Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007964.1 Hibiscus syriacus cultivar Beakdansim tig00110393_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: 1737572
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 6
Found at i:300385 original size:7 final size:7
Alignment explanation
Indices: 300373--300457 Score: 154
Period size: 7 Copynumber: 12.3 Consensus size: 7
300363 TACATGCCTG
300373 CTTTCTT
1 CTTTCTT
300380 CTTTCTT
1 CTTTCTT
300387 CTTTCTT
1 CTTTCTT
300394 CTTTCTT
1 CTTTCTT
300401 CTTTCTT
1 CTTTCTT
300408 CTTTCTT
1 CTTTCTT
300415 CTTTCTT
1 CTTTCTT
300422 CTTTCTT
1 CTTTCTT
300429 CTTTCTT
1 CTTTCTT
*
300436 CTTTTTT
1 CTTTCTT
300443 CTTTCTT
1 CTTTCTT
300450 C-TTCTT
1 CTTTCTT
300456 CT
1 CT
300458 ACTTCTACGC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
6 6 0.08
7 69 0.92
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
CTTTCTT
Found at i:301487 original size:43 final size:43
Alignment explanation
Indices: 301362--301503 Score: 178
Period size: 43 Copynumber: 3.3 Consensus size: 43
301352 GCTAAAGTTC
* *
301362 GCGGCGTTTTTAAACAAAAAACGCCGCAATAGGTATTGATATTTA
1 GCGGCGTTTTT-CA-AAAAAATGCCGCAATAGGTATTGATATTTA
* ** * * *
301407 GCGGCGTTTGT-GTACAAATGCCGCAATAGATGTTGATATTTA
1 GCGGCGTTTTTCAAAAAAATGCCGCAATAGGTATTGATATTTA
*
301449 GCGGCGTTTTTCAAAAAAATGCCGCAATAGGTAATGATATTTA
1 GCGGCGTTTTTCAAAAAAATGCCGCAATAGGTATTGATATTTA
301492 GCGGCGTTTTTC
1 GCGGCGTTTTTC
301504 TCTAAAACGC
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 35 0.43
43 37 0.45
45 10 0.12
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (43 bp):
GCGGCGTTTTTCAAAAAAATGCCGCAATAGGTATTGATATTTA
Found at i:301545 original size:85 final size:85
Alignment explanation
Indices: 301377--301545 Score: 191
Period size: 85 Copynumber: 2.0 Consensus size: 85
301367 GTTTTTAAAC
* * * * *
301377 AAAAAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTGTACAAATGCCGCAATAGATGTTG
1 AAAAAACGCCGCAATAGGTAATGATATTTAGCGGCGTTTCTCTACAAACGCCGAAATAGATGTTG
* *
301442 ATATTTAGCGGCGTTTTTCA
66 ATATTTAGCGACGATTTTCA
* *
301462 AAAAAATGCCGCAATAGGTAATGATATTTAGCGGCGTTTTTCTCTA-AAACGCC-AAAGTAGGTG
1 AAAAAACGCCGCAATAGGTAATGATATTTAGCGGCG--TTTCTCTACAAACGCCGAAA-TAGATG
* *
301525 TTGATGTTTTGCGAC-ATTTTC
63 TTGATATTTAGCGACGATTTTC
301546 CCACAAACGC
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
85 41 0.59
86 23 0.33
87 6 0.09
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (85 bp):
AAAAAACGCCGCAATAGGTAATGATATTTAGCGGCGTTTCTCTACAAACGCCGAAATAGATGTTG
ATATTTAGCGACGATTTTCA
Found at i:301656 original size:43 final size:43
Alignment explanation
Indices: 301380--301671 Score: 209
Period size: 42 Copynumber: 6.9 Consensus size: 43
301370 TTTAAACAAA
* * *
301380 AAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTGT-AC
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTTCTCAC
* * * * ** *
301422 AAATGCCGCAATAGATGTTGATATTTAGCGGCGTTTTTCAAAA
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTTCTCAC
* * *
301465 AAATGCCGCAATAGGTAATGATATTTAGCGGCGTTTTTCTCTA-
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTTCTC-AC
* * * * * *
301508 AAACGCC-AAAGTAGGTGTTGATGTTTTGCGAC-ATTTTCCCAC
1 AAACGCCGCAA-TAGGTATTGATATTTTGCGGCGTTTTTCTCAC
* * * * * * *
301550 AAACGCCGTAGTAGATGTTGATGTTTTGCGGC-ATTTTCCCAC
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTTCTCAC
* * * * * * *
301592 AAACGCCTCAGTTGATTTTGATGTTTTGCAGCGTTTTTCTCAC
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTTCTCAC
* *
301635 AAATGCCGCAATAGGTATTGAT-TTTTTCGGCGTTTTT
1 AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTT
301672 GCTAAAAACA
Statistics
Matches: 204, Mismatches: 40, Indels: 12
0.80 0.16 0.05
Matches are distributed among these distances:
41 1 0.00
42 118 0.58
43 84 0.41
44 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (43 bp):
AAACGCCGCAATAGGTATTGATATTTTGCGGCGTTTTTCTCAC
Found at i:302139 original size:21 final size:21
Alignment explanation
Indices: 302086--302153 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
302076 TGATATGATA
* *
302086 CTTCTCTTTATGCTACCGCTG
1 CTTCTCTTTGTGCTGCCGCTG
*
302107 CTTCTCTCTGTGCTGCCGCTG
1 CTTCTCTTTGTGCTGCCGCTG
* *
302128 CTTCTCTTTGTGGTGCTGCTG
1 CTTCTCTTTGTGCTGCCGCTG
302149 CTTCT
1 CTTCT
302154 TTCTCTACTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.03, C:0.32, G:0.21, T:0.44
Consensus pattern (21 bp):
CTTCTCTTTGTGCTGCCGCTG
Found at i:302206 original size:21 final size:22
Alignment explanation
Indices: 302155--302206 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
302145 GCTGCTTCTT
*
302155 TCTCTACTT-TCGCTGCTGCTC
1 TCTCTACTTCTCGCTACTGCTC
** *
302176 TAGCTGCTTCT-GCTACTGCTC
1 TCTCTACTTCTCGCTACTGCTC
302197 TCTCTACTTC
1 TCTCTACTTC
302207 CCTTGCTTCA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.08, C:0.37, G:0.13, T:0.42
Consensus pattern (22 bp):
TCTCTACTTCTCGCTACTGCTC
Found at i:313226 original size:9 final size:11
Alignment explanation
Indices: 313202--313245 Score: 79
Period size: 11 Copynumber: 4.0 Consensus size: 11
313192 GGGGAGAAGT
313202 GTGTGTTTTAA
1 GTGTGTTTTAA
*
313213 GTGTGTTTTAT
1 GTGTGTTTTAA
313224 GTGTGTTTTAA
1 GTGTGTTTTAA
313235 GTGTGTTTTAA
1 GTGTGTTTTAA
313246 AATGATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.27, T:0.57
Consensus pattern (11 bp):
GTGTGTTTTAA
Found at i:313229 original size:22 final size:22
Alignment explanation
Indices: 313201--313244 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
313191 AGGGGAGAAG
313201 TGTGTGTTTTAAGTGTGTTTTA
1 TGTGTGTTTTAAGTGTGTTTTA
313223 TGTGTGTTTTAAGTGTGTTTTA
1 TGTGTGTTTTAAGTGTGTTTTA
313245 AAATGATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (22 bp):
TGTGTGTTTTAAGTGTGTTTTA
Found at i:317839 original size:40 final size:40
Alignment explanation
Indices: 317771--317944 Score: 172
Period size: 41 Copynumber: 4.3 Consensus size: 40
317761 ATTTAACATT
* * *
317771 TTGCGGCGTTTATAAAAAAATGCCACTATTGATTACAATA
1 TTGCGGCGTTTGTTAAAAAACGCCACTATTGATTACAATA
* * * *
317811 TTGTGGCATTTGTTAAAAAACGTCACTATTGATTAAAACTA
1 TTGCGGCGTTTGTTAAAAAACGCCACTATTGATTACAA-TA
* * * *
317852 TTGCGGCGTTT-TTCTAAAAATGCCACTAGTGATTAACACTA
1 TTGCGGCGTTTGTT-AAAAAACGCCACTATTGATT-ACAATA
* *
317893 TTGCGGCGTTTGTCT-AAAAACGCCACTATTTATTATCACTA
1 TTGCGGCGTTTGT-TAAAAAACGCCACTATTGATTA-CAATA
317934 TTGCGGCGTTT
1 TTGCGGCGTTT
317945 TAAGAATAAA
Statistics
Matches: 110, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
40 34 0.31
41 72 0.65
42 3 0.03
43 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (40 bp):
TTGCGGCGTTTGTTAAAAAACGCCACTATTGATTACAATA
Found at i:317934 original size:82 final size:81
Alignment explanation
Indices: 317771--317962 Score: 226
Period size: 82 Copynumber: 2.3 Consensus size: 81
317761 ATTTAACATT
* * * *
317771 TTGCGGCGTTTATAAAAAAATGCCACTATTGATTACAATATTGTGGCATTTGTTAAAAAACGTCA
1 TTGCGGCGTTTTTAAAAAAATGCCACTAGTGATTACAATATTGCGGCATTTGTTAAAAAACGCCA
317836 CTATTGATTAAAACTA
66 CTATTGATTAAAACTA
** * *
317852 TTGCGGCGTTTTTCTAAAAATGCCACTAGTGATTAACACTATTGCGGCGTTTGTCT-AAAAACGC
1 TTGCGGCGTTTTTAAAAAAATGCCACTAGTGATT-ACAATATTGCGGCATTTGT-TAAAAAACGC
* **
317916 CACTATTTATTATCACTA
64 CACTATTGATTAAAACTA
*
317934 TTGCGGCG-TTTTAAGAATAAATGTCACTA
1 TTGCGGCGTTTTTAA-AA-AAATGCCACTA
317963 TATGTGTATT
Statistics
Matches: 93, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
81 34 0.37
82 48 0.52
83 11 0.12
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (81 bp):
TTGCGGCGTTTTTAAAAAAATGCCACTAGTGATTACAATATTGCGGCATTTGTTAAAAAACGCCA
CTATTGATTAAAACTA
Found at i:318018 original size:42 final size:41
Alignment explanation
Indices: 317890--318080 Score: 135
Period size: 42 Copynumber: 4.6 Consensus size: 41
317880 GTGATTAACA
* * * *
317890 CTATTGCGGCGTTTGT-CTAAAAACGCCACTATTTATT-AT
1 CTATTGCGGCGTTTGTGGTATAAACGCCACTATATGTTAAT
* * * * *
317929 CACTATTGCGGCGTTT-TAAGAATAAATGTCACTATATGTGTATT
1 --CTATTGCGGCGTTTGT-GGTATAAACGCCACTATATGT-TAAT
*
317973 CTATTGCGGCGTTTGTGGTATAAACGCCGCTA-AT-TTACTGAT
1 CTATTGCGGCGTTTGTGGTATAAACGCCACTATATGTTA---AT
* **
318015 CTATTACAACGTTT-TGGCTA-AAACGCCACTATATGTTAAT
1 CTATTGCGGCGTTTGTGG-TATAAACGCCACTATATGTTAAT
*
318055 ATATTGCGGCGTTTGTGGTATAAACG
1 CTATTGCGGCGTTTGTGGTATAAACG
318081 GAAGTTTAGA
Statistics
Matches: 115, Mismatches: 22, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
39 2 0.02
40 16 0.14
41 37 0.32
42 54 0.47
43 5 0.04
44 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (41 bp):
CTATTGCGGCGTTTGTGGTATAAACGCCACTATATGTTAAT
Found at i:320191 original size:22 final size:22
Alignment explanation
Indices: 320157--320198 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
320147 ATAATTATTT
320157 AAAAAATTAAATA-AAAATACC
1 AAAAAATTAAATAGAAAATACC
*
320178 AAAAATATTTAATAGAAAATA
1 AAAAA-ATTAAATAGAAAATA
320199 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAAAATTAAATAGAAAATACC
Found at i:320876 original size:24 final size:24
Alignment explanation
Indices: 320846--320925 Score: 142
Period size: 24 Copynumber: 3.3 Consensus size: 24
320836 CGAACGGTTC
*
320846 AGCGGTTCCGCCCGGTTCACTAGT
1 AGCGGTTCCGGCCGGTTCACTAGT
320870 AGCGGTTCCGGCCGGTTCACTAGT
1 AGCGGTTCCGGCCGGTTCACTAGT
320894 AGCGGTTCCGGCCGGTTCACTAGT
1 AGCGGTTCCGGCCGGTTCACTAGT
*
320918 AACGGTTC
1 AGCGGTTC
320926 AACCGGTGTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.14, C:0.30, G:0.31, T:0.25
Consensus pattern (24 bp):
AGCGGTTCCGGCCGGTTCACTAGT
Found at i:333131 original size:114 final size:116
Alignment explanation
Indices: 332902--333139 Score: 446
Period size: 114 Copynumber: 2.1 Consensus size: 116
332892 AATCATAAGC
332902 ATTAAA-TTAAATTAGAAAGTTAAAGTCAAGTATTAATTTAAATTAAAAATAATTTTAAATATAT
1 ATTAAATTTAAATTAGAAAGTTAAAGTCAAGTATTAATTTAAATTAAAAATAA-TTTAAATATAT
332966 AATTAGATAAAATAATAATAAATACCAACTAAATAAAAAATAATATAAAAAT
65 AATTAGATAAAATAATAATAAATACCAACTAAATAAAAAATAATATAAAAAT
333018 ATTAAATTTAAATTAGAAAGTTAAAGTCAAGTATTAATTTAAATTAAAAATAA-TTAAA-ATATA
1 ATTAAATTTAAATTAGAAAGTTAAAGTCAAGTATTAATTTAAATTAAAAATAATTTAAATATATA
333081 ATTAGATAAAATAATAATAAATACCAACTAAATAAAAAATAATATAAAAAT
66 ATTAGATAAAATAATAATAAATACCAACTAAATAAAAAATAATATAAAAAT
333132 ATTAAATT
1 ATTAAATT
333140 GAACAAATAA
Statistics
Matches: 121, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
114 64 0.53
115 5 0.04
116 6 0.05
117 46 0.38
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (116 bp):
ATTAAATTTAAATTAGAAAGTTAAAGTCAAGTATTAATTTAAATTAAAAATAATTTAAATATATA
ATTAGATAAAATAATAATAAATACCAACTAAATAAAAAATAATATAAAAAT
Found at i:341341 original size:2 final size:2
Alignment explanation
Indices: 341336--341361 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
341326 AAAAAAATAC
341336 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
341362 TAATTAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:344310 original size:31 final size:31
Alignment explanation
Indices: 344275--344338 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
344265 ATTTAATTAA
*
344275 TTTAATCTTAATTT-TAATTTAATATAATAAT
1 TTTAATCTTAATTTAT-ATTTAATAAAATAAT
344306 TTTAATCTTAATTTATATTTAATAAAATAAT
1 TTTAATCTTAATTTATATTTAATAAAATAAT
344337 TT
1 TT
344339 AATACTCCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (31 bp):
TTTAATCTTAATTTATATTTAATAAAATAAT
Found at i:344311 original size:25 final size:26
Alignment explanation
Indices: 344277--344330 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
344267 TTAATTAATT
*
344277 TAATCTTAATTTTAATTTA-ATATAA
1 TAATCTTAATCTTAATTTATATATAA
* *
344302 TAATTTTAATCTTAATTTATATTTAA
1 TAATCTTAATCTTAATTTATATATAA
344328 TAA
1 TAA
344331 AATAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (26 bp):
TAATCTTAATCTTAATTTATATATAA
Found at i:344341 original size:5 final size:5
Alignment explanation
Indices: 344265--344328 Score: 53
Period size: 5 Copynumber: 12.4 Consensus size: 5
344255 TTACTTACAT
*
344265 ATTTA A-TTA ATTTA ATCTTA ATTTTA ATTTA ATATA A--TA ATTTTA
1 ATTTA ATTTA ATTTA AT-TTA A-TTTA ATTTA ATTTA ATTTA A-TTTA
344310 ATCTTA ATTTA TATTTA AT
1 AT-TTA ATTTA -ATTTA AT
344329 AAAATAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
3 3 0.06
4 4 0.08
5 21 0.42
6 21 0.42
7 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (5 bp):
ATTTA
Found at i:357395 original size:21 final size:20
Alignment explanation
Indices: 357310--357466 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
357300 AATGACCAAT
** *
357310 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
357329 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
357349 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
357369 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
357390 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
357411 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
357432 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
357452 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
357467 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:357495 original size:20 final size:20
Alignment explanation
Indices: 357433--357625 Score: 228
Period size: 20 Copynumber: 9.7 Consensus size: 20
357423 CGATTTTCCA
* ** *
357433 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
357453 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
357473 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
357493 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
357513 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
357533 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
357553 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
357573 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
357593 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
357613 AAATCGCAACGCG
1 AAATCGCAACGCG
357626 ATATTTAAAG
Statistics
Matches: 148, Mismatches: 21, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 144 0.97
21 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:358152 original size:20 final size:20
Alignment explanation
Indices: 358127--358213 Score: 80
Period size: 19 Copynumber: 4.7 Consensus size: 20
358117 CAGAAGAGTT
***
358127 GCAACGAGAGAATGACTGTC
1 GCAACGAGAGAATGAAAATC
358147 GCAACGAGAGAAATGAAAATC
1 GCAACGAGAG-AATGAAAATC
358168 GCAAC--GAG-A-G--AATC
1 GCAACGAGAGAATGAAAATC
*
358182 GCAACGCGA-AATGAAAATC
1 GCAACGAGAGAATGAAAATC
358201 GCAACGAGAGAAT
1 GCAACGAGAGAAT
358214 CGCAACGCGA
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
14 9 0.16
16 4 0.07
17 2 0.04
19 15 0.27
20 13 0.24
21 12 0.22
ACGTcount: A:0.45, C:0.18, G:0.26, T:0.10
Consensus pattern (20 bp):
GCAACGAGAGAATGAAAATC
Found at i:358169 original size:21 final size:21
Alignment explanation
Indices: 358127--358179 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
358117 CAGAAGAGTT
***
358127 GCAACGAGAG-AATGACTGTC
1 GCAACGAGAGAAATGAAAATC
358147 GCAACGAGAGAAATGAAAATC
1 GCAACGAGAGAAATGAAAATC
358168 GCAACGAGAGAA
1 GCAACGAGAGAA
358180 TCGCAACGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.45, C:0.17, G:0.28, T:0.09
Consensus pattern (21 bp):
GCAACGAGAGAAATGAAAATC
Found at i:358183 original size:14 final size:14
Alignment explanation
Indices: 358164--358220 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
358154 GAGAAATGAA
358164 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
358178 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
358197 AATCGCAACGAGAG
1 AATCGCAACGAGAG
358211 AATCGCAACG
1 AATCGCAACG
358221 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:358196 original size:33 final size:33
Alignment explanation
Indices: 358156--358236 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
358146 CGCAACGAGA
358156 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
358189 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
358222 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
358237 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:358254 original size:19 final size:19
Alignment explanation
Indices: 358232--358329 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
358222 GAAACCAAAA
*
358232 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
358251 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
358265 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
358284 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
358298 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
358317 TCGCGTTGCGATT
1 TCGCGTTGCGATT
358330 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:358273 original size:14 final size:14
Alignment explanation
Indices: 358254--358343 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
358244 TTTCATTTCG
358254 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
358268 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
358287 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
358301 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
358320 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
358334 CGTTGCGATT
1 CGTTGCGATT
358344 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:358279 original size:33 final size:33
Alignment explanation
Indices: 358237--358351 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
358227 CAAAATCGCA
358237 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
358270 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
358303 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
358336 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
358352 AACCCAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:360209 original size:93 final size:93
Alignment explanation
Indices: 360050--360533 Score: 968
Period size: 93 Copynumber: 5.2 Consensus size: 93
360040 TAGATTGCTT
360050 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
360115 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
360143 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
360208 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
360236 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
360301 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
360329 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
360394 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
360422 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
360487 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
360515 AGTAAATTTGTTCGGTTGC
1 AGTAAATTTGTTCGGTTGC
360534 GATTCTTTCG
Statistics
Matches: 391, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 391 1.00
ACGTcount: A:0.21, C:0.13, G:0.20, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:360566 original size:19 final size:19
Alignment explanation
Indices: 360542--360640 Score: 109
Period size: 19 Copynumber: 5.4 Consensus size: 19
360532 GCGATTCTTT
360542 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
360561 CGTTGCGATTCT-G--T--
1 CGTTGCGATTTTGGTTTCG
**
360575 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTGGTTTCG
360594 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTGGTTTCG
*
360613 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-GGTTTCG
*
360633 TGTTGCGA
1 CGTTGCGA
360641 AAGTAAACTA
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
14 11 0.16
16 1 0.01
17 1 0.01
18 1 0.01
19 40 0.60
20 13 0.19
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTGGTTTCG
Found at i:360566 original size:33 final size:33
Alignment explanation
Indices: 360525--360603 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
360515 AGTAAATTTG
* **
360525 TTCG-GTTGCGATTCTTTCGTTGCGATTTTGGT
1 TTCGCGTTGCGATTCTGTCGTTGCGATTTTCAT
360557 TTCGCGTTGCGATTCTGTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTCTGTCGTTGCGATTTTCAT
360590 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
360604 TTGGTTTCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 4 0.09
33 39 0.91
ACGTcount: A:0.08, C:0.19, G:0.27, T:0.47
Consensus pattern (33 bp):
TTCGCGTTGCGATTCTGTCGTTGCGATTTTCAT
Found at i:362664 original size:12 final size:12
Alignment explanation
Indices: 362647--362671 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
362637 TCTTCGGGGA
362647 CTTTTTCTTCTT
1 CTTTTTCTTCTT
362659 CTTTTTCTTCTT
1 CTTTTTCTTCTT
362671 C
1 C
362672 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:362880 original size:24 final size:24
Alignment explanation
Indices: 362846--362892 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
362836 CTGAAACATC
362846 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
362870 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
362893 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:363629 original size:20 final size:20
Alignment explanation
Indices: 363604--363809 Score: 247
Period size: 20 Copynumber: 10.3 Consensus size: 20
363594 TGCCCTACCG
* *
363604 GATTTACAGATTCTCGTTGC
1 GATTTACGGATACTCGTTGC
363624 GATTTACGGATTA-TCGTTGC
1 GATTTACGGA-TACTCGTTGC
363644 GATTTACGGATTA-TCGTTGC
1 GATTTACGGA-TACTCGTTGC
* *
363664 GATTTACAGATTCTCGTTGC
1 GATTTACGGATACTCGTTGC
363684 GATTTACGGATTA-TCGTTGC
1 GATTTACGGA-TACTCGTTGC
*
363704 GATTTACGGATACGCGTTGC
1 GATTTACGGATACTCGTTGC
* * *
363724 GATATACGGATACGCATTGC
1 GATTTACGGATACTCGTTGC
** *
363744 GATTTACCCATACGCGTTGC
1 GATTTACGGATACTCGTTGC
*
363764 GATTTACGGATACACGTTGC
1 GATTTACGGATACTCGTTGC
*
363784 GATTTACGGATACGCGTTGC
1 GATTTACGGATACTCGTTGC
363804 GATTTA
1 GATTTA
363810 TGTGTTCGCG
Statistics
Matches: 165, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.02
20 160 0.97
21 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (20 bp):
GATTTACGGATACTCGTTGC
Found at i:363837 original size:20 final size:20
Alignment explanation
Indices: 363796--363839 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
363786 TTTACGGATA
* *
363796 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTTATATATT
363816 CGCGTTGCGATTT-TCATATT
1 CGCGTTGCGATTTAT-ATATT
363836 CGCG
1 CGCG
363840 ATTTTGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.11, C:0.20, G:0.27, T:0.41
Consensus pattern (20 bp):
CGCGTTGCGATTTATATATT
Found at i:369479 original size:12 final size:12
Alignment explanation
Indices: 369462--369486 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
369452 AACAAATTAA
369462 TTTGAACAATGT
1 TTTGAACAATGT
369474 TTTGAACAATGT
1 TTTGAACAATGT
369486 T
1 T
369487 CATGCATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTTGAACAATGT
Found at i:370743 original size:20 final size:20
Alignment explanation
Indices: 370707--370744 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
370697 ATCCTATTCC
**
370707 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
370727 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
370745 GTTAACCAAA
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:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:374976 original size:22 final size:22
Alignment explanation
Indices: 374916--374977 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
374906 AAATTAATAT
* *
374916 TAAAAATATATTAATATTTTAA
1 TAAAAATATATTAATATATGAA
* *
374938 CAAAAATAT-TTAAATATATGGA
1 TAAAAATATATT-AATATATGAA
*
374960 TAAAAATATATTTATATA
1 TAAAAATATATTAATATA
374978 AATATATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (22 bp):
TAAAAATATATTAATATATGAA
Found at i:375011 original size:16 final size:16
Alignment explanation
Indices: 374960--375016 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
374950 AATATATGGA
* *
374960 TAAAAATATATTTATA
1 TAAATATATATTTATT
374976 TAAATATATATTTGTATT
1 TAAATATATA-TT-TATT
*
374994 TAAATGTATATTTATT
1 TAAATATATATTTATT
*
375010 TATATAT
1 TAAATAT
375017 TTTAATATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 18 0.53
17 4 0.12
18 12 0.35
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (16 bp):
TAAATATATATTTATT
Found at i:375273 original size:19 final size:20
Alignment explanation
Indices: 375251--375289 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
375241 TAATAAACAA
*
375251 TAAAATTATTAA-TTAAAAT
1 TAAAATTACTAATTTAAAAT
375270 TAAAATTACTAATTTAAAAT
1 TAAAATTACTAATTTAAAAT
375290 CATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAATTACTAATTTAAAAT
Found at i:378742 original size:85 final size:83
Alignment explanation
Indices: 378601--378790 Score: 224
Period size: 85 Copynumber: 2.3 Consensus size: 83
378591 TGGATTAATC
* *
378601 TCAAGTTTTAGGATAATATTTT-AAACATTATATTTTATTTCTGTTTTAGATATTTTAGTTTAAA
1 TCAAGATTTAGGATATTATTTTAAAACATTATATTTTATTTCTGTTTTAGATATTTTAGTTTAAA
378665 TAGATGTT-AGTATTTCAA
66 TAG-TGTTAAGTATTTCAA
* * *
378683 TCAAGATTTAGGATATTATTTTAAATAGTATTTTATTTTATATT-TGTTTTAGGTATTTTAGTTT
1 TCAAGATTTAGGATATTATTTTAAA-A-CATTATATTTTAT-TTCTGTTTTAGATATTTTAGTTT
* *
378747 AAATAGTTTTAAGTATTTTAA
63 AAATAGTGTTAAGTATTTCAA
* * * *
378768 TTAGGATTTAAGATGTTATTTTA
1 TCAAGATTTAGGATATTATTTTA
378791 GGAATTATCT
Statistics
Matches: 92, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
82 20 0.22
83 2 0.02
84 4 0.04
85 64 0.70
86 2 0.02
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (83 bp):
TCAAGATTTAGGATATTATTTTAAAACATTATATTTTATTTCTGTTTTAGATATTTTAGTTTAAA
TAGTGTTAAGTATTTCAA
Found at i:378762 original size:24 final size:25
Alignment explanation
Indices: 378709--378766 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
378699 TATTTTAAAT
* * *
378709 AGTATTTTATTTTATATTTGTTTTA
1 AGTATTTTAGTTTATAATAGTTTTA
*
378734 GGTATTTTAGTTTA-AATAGTTTTA
1 AGTATTTTAGTTTATAATAGTTTTA
378758 AGTATTTTA
1 AGTATTTTA
378767 ATTAGGATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (25 bp):
AGTATTTTAGTTTATAATAGTTTTA
Found at i:380245 original size:14 final size:13
Alignment explanation
Indices: 380223--380265 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
380213 TTATCGTCAT
380223 AATTAAAAATATA
1 AATTAAAAATATA
*
380236 AATATAAAAATAATT
1 AAT-TAAAAAT-ATA
*
380251 AATTTAAAATATA
1 AATTAAAAATATA
380264 AA
1 AA
380266 AACTGAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 7 0.28
14 13 0.52
15 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATTAAAAATATA
Found at i:390864 original size:134 final size:137
Alignment explanation
Indices: 390579--391137 Score: 490
Period size: 134 Copynumber: 4.1 Consensus size: 137
390569 ACGTTTGTGA
* ** * *
390579 ACTGAAAAGTTTCTATCATGGTGCATTATTTTGCCTATGAGAAATACACATTTTTTATGATATGA
1 ACTGAAAAGTTTATGCCATGGTGCATTATTTTGCC--T-AGAAAT-GAC---TTTTGTGATATGA
* * * *
390644 A--GATATATCAACACTGAAAAGTTTGCTGAAATGGGTTG--ATATCACCGAAAAGTT-ACTGAA
59 AGTGATATATCAACACTGGAAAGTTTGCTTAAATGAGTTGATATATCACTGAAAAGTTGA-TGAA
*
390704 GATAATTTATTGGCC
123 GATAATTAATTGGCC
* * *
390719 ACTGAAAAGTTTATGCCATGGTGCATTATTTTGCCT-G-CATG-TTTTTGTGTTATGAAGTGATA
1 ACTGAAAAGTTTATGCCATGGTGCATTATTTTGCCTAGAAATGACTTTTGTGATATGAAGTGATA
*
390781 TATCAGCACTGGAAAGTTTGCTTAAATGAGTTGATATATCACTGAAAAGTTGATGAAGATAATTA
66 TATCAACACTGGAAAGTTTGCTTAAATGAGTTGATATATCACTGAAAAGTTGATGAAGATAATTA
*
390846 ATTGACC
131 ATTGGCC
*
390853 ACTTG-AAAGTTTCA-GCCATGGTGTATTATTTTGCCTAGAAATGCACTTTTGTGATATGAAGTG
1 AC-TGAAAAGTTT-ATGCCATGGTGCATTATTTTGCCTAGAAATG-ACTTTTGTGATATGAAGTG
* * * *
390916 --ATATCACCA-TTGAAAGTTTG-TTGAGATGAGTTGATATATCATTGAAAAGTTG-TGAAGATA
63 ATATATCAACACTGGAAAGTTTGCTT-AAATGAGTTGATATATCACTGAAAAGTTGATGAAGATA
390976 ATTAATTGGCC
127 ATTAATTGGCC
* * *
390987 ACTGAAAAGTTTATGTCATGGTGCATTGTTTTGCCTATGAGAAATGCACGTTTTTTGTGATATAA
1 ACTGAAAAGTTTATGCCATGGTGCATTATTTTGCC--T-AGAAATG-AC---TTTTGTGATATGA
* * * * * * * * * *
391052 AGT-A-ATATCACCACTGAAAAGTTTG-AT-GAGGAGTTGATATATCAATCAAAAGTTGCTAAAT
59 AGTGATATATCAACACTGGAAAGTTTGCTTAAATGAGTTGATATATCACTGAAAAGTTGATGAAG
**
391113 ATAATTAATTATCC
124 ATAATTAATTGGCC
*
391127 ACTAAAAAGTT
1 ACTGAAAAGTT
391138 GACTTTTCTA
Statistics
Matches: 357, Mismatches: 39, Indels: 46
0.81 0.09 0.10
Matches are distributed among these distances:
130 12 0.03
132 33 0.09
133 3 0.01
134 109 0.31
135 44 0.12
136 13 0.04
137 10 0.03
138 17 0.05
139 25 0.07
140 81 0.23
141 10 0.03
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (137 bp):
ACTGAAAAGTTTATGCCATGGTGCATTATTTTGCCTAGAAATGACTTTTGTGATATGAAGTGATA
TATCAACACTGGAAAGTTTGCTTAAATGAGTTGATATATCACTGAAAAGTTGATGAAGATAATTA
ATTGGCC
Found at i:393002 original size:2 final size:2
Alignment explanation
Indices: 392995--393030 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
392985 TAAATTAGAT
392995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
393031 TTTAATTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:394593 original size:23 final size:26
Alignment explanation
Indices: 394567--394621 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 26
394557 CCTTTATAAA
*
394567 ATTTTCTTTT-TTTTCTC-TCTT-TT
1 ATTTTCTTTTATTTTCTCTTCTTCTC
*
394590 ATTTT-TTTTATTTTTTCTTCTTCTC
1 ATTTTCTTTTATTTTCTCTTCTTCTC
394615 ATTTTCT
1 ATTTTCT
394622 CTTAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.15
23 11 0.42
24 4 0.15
25 6 0.23
26 1 0.04
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.76
Consensus pattern (26 bp):
ATTTTCTTTTATTTTCTCTTCTTCTC
Found at i:395420 original size:25 final size:25
Alignment explanation
Indices: 395391--395452 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
395381 TTTCAACCAG
395391 GATTGCATGTTCTTTCTGGACAAGA
1 GATTGCATGTTCTTTCTGGACAAGA
*
395416 GATTGCATGTTCTTTCTGGACAAGG
1 GATTGCATGTTCTTTCTGGACAAGA
395441 GATTGCATGTTC
1 GATTGCATGTTC
395453 ATTTAACTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (25 bp):
GATTGCATGTTCTTTCTGGACAAGA
Found at i:397149 original size:14 final size:14
Alignment explanation
Indices: 397132--397173 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
397122 CGTTCGTGAA
397132 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
397146 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
*
397160 CGTTCATTTATGTT
1 CGTTCGTTTATGTT
397174 TAACCCAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.10, C:0.14, G:0.19, T:0.57
Consensus pattern (14 bp):
CGTTCGTTTATGTT
Found at i:398352 original size:17 final size:17
Alignment explanation
Indices: 398330--398391 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
398320 ATAAATATCT
398330 CGAAGGACCTATCATCC
1 CGAAGGACCTATCATCC
** *
398347 CGAAGGATGTCATCTGTGTCC
1 CGAAGGACCT-ATC---ATCC
*
398368 CGAAGGACCTGTCATCC
1 CGAAGGACCTATCATCC
398385 CGAAGGA
1 CGAAGGA
398392 TGTAATCTGT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
17 18 0.53
18 3 0.09
20 2 0.06
21 11 0.32
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.19
Consensus pattern (17 bp):
CGAAGGACCTATCATCC
Found at i:398383 original size:38 final size:38
Alignment explanation
Indices: 398330--398420 Score: 146
Period size: 38 Copynumber: 2.4 Consensus size: 38
398320 ATAAATATCT
* *
398330 CGAAGGACCTATCATCCCGAAGGATGTCATCTGTGTCC
1 CGAAGGACCTATCATCCCGAAGGATGTAATCTGTGCCC
*
398368 CGAAGGACCTGTCATCCCGAAGGATGTAATCTGTGCCC
1 CGAAGGACCTATCATCCCGAAGGATGTAATCTGTGCCC
*
398406 CGTAGGACCTATCAT
1 CGAAGGACCTATCAT
398421 ATGTCTTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (38 bp):
CGAAGGACCTATCATCCCGAAGGATGTAATCTGTGCCC
Found at i:398929 original size:20 final size:20
Alignment explanation
Indices: 398904--398961 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
398894 ATCAGATTGT
398904 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
398924 CCAGGGGGAACAGATT-CCC
1 CCAGGGGGTACAGATTCCCC
398943 CCA-GGGGTATC-GATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
398962 GGGTACAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 9 0.26
19 10 0.29
20 15 0.44
ACGTcount: A:0.21, C:0.34, G:0.29, T:0.16
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:399193 original size:21 final size:21
Alignment explanation
Indices: 399160--399199 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
399150 TTTTTGTAGA
*
399160 AAAATCATTCCCAAACGGCTCT
1 AAAATCA-TCCCCAACGGCTCT
399182 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
399200 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCT
Found at i:399453 original size:34 final size:32
Alignment explanation
Indices: 399414--399483 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
399404 TTTTGTAAAG
*
399414 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
399448 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
399480 GGGA
1 GGGA
399484 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:400474 original size:3 final size:3
Alignment explanation
Indices: 400453--400499 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
400443 TGAAGAAAGG
* *
400453 GAA G-A GAA GAA AAA CAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
400500 TGATGACGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.68, C:0.02, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:402541 original size:216 final size:215
Alignment explanation
Indices: 402177--402610 Score: 766
Period size: 216 Copynumber: 2.0 Consensus size: 215
402167 AATATTTTGA
402177 TGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAATTTTCTAAGTATATTCG
1 TGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAATTTTCTAAGTATATTC-
402242 ATGTAATTATTCGAATATCAAAATATTACTCCAAGTCTTTCAAAGTTCATTTTAATCCTTACTAA
65 A-GTAATTATTCGAATATCAAAATATTACTCCAAGTCTTTCAAAGTTCATTTTAATCCTTACTAA
* *
402307 AGTGTAAAATTGTGTTTTATACTTAATCTATTTTAAAACAATTTTACAAAGTATTTCGAGCCTTA
129 AGTGTAAAATTATGTTTTATACTTAAACTATTTTAAAACAATTTTACAAAGTATTTCGAGCCTTA
402372 ATCGAGCCAAAAATATTTTCTT
194 ATCGAGCCAAAAATATTTTCTT
402394 TGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAAAGATTTTCTAAGTATAT
1 TGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTAC--AA-ATTTTCTAAGTATA-
402459 TTC-G-AATTATTCGAATATC-AAATATTACTCCAAGTCTTTCAAAGTTCATTTTAATCCTTACT
62 TTCAGTAATTATTCGAATATCAAAATATTACTCCAAGTCTTTCAAAGTTCATTTTAATCCTTACT
402521 AAAGTGTAAAATTATGTTTTATACTTAAACTATTTTAAAACAATTTTACAAAGTATTTCGAGCCT
127 AAAGTGTAAAATTATGTTTTATACTTAAACTATTTTAAAACAATTTTACAAAGTATTTCGAGCCT
*
402586 TAATCGAGCCAAACATATTTTCTT
192 TAATCGAGCCAAAAATATTTTCTT
402610 T
1 T
402611 TTATAGGGTT
Statistics
Matches: 210, Mismatches: 3, Indels: 9
0.95 0.01 0.04
Matches are distributed among these distances:
216 130 0.62
217 60 0.29
218 1 0.00
219 2 0.01
220 14 0.07
221 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (215 bp):
TGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAATTTTCTAAGTATATTCA
GTAATTATTCGAATATCAAAATATTACTCCAAGTCTTTCAAAGTTCATTTTAATCCTTACTAAAG
TGTAAAATTATGTTTTATACTTAAACTATTTTAAAACAATTTTACAAAGTATTTCGAGCCTTAAT
CGAGCCAAAAATATTTTCTT
Found at i:402687 original size:20 final size:21
Alignment explanation
Indices: 402640--402681 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
402630 ATCAGATTGT
*
402640 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGAACAGATTCCCCC
402661 CCAGGGGGAACAGATTCCCCC
1 CCAGGGGGAACAGATTCCCCC
402682 TAGGGGTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.38, G:0.29, T:0.12
Consensus pattern (21 bp):
CCAGGGGGAACAGATTCCCCC
Found at i:402722 original size:33 final size:34
Alignment explanation
Indices: 402666--402749 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 34
402656 CCCCCCCAGG
402666 GGGAACAGATTCCCCCTAGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTAGGGGTATCGATTCCCC
* *
402700 GGGAACAAATTCTCCC-AGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTAGGGGTATCGATTCCCC
*
402733 GGGTACAGATTCCCCCT
1 GGGAACAGATTCCCCCT
402750 GTATGGTTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 30 0.68
34 14 0.32
ACGTcount: A:0.21, C:0.32, G:0.25, T:0.21
Consensus pattern (34 bp):
GGGAACAGATTCCCCCTAGGGGTATCGATTCCCC
Found at i:402743 original size:15 final size:15
Alignment explanation
Indices: 402692--402747 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
402682 TAGGGGTATC
*
402692 GATTCCCCGGGAACA
1 GATTCCCCGGGTACA
*
402707 AATTCTCCCAGGGGTATC-
1 GATTC-CCC--GGGTA-CA
402725 GATTCCCCGGGTACA
1 GATTCCCCGGGTACA
402740 GATTCCCC
1 GATTCCCC
402748 CTGTATGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 1 0.03
15 17 0.52
16 3 0.09
17 3 0.09
18 8 0.24
19 1 0.03
ACGTcount: A:0.21, C:0.34, G:0.23, T:0.21
Consensus pattern (15 bp):
GATTCCCCGGGTACA
Found at i:402965 original size:21 final size:21
Alignment explanation
Indices: 402931--402970 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
402921 TTTTTGTAGA
*
402931 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
402953 AAAAT-ATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
402971 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 1 0.06
22 5 0.29
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:407983 original size:24 final size:23
Alignment explanation
Indices: 407930--407993 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
407920 TTTGTGTTGG
407930 TCGTTTATGTTCGTTTATTGTGT
1 TCGTTTATGTTCGTTTATTGTGT
* *
407953 TCATTTATGTTTGTTCGT-TTGTGT
1 TCGTTTATGTTCGTT--TATTGTGT
*
407977 TCGTTTACGTTCGTTTA
1 TCGTTTATGTTCGTTTA
407994 CATTTAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
22 1 0.03
23 13 0.39
24 18 0.55
25 1 0.03
ACGTcount: A:0.09, C:0.11, G:0.20, T:0.59
Consensus pattern (23 bp):
TCGTTTATGTTCGTTTATTGTGT
Found at i:417554 original size:22 final size:22
Alignment explanation
Indices: 417526--417577 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
417516 AAGATACTTG
417526 GTCTTCTTATTTTATTCTTTAA
1 GTCTTCTTATTTTATTCTTTAA
417548 GTCTTCTTATTTTATTCTTTAA
1 GTCTTCTTATTTTATTCTTTAA
417570 GTCTTCTT
1 GTCTTCTT
417578 TTAAAGGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.15, C:0.15, G:0.06, T:0.63
Consensus pattern (22 bp):
GTCTTCTTATTTTATTCTTTAA
Found at i:435308 original size:25 final size:25
Alignment explanation
Indices: 435280--435328 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
435270 AAACACAATA
435280 ATTT-GAAAATTAACAATTTTTTTTT
1 ATTTCGAAAATTAA-AATTTTTTTTT
*
435305 ATTTCGAAAATTTAAATTTTTTTT
1 ATTTCGAAAATTAAAATTTTTTTT
435329 GGAAAATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (25 bp):
ATTTCGAAAATTAAAATTTTTTTTT
Found at i:435735 original size:23 final size:23
Alignment explanation
Indices: 435705--435766 Score: 124
Period size: 23 Copynumber: 2.7 Consensus size: 23
435695 TTCCCCTGTG
435705 GGGGGAATCGGTTCCCATTCAAA
1 GGGGGAATCGGTTCCCATTCAAA
435728 GGGGGAATCGGTTCCCATTCAAA
1 GGGGGAATCGGTTCCCATTCAAA
435751 GGGGGAATCGGTTCCC
1 GGGGGAATCGGTTCCC
435767 TCATGGGGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.23, C:0.23, G:0.34, T:0.21
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCATTCAAA
Found at i:442188 original size:28 final size:28
Alignment explanation
Indices: 442148--442208 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
442138 TTCATAAGTT
442148 TGTATATTGATGACATGTTGTTATTCAG
1 TGTATATTGATGACATGTTGTTATTCAG
*
442176 TGTATGTTGATGACATGTTGTTATTCAG
1 TGTATATTGATGACATGTTGTTATTCAG
442204 TGTAT
1 TGTAT
442209 TAACAAAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.48
Consensus pattern (28 bp):
TGTATATTGATGACATGTTGTTATTCAG
Found at i:445964 original size:9 final size:9
Alignment explanation
Indices: 445950--446024 Score: 86
Period size: 9 Copynumber: 8.8 Consensus size: 9
445940 ATGCTTATTA
445950 AATATTTTT
1 AATATTTTT
**
445959 AATATTTAA
1 AATATTTTT
445968 AATATTTTT
1 AATATTTTT
*
445977 AATA--TTA
1 AATATTTTT
445984 AATATTTTT
1 AATATTTTT
445993 AATATTTTT
1 AATATTTTT
*
446002 AATA--TTA
1 AATATTTTT
446009 AATATTTTT
1 AATATTTTT
446018 AATATTT
1 AATATTT
446025 AAATCTAGTT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
7 12 0.22
9 42 0.78
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
AATATTTTT
Found at i:445987 original size:25 final size:25
Alignment explanation
Indices: 445959--446024 Score: 114
Period size: 25 Copynumber: 2.6 Consensus size: 25
445949 AAATATTTTT
**
445959 AATATTTAAAATATTTTTAATATTA
1 AATATTTTTAATATTTTTAATATTA
445984 AATATTTTTAATATTTTTAATATTA
1 AATATTTTTAATATTTTTAATATTA
446009 AATATTTTTAATATTT
1 AATATTTTTAATATTT
446025 AAATCTAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
AATATTTTTAATATTTTTAATATTA
Found at i:445988 original size:16 final size:16
Alignment explanation
Indices: 445945--446028 Score: 92
Period size: 16 Copynumber: 5.5 Consensus size: 16
445935 TATGTATGCT
445945 TATTAAATATTTTTAA
1 TATTAAATATTTTTAA
445961 TATTTAAAATATTTTTAA
1 TA-TT-AAATATTTTTAA
445979 TATTAAATA---TT--
1 TATTAAATATTTTTAA
445990 T-TT-AATATTTTTAA
1 TATTAAATATTTTTAA
446004 TATTAAATATTTTTAA
1 TATTAAATATTTTTAA
446020 TATTTAAAT
1 TA-TTAAAT
446029 CTAGTTGATC
Statistics
Matches: 58, Mismatches: 0, Indels: 19
0.75 0.00 0.25
Matches are distributed among these distances:
9 4 0.07
10 2 0.03
11 1 0.02
12 2 0.03
13 2 0.03
14 1 0.02
15 2 0.03
16 20 0.34
17 10 0.17
18 14 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTAAATATTTTTAA
Found at i:446810 original size:11 final size:12
Alignment explanation
Indices: 446786--446811 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
446776 AACAGTGCAG
446786 AAAAGCCTGAAA
1 AAAAGCCTGAAA
446798 AAAAGCCTGAAA
1 AAAAGCCTGAAA
446810 AA
1 AA
446812 CAACAAGCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAAGCCTGAAA
Found at i:449425 original size:55 final size:55
Alignment explanation
Indices: 449347--449509 Score: 272
Period size: 55 Copynumber: 3.0 Consensus size: 55
449337 TGATAAAAGG
* *
449347 AGTGATGAGTGAATCAAACTATGTGACATGTTGCTTCACTACACATTTTTGATAT
1 AGTGGTGAGTGAATCAAACTATGTGACATGTTGCTTCACTACACAATTTTGATAT
449402 AGTGGTGAGTGAATCAAACTATGTGACATGTTGCTTCACTACACAATTTTGATAT
1 AGTGGTGAGTGAATCAAACTATGTGACATGTTGCTTCACTACACAATTTTGATAT
* ***
449457 AGTGGTGAGTGAATCAAACTATGTGACAGGTTGCTTTGTTACACAATTTTGAT
1 AGTGGTGAGTGAATCAAACTATGTGACATGTTGCTTCACTACACAATTTTGAT
449510 TATATCAACA
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 102 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (55 bp):
AGTGGTGAGTGAATCAAACTATGTGACATGTTGCTTCACTACACAATTTTGATAT
Found at i:464356 original size:22 final size:23
Alignment explanation
Indices: 464308--464367 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
464298 TGGTGCAGGA
* *
464308 GGAATCGATACCCCC-TTGAAGG
1 GGAACCGATTCCCCCTTTGAAGG
464330 GGAACCGATTCCCCCTTTGAA-G
1 GGAACCGATTCCCCCTTTGAAGG
* *
464352 TGAACTGATTCCCCCT
1 GGAACCGATTCCCCCT
464368 GGAGGTGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (23 bp):
GGAACCGATTCCCCCTTTGAAGG
Found at i:464375 original size:21 final size:22
Alignment explanation
Indices: 464313--464375 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
464303 CAGGAGGAAT
* *
464313 CGATACCCCCTT-GAAGGGGAAC
1 CGATTCCCCCTTGGAA-GTGAAC
*
464335 CGATTCCCCCTTTGAAGTGAAC
1 CGATTCCCCCTTGGAAGTGAAC
* *
464357 TGATTCCCCC-TGGAGGTGA
1 CGATTCCCCCTTGGAAGTGA
464376 TACCCCCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 7 0.20
22 25 0.71
23 3 0.09
ACGTcount: A:0.22, C:0.30, G:0.25, T:0.22
Consensus pattern (22 bp):
CGATTCCCCCTTGGAAGTGAAC
Found at i:468695 original size:83 final size:83
Alignment explanation
Indices: 468432--468966 Score: 519
Period size: 83 Copynumber: 6.4 Consensus size: 83
468422 TAATAATGGA
* * * * * * * *
468432 AAACACACTTTTCATTTCGGATGGGATGAAACACTCTGGCATGGA-A-AATATTCTTTGAATAAT
1 AAACACGCCTTTCATTTCGGATGGGATGGAATACTATGACAT-GATAGAA-ATTATCTGAATAAT
* *
468495 AAAGGAAAAAGT-TTTCCCCG
64 AATGG-AAAACTCTTTCCCCG
* **
468515 AAATACGCCTTTCATTTCAAATGGGATGGAATACTATGACATGATAGAAATTATCTGAA-AATAA
1 AAACACGCCTTTCATTTCGGATGGGATGGAATACTATGACATGATAGAAATTATCTGAATAATAA
468579 TGGAAAACTCTTTCCCCG
66 TGGAAAACTCTTTCCCCG
*
468597 AAACACGCCTTTCATTTTGGATGGGATGGAATACTATGACATGATAGAAATTATCTGAATAATAA
1 AAACACGCCTTTCATTTCGGATGGGATGGAATACTATGACATGATAGAAATTATCTGAATAATAA
468662 TGGAAAACTCTTTCCCCG
66 TGGAAAACTCTTTCCCCG
* * * * * * *
468680 AAACACGCCTTTCATTTTGGATGGGATGAAACACTCTGACATGATAGAGATTCTCTAAATAATAA
1 AAACACGCCTTTCATTTCGGATGGGATGGAATACTATGACATGATAGAAATTATCTGAATAATAA
* **
468745 TGGAAAACACTTTCCTTG
66 TGGAAAACTCTTTCCCCG
* * * * * * * * *
468763 AAATACGCCTTTCACTTCGAATGGGATGGAACACTCTGACATGACAGAGATTTTCTAAATAATAA
1 AAACACGCCTTTCATTTCGGATGGGATGGAATACTATGACATGATAGAAATTATCTGAATAATAA
*
468828 TGGAAAACTCTTAT-CCTG
66 TGGAAAACTCTT-TCCCCG
* * * * * * * ** *
468846 AAACGCGCCTTTTATTTCGGACGAGATGGATTACTAT--TATAATCCAATGATTCTCTGAATAAT
1 AAACACGCCTTTCATTTCGGATGGGATGGAATACTATGACATGATAGAA--ATTATCTGAATAAT
*
468909 AATGGAAAAATGC-TTCCCCTG
64 AATGGAAAACT-CTTTCCCC-G
* *
468930 GAACACGCCTTTCATTTCGGATGGGATGGATTACTAT
1 AAACACGCCTTTCATTTCGGATGGGATGGAATACTAT
468967 TATAATCCAG
Statistics
Matches: 382, Mismatches: 60, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
81 9 0.02
82 73 0.19
83 263 0.69
84 37 0.10
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (83 bp):
AAACACGCCTTTCATTTCGGATGGGATGGAATACTATGACATGATAGAAATTATCTGAATAATAA
TGGAAAACTCTTTCCCCG
Found at i:468826 original size:166 final size:164
Alignment explanation
Indices: 468432--468863 Score: 485
Period size: 165 Copynumber: 2.6 Consensus size: 164
468422 TAATAATGGA
* * * *
468432 AAACACACTTTTCATTTCGGATGGGATGAAACACTCTGGCATGGAA-AATATTCTT-TGAATAAT
1 AAACACGCCTTTCATTTCGGATGGGATGGAACACTCTGACAT-GAAGAA-ATT-TTCTGAATAAT
* * * * *
468495 AAAGGAAAAAGT-TTTCCCCGAAATACGCCTTTCATTTCAAATGGGATGGAATACTATGACATGA
63 AATGG-AAAACTCTTTCCCCGAAACACGCCTTTCATTTCAAATGGGATGAAACACTATGACATGA
* *
468559 TAGAAATTATCTGAAAATAATGGAAAACTCTTTCCCCG
127 TAGAAATTATCTAAAAATAATGGAAAACACTTTCCCCG
* * * *
468597 AAACACGCCTTTCATTTTGGATGGGATGGAATACTATGACATGATAGAAATTATCTGAATAATAA
1 AAACACGCCTTTCATTTCGGATGGGATGGAACACTCTGACATGA-AGAAATTTTCTGAATAATAA
*** *
468662 TGGAAAACTCTTTCCCCGAAACACGCCTTTCATTTTGGATGGGATGAAACACTCTGACATGATAG
65 TGGAAAACTCTTTCCCCGAAACACGCCTTTCATTTCAAATGGGATGAAACACTATGACATGATAG
* * **
468727 AGATTCTCTAAATAATAATGGAAAACACTTTCCTTG
130 AAATTATCTAAA-AATAATGGAAAACACTTTCCCCG
* * * * *
468763 AAATACGCCTTTCACTTCGAATGGGATGGAACACTCTGACATGACAGAGATTTTCTAAATAATAA
1 AAACACGCCTTTCATTTCGGATGGGATGGAACACTCTGACATGA-AGAAATTTTCTGAATAATAA
* * *
468828 TGGAAAACTCTTAT-CCTGAAACGCGCCTTTTATTTC
65 TGGAAAACTCTT-TCCCCGAAACACGCCTTTCATTTC
468864 GGACGAGATG
Statistics
Matches: 224, Mismatches: 37, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
164 8 0.04
165 108 0.48
166 107 0.48
167 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (164 bp):
AAACACGCCTTTCATTTCGGATGGGATGGAACACTCTGACATGAAGAAATTTTCTGAATAATAAT
GGAAAACTCTTTCCCCGAAACACGCCTTTCATTTCAAATGGGATGAAACACTATGACATGATAGA
AATTATCTAAAAATAATGGAAAACACTTTCCCCG
Found at i:469748 original size:26 final size:27
Alignment explanation
Indices: 469713--469767 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
469703 AGGACTATAA
*
469713 AAACAACAAACCATGAA-CATTACATT
1 AAACAACAAACCATGAATCATGACATT
* *
469739 AAACAACAAACTATTAATCATGACATT
1 AAACAACAAACCATGAATCATGACATT
469766 AA
1 AA
469768 GAATACCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.55, C:0.20, G:0.04, T:0.22
Consensus pattern (27 bp):
AAACAACAAACCATGAATCATGACATT
Found at i:471916 original size:2 final size:2
Alignment explanation
Indices: 471909--471953 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
471899 CACCAAATTA
*
471909 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
471949 AT AT A
1 AT AT A
471954 AAATATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:474114 original size:27 final size:28
Alignment explanation
Indices: 474061--474120 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
474051 TTTGACAATC
* * *
474061 TTAATTTCATGATTTTTTTTAATTCAAA
1 TTAAATTCATGATATTTTTTAAATCAAA
474089 TTAAATTCATGA-ATTTTTTAAATCAAA
1 TTAAATTCATGATATTTTTTAAATCAAA
474116 TTAAA
1 TTAAA
474121 CTCAACTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (28 bp):
TTAAATTCATGATATTTTTTAAATCAAA
Found at i:484031 original size:29 final size:29
Alignment explanation
Indices: 483999--484073 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
483989 AAAAAAAGAG
*
483999 AAAAAAAG--AAAAATAA-CAGTTCGAAA
1 AAAAAAAGAAAAAAAAAAGCAGTTCGAAA
*
484025 AAAAAAAGAAAAAAAAAAGCTGTTCGAAA
1 AAAAAAAGAAAAAAAAAAGCAGTTCGAAA
* *
484054 GAAAAAGAGAGAGAAAAAAA
1 -AAAAAAAGA-AAAAAAAAA
484074 CACATGAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 8 0.20
28 7 0.17
29 9 0.22
30 8 0.20
31 8 0.20
ACGTcount: A:0.71, C:0.05, G:0.16, T:0.08
Consensus pattern (29 bp):
AAAAAAAGAAAAAAAAAAGCAGTTCGAAA
Found at i:500073 original size:25 final size:25
Alignment explanation
Indices: 500045--500097 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
500035 ATTTAAGGAT
*
500045 TTTAATTTTTTTAGAAATTATAAAA
1 TTTAAATTTTTTAGAAATTATAAAA
* * *
500070 TTTAAATTTTTTATACATTTTAAAA
1 TTTAAATTTTTTAGAAATTATAAAA
500095 TTT
1 TTT
500098 TGTGTTTGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
TTTAAATTTTTTAGAAATTATAAAA
Found at i:502764 original size:18 final size:18
Alignment explanation
Indices: 502737--502773 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
502727 TTTACGAGGG
*
502737 AATTGAAATCTGTGAAGA
1 AATTGAAATCTGTCAAGA
*
502755 AATTGGAATCTGTCAAGA
1 AATTGAAATCTGTCAAGA
502773 A
1 A
502774 TTATAATCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (18 bp):
AATTGAAATCTGTCAAGA
Found at i:508880 original size:19 final size:19
Alignment explanation
Indices: 508853--508899 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
508843 TGTCGAGTTC
*
508853 GATGAAGCAGAATATTGGA
1 GATGGAGCAGAATATTGGA
508872 GATGGAGCAGAATATTGGA
1 GATGGAGCAGAATATTGGA
508891 GATGGAGCA
1 GATGGAGCA
508900 AAGAGGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.36, T:0.19
Consensus pattern (19 bp):
GATGGAGCAGAATATTGGA
Found at i:511457 original size:21 final size:21
Alignment explanation
Indices: 511416--511456 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
511406 AAACATATTT
*
511416 TGAAAAATGATTTTCTTAAAA
1 TGAAAAATCATTTTCTTAAAA
*
511437 TGAAAAA-CATTTTTTTAAAA
1 TGAAAAATCATTTTCTTAAAA
511457 AAATATTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (21 bp):
TGAAAAATCATTTTCTTAAAA
Found at i:536825 original size:130 final size:130
Alignment explanation
Indices: 536587--536848 Score: 445
Period size: 130 Copynumber: 2.0 Consensus size: 130
536577 GCTTAATTTA
* *
536587 AAACCATTTAAAACTTAACATTTATAATATTCATTTAAAAATACAATTATAACTAAAATTAGCCA
1 AAACCATTTAAAACTAAACATTTATAATATTCATTTAAAAATACAATTATAACTAAAATTAACCA
*
536652 AAATTAAAATAATTCTAAATTACTATTACAAACTTTTTAAAATAAATTCGATAAAGTAACCCAAC
66 AAATTAAAATAATCCTAAATTACTATTACAAACTTTTTAAAATAAATTCGATAAAGTAACCCAAC
* * *
536717 AAACCATTTAAGACTAAACATTTATAATATTCATTTAAGAATACGATTATAACTAAAATTAACCA
1 AAACCATTTAAAACTAAACATTTATAATATTCATTTAAAAATACAATTATAACTAAAATTAACCA
*
536782 AAATTAAAATAATCCTAAATTACTATTACAAACATTTTT-AAATAAATTCGATAAAGTAATCCAA
66 AAATTAAAATAATCCTAAATTACTATTACAAAC-TTTTTAAAATAAATTCGATAAAGTAACCCAA
536846 C
130 C
536847 AA
1 AA
536849 TATAATGTAC
Statistics
Matches: 124, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
130 119 0.96
131 5 0.04
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (130 bp):
AAACCATTTAAAACTAAACATTTATAATATTCATTTAAAAATACAATTATAACTAAAATTAACCA
AAATTAAAATAATCCTAAATTACTATTACAAACTTTTTAAAATAAATTCGATAAAGTAACCCAAC
Found at i:539745 original size:29 final size:31
Alignment explanation
Indices: 539661--539745 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 31
539651 TTAATTTTCT
* * *
539661 AAATTTACATTTTTAGTCCCTAAACTTTTACA
1 AAATTTA-AATTTTAGTCACTAAACTATTACA
* *
539693 AAATTTATATTTTAGCCA-TCAAAC-ATT-CA
1 AAATTTAAATTTTAGTCACT-AAACTATTACA
539722 AAATTTAAATTTTAGTCACTAAAC
1 AAATTTAAATTTTAGTCACTAAAC
539746 CAAAATTTGA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
29 22 0.50
30 4 0.09
31 11 0.25
32 7 0.16
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (31 bp):
AAATTTAAATTTTAGTCACTAAACTATTACA
Found at i:541747 original size:32 final size:32
Alignment explanation
Indices: 541688--541748 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
541678 GATCTATTAC
* *
541688 AAAATAATCATTAAATTTTATTGAATTTTTAT
1 AAAATAATCATTAAATTTGATTAAATTTTTAT
*
541720 AAAATAATCATTATA-TTGATCTAAATTTT
1 AAAATAATCATTAAATTTGAT-TAAATTTT
541749 ACACCTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 4 0.16
32 21 0.84
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (32 bp):
AAAATAATCATTAAATTTGATTAAATTTTTAT
Found at i:542124 original size:2 final size:2
Alignment explanation
Indices: 542117--542147 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
542107 ATTTTATGAT
542117 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 T
542148 TTCTTCATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:543631 original size:2 final size:2
Alignment explanation
Indices: 543626--543654 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
543616 TAAAAAAAAC
543626 AT 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 AT A
543655 CCCCCATCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:543878 original size:24 final size:24
Alignment explanation
Indices: 543851--543931 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
543841 TATATCAAAA
*
543851 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAATCATAAATCAGGTCAAGT
* *
543875 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAATCATAAATCAGGTCAAGT
* * *
543899 AACAGATCAT-AATCCAAGTCAAGT
1 ATCAAATCATAAAT-CAGGTCAAGT
*
543923 ATCAGATCA
1 ATCAAATCA
543932 GAATCCATGT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 3 0.06
24 45 0.94
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAATCATAAATCAGGTCAAGT
Found at i:543936 original size:24 final size:24
Alignment explanation
Indices: 543868--543982 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
543858 CATAAATCAG
* *
543868 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* * *
543892 GTCAAGTAACAGATCATAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
543916 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
543940 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
543964 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
543983 ATCAAATCAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 5 0.06
24 74 0.91
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:543999 original size:48 final size:48
Alignment explanation
Indices: 543868--543999 Score: 151
Period size: 48 Copynumber: 2.8 Consensus size: 48
543858 CATAAATCAG
* * * *
543868 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CAGATCATAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAA-AAATCAGATCAGAATCCAA
* * * *
543916 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCAAAAATCAGATCAGAATCCAA
*
543964 GTCAAGTATCAGATCAGAAATCAAATCAAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTCAAAAATCAG
544000 GTAAAATATT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
47 4 0.06
48 63 0.90
49 3 0.04
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAAATCAGATCAGAATCCAA
Found at i:544987 original size:26 final size:26
Alignment explanation
Indices: 544958--545007 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
544948 TTTATTCCAT
544958 TCATTTCAGAGCTCGAGGATATTCAA
1 TCATTTCAGAGCTCGAGGATATTCAA
* * *
544984 TCATTTCTGAGCTTGGGGATATTC
1 TCATTTCAGAGCTCGAGGATATTC
545008 TTGGGTCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (26 bp):
TCATTTCAGAGCTCGAGGATATTCAA
Found at i:546442 original size:7 final size:7
Alignment explanation
Indices: 546430--546469 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
546420 TGGTCAACTC
546430 CGGTCAA
1 CGGTCAA
546437 CGGTCAA
1 CGGTCAA
546444 CGGGTCAA
1 C-GGTCAA
*
546452 CGGTTAA
1 CGGTCAA
546459 CGGGTCAA
1 C-GGTCAA
546467 CGG
1 CGG
546470 GTCGGGTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 16 0.55
8 13 0.45
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:546451 original size:15 final size:15
Alignment explanation
Indices: 546431--546469 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
546421 GGTCAACTCC
546431 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
546446 GGTCAACGGTTAACG
1 GGTCAACGGTCAACG
546461 GGTCAACGG
1 GGTCAACGG
546470 GTCGGGTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.36, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:546477 original size:13 final size:13
Alignment explanation
Indices: 546472--546508 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
546462 GTCAACGGGT
546472 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
546485 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
546498 CGGGTCGGGTC
1 CGGGTCGGGTC
546509 GGGTCGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.22, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:546482 original size:18 final size:18
Alignment explanation
Indices: 546459--546494 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
546449 CAACGGTTAA
546459 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
546477 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
546495 AAACGGGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:546490 original size:8 final size:8
Alignment explanation
Indices: 546431--546472 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
546421 GGTCAACTCC
546431 GGTCAAC-
1 GGTCAACG
546438 GGTCAACG
1 GGTCAACG
546446 GGTCAAC-
1 GGTCAACG
*
546453 GGTTAACG
1 GGTCAACG
546461 GGTCAACG
1 GGTCAACG
546469 GGTC
1 GGTC
546473 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 13 0.42
8 18 0.58
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:546500 original size:31 final size:32
Alignment explanation
Indices: 546444--546513 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
546434 CAACGGTCAA
* *
546444 CGGGTCAACGGTTAACGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGT-ACGGGTAAACGGGTCGGGT
546477 CGGGTCAACGGGT-CGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTACGGGTAAACGGGTCGGGT
546508 CGGGTC
1 CGGGTC
546514 GGGTTATGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 23 0.66
33 12 0.34
ACGTcount: A:0.16, C:0.21, G:0.46, T:0.17
Consensus pattern (32 bp):
CGGGTCAACGGGTACGGGTAAACGGGTCGGGT
Found at i:548716 original size:24 final size:24
Alignment explanation
Indices: 548689--548769 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
548679 TATATCAAAA
*
548689 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAATCATAAATCAGGTCAAGT
* *
548713 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAATCATAAATCAGGTCAAGT
* * *
548737 AACAGATCAT-AATCCAAGTCAAGT
1 ATCAAATCATAAAT-CAGGTCAAGT
*
548761 ATCAGATCA
1 ATCAAATCA
548770 GAATCCATGT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 3 0.06
24 45 0.94
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAATCATAAATCAGGTCAAGT
Found at i:548774 original size:24 final size:24
Alignment explanation
Indices: 548706--548820 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
548696 CATAAATCAG
* *
548706 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* * *
548730 GTCAAGTAACAGATCATAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
548754 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
548778 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
548802 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
548821 ATCAAATCAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 5 0.06
24 74 0.91
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:548837 original size:48 final size:48
Alignment explanation
Indices: 548706--548837 Score: 151
Period size: 48 Copynumber: 2.8 Consensus size: 48
548696 CATAAATCAG
* * * *
548706 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CAGATCATAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAA-AAATCAGATCAGAATCCAA
* * * *
548754 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCAAAAATCAGATCAGAATCCAA
*
548802 GTCAAGTATCAGATCAGAAATCAAATCAAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTCAAAAATCAG
548838 GTAAAATATT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
47 4 0.06
48 63 0.90
49 3 0.04
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAAATCAGATCAGAATCCAA
Found at i:549826 original size:26 final size:26
Alignment explanation
Indices: 549794--549843 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
549784 TTTATTCCAT
549794 TCATTTCAGAGCTCGAGGATATTCAA
1 TCATTTCAGAGCTCGAGGATATTCAA
* * *
549820 TCATTTCTGAGCTTGGGGATATTC
1 TCATTTCAGAGCTCGAGGATATTC
549844 TTGGGTCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (26 bp):
TCATTTCAGAGCTCGAGGATATTCAA
Found at i:551273 original size:7 final size:7
Alignment explanation
Indices: 551261--551300 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
551251 TGGTCAACTC
551261 CGGTCAA
1 CGGTCAA
551268 CGGTCAA
1 CGGTCAA
551275 CGGGTCAA
1 C-GGTCAA
*
551283 CGGTTAA
1 CGGTCAA
551290 CGGGTCAA
1 C-GGTCAA
551298 CGG
1 CGG
551301 GTCGGGTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 16 0.55
8 13 0.45
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:551282 original size:8 final size:8
Alignment explanation
Indices: 551262--551303 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
551252 GGTCAACTCC
551262 GGTCAAC-
1 GGTCAACG
551269 GGTCAACG
1 GGTCAACG
551277 GGTCAAC-
1 GGTCAACG
*
551284 GGTTAACG
1 GGTCAACG
551292 GGTCAACG
1 GGTCAACG
551300 GGTC
1 GGTC
551304 GGGTCGGGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
7 13 0.42
8 18 0.58
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:551282 original size:15 final size:15
Alignment explanation
Indices: 551262--551300 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
551252 GGTCAACTCC
551262 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
551277 GGTCAACGGTTAACG
1 GGTCAACGGTCAACG
551292 GGTCAACGG
1 GGTCAACGG
551301 GTCGGGTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.36, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:551308 original size:13 final size:13
Alignment explanation
Indices: 551303--551351 Score: 98
Period size: 13 Copynumber: 3.8 Consensus size: 13
551293 GTCAACGGGT
551303 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
551316 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
551329 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
551342 CGGGTCGGGT
1 CGGGTCGGGT
551352 CGGGTCGGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.18, C:0.16, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:551355 original size:18 final size:18
Alignment explanation
Indices: 551290--551325 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
551280 CAACGGTTAA
*
551290 CGGGTCAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGT
551308 CGGGTAAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGT
551326 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.19, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTAAACGGGTCGGGT
Found at i:552972 original size:20 final size:20
Alignment explanation
Indices: 552947--552992 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
552937 CTACAGGTAA
552947 AGTATCGATATTATTGGGAT
1 AGTATCGATATTATTGGGAT
552967 AGTATCGATATTATTGGGAT
1 AGTATCGATATTATTGGGAT
552987 AGTATC
1 AGTATC
552993 AATACTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.07, G:0.24, T:0.39
Consensus pattern (20 bp):
AGTATCGATATTATTGGGAT
Found at i:553210 original size:20 final size:20
Alignment explanation
Indices: 553132--553210 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 20
553122 AATGTTTAAA
* * *
553132 AGTATCGATACTTATATA-A
1 AGTATCGATACTTTTAGACT
* *
553151 AGTATCGAAACTTTT-GCAGT
1 AGTATCGATACTTTTAG-ACT
* * *
553171 AGTATTGATACTCTTGGACT
1 AGTATCGATACTTTTAGACT
553191 AGTATCGATACTTTTAGACT
1 AGTATCGATACTTTTAGACT
553211 GTTTTGGGCA
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
19 14 0.30
20 31 0.67
21 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (20 bp):
AGTATCGATACTTTTAGACT
Found at i:553499 original size:28 final size:28
Alignment explanation
Indices: 553458--553524 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
553448 CTTAGGTAGG
*
553458 GTCGAGGCCCTTATGACTAACTATGTTT
1 GTCGAGGCCTTTATGACTAACTATGTTT
* *
553486 GTCGAGACCTTTATGACTTACTATGTTT
1 GTCGAGGCCTTTATGACTAACTATGTTT
553514 GTCGAGGCCTT
1 GTCGAGGCCTT
553525 AACACTCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (28 bp):
GTCGAGGCCTTTATGACTAACTATGTTT
Found at i:554306 original size:15 final size:17
Alignment explanation
Indices: 554276--554322 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
554266 TTAAAAATCT
554276 AATTAACTATTTATTTG
1 AATTAACTATTTATTTG
* *
554293 AATTAA-TATTATTTTTA
1 AATTAACTATT-TATTTG
*
554310 AATTATCTATTTA
1 AATTAACTATTTA
554323 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
AATTAACTATTTATTTG
Found at i:554478 original size:19 final size:22
Alignment explanation
Indices: 554417--554478 Score: 74
Period size: 23 Copynumber: 2.9 Consensus size: 22
554407 GATAATTTAA
* *
554417 AAATAATATTATTTCAAATAAAT
1 AAATAATATGATTTTAAA-AAAT
*
554440 AAATAATATGGTTTTAAAAAAT
1 AAATAATATGATTTTAAAAAAT
554462 AAATAA-AT-ATTTTAAAA
1 AAATAATATGATTTTAAAA
554479 TATTTTCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.23
21 2 0.06
22 10 0.29
23 15 0.43
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (22 bp):
AAATAATATGATTTTAAAAAAT
Found at i:555562 original size:21 final size:21
Alignment explanation
Indices: 555523--555563 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
555513 GGTATAAAAT
* *
555523 TACCTAAAACATTATTATTTC
1 TACCTAAAACATCAATATTTC
555544 TACCTAAAACATCAATATTT
1 TACCTAAAACATCAATATTT
555564 TTTAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTC
Found at i:557117 original size:36 final size:36
Alignment explanation
Indices: 557077--557188 Score: 90
Period size: 36 Copynumber: 3.1 Consensus size: 36
557067 ACAGAACCAA
557077 TCAAGAAATCGAGTCGCCAGTGCAAATTCCGAGCGC
1 TCAAGAAATCGAGTCGCCAGTGCAAATTCCGAGCGC
* * * ** * *
557113 TCAAGTGAAGCCAGT--CCATGTTTAAA--CAGAAC-C
1 TCAAG-AAATCGAGTCGCCA-GTGCAAATTCCGAGCGC
557146 AATCAAGAAATCGAGTCGCCAGTGCAAATTCCGAGCGC
1 --TCAAGAAATCGAGTCGCCAGTGCAAATTCCGAGCGC
557184 TCAAG
1 TCAAG
557189 TAACAAAGCC
Statistics
Matches: 53, Mismatches: 14, Indels: 18
0.62 0.16 0.21
Matches are distributed among these distances:
33 1 0.02
34 10 0.19
35 13 0.25
36 18 0.34
37 10 0.19
38 1 0.02
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (36 bp):
TCAAGAAATCGAGTCGCCAGTGCAAATTCCGAGCGC
Found at i:557163 original size:71 final size:71
Alignment explanation
Indices: 557047--557189 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
557037 ACTAGAAAAC
557047 TGAAGCCAGTCCATGTTTAAACAGAACCAATCAAGAAATCGAGTCGCCAGTGCAAATTCCGAGCG
1 TGAAGCCAGTCCATGTTTAAACAGAACCAATCAAGAAATCGAGTCGCCAGTGCAAATTCCGAGCG
557112 CTCAAG
66 CTCAAG
557118 TGAAGCCAGTCCATGTTTAAACAGAACCAATCAAGAAATCGAGTCGCCAGTGCAAATTCCGAGCG
1 TGAAGCCAGTCCATGTTTAAACAGAACCAATCAAGAAATCGAGTCGCCAGTGCAAATTCCGAGCG
557183 CTCAAG
66 CTCAAG
557189 T
1 T
557190 AACAAAGCCG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (71 bp):
TGAAGCCAGTCCATGTTTAAACAGAACCAATCAAGAAATCGAGTCGCCAGTGCAAATTCCGAGCG
CTCAAG
Found at i:569470 original size:63 final size:63
Alignment explanation
Indices: 569371--569497 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
569361 AAGGGGGAGT
569371 TTGTTTGAGAGGATCACGGTCAAGGACGGGAAACCTTGCTTGTTTGATTTTATATGAAACTTG
1 TTGTTTGAGAGGATCACGGTCAAGGACGGGAAACCTTGCTTGTTTGATTTTATATGAAACTTG
569434 TTGTTTGAGAGGATCACGGTCAAGGACGGGAAACCTTGCTTGTTTGATTTTATATGAAACTTG
1 TTGTTTGAGAGGATCACGGTCAAGGACGGGAAACCTTGCTTGTTTGATTTTATATGAAACTTG
569497 T
1 T
569498 CTCTTGTGCG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (63 bp):
TTGTTTGAGAGGATCACGGTCAAGGACGGGAAACCTTGCTTGTTTGATTTTATATGAAACTTG
Found at i:569619 original size:17 final size:18
Alignment explanation
Indices: 569567--569613 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
569557 GAATTATAAG
*
569567 AATTTTTTTTCAAA--TT
1 AATTTTTTTTAAAATTTT
569583 AATTTTTTTTAGAAATTTT
1 AATTTTTTTTA-AAATTTT
569602 AATTTTTTTTAA
1 AATTTTTTTTAA
569614 GTTTTACAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 10 0.37
17 3 0.11
18 1 0.04
19 13 0.48
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
AATTTTTTTTAAAATTTT
Found at i:575658 original size:68 final size:70
Alignment explanation
Indices: 575521--575661 Score: 196
Period size: 68 Copynumber: 2.0 Consensus size: 70
575511 AATCATACAT
*
575521 ACCTTATAACACACTGTAGTATCTCTATCTTGTGTGAAATAAATGGCTATCAAAAGAGTGCACCA
1 ACCTTATAACACACTGTAGTATCTCTATCTCGTGT-AAATAAATGGCTATCAAAAGAGTGCACCA
575586 CAGTGG
65 CAGTGG
* * * * * *
575592 ACCTTATAAGACGCTGTATTATCTCTATCTCGTGT-CA-AAATGGCTATCGAAAGAGTGCACCGC
1 ACCTTATAACACACTGTAGTATCTCTATCTCGTGTAAATAAATGGCTATCAAAAGAGTGCACCAC
575655 AGTGG
66 AGTGG
575660 AC
1 AC
575662 ATTAATTTGT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
68 31 0.49
69 1 0.02
71 31 0.49
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (70 bp):
ACCTTATAACACACTGTAGTATCTCTATCTCGTGTAAATAAATGGCTATCAAAAGAGTGCACCAC
AGTGG
Found at i:576337 original size:12 final size:12
Alignment explanation
Indices: 576320--576350 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
576310 CGCAGTACCC
576320 GATGCTGGTGCT
1 GATGCTGGTGCT
576332 GATGCTGGTGCT
1 GATGCTGGTGCT
*
576344 GTTGCTG
1 GATGCTG
576351 CTGCATAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.42, T:0.35
Consensus pattern (12 bp):
GATGCTGGTGCT
Found at i:586782 original size:21 final size:21
Alignment explanation
Indices: 586739--586791 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
586729 ATTCTGACTA
586739 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * **
586760 TCGCGTTGCGATTTTCCTGAT
1 TCGCATTGCGATTTCCCAAAT
*
586781 TCGCAATGCGA
1 TCGCATTGCGA
586792 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:586806 original size:20 final size:20
Alignment explanation
Indices: 586781--586853 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
586771 TTTTCCTGAT
586781 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
586801 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
586821 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
586841 TCGCAATGCGAAT
1 TCGCAATGCGAAT
586854 CTGACTATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:587465 original size:20 final size:20
Alignment explanation
Indices: 587440--587488 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
587430 CAACGAGTGA
587440 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
587460 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
587480 ATCGCAACG
1 ATCGCAACG
587489 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:587586 original size:20 final size:20
Alignment explanation
Indices: 587501--587587 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
587491 AGAATCGCAA
587501 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
587520 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** * *
587540 TGCGATAGTCATTTTTGTGT
1 TGCGATTTTCATTTTCGCGT
*
587560 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
587580 TGCGATTT
1 TGCGATTT
587588 AAAGTTTCAG
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
19 9 0.16
20 48 0.84
ACGTcount: A:0.15, C:0.16, G:0.23, T:0.46
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Done.