Multiple sequence alignment - TraesCS2D01G230400

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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 TraesCS2D01G230400 chr2D 100.000 4474 0 0 1 4474 201091457 201095930 0.000000e+00 8263
1 TraesCS2D01G230400 chr2D 91.845 233 19 0 4242 4474 201112079 201112311 4.320000e-85 326
2 TraesCS2D01G230400 chr2B 93.473 3585 121 45 730 4222 377334414 377337977 0.000000e+00 5219
3 TraesCS2D01G230400 chr2B 87.972 715 81 4 1 711 377333649 377334362 0.000000e+00 839
4 TraesCS2D01G230400 chr2B 77.293 229 46 5 366 591 767689734 767689959 3.630000e-26 130
5 TraesCS2D01G230400 chr2A 94.466 3343 98 45 727 4014 222191369 222194679 0.000000e+00 5068
6 TraesCS2D01G230400 chr2A 96.104 77 2 1 4037 4113 222194893 222194968 1.690000e-24 124
7 TraesCS2D01G230400 chr5A 92.766 235 16 1 4241 4474 679412305 679412071 5.540000e-89 339
8 TraesCS2D01G230400 chr4B 91.915 235 16 3 4242 4474 619384352 619384585 4.320000e-85 326
9 TraesCS2D01G230400 chr4B 89.362 235 22 3 4242 4474 619390253 619390486 4.380000e-75 292
10 TraesCS2D01G230400 chr3D 91.139 237 20 1 4239 4474 271834309 271834545 2.010000e-83 320
11 TraesCS2D01G230400 chr3D 80.519 231 37 6 375 601 49042155 49042381 2.140000e-38 171
12 TraesCS2D01G230400 chr5B 91.064 235 17 4 4242 4474 683117742 683117974 9.340000e-82 315
13 TraesCS2D01G230400 chr5B 88.983 236 20 6 4242 4474 7945882 7945650 2.040000e-73 287
14 TraesCS2D01G230400 chr5B 79.556 225 33 6 373 590 478326484 478326702 1.000000e-31 148
15 TraesCS2D01G230400 chr3B 88.983 236 21 5 4242 4474 28268285 28268518 2.040000e-73 287
16 TraesCS2D01G230400 chr7A 88.889 234 23 3 4242 4474 431908344 431908575 7.320000e-73 285
17 TraesCS2D01G230400 chr4A 82.833 233 32 5 372 597 121480427 121480196 7.590000e-48 202
18 TraesCS2D01G230400 chr4A 80.531 226 39 4 372 594 642955660 642955437 7.700000e-38 169
19 TraesCS2D01G230400 chr6D 81.197 234 38 6 372 601 434464513 434464282 2.750000e-42 183
20 TraesCS2D01G230400 chr6A 78.733 221 43 3 381 598 37060501 37060720 1.300000e-30 145
21 TraesCS2D01G230400 chr7D 77.215 237 47 7 368 598 536515980 536516215 1.010000e-26 132


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 TraesCS2D01G230400 chr2D 201091457 201095930 4473 False 8263 8263 100.0000 1 4474 1 chr2D.!!$F1 4473
1 TraesCS2D01G230400 chr2B 377333649 377337977 4328 False 3029 5219 90.7225 1 4222 2 chr2B.!!$F2 4221
2 TraesCS2D01G230400 chr2A 222191369 222194968 3599 False 2596 5068 95.2850 727 4113 2 chr2A.!!$F1 3386

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
205 207 0.094730 GCGAACGTGCACTGAATACC 59.905 55.0 16.19 0.0 34.15 2.73 F
515 518 0.951558 GGCGTGACATCCAAAGTTGT 59.048 50.0 0.00 0.0 0.00 3.32 F
2307 2369 0.041982 AGTGGAAGGAGGAGGAGACC 59.958 60.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2013 0.173708 GTGCGGAAGGAGAAGACGAT 59.826 55.0 0.00 0.0 0.0 3.73 R
2382 2444 0.249120 CACGGGTAGCCAAGATGTCA 59.751 55.0 12.31 0.0 0.0 3.58 R
4259 4611 0.030909 TGGGCCTCCTCCGGTTATAA 60.031 55.0 4.53 0.0 0.0 0.98 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
59 60 7.373441 GCGAACATCTTTATGGTAAATTCTTCG 59.627 37.037 0.00 0.00 37.43 3.79
60 61 7.850982 CGAACATCTTTATGGTAAATTCTTCGG 59.149 37.037 0.00 0.00 37.43 4.30
63 64 6.920569 TCTTTATGGTAAATTCTTCGGAGC 57.079 37.500 0.00 0.00 0.00 4.70
96 97 9.382275 GGCAATTTTGACAACATAGGATATTTT 57.618 29.630 0.00 0.00 35.83 1.82
118 120 3.472652 TGTGAAATTACCGTGCTCACTT 58.527 40.909 5.93 0.00 37.79 3.16
123 125 5.066634 TGAAATTACCGTGCTCACTTGAAAA 59.933 36.000 0.00 0.00 0.00 2.29
138 140 3.311486 TGAAAATTTCGCCATGTTCCC 57.689 42.857 0.97 0.00 0.00 3.97
185 187 0.447406 CGTTTTGCCATGCATCTCGA 59.553 50.000 0.00 0.00 38.76 4.04
194 196 1.142185 ATGCATCTCGAGCGAACGTG 61.142 55.000 7.81 0.88 33.85 4.49
205 207 0.094730 GCGAACGTGCACTGAATACC 59.905 55.000 16.19 0.00 34.15 2.73
210 212 4.270084 CGAACGTGCACTGAATACCATTAT 59.730 41.667 16.19 0.00 0.00 1.28
260 262 6.422776 AGTATTTCAGTTATTGCACTTCGG 57.577 37.500 0.00 0.00 0.00 4.30
273 275 2.343101 CACTTCGGGTCTTGCGAATTA 58.657 47.619 0.00 0.00 0.00 1.40
276 278 1.717194 TCGGGTCTTGCGAATTACAC 58.283 50.000 0.00 0.00 0.00 2.90
288 290 7.967854 TCTTGCGAATTACACAAGGATTATTTG 59.032 33.333 12.23 0.00 40.90 2.32
326 328 3.241701 CATGTGCACCCGAAATTTACAC 58.758 45.455 15.69 0.00 0.00 2.90
330 332 2.034812 TGCACCCGAAATTTACACAACC 59.965 45.455 0.00 0.00 0.00 3.77
337 339 5.460748 CCCGAAATTTACACAACCTTTTGTC 59.539 40.000 0.00 0.00 44.57 3.18
340 342 6.469595 CGAAATTTACACAACCTTTTGTCGAA 59.530 34.615 0.00 0.00 44.57 3.71
343 345 8.710835 AATTTACACAACCTTTTGTCGAATTT 57.289 26.923 0.00 0.00 44.57 1.82
391 393 4.041075 TCTCAAATGGTAAGTGCCACACTA 59.959 41.667 0.00 0.00 44.62 2.74
394 396 5.012251 TCAAATGGTAAGTGCCACACTAGTA 59.988 40.000 0.00 0.00 44.62 1.82
418 420 1.363744 GAAGCAATCTGACCCTGACG 58.636 55.000 0.00 0.00 0.00 4.35
437 439 8.911662 CCCTGACGATTTTTACAAATAAAGTTG 58.088 33.333 0.00 0.00 32.35 3.16
443 445 8.920665 CGATTTTTACAAATAAAGTTGCCATCA 58.079 29.630 0.00 0.00 32.35 3.07
446 448 4.806640 ACAAATAAAGTTGCCATCAGGG 57.193 40.909 0.00 0.00 40.85 4.45
447 449 3.515104 ACAAATAAAGTTGCCATCAGGGG 59.485 43.478 0.00 0.00 37.04 4.79
496 499 6.182039 TGCCATTCGAAAAGAAGTTATCAG 57.818 37.500 0.00 0.00 42.92 2.90
499 502 4.921470 TTCGAAAAGAAGTTATCAGGCG 57.079 40.909 0.00 0.00 34.26 5.52
515 518 0.951558 GGCGTGACATCCAAAGTTGT 59.048 50.000 0.00 0.00 0.00 3.32
525 528 1.071542 TCCAAAGTTGTCATCCTCGCA 59.928 47.619 0.00 0.00 0.00 5.10
529 532 2.996249 AGTTGTCATCCTCGCATCAT 57.004 45.000 0.00 0.00 0.00 2.45
534 537 5.824624 AGTTGTCATCCTCGCATCATTAAAT 59.175 36.000 0.00 0.00 0.00 1.40
537 540 7.800155 TGTCATCCTCGCATCATTAAATTTA 57.200 32.000 0.00 0.00 0.00 1.40
541 544 7.448161 TCATCCTCGCATCATTAAATTTACCAT 59.552 33.333 0.00 0.00 0.00 3.55
570 573 1.511850 TCAGAGTTGCCATGTGTTCG 58.488 50.000 0.00 0.00 0.00 3.95
670 673 9.175312 TGTAATAGTGAGTTTGTTTTGTGGTAA 57.825 29.630 0.00 0.00 0.00 2.85
671 674 9.442033 GTAATAGTGAGTTTGTTTTGTGGTAAC 57.558 33.333 0.00 0.00 0.00 2.50
711 716 5.503927 AGGTCATGCTACAGTGATTTTGAT 58.496 37.500 0.00 0.00 0.00 2.57
712 717 5.948162 AGGTCATGCTACAGTGATTTTGATT 59.052 36.000 0.00 0.00 0.00 2.57
716 721 8.430063 GTCATGCTACAGTGATTTTGATTTTTG 58.570 33.333 0.00 0.00 0.00 2.44
717 722 8.358895 TCATGCTACAGTGATTTTGATTTTTGA 58.641 29.630 0.00 0.00 0.00 2.69
718 723 8.644619 CATGCTACAGTGATTTTGATTTTTGAG 58.355 33.333 0.00 0.00 0.00 3.02
719 724 7.147312 TGCTACAGTGATTTTGATTTTTGAGG 58.853 34.615 0.00 0.00 0.00 3.86
720 725 6.587608 GCTACAGTGATTTTGATTTTTGAGGG 59.412 38.462 0.00 0.00 0.00 4.30
721 726 5.857268 ACAGTGATTTTGATTTTTGAGGGG 58.143 37.500 0.00 0.00 0.00 4.79
722 727 5.366477 ACAGTGATTTTGATTTTTGAGGGGT 59.634 36.000 0.00 0.00 0.00 4.95
724 729 7.070571 ACAGTGATTTTGATTTTTGAGGGGTAA 59.929 33.333 0.00 0.00 0.00 2.85
725 730 8.096414 CAGTGATTTTGATTTTTGAGGGGTAAT 58.904 33.333 0.00 0.00 0.00 1.89
726 731 8.659527 AGTGATTTTGATTTTTGAGGGGTAATT 58.340 29.630 0.00 0.00 0.00 1.40
728 733 9.936759 TGATTTTGATTTTTGAGGGGTAATTAC 57.063 29.630 7.09 7.09 0.00 1.89
730 735 9.719355 ATTTTGATTTTTGAGGGGTAATTACAC 57.281 29.630 17.16 13.61 0.00 2.90
731 736 8.485578 TTTGATTTTTGAGGGGTAATTACACT 57.514 30.769 17.19 13.66 0.00 3.55
833 872 2.286772 CGTGTTTCTTGTTTCTTCCCCG 60.287 50.000 0.00 0.00 0.00 5.73
1018 1080 2.862541 CAATGTCAGTTCAGGACCCAA 58.137 47.619 0.00 0.00 34.36 4.12
1743 1805 2.131709 CCCGGGATCGCTCCTTGTA 61.132 63.158 18.48 0.00 41.74 2.41
1951 2013 0.806884 GGTGTTCGACGTCCACAACA 60.807 55.000 20.54 17.76 0.00 3.33
1986 2048 3.946201 ACGCTCAAGGCAGCCAGT 61.946 61.111 15.80 0.00 41.91 4.00
2307 2369 0.041982 AGTGGAAGGAGGAGGAGACC 59.958 60.000 0.00 0.00 0.00 3.85
2382 2444 1.302832 CGAGTTCTTGCCCCTGCTT 60.303 57.895 0.00 0.00 38.71 3.91
2558 2621 3.405170 AACAACTTGCTCAGTTTCACG 57.595 42.857 0.00 0.00 43.89 4.35
2618 2681 5.772672 TGTAGCAATTTAACATGGTGAAGGT 59.227 36.000 0.00 0.00 0.00 3.50
2757 2837 4.270084 CAGTGAAAGCTCGACAGTTTGTAA 59.730 41.667 0.00 0.00 0.00 2.41
2869 2978 4.104831 AGTAAAGGGAGCAGTATCCTTGT 58.895 43.478 0.00 0.00 40.42 3.16
2887 2996 8.608844 ATCCTTGTACTAACACTTTCTGAAAG 57.391 34.615 24.58 24.58 44.10 2.62
2888 2997 6.482308 TCCTTGTACTAACACTTTCTGAAAGC 59.518 38.462 25.76 10.57 42.27 3.51
2890 2999 7.656137 CCTTGTACTAACACTTTCTGAAAGCTA 59.344 37.037 25.76 15.27 42.27 3.32
2891 3000 9.209175 CTTGTACTAACACTTTCTGAAAGCTAT 57.791 33.333 25.76 15.70 42.27 2.97
2892 3001 8.534333 TGTACTAACACTTTCTGAAAGCTATG 57.466 34.615 25.76 19.50 42.27 2.23
2893 3002 6.487689 ACTAACACTTTCTGAAAGCTATGC 57.512 37.500 25.76 0.00 42.27 3.14
2894 3003 5.997746 ACTAACACTTTCTGAAAGCTATGCA 59.002 36.000 25.76 10.47 42.27 3.96
2896 3005 5.557891 ACACTTTCTGAAAGCTATGCATC 57.442 39.130 25.76 0.00 42.27 3.91
2897 3006 5.005740 ACACTTTCTGAAAGCTATGCATCA 58.994 37.500 25.76 0.00 42.27 3.07
2899 3008 6.825213 ACACTTTCTGAAAGCTATGCATCATA 59.175 34.615 25.76 0.00 42.27 2.15
2900 3009 7.501559 ACACTTTCTGAAAGCTATGCATCATAT 59.498 33.333 25.76 3.19 42.27 1.78
2901 3010 8.350722 CACTTTCTGAAAGCTATGCATCATATT 58.649 33.333 25.76 2.79 42.27 1.28
2902 3011 8.350722 ACTTTCTGAAAGCTATGCATCATATTG 58.649 33.333 25.76 2.08 42.27 1.90
2903 3012 6.250344 TCTGAAAGCTATGCATCATATTGC 57.750 37.500 0.19 0.00 43.07 3.56
2970 3088 4.202202 TGGAAACACACATGGAATTGGTTC 60.202 41.667 0.00 2.70 35.34 3.62
2971 3089 4.202202 GGAAACACACATGGAATTGGTTCA 60.202 41.667 14.19 0.00 37.40 3.18
2974 3092 3.318839 ACACACATGGAATTGGTTCACTG 59.681 43.478 0.00 0.00 36.01 3.66
2985 3103 0.106519 GGTTCACTGCCCATAGCCAT 60.107 55.000 0.00 0.00 42.71 4.40
2987 3105 2.498167 GTTCACTGCCCATAGCCATAG 58.502 52.381 0.00 0.00 42.71 2.23
2988 3106 0.397941 TCACTGCCCATAGCCATAGC 59.602 55.000 0.00 0.00 42.71 2.97
2989 3107 0.607489 CACTGCCCATAGCCATAGCC 60.607 60.000 0.00 0.00 42.71 3.93
2990 3108 1.001641 CTGCCCATAGCCATAGCCC 60.002 63.158 0.00 0.00 42.71 5.19
2991 3109 1.773804 TGCCCATAGCCATAGCCCA 60.774 57.895 0.00 0.00 42.71 5.36
3031 3149 3.851458 ATGAGTTGGATGCAGCTATCA 57.149 42.857 2.99 0.00 0.00 2.15
3058 3176 2.093658 AGATGGCGTAATTCAGTTCGGT 60.094 45.455 0.00 0.00 0.00 4.69
3071 3193 1.204704 AGTTCGGTCATTGATGCTCGA 59.795 47.619 0.00 0.00 33.04 4.04
3115 3237 5.238214 GTGGATTCAGCTAATTCATGACTCC 59.762 44.000 12.97 12.97 41.03 3.85
3299 3421 1.751924 ACCCACAAGAGCTCGTATCTC 59.248 52.381 8.37 0.00 0.00 2.75
3565 3695 2.622064 AATTACCGAGCATCTGGGAC 57.378 50.000 1.86 0.00 33.49 4.46
3622 3756 0.889186 AAAGAACTGCGGCGATTGGT 60.889 50.000 12.98 0.00 0.00 3.67
3913 4072 3.509442 TCCCTGGAAAGCAAAATGATGT 58.491 40.909 0.00 0.00 0.00 3.06
3914 4073 3.903090 TCCCTGGAAAGCAAAATGATGTT 59.097 39.130 0.00 0.00 0.00 2.71
4126 4478 2.500098 TCCTTCCTTCCTGGTGAATACG 59.500 50.000 0.00 0.00 37.07 3.06
4152 4504 2.050077 GCACCGCAAGCCTGTTTC 60.050 61.111 0.00 0.00 0.00 2.78
4153 4505 2.844451 GCACCGCAAGCCTGTTTCA 61.844 57.895 0.00 0.00 0.00 2.69
4154 4506 1.283793 CACCGCAAGCCTGTTTCAG 59.716 57.895 0.00 0.00 0.00 3.02
4155 4507 2.256461 CCGCAAGCCTGTTTCAGC 59.744 61.111 0.00 0.00 0.00 4.26
4179 4531 6.494842 CAATGTACAAACGGGGAAATATCAG 58.505 40.000 0.00 0.00 0.00 2.90
4193 4545 3.520691 ATATCAGGTGCAATGCTCCAT 57.479 42.857 25.58 14.84 43.69 3.41
4211 4563 6.317140 TGCTCCATGCTCTAACTTTGATAAAG 59.683 38.462 0.05 0.05 42.42 1.85
4230 4582 9.844790 TGATAAAGCAGATTGTAATGTTTCAAG 57.155 29.630 0.00 0.00 0.00 3.02
4243 4595 3.145212 GTTTCAAGAAACCGCACTTGT 57.855 42.857 13.34 0.00 43.52 3.16
4244 4596 3.507786 GTTTCAAGAAACCGCACTTGTT 58.492 40.909 13.34 0.00 43.52 2.83
4245 4597 4.664188 GTTTCAAGAAACCGCACTTGTTA 58.336 39.130 13.34 0.00 43.52 2.41
4246 4598 5.278604 GTTTCAAGAAACCGCACTTGTTAT 58.721 37.500 13.34 0.00 43.52 1.89
4247 4599 4.481930 TCAAGAAACCGCACTTGTTATG 57.518 40.909 0.00 0.00 42.50 1.90
4248 4600 4.130857 TCAAGAAACCGCACTTGTTATGA 58.869 39.130 0.00 0.00 42.50 2.15
4249 4601 4.024387 TCAAGAAACCGCACTTGTTATGAC 60.024 41.667 0.00 0.00 42.50 3.06
4250 4602 2.812011 AGAAACCGCACTTGTTATGACC 59.188 45.455 0.00 0.00 0.00 4.02
4251 4603 1.153353 AACCGCACTTGTTATGACCG 58.847 50.000 0.00 0.00 0.00 4.79
4252 4604 0.672401 ACCGCACTTGTTATGACCGG 60.672 55.000 0.00 0.00 40.01 5.28
4253 4605 0.672401 CCGCACTTGTTATGACCGGT 60.672 55.000 6.92 6.92 0.00 5.28
4254 4606 1.153353 CGCACTTGTTATGACCGGTT 58.847 50.000 9.42 0.00 0.00 4.44
4255 4607 1.533731 CGCACTTGTTATGACCGGTTT 59.466 47.619 9.42 1.66 0.00 3.27
4256 4608 2.737783 CGCACTTGTTATGACCGGTTTA 59.262 45.455 9.42 0.66 0.00 2.01
4257 4609 3.181524 CGCACTTGTTATGACCGGTTTAG 60.182 47.826 9.42 1.31 0.00 1.85
4258 4610 3.425758 GCACTTGTTATGACCGGTTTAGC 60.426 47.826 9.42 6.98 0.00 3.09
4259 4611 4.000988 CACTTGTTATGACCGGTTTAGCT 58.999 43.478 9.42 0.00 0.00 3.32
4260 4612 4.454504 CACTTGTTATGACCGGTTTAGCTT 59.545 41.667 9.42 0.00 0.00 3.74
4261 4613 5.640357 CACTTGTTATGACCGGTTTAGCTTA 59.360 40.000 9.42 0.00 0.00 3.09
4262 4614 6.315393 CACTTGTTATGACCGGTTTAGCTTAT 59.685 38.462 9.42 0.00 0.00 1.73
4263 4615 7.493320 CACTTGTTATGACCGGTTTAGCTTATA 59.507 37.037 9.42 0.00 0.00 0.98
4264 4616 8.042515 ACTTGTTATGACCGGTTTAGCTTATAA 58.957 33.333 9.42 3.34 0.00 0.98
4265 4617 7.775397 TGTTATGACCGGTTTAGCTTATAAC 57.225 36.000 9.42 14.49 32.96 1.89
4266 4618 6.762661 TGTTATGACCGGTTTAGCTTATAACC 59.237 38.462 9.42 12.60 40.31 2.85
4285 4637 2.122989 GAGGAGGCCCACCGGATA 60.123 66.667 9.46 0.00 42.76 2.59
4286 4638 2.122813 AGGAGGCCCACCGGATAG 60.123 66.667 9.46 0.00 42.76 2.08
4287 4639 2.446036 GGAGGCCCACCGGATAGT 60.446 66.667 9.46 0.00 42.76 2.12
4288 4640 1.152398 GGAGGCCCACCGGATAGTA 60.152 63.158 9.46 0.00 42.76 1.82
4289 4641 1.186267 GGAGGCCCACCGGATAGTAG 61.186 65.000 9.46 0.00 42.76 2.57
4290 4642 0.469518 GAGGCCCACCGGATAGTAGT 60.470 60.000 9.46 0.00 42.76 2.73
4291 4643 0.031414 AGGCCCACCGGATAGTAGTT 60.031 55.000 9.46 0.00 42.76 2.24
4292 4644 1.218704 AGGCCCACCGGATAGTAGTTA 59.781 52.381 9.46 0.00 42.76 2.24
4293 4645 1.617357 GGCCCACCGGATAGTAGTTAG 59.383 57.143 9.46 0.00 0.00 2.34
4294 4646 2.590821 GCCCACCGGATAGTAGTTAGA 58.409 52.381 9.46 0.00 0.00 2.10
4295 4647 2.557490 GCCCACCGGATAGTAGTTAGAG 59.443 54.545 9.46 0.00 0.00 2.43
4296 4648 3.155501 CCCACCGGATAGTAGTTAGAGG 58.844 54.545 9.46 0.00 0.00 3.69
4297 4649 2.557490 CCACCGGATAGTAGTTAGAGGC 59.443 54.545 9.46 0.00 0.00 4.70
4298 4650 3.488363 CACCGGATAGTAGTTAGAGGCT 58.512 50.000 9.46 0.00 0.00 4.58
4299 4651 3.890147 CACCGGATAGTAGTTAGAGGCTT 59.110 47.826 9.46 0.00 0.00 4.35
4300 4652 3.890147 ACCGGATAGTAGTTAGAGGCTTG 59.110 47.826 9.46 0.00 0.00 4.01
4301 4653 3.256136 CCGGATAGTAGTTAGAGGCTTGG 59.744 52.174 0.00 0.00 0.00 3.61
4302 4654 3.305471 CGGATAGTAGTTAGAGGCTTGGC 60.305 52.174 0.00 0.00 0.00 4.52
4318 4670 6.272822 GGCTTGGCCCATAAATTATCTTAG 57.727 41.667 0.00 0.00 44.06 2.18
4319 4671 5.185828 GGCTTGGCCCATAAATTATCTTAGG 59.814 44.000 0.00 0.00 44.06 2.69
4320 4672 5.336770 GCTTGGCCCATAAATTATCTTAGGC 60.337 44.000 0.00 0.00 38.45 3.93
4321 4673 5.599048 TGGCCCATAAATTATCTTAGGCT 57.401 39.130 0.00 0.00 39.17 4.58
4322 4674 6.712114 TGGCCCATAAATTATCTTAGGCTA 57.288 37.500 0.00 0.00 39.17 3.93
4323 4675 7.284014 TGGCCCATAAATTATCTTAGGCTAT 57.716 36.000 0.00 0.00 39.17 2.97
4324 4676 7.708624 TGGCCCATAAATTATCTTAGGCTATT 58.291 34.615 0.00 0.00 39.17 1.73
4325 4677 7.834181 TGGCCCATAAATTATCTTAGGCTATTC 59.166 37.037 0.00 0.00 39.17 1.75
4326 4678 7.012421 GGCCCATAAATTATCTTAGGCTATTCG 59.988 40.741 0.00 0.00 39.17 3.34
4327 4679 7.553044 GCCCATAAATTATCTTAGGCTATTCGT 59.447 37.037 0.00 0.00 36.22 3.85
4328 4680 9.449719 CCCATAAATTATCTTAGGCTATTCGTT 57.550 33.333 0.00 0.00 0.00 3.85
4334 4686 8.608844 ATTATCTTAGGCTATTCGTTTTGAGG 57.391 34.615 0.00 0.00 0.00 3.86
4335 4687 5.416271 TCTTAGGCTATTCGTTTTGAGGT 57.584 39.130 0.00 0.00 0.00 3.85
4336 4688 5.801380 TCTTAGGCTATTCGTTTTGAGGTT 58.199 37.500 0.00 0.00 0.00 3.50
4337 4689 6.938507 TCTTAGGCTATTCGTTTTGAGGTTA 58.061 36.000 0.00 0.00 0.00 2.85
4338 4690 7.562135 TCTTAGGCTATTCGTTTTGAGGTTAT 58.438 34.615 0.00 0.00 0.00 1.89
4339 4691 8.698210 TCTTAGGCTATTCGTTTTGAGGTTATA 58.302 33.333 0.00 0.00 0.00 0.98
4340 4692 9.321562 CTTAGGCTATTCGTTTTGAGGTTATAA 57.678 33.333 0.00 0.00 0.00 0.98
4341 4693 9.669887 TTAGGCTATTCGTTTTGAGGTTATAAA 57.330 29.630 0.00 0.00 0.00 1.40
4342 4694 8.747538 AGGCTATTCGTTTTGAGGTTATAAAT 57.252 30.769 0.00 0.00 0.00 1.40
4343 4695 9.841295 AGGCTATTCGTTTTGAGGTTATAAATA 57.159 29.630 0.00 0.00 0.00 1.40
4344 4696 9.874215 GGCTATTCGTTTTGAGGTTATAAATAC 57.126 33.333 0.00 0.00 0.00 1.89
4350 4702 9.590451 TCGTTTTGAGGTTATAAATACTAGGTG 57.410 33.333 0.00 0.00 0.00 4.00
4351 4703 9.374838 CGTTTTGAGGTTATAAATACTAGGTGT 57.625 33.333 0.00 0.00 0.00 4.16
4373 4725 8.282124 GTGTAAAACACCTTTTGAGATTAAGC 57.718 34.615 0.00 0.00 43.05 3.09
4374 4726 7.918562 GTGTAAAACACCTTTTGAGATTAAGCA 59.081 33.333 0.00 0.00 43.05 3.91
4375 4727 8.470805 TGTAAAACACCTTTTGAGATTAAGCAA 58.529 29.630 0.00 0.00 31.74 3.91
4376 4728 9.476202 GTAAAACACCTTTTGAGATTAAGCAAT 57.524 29.630 0.00 0.00 31.74 3.56
4380 4732 9.696917 AACACCTTTTGAGATTAAGCAATAAAG 57.303 29.630 0.00 0.00 0.00 1.85
4381 4733 9.077885 ACACCTTTTGAGATTAAGCAATAAAGA 57.922 29.630 10.89 0.00 0.00 2.52
4404 4756 8.986929 AGATATTTATTATCCCTATTGCAGGC 57.013 34.615 0.00 0.00 43.98 4.85
4405 4757 8.785859 AGATATTTATTATCCCTATTGCAGGCT 58.214 33.333 0.00 0.00 43.98 4.58
4406 4758 8.986929 ATATTTATTATCCCTATTGCAGGCTC 57.013 34.615 0.00 0.00 43.98 4.70
4407 4759 3.728385 ATTATCCCTATTGCAGGCTCC 57.272 47.619 0.00 0.00 43.98 4.70
4408 4760 1.362224 TATCCCTATTGCAGGCTCCC 58.638 55.000 0.00 0.00 43.98 4.30
4409 4761 0.698886 ATCCCTATTGCAGGCTCCCA 60.699 55.000 0.00 0.00 43.98 4.37
4410 4762 1.150081 CCCTATTGCAGGCTCCCAG 59.850 63.158 0.00 0.00 43.98 4.45
4411 4763 1.348008 CCCTATTGCAGGCTCCCAGA 61.348 60.000 0.00 0.00 43.98 3.86
4412 4764 0.108207 CCTATTGCAGGCTCCCAGAG 59.892 60.000 0.00 0.00 37.70 3.35
4413 4765 0.108207 CTATTGCAGGCTCCCAGAGG 59.892 60.000 0.00 0.00 0.00 3.69
4414 4766 0.326522 TATTGCAGGCTCCCAGAGGA 60.327 55.000 0.00 0.00 41.08 3.71
4422 4774 4.436368 TCCCAGAGGAGTCGGAAC 57.564 61.111 0.00 0.00 37.19 3.62
4423 4775 1.305046 TCCCAGAGGAGTCGGAACC 60.305 63.158 0.00 0.00 37.19 3.62
4424 4776 2.359967 CCCAGAGGAGTCGGAACCC 61.360 68.421 0.00 0.00 33.47 4.11
4425 4777 1.305381 CCAGAGGAGTCGGAACCCT 60.305 63.158 0.00 0.00 0.00 4.34
4426 4778 1.608717 CCAGAGGAGTCGGAACCCTG 61.609 65.000 4.40 8.32 0.00 4.45
4427 4779 1.305381 AGAGGAGTCGGAACCCTGG 60.305 63.158 4.40 0.00 0.00 4.45
4428 4780 3.003763 AGGAGTCGGAACCCTGGC 61.004 66.667 0.00 0.00 0.00 4.85
4429 4781 4.097361 GGAGTCGGAACCCTGGCC 62.097 72.222 0.00 0.00 0.00 5.36
4444 4796 4.858680 GCCGCCTCCAGCCCTAAC 62.859 72.222 0.00 0.00 38.78 2.34
4445 4797 4.176752 CCGCCTCCAGCCCTAACC 62.177 72.222 0.00 0.00 38.78 2.85
4446 4798 4.530857 CGCCTCCAGCCCTAACCG 62.531 72.222 0.00 0.00 38.78 4.44
4447 4799 4.858680 GCCTCCAGCCCTAACCGC 62.859 72.222 0.00 0.00 34.35 5.68
4448 4800 4.176752 CCTCCAGCCCTAACCGCC 62.177 72.222 0.00 0.00 0.00 6.13
4449 4801 4.530857 CTCCAGCCCTAACCGCCG 62.531 72.222 0.00 0.00 0.00 6.46
4471 4823 4.507916 CCTCCTCCTCCCTCGCGA 62.508 72.222 9.26 9.26 0.00 5.87
4472 4824 3.213402 CTCCTCCTCCCTCGCGAC 61.213 72.222 3.71 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.402968 CAAATGGCATCCCTCTCAACG 59.597 52.381 0.00 0.00 0.00 4.10
59 60 2.297033 TCAAAATTGCCAAGTCTGCTCC 59.703 45.455 0.00 0.00 0.00 4.70
60 61 3.243501 TGTCAAAATTGCCAAGTCTGCTC 60.244 43.478 0.00 0.00 0.00 4.26
63 64 4.431809 TGTTGTCAAAATTGCCAAGTCTG 58.568 39.130 0.00 0.00 0.00 3.51
96 97 3.472652 AGTGAGCACGGTAATTTCACAA 58.527 40.909 6.88 0.00 40.35 3.33
98 99 3.496884 TCAAGTGAGCACGGTAATTTCAC 59.503 43.478 0.00 0.00 38.68 3.18
106 108 3.548014 CGAAATTTTCAAGTGAGCACGGT 60.548 43.478 9.66 0.00 36.20 4.83
118 120 2.352225 CGGGAACATGGCGAAATTTTCA 60.352 45.455 9.66 0.00 0.00 2.69
123 125 1.247419 TTGCGGGAACATGGCGAAAT 61.247 50.000 0.00 0.00 0.00 2.17
161 163 1.325338 GATGCATGGCAAAACGAATGC 59.675 47.619 2.46 0.00 43.62 3.56
185 187 1.068474 GTATTCAGTGCACGTTCGCT 58.932 50.000 12.01 0.00 0.00 4.93
210 212 7.038154 GCATTAGTGCCCATTAAAGATACAA 57.962 36.000 0.00 0.00 45.76 2.41
249 251 1.577328 CGCAAGACCCGAAGTGCAAT 61.577 55.000 0.00 0.00 43.02 3.56
273 275 5.222130 ACCACTCTCCAAATAATCCTTGTGT 60.222 40.000 0.00 0.00 0.00 3.72
276 278 5.711976 ACAACCACTCTCCAAATAATCCTTG 59.288 40.000 0.00 0.00 0.00 3.61
288 290 2.289694 ACATGTGCTACAACCACTCTCC 60.290 50.000 0.00 0.00 34.38 3.71
313 315 5.353111 ACAAAAGGTTGTGTAAATTTCGGG 58.647 37.500 0.00 0.00 46.40 5.14
326 328 5.455525 GTGACTGAAATTCGACAAAAGGTTG 59.544 40.000 0.00 0.00 40.84 3.77
330 332 9.450807 AAAATAGTGACTGAAATTCGACAAAAG 57.549 29.630 0.00 0.00 0.00 2.27
372 374 4.367039 ACTAGTGTGGCACTTACCATTT 57.633 40.909 19.83 0.00 42.59 2.32
391 393 2.611518 GTCAGATTGCTTCGTGCTACT 58.388 47.619 5.00 0.00 43.37 2.57
394 396 0.674895 GGGTCAGATTGCTTCGTGCT 60.675 55.000 5.00 0.00 43.37 4.40
408 410 7.747155 TTATTTGTAAAAATCGTCAGGGTCA 57.253 32.000 0.00 0.00 0.00 4.02
410 412 8.173542 ACTTTATTTGTAAAAATCGTCAGGGT 57.826 30.769 0.00 0.00 0.00 4.34
411 413 8.911662 CAACTTTATTTGTAAAAATCGTCAGGG 58.088 33.333 0.00 0.00 0.00 4.45
452 454 4.094739 GCAAGTGCCAGTTTTCATTTTGTT 59.905 37.500 0.00 0.00 34.31 2.83
453 455 3.622612 GCAAGTGCCAGTTTTCATTTTGT 59.377 39.130 0.00 0.00 34.31 2.83
468 470 2.704725 TCTTTTCGAATGGCAAGTGC 57.295 45.000 0.00 0.00 41.14 4.40
496 499 0.951558 ACAACTTTGGATGTCACGCC 59.048 50.000 0.00 0.00 0.00 5.68
515 518 6.770303 TGGTAAATTTAATGATGCGAGGATGA 59.230 34.615 0.00 0.00 0.00 2.92
579 582 2.158871 TGAACCCTGGTAAGTGTCACAC 60.159 50.000 0.00 0.00 34.10 3.82
582 585 2.404559 ACTGAACCCTGGTAAGTGTCA 58.595 47.619 4.30 0.00 0.00 3.58
634 637 9.268268 ACAAACTCACTATTACAGATTTTCGAA 57.732 29.630 0.00 0.00 0.00 3.71
647 650 8.057536 TGTTACCACAAAACAAACTCACTATT 57.942 30.769 0.00 0.00 34.04 1.73
651 654 5.798434 GTCTGTTACCACAAAACAAACTCAC 59.202 40.000 0.00 0.00 36.46 3.51
686 691 6.108687 TCAAAATCACTGTAGCATGACCTAG 58.891 40.000 0.00 0.00 0.00 3.02
695 700 6.587608 CCCTCAAAAATCAAAATCACTGTAGC 59.412 38.462 0.00 0.00 0.00 3.58
701 706 8.846943 AATTACCCCTCAAAAATCAAAATCAC 57.153 30.769 0.00 0.00 0.00 3.06
711 716 6.488683 CAGTCAGTGTAATTACCCCTCAAAAA 59.511 38.462 13.01 0.00 0.00 1.94
712 717 6.001460 CAGTCAGTGTAATTACCCCTCAAAA 58.999 40.000 13.01 0.00 0.00 2.44
716 721 5.615925 ATCAGTCAGTGTAATTACCCCTC 57.384 43.478 13.01 1.91 0.00 4.30
717 722 5.487488 TCAATCAGTCAGTGTAATTACCCCT 59.513 40.000 13.01 6.16 0.00 4.79
718 723 5.741011 TCAATCAGTCAGTGTAATTACCCC 58.259 41.667 13.01 3.95 0.00 4.95
719 724 6.260936 CCATCAATCAGTCAGTGTAATTACCC 59.739 42.308 13.01 1.23 0.00 3.69
720 725 6.823689 ACCATCAATCAGTCAGTGTAATTACC 59.176 38.462 13.01 4.78 0.00 2.85
721 726 7.849804 ACCATCAATCAGTCAGTGTAATTAC 57.150 36.000 8.75 8.75 0.00 1.89
722 727 8.758829 ACTACCATCAATCAGTCAGTGTAATTA 58.241 33.333 0.00 0.00 0.00 1.40
724 729 7.187824 ACTACCATCAATCAGTCAGTGTAAT 57.812 36.000 0.00 0.00 0.00 1.89
725 730 6.605471 ACTACCATCAATCAGTCAGTGTAA 57.395 37.500 0.00 0.00 0.00 2.41
726 731 6.661805 TGTACTACCATCAATCAGTCAGTGTA 59.338 38.462 0.00 0.00 0.00 2.90
728 733 5.965922 TGTACTACCATCAATCAGTCAGTG 58.034 41.667 0.00 0.00 0.00 3.66
730 735 6.809869 TCATGTACTACCATCAATCAGTCAG 58.190 40.000 0.00 0.00 0.00 3.51
731 736 6.790232 TCATGTACTACCATCAATCAGTCA 57.210 37.500 0.00 0.00 0.00 3.41
927 976 2.125350 CTCTTCCTCGGCTGTGGC 60.125 66.667 8.86 0.00 37.82 5.01
1951 2013 0.173708 GTGCGGAAGGAGAAGACGAT 59.826 55.000 0.00 0.00 0.00 3.73
1986 2048 0.609151 TCAAATCCTTGCGACCGGTA 59.391 50.000 7.34 0.00 32.14 4.02
2286 2348 1.828595 GTCTCCTCCTCCTTCCACTTC 59.171 57.143 0.00 0.00 0.00 3.01
2382 2444 0.249120 CACGGGTAGCCAAGATGTCA 59.751 55.000 12.31 0.00 0.00 3.58
2424 2486 2.031012 TTGGTGGTGAGCAGCTCG 59.969 61.111 17.81 0.00 32.35 5.03
2460 2522 2.696707 ACTGAACGTTACCTTCACAGGA 59.303 45.455 0.00 0.00 44.19 3.86
2558 2621 3.791245 TCTTGTCAAATTTGCACAACCC 58.209 40.909 21.75 5.26 30.68 4.11
2618 2681 5.581126 AACTTCTGAGTGTTGAAATTGCA 57.419 34.783 0.00 0.00 35.91 4.08
2757 2837 9.247861 AGCATCTGAACTTATAAATTGTTTCCT 57.752 29.630 0.00 0.00 0.00 3.36
2869 2978 7.158697 TGCATAGCTTTCAGAAAGTGTTAGTA 58.841 34.615 21.61 7.65 40.64 1.82
2892 3001 7.519843 CATAGTCTTCAGAAGCAATATGATGC 58.480 38.462 16.79 0.00 46.78 3.91
2893 3002 7.172703 TGCATAGTCTTCAGAAGCAATATGATG 59.827 37.037 21.56 12.88 0.00 3.07
2894 3003 7.222161 TGCATAGTCTTCAGAAGCAATATGAT 58.778 34.615 21.56 4.25 0.00 2.45
2896 3005 6.856135 TGCATAGTCTTCAGAAGCAATATG 57.144 37.500 17.13 17.13 0.00 1.78
2897 3006 7.222161 TGATGCATAGTCTTCAGAAGCAATAT 58.778 34.615 0.00 1.84 33.91 1.28
2899 3008 5.434408 TGATGCATAGTCTTCAGAAGCAAT 58.566 37.500 0.00 0.00 33.91 3.56
2900 3009 4.835678 TGATGCATAGTCTTCAGAAGCAA 58.164 39.130 0.00 0.00 33.91 3.91
2901 3010 4.476628 TGATGCATAGTCTTCAGAAGCA 57.523 40.909 0.00 0.01 34.78 3.91
2902 3011 7.519843 CAATATGATGCATAGTCTTCAGAAGC 58.480 38.462 0.00 1.15 29.42 3.86
2903 3012 7.519843 GCAATATGATGCATAGTCTTCAGAAG 58.480 38.462 0.00 3.45 45.70 2.85
2962 3080 2.102578 GCTATGGGCAGTGAACCAATT 58.897 47.619 10.54 0.00 40.73 2.32
2974 3092 1.001641 CTGGGCTATGGCTATGGGC 60.002 63.158 11.41 11.41 39.25 5.36
2985 3103 5.841267 TCTTATGAATAATGCCTGGGCTA 57.159 39.130 13.05 0.00 42.51 3.93
2987 3105 5.990120 ATTCTTATGAATAATGCCTGGGC 57.010 39.130 4.43 4.43 40.77 5.36
2988 3106 9.246670 TCATAATTCTTATGAATAATGCCTGGG 57.753 33.333 7.03 0.00 46.54 4.45
3031 3149 5.599999 ACTGAATTACGCCATCTCTAGTT 57.400 39.130 0.00 0.00 0.00 2.24
3058 3176 5.823209 AAATCACAATCGAGCATCAATGA 57.177 34.783 0.00 0.00 33.17 2.57
3071 3193 6.179756 TCCACACATAGCACTAAATCACAAT 58.820 36.000 0.00 0.00 0.00 2.71
3115 3237 0.998226 CGCAACCTGCATCAACAACG 60.998 55.000 0.00 0.00 45.36 4.10
3622 3756 3.507411 AGAGGTTCCACACTAGCTGTTA 58.493 45.455 0.00 0.00 0.00 2.41
3816 3954 3.995048 TCAAACACAACAGACGTACACAA 59.005 39.130 0.00 0.00 0.00 3.33
4103 4455 2.951229 TTCACCAGGAAGGAAGGAAC 57.049 50.000 0.00 0.00 41.22 3.62
4126 4478 1.912371 GCTTGCGGTGCCAACTCTAC 61.912 60.000 0.00 0.00 0.00 2.59
4146 4498 3.974401 CCGTTTGTACATTGCTGAAACAG 59.026 43.478 0.00 0.00 34.12 3.16
4147 4499 3.243234 CCCGTTTGTACATTGCTGAAACA 60.243 43.478 0.00 0.00 0.00 2.83
4148 4500 3.305110 CCCGTTTGTACATTGCTGAAAC 58.695 45.455 0.00 0.00 0.00 2.78
4149 4501 2.294791 CCCCGTTTGTACATTGCTGAAA 59.705 45.455 0.00 0.00 0.00 2.69
4150 4502 1.883275 CCCCGTTTGTACATTGCTGAA 59.117 47.619 0.00 0.00 0.00 3.02
4151 4503 1.072489 TCCCCGTTTGTACATTGCTGA 59.928 47.619 0.00 0.00 0.00 4.26
4152 4504 1.529226 TCCCCGTTTGTACATTGCTG 58.471 50.000 0.00 0.00 0.00 4.41
4153 4505 2.279935 TTCCCCGTTTGTACATTGCT 57.720 45.000 0.00 0.00 0.00 3.91
4154 4506 3.586100 ATTTCCCCGTTTGTACATTGC 57.414 42.857 0.00 0.00 0.00 3.56
4155 4507 6.443934 TGATATTTCCCCGTTTGTACATTG 57.556 37.500 0.00 0.00 0.00 2.82
4193 4545 7.391554 ACAATCTGCTTTATCAAAGTTAGAGCA 59.608 33.333 10.95 0.00 40.64 4.26
4211 4563 6.088085 CGGTTTCTTGAAACATTACAATCTGC 59.912 38.462 22.51 5.16 34.46 4.26
4222 4574 2.490115 ACAAGTGCGGTTTCTTGAAACA 59.510 40.909 22.51 5.07 42.22 2.83
4223 4575 3.145212 ACAAGTGCGGTTTCTTGAAAC 57.855 42.857 15.53 15.53 42.22 2.78
4224 4576 3.859411 AACAAGTGCGGTTTCTTGAAA 57.141 38.095 11.07 0.00 42.22 2.69
4225 4577 4.576873 TCATAACAAGTGCGGTTTCTTGAA 59.423 37.500 11.07 1.07 42.22 2.69
4226 4578 4.024387 GTCATAACAAGTGCGGTTTCTTGA 60.024 41.667 11.07 0.00 42.22 3.02
4227 4579 4.219033 GTCATAACAAGTGCGGTTTCTTG 58.781 43.478 0.00 0.00 44.29 3.02
4228 4580 3.252458 GGTCATAACAAGTGCGGTTTCTT 59.748 43.478 0.00 0.00 0.00 2.52
4229 4581 2.812011 GGTCATAACAAGTGCGGTTTCT 59.188 45.455 0.00 0.00 0.00 2.52
4230 4582 2.412325 CGGTCATAACAAGTGCGGTTTC 60.412 50.000 0.00 0.00 0.00 2.78
4231 4583 1.533731 CGGTCATAACAAGTGCGGTTT 59.466 47.619 0.00 0.00 0.00 3.27
4232 4584 1.153353 CGGTCATAACAAGTGCGGTT 58.847 50.000 0.00 0.00 0.00 4.44
4233 4585 0.672401 CCGGTCATAACAAGTGCGGT 60.672 55.000 0.00 0.00 0.00 5.68
4234 4586 0.672401 ACCGGTCATAACAAGTGCGG 60.672 55.000 0.00 0.00 0.00 5.69
4235 4587 1.153353 AACCGGTCATAACAAGTGCG 58.847 50.000 8.04 0.00 0.00 5.34
4236 4588 3.425758 GCTAAACCGGTCATAACAAGTGC 60.426 47.826 8.04 0.00 0.00 4.40
4237 4589 4.000988 AGCTAAACCGGTCATAACAAGTG 58.999 43.478 8.04 0.00 0.00 3.16
4238 4590 4.281898 AGCTAAACCGGTCATAACAAGT 57.718 40.909 8.04 0.00 0.00 3.16
4239 4591 6.920569 ATAAGCTAAACCGGTCATAACAAG 57.079 37.500 8.04 0.00 0.00 3.16
4240 4592 7.280652 GGTTATAAGCTAAACCGGTCATAACAA 59.719 37.037 8.04 0.00 36.12 2.83
4241 4593 6.762661 GGTTATAAGCTAAACCGGTCATAACA 59.237 38.462 8.04 0.00 36.12 2.41
4242 4594 7.182361 GGTTATAAGCTAAACCGGTCATAAC 57.818 40.000 8.04 12.33 36.12 1.89
4251 4603 4.502777 CCTCCTCCGGTTATAAGCTAAACC 60.503 50.000 12.54 13.14 41.48 3.27
4252 4604 4.629092 CCTCCTCCGGTTATAAGCTAAAC 58.371 47.826 12.54 0.00 0.00 2.01
4253 4605 3.070590 GCCTCCTCCGGTTATAAGCTAAA 59.929 47.826 12.54 0.00 0.00 1.85
4254 4606 2.631545 GCCTCCTCCGGTTATAAGCTAA 59.368 50.000 12.54 0.24 0.00 3.09
4255 4607 2.245582 GCCTCCTCCGGTTATAAGCTA 58.754 52.381 12.54 0.53 0.00 3.32
4256 4608 1.049402 GCCTCCTCCGGTTATAAGCT 58.951 55.000 12.54 0.00 0.00 3.74
4257 4609 0.035036 GGCCTCCTCCGGTTATAAGC 59.965 60.000 0.00 4.53 0.00 3.09
4258 4610 0.685660 GGGCCTCCTCCGGTTATAAG 59.314 60.000 0.84 0.00 0.00 1.73
4259 4611 0.030909 TGGGCCTCCTCCGGTTATAA 60.031 55.000 4.53 0.00 0.00 0.98
4260 4612 0.761702 GTGGGCCTCCTCCGGTTATA 60.762 60.000 4.53 0.00 0.00 0.98
4261 4613 2.070650 GTGGGCCTCCTCCGGTTAT 61.071 63.158 4.53 0.00 0.00 1.89
4262 4614 2.686106 GTGGGCCTCCTCCGGTTA 60.686 66.667 4.53 0.00 0.00 2.85
4267 4619 3.768833 TATCCGGTGGGCCTCCTCC 62.769 68.421 21.55 9.79 41.95 4.30
4268 4620 2.122989 TATCCGGTGGGCCTCCTC 60.123 66.667 21.55 1.90 0.00 3.71
4269 4621 1.661990 TACTATCCGGTGGGCCTCCT 61.662 60.000 21.55 6.59 0.00 3.69
4270 4622 1.152398 TACTATCCGGTGGGCCTCC 60.152 63.158 14.77 14.77 0.00 4.30
4271 4623 0.469518 ACTACTATCCGGTGGGCCTC 60.470 60.000 4.53 0.00 0.00 4.70
4272 4624 0.031414 AACTACTATCCGGTGGGCCT 60.031 55.000 4.53 0.00 0.00 5.19
4273 4625 1.617357 CTAACTACTATCCGGTGGGCC 59.383 57.143 0.00 0.00 0.00 5.80
4274 4626 2.557490 CTCTAACTACTATCCGGTGGGC 59.443 54.545 0.00 0.00 0.00 5.36
4275 4627 3.155501 CCTCTAACTACTATCCGGTGGG 58.844 54.545 0.00 0.00 0.00 4.61
4276 4628 2.557490 GCCTCTAACTACTATCCGGTGG 59.443 54.545 0.00 0.00 0.00 4.61
4277 4629 3.488363 AGCCTCTAACTACTATCCGGTG 58.512 50.000 0.00 0.00 0.00 4.94
4278 4630 3.880168 AGCCTCTAACTACTATCCGGT 57.120 47.619 0.00 0.00 0.00 5.28
4279 4631 3.256136 CCAAGCCTCTAACTACTATCCGG 59.744 52.174 0.00 0.00 0.00 5.14
4280 4632 3.305471 GCCAAGCCTCTAACTACTATCCG 60.305 52.174 0.00 0.00 0.00 4.18
4281 4633 3.007074 GGCCAAGCCTCTAACTACTATCC 59.993 52.174 0.00 0.00 46.69 2.59
4282 4634 4.260139 GGCCAAGCCTCTAACTACTATC 57.740 50.000 0.00 0.00 46.69 2.08
4296 4648 5.336770 GCCTAAGATAATTTATGGGCCAAGC 60.337 44.000 11.89 0.00 33.07 4.01
4297 4649 6.012745 AGCCTAAGATAATTTATGGGCCAAG 58.987 40.000 11.89 0.00 39.17 3.61
4298 4650 5.964288 AGCCTAAGATAATTTATGGGCCAA 58.036 37.500 11.89 0.00 39.17 4.52
4299 4651 5.599048 AGCCTAAGATAATTTATGGGCCA 57.401 39.130 9.61 9.61 39.17 5.36
4300 4652 7.012421 CGAATAGCCTAAGATAATTTATGGGCC 59.988 40.741 0.00 0.00 39.17 5.80
4301 4653 7.553044 ACGAATAGCCTAAGATAATTTATGGGC 59.447 37.037 0.00 0.00 38.71 5.36
4302 4654 9.449719 AACGAATAGCCTAAGATAATTTATGGG 57.550 33.333 0.00 0.00 0.00 4.00
4308 4660 9.057089 CCTCAAAACGAATAGCCTAAGATAATT 57.943 33.333 0.00 0.00 0.00 1.40
4309 4661 8.211629 ACCTCAAAACGAATAGCCTAAGATAAT 58.788 33.333 0.00 0.00 0.00 1.28
4310 4662 7.562135 ACCTCAAAACGAATAGCCTAAGATAA 58.438 34.615 0.00 0.00 0.00 1.75
4311 4663 7.120923 ACCTCAAAACGAATAGCCTAAGATA 57.879 36.000 0.00 0.00 0.00 1.98
4312 4664 5.990668 ACCTCAAAACGAATAGCCTAAGAT 58.009 37.500 0.00 0.00 0.00 2.40
4313 4665 5.416271 ACCTCAAAACGAATAGCCTAAGA 57.584 39.130 0.00 0.00 0.00 2.10
4314 4666 7.787725 ATAACCTCAAAACGAATAGCCTAAG 57.212 36.000 0.00 0.00 0.00 2.18
4315 4667 9.669887 TTTATAACCTCAAAACGAATAGCCTAA 57.330 29.630 0.00 0.00 0.00 2.69
4316 4668 9.841295 ATTTATAACCTCAAAACGAATAGCCTA 57.159 29.630 0.00 0.00 0.00 3.93
4317 4669 8.747538 ATTTATAACCTCAAAACGAATAGCCT 57.252 30.769 0.00 0.00 0.00 4.58
4318 4670 9.874215 GTATTTATAACCTCAAAACGAATAGCC 57.126 33.333 0.00 0.00 0.00 3.93
4324 4676 9.590451 CACCTAGTATTTATAACCTCAAAACGA 57.410 33.333 0.00 0.00 0.00 3.85
4325 4677 9.374838 ACACCTAGTATTTATAACCTCAAAACG 57.625 33.333 0.00 0.00 0.00 3.60
4349 4701 8.001881 TGCTTAATCTCAAAAGGTGTTTTACA 57.998 30.769 0.00 0.00 33.93 2.41
4350 4702 8.865590 TTGCTTAATCTCAAAAGGTGTTTTAC 57.134 30.769 0.00 0.00 33.93 2.01
4354 4706 9.696917 CTTTATTGCTTAATCTCAAAAGGTGTT 57.303 29.630 0.00 0.00 0.00 3.32
4355 4707 9.077885 TCTTTATTGCTTAATCTCAAAAGGTGT 57.922 29.630 0.00 0.00 0.00 4.16
4393 4745 3.265645 CCTCTGGGAGCCTGCAATAGG 62.266 61.905 0.00 0.00 41.68 2.57
4394 4746 0.108207 CCTCTGGGAGCCTGCAATAG 59.892 60.000 0.00 0.00 33.58 1.73
4395 4747 0.326522 TCCTCTGGGAGCCTGCAATA 60.327 55.000 0.00 0.00 36.57 1.90
4396 4748 1.617536 TCCTCTGGGAGCCTGCAAT 60.618 57.895 0.00 0.00 36.57 3.56
4397 4749 2.203983 TCCTCTGGGAGCCTGCAA 60.204 61.111 0.00 0.00 36.57 4.08
4405 4757 1.305046 GGTTCCGACTCCTCTGGGA 60.305 63.158 0.00 0.00 39.70 4.37
4406 4758 2.359967 GGGTTCCGACTCCTCTGGG 61.360 68.421 0.00 0.00 0.00 4.45
4407 4759 1.305381 AGGGTTCCGACTCCTCTGG 60.305 63.158 0.00 0.00 0.00 3.86
4408 4760 1.608717 CCAGGGTTCCGACTCCTCTG 61.609 65.000 0.00 0.00 0.00 3.35
4409 4761 1.305381 CCAGGGTTCCGACTCCTCT 60.305 63.158 0.00 0.00 0.00 3.69
4410 4762 3.020237 GCCAGGGTTCCGACTCCTC 62.020 68.421 0.00 0.00 0.00 3.71
4411 4763 3.003763 GCCAGGGTTCCGACTCCT 61.004 66.667 0.00 0.00 0.00 3.69
4412 4764 4.097361 GGCCAGGGTTCCGACTCC 62.097 72.222 0.00 0.00 0.00 3.85
4427 4779 4.858680 GTTAGGGCTGGAGGCGGC 62.859 72.222 0.00 0.00 42.94 6.53
4428 4780 4.176752 GGTTAGGGCTGGAGGCGG 62.177 72.222 0.00 0.00 42.94 6.13
4429 4781 4.530857 CGGTTAGGGCTGGAGGCG 62.531 72.222 0.00 0.00 42.94 5.52
4430 4782 4.858680 GCGGTTAGGGCTGGAGGC 62.859 72.222 0.00 0.00 40.90 4.70
4431 4783 4.176752 GGCGGTTAGGGCTGGAGG 62.177 72.222 0.00 0.00 0.00 4.30
4432 4784 4.530857 CGGCGGTTAGGGCTGGAG 62.531 72.222 0.00 0.00 33.11 3.86
4454 4806 4.507916 TCGCGAGGGAGGAGGAGG 62.508 72.222 3.71 0.00 0.00 4.30
4455 4807 3.213402 GTCGCGAGGGAGGAGGAG 61.213 72.222 10.24 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.