Multiple sequence alignment - TraesCS2D01G563200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G563200 chr2D 100.000 3205 0 0 1 3205 634576784 634573580 0.000000e+00 5919.0
1 TraesCS2D01G563200 chr2D 80.776 1186 113 62 966 2082 634482759 634481620 0.000000e+00 821.0
2 TraesCS2D01G563200 chr2D 87.838 666 48 17 1423 2082 634658675 634658037 0.000000e+00 750.0
3 TraesCS2D01G563200 chr2D 86.076 632 57 16 1462 2082 634556410 634555799 0.000000e+00 651.0
4 TraesCS2D01G563200 chr2D 78.182 440 50 25 762 1185 634659339 634658930 4.130000e-59 239.0
5 TraesCS2D01G563200 chr2D 79.211 380 30 25 603 962 634483144 634482794 5.380000e-53 219.0
6 TraesCS2D01G563200 chr2D 95.714 70 3 0 1 70 459856528 459856597 2.610000e-21 113.0
7 TraesCS2D01G563200 chr2B 85.564 2002 153 71 133 2082 777620037 777618120 0.000000e+00 1971.0
8 TraesCS2D01G563200 chr2B 77.712 1678 201 94 825 2399 777549974 777548367 0.000000e+00 867.0
9 TraesCS2D01G563200 chr2B 80.576 1076 118 65 1023 2082 777659174 777658174 0.000000e+00 745.0
10 TraesCS2D01G563200 chr2B 82.250 569 54 25 1298 1849 777521925 777521387 6.310000e-122 448.0
11 TraesCS2D01G563200 chr2B 90.820 305 25 3 2903 3205 777615902 777615599 3.850000e-109 405.0
12 TraesCS2D01G563200 chr2B 89.836 305 28 3 2903 3205 777604440 777604137 3.880000e-104 388.0
13 TraesCS2D01G563200 chr2B 85.352 355 32 10 1723 2070 777634018 777633677 1.830000e-92 350.0
14 TraesCS2D01G563200 chr2B 86.557 305 35 6 2199 2500 777605610 777605309 6.630000e-87 331.0
15 TraesCS2D01G563200 chr2B 80.493 487 43 29 495 960 777608055 777607600 3.080000e-85 326.0
16 TraesCS2D01G563200 chr2B 87.795 254 22 6 2605 2850 777605081 777604829 4.050000e-74 289.0
17 TraesCS2D01G563200 chr2B 87.209 258 25 6 2246 2500 777617003 777616751 1.450000e-73 287.0
18 TraesCS2D01G563200 chr2B 92.353 170 13 0 2080 2249 777618086 777617917 3.190000e-60 243.0
19 TraesCS2D01G563200 chr2B 77.064 436 57 23 870 1290 777635559 777635152 9.010000e-51 211.0
20 TraesCS2D01G563200 chr2B 77.844 334 38 16 957 1271 777522238 777521922 1.180000e-39 174.0
21 TraesCS2D01G563200 chr2B 88.636 132 15 0 1193 1324 777605801 777605670 9.200000e-36 161.0
22 TraesCS2D01G563200 chr2B 83.735 166 12 8 239 399 777550425 777550270 3.330000e-30 143.0
23 TraesCS2D01G563200 chr2B 84.138 145 6 6 821 952 777659358 777659218 1.210000e-24 124.0
24 TraesCS2D01G563200 chr2B 77.291 251 25 14 2624 2855 777532497 777532260 5.620000e-23 119.0
25 TraesCS2D01G563200 chr2B 83.696 92 4 6 1991 2082 777521311 777521231 3.430000e-10 76.8
26 TraesCS2D01G563200 chr2A 88.782 1141 73 20 957 2065 778788578 778789695 0.000000e+00 1347.0
27 TraesCS2D01G563200 chr2A 89.597 596 40 9 1493 2082 778760227 778760806 0.000000e+00 737.0
28 TraesCS2D01G563200 chr2A 79.076 1190 126 77 957 2082 778914421 778915551 0.000000e+00 704.0
29 TraesCS2D01G563200 chr2A 77.375 1379 153 89 1052 2331 778876133 778877451 0.000000e+00 671.0
30 TraesCS2D01G563200 chr2A 86.364 638 50 18 1462 2082 778827463 778828080 0.000000e+00 662.0
31 TraesCS2D01G563200 chr2A 85.349 587 32 21 390 960 778787987 778788535 2.790000e-155 558.0
32 TraesCS2D01G563200 chr2A 81.784 527 39 29 1848 2326 778814331 778814848 3.880000e-104 388.0
33 TraesCS2D01G563200 chr2A 92.623 244 12 2 133 376 778787692 778787929 2.370000e-91 346.0
34 TraesCS2D01G563200 chr2A 87.645 259 23 3 2605 2855 778815328 778815585 3.130000e-75 292.0
35 TraesCS2D01G563200 chr2A 90.722 194 14 3 2858 3050 778815657 778815847 4.100000e-64 255.0
36 TraesCS2D01G563200 chr2A 87.435 191 11 4 957 1145 778826971 778827150 1.170000e-49 207.0
37 TraesCS2D01G563200 chr2A 89.404 151 13 2 2352 2499 778814904 778815054 1.520000e-43 187.0
38 TraesCS2D01G563200 chr2A 83.516 182 14 10 762 932 778759566 778759742 4.280000e-34 156.0
39 TraesCS2D01G563200 chr2A 85.430 151 15 3 253 398 778759131 778759279 1.990000e-32 150.0
40 TraesCS2D01G563200 chr2A 88.430 121 13 1 2492 2611 545171435 545171315 9.270000e-31 145.0
41 TraesCS2D01G563200 chr2A 88.119 101 2 3 196 296 778868997 778869087 9.400000e-21 111.0
42 TraesCS2D01G563200 chr2A 82.482 137 12 5 957 1088 778814189 778814318 3.380000e-20 110.0
43 TraesCS2D01G563200 chr7A 89.256 121 12 1 2492 2611 435059368 435059488 1.990000e-32 150.0
44 TraesCS2D01G563200 chr7A 88.430 121 13 1 2492 2611 460048448 460048568 9.270000e-31 145.0
45 TraesCS2D01G563200 chr6A 89.256 121 12 1 2492 2611 172036119 172035999 1.990000e-32 150.0
46 TraesCS2D01G563200 chr4A 90.435 115 10 1 2494 2607 469243063 469242949 1.990000e-32 150.0
47 TraesCS2D01G563200 chr4A 88.430 121 13 1 2492 2611 252243732 252243852 9.270000e-31 145.0
48 TraesCS2D01G563200 chr4A 88.430 121 13 1 2492 2611 384826093 384826213 9.270000e-31 145.0
49 TraesCS2D01G563200 chr4A 97.143 70 2 0 1 70 591598884 591598815 5.620000e-23 119.0
50 TraesCS2D01G563200 chr3A 89.076 119 12 1 2494 2611 513027117 513027235 2.580000e-31 147.0
51 TraesCS2D01G563200 chr3A 88.430 121 12 2 2492 2611 350477058 350477177 9.270000e-31 145.0
52 TraesCS2D01G563200 chr3D 84.000 125 10 7 1 115 250915534 250915410 9.400000e-21 111.0
53 TraesCS2D01G563200 chr3D 94.286 70 4 0 1 70 328303497 328303566 1.220000e-19 108.0
54 TraesCS2D01G563200 chrUn 94.286 70 4 0 1 70 10180739 10180808 1.220000e-19 108.0
55 TraesCS2D01G563200 chr6D 94.286 70 4 0 1 70 27667354 27667285 1.220000e-19 108.0
56 TraesCS2D01G563200 chr6D 94.286 70 4 0 1 70 40836409 40836340 1.220000e-19 108.0
57 TraesCS2D01G563200 chr1D 94.286 70 4 0 1 70 302252743 302252674 1.220000e-19 108.0
58 TraesCS2D01G563200 chr1D 94.286 70 4 0 1 70 333223327 333223258 1.220000e-19 108.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G563200 chr2D 634573580 634576784 3204 True 5919.000000 5919 100.000000 1 3205 1 chr2D.!!$R2 3204
1 TraesCS2D01G563200 chr2D 634555799 634556410 611 True 651.000000 651 86.076000 1462 2082 1 chr2D.!!$R1 620
2 TraesCS2D01G563200 chr2D 634481620 634483144 1524 True 520.000000 821 79.993500 603 2082 2 chr2D.!!$R3 1479
3 TraesCS2D01G563200 chr2D 634658037 634659339 1302 True 494.500000 750 83.010000 762 2082 2 chr2D.!!$R4 1320
4 TraesCS2D01G563200 chr2B 777615599 777620037 4438 True 726.500000 1971 88.986500 133 3205 4 chr2B.!!$R5 3072
5 TraesCS2D01G563200 chr2B 777548367 777550425 2058 True 505.000000 867 80.723500 239 2399 2 chr2B.!!$R3 2160
6 TraesCS2D01G563200 chr2B 777658174 777659358 1184 True 434.500000 745 82.357000 821 2082 2 chr2B.!!$R7 1261
7 TraesCS2D01G563200 chr2B 777604137 777608055 3918 True 299.000000 388 86.663400 495 3205 5 chr2B.!!$R4 2710
8 TraesCS2D01G563200 chr2B 777633677 777635559 1882 True 280.500000 350 81.208000 870 2070 2 chr2B.!!$R6 1200
9 TraesCS2D01G563200 chr2B 777521231 777522238 1007 True 232.933333 448 81.263333 957 2082 3 chr2B.!!$R2 1125
10 TraesCS2D01G563200 chr2A 778787692 778789695 2003 False 750.333333 1347 88.918000 133 2065 3 chr2A.!!$F5 1932
11 TraesCS2D01G563200 chr2A 778914421 778915551 1130 False 704.000000 704 79.076000 957 2082 1 chr2A.!!$F3 1125
12 TraesCS2D01G563200 chr2A 778876133 778877451 1318 False 671.000000 671 77.375000 1052 2331 1 chr2A.!!$F2 1279
13 TraesCS2D01G563200 chr2A 778826971 778828080 1109 False 434.500000 662 86.899500 957 2082 2 chr2A.!!$F7 1125
14 TraesCS2D01G563200 chr2A 778759131 778760806 1675 False 347.666667 737 86.181000 253 2082 3 chr2A.!!$F4 1829
15 TraesCS2D01G563200 chr2A 778814189 778815847 1658 False 246.400000 388 86.407400 957 3050 5 chr2A.!!$F6 2093

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
126 127 0.104672 TCCCCTTCTTCCACAGTGGA 60.105 55.0 19.21 19.21 46.61 4.02 F
1070 1357 0.109342 GATCCGTCAGCCCCATCATT 59.891 55.0 0.00 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 4590 0.106967 GGAATGGGAAGACTGGGAGC 60.107 60.0 0.0 0.0 0.0 4.70 R
2815 6876 0.370273 GCACACTATCAAGGCGTTCG 59.630 55.0 0.0 0.0 0.0 3.95 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.884037 ACTCCCATTCTCTTGTTTGGT 57.116 42.857 0.00 0.00 0.00 3.67
21 22 3.490348 ACTCCCATTCTCTTGTTTGGTG 58.510 45.455 0.00 0.00 0.00 4.17
22 23 3.117512 ACTCCCATTCTCTTGTTTGGTGT 60.118 43.478 0.00 0.00 0.00 4.16
23 24 4.104102 ACTCCCATTCTCTTGTTTGGTGTA 59.896 41.667 0.00 0.00 0.00 2.90
24 25 5.222130 ACTCCCATTCTCTTGTTTGGTGTAT 60.222 40.000 0.00 0.00 0.00 2.29
25 26 5.009631 TCCCATTCTCTTGTTTGGTGTATG 58.990 41.667 0.00 0.00 0.00 2.39
26 27 5.009631 CCCATTCTCTTGTTTGGTGTATGA 58.990 41.667 0.00 0.00 0.00 2.15
27 28 5.653769 CCCATTCTCTTGTTTGGTGTATGAT 59.346 40.000 0.00 0.00 0.00 2.45
28 29 6.405065 CCCATTCTCTTGTTTGGTGTATGATG 60.405 42.308 0.00 0.00 0.00 3.07
29 30 6.405065 CCATTCTCTTGTTTGGTGTATGATGG 60.405 42.308 0.00 0.00 0.00 3.51
30 31 4.588899 TCTCTTGTTTGGTGTATGATGGG 58.411 43.478 0.00 0.00 0.00 4.00
31 32 4.288366 TCTCTTGTTTGGTGTATGATGGGA 59.712 41.667 0.00 0.00 0.00 4.37
32 33 4.991776 TCTTGTTTGGTGTATGATGGGAA 58.008 39.130 0.00 0.00 0.00 3.97
33 34 5.579047 TCTTGTTTGGTGTATGATGGGAAT 58.421 37.500 0.00 0.00 0.00 3.01
34 35 6.015918 TCTTGTTTGGTGTATGATGGGAATT 58.984 36.000 0.00 0.00 0.00 2.17
35 36 6.496565 TCTTGTTTGGTGTATGATGGGAATTT 59.503 34.615 0.00 0.00 0.00 1.82
36 37 7.671819 TCTTGTTTGGTGTATGATGGGAATTTA 59.328 33.333 0.00 0.00 0.00 1.40
37 38 7.164230 TGTTTGGTGTATGATGGGAATTTAC 57.836 36.000 0.00 0.00 0.00 2.01
38 39 6.127869 TGTTTGGTGTATGATGGGAATTTACG 60.128 38.462 0.00 0.00 0.00 3.18
39 40 5.105567 TGGTGTATGATGGGAATTTACGT 57.894 39.130 0.00 0.00 0.00 3.57
40 41 4.878971 TGGTGTATGATGGGAATTTACGTG 59.121 41.667 0.00 0.00 0.00 4.49
41 42 4.274950 GGTGTATGATGGGAATTTACGTGG 59.725 45.833 0.00 0.00 0.00 4.94
42 43 4.274950 GTGTATGATGGGAATTTACGTGGG 59.725 45.833 0.00 0.00 0.00 4.61
43 44 3.943671 ATGATGGGAATTTACGTGGGA 57.056 42.857 0.00 0.00 0.00 4.37
44 45 3.943671 TGATGGGAATTTACGTGGGAT 57.056 42.857 0.00 0.00 0.00 3.85
45 46 5.576563 ATGATGGGAATTTACGTGGGATA 57.423 39.130 0.00 0.00 0.00 2.59
46 47 5.375283 TGATGGGAATTTACGTGGGATAA 57.625 39.130 0.00 0.00 0.00 1.75
47 48 5.756918 TGATGGGAATTTACGTGGGATAAA 58.243 37.500 0.00 0.00 0.00 1.40
48 49 6.188407 TGATGGGAATTTACGTGGGATAAAA 58.812 36.000 0.00 0.00 0.00 1.52
49 50 5.900865 TGGGAATTTACGTGGGATAAAAC 57.099 39.130 0.00 0.00 0.00 2.43
50 51 5.572252 TGGGAATTTACGTGGGATAAAACT 58.428 37.500 0.00 0.00 0.00 2.66
51 52 5.648960 TGGGAATTTACGTGGGATAAAACTC 59.351 40.000 0.00 0.00 0.00 3.01
52 53 5.884232 GGGAATTTACGTGGGATAAAACTCT 59.116 40.000 0.00 0.00 0.00 3.24
53 54 6.183360 GGGAATTTACGTGGGATAAAACTCTG 60.183 42.308 0.00 0.00 0.00 3.35
54 55 5.813080 ATTTACGTGGGATAAAACTCTGC 57.187 39.130 0.00 0.00 0.00 4.26
55 56 4.546829 TTACGTGGGATAAAACTCTGCT 57.453 40.909 0.00 0.00 0.00 4.24
56 57 2.973945 ACGTGGGATAAAACTCTGCTC 58.026 47.619 0.00 0.00 0.00 4.26
57 58 2.301870 ACGTGGGATAAAACTCTGCTCA 59.698 45.455 0.00 0.00 0.00 4.26
58 59 2.673368 CGTGGGATAAAACTCTGCTCAC 59.327 50.000 0.00 0.00 0.00 3.51
59 60 2.673368 GTGGGATAAAACTCTGCTCACG 59.327 50.000 0.00 0.00 0.00 4.35
60 61 2.565391 TGGGATAAAACTCTGCTCACGA 59.435 45.455 0.00 0.00 0.00 4.35
61 62 3.007506 TGGGATAAAACTCTGCTCACGAA 59.992 43.478 0.00 0.00 0.00 3.85
62 63 4.192317 GGGATAAAACTCTGCTCACGAAT 58.808 43.478 0.00 0.00 0.00 3.34
63 64 4.636206 GGGATAAAACTCTGCTCACGAATT 59.364 41.667 0.00 0.00 0.00 2.17
64 65 5.815740 GGGATAAAACTCTGCTCACGAATTA 59.184 40.000 0.00 0.00 0.00 1.40
65 66 6.315393 GGGATAAAACTCTGCTCACGAATTAA 59.685 38.462 0.00 0.00 0.00 1.40
66 67 7.180748 GGATAAAACTCTGCTCACGAATTAAC 58.819 38.462 0.00 0.00 0.00 2.01
67 68 7.148474 GGATAAAACTCTGCTCACGAATTAACA 60.148 37.037 0.00 0.00 0.00 2.41
68 69 5.597813 AAACTCTGCTCACGAATTAACAG 57.402 39.130 0.00 0.00 0.00 3.16
69 70 3.589988 ACTCTGCTCACGAATTAACAGG 58.410 45.455 0.00 0.00 0.00 4.00
70 71 2.346803 TCTGCTCACGAATTAACAGGC 58.653 47.619 0.00 0.00 0.00 4.85
71 72 2.076100 CTGCTCACGAATTAACAGGCA 58.924 47.619 0.00 0.00 0.00 4.75
72 73 1.804151 TGCTCACGAATTAACAGGCAC 59.196 47.619 0.00 0.00 0.00 5.01
73 74 1.130561 GCTCACGAATTAACAGGCACC 59.869 52.381 0.00 0.00 0.00 5.01
74 75 2.422597 CTCACGAATTAACAGGCACCA 58.577 47.619 0.00 0.00 0.00 4.17
75 76 2.811431 CTCACGAATTAACAGGCACCAA 59.189 45.455 0.00 0.00 0.00 3.67
76 77 3.215151 TCACGAATTAACAGGCACCAAA 58.785 40.909 0.00 0.00 0.00 3.28
77 78 3.632604 TCACGAATTAACAGGCACCAAAA 59.367 39.130 0.00 0.00 0.00 2.44
78 79 4.098044 TCACGAATTAACAGGCACCAAAAA 59.902 37.500 0.00 0.00 0.00 1.94
97 98 2.532250 AAAAATCGATGGGCTTCCCT 57.468 45.000 0.00 0.00 45.70 4.20
98 99 3.662759 AAAAATCGATGGGCTTCCCTA 57.337 42.857 0.00 0.00 45.70 3.53
99 100 3.662759 AAAATCGATGGGCTTCCCTAA 57.337 42.857 0.00 0.00 45.70 2.69
100 101 2.640316 AATCGATGGGCTTCCCTAAC 57.360 50.000 0.00 0.00 45.70 2.34
101 102 1.807814 ATCGATGGGCTTCCCTAACT 58.192 50.000 0.00 0.00 45.70 2.24
102 103 1.120530 TCGATGGGCTTCCCTAACTC 58.879 55.000 3.27 0.00 45.70 3.01
103 104 0.106894 CGATGGGCTTCCCTAACTCC 59.893 60.000 3.27 0.00 45.70 3.85
104 105 0.474614 GATGGGCTTCCCTAACTCCC 59.525 60.000 3.27 0.00 45.70 4.30
105 106 1.162329 TGGGCTTCCCTAACTCCCA 59.838 57.895 3.27 0.00 45.70 4.37
106 107 0.253630 TGGGCTTCCCTAACTCCCAT 60.254 55.000 3.27 0.00 45.70 4.00
107 108 0.927029 GGGCTTCCCTAACTCCCATT 59.073 55.000 0.00 0.00 41.34 3.16
108 109 1.133761 GGGCTTCCCTAACTCCCATTC 60.134 57.143 0.00 0.00 41.34 2.67
109 110 1.133761 GGCTTCCCTAACTCCCATTCC 60.134 57.143 0.00 0.00 0.00 3.01
110 111 1.133761 GCTTCCCTAACTCCCATTCCC 60.134 57.143 0.00 0.00 0.00 3.97
111 112 1.495148 CTTCCCTAACTCCCATTCCCC 59.505 57.143 0.00 0.00 0.00 4.81
112 113 0.728843 TCCCTAACTCCCATTCCCCT 59.271 55.000 0.00 0.00 0.00 4.79
113 114 1.083912 TCCCTAACTCCCATTCCCCTT 59.916 52.381 0.00 0.00 0.00 3.95
114 115 1.495148 CCCTAACTCCCATTCCCCTTC 59.505 57.143 0.00 0.00 0.00 3.46
115 116 2.493091 CCTAACTCCCATTCCCCTTCT 58.507 52.381 0.00 0.00 0.00 2.85
116 117 2.853077 CCTAACTCCCATTCCCCTTCTT 59.147 50.000 0.00 0.00 0.00 2.52
117 118 3.117851 CCTAACTCCCATTCCCCTTCTTC 60.118 52.174 0.00 0.00 0.00 2.87
118 119 1.299939 ACTCCCATTCCCCTTCTTCC 58.700 55.000 0.00 0.00 0.00 3.46
119 120 1.298953 CTCCCATTCCCCTTCTTCCA 58.701 55.000 0.00 0.00 0.00 3.53
120 121 0.999712 TCCCATTCCCCTTCTTCCAC 59.000 55.000 0.00 0.00 0.00 4.02
121 122 0.704076 CCCATTCCCCTTCTTCCACA 59.296 55.000 0.00 0.00 0.00 4.17
122 123 1.341383 CCCATTCCCCTTCTTCCACAG 60.341 57.143 0.00 0.00 0.00 3.66
123 124 1.355720 CCATTCCCCTTCTTCCACAGT 59.644 52.381 0.00 0.00 0.00 3.55
124 125 2.440409 CATTCCCCTTCTTCCACAGTG 58.560 52.381 0.00 0.00 0.00 3.66
125 126 0.771127 TTCCCCTTCTTCCACAGTGG 59.229 55.000 14.19 14.19 39.43 4.00
126 127 0.104672 TCCCCTTCTTCCACAGTGGA 60.105 55.000 19.21 19.21 46.61 4.02
149 150 0.242825 GTGTCCGAGATTCACCGTCA 59.757 55.000 0.00 0.00 0.00 4.35
205 206 2.099098 AGAACGCAGAAACAAAACCCAG 59.901 45.455 0.00 0.00 0.00 4.45
306 311 0.181587 TGTCCTCTCTCTCGCCTAGG 59.818 60.000 3.67 3.67 0.00 3.02
307 312 1.149627 TCCTCTCTCTCGCCTAGGC 59.850 63.158 24.75 24.75 37.85 3.93
308 313 1.150536 CCTCTCTCTCGCCTAGGCT 59.849 63.158 30.55 0.00 39.32 4.58
309 314 0.398696 CCTCTCTCTCGCCTAGGCTA 59.601 60.000 30.55 19.92 39.32 3.93
310 315 1.004277 CCTCTCTCTCGCCTAGGCTAT 59.996 57.143 30.55 0.00 39.32 2.97
455 512 1.096967 GTGGATGGATGCATGCGTCA 61.097 55.000 34.49 23.11 36.06 4.35
464 521 1.669115 GCATGCGTCAGTGTCACCT 60.669 57.895 0.00 0.00 0.00 4.00
565 623 1.002142 CCACTCGCCGATCACGTATAA 60.002 52.381 5.18 0.00 37.88 0.98
698 770 3.863142 GCAAGTTGCAAGATTCCATCT 57.137 42.857 22.90 0.00 44.26 2.90
726 813 0.462225 CGACCGAGAGCTCTCCAGTA 60.462 60.000 32.86 0.00 39.79 2.74
727 814 1.305201 GACCGAGAGCTCTCCAGTAG 58.695 60.000 32.86 20.34 39.79 2.57
728 815 0.621609 ACCGAGAGCTCTCCAGTAGT 59.378 55.000 32.86 20.73 39.79 2.73
731 818 1.407575 CGAGAGCTCTCCAGTAGTCCA 60.408 57.143 32.86 0.00 39.79 4.02
732 819 2.297701 GAGAGCTCTCCAGTAGTCCAG 58.702 57.143 30.10 0.00 37.02 3.86
733 820 1.638589 AGAGCTCTCCAGTAGTCCAGT 59.361 52.381 11.45 0.00 0.00 4.00
734 821 2.021457 GAGCTCTCCAGTAGTCCAGTC 58.979 57.143 6.43 0.00 0.00 3.51
735 822 1.638589 AGCTCTCCAGTAGTCCAGTCT 59.361 52.381 0.00 0.00 0.00 3.24
736 823 2.021457 GCTCTCCAGTAGTCCAGTCTC 58.979 57.143 0.00 0.00 0.00 3.36
759 858 2.747022 CACACCATGGACACCCGA 59.253 61.111 21.47 0.00 34.29 5.14
762 861 2.203938 ACCATGGACACCCGACCT 60.204 61.111 21.47 0.00 34.29 3.85
808 915 3.453717 TGAACGCTCCTACTCTACTCCTA 59.546 47.826 0.00 0.00 0.00 2.94
1009 1264 2.737679 GCACGTCCTCACATAGGTTACC 60.738 54.545 0.00 0.00 46.62 2.85
1062 1343 1.370657 GTCGATCGATCCGTCAGCC 60.371 63.158 22.50 0.53 0.00 4.85
1070 1357 0.109342 GATCCGTCAGCCCCATCATT 59.891 55.000 0.00 0.00 0.00 2.57
1188 3075 4.750952 CTCGATCGGTTAGAGCTAATCA 57.249 45.455 16.41 0.00 32.02 2.57
1189 3076 4.468643 CTCGATCGGTTAGAGCTAATCAC 58.531 47.826 16.41 0.00 32.02 3.06
1273 3218 3.780173 GCTCCAGCTTCCGCCTCT 61.780 66.667 0.00 0.00 38.21 3.69
1414 3383 4.346734 ACTTACATGACTACACGTACGG 57.653 45.455 21.06 11.05 0.00 4.02
1632 3653 4.873129 CGCCGCTACTGGACGCAT 62.873 66.667 0.00 0.00 0.00 4.73
1776 4584 4.468615 ACGCGCGCTCTCTCAGAC 62.469 66.667 32.58 0.00 0.00 3.51
1778 4586 4.121669 GCGCGCTCTCTCAGACCA 62.122 66.667 26.67 0.00 0.00 4.02
1779 4587 2.804167 CGCGCTCTCTCAGACCAT 59.196 61.111 5.56 0.00 0.00 3.55
1780 4588 1.299014 CGCGCTCTCTCAGACCATC 60.299 63.158 5.56 0.00 0.00 3.51
1781 4589 1.067250 GCGCTCTCTCAGACCATCC 59.933 63.158 0.00 0.00 0.00 3.51
1782 4590 1.358402 CGCTCTCTCAGACCATCCG 59.642 63.158 0.00 0.00 0.00 4.18
1783 4591 1.067250 GCTCTCTCAGACCATCCGC 59.933 63.158 0.00 0.00 0.00 5.54
1784 4592 1.391157 GCTCTCTCAGACCATCCGCT 61.391 60.000 0.00 0.00 0.00 5.52
1785 4593 0.667993 CTCTCTCAGACCATCCGCTC 59.332 60.000 0.00 0.00 0.00 5.03
1786 4594 0.753479 TCTCTCAGACCATCCGCTCC 60.753 60.000 0.00 0.00 0.00 4.70
1787 4595 1.743321 CTCTCAGACCATCCGCTCCC 61.743 65.000 0.00 0.00 0.00 4.30
1788 4596 2.038813 TCAGACCATCCGCTCCCA 59.961 61.111 0.00 0.00 0.00 4.37
1789 4597 2.025767 CTCAGACCATCCGCTCCCAG 62.026 65.000 0.00 0.00 0.00 4.45
1790 4598 2.039624 AGACCATCCGCTCCCAGT 59.960 61.111 0.00 0.00 0.00 4.00
1809 4617 1.486726 GTCTTCCCATTCCTCACCGAT 59.513 52.381 0.00 0.00 0.00 4.18
1811 4619 0.546122 TTCCCATTCCTCACCGATGG 59.454 55.000 0.00 0.00 39.99 3.51
1883 4700 3.991051 ACCAGCGACCACAGACCG 61.991 66.667 0.00 0.00 0.00 4.79
2070 4931 2.348666 CGTTCGAGGCTCCTGTTTTATG 59.651 50.000 9.32 0.00 0.00 1.90
2189 5103 2.279582 GCTAGCAAGCGTCTGAGTAA 57.720 50.000 10.63 0.00 39.39 2.24
2197 5111 0.458716 GCGTCTGAGTAACCAGGCTC 60.459 60.000 0.00 0.00 36.67 4.70
2218 5134 4.563061 TCGCTGTTAAGTACTTTTCCTCC 58.437 43.478 14.49 0.00 0.00 4.30
2236 5161 1.351017 TCCTGGTTTTGGTGCTCTAGG 59.649 52.381 0.00 0.00 0.00 3.02
2250 6098 5.394333 GGTGCTCTAGGTAAACCTCAGTAAG 60.394 48.000 4.57 0.00 44.77 2.34
2264 6113 5.230942 CCTCAGTAAGGGAATAGTAATGCG 58.769 45.833 0.00 0.00 42.03 4.73
2282 6131 1.071605 CGTGCAACTTGAGTCTAGCC 58.928 55.000 1.16 0.00 31.75 3.93
2286 6135 1.399791 GCAACTTGAGTCTAGCCATGC 59.600 52.381 10.23 10.23 0.00 4.06
2326 6176 3.011949 GCAATGGCGTTTTCTTCTTCA 57.988 42.857 0.00 0.00 0.00 3.02
2337 6187 7.096599 GGCGTTTTCTTCTTCAAACTATTCAAC 60.097 37.037 0.00 0.00 31.75 3.18
2350 6230 5.056894 ACTATTCAACTGGTAGTGACGAC 57.943 43.478 0.00 0.00 0.00 4.34
2378 6258 3.749665 CTGAAAGCATAGGAGGAGAGG 57.250 52.381 0.00 0.00 0.00 3.69
2387 6267 0.257616 AGGAGGAGAGGGAGAGAACG 59.742 60.000 0.00 0.00 0.00 3.95
2399 6279 3.117046 GGAGAGAACGATTTCGGATGAC 58.883 50.000 4.84 0.00 44.95 3.06
2418 6299 7.374228 CGGATGACAAAAATCGACTTGAATATG 59.626 37.037 9.92 0.00 0.00 1.78
2474 6357 7.472100 GCATACTCACTGGTTGGTATTATCTCT 60.472 40.741 0.00 0.00 0.00 3.10
2475 6358 6.472686 ACTCACTGGTTGGTATTATCTCTC 57.527 41.667 0.00 0.00 0.00 3.20
2504 6387 7.364200 ACATCTGTATCTAGACAAATACTCGC 58.636 38.462 0.00 0.00 31.11 5.03
2506 6389 7.192148 TCTGTATCTAGACAAATACTCGCTC 57.808 40.000 0.00 0.00 31.11 5.03
2507 6390 6.205076 TCTGTATCTAGACAAATACTCGCTCC 59.795 42.308 0.00 0.00 31.11 4.70
2510 6393 3.693085 TCTAGACAAATACTCGCTCCGTT 59.307 43.478 0.00 0.00 0.00 4.44
2511 6394 3.314541 AGACAAATACTCGCTCCGTTT 57.685 42.857 0.00 0.00 0.00 3.60
2512 6395 2.993899 AGACAAATACTCGCTCCGTTTG 59.006 45.455 0.00 0.00 36.23 2.93
2522 6541 6.823678 ACTCGCTCCGTTTGTAAATATAAG 57.176 37.500 0.00 0.00 0.00 1.73
2525 6544 5.750067 TCGCTCCGTTTGTAAATATAAGACC 59.250 40.000 0.00 0.00 0.00 3.85
2547 6566 9.159364 AGACCTTTTAAAGATGTTAATACGGAC 57.841 33.333 6.24 0.00 0.00 4.79
2548 6567 9.159364 GACCTTTTAAAGATGTTAATACGGACT 57.841 33.333 6.24 0.00 0.00 3.85
2602 6643 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2603 6644 5.412594 GTGTAGATTCACTCATTTTGCTCCA 59.587 40.000 0.00 0.00 35.68 3.86
2616 6668 8.347004 TCATTTTGCTCCATATAAGTTTGACA 57.653 30.769 0.00 0.00 0.00 3.58
2622 6674 8.893219 TGCTCCATATAAGTTTGACATCTAAG 57.107 34.615 0.00 0.00 0.00 2.18
2815 6876 5.786401 TTTTGTTTTGTACAACACCATGC 57.214 34.783 19.46 0.00 46.09 4.06
2834 6895 0.370273 CGAACGCCTTGATAGTGTGC 59.630 55.000 0.00 0.00 0.00 4.57
2855 6916 4.225208 GCGATCCTACTCGTATGTTAACC 58.775 47.826 2.48 0.00 40.73 2.85
2856 6917 4.791974 CGATCCTACTCGTATGTTAACCC 58.208 47.826 2.48 0.00 34.00 4.11
2886 7316 5.948742 AGGCCAAGGCTCTATATTCTATC 57.051 43.478 5.01 0.00 41.60 2.08
2887 7317 4.719273 AGGCCAAGGCTCTATATTCTATCC 59.281 45.833 5.01 0.00 41.60 2.59
2888 7318 4.471386 GGCCAAGGCTCTATATTCTATCCA 59.529 45.833 11.40 0.00 41.60 3.41
2889 7319 5.131809 GGCCAAGGCTCTATATTCTATCCAT 59.868 44.000 11.40 0.00 41.60 3.41
2890 7320 6.327626 GGCCAAGGCTCTATATTCTATCCATA 59.672 42.308 11.40 0.00 41.60 2.74
2891 7321 7.441017 GCCAAGGCTCTATATTCTATCCATAG 58.559 42.308 3.29 0.00 38.26 2.23
2892 7322 7.288852 GCCAAGGCTCTATATTCTATCCATAGA 59.711 40.741 3.29 0.00 36.57 1.98
3061 7514 9.512435 CATCTAGAAAATCTTGGCTGTAAAATG 57.488 33.333 0.00 0.00 0.00 2.32
3078 7531 3.872511 AATGGGCACATGTACACATTG 57.127 42.857 22.96 0.00 37.40 2.82
3086 7539 3.063861 CACATGTACACATTGACCATCGG 59.936 47.826 0.00 0.00 33.61 4.18
3089 7542 4.009370 TGTACACATTGACCATCGGAAA 57.991 40.909 0.00 0.00 0.00 3.13
3124 7578 4.734398 TGTTTCCATCCATATTTGCACC 57.266 40.909 0.00 0.00 0.00 5.01
3202 7656 4.286297 TCTCCTCACACCAACCAAATAG 57.714 45.455 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.117512 ACACCAAACAAGAGAATGGGAGT 60.118 43.478 0.00 0.00 37.26 3.85
1 2 3.490348 ACACCAAACAAGAGAATGGGAG 58.510 45.455 0.00 0.00 37.26 4.30
2 3 3.593442 ACACCAAACAAGAGAATGGGA 57.407 42.857 0.00 0.00 37.26 4.37
4 5 6.405065 CCATCATACACCAAACAAGAGAATGG 60.405 42.308 0.00 0.00 38.91 3.16
6 7 5.653769 CCCATCATACACCAAACAAGAGAAT 59.346 40.000 0.00 0.00 0.00 2.40
7 8 5.009631 CCCATCATACACCAAACAAGAGAA 58.990 41.667 0.00 0.00 0.00 2.87
8 9 4.288366 TCCCATCATACACCAAACAAGAGA 59.712 41.667 0.00 0.00 0.00 3.10
9 10 4.588899 TCCCATCATACACCAAACAAGAG 58.411 43.478 0.00 0.00 0.00 2.85
10 11 4.649267 TCCCATCATACACCAAACAAGA 57.351 40.909 0.00 0.00 0.00 3.02
11 12 5.920193 ATTCCCATCATACACCAAACAAG 57.080 39.130 0.00 0.00 0.00 3.16
12 13 6.678568 AAATTCCCATCATACACCAAACAA 57.321 33.333 0.00 0.00 0.00 2.83
13 14 6.127869 CGTAAATTCCCATCATACACCAAACA 60.128 38.462 0.00 0.00 0.00 2.83
14 15 6.127842 ACGTAAATTCCCATCATACACCAAAC 60.128 38.462 0.00 0.00 0.00 2.93
15 16 5.946972 ACGTAAATTCCCATCATACACCAAA 59.053 36.000 0.00 0.00 0.00 3.28
16 17 5.355630 CACGTAAATTCCCATCATACACCAA 59.644 40.000 0.00 0.00 0.00 3.67
17 18 4.878971 CACGTAAATTCCCATCATACACCA 59.121 41.667 0.00 0.00 0.00 4.17
18 19 4.274950 CCACGTAAATTCCCATCATACACC 59.725 45.833 0.00 0.00 0.00 4.16
19 20 4.274950 CCCACGTAAATTCCCATCATACAC 59.725 45.833 0.00 0.00 0.00 2.90
20 21 4.164413 TCCCACGTAAATTCCCATCATACA 59.836 41.667 0.00 0.00 0.00 2.29
21 22 4.710324 TCCCACGTAAATTCCCATCATAC 58.290 43.478 0.00 0.00 0.00 2.39
22 23 5.576563 ATCCCACGTAAATTCCCATCATA 57.423 39.130 0.00 0.00 0.00 2.15
23 24 3.943671 TCCCACGTAAATTCCCATCAT 57.056 42.857 0.00 0.00 0.00 2.45
24 25 3.943671 ATCCCACGTAAATTCCCATCA 57.056 42.857 0.00 0.00 0.00 3.07
25 26 6.320418 AGTTTTATCCCACGTAAATTCCCATC 59.680 38.462 0.00 0.00 0.00 3.51
26 27 6.192044 AGTTTTATCCCACGTAAATTCCCAT 58.808 36.000 0.00 0.00 0.00 4.00
27 28 5.572252 AGTTTTATCCCACGTAAATTCCCA 58.428 37.500 0.00 0.00 0.00 4.37
28 29 5.884232 AGAGTTTTATCCCACGTAAATTCCC 59.116 40.000 0.00 0.00 0.00 3.97
29 30 6.677187 GCAGAGTTTTATCCCACGTAAATTCC 60.677 42.308 0.00 0.00 0.00 3.01
30 31 6.093633 AGCAGAGTTTTATCCCACGTAAATTC 59.906 38.462 0.00 0.00 0.00 2.17
31 32 5.944007 AGCAGAGTTTTATCCCACGTAAATT 59.056 36.000 0.00 0.00 0.00 1.82
32 33 5.497474 AGCAGAGTTTTATCCCACGTAAAT 58.503 37.500 0.00 0.00 0.00 1.40
33 34 4.901868 AGCAGAGTTTTATCCCACGTAAA 58.098 39.130 0.00 0.00 0.00 2.01
34 35 4.020928 TGAGCAGAGTTTTATCCCACGTAA 60.021 41.667 0.00 0.00 0.00 3.18
35 36 3.512329 TGAGCAGAGTTTTATCCCACGTA 59.488 43.478 0.00 0.00 0.00 3.57
36 37 2.301870 TGAGCAGAGTTTTATCCCACGT 59.698 45.455 0.00 0.00 0.00 4.49
37 38 2.673368 GTGAGCAGAGTTTTATCCCACG 59.327 50.000 0.00 0.00 0.00 4.94
38 39 2.673368 CGTGAGCAGAGTTTTATCCCAC 59.327 50.000 0.00 0.00 0.00 4.61
39 40 2.565391 TCGTGAGCAGAGTTTTATCCCA 59.435 45.455 0.00 0.00 0.00 4.37
40 41 3.247006 TCGTGAGCAGAGTTTTATCCC 57.753 47.619 0.00 0.00 0.00 3.85
41 42 5.803020 AATTCGTGAGCAGAGTTTTATCC 57.197 39.130 0.00 0.00 0.00 2.59
42 43 7.739295 TGTTAATTCGTGAGCAGAGTTTTATC 58.261 34.615 0.00 0.00 0.00 1.75
43 44 7.148407 CCTGTTAATTCGTGAGCAGAGTTTTAT 60.148 37.037 0.00 0.00 0.00 1.40
44 45 6.147164 CCTGTTAATTCGTGAGCAGAGTTTTA 59.853 38.462 0.00 0.00 0.00 1.52
45 46 5.049405 CCTGTTAATTCGTGAGCAGAGTTTT 60.049 40.000 0.00 0.00 0.00 2.43
46 47 4.452455 CCTGTTAATTCGTGAGCAGAGTTT 59.548 41.667 0.00 0.00 0.00 2.66
47 48 3.997021 CCTGTTAATTCGTGAGCAGAGTT 59.003 43.478 0.00 0.00 0.00 3.01
48 49 3.589988 CCTGTTAATTCGTGAGCAGAGT 58.410 45.455 0.00 0.00 0.00 3.24
49 50 2.349886 GCCTGTTAATTCGTGAGCAGAG 59.650 50.000 0.00 0.00 0.00 3.35
50 51 2.289382 TGCCTGTTAATTCGTGAGCAGA 60.289 45.455 0.00 0.00 0.00 4.26
51 52 2.076100 TGCCTGTTAATTCGTGAGCAG 58.924 47.619 0.00 0.00 0.00 4.24
52 53 1.804151 GTGCCTGTTAATTCGTGAGCA 59.196 47.619 0.00 0.00 0.00 4.26
53 54 1.130561 GGTGCCTGTTAATTCGTGAGC 59.869 52.381 0.00 0.00 0.00 4.26
54 55 2.422597 TGGTGCCTGTTAATTCGTGAG 58.577 47.619 0.00 0.00 0.00 3.51
55 56 2.552599 TGGTGCCTGTTAATTCGTGA 57.447 45.000 0.00 0.00 0.00 4.35
56 57 3.634568 TTTGGTGCCTGTTAATTCGTG 57.365 42.857 0.00 0.00 0.00 4.35
57 58 4.657436 TTTTTGGTGCCTGTTAATTCGT 57.343 36.364 0.00 0.00 0.00 3.85
88 89 0.927029 AATGGGAGTTAGGGAAGCCC 59.073 55.000 0.00 0.00 45.90 5.19
89 90 1.133761 GGAATGGGAGTTAGGGAAGCC 60.134 57.143 0.00 0.00 0.00 4.35
90 91 1.133761 GGGAATGGGAGTTAGGGAAGC 60.134 57.143 0.00 0.00 0.00 3.86
91 92 1.495148 GGGGAATGGGAGTTAGGGAAG 59.505 57.143 0.00 0.00 0.00 3.46
92 93 1.083912 AGGGGAATGGGAGTTAGGGAA 59.916 52.381 0.00 0.00 0.00 3.97
93 94 0.728843 AGGGGAATGGGAGTTAGGGA 59.271 55.000 0.00 0.00 0.00 4.20
94 95 1.495148 GAAGGGGAATGGGAGTTAGGG 59.505 57.143 0.00 0.00 0.00 3.53
95 96 2.493091 AGAAGGGGAATGGGAGTTAGG 58.507 52.381 0.00 0.00 0.00 2.69
96 97 3.117851 GGAAGAAGGGGAATGGGAGTTAG 60.118 52.174 0.00 0.00 0.00 2.34
97 98 2.850568 GGAAGAAGGGGAATGGGAGTTA 59.149 50.000 0.00 0.00 0.00 2.24
98 99 1.641192 GGAAGAAGGGGAATGGGAGTT 59.359 52.381 0.00 0.00 0.00 3.01
99 100 1.299939 GGAAGAAGGGGAATGGGAGT 58.700 55.000 0.00 0.00 0.00 3.85
100 101 1.064389 GTGGAAGAAGGGGAATGGGAG 60.064 57.143 0.00 0.00 0.00 4.30
101 102 0.999712 GTGGAAGAAGGGGAATGGGA 59.000 55.000 0.00 0.00 0.00 4.37
102 103 0.704076 TGTGGAAGAAGGGGAATGGG 59.296 55.000 0.00 0.00 0.00 4.00
103 104 1.355720 ACTGTGGAAGAAGGGGAATGG 59.644 52.381 0.00 0.00 0.00 3.16
104 105 2.440409 CACTGTGGAAGAAGGGGAATG 58.560 52.381 0.00 0.00 0.00 2.67
105 106 1.355720 CCACTGTGGAAGAAGGGGAAT 59.644 52.381 22.33 0.00 39.56 3.01
106 107 0.771127 CCACTGTGGAAGAAGGGGAA 59.229 55.000 22.33 0.00 39.56 3.97
107 108 0.104672 TCCACTGTGGAAGAAGGGGA 60.105 55.000 26.54 0.75 45.00 4.81
108 109 2.463441 TCCACTGTGGAAGAAGGGG 58.537 57.895 26.54 0.00 45.00 4.79
119 120 3.991051 CGGACACGGCTCCACTGT 61.991 66.667 1.95 0.00 38.94 3.55
120 121 3.633094 CTCGGACACGGCTCCACTG 62.633 68.421 1.95 0.00 41.39 3.66
121 122 3.374402 CTCGGACACGGCTCCACT 61.374 66.667 1.95 0.00 41.39 4.00
122 123 2.227089 AATCTCGGACACGGCTCCAC 62.227 60.000 1.95 0.00 41.39 4.02
123 124 1.945354 GAATCTCGGACACGGCTCCA 61.945 60.000 1.95 0.00 41.39 3.86
124 125 1.227002 GAATCTCGGACACGGCTCC 60.227 63.158 0.00 0.00 41.39 4.70
125 126 0.802607 GTGAATCTCGGACACGGCTC 60.803 60.000 0.00 0.00 41.39 4.70
126 127 1.215647 GTGAATCTCGGACACGGCT 59.784 57.895 0.00 0.00 41.39 5.52
127 128 1.810030 GGTGAATCTCGGACACGGC 60.810 63.158 0.00 0.00 41.39 5.68
128 129 1.516386 CGGTGAATCTCGGACACGG 60.516 63.158 0.00 0.00 41.39 4.94
129 130 0.797249 GACGGTGAATCTCGGACACG 60.797 60.000 0.00 0.00 42.74 4.49
130 131 0.242825 TGACGGTGAATCTCGGACAC 59.757 55.000 0.00 0.00 0.00 3.67
131 132 0.242825 GTGACGGTGAATCTCGGACA 59.757 55.000 0.00 0.00 0.00 4.02
306 311 1.300233 CGGAGGTTGGCGAGATAGC 60.300 63.158 0.00 0.00 0.00 2.97
455 512 2.561956 CCGGACACGAGGTGACACT 61.562 63.158 5.39 0.00 44.60 3.55
565 623 2.800629 CGACCCAACTGTTCTGTACGTT 60.801 50.000 0.00 0.00 0.00 3.99
698 770 1.381928 GCTCTCGGTCGTGGTGGATA 61.382 60.000 0.00 0.00 0.00 2.59
726 813 0.780637 TGTGGAGAGGAGACTGGACT 59.219 55.000 0.00 0.00 44.43 3.85
727 814 0.892063 GTGTGGAGAGGAGACTGGAC 59.108 60.000 0.00 0.00 44.43 4.02
728 815 0.251832 GGTGTGGAGAGGAGACTGGA 60.252 60.000 0.00 0.00 44.43 3.86
759 858 2.281276 GGAAACCGAACGGCAGGT 60.281 61.111 13.32 0.00 43.68 4.00
762 861 2.356553 CGAGGAAACCGAACGGCA 60.357 61.111 13.32 0.00 39.32 5.69
808 915 1.986882 GGCCATGCCTTATTAGCAGT 58.013 50.000 0.00 0.00 46.69 4.40
998 1253 4.875389 TGGCTACTAGTGGTAACCTATGT 58.125 43.478 5.39 0.00 37.50 2.29
1070 1357 2.280797 GGCGGCGGCAATCAGATA 60.281 61.111 29.41 0.00 42.47 1.98
1329 3274 2.409651 GCTCAGTAGCGTCGGAGG 59.590 66.667 11.42 0.00 39.39 4.30
1372 3341 2.033755 GCAGTGAGCAGAGCAGTGG 61.034 63.158 0.00 0.00 44.79 4.00
1414 3383 0.721718 GCATCAGTACGTGGAGTTGC 59.278 55.000 0.00 0.80 0.00 4.17
1441 3444 0.321671 ACCTGATCACCAGTTCACCG 59.678 55.000 0.00 0.00 41.33 4.94
1747 4537 4.070552 GCGCGTCTCCTCCAGGTT 62.071 66.667 8.43 0.00 36.34 3.50
1767 4575 0.753479 GGAGCGGATGGTCTGAGAGA 60.753 60.000 0.00 0.00 42.30 3.10
1771 4579 2.038813 TGGGAGCGGATGGTCTGA 59.961 61.111 0.00 0.00 42.30 3.27
1776 4584 1.144936 GAAGACTGGGAGCGGATGG 59.855 63.158 0.00 0.00 0.00 3.51
1777 4585 1.144936 GGAAGACTGGGAGCGGATG 59.855 63.158 0.00 0.00 0.00 3.51
1778 4586 2.066999 GGGAAGACTGGGAGCGGAT 61.067 63.158 0.00 0.00 0.00 4.18
1779 4587 2.683933 GGGAAGACTGGGAGCGGA 60.684 66.667 0.00 0.00 0.00 5.54
1780 4588 1.915078 AATGGGAAGACTGGGAGCGG 61.915 60.000 0.00 0.00 0.00 5.52
1781 4589 0.462759 GAATGGGAAGACTGGGAGCG 60.463 60.000 0.00 0.00 0.00 5.03
1782 4590 0.106967 GGAATGGGAAGACTGGGAGC 60.107 60.000 0.00 0.00 0.00 4.70
1783 4591 1.488393 GAGGAATGGGAAGACTGGGAG 59.512 57.143 0.00 0.00 0.00 4.30
1784 4592 1.203428 TGAGGAATGGGAAGACTGGGA 60.203 52.381 0.00 0.00 0.00 4.37
1785 4593 1.065126 GTGAGGAATGGGAAGACTGGG 60.065 57.143 0.00 0.00 0.00 4.45
1786 4594 1.065126 GGTGAGGAATGGGAAGACTGG 60.065 57.143 0.00 0.00 0.00 4.00
1787 4595 1.406069 CGGTGAGGAATGGGAAGACTG 60.406 57.143 0.00 0.00 0.00 3.51
1788 4596 0.905357 CGGTGAGGAATGGGAAGACT 59.095 55.000 0.00 0.00 0.00 3.24
1789 4597 0.902531 TCGGTGAGGAATGGGAAGAC 59.097 55.000 0.00 0.00 0.00 3.01
1790 4598 1.486310 CATCGGTGAGGAATGGGAAGA 59.514 52.381 0.00 0.00 0.00 2.87
2070 4931 1.520342 GACACAGGAGGCTGCGATC 60.520 63.158 0.00 0.00 0.00 3.69
2181 5095 0.612174 AGCGAGCCTGGTTACTCAGA 60.612 55.000 0.00 0.00 36.93 3.27
2182 5096 0.459237 CAGCGAGCCTGGTTACTCAG 60.459 60.000 0.00 0.00 37.93 3.35
2189 5103 1.067071 GTACTTAACAGCGAGCCTGGT 60.067 52.381 0.00 0.00 46.14 4.00
2197 5111 4.389077 CAGGAGGAAAAGTACTTAACAGCG 59.611 45.833 8.92 0.00 0.00 5.18
2218 5134 2.568623 ACCTAGAGCACCAAAACCAG 57.431 50.000 0.00 0.00 0.00 4.00
2236 5161 9.543783 CATTACTATTCCCTTACTGAGGTTTAC 57.456 37.037 0.00 0.00 44.71 2.01
2250 6098 2.943033 AGTTGCACGCATTACTATTCCC 59.057 45.455 0.00 0.00 0.00 3.97
2264 6113 2.169832 TGGCTAGACTCAAGTTGCAC 57.830 50.000 0.00 0.00 0.00 4.57
2282 6131 8.183536 TGCTTTGACTAATTACTAACATGCATG 58.816 33.333 25.09 25.09 0.00 4.06
2286 6135 9.507280 CCATTGCTTTGACTAATTACTAACATG 57.493 33.333 0.00 0.00 0.00 3.21
2326 6176 5.924825 GTCGTCACTACCAGTTGAATAGTTT 59.075 40.000 0.00 0.00 0.00 2.66
2337 6187 2.922758 GCTCACAAGTCGTCACTACCAG 60.923 54.545 0.00 0.00 30.14 4.00
2350 6230 3.603532 TCCTATGCTTTCAGCTCACAAG 58.396 45.455 0.00 0.00 42.97 3.16
2377 6257 2.100916 TCATCCGAAATCGTTCTCTCCC 59.899 50.000 1.79 0.00 37.74 4.30
2378 6258 3.117046 GTCATCCGAAATCGTTCTCTCC 58.883 50.000 1.79 0.00 37.74 3.71
2387 6267 5.869350 AGTCGATTTTTGTCATCCGAAATC 58.131 37.500 0.00 0.00 35.95 2.17
2418 6299 4.883006 ACCGACTAGGATTGTCTCTAACTC 59.117 45.833 0.00 0.00 45.00 3.01
2500 6383 6.074463 GGTCTTATATTTACAAACGGAGCGAG 60.074 42.308 0.00 0.00 0.00 5.03
2501 6384 5.750067 GGTCTTATATTTACAAACGGAGCGA 59.250 40.000 0.00 0.00 0.00 4.93
2502 6385 5.751990 AGGTCTTATATTTACAAACGGAGCG 59.248 40.000 0.00 0.00 0.00 5.03
2522 6541 9.159364 AGTCCGTATTAACATCTTTAAAAGGTC 57.841 33.333 0.00 0.00 0.00 3.85
2579 6620 5.412594 TGGAGCAAAATGAGTGAATCTACAC 59.587 40.000 0.00 0.00 40.60 2.90
2580 6621 5.559770 TGGAGCAAAATGAGTGAATCTACA 58.440 37.500 0.00 0.00 0.00 2.74
2581 6622 6.690194 ATGGAGCAAAATGAGTGAATCTAC 57.310 37.500 0.00 0.00 0.00 2.59
2583 6624 8.985315 TTATATGGAGCAAAATGAGTGAATCT 57.015 30.769 0.00 0.00 0.00 2.40
2584 6625 8.844244 ACTTATATGGAGCAAAATGAGTGAATC 58.156 33.333 0.00 0.00 0.00 2.52
2585 6626 8.757982 ACTTATATGGAGCAAAATGAGTGAAT 57.242 30.769 0.00 0.00 0.00 2.57
2586 6627 8.579850 AACTTATATGGAGCAAAATGAGTGAA 57.420 30.769 0.00 0.00 0.00 3.18
2588 6629 8.461222 TCAAACTTATATGGAGCAAAATGAGTG 58.539 33.333 0.00 0.00 0.00 3.51
2589 6630 8.462016 GTCAAACTTATATGGAGCAAAATGAGT 58.538 33.333 0.00 0.00 0.00 3.41
2590 6631 8.461222 TGTCAAACTTATATGGAGCAAAATGAG 58.539 33.333 0.00 0.00 0.00 2.90
2591 6632 8.347004 TGTCAAACTTATATGGAGCAAAATGA 57.653 30.769 0.00 0.00 0.00 2.57
2592 6633 9.241317 GATGTCAAACTTATATGGAGCAAAATG 57.759 33.333 0.00 0.00 0.00 2.32
2593 6634 9.193806 AGATGTCAAACTTATATGGAGCAAAAT 57.806 29.630 0.00 0.00 0.00 1.82
2594 6635 8.579850 AGATGTCAAACTTATATGGAGCAAAA 57.420 30.769 0.00 0.00 0.00 2.44
2596 6637 9.330063 CTTAGATGTCAAACTTATATGGAGCAA 57.670 33.333 0.00 0.00 0.00 3.91
2597 6638 8.704668 TCTTAGATGTCAAACTTATATGGAGCA 58.295 33.333 0.00 0.00 0.00 4.26
2598 6639 9.547753 TTCTTAGATGTCAAACTTATATGGAGC 57.452 33.333 0.00 0.00 0.00 4.70
2664 6716 7.083875 TGAAATCGGCTTTCTTCGAATAAAT 57.916 32.000 8.90 0.00 43.14 1.40
2815 6876 0.370273 GCACACTATCAAGGCGTTCG 59.630 55.000 0.00 0.00 0.00 3.95
2884 7314 9.797642 TTGCACATAAATGATAGTTCTATGGAT 57.202 29.630 0.00 0.00 0.00 3.41
2885 7315 9.625747 TTTGCACATAAATGATAGTTCTATGGA 57.374 29.630 0.00 0.00 0.00 3.41
2886 7316 9.888878 CTTTGCACATAAATGATAGTTCTATGG 57.111 33.333 0.00 0.00 0.00 2.74
2890 7320 9.236006 AGAACTTTGCACATAAATGATAGTTCT 57.764 29.630 0.00 0.00 37.05 3.01
2896 7326 8.970020 TGGAATAGAACTTTGCACATAAATGAT 58.030 29.630 0.00 0.00 0.00 2.45
2897 7327 8.347004 TGGAATAGAACTTTGCACATAAATGA 57.653 30.769 0.00 0.00 0.00 2.57
2898 7328 8.461222 TCTGGAATAGAACTTTGCACATAAATG 58.539 33.333 0.00 0.00 30.84 2.32
2899 7329 8.579850 TCTGGAATAGAACTTTGCACATAAAT 57.420 30.769 0.00 0.00 30.84 1.40
2900 7330 7.994425 TCTGGAATAGAACTTTGCACATAAA 57.006 32.000 0.00 0.00 30.84 1.40
2901 7331 7.994425 TTCTGGAATAGAACTTTGCACATAA 57.006 32.000 0.00 0.00 40.43 1.90
2991 7443 2.833631 ACTCAAGTAAGGGAACACGG 57.166 50.000 0.00 0.00 0.00 4.94
3030 7483 5.065731 CAGCCAAGATTTTCTAGATGGTCAC 59.934 44.000 9.09 0.00 27.42 3.67
3031 7484 5.188434 CAGCCAAGATTTTCTAGATGGTCA 58.812 41.667 9.09 0.00 27.42 4.02
3061 7514 1.472480 GGTCAATGTGTACATGTGCCC 59.528 52.381 9.11 0.00 36.56 5.36
3112 7566 3.367292 GGCCATAATCGGTGCAAATATGG 60.367 47.826 15.08 15.08 43.74 2.74
3124 7578 9.874205 ATTTTATAAATTGGATGGCCATAATCG 57.126 29.630 20.84 0.00 45.46 3.34
3163 7617 1.869452 AAGGAGGGGGAGGAGTCCT 60.869 63.158 12.85 12.85 43.36 3.85
3168 7622 1.550374 AGGAGAAGGAGGGGGAGGA 60.550 63.158 0.00 0.00 0.00 3.71


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.