Multiple sequence alignment - TraesCS7D01G242600

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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 TraesCS7D01G242600 chr7D 100.000 4424 0 0 1 4424 208226435 208222012 0.000000e+00 8170.0
1 TraesCS7D01G242600 chr7D 89.702 369 37 1 2948 3316 512747072 512746705 1.860000e-128 470.0
2 TraesCS7D01G242600 chr7D 93.701 254 16 0 4077 4330 209496845 209496592 8.980000e-102 381.0
3 TraesCS7D01G242600 chr7D 91.481 270 23 0 4077 4346 27980628 27980359 5.400000e-99 372.0
4 TraesCS7D01G242600 chr7D 90.288 278 25 2 4077 4354 276255176 276254901 3.250000e-96 363.0
5 TraesCS7D01G242600 chr7D 100.000 31 0 0 545 575 603188899 603188929 1.720000e-04 58.4
6 TraesCS7D01G242600 chr7A 93.541 3917 178 37 1 3872 221270266 221266380 0.000000e+00 5762.0
7 TraesCS7D01G242600 chr7A 89.160 369 39 1 2948 3316 585356882 585356515 4.030000e-125 459.0
8 TraesCS7D01G242600 chr7A 95.726 117 4 1 3951 4067 221265939 221265824 2.100000e-43 187.0
9 TraesCS7D01G242600 chr7A 94.030 67 4 0 4356 4422 221265797 221265731 7.830000e-18 102.0
10 TraesCS7D01G242600 chr7A 100.000 31 0 0 545 575 85588229 85588259 1.720000e-04 58.4
11 TraesCS7D01G242600 chr7B 96.719 1981 45 9 651 2616 193308497 193310472 0.000000e+00 3280.0
12 TraesCS7D01G242600 chr7B 90.054 1478 79 29 2600 4062 193310486 193311910 0.000000e+00 1853.0
13 TraesCS7D01G242600 chr7B 90.756 595 47 7 73 665 193305259 193305847 0.000000e+00 787.0
14 TraesCS7D01G242600 chr7B 89.973 369 36 1 2948 3316 544481053 544480686 4.000000e-130 475.0
15 TraesCS7D01G242600 chr7B 96.104 77 3 0 4346 4422 193312181 193312257 4.650000e-25 126.0
16 TraesCS7D01G242600 chr7B 97.872 47 1 0 1 47 193305214 193305260 1.020000e-11 82.4
17 TraesCS7D01G242600 chr7B 96.774 31 1 0 545 575 617832631 617832661 8.000000e-03 52.8
18 TraesCS7D01G242600 chr5B 94.370 373 21 0 2949 3321 446996505 446996877 1.380000e-159 573.0
19 TraesCS7D01G242600 chr5B 92.517 147 8 1 1636 1782 446993005 446993148 1.610000e-49 207.0
20 TraesCS7D01G242600 chr5A 94.550 367 20 0 2949 3315 476225335 476225701 6.420000e-158 568.0
21 TraesCS7D01G242600 chr5D 94.278 367 21 0 2949 3315 374391716 374392082 2.990000e-156 562.0
22 TraesCS7D01G242600 chr5D 92.593 270 20 0 4077 4346 209326747 209326478 5.370000e-104 388.0
23 TraesCS7D01G242600 chr5D 91.481 270 23 0 4077 4346 276916222 276915953 5.400000e-99 372.0
24 TraesCS7D01G242600 chr5D 91.156 147 10 1 1636 1782 374388287 374388430 3.490000e-46 196.0
25 TraesCS7D01G242600 chr2A 92.251 271 21 0 4077 4347 470535666 470535936 6.940000e-103 385.0
26 TraesCS7D01G242600 chr1D 91.039 279 25 0 4070 4348 413352094 413352372 1.160000e-100 377.0
27 TraesCS7D01G242600 chr6A 91.481 270 23 0 4077 4346 55294556 55294825 5.400000e-99 372.0
28 TraesCS7D01G242600 chr4D 90.036 281 26 2 4068 4346 4142202 4142482 3.250000e-96 363.0
29 TraesCS7D01G242600 chr3D 94.595 37 2 0 546 582 576602221 576602257 1.720000e-04 58.4
30 TraesCS7D01G242600 chr3D 96.875 32 1 0 1571 1602 414507002 414506971 2.000000e-03 54.7
31 TraesCS7D01G242600 chr6D 96.774 31 1 0 545 575 112960363 112960333 8.000000e-03 52.8


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 TraesCS7D01G242600 chr7D 208222012 208226435 4423 True 8170.00 8170 100.000000 1 4424 1 chr7D.!!$R2 4423
1 TraesCS7D01G242600 chr7A 221265731 221270266 4535 True 2017.00 5762 94.432333 1 4422 3 chr7A.!!$R2 4421
2 TraesCS7D01G242600 chr7B 193305214 193312257 7043 False 1225.68 3280 94.301000 1 4422 5 chr7B.!!$F2 4421
3 TraesCS7D01G242600 chr5B 446993005 446996877 3872 False 390.00 573 93.443500 1636 3321 2 chr5B.!!$F1 1685
4 TraesCS7D01G242600 chr5D 374388287 374392082 3795 False 379.00 562 92.717000 1636 3315 2 chr5D.!!$F1 1679

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
649 660 0.109412 AAGCCGGACGTTCTCTTACG 60.109 55.0 5.05 0.0 46.52 3.18 F
1103 3785 0.030705 CATCTCCCTCCTCCCTTCCA 60.031 60.0 0.00 0.0 0.00 3.53 F
1333 4021 0.873312 CTCCGACTCCGACGACGATA 60.873 60.0 9.28 0.0 42.66 2.92 F
2746 8279 0.179045 ACGGCTAGGGCTTTGCATAG 60.179 55.0 5.35 0.0 38.73 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 4392 0.032117 TGGGACCGATGAGGATCTGT 60.032 55.000 0.0 0.0 45.00 3.41 R
2725 8258 2.046314 GCAAAGCCCTAGCCGTGA 60.046 61.111 0.0 0.0 41.25 4.35 R
2796 8337 2.665052 GCTTGTAGGTTTTCGTACTCCG 59.335 50.000 0.0 0.0 40.50 4.63 R
4351 10281 0.698238 AGGTTGGGCTGTATGCTTGA 59.302 50.000 0.0 0.0 42.39 3.02 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
39 40 6.682863 CCATTTGCGAGTAATCTTTAGAAACG 59.317 38.462 0.00 0.00 0.00 3.60
45 46 5.220416 CGAGTAATCTTTAGAAACGCCAAGG 60.220 44.000 0.00 0.00 0.00 3.61
46 47 5.557866 AGTAATCTTTAGAAACGCCAAGGT 58.442 37.500 0.00 0.00 0.00 3.50
47 48 6.704310 AGTAATCTTTAGAAACGCCAAGGTA 58.296 36.000 0.00 0.00 0.00 3.08
48 49 7.163441 AGTAATCTTTAGAAACGCCAAGGTAA 58.837 34.615 0.00 0.00 0.00 2.85
50 51 5.873179 TCTTTAGAAACGCCAAGGTAATG 57.127 39.130 0.00 0.00 0.00 1.90
52 53 2.871096 AGAAACGCCAAGGTAATGGA 57.129 45.000 0.00 0.00 43.54 3.41
55 56 4.086457 AGAAACGCCAAGGTAATGGAAAT 58.914 39.130 0.00 0.00 43.54 2.17
56 57 3.866883 AACGCCAAGGTAATGGAAATG 57.133 42.857 0.00 0.00 43.54 2.32
119 120 6.899393 ACATTCTTTTTCAATGTGCTCCTA 57.101 33.333 0.00 0.00 41.86 2.94
182 186 1.134220 GGGTGCCGAATTCCATGTCTA 60.134 52.381 0.00 0.00 0.00 2.59
183 187 2.213499 GGTGCCGAATTCCATGTCTAG 58.787 52.381 0.00 0.00 0.00 2.43
258 262 3.506067 CCCTCTTTTGTGGCGATAACTTT 59.494 43.478 0.00 0.00 0.00 2.66
403 409 2.444624 CGACATCCGGTGTTCTGCG 61.445 63.158 0.00 1.74 42.36 5.18
426 432 3.935203 CGAGATCAAATGCCTACACACTT 59.065 43.478 0.00 0.00 0.00 3.16
637 648 6.591750 TTGGTTCATTAATTTAAAGCCGGA 57.408 33.333 5.05 0.00 0.00 5.14
642 653 5.871539 TCATTAATTTAAAGCCGGACGTTC 58.128 37.500 5.05 0.00 0.00 3.95
644 655 5.535043 TTAATTTAAAGCCGGACGTTCTC 57.465 39.130 5.05 0.00 0.00 2.87
646 657 2.825861 TTAAAGCCGGACGTTCTCTT 57.174 45.000 5.05 0.00 0.00 2.85
648 659 2.075979 AAAGCCGGACGTTCTCTTAC 57.924 50.000 5.05 0.00 0.00 2.34
649 660 0.109412 AAGCCGGACGTTCTCTTACG 60.109 55.000 5.05 0.00 46.52 3.18
655 3331 2.090195 CGGACGTTCTCTTACGCTTTTC 59.910 50.000 0.00 0.00 45.06 2.29
657 3333 3.739810 GGACGTTCTCTTACGCTTTTCTT 59.260 43.478 0.00 0.00 45.06 2.52
658 3334 4.143368 GGACGTTCTCTTACGCTTTTCTTC 60.143 45.833 0.00 0.00 45.06 2.87
674 3350 7.201266 CGCTTTTCTTCAAAGAATTTATGACGG 60.201 37.037 6.05 0.00 44.40 4.79
691 3367 0.390472 CGGAAGGAAGCAGTGTCCTC 60.390 60.000 2.90 0.00 45.12 3.71
1103 3785 0.030705 CATCTCCCTCCTCCCTTCCA 60.031 60.000 0.00 0.00 0.00 3.53
1236 3924 4.075793 CCCTCCCCTCCACTCCGA 62.076 72.222 0.00 0.00 0.00 4.55
1333 4021 0.873312 CTCCGACTCCGACGACGATA 60.873 60.000 9.28 0.00 42.66 2.92
1358 4046 2.816958 CTGCTGCTACCACCTGCG 60.817 66.667 0.00 0.00 0.00 5.18
1809 4540 4.392047 TCATTTGCAGCTTCTCTTCTTGA 58.608 39.130 0.00 0.00 0.00 3.02
1842 4717 5.126067 ACATCTTGGGCACATGTAGTAATC 58.874 41.667 0.00 0.00 0.00 1.75
2022 6133 3.441290 GCCAGGAGCTGCAGCAAG 61.441 66.667 38.24 23.61 45.16 4.01
2189 6363 8.762645 TCAGTCAATCAGATTACTTTCTACCAT 58.237 33.333 0.00 0.00 0.00 3.55
2603 8105 5.618056 TTCTCTGCTTGCAAACTGATTAG 57.382 39.130 9.49 0.28 0.00 1.73
2662 8195 3.190327 CAGTTTGGTCACAACTCACACAA 59.810 43.478 0.00 0.00 36.06 3.33
2669 8202 5.295787 TGGTCACAACTCACACAAACTTATC 59.704 40.000 0.00 0.00 0.00 1.75
2676 8209 8.204836 ACAACTCACACAAACTTATCTACTCTT 58.795 33.333 0.00 0.00 0.00 2.85
2706 8239 3.325293 AGTCATCAGTCATCACACCAC 57.675 47.619 0.00 0.00 0.00 4.16
2708 8241 2.738846 GTCATCAGTCATCACACCACAC 59.261 50.000 0.00 0.00 0.00 3.82
2730 8263 3.060978 CATCAGTGCATTCAATCACGG 57.939 47.619 0.00 0.00 38.19 4.94
2745 8278 0.463654 CACGGCTAGGGCTTTGCATA 60.464 55.000 5.35 0.00 38.73 3.14
2746 8279 0.179045 ACGGCTAGGGCTTTGCATAG 60.179 55.000 5.35 0.00 38.73 2.23
2747 8280 0.179045 CGGCTAGGGCTTTGCATAGT 60.179 55.000 5.35 0.00 38.73 2.12
2748 8281 1.070134 CGGCTAGGGCTTTGCATAGTA 59.930 52.381 5.35 0.00 38.73 1.82
2835 8380 9.315525 CCTACAAGCATATGATATGATCTGAAG 57.684 37.037 16.22 6.10 0.00 3.02
2838 8383 9.570468 ACAAGCATATGATATGATCTGAAGTTT 57.430 29.630 16.22 0.00 0.00 2.66
2907 8452 8.748582 GTCCAAACTCCAAACTAAAATTTAACG 58.251 33.333 0.00 0.00 0.00 3.18
3081 8628 1.024579 GCCGGAACAACATCGACCAT 61.025 55.000 5.05 0.00 0.00 3.55
3084 8631 1.674519 CGGAACAACATCGACCATCCA 60.675 52.381 0.00 0.00 0.00 3.41
3288 8835 4.717629 TCGCTCAAGGACCACGCG 62.718 66.667 3.53 3.53 44.63 6.01
3506 9053 0.790207 CACGCACGAGCAAACACTAT 59.210 50.000 5.50 0.00 42.27 2.12
3508 9055 2.603110 CACGCACGAGCAAACACTATAT 59.397 45.455 5.50 0.00 42.27 0.86
3510 9057 3.795101 ACGCACGAGCAAACACTATATAC 59.205 43.478 5.50 0.00 42.27 1.47
3512 9059 4.444388 CGCACGAGCAAACACTATATACAT 59.556 41.667 5.50 0.00 42.27 2.29
3513 9060 5.627780 CGCACGAGCAAACACTATATACATA 59.372 40.000 5.50 0.00 42.27 2.29
3514 9061 6.308041 CGCACGAGCAAACACTATATACATAT 59.692 38.462 5.50 0.00 42.27 1.78
3579 9132 1.517242 CTCTGTGGCTCTTGTTGTCC 58.483 55.000 0.00 0.00 0.00 4.02
3633 9186 6.192044 AGGGTTTGTGGAAGTTTTCTTTAGA 58.808 36.000 0.00 0.00 40.61 2.10
3708 9267 6.042777 TCTCAATCGATCACACCATTAACTC 58.957 40.000 0.00 0.00 0.00 3.01
3729 9288 2.183478 TGGAGCAATAGGTGTGTGTG 57.817 50.000 0.00 0.00 0.00 3.82
3730 9289 1.419762 TGGAGCAATAGGTGTGTGTGT 59.580 47.619 0.00 0.00 0.00 3.72
3731 9290 1.806542 GGAGCAATAGGTGTGTGTGTG 59.193 52.381 0.00 0.00 0.00 3.82
3732 9291 2.494059 GAGCAATAGGTGTGTGTGTGT 58.506 47.619 0.00 0.00 0.00 3.72
3734 9293 3.287222 AGCAATAGGTGTGTGTGTGTTT 58.713 40.909 0.00 0.00 0.00 2.83
3735 9294 3.315191 AGCAATAGGTGTGTGTGTGTTTC 59.685 43.478 0.00 0.00 0.00 2.78
3736 9295 3.315191 GCAATAGGTGTGTGTGTGTTTCT 59.685 43.478 0.00 0.00 0.00 2.52
3737 9296 4.202010 GCAATAGGTGTGTGTGTGTTTCTT 60.202 41.667 0.00 0.00 0.00 2.52
3738 9297 5.273170 CAATAGGTGTGTGTGTGTTTCTTG 58.727 41.667 0.00 0.00 0.00 3.02
3739 9298 2.790433 AGGTGTGTGTGTGTTTCTTGT 58.210 42.857 0.00 0.00 0.00 3.16
3750 9309 3.823873 TGTGTTTCTTGTTTGTGTGTCCT 59.176 39.130 0.00 0.00 0.00 3.85
3761 9320 3.025322 TGTGTGTCCTTGAATTTGGGT 57.975 42.857 0.00 0.00 0.00 4.51
3763 9322 3.383185 TGTGTGTCCTTGAATTTGGGTTC 59.617 43.478 0.00 0.00 0.00 3.62
3805 9364 6.592607 AGCATGTTCTGAGCAATTTTTATTGG 59.407 34.615 0.00 0.00 32.43 3.16
3810 9369 9.206870 TGTTCTGAGCAATTTTTATTGGAAATC 57.793 29.630 0.00 0.00 32.43 2.17
3830 9389 4.736126 TCTTGGCTATTCATGAACTCGA 57.264 40.909 11.07 0.00 0.00 4.04
3831 9390 5.282055 TCTTGGCTATTCATGAACTCGAT 57.718 39.130 11.07 0.00 0.00 3.59
3832 9391 5.292765 TCTTGGCTATTCATGAACTCGATC 58.707 41.667 11.07 0.00 0.00 3.69
3833 9392 3.642705 TGGCTATTCATGAACTCGATCG 58.357 45.455 11.07 9.36 0.00 3.69
3834 9393 3.068165 TGGCTATTCATGAACTCGATCGT 59.932 43.478 15.94 0.00 0.00 3.73
3837 9396 5.117287 GGCTATTCATGAACTCGATCGTAAC 59.883 44.000 15.94 6.24 0.00 2.50
3840 9402 3.435566 TCATGAACTCGATCGTAACTGC 58.564 45.455 15.94 2.08 0.00 4.40
3876 9438 5.970317 ATGCAGACATCAACTTTTCATCA 57.030 34.783 0.00 0.00 0.00 3.07
3877 9439 5.771153 TGCAGACATCAACTTTTCATCAA 57.229 34.783 0.00 0.00 0.00 2.57
3878 9440 6.335471 TGCAGACATCAACTTTTCATCAAT 57.665 33.333 0.00 0.00 0.00 2.57
3879 9441 6.384224 TGCAGACATCAACTTTTCATCAATC 58.616 36.000 0.00 0.00 0.00 2.67
3880 9442 5.803967 GCAGACATCAACTTTTCATCAATCC 59.196 40.000 0.00 0.00 0.00 3.01
3883 9445 7.701078 CAGACATCAACTTTTCATCAATCCATC 59.299 37.037 0.00 0.00 0.00 3.51
3896 9458 9.939802 TTCATCAATCCATCTATATTCTCTGTG 57.060 33.333 0.00 0.00 0.00 3.66
3897 9459 8.537858 TCATCAATCCATCTATATTCTCTGTGG 58.462 37.037 0.00 0.00 0.00 4.17
3901 9463 4.109600 TCCATCTATATTCTCTGTGGGGGA 59.890 45.833 0.00 0.00 0.00 4.81
3902 9464 4.469227 CCATCTATATTCTCTGTGGGGGAG 59.531 50.000 0.00 0.00 0.00 4.30
3903 9465 4.834406 TCTATATTCTCTGTGGGGGAGT 57.166 45.455 0.00 0.00 33.06 3.85
3905 9467 5.893500 TCTATATTCTCTGTGGGGGAGTAG 58.106 45.833 0.00 0.00 33.06 2.57
3906 9468 2.950990 ATTCTCTGTGGGGGAGTAGT 57.049 50.000 0.00 0.00 33.06 2.73
3907 9469 5.681494 ATATTCTCTGTGGGGGAGTAGTA 57.319 43.478 0.00 0.00 33.06 1.82
3908 9470 4.561254 ATTCTCTGTGGGGGAGTAGTAT 57.439 45.455 0.00 0.00 33.06 2.12
3911 9473 3.789840 TCTCTGTGGGGGAGTAGTATGTA 59.210 47.826 0.00 0.00 33.06 2.29
3912 9474 4.231195 TCTCTGTGGGGGAGTAGTATGTAA 59.769 45.833 0.00 0.00 33.06 2.41
3913 9475 4.950361 TCTGTGGGGGAGTAGTATGTAAA 58.050 43.478 0.00 0.00 0.00 2.01
3915 9477 6.685541 TCTGTGGGGGAGTAGTATGTAAATA 58.314 40.000 0.00 0.00 0.00 1.40
3917 9479 8.458575 TCTGTGGGGGAGTAGTATGTAAATATA 58.541 37.037 0.00 0.00 0.00 0.86
3918 9480 9.096823 CTGTGGGGGAGTAGTATGTAAATATAA 57.903 37.037 0.00 0.00 0.00 0.98
3919 9481 9.449896 TGTGGGGGAGTAGTATGTAAATATAAA 57.550 33.333 0.00 0.00 0.00 1.40
3920 9482 9.939802 GTGGGGGAGTAGTATGTAAATATAAAG 57.060 37.037 0.00 0.00 0.00 1.85
3940 9870 2.039879 AGAGTAAAGAACAATGGCCGGT 59.960 45.455 1.90 0.00 0.00 5.28
3941 9871 3.262405 AGAGTAAAGAACAATGGCCGGTA 59.738 43.478 1.90 0.00 0.00 4.02
3943 9873 3.754850 AGTAAAGAACAATGGCCGGTAAC 59.245 43.478 1.90 0.00 0.00 2.50
3944 9874 2.279935 AAGAACAATGGCCGGTAACA 57.720 45.000 1.90 0.00 0.00 2.41
3945 9875 2.279935 AGAACAATGGCCGGTAACAA 57.720 45.000 1.90 0.00 0.00 2.83
3946 9876 2.802719 AGAACAATGGCCGGTAACAAT 58.197 42.857 1.90 0.00 0.00 2.71
3947 9877 2.491693 AGAACAATGGCCGGTAACAATG 59.508 45.455 1.90 6.39 0.00 2.82
3948 9878 2.208132 ACAATGGCCGGTAACAATGA 57.792 45.000 14.90 0.00 0.00 2.57
3949 9879 2.520069 ACAATGGCCGGTAACAATGAA 58.480 42.857 14.90 0.00 0.00 2.57
3956 9886 1.816224 CCGGTAACAATGAACAAGGGG 59.184 52.381 0.00 0.00 0.00 4.79
4039 9969 3.634397 TCCAACCTATCTTTCCTGCTG 57.366 47.619 0.00 0.00 0.00 4.41
4082 10012 6.212888 TCAACGTATCCTTTTCTACTACCC 57.787 41.667 0.00 0.00 0.00 3.69
4083 10013 5.716228 TCAACGTATCCTTTTCTACTACCCA 59.284 40.000 0.00 0.00 0.00 4.51
4085 10015 7.560991 TCAACGTATCCTTTTCTACTACCCATA 59.439 37.037 0.00 0.00 0.00 2.74
4086 10016 7.902920 ACGTATCCTTTTCTACTACCCATAA 57.097 36.000 0.00 0.00 0.00 1.90
4087 10017 8.488308 ACGTATCCTTTTCTACTACCCATAAT 57.512 34.615 0.00 0.00 0.00 1.28
4089 10019 8.582437 CGTATCCTTTTCTACTACCCATAATGA 58.418 37.037 0.00 0.00 0.00 2.57
4090 10020 9.930693 GTATCCTTTTCTACTACCCATAATGAG 57.069 37.037 0.00 0.00 0.00 2.90
4091 10021 8.798975 ATCCTTTTCTACTACCCATAATGAGA 57.201 34.615 0.00 0.00 0.00 3.27
4093 10023 7.844779 TCCTTTTCTACTACCCATAATGAGAGT 59.155 37.037 0.00 0.00 0.00 3.24
4097 10027 9.483489 TTTCTACTACCCATAATGAGAGTAACA 57.517 33.333 0.00 0.00 0.00 2.41
4098 10028 9.656323 TTCTACTACCCATAATGAGAGTAACAT 57.344 33.333 0.00 0.00 0.00 2.71
4103 10033 9.529823 CTACCCATAATGAGAGTAACATAGGTA 57.470 37.037 0.00 0.00 0.00 3.08
4104 10034 8.423906 ACCCATAATGAGAGTAACATAGGTAG 57.576 38.462 0.00 0.00 0.00 3.18
4105 10035 8.011290 ACCCATAATGAGAGTAACATAGGTAGT 58.989 37.037 0.00 0.00 0.00 2.73
4106 10036 9.529823 CCCATAATGAGAGTAACATAGGTAGTA 57.470 37.037 0.00 0.00 0.00 1.82
4157 10087 9.590451 AAATGATGTGGCAAGTAATAAATGAAG 57.410 29.630 0.00 0.00 0.00 3.02
4159 10089 8.347004 TGATGTGGCAAGTAATAAATGAAGAA 57.653 30.769 0.00 0.00 0.00 2.52
4160 10090 8.801299 TGATGTGGCAAGTAATAAATGAAGAAA 58.199 29.630 0.00 0.00 0.00 2.52
4161 10091 9.294030 GATGTGGCAAGTAATAAATGAAGAAAG 57.706 33.333 0.00 0.00 0.00 2.62
4163 10093 8.514594 TGTGGCAAGTAATAAATGAAGAAAGAG 58.485 33.333 0.00 0.00 0.00 2.85
4164 10094 7.970614 GTGGCAAGTAATAAATGAAGAAAGAGG 59.029 37.037 0.00 0.00 0.00 3.69
4165 10095 7.122650 TGGCAAGTAATAAATGAAGAAAGAGGG 59.877 37.037 0.00 0.00 0.00 4.30
4166 10096 7.416777 GGCAAGTAATAAATGAAGAAAGAGGGG 60.417 40.741 0.00 0.00 0.00 4.79
4167 10097 7.484140 CAAGTAATAAATGAAGAAAGAGGGGC 58.516 38.462 0.00 0.00 0.00 5.80
4168 10098 6.731467 AGTAATAAATGAAGAAAGAGGGGCA 58.269 36.000 0.00 0.00 0.00 5.36
4169 10099 7.357471 AGTAATAAATGAAGAAAGAGGGGCAT 58.643 34.615 0.00 0.00 0.00 4.40
4170 10100 6.475596 AATAAATGAAGAAAGAGGGGCATG 57.524 37.500 0.00 0.00 0.00 4.06
4171 10101 3.463048 AATGAAGAAAGAGGGGCATGT 57.537 42.857 0.00 0.00 0.00 3.21
4172 10102 2.205022 TGAAGAAAGAGGGGCATGTG 57.795 50.000 0.00 0.00 0.00 3.21
4173 10103 1.272092 TGAAGAAAGAGGGGCATGTGG 60.272 52.381 0.00 0.00 0.00 4.17
4174 10104 0.779997 AAGAAAGAGGGGCATGTGGT 59.220 50.000 0.00 0.00 0.00 4.16
4177 10107 2.092323 GAAAGAGGGGCATGTGGTAAC 58.908 52.381 0.00 0.00 0.00 2.50
4196 10126 8.585471 TGGTAACATAGTTAGTTACTAGCAGT 57.415 34.615 8.82 1.98 46.49 4.40
4202 10132 9.629878 ACATAGTTAGTTACTAGCAGTATGAGT 57.370 33.333 18.44 2.98 42.44 3.41
4210 10140 8.563289 GTTACTAGCAGTATGAGTAACATCAC 57.437 38.462 15.71 0.00 46.87 3.06
4211 10141 6.775594 ACTAGCAGTATGAGTAACATCACA 57.224 37.500 0.00 0.00 39.69 3.58
4212 10142 6.565234 ACTAGCAGTATGAGTAACATCACAC 58.435 40.000 0.00 0.00 39.69 3.82
4217 10147 7.869937 AGCAGTATGAGTAACATCACACATATC 59.130 37.037 0.00 0.00 39.69 1.63
4218 10148 7.653311 GCAGTATGAGTAACATCACACATATCA 59.347 37.037 0.00 0.00 39.69 2.15
4219 10149 9.533253 CAGTATGAGTAACATCACACATATCAA 57.467 33.333 0.00 0.00 39.69 2.57
4220 10150 9.755804 AGTATGAGTAACATCACACATATCAAG 57.244 33.333 0.00 0.00 40.07 3.02
4221 10151 8.982685 GTATGAGTAACATCACACATATCAAGG 58.017 37.037 0.00 0.00 40.07 3.61
4224 10154 8.536175 TGAGTAACATCACACATATCAAGGTAA 58.464 33.333 0.00 0.00 0.00 2.85
4225 10155 8.948631 AGTAACATCACACATATCAAGGTAAG 57.051 34.615 0.00 0.00 0.00 2.34
4228 10158 8.442632 AACATCACACATATCAAGGTAAGATG 57.557 34.615 0.00 0.00 36.61 2.90
4229 10159 7.795047 ACATCACACATATCAAGGTAAGATGA 58.205 34.615 0.00 0.00 35.32 2.92
4230 10160 7.930325 ACATCACACATATCAAGGTAAGATGAG 59.070 37.037 0.00 0.00 35.32 2.90
4231 10161 7.423844 TCACACATATCAAGGTAAGATGAGT 57.576 36.000 0.00 0.00 0.00 3.41
4232 10162 7.492524 TCACACATATCAAGGTAAGATGAGTC 58.507 38.462 0.00 0.00 0.00 3.36
4233 10163 7.343057 TCACACATATCAAGGTAAGATGAGTCT 59.657 37.037 0.00 0.00 35.82 3.24
4234 10164 8.633561 CACACATATCAAGGTAAGATGAGTCTA 58.366 37.037 0.00 0.00 33.30 2.59
4235 10165 9.373450 ACACATATCAAGGTAAGATGAGTCTAT 57.627 33.333 0.00 0.00 33.30 1.98
4239 10169 9.989296 ATATCAAGGTAAGATGAGTCTATAGCT 57.011 33.333 0.00 0.00 33.30 3.32
4242 10172 9.642343 TCAAGGTAAGATGAGTCTATAGCTTAA 57.358 33.333 0.00 0.00 35.93 1.85
4262 10192 7.894847 GCTTAATAAATAAAGCGTTGCATGTT 58.105 30.769 0.00 0.00 38.80 2.71
4265 10195 7.749539 AATAAATAAAGCGTTGCATGTTACC 57.250 32.000 0.00 0.00 0.00 2.85
4266 10196 4.775058 AATAAAGCGTTGCATGTTACCA 57.225 36.364 0.00 0.00 0.00 3.25
4267 10197 2.415697 AAAGCGTTGCATGTTACCAC 57.584 45.000 0.00 0.00 0.00 4.16
4268 10198 1.313772 AAGCGTTGCATGTTACCACA 58.686 45.000 0.00 0.00 37.31 4.17
4269 10199 0.591170 AGCGTTGCATGTTACCACAC 59.409 50.000 0.00 0.00 35.03 3.82
4270 10200 0.309302 GCGTTGCATGTTACCACACA 59.691 50.000 0.00 0.00 35.03 3.72
4272 10202 2.160615 GCGTTGCATGTTACCACACATA 59.839 45.455 0.00 0.00 35.51 2.29
4274 10204 4.341935 CGTTGCATGTTACCACACATATG 58.658 43.478 0.00 0.00 35.51 1.78
4275 10205 4.142708 CGTTGCATGTTACCACACATATGT 60.143 41.667 1.41 1.41 40.80 2.29
4277 10207 6.402658 CGTTGCATGTTACCACACATATGTTA 60.403 38.462 5.37 0.00 36.72 2.41
4278 10208 6.429791 TGCATGTTACCACACATATGTTAC 57.570 37.500 5.37 0.00 36.72 2.50
4279 10209 6.176896 TGCATGTTACCACACATATGTTACT 58.823 36.000 5.37 0.00 36.72 2.24
4280 10210 6.315144 TGCATGTTACCACACATATGTTACTC 59.685 38.462 5.37 0.00 36.72 2.59
4282 10212 5.736813 TGTTACCACACATATGTTACTCCC 58.263 41.667 5.37 0.00 36.72 4.30
4283 10213 3.926058 ACCACACATATGTTACTCCCC 57.074 47.619 5.37 0.00 36.72 4.81
4284 10214 3.186283 ACCACACATATGTTACTCCCCA 58.814 45.455 5.37 0.00 36.72 4.96
4285 10215 3.054655 ACCACACATATGTTACTCCCCAC 60.055 47.826 5.37 0.00 36.72 4.61
4286 10216 3.199946 CCACACATATGTTACTCCCCACT 59.800 47.826 5.37 0.00 36.72 4.00
4287 10217 4.407621 CCACACATATGTTACTCCCCACTA 59.592 45.833 5.37 0.00 36.72 2.74
4288 10218 5.071788 CCACACATATGTTACTCCCCACTAT 59.928 44.000 5.37 0.00 36.72 2.12
4290 10220 7.378966 CACACATATGTTACTCCCCACTATAG 58.621 42.308 5.37 0.00 36.72 1.31
4292 10222 7.451877 ACACATATGTTACTCCCCACTATAGAG 59.548 40.741 5.37 0.00 34.46 2.43
4293 10223 6.954684 ACATATGTTACTCCCCACTATAGAGG 59.045 42.308 6.78 8.10 31.70 3.69
4295 10225 5.999987 TGTTACTCCCCACTATAGAGGTA 57.000 43.478 14.29 2.62 31.70 3.08
4296 10226 5.950023 TGTTACTCCCCACTATAGAGGTAG 58.050 45.833 14.29 12.87 31.70 3.18
4299 10229 7.129349 TGTTACTCCCCACTATAGAGGTAGTAA 59.871 40.741 23.15 23.15 33.91 2.24
4300 10230 5.951204 ACTCCCCACTATAGAGGTAGTAAC 58.049 45.833 14.29 0.00 33.29 2.50
4301 10231 5.434376 ACTCCCCACTATAGAGGTAGTAACA 59.566 44.000 14.29 0.00 33.29 2.41
4302 10232 6.104392 ACTCCCCACTATAGAGGTAGTAACAT 59.896 42.308 14.29 0.00 33.29 2.71
4303 10233 7.296628 ACTCCCCACTATAGAGGTAGTAACATA 59.703 40.741 14.29 0.00 33.29 2.29
4304 10234 7.696981 TCCCCACTATAGAGGTAGTAACATAG 58.303 42.308 14.29 0.00 33.29 2.23
4306 10236 6.890814 CCCACTATAGAGGTAGTAACATAGGG 59.109 46.154 14.29 0.00 33.29 3.53
4307 10237 7.468496 CCACTATAGAGGTAGTAACATAGGGT 58.532 42.308 6.78 0.00 33.29 4.34
4309 10239 9.669887 CACTATAGAGGTAGTAACATAGGGTAG 57.330 40.741 6.78 0.00 33.29 3.18
4310 10240 9.404077 ACTATAGAGGTAGTAACATAGGGTAGT 57.596 37.037 6.78 0.00 33.29 2.73
4315 10245 8.509441 AGAGGTAGTAACATAGGGTAGTAACAT 58.491 37.037 5.22 0.00 0.00 2.71
4316 10246 8.474710 AGGTAGTAACATAGGGTAGTAACATG 57.525 38.462 5.22 0.00 0.00 3.21
4317 10247 8.284435 AGGTAGTAACATAGGGTAGTAACATGA 58.716 37.037 5.22 0.00 0.00 3.07
4319 10249 7.052142 AGTAACATAGGGTAGTAACATGAGC 57.948 40.000 0.00 0.00 0.00 4.26
4320 10250 5.950544 AACATAGGGTAGTAACATGAGCA 57.049 39.130 0.00 0.00 0.00 4.26
4321 10251 6.500589 AACATAGGGTAGTAACATGAGCAT 57.499 37.500 0.00 0.00 0.00 3.79
4336 10266 6.395426 CATGAGCATGTTATTACCCATTGT 57.605 37.500 2.34 0.00 34.23 2.71
4337 10267 5.833406 TGAGCATGTTATTACCCATTGTG 57.167 39.130 0.00 0.00 0.00 3.33
4338 10268 4.644234 TGAGCATGTTATTACCCATTGTGG 59.356 41.667 0.00 0.00 37.25 4.17
4339 10269 3.384467 AGCATGTTATTACCCATTGTGGC 59.616 43.478 0.00 0.00 35.79 5.01
4340 10270 3.384467 GCATGTTATTACCCATTGTGGCT 59.616 43.478 0.00 0.00 35.79 4.75
4341 10271 4.582656 GCATGTTATTACCCATTGTGGCTA 59.417 41.667 0.00 0.00 35.79 3.93
4342 10272 5.278463 GCATGTTATTACCCATTGTGGCTAG 60.278 44.000 0.00 0.00 35.79 3.42
4343 10273 5.444744 TGTTATTACCCATTGTGGCTAGT 57.555 39.130 0.00 0.00 35.79 2.57
4344 10274 5.433526 TGTTATTACCCATTGTGGCTAGTC 58.566 41.667 0.00 0.00 35.79 2.59
4351 10281 2.355513 CCATTGTGGCTAGTCTTCTGCT 60.356 50.000 0.00 0.00 0.00 4.24
4422 10359 6.428159 ACATATTCCAAGAAAGTCTGTGTGTC 59.572 38.462 0.00 0.00 0.00 3.67
4423 10360 3.194005 TCCAAGAAAGTCTGTGTGTCC 57.806 47.619 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.706086 ACATCCATTTCCATTACCTTGGC 59.294 43.478 0.00 0.00 36.66 4.52
45 46 4.160252 AGGCACAACATCCATTTCCATTAC 59.840 41.667 0.00 0.00 0.00 1.89
46 47 4.352009 AGGCACAACATCCATTTCCATTA 58.648 39.130 0.00 0.00 0.00 1.90
47 48 3.175594 AGGCACAACATCCATTTCCATT 58.824 40.909 0.00 0.00 0.00 3.16
48 49 2.823959 AGGCACAACATCCATTTCCAT 58.176 42.857 0.00 0.00 0.00 3.41
50 51 3.683365 AAAGGCACAACATCCATTTCC 57.317 42.857 0.00 0.00 0.00 3.13
52 53 4.128643 CACAAAAGGCACAACATCCATTT 58.871 39.130 0.00 0.00 0.00 2.32
55 56 1.202510 GCACAAAAGGCACAACATCCA 60.203 47.619 0.00 0.00 0.00 3.41
56 57 1.069049 AGCACAAAAGGCACAACATCC 59.931 47.619 0.00 0.00 0.00 3.51
119 120 5.163311 CCCTGAAACTCCAAAGGAATTTTGT 60.163 40.000 0.00 0.00 43.78 2.83
182 186 0.995024 ACCAGCAGGGCTAATTGTCT 59.005 50.000 0.00 0.00 42.05 3.41
183 187 1.383523 GACCAGCAGGGCTAATTGTC 58.616 55.000 0.00 0.00 41.07 3.18
221 225 0.953960 GAGGGCACAACCAACCTACG 60.954 60.000 0.00 0.00 42.05 3.51
250 254 2.227865 TGTCCAAAGCGCCAAAGTTATC 59.772 45.455 2.29 0.00 0.00 1.75
258 262 0.394938 TCTAGTTGTCCAAAGCGCCA 59.605 50.000 2.29 0.00 0.00 5.69
348 352 3.861840 TCTTTCTAGAGGCGTTGAATGG 58.138 45.455 0.00 0.00 0.00 3.16
395 401 1.394572 CATTTGATCTCGCGCAGAACA 59.605 47.619 8.75 11.58 33.62 3.18
403 409 2.030946 GTGTGTAGGCATTTGATCTCGC 59.969 50.000 0.00 0.00 0.00 5.03
500 508 6.017109 TGAGGCTGAAATGAAACAAAGACTAC 60.017 38.462 0.00 0.00 0.00 2.73
512 520 2.449464 CCACCATTGAGGCTGAAATGA 58.551 47.619 17.09 0.00 43.14 2.57
613 624 7.039270 GTCCGGCTTTAAATTAATGAACCAAT 58.961 34.615 0.00 0.00 0.00 3.16
637 648 4.365723 TGAAGAAAAGCGTAAGAGAACGT 58.634 39.130 0.00 0.00 44.64 3.99
655 3331 7.377766 TCCTTCCGTCATAAATTCTTTGAAG 57.622 36.000 0.00 0.00 0.00 3.02
657 3333 6.128007 GCTTCCTTCCGTCATAAATTCTTTGA 60.128 38.462 0.00 0.00 0.00 2.69
658 3334 6.030228 GCTTCCTTCCGTCATAAATTCTTTG 58.970 40.000 0.00 0.00 0.00 2.77
674 3350 1.016653 GCGAGGACACTGCTTCCTTC 61.017 60.000 0.00 0.00 44.03 3.46
691 3367 5.152097 CGTATAGTAGTATTTGTCCAGGCG 58.848 45.833 0.00 0.00 0.00 5.52
1086 3768 0.252742 GTTGGAAGGGAGGAGGGAGA 60.253 60.000 0.00 0.00 0.00 3.71
1103 3785 1.683365 TAGAGGGCGGCGTAAGGTT 60.683 57.895 9.37 0.00 38.28 3.50
1333 4021 0.105964 TGGTAGCAGCAGTCGTTGTT 59.894 50.000 0.00 0.00 0.00 2.83
1407 4095 1.741770 GCAGTTGAGGTCGGCGAAT 60.742 57.895 12.92 2.59 0.00 3.34
1632 4320 0.034767 TCGAAGAGAACCCTAGCGGA 60.035 55.000 4.45 0.00 34.64 5.54
1704 4392 0.032117 TGGGACCGATGAGGATCTGT 60.032 55.000 0.00 0.00 45.00 3.41
1809 4540 3.760684 GTGCCCAAGATGTTCAAGAAGAT 59.239 43.478 0.00 0.00 0.00 2.40
2022 6133 4.078342 GATGCATGCATGGCTAGCTAGC 62.078 54.545 36.73 33.40 41.59 3.42
2189 6363 7.070571 GGAGTACTAGTACTACCCTACTGAGAA 59.929 44.444 30.80 0.00 45.63 2.87
2307 6768 2.485814 GCTTCCGAAACATGAGAAAGCT 59.514 45.455 0.00 0.00 0.00 3.74
2676 8209 8.585018 TGTGATGACTGATGACTTTAGAGTTTA 58.415 33.333 0.00 0.00 35.88 2.01
2680 8213 5.809562 GGTGTGATGACTGATGACTTTAGAG 59.190 44.000 0.00 0.00 0.00 2.43
2681 8214 5.245977 TGGTGTGATGACTGATGACTTTAGA 59.754 40.000 0.00 0.00 0.00 2.10
2683 8216 5.221621 TGTGGTGTGATGACTGATGACTTTA 60.222 40.000 0.00 0.00 0.00 1.85
2685 8218 3.071457 TGTGGTGTGATGACTGATGACTT 59.929 43.478 0.00 0.00 0.00 3.01
2686 8219 2.634453 TGTGGTGTGATGACTGATGACT 59.366 45.455 0.00 0.00 0.00 3.41
2687 8220 2.738846 GTGTGGTGTGATGACTGATGAC 59.261 50.000 0.00 0.00 0.00 3.06
2725 8258 2.046314 GCAAAGCCCTAGCCGTGA 60.046 61.111 0.00 0.00 41.25 4.35
2730 8263 5.552178 AGTAATACTATGCAAAGCCCTAGC 58.448 41.667 0.00 0.00 40.32 3.42
2796 8337 2.665052 GCTTGTAGGTTTTCGTACTCCG 59.335 50.000 0.00 0.00 40.50 4.63
2798 8339 6.755141 TCATATGCTTGTAGGTTTTCGTACTC 59.245 38.462 0.00 0.00 40.50 2.59
2868 8413 5.048504 TGGAGTTTGGACACGTAACTACTAG 60.049 44.000 10.84 0.00 34.51 2.57
2875 8420 3.876341 AGTTTGGAGTTTGGACACGTAA 58.124 40.909 0.00 0.00 0.00 3.18
3425 8972 2.225727 CGATGGAATGATCGACGACCTA 59.774 50.000 0.00 0.00 46.72 3.08
3429 8976 1.029681 ACCGATGGAATGATCGACGA 58.970 50.000 0.00 0.00 46.72 4.20
3468 9015 0.895100 GTGGCATGGCTTGACTGGAA 60.895 55.000 21.08 0.00 32.91 3.53
3579 9132 1.322040 GCAAAAACGACAACAAACGGG 59.678 47.619 0.00 0.00 0.00 5.28
3645 9198 4.219507 CAGAGCGATGGATTGATAGTACCT 59.780 45.833 0.00 0.00 0.00 3.08
3655 9214 2.501723 ACACCTTACAGAGCGATGGATT 59.498 45.455 0.00 0.00 0.00 3.01
3708 9267 2.421073 CACACACACCTATTGCTCCATG 59.579 50.000 0.00 0.00 0.00 3.66
3729 9288 4.434713 AGGACACACAAACAAGAAACAC 57.565 40.909 0.00 0.00 0.00 3.32
3730 9289 4.520874 TCAAGGACACACAAACAAGAAACA 59.479 37.500 0.00 0.00 0.00 2.83
3731 9290 5.054390 TCAAGGACACACAAACAAGAAAC 57.946 39.130 0.00 0.00 0.00 2.78
3732 9291 5.713792 TTCAAGGACACACAAACAAGAAA 57.286 34.783 0.00 0.00 0.00 2.52
3734 9293 5.913137 AATTCAAGGACACACAAACAAGA 57.087 34.783 0.00 0.00 0.00 3.02
3735 9294 5.291614 CCAAATTCAAGGACACACAAACAAG 59.708 40.000 0.00 0.00 0.00 3.16
3736 9295 5.174395 CCAAATTCAAGGACACACAAACAA 58.826 37.500 0.00 0.00 0.00 2.83
3737 9296 4.382470 CCCAAATTCAAGGACACACAAACA 60.382 41.667 0.00 0.00 0.00 2.83
3738 9297 4.119136 CCCAAATTCAAGGACACACAAAC 58.881 43.478 0.00 0.00 0.00 2.93
3739 9298 3.772025 ACCCAAATTCAAGGACACACAAA 59.228 39.130 0.00 0.00 0.00 2.83
3750 9309 5.815233 TGCTTAATGGAACCCAAATTCAA 57.185 34.783 0.00 0.00 36.95 2.69
3761 9320 8.696043 ACATGCTAAAGATATGCTTAATGGAA 57.304 30.769 0.00 0.00 35.24 3.53
3763 9322 8.790718 AGAACATGCTAAAGATATGCTTAATGG 58.209 33.333 0.00 0.00 35.24 3.16
3805 9364 6.258727 TCGAGTTCATGAATAGCCAAGATTTC 59.741 38.462 12.12 0.00 0.00 2.17
3810 9369 4.149571 CGATCGAGTTCATGAATAGCCAAG 59.850 45.833 10.26 0.00 0.00 3.61
3819 9378 3.119637 TGCAGTTACGATCGAGTTCATGA 60.120 43.478 24.34 0.00 0.00 3.07
3840 9402 8.036273 TGATGTCTGCATATATAACTGCATTG 57.964 34.615 10.64 2.46 46.48 2.82
3872 9434 7.769507 CCCACAGAGAATATAGATGGATTGATG 59.230 40.741 0.00 0.00 0.00 3.07
3873 9435 7.092533 CCCCACAGAGAATATAGATGGATTGAT 60.093 40.741 0.00 0.00 0.00 2.57
3874 9436 6.214208 CCCCACAGAGAATATAGATGGATTGA 59.786 42.308 0.00 0.00 0.00 2.57
3875 9437 6.413052 CCCCACAGAGAATATAGATGGATTG 58.587 44.000 0.00 0.00 0.00 2.67
3876 9438 5.490357 CCCCCACAGAGAATATAGATGGATT 59.510 44.000 0.00 0.00 0.00 3.01
3877 9439 5.035556 CCCCCACAGAGAATATAGATGGAT 58.964 45.833 0.00 0.00 0.00 3.41
3878 9440 4.109600 TCCCCCACAGAGAATATAGATGGA 59.890 45.833 0.00 0.00 0.00 3.41
3879 9441 4.429505 TCCCCCACAGAGAATATAGATGG 58.570 47.826 0.00 0.00 0.00 3.51
3880 9442 5.090139 ACTCCCCCACAGAGAATATAGATG 58.910 45.833 0.00 0.00 35.27 2.90
3883 9445 5.646215 ACTACTCCCCCACAGAGAATATAG 58.354 45.833 0.00 0.00 35.27 1.31
3889 9451 2.585900 ACATACTACTCCCCCACAGAGA 59.414 50.000 0.00 0.00 35.27 3.10
3890 9452 3.033659 ACATACTACTCCCCCACAGAG 57.966 52.381 0.00 0.00 37.39 3.35
3891 9453 4.613265 TTACATACTACTCCCCCACAGA 57.387 45.455 0.00 0.00 0.00 3.41
3892 9454 5.888982 ATTTACATACTACTCCCCCACAG 57.111 43.478 0.00 0.00 0.00 3.66
3912 9474 8.621286 CGGCCATTGTTCTTTACTCTTTATATT 58.379 33.333 2.24 0.00 0.00 1.28
3913 9475 7.228706 CCGGCCATTGTTCTTTACTCTTTATAT 59.771 37.037 2.24 0.00 0.00 0.86
3915 9477 5.357032 CCGGCCATTGTTCTTTACTCTTTAT 59.643 40.000 2.24 0.00 0.00 1.40
3917 9479 3.506067 CCGGCCATTGTTCTTTACTCTTT 59.494 43.478 2.24 0.00 0.00 2.52
3918 9480 3.081804 CCGGCCATTGTTCTTTACTCTT 58.918 45.455 2.24 0.00 0.00 2.85
3919 9481 2.039879 ACCGGCCATTGTTCTTTACTCT 59.960 45.455 0.00 0.00 0.00 3.24
3920 9482 2.433436 ACCGGCCATTGTTCTTTACTC 58.567 47.619 0.00 0.00 0.00 2.59
3937 9867 1.816224 CCCCCTTGTTCATTGTTACCG 59.184 52.381 0.00 0.00 0.00 4.02
3956 9886 1.482593 AGAACATCCAGTCGTCATCCC 59.517 52.381 0.00 0.00 0.00 3.85
4039 9969 8.189460 ACGTTGATATAGTAGAAACTTGACTCC 58.811 37.037 0.00 0.00 37.15 3.85
4067 9997 7.844779 ACTCTCATTATGGGTAGTAGAAAAGGA 59.155 37.037 0.00 0.00 0.00 3.36
4068 9998 8.024145 ACTCTCATTATGGGTAGTAGAAAAGG 57.976 38.462 0.00 0.00 0.00 3.11
4072 10002 9.656323 ATGTTACTCTCATTATGGGTAGTAGAA 57.344 33.333 0.00 0.00 0.00 2.10
4076 10006 8.011290 ACCTATGTTACTCTCATTATGGGTAGT 58.989 37.037 0.00 0.00 0.00 2.73
4078 10008 9.529823 CTACCTATGTTACTCTCATTATGGGTA 57.470 37.037 0.00 0.00 0.00 3.69
4079 10009 8.011290 ACTACCTATGTTACTCTCATTATGGGT 58.989 37.037 0.00 0.00 0.00 4.51
4080 10010 8.423906 ACTACCTATGTTACTCTCATTATGGG 57.576 38.462 0.00 0.00 0.00 4.00
4131 10061 9.590451 CTTCATTTATTACTTGCCACATCATTT 57.410 29.630 0.00 0.00 0.00 2.32
4133 10063 8.523915 TCTTCATTTATTACTTGCCACATCAT 57.476 30.769 0.00 0.00 0.00 2.45
4135 10065 9.294030 CTTTCTTCATTTATTACTTGCCACATC 57.706 33.333 0.00 0.00 0.00 3.06
4137 10067 8.402798 TCTTTCTTCATTTATTACTTGCCACA 57.597 30.769 0.00 0.00 0.00 4.17
4138 10068 7.970614 CCTCTTTCTTCATTTATTACTTGCCAC 59.029 37.037 0.00 0.00 0.00 5.01
4140 10070 7.416777 CCCCTCTTTCTTCATTTATTACTTGCC 60.417 40.741 0.00 0.00 0.00 4.52
4141 10071 7.484140 CCCCTCTTTCTTCATTTATTACTTGC 58.516 38.462 0.00 0.00 0.00 4.01
4142 10072 7.122650 TGCCCCTCTTTCTTCATTTATTACTTG 59.877 37.037 0.00 0.00 0.00 3.16
4144 10074 6.731467 TGCCCCTCTTTCTTCATTTATTACT 58.269 36.000 0.00 0.00 0.00 2.24
4145 10075 7.068716 ACATGCCCCTCTTTCTTCATTTATTAC 59.931 37.037 0.00 0.00 0.00 1.89
4146 10076 7.068593 CACATGCCCCTCTTTCTTCATTTATTA 59.931 37.037 0.00 0.00 0.00 0.98
4149 10079 4.706476 CACATGCCCCTCTTTCTTCATTTA 59.294 41.667 0.00 0.00 0.00 1.40
4151 10081 3.094572 CACATGCCCCTCTTTCTTCATT 58.905 45.455 0.00 0.00 0.00 2.57
4154 10084 1.272147 ACCACATGCCCCTCTTTCTTC 60.272 52.381 0.00 0.00 0.00 2.87
4157 10087 2.092323 GTTACCACATGCCCCTCTTTC 58.908 52.381 0.00 0.00 0.00 2.62
4159 10089 1.072266 TGTTACCACATGCCCCTCTT 58.928 50.000 0.00 0.00 0.00 2.85
4160 10090 1.298953 ATGTTACCACATGCCCCTCT 58.701 50.000 0.00 0.00 42.46 3.69
4161 10091 2.172717 ACTATGTTACCACATGCCCCTC 59.827 50.000 0.00 0.00 43.92 4.30
4163 10093 2.729028 ACTATGTTACCACATGCCCC 57.271 50.000 0.00 0.00 43.92 5.80
4164 10094 4.777463 ACTAACTATGTTACCACATGCCC 58.223 43.478 0.00 0.00 43.92 5.36
4165 10095 7.046033 AGTAACTAACTATGTTACCACATGCC 58.954 38.462 11.59 0.00 46.31 4.40
4166 10096 9.245962 CTAGTAACTAACTATGTTACCACATGC 57.754 37.037 11.59 0.00 46.31 4.06
4167 10097 9.245962 GCTAGTAACTAACTATGTTACCACATG 57.754 37.037 11.59 0.00 46.31 3.21
4168 10098 8.974238 TGCTAGTAACTAACTATGTTACCACAT 58.026 33.333 11.59 0.00 46.31 3.21
4169 10099 8.352137 TGCTAGTAACTAACTATGTTACCACA 57.648 34.615 11.59 6.55 46.31 4.17
4170 10100 8.465201 ACTGCTAGTAACTAACTATGTTACCAC 58.535 37.037 11.59 4.59 46.31 4.16
4171 10101 8.585471 ACTGCTAGTAACTAACTATGTTACCA 57.415 34.615 11.59 4.47 46.31 3.25
4186 10116 8.188799 GTGTGATGTTACTCATACTGCTAGTAA 58.811 37.037 0.00 0.00 36.83 2.24
4188 10118 6.152831 TGTGTGATGTTACTCATACTGCTAGT 59.847 38.462 10.75 0.00 37.92 2.57
4190 10120 6.524101 TGTGTGATGTTACTCATACTGCTA 57.476 37.500 10.75 0.00 37.92 3.49
4191 10121 5.405935 TGTGTGATGTTACTCATACTGCT 57.594 39.130 10.75 0.00 37.92 4.24
4192 10122 7.653311 TGATATGTGTGATGTTACTCATACTGC 59.347 37.037 10.75 0.00 38.84 4.40
4193 10123 9.533253 TTGATATGTGTGATGTTACTCATACTG 57.467 33.333 10.75 0.00 38.84 2.74
4194 10124 9.755804 CTTGATATGTGTGATGTTACTCATACT 57.244 33.333 10.75 3.32 38.84 2.12
4196 10126 8.704668 ACCTTGATATGTGTGATGTTACTCATA 58.295 33.333 0.00 0.00 39.73 2.15
4198 10128 6.946340 ACCTTGATATGTGTGATGTTACTCA 58.054 36.000 0.00 0.00 0.00 3.41
4199 10129 8.942338 TTACCTTGATATGTGTGATGTTACTC 57.058 34.615 0.00 0.00 0.00 2.59
4200 10130 8.758829 TCTTACCTTGATATGTGTGATGTTACT 58.241 33.333 0.00 0.00 0.00 2.24
4201 10131 8.942338 TCTTACCTTGATATGTGTGATGTTAC 57.058 34.615 0.00 0.00 0.00 2.50
4202 10132 9.546428 CATCTTACCTTGATATGTGTGATGTTA 57.454 33.333 0.00 0.00 0.00 2.41
4203 10133 8.267183 TCATCTTACCTTGATATGTGTGATGTT 58.733 33.333 0.00 0.00 32.47 2.71
4204 10134 7.795047 TCATCTTACCTTGATATGTGTGATGT 58.205 34.615 0.00 0.00 32.47 3.06
4205 10135 7.930325 ACTCATCTTACCTTGATATGTGTGATG 59.070 37.037 0.00 0.00 32.17 3.07
4206 10136 8.027524 ACTCATCTTACCTTGATATGTGTGAT 57.972 34.615 0.00 0.00 0.00 3.06
4207 10137 7.343057 AGACTCATCTTACCTTGATATGTGTGA 59.657 37.037 0.00 0.00 0.00 3.58
4208 10138 7.495901 AGACTCATCTTACCTTGATATGTGTG 58.504 38.462 0.00 0.00 0.00 3.82
4209 10139 7.667575 AGACTCATCTTACCTTGATATGTGT 57.332 36.000 0.00 0.00 0.00 3.72
4234 10164 9.398170 CATGCAACGCTTTATTTATTAAGCTAT 57.602 29.630 10.58 0.00 43.49 2.97
4235 10165 8.402472 ACATGCAACGCTTTATTTATTAAGCTA 58.598 29.630 10.58 0.00 43.49 3.32
4236 10166 7.257722 ACATGCAACGCTTTATTTATTAAGCT 58.742 30.769 10.58 0.00 43.49 3.74
4237 10167 7.449934 ACATGCAACGCTTTATTTATTAAGC 57.550 32.000 0.00 3.94 42.51 3.09
4239 10169 9.291664 GGTAACATGCAACGCTTTATTTATTAA 57.708 29.630 0.00 0.00 0.00 1.40
4242 10172 6.857956 TGGTAACATGCAACGCTTTATTTAT 58.142 32.000 0.00 0.00 46.17 1.40
4245 10175 4.775058 TGGTAACATGCAACGCTTTATT 57.225 36.364 0.00 0.00 46.17 1.40
4262 10192 4.162698 GTGGGGAGTAACATATGTGTGGTA 59.837 45.833 9.63 0.00 38.92 3.25
4264 10194 3.199946 AGTGGGGAGTAACATATGTGTGG 59.800 47.826 9.63 0.00 38.92 4.17
4265 10195 4.487714 AGTGGGGAGTAACATATGTGTG 57.512 45.455 9.63 0.00 38.92 3.82
4266 10196 7.302948 TCTATAGTGGGGAGTAACATATGTGT 58.697 38.462 9.63 2.63 41.28 3.72
4267 10197 7.093727 CCTCTATAGTGGGGAGTAACATATGTG 60.094 44.444 9.63 0.00 0.00 3.21
4268 10198 6.954684 CCTCTATAGTGGGGAGTAACATATGT 59.045 42.308 12.29 1.41 0.00 2.29
4269 10199 6.954684 ACCTCTATAGTGGGGAGTAACATATG 59.045 42.308 21.82 0.00 33.22 1.78
4270 10200 7.117331 ACCTCTATAGTGGGGAGTAACATAT 57.883 40.000 21.82 0.00 33.22 1.78
4272 10202 5.420215 ACCTCTATAGTGGGGAGTAACAT 57.580 43.478 21.82 0.00 33.22 2.71
4274 10204 5.951204 ACTACCTCTATAGTGGGGAGTAAC 58.049 45.833 22.09 0.00 34.02 2.50
4275 10205 7.129349 TGTTACTACCTCTATAGTGGGGAGTAA 59.871 40.741 28.26 28.26 38.03 2.24
4277 10207 5.434376 TGTTACTACCTCTATAGTGGGGAGT 59.566 44.000 24.72 24.72 36.09 3.85
4278 10208 5.950023 TGTTACTACCTCTATAGTGGGGAG 58.050 45.833 21.82 20.04 36.09 4.30
4279 10209 5.999987 TGTTACTACCTCTATAGTGGGGA 57.000 43.478 21.82 11.28 36.09 4.81
4280 10210 6.890814 CCTATGTTACTACCTCTATAGTGGGG 59.109 46.154 21.82 16.35 36.09 4.96
4282 10212 7.468496 ACCCTATGTTACTACCTCTATAGTGG 58.532 42.308 17.49 17.49 36.09 4.00
4283 10213 9.669887 CTACCCTATGTTACTACCTCTATAGTG 57.330 40.741 0.00 0.00 36.09 2.74
4284 10214 9.404077 ACTACCCTATGTTACTACCTCTATAGT 57.596 37.037 0.00 0.00 38.89 2.12
4288 10218 9.003145 TGTTACTACCCTATGTTACTACCTCTA 57.997 37.037 0.00 0.00 0.00 2.43
4290 10220 8.574737 CATGTTACTACCCTATGTTACTACCTC 58.425 40.741 0.00 0.00 0.00 3.85
4292 10222 8.469309 TCATGTTACTACCCTATGTTACTACC 57.531 38.462 0.00 0.00 0.00 3.18
4293 10223 8.081025 GCTCATGTTACTACCCTATGTTACTAC 58.919 40.741 0.00 0.00 0.00 2.73
4295 10225 6.610020 TGCTCATGTTACTACCCTATGTTACT 59.390 38.462 0.00 0.00 0.00 2.24
4296 10226 6.812998 TGCTCATGTTACTACCCTATGTTAC 58.187 40.000 0.00 0.00 0.00 2.50
4299 10229 5.858381 CATGCTCATGTTACTACCCTATGT 58.142 41.667 1.84 0.00 34.23 2.29
4312 10242 9.033463 CCACAATGGGTAATAACATGCTCATGT 62.033 40.741 9.52 9.52 42.99 3.21
4313 10243 6.210796 CACAATGGGTAATAACATGCTCATG 58.789 40.000 8.21 8.21 44.15 3.07
4315 10245 4.644234 CCACAATGGGTAATAACATGCTCA 59.356 41.667 0.00 0.00 32.67 4.26
4316 10246 4.499696 GCCACAATGGGTAATAACATGCTC 60.500 45.833 0.00 0.00 38.19 4.26
4317 10247 3.384467 GCCACAATGGGTAATAACATGCT 59.616 43.478 0.00 0.00 38.19 3.79
4330 10260 2.012673 GCAGAAGACTAGCCACAATGG 58.987 52.381 0.00 0.00 41.55 3.16
4331 10261 2.935201 GAGCAGAAGACTAGCCACAATG 59.065 50.000 0.00 0.00 0.00 2.82
4332 10262 2.568956 TGAGCAGAAGACTAGCCACAAT 59.431 45.455 0.00 0.00 0.00 2.71
4333 10263 1.970640 TGAGCAGAAGACTAGCCACAA 59.029 47.619 0.00 0.00 0.00 3.33
4334 10264 1.632589 TGAGCAGAAGACTAGCCACA 58.367 50.000 0.00 0.00 0.00 4.17
4335 10265 2.615869 CTTGAGCAGAAGACTAGCCAC 58.384 52.381 0.00 0.00 0.00 5.01
4336 10266 1.066573 GCTTGAGCAGAAGACTAGCCA 60.067 52.381 0.00 0.00 41.59 4.75
4337 10267 1.650825 GCTTGAGCAGAAGACTAGCC 58.349 55.000 0.00 0.00 41.59 3.93
4351 10281 0.698238 AGGTTGGGCTGTATGCTTGA 59.302 50.000 0.00 0.00 42.39 3.02


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

AutoCloner maintained by Alex Coulton.