Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, 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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 113 of 131
Found at i:20203222 original size:219 final size:219
Alignment explanation
Indices: 20202822--20203541 Score: 668
Period size: 219 Copynumber: 3.3 Consensus size: 219
20202812 ATGACAGTAG
* *
20202822 ATAGTTCAGCTGAGAAGATGA-AGAAAGAGACTGC-CATGACAGTAAATAGCTCGGCTGAGAAGA
1 ATAGCTCAGCTGAGAAGATGAGA-AAAGAGA-T-CAC-T-ACAGTAAATAGCTCAGCTGAGAAGA
* * * * *
20202885 T-TAGAAAAGAGACGG--TT-ACAGTAAATAGCTCAGCTGAGAAGATGAAG-AAGGAG-ATGGCC
61 TGAAG-AAAGAGACGGCCTTGACAATTAATAGCTCAGCTGACAAGATGAAGAAAGAAGCA--GCC
* * * * * **
20202944 TTGACAATTAATAGCTCAGCTGAGAAGATTAGAA-AG-GAGGCACATACAGTATTTAGCTCAGCT
123 ATGACAGTAAATAGCTCAGCTGAGAAGATGAGAAGAGAGAGG-AC-TACAATAAATAGCTCAGCT
* * *
20203007 GAGAGGATGAAGAAGGAGACGGCCTTGACAATTA
186 GAGAAGATGAAGAAAGAGACAGCCTTGACAATTA
* * ** *
20203041 GTAGCTCAGCTGAGAAGATTAGAAAAGAGA-CACCTACAGTATTTAGCTCAGCTGAGAGGATGAA
1 ATAGCTCAGCTGAGAAGATGAGAAAAGAGATCA-CTACAGTAAATAGCTCAGCTGAGAAGATGAA
* * * *
20203105 GAAGGAGACGGCCTTGATAATTAGTAGCTCAGCTGACAAGAT-TAGAAA-AGAGACA-CC-T-AC
65 GAAAGAGACGGCCTTGACAATTAATAGCTCAGCTGACAAGATGAAGAAAGA-AG-CAGCCATGAC
** * * *
20203165 AGTATTTAGCTCAGCTGAGAGGATGAAGAAG-GAGACGGCCTTGACAATTAATAGCTCAGCTGAG
128 AGTAAATAGCTCAGCTGAGAAGATG-AGAAGAGAGA-GGAC-T-ACAATAAATAGCTCAGCTGAG
* * * *
20203229 AAGATGAAGAAAGAGGCAGCCATGACAGTAA
189 AAGATGAAGAAAGAGACAGCCTTGACAATTA
* * *
20203260 ATAGCTCAGCTGAGAAGATGAGACAAGAGATGACTACAGTAAATAGCTCAGCTGAGAAGCTGAAG
1 ATAGCTCAGCTGAGAAGATGAGAAAAGAGATCACTACAGTAAATAGCTCAGCTGAGAAGATGAAG
* * *
20203325 AAAGAGACGGTCTTGACAATTAATAGCTCAGCTGAGAAGATGAAGAAAGAAGCAGCCATGACGGT
66 AAAGAGACGGCCTTGACAATTAATAGCTCAGCTGACAAGATGAAGAAAGAAGCAGCCATGACAGT
* * * *
20203390 AAATAGCTCAGCTGAGAAGATGAGACGAGAGATGACTACAGTAAATAGCTCAGCTGAGAAGCTGA
131 AAATAGCTCAGCTGAGAAGATGAGAAGAGAGAGGACTACAATAAATAGCTCAGCTGAGAAGATGA
20203455 AGAAAGAGACAGCCTTGAC-ATTAA
196 AGAAAGAGACAGCCTTGACAATT-A
** * *
20203479 ATAGCTCAGCTGAGAAGATGA-AGAAAGAGATGGCTACGGCAGTGAATGGCTCAGCTGAGAAGA
1 ATAGCTCAGCTGAGAAGATGAGA-AAAGAGAT--C-ACTACAGTAAATAGCTCAGCTGAGAAGA
20203542 CAGAGAAACA
Statistics
Matches: 403, Mismatches: 70, Indels: 53
0.77 0.13 0.10
Matches are distributed among these distances:
216 53 0.13
217 9 0.02
218 13 0.03
219 257 0.64
220 12 0.03
221 9 0.02
222 50 0.12
ACGTcount: A:0.39, C:0.15, G:0.28, T:0.18
Consensus pattern (219 bp):
ATAGCTCAGCTGAGAAGATGAGAAAAGAGATCACTACAGTAAATAGCTCAGCTGAGAAGATGAAG
AAAGAGACGGCCTTGACAATTAATAGCTCAGCTGACAAGATGAAGAAAGAAGCAGCCATGACAGT
AAATAGCTCAGCTGAGAAGATGAGAAGAGAGAGGACTACAATAAATAGCTCAGCTGAGAAGATGA
AGAAAGAGACAGCCTTGACAATTA
Found at i:20203531 original size:45 final size:45
Alignment explanation
Indices: 20202782--20203541 Score: 574
Period size: 45 Copynumber: 17.3 Consensus size: 45
20202772 CCTAAACAGT
** ** * * * *
20202782 TCAGCTGAGAAGACAAACCAAGAGATGGCCATGACAGTAGATAGT
1 TCAGCTGAGAAGATGAAGAAAGAGACGGCTATGACAGTAAATAGC
* *
20202827 TCAGCTGAGAAGATGAAGAAAGAGACTGCCATGACAGTAAATAGC
1 TCAGCTGAGAAGATGAAGAAAGAGACGGCTATGACAGTAAATAGC
* *
20202872 TCGGCTGAGAAGAT-TAGAAAAGAGACGG-T-T-ACAGTAAATAGC
1 TCAGCTGAGAAGATGAAG-AAAGAGACGGCTATGACAGTAAATAGC
* * * *
20202914 TCAGCTGAGAAGATGAAGAAGGAGATGGCCT-TGACAATTAATAGC
1 TCAGCTGAGAAGATGAAGAAAGAGACGG-CTATGACAGTAAATAGC
* * **
20202959 TCAGCTGAGAAGAT-TAGAAAG-GA-GGCACAT-ACAGTATTTAGC
1 TCAGCTGAGAAGATGAAGAAAGAGACGGC-TATGACAGTAAATAGC
* * * * *
20203001 TCAGCTGAGAGGATGAAGAAGGAGACGGCCT-TGACAATTAGTAGC
1 TCAGCTGAGAAGATGAAGAAAGAGACGG-CTATGACAGTAAATAGC
* * * **
20203046 TCAGCTGAGAAGAT-TAGAAAAGAGAC-AC-CT-ACAGTATTTAGC
1 TCAGCTGAGAAGATGAAG-AAAGAGACGGCTATGACAGTAAATAGC
* * * * * *
20203088 TCAGCTGAGAGGATGAAGAAGGAGACGGCCT-TGATAATTAGTAGC
1 TCAGCTGAGAAGATGAAGAAAGAGACGG-CTATGACAGTAAATAGC
* * * * **
20203133 TCAGCTGACAAGAT-TAGAAAAGAGAC-AC-CT-ACAGTATTTAGC
1 TCAGCTGAGAAGATGAAG-AAAGAGACGGCTATGACAGTAAATAGC
* * * *
20203175 TCAGCTGAGAGGATGAAGAAGGAGACGGCCT-TGACAATTAATAGC
1 TCAGCTGAGAAGATGAAGAAAGAGACGG-CTATGACAGTAAATAGC
* * *
20203220 TCAGCTGAGAAGATGAAGAAAGAGGCAGCCATGACAGTAAATAGC
1 TCAGCTGAGAAGATGAAGAAAGAGACGGCTATGACAGTAAATAGC
* *
20203265 TCAGCTGAGAAGATG-AGACAAGAGATGAC--T-ACAGTAAATAGC
1 TCAGCTGAGAAGATGAAGA-AAGAGACGGCTATGACAGTAAATAGC
* * *
20203307 TCAGCTGAGAAGCTGAAGAAAGAGACGGTCT-TGACAATTAATAGC
1 TCAGCTGAGAAGATGAAGAAAGAGACGG-CTATGACAGTAAATAGC
* * *
20203352 TCAGCTGAGAAGATGAAGAAAGA-AGCAGCCATGACGGTAAATAGC
1 TCAGCTGAGAAGATGAAGAAAGAGA-CGGCTATGACAGTAAATAGC
* * *
20203397 TCAGCTGAGAAGATG-AGACGAGAGATGAC--T-ACAGTAAATAGC
1 TCAGCTGAGAAGATGAAGA-AAGAGACGGCTATGACAGTAAATAGC
* * *
20203439 TCAGCTGAGAAGCTGAAGAAAGAGACAGCCT-TGACATTAAATAGC
1 TCAGCTGAGAAGATGAAGAAAGAGAC-GGCTATGACAGTAAATAGC
* * * * *
20203484 TCAGCTGAGAAGATGAAGAAAGAGATGGCTACGGCAGTGAATGGC
1 TCAGCTGAGAAGATGAAGAAAGAGACGGCTATGACAGTAAATAGC
20203529 TCAGCTGAGAAGA
1 TCAGCTGAGAAGA
20203542 CAGAGAAACA
Statistics
Matches: 565, Mismatches: 109, Indels: 82
0.75 0.14 0.11
Matches are distributed among these distances:
41 1 0.00
42 173 0.31
43 30 0.05
44 34 0.06
45 325 0.58
46 2 0.00
ACGTcount: A:0.39, C:0.15, G:0.28, T:0.18
Consensus pattern (45 bp):
TCAGCTGAGAAGATGAAGAAAGAGACGGCTATGACAGTAAATAGC
Found at i:20203531 original size:132 final size:131
Alignment explanation
Indices: 20202782--20203559 Score: 760
Period size: 132 Copynumber: 5.9 Consensus size: 131
20202772 CCTAAACAGT
** ** * * * *
20202782 TCAGCTGAGAAGACAAACCAAGAGATGGCCATGAC-AGTAGATAGTTCAGCTGAGAAGATGAAGA
1 TCAGCTGAGAAGATGAAGAAAGAGACGGCCTTGACAATTA-ATAGCTCAGCTGAGAAGATGAAGA
* * * * **
20202846 AAGAGACTGCCATGACAGTAAATAGCTCGGCTGAGAAGATTAGAAAAGAGACGGTTACAGTAAAT
65 AAGAGA-GGCCATGACAGTAAATAGCTCAGCTGAGAAGATGAGAAAAGAGATGACTACAGTAAAT
20202911 AGC
129 AGC
* * *
20202914 TCAGCTGAGAAGATGAAGAAGGAGATGGCCTTGACAATTAATAGCTCAGCTGAGAAGAT-TAGAA
1 TCAGCTGAGAAGATGAAGAAAGAGACGGCCTTGACAATTAATAGCTCAGCTGAGAAGATGAAGAA
** * * * * * *
20202978 AG-GAGGCACAT-ACAGTATTTAGCTCAGCTGAGAGGATGA-AGAAGGAGACGGCCTTGACAATT
66 AGAGAGGC-CATGACAGTAAATAGCTCAGCTGAGAAGATGAGA-AAAGAGA-TGAC-T-ACAGTA
*
20203040 AGTAGC
126 AATAGC
* * *
20203046 TCAGCTGAGAAGAT-TAGAAAAGAGAC-ACC-T-ACAGTATT--TAGCTCAGCTGAGAGGATGAA
1 TCAGCTGAGAAGATGAAG-AAAGAGACGGCCTTGACA--ATTAATAGCTCAGCTGAGAAGATGAA
* * * * * * * * *
20203105 GAAGGAGACGGCCTTGATAATTAGTAGCTCAGCTGACAAGATTAGAAAAGAGA-CACCTACAGTA
63 GAAAGAGA-GGCCATGACAGTAAATAGCTCAGCTGAGAAGATGAGAAAAGAGATGA-CTACAGTA
**
20203169 TTTAGC
126 AATAGC
* *
20203175 TCAGCTGAGAGGATGAAGAAGGAGACGGCCTTGACAATTAATAGCTCAGCTGAGAAGATGAAGAA
1 TCAGCTGAGAAGATGAAGAAAGAGACGGCCTTGACAATTAATAGCTCAGCTGAGAAGATGAAGAA
*
20203240 AGAG-GCAGCCATGACAGTAAATAGCTCAGCTGAGAAGATGAGACAAGAGATGACTACAGTAAAT
66 AGAGAG--GCCATGACAGTAAATAGCTCAGCTGAGAAGATGAGAAAAGAGATGACTACAGTAAAT
20203304 AGC
129 AGC
* *
20203307 TCAGCTGAGAAGCTGAAGAAAGAGACGGTCTTGACAATTAATAGCTCAGCTGAGAAGATGAAGAA
1 TCAGCTGAGAAGATGAAGAAAGAGACGGCCTTGACAATTAATAGCTCAGCTGAGAAGATGAAGAA
* **
20203372 AGA-AGCAGCCATGACGGTAAATAGCTCAGCTGAGAAGATGAGACGAGAGATGACTACAGTAAAT
66 AGAGAG--GCCATGACAGTAAATAGCTCAGCTGAGAAGATGAGAAAAGAGATGACTACAGTAAAT
20203436 AGC
129 AGC
* *
20203439 TCAGCTGAGAAGCTGAAGAAAGAGACAGCCTTGAC-ATTAAATAGCTCAGCTGAGAAGATGAAGA
1 TCAGCTGAGAAGATGAAGAAAGAGACGGCCTTGACAATT-AATAGCTCAGCTGAGAAGATGAAGA
* * * * * * *
20203503 AAGAGATGGCTACGGCAGTGAATGGCTCAGCTGAGAAGA-CAGAGAAACAGATGACTA
65 AAGAGA-GGCCATGACAGTAAATAGCTCAGCTGAGAAGATGAGA-AAAGAGATGACTA
20203560 TGGCAGTTTC
Statistics
Matches: 537, Mismatches: 80, Indels: 58
0.80 0.12 0.09
Matches are distributed among these distances:
128 1 0.00
129 79 0.15
130 21 0.04
131 26 0.05
132 403 0.75
133 6 0.01
134 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.28, T:0.18
Consensus pattern (131 bp):
TCAGCTGAGAAGATGAAGAAAGAGACGGCCTTGACAATTAATAGCTCAGCTGAGAAGATGAAGAA
AGAGAGGCCATGACAGTAAATAGCTCAGCTGAGAAGATGAGAAAAGAGATGACTACAGTAAATAG
C
Found at i:20204926 original size:3 final size:3
Alignment explanation
Indices: 20204918--20204942 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20204908 TTTTAGTTAA
20204918 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
20204943 TAACAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20205225 original size:12 final size:12
Alignment explanation
Indices: 20205216--20205240 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20205206 ATTCATAAGA
20205216 ATTTGAATAATG
1 ATTTGAATAATG
20205228 ATTTGAATAATG
1 ATTTGAATAATG
20205240 A
1 A
20205241 CAGATTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
ATTTGAATAATG
Found at i:20210403 original size:20 final size:20
Alignment explanation
Indices: 20210380--20210418 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20210370 TTAATTTTTA
20210380 TATTTAAATTTAAATTCGAT
1 TATTTAAATTTAAATTCGAT
**
20210400 TATTTATGTTTAAATTCGA
1 TATTTAAATTTAAATTCGA
20210419 GTTCGAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (20 bp):
TATTTAAATTTAAATTCGAT
Found at i:20210478 original size:9 final size:9
Alignment explanation
Indices: 20210464--20210493 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
20210454 AATAATTTTT
20210464 TAATTAAAA
1 TAATTAAAA
20210473 TAATTAAAA
1 TAATTAAAA
20210482 TATATTAAAA
1 TA-ATTAAAA
20210492 TA
1 TA
20210494 TAAAAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:20210490 original size:10 final size:10
Alignment explanation
Indices: 20210466--20210495 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
20210456 TAATTTTTTA
20210466 ATTAAAATA-
1 ATTAAAATAT
20210475 ATTAAAATAT
1 ATTAAAATAT
20210485 ATTAAAATAT
1 ATTAAAATAT
20210495 A
1 A
20210496 AAAACTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:20223558 original size:85 final size:85
Alignment explanation
Indices: 20223414--20223569 Score: 215
Period size: 85 Copynumber: 1.8 Consensus size: 85
20223404 TTCCAATTGA
* * *
20223414 CAATTTACCAGTGTAAGCACTACTATATCTGCTCACATGTTTAAAACAGAACTTCATGTGATTAA
1 CAATTTACCAATGTAAGCACTACTACATCTGCTCACATGTTTAAAACACAACTTCATGTGATTAA
20223479 CAATACTAAATTAATGCGAC
66 CAATACTAAATTAATGCGAC
* * * * * *
20223499 CAATTTACCAATGTGAGCATTAGTACATCTG-TCCACATGTTTATAAGACAACTTGATGTGATTA
1 CAATTTACCAATGTAAGCACTACTACATCTGCT-CACATGTTTAAAACACAACTTCATGTGATTA
20223563 ACAATAC
65 ACAATAC
20223570 AGAACAAGCA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 1 0.02
85 60 0.98
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (85 bp):
CAATTTACCAATGTAAGCACTACTACATCTGCTCACATGTTTAAAACACAACTTCATGTGATTAA
CAATACTAAATTAATGCGAC
Found at i:20224104 original size:5 final size:5
Alignment explanation
Indices: 20224090--20224119 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
20224080 TAATTCCTCA
20224090 AAAAG AAAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAA
20224120 CATCTGAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:20225354 original size:17 final size:18
Alignment explanation
Indices: 20225322--20225356 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20225312 TTGAGTATTA
20225322 CAAAATATTATCTTAATT
1 CAAAATATTATCTTAATT
*
20225340 CAAATTATTAT-TTAATT
1 CAAAATATTATCTTAATT
20225357 AATTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
CAAAATATTATCTTAATT
Found at i:20227714 original size:22 final size:21
Alignment explanation
Indices: 20227689--20227734 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
20227679 TTACCTTAAA
*
20227689 AAATTAAAAATATAAATAATAT
1 AAATTAAAAATA-AAATAAAAT
*
20227711 AAATTAACAATAAAATAAAAT
1 AAATTAAAAATAAAATAAAAT
20227732 AAA
1 AAA
20227735 AAGAATAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATTAAAAATAAAATAAAAT
Found at i:20230449 original size:18 final size:17
Alignment explanation
Indices: 20230412--20230447 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
20230402 TCATTTTTTT
20230412 TCTTCATTTTTCTTCTC
1 TCTTCATTTTTCTTCTC
*
20230429 TCTTC-TTTTTCTTTTC
1 TCTTCATTTTTCTTCTC
20230445 TCT
1 TCT
20230448 CTCTCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (17 bp):
TCTTCATTTTTCTTCTC
Found at i:20237437 original size:17 final size:17
Alignment explanation
Indices: 20237395--20237438 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
20237385 TTAAAATTTT
*
20237395 TTAATATAATATCTGAA
1 TTAATATAATATATGAA
*
20237412 TT-ATA-AATATATTAA
1 TTAATATAATATATGAA
20237427 TTAATATAATAT
1 TTAATATAATAT
20237439 TTATTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 10 0.43
16 6 0.26
17 7 0.30
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TTAATATAATATATGAA
Found at i:20238706 original size:16 final size:17
Alignment explanation
Indices: 20238687--20238728 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
20238677 TATTACCTTA
20238687 TTAATTTCA-TAATAAT
1 TTAATTTCATTAATAAT
20238703 TTAATTTCATTAATAAT
1 TTAATTTCATTAATAAT
20238720 TTAATTTCA
1 TTAATTTCA
20238729 CTAACAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAATTTCATTAATAAT
Found at i:20239788 original size:16 final size:16
Alignment explanation
Indices: 20239767--20239798 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20239757 TTTAAACATG
*
20239767 TATATTTATATGTATT
1 TATATTTATATATATT
20239783 TATATTTATATATATT
1 TATATTTATATATATT
20239799 AATAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TATATTTATATATATT
Found at i:20239835 original size:20 final size:19
Alignment explanation
Indices: 20239795--20239837 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
20239785 TATTTATATA
* *
20239795 TATT-AATAAATAATTTTT
1 TATTAAATAAATAAATTAT
20239813 TATTAAATAATATAAATTAT
1 TATTAAATAA-ATAAATTAT
20239833 TATTA
1 TATTA
20239838 TTTTAGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 5 0.24
20 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTAAATAAATAAATTAT
Found at i:20242022 original size:14 final size:14
Alignment explanation
Indices: 20242014--20242053 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
20242004 AATATTATTT
20242014 TTTAAATATAAATA
1 TTTAAATATAAATA
20242028 TTTAAATATATAATTA
1 TTTAAATATA-AA-TA
*
20242044 TATAAATATA
1 TTTAAATATA
20242054 TATAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 2 0.09
16 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAAATATAAATA
Found at i:20242035 original size:8 final size:8
Alignment explanation
Indices: 20242019--20242055 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
20242009 TATTTTTTAA
20242019 ATATAAAT
1 ATATAAAT
*
20242027 ATTTAAAT
1 ATATAAAT
*
20242035 ATATAATT
1 ATATAAAT
20242043 ATATAAAT
1 ATATAAAT
20242051 ATATA
1 ATATA
20242056 TAAATTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATAAAT
Found at i:20242066 original size:16 final size:18
Alignment explanation
Indices: 20242019--20242060 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
20242009 TATTTTTTAA
*
20242019 ATATAAATAT-TTAA-AT
1 ATATAAATATATAAATAT
*
20242035 ATATAATTATATAAATAT
1 ATATAAATATATAAATAT
20242053 ATATAAAT
1 ATATAAAT
20242061 TAAAATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 9 0.43
17 3 0.14
18 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAAATATATAAATAT
Found at i:20242625 original size:27 final size:27
Alignment explanation
Indices: 20242594--20242662 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
20242584 AAATAAAAAT
*
20242594 AATATTAATTAATAAA-TTTATAATTTA
1 AATATTAATTAAAAAATTTTA-AATTTA
* *
20242621 GATATAAATTAAAAAATTTTCAAATTTA
1 AATATTAATTAAAAAATTTT-AAATTTA
20242649 AATATTATATTAAA
1 AATATTA-ATTAAA
20242663 TATTTTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 13 0.38
28 14 0.41
29 7 0.21
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (27 bp):
AATATTAATTAAAAAATTTTAAATTTA
Found at i:20242673 original size:17 final size:17
Alignment explanation
Indices: 20242651--20242707 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
20242641 CAAATTTAAA
20242651 TATTATATTAAATATTT
1 TATTATATTAAATATTT
*
20242668 TATTATAATTTAAAAATTATT
1 TATTAT-A-TTAAATA-T-TT
*
20242689 TATAATATTAAAT-TTT
1 TATTATATTAAATATTT
20242705 TAT
1 TAT
20242708 AAGAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
16 5 0.15
17 7 0.21
18 1 0.03
19 11 0.33
20 2 0.06
21 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTATATTAAATATTT
Found at i:20243570 original size:16 final size:17
Alignment explanation
Indices: 20243539--20243571 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20243529 ATATTTTATT
20243539 AATTAAAATAATAAAAA
1 AATTAAAATAATAAAAA
*
20243556 AATTTAAAT-ATAAAAA
1 AATTAAAATAATAAAAA
20243572 CTCGATTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATTAAAATAATAAAAA
Found at i:20244512 original size:17 final size:17
Alignment explanation
Indices: 20244492--20244524 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
20244482 AATAACCCTC
20244492 AAAAAAATAAAAGAGAG
1 AAAAAAATAAAAGAGAG
20244509 AAAAAAATAAAAGAGA
1 AAAAAAATAAAAGAGA
20244525 TGATATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (17 bp):
AAAAAAATAAAAGAGAG
Found at i:20247038 original size:20 final size:21
Alignment explanation
Indices: 20247013--20247053 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20247003 CCCAATTCAC
20247013 TTTTAAATA-GATATGATAAT
1 TTTTAAATATGATATGATAAT
20247033 TTTTAAATATGATATGATAAT
1 TTTTAAATATGATATGATAAT
20247054 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTTAAATATGATATGATAAT
Found at i:20250735 original size:33 final size:33
Alignment explanation
Indices: 20250698--20250762 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
20250688 TTGCAACTAA
20250698 CTGCTCCTTCTTTTTTTGTTATTGTTTATACAG
1 CTGCTCCTTCTTTTTTTGTTATTGTTTATACAG
*
20250731 CTGCTGCTTCTTTTTTTGTTATTGTTTATACA
1 CTGCTCCTTCTTTTTTTGTTATTGTTTATACA
20250763 TATATGATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.12, C:0.17, G:0.12, T:0.58
Consensus pattern (33 bp):
CTGCTCCTTCTTTTTTTGTTATTGTTTATACAG
Found at i:20253386 original size:11 final size:12
Alignment explanation
Indices: 20253359--20253384 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20253349 AGTCAAATAT
20253359 TTTATCAATAGA
1 TTTATCAATAGA
20253371 TTTATCAATAGA
1 TTTATCAATAGA
20253383 TT
1 TT
20253385 ATACGATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
TTTATCAATAGA
Found at i:20259013 original size:22 final size:22
Alignment explanation
Indices: 20258985--20259027 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20258975 ATGGATAATT
*
20258985 TATATAT-TTTTAGTTATATATA
1 TATATATGCTTTA-TTATATATA
20259007 TATATATGCTTTATTATATAT
1 TATATATGCTTTATTATATAT
20259028 CGATTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (22 bp):
TATATATGCTTTATTATATATA
Found at i:20265600 original size:60 final size:60
Alignment explanation
Indices: 20265489--20265602 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
20265479 TTAATGCATT
* * * * * *
20265489 TTGATAATTTTATTTAAAAAAAAAATTGATATTTTCAATTTTTTCTTAAAAATGTTTTTC
1 TTGAAAATTTTATTTAAAAAAAAAATTGATACTTTAAACTTTTCCTAAAAAATGTTTTTC
** * *
20265549 TTGAAAATTTTATTTTCAAAGAAAATTGGTACTTTAAACTTTTCCTAAAAAATG
1 TTGAAAATTTTATTTAAAAAAAAAATTGATACTTTAAACTTTTCCTAAAAAATG
20265603 CTTTATTAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (60 bp):
TTGAAAATTTTATTTAAAAAAAAAATTGATACTTTAAACTTTTCCTAAAAAATGTTTTTC
Found at i:20265631 original size:94 final size:94
Alignment explanation
Indices: 20265521--20265693 Score: 278
Period size: 94 Copynumber: 1.8 Consensus size: 94
20265511 AAATTGATAT
* *
20265521 TTTCAATTTTTTCTTAAAAATG-TTTTTCTTGAAAATTTTATTTTCAA-AGAAAATTGGTACTTT
1 TTTCAACTTTTACTTAAAAATGCTTTTT-TTGAAAATTTTATTTTCAAGA-AAAATTGGTACTTT
20265584 AAACTTTTCCTAAAAAATGCTTTATTAATAC
64 AAACTTTTCCTAAAAAATGCTTTATTAATAC
*
20265615 TTTCAACTTTTACTTAAAAATGCTTTTTTTGAAAATTTTATTTTCAAGAAAAATTGGTACTTTTA
1 TTTCAACTTTTACTTAAAAATGCTTTTTTTGAAAATTTTATTTTCAAGAAAAATTGGTACTTTAA
*
20265680 ACTTTTCCTCAAAA
66 ACTTTTCCTAAAAA
20265694 TATTTTTTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
94 67 0.92
95 6 0.08
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (94 bp):
TTTCAACTTTTACTTAAAAATGCTTTTTTTGAAAATTTTATTTTCAAGAAAAATTGGTACTTTAA
ACTTTTCCTAAAAAATGCTTTATTAATAC
Found at i:20265762 original size:60 final size:58
Alignment explanation
Indices: 20265611--20265785 Score: 208
Period size: 59 Copynumber: 3.0 Consensus size: 58
20265601 TGCTTTATTA
* * ** * *
20265611 ATACTTTCAACTTTTACTTAAAAATGCTTTTTTTGAAAATTTTATTTTCAAGAAAAATTG
1 ATACTTTCAACTTTTCCTCAAAAATATTTTTTTTG-AATTTTTATTTT-AAAAAAAATTG
* * *
20265671 GTACTTTTAACTTTTCCTC-AAAATATTTTTTTTGAAGTTTTTATTTTTTAAAAAAATTG
1 ATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAA-TTTTTA-TTTTAAAAAAAATTG
* *
20265730 ATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAATTTTTGTTTTAAAAAAAAT
1 ATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAATTTTTATTTTAAAAAAAAT
20265786 CATTGAAAAT
Statistics
Matches: 98, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
58 14 0.14
59 49 0.50
60 35 0.36
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.50
Consensus pattern (58 bp):
ATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAATTTTTATTTTAAAAAAAATTG
Found at i:20266997 original size:73 final size:73
Alignment explanation
Indices: 20266860--20266998 Score: 163
Period size: 73 Copynumber: 1.9 Consensus size: 73
20266850 ATCTAAAATA
* * ** * * * * *
20266860 AAATGACCTGGATTAAATCGAAGTCTGAAATAAATGGCTTGGACTGAATTGAAGAACGATCTAAC
1 AAATGACCTGGACTAAATCAAAGTCTGAAATAAATAACTTAGACTGAATCGAAAAAAGACCTAAC
20266925 ACATGCTG
66 ACATGCTG
* *
20266933 AAATGACCTGGACTAAATCAAAGTTTGAAATGAATAACTTAGACT-AAGTCGAAAAAAGACCTAA
1 AAATGACCTGGACTAAATCAAAGTCTGAAATAAATAACTTAGACTGAA-TCGAAAAAAGACCTAA
20266997 CA
65 CA
20266999 TAAGTCGAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
72 2 0.04
73 52 0.96
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (73 bp):
AAATGACCTGGACTAAATCAAAGTCTGAAATAAATAACTTAGACTGAATCGAAAAAAGACCTAAC
ACATGCTG
Found at i:20267444 original size:255 final size:252
Alignment explanation
Indices: 20266933--20267576 Score: 663
Period size: 255 Copynumber: 2.5 Consensus size: 252
20266923 ACACATGCTG
* * * * * **
20266933 AAATGACCTGGACTAAATCAAAGTTTGAAATGAATAACTTAGACTAAGTCGAAAAAAGACCTAAC
1 AAATAACCTGGACTAAATCGAAGTCTGAAATGAATAACTTGGACTAAGTCG-AAGAAGA-CTGGC
* ** * *
20266998 ATAAGTCGAAACCCGAAAACAAAATGACCTGGACTGAACCAAAGTT-TGAAATAAATAACTT-GA
64 AT-AGACGAAACCTAAAAACAAAATGACCTGGATTGAACCGAA-TTCTGAAAT-AATAACTTGGA
* * * * ***
20267061 CTAAGCTGAAGAGAGATCTGACAGAGGTCAAAATTCGAAATAAAATGACCTGGATGAAACTGCAG
126 CTAAGCTCAAGAGAGATCTAACAGAGGTCAAAATCCGAAATAAAATGACCTAGATGAAACCAAAG
* * * * * *
20267126 TCTAAAAAGAATAACTTGGACTAAGTCGAAGAAGGATCTGACATAAGTCAAAATTCAAAAACA
191 TCTAAAAAAAATAACTTGGACTAAGCCGAAAAAAGATCTAACACAAGTCAAAATT-AAAAACA
* * * *
20267189 AAATAACTTGGACTAAATCGAAGTCTGAAATGAATAACTTGGACTAAATCCAAGAGAGATATGGC
1 AAATAACCTGGACTAAATCGAAGTCTGAAATGAATAACTTGGACTAAGTCGAAGA-AGA-CTGGC
* *
20267254 ATAGGACGAAACCTAAAAATAAAATGACTTGGATTGAACCGAATTCTGAAATAAGTAACTTGGAC
64 ATA-GACGAAACCTAAAAACAAAATGACCTGGATTGAACCGAATTCTGAAATAA-TAACTTGGAC
* * *
20267319 TAAG-TCAA-AGAGATCTAACATAGG-CTAAAATCCTAAATAAAATTACCTAGATGAAACCAAAG
127 TAAGCTCAAGAGAGATCTAACAGAGGTC-AAAATCCGAAATAAAATGACCTAGATGAAACCAAAG
**
20267381 TCTAAAAAAAATAACTTGGACTAAGCCGAAAAAAGATCTAACACAAGTCGAGACCTT-AAAACA
191 TCTAAAAAAAATAACTTGGACTAAGCCGAAAAAAGATCTAACACAAGTC-A-AAATTAAAAACA
* * * * *
20267444 AAATGACCTAGA-TGGAATCGAAGTCTGAAAAGAATAACTTGGACTAAGTTGAAGAAGGACTGGA
1 AAATAACCTGGACT-AAATCGAAGTCTGAAATGAATAACTTGGACTAAGTCGAAGAA-GACTGG-
* * * * *
20267508 CATAAATCGAAACCTAAAAACAAATTGACCTGAATTGAACTGAAGTCTGAAATGAATAACTTGGA
63 CATAGA-CGAAACCTAAAAACAAAATGACCTGGATTGAACCGAATTCTGAAAT-AATAACTTGGA
20267573 CTAA
126 CTAA
20267577 ACTGAAAAAA
Statistics
Matches: 322, Mismatches: 53, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
254 7 0.02
255 204 0.63
256 101 0.31
257 10 0.03
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (252 bp):
AAATAACCTGGACTAAATCGAAGTCTGAAATGAATAACTTGGACTAAGTCGAAGAAGACTGGCAT
AGACGAAACCTAAAAACAAAATGACCTGGATTGAACCGAATTCTGAAATAATAACTTGGACTAAG
CTCAAGAGAGATCTAACAGAGGTCAAAATCCGAAATAAAATGACCTAGATGAAACCAAAGTCTAA
AAAAAATAACTTGGACTAAGCCGAAAAAAGATCTAACACAAGTCAAAATTAAAAACA
Found at i:20267750 original size:86 final size:85
Alignment explanation
Indices: 20266933--20267750 Score: 571
Period size: 86 Copynumber: 9.6 Consensus size: 85
20266923 ACACATGCTG
* * * * * * * * *
20266933 AAATGACCTGGACTAAATCAAAGTTTGAAATGAATAACTTAGACTAAGTCGAAAAAAGACCTAAC
1 AAATGACCTGGACTGAACCGAAGTCTGAAATGAATAACTTGGACTAAG-CCAAAGAAGATCTGAC
*
20266998 ATAAGTCGAAACCCGAAAACA
65 ATAAGTCAAAACCCGAAAACA
* * * **
20267019 AAATGACCTGGACTGAACCAAAGTTTGAAATAAATAACTT-GACTAAGCTGAAGAGAGATCTGAC
1 AAATGACCTGGACTGAACCGAAGTCTGAAATGAATAACTTGGACTAAGCCAAAGA-AGATCTGAC
* * ** *
20267083 AGAGGTCAAAATTCG-AAATA
65 ATAAGTCAAAACCCGAAAACA
* * * * * *
20267103 AAATGACCTGGA-TGAAACTGCAGTCTAAAAAGAATAACTTGGACTAAGTCGAAGAAGGATCTGA
1 AAATGACCTGGACTG-AACCGAAGTCTGAAATGAATAACTTGGACTAAGCCAAAGAA-GATCTGA
** *
20267167 CATAAGTCAAAATTCAAAAACA
64 CATAAGTCAAAACCCGAAAACA
* * * * * * *
20267189 AAATAACTTGGACTAAATCGAAGTCTGAAATGAATAACTTGGACTAAATCC-AAGAGAGATATGG
1 AAATGACCTGGACTGAACCGAAGTCTGAAATGAATAACTTGGACT-AAGCCAAAGA-AGATCTGA
* * * ** *
20267253 CATAGGACGAAACCTAAAAATA
64 CATAAGTCAAAACCCGAAAACA
* * * * *
20267275 AAATGACTTGGATTGAACCGAATTCTGAAAT-AAGTAACTTGGACTAAGTCAAAG-AGATCTAAC
1 AAATGACCTGGACTGAACCGAAGTCTGAAATGAA-TAACTTGGACTAAGCCAAAGAAGATCTGAC
* * * *
20267338 AT-AGGCTAAAATCC-TAAATA
65 ATAAGTC-AAAACCCGAAAACA
* * * * ** * *
20267358 AAATTACCTAGA-TGAAACCAAAGTCTAAAAAAAATAACTTGGACTAAGCCGAAAAAAGATCTAA
1 AAATGACCTGGACTG-AACCGAAGTCTGAAATGAATAACTTGGACTAAGCC-AAAGAAGATCTGA
* * * **
20267422 CACAAGTCGAGACCTTAAAACA
64 CATAAGTCAAAACCCGAAAACA
* * * ***
20267444 AAATGACCTAGA-TGGAATCGAAGTCTGAAAAGAATAACTTGGACTAAGTTGAAGAAGGA-CTGG
1 AAATGACCTGGACT-GAACCGAAGTCTGAAATGAATAACTTGGACTAAGCCAAAGAA-GATCT-G
* * **
20267507 ACATAAATCGAAACCTAAAAACA
63 ACATAAGTCAAAACCCGAAAACA
* * * * * * * * *
20267530 AATTGACCTGAATTGAACTGAAGTCTGAAATGAATAACTTGGACTAAACTGAAAAAAAATTTGAC
1 AAATGACCTGGACTGAACCGAAGTCTGAAATGAATAACTTGGACTAAGC-CAAAGAAGATCTGAC
*
20267595 ATAAATCAAAACCCGAAAACA
65 ATAAGTCAAAACCCGAAAACA
* * * * * *
20267616 AAATAACTTGGACTGAATCGAAGTTTGAAATGAATAACTTAGACTAAGCCAAAGAAGTATTTGAC
1 AAATGACCTGGACTGAACCGAAGTCTGAAATGAATAACTTGGACTAAGCCAAAGAAG-ATCTGAC
*
20267681 ATAAGTCAAAACCCGAAAATA
65 ATAAGTCAAAACCCGAAAACA
* *
20267702 AAATGACCTAGACTGAACCGAAGTCTAAAATGAATAA-TCTGGACTAAGC
1 AAATGACCTGGACTGAACCGAAGTCTGAAATGAATAACT-TGGACTAAGC
20267751 TAACATACGT
Statistics
Matches: 576, Mismatches: 131, Indels: 50
0.76 0.17 0.07
Matches are distributed among these distances:
82 2 0.00
83 45 0.08
84 56 0.10
85 86 0.15
86 375 0.65
87 12 0.02
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (85 bp):
AAATGACCTGGACTGAACCGAAGTCTGAAATGAATAACTTGGACTAAGCCAAAGAAGATCTGACA
TAAGTCAAAACCCGAAAACA
Found at i:20268686 original size:47 final size:46
Alignment explanation
Indices: 20268610--20268765 Score: 129
Period size: 47 Copynumber: 3.2 Consensus size: 46
20268600 TTTTTTTTTG
* *
20268610 TTTTATTTTTGAACTTAAATGACCCTTTAC-GAGTTTTCAATTTGAA
1 TTTTTTTTTTGAACTCAAATGACCCTTTACAG-GTTTTCAATTTGAA
* *
20268656 TTTTTTTTATTGAACTCAAACTG-CCTTTTACAGGTTTTCAATTTGAGTTTTTT
1 TTTTTTTT-TTGAACTCAAA-TGACCCTTTACAGGTTTTCAATTTGA------A
* *
20268709 TTTTTTTTTTGAACTTAAATTG-CCCTTTATAGGTTTTCAATTTGAGA
1 TTTTTTTTTTGAACTCAAA-TGACCCTTTACAGGTTTTCAATTTGA-A
*
20268756 TCTTTTTTTT
1 TTTTTTTTTT
20268766 ATTAAAAAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 17
0.76 0.09 0.14
Matches are distributed among these distances:
46 7 0.08
47 39 0.43
48 3 0.03
52 33 0.37
53 8 0.09
ACGTcount: A:0.22, C:0.12, G:0.11, T:0.54
Consensus pattern (46 bp):
TTTTTTTTTTGAACTCAAATGACCCTTTACAGGTTTTCAATTTGAA
Found at i:20268743 original size:52 final size:50
Alignment explanation
Indices: 20268602--20268765 Score: 158
Period size: 52 Copynumber: 3.2 Consensus size: 50
20268592 GCTATTTTTT
*
20268602 TTTTTTTGTTTTATTTTTGAACTTAAATGACCCTTTACGAGTTTTCAATTTGA-
1 TTTTTTT-TTTT-TTTTTGAACTTAAATG-CCCTTTAAG-GTTTTCAATTTGAG
* * * *
20268655 ----ATTTTTTTTATTGAACTCAAACTGCCTTTTACAGGTTTTCAATTTGAG
1 TTTTTTTTTTTTTTTTGAACTTAAA-TGCCCTTTA-AGGTTTTCAATTTGAG
20268703 TTTTTTTTTTTTTTTTGAACTTAAATTGCCCTTTATAGGTTTTCAATTTGAG
1 TTTTTTTTTTTTTTTTGAACTTAAA-TGCCCTTTA-AGGTTTTCAATTTGAG
* *
20268755 ATCTTTTTTTT
1 TTTTTTTTTTT
20268766 ATTAAAAAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
47 31 0.34
48 7 0.08
49 2 0.02
52 51 0.56
ACGTcount: A:0.21, C:0.12, G:0.11, T:0.56
Consensus pattern (50 bp):
TTTTTTTTTTTTTTTTGAACTTAAATGCCCTTTAAGGTTTTCAATTTGAG
Found at i:20268783 original size:99 final size:101
Alignment explanation
Indices: 20268602--20268783 Score: 225
Period size: 99 Copynumber: 1.8 Consensus size: 101
20268592 GCTATTTTTT
*
20268602 TTTTTTTGTTTTATTTTTGAACTTAAATGACCCTTTACGAGTTTTCAATTTGAATTTTTTTTATT
1 TTTTTTTGTTTTATTTTTGAACTTAAATGACCCTTTAAGAGTTTTCAATTTGAATTTTTTTTATT
** * *
20268667 GAACTCAAACTGCCTTTTACAGGTTTTCAATTTGAG
66 GAACAAAAAATGACTTTTACAGGTTTTCAATTTGAG
20268703 TTTTTTT-TTTT-TTTTTGAACTTAAATTG-CCCTTTATAG-GTTTTCAATTTGAGATCTTTTTT
1 TTTTTTTGTTTTATTTTTGAACTTAAA-TGACCCTTTA-AGAGTTTTCAATTTGA-A--TTTTTT
20268764 TTATT-AA-AAAAAAT-ACTTTT
61 TTATTGAACAAAAAATGACTTTT
20268784 TCACAGCATC
Statistics
Matches: 71, Mismatches: 5, Indels: 12
0.81 0.06 0.14
Matches are distributed among these distances:
99 39 0.55
100 12 0.17
101 9 0.13
102 11 0.15
ACGTcount: A:0.25, C:0.11, G:0.10, T:0.54
Consensus pattern (101 bp):
TTTTTTTGTTTTATTTTTGAACTTAAATGACCCTTTAAGAGTTTTCAATTTGAATTTTTTTTATT
GAACAAAAAATGACTTTTACAGGTTTTCAATTTGAG
Found at i:20282451 original size:25 final size:26
Alignment explanation
Indices: 20282423--20282487 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
20282413 ATTAAAAATT
20282423 AATAAACTTAATTTAA-TTAATAAAA
1 AATAAACTTAATTTAATTTAATAAAA
* ***
20282448 AAT-AACATAATTTAATTTAATTTTA
1 AATAAACTTAATTTAATTTAATAAAA
20282473 AATAAA-TTAATTTAA
1 AATAAACTTAATTTAA
20282488 AATTAACGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 11 0.33
25 20 0.61
26 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (26 bp):
AATAAACTTAATTTAATTTAATAAAA
Found at i:20288043 original size:23 final size:23
Alignment explanation
Indices: 20288013--20288057 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
20288003 GTTGGTTTGT
20288013 GAGTTGTTACCAACTATTTGGAA
1 GAGTTGTTACCAACTATTTGGAA
20288036 GAGTTGTTACCAACTATTTGGA
1 GAGTTGTTACCAACTATTTGGA
20288058 TGATGGTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (23 bp):
GAGTTGTTACCAACTATTTGGAA
Found at i:20294675 original size:14 final size:15
Alignment explanation
Indices: 20294650--20294678 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20294640 ATTAATTAAC
20294650 ATATTATTAAAATTA
1 ATATTATTAAAATTA
20294665 ATATT-TTAAAATTA
1 ATATTATTAAAATTA
20294679 CGAAATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATTATTAAAATTA
Found at i:20294778 original size:20 final size:20
Alignment explanation
Indices: 20294735--20294779 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
20294725 AATAAAATAA
* * **
20294735 AAAAATTTTAAAGATAAATT
1 AAAAATTTTAAAAACAAAAG
20294755 AAAAATTTTAAAAACAAAAG
1 AAAAATTTTAAAAACAAAAG
20294775 AAAAA
1 AAAAA
20294780 ATAACACGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
AAAAATTTTAAAAACAAAAG
Found at i:20295152 original size:14 final size:13
Alignment explanation
Indices: 20295117--20295266 Score: 55
Period size: 14 Copynumber: 11.5 Consensus size: 13
20295107 TTTATTACTC
20295117 AATTAATTCAAA--
1 AATTAATT-AAATT
20295129 AATTAATTAAATT
1 AATTAATTAAATT
20295142 AATTGAATTAAATTT
1 AATT-AATTAAA-TT
*
20295157 AATCAATTAAAATT
1 AATTAATT-AAATT
*
20295171 --TTAAATTTAATTT
1 AATT-AA-TTAAATT
*
20295184 AATTTAATTTAATT
1 AA-TTAATTAAATT
* * *
20295198 AATAAAAATAAAAT
1 AAT-TAATTAAATT
20295212 AATTTAATT-AATT
1 AA-TTAATTAAATT
* * *
20295225 TATT-TTTAAATA
1 AATTAATTAAATT
*
20295237 AATTAATTTAA--
1 AATTAATTAAATT
**
20295248 AATTAACAAAATT
1 AATTAATTAAATT
20295261 AATTAA
1 AATTAA
20295267 ATGAACATAC
Statistics
Matches: 101, Mismatches: 21, Indels: 31
0.66 0.14 0.20
Matches are distributed among these distances:
11 13 0.13
12 17 0.17
13 25 0.25
14 33 0.33
15 11 0.11
16 2 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (13 bp):
AATTAATTAAATT
Found at i:20295193 original size:37 final size:36
Alignment explanation
Indices: 20295126--20295206 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 36
20295116 CAATTAATTC
20295126 AAAAATTAATTAAATTAATTGAATTAAATTTAATCAAT
1 AAAAATT--TTAAATTAATTGAATTAAATTTAATCAAT
* * * *
20295164 TAAAATTTTAAATTTAATTTAATTTAATTTAATTAAT
1 AAAAATTTTAAA-TTAATTGAATTAAATTTAATCAAT
20295201 AAAAAT
1 AAAAAT
20295207 AAAATAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 5 0.14
37 26 0.70
38 6 0.16
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (36 bp):
AAAAATTTTAAATTAATTGAATTAAATTTAATCAAT
Found at i:20295268 original size:9 final size:9
Alignment explanation
Indices: 20295128--20295268 Score: 60
Period size: 9 Copynumber: 15.4 Consensus size: 9
20295118 ATTAATTCAA
20295128 AAATTAATT
1 AAATTAATT
20295137 AAATTAATT
1 AAATTAATT
*
20295146 GAATTAAATT
1 AAATT-AATT
* *
20295156 TAATCAATT
1 AAATTAATT
20295165 AAAATT--TT
1 -AAATTAATT
20295173 AAATTTAATTT
1 AAA-TTAA-TT
*
20295184 AATTTAATT
1 AAATTAATT
*
20295193 TAATTAA-T
1 AAATTAATT
20295201 AAA--AA-T
1 AAATTAATT
*
20295207 AAAATAATT
1 AAATTAATT
*
20295216 TAATTAATTT
1 AAATTAA-TT
** *
20295226 ATTTTTAAAT
1 A-AATTAATT
20295236 AAATTAATTT
1 AAATTAA-TT
**
20295246 AAAATTAACA
1 -AAATTAATT
20295256 AAATTAATT
1 AAATTAATT
20295265 AAAT
1 AAAT
20295269 GAACATACTA
Statistics
Matches: 97, Mismatches: 22, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
6 6 0.06
7 3 0.03
8 9 0.09
9 45 0.46
10 19 0.20
11 15 0.15
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (9 bp):
AAATTAATT
Found at i:20297002 original size:20 final size:20
Alignment explanation
Indices: 20296974--20297015 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
20296964 TGAATTAAGA
20296974 AAGAAAATTGATAGCAAAAG
1 AAGAAAATTGATAGCAAAAG
*
20296994 AAGATAATTGATAGCAAAAG
1 AAGAAAATTGATAGCAAAAG
20297014 AA
1 AA
20297016 ACGTCTAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.05, G:0.19, T:0.17
Consensus pattern (20 bp):
AAGAAAATTGATAGCAAAAG
Found at i:20297388 original size:48 final size:49
Alignment explanation
Indices: 20297326--20297419 Score: 127
Period size: 48 Copynumber: 1.9 Consensus size: 49
20297316 TTTTTAATGA
*
20297326 TTATACTGAAAAAGCTCCTCTAAGCTAAGACTCAACAACTTTAAAAATC
1 TTATACTGAAAAAGCTCCTCTAAGCAAAGACTCAACAACTTTAAAAATC
* * * **
20297375 TTAT-CTGGAAAAGCTCTTCTAAGCAAAGGCTCAATGACTTTAAAA
1 TTATACTGAAAAAGCTCCTCTAAGCAAAGACTCAACAACTTTAAAA
20297420 CTTTCCTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 35 0.90
49 4 0.10
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (49 bp):
TTATACTGAAAAAGCTCCTCTAAGCAAAGACTCAACAACTTTAAAAATC
Found at i:20297472 original size:24 final size:24
Alignment explanation
Indices: 20297440--20297486 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
20297430 AGAAAAGTTT
* *
20297440 CTCTTAGCAGAAGCTCAACAACTC
1 CTCTCAGCAAAAGCTCAACAACTC
20297464 CTCTCAGCAAAAGCTCAACAACT
1 CTCTCAGCAAAAGCTCAACAACT
20297487 TTAAAATCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.34, G:0.11, T:0.19
Consensus pattern (24 bp):
CTCTCAGCAAAAGCTCAACAACTC
Found at i:20297582 original size:50 final size:48
Alignment explanation
Indices: 20297463--20297684 Score: 147
Period size: 50 Copynumber: 4.6 Consensus size: 48
20297453 CTCAACAACT
* *
20297463 CCTCTCAGCAAAAGCTCAACAACTTTAAAATCTCATATTGAAAAAGTC
1 CCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATATTGAAAAAGTC
* * * *
20297511 CCTTTTAGCAGAGGCTCAACAATTTTAAAATCTCATCATCTTAGAAAAG-C
1 CCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCAT-AT-TGA-AAAAGTC
* * *
20297561 TCCTCTCA-CAGAGGTTCAACAACTTTAAAA----A-ATTTAAAAAGGC
1 -CCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATATTGAAAAAGTC
* * *
20297604 TCATCTAAGCAGAGGCTTAACAACTTTAAAAT-TCATCATCCTGAAAAAG-C
1 -CCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCAT-AT--TGAAAAAGTC
* * * * *
20297654 TCCTTTAAGTAAAGGCTTAACAACTTTAAAA
1 -CCTCTCAGCAGAGGCTCAACAACTTTAAAA
20297685 ATCTTATCTG
Statistics
Matches: 142, Mismatches: 19, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
42 5 0.04
43 10 0.07
44 22 0.15
46 1 0.01
47 1 0.01
48 31 0.22
49 4 0.03
50 51 0.36
51 17 0.12
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (48 bp):
CCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATATTGAAAAAGTC
Found at i:20297756 original size:80 final size:78
Alignment explanation
Indices: 20297618--20297770 Score: 191
Period size: 80 Copynumber: 1.9 Consensus size: 78
20297608 CTAAGCAGAG
** *
20297618 GCTTAACAACTTTAAAATTCATCATCCTGAAAAAGCTCCTTTAAGTAAAGGCTTAACAACTTTAA
1 GCTTAACAACTTTAAAATTCATCATCCTGAAAAAGCTCCACTAAGTAAAGGCTCAACAACTTT-A
20297683 AAATCTTATCTGAA
65 AAATCTTATCTGAA
* * * * * *
20297697 GCTTAACAATTTTAAAGTCTCATTAT-CTTAGAAAAGCTCCACTCAGTAGAGGCTCAACAACTTT
1 GCTTAACAACTTTAAAAT-TCATCATCCTGA-AAAAGCTCCACTAAGTAAAGGCTCAACAACTTT
20297761 AAAATCTTAT
64 AAAATCTTAT
20297771 ATTGGAAAAG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
79 29 0.46
80 34 0.54
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (78 bp):
GCTTAACAACTTTAAAATTCATCATCCTGAAAAAGCTCCACTAAGTAAAGGCTCAACAACTTTAA
AATCTTATCTGAA
Found at i:20297790 original size:48 final size:47
Alignment explanation
Indices: 20297721--20297965 Score: 258
Period size: 48 Copynumber: 5.1 Consensus size: 47
20297711 AAGTCTCATT
* * *
20297721 ATCTTAGAAAAGCTCCACTCAGTAGAGGCTCAACAACTTTAAAATCTT
1 ATCTTGGAAAAGCTCCTCTCAGTAGAGGCTCAACAACTTTAAAAT-TC
*
20297769 ATATTGGAAAAGCTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATTC
1 ATCTTGGAAAAGCTCCTCTCAGTAGAGGCTCAACAACTTT-AAAATTC
* * * * * *
20297817 ATCTTGGAAAAGCTCTTCTTAGCAAAGGCTCAATAATTTTAAAAATTC
1 ATCTTGGAAAAGCTCCTCTCAGTAGAGGCTCAACAACTTT-AAAATTC
* * * * * *
20297865 ATTTTGAAAAAGCTTCTTTAAGTAGAGGCTCAACAACTTTTAAAATTT
1 ATCTTGGAAAAGCTCCTCTCAGTAGAGGCTCAACAAC-TTTAAAATTC
* * *
20297913 ATCTTGG-AAAGTTTTCTCTCAGCAGAGGCTCAACAACTTTAAAGATTC
1 ATCTTGGAAAAG-CTCCTCTCAGTAGAGGCTCAACAACTTTAAA-ATTC
20297961 ATCTT
1 ATCTT
20297966 TTTCTCGAAA
Statistics
Matches: 164, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
47 10 0.06
48 146 0.89
49 8 0.05
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (47 bp):
ATCTTGGAAAAGCTCCTCTCAGTAGAGGCTCAACAACTTTAAAATTC
Found at i:20311417 original size:7 final size:8
Alignment explanation
Indices: 20311393--20311444 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
20311383 AGAAAGAAAG
*
20311393 AATAAAAA
1 AATATAAA
20311401 AATATAAA
1 AATATAAA
20311409 AATATAAA
1 AATATAAA
*
20311417 AAAATAAA
1 AATATAAA
20311425 TAATAATAATA
1 -AAT-ATAA-A
*
20311436 AATACAAA
1 AATATAAA
20311444 A
1 A
20311445 TAGTGTTTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
8 24 0.65
9 5 0.14
10 7 0.19
11 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (8 bp):
AATATAAA
Found at i:20311433 original size:18 final size:19
Alignment explanation
Indices: 20311393--20311433 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
20311383 AGAAAGAAAG
20311393 AATAAAAAAATATAAAAAT
1 AATAAAAAAATATAAAAAT
*
20311412 -ATAAAAAAATA-AATAAT
1 AATAAAAAAATATAAAAAT
20311429 AATAA
1 AATAA
20311434 TAAATACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (19 bp):
AATAAAAAAATATAAAAAT
Found at i:20315789 original size:8 final size:10
Alignment explanation
Indices: 20315762--20315794 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
20315752 CATATGCCTT
20315762 ATTATTTTTA
1 ATTATTTTTA
20315772 ATTATTTTTA
1 ATTATTTTTA
*
20315782 ATT-TTTTAA
1 ATTATTTTTA
20315791 ATTA
1 ATTA
20315795 CCTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
ATTATTTTTA
Found at i:20318073 original size:21 final size:23
Alignment explanation
Indices: 20318038--20318104 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 23
20318028 AATCATAAAC
*
20318038 AAAATATATAAAAATTCAAATATT
1 AAAA-ATAAAAAAATTCAAATATT
* *
20318062 -GAAAT-AAAAAATAT-AACTATT
1 AAAAATAAAAAAAT-TCAAATATT
20318083 AAAAATAAAAGAAATTCAAATA
1 AAAAATAAAA-AAATTCAAATA
20318105 CTTTTATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
21 12 0.36
22 7 0.21
23 6 0.18
24 8 0.24
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (23 bp):
AAAAATAAAAAAATTCAAATATT
Found at i:20320658 original size:145 final size:147
Alignment explanation
Indices: 20320482--20320793 Score: 565
Period size: 145 Copynumber: 2.1 Consensus size: 147
20320472 ATTCAAAAGT
*
20320482 GAAATTTAAATTTTTTAAAAATAATATATATTATTTTTAAAAAATAAAAAATTGAAAAAAATAAA
1 GAAATATAAATTTTTT-AAAATAATATATATTATTTTTAAAAAATAAAAAATTGAAAAAAATAAA
20320547 GTTAATATTTTTAAAAT-AAAAAATCTAAATAATTCAAA-TTTTTATTTTTTAAAATTGAAATCC
65 GTTAATATTTTTAAAATAAAAAAATCTAAATAATTCAAATTTTTTATTTTTTAAAATTGAAATCC
20320610 GATTGTTAAAAAATTCAA
130 GATTGTTAAAAAATTCAA
20320628 GAAATATAAATTTTTTAAAATAATATATATTATTTTTAAAAAATAAAAAATTGAAAAAAATAAAG
1 GAAATATAAATTTTTTAAAATAATATATATTATTTTTAAAAAATAAAAAATTGAAAAAAATAAAG
*
20320693 TTAATATTTTTAAAATAAAAAAAATCTAAATAATTCAAATTTTTTATTTTTTTAAATTGAAATCC
66 TTAATATTTTTAAAAT-AAAAAAATCTAAATAATTCAAATTTTTTATTTTTTAAAATTGAAATCC
20320758 GATTGTTAAAAAATTCAA
130 GATTGTTAAAAAATTCAA
*
20320776 GAAATATAATTTTTTTAA
1 GAAATATAAATTTTTTAA
20320794 GGTTTTTAAA
Statistics
Matches: 160, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
145 65 0.41
146 15 0.09
147 21 0.13
148 59 0.37
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (147 bp):
GAAATATAAATTTTTTAAAATAATATATATTATTTTTAAAAAATAAAAAATTGAAAAAAATAAAG
TTAATATTTTTAAAATAAAAAAATCTAAATAATTCAAATTTTTTATTTTTTAAAATTGAAATCCG
ATTGTTAAAAAATTCAA
Found at i:20321302 original size:15 final size:16
Alignment explanation
Indices: 20321282--20321311 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20321272 TTATAATTTG
20321282 ATGTCA-TTAATATTA
1 ATGTCATTTAATATTA
20321297 ATGTCATTTAATATT
1 ATGTCATTTAATATT
20321312 TTATTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (16 bp):
ATGTCATTTAATATTA
Found at i:20323387 original size:20 final size:17
Alignment explanation
Indices: 20323351--20323402 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 17
20323341 GATATATAAT
20323351 AAAATAAAAAAAATTTA
1 AAAATAAAAAAAATTTA
20323368 AAAATAAACTAAAAACTTTA
1 AAAATAAA--AAAAA-TTTA
*
20323388 AAAACAGAAAAAAAT
1 AAAATA-AAAAAAAT
20323403 ATTATATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 8 0.27
18 1 0.03
19 10 0.33
20 9 0.30
21 2 0.07
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAATAAAAAAAATTTA
Found at i:20324419 original size:11 final size:11
Alignment explanation
Indices: 20324397--20324438 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
20324387 GATTCATTAA
20324397 TTTTTAA-ATT
1 TTTTTAATATT
20324407 TTTTT-ATATT
1 TTTTTAATATT
*
20324417 TTTTTAATATGA
1 TTTTTAATAT-T
20324429 TTTTTAATAT
1 TTTTTAATAT
20324439 ATTTAAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 1 0.04
10 13 0.46
11 4 0.14
12 10 0.36
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (11 bp):
TTTTTAATATT
Found at i:20324442 original size:11 final size:11
Alignment explanation
Indices: 20324396--20324442 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
20324386 CGATTCATTA
20324396 ATTTTTAA-AT
1 ATTTTTAATAT
*
20324406 -TTTTTTATAT
1 ATTTTTAATAT
*
20324416 TTTTTTAATAT
1 ATTTTTAATAT
20324427 GATTTTTAATAT
1 -ATTTTTAATAT
20324439 ATTT
1 ATTT
20324443 AAATAGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 13 0.42
12 10 0.32
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:20329799 original size:19 final size:18
Alignment explanation
Indices: 20329772--20329817 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
20329762 AAAAGTGATA
20329772 AATCA-TAAGCATGTATAT
1 AATCATTAAGCATGT-TAT
* *
20329790 AATCGTTAAG-TTGTTAT
1 AATCATTAAGCATGTTAT
20329807 AATCATTAAGC
1 AATCATTAAGC
20329818 TAATTGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 12 0.52
18 7 0.30
19 4 0.17
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (18 bp):
AATCATTAAGCATGTTAT
Found at i:20330553 original size:3 final size:3
Alignment explanation
Indices: 20330545--20330580 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
20330535 AGAATTGTTT
20330545 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
20330581 GATATAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20332194 original size:21 final size:23
Alignment explanation
Indices: 20332168--20332227 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
20332158 CAACATACAT
*
20332168 AAAAATTCAAATATT-GAAAT-A
1 AAAAATTCAAATATTAAAAATAA
*
20332189 AAAAATAT-AACTATTAAAAATAA
1 AAAAAT-TCAAATATTAAAAATAA
20332212 AAGAAATTCAAATATT
1 AA-AAATTCAAATATT
20332228 TTATTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 12 0.39
22 5 0.16
23 4 0.13
24 10 0.32
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.28
Consensus pattern (23 bp):
AAAAATTCAAATATTAAAAATAA
Found at i:20335484 original size:21 final size:20
Alignment explanation
Indices: 20335438--20335485 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
20335428 ATAATAAAAT
* *
20335438 AAAAAAATTTTAAAAATAAA
1 AAAAAAACTTTAAAAACAAA
**
20335458 CTAAAAACTTTAAAAACAGAA
1 AAAAAAACTTTAAAAACA-AA
20335479 AAAAAAA
1 AAAAAAA
20335486 TGATATTTTT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAAAAACTTTAAAAACAAA
Found at i:20335853 original size:14 final size:14
Alignment explanation
Indices: 20335829--20335898 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
20335819 TTAATTCAAA
20335829 AATTG-ATTAAATT
1 AATTGAATTAAATT
20335842 AATTGAATTAAATTT
1 AATTGAATTAAA-TT
*
20335857 AA-TCAATTAAAATT
1 AATTGAATT-AAATT
*
20335871 --TTAAATT-AATT
1 AATTGAATTAAATT
* *
20335882 AATTTAATTTAATT
1 AATTGAATTAAATT
20335896 AAT
1 AAT
20335899 AAAAATAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
11 4 0.09
13 16 0.34
14 20 0.43
15 7 0.15
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (14 bp):
AATTGAATTAAATT
Found at i:20335883 original size:9 final size:9
Alignment explanation
Indices: 20335828--20335962 Score: 67
Period size: 9 Copynumber: 14.4 Consensus size: 9
20335818 ATTAATTCAA
*
20335828 AAATTGATT
1 AAATTAATT
20335837 AAATTAATT
1 AAATTAATT
*
20335846 GAATTAAATT
1 AAATT-AATT
* *
20335856 TAATCAATT
1 AAATTAATT
20335865 AAAATT--TT
1 -AAATTAATT
20335873 AAATTAATT
1 AAATTAATT
*
20335882 AATTTAATT
1 AAATTAATT
* *
20335891 TAATTAATAA
1 AAATTAAT-T
* *
20335901 AAATAAAAT
1 AAATTAATT
20335910 AAATTAATTT
1 AAATTAA-TT
** *
20335920 ACTTTCAAAT
1 AAATT-AATT
20335930 AAATTAATTT
1 AAATTAA-TT
**
20335940 AAAATTAACG
1 -AAATTAATT
20335950 AAATTAATT
1 AAATTAATT
20335959 AAAT
1 AAAT
20335963 GAACATACTA
Statistics
Matches: 91, Mismatches: 26, Indels: 18
0.67 0.19 0.13
Matches are distributed among these distances:
7 5 0.05
8 2 0.02
9 51 0.56
10 24 0.26
11 9 0.10
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (9 bp):
AAATTAATT
Found at i:20339968 original size:23 final size:23
Alignment explanation
Indices: 20339938--20339982 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
20339928 TAAAGCTTTA
*
20339938 TGGGATTCAAATCCTAGATTTTT
1 TGGGATTCAAATCCTAAATTTTT
*
20339961 TGGGATTCAAATCTTAAATTTT
1 TGGGATTCAAATCCTAAATTTT
20339983 CAAGCCGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (23 bp):
TGGGATTCAAATCCTAAATTTTT
Found at i:20340143 original size:10 final size:10
Alignment explanation
Indices: 20340116--20340171 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
20340106 ACCGAATAAG
*
20340116 GAAAGAAGAA
1 GAAAGAAAAA
*
20340126 GAAGGAAAAA
1 GAAAGAAAAA
20340136 GAAAGAAAGAA
1 GAAAGAAA-AA
*
20340147 GAAAAAAAATA
1 GAAAGAAAA-A
20340158 GAAA-AATAAA
1 GAAAGAA-AAA
20340168 GAAA
1 GAAA
20340172 AAATAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 23 0.59
11 16 0.41
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (10 bp):
GAAAGAAAAA
Found at i:20340155 original size:21 final size:22
Alignment explanation
Indices: 20340116--20340174 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
20340106 ACCGAATAAG
**
20340116 GAAAG-AAGAAGAAGGAAAA-A
1 GAAAGAAAGAAGAAAAAAAATA
20340136 GAAAGAAAGAAGAAAAAAAATA
1 GAAAGAAAGAAGAAAAAAAATA
20340158 GAAA-AATA-AAGAAAAAA
1 GAAAGAA-AGAAGAAAAAA
20340175 TAAATAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 5 0.15
21 23 0.68
22 6 0.18
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.03
Consensus pattern (22 bp):
GAAAGAAAGAAGAAAAAAAATA
Found at i:20340160 original size:11 final size:10
Alignment explanation
Indices: 20340131--20340174 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
20340121 AAGAAGAAGG
20340131 AAAAAGAAAGA
1 AAAAAGAAA-A
*
20340142 AAGAAGAAAA
1 AAAAAGAAAA
20340152 AAAATAGAAAA
1 AAAA-AGAAAA
*
20340163 ATAAAGAAAA
1 AAAAAGAAAA
20340173 AA
1 AA
20340175 TAAATAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
10 11 0.39
11 17 0.61
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:20340160 original size:18 final size:18
Alignment explanation
Indices: 20340124--20340161 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
20340114 AGGAAAGAAG
*
20340124 AAGAAGGAAAAAGAAAGA
1 AAGAAGGAAAAAAAAAGA
20340142 AAGAA-GAAAAAAAATAGA
1 AAGAAGGAAAAAAAA-AGA
20340160 AA
1 AA
20340162 AATAAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (18 bp):
AAGAAGGAAAAAAAAAGA
Found at i:20340443 original size:50 final size:49
Alignment explanation
Indices: 20340367--20340750 Score: 264
Period size: 50 Copynumber: 7.8 Consensus size: 49
20340357 TTAAAAATTT
* * *
20340367 AAAAAGCTCATCTAAGCAGA-AGCTCAACAACTTTAAAATGTATCATCCTG
1 AAAAAACTCTTCTAAGCAGAGA-CTCAACAACTTTAAAATATATCAT-CTG
* * *
20340417 AAAAAGCTCTTCTAAGCAGAGACTCAACAACTTTAAAA-ATTTTATCTG
1 AAAAAACTCTTCTAAGCAGAGACTCAACAACTTTAAAATATATCATCTG
* * * * *
20340465 AAAAAAAATCCTCTAAACA-AAAGCTCAACAACTTTAAAA-ATCTCATCTG
1 -AAAAAACTCTTCTAAGCAGAGA-CTCAACAACTTTAAAATATATCATCTG
* * *
20340514 AAAAAAATTTTTCTAAGCAGAGACTCAATAACTTTAAAAT-TCATCATCATG
1 -AAAAAACTCTTCTAAGCAGAGACTCAACAACTTTAAAATAT-ATCATC-TG
* * * * * * *
20340565 AAAAAAATCCTCTAAACAAATG-CTTAACAACTTTAAAA-ATCTCATATAG
1 AAAAAACTCTTCTAAGCAGA-GACTCAACAACTTTAAAATATATCATCT-G
* * **
20340614 AAAAAAAC-CTCTCTAAGCAGAGGCTCAATAACTTTAAAATCCATCATCATG
1 -AAAAAACTCT-TCTAAGCAGAGACTCAACAACTTTAAAATATATCATC-TG
* * * * * * *
20340665 AAAAAGCTCCTCTAAGTAGAGGCTCAATAACTTTAAAA-ATCTGATCTG
1 AAAAAACTCTTCTAAGCAGAGACTCAACAACTTTAAAATATATCATCTG
* * * * *
20340713 AAAAAGCTCTTTTAAGCAGAGGCTTAATAACTTTAAAA
1 AAAAAACTCTTCTAAGCAGAGACTCAACAACTTTAAAA
20340751 CTTTCATTTT
Statistics
Matches: 270, Mismatches: 48, Indels: 34
0.77 0.14 0.10
Matches are distributed among these distances:
48 42 0.16
49 84 0.31
50 133 0.49
51 10 0.04
52 1 0.00
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (49 bp):
AAAAAACTCTTCTAAGCAGAGACTCAACAACTTTAAAATATATCATCTG
Found at i:20340579 original size:148 final size:143
Alignment explanation
Indices: 20340367--20340830 Score: 430
Period size: 148 Copynumber: 3.1 Consensus size: 143
20340357 TTAAAAATTT
* * *
20340367 AAAAAGCTCATCTAAGCAGA-AGCTCAACAACTTTAAAATGT-ATCATCCTGAAAAAGCTCTTCT
1 AAAAAACTCCTCTAAGCAGAGA-CTCAATAACTTTAAAAT-TCATCAT-CTGAAAAAGCTCTTCT
* * * *
20340430 AAGCAGAGACTCAACAACTTTAAAAATTTTATCTGAAAAAAAATCCTCTAAACAAAAGCTCAACA
63 AAGCAGAG-CTTAACAACTTTAAAAATTTCATAT-AAAAAAAATCCTCTAAACAAAAGCTCAATA
20340495 ACTTTAAAAATCTCATCTG
126 ACTTT-AAAATCTCATCTG
* ** ** *
20340514 AAAAAAATTTTTCTAAGCAGAGACTCAATAACTTTAAAATTCATCATCATGAAAAAAATCCTCTA
1 -AAAAAACTCCTCTAAGCAGAGACTCAATAACTTTAAAATTCATCATC-TGAAAAAGCTCTTCTA
* * * * * * *
20340579 AACAAATGCTTAACAACTTTAAAAATCTCATATAGAAAAAAACCTCTCTAAGCAGAGGCTCAATA
64 AGCAGA-GCTTAACAACTTTAAAAATTTCATATA-AAAAAAATC-CTCTAAACAAAAGCTCAATA
20340644 ACTTTAAAATCCATCATCATG
126 ACTTTAAAAT-C-TCATC-TG
* * * * * *
20340665 AAAAAGCTCCTCTAAGTAGAGGCTCAATAACTTTAAAAATC-TGATCTGAAAAAGCTCTTTTAAG
1 AAAAAACTCCTCTAAGCAGAGACTCAATAACTTTAAAATTCATCATCTGAAAAAGCTCTTCTAAG
* * * * ** * *
20340729 CAGAGGCTTAATAACTTTAAAACTTTCATTTTAGAAAAGCTCATCTCAACAAAAGCTCAATAACT
66 CAGA-GCTTAACAACTTTAAAAATTTCA-TATAAAAAAAATCCTCTAAACAAAAGCTCAATAACT
20340794 TTAAAATCTCATCTTG
129 TTAAAATCTCATC-TG
* *
20340810 GAAAAACTCCTCTCAGCAGAG
1 AAAAAACTCCTCTAAGCAGAG
20340831 GCTTAACAAC
Statistics
Matches: 254, Mismatches: 52, Indels: 23
0.77 0.16 0.07
Matches are distributed among these distances:
145 24 0.09
146 1 0.00
147 28 0.11
148 129 0.51
149 31 0.12
150 39 0.15
151 2 0.01
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (143 bp):
AAAAAACTCCTCTAAGCAGAGACTCAATAACTTTAAAATTCATCATCTGAAAAAGCTCTTCTAAG
CAGAGCTTAACAACTTTAAAAATTTCATATAAAAAAAATCCTCTAAACAAAAGCTCAATAACTTT
AAAATCTCATCTG
Found at i:20340647 original size:100 final size:100
Alignment explanation
Indices: 20340377--20340807 Score: 420
Period size: 100 Copynumber: 4.4 Consensus size: 100
20340367 AAAAAGCTCA
* * * *
20340377 TCTAAGCAGAAGCTCAACAACTTTAAAATGTATCATCCTG--AAAAAGCTCTTCTAAGCAGAGAC
1 TCTAAACAAAAGCTCAACAACTTTAAAA-ATCTCAT-CTGAAAAAAAGCTCTTCTAAGCAGAGAC
* *
20340440 TCAACAACTTTAAAAATT--TTATC-TGAAAAAAAATCC
64 TCAATAACTTT-AAAATTCATCATCATG-AAAAAAATCC
* *
20340476 TCTAAACAAAAGCTCAACAACTTTAAAAATCTCATCTGAAAAAAA-TTTTTCTAAGCAGAGACTC
1 TCTAAACAAAAGCTCAACAACTTTAAAAATCTCATCTGAAAAAAAGCTCTTCTAAGCAGAGACTC
20340540 AATAACTTTAAAATTCATCATCATGAAAAAAATCC
66 AATAACTTTAAAATTCATCATCATGAAAAAAATCC
* * * * *
20340575 TCTAAACAAATGCTTAACAACTTTAAAAATCTCATATAGAAAAAAACCTC-TCTAAGCAGAGGCT
1 TCTAAACAAAAGCTCAACAACTTTAAAAATCTCATCT-GAAAAAAAGCTCTTCTAAGCAGAGACT
* **
20340639 CAATAACTTTAAAATCCATCATCATGAAAAAGCTCC
65 CAATAACTTTAAAATTCATCATCATGAAAAAAATCC
** * * * * * * *
20340675 TCTAAGTAGAGGCTCAATAACTTTAAAAATCTGATCTG--AAAAAGCTCTTTTAAGCAGAGGCTT
1 TCTAAACAAAAGCTCAACAACTTTAAAAATCTCATCTGAAAAAAAGCTCTTCTAAGCAGAGACTC
* * ** *
20340738 AATAACTTTAAAACTT--TCAT-TTTAGAAAAGCTCA
66 AATAACTTTAAAA-TTCATCATCATGA-AAAAAATCC
* *
20340772 TCTCAACAAAAGCTCAATAACTTT-AAAATCTCATCT
1 TCTAAACAAAAGCTCAACAACTTTAAAAATCTCATCT
20340808 TGGAAAAACT
Statistics
Matches: 284, Mismatches: 38, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
96 13 0.05
97 48 0.17
98 56 0.20
99 81 0.29
100 85 0.30
101 1 0.00
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.28
Consensus pattern (100 bp):
TCTAAACAAAAGCTCAACAACTTTAAAAATCTCATCTGAAAAAAAGCTCTTCTAAGCAGAGACTC
AATAACTTTAAAATTCATCATCATGAAAAAAATCC
Found at i:20340654 original size:49 final size:49
Alignment explanation
Indices: 20340367--20340805 Score: 244
Period size: 49 Copynumber: 8.9 Consensus size: 49
20340357 TTAAAAATTT
* * * ****
20340367 AAAAAGCTCATCTAAGCAGAAGCTCAACAACTTTAAAATGT-ATCATCCTG
1 AAAAAGCTC-TCTAAGCAGAGGCTCAATAACTTTAAAATCTCAT-ATAGAA
* * * * *
20340417 AAAAAGCTCTTCTAAGCAGAGACTCAACAACTTTAAAAATTTTATCT-GAA
1 AAAAAGCTC-TCTAAGCAGAGGCTCAATAACTTT-AAAATCTCATATAGAA
* * * * * *
20340467 AAAAA-ATCCTCTAAACAAAAGCTCAACAACTTTAAAAATCTCATCT-GAA
1 AAAAAGCT-CTCTAAGCAGAGGCTCAATAACTTT-AAAATCTCATATAGAA
** * *
20340516 AAAAATTTTTCTAAGCAGAGACTCAATAACTTTAAAAT-TCATCATCATGAA
1 AAAAAGCTCTCTAAGCAGAGGCTCAATAACTTTAAAATCTCAT-AT-A-GAA
* * * * * *
20340567 AAAAATC-CTCTAAACAAATGCTTAACAACTTTAAAAATCTCATATAGAA
1 AAAAAGCTCTCTAAGCAGAGGCTCAATAACTTT-AAAATCTCATATAGAA
*
20340616 AAAAACCTCTCTAAGCAGAGGCTCAATAACTTTAAAATC-CATCATCATG--
1 AAAAAGCTCTCTAAGCAGAGGCTCAATAACTTTAAAATCTCAT-AT-A-GAA
* * *
20340665 AAAAAGCTCCTCTAAGTAGAGGCTCAATAACTTTAAAAATCTGATCT-G--
1 AAAAAGCT-CTCTAAGCAGAGGCTCAATAACTTT-AAAATCTCATATAGAA
* * * *
20340713 AAAAAGCTCTTTTAAGCAGAGGCTTAATAACTTTAAAACTTTCATTTTAG--
1 AAAAAGCTC-TCTAAGCAGAGGCTCAATAACTTTAAAA-TCTCA-TATAGAA
* *
20340763 -AAAAGCTCATCTCAA-CAAAAGCTCAATAACTTTAAAATCTCAT
1 AAAAAGCTC-TCT-AAGCAGAGGCTCAATAACTTTAAAATCTCAT
20340806 CTTGGAAAAA
Statistics
Matches: 314, Mismatches: 53, Indels: 47
0.76 0.13 0.11
Matches are distributed among these distances:
47 10 0.03
48 46 0.15
49 114 0.36
50 105 0.33
51 31 0.10
52 8 0.03
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (49 bp):
AAAAAGCTCTCTAAGCAGAGGCTCAATAACTTTAAAATCTCATATAGAA
Found at i:20340862 original size:24 final size:24
Alignment explanation
Indices: 20340814--20340865 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
20340804 ATCTTGGAAA
* *
20340814 AACTCCTCTCAGCAGAGGCTTAAC
1 AACTCCTCTCAGCAAAGGCTCAAC
20340838 AACTCCTCTCAGCAAAAGG-TCAAC
1 AACTCCTCTCAGC-AAAGGCTCAAC
20340862 AACT
1 AACT
20340866 TTAAAATCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.35, C:0.33, G:0.13, T:0.19
Consensus pattern (24 bp):
AACTCCTCTCAGCAAAGGCTCAAC
Found at i:20340905 original size:72 final size:72
Alignment explanation
Indices: 20340772--20340913 Score: 187
Period size: 72 Copynumber: 2.0 Consensus size: 72
20340762 GAAAAGCTCA
* * * * *
20340772 TCTCAACAAAAGCTCAATAACTTTAAAATCTCATCTTGGAAAAACTCCTCTCAGCAGAGGCTTAA
1 TCTCAACAAAAGCTCAACAACTTTAAAATCTCATCTTGGAAAAACTCATCTCAACAAAGGCTCAA
20340837 CAACTCC
66 CAACTCC
* * * *
20340844 TCTCAGCAAAAGGTCAACAACTTTAAAATCTCATCTT-GAAAAAGCTCATTTCAATAAAGGCTCA
1 TCTCAACAAAAGCTCAACAACTTTAAAATCTCATCTTGGAAAAA-CTCATCTCAACAAAGGCTCA
20340908 ACAACT
65 ACAACT
20340914 TTAAAATCTC
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
71 6 0.10
72 54 0.90
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.25
Consensus pattern (72 bp):
TCTCAACAAAAGCTCAACAACTTTAAAATCTCATCTTGGAAAAACTCATCTCAACAAAGGCTCAA
CAACTCC
Found at i:20341070 original size:49 final size:49
Alignment explanation
Indices: 20340976--20341563 Score: 494
Period size: 48 Copynumber: 12.2 Consensus size: 49
20340966 GAGCTCAATG
* * * *
20340976 ACTTT-AAAATCTCATCATCTTAGAAAAGCTCCTCTAAGCAAAGGCTCAACA
1 ACTTTAAAAATCTCATC-T-TGA-AAAAGCTTCTCTAAGTAGAGGCTCAACA
* *
20341027 ACTTTAAAAATCTAAT-TTGAAAAAAGCTTATCTAAGTAGAGGCTCAACA
1 ACTTTAAAAATCTCATCTTG-AAAAAGCTTCTCTAAGTAGAGGCTCAACA
* *
20341076 ACTTTAAAAA--T--T-TTAAAAAAGTTTCTCTAAGTAGAGGCTCAACA
1 ACTTTAAAAATCTCATCTTGAAAAAGCTTCTCTAAGTAGAGGCTCAACA
* * * * *
20341120 ACTTTAAAATTCATCATCCTGGAAAAG-TTCCTCTAAGCAAAGGCTCAACA
1 ACTTTAAAAATC-TCATCTTGAAAAAGCTT-CTCTAAGTAGAGGCTCAACA
* * * * *
20341170 ACTTTAAAAATCTTAT-ATGGAAAAGC-TCTTTTAAGCAGAGGCTCAA-A
1 ACTTTAAAAATCTCATCTTGAAAAAGCTTC-TCTAAGTAGAGGCTCAACA
* * * * * *
20341217 ACTTTAAAACTTTCATCTTGGAAAAGC-TCATCTCAGCAGAGACTCAACA
1 ACTTTAAAAATCTCATCTTGAAAAAGCTTC-TCTAAGTAGAGGCTCAACA
* * * * *
20341266 ACTTT-AAAATCTCATCTTGAAAAAGTTTCTCTCAGAAAAGGCTCAATA
1 ACTTTAAAAATCTCATCTTGAAAAAGCTTCTCTAAGTAGAGGCTCAACA
* * * *
20341314 ACTTT-AAAATCTCATCTTAAAAAAGCTTATCTCAA-TAGAAGCTTAACA
1 ACTTTAAAAATCTCATCTTGAAAAAGCTTCTCT-AAGTAGAGGCTCAACA
* * * * **
20341362 ATTTTAAAAAT-TTATCTTGGAAAAGCTCCTCTAAACAGAGGCTCAACA
1 ACTTTAAAAATCTCATCTTGAAAAAGCTTCTCTAAGTAGAGGCTCAACA
* * * * * *
20341410 ACTTTAAAAGT-TGATCTTGGACAAAGCTTTTCTAAGTAAAGGCTCAATA
1 ACTTTAAAAATCTCATCTT-GAAAAAGCTTCTCTAAGTAGAGGCTCAACA
20341459 ACTTT-AAAATCTCATCTTGAAAAAGGCTTCTCTAAGTAGAGGCTCAACA
1 ACTTTAAAAATCTCATCTTGAAAAA-GCTTCTCTAAGTAGAGGCTCAACA
* * * * *
20341508 ACTTTACAAAT-TCATTTTGGAAAAGCTCCTTTAAGTAGAGGCTCAACA
1 ACTTTAAAAATCTCATCTTGAAAAAGCTTCTCTAAGTAGAGGCTCAACA
20341556 ACTTTAAA
1 ACTTTAAA
20341564 GATTCATTTT
Statistics
Matches: 439, Mismatches: 77, Indels: 45
0.78 0.14 0.08
Matches are distributed among these distances:
44 36 0.08
45 3 0.01
47 19 0.04
48 201 0.46
49 125 0.28
50 41 0.09
51 5 0.01
52 9 0.02
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (49 bp):
ACTTTAAAAATCTCATCTTGAAAAAGCTTCTCTAAGTAGAGGCTCAACA
Found at i:20353671 original size:22 final size:21
Alignment explanation
Indices: 20353631--20353680 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
20353621 TTTTACAAGG
20353631 TTTCTTTTTTTTTACAAAAAGT
1 TTTCTTTTTTTTTACAAAAA-T
*
20353653 TTTCTTTTTTATTT-TAAAAAT
1 TTTCTTTTTT-TTTACAAAAAT
20353674 TTT-TTTT
1 TTTCTTTT
20353681 GGTAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 15 0.58
23 3 0.12
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTCTTTTTTTTTACAAAAAT
Found at i:20362575 original size:15 final size:16
Alignment explanation
Indices: 20362555--20362584 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20362545 TTATAATTTG
20362555 ATGTCA-TTAATATTA
1 ATGTCATTTAATATTA
20362570 ATGTCATTTAATATT
1 ATGTCATTTAATATT
20362585 TTATTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (16 bp):
ATGTCATTTAATATTA
Found at i:20363964 original size:10 final size:10
Alignment explanation
Indices: 20363949--20364014 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 10
20363939 NNNNNNNTTC
20363949 TTTTCATTTT
1 TTTTCATTTT
20363959 TTTTCA-TTT
1 TTTTCATTTT
20363968 TTTT-ATTTT
1 TTTTCATTTT
20363977 TCCATTT--TTTCT
1 T---TTTCATTT-T
20363989 TATTTCATTTT
1 T-TTTCATTTT
20364000 TTTTC-TTTT
1 TTTTCATTTT
20364009 TTTTCA
1 TTTTCA
20364015 AGCATAGTAC
Statistics
Matches: 48, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
8 1 0.02
9 20 0.42
10 14 0.29
11 5 0.10
12 8 0.17
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTCATTTT
Found at i:20363968 original size:8 final size:8
Alignment explanation
Indices: 20363957--20364001 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
20363947 TCTTTTCATT
20363957 TTTTTTCA
1 TTTTTTCA
*
20363965 TTTTTTTA
1 TTTTTTCA
*
20363973 TTTTTCCA
1 TTTTTTCA
20363981 TTTTTTC-
1 TTTTTTCA
*
20363988 TTATTTCA
1 TTTTTTCA
20363996 TTTTTT
1 TTTTTT
20364002 TTCTTTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:20363978 original size:15 final size:14
Alignment explanation
Indices: 20363955--20364008 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
20363945 NTTCTTTTCA
20363955 TTTTTTTTCATTTT
1 TTTTTTTTCATTTT
20363969 TTTATTTTTCCATTTT
1 TTT-TTTTT-CATTTT
*
20363985 TTCTTATTTCATTTT
1 TT-TTTTTTCATTTT
20364000 TTTTCTTTT
1 TTTT-TTTT
20364009 TTTTCAAGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 5 0.15
15 16 0.47
16 12 0.35
17 1 0.03
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTTTCATTTT
Found at i:20363983 original size:26 final size:25
Alignment explanation
Indices: 20363949--20364014 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 25
20363939 NNNNNNNTTC
*
20363949 TTTTCATTTTTTTTCATTT-TTTTAT
1 TTTTCATTTTTTTTCATTTCATTT-T
20363974 TTTTCCATTTTTTCTT-ATTTCATTTT
1 TTTT-CATTTTTT-TTCATTTCATTTT
20364000 TTTTC-TTTTTTTTCA
1 TTTTCATTTTTTTTCA
20364015 AGCATAGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
23 2 0.06
24 7 0.19
25 5 0.14
26 17 0.47
27 5 0.14
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTCATTTTTTTTCATTTCATTTT
Found at i:20367878 original size:31 final size:31
Alignment explanation
Indices: 20367840--20367917 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
20367830 AAATATCCGA
20367840 ACCCGACCTGACCCGATACTATGTAAATCGT
1 ACCCGACCTGACCCGATACTATGTAAATCGT
*
20367871 ACCCGACCTGACCTGATACTATGTAAATCGT
1 ACCCGACCTGACCCGATACTATGTAAATCGT
*
20367902 ACCCGACCCGACCCGA
1 ACCCGACCTGACCCGA
20367918 AATTAATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.28, C:0.36, G:0.17, T:0.19
Consensus pattern (31 bp):
ACCCGACCTGACCCGATACTATGTAAATCGT
Found at i:20367959 original size:20 final size:21
Alignment explanation
Indices: 20367923--20367974 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
20367913 CCCGAAATTA
20367923 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
20367945 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
20367966 AT-AAATATT
1 ATAAAATATT
20367975 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:20367965 original size:21 final size:22
Alignment explanation
Indices: 20367923--20367974 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
20367913 CCCGAAATTA
20367923 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
20367945 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
20367966 AT-AAATATT
1 ATAAAATATT
20367975 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:20367982 original size:30 final size:32
Alignment explanation
Indices: 20367947--20368009 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
20367937 TTTAAAATAT
* * *
20367947 AAAATATTATTTTTTAAATATA-A-ATATTTA
1 AAAATATCATTATATAAATATATATATATTTA
20367977 AAAATATCATTATATAAATATATATATATTTA
1 AAAATATCATTATATAAATATATATATATTTA
20368009 A
1 A
20368010 TTAATTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 19 0.68
31 1 0.04
32 8 0.29
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (32 bp):
AAAATATCATTATATAAATATATATATATTTA
Found at i:20367983 original size:16 final size:16
Alignment explanation
Indices: 20367962--20368009 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
20367952 ATTATTTTTT
20367962 AAATATAAATATTTAA
1 AAATATAAATATTTAA
* * *
20367978 AAATATCATTATATAA
1 AAATATAAATATTTAA
* *
20367994 ATATATATATATTTAA
1 AAATATAAATATTTAA
20368010 TTAATTAATT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATAAATATTTAA
Found at i:20375931 original size:22 final size:22
Alignment explanation
Indices: 20375891--20376009 Score: 102
Period size: 22 Copynumber: 5.4 Consensus size: 22
20375881 AAAGATAAAA
*
20375891 ATAAA-AAT-ATATATTAATAG
1 ATAAATAATAATATATGAATAG
20375911 ATAAATAATAATATATGAATAG
1 ATAAATAATAATATATGAATAG
*
20375933 ATAAATAATAAAATATGTTAATAG
1 ATAAATAATAATATATG--AATAG
* * *
20375957 GTAAATAAAAATATATGTATTA-
1 ATAAATAATAATATATG-AATAG
* *
20375979 ATAAACAATAATAGTAAT-AATAA
1 ATAAATAATAATA-T-ATGAATAG
20376002 ATAAATAA
1 ATAAATAA
20376010 ATAAAAATAC
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.06
21 3 0.04
22 40 0.49
23 12 0.15
24 21 0.26
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.32
Consensus pattern (22 bp):
ATAAATAATAATATATGAATAG
Found at i:20375973 original size:24 final size:24
Alignment explanation
Indices: 20375889--20375974 Score: 115
Period size: 24 Copynumber: 3.7 Consensus size: 24
20375879 AAAAAGATAA
*
20375889 AAATAAAAATATATATTAATAGAT
1 AAATAAAAATATATGTTAATAGAT
*
20375913 AAATAATAATATATG--AATAGAT
1 AAATAAAAATATATGTTAATAGAT
*
20375935 AAATAATAAA-ATATGTTAATAGGT
1 AAATAA-AAATATATGTTAATAGAT
20375959 AAATAAAAATATATGT
1 AAATAAAAATATATGT
20375975 ATTAATAAAC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
22 18 0.33
23 5 0.09
24 31 0.57
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (24 bp):
AAATAAAAATATATGTTAATAGAT
Found at i:20375983 original size:46 final size:47
Alignment explanation
Indices: 20375889--20376018 Score: 133
Period size: 46 Copynumber: 2.8 Consensus size: 47
20375879 AAAAAGATAA
*
20375889 AAATAA-AAATATATATTAATAGATAAATAATAATATATGAATAGAT
1 AAATAATAAATATATATTAATAGATAAATAAAAATATATGAATAGAT
* * *
20375935 AAATAATAAA-ATATGTTAATAGGTAAATAAAAATATATGTATTA-AT
1 AAATAATAAATATATATTAATAGATAAATAAAAATATATG-AATAGAT
* * *
20375981 AAACAAT-AATAGTAATAATAAATAAATAAATAAAAATA
1 AAATAATAAATA-T-AT-ATTAATAGATAAATAAAAATA
20376019 CAAATAAACT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
45 2 0.03
46 41 0.59
47 7 0.10
48 2 0.03
49 17 0.25
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (47 bp):
AAATAATAAATATATATTAATAGATAAATAAAAATATATGAATAGAT
Found at i:20375999 original size:19 final size:18
Alignment explanation
Indices: 20375960--20376002 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
20375950 TTAATAGGTA
*
20375960 AATAAAAATATATGTATT
1 AATAAAAATATATGTAAT
20375978 AATAAACAATA-ATAGTAAT
1 AATAAA-AATATAT-GTAAT
20375997 AATAAA
1 AATAAA
20376003 TAAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (18 bp):
AATAAAAATATATGTAAT
Found at i:20376542 original size:21 final size:23
Alignment explanation
Indices: 20376516--20376575 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
20376506 CAACATACAT
*
20376516 AAAAATTCAAATATT-GAAAT-A
1 AAAAATTCAAATATTAAAAATAA
*
20376537 AAAAATAT-AACTATTAAAAATAA
1 AAAAAT-TCAAATATTAAAAATAA
20376560 AAGAAATTCAAATATT
1 AA-AAATTCAAATATT
20376576 TTATTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 12 0.39
22 5 0.16
23 4 0.13
24 10 0.32
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.28
Consensus pattern (23 bp):
AAAAATTCAAATATTAAAAATAA
Found at i:20378735 original size:149 final size:146
Alignment explanation
Indices: 20378463--20378763 Score: 489
Period size: 149 Copynumber: 2.0 Consensus size: 146
20378453 TAAGTTTTTT
* *
20378463 AAAACTAATATATATTATTTTTAAAAAATAAAAAATTGATAAAAATAAAGTTAATATTTTAAAAA
1 AAAAATAATATATATTATTTTTAAAAAATAAAAAATTGAAAAAAATAAAGTTAATATTTTAAAAA
*
20378528 AAAAAATCTAAATAATTCAAATTTTTTATTTTTTACAATTGAAATCCAATTGCTAAAAAATTCAA
66 AAAAAATCTAAACAATTCAAATTTTTTATTTTTTACAATTGAAATCCAATTGCTAAAAAATTCAA
20378593 GAAATATAA-TTTTAA
131 GAAATATAATTTTTAA
*
20378608 AAAAATAATATATATTGTTTTTAAAAAATAAAAAATTGAAAAAAAATAAAGTTAATATTTTTAAA
1 AAAAATAATATATATTATTTTTAAAAAATAAAAAATTG-AAAAAAATAAAGTTAATA-TTTTAAA
* *
20378673 ATAAAAAAATCTAAACAATTCAAAATTTTTTATTTTTTTA-AATTGAAATCCGATTGTTAAAAAA
64 A-AAAAAAATCTAAACAATTC-AAATTTTTTA-TTTTTTACAATTGAAATCCAATTGCTAAAAAA
20378737 TTCAAGAAATATAATTTTTAA
126 TTCAAGAAATATAATTTTTAA
20378758 AAAAAT
1 AAAAAT
20378764 TAAAATATTG
Statistics
Matches: 144, Mismatches: 6, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
145 36 0.25
146 17 0.12
147 8 0.06
148 18 0.12
149 46 0.32
150 19 0.13
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (146 bp):
AAAAATAATATATATTATTTTTAAAAAATAAAAAATTGAAAAAAATAAAGTTAATATTTTAAAAA
AAAAAATCTAAACAATTCAAATTTTTTATTTTTTACAATTGAAATCCAATTGCTAAAAAATTCAA
GAAATATAATTTTTAA
Found at i:20379043 original size:122 final size:119
Alignment explanation
Indices: 20378802--20379046 Score: 438
Period size: 122 Copynumber: 2.0 Consensus size: 119
20378792 GTTTTTAAAA
20378802 AATTCAAAAAAGCTTAAAAATCAATATTTTTTAATTTTTTTTAAATTTCTTTTAGGATATTTTTA
1 AATTCAAAAAAGCTTAAAAATCAATATTTTTTAATTTTTTTTAAATTTCTTTTAGGATATTTTTA
20378867 ATTTTAAGATTTAAAAAAAAAATTAGAGTCACGTAAGCAAAATTAATGGAGAGT
66 ATTTTAAGATTTAAAAAAAAAATTAGAGTCACGTAAGCAAAATTAATGGAGAGT
20378921 AATTCAAAAAAGCTTAAAAATCAATATTTTTTTAATTTTTTTTAAAAAATTTCTTTTAGGATATT
1 AATTCAAAAAAGCTTAAAAATCAATA-TTTTTTAATTTTTTTT---AAATTTCTTTTAGGATATT
*
20378986 TTTAATTTTAAG-TTTTAAAAAAAAATTAGAGTCACGTAAGCAAAATTAATGGAGAGT
62 TTTAATTTTAAGATTTAAAAAAAAAATTAGAGTCACGTAAGCAAAATTAATGGAGAGT
20379043 AATT
1 AATT
20379047 AATCTTATTA
Statistics
Matches: 121, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
119 26 0.21
120 16 0.13
122 48 0.40
123 31 0.26
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.41
Consensus pattern (119 bp):
AATTCAAAAAAGCTTAAAAATCAATATTTTTTAATTTTTTTTAAATTTCTTTTAGGATATTTTTA
ATTTTAAGATTTAAAAAAAAAATTAGAGTCACGTAAGCAAAATTAATGGAGAGT
Found at i:20379398 original size:15 final size:16
Alignment explanation
Indices: 20379378--20379407 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20379368 TTATAATTTG
20379378 ATGTCA-TTAATATTA
1 ATGTCATTTAATATTA
20379393 ATGTCATTTAATATT
1 ATGTCATTTAATATT
20379408 TTATTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (16 bp):
ATGTCATTTAATATTA
Found at i:20380770 original size:17 final size:16
Alignment explanation
Indices: 20380736--20380775 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
20380726 AAATCAAATT
*
20380736 TTTTTAATTTTTGGGA
1 TTTTTAATTTTTGAGA
*
20380752 TTTCTTAATTTTTTAGA
1 TTT-TTAATTTTTGAGA
20380769 TTTTTAA
1 TTTTTAA
20380776 AAAATTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (16 bp):
TTTTTAATTTTTGAGA
Found at i:20381233 original size:15 final size:16
Alignment explanation
Indices: 20381213--20381242 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20381203 TTATAATTTG
20381213 ATGTCA-TTAATATTA
1 ATGTCATTTAATATTA
20381228 ATGTCATTTAATATT
1 ATGTCATTTAATATT
20381243 TTATTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (16 bp):
ATGTCATTTAATATTA
Found at i:20381502 original size:20 final size:17
Alignment explanation
Indices: 20381466--20381516 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
20381456 GATATATAAT
20381466 AAAATAAAAAAAATTTA
1 AAAATAAAAAAAATTTA
20381483 AAAATAAACTAAAAACTTTA
1 AAAATAAA--AAAAA-TTTA
*
20381503 AAAACAGAAAAAAA
1 AAAATA-AAAAAAA
20381517 ATAATATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 8 0.28
19 10 0.34
20 9 0.31
21 2 0.07
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.18
Consensus pattern (17 bp):
AAAATAAAAAAAATTTA
Found at i:20381517 original size:20 final size:18
Alignment explanation
Indices: 20381471--20381518 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
20381461 ATAATAAAAT
*
20381471 AAAAAAAATTTAAAAATA
1 AAAAAAAATTTAAAAACA
*
20381489 AACTAAAAACTTTAAAAACA
1 AA--AAAAAATTTAAAAACA
20381509 GAAAAAAAAT
1 -AAAAAAAAT
20381519 AATATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
18 2 0.08
19 6 0.25
20 14 0.58
21 2 0.08
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAAAAATTTAAAAACA
Found at i:20381865 original size:9 final size:9
Alignment explanation
Indices: 20381866--20382014 Score: 73
Period size: 9 Copynumber: 15.4 Consensus size: 9
20381856 ATTAATTCAA
20381866 AAATTAATT
1 AAATTAATT
20381875 AAATTAATT
1 AAATTAATT
20381884 AAATTAATT
1 AAATTAATT
*
20381893 GAATTAAATT
1 AAATT-AATT
* *
20381903 TAATCAATT
1 AAATTAATT
*
20381912 AAAATTTTAAAAT
1 -AAA--TT-AATT
*
20381925 GAATTAATT
1 AAATTAATT
* *
20381934 TAATTAATA
1 AAATTAATT
*
20381943 AAAATAATTT
1 AAATTAA-TT
*
20381953 AATTTAATT
1 AAATTAATT
*
20381962 TAATTAATTT
1 AAATTAA-TT
** *
20381972 ACTTTTAAAT
1 A-AATTAATT
20381982 AAATTAATTT
1 AAATTAA-TT
**
20381992 AAAATTAACG
1 -AAATTAATT
20382002 AAATTAATT
1 AAATTAATT
20382011 AAAT
1 AAAT
20382015 GAACATACTA
Statistics
Matches: 102, Mismatches: 28, Indels: 20
0.68 0.19 0.13
Matches are distributed among these distances:
9 63 0.62
10 22 0.22
11 11 0.11
12 3 0.03
13 3 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (9 bp):
AAATTAATT
Found at i:20381971 original size:14 final size:14
Alignment explanation
Indices: 20381869--20381993 Score: 58
Period size: 15 Copynumber: 8.6 Consensus size: 14
20381859 AATTCAAAAA
*
20381869 TTAATTAAATTAA-
1 TTAATTTAATTAAT
*
20381882 TTAAATTAATTGAAT
1 TTAATTTAATT-AAT
* *
20381897 TAAATTTAATCAAT
1 TTAATTTAATTAAT
* *
20381911 TAAAATTTTAAAATGAA-
1 T-TAA-TTT--AATTAAT
20381928 TTAATTTAATTAA-
1 TTAATTTAATTAAT
* **
20381941 TAAAAATAATTTAAT
1 TTAATTTAA-TTAAT
20381956 TTAATTTAATTAAT
1 TTAATTTAATTAAT
* * *
20381970 TTACTTTTAAATAAA
1 TTA-ATTTAATTAAT
20381985 TTAATTTAA
1 TTAATTTAA
20381994 AATTAACGAA
Statistics
Matches: 85, Mismatches: 18, Indels: 17
0.71 0.15 0.14
Matches are distributed among these distances:
13 20 0.24
14 23 0.27
15 31 0.36
16 5 0.06
17 1 0.01
18 5 0.06
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (14 bp):
TTAATTTAATTAAT
Found at i:20382010 original size:59 final size:60
Alignment explanation
Indices: 20381866--20382010 Score: 163
Period size: 59 Copynumber: 2.5 Consensus size: 60
20381856 ATTAATTCAA
*
20381866 AAATTAA-TTAAATTAATTAAATTAATTGAATTAAATTTAATCAATTAAAATTTTAAAAT
1 AAATTAATTTAAATTAATAAAATTAATTGAATTAAATTTAATCAATTAAAATTTTAAAAT
* * * * * * *
20381925 GAATTAATTT-AATTAATAAAAATAATTTAATTTAATTTAATTAATT-TACTTTT-AAAT
1 AAATTAATTTAAATTAATAAAATTAATTGAATTAAATTTAATCAATTAAAATTTTAAAAT
**
20381982 AAATTAATTTAAAATTAACGAAATTAATT
1 AAATTAATTT-AAATTAATAAAATTAATT
20382011 AAATGAACAT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
57 13 0.18
58 5 0.07
59 51 0.72
60 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (60 bp):
AAATTAATTTAAATTAATAAAATTAATTGAATTAAATTTAATCAATTAAAATTTTAAAAT
Found at i:20382583 original size:23 final size:22
Alignment explanation
Indices: 20382541--20382587 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
20382531 GTCTTTTATT
*
20382541 TTTTTTATATTCTTTTAATATGA
1 TTTTTAATATTCTTTTAATA-GA
20382564 TTTTTAATA-TCTTTTAAATAGA
1 TTTTTAATATTCTTTT-AATAGA
20382586 TT
1 TT
20382588 AGTTCTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTTAATATTCTTTTAATAGA
Found at i:20385972 original size:23 final size:23
Alignment explanation
Indices: 20385942--20385986 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
20385932 TAAAGCTTTA
*
20385942 TGGGATTCAAATCCTAGATTTTT
1 TGGGATTCAAATCCTAAATTTTT
*
20385965 TGGGATTCAAATCTTAAATTTT
1 TGGGATTCAAATCCTAAATTTT
20385987 CAAGCTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (23 bp):
TGGGATTCAAATCCTAAATTTTT
Found at i:20386161 original size:24 final size:24
Alignment explanation
Indices: 20386119--20386170 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
20386109 ATCGGGTAAG
20386119 GAAAGAAGAAGAAAGAAAAAGAAA
1 GAAAGAAGAAGAAAGAAAAAGAAA
* *
20386143 GAAAGAAGTA-AAAGAAAAAATAAA
1 GAAAGAAGAAGAAAG-AAAAAGAAA
20386167 GAAA
1 GAAA
20386171 AAATAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (24 bp):
GAAAGAAGAAGAAAGAAAAAGAAA
Found at i:20386169 original size:11 final size:11
Alignment explanation
Indices: 20386130--20386177 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
20386120 AAAGAAGAAG
*
20386130 AAAG-AAAAAG
1 AAAGAAAAAAT
*
20386140 AAAGAAAGAAGT
1 AAAGAAA-AAAT
20386152 AAAAGAAAAAAT
1 -AAAGAAAAAAT
20386164 AAAGAAAAAAT
1 AAAGAAAAAAT
20386175 AAA
1 AAA
20386178 TAATAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 4 0.12
11 16 0.50
12 5 0.16
13 7 0.22
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (11 bp):
AAAGAAAAAAT
Found at i:20386172 original size:17 final size:17
Alignment explanation
Indices: 20386120--20386172 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
20386110 TCGGGTAAGG
*
20386120 AAAG-AAGAAGAAAGAA
1 AAAGAAAGAAAAAAGAA
* *
20386136 AAAGAAAGAAAGAAGTA
1 AAAGAAAGAAAAAAGAA
20386153 AAAGAAA-AAATAAAGAA
1 AAAGAAAGAAA-AAAGAA
20386170 AAA
1 AAA
20386173 ATAAATAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 7 0.23
17 23 0.77
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (17 bp):
AAAGAAAGAAAAAAGAA
Found at i:20386491 original size:99 final size:99
Alignment explanation
Indices: 20386387--20386748 Score: 310
Period size: 99 Copynumber: 3.7 Consensus size: 99
20386377 CTAAGTAGAA
* * * ** *
20386387 GCTCAATAACTTTAAAATGTATCATCCT-AAAAAAG-TTCTTTTAAGTAGAGACTCAACAATTTT
1 GCTCAACAACTTTAAAA-ATATCAT-CTGAAAAAAGCTTC-TCTAAACAGAGACTCAACAACTTT
* * *
20386450 AAAAATC-TTATC-TGGAAAAAAATCTTTTAAACAAAG
63 AAAAATCATCATCAT-GAAAAAAATCCTCTAAACAAAG
* * *
20386486 GCTCAACAACTTTAAAAATCTCATCTGAAAAAAGCTTCTCTAAACAGAGGCTCAATAACTTTAAA
1 GCTCAACAACTTTAAAAATATCATCTGAAAAAAGCTTCTCTAAACAGAGACTCAACAACTTTAAA
* *
20386551 ATTCATCATCATGAAAAAAATCCTCTAAACAAAT
66 AATCATCATCATGAAAAAAATCCTCTAAACAAAG
* * * * * *
20386585 GCTCAACAACTTTAAAAATCTCATATGAAAAAAGCTTCTCTAAGCAAATG-TTCAATAACTTT-A
1 GCTCAACAACTTTAAAAATATCATCTGAAAAAAGCTTCTCTAAACAGA-GACTCAACAACTTTAA
* ** ** *
20386648 AAATCCATCATTATGAAAAAGCTCCTCTAAGTAAAT
65 AAAT-CATCATCATGAAAAAAATCCTCTAAACAAAG
* * * * *
20386684 GCTCAACAACTTTAAAAATTTTATCTG-AAAAAGC-TCTTTTAAGCAGATG-CTCAATAACTTTA
1 GCTCAACAACTTTAAAAATATCATCTGAAAAAAGCTTC-TCTAAACAGA-GACTCAACAACTTTA
20386746 AAA
64 AAA
20386749 CTTTCATTTT
Statistics
Matches: 225, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
97 4 0.02
98 68 0.30
99 151 0.67
100 2 0.01
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (99 bp):
GCTCAACAACTTTAAAAATATCATCTGAAAAAAGCTTCTCTAAACAGAGACTCAACAACTTTAAA
AATCATCATCATGAAAAAAATCCTCTAAACAAAG
Found at i:20386651 original size:48 final size:48
Alignment explanation
Indices: 20386438--20386899 Score: 323
Period size: 48 Copynumber: 9.5 Consensus size: 48
20386428 TAAGTAGAGA
* * * * * *
20386438 CTCAACAATTTTAAAAATCTTATCTGGAAAAAAATCTT-T-TAAACAAAGG
1 CTCAACAACTTT-AAAATCTCATAT-G-AAAAAAGCTTCTCTAAGCAAATG
* * * *
20386487 CTCAACAACTTTAAAAATCTCATCTGAAAAAAGCTTCTCTAAACAGAGG
1 CTCAACAACTTT-AAAATCTCATATGAAAAAAGCTTCTCTAAGCAAATG
* * * *
20386536 CTCAATAACTTTAAAATTCATCATCATGAAAAAA-ATCCTCTAAACAAATG
1 CTCAACAACTTTAAAA-TC-TCAT-ATGAAAAAAGCTTCTCTAAGCAAATG
20386586 CTCAACAACTTTAAAAATCTCATATGAAAAAAGCTTCTCTAAGCAAATG
1 CTCAACAACTTT-AAAATCTCATATGAAAAAAGCTTCTCTAAGCAAATG
* * * *
20386635 TTCAATAACTTTAAAATCCATCATTATG-AAAAAGCTCCTCTAAGTAAATG
1 CTCAACAACTTTAAAAT-C-TCA-TATGAAAAAAGCTTCTCTAAGCAAATG
* * * * *
20386685 CTCAACAACTTTAAAAATTTTATCTG-AAAAAGC-TCTTTTAAGCAGATG
1 CTCAACAACTTT-AAAATCTCATATGAAAAAAGCTTC-TCTAAGCAAATG
* * * * * * * *
20386733 CTCAATAACTTTAAAACTTTCATTTTAGAAAAGCTTCTCTTAGTAAAAG
1 CTCAACAACTTTAAAA-TCTCATATGAAAAAAGCTTCTCTAAGCAAATG
* * * * *
20386782 TTCAACAACTTTAAAATCTCATCTTGAAAAAA-CTCCTCTTAGCAAAAG
1 CTCAACAACTTTAAAATCTCAT-ATGAAAAAAGCTTCTCTAAGCAAATG
* * * *
20386830 GTCAACAACTTTAAAATCTCATCTTG-AAAAAGC-TCATCTCAA-CAGAGG
1 CTCAACAACTTTAAAATCTCAT-ATGAAAAAAGCTTC-TCT-AAGCAAATG
*
20386878 CTTAACAACTTTAAAATCTCAT
1 CTCAACAACTTTAAAATCTCAT
20386900 CATCTTAGAA
Statistics
Matches: 343, Mismatches: 51, Indels: 39
0.79 0.12 0.09
Matches are distributed among these distances:
47 20 0.06
48 128 0.37
49 110 0.32
50 64 0.19
51 21 0.06
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (48 bp):
CTCAACAACTTTAAAATCTCATATGAAAAAAGCTTCTCTAAGCAAATG
Found at i:20386810 original size:97 final size:98
Alignment explanation
Indices: 20386486--20386900 Score: 398
Period size: 99 Copynumber: 4.3 Consensus size: 98
20386476 TTAAACAAAG
* * *
20386486 GCTCAACAACTTTAAAAATCTCATCTGAAAAAAGCTTCTCTAAACAGAGGCTCAATAACTTTAAA
1 GCTCAACAACTTTAAAAATCTCATCTG-AAAAAGCTTCTCTAAGCAAATGCTCAATAACTTTAAA
* * ** ** *
20386551 ATTCATCATCATGAAAAAAATCCTCTAAACAAAT
65 ATCCATCATTATGAAAAAGCTCCTCTAAGTAAAA
* *
20386585 GCTCAACAACTTTAAAAATCTCATATGAAAAAAGCTTCTCTAAGCAAATGTTCAATAACTTTAAA
1 GCTCAACAACTTTAAAAATCTCATCTG-AAAAAGCTTCTCTAAGCAAATGCTCAATAACTTTAAA
*
20386650 ATCCATCATTATGAAAAAGCTCCTCTAAGTAAAT
65 ATCCATCATTATGAAAAAGCTCCTCTAAGTAAAA
* * * *
20386684 GCTCAACAACTTTAAAAATTTTATCTGAAAAAGC-TCTTTTAAGCAGATGCTCAATAACTTTAAA
1 GCTCAACAACTTTAAAAATCTCATCTGAAAAAGCTTC-TCTAAGCAAATGCTCAATAACTTTAAA
** * * *
20386748 A-CTTTCATT-TTAGAAAAGCTTCTCTTAGTAAAA
65 ATCCATCATTATGA-AAAAGCTCCTCTAAGTAAAA
* * * * * * *
20386781 GTTCAACAACTTT-AAAATCTCATCTTGAAAAAACTCCTCTTAGCAAAAGGTCAACAACTTTAAA
1 GCTCAACAACTTTAAAAATCTCATC-TGAAAAAGCTTCTCTAAGCAAATGCTCAATAACTTTAAA
* * * *
20386845 AT-C-TCATCT-TGAAAAAGCTCATCTCAA-CAGAG
65 ATCCATCAT-TATGAAAAAGCTCCTCT-AAGTAAAA
*
20386877 GCTTAACAACTTT-AAAATCTCATC
1 GCTCAACAACTTTAAAAATCTCATC
20386901 ATCTTAGAAA
Statistics
Matches: 265, Mismatches: 44, Indels: 17
0.81 0.13 0.05
Matches are distributed among these distances:
96 49 0.18
97 71 0.27
98 33 0.12
99 112 0.42
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (98 bp):
GCTCAACAACTTTAAAAATCTCATCTGAAAAAGCTTCTCTAAGCAAATGCTCAATAACTTTAAAA
TCCATCATTATGAAAAAGCTCCTCTAAGTAAAA
Found at i:20387047 original size:49 final size:50
Alignment explanation
Indices: 20386942--20387595 Score: 567
Period size: 48 Copynumber: 13.5 Consensus size: 50
20386932 ATAACTTTGA
* * * * *
20386942 GCTCAACGACTTTAAAATCTCATCATCTTAGAAAAA-CTCCTCTAAGTAAAG
1 GCTCAACAACTTTAAAA-ATC-TCATCTTAGAAAAAGCTTCTCTAAGCAGAG
* *
20386993 GCTCAACAACTTTAAAAATCTCAT-TTAGAAAAAGCTTATCTAAGTAGAG
1 GCTCAACAACTTTAAAAATCTCATCTTAGAAAAAGCTTCTCTAAGCAGAG
* *
20387042 GCTCAACAACTTTAAAAA--T--T-TTA-AAAAGGCTTCTCTAAGTAGAG
1 GCTCAACAACTTTAAAAATCTCATCTTAGAAAAAGCTTCTCTAAGCAGAG
* * * * * *
20387086 GCTCAACAATTTTAAAATTCATCATCCT-GGAAAAGTTTCTCTAAGCAAAG
1 GCTCAACAACTTTAAAAATC-TCATCTTAGAAAAAGCTTCTCTAAGCAGAG
* *
20387136 GCTCAACAACTTTAAAAATCTTATC-T-GAAAAAGC-TCTTTTAAGCAGAG
1 GCTCAACAACTTTAAAAATCTCATCTTAGAAAAAGCTTC-TCTAAGCAGAG
* * * * * *
20387184 ACTCAATAACTTTAAAACTTTCATCTT-GAAAAAGCTCCTCTCAGCAGAG
1 GCTCAACAACTTTAAAAATCTCATCTTAGAAAAAGCTTCTCTAAGCAGAG
* * * *
20387233 ACTCAACAACTTT-AAAATCTCATCTTAG-AAAAGTTTCTCTCAGCAAAG
1 GCTCAACAACTTTAAAAATCTCATCTTAGAAAAAGCTTCTCTAAGCAGAG
* * * *
20387281 GCTCAATAACTTT--AAATCTCATCTTAG-AAAAGCTTATCTCAGTAGAG
1 GCTCAACAACTTTAAAAATCTCATCTTAGAAAAAGCTTCTCTAAGCAGAG
* * * *
20387328 GCTCAACAACTTTAAAAAT-TTATCTT-GGAAAAG-TTCCTCTAAGTATAG
1 GCTCAACAACTTTAAAAATCTCATCTTAGAAAAAGCTT-CTCTAAGCAGAG
* * * *
20387376 GCTTAACAACTTTAAAAGT-TCATCTTAGACAAAGC-TCTTCTAAGCAAAG
1 GCTCAACAACTTTAAAAATCTCATCTTAGAAAAAGCTTC-TCTAAGCAGAG
*
20387425 GCTCAATAACTTT-AAAATCTCATCTT-GAAAAAGGCTTCTCTAAGCAGAG
1 GCTCAACAACTTTAAAAATCTCATCTTAGAAAAA-GCTTCTCTAAGCAGAG
* * * * *
20387474 GCTCAACAACTTTACAAAT-TCAT-TTTGGAAAAGCTCCTCTAAGTAGAG
1 GCTCAACAACTTTAAAAATCTCATCTTAGAAAAAGCTTCTCTAAGCAGAG
* * * * *
20387522 GCTCAACAATTTTAAAAAT-TCAT-TTTGGAAAAGTTTCTCTCAGCAGAG
1 GCTCAACAACTTTAAAAATCTCATCTTAGAAAAAGCTTCTCTAAGCAGAG
* *
20387570 GTTCAACAACTTTAAAGAT-TCATCTT
1 GCTCAACAACTTTAAAAATCTCATCTT
20387596 TTTCTCGAAA
Statistics
Matches: 505, Mismatches: 73, Indels: 52
0.80 0.12 0.08
Matches are distributed among these distances:
44 35 0.07
45 4 0.01
47 49 0.10
48 215 0.43
49 142 0.28
50 44 0.09
51 16 0.03
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (50 bp):
GCTCAACAACTTTAAAAATCTCATCTTAGAAAAAGCTTCTCTAAGCAGAG
Found at i:20387244 original size:97 final size:95
Alignment explanation
Indices: 20386982--20387595 Score: 486
Period size: 97 Copynumber: 6.4 Consensus size: 95
20386972 GAAAAACTCC
* * * ** *
20386982 TCTAAGTAAAGGCTCAACAACTTTAAAAATCTCAT-TTAGAAAAAGCTTATCTAAGTAGAGGCTC
1 TCTAAGCAGAGGCTCAACAACTTT-AAAATTTCATCTT-GAAAAAGCTCCTCTAAGCAGAGGCTC
20387046 AACAACTTTAAAAA--TT-T-T-AAAAAGGCTT
64 AACAACTTTAAAAATCTTATCTGAAAAA-GCTT
* * * * * * *
20387074 CTCTAAGTAGAGGCTCAACAATTTTAAAATTCATCATCCTGGAAAAGTTTCTCTAAGCAAAGGCT
1 -TCTAAGCAGAGGCTCAACAACTTTAAAATT--TCATCTTGAAAAAGCTCCTCTAAGCAGAGGCT
20387139 CAACAACTTTAAAAATCTTATCTGAAAAAGCTCT
63 CAACAACTTTAAAAATCTTATCTGAAAAAGCT-T
* * * * *
20387173 TTTAAGCAGAGACTCAATAACTTTAAAACTTTCATCTTGAAAAAGCTCCTCTCAGCAGAGACTCA
1 TCTAAGCAGAGGCTCAACAACTTTAAAA-TTTCATCTTGAAAAAGCTCCTCTAAGCAGAGGCTCA
* * *
20387238 ACAACTTT-AAAATCTCATCTTAGAAAAGTTT
65 ACAACTTTAAAAATCTTATCTGA-AAAAGCTT
* * * * ** * *
20387269 CTCTCAGCAAAGGCTCAATAACTTT-AAATCTCATCTT-AGAAAAGCTTATCTCAGTAGAGGCTC
1 -TCTAAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGA-AAAAGCTCCTCTAAGCAGAGGCTC
*
20387332 AACAACTTTAAAAAT-TTATCTTGGAAAAG-TT
64 AACAACTTTAAAAATCTTATC-TGAAAAAGCTT
* * * * * * *
20387363 CCTCTAAGTATAGGCTTAACAACTTTAAAAGTTCATCTTAGACAAAGCTCTTCTAAGCAAAGGCT
1 --TCTAAGCAGAGGCTCAACAACTTTAAAATTTCATCTT-GAAAAAGCTCCTCTAAGCAGAGGCT
* *
20387428 CAATAACTTT-AAAATCTCATCTTGAAAAAGGCTT
63 CAACAACTTTAAAAATCTTATC-TGAAAAA-GCTT
* * *
20387462 CTCTAAGCAGAGGCTCAACAACTTTACAAA-TTCATTTTGGAAAAGCTCCTCTAAGTAGAGGCTC
1 -TCTAAGCAGAGGCTCAACAACTTTA-AAATTTCATCTTGAAAAAGCTCCTCTAAGCAGAGGCTC
* * *
20387526 AACAATTTTAAAAATTCATT-T-TGGAAAAGTTT
64 AACAACTTTAAAAA-TC-TTATCTGAAAAAGCTT
* *
20387558 CTCTCAGCAGAGGTTCAACAACTTTAAAGA-TTCATCTT
1 -TCTAAGCAGAGGCTCAACAACTTTAAA-ATTTCATCTT
20387596 TTTCTCGAAA
Statistics
Matches: 425, Mismatches: 69, Indels: 51
0.78 0.13 0.09
Matches are distributed among these distances:
92 5 0.01
93 22 0.05
94 42 0.10
95 69 0.16
96 74 0.17
97 133 0.31
98 63 0.15
99 16 0.04
100 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.30
Consensus pattern (95 bp):
TCTAAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTAAGCAGAGGCTCAA
CAACTTTAAAAATCTTATCTGAAAAAGCTT
Found at i:20400024 original size:21 final size:21
Alignment explanation
Indices: 20399999--20400052 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
20399989 TAACATACAT
20399999 AAATATTAAAAATAATA-ATTA
1 AAATATTAAAAATAATATA-TA
**
20400020 AAATAACAAAAATAATATATA
1 AAATATTAAAAATAATATATA
20400041 AAA-ATCTAAAAA
1 AAATAT-TAAAAA
20400053 AAATTTTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATATTAAAAATAATATATA
Found at i:20404231 original size:15 final size:15
Alignment explanation
Indices: 20404183--20404236 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
20404173 AACTGAATCG
*
20404183 AGAAAGGAAAGAAG-A
1 AGAAA-GAAAAAAGAA
20404198 AGAAAGAAAAAAGAA
1 AGAAAGAAAAAAGAA
20404213 AGAAAGAAAAAA-AA
1 AGAAAGAAAAAAGAA
20404227 TAGAAA-AAAA
1 -AGAAAGAAAA
20404237 TAATAATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
14 13 0.36
15 23 0.64
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (15 bp):
AGAAAGAAAAAAGAA
Found at i:20413492 original size:21 final size:19
Alignment explanation
Indices: 20413459--20413500 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
20413449 AAATTCAAGA
20413459 AATATAATTTTTTAAAAAT
1 AATATAATTTTTTAAAAAT
*
20413478 AATATATATTATTTTTAAAAT
1 AATATA-ATT-TTTTAAAAAT
20413499 AA
1 AA
20413501 AAAAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 3 0.15
21 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATATAATTTTTTAAAAAT
Found at i:20413635 original size:148 final size:144
Alignment explanation
Indices: 20413354--20413624 Score: 470
Period size: 148 Copynumber: 1.9 Consensus size: 144
20413344 ATATATTATT
* *
20413354 TAAAAAAATTGAAAAAAAAAGTTATTATTTTTAAAATAAAAAAATCTAAATAATTCAATTTTTTT
1 TAAAAAAATTGAAAAAAAAAGTTAATATTTTTAAAATAAAAAAATCTAAATAATTCAAATTTTTT
20413419 ATTTTTTAAAATTGAAATCCGATTGTTAAAAAATTCAAGAAATATAATTTTTTAAAAATAATATA
66 ATTTTTTAAAATTGAAATCCGATTGTTAAAAAATTCAAGAAATATAATTTTTTAAAAATAATATA
20413484 TATTATTTTTAAAA
131 TATTATTTTTAAAA
20413498 TAAAAAAATTGAAAAAAATAAAGTTAATATTTTTAAAATAAAAAAAAATCTAAATAATTCAAATT
1 TAAAAAAATTG-AAAAAA-AAAGTTAATATTTTTAAAAT--AAAAAAATCTAAATAATTCAAATT
* *
20413563 TTTTATTTTTTTAAATTGAAATCCGATTGTTAAAAAATTCAAGAAATATAATTTTTTTAAAA
62 TTTTATTTTTTAAAATTGAAATCCGATTGTTAAAAAATTCAAGAAATATAATTTTTTAAAAA
20413625 GTTAAAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
144 11 0.09
145 6 0.05
146 19 0.16
148 83 0.70
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (144 bp):
TAAAAAAATTGAAAAAAAAAGTTAATATTTTTAAAATAAAAAAATCTAAATAATTCAAATTTTTT
ATTTTTTAAAATTGAAATCCGATTGTTAAAAAATTCAAGAAATATAATTTTTTAAAAATAATATA
TATTATTTTTAAAA
Found at i:20413713 original size:21 final size:22
Alignment explanation
Indices: 20413688--20413729 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
20413678 CTTAAAAATC
*
20413688 AAATTTTTTTA-ATTTTTTTTT
1 AAATTATTTTAGATTTTTTTTT
20413709 AAATTATTTTAGGATTTTTTT
1 AAATTATTTTA-GATTTTTTT
20413730 AATTTTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
AAATTATTTTAGATTTTTTTTT
Found at i:20414159 original size:15 final size:16
Alignment explanation
Indices: 20414139--20414168 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20414129 TTATAATTTG
20414139 ATGTCA-TTAATATTA
1 ATGTCATTTAATATTA
20414154 ATGTCATTTAATATT
1 ATGTCATTTAATATT
20414169 TTATTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (16 bp):
ATGTCATTTAATATTA
Found at i:20418105 original size:14 final size:14
Alignment explanation
Indices: 20418088--20418147 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
20418078 AGATTTGAAT
20418088 TTTAAGGTTTTGGA
1 TTTAAGGTTTTGGA
**
20418102 TTTAAGGTTCGGGA
1 TTTAAGGTTTTGGA
*
20418116 TTT-TGGATTTTAGGA
1 TTTAAGG-TTTT-GGA
* *
20418131 TTTGAGATTTTGGA
1 TTTAAGGTTTTGGA
20418145 TTT
1 TTT
20418148 TGGGGTTTCG
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
13 2 0.06
14 23 0.64
15 10 0.28
16 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.28, T:0.50
Consensus pattern (14 bp):
TTTAAGGTTTTGGA
Done.