Multiple sequence alignment - TraesCS1A01G019800

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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 TraesCS1A01G019800 chr1A 100.000 4208 0 0 1 4208 9938053 9942260 0.000000e+00 7771
1 TraesCS1A01G019800 chr1A 89.421 1711 155 13 1741 3440 9856941 9858636 0.000000e+00 2134
2 TraesCS1A01G019800 chr1A 95.157 351 17 0 946 1296 9855866 9856216 4.750000e-154 555
3 TraesCS1A01G019800 chr1A 77.755 971 144 41 2273 3219 10005927 10005005 8.010000e-147 531
4 TraesCS1A01G019800 chr1A 99.194 124 1 0 1 124 9928057 9927934 1.520000e-54 224
5 TraesCS1A01G019800 chr1A 88.435 147 12 4 805 949 9855333 9855476 5.590000e-39 172
6 TraesCS1A01G019800 chr1A 97.561 82 2 0 1638 1719 9856788 9856869 1.580000e-29 141
7 TraesCS1A01G019800 chr1D 95.038 1713 51 5 1713 3411 8321551 8323243 0.000000e+00 2662
8 TraesCS1A01G019800 chr1D 90.154 1554 108 24 189 1719 8319993 8321524 0.000000e+00 1980
9 TraesCS1A01G019800 chr1D 95.122 328 16 0 3881 4208 8323644 8323971 6.240000e-143 518
10 TraesCS1A01G019800 chr1B 90.801 1261 63 16 28 1281 11216025 11217239 0.000000e+00 1637
11 TraesCS1A01G019800 chr1B 90.155 1097 75 13 1741 2833 11217574 11218641 0.000000e+00 1397
12 TraesCS1A01G019800 chr1B 83.181 547 63 20 2903 3440 11218679 11219205 1.370000e-129 473
13 TraesCS1A01G019800 chr1B 82.322 379 57 8 926 1297 29263115 29263490 1.890000e-83 320
14 TraesCS1A01G019800 chr3B 81.429 1050 122 33 1788 2800 4518795 4519808 0.000000e+00 791
15 TraesCS1A01G019800 chr3B 89.310 290 27 3 991 1276 4513255 4513544 1.110000e-95 361


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 TraesCS1A01G019800 chr1A 9938053 9942260 4207 False 7771.0 7771 100.000000 1 4208 1 chr1A.!!$F1 4207
1 TraesCS1A01G019800 chr1A 9855333 9858636 3303 False 750.5 2134 92.643500 805 3440 4 chr1A.!!$F2 2635
2 TraesCS1A01G019800 chr1A 10005005 10005927 922 True 531.0 531 77.755000 2273 3219 1 chr1A.!!$R2 946
3 TraesCS1A01G019800 chr1D 8319993 8323971 3978 False 1720.0 2662 93.438000 189 4208 3 chr1D.!!$F1 4019
4 TraesCS1A01G019800 chr1B 11216025 11219205 3180 False 1169.0 1637 88.045667 28 3440 3 chr1B.!!$F2 3412
5 TraesCS1A01G019800 chr3B 4518795 4519808 1013 False 791.0 791 81.429000 1788 2800 1 chr3B.!!$F2 1012

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
562 580 0.036732 TGAAGATTTGGCCAGCGAGT 59.963 50.000 5.11 0.00 0.00 4.18 F
796 818 0.654472 GCAAAGACTCAACACGCGTG 60.654 55.000 35.99 35.99 0.00 5.34 F
1437 2107 0.937304 CAGACATATTTCGGCCCACG 59.063 55.000 0.00 0.00 46.11 4.94 F
2561 3339 1.202417 ACACAACTCACTCACACCTCG 60.202 52.381 0.00 0.00 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2561 3339 0.179163 GCCTGTAACAATGAAGCGGC 60.179 55.000 0.0 0.0 0.0 6.53 R
2852 3631 4.581824 ACCACTCCATGCACATATCATTTC 59.418 41.667 0.0 0.0 0.0 2.17 R
3152 3942 1.899814 TCTCTTGTATTGCCACTCCGT 59.100 47.619 0.0 0.0 0.0 4.69 R
3603 4434 0.195096 TCCCCCTACCCAGTTTCACT 59.805 55.000 0.0 0.0 0.0 3.41 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
160 161 3.228453 AGCTAGCGGCAGTAACCTATAA 58.772 45.455 9.55 0.00 44.79 0.98
167 168 4.630069 GCGGCAGTAACCTATAATACATGG 59.370 45.833 0.00 0.00 0.00 3.66
241 243 8.786898 TCAAAAGTTTGAACTGATGAAGATAGG 58.213 33.333 4.00 0.00 43.62 2.57
270 272 7.805071 GGCAATATATTTCAACATTTCTCCTCG 59.195 37.037 0.00 0.00 0.00 4.63
282 284 1.725641 TCTCCTCGCGTCTACGTTTA 58.274 50.000 5.77 0.00 42.22 2.01
283 285 1.394917 TCTCCTCGCGTCTACGTTTAC 59.605 52.381 5.77 0.00 42.22 2.01
308 310 2.095161 GTCCATAGACGTGGGATCGATC 60.095 54.545 17.36 17.36 39.80 3.69
322 324 3.243201 GGATCGATCAAGGCCACAAAATC 60.243 47.826 25.93 0.00 0.00 2.17
360 362 2.859165 TTGGCAGGGTCTTGAACTAG 57.141 50.000 0.00 0.00 0.00 2.57
470 485 5.621197 TGTTTCCATTTTGGTCTGATACG 57.379 39.130 0.00 0.00 39.03 3.06
487 502 5.849510 TGATACGGATCGGTAATGTGATTT 58.150 37.500 16.07 0.00 34.49 2.17
497 512 9.398170 GATCGGTAATGTGATTTCCAATAATTG 57.602 33.333 0.00 0.00 30.85 2.32
502 517 9.965824 GTAATGTGATTTCCAATAATTGTAGGG 57.034 33.333 0.00 0.00 0.00 3.53
503 518 8.837099 AATGTGATTTCCAATAATTGTAGGGA 57.163 30.769 0.00 0.00 0.00 4.20
504 519 7.880160 TGTGATTTCCAATAATTGTAGGGAG 57.120 36.000 0.00 0.00 0.00 4.30
505 520 6.833416 TGTGATTTCCAATAATTGTAGGGAGG 59.167 38.462 0.00 0.00 0.00 4.30
506 521 7.060421 GTGATTTCCAATAATTGTAGGGAGGA 58.940 38.462 0.00 0.00 0.00 3.71
507 522 7.559897 GTGATTTCCAATAATTGTAGGGAGGAA 59.440 37.037 0.00 0.00 32.51 3.36
508 523 7.779798 TGATTTCCAATAATTGTAGGGAGGAAG 59.220 37.037 0.00 0.00 35.55 3.46
509 524 5.646692 TCCAATAATTGTAGGGAGGAAGG 57.353 43.478 0.00 0.00 0.00 3.46
510 525 4.415512 TCCAATAATTGTAGGGAGGAAGGG 59.584 45.833 0.00 0.00 0.00 3.95
511 526 4.415512 CCAATAATTGTAGGGAGGAAGGGA 59.584 45.833 0.00 0.00 0.00 4.20
556 574 2.627699 GTTGTCCTTGAAGATTTGGCCA 59.372 45.455 0.00 0.00 0.00 5.36
558 576 1.203287 GTCCTTGAAGATTTGGCCAGC 59.797 52.381 5.11 0.00 0.00 4.85
562 580 0.036732 TGAAGATTTGGCCAGCGAGT 59.963 50.000 5.11 0.00 0.00 4.18
597 615 3.367910 GGGAGTCTGAACACACTGATCTC 60.368 52.174 0.00 0.00 0.00 2.75
738 759 3.752222 ACGTGTAAACCACAAAAGTCACA 59.248 39.130 0.00 0.00 44.78 3.58
796 818 0.654472 GCAAAGACTCAACACGCGTG 60.654 55.000 35.99 35.99 0.00 5.34
887 913 4.091939 GGCCACCAGGACCGTACC 62.092 72.222 0.00 0.00 36.69 3.34
888 914 3.315949 GCCACCAGGACCGTACCA 61.316 66.667 0.00 0.00 36.89 3.25
889 915 2.886134 GCCACCAGGACCGTACCAA 61.886 63.158 0.00 0.00 36.89 3.67
897 923 0.958382 GGACCGTACCAATGCTGCAA 60.958 55.000 6.36 0.00 0.00 4.08
935 963 6.619801 ACTATCTTCACTTTTTCGCAAGTT 57.380 33.333 0.00 0.00 34.60 2.66
976 1397 1.153549 CCGCAGCAGAGTAGTTCCC 60.154 63.158 0.00 0.00 0.00 3.97
993 1414 2.967076 CGCGGGCATTACATCGCT 60.967 61.111 0.00 0.00 45.11 4.93
1413 2083 6.839134 AGGGATATGGTAGGGTTCAAAATTTC 59.161 38.462 0.00 0.00 0.00 2.17
1437 2107 0.937304 CAGACATATTTCGGCCCACG 59.063 55.000 0.00 0.00 46.11 4.94
1462 2132 6.318648 GCCAAAATATCAGTCACTTCCACATA 59.681 38.462 0.00 0.00 0.00 2.29
1580 2260 8.879759 GTTCAAATTTTAGATCATGGACGACTA 58.120 33.333 0.00 0.00 0.00 2.59
1603 2283 5.975988 TGGTAGCAGGAGGAAGAAAATAT 57.024 39.130 0.00 0.00 0.00 1.28
2076 2808 1.299541 CGAAAAGTGTCAGCAGTGGT 58.700 50.000 0.00 0.00 0.00 4.16
2285 3026 3.074504 CATGTGTAATGCATGCAGGTC 57.925 47.619 26.69 17.36 37.50 3.85
2561 3339 1.202417 ACACAACTCACTCACACCTCG 60.202 52.381 0.00 0.00 0.00 4.63
2852 3631 6.599445 AGGAGGGATGTCTATTCATTCAAAG 58.401 40.000 0.00 0.00 0.00 2.77
2876 3655 2.921821 TGATATGTGCATGGAGTGGTG 58.078 47.619 0.00 0.00 0.00 4.17
2899 3678 2.491022 TTTTTGGGGGAACGTGCCG 61.491 57.895 6.46 0.00 0.00 5.69
2901 3680 2.700407 TTTTGGGGGAACGTGCCGAT 62.700 55.000 6.46 0.00 0.00 4.18
2906 3685 2.584143 GGAACGTGCCGATACCCG 60.584 66.667 0.00 0.00 38.18 5.28
3151 3941 4.754114 CAGAGGAAAGTCAAGTTCAAGGAG 59.246 45.833 0.00 0.00 0.00 3.69
3152 3942 4.656112 AGAGGAAAGTCAAGTTCAAGGAGA 59.344 41.667 0.00 0.00 0.00 3.71
3153 3943 4.709250 AGGAAAGTCAAGTTCAAGGAGAC 58.291 43.478 0.00 0.00 0.00 3.36
3154 3944 3.495001 GGAAAGTCAAGTTCAAGGAGACG 59.505 47.826 0.00 0.00 34.56 4.18
3155 3945 2.821991 AGTCAAGTTCAAGGAGACGG 57.178 50.000 0.00 0.00 34.56 4.79
3156 3946 2.317040 AGTCAAGTTCAAGGAGACGGA 58.683 47.619 0.00 0.00 34.56 4.69
3157 3947 2.297597 AGTCAAGTTCAAGGAGACGGAG 59.702 50.000 0.00 0.00 34.56 4.63
3241 4057 9.729023 CTAACACATGTTAAATTGACAAGACAA 57.271 29.630 0.00 0.00 39.70 3.18
3361 4192 9.119418 CCATGTTGATTTGGATACTAATACACA 57.881 33.333 0.00 0.30 42.20 3.72
3404 4235 6.812160 ACACTTCAACCGTCAATATAGAAGAC 59.188 38.462 0.00 0.00 36.00 3.01
3449 4280 9.898152 TGTACAAATAATGAATAGATGGTCACA 57.102 29.630 0.00 0.00 0.00 3.58
3459 4290 8.996651 TGAATAGATGGTCACAGTATTAGAGA 57.003 34.615 0.00 0.00 0.00 3.10
3460 4291 9.593565 TGAATAGATGGTCACAGTATTAGAGAT 57.406 33.333 0.00 0.00 0.00 2.75
3466 4297 9.988815 GATGGTCACAGTATTAGAGATTTATGT 57.011 33.333 0.00 0.00 0.00 2.29
3523 4354 9.695155 ATAAGCTTACCATTTTAGTTGGTATGT 57.305 29.630 8.70 2.72 46.36 2.29
3524 4355 8.417273 AAGCTTACCATTTTAGTTGGTATGTT 57.583 30.769 0.00 7.90 46.36 2.71
3525 4356 8.051901 AGCTTACCATTTTAGTTGGTATGTTC 57.948 34.615 13.84 3.15 46.36 3.18
3526 4357 7.122204 AGCTTACCATTTTAGTTGGTATGTTCC 59.878 37.037 13.84 2.65 46.36 3.62
3527 4358 7.122204 GCTTACCATTTTAGTTGGTATGTTCCT 59.878 37.037 13.84 0.00 46.36 3.36
3528 4359 8.943594 TTACCATTTTAGTTGGTATGTTCCTT 57.056 30.769 3.58 0.00 46.36 3.36
3529 4360 7.849322 ACCATTTTAGTTGGTATGTTCCTTT 57.151 32.000 0.00 0.00 45.62 3.11
3530 4361 7.666623 ACCATTTTAGTTGGTATGTTCCTTTG 58.333 34.615 0.00 0.00 45.62 2.77
3531 4362 7.289084 ACCATTTTAGTTGGTATGTTCCTTTGT 59.711 33.333 0.00 0.00 45.62 2.83
3532 4363 8.798402 CCATTTTAGTTGGTATGTTCCTTTGTA 58.202 33.333 0.00 0.00 0.00 2.41
3538 4369 8.964476 AGTTGGTATGTTCCTTTGTATAGATG 57.036 34.615 0.00 0.00 0.00 2.90
3539 4370 7.993183 AGTTGGTATGTTCCTTTGTATAGATGG 59.007 37.037 0.00 0.00 0.00 3.51
3540 4371 7.446106 TGGTATGTTCCTTTGTATAGATGGT 57.554 36.000 0.00 0.00 0.00 3.55
3541 4372 7.506114 TGGTATGTTCCTTTGTATAGATGGTC 58.494 38.462 0.00 0.00 0.00 4.02
3542 4373 7.126573 TGGTATGTTCCTTTGTATAGATGGTCA 59.873 37.037 0.00 0.00 0.00 4.02
3543 4374 7.441458 GGTATGTTCCTTTGTATAGATGGTCAC 59.559 40.741 0.00 0.00 0.00 3.67
3544 4375 6.367374 TGTTCCTTTGTATAGATGGTCACA 57.633 37.500 0.00 0.00 0.00 3.58
3545 4376 6.406370 TGTTCCTTTGTATAGATGGTCACAG 58.594 40.000 0.00 0.00 0.00 3.66
3546 4377 6.013725 TGTTCCTTTGTATAGATGGTCACAGT 60.014 38.462 0.00 0.00 0.00 3.55
3547 4378 7.179516 TGTTCCTTTGTATAGATGGTCACAGTA 59.820 37.037 0.00 0.00 0.00 2.74
3548 4379 7.914427 TCCTTTGTATAGATGGTCACAGTAT 57.086 36.000 0.00 0.00 0.00 2.12
3549 4380 8.319057 TCCTTTGTATAGATGGTCACAGTATT 57.681 34.615 0.00 0.00 0.00 1.89
3550 4381 8.204160 TCCTTTGTATAGATGGTCACAGTATTG 58.796 37.037 0.00 0.00 0.00 1.90
3551 4382 8.204160 CCTTTGTATAGATGGTCACAGTATTGA 58.796 37.037 0.00 0.00 0.00 2.57
3552 4383 9.599866 CTTTGTATAGATGGTCACAGTATTGAA 57.400 33.333 0.00 0.00 0.00 2.69
3554 4385 9.546428 TTGTATAGATGGTCACAGTATTGAATG 57.454 33.333 0.00 0.00 0.00 2.67
3555 4386 8.704668 TGTATAGATGGTCACAGTATTGAATGT 58.295 33.333 0.00 0.00 0.00 2.71
3556 4387 9.547753 GTATAGATGGTCACAGTATTGAATGTT 57.452 33.333 0.00 0.00 0.00 2.71
3558 4389 7.149569 AGATGGTCACAGTATTGAATGTTTG 57.850 36.000 0.00 0.00 0.00 2.93
3559 4390 6.942005 AGATGGTCACAGTATTGAATGTTTGA 59.058 34.615 0.00 0.00 0.00 2.69
3560 4391 6.312399 TGGTCACAGTATTGAATGTTTGAC 57.688 37.500 0.00 0.00 0.00 3.18
3561 4392 6.061441 TGGTCACAGTATTGAATGTTTGACT 58.939 36.000 7.91 0.00 0.00 3.41
3562 4393 7.220740 TGGTCACAGTATTGAATGTTTGACTA 58.779 34.615 7.91 1.74 0.00 2.59
3563 4394 7.717436 TGGTCACAGTATTGAATGTTTGACTAA 59.283 33.333 7.91 0.00 0.00 2.24
3564 4395 8.730680 GGTCACAGTATTGAATGTTTGACTAAT 58.269 33.333 7.91 0.00 0.00 1.73
3578 4409 8.749026 TGTTTGACTAATTTTAGGGTAACACA 57.251 30.769 2.63 0.00 35.08 3.72
3579 4410 8.842280 TGTTTGACTAATTTTAGGGTAACACAG 58.158 33.333 2.63 0.00 35.08 3.66
3580 4411 9.059260 GTTTGACTAATTTTAGGGTAACACAGA 57.941 33.333 2.63 0.00 35.08 3.41
3581 4412 9.629878 TTTGACTAATTTTAGGGTAACACAGAA 57.370 29.630 2.63 0.00 35.08 3.02
3582 4413 9.802039 TTGACTAATTTTAGGGTAACACAGAAT 57.198 29.630 2.63 0.00 35.08 2.40
3594 4425 9.374838 AGGGTAACACAGAATATAAAACTAACG 57.625 33.333 0.00 0.00 39.74 3.18
3595 4426 9.154847 GGGTAACACAGAATATAAAACTAACGT 57.845 33.333 0.00 0.00 39.74 3.99
3596 4427 9.962759 GGTAACACAGAATATAAAACTAACGTG 57.037 33.333 0.00 0.00 0.00 4.49
3600 4431 9.918630 ACACAGAATATAAAACTAACGTGTACT 57.081 29.630 0.00 0.00 32.49 2.73
3610 4441 7.920908 AAACTAACGTGTACTCTAGTGAAAC 57.079 36.000 0.00 0.00 0.00 2.78
3622 4453 2.781631 GTGAAACTGGGTAGGGGGA 58.218 57.895 0.00 0.00 0.00 4.81
3623 4454 0.618981 GTGAAACTGGGTAGGGGGAG 59.381 60.000 0.00 0.00 0.00 4.30
3624 4455 0.549169 TGAAACTGGGTAGGGGGAGG 60.549 60.000 0.00 0.00 0.00 4.30
3625 4456 0.549413 GAAACTGGGTAGGGGGAGGT 60.549 60.000 0.00 0.00 0.00 3.85
3626 4457 0.801574 AAACTGGGTAGGGGGAGGTA 59.198 55.000 0.00 0.00 0.00 3.08
3627 4458 0.801574 AACTGGGTAGGGGGAGGTAA 59.198 55.000 0.00 0.00 0.00 2.85
3628 4459 0.342313 ACTGGGTAGGGGGAGGTAAG 59.658 60.000 0.00 0.00 0.00 2.34
3629 4460 0.640495 CTGGGTAGGGGGAGGTAAGA 59.360 60.000 0.00 0.00 0.00 2.10
3630 4461 0.640495 TGGGTAGGGGGAGGTAAGAG 59.360 60.000 0.00 0.00 0.00 2.85
3631 4462 0.641048 GGGTAGGGGGAGGTAAGAGT 59.359 60.000 0.00 0.00 0.00 3.24
3632 4463 1.009306 GGGTAGGGGGAGGTAAGAGTT 59.991 57.143 0.00 0.00 0.00 3.01
3633 4464 2.563828 GGGTAGGGGGAGGTAAGAGTTT 60.564 54.545 0.00 0.00 0.00 2.66
3634 4465 2.770802 GGTAGGGGGAGGTAAGAGTTTC 59.229 54.545 0.00 0.00 0.00 2.78
3635 4466 3.568333 GGTAGGGGGAGGTAAGAGTTTCT 60.568 52.174 0.00 0.00 0.00 2.52
3636 4467 2.835389 AGGGGGAGGTAAGAGTTTCTC 58.165 52.381 0.00 0.00 0.00 2.87
3637 4468 2.387510 AGGGGGAGGTAAGAGTTTCTCT 59.612 50.000 0.00 0.00 43.37 3.10
3638 4469 2.767394 GGGGGAGGTAAGAGTTTCTCTC 59.233 54.545 0.00 0.00 40.28 3.20
3673 4504 8.814038 AAAAATAATGAGTCCTGAGTAAGCAT 57.186 30.769 0.00 0.00 0.00 3.79
3674 4505 7.798596 AAATAATGAGTCCTGAGTAAGCATG 57.201 36.000 0.00 0.00 0.00 4.06
3675 4506 6.737720 ATAATGAGTCCTGAGTAAGCATGA 57.262 37.500 0.00 0.00 0.00 3.07
3676 4507 5.426689 AATGAGTCCTGAGTAAGCATGAA 57.573 39.130 0.00 0.00 0.00 2.57
3677 4508 4.890158 TGAGTCCTGAGTAAGCATGAAA 57.110 40.909 0.00 0.00 0.00 2.69
3678 4509 5.227569 TGAGTCCTGAGTAAGCATGAAAA 57.772 39.130 0.00 0.00 0.00 2.29
3679 4510 5.620206 TGAGTCCTGAGTAAGCATGAAAAA 58.380 37.500 0.00 0.00 0.00 1.94
3680 4511 5.470098 TGAGTCCTGAGTAAGCATGAAAAAC 59.530 40.000 0.00 0.00 0.00 2.43
3681 4512 4.452455 AGTCCTGAGTAAGCATGAAAAACG 59.548 41.667 0.00 0.00 0.00 3.60
3682 4513 4.451096 GTCCTGAGTAAGCATGAAAAACGA 59.549 41.667 0.00 0.00 0.00 3.85
3683 4514 5.122396 GTCCTGAGTAAGCATGAAAAACGAT 59.878 40.000 0.00 0.00 0.00 3.73
3684 4515 5.122239 TCCTGAGTAAGCATGAAAAACGATG 59.878 40.000 0.00 0.00 0.00 3.84
3685 4516 5.106555 CCTGAGTAAGCATGAAAAACGATGT 60.107 40.000 0.00 0.00 0.00 3.06
3686 4517 6.312399 TGAGTAAGCATGAAAAACGATGTT 57.688 33.333 0.00 0.00 0.00 2.71
3687 4518 7.360861 CCTGAGTAAGCATGAAAAACGATGTTA 60.361 37.037 0.00 0.00 0.00 2.41
3688 4519 7.866729 TGAGTAAGCATGAAAAACGATGTTAA 58.133 30.769 0.00 0.00 0.00 2.01
3689 4520 8.346300 TGAGTAAGCATGAAAAACGATGTTAAA 58.654 29.630 0.00 0.00 0.00 1.52
3690 4521 9.341899 GAGTAAGCATGAAAAACGATGTTAAAT 57.658 29.630 0.00 0.00 0.00 1.40
3691 4522 9.128107 AGTAAGCATGAAAAACGATGTTAAATG 57.872 29.630 0.00 0.00 0.00 2.32
3692 4523 6.949578 AGCATGAAAAACGATGTTAAATGG 57.050 33.333 0.00 0.00 0.00 3.16
3693 4524 6.454795 AGCATGAAAAACGATGTTAAATGGT 58.545 32.000 0.00 0.00 0.00 3.55
3694 4525 6.586082 AGCATGAAAAACGATGTTAAATGGTC 59.414 34.615 0.00 0.00 0.00 4.02
3695 4526 6.586082 GCATGAAAAACGATGTTAAATGGTCT 59.414 34.615 0.00 0.00 0.00 3.85
3696 4527 7.116233 GCATGAAAAACGATGTTAAATGGTCTT 59.884 33.333 0.00 0.00 0.00 3.01
3697 4528 8.977505 CATGAAAAACGATGTTAAATGGTCTTT 58.022 29.630 0.00 0.00 0.00 2.52
3698 4529 8.934507 TGAAAAACGATGTTAAATGGTCTTTT 57.065 26.923 0.00 0.00 0.00 2.27
3699 4530 9.372369 TGAAAAACGATGTTAAATGGTCTTTTT 57.628 25.926 0.00 0.00 0.00 1.94
3762 4593 9.734620 TCTTGACAAAGAAGACATAAAATGTTG 57.265 29.630 0.00 0.00 40.57 3.33
3763 4594 9.734620 CTTGACAAAGAAGACATAAAATGTTGA 57.265 29.630 0.00 0.00 38.52 3.18
3765 4596 9.897744 TGACAAAGAAGACATAAAATGTTGATC 57.102 29.630 0.00 0.00 45.03 2.92
3766 4597 9.346725 GACAAAGAAGACATAAAATGTTGATCC 57.653 33.333 0.00 0.00 45.03 3.36
3767 4598 9.082313 ACAAAGAAGACATAAAATGTTGATCCT 57.918 29.630 0.00 0.00 45.03 3.24
3768 4599 9.350357 CAAAGAAGACATAAAATGTTGATCCTG 57.650 33.333 0.00 0.00 45.03 3.86
3769 4600 7.093322 AGAAGACATAAAATGTTGATCCTGC 57.907 36.000 0.00 0.00 45.03 4.85
3770 4601 6.888632 AGAAGACATAAAATGTTGATCCTGCT 59.111 34.615 0.00 0.00 45.03 4.24
3771 4602 6.446781 AGACATAAAATGTTGATCCTGCTG 57.553 37.500 0.00 0.00 45.03 4.41
3772 4603 6.182627 AGACATAAAATGTTGATCCTGCTGA 58.817 36.000 0.00 0.00 45.03 4.26
3773 4604 6.832384 AGACATAAAATGTTGATCCTGCTGAT 59.168 34.615 0.00 0.00 45.03 2.90
3774 4605 7.013083 AGACATAAAATGTTGATCCTGCTGATC 59.987 37.037 9.15 9.15 45.79 2.92
3786 4617 2.630158 CTGCTGATCAGGAACTTGAGG 58.370 52.381 23.89 3.99 39.15 3.86
3787 4618 1.280133 TGCTGATCAGGAACTTGAGGG 59.720 52.381 23.89 0.00 34.60 4.30
3788 4619 1.407989 GCTGATCAGGAACTTGAGGGG 60.408 57.143 23.89 0.00 34.60 4.79
3789 4620 2.191400 CTGATCAGGAACTTGAGGGGA 58.809 52.381 15.38 0.00 34.60 4.81
3790 4621 2.573462 CTGATCAGGAACTTGAGGGGAA 59.427 50.000 15.38 0.00 34.60 3.97
3791 4622 2.986019 TGATCAGGAACTTGAGGGGAAA 59.014 45.455 0.00 0.00 34.60 3.13
3792 4623 3.397618 TGATCAGGAACTTGAGGGGAAAA 59.602 43.478 0.00 0.00 34.60 2.29
3795 4626 4.151883 TCAGGAACTTGAGGGGAAAAATG 58.848 43.478 0.00 0.00 34.60 2.32
3796 4627 3.897505 CAGGAACTTGAGGGGAAAAATGT 59.102 43.478 0.00 0.00 34.60 2.71
3798 4629 5.538433 CAGGAACTTGAGGGGAAAAATGTTA 59.462 40.000 0.00 0.00 34.60 2.41
3800 4631 6.787458 AGGAACTTGAGGGGAAAAATGTTATT 59.213 34.615 0.00 0.00 27.25 1.40
3802 4633 7.936847 GGAACTTGAGGGGAAAAATGTTATTTT 59.063 33.333 0.00 0.00 35.29 1.82
3803 4634 9.337396 GAACTTGAGGGGAAAAATGTTATTTTT 57.663 29.630 10.94 10.94 32.85 1.94
3804 4635 8.902540 ACTTGAGGGGAAAAATGTTATTTTTC 57.097 30.769 22.29 22.29 43.78 2.29
3829 4660 9.453572 TCCATTCTTTATCACCAGATATAATGC 57.546 33.333 0.00 0.00 36.65 3.56
3830 4661 8.680903 CCATTCTTTATCACCAGATATAATGCC 58.319 37.037 0.00 0.00 36.65 4.40
3831 4662 9.234827 CATTCTTTATCACCAGATATAATGCCA 57.765 33.333 0.00 0.00 36.65 4.92
3832 4663 9.812347 ATTCTTTATCACCAGATATAATGCCAA 57.188 29.630 0.00 0.00 36.65 4.52
3833 4664 9.639563 TTCTTTATCACCAGATATAATGCCAAA 57.360 29.630 0.00 0.00 36.65 3.28
3834 4665 9.639563 TCTTTATCACCAGATATAATGCCAAAA 57.360 29.630 0.00 0.00 36.65 2.44
3850 4681 7.643569 ATGCCAAAATATTATCAGTGTCACA 57.356 32.000 5.62 0.00 0.00 3.58
3851 4682 7.087409 TGCCAAAATATTATCAGTGTCACAG 57.913 36.000 5.62 0.00 0.00 3.66
3852 4683 6.095300 TGCCAAAATATTATCAGTGTCACAGG 59.905 38.462 5.62 0.00 0.00 4.00
3853 4684 6.460123 GCCAAAATATTATCAGTGTCACAGGG 60.460 42.308 5.62 0.00 0.00 4.45
3854 4685 6.603201 CCAAAATATTATCAGTGTCACAGGGT 59.397 38.462 5.62 0.00 0.00 4.34
3855 4686 7.415541 CCAAAATATTATCAGTGTCACAGGGTG 60.416 40.741 5.62 0.00 34.45 4.61
3856 4687 2.472695 TTATCAGTGTCACAGGGTGC 57.527 50.000 5.62 0.00 32.98 5.01
3857 4688 1.347062 TATCAGTGTCACAGGGTGCA 58.653 50.000 5.62 0.00 32.98 4.57
3858 4689 0.473755 ATCAGTGTCACAGGGTGCAA 59.526 50.000 5.62 0.00 32.98 4.08
3859 4690 0.254462 TCAGTGTCACAGGGTGCAAA 59.746 50.000 5.62 0.00 32.98 3.68
3860 4691 1.102154 CAGTGTCACAGGGTGCAAAA 58.898 50.000 5.62 0.00 32.98 2.44
3861 4692 1.682854 CAGTGTCACAGGGTGCAAAAT 59.317 47.619 5.62 0.00 32.98 1.82
3862 4693 1.682854 AGTGTCACAGGGTGCAAAATG 59.317 47.619 5.62 0.00 32.98 2.32
3863 4694 1.408702 GTGTCACAGGGTGCAAAATGT 59.591 47.619 0.00 0.00 32.98 2.71
3864 4695 2.621055 GTGTCACAGGGTGCAAAATGTA 59.379 45.455 0.00 0.00 32.98 2.29
3865 4696 2.621055 TGTCACAGGGTGCAAAATGTAC 59.379 45.455 0.00 0.00 32.98 2.90
3897 4728 2.031870 GCCACCAAATTATCCTCCCAC 58.968 52.381 0.00 0.00 0.00 4.61
3899 4730 2.356741 CCACCAAATTATCCTCCCACGT 60.357 50.000 0.00 0.00 0.00 4.49
3914 4745 4.018490 TCCCACGTAGAATTAGCTGTACA 58.982 43.478 0.00 0.00 0.00 2.90
4076 4907 8.311836 TCGATGAACCTTCTCTTAGTTAACAAT 58.688 33.333 8.61 0.00 0.00 2.71
4081 4912 9.162764 GAACCTTCTCTTAGTTAACAATGCATA 57.837 33.333 8.61 0.00 0.00 3.14
4118 4949 2.910688 ACTTGTAGGGCCGACATATG 57.089 50.000 20.45 14.99 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 1.000359 CCCCATGTCTTGTTCCCCC 60.000 63.158 0.00 0.00 0.00 5.40
160 161 4.994852 GTGTTCATACCGTATGCCATGTAT 59.005 41.667 12.94 0.00 36.14 2.29
234 236 5.815581 TGAAATATATTGCCCGCCTATCTT 58.184 37.500 0.00 0.00 0.00 2.40
241 243 6.215845 AGAAATGTTGAAATATATTGCCCGC 58.784 36.000 0.00 0.00 0.00 6.13
270 272 2.095567 TGGACTGAGTAAACGTAGACGC 60.096 50.000 1.14 0.00 44.43 5.19
282 284 1.005569 TCCCACGTCTATGGACTGAGT 59.994 52.381 7.68 0.00 43.02 3.41
283 285 1.763968 TCCCACGTCTATGGACTGAG 58.236 55.000 7.68 0.48 43.02 3.35
304 306 3.012518 AGAGATTTTGTGGCCTTGATCG 58.987 45.455 3.32 0.00 0.00 3.69
334 336 2.364970 TCAAGACCCTGCCAAAACATTG 59.635 45.455 0.00 0.00 0.00 2.82
336 338 2.365293 GTTCAAGACCCTGCCAAAACAT 59.635 45.455 0.00 0.00 0.00 2.71
338 340 2.031870 AGTTCAAGACCCTGCCAAAAC 58.968 47.619 0.00 0.00 0.00 2.43
347 349 4.087907 AGGAGTACACTAGTTCAAGACCC 58.912 47.826 0.00 0.00 0.00 4.46
463 475 4.499037 TCACATTACCGATCCGTATCAG 57.501 45.455 0.00 0.00 31.93 2.90
464 476 5.462530 AATCACATTACCGATCCGTATCA 57.537 39.130 0.00 0.00 31.93 2.15
470 485 7.504924 TTATTGGAAATCACATTACCGATCC 57.495 36.000 0.00 0.00 0.00 3.36
487 502 4.415512 CCCTTCCTCCCTACAATTATTGGA 59.584 45.833 9.88 0.00 34.12 3.53
497 512 0.694783 CCCCTTCCCTTCCTCCCTAC 60.695 65.000 0.00 0.00 0.00 3.18
502 517 2.442262 ATATCCCCCTTCCCTTCCTC 57.558 55.000 0.00 0.00 0.00 3.71
503 518 2.940011 AATATCCCCCTTCCCTTCCT 57.060 50.000 0.00 0.00 0.00 3.36
504 519 5.162870 ACATTAAATATCCCCCTTCCCTTCC 60.163 44.000 0.00 0.00 0.00 3.46
505 520 5.965486 ACATTAAATATCCCCCTTCCCTTC 58.035 41.667 0.00 0.00 0.00 3.46
506 521 5.162870 GGACATTAAATATCCCCCTTCCCTT 60.163 44.000 0.00 0.00 0.00 3.95
507 522 4.357097 GGACATTAAATATCCCCCTTCCCT 59.643 45.833 0.00 0.00 0.00 4.20
508 523 4.107311 TGGACATTAAATATCCCCCTTCCC 59.893 45.833 1.70 0.00 0.00 3.97
509 524 5.333566 TGGACATTAAATATCCCCCTTCC 57.666 43.478 1.70 0.00 0.00 3.46
510 525 7.344612 ACTTTTGGACATTAAATATCCCCCTTC 59.655 37.037 1.70 0.00 0.00 3.46
511 526 7.196187 ACTTTTGGACATTAAATATCCCCCTT 58.804 34.615 1.70 0.00 0.00 3.95
556 574 2.166254 CCCAAAATGCCAATTACTCGCT 59.834 45.455 0.00 0.00 0.00 4.93
558 576 3.443681 ACTCCCAAAATGCCAATTACTCG 59.556 43.478 0.00 0.00 0.00 4.18
562 580 4.671831 TCAGACTCCCAAAATGCCAATTA 58.328 39.130 0.00 0.00 0.00 1.40
597 615 0.583438 CAGTTGAAGCAGGTGTGACG 59.417 55.000 0.00 0.00 0.00 4.35
755 776 1.659098 GCCTGAATTAGTCGTCCAACG 59.341 52.381 0.00 0.00 44.19 4.10
796 818 3.622612 GGTTAGTCGAGACTGGAGAGTAC 59.377 52.174 15.36 0.00 42.52 2.73
849 871 5.172205 GCCTATTTGTATGGAGCTAGTAGC 58.828 45.833 14.62 14.62 42.84 3.58
886 912 1.606224 GGTTCTGGTTTGCAGCATTGG 60.606 52.381 0.00 0.00 0.00 3.16
887 913 1.068895 TGGTTCTGGTTTGCAGCATTG 59.931 47.619 0.00 0.00 0.00 2.82
888 914 1.412079 TGGTTCTGGTTTGCAGCATT 58.588 45.000 0.00 0.00 0.00 3.56
889 915 1.069049 GTTGGTTCTGGTTTGCAGCAT 59.931 47.619 0.00 0.00 0.00 3.79
897 923 5.011329 TGAAGATAGTACGTTGGTTCTGGTT 59.989 40.000 0.00 0.00 0.00 3.67
935 963 2.070028 GTGTGTGTGTGTGTGTGTGTA 58.930 47.619 0.00 0.00 0.00 2.90
1023 1444 0.037697 TTGCTACTGCCACCACGTAG 60.038 55.000 0.00 0.00 38.71 3.51
1413 2083 4.024048 GTGGGCCGAAATATGTCTGTATTG 60.024 45.833 0.00 0.00 0.00 1.90
1437 2107 4.458989 TGTGGAAGTGACTGATATTTTGGC 59.541 41.667 0.00 0.00 0.00 4.52
1462 2132 8.708742 GCTTTAGCCAAAAATCGTCTAAATTTT 58.291 29.630 0.00 0.00 35.22 1.82
1465 2135 6.919721 TGCTTTAGCCAAAAATCGTCTAAAT 58.080 32.000 0.00 0.00 41.18 1.40
1557 2237 8.285394 CCATAGTCGTCCATGATCTAAAATTTG 58.715 37.037 0.00 0.00 0.00 2.32
1563 2243 5.183331 GCTACCATAGTCGTCCATGATCTAA 59.817 44.000 0.00 0.00 0.00 2.10
1580 2260 4.870021 ATTTTCTTCCTCCTGCTACCAT 57.130 40.909 0.00 0.00 0.00 3.55
1603 2283 4.287326 ACCACCCCTTTTTCTTTTCACAAA 59.713 37.500 0.00 0.00 0.00 2.83
1739 2471 5.125900 TCAAACTATGACCATGGATGCAAAG 59.874 40.000 21.47 10.07 31.50 2.77
2076 2808 0.690192 TTCCTTTGATCCACTCGGCA 59.310 50.000 0.00 0.00 0.00 5.69
2285 3026 5.828299 TTGGATATTCTTTAAGCAACGGG 57.172 39.130 0.00 0.00 0.00 5.28
2516 3291 3.930336 TCAGCCTCATCACTTTGTACAG 58.070 45.455 0.00 0.00 0.00 2.74
2561 3339 0.179163 GCCTGTAACAATGAAGCGGC 60.179 55.000 0.00 0.00 0.00 6.53
2852 3631 4.581824 ACCACTCCATGCACATATCATTTC 59.418 41.667 0.00 0.00 0.00 2.17
2899 3678 5.632244 TTTTCTTTGGCTTTACGGGTATC 57.368 39.130 0.00 0.00 0.00 2.24
2901 3680 6.149807 CAGTATTTTCTTTGGCTTTACGGGTA 59.850 38.462 0.00 0.00 0.00 3.69
2906 3685 6.914259 AGAGCAGTATTTTCTTTGGCTTTAC 58.086 36.000 0.00 0.00 0.00 2.01
3008 3788 9.545105 TGCAAAACAAAGAGTATTTTGATCATT 57.455 25.926 11.72 0.00 43.07 2.57
3123 3913 2.695585 ACTTGACTTTCCTCTGGGACT 58.304 47.619 0.00 0.00 42.05 3.85
3151 3941 2.094182 TCTCTTGTATTGCCACTCCGTC 60.094 50.000 0.00 0.00 0.00 4.79
3152 3942 1.899814 TCTCTTGTATTGCCACTCCGT 59.100 47.619 0.00 0.00 0.00 4.69
3153 3943 2.672961 TCTCTTGTATTGCCACTCCG 57.327 50.000 0.00 0.00 0.00 4.63
3154 3944 4.072131 TGTTTCTCTTGTATTGCCACTCC 58.928 43.478 0.00 0.00 0.00 3.85
3155 3945 4.377431 CGTGTTTCTCTTGTATTGCCACTC 60.377 45.833 0.00 0.00 0.00 3.51
3156 3946 3.498397 CGTGTTTCTCTTGTATTGCCACT 59.502 43.478 0.00 0.00 0.00 4.00
3157 3947 3.496884 TCGTGTTTCTCTTGTATTGCCAC 59.503 43.478 0.00 0.00 0.00 5.01
3158 3948 3.734463 TCGTGTTTCTCTTGTATTGCCA 58.266 40.909 0.00 0.00 0.00 4.92
3159 3949 4.451096 TCTTCGTGTTTCTCTTGTATTGCC 59.549 41.667 0.00 0.00 0.00 4.52
3160 3950 5.389935 CCTCTTCGTGTTTCTCTTGTATTGC 60.390 44.000 0.00 0.00 0.00 3.56
3161 3951 5.389935 GCCTCTTCGTGTTTCTCTTGTATTG 60.390 44.000 0.00 0.00 0.00 1.90
3162 3952 4.691216 GCCTCTTCGTGTTTCTCTTGTATT 59.309 41.667 0.00 0.00 0.00 1.89
3163 3953 4.246458 GCCTCTTCGTGTTTCTCTTGTAT 58.754 43.478 0.00 0.00 0.00 2.29
3164 3954 3.069016 TGCCTCTTCGTGTTTCTCTTGTA 59.931 43.478 0.00 0.00 0.00 2.41
3165 3955 2.158957 TGCCTCTTCGTGTTTCTCTTGT 60.159 45.455 0.00 0.00 0.00 3.16
3166 3956 2.478134 CTGCCTCTTCGTGTTTCTCTTG 59.522 50.000 0.00 0.00 0.00 3.02
3167 3957 2.365617 TCTGCCTCTTCGTGTTTCTCTT 59.634 45.455 0.00 0.00 0.00 2.85
3168 3958 1.964223 TCTGCCTCTTCGTGTTTCTCT 59.036 47.619 0.00 0.00 0.00 3.10
3169 3959 2.440539 TCTGCCTCTTCGTGTTTCTC 57.559 50.000 0.00 0.00 0.00 2.87
3170 3960 2.103263 AGTTCTGCCTCTTCGTGTTTCT 59.897 45.455 0.00 0.00 0.00 2.52
3361 4192 4.448210 AGTGTAACATTGAAGGTCGTGTT 58.552 39.130 0.00 0.00 41.43 3.32
3440 4271 9.988815 ACATAAATCTCTAATACTGTGACCATC 57.011 33.333 0.00 0.00 0.00 3.51
3506 4337 7.666623 ACAAAGGAACATACCAACTAAAATGG 58.333 34.615 0.00 0.00 43.84 3.16
3513 4344 7.993183 CCATCTATACAAAGGAACATACCAACT 59.007 37.037 0.00 0.00 0.00 3.16
3514 4345 7.773690 ACCATCTATACAAAGGAACATACCAAC 59.226 37.037 0.00 0.00 0.00 3.77
3515 4346 7.867921 ACCATCTATACAAAGGAACATACCAA 58.132 34.615 0.00 0.00 0.00 3.67
3516 4347 7.126573 TGACCATCTATACAAAGGAACATACCA 59.873 37.037 0.00 0.00 0.00 3.25
3517 4348 7.441458 GTGACCATCTATACAAAGGAACATACC 59.559 40.741 0.00 0.00 0.00 2.73
3518 4349 7.985184 TGTGACCATCTATACAAAGGAACATAC 59.015 37.037 0.00 0.00 0.00 2.39
3519 4350 8.084985 TGTGACCATCTATACAAAGGAACATA 57.915 34.615 0.00 0.00 0.00 2.29
3520 4351 6.957631 TGTGACCATCTATACAAAGGAACAT 58.042 36.000 0.00 0.00 0.00 2.71
3521 4352 6.013725 ACTGTGACCATCTATACAAAGGAACA 60.014 38.462 0.00 0.00 0.00 3.18
3522 4353 6.407202 ACTGTGACCATCTATACAAAGGAAC 58.593 40.000 0.00 0.00 0.00 3.62
3523 4354 6.620877 ACTGTGACCATCTATACAAAGGAA 57.379 37.500 0.00 0.00 0.00 3.36
3524 4355 7.914427 ATACTGTGACCATCTATACAAAGGA 57.086 36.000 0.00 0.00 0.00 3.36
3525 4356 8.204160 TCAATACTGTGACCATCTATACAAAGG 58.796 37.037 0.00 0.00 0.00 3.11
3526 4357 9.599866 TTCAATACTGTGACCATCTATACAAAG 57.400 33.333 0.00 0.00 0.00 2.77
3528 4359 9.546428 CATTCAATACTGTGACCATCTATACAA 57.454 33.333 0.00 0.00 0.00 2.41
3529 4360 8.704668 ACATTCAATACTGTGACCATCTATACA 58.295 33.333 0.00 0.00 0.00 2.29
3530 4361 9.547753 AACATTCAATACTGTGACCATCTATAC 57.452 33.333 0.00 0.00 0.00 1.47
3532 4363 8.896744 CAAACATTCAATACTGTGACCATCTAT 58.103 33.333 0.00 0.00 0.00 1.98
3533 4364 8.100164 TCAAACATTCAATACTGTGACCATCTA 58.900 33.333 0.00 0.00 0.00 1.98
3534 4365 6.942005 TCAAACATTCAATACTGTGACCATCT 59.058 34.615 0.00 0.00 0.00 2.90
3535 4366 7.023575 GTCAAACATTCAATACTGTGACCATC 58.976 38.462 0.00 0.00 0.00 3.51
3536 4367 6.716628 AGTCAAACATTCAATACTGTGACCAT 59.283 34.615 0.00 0.00 0.00 3.55
3537 4368 6.061441 AGTCAAACATTCAATACTGTGACCA 58.939 36.000 0.00 0.00 0.00 4.02
3538 4369 6.560253 AGTCAAACATTCAATACTGTGACC 57.440 37.500 0.00 0.00 0.00 4.02
3552 4383 9.357161 TGTGTTACCCTAAAATTAGTCAAACAT 57.643 29.630 11.36 0.00 31.90 2.71
3553 4384 8.749026 TGTGTTACCCTAAAATTAGTCAAACA 57.251 30.769 0.00 4.24 0.00 2.83
3554 4385 9.059260 TCTGTGTTACCCTAAAATTAGTCAAAC 57.941 33.333 0.00 2.16 0.00 2.93
3555 4386 9.629878 TTCTGTGTTACCCTAAAATTAGTCAAA 57.370 29.630 0.00 0.00 0.00 2.69
3556 4387 9.802039 ATTCTGTGTTACCCTAAAATTAGTCAA 57.198 29.630 0.00 0.00 0.00 3.18
3568 4399 9.374838 CGTTAGTTTTATATTCTGTGTTACCCT 57.625 33.333 0.00 0.00 0.00 4.34
3569 4400 9.154847 ACGTTAGTTTTATATTCTGTGTTACCC 57.845 33.333 0.00 0.00 0.00 3.69
3570 4401 9.962759 CACGTTAGTTTTATATTCTGTGTTACC 57.037 33.333 0.00 0.00 0.00 2.85
3574 4405 9.918630 AGTACACGTTAGTTTTATATTCTGTGT 57.081 29.630 0.00 0.00 39.78 3.72
3584 4415 9.450807 GTTTCACTAGAGTACACGTTAGTTTTA 57.549 33.333 0.00 0.00 0.00 1.52
3585 4416 8.193438 AGTTTCACTAGAGTACACGTTAGTTTT 58.807 33.333 0.00 0.00 0.00 2.43
3586 4417 7.646922 CAGTTTCACTAGAGTACACGTTAGTTT 59.353 37.037 0.00 0.00 0.00 2.66
3587 4418 7.137426 CAGTTTCACTAGAGTACACGTTAGTT 58.863 38.462 0.00 0.00 0.00 2.24
3588 4419 6.293845 CCAGTTTCACTAGAGTACACGTTAGT 60.294 42.308 0.00 0.00 0.00 2.24
3589 4420 6.084925 CCAGTTTCACTAGAGTACACGTTAG 58.915 44.000 0.00 0.00 0.00 2.34
3590 4421 5.048504 CCCAGTTTCACTAGAGTACACGTTA 60.049 44.000 0.00 0.00 0.00 3.18
3591 4422 4.261909 CCCAGTTTCACTAGAGTACACGTT 60.262 45.833 0.00 0.00 0.00 3.99
3592 4423 3.255149 CCCAGTTTCACTAGAGTACACGT 59.745 47.826 0.00 0.00 0.00 4.49
3593 4424 3.255149 ACCCAGTTTCACTAGAGTACACG 59.745 47.826 0.00 0.00 0.00 4.49
3594 4425 4.868314 ACCCAGTTTCACTAGAGTACAC 57.132 45.455 0.00 0.00 0.00 2.90
3595 4426 5.014858 CCTACCCAGTTTCACTAGAGTACA 58.985 45.833 0.00 0.00 0.00 2.90
3596 4427 4.401837 CCCTACCCAGTTTCACTAGAGTAC 59.598 50.000 0.00 0.00 0.00 2.73
3597 4428 4.571362 CCCCTACCCAGTTTCACTAGAGTA 60.571 50.000 0.00 0.00 0.00 2.59
3598 4429 3.442076 CCCTACCCAGTTTCACTAGAGT 58.558 50.000 0.00 0.00 0.00 3.24
3599 4430 2.766828 CCCCTACCCAGTTTCACTAGAG 59.233 54.545 0.00 0.00 0.00 2.43
3600 4431 2.561297 CCCCCTACCCAGTTTCACTAGA 60.561 54.545 0.00 0.00 0.00 2.43
3601 4432 1.838077 CCCCCTACCCAGTTTCACTAG 59.162 57.143 0.00 0.00 0.00 2.57
3602 4433 1.437945 TCCCCCTACCCAGTTTCACTA 59.562 52.381 0.00 0.00 0.00 2.74
3603 4434 0.195096 TCCCCCTACCCAGTTTCACT 59.805 55.000 0.00 0.00 0.00 3.41
3604 4435 0.618981 CTCCCCCTACCCAGTTTCAC 59.381 60.000 0.00 0.00 0.00 3.18
3605 4436 0.549169 CCTCCCCCTACCCAGTTTCA 60.549 60.000 0.00 0.00 0.00 2.69
3606 4437 0.549413 ACCTCCCCCTACCCAGTTTC 60.549 60.000 0.00 0.00 0.00 2.78
3607 4438 0.801574 TACCTCCCCCTACCCAGTTT 59.198 55.000 0.00 0.00 0.00 2.66
3608 4439 0.801574 TTACCTCCCCCTACCCAGTT 59.198 55.000 0.00 0.00 0.00 3.16
3609 4440 0.342313 CTTACCTCCCCCTACCCAGT 59.658 60.000 0.00 0.00 0.00 4.00
3610 4441 0.640495 TCTTACCTCCCCCTACCCAG 59.360 60.000 0.00 0.00 0.00 4.45
3611 4442 0.640495 CTCTTACCTCCCCCTACCCA 59.360 60.000 0.00 0.00 0.00 4.51
3612 4443 0.641048 ACTCTTACCTCCCCCTACCC 59.359 60.000 0.00 0.00 0.00 3.69
3613 4444 2.564872 AACTCTTACCTCCCCCTACC 57.435 55.000 0.00 0.00 0.00 3.18
3614 4445 3.705579 GAGAAACTCTTACCTCCCCCTAC 59.294 52.174 0.00 0.00 0.00 3.18
3615 4446 3.601537 AGAGAAACTCTTACCTCCCCCTA 59.398 47.826 0.00 0.00 37.60 3.53
3616 4447 2.387510 AGAGAAACTCTTACCTCCCCCT 59.612 50.000 0.00 0.00 37.60 4.79
3617 4448 2.767394 GAGAGAAACTCTTACCTCCCCC 59.233 54.545 2.80 0.00 41.35 5.40
3648 4479 8.680903 CATGCTTACTCAGGACTCATTATTTTT 58.319 33.333 0.00 0.00 0.00 1.94
3649 4480 8.049117 TCATGCTTACTCAGGACTCATTATTTT 58.951 33.333 0.00 0.00 0.00 1.82
3650 4481 7.568349 TCATGCTTACTCAGGACTCATTATTT 58.432 34.615 0.00 0.00 0.00 1.40
3651 4482 7.129457 TCATGCTTACTCAGGACTCATTATT 57.871 36.000 0.00 0.00 0.00 1.40
3652 4483 6.737720 TCATGCTTACTCAGGACTCATTAT 57.262 37.500 0.00 0.00 0.00 1.28
3653 4484 6.544928 TTCATGCTTACTCAGGACTCATTA 57.455 37.500 0.00 0.00 0.00 1.90
3654 4485 5.426689 TTCATGCTTACTCAGGACTCATT 57.573 39.130 0.00 0.00 0.00 2.57
3655 4486 5.426689 TTTCATGCTTACTCAGGACTCAT 57.573 39.130 0.00 0.00 0.00 2.90
3656 4487 4.890158 TTTCATGCTTACTCAGGACTCA 57.110 40.909 0.00 0.00 0.00 3.41
3657 4488 5.389935 CGTTTTTCATGCTTACTCAGGACTC 60.390 44.000 0.00 0.00 0.00 3.36
3658 4489 4.452455 CGTTTTTCATGCTTACTCAGGACT 59.548 41.667 0.00 0.00 0.00 3.85
3659 4490 4.451096 TCGTTTTTCATGCTTACTCAGGAC 59.549 41.667 0.00 0.00 0.00 3.85
3660 4491 4.637276 TCGTTTTTCATGCTTACTCAGGA 58.363 39.130 0.00 0.00 0.00 3.86
3661 4492 5.106555 ACATCGTTTTTCATGCTTACTCAGG 60.107 40.000 0.00 0.00 0.00 3.86
3662 4493 5.931532 ACATCGTTTTTCATGCTTACTCAG 58.068 37.500 0.00 0.00 0.00 3.35
3663 4494 5.940192 ACATCGTTTTTCATGCTTACTCA 57.060 34.783 0.00 0.00 0.00 3.41
3664 4495 8.722342 TTTAACATCGTTTTTCATGCTTACTC 57.278 30.769 0.00 0.00 0.00 2.59
3665 4496 9.128107 CATTTAACATCGTTTTTCATGCTTACT 57.872 29.630 0.00 0.00 0.00 2.24
3666 4497 8.372521 CCATTTAACATCGTTTTTCATGCTTAC 58.627 33.333 0.00 0.00 0.00 2.34
3667 4498 8.085296 ACCATTTAACATCGTTTTTCATGCTTA 58.915 29.630 0.00 0.00 0.00 3.09
3668 4499 6.928492 ACCATTTAACATCGTTTTTCATGCTT 59.072 30.769 0.00 0.00 0.00 3.91
3669 4500 6.454795 ACCATTTAACATCGTTTTTCATGCT 58.545 32.000 0.00 0.00 0.00 3.79
3670 4501 6.586082 AGACCATTTAACATCGTTTTTCATGC 59.414 34.615 0.00 0.00 0.00 4.06
3671 4502 8.519492 AAGACCATTTAACATCGTTTTTCATG 57.481 30.769 0.00 0.00 0.00 3.07
3672 4503 9.541143 AAAAGACCATTTAACATCGTTTTTCAT 57.459 25.926 0.00 0.00 0.00 2.57
3673 4504 8.934507 AAAAGACCATTTAACATCGTTTTTCA 57.065 26.923 0.00 0.00 0.00 2.69
3736 4567 9.734620 CAACATTTTATGTCTTCTTTGTCAAGA 57.265 29.630 0.00 0.00 44.07 3.02
3737 4568 9.734620 TCAACATTTTATGTCTTCTTTGTCAAG 57.265 29.630 0.00 0.00 44.07 3.02
3739 4570 9.897744 GATCAACATTTTATGTCTTCTTTGTCA 57.102 29.630 0.00 0.00 44.07 3.58
3740 4571 9.346725 GGATCAACATTTTATGTCTTCTTTGTC 57.653 33.333 0.00 0.00 44.07 3.18
3741 4572 9.082313 AGGATCAACATTTTATGTCTTCTTTGT 57.918 29.630 0.00 0.00 44.07 2.83
3742 4573 9.350357 CAGGATCAACATTTTATGTCTTCTTTG 57.650 33.333 0.00 0.00 44.07 2.77
3743 4574 8.031277 GCAGGATCAACATTTTATGTCTTCTTT 58.969 33.333 0.00 0.00 44.07 2.52
3744 4575 7.395489 AGCAGGATCAACATTTTATGTCTTCTT 59.605 33.333 0.00 0.00 44.07 2.52
3745 4576 6.888632 AGCAGGATCAACATTTTATGTCTTCT 59.111 34.615 0.00 0.00 44.07 2.85
3746 4577 6.971184 CAGCAGGATCAACATTTTATGTCTTC 59.029 38.462 0.00 0.00 44.07 2.87
3747 4578 6.660521 TCAGCAGGATCAACATTTTATGTCTT 59.339 34.615 0.00 0.00 44.07 3.01
3748 4579 6.182627 TCAGCAGGATCAACATTTTATGTCT 58.817 36.000 0.00 0.00 44.07 3.41
3749 4580 6.441093 TCAGCAGGATCAACATTTTATGTC 57.559 37.500 0.00 0.00 44.07 3.06
3766 4597 2.630158 CCTCAAGTTCCTGATCAGCAG 58.370 52.381 17.76 4.89 44.49 4.24
3767 4598 1.280133 CCCTCAAGTTCCTGATCAGCA 59.720 52.381 17.76 0.00 0.00 4.41
3768 4599 1.407989 CCCCTCAAGTTCCTGATCAGC 60.408 57.143 17.76 3.91 0.00 4.26
3769 4600 2.191400 TCCCCTCAAGTTCCTGATCAG 58.809 52.381 16.24 16.24 0.00 2.90
3770 4601 2.342406 TCCCCTCAAGTTCCTGATCA 57.658 50.000 0.00 0.00 0.00 2.92
3771 4602 3.721087 TTTCCCCTCAAGTTCCTGATC 57.279 47.619 0.00 0.00 0.00 2.92
3772 4603 4.469469 TTTTTCCCCTCAAGTTCCTGAT 57.531 40.909 0.00 0.00 0.00 2.90
3773 4604 3.963476 TTTTTCCCCTCAAGTTCCTGA 57.037 42.857 0.00 0.00 0.00 3.86
3774 4605 3.897505 ACATTTTTCCCCTCAAGTTCCTG 59.102 43.478 0.00 0.00 0.00 3.86
3775 4606 4.199002 ACATTTTTCCCCTCAAGTTCCT 57.801 40.909 0.00 0.00 0.00 3.36
3776 4607 4.955811 AACATTTTTCCCCTCAAGTTCC 57.044 40.909 0.00 0.00 0.00 3.62
3777 4608 8.902540 AAAATAACATTTTTCCCCTCAAGTTC 57.097 30.769 0.00 0.00 0.00 3.01
3778 4609 9.337396 GAAAAATAACATTTTTCCCCTCAAGTT 57.663 29.630 19.43 0.00 40.58 2.66
3779 4610 8.902540 GAAAAATAACATTTTTCCCCTCAAGT 57.097 30.769 19.43 0.00 40.58 3.16
3803 4634 9.453572 GCATTATATCTGGTGATAAAGAATGGA 57.546 33.333 13.87 0.00 38.50 3.41
3804 4635 8.680903 GGCATTATATCTGGTGATAAAGAATGG 58.319 37.037 13.87 0.00 38.50 3.16
3808 4639 9.639563 TTTTGGCATTATATCTGGTGATAAAGA 57.360 29.630 0.00 0.00 38.50 2.52
3824 4655 9.183368 TGTGACACTGATAATATTTTGGCATTA 57.817 29.630 7.20 0.00 0.00 1.90
3825 4656 8.065473 TGTGACACTGATAATATTTTGGCATT 57.935 30.769 7.20 0.00 0.00 3.56
3826 4657 7.201848 CCTGTGACACTGATAATATTTTGGCAT 60.202 37.037 13.56 0.00 0.00 4.40
3827 4658 6.095300 CCTGTGACACTGATAATATTTTGGCA 59.905 38.462 13.56 0.00 0.00 4.92
3828 4659 6.460123 CCCTGTGACACTGATAATATTTTGGC 60.460 42.308 13.56 0.00 0.00 4.52
3829 4660 6.603201 ACCCTGTGACACTGATAATATTTTGG 59.397 38.462 13.56 5.12 0.00 3.28
3830 4661 7.475015 CACCCTGTGACACTGATAATATTTTG 58.525 38.462 13.56 0.00 35.23 2.44
3831 4662 6.095440 GCACCCTGTGACACTGATAATATTTT 59.905 38.462 13.56 0.00 35.23 1.82
3832 4663 5.590259 GCACCCTGTGACACTGATAATATTT 59.410 40.000 13.56 0.00 35.23 1.40
3833 4664 5.126067 GCACCCTGTGACACTGATAATATT 58.874 41.667 13.56 0.00 35.23 1.28
3834 4665 4.164030 TGCACCCTGTGACACTGATAATAT 59.836 41.667 13.56 0.00 35.23 1.28
3835 4666 3.517500 TGCACCCTGTGACACTGATAATA 59.482 43.478 13.56 0.00 35.23 0.98
3836 4667 2.305635 TGCACCCTGTGACACTGATAAT 59.694 45.455 13.56 0.00 35.23 1.28
3837 4668 1.696884 TGCACCCTGTGACACTGATAA 59.303 47.619 13.56 0.00 35.23 1.75
3838 4669 1.347062 TGCACCCTGTGACACTGATA 58.653 50.000 13.56 0.00 35.23 2.15
3839 4670 0.473755 TTGCACCCTGTGACACTGAT 59.526 50.000 13.56 0.00 35.23 2.90
3840 4671 0.254462 TTTGCACCCTGTGACACTGA 59.746 50.000 13.56 0.00 35.23 3.41
3841 4672 1.102154 TTTTGCACCCTGTGACACTG 58.898 50.000 7.20 6.31 35.23 3.66
3842 4673 1.682854 CATTTTGCACCCTGTGACACT 59.317 47.619 7.20 0.00 35.23 3.55
3843 4674 1.408702 ACATTTTGCACCCTGTGACAC 59.591 47.619 0.00 0.00 35.23 3.67
3844 4675 1.774110 ACATTTTGCACCCTGTGACA 58.226 45.000 0.00 0.00 35.23 3.58
3845 4676 2.030274 GGTACATTTTGCACCCTGTGAC 60.030 50.000 0.00 0.00 35.23 3.67
3846 4677 2.235016 GGTACATTTTGCACCCTGTGA 58.765 47.619 0.00 0.00 35.23 3.58
3847 4678 1.959985 TGGTACATTTTGCACCCTGTG 59.040 47.619 0.00 0.00 32.75 3.66
3848 4679 1.960689 GTGGTACATTTTGCACCCTGT 59.039 47.619 0.00 0.00 44.52 4.00
3849 4680 1.959985 TGTGGTACATTTTGCACCCTG 59.040 47.619 0.00 0.00 44.52 4.45
3850 4681 2.373335 TGTGGTACATTTTGCACCCT 57.627 45.000 0.00 0.00 44.52 4.34
3851 4682 3.676291 ATTGTGGTACATTTTGCACCC 57.324 42.857 0.00 0.00 44.52 4.61
3852 4683 6.162777 ACATAATTGTGGTACATTTTGCACC 58.837 36.000 7.15 0.00 44.52 5.01
3867 4698 6.383726 AGGATAATTTGGTGGCACATAATTGT 59.616 34.615 26.21 22.54 44.52 2.71
3868 4699 6.819284 AGGATAATTTGGTGGCACATAATTG 58.181 36.000 26.21 0.00 44.52 2.32
3869 4700 6.041979 GGAGGATAATTTGGTGGCACATAATT 59.958 38.462 23.52 23.52 44.52 1.40
3870 4701 5.539955 GGAGGATAATTTGGTGGCACATAAT 59.460 40.000 20.82 14.43 44.52 1.28
3871 4702 4.892934 GGAGGATAATTTGGTGGCACATAA 59.107 41.667 20.82 12.71 44.52 1.90
3872 4703 4.469657 GGAGGATAATTTGGTGGCACATA 58.530 43.478 20.82 4.71 44.52 2.29
3873 4704 3.299503 GGAGGATAATTTGGTGGCACAT 58.700 45.455 20.82 2.41 44.52 3.21
3874 4705 2.622977 GGGAGGATAATTTGGTGGCACA 60.623 50.000 20.82 2.61 0.00 4.57
3875 4706 2.031870 GGGAGGATAATTTGGTGGCAC 58.968 52.381 9.70 9.70 0.00 5.01
3876 4707 1.643286 TGGGAGGATAATTTGGTGGCA 59.357 47.619 0.00 0.00 0.00 4.92
3877 4708 2.031870 GTGGGAGGATAATTTGGTGGC 58.968 52.381 0.00 0.00 0.00 5.01
3878 4709 2.297701 CGTGGGAGGATAATTTGGTGG 58.702 52.381 0.00 0.00 0.00 4.61
3879 4710 2.999331 ACGTGGGAGGATAATTTGGTG 58.001 47.619 0.00 0.00 0.00 4.17
3897 4728 7.757097 ATGAAGTTGTACAGCTAATTCTACG 57.243 36.000 13.01 0.00 30.57 3.51
3925 4756 4.398988 TGCCTCGATTGCACATTATTTTCT 59.601 37.500 5.73 0.00 32.85 2.52
4013 4844 5.949735 TGCTTCTGATTTTACGGGATTTTC 58.050 37.500 0.00 0.00 0.00 2.29
4076 4907 4.071961 ACAATGATCTAACGGCTATGCA 57.928 40.909 0.00 0.00 0.00 3.96
4081 4912 5.488341 ACAAGTTACAATGATCTAACGGCT 58.512 37.500 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.