Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 62 of 141
Found at i:20195568 original size:23 final size:23
Alignment explanation
Indices: 20195536--20195587 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
20195526 ATTAAATATG
*
20195536 AAAAAGAAA-TAATAAAGAAATAA
1 AAAAACAAATTAATAAA-AAATAA
*
20195559 AAAAACAAATTAATTAAAAATAA
1 AAAAACAAATTAATAAAAAATAA
20195582 AGAAAA
1 A-AAAA
20195588 TAAAAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (23 bp):
AAAAACAAATTAATAAAAAATAA
Found at i:20196152 original size:21 final size:21
Alignment explanation
Indices: 20196110--20196169 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
20196100 TACAAAATCA
*
20196110 CATATTCTAAGATT--ACATAT
1 CATA-TCTAAGATTGCATATAT
20196130 CATATCTAAGATTGCATATAT
1 CATATCTAAGATTGCATATAT
20196151 CATATCTAAGATTGCATAT
1 CATATCTAAGATTGCATAT
20196170 CCTCGAAGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
19 9 0.24
20 4 0.11
21 24 0.65
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (21 bp):
CATATCTAAGATTGCATATAT
Found at i:20197654 original size:9 final size:9
Alignment explanation
Indices: 20197640--20197706 Score: 73
Period size: 9 Copynumber: 7.4 Consensus size: 9
20197630 TTTGGTTAAA
20197640 AATTAACCG
1 AATTAACCG
*
20197649 AATTAAACG
1 AATTAACCG
*
20197658 AATTAACCT
1 AATTAACCG
*
20197667 AATT-ACTTG
1 AATTAAC-CG
20197676 AATTAACCG
1 AATTAACCG
*
20197685 AATTACCCG
1 AATTAACCG
*
20197694 AATTAATCG
1 AATTAACCG
20197703 AATT
1 AATT
20197707 GAATCACTAC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
8 2 0.04
9 43 0.91
10 2 0.04
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (9 bp):
AATTAACCG
Found at i:20198341 original size:2 final size:2
Alignment explanation
Indices: 20198334--20198362 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20198324 CTTTATATTT
20198334 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20198363 GTCTTTGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20208516 original size:25 final size:25
Alignment explanation
Indices: 20208488--20208536 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
20208478 TTCAAGTGAG
20208488 CTATATCAGGAAGCTCACAAAGAGC
1 CTATATCAGGAAGCTCACAAAGAGC
* *
20208513 CTATATCAGGACGCTCATAAAGAG
1 CTATATCAGGAAGCTCACAAAGAG
20208537 TTGTGGTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (25 bp):
CTATATCAGGAAGCTCACAAAGAGC
Found at i:20208623 original size:64 final size:64
Alignment explanation
Indices: 20208514--20208640 Score: 148
Period size: 64 Copynumber: 2.0 Consensus size: 64
20208504 ACAAAGAGCC
* * * * * ** *
20208514 TATATCAGGACGCTCATAAAGAGTTGTGGTATGTCCGCATTATATGC-AGGATCCATACCGATCA
1 TATAACAGGACGCTCACAAAGAGCTGCGGTATGACCGCAACATATGCAAGG-TCAATACCGATCA
* *
20208578 TATAACAGGATGCTCACAAAGAGCTGCGGTATGACTGCAACATATGCAAGGTCAATACCGATC
1 TATAACAGGACGCTCACAAAGAGCTGCGGTATGACCGCAACATATGCAAGGTCAATACCGATC
20208641 GGGATGCTTG
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
64 49 0.94
65 3 0.06
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (64 bp):
TATAACAGGACGCTCACAAAGAGCTGCGGTATGACCGCAACATATGCAAGGTCAATACCGATCA
Found at i:20212984 original size:22 final size:22
Alignment explanation
Indices: 20212933--20212984 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
20212923 TAACAACCTT
*
20212933 TAAACATGTTCAAAACATCCCA
1 TAAACATGTTCAAAACATACCA
20212955 -AAACCATG-TCAAAACATACCA
1 TAAA-CATGTTCAAAACATACCA
20212976 TAAATCATG
1 TAAA-CATG
20212985 ATCCCAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.48, C:0.25, G:0.06, T:0.21
Consensus pattern (22 bp):
TAAACATGTTCAAAACATACCA
Found at i:20214070 original size:23 final size:23
Alignment explanation
Indices: 20214044--20214088 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
20214034 CTATATAGTA
20214044 ATTCATTTCGATTTATCAATTCT
1 ATTCATTTCGATTTATCAATTCT
20214067 ATTCATTTCGATTTATCAATTC
1 ATTCATTTCGATTTATCAATTC
20214089 AAACTACCTT
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:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (23 bp):
ATTCATTTCGATTTATCAATTCT
Found at i:20217876 original size:21 final size:22
Alignment explanation
Indices: 20217852--20217903 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
20217842 TGGCCAGTAC
*
20217852 AAATAACAA-AAACAATAGC-AA
1 AAATAACAACAAA-AACAGCAAA
20217873 AAATAACAACAAAAACAGCAGAA
1 AAATAACAACAAAAACAGCA-AA
20217896 AAATAACA
1 AAATAACA
20217904 CCACCAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 14 0.52
22 3 0.11
23 10 0.37
ACGTcount: A:0.71, C:0.15, G:0.06, T:0.08
Consensus pattern (22 bp):
AAATAACAACAAAAACAGCAAA
Found at i:20217897 original size:23 final size:24
Alignment explanation
Indices: 20217856--20217903 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
20217846 CAGTACAAAT
*
20217856 AACAAAAACAATAGCAAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
*
20217880 AACAAAAACAGCAG-AAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
20217903 A
1 A
20217904 CCACCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.71, C:0.17, G:0.06, T:0.06
Consensus pattern (24 bp):
AACAAAAACAACAGCAAAAATAAC
Found at i:20218439 original size:25 final size:26
Alignment explanation
Indices: 20218405--20218455 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
20218395 TTTGACTCTA
*
20218405 ATTTTTTTTAAATTTCTC-TCAATTT
1 ATTTTTTTTAAATTTATCGTCAATTT
*
20218430 ATTTTTTTTAACTTTATCGTCAATTT
1 ATTTTTTTTAAATTTATCGTCAATTT
20218456 GCTTTAGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.24, C:0.12, G:0.02, T:0.63
Consensus pattern (26 bp):
ATTTTTTTTAAATTTATCGTCAATTT
Found at i:20218548 original size:11 final size:11
Alignment explanation
Indices: 20218528--20218571 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
20218518 CTCAACACCA
20218528 AAATTGAGAGG
1 AAATTGAGAGG
*
20218539 AAATTTAGAGG
1 AAATTGAGAGG
*
20218550 AAACTGAGAGG
1 AAATTGAGAGG
20218561 AAATTTGAGAG
1 AAA-TTGAGAG
20218572 ATGATTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 22 0.79
12 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.32, T:0.20
Consensus pattern (11 bp):
AAATTGAGAGG
Found at i:20219680 original size:3 final size:3
Alignment explanation
Indices: 20219672--20219703 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20219662 TCTATCTACC
20219672 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
20219704 CCATCACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:20224733 original size:31 final size:32
Alignment explanation
Indices: 20224683--20224742 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
20224673 TTGCTTGGCA
* *
20224683 AAGTGGAATGAAAATTAGAAAGATGGAAATTG
1 AAGTGGAATGAAAAATAGAAAGATAGAAATTG
* *
20224715 AAGTGGTA-GAAAAATAGAAGGATAGAAA
1 AAGTGGAATGAAAAATAGAAAGATAGAAA
20224743 ATATAATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 17 0.71
32 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.18
Consensus pattern (32 bp):
AAGTGGAATGAAAAATAGAAAGATAGAAATTG
Found at i:20232663 original size:24 final size:24
Alignment explanation
Indices: 20232635--20232680 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
20232625 AGAACAGTCC
* *
20232635 CAAAAGTAAATGCAGGAGCAGCTT
1 CAAAAGAAAATGAAGGAGCAGCTT
*
20232659 CAAAAGAAAATGAATGAGCAGC
1 CAAAAGAAAATGAAGGAGCAGC
20232681 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.15, G:0.24, T:0.13
Consensus pattern (24 bp):
CAAAAGAAAATGAAGGAGCAGCTT
Found at i:20240764 original size:44 final size:45
Alignment explanation
Indices: 20240705--20241036 Score: 167
Period size: 44 Copynumber: 7.6 Consensus size: 45
20240695 CACATCTAGT
**
20240705 CTTATCTCTTTGAAGTTGCAGTGGAGTAGACT-AAG-TAAGCAAATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAT-AGCAAA-C
* *
20240750 C-TATCTTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGA-GTAGACTGAAGATAGCAAAC
* ** * *
20240794 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAGCT-G-ATAATC
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCA-AA-C
* * ** * * **** *
20240839 C-TATCTCCCTAAAGTTGTAGTGGAGCGGA-TTAAAATATTGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCAAAC
* * * * * * *
20240882 CTTATCTCTCTGAAGTTGTAG-AGAGCAGA-TCG--CAT--CTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACT-GAAGATAGCAAAC
* * **
20240922 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGTAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAT-AGCAAAC
* * *
20240966 CTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAAC
1 CTTATCTC-CCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCAAAC
20241011 CTTATCTCCCTGAAGTTGCAGTGGAG
1 CTTATCTCCCTGAAGTTGCAGTGGAG
20241037 CAGGTTAAAG
Statistics
Matches: 222, Mismatches: 43, Indels: 44
0.72 0.14 0.14
Matches are distributed among these distances:
40 21 0.09
41 8 0.04
42 3 0.01
43 16 0.07
44 102 0.46
45 67 0.30
46 5 0.02
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCAAAC
Found at i:20240999 original size:217 final size:217
Alignment explanation
Indices: 20240619--20241368 Score: 891
Period size: 217 Copynumber: 3.5 Consensus size: 217
20240609 AAAGCCAATG
*
20240619 ATCCTATCTCCCTGAAGTTGCACTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGC
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGC
* * ** * * *
20240684 AGAGAGCAGATCACATCTAGTCTTATCTCTTTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAAT
66 AGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGT
* * * *
20240749 CCTATCTTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCA
131 CTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCA
20240814 GTGGAGCAGGTTAAAGCTGATA
196 GTGGAGCAGGTTAAAGCTGATA
* * **
20240836 ATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAAT-ATTGGATCTTATCTCTCTGAAGTTG
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCA-CAGATCTTATCTCTCTGAAGTTG
*
20240900 TAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAG
65 CAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAG
20240965 TCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGC
130 TCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGC
20241030 AGTGGAGCAGGTTAAA---G---
195 AGTGGAGCAGGTTAAAGCTGATA
** * * *
20241047 -----------CTGAAGTTGCAGTGGAGTAGACTAAGTAAGCA-A-ATCCTATCT-TCCTGAAGT
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA--AATCACAGATCTTATCTCT-CTGAAGT
* * * * *
20241098 TGCAGTGAGGTAGA-CTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG
63 TGCAGAGA-GCAGATC-G--CAT--CTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG
* **
20241162 TAAGTAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGAAAATATTATCTCCCT
122 TAAGTAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCT
* * **
20241227 GAAGTTGCAGTGGAGCAGATTAAGGCCAATA
187 GAAGTTGCAGTGGAGCAGGTTAAAGCTGATA
** *
20241258 ATATTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTAC
1 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGC
*
20241323 AGAG-GCAGATCGCATCTAGTCTTATCTCCCTGACA-TTGCAGTGGAG
66 AGAGAGCAGATCGCATCTAATCTTATCTCCCTGA-AGTTGCAGTGGAG
20241369 TACACAGCAG
Statistics
Matches: 451, Mismatches: 49, Indels: 67
0.80 0.09 0.12
Matches are distributed among these distances:
199 1 0.00
200 42 0.09
201 5 0.01
202 2 0.00
203 3 0.01
205 122 0.27
214 1 0.00
216 27 0.06
217 192 0.43
218 2 0.00
220 9 0.02
221 2 0.00
222 42 0.09
223 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (217 bp):
ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGC
AGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGT
CTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCA
GTGGAGCAGGTTAAAGCTGATA
Found at i:20241135 original size:116 final size:116
Alignment explanation
Indices: 20240931--20241155 Score: 387
Period size: 116 Copynumber: 1.9 Consensus size: 116
20240921 TCTTATCTCC
* * * *
20240931 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGA
1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCCTCCTGAAGTTGCAGTGAGGCAGA
20240996 CTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAG
66 CTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAG
* * *
20241047 CTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAATCCTATCTTCCTGAAGTTGCAGTGAGGTAGA
1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCCTCCTGAAGTTGCAGTGAGGCAGA
20241112 CTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAG
66 CTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAG
20241156 ACTAAGTAAG
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 102 1.00
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (116 bp):
CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCCTATCCTCCTGAAGTTGCAGTGAGGCAGA
CTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTAAAG
Found at i:20241140 original size:45 final size:44
Alignment explanation
Indices: 20241047--20241286 Score: 199
Period size: 44 Copynumber: 5.4 Consensus size: 44
20241037 CAGGTTAAAG
* *
20241047 CTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAATCC-TATCTTC
1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAA-CCTTATCTCC
* *
20241091 CTGAAGTTGCAGT-GAGGTAGACTGAAG-ATGGCAAACCTTATCTCC
1 CTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGCAAACCTTATCTCC
* **
20241136 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCTTATC-CTC
1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAACCTTATCTC-C
* * * **
20241180 CTGAAGTTGCAGTGGGGCAGACTGAAG-ATGGAAAATATTATCTCC
1 CTGAAGTTGCAGTGGAGCAGACT-AAGTA-AGCAAACCTTATCTCC
* **
20241225 CTGAAGTTGCAGTGGAGCAGATTAAG---GCCAATAATATTATCTCC
1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAG-C-A-AACCTTATCTCC
20241269 CTGAAGTTGCAGTGGAGC
1 CTGAAGTTGCAGTGGAGC
20241287 GGATTAAAAT
Statistics
Matches: 168, Mismatches: 15, Indels: 26
0.80 0.07 0.12
Matches are distributed among these distances:
41 1 0.01
43 4 0.02
44 92 0.55
45 68 0.40
46 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAACCTTATCTCC
Found at i:20241202 original size:89 final size:88
Alignment explanation
Indices: 20241047--20241283 Score: 307
Period size: 89 Copynumber: 2.7 Consensus size: 88
20241037 CAGGTTAAAG
* * * * * *
20241047 CTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAATCCTATCTTCCTGAAGTTGCAGTGAGGTAGA
1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAG-TAATCTTATCCTCCTGAAGTTGCAGTGGGGCAGA
* *
20241112 CTGAAGATGGCAAACCTTATCTCC
65 CTGAAGATGGAAAACATTATCTCC
20241136 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGA
1 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAA-TCTTATCCTCCTGAAGTTGCAGTGGGGCAGA
*
20241201 CTGAAGATGGAAAATATTATCTCC
65 CTGAAGATGGAAAACATTATCTCC
* * *
20241225 CTGAAGTTGCAGTGGAGCAGATTAAGGCCAA-TAATATTAT-CTCCCTGAAGTTGCAGTGG
1 CTGAAGTTGCAGTGGAGCAGACTAA-G-TAAGTAATCTTATCCT-CCTGAAGTTGCAGTGG
20241284 AGCGGATTAA
Statistics
Matches: 132, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
88 4 0.03
89 122 0.92
90 4 0.03
91 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (88 bp):
CTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAATCTTATCCTCCTGAAGTTGCAGTGGGGCAGAC
TGAAGATGGAAAACATTATCTCC
Found at i:20241309 original size:44 final size:43
Alignment explanation
Indices: 20241047--20241320 Score: 173
Period size: 44 Copynumber: 6.2 Consensus size: 43
20241037 CAGGTTAAAG
* * * * *
20241047 CTGAAGTTGCAGTGGAGTAGACTAAGTAAGC-AAATCCTATCTTC
1 CTGAAGTTGCAGTGGAGCAGATTAA--AATCAAAATCTTATCTCC
* * * *
20241091 CTGAAGTTGCAGT-GAGGTAGACTGAAGATGGC-AAACCTTATCTCC
1 CTGAAGTTGCAGTGGA-GCAGA-TTAAAAT--CAAAATCTTATCTCC
* *
20241136 CTGAAGTTGCAGTGGAGCAGACTAAGTAAGT--AAGTCTTATC-CTC
1 CTGAAGTTGCAGTGGAGCAGATTAA--AA-TCAAAATCTTATCTC-C
* * * * *
20241180 CTGAAGTTGCAGTGGGGCAGACTGAAGATGGAAAATATTATCTCC
1 CTGAAGTTGCAGTGGAGCAGA-TTAAAAT-CAAAATCTTATCTCC
*** *
20241225 CTGAAGTTGCAGTGGAGCAGATTAAGGCCAATAATATTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTAAAATCAA-AATCTTATCTCC
* * *
20241269 CTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCT
1 CTGAAGTTGCAGTGGAGCAGATTAAAATCA-AAATCTTATCTCC
20241313 CTGAAGTT
1 CTGAAGTT
20241321 ACAGAGGCAG
Statistics
Matches: 183, Mismatches: 31, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
42 1 0.01
43 7 0.04
44 108 0.59
45 62 0.34
46 4 0.02
47 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (43 bp):
CTGAAGTTGCAGTGGAGCAGATTAAAATCAAAATCTTATCTCC
Found at i:20243107 original size:16 final size:17
Alignment explanation
Indices: 20243062--20243108 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
20243052 TCATGTACTT
20243062 TTTATATTTTTTTGCTA
1 TTTATATTTTTTTGCTA
*
20243079 TTTAT-TTGTTTTTTC-A
1 TTTATATT-TTTTTGCTA
*
20243095 TTTATATTATTTTG
1 TTTATATTTTTTTG
20243109 TTCGTTTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTATATTTTTTTGCTA
Found at i:20248265 original size:31 final size:32
Alignment explanation
Indices: 20248230--20248290 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
20248220 ATAAATTGCT
*
20248230 CTCCCTTA-ATAAAATTCATTTTCAATTTAAG
1 CTCCCCTATATAAAATTCATTTTCAATTTAAG
20248261 CTCCCCTATATAAAATTCATTTTCAATTTA
1 CTCCCCTATATAAAATTCATTTTCAATTTA
20248291 GGGCTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 7 0.25
32 21 0.75
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (32 bp):
CTCCCCTATATAAAATTCATTTTCAATTTAAG
Found at i:20250731 original size:41 final size:41
Alignment explanation
Indices: 20250685--20250809 Score: 162
Period size: 41 Copynumber: 3.0 Consensus size: 41
20250675 AGAATAATGA
* *
20250685 TGAATTGCACATACGTGTCCCTGTTTGTACTTCGGTACCCT
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCT
*
20250726 TGAATTGCACATACGTGCCCCTATTTGTACTTCAGTAACCC-
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGT-ACCCT
* * * * *
20250767 TGTATTGCATAGACGTGCCCCTCTTTGTACTTTGGTACCCT
1 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCT
20250808 TG
1 TG
20250810 GATGTACTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
40 4 0.05
41 65 0.89
42 4 0.05
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCT
Found at i:20252615 original size:51 final size:50
Alignment explanation
Indices: 20252455--20252641 Score: 166
Period size: 51 Copynumber: 3.7 Consensus size: 50
20252445 AGTGAAAGTG
* * * * *
20252455 ATGGTCACATGTTTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGACTACTACGTATATCGG-ATGGT
** * * *
20252506 A-GGTTGCATGTGTAGTACTATGTACAGGCTACTATGCGTAT-T-GGATAGT
1 ATGGTCACATGTGTAGTACTATGTGCAGACTACTA--CGTATATCGGATGGT
* ** *
20252555 TTCAATCACATGTGTAGTACTATGTGCAGACTACTACGTATATCTGATGGT
1 AT-GGTCACATGTGTAGTACTATGTGCAGACTACTACGTATATCGGATGGT
20252606 AATGGTCACATGTGTAGTACTATGTGCA-AGCTACTA
1 -ATGGTCACATGTGTAGTACTATGTGCAGA-CTACTA
20252642 TTTGAACTAA
Statistics
Matches: 108, Mismatches: 20, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
49 8 0.07
50 33 0.31
51 62 0.57
52 5 0.05
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGACTACTACGTATATCGGATGGT
Found at i:20257979 original size:51 final size:51
Alignment explanation
Indices: 20257916--20258047 Score: 158
Period size: 51 Copynumber: 2.6 Consensus size: 51
20257906 TGATAGGTCG
* *
20257916 CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGT-TTCGATCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGAATAGTAAT-GATCA
* * * * * * *
20257967 CGTGTGTAGTACTATGTACAGGCTTCTACGTGTATCGAATGGTAATGGTCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGAATAGTAATGATCA
*
20258018 CATGTGTAGTACTATGTGTAGGCTACTATG
1 CATGTGTAGTACTATGTGCAGGCTACTATG
20258048 TGAACCAAAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
51 65 0.98
52 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (51 bp):
CATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGAATAGTAATGATCA
Found at i:20258007 original size:100 final size:102
Alignment explanation
Indices: 20257864--20258047 Score: 293
Period size: 102 Copynumber: 1.8 Consensus size: 102
20257854 AAAGTGATGG
* *
20257864 TCACGTGTGTAGTACATGTGCAGGCTTCTACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGTA
1 TCACGTGTGTAGTACATGTACAGGCTTCTACGTGTACCGGAATGATAATGGTCACATGTGTAGTA
20257927 CTATGTGCAGGCTACTATGCGTATCGGATAGTTTCGA
66 CTATGTGCAGGCTACTATGCGTATCGGATAGTTTCGA
* *
20257964 TCACGTGTGTAGTACTATGTACAGGCTTCTACGTGTATC-GAATGGTAATGGTCACATGTGTAGT
1 TCACGTGTGTAGTAC-ATGTACAGGCTTCTACGTGTACCGGAATGATAATGGTCACATGTGTAGT
*
20258028 ACTATGTGTAGGCTACTATG
65 ACTATGTGCAGGCTACTATG
20258048 TGAACCAAAC
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
100 21 0.28
101 22 0.29
102 33 0.43
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.33
Consensus pattern (102 bp):
TCACGTGTGTAGTACATGTACAGGCTTCTACGTGTACCGGAATGATAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTATCGGATAGTTTCGA
Found at i:20258107 original size:45 final size:45
Alignment explanation
Indices: 20258056--20258144 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
20258046 TGTGAACCAA
* * *
20258056 ACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCGG
20258101 ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCG
20258145 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCGG
Found at i:20276705 original size:39 final size:39
Alignment explanation
Indices: 20276649--20276903 Score: 308
Period size: 39 Copynumber: 6.5 Consensus size: 39
20276639 AGATGTTTTG
* *
20276649 AGTATTGTGATATATGCTTAAGTATTATGAGATTATATGT
1 AGTATTGTGATATATGCTTAA-TGTTATGTGATTATATGT
* *
20276689 A-TATTGTGATATATGCTTGAATATTATGTGATTATACG-
1 AGTATTGTGATATATGCTT-AATGTTATGTGATTATATGT
*
20276727 AGTATTGTGATATATGCTTACATGTTATGAGATTATATGT
1 AGTATTGTGATATATGCTTA-ATGTTATGTGATTATATGT
* *
20276767 A-TATTATGATATATGCTTGAATGTTATGTGATTATA-CT
1 AGTATTGTGATATATGCTT-AATGTTATGTGATTATATGT
20276805 AGTATTGTGATATATGCTTAAATGTTATGTGATTATATG-
1 AGTATTGTGATATATGCTT-AATGTTATGTGATTATATGT
* *
20276844 AGTATTGTGATATATGCTTGGATGTTAGGTGATTATATGT
1 AGTATTGTGATATATGCTT-AATGTTATGTGATTATATGT
*
20276884 -GTAATAG-GATATATGCTTAA
1 AGT-ATTGTGATATATGCTTAA
20276904 AAGTGAATAT
Statistics
Matches: 190, Mismatches: 16, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
38 5 0.03
39 177 0.93
40 8 0.04
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (39 bp):
AGTATTGTGATATATGCTTAATGTTATGTGATTATATGT
Found at i:20276862 original size:117 final size:117
Alignment explanation
Indices: 20276651--20276903 Score: 348
Period size: 117 Copynumber: 2.2 Consensus size: 117
20276641 ATGTTTTGAG
* * *
20276651 TATTGTGATATATGCTTAAGTATTATGAGATTATATGTATATTGTGATATATGCTTGAATATTAT
1 TATTATGATATATGCTTAAGTATTATGAGATTATATCTATATTGTGATATATGCTTAAATATTAT
*
20276716 GTGATTATACGAGTATTGTGATATATGCTTACATGTTATGAGATTATATGTA
66 GTGATTATACGAGTATTGTGATATATGCTTACATGTTAGGAGATTATATGTA
* * *
20276768 TATTATGATATATGCTTGAA-TGTTATGTGATTATA-CTAGTATTGTGATATATGCTTAAATGTT
1 TATTATGATATATGCTT-AAGTATTATGAGATTATATCTA-TATTGTGATATATGCTTAAATATT
* ** * *
20276831 ATGTGATTATATGAGTATTGTGATATATGCTTGGATGTTAGGTGATTATATGTG
64 ATGTGATTATACGAGTATTGTGATATATGCTTACATGTTAGGAGATTATATGTA
* *
20276885 TAATAGGATATATGCTTAA
1 TATTATGATATATGCTTAA
20276904 AAGTGAATAT
Statistics
Matches: 120, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
116 4 0.03
117 114 0.95
118 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (117 bp):
TATTATGATATATGCTTAAGTATTATGAGATTATATCTATATTGTGATATATGCTTAAATATTAT
GTGATTATACGAGTATTGTGATATATGCTTACATGTTAGGAGATTATATGTA
Found at i:20276904 original size:78 final size:78
Alignment explanation
Indices: 20276647--20276904 Score: 369
Period size: 78 Copynumber: 3.3 Consensus size: 78
20276637 AAAGATGTTT
* * *
20276647 TGAGTATTGTGATATATGCTTAAGTATTATGAGATTATATGTATATTGTGATATATGCTTGAATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGTATATTGTGATATATGCTTGAATG
20276712 TTATGTGATTATA
66 TTATGTGATTATA
* * *
20276725 CGAGTATTGTGATATATGCTTACATGTTATGAGATTATATGTATATTATGATATATGCTTGAATG
1 TGAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGTATATTGTGATATATGCTTGAATG
20276790 TTATGTGATTATA
66 TTATGTGATTATA
* *
20276803 CT-AGTATTGTGATATATGCTTAAATGTTATGTGATTATATG-AGTATTGTGATATATGCTTGGA
1 -TGAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGTA-TATTGTGATATATGCTTGAA
*
20276866 TGTTAGGTGATTATA
64 TGTTATGTGATTATA
* *
20276881 TGTGTAATAG-GATATATGCTTAAA
1 TGAGT-ATTGTGATATATGCTTAAA
20276905 AGTGAATATA
Statistics
Matches: 162, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
77 2 0.01
78 157 0.97
79 3 0.02
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.45
Consensus pattern (78 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGAGATTATATGTATATTGTGATATATGCTTGAATG
TTATGTGATTATA
Found at i:20283650 original size:19 final size:20
Alignment explanation
Indices: 20283626--20283665 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
20283616 AAATACATGA
*
20283626 TTTTTTATTTTATC-TGAGT
1 TTTTTTATGTTATCTTGAGT
20283645 TTTTTTATGTTATCTTGAGT
1 TTTTTTATGTTATCTTGAGT
20283665 T
1 T
20283666 ATGGAATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.15, C:0.05, G:0.12, T:0.68
Consensus pattern (20 bp):
TTTTTTATGTTATCTTGAGT
Found at i:20295709 original size:116 final size:116
Alignment explanation
Indices: 20295505--20295778 Score: 406
Period size: 116 Copynumber: 2.4 Consensus size: 116
20295495 TCATCGATCA
* ***
20295505 ATGAAAAATGATGGTTTTGACCATCGATTATGAAAAGGGATAGTTTCGACTATCGACTATGAAAA
1 ATGAAAAAGGATGGTGACGACCATCGATTATGAAAAGGGATAGTTTCGACTATCGACTATGAAAA
* *
20295570 GGGATGGTCACGACCATCAACTATGAAAAGGGATGGTGACGACTATAAACT
66 GGGATGGTCACGACCATCAACTATGAAAAGGGATGGTAACGACCATAAACT
* *
20295621 ATGAAAAGGGATGGTGACGACCATCG-TATATGAAAAGGGATAGTTTTGACTATCGACTATGAAA
1 ATGAAAAAGGATGGTGACGACCATCGAT-TATGAAAAGGGATAGTTTCGACTATCGACTATGAAA
* **
20295685 AGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTAACGACCATCTACT
65 AGGGATGGTCACGACCATCAACTATGAAAAGGGATGGTAACGACCATAAACT
* *
20295737 ATGAAAAAGGATGGTGACAACCATCGATTAATGAAAAAGGAT
1 ATGAAAAAGGATGGTGACGACCATCGATT-ATGAAAAGGGAT
20295779 GGTGACGACC
Statistics
Matches: 141, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
115 1 0.01
116 128 0.91
117 12 0.09
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (116 bp):
ATGAAAAAGGATGGTGACGACCATCGATTATGAAAAGGGATAGTTTCGACTATCGACTATGAAAA
GGGATGGTCACGACCATCAACTATGAAAAGGGATGGTAACGACCATAAACT
Found at i:20295799 original size:29 final size:29
Alignment explanation
Indices: 20295523--20295807 Score: 302
Period size: 29 Copynumber: 9.8 Consensus size: 29
20295513 TGATGGTTTT
* * * **
20295523 GACCATCGATTATGAAAAGGGATAGTTTC
1 GACCATCAACTATGAAAAGGGATGGTGAC
* * *
20295552 GACTATCGACTATGAAAAGGGATGGTCAC
1 GACCATCAACTATGAAAAGGGATGGTGAC
20295581 GACCATCAACTATGAAAAGGGATGGTGAC
1 GACCATCAACTATGAAAAGGGATGGTGAC
* *
20295610 GACTATAAACTATGAAAAGGGATGGTGAC
1 GACCATCAACTATGAAAAGGGATGGTGAC
* * ***
20295639 GACCATCGTA-TATGAAAAGGGATAGTTTT
1 GACCATC-AACTATGAAAAGGGATGGTGAC
* *
20295668 GACTATCGACTATGAAAAGGGATGGTGAC
1 GACCATCAACTATGAAAAGGGATGGTGAC
*
20295697 GACCATCAACTATGAAAAGGGATGGTAAC
1 GACCATCAACTATGAAAAGGGATGGTGAC
* *
20295726 GACCATCTACTATGAAAAAGGATGGTGAC
1 GACCATCAACTATGAAAAGGGATGGTGAC
* * * *
20295755 AACCATCGATTAATGAAAAAGGATGGTGAC
1 GACCATCAACT-ATGAAAAGGGATGGTGAC
** *
20295785 GACCATCAAAAATGAAAGGGGAT
1 GACCATCAACTATGAAAAGGGAT
20295808 AGTTATGATC
Statistics
Matches: 215, Mismatches: 38, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
28 1 0.00
29 188 0.87
30 26 0.12
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.21
Consensus pattern (29 bp):
GACCATCAACTATGAAAAGGGATGGTGAC
Found at i:20305381 original size:16 final size:15
Alignment explanation
Indices: 20305356--20305389 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
20305346 AAGTTTGATA
*
20305356 ATAATTAATATATATT
1 ATAATCAATATA-ATT
20305372 ATAATCAATATAATT
1 ATAATCAATATAATT
20305387 ATA
1 ATA
20305390 CACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATCAATATAATT
Found at i:20305638 original size:16 final size:15
Alignment explanation
Indices: 20305613--20305646 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
20305603 AAGTTTGATA
*
20305613 ATAATTAATATATATT
1 ATAATCAATATA-ATT
20305629 ATAATCAATATAATT
1 ATAATCAATATAATT
20305644 ATA
1 ATA
20305647 CACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATCAATATAATT
Found at i:20305657 original size:125 final size:125
Alignment explanation
Indices: 20305271--20305659 Score: 332
Period size: 125 Copynumber: 3.1 Consensus size: 125
20305261 ACATATTACT
20305271 TTATTATTTGCTACTAATTTATTGAAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTA
1 TTATTATTTGCTACTAATTTATTGAAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTA
20305336 ATTCTATGCAAAGTTTGATAATAATTAATATATATTATAATCAATATAATTATACACTAG
66 ATTCTATGCAAAGTTTGATAATAATTAATATATATTATAATCAATATAATTATACACTAG
* * ** * * * * * *
20305396 TTATTATCAT-CTTATTTGTTAAATT-AAATTAAAAAC-ATTTATTCCTAGATGC-CTTTGAAAA
1 TTATTAT-TTGC-TACTAATT-TATTGAAA-TAAAAACTA-TGAAT-AT-GAT-CAATTT-TAAA
* ** **** * * * *
20305457 T-ATTTACAAAAAGAGACGTCTAA-TTT-TTAATAAAGTTAATACA-ATTAATAAAT-AATATAA
57 TGA-AT-CCTAATTCTATG-CAAAGTTTGATAAT-AA-TTAATATATATT-AT-AATCAATATAA
* *
20305517 TACATATTACT--
115 T-TATA-CACTAG
20305528 TTATTATTTGCTACTAATTTATTGAAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTA
1 TTATTATTTGCTACTAATTTATTGAAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTA
20305593 ATTCTATGCAAAGTTTGATAATAATTAATATATATTATAATCAATATAATTATACACTAG
66 ATTCTATGCAAAGTTTGATAATAATTAATATATATTATAATCAATATAATTATACACTAG
20305653 TTATTAT
1 TTATTAT
20305660 CATCTTATTT
Statistics
Matches: 189, Mismatches: 46, Indels: 58
0.65 0.16 0.20
Matches are distributed among these distances:
123 3 0.02
124 6 0.03
125 35 0.19
126 23 0.12
127 23 0.12
128 8 0.04
129 8 0.04
130 23 0.12
131 23 0.12
132 28 0.15
133 6 0.03
134 3 0.02
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (125 bp):
TTATTATTTGCTACTAATTTATTGAAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTA
ATTCTATGCAAAGTTTGATAATAATTAATATATATTATAATCAATATAATTATACACTAG
Found at i:20305696 original size:257 final size:258
Alignment explanation
Indices: 20305230--20305745 Score: 1025
Period size: 257 Copynumber: 2.0 Consensus size: 258
20305220 AATTCTACAC
20305230 AAAGTTAATAACAATTAATAAATAATATAATACATATTACTTTATTATTTGCTACTAATTTATTG
1 AAAGTTAATAACAATTAATAAATAATATAATACATATTACTTTATTATTTGCTACTAATTTATTG
20305295 AAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTAATTCTATGCAAAGTTTGATAATAA
66 AAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTAATTCTATGCAAAGTTTGATAATAA
20305360 TTAATATATATTATAATCAATATAATTATACACTAGTTATTATCATCTTATTTGTTAAATTAAAT
131 TTAATATATATTATAATCAATATAATTATACACTAGTTATTATCATCTTATTTGTTAAATTAAAT
20305425 TAAAAACATTTATTCCTAGATGCCTTTGAAAATATTTACAAAAAGAGACGTCTAATTTTTAAT
196 TAAAAACATTTATTCCTAGATGCCTTTGAAAATATTTACAAAAAGAGACGTCTAATTTTTAAT
20305488 AAAGTTAAT-ACAATTAATAAATAATATAATACATATTACTTTATTATTTGCTACTAATTTATTG
1 AAAGTTAATAACAATTAATAAATAATATAATACATATTACTTTATTATTTGCTACTAATTTATTG
20305552 AAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTAATTCTATGCAAAGTTTGATAATAA
66 AAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTAATTCTATGCAAAGTTTGATAATAA
20305617 TTAATATATATTATAATCAATATAATTATACACTAGTTATTATCATCTTATTTGTTAAATTAAAT
131 TTAATATATATTATAATCAATATAATTATACACTAGTTATTATCATCTTATTTGTTAAATTAAAT
20305682 TAAAAACATTTATTCCTAGATGCCTTTGAAAATATTTACAAAAAGAGACGTCTAATTTTTAAT
196 TAAAAACATTTATTCCTAGATGCCTTTGAAAATATTTACAAAAAGAGACGTCTAATTTTTAAT
20305745 A
1 A
20305746 TTTACAAAAA
Statistics
Matches: 258, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
257 249 0.97
258 9 0.03
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (258 bp):
AAAGTTAATAACAATTAATAAATAATATAATACATATTACTTTATTATTTGCTACTAATTTATTG
AAATAAAAACTATGAATATGATCAATTTTAAATGAATCCTAATTCTATGCAAAGTTTGATAATAA
TTAATATATATTATAATCAATATAATTATACACTAGTTATTATCATCTTATTTGTTAAATTAAAT
TAAAAACATTTATTCCTAGATGCCTTTGAAAATATTTACAAAAAGAGACGTCTAATTTTTAAT
Found at i:20321815 original size:43 final size:43
Alignment explanation
Indices: 20321779--20321878 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 43
20321769 TCCCGGGCAG
*
20321779 GGTCTTACACGAAAACACAAGTCAATTCCAACGTCCCAAACGT
1 GGTCTTACACGAAAACACAAGTCAATGCCAACGTCCCAAACGT
* * * * *
20321822 GGTCTTACATGAAAACATAAGTCAATGCCAACATTCCAGACGT
1 GGTCTTACACGAAAACACAAGTCAATGCCAACGTCCCAAACGT
20321865 GGTCTTACACGAAA
1 GGTCTTACACGAAA
20321879 TCACTTATCA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (43 bp):
GGTCTTACACGAAAACACAAGTCAATGCCAACGTCCCAAACGT
Found at i:20330113 original size:43 final size:43
Alignment explanation
Indices: 20330066--20330165 Score: 155
Period size: 43 Copynumber: 2.3 Consensus size: 43
20330056 TCCTGGACAG
*
20330066 GGTCTTACACGAAAACACAAGTCAATGCCAACGACTCAGACGT
1 GGTCTTACACGAAAACACAAGTCAATGCCAACGACCCAGACGT
* ***
20330109 GGTCTTACACGAAAACACAAGTCGATGCCAATTTCCCAGACGT
1 GGTCTTACACGAAAACACAAGTCAATGCCAACGACCCAGACGT
20330152 GGTCTTACACGAAA
1 GGTCTTACACGAAA
20330166 TCACTTATCA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (43 bp):
GGTCTTACACGAAAACACAAGTCAATGCCAACGACCCAGACGT
Found at i:20335064 original size:30 final size:30
Alignment explanation
Indices: 20335008--20335064 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
20334998 CATAGTCTGG
* *
20335008 CACATGGCCATGTGTCCACCAGGTGTGGCT
1 CACACGGCCATGTGTCCACCACGTGTGGCT
*
20335038 CACACGGCCGTGTGTCCAGCC-CGTGTG
1 CACACGGCCATGTGTCCA-CCACGTGTG
20335065 ACTCTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 21 0.91
31 2 0.09
ACGTcount: A:0.14, C:0.33, G:0.32, T:0.21
Consensus pattern (30 bp):
CACACGGCCATGTGTCCACCACGTGTGGCT
Found at i:20342322 original size:12 final size:13
Alignment explanation
Indices: 20342289--20342319 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20342279 ATATGGTTCA
20342289 TAAAAACATAGCT
1 TAAAAACATAGCT
*
20342302 TAAAAACATATCT
1 TAAAAACATAGCT
20342315 TAAAA
1 TAAAA
20342320 CATTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (13 bp):
TAAAAACATAGCT
Found at i:20345318 original size:4 final size:4
Alignment explanation
Indices: 20345306--20345372 Score: 125
Period size: 4 Copynumber: 16.8 Consensus size: 4
20345296 TTTATGCATG
*
20345306 CATA TATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
20345354 CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CAT
20345373 GGCTTTTCAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:20353473 original size:24 final size:24
Alignment explanation
Indices: 20353445--20353490 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
20353435 AGTTGTAAAT
20353445 CATCCATTGTTCCATTGTATTTTG
1 CATCCATTGTTCCATTGTATTTTG
20353469 CATCCATTGTTCCATTGTATTT
1 CATCCATTGTTCCATTGTATTT
20353491 AAAAGAGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.11, T:0.50
Consensus pattern (24 bp):
CATCCATTGTTCCATTGTATTTTG
Found at i:20353604 original size:50 final size:50
Alignment explanation
Indices: 20353545--20353640 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
20353535 CGATTTGCAC
*
20353545 GAGGCACTGCTAAGAAGTGTGTTAGAGAGTTTAAAGAACTTATGCTTCAA
1 GAGGCACTGCTAAGAAGTATGTTAGAGAGTTTAAAGAACTTATGCTTCAA
** * *
20353595 GAGGCACTGCTGGGGAGTATGTTCGAGAGTTTAAAGAACTTATGCT
1 GAGGCACTGCTAAGAAGTATGTTAGAGAGTTTAAAGAACTTATGCT
20353641 CCAAATTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.28
Consensus pattern (50 bp):
GAGGCACTGCTAAGAAGTATGTTAGAGAGTTTAAAGAACTTATGCTTCAA
Found at i:20361570 original size:22 final size:22
Alignment explanation
Indices: 20361545--20361594 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
20361535 TTTTTTTCCT
*
20361545 TATTTTCATTGATTTTCTAATC
1 TATTTTCATTGATTTACTAATC
**
20361567 TATTTTTGTTGATTTACTAATC
1 TATTTTCATTGATTTACTAATC
*
20361589 TGTTTT
1 TATTTT
20361595 GGTCTCTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.62
Consensus pattern (22 bp):
TATTTTCATTGATTTACTAATC
Found at i:20365463 original size:8 final size:8
Alignment explanation
Indices: 20365450--20365477 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
20365440 ATAATTTAAA
20365450 AAAATTCT
1 AAAATTCT
20365458 AAAATTCT
1 AAAATTCT
20365466 AAAATTCT
1 AAAATTCT
20365474 AAAA
1 AAAA
20365478 AATATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (8 bp):
AAAATTCT
Found at i:20365520 original size:21 final size:20
Alignment explanation
Indices: 20365496--20365538 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
20365486 TATAAACTTT
*
20365496 AAAAATTCAAAATAATATATA
1 AAAAATTAAAAAT-ATATATA
* *
20365517 AAAATTTAAAAATATATTTA
1 AAAAATTAAAAATATATATA
20365537 AA
1 AA
20365539 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTAAAAATATATATA
Found at i:20365532 original size:18 final size:18
Alignment explanation
Indices: 20365495--20365546 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
20365485 ATATAAACTT
*
20365495 TAAAAATTCAAAATAATATA
1 TAAAAATT-TAAA-AATATA
20365515 TAAAAATTTAAAAATATA
1 TAAAAATTTAAAAATATA
**
20365533 TTTAAATTTAAAAA
1 TAAAAATTTAAAAA
20365547 ATNNNNNNNN
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 18 0.62
19 3 0.10
20 8 0.28
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAAATTTAAAAATATA
Found at i:20366368 original size:14 final size:14
Alignment explanation
Indices: 20366349--20366377 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20366339 GATATGTTCT
20366349 CACACTTATCTTAA
1 CACACTTATCTTAA
20366363 CACACTTATCTTAA
1 CACACTTATCTTAA
20366377 C
1 C
20366378 TTTTCTGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (14 bp):
CACACTTATCTTAA
Found at i:20367016 original size:42 final size:42
Alignment explanation
Indices: 20366910--20367072 Score: 272
Period size: 42 Copynumber: 3.9 Consensus size: 42
20366900 TTATAAGAAA
* *
20366910 AAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTGCCCAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTG-CCAC
* * *
20366953 AAACGCCGCTAAAAAATATGACCTTTAGTGGCGCTTTGCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCCAC
20366995 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCCAC
20367037 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTT
20367073 ATGAAAAAAC
Statistics
Matches: 112, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
42 78 0.70
43 34 0.30
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCCAC
Found at i:20367083 original size:42 final size:42
Alignment explanation
Indices: 20366908--20367090 Score: 269
Period size: 42 Copynumber: 4.3 Consensus size: 42
20366898 ATTTATAAGA
*
20366908 AAAAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTGCCC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTG-CC
* * *
20366951 AAAAACGCCGCTAAAAAATATGACCTTTAGTGGCGCTTTGCC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCC
*
20366993 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCC
* *
20367035 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTATG-A
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTT-TGCC
*
20367077 AAAAACGCGGCTAA
1 AAAAACGCCGCTAA
20367091 TTTTGACAAA
Statistics
Matches: 128, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
42 90 0.70
43 38 0.30
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.19
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTGCC
Found at i:20368289 original size:86 final size:85
Alignment explanation
Indices: 20368140--20368468 Score: 394
Period size: 86 Copynumber: 3.8 Consensus size: 85
20368130 GTTTATGTGA
* ** *** * *
20368140 AACAAATTAGCAAAAATCAACTATTCATAGTTCATATATTTACCGGTAA-TAGGGCTAAATTTTC
1 AACAAATTAGCAAAAATCAACTGTTCA-AGTTCATGCATTTACCAACAACCA-GACTAAATTTTC
* *
20368204 AATTTCTATAACGATTTATATGC
64 AATTT-TATAACAACTTATATGC
* * * *
20368227 AACAAATTAGCAAAAATCAA-TGGTTCAAGTTCATGTATTTACCAAAAATCAGACTAATTTTTCA
1 AACAAATTAGCAAAAATCAACT-GTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCA
20368291 ATATTTATAACAACTTATATGC
65 AT-TTTATAACAACTTATATGC
*
20368313 AACAAATTAGCAAAAAT-AAATGGTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCA
1 AACAAATTAGCAAAAATCAACT-GTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCA
*
20368377 ATTTTTATAACAACTTATGTGC
65 A-TTTTATAACAACTTATATGC
* * *
20368399 AACAAATTAGAAAAAATCAACTGTTCAAGTTCATGCATTCACCAACAACCAGACCAAATTTTCAA
1 AACAAATTAGCAAAAATCAACTGTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCAA
20368464 CTTTT
66 -TTTT
20368469 TTAAAGTAGA
Statistics
Matches: 216, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
85 2 0.01
86 183 0.85
87 31 0.14
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (85 bp):
AACAAATTAGCAAAAATCAACTGTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCAA
TTTTATAACAACTTATATGC
Found at i:20373983 original size:11 final size:11
Alignment explanation
Indices: 20373967--20374026 Score: 65
Period size: 10 Copynumber: 5.7 Consensus size: 11
20373957 AAAATGAAAG
20373967 TTTAAAATCTT
1 TTTAAAATCTT
20373978 TTTAAAA--TT
1 TTTAAAATCTT
*
20373987 TTTAAAA-ATT
1 TTTAAAATCTT
20373997 TTTAAAATC-T
1 TTTAAAATCTT
*
20374007 TTTAAAATTCAT
1 TTTAAAA-TCTT
20374019 TTTAAAAT
1 TTTAAAAT
20374027 TTTAAATCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
9 9 0.20
10 17 0.39
11 10 0.23
12 8 0.18
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAAATCTT
Found at i:20374032 original size:20 final size:19
Alignment explanation
Indices: 20373967--20374029 Score: 74
Period size: 19 Copynumber: 3.1 Consensus size: 19
20373957 AAAATGAAAG
20373967 TTTAAAATCTTTTTAAAATT
1 TTTAAAATC-TTTTAAAATT
20373987 TTTAAAAAT-TTTTAAAATCT
1 TTT-AAAATCTTTTAAAAT-T
20374007 TTTAAAATTCATTTTAAAATT
1 TTTAAAA-TC-TTTTAAAATT
20374028 TT
1 TT
20374030 AAATCATGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
19 13 0.34
20 8 0.21
21 8 0.21
22 9 0.24
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAAAATCTTTTAAAATT
Found at i:20374225 original size:40 final size:40
Alignment explanation
Indices: 20374179--20374258 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
20374169 TGTTTTTAAA
20374179 CAATGAAATGGGTGATTCGGGTAAAACGAGCTTAAAGTTG
1 CAATGAAATGGGTGATTCGGGTAAAACGAGCTTAAAGTTG
* *
20374219 CAATGAAATGGGTGATTTGGGTAAAACGAGCTTGAAGTTG
1 CAATGAAATGGGTGATTCGGGTAAAACGAGCTTAAAGTTG
20374259 GAAAAGTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (40 bp):
CAATGAAATGGGTGATTCGGGTAAAACGAGCTTAAAGTTG
Found at i:20374632 original size:15 final size:15
Alignment explanation
Indices: 20374585--20374635 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
20374575 CTAGTTAATC
20374585 TAAACCCT-AAACCA
1 TAAACCCTAAAACCA
**
20374599 TAAA-CCTAAGCCCCA
1 TAAACCCTAA-AACCA
20374614 -AAACCCTAAAACCA
1 TAAACCCTAAAACCA
20374628 TAAACCCT
1 TAAACCCT
20374636 TAACACATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 3 0.10
14 11 0.38
15 15 0.52
ACGTcount: A:0.47, C:0.37, G:0.02, T:0.14
Consensus pattern (15 bp):
TAAACCCTAAAACCA
Found at i:20374844 original size:41 final size:41
Alignment explanation
Indices: 20374736--20374896 Score: 227
Period size: 41 Copynumber: 3.9 Consensus size: 41
20374726 TTTTAAATCC
* * *
20374736 CTGAGCATTAGTGGCGCTTTTTAGAAAACGCCGCT-AAA-A
1 CTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACA
*
20374775 GTAGAGCATTAGCGGCGCTTTCTCAAAAAACGCCGCTAAAACA
1 CT-GAGCATTAGCGGCGCTTTCT-AAAAAACGCCGCTAAAACA
*
20374818 CTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACC
1 CTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACA
* *
20374859 CTGAGCATTAGCGGCGCTTTCTTAAAAATGCCGCTAAA
1 CTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAA
20374897 GCCCCAAAAG
Statistics
Matches: 110, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
39 1 0.01
40 18 0.16
41 66 0.60
42 23 0.21
43 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (41 bp):
CTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACA
Found at i:20375003 original size:39 final size:40
Alignment explanation
Indices: 20374976--20375070 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
20374966 AATGCTTATT
* * *
20374976 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATTCTCGATC
1 TTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATTCTCGATA
* * *
20375016 TTTAGTGGCATTTTCCAAAAAGCGCCGCTAATTCTCGATA
1 TTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATTCTCGATA
*
20375056 TTTAGCGACGTTTTT
1 TTTAGCGGCGTTTTT
20375071 TATCCAAACG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTCAAAAAGCGCCGCTAATTCTCGATA
Found at i:20384353 original size:22 final size:21
Alignment explanation
Indices: 20384321--20384362 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
20384311 AATTAATTTC
20384321 ATAAAGAAGAAATTAAAGAAA
1 ATAAAGAAGAAATTAAAGAAA
* *
20384342 ATAAATGAAGAACTTTAAGAA
1 ATAAA-GAAGAAATTAAAGAA
20384363 GCTTTTGCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.64, C:0.02, G:0.14, T:0.19
Consensus pattern (21 bp):
ATAAAGAAGAAATTAAAGAAA
Found at i:20385416 original size:22 final size:22
Alignment explanation
Indices: 20385391--20385434 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
20385381 AGTTTGAAGG
* *
20385391 TTAAGAGGGTTTTAGGTTTTAA
1 TTAAAAGGGTTTTAGGATTTAA
* *
20385413 TTAAAAGTGTTTTGGGATTTAA
1 TTAAAAGGGTTTTAGGATTTAA
20385435 ATAGGGTAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (22 bp):
TTAAAAGGGTTTTAGGATTTAA
Found at i:20385464 original size:23 final size:23
Alignment explanation
Indices: 20385433--20385479 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
20385423 TTTGGGATTT
20385433 AAATAGGGT-AAGTTAAGGGTTTA
1 AAATAGGGTGAAGTTAA-GGTTTA
* *
20385456 AAATTGGGTGAATTTAAGGTTTA
1 AAATAGGGTGAAGTTAAGGTTTA
20385479 A
1 A
20385480 TTAACTGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (23 bp):
AAATAGGGTGAAGTTAAGGTTTA
Found at i:20387137 original size:9 final size:9
Alignment explanation
Indices: 20387123--20387159 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
20387113 TATAGTTTGA
20387123 TATTCGAAT
1 TATTCGAAT
20387132 TATTCGAAT
1 TATTCGAAT
*
20387141 TATTCGAGT
1 TATTCGAAT
*
20387150 TATTCAAAT
1 TATTCGAAT
20387159 T
1 T
20387160 TGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:20388765 original size:18 final size:18
Alignment explanation
Indices: 20388722--20388757 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20388712 TGAATTTAAT
20388722 AAATAAAACACGAAAGAA
1 AAATAAAACACGAAAGAA
*
20388740 AAATAAAACATGAAAGAA
1 AAATAAAACACGAAAGAA
20388758 TTATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.11, T:0.08
Consensus pattern (18 bp):
AAATAAAACACGAAAGAA
Found at i:20394118 original size:21 final size:22
Alignment explanation
Indices: 20394079--20394119 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20394069 CTTTATTTAA
* *
20394079 TTATTAAATTACCTTAATAACC
1 TTATTAAATTAACTAAATAACC
20394101 TTATT-AATTAACTAAATAA
1 TTATTAAATTAACTAAATAA
20394120 AACATCTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (22 bp):
TTATTAAATTAACTAAATAACC
Found at i:20397149 original size:21 final size:21
Alignment explanation
Indices: 20397102--20397149 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
20397092 CATGTGACCC
* *
20397102 TTGTTTCCCAATTTTTGTAAT
1 TTGTTTCCCAAATTTTCTAAT
* *
20397123 TT-TTTCCTAAATTTTCTGAT
1 TTGTTTCCCAAATTTTCTAAT
20397143 TTGTTTC
1 TTGTTTC
20397150 AAATTGGTCC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.17, C:0.15, G:0.08, T:0.60
Consensus pattern (21 bp):
TTGTTTCCCAAATTTTCTAAT
Found at i:20399127 original size:13 final size:13
Alignment explanation
Indices: 20399109--20399134 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20399099 TAATGAGAAG
20399109 ATATCATTTACCC
1 ATATCATTTACCC
20399122 ATATCATTTACCC
1 ATATCATTTACCC
20399135 TTTTCTTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATCATTTACCC
Found at i:20414248 original size:22 final size:22
Alignment explanation
Indices: 20414222--20414267 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
20414212 ATTTTTTTAA
20414222 TTTC-AAATTTTTTTCGAATTTT
1 TTTCAAAATTTTTTT-GAATTTT
20414244 TTTCAAAATTTTTTTGAATTTT
1 TTTCAAAATTTTTTTGAATTTT
20414266 TT
1 TT
20414268 GAATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTCAAAATTTTTTTGAATTTT
Found at i:20414277 original size:10 final size:11
Alignment explanation
Indices: 20414222--20414278 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
20414212 ATTTTTTTAA
*
20414222 TTTCAAATTTT
1 TTTCGAATTTT
20414233 TTTCGAATTTT
1 TTTCGAATTTT
*
20414244 TTTCAAAATTTT
1 TTTC-GAATTTT
20414256 TTT-GAA-TTT
1 TTTCGAATTTT
20414265 TTT-GAATTTT
1 TTTCGAATTTT
20414275 TTTC
1 TTTC
20414279 ACGTACCTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 9 0.22
10 8 0.20
11 14 0.35
12 9 0.22
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.65
Consensus pattern (11 bp):
TTTCGAATTTT
Found at i:20414505 original size:22 final size:22
Alignment explanation
Indices: 20414480--20414597 Score: 94
Period size: 23 Copynumber: 5.2 Consensus size: 22
20414470 TTAGCTAGGG
20414480 AATGGTATTGGTTTTGGTACGA
1 AATGGTATTGGTTTTGGTACGA
* *
20414502 AATGGGGT-TTGGTATAGGTACGA
1 AAT--GGTATTGGTTTTGGTACGA
* *
20414525 AATGGTATAGGTTTTGGTATGA
1 AATGGTATTGGTTTTGGTACGA
* * * **
20414547 AATGAATTTTGGTGTAAGTACGA
1 AATG-GTATTGGTTTTGGTACGA
* *
20414570 AAGGGTATAGGTTTTGGTACGGA
1 AATGGTATTGGTTTTGGTAC-GA
20414593 AATGG
1 AATGG
20414598 ATCAAAAAGG
Statistics
Matches: 70, Mismatches: 21, Indels: 9
0.70 0.21 0.09
Matches are distributed among these distances:
21 3 0.04
22 28 0.40
23 36 0.51
24 3 0.04
ACGTcount: A:0.28, C:0.03, G:0.34, T:0.35
Consensus pattern (22 bp):
AATGGTATTGGTTTTGGTACGA
Found at i:20414530 original size:45 final size:45
Alignment explanation
Indices: 20414480--20414598 Score: 157
Period size: 45 Copynumber: 2.6 Consensus size: 45
20414470 TTAGCTAGGG
* * *
20414480 AATGGTATTGGTTTTGGTACGAAATGGGGTTTGGTATAGGTACGA
1 AATGGTATAGGTTTTGGTACGAAATGGAGTTTGGTATAAGTACGA
* * * *
20414525 AATGGTATAGGTTTTGGTATGAAATGAATTTTGGTGTAAGTACGA
1 AATGGTATAGGTTTTGGTACGAAATGGAGTTTGGTATAAGTACGA
*
20414570 AAGGGTATAGGTTTTGGTACGGAAATGGA
1 AATGGTATAGGTTTTGGTAC-GAAATGGA
20414599 TCAAAAAGGT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
45 56 0.89
46 7 0.11
ACGTcount: A:0.29, C:0.03, G:0.34, T:0.34
Consensus pattern (45 bp):
AATGGTATAGGTTTTGGTACGAAATGGAGTTTGGTATAAGTACGA
Found at i:20415495 original size:20 final size:20
Alignment explanation
Indices: 20415470--20415514 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
20415460 TAAATTCACA
20415470 TAATTAAAACT-AGACACAAT
1 TAATT-AAACTAAGACACAAT
**
20415490 TAATTAAGTTAAGACACAAT
1 TAATTAAACTAAGACACAAT
20415510 TAATT
1 TAATT
20415515 CGGTTAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
TAATTAAACTAAGACACAAT
Found at i:20418861 original size:38 final size:40
Alignment explanation
Indices: 20418778--20418862 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 40
20418768 CTCATTGATT
** *
20418778 TCTTTTTTTACTCTCTTTTCATTTTCTTTTGCAATTTTCCC
1 TCTTTTTTTACTCAATTTTCATTTTCTTTTG-AATTTTCAC
20418819 TCTTTTTTT-CTCAATTTT-ATTTTCCTTTTG-ATTTTCAC
1 TCTTTTTTTACTCAATTTTCATTTT-CTTTTGAATTTTCAC
20418857 TCTTTT
1 TCTTTT
20418863 CTTTTGTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
38 13 0.32
39 5 0.12
40 13 0.32
41 9 0.22
ACGTcount: A:0.11, C:0.21, G:0.02, T:0.66
Consensus pattern (40 bp):
TCTTTTTTTACTCAATTTTCATTTTCTTTTGAATTTTCAC
Found at i:20421407 original size:44 final size:45
Alignment explanation
Indices: 20421253--20421416 Score: 213
Period size: 45 Copynumber: 3.6 Consensus size: 45
20421243 TTAATTATGG
* * * * *
20421253 AATGATATCGGTTTTGGTAGGAAATGGGTTTTGGTATAGGTACGA
1 AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA
* * *
20421298 AATGATATAGGTTTTGGTACAAAATAGATTTTGGTGTAGGTACGA
1 AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA
*
20421343 AATGGTATAGGTTTTGGTACGACATGGATTTTGGTGTAGGTAC-A
1 AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA
* *
20421387 AAAGGTATAAGTTTTGGTACGAAAATGGAT
1 AATGGTATAGGTTTTGGTACG-AAATGGAT
20421417 CAAAAAGGTC
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
44 20 0.19
45 85 0.81
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (45 bp):
AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA
Found at i:20422327 original size:20 final size:20
Alignment explanation
Indices: 20422302--20422346 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20422292 TAAATTCACA
20422302 TAATTAAAACAAGACACAAT
1 TAATTAAAACAAGACACAAT
***
20422322 TAATTAAGTTAAGACACAAT
1 TAATTAAAACAAGACACAAT
20422342 TAATT
1 TAATT
20422347 CGGTTAGGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29
Consensus pattern (20 bp):
TAATTAAAACAAGACACAAT
Found at i:20425697 original size:38 final size:40
Alignment explanation
Indices: 20425614--20425698 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 40
20425604 CTCATTGATT
** *
20425614 TCTTTTTTTACTCTCTTTTCATTTTCTTTTGCAATTTTCCC
1 TCTTTTTTTACTCAATTTTCATTTTCTTTTG-AATTTTCAC
20425655 TCTTTTTTT-CTCAATTTT-ATTTTCCTTTTG-ATTTTCAC
1 TCTTTTTTTACTCAATTTTCATTTT-CTTTTGAATTTTCAC
20425693 TCTTTT
1 TCTTTT
20425699 CTTTTGTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
38 13 0.32
39 5 0.12
40 13 0.32
41 9 0.22
ACGTcount: A:0.11, C:0.21, G:0.02, T:0.66
Consensus pattern (40 bp):
TCTTTTTTTACTCAATTTTCATTTTCTTTTGAATTTTCAC
Found at i:20428240 original size:44 final size:45
Alignment explanation
Indices: 20428086--20428249 Score: 213
Period size: 45 Copynumber: 3.6 Consensus size: 45
20428076 TTAATTATGG
* * * * *
20428086 AATGATATCGGTTTTGGTAGGAAATGGGTTTTGGTATAGGTACGA
1 AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA
* * *
20428131 AATGATATAGGTTTTGGTACAAAATAGATTTTGGTGTAGGTACGA
1 AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA
*
20428176 AATGGTATAGGTTTTGGTACGACATGGATTTTGGTGTAGGTAC-A
1 AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA
* *
20428220 AAAGGTATAAGTTTTGGTACGAAAATGGAT
1 AATGGTATAGGTTTTGGTACG-AAATGGAT
20428250 CAAAAAGGTC
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
44 20 0.19
45 85 0.81
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (45 bp):
AATGGTATAGGTTTTGGTACGAAATGGATTTTGGTGTAGGTACGA
Found at i:20429160 original size:20 final size:20
Alignment explanation
Indices: 20429135--20429179 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20429125 TAAATTCACA
20429135 TAATTAAAACAAGACACAAT
1 TAATTAAAACAAGACACAAT
***
20429155 TAATTAAGTTAAGACACAAT
1 TAATTAAAACAAGACACAAT
20429175 TAATT
1 TAATT
20429180 CGGTTAGGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29
Consensus pattern (20 bp):
TAATTAAAACAAGACACAAT
Found at i:20432530 original size:38 final size:40
Alignment explanation
Indices: 20432447--20432531 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 40
20432437 CTCATTGATT
** *
20432447 TCTTTTTTTACTCTCTTTTCATTTTCTTTTGCAATTTTCCC
1 TCTTTTTTTACTCAATTTTCATTTTCTTTTG-AATTTTCAC
20432488 TCTTTTTTT-CTCAATTTT-ATTTTCCTTTTG-ATTTTCAC
1 TCTTTTTTTACTCAATTTTCATTTT-CTTTTGAATTTTCAC
20432526 TCTTTT
1 TCTTTT
20432532 CTTTTGTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
38 13 0.32
39 5 0.12
40 13 0.32
41 9 0.22
ACGTcount: A:0.11, C:0.21, G:0.02, T:0.66
Consensus pattern (40 bp):
TCTTTTTTTACTCAATTTTCATTTTCTTTTGAATTTTCAC
Found at i:20434968 original size:45 final size:45
Alignment explanation
Indices: 20434919--20435028 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 45
20434909 TTAATTATGG
* ** * *
20434919 AATGATATCGGTTTTGGTAGGAAATGGGTTTTGGTATAGGTACGA
1 AATGATATAGGTTTTGGTACAAAATAGATTTTGGTATAGGTACGA
*
20434964 AATGATATAGGTTTTGGTACAAAATAGATTTTGGTGTAGGTACGA
1 AATGATATAGGTTTTGGTACAAAATAGATTTTGGTATAGGTACGA
*
20435009 AATGGTATAGGTTTTGGTAC
1 AATGATATAGGTTTTGGTAC
20435029 GACATGTGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.29, C:0.05, G:0.30, T:0.36
Consensus pattern (45 bp):
AATGATATAGGTTTTGGTACAAAATAGATTTTGGTATAGGTACGA
Found at i:20435005 original size:23 final size:22
Alignment explanation
Indices: 20434947--20435012 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 22
20434937 AGGAAATGGG
20434947 TTTTGGTATAGGTACGAAATGA
1 TTTTGGTATAGGTACGAAATGA
* * * * *
20434969 TATAGGTTTTGGTACAAAATAGA
1 TTTTGGTATAGGTACGAAAT-GA
*
20434992 TTTTGGTGTAGGTACGAAATG
1 TTTTGGTATAGGTACGAAATG
20435013 GTATAGGTTT
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
22 16 0.48
23 17 0.52
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (22 bp):
TTTTGGTATAGGTACGAAATGA
Found at i:20435029 original size:22 final size:22
Alignment explanation
Indices: 20434919--20435030 Score: 89
Period size: 22 Copynumber: 5.0 Consensus size: 22
20434909 TTAATTATGG
* *
20434919 AATGATATCGGTTTTGGTAGGA
1 AATGATATAGGTTTTGGTACGA
* * * * *
20434941 AATGGGTTTTGGTATAGGTACGA
1 AAT-GATATAGGTTTTGGTACGA
*
20434964 AATGATATAGGTTTTGGTACAA
1 AATGATATAGGTTTTGGTACGA
* * * *
20434986 AATAGATTTTGGTGTAGGTACGA
1 AAT-GATATAGGTTTTGGTACGA
*
20435009 AATGGTATAGGTTTTGGTACGA
1 AATGATATAGGTTTTGGTACGA
20435031 CATGTGAACA
Statistics
Matches: 66, Mismatches: 22, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
22 33 0.50
23 33 0.50
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.36
Consensus pattern (22 bp):
AATGATATAGGTTTTGGTACGA
Found at i:20435101 original size:20 final size:20
Alignment explanation
Indices: 20435076--20435120 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
20435066 TAAATTCACA
20435076 TAATTAAAACT-AGACACAAT
1 TAATT-AAACTAAGACACAAT
**
20435096 TAATTAAGTTAAGACACAAT
1 TAATTAAACTAAGACACAAT
20435116 TAATT
1 TAATT
20435121 CGGTTAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (20 bp):
TAATTAAACTAAGACACAAT
Found at i:20438754 original size:191 final size:192
Alignment explanation
Indices: 20438429--20438811 Score: 750
Period size: 191 Copynumber: 2.0 Consensus size: 192
20438419 ATTTTTCTTA
20438429 AATCCTACAGCTCATTAATAAGCTTATTGCATGTTTTTAATATGTTTTTTGTTCTAACCGAATTA
1 AATCCTACAGCTCATTAATAAGCTTATTGCATGTTTTTAATATGTTTTTTGTTCTAACCGAATTA
20438494 CTGGTGTCTTAGCTTAATTAAACTTGTCTAGTTTTTTTTTAATTATGTGTATTTAAATTGTCCAA
66 CTGGTGTCTTAGCTTAATTAAACTTGTCTAGTTTTTTTTTAATTATGTGTATTTAAATTGTCCAA
20438559 GTTATGTTTTCAATTATGTTCAACTGAATGTGAATTAATTTAAGTTGGTTCATCTATGTTTG
131 GTTATGTTTTCAATTATGTTCAACTGAATGTGAATTAATTTAAGTTGGTTCATCTATGTTTG
20438621 AATCCTACAG-TCATTAATAAGCTTATTGCATGTTTTTAATATGTTTTTTGTTCTAACCGAATTA
1 AATCCTACAGCTCATTAATAAGCTTATTGCATGTTTTTAATATGTTTTTTGTTCTAACCGAATTA
20438685 CTGGTGTCTTAGCTTAATTAAACTTGTCTAGTTTTTTTTTAATTATGTGTATTTAAATTGTCCAA
66 CTGGTGTCTTAGCTTAATTAAACTTGTCTAGTTTTTTTTTAATTATGTGTATTTAAATTGTCCAA
*
20438750 GTTATGTTTTCAATTATGTTCAGCTGAATGTGAATTAATTTAAGTTGGTTCATCTATGTTTG
131 GTTATGTTTTCAATTATGTTCAACTGAATGTGAATTAATTTAAGTTGGTTCATCTATGTTTG
20438812 TAGGTTGGCC
Statistics
Matches: 190, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
191 180 0.95
192 10 0.05
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.48
Consensus pattern (192 bp):
AATCCTACAGCTCATTAATAAGCTTATTGCATGTTTTTAATATGTTTTTTGTTCTAACCGAATTA
CTGGTGTCTTAGCTTAATTAAACTTGTCTAGTTTTTTTTTAATTATGTGTATTTAAATTGTCCAA
GTTATGTTTTCAATTATGTTCAACTGAATGTGAATTAATTTAAGTTGGTTCATCTATGTTTG
Found at i:20451194 original size:6 final size:6
Alignment explanation
Indices: 20451183--20451215 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
20451173 ACAAAAATGT
*
20451183 AATGAC AATGAC AATGAA AATG-C AATGAC AATG
1 AATGAC AATGAC AATGAC AATGAC AATGAC AATG
20451216 TATACTTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.52, C:0.12, G:0.18, T:0.18
Consensus pattern (6 bp):
AATGAC
Found at i:20463180 original size:39 final size:39
Alignment explanation
Indices: 20463137--20463263 Score: 143
Period size: 40 Copynumber: 3.3 Consensus size: 39
20463127 AACCTATGTT
* * *
20463137 TTATATTACCTGAGAATCC-ACGACAAGGGTTGGATCTCA
1 TTATATTACCTGAGAATCCTACAACAA-GGCTAGATCTCA
* *
20463176 TTATATTGCCTGAGAA-CCTGCAACAAGGCTAGATCTCA
1 TTATATTACCTGAGAATCCTACAACAAGGCTAGATCTCA
*
20463214 TTATATTACCCTTGAGAAT-CTGCAACAAGGCTAGATCTCA
1 TTATATTA-CC-TGAGAATCCTACAACAAGGCTAGATCTCA
*
20463254 TTGTATTACC
1 TTATATTACC
20463264 CCAAGAATCT
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
38 19 0.25
39 24 0.31
40 34 0.44
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (39 bp):
TTATATTACCTGAGAATCCTACAACAAGGCTAGATCTCA
Found at i:20463220 original size:38 final size:40
Alignment explanation
Indices: 20463169--20463264 Score: 151
Period size: 40 Copynumber: 2.5 Consensus size: 40
20463159 ACAAGGGTTG
*
20463169 GATCTCATTATATT-GCC-TGAGAACCTGCAACAAGGCTA
1 GATCTCATTATATTACCCTTGAGAACCTGCAACAAGGCTA
*
20463207 GATCTCATTATATTACCCTTGAGAATCTGCAACAAGGCTA
1 GATCTCATTATATTACCCTTGAGAACCTGCAACAAGGCTA
*
20463247 GATCTCATTGTATTACCC
1 GATCTCATTATATTACCC
20463265 CAAGAATCTG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
38 14 0.26
39 2 0.04
40 37 0.70
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (40 bp):
GATCTCATTATATTACCCTTGAGAACCTGCAACAAGGCTA
Found at i:20463240 original size:40 final size:39
Alignment explanation
Indices: 20463137--20463280 Score: 166
Period size: 39 Copynumber: 3.7 Consensus size: 39
20463127 AACCTATGTT
** * * *
20463137 TTATATTA-CCTGAGAATCCACGACAAGGGTTGGATCTCA
1 TTATATTACCCTGAGAATCTGCAACAA-GGCTAGATCTCA
* *
20463176 TTATATT-GCCTGAGAACCTGCAACAAGGCTAGATCTCA
1 TTATATTACCCTGAGAATCTGCAACAAGGCTAGATCTCA
20463214 TTATATTACCCTTGAGAATCTGCAACAAGGCTAGATCTCA
1 TTATATTACCC-TGAGAATCTGCAACAAGGCTAGATCTCA
* **
20463254 TTGTATTACCCCAAGAATCTGCAACAA
1 TTATATTACCCTGAGAATCTGCAACAA
20463281 AAACTAGATA
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
38 17 0.19
39 37 0.41
40 37 0.41
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (39 bp):
TTATATTACCCTGAGAATCTGCAACAAGGCTAGATCTCA
Found at i:20463288 original size:40 final size:40
Alignment explanation
Indices: 20463169--20463298 Score: 122
Period size: 40 Copynumber: 3.3 Consensus size: 40
20463159 ACAAGGGTTG
* * * **
20463169 GATCTCATTATATT-GCCT-GAGAACCTGCAACAAGGCTA
1 GATCTCATTATATTACCCTCAAGAATCTGCAACAAAACTA
** **
20463207 GATCTCATTATATTACCCTTGAGAATCTGCAACAAGGCTA
1 GATCTCATTATATTACCCTCAAGAATCTGCAACAAAACTA
*
20463247 GATCTCATTGTATTACCC-CAAGAATCTGCAACAAAAACTA
1 GATCTCATTATATTACCCTCAAGAATCTGCAAC-AAAACTA
* *
20463287 GATATTATTATA
1 GATCTCATTATA
20463299 ATCTATAATA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
38 14 0.18
39 15 0.19
40 50 0.63
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (40 bp):
GATCTCATTATATTACCCTCAAGAATCTGCAACAAAACTA
Found at i:20464401 original size:21 final size:22
Alignment explanation
Indices: 20464364--20464404 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20464354 TGTTTAATCA
*
20464364 AATTTTAATATATATTTTTAAT
1 AATTTTAATAAATATTTTTAAT
20464386 AATTTT-ATAAATATTTTTA
1 AATTTTAATAAATATTTTTA
20464405 TTTTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AATTTTAATAAATATTTTTAAT
Found at i:20464955 original size:21 final size:22
Alignment explanation
Indices: 20464916--20464956 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20464906 ACATTTTAAA
*
20464916 TAAAAAATAATCTAGTTAATTT
1 TAAAAAAAAATCTAGTTAATTT
*
20464938 TAAAAAAAAATTTA-TTAAT
1 TAAAAAAAAATCTAGTTAAT
20464957 GTGAAGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
TAAAAAAAAATCTAGTTAATTT
Found at i:20466812 original size:43 final size:43
Alignment explanation
Indices: 20466758--20466888 Score: 208
Period size: 43 Copynumber: 3.0 Consensus size: 43
20466748 TTTTCTTTGC
* * *
20466758 AACGCCGCTATAAACCATGGTCTTTAGCGGCGCTTAGCCTAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAA
*
20466801 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCGAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAA
* *
20466844 AACGCCACTATAGACGATGGTCTTTAGCGGCGCTTATCCAAAA
1 AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAA
20466887 AA
1 AA
20466889 TGCCGCTAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 82 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (43 bp):
AACGCCACTATAGACCATGGTCTTTAGCGGCGCTTAGCCAAAA
Found at i:20467244 original size:21 final size:21
Alignment explanation
Indices: 20467196--20467253 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
20467186 TTATGCTATT
* * *
20467196 CTACTTCCCTCGCTGTAGCCT
1 CTACTTCCCTCGCTGCAACCG
20467217 CTACTTCCCTCGCTGCAACCG
1 CTACTTCCCTCGCTGCAACCG
* *
20467238 CTGCTTCTCTCGCTGC
1 CTACTTCCCTCGCTGC
20467254 CGCATCTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.09, C:0.45, G:0.16, T:0.31
Consensus pattern (21 bp):
CTACTTCCCTCGCTGCAACCG
Found at i:20467355 original size:66 final size:64
Alignment explanation
Indices: 20467240--20467404 Score: 190
Period size: 65 Copynumber: 2.5 Consensus size: 64
20467230 TGCAACCGCT
* **
20467240 GCTTCTCTCGCTGCCGCATCTTCTTTAAGCTACTGCTGCAGTTGCTCATA-CTTTCGTTGAACCT
1 GCTTCTCTCGCTGCCGCATCTGCTTTAAG-TTGTGCTGCAGTTGCTCATATCTTT--TTGAACCT
20467304 CA
63 CA
*
20467306 GCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTT-CTTCATATCTTTTTGAACCTC
1 GCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGT-GCTGCAGTTGC-TCATATCTTTTTGAACCTC
20467370 A
64 A
* ** * *
20467371 GCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGTG
1 GCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTG
20467405 TAATTTGCTC
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
64 1 0.01
65 41 0.47
66 41 0.47
67 4 0.05
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.39
Consensus pattern (64 bp):
GCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTGCTGCAGTTGCTCATATCTTTTTGAACCTCA
Found at i:20478499 original size:113 final size:113
Alignment explanation
Indices: 20478314--20478659 Score: 631
Period size: 113 Copynumber: 3.1 Consensus size: 113
20478304 GCTTAACGCT
* * *
20478314 AAACGCCGCTAAAGAACGGA-TTATTAGCGGCGTTTGGGCAAAAACCGCCACTAGTGTTCCCAAA
1 AAACGCCGCTGAAGAACGGAGTT-TTAGCGGCGCTTGGG-AAAAACCGCCACTAATGTTCCCAAA
20478378 TATATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTATA
64 TATATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTATA
20478428 AAACGCCGCTGAAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA
1 AAACGCCGCTGAAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA
20478493 TATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTATA
66 TATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTATA
20478541 AAACGCCGCTGAAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA
1 AAACGCCGCTGAAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA
*
20478606 TATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTGTA
66 TATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTATA
20478654 AAACGC
1 AAACGC
20478660 TGCTAATGCT
Statistics
Matches: 227, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
113 192 0.85
114 33 0.15
115 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (113 bp):
AAACGCCGCTGAAGAACGGAGTTTTAGCGGCGCTTGGGAAAAACCGCCACTAATGTTCCCAAATA
TATGAAAACAGCGTCATTCTGTGTGACTCTATTGCGGCGCTTTTTATA
Found at i:20478783 original size:41 final size:40
Alignment explanation
Indices: 20478697--20478786 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
20478687 TTTTATGTAG
* *
20478697 CGCCGCTAATGCTCGATATTTTGAGGCGTTTTTCGTAAAA
1 CGCCGCTAATGCTCGATATTTAGAGGCATTTTTCGTAAAA
* * * *
20478737 TGCCGCTAATGCTCGAT-TATTAGTGGCATTTTTTGTCCAAA
1 CGCCGCTAATGCTCGATAT-TTAGAGGCATTTTTCGT-AAAA
20478778 CGCCGCTAA
1 CGCCGCTAA
20478787 AAGTGCCGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.02
40 29 0.71
41 11 0.27
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (40 bp):
CGCCGCTAATGCTCGATATTTAGAGGCATTTTTCGTAAAA
Found at i:20483497 original size:27 final size:27
Alignment explanation
Indices: 20483439--20483526 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
20483429 ATGGTATCAA
* * *
20483439 AGATAGTTCGACGAGATGTTAAACA-A
1 AGATAGTTCGATGGGATGTTAAACACG
20483465 ATGATAGTTCGATGGGATGTTAAACACG
1 A-GATAGTTCGATGGGATGTTAAACACG
*
20483493 GGATAG-TCTGATGGGATGTTAAACACG
1 AGATAGTTC-GATGGGATGTTAAACACG
20483520 AGATAGT
1 AGATAGT
20483527 CCACTAGGAC
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
26 3 0.06
27 50 0.94
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.26
Consensus pattern (27 bp):
AGATAGTTCGATGGGATGTTAAACACG
Found at i:20486629 original size:201 final size:201
Alignment explanation
Indices: 20486284--20486652 Score: 711
Period size: 201 Copynumber: 1.8 Consensus size: 201
20486274 TACTCGAATG
*
20486284 TTGTTGATTAATGATATATATTACATTGTGTTGTATTGAATGGTATCAAAATTAATGATTGTTAC
1 TTGTTGATTAATGATACATATTACATTGTGTTGTATTGAATGGTATCAAAATTAATGATTGTTAC
20486349 TCGAGTGAATGATGACCTATGCTCATACACCATTTGACATCAATTTGATAGTGGCTATGTAATGA
66 TCGAGTGAATGATGACCTATGCTCATACACCATTTGACATCAATTTGATAGTGGCTATGTAATGA
20486414 TATGAAATTCTAATGATGGTTTTGTGTTCTTCTGATAATGCTAACATGTTTCAATATATTTGATA
131 TATGAAATTCTAATGATGGTTTTGTGTTCTTCTGATAATGCTAACATGTTTCAATATATTTGATA
20486479 TTTATC
196 TTTATC
*
20486485 TTGTTGATTAATGATACATATTGCATTGTGTTGTATTGAATGGTATCAAAATTAATGATTGTTAC
1 TTGTTGATTAATGATACATATTACATTGTGTTGTATTGAATGGTATCAAAATTAATGATTGTTAC
*
20486550 TCGAGTGAATGATGACCTATGCTCATACACCATTTGGCATCAATTTGATAGTGGCTATGTAATGA
66 TCGAGTGAATGATGACCTATGCTCATACACCATTTGACATCAATTTGATAGTGGCTATGTAATGA
20486615 TATGAAATTCTAATGATGGTTTTGTGTTCTTCTGATAA
131 TATGAAATTCTAATGATGGTTTTGTGTTCTTCTGATAA
20486653 CTCACACTGA
Statistics
Matches: 165, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
201 165 1.00
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (201 bp):
TTGTTGATTAATGATACATATTACATTGTGTTGTATTGAATGGTATCAAAATTAATGATTGTTAC
TCGAGTGAATGATGACCTATGCTCATACACCATTTGACATCAATTTGATAGTGGCTATGTAATGA
TATGAAATTCTAATGATGGTTTTGTGTTCTTCTGATAATGCTAACATGTTTCAATATATTTGATA
TTTATC
Found at i:20487788 original size:15 final size:15
Alignment explanation
Indices: 20487768--20487799 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20487758 ACATTTCATG
*
20487768 TTATGTCTTTTATAT
1 TTATGTCTTTCATAT
20487783 TTATGTCTTTCATAT
1 TTATGTCTTTCATAT
20487798 TT
1 TT
20487800 TGCATTCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.09, G:0.06, T:0.66
Consensus pattern (15 bp):
TTATGTCTTTCATAT
Found at i:20495827 original size:69 final size:69
Alignment explanation
Indices: 20495716--20495868 Score: 288
Period size: 69 Copynumber: 2.2 Consensus size: 69
20495706 CAGGACTAAA
20495716 ACCATAGTTGGACTATGGCATCCTAGTACTCTACCAAAAAAATAAACACGGTGAAACATAAGGTG
1 ACCATAGTTGGACTATGGCATCCTAGTACTCTACCAAAAAAATAAACACGGTGAAACATAAGGTG
20495781 TAAG
66 TAAG
*
20495785 ACCATAGTTGGACTATGGCATCCTAGTACTCTACCAAGAAAATAAACACGGTGAAACATAAGGTG
1 ACCATAGTTGGACTATGGCATCCTAGTACTCTACCAAAAAAATAAACACGGTGAAACATAAGGTG
20495850 TAAG
66 TAAG
*
20495854 ACCATAGCTGGACTA
1 ACCATAGTTGGACTA
20495869 AAGCCACTGC
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 82 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (69 bp):
ACCATAGTTGGACTATGGCATCCTAGTACTCTACCAAAAAAATAAACACGGTGAAACATAAGGTG
TAAG
Found at i:20496039 original size:27 final size:27
Alignment explanation
Indices: 20496008--20496060 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
20495998 ACGACAACAA
*
20496008 AGATAGTCTGACGGGACATTAAACATG
1 AGATAGTCTGACGGGACATCAAACATG
*
20496035 AGATAGTTTGACGGGACATCAAACAT
1 AGATAGTCTGACGGGACATCAAACAT
20496061 AGGGTTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (27 bp):
AGATAGTCTGACGGGACATCAAACATG
Found at i:20498532 original size:42 final size:43
Alignment explanation
Indices: 20498446--20498567 Score: 169
Period size: 42 Copynumber: 2.9 Consensus size: 43
20498436 GGCTCGTACA
* * *
20498446 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACAGATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACACAAATCG
*
20498489 ATGCC-ACTGTCCCAGACAG-GGT-TTACAAGAAAACACAAATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAAACACAAATCG
20498531 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACAC
20498568 TTTTCGAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
41 1 0.01
42 35 0.51
43 32 0.46
44 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGAAAACACAAATCG
Found at i:20502509 original size:27 final size:27
Alignment explanation
Indices: 20502412--20502509 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 27
20502402 TTGCAACTCA
*
20502412 ACTGGCAAACCCC-GGTTCGCCAAATAG
1 ACTGGCAAACCCCAGCTT-GCCAAATAG
* ** * *
20502439 AATGGTGAACCCCAACTAGCCAAATAG
1 ACTGGCAAACCCCAGCTTGCCAAATAG
* * *
20502466 ACTAGCAAACCCTAGCTTGCCAAACAG
1 ACTGGCAAACCCCAGCTTGCCAAATAG
*
20502493 ACTGGCGAACCCCAGCT
1 ACTGGCAAACCCCAGCT
20502510 CATCAGCACG
Statistics
Matches: 53, Mismatches: 17, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
27 52 0.98
28 1 0.02
ACGTcount: A:0.34, C:0.33, G:0.19, T:0.14
Consensus pattern (27 bp):
ACTGGCAAACCCCAGCTTGCCAAATAG
Found at i:20502941 original size:9 final size:9
Alignment explanation
Indices: 20502927--20502957 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20502917 GTTAAACGAA
20502927 TCGAGTTAT
1 TCGAGTTAT
*
20502936 TCGAGTTAA
1 TCGAGTTAT
20502945 TCGAGTTAT
1 TCGAGTTAT
20502954 TCGA
1 TCGA
20502958 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:20503027 original size:9 final size:9
Alignment explanation
Indices: 20503010--20503046 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20503000 TGAGTTTTCA
20503010 AATTCGAAT
1 AATTCGAAT
*
20503019 AACTCGAAT
1 AATTCGAAT
20503028 AATTCGAAT
1 AATTCGAAT
20503037 AATTCGAAT
1 AATTCGAAT
20503046 A
1 A
20503047 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:20504361 original size:7 final size:7
Alignment explanation
Indices: 20504349--20504394 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
20504339 TAAATTTGAA
*
20504349 TAAACCT
1 TAAACCC
20504356 TAAACCC
1 TAAACCC
*
20504363 TAAATCC
1 TAAACCC
20504370 TAAACCC
1 TAAACCC
*
20504377 TAAATCC
1 TAAACCC
20504384 TAAACCC
1 TAAACCC
20504391 TAAA
1 TAAA
20504395 AAATTAAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:20504373 original size:14 final size:14
Alignment explanation
Indices: 20504356--20504394 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
20504346 GAATAAACCT
20504356 TAAACCCTAAATCC
1 TAAACCCTAAATCC
20504370 TAAACCCTAAATCC
1 TAAACCCTAAATCC
20504384 TAAACCCTAAA
1 TAAACCCTAAA
20504395 AAATTAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAATCC
Found at i:20513111 original size:30 final size:30
Alignment explanation
Indices: 20513070--20513130 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
20513060 AAACCTCTTT
20513070 ACTTTCCCCCAAAACTTTTACT-CCCTTCC
1 ACTTTCCCCCAAAACTTTTACTCCCCTTCC
*
20513099 ACTTTCCCCCCAAAACTTTTTCTCCCCTTCC
1 ACTTT-CCCCCAAAACTTTTACTCCCCTTCC
20513130 A
1 A
20513131 TCCCACCCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 5 0.17
30 16 0.55
31 8 0.28
ACGTcount: A:0.20, C:0.46, G:0.00, T:0.34
Consensus pattern (30 bp):
ACTTTCCCCCAAAACTTTTACTCCCCTTCC
Found at i:20513140 original size:31 final size:30
Alignment explanation
Indices: 20513075--20513140 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
20513065 TCTTTACTTT
**
20513075 CCCCCAAAACTTTTACTCCCTTCCACTTTC
1 CCCCCAAAACTTTTACTCCCTTCCACTCCC
*
20513105 CCCCCAAAACTTTTTCTCCCCTTCCA-TCCC
1 CCCCCAAAACTTTTACT-CCCTTCCACTCCC
20513135 ACCCCC
1 -CCCCC
20513141 TTCTACCCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.18, C:0.53, G:0.00, T:0.29
Consensus pattern (30 bp):
CCCCCAAAACTTTTACTCCCTTCCACTCCC
Found at i:20513260 original size:18 final size:19
Alignment explanation
Indices: 20513228--20513265 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
20513218 AATCCCTCAA
20513228 CCCCCAAAACTTTTTATTT
1 CCCCCAAAACTTTTTATTT
20513247 CCCCCAAAAC-TTTTATTT
1 CCCCCAAAACTTTTTATTT
20513265 C
1 C
20513266 TCACCTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.39
Consensus pattern (19 bp):
CCCCCAAAACTTTTTATTT
Found at i:20514601 original size:2 final size:2
Alignment explanation
Indices: 20514596--20514633 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
20514586 AAAAAAAAAA
*
20514596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20514634 TAATAAAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20515395 original size:30 final size:31
Alignment explanation
Indices: 20515331--20515400 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
20515321 ATTCAAAAAA
*
20515331 TTTTATTTAAGCCACTGAACTATTTAAAAGT
1 TTTTATTTAAGCCACTGAACTAGTTAAAAGT
* *
20515362 TTTTATTTAAGTCATTGAACT-GTT-AAA-T
1 TTTTATTTAAGCCACTGAACTAGTTAAAAGT
*
20515390 TTTTTTTTAAG
1 TTTTATTTAAG
20515401 TTTCACCACT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.31
29 3 0.09
30 2 0.06
31 19 0.54
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.50
Consensus pattern (31 bp):
TTTTATTTAAGCCACTGAACTAGTTAAAAGT
Found at i:20523122 original size:48 final size:47
Alignment explanation
Indices: 20522997--20523131 Score: 144
Period size: 48 Copynumber: 2.8 Consensus size: 47
20522987 CTATTTACCT
* * * * **
20522997 TGTAGATTTAACCCTAACGGGTAACTAGACACTATTACTCATTATTTG
1 TGTAGGTTTAACCCTAAC-GGTAACCAGGCACTATTATTCATTATTCA
* * *
20523045 TGTAGGTTTAACCTTGACGAGTAATCAGGCACTATTATTCATTATTCA
1 TGTAGGTTTAACCCTAACG-GTAACCAGGCACTATTATTCATTATTCA
**
20523093 TGTAGGTTTAACCGAAACAGGTAACCAGGCACTATTATT
1 TGTAGGTTTAACCCTAAC-GGTAACCAGGCACTATTATT
20523132 TTCACCTGTG
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
47 1 0.01
48 70 0.97
49 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (47 bp):
TGTAGGTTTAACCCTAACGGTAACCAGGCACTATTATTCATTATTCA
Found at i:20526806 original size:28 final size:28
Alignment explanation
Indices: 20526766--20526822 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
20526756 AGTAAGTCTA
*
20526766 TTGGGACAGTAAACACGAGCTAGGTTTG
1 TTGGGACAGTAAACACGAGCTAAGTTTG
*
20526794 TTGGGACAGTAAACACGAGGTAAGTTTG
1 TTGGGACAGTAAACACGAGCTAAGTTTG
20526822 T
1 T
20526823 CGGGGTACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.12, G:0.32, T:0.26
Consensus pattern (28 bp):
TTGGGACAGTAAACACGAGCTAAGTTTG
Found at i:20530739 original size:43 final size:42
Alignment explanation
Indices: 20530692--20530793 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 42
20530682 TCTAGAACAT
* * * *
20530692 TGGCATTGATATGAGATTACGTGTAAGACCCTGTTTGGGACA
1 TGGCATTGATATGAGATAACATGTAAGACCATATTTGGGACA
* * *
20530734 GTGGCATCGATATGTGATAACATGTAAGACCATATTTGGGATA
1 -TGGCATTGATATGAGATAACATGTAAGACCATATTTGGGACA
*
20530777 TGGCATTG-TATGTGATA
1 TGGCATTGATATGAGATA
20530794 TATGTGTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 9 0.18
42 7 0.14
43 35 0.69
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.32
Consensus pattern (42 bp):
TGGCATTGATATGAGATAACATGTAAGACCATATTTGGGACA
Found at i:20531577 original size:35 final size:34
Alignment explanation
Indices: 20531510--20531577 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 34
20531500 TATTAAAGTG
*
20531510 TGGTTGTTTTACATATTACAATGATATCCAAATA
1 TGGTTGTTTTACATATTACAATGATATACAAATA
* * * *
20531544 TGGTTGTTTTTACATGTTATAATGTTGTACAAAT
1 TGGTTG-TTTTACATATTACAATGATATACAAAT
20531578 TAGTGCTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 6 0.21
35 22 0.79
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.46
Consensus pattern (34 bp):
TGGTTGTTTTACATATTACAATGATATACAAATA
Found at i:20535677 original size:54 final size:52
Alignment explanation
Indices: 20535611--20535765 Score: 161
Period size: 54 Copynumber: 2.9 Consensus size: 52
20535601 TGGCCATGGG
*
20535611 AAGAAGACCATATAGTGTAAGACCTAATCTGGGACTATGGCATCATAT-AGGA
1 AAGAAGA-CATATAGTGTAAGACCTAGTCTGGGACTATGGCATCATATAAGGA
* *
20535663 AACTGAAGATCATATAGTGTAAGACCTAGTCATTATGG-CCATGGCATCATATAAGGA
1 AA--GAAGA-CATATAGTGTAAGACCTAGTC--T-GGGACTATGGCATCATATAAGGA
* * * *
20535720 AAGAAGACTACATAGTGTAAGACCTAGTTTGAGACTATGGTATCAT
1 AAGAAGAC-ATATAGTGTAAGACCTAGTCTGGGACTATGGCATCAT
20535766 GTGGGAAAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
52 3 0.04
53 11 0.13
54 26 0.31
55 23 0.27
56 14 0.16
57 8 0.09
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (52 bp):
AAGAAGACATATAGTGTAAGACCTAGTCTGGGACTATGGCATCATATAAGGA
Found at i:20537840 original size:43 final size:43
Alignment explanation
Indices: 20537793--20537903 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 43
20537783 AAATAGAAGA
*
20537793 AAATATACTGGCACACACAGTGCATCATTGGACAAACCAAAGC
1 AAATATACTGGAACACACAGTGCATCATTGGACAAACCAAAGC
* * * * * * *
20537836 AAATATACTAGTATAGACATTGTATCATTGGACGAACCAAAGC
1 AAATATACTGGAACACACAGTGCATCATTGGACAAACCAAAGC
20537879 AAATATACTGGAACACGA-AGTGCAT
1 AAATATACTGGAACAC-ACAGTGCAT
20537904 AAACCCGTAC
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
43 53 0.98
44 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (43 bp):
AAATATACTGGAACACACAGTGCATCATTGGACAAACCAAAGC
Found at i:20542099 original size:555 final size:555
Alignment explanation
Indices: 20541049--20542159 Score: 2222
Period size: 555 Copynumber: 2.0 Consensus size: 555
20541039 ACATAAGCAA
20541049 CTAGTGCTTAGTAAGCTCATATAAATCATAAACGTAAACTTACCAAATAGGCTCAATTTATACAA
1 CTAGTGCTTAGTAAGCTCATATAAATCATAAACGTAAACTTACCAAATAGGCTCAATTTATACAA
20541114 TTCATTCATAATTTCATTAACAAGTTCACAAGTTTATTCAATTCCTGTACACATCACAAATCTCA
66 TTCATTCATAATTTCATTAACAAGTTCACAAGTTTATTCAATTCCTGTACACATCACAAATCTCA
20541179 CAAGTTAGTGAGTTCACATTTATATAAGAACATAAAACCATATCATATCATATAATGTTCATAAA
131 CAAGTTAGTGAGTTCACATTTATATAAGAACATAAAACCATATCATATCATATAATGTTCATAAA
20541244 TAACAATTGTAATTTAATCATCCATCTTATGCCGATCATATGTGACACATTCCATTCAATGTTTG
196 TAACAATTGTAATTTAATCATCCATCTTATGCCGATCATATGTGACACATTCCATTCAATGTTTG
20541309 ATACCATATAACCATTTCAGAAATGTCCTTTTCATAAATCAAATTACATATAGCCATTTCATATA
261 ATACCATATAACCATTTCAGAAATGTCCTTTTCATAAATCAAATTACATATAGCCATTTCATATA
20541374 ACTCATTTGTATATCACTTAATACCCGATGAACCATAGTGATATAACATTGGATACATGGGAAAA
326 ACTCATTTGTATATCACTTAATACCCGATGAACCATAGTGATATAACATTGGATACATGGGAAAA
20541439 TGCTCACACGAGCTGTAACTGTAAATGCTCATATGATTTGTAACTGTAAATGCTTACACAAGCTG
391 TGCTCACACGAGCTGTAACTGTAAATGCTCATATGATTTGTAACTGTAAATGCTTACACAAGCTG
20541504 TGAAATGGGCCTACTCGCACGAGCTATGGGTCAGGATGCTAGGCTACACGATGCTGCTCACATGA
456 TGAAATGGGCCTACTCGCACGAGCTATGGGTCAGGATGCTAGGCTACACGATGCTGCTCACATGA
20541569 GTTGTGAAGAGTCCACAACAAATGCAAGACCTTAG
521 GTTGTGAAGAGTCCACAACAAATGCAAGACCTTAG
20541604 CTAGTGCTTAGTAAGCTCATATAAATCATAAACGTAAACTTACCAAATAGGCTCAATTTATACAA
1 CTAGTGCTTAGTAAGCTCATATAAATCATAAACGTAAACTTACCAAATAGGCTCAATTTATACAA
20541669 TTCATTCATAATTTCATTAACAAGTTCACAAGTTTATTCAATTCCTGTACACATCACAAATCTCA
66 TTCATTCATAATTTCATTAACAAGTTCACAAGTTTATTCAATTCCTGTACACATCACAAATCTCA
20541734 CAAGTTAGTGAGTTCACATTTATATAAGAACATAAAACCATATCATATCATATAATGTTCATAAA
131 CAAGTTAGTGAGTTCACATTTATATAAGAACATAAAACCATATCATATCATATAATGTTCATAAA
20541799 TAACAATTGTAATTTAATCATCCATCTTATGCCGATCATATGTGACACATTCCATTCAATGTTTG
196 TAACAATTGTAATTTAATCATCCATCTTATGCCGATCATATGTGACACATTCCATTCAATGTTTG
20541864 ATACCATATAACCATTTCAGAAATGTCCTTTTCATAAATCAAATTACATATAGCCATTTCATATA
261 ATACCATATAACCATTTCAGAAATGTCCTTTTCATAAATCAAATTACATATAGCCATTTCATATA
20541929 ACTCATTTGTATATCACTTAATACCCGATGAACCATAGTGATATAACATTGGATACATGGGAAAA
326 ACTCATTTGTATATCACTTAATACCCGATGAACCATAGTGATATAACATTGGATACATGGGAAAA
20541994 TGCTCACACGAGCTGTAACTGTAAATGCTCATATGATTTGTAACTGTAAATGCTTACACAAGCTG
391 TGCTCACACGAGCTGTAACTGTAAATGCTCATATGATTTGTAACTGTAAATGCTTACACAAGCTG
20542059 TGAAATGGGCCTACTCGCACGAGCTATGGGTCAGGATGCTAGGCTACACGATGCTGCTCACATGA
456 TGAAATGGGCCTACTCGCACGAGCTATGGGTCAGGATGCTAGGCTACACGATGCTGCTCACATGA
20542124 GTTGTGAAGAGTCCACAACAAATGCAAGACCTTAG
521 GTTGTGAAGAGTCCACAACAAATGCAAGACCTTAG
20542159 C
1 C
20542160 CACCGGTAGG
Statistics
Matches: 556, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
555 556 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.31
Consensus pattern (555 bp):
CTAGTGCTTAGTAAGCTCATATAAATCATAAACGTAAACTTACCAAATAGGCTCAATTTATACAA
TTCATTCATAATTTCATTAACAAGTTCACAAGTTTATTCAATTCCTGTACACATCACAAATCTCA
CAAGTTAGTGAGTTCACATTTATATAAGAACATAAAACCATATCATATCATATAATGTTCATAAA
TAACAATTGTAATTTAATCATCCATCTTATGCCGATCATATGTGACACATTCCATTCAATGTTTG
ATACCATATAACCATTTCAGAAATGTCCTTTTCATAAATCAAATTACATATAGCCATTTCATATA
ACTCATTTGTATATCACTTAATACCCGATGAACCATAGTGATATAACATTGGATACATGGGAAAA
TGCTCACACGAGCTGTAACTGTAAATGCTCATATGATTTGTAACTGTAAATGCTTACACAAGCTG
TGAAATGGGCCTACTCGCACGAGCTATGGGTCAGGATGCTAGGCTACACGATGCTGCTCACATGA
GTTGTGAAGAGTCCACAACAAATGCAAGACCTTAG
Found at i:20546881 original size:5 final size:5
Alignment explanation
Indices: 20546871--20546895 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
20546861 AGCTTGCACC
20546871 AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT
20546896 TTATTTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Done.