Multiple sequence alignment - TraesCS5D01G378900

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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 TraesCS5D01G378900 chr5D 100.000 6047 0 0 1 6047 450211621 450205575 0.000000e+00 11167.0
1 TraesCS5D01G378900 chr5A 94.581 4355 154 33 1272 5603 569550169 569545874 0.000000e+00 6660.0
2 TraesCS5D01G378900 chr5A 88.081 495 35 10 790 1275 569550677 569550198 3.160000e-157 566.0
3 TraesCS5D01G378900 chr5A 91.337 404 25 5 5647 6046 569545877 569545480 1.480000e-150 544.0
4 TraesCS5D01G378900 chr5A 82.181 376 50 12 3 367 569551515 569551146 2.120000e-79 307.0
5 TraesCS5D01G378900 chr5A 97.222 36 1 0 5616 5651 606169540 606169505 1.820000e-05 62.1
6 TraesCS5D01G378900 chr5A 97.143 35 1 0 5616 5650 458475434 458475400 6.550000e-05 60.2
7 TraesCS5D01G378900 chr5B 94.864 4167 157 30 1272 5423 550229908 550225784 0.000000e+00 6457.0
8 TraesCS5D01G378900 chr5B 85.909 809 56 31 5266 6047 550224387 550223610 0.000000e+00 809.0
9 TraesCS5D01G378900 chr5B 92.683 492 24 3 786 1275 550230418 550229937 0.000000e+00 699.0
10 TraesCS5D01G378900 chr5B 86.817 311 11 13 5651 5948 550225643 550225350 2.720000e-83 320.0
11 TraesCS5D01G378900 chr5B 96.809 94 3 0 525 618 386542047 386541954 2.260000e-34 158.0
12 TraesCS5D01G378900 chr5B 90.541 74 6 1 18 90 550231803 550231730 4.990000e-16 97.1
13 TraesCS5D01G378900 chr5B 90.164 61 5 1 5477 5537 713016351 713016410 1.810000e-10 78.7
14 TraesCS5D01G378900 chr4B 85.139 397 49 9 3135 3526 9359064 9359455 1.220000e-106 398.0
15 TraesCS5D01G378900 chr4B 95.876 97 3 1 531 626 498537655 498537559 8.110000e-34 156.0
16 TraesCS5D01G378900 chr3A 80.361 499 51 24 5382 5853 30182185 30182663 9.710000e-88 335.0
17 TraesCS5D01G378900 chr7B 96.939 98 3 0 527 624 54323441 54323344 1.350000e-36 165.0
18 TraesCS5D01G378900 chr2B 97.802 91 2 0 529 619 85695568 85695658 2.260000e-34 158.0
19 TraesCS5D01G378900 chr3B 95.876 97 3 1 528 624 798639476 798639381 8.110000e-34 156.0
20 TraesCS5D01G378900 chr3D 96.739 92 3 0 527 618 535746852 535746943 2.920000e-33 154.0
21 TraesCS5D01G378900 chr1D 92.593 108 4 3 532 635 195609573 195609680 1.050000e-32 152.0
22 TraesCS5D01G378900 chr6A 95.652 92 4 0 528 619 20747003 20747094 1.360000e-31 148.0
23 TraesCS5D01G378900 chr6A 92.537 67 5 0 3187 3253 381033194 381033128 4.990000e-16 97.1
24 TraesCS5D01G378900 chr2A 90.909 110 6 4 532 638 629643988 629644096 1.760000e-30 145.0
25 TraesCS5D01G378900 chr2A 88.679 53 5 1 5596 5648 197673901 197673850 5.060000e-06 63.9
26 TraesCS5D01G378900 chr2A 94.595 37 2 0 5615 5651 44768536 44768572 2.350000e-04 58.4
27 TraesCS5D01G378900 chr1B 95.312 64 3 0 3187 3250 624085362 624085425 1.070000e-17 102.0
28 TraesCS5D01G378900 chr6D 92.537 67 5 0 3187 3253 267518381 267518315 4.990000e-16 97.1
29 TraesCS5D01G378900 chr6D 94.872 39 1 1 5616 5654 406619797 406619760 6.550000e-05 60.2
30 TraesCS5D01G378900 chr6B 92.537 67 5 0 3187 3253 415867348 415867282 4.990000e-16 97.1
31 TraesCS5D01G378900 chr2D 92.857 42 2 1 5609 5650 544500939 544500899 6.550000e-05 60.2
32 TraesCS5D01G378900 chrUn 94.595 37 2 0 5615 5651 369681437 369681473 2.350000e-04 58.4
33 TraesCS5D01G378900 chrUn 94.595 37 2 0 5615 5651 382726918 382726882 2.350000e-04 58.4
34 TraesCS5D01G378900 chr1A 92.500 40 2 1 5616 5654 125146253 125146292 8.470000e-04 56.5


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 TraesCS5D01G378900 chr5D 450205575 450211621 6046 True 11167.00 11167 100.0000 1 6047 1 chr5D.!!$R1 6046
1 TraesCS5D01G378900 chr5A 569545480 569551515 6035 True 2019.25 6660 89.0450 3 6046 4 chr5A.!!$R3 6043
2 TraesCS5D01G378900 chr5B 550223610 550231803 8193 True 1676.42 6457 90.1628 18 6047 5 chr5B.!!$R2 6029

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
246 409 0.099259 CGGTGGCTTGTGCATATGTG 59.901 55.000 4.29 0.00 41.91 3.21 F
468 655 0.324943 CCGTTGTCATGTCTCCCCTT 59.675 55.000 0.00 0.00 0.00 3.95 F
1303 2072 0.161024 GCGTTTAGAGTGTCGTGTGC 59.839 55.000 0.00 0.00 0.00 4.57 F
1321 2090 0.249826 GCCTGATGCTAGACCTGCTC 60.250 60.000 0.00 0.00 36.87 4.26 F
1468 2238 0.959553 GTGTCCGTGGTTCTCTCTCA 59.040 55.000 0.00 0.00 0.00 3.27 F
1666 2437 2.898729 AGTGAGAACTATGGATGGCG 57.101 50.000 0.00 0.00 0.00 5.69 F
1685 2456 3.098636 GCGTTTTCAGAATATTCGGCAC 58.901 45.455 10.39 6.55 0.00 5.01 F
3380 4165 1.658994 ACGACTTTCTGCGGAAAACA 58.341 45.000 20.77 0.00 40.41 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 2053 0.161024 GCACACGACACTCTAAACGC 59.839 55.000 0.00 0.0 0.00 4.84 R
1421 2190 0.542702 ACAGGGGCAATTTGGTCCAG 60.543 55.000 0.00 0.0 32.89 3.86 R
3080 3861 1.280457 AGCTTCCTTGTGGAGGTAGG 58.720 55.000 1.70 0.0 46.39 3.18 R
3178 3962 2.187707 CACAGCTGCAAAAACACTCAC 58.812 47.619 15.27 0.0 0.00 3.51 R
3362 4147 1.660333 GCTGTTTTCCGCAGAAAGTCG 60.660 52.381 0.00 0.0 42.78 4.18 R
3380 4165 1.858739 TTGGAAATGGGCGGTAGGCT 61.859 55.000 0.00 0.0 42.94 4.58 R
3561 4346 5.251700 AGAAAGAACCCAGTCCAAGATATGT 59.748 40.000 0.00 0.0 0.00 2.29 R
5300 6096 1.250154 CGAATTTGCCCCAGCTTCCA 61.250 55.000 0.00 0.0 40.80 3.53 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
52 53 8.571336 CAAATGCAAGAAATACCCTAATAGAGG 58.429 37.037 0.00 0.00 46.25 3.69
61 62 8.425237 AAATACCCTAATAGAGGTTCTAGAGC 57.575 38.462 0.00 0.00 45.03 4.09
63 64 5.390387 ACCCTAATAGAGGTTCTAGAGCAG 58.610 45.833 8.96 0.00 45.03 4.24
122 284 4.162320 AGAGTATATGTGTCAACCAGTGGG 59.838 45.833 15.21 0.00 41.29 4.61
138 300 4.144297 CAGTGGGTTCTTTCTGATTTCCA 58.856 43.478 0.00 0.00 0.00 3.53
139 301 4.768968 CAGTGGGTTCTTTCTGATTTCCAT 59.231 41.667 0.00 0.00 0.00 3.41
142 304 4.044571 TGGGTTCTTTCTGATTTCCATCCT 59.955 41.667 0.00 0.00 0.00 3.24
144 306 5.105595 GGGTTCTTTCTGATTTCCATCCTTG 60.106 44.000 0.00 0.00 0.00 3.61
174 337 0.536233 TTGGCACCGCTCTTTGCTTA 60.536 50.000 0.00 0.00 38.85 3.09
182 345 3.826729 ACCGCTCTTTGCTTAATCCTTTT 59.173 39.130 0.00 0.00 40.11 2.27
184 347 4.091424 CGCTCTTTGCTTAATCCTTTTCG 58.909 43.478 0.00 0.00 40.11 3.46
185 348 4.378459 CGCTCTTTGCTTAATCCTTTTCGT 60.378 41.667 0.00 0.00 40.11 3.85
187 350 5.569441 GCTCTTTGCTTAATCCTTTTCGTTC 59.431 40.000 0.00 0.00 38.95 3.95
197 360 9.118236 CTTAATCCTTTTCGTTCACAAATCTTC 57.882 33.333 0.00 0.00 0.00 2.87
203 366 6.384258 TTTCGTTCACAAATCTTCCATCAA 57.616 33.333 0.00 0.00 0.00 2.57
219 382 4.289410 TCCATCAATCTTGTCCTTGAAGGA 59.711 41.667 10.46 10.46 43.32 3.36
233 396 4.455877 CCTTGAAGGATTATAATCGGTGGC 59.544 45.833 17.25 5.24 37.67 5.01
234 397 4.974645 TGAAGGATTATAATCGGTGGCT 57.025 40.909 17.25 7.23 36.27 4.75
242 405 2.700722 TAATCGGTGGCTTGTGCATA 57.299 45.000 0.00 0.00 41.91 3.14
246 409 0.099259 CGGTGGCTTGTGCATATGTG 59.901 55.000 4.29 0.00 41.91 3.21
275 439 6.914215 CGTAATGATCACATCAATTTTCCAGG 59.086 38.462 0.00 0.00 43.50 4.45
282 446 4.708421 CACATCAATTTTCCAGGGTCTCAT 59.292 41.667 0.00 0.00 0.00 2.90
288 452 0.613260 TTCCAGGGTCTCATTGGTCG 59.387 55.000 0.00 0.00 33.65 4.79
319 483 7.120138 TGCATGGACATGTATATTGCTAGAATG 59.880 37.037 17.90 0.00 40.80 2.67
323 487 6.875726 GGACATGTATATTGCTAGAATGCTCA 59.124 38.462 0.00 0.00 0.00 4.26
324 488 7.551974 GGACATGTATATTGCTAGAATGCTCAT 59.448 37.037 0.00 0.00 0.00 2.90
329 499 9.813446 TGTATATTGCTAGAATGCTCATATCAG 57.187 33.333 0.00 0.00 0.00 2.90
387 565 5.084818 CACTAAGGTGGACATGTGATACA 57.915 43.478 1.15 0.00 39.59 2.29
404 582 6.128580 TGTGATACACATGACAGAAAATCACG 60.129 38.462 0.00 0.00 42.98 4.35
405 583 3.542712 ACACATGACAGAAAATCACGC 57.457 42.857 0.00 0.00 0.00 5.34
406 584 2.226437 ACACATGACAGAAAATCACGCC 59.774 45.455 0.00 0.00 0.00 5.68
408 586 1.133025 CATGACAGAAAATCACGCCCC 59.867 52.381 0.00 0.00 0.00 5.80
409 587 0.608035 TGACAGAAAATCACGCCCCC 60.608 55.000 0.00 0.00 0.00 5.40
433 614 6.439058 CCCCACCCTAGATTTGTATTTTTGAA 59.561 38.462 0.00 0.00 0.00 2.69
462 649 4.003648 GGAAGAAATCCGTTGTCATGTCT 58.996 43.478 0.00 0.00 38.79 3.41
467 654 0.544357 TCCGTTGTCATGTCTCCCCT 60.544 55.000 0.00 0.00 0.00 4.79
468 655 0.324943 CCGTTGTCATGTCTCCCCTT 59.675 55.000 0.00 0.00 0.00 3.95
469 656 1.271379 CCGTTGTCATGTCTCCCCTTT 60.271 52.381 0.00 0.00 0.00 3.11
470 657 1.806542 CGTTGTCATGTCTCCCCTTTG 59.193 52.381 0.00 0.00 0.00 2.77
471 658 2.549992 CGTTGTCATGTCTCCCCTTTGA 60.550 50.000 0.00 0.00 0.00 2.69
472 659 2.814336 GTTGTCATGTCTCCCCTTTGAC 59.186 50.000 0.00 0.00 37.73 3.18
475 662 3.244561 TGTCATGTCTCCCCTTTGACTTC 60.245 47.826 0.00 0.00 38.00 3.01
476 663 3.008485 GTCATGTCTCCCCTTTGACTTCT 59.992 47.826 0.00 0.00 35.09 2.85
477 664 3.652869 TCATGTCTCCCCTTTGACTTCTT 59.347 43.478 0.00 0.00 34.57 2.52
478 665 3.492102 TGTCTCCCCTTTGACTTCTTG 57.508 47.619 0.00 0.00 34.57 3.02
479 666 2.106511 TGTCTCCCCTTTGACTTCTTGG 59.893 50.000 0.00 0.00 34.57 3.61
517 705 5.063880 AGAGACAAGTTCAACCCACAATAC 58.936 41.667 0.00 0.00 0.00 1.89
552 960 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
553 961 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
554 962 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
555 963 3.178865 TCCCTCCGTTCCAAATTACTCT 58.821 45.455 0.00 0.00 0.00 3.24
556 964 3.585732 TCCCTCCGTTCCAAATTACTCTT 59.414 43.478 0.00 0.00 0.00 2.85
558 966 3.617263 CCTCCGTTCCAAATTACTCTTCG 59.383 47.826 0.00 0.00 0.00 3.79
560 968 3.991773 TCCGTTCCAAATTACTCTTCGTG 59.008 43.478 0.00 0.00 0.00 4.35
561 969 3.124636 CCGTTCCAAATTACTCTTCGTGG 59.875 47.826 0.00 0.00 0.00 4.94
562 970 3.744426 CGTTCCAAATTACTCTTCGTGGT 59.256 43.478 0.00 0.00 0.00 4.16
566 974 7.518689 CGTTCCAAATTACTCTTCGTGGTTTTA 60.519 37.037 0.00 0.00 0.00 1.52
567 975 7.804843 TCCAAATTACTCTTCGTGGTTTTAA 57.195 32.000 0.00 0.00 0.00 1.52
568 976 8.398878 TCCAAATTACTCTTCGTGGTTTTAAT 57.601 30.769 0.00 0.00 0.00 1.40
570 978 9.124807 CCAAATTACTCTTCGTGGTTTTAATTC 57.875 33.333 0.00 0.00 0.00 2.17
571 979 9.672086 CAAATTACTCTTCGTGGTTTTAATTCA 57.328 29.630 0.00 0.00 0.00 2.57
592 1000 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
593 1001 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
594 1002 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
595 1003 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
599 1048 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
602 1051 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
640 1216 4.866921 CATACATGCCCACATCAAATGAG 58.133 43.478 0.00 0.00 32.87 2.90
677 1253 1.680105 CGTTCGGTTTCGTATGCGCT 61.680 55.000 9.73 0.00 38.14 5.92
680 1256 1.060308 CGGTTTCGTATGCGCTTGG 59.940 57.895 9.73 0.00 38.14 3.61
683 1259 1.733360 GGTTTCGTATGCGCTTGGTAA 59.267 47.619 9.73 0.00 38.14 2.85
684 1260 2.353579 GGTTTCGTATGCGCTTGGTAAT 59.646 45.455 9.73 0.00 38.14 1.89
685 1261 3.545426 GGTTTCGTATGCGCTTGGTAATC 60.545 47.826 9.73 0.00 38.14 1.75
687 1263 2.739292 TCGTATGCGCTTGGTAATCTC 58.261 47.619 9.73 0.00 38.14 2.75
688 1264 2.100087 TCGTATGCGCTTGGTAATCTCA 59.900 45.455 9.73 0.00 38.14 3.27
689 1265 3.059884 CGTATGCGCTTGGTAATCTCAT 58.940 45.455 9.73 0.00 0.00 2.90
690 1266 4.022676 TCGTATGCGCTTGGTAATCTCATA 60.023 41.667 9.73 0.00 38.14 2.15
691 1267 4.864806 CGTATGCGCTTGGTAATCTCATAT 59.135 41.667 9.73 0.00 0.00 1.78
692 1268 6.033966 CGTATGCGCTTGGTAATCTCATATA 58.966 40.000 9.73 0.00 0.00 0.86
707 1284 5.670485 TCTCATATAGTTCGTGCCATTGTT 58.330 37.500 0.00 0.00 0.00 2.83
709 1286 4.506288 TCATATAGTTCGTGCCATTGTTCG 59.494 41.667 0.00 0.00 0.00 3.95
712 1289 1.673920 AGTTCGTGCCATTGTTCGTTT 59.326 42.857 0.00 0.00 0.00 3.60
714 1291 3.500680 AGTTCGTGCCATTGTTCGTTTAT 59.499 39.130 0.00 0.00 0.00 1.40
715 1292 4.691685 AGTTCGTGCCATTGTTCGTTTATA 59.308 37.500 0.00 0.00 0.00 0.98
716 1293 4.850859 TCGTGCCATTGTTCGTTTATAG 57.149 40.909 0.00 0.00 0.00 1.31
717 1294 4.496360 TCGTGCCATTGTTCGTTTATAGA 58.504 39.130 0.00 0.00 0.00 1.98
718 1295 4.327898 TCGTGCCATTGTTCGTTTATAGAC 59.672 41.667 0.00 0.00 0.00 2.59
719 1296 4.092237 CGTGCCATTGTTCGTTTATAGACA 59.908 41.667 0.00 0.00 0.00 3.41
720 1297 5.321516 GTGCCATTGTTCGTTTATAGACAC 58.678 41.667 0.00 0.00 0.00 3.67
721 1298 5.121768 GTGCCATTGTTCGTTTATAGACACT 59.878 40.000 0.00 0.00 0.00 3.55
722 1299 5.121611 TGCCATTGTTCGTTTATAGACACTG 59.878 40.000 0.00 0.00 0.00 3.66
723 1300 5.350365 GCCATTGTTCGTTTATAGACACTGA 59.650 40.000 0.00 0.00 0.00 3.41
729 1306 8.651391 TGTTCGTTTATAGACACTGAGAAAAA 57.349 30.769 0.00 0.00 0.00 1.94
733 1310 6.402226 CGTTTATAGACACTGAGAAAAAGGCC 60.402 42.308 0.00 0.00 0.00 5.19
738 1315 3.096092 ACACTGAGAAAAAGGCCAAACA 58.904 40.909 5.01 0.00 0.00 2.83
758 1335 8.133627 CCAAACATTGCAAATTCCATAAAAACA 58.866 29.630 1.71 0.00 0.00 2.83
815 1538 1.817099 CAGGCCTGGCACGAATCTC 60.817 63.158 26.14 0.00 0.00 2.75
849 1572 2.509052 GGTCAAAAGTCAAACCCAGC 57.491 50.000 0.00 0.00 0.00 4.85
850 1573 1.754226 GGTCAAAAGTCAAACCCAGCA 59.246 47.619 0.00 0.00 0.00 4.41
851 1574 2.481276 GGTCAAAAGTCAAACCCAGCAC 60.481 50.000 0.00 0.00 0.00 4.40
852 1575 1.754226 TCAAAAGTCAAACCCAGCACC 59.246 47.619 0.00 0.00 0.00 5.01
853 1576 1.480137 CAAAAGTCAAACCCAGCACCA 59.520 47.619 0.00 0.00 0.00 4.17
868 1591 2.068821 ACCAGCAGCATCCGATCCT 61.069 57.895 0.00 0.00 0.00 3.24
949 1683 3.864983 TTTCCCCCACCTCGCCTCT 62.865 63.158 0.00 0.00 0.00 3.69
950 1684 4.779733 TCCCCCACCTCGCCTCTC 62.780 72.222 0.00 0.00 0.00 3.20
952 1686 4.787280 CCCCACCTCGCCTCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
953 1687 3.151022 CCCACCTCGCCTCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
954 1688 3.151022 CCACCTCGCCTCTCCTCC 61.151 72.222 0.00 0.00 0.00 4.30
955 1689 3.151022 CACCTCGCCTCTCCTCCC 61.151 72.222 0.00 0.00 0.00 4.30
956 1690 3.351885 ACCTCGCCTCTCCTCCCT 61.352 66.667 0.00 0.00 0.00 4.20
957 1691 2.520741 CCTCGCCTCTCCTCCCTC 60.521 72.222 0.00 0.00 0.00 4.30
1113 1848 1.890489 GTAAACAGACGCCCCCATTTT 59.110 47.619 0.00 0.00 0.00 1.82
1119 1854 1.928714 GACGCCCCCATTTTCCCCTA 61.929 60.000 0.00 0.00 0.00 3.53
1272 2008 1.298413 CGCGGTCCGTGTAGATCTG 60.298 63.158 16.85 0.00 32.40 2.90
1275 2011 1.065928 GGTCCGTGTAGATCTGGCG 59.934 63.158 5.18 6.94 0.00 5.69
1277 2013 2.049767 TCCGTGTAGATCTGGCGCA 61.050 57.895 10.83 0.00 0.00 6.09
1303 2072 0.161024 GCGTTTAGAGTGTCGTGTGC 59.839 55.000 0.00 0.00 0.00 4.57
1321 2090 0.249826 GCCTGATGCTAGACCTGCTC 60.250 60.000 0.00 0.00 36.87 4.26
1396 2165 3.681705 CTGTTACAGCCAACATGCG 57.318 52.632 0.00 0.00 37.75 4.73
1421 2190 2.870411 AGCGTCGGTTAAATTAGGATGC 59.130 45.455 0.00 6.79 39.35 3.91
1433 2202 5.603170 AATTAGGATGCTGGACCAAATTG 57.397 39.130 0.00 0.00 0.00 2.32
1443 2213 2.252714 GGACCAAATTGCCCCTGTAAA 58.747 47.619 0.00 0.00 0.00 2.01
1449 2219 4.937015 CCAAATTGCCCCTGTAAATTCTTG 59.063 41.667 0.00 0.00 0.00 3.02
1454 2224 2.492088 GCCCCTGTAAATTCTTGTGTCC 59.508 50.000 0.00 0.00 0.00 4.02
1468 2238 0.959553 GTGTCCGTGGTTCTCTCTCA 59.040 55.000 0.00 0.00 0.00 3.27
1479 2249 3.008049 GGTTCTCTCTCAGGCCTTGTTTA 59.992 47.826 0.00 0.00 0.00 2.01
1488 2259 5.071250 TCTCAGGCCTTGTTTACTTGAGTTA 59.929 40.000 0.00 0.00 0.00 2.24
1490 2261 5.071250 TCAGGCCTTGTTTACTTGAGTTAGA 59.929 40.000 0.00 0.00 0.00 2.10
1495 2266 5.179555 CCTTGTTTACTTGAGTTAGAGTGCC 59.820 44.000 0.00 0.00 0.00 5.01
1497 2268 5.539048 TGTTTACTTGAGTTAGAGTGCCTC 58.461 41.667 0.00 0.00 0.00 4.70
1499 2270 5.801531 TTACTTGAGTTAGAGTGCCTCAA 57.198 39.130 0.00 0.00 41.55 3.02
1501 2272 7.476540 TTACTTGAGTTAGAGTGCCTCAATA 57.523 36.000 0.00 0.00 42.51 1.90
1536 2307 6.673154 TCAGCTTATCATGATGTTGTTGAG 57.327 37.500 18.72 0.00 0.00 3.02
1589 2360 6.458342 GCACCTATGTTCACTGCCTAAAATAC 60.458 42.308 0.00 0.00 0.00 1.89
1666 2437 2.898729 AGTGAGAACTATGGATGGCG 57.101 50.000 0.00 0.00 0.00 5.69
1685 2456 3.098636 GCGTTTTCAGAATATTCGGCAC 58.901 45.455 10.39 6.55 0.00 5.01
1693 2464 7.946655 TTCAGAATATTCGGCACTGTATTAG 57.053 36.000 10.39 0.00 0.00 1.73
1746 2517 7.705325 CGTGTAGCATACTAAGTGGTATTTTCT 59.295 37.037 0.00 0.00 43.54 2.52
1790 2561 7.408756 TCAGGTAAGCTATTTTTGCATGATT 57.591 32.000 0.00 0.00 28.67 2.57
1795 2566 9.971922 GGTAAGCTATTTTTGCATGATTCTATT 57.028 29.630 0.00 0.00 0.00 1.73
1824 2595 9.653287 TGCTATATAGGTTTATTACTGTGATGC 57.347 33.333 11.72 0.00 0.00 3.91
1825 2596 9.877178 GCTATATAGGTTTATTACTGTGATGCT 57.123 33.333 11.72 0.00 0.00 3.79
1831 2602 8.438676 AGGTTTATTACTGTGATGCTAATGTC 57.561 34.615 0.00 0.00 0.00 3.06
1832 2603 7.499232 AGGTTTATTACTGTGATGCTAATGTCC 59.501 37.037 0.00 0.00 0.00 4.02
1833 2604 7.345192 GTTTATTACTGTGATGCTAATGTCCG 58.655 38.462 0.00 0.00 0.00 4.79
1834 2605 4.729227 TTACTGTGATGCTAATGTCCGA 57.271 40.909 0.00 0.00 0.00 4.55
1835 2606 3.827008 ACTGTGATGCTAATGTCCGAT 57.173 42.857 0.00 0.00 0.00 4.18
1853 2624 5.795441 GTCCGATTCTGTGCTTTGTTTATTC 59.205 40.000 0.00 0.00 0.00 1.75
1866 2637 6.417930 GCTTTGTTTATTCTGTGTTCCACTTC 59.582 38.462 0.00 0.00 35.11 3.01
1868 2639 7.581213 TTGTTTATTCTGTGTTCCACTTCAT 57.419 32.000 0.00 0.00 35.11 2.57
2312 3086 7.307694 TGAATTTGTTCATTCTGCAGACATAC 58.692 34.615 18.03 12.56 34.66 2.39
2346 3120 7.201617 GCTTATGTTCCTTGGTTACTCATGTAC 60.202 40.741 0.00 0.00 0.00 2.90
2549 3330 6.263344 GTGGTTTGAAGTCTACAAGGTTTTC 58.737 40.000 0.00 0.00 0.00 2.29
2626 3407 8.233692 GTGTTAACACAAACATGTCTTTTTGA 57.766 30.769 29.46 0.00 45.75 2.69
2647 3428 6.668541 TGAAAAGTGCATGCTAGTTATCTC 57.331 37.500 20.33 11.44 0.00 2.75
2850 3631 5.244851 TCAGATCCACCTGATATTGTCTAGC 59.755 44.000 0.00 0.00 38.18 3.42
2856 3637 6.382859 TCCACCTGATATTGTCTAGCAACTAA 59.617 38.462 2.35 0.00 40.28 2.24
3380 4165 1.658994 ACGACTTTCTGCGGAAAACA 58.341 45.000 20.77 0.00 40.41 2.83
3561 4346 7.039313 TCTCTGTGCGCTTATTCTTCTATAA 57.961 36.000 9.73 0.00 0.00 0.98
3703 4488 4.160065 TGGGTGCTCATAATTTGGTTCATG 59.840 41.667 0.00 0.00 0.00 3.07
3816 4601 7.056635 AGAACATTCTCCTTGTTTCTTCAGAA 58.943 34.615 0.00 0.00 37.43 3.02
3888 4673 6.170506 TCGAATAACTGTTAAGTTGCAGGAT 58.829 36.000 4.11 4.60 46.30 3.24
3935 4720 6.265196 ACCATGTTCAAAGCAGATAAAAGTCA 59.735 34.615 0.00 0.00 0.00 3.41
3954 4739 9.561069 AAAAGTCATGTTCAGTATAGTTCTGTT 57.439 29.630 0.00 0.00 34.86 3.16
4173 4958 5.125900 TGAATTTGGACATGACTGGCTATTG 59.874 40.000 0.00 0.00 0.00 1.90
4187 4972 2.618709 GGCTATTGGGTGCACATACTTC 59.381 50.000 20.43 0.00 0.00 3.01
4194 4979 3.244875 TGGGTGCACATACTTCTGATTGT 60.245 43.478 20.43 0.00 0.00 2.71
4200 4986 8.028938 GGTGCACATACTTCTGATTGTTTTATT 58.971 33.333 20.43 0.00 0.00 1.40
4232 5018 3.314693 ACTGACTTTCCCTGGTCTTGTA 58.685 45.455 0.00 0.00 34.01 2.41
4253 5039 4.468689 GGGCACGGGTGGAGCTAC 62.469 72.222 0.43 0.00 0.00 3.58
4309 5095 2.010145 GAGCTTTGCTCGGTATGTGA 57.990 50.000 3.73 0.00 45.85 3.58
4498 5285 8.496751 GGAAAGAGCCGAGTATGTTTATTAATC 58.503 37.037 0.00 0.00 0.00 1.75
4715 5508 0.814010 ACGCAAACAGGACGAGCTTT 60.814 50.000 0.00 0.00 0.00 3.51
4740 5533 5.449553 CCTATTAGTTTCTGGGGCATTTCT 58.550 41.667 0.00 0.00 0.00 2.52
4819 5613 7.970614 GGATTCAAGATGTATTTGTGTTTCTCC 59.029 37.037 0.00 0.00 0.00 3.71
4820 5614 7.815840 TTCAAGATGTATTTGTGTTTCTCCA 57.184 32.000 0.00 0.00 0.00 3.86
5239 6035 7.548075 GTGTGTTGTGGCTTTATGTACTATAGT 59.452 37.037 10.87 10.87 0.00 2.12
5300 6096 0.537188 CTGGTATGTTCCCTCGCAGT 59.463 55.000 0.00 0.00 0.00 4.40
5326 7668 2.612721 GCTGGGGCAAATTCGAACAAAT 60.613 45.455 0.00 0.00 38.54 2.32
5423 7765 6.122277 TCTTCTGGTGTTTTCTGTTTGAGAT 58.878 36.000 0.00 0.00 0.00 2.75
5424 7766 5.756195 TCTGGTGTTTTCTGTTTGAGATG 57.244 39.130 0.00 0.00 0.00 2.90
5425 7767 5.436175 TCTGGTGTTTTCTGTTTGAGATGA 58.564 37.500 0.00 0.00 0.00 2.92
5426 7768 5.528690 TCTGGTGTTTTCTGTTTGAGATGAG 59.471 40.000 0.00 0.00 0.00 2.90
5427 7769 5.436175 TGGTGTTTTCTGTTTGAGATGAGA 58.564 37.500 0.00 0.00 0.00 3.27
5584 7940 0.165944 GTCACGGAAGCCATTCAACG 59.834 55.000 0.00 0.00 37.15 4.10
5585 7941 0.250124 TCACGGAAGCCATTCAACGT 60.250 50.000 0.00 0.00 37.15 3.99
5597 7953 7.270757 AGCCATTCAACGTAATGCATATTTA 57.729 32.000 0.00 0.00 35.85 1.40
5598 7954 7.138736 AGCCATTCAACGTAATGCATATTTAC 58.861 34.615 0.00 0.00 35.85 2.01
5599 7955 7.013274 AGCCATTCAACGTAATGCATATTTACT 59.987 33.333 0.00 0.00 35.85 2.24
5600 7956 8.286800 GCCATTCAACGTAATGCATATTTACTA 58.713 33.333 0.00 0.00 35.85 1.82
5605 7961 7.654520 TCAACGTAATGCATATTTACTACTCCC 59.345 37.037 0.00 0.00 0.00 4.30
5606 7962 7.299246 ACGTAATGCATATTTACTACTCCCT 57.701 36.000 0.00 0.00 0.00 4.20
5607 7963 7.732996 ACGTAATGCATATTTACTACTCCCTT 58.267 34.615 0.00 0.00 0.00 3.95
5609 7965 9.871238 CGTAATGCATATTTACTACTCCCTTAT 57.129 33.333 0.00 0.00 0.00 1.73
5682 8039 5.050126 TGTATGGTCAGGGTTGTTTTGTA 57.950 39.130 0.00 0.00 0.00 2.41
5723 8081 3.119137 GGTATTACCAGCCAGCCAAAAAG 60.119 47.826 8.03 0.00 38.42 2.27
5772 8132 4.623932 ATCACACTCAAGCTTAGTTGGA 57.376 40.909 0.00 4.22 0.00 3.53
5843 8203 3.127425 ACTGTTCTGTGTAAAGGAGGC 57.873 47.619 0.00 0.00 0.00 4.70
5869 8229 4.523083 CAGTAAAAGGCCAGCCAACTATA 58.477 43.478 12.03 0.00 38.92 1.31
5870 8230 4.335594 CAGTAAAAGGCCAGCCAACTATAC 59.664 45.833 12.03 6.71 38.92 1.47
5882 8242 2.235402 CCAACTATACGACCCTGGTTGT 59.765 50.000 13.59 13.59 44.23 3.32
5883 8243 3.518590 CAACTATACGACCCTGGTTGTC 58.481 50.000 12.50 0.00 41.43 3.18
5967 8336 1.308998 CCTGGTTGGTGAACACTGAC 58.691 55.000 4.96 4.34 33.27 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 8.637281 TTTCTTGCATTTGTGCATATATCAAG 57.363 30.769 3.73 13.78 44.94 3.02
23 24 4.192429 AGGGTATTTCTTGCATTTGTGC 57.808 40.909 0.00 0.00 0.00 4.57
116 278 4.144297 TGGAAATCAGAAAGAACCCACTG 58.856 43.478 0.00 0.00 0.00 3.66
122 284 5.405797 GCAAGGATGGAAATCAGAAAGAAC 58.594 41.667 0.00 0.00 0.00 3.01
128 290 1.925255 AGGGCAAGGATGGAAATCAGA 59.075 47.619 0.00 0.00 0.00 3.27
138 300 2.621668 GCCAACTTCTAAGGGCAAGGAT 60.622 50.000 0.00 0.00 45.70 3.24
139 301 1.271926 GCCAACTTCTAAGGGCAAGGA 60.272 52.381 0.00 0.00 45.70 3.36
144 306 1.305930 CGGTGCCAACTTCTAAGGGC 61.306 60.000 0.00 0.00 46.58 5.19
174 337 6.040391 TGGAAGATTTGTGAACGAAAAGGATT 59.960 34.615 0.00 0.00 0.00 3.01
182 345 5.939883 AGATTGATGGAAGATTTGTGAACGA 59.060 36.000 0.00 0.00 0.00 3.85
184 347 7.373493 ACAAGATTGATGGAAGATTTGTGAAC 58.627 34.615 0.00 0.00 0.00 3.18
185 348 7.309377 GGACAAGATTGATGGAAGATTTGTGAA 60.309 37.037 0.00 0.00 0.00 3.18
187 350 6.152323 AGGACAAGATTGATGGAAGATTTGTG 59.848 38.462 0.00 0.00 0.00 3.33
197 360 4.592942 TCCTTCAAGGACAAGATTGATGG 58.407 43.478 0.34 11.58 45.38 3.51
219 382 3.550820 TGCACAAGCCACCGATTATAAT 58.449 40.909 0.00 0.00 41.13 1.28
220 383 2.992593 TGCACAAGCCACCGATTATAA 58.007 42.857 0.00 0.00 41.13 0.98
233 396 6.541969 TCATTACGAAACACATATGCACAAG 58.458 36.000 1.58 0.00 0.00 3.16
234 397 6.487689 TCATTACGAAACACATATGCACAA 57.512 33.333 1.58 0.00 0.00 3.33
246 409 8.798153 GGAAAATTGATGTGATCATTACGAAAC 58.202 33.333 0.00 0.00 39.39 2.78
319 483 6.346896 TCATATCTGGAATGCTGATATGAGC 58.653 40.000 27.39 7.29 46.46 4.26
367 545 5.084818 TGTGTATCACATGTCCACCTTAG 57.915 43.478 0.00 0.00 39.62 2.18
386 564 2.414559 GGGCGTGATTTTCTGTCATGTG 60.415 50.000 0.00 0.00 35.52 3.21
387 565 1.812571 GGGCGTGATTTTCTGTCATGT 59.187 47.619 0.00 0.00 35.52 3.21
392 570 4.415783 GGGGGCGTGATTTTCTGT 57.584 55.556 0.00 0.00 0.00 3.41
408 586 5.955355 TCAAAAATACAAATCTAGGGTGGGG 59.045 40.000 0.00 0.00 0.00 4.96
409 587 7.475137 TTCAAAAATACAAATCTAGGGTGGG 57.525 36.000 0.00 0.00 0.00 4.61
433 614 7.519032 TGACAACGGATTTCTTCCTTTTAAT 57.481 32.000 0.00 0.00 42.99 1.40
449 636 0.324943 AAGGGGAGACATGACAACGG 59.675 55.000 0.00 0.00 0.00 4.44
451 638 2.814336 GTCAAAGGGGAGACATGACAAC 59.186 50.000 0.00 0.00 40.02 3.32
460 647 2.418669 ACCAAGAAGTCAAAGGGGAGA 58.581 47.619 0.00 0.00 0.00 3.71
462 649 2.512056 TCAACCAAGAAGTCAAAGGGGA 59.488 45.455 0.00 0.00 0.00 4.81
467 654 5.420421 TGGTGATTTCAACCAAGAAGTCAAA 59.580 36.000 3.92 0.00 43.07 2.69
468 655 4.952957 TGGTGATTTCAACCAAGAAGTCAA 59.047 37.500 3.92 0.00 43.07 3.18
469 656 4.338118 GTGGTGATTTCAACCAAGAAGTCA 59.662 41.667 0.00 0.00 40.50 3.41
470 657 4.338118 TGTGGTGATTTCAACCAAGAAGTC 59.662 41.667 0.00 0.00 35.53 3.01
471 658 4.277476 TGTGGTGATTTCAACCAAGAAGT 58.723 39.130 0.00 0.00 35.05 3.01
472 659 4.916983 TGTGGTGATTTCAACCAAGAAG 57.083 40.909 0.00 0.00 35.05 2.85
475 662 4.580167 TCTCTTGTGGTGATTTCAACCAAG 59.420 41.667 15.15 15.15 40.24 3.61
476 663 4.338118 GTCTCTTGTGGTGATTTCAACCAA 59.662 41.667 0.00 0.00 35.05 3.67
477 664 3.882888 GTCTCTTGTGGTGATTTCAACCA 59.117 43.478 0.00 0.00 31.06 3.67
478 665 3.882888 TGTCTCTTGTGGTGATTTCAACC 59.117 43.478 0.00 0.00 31.06 3.77
479 666 5.066505 ACTTGTCTCTTGTGGTGATTTCAAC 59.933 40.000 0.00 0.00 0.00 3.18
517 705 1.209128 GGAGTACATTCGATGTGCCG 58.791 55.000 9.77 0.00 45.45 5.69
552 960 9.243637 TCAAATTTGAATTAAAACCACGAAGAG 57.756 29.630 18.45 0.00 33.55 2.85
553 961 9.587772 TTCAAATTTGAATTAAAACCACGAAGA 57.412 25.926 26.01 1.80 41.88 2.87
568 976 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
570 978 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
571 979 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
574 982 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
575 983 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
576 984 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
579 987 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
580 988 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
583 991 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
584 992 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
585 993 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
586 994 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
587 995 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
590 998 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
591 999 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
592 1000 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
593 1001 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
594 1002 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
595 1003 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
599 1048 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
602 1051 1.340568 GTATGCTACTCCCTCCGTTCC 59.659 57.143 0.00 0.00 0.00 3.62
640 1216 6.364435 ACCGAACGAAGAGTTTATACAAGTTC 59.636 38.462 0.00 0.00 44.35 3.01
654 1230 1.987770 GCATACGAAACCGAACGAAGA 59.012 47.619 0.00 0.00 0.00 2.87
657 1233 1.676438 GCGCATACGAAACCGAACGA 61.676 55.000 0.30 0.00 43.93 3.85
677 1253 6.183360 TGGCACGAACTATATGAGATTACCAA 60.183 38.462 0.00 0.00 0.00 3.67
680 1256 7.385205 ACAATGGCACGAACTATATGAGATTAC 59.615 37.037 0.00 0.00 0.00 1.89
683 1259 5.858381 ACAATGGCACGAACTATATGAGAT 58.142 37.500 0.00 0.00 0.00 2.75
684 1260 5.276461 ACAATGGCACGAACTATATGAGA 57.724 39.130 0.00 0.00 0.00 3.27
685 1261 5.332581 CGAACAATGGCACGAACTATATGAG 60.333 44.000 0.00 0.00 0.00 2.90
687 1263 4.270084 ACGAACAATGGCACGAACTATATG 59.730 41.667 1.25 0.00 0.00 1.78
688 1264 4.439057 ACGAACAATGGCACGAACTATAT 58.561 39.130 1.25 0.00 0.00 0.86
689 1265 3.852286 ACGAACAATGGCACGAACTATA 58.148 40.909 1.25 0.00 0.00 1.31
690 1266 2.695359 ACGAACAATGGCACGAACTAT 58.305 42.857 1.25 0.00 0.00 2.12
691 1267 2.157834 ACGAACAATGGCACGAACTA 57.842 45.000 1.25 0.00 0.00 2.24
692 1268 1.305201 AACGAACAATGGCACGAACT 58.695 45.000 1.25 0.00 0.00 3.01
707 1284 6.367969 GCCTTTTTCTCAGTGTCTATAAACGA 59.632 38.462 0.00 0.00 0.00 3.85
709 1286 6.430000 TGGCCTTTTTCTCAGTGTCTATAAAC 59.570 38.462 3.32 0.00 0.00 2.01
712 1289 5.755409 TGGCCTTTTTCTCAGTGTCTATA 57.245 39.130 3.32 0.00 0.00 1.31
714 1291 4.431416 TTGGCCTTTTTCTCAGTGTCTA 57.569 40.909 3.32 0.00 0.00 2.59
715 1292 3.297134 TTGGCCTTTTTCTCAGTGTCT 57.703 42.857 3.32 0.00 0.00 3.41
716 1293 3.130340 TGTTTGGCCTTTTTCTCAGTGTC 59.870 43.478 3.32 0.00 0.00 3.67
717 1294 3.096092 TGTTTGGCCTTTTTCTCAGTGT 58.904 40.909 3.32 0.00 0.00 3.55
718 1295 3.799281 TGTTTGGCCTTTTTCTCAGTG 57.201 42.857 3.32 0.00 0.00 3.66
719 1296 4.696455 CAATGTTTGGCCTTTTTCTCAGT 58.304 39.130 3.32 0.00 0.00 3.41
720 1297 3.495753 GCAATGTTTGGCCTTTTTCTCAG 59.504 43.478 3.32 0.00 0.00 3.35
721 1298 3.118482 TGCAATGTTTGGCCTTTTTCTCA 60.118 39.130 3.32 0.00 0.00 3.27
722 1299 3.465871 TGCAATGTTTGGCCTTTTTCTC 58.534 40.909 3.32 0.00 0.00 2.87
723 1300 3.557228 TGCAATGTTTGGCCTTTTTCT 57.443 38.095 3.32 0.00 0.00 2.52
729 1306 2.106166 TGGAATTTGCAATGTTTGGCCT 59.894 40.909 3.32 0.00 0.00 5.19
733 1310 9.512435 TTGTTTTTATGGAATTTGCAATGTTTG 57.488 25.926 0.00 0.00 0.00 2.93
738 1315 8.462589 AACCTTGTTTTTATGGAATTTGCAAT 57.537 26.923 0.00 0.00 0.00 3.56
772 1349 1.861982 AGGTACTACAGCGTTGGGAT 58.138 50.000 3.74 0.00 36.02 3.85
780 1357 3.492829 GGCCTGATGTTAGGTACTACAGC 60.493 52.174 0.00 0.00 42.67 4.40
847 1570 2.937379 GATCGGATGCTGCTGGTGCT 62.937 60.000 0.00 0.00 40.48 4.40
848 1571 2.515523 ATCGGATGCTGCTGGTGC 60.516 61.111 0.00 0.00 40.20 5.01
849 1572 1.890979 GGATCGGATGCTGCTGGTG 60.891 63.158 1.86 0.00 0.00 4.17
850 1573 2.037620 GAGGATCGGATGCTGCTGGT 62.038 60.000 17.16 0.00 0.00 4.00
851 1574 1.301558 GAGGATCGGATGCTGCTGG 60.302 63.158 17.16 0.00 0.00 4.85
852 1575 0.879400 GTGAGGATCGGATGCTGCTG 60.879 60.000 17.16 0.00 38.61 4.41
853 1576 1.445095 GTGAGGATCGGATGCTGCT 59.555 57.895 17.16 0.00 38.61 4.24
868 1591 2.604152 GTGGGTTGGGTTGGGTGA 59.396 61.111 0.00 0.00 0.00 4.02
949 1683 4.075793 CACGGGAGGGAGGGAGGA 62.076 72.222 0.00 0.00 32.31 3.71
951 1685 4.787280 AGCACGGGAGGGAGGGAG 62.787 72.222 0.00 0.00 32.31 4.30
952 1686 4.779733 GAGCACGGGAGGGAGGGA 62.780 72.222 0.00 0.00 32.31 4.20
990 1725 3.124921 GTCGCCATCGGTGGGTTG 61.125 66.667 18.38 0.00 46.14 3.77
1113 1848 2.533916 CAGAGCAGAGCATATAGGGGA 58.466 52.381 0.00 0.00 0.00 4.81
1119 1854 2.036217 GTCAGAGCAGAGCAGAGCATAT 59.964 50.000 0.00 0.00 0.00 1.78
1275 2011 2.484264 ACACTCTAAACGCTGGATTTGC 59.516 45.455 0.00 0.00 0.00 3.68
1277 2013 2.993899 CGACACTCTAAACGCTGGATTT 59.006 45.455 0.00 0.00 0.00 2.17
1284 2053 0.161024 GCACACGACACTCTAAACGC 59.839 55.000 0.00 0.00 0.00 4.84
1303 2072 1.068895 CTGAGCAGGTCTAGCATCAGG 59.931 57.143 0.38 0.00 35.52 3.86
1321 2090 5.357314 AGTTCAATCAATCAATCTCAGCCTG 59.643 40.000 0.00 0.00 0.00 4.85
1328 2097 7.013083 GGTATCTGCAGTTCAATCAATCAATCT 59.987 37.037 14.67 0.00 0.00 2.40
1388 2157 4.465512 GACGCTGGCCGCATGTTG 62.466 66.667 17.57 5.43 41.76 3.33
1395 2164 1.641123 AATTTAACCGACGCTGGCCG 61.641 55.000 0.00 0.00 44.21 6.13
1396 2165 1.329599 CTAATTTAACCGACGCTGGCC 59.670 52.381 0.00 0.00 0.00 5.36
1401 2170 2.870411 AGCATCCTAATTTAACCGACGC 59.130 45.455 0.00 0.00 0.00 5.19
1409 2178 6.406849 GCAATTTGGTCCAGCATCCTAATTTA 60.407 38.462 0.00 0.00 37.17 1.40
1421 2190 0.542702 ACAGGGGCAATTTGGTCCAG 60.543 55.000 0.00 0.00 32.89 3.86
1433 2202 2.492088 GGACACAAGAATTTACAGGGGC 59.508 50.000 0.00 0.00 0.00 5.80
1443 2213 2.368875 AGAGAACCACGGACACAAGAAT 59.631 45.455 0.00 0.00 0.00 2.40
1449 2219 0.959553 TGAGAGAGAACCACGGACAC 59.040 55.000 0.00 0.00 0.00 3.67
1454 2224 1.216710 GGCCTGAGAGAGAACCACG 59.783 63.158 0.00 0.00 0.00 4.94
1468 2238 5.071923 ACTCTAACTCAAGTAAACAAGGCCT 59.928 40.000 0.00 0.00 0.00 5.19
1495 2266 6.893958 AGCTGAAAGTTGTACGATATTGAG 57.106 37.500 0.00 0.00 35.30 3.02
1497 2268 8.817100 TGATAAGCTGAAAGTTGTACGATATTG 58.183 33.333 0.00 0.00 35.30 1.90
1499 2270 8.982685 CATGATAAGCTGAAAGTTGTACGATAT 58.017 33.333 0.00 0.00 35.30 1.63
1501 2272 7.041721 TCATGATAAGCTGAAAGTTGTACGAT 58.958 34.615 0.00 0.00 35.30 3.73
1589 2360 5.195940 AGATCCACCCAAGTATTTCACATG 58.804 41.667 0.00 0.00 0.00 3.21
1666 2437 5.296813 ACAGTGCCGAATATTCTGAAAAC 57.703 39.130 13.45 6.75 0.00 2.43
1685 2456 7.148474 ACGTGTAAATTTGAGCCACTAATACAG 60.148 37.037 0.00 0.00 0.00 2.74
1693 2464 3.429543 TCGTACGTGTAAATTTGAGCCAC 59.570 43.478 16.05 2.04 0.00 5.01
1746 2517 8.177119 ACCTGAAAGCACTCATATTAACAAAA 57.823 30.769 0.00 0.00 0.00 2.44
1821 2592 2.874701 GCACAGAATCGGACATTAGCAT 59.125 45.455 0.00 0.00 0.00 3.79
1822 2593 2.093500 AGCACAGAATCGGACATTAGCA 60.093 45.455 0.00 0.00 0.00 3.49
1823 2594 2.555199 AGCACAGAATCGGACATTAGC 58.445 47.619 0.00 0.00 0.00 3.09
1824 2595 4.393062 ACAAAGCACAGAATCGGACATTAG 59.607 41.667 0.00 0.00 0.00 1.73
1825 2596 4.323417 ACAAAGCACAGAATCGGACATTA 58.677 39.130 0.00 0.00 0.00 1.90
1826 2597 3.149196 ACAAAGCACAGAATCGGACATT 58.851 40.909 0.00 0.00 0.00 2.71
1827 2598 2.783135 ACAAAGCACAGAATCGGACAT 58.217 42.857 0.00 0.00 0.00 3.06
1828 2599 2.254546 ACAAAGCACAGAATCGGACA 57.745 45.000 0.00 0.00 0.00 4.02
1829 2600 3.626028 AAACAAAGCACAGAATCGGAC 57.374 42.857 0.00 0.00 0.00 4.79
1830 2601 5.705441 AGAATAAACAAAGCACAGAATCGGA 59.295 36.000 0.00 0.00 0.00 4.55
1831 2602 5.796935 CAGAATAAACAAAGCACAGAATCGG 59.203 40.000 0.00 0.00 0.00 4.18
1832 2603 6.303970 CACAGAATAAACAAAGCACAGAATCG 59.696 38.462 0.00 0.00 0.00 3.34
1833 2604 7.141363 ACACAGAATAAACAAAGCACAGAATC 58.859 34.615 0.00 0.00 0.00 2.52
1834 2605 7.042797 ACACAGAATAAACAAAGCACAGAAT 57.957 32.000 0.00 0.00 0.00 2.40
1835 2606 6.449635 ACACAGAATAAACAAAGCACAGAA 57.550 33.333 0.00 0.00 0.00 3.02
1916 2687 4.261614 GCCTACACACATCGATCACTCATA 60.262 45.833 0.00 0.00 0.00 2.15
1917 2688 3.491619 GCCTACACACATCGATCACTCAT 60.492 47.826 0.00 0.00 0.00 2.90
2312 3086 2.936498 CAAGGAACATAAGCAGGTACCG 59.064 50.000 6.18 2.66 0.00 4.02
2476 3257 9.945904 AAATGTAAAAACCCTACACAAGAAAAA 57.054 25.926 0.00 0.00 32.27 1.94
2626 3407 6.176183 ACAGAGATAACTAGCATGCACTTTT 58.824 36.000 21.98 9.58 0.00 2.27
3080 3861 1.280457 AGCTTCCTTGTGGAGGTAGG 58.720 55.000 1.70 0.00 46.39 3.18
3178 3962 2.187707 CACAGCTGCAAAAACACTCAC 58.812 47.619 15.27 0.00 0.00 3.51
3362 4147 1.660333 GCTGTTTTCCGCAGAAAGTCG 60.660 52.381 0.00 0.00 42.78 4.18
3380 4165 1.858739 TTGGAAATGGGCGGTAGGCT 61.859 55.000 0.00 0.00 42.94 4.58
3561 4346 5.251700 AGAAAGAACCCAGTCCAAGATATGT 59.748 40.000 0.00 0.00 0.00 2.29
3703 4488 4.931601 TCAAGATACATGACACAGAAGCAC 59.068 41.667 0.00 0.00 0.00 4.40
3864 4649 5.543714 TCCTGCAACTTAACAGTTATTCGA 58.456 37.500 0.00 0.00 41.69 3.71
3954 4739 6.918892 ATAATGCAGCGTGTTGTATCTAAA 57.081 33.333 0.00 0.00 0.00 1.85
3958 4743 6.020678 GGAAAAATAATGCAGCGTGTTGTATC 60.021 38.462 0.00 0.00 0.00 2.24
4173 4958 3.347216 ACAATCAGAAGTATGTGCACCC 58.653 45.455 15.69 1.97 0.00 4.61
4232 5018 3.043999 GCTCCACCCGTGCCCTAAT 62.044 63.158 0.00 0.00 0.00 1.73
4253 5039 4.643334 CCAATGCTCCATATATCACATGGG 59.357 45.833 0.00 0.00 42.79 4.00
4309 5095 7.556844 AGACAAAGACGGACAAGATATACAAT 58.443 34.615 0.00 0.00 0.00 2.71
4715 5508 2.853430 TGCCCCAGAAACTAATAGGGA 58.147 47.619 0.00 0.00 42.25 4.20
5239 6035 8.400947 CAGTGAGACTTTTGAATTCTCTTTCAA 58.599 33.333 7.05 0.00 42.33 2.69
5300 6096 1.250154 CGAATTTGCCCCAGCTTCCA 61.250 55.000 0.00 0.00 40.80 3.53
5326 7668 2.717580 AACATACACAGCTTCGACGA 57.282 45.000 0.00 0.00 0.00 4.20
5423 7765 3.199946 ACCCGCAAGATTTAGGATTCTCA 59.800 43.478 0.00 0.00 43.02 3.27
5424 7766 3.561725 CACCCGCAAGATTTAGGATTCTC 59.438 47.826 0.00 0.00 43.02 2.87
5425 7767 3.199946 TCACCCGCAAGATTTAGGATTCT 59.800 43.478 0.00 0.00 43.02 2.40
5426 7768 3.541632 TCACCCGCAAGATTTAGGATTC 58.458 45.455 0.00 0.00 43.02 2.52
5427 7769 3.644966 TCACCCGCAAGATTTAGGATT 57.355 42.857 0.00 0.00 43.02 3.01
5553 7908 2.825861 TCCGTGACTAAACCTGGTTC 57.174 50.000 13.36 0.46 0.00 3.62
5630 7986 8.930846 ACAGTAAGTACTCCTTCTGTAAACTA 57.069 34.615 15.49 0.00 38.56 2.24
5631 7987 7.836479 ACAGTAAGTACTCCTTCTGTAAACT 57.164 36.000 15.49 0.00 38.56 2.66
5632 7988 8.883954 AAACAGTAAGTACTCCTTCTGTAAAC 57.116 34.615 16.61 0.00 38.99 2.01
5723 8081 2.618045 CCAGTGGTAACCATCTTGACCC 60.618 54.545 0.00 0.00 35.28 4.46
5843 8203 1.305930 GGCTGGCCTTTTACTGGACG 61.306 60.000 3.32 0.00 34.69 4.79
5869 8229 0.321671 CATGAGACAACCAGGGTCGT 59.678 55.000 0.00 0.00 40.20 4.34
5870 8230 0.321671 ACATGAGACAACCAGGGTCG 59.678 55.000 0.00 0.00 40.20 4.79
5882 8242 4.284490 AGTGCTGTTCCTTAAGACATGAGA 59.716 41.667 3.36 0.00 0.00 3.27
5883 8243 4.573900 AGTGCTGTTCCTTAAGACATGAG 58.426 43.478 3.36 0.00 0.00 2.90
5972 8341 8.764287 CGTCATCTACAAATAGCAAACATGATA 58.236 33.333 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.