Multiple sequence alignment - TraesCS7A01G091600

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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 TraesCS7A01G091600 chr7A 100.000 4334 0 0 1 4334 55892030 55887697 0.000000e+00 8004.0
1 TraesCS7A01G091600 chr7D 94.416 2883 141 5 395 3270 53506044 53503175 0.000000e+00 4414.0
2 TraesCS7A01G091600 chr7D 86.323 775 77 19 3579 4334 53501892 53501128 0.000000e+00 817.0
3 TraesCS7A01G091600 chr7D 95.926 270 10 1 1 269 53506468 53506199 1.850000e-118 436.0
4 TraesCS7A01G091600 chr7D 90.187 214 18 3 441 653 46767849 46768060 4.270000e-70 276.0
5 TraesCS7A01G091600 chr7D 92.373 118 8 1 3269 3385 53502237 53502120 2.680000e-37 167.0
6 TraesCS7A01G091600 chr7D 100.000 33 0 0 265 297 53506089 53506057 1.300000e-05 62.1
7 TraesCS7A01G091600 chr4A 95.612 1504 64 1 1769 3270 668154894 668153391 0.000000e+00 2410.0
8 TraesCS7A01G091600 chr4A 92.789 527 36 2 268 793 668155947 668155422 0.000000e+00 761.0
9 TraesCS7A01G091600 chr4A 85.294 340 32 14 3803 4129 668152133 668151799 6.940000e-88 335.0
10 TraesCS7A01G091600 chr4A 89.352 216 23 0 439 654 165816330 165816545 5.520000e-69 272.0
11 TraesCS7A01G091600 chr5D 78.899 2270 438 27 1024 3271 423833718 423835968 0.000000e+00 1500.0
12 TraesCS7A01G091600 chr5D 80.606 165 28 3 2348 2510 438661776 438661938 1.640000e-24 124.0
13 TraesCS7A01G091600 chr5D 85.047 107 16 0 2404 2510 438725724 438725830 4.580000e-20 110.0
14 TraesCS7A01G091600 chr5B 79.137 2224 419 34 1071 3271 511605900 511608101 0.000000e+00 1495.0
15 TraesCS7A01G091600 chr5B 88.158 228 25 2 439 664 121249716 121249489 1.990000e-68 270.0
16 TraesCS7A01G091600 chr5B 77.578 223 50 0 2348 2570 533526339 533526561 7.560000e-28 135.0
17 TraesCS7A01G091600 chr5B 76.078 255 51 8 2348 2595 533576374 533576625 1.640000e-24 124.0
18 TraesCS7A01G091600 chr3B 90.952 210 18 1 444 653 519860864 519860656 9.180000e-72 281.0
19 TraesCS7A01G091600 chr2A 91.133 203 15 2 451 653 468290446 468290645 5.520000e-69 272.0
20 TraesCS7A01G091600 chr2A 89.352 216 23 0 439 654 566591822 566592037 5.520000e-69 272.0
21 TraesCS7A01G091600 chr5A 88.210 229 24 3 439 664 115095340 115095112 1.990000e-68 270.0


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 TraesCS7A01G091600 chr7A 55887697 55892030 4333 True 8004.000000 8004 100.000000 1 4334 1 chr7A.!!$R1 4333
1 TraesCS7A01G091600 chr7D 53501128 53506468 5340 True 1179.220000 4414 93.807600 1 4334 5 chr7D.!!$R1 4333
2 TraesCS7A01G091600 chr4A 668151799 668155947 4148 True 1168.666667 2410 91.231667 268 4129 3 chr4A.!!$R1 3861
3 TraesCS7A01G091600 chr5D 423833718 423835968 2250 False 1500.000000 1500 78.899000 1024 3271 1 chr5D.!!$F1 2247
4 TraesCS7A01G091600 chr5B 511605900 511608101 2201 False 1495.000000 1495 79.137000 1071 3271 1 chr5B.!!$F1 2200

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
711 828 0.250640 CCAACAGAGAAGTGCTGGCT 60.251 55.000 0.00 0.0 37.69 4.75 F
955 1076 0.394080 GGCCAGAGCTTCAGATTGCT 60.394 55.000 0.00 0.0 42.82 3.91 F
1088 1212 0.697079 TCCACCACGACTACCTCTCT 59.303 55.000 0.00 0.0 0.00 3.10 F
1139 1266 0.835276 TGCATCACAGATGAGAGGGG 59.165 55.000 10.95 0.0 38.57 4.79 F
1269 1396 0.957395 CAGGCCATGTCGTCAAGCTT 60.957 55.000 5.01 0.0 0.00 3.74 F
1621 1867 1.344438 TCTCATGGTTGTTGCGTCTCT 59.656 47.619 0.00 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2493 2741 1.144093 ACACTCCAAAACCAATCCGGA 59.856 47.619 6.61 6.61 38.63 5.14 R
2611 2859 3.480470 CAGTGAGGTTGTTGGAGTTCAT 58.520 45.455 0.00 0.00 0.00 2.57 R
2961 3209 1.089112 TGTGCGCAAGATCATGAAGG 58.911 50.000 14.00 0.00 43.02 3.46 R
2964 3212 1.521580 TGTTGTGCGCAAGATCATGA 58.478 45.000 14.00 0.00 43.02 3.07 R
2966 3214 1.881973 AGTTGTTGTGCGCAAGATCAT 59.118 42.857 14.00 0.00 43.02 2.45 R
3386 4581 1.134037 AGTTGTTTAAGCACACCCGGA 60.134 47.619 0.73 0.00 0.00 5.14 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
152 154 1.337260 GCCGTCATGACTTCAGACAGT 60.337 52.381 22.95 0.00 32.68 3.55
185 187 4.075682 TCTCTATCTGATAGGTGCCTTCG 58.924 47.826 21.28 0.00 33.64 3.79
192 194 2.094182 TGATAGGTGCCTTCGTTGACTC 60.094 50.000 0.00 0.00 0.00 3.36
198 200 0.384353 GCCTTCGTTGACTCGTTTGC 60.384 55.000 0.00 0.00 0.00 3.68
208 210 3.599792 CTCGTTTGCCAGCTTGCGG 62.600 63.158 5.19 0.00 0.00 5.69
261 263 5.827797 CAGGGCCAGAGCTTTATATTGTTAA 59.172 40.000 6.18 0.00 39.73 2.01
299 415 7.988904 TGACTTGGTAAAACAAAAATAACGG 57.011 32.000 0.00 0.00 0.00 4.44
300 416 7.545489 TGACTTGGTAAAACAAAAATAACGGT 58.455 30.769 0.00 0.00 0.00 4.83
302 418 6.757478 ACTTGGTAAAACAAAAATAACGGTGG 59.243 34.615 0.00 0.00 0.00 4.61
326 442 5.528690 GGTTTTGCAGCTCAGATGTCATATA 59.471 40.000 0.00 0.00 0.00 0.86
329 445 8.944029 GTTTTGCAGCTCAGATGTCATATATAT 58.056 33.333 0.00 0.00 0.00 0.86
344 460 9.074576 TGTCATATATATAGAACCGTCACTTGT 57.925 33.333 0.00 0.00 0.00 3.16
416 533 4.531339 GGGAAAGTAGTACTCCCTCTGTTT 59.469 45.833 16.89 0.74 44.81 2.83
460 577 1.676006 AGACTTTGCCAACTTTGACCG 59.324 47.619 0.00 0.00 0.00 4.79
468 585 3.252215 TGCCAACTTTGACCGAGTTTATG 59.748 43.478 0.00 0.00 35.26 1.90
586 703 6.983474 AAATGTTTTTCTCCACAAACTTGG 57.017 33.333 0.00 0.00 38.10 3.61
711 828 0.250640 CCAACAGAGAAGTGCTGGCT 60.251 55.000 0.00 0.00 37.69 4.75
766 883 3.220110 TCTGTCACACTAGTCTTCGGTT 58.780 45.455 0.00 0.00 0.00 4.44
796 913 0.968405 GGGGCTTTCATTCAGCACAA 59.032 50.000 0.00 0.00 43.07 3.33
859 976 2.008329 TCGTTACAGTGGCACGTTTTT 58.992 42.857 17.48 3.24 35.40 1.94
860 977 2.030701 TCGTTACAGTGGCACGTTTTTC 59.969 45.455 17.48 6.18 35.40 2.29
907 1024 3.599792 CTTTGTCAGCTTGCGGCCG 62.600 63.158 24.05 24.05 43.05 6.13
949 1070 0.615331 TACCAAGGCCAGAGCTTCAG 59.385 55.000 5.01 0.00 39.73 3.02
955 1076 0.394080 GGCCAGAGCTTCAGATTGCT 60.394 55.000 0.00 0.00 42.82 3.91
970 1091 4.277174 CAGATTGCTATACGTCCTCAGAGT 59.723 45.833 0.00 0.00 0.00 3.24
977 1098 5.163581 GCTATACGTCCTCAGAGTACCAAAA 60.164 44.000 0.00 0.00 0.00 2.44
1007 1131 8.370321 GCTTAGTAAAACAAAAATAATGGCGAC 58.630 33.333 0.00 0.00 0.00 5.19
1062 1186 1.458209 AGCCCTTTGCCTTGTGCTT 60.458 52.632 0.00 0.00 42.71 3.91
1069 1193 4.646492 CCCTTTGCCTTGTGCTTATTCTAT 59.354 41.667 0.00 0.00 42.00 1.98
1088 1212 0.697079 TCCACCACGACTACCTCTCT 59.303 55.000 0.00 0.00 0.00 3.10
1139 1266 0.835276 TGCATCACAGATGAGAGGGG 59.165 55.000 10.95 0.00 38.57 4.79
1188 1315 2.166459 CAGAAGCGATCCACAGAACCTA 59.834 50.000 0.00 0.00 0.00 3.08
1269 1396 0.957395 CAGGCCATGTCGTCAAGCTT 60.957 55.000 5.01 0.00 0.00 3.74
1293 1420 2.338500 GTCCGCAACGATCTCTTCTTT 58.662 47.619 0.00 0.00 0.00 2.52
1401 1528 5.913946 TGGAGTATCTAGATCTGAGTGGA 57.086 43.478 8.95 0.00 33.73 4.02
1565 1802 4.137543 GACCTCAACAACAACTGGAATCT 58.862 43.478 0.00 0.00 0.00 2.40
1612 1858 4.590647 ACATCGAGGATATCTCATGGTTGT 59.409 41.667 3.06 0.66 42.55 3.32
1621 1867 1.344438 TCTCATGGTTGTTGCGTCTCT 59.656 47.619 0.00 0.00 0.00 3.10
1647 1893 2.930682 GCTAAGGTTTCTCGACATGACC 59.069 50.000 0.00 0.00 0.00 4.02
1719 1965 8.282455 TGCTATATAATCTAAGAGTCCTTCGG 57.718 38.462 0.00 0.00 33.94 4.30
1758 2004 5.299279 ACTTGTTTTTCCACAGACACCTATG 59.701 40.000 0.00 0.00 0.00 2.23
1783 2029 4.021807 TGCGTTCTAACCTCACATCACTTA 60.022 41.667 0.00 0.00 0.00 2.24
1940 2186 2.251893 GACTTCGCTTGAGGTACTTCG 58.748 52.381 0.05 0.00 41.55 3.79
2056 2302 8.828644 TCAATCAAGACATTTCACAATTTTTGG 58.171 29.630 0.00 0.00 34.12 3.28
2217 2463 4.336713 GGATCAGTACCTTCAGAAATTGGC 59.663 45.833 0.00 0.00 0.00 4.52
2225 2471 1.825090 TCAGAAATTGGCATGCTCGT 58.175 45.000 18.92 0.15 0.00 4.18
2229 2475 2.756760 AGAAATTGGCATGCTCGTCAAT 59.243 40.909 18.92 15.11 42.89 2.57
2237 2483 2.417933 GCATGCTCGTCAATCTCAAACT 59.582 45.455 11.37 0.00 0.00 2.66
2238 2484 3.120060 GCATGCTCGTCAATCTCAAACTT 60.120 43.478 11.37 0.00 0.00 2.66
2262 2508 7.766219 TTTGTATCTAGACGGCAACTATTTC 57.234 36.000 0.00 0.00 0.00 2.17
2293 2539 8.637986 GTTCTATATCAGAGGAACATCTTGACT 58.362 37.037 0.00 0.00 38.23 3.41
2345 2591 4.282703 GTCTTACAACTCCCTACACCTGAA 59.717 45.833 0.00 0.00 0.00 3.02
2370 2618 1.648037 AGCTCAAATTGGATTCCCCCT 59.352 47.619 0.00 0.00 0.00 4.79
2469 2717 6.549364 AGGGTGTTGTTTATCTTGACATTTCA 59.451 34.615 0.00 0.00 0.00 2.69
2493 2741 4.235079 TGCAGGCATAGTTGATAACCTT 57.765 40.909 0.00 0.00 0.00 3.50
2605 2853 7.038048 TGAGTTTATGTCTTCAGCAGTGATAG 58.962 38.462 0.00 0.00 30.85 2.08
2611 2859 6.530019 TGTCTTCAGCAGTGATAGTTGATA 57.470 37.500 0.00 0.00 30.85 2.15
2728 2976 2.602217 CGAAACTTTGGAGCTCCGTTTG 60.602 50.000 30.29 21.46 39.43 2.93
2865 3113 3.454447 TCCCTGTCTGTTCAGAAGAAACA 59.546 43.478 3.99 0.00 37.61 2.83
2949 3197 4.104383 TCCTTCATTTTTGGAGAGCTGT 57.896 40.909 0.00 0.00 0.00 4.40
2953 3201 5.221303 CCTTCATTTTTGGAGAGCTGTTCAA 60.221 40.000 0.00 0.00 0.00 2.69
2961 3209 2.550180 GGAGAGCTGTTCAAAGTTGGTC 59.450 50.000 0.00 0.00 0.00 4.02
2964 3212 2.952310 GAGCTGTTCAAAGTTGGTCCTT 59.048 45.455 0.00 0.00 0.00 3.36
2966 3214 2.687935 GCTGTTCAAAGTTGGTCCTTCA 59.312 45.455 0.00 0.00 0.00 3.02
3054 3302 1.448540 CTACCTCAGGTTGCGGCAG 60.449 63.158 0.00 0.00 37.09 4.85
3144 3392 5.112686 GCAGATAACCGAATATCAGGATCC 58.887 45.833 2.48 2.48 35.22 3.36
3154 3402 6.279123 CGAATATCAGGATCCATACCTCATG 58.721 44.000 15.82 0.26 35.35 3.07
3161 3409 0.908910 TCCATACCTCATGCGTTGGT 59.091 50.000 5.76 5.76 37.83 3.67
3267 3518 7.825681 ACACGAATGATTCACCAAAATATGAA 58.174 30.769 5.95 0.00 39.09 2.57
3326 4521 8.325787 TGTCTATATTGTTTTAGATGGTGGTGT 58.674 33.333 0.00 0.00 0.00 4.16
3340 4535 5.255710 TGGTGGTGTTGTCTAAATTGTTG 57.744 39.130 0.00 0.00 0.00 3.33
3357 4552 8.524870 AAATTGTTGTATTCTTGATTCTGTGC 57.475 30.769 0.00 0.00 0.00 4.57
3358 4553 6.882610 TTGTTGTATTCTTGATTCTGTGCT 57.117 33.333 0.00 0.00 0.00 4.40
3359 4554 7.977789 TTGTTGTATTCTTGATTCTGTGCTA 57.022 32.000 0.00 0.00 0.00 3.49
3360 4555 7.364522 TGTTGTATTCTTGATTCTGTGCTAC 57.635 36.000 0.00 0.00 0.00 3.58
3361 4556 7.161404 TGTTGTATTCTTGATTCTGTGCTACT 58.839 34.615 0.00 0.00 0.00 2.57
3362 4557 7.118245 TGTTGTATTCTTGATTCTGTGCTACTG 59.882 37.037 0.00 0.00 0.00 2.74
3363 4558 5.582269 TGTATTCTTGATTCTGTGCTACTGC 59.418 40.000 0.00 0.00 40.20 4.40
3402 4597 3.439895 TTTTTCCGGGTGTGCTTAAAC 57.560 42.857 0.00 0.00 0.00 2.01
3403 4598 2.054232 TTTCCGGGTGTGCTTAAACA 57.946 45.000 0.00 0.00 0.00 2.83
3404 4599 2.054232 TTCCGGGTGTGCTTAAACAA 57.946 45.000 0.00 0.00 0.00 2.83
3405 4600 1.310904 TCCGGGTGTGCTTAAACAAC 58.689 50.000 0.00 0.00 37.01 3.32
3406 4601 1.134037 TCCGGGTGTGCTTAAACAACT 60.134 47.619 0.00 0.00 37.90 3.16
3407 4602 2.104451 TCCGGGTGTGCTTAAACAACTA 59.896 45.455 0.00 0.00 37.90 2.24
3408 4603 2.482721 CCGGGTGTGCTTAAACAACTAG 59.517 50.000 0.00 0.00 37.90 2.57
3409 4604 2.482721 CGGGTGTGCTTAAACAACTAGG 59.517 50.000 0.00 0.00 37.90 3.02
3410 4605 3.746940 GGGTGTGCTTAAACAACTAGGA 58.253 45.455 0.00 0.00 37.90 2.94
3411 4606 3.751698 GGGTGTGCTTAAACAACTAGGAG 59.248 47.826 0.00 0.00 37.90 3.69
3412 4607 4.386711 GGTGTGCTTAAACAACTAGGAGT 58.613 43.478 0.00 0.00 34.79 3.85
3413 4608 4.820173 GGTGTGCTTAAACAACTAGGAGTT 59.180 41.667 0.00 0.00 39.39 3.01
3414 4609 5.298527 GGTGTGCTTAAACAACTAGGAGTTT 59.701 40.000 15.94 15.94 36.03 2.66
3415 4610 6.183360 GGTGTGCTTAAACAACTAGGAGTTTT 60.183 38.462 16.61 3.88 36.03 2.43
3416 4611 7.255569 GTGTGCTTAAACAACTAGGAGTTTTT 58.744 34.615 16.61 2.41 36.03 1.94
3440 4635 3.875134 CCGGGTATGCTTAAACAACTAGG 59.125 47.826 0.00 0.00 0.00 3.02
3452 4647 5.376854 AAACAACTAGGACATGATGTTGC 57.623 39.130 0.00 0.00 40.88 4.17
3463 4658 5.858581 GGACATGATGTTGCTTAAACTGTTC 59.141 40.000 0.00 0.00 39.70 3.18
3486 4681 6.518493 TCTAGACGGTGTTGTTGTCTAAATT 58.482 36.000 3.29 0.00 42.75 1.82
3492 4687 6.127842 ACGGTGTTGTTGTCTAAATTGTTTCT 60.128 34.615 0.00 0.00 0.00 2.52
3495 4690 8.931775 GGTGTTGTTGTCTAAATTGTTTCTTTT 58.068 29.630 0.00 0.00 0.00 2.27
3496 4691 9.739786 GTGTTGTTGTCTAAATTGTTTCTTTTG 57.260 29.630 0.00 0.00 0.00 2.44
3533 4728 8.951787 TTTGTTTAGACTTGAGTACTGCTTTA 57.048 30.769 0.00 0.00 0.00 1.85
3534 4729 9.555727 TTTGTTTAGACTTGAGTACTGCTTTAT 57.444 29.630 0.00 0.00 0.00 1.40
3536 4731 8.988934 TGTTTAGACTTGAGTACTGCTTTATTG 58.011 33.333 0.00 0.00 0.00 1.90
3537 4732 9.204570 GTTTAGACTTGAGTACTGCTTTATTGA 57.795 33.333 0.00 0.00 0.00 2.57
3538 4733 9.944376 TTTAGACTTGAGTACTGCTTTATTGAT 57.056 29.630 0.00 0.00 0.00 2.57
3540 4735 8.261492 AGACTTGAGTACTGCTTTATTGATTG 57.739 34.615 0.00 0.00 0.00 2.67
3541 4736 7.880195 AGACTTGAGTACTGCTTTATTGATTGT 59.120 33.333 0.00 0.00 0.00 2.71
3544 4739 9.334693 CTTGAGTACTGCTTTATTGATTGTTTC 57.665 33.333 0.00 0.00 0.00 2.78
3545 4740 7.518161 TGAGTACTGCTTTATTGATTGTTTCG 58.482 34.615 0.00 0.00 0.00 3.46
3546 4741 7.386573 TGAGTACTGCTTTATTGATTGTTTCGA 59.613 33.333 0.00 0.00 0.00 3.71
3547 4742 8.094798 AGTACTGCTTTATTGATTGTTTCGAA 57.905 30.769 0.00 0.00 0.00 3.71
3553 4748 9.737427 TGCTTTATTGATTGTTTCGAAAAGTTA 57.263 25.926 13.10 0.00 0.00 2.24
3574 4769 8.209917 AGTTATCTATTTTTCCGATGGTGTTC 57.790 34.615 0.00 0.00 0.00 3.18
3592 4902 4.046462 TGTTCTCAAGTACGAAGAAACCG 58.954 43.478 8.56 0.00 0.00 4.44
3626 4937 6.422776 TCTTTTGCGATTTTGGATCTCTAC 57.577 37.500 0.00 0.00 0.00 2.59
3632 4943 4.492570 GCGATTTTGGATCTCTACGTGTTG 60.493 45.833 0.00 0.00 0.00 3.33
3644 4955 4.593157 TCTACGTGTTGCATTGAACAAAC 58.407 39.130 0.00 0.00 37.58 2.93
3661 4972 6.936900 TGAACAAACACCTTCATTTTTGGAAA 59.063 30.769 0.00 0.00 33.98 3.13
3662 4973 6.735678 ACAAACACCTTCATTTTTGGAAAC 57.264 33.333 0.00 0.00 33.98 2.78
3664 4975 6.939730 ACAAACACCTTCATTTTTGGAAACTT 59.060 30.769 0.00 0.00 33.98 2.66
3688 4999 5.996271 ATATATCCTAGAGACCGGATCCA 57.004 43.478 9.46 0.00 40.40 3.41
3689 5000 2.595750 ATCCTAGAGACCGGATCCAG 57.404 55.000 9.46 2.18 35.08 3.86
3706 5017 6.294176 CGGATCCAGCTAAATAATTTGGGAAG 60.294 42.308 13.41 0.00 0.00 3.46
3712 5023 7.322664 CAGCTAAATAATTTGGGAAGCAAAGA 58.677 34.615 0.00 0.00 0.00 2.52
3743 5054 6.613755 TTCTAGTTTTTGTCCTAGTTGTGC 57.386 37.500 0.00 0.00 33.81 4.57
3744 5055 3.963383 AGTTTTTGTCCTAGTTGTGCG 57.037 42.857 0.00 0.00 0.00 5.34
3756 5067 4.452455 CCTAGTTGTGCGATGAAGAAACTT 59.548 41.667 0.00 0.00 0.00 2.66
3759 5070 5.057149 AGTTGTGCGATGAAGAAACTTAGT 58.943 37.500 0.00 0.00 0.00 2.24
3762 5073 4.927425 TGTGCGATGAAGAAACTTAGTACC 59.073 41.667 0.00 0.00 0.00 3.34
3779 5090 1.038130 ACCTGTCCTAGCTAGCCACG 61.038 60.000 15.74 9.87 0.00 4.94
3824 5142 1.270550 CATCCAGCAAGGTTGAACCAC 59.729 52.381 17.83 5.54 41.95 4.16
3830 5148 1.270550 GCAAGGTTGAACCACTCCATG 59.729 52.381 17.83 6.53 41.95 3.66
3831 5149 1.270550 CAAGGTTGAACCACTCCATGC 59.729 52.381 17.83 0.00 41.95 4.06
3832 5150 0.478072 AGGTTGAACCACTCCATGCA 59.522 50.000 17.83 0.00 41.95 3.96
3837 5155 2.989909 TGAACCACTCCATGCACTATG 58.010 47.619 0.00 0.00 36.50 2.23
3861 5179 9.687210 ATGTATGTTTGATGCATATGTTTCATC 57.313 29.630 0.00 12.40 37.65 2.92
3880 5198 2.892425 CGAGATGGGCAACGGCTC 60.892 66.667 0.00 0.00 42.48 4.70
3882 5200 1.078143 GAGATGGGCAACGGCTCTT 60.078 57.895 0.00 0.00 42.67 2.85
3883 5201 1.372087 GAGATGGGCAACGGCTCTTG 61.372 60.000 0.00 0.00 42.67 3.02
3885 5203 0.960364 GATGGGCAACGGCTCTTGAA 60.960 55.000 0.00 0.00 42.67 2.69
3886 5204 1.244019 ATGGGCAACGGCTCTTGAAC 61.244 55.000 0.00 0.00 42.67 3.18
3887 5205 1.600916 GGGCAACGGCTCTTGAACT 60.601 57.895 0.00 0.00 37.60 3.01
3888 5206 0.321298 GGGCAACGGCTCTTGAACTA 60.321 55.000 0.00 0.00 37.60 2.24
3889 5207 1.079503 GGCAACGGCTCTTGAACTAG 58.920 55.000 0.00 0.00 40.87 2.57
3890 5208 1.608283 GGCAACGGCTCTTGAACTAGT 60.608 52.381 0.00 0.00 40.87 2.57
3891 5209 2.353406 GGCAACGGCTCTTGAACTAGTA 60.353 50.000 0.00 0.00 40.87 1.82
3892 5210 2.924290 GCAACGGCTCTTGAACTAGTAG 59.076 50.000 0.00 0.00 36.96 2.57
3893 5211 3.614390 GCAACGGCTCTTGAACTAGTAGT 60.614 47.826 0.00 0.00 36.96 2.73
3894 5212 4.380233 GCAACGGCTCTTGAACTAGTAGTA 60.380 45.833 2.50 0.00 36.96 1.82
3895 5213 4.961435 ACGGCTCTTGAACTAGTAGTAC 57.039 45.455 2.50 0.00 0.00 2.73
3896 5214 4.330250 ACGGCTCTTGAACTAGTAGTACA 58.670 43.478 2.50 0.00 0.00 2.90
3897 5215 4.948621 ACGGCTCTTGAACTAGTAGTACAT 59.051 41.667 2.50 0.00 0.00 2.29
3905 5223 9.595823 TCTTGAACTAGTAGTACATTTAATGGC 57.404 33.333 9.88 2.19 33.60 4.40
3907 5225 7.774134 TGAACTAGTAGTACATTTAATGGCGA 58.226 34.615 9.88 0.00 33.60 5.54
3912 5230 9.256477 CTAGTAGTACATTTAATGGCGATGAAA 57.744 33.333 9.88 0.00 33.60 2.69
3961 5290 0.037046 AACATACGTGTCCGGGGAAC 60.037 55.000 0.00 0.00 37.67 3.62
3981 5310 1.136147 GCTCGCGGTCTTCGTTCTA 59.864 57.895 6.13 0.00 41.72 2.10
4014 5343 9.843334 AGATAAACTAAACTAGACGTTTGAGAG 57.157 33.333 0.00 0.00 45.10 3.20
4036 5365 4.589798 AGTTGAGATCAGAGATCAGATGGG 59.410 45.833 9.43 0.00 0.00 4.00
4107 5436 4.116238 CCAAATTAAACAACAAGCCACGT 58.884 39.130 0.00 0.00 0.00 4.49
4108 5437 4.568760 CCAAATTAAACAACAAGCCACGTT 59.431 37.500 0.00 0.00 0.00 3.99
4112 5443 2.461897 AACAACAAGCCACGTTTACG 57.538 45.000 0.00 0.00 46.33 3.18
4129 5460 5.003778 CGTTTACGGTTTGATTAGTACTCCG 59.996 44.000 13.60 13.60 41.77 4.63
4141 5472 0.321034 GTACTCCGTTTCACACCCCC 60.321 60.000 0.00 0.00 0.00 5.40
4142 5473 0.472352 TACTCCGTTTCACACCCCCT 60.472 55.000 0.00 0.00 0.00 4.79
4155 5486 0.194587 ACCCCCTATGATCCAGGAGG 59.805 60.000 11.22 10.03 37.10 4.30
4163 5494 2.550277 TGATCCAGGAGGCTTGAGTA 57.450 50.000 0.00 0.00 33.74 2.59
4187 5518 5.163622 ACAAGTTCATCTTTCCTTGTGTGTG 60.164 40.000 3.32 0.00 44.19 3.82
4191 5522 7.450074 AGTTCATCTTTCCTTGTGTGTGTATA 58.550 34.615 0.00 0.00 0.00 1.47
4198 5529 5.183014 TCCTTGTGTGTGTATATAGCTCG 57.817 43.478 0.00 0.00 0.00 5.03
4204 5535 7.733402 TGTGTGTGTATATAGCTCGTATGTA 57.267 36.000 0.00 0.00 0.00 2.29
4206 5537 8.287503 TGTGTGTGTATATAGCTCGTATGTAAG 58.712 37.037 0.00 0.00 0.00 2.34
4212 5543 9.169592 TGTATATAGCTCGTATGTAAGTATGCA 57.830 33.333 0.00 0.00 0.00 3.96
4216 5547 3.179795 GCTCGTATGTAAGTATGCACACG 59.820 47.826 0.00 0.00 42.39 4.49
4228 5559 1.017177 TGCACACGAATAACCCTCGC 61.017 55.000 0.00 0.00 39.97 5.03
4229 5560 1.702491 GCACACGAATAACCCTCGCC 61.702 60.000 0.00 0.00 39.97 5.54
4234 5565 0.107848 CGAATAACCCTCGCCCAACT 60.108 55.000 0.00 0.00 0.00 3.16
4235 5566 1.664873 GAATAACCCTCGCCCAACTC 58.335 55.000 0.00 0.00 0.00 3.01
4237 5568 0.912487 ATAACCCTCGCCCAACTCCA 60.912 55.000 0.00 0.00 0.00 3.86
4239 5570 1.789576 AACCCTCGCCCAACTCCAAT 61.790 55.000 0.00 0.00 0.00 3.16
4255 5586 5.220381 ACTCCAATACAGTCGCATAATACG 58.780 41.667 0.00 0.00 0.00 3.06
4317 5650 1.202114 CACACACATACATGGGTTGGC 59.798 52.381 0.00 0.00 42.97 4.52
4323 5656 0.704076 ATACATGGGTTGGCCACTGT 59.296 50.000 3.88 7.13 35.79 3.55
4326 5659 0.540365 CATGGGTTGGCCACTGTCTT 60.540 55.000 3.88 0.00 36.17 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 4.756084 AGCTAAACTGTGCTGAATGAAC 57.244 40.909 0.00 0.00 38.21 3.18
127 129 1.462283 CTGAAGTCATGACGGCAACAG 59.538 52.381 19.85 18.79 36.20 3.16
152 154 8.762645 ACCTATCAGATAGAGAAAAATGTGTCA 58.237 33.333 17.91 0.00 34.77 3.58
185 187 0.663153 AAGCTGGCAAACGAGTCAAC 59.337 50.000 0.00 0.00 0.00 3.18
198 200 2.182537 GAATTGGCCGCAAGCTGG 59.817 61.111 0.00 0.00 43.05 4.85
261 263 4.595986 ACCAAGTCAACTTTGGTACTGTT 58.404 39.130 7.82 0.00 36.39 3.16
297 413 2.133742 CTGAGCTGCAAAACCCACCG 62.134 60.000 1.02 0.00 0.00 4.94
299 415 1.068055 CATCTGAGCTGCAAAACCCAC 60.068 52.381 1.02 0.00 0.00 4.61
300 416 1.250328 CATCTGAGCTGCAAAACCCA 58.750 50.000 1.02 0.00 0.00 4.51
302 418 1.881973 TGACATCTGAGCTGCAAAACC 59.118 47.619 1.02 0.00 0.00 3.27
326 442 6.216801 TGCTAACAAGTGACGGTTCTATAT 57.783 37.500 0.00 0.00 0.00 0.86
329 445 4.530710 ATGCTAACAAGTGACGGTTCTA 57.469 40.909 0.00 0.00 0.00 2.10
372 489 4.194640 CCTGAACTGTGATGGGATAACTG 58.805 47.826 0.00 0.00 0.00 3.16
624 741 4.929808 CCTCCGTTCCATAATATAGTGCAC 59.070 45.833 9.40 9.40 0.00 4.57
680 797 9.162764 GCACTTCTCTGTTGGAATAGTTAAATA 57.837 33.333 0.00 0.00 0.00 1.40
695 812 0.471617 ACAAGCCAGCACTTCTCTGT 59.528 50.000 0.00 0.00 0.00 3.41
751 868 2.480845 GCAACAACCGAAGACTAGTGT 58.519 47.619 0.00 0.00 0.00 3.55
796 913 3.407424 TGTGTTGACTTGCAGCTAGAT 57.593 42.857 11.12 0.00 0.00 1.98
859 976 3.204158 AGAAGGCACCTATCAGAGAGAGA 59.796 47.826 0.00 0.00 0.00 3.10
860 977 3.565307 AGAAGGCACCTATCAGAGAGAG 58.435 50.000 0.00 0.00 0.00 3.20
930 1047 0.615331 CTGAAGCTCTGGCCTTGGTA 59.385 55.000 3.32 0.00 39.73 3.25
931 1048 1.130054 TCTGAAGCTCTGGCCTTGGT 61.130 55.000 3.32 0.00 39.73 3.67
932 1049 0.255318 ATCTGAAGCTCTGGCCTTGG 59.745 55.000 3.32 0.00 39.73 3.61
933 1050 1.743958 CAATCTGAAGCTCTGGCCTTG 59.256 52.381 3.32 0.00 39.73 3.61
934 1051 1.954258 GCAATCTGAAGCTCTGGCCTT 60.954 52.381 3.32 0.00 39.73 4.35
949 1070 4.839668 ACTCTGAGGACGTATAGCAATC 57.160 45.455 9.85 0.00 0.00 2.67
955 1076 7.262772 CAATTTTGGTACTCTGAGGACGTATA 58.737 38.462 13.67 0.57 0.00 1.47
1007 1131 0.876342 GGATACCGGAGCTGCGAAAG 60.876 60.000 30.34 15.01 0.00 2.62
1062 1186 5.057843 AGGTAGTCGTGGTGGATAGAATA 57.942 43.478 0.00 0.00 0.00 1.75
1069 1193 0.697079 AGAGAGGTAGTCGTGGTGGA 59.303 55.000 0.00 0.00 0.00 4.02
1088 1212 4.642437 TGTTGGTTTCTTGTGCATAGACAA 59.358 37.500 0.00 0.00 34.64 3.18
1139 1266 1.530293 CTCTGAAAGACAGCAGTGCAC 59.470 52.381 19.20 9.40 45.38 4.57
1310 1437 5.707298 CCATGAGAATTTTCACTGTACCAGT 59.293 40.000 0.00 0.00 46.51 4.00
1401 1528 2.816411 TCCACTCCACCGAGATAGTTT 58.184 47.619 0.00 0.00 38.52 2.66
1565 1802 6.979817 GTGCAACATCATGCCATAAGAATTAA 59.020 34.615 0.00 0.00 45.83 1.40
1612 1858 2.037251 ACCTTAGCAAAGAGAGACGCAA 59.963 45.455 0.00 0.00 34.37 4.85
1621 1867 4.330944 TGTCGAGAAACCTTAGCAAAGA 57.669 40.909 0.00 0.00 34.37 2.52
1647 1893 4.142534 CCAATGGCACTAAGATTCACACTG 60.143 45.833 0.00 0.00 0.00 3.66
1719 1965 1.300697 AAGTCCACAACGACGGAGC 60.301 57.895 0.00 0.00 37.85 4.70
1758 2004 2.000447 GATGTGAGGTTAGAACGCACC 59.000 52.381 11.89 0.00 35.41 5.01
1763 2009 7.201565 GCATCTTAAGTGATGTGAGGTTAGAAC 60.202 40.741 1.63 0.00 44.02 3.01
1783 2029 7.215789 CCAGTATCACTTAGATCAAGCATCTT 58.784 38.462 0.00 0.00 38.95 2.40
1908 2154 4.816385 TCAAGCGAAGTCATATTTCCCATC 59.184 41.667 0.00 0.00 0.00 3.51
1940 2186 2.941720 GTGAGATGATTGCCTCCAAGAC 59.058 50.000 0.00 0.00 33.80 3.01
2217 2463 4.675190 AAGTTTGAGATTGACGAGCATG 57.325 40.909 0.00 0.00 0.00 4.06
2225 2471 9.140286 CGTCTAGATACAAAAGTTTGAGATTGA 57.860 33.333 10.66 0.06 40.55 2.57
2229 2475 5.867716 GCCGTCTAGATACAAAAGTTTGAGA 59.132 40.000 10.66 0.17 40.55 3.27
2237 2483 7.820386 TGAAATAGTTGCCGTCTAGATACAAAA 59.180 33.333 0.00 0.00 0.00 2.44
2238 2484 7.324935 TGAAATAGTTGCCGTCTAGATACAAA 58.675 34.615 0.00 0.00 0.00 2.83
2262 2508 5.902681 TGTTCCTCTGATATAGAACCGTTG 58.097 41.667 0.00 0.00 38.24 4.10
2293 2539 7.176690 GTCCAATTCCTCCAAATTCACTAAAGA 59.823 37.037 0.00 0.00 0.00 2.52
2345 2591 4.213513 GGGAATCCAATTTGAGCTGATCT 58.786 43.478 0.09 0.00 0.00 2.75
2370 2618 4.580835 GCCCGGCGCAATTTAAAA 57.419 50.000 10.83 0.00 37.47 1.52
2469 2717 4.103785 AGGTTATCAACTATGCCTGCATCT 59.896 41.667 8.09 0.00 37.82 2.90
2493 2741 1.144093 ACACTCCAAAACCAATCCGGA 59.856 47.619 6.61 6.61 38.63 5.14
2605 2853 5.705441 TGAGGTTGTTGGAGTTCATATCAAC 59.295 40.000 0.00 0.00 39.68 3.18
2611 2859 3.480470 CAGTGAGGTTGTTGGAGTTCAT 58.520 45.455 0.00 0.00 0.00 2.57
2728 2976 5.065218 TCTCAGAAAGCAACAACTCTTCAAC 59.935 40.000 0.00 0.00 0.00 3.18
2865 3113 9.336171 GCTCTAATGGATCTATTCAGTTCTTTT 57.664 33.333 7.68 0.00 0.00 2.27
2949 3197 5.634118 AGATCATGAAGGACCAACTTTGAA 58.366 37.500 0.00 0.00 0.00 2.69
2953 3201 3.760684 GCAAGATCATGAAGGACCAACTT 59.239 43.478 0.00 0.00 0.00 2.66
2961 3209 1.089112 TGTGCGCAAGATCATGAAGG 58.911 50.000 14.00 0.00 43.02 3.46
2964 3212 1.521580 TGTTGTGCGCAAGATCATGA 58.478 45.000 14.00 0.00 43.02 3.07
2966 3214 1.881973 AGTTGTTGTGCGCAAGATCAT 59.118 42.857 14.00 0.00 43.02 2.45
3144 3392 2.022764 TGACCAACGCATGAGGTATG 57.977 50.000 0.00 0.00 39.88 2.39
3154 3402 3.073144 TGCTTTTAAGTTGACCAACGC 57.927 42.857 7.18 4.69 45.50 4.84
3161 3409 7.121168 CCTCCTGTATCATTGCTTTTAAGTTGA 59.879 37.037 0.00 0.00 0.00 3.18
3340 4535 6.042144 GCAGTAGCACAGAATCAAGAATAC 57.958 41.667 0.00 0.00 41.58 1.89
3382 4577 2.758979 TGTTTAAGCACACCCGGAAAAA 59.241 40.909 0.73 0.00 0.00 1.94
3383 4578 2.376109 TGTTTAAGCACACCCGGAAAA 58.624 42.857 0.73 0.00 0.00 2.29
3384 4579 2.054232 TGTTTAAGCACACCCGGAAA 57.946 45.000 0.73 0.00 0.00 3.13
3385 4580 1.677052 GTTGTTTAAGCACACCCGGAA 59.323 47.619 0.73 0.00 0.00 4.30
3386 4581 1.134037 AGTTGTTTAAGCACACCCGGA 60.134 47.619 0.73 0.00 0.00 5.14
3387 4582 1.314730 AGTTGTTTAAGCACACCCGG 58.685 50.000 0.00 0.00 0.00 5.73
3388 4583 2.482721 CCTAGTTGTTTAAGCACACCCG 59.517 50.000 0.00 0.00 0.00 5.28
3389 4584 3.746940 TCCTAGTTGTTTAAGCACACCC 58.253 45.455 0.00 0.00 0.00 4.61
3390 4585 4.386711 ACTCCTAGTTGTTTAAGCACACC 58.613 43.478 0.00 0.00 0.00 4.16
3391 4586 6.373186 AAACTCCTAGTTGTTTAAGCACAC 57.627 37.500 8.10 0.00 38.66 3.82
3392 4587 7.399245 AAAAACTCCTAGTTGTTTAAGCACA 57.601 32.000 9.70 0.00 38.66 4.57
3413 4608 5.302313 AGTTGTTTAAGCATACCCGGAAAAA 59.698 36.000 0.73 0.00 0.00 1.94
3414 4609 4.828387 AGTTGTTTAAGCATACCCGGAAAA 59.172 37.500 0.73 0.00 0.00 2.29
3415 4610 4.400120 AGTTGTTTAAGCATACCCGGAAA 58.600 39.130 0.73 0.00 0.00 3.13
3416 4611 4.023726 AGTTGTTTAAGCATACCCGGAA 57.976 40.909 0.73 0.00 0.00 4.30
3417 4612 3.706600 AGTTGTTTAAGCATACCCGGA 57.293 42.857 0.73 0.00 0.00 5.14
3418 4613 3.875134 CCTAGTTGTTTAAGCATACCCGG 59.125 47.826 0.00 0.00 0.00 5.73
3419 4614 4.569564 GTCCTAGTTGTTTAAGCATACCCG 59.430 45.833 0.00 0.00 0.00 5.28
3420 4615 5.493809 TGTCCTAGTTGTTTAAGCATACCC 58.506 41.667 0.00 0.00 0.00 3.69
3421 4616 6.821665 TCATGTCCTAGTTGTTTAAGCATACC 59.178 38.462 0.00 0.00 0.00 2.73
3422 4617 7.843490 TCATGTCCTAGTTGTTTAAGCATAC 57.157 36.000 0.00 0.00 0.00 2.39
3423 4618 8.046708 ACATCATGTCCTAGTTGTTTAAGCATA 58.953 33.333 0.00 0.00 0.00 3.14
3424 4619 6.886459 ACATCATGTCCTAGTTGTTTAAGCAT 59.114 34.615 0.00 0.00 0.00 3.79
3425 4620 6.237901 ACATCATGTCCTAGTTGTTTAAGCA 58.762 36.000 0.00 0.00 0.00 3.91
3426 4621 6.743575 ACATCATGTCCTAGTTGTTTAAGC 57.256 37.500 0.00 0.00 0.00 3.09
3427 4622 7.023575 GCAACATCATGTCCTAGTTGTTTAAG 58.976 38.462 0.00 0.00 41.07 1.85
3428 4623 6.714810 AGCAACATCATGTCCTAGTTGTTTAA 59.285 34.615 0.00 0.00 41.07 1.52
3429 4624 6.237901 AGCAACATCATGTCCTAGTTGTTTA 58.762 36.000 0.00 0.00 41.07 2.01
3430 4625 5.072741 AGCAACATCATGTCCTAGTTGTTT 58.927 37.500 0.00 6.30 41.07 2.83
3431 4626 4.655963 AGCAACATCATGTCCTAGTTGTT 58.344 39.130 0.00 9.44 41.07 2.83
3432 4627 4.292186 AGCAACATCATGTCCTAGTTGT 57.708 40.909 0.00 0.00 41.07 3.32
3433 4628 6.741992 TTAAGCAACATCATGTCCTAGTTG 57.258 37.500 0.00 0.00 41.71 3.16
3434 4629 6.942576 AGTTTAAGCAACATCATGTCCTAGTT 59.057 34.615 0.00 0.00 37.93 2.24
3440 4635 6.672147 AGAACAGTTTAAGCAACATCATGTC 58.328 36.000 0.00 0.00 37.93 3.06
3452 4647 5.751990 ACAACACCGTCTAGAACAGTTTAAG 59.248 40.000 0.00 0.00 0.00 1.85
3463 4658 6.202188 ACAATTTAGACAACAACACCGTCTAG 59.798 38.462 0.00 0.00 41.80 2.43
3504 4699 8.345565 AGCAGTACTCAAGTCTAAACAAATTTG 58.654 33.333 16.67 16.67 0.00 2.32
3505 4700 8.451908 AGCAGTACTCAAGTCTAAACAAATTT 57.548 30.769 0.00 0.00 0.00 1.82
3508 4703 7.859325 AAAGCAGTACTCAAGTCTAAACAAA 57.141 32.000 0.00 0.00 0.00 2.83
3517 4712 7.986085 ACAATCAATAAAGCAGTACTCAAGT 57.014 32.000 0.00 0.00 0.00 3.16
3518 4713 9.334693 GAAACAATCAATAAAGCAGTACTCAAG 57.665 33.333 0.00 0.00 0.00 3.02
3526 4721 8.285776 ACTTTTCGAAACAATCAATAAAGCAG 57.714 30.769 10.79 2.61 0.00 4.24
3527 4722 8.641499 AACTTTTCGAAACAATCAATAAAGCA 57.359 26.923 10.79 0.00 0.00 3.91
3540 4735 9.815936 TCGGAAAAATAGATAACTTTTCGAAAC 57.184 29.630 10.79 0.00 39.08 2.78
3544 4739 8.395633 ACCATCGGAAAAATAGATAACTTTTCG 58.604 33.333 0.00 0.00 39.08 3.46
3545 4740 9.503427 CACCATCGGAAAAATAGATAACTTTTC 57.497 33.333 0.00 0.00 38.01 2.29
3546 4741 9.020731 ACACCATCGGAAAAATAGATAACTTTT 57.979 29.630 0.00 0.00 0.00 2.27
3547 4742 8.575649 ACACCATCGGAAAAATAGATAACTTT 57.424 30.769 0.00 0.00 0.00 2.66
3553 4748 6.414732 TGAGAACACCATCGGAAAAATAGAT 58.585 36.000 0.00 0.00 0.00 1.98
3559 4754 3.815809 ACTTGAGAACACCATCGGAAAA 58.184 40.909 0.00 0.00 0.00 2.29
3563 4758 2.094906 TCGTACTTGAGAACACCATCGG 60.095 50.000 0.00 0.00 0.00 4.18
3564 4759 3.211803 TCGTACTTGAGAACACCATCG 57.788 47.619 0.00 0.00 0.00 3.84
3574 4769 5.399604 AAAACGGTTTCTTCGTACTTGAG 57.600 39.130 6.57 0.00 40.18 3.02
3603 4914 5.063438 CGTAGAGATCCAAAATCGCAAAAGA 59.937 40.000 0.00 0.00 0.00 2.52
3611 4922 4.391830 TGCAACACGTAGAGATCCAAAATC 59.608 41.667 0.00 0.00 0.00 2.17
3626 4937 2.281234 GGTGTTTGTTCAATGCAACACG 59.719 45.455 7.68 0.00 35.97 4.49
3632 4943 5.989551 AAATGAAGGTGTTTGTTCAATGC 57.010 34.783 0.00 0.00 36.31 3.56
3661 4972 8.000127 GGATCCGGTCTCTAGGATATATAAAGT 59.000 40.741 0.00 0.00 46.42 2.66
3662 4973 7.999545 TGGATCCGGTCTCTAGGATATATAAAG 59.000 40.741 7.39 0.00 46.42 1.85
3664 4975 7.461633 TGGATCCGGTCTCTAGGATATATAA 57.538 40.000 7.39 0.00 46.42 0.98
3668 4979 3.626222 GCTGGATCCGGTCTCTAGGATAT 60.626 52.174 21.88 0.00 46.42 1.63
3678 4989 5.048713 CCAAATTATTTAGCTGGATCCGGTC 60.049 44.000 21.88 13.77 0.00 4.79
3679 4990 4.827284 CCAAATTATTTAGCTGGATCCGGT 59.173 41.667 21.88 16.30 0.00 5.28
3681 4992 5.070001 TCCCAAATTATTTAGCTGGATCCG 58.930 41.667 7.39 3.14 0.00 4.18
3688 4999 7.323420 GTCTTTGCTTCCCAAATTATTTAGCT 58.677 34.615 10.33 0.00 42.22 3.32
3689 5000 6.253512 CGTCTTTGCTTCCCAAATTATTTAGC 59.746 38.462 3.90 3.90 42.22 3.09
3706 5017 3.831715 ACTAGAAAATGGCGTCTTTGC 57.168 42.857 0.00 0.00 0.00 3.68
3712 5023 4.583073 AGGACAAAAACTAGAAAATGGCGT 59.417 37.500 0.00 0.00 0.00 5.68
3743 5054 5.805994 GGACAGGTACTAAGTTTCTTCATCG 59.194 44.000 0.00 0.00 36.02 3.84
3744 5055 6.937392 AGGACAGGTACTAAGTTTCTTCATC 58.063 40.000 0.00 0.00 36.02 2.92
3756 5067 2.781757 TGGCTAGCTAGGACAGGTACTA 59.218 50.000 22.10 0.00 36.02 1.82
3759 5070 1.749635 CGTGGCTAGCTAGGACAGGTA 60.750 57.143 22.10 0.00 36.15 3.08
3762 5073 0.101399 CACGTGGCTAGCTAGGACAG 59.899 60.000 25.06 11.70 0.00 3.51
3800 5111 1.909700 TCAACCTTGCTGGATGAACC 58.090 50.000 6.77 0.00 43.39 3.62
3812 5130 1.133513 TGCATGGAGTGGTTCAACCTT 60.134 47.619 8.40 0.00 39.58 3.50
3824 5142 6.665465 CATCAAACATACATAGTGCATGGAG 58.335 40.000 0.00 0.00 39.13 3.86
3830 5148 7.587629 ACATATGCATCAAACATACATAGTGC 58.412 34.615 0.19 0.00 33.03 4.40
3831 5149 9.955208 AAACATATGCATCAAACATACATAGTG 57.045 29.630 0.19 0.00 33.03 2.74
3837 5155 7.596248 GGGATGAAACATATGCATCAAACATAC 59.404 37.037 17.99 4.02 40.03 2.39
3870 5188 1.079503 CTAGTTCAAGAGCCGTTGCC 58.920 55.000 0.00 0.00 38.69 4.52
3880 5198 8.540492 CGCCATTAAATGTACTACTAGTTCAAG 58.460 37.037 0.00 0.00 29.44 3.02
3882 5200 7.774134 TCGCCATTAAATGTACTACTAGTTCA 58.226 34.615 0.00 0.00 30.18 3.18
3883 5201 8.700644 CATCGCCATTAAATGTACTACTAGTTC 58.299 37.037 0.00 0.00 0.00 3.01
3885 5203 7.948357 TCATCGCCATTAAATGTACTACTAGT 58.052 34.615 0.00 0.00 0.00 2.57
3886 5204 8.812147 TTCATCGCCATTAAATGTACTACTAG 57.188 34.615 0.00 0.00 0.00 2.57
3887 5205 9.772973 ATTTCATCGCCATTAAATGTACTACTA 57.227 29.630 0.00 0.00 0.00 1.82
3888 5206 8.677148 ATTTCATCGCCATTAAATGTACTACT 57.323 30.769 0.00 0.00 0.00 2.57
3894 5212 9.814899 TCAAAATATTTCATCGCCATTAAATGT 57.185 25.926 0.10 0.00 0.00 2.71
3897 5215 9.515020 GAGTCAAAATATTTCATCGCCATTAAA 57.485 29.630 0.10 0.00 0.00 1.52
3905 5223 5.967674 GCACTGGAGTCAAAATATTTCATCG 59.032 40.000 0.10 0.00 0.00 3.84
3907 5225 5.163622 CCGCACTGGAGTCAAAATATTTCAT 60.164 40.000 0.10 0.00 42.00 2.57
3912 5230 3.350219 ACCGCACTGGAGTCAAAATAT 57.650 42.857 0.00 0.00 42.00 1.28
3961 5290 2.430921 AACGAAGACCGCGAGCTG 60.431 61.111 8.23 0.00 43.32 4.24
3981 5310 7.614974 ACGTCTAGTTTAGTTTATCTCCTTCCT 59.385 37.037 0.00 0.00 0.00 3.36
4014 5343 4.262549 CCCCATCTGATCTCTGATCTCAAC 60.263 50.000 8.71 0.00 33.14 3.18
4036 5365 1.459592 CAGTCAACCGTTGTTCGATCC 59.540 52.381 11.01 0.00 42.86 3.36
4112 5443 5.697633 TGTGAAACGGAGTACTAATCAAACC 59.302 40.000 0.00 0.00 45.00 3.27
4129 5460 2.241176 TGGATCATAGGGGGTGTGAAAC 59.759 50.000 0.00 0.00 28.82 2.78
4141 5472 2.971330 ACTCAAGCCTCCTGGATCATAG 59.029 50.000 0.00 0.00 34.57 2.23
4142 5473 3.051940 ACTCAAGCCTCCTGGATCATA 57.948 47.619 0.00 0.00 34.57 2.15
4170 5501 7.712639 AGCTATATACACACACAAGGAAAGATG 59.287 37.037 0.00 0.00 0.00 2.90
4187 5518 9.435802 GTGCATACTTACATACGAGCTATATAC 57.564 37.037 0.00 0.00 0.00 1.47
4191 5522 6.150318 GTGTGCATACTTACATACGAGCTAT 58.850 40.000 6.31 0.00 0.00 2.97
4198 5529 7.306983 GGGTTATTCGTGTGCATACTTACATAC 60.307 40.741 12.05 3.18 0.00 2.39
4204 5535 4.189231 GAGGGTTATTCGTGTGCATACTT 58.811 43.478 12.05 0.00 0.00 2.24
4206 5537 2.538449 CGAGGGTTATTCGTGTGCATAC 59.462 50.000 3.05 3.05 33.57 2.39
4209 5540 1.017177 GCGAGGGTTATTCGTGTGCA 61.017 55.000 0.00 0.00 40.08 4.57
4212 5543 1.219935 GGGCGAGGGTTATTCGTGT 59.780 57.895 0.00 0.00 40.08 4.49
4216 5547 1.664873 GAGTTGGGCGAGGGTTATTC 58.335 55.000 0.00 0.00 0.00 1.75
4228 5559 1.338674 TGCGACTGTATTGGAGTTGGG 60.339 52.381 0.00 0.00 0.00 4.12
4229 5560 2.093306 TGCGACTGTATTGGAGTTGG 57.907 50.000 0.00 0.00 0.00 3.77
4234 5565 3.985279 GCGTATTATGCGACTGTATTGGA 59.015 43.478 6.92 0.00 0.00 3.53
4235 5566 4.307834 GCGTATTATGCGACTGTATTGG 57.692 45.455 6.92 0.00 0.00 3.16
4255 5586 1.443702 GGATTTGTTCCGCAACCGC 60.444 57.895 0.00 0.00 36.72 5.68
4264 5595 0.034863 TGTAGCCCCCGGATTTGTTC 60.035 55.000 0.73 0.00 0.00 3.18
4277 5608 4.342951 TGTGTATGTATGTAGGGTGTAGCC 59.657 45.833 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.