Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 121 of 130
Found at i:24041717 original size:22 final size:22
Alignment explanation
Indices: 24041677--24041726 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
24041667 GGACCATGTT
* *
24041677 TTATTA-TATTATATTATAGTA
1 TTATTATTACTATATGATAGTA
24041698 TTATTATTACTATATGATAGTA
1 TTATTATTACTATATGATAGTA
*
24041720 TCATTAT
1 TTATTAT
24041727 CATATTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (22 bp):
TTATTATTACTATATGATAGTA
Found at i:24042195 original size:21 final size:20
Alignment explanation
Indices: 24042166--24042208 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
24042156 AAAGATTATG
* *
24042166 GGTTAGATTTAGGTTTCTGGA
1 GGTTAGATTAAGATTT-TGGA
*
24042187 GGTTGGATTAAGATTTTGGA
1 GGTTAGATTAAGATTTTGGA
24042207 GG
1 GG
24042209 ATACTAGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.21, C:0.02, G:0.37, T:0.40
Consensus pattern (20 bp):
GGTTAGATTAAGATTTTGGA
Found at i:24043515 original size:11 final size:11
Alignment explanation
Indices: 24043499--24043525 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
24043489 CTGGTACTAT
24043499 GGGTGTTGTAA
1 GGGTGTTGTAA
24043510 GGGTGTTGTAA
1 GGGTGTTGTAA
24043521 GGGTG
1 GGGTG
24043526 CTATAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (11 bp):
GGGTGTTGTAA
Found at i:24047371 original size:3 final size:3
Alignment explanation
Indices: 24047363--24047406 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
24047353 CAGCAACATC
24047363 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
24047407 ATTAAACATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:24057152 original size:18 final size:18
Alignment explanation
Indices: 24057129--24057174 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
24057119 TATTTTAAAA
*
24057129 TTTTAAAAATATTACTAT
1 TTTTAAAAATATTAATAT
* *
24057147 TTTTAAATATTTTAATAT
1 TTTTAAAAATATTAATAT
24057165 TTGTTAAAAA
1 TT-TTAAAAA
24057175 AATCGGGCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTTAAAAATATTAATAT
Found at i:24076397 original size:22 final size:23
Alignment explanation
Indices: 24076371--24076420 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
24076361 TTAAGATGAT
*
24076371 TATATAATTTCTTATCATTATAA
1 TATATAATTTATTATCATTATAA
*
24076394 -ATATTATTTATTATCATTATAA
1 TATATAATTTATTATCATTATAA
24076416 TATAT
1 TATAT
24076421 TATTGTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATAATTTATTATCATTATAA
Found at i:24076846 original size:20 final size:20
Alignment explanation
Indices: 24076818--24076860 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
24076808 AACAATGATG
*
24076818 TATTATATTAATATTATTTA
1 TATTATATTAATATTATTAA
* *
24076838 TATTGTATTTATATTATTAA
1 TATTATATTAATATTATTAA
24076858 TAT
1 TAT
24076861 AAAAATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TATTATATTAATATTATTAA
Found at i:24082676 original size:88 final size:88
Alignment explanation
Indices: 24082516--24082676 Score: 191
Period size: 88 Copynumber: 1.8 Consensus size: 88
24082506 TACTATTCAG
* * * *
24082516 TATACGATTCAGCCTCCTAATTTCATACAAACCCATTTAGCAAAACAATATCAGACAACAAGATT
1 TATACGATTCAGACTCCCAATATCATACAAACCCATTCAGCAAAACAATATCAGACAACAAGATT
* *
24082581 GAGCAAACTATTTAGCATATATA
66 CAACAAACTATTTAGCATATATA
* * ** *
24082604 TATATGATTCAGACTCCCAATATCATACAATA-CCATTCGGCATTACAATATCAGATAACAAGGA
1 TATACGATTCAGACTCCCAATATCATACAA-ACCCATTCAGCAAAACAATATCAGACAACAA-GA
24082668 -TCAACAAAC
64 TTCAACAAAC
24082677 CACAATAGTT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
88 57 0.95
89 3 0.05
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.26
Consensus pattern (88 bp):
TATACGATTCAGACTCCCAATATCATACAAACCCATTCAGCAAAACAATATCAGACAACAAGATT
CAACAAACTATTTAGCATATATA
Found at i:24083924 original size:356 final size:356
Alignment explanation
Indices: 24083259--24083946 Score: 988
Period size: 356 Copynumber: 1.9 Consensus size: 356
24083249 ATACCTTCAT
* *
24083259 TAATTATCTACAAAATCTAATAGGAATTATTAAAGATATTTTTCTTAAATATACGCCTTCAATAA
1 TAATTATCTACAAAATCTAATAGGAATTATTAAAGATATTTTGCTTAAATATACACCTTCAATAA
*
24083324 CCGTGTTAAAATTTGTGGGACGGTATATTAAAGGCATTTTACATTAAAAGACGCCTTTAATAATT
66 CCGTGTTAAAATTTGTGGGACGGTATATTAAAGGCATTTTACAGTAAAAGACGCCTTTAATAATT
* * ** * *
24083389 CTTAAAATTTTTTGAAAGAAAATATTGAAGGCGTCTGTTGTTAACAAATGCCTTCAGTAATGGAT
131 CTCAAAATTTTTAGAAAGAAAATATTGAAAACGTCTGTTATTAACAAACGCCTTCAGTAATGGAT
* * * * * *
24083454 TAACTAAGTTTAAAGGTATATTGAAGGTGTTTTTTCGAATAAACATCTTCTATAACCATCGTGAT
196 TAACTAAGTTTAAAGATATATTAAAGGTGCTTTTTCAAATAAACACCTTCTATAACCACCGTGAT
* * ** * *
24083519 ATATTGAATGTATTTTATAATAAAAGATGTCTTTAATAATCTTAAAATTTTTTTATGAAAATTAT
261 ATATTGAAGGCATTTTATAATAAAAGATACCTTTAATAATCTAAAAATTTTTTTAAGAAAATTAT
24083584 TAAAGGTGTTGTTATCTGCAAACGCCTGCAC
326 TAAAGGTGTTGTTATCTGCAAACGCCTGCAC
* * *
24083615 TAATTATCTACAATATCTAATAGGAATTATTAAAGGA-ATTTTGCTTGAATATACACTTTCAATA
1 TAATTATCTACAAAATCTAATAGGAATTATTAAA-GATATTTTGCTTAAATATACACCTTCAATA
* * * * * *
24083679 ACCGTGTTAAAATTTGTGTGATGGTATATTAAAGGTATTTTACAGTAGAATACGTCTTTAATAAT
65 ACCGTGTTAAAATTTGTGGGACGGTATATTAAAGGCATTTTACAGTAAAAGACGCCTTTAATAAT
* *
24083744 TCTCAAAATTTTTAGTAAA-AATATATT-AAAACTGTCTGTTATTAACATACGCCTTCAGTAATG
130 TCTCAAAATTTTTAG-AAAGAAAATATTGAAAAC-GTCTGTTATTAACAAACGCCTTCAGTAATG
**
24083807 GATT-ACTAAGTTTAAAGATATATTAAAGGTGCTTTTTCAAATAAATGCCTTCTATAACCACCGT
193 GATTAACTAAGTTTAAAGATATATTAAAGGTGCTTTTTCAAATAAACACCTTCTATAACCACCGT
*
24083871 GGTATATTGAAGGCATTTTATAATAAAAGATACCTTTAATAATCCTAAAAATTTTTTTAAGAAAA
258 GATATATTGAAGGCATTTTATAATAAAAGATACCTTTAATAAT-CTAAAAATTTTTTTAAGAAAA
*
24083936 TTATTGAAGGT
322 TTATTAAAGGT
24083947 ATTTTTCTTG
Statistics
Matches: 292, Mismatches: 36, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
355 93 0.32
356 194 0.66
357 5 0.02
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.38
Consensus pattern (356 bp):
TAATTATCTACAAAATCTAATAGGAATTATTAAAGATATTTTGCTTAAATATACACCTTCAATAA
CCGTGTTAAAATTTGTGGGACGGTATATTAAAGGCATTTTACAGTAAAAGACGCCTTTAATAATT
CTCAAAATTTTTAGAAAGAAAATATTGAAAACGTCTGTTATTAACAAACGCCTTCAGTAATGGAT
TAACTAAGTTTAAAGATATATTAAAGGTGCTTTTTCAAATAAACACCTTCTATAACCACCGTGAT
ATATTGAAGGCATTTTATAATAAAAGATACCTTTAATAATCTAAAAATTTTTTTAAGAAAATTAT
TAAAGGTGTTGTTATCTGCAAACGCCTGCAC
Found at i:24084093 original size:125 final size:124
Alignment explanation
Indices: 24083871--24084100 Score: 266
Period size: 125 Copynumber: 1.8 Consensus size: 124
24083861 TAACCACCGT
* *
24083871 GGTATATTGAAGGCATTTTATAATAAAAGATACCTTTAATAATCCTAAAAATTTTTTTAAGAAAA
1 GGTATATTAAAGGCATTTTACAATAAAAGATACCTTTAATAATCCTAAAAA-TTTTTTAAGAAAA
* * * * *
24083936 TTATTGAAGGTATTTTTCTTGAATATACGCCTTCAATAATCGTGTTAAAATTTGTGTGAC
65 ATATTGAAGGCATTGTTATTGAACATACGCCTTCAATAATCGTGTTAAAATTTGTGTGAC
* * * * ** *
24083996 GGTATATTAAAGGCATTTTACAGTAGAATATGCCTTTAATAATTTTTAAAA-TTTTTAGAGAAAA
1 GGTATATTAAAGGCATTTTACAATAAAAGATACCTTTAATAATCCTAAAAATTTTTTA-AG-AAA
* *
24084060 AATATTGAAGGCATCTGTTATT-AACATATGCCTTCAGTAAT
64 AATATTGAAGGCAT-TGTTATTGAACATACGCCTTCAATAAT
24084101 GGATTACTAA
Statistics
Matches: 86, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
123 6 0.07
124 2 0.02
125 73 0.85
126 5 0.06
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (124 bp):
GGTATATTAAAGGCATTTTACAATAAAAGATACCTTTAATAATCCTAAAAATTTTTTAAGAAAAA
TATTGAAGGCATTGTTATTGAACATACGCCTTCAATAATCGTGTTAAAATTTGTGTGAC
Found at i:24086444 original size:324 final size:325
Alignment explanation
Indices: 24085834--24086472 Score: 935
Period size: 324 Copynumber: 2.0 Consensus size: 325
24085824 CTGAGAAAAG
* *
24085834 AAGTATCAAAGTTTTATAGGTTGCTTGAAAAAATGAATGAATAACTTTTTGAGGGATCAAAGCAT
1 AAGTATCAAAGTTTTATAGCTTGCTTGAAAAAATGAATGAATAACTTTTTAAGGGATCAAAGCAT
* * * * * *
24085899 TCAATGTTATCTTTCTGTGTTCGTCTTTTTCATTTGAAATGCTTATGTGGATGGATAAAAAACTC
66 TCAAGGTTATCTTTCTGTGTTCATCTTTTTCACTTGAAATGCTTATATGAATGGACAAAAAACTC
* * ** * **
24085964 TTTGACTTTATTATTATAGTTTATGAAAGTAATGTTTTCTTTTGTAAAATTCTCTGAATCTTGTA
131 TCTGACTTTATTATTACAGTTTATGAAAAAAATATTTTCTTTTCAAAAATTCTCTGAATCTTGTA
* ** * * *
24086029 AGGAATTAAAATAGATGATCAAAGATTTAGGTCTTGGATATGAAAAAATTTATAGTTGTCTCAAT
196 AGGAATCAAAATAGATGATCAAAGATTTAGGTCTCAGATATGAAAAAATTCATAATTGTCCCAAT
* * * *
24086094 GATTGCATGTTGTTTTGAAGGAATAGAAAAAATCAAGAATCTTGTCATTTGTGTGGTATTTGGAA
261 GATTACATGTTGTTTGGAAGGAATAGAAAAAATAAAAAATCTTGTCATTTGTGTGGTATTTGGAA
* ** *
24086159 AAGTATTAAAGTTTTATAGCTTGCTTGAGGAGATGAATGAATAACTTTTTAAGGGATCAAAGCAT
1 AAGTATCAAAGTTTTATAGCTTGCTTGAAAAAATGAATGAATAACTTTTTAAGGGATCAAAGCAT
24086224 TCAAGGTTATCTTTCTGTGTTCATCTTTTTCACTTGAAAT-CTTATATGAATGGACAAAAAACTC
66 TCAAGGTTATCTTTCTGTGTTCATCTTTTTCACTTGAAATGCTTATATGAATGGACAAAAAACTC
*
24086288 TCTGACTTTATTATTACAGTTTATGAAAAAAATATTTTCTTTTACAAAAATT-TTTGAATCTTGT
131 TCTGACTTTATTATTACAGTTTATGAAAAAAATATTTTCTTTT-CAAAAATTCTCTGAATCTTGT
*
24086352 AAGGAATCAAAGA-AGATGATCAAGGATTTAGGTCTCAGATATGAAAAAATTCATAATTGTCCCA
195 AAGGAATCAAA-ATAGATGATCAAAGATTTAGGTCTCAGATATGAAAAAATTCATAATTGTCCCA
*
24086416 ATTATTACATGTTGTATTGGAA-GAATAGAAAAAATAAAAAATCTTGTCATTTGTGTG
259 ATGATTACATGTTGT-TTGGAAGGAATAGAAAAAATAAAAAATCTTGTCATTTGTGTG
24086473 ATATATCTCG
Statistics
Matches: 279, Mismatches: 32, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
324 171 0.61
325 108 0.39
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (325 bp):
AAGTATCAAAGTTTTATAGCTTGCTTGAAAAAATGAATGAATAACTTTTTAAGGGATCAAAGCAT
TCAAGGTTATCTTTCTGTGTTCATCTTTTTCACTTGAAATGCTTATATGAATGGACAAAAAACTC
TCTGACTTTATTATTACAGTTTATGAAAAAAATATTTTCTTTTCAAAAATTCTCTGAATCTTGTA
AGGAATCAAAATAGATGATCAAAGATTTAGGTCTCAGATATGAAAAAATTCATAATTGTCCCAAT
GATTACATGTTGTTTGGAAGGAATAGAAAAAATAAAAAATCTTGTCATTTGTGTGGTATTTGGAA
Found at i:24092800 original size:31 final size:32
Alignment explanation
Indices: 24092742--24092807 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
24092732 ATAAATGTCA
* **
24092742 CTAATATTGAGGTATTTTTTTTGAAAATATCG
1 CTAATATTGAGGCATTTTTTTCAAAAATATCG
24092774 CTAATATTGAGGCA-TTTTTTCAAAAATATCG
1 CTAATATTGAGGCATTTTTTTCAAAAATATCG
24092805 CTA
1 CTA
24092808 TTTACTACGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (32 bp):
CTAATATTGAGGCATTTTTTTCAAAAATATCG
Found at i:24093091 original size:15 final size:15
Alignment explanation
Indices: 24093033--24093102 Score: 59
Period size: 15 Copynumber: 4.4 Consensus size: 15
24093023 TTTATATTTT
24093033 TATTTTTAATTTAAA
1 TATTTTTAATTTAAA
* * *
24093048 TTAAATTATAATTATAAT
1 -T-ATTTTTAATT-TAAA
**
24093066 TATAATTAATTTAAA
1 TATTTTTAATTTAAA
24093081 TATTTTTAATTTAAA
1 TATTTTTAATTTAAA
24093096 TAATTTT
1 T-ATTTT
24093103 GATCTAATAA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
15 17 0.41
16 12 0.29
17 9 0.22
18 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTTTAATTTAAA
Found at i:24095066 original size:125 final size:126
Alignment explanation
Indices: 24094915--24095162 Score: 315
Period size: 131 Copynumber: 2.0 Consensus size: 126
24094905 AGAACTTGCC
*
24094915 TGGAAACCGAAGGAAACTA-T-TT-TCTTGGTCTTGGTCATTGTTAAGTCGAAAAAGCAATGGAA
1 TGGAAACCGAAGGAAACTATTCTTGTCTTGGTCTTGGTCATTGCTAAGTCGAAAAAGCAATGGAA
* **
24094977 AGCCCCTTCAATTATTGGGCAATATACCCCA-CTTAACTTTTATGACTACCACATAACTTACA
66 AACCCCTTCAATTATTCCGCAATATA-CCCATCTTAAC-TTTATGACTACCACATAACTTACA
* * **
24095039 TGGAAACCGGAAGGAAATTCTTTTCTTGGTCTTGGTCTTGGTCATTGCTCAGTCGAAAGGGCAAT
1 TGGAAACC-GAAGGAAA--CTATTCTT-GTCTTGGTCTTGGTCATTGCTAAGTCGAAAAAGCAAT
* * *
24095104 GGAAAACTCCTTCAATTATTCCGCTATATACCCATCTTAACTTTATGACTACGACATAA
62 GGAAAACCCCTTCAATTATTCCGCAATATACCCATCTTAACTTTATGACTACCACATAA
24095163 AAAAAAAGAA
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
124 8 0.08
125 8 0.08
127 2 0.02
128 1 0.01
129 2 0.02
130 21 0.20
131 63 0.60
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (126 bp):
TGGAAACCGAAGGAAACTATTCTTGTCTTGGTCTTGGTCATTGCTAAGTCGAAAAAGCAATGGAA
AACCCCTTCAATTATTCCGCAATATACCCATCTTAACTTTATGACTACCACATAACTTACA
Found at i:24097611 original size:111 final size:111
Alignment explanation
Indices: 24097407--24097630 Score: 315
Period size: 111 Copynumber: 2.0 Consensus size: 111
24097397 CCAAATTGCA
* * ** *
24097407 GCTGTCTGTTCCCAAGGCAAGTGGGTCGCGATTGACTGAGCTACGGAAGGAAGAAGAATGGGCAG
1 GCTGTCTGTTCCCAAGGCAAGTGGGTCGCGATTGACCGAGCCACAAAAGGAAGAAGAATGGACAG
* * ** *
24097472 CTAGAGAGATCCATTTAACAGGTGATAAACATAACGTGTCTGAGCT
66 CCAAAGAGATCCATTTAACAGGCAATAAACATAACGTGTCGGAGCT
*
24097518 GCTGTCTGTTCCTAAGGCAAGTGGGTCAG-GATTGACCGAGCCACAAAAGGAAGAAGAATGGACA
1 GCTGTCTGTTCCCAAGGCAAGTGGGTC-GCGATTGACCGAGCCACAAAAGGAAGAAGAATGGACA
* *
24097582 GCCAAAGAGATCCATTTTACCGGCAATAAACATAACGTGTCGGAGCT
65 GCCAAAGAGATCCATTTAACAGGCAATAAACATAACGTGTCGGAGCT
24097629 GC
1 GC
24097631 CAAAATCTCC
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
111 98 0.99
112 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (111 bp):
GCTGTCTGTTCCCAAGGCAAGTGGGTCGCGATTGACCGAGCCACAAAAGGAAGAAGAATGGACAG
CCAAAGAGATCCATTTAACAGGCAATAAACATAACGTGTCGGAGCT
Found at i:24100491 original size:13 final size:13
Alignment explanation
Indices: 24100475--24100515 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
24100465 TTTAAATTTT
*
24100475 TTATTTTTATATA
1 TTATTTTAATATA
24100488 TTATTTTAATATA
1 TTATTTTAATATA
**
24100501 AAATTTTAATATA
1 TTATTTTAATATA
24100514 TT
1 TT
24100516 TAAATAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTATTTTAATATA
Found at i:24100505 original size:33 final size:32
Alignment explanation
Indices: 24100468--24100549 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
24100458 TTTTAAATTT
* *
24100468 AAATTTTTTATTTTTATATATTATTTTAATATA
1 AAATTTTTTATTTTTAAATA-AATTTTAATATA
* * *
24100501 AAATTTTAATATATTTAAATAAATTTTGATATA
1 AAATTTT-TTATTTTTAAATAAATTTTAATATA
*
24100534 AAA-TTATTATTTTTAA
1 AAATTTTTTATTTTTAA
24100550 TTTATAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
31 8 0.20
32 2 0.05
33 20 0.50
34 10 0.25
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
AAATTTTTTATTTTTAAATAAATTTTAATATA
Found at i:24102608 original size:7 final size:7
Alignment explanation
Indices: 24102596--24102631 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
24102586 CTCAATTATA
24102596 AAAAAAT
1 AAAAAAT
24102603 AAAAAAT
1 AAAAAAT
24102610 AAAAAAT
1 AAAAAAT
24102617 AAATAAAAT
1 -AA-AAAAT
24102626 AAAAAA
1 AAAAAA
24102632 GGATGCTCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 18 0.67
8 4 0.15
9 5 0.19
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:24102624 original size:16 final size:14
Alignment explanation
Indices: 24102596--24102631 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
24102586 CTCAATTATA
24102596 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
24102610 AAAAAATAAATAAAAT
1 AAAAAAT-AA-AAAAT
24102626 AAAAAA
1 AAAAAA
24102632 GGATGCTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.35
15 2 0.10
16 11 0.55
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAATAAAAAAT
Found at i:24110670 original size:16 final size:16
Alignment explanation
Indices: 24110651--24110691 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
24110641 TTTTATTAGT
24110651 TATTTATAT-ATATTTA
1 TATTTATATAAT-TTTA
24110667 TATTTATATAATTTTA
1 TATTTATATAATTTTA
*
24110683 TAATTATAT
1 TATTTATAT
24110692 TAAAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTATATAATTTTA
Found at i:24110736 original size:23 final size:22
Alignment explanation
Indices: 24110662--24110730 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 22
24110652 ATTTATATAT
* * *
24110662 ATTTATATTTATATAATTTTATA
1 ATTTATATTT-TAAAATATAATA
24110685 A-TTATA--TTAAAATATAATA
1 ATTTATATTTTAAAATATAATA
24110704 ATTTATATTTTAAAA-ATAATA
1 ATTTATATTTTAAAATATAATA
*
24110725 TTTTAT
1 ATTTAT
24110731 TAATTTCGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 10 0.26
20 6 0.15
21 11 0.28
22 11 0.28
23 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTATATTTTAAAATATAATA
Found at i:24111470 original size:20 final size:20
Alignment explanation
Indices: 24111431--24111471 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
24111421 GATATAAAAC
**
24111431 ATTAAATTTTATTATTTAAT
1 ATTAAATTTTATTACATAAT
24111451 ATTAAATTTTATTACATAAT
1 ATTAAATTTTATTACATAAT
24111471 A
1 A
24111472 ATTTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTAAATTTTATTACATAAT
Found at i:24111913 original size:18 final size:18
Alignment explanation
Indices: 24111890--24111925 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
24111880 AATTAAAATA
24111890 TTTTTTT-ATTATTTTAAT
1 TTTTTTTAATT-TTTTAAT
24111908 TTTTTTTAATTTTTTAAT
1 TTTTTTTAATTTTTTAAT
24111926 CAAACAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTTAATTTTTTAAT
Found at i:24114107 original size:2 final size:2
Alignment explanation
Indices: 24114100--24114126 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24114090 TATTATTAAT
24114100 TA 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 T
24114127 TAGTTGAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24125008 original size:11 final size:10
Alignment explanation
Indices: 24124989--24125023 Score: 54
Period size: 11 Copynumber: 3.5 Consensus size: 10
24124979 TCATCCTATA
24124989 TTTTTTTCTT
1 TTTTTTTCTT
24124999 TTTGTTTTCTT
1 TTT-TTTTCTT
24125010 TTTTTTT-TT
1 TTTTTTTCTT
24125019 TTTTT
1 TTTTT
24125024 CTGATAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.29
10 7 0.29
11 10 0.42
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:24125017 original size:17 final size:18
Alignment explanation
Indices: 24124990--24125025 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
24124980 CATCCTATAT
24124990 TTTTTTCTTTTTGTTTTC
1 TTTTTTCTTTTTGTTTTC
*
24125008 TTTTTT-TTTTTTTTTTC
1 TTTTTTCTTTTTGTTTTC
24125025 T
1 T
24125026 GATAAGCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (18 bp):
TTTTTTCTTTTTGTTTTC
Found at i:24128116 original size:22 final size:22
Alignment explanation
Indices: 24128076--24128117 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
24128066 TGTAAATTTA
** *
24128076 TATTTGTATCTTTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
24128098 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
24128118 GGATAGATAA
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:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:24128390 original size:16 final size:16
Alignment explanation
Indices: 24128369--24128400 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
24128359 TTGTCGAATC
24128369 CTGTTTAGGCCTTCAT
1 CTGTTTAGGCCTTCAT
24128385 CTGTTTAGGCCTTCAT
1 CTGTTTAGGCCTTCAT
24128401 TGCCGAACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (16 bp):
CTGTTTAGGCCTTCAT
Found at i:24132071 original size:22 final size:22
Alignment explanation
Indices: 24132045--24132087 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
24132035 CTGTATATTT
* *
24132045 ATATTTGTATCTCTAGAATTAA
1 ATATTTGTATCCCTAAAATTAA
24132067 ATATTTGTATCCCTAAAATTA
1 ATATTTGTATCCCTAAAATTA
24132088 GGATAGACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (22 bp):
ATATTTGTATCCCTAAAATTAA
Found at i:24147155 original size:2 final size:2
Alignment explanation
Indices: 24147143--24147207 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
24147133 TAGCTGGAGA
* *
24147143 TC TC AC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
24147185 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
24147208 TTACTTTCGC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.02, C:0.48, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:24150174 original size:20 final size:18
Alignment explanation
Indices: 24150149--24150185 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
24150139 TTTGCATGAA
24150149 TTTGTATGACTAATATTATC
1 TTTGTATGA-TAAT-TTATC
24150169 TTTGTATGATAATTTAT
1 TTTGTATGATAATTTAT
24150186 TTGCCTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTGTATGATAATTTATC
Found at i:24150258 original size:20 final size:20
Alignment explanation
Indices: 24150191--24150358 Score: 113
Period size: 20 Copynumber: 7.5 Consensus size: 20
24150181 TTTATTTGCC
* *
24150191 TAATATATTTGTTTGCATGAT
1 TAATATATTTATTTG-ATTAT
24150212 TAATATATTTATTTGTGTGATTTAT
1 TAATATATTTA--T-T-TGA-TTAT
*
24150237 TAATATATTTATATGATTAT
1 TAATATATTTATTTGATTAT
24150257 TAATATATTTATTTGTATTAT
1 TAATATATTTATTTG-ATTAT
* *
24150278 CATATTTAATTTGATTGCATGATTAT
1 TA-ATAT-ATTT-ATT---TGATTAT
24150304 TAATATATTTAATTGCTTGATTAT
1 TAATATATTT-A-T--TTGATTAT
*
24150328 TAATATATTTATTTGCATGAT
1 TAATATATTTATTTG-ATTAT
24150349 T-ATATATTTA
1 TAATATATTTA
24150359 ATTGCATTTT
Statistics
Matches: 121, Mismatches: 10, Indels: 33
0.74 0.06 0.20
Matches are distributed among these distances:
20 30 0.25
21 24 0.20
22 4 0.03
23 7 0.06
24 27 0.22
25 20 0.17
26 6 0.05
27 3 0.02
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (20 bp):
TAATATATTTATTTGATTAT
Found at i:24150318 original size:24 final size:24
Alignment explanation
Indices: 24150210--24150365 Score: 127
Period size: 24 Copynumber: 6.8 Consensus size: 24
24150200 TGTTTGCATG
* **
24150210 ATTAATATATTTATTTGTGTGATTT
1 ATTAATATATTTAATTGCATGA-TT
24150235 ATTAATATATTT-A-T--ATGATT
1 ATTAATATATTTAATTGCATGATT
*
24150255 ATTAATATATTTATTTG--T-ATT
1 ATTAATATATTTAATTGCATGATT
* * *
24150276 ATCATATTTAATTTGATTGCATGATT
1 ATTA-ATAT-ATTTAATTGCATGATT
*
24150302 ATTAATATATTTAATTGCTTGATT
1 ATTAATATATTTAATTGCATGATT
*
24150326 ATTAATATATTTATTTGCATG---
1 ATTAATATATTTAATTGCATGATT
24150347 ATT-ATATATTTAATTGCAT
1 ATTAATATATTTAATTGCAT
24150366 TTTTTTGCAT
Statistics
Matches: 109, Mismatches: 14, Indels: 21
0.76 0.10 0.15
Matches are distributed among these distances:
20 29 0.27
21 12 0.11
22 5 0.05
23 8 0.07
24 33 0.30
25 16 0.15
26 6 0.06
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.55
Consensus pattern (24 bp):
ATTAATATATTTAATTGCATGATT
Found at i:24150450 original size:53 final size:53
Alignment explanation
Indices: 24150340--24150465 Score: 132
Period size: 53 Copynumber: 2.4 Consensus size: 53
24150330 ATATATTTAT
* * * **
24150340 TTGCATGATTATATATTTAATTGCATTTTTTTGCATGATTTATATATTATTGT
1 TTGCATGATTATATATTTAATTGCATTTTATTACATGATTTATACATTATTAA
* * *
24150393 TTGCATAATTATATATTTACTTGCATGTTTAATTACAT-ATTT-TACATTCTTAA
1 TTGCATGATTATATATTTAATTGCAT-TTT-ATTACATGATTTATACATTATTAA
24150446 TTGCATGATTAT-TAATTTAA
1 TTGCATGATTATAT-ATTTAA
24150466 ATATTTGCAT
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
52 1 0.02
53 47 0.78
54 7 0.12
55 5 0.08
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (53 bp):
TTGCATGATTATATATTTAATTGCATTTTATTACATGATTTATACATTATTAA
Found at i:24150537 original size:3 final size:3
Alignment explanation
Indices: 24150529--24150563 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
24150519 TATTTATTTG
24150529 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
24150564 GCATGATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:24150596 original size:19 final size:19
Alignment explanation
Indices: 24150559--24150597 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
24150549 ATTATTATTA
* * *
24150559 TTATTGCATGATTTTATAT
1 TTATTGCATAATATGATAT
24150578 TTATTGCATAATATGATAT
1 TTATTGCATAATATGATAT
24150597 T
1 T
24150598 ATATGTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (19 bp):
TTATTGCATAATATGATAT
Found at i:24150620 original size:24 final size:24
Alignment explanation
Indices: 24150572--24150627 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
24150562 TTGCATGATT
*
24150572 TTATATTTATTGCATAATATGATA
1 TTATATTTATTGCATAATATAATA
*
24150596 TTATATGTTATTGCATGAT-TAATA
1 TTATAT-TTATTGCATAATATAATA
24150620 TTATATTT
1 TTATATTT
24150628 GAATGATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 16 0.55
25 11 0.38
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.54
Consensus pattern (24 bp):
TTATATTTATTGCATAATATAATA
Found at i:24156831 original size:12 final size:11
Alignment explanation
Indices: 24156794--24156876 Score: 53
Period size: 12 Copynumber: 7.3 Consensus size: 11
24156784 AGAGGTGTGC
24156794 AAAAAAAATAA
1 AAAAAAAATAA
* *
24156805 ATAAATAAGTAAA
1 A-AAAAAAAT-AA
24156818 AAAACAAAATAA
1 AAAA-AAAATAA
24156830 AAATAAAAATAA
1 AAA-AAAAATAA
*
24156842 AAAAGTAAA-AA
1 AAAA-AAAATAA
*
24156853 AGAAAAAA-AA
1 AAAAAAAATAA
* *
24156863 AAGAAAAAGAA
1 AAAAAAAATAA
24156874 AAA
1 AAA
24156877 CTTAAACTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
10 11 0.20
11 11 0.20
12 27 0.48
13 7 0.12
ACGTcount: A:0.83, C:0.01, G:0.06, T:0.10
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:24156832 original size:6 final size:6
Alignment explanation
Indices: 24156803--24156876 Score: 51
Period size: 6 Copynumber: 11.5 Consensus size: 6
24156793 CAAAAAAAAT
*
24156803 AAATAA ATAAGTAA AAAAACA AAATAA AAATAA AAATAAA AAAGTAA AAA-AGA
1 AAATAA A-AA-TAA AAATA-A AAATAA AAATAA AAAT-AA AAA-TAA AAATA-A
* * *
24156856 AAAAAA AAAGAA AAAGAA AAA
1 AAATAA AAATAA AAATAA AAA
24156877 CTTAAACTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
5 1 0.02
6 32 0.55
7 20 0.34
8 5 0.09
ACGTcount: A:0.82, C:0.01, G:0.07, T:0.09
Consensus pattern (6 bp):
AAATAA
Found at i:24156840 original size:33 final size:32
Alignment explanation
Indices: 24156795--24156876 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 32
24156785 GAGGTGTGCA
* *
24156795 AAAAAAATAAATAAATAAGTAAAAAA-ACAAAA
1 AAAAAAAAAAATAAAAAAGTAAAAAAGA-AAAA
*
24156827 TAAAAATAAAAATAAAAAAGTAAAAAAGAAAAA
1 -AAAAAAAAAAATAAAAAAGTAAAAAAGAAAAA
* *
24156860 AAAAAGAAAAAGAAAAA
1 AAAAAAAAAAATAAAAA
24156877 CTTAAACTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 15 0.35
33 27 0.63
34 1 0.02
ACGTcount: A:0.83, C:0.01, G:0.06, T:0.10
Consensus pattern (32 bp):
AAAAAAAAAAATAAAAAAGTAAAAAAGAAAAA
Found at i:24156860 original size:17 final size:17
Alignment explanation
Indices: 24156816--24156876 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 17
24156806 TAAATAAGTA
* *
24156816 AAAAAACAAAATAAAAATA
1 AAAAAA-AAAAGAAAAA-G
24156835 AAAATAAAAAAGTAAAAAAG
1 AAAA-AAAAAAG--AAAAAG
24156855 AAAAAAAAAAGAAAAAG
1 AAAAAAAAAAGAAAAAG
24156872 AAAAA
1 AAAAA
24156877 CTTAAACTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 11 0.30
19 15 0.41
20 6 0.16
21 5 0.14
ACGTcount: A:0.85, C:0.02, G:0.07, T:0.07
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAAG
Found at i:24158429 original size:42 final size:43
Alignment explanation
Indices: 24158311--24158637 Score: 303
Period size: 42 Copynumber: 7.9 Consensus size: 43
24158301 AAGAGTGATC
* *
24158311 TCATTTTATTTTTCAAAAATTTCAAAGCCTCAGTTGT-AGGGGA
1 TCATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTGTGA-GGGA
* *
24158354 GCATTTTTATTTTTCAAAAGTTTCAAAGCCTCAATTGTGATGGA
1 TCA-TTTTATTTTTCAAAAGTTTCAAAGCCTCAATTGTGAGGGA
* *
24158398 TCATTTTATTTTTC-AAAGTTTCAAAGCCTCAATTATG-GAGA
1 TCATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTGTGAGGGA
* *
24158439 TCA--TT-TTTTTCAAAAGTTTTAAAAG-TTCAATTGTG-GAGGA
1 TCATTTTATTTTTCAAAAG-TTTCAAAGCCTCAATTGTGAG-GGA
* * *
24158479 GT-ATTTTATTTTTCAAAAG--T-AAA-CCTTAGTTGTGGGGGA
1 -TCATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTGTGAGGGA
* * *
24158518 ACATTTTA-TTTTCAAAAGTTTCAAAGCCTCAGTTGTGGGGGA
1 TCATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTGTGAGGGA
* *
24158560 ACATTTTATTTTTC-AAAGTTTTAAAGCCTCAATTGTG-GGAGA
1 TCATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTGTGAGG-GA
* *
24158602 GT-ATTTTA-TTTTCAAAAGTTTTAAAGTCTCAATTGT
1 -TCATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTGT
24158638 ATAAAGCATT
Statistics
Matches: 243, Mismatches: 21, Indels: 41
0.80 0.07 0.13
Matches are distributed among these distances:
38 16 0.07
39 34 0.14
40 13 0.05
41 16 0.07
42 97 0.40
43 29 0.12
44 37 0.15
45 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (43 bp):
TCATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTGTGAGGGA
Found at i:24158472 original size:81 final size:85
Alignment explanation
Indices: 24158311--24158663 Score: 322
Period size: 81 Copynumber: 4.2 Consensus size: 85
24158301 AAGAGTGATC
* * * *
24158311 TCATTTTATTTTTCAAAAATTTCAAAGCCTCAGTTGTAGGG-GAGCATTTTTATTTTTCAAAAGT
1 TCATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTAT-GGGAGATCA-TTTTA-TTTTCAAAAGT
24158375 TTCAAAGCCTCAATTGTGATGGA
63 TTCAAAGCCTCAATTGTGATGGA
24158398 TCATTTTATTTTTC-AAAGTTTCAAAGCCTCAATTAT-GGAGATCA-TTT-TTTTCAAAAGTTTT
1 TCATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTATGGGAGATCATTTTATTTTCAAAAG-TTT
* *
24158459 AAAAG-TTCAATTGTGGA-GGA
65 CAAAGCCTCAATTGT-GATGGA
* * * * *
24158479 GT-ATTTTATTTTTCAAAAG--T-AAA-CCTTAGTTGTGGGGGAACATTTTATTTTCAAAAGTTT
1 -TCATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTATGGGAGATCATTTTATTTTCAAAAGTTT
* **
24158539 CAAAGCCTCAGTTGTGGGGGA
65 CAAAGCCTCAATTGTGATGGA
* * *
24158560 ACATTTTATTTTTC-AAAGTTTTAAAGCCTCAATTGTGGGAGAGT-ATTTTATTTTCAAAAGTTT
1 TCATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTATGGGAGA-TCATTTTATTTTCAAAAGTTT
* * **
24158623 TAAAGTCTCAATTGT-ATAAA
65 CAAAGCCTCAATTGTGATGGA
* **
24158643 GCATTTTATTTTAGAAAAGTT
1 TCATTTTATTTTTCAAAAGTT
24158664 CATTTTTCAA
Statistics
Matches: 219, Mismatches: 30, Indels: 37
0.77 0.10 0.13
Matches are distributed among these distances:
78 7 0.03
79 9 0.04
80 16 0.07
81 65 0.30
82 15 0.07
83 18 0.08
84 52 0.24
85 4 0.02
86 19 0.09
87 14 0.06
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (85 bp):
TCATTTTATTTTTCAAAAGTTTCAAAGCCTCAATTATGGGAGATCATTTTATTTTCAAAAGTTTC
AAAGCCTCAATTGTGATGGA
Found at i:24158544 original size:162 final size:171
Alignment explanation
Indices: 24158313--24158637 Score: 465
Period size: 162 Copynumber: 2.0 Consensus size: 171
24158303 GAGTGATCTC
* *
24158313 ATTTTATTTTTCAAAAATTTCAAAGCCTCAGTTGTAGGGGAGCATTTTTATTTTTCAAAAGTTTC
1 ATTTTATTTTTCAAAAATGTCAAAGCCTCAGTTGTAGGGGAACATTTTTATTTTTCAAAAGTTTC
* *
24158378 AAAGCCTCAATTGTGATGGATCATTTTATTTTTCAAAGTTTCAAAGCCTCAATTAT-GGAGA-TC
66 AAAGCCTCAATTGTGAGGGAACATTTTATTTTTCAAAGTTTCAAAGCCTCAATTATGGGAGAGT-
24158441 A-TTT-TTTTCAAAAGTTTTAAAAGT-TCAATTGTGGAGGAGT
130 ATTTTATTTTCAAAAGTTTT-AAAGTCTCAATTGTGGAGGAGT
* *
24158481 ATTTTATTTTTC-AAAA-GT-AAA-CCTTAGTTGTGGGGGAACA-TTTTA-TTTTCAAAAGTTTC
1 ATTTTATTTTTCAAAAATGTCAAAGCCTCAGTTGTAGGGGAACATTTTTATTTTTCAAAAGTTTC
* * * *
24158540 AAAGCCTCAGTTGTGGGGGAACATTTTATTTTTCAAAGTTTTAAAGCCTCAATTGTGGGAGAGTA
66 AAAGCCTCAATTGTGAGGGAACATTTTATTTTTCAAAGTTTCAAAGCCTCAATTATGGGAGAGTA
24158605 TTTTATTTTCAAAAGTTTTAAAGTCTCAATTGT
131 TTTTATTTTCAAAAGTTTTAAAGTCTCAATTGT
24158638 ATAAAGCATT
Statistics
Matches: 142, Mismatches: 10, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
162 64 0.45
163 11 0.08
164 25 0.18
165 25 0.18
166 1 0.01
167 4 0.03
168 12 0.08
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (171 bp):
ATTTTATTTTTCAAAAATGTCAAAGCCTCAGTTGTAGGGGAACATTTTTATTTTTCAAAAGTTTC
AAAGCCTCAATTGTGAGGGAACATTTTATTTTTCAAAGTTTCAAAGCCTCAATTATGGGAGAGTA
TTTTATTTTCAAAAGTTTTAAAGTCTCAATTGTGGAGGAGT
Found at i:24158649 original size:41 final size:42
Alignment explanation
Indices: 24158312--24158876 Score: 284
Period size: 42 Copynumber: 13.4 Consensus size: 42
24158302 AGAGTGATCT
* * * *
24158312 CATTTTATTTTTCAAAAATTTCAAAGCCTCAGTTGTAGGG-GAG
1 CATTTTA-TTTTCAAAAGTTTTAAAGCCTCAATTGT-GGGAAAG
* *
24158355 CATTTTTATTTTTCAAAAGTTTCAAAGCCTCAATTGTGATGG--AT
1 CA-TTTTA-TTTTCAAAAGTTTTAAAGCCTCAATTGTG--GGAAAG
* * * *
24158399 CATTTTATTTTTC-AAAGTTTCAAAGCCTCAATTAT-GGAGAT
1 CATTTTA-TTTTCAAAAGTTTTAAAGCCTCAATTGTGGGAAAG
* *
24158440 CA-TTT-TTTTCAAAAGTTTTAAAAG-TTCAATTGT-GGAGGAG
1 CATTTTATTTTCAAAAGTTTT-AAAGCCTCAATTGTGGGA-AAG
* * * *
24158480 TATTTTATTTTTCAAAAG---TAAA-CCTTAGTTGTGGGGGAA-
1 CATTTTA-TTTTCAAAAGTTTTAAAGCCTCAATTGT-GGGAAAG
* * *
24158519 CATTTTATTTTCAAAAGTTTCAAAGCCTCAGTTGTGGGGGAA-
1 CATTTTATTTTCAAAAGTTTTAAAGCCTCAATTGT-GGGAAAG
*
24158561 CATTTTATTTTTC-AAAGTTTTAAAGCCTCAATTGTGGGAGAG
1 CATTTTA-TTTTCAAAAGTTTTAAAGCCTCAATTGTGGGAAAG
* * **
24158603 TATTTTATTTTCAAAAGTTTTAAAGTCTCAATTGT-ATAAAG
1 CATTTTATTTTCAAAAGTTTTAAAGCCTCAATTGTGGGAAAG
* * *
24158644 CATTTTATTTTAGAAAAGTTCATTTTTCAAAGTTTTAAAGCCTCAATTATGGGAGAG
1 CATTTTATTTT-CAAAAG-------TT-------TTAAAGCCTCAATTGTGGGAAAG
* * **
24158701 TATTTTATTTTCAAAAGTTTTAAAGTCTCAATTGTAAG-AAG
1 CATTTTATTTTCAAAAGTTTTAAAGCCTCAATTGTGGGAAAG
** * * *
24158742 CATTTTATTTTACAAAAGTTCCAAAGCCTTAGTTGTGGG-GAG
1 CATTTTATTTT-CAAAAGTTTTAAAGCCTCAATTGTGGGAAAG
* * * * *
24158784 CGTTTTATTTTCAAAAGTTCTAACA-CCTCAGTTGTAGGAAAA
1 CATTTTATTTTCAAAAGTTTTAA-AGCCTCAATTGTGGGAAAG
* *
24158826 CA--TT-TTTT-AAAAGTTTTAAAGCTTCAGTTGTGGG-AAG
1 CATTTTATTTTCAAAAGTTTTAAAGCCTCAATTGTGGGAAAG
24158863 CA-TTT-TTTTCAAAA
1 CATTTTATTTTCAAAA
24158877 AAAAAAAAAG
Statistics
Matches: 419, Mismatches: 60, Indels: 90
0.74 0.11 0.16
Matches are distributed among these distances:
37 5 0.01
38 42 0.10
39 42 0.10
40 14 0.03
41 68 0.16
42 146 0.35
43 29 0.07
44 35 0.08
45 2 0.00
49 4 0.01
56 19 0.05
57 13 0.03
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (42 bp):
CATTTTATTTTCAAAAGTTTTAAAGCCTCAATTGTGGGAAAG
Found at i:24158717 original size:56 final size:57
Alignment explanation
Indices: 24158610--24158719 Score: 134
Period size: 56 Copynumber: 1.9 Consensus size: 57
24158600 GAGTATTTTA
* * * *
24158610 TTTTCAAAAGTTTTAAAGTCTCAATTGTATAAAGCATTTTATTTTAGAAAAGTTCAT
1 TTTTCAAAAGTTTTAAAGCCTCAATTATAGAAAGCATTTTATTTTACAAAAGTTCAT
* * *
24158667 TTTTC-AAAGTTTTAAAGCCTCAATTATGGGAGAGTATTTTATTTT-CAAAAGTT
1 TTTTCAAAAGTTTTAAAGCCTCAATTAT-AGAAAGCATTTTATTTTACAAAAGTT
24158720 TTAAAGTCTC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
56 27 0.60
57 18 0.40
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.44
Consensus pattern (57 bp):
TTTTCAAAAGTTTTAAAGCCTCAATTATAGAAAGCATTTTATTTTACAAAAGTTCAT
Found at i:24158736 original size:98 final size:98
Alignment explanation
Indices: 24158567--24158762 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
24158557 GGAACATTTT
*
24158567 ATTTTTCAAAGTTTTAAAGCCTCAATTGTGGGAGAGTATTTTATTTTCAAAAGTTTTAAAGTCTC
1 ATTTTTCAAAGTTTTAAAGCCTCAATTATGGGAGAGTATTTTATTTTCAAAAGTTTTAAAGTCTC
*
24158632 AATTGTATA-AAGCATTTTATTTTAGAAAAGTTC
66 AATTGTA-AGAAGCATTTTATTTTACAAAAGTTC
24158665 ATTTTTCAAAGTTTTAAAGCCTCAATTATGGGAGAGTATTTTATTTTCAAAAGTTTTAAAGTCTC
1 ATTTTTCAAAGTTTTAAAGCCTCAATTATGGGAGAGTATTTTATTTTCAAAAGTTTTAAAGTCTC
24158730 AATTGTAAGAAGCATTTTATTTTACAAAAGTTC
66 AATTGTAAGAAGCATTTTATTTTACAAAAGTTC
24158763 CAAAGCCTTA
Statistics
Matches: 95, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
97 1 0.01
98 94 0.99
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (98 bp):
ATTTTTCAAAGTTTTAAAGCCTCAATTATGGGAGAGTATTTTATTTTCAAAAGTTTTAAAGTCTC
AATTGTAAGAAGCATTTTATTTTACAAAAGTTC
Found at i:24158790 original size:140 final size:140
Alignment explanation
Indices: 24158526--24158803 Score: 319
Period size: 140 Copynumber: 2.0 Consensus size: 140
24158516 GAACATTTTA
* * *
24158526 TTTTCAAAAGTTTCAAAGCCTCAGTTGTGGGGGAACATTTTATTTTTCAAAGTTTTAAAGCCTCA
1 TTTTCAAAAGTTTCAAAGCCTCAATTATGGGAGAACATTTTATTTTTCAAAGTTTTAAAGCCTCA
** * ** * *
24158591 ATTGTGGGAGAGTATTTTATTTTCAAAAGTTTTAAAGTCTCAATTGTATAAAGCATTTTATTTTA
66 ATTGTAAGAGAGCATTTTATTTTCAAAAGTTCCAAAGCCTCAATTGTAGAAAGCATTTTATTTT-
*
24158656 GAAAAGTTCAT
130 CAAAAGTTCAT
* ** *
24158667 TTTTC-AAAGTTTTAAAGCCTCAATTATGGGAGAGTATTTTA-TTTTCAAAAGTTTTAAAGTCTC
1 TTTTCAAAAGTTTCAAAGCCTCAATTATGGGAGAACATTTTATTTTTC-AAAGTTTTAAAGCCTC
* * * ** *
24158730 AATTGTAAGA-AGCATTTTATTTTACAAAAGTTCCAAAGCCTTAGTTGTGGGGAGCGTTTTATTT
65 AATTGTAAGAGAGCATTTTATTTT-CAAAAGTTCCAAAGCCTCAATTGTAGAAAGCATTTTATTT
24158794 TCAAAAGTTC
129 TCAAAAGTTC
24158804 TAACACCTCA
Statistics
Matches: 114, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
139 25 0.22
140 84 0.74
141 5 0.04
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.41
Consensus pattern (140 bp):
TTTTCAAAAGTTTCAAAGCCTCAATTATGGGAGAACATTTTATTTTTCAAAGTTTTAAAGCCTCA
ATTGTAAGAGAGCATTTTATTTTCAAAAGTTCCAAAGCCTCAATTGTAGAAAGCATTTTATTTTC
AAAAGTTCAT
Found at i:24159855 original size:24 final size:23
Alignment explanation
Indices: 24159775--24159936 Score: 120
Period size: 24 Copynumber: 7.1 Consensus size: 23
24159765 TTTATTTGCC
* *
24159775 TAATATATTTGTTTGCATGA-T-
1 TAATATATTTATTTGTATGATTA
* *
24159796 TAATATATTTATTTATGTGATT-
1 TAATATATTTATTTGTATGATTA
* *
24159818 TATTA-ATATATTTGTATGATTA
1 TAATATATTTATTTGTATGATTA
24159840 GTAATATATTTATTTGTATGATTA
1 -TAATATATTTATTTGTATGATTA
* *
24159864 T-ATTTAATTTGA-TTGCATGATTA
1 TAATAT-ATTT-ATTTGTATGATTA
* * *
24159887 TTAATATAATTAATTGTTTGATTA
1 -TAATATATTTATTTGTATGATTA
**
24159911 TTAATATATTTATTTACATGATTA
1 -TAATATATTTATTTGTATGATTA
24159935 TA
1 TA
24159937 TATTTAATTG
Statistics
Matches: 111, Mismatches: 21, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
21 29 0.26
22 8 0.07
23 22 0.20
24 49 0.44
25 3 0.03
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (23 bp):
TAATATATTTATTTGTATGATTA
Found at i:24159892 original size:47 final size:46
Alignment explanation
Indices: 24159775--24159921 Score: 140
Period size: 47 Copynumber: 3.2 Consensus size: 46
24159765 TTTATTTGCC
** * * *
24159775 TAATATATTTGTTTGCATGATTAATATATTTATTTATGTGATT-TAT
1 TAATATATTTGCATG-ATTATTAATATATTTATTTGTATGATTATAT
* *
24159821 TAATATATTTGTATGATTAGTAATATATTTATTTGTATGATTATATT
1 TAATATATTTGCATGATTATTAATATATTTATTTGTATGATTATA-T
* * * *
24159868 TAATTTGA-TTGCATGATTATTAATATAATTAATTGTTTGA-T-TAT
1 TAATAT-ATTTGCATGATTATTAATATATTTATTTGTATGATTATAT
24159912 TAATATATTT
1 TAATATATTT
24159922 ATTTACATGA
Statistics
Matches: 85, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
43 1 0.01
44 8 0.09
45 25 0.29
46 17 0.20
47 33 0.39
48 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.10, T:0.55
Consensus pattern (46 bp):
TAATATATTTGCATGATTATTAATATATTTATTTGTATGATTATAT
Found at i:24159983 original size:23 final size:21
Alignment explanation
Indices: 24159952--24160006 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
24159942 AATTGAATTT
*
24159952 TTTGTATGATTTATATGTTATAA
1 TTTGCATGATTTATAT-TT-TAA
24159975 TTTGCATGA-TTATATTTTAA
1 TTTGCATGATTTATATTTTAA
24159995 -TTGCATG-TTTAT
1 TTTGCATGATTTAT
24160007 TTACATGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 11 0.37
20 3 0.10
21 2 0.07
22 6 0.20
23 8 0.27
ACGTcount: A:0.27, C:0.04, G:0.13, T:0.56
Consensus pattern (21 bp):
TTTGCATGATTTATATTTTAA
Found at i:24160665 original size:2 final size:2
Alignment explanation
Indices: 24160658--24160690 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
24160648 TAGATTTTCA
*
24160658 AT AT AT AT AT AT AT AA AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24160691 TAATCTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:24161795 original size:20 final size:20
Alignment explanation
Indices: 24161745--24161795 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
24161735 TTTGTTAACA
*
24161745 ATAAATAAAAATTAATTAAT
1 ATAAATAAAAAATAATTAAT
*
24161765 AT-ATTAAAAAATAA-TAAT
1 ATAAATAAAAAATAATTAAT
24161783 ATAAATAAGAAAA
1 ATAAATAA-AAAA
24161796 AAGAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.23
19 14 0.54
20 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
ATAAATAAAAAATAATTAAT
Found at i:24162277 original size:20 final size:21
Alignment explanation
Indices: 24162236--24162277 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
24162226 ATAATATTTG
*
24162236 AAAATAAAAACAATAAATAAA
1 AAAATAAAAACAATAAAGAAA
*
24162257 AAAATAAAAA-AATCAAGAAA
1 AAAATAAAAACAATAAAGAAA
24162277 A
1 A
24162278 TTAATTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12
Consensus pattern (21 bp):
AAAATAAAAACAATAAAGAAA
Found at i:24162378 original size:30 final size:30
Alignment explanation
Indices: 24162342--24162403 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
24162332 TGTAGTTAAT
24162342 TGGTACCCTCTTAGACGGGCGCTGTGGAGG
1 TGGTACCCTCTTAGACGGGCGCTGTGGAGG
24162372 TGGTACCCTCTTAGACGGGCGCTGTGGAGG
1 TGGTACCCTCTTAGACGGGCGCTGTGGAGG
24162402 TG
1 TG
24162404 CTTATCCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.13, C:0.23, G:0.40, T:0.24
Consensus pattern (30 bp):
TGGTACCCTCTTAGACGGGCGCTGTGGAGG
Found at i:24162785 original size:23 final size:22
Alignment explanation
Indices: 24162759--24162801 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
24162749 AAAAGGGTCA
24162759 AAAATAAAAAACAAAACAAATCG
1 AAAATAAAAAACAAAA-AAATCG
*
24162782 AAAATAAAAAGCAAAAAAAT
1 AAAATAAAAAACAAAAAAAT
24162802 TCACACACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.77, C:0.09, G:0.05, T:0.09
Consensus pattern (22 bp):
AAAATAAAAAACAAAAAAATCG
Found at i:24173976 original size:100 final size:100
Alignment explanation
Indices: 24173793--24174383 Score: 433
Period size: 100 Copynumber: 5.8 Consensus size: 100
24173783 CAGATAAAAA
* * * *
24173793 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTCTTTCCAAAATGAGATTTTAAGGTTGTTGAG
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTCTTTACAAAATAAAATTTTAAAGTTGTTGAG
24173858 CCTCTGCTGAGAAGAGCCC-TTTCAAAGAT-GAGAT
66 CCTCTGCTGAGAAGAGCCCTTTTC-AAGATAGAGAT
* * *
24173892 TTTTAAAGTTGTTGAGCCTCTGTTGAGATGAGC-CATTTACAAAATAAAAATTTTAAATTTGTTG
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTC-TTTACAAAAT-AAAATTTTAAAGTTGTTG
*
24173956 AGCCTCTGCTGAGATGAGCCCTTTTCAAGATGAGAGAT
64 AGCCTCTGCTGAGAAGAGCCCTTTTCAAGAT-AGAGAT
** * * * * *
24173994 TTTTAAAGTTGTTGAGCCTCTATTGGGAGGAGCT-TTTCCAAGATGAGAGATTTTTTTAAAGTTA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTCTTTACAAAAT-A-A-A--ATTTTAAAGTTG
* ** *
24174058 TTGAGCCTCTGTTGA-AAGA-AACTTTTCTAAGAT-TAGAT
61 TTGAGCCTCTGCTGAGAAGAGCCCTTTTC-AAGATAGAGAT
* * * *
24174096 TTTTAAAGTTAAAGTTATTGAGCCTCTGCTGAGAGGAGCT-TTTCCAAGATGAGAGATTTTTTAA
1 TTTTAAAGTT---G---TTGAGCCTCTGCTGAGAGGAGCTCTTTACAAAAT-A-A-AATTTTAAA
* * ** *
24174160 GTTGTTGAGCCTTTGTTGAGAA-A-AACTTTTACAAGATA-AGAA
57 GTTGTTGAGCCTCTGCTGAGAAGAGCCCTTTT-CAAGATAGAGAT
* ** * * *
24174202 TTTTAAAGTTATTGAGTTTCTGCTGAGAGGAGCT-TTTTCAAGATGAGAGATTTTTAAAGTTGTT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTCTTTACAAAAT-A-A-AATTTTAAAGTTGTT
* * * * * * *
24174266 GAGTCTTTGTTAAGAGGAG--CTTTTACAAGATA-AAAA
63 GAGCCTCTGCTGAGAAGAGCCCTTTT-CAAGATAGAGAT
**
24174302 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCT-TTT-TTAAATAAAATTTTTAAAGTTGTTGA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTCTTTACAAAATAAAA-TTTTAAAGTTGTTGA
* *
24174365 GCCTCTGCTAAGAGGAGCC
65 GCCTCTGCTGAGAAGAGCC
24174384 ATTTAAATTT
Statistics
Matches: 419, Mismatches: 48, Indels: 50
0.81 0.09 0.10
Matches are distributed among these distances:
96 1 0.00
97 30 0.07
98 2 0.00
99 43 0.10
100 151 0.36
101 14 0.03
102 50 0.12
103 7 0.02
104 8 0.02
105 24 0.06
106 50 0.12
107 3 0.01
108 36 0.09
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (100 bp):
TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTCTTTACAAAATAAAATTTTAAAGTTGTTGAG
CCTCTGCTGAGAAGAGCCCTTTTCAAGATAGAGAT
Found at i:24174041 original size:51 final size:50
Alignment explanation
Indices: 24173793--24174382 Score: 534
Period size: 49 Copynumber: 11.7 Consensus size: 50
24173783 CAGATAAAAA
*
24173793 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTCTTTCCAAAAT-GAGA-
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCT-TTTCCAAGATAGAGAT
* * * *
24173842 TTTTAAGGTTGTTGAGCCTCTGCTGAGAAGAGCCCTTTCAAAGAT-GAGAT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTCCAAGATAGAGAT
* * * * * * *
24173892 TTTTAAAGTTGTTGAGCCTCTGTTGAGATGAGCCATTTACAAAATA-AAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTCCAAGATAGAGAT
* *
24173942 TTTTAAATTTGTTGAGCCTCTGCTGAGATGAGCCCTTTT-CAAGATGAGAGAT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG--CTTTTCCAAGAT-AGAGAT
** *
24173994 TTTTAAAGTTGTTGAGCCTCTATTGGGAGGAGCTTTTCCAAGATGAGAGATTT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGAT-AGAGA--T
* * * * * * *
24174047 TTTTAAAGTTATTGAGCCTCTGTTGAAAGAAACTTTTCTAAGAT-TAGAT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATAGAGAT
24174096 TTTTAAAGTTAAAGTTATTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAGAT
1 TTTTAAAGTT---G---TTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGAT-AGAGAT
* * * ** * * *
24174153 TTTTTAAGTTGTTGAGCCTTTGTTGAGAAAAACTTTTACAAGATA-AGAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATAGAGAT
* ** *
24174202 TTTTAAAGTTATTGAGTTTCTGCTGAGAGGAGCTTTTTCAAGATGAGAGAT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGAT-AGAGAT
* * * * * * *
24174253 TTTTAAAGTTGTTGAGTCTTTGTTAAGAGGAGCTTTTACAAGATA-AAAA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATAGAGAT
** *
24174302 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTTAA-ATA-AAAT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATAGAGAT
*
24174350 TTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGC
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC
24174383 CATTTAAATT
Statistics
Matches: 447, Mismatches: 75, Indels: 39
0.80 0.13 0.07
Matches are distributed among these distances:
48 38 0.09
49 127 0.28
50 84 0.19
51 89 0.20
52 29 0.06
53 38 0.09
54 1 0.00
55 28 0.06
57 13 0.03
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (50 bp):
TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATAGAGAT
Found at i:24174120 original size:55 final size:54
Alignment explanation
Indices: 24174049--24174212 Score: 160
Period size: 55 Copynumber: 3.1 Consensus size: 54
24174039 AGAGATTTTT
* *
24174049 TTAAAGTTATTGAGCCTCTGTTGAAAGAAACTTTTCTAAGATTAGATTTTTAAAG
1 TTAAAGTTATTGAGCCTCTGTTGAAAGAAACTTTTC-AAGATAAGAATTTTAAAG
* * * * *
24174104 TTAAAGTTATTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGAGATTTT----
1 TTAAAGTTATTGAGCCTCTGTTGAAAGAAACTTTT-CAAGATAAGA-ATTTTAAAG
* *
24174156 TT-AAGTTGTTGAGCCTTTGTTGAGAA-AAACTTTTACAAGATAAGAATTTTAAAG
1 TTAAAGTTATTGAGCCTCTGTTGA-AAGAAACTTTT-CAAGATAAGAATTTTAAAG
24174210 TTA
1 TTA
24174213 TTGAGTTTCT
Statistics
Matches: 87, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
50 5 0.06
51 33 0.38
52 3 0.03
54 2 0.02
55 39 0.45
56 5 0.06
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (54 bp):
TTAAAGTTATTGAGCCTCTGTTGAAAGAAACTTTTCAAGATAAGAATTTTAAAG
Found at i:24174618 original size:4 final size:4
Alignment explanation
Indices: 24174611--24174659 Score: 54
Period size: 4 Copynumber: 13.5 Consensus size: 4
24174601 TTTTTATTTT
*
24174611 TTTC TTTC -TTC TTTC TTTC TTTC TTTC -TT- TTTC CTTC -TTC -TTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
24174654 TTTC TT
1 TTTC TT
24174660 ATCCGATTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
3 13 0.32
4 27 0.68
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:24174622 original size:7 final size:7
Alignment explanation
Indices: 24174612--24174659 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
24174602 TTTTATTTTT
24174612 TTCTTTC
1 TTCTTTC
24174619 TTCTTTC
1 TTCTTTC
*
24174626 TT-TCT-
1 TTCTTTC
24174631 TTCTTTC
1 TTCTTTC
24174638 TT-TTTCC
1 TTCTTT-C
24174645 TTC-TTC
1 TTCTTTC
24174651 TTCTTTC
1 TTCTTTC
24174658 TT
1 TT
24174660 ATCCGATTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
5 2 0.06
6 11 0.32
7 21 0.62
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCTTTC
Found at i:24175880 original size:20 final size:20
Alignment explanation
Indices: 24175830--24175880 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
24175820 TTTGTTAACA
*
24175830 ATAAATAAAAATTAATTAAT
1 ATAAATAAAAAATAATTAAT
*
24175850 AT-ATTAAAAAATAA-TAAT
1 ATAAATAAAAAATAATTAAT
24175868 ATAAATAAGAAAA
1 ATAAATAA-AAAA
24175881 AAAGAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.23
19 14 0.54
20 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
ATAAATAAAAAATAATTAAT
Found at i:24176062 original size:16 final size:16
Alignment explanation
Indices: 24176032--24176074 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
24176022 TTTTTCCTTC
24176032 AAAATTAA-AAATAAA
1 AAAATTAATAAATAAA
*
24176047 AAAATTAATTAATAAA
1 AAAATTAATAAATAAA
*
24176063 ATAATTAATAAA
1 AAAATTAATAAA
24176075 ATTTTTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATTAATAAATAAA
Found at i:24176069 original size:12 final size:12
Alignment explanation
Indices: 24176047--24176076 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
24176037 TAAAAATAAA
24176047 AAAATTAATTAAT
1 AAAA-TAATTAAT
24176060 AAAATAATTAAT
1 AAAATAATTAAT
24176072 AAAAT
1 AAAAT
24176077 TTTTGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATAATTAAT
Found at i:24176360 original size:20 final size:21
Alignment explanation
Indices: 24176319--24176360 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
24176309 ATAATATTTG
*
24176319 AAAATAAAAACAATAAATAAA
1 AAAATAAAAACAATAAAGAAA
*
24176340 AAAATAAAAA-AATCAAGAAA
1 AAAATAAAAACAATAAAGAAA
24176360 A
1 A
24176361 TTAATTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12
Consensus pattern (21 bp):
AAAATAAAAACAATAAAGAAA
Found at i:24185923 original size:13 final size:13
Alignment explanation
Indices: 24185905--24185929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24185895 AGCTGCTAAT
24185905 GTGTGATTTCTGG
1 GTGTGATTTCTGG
24185918 GTGTGATTTCTG
1 GTGTGATTTCTG
24185930 AGTTATTGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.36, T:0.48
Consensus pattern (13 bp):
GTGTGATTTCTGG
Found at i:24189513 original size:2 final size:2
Alignment explanation
Indices: 24189506--24189535 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24189496 TCAAATTCTA
24189506 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
24189536 TTTCAGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24192758 original size:125 final size:125
Alignment explanation
Indices: 24192533--24192774 Score: 369
Period size: 125 Copynumber: 1.9 Consensus size: 125
24192523 TGTGTTTAAA
* * * * *
24192533 TAAATAAGATACATATGTTTGTTTGAGGAACATCAAGCATACAGATCTACAGAACAGGAAGAGCT
1 TAAATAAGATACATATCTTCGTTAGAGAAACATCAAGCATACAGATCTACAGAACAAGAAGAGCT
* ** *
24192598 GGGTGATTTTCTGGCAAAGATGAGAAAGAATTTCTAAAGCACAGAAATATAATATGTGTT
66 GGATGATTTTCCAGCAAAGATGAGAAAGAAGTTCTAAAGCACAGAAATATAATATGTGTT
*
24192658 TAAATAAGATACATATCTTCGTTAGTA-AAACATCAAGCATACAGATCTACAGAACAAGAAGAGT
1 TAAATAAGATACATATCTTCGTTAG-AGAAACATCAAGCATACAGATCTACAGAACAAGAAGAGC
*
24192722 TGGATTATTTTCCAGCAAAGATGAGAAAGAAGTTCTAAAGCACAGAAATATAA
65 TGGATGATTTTCCAGCAAAGATGAGAAAGAAGTTCTAAAGCACAGAAATATAA
24192775 GAAGACTTCT
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
125 104 0.99
126 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (125 bp):
TAAATAAGATACATATCTTCGTTAGAGAAACATCAAGCATACAGATCTACAGAACAAGAAGAGCT
GGATGATTTTCCAGCAAAGATGAGAAAGAAGTTCTAAAGCACAGAAATATAATATGTGTT
Found at i:24201588 original size:163 final size:163
Alignment explanation
Indices: 24201319--24201647 Score: 606
Period size: 163 Copynumber: 2.0 Consensus size: 163
24201309 AAATACGGAT
*
24201319 TTCTTTTGATATCTACAAAAAAAAAAAAATATGCAATCAAGGTAGTAAGCAGTGGAGGTTCATAA
1 TTCTTTTGATATCTACAAAAAAAAAAAAATACGCAATCAAGGTAGTAAGCAGTGGAGGTTCATAA
24201384 AGGGTGTGGCATCGAATGCATCAAACAGTTTGATGTATATGATTTT-AAAAAAAAAAAAATCCAA
66 AGGGTGTGGCATCGAATGCATCAAACAGTTTGATGTATATGATTTTAAAAAAAAAAAAAATCCAA
24201448 CAGCAGGCAAAACCCCAAAGAATTGCAATGAAA
131 CAGCAGGCAAAACCCCAAAGAATTGCAATGAAA
*
24201481 TTCTTTTGATATCTACAAGAAAAATAAAAATACGCAATCAAGGTAGTAAGCAGTGGAGGTTCATA
1 TTCTTTTGATATCTACAA-AAAAAAAAAAATACGCAATCAAGGTAGTAAGCAGTGGAGGTTCATA
*
24201546 AAGGGTGTGGCATCGAATGCATCAAATAGTTTGATGTATATGATTTTAAAAAAAAAAAAAAATCC
65 AAGGGTGTGGCATCGAATGCATCAAACAGTTTGATGTATATGATTTT-AAAAAAAAAAAAAATCC
24201611 AACAGCAGGCAAAACCCCAAAGAATTGCAATGAAA
129 AACAGCAGGCAAAACCCCAAAGAATTGCAATGAAA
24201646 TT
1 TT
24201648 GGAAGAGAAA
Statistics
Matches: 161, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
162 18 0.11
163 90 0.56
165 53 0.33
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (163 bp):
TTCTTTTGATATCTACAAAAAAAAAAAAATACGCAATCAAGGTAGTAAGCAGTGGAGGTTCATAA
AGGGTGTGGCATCGAATGCATCAAACAGTTTGATGTATATGATTTTAAAAAAAAAAAAAATCCAA
CAGCAGGCAAAACCCCAAAGAATTGCAATGAAA
Found at i:24202705 original size:15 final size:16
Alignment explanation
Indices: 24202681--24202715 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
24202671 TTTGTTTATT
*
24202681 AAATATTATCTTTTTA
1 AAATATTATCTGTTTA
24202697 AAATA-TATCTGTTTA
1 AAATATTATCTGTTTA
24202712 AAAT
1 AAAT
24202716 TAAAAGTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (16 bp):
AAATATTATCTGTTTA
Found at i:24206799 original size:2 final size:2
Alignment explanation
Indices: 24206794--24206833 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
24206784 TTATTGAGCA
24206794 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
24206834 AAACATCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:24214030 original size:29 final size:29
Alignment explanation
Indices: 24213998--24214057 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
24213988 AAATTACAAT
* *
24213998 AAAATATATAATATGATATTTTAATTTTA
1 AAAATATATAATATGATATTTAAATTATA
* *
24214027 AAAATTTTTAATATGATATTTAAATTATA
1 AAAATATATAATATGATATTTAAATTATA
24214056 AA
1 AA
24214058 TAAATTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (29 bp):
AAAATATATAATATGATATTTAAATTATA
Found at i:24214065 original size:28 final size:28
Alignment explanation
Indices: 24213998--24214066 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
24213988 AAATTACAAT
* *
24213998 AAAATATATAATATGATATTTTAATTTTA
1 AAAATAT-TAATATGATATTTAAATTATA
*
24214027 AAAATTTTTAATATGATATTTAAATTATA
1 AAAA-TATTAATATGATATTTAAATTATA
24214056 AATAA-ATTAAT
1 AA-AATATTAAT
24214067 TAATATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
28 5 0.15
29 25 0.74
30 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (28 bp):
AAAATATTAATATGATATTTAAATTATA
Found at i:24216189 original size:17 final size:18
Alignment explanation
Indices: 24216150--24216198 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
24216140 GAGAAAAAAA
*
24216150 TATTTTTTTT-TTTTTAG
1 TATTTTTTTTGTTTTGAG
*
24216167 TGTTTTTTTTGTTTTGAG
1 TATTTTTTTTGTTTTGAG
24216185 -A-TTTTTTTGTTTTG
1 TATTTTTTTTGTTTTG
24216199 TTTTGTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.46
17 9 0.32
18 6 0.21
ACGTcount: A:0.08, C:0.00, G:0.14, T:0.78
Consensus pattern (18 bp):
TATTTTTTTTGTTTTGAG
Found at i:24216656 original size:23 final size:22
Alignment explanation
Indices: 24216626--24216668 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
24216616 ATGTGTGTGA
24216626 ATTTTTTTGCTTTTTATTTTCG
1 ATTTTTTTGCTTTTTATTTTCG
*
24216648 ATTTGTTTTGTTTTTTATTTT
1 ATTT-TTTTGCTTTTTATTTT
24216669 TGACCCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.09, C:0.05, G:0.09, T:0.77
Consensus pattern (22 bp):
ATTTTTTTGCTTTTTATTTTCG
Found at i:24217636 original size:18 final size:19
Alignment explanation
Indices: 24217613--24217648 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
24217603 TTTTCTTATT
*
24217613 TATATT-ATTATTTTTTAA
1 TATATTAATTAATTTTTAA
24217631 TATATTAATTAATTTTTA
1 TATATTAATTAATTTTTA
24217649 TTTATTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATATTAATTAATTTTTAA
Found at i:24217855 original size:204 final size:205
Alignment explanation
Indices: 24217456--24217855 Score: 458
Period size: 204 Copynumber: 2.0 Consensus size: 205
24217446 ATTTTGAAGG
* ***
24217456 AAAAAAAATTTTATTGTATTGAAGTTTTTTCTATAAATATTCTAATACACTGGTAATATTTTAAA
1 AAAAAAAAATTTATTGTATTGAAAAATTTTCTATAAATATTCTAATACACTGGTAATATTTTAAA
* ** *
24217521 AAAAATCTTCTCACCTAGAGATTTCTTAAAGCATCTTTACTCAAAATACTTTTGGAATCCTATCA
66 AAAAATCTTCTCACCTAGAGATTTCATAAAGCATCACTACTCAAAATACTTTTGAAATCCTATCA
** * * * **
24217586 TTGGATAAAATTTTCTTTTTTCTTATTTATATTATTATTTTTTAATATATTAATTAATTTTTATT
131 TTGGATAAAATTCCCTTTTTTATTATTTATATTATTATTTATTAATATATTAATAAAAATTTATT
24217651 TATTGTTAAC
196 TATTGTTAAC
*
24217661 AAAAAAAAATTTATTGTATTGAAAAATTTT-TATAAATACTTC-AATACACTGGTAGTA-TTTAA
1 AAAAAAAAATTTATTGTATTGAAAAATTTTCTATAAATA-TTCTAATACACTGGTAATATTTTAA
* * * * **
24217723 AAAAATTCTTCTCATCTAGAGATTTCAT-AGGCATCACTGCTCGGAATACTTTT-AAAT-CTCAT
65 AAAAAATCTTCTCACCTAGAGATTTCATAAAGCATCACTACTCAAAATACTTTTGAAATCCT-AT
*
24217785 CATTGGATAAAATTCCCTTTTCTTATATTTTTTATCAATT-TTATATTATTAA-ATATT-ATAAA
129 CATTGGATAAAATTCCC-TTT-TT-TATTATTTAT--ATTATTAT-TTATTAATATATTAATAAA
24217847 AATTTATTT
188 AATTTATTT
24217856 TGATAAATTT
Statistics
Matches: 164, Mismatches: 23, Indels: 17
0.80 0.11 0.08
Matches are distributed among these distances:
200 2 0.01
201 20 0.12
202 22 0.13
203 32 0.20
204 41 0.25
205 38 0.23
206 9 0.05
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (205 bp):
AAAAAAAAATTTATTGTATTGAAAAATTTTCTATAAATATTCTAATACACTGGTAATATTTTAAA
AAAAATCTTCTCACCTAGAGATTTCATAAAGCATCACTACTCAAAATACTTTTGAAATCCTATCA
TTGGATAAAATTCCCTTTTTTATTATTTATATTATTATTTATTAATATATTAATAAAAATTTATT
TATTGTTAAC
Found at i:24219413 original size:19 final size:22
Alignment explanation
Indices: 24219391--24219445 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 22
24219381 AATCATGTAA
24219391 ATAAACATGC-AATTA-AA-AT
1 ATAAACATGCAAATTATAACAT
*
24219410 ATAATCATGCAAATTATAACAT
1 ATAAACATGCAAATTATAACAT
*
24219432 ATAAATCATACAAA
1 ATAAA-CATGCAAA
24219446 AATATTCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 9 0.31
20 5 0.17
21 2 0.07
22 6 0.21
23 7 0.24
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.27
Consensus pattern (22 bp):
ATAAACATGCAAATTATAACAT
Found at i:24219420 original size:54 final size:52
Alignment explanation
Indices: 24219341--24219474 Score: 164
Period size: 54 Copynumber: 2.5 Consensus size: 52
24219331 ATCATGTAAT
* *
24219341 CATGCAATTAAATATATAATTATGCAATTATTAATACATAAATCATGTA-AATAAA
1 CATGCAATTAAATATATAATCATGCAATTA-TAACACATAAATCA--TACAA-AAA
*
24219396 CATGCAATTAAA-ATATAATCATGCAAATTATAACATATAAATCATACAAAAA
1 CATGCAATTAAATATATAATCATGC-AATTATAACACATAAATCATACAAAAA
* *
24219448 TATTCAATTAAATATATAATCATGCAA
1 CATGCAATTAAATATATAATCATGCAA
24219475 ATAAATATAT
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
52 17 0.24
53 14 0.20
54 23 0.32
55 17 0.24
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.32
Consensus pattern (52 bp):
CATGCAATTAAATATATAATCATGCAATTATAACACATAAATCATACAAAAA
Found at i:24219440 original size:23 final size:21
Alignment explanation
Indices: 24219391--24219445 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 21
24219381 AATCATGTAA
24219391 ATAAA-CATGC-AATTAAAAT
1 ATAAATCATGCAAATTAAAAT
24219410 AT-AATCATGCAAATTATAACAT
1 ATAAATCATGCAAATTA-AA-AT
*
24219432 ATAAATCATACAAA
1 ATAAATCATGCAAA
24219446 AATATTCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.07
19 7 0.23
20 5 0.17
21 2 0.07
22 4 0.13
23 10 0.33
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAAATCATGCAAATTAAAAT
Found at i:24219490 original size:24 final size:24
Alignment explanation
Indices: 24219463--24219622 Score: 119
Period size: 24 Copynumber: 7.0 Consensus size: 24
24219453 AATTAAATAT
24219463 ATAATCATGCAAATAAATATATTA
1 ATAATCATGCAAATAAATATATTA
** * *
24219487 ATAATCAAACAATTAATTATATTA
1 ATAATCATGCAAATAAATATATTA
*
24219511 ATAATCATGC-AATCAAAT-TA-AA
1 ATAATCATGCAAAT-AAATATATTA
*
24219533 TATAATCATACAAATAAATATATTA
1 -ATAATCATGCAAATAAATATATTA
* *
24219558 CTAATCAT----ACAAATATATTA
1 ATAATCATGCAAATAAATATATTA
24219578 ATAAATCA--CATAATAAATATA-T-
1 AT-AATCATGCA-AATAAATATATTA
*
24219600 -TAATCATGCAAAAAAATATATTA
1 ATAATCATGCAAATAAATATATTA
24219623 GGCAAATAAA
Statistics
Matches: 106, Mismatches: 16, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
20 17 0.16
21 15 0.14
22 4 0.04
23 18 0.17
24 51 0.48
25 1 0.01
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
ATAATCATGCAAATAAATATATTA
Found at i:24219511 original size:53 final size:52
Alignment explanation
Indices: 24219400--24219522 Score: 139
Period size: 48 Copynumber: 2.4 Consensus size: 52
24219390 AATAAACATG
*
24219400 CAATTAAAATATAATCATGCAAATTATAACATATAAATCATACAAAAATATT
1 CAATTAAAATATAATCATGCAAATTATAACATATAAATAATACAAAAATATT
* * *
24219452 CAATTAAATATATAATCATGCAAA-TA-AATATATTAATAAT-CAAACA-ATT
1 CAATTAAA-ATATAATCATGCAAATTATAACATATAAATAATACAAAAATATT
* *
24219501 -AATTATATTAATAATCATGCAA
1 CAATTAAAAT-ATAATCATGCAA
24219523 TCAAATTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
47 1 0.02
48 18 0.29
49 3 0.05
50 5 0.08
51 11 0.17
52 10 0.16
53 15 0.24
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (52 bp):
CAATTAAAATATAATCATGCAAATTATAACATATAAATAATACAAAAATATT
Found at i:24219536 original size:71 final size:66
Alignment explanation
Indices: 24219461--24219622 Score: 184
Period size: 71 Copynumber: 2.4 Consensus size: 66
24219451 TCAATTAAAT
**
24219461 ATATAATCATGCAAATAAATATATTAATAATCAAACAATTAATTATATTAAT-AATCATGCAATC
1 ATATAATCATGCAAATAAATATATTAATAATCAAAC-A--AA-TATATTAATAAATCACACAAT-
24219525 AAATTAA
61 AAA-TAA
* * * *
24219532 ATATAATCATACAAATAAATATATTACTAATCATACAAATATATTAATAAATCACATAATAAATA
1 ATATAATCATGCAAATAAATATATTAATAATCAAACAAATATATTAATAAATCACACAATAAATA
*
24219597 T
66 A
*
24219598 AT-TAATCATGCAAAAAAATATATTA
1 ATATAATCATGCAAATAAATATATTA
24219623 GGCAAATAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
65 21 0.26
66 4 0.05
67 12 0.15
68 10 0.12
70 1 0.01
71 33 0.41
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (66 bp):
ATATAATCATGCAAATAAATATATTAATAATCAAACAAATATATTAATAAATCACACAATAAATA
A
Found at i:24219555 original size:47 final size:45
Alignment explanation
Indices: 24219463--24219603 Score: 135
Period size: 47 Copynumber: 3.0 Consensus size: 45
24219453 AATTAAATAT
* * * *
24219463 ATAATCATGCAAATAAATATATTAATAATCAAACAATTAATTATATTA
1 ATAATCATACAAATAAAT-TAAT-ATAATC-AACAAATAAATATATTA
*
24219511 ATAATCATGC-AATCAAATTAAATATAATCATACAAATAAATATATTA
1 ATAATCATACAAAT-AAATT-AATATAATCA-ACAAATAAATATATTA
* *
24219558 CTAATCATACAAATATATTAATA-AATC-ACATAATAAATATATTA
1 ATAATCATACAAATAAATTAATATAATCAACA-AATAAATATATTA
24219602 AT
1 AT
24219604 CATGCAAAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
43 3 0.04
44 14 0.17
45 4 0.05
46 5 0.06
47 36 0.44
48 19 0.23
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.34
Consensus pattern (45 bp):
ATAATCATACAAATAAATTAATATAATCAACAAATAAATATATTA
Found at i:24220601 original size:37 final size:38
Alignment explanation
Indices: 24220521--24220600 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
24220511 TTTTTTTTGA
*
24220521 AAAAAATG-CTTCCCACAACTGAAGCTTTAAAACTTTT
1 AAAAAATGTTTTCCCACAACTGAAGCTTTAAAACTTTT
* * * *
24220558 AAAAAATGTTTTCCTACAACTGAGGTTTTAGAACTTTT
1 AAAAAATGTTTTCCCACAACTGAAGCTTTAAAACTTTT
*
24220596 GAAAA
1 AAAAA
24220601 TAAAACGCTC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 8 0.22
38 28 0.78
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (38 bp):
AAAAAATGTTTTCCCACAACTGAAGCTTTAAAACTTTT
Found at i:24220633 original size:41 final size:41
Alignment explanation
Indices: 24220573--24220724 Score: 144
Period size: 42 Copynumber: 3.7 Consensus size: 41
24220563 ATGTTTTCCT
*
24220573 ACAACTGAGGTTTTAGAACTTTTGAAAATAAAACGCTCCCC
1 ACAACTGAGGCTTTAGAACTTTTGAAAATAAAACGCTCCCC
* * * * **
24220614 ACAACTAAGGCTTTGGAACTTTTGTAAAATAAAATGCTTCTT
1 ACAACTGAGGCTTTAGAACTTTTG-AAAATAAAACGCTCCCC
* * * **
24220656 ACAATTGAGACTTTAAAACTTTTGAAAATAAAATACTCTCCC
1 ACAACTGAGGCTTTAGAACTTTTGAAAATAAAACGCTC-CCC
* * *
24220698 ATAATTGAGGCTTTAAAAC-TTTGAAAA
1 ACAACTGAGGCTTTAGAACTTTTGAAAA
24220725 ATGAACTTTT
Statistics
Matches: 91, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
41 41 0.45
42 50 0.55
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.32
Consensus pattern (41 bp):
ACAACTGAGGCTTTAGAACTTTTGAAAATAAAACGCTCCCC
Found at i:24220783 original size:41 final size:41
Alignment explanation
Indices: 24220737--24221078 Score: 186
Period size: 42 Copynumber: 8.3 Consensus size: 41
24220727 GAACTTTTCT
* *
24220737 AAAATAAAATGCT-TTATACAATTGAGACTTTAAAACTTTG
1 AAAATAAAATGCTCTCACACAATTGAGACTTTAAAACTTTG
* * *
24220777 AAAAATAAAATACTCTCCCACAATTGAGGCTTTAAAACTTTG
1 -AAAATAAAATGCTCTCACACAATTGAGACTTTAAAACTTTG
* * * * * *
24220819 AAAATAAAATGTTCCCCCACAACTGAGGCTTTGAAACTTTTG
1 AAAATAAAATGCTCTCACACAATTGAGACTTTAAAAC-TTTG
* * * * * *
24220861 AAAATAAAATGTTCCCCCACAACTAAG-GTTT---ACTTTTG
1 AAAATAAAATGCTCTCACACAATTGAGACTTTAAAAC-TTTG
* *
24220899 AAAAATAAAATACTCCTC-CATAATTGA-ACTTTTAAAACTTTTG
1 -AAAATAAAATGCT-CTCACACAATTGAGAC-TTTAAAAC-TTTG
* * * *
24220942 -AAA-AAAATGATCTC-CATAATTGAGGCTTTGAAACTTTG
1 AAAATAAAATGCTCTCACACAATTGAGACTTTAAAACTTTG
* * *
24220980 AAAAATAAAATGATC-CATCACAATTGAGGCTTTGAAACTTTTG
1 -AAAATAAAATGCTCTCA-CACAATTGAGACTTTAAAAC-TTTG
* * * **
24221023 AAAAATAAAAATGCTC-CCCTACAACTGAGGCTTTGAAATTTTTG
1 -AAAAT-AAAATGCTCTCAC-ACAATTGAGACTTT-AAAACTTTG
24221067 AAAAATAAAATG
1 -AAAATAAAATG
24221079 AGATCACTCT
Statistics
Matches: 252, Mismatches: 30, Indels: 36
0.79 0.09 0.11
Matches are distributed among these distances:
38 11 0.04
39 36 0.14
40 16 0.06
41 59 0.23
42 72 0.29
43 24 0.10
44 32 0.13
45 2 0.01
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (41 bp):
AAAATAAAATGCTCTCACACAATTGAGACTTTAAAACTTTG
Found at i:24220802 original size:98 final size:98
Alignment explanation
Indices: 24220629--24220822 Score: 338
Period size: 98 Copynumber: 2.0 Consensus size: 98
24220619 TAAGGCTTTG
*
24220629 GAACTTTTGTAAAATAAAATGCTTCTTACAATTGAGACTTTAAAACTTTTGAAAATAAAATACTC
1 GAACTTTTCTAAAATAAAATGCTTCTTACAATTGAGACTTTAAAACTTTTGAAAATAAAATACTC
*
24220694 TCCCATAATTGAGGCTTTAAAACTTTGAAAAAT
66 TCCCACAATTGAGGCTTTAAAACTTTGAAAAAT
24220727 GAACTTTTCTAAAATAAAATGCTT-TATACAATTGAGACTTTAAAAC-TTTGAAAAATAAAATAC
1 GAACTTTTCTAAAATAAAATGCTTCT-TACAATTGAGACTTTAAAACTTTTG-AAAATAAAATAC
24220790 TCTCCCACAATTGAGGCTTTAAAACTTTGAAAA
64 TCTCCCACAATTGAGGCTTTAAAACTTTGAAAA
24220823 TAAAATGTTC
Statistics
Matches: 92, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
97 5 0.05
98 87 0.95
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.34
Consensus pattern (98 bp):
GAACTTTTCTAAAATAAAATGCTTCTTACAATTGAGACTTTAAAACTTTTGAAAATAAAATACTC
TCCCACAATTGAGGCTTTAAAACTTTGAAAAAT
Found at i:24220980 original size:81 final size:85
Alignment explanation
Indices: 24220737--24221079 Score: 263
Period size: 81 Copynumber: 4.1 Consensus size: 85
24220727 GAACTTTTCT
* ** *
24220737 AAAATAAAATGCTTTAT-ACAATTGAGACTTTAAAAC-TTTGAAAAATAAAAT-ACTCTCCC-AC
1 AAAATAAAATGATCCATCACAATTGAGACTTTAAAACTTTTGAAATA-AAAATGA-TC-CCCTAC
* *
24220798 AATTGAGGCTTT-AAAACTTTG-
63 AACTGAGGCTTTGAAATCTTTGA
* ** * * * * *
24220819 AAAATAAAATGTTCCCCCACAACTGAGGCTTTGAAACTTTTGAAA-ATAAAATGTTCCCCCACAA
1 AAAATAAAATGATCCATCACAATTGAGACTTTAAAACTTTTGAAATA-AAAATGATCCCCTACAA
* *
24220883 CTAAGG-TTT--ACT-TTTGA
65 CTGAGGCTTTGAAATCTTTGA
* * *
24220900 AAAATAAAAT-ACTCC-TCCATAATTGA-ACTTTTAAAACTTTTG-AA-AAAAATGATCTCC-AT
1 AAAATAAAATGA-TCCAT-CACAATTGAGAC-TTTAAAACTTTTGAAATAAAAATGATCCCCTAC
*
24220959 AATTGAGGCTTTGAAA-CTTTGA
63 AACTGAGGCTTTGAAATCTTTGA
* * *
24220981 AAAATAAAATGATCCATCACAATTGAGGCTTTGAAACTTTTGAAAAATAAAAATGCTCCCCTACA
1 AAAATAAAATGATCCATCACAATTGAGACTTTAAAACTTTTG--AAATAAAAATGATCCCCTACA
*
24221046 ACTGAGGCTTTGAAATTTTTGA
64 ACTGAGGCTTTGAAATCTTTGA
24221068 AAAATAAAATGA
1 AAAATAAAATGA
24221080 GATCACTCTT
Statistics
Matches: 207, Mismatches: 33, Indels: 37
0.75 0.12 0.13
Matches are distributed among these distances:
78 7 0.03
79 13 0.06
80 8 0.04
81 72 0.35
82 21 0.10
83 33 0.16
84 9 0.04
85 11 0.05
86 16 0.08
87 17 0.08
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (85 bp):
AAAATAAAATGATCCATCACAATTGAGACTTTAAAACTTTTGAAATAAAAATGATCCCCTACAAC
TGAGGCTTTGAAATCTTTGA
Found at i:24222549 original size:32 final size:32
Alignment explanation
Indices: 24222513--24222593 Score: 110
Period size: 32 Copynumber: 2.5 Consensus size: 32
24222503 TTAGTTTAAG
* * *
24222513 TTTTTCTTTTTCTTTTTTTTTTCTTTTTTACT
1 TTTTTATTTTTATTTTTATTTTCTTTTTTACT
*
24222545 TTTTTATTTTTATTTTTATTTTGTTTTTTACT
1 TTTTTATTTTTATTTTTATTTTCTTTTTTACT
24222577 TTTTTATTTATT-TTTTT
1 TTTTTATTT-TTATTTTT
24222594 GCACACCTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 42 0.95
33 2 0.05
ACGTcount: A:0.09, C:0.06, G:0.01, T:0.84
Consensus pattern (32 bp):
TTTTTATTTTTATTTTTATTTTCTTTTTTACT
Found at i:24222554 original size:5 final size:6
Alignment explanation
Indices: 24222513--24222591 Score: 56
Period size: 6 Copynumber: 12.8 Consensus size: 6
24222503 TTAGTTTAAG
* * *
24222513 TTTTTC TTTTTC TTTTT- TTTTTCT TTTTTA CTTTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTT-A TTTTTA --TTTTTA TTTTTA TTTTTA
*
24222563 TTTTGT- TTTTTA CTTTTT- TATTTA TTTTT
1 TTTT-TA TTTTTA -TTTTTA TTTTTA TTTTT
24222592 TTGCACACCT
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
5 10 0.16
6 35 0.56
7 11 0.18
8 6 0.10
ACGTcount: A:0.09, C:0.06, G:0.01, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:24228792 original size:24 final size:24
Alignment explanation
Indices: 24228762--24228823 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
24228752 AATATCATTC
*
24228762 AAATATAATATTA-ATCATGCAAT
1 AAATATAATATCATATCATGCAAT
*
24228785 AACATATAATATCATATTATGCAAT
1 AA-ATATAATATCATATCATGCAAT
*
24228810 AAATATAAAATCAT
1 AAATATAATATCAT
24228824 GCAATAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.06
24 21 0.62
25 11 0.32
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (24 bp):
AAATATAATATCATATCATGCAAT
Found at i:24228834 original size:3 final size:3
Alignment explanation
Indices: 24228826--24228893 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
24228816 AAAATCATGC
24228826 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24228874 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
24228894 CAAATAAATA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:24229099 original size:24 final size:24
Alignment explanation
Indices: 24229072--24229231 Score: 144
Period size: 24 Copynumber: 7.0 Consensus size: 24
24229062 ATTAAATATG
24229072 TAATCATGCAAATAAATATATTAA
1 TAATCATGCAAATAAATATATTAA
* *
24229096 TAATCAAGCAATTAAATATATTAA
1 TAATCATGCAAATAAATATATTAA
24229120 TAATCATGC-AATCAAAT-TA--AA
1 TAATCATGCAAAT-AAATATATTAA
* *
24229141 TATGATAATACAAATAAATATATTAA
1 TA--ATCATGCAAATAAATATATTAA
24229167 TAATCAT----ATAAATATATTAA
1 TAATCATGCAAATAAATATATTAA
**
24229187 TAAATCACACAAATAAATATA-T--
1 T-AATCATGCAAATAAATATATTAA
*
24229209 TAATCATGCAAACAAATATATTA
1 TAATCATGCAAATAAATATATTA
24229232 GGCAAATAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 29
0.74 0.07 0.19
Matches are distributed among these distances:
20 14 0.13
21 25 0.23
22 2 0.02
23 13 0.12
24 44 0.40
25 9 0.08
26 4 0.04
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (24 bp):
TAATCATGCAAATAAATATATTAA
Found at i:24229115 original size:73 final size:73
Alignment explanation
Indices: 24229003--24229231 Score: 168
Period size: 73 Copynumber: 3.3 Consensus size: 73
24228993 TGTAATTAAA
* * *
24229003 CATGCAAGTAAATATA-TAATTATGCAAACAATAATATATA-AATCATGCAAAAAAATGC-AATT
1 CATGCAAATAAATATATTAATAAT-CAAACAATAATATATATAATAAT-C-AAAAAAT-CAAATT
24229065 AAATATG-TAAT
62 AAATATGATAAT
* ***
24229076 CATGCAAATAAATATATTAATAATCAAGCAATTAA-ATATATTAATAATCATGCAATCAAATTAA
1 CATGCAAATAAATATATTAATAATCAAACAA-TAATATATA-TAATAATCAAAAAATCAAATTAA
24229140 ATATGATAAT
64 ATATGATAAT
* * *
24229150 -A--CAAATAAATATATTAATAATCATA-TA-AATATAT-TAATAAATC---ACA-CAAA-TAAA
1 CATGCAAATAAATATATTAATAATCAAACAATAATATATATAAT-AATCAAAAAATCAAATTAAA
24229204 TAT-ATTAAT
65 TATGA-TAAT
*
24229213 CATGCAAACAAATATATTA
1 CATGCAAATAAATATATTA
24229232 GGCAAATAAA
Statistics
Matches: 131, Mismatches: 13, Indels: 31
0.75 0.07 0.18
Matches are distributed among these distances:
62 1 0.01
63 11 0.08
64 5 0.04
65 1 0.01
66 14 0.11
67 4 0.03
68 6 0.05
69 4 0.03
70 1 0.01
71 22 0.17
72 1 0.01
73 42 0.32
74 14 0.11
75 5 0.04
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.31
Consensus pattern (73 bp):
CATGCAAATAAATATATTAATAATCAAACAATAATATATATAATAATCAAAAAATCAAATTAAAT
ATGATAAT
Found at i:24229167 original size:18 final size:19
Alignment explanation
Indices: 24229130--24229231 Score: 73
Period size: 20 Copynumber: 4.9 Consensus size: 19
24229120 TAATCATGCA
24229130 ATCAAATTAAATATGA-TAAT
1 ATCAAA-TAAATAT-ATTAAT
24229150 A-CAAATAAATATATTAAT
1 ATCAAATAAATATATTAAT
*
24229168 AATCATATAAATATATTAAT
1 -ATCAAATAAATATATTAAT
24229188 AAATCACACAAATAAATATATTAAT
1 --AT----CAAATAAATATATTAAT
*
24229213 CATGCAAACAAATATATTA
1 -AT-CAAATAAATATATTA
24229232 GGCAAATAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
17 1 0.01
18 11 0.16
19 5 0.07
20 17 0.25
21 17 0.25
24 2 0.03
25 16 0.23
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (19 bp):
ATCAAATAAATATATTAAT
Found at i:24229186 original size:47 final size:46
Alignment explanation
Indices: 24229108--24229231 Score: 135
Period size: 45 Copynumber: 2.7 Consensus size: 46
24229098 ATCAAGCAAT
* * * *
24229108 TAAATATATTAATAATCATGC-AATCAAATTAAATATGATAATACAAA
1 TAAATATATTAATAATCATACAAAT-ATATTAAATA-AATAACACAAA
* *
24229155 TAAATATATTAATAATCATATAAATATATT-AATAAATCACACAAA
1 TAAATATATTAATAATCATACAAATATATTAAATAAATAACACAAA
* *
24229200 TAAATATATTAATCATGCAAACAAATATATTA
1 TAAATATATTAATAAT-CATACAAATATATTA
24229232 GGCAAATAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
45 23 0.35
46 16 0.25
47 23 0.35
48 3 0.05
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (46 bp):
TAAATATATTAATAATCATACAAATATATTAAATAAATAACACAAA
Found at i:24229213 original size:21 final size:20
Alignment explanation
Indices: 24229150--24229231 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 20
24229140 ATATGATAAT
24229150 ACAAATAAATATATTAAT-A
1 ACAAATAAATATATTAATCA
*
24229169 ATCATATAAATATATTAATAAATCA
1 A-CAAATAAATATA-T--T-AATCA
24229194 CACAAATAAATATATTAATCA
1 -ACAAATAAATATATTAATCA
* *
24229215 TGCAAACAAATATATTA
1 -ACAAATAAATATATTA
24229232 GGCAAATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
19 1 0.02
20 11 0.22
21 20 0.39
22 1 0.02
23 1 0.02
24 4 0.08
25 12 0.24
26 1 0.02
ACGTcount: A:0.57, C:0.10, G:0.01, T:0.32
Consensus pattern (20 bp):
ACAAATAAATATATTAATCA
Found at i:24229270 original size:20 final size:18
Alignment explanation
Indices: 24229237--24229273 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
24229227 TATTAGGCAA
24229237 ATAAATTATCATACAAAG
1 ATAAATTATCATACAAAG
24229255 ATAATATTAGTCATACAAA
1 ATAA-ATTA-TCATACAAA
24229274 TTCATGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (18 bp):
ATAAATTATCATACAAAG
Found at i:24229897 original size:12 final size:12
Alignment explanation
Indices: 24229880--24229909 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
24229870 ACTAAAAAAA
24229880 CAAAAATTAAAC
1 CAAAAATTAAAC
24229892 CAAAAATTAAAC
1 CAAAAATTAAAC
*
24229904 TAAAAA
1 CAAAAA
24229910 AATTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (12 bp):
CAAAAATTAAAC
Found at i:24232199 original size:2 final size:2
Alignment explanation
Indices: 24232192--24232240 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
24232182 GCGAAAGTAA
24232192 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
24232234 AG AG AG A
1 AG AG AG A
24232241 TCTCCAGCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:24241999 original size:3 final size:3
Alignment explanation
Indices: 24241993--24242020 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
24241983 CGAACTCAAT
24241993 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
24242021 ACAGAATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:24242501 original size:33 final size:33
Alignment explanation
Indices: 24242436--24242501 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
24242426 TCCACAAGTT
**
24242436 CACCTTCACATATTTCCAAAAAGTACTTTACAC
1 CACCTTCACATATTTCCAAAAAGTACCATACAC
* * * *
24242469 CACCTTCCCATGTTTCGAAACAGTACCATACAC
1 CACCTTCACATATTTCCAAAAAGTACCATACAC
24242502 GAGAATCCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.27
Consensus pattern (33 bp):
CACCTTCACATATTTCCAAAAAGTACCATACAC
Found at i:24242827 original size:2 final size:2
Alignment explanation
Indices: 24242820--24242855 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24242810 CGATAATGAC
24242820 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24242856 AACAATACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24250158 original size:20 final size:20
Alignment explanation
Indices: 24250130--24250197 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
24250120 TATAAATAAT
*
24250130 TTTTTTAATTATTTATTTAA
1 TTTTATAATTATTTATTTAA
*
24250150 TTTTATAATTATTTATAT-A
1 TTTTATAATTATTTATTTAA
*
24250169 -TTTAT-A-TATATATTTAA
1 TTTTATAATTATTTATTTAA
*
24250186 TTTTATATTTAT
1 TTTTATAATTAT
24250198 ATTAAAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
16 7 0.18
17 2 0.05
18 10 0.26
19 1 0.03
20 19 0.49
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATAATTATTTATTTAA
Found at i:24250174 original size:6 final size:6
Alignment explanation
Indices: 24250139--24250200 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
24250129 TTTTTTTAAT
* * *
24250139 TATTTA T-TTAA T-TTTA TAATTA T-TTATA TATTTA TATATA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATT-TA TATTTA TATTTA TATTTA
24250185 -ATTTTA TATTTA TATT
1 TA-TTTA TATTTA TATT
24250201 AAAAATAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
5 10 0.22
6 32 0.71
7 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TATTTA
Found at i:24250180 original size:24 final size:24
Alignment explanation
Indices: 24250153--24250217 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
24250143 TATTTAATTT
24250153 TATAATT-ATTTATATATTTATATA
1 TATAATTAATTT-TATATTTATATA
*
24250177 TATATTTAATTTTATATTTATAT-
1 TATAATTAATTTTATATTTATATA
* * *
24250200 TAAAAATAATATTATATT
1 TATAATTAATTTTATATT
24250218 AATTTCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 14 0.40
24 17 0.49
25 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATAATTAATTTTATATTTATATA
Found at i:24250198 original size:20 final size:19
Alignment explanation
Indices: 24250132--24250200 Score: 69
Period size: 18 Copynumber: 3.8 Consensus size: 19
24250122 TAAATAATTT
*
24250132 TTTTA-ATTATTTATTTAA
1 TTTTATATTATATATTTAA
24250150 TTTTATA--AT-TATTTATA
1 TTTTATATTATATATTTA-A
24250167 TATTTATA-TATATATTTAA
1 T-TTTATATTATATATTTAA
24250186 TTTTATATT-TATATT
1 TTTTATATTATATATT
24250201 AAAAATAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.13
17 4 0.09
18 23 0.51
19 6 0.13
20 6 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATATTATATATTTAA
Found at i:24250804 original size:12 final size:12
Alignment explanation
Indices: 24250789--24250813 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24250779 TTTAATGATT
24250789 AAAAATATTAAA
1 AAAAATATTAAA
24250801 AAAAATATTAAA
1 AAAAATATTAAA
24250813 A
1 A
24250814 TATTAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATATTAAA
Found at i:24251902 original size:22 final size:22
Alignment explanation
Indices: 24251876--24251926 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
24251866 TATTTTAAAT
24251876 TTTTATAAAATAAAAATAATTA
1 TTTTATAAAATAAAAATAATTA
* * *
24251898 TTTTAT-ATATAAATATATTTA
1 TTTTATAAAATAAAAATAATTA
24251919 TATTTATA
1 T-TTTATA
24251927 TTTAAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTATAAAATAAAAATAATTA
Found at i:24251927 original size:22 final size:21
Alignment explanation
Indices: 24251876--24251934 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
24251866 TATTTTAAAT
* *
24251876 TTTTATAAAATAAAAATAATTA
1 TTTTAT-ATATAAATATAATTA
*
24251898 TTTTATATATAAATATATTTA
1 TTTTATATATAAATATAATTA
*
24251919 TATTTATATTTAAATA
1 T-TTTATATATAAATA
24251935 ATATATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 13 0.41
22 19 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTATATATAAATATAATTA
Found at i:24253647 original size:25 final size:24
Alignment explanation
Indices: 24253619--24253676 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
24253609 TGATTTTAAT
24253619 TTTAATTTTAATTTTAATTTT-TAGA
1 TTTAATTTT-ATTTTAATTTTGT-GA
*
24253644 TTTAGTTTGTATTTTAATTTTGTGA
1 TTTAATTT-TATTTTAATTTTGTGA
24253669 TTT-ATTTT
1 TTTAATTTT
24253677 GATTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 1 0.03
24 3 0.10
25 23 0.79
26 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (24 bp):
TTTAATTTTATTTTAATTTTGTGA
Found at i:24253664 original size:6 final size:6
Alignment explanation
Indices: 24253611--24253639 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
24253601 TTGTAAATTG
24253611 ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
24253640 TAGATTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
ATTTTA
Found at i:24253666 original size:13 final size:12
Alignment explanation
Indices: 24253611--24253664 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
24253601 TTGTAAATTG
*
24253611 ATTTTAATTTTA
1 ATTTTTATTTTA
*
24253623 ATTTTAATTTTA
1 ATTTTTATTTTA
*
24253635 ATTTTTAGATTTA
1 ATTTTTA-TTTTA
* *
24253648 GTTTGTATTTTA
1 ATTTTTATTTTA
24253660 ATTTT
1 ATTTT
24253665 GTGATTTATT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
12 25 0.74
13 9 0.26
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (12 bp):
ATTTTTATTTTA
Found at i:24253677 original size:25 final size:25
Alignment explanation
Indices: 24253629--24253677 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
24253619 TTTAATTTTA
24253629 ATTTTAATTTTTAGATTTAGTTTGT
1 ATTTTAATTTTTAGATTTAGTTTGT
*
24253654 ATTTTAATTTTGT-GATTTATTTTG
1 ATTTTAATTTT-TAGATTTAGTTTG
24253678 ATTAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.65
Consensus pattern (25 bp):
ATTTTAATTTTTAGATTTAGTTTGT
Found at i:24253701 original size:16 final size:16
Alignment explanation
Indices: 24253680--24253710 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24253670 TTATTTTGAT
24253680 TAAAAAAAATCAAAAG
1 TAAAAAAAATCAAAAG
*
24253696 TAAAAAAAATGAAAA
1 TAAAAAAAATCAAAA
24253711 ACTTGAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.13
Consensus pattern (16 bp):
TAAAAAAAATCAAAAG
Found at i:24255954 original size:10 final size:10
Alignment explanation
Indices: 24255939--24255968 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
24255929 TCTCTGCTAA
24255939 AACCTTTCTT
1 AACCTTTCTT
24255949 AACCTTTCTT
1 AACCTTTCTT
*
24255959 AACCTCTCTT
1 AACCTTTCTT
24255969 TTCAACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (10 bp):
AACCTTTCTT
Found at i:24257276 original size:30 final size:31
Alignment explanation
Indices: 24257235--24257302 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 31
24257225 TCACTTTTTT
* * *
24257235 AAATAATTTTTTTATATTTTTATTT-TGTCC
1 AAATAAATTTTTTAAATTTTGATTTGTGTCC
* *
24257265 AAATAAA-TTTTTAAATTTTGATTTGTTTCT
1 AAATAAATTTTTTAAATTTTGATTTGTGTCC
24257295 AAATAAAT
1 AAATAAAT
24257303 CTTTATTTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (31 bp):
AAATAAATTTTTTAAATTTTGATTTGTGTCC
Found at i:24257288 original size:29 final size:30
Alignment explanation
Indices: 24257243--24257307 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
24257233 TTAAATAATT
* *
24257243 TTTTTATATTTTTATTT-TGTCCAAATAAA
1 TTTTTAAATTTTGATTTGTGTCCAAATAAA
* *
24257272 TTTTTAAATTTTGATTTGTTTCTAAATAAA
1 TTTTTAAATTTTGATTTGTGTCCAAATAAA
*
24257302 TCTTTA
1 TTTTTA
24257308 TTTCAAATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.31, C:0.06, G:0.05, T:0.58
Consensus pattern (30 bp):
TTTTTAAATTTTGATTTGTGTCCAAATAAA
Found at i:24257435 original size:30 final size:31
Alignment explanation
Indices: 24257349--24257451 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 31
24257339 TTTATTTAGT
* *
24257349 TATATATTAAAAGTTTAAAA-ACTTATTT-AGA
1 TATAAATTAAAA-ATTAAAAGACTTATTTGA-A
* *
24257380 TATAAATTAAAGA-TCAAAGACTTATTTGAA
1 TATAAATTAAAAATTAAAAGACTTATTTGAA
*
24257410 TATAAATTAAAAATTAAAAG-TTTATTTGAA
1 TATAAATTAAAAATTAAAAGACTTATTTGAA
24257440 TAT-AA-TAAAAAT
1 TATAAATTAAAAAT
24257452 ACAAATATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
28 7 0.11
29 6 0.10
30 33 0.53
31 16 0.26
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (31 bp):
TATAAATTAAAAATTAAAAGACTTATTTGAA
Done.