found at i:5873205 original size:18 final size:18
Alignment explanation
Indices: 5873163--5873205 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5873153 GTCGGGTCAA
* *
5873163 CGGGTCAGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
*
5873181 CGGGTCGGGTAAAGGGGT
1 CGGGTCGGGTAAACGGGT
5873199 CGGGTCG
1 CGGGTCG
5873206 TGACTGGTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.51, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:5883321 original size:63 final size:63
Alignment explanation
Indices: 5883222--5883347 Score: 198
Period size: 63 Copynumber: 2.0 Consensus size: 63
5883212 TTCCGGTGCA
* * *
5883222 CAGATTCTCAGAAGCTTCTGACAGGATTTTCTTTATTTAAGGTGATATGTTTTGCATATAACT
1 CAGATTCTCAGAAGCTTCTGACAAGATTTTCTTTATTTAAGGCGATATGTTCTGCATATAACT
* * *
5883285 CAGATTCTTAGAAGCTTCTGATAAGATTTTCTTTATTTAAGGCGATATGTTCTGCGTATAACT
1 CAGATTCTCAGAAGCTTCTGACAAGATTTTCTTTATTTAAGGCGATATGTTCTGCATATAACT
5883348 TATAATAGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (63 bp):
CAGATTCTCAGAAGCTTCTGACAAGATTTTCTTTATTTAAGGCGATATGTTCTGCATATAACT
Found at i:5899178 original size:28 final size:29
Alignment explanation
Indices: 5899146--5899214 Score: 104
Period size: 28 Copynumber: 2.3 Consensus size: 29
5899136 CAACTATCAT
5899146 TAATTTTAATAAAATTATCGAGAGT-CAA
1 TAATTTTAATAAAATTATCGAGAGTACAA
*
5899174 TAATTTTAATAAAATTATCGAGGGTCGACAA
1 TAATTTTAATAAAATTATCGAGAGT--ACAA
5899205 TAATTTTAAT
1 TAATTTTAAT
5899215 TCACTCGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 24 0.65
31 13 0.35
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (29 bp):
TAATTTTAATAAAATTATCGAGAGTACAA
Found at i:5899839 original size:22 final size:22
Alignment explanation
Indices: 5899800--5899841 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5899790 TTAAGACAAT
* **
5899800 TTTAATTTAAAATGTTATATTA
1 TTTAATCTAAAAAATTATATTA
5899822 TTTAATCTAAAAAATTATAT
1 TTTAATCTAAAAAATTATAT
5899842 AAATTTATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAATCTAAAAAATTATATTA
Found at i:5909069 original size:2 final size:2
Alignment explanation
Indices: 5909064--5909089 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5909054 TCCTATACCA
5909064 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5909090 GATCATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5912363 original size:42 final size:42
Alignment explanation
Indices: 5912316--5912441 Score: 234
Period size: 42 Copynumber: 3.0 Consensus size: 42
5912306 AAAACAATGA
5912316 GTAACTATTTACATGATGACGTTACTCTTTATCGATAGAAAG
1 GTAACTATTTACATGATGACGTTACTCTTTATCGATAGAAAG
5912358 GTAACTATTTACATGATGACGTTACTCTTTATCGATAGAAAG
1 GTAACTATTTACATGATGACGTTACTCTTTATCGATAGAAAG
* *
5912400 GTAACTATTTACATGATGACGTTACTTTTTATCGATCGAAAG
1 GTAACTATTTACATGATGACGTTACTCTTTATCGATAGAAAG
5912442 ATAAAATGTG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (42 bp):
GTAACTATTTACATGATGACGTTACTCTTTATCGATAGAAAG
Found at i:5914609 original size:702 final size:696
Alignment explanation
Indices: 5913290--5914912 Score: 2181
Period size: 702 Copynumber: 2.3 Consensus size: 696
5913280 ATGTTACTCT
* ** *
5913290 TTATCGATGAAAAGGTAAATTGTGTGATACCTATACATTTTTTATATAAAAAATATGGGTAACTA
1 TTATCGATGAAAAGGTAAATTGTGTGATACCTATACATTTTATCCATAAAAAATATGAGTAACTA
* * *
5913355 TTTACATGATGAGGGTTACTCTATATCGAGGTAAAATAAAATTATCTTGATACCTTAGCTACCCA
66 TTTACATGATGA-GGTTACTCTCTATCGAGGTAAAATAAAATTATCTTGATACCTTGGCTACACA
** *
5913420 TTTTAGATATAGAATATTGAGTCTTTAGAAGAT-GTTTTTCAGTATTATAGGCTCCTTAATTTAA
130 TTTTAGATATAGAATATTGAGTCTTTAGAAGATGGTTTTT-AGTATTAGGGGCTCCTGAATTTAA
* * * * *
5913484 TAAGAATATTTATCCGATTTTTGAAGCACTTTACTATAGCTTGTCTTTGCGCCTAAGGACTTTTG
194 AAAGAATATTTTTCTGAGTTTTGAAGCACTTTACTATAGCTTGTCTTTGCACCTAAGGACTTTTG
*
5913549 CTTATATTACTAATATTTGTTACTTAATGTAAGTTAAAAAAACATTTACAAATTCAGTGCACATG
259 CTTATATTACTAATATTTGCTACTTAATGTAAGTTAAAAAAACATTTACAAATTCAGTGCACATG
*
5913614 ATTTACATGATATGACTTATGTTTTATCTGCAAACATAATATGATGTGTAATTATTTACATGATG
324 ATTTACATGAAATGACTTATGTTTTATCTGCAAACATAATATGATGTGTAATTATTTACATGATG
* *
5913679 AGGGTTACTCAAAGTTGAGGTAAATTATCATATAATGTTACTTTCTATTCTAGATATAGATTCAT
389 AGGGTTACTCAAAGTTAAGGTAAATTATCATATAATGTTACTTTCTATTCTAGA-ACAGATTCAT
* ** * *
5913744 GTCGAGTCTTTGGAATATGTTTTGAACATTAGGGGCTCTTGAAGTTGAGGAGTATGTTATTATGA
453 GTCGAGTCTTTGGAATATGTTTTGAACATCAAAGGCTCCTGAAGTTGAGAAGTATGTTATTATGA
* *
5913809 TTTTTGAAGTATTTTGCTACATCTTATCTCCATTCATAATAAGATTTTTCTTTTATTACTAAATC
518 TTTTTGAAGTATTTTACTACATCTTATCTCCATTCATAATAAGATTTTTCTTCTATTACTAAATC
* * * * * *
5913874 TTGACAAGTTGCTTAGAATCAAATAATTTTTGTAAGTTCAGCTTACATGCTTTCTATGATATTTA
583 CTGACAAATTGCTAAGAATCAAATAACTTTTGTAACTTCAGCTTACATGCTTTCTATGATACTTA
*
5913939 TACATTTTCTCTCTAAAAACAATGAGTAACTATTTAC-ATGACG-A-CG
648 TACACTTTCTCTCTAAAAACAATGAGTAACTATTTACAATGACGTACCG
* * *
5913985 TT-T-GATGGAAAGGTAAATTGTGTGATACCTATATATTTTATCCCTAAAAGTAATATGAGTAAC
1 TTATCGATGAAAAGGTAAATTGTGTGATACCTATACATTTTATCCATAAAA--AATATGAGTAAC
* *
5914048 TATTTACATGATGAGAGTTACTTTCTATCGAGGTAAAATAAAATTATCTTGATTCCTTGGCTACA
64 TATTTACATGATGAG-GTTACTCTCTATCGAGGTAAAATAAAATTATCTTGATACCTTGGCTACA
* *
5914113 CATTTTAGATATA-AAAATTTGAGTGTTTAGAAGATGGTTTTTAGTATTAGGGGCTCCTGAATTT
128 CATTTTAGATATAGAATA-TTGAGTCTTTAGAAGATGGTTTTTAGTATTAGGGGCTCCTGAATTT
* * * ** * * *
5914177 GAGAAGAATATTTTTTTTTGAGTTTTGAAGCACTTTGTTATATCTTGTCTTTGTA-CTCGAGGAC
192 AAAAAGAATA--TTTTTCTGAGTTTTGAAGCACTTTACTATAGCTTGTCTTTGCACCT-AAGGAC
* *
5914241 TTTTGCTTATATTACTAATGTTTGCTACTTAATGTAAGTTAAAAAAAAAACTTTTACAAATTCAG
254 TTTTGCTTATATTACTAATATTTGCTACTTAATGTAAGTT---AAAAAAACATTTACAAATTCAG
* ** * *
5914306 TGCCCATTTTTTTGCATGAAATGACTTATGTTTTATCTGCAAACATAATTTGATGTGTAATTATT
316 TGCACA-TGATTTACATGAAATGACTTATGTTTTATCTGCAAACATAATATGATGTGTAATTATT
* *
5914371 TACATGATGAGGGTTACTCAAAGTTAAGGTAAATTATATATATAATGTTACTTTCTATTTTAG-A
380 TACATGATGAGGGTTACTCAAAGTTAAGGTAAATTAT-CATATAATGTTACTTTCTATTCTAGAA
* *
5914435 CAGATTCATGTCTAGTCTTTGGAATATGGTTTTTTAACATCAAAGGCTCCTGAAGTTGAGAAGTA
444 CAGATTCATGTCGAGTCTTTGGAATAT-G-TTTTGAACATCAAAGGCTCCTGAAGTTGAGAAGTA
* * *
5914500 TGTTATTATGATTTTTGAAGTATTTTACTACATCTTGTCTCCATTCATAATGAGCGTTTTT-TTC
507 TGTTATTATGATTTTTGAAGTATTTTACTACATCTTATCTCCATTCATAATAAG-ATTTTTCTTC
* *
5914564 TATTAGTAAATCCTGACAAATTGCTAAGAATCAAATAACTTTTGTAACTTCAGCTTGCATGCTTT
571 TATTACTAAATCCTGACAAATTGCTAAGAATCAAATAACTTTTGTAACTTCAGCTTACATGCTTT
* * * *
5914629 CTATTATACTTATACACTTTCTCTCTAAAAACATTGAGTAACTATTTACATGATGATGTTACTCT
636 CTATGATACTTATACACTTTCTCTCTAAAAACAATGAGTAACTATTTACA--ATGACG-TAC-CG
* * * * * * *
5914694 TTATCGATGAAAATGTTAACTGTTTGATACCTCTGCATTTTATCCATAGAAACAATATAAGTAAC
1 TTATCGATGAAAAGGTAAATTGTGTGATACCTATACATTTTATCCATA-AAA-AATATGAGTAAC
* * *
5914759 TATTTACATGATGAGGATTACTCTCTGTC-AAG-AAAAAAAAATTATCTTGATACCTTGGCTACA
64 TATTTACATGATGAGG-TTACTCTCTATCGAGGTAAAATAAAATTATCTTGATACCTTGGCTACA
* * * * * *
5914822 CATTTTAGATATTGAATGTTTAGTCTTTAGAAAATGGTTTTCAGTATTAGGGACTCCTGAATTTA
128 CATTTTAGATATAGAATATTGAGTCTTTAGAAGATGGTTTTTAGTATTAGGGGCTCCTGAATTTA
5914887 AAAAGAATATTTTTCTGAGTTTTGAA
193 AAAAGAATATTTTTCTGAGTTTTGAA
5914913 ACATTTCAGC
Statistics
Matches: 806, Mismatches: 94, Indels: 44
0.85 0.10 0.05
Matches are distributed among these distances:
693 40 0.05
694 5 0.01
695 127 0.16
696 8 0.01
697 77 0.10
700 52 0.06
701 90 0.11
702 208 0.26
703 5 0.01
705 5 0.01
707 17 0.02
709 93 0.12
710 6 0.01
711 70 0.09
712 3 0.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (696 bp):
TTATCGATGAAAAGGTAAATTGTGTGATACCTATACATTTTATCCATAAAAAATATGAGTAACTA
TTTACATGATGAGGTTACTCTCTATCGAGGTAAAATAAAATTATCTTGATACCTTGGCTACACAT
TTTAGATATAGAATATTGAGTCTTTAGAAGATGGTTTTTAGTATTAGGGGCTCCTGAATTTAAAA
AGAATATTTTTCTGAGTTTTGAAGCACTTTACTATAGCTTGTCTTTGCACCTAAGGACTTTTGCT
TATATTACTAATATTTGCTACTTAATGTAAGTTAAAAAAACATTTACAAATTCAGTGCACATGAT
TTACATGAAATGACTTATGTTTTATCTGCAAACATAATATGATGTGTAATTATTTACATGATGAG
GGTTACTCAAAGTTAAGGTAAATTATCATATAATGTTACTTTCTATTCTAGAACAGATTCATGTC
GAGTCTTTGGAATATGTTTTGAACATCAAAGGCTCCTGAAGTTGAGAAGTATGTTATTATGATTT
TTGAAGTATTTTACTACATCTTATCTCCATTCATAATAAGATTTTTCTTCTATTACTAAATCCTG
ACAAATTGCTAAGAATCAAATAACTTTTGTAACTTCAGCTTACATGCTTTCTATGATACTTATAC
ACTTTCTCTCTAAAAACAATGAGTAACTATTTACAATGACGTACCG
Found at i:5916200 original size:75 final size:74
Alignment explanation
Indices: 5916057--5916205 Score: 244
Period size: 75 Copynumber: 2.0 Consensus size: 74
5916047 TAAAGGTAAA
* *
5916057 TTATCTAGATAAACAACTCATTTTTAGAAATAGTTCATGTTGAGTCTCTTGAACACATTCTTCAG
1 TTATCTAGATAAACAACTCATTTTTAGAAATAGTTCATGTTGAGTCTCTGGAACACAGTCTTCAG
5916122 TATTAGGGG
66 TATTAGGGG
* * *
5916131 TTATCTAGATAAACAACTCCTTTTTAGATATAGATTCATGTTGAGTCTCTGGAGCACAGTCTTCA
1 TTATCTAGATAAACAACTCATTTTTAGAAATAG-TTCATGTTGAGTCTCTGGAACACAGTCTTCA
5916196 GTATTAGGGG
65 GTATTAGGGG
5916206 CCTTGAAATT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
74 31 0.45
75 38 0.55
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (74 bp):
TTATCTAGATAAACAACTCATTTTTAGAAATAGTTCATGTTGAGTCTCTGGAACACAGTCTTCAG
TATTAGGGG
Found at i:5920175 original size:705 final size:710
Alignment explanation
Indices: 5917791--5921575 Score: 5948
Period size: 705 Copynumber: 5.4 Consensus size: 710
5917781 TTTATCACAT
* * * *
5917791 AATGGAAACCTATTAAATTATTTAGAGGGGTACTAATATTCGTCATCTACTTTTTGCAGATGACT
1 AATGGAAACCTATTAAATTGTCTAGAGGGGTACTAATATTAGTCATCTATTTTTTGCAGATGACT
* * * *
5917856 TACTTTTATTCTTCGAAGCTACAAGGGATCAAATTATTGAAGTAAAGAATTGCTTAAAGGCCTTC
66 TACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAAGAATTGCTTAAAGACTTTC
* ** * *
5917921 ATCAAAGCTTCAAGGCTCGAAATAAATCTTTAAAAGTTAAAAATGTTTATATCAACAAACGT-AA
131 AGCAAAGCTTCGGGGCTTGAAATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAACGTAAA
5917985 CAACGAGAATGCTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTTGGGGGTGT
196 CAACGAGAATGCTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTTGGGGGTGT
* *
5918050 ATCTTGGAGTTCTGATTTTGCATAAGAGGAGAATCACTTGCACTTATGCGCCTCATTGTAGAAAA
261 ATCTTGGAGTTCCGATTCTGCATAAGAGGAGAATCACTTGCACTTATGCGCCTC-TTGTAGAAAA
*
5918115 AGTTGTGAGAAAAATGGTTGGGTGGAAGGGTAAGCCTTATCAAAACAATTTATTACCAGGAAGAA
325 AGTTGTGAGAAAAATGGTTGGGTGGAAGGGTAAGCCTTATCAAAACAATTTCTTACCAGGAAGAA
*
5918180 ATACCTCTGATAATATTTTTGTTGTGTAGGAAGCAGTCTACACATTTTCAAACTTAC----AAGG
390 ATACCTCTGATAATATTTTCGTTGTGTAGGAAGCAGTCTACACATTTTCAAACTTACAAGGAAGG
*
5918241 AAAGGTGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTACTAAAGGAGACT
455 AAAGGTGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTAAAGGAGACT
* * *
5918306 TTAATATATTTCAATTTGCCCGAGAAGATGATTGTCTAATTATGTTCCGCATCAATAACAGTACC
520 TTAATAGATTTCAATTTGCCCGAGAAGATGATTGTCTAATTATGTTCTGCATCAAAAACAGTACC
5918371 ATTGAACCATTGTGGAACAGAGACAGAACAAAGAGCTTCAAACCGGAACAAAGACTCATTCAGGG
585 ATTGAACCATTGTGGAACAGAGACAGAACAAAGAGCTTCAAACCGGAACAAAGACTCATTCAGGG
** **
5918436 AGATCTATTCTCATTATGGAACGTTTATCGTATATATTATTAGAAAAAATAGAAAGGGAAC
650 AGATCCGTTCTCATTATGGAACGTTTATCACATATATTATTAGAAAAAATAGAAAGGGAAC
5918497 AATGGAAACCTATTAAATTGTCTAGAGGGGTACTAATATTAGTCATCTATTTTTTGCAGATGAC-
1 AATGGAAACCTATTAAATTGTCTAGAGGGGTACTAATATTAGTCATCTATTTTTTGCAGATGACT
* * * *
5918561 AACTTTTATTCTTCGAAGCTGCAAGGGGTAAAATCATTGAAGTGAAGAATTGCTTAAAGACTTTC
66 TACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAAGAATTGCTTAAAGACTTTC
* *
5918626 AACAAAGCTTTGGGGCTTGAAATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAACGTAAA
131 AGCAAAGCTTCGGGGCTTGAAATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAACGTAAA
* * *
5918691 CAACGAGATTGCTGATCAGCTGAGTTAACTCAGTGGAATTATAAGAACTGGAAATTTGGGGGTGT
196 CAACGAGAATGCTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTTGGGGGTGT
5918756 ATCTTGGAGTTCCGATTCTGCATAAGAGGAGAATCACTTGCACTTATGCGCCTCTTGTAGAAAAA
261 ATCTTGGAGTTCCGATTCTGCATAAGAGGAGAATCACTTGCACTTATGCGCCTCTTGTAGAAAAA
* * *
5918821 GTTATGAGAAAAATGGCTGGGTGGAAGGGTAAGCCTTATCAAAACAATTTCTTACCAAGAAGAAA
326 GTTGTGAGAAAAATGGTTGGGTGGAAGGGTAAGCCTTATCAAAACAATTTCTTACCAGGAAGAAA
* *
5918886 TACCTCTGATAATATTTTCATTGTGTAGGAAGCAGTCTACACATTTTCAAACTTACTAGGAAGGA
391 TACCTCTGATAATATTTTCGTTGTGTAGGAAGCAGTCTACACATTTTCAAACTTACAAGGAAGGA
*
5918951 AAGGTGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTAAATGAGACTT
456 AAGGTGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTAAAGGAGACTT
* * *
5919016 TAATTAG-TTTCAATTTGCCCAAGAAGATGATTGTCTAATCATGTTTTGCATCAAAAACAGTACC
521 TAA-TAGATTTCAATTTGCCCGAGAAGATGATTGTCTAATTATGTTCTGCATCAAAAACAGTACC
* * *
5919080 ATT-AACCATTGTGGTACGGAGACAGAACAAAGAGCTTCAAACCGGAACAAAGACTCATTTAGGG
585 ATTGAACCATTGTGGAACAGAGACAGAACAAAGAGCTTCAAACCGGAACAAAGACTCATTCAGGG
*
5919144 AGATCCGTTCTCATTATGGAACGTTTATAACATATATTATTAGAAAAAATAGAAAGGGAAC
650 AGATCCGTTCTCATTATGGAACGTTTATCACATATATTATTAGAAAAAATAGAAAGGGAAC
5919205 AATGGAGAAACCTATTAAATTGTCTAGAGGGGTACTAATATTAGTCATCTATTTTTTGCAGATGA
1 AAT-G-GAAACCTATTAAATTGTCTAGAGGGGTACTAATATTAGTCATCTATTTTTTGCAGATGA
*
5919270 CTTACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAATAATTGCTTAAAGACTT
64 CTTACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAAGAATTGCTTAAAGACTT
*
5919335 TCAGCAAAGCTTCGGGGCTTGAAATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAACATA
129 TCAGCAAAGCTTCGGGGCTTGAAATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAACGTA
5919400 AACAACGAGAATGCTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTTGGGGGT
194 AACAACGAGAATGCTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTTGGGGGT
* *
5919465 GTATCTTGGAGTTCCGATTCTGC-TTA-A-GAGAATCACGTGCACTTATGCGCCTCTTGTAGAAA
259 GTATCTTGGAGTTCCGATTCTGCATAAGAGGAGAATCACTTGCACTTATGCGCCTCTTGTAGAAA
*
5919527 AAG-T-TGAGAAAAATGGTTGGGTGGAAGGGTAAGCCTTATCAAAACAATTTCTTTCCAGGAAGA
324 AAGTTGTGAGAAAAATGGTTGGGTGGAAGGGTAAGCCTTATCAAAACAATTTCTTACCAGGAAGA
* *
5919590 AATACCTCTGATAATATTTTCGTTTTGCAGGAAGCAGTCTACACATTTTCAAACTTACAAGGAAG
389 AATACCTCTGATAATATTTTCGTTGTGTAGGAAGCAGTCTACACATTTTCAAACTTACAAGGAAG
* * *
5919655 GAAAGGCGCTGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTAAAGAAGAC
454 GAAAGGTGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTAAAGGAGAC
5919720 TTTAATAGATTTCAATTTGCCCGAGAAGATGATTGTCTAATTATGTTCTGCATCAAAAACAGTAC
519 TTTAATAGATTTCAATTTGCCCGAGAAGATGATTGTCTAATTATGTTCTGCATCAAAAACAGTAC
** **
5919785 CATTGAACCATTGTGGAACAGAGACAGAACAAAGAGCTTCAAACCATAACAAAGACTCAGACAGG
584 CATTGAACCATTGTGGAACAGAGACAGAACAAAGAGCTTCAAACCGGAACAAAGACTCATTCAGG
* * * *
5919850 GAGATCCGTTCTCATTATTGAACATTTATCACATATAATATTAGAAAAAATAGAAAGGAAAC
649 GAGATCCGTTCTCATTATGGAACGTTTATCACATATATTATTAGAAAAAATAGAAAGGGAAC
*
5919912 AATGGAAACCTATTAAATTGTCTAGAGGGGTACTAAAATTAGTCATCTATTTTTTGCAGATGACT
1 AATGGAAACCTATTAAATTGTCTAGAGGGGTACTAATATTAGTCATCTATTTTTTGCAGATGACT
*
5919977 TACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAAGAATTGCTTAAAGGCTTTC
66 TACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAAGAATTGCTTAAAGACTTTC
*
5920042 AGCAAAGCTTCGGGGATTGAAATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAACGTAAA
131 AGCAAAGCTTCGGGGCTTGAAATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAACGTAAA
* *
5920107 CAACGAGAATACTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAATTGGAAATTTGGGGGTGT
196 CAACGAGAATGCTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTTGGGGGTGT
*
5920172 ATCTTGGAGTTTCGATTCTGCATAAGAGGAGAATCACTTGCACTTATGCGCCTCTTGTAGAAAAA
261 ATCTTGGAGTTCCGATTCTGCATAAGAGGAGAATCACTTGCACTTATGCGCCTCTTGTAGAAAAA
* *
5920237 G-T-TGACAAAAA----TGGCT----GGGT--G------------------------GGAAGAAA
326 GTTGTGAGAAAAATGGTTGGGTGGAAGGGTAAGCCTTATCAAAACAATTTCTTACCAGGAAGAAA
*
5920266 TACCTCTGATAATATTTTCGTTGTGTAGGAAGCAGTCTACACATTTTCAAACTTACTAGGAAGGA
391 TACCTCTGATAATATTTTCGTTGTGTAGGAAGCAGTCTACACATTTTCAAACTTACAAGGAAGGA
5920331 AAGGTGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTAAAGGAGACTT
456 AAGGTGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTAAAGGAGACTT
* * *
5920396 TAATTAG-TTTCAATTTGCCCAAGAAGATGATTGTCTAATCATGTTTTGCATCAAAAACAGTACC
521 TAA-TAGATTTCAATTTGCCCGAGAAGATGATTGTCTAATTATGTTCTGCATCAAAAACAGTACC
* * *
5920460 ATTGAACCATTGTGGTACGGAGACAGAACAAAGAGCTTCAAACCGGAACAAAGACTCATTTAGGG
585 ATTGAACCATTGTGGAACAGAGACAGAACAAAGAGCTTCAAACCGGAACAAAGACTCATTCAGGG
5920525 AGATCCGTTCTCATTATGGAACGTTTATCACATATATTATTAGAAAAAATAGAAAGGGAAC
650 AGATCCGTTCTCATTATGGAACGTTTATCACATATATTATTAGAAAAAATAGAAAGGGAAC
5920586 AATGGAGAAACCTATTAAATTGTCTAGAGGGGTACTAATATTAGTCATCTATTTTTTGCAGATGA
1 AAT-G-GAAACCTATTAAATTGTCTAGAGGGGTACTAATATTAGTCATCTATTTTTTGCAGATGA
*
5920651 CTTACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAACGAATTGCTT----A---
64 CTTACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAAGAATTGCTTAAAGACTT
* *
5920709 --A--AAA--------G-TT----T-CAT-TTCAAAAGTTAAAAATGTTTATATCAACAAACATA
129 TCAGCAAAGCTTCGGGGCTTGAAATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAACGTA
* * *
5920755 AACAACGAGAATGTTGATCAGCTGAGTCAACTCAGTGAAATTATAAGAACTGGAAATTTGGGGGT
194 AACAACGAGAATGCTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTTGGGGGT
*
5920820 GTATCTTGGAGTTCTGATTCTGCATAA-A--AGAATCACTTGCACTTATGCGCCTCTTGTAGAAA
259 GTATCTTGGAGTTCCGATTCTGCATAAGAGGAGAATCACTTGCACTTATGCGCCTCTTGTAGAAA
* **
5920882 AAGTTGTGAGAAAAATGGTTGGGTGGAAGGGTAAGCCTTATCAAAACAATTTCTTTCTGGGAAGA
324 AAGTTGTGAGAAAAATGGTTGGGTGGAAGGGTAAGCCTTATCAAAACAATTTCTTACCAGGAAGA
* * *
5920947 AATACCTCTGATAATATTTTCGTTGTGCAGGAAGCAGTCTATATATTTTCAAACTTACAAGGAAG
389 AATACCTCTGATAATATTTTCGTTGTGTAGGAAGCAGTCTACACATTTTCAAACTTACAAGGAAG
*
5921012 GAAAGGCGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTAAAGGAGAC
454 GAAAGGTGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTAAAGGAGAC
* *
5921077 TTTAATAGATTTCAATTTGCCCGAGAAGATGATTGTCTAATTATGTTCTACATCAAAAATAGTAC
519 TTTAATAGATTTCAATTTGCCCGAGAAGATGATTGTCTAATTATGTTCTGCATCAAAAACAGTAC
* **
5921142 CATTGAACCATTGTGGAACAGAGACAGAATAAAGAGCTTCAAACCGGAACAAAGACTCAGACAGG
584 CATTGAACCATTGTGGAACAGAGACAGAACAAAGAGCTTCAAACCGGAACAAAGACTCATTCAGG
* * ** * **
5921207 GAGATCTGTTCTCATTATTGAATATTTATCACATATAATATTAGAAAAAATAGAAAGTAAAC
649 GAGATCCGTTCTCATTATGGAACGTTTATCACATATATTATTAGAAAAAATAGAAAGGGAAC
*
5921269 AATGGAAACCTATTAAATTGTCTAGAGGGGTACTAAAATTAGTCATCTATTTTTTGCAGATGACT
1 AATGGAAACCTATTAAATTGTCTAGAGGGGTACTAATATTAGTCATCTATTTTTTGCAGATGACT
*
5921334 TACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAAAAATTGCTTAAAGACTTTC
66 TACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAAGAATTGCTTAAAGACTTTC
5921399 AGCAAAGCTTCGGGGCTTGAAATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAACGTAAA
131 AGCAAAGCTTCGGGGCTTGAAATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAACGTAAA
*
5921464 CAACGAGAATGTTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTT-GGGGTGT
196 CAACGAGAATGCTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTTGGGGGTGT
* *
5921528 ATCTTGGAGTTTCGATTTTGCATAAGAGGAGAATCACTTGCACTTATG
261 ATCTTGGAGTTCCGATTCTGCATAAGAGGAGAATCACTTGCACTTATG
5921576 TGATAATGAA
Statistics
Matches: 2833, Mismatches: 163, Indels: 163
0.90 0.05 0.05
Matches are distributed among these distances:
647 37 0.01
648 1 0.00
649 9 0.00
650 119 0.04
651 2 0.00
652 1 0.00
653 4 0.00
656 2 0.00
657 5 0.00
659 1 0.00
665 3 0.00
667 1 0.00
674 307 0.11
675 4 0.00
676 114 0.04
681 113 0.04
682 4 0.00
683 304 0.11
685 1 0.00
690 1 0.00
692 3 0.00
698 1 0.00
700 5 0.00
701 2 0.00
704 4 0.00
705 512 0.18
706 450 0.16
707 207 0.07
708 200 0.07
709 147 0.05
710 64 0.02
711 205 0.07
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (710 bp):
AATGGAAACCTATTAAATTGTCTAGAGGGGTACTAATATTAGTCATCTATTTTTTGCAGATGACT
TACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAAGAATTGCTTAAAGACTTTC
AGCAAAGCTTCGGGGCTTGAAATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAACGTAAA
CAACGAGAATGCTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTTGGGGGTGT
ATCTTGGAGTTCCGATTCTGCATAAGAGGAGAATCACTTGCACTTATGCGCCTCTTGTAGAAAAA
GTTGTGAGAAAAATGGTTGGGTGGAAGGGTAAGCCTTATCAAAACAATTTCTTACCAGGAAGAAA
TACCTCTGATAATATTTTCGTTGTGTAGGAAGCAGTCTACACATTTTCAAACTTACAAGGAAGGA
AAGGTGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTAAAGGAGACTT
TAATAGATTTCAATTTGCCCGAGAAGATGATTGTCTAATTATGTTCTGCATCAAAAACAGTACCA
TTGAACCATTGTGGAACAGAGACAGAACAAAGAGCTTCAAACCGGAACAAAGACTCATTCAGGGA
GATCCGTTCTCATTATGGAACGTTTATCACATATATTATTAGAAAAAATAGAAAGGGAAC
Found at i:5921098 original size:683 final size:689
Alignment explanation
Indices: 5920256--5921575 Score: 2018
Period size: 683 Copynumber: 1.9 Consensus size: 689
5920246 AATGGCTGGG
*
5920256 TGGGAAGAAATACCTCTGATAATATTTTCGTTGTGTAGGAAGCAGTCTACACATTTTCAAACTTA
1 TGGGAAGAAATACCTCTGATAATATTTTCGTTGTGCAGGAAGCAGTCTACACATTTTCAAACTTA
* *
5920321 CTAGGAAGGAAAGGTGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTA
66 CAAGGAAGGAAAGGCGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTA
* * *
5920386 AAGGAGACTTTAATTAG-TTTCAATTTGCCCAAGAAGATGATTGTCTAATCATGTTTTGCATCAA
131 AAGGAGACTTTAA-TAGATTTCAATTTGCCCGAGAAGATGATTGTCTAATTATGTTCTGCATCAA
* *
5920450 AAACAGTACCATTGAACCATTGTGGTACGGAGACAGAACAAAGAGCTTCAAACCGGAACAAAGAC
195 AAACAGTACCATTGAACCATTGTGGAACAGAGACAGAACAAAGAGCTTCAAACCGGAACAAAGAC
*** * * *
5920515 TCATTTAGGGAGATCCGTTCTCATTATGGAACGTTTATCACATATATTATTAGAAAAAATAGAAA
260 TCAGACAGGGAGATCCGTTCTCATTATTGAACATTTATCACATATAATATTAGAAAAAATAGAAA
* *
5920580 GGGAACAATGGAGAAACCTATTAAATTGTCTAGAGGGGTACTAATATTAGTCATCTATTTTTTGC
325 GGAAACAAT-G-GAAACCTATTAAATTGTCTAGAGGGGTACTAAAATTAGTCATCTATTTTTTGC
*
5920645 AGATGACTTACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAACGAATTGCTT-A
388 AGATGACTTACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAAGAATTGCTTAA
*
5920709 -A-AAA-G-TT-T-CAT-TTCAAAAGTTAAAAATGTTTATATCAACAAACATAAACAACGAGAAT
453 TACAAAGGATTATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAACATAAACAACGAGAAT
* * *
5920767 GTTGATCAGCTGAGTCAACTCAGTGAAATTATAAGAACTGGAAATTTGGGGGTGTATCTTGGAG-
518 GCTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTTGGGGGTGTATCTTGGAGT
5920831 TTCTGATTCTGCATAA-A-AGAATCACTTGCACTTATGCGCCTCTTGTAGAAAAAGTTGTGAGAA
583 TTC-GATTCTGCATAAGAGAGAATCACTTGCACTTATGCGCCTCTTGTAGAAAAAG-T-TGAGAA
5920894 AAATGGTTGGGTGGAAGGGTAAGCCTTATCAAAACAATTTCTTTC
645 AAATGGTTGGGTGGAAGGGTAAGCCTTATCAAAACAATTTCTTTC
* *
5920939 TGGGAAGAAATACCTCTGATAATATTTTCGTTGTGCAGGAAGCAGTCTATATATTTTCAAACTTA
1 TGGGAAGAAATACCTCTGATAATATTTTCGTTGTGCAGGAAGCAGTCTACACATTTTCAAACTTA
5921004 CAAGGAAGGAAAGGCGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTA
66 CAAGGAAGGAAAGGCGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTA
*
5921069 AAGGAGACTTTAATAGATTTCAATTTGCCCGAGAAGATGATTGTCTAATTATGTTCTACATCAAA
131 AAGGAGACTTTAATAGATTTCAATTTGCCCGAGAAGATGATTGTCTAATTATGTTCTGCATCAAA
* *
5921134 AATAGTACCATTGAACCATTGTGGAACAGAGACAGAATAAAGAGCTTCAAACCGGAACAAAGACT
196 AACAGTACCATTGAACCATTGTGGAACAGAGACAGAACAAAGAGCTTCAAACCGGAACAAAGACT
* *
5921199 CAGACAGGGAGATCTGTTCTCATTATTGAATATTTATCACATATAATATTAGAAAAAATAGAAAG
261 CAGACAGGGAGATCCGTTCTCATTATTGAACATTTATCACATATAATATTAGAAAAAATAGAAAG
*
5921264 TAAACAATGGAAACCTATTAAATTGTCTAGAGGGGTACTAAAATTAGTCATCTATTTTTTGCAGA
326 GAAACAATGGAAACCTATTAAATTGTCTAGAGGGGTACTAAAATTAGTCATCTATTTTTTGCAGA
*
5921329 TGACTTACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAAAAATTGCTTAAAGA
391 TGACTTACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAAGAATTGCTT--A-A
*
5921394 CTTTCAGCAAAGCTTCGGGGCTTGAAATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAAC
453 ---T-A-CAAA-------GGATT---ATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAAC
* *
5921459 GTAAACAACGAGAATGTTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTT-GG
503 ATAAACAACGAGAATGCTGATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTTGGG
*
5921523 GGTGTATCTTGGAGTTTCGATTTTGCATAAGAGGAGAATCACTTGCACTTATG
568 GGTGTATCTTGGAGTTTCGATTCTGCATAAGA-GAGAATCACTTGCACTTATG
5921576 TGATAATGAA
Statistics
Matches: 575, Mismatches: 31, Indels: 36
0.90 0.05 0.06
Matches are distributed among these distances:
681 113 0.20
682 4 0.01
683 306 0.53
685 1 0.00
690 1 0.00
692 3 0.01
700 1 0.00
701 2 0.00
705 1 0.00
706 29 0.05
707 95 0.17
709 19 0.03
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (689 bp):
TGGGAAGAAATACCTCTGATAATATTTTCGTTGTGCAGGAAGCAGTCTACACATTTTCAAACTTA
CAAGGAAGGAAAGGCGCCGTGATAATGAAGATTGACCTACAGTAAGCCTAAACTGGCAATTCCTA
AAGGAGACTTTAATAGATTTCAATTTGCCCGAGAAGATGATTGTCTAATTATGTTCTGCATCAAA
AACAGTACCATTGAACCATTGTGGAACAGAGACAGAACAAAGAGCTTCAAACCGGAACAAAGACT
CAGACAGGGAGATCCGTTCTCATTATTGAACATTTATCACATATAATATTAGAAAAAATAGAAAG
GAAACAATGGAAACCTATTAAATTGTCTAGAGGGGTACTAAAATTAGTCATCTATTTTTTGCAGA
TGACTTACTTTTATTCTTCGAAGCTGCAAGGGATCAAATCATTGAAGTAAAGAATTGCTTAATAC
AAAGGATTATAAATCTTCAAAAGTTAAAAATGTTTATATCAACAAACATAAACAACGAGAATGCT
GATCAGCTGAGTCAACTCAGTGGAATTACAAGAACTGGAAATTTGGGGGTGTATCTTGGAGTTTC
GATTCTGCATAAGAGAGAATCACTTGCACTTATGCGCCTCTTGTAGAAAAAGTTGAGAAAAATGG
TTGGGTGGAAGGGTAAGCCTTATCAAAACAATTTCTTTC
Found at i:5922586 original size:34 final size:34
Alignment explanation
Indices: 5922543--5922611 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
5922533 TATTAAATTG
5922543 TCTAGAGGGGTACTAAAATTAGTCATCTATATTT
1 TCTAGAGGGGTACTAAAATTAGTCATCTATATTT
*
5922577 TCTAGAGGGGTACTAAAATTAGTCATCTATTTTT
1 TCTAGAGGGGTACTAAAATTAGTCATCTATATTT
5922611 T
1 T
5922612 ACAGATGACT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (34 bp):
TCTAGAGGGGTACTAAAATTAGTCATCTATATTT
Found at i:5925444 original size:17 final size:18
Alignment explanation
Indices: 5925408--5925446 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5925398 ATATTATGTA
*
5925408 TTTAATTTATTTAAGCAT
1 TTTAATTTATTTAAGAAT
*
5925426 TTTACTTTATTTAA-AAT
1 TTTAATTTATTTAAGAAT
5925443 TTTA
1 TTTA
5925447 TTAATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTAATTTATTTAAGAAT
Found at i:5928833 original size:18 final size:18
Alignment explanation
Indices: 5928806--5928845 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5928796 ACAGCAGCCA
*
5928806 CCGCAGCCATTTATGATG
1 CCGCAGCCATATATGATG
*
5928824 CCGCATCCATATATGATG
1 CCGCAGCCATATATGATG
5928842 CCGC
1 CCGC
5928846 CACCTTTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.25
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:5929410 original size:26 final size:24
Alignment explanation
Indices: 5929339--5929410 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
5929329 TTATATTTGT
5929339 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
5929364 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
5929386 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
5929411 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:5935000 original size:22 final size:22
Alignment explanation
Indices: 5934975--5935023 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
5934965 ATATATTTAT
5934975 TAATATTTCTAATAATATAATA
1 TAATATTTCTAATAATATAATA
* *
5934997 TAATATTTTTAATATTATAATA
1 TAATATTTCTAATAATATAATA
*
5935019 AAATA
1 TAATA
5935024 ATCAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATTTCTAATAATATAATA
Found at i:5935009 original size:31 final size:30
Alignment explanation
Indices: 5934962--5935025 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
5934952 AAATATTTAA
* *
5934962 AATATATATTTATTAATATTTCTAATAATAT
1 AATATATATTTATTAATA-TTATAATAAAAT
5934993 AATATAATATTT-TTAATATTATAATAAAAT
1 AATAT-ATATTTATTAATATTATAATAAAAT
5935023 AAT
1 AAT
5935026 CAATTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 13 0.43
31 11 0.37
32 6 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
AATATATATTTATTAATATTATAATAAAAT
Found at i:5935087 original size:29 final size:29
Alignment explanation
Indices: 5934984--5935075 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 29
5934974 TTAATATTTC
* *
5934984 TAATAATAT-A-ATATAATATTTTTAATA
1 TAATAATATAAGATATTATATTTTTATTA
* * *
5935011 TTATAATA-AA-ATA--ATCAATTATATTA
1 TAATAATATAAGATATTAT-ATTTTTATTA
*
5935037 TAATAATATAAGATATTATATTTTTATTT
1 TAATAATATAAGATATTATATTTTTATTA
5935066 TAATAATATA
1 TAATAATATA
5935076 TAATAATTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
25 2 0.04
26 14 0.27
27 13 0.25
28 3 0.06
29 17 0.33
30 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (29 bp):
TAATAATATAAGATATTATATTTTTATTA
Found at i:5935208 original size:23 final size:23
Alignment explanation
Indices: 5935189--5935233 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5935179 AATAATATTT
5935189 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
5935212 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
5935234 ATATGACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:5935330 original size:14 final size:14
Alignment explanation
Indices: 5935311--5935355 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
5935301 TCCAATATTA
*
5935311 AAAATTTTATTAAT
1 AAAATTTTAATAAT
* *
5935325 AAAATTATAAAAAT
1 AAAATTTTAATAAT
*
5935339 AATATTTTAATAAT
1 AAAATTTTAATAAT
5935353 AAA
1 AAA
5935356 TAAATTATTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATTTTAATAAT
Found at i:5936481 original size:32 final size:32
Alignment explanation
Indices: 5936439--5936506 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
5936429 TTATGGTACC
5936439 TTTTTATCTAATTTGATACATGAATTTATCAT
1 TTTTTATCTAATTTGATACATGAATTTATCAT
* * * *
5936471 TTTTTTTCTAATTTGATTCATGCATTTTTCAT
1 TTTTTATCTAATTTGATACATGAATTTATCAT
5936503 TTTT
1 TTTT
5936507 CTAGTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.60
Consensus pattern (32 bp):
TTTTTATCTAATTTGATACATGAATTTATCAT
Done.