Multiple sequence alignment - TraesCS7A01G300300

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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 TraesCS7A01G300300 chr7A 100.000 4874 0 0 1 4874 416422529 416427402 0.000000e+00 9001.0
1 TraesCS7A01G300300 chr7A 88.417 259 23 2 4623 4874 702248498 702248756 6.130000e-79 305.0
2 TraesCS7A01G300300 chr7A 89.216 204 21 1 4672 4874 478588314 478588517 2.250000e-63 254.0
3 TraesCS7A01G300300 chr7B 95.112 2578 81 29 820 3374 367015332 367017887 0.000000e+00 4021.0
4 TraesCS7A01G300300 chr7B 94.982 817 33 2 3368 4184 367017995 367018803 0.000000e+00 1275.0
5 TraesCS7A01G300300 chr7B 84.507 355 45 9 1 354 366561245 366561590 4.670000e-90 342.0
6 TraesCS7A01G300300 chr7B 92.857 112 8 0 2587 2698 570465256 570465367 3.900000e-36 163.0
7 TraesCS7A01G300300 chr7B 86.508 126 13 4 2569 2693 664916955 664917077 8.510000e-28 135.0
8 TraesCS7A01G300300 chr7D 95.670 1755 57 12 838 2589 371787748 371789486 0.000000e+00 2802.0
9 TraesCS7A01G300300 chr7D 94.641 821 41 3 1 820 371784625 371785443 0.000000e+00 1269.0
10 TraesCS7A01G300300 chr7D 94.444 684 30 7 2695 3374 371789486 371790165 0.000000e+00 1046.0
11 TraesCS7A01G300300 chr7D 95.915 563 19 3 3368 3930 371790284 371790842 0.000000e+00 909.0
12 TraesCS7A01G300300 chr7D 89.174 702 50 11 3926 4623 371827586 371828265 0.000000e+00 852.0
13 TraesCS7A01G300300 chr7D 87.166 187 21 3 3 187 482701139 482700954 4.940000e-50 209.0
14 TraesCS7A01G300300 chr7D 86.170 188 24 2 1 187 315413866 315414052 8.270000e-48 202.0
15 TraesCS7A01G300300 chr7D 94.915 59 3 0 4618 4676 380186116 380186058 5.190000e-15 93.5
16 TraesCS7A01G300300 chr5A 76.649 561 90 17 188 745 312508518 312509040 6.220000e-69 272.0
17 TraesCS7A01G300300 chr5A 90.909 110 9 1 2588 2697 378505310 378505418 3.930000e-31 147.0
18 TraesCS7A01G300300 chr6D 90.686 204 18 1 4672 4874 431324588 431324791 2.240000e-68 270.0
19 TraesCS7A01G300300 chr6D 89.216 204 20 2 4672 4874 7081442 7081240 2.250000e-63 254.0
20 TraesCS7A01G300300 chr6D 88.043 184 19 3 1 182 428076090 428076272 1.060000e-51 215.0
21 TraesCS7A01G300300 chr6D 90.265 113 9 2 2588 2700 132306872 132306982 3.930000e-31 147.0
22 TraesCS7A01G300300 chr6D 100.000 52 0 0 4622 4673 3770088 3770139 4.020000e-16 97.1
23 TraesCS7A01G300300 chr6B 85.214 257 33 5 4621 4874 668143861 668144115 4.840000e-65 259.0
24 TraesCS7A01G300300 chr6B 93.519 108 7 0 2588 2695 617173819 617173712 1.400000e-35 161.0
25 TraesCS7A01G300300 chr6B 92.453 106 8 0 2588 2693 281336070 281335965 8.450000e-33 152.0
26 TraesCS7A01G300300 chr3D 89.655 203 20 1 4673 4874 520803498 520803296 1.740000e-64 257.0
27 TraesCS7A01G300300 chr3D 92.308 65 3 2 4623 4685 64288062 64287998 1.870000e-14 91.6
28 TraesCS7A01G300300 chr5D 89.268 205 18 4 4672 4874 33866809 33866607 2.250000e-63 254.0
29 TraesCS7A01G300300 chr5D 89.216 204 21 1 4672 4874 484559936 484559733 2.250000e-63 254.0
30 TraesCS7A01G300300 chr5D 88.333 60 4 2 3598 3654 532636093 532636152 8.750000e-08 69.4
31 TraesCS7A01G300300 chr1D 84.231 260 33 4 4623 4874 465355975 465356234 3.770000e-61 246.0
32 TraesCS7A01G300300 chr1D 78.141 398 68 13 188 578 221080625 221080240 8.160000e-58 235.0
33 TraesCS7A01G300300 chr1D 100.000 29 0 0 3612 3640 258092032 258092060 2.000000e-03 54.7
34 TraesCS7A01G300300 chr6A 88.830 188 16 4 1 187 211635177 211635360 4.910000e-55 226.0
35 TraesCS7A01G300300 chr6A 86.702 188 22 3 1 187 42001410 42001225 6.390000e-49 206.0
36 TraesCS7A01G300300 chr6A 96.491 57 2 0 4617 4673 196008871 196008927 1.440000e-15 95.3
37 TraesCS7A01G300300 chr5B 86.702 188 22 3 1 187 415675606 415675791 6.390000e-49 206.0
38 TraesCS7A01G300300 chr4B 86.957 184 21 3 4 185 182804266 182804084 2.300000e-48 204.0
39 TraesCS7A01G300300 chr4B 91.509 106 8 1 2588 2693 585803174 585803070 1.410000e-30 145.0
40 TraesCS7A01G300300 chr1A 86.667 135 15 3 435 567 285652442 285652309 3.930000e-31 147.0
41 TraesCS7A01G300300 chr1A 100.000 29 0 0 3612 3640 343421472 343421444 2.000000e-03 54.7
42 TraesCS7A01G300300 chr2B 82.667 150 19 5 2554 2699 476564389 476564243 5.120000e-25 126.0
43 TraesCS7A01G300300 chr2B 83.721 129 19 2 430 558 102121705 102121831 2.380000e-23 121.0
44 TraesCS7A01G300300 chr2D 83.740 123 17 2 640 759 68731206 68731328 3.990000e-21 113.0
45 TraesCS7A01G300300 chrUn 98.182 55 1 0 4619 4673 81909400 81909454 4.020000e-16 97.1
46 TraesCS7A01G300300 chr4D 100.000 51 0 0 4623 4673 246473204 246473154 1.440000e-15 95.3
47 TraesCS7A01G300300 chr1B 100.000 29 0 0 3612 3640 354987460 354987432 2.000000e-03 54.7


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 TraesCS7A01G300300 chr7A 416422529 416427402 4873 False 9001.0 9001 100.0000 1 4874 1 chr7A.!!$F1 4873
1 TraesCS7A01G300300 chr7B 367015332 367018803 3471 False 2648.0 4021 95.0470 820 4184 2 chr7B.!!$F4 3364
2 TraesCS7A01G300300 chr7D 371784625 371790842 6217 False 1506.5 2802 95.1675 1 3930 4 chr7D.!!$F3 3929
3 TraesCS7A01G300300 chr7D 371827586 371828265 679 False 852.0 852 89.1740 3926 4623 1 chr7D.!!$F2 697
4 TraesCS7A01G300300 chr5A 312508518 312509040 522 False 272.0 272 76.6490 188 745 1 chr5A.!!$F1 557

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
230 232 0.478072 ATGAGAGTGCCAACCCAACA 59.522 50.0 0.0 0.0 0.0 3.33 F
994 3288 0.674895 GAAGGAAGTGCAGTGCGGAT 60.675 55.0 11.2 0.0 0.0 4.18 F
995 3289 0.957395 AAGGAAGTGCAGTGCGGATG 60.957 55.0 11.2 0.0 0.0 3.51 F
2067 4374 1.151668 CAGCCTCAACCTTGTCTTCG 58.848 55.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1399 3696 0.178975 AATTGGTGGACTTGCGGGAA 60.179 50.000 0.00 0.0 0.00 3.97 R
2067 4374 2.454538 TCTTCCTCCGGTTCCTAAGAC 58.545 52.381 0.00 0.0 0.00 3.01 R
2667 4979 3.187700 CTCCTTCCCGAATTACTTGTCG 58.812 50.000 0.00 0.0 37.01 4.35 R
3905 6347 0.236711 CCGTGCAGCAAGAGAACAAG 59.763 55.000 10.26 0.0 0.00 3.16 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
40 41 5.007039 CACTATGTCATCTTGCTTAATGCGT 59.993 40.000 0.00 0.00 46.63 5.24
48 49 5.530519 TCTTGCTTAATGCGTTTACTCTG 57.469 39.130 0.00 0.00 46.63 3.35
82 83 8.737168 AACTTAATACTTTGAGATGCATGCTA 57.263 30.769 20.33 5.73 0.00 3.49
103 104 2.428890 AGATAGCGGTCTTGAGTTGGAG 59.571 50.000 0.00 0.00 0.00 3.86
108 109 2.673368 GCGGTCTTGAGTTGGAGTAATG 59.327 50.000 0.00 0.00 0.00 1.90
109 110 3.864921 GCGGTCTTGAGTTGGAGTAATGT 60.865 47.826 0.00 0.00 0.00 2.71
110 111 4.619863 GCGGTCTTGAGTTGGAGTAATGTA 60.620 45.833 0.00 0.00 0.00 2.29
111 112 5.103000 CGGTCTTGAGTTGGAGTAATGTAG 58.897 45.833 0.00 0.00 0.00 2.74
112 113 5.336531 CGGTCTTGAGTTGGAGTAATGTAGT 60.337 44.000 0.00 0.00 0.00 2.73
113 114 6.127814 CGGTCTTGAGTTGGAGTAATGTAGTA 60.128 42.308 0.00 0.00 0.00 1.82
114 115 7.259161 GGTCTTGAGTTGGAGTAATGTAGTAG 58.741 42.308 0.00 0.00 0.00 2.57
115 116 7.122353 GGTCTTGAGTTGGAGTAATGTAGTAGA 59.878 40.741 0.00 0.00 0.00 2.59
116 117 7.969508 GTCTTGAGTTGGAGTAATGTAGTAGAC 59.030 40.741 0.00 0.00 0.00 2.59
117 118 7.668469 TCTTGAGTTGGAGTAATGTAGTAGACA 59.332 37.037 0.00 0.00 43.97 3.41
145 147 8.828688 AGTAAGTTGAATGGTCTACTTGTTAC 57.171 34.615 11.97 4.80 45.55 2.50
150 152 3.881937 ATGGTCTACTTGTTACGGACC 57.118 47.619 0.00 0.00 44.57 4.46
208 210 8.292444 TCTTGGGTTAAGAAATATGGTCATTG 57.708 34.615 0.00 0.00 42.31 2.82
230 232 0.478072 ATGAGAGTGCCAACCCAACA 59.522 50.000 0.00 0.00 0.00 3.33
236 238 1.064314 AGTGCCAACCCAACACACTTA 60.064 47.619 0.00 0.00 38.38 2.24
265 267 4.314740 TTGTCTTTTCACCGAAATTGGG 57.685 40.909 0.00 0.00 31.34 4.12
274 276 3.009695 TCACCGAAATTGGGGTATCTTGT 59.990 43.478 0.00 0.00 33.95 3.16
294 296 2.503869 AGATGCCCCCTATCTTCAGT 57.496 50.000 0.00 0.00 30.98 3.41
310 312 2.183555 GTAAGCACCTCGTCCCCG 59.816 66.667 0.00 0.00 0.00 5.73
341 343 0.677288 TCACCCTCACGACGAACAAT 59.323 50.000 0.00 0.00 0.00 2.71
375 377 2.762043 TCACCGCCCGGATGATCA 60.762 61.111 14.44 0.00 38.96 2.92
472 474 0.836606 TCAAGTTGGTGAGTCCTGCA 59.163 50.000 2.34 0.00 37.07 4.41
476 478 1.212935 AGTTGGTGAGTCCTGCAAACT 59.787 47.619 1.17 1.17 37.07 2.66
499 501 5.089970 TGAAGGTGATCGTCTTCATCAAT 57.910 39.130 19.96 0.00 42.81 2.57
580 582 3.726790 TGAGGGTGCTTAGGGTGTTATA 58.273 45.455 0.00 0.00 0.00 0.98
633 635 7.225931 GTCATGTTTGAAGACTTTGTGGTACTA 59.774 37.037 0.00 0.00 32.48 1.82
745 748 6.763610 TGACTATTATGTTGTTGTGTGTGTGA 59.236 34.615 0.00 0.00 0.00 3.58
771 774 5.070714 GGTAAACCCACCAAAAAGTTACCAT 59.929 40.000 0.00 0.00 38.55 3.55
812 815 4.989279 ACCAAGCAAACATATAGGCAAG 57.011 40.909 0.00 0.00 0.00 4.01
876 3165 1.002134 ATGGTTTGAGTCGGGCCAG 60.002 57.895 4.39 0.00 32.28 4.85
986 3280 2.592993 CCCCGAGGAAGGAAGTGCA 61.593 63.158 0.00 0.00 33.47 4.57
993 3287 1.301716 GAAGGAAGTGCAGTGCGGA 60.302 57.895 11.20 0.00 0.00 5.54
994 3288 0.674895 GAAGGAAGTGCAGTGCGGAT 60.675 55.000 11.20 0.00 0.00 4.18
995 3289 0.957395 AAGGAAGTGCAGTGCGGATG 60.957 55.000 11.20 0.00 0.00 3.51
997 3291 3.044059 GAAGTGCAGTGCGGATGGC 62.044 63.158 11.20 0.00 43.96 4.40
1078 3372 4.074526 GCCTCTGCTCAGCCGACA 62.075 66.667 0.00 0.00 33.53 4.35
1119 3413 2.750166 CTGTCATACGTCACTCCACTCT 59.250 50.000 0.00 0.00 0.00 3.24
1180 3474 1.396301 CGACATGCTTTGCTTCTCTCC 59.604 52.381 0.00 0.00 0.00 3.71
1292 3588 2.438795 CCGGTCCACAAACCCCAT 59.561 61.111 0.00 0.00 35.79 4.00
1301 3597 1.287739 CACAAACCCCATACCCTCCAT 59.712 52.381 0.00 0.00 0.00 3.41
1302 3598 1.569072 ACAAACCCCATACCCTCCATC 59.431 52.381 0.00 0.00 0.00 3.51
1303 3599 1.852965 CAAACCCCATACCCTCCATCT 59.147 52.381 0.00 0.00 0.00 2.90
1304 3600 2.244769 CAAACCCCATACCCTCCATCTT 59.755 50.000 0.00 0.00 0.00 2.40
1305 3601 3.448277 AACCCCATACCCTCCATCTTA 57.552 47.619 0.00 0.00 0.00 2.10
1306 3602 3.674358 ACCCCATACCCTCCATCTTAT 57.326 47.619 0.00 0.00 0.00 1.73
1316 3613 4.837860 ACCCTCCATCTTATCTCATCTCAC 59.162 45.833 0.00 0.00 0.00 3.51
1402 3699 1.327303 TGTGGGCACAACAGATTTCC 58.673 50.000 0.00 0.00 38.56 3.13
1556 3853 6.207928 TGTTGTTGTTGATTTCTGCAGTATG 58.792 36.000 14.67 0.00 40.87 2.39
1572 3869 4.337555 GCAGTATGTCAGGAATGCATTCTT 59.662 41.667 32.48 25.73 39.31 2.52
1592 3889 4.701651 TCTTCATGATTGGACGCATCTTTT 59.298 37.500 0.00 0.00 0.00 2.27
1601 3898 4.832248 TGGACGCATCTTTTTAGTCATCT 58.168 39.130 0.00 0.00 33.84 2.90
1602 3899 5.972935 TGGACGCATCTTTTTAGTCATCTA 58.027 37.500 0.00 0.00 33.84 1.98
1758 4055 3.187227 GTCAGCGTCATGTCAATCAAACT 59.813 43.478 0.00 0.00 0.00 2.66
1797 4094 3.791245 TCCAAACACTGCATTTTGTTCC 58.209 40.909 8.47 0.00 34.82 3.62
1970 4270 3.670055 GCATGTGTGTGTATGCTGAAAAC 59.330 43.478 0.00 0.00 44.70 2.43
2067 4374 1.151668 CAGCCTCAACCTTGTCTTCG 58.848 55.000 0.00 0.00 0.00 3.79
2191 4498 3.732212 TCAGATGCCCGTTATCTCATTG 58.268 45.455 0.00 0.00 32.75 2.82
2328 4636 6.390721 GCTGAAGACCGCTTATATAATCAGA 58.609 40.000 17.98 0.00 33.61 3.27
2406 4714 9.132923 TCTGTACCTCTAATACACTCCTTTATG 57.867 37.037 0.00 0.00 0.00 1.90
2450 4762 8.289939 ACTCGTACTGATCCAACTTATCTTTA 57.710 34.615 0.00 0.00 0.00 1.85
2551 4863 5.185056 TGGTTAAGCCCTTTCTAATGCTTTC 59.815 40.000 1.51 0.00 40.98 2.62
2597 4909 9.442062 TTCTAATGTTAATATGTACTCCCTCCA 57.558 33.333 0.00 0.00 0.00 3.86
2614 4926 3.555956 CCTCCATTCCGAATTACTTGTCG 59.444 47.826 0.00 0.00 37.01 4.35
2617 4929 3.126171 CCATTCCGAATTACTTGTCGCAA 59.874 43.478 0.00 0.00 35.93 4.85
2633 4945 6.603237 TGTCGCAAAAATGGATGTATCTAG 57.397 37.500 0.00 0.00 0.00 2.43
2635 4947 6.821160 TGTCGCAAAAATGGATGTATCTAGAA 59.179 34.615 0.00 0.00 0.00 2.10
2639 4951 8.826710 CGCAAAAATGGATGTATCTAGAACTAA 58.173 33.333 0.00 0.00 0.00 2.24
2684 4996 2.028839 TCTGCGACAAGTAATTCGGGAA 60.029 45.455 0.00 0.00 35.73 3.97
2693 5005 1.129058 TAATTCGGGAAGGAGGGAGC 58.871 55.000 0.00 0.00 0.00 4.70
2866 5179 7.678837 TCAAAGCTTGATCAAACCCATATTTT 58.321 30.769 9.88 0.00 34.08 1.82
2873 5186 9.270640 CTTGATCAAACCCATATTTTCAAAACA 57.729 29.630 9.88 0.00 0.00 2.83
2965 5280 0.907486 TCCCTCAGAGTGCATTCCAG 59.093 55.000 5.47 2.38 0.00 3.86
3046 5361 4.456911 CAGGTGTGTCTGCTATTTGTCAAT 59.543 41.667 0.00 0.00 0.00 2.57
3068 5383 4.746535 TTTCAGAGTCTGTGGTGTGTTA 57.253 40.909 19.53 0.00 32.61 2.41
3147 5464 4.742167 CGTAGCCTTCAGAGTATTCATGTG 59.258 45.833 0.00 0.00 0.00 3.21
3189 5506 7.944061 TCATCATTTATATTTGAAGCCACCTG 58.056 34.615 0.00 0.00 0.00 4.00
3255 5572 6.819146 TGCATGACTAACGATATGTTTTGGTA 59.181 34.615 0.00 0.00 42.09 3.25
3381 5823 6.202954 GTGTTAAGCATGTACTCCATATGGAC 59.797 42.308 20.98 12.38 39.78 4.02
3528 5970 4.839668 AAACCAGTACGCTTATTGCAAA 57.160 36.364 1.71 0.00 43.06 3.68
3566 6008 1.299541 GTGCGTTATGGACCATCTGG 58.700 55.000 11.17 2.21 42.17 3.86
3588 6030 7.119699 TCTGGCAATGTTAAGAGTCAATTACTG 59.880 37.037 0.00 0.00 39.07 2.74
3589 6031 6.939730 TGGCAATGTTAAGAGTCAATTACTGA 59.060 34.615 0.00 0.00 39.07 3.41
3590 6032 7.611467 TGGCAATGTTAAGAGTCAATTACTGAT 59.389 33.333 0.00 0.00 39.07 2.90
3591 6033 8.462016 GGCAATGTTAAGAGTCAATTACTGATT 58.538 33.333 0.00 0.00 39.07 2.57
3610 6052 8.617290 ACTGATTAACTTTGTACTAAACCAGG 57.383 34.615 0.00 0.00 0.00 4.45
3611 6053 7.664318 ACTGATTAACTTTGTACTAAACCAGGG 59.336 37.037 0.00 0.00 0.00 4.45
3628 6070 6.786843 ACCAGGGTCAATTAATATGGATCT 57.213 37.500 0.00 0.00 0.00 2.75
3702 6144 0.899717 GCATTGCCCCTCCAACTTCA 60.900 55.000 0.00 0.00 0.00 3.02
3710 6152 1.408266 CCCTCCAACTTCAATACCGGG 60.408 57.143 6.32 0.00 0.00 5.73
3753 6195 4.624364 CAGGACACGCACAGGGCA 62.624 66.667 0.00 0.00 45.17 5.36
3905 6347 2.376032 GTTGCTTGCTTGTCTCGTTTC 58.624 47.619 0.00 0.00 0.00 2.78
3915 6357 4.271291 GCTTGTCTCGTTTCTTGTTCTCTT 59.729 41.667 0.00 0.00 0.00 2.85
3922 6364 3.366719 GTTTCTTGTTCTCTTGCTGCAC 58.633 45.455 0.00 0.00 0.00 4.57
3952 6394 2.333706 GACGAGGCTACTGGTACGGC 62.334 65.000 0.00 0.00 39.14 5.68
3967 6409 0.317479 ACGGCAGTGTAAGTGTCTCC 59.683 55.000 0.00 0.00 40.50 3.71
4026 6468 2.485479 GCTGGTGAGGTCTGAACTTTGA 60.485 50.000 0.00 0.00 0.00 2.69
4027 6469 3.808728 CTGGTGAGGTCTGAACTTTGAA 58.191 45.455 0.00 0.00 0.00 2.69
4028 6470 4.199310 CTGGTGAGGTCTGAACTTTGAAA 58.801 43.478 0.00 0.00 0.00 2.69
4029 6471 4.594970 TGGTGAGGTCTGAACTTTGAAAA 58.405 39.130 0.00 0.00 0.00 2.29
4034 6476 6.693113 GTGAGGTCTGAACTTTGAAAAACATC 59.307 38.462 0.00 0.00 0.00 3.06
4269 6711 5.178252 CGGCGATCAGTATTCATCAGAAAAT 59.822 40.000 0.00 0.00 37.29 1.82
4320 6762 1.856265 GCACCTGCCTTTTCCGTCAG 61.856 60.000 0.00 0.00 34.31 3.51
4335 6777 2.228822 CCGTCAGAAAAATCACAAGGGG 59.771 50.000 0.00 0.00 0.00 4.79
4370 6812 8.182881 AGTGTACAGAAGTTATTTAGCGAGTAG 58.817 37.037 0.00 0.00 0.00 2.57
4388 6832 7.039644 AGCGAGTAGATAGCATAAAACTACCAT 60.040 37.037 0.00 0.00 35.48 3.55
4390 6834 9.776158 CGAGTAGATAGCATAAAACTACCATAG 57.224 37.037 0.00 0.00 35.48 2.23
4406 6850 3.740115 CCATAGTTTGGGTAGGATTCCG 58.260 50.000 0.00 0.00 42.33 4.30
4407 6851 3.389983 CCATAGTTTGGGTAGGATTCCGA 59.610 47.826 0.00 0.00 42.33 4.55
4408 6852 4.141574 CCATAGTTTGGGTAGGATTCCGAA 60.142 45.833 0.00 0.00 42.33 4.30
4409 6853 5.433526 CATAGTTTGGGTAGGATTCCGAAA 58.566 41.667 0.00 0.00 32.04 3.46
4410 6854 4.376225 AGTTTGGGTAGGATTCCGAAAA 57.624 40.909 0.00 0.00 35.23 2.29
4411 6855 4.732065 AGTTTGGGTAGGATTCCGAAAAA 58.268 39.130 0.00 0.00 35.23 1.94
4412 6856 4.521639 AGTTTGGGTAGGATTCCGAAAAAC 59.478 41.667 0.00 5.90 35.23 2.43
4413 6857 4.376225 TTGGGTAGGATTCCGAAAAACT 57.624 40.909 0.00 0.00 0.00 2.66
4414 6858 3.681593 TGGGTAGGATTCCGAAAAACTG 58.318 45.455 0.00 0.00 0.00 3.16
4415 6859 3.328343 TGGGTAGGATTCCGAAAAACTGA 59.672 43.478 0.00 0.00 0.00 3.41
4416 6860 3.688185 GGGTAGGATTCCGAAAAACTGAC 59.312 47.826 0.00 0.00 0.00 3.51
4417 6861 4.320870 GGTAGGATTCCGAAAAACTGACA 58.679 43.478 0.00 0.00 0.00 3.58
4418 6862 4.153655 GGTAGGATTCCGAAAAACTGACAC 59.846 45.833 0.00 0.00 0.00 3.67
4500 6944 5.998981 TGTTGAATCCTTACGTTGTAATGGT 59.001 36.000 0.00 0.00 0.00 3.55
4502 6946 4.938832 TGAATCCTTACGTTGTAATGGTGG 59.061 41.667 0.00 0.00 0.00 4.61
4505 6949 4.317488 TCCTTACGTTGTAATGGTGGTTC 58.683 43.478 0.00 0.00 0.00 3.62
4511 6955 3.751175 CGTTGTAATGGTGGTTCTGACAT 59.249 43.478 0.00 0.00 0.00 3.06
4517 6961 0.962356 GGTGGTTCTGACATGCCTGG 60.962 60.000 0.00 0.00 0.00 4.45
4518 6962 0.036732 GTGGTTCTGACATGCCTGGA 59.963 55.000 0.00 0.00 0.00 3.86
4525 6969 1.377725 GACATGCCTGGACCACCTG 60.378 63.158 0.00 0.00 37.04 4.00
4535 6979 2.532715 ACCACCTGTCAGGGCCAT 60.533 61.111 23.06 0.00 40.58 4.40
4536 6980 2.044650 CCACCTGTCAGGGCCATG 60.045 66.667 23.06 12.23 40.58 3.66
4538 6982 1.377725 CACCTGTCAGGGCCATGTC 60.378 63.158 23.06 12.90 40.58 3.06
4557 7001 3.450115 GCTAGGGACAGACGGCGT 61.450 66.667 14.65 14.65 0.00 5.68
4587 7033 3.376078 TCGTTAGGGCGCCGTTCT 61.376 61.111 28.71 18.01 0.00 3.01
4590 7036 1.153429 GTTAGGGCGCCGTTCTGAT 60.153 57.895 28.71 5.65 0.00 2.90
4592 7038 2.622903 TTAGGGCGCCGTTCTGATCG 62.623 60.000 28.71 1.25 0.00 3.69
4623 7069 1.522092 CCAAGCCGGCTCACTATCA 59.478 57.895 32.93 0.00 0.00 2.15
4624 7070 0.811616 CCAAGCCGGCTCACTATCAC 60.812 60.000 32.93 0.00 0.00 3.06
4625 7071 0.176680 CAAGCCGGCTCACTATCACT 59.823 55.000 32.93 7.72 0.00 3.41
4626 7072 1.409064 CAAGCCGGCTCACTATCACTA 59.591 52.381 32.93 0.00 0.00 2.74
4627 7073 1.323412 AGCCGGCTCACTATCACTAG 58.677 55.000 27.08 0.00 0.00 2.57
4628 7074 1.033574 GCCGGCTCACTATCACTAGT 58.966 55.000 22.15 0.00 38.79 2.57
4637 7083 3.439293 CACTATCACTAGTGCAGAACCG 58.561 50.000 23.37 9.66 46.13 4.44
4638 7084 2.427453 ACTATCACTAGTGCAGAACCGG 59.573 50.000 23.37 0.00 36.81 5.28
4639 7085 0.537188 ATCACTAGTGCAGAACCGGG 59.463 55.000 18.45 0.00 0.00 5.73
4640 7086 0.541063 TCACTAGTGCAGAACCGGGA 60.541 55.000 18.45 0.00 0.00 5.14
4641 7087 0.537188 CACTAGTGCAGAACCGGGAT 59.463 55.000 10.54 0.00 0.00 3.85
4642 7088 1.754803 CACTAGTGCAGAACCGGGATA 59.245 52.381 10.54 0.00 0.00 2.59
4643 7089 2.365617 CACTAGTGCAGAACCGGGATAT 59.634 50.000 10.54 0.00 0.00 1.63
4644 7090 3.572682 CACTAGTGCAGAACCGGGATATA 59.427 47.826 10.54 0.00 0.00 0.86
4645 7091 3.827302 ACTAGTGCAGAACCGGGATATAG 59.173 47.826 6.32 0.00 0.00 1.31
4646 7092 1.344763 AGTGCAGAACCGGGATATAGC 59.655 52.381 6.32 2.35 0.00 2.97
4647 7093 1.070134 GTGCAGAACCGGGATATAGCA 59.930 52.381 6.32 5.36 0.00 3.49
4648 7094 1.070134 TGCAGAACCGGGATATAGCAC 59.930 52.381 6.32 0.00 0.00 4.40
4649 7095 1.608283 GCAGAACCGGGATATAGCACC 60.608 57.143 6.32 0.00 0.00 5.01
4650 7096 0.966920 AGAACCGGGATATAGCACCG 59.033 55.000 6.32 9.96 46.79 4.94
4654 7100 3.509388 CGGGATATAGCACCGGTTC 57.491 57.895 2.97 0.00 43.69 3.62
4655 7101 0.388134 CGGGATATAGCACCGGTTCG 60.388 60.000 2.97 0.00 43.69 3.95
4656 7102 0.677842 GGGATATAGCACCGGTTCGT 59.322 55.000 2.97 0.00 0.00 3.85
4657 7103 1.888512 GGGATATAGCACCGGTTCGTA 59.111 52.381 2.97 0.00 0.00 3.43
4658 7104 2.297033 GGGATATAGCACCGGTTCGTAA 59.703 50.000 2.97 0.00 0.00 3.18
4659 7105 3.572584 GGATATAGCACCGGTTCGTAAG 58.427 50.000 2.97 0.00 0.00 2.34
4660 7106 3.572584 GATATAGCACCGGTTCGTAAGG 58.427 50.000 2.97 0.00 38.47 2.69
4661 7107 0.462789 ATAGCACCGGTTCGTAAGGG 59.537 55.000 2.97 0.00 38.47 3.95
4662 7108 2.229690 TAGCACCGGTTCGTAAGGGC 62.230 60.000 2.97 1.90 38.47 5.19
4663 7109 2.435410 CACCGGTTCGTAAGGGCC 60.435 66.667 2.97 0.00 38.47 5.80
4664 7110 2.605601 ACCGGTTCGTAAGGGCCT 60.606 61.111 0.00 0.00 38.47 5.19
4665 7111 2.219164 ACCGGTTCGTAAGGGCCTT 61.219 57.895 24.44 24.44 38.47 4.35
4666 7112 1.002990 CCGGTTCGTAAGGGCCTTT 60.003 57.895 26.29 5.08 38.47 3.11
4667 7113 0.249955 CCGGTTCGTAAGGGCCTTTA 59.750 55.000 26.29 2.60 38.47 1.85
4668 7114 1.648504 CGGTTCGTAAGGGCCTTTAG 58.351 55.000 26.29 18.30 38.47 1.85
4669 7115 1.066645 CGGTTCGTAAGGGCCTTTAGT 60.067 52.381 26.29 1.50 38.47 2.24
4670 7116 2.353323 GGTTCGTAAGGGCCTTTAGTG 58.647 52.381 26.29 11.88 38.47 2.74
4671 7117 1.736126 GTTCGTAAGGGCCTTTAGTGC 59.264 52.381 26.29 8.97 38.47 4.40
4681 7127 4.913335 GGCCTTTAGTGCCCTTTAATAC 57.087 45.455 0.00 0.00 43.33 1.89
4682 7128 3.635373 GGCCTTTAGTGCCCTTTAATACC 59.365 47.826 0.00 0.00 43.33 2.73
4683 7129 3.314357 GCCTTTAGTGCCCTTTAATACCG 59.686 47.826 0.00 0.00 0.00 4.02
4684 7130 3.881089 CCTTTAGTGCCCTTTAATACCGG 59.119 47.826 0.00 0.00 0.00 5.28
4685 7131 4.520179 CTTTAGTGCCCTTTAATACCGGT 58.480 43.478 13.98 13.98 0.00 5.28
4686 7132 4.573021 TTAGTGCCCTTTAATACCGGTT 57.427 40.909 15.04 0.00 0.00 4.44
4687 7133 3.444792 AGTGCCCTTTAATACCGGTTT 57.555 42.857 15.04 9.90 0.00 3.27
4688 7134 3.770046 AGTGCCCTTTAATACCGGTTTT 58.230 40.909 15.04 14.93 0.00 2.43
4689 7135 3.508402 AGTGCCCTTTAATACCGGTTTTG 59.492 43.478 15.04 0.00 0.00 2.44
4690 7136 2.231721 TGCCCTTTAATACCGGTTTTGC 59.768 45.455 15.04 11.20 0.00 3.68
4691 7137 2.231721 GCCCTTTAATACCGGTTTTGCA 59.768 45.455 15.04 0.00 0.00 4.08
4692 7138 3.840468 CCCTTTAATACCGGTTTTGCAC 58.160 45.455 15.04 0.00 0.00 4.57
4693 7139 3.494232 CCTTTAATACCGGTTTTGCACG 58.506 45.455 15.04 0.42 0.00 5.34
4694 7140 3.188873 CCTTTAATACCGGTTTTGCACGA 59.811 43.478 15.04 0.00 0.00 4.35
4695 7141 4.320348 CCTTTAATACCGGTTTTGCACGAA 60.320 41.667 15.04 0.00 0.00 3.85
4696 7142 2.691984 AATACCGGTTTTGCACGAAC 57.308 45.000 15.04 4.01 0.00 3.95
4697 7143 0.876399 ATACCGGTTTTGCACGAACC 59.124 50.000 15.04 17.39 42.47 3.62
4700 7146 2.719354 GGTTTTGCACGAACCGCT 59.281 55.556 13.69 0.00 37.41 5.52
4701 7147 1.657181 GGTTTTGCACGAACCGCTG 60.657 57.895 13.69 0.00 37.41 5.18
4702 7148 2.025441 TTTTGCACGAACCGCTGC 59.975 55.556 0.00 0.00 35.63 5.25
4703 7149 2.477176 TTTTGCACGAACCGCTGCT 61.477 52.632 0.00 0.00 35.89 4.24
4704 7150 1.160946 TTTTGCACGAACCGCTGCTA 61.161 50.000 0.00 5.33 35.89 3.49
4705 7151 1.160946 TTTGCACGAACCGCTGCTAA 61.161 50.000 0.00 9.45 35.89 3.09
4706 7152 1.160946 TTGCACGAACCGCTGCTAAA 61.161 50.000 0.00 1.60 35.89 1.85
4707 7153 1.132640 GCACGAACCGCTGCTAAAG 59.867 57.895 0.00 0.00 33.64 1.85
4708 7154 1.289109 GCACGAACCGCTGCTAAAGA 61.289 55.000 0.00 0.00 33.64 2.52
4709 7155 0.716108 CACGAACCGCTGCTAAAGAG 59.284 55.000 0.00 0.00 0.00 2.85
4762 7208 3.242549 GGAGACCTTTAGTACCGGTTG 57.757 52.381 15.04 0.00 0.00 3.77
4763 7209 2.093816 GGAGACCTTTAGTACCGGTTGG 60.094 54.545 15.04 8.59 42.84 3.77
4791 7237 4.664188 CCGACCGGTATTAAAATGTTTGG 58.336 43.478 7.34 0.00 0.00 3.28
4792 7238 4.395542 CCGACCGGTATTAAAATGTTTGGA 59.604 41.667 7.34 0.00 0.00 3.53
4793 7239 5.448089 CCGACCGGTATTAAAATGTTTGGAG 60.448 44.000 7.34 0.00 0.00 3.86
4794 7240 5.448089 CGACCGGTATTAAAATGTTTGGAGG 60.448 44.000 7.34 0.00 0.00 4.30
4795 7241 4.707934 ACCGGTATTAAAATGTTTGGAGGG 59.292 41.667 4.49 0.00 0.00 4.30
4796 7242 4.707934 CCGGTATTAAAATGTTTGGAGGGT 59.292 41.667 0.00 0.00 0.00 4.34
4797 7243 5.186215 CCGGTATTAAAATGTTTGGAGGGTT 59.814 40.000 0.00 0.00 0.00 4.11
4798 7244 6.295405 CCGGTATTAAAATGTTTGGAGGGTTT 60.295 38.462 0.00 0.00 0.00 3.27
4799 7245 7.156000 CGGTATTAAAATGTTTGGAGGGTTTT 58.844 34.615 0.00 0.00 0.00 2.43
4800 7246 7.117092 CGGTATTAAAATGTTTGGAGGGTTTTG 59.883 37.037 0.00 0.00 0.00 2.44
4801 7247 8.151596 GGTATTAAAATGTTTGGAGGGTTTTGA 58.848 33.333 0.00 0.00 0.00 2.69
4802 7248 9.719355 GTATTAAAATGTTTGGAGGGTTTTGAT 57.281 29.630 0.00 0.00 0.00 2.57
4804 7250 9.639563 ATTAAAATGTTTGGAGGGTTTTGATTT 57.360 25.926 0.00 0.00 0.00 2.17
4805 7251 7.953005 AAAATGTTTGGAGGGTTTTGATTTT 57.047 28.000 0.00 0.00 0.00 1.82
4807 7253 9.639563 AAAATGTTTGGAGGGTTTTGATTTTAT 57.360 25.926 0.00 0.00 0.00 1.40
4808 7254 8.620116 AATGTTTGGAGGGTTTTGATTTTATG 57.380 30.769 0.00 0.00 0.00 1.90
4809 7255 7.366847 TGTTTGGAGGGTTTTGATTTTATGA 57.633 32.000 0.00 0.00 0.00 2.15
4810 7256 7.972301 TGTTTGGAGGGTTTTGATTTTATGAT 58.028 30.769 0.00 0.00 0.00 2.45
4811 7257 8.093927 TGTTTGGAGGGTTTTGATTTTATGATC 58.906 33.333 0.00 0.00 0.00 2.92
4812 7258 8.314021 GTTTGGAGGGTTTTGATTTTATGATCT 58.686 33.333 0.00 0.00 0.00 2.75
4813 7259 9.540538 TTTGGAGGGTTTTGATTTTATGATCTA 57.459 29.630 0.00 0.00 0.00 1.98
4814 7260 9.713684 TTGGAGGGTTTTGATTTTATGATCTAT 57.286 29.630 0.00 0.00 0.00 1.98
4815 7261 9.713684 TGGAGGGTTTTGATTTTATGATCTATT 57.286 29.630 0.00 0.00 0.00 1.73
4861 7307 9.913451 TTTCATTTAATTCTTTTTCGTTTGCTG 57.087 25.926 0.00 0.00 0.00 4.41
4862 7308 8.071122 TCATTTAATTCTTTTTCGTTTGCTGG 57.929 30.769 0.00 0.00 0.00 4.85
4863 7309 7.708752 TCATTTAATTCTTTTTCGTTTGCTGGT 59.291 29.630 0.00 0.00 0.00 4.00
4864 7310 8.973378 CATTTAATTCTTTTTCGTTTGCTGGTA 58.027 29.630 0.00 0.00 0.00 3.25
4865 7311 9.705290 ATTTAATTCTTTTTCGTTTGCTGGTAT 57.295 25.926 0.00 0.00 0.00 2.73
4866 7312 9.535878 TTTAATTCTTTTTCGTTTGCTGGTATT 57.464 25.926 0.00 0.00 0.00 1.89
4867 7313 9.535878 TTAATTCTTTTTCGTTTGCTGGTATTT 57.464 25.926 0.00 0.00 0.00 1.40
4868 7314 8.432110 AATTCTTTTTCGTTTGCTGGTATTTT 57.568 26.923 0.00 0.00 0.00 1.82
4869 7315 9.535878 AATTCTTTTTCGTTTGCTGGTATTTTA 57.464 25.926 0.00 0.00 0.00 1.52
4870 7316 7.917720 TCTTTTTCGTTTGCTGGTATTTTAC 57.082 32.000 0.00 0.00 0.00 2.01
4871 7317 6.633634 TCTTTTTCGTTTGCTGGTATTTTACG 59.366 34.615 0.00 0.00 0.00 3.18
4872 7318 5.670149 TTTCGTTTGCTGGTATTTTACGA 57.330 34.783 0.00 0.00 35.11 3.43
4873 7319 5.866335 TTCGTTTGCTGGTATTTTACGAT 57.134 34.783 0.00 0.00 36.58 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 5.663795 ACGCATTAAGCAAGATGACATAG 57.336 39.130 0.00 0.00 46.13 2.23
82 83 2.428890 CTCCAACTCAAGACCGCTATCT 59.571 50.000 0.00 0.00 0.00 1.98
110 111 9.036980 AGACCATTCAACTTACTAATGTCTACT 57.963 33.333 0.00 0.00 0.00 2.57
113 114 9.036980 AGTAGACCATTCAACTTACTAATGTCT 57.963 33.333 0.00 0.00 31.79 3.41
114 115 9.654663 AAGTAGACCATTCAACTTACTAATGTC 57.345 33.333 0.00 0.00 30.62 3.06
115 116 9.436957 CAAGTAGACCATTCAACTTACTAATGT 57.563 33.333 0.00 0.00 31.20 2.71
116 117 9.436957 ACAAGTAGACCATTCAACTTACTAATG 57.563 33.333 0.00 0.00 31.20 1.90
124 126 5.011329 TCCGTAACAAGTAGACCATTCAACT 59.989 40.000 0.00 0.00 0.00 3.16
177 179 6.015940 CCATATTTCTTAACCCAAGAGCATCC 60.016 42.308 0.00 0.00 44.10 3.51
182 184 8.408601 CAATGACCATATTTCTTAACCCAAGAG 58.591 37.037 0.00 0.00 44.10 2.85
208 210 2.048603 GGGTTGGCACTCTCATGGC 61.049 63.158 0.00 0.00 45.14 4.40
230 232 8.352942 GGTGAAAAGACAATCTTTCATAAGTGT 58.647 33.333 4.36 0.00 45.19 3.55
236 238 6.633500 TTCGGTGAAAAGACAATCTTTCAT 57.367 33.333 4.36 0.00 45.19 2.57
265 267 2.339769 AGGGGGCATCTACAAGATACC 58.660 52.381 0.00 0.00 37.41 2.73
274 276 3.637821 ACTGAAGATAGGGGGCATCTA 57.362 47.619 0.00 0.00 32.40 1.98
310 312 1.891150 TGAGGGTGAACTCCGTTAGAC 59.109 52.381 0.00 0.00 36.66 2.59
326 328 0.670546 AGCCATTGTTCGTCGTGAGG 60.671 55.000 0.00 0.00 0.00 3.86
402 404 1.776662 AGCTACATAGAAGCCGACCA 58.223 50.000 0.00 0.00 41.02 4.02
472 474 4.703897 TGAAGACGATCACCTTCAAGTTT 58.296 39.130 18.81 0.00 43.84 2.66
499 501 2.200370 ACCACCTCACCGTCCTCA 59.800 61.111 0.00 0.00 0.00 3.86
745 748 7.320435 TGGTAACTTTTTGGTGGGTTTACCAT 61.320 38.462 6.27 0.00 46.03 3.55
812 815 3.572255 TCCATTCCCTTTAGTGTGTTTGC 59.428 43.478 0.00 0.00 0.00 3.68
856 3145 2.700773 GGCCCGACTCAAACCATGC 61.701 63.158 0.00 0.00 0.00 4.06
986 3280 4.552365 CCATCCGCCATCCGCACT 62.552 66.667 0.00 0.00 37.30 4.40
1119 3413 2.406002 GACGAGGGAAGTTGGGGCAA 62.406 60.000 0.00 0.00 0.00 4.52
1180 3474 1.873903 CGATCCTTGCCCGAACCTATG 60.874 57.143 0.00 0.00 0.00 2.23
1292 3588 6.013379 GTGAGATGAGATAAGATGGAGGGTA 58.987 44.000 0.00 0.00 0.00 3.69
1301 3597 8.093307 GCATTTATGAGGTGAGATGAGATAAGA 58.907 37.037 0.00 0.00 0.00 2.10
1302 3598 7.876582 TGCATTTATGAGGTGAGATGAGATAAG 59.123 37.037 0.00 0.00 0.00 1.73
1303 3599 7.738847 TGCATTTATGAGGTGAGATGAGATAA 58.261 34.615 0.00 0.00 0.00 1.75
1304 3600 7.015974 ACTGCATTTATGAGGTGAGATGAGATA 59.984 37.037 0.00 0.00 0.00 1.98
1305 3601 6.183361 ACTGCATTTATGAGGTGAGATGAGAT 60.183 38.462 0.00 0.00 0.00 2.75
1306 3602 5.129980 ACTGCATTTATGAGGTGAGATGAGA 59.870 40.000 0.00 0.00 0.00 3.27
1316 3613 3.004419 CAGCCATGACTGCATTTATGAGG 59.996 47.826 9.99 0.00 30.68 3.86
1399 3696 0.178975 AATTGGTGGACTTGCGGGAA 60.179 50.000 0.00 0.00 0.00 3.97
1402 3699 1.080569 GCAATTGGTGGACTTGCGG 60.081 57.895 7.72 0.00 36.31 5.69
1556 3853 5.769484 ATCATGAAGAATGCATTCCTGAC 57.231 39.130 31.05 20.61 24.93 3.51
1572 3869 5.647658 ACTAAAAAGATGCGTCCAATCATGA 59.352 36.000 1.23 0.00 0.00 3.07
1743 4040 6.484288 ACCTTGGATAGTTTGATTGACATGA 58.516 36.000 0.00 0.00 0.00 3.07
1758 4055 6.780031 TGTTTGGATTTTGAAGACCTTGGATA 59.220 34.615 0.00 0.00 0.00 2.59
1970 4270 6.267817 CACATATTTGTATCAGGCAAACCAG 58.732 40.000 0.00 0.00 38.44 4.00
2067 4374 2.454538 TCTTCCTCCGGTTCCTAAGAC 58.545 52.381 0.00 0.00 0.00 3.01
2191 4498 5.049612 GCAAAAACAGTACCTTCTCCACTAC 60.050 44.000 0.00 0.00 0.00 2.73
2328 4636 4.103627 TGCAGTGATGAGGATACATGGAAT 59.896 41.667 0.00 0.00 41.41 3.01
2450 4762 7.653311 GCAAGATAAACCTGTTTCAGAACATTT 59.347 33.333 0.00 0.00 44.30 2.32
2551 4863 3.420839 AAGTGCTTCCGTTCACAAAAG 57.579 42.857 0.00 0.00 35.76 2.27
2597 4909 5.365403 TTTTGCGACAAGTAATTCGGAAT 57.635 34.783 0.00 0.00 43.71 3.01
2599 4911 4.815040 TTTTTGCGACAAGTAATTCGGA 57.185 36.364 0.00 0.00 35.73 4.55
2642 4954 8.346300 CGCAGAAATGGATATATCTAGACGTAT 58.654 37.037 12.42 0.00 0.00 3.06
2645 4957 6.689241 GTCGCAGAAATGGATATATCTAGACG 59.311 42.308 12.42 5.95 39.69 4.18
2646 4958 7.539436 TGTCGCAGAAATGGATATATCTAGAC 58.461 38.462 12.42 8.56 39.69 2.59
2655 4967 6.019075 CGAATTACTTGTCGCAGAAATGGATA 60.019 38.462 0.00 0.00 39.69 2.59
2667 4979 3.187700 CTCCTTCCCGAATTACTTGTCG 58.812 50.000 0.00 0.00 37.01 4.35
2684 4996 4.507342 ACCAGAATATTATGCTCCCTCCT 58.493 43.478 4.49 0.00 0.00 3.69
2757 5069 3.834938 AGTACACAGTATAGAGAGCCCC 58.165 50.000 0.00 0.00 0.00 5.80
2873 5186 9.638176 AGCTGGAAGAAGAATATCATTAATGTT 57.362 29.630 14.97 9.56 34.07 2.71
2965 5280 3.609409 GCAAATCACGAGGTTTCAACTCC 60.609 47.826 0.00 0.00 0.00 3.85
3041 5356 4.576463 ACACCACAGACTCTGAAAATTGAC 59.424 41.667 13.25 0.00 35.18 3.18
3046 5361 3.627395 ACACACCACAGACTCTGAAAA 57.373 42.857 13.25 0.00 35.18 2.29
3147 5464 8.483307 AAATGATGAAAATGTTATCTGTTGCC 57.517 30.769 0.00 0.00 0.00 4.52
3189 5506 6.097129 AGTCTTAGTAGAGCCAACAAGGTATC 59.903 42.308 0.00 0.00 40.61 2.24
3255 5572 6.103997 GTGAGCCAATGTCATGATCAAATTT 58.896 36.000 0.00 0.00 0.00 1.82
3263 5580 4.523558 TGATTTTGTGAGCCAATGTCATGA 59.476 37.500 0.00 0.00 31.81 3.07
3381 5823 2.676839 ACCTCGTACAGTGATACTCGTG 59.323 50.000 0.00 0.00 0.00 4.35
3528 5970 4.271049 CGCACATGAATAGTTTCGGAAGAT 59.729 41.667 0.00 0.00 41.60 2.40
3588 6030 7.662669 TGACCCTGGTTTAGTACAAAGTTAATC 59.337 37.037 0.00 0.00 0.00 1.75
3589 6031 7.519927 TGACCCTGGTTTAGTACAAAGTTAAT 58.480 34.615 0.00 0.00 0.00 1.40
3590 6032 6.897986 TGACCCTGGTTTAGTACAAAGTTAA 58.102 36.000 0.00 0.00 0.00 2.01
3591 6033 6.497624 TGACCCTGGTTTAGTACAAAGTTA 57.502 37.500 0.00 0.00 0.00 2.24
3610 6052 7.020827 TCCCTCAGATCCATATTAATTGACC 57.979 40.000 0.00 0.00 0.00 4.02
3611 6053 7.684529 ACTCCCTCAGATCCATATTAATTGAC 58.315 38.462 0.00 0.00 0.00 3.18
3628 6070 4.999310 TCAGAGAAGAAACTACTCCCTCA 58.001 43.478 0.00 0.00 0.00 3.86
3702 6144 4.411212 ACCAGCTTATAACTTCCCGGTATT 59.589 41.667 0.00 0.00 0.00 1.89
3710 6152 4.379499 GGCACAACACCAGCTTATAACTTC 60.379 45.833 0.00 0.00 0.00 3.01
3753 6195 1.215647 GACCATCCGCGTCAACTCT 59.784 57.895 4.92 0.00 0.00 3.24
3905 6347 0.236711 CCGTGCAGCAAGAGAACAAG 59.763 55.000 10.26 0.00 0.00 3.16
3915 6357 2.110352 CATCATGAGCCGTGCAGCA 61.110 57.895 0.09 0.00 34.23 4.41
3922 6364 1.953138 GCCTCGTCATCATGAGCCG 60.953 63.158 0.09 3.34 34.62 5.52
3952 6394 5.120208 CCAATTAACGGAGACACTTACACTG 59.880 44.000 0.00 0.00 0.00 3.66
3967 6409 2.721603 CGATCTCGCTCTCCAATTAACG 59.278 50.000 0.00 0.00 0.00 3.18
4026 6468 4.380867 CCGCTTTGCTCTATGGATGTTTTT 60.381 41.667 0.00 0.00 0.00 1.94
4027 6469 3.129287 CCGCTTTGCTCTATGGATGTTTT 59.871 43.478 0.00 0.00 0.00 2.43
4028 6470 2.684881 CCGCTTTGCTCTATGGATGTTT 59.315 45.455 0.00 0.00 0.00 2.83
4029 6471 2.092968 TCCGCTTTGCTCTATGGATGTT 60.093 45.455 0.00 0.00 0.00 2.71
4034 6476 3.062763 CACTATCCGCTTTGCTCTATGG 58.937 50.000 0.00 0.00 0.00 2.74
4161 6603 4.792068 TGGCTAATTTTATGGGGAGAGTG 58.208 43.478 0.00 0.00 0.00 3.51
4269 6711 7.874528 CAGTGTCATGTTGATAGCCTATCATAA 59.125 37.037 14.91 7.20 44.06 1.90
4279 6721 3.314357 CCATGCCAGTGTCATGTTGATAG 59.686 47.826 12.80 0.00 39.60 2.08
4346 6788 8.272545 TCTACTCGCTAAATAACTTCTGTACA 57.727 34.615 0.00 0.00 0.00 2.90
4352 6794 8.973835 ATGCTATCTACTCGCTAAATAACTTC 57.026 34.615 0.00 0.00 0.00 3.01
4363 6805 6.444633 TGGTAGTTTTATGCTATCTACTCGC 58.555 40.000 0.00 0.00 33.69 5.03
4364 6806 9.776158 CTATGGTAGTTTTATGCTATCTACTCG 57.224 37.037 0.00 0.00 33.69 4.18
4388 6832 5.502089 TTTTCGGAATCCTACCCAAACTA 57.498 39.130 0.00 0.00 0.00 2.24
4390 6834 4.521639 AGTTTTTCGGAATCCTACCCAAAC 59.478 41.667 0.00 0.21 0.00 2.93
4396 6840 4.995487 AGTGTCAGTTTTTCGGAATCCTAC 59.005 41.667 0.00 0.00 0.00 3.18
4397 6841 5.223449 AGTGTCAGTTTTTCGGAATCCTA 57.777 39.130 0.00 0.00 0.00 2.94
4398 6842 4.086706 AGTGTCAGTTTTTCGGAATCCT 57.913 40.909 0.00 0.00 0.00 3.24
4469 6913 3.744426 ACGTAAGGATTCAACAACTTCGG 59.256 43.478 0.00 0.00 46.39 4.30
4470 6914 4.985044 ACGTAAGGATTCAACAACTTCG 57.015 40.909 0.00 0.00 46.39 3.79
4471 6915 6.056428 ACAACGTAAGGATTCAACAACTTC 57.944 37.500 0.00 0.00 46.39 3.01
4472 6916 7.556733 TTACAACGTAAGGATTCAACAACTT 57.443 32.000 0.00 0.00 46.39 2.66
4500 6944 0.036732 GTCCAGGCATGTCAGAACCA 59.963 55.000 0.00 0.00 0.00 3.67
4502 6946 0.036732 TGGTCCAGGCATGTCAGAAC 59.963 55.000 0.00 0.00 0.00 3.01
4505 6949 1.377725 GGTGGTCCAGGCATGTCAG 60.378 63.158 0.00 0.00 0.00 3.51
4511 6955 2.447572 TGACAGGTGGTCCAGGCA 60.448 61.111 0.00 0.00 46.38 4.75
4518 6962 2.532715 ATGGCCCTGACAGGTGGT 60.533 61.111 20.24 0.67 31.93 4.16
4525 6969 0.179062 CTAGCTGACATGGCCCTGAC 60.179 60.000 15.66 9.32 0.00 3.51
4535 6979 0.965866 CCGTCTGTCCCTAGCTGACA 60.966 60.000 11.45 11.45 40.28 3.58
4536 6980 1.810532 CCGTCTGTCCCTAGCTGAC 59.189 63.158 0.00 0.00 0.00 3.51
4538 6982 2.496817 GCCGTCTGTCCCTAGCTG 59.503 66.667 0.00 0.00 0.00 4.24
4557 7001 2.149803 CTAACGACCGTGAGTGGCCA 62.150 60.000 0.00 0.00 0.00 5.36
4570 7014 3.376078 AGAACGGCGCCCTAACGA 61.376 61.111 23.46 0.00 34.06 3.85
4571 7015 2.901051 ATCAGAACGGCGCCCTAACG 62.901 60.000 23.46 11.58 0.00 3.18
4607 7053 1.683917 CTAGTGATAGTGAGCCGGCTT 59.316 52.381 33.34 18.32 0.00 4.35
4623 7069 2.154567 TATCCCGGTTCTGCACTAGT 57.845 50.000 0.00 0.00 0.00 2.57
4624 7070 3.367498 GCTATATCCCGGTTCTGCACTAG 60.367 52.174 0.00 0.00 0.00 2.57
4625 7071 2.561419 GCTATATCCCGGTTCTGCACTA 59.439 50.000 0.00 0.00 0.00 2.74
4626 7072 1.344763 GCTATATCCCGGTTCTGCACT 59.655 52.381 0.00 0.00 0.00 4.40
4627 7073 1.070134 TGCTATATCCCGGTTCTGCAC 59.930 52.381 0.00 0.00 0.00 4.57
4628 7074 1.070134 GTGCTATATCCCGGTTCTGCA 59.930 52.381 0.00 0.00 0.00 4.41
4629 7075 1.608283 GGTGCTATATCCCGGTTCTGC 60.608 57.143 0.00 0.00 0.00 4.26
4630 7076 1.336887 CGGTGCTATATCCCGGTTCTG 60.337 57.143 0.00 0.00 38.09 3.02
4631 7077 0.966920 CGGTGCTATATCCCGGTTCT 59.033 55.000 0.00 0.00 38.09 3.01
4632 7078 3.509388 CGGTGCTATATCCCGGTTC 57.491 57.895 0.00 0.00 38.09 3.62
4636 7082 0.388134 CGAACCGGTGCTATATCCCG 60.388 60.000 8.52 0.00 41.37 5.14
4637 7083 0.677842 ACGAACCGGTGCTATATCCC 59.322 55.000 8.52 0.00 0.00 3.85
4638 7084 3.572584 CTTACGAACCGGTGCTATATCC 58.427 50.000 8.52 0.00 0.00 2.59
4639 7085 3.572584 CCTTACGAACCGGTGCTATATC 58.427 50.000 8.52 0.00 0.00 1.63
4640 7086 2.298163 CCCTTACGAACCGGTGCTATAT 59.702 50.000 8.52 0.00 0.00 0.86
4641 7087 1.682854 CCCTTACGAACCGGTGCTATA 59.317 52.381 8.52 0.00 0.00 1.31
4642 7088 0.462789 CCCTTACGAACCGGTGCTAT 59.537 55.000 8.52 0.00 0.00 2.97
4643 7089 1.892338 CCCTTACGAACCGGTGCTA 59.108 57.895 8.52 0.00 0.00 3.49
4644 7090 2.660802 CCCTTACGAACCGGTGCT 59.339 61.111 8.52 0.00 0.00 4.40
4645 7091 3.122971 GCCCTTACGAACCGGTGC 61.123 66.667 8.52 4.53 0.00 5.01
4646 7092 2.435410 GGCCCTTACGAACCGGTG 60.435 66.667 8.52 0.00 0.00 4.94
4647 7093 1.771783 AAAGGCCCTTACGAACCGGT 61.772 55.000 0.00 0.00 0.00 5.28
4648 7094 0.249955 TAAAGGCCCTTACGAACCGG 59.750 55.000 0.00 0.00 0.00 5.28
4649 7095 1.066645 ACTAAAGGCCCTTACGAACCG 60.067 52.381 0.00 0.00 0.00 4.44
4650 7096 2.353323 CACTAAAGGCCCTTACGAACC 58.647 52.381 0.00 0.00 0.00 3.62
4651 7097 1.736126 GCACTAAAGGCCCTTACGAAC 59.264 52.381 0.00 0.00 0.00 3.95
4652 7098 1.339342 GGCACTAAAGGCCCTTACGAA 60.339 52.381 0.00 0.00 45.87 3.85
4653 7099 0.251073 GGCACTAAAGGCCCTTACGA 59.749 55.000 0.00 0.00 45.87 3.43
4654 7100 2.776659 GGCACTAAAGGCCCTTACG 58.223 57.895 0.00 0.00 45.87 3.18
4661 7107 3.314357 CGGTATTAAAGGGCACTAAAGGC 59.686 47.826 0.00 0.00 0.00 4.35
4662 7108 3.881089 CCGGTATTAAAGGGCACTAAAGG 59.119 47.826 0.00 0.00 0.00 3.11
4663 7109 4.520179 ACCGGTATTAAAGGGCACTAAAG 58.480 43.478 4.49 0.00 0.00 1.85
4664 7110 4.573021 ACCGGTATTAAAGGGCACTAAA 57.427 40.909 4.49 0.00 0.00 1.85
4665 7111 4.573021 AACCGGTATTAAAGGGCACTAA 57.427 40.909 8.00 0.00 0.00 2.24
4666 7112 4.573021 AAACCGGTATTAAAGGGCACTA 57.427 40.909 8.00 0.00 0.00 2.74
4667 7113 3.444792 AAACCGGTATTAAAGGGCACT 57.555 42.857 8.00 0.00 0.00 4.40
4668 7114 3.840468 CAAAACCGGTATTAAAGGGCAC 58.160 45.455 8.00 0.00 0.00 5.01
4669 7115 2.231721 GCAAAACCGGTATTAAAGGGCA 59.768 45.455 8.00 0.00 0.00 5.36
4670 7116 2.231721 TGCAAAACCGGTATTAAAGGGC 59.768 45.455 8.00 4.20 0.00 5.19
4671 7117 3.671164 CGTGCAAAACCGGTATTAAAGGG 60.671 47.826 8.00 0.00 0.00 3.95
4672 7118 3.188873 TCGTGCAAAACCGGTATTAAAGG 59.811 43.478 8.00 0.00 0.00 3.11
4673 7119 4.407496 TCGTGCAAAACCGGTATTAAAG 57.593 40.909 8.00 0.00 0.00 1.85
4674 7120 4.535116 GTTCGTGCAAAACCGGTATTAAA 58.465 39.130 8.00 0.00 0.00 1.52
4675 7121 3.058363 GGTTCGTGCAAAACCGGTATTAA 60.058 43.478 8.00 0.00 37.06 1.40
4676 7122 2.483491 GGTTCGTGCAAAACCGGTATTA 59.517 45.455 8.00 0.00 37.06 0.98
4677 7123 1.267533 GGTTCGTGCAAAACCGGTATT 59.732 47.619 8.00 1.22 37.06 1.89
4678 7124 0.876399 GGTTCGTGCAAAACCGGTAT 59.124 50.000 8.00 0.00 37.06 2.73
4679 7125 2.319219 GGTTCGTGCAAAACCGGTA 58.681 52.632 8.00 0.00 37.06 4.02
4680 7126 3.112842 GGTTCGTGCAAAACCGGT 58.887 55.556 14.57 0.00 37.06 5.28
4683 7129 1.657181 CAGCGGTTCGTGCAAAACC 60.657 57.895 18.20 18.20 42.30 3.27
4684 7130 2.292916 GCAGCGGTTCGTGCAAAAC 61.293 57.895 4.94 4.94 39.62 2.43
4685 7131 1.160946 TAGCAGCGGTTCGTGCAAAA 61.161 50.000 13.73 0.00 42.47 2.44
4686 7132 1.160946 TTAGCAGCGGTTCGTGCAAA 61.161 50.000 13.73 0.00 42.47 3.68
4687 7133 1.160946 TTTAGCAGCGGTTCGTGCAA 61.161 50.000 13.73 6.63 42.47 4.08
4688 7134 1.565156 CTTTAGCAGCGGTTCGTGCA 61.565 55.000 13.73 0.00 42.47 4.57
4689 7135 1.132640 CTTTAGCAGCGGTTCGTGC 59.867 57.895 0.00 6.72 40.17 5.34
4690 7136 0.716108 CTCTTTAGCAGCGGTTCGTG 59.284 55.000 0.00 0.00 0.00 4.35
4691 7137 3.123674 CTCTTTAGCAGCGGTTCGT 57.876 52.632 0.00 0.00 0.00 3.85
4735 7181 2.689771 TAAAGGTCTCCCCGGCCC 60.690 66.667 0.00 0.00 38.74 5.80
4736 7182 0.688749 TACTAAAGGTCTCCCCGGCC 60.689 60.000 0.00 0.00 38.74 6.13
4737 7183 0.463204 GTACTAAAGGTCTCCCCGGC 59.537 60.000 0.00 0.00 38.74 6.13
4738 7184 1.117994 GGTACTAAAGGTCTCCCCGG 58.882 60.000 0.00 0.00 38.74 5.73
4739 7185 0.743097 CGGTACTAAAGGTCTCCCCG 59.257 60.000 0.00 0.00 38.74 5.73
4740 7186 1.117994 CCGGTACTAAAGGTCTCCCC 58.882 60.000 0.00 0.00 0.00 4.81
4741 7187 1.857965 ACCGGTACTAAAGGTCTCCC 58.142 55.000 4.49 0.00 31.69 4.30
4742 7188 2.093816 CCAACCGGTACTAAAGGTCTCC 60.094 54.545 8.00 0.00 37.26 3.71
4743 7189 2.564504 ACCAACCGGTACTAAAGGTCTC 59.435 50.000 8.00 0.00 46.71 3.36
4744 7190 2.613129 ACCAACCGGTACTAAAGGTCT 58.387 47.619 8.00 0.00 46.71 3.85
4758 7204 1.668793 CCGGTCGGTGTTACCAACC 60.669 63.158 0.55 0.00 42.01 3.77
4759 7205 3.955775 CCGGTCGGTGTTACCAAC 58.044 61.111 0.55 0.00 38.47 3.77
4760 7206 3.259374 TTAATACCGGTCGGTGTTACCAA 59.741 43.478 24.26 13.73 46.51 3.67
4761 7207 2.828520 TTAATACCGGTCGGTGTTACCA 59.171 45.455 24.26 12.93 46.51 3.25
4762 7208 3.518634 TTAATACCGGTCGGTGTTACC 57.481 47.619 24.26 0.00 46.51 2.85
4763 7209 5.351189 ACATTTTAATACCGGTCGGTGTTAC 59.649 40.000 24.26 0.00 46.51 2.50
4769 7215 4.395542 TCCAAACATTTTAATACCGGTCGG 59.604 41.667 12.40 7.97 42.03 4.79
4770 7216 5.448089 CCTCCAAACATTTTAATACCGGTCG 60.448 44.000 12.40 0.00 0.00 4.79
4771 7217 5.163591 CCCTCCAAACATTTTAATACCGGTC 60.164 44.000 12.40 0.00 0.00 4.79
4772 7218 4.707934 CCCTCCAAACATTTTAATACCGGT 59.292 41.667 13.98 13.98 0.00 5.28
4773 7219 4.707934 ACCCTCCAAACATTTTAATACCGG 59.292 41.667 0.00 0.00 0.00 5.28
4774 7220 5.907866 ACCCTCCAAACATTTTAATACCG 57.092 39.130 0.00 0.00 0.00 4.02
4775 7221 8.151596 TCAAAACCCTCCAAACATTTTAATACC 58.848 33.333 0.00 0.00 0.00 2.73
4776 7222 9.719355 ATCAAAACCCTCCAAACATTTTAATAC 57.281 29.630 0.00 0.00 0.00 1.89
4778 7224 9.639563 AAATCAAAACCCTCCAAACATTTTAAT 57.360 25.926 0.00 0.00 0.00 1.40
4779 7225 9.467796 AAAATCAAAACCCTCCAAACATTTTAA 57.532 25.926 0.00 0.00 0.00 1.52
4781 7227 7.953005 AAAATCAAAACCCTCCAAACATTTT 57.047 28.000 0.00 0.00 0.00 1.82
4782 7228 9.065798 CATAAAATCAAAACCCTCCAAACATTT 57.934 29.630 0.00 0.00 0.00 2.32
4783 7229 8.435982 TCATAAAATCAAAACCCTCCAAACATT 58.564 29.630 0.00 0.00 0.00 2.71
4784 7230 7.972301 TCATAAAATCAAAACCCTCCAAACAT 58.028 30.769 0.00 0.00 0.00 2.71
4785 7231 7.366847 TCATAAAATCAAAACCCTCCAAACA 57.633 32.000 0.00 0.00 0.00 2.83
4786 7232 8.314021 AGATCATAAAATCAAAACCCTCCAAAC 58.686 33.333 0.00 0.00 0.00 2.93
4787 7233 8.434589 AGATCATAAAATCAAAACCCTCCAAA 57.565 30.769 0.00 0.00 0.00 3.28
4788 7234 9.713684 ATAGATCATAAAATCAAAACCCTCCAA 57.286 29.630 0.00 0.00 0.00 3.53
4789 7235 9.713684 AATAGATCATAAAATCAAAACCCTCCA 57.286 29.630 0.00 0.00 0.00 3.86
4835 7281 9.913451 CAGCAAACGAAAAAGAATTAAATGAAA 57.087 25.926 0.00 0.00 0.00 2.69
4836 7282 8.547069 CCAGCAAACGAAAAAGAATTAAATGAA 58.453 29.630 0.00 0.00 0.00 2.57
4837 7283 7.708752 ACCAGCAAACGAAAAAGAATTAAATGA 59.291 29.630 0.00 0.00 0.00 2.57
4838 7284 7.850501 ACCAGCAAACGAAAAAGAATTAAATG 58.149 30.769 0.00 0.00 0.00 2.32
4839 7285 9.705290 ATACCAGCAAACGAAAAAGAATTAAAT 57.295 25.926 0.00 0.00 0.00 1.40
4840 7286 9.535878 AATACCAGCAAACGAAAAAGAATTAAA 57.464 25.926 0.00 0.00 0.00 1.52
4841 7287 9.535878 AAATACCAGCAAACGAAAAAGAATTAA 57.464 25.926 0.00 0.00 0.00 1.40
4842 7288 9.535878 AAAATACCAGCAAACGAAAAAGAATTA 57.464 25.926 0.00 0.00 0.00 1.40
4843 7289 8.432110 AAAATACCAGCAAACGAAAAAGAATT 57.568 26.923 0.00 0.00 0.00 2.17
4844 7290 8.974408 GTAAAATACCAGCAAACGAAAAAGAAT 58.026 29.630 0.00 0.00 0.00 2.40
4845 7291 7.166142 CGTAAAATACCAGCAAACGAAAAAGAA 59.834 33.333 0.00 0.00 0.00 2.52
4846 7292 6.633634 CGTAAAATACCAGCAAACGAAAAAGA 59.366 34.615 0.00 0.00 0.00 2.52
4847 7293 6.633634 TCGTAAAATACCAGCAAACGAAAAAG 59.366 34.615 0.00 0.00 35.23 2.27
4848 7294 6.493116 TCGTAAAATACCAGCAAACGAAAAA 58.507 32.000 0.00 0.00 35.23 1.94
4849 7295 6.057627 TCGTAAAATACCAGCAAACGAAAA 57.942 33.333 0.00 0.00 35.23 2.29
4850 7296 5.670149 TCGTAAAATACCAGCAAACGAAA 57.330 34.783 0.00 0.00 35.23 3.46
4851 7297 5.866335 ATCGTAAAATACCAGCAAACGAA 57.134 34.783 0.00 0.00 40.71 3.85


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

AutoCloner maintained by Alex Coulton.