Multiple sequence alignment - TraesCS5B01G335700

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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 TraesCS5B01G335700 chr5B 100.000 5857 0 0 1 5857 518954469 518960325 0.000000e+00 10816.0
1 TraesCS5B01G335700 chr5B 100.000 76 0 0 3678 3753 518958108 518958183 2.200000e-29 141.0
2 TraesCS5B01G335700 chr5B 100.000 76 0 0 3640 3715 518958146 518958221 2.200000e-29 141.0
3 TraesCS5B01G335700 chr5B 100.000 38 0 0 3716 3753 518958108 518958145 2.930000e-08 71.3
4 TraesCS5B01G335700 chr5B 100.000 38 0 0 3640 3677 518958184 518958221 2.930000e-08 71.3
5 TraesCS5B01G335700 chr5B 100.000 30 0 0 5132 5161 518959508 518959537 8.200000e-04 56.5
6 TraesCS5B01G335700 chr5B 100.000 30 0 0 5040 5069 518959600 518959629 8.200000e-04 56.5
7 TraesCS5B01G335700 chr5D 93.720 1672 71 11 1802 3456 429710784 429712438 0.000000e+00 2475.0
8 TraesCS5B01G335700 chr5D 94.951 1327 51 8 3716 5034 429712592 429713910 0.000000e+00 2065.0
9 TraesCS5B01G335700 chr5D 95.027 1307 49 8 1 1295 429708811 429710113 0.000000e+00 2039.0
10 TraesCS5B01G335700 chr5D 91.765 340 22 5 1295 1630 429710147 429710484 8.890000e-128 468.0
11 TraesCS5B01G335700 chr5D 88.654 379 14 9 5485 5854 429714335 429714693 9.010000e-118 435.0
12 TraesCS5B01G335700 chr5D 80.098 407 36 23 5090 5485 429713911 429714283 1.620000e-65 261.0
13 TraesCS5B01G335700 chr5D 95.833 144 6 0 1666 1809 429710481 429710624 3.530000e-57 233.0
14 TraesCS5B01G335700 chr5D 97.321 112 3 0 3566 3677 429712518 429712629 2.150000e-44 191.0
15 TraesCS5B01G335700 chr5D 100.000 33 0 0 3457 3489 429712485 429712517 1.760000e-05 62.1
16 TraesCS5B01G335700 chr5D 100.000 30 0 0 5040 5069 429713953 429713982 8.200000e-04 56.5
17 TraesCS5B01G335700 chr5A 95.603 1319 45 8 3716 5034 545563172 545564477 0.000000e+00 2102.0
18 TraesCS5B01G335700 chr5A 93.783 933 44 7 2533 3456 545562016 545562943 0.000000e+00 1389.0
19 TraesCS5B01G335700 chr5A 87.647 1020 74 27 301 1295 545559607 545560599 0.000000e+00 1138.0
20 TraesCS5B01G335700 chr5A 95.603 705 21 3 1716 2419 545561322 545562017 0.000000e+00 1122.0
21 TraesCS5B01G335700 chr5A 87.451 773 72 21 5090 5854 545564478 545565233 0.000000e+00 867.0
22 TraesCS5B01G335700 chr5A 93.862 391 21 2 1300 1688 545560938 545561327 2.350000e-163 586.0
23 TraesCS5B01G335700 chr5A 93.213 221 14 1 3457 3677 545562990 545563209 2.040000e-84 324.0
24 TraesCS5B01G335700 chr2A 79.861 144 17 7 174 308 364465720 364465580 1.740000e-15 95.3
25 TraesCS5B01G335700 chr2D 78.621 145 18 8 174 308 295798100 295797959 3.760000e-12 84.2
26 TraesCS5B01G335700 chr2D 88.000 50 5 1 3457 3505 603925180 603925229 2.280000e-04 58.4
27 TraesCS5B01G335700 chr2B 81.553 103 16 2 171 273 352290492 352290591 1.350000e-11 82.4
28 TraesCS5B01G335700 chr2B 100.000 32 0 0 3415 3446 383646725 383646694 6.340000e-05 60.2
29 TraesCS5B01G335700 chr3D 96.875 32 1 0 3415 3446 444075765 444075734 3.000000e-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 TraesCS5B01G335700 chr5B 518954469 518960325 5856 False 1621.942857 10816 100.000000 1 5857 7 chr5B.!!$F1 5856
1 TraesCS5B01G335700 chr5D 429708811 429714693 5882 False 828.560000 2475 93.736900 1 5854 10 chr5D.!!$F1 5853
2 TraesCS5B01G335700 chr5A 545559607 545565233 5626 False 1075.428571 2102 92.451714 301 5854 7 chr5A.!!$F1 5553

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
198 206 0.536260 CAGGCAGAGTGCTAGAAGCT 59.464 55.0 0.00 0.0 44.28 3.74 F
1284 1340 0.251165 CGAGGGTTCCATTTGTGGGT 60.251 55.0 0.00 0.0 0.00 4.51 F
1893 2456 0.178992 TATGCTATGTTGGGCTGGGC 60.179 55.0 0.00 0.0 0.00 5.36 F
2653 3219 0.319555 CAACTTGAGACGGCGAGGAA 60.320 55.0 16.62 0.0 0.00 3.36 F
3646 4273 0.250640 AAGAGCTCACCTGTGCTTGG 60.251 55.0 17.77 0.0 43.90 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 2453 0.324275 TAGGAAATGCCCACTTGCCC 60.324 55.0 0.00 0.0 37.37 5.36 R
2523 3087 0.240145 TTACTGTCGTCAGACTGCCG 59.760 55.0 16.64 0.0 46.27 5.69 R
3583 4210 0.099436 GGATTGACGCACCAGAATGC 59.901 55.0 0.00 0.0 42.48 3.56 R
3668 4295 0.110295 TGCCCAAGCACTTCTTAGCA 59.890 50.0 0.00 0.0 46.52 3.49 R
5083 5720 0.371645 CTGAAGGAGAACAATCGCGC 59.628 55.0 0.00 0.0 0.00 6.86 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
43 44 3.930336 TGTGTCCATTGCACAAACAAAA 58.070 36.364 0.00 0.00 42.96 2.44
46 47 4.153117 GTGTCCATTGCACAAACAAAAACA 59.847 37.500 0.00 0.00 36.88 2.83
99 100 6.824196 AGCCTAGTTGCTACCTTATTTCTTTC 59.176 38.462 0.00 0.00 40.56 2.62
136 144 5.624159 TCATCTCCATTAGCTGGGTTAATG 58.376 41.667 0.00 0.00 45.98 1.90
139 147 3.287222 TCCATTAGCTGGGTTAATGTGC 58.713 45.455 0.00 0.00 45.98 4.57
152 160 5.393027 GGGTTAATGTGCATGTCTAAAGGTG 60.393 44.000 0.00 0.00 0.00 4.00
157 165 3.181455 TGTGCATGTCTAAAGGTGTGTCT 60.181 43.478 0.00 0.00 0.00 3.41
159 167 2.744202 GCATGTCTAAAGGTGTGTCTGG 59.256 50.000 0.00 0.00 0.00 3.86
182 190 6.487668 TGGCATCTACATCAATAAATGACAGG 59.512 38.462 0.00 0.00 41.93 4.00
198 206 0.536260 CAGGCAGAGTGCTAGAAGCT 59.464 55.000 0.00 0.00 44.28 3.74
274 282 3.254166 CCCAATGCAATGTATAGAGGCAC 59.746 47.826 0.21 0.00 37.30 5.01
332 340 0.689080 CTGCCAGGCCTCTCCTTCTA 60.689 60.000 9.64 0.00 44.75 2.10
347 355 6.577103 TCTCCTTCTAGCATCTACAACAATG 58.423 40.000 0.00 0.00 0.00 2.82
348 356 5.118990 TCCTTCTAGCATCTACAACAATGC 58.881 41.667 0.00 0.00 46.84 3.56
884 939 3.188786 GGATCGCCGTGAGCACAC 61.189 66.667 3.95 3.95 44.04 3.82
904 959 6.036953 GCACACTAAAATCATCTTCTCCTCTG 59.963 42.308 0.00 0.00 0.00 3.35
911 966 3.897239 TCATCTTCTCCTCTGTCTCTCC 58.103 50.000 0.00 0.00 0.00 3.71
1179 1234 2.745308 CCGAGCACCCCATCCATCA 61.745 63.158 0.00 0.00 0.00 3.07
1284 1340 0.251165 CGAGGGTTCCATTTGTGGGT 60.251 55.000 0.00 0.00 0.00 4.51
1295 1351 4.141135 TCCATTTGTGGGTTGGTTCTTAGA 60.141 41.667 0.00 0.00 0.00 2.10
1297 1353 2.561478 TGTGGGTTGGTTCTTAGAGC 57.439 50.000 0.00 0.00 0.00 4.09
1298 1354 1.270625 TGTGGGTTGGTTCTTAGAGCG 60.271 52.381 0.00 0.00 0.00 5.03
1313 1703 1.202627 AGAGCGAGGATGCAAGGATTC 60.203 52.381 0.00 0.00 37.31 2.52
1415 1809 7.176690 TGGACCCTTCAGATTTTCTTATGAAAC 59.823 37.037 3.41 0.00 41.34 2.78
1488 1882 5.523916 GTGGTTGAGTATTAGTATGCAGGTG 59.476 44.000 0.00 0.00 0.00 4.00
1516 1910 5.581874 CCATTGGTTAGTTTCATGATTTGGC 59.418 40.000 0.00 0.00 0.00 4.52
1557 1951 4.297299 AGCAGGCAAATAATCGACAATG 57.703 40.909 0.00 0.00 0.00 2.82
1604 1998 8.757982 AGAATGGCTGAATTGAATACAATACT 57.242 30.769 0.00 0.00 44.67 2.12
1638 2032 6.075762 TGACTGCTGTACGAAACTAACTTA 57.924 37.500 0.00 0.00 0.00 2.24
1700 2096 7.673926 TCCTGAAATTTTACCTTCCAAGCTTAT 59.326 33.333 0.00 0.00 0.00 1.73
1727 2123 5.414454 CCATACTTTTTCTTTCACGGGATCA 59.586 40.000 0.00 0.00 0.00 2.92
1844 2407 7.486407 AAATAGGCTTCTGGAAATTGTTGAT 57.514 32.000 0.00 0.00 0.00 2.57
1891 2454 4.734398 TTTTTATGCTATGTTGGGCTGG 57.266 40.909 0.00 0.00 0.00 4.85
1892 2455 2.363306 TTATGCTATGTTGGGCTGGG 57.637 50.000 0.00 0.00 0.00 4.45
1893 2456 0.178992 TATGCTATGTTGGGCTGGGC 60.179 55.000 0.00 0.00 0.00 5.36
1894 2457 2.044053 GCTATGTTGGGCTGGGCA 60.044 61.111 0.00 0.00 0.00 5.36
1895 2458 1.682005 GCTATGTTGGGCTGGGCAA 60.682 57.895 0.00 0.00 0.00 4.52
1896 2459 1.669999 GCTATGTTGGGCTGGGCAAG 61.670 60.000 0.00 0.00 0.00 4.01
2147 2710 4.990543 TCGTGCTGTATGTTTCTTGAAG 57.009 40.909 0.00 0.00 0.00 3.02
2170 2733 6.365520 AGTTGGTAAGACATTTTTCTGGTCT 58.634 36.000 0.00 0.00 43.35 3.85
2336 2900 9.338622 CTTTTATCTACGGTTTATCCATTCCTT 57.661 33.333 0.00 0.00 35.57 3.36
2490 3054 9.256477 TGCGTCCTTATTATTTAGTGTAAGATG 57.744 33.333 0.00 0.00 0.00 2.90
2508 3072 8.145122 TGTAAGATGTACGGAACAATATGCATA 58.855 33.333 9.27 9.27 42.70 3.14
2523 3087 1.699634 TGCATAGGGAATACAGAGGCC 59.300 52.381 0.00 0.00 0.00 5.19
2530 3094 0.530870 GAATACAGAGGCCGGCAGTC 60.531 60.000 30.85 23.71 0.00 3.51
2531 3095 0.978146 AATACAGAGGCCGGCAGTCT 60.978 55.000 30.85 25.65 0.00 3.24
2533 3097 2.781431 TACAGAGGCCGGCAGTCTGA 62.781 60.000 42.34 29.95 40.21 3.27
2563 3129 4.833478 AATGCCTTTAGCTTCTCTCTCA 57.167 40.909 0.00 0.00 44.23 3.27
2593 3159 5.943416 TCTTCTCGTTTCTCTGATCTCTCTT 59.057 40.000 0.00 0.00 0.00 2.85
2653 3219 0.319555 CAACTTGAGACGGCGAGGAA 60.320 55.000 16.62 0.00 0.00 3.36
2677 3243 4.740822 GGGCTGCGGTGATTGGGT 62.741 66.667 0.00 0.00 0.00 4.51
2688 3262 2.911509 ATTGGGTGCTGCAACGCA 60.912 55.556 12.13 13.55 40.81 5.24
2696 3270 2.046023 CTGCAACGCATGGGGAGA 60.046 61.111 14.94 0.00 38.13 3.71
2717 3291 3.495331 AGGTGTTGTTTACATGGATGCA 58.505 40.909 0.00 0.00 39.39 3.96
2758 3332 0.989212 TAGTCTCCCTCCTCGGCTCT 60.989 60.000 0.00 0.00 0.00 4.09
2770 3344 3.715097 GGCTCTGGCTGCCTGAGT 61.715 66.667 38.76 0.00 46.71 3.41
2790 3364 2.825836 CTGATCACGCAAGCCCCC 60.826 66.667 0.00 0.00 45.62 5.40
2819 3393 1.903877 CGGGCAGAGGTTGTGGATCT 61.904 60.000 0.00 0.00 0.00 2.75
2862 3440 3.767230 CCGACGTGCGCTGAGTTG 61.767 66.667 9.73 9.68 39.11 3.16
2878 3456 1.145738 AGTTGGTGCAGGTGGATTCTT 59.854 47.619 0.00 0.00 0.00 2.52
2932 3510 3.450457 TGGTTCCTTGTTTGCTTGACAAT 59.550 39.130 0.00 0.00 38.31 2.71
3000 3578 2.219080 TTGATTTCCTGCTGCATCCA 57.781 45.000 1.31 0.00 0.00 3.41
3055 3633 9.663904 GAATCGATAATTTATTTGTAGCAGCAA 57.336 29.630 0.00 0.00 0.00 3.91
3080 3661 2.171237 TGCTGGATGGGTCATCAACTAG 59.829 50.000 9.68 0.00 42.13 2.57
3084 3665 3.118775 TGGATGGGTCATCAACTAGTTCG 60.119 47.826 4.77 2.02 42.13 3.95
3133 3714 4.671831 TCAACTTTTATTCCCCATGCAGA 58.328 39.130 0.00 0.00 0.00 4.26
3165 3746 5.064579 GTGCAAAGGTTTTTACTGCACAATT 59.935 36.000 17.90 0.00 46.92 2.32
3252 3833 6.753744 GCCAAGATTGATTTAGTGAAACATCC 59.246 38.462 0.00 0.00 41.43 3.51
3262 3843 2.892852 AGTGAAACATCCATTGTGGTGG 59.107 45.455 0.00 0.00 41.43 4.61
3426 4007 1.973515 TCAGGATAGATGCAAGCGGAT 59.026 47.619 0.00 0.00 0.00 4.18
3492 4119 3.945434 CATGCAGATGCCGTCCGC 61.945 66.667 1.72 0.00 41.18 5.54
3524 4151 3.374764 AGGATAGCAGTACCATGTGTCA 58.625 45.455 0.00 0.00 0.00 3.58
3535 4162 2.559668 ACCATGTGTCAGCCAGAAATTG 59.440 45.455 0.00 0.00 0.00 2.32
3645 4272 1.602311 AAAGAGCTCACCTGTGCTTG 58.398 50.000 17.77 0.00 43.90 4.01
3646 4273 0.250640 AAGAGCTCACCTGTGCTTGG 60.251 55.000 17.77 0.00 43.90 3.61
3647 4274 1.673665 GAGCTCACCTGTGCTTGGG 60.674 63.158 9.40 0.00 43.90 4.12
3648 4275 3.368571 GCTCACCTGTGCTTGGGC 61.369 66.667 0.00 0.00 39.26 5.36
3666 4293 3.845781 GGCACCCTTCTTGATATCTCA 57.154 47.619 3.98 0.00 0.00 3.27
3667 4294 4.363991 GGCACCCTTCTTGATATCTCAT 57.636 45.455 3.98 0.00 0.00 2.90
3668 4295 4.723309 GGCACCCTTCTTGATATCTCATT 58.277 43.478 3.98 0.00 0.00 2.57
3669 4296 4.518211 GGCACCCTTCTTGATATCTCATTG 59.482 45.833 3.98 0.00 0.00 2.82
3670 4297 4.023365 GCACCCTTCTTGATATCTCATTGC 60.023 45.833 3.98 0.00 0.00 3.56
3671 4298 5.374921 CACCCTTCTTGATATCTCATTGCT 58.625 41.667 3.98 0.00 0.00 3.91
3672 4299 6.528321 CACCCTTCTTGATATCTCATTGCTA 58.472 40.000 3.98 0.00 0.00 3.49
3673 4300 6.994496 CACCCTTCTTGATATCTCATTGCTAA 59.006 38.462 3.98 0.00 0.00 3.09
3674 4301 7.172875 CACCCTTCTTGATATCTCATTGCTAAG 59.827 40.741 3.98 0.00 0.00 2.18
3675 4302 7.071698 ACCCTTCTTGATATCTCATTGCTAAGA 59.928 37.037 3.98 0.00 0.00 2.10
3676 4303 7.935755 CCCTTCTTGATATCTCATTGCTAAGAA 59.064 37.037 3.98 7.23 0.00 2.52
3677 4304 8.991026 CCTTCTTGATATCTCATTGCTAAGAAG 58.009 37.037 20.50 20.50 37.98 2.85
3678 4305 9.545105 CTTCTTGATATCTCATTGCTAAGAAGT 57.455 33.333 19.79 0.00 35.77 3.01
3679 4306 8.883954 TCTTGATATCTCATTGCTAAGAAGTG 57.116 34.615 3.98 0.00 0.00 3.16
3680 4307 7.440556 TCTTGATATCTCATTGCTAAGAAGTGC 59.559 37.037 3.98 0.00 0.00 4.40
3681 4308 6.824553 TGATATCTCATTGCTAAGAAGTGCT 58.175 36.000 3.98 0.00 0.00 4.40
3682 4309 7.278135 TGATATCTCATTGCTAAGAAGTGCTT 58.722 34.615 3.98 0.00 40.68 3.91
3683 4310 5.814764 ATCTCATTGCTAAGAAGTGCTTG 57.185 39.130 0.00 0.00 37.42 4.01
3684 4311 4.005650 TCTCATTGCTAAGAAGTGCTTGG 58.994 43.478 0.00 0.00 37.42 3.61
3685 4312 3.084039 TCATTGCTAAGAAGTGCTTGGG 58.916 45.455 0.00 0.00 37.42 4.12
3686 4313 1.247567 TTGCTAAGAAGTGCTTGGGC 58.752 50.000 0.00 0.00 37.42 5.36
3704 4331 3.845781 GGCACCCTTCTTGATATCTCA 57.154 47.619 3.98 0.00 0.00 3.27
3705 4332 4.363991 GGCACCCTTCTTGATATCTCAT 57.636 45.455 3.98 0.00 0.00 2.90
3706 4333 4.723309 GGCACCCTTCTTGATATCTCATT 58.277 43.478 3.98 0.00 0.00 2.57
3707 4334 4.518211 GGCACCCTTCTTGATATCTCATTG 59.482 45.833 3.98 0.00 0.00 2.82
3708 4335 4.023365 GCACCCTTCTTGATATCTCATTGC 60.023 45.833 3.98 0.00 0.00 3.56
3709 4336 5.374921 CACCCTTCTTGATATCTCATTGCT 58.625 41.667 3.98 0.00 0.00 3.91
3710 4337 6.528321 CACCCTTCTTGATATCTCATTGCTA 58.472 40.000 3.98 0.00 0.00 3.49
3711 4338 6.994496 CACCCTTCTTGATATCTCATTGCTAA 59.006 38.462 3.98 0.00 0.00 3.09
3712 4339 7.172875 CACCCTTCTTGATATCTCATTGCTAAG 59.827 40.741 3.98 0.00 0.00 2.18
3713 4340 7.071698 ACCCTTCTTGATATCTCATTGCTAAGA 59.928 37.037 3.98 0.00 0.00 2.10
3714 4341 7.935755 CCCTTCTTGATATCTCATTGCTAAGAA 59.064 37.037 3.98 7.23 0.00 2.52
3715 4342 8.991026 CCTTCTTGATATCTCATTGCTAAGAAG 58.009 37.037 20.50 20.50 37.98 2.85
3716 4343 9.545105 CTTCTTGATATCTCATTGCTAAGAAGT 57.455 33.333 19.79 0.00 35.77 3.01
3717 4344 8.883954 TCTTGATATCTCATTGCTAAGAAGTG 57.116 34.615 3.98 0.00 0.00 3.16
3718 4345 7.440556 TCTTGATATCTCATTGCTAAGAAGTGC 59.559 37.037 3.98 0.00 0.00 4.40
3719 4346 6.824553 TGATATCTCATTGCTAAGAAGTGCT 58.175 36.000 3.98 0.00 0.00 4.40
3720 4347 7.278135 TGATATCTCATTGCTAAGAAGTGCTT 58.722 34.615 3.98 0.00 40.68 3.91
3767 4394 4.025229 TGCTAAGAACTGTGCTGTTAAACG 60.025 41.667 0.00 0.00 0.00 3.60
3998 4625 4.152045 CGCTTGAGCTGAATCCTTCATATC 59.848 45.833 0.00 0.00 39.30 1.63
4168 4795 4.020543 TGTTCCACCAGTGCTAAGTTTTT 58.979 39.130 0.00 0.00 0.00 1.94
4169 4796 4.142271 TGTTCCACCAGTGCTAAGTTTTTG 60.142 41.667 0.00 0.00 0.00 2.44
4170 4797 3.892284 TCCACCAGTGCTAAGTTTTTGA 58.108 40.909 0.00 0.00 0.00 2.69
4171 4798 3.882888 TCCACCAGTGCTAAGTTTTTGAG 59.117 43.478 0.00 0.00 0.00 3.02
4172 4799 3.550842 CCACCAGTGCTAAGTTTTTGAGC 60.551 47.826 0.00 0.00 36.72 4.26
4185 4812 6.225981 AGTTTTTGAGCATTGTTCCTCTTT 57.774 33.333 0.00 0.00 0.00 2.52
4458 5085 1.069296 ACGGCATTCACGATTGTGTTG 60.069 47.619 12.90 12.34 46.49 3.33
4462 5089 4.671508 CGGCATTCACGATTGTGTTGTTAT 60.672 41.667 12.90 0.00 46.49 1.89
4591 5218 6.628844 GCAAAAATGGATTATTCAGCAGGAGT 60.629 38.462 0.00 0.00 0.00 3.85
4636 5263 4.949238 CACCATGGTTCTGTCATATGGAAA 59.051 41.667 16.84 0.00 40.52 3.13
4683 5310 0.108585 GCACCCTCAGACCTTGTGAA 59.891 55.000 0.00 0.00 0.00 3.18
4719 5346 4.541973 ATTCTTTGCTCATGTTTTCCCC 57.458 40.909 0.00 0.00 0.00 4.81
4724 5351 2.449464 TGCTCATGTTTTCCCCATCTG 58.551 47.619 0.00 0.00 0.00 2.90
4864 5493 7.707035 CGTTTCTTTCCAGAAGTAGTAGCATAT 59.293 37.037 0.00 0.00 40.28 1.78
4898 5527 8.632906 ATGAATTTTACAGAGGATCATGGATC 57.367 34.615 0.00 0.00 37.82 3.36
4918 5555 1.208165 GGTGTCCATTGAGGGGGAGT 61.208 60.000 0.00 0.00 38.24 3.85
4955 5592 1.401905 GAATCCTGGTGGCGATTGTTC 59.598 52.381 0.00 0.00 0.00 3.18
4985 5622 5.186198 AGTTATGTAATGGTCTTGCACTCC 58.814 41.667 0.00 0.00 0.00 3.85
5002 5639 1.005748 CCTGCAGTCAGAACGCTCA 60.006 57.895 13.81 0.00 42.95 4.26
5012 5649 3.579709 TCAGAACGCTCAATCTGAAGAC 58.420 45.455 3.16 0.00 46.67 3.01
5034 5671 0.606604 GCCTGACCGTTCTTGGACTA 59.393 55.000 0.00 0.00 0.00 2.59
5035 5672 1.207329 GCCTGACCGTTCTTGGACTAT 59.793 52.381 0.00 0.00 0.00 2.12
5036 5673 2.354805 GCCTGACCGTTCTTGGACTATT 60.355 50.000 0.00 0.00 0.00 1.73
5037 5674 3.868754 GCCTGACCGTTCTTGGACTATTT 60.869 47.826 0.00 0.00 0.00 1.40
5038 5675 3.684788 CCTGACCGTTCTTGGACTATTTG 59.315 47.826 0.00 0.00 0.00 2.32
5039 5676 4.315803 CTGACCGTTCTTGGACTATTTGT 58.684 43.478 0.00 0.00 0.00 2.83
5040 5677 4.710324 TGACCGTTCTTGGACTATTTGTT 58.290 39.130 0.00 0.00 0.00 2.83
5041 5678 4.513692 TGACCGTTCTTGGACTATTTGTTG 59.486 41.667 0.00 0.00 0.00 3.33
5042 5679 3.252458 ACCGTTCTTGGACTATTTGTTGC 59.748 43.478 0.00 0.00 0.00 4.17
5043 5680 3.502211 CCGTTCTTGGACTATTTGTTGCT 59.498 43.478 0.00 0.00 0.00 3.91
5044 5681 4.466828 CGTTCTTGGACTATTTGTTGCTG 58.533 43.478 0.00 0.00 0.00 4.41
5045 5682 4.229876 GTTCTTGGACTATTTGTTGCTGC 58.770 43.478 0.00 0.00 0.00 5.25
5046 5683 2.819608 TCTTGGACTATTTGTTGCTGCC 59.180 45.455 0.00 0.00 0.00 4.85
5047 5684 2.584835 TGGACTATTTGTTGCTGCCT 57.415 45.000 0.00 0.00 0.00 4.75
5048 5685 3.712016 TGGACTATTTGTTGCTGCCTA 57.288 42.857 0.00 0.00 0.00 3.93
5049 5686 3.609853 TGGACTATTTGTTGCTGCCTAG 58.390 45.455 0.00 0.00 0.00 3.02
5050 5687 2.945668 GGACTATTTGTTGCTGCCTAGG 59.054 50.000 3.67 3.67 0.00 3.02
5051 5688 2.356069 GACTATTTGTTGCTGCCTAGGC 59.644 50.000 27.71 27.71 42.35 3.93
5065 5702 4.848562 GCCTAGGCACTAAGTTGTTTTT 57.151 40.909 29.33 0.00 42.17 1.94
5066 5703 4.546570 GCCTAGGCACTAAGTTGTTTTTG 58.453 43.478 29.33 0.00 42.17 2.44
5067 5704 4.037565 GCCTAGGCACTAAGTTGTTTTTGT 59.962 41.667 29.33 0.00 42.17 2.83
5068 5705 5.239963 GCCTAGGCACTAAGTTGTTTTTGTA 59.760 40.000 29.33 0.00 42.17 2.41
5069 5706 6.072119 GCCTAGGCACTAAGTTGTTTTTGTAT 60.072 38.462 29.33 0.00 42.17 2.29
5070 5707 7.305474 CCTAGGCACTAAGTTGTTTTTGTATG 58.695 38.462 0.00 0.00 42.17 2.39
5071 5708 6.952773 AGGCACTAAGTTGTTTTTGTATGA 57.047 33.333 0.00 0.00 36.02 2.15
5072 5709 7.524717 AGGCACTAAGTTGTTTTTGTATGAT 57.475 32.000 0.00 0.00 36.02 2.45
5073 5710 8.630054 AGGCACTAAGTTGTTTTTGTATGATA 57.370 30.769 0.00 0.00 36.02 2.15
5074 5711 8.512138 AGGCACTAAGTTGTTTTTGTATGATAC 58.488 33.333 0.00 0.00 36.02 2.24
5075 5712 7.480542 GGCACTAAGTTGTTTTTGTATGATACG 59.519 37.037 0.00 0.00 0.00 3.06
5076 5713 7.007099 GCACTAAGTTGTTTTTGTATGATACGC 59.993 37.037 0.00 0.00 0.00 4.42
5077 5714 8.012809 CACTAAGTTGTTTTTGTATGATACGCA 58.987 33.333 0.00 0.00 0.00 5.24
5078 5715 8.726988 ACTAAGTTGTTTTTGTATGATACGCAT 58.273 29.630 0.00 0.00 41.08 4.73
5079 5716 7.795431 AAGTTGTTTTTGTATGATACGCATG 57.205 32.000 0.00 0.00 37.87 4.06
5080 5717 6.321717 AGTTGTTTTTGTATGATACGCATGG 58.678 36.000 0.00 0.00 37.87 3.66
5081 5718 5.888691 TGTTTTTGTATGATACGCATGGT 57.111 34.783 0.00 0.00 37.87 3.55
5082 5719 5.635866 TGTTTTTGTATGATACGCATGGTG 58.364 37.500 0.00 0.00 37.87 4.17
5083 5720 4.891627 TTTTGTATGATACGCATGGTGG 57.108 40.909 0.00 0.00 37.87 4.61
5084 5721 1.877637 TGTATGATACGCATGGTGGC 58.122 50.000 0.00 0.00 37.87 5.01
5101 5738 1.019278 GGCGCGATTGTTCTCCTTCA 61.019 55.000 12.10 0.00 0.00 3.02
5165 5803 5.230516 GGCACTAAGTTGTTTTTGTAAACGG 59.769 40.000 0.00 0.00 45.29 4.44
5183 5821 6.828502 AAACGGCTCTTCATTTTTCTTTTC 57.171 33.333 0.00 0.00 0.00 2.29
5185 5823 6.149129 ACGGCTCTTCATTTTTCTTTTCTT 57.851 33.333 0.00 0.00 0.00 2.52
5217 5855 4.493220 GCACTATCTGTTGTCGAATTGCTC 60.493 45.833 0.00 0.00 0.00 4.26
5230 5868 3.120752 CGAATTGCTCTTATGGCAGATCG 60.121 47.826 0.00 0.00 40.90 3.69
5285 5928 5.975693 TTTATTTGCCCTACAAGGAACAG 57.024 39.130 0.00 0.00 40.06 3.16
5293 5936 4.767409 GCCCTACAAGGAACAGAGAAATTT 59.233 41.667 0.00 0.00 37.67 1.82
5307 5954 2.298163 AGAAATTTGCTTGGCCTGTCAG 59.702 45.455 3.32 0.00 0.00 3.51
5310 5957 1.174712 TTTGCTTGGCCTGTCAGAGC 61.175 55.000 3.32 2.78 0.00 4.09
5332 5980 4.693283 CGTAATCATGCTAGGGAGTTCAA 58.307 43.478 0.00 0.00 0.00 2.69
5343 5991 3.425659 AGGGAGTTCAATTTTGAGCCTC 58.574 45.455 3.86 8.03 38.94 4.70
5393 6041 0.744414 ATCGCCAGTGATGGGTTTCG 60.744 55.000 0.00 0.00 0.00 3.46
5398 6046 2.076863 CCAGTGATGGGTTTCGACTTC 58.923 52.381 0.00 0.00 0.00 3.01
5406 6054 1.468914 GGGTTTCGACTTCATGCCTTC 59.531 52.381 0.00 0.00 0.00 3.46
5441 6092 6.126568 GCAATTTTGCGTAAACTATAGGGA 57.873 37.500 4.43 0.00 45.11 4.20
5442 6093 6.557110 GCAATTTTGCGTAAACTATAGGGAA 58.443 36.000 4.43 0.00 45.11 3.97
5495 6205 0.319555 ATATGCAGTATTCGCCGCGT 60.320 50.000 13.39 0.00 0.00 6.01
5498 6208 2.578713 CAGTATTCGCCGCGTCGT 60.579 61.111 10.12 0.00 0.00 4.34
5626 6336 4.333926 GCAATGTACAAAGCCCAAACAAAA 59.666 37.500 0.00 0.00 0.00 2.44
5627 6337 5.729176 GCAATGTACAAAGCCCAAACAAAAC 60.729 40.000 0.00 0.00 0.00 2.43
5628 6338 3.512680 TGTACAAAGCCCAAACAAAACG 58.487 40.909 0.00 0.00 0.00 3.60
5854 6573 2.125912 CGCTCCAGGTTGTCCTCG 60.126 66.667 0.00 0.00 43.07 4.63
5855 6574 2.636412 CGCTCCAGGTTGTCCTCGA 61.636 63.158 0.00 0.00 43.07 4.04
5856 6575 1.079750 GCTCCAGGTTGTCCTCGAC 60.080 63.158 0.00 0.00 43.07 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.765036 TGCAATGGACACAATGTTTAATGTTT 59.235 30.769 0.00 0.00 30.07 2.83
64 65 7.724287 AGGTAGCAACTAGGCTTAGTAATTAC 58.276 38.462 9.17 7.57 42.71 1.89
67 68 6.809976 AAGGTAGCAACTAGGCTTAGTAAT 57.190 37.500 9.17 1.28 42.71 1.89
99 100 2.965147 GGAGATGAGAGGAGGAAGAAGG 59.035 54.545 0.00 0.00 0.00 3.46
136 144 3.187227 CAGACACACCTTTAGACATGCAC 59.813 47.826 0.00 0.00 0.00 4.57
139 147 2.744202 GCCAGACACACCTTTAGACATG 59.256 50.000 0.00 0.00 0.00 3.21
152 160 6.925610 TTTATTGATGTAGATGCCAGACAC 57.074 37.500 0.00 0.00 0.00 3.67
157 165 6.487668 CCTGTCATTTATTGATGTAGATGCCA 59.512 38.462 0.00 0.00 36.54 4.92
159 167 6.016860 TGCCTGTCATTTATTGATGTAGATGC 60.017 38.462 0.00 0.00 36.54 3.91
182 190 0.179086 GGGAGCTTCTAGCACTCTGC 60.179 60.000 1.09 0.00 45.56 4.26
216 224 6.490040 GCTTGCCTTATATAATCCTTCACCAA 59.510 38.462 0.00 0.00 0.00 3.67
274 282 3.490761 CCACTTGTGCCAAAAGTAAGGTG 60.491 47.826 0.00 0.00 35.70 4.00
297 305 2.037251 TGGCAGAGTGTTGAAGTACTCC 59.963 50.000 0.00 0.00 43.32 3.85
332 340 3.595173 TGTACGCATTGTTGTAGATGCT 58.405 40.909 6.73 0.00 44.90 3.79
551 561 5.298276 TGGGAAAATTGTTCTGACTACACAC 59.702 40.000 0.00 0.00 0.00 3.82
690 712 9.668497 GAGTACTTAAGACAAATACCCTCAAAT 57.332 33.333 10.09 0.00 0.00 2.32
884 939 8.010733 AGAGACAGAGGAGAAGATGATTTTAG 57.989 38.462 0.00 0.00 0.00 1.85
1179 1234 3.790089 AATCAAGAAGGAGAACGGGTT 57.210 42.857 0.00 0.00 0.00 4.11
1278 1334 1.270625 CGCTCTAAGAACCAACCCACA 60.271 52.381 0.00 0.00 0.00 4.17
1284 1340 2.418746 GCATCCTCGCTCTAAGAACCAA 60.419 50.000 0.00 0.00 0.00 3.67
1295 1351 0.531532 CGAATCCTTGCATCCTCGCT 60.532 55.000 0.00 0.00 0.00 4.93
1297 1353 2.223829 ACTACGAATCCTTGCATCCTCG 60.224 50.000 0.00 0.00 0.00 4.63
1298 1354 3.460857 ACTACGAATCCTTGCATCCTC 57.539 47.619 0.00 0.00 0.00 3.71
1313 1703 8.298030 TCATCAATTATCATGCACTAACTACG 57.702 34.615 0.00 0.00 0.00 3.51
1426 1820 7.933577 CAGGACAATATCATCTAGTAAGGCAAA 59.066 37.037 0.00 0.00 0.00 3.68
1488 1882 3.509575 TCATGAAACTAACCAATGGTGCC 59.490 43.478 5.34 0.00 35.34 5.01
1496 1890 3.823873 ACGCCAAATCATGAAACTAACCA 59.176 39.130 0.00 0.00 0.00 3.67
1516 1910 2.586258 ACATCCGAGGAATGAGAACG 57.414 50.000 0.00 0.00 0.00 3.95
1583 1977 7.568349 AGAGAGTATTGTATTCAATTCAGCCA 58.432 34.615 2.68 0.00 43.12 4.75
1604 1998 6.231211 TCGTACAGCAGTCATATGATAGAGA 58.769 40.000 9.02 0.00 0.00 3.10
1664 2060 6.015940 AGGTAAAATTTCAGGAACAAGCTCTG 60.016 38.462 0.00 0.00 0.00 3.35
1700 2096 5.828859 TCCCGTGAAAGAAAAAGTATGGAAA 59.171 36.000 0.00 0.00 0.00 3.13
1837 2400 6.998074 AGTAAGACATGAAGTTCCATCAACAA 59.002 34.615 0.00 0.00 37.48 2.83
1844 2407 6.108687 CAGCATAGTAAGACATGAAGTTCCA 58.891 40.000 0.00 0.00 0.00 3.53
1889 2452 1.912763 GGAAATGCCCACTTGCCCA 60.913 57.895 0.00 0.00 0.00 5.36
1890 2453 0.324275 TAGGAAATGCCCACTTGCCC 60.324 55.000 0.00 0.00 37.37 5.36
1891 2454 1.106285 CTAGGAAATGCCCACTTGCC 58.894 55.000 0.00 0.00 37.37 4.52
1892 2455 2.019984 CTCTAGGAAATGCCCACTTGC 58.980 52.381 0.00 0.00 37.37 4.01
1893 2456 2.019984 GCTCTAGGAAATGCCCACTTG 58.980 52.381 0.00 0.00 37.37 3.16
1894 2457 1.635487 TGCTCTAGGAAATGCCCACTT 59.365 47.619 0.00 0.00 37.37 3.16
1895 2458 1.289160 TGCTCTAGGAAATGCCCACT 58.711 50.000 0.00 0.00 37.37 4.00
1896 2459 2.225467 GATGCTCTAGGAAATGCCCAC 58.775 52.381 0.00 0.00 37.37 4.61
2147 2710 6.039382 ACAGACCAGAAAAATGTCTTACCAAC 59.961 38.462 0.00 0.00 37.25 3.77
2170 2733 1.116308 TGTCCTCCGAGTTGTCAACA 58.884 50.000 17.78 0.00 0.00 3.33
2385 2949 0.251634 GCTGCTCCCTGCTTTCTACT 59.748 55.000 0.00 0.00 43.37 2.57
2436 3000 2.119495 AGGTATCTGGATGGTCCACAC 58.881 52.381 0.00 0.00 42.67 3.82
2455 3019 3.753294 AATAAGGACGCACATCCCTAG 57.247 47.619 0.00 0.00 39.91 3.02
2490 3054 4.890088 TCCCTATGCATATTGTTCCGTAC 58.110 43.478 6.92 0.00 0.00 3.67
2494 3058 7.168219 TCTGTATTCCCTATGCATATTGTTCC 58.832 38.462 6.92 0.00 0.00 3.62
2508 3072 2.444256 GCCGGCCTCTGTATTCCCT 61.444 63.158 18.11 0.00 0.00 4.20
2523 3087 0.240145 TTACTGTCGTCAGACTGCCG 59.760 55.000 16.64 0.00 46.27 5.69
2530 3094 4.201724 GCTAAAGGCATTTACTGTCGTCAG 60.202 45.833 8.17 8.17 42.83 3.51
2531 3095 3.682858 GCTAAAGGCATTTACTGTCGTCA 59.317 43.478 0.00 0.00 41.35 4.35
2533 3097 3.939066 AGCTAAAGGCATTTACTGTCGT 58.061 40.909 0.00 0.00 44.79 4.34
2563 3129 5.651387 TCAGAGAAACGAGAAGATGTGAT 57.349 39.130 0.00 0.00 0.00 3.06
2593 3159 1.841556 GCCCCATCCCATCGGTAGA 60.842 63.158 0.00 0.00 0.00 2.59
2688 3262 2.714250 TGTAAACAACACCTCTCCCCAT 59.286 45.455 0.00 0.00 31.43 4.00
2696 3270 3.495331 TGCATCCATGTAAACAACACCT 58.505 40.909 0.00 0.00 42.09 4.00
2758 3332 1.196766 ATCAGTCACTCAGGCAGCCA 61.197 55.000 15.80 0.00 0.00 4.75
2770 3344 1.375908 GGGCTTGCGTGATCAGTCA 60.376 57.895 0.00 0.00 0.00 3.41
2798 3372 4.641645 CCACAACCTCTGCCCGCA 62.642 66.667 0.00 0.00 0.00 5.69
2819 3393 1.761174 GGAGTCAAGGGACAAGCCA 59.239 57.895 0.00 0.00 46.80 4.75
2862 3440 0.251341 ACCAAGAATCCACCTGCACC 60.251 55.000 0.00 0.00 0.00 5.01
2932 3510 4.792068 TCCAAAGAAGAAGAAAAGGAGCA 58.208 39.130 0.00 0.00 0.00 4.26
3000 3578 3.880047 ATGCAGCACTACAAATTGCAT 57.120 38.095 0.00 4.57 46.89 3.96
3055 3633 0.254178 GATGACCCATCCAGCACTGT 59.746 55.000 0.00 0.00 35.07 3.55
3080 3661 4.184629 ACAAATGCTCTAGACATCCGAAC 58.815 43.478 7.86 0.00 0.00 3.95
3084 3665 6.259550 ACAAAACAAATGCTCTAGACATCC 57.740 37.500 7.86 0.00 0.00 3.51
3133 3714 3.535280 AAAACCTTTGCACGAAATGGT 57.465 38.095 0.00 0.00 30.64 3.55
3179 3760 7.056006 AGTACAAGATATTGGCATGAATGTGA 58.944 34.615 4.88 0.00 0.00 3.58
3180 3761 7.268199 AGTACAAGATATTGGCATGAATGTG 57.732 36.000 4.88 0.00 0.00 3.21
3181 3762 7.886629 AAGTACAAGATATTGGCATGAATGT 57.113 32.000 4.88 0.00 0.00 2.71
3182 3763 8.407832 TCAAAGTACAAGATATTGGCATGAATG 58.592 33.333 4.88 0.00 0.00 2.67
3183 3764 8.408601 GTCAAAGTACAAGATATTGGCATGAAT 58.591 33.333 4.88 0.00 0.00 2.57
3252 3833 2.231721 TGATTGCATCACCACCACAATG 59.768 45.455 0.00 0.00 33.59 2.82
3262 3843 6.485984 AGATTAGGACAGATTGATTGCATCAC 59.514 38.462 0.00 0.00 39.39 3.06
3492 4119 4.348863 ACTGCTATCCTAAGGATGCAAG 57.651 45.455 2.71 0.58 43.06 4.01
3501 4128 4.959839 TGACACATGGTACTGCTATCCTAA 59.040 41.667 0.00 0.00 0.00 2.69
3524 4151 5.105146 TGTGGTGTTTAAACAATTTCTGGCT 60.105 36.000 22.14 0.00 41.21 4.75
3552 4179 8.898761 AGTGTTGTATGTGTTCAGTATTTTTCA 58.101 29.630 0.00 0.00 0.00 2.69
3583 4210 0.099436 GGATTGACGCACCAGAATGC 59.901 55.000 0.00 0.00 42.48 3.56
3645 4272 2.439507 TGAGATATCAAGAAGGGTGCCC 59.560 50.000 5.32 0.00 0.00 5.36
3646 4273 3.845781 TGAGATATCAAGAAGGGTGCC 57.154 47.619 5.32 0.00 0.00 5.01
3647 4274 4.023365 GCAATGAGATATCAAGAAGGGTGC 60.023 45.833 5.32 0.22 0.00 5.01
3648 4275 5.374921 AGCAATGAGATATCAAGAAGGGTG 58.625 41.667 5.32 0.00 0.00 4.61
3649 4276 5.643421 AGCAATGAGATATCAAGAAGGGT 57.357 39.130 5.32 0.00 0.00 4.34
3650 4277 7.448420 TCTTAGCAATGAGATATCAAGAAGGG 58.552 38.462 5.32 0.00 0.00 3.95
3651 4278 8.899427 TTCTTAGCAATGAGATATCAAGAAGG 57.101 34.615 5.32 0.00 0.00 3.46
3652 4279 9.545105 ACTTCTTAGCAATGAGATATCAAGAAG 57.455 33.333 23.24 23.24 46.69 2.85
3653 4280 9.322773 CACTTCTTAGCAATGAGATATCAAGAA 57.677 33.333 5.32 7.74 31.84 2.52
3654 4281 7.440556 GCACTTCTTAGCAATGAGATATCAAGA 59.559 37.037 5.32 0.00 0.00 3.02
3655 4282 7.441760 AGCACTTCTTAGCAATGAGATATCAAG 59.558 37.037 5.32 0.00 0.00 3.02
3656 4283 7.278135 AGCACTTCTTAGCAATGAGATATCAA 58.722 34.615 5.32 0.00 0.00 2.57
3657 4284 6.824553 AGCACTTCTTAGCAATGAGATATCA 58.175 36.000 5.32 0.00 0.00 2.15
3658 4285 7.307870 CCAAGCACTTCTTAGCAATGAGATATC 60.308 40.741 0.00 0.00 32.74 1.63
3659 4286 6.485984 CCAAGCACTTCTTAGCAATGAGATAT 59.514 38.462 0.00 0.00 32.74 1.63
3660 4287 5.819379 CCAAGCACTTCTTAGCAATGAGATA 59.181 40.000 0.00 0.00 32.74 1.98
3661 4288 4.639310 CCAAGCACTTCTTAGCAATGAGAT 59.361 41.667 0.00 0.00 32.74 2.75
3662 4289 4.005650 CCAAGCACTTCTTAGCAATGAGA 58.994 43.478 0.00 0.00 32.74 3.27
3663 4290 3.128242 CCCAAGCACTTCTTAGCAATGAG 59.872 47.826 0.00 0.00 32.74 2.90
3664 4291 3.084039 CCCAAGCACTTCTTAGCAATGA 58.916 45.455 0.00 0.00 32.74 2.57
3665 4292 2.416431 GCCCAAGCACTTCTTAGCAATG 60.416 50.000 0.00 0.00 39.53 2.82
3666 4293 1.821136 GCCCAAGCACTTCTTAGCAAT 59.179 47.619 0.00 0.00 39.53 3.56
3667 4294 1.247567 GCCCAAGCACTTCTTAGCAA 58.752 50.000 0.00 0.00 39.53 3.91
3668 4295 0.110295 TGCCCAAGCACTTCTTAGCA 59.890 50.000 0.00 0.00 46.52 3.49
3669 4296 2.946947 TGCCCAAGCACTTCTTAGC 58.053 52.632 0.00 0.00 46.52 3.09
3679 4306 0.613012 ATCAAGAAGGGTGCCCAAGC 60.613 55.000 10.26 0.00 38.92 4.01
3680 4307 2.806945 TATCAAGAAGGGTGCCCAAG 57.193 50.000 10.26 0.00 38.92 3.61
3681 4308 2.852449 AGATATCAAGAAGGGTGCCCAA 59.148 45.455 10.26 0.00 38.92 4.12
3682 4309 2.439507 GAGATATCAAGAAGGGTGCCCA 59.560 50.000 10.26 0.00 38.92 5.36
3683 4310 2.439507 TGAGATATCAAGAAGGGTGCCC 59.560 50.000 5.32 0.00 0.00 5.36
3684 4311 3.845781 TGAGATATCAAGAAGGGTGCC 57.154 47.619 5.32 0.00 0.00 5.01
3685 4312 4.023365 GCAATGAGATATCAAGAAGGGTGC 60.023 45.833 5.32 0.22 0.00 5.01
3686 4313 5.374921 AGCAATGAGATATCAAGAAGGGTG 58.625 41.667 5.32 0.00 0.00 4.61
3687 4314 5.643421 AGCAATGAGATATCAAGAAGGGT 57.357 39.130 5.32 0.00 0.00 4.34
3688 4315 7.448420 TCTTAGCAATGAGATATCAAGAAGGG 58.552 38.462 5.32 0.00 0.00 3.95
3689 4316 8.899427 TTCTTAGCAATGAGATATCAAGAAGG 57.101 34.615 5.32 0.00 0.00 3.46
3690 4317 9.545105 ACTTCTTAGCAATGAGATATCAAGAAG 57.455 33.333 23.24 23.24 46.69 2.85
3691 4318 9.322773 CACTTCTTAGCAATGAGATATCAAGAA 57.677 33.333 5.32 7.74 31.84 2.52
3692 4319 7.440556 GCACTTCTTAGCAATGAGATATCAAGA 59.559 37.037 5.32 0.00 0.00 3.02
3693 4320 7.441760 AGCACTTCTTAGCAATGAGATATCAAG 59.558 37.037 5.32 0.00 0.00 3.02
3694 4321 7.278135 AGCACTTCTTAGCAATGAGATATCAA 58.722 34.615 5.32 0.00 0.00 2.57
3695 4322 6.824553 AGCACTTCTTAGCAATGAGATATCA 58.175 36.000 5.32 0.00 0.00 2.15
3696 4323 7.307870 CCAAGCACTTCTTAGCAATGAGATATC 60.308 40.741 0.00 0.00 32.74 1.63
3697 4324 6.485984 CCAAGCACTTCTTAGCAATGAGATAT 59.514 38.462 0.00 0.00 32.74 1.63
3698 4325 5.819379 CCAAGCACTTCTTAGCAATGAGATA 59.181 40.000 0.00 0.00 32.74 1.98
3699 4326 4.639310 CCAAGCACTTCTTAGCAATGAGAT 59.361 41.667 0.00 0.00 32.74 2.75
3700 4327 4.005650 CCAAGCACTTCTTAGCAATGAGA 58.994 43.478 0.00 0.00 32.74 3.27
3701 4328 3.128242 CCCAAGCACTTCTTAGCAATGAG 59.872 47.826 0.00 0.00 32.74 2.90
3702 4329 3.084039 CCCAAGCACTTCTTAGCAATGA 58.916 45.455 0.00 0.00 32.74 2.57
3703 4330 2.416431 GCCCAAGCACTTCTTAGCAATG 60.416 50.000 0.00 0.00 39.53 2.82
3704 4331 1.821136 GCCCAAGCACTTCTTAGCAAT 59.179 47.619 0.00 0.00 39.53 3.56
3705 4332 1.247567 GCCCAAGCACTTCTTAGCAA 58.752 50.000 0.00 0.00 39.53 3.91
3706 4333 0.110295 TGCCCAAGCACTTCTTAGCA 59.890 50.000 0.00 0.00 46.52 3.49
3707 4334 2.946947 TGCCCAAGCACTTCTTAGC 58.053 52.632 0.00 0.00 46.52 3.09
3717 4344 0.613012 ATCAAGAAGGGTGCCCAAGC 60.613 55.000 10.26 0.00 38.92 4.01
3718 4345 2.806945 TATCAAGAAGGGTGCCCAAG 57.193 50.000 10.26 0.00 38.92 3.61
3719 4346 2.852449 AGATATCAAGAAGGGTGCCCAA 59.148 45.455 10.26 0.00 38.92 4.12
3720 4347 2.439507 GAGATATCAAGAAGGGTGCCCA 59.560 50.000 10.26 0.00 38.92 5.36
3728 4355 9.545105 AGTTCTTAGCAATGAGATATCAAGAAG 57.455 33.333 5.32 0.00 32.96 2.85
3740 4367 3.743521 ACAGCACAGTTCTTAGCAATGA 58.256 40.909 0.00 0.00 0.00 2.57
3767 4394 2.990066 AACATGGCCTAGTCTAGCAC 57.010 50.000 3.32 0.00 0.00 4.40
3838 4465 5.730550 ACGCTCATTCAAGTACATAAAGGA 58.269 37.500 0.00 0.00 0.00 3.36
3888 4515 3.799281 TGCGTGTGATGAGATATGACA 57.201 42.857 0.00 0.00 0.00 3.58
3898 4525 1.069703 CACCAGAGTTTGCGTGTGATG 60.070 52.381 0.00 0.00 0.00 3.07
4168 4795 2.555325 CTGCAAAGAGGAACAATGCTCA 59.445 45.455 0.26 0.00 45.74 4.26
4169 4796 2.816087 TCTGCAAAGAGGAACAATGCTC 59.184 45.455 0.00 0.00 43.82 4.26
4170 4797 2.867624 TCTGCAAAGAGGAACAATGCT 58.132 42.857 0.00 0.00 37.86 3.79
4171 4798 3.863142 ATCTGCAAAGAGGAACAATGC 57.137 42.857 0.00 0.00 37.52 3.56
4172 4799 6.688637 TCATATCTGCAAAGAGGAACAATG 57.311 37.500 0.00 0.00 0.00 2.82
4348 4975 6.017440 GTGAACTACACTGGAAGCATAAACAA 60.017 38.462 0.00 0.00 45.13 2.83
4410 5037 5.070981 ACCAAATATCATCATCGACAGGACT 59.929 40.000 0.00 0.00 0.00 3.85
4416 5043 5.207768 GTGCAACCAAATATCATCATCGAC 58.792 41.667 0.00 0.00 0.00 4.20
4458 5085 6.544038 AAGAAAATTGTGCCAGCAAATAAC 57.456 33.333 0.00 0.00 31.63 1.89
4462 5089 5.523188 CACTAAAGAAAATTGTGCCAGCAAA 59.477 36.000 0.00 0.00 31.63 3.68
4501 5128 6.530120 TGGTACATTCACGGCATATATTCTT 58.470 36.000 0.00 0.00 0.00 2.52
4509 5136 2.722094 ACATTGGTACATTCACGGCAT 58.278 42.857 0.00 0.00 39.30 4.40
4566 5193 5.663456 TCCTGCTGAATAATCCATTTTTGC 58.337 37.500 0.00 0.00 0.00 3.68
4573 5200 4.968719 TCCTTACTCCTGCTGAATAATCCA 59.031 41.667 0.00 0.00 0.00 3.41
4683 5310 9.932207 TGAGCAAAGAATAAATCAATCAAATGT 57.068 25.926 0.00 0.00 0.00 2.71
4719 5346 5.827666 TGCTGCATCACATAAATTCAGATG 58.172 37.500 0.00 0.00 39.17 2.90
4724 5351 5.107133 AGCTTTGCTGCATCACATAAATTC 58.893 37.500 1.84 0.00 37.57 2.17
4867 5496 8.985315 TGATCCTCTGTAAAATTCATTATGCT 57.015 30.769 0.00 0.00 0.00 3.79
4880 5509 3.321968 CACCGATCCATGATCCTCTGTAA 59.678 47.826 0.00 0.00 35.83 2.41
4887 5516 0.758734 TGGACACCGATCCATGATCC 59.241 55.000 0.00 2.89 44.14 3.36
4896 5525 1.635817 CCCCCTCAATGGACACCGAT 61.636 60.000 0.00 0.00 38.35 4.18
4898 5527 2.257409 CTCCCCCTCAATGGACACCG 62.257 65.000 0.00 0.00 38.35 4.94
4918 5555 6.270927 CCAGGATTCAAAGGATATACTGGAGA 59.729 42.308 6.73 0.00 44.26 3.71
4955 5592 8.839343 TGCAAGACCATTACATAACTTATCATG 58.161 33.333 0.00 0.00 0.00 3.07
4985 5622 1.392853 GATTGAGCGTTCTGACTGCAG 59.607 52.381 13.48 13.48 43.67 4.41
5002 5639 1.205893 GGTCAGGCTCGTCTTCAGATT 59.794 52.381 0.00 0.00 0.00 2.40
5012 5649 1.738099 CCAAGAACGGTCAGGCTCG 60.738 63.158 1.87 0.00 0.00 5.03
5044 5681 4.037565 ACAAAAACAACTTAGTGCCTAGGC 59.962 41.667 27.71 27.71 42.35 3.93
5045 5682 5.767816 ACAAAAACAACTTAGTGCCTAGG 57.232 39.130 3.67 3.67 0.00 3.02
5046 5683 8.094798 TCATACAAAAACAACTTAGTGCCTAG 57.905 34.615 0.00 0.00 0.00 3.02
5047 5684 8.630054 ATCATACAAAAACAACTTAGTGCCTA 57.370 30.769 0.00 0.00 0.00 3.93
5048 5685 6.952773 TCATACAAAAACAACTTAGTGCCT 57.047 33.333 0.00 0.00 0.00 4.75
5049 5686 7.480542 CGTATCATACAAAAACAACTTAGTGCC 59.519 37.037 0.00 0.00 0.00 5.01
5050 5687 7.007099 GCGTATCATACAAAAACAACTTAGTGC 59.993 37.037 0.00 0.00 0.00 4.40
5051 5688 8.012809 TGCGTATCATACAAAAACAACTTAGTG 58.987 33.333 0.00 0.00 0.00 2.74
5052 5689 8.090250 TGCGTATCATACAAAAACAACTTAGT 57.910 30.769 0.00 0.00 0.00 2.24
5053 5690 8.998989 CATGCGTATCATACAAAAACAACTTAG 58.001 33.333 0.00 0.00 33.19 2.18
5054 5691 7.965655 CCATGCGTATCATACAAAAACAACTTA 59.034 33.333 0.00 0.00 33.19 2.24
5055 5692 6.806249 CCATGCGTATCATACAAAAACAACTT 59.194 34.615 0.00 0.00 33.19 2.66
5056 5693 6.072175 ACCATGCGTATCATACAAAAACAACT 60.072 34.615 0.00 0.00 33.19 3.16
5057 5694 6.033407 CACCATGCGTATCATACAAAAACAAC 59.967 38.462 0.00 0.00 33.19 3.32
5058 5695 6.089476 CACCATGCGTATCATACAAAAACAA 58.911 36.000 0.00 0.00 33.19 2.83
5059 5696 5.392487 CCACCATGCGTATCATACAAAAACA 60.392 40.000 0.00 0.00 33.19 2.83
5060 5697 5.034152 CCACCATGCGTATCATACAAAAAC 58.966 41.667 0.00 0.00 33.19 2.43
5061 5698 4.439426 GCCACCATGCGTATCATACAAAAA 60.439 41.667 0.00 0.00 33.19 1.94
5062 5699 3.066064 GCCACCATGCGTATCATACAAAA 59.934 43.478 0.00 0.00 33.19 2.44
5063 5700 2.616376 GCCACCATGCGTATCATACAAA 59.384 45.455 0.00 0.00 33.19 2.83
5064 5701 2.217750 GCCACCATGCGTATCATACAA 58.782 47.619 0.00 0.00 33.19 2.41
5065 5702 1.877637 GCCACCATGCGTATCATACA 58.122 50.000 0.00 0.00 33.19 2.29
5075 5712 3.340953 AACAATCGCGCCACCATGC 62.341 57.895 0.00 0.00 0.00 4.06
5076 5713 1.226379 GAACAATCGCGCCACCATG 60.226 57.895 0.00 0.00 0.00 3.66
5077 5714 1.369091 GAGAACAATCGCGCCACCAT 61.369 55.000 0.00 0.00 0.00 3.55
5078 5715 2.031919 AGAACAATCGCGCCACCA 59.968 55.556 0.00 0.00 0.00 4.17
5079 5716 2.750888 GGAGAACAATCGCGCCACC 61.751 63.158 0.00 0.00 0.00 4.61
5080 5717 1.298859 AAGGAGAACAATCGCGCCAC 61.299 55.000 0.00 0.00 0.00 5.01
5081 5718 1.003839 AAGGAGAACAATCGCGCCA 60.004 52.632 0.00 0.00 0.00 5.69
5082 5719 1.019278 TGAAGGAGAACAATCGCGCC 61.019 55.000 0.00 0.00 0.00 6.53
5083 5720 0.371645 CTGAAGGAGAACAATCGCGC 59.628 55.000 0.00 0.00 0.00 6.86
5084 5721 1.391485 CACTGAAGGAGAACAATCGCG 59.609 52.381 0.00 0.00 0.00 5.87
5085 5722 1.129437 GCACTGAAGGAGAACAATCGC 59.871 52.381 0.00 0.00 0.00 4.58
5086 5723 2.693069 AGCACTGAAGGAGAACAATCG 58.307 47.619 0.00 0.00 0.00 3.34
5087 5724 4.516698 TGAAAGCACTGAAGGAGAACAATC 59.483 41.667 0.00 0.00 0.00 2.67
5088 5725 4.276926 GTGAAAGCACTGAAGGAGAACAAT 59.723 41.667 0.00 0.00 41.84 2.71
5091 5728 2.221981 CGTGAAAGCACTGAAGGAGAAC 59.778 50.000 0.00 0.00 42.93 3.01
5121 5758 2.033801 CCTAGGCAGCAAATGTACATGC 59.966 50.000 9.63 11.33 42.87 4.06
5165 5803 8.919661 CCATACAAGAAAAGAAAAATGAAGAGC 58.080 33.333 0.00 0.00 0.00 4.09
5183 5821 5.819379 ACAACAGATAGTGCATCCATACAAG 59.181 40.000 0.00 0.00 33.75 3.16
5185 5823 5.357742 ACAACAGATAGTGCATCCATACA 57.642 39.130 0.00 0.00 33.75 2.29
5217 5855 4.626042 AGAAGCTAACGATCTGCCATAAG 58.374 43.478 0.00 0.00 0.00 1.73
5230 5868 3.067833 GACCAACAGGTGAGAAGCTAAC 58.932 50.000 0.00 0.00 35.25 2.34
5285 5928 2.297033 TGACAGGCCAAGCAAATTTCTC 59.703 45.455 5.01 0.00 0.00 2.87
5293 5936 2.033141 GCTCTGACAGGCCAAGCA 59.967 61.111 5.01 0.00 33.21 3.91
5307 5954 2.297597 ACTCCCTAGCATGATTACGCTC 59.702 50.000 0.00 0.00 39.70 5.03
5310 5957 4.322080 TGAACTCCCTAGCATGATTACG 57.678 45.455 0.00 0.00 0.00 3.18
5332 5980 1.066605 GCATGATGCGAGGCTCAAAAT 59.933 47.619 15.95 4.27 31.71 1.82
5427 6078 6.808212 TCACGTTTTCTTCCCTATAGTTTACG 59.192 38.462 0.00 0.00 0.00 3.18
5429 6080 7.669427 TGTCACGTTTTCTTCCCTATAGTTTA 58.331 34.615 0.00 0.00 0.00 2.01
5435 6086 5.374071 AGTTTGTCACGTTTTCTTCCCTAT 58.626 37.500 0.00 0.00 0.00 2.57
5436 6087 4.773013 AGTTTGTCACGTTTTCTTCCCTA 58.227 39.130 0.00 0.00 0.00 3.53
5441 6092 7.383843 ACAATGAAAAGTTTGTCACGTTTTCTT 59.616 29.630 11.80 5.94 37.22 2.52
5442 6093 6.866248 ACAATGAAAAGTTTGTCACGTTTTCT 59.134 30.769 11.80 0.87 37.22 2.52
5495 6205 1.593209 GGTTTCAGCCACGACACGA 60.593 57.895 0.00 0.00 0.00 4.35
5498 6208 0.393132 TGTTGGTTTCAGCCACGACA 60.393 50.000 0.00 0.00 38.42 4.35
5751 6470 2.361357 ACCTCTACGACCGCTGCT 60.361 61.111 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.