Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009281.1 Hibiscus syriacus cultivar Beakdansim tig00112968_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: 390849
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:17959 original size:18 final size:18
Alignment explanation
Indices: 17936--17992 Score: 78
Period size: 18 Copynumber: 3.0 Consensus size: 18
17926 TATATTTTCC
17936 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
*
17954 AACAATTGATATCCTTTTGTT
1 AACAATTGGTAT-C-TTT-TT
17975 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
17993 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 13 0.38
19 4 0.12
20 4 0.12
21 13 0.38
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (18 bp):
AACAATTGGTATCTTTTT
Found at i:17978 original size:21 final size:20
Alignment explanation
Indices: 17936--17992 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 20
17926 TATATTTTCC
17936 AACAATTGGTAT-C-TTTTT
1 AACAATTGGTATCCTTTTTT
*
17954 AACAATTGATATCCTTTTGTT
1 AACAATTGGTATCCTTTT-TT
17975 AACAATTGGTAT-CTTTTT
1 AACAATTGGTATCCTTTTT
17993 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 11 0.32
19 2 0.06
20 8 0.24
21 13 0.38
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (20 bp):
AACAATTGGTATCCTTTTTT
Found at i:18508 original size:20 final size:21
Alignment explanation
Indices: 18449--18509 Score: 97
Period size: 21 Copynumber: 2.9 Consensus size: 21
18439 TTTTTGCAGA
*
18449 AAAATCATCCCCAAAAGGCTCT
1 AAAA-CATCCCCAAACGGCTCT
18471 AAAACATCCCCAAACGGCTCT
1 AAAACATCCCCAAACGGCTCT
18492 AAAACATCCCC-AACGGCT
1 AAAACATCCCCAAACGGCT
18510 AGATAAGACT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 7 0.18
21 27 0.71
22 4 0.11
ACGTcount: A:0.39, C:0.36, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAACATCCCCAAACGGCTCT
Found at i:25543 original size:16 final size:16
Alignment explanation
Indices: 25522--25554 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
25512 TTTACAACGA
25522 TTAATTCAAGGAGACC
1 TTAATTCAAGGAGACC
25538 TTAATTCAAGGAGACC
1 TTAATTCAAGGAGACC
25554 T
1 T
25555 AGTAAGAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (16 bp):
TTAATTCAAGGAGACC
Found at i:28445 original size:19 final size:20
Alignment explanation
Indices: 28421--28478 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 20
28411 TTTGGTGCAG
*
28421 AGGGAATCGATTCCCCTTT-
1 AGGGAACCGATTCCCCTTTA
28440 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATT-CCCCTTT-A
28462 AGGGGAACCGATTCCCC
1 A-GGGAACCGATTCCCC
28479 CCACAGGGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 11 0.32
20 7 0.21
22 5 0.15
23 11 0.32
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.22
Consensus pattern (20 bp):
AGGGAACCGATTCCCCTTTA
Found at i:28470 original size:23 final size:20
Alignment explanation
Indices: 28421--28479 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 20
28411 TTTGGTGCAG
*
28421 AGGGAATCGATT-CCCCTTT
1 AGGGAACCGATTCCCCCTTT
28440 AGGGAACCGATTCCCCCTTT
1 AGGGAACCGATTCCCCCTTT
28460 GAAGGGGAACCGATTCCCCC
1 --A-GGGAACCGATTCCCCC
28480 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 11 0.31
20 7 0.20
22 1 0.03
23 16 0.46
ACGTcount: A:0.22, C:0.32, G:0.24, T:0.22
Consensus pattern (20 bp):
AGGGAACCGATTCCCCCTTT
Found at i:36176 original size:18 final size:18
Alignment explanation
Indices: 36153--36187 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
36143 CTGAGTCACC
36153 GATGCTCCACAGCATTGG
1 GATGCTCCACAGCATTGG
*
36171 GATGCTCCATAGCATTG
1 GATGCTCCACAGCATTG
36188 AAATGACACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (18 bp):
GATGCTCCACAGCATTGG
Found at i:39088 original size:67 final size:67
Alignment explanation
Indices: 38980--39113 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
38970 GCGCCAATGG
*
38980 GGTTTCCTTAATTATTAAAATATTTCAATCTAAATCCATCTATTGCTAGTAAGGGGTAAATATTT
1 GGTTTCCTTAATTATTAAAATATTTCAATCTAAATCCATCTACTGCTAGTAAGGGGTAAATATTT
39045 TT
66 TT
39047 GGTTTCCTTAATTATTAAAATATTTCAATCTAAATCCATCTACTGCTAGTAAGGGGTAAATATTT
1 GGTTTCCTTAATTATTAAAATATTTCAATCTAAATCCATCTACTGCTAGTAAGGGGTAAATATTT
39112 TT
66 TT
39114 AATATAATTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.43
Consensus pattern (67 bp):
GGTTTCCTTAATTATTAAAATATTTCAATCTAAATCCATCTACTGCTAGTAAGGGGTAAATATTT
TT
Found at i:43179 original size:13 final size:13
Alignment explanation
Indices: 43163--43187 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43153 TTCAGCTAAT
43163 TCAATTAATTCGG
1 TCAATTAATTCGG
43176 TCAATTAATTCG
1 TCAATTAATTCG
43188 ATGTAAACCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (13 bp):
TCAATTAATTCGG
Found at i:64752 original size:11 final size:11
Alignment explanation
Indices: 64729--64765 Score: 58
Period size: 12 Copynumber: 3.4 Consensus size: 11
64719 ACAATTCTGC
64729 TTCTTTT-TTT
1 TTCTTTTGTTT
64739 TTCTTTTGTTT
1 TTCTTTTGTTT
64750 TTCTTTTTGTTT
1 TTC-TTTTGTTT
64762 TTCT
1 TTCT
64766 AATGAAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 7 0.28
11 7 0.28
12 11 0.44
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (11 bp):
TTCTTTTGTTT
Found at i:70370 original size:12 final size:11
Alignment explanation
Indices: 70352--70386 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
70342 ACCTTCGACC
70352 AAAAAAAACAA
1 AAAAAAAACAA
70363 AAACAAAAACAA
1 AAA-AAAAACAA
70375 AAAAAATAACAA
1 AAAAAA-AACAA
70387 GAGTACTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:72955 original size:10 final size:10
Alignment explanation
Indices: 72940--72982 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
72930 ATAGTAGTAG
*
72940 TAATAACAAT
1 TAATAATAAT
72950 TAATAATAAT
1 TAATAATAAT
*
72960 TAATTATAAT
1 TAATAATAAT
*
72970 AAATAATAAT
1 TAATAATAAT
72980 TAA
1 TAA
72983 AATCCAGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (10 bp):
TAATAATAAT
Found at i:81213 original size:27 final size:25
Alignment explanation
Indices: 81181--81251 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 25
81171 AATAAAATTT
*
81181 ATATTATTTATTATTTTCATAGAAATA
1 ATATTATTTATTATTTTAAT-G-AATA
* *
81208 ATATTATTAAATTATTAATAATGAATA
1 ATATTATT-TATTATT-TTAATGAATA
81235 ATATTATTTATATATTT
1 ATATTATTTAT-TATTT
81252 ACTATTTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
26 2 0.06
27 24 0.67
28 7 0.19
29 3 0.08
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (25 bp):
ATATTATTTATTATTTTAATGAATA
Found at i:99639 original size:16 final size:17
Alignment explanation
Indices: 99611--99644 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
99601 AATAGCACTC
99611 TTACCCAGACATGCTTT
1 TTACCCAGACATGCTTT
99628 TTACCC-GACATGCTTT
1 TTACCCAGACATGCTTT
99644 T
1 T
99645 ATTTCAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (17 bp):
TTACCCAGACATGCTTT
Found at i:104351 original size:72 final size:72
Alignment explanation
Indices: 104234--104373 Score: 217
Period size: 72 Copynumber: 1.9 Consensus size: 72
104224 AATAAAGCTT
* * *
104234 GAGTTATCCCCCTAAAGCAATTGGTTAATAGCTCCGACTTTATGGATAATATTTAGCTAGTCTGT
1 GAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTAGCCTGT
104299 TATGCTC
66 TATGCTC
* * * *
104306 GAGTTGTCCCTCTAAAGCAATTGGTTAATCGCCCCGGCTTTATGGATAATATTCAGCTAGCCTGT
1 GAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTAGCCTGT
104371 TAT
66 TAT
104374 ACTATTATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (72 bp):
GAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTAGCCTGT
TATGCTC
Found at i:107427 original size:22 final size:22
Alignment explanation
Indices: 107399--107441 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
107389 ATACATCTAC
107399 ATTCTTCAAAGATGATAGATTT
1 ATTCTTCAAAGATGATAGATTT
107421 ATTCTTCAAAGATGATAGATT
1 ATTCTTCAAAGATGATAGATT
107442 ATCTTTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (22 bp):
ATTCTTCAAAGATGATAGATTT
Found at i:108150 original size:44 final size:46
Alignment explanation
Indices: 108087--108176 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 46
108077 CTATTTCCCA
*
108087 CATCTGTAAGACCTTCAGTGTAGGATGTTTTC-AAA-CCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAGCCTTCGGGT
* *
108131 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCGAAAAGCCTTCGGG
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTC-AAAAGCCTTCGGG
108177 AGCTTTTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 29 0.73
46 3 0.08
47 8 0.20
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (46 bp):
CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAAGCCTTCGGGT
Found at i:108253 original size:45 final size:45
Alignment explanation
Indices: 108184--108286 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 45
108174 GGGAGCTTTT
* * * ** *
108184 TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGTCCTACAGTGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCA
108229 TGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCA
*
108274 GGATGTTTTCAAA
1 TGATGTTTTCAAA
108287 GAAGCCTTCG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCA
Found at i:108305 original size:121 final size:121
Alignment explanation
Indices: 108087--108484 Score: 604
Period size: 121 Copynumber: 3.3 Consensus size: 121
108077 CTATTTCCCA
* * * ** * *
108087 CATCTGTAAGACCTTCAGTGTAGGATGTTTTC-AAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTG
* * *
108151 CATGATGTTTTCGAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTTCGGGT
66 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
* *
108207 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTG
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTG
108272 CAGGATGTTTTCAAAGAAGCCTTCGGGAG-TTTTTGATGTTTTCAAAGCCTTCGGGT
66 CAGGATGTTTTCAAA-AAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
* *
108328 CACCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTG
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTG
* *
108393 CAGGAT-TTTTCAAAAAAGCCTTAGGGAGCTTTTTGATGTTTTCAAAGCCTTCAGGT
66 CAGGATGTTTTC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
*
108449 CATCTATAAGACCTACAGTGCAGGATGTTTTCAAAA
1 CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAA
108485 AGCCTTCGGG
Statistics
Matches: 255, Mismatches: 19, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
120 45 0.18
121 197 0.77
122 13 0.05
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (121 bp):
CATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTG
CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
Found at i:108374 original size:45 final size:45
Alignment explanation
Indices: 108305--108407 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
108295 CGGGAGTTTT
* * *
108305 TGATGTTTTCAAAGCCTTCGGGTCA-CCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCC-ATAAGACCTACAGTGCA
108350 TGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCA
*
108395 GGAT-TTTTCAAAA
1 TGATGTTTTCAAAA
108408 AAGCCTTAGG
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
44 9 0.17
45 42 0.79
46 2 0.04
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCA
Found at i:108550 original size:74 final size:76
Alignment explanation
Indices: 108350--108566 Score: 282
Period size: 76 Copynumber: 2.9 Consensus size: 76
108340 CTACAGTGCA
* * *
108350 TGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCAGGAT-TTTTCAAAAAAGCCT
1 TGATGATTTCAAAGCCTTCAGGTCATCTATAAGACCTACAGTGCAGGATGTTTTC-AAAAAGCCT
*
108414 TAGGGAGCTTTT
65 TCGGGAGCTTTT
*
108426 TGATGTTTTCAAAGCCTTCAGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGATTTCAAAGCCTTCAGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
108491 CGGGAGCTTTT
66 CGGGAGCTTTT
* * ** ** *
108502 TGAT-ATTT-AAAGCCTTCGGGTCATCTGTAATCCCTTTAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATGATTTCAAAGCCTTCAGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
108563 CGGG
66 CGGG
108567 TCATCTGTAA
Statistics
Matches: 129, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
72 8 0.06
73 4 0.03
74 38 0.29
75 3 0.02
76 71 0.55
77 5 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (76 bp):
TGATGATTTCAAAGCCTTCAGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTTTT
Found at i:108648 original size:45 final size:45
Alignment explanation
Indices: 108510--108659 Score: 221
Period size: 45 Copynumber: 3.4 Consensus size: 45
108500 TTTGATATTT
* *
108510 AAAGCCTTCGGGTCATCTGTAATCCCTTTAGTGCATGATGTTTTC
1 AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC
* *
108555 AAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTC
1 AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC
* * *
108600 AAAGCCTTCGGGTTATCTGTAAGACCTTCAGTGCATAATGTTTTC
1 AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC
*
108645 AAAGCATTC-GGTCAT
1 AAAGCCTTCGGGTCAT
108660 TAAGACCTAC
Statistics
Matches: 94, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
44 5 0.05
45 89 0.95
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (45 bp):
AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC
Found at i:110317 original size:2 final size:2
Alignment explanation
Indices: 110304--110337 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
110294 CATATTAGTC
*
110304 AT AT AA AT 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 AT AT AT AT
110338 TTGTTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:114337 original size:3 final size:3
Alignment explanation
Indices: 114329--114356 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
114319 ATAAATATTG
114329 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
114357 TTGAGAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:115686 original size:15 final size:14
Alignment explanation
Indices: 115647--115696 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
115637 TAATTCATGT
*
115647 TATTTAATTTCCAG
1 TATTTAAATTCCAG
*
115661 TATTTACATTCCAG
1 TATTTAAATTCCAG
* *
115675 TCCTTTAAATTCCAA
1 T-ATTTAAATTCCAG
115690 TATTTAA
1 TATTTAA
115697 CTTTTTGTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (14 bp):
TATTTAAATTCCAG
Found at i:124259 original size:27 final size:27
Alignment explanation
Indices: 124240--124291 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
124230 TAGTTTTAAT
124240 AGGTTCCTTACTAGAGATAGCCTAAAA
1 AGGTTCCTTACTAGAGATAGCCTAAAA
124267 AGGTTCCTTACTAGAGATAGCCTAA
1 AGGTTCCTTACTAGAGATAGCCTAA
124292 GAACACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (27 bp):
AGGTTCCTTACTAGAGATAGCCTAAAA
Found at i:133634 original size:25 final size:25
Alignment explanation
Indices: 133606--133696 Score: 71
Period size: 25 Copynumber: 3.6 Consensus size: 25
133596 ATTTGTAACA
133606 AAAAAAGAA-AAAGAAAGAAAAAAGG
1 AAAAAAGAACAAAGAAAGAAAAAA-G
** * *
133631 AAAATTGAA-AAAGAAAAATAAAAAT
1 AAAAAAGAACAAAGAAAGA-AAAAAG
*
133656 AAAAAAGAAAGAAAGAAATGAAAAGAAG
1 AAAAAAG-AACAAAGAAA-GAAAA-AAG
133684 -AAAAAGAACAAAG
1 AAAAAAGAACAAAG
133697 TGAAAGCCCG
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
25 20 0.38
26 13 0.25
27 16 0.31
28 3 0.06
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.05
Consensus pattern (25 bp):
AAAAAAGAACAAAGAAAGAAAAAAG
Found at i:134450 original size:116 final size:115
Alignment explanation
Indices: 134210--134612 Score: 352
Period size: 116 Copynumber: 3.5 Consensus size: 115
134200 ATAAAAGGGA
* * * * *
134210 TCATAATGAGAAGAACTCGTCCGACAAGGGAGAAGAAGTTTATAATAAGAAGAAC-TATTTCAA-
1 TCATAATGAGAAGAACTCGTCTGATAAGGGAGAATAAGTTCATAATGAGAAGAACATA-TTCAAC
** ** * * * *
134273 TTTTTCTTACTTCTATCATAGATGGAGGTGGATCA-GTATCTCCAATGGAGGAGT
65 ACTGGC-T-CATCCATCACAGAAGGAGGTGGATCACGT-T-TCCAATGGAGGAGT
* * * * * * *
134327 TCA-AATGAGAAGAACTCATCTGATAAGAGAAAAGAAGTTCATAATGAGAAGAACCTATTCATCC
1 TCATAATGAGAAGAACTCGTCTGATAAGGGAGAATAAGTTCATAATGAGAAGAACATATTCAACA
134391 CTGGCTCATCCATCACAGAAGGAGGTGGATCAACGTTTCCAATGGAGGAGT
66 CTGGCTCATCCATCACAGAAGGAGGTGGATC-ACGTTTCCAATGGAGGAGT
* * * *
134442 TCATAATGA-AAGGAACTTGTCCTGA-GAGGGAGAATAAGTTCATAATGAGAAGAATATGTTCAA
1 TCATAATGAGAA-GAACTCGT-CTGATAAGGGAGAATAAGTTCATAATGAGAAGAACATATTCAA
* * * * ** * *
134505 CATTGTCTCATCCATCACAAAAGGAGGAGGATTGGCATTTCCAATAGAAGG-GT
64 CACTGGCTCATCCATCACAGAAGGAGGTGGA-TCACGTTTCCAAT-GGAGGAGT
* * *
134558 TCATAACGAGAAGAACTCGTCCGATAAGGGAGAATAAGTTTATAATGAGAAGAAC
1 TCATAATGAGAAGAACTCGTCTGATAAGGGAGAATAAGTTCATAATGAGAAGAAC
134613 TGTCATACCC
Statistics
Matches: 234, Mismatches: 41, Indels: 23
0.79 0.14 0.08
Matches are distributed among these distances:
115 43 0.18
116 171 0.73
117 20 0.09
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (115 bp):
TCATAATGAGAAGAACTCGTCTGATAAGGGAGAATAAGTTCATAATGAGAAGAACATATTCAACA
CTGGCTCATCCATCACAGAAGGAGGTGGATCACGTTTCCAATGGAGGAGT
Found at i:135369 original size:19 final size:19
Alignment explanation
Indices: 135323--135404 Score: 101
Period size: 19 Copynumber: 4.3 Consensus size: 19
135313 GAGCATTTTA
*
135323 GAACCGGTCCAGGCAGACC
1 GAACCGGTCCAGTCAGACC
** *
135342 GAATTGGTCCAGTCAGATC
1 GAACCGGTCCAGTCAGACC
**
135361 GAACCGGTCCAGTCAGTTC
1 GAACCGGTCCAGTCAGACC
*
135380 GAACCGGTCCAGTCAAACC
1 GAACCGGTCCAGTCAGACC
135399 GAACCG
1 GAACCG
135405 ATCTAGTTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.27, C:0.32, G:0.27, T:0.15
Consensus pattern (19 bp):
GAACCGGTCCAGTCAGACC
Found at i:135416 original size:19 final size:19
Alignment explanation
Indices: 135349--135417 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
135339 ACCGAATTGG
* * *
135349 TCCAGTCAGATCGAACCGG
1 TCCAGTCAAACCGAACCGA
*** *
135368 TCCAGTCAGTTCGAACCGG
1 TCCAGTCAAACCGAACCGA
135387 TCCAGTCAAACCGAACCGA
1 TCCAGTCAAACCGAACCGA
* *
135406 TCTAGTTAAACC
1 TCCAGTCAAACC
135418 AATCTAAACC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.29, C:0.32, G:0.20, T:0.19
Consensus pattern (19 bp):
TCCAGTCAAACCGAACCGA
Found at i:142238 original size:16 final size:16
Alignment explanation
Indices: 142217--142247 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
142207 GTATTACTCG
142217 ACATGTTTTCAACCTA
1 ACATGTTTTCAACCTA
142233 ACATGTTTTCAACCT
1 ACATGTTTTCAACCT
142248 GACTTGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (16 bp):
ACATGTTTTCAACCTA
Found at i:143596 original size:8 final size:8
Alignment explanation
Indices: 143585--143712 Score: 62
Period size: 8 Copynumber: 16.4 Consensus size: 8
143575 TATATAACTC
143585 TATATTTA
1 TATATTTA
143593 TATATTT-
1 TATATTTA
143600 TAATACTTTA
1 T-ATA-TTTA
*
143610 TAT-TGTA
1 TATATTTA
143617 TACTTATATTA
1 TA--TAT-TTA
143628 TATAGTTT-
1 TATA-TTTA
* *
143636 GATACTT-
1 TATATTTA
143643 TATA-TTA
1 TATATTTA
*
143650 TATACTTA
1 TATATTTA
*
143658 TATACTTA
1 TATATTTA
143666 TATA-TT-
1 TATATTTA
143672 TATATTTA
1 TATATTTA
143680 -ATA-TT-
1 TATATTTA
143685 TATATTTA
1 TATATTTA
143693 TATACTTTA
1 TATA-TTTA
143702 -ATACTTTA
1 TATA-TTTA
143710 TAT
1 TAT
143713 GGTATACTTT
Statistics
Matches: 98, Mismatches: 5, Indels: 33
0.72 0.04 0.24
Matches are distributed among these distances:
6 11 0.11
7 24 0.24
8 40 0.41
9 16 0.16
10 3 0.03
11 4 0.04
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.57
Consensus pattern (8 bp):
TATATTTA
Found at i:143618 original size:22 final size:22
Alignment explanation
Indices: 143593--143763 Score: 85
Period size: 22 Copynumber: 7.7 Consensus size: 22
143583 TCTATATTTA
143593 TATATTTTAATACTTT-ATATT
1 TATATTTTAATACTTTAATATT
* *
143614 GTATACTTATATTATATAGTTTGATACTT
1 -TATA--T-T-TTA-ATACTTTAATA-TT
* *
143643 TATATTAT-ATAC-TTATATACT
1 TATATTTTAATACTTTA-ATATT
143664 TATATATTT-ATA-TTTAATATT
1 TATAT-TTTAATACTTTAATATT
143685 TATA-TTTATATACTTTAATACTT
1 TATATTTTA-ATACTTTAATA-TT
**
143708 TATATGGT-ATACTTTAATACTT
1 TATATTTTAATACTTTAATA-TT
143730 TA-A-TTTAATAC-TT-ATATT
1 TATATTTTAATACTTTAATATT
*
143748 ATATAGTTTAATACTT
1 -TATATTTTAATACTT
143764 ATAACATATA
Statistics
Matches: 118, Mismatches: 11, Indels: 40
0.70 0.07 0.24
Matches are distributed among these distances:
18 2 0.02
19 8 0.07
20 4 0.03
21 32 0.27
22 42 0.36
23 6 0.05
24 3 0.03
25 2 0.02
26 4 0.03
27 6 0.05
28 7 0.06
29 2 0.02
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (22 bp):
TATATTTTAATACTTTAATATT
Found at i:143625 original size:13 final size:14
Alignment explanation
Indices: 143602--143918 Score: 87
Period size: 14 Copynumber: 21.8 Consensus size: 14
143592 ATATATTTTA
*
143602 ATACTTTATATTGT
1 ATACTTTATATTAT
143616 ATAC-TTATATTAT
1 ATACTTTATATTAT
*
143629 ATAGTTTGATACTT-T
1 ATACTTT-ATA-TTAT
143644 ATA-TTATATACTTAT
1 ATACTT-TATA-TTAT
143659 ATACTTATATATT-T
1 ATACTT-TATATTAT
143673 ATA-TTTAATATT-T
1 ATACTTT-ATATTAT
*
143686 ATA-TTTATATACTTT
1 ATACTTTATAT--TAT
**
143701 AATACTTTATATGGT
1 -ATACTTTATATTAT
143716 ATACTTTAATACTTTAATTT
1 ATACTTT-ATA--TT-A--T
143736 AATAC-TTATATTAT
1 -ATACTTTATATTAT
*
143750 ATAGTTTAATACTTAT
1 ATACTTT-ATA-TTAT
*
143766 A-AC-ATATATATAT
1 ATACTTTATAT-TAT
*
143779 ATA-TATATATATAT
1 ATACTTTATAT-TAT
*
143793 ATACTTTTTAGTT-T
1 ATACTTTATA-TTAT
*
143807 ATA---TATACT-T
1 ATACTTTATATTAT
143817 ATACTTTATATGTATAT
1 ATACTTTATA--T-TAT
*
143834 ATACTTTTATAATAT
1 ATAC-TTTATATTAT
* *
143849 AAAGTTTATA-TACTT
1 ATACTTTATATTA--T
143864 ATACTTTATATGTATAT
1 ATACTTTATA--T-TAT
*
143881 ATACTTTTATACTAT
1 ATAC-TTTATATTAT
*
143896 ATAGTTTATA-TAT
1 ATACTTTATATTAT
143909 ATAC-TTATAT
1 ATACTTTATAT
143919 ACTTTATATT
Statistics
Matches: 238, Mismatches: 22, Indels: 87
0.69 0.06 0.25
Matches are distributed among these distances:
10 5 0.02
11 3 0.01
12 11 0.05
13 47 0.20
14 60 0.25
15 48 0.20
16 20 0.08
17 20 0.08
18 12 0.05
19 5 0.02
20 3 0.01
21 4 0.02
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (14 bp):
ATACTTTATATTAT
Found at i:143629 original size:35 final size:34
Alignment explanation
Indices: 143575--143752 Score: 133
Period size: 35 Copynumber: 5.2 Consensus size: 34
143565 TAATTTAATA
143575 TATATAACTCTATATTTATATATTTTAATACTTTATAT
1 TATAT-ACT-TATA-TTATATA-TTTAATACTTTATAT
* *
143613 TGTATACTTATATTATATAGTTTGATACTTTATAT
1 TATATACTTATATTATATA-TTTAATACTTTATAT
143648 TATATACTTATATACTTATATATTT-ATA-TTTAATAT
1 TATATAC-T-TATA-TTATATATTTAATACTTT-ATAT
*
143684 T-TATA-TT-TA-TATA-CTTTAATACTTTATAT
1 TATATACTTATATTATATATTTAATACTTTATAT
**
143713 GGTATACTTTAATACTT-TA-ATTTAATAC-TTATAT
1 TATATAC-TT-ATA-TTATATATTTAATACTTTATAT
143747 TATATA
1 TATATA
143753 GTTTAATACT
Statistics
Matches: 118, Mismatches: 9, Indels: 30
0.75 0.06 0.19
Matches are distributed among these distances:
28 3 0.03
29 11 0.09
30 7 0.06
31 2 0.02
32 3 0.03
33 1 0.01
34 12 0.10
35 44 0.37
36 14 0.12
37 10 0.08
38 11 0.09
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (34 bp):
TATATACTTATATTATATATTTAATACTTTATAT
Found at i:143663 original size:43 final size:42
Alignment explanation
Indices: 143585--143746 Score: 138
Period size: 43 Copynumber: 3.8 Consensus size: 42
143575 TATATAACTC
* *
143585 TATATTTATATATTTTAATACTT-TATA-TTGTATACTTATATTA
1 TATATTTA-ATACTTT-ATA-TTATATACTTATATACTTATATTA
* *
143628 TATAGTTTGATACTTTATATTATATACTTATATACTTATATATT
1 TATA-TTTAATACTTTATATTATATACTTATATACTTATAT-TA
**
143672 TATATTTAATA-TTTATATTTATATACTT-TAATACTTTATATGG
1 TATATTTAATACTTTATA-TTATATACTTAT-ATAC-TTATATTA
143715 TATACTTTAATACTTTA-ATT-TAATACTTATAT
1 TATA-TTTAATACTTTATATTAT-ATACTTATAT
143747 TATATAGTTT
Statistics
Matches: 101, Mismatches: 7, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
41 2 0.02
42 15 0.15
43 57 0.56
44 23 0.23
45 4 0.04
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (42 bp):
TATATTTAATACTTTATATTATATACTTATATACTTATATTA
Found at i:143758 original size:34 final size:35
Alignment explanation
Indices: 143698--143763 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
143688 ATTTATATAC
*
143698 TTTAATACTTTATATGGTATACTTTAATACTTTAA
1 TTTAATACTTTATATGATATACTTTAATACTTTAA
* *
143733 TTTAATAC-TTATATTATATAGTTTAATACTT
1 TTTAATACTTTATATGATATACTTTAATACTT
143764 ATAACATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 20 0.71
35 8 0.29
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.53
Consensus pattern (35 bp):
TTTAATACTTTATATGATATACTTTAATACTTTAA
Found at i:143813 original size:2 final size:2
Alignment explanation
Indices: 143769--143795 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
143759 TACTTATAAC
143769 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
143796 CTTTTTAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:143859 original size:47 final size:47
Alignment explanation
Indices: 143808--143919 Score: 183
Period size: 47 Copynumber: 2.4 Consensus size: 47
143798 TTTTAGTTTA
143808 TATATACTTATACTTTATATGTATATATACTTTTATAATATAAAGTT
1 TATATACTTATACTTTATATGTATATATACTTTTATAATATAAAGTT
* *
143855 TATATACTTATACTTTATATGTATATATACTTTTATACTATATAGTT
1 TATATACTTATACTTTATATGTATATATACTTTTATAATATAAAGTT
143902 TATATA--TATACTTATATA
1 TATATACTTATACTT-TATA
143920 CTTTATATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
45 7 0.11
46 4 0.06
47 51 0.82
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.52
Consensus pattern (47 bp):
TATATACTTATACTTTATATGTATATATACTTTTATAATATAAAGTT
Found at i:143919 original size:21 final size:20
Alignment explanation
Indices: 143615--143939 Score: 86
Period size: 21 Copynumber: 16.2 Consensus size: 20
143605 CTTTATATTG
* *
143615 TATAC-TTATATTATATAGTT
1 TATACTTTATA-TATATACTA
143635 TGATACTTTATATTATATACTTA
1 T-ATACTTTATA-TATATAC-TA
* *
143658 TATACTTATATATTTATA-TT
1 TATACTT-TATATATATACTA
*
143678 TAATA-TTTATATTTATATACTT
1 T-ATACTTTATA--TATATACTA
* *
143700 TAATACTTTATATGGTATACTT
1 T-ATACTTTATAT-ATATACTA
*
143722 TAATACTTTA-ATTTAATACT-
1 T-ATACTTTATATAT-ATACTA
*
143742 TATA-TTATATAGTTTAATACT-
1 TATACTT-TATA-TAT-ATACTA
143763 TATAAC---ATATATATA-TA
1 TAT-ACTTTATATATATACTA
* *
143780 TATA-TATATATATATACTT
1 TATACTTTATATATATACTA
* *
143799 TTTA-GTT-TATATATACT-
1 TATACTTTATATATATACTA
*
143816 TATAC-TT-TATATGTA-TA
1 TATACTTTATATATATACTA
143833 TATACTTT-TATA-ATA-TA
1 TATACTTTATATATATACTA
* *
143850 -A-AGTTTATATACTTATACTT
1 TATACTTTATATA--TATACTA
143870 TATA-TGTATATATACTTTTATACTA
1 TATACT-T-TATATA----TATACTA
*
143895 TATAGTTTATATATATACTTA
1 TATACTTTATATATATAC-TA
* *
143916 TATACTTTATATTTAAACTA
1 TATACTTTATATATATACTA
143936 TATA
1 TATA
143940 AACTATATAA
Statistics
Matches: 246, Mismatches: 22, Indels: 74
0.72 0.06 0.22
Matches are distributed among these distances:
15 4 0.02
16 8 0.03
17 27 0.11
18 29 0.12
19 20 0.08
20 20 0.08
21 51 0.21
22 50 0.20
23 18 0.07
24 6 0.02
25 12 0.05
26 1 0.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (20 bp):
TATACTTTATATATATACTA
Found at i:143939 original size:28 final size:25
Alignment explanation
Indices: 143602--143931 Score: 122
Period size: 27 Copynumber: 12.9 Consensus size: 25
143592 ATATATTTTA
*
143602 ATACTTTATA-TTGTATACTTATATTAT
1 ATACTTTATACTT-TATA-TT-TAATAT
*
143629 ATAGTTTGATACTTTATATTATATACTTAT
1 ATACTTT-ATACTTTATATT-TA-A--TAT
143659 ATACTTATATA-TTTATATTTAATATTT
1 ATACTT-TATACTTTATATTTAATA--T
* *
143686 ATATTTATATACTTTAATACTTTATATGGT
1 ATACTT-TATACTTT-ATA-TTTA-AT-AT
143716 ATACTTTAATACTTTA-ATTTAATACTT
1 ATACTTT-ATACTTTATATTTAATA--T
* *
143743 ATA-TTATATAGTTTAATACTT-ATA-
1 ATACTT-TATACTTT-ATATTTAATAT
* * * *
143767 ACA-TATATA-TATATATAT-ATAT
1 ATACTTTATACTTTATATTTAATAT
*
143789 ATA---TATACTTTTTAGTTT-ATAT
1 ATACTTTATACTTTATA-TTTAATAT
*
143811 ATAC-TTATACTTTATATGT-ATAT
1 ATACTTTATACTTTATATTTAATAT
* * * *
143834 ATACTTTTATAATATAAAGTT--TAT
1 ATAC-TTTATACTTTATATTTAATAT
*
143858 ATAC-TTATACTTTATATGT-ATAT
1 ATACTTTATACTTTATATTTAATAT
*
143881 ATACTTTTATACTATATAGTTTATATAT
1 ATAC-TTTATACTTTATA-TTTA-ATAT
143909 ATACTTATATACTTTATATTTAA
1 ATACTT-TATACTTTATATTTAA
143932 ACTATATAAA
Statistics
Matches: 237, Mismatches: 33, Indels: 67
0.70 0.10 0.20
Matches are distributed among these distances:
20 4 0.02
21 11 0.05
22 23 0.10
23 21 0.09
24 20 0.08
25 23 0.10
26 13 0.05
27 42 0.18
28 34 0.14
29 15 0.06
30 28 0.12
31 3 0.01
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (25 bp):
ATACTTTATACTTTATATTTAATAT
Found at i:143948 original size:22 final size:22
Alignment explanation
Indices: 143886--144010 Score: 72
Period size: 22 Copynumber: 6.0 Consensus size: 22
143876 TATATATACT
* *
143886 TTTATACTATAT--AGTTTATA
1 TTTATACTATATAAACTATATA
* * *
143906 TATATACT-TATATACTTTATA
1 TTTATACTATATAAACTATATA
*
143927 TTTAAACTATATAAACTATATAA
1 TTTATACTATATAAACTATAT-A
*
143950 TTTATAC-ATGGT--A-TATATA
1 TTTATACTAT-ATAAACTATATA
*
143969 ATT-TA-TATATAAACTATATAA
1 TTTATACTATATAAACTATAT-A
*
143990 TTTATATTA-ATAAACTATATA
1 TTTATACTATATAAACTATATA
144011 GTTTTTCTAT
Statistics
Matches: 82, Mismatches: 11, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
17 1 0.01
18 4 0.05
19 7 0.09
20 17 0.21
21 18 0.22
22 25 0.30
23 10 0.12
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTATACTATATAAACTATATA
Found at i:143986 original size:20 final size:20
Alignment explanation
Indices: 143934--144010 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
143924 ATATTTAAAC
143934 TATATAAACTATATAATTTA
1 TATATAAACTATATAATTTA
* **
143954 TACATGGTA-TATATAATTTA
1 TATAT-AAACTATATAATTTA
143974 TATATAAACTATATAATTTA
1 TATATAAACTATATAATTTA
143994 TATTAATAAACTATATA
1 TA-T-ATAAACTATATA
144011 GTTTTTCTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.02
20 32 0.68
21 2 0.04
22 12 0.26
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (20 bp):
TATATAAACTATATAATTTA
Found at i:144414 original size:27 final size:28
Alignment explanation
Indices: 144379--144432 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
144369 TATTTAATTT
144379 TTTACTTC-T-AATTTCATATTTGTTCAA
1 TTTACTTCTTAAATTT-ATATTTGTTCAA
* *
144406 TTTAGTTCTTAAATTTATATTTTTTCA
1 TTTACTTCTTAAATTTATATTTGTTCA
144433 TAAAATTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 11 0.48
29 5 0.22
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.59
Consensus pattern (28 bp):
TTTACTTCTTAAATTTATATTTGTTCAA
Found at i:145884 original size:18 final size:18
Alignment explanation
Indices: 145858--145899 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
145848 GGAAGGTAAA
* *
145858 ATTATTAACGAGAATAAG
1 ATTAATAACCAGAATAAG
145876 ATTAATAACCAGAATAAG
1 ATTAATAACCAGAATAAG
145894 ATTAAT
1 ATTAAT
145900 GAAAATATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (18 bp):
ATTAATAACCAGAATAAG
Found at i:146528 original size:29 final size:29
Alignment explanation
Indices: 146461--146529 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
146451 ATTATTTCTA
*
146461 TCTTTAAATTTCCACATTTGAATTTTTAT
1 TCTTTAAATTTCCACATTTGAATTTTTAC
* * *
146490 TACTTT-AATTTCTAC-TTTTACATTTTTGC
1 T-CTTTAAATTTCCACATTTGA-ATTTTTAC
146519 TCTTTAAATTT
1 TCTTTAAATTT
146530 TATGTATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
28 8 0.24
29 21 0.64
30 4 0.12
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (29 bp):
TCTTTAAATTTCCACATTTGAATTTTTAC
Found at i:150116 original size:31 final size:30
Alignment explanation
Indices: 150081--150195 Score: 110
Period size: 30 Copynumber: 3.8 Consensus size: 30
150071 TTAAATTCAA
150081 ATCTTAACACTTAAAAATATATTTTATTTTT
1 ATCTTAA-ACTTAAAAATATATTTTATTTTT
* * *
150112 ATCTT-AACTTATTAAATATATTTTACTGTT
1 ATCTTAAACTTA-AAAATATATTTTATTTTT
*
150142 AT-TTTAACTTAAAAATATATTTT-TTTCTT
1 ATCTTAAACTTAAAAATATATTTTATTT-TT
** *
150171 ATCTTAATTTTTACAAATATATTTT
1 ATCTTAA-ACTTAAAAATATATTTT
150196 TAATTAAATT
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.01
29 22 0.32
30 27 0.39
31 19 0.28
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.55
Consensus pattern (30 bp):
ATCTTAAACTTAAAAATATATTTTATTTTT
Found at i:150211 original size:59 final size:58
Alignment explanation
Indices: 150088--150211 Score: 137
Period size: 59 Copynumber: 2.1 Consensus size: 58
150078 CAAATCTTAA
* **
150088 CACTTAAAAATATATTTTATTTTTATCTTAACTTATTAAATATATTTTACTGTTATTTT
1 CACTTAAAAATATATTTTATTTTTATCTTAACTTATTAAATATATTTTAC-ATTAAATT
* *
150147 AACTTAAAAATATATTTT-TTTCTTATCTTAA-TTTTTACAAATATATTTTTA-ATTAAATT
1 CACTTAAAAATATATTTTATTT-TTATCTTAACTTATT--AAATATA-TTTTACATTAAATT
150206 CACTTA
1 CACTTA
150212 TTAAAATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
58 7 0.13
59 36 0.65
60 7 0.13
61 5 0.09
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (58 bp):
CACTTAAAAATATATTTTATTTTTATCTTAACTTATTAAATATATTTTACATTAAATT
Found at i:150294 original size:28 final size:30
Alignment explanation
Indices: 150248--150317 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 30
150238 TTAACTTATT
* *
150248 AATTATATTTTATTCTTATTTTA-ATTTAAA
1 AATTAT-TTTTAATCTTATTTTAGATTAAAA
*
150278 AA-TATTTTTAATCTTATTTTAGCTTAAAA
1 AATTATTTTTAATCTTATTTTAGATTAAAA
150307 AATTATTTTTA
1 AATTATTTTTA
150318 TATTAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 15 0.43
29 10 0.29
30 10 0.29
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (30 bp):
AATTATTTTTAATCTTATTTTAGATTAAAA
Found at i:150392 original size:31 final size:31
Alignment explanation
Indices: 150356--150432 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
150346 TAGTTTTATT
*
150356 TAAGATATATTTTTAAAAGTTAATATAAGAA
1 TAAGATATATTTTTAAAAGTTAAAATAAGAA
* * *
150387 TAAGATATCTTATT--AAGTTAAAATAAGAT
1 TAAGATATATTTTTAAAAGTTAAAATAAGAA
* *
150416 TAAAATATTTTTTTAAA
1 TAAGATATATTTTTAAA
150433 TAAAATATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 24 0.65
31 13 0.35
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.42
Consensus pattern (31 bp):
TAAGATATATTTTTAAAAGTTAAAATAAGAA
Found at i:150466 original size:30 final size:31
Alignment explanation
Indices: 150430--150488 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
150420 ATATTTTTTT
150430 AAATAAAATATATTTAAT-AAGTTAAGATAA
1 AAATAAAATATATTTAATAAAGTTAAGATAA
**
150460 AAATAAAATATATTTTCTAAAGTTAAGAT
1 AAATAAAATATATTTAATAAAGTTAAGAT
150489 GTGAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (31 bp):
AAATAAAATATATTTAATAAAGTTAAGATAA
Found at i:154958 original size:2 final size:2
Alignment explanation
Indices: 154951--154975 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
154941 AATTTTCAAG
154951 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
154976 CCTATCCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:155218 original size:19 final size:21
Alignment explanation
Indices: 155191--155239 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
155181 TGGTTTCTTT
*
155191 ATAATTATATTATTATTA-TA
1 ATAATTATATTATTATAATTA
155211 AT-ATTATATTATTATAATTA
1 ATAATTATATTATTATAATTA
155231 ATAATTATA
1 ATAATTATA
155240 ATTTTAGAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 14 0.54
20 6 0.23
21 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAATTATATTATTATAATTA
Found at i:155237 original size:16 final size:16
Alignment explanation
Indices: 155189--155238 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
155179 TTTGGTTTCT
*
155189 TTATAATTATATTATTA
1 TTATAATTA-ATAATTA
*
155206 TTATAA-TATTATATTA
1 TTATAATTAATA-ATTA
155222 TTATAATTAATAATTA
1 TTATAATTAATAATTA
155238 T
1 T
155239 AATTTTAGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 1 0.04
16 17 0.61
17 10 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATAATTAATAATTA
Found at i:155240 original size:6 final size:6
Alignment explanation
Indices: 155189--155242 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
155179 TTTGGTTTCT
* * *
155189 TTATAA TTAT-A TTATTA TTATAA -TATTA -TATTA TTATAA TTAATAA
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TT-ATAA
155235 TTATAA TT
1 TTATAA TT
155243 TTAGAGGCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
5 14 0.33
6 22 0.52
7 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTATAA
Found at i:155298 original size:30 final size:31
Alignment explanation
Indices: 155249--155424 Score: 286
Period size: 31 Copynumber: 5.8 Consensus size: 31
155239 AATTTTAGAG
*
155249 GCCAAATTACAACCCGAAGGCCCAAATACAA
1 GCCAAATAACAACCCGAAGGCCCAAATACAA
155280 GCCAAATAACAA-CCGAAGGCCCAAATACAA
1 GCCAAATAACAACCCGAAGGCCCAAATACAA
155310 GCCAAATAACAACCCGAAGGCCCAAATACAA
1 GCCAAATAACAACCCGAAGGCCCAAATACAA
155341 GCCAAATAACAA-CCGAAGGCCCAAATACAA
1 GCCAAATAACAACCCGAAGGCCCAAATACAA
155371 GCCAAATAACAACCCGAAGGCCCAAATACAA
1 GCCAAATAACAACCCGAAGGCCCAAATACAA
** * *
155402 AACAAATTACAACCC-AAAGCCCA
1 GCCAAATAACAACCCGAAGGCCCA
155425 TGTTACAACC
Statistics
Matches: 138, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
30 67 0.49
31 71 0.51
ACGTcount: A:0.49, C:0.32, G:0.12, T:0.07
Consensus pattern (31 bp):
GCCAAATAACAACCCGAAGGCCCAAATACAA
Found at i:155344 original size:61 final size:61
Alignment explanation
Indices: 155249--155424 Score: 298
Period size: 61 Copynumber: 2.9 Consensus size: 61
155239 AATTTTAGAG
*
155249 GCCAAATTACAACCCGAAGGCCCAAATACAAGCCAAATAACAACCGAAGGCCCAAATACAA
1 GCCAAATAACAACCCGAAGGCCCAAATACAAGCCAAATAACAACCGAAGGCCCAAATACAA
155310 GCCAAATAACAACCCGAAGGCCCAAATACAAGCCAAATAACAACCGAAGGCCCAAATACAA
1 GCCAAATAACAACCCGAAGGCCCAAATACAAGCCAAATAACAACCGAAGGCCCAAATACAA
** * * *
155371 GCCAAATAACAACCCGAAGGCCCAAATACAAAACAAATTACAACCCAAAGCCCA
1 GCCAAATAACAACCCGAAGGCCCAAATACAAGCCAAATAACAACCGAAGGCCCA
155425 TGTTACAACC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 109 1.00
ACGTcount: A:0.49, C:0.32, G:0.12, T:0.07
Consensus pattern (61 bp):
GCCAAATAACAACCCGAAGGCCCAAATACAAGCCAAATAACAACCGAAGGCCCAAATACAA
Found at i:156431 original size:26 final size:24
Alignment explanation
Indices: 156373--156432 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
156363 TTATTCACTA
156373 AATATATTAATATTTTAAATAAAT
1 AATATATTAATATTTTAAATAAAT
* * *
156397 -ATAGGATTATTTTATTTATAATAAAT
1 AATA-TATTAATAT-TTTA-AATAAAT
156423 AATATATTAA
1 AATATATTAA
156433 GTAATATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
23 3 0.11
24 6 0.22
25 4 0.15
26 11 0.41
27 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (24 bp):
AATATATTAATATTTTAAATAAAT
Found at i:165982 original size:133 final size:131
Alignment explanation
Indices: 165698--165984 Score: 360
Period size: 131 Copynumber: 2.2 Consensus size: 131
165688 GAAGATTTGG
* * * * *
165698 TCTCCACGGAAGAGTATTGGAAGAAAATCAACCTCAAATTTTATCTTCACGAAAGAATAGTGAAG
1 TCTCCACGGAAGAGTAGTGGAATAAAATCAACCTCAAATGTGATCTTCACGAAAGAATAGTGAAA
* * * * * *
165763 CATATTCTTTTCAAGCAATACAACCTTCACAGAAGAGTAGTGAGCAGGAATAGACCAAAAGTTCG
66 CAGATTCTTCTCAAACAATACAACCTTCACAAAAGAGTAGTGAGCAAGAATAGACCAAAAGCTCG
165828 A
131 A
* ** * *
165829 TCTCCACGGAAGAGTAGTGGAATAAAATCAATCTTGAATGTGATCTTCACGGAAGAGTAGTGAAA
1 TCTCCACGGAAGAGTAGTGGAATAAAATCAACCTCAAATGTGATCTTCACGAAAGAATAGTGAAA
* * **
165894 TAGATTCTTCTCAAACAAATACATCCTTCACAAAAGAGTAGTGAAGCAAG-ATCAGATTAAAAGC
66 CAGATTCTTCTCAAAC-AATACAACCTTCACAAAAGAGTAGTG-AGCAAGAAT-AGACCAAAAGC
165958 TCGA
128 TCGA
165962 TCTCCACGGAAGAGTAGTGGAAT
1 TCTCCACGGAAGAGTAGTGGAAT
165985 GAATTTTTAT
Statistics
Matches: 133, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
131 67 0.50
132 26 0.20
133 40 0.30
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (131 bp):
TCTCCACGGAAGAGTAGTGGAATAAAATCAACCTCAAATGTGATCTTCACGAAAGAATAGTGAAA
CAGATTCTTCTCAAACAATACAACCTTCACAAAAGAGTAGTGAGCAAGAATAGACCAAAAGCTCG
A
Found at i:166184 original size:28 final size:29
Alignment explanation
Indices: 166144--166212 Score: 122
Period size: 28 Copynumber: 2.4 Consensus size: 29
166134 ATATTATATT
166144 ATATCATATCACATCACATCACAT-CATC
1 ATATCATATCACATCACATCACATACATC
166172 ATATCATATCACATCACATCACATCACATC
1 ATATCATATCACATCACATCACAT-ACATC
166202 ATATCATATCA
1 ATATCATATCA
166213 TATTATATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 24 0.62
30 15 0.38
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.29
Consensus pattern (29 bp):
ATATCATATCACATCACATCACATACATC
Found at i:166188 original size:33 final size:34
Alignment explanation
Indices: 166139--166215 Score: 120
Period size: 33 Copynumber: 2.3 Consensus size: 34
166129 TTATTATATT
* *
166139 ATATTATATCATATCACATCACATCACATC-ATC
1 ATATCATATCACATCACATCACATCACATCAATC
166172 ATATCATATCACATCACATCACATCACATCATATC
1 ATATCATATCACATCACATCACATCACATCA-ATC
166207 ATATCATAT
1 ATATCATAT
166216 TATATTATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 28 0.70
35 12 0.30
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.32
Consensus pattern (34 bp):
ATATCATATCACATCACATCACATCACATCAATC
Found at i:166220 original size:15 final size:15
Alignment explanation
Indices: 166144--166212 Score: 88
Period size: 15 Copynumber: 4.7 Consensus size: 15
166134 ATATTATATT
166144 ATATCATATCACATC
1 ATATCATATCACATC
* *
166159 ACATCACAT--CATC
1 ATATCATATCACATC
166172 ATATCATATCACATC
1 ATATCATATCACATC
* *
166187 ACATCACATCACATC
1 ATATCATATCACATC
166202 ATATCATATCA
1 ATATCATATCA
166213 TATTATATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.25
15 33 0.75
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.29
Consensus pattern (15 bp):
ATATCATATCACATC
Found at i:166223 original size:5 final size:5
Alignment explanation
Indices: 166134--166220 Score: 70
Period size: 5 Copynumber: 17.8 Consensus size: 5
166124 TAATATTATT
* * * * *
166134 ATATT ATATT ATATC ATATC ACATC ACATC ACATC --ATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
* * * * *
166182 ACATC ACATC ACATC ACATC ATATC ATATC ATATT ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATAT
166221 TATTATAATT
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
3 3 0.04
5 72 0.96
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (5 bp):
ATATC
Found at i:171848 original size:40 final size:42
Alignment explanation
Indices: 171802--171988 Score: 103
Period size: 40 Copynumber: 4.4 Consensus size: 42
171792 TTGAAGCGGC
*
171802 TCCTACGTGATGAGGAGATCTAGTCA-GT-GGATGACATGGT
1 TCCTACGTGATGAGGAGATCTAGTCAGGTAGGATGACACGGT
* * * * * * *
171842 TCCTACGTGATTAGGATGGTTGACCATATTTAGGTATGATAACATGGT
1 TCCTACGTGA-T--GA-GG-AGATC-TAGTCAGGTAGGATGACACGGT
* * * * ** * *
171890 TCCTACGTGATGAGGACAACTGGTTATCTAAGGGTGACACGGC
1 TCCTACGTGATGAGGAGATCTAGTCAGGT-AGGATGACACGGT
* *
171933 TCCTACGTGATGAGGAGGTCTGGTCA-GT-GGATGACACGGT
1 TCCTACGTGATGAGGAGATCTAGTCAGGTAGGATGACACGGT
* *
171973 TCCAACGCGATGAGGA
1 TCCTACGTGATGAGGA
171989 TGACATGCCA
Statistics
Matches: 111, Mismatches: 27, Indels: 18
0.71 0.17 0.12
Matches are distributed among these distances:
40 34 0.31
41 1 0.01
42 6 0.05
43 34 0.31
44 4 0.04
45 5 0.05
46 4 0.04
47 3 0.03
48 20 0.18
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (42 bp):
TCCTACGTGATGAGGAGATCTAGTCAGGTAGGATGACACGGT
Found at i:171874 original size:132 final size:130
Alignment explanation
Indices: 171646--171990 Score: 435
Period size: 131 Copynumber: 2.6 Consensus size: 130
171636 TTGAGGAAGT
* * * * *
171646 CTGGCTATCTAAGGGTGACACAGCTCCTACATGATGAGGAGATCTGGTC-GATAGAAGACACGGT
1 CTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAG-TGGATGACACGGT
* * * *
171710 TTCTACACGATGATGAAGGTTGACCATATTTAGGATGATGATAACATGATTCCTA-TGCATGAGG
65 TCCTACGCGATGAGGATGGTTGACCATATTTAGG-T-ATGATAACATGATTCCTACTG-ATGAGG
**
171774 ACGG
127 ACAA
* * * *
171778 CTGGTTGTCTAAGGTTGA-AGCGGCTCCTACGTGATGAGGAGATCTAGTCAGTGGATGACATGGT
1 CTGGTTATCTAAGGGTGACA-CGGCTCCTACGTGATGAGGAGATCTGGTCAGTGGATGACACGGT
* * *
171842 TCCTACGTGATTAGGATGGTTGACCATATTTAGGTATGATAACATGGTTCCTACGTGATGAGGAC
65 TCCTACGCGATGAGGATGGTTGACCATATTTAGGTATGATAACATGATTCCTAC-TGATGAGGAC
171907 AA
129 AA
*
171909 CTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCAGTGGATGACACGGTT
1 CTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGTGGATGACACGGTT
*
171974 CCAACGCGATGAGGATG
66 CCTACGCGATGAGGATG
171991 ACATGCCATC
Statistics
Matches: 182, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
130 17 0.09
131 82 0.45
132 82 0.45
133 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (130 bp):
CTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGTGGATGACACGGTT
CCTACGCGATGAGGATGGTTGACCATATTTAGGTATGATAACATGATTCCTACTGATGAGGACAA
Found at i:172006 original size:131 final size:133
Alignment explanation
Indices: 171624--171990 Score: 451
Period size: 132 Copynumber: 2.8 Consensus size: 133
171614 GAGATAGCAC
* * * * *
171624 GGTTCCTACGTGTTGAGGA-AGTCTGGCTATCTAAGGGTGACACAGCTCCTACATGATGAGGAGA
1 GGTTCCTACGTGATGAGGACA-ACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGA
* * * * * *
171688 TCTGGTC-GATAGAAGACACGGTTTCTACACGATGATGAAGGTTGACCATATTTAGGATGATGAT
65 TCTGGTCAG-TGGATGACACGGTTCCTACGCGATGAGGATGGTTGACCATATTTAGGATGATGAT
171752 AACAT
129 AACAT
* ** * *
171757 GATTCCTA--TGCATGAGGACGGCTGGTTGTCTAAGGTTGA-AGCGGCTCCTACGTGATGAGGAG
1 GGTTCCTACGTG-ATGAGGACAACTGGTTATCTAAGGGTGACA-CGGCTCCTACGTGATGAGGAG
* * * *
171819 ATCTAGTCAGTGGATGACATGGTTCCTACGTGATTAGGATGGTTGACCATATTTAGG-T-ATGAT
64 ATCTGGTCAGTGGATGACACGGTTCCTACGCGATGAGGATGGTTGACCATATTTAGGATGATGAT
171882 AACAT
129 AACAT
*
171887 GGTTCCTACGTGATGAGGACAACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGGT
1 GGTTCCTACGTGATGAGGACAACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGAT
*
171952 CTGGTCAGTGGATGACACGGTTCCAACGCGATGAGGATG
66 CTGGTCAGTGGATGACACGGTTCCTACGCGATGAGGATG
171991 ACATGCCATC
Statistics
Matches: 197, Mismatches: 30, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
130 17 0.09
131 84 0.43
132 88 0.45
133 8 0.04
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.27
Consensus pattern (133 bp):
GGTTCCTACGTGATGAGGACAACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGAT
CTGGTCAGTGGATGACACGGTTCCTACGCGATGAGGATGGTTGACCATATTTAGGATGATGATAA
CAT
Found at i:172061 original size:36 final size:36
Alignment explanation
Indices: 172010--172191 Score: 117
Period size: 36 Copynumber: 5.4 Consensus size: 36
172000 CTTTAGGGAC
* *
172010 TTGTTTTAAGAGAAACTGTCTTAAGAGAGACAAAAT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
* *
172046 TTGTTTCAAGGGAAACTATCTCAA-AGATG-----A-
1 TTGTTTCAAGAGAAACTGTCTCAAGAGA-GACAAAAT
172076 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
* * *
172111 TTGTTTTAAGGGAAA-TGATCTC-A-A-AG--ATAA-
1 TTGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAAT
* * * *
172141 -TGATTCAAGAGAAACTATCTAAAGAGAGACTAAATT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAAT
*
172177 TTGTTTCAAGGGAAA
1 TTGTTTCAAGAGAAA
172192 TAAACTCAAA
Statistics
Matches: 109, Mismatches: 18, Indels: 37
0.66 0.11 0.23
Matches are distributed among these distances:
29 36 0.33
30 5 0.05
31 5 0.05
32 2 0.02
33 2 0.02
34 2 0.02
35 8 0.07
36 37 0.34
37 12 0.11
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (36 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
Found at i:172115 original size:65 final size:65
Alignment explanation
Indices: 172011--172204 Score: 273
Period size: 65 Copynumber: 3.0 Consensus size: 65
172001 TTTAGGGACT
* * *
172011 TGTTTTAAGAGAAACTGTCTTAAGAGAGACAAAATTTGTTTCAAGGGAAACT-ATCTCAAAGATG
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGGGAAA-TAATCTCAAAGATA
172075 A
65 A
* * *
172076 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATGATCTCAAAGATAA
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGGGAAATAATCTCAAAGATAA
* * * *
172141 TGATTCAAGAGAAACTATCTAAAGAGAGACTAAATTTTGTTTCAAGGGAAATAAACTCAAAGAT
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGAC-AAAATTTGTTTCAAGGGAAATAATCTCAAAGAT
172205 TTTTTTTTTG
Statistics
Matches: 116, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
64 1 0.01
65 86 0.74
66 29 0.25
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGGGAAATAATCTCAAAGATAA
Found at i:179455 original size:3 final size:3
Alignment explanation
Indices: 179447--179493 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
179437 GTTATTAAGT
179447 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
179494 TTTTTAAGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:189820 original size:7 final size:7
Alignment explanation
Indices: 189810--189903 Score: 59
Period size: 7 Copynumber: 13.1 Consensus size: 7
189800 GAGAACAGAG
189810 AAAGAAA
1 AAAGAAA
189817 AAAG--A
1 AAAGAAA
*
189822 ATAGAAA
1 AAAGAAA
*
189829 AAAGAAG
1 AAAGAAA
*
189836 AAAGATA
1 AAAGAAA
*
189843 AAAGATA
1 AAAGAAA
189850 AAAGATAA
1 AAAGA-AA
*
189858 AAATAAGA
1 AAAGAA-A
*
189866 ATAGAGAA
1 AAAGA-AA
189874 AAAGAAA
1 AAAGAAA
*
189881 GAAAGAAT
1 -AAAGAAA
189889 AAAGAAGA
1 AAAGAA-A
189897 AAA-AAA
1 AAAGAAA
189903 A
1 A
189904 TGAATCAAGT
Statistics
Matches: 68, Mismatches: 12, Indels: 15
0.72 0.13 0.16
Matches are distributed among these distances:
5 4 0.06
6 2 0.03
7 38 0.56
8 23 0.34
9 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (7 bp):
AAAGAAA
Found at i:189845 original size:14 final size:14
Alignment explanation
Indices: 189808--189903 Score: 83
Period size: 14 Copynumber: 6.8 Consensus size: 14
189798 TCGAGAACAG
189808 AGAAAGAAAAAAG-
1 AGAAAGAAAAAAGA
*
189821 A-ATAGAAAAAAGA
1 AGAAAGAAAAAAGA
*
189834 AGAAAGATAAAAGA
1 AGAAAGAAAAAAGA
*
189848 TA-AAAGATAAAAATA
1 -AGAAAGA-AAAAAGA
189863 AGAATAGAGAAAAAGAA
1 AGAA-AGA-AAAAAG-A
*
189880 AGAAAGAATAAAGA
1 AGAAAGAAAAAAGA
189894 AGAAA-AAAAA
1 AGAAAGAAAAA
189904 TGAATCAAGT
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
12 10 0.15
13 6 0.09
14 22 0.33
15 13 0.19
16 11 0.16
17 5 0.07
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (14 bp):
AGAAAGAAAAAAGA
Found at i:193116 original size:65 final size:66
Alignment explanation
Indices: 193008--193180 Score: 226
Period size: 65 Copynumber: 2.6 Consensus size: 66
192998 ATTCTGAGAA
* * * *
193008 TGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGATAATTTCTTTTCG-AACATAAACC-TGAA
1 TGTTTCTCTCAAAACAAAGTTTTATCTTGCTTGAGACAATTTCTTTT-GAAACATAAACCTTGAA
193071 AT
65 AT
* * *
193073 TGTTTCTCTCTAAACAAAGTTTTATCTTGCTTGAGACAGTTTCTTTTGAAACATAAACCTTTGAG
1 TGTTTCTCTCAAAACAAAGTTTTATCTTGCTTGAGACAATTTCTTTTGAAACATAAACC-TTGAA
193138 AT
65 AT
* *
193140 TATTTCTCTCAAAACAAA-TTTCATCTTGCTTGAGACAATTT
1 TGTTTCTCTCAAAACAAAGTTTTATCTTGCTTGAGACAATTT
193181 TCCCTCGAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 1 0.01
65 52 0.55
66 21 0.22
67 21 0.22
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.40
Consensus pattern (66 bp):
TGTTTCTCTCAAAACAAAGTTTTATCTTGCTTGAGACAATTTCTTTTGAAACATAAACCTTGAAA
T
Found at i:194298 original size:3 final size:3
Alignment explanation
Indices: 194290--194323 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
194280 TTTTAATTGT
194290 TTA TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
194324 ACAATATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:199814 original size:14 final size:13
Alignment explanation
Indices: 199779--199817 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
199769 TGTCCAAAAG
199779 TAAAGA-ATAAA-
1 TAAAGAGATAAAT
199790 TAAAGAGATAAAT
1 TAAAGAGATAAAT
199803 TAAAGAAGATAAAT
1 TAAAG-AGATAAAT
199817 T
1 T
199818 GATATGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.24
12 5 0.20
13 5 0.20
14 9 0.36
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (13 bp):
TAAAGAGATAAAT
Found at i:200740 original size:83 final size:83
Alignment explanation
Indices: 200601--200767 Score: 289
Period size: 83 Copynumber: 2.0 Consensus size: 83
200591 TTTGAATTTA
*
200601 CGGCTAAATCTTCTGTTTTCACAAAAATATTGATTGGACCTTCTAGAAGGTGCTGACTGGATGCC
1 CGGCTAAATCTTCTGCTTTCACAAAAATATTGATTGGACCTTCTAGAAGGTGCTGACTGGATGCC
200666 ACATAAGCAGAGTCATGC
66 ACATAAGCAGAGTCATGC
* * * *
200684 CGGCTAAATCTTCTGCTTTCACAAAAATGTTGATTGGATCTTTTAGAAGGTGCTGACTGGATGGC
1 CGGCTAAATCTTCTGCTTTCACAAAAATATTGATTGGACCTTCTAGAAGGTGCTGACTGGATGCC
200749 ACATAAGCAGAGTCATGC
66 ACATAAGCAGAGTCATGC
200767 C
1 C
200768 CAAGTCAATG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (83 bp):
CGGCTAAATCTTCTGCTTTCACAAAAATATTGATTGGACCTTCTAGAAGGTGCTGACTGGATGCC
ACATAAGCAGAGTCATGC
Found at i:201530 original size:19 final size:19
Alignment explanation
Indices: 201483--201532 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
201473 TGAAGGCTTT
201483 TTTCTTTTTTCTTTTCTCCC
1 TTTC-TTTTTCTTTTCTCCC
*
201503 TTT-TGTTTTCTTTTGTCCC
1 TTTCT-TTTTCTTTTCTCCC
201522 TTTCTTTTTCT
1 TTTCTTTTTCT
201533 GCTTTTATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.04
19 22 0.81
20 4 0.15
ACGTcount: A:0.00, C:0.24, G:0.04, T:0.72
Consensus pattern (19 bp):
TTTCTTTTTCTTTTCTCCC
Found at i:201556 original size:26 final size:25
Alignment explanation
Indices: 201526--201589 Score: 65
Period size: 28 Copynumber: 2.4 Consensus size: 25
201516 TGTCCCTTTC
* *
201526 TTTTTCTGCTTTTATTCGAATTTGTT
1 TTTTTCTGCTTGTATTCGAA-CTGTT
201552 TTTTTCTTTGCATTGTATTCGAACTGTT
1 TTTTTC--TGC-TTGTATTCGAACTGTT
*
201580 TTTTTTTGCT
1 TTTTTCTGCT
201590 ATTCGAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 1 0.03
26 9 0.28
28 12 0.38
29 10 0.31
ACGTcount: A:0.11, C:0.12, G:0.12, T:0.64
Consensus pattern (25 bp):
TTTTTCTGCTTGTATTCGAACTGTT
Found at i:219473 original size:21 final size:22
Alignment explanation
Indices: 219449--219489 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
219439 AGAGTCAAAC
* *
219449 AAACAATTTGAAGAA-AAATGG
1 AAACAACTAGAAGAAGAAATGG
219470 AAACAACTAGAAGAAGAAAT
1 AAACAACTAGAAGAAGAAAT
219490 TAGGGCTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.61, C:0.07, G:0.17, T:0.15
Consensus pattern (22 bp):
AAACAACTAGAAGAAGAAATGG
Found at i:225909 original size:4 final size:4
Alignment explanation
Indices: 225865--225949 Score: 72
Period size: 4 Copynumber: 21.8 Consensus size: 4
225855 AAGAAAAGAA
* *
225865 AAAG AAA- AAAG AAAG AGAA- AAA- AAA- AAAA AAAG -AAG GAAG AAAG
1 AAAG AAAG AAAG AAAG A-AAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
* *
225909 AAAG AAAG AAAG AAAG AAATA AAAG AAAA AAAG AAAAG AAA
1 AAAG AAAG AAAG AAAG AAA-G AAAG AAAG AAAG -AAAG AAA
225950 ATAAGGAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
3 14 0.20
4 46 0.67
5 9 0.13
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:227580 original size:134 final size:134
Alignment explanation
Indices: 227151--227750 Score: 729
Period size: 136 Copynumber: 4.4 Consensus size: 134
227141 AATTTAATCC
* * *
227151 TTCAGATTTAGTCTTCCTGAAGAAGTAACGAAGCAAATCAAGTTCGATTCAATCTTCCTTGAAGA
1 TTCAAATTTAGTCTTCCTGAAGAA-CAGCGAAGCAAATCAAGTTCGATTCAATCTTCCTTGAAGA
* * ** *
227216 GCAGTGAAGTGGATCAAAATTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGAGGAGCATATTCT
65 GCAGCGAAGTGGATAAAAAAATTTCTCGAGTCTGATCT-CCCTAAAGAGTAGAGGAGCAGATTCT
227281 TCTTCT
129 TCTTCT
* * * *
227287 TTCAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATGAAGTTCGATTTAATCTTCCTTGAAGA
1 TTCAAATTTAGTCTTCCTGAAGAA-CAGCGAAGCAAATCAAGTTCGATTCAATCTTCCTTGAAGA
* * * * *
227352 GTAGCGAAGTGGATCAAAAAAAATTCTCGAGTCTGAGAAC-CCCTAAAGAGTAGCGGAACAGATT
65 GCAGCGAAGTGGAT-AAAAAAATTTCTCGAGTCT--GATCTCCCTAAAGAGTAGAGGAGCAGATT
*
227416 CTTGTTCT
127 CTTCTTCT
* *
227424 TTCAAATTTGGTCTTCCTGAAGAACAGCGAAGCAAATCAAGTTCAATTCAATCTTCCTTGAAGAG
1 TTCAAATTTAGTCTTCCTGAAGAACAGCGAAGCAAATCAAGTTCGATTCAATCTTCCTTGAAGAG
* * * *
227489 CAGCGAAGTGGGTAAAAAAATTTCTCGAGTCTGATCTCCCTAAAGAGTAGCGGAGCATATTGTTC
66 CAGCGAAGTGGATAAAAAAATTTCTCGAGTCTGATCTCCCTAAAGAGTAGAGGAGCAGATTCTTC
227554 TTCT
131 TTCT
* ** * *
227558 TTCAAATTTAGTCTTCTTGAAGAACAGCGAAGCAAATCAAGTTTTAGTCAATCTTCCCTGAAGAG
1 TTCAAATTTAGTCTTCCTGAAGAACAGCGAAGCAAATCAAGTTCGATTCAATCTTCCTTGAAGAG
* ** * *
227623 CAGCGAAGTGGATCAAAATTTTTCTCGAGTCTGATTTTCCCTAAAGAGTAAAGGAGCAGATTCTT
66 CAGCGAAGTGGATAAAAAAATTTCTCGAGTCTGA-TCTCCCTAAAGAGTAGAGGAGCAGATTCTT
*
227688 CTCCT
130 CTTCT
* * * ** *
227693 TTCATATTT-GATCTTCTTGAAGAGA-AGTGAAGCAAATCAACCTCGATTCAATTTTCCT
1 TTCAAATTTAG-TCTTCCTGAAGA-ACAGCGAAGCAAATCAAGTTCGATTCAATCTTCCT
227751 AGACTAACTT
Statistics
Matches: 404, Mismatches: 53, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
133 3 0.01
134 118 0.29
135 92 0.23
136 122 0.30
137 66 0.16
139 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (134 bp):
TTCAAATTTAGTCTTCCTGAAGAACAGCGAAGCAAATCAAGTTCGATTCAATCTTCCTTGAAGAG
CAGCGAAGTGGATAAAAAAATTTCTCGAGTCTGATCTCCCTAAAGAGTAGAGGAGCAGATTCTTC
TTCT
Found at i:228460 original size:16 final size:15
Alignment explanation
Indices: 228439--228480 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
228429 GAGACATAAA
228439 GAAAAAAAAAGGGAAC
1 GAAAAAAAAA-GGAAC
*
228455 GAAAAAAATA-GAAC
1 GAAAAAAAAAGGAAC
228469 GAAAAAGAAAAG
1 GAAAAA-AAAAG
228481 AAAAAAGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.45
15 3 0.14
16 9 0.41
ACGTcount: A:0.71, C:0.05, G:0.21, T:0.02
Consensus pattern (15 bp):
GAAAAAAAAAGGAAC
Found at i:230789 original size:34 final size:34
Alignment explanation
Indices: 230751--230973 Score: 151
Period size: 34 Copynumber: 5.9 Consensus size: 34
230741 CCTTAGCTTA
230751 AATGCATATGGGTGCATTATCAGCATAAAAGAGT
1 AATGCATATGGGTGCATTATCAGCATAAAAGAGT
* *
230785 AATGCATATGGGTGTATTATTAGCATGAAAGGATGCCTTAGCT
1 AATGCATATGGGTGCATTATCAGCAT-AAA--A-G----AG-T
*
230828 GAAATGCATATGGGTGCATTATC-GACATAAAAGAAT
1 --AATGCATATGGGTGCATTATCAG-CATAAAAGAGT
* **
230864 AATACATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCT
1 AATGCATATGGGTGCATTATCAGCAT-AAA--A-G----AG-T
* *
230907 GAAATGCATATGGGTGCATTATCGGCATAAAAGATT
1 --AATGCATATGGGTGCATTATCAGCATAAAAGAGT
*
230943 AATGCATATGGGTGCATTATCAACATAAAAG
1 AATGCATATGGGTGCATTATCAGCATAAAAG
230974 TATGCTATAA
Statistics
Matches: 152, Mismatches: 13, Indels: 48
0.71 0.06 0.23
Matches are distributed among these distances:
34 75 0.49
35 7 0.05
36 2 0.01
37 4 0.03
38 2 0.01
41 2 0.01
42 5 0.03
43 2 0.01
44 7 0.05
45 46 0.30
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCAGCATAAAAGAGT
Found at i:230849 original size:45 final size:45
Alignment explanation
Indices: 230785--230928 Score: 150
Period size: 45 Copynumber: 3.4 Consensus size: 45
230775 ATAAAAGAGT
*
230785 AATGCATATGGGTGTATTATTAGCATGAAAGGATGCCTTAGCTGA
1 AATGCATATGGGTGCATTATTAGCATGAAAGGATGCCTTAGCTGA
* *
230830 AATGCATATGGGTGCATTA-TCGACAT-AAA--A-G----A-AT--
1 AATGCATATGGGTGCATTATTAG-CATGAAAGGATGCCTTAGCTGA
* *
230864 AATACATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGA
1 AATGCATATGGGTGCATTATTAGCATGAAAGGATGCCTTAGCTGA
230909 AATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
230929 CGGCATAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 26
0.71 0.06 0.23
Matches are distributed among these distances:
34 21 0.27
35 5 0.06
36 1 0.01
37 2 0.03
38 1 0.01
41 1 0.01
42 2 0.03
43 1 0.01
44 5 0.06
45 40 0.51
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTAGCATGAAAGGATGCCTTAGCTGA
Found at i:230989 original size:79 final size:79
Alignment explanation
Indices: 230697--230962 Score: 451
Period size: 79 Copynumber: 3.4 Consensus size: 79
230687 AACGAATGAG
* *
230697 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTTAAATGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTAGCATGAAAGGATGCCTTAGCTGAAATGCATATGG
*
230762 GTGCATTATCAGCA
66 GTGCATTATCGGCA
* *
230776 TAAAAGAGTAATGCATATGGGTGTATTATTAGCATGAAAGGATGCCTTAGCTGAAATGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTAGCATGAAAGGATGCCTTAGCTGAAATGCATATGG
*
230841 GTGCATTATCGACA
66 GTGCATTATCGGCA
* *
230855 TAAAAGAATAATACATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTAGCATGAAAGGATGCCTTAGCTGAAATGCATATGG
230920 GTGCATTATCGGCA
66 GTGCATTATCGGCA
*
230934 TAAAAGATTAATGCATATGGGTGCATTAT
1 TAAAAGAATAATGCATATGGGTGCATTAT
230963 CAACATAAAA
Statistics
Matches: 174, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 174 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (79 bp):
TAAAAGAATAATGCATATGGGTGCATTATTAGCATGAAAGGATGCCTTAGCTGAAATGCATATGG
GTGCATTATCGGCA
Found at i:230989 original size:158 final size:159
Alignment explanation
Indices: 230697--231005 Score: 480
Period size: 158 Copynumber: 1.9 Consensus size: 159
230687 AACGAATGAG
* *
230697 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTTAAATGCATATGG
1 TAAAAGAATAATACATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGCATATGG
* * * * *
230762 GTGCATTATCAGCATAAAAGAGTAATGCATATGGGTGTATTATTAGCATGAAAGGATGCCTTAGC
66 GTGCATTATCAGCATAAAAGAGTAATGCATATGGGTGCATTATCAACATAAAAGGATGCCTTAAC
230827 TG-AAATGCAT-ATGGGTGCATTATCGACA
131 TGAAAATGCATAAT-GGTGCATTATCGACA
230855 TAAAAGAATAATACATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGCATATGG
1 TAAAAGAATAATACATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGCATATGG
* * *
230920 GTGCATTATCGGCATAAAAGATTAATGCATATGGGTGCATTATCAACATAAAAGTATG-CTATAA
66 GTGCATTATCAGCATAAAAGAGTAATGCATATGGGTGCATTATCAACATAAAAGGATGCCT-TAA
*
230984 TTGAAAATGCATAATGGTGCAT
130 CTGAAAATGCATAATGGTGCAT
231006 GATAAACGTA
Statistics
Matches: 137, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
157 2 0.01
158 118 0.86
159 15 0.11
160 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (159 bp):
TAAAAGAATAATACATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGCATATGG
GTGCATTATCAGCATAAAAGAGTAATGCATATGGGTGCATTATCAACATAAAAGGATGCCTTAAC
TGAAAATGCATAATGGTGCATTATCGACA
Found at i:232590 original size:34 final size:34
Alignment explanation
Indices: 232547--232620 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
232537 ACCATTTTGA
232547 CATTATCAGTATAAAAGAATAATGCATATGGGTG
1 CATTATCAGTATAAAAGAATAATGCATATGGGTG
232581 CATTATCAGTATAAAAGAATAATGCATATGGGTG
1 CATTATCAGTATAAAAGAATAATGCATATGGGTG
232615 CATTAT
1 CATTAT
232621 TGGCATGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (34 bp):
CATTATCAGTATAAAAGAATAATGCATATGGGTG
Found at i:232652 original size:45 final size:41
Alignment explanation
Indices: 232601--232742 Score: 136
Period size: 45 Copynumber: 3.4 Consensus size: 41
232591 ATAAAAGAAT
*
232601 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GA-GCC--AGATGA
232646 AATGCATATGGGTGCATTATTGGCAT-AAA-AG--A-AT--
1 AATGCATATGGGTGCATTATTGGCATGAAAGAGCCAGATGA
* *
232680 AATGTATATGGGTGCATTATTGGCATGAAAGGACGCCAAAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GA-GCC--AGATGA
232725 AATGCATATGGGTGCATT
1 AATGCATATGGGTGCATT
232743 TTCAACATAA
Statistics
Matches: 82, Mismatches: 4, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
34 25 0.30
35 3 0.04
36 1 0.01
37 2 0.02
38 1 0.01
41 1 0.01
42 2 0.02
43 1 0.01
44 3 0.04
45 43 0.52
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (41 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGAGCCAGATGA
Found at i:232694 original size:34 final size:34
Alignment explanation
Indices: 232646--232710 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
232636 CCTTAGCTGA
232646 AATGCATATGGGTGCATTATTGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATTGGCATAAAAGAAT
* *
232680 AATGTATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATTGGCATAAAAG
232711 GACGCCAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATTGGCATAAAAGAAT
Found at i:232698 original size:79 final size:79
Alignment explanation
Indices: 232567--232755 Score: 279
Period size: 79 Copynumber: 2.4 Consensus size: 79
232557 ATAAAAGAAT
* *
232567 AATGCATATGGGTGCATTATCAGTATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAT
1 AATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAG
* **
232632 GATGCCTTAGCTGA
66 GACGCCAAAGCTGA
** *
232646 AATGCATATGGGTGCATTATTGGCATAAAAGAATAATGTATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAG
*
232711 GACGCCAAAGTTGA
66 GACGCCAAAGCTGA
* *
232725 AATGCATATGGGTGCATTTTCAACATAAAAG
1 AATGCATATGGGTGCATTATCAGCATAAAAG
232756 TATGCTATAA
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 97 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.29
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAG
GACGCCAAAGCTGA
Found at i:234306 original size:20 final size:19
Alignment explanation
Indices: 234269--234320 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
234259 TAATTCAATC
* *
234269 AGTATCAATACCGAAGGGGG
1 AGTATCGATACCGAA-GGGA
* *
234289 AGTATCGATACTGTAGGGA
1 AGTATCGATACCGAAGGGA
234308 AGGTATCGATACC
1 A-GTATCGATACC
234321 ATTTTGAAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTATCGATACCGAAGGGA
Found at i:234396 original size:22 final size:20
Alignment explanation
Indices: 234345--234415 Score: 56
Period size: 22 Copynumber: 3.5 Consensus size: 20
234335 TGTAAAAACG
* * *
234345 GTATCGATACCATGGGAAG-
1 GTATCGATACCATAGTAGGA
234364 GTATC-AGTACCATAGTATTGGA
1 GTATCGA-TACCATAGTA--GGA
* *
234386 GTATCGATACCATGGTAGGG
1 GTATCGATACCATAGTAGGA
234406 GTATCGATAC
1 GTATCGATAC
234416 TGAGGAACCA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 1 0.02
19 13 0.31
20 12 0.29
21 1 0.02
22 14 0.33
23 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (20 bp):
GTATCGATACCATAGTAGGA
Found at i:235012 original size:33 final size:34
Alignment explanation
Indices: 234956--235042 Score: 167
Period size: 33 Copynumber: 2.6 Consensus size: 34
234946 TCTTAGCTGA
234956 AATGCATATGGGTGCATTATCAGTATAAAAGAAT
1 AATGCATATGGGTGCATTATCAGTATAAAAGAAT
234990 AATGCATATGGGT-CATTATCAGTATAAAAGAAT
1 AATGCATATGGGTGCATTATCAGTATAAAAGAAT
235023 AATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
235043 TGGCATGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
33 33 0.63
34 19 0.37
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCAGTATAAAAGAAT
Found at i:235022 original size:112 final size:113
Alignment explanation
Indices: 234881--235121 Score: 369
Period size: 112 Copynumber: 2.1 Consensus size: 113
234871 AGTTGAAATA
* *
234881 CATATGGGTGCATTATCAGCATAAAAGAATAATGCATATGGGTTCATTGTTAGAATGAAAAT-AT
1 CATATGGGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTAGAATG-AAATGAT
* *
234945 GTCTTAGCTGAAATGCATATGGGTGCATTATCAGTATAAAAGAATAATG
65 GCCTTAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATG
* * *
234994 CATATGGGT-CATTATCAGTATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATG
1 CATATGGGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTAGAATGAAATGATG
**
235058 CCTTAGCTGAAATGCATATGGGTGCATTATTGGCATAAAAGAATAATG
66 CCTTAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATG
*
235106 TATATGGGTGCATTAT
1 CATATGGGTGCATTAT
235122 TGGCATGAAA
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
111 4 0.03
112 97 0.84
113 15 0.13
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (113 bp):
CATATGGGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTAGAATGAAATGATG
CCTTAGCTGAAATGCATATGGGTGCATTATCAGCATAAAAGAATAATG
Found at i:235074 original size:45 final size:41
Alignment explanation
Indices: 235023--235164 Score: 136
Period size: 45 Copynumber: 3.4 Consensus size: 41
235013 ATAAAAGAAT
*
235023 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GA-GCC--AGATGA
235068 AATGCATATGGGTGCATTATTGGCAT-AAA-AG--A-AT--
1 AATGCATATGGGTGCATTATTGGCATGAAAGAGCCAGATGA
* *
235102 AATGTATATGGGTGCATTATTGGCATGAAAGGACGCCAAAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GA-GCC--AGATGA
235147 AATGCATATGGGTGCATT
1 AATGCATATGGGTGCATT
235165 TTCAACATAA
Statistics
Matches: 82, Mismatches: 4, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
34 25 0.30
35 3 0.04
36 1 0.01
37 2 0.02
38 1 0.01
41 1 0.01
42 2 0.02
43 1 0.01
44 3 0.04
45 43 0.52
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (41 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGAGCCAGATGA
Found at i:235098 original size:79 final size:79
Alignment explanation
Indices: 234990--235177 Score: 270
Period size: 79 Copynumber: 2.4 Consensus size: 79
234980 ATAAAAGAAT
* *
234990 AATGCATATGGGT-CATTATCAGTATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAT
1 AATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAG
* **
235054 GATGCCTTAGCTGA
66 GACGCCAAAGCTGA
** *
235068 AATGCATATGGGTGCATTATTGGCATAAAAGAATAATGTATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAG
*
235133 GACGCCAAAGTTGA
66 GACGCCAAAGCTGA
* *
235147 AATGCATATGGGTGCATTTTCAACATAAAAG
1 AATGCATATGGGTGCATTATCAGCATAAAAG
235178 TATGCTATAA
Statistics
Matches: 96, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
78 13 0.14
79 83 0.86
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATCAGCATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAG
GACGCCAAAGCTGA
Found at i:235116 original size:34 final size:34
Alignment explanation
Indices: 235068--235132 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
235058 CCTTAGCTGA
235068 AATGCATATGGGTGCATTATTGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATTGGCATAAAAGAAT
* *
235102 AATGTATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATTGGCATAAAAG
235133 GACGCCAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATTGGCATAAAAGAAT
Found at i:235177 original size:191 final size:191
Alignment explanation
Indices: 234829--235177 Score: 509
Period size: 191 Copynumber: 1.8 Consensus size: 191
234819 TGAATAATAT
*
234829 AATAATACATATGGGTGCATTATTGGCATGAAATGATACCTTAGTTGAAATACATATGGGTGCAT
1 AATAATACATATGGGTGCATTATTGGCATGAAATGATACCTTAGCTGAAATACATATGGGTGCAT
* * * * * **
234894 TATCAGCATAAAAGAATAATGCATATGGGTTCATTGTTAGAATGAAAATATGTCTTAGCTGAAAT
66 TATCAGCATAAAAGAATAATGCATATGGGTGCATTATTAGAATGAAAAGACGCCAAAGCTGAAAT
**
234959 GCATATGGGTGCATTATCAGTATAAAAGAATAATGCATATGGGTCATTATCAGTATAAAAG
131 GCATATGGGTGCATTATCAACATAAAAGAATAATGCATATGGGTCATTATCAGTATAAAAG
* * *
235020 AATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGAAATGCATATGGGTGCAT
1 AATAATACATATGGGTGCATTATTGGCATGAAATGATACCTTAGCTGAAATACATATGGGTGCAT
** * * * * *
235085 TATTGGCATAAAAGAATAATGTATATGGGTGCATTATTGGCATGAAAGGACGCCAAAGTTGAAAT
66 TATCAGCATAAAAGAATAATGCATATGGGTGCATTATTAGAATGAAAAGACGCCAAAGCTGAAAT
*
235150 GCATATGGGTGCATTTTCAACATAAAAG
131 GCATATGGGTGCATTATCAACATAAAAG
235178 TATGCTATAA
Statistics
Matches: 137, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
191 137 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (191 bp):
AATAATACATATGGGTGCATTATTGGCATGAAATGATACCTTAGCTGAAATACATATGGGTGCAT
TATCAGCATAAAAGAATAATGCATATGGGTGCATTATTAGAATGAAAAGACGCCAAAGCTGAAAT
GCATATGGGTGCATTATCAACATAAAAGAATAATGCATATGGGTCATTATCAGTATAAAAG
Found at i:241300 original size:20 final size:20
Alignment explanation
Indices: 241275--241343 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
241265 ATCGATACTG
241275 ATCGATACCGAAGGTGGAGT
1 ATCGATACCGAAGGTGGAGT
*
241295 ATCGATACCAAAGGTGGAGT
1 ATCGATACCGAAGGTGGAGT
*
241315 ATCGATACCGAAGG-GAAGGT
1 ATCGATACCGAAGGTGGA-GT
241335 ATCGATACC
1 ATCGATACC
241344 ATTTTAAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 2 0.04
20 43 0.96
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.19
Consensus pattern (20 bp):
ATCGATACCGAAGGTGGAGT
Found at i:241419 original size:22 final size:20
Alignment explanation
Indices: 241368--241438 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 20
241358 TGCAAAAACG
* * *
241368 GTATCGATACCATGGGAAG-
1 GTATCGATACCATAGTAGGA
*
241387 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGTA-GG-A
* *
241409 GTATCGATACCATGGTAGGG
1 GTATCGATACCATAGTAGGA
241429 GTATCGATAC
1 GTATCGATAC
241439 TGAGGAACCA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 14 0.33
20 11 0.26
21 2 0.05
22 15 0.36
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.27
Consensus pattern (20 bp):
GTATCGATACCATAGTAGGA
Found at i:241954 original size:34 final size:34
Alignment explanation
Indices: 241901--242123 Score: 140
Period size: 34 Copynumber: 5.9 Consensus size: 34
241891 CCTTAGCTGA
*
241901 AATGAATATGGGTGCATTATTGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATTGGCATAAAAGAAT
* * *
241935 AATTCATATGGGTGTATTATTGGCATGAAAGGATGCCTTAGCT
1 AATGCATATGGGTGCATTATTGGCAT-AAA--A-G----A-AT
* * *
241978 GAAATGTATGTGGGTTCATTATTGGCATAAAAGAAT
1 --AATGCATATGGGTGCATTATTGGCATAAAAGAAT
* *
242014 AATACATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCT
1 AATGCATATGGGTGCATTATTGGCAT-AAA--A-G----A-AT
**
242057 GAAATGCATATGGGTGTTTTATTGGCATAAAAGAAT
1 --AATGCATATGGGTGCATTATTGGCATAAAAGAAT
*
242093 AATGCATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATTGGCATAAAAG
242124 GACGCCAAAG
Statistics
Matches: 145, Mismatches: 22, Indels: 44
0.69 0.10 0.21
Matches are distributed among these distances:
34 73 0.50
35 6 0.04
36 2 0.01
37 4 0.03
38 2 0.01
41 2 0.01
42 4 0.03
43 2 0.01
44 6 0.04
45 44 0.30
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.32
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATTGGCATAAAAGAAT
Found at i:242168 original size:79 final size:79
Alignment explanation
Indices: 241846--242153 Score: 481
Period size: 79 Copynumber: 3.9 Consensus size: 79
241836 GAATGAATGA
* * *
241846 ATAAAAGAATAATGCATATGGGTACATTATTGGAATGAAAGGATGCCTTAGCTGAAATGAATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGCATATG
241911 GGTGCATTATTGGC
66 GGTGCATTATTGGC
* * * *
241925 ATAAAAGAATAATTCATATGGGTGTATTATTGGCATGAAAGGATGCCTTAGCTGAAATGTATGTG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGCATATG
*
241990 GGTTCATTATTGGC
66 GGTGCATTATTGGC
*
242004 ATAAAAGAATAATACATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGCATATG
**
242069 GGTGTTTTATTGGC
66 GGTGCATTATTGGC
* ** *
242083 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGACGCCAAAGTTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGCATATG
242148 GGTGCA
66 GGTGCA
242154 GTGTCAACAT
Statistics
Matches: 208, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 208 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.30
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGCATATG
GGTGCATTATTGGC
Found at i:245386 original size:31 final size:30
Alignment explanation
Indices: 245321--245427 Score: 117
Period size: 31 Copynumber: 3.4 Consensus size: 30
245311 TGTATTATCT
* *
245321 ACTATATATAATATATATTACTTTTATTTTCAAA
1 ACTATATAT-ATATATA-TA--TATACTTTCAAA
* *
245355 ACTATATCTATAATATATATCTACTTTCAAA
1 ACTATATATAT-ATATATATATACTTTCAAA
245386 ACTATATATATATATATATATACTTTC-AA
1 ACTATATATATATATATATATACTTTCAAA
*
245415 ACTAAATATATAT
1 ACTATATATATAT
245428 TATTTCAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
29 14 0.21
30 15 0.23
31 20 0.30
33 4 0.06
34 13 0.20
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.45
Consensus pattern (30 bp):
ACTATATATATATATATATATACTTTCAAA
Found at i:246998 original size:30 final size:29
Alignment explanation
Indices: 246964--247115 Score: 127
Period size: 30 Copynumber: 5.2 Consensus size: 29
246954 TTAAATTATT
246964 AAATATATTTTATTCTTAATTTAATTTTAA
1 AAATATATTTTATTCTTAATTTAA-TTTAA
* * *
246994 AAATATATTTTATTCTTATTTTAGTTTTTTTA
1 AAATATATTTTATTCTTAATTTA---ATTTAA
* *
247026 AAA-A-A--TTATTCTTATTTTAACTTAA
1 AAATATATTTTATTCTTAATTTAATTTAA
*
247051 AAATATATTTTATTCTCGT-ATTTACTTTAA
1 AAATATATTTTATTCT--TAATTTAATTTAA
* *
247081 AAATATATTTTATT-TTTATCTTAAATTAA
1 AAATATATTTTATTCTTAAT-TTAATTTAA
247110 AAATAT
1 AAATAT
247116 TAAAAATATA
Statistics
Matches: 100, Mismatches: 11, Indels: 23
0.75 0.08 0.17
Matches are distributed among these distances:
25 6 0.06
26 1 0.01
27 2 0.02
28 16 0.16
29 21 0.21
30 45 0.45
31 2 0.02
32 7 0.07
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.55
Consensus pattern (29 bp):
AAATATATTTTATTCTTAATTTAATTTAA
Found at i:247120 original size:38 final size:41
Alignment explanation
Indices: 247079--247156 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 41
247069 TATTTACTTT
* *
247079 AAAA-ATATATTTTATTTTTATCTTAAATTAA-AAATATTA
1 AAAATATATATTTTATTATTATATTAAATTAATAAATATTA
*
247118 AAAATATATATTTTATTATTATATTAACTTAATAAATAT
1 AAAATATATATTTTATTATTATATTAAATTAATAAATAT
247157 ATTTTATTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 4 0.12
40 24 0.71
41 6 0.18
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (41 bp):
AAAATATATATTTTATTATTATATTAAATTAATAAATATTA
Found at i:247159 original size:30 final size:30
Alignment explanation
Indices: 247123--247184 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
247113 TATTAAAAAT
*
247123 ATATATTTTATTATTATATTAACTTAATAA
1 ATATATTTTATTATTACATTAACTTAATAA
* * *
247153 ATATATTTTATTCTTACCTTAACTTATTAA
1 ATATATTTTATTATTACATTAACTTAATAA
247183 AT
1 AT
247185 GTATGTTGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (30 bp):
ATATATTTTATTATTACATTAACTTAATAA
Found at i:247468 original size:61 final size:59
Alignment explanation
Indices: 247393--247543 Score: 175
Period size: 61 Copynumber: 2.5 Consensus size: 59
247383 TAAATAAATT
* *
247393 TTTTGAAGTTAAGATAAGAATAAAGTATTTATTTCTAA-TTAAAATAAGAATAGAATATAC
1 TTTTAAAGTTAAGATAAGAATAAAGTATTTATTT-TAAGTTAAAATAAGAATAAAATAT-C
* *
247453 ATTTTAAAGTTAAGATGAGAATAAAGTATGTT-TTTTAAGTTAAAATAAGATTAAAATATC
1 -TTTTAAAGTTAAGATAAGAATAAAGTAT-TTATTTTAAGTTAAAATAAGAATAAAATATC
*
247513 -TTTAAA-TTAAGATAAAAATAAATTGTATTTA
1 TTTTAAAGTTAAGATAAGAATAAA--GTATTTA
247544 ATAATGTAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
57 14 0.18
58 8 0.10
59 4 0.05
60 4 0.05
61 47 0.59
62 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.38
Consensus pattern (59 bp):
TTTTAAAGTTAAGATAAGAATAAAGTATTTATTTTAAGTTAAAATAAGAATAAAATATC
Found at i:247489 original size:31 final size:29
Alignment explanation
Indices: 247390--247534 Score: 109
Period size: 30 Copynumber: 4.9 Consensus size: 29
247380 AAATAAATAA
*
247390 ATTTTTTGAAGTTAAGATAAGAATAAAGT
1 ATTTTTTTAAGTTAAGATAAGAATAAAGT
*
247419 ATTTATTTCTAA-TTAAAATAAGAATAGAA-T
1 ATTT-TTT-TAAGTTAAGATAAGAATA-AAGT
* * *
247449 ATACATTTTAAAGTTAAGATGAGAATAAAGT
1 AT--TTTTTTAAGTTAAGATAAGAATAAAGT
* *
247480 ATGTTTTTTAAGTTAAAATAAGATTAAA--
1 AT-TTTTTTAAGTTAAGATAAGAATAAAGT
* * * *
247508 ATATCTTTAAATTAAGATAAAAATAAA
1 ATTTTTTTAAGTTAAGATAAGAATAAA
247535 TTGTATTTAA
Statistics
Matches: 91, Mismatches: 18, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
27 19 0.21
28 2 0.02
29 4 0.04
30 43 0.47
31 22 0.24
32 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (29 bp):
ATTTTTTTAAGTTAAGATAAGAATAAAGT
Found at i:247584 original size:2 final size:2
Alignment explanation
Indices: 247577--247630 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
247567 ACATACATAC
* * * *
247577 AT AT AT AT AT AT AT AT AT AT AT AT GT GT GT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
247619 AT AT AT A- AT AT A
1 AT AT AT AT AT AT A
247631 AAAATCAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (2 bp):
AT
Found at i:251559 original size:2 final size:2
Alignment explanation
Indices: 251495--251540 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
251485 ATTAGGGTGG
251495 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
251537 AT AT
1 AT AT
251541 TTAACACGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:252735 original size:15 final size:15
Alignment explanation
Indices: 252717--252757 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
252707 CAAAGCAATA
*
252717 AAAATTTGTATCTAC
1 AAAACTTGTATCTAC
252732 AAAACTTGTATCTAC
1 AAAACTTGTATCTAC
252747 AAAACTTGTAT
1 AAAACTTGTAT
252758 ATTATATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (15 bp):
AAAACTTGTATCTAC
Found at i:253369 original size:7 final size:7
Alignment explanation
Indices: 253357--253395 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
253347 ATATTACTGT
253357 TATATTA
1 TATATTA
253364 TATATT-
1 TATATTA
253370 TATATTA
1 TATATTA
253377 TATATT-
1 TATATTA
253383 TATATTA
1 TATATTA
*
253390 CATATT
1 TATATT
253396 GGTTTATGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (7 bp):
TATATTA
Found at i:253394 original size:15 final size:13
Alignment explanation
Indices: 253356--253395 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
253346 TATATTACTG
253356 TTATATTATATAT
1 TTATATTATATAT
253369 TTATATTATATAT
1 TTATATTATATAT
*
253382 TTATATTACATAT
1 TTATATTATATAT
253395 T
1 T
253396 GGTTTATGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATATTATATAT
Found at i:254399 original size:21 final size:21
Alignment explanation
Indices: 254374--254437 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
254364 AAAATTTAAC
254374 CTTTTTTATTATTATTATTTTA
1 CTTTTTTATT-TTATTATTTTA
* *
254396 -TTTTTTCGTTTTCTTATTTTA
1 CTTTTTT-ATTTTATTATTTTA
*
254417 CTTATTTTATTTTTTTATTTT
1 CTT-TTTTATTTTATTATTTT
254438 TTACTAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 16 0.46
22 15 0.43
23 4 0.11
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.77
Consensus pattern (21 bp):
CTTTTTTATTTTATTATTTTA
Found at i:254422 original size:9 final size:8
Alignment explanation
Indices: 254375--254493 Score: 59
Period size: 8 Copynumber: 14.5 Consensus size: 8
254365 AAATTTAACC
254375 TTTT-TTA
1 TTTTATTA
254382 TTATTATTA
1 TT-TTATTA
254391 TTTTA-T-
1 TTTTATTA
**
254397 TTTT-TCG
1 TTTTATTA
*
254404 TTTTCTTA
1 TTTTATTA
254412 TTTTACTTA
1 TTTTA-TTA
*
254421 TTTTATTT
1 TTTTATTA
254429 TTTTATT-
1 TTTTATTA
*
254436 TTTTACTAAA
1 TTTTA-T-TA
254446 TTTTATTTA
1 TTTTA-TTA
254455 TCTTTATTTA
1 T-TTTA-TTA
254465 TTTTATTA
1 TTTTATTA
*
254473 TTATTAGTA
1 TT-TTATTA
* *
254482 TATTAATA
1 TTTTATTA
254490 TTTT
1 TTTT
254494 TTTTTTTTCA
Statistics
Matches: 89, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
6 4 0.04
7 12 0.13
8 33 0.37
9 25 0.28
10 15 0.17
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (8 bp):
TTTTATTA
Found at i:254422 original size:30 final size:29
Alignment explanation
Indices: 254375--254440 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
254365 AAATTTAACC
254375 TTTTTTATTATTATTATTTTATTTTTTCG
1 TTTTTTATTATTATTATTTTATTTTTTCG
**
254404 TTTTCTTATT-TTACTTATTTTATTTTTTTA
1 TTTT-TTATTATTA-TTATTTTATTTTTTCG
254434 TTTTTTA
1 TTTTTTA
254441 CTAAATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (29 bp):
TTTTTTATTATTATTATTTTATTTTTTCG
Found at i:254432 original size:25 final size:25
Alignment explanation
Indices: 254412--254463 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
254402 CGTTTTCTTA
*
254412 TTTTACT-TATTTTATTTTTTTATT
1 TTTTACTAAATTTTATTTTTTTATT
254436 TTTTACTAAATTTTATTTATCTTTATT
1 TTTTACTAAATTTTATTT-T-TTTATT
254463 T
1 T
254464 ATTTTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 9 0.38
26 1 0.04
27 7 0.29
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTACTAAATTTTATTTTTTTATT
Found at i:254460 original size:10 final size:9
Alignment explanation
Indices: 254378--254471 Score: 61
Period size: 9 Copynumber: 10.2 Consensus size: 9
254368 TTTAACCTTT
254378 TTTATTATTA
1 TTTATT-TTA
254388 -TTATTTTA
1 TTTATTTTA
* *
254396 TTTTTTCGTTT
1 TTTATT--TTA
254407 TCTTATTTTA
1 T-TTATTTTA
*
254417 CTTATTTTA
1 TTTATTTTA
254426 TTT-TTTTA
1 TTTATTTTA
254434 -TT-TTTTA
1 TTTATTTTA
**
254441 CTAAATTTTA
1 -TTTATTTTA
254451 TTTATCTTTA
1 TTTAT-TTTA
254461 TTTATTTTA
1 TTTATTTTA
254470 TT
1 TT
254472 ATTATTAGTA
Statistics
Matches: 66, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
7 7 0.11
8 8 0.12
9 28 0.42
10 16 0.24
11 3 0.05
12 4 0.06
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.73
Consensus pattern (9 bp):
TTTATTTTA
Found at i:254492 original size:39 final size:34
Alignment explanation
Indices: 254418--254501 Score: 82
Period size: 36 Copynumber: 2.4 Consensus size: 34
254408 CTTATTTTAC
*
254418 TTATTTTATTTTTTTATTTTTTACTAAATTTTAT
1 TTATTTTATTTTTTTATTTTTTACTAAATTATAT
* *
254452 TTATCTTTATTTATTTTATTATTATTAGTATATTAATAT
1 TTAT-TTTATTT-TTTTATT-TT-TTACTAAATT-ATAT
254491 TT-TTTT-TTTTT
1 TTATTTTATTTTT
254502 CATATTTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
34 4 0.10
35 9 0.21
36 10 0.24
37 5 0.12
38 9 0.21
39 5 0.12
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.73
Consensus pattern (34 bp):
TTATTTTATTTTTTTATTTTTTACTAAATTATAT
Found at i:254527 original size:18 final size:17
Alignment explanation
Indices: 254487--254519 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
254477 TAGTATATTA
254487 ATATTT-TTTTTTTTTC
1 ATATTTATTTTTTTTTC
254503 ATATTTATTTTTATTTT
1 ATATTTATTTTT-TTTT
254520 ATCATTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (17 bp):
ATATTTATTTTTTTTTC
Found at i:254616 original size:13 final size:13
Alignment explanation
Indices: 254598--254622 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
254588 TCGGGTTTTT
254598 AATTTTTTATTTA
1 AATTTTTTATTTA
254611 AATTTTTTATTT
1 AATTTTTTATTT
254623 TTCGTAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
AATTTTTTATTTA
Done.