Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008709.1 Hibiscus syriacus cultivar Beakdansim tig00111758_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3030657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 15
Found at i:2298778 original size:32 final size:32
Alignment explanation
Indices: 2298717--2298778 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
2298707 GTTATAATTT
* **
2298717 TATCATGTTTAAATGTTTAATTTTTTTAATAG
1 TATCATGTTTAAATGTTAAATTTCATTAATAG
2298749 TATCATGTTTAAAT-TTAAATATTCATTAAT
1 TATCATGTTTAAATGTTAAAT-TTCATTAAT
2298779 TAAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 5 0.19
32 21 0.81
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.53
Consensus pattern (32 bp):
TATCATGTTTAAATGTTAAATTTCATTAATAG
Found at i:2299085 original size:2 final size:2
Alignment explanation
Indices: 2299080--2299104 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2299070 TTTAATGTTG
2299080 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 T
2299105 TGTACCAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2300107 original size:2 final size:2
Alignment explanation
Indices: 2300100--2300126 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2300090 CATATACAAC
2300100 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2300127 AAGTATTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2300308 original size:32 final size:32
Alignment explanation
Indices: 2300271--2300334 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
2300261 TCCCAAAGGA
*
2300271 CCTGTCCATATGTCCCGAAGGACATAGGTAAT
1 CCTGTCCATATGTCCCGAAGAACATAGGTAAT
*
2300303 CCTGTCCATATGTCCCGGAGAACATAGGTAAT
1 CCTGTCCATATGTCCCGAAGAACATAGGTAAT
2300335 GTAACATCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (32 bp):
CCTGTCCATATGTCCCGAAGAACATAGGTAAT
Found at i:2301920 original size:7 final size:7
Alignment explanation
Indices: 2301908--2301951 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
2301898 ACTAAGATCA
2301908 ATGTGAT
1 ATGTGAT
*
2301915 ATGTGAC
1 ATGTGAT
2301922 ATGTGAAT
1 ATGTG-AT
2301930 ATGTGAT
1 ATGTGAT
*
2301937 ATGAGAT
1 ATGTGAT
*
2301944 ATATGAT
1 ATGTGAT
2301951 A
1 A
2301952 ATGAAAACTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (7 bp):
ATGTGAT
Found at i:2302026 original size:12 final size:12
Alignment explanation
Indices: 2302009--2302038 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2301999 GCCATGAGCT
2302009 TATATGAATATG
1 TATATGAATATG
*
2302021 TATATGAATGTG
1 TATATGAATATG
2302033 TATATG
1 TATATG
2302039 TGAAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (12 bp):
TATATGAATATG
Found at i:2302184 original size:30 final size:30
Alignment explanation
Indices: 2302116--2302207 Score: 114
Period size: 30 Copynumber: 3.0 Consensus size: 30
2302106 AGAGTCGAGG
* * *
2302116 GTTACCTATGTCTTTCGAGACATATATATA
1 GTTACCTATGTCTTTCGGGACATATGTACA
*
2302146 GTTTACCTATGTCTTTCGGGACATATGGACA
1 G-TTACCTATGTCTTTCGGGACATATGTACA
*
2302177 GTTACCTATGT-TCTTCGGAACATATGTACA
1 GTTACCTATGTCT-TTCGGGACATATGTACA
2302207 G
1 G
2302208 GTCCTTCGGG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.02
30 27 0.50
31 26 0.48
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (30 bp):
GTTACCTATGTCTTTCGGGACATATGTACA
Found at i:2308973 original size:54 final size:54
Alignment explanation
Indices: 2308891--2308999 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
2308881 AGGTAGTTAA
2308891 GAGAGCCTTAGATAGGCAGACTAGGCAGTATAGTAAGGGTACAAGACAGGTCAG
1 GAGAGCCTTAGATAGGCAGACTAGGCAGTATAGTAAGGGTACAAGACAGGTCAG
2308945 GAGAGCCTTAGATAGGCAGACTAGGCAGTATAGTAAGGGTACAAGACAGGTCAG
1 GAGAGCCTTAGATAGGCAGACTAGGCAGTATAGTAAGGGTACAAGACAGGTCAG
2308999 G
1 G
2309000 GTTCTTCAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.35, C:0.15, G:0.34, T:0.17
Consensus pattern (54 bp):
GAGAGCCTTAGATAGGCAGACTAGGCAGTATAGTAAGGGTACAAGACAGGTCAG
Found at i:2323049 original size:20 final size:20
Alignment explanation
Indices: 2323024--2323061 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2323014 ATACTTGATC
* *
2323024 CTAGAGTATCGATACTACAA
1 CTAGAGTACCAATACTACAA
2323044 CTAGAGTACCAATACTAC
1 CTAGAGTACCAATACTAC
2323062 CCATCTCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (20 bp):
CTAGAGTACCAATACTACAA
Found at i:2324101 original size:32 final size:32
Alignment explanation
Indices: 2324056--2324145 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
2324046 AGCTTGTGTG
2324056 ATGCATAGAAGAGTCAATATTGCATTCAAATA
1 ATGCATAGAAGAGTCAATATTGCATTCAAATA
* * *
2324088 ATGCATAGTAGAGTCAATATTGTATTCAGATA
1 ATGCATAGAAGAGTCAATATTGCATTCAAATA
* *
2324120 ATGTATAGAAGAGTTAATATTGCATT
1 ATGCATAGAAGAGTCAATATTGCATT
2324146 TAGACAGTGC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (32 bp):
ATGCATAGAAGAGTCAATATTGCATTCAAATA
Found at i:2327162 original size:8 final size:8
Alignment explanation
Indices: 2327146--2327179 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
2327136 TTTTTTTCAT
2327146 TATTATTA
1 TATTATTA
*
2327154 TAATATTA
1 TATTATTA
2327162 TATTATTAA
1 TATTATT-A
2327171 TATTATTA
1 TATTATTA
2327179 T
1 T
2327180 TATAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATTA
Found at i:2328450 original size:3 final size:3
Alignment explanation
Indices: 2328440--2328498 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
2328430 TTTGCAATAA
* * *
2328440 TAT T-T TAT TAT TAT TAT TAT TGCT T-T AAT TAT TAT T-T CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
*
2328483 TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT T
2328499 TATATAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
2 4 0.09
3 39 0.87
4 2 0.04
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2328458 original size:29 final size:30
Alignment explanation
Indices: 2328413--2328490 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 30
2328403 TTTTAATTCC
*
2328413 TTTTATT-TTAATCATTATTTGCAATAA-TA
1 TTTTATTATT-ATTATTATTTGCAATAATTA
**
2328442 TTTTATTATTATTATTA-TTGCTTTAATTA
1 TTTTATTATTATTATTATTTGCAATAATTA
*
2328471 TTATT-TCATTATTATTATTT
1 TT-TTATTATTATTATTATTT
2328491 TTATTATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 7 0.17
29 28 0.68
30 6 0.15
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (30 bp):
TTTTATTATTATTATTATTTGCAATAATTA
Found at i:2328512 original size:23 final size:22
Alignment explanation
Indices: 2328468--2328524 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
2328458 ATTGCTTTAA
* *
2328468 TTATTATTTCATTATTATTATTT
1 TTATTATTT-ATTAATAATATTT
2328491 TTATTATTTATATAATAATATTT
1 TTATTATTTAT-TAATAATATTT
*
2328514 GT-TTATTTATT
1 TTATTATTTATT
2328525 CTATTGTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 10 0.33
23 19 0.63
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTATTTATTAATAATATTT
Found at i:2330928 original size:12 final size:12
Alignment explanation
Indices: 2330911--2330938 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2330901 ACATTCACAT
2330911 ATTTACATTTGC
1 ATTTACATTTGC
2330923 ATTTACATTTGC
1 ATTTACATTTGC
2330935 ATTT
1 ATTT
2330939 TTTATGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:2333595 original size:11 final size:11
Alignment explanation
Indices: 2333581--2333622 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
2333571 GAAGAAGGAA
2333581 AAAGAAAAAAG
1 AAAGAAAAAAG
2333592 AAAGAAAAAAG
1 AAAGAAAAAAG
* *
2333603 AAAAAAAGAAAA
1 AAAGAAA-AAAG
2333615 AAAGAAAA
1 AAAGAAAA
2333623 GAAAAAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:2333596 original size:28 final size:28
Alignment explanation
Indices: 2333564--2333656 Score: 99
Period size: 27 Copynumber: 3.4 Consensus size: 28
2333554 CTCATCCAGC
2333564 AAAGAAAGAAGAAGGAAAAAGAAAAAAG-
1 AAAGAAA-AAGAAGGAAAAAGAAAAAAGA
2333592 AAAGAAAAAAGAA--AAAAAGAAAAAAAGA
1 AAAG-AAAAAGAAGGAAAAAG-AAAAAAGA
*
2333620 AAAGAAAAA-AAGG-AAAAGAAAAAAAGG
1 AAAGAAAAAGAAGGAAAAAG-AAAAAAGA
2333647 AAA-AAAAAGA
1 AAAGAAAAAGA
2333657 GGAGAAATTG
Statistics
Matches: 58, Mismatches: 1, Indels: 13
0.81 0.01 0.18
Matches are distributed among these distances:
26 13 0.22
27 29 0.50
28 13 0.22
29 3 0.05
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (28 bp):
AAAGAAAAAGAAGGAAAAAGAAAAAAGA
Found at i:2333607 original size:8 final size:8
Alignment explanation
Indices: 2333579--2333653 Score: 78
Period size: 8 Copynumber: 8.6 Consensus size: 8
2333569 AAGAAGAAGG
2333579 AAAAAGAA
1 AAAAAGAA
*
2333587 AAAAGAAAGA
1 AAAA-AGA-A
2333597 AAAAAGAA
1 AAAAAGAA
2333605 AAAAAGAA
1 AAAAAGAA
2333613 AAAAAGAA
1 AAAAAGAA
*
2333621 AAGAAAAAA
1 AA-AAAGAA
2333630 AGGAAAAGAA
1 A--AAAAGAA
2333640 AAAAAGGAA
1 AAAAA-GAA
2333649 AAAAA
1 AAAAA
2333654 AGAGGAGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 27 0.47
9 18 0.32
10 11 0.19
11 1 0.02
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:2333622 original size:14 final size:14
Alignment explanation
Indices: 2333564--2333651 Score: 85
Period size: 15 Copynumber: 6.2 Consensus size: 14
2333554 CTCATCCAGC
2333564 AAAGAAAGAAGAAGGAA
1 AAAGAAA-AA-AA-GAA
2333581 AAAG-AAAAAAG--
1 AAAGAAAAAAAGAA
*
2333592 AAAGAAAAAAGAAAA
1 AAAGAAAAAA-AGAA
2333607 AAAGAAAAAAAG-A
1 AAAGAAAAAAAGAA
*
2333620 AAAGAAAAAAAGGA
1 AAAGAAAAAAAGAA
2333634 AAAGAAAAAAAGGAA
1 AAAGAAAAAAA-GAA
2333649 AAA
1 AAA
2333652 AAAGAGGAGA
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
11 4 0.06
12 5 0.08
13 15 0.24
14 15 0.24
15 17 0.27
16 2 0.03
17 4 0.06
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAGAA
Found at i:2333650 original size:6 final size:5
Alignment explanation
Indices: 2333580--2333656 Score: 58
Period size: 5 Copynumber: 16.2 Consensus size: 5
2333570 AGAAGAAGGA
* *
2333580 AAAAG AAAAA AGAAAG AAAA- AAGAAA AAAAG -AAA- AAAAG AAAAG AAAA-
1 AAAAG AAAAG A-AAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG
* *
2333628 AAAGG AAAAG AAAA- AAAGG AAAA- AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
2333657 GGAGAAATTG
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
4 18 0.32
5 33 0.58
6 6 0.11
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2333651 original size:7 final size:7
Alignment explanation
Indices: 2333579--2333643 Score: 59
Period size: 7 Copynumber: 9.7 Consensus size: 7
2333569 AAGAAGAAGG
2333579 AAAAAGA
1 AAAAAGA
2333586 AAAAAG-
1 AAAAAGA
2333592 --AAAGA
1 AAAAAGA
2333597 AAAAAGAA
1 AAAAAG-A
2333605 AAAAAGA
1 AAAAAGA
2333612 AAAAA-A
1 AAAAAGA
*
2333618 GAAAAGA
1 AAAAAGA
2333625 AAAAA-A
1 AAAAAGA
*
2333631 GGAAAAGA
1 -AAAAAGA
2333639 AAAAA
1 AAAAA
2333644 AGGAAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
4 4 0.09
6 6 0.13
7 29 0.62
8 8 0.17
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:2333663 original size:23 final size:22
Alignment explanation
Indices: 2333585--2333656 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
2333575 AAGGAAAAAG
2333585 AAAAAAG-AAAG-AAAAAAG-A
1 AAAAAAGAAAAGAAAAAAAGAA
2333604 AAAAAAGAAAA-AAAGAAAAGAA
1 AAAAAAGAAAAGAAA-AAAAGAA
*
2333626 AAAAAGGAAAAGAAAAAAAGGAA
1 AAAAAAGAAAAGAAAAAAA-GAA
2333649 AAAAAAGA
1 AAAAAAGA
2333657 GGAGAAATTG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
19 7 0.16
20 5 0.11
21 5 0.11
22 15 0.33
23 13 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAAGAAAAAAAGAA
Found at i:2334937 original size:21 final size:21
Alignment explanation
Indices: 2334895--2334937 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2334885 TTTTCGGGCT
* * *
2334895 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
2334916 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
2334937 A
1 A
2334938 CAAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:2335021 original size:64 final size:65
Alignment explanation
Indices: 2334917--2335062 Score: 217
Period size: 64 Copynumber: 2.3 Consensus size: 65
2334907 ACCCATTCAA
* *
2334917 GGGGAACCGATACCCCCTCAACAAATATGAATTTCCAGAATGCTAGA-GGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAACCG-TA-CCCCA
2334981 -G
64 GG
*
2334982 GGGGAACCGATACCCCCTCAAC-GATATGAAATTCCAGAATGCTAGAGGGGAACCGTACCCCAGG
1 GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAACCGTACCCCAGG
*
2335046 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
2335063 ATTAGAAAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
63 5 0.07
64 41 0.55
65 29 0.39
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (65 bp):
GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAACCGTACCCCAGG
Found at i:2335738 original size:23 final size:23
Alignment explanation
Indices: 2335671--2335730 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
2335661 ATCATTATAT
*
2335671 GGCACTACGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
2335694 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
2335717 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
2335731 TTTATACGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:2341817 original size:21 final size:21
Alignment explanation
Indices: 2341775--2341817 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2341765 TTTTCGGGCT
* * *
2341775 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
2341796 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
2341817 A
1 A
2341818 CAAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:2341878 original size:67 final size:68
Alignment explanation
Indices: 2341797--2341948 Score: 252
Period size: 67 Copynumber: 2.2 Consensus size: 68
2341787 ACCCATTCAA
* *
2341797 GGGGAACCGATACCCCCTCAACAAATATGAATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCCA
2341862 -GG
66 GGG
**
2341864 GGGGAACCGATACCCCCTCAACGGATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCCA
2341929 GGG
66 GGG
*
2341932 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
2341949 ATTAGAAAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
67 61 0.77
68 18 0.23
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.14
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAACCGATACCCCCA
GGG
Found at i:2342626 original size:23 final size:23
Alignment explanation
Indices: 2342559--2342618 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
2342549 ATCATTAAAT
*
2342559 GGCACTACGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
2342582 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
2342605 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
2342619 TTTATACGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:2345010 original size:114 final size:114
Alignment explanation
Indices: 2344810--2345038 Score: 404
Period size: 114 Copynumber: 2.0 Consensus size: 114
2344800 AAGTGCCACA
* *
2344810 TTCTCATAGTAGAAATAAGGAGACCCAATATCATCTTTTGGAAGTGTTCTTTGAGTTATATGATC
1 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATC
* *
2344875 TAGTTTGGTATGAACCCTAAAACCGATCATTGGATTTGAAAGATGAATT
66 TAGTTTGGTATGAACCCTAAAACCAATCATTAGATTTGAAAGATGAATT
*
2344924 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATC
*
2344989 TGGTTTGGTATGAACCCTAAAACCAATCATTAGATTTGAAAGATGAATT
66 TAGTTTGGTATGAACCCTAAAACCAATCATTAGATTTGAAAGATGAATT
2345038 T
1 T
2345039 GATGATAGTC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 109 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Consensus pattern (114 bp):
TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATATGATC
TAGTTTGGTATGAACCCTAAAACCAATCATTAGATTTGAAAGATGAATT
Found at i:2346054 original size:76 final size:76
Alignment explanation
Indices: 2345973--2346144 Score: 222
Period size: 76 Copynumber: 2.3 Consensus size: 76
2345963 TAACAAGAAG
* *
2345973 CAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATATTGAAGTATTTTGAATA
1 CAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATATTGAAGCATTTTGAACA
*
2346038 TTTATATCAG-
66 CTTATATCAGT
* * * * * *
2346048 CAAAATGCTGGGGCATGATGAAAGCCCTTTTCAATCAGAATCAGGACTGTTGATGCATTTTGAAC
1 C-AAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATATTGAAGCATTTTGAAC
* *
2346113 ACTTGTATTAGT
65 ACTTATATCAGT
2346125 C-AATGTTGGGGCATGCTGAA
1 CAAATGTTGGGGCATGCTGAA
2346145 GGCCCATATC
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
75 18 0.22
76 63 0.77
77 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (76 bp):
CAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATATTGAAGCATTTTGAACA
CTTATATCAGT
Found at i:2347531 original size:22 final size:22
Alignment explanation
Indices: 2347483--2347525 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2347473 CTACACTCTT
2347483 CAAAGATGATAGATTCTCTTTG
1 CAAAGATGATAGATTCTCTTTG
2347505 CAAAGATGATAGATTCTCTTT
1 CAAAGATGATAGATTCTCTTT
2347526 TTAAAGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (22 bp):
CAAAGATGATAGATTCTCTTTG
Found at i:2348332 original size:76 final size:76
Alignment explanation
Indices: 2348206--2349009 Score: 1371
Period size: 76 Copynumber: 10.6 Consensus size: 76
2348196 CTATTTCCCA
* *
2348206 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGCTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2348271 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2348282 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2348347 AGCCTTAGTGT
66 AGCCTTAGGGT
2348358 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2348423 AGCCTTAGGGT
66 AGCCTTAGGGT
2348434 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2348499 AGCCTTAGGGT
66 AGCCTTAGGGT
2348510 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2348575 AGCCTTAGGGT
66 AGCCTTAGGGT
* * * *
2348586 CATCTGTAAGTCCTGCACTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAT
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2348651 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2348662 CATATGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2348727 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2348738 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2348803 AGCCTTATGGT
66 AGCCTTAGGGT
*
2348814 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
2348879 ATCCTTATGGT
66 AGCCTTAGGGT
*
2348890 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* **
2348955 AACCTTCTGGT
66 AGCCTTAGGGT
* * * * *
2348966 CGTCTATAAG-CCTTTCAGTGCATGATATTTTC-AAAA-CCTTCGGG
1 CATCTGTAAGTCC-TACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
2349010 TCATCTATAA
Statistics
Matches: 697, Mismatches: 30, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
74 8 0.01
75 6 0.01
76 683 0.98
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:2349004 original size:45 final size:45
Alignment explanation
Indices: 2348943--2349045 Score: 161
Period size: 45 Copynumber: 2.3 Consensus size: 45
2348933 GGGAGCTTTT
* * * *
2348943 TGATGTTTTTAAAACCTTCTGGTCGTCTATAAGCCTTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
*
2348988 TGATATTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
2349033 TGATGTTTTCAAA
1 TGATGTTTTCAAA
2349046 CATTTACATC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCA
Found at i:2349172 original size:3 final size:3
Alignment explanation
Indices: 2349164--2349264 Score: 193
Period size: 3 Copynumber: 33.3 Consensus size: 3
2349154 CAATTTTTTC
2349164 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2349212 ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT
2349258 ATT ATT A
1 ATT ATT A
2349265 AATAAAAAAT
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 94 0.97
4 3 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2350500 original size:12 final size:11
Alignment explanation
Indices: 2350485--2350559 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
2350475 TTAATTCCTT
2350485 TTATTTTAATCA
1 TTATTTTAAT-A
*
2350497 TTATTTGCAATA
1 TTATTT-TAATA
*
2350509 TTATTTTATTA
1 TTATTTTAATA
*
2350520 TTATTATTATTA
1 TTATT-TTAATA
**
2350532 TTGCTTTAATTA
1 TTATTTTAA-TA
* *
2350544 TTATTTCATTA
1 TTATTTTAATA
2350555 TTATT
1 TTATT
2350560 ATTTTTATTA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
11 18 0.36
12 29 0.58
13 3 0.06
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:2350520 original size:3 final size:3
Alignment explanation
Indices: 2350507--2350571 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
2350497 TTATTTGCAA
* *
2350507 TAT TAT T-T TAT TAT TAT TAT TAT TAT TGCT T-T AAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
* *
2350550 CAT TAT TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
2350572 TATATAATAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
2 4 0.08
3 45 0.88
4 2 0.04
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2350532 original size:32 final size:34
Alignment explanation
Indices: 2350496--2350568 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 34
2350486 TATTTTAATC
*
2350496 ATTATTTGC-AA-TATTATTTTATTATTATTATT
1 ATTATTTGCTAATTATTATTTCATTATTATTATT
2350528 ATTA-TTGCTTTAATTATTATTTCATTATTATTATT
1 ATTATTTGC--TAATTATTATTTCATTATTATTATT
*
2350563 TTTATT
1 ATTATT
2350569 ATTTATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 4 0.12
32 4 0.12
34 2 0.06
35 23 0.68
36 1 0.03
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (34 bp):
ATTATTTGCTAATTATTATTTCATTATTATTATT
Found at i:2352064 original size:27 final size:27
Alignment explanation
Indices: 2352026--2352095 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
2352016 ATTATGTCAT
2352026 TGCACGGAGTAATGTTTTTTTAAAGAA
1 TGCACGGAGTAATGTTTTTTTAAAGAA
2352053 TGCACGGAGTAATGTTTTTTTAAAGAA
1 TGCACGGAGTAATGTTTTTTTAAAGAA
*
2352080 TGCACGGAGCAATGTT
1 TGCACGGAGTAATGTT
2352096 AAGACCATTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.34
Consensus pattern (27 bp):
TGCACGGAGTAATGTTTTTTTAAAGAA
Found at i:2355818 original size:19 final size:19
Alignment explanation
Indices: 2355794--2355832 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2355784 ACAAGCGCTC
2355794 TACGGAACACCTTCATGAT
1 TACGGAACACCTTCATGAT
2355813 TACGGAACACCTTCATGAT
1 TACGGAACACCTTCATGAT
2355832 T
1 T
2355833 CCTTTTCGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (19 bp):
TACGGAACACCTTCATGAT
Found at i:2357765 original size:30 final size:30
Alignment explanation
Indices: 2357729--2357786 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2357719 AGTGAACCGG
*
2357729 CGGTTCAAACTGGTTTTACCGGTTTTCAGC
1 CGGTTCAAACCGGTTTTACCGGTTTTCAGC
** *
2357759 CGGTTCACCCCGGTTTTCCCGGTTTTCA
1 CGGTTCAAACCGGTTTTACCGGTTTTCA
2357787 ATCGGTTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.12, C:0.29, G:0.22, T:0.36
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTACCGGTTTTCAGC
Found at i:2360081 original size:14 final size:15
Alignment explanation
Indices: 2360062--2360101 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
2360052 TTTCTGTCTA
*
2360062 TATGCAGAGATTT-T
1 TATGCAGGGATTTAT
2360076 TATGCAGGGATTTAT
1 TATGCAGGGATTTAT
2360091 T-TGCAGGGATT
1 TATGCAGGGATT
2360102 ACTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.25, C:0.07, G:0.28, T:0.40
Consensus pattern (15 bp):
TATGCAGGGATTTAT
Found at i:2360574 original size:14 final size:15
Alignment explanation
Indices: 2360555--2360583 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2360545 CGTTGCCTTG
2360555 ATTTTCATAT-TTCT
1 ATTTTCATATATTCT
2360569 ATTTTCATATATTCT
1 ATTTTCATATATTCT
2360584 CTGTTCTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTCATATATTCT
Found at i:2363979 original size:18 final size:18
Alignment explanation
Indices: 2363937--2363984 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
2363927 TGTTTTTGAG
*
2363937 GGAATTAGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
2363955 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
2363973 GGAATTGAAATC
1 GGAATTGGAATC
2363985 CAATTCTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.38, C:0.06, G:0.29, T:0.27
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:2364177 original size:13 final size:13
Alignment explanation
Indices: 2364159--2364186 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2364149 ATTACATGTT
2364159 AATAAATTATAAA
1 AATAAATTATAAA
2364172 AATAAATTATAAA
1 AATAAATTATAAA
2364185 AA
1 AA
2364187 ATTTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAAATTATAAA
Found at i:2364869 original size:229 final size:231
Alignment explanation
Indices: 2364397--2364877 Score: 670
Period size: 229 Copynumber: 2.1 Consensus size: 231
2364387 TGAATTAGAA
* *
2364397 ACCCGACCCGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGTTACTTAATTGGAAAAAA
1 ACCCGACCCGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
* * *
2364462 ATATATATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATCTTT
66 AAATATATATATAGAGGGGTATTATTGTAATTATTCATAAATATATAAGGTAAAATTATA--TTA
* *
2364527 TTTGGGTTGGGTCGGGTCGGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCCGAACCGAAT
129 TAT--GTT--GTCAGGTCGGGTATTTTTCACCCTAAACCCAAACCCGACCCGA-CC--ACCGAAT
* *
2364592 ATCACACTTAAAAAAACTGACCCGACCAAAATAAAGTTTCACCCG
187 ATCACACTTAAAAAAACCGACCCGACCAAAACAAAGTTTCACCCG
*
2364637 ACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAA-AGTGACTTAATTGAAAAAAA
1 ACCCGACCCGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
2364701 AAAT-TATATATAGAGGGGTATTATTGTAATTATTCATAAATATATAAGGTAAAATTATA-TATA
66 AAATATATATATAGAGGGGTATTATTGTAATTATTCATAAATATATAAGGTAAAATTATATTATA
* * *
2364764 T-TT-TCAGGTCGGTTATTTTTCACCCTAAACCCGAACTCGACCCGA-C-CCGAATATCACACTT
131 TGTTGTCAGGTCGGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCACCGAATATCACACTT
2364825 AAAAAAACCGAACCGACCCGACCAAAACAAAGTTTCACCCG
196 --AAAAA---AACCGACCCGACCAAAACAAAGTTTCACCCG
2364866 ACCCGACCCGAA
1 ACCCGACCCGAA
2364878 TATATGAATT
Statistics
Matches: 223, Mismatches: 13, Indels: 21
0.87 0.05 0.08
Matches are distributed among these distances:
224 15 0.07
226 5 0.02
227 1 0.00
229 79 0.35
232 2 0.01
235 3 0.01
238 54 0.24
239 21 0.09
240 43 0.19
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.27
Consensus pattern (231 bp):
ACCCGACCCGAAATAATAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
AAATATATATATAGAGGGGTATTATTGTAATTATTCATAAATATATAAGGTAAAATTATATTATA
TGTTGTCAGGTCGGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCACCGAATATCACACTT
AAAAAAACCGACCCGACCAAAACAAAGTTTCACCCG
Found at i:2376806 original size:31 final size:31
Alignment explanation
Indices: 2376768--2376853 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
2376758 TAAATTAAGG
* *
2376768 TTTAGTACCTAAACTATCAATTTTGGTTTGT
1 TTTAGTACCTAAACTTTCAATTTTGGTCTGT
2376799 TTTAGTACCTAAACTTTCAATTTTGGTCTGT
1 TTTAGTACCTAAACTTTCAATTTTGGTCTGT
* *
2376830 TTTAGAACCCAAACTTTCAATTTT
1 TTTAGTACCTAAACTTTCAATTTT
2376854 TTCAAACTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (31 bp):
TTTAGTACCTAAACTTTCAATTTTGGTCTGT
Found at i:2378890 original size:20 final size:20
Alignment explanation
Indices: 2378865--2378902 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2378855 TGTTTAAAAG
2378865 CTCATTTA-TGTGCATTTAGT
1 CTCATTTAGT-TGCATTTAGT
2378885 CTCATTTAGTTGCATTTA
1 CTCATTTAGTTGCATTTA
2378903 TCATACTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.50
Consensus pattern (20 bp):
CTCATTTAGTTGCATTTAGT
Found at i:2384207 original size:20 final size:20
Alignment explanation
Indices: 2384166--2384218 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2384156 TTGATACTTT
*
2384166 TCAAGAGTTTCGAAACTATC
1 TCAAGAGTTTCAAAACTATC
* *
2384186 TCAAGAGTTTCAAAATTTTC
1 TCAAGAGTTTCAAAACTATC
2384206 TCTAA-AGTTTCAA
1 TC-AAGAGTTTCAA
2384219 TACTTTGGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (20 bp):
TCAAGAGTTTCAAAACTATC
Found at i:2397818 original size:22 final size:21
Alignment explanation
Indices: 2397790--2397835 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2397780 TCGGAAATGT
* *
2397790 TAAAAAATATTAATGTTTTAGG
1 TAAAAAA-AATAATATTTTAGG
2397812 TAAAAAAAATAATATTTTAGG
1 TAAAAAAAATAATATTTTAGG
2397833 TAA
1 TAA
2397836 TATTTTACCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (21 bp):
TAAAAAAAATAATATTTTAGG
Found at i:2402896 original size:31 final size:31
Alignment explanation
Indices: 2402823--2402896 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 31
2402813 TTTTACAAGC
* * *
2402823 TTTGGAAAAA-TTCAGGGATCATTTTGTAAT
1 TTTGGAAAAAGTTGAGGGACCAATTTGTAAT
*
2402853 TTTTG-AAAAGTTGAGGGACCAATTTGTAAT
1 TTTGGAAAAAGTTGAGGGACCAATTTGTAAT
2402883 TTTGGAAAAAGTTG
1 TTTGGAAAAAGTTG
2402897 GGAATGGTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 4 0.11
30 25 0.68
31 8 0.22
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (31 bp):
TTTGGAAAAAGTTGAGGGACCAATTTGTAAT
Found at i:2404286 original size:38 final size:38
Alignment explanation
Indices: 2404227--2404389 Score: 192
Period size: 38 Copynumber: 4.4 Consensus size: 38
2404217 CTTAAGGAGT
* *
2404227 GGTCCTAT-GGGACACATATGACATCCTTCGAGATAATA
1 GGTCCT-TCGGGACACATATGACATCCTTCGGGATGATA
* * *
2404265 AGT-CTTACGGGACACAGATGACATCCTGCGGGATGATA
1 GGTCCTT-CGGGACACATATGACATCCTTCGGGATGATA
*
2404303 GGTCCTTCGGGACACATATCACATCCTTCGGGATGATA
1 GGTCCTTCGGGACACATATGACATCCTTCGGGATGATA
* *
2404341 GGTCCTTCGGGACAC--AT-ACATCCTTTGGGATTATA
1 GGTCCTTCGGGACACATATGACATCCTTCGGGATGATA
*
2404376 GGTTCTTCGGGACA
1 GGTCCTTCGGGACA
2404390 TTTATACGAG
Statistics
Matches: 110, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
35 29 0.26
36 3 0.03
37 2 0.02
38 73 0.66
39 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (38 bp):
GGTCCTTCGGGACACATATGACATCCTTCGGGATGATA
Found at i:2404481 original size:12 final size:12
Alignment explanation
Indices: 2404464--2404495 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2404454 CTCAGTACTG
2404464 TACATGGGCTAA
1 TACATGGGCTAA
*
2404476 TACATGGACTAA
1 TACATGGGCTAA
2404488 TACATGGG
1 TACATGGG
2404496 ATTATAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (12 bp):
TACATGGGCTAA
Found at i:2404750 original size:18 final size:18
Alignment explanation
Indices: 2404727--2404792 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 18
2404717 AAATGTATTA
*
2404727 CATGATAATAATAGAGAT
1 CATGATAATGATAGAGAT
**
2404745 CATGATAATGATATTGAT
1 CATGATAATGATAGAGAT
** *
2404763 GTTGATAATGATAGATAT
1 CATGATAATGATAGAGAT
2404781 CATGATAATGAT
1 CATGATAATGAT
2404793 GTTGATAATG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (18 bp):
CATGATAATGATAGAGAT
Found at i:2404777 original size:36 final size:36
Alignment explanation
Indices: 2404729--2404798 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
2404719 ATGTATTACA
2404729 TGATAATAATAGAGATCATGATAATGATATTGATGT
1 TGATAATAATAGAGATCATGATAATGATATTGATGT
* * *
2404765 TGATAATGATAGATATCATGATAATGATGTTGAT
1 TGATAATAATAGAGATCATGATAATGATATTGAT
2404799 AATGAGGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (36 bp):
TGATAATAATAGAGATCATGATAATGATATTGATGT
Found at i:2404803 original size:18 final size:18
Alignment explanation
Indices: 2404746--2404803 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
2404736 AATAGAGATC
* *
2404746 ATGATAATGATATTGATG
1 ATGATAATGATGTTGATA
* * *
2404764 TTGATAATGATAGAT-ATC
1 ATGATAATGAT-GTTGATA
2404782 ATGATAATGATGTTGATA
1 ATGATAATGATGTTGATA
2404800 ATGA
1 ATGA
2404804 GGCATATATA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
17 2 0.06
18 28 0.90
19 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.38
Consensus pattern (18 bp):
ATGATAATGATGTTGATA
Found at i:2407383 original size:13 final size:13
Alignment explanation
Indices: 2407352--2407376 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2407342 TTATTTCACT
2407352 GAAAATATTTTTA
1 GAAAATATTTTTA
2407365 GAAAATATTTTT
1 GAAAATATTTTT
2407377 GTAAAATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
GAAAATATTTTTA
Found at i:2407525 original size:22 final size:24
Alignment explanation
Indices: 2407491--2407550 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
2407481 ATATAATAAA
2407491 TAATATTATTTATTATAAAAAT-T
1 TAATATTATTTATTATAAAAATAT
*
2407514 TAATATTA-TTATTTTAAAAATAT
1 TAATATTATTTATTATAAAAATAT
* *
2407537 TAAAATAATTTATT
1 TAATATTATTTATT
2407551 TAATATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.38
23 15 0.47
24 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TAATATTATTTATTATAAAAATAT
Found at i:2407735 original size:23 final size:22
Alignment explanation
Indices: 2407675--2407736 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
2407665 TCTTTAAAAA
*
2407675 TAAAA-TA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
2407695 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
2407718 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
2407737 TATAATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 5 0.15
21 2 0.06
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:2407809 original size:23 final size:22
Alignment explanation
Indices: 2407765--2407853 Score: 63
Period size: 23 Copynumber: 3.8 Consensus size: 22
2407755 ATATAAATAT
* * *
2407765 ATAAATAA-AATATTACTGTTA
1 ATAATTAATAATATTATTTTTA
2407786 ATAATTCAATAATATTATTTTTA
1 ATAATT-AATAATATTATTTTTA
* *
2407809 AGAATTAATAAAATATAACTTTTTA
1 ATAATTAAT--AATATTA-TTTTTA
*
2407834 ATAATTTATTATATATTATT
1 ATAA-TTAATA-ATATTATT
2407854 AAAATAAGAA
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
21 5 0.09
22 5 0.09
23 16 0.30
24 9 0.17
25 14 0.26
26 4 0.08
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (22 bp):
ATAATTAATAATATTATTTTTA
Found at i:2408269 original size:265 final size:271
Alignment explanation
Indices: 2407951--2408456 Score: 897
Period size: 270 Copynumber: 1.9 Consensus size: 271
2407941 TAATAATATG
2407951 TTAATAATAATATTTTTATTAAATGATAATAAAATATCAATTAATATTAAATTTATAAAATAATA
1 TTAATAATAATATTTTTATTAAATGATAATAAAATATCAATTAATATTAAATTTATAAAATAATA
2408016 TTATTTTGAGTATTTA-GTTTTAAACTGAAAAG-TTAAAAAATAACTTAC-AAAAATTAAATCAT
66 -T-TTTTGAGTATTTATGTTTTAAACTGAAAAGTTTAAAAAATAACTTACAAAAAATTAAATCAT
2408078 AAGTTAATTTTAG-AAA-ATAAAAAAATTA-TGATCAAAAA-ATATTTTACATTGTTCAATCTGT
129 AAGTTAATTTTAGAAAATATAAAAAAATTATTGATCAAAAATATATTTTACATTGTTCAATCTGT
2408139 TTTCTTCCAACCAAATATTAAAAAATGAG-AAAATATTTTTCAAAAAAATATATTGTTATATTAT
194 TTTCTTCCAACCAAATATTAAAAAATGAGAAAAATATTTTTCAAAAAAATATATTGTTATATTAT
2408203 ATTATTAAAAATA
259 ATTATTAAAAATA
2408216 TTAATAATTAATATTTTTATTAAAATGATAATAAAATATC-A-TAATATTAAATTTATAAAATAA
1 TTAATAA-TAATATTTTTATT-AAATGATAATAAAATATCAATTAATATTAAATTTATAAAATAA
2408279 TATTTTTGAGTATTTATGTTTTAAACTGAAAAGTTTAAAAAATAACTTACAAAAAATTAAATCAT
64 TATTTTTGAGTATTTATGTTTTAAACTGAAAAGTTTAAAAAATAACTTACAAAAAATTAAATCAT
*
2408344 AAGTTAATTTTAGAAAATATAAAAAAATTATTGATCAAAAATATATTTTACATTGTTCGATCTGT
129 AAGTTAATTTTAGAAAATATAAAAAAATTATTGATCAAAAATATATTTTACATTGTTCAATCTGT
2408409 TTTCTTCCAACCAAATATTAAAAAATGAGAAAAATATTTTTCAAAAAA
194 TTTCTTCCAACCAAATATTAAAAAATGAGAAAAATATTTTTCAAAAAA
2408457 TATTTTTATT
Statistics
Matches: 230, Mismatches: 1, Indels: 14
0.94 0.00 0.06
Matches are distributed among these distances:
263 13 0.06
264 17 0.07
265 47 0.20
266 41 0.18
267 21 0.09
268 12 0.05
269 10 0.04
270 51 0.22
271 18 0.08
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (271 bp):
TTAATAATAATATTTTTATTAAATGATAATAAAATATCAATTAATATTAAATTTATAAAATAATA
TTTTTGAGTATTTATGTTTTAAACTGAAAAGTTTAAAAAATAACTTACAAAAAATTAAATCATAA
GTTAATTTTAGAAAATATAAAAAAATTATTGATCAAAAATATATTTTACATTGTTCAATCTGTTT
TCTTCCAACCAAATATTAAAAAATGAGAAAAATATTTTTCAAAAAAATATATTGTTATATTATAT
TATTAAAAATA
Found at i:2408467 original size:39 final size:39
Alignment explanation
Indices: 2408424--2408503 Score: 128
Period size: 40 Copynumber: 2.1 Consensus size: 39
2408414 TCCAACCAAA
2408424 TATT-AAAAAATGAGAAAA-ATATTTTTCAAAAAATATTTT
1 TATTAAAAAAATGAGAAAATAT-TTTTTC-AAAAATATTTT
2408463 TATTAAAAAAATGAGAAAATATTTTTTCAAAAATATTTT
1 TATTAAAAAAATGAGAAAATATTTTTTCAAAAATATTTT
2408502 TA
1 TA
2408504 AGTAAATACC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
39 17 0.44
40 20 0.51
41 2 0.05
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (39 bp):
TATTAAAAAAATGAGAAAATATTTTTTCAAAAATATTTT
Found at i:2413239 original size:20 final size:21
Alignment explanation
Indices: 2413216--2413256 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2413206 TATTATATGT
**
2413216 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
2413236 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
2413257 TAAAATATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:2414166 original size:19 final size:19
Alignment explanation
Indices: 2414142--2414178 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2414132 TTTTTTTTTT
2414142 TTTTTTTTTTCTTTCTCTG
1 TTTTTTTTTTCTTTCTCTG
2414161 TTTTTTTTTTCTTTCTCT
1 TTTTTTTTTTCTTTCTCT
2414179 CCGGTTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (19 bp):
TTTTTTTTTTCTTTCTCTG
Found at i:2414461 original size:15 final size:15
Alignment explanation
Indices: 2414441--2414479 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
2414431 CGCCGCGTGG
2414441 CCCTAGGGTATCAAA
1 CCCTAGGGTATCAAA
2414456 CCCTAGGGTATCAAA
1 CCCTAGGGTATCAAA
2414471 CCCTAGGGT
1 CCCTAGGGT
2414480 TTCCCTCTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (15 bp):
CCCTAGGGTATCAAA
Found at i:2414702 original size:3 final size:3
Alignment explanation
Indices: 2414694--2414779 Score: 145
Period size: 3 Copynumber: 28.7 Consensus size: 3
2414684 AATATATATT
*
2414694 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2414742 TAA TAA TAA TAG TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2414780 TGGATAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2415138 original size:114 final size:115
Alignment explanation
Indices: 2414917--2415671 Score: 1048
Period size: 114 Copynumber: 6.6 Consensus size: 115
2414907 ATTGAATAAA
* * ** * *
2414917 TTCTTC-TCTTTCTTCAGAT-GAGTTCTTCTCATTATGAACTTTCT-GCTGGGGATGATGATCCA
1 TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAAC--TCTACCTGGCAAAGATAATCCA
* * * *
2414979 TCAA-ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
64 TCAACTTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * *
2415030 TTC-TCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCT-GCAATGTTGATCCA
1 TTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
* * * *
2415093 TCAA-ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
64 TCAACTTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
2415144 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
1 TTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
* *
2415209 TCAACTTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
64 TCAACTTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
2415261 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
1 TTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
**
2415326 TCAACTTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
64 TCAACTTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * *
2415378 TTATTCTTCCTTCTTCAGATA-AGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATAATCCAT
1 TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATAATCCAT
* *
2415441 CAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 CAACTTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
2415492 TTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATAATCCAT
1 TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATAATCCAT
* *
2415555 CAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 CAACTTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
2415606 TTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACTTTACCTGGCAAAGATAATCTATC
1 TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATC
2415670 AA
66 AA
2415672 ATGATAGATT
Statistics
Matches: 605, Mismatches: 25, Indels: 23
0.93 0.04 0.04
Matches are distributed among these distances:
112 2 0.00
113 17 0.03
114 323 0.53
115 50 0.08
116 36 0.06
117 177 0.29
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (115 bp):
TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATC
AACTTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:2415405 original size:231 final size:229
Alignment explanation
Indices: 2414916--2415676 Score: 1063
Period size: 231 Copynumber: 3.3 Consensus size: 229
2414906 TATTGAATAA
* * ** * *
2414916 ATTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT-GCTGGGGATGATGATCCAT
1 ATTCTTC-C-TTCTTCAGATAAGTTCTTCTCATTATGAAC--TCTACCTGGCAAAGATAATCCAT
* *
2414980 CAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTC-TCTTCCTTCTT
62 CAATTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
* * * *
2415044 CAGATGACGAGTTCTTCTCATTATGAACTCTACCT-GCAATGTTGATCCATCAAATGATGAATTC
127 CAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAATTGATGAATTC
* * *
2415108 A-AGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTT
192 AGA-AAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
*
2415146 CTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATC
1 ATTCTTCCTTCTTCAGAT-A--AGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATC
2415211 AACTTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
63 AA-TTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
2415276 CAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATGAATT
127 CAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAA-TTGATGAATT
2415341 CAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
191 CAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
* *
2415380 ATTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATAATCCATCAA
1 ATTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATAATCCATCAA
* * *
2415444 TTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
65 -TTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* *
2415509 GAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTC
129 GATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGATAATCCATCAA-TTGATGAATTC
**
2415570 AGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
192 AGAAAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
* * * * *
2415608 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGCAAAGATAATCTATCAAA
1 ATTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAAT
2415673 TGAT
66 TGAT
2415677 AGATTTGAAT
Statistics
Matches: 485, Mismatches: 34, Indels: 27
0.89 0.06 0.05
Matches are distributed among these distances:
227 7 0.01
228 153 0.32
229 6 0.01
230 25 0.05
231 171 0.35
232 46 0.09
233 16 0.03
234 60 0.12
235 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (229 bp):
ATTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAAT
TGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAATTGATGAATTCAGAA
AAAAGGTTGAACAAATTCTTCTCATTATGAACTT
Found at i:2415949 original size:117 final size:116
Alignment explanation
Indices: 2415796--2416551 Score: 1026
Period size: 114 Copynumber: 6.6 Consensus size: 116
2415786 ATTGAATAAA
* * ** * *
2415796 TTCTTC-TCTTTCTTCAGAT-GAGTTCTTCTCATTATGAACTTTCT-GCTGGGGATGATGATCCA
1 TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAAC-TTCTACCTGGCAAAGATAATCCA
* *
2415858 TCAA-ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 TCAACTTGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
* * *
2415909 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAAC-TCTACCT-GCAATGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTTCTACCTGGCAAAGATAATCC
* *
2415972 ATCAA-ATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
64 ATCAACTTGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
2416024 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAAC-TCTACCTGGCAAAGATAATCC
1 TTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTTCTACCTGGCAAAGATAATCC
* *
2416088 ATCAACTTGATGAATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
64 ATCAACTTGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
2416141 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAAC-TCTACCTGGCAAAGATAATCC
1 TTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTTCTACCTGGCAAAGATAATCC
* *
2416205 ATCAACTTGATGAATTC-AGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
64 ATCAACTTGATGAATTCAAG-CAAAAGATTGAACAAATTCTTCTCATTATGAAC
* *
2416258 TTATTCTTCCTTCTTCAGATA-AGTTCTTCTCATTATGAACTT-T-CTCTGGAAAAGATAATCCA
1 TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTTCTAC-CTGGCAAAGATAATCCA
* * * * *
2416320 TCAATTTGATGAATTTAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 TCAACTTGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
*
2416372 TTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACCTTCT--CTGGAAAAGATAATCCA
1 TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAA-CTTCTACCTGGCAAAGATAATCCA
* * * *
2416434 TCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAAC
65 TCAACTTGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
*
2416486 TTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACTT-TACCTGGCAAAGATAATCTAT
1 TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTTCTACCTGGCAAAGATAATCCAT
2416549 CAA
66 CAA
2416552 ATGATAGATT
Statistics
Matches: 603, Mismatches: 24, Indels: 31
0.92 0.04 0.05
Matches are distributed among these distances:
112 1 0.00
113 10 0.02
114 257 0.43
115 120 0.20
116 20 0.03
117 195 0.32
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (116 bp):
TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTTCTACCTGGCAAAGATAATCCAT
CAACTTGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
Found at i:2416595 original size:880 final size:879
Alignment explanation
Indices: 2414896--2416660 Score: 3512
Period size: 880 Copynumber: 2.0 Consensus size: 879
2414886 TACTTTGATC
2414896 ATGATGGAAATATTGAATAAATTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1 ATGATGGAAATATTGAATAAATTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
2414961 GCTGGGGATGATGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTAT
66 GCTGGGGATGATGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTAT
2415026 GAACTTCTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGCAATGTTGATC
131 GAACTTCTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGCAATGTTGATC
2415091 CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT
196 CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT
2415156 CTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATGA
261 CTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATGA
2415221 ATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGA
326 ATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGA
2415286 GTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATGAATTCAGAAAAAAG
391 GTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATGAATTCAGAAAAAAG
2415351 GTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
456 GTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
2415416 ACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTC
521 ACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTC
2415481 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAG
586 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAG
2415546 ATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT
651 ATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT
2415611 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGCAAAGATAATCTATCAAATGA
716 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGCAAAGATAATCTATCAAATGA
2415676 TAGATTTGAATCTTTGCTAAAATCTTTGAAATTCCTGTTAAAAATTCAACAAGAATAAAAATGAA
781 TAGATTTGAATCTTTGCTAAAATCTTTGAAATTCCTGTTAAAAATTCAACAAGAATAAAAATGAA
2415741 TGAAAATGCACCTATTTTTGTAAACACCTAAAAT
846 TGAAAATGCACCTATTTTTGTAAACACCTAAAAT
2415775 ATGATGGAAATATTGAATAAATTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
1 ATGATGGAAATATTGAATAAATTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
2415840 GCTGGGGATGATGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTAT
66 GCTGGGGATGATGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTAT
2415905 GAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGCAATGTTGAT
131 GAACTTC-TCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGCAATGTTGAT
2415970 CCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
195 CCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
2416035 TCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATG
260 TCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATG
2416100 AATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACG
325 AATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACG
2416165 AGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATGAATTCAGAAAAAA
390 AGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATGAATTCAGAAAAAA
2416230 GGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATAAGTTCTTCTCATTATG
455 GGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATAAGTTCTTCTCATTATG
*
2416295 AACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTTAGGTAAAAGGTTGAACAAATTCTT
520 AACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTT
2416360 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAA
585 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAA
2416425 GATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT
650 GATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT
2416490 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGCAAAGATAATCTATCAAATG
715 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGCAAAGATAATCTATCAAATG
2416555 ATAGATTTGAATCTTTGCTAAAATCTTTGAAATTCCTGTTAAAAATTCAACAAGAATAAAAATGA
780 ATAGATTTGAATCTTTGCTAAAATCTTTGAAATTCCTGTTAAAAATTCAACAAGAATAAAAATGA
2416620 ATGAAAATGCACCTATTTTTGTAAACACCTAAAAT
845 ATGAAAATGCACCTATTTTTGTAAACACCTAAAAT
2416655 ATGATG
1 ATGATG
2416661 CATGAATTTT
Statistics
Matches: 884, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
879 137 0.15
880 747 0.85
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (879 bp):
ATGATGGAAATATTGAATAAATTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCT
GCTGGGGATGATGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTAT
GAACTTCTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGCAATGTTGATC
CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT
CTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATGA
ATTCAGGCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGA
GTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCATCAACTTGATGAATTCAGAAAAAAG
GTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGA
ACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTC
TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAG
ATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT
CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTACCTGGCAAAGATAATCTATCAAATGA
TAGATTTGAATCTTTGCTAAAATCTTTGAAATTCCTGTTAAAAATTCAACAAGAATAAAAATGAA
TGAAAATGCACCTATTTTTGTAAACACCTAAAAT
Found at i:2417546 original size:167 final size:166
Alignment explanation
Indices: 2417294--2417616 Score: 619
Period size: 167 Copynumber: 1.9 Consensus size: 166
2417284 CCTACTGAAT
*
2417294 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCCAAATTCAA
2417359 TGATTGGTTCTGTCTAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
66 TGATTGGTTCTGTCTAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
2417424 TTCATCTTCCAAATTCAATGATTGGTTCTGCCAATC
131 TTCATCTTCCAAATTCAATGATTGGTTCTGCCAATC
*
2417460 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACAAATTCATCTTCCAAATTCA
2417525 ATGATTGGTTCTGTCTAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAA
65 ATGATTGGTTCTGTCTAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAA
2417590 ATTCATCTTCCAAATTCAATGATTGGT
130 ATTCATCTTCCAAATTCAATGATTGGT
2417617 CTATGATATC
Statistics
Matches: 154, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
166 39 0.25
167 115 0.75
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (166 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACAAATTCATCTTCCAAATTCAA
TGATTGGTTCTGTCTAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
TTCATCTTCCAAATTCAATGATTGGTTCTGCCAATC
Found at i:2417549 original size:84 final size:83
Alignment explanation
Indices: 2417294--2417616 Score: 569
Period size: 83 Copynumber: 3.9 Consensus size: 83
2417284 CCTACTGAAT
*
2417294 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCCAAATTCA
2417358 ATGATTGGTTCTGTCTAAC
65 ATGATTGGTTCTGTCTAAC
*
2417377 CAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
*
2417442 TGATTGGTTCTG-CCAATC
66 TGATTGGTTCTGTCTAA-C
2417460 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-CAAATTCATCTTCCAAATTCA
2417525 ATGATTGGTTCTGTCTAAC
65 ATGATTGGTTCTGTCTAAC
*
2417544 CAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
2417609 TGATTGGT
66 TGATTGGT
2417617 CTATGATATC
Statistics
Matches: 230, Mismatches: 6, Indels: 8
0.94 0.02 0.03
Matches are distributed among these distances:
82 3 0.01
83 145 0.63
84 79 0.34
85 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
TGATTGGTTCTGTCTAAC
Found at i:2418746 original size:1 final size:1
Alignment explanation
Indices: 2418742--2418787 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
2418732 TTGACCCCCC
* * * *
2418742 TTTTTTCTTTTTTCTTTTTTTTTTTATTTTTTTTTTATTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2418788 CAAGCATAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.04, C:0.04, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:2418765 original size:11 final size:11
Alignment explanation
Indices: 2418757--2418787 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
2418747 TCTTTTTTCT
2418757 TTTTTTTTTTA
1 TTTTTTTTTTA
2418768 TTTTTTTTTTA
1 TTTTTTTTTTA
2418779 TTTTTTTTT
1 TTTTTTTTT
2418788 CAAGCATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.06, C:0.00, G:0.00, T:0.94
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:2430119 original size:20 final size:21
Alignment explanation
Indices: 2430096--2430136 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2430086 TATTATATGT
**
2430096 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
2430116 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
2430137 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:2431054 original size:18 final size:18
Alignment explanation
Indices: 2431031--2431065 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2431021 TTGTTGTTGT
2431031 TTTTTTTTTCTTTCTCTG
1 TTTTTTTTTCTTTCTCTG
2431049 TTTTTTTTTCTTTCTCT
1 TTTTTTTTTCTTTCTCT
2431066 CCGGTTCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTTTTTTCTTTCTCTG
Found at i:2431574 original size:3 final size:3
Alignment explanation
Indices: 2431566--2431660 Score: 145
Period size: 3 Copynumber: 31.7 Consensus size: 3
2431556 AATATATATT
* * *
2431566 TAA TAA TAA TAA TAA TAA TGA TGA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
2431614 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2431661 TGGATAAAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2435004 original size:2 final size:2
Alignment explanation
Indices: 2434997--2435053 Score: 80
Period size: 2 Copynumber: 28.5 Consensus size: 2
2434987 TTATAATTCT
2434997 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2435038 TA AA AA TA TGA TA TA T
1 TA TA TA TA T-A TA TA T
2435054 TAGCATGATA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.94
3 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2440767 original size:40 final size:41
Alignment explanation
Indices: 2440723--2440956 Score: 259
Period size: 40 Copynumber: 5.8 Consensus size: 41
2440713 AACCTAGTTT
* *
2440723 TCAAATTCGCAACGCAAATTTGT-AAA-TCGCAACACATAAG
1 TCAAATTCGCAACGCAAA-TAGTCAAATTCGCAACACAAAAG
* *
2440763 TCAAATTCGCAACGC-GATAGTCAAATTCACAACACAAAAG
1 TCAAATTCGCAACGCAAATAGTCAAATTCGCAACACAAAAG
* * * *
2440803 TCAAATTCGCAACACAAA-AGTCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACGCAAATAGTCAAATTCGCAACACAAAAG
* * *
2440843 TCAAATTCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAG
1 TCAAATTCGCAACGC-AAATAGTCAAATTCGCAACACAAAAG
* *
2440883 TCAAATTCGTAACGC-TATAGTCAAATTCGCAACACAAAAG
1 TCAAATTCGCAACGCAAATAGTCAAATTCGCAACACAAAAG
*
2440923 TCAAATTCGCAACGCAGAAT-TTCAAATTCGCAAC
1 TCAAATTCGCAACGCA-AATAGTCAAATTCGCAAC
2440957 TAGATTTTCG
Statistics
Matches: 160, Mismatches: 25, Indels: 17
0.79 0.12 0.08
Matches are distributed among these distances:
38 6 0.04
39 7 0.04
40 124 0.77
41 19 0.12
42 4 0.03
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.21
Consensus pattern (41 bp):
TCAAATTCGCAACGCAAATAGTCAAATTCGCAACACAAAAG
Found at i:2440772 original size:20 final size:20
Alignment explanation
Indices: 2440749--2440956 Score: 192
Period size: 20 Copynumber: 10.3 Consensus size: 20
2440739 AATTTGTAAA
2440749 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
2440769 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
* *
2440789 TCACAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
2440809 TCGCAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
2440829 TCGCAACGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
* **
2440849 TCGCAACGCGAATTTGT-AAA-
1 TCGCAACAC--ATAAGTCAAAT
*
2440869 TCGCAACACAGAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
* *
2440889 TCGTAACGC-TATAGTCAAAT
1 TCGCAACACATA-AGTCAAAT
*
2440909 TCGCAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
* * *
2440929 TCGCAACGCAGAATTTCAAAT
1 TCGCAACACATAA-GTCAAAT
2440950 TCGCAAC
1 TCGCAAC
2440957 TAGATTTTCG
Statistics
Matches: 156, Mismatches: 22, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
18 3 0.02
19 5 0.03
20 124 0.79
21 22 0.14
22 2 0.01
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.20
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:2440787 original size:60 final size:60
Alignment explanation
Indices: 2440723--2440920 Score: 283
Period size: 60 Copynumber: 3.3 Consensus size: 60
2440713 AACCTAGTTT
* *
2440723 TCAAATTCGCAACGCAAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACACAAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAG
* *
2440783 TCAAATTCACAACACAAA--AGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACACAAATTTGT-AAA-TCGCAACACAAAAGTCAAATTCGCAACGCGATAG
* * * * *
2440843 TCAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGTAACGCTATAG
1 TCAAATTCGCAACACAAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAG
2440903 TCAAATTCGCAACACAAA
1 TCAAATTCGCAACACAAA
2440921 AGTCAAATTC
Statistics
Matches: 121, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
58 2 0.02
59 3 0.02
60 111 0.92
61 3 0.02
62 2 0.02
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (60 bp):
TCAAATTCGCAACACAAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAG
Found at i:2440933 original size:60 final size:58
Alignment explanation
Indices: 2440723--2440956 Score: 279
Period size: 60 Copynumber: 3.9 Consensus size: 58
2440713 AACCTAGTTT
* * *
2440723 TCAAATTCGCAACGCAAATTTGTAAATCGCAACACATAAGTCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACACAAA--AGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAG
* *
2440783 TCAAATTCACAACACAAAAGTCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACACAAAAGT-AAA-TCGCAACACAGAAGTCAAATTCGCAACGCGATAG
* ** * *
2440843 TCAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGTAACGCTATAG
1 TCAAATTCGCAACAC-AA-AAGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAG
* *
2440903 TCAAATTCGCAACACAAAAGTCAAATTCGCAACGCAGAATTTCAAATTCGCAAC
1 TCAAATTCGCAACACAAAAGT-AAA-TCGCAACACAGAA-GTCAAATTCGCAAC
2440957 TAGATTTTCG
Statistics
Matches: 150, Mismatches: 17, Indels: 13
0.83 0.09 0.07
Matches are distributed among these distances:
58 4 0.03
59 8 0.05
60 119 0.79
61 17 0.11
62 2 0.01
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.21
Consensus pattern (58 bp):
TCAAATTCGCAACACAAAAGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAG
Found at i:2440993 original size:19 final size:19
Alignment explanation
Indices: 2440969--2441015 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
2440959 GATTTTCGAA
2440969 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
2440988 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
2441006 TTCGCAACAC
1 TTCGCAACAC
2441016 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:2441171 original size:14 final size:15
Alignment explanation
Indices: 2441152--2441189 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2441142 TCCCCATCTC
2441152 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
2441166 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
2441182 TAATTTTT
1 TAATTTTT
2441190 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:2442785 original size:20 final size:20
Alignment explanation
Indices: 2442762--2442824 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
2442752 AAACTTAAAT
2442762 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
2442782 TCGCAACGAGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
2442802 TCGCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
2442821 TCGC
1 TCGC
2442825 GTTGCGATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 8 0.20
20 32 0.80
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:2443286 original size:22 final size:22
Alignment explanation
Indices: 2443224--2443288 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
2443214 TCTGAGAGAT
*
2443224 GGAGAT-A-GACGGATTTCGCC
1 GGAGATGAGGACGGATTTCGTC
**
2443244 GGAGATGAGGACATATTTCGTC
1 GGAGATGAGGACGGATTTCGTC
* *
2443266 GGAGATGGGGACGGATGTCGTC
1 GGAGATGAGGACGGATTTCGTC
2443288 G
1 G
2443289 TAGAGAGTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 6 0.17
21 1 0.03
22 29 0.81
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.22
Consensus pattern (22 bp):
GGAGATGAGGACGGATTTCGTC
Found at i:2443469 original size:40 final size:40
Alignment explanation
Indices: 2443393--2443507 Score: 169
Period size: 40 Copynumber: 2.9 Consensus size: 40
2443383 ATATTGTGTT
* * *
2443393 TCGCATTGCGAATTTGAAATTCAGTGTTGCGAATTTGACTA
1 TCGCATTGCGAATTTG-ACTTCTGTGTTGCGGATTTGACTA
* *
2443434 TCGCGTTGCGAATTTGACTTTTGTGTTGCGGATTTGACTA
1 TCGCATTGCGAATTTGACTTCTGTGTTGCGGATTTGACTA
2443474 TCGCATTGCGAATTTGACTTCTGTGTTGC-GATTT
1 TCGCATTGCGAATTTGACTTCTGTGTTGCGGATTT
2443508 ACAAATTCGC
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 5 0.07
40 47 0.70
41 15 0.22
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (40 bp):
TCGCATTGCGAATTTGACTTCTGTGTTGCGGATTTGACTA
Found at i:2443502 original size:20 final size:19
Alignment explanation
Indices: 2443398--2443504 Score: 106
Period size: 20 Copynumber: 5.3 Consensus size: 19
2443388 GTGTTTCGCA
*
2443398 TTGCGAATTTGAAATTCAGTG
1 TTGCGAATTTG-ACTTC-GTG
*
2443419 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACT-TCGTG
*
2443439 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGAC-TTCGTG
* **
2443459 TTGCGGATTTGACTATCGCA
1 TTGCGAATTTGACT-TCGTG
2443479 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTC-GTG
2443499 TTGCGA
1 TTGCGA
2443505 TTTACAAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.04
20 54 0.76
21 14 0.20
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.40
Consensus pattern (19 bp):
TTGCGAATTTGACTTCGTG
Found at i:2443525 original size:40 final size:40
Alignment explanation
Indices: 2443400--2443528 Score: 118
Period size: 40 Copynumber: 3.2 Consensus size: 40
2443390 GTTTCGCATT
* * * * ***
2443400 GCGAATTTGAAATTCAGTGTTGCGAATTTGACTATCGCGTT
1 GCGAATTTG-ACTTCTGTGTTGCGGATTTGACAATCGCAAC
* * **
2443441 GCGAATTTGACTTTTGTGTTGCGGATTTGACTATCGCATT
1 GCGAATTTGACTTCTGTGTTGCGGATTTGACAATCGCAAC
2443481 GCGAATTTGACTTCTGTGTTGC-GATTT-ACAAATTCGCAAC
1 GCGAATTTGACTTCTGTGTTGCGGATTTGAC-AA-TCGCAAC
2443521 GCGAATTT
1 GCGAATTT
2443529 AGAAAATTGC
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.03
39 6 0.08
40 60 0.78
41 9 0.12
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.38
Consensus pattern (40 bp):
GCGAATTTGACTTCTGTGTTGCGGATTTGACAATCGCAAC
Found at i:2443528 original size:21 final size:20
Alignment explanation
Indices: 2443501--2443558 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
2443491 CTTCTGTGTT
2443501 GCGATTTACAAATTCGCAAC
1 GCGATTTACAAATTCGCAAC
* *
2443521 GCGAATTTAGAAAATT-GCAAT
1 GCG-ATTTA-CAAATTCGCAAC
*
2443542 GCGATTTACATATTCGC
1 GCGATTTACAAATTCGC
2443559 GTTGCGAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 4 0.13
20 10 0.32
21 12 0.39
22 5 0.16
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (20 bp):
GCGATTTACAAATTCGCAAC
Found at i:2444888 original size:18 final size:19
Alignment explanation
Indices: 2444853--2444889 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2444843 CACGGAATGT
2444853 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2444873 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2444890 TGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2445078 original size:36 final size:38
Alignment explanation
Indices: 2445029--2445105 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
2445019 ATAATATTAC
2445029 AAATTGTAAAATATTTATAT-ATTTTCTTTAAAAAATT
1 AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
* * *
2445066 AAATT-TATAATATTTATATAATTTTTTTTACAAAATT
1 AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
2445103 AAA
1 AAA
2445106 AATATAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 13 0.36
37 23 0.64
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (38 bp):
AAATTGTAAAATATTTATATAATTTTCTTTAAAAAATT
Found at i:2445512 original size:21 final size:22
Alignment explanation
Indices: 2445487--2445535 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
2445477 ACCAAACACC
2445487 CCCTAAATC-C-AAAATATCAAA
1 CCCTAAATCACTAAAATAT-AAA
*
2445508 CCCT-AATCACTAAACTATAAA
1 CCCTAAATCACTAAAATATAAA
2445529 CCCTAAA
1 CCCTAAA
2445536 CCTTAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 12 0.50
22 8 0.33
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (22 bp):
CCCTAAATCACTAAAATATAAA
Found at i:2452915 original size:45 final size:44
Alignment explanation
Indices: 2452864--2452953 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
2452854 GGTGGCGGGT
* *
2452864 GGTGAGGGTGTTGTTGATGAACCAGTTGT-TGTGGGTGGAGGTGGG
1 GGTGAGGGTGTTGTTAATG-ACCAGTTGTGGGTGGG-GGAGGTGGG
*
2452909 GGTGAGGGTGTTGTTAATGACCAGTTGTGGGTGGGGGTGGTGGG
1 GGTGAGGGTGTTGTTAATGACCAGTTGTGGGTGGGGGAGGTGGG
2452953 G
1 G
2452954 CTGGTGCTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
44 18 0.44
45 23 0.56
ACGTcount: A:0.12, C:0.04, G:0.53, T:0.30
Consensus pattern (44 bp):
GGTGAGGGTGTTGTTAATGACCAGTTGTGGGTGGGGGAGGTGGG
Found at i:2453278 original size:45 final size:44
Alignment explanation
Indices: 2453176--2453374 Score: 163
Period size: 45 Copynumber: 4.5 Consensus size: 44
2453166 TGGTGTGGGT
*
2453176 GGTGCTGATGATGATACAGTTGGGGCTTGTGGTGGGCGTGGTGC
1 GGTGCTGATGATGATACAGTTGGGGCTTGTGGTGGGGGTGGTGC
* * * * *
2453220 AGTGCTTAATGAT-ATA-A-TTAGGGCTTGTTGTGGGGGTGGTGTG
1 GGTGC-TGATGATGATACAGTTGGGGCTTGTGGTGGGGGTGGTG-C
* *
2453263 GGTGCTGATGATGATACAGTTGGGGCTCGAGGTGGGGGTGGTGC
1 GGTGCTGATGATGATACAGTTGGGGCTTGTGGTGGGGGTGGTGC
* * * * * * *
2453307 AGATGCTGATGAGGAAATA-TTGGGGCTTCTGGTTGGGGTGATGC
1 -GGTGCTGATGATGATACAGTTGGGGCTTGTGGTGGGGGTGGTGC
* * * *
2453351 GACTGATGATAATGAAACAGTTGG
1 G-GTGCTGATGATGATACAGTTGG
2453375 ACCAGTTATA
Statistics
Matches: 120, Mismatches: 27, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
42 27 0.22
43 9 0.08
44 40 0.33
45 44 0.37
ACGTcount: A:0.19, C:0.09, G:0.43, T:0.30
Consensus pattern (44 bp):
GGTGCTGATGATGATACAGTTGGGGCTTGTGGTGGGGGTGGTGC
Found at i:2465612 original size:22 final size:23
Alignment explanation
Indices: 2465587--2465632 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
2465577 AACTTAAAGG
2465587 ATTAAAATGGC-AAAA-ACAGAAA
1 ATTAAAA-GGCTAAAATACAGAAA
*
2465609 ATTAAAAGGCTAAAATAGAGAAA
1 ATTAAAAGGCTAAAATACAGAAA
2465632 A
1 A
2465633 CAGAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 11 0.52
23 7 0.33
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (23 bp):
ATTAAAAGGCTAAAATACAGAAA
Found at i:2465614 original size:30 final size:30
Alignment explanation
Indices: 2465580--2465685 Score: 117
Period size: 30 Copynumber: 3.5 Consensus size: 30
2465570 AAACATGAAC
* *
2465580 TTAAAGGATTAAAATGGCAAAAACAGAAAA
1 TTAAAGGACTAAAATAGCAAAAACAGAAAA
*
2465610 TTAAAAGG-CTAAAATAG-AGAAAACAGAAAT
1 TT-AAAGGACTAAAATAGCA-AAAACAGAAAA
* *
2465640 TTAAAGGACAAAAATAGCAAAAACAGAAAC
1 TTAAAGGACTAAAATAGCAAAAACAGAAAA
* *
2465670 TTAGATGACTAAAATA
1 TTAAAGGACTAAAATA
2465686 AAATATTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
29 6 0.09
30 52 0.81
31 6 0.09
ACGTcount: A:0.59, C:0.08, G:0.15, T:0.17
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGCAAAAACAGAAAA
Found at i:2487947 original size:3 final size:3
Alignment explanation
Indices: 2487934--2487977 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
2487924 TTAAAAAATA
* *
2487934 TAT TA- TAT TAT TAT AAT TACT TAT TAT TAT TAG TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA
2487978 ATTTATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:2488961 original size:11 final size:11
Alignment explanation
Indices: 2488940--2488977 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
2488930 ATATTCTTAA
2488940 TTTTA-TTTAT
1 TTTTATTTTAT
2488950 TTTTATTTTATT
1 TTTTATTTTA-T
2488962 TTTTATTTTAT
1 TTTTATTTTAT
*
2488973 ATTTA
1 TTTTA
2488978 CATATTACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 5 0.20
11 9 0.36
12 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:2488964 original size:12 final size:12
Alignment explanation
Indices: 2488940--2488972 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2488930 ATATTCTTAA
2488940 TTTTA-TTTA-T
1 TTTTATTTTATT
2488950 TTTTATTTTATT
1 TTTTATTTTATT
2488962 TTTTATTTTAT
1 TTTTATTTTAT
2488973 ATTTACATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.24
11 4 0.19
12 12 0.57
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:2492814 original size:106 final size:106
Alignment explanation
Indices: 2492623--2493835 Score: 2094
Period size: 106 Copynumber: 11.5 Consensus size: 106
2492613 TTTTTGCAGT
2492623 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
*
2492688 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
* * *
2492729 TTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
* *
2492794 ACGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
2492835 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
*
2492900 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
*
2492941 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
*
2493006 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
*
2493047 TTTCAGAGCCAATTTCAACTTCACAACG-AGTGATATTGGACTCCAGACAACGCATGTTCAACTT
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAG-GATATTGGACTCCAGACAACGCATGTTCAACTT
2493111 CACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAA
65 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
*
2493152 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
2493217 ACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
2493257 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
2493322 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
* *
2493363 TTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACGTATGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
* *
2493428 ATGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
* *
2493469 TTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCATGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
2493534 ACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
* *
2493574 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAAAACGCAAGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
*
2493639 ACGACGAAGGGACTGCTGGTTGTCAAC-AACAACTTCCCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
* * * * *
2493679 TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAAATTC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
* ** *
2493744 ACAACGAAGGGAAGGCTGGTTGTCAACAAACAATTTCCCAA
66 ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
* * *
2493785 TTTCGGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAAC
1 TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAC
2493836 ACAACTTTCA
Statistics
Matches: 1059, Mismatches: 44, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
105 401 0.38
106 658 0.62
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (106 bp):
TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTC
ACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAA
Found at i:2493409 original size:422 final size:422
Alignment explanation
Indices: 2492623--2493835 Score: 2176
Period size: 422 Copynumber: 2.9 Consensus size: 422
2492613 TTTTTGCAGT
*
2492623 TTTCAGAGCCAATTTCAACTTCACAGCGAAG-GATATTGGACTCCAGACAACGCATGTTCAACTT
1 TTTCAGAGCCAATTTCAACTTCACAACG-AGTGATATTGGACTCCAGACAACGCATGTTCAACTT
* *
2492687 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGCCAATTTCAACTTCA
65 CACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
* *
2492752 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGT
129 CAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
*
2492817 CAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
194 CAA-CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
*
2492882 CAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
258 CAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
2492947 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACGACG
323 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACGACG
2493012 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAA
388 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAA
2493047 TTTCAGAGCCAATTTCAACTTCACAACGAGTGATATTGGACTCCAGACAACGCATGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAACGAGTGATATTGGACTCCAGACAACGCATGTTCAACTTC
2493112 ACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 ACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
2493177 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
131 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
2493242 ACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAA
196 ACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAA
2493307 CGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
261 CGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* *
2493372 CAATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACGTATGTTCAACTTCATGACGAAG
326 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACGACGAAG
2493437 GGACCGCTGGTTGTCAACAAACAACTTCTCAA
391 GGACCGCTGGTTGTCAACAAACAACTTCTCAA
*
2493469 TTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCATGTTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAACGAGTGATATTGGACTCCAGACAACGCATGTTCAACTTC
2493534 ACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 ACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
* *
2493599 GCGAAGGATATTGGACTCCAGAAAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCA
131 GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
2493664 ACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAA
196 ACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAA
* * * * ** * *
2493729 CACAAGTTCAAATTCACAACGAAGGGAAGGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGC
261 CGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* *
2493794 CAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAAC
326 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAC
2493836 ACAACTTTCA
Statistics
Matches: 763, Mismatches: 25, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
422 573 0.75
423 102 0.13
424 88 0.12
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (422 bp):
TTTCAGAGCCAATTTCAACTTCACAACGAGTGATATTGGACTCCAGACAACGCATGTTCAACTTC
ACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
GCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
ACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAA
CGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAACAAACAACTTCTCAA
Found at i:2494766 original size:3 final size:3
Alignment explanation
Indices: 2494753--2494805 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
2494743 TTAAAAAATA
* *
2494753 TAT TA- TAT TAT TAT TAT TAT TAT AAT TACT TAT TAT TAT TAG TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
2494798 TAT TAT TA
1 TAT TAT TA
2494806 ATTTATATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:2494785 original size:22 final size:22
Alignment explanation
Indices: 2494760--2494802 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2494750 ATATATTATA
*
2494760 TTATTATTATTATTATAATTAC
1 TTATTATTATTAGTATAATTAC
*
2494782 TTATTATTATTAGTATTATTA
1 TTATTATTATTAGTATAATTA
2494803 TTAATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATTATTATTAGTATAATTAC
Found at i:2494792 original size:25 final size:25
Alignment explanation
Indices: 2494758--2494805 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2494748 AAATATATTA
*
2494758 TATTATTATTATTATTATAATTACT
1 TATTATTATTAGTATTATAATTACT
*
2494783 TATTATTATTAGTATTATTATTA
1 TATTATTATTAGTATTATAATTA
2494806 ATTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TATTATTATTAGTATTATAATTACT
Found at i:2495791 original size:7 final size:7
Alignment explanation
Indices: 2495775--2495814 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
2495765 CTTAATTTTA
2495775 TTTA-TT
1 TTTATTT
2495781 TTTATTT
1 TTTATTT
2495788 TTTA-TT
1 TTTATTT
2495794 TTTATTT
1 TTTATTT
2495801 TTTATTT
1 TTTATTT
2495808 TTTATTT
1 TTTATTT
2495815 ACATATTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 10 0.31
7 22 0.69
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTATTT
Found at i:2495793 original size:13 final size:13
Alignment explanation
Indices: 2495775--2495814 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
2495765 CTTAATTTTA
2495775 TTTATTTTTATTT
1 TTTATTTTTATTT
2495788 TTTATTTTTATTT
1 TTTATTTTTATTT
2495801 TTTATTTTTTATTT
1 TTTA-TTTTTATTT
2495815 ACATATTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTATTTTTATTT
Found at i:2498351 original size:34 final size:34
Alignment explanation
Indices: 2498304--2498368 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
2498294 TATATTTAAT
* *
2498304 CATCCAATTGAATGATGTCGTGTCATTGGTGTCA
1 CATCCAATCGAATGATGTCGCGTCATTGGTGTCA
2498338 CATCCAATCGAATGATGTCGCGTCATTGGTG
1 CATCCAATCGAATGATGTCGCGTCATTGGTG
2498369 CCACGTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (34 bp):
CATCCAATCGAATGATGTCGCGTCATTGGTGTCA
Found at i:2506068 original size:17 final size:18
Alignment explanation
Indices: 2506046--2506084 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2506036 AATCACTCTC
* *
2506046 ATCATGCCAT-TGTAAAG
1 ATCATGCAATATGCAAAG
2506063 ATCATGCAATATGCAAAG
1 ATCATGCAATATGCAAAG
2506081 ATCA
1 ATCA
2506085 GGATAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (18 bp):
ATCATGCAATATGCAAAG
Found at i:2506664 original size:18 final size:18
Alignment explanation
Indices: 2506641--2506677 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2506631 AACCTTAGAC
*
2506641 AGTTTCCAGAAGCATTGG
1 AGTTTCCAAAAGCATTGG
2506659 AGTTTCCAAAAGCATTGG
1 AGTTTCCAAAAGCATTGG
2506677 A
1 A
2506678 ATACAATGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (18 bp):
AGTTTCCAAAAGCATTGG
Found at i:2525862 original size:16 final size:16
Alignment explanation
Indices: 2525837--2525867 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2525827 AAATATGTTC
*
2525837 AAATCTAAAAGCAATA
1 AAATCAAAAAGCAATA
2525853 AAATCAAAAAGCAAT
1 AAATCAAAAAGCAAT
2525868 TAGTTAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.13, G:0.06, T:0.16
Consensus pattern (16 bp):
AAATCAAAAAGCAATA
Found at i:2527618 original size:4 final size:4
Alignment explanation
Indices: 2527609--2527643 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
2527599 TTCGAACATA
* *
2527609 AAAT AAAT AAAT AAAT AAGT AAAG AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2527644 AATTAGCAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:2533377 original size:22 final size:21
Alignment explanation
Indices: 2533345--2533386 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2533335 TTCAGAAAGA
2533345 AAATAAAATAA-ATAAATAAAT
1 AAATAAAATAATA-AAATAAAT
2533366 AAATAAAAATAATAAAATAAA
1 AAAT-AAAATAATAAAATAAA
2533387 CATATACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 14 0.74
23 1 0.05
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (21 bp):
AAATAAAATAATAAAATAAAT
Found at i:2535801 original size:20 final size:20
Alignment explanation
Indices: 2535772--2535810 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2535762 ATTTCACCAC
*
2535772 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
2535792 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
2535811 TATGAGCTCT
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:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:2536099 original size:16 final size:16
Alignment explanation
Indices: 2536078--2536110 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2536068 TGGGTGTGTG
*
2536078 CGTGTTTGTATCAAGT
1 CGTGTTTGTATAAAGT
2536094 CGTGTTTGTATAAAGT
1 CGTGTTTGTATAAAGT
2536110 C
1 C
2536111 CATGCTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.42
Consensus pattern (16 bp):
CGTGTTTGTATAAAGT
Found at i:2543145 original size:2 final size:2
Alignment explanation
Indices: 2543093--2543129 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2543083 AGCTTTATTG
*
2543093 TA TA CA TA 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 TA TA TA TA T
2543130 TTTGTCTGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2547946 original size:20 final size:20
Alignment explanation
Indices: 2547904--2547947 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2547894 GAACTGAAAC
* *
2547904 AAAACAAATAAAAGTTAGTA
1 AAAACAAATAAAAGTCAGAA
2547924 AAAACAAAATAAAAG-CAGAA
1 AAAAC-AAATAAAAGTCAGAA
2547944 AAAA
1 AAAA
2547948 ATAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.73, C:0.07, G:0.09, T:0.11
Consensus pattern (20 bp):
AAAACAAATAAAAGTCAGAA
Found at i:2549176 original size:3 final size:3
Alignment explanation
Indices: 2549153--2549210 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
2549143 CATGGAGCCT
* *
2549153 ATA AAA ATA TTA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2549199 AT- ATA AT- ATA AT
1 ATA ATA ATA ATA AT
2549211 GCTTTTATAG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2551097 original size:21 final size:21
Alignment explanation
Indices: 2551071--2551112 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2551061 ATTGGCCCTT
2551071 GCTCTCTAATCACCGGTCCTC
1 GCTCTCTAATCACCGGTCCTC
2551092 GCTCTCTAATCACCGGTCCTC
1 GCTCTCTAATCACCGGTCCTC
2551113 AATCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.14, T:0.29
Consensus pattern (21 bp):
GCTCTCTAATCACCGGTCCTC
Found at i:2552299 original size:25 final size:25
Alignment explanation
Indices: 2552265--2552321 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
2552255 TGAAAAAAAT
2552265 GAAAACTTATAGACAACGTCGGAAA
1 GAAAACTTATAGACAACGTCGGAAA
2552290 GAAAACTTATAGACAACGTCGGAAA
1 GAAAACTTATAGACAACGTCGGAAA
2552315 GAAAACT
1 GAAAACT
2552322 CAAATCGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (25 bp):
GAAAACTTATAGACAACGTCGGAAA
Found at i:2554601 original size:355 final size:358
Alignment explanation
Indices: 2554114--2554761 Score: 1016
Period size: 355 Copynumber: 1.8 Consensus size: 358
2554104 TACCTCGTAA
* * *
2554114 ATGAAGCTAAGAATGAAGATTTATGACAGAACCAATGTAGAAAAATGAGAAGGATATGAGATAAG
1 ATGAAGCTAAGAATGAAGATTTATGACAAAACCAATGTAAAAAAATGAAAAGGATATGAGATAAG
* * * **
2554179 GAAGATAGTGACATAAACAGTTAAGATTAGAAGATTTAAGCAATTCAAAAATAATAGTAAGATAA
66 AAAGATAGTGACATAAACAATGAAGATTAGAAGATACAAGCAATTCAAAAATAATAGTAAGATAA
*
2554244 TTGGATTGTTTTTAAAGTATATTTTTGAAAATTTGAAAGCTCATTATATTCAACATAAATATTAA
131 TTGGATTGTTTTTAAAGTATATTTTTGAAAATTTGAAAGATCATTATATTCAACATAAATATTAA
* ** * *
2554309 AATAATATAATATTGATTTATTATATAAATTACTTTAATTGTT-AAAAA-A-TGTTATTTTATAG
196 AATAACATAATATTGAAATATTATATAAATTACTCTAATCGTTAAAAAATAGTGTTATTTT-TAG
*
2554371 AAGTCTCAAGTTTGAACACAAATAACTGCATAATAATAAAGGTGAATGAACTTTCATTATCAAAT
260 AAGTCTCAAGTTTAAACACAAATAACTGCATAATAATAAAGGTGAATGAACTTTCATTATCAAAT
2554436 GATTAAGTTTGCCATAAATCAATACTCCATGACT
325 GATTAAGTTTGCCATAAATCAATACTCCATGACT
* *
2554470 ATGAAGCTAAGAATGAAGATTTATGACAAAATCAATG-AAAAAAATGAAAAGGATTTGAGATAAG
1 ATGAAGCTAAGAATGAAGATTTATGACAAAACCAATGTAAAAAAATGAAAAGGATATGAGATAAG
* * *
2554534 AAAGATAGTGAGATAAATAATGAAGATTAGAAGGTACAAGCAATTCAAAAATAATAGTAAGATAA
66 AAAGATAGTGACATAAACAATGAAGATTAGAAGATACAAGCAATTCAAAAATAATAGTAAGATAA
* *
2554599 TTGGATTGTTTTTAAAGTATATTTTTGAAAATTTGAAAGATCTTTATATTCAACATAGATATTAA
131 TTGGATTGTTTTTAAAGTATATTTTTGAAAATTTGAAAGATCATTATATTCAACATAAATATTAA
2554664 AATAACATAATATTGAAATATTATATAAATTACTCTAATCGTTGAAAAAATAGTTGTTATTTTTA
196 AATAACATAATATTGAAATATTATATAAATTACTCTAATCGTT-AAAAAATAG-TGTTATTTTTA
* * *
2554729 GAAGTTTCAAGTTTAAACACAAATGATTGCATA
259 GAAGTCTCAAGTTTAAACACAAATAACTGCATA
2554762 TCAAAGACGA
Statistics
Matches: 262, Mismatches: 25, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
355 181 0.69
356 35 0.13
357 5 0.02
358 1 0.00
359 31 0.12
360 9 0.03
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (358 bp):
ATGAAGCTAAGAATGAAGATTTATGACAAAACCAATGTAAAAAAATGAAAAGGATATGAGATAAG
AAAGATAGTGACATAAACAATGAAGATTAGAAGATACAAGCAATTCAAAAATAATAGTAAGATAA
TTGGATTGTTTTTAAAGTATATTTTTGAAAATTTGAAAGATCATTATATTCAACATAAATATTAA
AATAACATAATATTGAAATATTATATAAATTACTCTAATCGTTAAAAAATAGTGTTATTTTTAGA
AGTCTCAAGTTTAAACACAAATAACTGCATAATAATAAAGGTGAATGAACTTTCATTATCAAATG
ATTAAGTTTGCCATAAATCAATACTCCATGACT
Done.