Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008057.1 Hibiscus syriacus cultivar Beakdansim tig00110552_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: 141434
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:16770 original size:3 final size:3
Alignment explanation
Indices: 16762--16793 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
16752 TACCAATACA
16762 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16794 ATAAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21574 original size:27 final size:27
Alignment explanation
Indices: 21526--21643 Score: 101
Period size: 27 Copynumber: 4.4 Consensus size: 27
21516 AATATACATC
* * ** *
21526 ATTCAACTATTAATATCCATCATATTA
1 ATTCAAATATTGATATTAATCACATTA
* *
21553 ATTCAAATATTGATAATAATCACAATA
1 ATTCAAATATTGATATTAATCACATTA
* * * *
21580 ATTCAACTATTTATATTATTCACATTC
1 ATTCAAATATTGATATTAATCACATTA
* * *
21607 ATTCAACTATTGATATTAATCATATTC
1 ATTCAAATATTGATATTAATCACATTA
*
21634 ATTAAAATAT
1 ATTCAAATAT
21644 AAAGTTACAA
Statistics
Matches: 73, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (27 bp):
ATTCAAATATTGATATTAATCACATTA
Found at i:21585 original size:54 final size:54
Alignment explanation
Indices: 21526--21628 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
21516 AATATACATC
*
21526 ATTCAACTATTAATATCCA-TCATATTAATTCAAATATTGATAATAATCACAATA
1 ATTCAACTATTAATAT-CATTCACATTAATTCAAATATTGATAATAATCACAATA
* * * * *
21580 ATTCAACTATTTATATTATTCACATTCATTCAACTATTGATATTAATCA
1 ATTCAACTATTAATATCATTCACATTAATTCAAATATTGATAATAATCA
21629 TATTCATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 1 0.02
54 41 0.98
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.41
Consensus pattern (54 bp):
ATTCAACTATTAATATCATTCACATTAATTCAAATATTGATAATAATCACAATA
Found at i:22409 original size:46 final size:46
Alignment explanation
Indices: 22359--22567 Score: 339
Period size: 46 Copynumber: 4.5 Consensus size: 46
22349 CACATTAACA
*
22359 CATCCATTT-ATGCATTTTAATTATGACATTCTTTCATGCCTTAATG
1 CATCC-TTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATG
* *
22405 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAGTG
1 CATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATG
*
22451 CATCCTTTCATACATTTTAATTATGACATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATG
* *
22497 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCACGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATG
*
22543 CATTCTTTCATGCATTTTAATTATG
1 CATCCTTTCATGCATTTTAATTATG
22568 TATTCGATTT
Statistics
Matches: 152, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 3 0.02
46 149 0.98
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.44
Consensus pattern (46 bp):
CATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATG
Found at i:22414 original size:20 final size:20
Alignment explanation
Indices: 22389--22555 Score: 109
Period size: 20 Copynumber: 7.5 Consensus size: 20
22379 TTATGACATT
22389 CTTTCATGCCTTAATGCATC
1 CTTTCATGCCTTAATGCATC
*
22409 CTTTCATGCATTTTAATTATGGCATC
1 CTTTCATGC--CTT-A--AT-GCATC
*
22435 CTTTCATGCCTTAGTGCATC
1 CTTTCATGCCTTAATGCATC
* *
22455 CTTTCATACATTTTAATTATGACATC
1 CTTTCATGC--CTT-A--ATG-CATC
22481 CTTTCATGCCTTAATGCATC
1 CTTTCATGCCTTAATGCATC
*
22501 CTTTCATGCATTTTAATTATGGCATC
1 CTTTCATGC--CTT-A--AT-GCATC
* *
22527 CTTTCACGCCTTAATGCATT
1 CTTTCATGCCTTAATGCATC
22547 CTTTCATGC
1 CTTTCATGC
22556 ATTTTAATTA
Statistics
Matches: 116, Mismatches: 13, Indels: 36
0.70 0.08 0.22
Matches are distributed among these distances:
20 47 0.41
21 6 0.05
22 6 0.05
23 6 0.05
24 6 0.05
25 6 0.05
26 39 0.34
ACGTcount: A:0.22, C:0.25, G:0.10, T:0.43
Consensus pattern (20 bp):
CTTTCATGCCTTAATGCATC
Found at i:24052 original size:21 final size:21
Alignment explanation
Indices: 24028--24070 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
24018 CTTTAAAAAT
*
24028 ATTTTC-TTTATTTTTACTTTA
1 ATTTTCTTTTATTATTA-TTTA
24049 ATTTTCTTTTATTATTATTTA
1 ATTTTCTTTTATTATTATTTA
24070 A
1 A
24071 ATATCCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTCTTTTATTATTATTTA
Found at i:31903 original size:10 final size:11
Alignment explanation
Indices: 31887--31913 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
31877 AATACATGAG
31887 AAAAAAACAAT
1 AAAAAAACAAT
31898 AAAAAAACAAT
1 AAAAAAACAAT
31909 AAAAA
1 AAAAA
31914 TGTGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAAACAAT
Found at i:42078 original size:22 final size:23
Alignment explanation
Indices: 42052--42098 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
42042 AAATATTTTC
* *
42052 TTTATTTTTACTTTAAT-TCATT
1 TTTATTATTACTTAAATATCATT
*
42074 TTTATTATTAGTTAAATATCATT
1 TTTATTATTACTTAAATATCATT
42097 TT
1 TT
42099 ACCAACACCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTATTATTACTTAAATATCATT
Found at i:42237 original size:20 final size:19
Alignment explanation
Indices: 42212--42264 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
42202 TGTTTTGAAA
42212 TGGTATCGATATCTTCCCT-T
1 TGGTATCGATA-C-TCCCTCT
42232 TGGTATCGATACTCCCTCGT
1 TGGTATCGATACTCCCTC-T
42252 TGGTATCGATACT
1 TGGTATCGATACT
42265 GATTGAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.16
19 1 0.03
20 25 0.81
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.40
Consensus pattern (19 bp):
TGGTATCGATACTCCCTCT
Found at i:42284 original size:21 final size:22
Alignment explanation
Indices: 42254--42327 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
42244 TCCCTCGTTG
42254 GTATCGATACTGATTGAATCAA
1 GTATCGATACTGATTGAATCAA
*
42276 -TATCAATACTGATTGAAT-AA
1 GTATCGATACTGATTGAATCAA
* *
42296 GTATCGATATTGTTTGAATC-A
1 GTATCGATACTGATTGAATCAA
*
42317 GTATTGATACT
1 GTATCGATACT
42328 ACTCATCTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.05
21 42 0.95
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (22 bp):
GTATCGATACTGATTGAATCAA
Found at i:48404 original size:46 final size:46
Alignment explanation
Indices: 48354--48504 Score: 232
Period size: 46 Copynumber: 3.3 Consensus size: 46
48344 CAGATTAACA
*
48354 CATCCATTT-ATGCATTTTAATTATGTCATTCTTTCATACCTTAATG
1 CATCC-TTTCATGCATTTTAATTATGTCATTCTTTCATGCCTTAATG
48400 CATCCTTTCATGCATTTTAATTATGTCATTCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGTCATTCTTTCATGCCTTAATG
* * * *
48446 CATTCTTTCATGCATTTTAATTATGACATCCTTTAATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGTCATTCTTTCATGCCTTAATG
*
48492 CAACCTTTCATGC
1 CATCCTTTCATGC
48505 CTTAATGCAT
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
45 3 0.03
46 94 0.97
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.46
Consensus pattern (46 bp):
CATCCTTTCATGCATTTTAATTATGTCATTCTTTCATGCCTTAATG
Found at i:48500 original size:66 final size:66
Alignment explanation
Indices: 48430--48559 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
48420 TTATGTCATT
48430 CTTTCATGCCTTAATGCATTC-TTTCATGCATTTTAATTATGACATCCTTTAATGCCTTAATGCA
1 CTTTCATGCCTTAATGCA-TCATTTCATGCATTTTAATTATGACATCCTTTAATGCCTTAATGCA
48494 AC
65 AC
* *
48496 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCA
1 CTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGACATCCTTTAATGCCTTAATGCA
48560 TTATTTAATG
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 2 0.03
66 59 0.97
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (66 bp):
CTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGACATCCTTTAATGCCTTAATGCAA
C
Found at i:48523 original size:20 final size:20
Alignment explanation
Indices: 48384--48560 Score: 111
Period size: 20 Copynumber: 8.0 Consensus size: 20
48374 TTATGTCATT
*
48384 CTTTCATACCTTAATGCATC
1 CTTTCATGCCTTAATGCATC
* *
48404 CTTTCATGCATTTTAATTATGTCATT
1 CTTTCATGC--CTT-A--ATG-CATC
*
48430 CTTTCATGCCTTAATGCATT
1 CTTTCATGCCTTAATGCATC
*
48450 CTTTCATGCATTTTAATTATGACATC
1 CTTTCATGC--CTT-A--ATG-CATC
* *
48476 CTTTAATGCCTTAATGCAAC
1 CTTTCATGCCTTAATGCATC
48496 CTTTCATGCCTTAATGCATC
1 CTTTCATGCCTTAATGCATC
* *
48516 ATTTCATGCATTTTAATTATGGCATC
1 CTTTCATGC--CTT-A--AT-GCATC
48542 CTTTCATGCCTTAATGCAT
1 CTTTCATGCCTTAATGCAT
48561 TATTTAATGC
Statistics
Matches: 124, Mismatches: 15, Indels: 36
0.71 0.09 0.21
Matches are distributed among these distances:
20 54 0.44
21 8 0.06
22 6 0.05
23 6 0.05
24 6 0.05
25 8 0.06
26 36 0.29
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (20 bp):
CTTTCATGCCTTAATGCATC
Found at i:48545 original size:46 final size:46
Alignment explanation
Indices: 48495--48583 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
48485 CTTAATGCAA
*
48495 CCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCAT
1 CCTTTCATGCCTTAATGCATCATTTAATGCATTTTAATTATGGCAT
*
48541 CCTTTCATGCCTTAATGCATTATTTAATGCATTTTAATTATGG
1 CCTTTCATGCCTTAATGCATCATTTAATGCATTTTAATTATGG
48584 ATTCGATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (46 bp):
CCTTTCATGCCTTAATGCATCATTTAATGCATTTTAATTATGGCAT
Found at i:50883 original size:14 final size:14
Alignment explanation
Indices: 50842--50876 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
50832 TAATTCTTAC
50842 CAATATGACAGATA
1 CAATATGACAGATA
50856 CAATATGACAGATA
1 CAATATGACAGATA
50870 CAATATG
1 CAATATG
50877 TGGGATATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (14 bp):
CAATATGACAGATA
Found at i:52803 original size:37 final size:38
Alignment explanation
Indices: 52762--52842 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
52752 TCCAGTTCAA
* *
52762 CACCAACCTACCCA-GGCATTAATGGATG-ATTAATAAC
1 CACCAACATACCCATAGCATTAATGGA-GAATTAATAAC
**
52799 CACCAACATACCCATATTATTAATGGAGAATTAATAAC
1 CACCAACATACCCATAGCATTAATGGAGAATTAATAAC
52837 CACCAA
1 CACCAA
52843 TCATCACCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 14 0.37
38 24 0.63
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.22
Consensus pattern (38 bp):
CACCAACATACCCATAGCATTAATGGAGAATTAATAAC
Found at i:52878 original size:44 final size:45
Alignment explanation
Indices: 52796--52909 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 45
52786 GATGATTAAT
* *** *
52796 AACCACCAACATACCCATATTATTAATGGAGAATTAATAACCACC
1 AACCACCAACCTACCCGGGTTATTAATGAAGAATTAATAACCACC
* * * * *
52841 AATCATC-ACCTATCTGGGTTATTAATGAATAATTAATAACCACC
1 AACCACCAACCTACCCGGGTTATTAATGAAGAATTAATAACCACC
52885 AACCACCAACCTACCCGGGTTATTA
1 AACCACCAACCTACCCGGGTTATTA
52910 TCGCATCATT
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
44 34 0.63
45 20 0.37
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.25
Consensus pattern (45 bp):
AACCACCAACCTACCCGGGTTATTAATGAAGAATTAATAACCACC
Found at i:53179 original size:44 final size:45
Alignment explanation
Indices: 53112--53196 Score: 145
Period size: 44 Copynumber: 1.9 Consensus size: 45
53102 TCGTTCAACA
*
53112 ACCAACCACCAACCTACTAGGGTTATTAATGGATAATTAATAATC
1 ACCAACCACCAACCTACTAGGGTTATTAATAGATAATTAATAATC
*
53157 ACCAACCACC-ACCTACTCGGGTTATTAATAGATAATTAAT
1 ACCAACCACCAACCTACTAGGGTTATTAATAGATAATTAAT
53197 GTTGCCGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 28 0.74
45 10 0.26
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.27
Consensus pattern (45 bp):
ACCAACCACCAACCTACTAGGGTTATTAATAGATAATTAATAATC
Found at i:53792 original size:200 final size:198
Alignment explanation
Indices: 53443--53839 Score: 570
Period size: 200 Copynumber: 2.0 Consensus size: 198
53433 AGTTTCTTCC
* * *
53443 GACAAGTTGATGTTATAAAAAAACCTTTTCAAATTTCTTACTCACTTCTTTTTTACATGCAACAA
1 GACAACTTGATGTTATAAAAAAACCTTTTCAAATTTCTTAATCACTTATTTTTTACATGCAACAA
* * *
53508 CATATTAAAAAATATTTTAATAACTTTTCCGAAATAGAGATATATTATTCGAATACGAGTAAAAT
66 CATATTAAAAAATATTTTAAAAACCTTTCCGAAATAGAGATATATTATTCGAATACGAATAAAAT
*
53573 TTATTCCAATAATACTTACAGATTATAGATT-GAAAGAAAATTTTGTTCAAAATTTTCTCTACTA
131 TTATTCCAATAATACTTACAGA-T-TAGATTAG-AAGAAAATTTCGTTCAAAATTTTCTCTACTA
53637 TTCTTT
193 TTCTTT
* * *
53643 GACAACTTGATGTTAT-TAAAAA-CTTCTCTCGAATTTCTTAATCACTTATTTTTTACCTGCAAC
1 GACAACTTGATGTTATAAAAAAACCTT-T-TCAAATTTCTTAATCACTTATTTTTTACATGCAAC
* * *
53706 AATATATTAAAACAATATTTTAAAAACCTTTCCG-AA-AGAGATATTTTATTCTAATACGAATAA
64 AACATATTAAAA-AATATTTTAAAAACCTTTCCGAAATAGAGATATATTATTCGAATACGAATAA
*
53769 AATTTTATTCGAATAATACTTACAGATTAGATTAGAAGAAAATTTCGTTCAAAATTTTCTCTACT
128 AA-TTTATTCCAATAATACTTACAGATTAGATTAGAAGAAAATTTCGTTCAAAATTTTCTCTACT
53834 ATTCTT
192 ATTCTT
53840 CTCGGATGCT
Statistics
Matches: 178, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
198 44 0.25
199 34 0.19
200 81 0.46
201 19 0.11
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.40
Consensus pattern (198 bp):
GACAACTTGATGTTATAAAAAAACCTTTTCAAATTTCTTAATCACTTATTTTTTACATGCAACAA
CATATTAAAAAATATTTTAAAAACCTTTCCGAAATAGAGATATATTATTCGAATACGAATAAAAT
TTATTCCAATAATACTTACAGATTAGATTAGAAGAAAATTTCGTTCAAAATTTTCTCTACTATTC
TTT
Found at i:64608 original size:61 final size:64
Alignment explanation
Indices: 64492--64612 Score: 203
Period size: 61 Copynumber: 1.9 Consensus size: 64
64482 TAAACAATAC
*
64492 AAACAACCATTAAAAATATGTATCATCTCATCAAATATGCAAAAGCTTAAATATAACACAAATT
1 AAACAACCATTAAAAATATGTATCATCTCATCAAATATGCAAAAGCATAAATATAACACAAATT
*
64556 AAACAACCATT-AAAA-ATGTATCATCTCATC-AATATGTAAAAGCATAAATATAACACA
1 AAACAACCATTAAAAATATGTATCATCTCATCAAATATGCAAAAGCATAAATATAACACA
64613 TTAATTTATT
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
61 25 0.45
62 15 0.27
63 4 0.07
64 11 0.20
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.26
Consensus pattern (64 bp):
AAACAACCATTAAAAATATGTATCATCTCATCAAATATGCAAAAGCATAAATATAACACAAATT
Found at i:64875 original size:23 final size:23
Alignment explanation
Indices: 64806--64875 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
64796 GTCACGATAA
* *
64806 GATACCAAAGTATCCATCATTAG
1 GATACCAAAGTATCAATCAATAG
* * *
64829 GATACCGAAGTACCAAACAATAG
1 GATACCAAAGTATCAATCAATAG
* * *
64852 GATACCTAAGTATTAATCACTAG
1 GATACCAAAGTATCAATCAATAG
64875 G
1 G
64876 GTATTGTAAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (23 bp):
GATACCAAAGTATCAATCAATAG
Found at i:64892 original size:23 final size:22
Alignment explanation
Indices: 64866--64916 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 22
64856 CCTAAGTATT
64866 AATCACTAGGGTATTGTAA-TACC
1 AATCACTA-GGTATTG-AAGTACC
64889 AATCAC---GTATTGAAGTACC
1 AATCACTAGGTATTGAAGTACC
64908 AATCACTAG
1 AATCACTAG
64917 ATAACTACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
18 2 0.08
19 16 0.67
23 6 0.25
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (22 bp):
AATCACTAGGTATTGAAGTACC
Found at i:64900 original size:19 final size:19
Alignment explanation
Indices: 64876--64913 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
64866 AATCACTAGG
64876 GTATTGTAA-TACCAATCAC
1 GTATTG-AAGTACCAATCAC
64895 GTATTGAAGTACCAATCAC
1 GTATTGAAGTACCAATCAC
64914 TAGATAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (19 bp):
GTATTGAAGTACCAATCAC
Found at i:75193 original size:26 final size:26
Alignment explanation
Indices: 75164--75215 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
75154 AGACAAGCCT
75164 CAGAAAACTCAACGAGAAATGGGCCA
1 CAGAAAACTCAACGAGAAATGGGCCA
* ** *
75190 CAGAAAATTCAGTGAGAGATGGGCCA
1 CAGAAAACTCAACGAGAAATGGGCCA
75216 AACAGGAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.27, T:0.12
Consensus pattern (26 bp):
CAGAAAACTCAACGAGAAATGGGCCA
Found at i:76779 original size:23 final size:23
Alignment explanation
Indices: 76747--76862 Score: 142
Period size: 23 Copynumber: 5.0 Consensus size: 23
76737 GTCACGATAA
* **
76747 GATACTGAAGTATCAATTACTAG
1 GATACCGAAGTATCAAACACTAG
*
76770 GATACCGAAGTATCAAACACTAA
1 GATACCGAAGTATCAAACACTAG
* *
76793 GATAACGAAGTATCAATCACTAG
1 GATACCGAAGTATCAAACACTAG
* *
76816 GATACAGAAGTATCAAACATTAG
1 GATACCGAAGTATCAAACACTAG
* *
76839 GATACCAAAGTATCAACCACTAG
1 GATACCGAAGTATCAAACACTAG
76862 G
1 G
76863 GTATCATAGT
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 78 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (23 bp):
GATACCGAAGTATCAAACACTAG
Found at i:76815 original size:46 final size:46
Alignment explanation
Indices: 76744--76862 Score: 159
Period size: 46 Copynumber: 2.6 Consensus size: 46
76734 CGAGTCACGA
* *
76744 TAAGAT-ACTGAAGTATCAATTACTAGGATACCGAAGTATCAAACAC
1 TAAGATAAC-GAAGTATCAATCACTAGGATACAGAAGTATCAAACAC
*
76790 TAAGATAACGAAGTATCAATCACTAGGATACAGAAGTATCAAACAT
1 TAAGATAACGAAGTATCAATCACTAGGATACAGAAGTATCAAACAC
* * * *
76836 TAGGATACCAAAGTATCAACCACTAGG
1 TAAGATAACGAAGTATCAATCACTAGG
76863 GTATCATAGT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
46 63 0.97
47 2 0.03
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.22
Consensus pattern (46 bp):
TAAGATAACGAAGTATCAATCACTAGGATACAGAAGTATCAAACAC
Found at i:76873 original size:23 final size:22
Alignment explanation
Indices: 76754--76885 Score: 120
Period size: 23 Copynumber: 5.8 Consensus size: 22
76744 TAAGATACTG
* *
76754 AAGTATCAATTACTAGGATACCG
1 AAGTATCAATCACTAGGATA-CA
* * *
76777 AAGTATCAAACACTAAGATAACG
1 AAGTATCAATCACTAGGAT-ACA
76800 AAGTATCAATCACTAGGATACA
1 AAGTATCAATCACTAGGATACA
* *
76822 GAAGTATCAAACATTAGGATACCA
1 -AAGTATCAATCACTAGGATA-CA
* *
76846 AAGTATCAACCACTAGGGTATCA
1 AAGTATCAATCACTAGGATA-CA
* *
76869 TAGTACCAATCACTAGG
1 AAGTATCAATCACTAGG
76886 CAACTACTAG
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
22 2 0.02
23 86 0.95
24 3 0.03
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (22 bp):
AAGTATCAATCACTAGGATACA
Found at i:76879 original size:69 final size:69
Alignment explanation
Indices: 76747--76885 Score: 172
Period size: 69 Copynumber: 2.0 Consensus size: 69
76737 GTCACGATAA
* ** * *
76747 GATACTGAAGTATCAATTACTAGGATACCGAAGTATCAAACACTAAGATAACGAAGTATCAATCA
1 GATACAGAAGTATCAAACACTAGGATACCAAAGTATCAAACACTAAGATAACGAAGTACCAATCA
76812 CTAG
66 CTAG
* * * * *
76816 GATACAGAAGTATCAAACATTAGGATACCAAAGTATCAACCACTAGGGTATC-ATAGTACCAATC
1 GATACAGAAGTATCAAACACTAGGATACCAAAGTATCAAACACTAAGATAACGA-AGTACCAATC
76880 ACTAG
65 ACTAG
76885 G
1 G
76886 CAACTACTAG
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
68 1 0.02
69 58 0.98
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (69 bp):
GATACAGAAGTATCAAACACTAGGATACCAAAGTATCAAACACTAAGATAACGAAGTACCAATCA
CTAG
Found at i:80749 original size:28 final size:28
Alignment explanation
Indices: 80678--80770 Score: 109
Period size: 28 Copynumber: 3.4 Consensus size: 28
80668 ATATGTATCG
* *
80678 ATTACATATA-TATGTGTGTGTGTATAT
1 ATTACATATACAATATGTGTGTGTATAT
* *
80705 A-TATATATACAATATGTGTGTGAATAT
1 ATTACATATACAATATGTGTGTGTATAT
*
80732 ATTACATATCCAATATGTGTGTGTATAT
1 ATTACATATACAATATGTGTGTGTATAT
*
80760 ATATATATATA
1 AT-TACATATA
80771 TGTGTGTGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 7 0.13
27 16 0.30
28 25 0.46
29 6 0.11
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (28 bp):
ATTACATATACAATATGTGTGTGTATAT
Found at i:92245 original size:23 final size:23
Alignment explanation
Indices: 92219--92272 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
92209 AAAGGAAAAG
*
92219 ATAAAAAAAAAGAGT-GAAATGAA
1 ATAAAAAAAAAGAGTAAAAAT-AA
* *
92242 ATAAAAAGAATGAGTAAAAATAA
1 ATAAAAAAAAAGAGTAAAAATAA
92265 ATAAAAAA
1 ATAAAAAA
92273 GGATCAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (23 bp):
ATAAAAAAAAAGAGTAAAAATAA
Found at i:95176 original size:16 final size:16
Alignment explanation
Indices: 95155--95198 Score: 79
Period size: 16 Copynumber: 2.7 Consensus size: 16
95145 ATATTATGAT
95155 TCTTACTTTTATGCGC
1 TCTTACTTTTATGCGC
95171 TCTTACTTTTATGCGC
1 TCTTACTTTTATGCGC
95187 TCTTACATTTTA
1 TCTTAC-TTTTA
95199 ATCTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 22 0.81
17 5 0.19
ACGTcount: A:0.16, C:0.23, G:0.09, T:0.52
Consensus pattern (16 bp):
TCTTACTTTTATGCGC
Found at i:95697 original size:6 final size:6
Alignment explanation
Indices: 95686--95886 Score: 393
Period size: 6 Copynumber: 33.5 Consensus size: 6
95676 TTACATATCC
95686 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
95734 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
95782 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
*
95830 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATC
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
95878 TATATG TAT
1 TATATG TAT
95887 GTATGTATGT
Statistics
Matches: 193, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 193 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:95919 original size:24 final size:24
Alignment explanation
Indices: 95680--95921 Score: 218
Period size: 24 Copynumber: 10.0 Consensus size: 24
95670 TATATATTAC
* *
95680 ATATCCTATATGTATATGTATATGT
1 ATAT-CTATATGTATGTATATATGT
* * *
95705 ATATGTATATGTATATGTATATGT
1 ATATCTATATGTATGTATATATGT
* * *
95729 ATATGTATATGTATATGTATATGT
1 ATATCTATATGTATGTATATATGT
* * *
95753 ATATGTATATGTATATGTATATGT
1 ATATCTATATGTATGTATATATGT
* * *
95777 ATATGTATATGTATATGTATATGT
1 ATATCTATATGTATGTATATATGT
* * *
95801 ATATGTATATGTATATGTATATGT
1 ATATCTATATGTATGTATATATGT
* * *
95825 ATATGTATATGTATATGTATATGT
1 ATATCTATATGTATGTATATATGT
* * *
95849 ATATGTATATGTATATGTATATGT
1 ATATCTATATGTATGTATATATGT
*
95873 ATATCTATATGTATGTATGTATGT
1 ATATCTATATGTATGTATATATGT
*
95897 ATTAAT-TATATTTAT-TATATATGT
1 A-T-ATCTATATGTATGTATATATGT
95921 A
1 A
95922 ACCCCTTAGA
Statistics
Matches: 208, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
24 193 0.93
25 13 0.06
26 2 0.01
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.50
Consensus pattern (24 bp):
ATATCTATATGTATGTATATATGT
Found at i:104149 original size:13 final size:13
Alignment explanation
Indices: 104131--104156 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
104121 TGACTTTTTA
104131 GTCAAAGTCAACG
1 GTCAAAGTCAACG
104144 GTCAAAGTCAACG
1 GTCAAAGTCAACG
104157 TTAAACTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
GTCAAAGTCAACG
Found at i:105255 original size:2 final size:2
Alignment explanation
Indices: 105248--105286 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
105238 CATGCGCGTG
*
105248 TA TA TA TA TA TA TA TA TA TA TA TA TA -A CTT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA T
105287 GTGTATTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:106128 original size:22 final size:22
Alignment explanation
Indices: 106088--106133 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
106078 AAAAGTGTTG
*
106088 TTTTAATAAAATTAAAATTATT
1 TTTTAATAAAATGAAAATTATT
* * *
106110 TTTTATTAAAATGACAATTGTT
1 TTTTAATAAAATGAAAATTATT
106132 TT
1 TT
106134 GGGTGCCTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTTAATAAAATGAAAATTATT
Found at i:108491 original size:27 final size:27
Alignment explanation
Indices: 108435--108491 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
108425 ATTAAAGAAG
** * *
108435 AAAAAATGTTAAATTAAGAAATTAACA
1 AAAAAATGTTAAAAGAAAAAATAAACA
*
108462 AAAAAATGTTAAAAGAAAAAATAAATA
1 AAAAAATGTTAAAAGAAAAAATAAACA
108489 AAA
1 AAA
108492 TAAAATAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (27 bp):
AAAAAATGTTAAAAGAAAAAATAAACA
Found at i:109640 original size:16 final size:17
Alignment explanation
Indices: 109621--109659 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
109611 AAAAATTAAC
109621 AATAATAAA-AAAAATA
1 AATAATAAATAAAAATA
*
109637 AAT-ATAAATATAAATA
1 AATAATAAATAAAAATA
109653 AATAATA
1 AATAATA
109660 TTAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 12 0.60
17 3 0.15
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAATAAATAAAAATA
Found at i:109717 original size:17 final size:17
Alignment explanation
Indices: 109697--109729 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
109687 TAATATTATA
109697 TTTTCAAAAATAATATG
1 TTTTCAAAAATAATATG
*
109714 TTTTCAAAAATTATAT
1 TTTTCAAAAATAATAT
109730 ATTATATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTTCAAAAATAATATG
Found at i:109776 original size:35 final size:34
Alignment explanation
Indices: 109732--110007 Score: 130
Period size: 35 Copynumber: 7.5 Consensus size: 34
109722 AATTATATAT
* *
109732 TATATATGTTTCCAAAAAATCATTTAAAAAAACTA
1 TATATATGTTTTCAAAAAATCATTT-TAAAAACTA
* * *
109767 TATATATGTTTTCAAAATAT-GTTTTCAAAACTA
1 TATATATGTTTTCAAAAAATCATTTTAAAAACTA
*
109800 TATTATATACGTTTTC-AAAAATCATTTTTAAAACTATA
1 TA-TATAT--GTTTTCAAAAAATCATTTTAAAAAC--TA
**
109838 TATATTATACGTTTTC-AAAAATGTTTTTTCAAAATTA-TA
1 TATA-TAT--GTTTTCAAAAAAT-CATTTT-AAAA--ACTA
* * * *
109877 TAATATATGTTTTC-AAAAATGTATTTTCAAACCCA
1 T-ATATATGTTTTCAAAAAAT-CATTTTAAAAACTA
* * *
109912 TATTATGTGTTTTCAAAAACTGATTTTAAAAACTATA
1 TA-TATATGTTTTCAAAAAATCATTTTAAAAAC--TA
* * *
109949 TATTATATGCTTTCAAAAAAAACGTTTTCTAAAAACTATA
1 TA-TATATGTTTTC-AAAAAATC-ATTT-TAAAAAC--TA
109989 TATTATATGTTTTCAAAAA
1 TA-TATATGTTTTCAAAAA
110008 TTATTTATTT
Statistics
Matches: 193, Mismatches: 28, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
33 9 0.05
34 9 0.05
35 44 0.23
36 23 0.12
37 33 0.17
38 26 0.13
39 18 0.09
40 30 0.16
42 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (34 bp):
TATATATGTTTTCAAAAAATCATTTTAAAAACTA
Found at i:109788 original size:13 final size:13
Alignment explanation
Indices: 109770--109796 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
109760 AAAACTATAT
109770 ATATGTTTTCAAA
1 ATATGTTTTCAAA
109783 ATATGTTTTCAAA
1 ATATGTTTTCAAA
109796 A
1 A
109797 CTATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
ATATGTTTTCAAA
Found at i:109877 original size:37 final size:37
Alignment explanation
Indices: 109765--110008 Score: 216
Period size: 37 Copynumber: 6.6 Consensus size: 37
109755 TTAAAAAAAC
109765 TATA-TATATGTTTTCAAAATATG--TTTTCAAAACTA
1 TATATTATATGTTTTCAAAA-ATGTTTTTTCAAAACTA
* **
109800 TAT-TATATACGTTTTCAAAAATCATTTTT-AAAACTATA
1 TATAT-TATATGTTTTCAAAAATGTTTTTTCAAAAC--TA
* *
109838 TATATTATACGTTTTCAAAAATGTTTTTTCAAAATTA
1 TATATTATATGTTTTCAAAAATGTTTTTTCAAAACTA
* * *
109875 TATAATATATGTTTTCAAAAATGTATTTTC-AAAC-C
1 TATATTATATGTTTTCAAAAATGTTTTTTCAAAACTA
* * * *
109910 CATATTATGTGTTTTCAAAAACTG-ATTTTAAAAACTA
1 TATATTATATGTTTTCAAAAA-TGTTTTTTCAAAACTA
* * * *
109947 TATATTATATGCTTTCAAAAAAAACGTTTTCTAAAAACTA
1 TATATTATATGTTTTC---AAAAATGTTTTTTCAAAACTA
109987 TATATTATATGTTTTCAAAAAT
1 TATATTATATGTTTTCAAAAAT
110009 TATTTATTTA
Statistics
Matches: 171, Mismatches: 23, Indels: 28
0.77 0.10 0.13
Matches are distributed among these distances:
35 28 0.16
36 28 0.16
37 51 0.30
38 27 0.16
39 6 0.04
40 31 0.18
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (37 bp):
TATATTATATGTTTTCAAAAATGTTTTTTCAAAACTA
Found at i:109883 original size:111 final size:109
Alignment explanation
Indices: 109768--110032 Score: 277
Period size: 112 Copynumber: 2.4 Consensus size: 109
109758 AAAAAACTAT
*
109768 ATATATGTTTTCAAAATATGTTTTCAAAACTATATTATATACGTTTTCAAAAA-TCATTTTTAAA
1 ATATATGTTTTCAAAATATGTTTTCAAAACTATATTATAT--GTTTTCAAAAACTCATTTTAAAA
* * * * *
109832 ACTATATATATTATACGTTTTC-AAAAATGTTTTTTCAAAATTATATA
64 AC--TATATATTATACGCTTTCAAAAAACGTTTTCTAAAAACTATATA
* * * *
109879 ATATATGTTTTCAAAA-ATGTATTTTCAAACCCATATTATGTGTTTTCAAAAACTGATTTTAAAA
1 ATATATGTTTTCAAAATATG--TTTTCAAAACTATATTATATGTTTTCAAAAACTCATTTTAAAA
*
109943 ACTATATATTATATGCTTTCAAAAAAAACGTTTTCTAAAAACTATATA
64 ACTATATATTATACGCTTTC--AAAAAACGTTTTCTAAAAACTATATA
* * *
109991 TTATATGTTTTCAAAAATTAT-TTATTTAAAACTACATTATAT
1 ATATATGTTTTC-AAAA-TATGTT-TTCAAAACTATATTATAT
110033 TATTATATAT
Statistics
Matches: 127, Mismatches: 17, Indels: 18
0.78 0.10 0.11
Matches are distributed among these distances:
109 16 0.13
110 14 0.11
111 27 0.21
112 51 0.40
113 17 0.13
115 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (109 bp):
ATATATGTTTTCAAAATATGTTTTCAAAACTATATTATATGTTTTCAAAAACTCATTTTAAAAAC
TATATATTATACGCTTTCAAAAAACGTTTTCTAAAAACTATATA
Found at i:109949 original size:72 final size:71
Alignment explanation
Indices: 109711--110008 Score: 237
Period size: 72 Copynumber: 4.0 Consensus size: 71
109701 CAAAAATAAT
* * ** *
109711 ATGTTTTCAAAAATTATATATTATATATGTTTCCAAAAAATCATTTAAAAAAAC-TATATA-TAT
1 ATGTTTTC-AAAACTATATA--ATATATGTTTTC-AAAAATCATTTTCAAAACCATATATATTAT
109774 GTTTTCAAAA
62 GTTTTCAAAA
* * * *
109784 TATGTTTTCAAAACTATATTATATACGTTTTCAAAAATCATTTTTAAAACTATATATATTATACG
1 -ATGTTTTCAAAACTATATAATATATGTTTTCAAAAATCATTTTCAAAACCATATATATTAT--G
109849 TTTTCAAAA
63 TTTTCAAAA
* * * *
109858 ATGTTTTTTCAAAATTATATAATATATGTTTTCAAAAATGTATTTTCAAACCCATAT-TA-TGTG
1 ATG--TTTTCAAAACTATATAATATATGTTTTCAAAAAT-CATTTTCAAAACCATATATATTATG
109921 TTTTCAAAA
63 TTTTCAAAA
* * * * * *
109930 ACTGATTTTAAAAACTATATATTATATGCTTTCAAAAAAAACGTTTTCTAAAAAC-TATATATTA
1 A-TG-TTTTCAAAACTATATAATATATGTTTTC--AAAAATCATTTTC-AAAACCATATATA-T-
109994 TATGTTTTCAAAA
59 TATGTTTTCAAAA
110007 AT
1 AT
110009 TATTTATTTA
Statistics
Matches: 182, Mismatches: 27, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
70 15 0.08
71 16 0.09
72 38 0.21
73 22 0.12
74 31 0.17
75 33 0.18
76 14 0.08
77 13 0.07
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (71 bp):
ATGTTTTCAAAACTATATAATATATGTTTTCAAAAATCATTTTCAAAACCATATATATTATGTTT
TCAAAA
Found at i:110942 original size:13 final size:13
Alignment explanation
Indices: 110924--110970 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
110914 GGATACACGT
110924 ATTTTTAAAAAGC
1 ATTTTTAAAAAGC
*
110937 ATTTTT-AAAA-T
1 ATTTTTAAAAAGC
*
110948 A-TTTCAAAAAGC
1 ATTTTTAAAAAGC
110960 ATTTTTAAAAA
1 ATTTTTAAAAA
110971 ATTCTTCCGG
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
10 3 0.11
11 5 0.19
12 5 0.19
13 14 0.52
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (13 bp):
ATTTTTAAAAAGC
Found at i:111828 original size:21 final size:21
Alignment explanation
Indices: 111790--111830 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
111780 TTTTCTAGAA
*
111790 AAAGGATCGATCATTTGCTAT
1 AAAGGATCGATCACTTGCTAT
111811 AAAGGATCGATTC-CTTGCTA
1 AAAGGATCGA-TCACTTGCTA
111831 ATAATTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (21 bp):
AAAGGATCGATCACTTGCTAT
Found at i:119561 original size:14 final size:15
Alignment explanation
Indices: 119542--119583 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
119532 CCCTGAAAAT
119542 AAAATAA-AATAATA
1 AAAATAATAATAATA
*
119556 AAAATAATATTAATA
1 AAAATAATAATAATA
*
119571 AATAATGATAATA
1 AA-AATAATAATA
119584 TAATAATATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 7 0.30
15 8 0.35
16 8 0.35
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
AAAATAATAATAATA
Found at i:119574 original size:19 final size:18
Alignment explanation
Indices: 119537--119589 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
119527 TTGTACCCTG
* *
119537 AAAATAAAATAAAATAATA
1 AAAATAATATAATA-AATA
119556 AAAATAATATTAATAAATA
1 AAAATAATA-TAATAAATA
**
119575 ATGATAATATAATAA
1 AAAATAATATAATAA
119590 TATCTGAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 6 0.21
19 19 0.66
20 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAATAATATAATAAATA
Found at i:120703 original size:45 final size:45
Alignment explanation
Indices: 120625--121077 Score: 357
Period size: 45 Copynumber: 10.2 Consensus size: 45
120615 GATACCATAG
* * * *
120625 AAAGGTTGACTCTTCTTCAG-GAGAAAGTAAAAAAGGACAACACTA
1 AAAGATTGACTCCTCTTC-GCGAGAAAGTCAAGAAGGACAACACTA
* * * * * * *
120670 AAAGATTGACTCATCTTTGCGAGAGATTCAAAAAGGATAACACTG
1 AAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTA
* *
120715 AAAGATTGACTCCTCTCCGCGAGAAAGTCAAGAAGGATAACACTA
1 AAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTA
* * *
120760 AAAGATTTACTCATCTTCACGAGAAAGTCAAGAAGGACAACACTA
1 AAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTA
* * ** * **
120805 AAATATTAACTCCTCTTCATGAGAAATTCAAGGAA-GACAACACCG
1 AAAGATTGACTCCTCTTCGCGAGAAAGTCAA-GAAGGACAACACTA
* * * *
120850 AAAGACTGAATCCTC-TCTGAGAGAAAGTCAGGAAGGACAACACTA
1 AAAGATTGACTCCTCTTC-GCGAGAAAGTCAAGAAGGACAACACTA
* * * * *
120895 AAAGATTGACTTCTCTTCGCGAGAAAGTCAA-TA--ATAACATTG
1 AAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTA
* * * * * *
120937 AAAGATTGACTCCTCTTCACGAGAGAGTCAAG-A--ATAATATTT
1 AAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTA
* * ** * * *
120979 AAAGATTGACTCCTCTTCACGGGGGAGTCAAGAAAGACAATACTG
1 AAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTA
* ** * *
121024 AAAGATTGACTTCTCTTTACGAGAAAGTCAAGAATGACATCACTA
1 AAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTA
*
121069 AAAGGTTGA
1 AAAGATTGA
121078 TTTATCTTCA
Statistics
Matches: 333, Mismatches: 66, Indels: 18
0.80 0.16 0.04
Matches are distributed among these distances:
42 72 0.22
43 1 0.00
44 7 0.02
45 248 0.74
46 5 0.02
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (45 bp):
AAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGACAACACTA
Found at i:120834 original size:135 final size:134
Alignment explanation
Indices: 120625--121077 Score: 427
Period size: 135 Copynumber: 3.4 Consensus size: 134
120615 GATACCATAG
* * * * * **
120625 AAAGGTTGAC-TCTTCTTCAGGAGAAAGTAAAAAAGGACAACACTAAAAGATTGACTCATCTTTG
1 AAAGATTGACTTC-TCTTCACGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCCTCTTCA
*
120689 CGAGAGATTCAAAAAGGATAACACTGAAAGATTGACTCCTCTCCGCGAGAAAGTCAAGAAGGATA
65 CGAGAGATTC-AAAAGGATAACACTGAAAGATTGACTCCTCTCCGCGAGAAAGTCAAGAAGGACA
120754 ACACTA
129 ACACTA
* * *
120760 AAAGATTTAC-TCATCTTCACGAGAAAGTCAAGAAGGACAACACTAAAATATTAACTCCTCTTCA
1 AAAGATTGACTTC-TCTTCACGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCCTCTTCA
* * * * * * * * *
120824 TGAGAAATTCAAGGAA-GACAACACCGAAAGACTGAATCCTCTCTGAGAGAAAGTCAGGAAGGAC
65 CGAGAGATTCAA--AAGGATAACACTGAAAGATTGACTCCTCTCCGCGAGAAAGTCAAGAAGGAC
120888 AACACTA
128 AACACTA
* * * * *
120895 AAAGATTGACTTCTCTTCGCGAGAAAGTCAA-TA--ATAACATTGAAAGATTGACTCCTCTTCAC
1 AAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCCTCTTCAC
* * * * * * * * ** * *
120957 GAGAGAGTC--AAGAATAATATTTAAAGATTGACTCCTCTTCACGGGGGAGTCAAGAAAGACAAT
66 GAGAGATTCAAAAGGATAACACTGAAAGATTGACTCCTCTCCGCGAGAAAGTCAAGAAGGACAAC
*
121020 ACTG
131 ACTA
* * * *
121024 AAAGATTGACTTCTCTTTACGAGAAAGTCAAGAATGACATCACTAAAAGGTTGA
1 AAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAGGACAACACTAAAAGATTGA
121078 TTTATCTTCA
Statistics
Matches: 252, Mismatches: 59, Indels: 17
0.77 0.18 0.05
Matches are distributed among these distances:
128 2 0.01
129 65 0.26
130 1 0.00
132 43 0.17
134 3 0.01
135 134 0.53
136 4 0.02
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (134 bp):
AAAGATTGACTTCTCTTCACGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCCTCTTCAC
GAGAGATTCAAAAGGATAACACTGAAAGATTGACTCCTCTCCGCGAGAAAGTCAAGAAGGACAAC
ACTA
Found at i:120946 original size:42 final size:42
Alignment explanation
Indices: 120706--121187 Score: 251
Period size: 45 Copynumber: 11.1 Consensus size: 42
120696 TTCAAAAAGG
* * *
120706 ATAACACTGAAAGATTGACTCCTCTCCGCGAGAAAGTCAAGAA
1 ATAACATTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAG-A
* * * *
120749 GGATAACACTAAAAGATTTACTCATCTTCACGAGAAAGTCAAGAA
1 --ATAACATTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAG-A
* * * * * * *
120794 GGACAACACTAAAATATTAACTCCTCTTCATGAGAAATTCAAGGAA
1 --ATAACATTGAAAGATTGACTCCTCTTCACGAGAAAGTCAA-G-A
* ** * * * *
120840 GACAACACCGAAAGACTGAATCCTCTCTGA-GAGAAAGTCAGGAAGG
1 -ATAACATTGAAAGATTGACTCCTCT-TCACGAGAAAGTC---AAGA
* * * * * *
120886 ACAACACTAAAAGATTGACTTCTCTTCGCGAGAAAGTCAATA
1 ATAACATTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
*
120928 ATAACATTGAAAGATTGACTCCTCTTCACGAGAGAGTCAAGA
1 ATAACATTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* * * **
120970 ATAATATTTAAAGATTGACTCCTCTTCACGGGGGAGTCAAGA
1 ATAACATTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* *
121012 A-AGACAATACTGAAAGATTGACTTCTCTTTACGAGAAAGTCAAGA
1 ATA-AC-AT--TGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* * * * ** * **
121057 ATGACATCACTAAAAGGTTGATTTATCTTCATGA-AAAAACTAAGA
1 AT-A-A-CATTGAAAGATTGACTCCTCTTCACGAGAAAGTC-AAGA
* ** **
121102 ACAACATTGAAAGATTGACTCCTCTTCACGAGGGAGTCGGGA
1 ATAACATTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
* *
121144 ATAAC----AAAGATTCACAT-CTCTTCACGAGGAAGTCAAGA
1 ATAACATTGAAAGATTGAC-TCCTCTTCACGAGAAAGTCAAGA
121182 ATAACA
1 ATAACA
121188 AAGATTGACT
Statistics
Matches: 344, Mismatches: 76, Indels: 40
0.75 0.17 0.09
Matches are distributed among these distances:
38 32 0.09
39 1 0.00
41 1 0.00
42 103 0.30
43 5 0.01
44 6 0.02
45 184 0.53
46 5 0.01
47 4 0.01
48 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (42 bp):
ATAACATTGAAAGATTGACTCCTCTTCACGAGAAAGTCAAGA
Found at i:121052 original size:174 final size:176
Alignment explanation
Indices: 120633--121139 Score: 459
Period size: 174 Copynumber: 2.9 Consensus size: 176
120623 AGAAAGGTTG
* * * * * *
120633 ACTCTTCTTCAGGAGAAAGT-AAAAAAGGACAACACTAAAAGATTGAC-TCATCTTTGCGAGAGA
1 ACTCCTCTTCACGAGAAAGTCAAGAAA-GACAACACTGAAAGATTGACTTC-TCTTTACGAGAAA
* * * * * * * *
120696 TTCAAAAAGGATAACACTGAAAGATTGACTCCTCTCCGCGAGAAAGTCAAGAAGGATAACACTAA
64 GTCAAGAAGGACAACACTAAAAGATTGACTTCTCTTCGCGAGAAAGTCAA-AA--ATAACATTGA
* * * *
120761 AAGATTTACTCATCTTCACGAGAAAGTCAAGAAGGACAACACTAAAATATTA
126 AAGATTGACTCCTCTTCACGAGAGAGTCAAGAA-GACAACACTAAAAGATTA
* * * * * * * *
120813 ACTCCTCTTCATGAGAAATTCAAGGAAGACAACACCGAAAGACTGAATCCTCTCTGA-GAGAAAG
1 ACTCCTCTTCACGAGAAAGTCAAGAAAGACAACACTGAAAGATTGACTTCTCT-TTACGAGAAAG
* *
120877 TCAGGAAGGACAACACTAAAAGATTGACTTCTCTTCGCGAGAAAGTCAATAATAACATTGAAAGA
65 TCAAGAAGGACAACACTAAAAGATTGACTTCTCTTCGCGAGAAAGTCAAAAATAACATTGAAAGA
* * * * *
120942 TTGACTCCTCTTCACGAGAGAGTCAAG-A-ATAATATTTAAAGATTG
130 TTGACTCCTCTTCACGAGAGAGTCAAGAAGACAACACTAAAAGATTA
* ** *
120987 ACTCCTCTTCACGGGGGAGTCAAGAAAGACAATACTGAAAGATTGACTTCTCTTTACGAGAAAGT
1 ACTCCTCTTCACGAGAAAGTCAAGAAAGACAACACTGAAAGATTGACTTCTCTTTACGAGAAAGT
* * * * * ** ** * *
121052 CAAGAATGACATCACTAAAAGGTTGATTTATCTTCATGA-AAAAACTAAGAACAACATTGAAAGA
66 CAAGAAGGACAACACTAAAAGATTGACTTCTCTTCGCGAGAAAGTC-AAAAATAACATTGAAAGA
*
121116 TTGACTCCTCTTCACGAGGGAGTC
130 TTGACTCCTCTTCACGAGAGAGTC
121140 GGGAATAACA
Statistics
Matches: 265, Mismatches: 57, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
173 6 0.02
174 131 0.49
176 1 0.00
177 36 0.14
179 1 0.00
180 84 0.32
181 6 0.02
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (176 bp):
ACTCCTCTTCACGAGAAAGTCAAGAAAGACAACACTGAAAGATTGACTTCTCTTTACGAGAAAGT
CAAGAAGGACAACACTAAAAGATTGACTTCTCTTCGCGAGAAAGTCAAAAATAACATTGAAAGAT
TGACTCCTCTTCACGAGAGAGTCAAGAAGACAACACTAAAAGATTA
Found at i:121211 original size:38 final size:38
Alignment explanation
Indices: 121111--121233 Score: 147
Period size: 38 Copynumber: 3.2 Consensus size: 38
121101 AACAACATTG
* * **
121111 AAAGATTGACTCCTCTTCACGAGGGAGTCGGGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
121149 AAAGATTCACATCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
121187 AAAGATTGACTTCTATTCATGAGGAAGTAAAAAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
121225 GAAGATTGA
1 AAAGATTGA
121234 AGTTTTTAGA
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 72 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:122067 original size:41 final size:40
Alignment explanation
Indices: 121999--122103 Score: 115
Period size: 41 Copynumber: 2.6 Consensus size: 40
121989 ACTCGAGGGT
*
121999 CTTACAGATGGCCTGAAGGACTTATCATC-TCACTCAAAAGA
1 CTTACAGATGGCCCGAA-GACTTATCATCAT-ACTCAAAAGA
* * * *
122040 CTTACAGATGACCCGAAGATTTAATCATCATGCTCGAAAGA
1 CTTACAGATGGCCCGAAGACTT-ATCATCATACTCAAAAGA
122081 CTTACA-ATGGCCCGAAGGACTTA
1 CTTACAGATGGCCCGAA-GACTTA
122104 CCAATTTGGG
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
40 14 0.26
41 39 0.72
42 1 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (40 bp):
CTTACAGATGGCCCGAAGACTTATCATCATACTCAAAAGA
Found at i:122556 original size:512 final size:514
Alignment explanation
Indices: 121589--123629 Score: 2446
Period size: 512 Copynumber: 4.0 Consensus size: 514
121579 ATCTGATGTT
* * * * *
121589 CCAATTTTGAAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTAAAAAATT
1 CCAATTTGGGAAATAGTCTACTGGGTAAGAAACTTTGGAAATCGCTTTCTCACTTTTCAAAAATT
* * * *
121654 CATTTTCTGAAAACATTAAATAAGAAACTTTGAAAATTGCTTTCTCATCTTTTTTGTAAA-TCAT
66 CATTTTCTGAAAACACTAAATAAGAAACTTTGGAAATCGCTTTCTCA--TTTTTT-CAAATTCAT
* * ** *
121718 GTGAAAACATCCTACCTGAAGGTTTTTTAGATGGCCCGAA-GAACTTATCATCTTGCTCGAAAGA
128 GTGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAATG-ACTTATCATCTCGCTCGAAAGA
* * *
121782 -TGACAGATGACCCGAAGGATTTAATCATCATGCT-GAACAGAATTACTAATGGCCCAAAGGACT
192 CTAACAGATGACCCAAAGGATTTAATCATCATGCTCGAA-AGACTTACTAATGGCCCAAAGGACT
* * * *
121845 TCCCAATTTTGGAAATAGTTTATTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTCTTCAAAAA
256 TACCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTCTTCAAAAA
* * * * *
121910 TTTCATTTTCTGAAAAGATTTAAATGTGAAACTTTGGAAATC-ACTTTCTCCTTTTTTTGAAAAT
321 TTTCATTTTCTGAAAATA-CTAAATGAGAAACTTTGGAAATCGA-TTTCT-C-ATTTTTCAAAAT
* * * * * *
121974 -ATGTGAAAATATCCTACTCGAGGGTCTTACAGATGGCCTGAAGGACTTATCATCTCACTCAAAA
382 CATGTGAAAACATCATACCCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTCACTCGAAA
*
122038 GACTTACAGATGACCCGAA-GATTTAATCATCATGCTCGAAAGACTTAC-AATGGCCCGAAGGAC
447 GACTTACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGAC
122101 TTA
512 TTA
* *
122104 CCAATTTGGGAAATAGTCTACCGGGTAAGAAACTTTGGAAATCGTTTTCTCACTTTTCAAAAATT
1 CCAATTTGGGAAATAGTCTACTGGGTAAGAAACTTTGGAAATCGCTTTCTCACTTTTCAAAAATT
* * *
122169 CATTTTATGAGAATACTAAATAAGAAACTTTGGAAATCGCTTTCTCA-TTTTTCAAATTCATGTG
66 CATTTTCTGAAAACACTAAATAAGAAACTTTGGAAATCGCTTTCTCATTTTTTCAAATTCATGTG
* * * * *
122233 AAAACATCCTACCCGAAGGTCTTACGGATGG-CTGAATGACTTATCCTCTTGCTCGAAAGACTCA
131 AAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAATGACTTATCATCTCGCTCGAAAGACTAA
*
122297 CAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCA
196 CAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCAAAGGACTTACCA
* *
122362 ATTTTGGAAATAGATTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTCTTCAAAAATTTCA
261 ATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTCTTCAAAAATTTCA
* * * * *
122427 TTTTCTTAAAACACTAAATGAGAAACTTTGAAAATCGATTTATCATTTTTTTTGAAAATCATGTG
326 TTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGATTTCTCA---TTTTTCAAAATCATGTG
* * *
122492 AAAACATCATGCCCGAAGGTC-TATAGATGGCCCGAATGACTTATCATCTCACTCGAAAGACTTA
388 AAAACATCATACCCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTCACTCGAAAGACTTA
* * * *
122556 CAGATGACCCAAATGATTTAATCATCATTCTCAAAAGACTTACTAATGGCCTGAAGGACTTA
453 CAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
* *
122618 CCAATTTGGGAAATAGTCTACTGGGTAAGAAACTTTGGAAATTGCTTTCTCACTTTTCAAAATTT
1 CCAATTTGGGAAATAGTCTACTGGGTAAGAAACTTTGGAAATCGCTTTCTCACTTTTCAAAA-AT
* ** * *
122683 TCATTTTCTGAATACACTAAATGTGAAACTTTGGAAATCGCTTTCTCATTATTTTTATTGAAAAT
65 TCATTTTCTGAAAACACTAAATAAGAAACTTTGGAAATCGCTTTCTC---A-TTTT-TTCAAATT
* ** * * * *
122748 AATGTGAAAACATCCTGTCTGAAGGTCTTATAGATGGCACGAAGGACTTATCATCTCGCTCGAAA
125 CATGTGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAATGACTTATCATCTCGCTCGAAA
* * * * * * * *
122813 AACTTACAGACGACCCGAAGGATTTAATCACCATGCTAGAAAGACTTACTAATGGCCCGAATGAC
190 GACTAACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCAAAGGAC
* * *
122878 TTACCAATTTGGGAAATAGTCTACTGGGTAAGAAACTTTGGAAATCACTTTCTCACTTTTCAAAA
255 TTACCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTCTTCAAAA
* * * * * *
122943 ATTTCATTTTATGAAAATACTAAATGAAAAACTTTGGAAATTGCTTTTTCATTTTTCAAATTCAT
320 ATTTCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGATTTCTCATTTTTCAAAATCAT
* *
123008 ATG---A-A--A-A--C--A--TC---CA-A---CCCGAAGGACTTATCATCTCGCTCGAAAGAC
385 GTGAAAACATCATACCCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTCACTCGAAAGAC
* * * * *
123053 TTAAAAATGACCTAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTA
450 TTACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
* * * * * *
123118 CCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATTGTTTTCTTA-TTCTTCAAAAAT
1 CCAATTTGGGAAATAGTCTACTGGGTAAGAAACTTTGGAAATCGCTTTCTCACTT-TTCAAAAAT
* * * * * *
123182 ATCATTTTTTGAAAATACTAAATGAGAAACTTTAGAAATTGCTTTCTCA-TTTTTCAAATTCATA
65 -TCATTTTCTGAAAACACTAAATAAGAAACTTTGGAAATCGCTTTCTCATTTTTTCAAATTCATG
* *
123246 TGAAAACAT-CTACCCAAAGGTCTTACGGATGGCCCGAATGACTTATCATCTCGCTCGAAAGACT
129 TGAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAATGACTTATCATCTCGCTCGAAAGACT
* * * **
123310 AACAGATGA-CCAGAAAGATTTAATCATCATGCTCGAAAGATTTACTGATGGCCTGAAGGACTTA
194 AACAGATGACCCA-AAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCAAAGGACTTA
* * *
123374 CCAA-TTGGGAAATAGTTTACTGGGTAAGAAACTTTAGAAATCACTTTTTTACT-TGTCAAAATT
258 CCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTCT-TCAAAAAT
* *
123437 TTCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGT
322 TTCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGATTTCTCATTTTTCAAAATCATGT
* * * *
123502 GAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAGGACTTATTATCTTACTTGAAAGACTT
387 GAAAACATCATACCCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTCACTCGAAAGACTT
** * * ** *
123567 ACAGATGACCTGAAGGATTTAATTATCATGCTCGGAAGACTTACTGTTGGCCCGAACGACTTA
452 ACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
123630 AATGAGAAAC
Statistics
Matches: 1317, Mismatches: 166, Indels: 89
0.84 0.11 0.06
Matches are distributed among these distances:
491 1 0.00
492 115 0.09
493 101 0.08
494 17 0.01
495 4 0.00
496 1 0.00
497 1 0.00
499 4 0.00
500 182 0.14
501 1 0.00
503 2 0.00
504 1 0.00
505 2 0.00
506 2 0.00
508 3 0.00
509 1 0.00
510 2 0.00
511 52 0.04
512 318 0.24
513 52 0.04
514 76 0.06
515 142 0.11
516 1 0.00
518 1 0.00
519 14 0.01
520 3 0.00
521 37 0.03
522 181 0.14
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (514 bp):
CCAATTTGGGAAATAGTCTACTGGGTAAGAAACTTTGGAAATCGCTTTCTCACTTTTCAAAAATT
CATTTTCTGAAAACACTAAATAAGAAACTTTGGAAATCGCTTTCTCATTTTTTCAAATTCATGTG
AAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAATGACTTATCATCTCGCTCGAAAGACTAA
CAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCAAAGGACTTACCA
ATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTCTTCAAAAATTTCA
TTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGATTTCTCATTTTTCAAAATCATGTGAAA
ACATCATACCCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTCACTCGAAAGACTTACAG
ATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
Found at i:122561 original size:41 final size:42
Alignment explanation
Indices: 122515--122617 Score: 104
Period size: 42 Copynumber: 2.5 Consensus size: 42
122505 CGAAGGTCTA
*
122515 TAGATGGCCCGAATGACTTATCATC-TCACTCGAAAGACTTAC
1 TAGATGGCCCGAATGACTTATCATCAT-ACTCAAAAGACTTAC
* * * *
122557 -AGATGACCCAAATGATTTAATCATCATTCTCAAAAGACTTAC
1 TAGATGGCCCGAATGACTT-ATCATCATACTCAAAAGACTTAC
* *
122599 TA-ATGGCCTGAAGGACTTA
1 TAGATGGCCCGAATGACTTA
122618 CCAATTTGGG
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
41 16 0.33
42 30 0.62
43 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (42 bp):
TAGATGGCCCGAATGACTTATCATCATACTCAAAAGACTTAC
Found at i:122567 original size:259 final size:256
Alignment explanation
Indices: 121589--123629 Score: 2357
Period size: 259 Copynumber: 8.0 Consensus size: 256
121579 ATCTGATGTT
* * * *
121589 CCAATTTTGAAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACT-TTTAAAAAAT
1 CCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTCTTCAAAAATT
* * * * * **
121653 TCATTTTCTGAAAACATTAAATAAGAAACTTTGAAAATTGCTTTCTCATCTTTTTTGTAAATCAT
66 TCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCA---TTTTTCAAAATCAT
* * * * *
121718 GTGAAAACATCCTACCTGAAGGTTTTTTAGATGGCCCGAAGAACTTATCATCTTGCTCGAAAGA-
128 GTGAAAACATCCTACCCGAAGG-TCTATAGATGGCCCGAAGGACTTATCATCTCGCTCGAAAGAC
* * * *
121782 TGACAGATGACCCGAAGGATTTAATCATCATGCT-GAACAGAATTACTAATGGCCCAAAGGACTT
192 TTACAGATGACCCAAAGGATTTAATCATCATGCTCGAA-AGACTTACTAATGGCCCGAAGGACTT
*
121846 C
256 A
* *
121847 CCAATTTTGGAAATAGTTTATTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTCTTCAAAAATT
1 CCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTCTTCAAAAATT
* * * * * *
121912 TCATTTTCTGAAAAGATTTAAATGTGAAACTTTGGAAATCACTTTCTCCTTTTTTTGAAAAT-AT
66 TCATTTTCTGAAAATA-CTAAATGAGAAACTTTGGAAATCGCTTTCT-C-ATTTTTCAAAATCAT
* * * * * * *
121976 GTGAAAATATCCTACTCGAGGGTCTTACAGATGGCCTGAAGGACTTATCATCTCACTCAAAAGAC
128 GTGAAAACATCCTACCCGAAGGTC-TATAGATGGCCCGAAGGACTTATCATCTCGCTCGAAAGAC
*
122041 TTACAGATGACCCGAA-GATTTAATCATCATGCTCGAAAGACTTAC-AATGGCCCGAAGGACTTA
192 TTACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
* * * * *
122104 CCAATTTGGGAAATAGTCTACCGGGTAAGAAACTTTGGAAATCGTTTTCTCACTTTTCAAAAA-T
1 CCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTCTTCAAAAATT
* * * *
122168 TCATTTTATGAGAATACTAAATAAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTG
66 TCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATCATGTG
* * * * *
122233 AAAACATCCTACCCGAAGGTCT-TACGGATGG-CTGAATGACTTATCCTCTTGCTCGAAAGACTC
131 AAAACATCCTACCCGAAGGTCTATA--GATGGCCCGAAGGACTTATCATCTCGCTCGAAAGACTT
* *
122296 ACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTA
194 ACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
* * *
122359 CCAATTTTGGAAATAGATTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTCTTCAAAAATT
1 CCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTCTTCAAAAATT
* * * * * *
122424 TCATTTTCTTAAAACACTAAATGAGAAACTTTGAAAATCGATTTATCATTTTTTTTGAAAATCAT
66 TCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCA---TTTTTCAAAATCAT
* * * *
122489 GTGAAAACATCATGCCCGAAGGTCTATAGATGGCCCGAATGACTTATCATCTCACTCGAAAGACT
128 GTGAAAACATCCTACCCGAAGGTCTATAGATGGCCCGAAGGACTTATCATCTCGCTCGAAAGACT
* * * *
122554 TACAGATGACCCAAATGATTTAATCATCATTCTCAAAAGACTTACTAATGGCCTGAAGGACTTA
193 TACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
* * * * *
122618 CCAATTTGGGAAATAGTCTACTGGGTAAGAAACTTTGGAAATTGCTTTCTCACTTTTCAAAATTT
1 CCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTCTTCAAAAATT
* * * *
122683 TCATTTTCTGAATACACTAAATGTGAAACTTTGGAAATCGCTTTCTCATTATTTTTATTGAAAAT
66 TCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTC---A--TTT-TTCAAAAT
* ** * *
122748 AATGTGAAAACATCCTGTCTGAAGGTCTTATAGATGGCACGAAGGACTTATCATCTCGCTCGAAA
125 CATGTGAAAACATCCTACCCGAAGGTC-TATAGATGGCCCGAAGGACTTATCATCTCGCTCGAAA
* * * * * *
122813 AACTTACAGACGACCCGAAGGATTTAATCACCATGCTAGAAAGACTTACTAATGGCCCGAATGAC
189 GACTTACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGAC
122878 TTA
254 TTA
* * * *
122881 CCAATTTGGGAAATAGTCTACTGGGTAAGAAACTTTGGAAATCACTTTCTCACTTTTCAAAAATT
1 CCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTCTTCAAAAATT
* * * * * *
122946 TCATTTTATGAAAATACTAAATGAAAAACTTTGGAAATTGCTTTTTCATTTTTCAAATTCATATG
66 TCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATCATGTG
*
123011 AAAACA---T---C------C---A-A---CCCGAAGGACTTATCATCTCGCTCGAAAGACTTAA
131 AAAACATCCTACCCGAAGGTCTATAGATGGCCCGAAGGACTTATCATCTCGCTCGAAAGACTTAC
* * * *
123057 AAATGACCTAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTA
196 AGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
* * * * * *
123118 CCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATTGTTTTCTTATTCTTCAAAAATA
1 CCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTCTTCAAAAATT
* * * * *
123183 TCATTTTTTGAAAATACTAAATGAGAAACTTTAGAAATTGCTTTCTCATTTTTCAAATTCATATG
66 TCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATCATGTG
* * *
123248 AAAACAT-CTACCCAAAGGTCT-TACGGATGGCCCGAATGACTTATCATCTCGCTCGAAAGACTA
131 AAAACATCCTACCCGAAGGTCTATA--GATGGCCCGAAGGACTTATCATCTCGCTCGAAAGACTT
* * * *
123311 ACAGATGA-CCAGAAAGATTTAATCATCATGCTCGAAAGATTTACTGATGGCCTGAAGGACTTA
194 ACAGATGACCCA-AAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
* * * *
123374 CCAA-TTGGGAAATAGTTTACTGGGTAAGAAACTTTAGAAATCACTTTTTTACT-TGTCAAAATT
1 CCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTCT-TCAAAAAT
*
123437 TTCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGT
65 TTCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATCATGT
* * ** *
123502 GAAAACATCCTACCCGAAGGTCTTACAGATGGCCCGAAGGACTTATTATCTTACTTGAAAGACTT
130 GAAAACATCCTACCCGAAGGTC-TATAGATGGCCCGAAGGACTTATCATCTCGCTCGAAAGACTT
** * * ** *
123567 ACAGATGACCTGAAGGATTTAATTATCATGCTCGGAAGACTTACTGTTGGCCCGAACGACTTA
194 ACAGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
123630 AATGAGAAAC
Statistics
Matches: 1536, Mismatches: 199, Indels: 98
0.84 0.11 0.05
Matches are distributed among these distances:
237 206 0.13
239 1 0.00
240 1 0.00
241 1 0.00
242 1 0.00
245 1 0.00
248 1 0.00
250 1 0.00
252 1 0.00
253 50 0.03
254 60 0.04
255 215 0.14
256 241 0.16
257 91 0.06
258 137 0.09
259 268 0.17
260 28 0.02
261 6 0.00
262 32 0.02
263 194 0.13
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (256 bp):
CCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTCTTCAAAAATT
TCATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAAATCATGTG
AAAACATCCTACCCGAAGGTCTATAGATGGCCCGAAGGACTTATCATCTCGCTCGAAAGACTTAC
AGATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
Found at i:123113 original size:42 final size:41
Alignment explanation
Indices: 123025--123117 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
123015 CATCCAACCC
123025 GAAGGACTTATCATCTCGCTCGAAAGACTTAAAAATGACCT
1 GAAGGACTTATCATCTCGCTCGAAAGACTTAAAAATGACCT
* * *** *
123066 AAAGGATTTAATCATCAT-GCTCGAAAGACTTACTGATGGCCT
1 GAAGGACTT-ATCATC-TCGCTCGAAAGACTTAAAAATGACCT
123108 GAAGGACTTA
1 GAAGGACTTA
123118 CCAATTTTGG
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
41 8 0.19
42 33 0.79
43 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (41 bp):
GAAGGACTTATCATCTCGCTCGAAAGACTTAAAAATGACCT
Found at i:123202 original size:237 final size:236
Alignment explanation
Indices: 122787--123526 Score: 912
Period size: 237 Copynumber: 3.0 Consensus size: 236
122777 ATAGATGGCA
* * * * * *
122787 CGAAGGACTTATCATCTCGCTCGAAAAACTTACAGACGACCCGAAGGATTTAATCACCATGCTAG
1 CGAAGGACTTATCATCTCGCTCGAAAGACTTAAAGATGA-CCAAAGGATTTAATCATCATGCTCG
* * * *
122852 AAAGACTTACTAATGGCCCGAATGACTTACCAATTTGGGAAATAGTCTACTGGGTAAGAAACTTT
65 AAAGACTTACTGATGGCCTGAAGGACTTACCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTT
* * * *
122917 GGAAATCACTTTCTCACTTTTCAAAAATTTCATTTTATGAAAATACTAAATGAAAAACTTTGGAA
130 GGAAATAATTTTCTTACTTTTCAAAAATTTCATTTTATGAAAATACTAAATGAGAAACTTTGGAA
*
122982 ATTGCTTTTTCATTTTTCAAATTCATATGAAAACATCCAACC
195 ATTGCTTTCTCATTTTTCAAATTCATATGAAAACATCCAACC
*
123024 CGAAGGACTTATCATCTCGCTCGAAAGACTTAAAAATGACCTAAAGGATTTAATCATCATGCTCG
1 CGAAGGACTTATCATCTCGCTCGAAAGACTTAAAGATGACC-AAAGGATTTAATCATCATGCTCG
* *
123089 AAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTT
65 AAAGACTTACTGATGGCCTGAAGGACTTACCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTT
** * * *
123154 GGAAATTGTTTTCTTA-TTCTTCAAAAATATCATTTTTTGAAAATACTAAATGAGAAACTTTAGA
130 GGAAATAATTTTCTTACTT-TTCAAAAATTTCATTTTATGAAAATACTAAATGAGAAACTTTGGA
123218 AATTGCTTTCTCATTTTTCAAATTCATATGAAAACATCTACCCAAAGGTCTTACGGATGGCC
194 AATTGCTTTCTCATTTTTCAAATTCATATGAAAACA--T---C------C--A---A---CC
* *
123280 CGAATGACTTATCATCTCGCTCGAAAGAC-TAACAGATGACCAGAAAGATTTAATCATCATGCTC
1 CGAAGGACTTATCATCTCGCTCGAAAGACTTAA-AGATGACCA-AAGGATTTAATCATCATGCTC
*
123344 GAAAGATTTACTGATGGCCTGAAGGACTTACCAA-TTGGGAAATAGTTTACTGGGTAAGAAACTT
64 GAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTGGGAAATAGTTTACTGGGTAAGAAACTT
* * * * *
123408 TAGAAATCACTTTT-TTACTTGTCAAAATTTTCATTTTCTGAAAATACTAAATGAGAAACTTTGG
129 TGGAAAT-AATTTTCTTACTTTTCAAAAATTTCATTTTATGAAAATACTAAATGAGAAACTTTGG
* * *
123472 AAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTACC
193 AAATTGCTTTCTCATTTTTCAAATTCATATGAAAACATCCAACC
*
123516 CGAAGGTCTTA
1 CGAAGGACTTA
123527 CAGATGGCCC
Statistics
Matches: 437, Mismatches: 41, Indels: 51
0.83 0.08 0.10
Matches are distributed among these distances:
236 15 0.03
237 202 0.46
239 2 0.00
242 1 0.00
244 1 0.00
248 1 0.00
250 2 0.00
253 2 0.00
255 115 0.26
256 96 0.22
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (236 bp):
CGAAGGACTTATCATCTCGCTCGAAAGACTTAAAGATGACCAAAGGATTTAATCATCATGCTCGA
AAGACTTACTGATGGCCTGAAGGACTTACCAATTTGGGAAATAGTTTACTGGGTAAGAAACTTTG
GAAATAATTTTCTTACTTTTCAAAAATTTCATTTTATGAAAATACTAAATGAGAAACTTTGGAAA
TTGCTTTCTCATTTTTCAAATTCATATGAAAACATCCAACC
Found at i:123524 original size:256 final size:256
Alignment explanation
Indices: 123022--123629 Score: 875
Period size: 256 Copynumber: 2.4 Consensus size: 256
123012 AAACATCCAA
*
123022 CCCGAAGGACTTATCATCTCGCTCGAAAGACTTAA-AAATGACCTA-AAGGATTTAATCATCATG
1 CCCGAAGGACTTATCATCTCGCTCGAAAGAC-TAACAGATGACC-AGAAGGATTTAATCATCATG
*
123085 CTCGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAA
64 CTCGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTGGGAAATAGTTTACTAGGTAAGAAA
* ** * *
123150 CTTTGGAAATTGTTTTCTTATTCTTCAAAAATATCATTTTTTGAAAATACTAAATGAGAAACTTT
129 CTTTAGAAATACTTTTCTTATTCGTCAAAAATATCATTTTCTGAAAATACTAAATGAGAAACTTT
* *
123215 AGAAATTGCTTTCTCATTTTTCAAATTCATATGAAAACATCTACCCAAAGGTCTTACGGATGG
194 AGAAATCGCTTTCTCATTTTTCAAATTCATATGAAAACATCTACCCAAAGGTCTTACAGATGG
* *
123278 CCCGAATGACTTATCATCTCGCTCGAAAGACTAACAGATGACCAGAAAGATTTAATCATCATGCT
1 CCCGAAGGACTTATCATCTCGCTCGAAAGACTAACAGATGACCAGAAGGATTTAATCATCATGCT
* *
123343 CGAAAGATTTACTGATGGCCTGAAGGACTTACCAA-TTGGGAAATAGTTTACTGGGTAAGAAACT
66 CGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTGGGAAATAGTTTACTAGGTAAGAAACT
* *
123407 TTAGAAATCACTTTT-TTACTT-GTCAAAATTTTCATTTTCTGAAAATACTAAATGAGAAACTTT
131 TTAGAAAT-ACTTTTCTTA-TTCGTCAAAAATATCATTTTCTGAAAATACTAAATGAGAAACTTT
* * *
123470 GGAAATCGCTTTCTCATTTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACAGATGG
194 AGAAATCGCTTTCTCATTTTTCAAATTCATATGAAAACAT-CTACCCAAAGGTCTTACAGATGG
* ** * * * *
123534 CCCGAAGGACTTATTATCTTACTTGAAAGACTTACAGATGACCTGAAGGATTTAATTATCATGCT
1 CCCGAAGGACTTATCATCTCGCTCGAAAGACTAACAGATGACCAGAAGGATTTAATCATCATGCT
* * * *
123599 CGGAAGACTTACTGTTGGCCCGAACGACTTA
66 CGAAAGACTTACTGATGGCCTGAAGGACTTA
123630 AATGAGAAAC
Statistics
Matches: 315, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
255 116 0.37
256 199 0.63
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (256 bp):
CCCGAAGGACTTATCATCTCGCTCGAAAGACTAACAGATGACCAGAAGGATTTAATCATCATGCT
CGAAAGACTTACTGATGGCCTGAAGGACTTACCAATTTGGGAAATAGTTTACTAGGTAAGAAACT
TTAGAAATACTTTTCTTATTCGTCAAAAATATCATTTTCTGAAAATACTAAATGAGAAACTTTAG
AAATCGCTTTCTCATTTTTCAAATTCATATGAAAACATCTACCCAAAGGTCTTACAGATGG
Found at i:123606 original size:42 final size:41
Alignment explanation
Indices: 123523--123629 Score: 106
Period size: 42 Copynumber: 2.6 Consensus size: 41
123513 ACCCGAAGGT
* * *
123523 CTTACAGATGGCCCGAAGGACTTATTATCTTACTTGAAAGA
1 CTTACAGATGACCCGAAGGACTTATTATCATACTCGAAAGA
* * * *
123564 CTTACAGATGACCTGAAGGATTTAATTATCATGCTCGGAAGA
1 CTTACAGATGACCCGAAGGACTT-ATTATCATACTCGAAAGA
* * * *
123606 CTTACTGTTGGCCCGAACGACTTA
1 CTTACAGATGACCCGAAGGACTTA
123630 AATGAGAAAC
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 21 0.40
42 31 0.60
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (41 bp):
CTTACAGATGACCCGAAGGACTTATTATCATACTCGAAAGA
Found at i:138606 original size:3 final size:3
Alignment explanation
Indices: 138593--138645 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
138583 GTACCTTGAA
* *
138593 AAT AA- AAT AAT AAT AAT AAT AAT AA- AAT AAC ATT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
138637 AAAT AAT AA
1 -AAT AAT AA
138646 ATTATGACCC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.10
3 32 0.76
4 6 0.14
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:138618 original size:20 final size:21
Alignment explanation
Indices: 138593--138645 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
138583 GTACCTTGAA
138593 AATAAAATAATAATAAT-AAT
1 AATAAAATAATAATAATAAAT
* *
138613 AATAAAATAACATTAATAAAT
1 AATAAAATAATAATAATAAAT
138634 AAT-AAATAATAA
1 AATAAAATAATAA
138646 ATTATGACCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
AATAAAATAATAATAATAAAT
Found at i:138647 original size:14 final size:13
Alignment explanation
Indices: 138592--138647 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 13
138582 TGTACCTTGA
138592 AAATAA-AATAAT
1 AAATAATAATAAT
138604 -AATAATAATAAT
1 AAATAATAATAAT
* *
138616 AAAATAACATTAAT
1 -AAATAATAATAAT
138630 AAATAATAAATAAT
1 AAATAAT-AATAAT
138644 AAAT
1 AAAT
138648 TATGACCCAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 5 0.14
12 6 0.17
13 6 0.17
14 19 0.53
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:139141 original size:41 final size:41
Alignment explanation
Indices: 139096--139189 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
139086 ACCAAAACAT
* * * * *
139096 TTTTTTCATTAGTCTTAGTT-GGTGATTTGTGACGACAATTG
1 TTTTTTCACTAATCTTA-TTCGATGATTTATGACGACAATTA
139137 TTTTTTCACTAATCTTATTCGATGATTTATGACGACAATTA
1 TTTTTTCACTAATCTTATTCGATGATTTATGACGACAATTA
139178 TTTTTGTCACTA
1 TTTTT-TCACTA
139190 TTGAAGTGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 2 0.04
41 38 0.83
42 6 0.13
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (41 bp):
TTTTTTCACTAATCTTATTCGATGATTTATGACGACAATTA
Found at i:140243 original size:20 final size:21
Alignment explanation
Indices: 140201--140244 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
140191 TTATTAGTAG
* **
140201 TTTATTTTTTTAATTTATTAC
1 TTTATTTTTTTAATATAGGAC
140222 TTTA-TTTTTTAATATAGGAC
1 TTTATTTTTTTAATATAGGAC
140242 TTT
1 TTT
140245 CAACACAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTATTTTTTTAATATAGGAC
Done.