Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009573.1 Hibiscus syriacus cultivar Beakdansim tig00116938_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: 1247605
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:282476 original size:21 final size:21
Alignment explanation
Indices: 282417--282478 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
282407 CTTTGATTTA
*
282417 TTATTATGGATTTCAAGATTC
1 TTATTATGGATTTCAAGTTTC
*
282438 TTATTATGGATTTCAAGTTTG
1 TTATTATGGATTTCAAGTTTC
* *
282459 TTGTTATGGATGTCAAGTTT
1 TTATTATGGATTTCAAGTTT
282479 ATTGGATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.24, C:0.06, G:0.19, T:0.50
Consensus pattern (21 bp):
TTATTATGGATTTCAAGTTTC
Found at i:285510 original size:23 final size:23
Alignment explanation
Indices: 285474--285537 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
285464 CAACTCGTAT
285474 AAATGCACCGAAGTGCCACCTAG
1 AAATGCACCGAAGTGCCACCTAG
* * * *
285497 AATTGCACCTAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACCTAG
285520 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
285538 TATAAGATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACCTAG
Found at i:285716 original size:37 final size:37
Alignment explanation
Indices: 285665--285768 Score: 138
Period size: 36 Copynumber: 2.8 Consensus size: 37
285655 CATTTTCGTC
285665 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
285702 TTACTAGGATTCAAACTCCT-AAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
285738 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
285769 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 30 0.52
37 28 0.48
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:286165 original size:18 final size:17
Alignment explanation
Indices: 286126--286168 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
286116 ATTATATTGA
286126 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
286142 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
286160 TATTATTAT
1 TATTATTAT
286169 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:286231 original size:20 final size:20
Alignment explanation
Indices: 286156--286232 Score: 56
Period size: 20 Copynumber: 4.0 Consensus size: 20
286146 ATTATTCATG
*
286156 TTATTATTATTATATGTA-T
1 TTATTATTATTATATATATT
* *
286175 ATA-TA-TATTAAAT-TATT
1 TTATTATTATTATATATATT
*
286192 TTCATTTATT-TTTTACTATATT
1 TT-A-TTATTATTATA-TATATT
286214 TTATTATTATTATATATAT
1 TTATTATTATTATATATAT
286233 ATATTTCTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
16 2 0.05
17 9 0.20
18 3 0.07
19 2 0.05
20 15 0.34
21 7 0.16
22 6 0.14
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (20 bp):
TTATTATTATTATATATATT
Found at i:289214 original size:14 final size:14
Alignment explanation
Indices: 289195--289229 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
289185 AGACCCTGAA
289195 GGCACCTTACTTCG
1 GGCACCTTACTTCG
289209 GGCACCTTACTTCG
1 GGCACCTTACTTCG
289223 GGCACCT
1 GGCACCT
289230 GGTGGCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.14, C:0.37, G:0.23, T:0.26
Consensus pattern (14 bp):
GGCACCTTACTTCG
Found at i:290613 original size:183 final size:182
Alignment explanation
Indices: 290305--290841 Score: 923
Period size: 183 Copynumber: 2.9 Consensus size: 182
290295 ATTAAATCCG
290305 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCT-GCTTTATGA
* *
290370 ATAGATTATGTTAAAACTATGACACTGCTCGGACACTTGGAAATTCGGTGTTTGCTCCACTGCTT
65 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
290435 TTGTCAGGCCATAGACTTTGTGATGAGATGAACCCATCAGTGATTTGTCCCTC
130 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
290488 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTAGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCT-GCTTTATGA
290553 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
65 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
290618 TTGTCAAGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
130 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
290671 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGCCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTG-CTTTATGA
** * *
290736 ATAGATTACATTCAAA-TCATGACATTGCTCGAACACTTGGCAATTCGGTGTTTGCTCCACTGCT
65 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
* *
290800 TTTGTCAGGTCAAAGATTTTGTGATGAGATGAACCCTTCAGT
129 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
290842 TAAACCTGAT
Statistics
Matches: 337, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
182 2 0.01
183 335 0.99
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (182 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGCTTTATGAA
TAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTTT
TGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:292038 original size:36 final size:34
Alignment explanation
Indices: 291998--292111 Score: 95
Period size: 36 Copynumber: 3.2 Consensus size: 34
291988 CACTCAAATT
291998 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * * ** *
292034 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACA-ATTTGTCTCACTTGAGAC
*
292070 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
292106 TGTTTT
1 TGTTTT
292112 CACTCGAAAG
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 50 0.83
37 5 0.08
38 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:292073 original size:72 final size:76
Alignment explanation
Indices: 291982--292143 Score: 228
Period size: 72 Copynumber: 2.2 Consensus size: 76
291972 ATGCAGATGA
* * *
291982 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACTGTTTTCACTC
292044 GAAAGAA-G-AT
65 GAAAGAAGGCAT
*
292054 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACTGTTTTCACTCG
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACTGTTTTCACTCG
292118 AAAGAAGGCAT
66 AAAGAAGGCAT
292129 TTCATTTCACTCAAG
1 TT-ATTTCACTCAAG
292144 GCTATTTTTT
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
71 1 0.01
72 51 0.64
73 11 0.14
74 1 0.01
75 4 0.05
76 12 0.15
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (76 bp):
TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACTGTTTTCACTCG
AAAGAAGGCAT
Found at i:292216 original size:39 final size:39
Alignment explanation
Indices: 292173--292324 Score: 108
Period size: 39 Copynumber: 3.6 Consensus size: 39
292163 TTTATCTTGA
*
292173 TTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCC
1 TTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCCC
* * * *
292212 TTGAGACAATTTCTCTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCC
1 TTGAGACAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTC-CC
*
292264 -TGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCC
1 TTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCCC
* *
292302 TTGAGACAGTTTCTCTTGAAACA
1 TTGAGACAGTTTCCCTCGAAACA
292325 TAAACATTGA
Statistics
Matches: 86, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
38 2 0.02
39 43 0.50
40 5 0.06
41 2 0.02
42 1 0.01
48 1 0.01
49 2 0.02
50 5 0.06
51 23 0.27
52 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (39 bp):
TTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCCC
Found at i:292393 original size:105 final size:104
Alignment explanation
Indices: 292227--292545 Score: 500
Period size: 105 Copynumber: 3.1 Consensus size: 104
292217 ACAATTTCTC
* *
292227 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
292292 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
292331 TTGAAAACATTTCCCTTGAAATGATTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGA-ATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
*
292396 TTTTGTCTCCCTTGAGTCAGTTTCTCTTGAAACATAAACA
65 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * * *
292436 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGACAGCTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
** *
292498 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
292537 TTGAAAACA
1 TTGAAAACA
292546 ATTTAACGAA
Statistics
Matches: 200, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
101 47 0.23
103 1 0.00
104 51 0.25
105 101 0.50
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:292498 original size:36 final size:36
Alignment explanation
Indices: 292446--292516 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
292436 TTGAAAACAT
* *
292446 TTCCCTTGAAATGAATTTTATCTCGCTTGAGACAGC
1 TTCCCTTGAAACGAATTTTATCTCCCTTGAGACAGC
*
292482 TTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
292517 TTTCTCTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (36 bp):
TTCCCTTGAAACGAATTTTATCTCCCTTGAGACAGC
Found at i:292922 original size:105 final size:105
Alignment explanation
Indices: 292720--293350 Score: 880
Period size: 105 Copynumber: 6.0 Consensus size: 105
292710 ATATCATGAC
* * * * * *
292720 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAA-CAACAACTTCCC
292785 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
292826 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
292891 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** *
292931 ACTTTAGACAACGCAAGTTCAACTTCATAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
292996 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
293036 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
293101 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
293141 ACTCCAGACAACGCAAGTTCAACTCCACGAA-GAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC
1 ACTCCAGACAACGCAAGTTCAACTTCAC-AACGAAGGGACCGCTGCTTGTCAACAACAACTTCCC
* ** *
293202 -A-TTCAGAGTCAATTTCAACTTCACAGTGAATGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
293241 ACTCGAGACAACACAAGTTCAACTTCATAACGAAGAGACGGCTTG-TTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGC-TGCTTGTCAAC-AACAACTTCC
** * * *
293305 CGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
64 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
293347 ACTC
1 ACTC
293351 GGAACAATGC
Statistics
Matches: 473, Mismatches: 43, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
99 2 0.00
100 74 0.16
101 5 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 299 0.63
106 83 0.18
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:293985 original size:36 final size:36
Alignment explanation
Indices: 293893--293995 Score: 127
Period size: 36 Copynumber: 2.8 Consensus size: 36
293883 CATTTTCGTC
293893 CTACTAGGATTCAAACTCCTAACAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAA-AATAGGATAAAATT
* * *
293930 -TGCTAGGATTCAAACTCCTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAATAGGATAAAATT
* * *
293965 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAA-ATAGGAT
293996 CCACAAGAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
35 12 0.21
36 38 0.67
37 7 0.12
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.29
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAATAGGATAAAATT
Found at i:294391 original size:18 final size:17
Alignment explanation
Indices: 294352--294395 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
294342 ATTATATGGA
294352 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
294368 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
294386 TATTATTATT
1 TATTATTATT
294396 ATATATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 8 0.33
18 13 0.54
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:294503 original size:58 final size:63
Alignment explanation
Indices: 294382--294503 Score: 137
Period size: 64 Copynumber: 2.0 Consensus size: 63
294372 ATTATTCATG
* *** *
294382 TTATTATTATTATTATATATATATATATATATTAAATTATTTTCATTTATTTTTTTACTATATT
1 TTATTATTATTATTATATATATATATATATATTAAATTATTTTCACTTATAAATCTAC-ATATT
* *
294446 TTATTATTATTATTATATATATATAT-T-TCTTTAA-TATTTT-ACTTATAAATCTA-ATATT
1 TTATTATTATTATTATATATATATATATATATTAAATTATTTTCACTTATAAATCTACATATT
294504 ACTATATATA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
58 5 0.10
60 8 0.16
61 6 0.12
62 5 0.10
63 1 0.02
64 26 0.51
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (63 bp):
TTATTATTATTATTATATATATATATATATATTAAATTATTTTCACTTATAAATCTACATATT
Found at i:297655 original size:20 final size:20
Alignment explanation
Indices: 297630--297686 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
297620 ATCAATGGCT
297630 AAGATTTGCC-AAATCAATAC
1 AAGATTT-CCTAAATCAATAC
297650 AAGA-TTCCTTAAATCAATAC
1 AAGATTTCC-TAAATCAATAC
297670 AAGA-TTCCTTAAATCAA
1 AAGATTTCC-TAAATCAA
297687 GGAAACCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 31 0.89
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (20 bp):
AAGATTTCCTAAATCAATAC
Found at i:300554 original size:11 final size:11
Alignment explanation
Indices: 300538--300644 Score: 63
Period size: 11 Copynumber: 9.5 Consensus size: 11
300528 AAGCTCGAGA
*
300538 CTCGATTGAAG
1 CTCGATTCAAG
*
300549 CTCGATTCAAA
1 CTCGATTCAAG
* **
300560 CTCAATTTTGAG
1 CTCGA-TTCAAG
*
300572 CTAGATTCAAG
1 CTCGATTCAAG
* **
300583 CTCGTTTGTGAG
1 CTCGATT-CAAG
300595 CTCGATTCAAG
1 CTCGATTCAAG
**
300606 CTCGATTGTGAG
1 CTCGATT-CAAG
*
300618 CTCAATTCAAG
1 CTCGATTCAAG
300629 CTCGACTT-AAG
1 CTCGA-TTCAAG
300640 CTCGA
1 CTCGA
300645 GGATGGGTTA
Statistics
Matches: 69, Mismatches: 23, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
11 45 0.65
12 24 0.35
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (11 bp):
CTCGATTCAAG
Found at i:300632 original size:23 final size:23
Alignment explanation
Indices: 300538--300633 Score: 106
Period size: 23 Copynumber: 4.2 Consensus size: 23
300528 AAGCTCGAGA
* * *
300538 CTCGATTG-AAGCTCGATTCAAA
1 CTCGATTGTGAGCTCAATTCAAG
* *
300560 CTCAATTTTGAGCT-AGATTCAAG
1 CTCGATTGTGAGCTCA-ATTCAAG
* *
300583 CTCGTTTGTGAGCTCGATTCAAG
1 CTCGATTGTGAGCTCAATTCAAG
300606 CTCGATTGTGAGCTCAATTCAAG
1 CTCGATTGTGAGCTCAATTCAAG
300629 CTCGA
1 CTCGA
300634 CTTAAGCTCG
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
22 6 0.10
23 54 0.90
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (23 bp):
CTCGATTGTGAGCTCAATTCAAG
Found at i:303520 original size:60 final size:60
Alignment explanation
Indices: 303302--303505 Score: 239
Period size: 60 Copynumber: 3.4 Consensus size: 60
303292 TAGGATAACT
* * *
303302 ATTTTGTAATTTTTAATAGTCGGGGGACTCAACAAAATAGTGTCATATAGTAAATGAATC
1 ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAATAGTGTCATATAGTAGATGAATC
* * * * ** ** *
303362 ATTTTGTAACTCTTAATAGTTGTGGGATTCAACAAAATAGCATCATATAGCCGATGGATC
1 ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAATAGTGTCATATAGTAGATGAATC
* * * * *
303422 ATTTTGTAACTTTTAATAATCGAGTGACTTAACAAAGTAGTGTCATATAATTAGA-GAATC
1 ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAATAGTGTCATAT-AGTAGATGAATC
303482 ATTTTGTAACTTTTAATAGTCGAG
1 ATTTTGTAACTTTTAATAGTCGAG
303506 AGATTTAAGA
Statistics
Matches: 117, Mismatches: 26, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
60 114 0.97
61 3 0.03
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAATAGTGTCATATAGTAGATGAATC
Found at i:303531 original size:60 final size:60
Alignment explanation
Indices: 303419--303533 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
303409 TAGCCGATGG
* * **
303419 ATCATTTTGTAACTTTTAATAATCGAGTGACTTAACAAAGTAGTGTCATATAATTAGAGA
1 ATCATTTTGTAACTTTTAATAATCGAGAGACTTAACAAAGTAATACCATATAATTAGAGA
* * * *
303479 ATCATTTTGTAACTTTTAATAGTCGAGAGATTTAAGAAAGTAATACCCTATAATT
1 ATCATTTTGTAACTTTTAATAATCGAGAGACTTAACAAAGTAATACCATATAATT
303534 TGGAGACCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (60 bp):
ATCATTTTGTAACTTTTAATAATCGAGAGACTTAACAAAGTAATACCATATAATTAGAGA
Found at i:304532 original size:12 final size:12
Alignment explanation
Indices: 304515--304543 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
304505 TATTGTTATT
304515 ATAAAATATGAC
1 ATAAAATATGAC
304527 ATAAAATATGAC
1 ATAAAATATGAC
304539 ATAAA
1 ATAAA
304544 TTAAGTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (12 bp):
ATAAAATATGAC
Found at i:310834 original size:19 final size:20
Alignment explanation
Indices: 310790--310835 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
310780 TATAAGGTAA
*
310790 AATTATTTTTTTTATTATTT
1 AATTATTTCTTTTATTATTT
*
310810 TA-TATTTCTTTTA-TATTT
1 AATTATTTCTTTTATTATTT
310828 AATTATTT
1 AATTATTT
310836 GAACAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 6 0.27
19 15 0.68
20 1 0.05
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (20 bp):
AATTATTTCTTTTATTATTT
Found at i:329103 original size:16 final size:17
Alignment explanation
Indices: 329082--329114 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
329072 CAATTTCATA
329082 AATTTTA-TAATCAAGT
1 AATTTTAGTAATCAAGT
*
329098 AATTTTAGTATTCAAGT
1 AATTTTAGTAATCAAGT
329115 TTTTAACGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (17 bp):
AATTTTAGTAATCAAGT
Found at i:332006 original size:15 final size:15
Alignment explanation
Indices: 331970--332000 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
331960 TAAGAAAAAC
331970 TTCAGAGTACCAGGT
1 TTCAGAGTACCAGGT
331985 TTCAGAGTACCAGGT
1 TTCAGAGTACCAGGT
332000 T
1 T
332001 CAAGAGATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (15 bp):
TTCAGAGTACCAGGT
Found at i:341595 original size:28 final size:28
Alignment explanation
Indices: 341554--341634 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 28
341544 GTAGGACCAC
** *
341554 TATGTCCCAAAGGACCACATAGAACATA
1 TATGTCCCGTAGGACCACGTAGAACATA
341582 TATGTCCCGTAGGACCACGTAGAACATA
1 TATGTCCCGTAGGACCACGTAGAACATA
* * *
341610 TATATCTCGTAGGACTACGTAGAAC
1 TATGTCCCGTAGGACCACGTAGAAC
341635 CCTCGACTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (28 bp):
TATGTCCCGTAGGACCACGTAGAACATA
Found at i:345896 original size:27 final size:28
Alignment explanation
Indices: 345824--345903 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
345814 ATAGGACCAC
*
345824 TATGTCCCGAAGGACCACATAGAACACA
1 TATGTCCCGTAGGACCACATAGAACACA
345852 TATGTCCCGTAGGACCACATAGAACACA
1 TATGTCCCGTAGGACCACATAGAACACA
* *
345880 TATGT-CCGTATGACCACGTAGAAC
1 TATGTCCCGTAGGACCACATAGAAC
345904 CCTCGACTCT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 17 0.35
28 32 0.65
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.19
Consensus pattern (28 bp):
TATGTCCCGTAGGACCACATAGAACACA
Found at i:347503 original size:14 final size:14
Alignment explanation
Indices: 347484--347519 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
347474 CCCTTATAAT
347484 CCTTTCATATTTAC
1 CCTTTCATATTTAC
347498 CCTTTCATATTTAC
1 CCTTTCATATTTAC
347512 CCTTTCAT
1 CCTTTCAT
347520 CTAATACTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (14 bp):
CCTTTCATATTTAC
Found at i:349059 original size:19 final size:18
Alignment explanation
Indices: 349026--349081 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
349016 ACACCTTGCA
349026 TTTTGCATCTACATTTTAT
1 TTTTGCAT-TACATTTTAT
*
349045 TTTATGCATTACATTTTCT
1 TTT-TGCATTACATTTTAT
* *
349064 TTTTGAATTGCATTTTAT
1 TTTTGCATTACATTTTAT
349082 CCATTTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 12 0.38
19 15 0.47
20 5 0.16
ACGTcount: A:0.21, C:0.12, G:0.07, T:0.59
Consensus pattern (18 bp):
TTTTGCATTACATTTTAT
Found at i:349079 original size:18 final size:19
Alignment explanation
Indices: 349035--349081 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
349025 ATTTTGCATC
*
349035 TACATTTTATTTTATGCAT
1 TACATTTTATTTTATGAAT
*
349054 TACATTTTCTTTT-TGAAT
1 TACATTTTATTTTATGAAT
*
349072 TGCATTTTAT
1 TACATTTTAT
349082 CCATTTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (19 bp):
TACATTTTATTTTATGAAT
Found at i:353321 original size:18 final size:18
Alignment explanation
Indices: 353300--353336 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
353290 TGAAGAGGTC
353300 GAGGTCATCCCTATGATA
1 GAGGTCATCCCTATGATA
353318 GAGGTCATCCCTATGATA
1 GAGGTCATCCCTATGATA
353336 G
1 G
353337 TAGCCACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (18 bp):
GAGGTCATCCCTATGATA
Found at i:356803 original size:63 final size:64
Alignment explanation
Indices: 356729--356849 Score: 174
Period size: 63 Copynumber: 1.9 Consensus size: 64
356719 ATTGTTCAAG
* * *
356729 GTGTATCGATGCACATGAAGTGTATCGATGTACTACT-TTAAAATA-AAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCAC-ACTCTTAAAATACAAACATCGAATGCCATCA
* *
356792 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCTCTTAAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACACTCTTAAAATACAAACATCGAATG
356850 GGATTTATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
62 2 0.04
63 37 0.73
64 12 0.24
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACACTCTTAAAATACAAACATCGAATGCCATCA
Found at i:356877 original size:64 final size:63
Alignment explanation
Indices: 356766--356890 Score: 155
Period size: 64 Copynumber: 2.0 Consensus size: 63
356756 ATGTACTACT
* *
356766 TTAAAATAAAACATCGAATGCCATCAGTGTATCGATGCACAAGTAGTGCATCGATGCACCCTC
1 TTAAAATAAAACATCGAATGCCATCAGTGTACCGATGCACAAGTAGTGCATCGATCCACCCTC
** * *
356829 TTAAAATACAAACATCGAATGGGATTTA-TGTACCGATGCA-TAGATAGTGCATCGATCCACCC
1 TTAAAATA-AAACATCGAATGCCA-TCAGTGTACCGATGCACAAG-TAGTGCATCGATCCACCC
356891 GTCAAGGGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
63 10 0.19
64 41 0.77
65 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (63 bp):
TTAAAATAAAACATCGAATGCCATCAGTGTACCGATGCACAAGTAGTGCATCGATCCACCCTC
Found at i:357598 original size:23 final size:23
Alignment explanation
Indices: 357532--357590 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
357522 ATCTTATATA
*
357532 GCACTACGGTGCAATTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
* * *
357555 ACACTTCGGTTCAATTCTACGTG
1 GCACTTCGGTGCAATTCTACGCG
357578 GCACTTCGGTGCA
1 GCACTTCGGTGCA
357591 TTTATACGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:359291 original size:20 final size:19
Alignment explanation
Indices: 359262--359336 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 19
359252 TCGCGTTGCG
359262 ATTTGCGTTGCGATTTTCC
1 ATTTGCGTTGCGATTTTCC
* *
359281 ATTTCGCGTTGCGATAGTCTAC
1 ATTT-GCGTTGCGAT--TTTCC
*
359303 A-GTGTCGTTGCGATTTTCC
1 ATTTG-CGTTGCGATTTTCC
359322 ATTTCGCGTTGCGAT
1 ATTT-GCGTTGCGAT
359337 AGTTGAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
19 8 0.18
20 21 0.48
21 11 0.25
22 4 0.09
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.41
Consensus pattern (19 bp):
ATTTGCGTTGCGATTTTCC
Found at i:359977 original size:5 final size:5
Alignment explanation
Indices: 359967--360165 Score: 125
Period size: 5 Copynumber: 38.6 Consensus size: 5
359957 CGCCGCCGTC
*
359967 TCGGG TCGGG TTCGGG TCGGG TCGGGGG TAGGG TCGGG TC-GG TCGGG
1 TCGGG TCGGG -TCGGG TCGGG TC--GGG TCGGG TCGGG TCGGG TCGGG
* * * * *
360014 TCGGG TCGGG TCGGG TCGGG TCGGG TCGTG TCGTG TCGTG TCGTG TCGTG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG
* * * * * * * * * *
360064 TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG
* * *
360114 T-GTG T-GTG TCGTG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG-GG TCG-GG TCG-GG
360163 TCG
1 TCG
360166 TGGTAATACG
Statistics
Matches: 184, Mismatches: 4, Indels: 11
0.92 0.02 0.06
Matches are distributed among these distances:
4 12 0.07
5 129 0.70
6 39 0.21
7 4 0.02
ACGTcount: A:0.01, C:0.18, G:0.49, T:0.32
Consensus pattern (5 bp):
TCGGG
Found at i:360323 original size:41 final size:41
Alignment explanation
Indices: 360259--360412 Score: 215
Period size: 41 Copynumber: 3.8 Consensus size: 41
360249 ATTTTAGACT
*
360259 ATCGCAAACGACACTGTAGACTATCGCAACGCGAGATGGAAA
1 ATCGC-AACGACACTGTAGACTATCGCAACGCGAAATGGAAA
* * * *
360301 ATCGCAACGACAATGTACACTATCGCAACGCAAAACGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
*
360342 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGAAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
*
360383 AT---AACGACACTGTAGACTATTGCAACGCGA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGA
360413 TTTTCGACTA
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
38 27 0.27
41 69 0.68
42 5 0.05
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (41 bp):
ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
Found at i:360327 original size:21 final size:20
Alignment explanation
Indices: 360256--360371 Score: 76
Period size: 21 Copynumber: 5.6 Consensus size: 20
360246 TTTATTTTAG
*
360256 ACTATCGCAAACGACACTGTA
1 ACTATCGC-AACGACAATGTA
*
360277 GACTATCGCAACG-CGAGATGGA
1 -ACTATCGCAACGAC-A-ATGTA
*
360299 A-AATCGCAACGACAATGTA
1 ACTATCGCAACGACAATGTA
* * *
360318 CACTATCGCAACGCAAAACGGA
1 -ACTATCGCAACG-ACAATGTA
* *
360340 A-AATCGCAACGACACTGTA
1 ACTATCGCAACGACAATGTA
360359 GACTATCGCAACG
1 -ACTATCGCAACG
360372 CGAAATGAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 17
0.70 0.14 0.17
Matches are distributed among these distances:
19 8 0.11
20 22 0.31
21 26 0.36
22 16 0.22
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.15
Consensus pattern (20 bp):
ACTATCGCAACGACAATGTA
Found at i:364254 original size:13 final size:13
Alignment explanation
Indices: 364236--364261 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
364226 AAAGTTACAC
364236 TTTTACTCTTACT
1 TTTTACTCTTACT
364249 TTTTACTCTTACT
1 TTTTACTCTTACT
364262 GTGATGTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTACTCTTACT
Found at i:364947 original size:21 final size:21
Alignment explanation
Indices: 364923--364968 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
364913 AATCAATTTT
*
364923 TCAAAAGCATGCACCGATGCA
1 TCAAAACCATGCACCGATGCA
* *
364944 TCAATACCATGCATCGATGCA
1 TCAAAACCATGCACCGATGCA
364965 TCAA
1 TCAA
364969 TGAATAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (21 bp):
TCAAAACCATGCACCGATGCA
Found at i:364969 original size:21 final size:21
Alignment explanation
Indices: 364930--364969 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
364920 TTTTCAAAAG
364930 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
364951 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
364970 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:365019 original size:19 final size:19
Alignment explanation
Indices: 364995--365033 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
364985 TCGAATGCAT
* *
364995 TTCATGTACCGATGCACTC
1 TTCATGCACCAATGCACTC
*
365014 TTCATGCATCAATGCACTC
1 TTCATGCACCAATGCACTC
365033 T
1 T
365034 GATTTAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (19 bp):
TTCATGCACCAATGCACTC
Found at i:365084 original size:64 final size:65
Alignment explanation
Indices: 364930--365139 Score: 196
Period size: 64 Copynumber: 3.2 Consensus size: 65
364920 TTTTCAAAAG
* * *
364930 CATGCACCGATGCATCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGCA
1 CATGCACCGATGCA-CAA-ACCATGCATCGATGCACTC-ATGATTTAATTAAAACATCGAATGCA
364994 TTT
63 TTT
* **** *
364997 CATGTACCGATGCACTCTTCATGCATCAATGCACTC-TGATTTAATTAAAACATCGAATGCATTT
1 CATGCACCGATGCACAAACCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTT
* * * * * *
365061 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTT--TTCAAACATCGAATGCAC
1 CATGCACCGATGCACAAACCATGCATCGATGCACTCATG--ATTTAATTAAAACATCGAATGCAT
365123 TT
64 TT
*
365125 CATGCATCGATGCAC
1 CATGCACCGATGCAC
365140 TCTTAGTGCA
Statistics
Matches: 118, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
63 1 0.01
64 84 0.71
65 13 0.11
66 7 0.06
67 13 0.11
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (65 bp):
CATGCACCGATGCACAAACCATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTT
Found at i:365139 original size:17 final size:19
Alignment explanation
Indices: 365111--365159 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
365101 ATTTTTCAAA
365111 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
365129 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
365148 CACCGATGCACT
1 CATCGATGCACT
365160 AGGTGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:365155 original size:64 final size:63
Alignment explanation
Indices: 364980--365158 Score: 177
Period size: 64 Copynumber: 2.8 Consensus size: 63
364970 GAATAAATTG
* * * *
364980 AAACATCGAATGCATTTCATGTACCGATGCACTCTTCATGCATCAATGCA-CTCTGATTTAATTA
1 AAACATCGAATGCATTTCATGCATCGATGCACTCTT-ATGCATCGATGCACCGCTGATTT-ATTA
* * *
365044 AAACATCGAATGCATTTGATGCATCGATGCACAAGC-CATGCATCGATGCACCAGGCT-ATTT-T
1 AAACATCGAATGCATTTCATGCATCGATGCAC--TCTTATGCATCGATGCACC--GCTGATTTAT
*
365106 TC
62 TA
* *
365108 AAACATCGAATGCACTTCATGCATCGATGCACTCTTAGTGCACCGATGCAC
1 AAACATCGAATGCATTTCATGCATCGATGCACTCTTA-TGCATCGATGCAC
365159 TAGGTGTCCA
Statistics
Matches: 95, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 85 0.89
65 1 0.01
66 5 0.05
67 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (63 bp):
AAACATCGAATGCATTTCATGCATCGATGCACTCTTATGCATCGATGCACCGCTGATTTATTA
Found at i:367105 original size:20 final size:21
Alignment explanation
Indices: 367080--367126 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
367070 GGATTATGAG
*
367080 AAATGAT-TTTTAAAATAT-AA
1 AAATGATGTTTCAAAAT-TGAA
367100 AAATGATGTTTCAAAATTGAA
1 AAATGATGTTTCAAAATTGAA
367121 AAATGA
1 AAATGA
367127 AAACAAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.34
Consensus pattern (21 bp):
AAATGATGTTTCAAAATTGAA
Found at i:373547 original size:21 final size:21
Alignment explanation
Indices: 373523--373568 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
373513 AATCAATTTT
*
373523 TCAAAAGCATGCACCGATGCA
1 TCAAAACCATGCACCGATGCA
* *
373544 TCAATACCATGCATCGATGCA
1 TCAAAACCATGCACCGATGCA
373565 TCAA
1 TCAA
373569 TGAATAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (21 bp):
TCAAAACCATGCACCGATGCA
Found at i:373569 original size:21 final size:21
Alignment explanation
Indices: 373530--373569 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
373520 TTTTCAAAAG
373530 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
373551 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
373570 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:373619 original size:19 final size:19
Alignment explanation
Indices: 373595--373633 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
373585 TTGAATGCAT
373595 TTCATGCACCGATGCACTC
1 TTCATGCACCGATGCACTC
*
373614 TTCATGCATCGATGCACTC
1 TTCATGCACCGATGCACTC
373633 T
1 T
373634 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (19 bp):
TTCATGCACCGATGCACTC
Found at i:373664 original size:62 final size:65
Alignment explanation
Indices: 373530--373693 Score: 183
Period size: 62 Copynumber: 2.5 Consensus size: 65
373520 TTTTCAAAAG
* *
373530 CATGCACCGATGCATCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATTGAATGCA
1 CATGCACCGATGCA-CAA-GCCATGCATCGATGCACTC-ATGAATAAATTGAAACATCGAATGCA
373594 TTT
63 TTT
**** * *
373597 CATGCACCGATGCACTCTTCATGCATCGATGCACTC-TGATTTAATT-AAA-ATCGAATGCATTT
1 CATGCACCGATGCACAAGCCATGCATCGATGCACTCATGAATAAATTGAAACATCGAATGCATTT
* *
373659 GATGCATCGATGCACAAGCCATGCATCGATGCACT
1 CATGCACCGATGCACAAGCCATGCATCGATGCACT
373694 AGGCTATTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
62 41 0.49
63 3 0.04
64 8 0.10
65 14 0.17
66 3 0.04
67 14 0.17
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (65 bp):
CATGCACCGATGCACAAGCCATGCATCGATGCACTCATGAATAAATTGAAACATCGAATGCATTT
Found at i:373710 original size:62 final size:61
Alignment explanation
Indices: 373587--373735 Score: 167
Period size: 62 Copynumber: 2.4 Consensus size: 61
373577 TTGAAACATT
* ****
373587 GAATGCATTTCATGCACCGATGCACTCTTCATGCATCGATGCACTCTGATTTAATTAAAATC
1 GAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCTGATTT-ATTAAAATC
* *
373649 GAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTAGGCT-ATTT-TTCAAATC
1 GAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACT---CTGATTTATTAAAATC
* *
373711 GAATGCACTTCATACATCGATGCAC
1 GAATGCATTTCATGCATCGATGCAC
373736 TCTTAGTGCA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
62 68 0.92
64 4 0.05
65 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (61 bp):
GAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCTGATTTATTAAAATC
Found at i:375846 original size:124 final size:121
Alignment explanation
Indices: 375551--375803 Score: 319
Period size: 124 Copynumber: 2.0 Consensus size: 121
375541 TCATTTGAGG
* **
375551 TTAATCGC-TTCTTGAGTCAATTCGGGAAGAGTTACATCGATAATCAAGTCATCAATGGCCTCTA
1 TTAATCGCTTTCTGGAG-CAATTAAGGAAGAGTT--ATCGAT-ATCAAGTCATCAATGGCCTCTA
* *
375615 CTTCAAATCACGACGGTCTGATTCATTGCCGTCAACAAGCCTCCTTTCTTAAATGGAAGT
62 CTTCAAACCACGACGGTCTGATTCATTGCCGTCAACAAGCCTCCTTTCTTAAATGGAACT
* **
375675 TTAATCGCTTTCTTGAGTCAATTCGGGAAGAGTTTATCGATAATCAAGTCATCAATGGCCTCTAC
1 TTAATCGCTTTCTGGAG-CAATTAAGGAAGAG-TTATCGAT-ATCAAGTCATCAATGGCCTCTAC
375740 TTCAAACCACGACTTCGGTCTTGATTCATTGCCCGTCAACAAGCCTCCTTTCTTAAATGGAACT
63 TTCAAACCACGA---CGGTC-TGATTCATTG-CCGTCAACAAGCCTCCTTTCTTAAATGGAACT
375804 AATTATGCTT
Statistics
Matches: 120, Mismatches: 2, Indels: 9
0.92 0.02 0.07
Matches are distributed among these distances:
124 49 0.41
125 23 0.19
126 2 0.02
127 5 0.04
128 10 0.08
129 31 0.26
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (121 bp):
TTAATCGCTTTCTGGAGCAATTAAGGAAGAGTTATCGATATCAAGTCATCAATGGCCTCTACTTC
AAACCACGACGGTCTGATTCATTGCCGTCAACAAGCCTCCTTTCTTAAATGGAACT
Found at i:380678 original size:21 final size:23
Alignment explanation
Indices: 380649--380695 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
380639 GGGTGCATGA
380649 GGTATCGAT-ACCCCCTTGAATG
1 GGTATCGATCACCCCCTTGAATG
* *
380671 GGTA-CGATCACCCCTTTGAGTG
1 GGTATCGATCACCCCCTTGAATG
380693 GGT
1 GGT
380696 TTCAATACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (23 bp):
GGTATCGATCACCCCCTTGAATG
Found at i:380683 original size:22 final size:22
Alignment explanation
Indices: 380649--380704 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
380639 GGGTGCATGA
380649 GGTATCGATACCCCCTTGAATG
1 GGTATCGATACCCCCTTGAATG
* *
380671 GGTA-CGATCACCCCTTTGAGTG
1 GGTATCGAT-ACCCCCTTGAATG
* *
380693 GGTTTCAATACC
1 GGTATCGATACC
380705 TCCCCAGGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.14
22 21 0.75
23 3 0.11
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (22 bp):
GGTATCGATACCCCCTTGAATG
Found at i:381105 original size:10 final size:10
Alignment explanation
Indices: 381086--381115 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
381076 ATCAAAAACA
381086 CAAGATTTTT
1 CAAGATTTTT
*
381096 CAATATTTTT
1 CAAGATTTTT
381106 CAAGATTTTT
1 CAAGATTTTT
381116 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (10 bp):
CAAGATTTTT
Found at i:383029 original size:21 final size:22
Alignment explanation
Indices: 383003--383044 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
382993 TAACAAAAAG
383003 GGGGAG-AAGTGTTAAGAGTTA
1 GGGGAGTAAGTGTTAAGAGTTA
* *
383024 GGGGAGTAATTTTTAAGAGTT
1 GGGGAGTAAGTGTTAAGAGTT
383045 TTAAGAGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (22 bp):
GGGGAGTAAGTGTTAAGAGTTA
Found at i:383481 original size:55 final size:55
Alignment explanation
Indices: 383397--383554 Score: 271
Period size: 55 Copynumber: 2.9 Consensus size: 55
383387 GAAATAACAT
*
383397 ATTTGGCTCTAAGAAATTACAGATTGCTCGGAAGGTACCGATACCCCCATGTAAG
1 ATTTGGCTCTAAGAAATTACAGATTGCTCGGAGGGTACCGATACCCCCATGTAAG
* *
383452 ATTTGGCTCTAAGAAATTATAGACTGCTCGGAGGGTACCGATACCCCCATGTAAG
1 ATTTGGCTCTAAGAAATTACAGATTGCTCGGAGGGTACCGATACCCCCATGTAAG
* *
383507 ATTTGGCTCCAAGAAATAACAGATTGCTCGGAGGGTACCGATACCCCC
1 ATTTGGCTCTAAGAAATTACAGATTGCTCGGAGGGTACCGATACCCCC
383555 CAGGAGGTAC
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 96 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (55 bp):
ATTTGGCTCTAAGAAATTACAGATTGCTCGGAGGGTACCGATACCCCCATGTAAG
Found at i:384346 original size:44 final size:44
Alignment explanation
Indices: 384285--384548 Score: 343
Period size: 44 Copynumber: 6.0 Consensus size: 44
384275 ATACCATGAG
* * * *
384285 TGGCACCTTTTTGCCAATAATACACTGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
384329 TGGTACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* ** *
384373 TGGCATC-TTTCTGCCAATAATGCACTGTTATTAATTATCATTTA
1 TGGCA-CATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
384417 TGGCACTTTTCTGCCAATAATGCACCGTTAAGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
384461 TGGCACCTTTGTGCCAATAATGCACCATTATGTATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
384505 TGAC-CATTTCTGCCAATATTGCACCGTTATGCATTTTCAATTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
384548 T
1 T
384549 TACAGTAACA
Statistics
Matches: 191, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
43 35 0.18
44 155 0.81
45 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.41
Consensus pattern (44 bp):
TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:385061 original size:60 final size:60
Alignment explanation
Indices: 384984--385096 Score: 201
Period size: 61 Copynumber: 1.9 Consensus size: 60
384974 CAGGCTCAAT
384984 AGTATCGGTACCCTACCATGGTATT-ATACTTCTATACTATGGTATCAATACTCTCTTTC
1 AGTATCGGTACCCTACCATGGTATTGATACTTCTATACTATGGTATCAATACTCTCTTTC
*
385043 AGTATCGGTACCCCTACCATGGTATTGATACTTCTATACTATGGTATCGATACT
1 AGTATCGGTA-CCCTACCATGGTATTGATACTTCTATACTATGGTATCAATACT
385097 GGTATTGATA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
59 10 0.20
60 15 0.29
61 26 0.51
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (60 bp):
AGTATCGGTACCCTACCATGGTATTGATACTTCTATACTATGGTATCAATACTCTCTTTC
Found at i:390116 original size:13 final size:13
Alignment explanation
Indices: 390115--390140 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
390105 GTCAACGGGT
390115 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
390128 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
390141 ACTTGTCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:390121 original size:18 final size:18
Alignment explanation
Indices: 390085--390138 Score: 83
Period size: 18 Copynumber: 2.9 Consensus size: 18
390075 AATACCACCT
390085 GGTCAAC-GGTCGGGGGTCG
1 GGTCAACGGGTC--GGGTCG
390104 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
390122 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
390139 AAACTTGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 23 0.68
19 7 0.21
20 4 0.12
ACGTcount: A:0.11, C:0.22, G:0.50, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:397168 original size:13 final size:13
Alignment explanation
Indices: 397136--397176 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
397126 AATACCACTT
397136 GGTCAACGGGTCG
1 GGTCAACGGGTCG
397149 GGT---CGGGTCG
1 GGTCAACGGGTCG
397159 GGTCAACGGGTCG
1 GGTCAACGGGTCG
397172 GGTCA
1 GGTCA
397177 GACTGGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.40
13 15 0.60
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:397194 original size:21 final size:22
Alignment explanation
Indices: 397159--397202 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
397149 GGTCGGGTCG
* *
397159 GGTCAACGGGTCGGGTCAGACT
1 GGTCAACGAGTCGGGTCAAACT
397181 GGTCAAC-AGTCGGGTCAAACT
1 GGTCAACGAGTCGGGTCAAACT
397202 G
1 G
397203 ATTCAACCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.23, C:0.23, G:0.36, T:0.18
Consensus pattern (22 bp):
GGTCAACGAGTCGGGTCAAACT
Found at i:397219 original size:31 final size:29
Alignment explanation
Indices: 397181--397239 Score: 100
Period size: 31 Copynumber: 2.0 Consensus size: 29
397171 GGGTCAGACT
397181 GGTCAACAGTCGGGTCAAACTGATTCAACCC
1 GGTCAACAGTCGGGTCAAAC-GA-TCAACCC
397212 GGTCAACAGTCGGGTCAAACGATCAACC
1 GGTCAACAGTCGGGTCAAACGATCAACC
397240 GGTTCAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 6 0.21
30 2 0.07
31 20 0.71
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.17
Consensus pattern (29 bp):
GGTCAACAGTCGGGTCAAACGATCAACCC
Found at i:397254 original size:18 final size:18
Alignment explanation
Indices: 397226--397262 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
397216 AACAGTCGGG
397226 TCAAACGATC-AACCGGT
1 TCAAACGATCAAACCGGT
397243 TCAAACCGATCAAACCGGT
1 TCAAA-CGATCAAACCGGT
397262 T
1 T
397263 TCAAGATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 8 0.44
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.19
Consensus pattern (18 bp):
TCAAACGATCAAACCGGT
Found at i:400041 original size:44 final size:44
Alignment explanation
Indices: 399986--400295 Score: 440
Period size: 44 Copynumber: 7.0 Consensus size: 44
399976 ATACCATGAG
* * * *
399986 TGGCACTTTTCTTCCAATAGTGCATCATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
*
400030 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
400074 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
* * *
400118 TGGAACCTTTATGCCAATAATGCATCATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
* * * * *
400162 CGGCTCCTTTCTACCAATAATGCATCGTTATGCATTTTTATTTTT
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCA-TTTA
*
400207 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
* * * * *
400251 TGGCACCTATCTGTCAATAATGCACCATTATGCATTTTTATTTA
1 TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
400295 T
1 T
400296 TTCAGTAACA
Statistics
Matches: 238, Mismatches: 27, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
44 200 0.84
45 38 0.16
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
Found at i:404924 original size:60 final size:60
Alignment explanation
Indices: 404819--404931 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
404809 TATTTGGATG
* * * * * *
404819 AATTTGGGGATGAAACTGGAATGTTCAAAAGTTTAAGAACTAATTTAGAATGAGAGTCAT
1 AATTTGGGGATGAAACTAGAATATTAAAAAATATAAGAACTAATTTAAAATGAGAGTCAT
*
404879 AATTTGGGGATGAAATTAGAATATTAAAAAATATAAGGAAC-AATTTAAAATGA
1 AATTTGGGGATGAAACTAGAATATTAAAAAATATAA-GAACTAATTTAAAATGA
404932 AGGTTATAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
60 41 0.91
61 4 0.09
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.29
Consensus pattern (60 bp):
AATTTGGGGATGAAACTAGAATATTAAAAAATATAAGAACTAATTTAAAATGAGAGTCAT
Found at i:407231 original size:21 final size:20
Alignment explanation
Indices: 407145--407302 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
407135 AAATGACCAA
**
407145 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
407164 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
407184 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
407204 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
407225 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
407246 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
407266 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
407287 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
407303 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:407331 original size:20 final size:20
Alignment explanation
Indices: 407269--407462 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
407259 CGATTTTCCA
* ** *
407269 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
407289 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
407309 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
407329 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
407349 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
407369 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
407389 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * * *
407409 AAATCACAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
407429 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
407450 AAATCGCAACGCG
1 AAATCGCAACGCG
407463 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 16 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:407353 original size:60 final size:60
Alignment explanation
Indices: 407269--407462 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
407259 CGATTTTCCA
* ** * *
407269 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
407329 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * **
407389 ATATCGCAACGCGTATCCGTAAATCACAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
407450 AAATCGCAACGCG
1 AAATCGCAACGCG
407463 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:407883 original size:33 final size:33
Alignment explanation
Indices: 407844--407914 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
407834 TTCACTTAGA
* *
407844 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
407877 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
407910 TTTCA
1 TTTCA
407915 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:408020 original size:21 final size:20
Alignment explanation
Indices: 407994--408099 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
407984 TGCAGAAGAG
407994 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
408015 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
408035 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
408056 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
408070 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
408089 TCGCAACGAGA
1 TCGCAACGAGA
408100 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:408038 original size:20 final size:21
Alignment explanation
Indices: 407992--408070 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
407982 TTTGCAGAAG
*
407992 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
408014 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
408033 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
408055 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
408071 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:408051 original size:41 final size:38
Alignment explanation
Indices: 407987--408103 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
407977 TTCAATTTGC
* *
407987 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
408025 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
408066 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
408099 AGAAT
1 AGAAT
408104 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:408076 original size:14 final size:14
Alignment explanation
Indices: 408057--408110 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
408047 AAATGAAAAG
408057 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
408071 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
408090 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
408104 CGCAACG
1 CGCAACG
408111 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:408086 original size:33 final size:33
Alignment explanation
Indices: 408046--408115 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
408036 CGCAACGAGA
408046 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
408079 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
408112 GAAA
1 GAAA
408116 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:408122 original size:33 final size:33
Alignment explanation
Indices: 408052--408126 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
408042 GAGAGAAATG
* **
408052 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
408085 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
408118 AAAATCGCA
1 AAAATCGCA
408127 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:408144 original size:19 final size:19
Alignment explanation
Indices: 408122--408219 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
408112 GAAACCAAAA
*
408122 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
408141 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
408155 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
408174 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
408188 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
408207 TCGCGTTGCGATT
1 TCGCGTTGCGATT
408220 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:408163 original size:14 final size:14
Alignment explanation
Indices: 408144--408233 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
408134 TTTCATTTCG
408144 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
408158 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
408177 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
408191 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
408208 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
408224 CGTTGCGATT
1 CGTTGCGATT
408234 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:408169 original size:33 final size:33
Alignment explanation
Indices: 408127--408241 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
408117 CAAAATCGCA
408127 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
408160 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
408193 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
408226 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
408242 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:410241 original size:93 final size:93
Alignment explanation
Indices: 409936--410314 Score: 726
Period size: 93 Copynumber: 4.1 Consensus size: 93
409926 TAGATTGCTT
*
409936 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
410001 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
410029 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAC--TGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
410092 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
410120 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
410185 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
410213 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
410278 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
410306 AGTAAATTT
1 AGTAAATTT
410315 ATCCATTCAA
Statistics
Matches: 281, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
91 90 0.32
93 191 0.68
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:410245 original size:184 final size:185
Alignment explanation
Indices: 409936--410316 Score: 728
Period size: 184 Copynumber: 2.1 Consensus size: 185
409926 TAGATTGCTT
*
409936 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
410001 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
410066 GTGTATTCTTTAACAC-TGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
410120 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
410185 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
410250 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACAC-GTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
410306 AGTAAATTTAT
1 AGTAAATTTAT
410317 CCATTCAAGT
Statistics
Matches: 192, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
184 144 0.75
186 48 0.25
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:410398 original size:19 final size:19
Alignment explanation
Indices: 410358--410486 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
410348 TAGTTTACTT
* *
410358 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
410378 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
410397 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
410416 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
410430 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
410449 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
410463 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
410482 TCGCA
1 TCGCA
410487 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:410437 original size:33 final size:32
Alignment explanation
Indices: 410394--410486 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
410384 CGCGAAACCA
**
410394 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
410426 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
410459 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
410487 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:410484 original size:52 final size:52
Alignment explanation
Indices: 410358--410486 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
410348 TAGTTTACTT
**
410358 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
410410 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
410463 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
410487 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:410504 original size:19 final size:19
Alignment explanation
Indices: 410482--410616 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
410472 GAAACCAAAA
*
410482 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
410501 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
410517 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
410534 TCGCTTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
410550 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
410567 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
410586 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
410606 TCGTGTTGCGA
1 TCGCGTTGCGA
410617 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:410523 original size:14 final size:14
Alignment explanation
Indices: 410504--410560 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
410494 TTTCATTTCG
410504 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
410518 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
410535 CGCTTTGCGATTCTGT
1 CG--TTGCGATTCTTT
410551 CGTTGCGATT
1 CGTTGCGATT
410561 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:410529 original size:33 final size:33
Alignment explanation
Indices: 410487--410579 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
410477 CAAAATCGCA
*
410487 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
410520 TTGCGATTTTCATTTCGCTTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
410553 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
410580 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:412559 original size:14 final size:14
Alignment explanation
Indices: 412540--412575 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
412530 ATTGTTTAAT
412540 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
412554 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
412568 TGATTTGT
1 TGATTTGT
412576 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:412698 original size:19 final size:19
Alignment explanation
Indices: 412682--412779 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
412672 AAAAATGACT
412682 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
412701 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
412720 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
412734 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
412753 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
412773 ATCGCAA
1 ATCGCAA
412780 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:412811 original size:53 final size:53
Alignment explanation
Indices: 412682--412797 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
412672 AAAAATGACT
412682 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
412734 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
412787 ATCGCAATGCG
1 ATCGCAATGCG
412798 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:412841 original size:33 final size:33
Alignment explanation
Indices: 412804--412956 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
412794 TGCGTTTATA
412804 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
412837 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
412877 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
412908 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
412941 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
412957 TTCATTTCGC
Statistics
Matches: 97, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 52 0.54
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:412850 original size:19 final size:19
Alignment explanation
Indices: 412826--413042 Score: 231
Period size: 19 Copynumber: 12.4 Consensus size: 19
412816 GATTCTCTCG
412826 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
412845 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
412864 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
412878 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
412897 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
412916 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
412930 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
412949 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
412968 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
412982 TTGCGATTTTCATTTCCACA
1 TTGCGATTTTCATTT-CGCA
413002 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
413016 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
413035 TTGCGATT
1 TTGCGATT
413043 GTAATTTCCG
Statistics
Matches: 167, Mismatches: 10, Indels: 42
0.76 0.05 0.19
Matches are distributed among these distances:
14 29 0.17
16 22 0.13
17 20 0.12
18 2 0.01
19 82 0.49
20 12 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:412861 original size:52 final size:52
Alignment explanation
Indices: 412804--413014 Score: 404
Period size: 52 Copynumber: 4.0 Consensus size: 52
412794 TGCGTTTATA
412804 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
412856 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
412908 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
412960 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCACATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
413013 AT
1 AT
413015 GTTGGGATTT
Statistics
Matches: 157, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
52 141 0.90
53 16 0.10
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:412986 original size:33 final size:33
Alignment explanation
Indices: 412845--413042 Score: 188
Period size: 33 Copynumber: 5.8 Consensus size: 33
412835 TCATTTCGCA
412845 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
412878 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
412914 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
412949 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
412982 TTGCGATTTTCATTTCCACATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
413016 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
413043 GTAATTTCCG
Statistics
Matches: 135, Mismatches: 17, Indels: 26
0.76 0.10 0.15
Matches are distributed among these distances:
31 9 0.07
32 5 0.04
33 61 0.45
34 28 0.21
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.06
39 3 0.02
40 9 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:415339 original size:12 final size:12
Alignment explanation
Indices: 415322--415346 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
415312 TCTTCGGGGA
415322 CTTTTTCTTCTT
1 CTTTTTCTTCTT
415334 CTTTTTCTTCTT
1 CTTTTTCTTCTT
415346 C
1 C
415347 AGGATTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:415555 original size:24 final size:24
Alignment explanation
Indices: 415521--415567 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
415511 CTGAAACATC
415521 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
415545 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
415568 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:416278 original size:20 final size:20
Alignment explanation
Indices: 416250--416459 Score: 206
Period size: 20 Copynumber: 10.5 Consensus size: 20
416240 AAATTTCAGT
* * *
416250 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
416270 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
416290 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
416310 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
416330 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
416350 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
** *
416370 GTTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
416390 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
416410 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
416430 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
416450 GTTGCGATTT
1 GTTGCGATTT
416460 TGGAAAATCG
Statistics
Matches: 162, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 161 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:416476 original size:21 final size:20
Alignment explanation
Indices: 416426--416523 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
416416 ATTTATGTGT
* * * *
416426 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
416446 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
416467 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
416487 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
416508 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
416524 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:416499 original size:61 final size:60
Alignment explanation
Indices: 416426--416582 Score: 176
Period size: 61 Copynumber: 2.6 Consensus size: 60
416416 ATTTATGTGT
*
416426 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCA-ATGCGAATT-TGACTA
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAAT-G-ATATGCG-ATTCTGACGA
* * * * * **
416487 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAACTGATTTGCGATTCTGGGGA
1 TCGCGTTGCGATTTTC-ATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
*
416548 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTG
416583 TTGGTCATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 16 0.20
60 5 0.06
61 37 0.46
62 23 0.28
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
Found at i:416518 original size:41 final size:41
Alignment explanation
Indices: 416426--416582 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
416416 ATTTATGTGT
* * *
416426 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
416467 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
416508 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
416548 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
416583 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:417595 original size:15 final size:16
Alignment explanation
Indices: 417540--417597 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 16
417530 TTATATTTTT
417540 AATATTTTT-ATATTA
1 AATATTTTTAATATTA
417555 AAT-TTTTTCCGAATATTA
1 AATATTTTT---AATATTA
417573 ACATATTTTTAAT-TTA
1 A-ATATTTTTAATATTA
417589 AATATTTTT
1 AATATTTTT
417598 TATTTTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 4 0.11
17 3 0.08
18 7 0.19
19 2 0.05
20 5 0.14
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (16 bp):
AATATTTTTAATATTA
Found at i:417602 original size:15 final size:16
Alignment explanation
Indices: 417570--417602 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
417560 TTTCCGAATA
417570 TTAACATATTTTTAAT
1 TTAACATATTTTTAAT
*
417586 TTAA-ATATTTTTTAT
1 TTAACATATTTTTAAT
417601 TT
1 TT
417603 TAAAACAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAACATATTTTTAAT
Found at i:418185 original size:60 final size:59
Alignment explanation
Indices: 418110--418256 Score: 183
Period size: 60 Copynumber: 2.4 Consensus size: 59
418100 AATATAATGA
* *
418110 ATAGTCGAGTGATCATTTTGTAACTTTTAATAGTC-GAGGGACTCAATAAAGCAACT-TCCT
1 ATAGTCGAG-GATCATTTTGTAACTTTTAATAGCCTGA-GGACTCAACAAAGC-ACTATCCT
* *
418170 ATAGTCGATGGATCATTTTGTAACTTTTAATAGCCTTAGGACTCAACAAAGCAGTATCCT
1 ATAGTCGA-GGATCATTTTGTAACTTTTAATAGCCTGAGGACTCAACAAAGCACTATCCT
418230 ATAGTCGAGGGATCATTTGTGT-ACTTT
1 ATAGTCGA-GGATCATTT-TGTAACTTT
418257 GCCCTAATTC
Statistics
Matches: 78, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
59 2 0.03
60 71 0.91
61 5 0.06
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (59 bp):
ATAGTCGAGGATCATTTTGTAACTTTTAATAGCCTGAGGACTCAACAAAGCACTATCCT
Found at i:418202 original size:29 final size:28
Alignment explanation
Indices: 418109--418202 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
418099 GAATATAATG
418109 AATAGTCGAGTGATCATTTTGTAACTTTT
1 AATAGTCGAG-GATCATTTTGTAACTTTT
*** * *
418138 AATAGTCGAGGGACTCAATAAAGCAACTTCCT
1 AATAGTCGA-GGA-TC-ATTTTGTAACTT-TT
418170 -ATAGTCGATGGATCATTTTGTAACTTTT
1 AATAGTCGA-GGATCATTTTGTAACTTTT
418198 AATAG
1 AATAG
418203 CCTTAGGACT
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
28 1 0.02
29 23 0.47
30 5 0.10
31 19 0.39
32 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (28 bp):
AATAGTCGAGGATCATTTTGTAACTTTT
Found at i:418473 original size:2 final size:2
Alignment explanation
Indices: 418466--418517 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
418456 ATTAAACTTA
418466 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
418508 AT AT AT AT AT
1 AT AT AT AT AT
418518 TCACTTTAGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:418723 original size:15 final size:15
Alignment explanation
Indices: 418703--418732 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
418693 AACATTCATT
418703 CCCTCTCTCTATCTA
1 CCCTCTCTCTATCTA
418718 CCCTCTCTCTATCTA
1 CCCTCTCTCTATCTA
418733 TCTCGCTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (15 bp):
CCCTCTCTCTATCTA
Found at i:421636 original size:23 final size:23
Alignment explanation
Indices: 421610--421654 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
421600 CACTACAGCT
* *
421610 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* *
421633 CGTAGAATTACATCGAAGTGCC
1 CGTAGAAATACACCGAAGTGCC
421655 GTATAGAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:423135 original size:20 final size:22
Alignment explanation
Indices: 423110--423167 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
423100 TTCCCCTTGA
423110 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
423130 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
423153 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
423168 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:423306 original size:19 final size:19
Alignment explanation
Indices: 423282--423353 Score: 108
Period size: 19 Copynumber: 3.8 Consensus size: 19
423272 ATTTTAAAGG
423282 GTGCATCGATGCACTTCCT
1 GTGCATCGATGCACTTCCT
*
423301 GTGCATCTATGCACTTCCT
1 GTGCATCGATGCACTTCCT
* *
423320 ATGCATCTATGCACTTCCT
1 GTGCATCGATGCACTTCCT
*
423339 GTGCATCGATACACT
1 GTGCATCGATGCACT
423354 GAACAATTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (19 bp):
GTGCATCGATGCACTTCCT
Found at i:423313 original size:63 final size:63
Alignment explanation
Indices: 423154--423314 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
423144 TTCTTTAACA
* * * * *
423154 GGTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTCTCATTTTAAGG
1 GGTGCATCGATGCACTTCCTATGCATCGATGCACAAATTACATTCGATGTTCTCATTTTAAAG
* *
423217 GGATGCATCGATGCAC-TCCTTATGCATCGATGCACCAATTGCATTCGATGTT-TCCATTTTAAA
1 GG-TGCATCGATGCACTTCC-TATGCATCGATGCACAAATTACATTCGATGTTCT-CATTTTAAA
423280 G
63 G
* *
423281 GGTGCATCGATGCACTTCCTGTGCATCTATGCAC
1 GGTGCATCGATGCACTTCCTATGCATCGATGCAC
423315 TTCCTATGCA
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
63 31 0.36
64 54 0.64
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.31
Consensus pattern (63 bp):
GGTGCATCGATGCACTTCCTATGCATCGATGCACAAATTACATTCGATGTTCTCATTTTAAAG
Found at i:428286 original size:64 final size:62
Alignment explanation
Indices: 428198--428359 Score: 225
Period size: 64 Copynumber: 2.5 Consensus size: 62
428188 TTCTTTAACA
* *
428198 GGTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTAAGG
1 GGTGCATCGATGCACT-CCTATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAGG
* * * *
428261 GGATGCATTGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTTCATTTTAAGG
1 GG-TGCATCGATGCACTCC-TATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAGG
*
428325 GGTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GGTGCATCGATGCAC-TCCTATGCATCGATACACA
428360 CTGAACAATT
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 29 0.34
64 57 0.66
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (62 bp):
GGTGCATCGATGCACTCCTATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAGG
Found at i:431814 original size:60 final size:60
Alignment explanation
Indices: 431738--431920 Score: 210
Period size: 60 Copynumber: 3.0 Consensus size: 60
431728 ACACTATATG
* *
431738 TCCCTAAACTATGACTCTCATT-TCAAATTAATCCTTAAACTTTTAAATATT-TCAATTTCA
1 TCCCTAAACTATGACTCTCATTCT-AAATTAATCCTTAAACATTTAAACATTCT-AATTTCA
* * * *
431798 TCTCTAAACTATGACTCTCATTCTAAATGAGTCCTTAAACATTTGAACATTCTAATTTCA
1 TCCCTAAACTATGACTCTCATTCTAAATTAATCCTTAAACATTTAAACATTCTAATTTCA
* * * * * *
431858 TCCCTAAACCATGACTCTCATTCTAAATTGATCCTCAAACGTTTGAATC-TTCTAATTCCA
1 TCCCTAAACTATGACTCTCATTCTAAATTAATCCTTAAACATTT-AAACATTCTAATTTCA
431918 TCC
1 TCC
431921 TCAAATTCAT
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
60 100 0.96
61 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (60 bp):
TCCCTAAACTATGACTCTCATTCTAAATTAATCCTTAAACATTTAAACATTCTAATTTCA
Found at i:434114 original size:17 final size:17
Alignment explanation
Indices: 434066--434119 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
434056 TAATTTACTT
434066 TATATA-GTT-TATATA
1 TATATAGGTTATATATA
*
434081 TTTATAGGTTATATATA
1 TATATAGGTTATATATA
434098 TATATAGGTTATATATA
1 TATATAGGTTATATATA
434115 CTATA
1 -TATA
434120 CATGGTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 5 0.15
16 3 0.09
17 22 0.65
18 4 0.12
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (17 bp):
TATATAGGTTATATATA
Found at i:434487 original size:14 final size:14
Alignment explanation
Indices: 434468--434521 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
434458 TTCATTTATA
434468 TTAGGGTTTGTGAT
1 TTAGGGTTTGTGAT
* *
434482 TTAGGGTTTAGGGTT
1 TTAGGGTTT-GTGAT
*
434497 TATGAGGGTTTATGAT
1 T-T-AGGGTTTGTGAT
434513 TTAGGGTTT
1 TTAGGGTTT
434522 CTATAAACTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 16 0.50
15 5 0.16
16 4 0.12
17 7 0.22
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (14 bp):
TTAGGGTTTGTGAT
Found at i:434792 original size:2 final size:2
Alignment explanation
Indices: 434785--434965 Score: 110
Period size: 2 Copynumber: 92.0 Consensus size: 2
434775 ATAGTGTTTC
434785 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
434827 TC TA TA GA T- TA CT- TA TA T- TA GT- TA TA CA TA CA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * *
434867 T- TA TA T- TA -A TA TA AA T- TA TA -A TT TA TA AA CTA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* * * * * * *
434906 TA TA TA GTT TA TA CA TA TA TA GTT TA TA TA CA TA CA TA CA TA CA
1 TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
434950 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
434966 ATTAAAAGTA
Statistics
Matches: 134, Mismatches: 30, Indels: 30
0.69 0.15 0.15
Matches are distributed among these distances:
1 9 0.07
2 119 0.89
3 6 0.04
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:435183 original size:18 final size:20
Alignment explanation
Indices: 435160--435206 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 20
435150 GCGCAAACTT
*
435160 CTCTAAATTT-TCTATTT-C
1 CTCTAAATTTCTCAATTTCC
435178 CTCTAAATTTCTCAATTTCC
1 CTCTAAATTTCTCAATTTCC
435198 CTCTAAATT
1 CTCTAAATT
435207 CACAATTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 10 0.38
19 6 0.23
20 10 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (20 bp):
CTCTAAATTTCTCAATTTCC
Found at i:435217 original size:20 final size:20
Alignment explanation
Indices: 435160--435214 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
435150 GCGCAAACTT
* *
435160 CTCTAAATTT-TCTATTT-C
1 CTCTAAATTTCACAATTTCC
*
435178 CTCTAAATTTCTCAATTTCC
1 CTCTAAATTTCACAATTTCC
435198 CTCTAAA-TTCACAATTT
1 CTCTAAATTTCACAATTT
435215 TCCTATATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 10 0.30
19 15 0.45
20 8 0.24
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.47
Consensus pattern (20 bp):
CTCTAAATTTCACAATTTCC
Found at i:435234 original size:46 final size:45
Alignment explanation
Indices: 435165--435253 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 45
435155 AACTTCTCTA
* *
435165 AATTTTCTATTTCCTCTAAATTTCTCAATTTCCCTCTAAATTCAC
1 AATTTTCTATTTCCTCAAAATTTCCCAATTTCCCTCTAAATTCAC
435210 AATTTTCCTATATT-CTCAAAATTTCCCAATTTCCCTCTAAATTC
1 AATTTT-CTAT-TTCCTCAAAATTTCCCAATTTCCCTCTAAATTC
435254 TCAAATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
45 6 0.15
46 32 0.80
47 2 0.05
ACGTcount: A:0.28, C:0.27, G:0.00, T:0.45
Consensus pattern (45 bp):
AATTTTCTATTTCCTCAAAATTTCCCAATTTCCCTCTAAATTCAC
Found at i:435873 original size:21 final size:22
Alignment explanation
Indices: 435849--435893 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
435839 TTCAATTTTT
*
435849 TTATAATTTATAAATTATA-AA
1 TTATAATTTATAAACTATATAA
*
435870 TTATAGTTTATAAACTATATAA
1 TTATAATTTATAAACTATATAA
435892 TT
1 TT
435894 TTTATAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTATAATTTATAAACTATATAA
Done.