Multiple sequence alignment - TraesCS4A01G453100

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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 TraesCS4A01G453100 chr4A 100.000 7242 0 0 1 7242 717799670 717806911 0.000000e+00 13374.0
1 TraesCS4A01G453100 chr4A 95.907 3494 112 9 3370 6847 717261286 717257808 0.000000e+00 5631.0
2 TraesCS4A01G453100 chr4A 95.695 3275 130 8 1 3266 717264557 717261285 0.000000e+00 5256.0
3 TraesCS4A01G453100 chr4A 93.750 3472 158 19 3370 6799 717287641 717284187 0.000000e+00 5155.0
4 TraesCS4A01G453100 chr4A 94.992 3235 152 5 3370 6596 717752222 717755454 0.000000e+00 5068.0
5 TraesCS4A01G453100 chr4A 94.186 2993 133 6 3894 6847 717225661 717222671 0.000000e+00 4525.0
6 TraesCS4A01G453100 chr4A 94.183 2613 136 13 207 2809 717237356 717234750 0.000000e+00 3969.0
7 TraesCS4A01G453100 chr4A 93.950 2463 121 10 816 3266 717749777 717752223 0.000000e+00 3698.0
8 TraesCS4A01G453100 chr4A 92.916 1327 83 6 1 1322 717289138 717287818 0.000000e+00 1919.0
9 TraesCS4A01G453100 chr4A 92.028 715 56 1 1 714 717748670 717749384 0.000000e+00 1003.0
10 TraesCS4A01G453100 chr4A 94.098 305 10 2 6944 7240 717222519 717222215 2.380000e-124 457.0
11 TraesCS4A01G453100 chr4A 88.354 395 19 6 6854 7240 717257767 717257392 3.980000e-122 449.0
12 TraesCS4A01G453100 chr4A 93.174 293 12 3 6944 7228 717755753 717756045 2.420000e-114 424.0
13 TraesCS4A01G453100 chr4A 92.657 286 11 3 6962 7240 717284183 717283901 3.150000e-108 403.0
14 TraesCS4A01G453100 chr4A 97.857 140 3 0 6708 6847 717755454 717755593 7.260000e-60 243.0
15 TraesCS4A01G453100 chr4A 96.226 106 4 0 6854 6959 717755635 717755740 2.690000e-39 174.0
16 TraesCS4A01G453100 chr4A 96.939 98 3 0 6862 6959 717222630 717222533 1.620000e-36 165.0
17 TraesCS4A01G453100 chr4A 90.654 107 10 0 3265 3371 590945708 590945814 7.570000e-30 143.0
18 TraesCS4A01G453100 chr7A 93.029 3902 222 33 3370 7240 16426181 16430063 0.000000e+00 5653.0
19 TraesCS4A01G453100 chr7A 94.055 3011 150 12 3370 6371 16314086 16317076 0.000000e+00 4542.0
20 TraesCS4A01G453100 chr7A 92.327 2411 162 15 4298 6690 15822537 15820132 0.000000e+00 3406.0
21 TraesCS4A01G453100 chr7A 92.227 2380 161 17 901 3266 16311718 16314087 0.000000e+00 3349.0
22 TraesCS4A01G453100 chr7A 92.860 2297 127 20 980 3266 16378723 16380992 0.000000e+00 3299.0
23 TraesCS4A01G453100 chr7A 91.429 2380 175 20 901 3266 16423818 16426182 0.000000e+00 3238.0
24 TraesCS4A01G453100 chr7A 92.487 1544 97 9 3370 4895 16380991 16382533 0.000000e+00 2191.0
25 TraesCS4A01G453100 chr7A 93.257 875 37 2 5979 6847 16393096 16393954 0.000000e+00 1269.0
26 TraesCS4A01G453100 chr7A 88.341 669 70 4 1 665 15837556 15836892 0.000000e+00 797.0
27 TraesCS4A01G453100 chr7A 88.166 676 71 3 1 667 16377397 16378072 0.000000e+00 797.0
28 TraesCS4A01G453100 chr7A 87.537 674 74 7 1 668 15775474 15774805 0.000000e+00 771.0
29 TraesCS4A01G453100 chr7A 95.337 386 17 1 6854 7238 16317520 16317905 4.800000e-171 612.0
30 TraesCS4A01G453100 chr7A 93.557 388 24 1 6854 7240 16393992 16394379 1.750000e-160 577.0
31 TraesCS4A01G453100 chr7A 85.874 269 27 10 663 929 16423627 16423886 7.160000e-70 276.0
32 TraesCS4A01G453100 chr7A 92.157 102 8 0 3265 3366 252178398 252178499 2.110000e-30 145.0
33 TraesCS4A01G453100 chr7A 90.654 107 10 0 3265 3371 94782443 94782337 7.570000e-30 143.0
34 TraesCS4A01G453100 chr7A 91.346 104 9 0 3268 3371 704294010 704293907 7.570000e-30 143.0
35 TraesCS4A01G453100 chr7A 83.871 124 18 2 6322 6443 15789520 15789397 4.590000e-22 117.0
36 TraesCS4A01G453100 chr7A 83.871 124 18 2 6322 6443 15817404 15817281 4.590000e-22 117.0
37 TraesCS4A01G453100 chr7A 95.745 47 2 0 6801 6847 16429582 16429628 7.790000e-10 76.8
38 TraesCS4A01G453100 chr7D 95.504 3492 136 11 3370 6847 16761495 16758011 0.000000e+00 5559.0
39 TraesCS4A01G453100 chr7D 94.505 3494 175 7 3370 6847 17121120 17124612 0.000000e+00 5373.0
40 TraesCS4A01G453100 chr7D 93.959 3294 167 20 1 3266 16764783 16761494 0.000000e+00 4951.0
41 TraesCS4A01G453100 chr7D 93.254 2357 136 18 924 3266 17118774 17121121 0.000000e+00 3450.0
42 TraesCS4A01G453100 chr7D 93.380 2296 139 9 980 3266 16992267 16994558 0.000000e+00 3386.0
43 TraesCS4A01G453100 chr7D 94.261 1272 62 6 3370 4633 16994557 16995825 0.000000e+00 1934.0
44 TraesCS4A01G453100 chr7D 92.556 712 37 6 6539 7240 16995822 16996527 0.000000e+00 1007.0
45 TraesCS4A01G453100 chr7D 88.296 675 70 3 1 666 17117283 17117957 0.000000e+00 800.0
46 TraesCS4A01G453100 chr7D 95.396 391 14 3 6854 7240 16757969 16757579 2.870000e-173 619.0
47 TraesCS4A01G453100 chr7D 93.773 273 17 0 6968 7240 17124730 17125002 1.880000e-110 411.0
48 TraesCS4A01G453100 chr7D 87.547 265 27 6 663 923 16991986 16992248 1.180000e-77 302.0
49 TraesCS4A01G453100 chr7D 90.741 108 10 0 3265 3372 236821536 236821643 2.110000e-30 145.0
50 TraesCS4A01G453100 chr7D 90.741 108 9 1 3265 3371 294047665 294047772 7.570000e-30 143.0
51 TraesCS4A01G453100 chr7D 93.590 78 5 0 6857 6934 17124658 17124735 4.590000e-22 117.0
52 TraesCS4A01G453100 chr7D 97.143 35 0 1 940 973 16992188 16992222 2.820000e-04 58.4
53 TraesCS4A01G453100 chr7B 94.257 2159 113 6 4696 6845 655811492 655813648 0.000000e+00 3290.0
54 TraesCS4A01G453100 chr7B 92.361 2304 149 18 980 3266 655805498 655807791 0.000000e+00 3254.0
55 TraesCS4A01G453100 chr7B 88.095 672 71 5 1 666 655706509 655707177 0.000000e+00 789.0
56 TraesCS4A01G453100 chr7B 87.072 263 21 8 663 925 655805227 655805476 1.190000e-72 285.0
57 TraesCS4A01G453100 chr7B 86.590 261 25 9 663 923 655663043 655663293 5.530000e-71 279.0
58 TraesCS4A01G453100 chr7B 83.721 258 29 11 663 920 655750110 655750354 1.570000e-56 231.0
59 TraesCS4A01G453100 chr7B 90.244 164 15 1 760 923 655689561 655689723 5.690000e-51 213.0
60 TraesCS4A01G453100 chr7B 89.831 118 9 3 3265 3380 357651484 357651600 1.630000e-31 148.0
61 TraesCS4A01G453100 chr7B 97.297 37 0 1 938 973 655805412 655805448 2.180000e-05 62.1
62 TraesCS4A01G453100 chr7B 97.143 35 0 1 940 973 655663233 655663267 2.820000e-04 58.4
63 TraesCS4A01G453100 chr7B 97.143 35 0 1 940 973 655689663 655689697 2.820000e-04 58.4
64 TraesCS4A01G453100 chr7B 97.143 35 0 1 940 973 655707993 655708027 2.820000e-04 58.4
65 TraesCS4A01G453100 chr6D 90.090 111 11 0 3261 3371 302113640 302113750 2.110000e-30 145.0
66 TraesCS4A01G453100 chr4B 87.931 116 14 0 3264 3379 28196881 28196996 3.520000e-28 137.0


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 TraesCS4A01G453100 chr4A 717799670 717806911 7241 False 13374.000000 13374 100.000000 1 7242 1 chr4A.!!$F2 7241
1 TraesCS4A01G453100 chr4A 717234750 717237356 2606 True 3969.000000 3969 94.183000 207 2809 1 chr4A.!!$R1 2602
2 TraesCS4A01G453100 chr4A 717257392 717264557 7165 True 3778.666667 5631 93.318667 1 7240 3 chr4A.!!$R3 7239
3 TraesCS4A01G453100 chr4A 717283901 717289138 5237 True 2492.333333 5155 93.107667 1 7240 3 chr4A.!!$R4 7239
4 TraesCS4A01G453100 chr4A 717748670 717756045 7375 False 1768.333333 5068 94.704500 1 7228 6 chr4A.!!$F3 7227
5 TraesCS4A01G453100 chr4A 717222215 717225661 3446 True 1715.666667 4525 95.074333 3894 7240 3 chr4A.!!$R2 3346
6 TraesCS4A01G453100 chr7A 16311718 16317905 6187 False 2834.333333 4542 93.873000 901 7238 3 chr7A.!!$F2 6337
7 TraesCS4A01G453100 chr7A 16423627 16430063 6436 False 2310.950000 5653 91.519250 663 7240 4 chr7A.!!$F5 6577
8 TraesCS4A01G453100 chr7A 16377397 16382533 5136 False 2095.666667 3299 91.171000 1 4895 3 chr7A.!!$F3 4894
9 TraesCS4A01G453100 chr7A 15817281 15822537 5256 True 1761.500000 3406 88.099000 4298 6690 2 chr7A.!!$R6 2392
10 TraesCS4A01G453100 chr7A 16393096 16394379 1283 False 923.000000 1269 93.407000 5979 7240 2 chr7A.!!$F4 1261
11 TraesCS4A01G453100 chr7A 15836892 15837556 664 True 797.000000 797 88.341000 1 665 1 chr7A.!!$R3 664
12 TraesCS4A01G453100 chr7A 15774805 15775474 669 True 771.000000 771 87.537000 1 668 1 chr7A.!!$R1 667
13 TraesCS4A01G453100 chr7D 16757579 16764783 7204 True 3709.666667 5559 94.953000 1 7240 3 chr7D.!!$R1 7239
14 TraesCS4A01G453100 chr7D 17117283 17125002 7719 False 2030.200000 5373 92.683600 1 7240 5 chr7D.!!$F4 7239
15 TraesCS4A01G453100 chr7D 16991986 16996527 4541 False 1337.480000 3386 92.977400 663 7240 5 chr7D.!!$F3 6577
16 TraesCS4A01G453100 chr7B 655805227 655813648 8421 False 1722.775000 3290 92.746750 663 6845 4 chr7B.!!$F6 6182
17 TraesCS4A01G453100 chr7B 655706509 655708027 1518 False 423.700000 789 92.619000 1 973 2 chr7B.!!$F5 972

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
351 355 0.114364 TGTGTCTAGGAGTGGAGCCA 59.886 55.000 0.00 0.00 0.00 4.75 F
427 438 0.465460 GCAGGAATCATGGCCGGTTA 60.465 55.000 1.90 0.00 0.00 2.85 F
889 1993 0.472925 TGAAGTCCTAGGTGTGGGCA 60.473 55.000 9.08 0.00 0.00 5.36 F
1960 3124 1.338105 TGGCTTGTGAATCAGTCTCCG 60.338 52.381 0.00 0.00 0.00 4.63 F
2949 4122 0.602562 CACCAACCCAACGATGCAAT 59.397 50.000 0.00 0.00 0.00 3.56 F
4033 5225 0.689080 GACTCATGGAGGAGGCCTGA 60.689 60.000 12.00 0.00 36.92 3.86 F
4161 5360 0.756294 TGATTGCCGGTATCGTGGAT 59.244 50.000 1.90 0.00 33.95 3.41 F
4799 10365 1.053424 GTATCTGTGGGCCCCGAATA 58.947 55.000 22.27 9.22 0.00 1.75 F
5953 11521 0.903236 GTAACGGGGAAGCCTTCTCT 59.097 55.000 3.97 0.00 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 3124 2.601367 TCTTGGCAAGGCAAGGGC 60.601 61.111 28.67 0.0 40.13 5.19 R
2153 3318 7.001674 TCAAGTGCTTCCCAATTACTTCTTTA 58.998 34.615 0.00 0.0 29.34 1.85 R
2614 3783 0.537653 TATTGGTTGCGGATGGTCGA 59.462 50.000 0.00 0.0 0.00 4.20 R
3284 4464 0.109086 CATCCGTCTGAGCGACAAGT 60.109 55.000 0.00 0.0 42.98 3.16 R
4799 10365 0.178921 TGGCTCTTGTCTCCACCTCT 60.179 55.000 0.00 0.0 0.00 3.69 R
5200 10768 0.988832 AGCCTTCGGGTCCAAACATA 59.011 50.000 0.00 0.0 37.45 2.29 R
5802 11370 2.223249 GCCAAATGCACGGTGTATAGTG 60.223 50.000 12.14 12.5 40.77 2.74 R
6170 11738 1.329292 CGTCGCAAAACAAGGTTCTGA 59.671 47.619 0.00 0.0 0.00 3.27 R
7198 12955 1.281867 TCTGATACAGCTTTGGTGGGG 59.718 52.381 1.90 0.0 35.13 4.96 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
116 117 0.533032 TATCACCGTCGTTGGCATCA 59.467 50.000 0.00 0.00 0.00 3.07
117 118 1.019278 ATCACCGTCGTTGGCATCAC 61.019 55.000 0.00 0.00 0.00 3.06
134 135 3.998913 TCACCCACTTTGCTATCATCA 57.001 42.857 0.00 0.00 0.00 3.07
187 190 1.868997 GGGTGACGAGTGTTGCATG 59.131 57.895 0.00 0.00 0.00 4.06
252 255 2.840651 CAGTAGAGGGGTCTTGGTTGAT 59.159 50.000 0.00 0.00 0.00 2.57
297 301 9.747898 AAATATGGGTGAACAACTACAAGAATA 57.252 29.630 0.00 0.00 0.00 1.75
321 325 3.904717 AGGAGAACATCGAGTACCTCAT 58.095 45.455 0.00 0.00 33.94 2.90
351 355 0.114364 TGTGTCTAGGAGTGGAGCCA 59.886 55.000 0.00 0.00 0.00 4.75
372 376 1.674057 GGTGTCTGGTCAGTGAGGG 59.326 63.158 0.00 0.00 0.00 4.30
427 438 0.465460 GCAGGAATCATGGCCGGTTA 60.465 55.000 1.90 0.00 0.00 2.85
460 471 4.248859 CATGATGTCTTTCGTCTCCTTGT 58.751 43.478 0.00 0.00 33.55 3.16
529 548 3.186119 CAAACTGACCAAAACGCACAAT 58.814 40.909 0.00 0.00 0.00 2.71
533 552 3.044986 CTGACCAAAACGCACAATTCTG 58.955 45.455 0.00 0.00 0.00 3.02
753 1600 1.092921 CCCCTCTCTCTCTCGTCACG 61.093 65.000 0.00 0.00 0.00 4.35
889 1993 0.472925 TGAAGTCCTAGGTGTGGGCA 60.473 55.000 9.08 0.00 0.00 5.36
1098 2246 3.394836 GCCTCCACTTCGCCCTCT 61.395 66.667 0.00 0.00 0.00 3.69
1121 2269 7.568349 TCTGCTATCAACATTGAAGAAGGTAT 58.432 34.615 0.00 0.00 41.13 2.73
1374 2525 5.125900 TGGAATTCATGCTCCACATTGTTAG 59.874 40.000 7.93 0.00 36.79 2.34
1416 2567 4.868171 TGTTACACTCAGCGCCTTTATAAG 59.132 41.667 2.29 0.00 0.00 1.73
1528 2682 9.519191 CATCCCAAATACTCCAATTATATGTCA 57.481 33.333 0.00 0.00 0.00 3.58
1592 2746 4.993028 AGTTGGGTGGCAAGTTTATAAGA 58.007 39.130 0.00 0.00 0.00 2.10
1668 2824 7.285401 TCAAAATCAGAAAATAGCCTATGGACC 59.715 37.037 0.00 0.00 0.00 4.46
1675 2831 6.332901 AGAAAATAGCCTATGGACCAGGTTAT 59.667 38.462 0.00 1.81 40.22 1.89
1680 2836 5.880901 AGCCTATGGACCAGGTTATTATTG 58.119 41.667 0.00 0.00 35.45 1.90
1865 3025 2.203126 CTCCAAGCCGAGGATGCC 60.203 66.667 0.00 0.00 33.99 4.40
1925 3088 8.641499 ACGATAATTCTGATTTCAAGACTCTC 57.359 34.615 0.00 0.00 0.00 3.20
1960 3124 1.338105 TGGCTTGTGAATCAGTCTCCG 60.338 52.381 0.00 0.00 0.00 4.63
2153 3318 3.259123 GCCCAAGGACATTTGAACAATCT 59.741 43.478 0.00 0.00 0.00 2.40
2467 3635 7.287696 ACACCTTTGAAATAGATTTGGAGTGTT 59.712 33.333 0.00 0.00 0.00 3.32
2524 3693 5.302568 TGAAGAACAAAAGGCTGTCATCAAT 59.697 36.000 0.00 0.00 0.00 2.57
2527 3696 6.917533 AGAACAAAAGGCTGTCATCAATAAG 58.082 36.000 0.00 0.00 0.00 1.73
2528 3697 5.649782 ACAAAAGGCTGTCATCAATAAGG 57.350 39.130 0.00 0.00 0.00 2.69
2546 3715 9.042450 TCAATAAGGATTAGTTTAGAGACACCA 57.958 33.333 0.00 0.00 31.76 4.17
2614 3783 5.320277 ACCTGCTTTCTTAAGATGCTTTCT 58.680 37.500 22.84 8.03 35.70 2.52
2783 3953 1.473434 CGGCCAGGGATTTCAGTAGTC 60.473 57.143 2.24 0.00 0.00 2.59
2858 4028 0.677731 TGCTATGCACCTTGGTCTGC 60.678 55.000 0.00 0.00 31.71 4.26
2949 4122 0.602562 CACCAACCCAACGATGCAAT 59.397 50.000 0.00 0.00 0.00 3.56
3026 4199 1.439543 CAGGAAGGCCCCTTATAGCT 58.560 55.000 0.00 0.00 36.26 3.32
3264 4444 3.581332 GGCCATGGGAATCATCATGAATT 59.419 43.478 15.13 0.00 42.25 2.17
3265 4445 4.773674 GGCCATGGGAATCATCATGAATTA 59.226 41.667 15.13 0.00 42.25 1.40
3266 4446 5.337009 GGCCATGGGAATCATCATGAATTAC 60.337 44.000 15.13 0.00 42.25 1.89
3267 4447 5.479375 GCCATGGGAATCATCATGAATTACT 59.521 40.000 15.13 0.00 42.25 2.24
3268 4448 6.349944 GCCATGGGAATCATCATGAATTACTC 60.350 42.308 15.13 0.00 42.25 2.59
3269 4449 6.152323 CCATGGGAATCATCATGAATTACTCC 59.848 42.308 2.85 2.66 42.25 3.85
3270 4450 5.634118 TGGGAATCATCATGAATTACTCCC 58.366 41.667 19.19 19.19 40.43 4.30
3271 4451 5.373555 TGGGAATCATCATGAATTACTCCCT 59.626 40.000 23.27 0.00 40.62 4.20
3272 4452 6.126097 TGGGAATCATCATGAATTACTCCCTT 60.126 38.462 23.27 0.00 40.62 3.95
3273 4453 6.432472 GGGAATCATCATGAATTACTCCCTTC 59.568 42.308 18.92 0.89 37.57 3.46
3274 4454 7.000472 GGAATCATCATGAATTACTCCCTTCA 59.000 38.462 0.00 0.00 35.95 3.02
3275 4455 7.174599 GGAATCATCATGAATTACTCCCTTCAG 59.825 40.741 0.00 0.00 35.04 3.02
3276 4456 6.566079 TCATCATGAATTACTCCCTTCAGT 57.434 37.500 0.00 0.00 35.04 3.41
3277 4457 6.586344 TCATCATGAATTACTCCCTTCAGTC 58.414 40.000 0.00 0.00 35.04 3.51
3278 4458 6.385176 TCATCATGAATTACTCCCTTCAGTCT 59.615 38.462 0.00 0.00 35.04 3.24
3279 4459 7.565029 TCATCATGAATTACTCCCTTCAGTCTA 59.435 37.037 0.00 0.00 35.04 2.59
3280 4460 7.921041 TCATGAATTACTCCCTTCAGTCTAT 57.079 36.000 0.00 0.00 35.04 1.98
3281 4461 9.607333 ATCATGAATTACTCCCTTCAGTCTATA 57.393 33.333 0.00 0.00 35.04 1.31
3282 4462 9.607333 TCATGAATTACTCCCTTCAGTCTATAT 57.393 33.333 0.00 0.00 35.04 0.86
3289 4469 9.710818 TTACTCCCTTCAGTCTATATTACTTGT 57.289 33.333 0.00 0.00 0.00 3.16
3290 4470 8.240267 ACTCCCTTCAGTCTATATTACTTGTC 57.760 38.462 0.00 0.00 0.00 3.18
3291 4471 7.013464 ACTCCCTTCAGTCTATATTACTTGTCG 59.987 40.741 0.00 0.00 0.00 4.35
3292 4472 5.921408 CCCTTCAGTCTATATTACTTGTCGC 59.079 44.000 0.00 0.00 0.00 5.19
3293 4473 6.239064 CCCTTCAGTCTATATTACTTGTCGCT 60.239 42.308 0.00 0.00 0.00 4.93
3294 4474 6.858993 CCTTCAGTCTATATTACTTGTCGCTC 59.141 42.308 0.00 0.00 0.00 5.03
3295 4475 6.937436 TCAGTCTATATTACTTGTCGCTCA 57.063 37.500 0.00 0.00 0.00 4.26
3296 4476 6.960468 TCAGTCTATATTACTTGTCGCTCAG 58.040 40.000 0.00 0.00 0.00 3.35
3297 4477 6.766467 TCAGTCTATATTACTTGTCGCTCAGA 59.234 38.462 0.00 0.00 0.00 3.27
3307 4487 2.039327 GTCGCTCAGACGGATGTATC 57.961 55.000 0.00 0.00 40.43 2.24
3308 4488 1.604755 GTCGCTCAGACGGATGTATCT 59.395 52.381 0.00 0.00 40.43 1.98
3309 4489 2.806818 GTCGCTCAGACGGATGTATCTA 59.193 50.000 0.00 0.00 40.43 1.98
3310 4490 3.067833 TCGCTCAGACGGATGTATCTAG 58.932 50.000 0.00 0.00 0.00 2.43
3311 4491 2.413502 CGCTCAGACGGATGTATCTAGC 60.414 54.545 0.00 0.00 0.00 3.42
3312 4492 2.554462 GCTCAGACGGATGTATCTAGCA 59.446 50.000 0.00 0.00 0.00 3.49
3313 4493 3.610585 GCTCAGACGGATGTATCTAGCAC 60.611 52.174 0.00 0.00 0.00 4.40
3314 4494 3.818210 CTCAGACGGATGTATCTAGCACT 59.182 47.826 0.00 0.00 0.00 4.40
3315 4495 3.565902 TCAGACGGATGTATCTAGCACTG 59.434 47.826 0.00 0.00 0.00 3.66
3316 4496 3.565902 CAGACGGATGTATCTAGCACTGA 59.434 47.826 0.00 0.00 0.00 3.41
3317 4497 4.036852 CAGACGGATGTATCTAGCACTGAA 59.963 45.833 0.00 0.00 0.00 3.02
3318 4498 4.645136 AGACGGATGTATCTAGCACTGAAA 59.355 41.667 0.00 0.00 0.00 2.69
3319 4499 5.303078 AGACGGATGTATCTAGCACTGAAAT 59.697 40.000 0.00 0.00 0.00 2.17
3320 4500 6.490381 AGACGGATGTATCTAGCACTGAAATA 59.510 38.462 0.00 0.00 0.00 1.40
3321 4501 6.448006 ACGGATGTATCTAGCACTGAAATAC 58.552 40.000 0.00 0.00 0.00 1.89
3322 4502 6.040504 ACGGATGTATCTAGCACTGAAATACA 59.959 38.462 1.90 1.90 37.26 2.29
3323 4503 7.093354 CGGATGTATCTAGCACTGAAATACAT 58.907 38.462 9.54 9.54 42.96 2.29
3328 4508 9.574516 TGTATCTAGCACTGAAATACATCTAGA 57.425 33.333 0.00 0.00 36.86 2.43
3332 4512 9.574516 TCTAGCACTGAAATACATCTAGATACA 57.425 33.333 4.54 0.00 32.49 2.29
3335 4515 8.864087 AGCACTGAAATACATCTAGATACATCA 58.136 33.333 4.54 5.50 0.00 3.07
3336 4516 9.138062 GCACTGAAATACATCTAGATACATCAG 57.862 37.037 20.39 20.39 0.00 2.90
3343 4523 9.703892 AATACATCTAGATACATCAGTTTGAGC 57.296 33.333 4.54 0.00 0.00 4.26
3344 4524 6.212235 ACATCTAGATACATCAGTTTGAGCG 58.788 40.000 4.54 0.00 0.00 5.03
3345 4525 6.039829 ACATCTAGATACATCAGTTTGAGCGA 59.960 38.462 4.54 0.00 0.00 4.93
3346 4526 5.822278 TCTAGATACATCAGTTTGAGCGAC 58.178 41.667 0.00 0.00 0.00 5.19
3347 4527 4.456280 AGATACATCAGTTTGAGCGACA 57.544 40.909 0.00 0.00 0.00 4.35
3348 4528 4.820897 AGATACATCAGTTTGAGCGACAA 58.179 39.130 0.00 0.00 36.65 3.18
3349 4529 4.867047 AGATACATCAGTTTGAGCGACAAG 59.133 41.667 0.00 0.00 39.77 3.16
3350 4530 2.838736 ACATCAGTTTGAGCGACAAGT 58.161 42.857 0.00 0.00 39.77 3.16
3351 4531 3.990092 ACATCAGTTTGAGCGACAAGTA 58.010 40.909 0.00 0.00 39.77 2.24
3352 4532 4.377021 ACATCAGTTTGAGCGACAAGTAA 58.623 39.130 0.00 0.00 39.77 2.24
3353 4533 4.997395 ACATCAGTTTGAGCGACAAGTAAT 59.003 37.500 0.00 0.00 39.77 1.89
3354 4534 6.163476 ACATCAGTTTGAGCGACAAGTAATA 58.837 36.000 0.00 0.00 39.77 0.98
3355 4535 6.818644 ACATCAGTTTGAGCGACAAGTAATAT 59.181 34.615 0.00 0.00 39.77 1.28
3356 4536 6.647212 TCAGTTTGAGCGACAAGTAATATG 57.353 37.500 0.00 0.00 39.77 1.78
3357 4537 5.580691 TCAGTTTGAGCGACAAGTAATATGG 59.419 40.000 0.00 0.00 39.77 2.74
3358 4538 5.580691 CAGTTTGAGCGACAAGTAATATGGA 59.419 40.000 0.00 0.00 39.77 3.41
3359 4539 6.258727 CAGTTTGAGCGACAAGTAATATGGAT 59.741 38.462 0.00 0.00 39.77 3.41
3360 4540 6.480320 AGTTTGAGCGACAAGTAATATGGATC 59.520 38.462 0.00 0.00 39.77 3.36
3361 4541 4.546570 TGAGCGACAAGTAATATGGATCG 58.453 43.478 0.00 0.00 0.00 3.69
3362 4542 3.914312 AGCGACAAGTAATATGGATCGG 58.086 45.455 0.00 0.00 0.00 4.18
3363 4543 3.572682 AGCGACAAGTAATATGGATCGGA 59.427 43.478 0.00 0.00 0.00 4.55
3364 4544 3.921021 GCGACAAGTAATATGGATCGGAG 59.079 47.826 0.00 0.00 0.00 4.63
3365 4545 4.486090 CGACAAGTAATATGGATCGGAGG 58.514 47.826 0.00 0.00 0.00 4.30
3366 4546 4.022242 CGACAAGTAATATGGATCGGAGGT 60.022 45.833 0.00 0.00 0.00 3.85
3367 4547 5.182570 CGACAAGTAATATGGATCGGAGGTA 59.817 44.000 0.00 0.00 0.00 3.08
3368 4548 6.591750 ACAAGTAATATGGATCGGAGGTAG 57.408 41.667 0.00 0.00 0.00 3.18
3398 4578 6.327365 ACATTGATGTACCTCAGGTCATATGA 59.673 38.462 0.00 0.00 39.68 2.15
3464 4645 1.645919 ACCCTTGCCCTTACCATCATT 59.354 47.619 0.00 0.00 0.00 2.57
3515 4696 8.834465 CATCCACCTAAGATTATTGAAACTCTG 58.166 37.037 0.00 0.00 0.00 3.35
3576 4757 2.104170 TGGTATATGTGTGCACGAGGA 58.896 47.619 13.13 0.00 0.00 3.71
3770 4960 3.152341 CTCACCTCATGCCTTCTTGTTT 58.848 45.455 0.00 0.00 0.00 2.83
3798 4989 5.010933 CAGGACTCTTCTAACTAGGTGTCA 58.989 45.833 0.00 0.00 0.00 3.58
3824 5015 5.009710 CACAAACTCACTACCAGACTCACTA 59.990 44.000 0.00 0.00 0.00 2.74
3828 5019 5.761205 ACTCACTACCAGACTCACTATCAT 58.239 41.667 0.00 0.00 0.00 2.45
3886 5077 3.610911 CCAGGGATTGGTCAACTTACTC 58.389 50.000 0.00 0.00 42.41 2.59
4033 5225 0.689080 GACTCATGGAGGAGGCCTGA 60.689 60.000 12.00 0.00 36.92 3.86
4111 5305 1.203087 TGTCGAGTTCTACCCCCTTGA 60.203 52.381 0.00 0.00 0.00 3.02
4161 5360 0.756294 TGATTGCCGGTATCGTGGAT 59.244 50.000 1.90 0.00 33.95 3.41
4296 5501 1.648720 GTGCTTGCATGTCACGTGT 59.351 52.632 16.51 0.00 0.00 4.49
4367 5578 3.063997 CGTGTTTGAGTCAAGCTTGAGTT 59.936 43.478 32.04 22.21 40.75 3.01
4384 5595 9.765795 AGCTTGAGTTCAAATATGTAGTATACC 57.234 33.333 0.00 0.00 36.66 2.73
4537 5749 2.916527 CTTCCTTGGCCCGCCATCAT 62.917 60.000 9.70 0.00 46.64 2.45
4636 10201 3.587061 TGGGGATCTGAGTGTATGTGTTT 59.413 43.478 0.00 0.00 0.00 2.83
4647 10212 3.987220 GTGTATGTGTTTTTGGTGGATGC 59.013 43.478 0.00 0.00 0.00 3.91
4722 10288 9.865321 GTTTACCACTATCAGTGTAGAACAATA 57.135 33.333 5.65 0.00 44.50 1.90
4794 10360 1.696097 ATCACGTATCTGTGGGCCCC 61.696 60.000 22.27 11.72 40.31 5.80
4799 10365 1.053424 GTATCTGTGGGCCCCGAATA 58.947 55.000 22.27 9.22 0.00 1.75
4952 10518 4.521639 AGATGCACATTTCGATGGCAATAT 59.478 37.500 0.00 0.00 38.08 1.28
5125 10693 6.521151 AATTGTTGTCCTTTCATGATCCTC 57.479 37.500 0.00 0.00 0.00 3.71
5142 10710 5.713389 TGATCCTCAATGCAGAATTTGAAGT 59.287 36.000 2.36 0.00 0.00 3.01
5200 10768 1.667830 CATCTCCGTGCACCGTGTT 60.668 57.895 12.15 0.00 33.66 3.32
5460 11028 8.811017 CATTGATCCTGTATATCCAAGTACTCT 58.189 37.037 0.00 0.00 0.00 3.24
5540 11108 1.532523 TGGTCATGCGATTTTCTGCA 58.467 45.000 0.00 0.00 46.51 4.41
5617 11185 3.254166 CACCTTTCCCATTGAGTCAACTG 59.746 47.826 7.96 7.86 0.00 3.16
5671 11239 7.041780 GCGTCACCAGATTCATATCTATTTGTT 60.042 37.037 0.00 0.00 39.11 2.83
5802 11370 4.260784 GGTCATTATGAGGATGCGTCAAAC 60.261 45.833 8.47 0.00 32.06 2.93
5953 11521 0.903236 GTAACGGGGAAGCCTTCTCT 59.097 55.000 3.97 0.00 0.00 3.10
6170 11738 3.884037 ACCAAAATGAGGAGTTGGAGT 57.116 42.857 8.58 0.00 43.82 3.85
6245 11813 4.454678 CTTTGCAGCTTGGGTATGAGATA 58.545 43.478 0.00 0.00 0.00 1.98
6259 11828 3.615224 TGAGATAGTGTCATTGCAGCA 57.385 42.857 0.00 0.00 0.00 4.41
6384 11987 0.466555 TGTTTGCCACCCAGTGTACC 60.467 55.000 0.00 0.00 0.00 3.34
6438 12041 4.556699 GCTGTTTTCGCTGAACCTTGTTAT 60.557 41.667 0.00 0.00 0.00 1.89
6440 12043 6.621316 TGTTTTCGCTGAACCTTGTTATTA 57.379 33.333 0.00 0.00 0.00 0.98
6478 12081 2.886523 CAAGAGACAAGGGTTTGCATCA 59.113 45.455 0.00 0.00 37.85 3.07
6551 12167 0.250814 TGCACCATGTCAGATGTGCA 60.251 50.000 17.66 17.66 44.11 4.57
6617 12234 6.821388 TCTATTTGTAGCTTGATCTCCTTCC 58.179 40.000 0.00 0.00 0.00 3.46
6687 12304 5.534207 TCAAATGCAGATCTGTTTGGTTT 57.466 34.783 26.32 16.93 33.55 3.27
6847 12472 1.271597 GGTGACCTTGCAACTCTCCAT 60.272 52.381 12.59 0.00 0.00 3.41
6848 12473 2.027192 GGTGACCTTGCAACTCTCCATA 60.027 50.000 12.59 0.00 0.00 2.74
6849 12474 3.370953 GGTGACCTTGCAACTCTCCATAT 60.371 47.826 12.59 0.00 0.00 1.78
6850 12475 4.141711 GGTGACCTTGCAACTCTCCATATA 60.142 45.833 12.59 0.00 0.00 0.86
6851 12476 5.455326 GGTGACCTTGCAACTCTCCATATAT 60.455 44.000 12.59 0.00 0.00 0.86
6852 12477 5.468072 GTGACCTTGCAACTCTCCATATATG 59.532 44.000 5.68 5.68 0.00 1.78
6926 12591 3.564235 GCTCAAGCACATCACATGAAA 57.436 42.857 0.00 0.00 41.59 2.69
6990 12738 3.850173 TGAAAGGGAAGTTACAGGCCTAT 59.150 43.478 3.98 0.00 0.00 2.57
7147 12897 5.747565 TCTGTTTGTAATGCAAGTTTCGAG 58.252 37.500 0.00 0.00 38.47 4.04
7159 12916 4.551990 GCAAGTTTCGAGACGAACATTCAA 60.552 41.667 6.09 0.00 45.64 2.69
7198 12955 3.063997 CGACTGCAACATTGTAGAATCCC 59.936 47.826 15.48 0.70 42.54 3.85
7240 12997 1.599542 GCTAATCATCAACCGCACTCC 59.400 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 2.648059 GCTGATGATAGCAAAGTGGGT 58.352 47.619 0.00 0.00 43.17 4.51
134 135 1.204941 GTCCTATGTGTCGTCCTTGCT 59.795 52.381 0.00 0.00 0.00 3.91
187 190 3.244422 TGACAGTTGTGACCTCCATAACC 60.244 47.826 0.00 0.00 44.78 2.85
297 301 4.506937 AGGTACTCGATGTTCTCCTAGT 57.493 45.455 0.00 0.00 0.00 2.57
351 355 1.456892 TCACTGACCAGACACCCGT 60.457 57.895 3.76 0.00 0.00 5.28
372 376 2.621998 CCATCAGATGCCAATGACCTTC 59.378 50.000 4.68 0.00 0.00 3.46
427 438 3.000684 AGACATCATGCAACATGCTCT 57.999 42.857 7.91 7.47 45.31 4.09
460 471 0.770499 TCAATGTGAGGTGCTCCCAA 59.230 50.000 0.00 0.00 34.66 4.12
504 523 1.202245 GCGTTTTGGTCAGTTTGCTCA 60.202 47.619 0.00 0.00 0.00 4.26
520 539 3.684788 GTGTAGGATCAGAATTGTGCGTT 59.315 43.478 0.00 0.00 0.00 4.84
620 639 1.732259 CTGCATACGACAACAAGACCC 59.268 52.381 0.00 0.00 0.00 4.46
632 651 5.871524 AGATTATTATGTGAGCCTGCATACG 59.128 40.000 0.00 0.00 0.00 3.06
753 1600 4.735358 GGGGAAGGGGGAACGTGC 62.735 72.222 0.00 0.00 0.00 5.34
789 1828 2.819984 ATCATGGGCGGTTCAAGCGT 62.820 55.000 11.22 0.00 41.74 5.07
889 1993 1.545582 CAAATCTGGATGCGGTTGGTT 59.454 47.619 0.00 0.00 0.00 3.67
999 2147 3.794475 GCTTTCCTTCATCGCCAATCATG 60.794 47.826 0.00 0.00 0.00 3.07
1098 2246 6.543465 CCATACCTTCTTCAATGTTGATAGCA 59.457 38.462 0.00 0.00 37.00 3.49
1121 2269 3.695830 AAATAGTGCGAGTTCTTCCCA 57.304 42.857 0.00 0.00 0.00 4.37
1299 2450 6.116126 GCTAGTGTCCCATCAATACTTCTTT 58.884 40.000 0.00 0.00 0.00 2.52
1528 2682 3.306641 CCTGCTTCTAGCTCTTCAAGTGT 60.307 47.826 0.00 0.00 42.97 3.55
1699 2859 6.938698 TGAGGTGGGTAAACTAGTTGATTA 57.061 37.500 9.34 0.00 0.00 1.75
1708 2868 2.781174 TCAAGGTTGAGGTGGGTAAACT 59.219 45.455 0.00 0.00 32.50 2.66
1865 3025 3.118775 TGGACATGGTCATTTCCTCGTAG 60.119 47.826 14.82 0.00 38.25 3.51
1925 3088 5.580691 TCACAAGCCAGATAGTTTATGTTCG 59.419 40.000 0.00 0.00 0.00 3.95
1960 3124 2.601367 TCTTGGCAAGGCAAGGGC 60.601 61.111 28.67 0.00 40.13 5.19
2153 3318 7.001674 TCAAGTGCTTCCCAATTACTTCTTTA 58.998 34.615 0.00 0.00 29.34 1.85
2467 3635 2.650322 AGAGAGGTGAGGGTAGTGAAGA 59.350 50.000 0.00 0.00 0.00 2.87
2524 3693 7.580882 GCCTTGGTGTCTCTAAACTAATCCTTA 60.581 40.741 0.00 0.00 0.00 2.69
2527 3696 4.876679 GCCTTGGTGTCTCTAAACTAATCC 59.123 45.833 0.00 0.00 0.00 3.01
2528 3697 5.735766 AGCCTTGGTGTCTCTAAACTAATC 58.264 41.667 0.00 0.00 0.00 1.75
2614 3783 0.537653 TATTGGTTGCGGATGGTCGA 59.462 50.000 0.00 0.00 0.00 4.20
2799 3969 8.333984 TCGGTATGAGTAGATATGGGAAAGATA 58.666 37.037 0.00 0.00 0.00 1.98
2858 4028 1.344438 TCTATGGCTGCAATACGGAGG 59.656 52.381 0.50 0.00 32.67 4.30
2949 4122 0.457851 CCGTTGGGTTGAAAGTGCAA 59.542 50.000 0.00 0.00 0.00 4.08
3026 4199 8.539544 TGTTCTAGTGTGATCTTCATAATTGGA 58.460 33.333 0.00 0.00 0.00 3.53
3180 4360 3.056749 AGACGTCACATCTGGAGTTTACC 60.057 47.826 19.50 0.00 0.00 2.85
3264 4444 9.352191 GACAAGTAATATAGACTGAAGGGAGTA 57.648 37.037 0.00 0.00 0.00 2.59
3265 4445 7.013464 CGACAAGTAATATAGACTGAAGGGAGT 59.987 40.741 0.00 0.00 0.00 3.85
3266 4446 7.364200 CGACAAGTAATATAGACTGAAGGGAG 58.636 42.308 0.00 0.00 0.00 4.30
3267 4447 6.238953 GCGACAAGTAATATAGACTGAAGGGA 60.239 42.308 0.00 0.00 0.00 4.20
3268 4448 5.921408 GCGACAAGTAATATAGACTGAAGGG 59.079 44.000 0.00 0.00 0.00 3.95
3269 4449 6.740110 AGCGACAAGTAATATAGACTGAAGG 58.260 40.000 0.00 0.00 0.00 3.46
3270 4450 7.418408 TGAGCGACAAGTAATATAGACTGAAG 58.582 38.462 0.00 0.00 0.00 3.02
3271 4451 7.282450 TCTGAGCGACAAGTAATATAGACTGAA 59.718 37.037 0.00 0.00 0.00 3.02
3272 4452 6.766467 TCTGAGCGACAAGTAATATAGACTGA 59.234 38.462 0.00 0.00 0.00 3.41
3273 4453 6.853872 GTCTGAGCGACAAGTAATATAGACTG 59.146 42.308 0.00 0.00 42.37 3.51
3274 4454 6.292973 CGTCTGAGCGACAAGTAATATAGACT 60.293 42.308 0.00 0.00 42.98 3.24
3275 4455 5.846994 CGTCTGAGCGACAAGTAATATAGAC 59.153 44.000 0.00 0.00 42.98 2.59
3276 4456 5.049612 CCGTCTGAGCGACAAGTAATATAGA 60.050 44.000 0.00 0.00 42.98 1.98
3277 4457 5.049612 TCCGTCTGAGCGACAAGTAATATAG 60.050 44.000 0.00 0.00 42.98 1.31
3278 4458 4.818005 TCCGTCTGAGCGACAAGTAATATA 59.182 41.667 0.00 0.00 42.98 0.86
3279 4459 3.630769 TCCGTCTGAGCGACAAGTAATAT 59.369 43.478 0.00 0.00 42.98 1.28
3280 4460 3.011818 TCCGTCTGAGCGACAAGTAATA 58.988 45.455 0.00 0.00 42.98 0.98
3281 4461 1.816835 TCCGTCTGAGCGACAAGTAAT 59.183 47.619 0.00 0.00 42.98 1.89
3282 4462 1.241165 TCCGTCTGAGCGACAAGTAA 58.759 50.000 0.00 0.00 42.98 2.24
3283 4463 1.132453 CATCCGTCTGAGCGACAAGTA 59.868 52.381 0.00 0.00 42.98 2.24
3284 4464 0.109086 CATCCGTCTGAGCGACAAGT 60.109 55.000 0.00 0.00 42.98 3.16
3285 4465 0.109086 ACATCCGTCTGAGCGACAAG 60.109 55.000 0.00 0.00 42.98 3.16
3286 4466 1.170442 TACATCCGTCTGAGCGACAA 58.830 50.000 0.00 0.00 42.98 3.18
3287 4467 1.333931 GATACATCCGTCTGAGCGACA 59.666 52.381 0.00 0.00 42.98 4.35
3288 4468 1.604755 AGATACATCCGTCTGAGCGAC 59.395 52.381 0.00 0.00 39.33 5.19
3289 4469 1.968704 AGATACATCCGTCTGAGCGA 58.031 50.000 0.00 0.00 0.00 4.93
3290 4470 2.413502 GCTAGATACATCCGTCTGAGCG 60.414 54.545 0.00 0.00 0.00 5.03
3291 4471 2.554462 TGCTAGATACATCCGTCTGAGC 59.446 50.000 0.00 0.00 0.00 4.26
3292 4472 3.818210 AGTGCTAGATACATCCGTCTGAG 59.182 47.826 0.00 0.00 0.00 3.35
3293 4473 3.565902 CAGTGCTAGATACATCCGTCTGA 59.434 47.826 0.00 0.00 0.00 3.27
3294 4474 3.565902 TCAGTGCTAGATACATCCGTCTG 59.434 47.826 0.00 0.00 0.00 3.51
3295 4475 3.821748 TCAGTGCTAGATACATCCGTCT 58.178 45.455 0.00 0.00 0.00 4.18
3296 4476 4.569761 TTCAGTGCTAGATACATCCGTC 57.430 45.455 0.00 0.00 0.00 4.79
3297 4477 5.537300 ATTTCAGTGCTAGATACATCCGT 57.463 39.130 0.00 0.00 0.00 4.69
3298 4478 6.447162 TGTATTTCAGTGCTAGATACATCCG 58.553 40.000 0.00 0.00 30.60 4.18
3299 4479 8.472683 GATGTATTTCAGTGCTAGATACATCC 57.527 38.462 21.74 12.87 45.75 3.51
3302 4482 9.574516 TCTAGATGTATTTCAGTGCTAGATACA 57.425 33.333 0.00 0.00 37.53 2.29
3306 4486 9.574516 TGTATCTAGATGTATTTCAGTGCTAGA 57.425 33.333 15.79 0.00 38.41 2.43
3309 4489 8.864087 TGATGTATCTAGATGTATTTCAGTGCT 58.136 33.333 15.79 0.00 0.00 4.40
3310 4490 9.138062 CTGATGTATCTAGATGTATTTCAGTGC 57.862 37.037 15.79 0.00 0.00 4.40
3317 4497 9.703892 GCTCAAACTGATGTATCTAGATGTATT 57.296 33.333 15.79 0.00 0.00 1.89
3318 4498 8.026026 CGCTCAAACTGATGTATCTAGATGTAT 58.974 37.037 15.79 9.11 0.00 2.29
3319 4499 7.228706 TCGCTCAAACTGATGTATCTAGATGTA 59.771 37.037 15.79 4.44 0.00 2.29
3320 4500 6.039829 TCGCTCAAACTGATGTATCTAGATGT 59.960 38.462 15.79 0.32 0.00 3.06
3321 4501 6.362016 GTCGCTCAAACTGATGTATCTAGATG 59.638 42.308 15.79 0.00 0.00 2.90
3322 4502 6.039829 TGTCGCTCAAACTGATGTATCTAGAT 59.960 38.462 10.73 10.73 0.00 1.98
3323 4503 5.357032 TGTCGCTCAAACTGATGTATCTAGA 59.643 40.000 0.00 0.00 0.00 2.43
3324 4504 5.582550 TGTCGCTCAAACTGATGTATCTAG 58.417 41.667 0.00 0.00 0.00 2.43
3325 4505 5.576447 TGTCGCTCAAACTGATGTATCTA 57.424 39.130 0.00 0.00 0.00 1.98
3326 4506 4.456280 TGTCGCTCAAACTGATGTATCT 57.544 40.909 0.00 0.00 0.00 1.98
3327 4507 4.627467 ACTTGTCGCTCAAACTGATGTATC 59.373 41.667 0.00 0.00 35.48 2.24
3328 4508 4.569943 ACTTGTCGCTCAAACTGATGTAT 58.430 39.130 0.00 0.00 35.48 2.29
3329 4509 3.990092 ACTTGTCGCTCAAACTGATGTA 58.010 40.909 0.00 0.00 35.48 2.29
3330 4510 2.838736 ACTTGTCGCTCAAACTGATGT 58.161 42.857 0.00 0.00 35.48 3.06
3331 4511 4.990543 TTACTTGTCGCTCAAACTGATG 57.009 40.909 0.00 0.00 35.48 3.07
3332 4512 6.258727 CCATATTACTTGTCGCTCAAACTGAT 59.741 38.462 0.00 0.00 35.48 2.90
3333 4513 5.580691 CCATATTACTTGTCGCTCAAACTGA 59.419 40.000 0.00 0.00 35.48 3.41
3334 4514 5.580691 TCCATATTACTTGTCGCTCAAACTG 59.419 40.000 0.00 0.00 35.48 3.16
3335 4515 5.730550 TCCATATTACTTGTCGCTCAAACT 58.269 37.500 0.00 0.00 35.48 2.66
3336 4516 6.562270 CGATCCATATTACTTGTCGCTCAAAC 60.562 42.308 0.00 0.00 35.48 2.93
3337 4517 5.462068 CGATCCATATTACTTGTCGCTCAAA 59.538 40.000 0.00 0.00 35.48 2.69
3338 4518 4.982295 CGATCCATATTACTTGTCGCTCAA 59.018 41.667 0.00 0.00 34.61 3.02
3339 4519 4.546570 CGATCCATATTACTTGTCGCTCA 58.453 43.478 0.00 0.00 0.00 4.26
3340 4520 3.921021 CCGATCCATATTACTTGTCGCTC 59.079 47.826 0.00 0.00 0.00 5.03
3341 4521 3.572682 TCCGATCCATATTACTTGTCGCT 59.427 43.478 0.00 0.00 0.00 4.93
3342 4522 3.909430 TCCGATCCATATTACTTGTCGC 58.091 45.455 0.00 0.00 0.00 5.19
3343 4523 4.022242 ACCTCCGATCCATATTACTTGTCG 60.022 45.833 0.00 0.00 0.00 4.35
3344 4524 5.470047 ACCTCCGATCCATATTACTTGTC 57.530 43.478 0.00 0.00 0.00 3.18
3345 4525 6.075984 ACTACCTCCGATCCATATTACTTGT 58.924 40.000 0.00 0.00 0.00 3.16
3346 4526 6.591750 ACTACCTCCGATCCATATTACTTG 57.408 41.667 0.00 0.00 0.00 3.16
3347 4527 8.168725 TCTTACTACCTCCGATCCATATTACTT 58.831 37.037 0.00 0.00 0.00 2.24
3348 4528 7.611079 GTCTTACTACCTCCGATCCATATTACT 59.389 40.741 0.00 0.00 0.00 2.24
3349 4529 7.392673 TGTCTTACTACCTCCGATCCATATTAC 59.607 40.741 0.00 0.00 0.00 1.89
3350 4530 7.464273 TGTCTTACTACCTCCGATCCATATTA 58.536 38.462 0.00 0.00 0.00 0.98
3351 4531 6.312529 TGTCTTACTACCTCCGATCCATATT 58.687 40.000 0.00 0.00 0.00 1.28
3352 4532 5.888901 TGTCTTACTACCTCCGATCCATAT 58.111 41.667 0.00 0.00 0.00 1.78
3353 4533 5.314718 TGTCTTACTACCTCCGATCCATA 57.685 43.478 0.00 0.00 0.00 2.74
3354 4534 4.180377 TGTCTTACTACCTCCGATCCAT 57.820 45.455 0.00 0.00 0.00 3.41
3355 4535 3.657398 TGTCTTACTACCTCCGATCCA 57.343 47.619 0.00 0.00 0.00 3.41
3356 4536 4.583489 TCAATGTCTTACTACCTCCGATCC 59.417 45.833 0.00 0.00 0.00 3.36
3357 4537 5.769484 TCAATGTCTTACTACCTCCGATC 57.231 43.478 0.00 0.00 0.00 3.69
3358 4538 5.598830 ACATCAATGTCTTACTACCTCCGAT 59.401 40.000 0.00 0.00 35.87 4.18
3359 4539 4.954202 ACATCAATGTCTTACTACCTCCGA 59.046 41.667 0.00 0.00 35.87 4.55
3360 4540 5.263968 ACATCAATGTCTTACTACCTCCG 57.736 43.478 0.00 0.00 35.87 4.63
3361 4541 6.324254 AGGTACATCAATGTCTTACTACCTCC 59.676 42.308 7.05 0.00 37.60 4.30
3362 4542 7.349412 AGGTACATCAATGTCTTACTACCTC 57.651 40.000 7.05 0.00 37.60 3.85
3363 4543 6.895756 TGAGGTACATCAATGTCTTACTACCT 59.104 38.462 7.95 11.13 42.10 3.08
3364 4544 7.108841 TGAGGTACATCAATGTCTTACTACC 57.891 40.000 7.95 1.05 41.97 3.18
3365 4545 7.147880 ACCTGAGGTACATCAATGTCTTACTAC 60.148 40.741 11.87 0.00 41.97 2.73
3366 4546 6.895756 ACCTGAGGTACATCAATGTCTTACTA 59.104 38.462 11.87 0.00 41.97 1.82
3367 4547 5.721960 ACCTGAGGTACATCAATGTCTTACT 59.278 40.000 11.87 0.00 41.97 2.24
3368 4548 5.978814 ACCTGAGGTACATCAATGTCTTAC 58.021 41.667 11.87 0.00 41.97 2.34
3430 4611 1.939769 AAGGGTGCGTTGCGTTGTTT 61.940 50.000 0.00 0.00 0.00 2.83
3464 4645 1.742831 GCCGCCAGAATTGTATTGTGA 59.257 47.619 0.00 0.00 0.00 3.58
3515 4696 4.818534 TCTGAAACTCAGCAATGTGAAC 57.181 40.909 0.00 0.00 43.95 3.18
3576 4757 5.420409 CCGGATAGTTGAAGAGCTAGTTTT 58.580 41.667 0.00 0.00 0.00 2.43
3770 4960 5.491800 ACCTAGTTAGAAGAGTCCTGGTCTA 59.508 44.000 0.00 0.00 0.00 2.59
3798 4989 3.039011 AGTCTGGTAGTGAGTTTGTGGT 58.961 45.455 0.00 0.00 0.00 4.16
3875 5066 0.984995 AGCCAGGGGAGTAAGTTGAC 59.015 55.000 0.00 0.00 0.00 3.18
3886 5077 1.609783 CTCAAGGGTAAGCCAGGGG 59.390 63.158 0.00 0.00 36.17 4.79
3957 5149 1.492133 CCTCAACAAGGCTCCTCCCA 61.492 60.000 0.00 0.00 38.67 4.37
4033 5225 1.299976 GGCGGAGGTGATTCAAGGT 59.700 57.895 0.00 0.00 0.00 3.50
4111 5305 4.872691 GCTGCTTGTATGTACAACTCAGAT 59.127 41.667 21.86 0.00 40.93 2.90
4161 5360 0.193574 AGGAGGTGGGAAAGGTCTCA 59.806 55.000 0.00 0.00 0.00 3.27
4261 5465 4.771590 AGCACCAACTACATCATGTTTG 57.228 40.909 0.00 0.00 0.00 2.93
4262 5466 4.559300 GCAAGCACCAACTACATCATGTTT 60.559 41.667 0.00 0.00 0.00 2.83
4296 5501 6.854578 TGGTTAGTCCCCAAAGAAATAAAGA 58.145 36.000 0.00 0.00 34.77 2.52
4384 5595 8.616076 GGAAATTGACTTAACCTAGATCACATG 58.384 37.037 0.00 0.00 0.00 3.21
4554 5768 1.139734 GATGAGCGCGTCAGAGGAA 59.860 57.895 8.43 0.00 39.07 3.36
4636 10201 3.496711 GATCGCGCATCCACCAAA 58.503 55.556 8.75 0.00 0.00 3.28
4647 10212 3.863424 AGTATAAACACAACAGGATCGCG 59.137 43.478 0.00 0.00 0.00 5.87
4722 10288 9.880157 AAGTGCAAGCAATATTGAAATTCTAAT 57.120 25.926 19.73 0.00 31.55 1.73
4778 10344 3.467226 CGGGGCCCACAGATACGT 61.467 66.667 26.86 0.00 0.00 3.57
4794 10360 3.490078 GCTCTTGTCTCCACCTCTATTCG 60.490 52.174 0.00 0.00 0.00 3.34
4799 10365 0.178921 TGGCTCTTGTCTCCACCTCT 60.179 55.000 0.00 0.00 0.00 3.69
4952 10518 5.531122 ACACAGTAGAGCAAAGACTACAA 57.469 39.130 0.00 0.00 40.68 2.41
5097 10665 8.306761 GGATCATGAAAGGACAACAATTTTAGT 58.693 33.333 0.00 0.00 0.00 2.24
5125 10693 8.920509 TGATATCAACTTCAAATTCTGCATTG 57.079 30.769 1.98 0.00 0.00 2.82
5142 10710 6.035217 CGGTTGATGTTTTGCATGATATCAA 58.965 36.000 9.99 14.04 38.06 2.57
5200 10768 0.988832 AGCCTTCGGGTCCAAACATA 59.011 50.000 0.00 0.00 37.45 2.29
5277 10845 2.357009 GCGATGAATGCAAGAAGGTCAT 59.643 45.455 0.00 0.00 0.00 3.06
5460 11028 4.134623 GGGTCAAGCGACACAACA 57.865 55.556 0.00 0.00 45.58 3.33
5540 11108 5.453903 CCATAATGACAAGGGATCTCTCGTT 60.454 44.000 0.00 0.00 0.00 3.85
5617 11185 5.880332 TGGAGATATGAAGGTTTTGTAGCAC 59.120 40.000 0.00 0.00 0.00 4.40
5802 11370 2.223249 GCCAAATGCACGGTGTATAGTG 60.223 50.000 12.14 12.50 40.77 2.74
5953 11521 4.997395 GCAGGTTCAGTTGAGAAGTCAATA 59.003 41.667 0.00 0.00 44.58 1.90
6170 11738 1.329292 CGTCGCAAAACAAGGTTCTGA 59.671 47.619 0.00 0.00 0.00 3.27
6245 11813 2.949106 GCGTGCTGCAATGACACT 59.051 55.556 2.77 0.00 45.45 3.55
6259 11828 1.668751 ACGACAACAAGACAATTGCGT 59.331 42.857 5.05 0.61 35.36 5.24
6264 11833 2.033299 CAGCCAACGACAACAAGACAAT 59.967 45.455 0.00 0.00 0.00 2.71
6313 11890 2.388310 AAGGAGCGGAAACTAGAAGC 57.612 50.000 0.00 0.00 0.00 3.86
6364 11967 1.394618 GTACACTGGGTGGCAAACAA 58.605 50.000 0.00 0.00 37.94 2.83
6384 11987 2.035066 CACAAGTTTTGCCTCCAGGAAG 59.965 50.000 0.00 0.00 37.39 3.46
6478 12081 6.485171 ACCCAAGAAGCTAGTATTGTTTCAT 58.515 36.000 0.00 0.00 0.00 2.57
6551 12167 8.078060 AGCACATAACTAAAATAAAAGCCCAT 57.922 30.769 0.00 0.00 0.00 4.00
6581 12198 6.525629 AGCTACAAATAGATGTATGGACCAC 58.474 40.000 0.00 0.00 35.37 4.16
6617 12234 5.228635 GCGTGCATTTGATTATCTCTGTTTG 59.771 40.000 0.00 0.00 0.00 2.93
6687 12304 4.385825 ACAAAAACTAGGCAGACATCGAA 58.614 39.130 0.00 0.00 0.00 3.71
6960 12708 6.992715 CCTGTAACTTCCCTTTCATACATAGG 59.007 42.308 0.00 0.00 0.00 2.57
6990 12738 1.638070 TGGGCACTTGATAACATGGGA 59.362 47.619 0.00 0.00 0.00 4.37
7147 12897 6.706055 TGAGTAGTTCATTGAATGTTCGTC 57.294 37.500 4.93 0.00 0.00 4.20
7159 12916 6.756157 GCAGTCGCAGGATGAGTAGTTCAT 62.756 50.000 0.00 0.00 43.09 2.57
7198 12955 1.281867 TCTGATACAGCTTTGGTGGGG 59.718 52.381 1.90 0.00 35.13 4.96


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

AutoCloner maintained by Alex Coulton.