Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 62
Found at i:6586692 original size:3 final size:3
Alignment explanation
Indices: 6586680--6586754 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
6586670 AATATATATT
*
6586680 TAA T-A TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6586727 TAA TAA TAA TAA TAA -AA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
6586755 TGGGTAAAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 4 0.06
3 64 0.94
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6587352 original size:113 final size:113
Alignment explanation
Indices: 6587071--6587584 Score: 814
Period size: 113 Copynumber: 4.5 Consensus size: 113
6587061 GATAGAATTA
* *
6587071 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
6587136 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGCAAAAGG
66 CTTTCTCTAGAAAAGATAATCCATCAA-GTGATGAATTCAGGCAAAAGG
*
6587185 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
6587250 CTTTCTCTAGAAAAGCTGATCCATCAAGTAATGAATTCAGGTAAAAGG
66 CTTTCTCTAGAAAAGATAATCCATCAAGTGATGAATTCAGGCAAAAGG
6587298 TTGAACAAATTCTTCTCATTATGAACTT-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * * * *
6587362 ACTTTCTCTAGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGG
65 ACTTTCTCTAGAAAAGATAATCCATCAAGTGATGAATTCAGGCAAAAGG
*
6587411 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
6587476 CTTTCTCTGGAAAAAATAATCCATCAAGTGATGGATTCAGACAAAAGG
66 CTTTCTCTAGAAAAGATAATCCATCAAGTGATGAATTCAGGCAAAAGG
*
6587524 TTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
6587585 ACCTTCTCTG
Statistics
Matches: 371, Mismatches: 27, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
112 1 0.00
113 283 0.76
114 87 0.23
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (113 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTAGAAAAGATAATCCATCAAGTGATGAATTCAGGCAAAAGG
Found at i:6588473 original size:83 final size:83
Alignment explanation
Indices: 6588334--6589305 Score: 1833
Period size: 83 Copynumber: 11.7 Consensus size: 83
6588324 GTAGTTCCTA
6588334 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
6588399 ATTCAAAT-ATTGGTTCTG
66 ATTC-AATGATTGGTTCTG
6588417 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
6588482 A-TCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
6588499 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
*
6588564 AGTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
6588582 CCAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
6588647 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
6588665 CCAAACCAGATCAGATAACTCAAAG-ACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
6588729 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
6588747 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
6588812 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
6588830 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
6588895 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
6588913 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
6588978 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
6588996 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
6589061 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
6589079 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
6589144 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
6589162 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
6589227 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
6589245 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAATATGCTATGAACACATTCATCTT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTT
6589306 TCATTTAATT
Statistics
Matches: 871, Mismatches: 15, Indels: 6
0.98 0.02 0.01
Matches are distributed among these distances:
81 3 0.00
82 158 0.18
83 710 0.82
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:6590098 original size:16 final size:18
Alignment explanation
Indices: 6590060--6590104 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
6590050 TTCATAGAAG
*
6590060 AATAAATTGAATTTCCAA
1 AATAAATTGAATCTCCAA
6590078 AATAAATTGAATCT-C-A
1 AATAAATTGAATCTCCAA
6590094 AATAAATTGAA
1 AATAAATTGAA
6590105 CTTGAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 13 0.50
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (18 bp):
AATAAATTGAATCTCCAA
Found at i:6590445 original size:9 final size:9
Alignment explanation
Indices: 6590431--6590515 Score: 86
Period size: 9 Copynumber: 9.3 Consensus size: 9
6590421 TTGACCCCTC
6590431 TTTTTCTTT
1 TTTTTCTTT
6590440 TTTTTCTTT
1 TTTTTCTTT
*
6590449 TTTTT-TTC
1 TTTTTCTTT
*
6590457 TTCTTCTTCT
1 TTTTTCTT-T
6590467 TCTTTT-TTT
1 T-TTTTCTTT
*
6590476 TTCTT-TTT
1 TTTTTCTTT
6590484 TTTTTCTTT
1 TTTTTCTTT
6590493 TTTTTCTCTT
1 TTTTTCT-TT
6590503 TTCTTTCTTT
1 TT-TTTCTTT
6590513 TTT
1 TTT
6590516 CTTTCTTCAA
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
8 16 0.25
9 29 0.45
10 11 0.17
11 8 0.12
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:6590453 original size:11 final size:11
Alignment explanation
Indices: 6590437--6590522 Score: 97
Period size: 11 Copynumber: 8.0 Consensus size: 11
6590427 CCTCTTTTTC
6590437 TTTTTTTTCTT
1 TTTTTTTTCTT
6590448 TTTTTTTTCTT
1 TTTTTTTTCTT
* *
6590459 CTTCTTCTTC-T
1 -TTTTTTTTCTT
6590470 TTTTTTTTCTT
1 TTTTTTTTCTT
6590481 TTTTTTTTC--
1 TTTTTTTTCTT
*
6590490 TTTTTTTTCTC
1 TTTTTTTTCTT
*
6590501 TTTTCTTTCTT
1 TTTTTTTTCTT
*
6590512 TTTTCTTTCTT
1 TTTTTTTTCTT
6590523 CAAGCATAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
9 9 0.14
10 7 0.11
11 42 0.65
12 7 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:6590456 original size:20 final size:20
Alignment explanation
Indices: 6590431--6590522 Score: 112
Period size: 20 Copynumber: 4.4 Consensus size: 20
6590421 TTGACCCCTC
6590431 TTTTTCTTTTTTTTCTTTTT
1 TTTTTCTTTTTTTTCTTTTT
6590451 TTTTTCTTCTTCTTCTTCTTTTT
1 TTTTTCTT-TT-TT-TTCTTTTT
*
6590474 TTTTCTTTTTTTTTTCTTTTT
1 TTTT-TCTTTTTTTTCTTTTT
* *
6590495 TTTCTCTTTTCTTTCTTTTT
1 TTTTTCTTTTTTTTCTTTTT
*
6590515 TCTTTCTT
1 TTTTTCTT
6590523 CAAGCATAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
20 28 0.45
21 13 0.21
22 4 0.06
23 14 0.23
24 3 0.05
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTCTTTTTTTTCTTTTT
Found at i:6590515 original size:1 final size:1
Alignment explanation
Indices: 6590431--6590497 Score: 53
Period size: 1 Copynumber: 67.0 Consensus size: 1
6590421 TTGACCCCTC
* * * * * * * * *
6590431 TTTTTCTTTTTTTTCTTTTTTTTTTCTTCTTCTTCTTCTTTTTTTTTCTTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6590496 TT
1 TT
6590498 CTCTTTTCTT
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:6597715 original size:16 final size:16
Alignment explanation
Indices: 6597694--6597727 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
6597684 TGAATGATGA
*
6597694 ATGTATGCAAAAATGT
1 ATGTATGCAAAAAGGT
6597710 ATGTATGCAAAAAGGT
1 ATGTATGCAAAAAGGT
6597726 AT
1 AT
6597728 TGATCCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (16 bp):
ATGTATGCAAAAAGGT
Found at i:6601054 original size:17 final size:17
Alignment explanation
Indices: 6601032--6601076 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
6601022 ATAATAAAAC
*
6601032 ATATAAATATTATGAAA
1 ATATAAAAATTATGAAA
*
6601049 ATATAAAAATTTTGAAA
1 ATATAAAAATTATGAAA
*
6601066 AGA-AAAAATTA
1 ATATAAAAATTA
6601077 AATTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (17 bp):
ATATAAAAATTATGAAA
Found at i:6603116 original size:3 final size:3
Alignment explanation
Indices: 6603108--6603215 Score: 193
Period size: 3 Copynumber: 36.7 Consensus size: 3
6603098 AATATATATT
*
6603108 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA -AA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6603154 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6603202 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
6603216 TGGGTAAAAA
Statistics
Matches: 101, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 4 0.04
3 97 0.96
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6603721 original size:21 final size:22
Alignment explanation
Indices: 6603692--6603751 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 22
6603682 GTCATGTTTT
*
6603692 AGTCATTCGAGCACGATG-ATA
1 AGTCCTTCGAGCACGATGTATA
6603713 AGTCCTTCGAGC-C-ATGTATA
1 AGTCCTTCGAGCACGATGTATA
* *
6603733 AGACCTTCGAGCAAGATGT
1 AGTCCTTCGAGCACGATGT
6603752 TTTCATGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 3 0.09
20 15 0.45
21 11 0.33
22 4 0.12
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (22 bp):
AGTCCTTCGAGCACGATGTATA
Found at i:6604418 original size:42 final size:42
Alignment explanation
Indices: 6604357--6604460 Score: 181
Period size: 42 Copynumber: 2.5 Consensus size: 42
6604347 GCCATCAGAA
* * *
6604357 AGTCTTTCGAGCACGATGATTAAATCCTTAGGGTCATGTTTC
1 AGTCATTCTAGCAAGATGATTAAATCCTTAGGGTCATGTTTC
6604399 AGTCATTCTAGCAAGATGATTAAATCCTTAGGGTCATGTTTC
1 AGTCATTCTAGCAAGATGATTAAATCCTTAGGGTCATGTTTC
6604441 AGTCATTCTAGCAAGATGAT
1 AGTCATTCTAGCAAGATGAT
6604461 AAGTTCTTAG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (42 bp):
AGTCATTCTAGCAAGATGATTAAATCCTTAGGGTCATGTTTC
Found at i:6604665 original size:303 final size:300
Alignment explanation
Indices: 6604114--6604684 Score: 707
Period size: 303 Copynumber: 1.9 Consensus size: 300
6604104 ATTCAACATT
* * ** * *
6604114 ATGATTAAATCCTTTGGGTCATCTGTCATTGTTTCGAGTAAGATGATAAGTCCTTCGGGCCATCT
1 ATGATTAAATCCTTAGGGTCATCTGTCAGTCATTCGAGCAAGATGATAAGTCCTTAGGGCCATCT
* ** * * *
6604179 ATAAGGCATTCGGGTAAGATGTTTTAATATGATTTTTAGAAAATGAGAAAGCGATTTTCAAAGTT
66 ATAAGACATTCGGAAAAGATATGTTAATATGATTTTTAGAAAATGAGAAAACGATTTTCAAAGTT
*
6604244 TCTCATTTAATATTTTCAGAAAATAAAAATTTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCTT
131 TCTCATTTAATATTTTCAAAAAATAAAAATTTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCTT
* *
6604309 GCCAGGTAGACTATTTCCAAAATTGGTAAGTCCTTCAAGCCATCAGAAAGTCTTTCGAGCACGAT
196 ACCAGGTAGACTATTTCCAAAATTGGTAAGTCCTTCAAGCCATCAGAAAGTCTTTCAAGCACGAT
6604374 GATTAAATCCTTAGGGTCATGTTTCAGTCATTCTAGCAAG
261 GATTAAATCCTTAGGGTCATGTTTCAGTCATTCTAGCAAG
* * * *
6604414 ATGATTAAATCCTTAGGGTCATGTTTCAGTCATTCTAGCAAGATGATAAGTTCTTAGGGCCATCT
1 ATGATTAAATCCTTAGGGTCATCTGTCAGTCATTCGAGCAAGATGATAAGTCCTTAGGGCCATCT
* ** * * **
6604479 ATAAGACCTTCGGAAAAGATATGTTCTTGTGATTTTTGTGAAAAATGAGAAAATTATTTTCAAAG
66 ATAAGACATTCGGAAAAGATATGTTAATATGATTTTT-AG-AAAATGAGAAAACGATTTTCAAAG
* * * * * *
6604544 TTTTTCATTTAGTATTTTCAAAAAAATAAAATTTTTGAGAAGTAAGAAAGTG-TTCTTCAAAGTT
129 TTTCTCATTTAATATTTTC-AAAAAATAAAAATTTTGAAAAGTAAGAAAGAGATT-TCCAAAGTT
* * * * * *
6604608 TCTTACCTA-GTATATTATTTCCATAATTGGTAAGTCCTT-AAGGCGATTAGTAAGTCTTTCAAG
192 TCTTACC-AGGTAGACTATTTCCAAAATTGGTAAGTCCTTCAA-GCCATCAGAAAGTCTTTCAAG
**
6604671 CGTGATGATTAAAT
255 CACGATGATTAAAT
6604685 ACTATTGGTT
Statistics
Matches: 225, Mismatches: 40, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
300 83 0.37
301 1 0.00
302 42 0.19
303 98 0.44
304 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (300 bp):
ATGATTAAATCCTTAGGGTCATCTGTCAGTCATTCGAGCAAGATGATAAGTCCTTAGGGCCATCT
ATAAGACATTCGGAAAAGATATGTTAATATGATTTTTAGAAAATGAGAAAACGATTTTCAAAGTT
TCTCATTTAATATTTTCAAAAAATAAAAATTTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCTT
ACCAGGTAGACTATTTCCAAAATTGGTAAGTCCTTCAAGCCATCAGAAAGTCTTTCAAGCACGAT
GATTAAATCCTTAGGGTCATGTTTCAGTCATTCTAGCAAG
Found at i:6606222 original size:42 final size:42
Alignment explanation
Indices: 6606153--6606232 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
6606143 AATTGGTAAG
6606153 TCCTTTGGGTCATCAGTAAGTCATTTGAG-AATGATGATTAAA
1 TCCTTTGGGTCATCAGTAAGTCATTTGAGCAA-GATGATTAAA
* * *
6606195 TCCTTTGGGTCATCTGTCAGTCTTTTGAGCAAGATGAT
1 TCCTTTGGGTCATCAGTAAGTCATTTGAGCAAGATGAT
6606233 AAGTCCCTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (42 bp):
TCCTTTGGGTCATCAGTAAGTCATTTGAGCAAGATGATTAAA
Found at i:6606516 original size:773 final size:763
Alignment explanation
Indices: 6604843--6606868 Score: 2468
Period size: 774 Copynumber: 2.6 Consensus size: 763
6604833 GTTTTGACCT
*
6604843 GGTAGACTATTTCCAAAACTGGTAAGTCCTTTGAGCCATCAATAAGTCTTCCGAGCATGATGATT
1 GGTAGACTATTTCCAAAACTGGTAAGTCCTTTGAGCCATCAATAAGTCTTTCGAGCATGATGATT
* *
6604908 AAATCCTTAAGGTCGTGTTTCAGTCATTCGAGCAAGATGATAAGTCCATCAAGCCAACTATAAGA
66 -AATCCTTAGGGTCATGTTTCAGTCATTCGAGCAAGATGATAAGTCCAT-AAGCCAACTATAAGA
* * * *
6604973 CCTTCGAGCAAGATGTTTTCATGTGATATTTGTGAAAAATGAGAAAACAATATTCAAAGTTTTTC
129 CCTTCGGGCAAGATGTTTTCATGTGATATTTGTGAAAAATGAGAAAACGATTTTCAAAGGTTTTC
* * *
6605038 ATTTAGTA-TTTCA-AAAAGTTAAATTTTTGAAAAGTAAGAAAGCATTTTCCAAAGTTTCTTACC
194 ATTTAGGATTTTCAGAAAA-TGAAATTTTTGAAAAGTAAGAAAGCGTTTTCCAAAGTTTCTTACC
* * *
6605101 TAGTAGACTATTTCAAAAATTGGTAAGTCCTTAAGGCCATTAGTAAATCTTTCAAGCATGATGAT
258 TA-TAGACTATTTCCAAAATTGGTAAGTCCTTAAGGCCATTAATAAATCTTTCGAGCATGATGAT
*
6605166 TAAAAACTATTGGTCATCTGTCAGACTTTCGAGCAAGATTATAAGTCCTTGGGCCATCTATAAGA
322 TAAATACTATTGGTCATCTGTCAGACTTTCGAGC------AT-AGTCCTTGGGCCATCTATAAGA
* * *
6605231 CCTTTGGGTAGGATGTTTTCATATGATTTGTAACAAATGAGTAAACGATTTTCAAAATTTCTAAT
380 CCTTTGGGTAGGATGTTTTCATATGATTAGTAAAAAATGAGAAAACGATTTTCAAAATTTCTAAT
*
6605296 TTAAGAATTTTAGAAAATGAAAATTTTGAAAAGTAAGAAAGTGGTCTCCAAAGTTTCTTACCAAG
445 TTAAGAATTTTAGAAAATGAAAATTTTGAAAAGTAAGAAAGTGGTCTACAAAGTTTCTTACCAAG
* **
6605361 TAGACTTTTTCCAAAATTGGTAAGTCCTTTGGGTAATCAGTAAGTCATTCAAAATTCTGATTAAA
510 TAGACTTTTCCCAAAATTGGTAAGTCCTTTGGGTAATCAGTAAGTCATTCAAAATGATGATTAAA
* * **
6605426 TCCTTCGGGTCATCTGTAATTCTTTCAAGCAAGATGATAAGTCATTCTCCATCTATAAGTCATTC
575 TCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGTCATTCGCCATCTATAAAACATTC
* * * * * * *
6605491 AGGCATGATGTTTTAATTTGATTTGTAAAAAATGAGAAACCGATTTTCAAAGTTTCTCATTTTGG
640 AGGCAGGATATTTCAATATGATTTGAAAAAAATGAGAAACCGAATGTCAAAGTTTCTCATTTTGG
* *
6605556 ATTTTCAGAAAAATAAAAATTTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCTTGCTA
705 ATTTTCAGAAAAATAAAAATTTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCTTCCCA
6605615 GGTAGACTATTTCCAAAACTGGTAAGTCCTTTGAGCCATCAATATA-TCTTTCGAGCATGATGAT
1 GGTAGACTATTTCCAAAACTGGTAAGTCCTTTGAGCCATCAATA-AGTCTTTCGAGCATGATGAT
* * * *
6605679 TAGATCCTTAGGGTTATGTTTCAGTCATTCGAGCAAGATGATAAGTCCTTCAGGCCATCTATAAG
65 TA-ATCCTTAGGGTCATGTTTCAGTCATTCGAGCAAGATGATAAGTCCAT-AAGCCAACTATAAG
6605744 ACCTTCGGGCAAGATGTTTTCATGTGATATTTGTGAAAAATGAGAAAACGATTTTCAAAGGTTTT
128 ACCTTCGGGCAAGATGTTTTCATGTGATATTTGTGAAAAATGAGAAAACGATTTTCAAAGGTTTT
* *
6605809 AATTTAGGATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGTTTTCCAAAGTTTCTTACC
193 CATTTAGGATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGTTTTCCAAAGTTTCTTACC
* * * *
6605874 TACTAGACTATTTCCAAAACTGGTAAGTCCTTAAGGCCATTACTAAGTCTTTCGAGCATTATGAT
258 TA-TAGACTATTTCCAAAATTGGTAAGTCCTTAAGGCCATTAATAAATCTTTCGAGCATGATGAT
**
6605939 TAAATACTATTGGTCATCTGTCA-ATCTTTCGAGC-T-GTCCTTGGGCCATCTATAAGAGTTTTG
322 TAAATACTATTGGTCATCTGTCAGA-CTTTCGAGCATAGTCCTTGGGCCATCTATAAGACCTTTG
* * *
6606001 GGTTGGATGTTTTCATATGATTAGTAAAAAAAAATGAGAAAACGATTTTCAAAATTTTTCATTTA
386 GGTAGGATGTTTTCATATGATTAGT---AAAAAATGAGAAAACGATTTTCAAAATTTCTAATTTA
* * *
6606066 AGATTTTTAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGGTTTACAAAGTTTCTTACCAAGTAG
448 AGAATTTTAGAAAATGAAAATTTTGAAAAGTAAGAAAGTGGTCTACAAAGTTTCTTACCAAGTAG
* * *
6606131 ACTATTTCCCAAAATTGGTAAGTCCTTTGGGTCATCAGTAAGTCATTTGAGAATGATGATTAAAT
513 ACT-TTTCCCAAAATTGGTAAGTCCTTTGGGTAATCAGTAAGTCA-TTCAAAATGATGATTAAAT
* * ** * * * *
6606196 CCTTTGGGTCATCTGTCAGTCTTTTGAGCAAGATGATAAGTCCCTTGGGCTATCTATAAAACCTT
576 CCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGATAAGT-CATT-CGCCATCTATAAAACATT
** * *
6606261 CTTGCAGGATATTTCCATATGATATTTGAAAAAAAATGAGAAAGCGAATGTCAAAGTTTCTCATT
639 CAGGCAGGATATTTCAATATG--ATTTG-AAAAAAATGAGAAACCGAATGTCAAAGTTTCTCATT
* * * *
6606326 TAT-GATTTTCAG-AAAAT-GAAATTTCTGAAAAGTAAGAAAGCGATTTTCAAAGTTTTTTTACC
701 T-TGGATTTTCAGAAAAATAAAAATTT-TGAAAAGTAAGAAAGAGATTTCCAAAG-TTTCTT-CC
6606388 CA
762 CA
* * * * * *
6606390 -GTAGACTATTTCCAAAATTGCTAAGTCATTCGAGCCATCAATAAGTCTTTCAAGCGTGATGATT
1 GGTAGACTATTTCCAAAACTGGTAAGTCCTTTGAGCCATCAATAAGTCTTTCGAGCATGATGATT
* * * * *
6606454 CAATCCTTCGGGTCATCTTTCAGTCTTTCGAGCAAGATGATAAG-CCCTAATGCCACCTATAAGA
66 -AATCCTTAGGGTCATGTTTCAGTCATTCGAGCAAGATGATAAGTCCATAA-GCCAACTATAAGA
* * * ** ** *
6606518 CCTTCGGGTAAGATGTTTCCATATGATATTTGAAAAAAAATGAGAAAGTGGTTTTCAAA-GTTTC
129 CCTTCGGGCAAGATGTTTTCATGTGATATTTG-TGAAAAATGAGAAAACGATTTTCAAAGGTTT-
* * * *
6606582 TCATTTAAGATTTTTAGAAAATGAATTTTTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTAC
192 TCATTTAGGATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGTTTTCCAAAGTTTCTTAC
** * * *
6606647 CGTATAGACTATTTTCCAAAATTGGTAAGTCCTTCGGGCTATCAATAAATCTTTCGAGCATGATA
257 C-TATAGACTA-TTTCCAAAATTGGTAAGTCCTTAAGGCCATTAATAAATCTTTCGAGCATGATG
* * * * *
6606712 ATTAAAT-C-ATTCAGG-CTATTTGTTAGCCTTTCGAGCAAGATGATAAGTCCCTCGGTCCATCT
320 ATTAAATACTATT--GGTC-ATCTGTCAGACTTTCGAGC------AT-AGT-CCTTGGGCCATCT
* * * * *
6606774 ATAAGACCTTCT-GGCAGGATGTTTTCATATGATTTGTAAAAAGTGAGAAATA-AATTTTCAAAG
374 ATAAGACCTT-TGGGTAGGATGTTTTCATATGATTAGTAAAAAATGAGAAA-ACGATTTTCAAAA
* *
6606837 TTTCTCATTTAA-AATTTTCAAAAAAATGAAAA
437 TTTCTAATTTAAGAATTTT--AGAAAATGAAAA
6606869 AGGGAAAGGG
Statistics
Matches: 1086, Mismatches: 124, Indels: 77
0.84 0.10 0.06
Matches are distributed among these distances:
764 48 0.04
766 1 0.00
767 97 0.09
768 39 0.04
769 51 0.05
770 3 0.00
771 27 0.02
772 194 0.18
773 224 0.21
774 235 0.22
775 74 0.07
781 5 0.00
782 33 0.03
783 11 0.01
784 2 0.00
785 41 0.04
786 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (763 bp):
GGTAGACTATTTCCAAAACTGGTAAGTCCTTTGAGCCATCAATAAGTCTTTCGAGCATGATGATT
AATCCTTAGGGTCATGTTTCAGTCATTCGAGCAAGATGATAAGTCCATAAGCCAACTATAAGACC
TTCGGGCAAGATGTTTTCATGTGATATTTGTGAAAAATGAGAAAACGATTTTCAAAGGTTTTCAT
TTAGGATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGTTTTCCAAAGTTTCTTACCTAT
AGACTATTTCCAAAATTGGTAAGTCCTTAAGGCCATTAATAAATCTTTCGAGCATGATGATTAAA
TACTATTGGTCATCTGTCAGACTTTCGAGCATAGTCCTTGGGCCATCTATAAGACCTTTGGGTAG
GATGTTTTCATATGATTAGTAAAAAATGAGAAAACGATTTTCAAAATTTCTAATTTAAGAATTTT
AGAAAATGAAAATTTTGAAAAGTAAGAAAGTGGTCTACAAAGTTTCTTACCAAGTAGACTTTTCC
CAAAATTGGTAAGTCCTTTGGGTAATCAGTAAGTCATTCAAAATGATGATTAAATCCTTCGGGTC
ATCTGTAAGTCTTTCAAGCAAGATGATAAGTCATTCGCCATCTATAAAACATTCAGGCAGGATAT
TTCAATATGATTTGAAAAAAATGAGAAACCGAATGTCAAAGTTTCTCATTTTGGATTTTCAGAAA
AATAAAAATTTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCTTCCCA
Found at i:6606627 original size:261 final size:260
Alignment explanation
Indices: 6604830--6606867 Score: 2032
Period size: 261 Copynumber: 7.9 Consensus size: 260
6604820 CAGAAAAATA
* * * *
6604830 AAAGTTT-TGACCTGGTAGACTATTTCCAAAACTGGTAAGTCCTTTGAGCCATCAATAAGTCTTC
1 AAAGTTTCTTACCTAGTAGACTATTTCCAAAATTGGTAAGTCCTTTGAGCCATCAATAAGTCTTT
** * * * * * *
6604894 CGAGCATGATGATTAAATCCTTAAGGTCGTGTTTCAGTCATTCGAGCAAGATGATAAGTCCATCA
66 CGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCCTTA
* * * * * * *
6604959 AGCCAACTATAAGACCTTCGAGCAAGATGTTTTCATGTGATATTTGTGAAAAATGAGAAAACAAT
131 GGCCATCTATAAGACCTTCGGGCAGGATGTTTTCATATGATATTTGTAAAAAATGAGAAAACGAT
* * *
6605024 ATTCAAAGTTTTTCATTT-AG-TATTTCA-AAAAGTTAAATTTTTGAAAAGTAAGAAAGC-ATTT
196 TTTCAAAGTTTCTCATTTAAGAT-TTTCAGAAAA-TGAAATTTTTGAAAAGTAAGAAAGCGA-TT
6605085 TCC
258 TCC
* * * * *
6605088 AAAGTTTCTTACCTAGTAGACTATTTCAAAAATTGGTAAGTCC-TTAAGGCCATTAGTAAATCTT
1 AAAGTTTCTTACCTAGTAGACTATTTCCAAAATTGGTAAGTCCTTTGA-GCCATCAATAAGTCTT
* ** * * *
6605152 TCAAGCATGATGATTAAAAACTAT-TGGTCATCTGTCAGACTTTCGAGCAAGATTATAAGT-CCT
65 TCGAGCATGATGATTAAATCCT-TCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCCT
* * * * *
6605215 TGGGCCATCTATAAGACCTTTGGGTAGGATGTTTTCATATG--ATTTGTAACAAATGAGTAAACG
129 TAGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCATATGATATTTGTAAAAAATGAGAAAACG
* * * * * *
6605278 ATTTTCAAAATTTCTAATTTAAGAATTTT-AGAAAATGAAAATTTTGAAAAGTAAGAAAGTGGTC
194 ATTTTCAAAGTTTCTCATTTAAG-ATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATT
6605342 TCC
258 TCC
* * * ** * *
6605345 AAAGTTTCTTACCAAGTAGACTTTTTCCAAAATTGGTAAGTCCTTTGGGTAATCAGTAAGTCATT
1 AAAGTTTCTTACCTAGTAGACTATTTCCAAAATTGGTAAGTCCTTTGAGCCATCAATAAGTCTTT
** ** * * * *
6605410 C-AAAATTCTGATTAAATCCTTCGGGTCATCTGTAATTCTTTCAAGCAAGATGATAAGT-CATT-
66 CGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCCTTA
** * * * * * * *
6605472 CTCCATCTATAAGTCATTCAGGCATGATGTTTTAATTTG--ATTTGTAAAAAATGAGAAACCGAT
131 GGCCATCTATAAGACCTTCGGGCAGGATGTTTTCATATGATATTTGTAAAAAATGAGAAAACGAT
** * * *
6605535 TTTCAAAGTTTCTCATTTTGGATTTTCAGAAAAATAAAAATTTTGAAAAGTAAGAAAGAGATTTC
196 TTTCAAAGTTTCTCATTTAAGATTTTCAG-AAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTC
6605600 C
260 C
* *
6605601 AAAGTTTCTT-GCTAGGTAGACTATTTCCAAAACTGGTAAGTCCTTTGAGCCATCAATATA-TCT
1 AAAGTTTCTTACCTA-GTAGACTATTTCCAAAATTGGTAAGTCCTTTGAGCCATCAATA-AGTCT
* * * * * *
6605664 TTCGAGCATGATGATTAGATCCTTAGGGTTATGTTTCAGTCATTCGAGCAAGATGATAAGT-CCT
64 TTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCCT
* * *
6605728 TCAGGCCATCTATAAGACCTTCGGGCAAGATGTTTTCATGTGATATTTGTGAAAAATGAGAAAAC
129 T-AGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCATATGATATTTGTAAAAAATGAGAAAAC
* * * *
6605793 GATTTTCAAAGGTTT-TAATTTAGGATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGTT
193 GATTTTCAAA-GTTTCTCATTTAAGATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGAT
6605857 TTCC
257 TTCC
* * * * *
6605861 AAAGTTTCTTACCTACTAGACTATTTCCAAAACTGGTAAGTCC-TTAAGGCCATTACTAAGTCTT
1 AAAGTTTCTTACCTAGTAGACTATTTCCAAAATTGGTAAGTCCTTTGA-GCCATCAATAAGTCTT
* * * *
6605925 TCGAGCATTATGATTAAATACTAT-TGGTCATCTGTCAATCTTTCGAGC-------T--GT-CCT
65 TCGAGCATGATGATTAAATCCT-TCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCCT
* ** * ** * ***
6605979 TGGGCCATCTATAAGAGTTTTGGGTTGGATGTTTTCATATGATTAGTAAAAAAAAATGAGAAAAC
129 TAGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCATATGA-TATTTGTAAAAAATGAGAAAAC
* * * * *
6606044 GATTTTCAAAATTTTTCATTTAAGATTTTTAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGGTT
193 GATTTTCAAAGTTTCTCATTTAAGATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATT
*
6606109 TAC
258 TCC
* * * *
6606112 AAAGTTTCTTACCAAGTAGACTATTTCCCAAAATTGGTAAGTCCTTTGGGTCATCAGTAAGTCAT
1 AAAGTTTCTTACCTAGTAGACTATTT-CCAAAATTGGTAAGTCCTTTGAGCCATCAATAAGTC-T
* * *
6606177 TT-GAGAATGATGATTAAATCCTTTGGGTCATCTGTCAGTCTTTTGAGCAAGATGATAAGTCCCT
64 TTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCCT
* * * ** * * * *
6606241 TGGGCTATCTATAAAACCTTCTTGCAGGATATTTCCATATGATATTTGAAAAAAAATGAGAAAGC
129 TAGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCATATGATATTTG-TAAAAAATGAGAAAAC
* * * *
6606306 GAATGTCAAAGTTTCTCATTTATGATTTTCAGAAAATGAAATTTCTGAAAAGTAAGAAAGCGATT
193 GATTTTCAAAGTTTCTCATTTAAGATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATT
*
6606371 TTC
258 TCC
* * * * *
6606374 AAAGTTTTTTTACCCAGTAGACTATTTCCAAAATTGCTAAGTCATTCGAGCCATCAATAAGTCTT
1 AAAG-TTTCTTACCTAGTAGACTATTTCCAAAATTGGTAAGTCCTTTGAGCCATCAATAAGTCTT
* * * * *
6606439 TCAAGCGTGATGATTCAATCCTTCGGGTCATCTTTCAGTCTTTCGAGCAAGATGATAAG-CCCTA
65 TCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCCTT
* * * * * * **
6606503 ATGCCACCTATAAGACCTTCGGGTAAGATGTTTCCATATGATATTTGAAAAAAAATGAGAAAGTG
130 AGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCATATGATATTTG-TAAAAAATGAGAAAACG
* * *
6606568 GTTTTCAAAGTTTCTCATTTAAGATTTTTAGAAAATGAATTTTTTGAAAAGTAAGAAAGCGATTT
194 ATTTTCAAAGTTTCTCATTTAAGATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTT
6606633 CC
259 CC
* * * *
6606635 AAAGTTTCTTACCGTA-TAGACTATTTTCCAAAATTGGTAAGTCCTTCGGGCTATCAATAAATCT
1 AAAGTTTCTTACC-TAGTAGACTA-TTTCCAAAATTGGTAAGTCCTTTGAGCCATCAATAAGTCT
* * * * * *
6606699 TTCGAGCATGATAATTAAATCATTCAGG-CTATTTGTTAGCCTTTCGAGCAAGATGATAAGTCCC
64 TTCGAGCATGATGATTAAATCCTTCGGGTC-ATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCC
* * *
6606763 -TCGGTCCATCTATAAGACCTTCTGGCAGGATGTTTTCATATG--ATTTGTAAAAAGTGAGAAAT
128 TTAGG-CCATCTATAAGACCTTCGGGCAGGATGTTTTCATATGATATTTGTAAAAAATGAGAAA-
* * *
6606825 A-AATTTTCAAAGTTTCTCATTTAAAATTTTCAAAAAAATGAAA
191 ACGATTTTCAAAGTTTCTCATTTAAGATTTTC-AGAAAATGAAA
6606868 AAGGGAAAGG
Statistics
Matches: 1464, Mismatches: 266, Indels: 98
0.80 0.15 0.05
Matches are distributed among these distances:
250 36 0.02
251 106 0.07
252 65 0.04
253 6 0.00
254 5 0.00
255 72 0.05
256 164 0.11
257 130 0.09
258 53 0.04
259 166 0.11
260 149 0.10
261 262 0.18
262 230 0.16
263 20 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (260 bp):
AAAGTTTCTTACCTAGTAGACTATTTCCAAAATTGGTAAGTCCTTTGAGCCATCAATAAGTCTTT
CGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCCTTA
GGCCATCTATAAGACCTTCGGGCAGGATGTTTTCATATGATATTTGTAAAAAATGAGAAAACGAT
TTTCAAAGTTTCTCATTTAAGATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGATTTCC
Found at i:6608937 original size:30 final size:28
Alignment explanation
Indices: 6608903--6608959 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
6608893 ATTTTATATT
6608903 TTTATTTACATTTTCTCCCTTTTAATTTCA
1 TTTATTTACATTTT-TCCC-TTTAATTTCA
* *
6608933 TTTATTTTCATTTTTTCCTTTAATTTC
1 TTTATTTACATTTTTCCCTTTAATTTC
6608960 CAAAATTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.36
29 3 0.12
30 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTATTTACATTTTTCCCTTTAATTTCA
Found at i:6609726 original size:18 final size:18
Alignment explanation
Indices: 6609677--6609726 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
6609667 GTTTTAAATA
* *
6609677 TATGTGTACATATGTATTT
1 TATGTGAACAT-TTTATTT
*
6609696 TATGTGAATATTTTATTT
1 TATGTGAACATTTTATTT
*
6609714 TATGTGGACATTT
1 TATGTGAACATTT
6609727 CTTTATGTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (18 bp):
TATGTGAACATTTTATTT
Found at i:6610853 original size:20 final size:19
Alignment explanation
Indices: 6610807--6610862 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
6610797 ACCGATTCAA
*
6610807 GTGGTATCGATACCAAGAG
1 GTGGTATCGATACCATGAG
*
6610826 GGGAGTATCGATACCATGAG
1 GTG-GTATCGATACCATGAG
*
6610846 GATGGTATCGACACCAT
1 G-TGGTATCGATACCAT
6610863 TGAGCACTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.06
20 28 0.90
21 1 0.03
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.21
Consensus pattern (19 bp):
GTGGTATCGATACCATGAG
Found at i:6611419 original size:46 final size:46
Alignment explanation
Indices: 6611360--6611478 Score: 193
Period size: 46 Copynumber: 2.6 Consensus size: 46
6611350 TAAAATGAAT
* *
6611360 CCATAAATAAAATGCATGCAAGGATGCATTAAGGCATAAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATG
* *
6611406 CCATAAATGAAATGCATGAAAGGATTCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATG
*
6611452 GCATAAATGAAATGCATGAAAGGATGC
1 CCATAAATGAAATGCATGAAAGGATGC
6611479 CATCAATGAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.20
Consensus pattern (46 bp):
CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATG
Found at i:6611427 original size:26 final size:26
Alignment explanation
Indices: 6611393--6611536 Score: 132
Period size: 26 Copynumber: 6.0 Consensus size: 26
6611383 ATGCATTAAG
*
6611393 GCATAAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATGCCATAAATGAAAT
* *
6611419 GCATGAAAGGAT-TCAT---T--AAG
1 GCATGAAAGGATGCCATAAATGAAAT
*
6611439 GCATGAAAGGATGGCATAAATGAAAT
1 GCATGAAAGGATGCCATAAATGAAAT
*
6611465 GCATGAAAGGATGCCATCAATGAAAT
1 GCATGAAAGGATGCCATAAATGAAAT
* *
6611491 GTATGAAAGGATG-CAT---T--AAG
1 GCATGAAAGGATGCCATAAATGAAAT
*
6611511 GCATGAATGGATGCCATAAATGAAAT
1 GCATGAAAGGATGCCATAAATGAAAT
6611537 TAACGAATGG
Statistics
Matches: 94, Mismatches: 12, Indels: 24
0.72 0.09 0.18
Matches are distributed among these distances:
20 27 0.29
21 6 0.06
22 2 0.02
24 2 0.02
25 6 0.06
26 51 0.54
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (26 bp):
GCATGAAAGGATGCCATAAATGAAAT
Found at i:6611481 original size:72 final size:72
Alignment explanation
Indices: 6611393--6611536 Score: 234
Period size: 72 Copynumber: 2.0 Consensus size: 72
6611383 ATGCATTAAG
* *
6611393 GCATAAAAGGATGCCATAAATGAAATGCATGAAAGGATTCATTAAGGCATGAAAGGATGGCATAA
1 GCATAAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAA
6611458 ATGAAAT
66 ATGAAAT
* * * *
6611465 GCATGAAAGGATGCCATCAATGAAATGTATGAAAGGATGCATTAAGGCATGAATGGATGCCATAA
1 GCATAAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAA
6611530 ATGAAAT
66 ATGAAAT
6611537 TAACGAATGG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (72 bp):
GCATAAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAA
ATGAAAT
Found at i:6611765 original size:56 final size:55
Alignment explanation
Indices: 6611703--6611825 Score: 158
Period size: 56 Copynumber: 2.2 Consensus size: 55
6611693 AATTTTTTGT
* * * *
6611703 AATTCATAATAAGTTTATGAATTTCCATATGGGTACTATGTGTACAAA-ACTAAGAA
1 AATTCATAATAAGTGTATGAATTTCCATATGGGAAATATATGTACAAATA-TAAG-A
* *
6611759 AATTCATACTAAGTGTATGAATTTCCGTATGGGAAATATATGTACAAATATAAGA
1 AATTCATAATAAGTGTATGAATTTCCATATGGGAAATATATGTACAAATATAAGA
*
6611814 AGTTCATAATAA
1 AATTCATAATAA
6611826 TTAGGTGAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
55 11 0.19
56 46 0.79
57 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (55 bp):
AATTCATAATAAGTGTATGAATTTCCATATGGGAAATATATGTACAAATATAAGA
Found at i:6612140 original size:68 final size:68
Alignment explanation
Indices: 6612010--6612140 Score: 147
Period size: 68 Copynumber: 1.9 Consensus size: 68
6612000 TAATGGCCTA
* * * *
6612010 ACTGTGCATTTGACATAAATGTGTCAATCATGCCAGTTAAATGAAAGGCTAATTGCCTTTGAGGC
1 ACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAAATGAAAGGCTAAATGACTTTGAGGC
6612075 TTG
66 TTG
* * * * * * *
6612078 ACTGTGCATTTGATAGGAAGGTGTCAATGATGCTAGTTAGATGAACGGTTAAAT-ACTGTTGAG
1 ACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAAATGAAAGGCTAAATGACT-TTGAG
6612141 TAAAAGATTT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
67 2 0.04
68 49 0.96
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (68 bp):
ACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAAATGAAAGGCTAAATGACTTTGAGGC
TTG
Found at i:6616706 original size:2 final size:2
Alignment explanation
Indices: 6616699--6616784 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
6616689 TGAAACATGC
6616699 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6616741 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6616783 AT
1 AT
6616785 CATGGACTAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6617502 original size:20 final size:20
Alignment explanation
Indices: 6617477--6617517 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6617467 CATCCGAATC
6617477 AAAATGAACAAAATATAAAT
1 AAAATGAACAAAATATAAAT
**
6617497 AAAATGGTCAAAATATAAAT
1 AAAATGAACAAAATATAAAT
6617517 A
1 A
6617518 GAAACATTAT
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:0.66, C:0.05, G:0.07, T:0.22
Consensus pattern (20 bp):
AAAATGAACAAAATATAAAT
Found at i:6617566 original size:5 final size:5
Alignment explanation
Indices: 6617556--6617580 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6617546 AGAGGTGACC
6617556 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
6617581 CAGCCAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:6619467 original size:241 final size:241
Alignment explanation
Indices: 6619029--6620296 Score: 1665
Period size: 241 Copynumber: 5.3 Consensus size: 241
6619019 TCCTGAAGGT
* * ** *
6619029 CTTATAGATGGCCAGAAGGATTTGGGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
1 CTTATAGATGACCCGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* * * *
6619094 AATAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAGAAAAATAAATTTTCAGAAAATAT
66 ACTAAGTAAGAAATTTTGGAAATCATTTTCTTACTTTTCAAGAAAAATCAATTTTCAGAAAAGAT
* * * *
6619159 TTAAATCAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCATGCCCA
131 TTAAATGAGAAACTTTAGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCCA
* * * *
6619224 AAGGTCTTATGGATGGCCTGATGTACTTATTATCTTACTCGAAAGA
196 AAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGA
* * * *
6619270 CTTATAAATGACTCGAAGGATTTAAGCACCATGCTTGAAAGACTTACTAATGGCCCGAAGGACTT
1 CTTATAGATGACCCGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* ** * *
6619335 ACTAAGTAAGAAATTTTAGAAATTGTTTTCTTACTTTTCAAGAAAATTCAATTTTCAAAAAAGAT
66 ACTAAGTAAGAAATTTTGGAAATCATTTTCTTACTTTTCAAGAAAAATCAATTTTCAGAAAAGAT
* * *
6619400 TTAAATGAGAAAATTTAGAAATCACTTTCTCATTTTTCAAAAATCATGTGAAAACATCCTACCCA
131 TTAAATGAGAAACTTTAGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCCA
* * * *
6619465 AAGGTCTTATGGATGGCCTGATGTAATTATTATCTTGCTCGAAAGA
196 AAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGA
* *
6619511 CTTATAGATGACCCGAAGGATTTAAGAACCATGCTCGAAAGACTTACTGATGACCCGAAGGACTT
1 CTTATAGATGACCCGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* * *
6619576 ACTAAGTAATAAATTTTGGAAATCTTTTTCTTACTTTTCAAGAAAAATCAA-TTTCAAAAAAGAT
66 ACTAAGTAAGAAATTTTGGAAATCATTTTCTTACTTTTCAAGAAAAATCAATTTTCAGAAAAGAT
* ** *
6619640 TTAAATGAGAAAATTTAGAAATCACTTTCTCATTTTTAAAAAATCATGTGAAAACATCCTACCCA
131 TTAAATGAGAAACTTTAGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCCA
* *
6619705 AAGGTCTTATGAATGG-CTCGAAGGACTTATCATCTTGTTCGAAAGA
196 AAGGTCTTATGGATGGCCT-GAAGGACTTATCATCTTGCTCGAAAGA
* * *
6619751 CTTATAGATGACCCGAAGGATTTAAGAACCATGCTCGAAATACTTACTGATGGCCCAAAGGACTT
1 CTTATAGATGACCCGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* * *
6619816 ACTAAGTAAGAAACTTTT-TAAATCATTTTCTTA-ATTTC--CAAAAATCAATTTTCAGAAAAGA
66 ACTAAGTAAGAAA-TTTTGGAAATCATTTTCTTACTTTTCAAGAAAAATCAATTTTCAGAAAAGA
* ** *
6619877 TTTAAATGAGAAACTTT-GGAATC-CGCTCTCATTTTTTGAAAATCATGTGAAAACATCCTGCCC
130 TTTAAATGAGAAACTTTAGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCC
* * *
6619940 GAAGGTCTTATGGATGGTCC-GAAGCACTTATCATCATGCTCGAAAGA
195 AAAGGTCTTATGGATGG-CCTGAAGGACTTATCATCTTGCTCGAAAGA
* * ** * * * * *
6619987 CTTATAGATGACCTGAAGGATTTAAGCATCACACTTGAAAGACTTATTGATAGCTCGATGGACTT
1 CTTATAGATGACCCGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* * * * *
6620052 ACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAGAAAAATTAATTTTGAGAAAATAT
66 ACTAAGTAAGAAATTTTGGAAATCATTTTCTTACTTTTCAAGAAAAATCAATTTTCAGAAAAGAT
* * ** * *
6620117 TTAAATAAGAAACTTTGGAAATCGGTTTCTCATTTTTTTGAAAATCATGTGAAAACATCATGCCC
131 TTAAATGAGAAACTTTAGAAATCACTTTCTCA-TTTTTCGAAAATCATGTGAAAACATCCTGCCC
* * *
6620182 GAAGGTATTATGGATGG-CTCGAAGGACTTATCATCTTGCTCAAAAGA
195 AAAGGTCTTATGGATGGCCT-GAAGGACTTATCATCTTGCTCGAAAGA
* ** *
6620229 CTTATAGATGACCCGAAGGATTTAAGCACCATGCTCGAAAGACTTAGTGATAACCCAAAGGACTT
1 CTTATAGATGACCCGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
6620294 ACT
66 ACT
6620297 CATCAAGAAA
Statistics
Matches: 907, Mismatches: 106, Indels: 27
0.87 0.10 0.03
Matches are distributed among these distances:
235 3 0.00
236 153 0.17
237 18 0.02
238 28 0.03
239 41 0.05
240 207 0.23
241 328 0.36
242 129 0.14
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (241 bp):
CTTATAGATGACCCGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
ACTAAGTAAGAAATTTTGGAAATCATTTTCTTACTTTTCAAGAAAAATCAATTTTCAGAAAAGAT
TTAAATGAGAAACTTTAGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCCA
AAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGA
Found at i:6620246 original size:41 final size:41
Alignment explanation
Indices: 6620201--6620301 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 41
6620191 ATGGATGGCT
* *
6620201 CGAAGGACTTATCATCTTGCTCAAAAGACTTA-TAGATGACC
1 CGAAGGACTTATCATCATGCTCAAAAGACTTAGT-GATAACC
* * * *
6620242 CGAAGGATTTAAGCACCATGCTCGAAAGACTTAGTGATAACC
1 CGAAGGACTT-ATCATCATGCTCAAAAGACTTAGTGATAACC
*
6620284 CAAAGGACTTACTCATCA
1 CGAAGGACTTA-TCATCA
6620302 AGAAACCCTT
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
41 10 0.21
42 36 0.77
43 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (41 bp):
CGAAGGACTTATCATCATGCTCAAAAGACTTAGTGATAACC
Found at i:6620425 original size:57 final size:59
Alignment explanation
Indices: 6620296--6620454 Score: 200
Period size: 58 Copynumber: 2.7 Consensus size: 59
6620286 AAGGACTTAC
* * * * *
6620296 TCATCAAGAAACCCTTGAAAATCAAGCTTAGTTTC-TTAAAAACTTTCTTTTACAATTA
1 TCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTAAAAACTTTCTTTGACAATAA
* * *
6620354 TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAACAA-TTAT-TTTGA-AATAA
1 TCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTAAAAACTT-TCTTTGACAATAA
6620411 TCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTTAAAAA
1 TCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTC-TTTAAAAA
6620455 TTCATCATGT
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
57 37 0.43
58 43 0.49
59 7 0.08
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (59 bp):
TCATCAAGAAACCCCTAAAAATCAGGCTTAGTTTCTTTAAAAACTTTCTTTGACAATAA
Found at i:6620535 original size:55 final size:55
Alignment explanation
Indices: 6620464--6620791 Score: 440
Period size: 55 Copynumber: 6.0 Consensus size: 55
6620454 ATTCATCATG
* * **
6620464 TCAAGAAACCTCTGAAAATCAGACTTAGTTTATTTGAAAGCTCATTTAAAAATTT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCA
* * *
6620519 TCAAGAAACTTCTGAAAATAAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCA
* **
6620574 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTTATTTAAAAATTG
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCA
* * * *
6620629 CCAAGAAACTTCTGAAAATCAGACTTAGTTTATTTAAAAACTCATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCA
*
6620684 TCAAGAAACTTTTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCA
** * * * * ** *
6620739 TCAAGAAACTTCCAAAAACCGGACTTAGTCTCTTTCAAAATTTATTTAAAAAT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAAT
6620792 ATAAAAAAAC
Statistics
Matches: 238, Mismatches: 35, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 238 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (55 bp):
TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCA
Found at i:6620600 original size:110 final size:110
Alignment explanation
Indices: 6620464--6620791 Score: 494
Period size: 110 Copynumber: 3.0 Consensus size: 110
6620454 ATTCATCATG
* * *
6620464 TCAAGAAACCTCTGAAAATCAGACTTAGTTTATTTGAAAGCTCATTTAAAAATTTTCAAGAAACT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATTATCAAGAAACT
*
6620529 TCTGAAAATAAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
66 TCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* **
6620574 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTTATTTAAAAATTGCCAAGAAACT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATTATCAAGAAACT
*
6620639 TCTGAAAATCAGACTTAGTTTATTTAAAAACTCATTTAAAAATCA
66 TCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* *
6620684 TCAAGAAACTTTTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATTATCAAGAAACT
** * * * * * *
6620749 TCCAAAAACCGGACTTAGTCTCTTTCAAAATTTATTTAAAAAT
66 TCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAAT
6620792 ATAAAAAAAC
Statistics
Matches: 197, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
110 197 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (110 bp):
TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATTATCAAGAAACT
TCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCA
Found at i:6620636 original size:165 final size:165
Alignment explanation
Indices: 6620465--6620791 Score: 501
Period size: 165 Copynumber: 2.0 Consensus size: 165
6620455 TTCATCATGT
* * **
6620465 CAAGAAACCTCTGAAAATCAGACTTAGTTTATTTGAAAGCTCATTTAAAAATTTTCAAGAAACTT
1 CAAGAAACCTCTGAAAATCAGACTTAGTTTATTTAAAAACTCATTTAAAAATCATCAAGAAACTT
** *
6620530 CTGAAAATAAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTCTGAAAATCA
66 CTGAAAATAAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTCCAAAAACCA
* * *
6620595 GACTTAGTTTCTTTGAAAGCTTATTTAAAAATTGC
131 GACTTAGTCTCTTTCAAAACTTATTTAAAAATTGC
*
6620630 CAAGAAACTTCTGAAAATCAGACTTAGTTTATTTAAAAACTCATTTAAAAATCATCAAGAAACTT
1 CAAGAAACCTCTGAAAATCAGACTTAGTTTATTTAAAAACTCATTTAAAAATCATCAAGAAACTT
* * * * *
6620695 TTGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACTTCCAAAAACCG
66 CTGAAAATAAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTCCAAAAACCA
*
6620760 GACTTAGTCTCTTTCAAAATTTATTTAAAAAT
131 GACTTAGTCTCTTTCAAAACTTATTTAAAAAT
6620792 ATAAAAAAAC
Statistics
Matches: 145, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
165 145 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (165 bp):
CAAGAAACCTCTGAAAATCAGACTTAGTTTATTTAAAAACTCATTTAAAAATCATCAAGAAACTT
CTGAAAATAAGACTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTCCAAAAACCA
GACTTAGTCTCTTTCAAAACTTATTTAAAAATTGC
Found at i:6622619 original size:8 final size:8
Alignment explanation
Indices: 6622606--6622676 Score: 54
Period size: 8 Copynumber: 8.5 Consensus size: 8
6622596 TTCAATTTTC
6622606 TTTTCTTT
1 TTTTCTTT
6622614 TTTTCTTT
1 TTTTCTTT
* *
6622622 TATGCTTT
1 TTTTCTTT
6622630 TTCTTCTTT
1 TT-TTCTTT
*
6622639 TCATCTCTTT
1 T--TTTCTTT
6622649 TTTTCTTT
1 TTTTCTTT
*
6622657 TTAT-TTT
1 TTTTCTTT
*
6622664 TTTCCTTAT
1 TTTTCTT-T
6622673 TTTT
1 TTTT
6622677 TCCCTTTCCT
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
7 5 0.10
8 26 0.54
9 10 0.21
10 6 0.12
11 1 0.02
ACGTcount: A:0.06, C:0.15, G:0.01, T:0.77
Consensus pattern (8 bp):
TTTTCTTT
Found at i:6622654 original size:18 final size:18
Alignment explanation
Indices: 6622609--6622657 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
6622599 AATTTTCTTT
6622609 TCTTTTTTTCTTTTATGC
1 TCTTTTTTTCTTTTATGC
*
6622627 T-TTTTCTTCTTTTCAT-C
1 TCTTTTTTTCTTTT-ATGC
6622644 TCTTTTTTTCTTTT
1 TCTTTTTTTCTTTT
6622658 TATTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (18 bp):
TCTTTTTTTCTTTTATGC
Found at i:6625600 original size:12 final size:11
Alignment explanation
Indices: 6625583--6625616 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
6625573 CTCTGCGGGA
6625583 TACTCCATAAAT
1 TACTCC-TAAAT
6625595 TACTCCTAAAAT
1 TACTCCT-AAAT
6625607 TACTCCTAAA
1 TACTCCTAAA
6625617 ATTTCATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.32
Consensus pattern (11 bp):
TACTCCTAAAT
Found at i:6625617 original size:12 final size:12
Alignment explanation
Indices: 6625591--6625619 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
6625581 GATACTCCAT
6625591 AAATTACTCCTA
1 AAATTACTCCTA
6625603 AAATTACTCCTA
1 AAATTACTCCTA
6625615 AAATT
1 AAATT
6625620 TCATGATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATTACTCCTA
Found at i:6628444 original size:2 final size:2
Alignment explanation
Indices: 6628437--6628474 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6628427 TGAAACATGC
6628437 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6628475 CATGGGGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6629183 original size:20 final size:20
Alignment explanation
Indices: 6629158--6629201 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
6629148 GTATCCTAAT
6629158 TAAAATGAACAAAATATAAA
1 TAAAATGAACAAAATATAAA
**
6629178 TAAAATGGTCAAAATATAAA
1 TAAAATGAACAAAATATAAA
6629198 TAAA
1 TAAA
6629202 TAAAAGCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.23
Consensus pattern (20 bp):
TAAAATGAACAAAATATAAA
Found at i:6633087 original size:54 final size:53
Alignment explanation
Indices: 6633022--6633404 Score: 541
Period size: 54 Copynumber: 7.1 Consensus size: 53
6633012 TTTTGTACAA
* * * * * *
6633022 ATAGTGTCAATACAATAATTCACAAACTCATTATGAATTACTTGGGGTGCACAC
1 ATAGTGCCAATACAA-AATTCATAAACTAATTATGAATTTCTTAGGTTGCACAC
*
6633076 ATAGTGCCAATACAGAAATTCATAAACTAATTATGAATTTCTTAGGTTGCAAAC
1 ATAGTGCCAATACA-AAATTCATAAACTAATTATGAATTTCTTAGGTTGCACAC
* *
6633130 ATAGTGTCAATACGAAAATTCATAAACAAATTATGAATTTCTTAGGTTGCACAC
1 ATAGTGCCAATAC-AAAATTCATAAACTAATTATGAATTTCTTAGGTTGCACAC
* * *
6633184 ATAGTGCCAATAAGAAAATTCATATACTAATTATGAATTTCTTAGGTTGCACAG
1 ATAGTGCCAAT-ACAAAATTCATAAACTAATTATGAATTTCTTAGGTTGCACAC
* * *
6633238 ATAGTACCGATACGAAAATTCATAAACTAATTATGAATTTCTTAGGTTGTACAC
1 ATAGTGCCAATAC-AAAATTCATAAACTAATTATGAATTTCTTAGGTTGCACAC
*
6633292 ATAGTGCCAATATAGAAATTCATAAACTAATTATGAATTTCTTAGGTTGCACAC
1 ATAGTGCCAATACA-AAATTCATAAACTAATTATGAATTTCTTAGGTTGCACAC
* *
6633346 ATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCGCAC
1 ATAGTGCCAATAC-AAAATTCATAAACTAATTATGAATTTCTTAGGTTGCACAC
6633400 ATAGT
1 ATAGT
6633405 ACCCATTCGG
Statistics
Matches: 295, Mismatches: 28, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
53 2 0.01
54 289 0.98
55 4 0.01
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (53 bp):
ATAGTGCCAATACAAAATTCATAAACTAATTATGAATTTCTTAGGTTGCACAC
Found at i:6635833 original size:365 final size:363
Alignment explanation
Indices: 6635152--6635994 Score: 983
Period size: 365 Copynumber: 2.3 Consensus size: 363
6635142 CTGGAGGTTC
* * * **
6635152 AGTTGTTATGGATTGATGTTTTCATCTTCTTAAATTATCCATAATAGTTTCCTCGCTTAGTCTTG
1 AGTTGTTATGGATTGATGTTTTCGTCTTCTTAAA-T-TGCAAAATAGTTTCCTCGCTTAGTCCAG
* * * * * * * ** *
6635217 TGGAAACATCCCCAATTAGCTACTCCAGTTTCATCACTTCCTACAAAATAAATAATTCAAGCTTT
64 TGAAAACATCCCCAATTTGCTCCTCCAGCTCCAACAGTTCCTACAAAATAAATAACACAAGATTT
* *
6635282 TAAAACCCTAAGTAAATTCCATTGAACTCAAAACATTTGAGTGTTACCTTATAAGATATGTTATC
129 TAAAACCATAAGTAAATTCCATTGAACTCAAAACATTTGAGTGTTACCTCATAAGATATGTTATC
* *
6635347 GACATTAAGGCACATATCCTCAAGAATATCAAGATCCTCAGGTATGCCATACAAATATTAAGTAT
194 GACATTAAGGCACATATCCTCAAGAATATCAAGATCCTCAGGCATGCCATACAAATATGAAGTAT
* * * * * * *
6635412 TGATTACCATCACATCCTGACATATATTCTATGTTAGTGCGAAATCAGTATTAAACATTGATAAT
259 TGATTACAATCAAATCATGACATATATTCCATGTTAGCGCAAAATCAGTATTAAACATTGATAAG
* *
6635477 AATAGCATTGATTTCCTTCATATTCAAACATTGATATTCT
324 AATAGCATTGATTTCCTTCATATTCAAACATTAACATTCT
* * * **
6635517 AGTTGTTATGGACTAATGTTTTCGTCTTCTTATATTGGCAAAAATAGTTTCCTTACTTAGTCCAG
1 AGTTGTTATGGATTGATGTTTTCGTCTTCTTAAATT-GC-AAAATAGTTTCCTCGCTTAGTCCAG
* * * * *
6635582 TGAAAACATCCCCAATTTGCTCCTCCAACTCCAACAGTTCCGACAAAATAAGTGACACGAGATTT
64 TGAAAACATCCCCAATTTGCTCCTCCAGCTCCAACAGTTCCTACAAAATAAATAACACAAGATTT
* * *
6635647 TAAAACTATAAGT-AATTCCCATTGGACTCAAAATATTTGAGTGTTACCTCATAAGATATGTTAT
129 TAAAACCATAAGTAAATT-CCATTGAACTCAAAACATTTGAGTGTTACCTCATAAGATATGTTAT
* * * * * * *
6635711 CTACATCT-AGGTACATATCCTCCATAATATGAGGATCCTCAGGCATGCCTTACAAATATGAA-T
193 CGACAT-TAAGGCACATATCCTCAAGAATATCAAGATCCTCAGGCATGCCATACAAATATGAAGT
* * * * *
6635774 GATTGATTACAATCAAATCATGCCTTATATTCCATGTTGGCGCAAAATTAGTGTTAAACATTGAT
257 -ATTGATTACAATCAAATCATGACATATATTCCATGTTAGCGCAAAATCAGTATTAAACATTGAT
*
6635839 AAGAATAGCATTGATTTCCTTCATATTCAAACATTAACATTTT
321 AAGAATAGCATTGATTTCCTTCATATTCAAACATTAACATTCT
** * * * * ** **
6635882 AACTATTATGTATTGATATTTTCGTCTTCTTAGATTG-ACCATAGTTTCCTCGCTTAGTCCAACG
1 AGTTGTTATGGATTGATGTTTTCGTCTTCTTAAATTGCAAAATAGTTTCCTCGCTTAGTCCAGTG
* * * *
6635946 CAAACATCCCCAATTTGTTCTTCCAGCTCCTACAGTTCCTACAAAATAA
66 AAAACATCCCCAATTTGCTCCTCCAGCTCCAACAGTTCCTACAAAATAA
6635995 TCACAAGAAA
Statistics
Matches: 399, Mismatches: 74, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
362 64 0.16
363 1 0.00
364 8 0.02
365 325 0.81
366 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (363 bp):
AGTTGTTATGGATTGATGTTTTCGTCTTCTTAAATTGCAAAATAGTTTCCTCGCTTAGTCCAGTG
AAAACATCCCCAATTTGCTCCTCCAGCTCCAACAGTTCCTACAAAATAAATAACACAAGATTTTA
AAACCATAAGTAAATTCCATTGAACTCAAAACATTTGAGTGTTACCTCATAAGATATGTTATCGA
CATTAAGGCACATATCCTCAAGAATATCAAGATCCTCAGGCATGCCATACAAATATGAAGTATTG
ATTACAATCAAATCATGACATATATTCCATGTTAGCGCAAAATCAGTATTAAACATTGATAAGAA
TAGCATTGATTTCCTTCATATTCAAACATTAACATTCT
Found at i:6636590 original size:21 final size:20
Alignment explanation
Indices: 6636558--6636596 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
6636548 AATGTTACAG
6636558 TAATTTAGTTATTATATTAA
1 TAATTTAGTTATTATATTAA
* *
6636578 TAATATTATTTATTTTATT
1 TAAT-TTAGTTATTATATT
6636597 TAACATTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TAATTTAGTTATTATATTAA
Found at i:6641410 original size:26 final size:26
Alignment explanation
Indices: 6641374--6641459 Score: 122
Period size: 26 Copynumber: 3.3 Consensus size: 26
6641364 CACCAACGTG
*
6641374 ATAATATACATAAGGTTATGCCCACC
1 ATAATACACATAAGGTTATGCCCACC
6641400 ATAATACACATAA-GTTCATGCCCACC
1 ATAATACACATAAGGTT-ATGCCCACC
**
6641426 ATAATACACATAAGGTCGTGCCCACC
1 ATAATACACATAAGGTTATGCCCACC
6641452 AT-ATACAC
1 ATAATACAC
6641460 TTAGTGTTGT
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
25 9 0.16
26 44 0.80
27 2 0.04
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.23
Consensus pattern (26 bp):
ATAATACACATAAGGTTATGCCCACC
Found at i:6641696 original size:22 final size:23
Alignment explanation
Indices: 6641663--6641706 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
6641653 AATACCTGAA
* *
6641663 ATATCATTCATGTTAAATATCAT
1 ATATCATTCATGATAAACATCAT
6641686 ATAT-ATTCATGATAAACATCA
1 ATATCATTCATGATAAACATCA
6641707 AATGTAACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (23 bp):
ATATCATTCATGATAAACATCAT
Found at i:6644870 original size:23 final size:22
Alignment explanation
Indices: 6644844--6644896 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
6644834 ATTAGCAGCA
6644844 GAAAAAAAAACATGAAAAAAATG-
1 GAAAAAAAAACA--AAAAAAATGT
*
6644867 GAAAACAAAACAAAAAAAATGT
1 GAAAAAAAAACAAAAAAAATGT
6644889 GAAAAAAA
1 GAAAAAAA
6644897 TCGAATGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 9 0.33
22 7 0.26
23 11 0.41
ACGTcount: A:0.75, C:0.06, G:0.11, T:0.08
Consensus pattern (22 bp):
GAAAAAAAAACAAAAAAAATGT
Found at i:6648649 original size:22 final size:20
Alignment explanation
Indices: 6648610--6648664 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
6648600 TGAGATAAAG
* *
6648610 GTATCAGTACCATAGTATAGAA
1 GTATCAATACTATAGTAT-G-A
*
6648632 GTATCAATACTATGGTATGA
1 GTATCAATACTATAGTATGA
6648652 GTATCAATACTAT
1 GTATCAATACTAT
6648665 TGAACCTGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 14 0.47
21 1 0.03
22 15 0.50
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (20 bp):
GTATCAATACTATAGTATGA
Found at i:6649112 original size:44 final size:44
Alignment explanation
Indices: 6649064--6649292 Score: 316
Period size: 44 Copynumber: 5.2 Consensus size: 44
6649054 AAAACGAATT
6649064 CATAAATGAAATGCATAAAGGTGCATTAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAAAGGTGCATTAAGGCATGAAAGGATGC
* *
6649108 CATAAATGAAATGCATAACA-GTACATTAGGGCATGAAAGGATGC
1 CATAAATGAAATGCATAA-AGGTGCATTAAGGCATGAAAGGATGC
* * *
6649152 CATAAATGAAATGCATAACGGTGCATTAAAGTCATGAAAGGATTC
1 CATAAATGAAATGCATAAAGGTGCATT-AAGGCATGAAAGGATGC
* * * **
6649197 TATAAATGAAATGCATAAATGTCCATTAAGGCATGAAAGGATTA
1 CATAAATGAAATGCATAAAGGTGCATTAAGGCATGAAAGGATGC
* *
6649241 CATAAAGGAAATGCATAACGGTGCATTAATGGCATGAAAGGATGC
1 CATAAATGAAATGCATAAAGGTGCATTAA-GGCATGAAAGGATGC
6649286 CATAAAT
1 CATAAAT
6649293 AAAAATAATG
Statistics
Matches: 160, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
44 103 0.64
45 57 0.36
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (44 bp):
CATAAATGAAATGCATAAAGGTGCATTAAGGCATGAAAGGATGC
Found at i:6649214 original size:89 final size:89
Alignment explanation
Indices: 6649064--6649292 Score: 345
Period size: 89 Copynumber: 2.6 Consensus size: 89
6649054 AAAACGAATT
*
6649064 CATAAATGAAATGCATAAAGGTGCATT-AAGGCATGAAAGGATGCCATAAATGAAATGCATAACA
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAA-A
* *
6649128 -GTACATTAGGGCATGAAAGGATGC
65 TGTACATTAAGGCATGAAAGGATGA
* * *
6649152 CATAAATGAAATGCATAACGGTGCATTAAAGTCATGAAAGGATTCTATAAATGAAATGCATAAAT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAAAT
* *
6649217 GTCCATTAAGGCATGAAAGGATTA
66 GTACATTAAGGCATGAAAGGATGA
* *
6649241 CATAAAGGAAATGCATAACGGTGCATTAATGGCATGAAAGGATGCCATAAAT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAAT
6649293 AAAAATAATG
Statistics
Matches: 126, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
88 27 0.21
89 99 0.79
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (89 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAAAT
GTACATTAAGGCATGAAAGGATGA
Found at i:6650139 original size:8 final size:8
Alignment explanation
Indices: 6650126--6650152 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
6650116 AGAAATAGTG
6650126 ATAAATGT
1 ATAAATGT
6650134 ATAAATGT
1 ATAAATGT
6650142 ATAAATGT
1 ATAAATGT
6650150 ATA
1 ATA
6650153 GAGATGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (8 bp):
ATAAATGT
Found at i:6650527 original size:54 final size:54
Alignment explanation
Indices: 6650442--6650629 Score: 306
Period size: 54 Copynumber: 3.5 Consensus size: 54
6650432 AGTTGCACTT
* *
6650442 ATTTCTTAGGTTGCACAGATAGTACCGATACAGAAATTCATAAACTAATTATGA
1 ATTTCTTAGGTTGCACACATAGTACCAATACAGAAATTCATAAACTAATTATGA
* *
6650496 ATTTCTTAGGTTGCACACATAGTTCCAATACAAAAATTCATAAACTAATTATGA
1 ATTTCTTAGGTTGCACACATAGTACCAATACAGAAATTCATAAACTAATTATGA
* *
6650550 ATTTCTTAGGTTGCACACATAGTGCCAATAC-GAAAATTCATAAACTTATTATGA
1 ATTTCTTAGGTTGCACACATAGTACCAATACAG-AAATTCATAAACTAATTATGA
6650604 ATTTCTTAGGTTGCACACATAGTACC
1 ATTTCTTAGGTTGCACACATAGTACC
6650630 CATTCGGTAA
Statistics
Matches: 125, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
54 125 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (54 bp):
ATTTCTTAGGTTGCACACATAGTACCAATACAGAAATTCATAAACTAATTATGA
Found at i:6653061 original size:364 final size:365
Alignment explanation
Indices: 6652385--6653229 Score: 1036
Period size: 364 Copynumber: 2.3 Consensus size: 365
6652375 CTGGAGGTTC
* * *
6652385 AGTTGTTATGGATTGATGTTTTCATCTTCTTAAATT-ATCCAGAATAGTTTCCTCGCTTAGTCCT
1 AGTTGTTATGGACTGATGTTTTCATCTTCTTAAATTGA-CCAAAATAGTTTCCTCGCTTAGTCCA
* * * * * *
6652449 GTGGAAACATCCCCAATTAGCTACTCCAGCTTCATCAATTCCTACAAAATAAATGACTCAAGCTT
65 GTGAAAACATCCCCAATTTGCTCCTCCAGCTTCAACAGTTCCTACAAAATAAATGACACAAGCTT
* * *
6652514 TTAAAACCCTAAGTAATTTCCATTGAACTAAAAATATTTGAGTGTTACCTTATAAGATATGTTAT
130 TTAAAACCATAAGTAATTCCCATTGAACTAAAAATATTTGAGTGTTACCTCATAAGATATGTTAT
* * * * *
6652579 TGTCATCAAGGCACATATCCTCAAGAATATCAAGATCTTCAGGTATGCCATACAAATATTAAGTA
195 TGACATCAAGGCACATATCCTCAAGAATATCAAGATCCTCAGGCATACCATACAAATATGAAGTA
* * *
6652644 TTGATTACCATCACATCCTAACATATATTCTATGTTAGTGCGAAATCAGTGTTAAACATTGATAA
260 TTGATTACAATCACATCCTAACATATATTCCATGTTAGTGCGAAAACAGTGTTAAACATTGATAA
* * *
6652709 TAATAGCA-TGATTTCCTTCATATTCAAACATTGATATTCT
325 GAATAGCATTGATTTCCTTCATATTCAAACATTAACATTCT
* * * * * **
6652749 AGTTGTTATGTACTAATGTTTTCATCTTCTTATATTGGCGAAAATAGTTTCCTTACTTAGTCCAG
1 AGTTGTTATGGACTGATGTTTTCATCTTCTTAAATTGACCAAAATAGTTTCCTCGCTTAGTCCAG
* * *
6652814 TGAAAACATCCCCAATTTGCTCCTCCAGCTTCAACAGTTCCGACAAAATAAGTGACACGAGCTTT
66 TGAAAACATCCCCAATTTGCTCCTCCAGCTTCAACAGTTCCTACAAAATAAATGACACAAGCTTT
* * *
6652879 TAAAACTATAAGTAATTCCCATTGGACTCAAAATATTTGAGTGTTACCTCATAAGATATGTTATC
131 TAAAACCATAAGTAATTCCCATTGAACTAAAAATATTTGAGTGTTACCTCATAAGATATGTTAT-
* * * * * *
6652944 T-ACAT-ATAGGTACATATCCTCGATAATATGAGGATCCTCAGGCATACCTTACAAATATGAA-T
195 TGACATCA-AGGCACATATCCTCAAGAATATCAAGATCCTCAGGCATACCATACAAATATGAAGT
** * *
6653006 GATTGATTACAATCACATCCTGCCTTATATTCCATGTTGGTGC-AAAACAAGTGTTAAACATTGA
259 -ATTGATTACAATCACATCCTAACATATATTCCATGTTAGTGCGAAAAC-AGTGTTAAACATTGA
* *
6653070 TAAGAATAGCATTGATTTCCTTCATATTGAAACATTAACATTTT
322 TAAGAATAGCATTGATTTCCTTCATATTCAAACATTAACATTCT
** * * * * * * * *
6653114 AACTATTATGGACTGATATTTTCGTCTTCTCAGATTGACCATAATAGTTTCATCGCTTAGTCTAG
1 AGTTGTTATGGACTGATGTTTTCATCTTCTTAAATTGACCAAAATAGTTTCCTCGCTTAGTCCAG
* * * * *
6653179 CGCAAACATCCCCAATTTGCTCTTCCAGCTCCTACAGTTCCTACAAAATAA
66 TGAAAACATCCCCAATTTGCTCCTCCAGCTTCAACAGTTCCTACAAAATAA
6653230 TCACAATAAA
Statistics
Matches: 405, Mismatches: 70, Indels: 11
0.83 0.14 0.02
Matches are distributed among these distances:
363 6 0.01
364 276 0.68
365 123 0.30
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (365 bp):
AGTTGTTATGGACTGATGTTTTCATCTTCTTAAATTGACCAAAATAGTTTCCTCGCTTAGTCCAG
TGAAAACATCCCCAATTTGCTCCTCCAGCTTCAACAGTTCCTACAAAATAAATGACACAAGCTTT
TAAAACCATAAGTAATTCCCATTGAACTAAAAATATTTGAGTGTTACCTCATAAGATATGTTATT
GACATCAAGGCACATATCCTCAAGAATATCAAGATCCTCAGGCATACCATACAAATATGAAGTAT
TGATTACAATCACATCCTAACATATATTCCATGTTAGTGCGAAAACAGTGTTAAACATTGATAAG
AATAGCATTGATTTCCTTCATATTCAAACATTAACATTCT
Found at i:6654169 original size:26 final size:26
Alignment explanation
Indices: 6654133--6654213 Score: 110
Period size: 26 Copynumber: 3.1 Consensus size: 26
6654123 CACCAACAAG
*
6654133 ATAATATACATAAGGTTATGCCCACC
1 ATAATACACATAAGGTTATGCCCACC
*
6654159 ATAATACACATAA-GTTCTTGCCCACC
1 ATAATACACATAAGGTT-ATGCCCACC
**
6654185 ATAATACACATAAGGTCGTGCCCACC
1 ATAATACACATAAGGTTATGCCCACC
6654211 ATA
1 ATA
6654214 TAACTTACTG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.06
26 44 0.90
27 2 0.04
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.25
Consensus pattern (26 bp):
ATAATACACATAAGGTTATGCCCACC
Found at i:6654454 original size:22 final size:23
Alignment explanation
Indices: 6654421--6654464 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
6654411 AATACCCTAA
* *
6654421 ATATCATTCATGTTAAATATCAT
1 ATATCATTCATGATAAACATCAT
6654444 ATAT-ATTCATGATAAACATCA
1 ATATCATTCATGATAAACATCA
6654465 AATGTAACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (23 bp):
ATATCATTCATGATAAACATCAT
Found at i:6657475 original size:26 final size:26
Alignment explanation
Indices: 6657440--6657489 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
6657430 ATTGAAGTGC
*
6657440 TAATAAACATAAGGTTGTGCCCACCA
1 TAATAAACATAAGGTCGTGCCCACCA
*
6657466 TAATACACATAAGGTCGTGCCCAC
1 TAATAAACATAAGGTCGTGCCCAC
6657490 TATATGCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (26 bp):
TAATAAACATAAGGTCGTGCCCACCA
Found at i:6661202 original size:12 final size:12
Alignment explanation
Indices: 6661174--6661229 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
6661164 CAAGTATTAG
6661174 ATCAGAATCCAT
1 ATCAGAATCCAT
*
6661186 GTCAGATAT-CAT
1 ATCAGA-ATCCAT
6661198 ATCAGAATCCAT
1 ATCAGAATCCAT
* *
6661210 GTCA-AATATCAT
1 ATCAGAAT-CCAT
6661222 ATCAGAAT
1 ATCAGAAT
6661230 TCAAATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
11 5 0.14
12 25 0.71
13 5 0.14
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (12 bp):
ATCAGAATCCAT
Found at i:6661226 original size:24 final size:24
Alignment explanation
Indices: 6661111--6661229 Score: 132
Period size: 24 Copynumber: 5.0 Consensus size: 24
6661101 AAACATAATT
* *
6661111 CATGTCAAGTATCATGTCAAAATC
1 CATGTCAAGTATCATATCAGAATC
* * * *
6661135 CAGGTCAAGTATCAGATTAAAATC
1 CATGTCAAGTATCATATCAGAATC
* * *
6661159 CAAGTCAAGTATTAGATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
6661183 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
*
6661207 CATGTCAAATATCATATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
6661230 TCAAATAAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.02
24 78 0.96
25 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:6661244 original size:24 final size:24
Alignment explanation
Indices: 6661193--6661244 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
6661183 CATGTCAGAT
** * *
6661193 ATCATATCAGAATCCATGTCAAAT
1 ATCATATCAGAATCCAAATAAAAA
*
6661217 ATCATATCAGAATTCAAATAAAAA
1 ATCATATCAGAATCCAAATAAAAA
6661241 ATCA
1 ATCA
6661245 GATAAAATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.27
Consensus pattern (24 bp):
ATCATATCAGAATCCAAATAAAAA
Found at i:6663001 original size:21 final size:21
Alignment explanation
Indices: 6662977--6663025 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
6662967 GATCGTCGTG
*
6662977 AATCGACGAT-AAACTAACTGA
1 AATCGA-GATAAAACCAACTGA
*
6662998 AATCGAGTTAAAACCAACTGA
1 AATCGAGATAAAACCAACTGA
6663019 AATCGAG
1 AATCGAG
6663026 TTACAACTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (21 bp):
AATCGAGATAAAACCAACTGA
Found at i:6663026 original size:21 final size:21
Alignment explanation
Indices: 6662987--6663028 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6662977 AATCGACGAT
*
6662987 AAACTAACTGAAATCGAGTTA
1 AAACCAACTGAAATCGAGTTA
6663008 AAACCAACTGAAATCGAGTTA
1 AAACCAACTGAAATCGAGTTA
6663029 CAACTGACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (21 bp):
AAACCAACTGAAATCGAGTTA
Found at i:6668783 original size:12 final size:13
Alignment explanation
Indices: 6668761--6668796 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
6668751 TACCATTTTG
6668761 AATTTTCTTTTAA
1 AATTTTCTTTTAA
*
6668774 ACTTTT-TTTTAA
1 AATTTTCTTTTAA
6668786 AATTTTCTTTT
1 AATTTTCTTTT
6668797 TAATCTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (13 bp):
AATTTTCTTTTAA
Found at i:6668816 original size:26 final size:25
Alignment explanation
Indices: 6668761--6668817 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
6668751 TACCATTTTG
* *
6668761 AATTTTCTTTTAAACTTTTTTTTAA
1 AATTTTCTTTTAAACTTTCTTTGAA
*
6668786 AATTTTCTTTTTAA-TCTTCTTTGAA
1 AATTTTCTTTTAAACT-TTCTTTGAA
6668811 ATATTTT
1 A-ATTTT
6668818 TTCTTTCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 21 0.78
26 5 0.19
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (25 bp):
AATTTTCTTTTAAACTTTCTTTGAA
Found at i:6669850 original size:34 final size:34
Alignment explanation
Indices: 6669809--6669888 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 34
6669799 AGTAGAATTG
* *
6669809 TTTTGGTTCGAACAATAACAAAACAACAGTACAA
1 TTTTGGTTCGAACAATAAAAAAACAACAGAACAA
* * * * *
6669843 TTTTGGTTCAAACAGTAAAAAAATAGCAGAACAG
1 TTTTGGTTCGAACAATAAAAAAACAACAGAACAA
6669877 TTTTGGTTCGAA
1 TTTTGGTTCGAA
6669889 TAGAAAAAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (34 bp):
TTTTGGTTCGAACAATAAAAAAACAACAGAACAA
Found at i:6669897 original size:34 final size:34
Alignment explanation
Indices: 6669808--6669897 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 34
6669798 AAGTAGAATT
* *
6669808 GTTTTGGTTCGAACA-ATAACAAAACAACAGTACA
1 GTTTTGGTTCGAACAGA-AAAAAAACAACAGAACA
* * * * *
6669842 ATTTTGGTTCAAACAGTAAAAAAATAGCAGAACA
1 GTTTTGGTTCGAACAGAAAAAAAACAACAGAACA
*
6669876 GTTTTGGTTCGAATAGAAAAAA
1 GTTTTGGTTCGAACAGAAAAAA
6669898 GAAAAAAACA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.26
Consensus pattern (34 bp):
GTTTTGGTTCGAACAGAAAAAAAACAACAGAACA
Found at i:6671812 original size:13 final size:13
Alignment explanation
Indices: 6671794--6671820 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6671784 GTTTAAATGT
6671794 TTTAAGAATTATC
1 TTTAAGAATTATC
6671807 TTTAAGAATTATC
1 TTTAAGAATTATC
6671820 T
1 T
6671821 CTTGTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTAAGAATTATC
Found at i:6677099 original size:20 final size:20
Alignment explanation
Indices: 6677074--6677128 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
6677064 TCCAAAATTG
*
6677074 GTAAGTCTTTCGGGCCATCA
1 GTAAGTCTTTCGAGCCATCA
6677094 GTAAGTCTTTCGAGCCATCA
1 GTAAGTCTTTCGAGCCATCA
6677114 GTAAGTCTTTCGAGC
1 GTAAGTCTTTCGAGC
6677129 ATGATGACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
GTAAGTCTTTCGAGCCATCA
Found at i:6678006 original size:261 final size:258
Alignment explanation
Indices: 6677443--6678204 Score: 1010
Period size: 261 Copynumber: 2.9 Consensus size: 258
6677433 ATGATAAGTC
* * * * * **
6677443 TAAGACCTTCGGGTAGGATGTTTTCATATG--ATTTGCAAAAGATGAGAAAATGATTTTTGAAGT
1 TAAGACCTTCGGGTAGGATGTTTCCATATGATATTTGAAAAAAATGAGAAAGTGAGTTTCAAAGT
* * *
6677506 TTCTCATTTAAGATTTTCAGAAAATGAAAATATTGAAAAA-TAAGAAAGTGATTTCCAAAGTTTC
66 TTCTCATTTAAGATTTTCAGAAAAT-AAAATTTTTAAAAAGTAAGAAAGCGATTTCCAAAGTTTC
* * *
6677570 TTACCCAGTAGACTATTTCTCAAAATTGGTACGTCATTCGGGCCATCAGTATGTCTTTCGAGCAT
130 TTACCCAGTAGACTATTTC-CAAAATTGGTAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCAT
* *
6677635 GATGATTAAATCCTTCAGGTCATCTATCAATCTTTGGAGCAAGATGATAAGTCCCCCGGGCCATC
194 GATGATTAAATCCTT--GGTCATCTATCAATCTTTCGAGCAAGATGATAAGTCCCCCAGGCCATC
6677700 TA
257 TA
* * *
6677702 TAAAACCTTCGGGCAGGATGTTTCCATATGATATTTGAAAAAAATGAGAAAGCGAGTTTCAAAGT
1 TAAGACCTTCGGGTAGGATGTTTCCATATGATATTTGAAAAAAATGAGAAAGTGAGTTTCAAAGT
* * *
6677767 TTCTCATTTAAGATTTTCAGAAAATTAAATTTTTAAAAAGTAAGAAACCAATTTCCAAAGTTTCT
66 TTCTCATTTAAGATTTTCAGAAAATAAAATTTTTAAAAAGTAAGAAAGCGATTTCCAAAGTTTCT
* * ** *
6677832 TACCCAGTAGACTATTTCCAAAATTGATAAGTCCTTCAAGCCATCAATAAGTCTTTCGAGGATGA
131 TACCCAGTAGACTATTTCCAAAATTGGTAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGA
*
6677897 TGATTAAATCCGTTGGTTCATCTATCAATCTTTCGAGCAAGATGATAAGTCCCTCAGGCCATCTA
196 TGATTAAATCC-TTGG-TCATCTATCAATCTTTCGAGCAAGATGATAAGTCCCCCAGGCCATCTA
* * *
6677962 TAAGACCTTCTGGTAGGATCTTTCCATATGATATTTGAAAAAAAATGAGAAAGTG-GTTTTCACA
1 TAAGACCTTCGGGTAGGATGTTTCCATATGATATTTG-AAAAAAATGAGAAAGTGAG-TTTCAAA
* ** * * *
6678026 GTTTCTCATTTAAGATTTTCAGAGAACGAATTTTTTGAGAAGTAAGAAAGCGATTTCCAAAGTTT
64 GTTTCTCATTTAAGATTTTCAGAAAATAAAATTTTTAAAAAGTAAGAAAGCGATTTCCAAAGTTT
* * *
6678091 CTTACCCAATAGACTATTTCCAAAATTGGTAAGTCATTCGGGCCATCAATAAGCCTTTCAAGCAT
129 CTTACCCAGTAGACTATTTCCAAAATTGGTAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCAT
* * * * *
6678156 GATAATTATATCATTTGGGTCATCTGTCAGTCTTTCGAGCAAGATGATA
194 GATGATTAAATC-CTT-GGTCATCTATCAATCTTTCGAGCAAGATGATA
6678205 TTTGAAAACA
Statistics
Matches: 440, Mismatches: 54, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
259 29 0.07
260 140 0.32
261 269 0.61
262 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (258 bp):
TAAGACCTTCGGGTAGGATGTTTCCATATGATATTTGAAAAAAATGAGAAAGTGAGTTTCAAAGT
TTCTCATTTAAGATTTTCAGAAAATAAAATTTTTAAAAAGTAAGAAAGCGATTTCCAAAGTTTCT
TACCCAGTAGACTATTTCCAAAATTGGTAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCATGA
TGATTAAATCCTTGGTCATCTATCAATCTTTCGAGCAAGATGATAAGTCCCCCAGGCCATCTA
Found at i:6678258 original size:25 final size:23
Alignment explanation
Indices: 6678230--6678287 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 23
6678220 GAAAAATGAT
6678230 GAAAAAAGAGAAAATA-AAGAGAAAA
1 GAAAAAAGA-AAAA-AGAAGA-AAAA
6678255 GAAAAAAGAAAAAAGAAGAAAAA
1 GAAAAAAGAAAAAAGAAGAAAAA
6678278 G-AAAAAGAAA
1 GAAAAAAGAAA
6678288 TAAATGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.28
23 6 0.19
24 8 0.25
25 9 0.28
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (23 bp):
GAAAAAAGAAAAAAGAAGAAAAA
Found at i:6678264 original size:23 final size:22
Alignment explanation
Indices: 6678232--6678291 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
6678222 AAAATGATGA
6678232 AAAAAGAGAAAATAAAGAGAAAAG
1 AAAAA-AGAAAATAAAGA-AAAAG
*
6678256 AAAAAAGAAAAAAGAAGAAAAAG
1 AAAAAAGAAAATA-AAGAAAAAG
6678279 -AAAAAG-AAATAAA
1 AAAAAAGAAAATAAA
6678292 TGATAGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 4 0.12
22 6 0.18
23 12 0.36
24 9 0.27
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (22 bp):
AAAAAAGAAAATAAAGAAAAAG
Found at i:6678837 original size:14 final size:13
Alignment explanation
Indices: 6678800--6678826 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6678790 AAAACATTGG
6678800 ATACCCAAATTTA
1 ATACCCAAATTTA
6678813 ATACCCAAATTTA
1 ATACCCAAATTTA
6678826 A
1 A
6678827 ATGTCCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
ATACCCAAATTTA
Found at i:6680484 original size:29 final size:28
Alignment explanation
Indices: 6680452--6680506 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
6680442 TTTTATATTT
6680452 TTATTTACATTTTCTCCCTTTAATTTCTG
1 TTATTTACATTTT-TCCCTTTAATTTCTG
* *
6680481 TTATTTTCATTTTTGCCTTTAATTTC
1 TTATTTACATTTTTCCCTTTAATTTC
6680507 CAAAATTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.16, C:0.18, G:0.04, T:0.62
Consensus pattern (28 bp):
TTATTTACATTTTTCCCTTTAATTTCTG
Found at i:6685492 original size:104 final size:104
Alignment explanation
Indices: 6685312--6685513 Score: 260
Period size: 104 Copynumber: 1.9 Consensus size: 104
6685302 TGATATAGAG
* * * * * **
6685312 TTGGATTCATGCATTATACAACATGGAAATGTGTGCAGTCTCCTCGCCTGGATTAACTATTTAAC
1 TTGGATTCATGCATTAAACAACAAGGAAATGTGTGCAGTCTCCACGCCTGGATCAACGACGTAAC
* * *
6685377 TCCTACCATTAATGTGGCTTGTGTATTTACACATCCTTA
66 TACTACCATTAATGTGGCTCGTGTATTCACACATCCTTA
* * *
6685416 TTGGATTCATGCATTAAACAATAAGGAAATGTGTGCAGTCTCCACGCTTGGATCAACGCCGTAAC
1 TTGGATTCATGCATTAAACAACAAGGAAATGTGTGCAGTCTCCACGCCTGGATCAACGACGTAAC
* * *
6685481 TATTGCTATTAATGTGGCTCGTGTATTCACACA
66 TACTACCATTAATGTGGCTCGTGTATTCACACA
6685514 AGACTGTTGC
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
104 82 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (104 bp):
TTGGATTCATGCATTAAACAACAAGGAAATGTGTGCAGTCTCCACGCCTGGATCAACGACGTAAC
TACTACCATTAATGTGGCTCGTGTATTCACACATCCTTA
Found at i:6686808 original size:41 final size:40
Alignment explanation
Indices: 6686763--6686870 Score: 105
Period size: 41 Copynumber: 2.6 Consensus size: 40
6686753 TCACATATTT
* *
6686763 TTGCGGCGTTTATACAATAAGCGTCGCTATAT-TAC-ACTATA
1 TTGCGGCGTTT-TACAATAA-CGCCGCTAAATGT-CTACTATA
6686804 TTGCGGCGTTTTTAGCTAA-AACGCCGCTAAATGTCTACTATA
1 TTGCGGCG-TTTTA-C-AATAACGCCGCTAAATGTCTACTATA
*
6686846 TTGCGGCGTTTTACTATAAACGCCG
1 TTGCGGCGTTTTACAAT-AACGCCG
6686871 TTATTGTTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
39 1 0.02
40 1 0.02
41 32 0.56
42 21 0.37
43 2 0.04
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (40 bp):
TTGCGGCGTTTTACAATAACGCCGCTAAATGTCTACTATA
Found at i:6690018 original size:20 final size:20
Alignment explanation
Indices: 6690001--6690049 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
6689991 ACGAGTATTG
6690001 ATACTCACCCCTAGGTATCA
1 ATACTCACCCCTAGGTATCA
6690021 ATACTCACCCCTAGGTATCA
1 ATACTCACCCCTAGGTATCA
6690041 ATACTCACC
1 ATACTCACC
6690050 TTAAGTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.37, G:0.08, T:0.24
Consensus pattern (20 bp):
ATACTCACCCCTAGGTATCA
Found at i:6693436 original size:18 final size:18
Alignment explanation
Indices: 6693401--6693436 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6693391 TGTACATATG
*
6693401 TATTTTATGTGAATATTT
1 TATTTTATGTGAAGATTT
*
6693419 TATTTTATGTGGAGATTT
1 TATTTTATGTGAAGATTT
6693437 CTTTATGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (18 bp):
TATTTTATGTGAAGATTT
Found at i:6696076 original size:16 final size:16
Alignment explanation
Indices: 6696050--6696108 Score: 93
Period size: 16 Copynumber: 3.8 Consensus size: 16
6696040 AAATGAAAGC
6696050 TATAG-CTATGGGGAT
1 TATAGTCTATGGGGAT
6696065 TATAGTCTATGGGGAT
1 TATAGTCTATGGGGAT
* *
6696081 TATAGTGTATGGGTAT
1 TATAGTCTATGGGGAT
6696097 TATAGTCTATGG
1 TATAGTCTATGG
6696109 AACAATACCT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
15 5 0.12
16 35 0.88
ACGTcount: A:0.25, C:0.05, G:0.31, T:0.39
Consensus pattern (16 bp):
TATAGTCTATGGGGAT
Found at i:6697396 original size:13 final size:13
Alignment explanation
Indices: 6697378--6697471 Score: 55
Period size: 18 Copynumber: 6.3 Consensus size: 13
6697368 GTCACAACCC
6697378 GACCTGACCCGTT
1 GACCTGACCCGTT
6697391 GACCTGACCCGTT
1 GACCTGACCCGTT
6697404 GGCCCGACCTGACCCGTT
1 -----GACCTGACCCGTT
*
6697422 GGCCCGACCCGACCCGTT
1 -----GACCTGACCCGTT
6697440 GA-CTCGACCCGTT
1 GACCT-GACCCGTT
6697453 GACCGTTGACCCGTT
1 GACC--TGACCCGTT
6697468 GACC
1 GACC
6697472 GTCGTTGACC
Statistics
Matches: 70, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
12 1 0.01
13 25 0.36
14 1 0.01
15 12 0.17
16 1 0.01
18 30 0.43
ACGTcount: A:0.14, C:0.41, G:0.26, T:0.19
Consensus pattern (13 bp):
GACCTGACCCGTT
Found at i:6697412 original size:18 final size:18
Alignment explanation
Indices: 6697391--6697440 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
6697381 CTGACCCGTT
6697391 GACCTGACCCGTTGGCCC
1 GACCTGACCCGTTGGCCC
6697409 GACCTGACCCGTTGGCCC
1 GACCTGACCCGTTGGCCC
*
6697427 GACCCGACCCGTTG
1 GACCTGACCCGTTG
6697441 ACTCGACCCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.12, C:0.44, G:0.28, T:0.16
Consensus pattern (18 bp):
GACCTGACCCGTTGGCCC
Found at i:6697447 original size:18 final size:18
Alignment explanation
Indices: 6697391--6697450 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
6697381 CTGACCCGTT
*
6697391 GACCTGACCCGTTGGCCC
1 GACCCGACCCGTTGGCCC
*
6697409 GACCTGACCCGTTGGCCC
1 GACCCGACCCGTTGGCCC
* *
6697427 GACCCGACCCGTTGACTC
1 GACCCGACCCGTTGGCCC
6697445 GACCCG
1 GACCCG
6697451 TTGACCGTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.13, C:0.45, G:0.27, T:0.15
Consensus pattern (18 bp):
GACCCGACCCGTTGGCCC
Found at i:6697465 original size:15 final size:15
Alignment explanation
Indices: 6697431--6697475 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
6697421 TGGCCCGACC
6697431 CGACCCGTTGA-C-T
1 CGACCCGTTGACCGT
6697444 CGACCCGTTGACCGT
1 CGACCCGTTGACCGT
*
6697459 TGACCCGTTGACCGT
1 CGACCCGTTGACCGT
6697474 CG
1 CG
6697476 TTGACCACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 11 0.39
14 1 0.04
15 16 0.57
ACGTcount: A:0.13, C:0.38, G:0.27, T:0.22
Consensus pattern (15 bp):
CGACCCGTTGACCGT
Found at i:6697479 original size:10 final size:8
Alignment explanation
Indices: 6697445--6697491 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
6697435 CCGTTGACTC
6697445 GACCCGTT
1 GACCCGTT
6697453 GA-CCGTT
1 GACCCGTT
6697460 GACCCGTT
1 GACCCGTT
6697468 GACCGTCGTT
1 GACC--CGTT
6697478 GACCACTGTT
1 GACC-C-GTT
6697488 GACC
1 GACC
6697492 AAAACTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 11 0.32
9 1 0.03
10 15 0.44
ACGTcount: A:0.15, C:0.34, G:0.26, T:0.26
Consensus pattern (8 bp):
GACCCGTT
Found at i:6707270 original size:34 final size:32
Alignment explanation
Indices: 6707213--6707284 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 32
6707203 CTTGGCTTGC
*
6707213 TTTC-TTTTTGAATTTCTTTTTCTTTTCT-TCT
1 TTTCTTTTTTGAATTTCTTCTTCTTTT-TGTCT
6707244 TTTCTTTTTCTGAATTTTCTTCTTCTTTTTGTCT
1 TTTCTTTTT-TGAA-TTTCTTCTTCTTTTTGTCT
6707278 TTTCTTT
1 TTTCTTT
6707285 CTTTTTGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 4 0.11
32 4 0.11
33 5 0.14
34 23 0.64
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.74
Consensus pattern (32 bp):
TTTCTTTTTTGAATTTCTTCTTCTTTTTGTCT
Found at i:6707573 original size:19 final size:20
Alignment explanation
Indices: 6707545--6707584 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
6707535 GGATAATAAT
6707545 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
6707565 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
6707584 A
1 A
6707585 AGAAAGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:6709552 original size:11 final size:11
Alignment explanation
Indices: 6709536--6709570 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
6709526 AGTCATACAT
6709536 GTATAAAACAA
1 GTATAAAACAA
6709547 GTATAAAACAA
1 GTATAAAACAA
6709558 GTATAAAACAA
1 GTATAAAACAA
6709569 GT
1 GT
6709571 GAGTTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (11 bp):
GTATAAAACAA
Found at i:6710636 original size:29 final size:29
Alignment explanation
Indices: 6710602--6710660 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
6710592 CCTAAATTAA
6710602 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
6710631 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
6710660 T
1 T
6710661 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:6715235 original size:27 final size:28
Alignment explanation
Indices: 6715204--6715260 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
6715194 CCTAAATTAA
6715204 TTTGATGTCA-TGCTTACATCAATTTAG
1 TTTGATGTCATTGCTTACATCAATTTAG
6715231 TTTGATGTCATTGCTTACATCAATTTAG
1 TTTGATGTCATTGCTTACATCAATTTAG
6715259 TT
1 TT
6715261 AGGTGAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 10 0.34
28 19 0.66
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (28 bp):
TTTGATGTCATTGCTTACATCAATTTAG
Found at i:6717341 original size:60 final size:59
Alignment explanation
Indices: 6717264--6717438 Score: 167
Period size: 60 Copynumber: 2.9 Consensus size: 59
6717254 AGTATGACTC
* * * * *
6717264 TCATTTTAAATTGGTCCTTAAA-TTATTAAATATTTTAATTTCA-TCCCTAAACTATGGATA
1 TCATTCTAAATTGGTCCTAAAACTT-TTAAACATTTCAATTTCATTCCC-AAACTAT-GACA
* * *
6717324 TCATTCTAAATTAGTCCTAAAACTTTTGAACATTTCATTTTCATTCCCAAACTATGACA
1 TCATTCTAAATTGGTCCTAAAACTTTTAAACATTTCAATTTCATTCCCAAACTATGACA
** * * *
6717383 TACATTCTAAATTGGTCCCCAAACGTTTTGAACATTCCAATGTCA-TCCCAAACTAT
1 T-CATTCTAAATTGGTCCTAAAAC-TTTTAAACATTTCAATTTCATTCCCAAACTAT
6717439 ATGTACATAG
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
59 4 0.04
60 70 0.72
61 23 0.24
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.39
Consensus pattern (59 bp):
TCATTCTAAATTGGTCCTAAAACTTTTAAACATTTCAATTTCATTCCCAAACTATGACA
Found at i:6720988 original size:21 final size:20
Alignment explanation
Indices: 6720962--6721005 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
6720952 CATCCGAATC
6720962 AAAATGAAAAAAAATATAAAT
1 AAAATG-AAAAAAATATAAAT
***
6720983 AAAATGGTCAAAATATAAAT
1 AAAATGAAAAAAATATAAAT
6721003 AAA
1 AAA
6721006 TAGAAGCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAATGAAAAAAATATAAAT
Found at i:6721056 original size:5 final size:5
Alignment explanation
Indices: 6721046--6721070 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6721036 AGAGGTGGCC
6721046 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
6721071 CAGCCAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:6723010 original size:240 final size:241
Alignment explanation
Indices: 6722545--6723573 Score: 1345
Period size: 240 Copynumber: 4.3 Consensus size: 241
6722535 ACCCAAAGGT
** * ** * * *
6722545 CTTATAGATGACCCAAATGATTTGGGCATCATGCTCGAAAGACTTACTGATGGCCTAAAGAACAT
1 CTTATAGATGACCTGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCTAAAGGACTT
* * * *
6722610 AATAAGTAAGAAACTTTGGAAATCATTTTCTTGCTTTTCAAGAAAAATGAATTTTCAAAAAAGAT
66 ACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAGAAAAATCAATTTTCAAAAAAGAT
* * *
6722675 TTAAATTAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTGCCCA
131 TTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCATGCCCA
* * *
6722740 AAGGTATTATGGATGGCCTGATGTACTTATCATATTGCTCGAAAGA
196 AAGGTCTTATGGATGGCCTGAAGGACTTATCATATTGCTCGAAAGA
* *
6722786 CTTATAAAT-TCCTGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCTAAAGGACTT
1 CTTATAGATGACCTGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCTAAAGGACTT
*
6722850 ACTAAGTAAGAAACTTTGGAAATTGTTTTCTTACTTTTCAAGAAAAATCAATTTTCAAAAAAGAT
66 ACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAGAAAAATCAATTTTCAAAAAAGAT
* * * *
6722915 TTAAATGAGAAAATTTGAAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCCTACCCA
131 TTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCATGCCCA
* * * * * *
6722980 AAAGTCTTATGAATAGCCTGAAGGACTTATCATCTTGTTCAAAAGA
196 AAGGTCTTATGGATGGCCTGAAGGACTTATCATATTGCTCGAAAGA
* * **
6723026 CTTATAGATGACAC-GAAGGATTTAAGAACCATGCTCGAAATACTTACTGATGGCCCCAAGGACT
1 CTTATAGATGAC-CTGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCTAAAGGACT
* * * * *
6723090 TATTAAGTCATAAACTTTGGAAA-CGTTTTCTTACTTTTC-A-AAAAATAAATTTTCAGAAAAGA
65 TACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAGAAAAATCAATTTTCAAAAAAGA
* * * * * *
6723152 TTTGAATGAGAAACTTTGGAAACCGCTTTCACATTTTTTGAAAATCATGTGAAAACATCATGCTC
130 TTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCATGCCC
* *
6723217 AAAGGTCTTATGGATGGCCTGAAGGACTTATCATCA-TGTTCGAAAGG
195 AAAGGTCTTATGGATGGCCTGAAGGACTTATCAT-ATTGCTCGAAAGA
** * * * * *
6723264 CTTATAGATGACCTGAAGGAAATATGGCATCATGCTCGAAAGACTTACTGATGGCTTGATGGACT
1 CTTATAGATGACCTGAAGGATTTA-AGCACCATGCTCGAAAGACTTACTGATGGCCTAAAGGACT
* * * *
6723329 TACTAAGTAAGAAACTTTGGAAATCGTTTTCATATTTTTCAAGAAAAATCAATTTTTAGAAAAGA
65 TACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAGAAAAATCAATTTTCAAAAAAGA
*
6723394 TTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTTGAAAATCATGTGAAAACATCATGCCC
130 TTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCATGCCC
* * * * * *
6723459 GAAGGCCTTAAGGATGG-ATCGAAGGACTTATCATCTTGCTTGAAAGA
195 AAAGGTCTTATGGATGGCCT-GAAGGACTTATCATATTGCTCGAAAGA
* *
6723506 CTTATAGATGACCCGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGG-CTGGAAGGACT
1 CTTATAGATGACCTGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCT-AAAGGACT
6723570 TACT
65 TACT
6723574 CATCTAGAAA
Statistics
Matches: 683, Mismatches: 94, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
237 1 0.00
238 135 0.20
239 53 0.08
240 241 0.35
241 115 0.17
242 138 0.20
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (241 bp):
CTTATAGATGACCTGAAGGATTTAAGCACCATGCTCGAAAGACTTACTGATGGCCTAAAGGACTT
ACTAAGTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAGAAAAATCAATTTTCAAAAAAGAT
TTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCATGCCCA
AAGGTCTTATGGATGGCCTGAAGGACTTATCATATTGCTCGAAAGA
Found at i:6723268 original size:41 final size:41
Alignment explanation
Indices: 6723207--6723330 Score: 126
Period size: 43 Copynumber: 3.0 Consensus size: 41
6723197 CATGTGAAAA
6723207 CATCATGCTC-AAAGGTCTTATGGATGGCCTGAAGGACTTAT-
1 CATCATGCTCGAAAGG-CTTAT-GATGGCCTGAAGGACTTATG
* * **
6723248 CATCATGTTCGAAAGGCTTATAGATGACCTGAAGGAAATATGG
1 CATCATGCTCGAAAGGCTTAT-GATGGCCTGAAGGACTTAT-G
* * *
6723291 CATCATGCTCGAAAGACTTACTGATGGCTTGATGGACTTA
1 CATCATGCTCGAAAGGCTTA-TGATGGCCTGAAGGACTTA
6723331 CTAAGTAAGA
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 30 0.45
42 5 0.07
43 31 0.46
44 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (41 bp):
CATCATGCTCGAAAGGCTTATGATGGCCTGAAGGACTTATG
Found at i:6723305 original size:43 final size:41
Alignment explanation
Indices: 6723207--6723310 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 41
6723197 CATGTGAAAA
* * **
6723207 CATCATGCTC-AAAGGTCTTATGGATGGCCTGAAGGACTTAT
1 CATCATGCTCGAAAGG-CTTATAGATGACCTGAAGGAAATAT
*
6723248 CATCATGTTCGAAAGGCTTATAGATGACCTGAAGGAAATAT
1 CATCATGCTCGAAAGGCTTATAGATGACCTGAAGGAAATAT
*
6723289 GGCATCATGCTCGAAAGACTTA
1 --CATCATGCTCGAAAGGCTTA
6723311 CTGATGGCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
41 30 0.57
42 5 0.09
43 18 0.34
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (41 bp):
CATCATGCTCGAAAGGCTTATAGATGACCTGAAGGAAATAT
Found at i:6723667 original size:58 final size:57
Alignment explanation
Indices: 6723590--6723734 Score: 161
Period size: 57 Copynumber: 2.5 Consensus size: 57
6723580 GAAACCTTTG
* * * * *
6723590 AAAATCAAGCTTAGTTTC-TTAAAAACTTTCTTT-TACAATTATCATCAAGAAGCCCCTA
1 AAAATCAGGCTTAGCTTCTTTAAAAA--TTCTTTGGA-AATAATCATCAAGAAACCCCTA
* *
6723648 AAAATTAGGCTTAGCTTCTTTAACAATTCTTTGGAAATAATCATCAAGAAACCCCTA
1 AAAATCAGGCTTAGCTTCTTTAAAAATTCTTTGGAAATAATCATCAAGAAACCCCTA
6723705 AAAATCAGGCTTAGCATAT-TTTAAAAATTC
1 AAAATCAGGCTTAGC-T-TCTTTAAAAATTC
6723735 ATCATGTCAA
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
57 40 0.54
58 27 0.36
59 7 0.09
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (57 bp):
AAAATCAGGCTTAGCTTCTTTAAAAATTCTTTGGAAATAATCATCAAGAAACCCCTA
Found at i:6723812 original size:55 final size:55
Alignment explanation
Indices: 6723741--6724069 Score: 379
Period size: 55 Copynumber: 6.0 Consensus size: 55
6723731 ATTCATCATG
* * *
6723741 TCAAGAAACCTATGAAAATCAGACTCAGTTTATTTGAAAGCTCATTTAAAAATTA
1 TCAAGAAACTTATGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATTA
* * * * * *
6723796 TCAAGAAACTTTTGAAAACCTGACTTAGTTTCTTTAAAAACTCATTTAAAATTTCA
1 TCAAGAAACTTATGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATT-A
* * *
6723852 TCAAGAAACTTATGAAAATCATACTTAGTTTCTTTGAAAGCTTATTTAAAAATTG
1 TCAAGAAACTTATGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATTA
* * * * * * *
6723907 TCAAGAAACTTCTAAAAATCAGACTTAGTTTCTTTAAAAACTTATTTAAAAGTCA
1 TCAAGAAACTTATGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATTA
* * *
6723962 TCAAGAAACTTTTGAAAAACAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATAA
1 TCAAGAAACTTATGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATTA
*** * * ** *
6724017 TCAAGAAACTTCCAAAAATCAGACTTAGTCTCTTTCAAAATTAATTTAAAAAT
1 TCAAGAAACTTATGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAAT
6724070 ATAAAAAACC
Statistics
Matches: 230, Mismatches: 43, Indels: 2
0.84 0.16 0.01
Matches are distributed among these distances:
55 183 0.80
56 47 0.20
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (55 bp):
TCAAGAAACTTATGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATTA
Found at i:6724021 original size:110 final size:111
Alignment explanation
Indices: 6723741--6724067 Score: 469
Period size: 110 Copynumber: 3.0 Consensus size: 111
6723731 ATTCATCATG
* * *
6723741 TCAAGAAACCTATGAAAATCAGACTCAGTTTATTTGAAAGCTCATTTAAAAATTATCAAGAAACT
1 TCAAGAAACTTATGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATTATCAAGAAACT
* * * * * *
6723806 TTTGAAAACCTGACTTAGTTTCTTTAAAAACTCATTTAAAATTTCA
66 TCTAAAAATCAGACTTAGTTTCTTTAAAAACTTATTTAAAATGTCA
* * *
6723852 TCAAGAAACTTATGAAAATCATACTTAGTTTCTTTGAAAGCTTATTTAAAAATTGTCAAGAAACT
1 TCAAGAAACTTATGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATTATCAAGAAACT
6723917 TCTAAAAATCAGACTTAGTTTCTTTAAAAACTTATTTAAAA-GTCA
66 TCTAAAAATCAGACTTAGTTTCTTTAAAAACTTATTTAAAATGTCA
* * *
6723962 TCAAGAAACTTTTGAAAAACAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATAATCAAGAAACT
1 TCAAGAAACTTATGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATTATCAAGAAACT
* * *
6724027 TCCAAAAATCAGACTTAGTCTCTTTCAAAA-TTAATTTAAAA
66 TCTAAAAATCAGACTTAGTTTCTTTAAAAACTT-ATTTAAAA
6724068 ATATAAAAAA
Statistics
Matches: 194, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
109 2 0.01
110 97 0.50
111 95 0.49
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (111 bp):
TCAAGAAACTTATGAAAATCAGACTTAGTTTCTTTGAAAGCTCATTTAAAAATTATCAAGAAACT
TCTAAAAATCAGACTTAGTTTCTTTAAAAACTTATTTAAAATGTCA
Found at i:6725911 original size:9 final size:8
Alignment explanation
Indices: 6725893--6725952 Score: 59
Period size: 8 Copynumber: 7.2 Consensus size: 8
6725883 CTTTTCCCTA
6725893 TTTCTTTT
1 TTTCTTTT
6725901 TTTCATTTT
1 TTTC-TTTT
6725910 TTTCTTTT
1 TTTCTTTT
* *
6725918 CTTATTTT
1 TTTCTTTT
6725926 TCTTCTATTT
1 T-TTCT-TTT
*
6725936 TTT-TCTT
1 TTTCTTTT
6725943 TTTCTTTT
1 TTTCTTTT
6725951 TT
1 TT
6725953 CCATCTCCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
7 5 0.12
8 20 0.48
9 13 0.31
10 4 0.10
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTCTTTT
Found at i:6725935 original size:27 final size:25
Alignment explanation
Indices: 6725898--6725952 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 25
6725888 CCCTATTTCT
6725898 TTTTTTCATTTTTTTC-TTTTCTTAT
1 TTTTTTCATTTTTTTCTTTTTCTT-T
6725923 TTTTCTTCTATTTTTTTCTTTTTCTTT
1 TTTT-TTC-ATTTTTTTCTTTTTCTTT
6725950 TTT
1 TTT
6725953 CCATCTCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 4 0.15
26 3 0.11
27 13 0.48
28 7 0.26
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTTTCATTTTTTTCTTTTTCTTT
Found at i:6725950 original size:14 final size:13
Alignment explanation
Indices: 6725900--6725952 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 13
6725890 CTATTTCTTT
6725900 TTTTCATTTTTTTC
1 TTTTC-TTTTTTTC
6725914 TTTTCTTATTTTTC
1 TTTTCTT-TTTTTC
* *
6725928 TTCTATTTTTTTC
1 TTTTCTTTTTTTC
6725941 TTTTTCTTTTTT
1 -TTTTCTTTTTT
6725953 CCATCTCCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 8 0.24
14 25 0.76
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:6727484 original size:22 final size:21
Alignment explanation
Indices: 6727434--6727480 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
6727424 CCGTTAGACA
6727434 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
* *
6727455 GGGGGAATCTGTTCCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
6727476 GGGGG
1 GGGGG
6727481 GAATATATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.11, C:0.26, G:0.47, T:0.17
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:6727493 original size:22 final size:21
Alignment explanation
Indices: 6727445--6727495 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
6727435 GGGGAATCGG
* *
6727445 TACCCCCTGGGGGGGAATCTG
1 TACCCCCTGGGGGGGAATATA
*
6727466 TTCCCCCTGGGGGGGGAATATA
1 TACCCCCT-GGGGGGGAATATA
6727488 TACCCCCT
1 TACCCCCT
6727496 AGACAATCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.16, C:0.31, G:0.31, T:0.22
Consensus pattern (21 bp):
TACCCCCTGGGGGGGAATATA
Found at i:6732788 original size:4 final size:4
Alignment explanation
Indices: 6732779--6732805 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
6732769 TTCGAATATA
6732779 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
6732806 ATTAGCGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:6733187 original size:20 final size:20
Alignment explanation
Indices: 6733162--6733205 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
6733152 GCATCTGAAT
6733162 TAAAATGAACAAAATATAAA
1 TAAAATGAACAAAATATAAA
**
6733182 TAAAATGGTCAAAATATAAA
1 TAAAATGAACAAAATATAAA
6733202 TAAA
1 TAAA
6733206 CAAAAGCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.23
Consensus pattern (20 bp):
TAAAATGAACAAAATATAAA
Found at i:6734395 original size:17 final size:16
Alignment explanation
Indices: 6734373--6734412 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
6734363 GATAAATATG
6734373 TTTTATTACTATTATTA
1 TTTTATTA-TATTATTA
6734390 TTTTATT-TA-TATTA
1 TTTTATTATATTATTA
6734404 TTTTATTAT
1 TTTTATTAT
6734413 TATTGATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 12 0.55
15 3 0.14
17 7 0.32
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTATTATATTATTA
Found at i:6734416 original size:14 final size:14
Alignment explanation
Indices: 6734382--6734416 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
6734372 GTTTTATTAC
6734382 TATTATTATTTTAT
1 TATTATTATTTTAT
6734396 T-TATATTATTTTAT
1 TAT-TATTATTTTAT
6734410 TATTATT
1 TATTATT
6734417 GATAGAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.05
14 17 0.89
15 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTATTTTAT
Found at i:6736353 original size:21 final size:21
Alignment explanation
Indices: 6736327--6736382 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
6736317 TGACACTAGG
6736327 TACCTAGCTAGCTACCTACAC
1 TACCTAGCTAGCTACCTACAC
**
6736348 TACCTAGCTAGCTACCTATGC
1 TACCTAGCTAGCTACCTACAC
*
6736369 TACCTATCTAGCTA
1 TACCTAGCTAGCTA
6736383 AGTGACCTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.27, C:0.34, G:0.11, T:0.29
Consensus pattern (21 bp):
TACCTAGCTAGCTACCTACAC
Found at i:6744398 original size:22 final size:20
Alignment explanation
Indices: 6744353--6744408 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
6744343 TGGCCCTTCA
*
6744353 GTATCGATACCCCTACCATG
1 GTATCGATACCCCTACAATG
6744373 GTATCGATACTACCCTACTAAT-
1 GTATCGATAC--CCCTAC-AATG
*
6744395 GTATCAATACCCCT
1 GTATCGATACCCCT
6744409 TCCGGTATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 14 0.45
22 15 0.48
23 2 0.06
ACGTcount: A:0.29, C:0.32, G:0.11, T:0.29
Consensus pattern (20 bp):
GTATCGATACCCCTACAATG
Found at i:6755436 original size:125 final size:125
Alignment explanation
Indices: 6755214--6755463 Score: 464
Period size: 125 Copynumber: 2.0 Consensus size: 125
6755204 CTAGACTGAT
6755214 TTCCAGCTTTGTACAGAGGAGACAAGCTGTTAATATCAGGAGTTACAGGAGTTATTTGATTTAAT
1 TTCCAGCTTTGTACAGAGGAGACAAGCTGTTAATATCAGGAGTTACAGGAGTTATTTGATTTAAT
*
6755279 TCCATGGGTTACATGATATAATTCCGGGAGTTATAACAGCTGAACAATGATACAATGAAC
66 TCCATGGGTGACATGATATAATTCCGGGAGTTATAACAGCTGAACAATGATACAATGAAC
6755339 TTCCAGCTTTGTACAGAGGAGACAAGCTGTTAATATCAGGAGTTACAGGAGTTATTTGATTTAAT
1 TTCCAGCTTTGTACAGAGGAGACAAGCTGTTAATATCAGGAGTTACAGGAGTTATTTGATTTAAT
* * *
6755404 TCCATGGGTGACATGATATAATTTCGGGAGTTATAACAGTTGAACAATGATGCAATGAAC
66 TCCATGGGTGACATGATATAATTCCGGGAGTTATAACAGCTGAACAATGATACAATGAAC
6755464 CTGGACTATT
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
125 121 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (125 bp):
TTCCAGCTTTGTACAGAGGAGACAAGCTGTTAATATCAGGAGTTACAGGAGTTATTTGATTTAAT
TCCATGGGTGACATGATATAATTCCGGGAGTTATAACAGCTGAACAATGATACAATGAAC
Found at i:6760734 original size:6 final size:6
Alignment explanation
Indices: 6760717--6760747 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
6760707 TCGGATCGGC
*
6760717 TCGTGG TTGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
6760748 AATATGTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.13, G:0.48, T:0.39
Consensus pattern (6 bp):
TCGTGG
Found at i:6772239 original size:60 final size:60
Alignment explanation
Indices: 6772173--6772311 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 60
6772163 TAAATATTTT
* * * *
6772173 AATTTCATCCCTAAACTATGA-GTATCATTCTAAATTAGTCCTAAAAC-TTTCGAACATTTC
1 AATTTCATCCC-AAACTATGACATA-CATTCTAAATTAGTCCCAAAACTTTTAGAACATTCC
* * *
6772233 ATTTTCATCCCCAAACTATGACATACATTCTAAATTGGTCCCCAAACTTTTAGAACATTCC
1 AATTTCAT-CCCAAACTATGACATACATTCTAAATTAGTCCCAAAACTTTTAGAACATTCC
*
6772294 AATGTCATCCCAAACTAT
1 AATTTCATCCCAAACTAT
6772312 ATGTACATAG
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
60 45 0.67
61 22 0.33
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (60 bp):
AATTTCATCCCAAACTATGACATACATTCTAAATTAGTCCCAAAACTTTTAGAACATTCC
Found at i:6775194 original size:18 final size:18
Alignment explanation
Indices: 6775159--6775194 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6775149 TGTACATATG
*
6775159 TATTTTATGTGAATATTT
1 TATTTTATGTGAAGATTT
*
6775177 TATTTTATGTGGAGATTT
1 TATTTTATGTGAAGATTT
6775195 CTTTATGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (18 bp):
TATTTTATGTGAAGATTT
Found at i:6782384 original size:54 final size:54
Alignment explanation
Indices: 6782313--6782780 Score: 293
Period size: 54 Copynumber: 8.8 Consensus size: 54
6782303 TCAGACAACA
* * * * **
6782313 GGTTCACTCCCTATTCCTTCATGGAGTAGA-AACTCGTACAATCTTTTGCCTACG
1 GGTTCACTCCCTCTTCCTTCAGGGAGTATAGAACTCG-AAAATCTTTTGCAAACG
* * *
6782367 GGTTCGCTCCCTCTTCCTTCAGGGAGTATAGAACTTGAAAATCTTCTGCAAACG
1 GGTTCACTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTTTGCAAACG
* * **
6782421 GGTTCTCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTTTAAAAAACG
1 GGTTCACTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTTT-GCAAACG
* * * * * *
6782476 TG-TCTGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACATCTCTT-CAAACG
1 GGTTC-ACTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTTTGCAAACG
* * * * * *
6782529 GGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATC--TT-CAAACG
1 GGTTCACTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTTTGCAAACG
* * * * *
6782580 GGTTCGCTCCTTCTTTCTTTAGGGAGTATAGAACTCGAACATC--TT-C-AACTG
1 GGTTCACTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTTTGCAAAC-G
* * * * * * * * *
6782631 GGTTCGCTCCCTTCTTTCTTTAAGGAGTATGGAAGTCGGATATC--TT-CACACG
1 GGTTCACTCCC-TCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTTTGCAAACG
* * * * * *
6782683 GGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACT-TAGACATCTCTT-CAAACG
1 GGTTCACTCCCTCTTCCTTC-AGGGAGTATAGAACTCGA-AAATCTTTTGCAAACG
* * * * * * *
6782736 GGTTCGCTCCTTCTTTCTTTAAGGAGAATAGAACTCGAATATCTT
1 GGTTCACTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTT
6782781 CAACAATCGT
Statistics
Matches: 348, Mismatches: 53, Indels: 27
0.81 0.12 0.06
Matches are distributed among these distances:
50 4 0.01
51 87 0.25
52 42 0.12
53 80 0.23
54 88 0.25
55 47 0.14
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.33
Consensus pattern (54 bp):
GGTTCACTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTTTGCAAACG
Found at i:6782503 original size:55 final size:55
Alignment explanation
Indices: 6782364--6782836 Score: 285
Period size: 54 Copynumber: 8.9 Consensus size: 55
6782354 TCTTTTGCCT
* **
6782364 ACGGGTTC-GCTCCCTCTTCCTTCAGGGAGTATAGAACTTGAAAATCTTCTGCAA
1 ACGGGTTCTGCTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTCTAAAA
* *
6782418 ACGGGTTCT-CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTTTAAAAA
1 ACGGGTTCTGCTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTCT-AAAA
* * * * **
6782473 ACGTG-TCTGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACATC-TCTTCAA
1 ACGGGTTCTGCTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTCTAAAA
* * * * *
6782526 ACGGGTTC-GCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTC---AA
1 ACGGGTTCTGCTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTCTAAAA
* * * *
6782577 ACGGGTTC-GCTCCTTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTC----A
1 ACGGGTTCTGCTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTCTAAAA
* * * * * * * *
6782627 ACTGGGTTC-GCTCCCTTCTTTCTTTAAGGAGTATGGAAGTCGGATATCTTC---AC
1 AC-GGGTTCTGCTCCC-TCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTCTAAAA
* * * * **
6782680 ACGGGTTC-GCTCCCTCTTTC-TCTAGGGAGTATGGAACT-TAGACATC-TCTTCAA
1 ACGGGTTCTGCTCCCTCTTCCTTC-AGGGAGTATAGAACTCGA-AAATCTTCTAAAA
* * * * * *
6782733 ACGGGTTC-GCTCCTTCTTTCTTTAAGGAGAATAGAACTCGAATATCTTC-AACAA
1 ACGGGTTCTGCTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTCTAA-AA
* * * * * *
6782787 TCGTG-TCTGCTACCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTC
1 ACGGGTTCTGCTCCCTCTTCCTTCAGGGAGTATAGA-ACTCGAA-AATCTTC
6782837 AATAATTGTT
Statistics
Matches: 345, Mismatches: 54, Indels: 39
0.79 0.12 0.09
Matches are distributed among these distances:
50 6 0.02
51 84 0.24
52 42 0.12
53 79 0.23
54 89 0.26
55 45 0.13
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (55 bp):
ACGGGTTCTGCTCCCTCTTCCTTCAGGGAGTATAGAACTCGAAAATCTTCTAAAA
Found at i:6782557 original size:53 final size:53
Alignment explanation
Indices: 6782364--6782779 Score: 404
Period size: 51 Copynumber: 7.9 Consensus size: 53
6782354 TCTTTTGCCT
* * * * * * *
6782364 ACGGGTTCGCTCCCTCTTCCTTCAGGGAGTATAGAACTTGAAAATCTTCTGCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATC-TCTTCAA
* * * * * * *
6782418 ACGGGTTCTCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTTTAAAAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCTT--CAA
* * *
6782473 ACGTG-TCTGCTCC--CTATTCCTTCAGAGAGTATAGAACTCGAACATCTCTTCAA
1 ACGGGTTC-GCTCCTTCT-TTCTTTAAG-GAGTATAGAACTCGAACATCTCTTCAA
6782526 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACA--TCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCTTCAA
*
6782577 ACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATAGAACTCGAACA--TCTTC-A
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCTTCAA
* * * * *
6782627 ACTGGGTTCGCTCCCTTCTTTCTTTAAGGAGTATGGAAGTCG--GATATCTTCAC
1 AC-GGGTTCGCT-CCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCTTCAA
* * * * *
6782680 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACT-TAGACATCTCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGA-ACATCTCTTCAA
* *
6782733 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGAATAGAACTCGAATATCT
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCT
6782780 TCAACAATCG
Statistics
Matches: 306, Mismatches: 39, Indels: 35
0.81 0.10 0.09
Matches are distributed among these distances:
50 4 0.01
51 87 0.28
52 40 0.13
53 81 0.26
54 60 0.20
55 34 0.11
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (53 bp):
ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCTTCAA
Found at i:6782684 original size:103 final size:103
Alignment explanation
Indices: 6782364--6782783 Score: 456
Period size: 103 Copynumber: 4.0 Consensus size: 103
6782354 TCTTTTGCCT
* * * * *
6782364 ACGGGTTCGCTCCCTCTTCCT-TCAGGGAGTATAGAACTTGAAAATCTTCTGCAAACGGGTTCTC
1 ACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACA-C-TCTTCAAACGGGTTCGC
* * * * *
6782428 TCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTTTAAAAA
63 TCCTTCTTTCTTTAAGGAGTATAGAACTCGAATATC--TT--CAA
* * * *
6782473 ACGTG-TCTGCTCCCTATTCCT-TCAGAGAGTATAGAACTCGAACATCTCTTCAAACGGGTTCGC
1 ACGGGTTC-GCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACA-CTCTTCAAACGGGTTCGC
*
6782536 TCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
63 TCCTTCTTTCTTTAAGGAGTATAGAACTCGAATATCTTCAA
* *
6782577 ACGGGTTCGCTCCTTCTTTCTTTAGGGAGTATAGAACTCGAACA-TCTTC-AACTGGGTTCGCTC
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACACTCTTCAAAC-GGGTTCGCT-
* * * *
6782640 CCTTCTTTCTTTAAGGAGTATGGAAGTCGGATATCTTCAC
64 CCTTCTTTCTTTAAGGAGTATAGAACTCGAATATCTTCAA
* *
6782680 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACT-TAGACATCTCTTCAAACGGGTTCGCT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGA-ACA-CTCTTCAAACGGGTTCGCT
*
6782744 CCTTCTTTCTTTAAGGAGAATAGAACTCGAATATCTTCAA
64 CCTTCTTTCTTTAAGGAGTATAGAACTCGAATATCTTCAA
6782784 CAATCGTGTC
Statistics
Matches: 271, Mismatches: 31, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
101 3 0.01
102 15 0.06
103 73 0.27
104 71 0.26
105 17 0.06
106 5 0.02
108 49 0.18
109 38 0.14
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (103 bp):
ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACACTCTTCAAACGGGTTCGCTCC
TTCTTTCTTTAAGGAGTATAGAACTCGAATATCTTCAA
Found at i:6783790 original size:8 final size:8
Alignment explanation
Indices: 6783772--6783823 Score: 70
Period size: 8 Copynumber: 6.5 Consensus size: 8
6783762 GCTTCTTCTT
6783772 TTTTTTCCA
1 TTTTTT-CA
6783781 TTTTTTCA
1 TTTTTTCA
6783789 TTTTTT-A
1 TTTTTTCA
*
6783796 TTTTTTTA
1 TTTTTTCA
*
6783804 TTTTTTTA
1 TTTTTTCA
6783812 TTTTTTCA
1 TTTTTTCA
6783820 TTTT
1 TTTT
6783824 CACTCATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
7 7 0.17
8 28 0.68
9 6 0.15
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCA
Found at i:6799233 original size:7 final size:7
Alignment explanation
Indices: 6799221--6799246 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6799211 CCTATATAAA
6799221 TTATCAT
1 TTATCAT
6799228 TTATCAT
1 TTATCAT
6799235 TTATCAT
1 TTATCAT
6799242 TTATC
1 TTATC
6799247 TTCCATCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (7 bp):
TTATCAT
Found at i:6801356 original size:23 final size:23
Alignment explanation
Indices: 6801330--6801379 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
6801320 ACTTTTGGGG
*
6801330 TGAAATGAAATAACTATTTTTCA
1 TGAAAAGAAATAACTATTTTTCA
** *
6801353 TGAAAAGACTTAATTATTTTTCA
1 TGAAAAGAAATAACTATTTTTCA
6801376 TGAA
1 TGAA
6801380 TAGTCATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (23 bp):
TGAAAAGAAATAACTATTTTTCA
Found at i:6810470 original size:104 final size:104
Alignment explanation
Indices: 6810259--6810462 Score: 291
Period size: 104 Copynumber: 2.0 Consensus size: 104
6810249 TTGATATAGA
* * * * * * *
6810259 GTTGGATTCATGCATTATACAACATGGAAATGTGTGCAGTCTCCTCACTTGGGTCAACTCTTTAA
1 GTTGGATTCACGCATTAAACAACAAGGAAATGTGTGCAGTCTCCACACTTGGATCAACGCCTTAA
* *
6810324 CTCCTGCCATTAATGTGGCTTGTGTATTTACACATCACT
66 CTACTGCCATTAATGTGGCTTGTGTATTCACACATCACT
* * *
6810363 GTTGGATTCACGCATTAAACAATAAGGAAATGTGTGCAGTCTCCACGCTTGGATCAACGCCTTGA
1 GTTGGATTCACGCATTAAACAACAAGGAAATGTGTGCAGTCTCCACACTTGGATCAACGCCTTAA
*
6810428 CTACTGCTATTAATGTGGCTTGTGTATTCACACAT
66 CTACTGCCATTAATGTGGCTTGTGTATTCACACAT
6810463 GATTGTTGCT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
104 87 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (104 bp):
GTTGGATTCACGCATTAAACAACAAGGAAATGTGTGCAGTCTCCACACTTGGATCAACGCCTTAA
CTACTGCCATTAATGTGGCTTGTGTATTCACACATCACT
Found at i:6810834 original size:21 final size:21
Alignment explanation
Indices: 6810808--6810862 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
6810798 ATTTACCGTG
*
6810808 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGACGCT
6810829 ATTGCGGCCGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGACGCT
*
6810850 ATTGCGGTCGTCG
1 ATTGCGGCCGTCG
6810863 TAGGTTACTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.07, C:0.31, G:0.40, T:0.22
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGACGCT
Found at i:6812874 original size:4 final size:4
Alignment explanation
Indices: 6812867--6812892 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
6812857 GAGTGAGTAG
6812867 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
6812893 CGAGTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Done.