Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008643.1 Hibiscus syriacus cultivar Beakdansim tig00111619_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: 166505
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:13735 original size:37 final size:37
Alignment explanation
Indices: 13678--13774 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
13668 CATTTTCGTC
*
13678 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
13715 TTGCTAAGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* *
13752 CTACTAAGATTTAAATTCCTAAA
1 CTACTAAGATTCAAACTCCTAAA
13775 GATAAGATCC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.30
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:14164 original size:17 final size:18
Alignment explanation
Indices: 14138--14177 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
14128 ATTATATAGA
14138 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
14154 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
14172 TATTAT
1 TATTAT
14178 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:14292 original size:28 final size:29
Alignment explanation
Indices: 14273--14326 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
14263 ATTTTACTTA
14273 TAAGTCTAATATTACTATA-TATATATAT
1 TAAGTCTAATATTACTATATTATATATAT
14301 TAAGTCTAATATTACTATA-TATATAT
1 TAAGTCTAATATTACTATATTATATAT
14327 TAATTATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (29 bp):
TAAGTCTAATATTACTATATTATATATAT
Found at i:20625 original size:182 final size:183
Alignment explanation
Indices: 20189--20724 Score: 914
Period size: 182 Copynumber: 2.9 Consensus size: 183
20179 ATTAAATCCG
*
20189 TAAAGTTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
20254 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTACTCCACTACTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
**
20319 TTGTTTGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
*
20372 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCAAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
20437 ATAGATTATGTTCAAACTATGACACTGCTTGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
20502 TTGTCAGGCCAAAGAC-TTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
* * *
20554 TAAAGCTGATCTATCCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAATCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
20619 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
20683 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
20725 TAAACCTGAT
Statistics
Matches: 333, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
181 1 0.00
182 170 0.51
183 162 0.49
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:21311 original size:10 final size:10
Alignment explanation
Indices: 21298--21322 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
21288 TCTTTTTGAG
21298 ATTTTTCAAA
1 ATTTTTCAAA
21308 ATTTTTCAAA
1 ATTTTTCAAA
21318 ATTTT
1 ATTTT
21323 GAAAATTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTTCAAA
Found at i:21931 original size:36 final size:34
Alignment explanation
Indices: 21891--22004 Score: 86
Period size: 36 Copynumber: 3.2 Consensus size: 34
21881 CACTCAAATT
21891 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * * ** *
21927 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACA-ATTTGTCTCACTTGAGAC
*
21963 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
*
21999 CGTTTT
1 TGTTTT
22005 CACTCGAAAG
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 49 0.83
37 5 0.08
38 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:21967 original size:72 final size:75
Alignment explanation
Indices: 21875--22050 Score: 218
Period size: 72 Copynumber: 2.4 Consensus size: 75
21865 ATGCAGATGA
* * * *
21875 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
21937 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
21947 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
22012 AAGAAGGCAT
66 AAGAAGGCAT
** *
22022 TTCATTTCACTCAAGGCTGTTTTTTTTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
22051 GAAGATTTTA
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
71 1 0.01
72 50 0.56
73 11 0.12
74 1 0.01
75 4 0.04
76 23 0.26
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:22304 original size:106 final size:105
Alignment explanation
Indices: 22121--22440 Score: 506
Period size: 106 Copynumber: 3.1 Consensus size: 105
22111 ACAGTTTCTC
*
22121 TTGAAAACATTTCCCTTGAAAT-TAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAT
1 TTGAAAACATTTCCCTTGAAATATAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
*
22185 TTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
** *
22225 TTGAAAACATTTCCCTTGAAATGATTTTTTTTTCTCTCTTAAGATAGTTTCCCTCGAAACAGAAA
1 TTGAAAACATTTCCCTTGAAAT-ATAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAA
22290 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* *
22331 TTGAAAACATTTCCCTTGAAATA-AATTTTTTCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AA
1 TTGAAAACATTTCCCTTGAAATATAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
** *
22392 TTTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
22432 TTGAAAACA
1 TTGAAAACA
22441 ATTTAACGAA
Statistics
Matches: 201, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
101 48 0.24
103 1 0.00
104 52 0.26
105 1 0.00
106 99 0.49
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.38
Consensus pattern (105 bp):
TTGAAAACATTTCCCTTGAAATATAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:22387 original size:36 final size:36
Alignment explanation
Indices: 22340--22415 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
22330 ATTGAAAACA
* * * *
22340 TTTCCCTTGAAATAAATTTTTTCTCGCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
22376 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
22412 TTTC
1 TTTC
22416 TCTCCAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:22812 original size:105 final size:105
Alignment explanation
Indices: 22615--23245 Score: 934
Period size: 105 Copynumber: 6.0 Consensus size: 105
22605 ATACCGTGAC
* * * * * * *
22615 ACTCGAGACAACACAAGTTCAACTTCACAACAAAGGGACGGTTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
22680 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
22721 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
22786 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
22826 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
22891 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
22931 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAATAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
22996 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
23036 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* * *
23097 A-TTCAGTGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
23136 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTCT
** * * *
23199 CTGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
64 C-AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
23242 ACTC
1 ACTC
23246 GGAACAATGC
Statistics
Matches: 487, Mismatches: 30, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
99 2 0.00
100 80 0.16
101 3 0.01
102 3 0.01
103 5 0.01
104 2 0.00
105 310 0.64
106 82 0.17
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:23838 original size:37 final size:37
Alignment explanation
Indices: 23785--23889 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
23775 CATTTTCGTC
23785 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * *
23822 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
23859 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
23890 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:24285 original size:18 final size:17
Alignment explanation
Indices: 24246--24288 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
24236 ATTATATGAA
24246 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
24262 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
24280 TATTATTAT
1 TATTATTAT
24289 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:24298 original size:56 final size:59
Alignment explanation
Indices: 24245--24360 Score: 141
Period size: 62 Copynumber: 2.0 Consensus size: 59
24235 TATTATATGA
*
24245 ATATT-TTA-TTCATTTATTTTTATTA-T-TCATGTTATTATTATTATATGTATATATAT
1 ATATTATTATTTCATTTATTTTTATTACTAT-ATGTTATTATTATTATATATATATATAT
* *
24301 ATATTAAATTATTTTCATTTATTTTTTTTACTATATTTTATTATTATTATATATATATAT
1 ATATT--ATTA-TTTCATTTATTTTTATTACTATATGTTATTATTATTATATATATATAT
24361 TTCTTTAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
56 5 0.10
59 3 0.06
61 16 0.32
62 25 0.50
63 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (59 bp):
ATATTATTATTTCATTTATTTTTATTACTATATGTTATTATTATTATATATATATATAT
Found at i:44890 original size:23 final size:22
Alignment explanation
Indices: 44843--44888 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
44833 TGATCCGAAT
*
44843 TTATTTATTTTTTAAAATTACAA
1 TTATTTATGTTTTAAAATTA-AA
44866 TTATTTAATGTTTTATAAATTAA
1 TTATTT-ATGTTTTA-AAATTAA
44889 TTCAAATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 8 0.40
25 6 0.30
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTATTTATGTTTTAAAATTAAA
Found at i:48409 original size:186 final size:186
Alignment explanation
Indices: 48095--48451 Score: 579
Period size: 186 Copynumber: 1.9 Consensus size: 186
48085 TATGACGATG
* *
48095 TTCCTTCGTGTTGAGGAAATCTGATTGTCTGAGGATGACACTGCTCATTCATGTTGAGGAGATCG
1 TTCCTTCGTGATGAGGAAATCTGATTGTCTGAGGATGACACTGCTCATCCATGTTGAGGAGATCG
* * *
48160 GGTCAATTTGATGTTGAAGATGACACTGCTCATCCGTGTTGGAGAGATCGGGTCGTTTTCGATAA
66 AGTCAATTTGATGTTGAAGACGACACTGCTCATCCGTGTTGAAGAGATCGGGTCGTTTTCGATAA
** * *
48225 ATTATGACGTTGTTCCTTCGTGTTGAGGAAATTAGGTCAATTTGGGGACAATACGA
131 ATTATGACACTGTTCCTTCGCGTTGAGGAAATCAGGTCAATTTGGGGACAATACGA
* * * * *
48281 TTCCTTCGTGATGAGGAAGTCTGATTGTTTGATGATGACACTGCTCCTCCGTGTTGAGGAGATCG
1 TTCCTTCGTGATGAGGAAATCTGATTGTCTGAGGATGACACTGCTCATCCATGTTGAGGAGATCG
48346 AGTCAATTTGATGTTGAAGACGACACTGCTCATCCGTGTTGAAGAGATCGGGTCGTTTTCGATAA
66 AGTCAATTTGATGTTGAAGACGACACTGCTCATCCGTGTTGAAGAGATCGGGTCGTTTTCGATAA
*
48411 ATTATGACACTGTTCCTTCGCGTTGAGGAAATCGGGTCAAT
131 ATTATGACACTGTTCCTTCGCGTTGAGGAAATCAGGTCAAT
48452 CTGGAGATGA
Statistics
Matches: 156, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
186 156 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (186 bp):
TTCCTTCGTGATGAGGAAATCTGATTGTCTGAGGATGACACTGCTCATCCATGTTGAGGAGATCG
AGTCAATTTGATGTTGAAGACGACACTGCTCATCCGTGTTGAAGAGATCGGGTCGTTTTCGATAA
ATTATGACACTGTTCCTTCGCGTTGAGGAAATCAGGTCAATTTGGGGACAATACGA
Found at i:52117 original size:3 final size:3
Alignment explanation
Indices: 52109--52133 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
52099 GAATTGGGTT
52109 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
52134 AAGTTGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:58619 original size:103 final size:103
Alignment explanation
Indices: 58490--58707 Score: 366
Period size: 103 Copynumber: 2.1 Consensus size: 103
58480 ATAGAGGGTC
*
58490 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGA-GGTCTGGTGAGACACATA
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTAGAACATGTGT-ATGGTCTGGTGAGACACATA
*
58554 CTTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
65 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
58593 TATGTGGTCTTTCGAGCCATATATGTATTCTTTGGAACATGTGTATGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTAGAACATGTGTATGGTCTGGTGAGACACATAC
58658 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
58696 TATGTGTTCCTT
1 TATGTGGTCCTT
58708 ATGGACATTA
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 1 0.01
103 106 0.99
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (103 bp):
TATGTGGTCCTTCGAGACATATATGTATTCTTTAGAACATGTGTATGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:58757 original size:23 final size:23
Alignment explanation
Indices: 58724--58786 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
58714 ATTATTATAT
58724 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
58747 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
58770 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
58787 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:73505 original size:25 final size:24
Alignment explanation
Indices: 73461--73510 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
73451 TTATGGAAAC
*
73461 ATTAGTCAAACAAGACCACATCAAT
1 ATTAGTCAAACAAGAACACAT-AAT
73486 ATTAGTCAAACTAA-AACACATAAT
1 ATTAGTCAAAC-AAGAACACATAAT
73510 A
1 A
73511 AGGACAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 17 0.74
26 2 0.09
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.22
Consensus pattern (24 bp):
ATTAGTCAAACAAGAACACATAAT
Found at i:83786 original size:2 final size:2
Alignment explanation
Indices: 83779--83821 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
83769 CGAAATTAAC
83779 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
83821 A
1 A
83822 GTTTAACCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:89165 original size:18 final size:18
Alignment explanation
Indices: 89144--89216 Score: 86
Period size: 18 Copynumber: 4.4 Consensus size: 18
89134 TGACCGGTCA
89144 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
89162 CGACCCAACCCGTT----
1 CGACCCGACCCGTTGACC
*
89176 -TA-CCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
89192 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
89210 CGACCCG
1 CGACCCG
89217 TTGACCGTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
12 9 0.20
13 1 0.02
17 1 0.02
18 34 0.76
ACGTcount: A:0.18, C:0.49, G:0.21, T:0.12
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:89182 original size:30 final size:31
Alignment explanation
Indices: 89145--89222 Score: 131
Period size: 30 Copynumber: 2.5 Consensus size: 31
89135 GACCGGTCAC
89145 GACCCGACCCGTTGACCCGACCCAACCCGTT
1 GACCCGACCCGTTGACCCGACCCAACCCGTT
* *
89176 TA-CCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCAACCCGTT
89206 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
89223 GTTGACCGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 28 0.65
31 15 0.35
ACGTcount: A:0.18, C:0.47, G:0.21, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCAACCCGTT
Found at i:89186 original size:12 final size:13
Alignment explanation
Indices: 89163--89222 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 13
89153 CCGTTGACCC
*
89163 GACCCAACCCGTT
1 GACCCGACCCGTT
*
89176 TA-CCGACCCGTT
1 GACCCGACCCGTT
89188 GACCCGACCCGACCCGTT
1 GACCCG-----ACCCGTT
89206 GACCCGACCCGTT
1 GACCCGACCCGTT
89219 GACC
1 GACC
89223 GTTGACCGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
12 10 0.26
13 15 0.39
18 13 0.34
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:91777 original size:24 final size:24
Alignment explanation
Indices: 91683--91789 Score: 76
Period size: 24 Copynumber: 4.5 Consensus size: 24
91673 GAATATTTTA
* * *
91683 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTATGT
* * *
91707 TTTGACATCTGATCTGAA--ATCT
1 TCTGATATCTGATCTGAATTATGT
* * * *
91729 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTATGT
91753 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTATGT
* *
91777 TTTGATTTCTGAT
1 TCTGATATCTGAT
91790 ATCTCCGTTT
Statistics
Matches: 60, Mismatches: 19, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
21 1 0.02
22 13 0.22
24 45 0.75
25 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTATGT
Found at i:95132 original size:16 final size:16
Alignment explanation
Indices: 95111--95145 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
95101 AGGTAATATA
*
95111 ACAAATATTTCCAGCT
1 ACAAATATTTCAAGCT
95127 ACAAATATTTCAAGCT
1 ACAAATATTTCAAGCT
95143 ACA
1 ACA
95146 TAGACTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.29
Consensus pattern (16 bp):
ACAAATATTTCAAGCT
Found at i:102130 original size:17 final size:17
Alignment explanation
Indices: 102090--102133 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
102080 TTAGTACTTA
*
102090 CAACTTCTCACCAATTT
1 CAACTTGTCACCAATTT
102107 CAACTTGTCACCAATTT
1 CAACTTGTCACCAATTT
102124 CAACTTGTCA
1 CAACTTGTCA
102134 TCTCATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.30, C:0.32, G:0.05, T:0.34
Consensus pattern (17 bp):
CAACTTGTCACCAATTT
Found at i:104771 original size:2 final size:2
Alignment explanation
Indices: 104766--104792 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
104756 TTTAAAATAG
104766 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 T
104793 TAAGAGTAGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:115891 original size:15 final size:15
Alignment explanation
Indices: 115873--115919 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
115863 CTGCAAAAGT
*
115873 AATAAAAATTAATAC
1 AATAAAAATTAATAA
*
115888 AATAAAATTTAATAA
1 AATAAAAATTAATAA
*
115903 AATAATAAATTATTAA
1 AATAA-AAATTAATAA
115919 A
1 A
115920 TAATTATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAAAAATTAATAA
Found at i:121568 original size:2 final size:2
Alignment explanation
Indices: 121561--121587 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
121551 TCAATCTATG
121561 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
121588 CTCACACACA
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:135257 original size:21 final size:21
Alignment explanation
Indices: 135231--135287 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
135221 AGGGTGTCAA
*
135231 AGTGCATCCATGCACCCCTGT
1 AGTGCATCCATGCACCCCTGC
*
135252 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
135273 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
135288 TTGCACTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:135355 original size:20 final size:20
Alignment explanation
Indices: 135330--135423 Score: 118
Period size: 20 Copynumber: 4.7 Consensus size: 20
135320 AATGCAATTA
135330 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
135350 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
**
135370 GTGCATCGATGCATCAAGGT-T
1 GTGCATCGATGCATC--CTTCT
* *
135391 GTGCATCCATGCATCCTGCT
1 GTGCATCGATGCATCCTTCT
*
135411 GTGCATCCATGCA
1 GTGCATCGATGCA
135424 CGAAGGCTGC
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
20 49 0.75
21 15 0.23
22 1 0.02
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:136735 original size:19 final size:20
Alignment explanation
Indices: 136711--136758 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
136701 AATGATTTTC
*
136711 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
136730 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
136750 TTTTGAAAA
1 TTTTGAAAA
136759 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:137562 original size:26 final size:26
Alignment explanation
Indices: 137533--137604 Score: 117
Period size: 26 Copynumber: 2.8 Consensus size: 26
137523 ATATGCACTT
*
137533 AATTTTAACAAATGATATTGATATCA
1 AATTTTAACAAATGGTATTGATATCA
137559 AATTTTAACAAATGGTATTGATATCA
1 AATTTTAACAAATGGTATTGATATCA
* *
137585 AATTTCAACAATTGGTATTG
1 AATTTTAACAAATGGTATTG
137605 CATAAAGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (26 bp):
AATTTTAACAAATGGTATTGATATCA
Found at i:137956 original size:21 final size:21
Alignment explanation
Indices: 137930--137969 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
137920 AAACAATTGG
*
137930 TAACAATTGATATCATTTTGT
1 TAACAATTGACATCATTTTGT
*
137951 TAACAATTGACATCTTTTT
1 TAACAATTGACATCATTTT
137970 CATTAAACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (21 bp):
TAACAATTGACATCATTTTGT
Found at i:138217 original size:21 final size:21
Alignment explanation
Indices: 138191--138269 Score: 104
Period size: 21 Copynumber: 3.7 Consensus size: 21
138181 AGGGTATCAA
138191 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
138212 AGTGCATCCATGCATCCCTGT
1 AGTGCATCCATGCACCCCTGC
** *
138233 AGTGCATCCATGCACCTGTAC
1 AGTGCATCCATGCACCCCTGC
138254 TAGTGCATCCATGCAC
1 -AGTGCATCCATGCAC
138270 TCAAACACCG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 35 0.70
22 15 0.30
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:138316 original size:21 final size:21
Alignment explanation
Indices: 138290--138364 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
138280 AATGCAATTA
138290 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
138311 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
* * **
138332 TTGCATCAATGCATC-CTGCT
1 GTGCATCGATGCATCAAGGCT
*
138352 GTGCATCCATGCA
1 GTGCATCGATGCA
138365 CGAAGACTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 14 0.29
21 34 0.71
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.27
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:138473 original size:21 final size:21
Alignment explanation
Indices: 138418--138473 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
138408 ATGAAGAGCT
* *
138418 ATCGATACACCATAATAGTGC
1 ATCGATGCACCATGATAGTGC
*
138439 ACCGATGCACCATGATAGTGC
1 ATCGATGCACCATGATAGTGC
138460 ATCGATGCACCATG
1 ATCGATGCACCATG
138474 TTATGGGCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGATGCACCATGATAGTGC
Found at i:139561 original size:18 final size:19
Alignment explanation
Indices: 139525--139583 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
139515 TGATTTTTTA
139525 ATTTTATTAATAATTAATT
1 ATTTTATTAATAATTAATT
*
139544 ATTTTATTAAT-GTTAATT
1 ATTTTATTAATAATTAATT
** *
139562 AAGTCATTAATAATTAA-T
1 ATTTTATTAATAATTAATT
139580 ATTT
1 ATTT
139584 AAGACGGTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 17 0.53
19 15 0.47
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTTTATTAATAATTAATT
Found at i:139731 original size:16 final size:16
Alignment explanation
Indices: 139702--139741 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
139692 TCAAATTATG
139702 ACACGTGTCACTAGTA
1 ACACGTGTCACTAGTA
* *
139718 ACAGGTGTCGCTAGTA
1 ACACGTGTCACTAGTA
139734 ACACGTGT
1 ACACGTGT
139742 GAAGGAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (16 bp):
ACACGTGTCACTAGTA
Found at i:139821 original size:29 final size:29
Alignment explanation
Indices: 139787--139855 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
139777 AAACATACAC
139787 TCAATTATTGATCCAAAATCATTATATGA
1 TCAATTATTGATCCAAAATCATTATATGA
139816 TCAATTATTGATCCAAAATCATTATATGA
1 TCAATTATTGATCCAAAATCATTATATGA
*
139845 TCAATAATTGA
1 TCAATTATTGA
139856 CTCATATTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (29 bp):
TCAATTATTGATCCAAAATCATTATATGA
Found at i:142961 original size:2 final size:2
Alignment explanation
Indices: 142954--142981 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
142944 GAGCACTTTA
142954 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
142982 TGGTTGTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:148716 original size:26 final size:26
Alignment explanation
Indices: 148669--148718 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
148659 AGAAATATTT
* **
148669 TATTTATTAAAATATTCTAATAATAA
1 TATTGATTAAAATATTAGAATAATAA
*
148695 TATTGATTAAATTATTAGAATAAT
1 TATTGATTAAAATATTAGAATAAT
148719 TTAAACTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (26 bp):
TATTGATTAAAATATTAGAATAATAA
Found at i:152750 original size:29 final size:29
Alignment explanation
Indices: 152713--152873 Score: 229
Period size: 29 Copynumber: 5.7 Consensus size: 29
152703 CCACAGTCAA
** *
152713 AATTACCAAAATATCATTGTTTTAAAAAT
1 AATTACCAAAATATCACCGATTTAAAAAT
** *
152742 AATTACCAAAATATCATTGTTTTAAAAAT
1 AATTACCAAAATATCACCGATTTAAAAAT
152771 AATTACCAAAATATCACCGATTTAAAAAT
1 AATTACCAAAATATCACCGATTTAAAAAT
152800 AATTACCAAAATATCACCGATTTAAAAAT
1 AATTACCAAAATATCACCGATTTAAAAAT
*
152829 AAATACCAAAATATCACCG-TTTAAAAA-
1 AATTACCAAAATATCACCGATTTAAAAAT
*
152856 AA-TCCCAAAATATCACCG
1 AATTACCAAAATATCACCG
152874 GGTCGAGTCA
Statistics
Matches: 127, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
26 15 0.12
27 2 0.02
28 8 0.06
29 102 0.80
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.29
Consensus pattern (29 bp):
AATTACCAAAATATCACCGATTTAAAAAT
Found at i:159114 original size:27 final size:29
Alignment explanation
Indices: 159015--159198 Score: 213
Period size: 28 Copynumber: 6.6 Consensus size: 29
159005 CACAGTCAAA
* *
159015 AATTACAAAAATATCACTTTTTTAAAAAT
1 AATTACCAAAATATCACTGTTTTAAAAAT
* *
159044 AATTATCAAAATATCATTGTTTTAAAAA-
1 AATTACCAAAATATCACTGTTTTAAAAAT
159072 AATTACCAAAATATCACTGTTTTAAAAAT
1 AATTACCAAAATATCACTGTTTTAAAAAT
**
159101 AATTA-CAAAA-ATCACTAATTTAAAAAT
1 AATTACCAAAATATCACTGTTTTAAAAAT
* *
159128 AATTACC-AAATATCACCGATTTAAAAAT
1 AATTACCAAAATATCACTGTTTTAAAAAT
* *
159156 -TTTACCAAAATATCACCGTTTTAAAAA-
1 AATTACCAAAATATCACTGTTTTAAAAAT
159183 AA-T-CTCAAAATATCAC
1 AATTAC-CAAAATATCAC
159199 CGGGTTGGAT
Statistics
Matches: 136, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
26 1 0.01
27 40 0.29
28 66 0.49
29 29 0.21
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (29 bp):
AATTACCAAAATATCACTGTTTTAAAAAT
Found at i:159151 original size:55 final size:57
Alignment explanation
Indices: 159012--159200 Score: 192
Period size: 55 Copynumber: 3.4 Consensus size: 57
159002 GTCCACAGTC
* *** * **
159012 AAAAATTACAAAAATATCACTTTTTTAAAAATAATTATCAAAATATCATTGTTTTAA
1 AAAAATTACCAAAATATCACCGATTTAAAAATAATTATCAAAATATCACTAATTTAA
* *
159069 AAAAATTACCAAAATATCACTGTTTTAAAAATAATTA-CAAAA-ATCACTAATTTAA
1 AAAAATTACCAAAATATCACCGATTTAAAAATAATTATCAAAATATCACTAATTTAA
* * ***
159124 AAATAATTACC-AAATATCACCGATTTAAAAAT-TTTACCAAAATATCACCGTTTTAA
1 AAA-AATTACCAAAATATCACCGATTTAAAAATAATTATCAAAATATCACTAATTTAA
159180 AAAAA-T-CTCAAAATATCACCG
1 AAAAATTAC-CAAAATATCACCG
159201 GGTTGGATCG
Statistics
Matches: 116, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
53 1 0.01
54 5 0.04
55 50 0.43
56 25 0.22
57 35 0.30
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (57 bp):
AAAAATTACCAAAATATCACCGATTTAAAAATAATTATCAAAATATCACTAATTTAA
Found at i:159152 original size:83 final size:84
Alignment explanation
Indices: 159012--159198 Score: 245
Period size: 83 Copynumber: 2.2 Consensus size: 84
159002 GTCCACAGTC
** ** *
159012 AAAAATTACAAAAATATCACTTTTTTAAAAATAATTATCAAAATATCATTGTTTTAAAAAAATTA
1 AAAAATTAC-AAAATATCACTAATTTAAAAATAATTATCAAAATATCACCGATTTAAAAAAATTA
*
159077 CCAAAATATCACTGTTTTAA
65 CCAAAATATCACCGTTTTAA
* **
159097 AAATAATTACAAAA-ATCACTAATTTAAAAATAATTA-CCAAATATCACCGATTTAAAAATTTTA
1 AAA-AATTACAAAATATCACTAATTTAAAAATAATTATCAAAATATCACCGATTTAAAAAAATTA
159160 CCAAAATATCACCGTTTTAA
65 CCAAAATATCACCGTTTTAA
159180 AAAAATCT-CAAAATATCAC
1 AAAAAT-TACAAAATATCAC
159199 CGGGTTGGAT
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
82 8 0.09
83 49 0.54
84 20 0.22
85 7 0.08
86 6 0.07
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (84 bp):
AAAAATTACAAAATATCACTAATTTAAAAATAATTATCAAAATATCACCGATTTAAAAAAATTAC
CAAAATATCACCGTTTTAA
Found at i:162482 original size:22 final size:21
Alignment explanation
Indices: 162448--162488 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
162438 ATAATTATTT
162448 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
162469 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
162489 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:165994 original size:20 final size:19
Alignment explanation
Indices: 165969--166019 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
165959 CCATGTTCGA
*
165969 GTTGCGAATTTGGAATCTGT
1 GTTGCGAATTTGGAATC-GC
* * *
165989 GTTGCGAAATAGGAGTCGC
1 GTTGCGAATTTGGAATCGC
166008 GTTGCGAATTTG
1 GTTGCGAATTTG
166020 TTGGTTATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.22, C:0.12, G:0.33, T:0.33
Consensus pattern (19 bp):
GTTGCGAATTTGGAATCGC
Done.