Multiple sequence alignment - TraesCS3B01G243500

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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 TraesCS3B01G243500 chr3B 100.000 3683 0 0 1 3683 384908740 384912422 0.000000e+00 6802.0
1 TraesCS3B01G243500 chr3A 94.520 2427 49 24 961 3359 384319779 384322149 0.000000e+00 3668.0
2 TraesCS3B01G243500 chr3A 87.075 882 30 38 2 842 384318488 384319326 0.000000e+00 920.0
3 TraesCS3B01G243500 chr3A 81.250 688 112 14 1190 1867 88854786 88855466 1.160000e-149 540.0
4 TraesCS3B01G243500 chr3A 91.329 173 15 0 3511 3683 57468565 57468393 1.710000e-58 237.0
5 TraesCS3B01G243500 chr3A 89.024 82 8 1 3431 3511 57468701 57468620 2.340000e-17 100.0
6 TraesCS3B01G243500 chr3D 95.583 1562 44 6 730 2284 291765079 291766622 0.000000e+00 2479.0
7 TraesCS3B01G243500 chr3D 92.289 1219 34 14 2178 3370 291766567 291767751 0.000000e+00 1676.0
8 TraesCS3B01G243500 chr3D 90.072 1108 40 24 1 1084 291763986 291765047 0.000000e+00 1373.0
9 TraesCS3B01G243500 chr3D 78.621 856 160 20 1190 2032 75355829 75356674 2.500000e-151 545.0
10 TraesCS3B01G243500 chr3D 96.532 173 6 0 3511 3683 87329993 87329821 1.670000e-73 287.0
11 TraesCS3B01G243500 chr3D 96.341 82 2 1 3431 3511 87330129 87330048 2.310000e-27 134.0
12 TraesCS3B01G243500 chr3D 83.721 86 14 0 2393 2478 291766872 291766957 8.480000e-12 82.4
13 TraesCS3B01G243500 chr1D 77.450 949 179 27 1178 2107 119010745 119009813 5.410000e-148 534.0
14 TraesCS3B01G243500 chr1D 89.595 173 18 0 3511 3683 314005743 314005571 1.720000e-53 220.0
15 TraesCS3B01G243500 chr1B 77.158 950 180 29 1178 2107 181218220 181217288 5.450000e-143 518.0
16 TraesCS3B01G243500 chr1A 77.158 950 180 31 1178 2107 131521533 131520601 5.450000e-143 518.0
17 TraesCS3B01G243500 chr6D 77.870 723 134 22 1178 1884 60168240 60167528 3.400000e-115 425.0
18 TraesCS3B01G243500 chr6D 97.110 173 5 0 3511 3683 83112382 83112210 3.600000e-75 292.0
19 TraesCS3B01G243500 chr6D 95.122 82 3 1 3431 3511 83112518 83112437 1.070000e-25 128.0
20 TraesCS3B01G243500 chr6B 77.455 723 137 21 1178 1884 134000283 133999571 3.420000e-110 409.0
21 TraesCS3B01G243500 chr2D 93.642 173 11 0 3511 3683 545502465 545502637 3.650000e-65 259.0
22 TraesCS3B01G243500 chr2D 93.064 173 12 0 3511 3683 554348529 554348357 1.700000e-63 254.0
23 TraesCS3B01G243500 chr2A 91.908 173 14 0 3511 3683 687497089 687496917 3.670000e-60 243.0
24 TraesCS3B01G243500 chr2A 91.358 81 7 0 3431 3511 105412981 105412901 1.080000e-20 111.0
25 TraesCS3B01G243500 chr5A 90.751 173 16 0 3511 3683 558232432 558232260 7.950000e-57 231.0
26 TraesCS3B01G243500 chr5A 90.244 82 8 0 3430 3511 558232568 558232487 1.400000e-19 108.0
27 TraesCS3B01G243500 chr4A 90.230 174 16 1 3511 3683 54399266 54399093 3.700000e-55 226.0
28 TraesCS3B01G243500 chr6A 90.244 82 5 3 3431 3510 387970974 387971054 1.810000e-18 104.0
29 TraesCS3B01G243500 chr4B 87.805 82 9 1 3431 3511 630364943 630364862 1.090000e-15 95.3


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 TraesCS3B01G243500 chr3B 384908740 384912422 3682 False 6802.0 6802 100.00000 1 3683 1 chr3B.!!$F1 3682
1 TraesCS3B01G243500 chr3A 384318488 384322149 3661 False 2294.0 3668 90.79750 2 3359 2 chr3A.!!$F2 3357
2 TraesCS3B01G243500 chr3A 88854786 88855466 680 False 540.0 540 81.25000 1190 1867 1 chr3A.!!$F1 677
3 TraesCS3B01G243500 chr3D 291763986 291767751 3765 False 1402.6 2479 90.41625 1 3370 4 chr3D.!!$F2 3369
4 TraesCS3B01G243500 chr3D 75355829 75356674 845 False 545.0 545 78.62100 1190 2032 1 chr3D.!!$F1 842
5 TraesCS3B01G243500 chr1D 119009813 119010745 932 True 534.0 534 77.45000 1178 2107 1 chr1D.!!$R1 929
6 TraesCS3B01G243500 chr1B 181217288 181218220 932 True 518.0 518 77.15800 1178 2107 1 chr1B.!!$R1 929
7 TraesCS3B01G243500 chr1A 131520601 131521533 932 True 518.0 518 77.15800 1178 2107 1 chr1A.!!$R1 929
8 TraesCS3B01G243500 chr6D 60167528 60168240 712 True 425.0 425 77.87000 1178 1884 1 chr6D.!!$R1 706
9 TraesCS3B01G243500 chr6B 133999571 134000283 712 True 409.0 409 77.45500 1178 1884 1 chr6B.!!$R1 706

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
513 556 0.458197 GCACAAACAGCACAGCACAA 60.458 50.0 0.0 0.0 0.0 3.33 F
1176 1940 0.460311 CGTCCTACTCCTTCGCCAAT 59.540 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1320 2087 1.153978 GGCGACGACGGTGATGTAA 60.154 57.895 9.67 0.0 40.15 2.41 R
3082 3951 1.052768 GCAACGCGTCACAAATCGAC 61.053 55.000 14.44 0.0 0.00 4.20 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
303 342 3.518634 ATGGTTTATTTGCGCGGAAAT 57.481 38.095 35.11 35.11 0.00 2.17
304 343 4.640789 ATGGTTTATTTGCGCGGAAATA 57.359 36.364 33.15 33.15 0.00 1.40
305 344 3.760537 TGGTTTATTTGCGCGGAAATAC 58.239 40.909 35.55 29.04 29.41 1.89
306 345 3.440872 TGGTTTATTTGCGCGGAAATACT 59.559 39.130 35.55 20.97 29.41 2.12
307 346 4.033019 GGTTTATTTGCGCGGAAATACTC 58.967 43.478 35.55 29.21 29.41 2.59
308 347 3.955771 TTATTTGCGCGGAAATACTCC 57.044 42.857 35.55 6.47 41.40 3.85
309 348 2.038387 ATTTGCGCGGAAATACTCCT 57.962 45.000 33.02 12.55 42.85 3.69
310 349 2.676632 TTTGCGCGGAAATACTCCTA 57.323 45.000 22.36 0.00 42.85 2.94
311 350 2.902705 TTGCGCGGAAATACTCCTAT 57.097 45.000 11.75 0.00 42.85 2.57
312 351 4.325028 TTTGCGCGGAAATACTCCTATA 57.675 40.909 22.36 0.00 42.85 1.31
512 555 1.139308 GCACAAACAGCACAGCACA 59.861 52.632 0.00 0.00 0.00 4.57
513 556 0.458197 GCACAAACAGCACAGCACAA 60.458 50.000 0.00 0.00 0.00 3.33
551 597 2.961526 TTTTCTACTAGGGAGCGCAG 57.038 50.000 11.47 0.00 0.00 5.18
577 623 4.878397 AGCTAGCATCGCTTTCTTTGTTAT 59.122 37.500 18.83 0.00 40.44 1.89
659 707 2.289547 AGAAAACACCGTTCGTTGATGG 59.710 45.455 0.00 0.00 0.00 3.51
698 752 8.710835 AAAGAATCGTAAAAAGAAAAAGCCAA 57.289 26.923 0.00 0.00 0.00 4.52
700 754 8.887036 AGAATCGTAAAAAGAAAAAGCCAATT 57.113 26.923 0.00 0.00 0.00 2.32
701 755 9.974980 AGAATCGTAAAAAGAAAAAGCCAATTA 57.025 25.926 0.00 0.00 0.00 1.40
784 842 2.964310 GCTCCTCTTCCAGCTGCCA 61.964 63.158 8.66 0.00 32.48 4.92
793 851 2.110967 CCAGCTGCCAGTTGATCCG 61.111 63.158 10.40 0.00 0.00 4.18
794 852 1.376424 CAGCTGCCAGTTGATCCGT 60.376 57.895 1.85 0.00 0.00 4.69
795 853 0.957395 CAGCTGCCAGTTGATCCGTT 60.957 55.000 1.85 0.00 0.00 4.44
796 854 0.957395 AGCTGCCAGTTGATCCGTTG 60.957 55.000 0.00 0.00 0.00 4.10
873 940 2.818274 GCCGTCCGGTCCAATCAC 60.818 66.667 7.66 0.00 37.65 3.06
934 1001 1.360393 TGCTCCCCCATATGAACCCC 61.360 60.000 3.65 0.00 0.00 4.95
935 1002 1.360393 GCTCCCCCATATGAACCCCA 61.360 60.000 3.65 0.00 0.00 4.96
969 1370 2.969238 GAGCATCCATCCACGCCG 60.969 66.667 0.00 0.00 0.00 6.46
972 1373 3.274586 CATCCATCCACGCCGCAG 61.275 66.667 0.00 0.00 0.00 5.18
1031 1432 2.988684 GGCAATGGCGACCACCAA 60.989 61.111 0.50 0.00 44.65 3.67
1032 1433 2.568090 GCAATGGCGACCACCAAG 59.432 61.111 0.50 0.00 44.65 3.61
1033 1434 1.971167 GCAATGGCGACCACCAAGA 60.971 57.895 0.50 0.00 44.65 3.02
1034 1435 1.875963 CAATGGCGACCACCAAGAC 59.124 57.895 0.50 0.00 44.65 3.01
1035 1436 1.671054 AATGGCGACCACCAAGACG 60.671 57.895 0.50 0.00 44.65 4.18
1078 1836 4.671590 TCCTCGTCCCGCACCTCA 62.672 66.667 0.00 0.00 0.00 3.86
1165 1929 1.003355 TTCGTCGACCCGTCCTACT 60.003 57.895 10.58 0.00 0.00 2.57
1176 1940 0.460311 CGTCCTACTCCTTCGCCAAT 59.540 55.000 0.00 0.00 0.00 3.16
1324 2091 1.613928 TCCCAGGCGGACCATTACA 60.614 57.895 0.00 0.00 39.06 2.41
1683 2456 4.021650 GACAACGTCGGCAACTCA 57.978 55.556 0.00 0.00 0.00 3.41
1794 2567 1.855295 TACTCATGAACACCGGGCTA 58.145 50.000 6.32 0.00 0.00 3.93
2502 3365 0.033796 CACCAGAGGACCGGTACCTA 60.034 60.000 21.12 0.00 37.93 3.08
2505 3368 1.133575 CCAGAGGACCGGTACCTATCA 60.134 57.143 21.12 0.00 37.93 2.15
2800 3666 9.143631 CTTCTTCTTCTTCTTCATTCTTCTCTC 57.856 37.037 0.00 0.00 0.00 3.20
3079 3948 0.386858 CACGTTCACGATGAGACGGT 60.387 55.000 6.30 0.00 43.02 4.83
3080 3949 0.109873 ACGTTCACGATGAGACGGTC 60.110 55.000 6.30 0.00 43.02 4.79
3081 3950 0.797249 CGTTCACGATGAGACGGTCC 60.797 60.000 4.14 0.00 43.02 4.46
3082 3951 0.797249 GTTCACGATGAGACGGTCCG 60.797 60.000 10.48 10.48 37.61 4.79
3281 4159 3.242641 GCGCCTGTATAACTTAACCTTGC 60.243 47.826 0.00 0.00 0.00 4.01
3352 4230 0.657077 CGTCAACACCAACGTGCATG 60.657 55.000 3.82 3.82 44.40 4.06
3370 4248 1.108776 TGCGACTACTCCATGGTACC 58.891 55.000 12.58 4.43 0.00 3.34
3371 4249 1.108776 GCGACTACTCCATGGTACCA 58.891 55.000 18.99 18.99 0.00 3.25
3372 4250 1.202382 GCGACTACTCCATGGTACCAC 60.202 57.143 19.09 0.00 0.00 4.16
3373 4251 2.376109 CGACTACTCCATGGTACCACT 58.624 52.381 19.09 3.70 0.00 4.00
3374 4252 3.548770 CGACTACTCCATGGTACCACTA 58.451 50.000 19.09 4.52 0.00 2.74
3375 4253 3.949754 CGACTACTCCATGGTACCACTAA 59.050 47.826 19.09 4.15 0.00 2.24
3376 4254 4.201990 CGACTACTCCATGGTACCACTAAC 60.202 50.000 19.09 1.53 0.00 2.34
3377 4255 4.680407 ACTACTCCATGGTACCACTAACA 58.320 43.478 19.09 0.04 0.00 2.41
3378 4256 5.088730 ACTACTCCATGGTACCACTAACAA 58.911 41.667 19.09 0.99 0.00 2.83
3379 4257 4.553330 ACTCCATGGTACCACTAACAAG 57.447 45.455 19.09 11.32 0.00 3.16
3380 4258 3.908103 ACTCCATGGTACCACTAACAAGT 59.092 43.478 19.09 11.95 0.00 3.16
3381 4259 4.349930 ACTCCATGGTACCACTAACAAGTT 59.650 41.667 19.09 0.00 0.00 2.66
3382 4260 5.163131 ACTCCATGGTACCACTAACAAGTTT 60.163 40.000 19.09 0.00 0.00 2.66
3383 4261 5.697067 TCCATGGTACCACTAACAAGTTTT 58.303 37.500 19.09 0.00 0.00 2.43
3384 4262 6.130569 TCCATGGTACCACTAACAAGTTTTT 58.869 36.000 19.09 0.00 0.00 1.94
3425 4303 5.997385 GGTACCAGTAACAAGTTGAATGTG 58.003 41.667 10.54 1.79 0.00 3.21
3426 4304 5.529800 GGTACCAGTAACAAGTTGAATGTGT 59.470 40.000 10.54 2.33 0.00 3.72
3427 4305 5.499139 ACCAGTAACAAGTTGAATGTGTG 57.501 39.130 10.54 0.00 0.00 3.82
3428 4306 4.202010 ACCAGTAACAAGTTGAATGTGTGC 60.202 41.667 10.54 0.00 0.00 4.57
3429 4307 4.202000 CCAGTAACAAGTTGAATGTGTGCA 60.202 41.667 10.54 0.00 0.00 4.57
3430 4308 5.507817 CCAGTAACAAGTTGAATGTGTGCAT 60.508 40.000 10.54 0.00 36.80 3.96
3431 4309 5.978919 CAGTAACAAGTTGAATGTGTGCATT 59.021 36.000 10.54 0.00 46.99 3.56
3432 4310 6.476380 CAGTAACAAGTTGAATGTGTGCATTT 59.524 34.615 10.54 0.00 44.61 2.32
3433 4311 7.010367 CAGTAACAAGTTGAATGTGTGCATTTT 59.990 33.333 10.54 0.00 44.61 1.82
3434 4312 6.740411 AACAAGTTGAATGTGTGCATTTTT 57.260 29.167 10.54 0.00 44.61 1.94
3458 4336 8.519799 TTTTTCGGGAATCATAGAGCTTTATT 57.480 30.769 0.00 0.00 0.00 1.40
3459 4337 7.730364 TTTCGGGAATCATAGAGCTTTATTC 57.270 36.000 0.00 0.00 0.00 1.75
3460 4338 6.419484 TCGGGAATCATAGAGCTTTATTCA 57.581 37.500 0.00 0.00 0.00 2.57
3461 4339 6.826668 TCGGGAATCATAGAGCTTTATTCAA 58.173 36.000 0.00 0.00 0.00 2.69
3462 4340 7.453393 TCGGGAATCATAGAGCTTTATTCAAT 58.547 34.615 0.00 0.00 0.00 2.57
3463 4341 7.604164 TCGGGAATCATAGAGCTTTATTCAATC 59.396 37.037 0.00 0.00 0.00 2.67
3464 4342 7.388776 CGGGAATCATAGAGCTTTATTCAATCA 59.611 37.037 0.00 0.00 0.00 2.57
3465 4343 9.240734 GGGAATCATAGAGCTTTATTCAATCAT 57.759 33.333 0.00 0.00 0.00 2.45
3473 4351 8.977267 AGAGCTTTATTCAATCATTTCTAGCT 57.023 30.769 0.00 0.00 37.90 3.32
3474 4352 9.054922 AGAGCTTTATTCAATCATTTCTAGCTC 57.945 33.333 0.00 0.00 46.81 4.09
3475 4353 8.164058 AGCTTTATTCAATCATTTCTAGCTCC 57.836 34.615 0.00 0.00 29.98 4.70
3476 4354 7.776969 AGCTTTATTCAATCATTTCTAGCTCCA 59.223 33.333 0.00 0.00 29.98 3.86
3477 4355 8.074972 GCTTTATTCAATCATTTCTAGCTCCAG 58.925 37.037 0.00 0.00 0.00 3.86
3478 4356 7.502120 TTATTCAATCATTTCTAGCTCCAGC 57.498 36.000 0.00 0.00 42.49 4.85
3489 4367 4.519437 CTCCAGCGCGATCAGCCA 62.519 66.667 12.10 0.00 44.76 4.75
3490 4368 3.804153 CTCCAGCGCGATCAGCCAT 62.804 63.158 12.10 0.00 44.76 4.40
3491 4369 3.344215 CCAGCGCGATCAGCCATC 61.344 66.667 12.10 0.00 44.76 3.51
3492 4370 2.586914 CAGCGCGATCAGCCATCA 60.587 61.111 12.10 0.00 44.76 3.07
3493 4371 2.279985 AGCGCGATCAGCCATCAG 60.280 61.111 12.10 0.00 44.76 2.90
3494 4372 3.344215 GCGCGATCAGCCATCAGG 61.344 66.667 12.10 0.00 44.76 3.86
3504 4382 2.885113 CCATCAGGCTCGTCACGA 59.115 61.111 0.00 0.00 0.00 4.35
3516 4394 3.211803 TCGTCACGAGGAAACACATAG 57.788 47.619 0.00 0.00 0.00 2.23
3517 4395 2.094906 TCGTCACGAGGAAACACATAGG 60.095 50.000 0.00 0.00 0.00 2.57
3518 4396 2.352421 CGTCACGAGGAAACACATAGGT 60.352 50.000 0.00 0.00 0.00 3.08
3527 4405 4.919653 CACATAGGTGCGCTGAGT 57.080 55.556 9.73 0.00 38.37 3.41
3528 4406 3.143675 CACATAGGTGCGCTGAGTT 57.856 52.632 9.73 0.00 38.37 3.01
3529 4407 0.723414 CACATAGGTGCGCTGAGTTG 59.277 55.000 9.73 3.73 38.37 3.16
3530 4408 0.321671 ACATAGGTGCGCTGAGTTGT 59.678 50.000 9.73 4.43 0.00 3.32
3531 4409 1.270839 ACATAGGTGCGCTGAGTTGTT 60.271 47.619 9.73 0.00 0.00 2.83
3532 4410 1.129251 CATAGGTGCGCTGAGTTGTTG 59.871 52.381 9.73 0.00 0.00 3.33
3533 4411 0.602638 TAGGTGCGCTGAGTTGTTGG 60.603 55.000 9.73 0.00 0.00 3.77
3534 4412 2.050985 GTGCGCTGAGTTGTTGGC 60.051 61.111 9.73 0.00 0.00 4.52
3535 4413 2.203195 TGCGCTGAGTTGTTGGCT 60.203 55.556 9.73 0.00 0.00 4.75
3536 4414 1.823470 TGCGCTGAGTTGTTGGCTT 60.823 52.632 9.73 0.00 0.00 4.35
3537 4415 1.370900 GCGCTGAGTTGTTGGCTTG 60.371 57.895 0.00 0.00 0.00 4.01
3538 4416 2.024918 CGCTGAGTTGTTGGCTTGT 58.975 52.632 0.00 0.00 0.00 3.16
3539 4417 0.040958 CGCTGAGTTGTTGGCTTGTC 60.041 55.000 0.00 0.00 0.00 3.18
3540 4418 1.312815 GCTGAGTTGTTGGCTTGTCT 58.687 50.000 0.00 0.00 0.00 3.41
3541 4419 1.265365 GCTGAGTTGTTGGCTTGTCTC 59.735 52.381 0.00 0.00 0.00 3.36
3542 4420 2.564771 CTGAGTTGTTGGCTTGTCTCA 58.435 47.619 0.00 0.00 0.00 3.27
3543 4421 3.144506 CTGAGTTGTTGGCTTGTCTCAT 58.855 45.455 0.00 0.00 32.73 2.90
3544 4422 3.554934 TGAGTTGTTGGCTTGTCTCATT 58.445 40.909 0.00 0.00 0.00 2.57
3545 4423 4.713553 TGAGTTGTTGGCTTGTCTCATTA 58.286 39.130 0.00 0.00 0.00 1.90
3546 4424 4.515191 TGAGTTGTTGGCTTGTCTCATTAC 59.485 41.667 0.00 0.00 0.00 1.89
3547 4425 4.460263 AGTTGTTGGCTTGTCTCATTACA 58.540 39.130 0.00 0.00 0.00 2.41
3548 4426 5.072741 AGTTGTTGGCTTGTCTCATTACAT 58.927 37.500 0.00 0.00 0.00 2.29
3549 4427 6.237901 AGTTGTTGGCTTGTCTCATTACATA 58.762 36.000 0.00 0.00 0.00 2.29
3550 4428 6.886459 AGTTGTTGGCTTGTCTCATTACATAT 59.114 34.615 0.00 0.00 0.00 1.78
3551 4429 7.394359 AGTTGTTGGCTTGTCTCATTACATATT 59.606 33.333 0.00 0.00 0.00 1.28
3552 4430 7.087409 TGTTGGCTTGTCTCATTACATATTG 57.913 36.000 0.00 0.00 0.00 1.90
3553 4431 6.883756 TGTTGGCTTGTCTCATTACATATTGA 59.116 34.615 0.00 0.00 0.00 2.57
3554 4432 7.392953 TGTTGGCTTGTCTCATTACATATTGAA 59.607 33.333 0.00 0.00 0.00 2.69
3555 4433 7.320443 TGGCTTGTCTCATTACATATTGAAC 57.680 36.000 0.00 0.00 0.00 3.18
3556 4434 6.883756 TGGCTTGTCTCATTACATATTGAACA 59.116 34.615 0.00 0.00 0.00 3.18
3557 4435 7.392953 TGGCTTGTCTCATTACATATTGAACAA 59.607 33.333 0.00 0.00 0.00 2.83
3558 4436 7.698130 GGCTTGTCTCATTACATATTGAACAAC 59.302 37.037 0.00 0.00 0.00 3.32
3559 4437 8.236586 GCTTGTCTCATTACATATTGAACAACA 58.763 33.333 0.00 0.00 0.00 3.33
3576 4454 9.751542 TTGAACAACAAAACTAAGAAAAGTTGA 57.248 25.926 9.09 0.00 39.62 3.18
3577 4455 9.405587 TGAACAACAAAACTAAGAAAAGTTGAG 57.594 29.630 9.09 0.00 39.62 3.02
3578 4456 8.757164 AACAACAAAACTAAGAAAAGTTGAGG 57.243 30.769 9.09 0.00 39.62 3.86
3579 4457 6.811665 ACAACAAAACTAAGAAAAGTTGAGGC 59.188 34.615 9.09 0.00 39.62 4.70
3580 4458 6.775594 ACAAAACTAAGAAAAGTTGAGGCT 57.224 33.333 0.00 0.00 39.62 4.58
3581 4459 7.875327 ACAAAACTAAGAAAAGTTGAGGCTA 57.125 32.000 0.00 0.00 39.62 3.93
3582 4460 7.931275 ACAAAACTAAGAAAAGTTGAGGCTAG 58.069 34.615 0.00 0.00 39.62 3.42
3583 4461 6.561737 AAACTAAGAAAAGTTGAGGCTAGC 57.438 37.500 6.04 6.04 39.62 3.42
3584 4462 4.580868 ACTAAGAAAAGTTGAGGCTAGCC 58.419 43.478 27.19 27.19 0.00 3.93
3585 4463 2.498644 AGAAAAGTTGAGGCTAGCCC 57.501 50.000 30.42 21.06 36.58 5.19
3586 4464 8.168163 AACTAAGAAAAGTTGAGGCTAGCCCT 62.168 42.308 30.42 17.04 38.31 5.19
3587 4465 2.376855 AGAAAAGTTGAGGCTAGCCCTT 59.623 45.455 30.42 21.83 46.60 3.95
3588 4466 2.498644 AAAGTTGAGGCTAGCCCTTC 57.501 50.000 30.42 21.84 46.60 3.46
3589 4467 1.362224 AAGTTGAGGCTAGCCCTTCA 58.638 50.000 30.42 24.21 46.60 3.02
3590 4468 1.362224 AGTTGAGGCTAGCCCTTCAA 58.638 50.000 30.42 28.13 46.60 2.69
3591 4469 1.918957 AGTTGAGGCTAGCCCTTCAAT 59.081 47.619 30.43 20.35 46.60 2.57
3592 4470 2.310052 AGTTGAGGCTAGCCCTTCAATT 59.690 45.455 30.43 25.83 46.60 2.32
3593 4471 3.092301 GTTGAGGCTAGCCCTTCAATTT 58.908 45.455 30.43 13.53 46.60 1.82
3594 4472 3.004752 TGAGGCTAGCCCTTCAATTTC 57.995 47.619 30.42 18.17 46.60 2.17
3595 4473 1.943340 GAGGCTAGCCCTTCAATTTCG 59.057 52.381 30.42 0.00 46.60 3.46
3596 4474 1.559682 AGGCTAGCCCTTCAATTTCGA 59.440 47.619 30.42 0.00 43.06 3.71
3597 4475 1.943340 GGCTAGCCCTTCAATTTCGAG 59.057 52.381 24.19 0.00 0.00 4.04
3598 4476 2.420129 GGCTAGCCCTTCAATTTCGAGA 60.420 50.000 24.19 0.00 0.00 4.04
3599 4477 3.270877 GCTAGCCCTTCAATTTCGAGAA 58.729 45.455 2.29 0.00 0.00 2.87
3600 4478 3.311048 GCTAGCCCTTCAATTTCGAGAAG 59.689 47.826 2.29 5.41 40.64 2.85
3601 4479 3.703001 AGCCCTTCAATTTCGAGAAGA 57.297 42.857 12.36 0.00 42.95 2.87
3602 4480 4.021102 AGCCCTTCAATTTCGAGAAGAA 57.979 40.909 12.36 4.39 42.95 2.52
3603 4481 4.593956 AGCCCTTCAATTTCGAGAAGAAT 58.406 39.130 12.36 0.00 42.95 2.40
3604 4482 4.397417 AGCCCTTCAATTTCGAGAAGAATG 59.603 41.667 12.36 2.90 42.95 2.67
3605 4483 4.439289 GCCCTTCAATTTCGAGAAGAATGG 60.439 45.833 12.36 10.88 42.95 3.16
3606 4484 4.096984 CCCTTCAATTTCGAGAAGAATGGG 59.903 45.833 12.36 11.57 42.95 4.00
3607 4485 4.439289 CCTTCAATTTCGAGAAGAATGGGC 60.439 45.833 12.36 0.00 42.95 5.36
3608 4486 2.677836 TCAATTTCGAGAAGAATGGGCG 59.322 45.455 0.00 0.00 38.86 6.13
3609 4487 1.017387 ATTTCGAGAAGAATGGGCGC 58.983 50.000 0.00 0.00 38.86 6.53
3610 4488 0.036388 TTTCGAGAAGAATGGGCGCT 60.036 50.000 7.64 0.00 38.86 5.92
3611 4489 0.821517 TTCGAGAAGAATGGGCGCTA 59.178 50.000 7.64 0.00 33.14 4.26
3612 4490 1.040646 TCGAGAAGAATGGGCGCTAT 58.959 50.000 7.64 0.00 0.00 2.97
3613 4491 2.235891 TCGAGAAGAATGGGCGCTATA 58.764 47.619 7.64 0.00 0.00 1.31
3614 4492 2.626266 TCGAGAAGAATGGGCGCTATAA 59.374 45.455 7.64 0.00 0.00 0.98
3615 4493 2.731976 CGAGAAGAATGGGCGCTATAAC 59.268 50.000 7.64 0.00 0.00 1.89
3616 4494 3.728845 GAGAAGAATGGGCGCTATAACA 58.271 45.455 7.64 0.00 0.00 2.41
3617 4495 3.733337 AGAAGAATGGGCGCTATAACAG 58.267 45.455 7.64 0.00 0.00 3.16
3618 4496 3.388024 AGAAGAATGGGCGCTATAACAGA 59.612 43.478 7.64 0.00 0.00 3.41
3619 4497 3.393089 AGAATGGGCGCTATAACAGAG 57.607 47.619 7.64 0.00 0.00 3.35
3628 4506 3.861569 GCTATAACAGAGCGCGAAAAT 57.138 42.857 12.10 0.00 0.00 1.82
3629 4507 4.197107 GCTATAACAGAGCGCGAAAATT 57.803 40.909 12.10 0.00 0.00 1.82
3630 4508 3.962481 GCTATAACAGAGCGCGAAAATTG 59.038 43.478 12.10 2.32 0.00 2.32
3631 4509 4.494199 GCTATAACAGAGCGCGAAAATTGT 60.494 41.667 12.10 3.05 0.00 2.71
3632 4510 2.316119 AACAGAGCGCGAAAATTGTC 57.684 45.000 12.10 0.00 0.00 3.18
3633 4511 1.225855 ACAGAGCGCGAAAATTGTCA 58.774 45.000 12.10 0.00 0.00 3.58
3634 4512 1.069906 ACAGAGCGCGAAAATTGTCAC 60.070 47.619 12.10 0.00 0.00 3.67
3635 4513 0.163788 AGAGCGCGAAAATTGTCACG 59.836 50.000 12.10 1.57 0.00 4.35
3636 4514 0.162933 GAGCGCGAAAATTGTCACGA 59.837 50.000 12.10 0.00 0.00 4.35
3637 4515 0.163788 AGCGCGAAAATTGTCACGAG 59.836 50.000 12.10 2.42 0.00 4.18
3638 4516 0.110823 GCGCGAAAATTGTCACGAGT 60.111 50.000 12.10 0.00 0.00 4.18
3639 4517 1.659211 GCGCGAAAATTGTCACGAGTT 60.659 47.619 12.10 0.00 0.00 3.01
3640 4518 2.222624 CGCGAAAATTGTCACGAGTTC 58.777 47.619 0.00 0.00 0.00 3.01
3641 4519 2.571206 GCGAAAATTGTCACGAGTTCC 58.429 47.619 0.00 0.00 0.00 3.62
3642 4520 2.032377 GCGAAAATTGTCACGAGTTCCA 60.032 45.455 0.00 0.00 0.00 3.53
3643 4521 3.799035 CGAAAATTGTCACGAGTTCCAG 58.201 45.455 0.00 0.00 0.00 3.86
3644 4522 3.493129 CGAAAATTGTCACGAGTTCCAGA 59.507 43.478 0.00 0.00 0.00 3.86
3645 4523 4.376413 CGAAAATTGTCACGAGTTCCAGAG 60.376 45.833 0.00 0.00 0.00 3.35
3646 4524 3.753294 AATTGTCACGAGTTCCAGAGT 57.247 42.857 0.00 0.00 0.00 3.24
3647 4525 3.753294 ATTGTCACGAGTTCCAGAGTT 57.247 42.857 0.00 0.00 0.00 3.01
3648 4526 2.509052 TGTCACGAGTTCCAGAGTTG 57.491 50.000 0.00 0.00 0.00 3.16
3649 4527 1.754803 TGTCACGAGTTCCAGAGTTGT 59.245 47.619 0.00 0.00 0.00 3.32
3650 4528 2.953648 TGTCACGAGTTCCAGAGTTGTA 59.046 45.455 0.00 0.00 0.00 2.41
3651 4529 3.243301 TGTCACGAGTTCCAGAGTTGTAC 60.243 47.826 0.00 0.00 0.00 2.90
3652 4530 2.295349 TCACGAGTTCCAGAGTTGTACC 59.705 50.000 0.00 0.00 0.00 3.34
3653 4531 2.035449 CACGAGTTCCAGAGTTGTACCA 59.965 50.000 0.00 0.00 0.00 3.25
3654 4532 2.696707 ACGAGTTCCAGAGTTGTACCAA 59.303 45.455 0.00 0.00 0.00 3.67
3655 4533 3.057734 CGAGTTCCAGAGTTGTACCAAC 58.942 50.000 0.00 0.00 0.00 3.77
3656 4534 3.243771 CGAGTTCCAGAGTTGTACCAACT 60.244 47.826 9.24 9.24 0.00 3.16
3657 4535 4.308265 GAGTTCCAGAGTTGTACCAACTC 58.692 47.826 23.13 23.13 45.21 3.01
3658 4536 3.071167 AGTTCCAGAGTTGTACCAACTCC 59.929 47.826 25.57 14.45 45.82 3.85
3659 4537 2.684943 TCCAGAGTTGTACCAACTCCA 58.315 47.619 25.57 12.72 45.82 3.86
3660 4538 3.042682 TCCAGAGTTGTACCAACTCCAA 58.957 45.455 25.57 13.55 45.82 3.53
3661 4539 3.071023 TCCAGAGTTGTACCAACTCCAAG 59.929 47.826 25.57 18.09 45.82 3.61
3662 4540 2.808543 CAGAGTTGTACCAACTCCAAGC 59.191 50.000 25.57 8.49 45.82 4.01
3663 4541 2.438021 AGAGTTGTACCAACTCCAAGCA 59.562 45.455 25.57 0.00 45.82 3.91
3664 4542 3.118038 AGAGTTGTACCAACTCCAAGCAA 60.118 43.478 25.57 0.00 45.82 3.91
3665 4543 3.821033 GAGTTGTACCAACTCCAAGCAAT 59.179 43.478 21.04 0.00 40.46 3.56
3666 4544 3.821033 AGTTGTACCAACTCCAAGCAATC 59.179 43.478 3.85 0.00 0.00 2.67
3667 4545 3.788227 TGTACCAACTCCAAGCAATCT 57.212 42.857 0.00 0.00 0.00 2.40
3668 4546 4.901197 TGTACCAACTCCAAGCAATCTA 57.099 40.909 0.00 0.00 0.00 1.98
3669 4547 4.575885 TGTACCAACTCCAAGCAATCTAC 58.424 43.478 0.00 0.00 0.00 2.59
3670 4548 4.286032 TGTACCAACTCCAAGCAATCTACT 59.714 41.667 0.00 0.00 0.00 2.57
3671 4549 4.373156 ACCAACTCCAAGCAATCTACTT 57.627 40.909 0.00 0.00 0.00 2.24
3672 4550 4.327680 ACCAACTCCAAGCAATCTACTTC 58.672 43.478 0.00 0.00 0.00 3.01
3673 4551 4.202461 ACCAACTCCAAGCAATCTACTTCA 60.202 41.667 0.00 0.00 0.00 3.02
3674 4552 4.761739 CCAACTCCAAGCAATCTACTTCAA 59.238 41.667 0.00 0.00 0.00 2.69
3675 4553 5.241506 CCAACTCCAAGCAATCTACTTCAAA 59.758 40.000 0.00 0.00 0.00 2.69
3676 4554 5.948992 ACTCCAAGCAATCTACTTCAAAC 57.051 39.130 0.00 0.00 0.00 2.93
3677 4555 5.376625 ACTCCAAGCAATCTACTTCAAACA 58.623 37.500 0.00 0.00 0.00 2.83
3678 4556 5.239525 ACTCCAAGCAATCTACTTCAAACAC 59.760 40.000 0.00 0.00 0.00 3.32
3679 4557 4.518970 TCCAAGCAATCTACTTCAAACACC 59.481 41.667 0.00 0.00 0.00 4.16
3680 4558 4.278170 CCAAGCAATCTACTTCAAACACCA 59.722 41.667 0.00 0.00 0.00 4.17
3681 4559 5.215160 CAAGCAATCTACTTCAAACACCAC 58.785 41.667 0.00 0.00 0.00 4.16
3682 4560 4.718961 AGCAATCTACTTCAAACACCACT 58.281 39.130 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.091552 TCCTGACCACAATTAAGTAGGAGT 58.908 41.667 1.14 0.00 0.00 3.85
305 344 9.153721 CGTAATCCAACTAGAGTAGTATAGGAG 57.846 40.741 0.00 0.00 38.26 3.69
306 345 8.099537 CCGTAATCCAACTAGAGTAGTATAGGA 58.900 40.741 0.00 5.72 38.26 2.94
307 346 8.099537 TCCGTAATCCAACTAGAGTAGTATAGG 58.900 40.741 0.00 0.00 38.26 2.57
308 347 9.153721 CTCCGTAATCCAACTAGAGTAGTATAG 57.846 40.741 0.00 0.00 38.26 1.31
309 348 8.099537 CCTCCGTAATCCAACTAGAGTAGTATA 58.900 40.741 0.00 0.00 38.26 1.47
310 349 6.941436 CCTCCGTAATCCAACTAGAGTAGTAT 59.059 42.308 0.00 0.00 38.26 2.12
311 350 6.100279 TCCTCCGTAATCCAACTAGAGTAGTA 59.900 42.308 0.00 0.00 38.26 1.82
312 351 5.104193 TCCTCCGTAATCCAACTAGAGTAGT 60.104 44.000 0.00 0.00 41.73 2.73
551 597 2.147436 AGAAAGCGATGCTAGCTAGC 57.853 50.000 34.20 34.20 45.31 3.42
552 598 3.868077 ACAAAGAAAGCGATGCTAGCTAG 59.132 43.478 16.84 16.84 45.31 3.42
553 599 3.861840 ACAAAGAAAGCGATGCTAGCTA 58.138 40.909 17.23 2.58 45.31 3.32
673 727 8.710835 TTGGCTTTTTCTTTTTACGATTCTTT 57.289 26.923 0.00 0.00 0.00 2.52
700 754 8.977267 TGATGATTGATGACCAATGTTGTATA 57.023 30.769 0.00 0.00 45.00 1.47
701 755 7.776500 TCTGATGATTGATGACCAATGTTGTAT 59.224 33.333 0.00 0.00 45.00 2.29
784 842 0.036010 CTCCAGCCAACGGATCAACT 60.036 55.000 0.00 0.00 0.00 3.16
793 851 2.594592 ACCAACGCTCCAGCCAAC 60.595 61.111 0.00 0.00 37.91 3.77
794 852 2.281484 GACCAACGCTCCAGCCAA 60.281 61.111 0.00 0.00 37.91 4.52
795 853 4.329545 GGACCAACGCTCCAGCCA 62.330 66.667 0.00 0.00 37.91 4.75
796 854 3.628646 ATGGACCAACGCTCCAGCC 62.629 63.158 0.00 0.00 41.24 4.85
865 932 0.179032 ATAATGGCGCGGTGATTGGA 60.179 50.000 8.83 0.00 0.00 3.53
873 940 1.737793 GGGAATAGAATAATGGCGCGG 59.262 52.381 8.83 0.00 0.00 6.46
912 979 1.140312 GTTCATATGGGGGAGCAGGA 58.860 55.000 2.13 0.00 0.00 3.86
969 1370 3.969802 GGGCTGTGTGTGTGCTGC 61.970 66.667 0.00 0.00 0.00 5.25
1030 1431 2.364448 GAGGAGGAGGGGCGTCTT 60.364 66.667 0.00 0.00 0.00 3.01
1031 1432 2.864770 GAAGAGGAGGAGGGGCGTCT 62.865 65.000 0.00 0.00 0.00 4.18
1032 1433 2.364448 AAGAGGAGGAGGGGCGTC 60.364 66.667 0.00 0.00 0.00 5.19
1033 1434 2.364448 GAAGAGGAGGAGGGGCGT 60.364 66.667 0.00 0.00 0.00 5.68
1034 1435 3.157949 GGAAGAGGAGGAGGGGCG 61.158 72.222 0.00 0.00 0.00 6.13
1035 1436 1.764454 GAGGAAGAGGAGGAGGGGC 60.764 68.421 0.00 0.00 0.00 5.80
1036 1437 1.456705 CGAGGAAGAGGAGGAGGGG 60.457 68.421 0.00 0.00 0.00 4.79
1037 1438 2.131067 GCGAGGAAGAGGAGGAGGG 61.131 68.421 0.00 0.00 0.00 4.30
1320 2087 1.153978 GGCGACGACGGTGATGTAA 60.154 57.895 9.67 0.00 40.15 2.41
1401 2174 1.241990 CGTGGAAGACGGAGAGGTCA 61.242 60.000 0.00 0.00 44.85 4.02
2617 3480 3.554692 CGGCATCTTCCACGTCGC 61.555 66.667 0.00 0.00 0.00 5.19
2708 3571 9.645059 AAACTCGTATATGATCAGAATGTATGG 57.355 33.333 0.09 0.00 37.40 2.74
2800 3666 8.675705 AAAAACAAGAACAAATTAATGGGAGG 57.324 30.769 0.00 0.00 0.00 4.30
2843 3712 9.877137 CATTATCGAATCGATCTTCTATAGGAG 57.123 37.037 22.15 1.00 43.45 3.69
2844 3713 9.614792 TCATTATCGAATCGATCTTCTATAGGA 57.385 33.333 22.15 5.47 43.45 2.94
2845 3714 9.877137 CTCATTATCGAATCGATCTTCTATAGG 57.123 37.037 22.15 3.34 43.45 2.57
2857 3726 8.065557 TGATGAAACTTCTCATTATCGAATCG 57.934 34.615 0.00 0.00 36.15 3.34
3082 3951 1.052768 GCAACGCGTCACAAATCGAC 61.053 55.000 14.44 0.00 0.00 4.20
3140 4009 2.355599 CATCCAGCTAGCGCTCCG 60.356 66.667 16.34 7.90 45.15 4.63
3171 4040 2.684843 GCTTGACCTTGAGCTGGCG 61.685 63.158 0.00 0.00 36.01 5.69
3237 4114 4.282703 GCATCCATTTTGAGGAGCCATATT 59.717 41.667 0.00 0.00 38.83 1.28
3238 4115 3.830755 GCATCCATTTTGAGGAGCCATAT 59.169 43.478 0.00 0.00 38.83 1.78
3281 4159 2.299297 AGACGTGGGTAAAGTCAAGAGG 59.701 50.000 0.00 0.00 37.36 3.69
3352 4230 1.108776 TGGTACCATGGAGTAGTCGC 58.891 55.000 21.47 0.00 0.00 5.19
3391 4269 0.845337 ACTGGTACCCCCGTCAAAAA 59.155 50.000 10.07 0.00 35.15 1.94
3392 4270 1.727062 TACTGGTACCCCCGTCAAAA 58.273 50.000 10.07 0.00 35.15 2.44
3393 4271 1.347378 GTTACTGGTACCCCCGTCAAA 59.653 52.381 10.07 0.00 35.15 2.69
3394 4272 0.975887 GTTACTGGTACCCCCGTCAA 59.024 55.000 10.07 0.00 35.15 3.18
3395 4273 0.178938 TGTTACTGGTACCCCCGTCA 60.179 55.000 10.07 0.73 35.15 4.35
3396 4274 0.975887 TTGTTACTGGTACCCCCGTC 59.024 55.000 10.07 0.00 35.15 4.79
3397 4275 0.978907 CTTGTTACTGGTACCCCCGT 59.021 55.000 10.07 6.64 35.15 5.28
3398 4276 0.978907 ACTTGTTACTGGTACCCCCG 59.021 55.000 10.07 0.04 35.15 5.73
3399 4277 2.372837 TCAACTTGTTACTGGTACCCCC 59.627 50.000 10.07 0.00 0.00 5.40
3400 4278 3.775261 TCAACTTGTTACTGGTACCCC 57.225 47.619 10.07 0.00 0.00 4.95
3401 4279 5.048991 CACATTCAACTTGTTACTGGTACCC 60.049 44.000 10.07 0.00 0.00 3.69
3402 4280 5.529800 ACACATTCAACTTGTTACTGGTACC 59.470 40.000 4.43 4.43 0.00 3.34
3403 4281 6.427150 CACACATTCAACTTGTTACTGGTAC 58.573 40.000 0.00 0.00 0.00 3.34
3404 4282 5.008217 GCACACATTCAACTTGTTACTGGTA 59.992 40.000 0.00 0.00 0.00 3.25
3405 4283 4.202010 GCACACATTCAACTTGTTACTGGT 60.202 41.667 0.00 0.00 0.00 4.00
3406 4284 4.202000 TGCACACATTCAACTTGTTACTGG 60.202 41.667 0.00 0.00 0.00 4.00
3407 4285 4.919206 TGCACACATTCAACTTGTTACTG 58.081 39.130 0.00 0.00 0.00 2.74
3408 4286 5.772825 ATGCACACATTCAACTTGTTACT 57.227 34.783 0.00 0.00 30.07 2.24
3409 4287 6.826893 AAATGCACACATTCAACTTGTTAC 57.173 33.333 0.00 0.00 45.90 2.50
3410 4288 7.840342 AAAAATGCACACATTCAACTTGTTA 57.160 28.000 0.00 0.00 45.90 2.41
3411 4289 6.740411 AAAAATGCACACATTCAACTTGTT 57.260 29.167 0.00 0.00 45.90 2.83
3433 4311 8.519799 AATAAAGCTCTATGATTCCCGAAAAA 57.480 30.769 0.00 0.00 0.00 1.94
3434 4312 7.773224 TGAATAAAGCTCTATGATTCCCGAAAA 59.227 33.333 0.00 0.00 0.00 2.29
3435 4313 7.279615 TGAATAAAGCTCTATGATTCCCGAAA 58.720 34.615 0.00 0.00 0.00 3.46
3436 4314 6.826668 TGAATAAAGCTCTATGATTCCCGAA 58.173 36.000 0.00 0.00 0.00 4.30
3437 4315 6.419484 TGAATAAAGCTCTATGATTCCCGA 57.581 37.500 0.00 0.00 0.00 5.14
3438 4316 7.388776 TGATTGAATAAAGCTCTATGATTCCCG 59.611 37.037 0.00 0.00 0.00 5.14
3439 4317 8.627208 TGATTGAATAAAGCTCTATGATTCCC 57.373 34.615 0.00 0.00 0.00 3.97
3448 4326 8.977267 AGCTAGAAATGATTGAATAAAGCTCT 57.023 30.769 0.00 0.00 31.24 4.09
3450 4328 7.776969 TGGAGCTAGAAATGATTGAATAAAGCT 59.223 33.333 0.00 0.00 39.16 3.74
3451 4329 7.934457 TGGAGCTAGAAATGATTGAATAAAGC 58.066 34.615 0.00 0.00 0.00 3.51
3452 4330 8.074972 GCTGGAGCTAGAAATGATTGAATAAAG 58.925 37.037 0.00 0.00 38.21 1.85
3453 4331 7.254898 CGCTGGAGCTAGAAATGATTGAATAAA 60.255 37.037 0.00 0.00 39.32 1.40
3454 4332 6.203530 CGCTGGAGCTAGAAATGATTGAATAA 59.796 38.462 0.00 0.00 39.32 1.40
3455 4333 5.698089 CGCTGGAGCTAGAAATGATTGAATA 59.302 40.000 0.00 0.00 39.32 1.75
3456 4334 4.514441 CGCTGGAGCTAGAAATGATTGAAT 59.486 41.667 0.00 0.00 39.32 2.57
3457 4335 3.873361 CGCTGGAGCTAGAAATGATTGAA 59.127 43.478 0.00 0.00 39.32 2.69
3458 4336 3.461061 CGCTGGAGCTAGAAATGATTGA 58.539 45.455 0.00 0.00 39.32 2.57
3459 4337 2.032204 GCGCTGGAGCTAGAAATGATTG 60.032 50.000 0.00 0.00 39.32 2.67
3460 4338 2.216898 GCGCTGGAGCTAGAAATGATT 58.783 47.619 0.00 0.00 39.32 2.57
3461 4339 1.871408 CGCGCTGGAGCTAGAAATGAT 60.871 52.381 5.56 0.00 39.32 2.45
3462 4340 0.528466 CGCGCTGGAGCTAGAAATGA 60.528 55.000 5.56 0.00 39.32 2.57
3463 4341 0.528466 TCGCGCTGGAGCTAGAAATG 60.528 55.000 5.56 0.00 39.32 2.32
3464 4342 0.390860 ATCGCGCTGGAGCTAGAAAT 59.609 50.000 5.56 0.00 39.32 2.17
3465 4343 0.249073 GATCGCGCTGGAGCTAGAAA 60.249 55.000 5.56 0.00 39.32 2.52
3466 4344 1.360551 GATCGCGCTGGAGCTAGAA 59.639 57.895 5.56 0.00 39.32 2.10
3467 4345 1.790090 CTGATCGCGCTGGAGCTAGA 61.790 60.000 5.56 0.00 39.32 2.43
3468 4346 1.371512 CTGATCGCGCTGGAGCTAG 60.372 63.158 5.56 0.00 39.32 3.42
3469 4347 2.724377 CTGATCGCGCTGGAGCTA 59.276 61.111 5.56 0.00 39.32 3.32
3470 4348 4.887987 GCTGATCGCGCTGGAGCT 62.888 66.667 5.56 0.00 39.32 4.09
3472 4350 3.804153 ATGGCTGATCGCGCTGGAG 62.804 63.158 5.56 0.00 40.44 3.86
3473 4351 3.797225 GATGGCTGATCGCGCTGGA 62.797 63.158 5.56 0.00 40.44 3.86
3474 4352 3.344215 GATGGCTGATCGCGCTGG 61.344 66.667 5.56 0.00 40.44 4.85
3475 4353 2.586914 TGATGGCTGATCGCGCTG 60.587 61.111 5.56 0.00 40.44 5.18
3476 4354 2.279985 CTGATGGCTGATCGCGCT 60.280 61.111 5.56 0.00 40.44 5.92
3477 4355 3.344215 CCTGATGGCTGATCGCGC 61.344 66.667 0.00 0.00 40.44 6.86
3487 4365 1.226802 CTCGTGACGAGCCTGATGG 60.227 63.158 22.72 0.00 46.75 3.51
3488 4366 4.391539 CTCGTGACGAGCCTGATG 57.608 61.111 22.72 0.00 46.75 3.07
3496 4374 2.094906 CCTATGTGTTTCCTCGTGACGA 60.095 50.000 7.70 7.70 0.00 4.20
3497 4375 2.259618 CCTATGTGTTTCCTCGTGACG 58.740 52.381 0.00 0.00 0.00 4.35
3498 4376 2.993899 CACCTATGTGTTTCCTCGTGAC 59.006 50.000 0.00 0.00 37.72 3.67
3499 4377 2.611971 GCACCTATGTGTTTCCTCGTGA 60.612 50.000 0.00 0.00 44.65 4.35
3500 4378 1.732259 GCACCTATGTGTTTCCTCGTG 59.268 52.381 0.00 0.00 44.65 4.35
3501 4379 1.671850 CGCACCTATGTGTTTCCTCGT 60.672 52.381 0.00 0.00 44.65 4.18
3502 4380 0.999406 CGCACCTATGTGTTTCCTCG 59.001 55.000 0.00 0.00 44.65 4.63
3503 4381 0.727398 GCGCACCTATGTGTTTCCTC 59.273 55.000 0.30 0.00 44.65 3.71
3504 4382 0.324943 AGCGCACCTATGTGTTTCCT 59.675 50.000 11.47 0.00 44.65 3.36
3505 4383 0.447801 CAGCGCACCTATGTGTTTCC 59.552 55.000 11.47 0.00 44.65 3.13
3506 4384 1.394917 CTCAGCGCACCTATGTGTTTC 59.605 52.381 11.47 0.00 44.65 2.78
3507 4385 1.270839 ACTCAGCGCACCTATGTGTTT 60.271 47.619 11.47 0.00 44.65 2.83
3508 4386 0.321671 ACTCAGCGCACCTATGTGTT 59.678 50.000 11.47 0.00 44.65 3.32
3509 4387 0.321671 AACTCAGCGCACCTATGTGT 59.678 50.000 11.47 2.46 44.65 3.72
3510 4388 0.723414 CAACTCAGCGCACCTATGTG 59.277 55.000 11.47 1.73 45.65 3.21
3511 4389 0.321671 ACAACTCAGCGCACCTATGT 59.678 50.000 11.47 6.23 0.00 2.29
3512 4390 1.129251 CAACAACTCAGCGCACCTATG 59.871 52.381 11.47 5.50 0.00 2.23
3513 4391 1.442769 CAACAACTCAGCGCACCTAT 58.557 50.000 11.47 0.00 0.00 2.57
3514 4392 0.602638 CCAACAACTCAGCGCACCTA 60.603 55.000 11.47 0.00 0.00 3.08
3515 4393 1.893808 CCAACAACTCAGCGCACCT 60.894 57.895 11.47 0.00 0.00 4.00
3516 4394 2.639286 CCAACAACTCAGCGCACC 59.361 61.111 11.47 0.00 0.00 5.01
3517 4395 2.050985 GCCAACAACTCAGCGCAC 60.051 61.111 11.47 0.00 0.00 5.34
3518 4396 1.823470 AAGCCAACAACTCAGCGCA 60.823 52.632 11.47 0.00 0.00 6.09
3519 4397 1.370900 CAAGCCAACAACTCAGCGC 60.371 57.895 0.00 0.00 0.00 5.92
3520 4398 0.040958 GACAAGCCAACAACTCAGCG 60.041 55.000 0.00 0.00 0.00 5.18
3521 4399 1.265365 GAGACAAGCCAACAACTCAGC 59.735 52.381 0.00 0.00 0.00 4.26
3522 4400 2.564771 TGAGACAAGCCAACAACTCAG 58.435 47.619 0.00 0.00 32.04 3.35
3523 4401 2.708216 TGAGACAAGCCAACAACTCA 57.292 45.000 0.00 0.00 33.06 3.41
3524 4402 4.515191 TGTAATGAGACAAGCCAACAACTC 59.485 41.667 0.00 0.00 0.00 3.01
3525 4403 4.460263 TGTAATGAGACAAGCCAACAACT 58.540 39.130 0.00 0.00 0.00 3.16
3526 4404 4.829064 TGTAATGAGACAAGCCAACAAC 57.171 40.909 0.00 0.00 0.00 3.32
3527 4405 7.392953 TCAATATGTAATGAGACAAGCCAACAA 59.607 33.333 0.00 0.00 31.83 2.83
3528 4406 6.883756 TCAATATGTAATGAGACAAGCCAACA 59.116 34.615 0.00 0.00 31.83 3.33
3529 4407 7.320443 TCAATATGTAATGAGACAAGCCAAC 57.680 36.000 0.00 0.00 31.83 3.77
3530 4408 7.392953 TGTTCAATATGTAATGAGACAAGCCAA 59.607 33.333 0.00 0.00 31.83 4.52
3531 4409 6.883756 TGTTCAATATGTAATGAGACAAGCCA 59.116 34.615 0.00 0.00 31.83 4.75
3532 4410 7.320443 TGTTCAATATGTAATGAGACAAGCC 57.680 36.000 0.00 0.00 31.83 4.35
3533 4411 8.236586 TGTTGTTCAATATGTAATGAGACAAGC 58.763 33.333 0.00 0.00 32.54 4.01
3550 4428 9.751542 TCAACTTTTCTTAGTTTTGTTGTTCAA 57.248 25.926 0.00 0.00 36.24 2.69
3551 4429 9.405587 CTCAACTTTTCTTAGTTTTGTTGTTCA 57.594 29.630 0.00 0.00 36.24 3.18
3552 4430 8.860128 CCTCAACTTTTCTTAGTTTTGTTGTTC 58.140 33.333 0.00 0.00 36.24 3.18
3553 4431 7.330946 GCCTCAACTTTTCTTAGTTTTGTTGTT 59.669 33.333 0.00 0.00 36.24 2.83
3554 4432 6.811665 GCCTCAACTTTTCTTAGTTTTGTTGT 59.188 34.615 0.00 0.00 36.24 3.32
3555 4433 7.035612 AGCCTCAACTTTTCTTAGTTTTGTTG 58.964 34.615 0.00 0.00 36.24 3.33
3556 4434 7.170393 AGCCTCAACTTTTCTTAGTTTTGTT 57.830 32.000 0.00 0.00 36.24 2.83
3557 4435 6.775594 AGCCTCAACTTTTCTTAGTTTTGT 57.224 33.333 0.00 0.00 36.24 2.83
3558 4436 6.858478 GCTAGCCTCAACTTTTCTTAGTTTTG 59.142 38.462 2.29 0.00 36.24 2.44
3559 4437 6.016192 GGCTAGCCTCAACTTTTCTTAGTTTT 60.016 38.462 27.17 0.00 36.24 2.43
3560 4438 5.473846 GGCTAGCCTCAACTTTTCTTAGTTT 59.526 40.000 27.17 0.00 36.24 2.66
3561 4439 5.004448 GGCTAGCCTCAACTTTTCTTAGTT 58.996 41.667 27.17 0.00 38.87 2.24
3562 4440 4.565861 GGGCTAGCCTCAACTTTTCTTAGT 60.566 45.833 32.18 0.00 36.10 2.24
3563 4441 3.942115 GGGCTAGCCTCAACTTTTCTTAG 59.058 47.826 32.18 0.00 36.10 2.18
3564 4442 3.587506 AGGGCTAGCCTCAACTTTTCTTA 59.412 43.478 32.18 0.00 36.10 2.10
3565 4443 2.376855 AGGGCTAGCCTCAACTTTTCTT 59.623 45.455 32.18 1.81 36.10 2.52
3566 4444 1.988846 AGGGCTAGCCTCAACTTTTCT 59.011 47.619 32.18 15.03 36.10 2.52
3567 4445 2.498644 AGGGCTAGCCTCAACTTTTC 57.501 50.000 32.18 12.91 36.10 2.29
3568 4446 2.108250 TGAAGGGCTAGCCTCAACTTTT 59.892 45.455 32.18 14.94 36.10 2.27
3569 4447 1.705186 TGAAGGGCTAGCCTCAACTTT 59.295 47.619 32.18 16.54 36.10 2.66
3570 4448 1.362224 TGAAGGGCTAGCCTCAACTT 58.638 50.000 32.18 25.18 36.10 2.66
3571 4449 1.362224 TTGAAGGGCTAGCCTCAACT 58.638 50.000 32.18 18.38 36.10 3.16
3572 4450 2.426842 ATTGAAGGGCTAGCCTCAAC 57.573 50.000 30.43 20.95 34.52 3.18
3573 4451 3.356290 GAAATTGAAGGGCTAGCCTCAA 58.644 45.455 30.12 30.12 35.62 3.02
3574 4452 2.680805 CGAAATTGAAGGGCTAGCCTCA 60.681 50.000 32.18 25.24 36.10 3.86
3575 4453 1.943340 CGAAATTGAAGGGCTAGCCTC 59.057 52.381 32.18 22.95 36.10 4.70
3576 4454 1.559682 TCGAAATTGAAGGGCTAGCCT 59.440 47.619 32.18 14.96 36.10 4.58
3577 4455 1.943340 CTCGAAATTGAAGGGCTAGCC 59.057 52.381 26.55 26.55 0.00 3.93
3578 4456 2.906354 TCTCGAAATTGAAGGGCTAGC 58.094 47.619 6.04 6.04 0.00 3.42
3579 4457 4.759782 TCTTCTCGAAATTGAAGGGCTAG 58.240 43.478 11.05 0.00 39.85 3.42
3580 4458 4.819105 TCTTCTCGAAATTGAAGGGCTA 57.181 40.909 11.05 0.00 39.85 3.93
3581 4459 3.703001 TCTTCTCGAAATTGAAGGGCT 57.297 42.857 11.05 0.00 39.85 5.19
3582 4460 4.439289 CCATTCTTCTCGAAATTGAAGGGC 60.439 45.833 11.05 0.00 39.85 5.19
3583 4461 4.096984 CCCATTCTTCTCGAAATTGAAGGG 59.903 45.833 11.05 11.22 39.85 3.95
3584 4462 4.439289 GCCCATTCTTCTCGAAATTGAAGG 60.439 45.833 11.05 4.28 39.85 3.46
3585 4463 4.666237 GCCCATTCTTCTCGAAATTGAAG 58.334 43.478 5.93 5.93 40.53 3.02
3586 4464 3.126858 CGCCCATTCTTCTCGAAATTGAA 59.873 43.478 0.00 0.00 34.79 2.69
3587 4465 2.677836 CGCCCATTCTTCTCGAAATTGA 59.322 45.455 0.00 0.00 34.79 2.57
3588 4466 2.792542 GCGCCCATTCTTCTCGAAATTG 60.793 50.000 0.00 0.00 34.79 2.32
3589 4467 1.401905 GCGCCCATTCTTCTCGAAATT 59.598 47.619 0.00 0.00 34.79 1.82
3590 4468 1.017387 GCGCCCATTCTTCTCGAAAT 58.983 50.000 0.00 0.00 34.79 2.17
3591 4469 0.036388 AGCGCCCATTCTTCTCGAAA 60.036 50.000 2.29 0.00 34.79 3.46
3592 4470 0.821517 TAGCGCCCATTCTTCTCGAA 59.178 50.000 2.29 0.00 35.78 3.71
3593 4471 1.040646 ATAGCGCCCATTCTTCTCGA 58.959 50.000 2.29 0.00 0.00 4.04
3594 4472 2.724977 TATAGCGCCCATTCTTCTCG 57.275 50.000 2.29 0.00 0.00 4.04
3595 4473 3.728845 TGTTATAGCGCCCATTCTTCTC 58.271 45.455 2.29 0.00 0.00 2.87
3596 4474 3.388024 TCTGTTATAGCGCCCATTCTTCT 59.612 43.478 2.29 0.00 0.00 2.85
3597 4475 3.728845 TCTGTTATAGCGCCCATTCTTC 58.271 45.455 2.29 0.00 0.00 2.87
3598 4476 3.733337 CTCTGTTATAGCGCCCATTCTT 58.267 45.455 2.29 0.00 0.00 2.52
3599 4477 2.548920 GCTCTGTTATAGCGCCCATTCT 60.549 50.000 2.29 0.00 30.88 2.40
3600 4478 1.801178 GCTCTGTTATAGCGCCCATTC 59.199 52.381 2.29 0.00 30.88 2.67
3601 4479 1.884235 GCTCTGTTATAGCGCCCATT 58.116 50.000 2.29 0.00 30.88 3.16
3602 4480 3.614399 GCTCTGTTATAGCGCCCAT 57.386 52.632 2.29 0.00 30.88 4.00
3608 4486 3.861569 ATTTTCGCGCTCTGTTATAGC 57.138 42.857 5.56 0.00 36.60 2.97
3609 4487 5.143916 ACAATTTTCGCGCTCTGTTATAG 57.856 39.130 5.56 0.00 0.00 1.31
3610 4488 4.627900 TGACAATTTTCGCGCTCTGTTATA 59.372 37.500 5.56 0.00 0.00 0.98
3611 4489 3.435327 TGACAATTTTCGCGCTCTGTTAT 59.565 39.130 5.56 0.00 0.00 1.89
3612 4490 2.803386 TGACAATTTTCGCGCTCTGTTA 59.197 40.909 5.56 0.00 0.00 2.41
3613 4491 1.601903 TGACAATTTTCGCGCTCTGTT 59.398 42.857 5.56 0.00 0.00 3.16
3614 4492 1.069906 GTGACAATTTTCGCGCTCTGT 60.070 47.619 5.56 0.00 0.00 3.41
3615 4493 1.595609 GTGACAATTTTCGCGCTCTG 58.404 50.000 5.56 0.00 0.00 3.35
3616 4494 0.163788 CGTGACAATTTTCGCGCTCT 59.836 50.000 13.90 0.00 42.10 4.09
3617 4495 0.162933 TCGTGACAATTTTCGCGCTC 59.837 50.000 19.87 0.00 46.70 5.03
3618 4496 0.163788 CTCGTGACAATTTTCGCGCT 59.836 50.000 19.87 0.00 46.70 5.92
3619 4497 0.110823 ACTCGTGACAATTTTCGCGC 60.111 50.000 19.87 0.00 46.70 6.86
3621 4499 2.032377 TGGAACTCGTGACAATTTTCGC 60.032 45.455 0.00 0.00 0.00 4.70
3622 4500 3.493129 TCTGGAACTCGTGACAATTTTCG 59.507 43.478 0.00 0.00 0.00 3.46
3623 4501 4.511826 ACTCTGGAACTCGTGACAATTTTC 59.488 41.667 0.00 0.00 0.00 2.29
3624 4502 4.451900 ACTCTGGAACTCGTGACAATTTT 58.548 39.130 0.00 0.00 0.00 1.82
3625 4503 4.073293 ACTCTGGAACTCGTGACAATTT 57.927 40.909 0.00 0.00 0.00 1.82
3626 4504 3.753294 ACTCTGGAACTCGTGACAATT 57.247 42.857 0.00 0.00 0.00 2.32
3627 4505 3.181465 ACAACTCTGGAACTCGTGACAAT 60.181 43.478 0.00 0.00 0.00 2.71
3628 4506 2.167693 ACAACTCTGGAACTCGTGACAA 59.832 45.455 0.00 0.00 0.00 3.18
3629 4507 1.754803 ACAACTCTGGAACTCGTGACA 59.245 47.619 0.00 0.00 0.00 3.58
3630 4508 2.510768 ACAACTCTGGAACTCGTGAC 57.489 50.000 0.00 0.00 0.00 3.67
3631 4509 2.295349 GGTACAACTCTGGAACTCGTGA 59.705 50.000 0.00 0.00 0.00 4.35
3632 4510 2.035449 TGGTACAACTCTGGAACTCGTG 59.965 50.000 0.00 0.00 31.92 4.35
3633 4511 2.313317 TGGTACAACTCTGGAACTCGT 58.687 47.619 0.00 0.00 31.92 4.18
3647 4525 3.788227 AGATTGCTTGGAGTTGGTACA 57.212 42.857 0.00 0.00 0.00 2.90
3648 4526 4.833390 AGTAGATTGCTTGGAGTTGGTAC 58.167 43.478 0.00 0.00 0.00 3.34
3649 4527 5.012664 TGAAGTAGATTGCTTGGAGTTGGTA 59.987 40.000 0.00 0.00 0.00 3.25
3650 4528 4.202461 TGAAGTAGATTGCTTGGAGTTGGT 60.202 41.667 0.00 0.00 0.00 3.67
3651 4529 4.326826 TGAAGTAGATTGCTTGGAGTTGG 58.673 43.478 0.00 0.00 0.00 3.77
3652 4530 5.947228 TTGAAGTAGATTGCTTGGAGTTG 57.053 39.130 0.00 0.00 0.00 3.16
3653 4531 5.827797 TGTTTGAAGTAGATTGCTTGGAGTT 59.172 36.000 0.00 0.00 0.00 3.01
3654 4532 5.239525 GTGTTTGAAGTAGATTGCTTGGAGT 59.760 40.000 0.00 0.00 0.00 3.85
3655 4533 5.335191 GGTGTTTGAAGTAGATTGCTTGGAG 60.335 44.000 0.00 0.00 0.00 3.86
3656 4534 4.518970 GGTGTTTGAAGTAGATTGCTTGGA 59.481 41.667 0.00 0.00 0.00 3.53
3657 4535 4.278170 TGGTGTTTGAAGTAGATTGCTTGG 59.722 41.667 0.00 0.00 0.00 3.61
3658 4536 5.009010 AGTGGTGTTTGAAGTAGATTGCTTG 59.991 40.000 0.00 0.00 0.00 4.01
3659 4537 5.133221 AGTGGTGTTTGAAGTAGATTGCTT 58.867 37.500 0.00 0.00 0.00 3.91
3660 4538 4.718961 AGTGGTGTTTGAAGTAGATTGCT 58.281 39.130 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.