Multiple sequence alignment - TraesCS4A01G117400

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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 TraesCS4A01G117400 chr4A 100.000 3822 0 0 1 3822 143249724 143253545 0.000000e+00 7059.0
1 TraesCS4A01G117400 chr4A 100.000 38 0 0 3138 3175 143252823 143252860 1.900000e-08 71.3
2 TraesCS4A01G117400 chr4A 100.000 38 0 0 3100 3137 143252861 143252898 1.900000e-08 71.3
3 TraesCS4A01G117400 chr4D 96.107 2363 58 8 1 2340 327721985 327719634 0.000000e+00 3823.0
4 TraesCS4A01G117400 chr4D 96.433 785 23 2 2356 3140 327719649 327718870 0.000000e+00 1290.0
5 TraesCS4A01G117400 chr4B 94.763 2387 73 11 1 2340 407059559 407057178 0.000000e+00 3668.0
6 TraesCS4A01G117400 chr4B 95.302 1043 38 8 2356 3395 407057193 407056159 0.000000e+00 1644.0
7 TraesCS4A01G117400 chr4B 91.558 154 10 3 3500 3650 407056053 407055900 3.870000e-50 209.0
8 TraesCS4A01G117400 chr4B 97.561 41 1 0 3100 3140 407056416 407056376 1.900000e-08 71.3
9 TraesCS4A01G117400 chr4B 95.122 41 2 0 3138 3178 407056454 407056414 8.860000e-07 65.8
10 TraesCS4A01G117400 chr2B 95.280 339 12 2 2356 2693 188856053 188855718 5.620000e-148 534.0
11 TraesCS4A01G117400 chr2B 87.000 400 23 12 1958 2340 188856425 188856038 1.270000e-114 424.0
12 TraesCS4A01G117400 chr3B 94.100 339 16 2 2356 2693 554900341 554900676 2.630000e-141 512.0
13 TraesCS4A01G117400 chr3B 92.920 339 19 3 2356 2693 303334028 303333694 4.440000e-134 488.0
14 TraesCS4A01G117400 chr3B 88.279 401 17 13 1958 2340 554899968 554900356 1.620000e-123 453.0
15 TraesCS4A01G117400 chr3B 87.750 400 20 12 1958 2340 303334400 303334013 1.260000e-119 440.0
16 TraesCS4A01G117400 chr5B 93.805 339 17 2 2356 2693 299679708 299680043 1.230000e-139 507.0
17 TraesCS4A01G117400 chr5B 87.500 400 20 13 1958 2340 299679337 299679723 5.860000e-118 435.0
18 TraesCS4A01G117400 chr1A 98.830 171 2 0 3651 3821 520874814 520874644 4.800000e-79 305.0
19 TraesCS4A01G117400 chr1A 80.631 222 36 6 2578 2794 573818413 573818632 8.490000e-37 165.0
20 TraesCS4A01G117400 chr2A 97.143 175 5 0 3648 3822 47364043 47364217 2.890000e-76 296.0
21 TraesCS4A01G117400 chr7A 97.093 172 5 0 3651 3822 120741360 120741189 1.340000e-74 291.0
22 TraesCS4A01G117400 chr2D 89.535 172 13 1 3651 3822 408458923 408458757 2.990000e-51 213.0
23 TraesCS4A01G117400 chr1D 81.944 216 28 9 2586 2794 477480552 477480763 5.080000e-39 172.0
24 TraesCS4A01G117400 chr1B 81.567 217 29 9 2586 2795 665061697 665061909 6.570000e-38 169.0
25 TraesCS4A01G117400 chr3D 79.295 227 38 8 2576 2796 301414172 301414395 2.380000e-32 150.0


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 TraesCS4A01G117400 chr4A 143249724 143253545 3821 False 2400.533333 7059 100.0000 1 3822 3 chr4A.!!$F1 3821
1 TraesCS4A01G117400 chr4D 327718870 327721985 3115 True 2556.500000 3823 96.2700 1 3140 2 chr4D.!!$R1 3139
2 TraesCS4A01G117400 chr4B 407055900 407059559 3659 True 1131.620000 3668 94.8612 1 3650 5 chr4B.!!$R1 3649
3 TraesCS4A01G117400 chr2B 188855718 188856425 707 True 479.000000 534 91.1400 1958 2693 2 chr2B.!!$R1 735
4 TraesCS4A01G117400 chr3B 554899968 554900676 708 False 482.500000 512 91.1895 1958 2693 2 chr3B.!!$F1 735
5 TraesCS4A01G117400 chr3B 303333694 303334400 706 True 464.000000 488 90.3350 1958 2693 2 chr3B.!!$R1 735
6 TraesCS4A01G117400 chr5B 299679337 299680043 706 False 471.000000 507 90.6525 1958 2693 2 chr5B.!!$F1 735

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
568 569 0.534203 GTGGTGTCCAACGGTGACAT 60.534 55.000 0.00 0.00 43.98 3.06 F
859 879 1.068055 GCAGGGCAATCAAGTCACTTG 60.068 52.381 11.69 11.69 42.25 3.16 F
2361 2410 0.825840 TTTTTGCGGGGGACTTCAGG 60.826 55.000 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2347 2396 0.106894 CTATTCCTGAAGTCCCCCGC 59.893 60.0 0.00 0.00 0.00 6.13 R
2560 2609 1.207488 CCACCACTTCTCCATCCCCA 61.207 60.0 0.00 0.00 0.00 4.96 R
3456 3508 0.044161 GACCGCACGATCGAAAATCG 60.044 55.0 24.34 15.52 46.02 3.34 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
124 125 1.617322 TGAAGACACTGGTAGAGCGT 58.383 50.000 0.00 0.00 0.00 5.07
238 239 2.221906 TAACCGTTCCGCAGCTCCTC 62.222 60.000 0.00 0.00 0.00 3.71
275 276 3.251245 GGTCTCTGATATCACGACGACAT 59.749 47.826 17.64 0.00 0.00 3.06
457 458 9.295825 ACATTGATATTTTGGTCAGTAGTTCAA 57.704 29.630 0.00 0.00 0.00 2.69
513 514 4.756642 ACACCATCTGAACCATTATATGCG 59.243 41.667 0.00 0.00 0.00 4.73
567 568 1.153329 GTGGTGTCCAACGGTGACA 60.153 57.895 0.00 1.18 40.28 3.58
568 569 0.534203 GTGGTGTCCAACGGTGACAT 60.534 55.000 0.00 0.00 43.98 3.06
627 629 5.511088 AAACGAAATGAAGCTACTGTACG 57.489 39.130 0.00 0.00 0.00 3.67
748 768 5.258456 TCTACGGCCTTATACTTGTTCAG 57.742 43.478 0.00 0.00 0.00 3.02
859 879 1.068055 GCAGGGCAATCAAGTCACTTG 60.068 52.381 11.69 11.69 42.25 3.16
1051 1078 3.432588 CGTCGTCCTGCGTCTCCT 61.433 66.667 0.00 0.00 42.13 3.69
1057 1084 3.522731 CCTGCGTCTCCTCCGAGG 61.523 72.222 8.30 8.30 36.70 4.63
1109 1136 3.062466 CTCCACTCCCTCGTCGCA 61.062 66.667 0.00 0.00 0.00 5.10
1212 1239 1.297967 CTCATCGTGCGTCTCCGAG 60.298 63.158 0.00 0.00 36.41 4.63
1227 1254 2.829458 GAGGGCCGCTACGTCTCT 60.829 66.667 0.00 0.00 0.00 3.10
1391 1418 1.446966 GCCTCAGAGCGGAGAACAC 60.447 63.158 4.89 0.00 37.05 3.32
1662 1689 3.181511 CGAATTCACTGCTTTATTCCGCA 60.182 43.478 6.22 0.00 34.54 5.69
1752 1779 3.960102 AGTTCCAGTTCCTGCAAAATTCA 59.040 39.130 0.00 0.00 0.00 2.57
1801 1828 7.878547 TGTGATGCAATTAGATGGTGAAATA 57.121 32.000 0.00 0.00 0.00 1.40
1851 1878 7.176865 AGCTCTGGTAATACGATGCTCTATTTA 59.823 37.037 0.00 0.00 0.00 1.40
1908 1935 9.988350 ATGTTGAATTAGCTAATTTTGTACTCG 57.012 29.630 27.96 0.00 36.13 4.18
2157 2185 5.897377 AACACTTGACAGTTGTAGCTTTT 57.103 34.783 0.00 0.00 0.00 2.27
2180 2208 3.939066 ACCTACATAGTGTTGGCAGTTC 58.061 45.455 9.88 0.00 45.17 3.01
2211 2260 1.852067 AAGCCAAACTTACGCCGCAG 61.852 55.000 0.00 0.00 36.62 5.18
2272 2321 5.415701 ACAAATTCTTATCACGTCATGGCTT 59.584 36.000 0.00 0.00 0.00 4.35
2305 2354 5.689383 TCAATTGCAGGAAGAAACTGTAC 57.311 39.130 0.00 0.00 38.22 2.90
2324 2373 9.516314 AACTGTACTGAACTTGCTTAATTTTTC 57.484 29.630 6.77 0.00 0.00 2.29
2325 2374 8.903820 ACTGTACTGAACTTGCTTAATTTTTCT 58.096 29.630 6.77 0.00 0.00 2.52
2326 2375 9.736023 CTGTACTGAACTTGCTTAATTTTTCTT 57.264 29.630 0.00 0.00 0.00 2.52
2327 2376 9.730420 TGTACTGAACTTGCTTAATTTTTCTTC 57.270 29.630 0.00 0.00 0.00 2.87
2328 2377 9.730420 GTACTGAACTTGCTTAATTTTTCTTCA 57.270 29.630 0.00 0.00 0.00 3.02
2329 2378 8.862550 ACTGAACTTGCTTAATTTTTCTTCAG 57.137 30.769 0.00 0.00 38.58 3.02
2330 2379 7.922811 ACTGAACTTGCTTAATTTTTCTTCAGG 59.077 33.333 0.00 0.00 37.49 3.86
2331 2380 8.006298 TGAACTTGCTTAATTTTTCTTCAGGA 57.994 30.769 0.00 0.00 0.00 3.86
2332 2381 8.474025 TGAACTTGCTTAATTTTTCTTCAGGAA 58.526 29.630 0.00 0.00 0.00 3.36
2333 2382 9.481340 GAACTTGCTTAATTTTTCTTCAGGAAT 57.519 29.630 0.00 0.00 33.53 3.01
2361 2410 0.825840 TTTTTGCGGGGGACTTCAGG 60.826 55.000 0.00 0.00 0.00 3.86
2388 2437 5.488341 AGTATTGAATCGGCTACTTGTTGT 58.512 37.500 0.00 0.00 0.00 3.32
2389 2438 5.938125 AGTATTGAATCGGCTACTTGTTGTT 59.062 36.000 0.00 0.00 0.00 2.83
2390 2439 5.705609 ATTGAATCGGCTACTTGTTGTTT 57.294 34.783 0.00 0.00 0.00 2.83
2407 2456 7.231705 TGTTGTTTGCAATTTCATGTTACAG 57.768 32.000 0.00 0.00 36.92 2.74
2411 2460 6.696583 TGTTTGCAATTTCATGTTACAGAGTG 59.303 34.615 0.00 0.00 0.00 3.51
2420 2469 8.862325 TTTCATGTTACAGAGTGGTCATTAAT 57.138 30.769 0.00 0.00 0.00 1.40
2459 2508 5.195001 TGATTTGGCTAACTCACAAAACC 57.805 39.130 0.00 0.00 37.60 3.27
2480 2529 9.810545 AAAACCAAAAACTCAATTCGAGAAATA 57.189 25.926 10.61 0.00 45.45 1.40
2560 2609 3.155167 GGGGAGGACGAGGCGAAT 61.155 66.667 0.00 0.00 0.00 3.34
2744 2793 1.277580 CCTCCCCTGCCAGATGTTCT 61.278 60.000 0.00 0.00 0.00 3.01
2878 2927 2.426024 GTCTCCTACTGCCGTGTAATGA 59.574 50.000 0.00 0.00 0.00 2.57
2885 2934 2.027192 ACTGCCGTGTAATGACATCCTT 60.027 45.455 0.00 0.00 38.04 3.36
2934 2983 2.434709 TGCGCGCATGTCTGATGT 60.435 55.556 33.09 0.00 0.00 3.06
3258 3309 1.909532 CAAGTGTATCGTCGGTTCGTC 59.090 52.381 0.00 0.00 0.00 4.20
3259 3310 1.159285 AGTGTATCGTCGGTTCGTCA 58.841 50.000 0.00 0.00 0.00 4.35
3281 3332 9.087424 CGTCATTATCTTGTTGATCAGAACTAA 57.913 33.333 0.00 0.00 36.65 2.24
3286 3337 5.305585 TCTTGTTGATCAGAACTAACCCAC 58.694 41.667 0.00 0.00 0.00 4.61
3378 3430 6.430451 AGTGTTTTATGTTTCGAGAAAGCTG 58.570 36.000 0.00 0.00 0.00 4.24
3389 3441 1.194772 GAGAAAGCTGTTTTCCGACCG 59.805 52.381 12.51 0.00 45.15 4.79
3390 3442 1.202604 AGAAAGCTGTTTTCCGACCGA 60.203 47.619 12.51 0.00 45.15 4.69
3392 3444 1.892209 AAGCTGTTTTCCGACCGATT 58.108 45.000 0.00 0.00 0.00 3.34
3393 3445 1.439679 AGCTGTTTTCCGACCGATTC 58.560 50.000 0.00 0.00 0.00 2.52
3394 3446 1.002087 AGCTGTTTTCCGACCGATTCT 59.998 47.619 0.00 0.00 0.00 2.40
3395 3447 1.804748 GCTGTTTTCCGACCGATTCTT 59.195 47.619 0.00 0.00 0.00 2.52
3398 3450 4.083696 GCTGTTTTCCGACCGATTCTTTTA 60.084 41.667 0.00 0.00 0.00 1.52
3399 3451 5.561339 GCTGTTTTCCGACCGATTCTTTTAA 60.561 40.000 0.00 0.00 0.00 1.52
3400 3452 6.374565 TGTTTTCCGACCGATTCTTTTAAA 57.625 33.333 0.00 0.00 0.00 1.52
3402 3454 7.256286 TGTTTTCCGACCGATTCTTTTAAAAA 58.744 30.769 1.66 0.00 0.00 1.94
3420 3472 4.841443 AAAAAGCTATTTTCCGACCGTT 57.159 36.364 0.00 0.00 37.65 4.44
3421 3473 4.414999 AAAAGCTATTTTCCGACCGTTC 57.585 40.909 0.00 0.00 33.21 3.95
3422 3474 3.329929 AAGCTATTTTCCGACCGTTCT 57.670 42.857 0.00 0.00 0.00 3.01
3423 3475 2.618053 AGCTATTTTCCGACCGTTCTG 58.382 47.619 0.00 0.00 0.00 3.02
3424 3476 2.232941 AGCTATTTTCCGACCGTTCTGA 59.767 45.455 0.00 0.00 0.00 3.27
3425 3477 3.118738 AGCTATTTTCCGACCGTTCTGAT 60.119 43.478 0.00 0.00 0.00 2.90
3426 3478 3.245519 GCTATTTTCCGACCGTTCTGATC 59.754 47.826 0.00 0.00 0.00 2.92
3427 3479 3.611766 ATTTTCCGACCGTTCTGATCT 57.388 42.857 0.00 0.00 0.00 2.75
3450 3502 2.359981 TAGATCCGAACGGTCTGGAT 57.640 50.000 21.55 21.55 38.82 3.41
3451 3503 0.747255 AGATCCGAACGGTCTGGATG 59.253 55.000 24.90 0.00 37.32 3.51
3452 3504 0.460311 GATCCGAACGGTCTGGATGT 59.540 55.000 24.90 8.82 37.32 3.06
3453 3505 0.460311 ATCCGAACGGTCTGGATGTC 59.540 55.000 20.99 0.00 36.46 3.06
3454 3506 0.896479 TCCGAACGGTCTGGATGTCA 60.896 55.000 12.93 0.00 36.47 3.58
3455 3507 0.175760 CCGAACGGTCTGGATGTCAT 59.824 55.000 5.54 0.00 0.00 3.06
3456 3508 1.560923 CGAACGGTCTGGATGTCATC 58.439 55.000 4.06 4.06 0.00 2.92
3458 3510 1.134367 GAACGGTCTGGATGTCATCGA 59.866 52.381 6.74 2.00 0.00 3.59
3498 3550 1.202698 GCACGAGCCTCCCATAATTCT 60.203 52.381 0.00 0.00 33.58 2.40
3513 3592 6.461370 CCCATAATTCTGATTTCAATTGCGGA 60.461 38.462 0.00 0.00 0.00 5.54
3527 3607 8.641499 TTCAATTGCGGATTTATTAATTGACC 57.359 30.769 0.00 0.00 43.42 4.02
3530 3610 4.452825 TGCGGATTTATTAATTGACCCGA 58.547 39.130 17.44 5.69 38.10 5.14
3560 3641 6.197468 GTCTCATGACTCTTAATTAGCACGAC 59.803 42.308 0.00 0.00 39.94 4.34
3569 3650 9.865321 ACTCTTAATTAGCACGACTTAATTACA 57.135 29.630 0.00 0.00 0.00 2.41
3591 3672 7.458409 ACACCATATCTTAATTGGCATGATC 57.542 36.000 0.00 0.00 33.66 2.92
3630 3711 5.183228 ACGTGTACTGCCATTTAAAGCTAT 58.817 37.500 0.00 0.00 0.00 2.97
3636 3718 8.802267 TGTACTGCCATTTAAAGCTATCTTTTT 58.198 29.630 0.00 0.00 42.21 1.94
3674 3756 9.745880 AAGAGTTAATTACACCTATGATACACG 57.254 33.333 0.00 0.00 0.00 4.49
3675 3757 9.128404 AGAGTTAATTACACCTATGATACACGA 57.872 33.333 0.00 0.00 0.00 4.35
3676 3758 9.740239 GAGTTAATTACACCTATGATACACGAA 57.260 33.333 0.00 0.00 0.00 3.85
3677 3759 9.525409 AGTTAATTACACCTATGATACACGAAC 57.475 33.333 0.00 0.00 0.00 3.95
3678 3760 9.525409 GTTAATTACACCTATGATACACGAACT 57.475 33.333 0.00 0.00 0.00 3.01
3680 3762 8.420374 AATTACACCTATGATACACGAACTTG 57.580 34.615 0.00 0.00 0.00 3.16
3681 3763 5.401531 ACACCTATGATACACGAACTTGT 57.598 39.130 0.00 0.00 0.00 3.16
3682 3764 6.519679 ACACCTATGATACACGAACTTGTA 57.480 37.500 0.00 0.00 36.41 2.41
3683 3765 6.327934 ACACCTATGATACACGAACTTGTAC 58.672 40.000 0.00 0.00 34.79 2.90
3684 3766 5.454554 CACCTATGATACACGAACTTGTACG 59.545 44.000 0.00 0.00 34.79 3.67
3685 3767 4.974275 CCTATGATACACGAACTTGTACGG 59.026 45.833 0.00 0.00 34.79 4.02
3686 3768 3.921119 TGATACACGAACTTGTACGGT 57.079 42.857 0.00 0.00 34.79 4.83
3687 3769 3.567530 TGATACACGAACTTGTACGGTG 58.432 45.455 0.00 0.00 34.79 4.94
3688 3770 3.004629 TGATACACGAACTTGTACGGTGT 59.995 43.478 0.00 0.61 34.79 4.16
3689 3771 1.563111 ACACGAACTTGTACGGTGTG 58.437 50.000 0.00 7.32 0.00 3.82
3690 3772 1.135024 ACACGAACTTGTACGGTGTGT 60.135 47.619 0.00 8.20 34.52 3.72
3691 3773 2.098934 ACACGAACTTGTACGGTGTGTA 59.901 45.455 10.78 0.00 37.32 2.90
3705 3787 5.992729 ACGGTGTGTACAAATTCATACAAC 58.007 37.500 0.00 0.00 33.23 3.32
3706 3788 5.527951 ACGGTGTGTACAAATTCATACAACA 59.472 36.000 0.00 3.27 33.23 3.33
3707 3789 6.038382 ACGGTGTGTACAAATTCATACAACAA 59.962 34.615 0.00 0.00 33.23 2.83
3708 3790 6.358558 CGGTGTGTACAAATTCATACAACAAC 59.641 38.462 0.00 6.52 33.23 3.32
3709 3791 7.422399 GGTGTGTACAAATTCATACAACAACT 58.578 34.615 0.00 0.00 33.23 3.16
3710 3792 7.918562 GGTGTGTACAAATTCATACAACAACTT 59.081 33.333 0.00 0.00 33.23 2.66
3711 3793 8.742188 GTGTGTACAAATTCATACAACAACTTG 58.258 33.333 0.00 0.00 33.23 3.16
3712 3794 7.433719 TGTGTACAAATTCATACAACAACTTGC 59.566 33.333 0.00 0.00 33.23 4.01
3713 3795 7.433719 GTGTACAAATTCATACAACAACTTGCA 59.566 33.333 0.00 0.00 33.23 4.08
3714 3796 7.976175 TGTACAAATTCATACAACAACTTGCAA 59.024 29.630 0.00 0.00 0.00 4.08
3715 3797 7.467557 ACAAATTCATACAACAACTTGCAAG 57.532 32.000 24.84 24.84 0.00 4.01
3716 3798 7.264221 ACAAATTCATACAACAACTTGCAAGA 58.736 30.769 32.50 8.89 0.00 3.02
3717 3799 7.927629 ACAAATTCATACAACAACTTGCAAGAT 59.072 29.630 32.50 18.98 0.00 2.40
3718 3800 7.878477 AATTCATACAACAACTTGCAAGATG 57.122 32.000 32.50 30.57 35.23 2.90
3719 3801 6.631971 TTCATACAACAACTTGCAAGATGA 57.368 33.333 34.96 25.36 33.55 2.92
3720 3802 6.000891 TCATACAACAACTTGCAAGATGAC 57.999 37.500 34.96 0.00 33.55 3.06
3721 3803 5.530543 TCATACAACAACTTGCAAGATGACA 59.469 36.000 34.96 19.78 33.55 3.58
3722 3804 4.032703 ACAACAACTTGCAAGATGACAC 57.967 40.909 34.96 0.00 33.55 3.67
3723 3805 3.443329 ACAACAACTTGCAAGATGACACA 59.557 39.130 34.96 0.00 33.55 3.72
3724 3806 4.082300 ACAACAACTTGCAAGATGACACAA 60.082 37.500 34.96 0.00 33.55 3.33
3725 3807 4.717233 ACAACTTGCAAGATGACACAAA 57.283 36.364 34.96 0.00 33.55 2.83
3726 3808 5.266733 ACAACTTGCAAGATGACACAAAT 57.733 34.783 34.96 14.19 33.55 2.32
3727 3809 5.663456 ACAACTTGCAAGATGACACAAATT 58.337 33.333 34.96 13.54 33.55 1.82
3728 3810 5.521010 ACAACTTGCAAGATGACACAAATTG 59.479 36.000 34.96 23.96 35.86 2.32
3729 3811 5.518848 ACTTGCAAGATGACACAAATTGA 57.481 34.783 32.50 0.00 0.00 2.57
3730 3812 6.092955 ACTTGCAAGATGACACAAATTGAT 57.907 33.333 32.50 1.12 0.00 2.57
3731 3813 6.154445 ACTTGCAAGATGACACAAATTGATC 58.846 36.000 32.50 0.00 0.00 2.92
3732 3814 5.708877 TGCAAGATGACACAAATTGATCA 57.291 34.783 0.00 3.59 0.00 2.92
3733 3815 6.275494 TGCAAGATGACACAAATTGATCAT 57.725 33.333 14.14 14.14 34.50 2.45
3734 3816 7.393841 TGCAAGATGACACAAATTGATCATA 57.606 32.000 14.19 0.00 31.96 2.15
3735 3817 8.002984 TGCAAGATGACACAAATTGATCATAT 57.997 30.769 14.19 10.32 31.96 1.78
3736 3818 9.122779 TGCAAGATGACACAAATTGATCATATA 57.877 29.630 14.19 0.00 31.96 0.86
3737 3819 9.955208 GCAAGATGACACAAATTGATCATATAA 57.045 29.630 14.19 0.00 31.96 0.98
3750 3832 7.786178 TTGATCATATAACTTGAGTTTCGGG 57.214 36.000 0.00 0.00 39.31 5.14
3751 3833 6.288294 TGATCATATAACTTGAGTTTCGGGG 58.712 40.000 1.20 0.00 39.31 5.73
3752 3834 5.943349 TCATATAACTTGAGTTTCGGGGA 57.057 39.130 1.20 0.00 39.31 4.81
3753 3835 5.667466 TCATATAACTTGAGTTTCGGGGAC 58.333 41.667 1.20 0.00 39.31 4.46
3754 3836 5.188163 TCATATAACTTGAGTTTCGGGGACA 59.812 40.000 1.20 0.00 39.31 4.02
3755 3837 2.951229 AACTTGAGTTTCGGGGACAT 57.049 45.000 0.00 0.00 33.93 3.06
3756 3838 2.951229 ACTTGAGTTTCGGGGACATT 57.049 45.000 0.00 0.00 0.00 2.71
3757 3839 3.223674 ACTTGAGTTTCGGGGACATTT 57.776 42.857 0.00 0.00 0.00 2.32
3758 3840 3.146847 ACTTGAGTTTCGGGGACATTTC 58.853 45.455 0.00 0.00 0.00 2.17
3759 3841 2.940994 TGAGTTTCGGGGACATTTCA 57.059 45.000 0.00 0.00 0.00 2.69
3760 3842 2.778299 TGAGTTTCGGGGACATTTCAG 58.222 47.619 0.00 0.00 0.00 3.02
3761 3843 2.105821 TGAGTTTCGGGGACATTTCAGT 59.894 45.455 0.00 0.00 0.00 3.41
3762 3844 3.325425 TGAGTTTCGGGGACATTTCAGTA 59.675 43.478 0.00 0.00 0.00 2.74
3763 3845 3.671716 AGTTTCGGGGACATTTCAGTAC 58.328 45.455 0.00 0.00 0.00 2.73
3764 3846 3.071892 AGTTTCGGGGACATTTCAGTACA 59.928 43.478 0.00 0.00 0.00 2.90
3765 3847 3.773418 TTCGGGGACATTTCAGTACAA 57.227 42.857 0.00 0.00 0.00 2.41
3766 3848 3.992943 TCGGGGACATTTCAGTACAAT 57.007 42.857 0.00 0.00 0.00 2.71
3767 3849 4.295141 TCGGGGACATTTCAGTACAATT 57.705 40.909 0.00 0.00 0.00 2.32
3768 3850 4.658063 TCGGGGACATTTCAGTACAATTT 58.342 39.130 0.00 0.00 0.00 1.82
3769 3851 4.457603 TCGGGGACATTTCAGTACAATTTG 59.542 41.667 0.00 0.00 0.00 2.32
3770 3852 4.380444 CGGGGACATTTCAGTACAATTTGG 60.380 45.833 0.78 0.00 0.00 3.28
3771 3853 4.526650 GGGGACATTTCAGTACAATTTGGT 59.473 41.667 0.78 0.00 0.00 3.67
3772 3854 5.336451 GGGGACATTTCAGTACAATTTGGTC 60.336 44.000 0.78 0.00 0.00 4.02
3773 3855 5.242838 GGGACATTTCAGTACAATTTGGTCA 59.757 40.000 0.78 0.00 0.00 4.02
3774 3856 6.149633 GGACATTTCAGTACAATTTGGTCAC 58.850 40.000 0.78 0.00 0.00 3.67
3775 3857 6.016276 GGACATTTCAGTACAATTTGGTCACT 60.016 38.462 0.78 0.00 0.00 3.41
3776 3858 7.346751 ACATTTCAGTACAATTTGGTCACTT 57.653 32.000 0.78 0.00 0.00 3.16
3777 3859 8.458573 ACATTTCAGTACAATTTGGTCACTTA 57.541 30.769 0.78 0.00 0.00 2.24
3778 3860 8.349983 ACATTTCAGTACAATTTGGTCACTTAC 58.650 33.333 0.78 0.00 0.00 2.34
3788 3870 2.738013 GGTCACTTACCGTTAGTGCT 57.262 50.000 11.95 0.00 42.12 4.40
3789 3871 2.603953 GGTCACTTACCGTTAGTGCTC 58.396 52.381 11.95 8.00 42.12 4.26
3790 3872 2.603953 GTCACTTACCGTTAGTGCTCC 58.396 52.381 11.95 0.88 42.12 4.70
3791 3873 1.200716 TCACTTACCGTTAGTGCTCCG 59.799 52.381 11.95 0.00 42.12 4.63
3792 3874 1.068055 CACTTACCGTTAGTGCTCCGT 60.068 52.381 4.83 0.00 36.88 4.69
3793 3875 1.615392 ACTTACCGTTAGTGCTCCGTT 59.385 47.619 0.00 0.00 0.00 4.44
3794 3876 2.819608 ACTTACCGTTAGTGCTCCGTTA 59.180 45.455 0.00 0.00 0.00 3.18
3795 3877 2.919666 TACCGTTAGTGCTCCGTTAC 57.080 50.000 0.00 0.00 0.00 2.50
3796 3878 0.961019 ACCGTTAGTGCTCCGTTACA 59.039 50.000 0.00 0.00 0.00 2.41
3797 3879 1.547372 ACCGTTAGTGCTCCGTTACAT 59.453 47.619 0.00 0.00 0.00 2.29
3798 3880 2.028748 ACCGTTAGTGCTCCGTTACATT 60.029 45.455 0.00 0.00 0.00 2.71
3799 3881 2.601763 CCGTTAGTGCTCCGTTACATTC 59.398 50.000 0.00 0.00 0.00 2.67
3800 3882 2.278094 CGTTAGTGCTCCGTTACATTCG 59.722 50.000 0.00 0.00 0.00 3.34
3801 3883 3.248266 GTTAGTGCTCCGTTACATTCGT 58.752 45.455 0.00 0.00 0.00 3.85
3802 3884 1.992170 AGTGCTCCGTTACATTCGTC 58.008 50.000 0.00 0.00 0.00 4.20
3803 3885 1.544691 AGTGCTCCGTTACATTCGTCT 59.455 47.619 0.00 0.00 0.00 4.18
3804 3886 2.751259 AGTGCTCCGTTACATTCGTCTA 59.249 45.455 0.00 0.00 0.00 2.59
3805 3887 2.850647 GTGCTCCGTTACATTCGTCTAC 59.149 50.000 0.00 0.00 0.00 2.59
3806 3888 2.488937 TGCTCCGTTACATTCGTCTACA 59.511 45.455 0.00 0.00 0.00 2.74
3807 3889 3.129813 TGCTCCGTTACATTCGTCTACAT 59.870 43.478 0.00 0.00 0.00 2.29
3808 3890 4.110482 GCTCCGTTACATTCGTCTACATT 58.890 43.478 0.00 0.00 0.00 2.71
3809 3891 4.026804 GCTCCGTTACATTCGTCTACATTG 60.027 45.833 0.00 0.00 0.00 2.82
3810 3892 3.861113 TCCGTTACATTCGTCTACATTGC 59.139 43.478 0.00 0.00 0.00 3.56
3811 3893 3.615056 CCGTTACATTCGTCTACATTGCA 59.385 43.478 0.00 0.00 0.00 4.08
3812 3894 4.491924 CCGTTACATTCGTCTACATTGCAC 60.492 45.833 0.00 0.00 0.00 4.57
3813 3895 4.565229 GTTACATTCGTCTACATTGCACG 58.435 43.478 0.00 0.00 34.78 5.34
3814 3896 1.393539 ACATTCGTCTACATTGCACGC 59.606 47.619 0.00 0.00 33.46 5.34
3815 3897 1.660607 CATTCGTCTACATTGCACGCT 59.339 47.619 0.00 0.00 33.46 5.07
3816 3898 2.640346 TTCGTCTACATTGCACGCTA 57.360 45.000 0.00 0.00 33.46 4.26
3817 3899 2.188837 TCGTCTACATTGCACGCTAG 57.811 50.000 0.00 0.00 33.46 3.42
3818 3900 0.572590 CGTCTACATTGCACGCTAGC 59.427 55.000 4.06 4.06 0.00 3.42
3819 3901 0.572590 GTCTACATTGCACGCTAGCG 59.427 55.000 34.27 34.27 46.03 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 125 2.158957 GCCATCGACTGGGATCTTGTAA 60.159 50.000 13.51 0.00 46.06 2.41
457 458 7.389884 CCAGCAAGTATCAGTAATATTGAGCAT 59.610 37.037 0.00 0.00 0.00 3.79
513 514 2.601741 GCAGCTCTGAATTTAGCATCGC 60.602 50.000 0.29 6.49 41.32 4.58
567 568 4.878397 GGAACAGTAAAGAGCACTGCATAT 59.122 41.667 3.30 0.00 45.96 1.78
568 569 4.020218 AGGAACAGTAAAGAGCACTGCATA 60.020 41.667 3.30 0.00 45.96 3.14
627 629 6.262496 ACTTTTCTCCCAGTTACTGCTAAAAC 59.738 38.462 6.88 0.00 0.00 2.43
748 768 0.742635 GACCAGCTCCTGCACTAAGC 60.743 60.000 2.69 2.69 42.74 3.09
859 879 0.670854 GCGGTTTGAGAGACAGGTCC 60.671 60.000 0.00 0.00 0.00 4.46
1126 1153 3.726144 GAGCAGGCCTCCCTTGCT 61.726 66.667 15.74 15.74 43.57 3.91
1212 1239 3.902086 GGAGAGACGTAGCGGCCC 61.902 72.222 0.00 0.00 34.11 5.80
1391 1418 1.662438 GAGGAGGAGAGACAGGTGCG 61.662 65.000 0.00 0.00 0.00 5.34
1662 1689 4.697352 AGCAGATAAACAAAGCGATTCACT 59.303 37.500 0.00 0.00 0.00 3.41
1752 1779 7.391148 AACAAATTTGCTCCACGATTACTAT 57.609 32.000 18.12 0.00 0.00 2.12
1801 1828 7.444629 TCGTCTAATATCGCAGGTTTAGTAT 57.555 36.000 0.00 0.00 0.00 2.12
1851 1878 6.567321 GCTGCTTGATGCTATCGTCAAATTAT 60.567 38.462 3.05 0.00 44.83 1.28
1908 1935 3.487574 CGAAAGCAGAGTATGACGAATCC 59.512 47.826 0.00 0.00 0.00 3.01
2137 2165 6.038271 AGGTTAAAAGCTACAACTGTCAAGTG 59.962 38.462 0.00 0.00 33.85 3.16
2157 2185 5.484715 GAACTGCCAACACTATGTAGGTTA 58.515 41.667 0.00 0.00 0.00 2.85
2180 2208 5.712152 AAGTTTGGCTTACTTCATCAAGG 57.288 39.130 0.00 0.00 35.27 3.61
2207 2256 3.957468 GGAAATTCCTAATCAAGCTGCG 58.043 45.455 4.46 0.00 32.53 5.18
2231 2280 8.237811 AGAATTTGTGTGATTCCAACTTAACT 57.762 30.769 0.00 0.00 34.74 2.24
2244 2293 6.128309 CCATGACGTGATAAGAATTTGTGTGA 60.128 38.462 0.00 0.00 0.00 3.58
2272 2321 2.027929 CCTGCAATTGAATCCCAAGCAA 60.028 45.455 10.34 0.00 36.11 3.91
2305 2354 8.137437 TCCTGAAGAAAAATTAAGCAAGTTCAG 58.863 33.333 0.00 0.00 38.61 3.02
2342 2391 0.825840 CCTGAAGTCCCCCGCAAAAA 60.826 55.000 0.00 0.00 0.00 1.94
2343 2392 1.228429 CCTGAAGTCCCCCGCAAAA 60.228 57.895 0.00 0.00 0.00 2.44
2344 2393 1.710996 TTCCTGAAGTCCCCCGCAAA 61.711 55.000 0.00 0.00 0.00 3.68
2345 2394 1.497309 ATTCCTGAAGTCCCCCGCAA 61.497 55.000 0.00 0.00 0.00 4.85
2346 2395 0.619255 TATTCCTGAAGTCCCCCGCA 60.619 55.000 0.00 0.00 0.00 5.69
2347 2396 0.106894 CTATTCCTGAAGTCCCCCGC 59.893 60.000 0.00 0.00 0.00 6.13
2348 2397 1.497161 ACTATTCCTGAAGTCCCCCG 58.503 55.000 0.00 0.00 0.00 5.73
2349 2398 4.658901 TCAATACTATTCCTGAAGTCCCCC 59.341 45.833 0.00 0.00 0.00 5.40
2350 2399 5.888982 TCAATACTATTCCTGAAGTCCCC 57.111 43.478 0.00 0.00 0.00 4.81
2351 2400 6.647067 CGATTCAATACTATTCCTGAAGTCCC 59.353 42.308 0.00 0.00 31.70 4.46
2352 2401 6.647067 CCGATTCAATACTATTCCTGAAGTCC 59.353 42.308 0.00 0.00 31.70 3.85
2353 2402 6.146347 GCCGATTCAATACTATTCCTGAAGTC 59.854 42.308 0.00 0.00 31.70 3.01
2354 2403 5.992217 GCCGATTCAATACTATTCCTGAAGT 59.008 40.000 0.00 0.00 31.70 3.01
2361 2410 7.948278 ACAAGTAGCCGATTCAATACTATTC 57.052 36.000 0.00 0.00 0.00 1.75
2388 2437 6.183360 ACCACTCTGTAACATGAAATTGCAAA 60.183 34.615 1.71 0.00 0.00 3.68
2389 2438 5.301551 ACCACTCTGTAACATGAAATTGCAA 59.698 36.000 0.00 0.00 0.00 4.08
2390 2439 4.826733 ACCACTCTGTAACATGAAATTGCA 59.173 37.500 0.00 0.00 0.00 4.08
2407 2456 5.651530 TGTCTCTTCGATTAATGACCACTC 58.348 41.667 0.00 0.00 0.00 3.51
2411 2460 4.141914 ACCCTGTCTCTTCGATTAATGACC 60.142 45.833 0.00 0.00 0.00 4.02
2420 2469 5.419542 CAAATCAATACCCTGTCTCTTCGA 58.580 41.667 0.00 0.00 0.00 3.71
2480 2529 7.632861 TCATACGGATATGAATTCCCAATGAT 58.367 34.615 2.27 0.00 43.46 2.45
2560 2609 1.207488 CCACCACTTCTCCATCCCCA 61.207 60.000 0.00 0.00 0.00 4.96
2878 2927 0.905357 CAGGTCGGAGGAAAGGATGT 59.095 55.000 0.00 0.00 0.00 3.06
2885 2934 2.291043 GGAAGGCAGGTCGGAGGAA 61.291 63.158 0.00 0.00 0.00 3.36
2934 2983 0.397941 CAAGCAGTCCCTGGTGAAGA 59.602 55.000 0.00 0.00 41.59 2.87
3103 3154 0.961753 CTGTTTTCCTGCCCTGAACC 59.038 55.000 0.00 0.00 0.00 3.62
3248 3299 4.624024 TCAACAAGATAATGACGAACCGAC 59.376 41.667 0.00 0.00 0.00 4.79
3258 3309 8.616076 GGGTTAGTTCTGATCAACAAGATAATG 58.384 37.037 0.00 0.00 37.00 1.90
3259 3310 8.328758 TGGGTTAGTTCTGATCAACAAGATAAT 58.671 33.333 0.00 0.00 37.00 1.28
3281 3332 7.665559 CACCATATATACAAAGCTTATGTGGGT 59.334 37.037 19.95 14.51 38.32 4.51
3286 3337 8.896744 CCATCCACCATATATACAAAGCTTATG 58.103 37.037 0.00 3.17 0.00 1.90
3378 3430 7.682593 TTTTTAAAAGAATCGGTCGGAAAAC 57.317 32.000 0.14 0.00 0.00 2.43
3399 3451 4.517832 AGAACGGTCGGAAAATAGCTTTTT 59.482 37.500 0.00 0.00 34.73 1.94
3400 3452 4.070009 AGAACGGTCGGAAAATAGCTTTT 58.930 39.130 0.00 0.00 37.28 2.27
3402 3454 3.000727 CAGAACGGTCGGAAAATAGCTT 58.999 45.455 0.00 0.00 0.00 3.74
3403 3455 2.232941 TCAGAACGGTCGGAAAATAGCT 59.767 45.455 0.00 0.00 0.00 3.32
3404 3456 2.613691 TCAGAACGGTCGGAAAATAGC 58.386 47.619 0.00 0.00 0.00 2.97
3405 3457 4.683832 AGATCAGAACGGTCGGAAAATAG 58.316 43.478 7.55 0.00 31.40 1.73
3406 3458 4.730949 AGATCAGAACGGTCGGAAAATA 57.269 40.909 7.55 0.00 31.40 1.40
3407 3459 3.611766 AGATCAGAACGGTCGGAAAAT 57.388 42.857 7.55 0.00 31.40 1.82
3408 3460 3.396260 AAGATCAGAACGGTCGGAAAA 57.604 42.857 7.55 0.00 31.40 2.29
3409 3461 3.396260 AAAGATCAGAACGGTCGGAAA 57.604 42.857 7.55 0.00 31.40 3.13
3410 3462 4.730949 ATAAAGATCAGAACGGTCGGAA 57.269 40.909 7.55 0.00 31.40 4.30
3411 3463 5.128205 TCTATAAAGATCAGAACGGTCGGA 58.872 41.667 5.58 5.58 32.22 4.55
3412 3464 5.434352 TCTATAAAGATCAGAACGGTCGG 57.566 43.478 0.00 0.00 0.00 4.79
3424 3476 5.047943 CCAGACCGTTCGGATCTATAAAGAT 60.048 44.000 18.28 0.00 45.46 2.40
3425 3477 4.277672 CCAGACCGTTCGGATCTATAAAGA 59.722 45.833 18.28 0.00 35.80 2.52
3426 3478 4.277672 TCCAGACCGTTCGGATCTATAAAG 59.722 45.833 18.28 5.16 0.00 1.85
3427 3479 4.209538 TCCAGACCGTTCGGATCTATAAA 58.790 43.478 18.28 1.99 0.00 1.40
3456 3508 0.044161 GACCGCACGATCGAAAATCG 60.044 55.000 24.34 15.52 46.02 3.34
3458 3510 1.278238 GAGACCGCACGATCGAAAAT 58.722 50.000 24.34 2.53 0.00 1.82
3480 3532 2.398588 TCAGAATTATGGGAGGCTCGT 58.601 47.619 8.69 0.00 0.00 4.18
3567 3648 7.005902 TGATCATGCCAATTAAGATATGGTGT 58.994 34.615 0.00 0.00 36.57 4.16
3569 3650 8.528643 CATTGATCATGCCAATTAAGATATGGT 58.471 33.333 0.00 0.00 36.57 3.55
3570 3651 7.979537 CCATTGATCATGCCAATTAAGATATGG 59.020 37.037 0.00 0.00 37.29 2.74
3583 3664 0.186873 AGGACCCCATTGATCATGCC 59.813 55.000 0.00 0.00 0.00 4.40
3591 3672 3.881220 ACACGTAATTAGGACCCCATTG 58.119 45.455 11.96 0.98 0.00 2.82
3650 3732 9.740239 TTCGTGTATCATAGGTGTAATTAACTC 57.260 33.333 0.00 0.00 0.00 3.01
3651 3733 9.525409 GTTCGTGTATCATAGGTGTAATTAACT 57.475 33.333 0.00 0.00 0.00 2.24
3652 3734 9.525409 AGTTCGTGTATCATAGGTGTAATTAAC 57.475 33.333 0.00 0.00 0.00 2.01
3654 3736 9.524106 CAAGTTCGTGTATCATAGGTGTAATTA 57.476 33.333 0.00 0.00 0.00 1.40
3655 3737 8.038944 ACAAGTTCGTGTATCATAGGTGTAATT 58.961 33.333 0.00 0.00 0.00 1.40
3656 3738 7.553334 ACAAGTTCGTGTATCATAGGTGTAAT 58.447 34.615 0.00 0.00 0.00 1.89
3657 3739 6.927416 ACAAGTTCGTGTATCATAGGTGTAA 58.073 36.000 0.00 0.00 0.00 2.41
3658 3740 6.519679 ACAAGTTCGTGTATCATAGGTGTA 57.480 37.500 0.00 0.00 0.00 2.90
3659 3741 5.401531 ACAAGTTCGTGTATCATAGGTGT 57.598 39.130 0.00 0.00 0.00 4.16
3660 3742 5.454554 CGTACAAGTTCGTGTATCATAGGTG 59.545 44.000 2.48 0.00 36.42 4.00
3661 3743 5.449588 CCGTACAAGTTCGTGTATCATAGGT 60.450 44.000 2.48 0.00 36.42 3.08
3662 3744 4.974275 CCGTACAAGTTCGTGTATCATAGG 59.026 45.833 2.48 0.07 36.42 2.57
3663 3745 5.454554 CACCGTACAAGTTCGTGTATCATAG 59.545 44.000 2.48 0.00 36.42 2.23
3664 3746 5.106197 ACACCGTACAAGTTCGTGTATCATA 60.106 40.000 2.48 0.00 36.42 2.15
3665 3747 4.171005 CACCGTACAAGTTCGTGTATCAT 58.829 43.478 2.48 0.00 36.42 2.45
3666 3748 3.004629 ACACCGTACAAGTTCGTGTATCA 59.995 43.478 2.48 0.00 36.42 2.15
3667 3749 3.362831 CACACCGTACAAGTTCGTGTATC 59.637 47.826 2.48 0.00 36.42 2.24
3668 3750 3.243501 ACACACCGTACAAGTTCGTGTAT 60.244 43.478 7.13 0.00 36.42 2.29
3669 3751 2.098934 ACACACCGTACAAGTTCGTGTA 59.901 45.455 7.13 0.00 34.55 2.90
3670 3752 1.135024 ACACACCGTACAAGTTCGTGT 60.135 47.619 0.00 0.00 35.43 4.49
3671 3753 1.563111 ACACACCGTACAAGTTCGTG 58.437 50.000 0.00 0.00 0.00 4.35
3681 3763 6.704937 TGTTGTATGAATTTGTACACACCGTA 59.295 34.615 0.00 0.00 31.05 4.02
3682 3764 5.527951 TGTTGTATGAATTTGTACACACCGT 59.472 36.000 0.00 0.00 31.05 4.83
3683 3765 5.991568 TGTTGTATGAATTTGTACACACCG 58.008 37.500 0.00 0.00 31.05 4.94
3684 3766 7.422399 AGTTGTTGTATGAATTTGTACACACC 58.578 34.615 0.00 0.00 31.05 4.16
3685 3767 8.742188 CAAGTTGTTGTATGAATTTGTACACAC 58.258 33.333 0.00 6.52 31.05 3.82
3686 3768 7.433719 GCAAGTTGTTGTATGAATTTGTACACA 59.566 33.333 4.48 0.00 35.92 3.72
3687 3769 7.433719 TGCAAGTTGTTGTATGAATTTGTACAC 59.566 33.333 4.48 0.00 35.92 2.90
3688 3770 7.484140 TGCAAGTTGTTGTATGAATTTGTACA 58.516 30.769 4.48 0.00 35.92 2.90
3689 3771 7.922505 TGCAAGTTGTTGTATGAATTTGTAC 57.077 32.000 4.48 0.00 35.92 2.90
3690 3772 8.409371 TCTTGCAAGTTGTTGTATGAATTTGTA 58.591 29.630 25.19 0.00 35.92 2.41
3691 3773 7.264221 TCTTGCAAGTTGTTGTATGAATTTGT 58.736 30.769 25.19 0.00 35.92 2.83
3692 3774 7.697352 TCTTGCAAGTTGTTGTATGAATTTG 57.303 32.000 25.19 0.00 35.92 2.32
3693 3775 8.143193 TCATCTTGCAAGTTGTTGTATGAATTT 58.857 29.630 28.17 0.00 36.49 1.82
3694 3776 7.596248 GTCATCTTGCAAGTTGTTGTATGAATT 59.404 33.333 28.17 0.00 36.49 2.17
3695 3777 7.086376 GTCATCTTGCAAGTTGTTGTATGAAT 58.914 34.615 28.17 9.53 36.49 2.57
3696 3778 6.039159 TGTCATCTTGCAAGTTGTTGTATGAA 59.961 34.615 28.17 15.18 36.49 2.57
3697 3779 5.530543 TGTCATCTTGCAAGTTGTTGTATGA 59.469 36.000 28.17 22.35 37.03 2.15
3698 3780 5.626543 GTGTCATCTTGCAAGTTGTTGTATG 59.373 40.000 28.17 20.83 35.92 2.39
3699 3781 5.299028 TGTGTCATCTTGCAAGTTGTTGTAT 59.701 36.000 28.17 11.87 35.92 2.29
3700 3782 4.637977 TGTGTCATCTTGCAAGTTGTTGTA 59.362 37.500 28.17 12.97 35.92 2.41
3701 3783 3.443329 TGTGTCATCTTGCAAGTTGTTGT 59.557 39.130 28.17 8.71 35.92 3.32
3702 3784 4.031418 TGTGTCATCTTGCAAGTTGTTG 57.969 40.909 28.17 19.92 36.67 3.33
3703 3785 4.717233 TTGTGTCATCTTGCAAGTTGTT 57.283 36.364 28.17 11.35 0.00 2.83
3704 3786 4.717233 TTTGTGTCATCTTGCAAGTTGT 57.283 36.364 28.17 14.32 0.00 3.32
3705 3787 5.749588 TCAATTTGTGTCATCTTGCAAGTTG 59.250 36.000 25.26 25.26 38.79 3.16
3706 3788 5.904941 TCAATTTGTGTCATCTTGCAAGTT 58.095 33.333 25.19 15.14 0.00 2.66
3707 3789 5.518848 TCAATTTGTGTCATCTTGCAAGT 57.481 34.783 25.19 10.69 0.00 3.16
3708 3790 6.153756 TGATCAATTTGTGTCATCTTGCAAG 58.846 36.000 20.81 20.81 0.00 4.01
3709 3791 6.086785 TGATCAATTTGTGTCATCTTGCAA 57.913 33.333 0.00 0.00 0.00 4.08
3710 3792 5.708877 TGATCAATTTGTGTCATCTTGCA 57.291 34.783 0.00 0.00 0.00 4.08
3711 3793 9.955208 TTATATGATCAATTTGTGTCATCTTGC 57.045 29.630 17.19 0.00 33.13 4.01
3724 3806 8.840321 CCCGAAACTCAAGTTATATGATCAATT 58.160 33.333 0.00 0.00 37.25 2.32
3725 3807 7.445402 CCCCGAAACTCAAGTTATATGATCAAT 59.555 37.037 0.00 0.00 37.25 2.57
3726 3808 6.765989 CCCCGAAACTCAAGTTATATGATCAA 59.234 38.462 0.00 0.00 37.25 2.57
3727 3809 6.099125 TCCCCGAAACTCAAGTTATATGATCA 59.901 38.462 0.00 0.00 37.25 2.92
3728 3810 6.424207 GTCCCCGAAACTCAAGTTATATGATC 59.576 42.308 0.00 0.00 37.25 2.92
3729 3811 6.126883 TGTCCCCGAAACTCAAGTTATATGAT 60.127 38.462 0.00 0.00 37.25 2.45
3730 3812 5.188163 TGTCCCCGAAACTCAAGTTATATGA 59.812 40.000 0.00 0.00 37.25 2.15
3731 3813 5.424757 TGTCCCCGAAACTCAAGTTATATG 58.575 41.667 0.00 0.00 37.25 1.78
3732 3814 5.687166 TGTCCCCGAAACTCAAGTTATAT 57.313 39.130 0.00 0.00 37.25 0.86
3733 3815 5.687166 ATGTCCCCGAAACTCAAGTTATA 57.313 39.130 0.00 0.00 37.25 0.98
3734 3816 4.569719 ATGTCCCCGAAACTCAAGTTAT 57.430 40.909 0.00 0.00 37.25 1.89
3735 3817 4.360951 AATGTCCCCGAAACTCAAGTTA 57.639 40.909 0.00 0.00 37.25 2.24
3736 3818 2.951229 ATGTCCCCGAAACTCAAGTT 57.049 45.000 0.00 0.00 40.50 2.66
3737 3819 2.951229 AATGTCCCCGAAACTCAAGT 57.049 45.000 0.00 0.00 0.00 3.16
3738 3820 3.146066 TGAAATGTCCCCGAAACTCAAG 58.854 45.455 0.00 0.00 0.00 3.02
3739 3821 3.146066 CTGAAATGTCCCCGAAACTCAA 58.854 45.455 0.00 0.00 0.00 3.02
3740 3822 2.105821 ACTGAAATGTCCCCGAAACTCA 59.894 45.455 0.00 0.00 0.00 3.41
3741 3823 2.779506 ACTGAAATGTCCCCGAAACTC 58.220 47.619 0.00 0.00 0.00 3.01
3742 3824 2.951229 ACTGAAATGTCCCCGAAACT 57.049 45.000 0.00 0.00 0.00 2.66
3743 3825 3.404899 TGTACTGAAATGTCCCCGAAAC 58.595 45.455 0.00 0.00 0.00 2.78
3744 3826 3.773418 TGTACTGAAATGTCCCCGAAA 57.227 42.857 0.00 0.00 0.00 3.46
3745 3827 3.773418 TTGTACTGAAATGTCCCCGAA 57.227 42.857 0.00 0.00 0.00 4.30
3746 3828 3.992943 ATTGTACTGAAATGTCCCCGA 57.007 42.857 0.00 0.00 0.00 5.14
3747 3829 4.380444 CCAAATTGTACTGAAATGTCCCCG 60.380 45.833 0.00 0.00 0.00 5.73
3748 3830 4.526650 ACCAAATTGTACTGAAATGTCCCC 59.473 41.667 0.00 0.00 0.00 4.81
3749 3831 5.242838 TGACCAAATTGTACTGAAATGTCCC 59.757 40.000 0.00 0.00 0.00 4.46
3750 3832 6.016276 AGTGACCAAATTGTACTGAAATGTCC 60.016 38.462 0.00 0.00 0.00 4.02
3751 3833 6.970484 AGTGACCAAATTGTACTGAAATGTC 58.030 36.000 0.00 0.00 0.00 3.06
3752 3834 6.959639 AGTGACCAAATTGTACTGAAATGT 57.040 33.333 0.00 0.00 0.00 2.71
3753 3835 8.728088 GTAAGTGACCAAATTGTACTGAAATG 57.272 34.615 0.00 0.00 0.00 2.32
3769 3851 2.603953 GAGCACTAACGGTAAGTGACC 58.396 52.381 15.58 0.00 45.89 4.02
3770 3852 2.603953 GGAGCACTAACGGTAAGTGAC 58.396 52.381 15.58 9.41 45.89 3.67
3771 3853 1.200716 CGGAGCACTAACGGTAAGTGA 59.799 52.381 15.58 0.00 45.89 3.41
3772 3854 1.068055 ACGGAGCACTAACGGTAAGTG 60.068 52.381 9.05 9.05 45.80 3.16
3773 3855 1.251251 ACGGAGCACTAACGGTAAGT 58.749 50.000 0.00 0.00 0.00 2.24
3774 3856 2.358939 AACGGAGCACTAACGGTAAG 57.641 50.000 0.00 0.00 0.00 2.34
3775 3857 2.556189 TGTAACGGAGCACTAACGGTAA 59.444 45.455 0.00 0.00 30.97 2.85
3776 3858 2.158559 TGTAACGGAGCACTAACGGTA 58.841 47.619 0.00 0.00 0.00 4.02
3777 3859 0.961019 TGTAACGGAGCACTAACGGT 59.039 50.000 0.00 0.00 0.00 4.83
3778 3860 2.288961 ATGTAACGGAGCACTAACGG 57.711 50.000 0.00 0.00 0.00 4.44
3779 3861 2.278094 CGAATGTAACGGAGCACTAACG 59.722 50.000 0.00 0.00 0.00 3.18
3780 3862 3.248266 ACGAATGTAACGGAGCACTAAC 58.752 45.455 0.00 0.00 34.93 2.34
3781 3863 3.192001 AGACGAATGTAACGGAGCACTAA 59.808 43.478 0.00 0.00 34.93 2.24
3782 3864 2.751259 AGACGAATGTAACGGAGCACTA 59.249 45.455 0.00 0.00 34.93 2.74
3783 3865 1.544691 AGACGAATGTAACGGAGCACT 59.455 47.619 0.00 0.00 34.93 4.40
3784 3866 1.992170 AGACGAATGTAACGGAGCAC 58.008 50.000 0.00 0.00 34.93 4.40
3785 3867 2.488937 TGTAGACGAATGTAACGGAGCA 59.511 45.455 0.00 0.00 34.93 4.26
3786 3868 3.141002 TGTAGACGAATGTAACGGAGC 57.859 47.619 0.00 0.00 34.93 4.70
3787 3869 4.026804 GCAATGTAGACGAATGTAACGGAG 60.027 45.833 0.00 0.00 34.93 4.63
3788 3870 3.861113 GCAATGTAGACGAATGTAACGGA 59.139 43.478 0.00 0.00 34.93 4.69
3789 3871 3.615056 TGCAATGTAGACGAATGTAACGG 59.385 43.478 0.00 0.00 34.93 4.44
3790 3872 4.565229 GTGCAATGTAGACGAATGTAACG 58.435 43.478 0.00 0.00 0.00 3.18
3791 3873 4.565229 CGTGCAATGTAGACGAATGTAAC 58.435 43.478 0.00 0.00 35.05 2.50
3792 3874 3.061563 GCGTGCAATGTAGACGAATGTAA 59.938 43.478 0.00 0.00 35.05 2.41
3793 3875 2.601314 GCGTGCAATGTAGACGAATGTA 59.399 45.455 0.00 0.00 35.05 2.29
3794 3876 1.393539 GCGTGCAATGTAGACGAATGT 59.606 47.619 0.00 0.00 35.05 2.71
3795 3877 1.660607 AGCGTGCAATGTAGACGAATG 59.339 47.619 0.00 0.00 35.05 2.67
3796 3878 2.010145 AGCGTGCAATGTAGACGAAT 57.990 45.000 0.00 0.00 35.05 3.34
3797 3879 2.526077 CTAGCGTGCAATGTAGACGAA 58.474 47.619 0.00 0.00 35.05 3.85
3798 3880 1.797713 GCTAGCGTGCAATGTAGACGA 60.798 52.381 0.00 0.00 35.05 4.20
3799 3881 0.572590 GCTAGCGTGCAATGTAGACG 59.427 55.000 0.00 0.00 36.18 4.18
3800 3882 0.572590 CGCTAGCGTGCAATGTAGAC 59.427 55.000 28.66 0.00 34.35 2.59
3801 3883 2.957871 CGCTAGCGTGCAATGTAGA 58.042 52.632 28.66 0.00 34.35 2.59


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

AutoCloner maintained by Alex Coulton.