Multiple sequence alignment - TraesCS4D01G099700

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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 TraesCS4D01G099700 chr4D 100.000 3422 0 0 1 3422 77015873 77019294 0.000000e+00 6320.0
1 TraesCS4D01G099700 chr4D 95.512 1827 81 1 932 2758 76625059 76623234 0.000000e+00 2918.0
2 TraesCS4D01G099700 chr4D 87.829 304 32 3 542 840 335743769 335743466 5.430000e-93 351.0
3 TraesCS4D01G099700 chr4B 95.336 1844 78 4 922 2758 109053132 109051290 0.000000e+00 2922.0
4 TraesCS4D01G099700 chr4B 90.741 216 20 0 259 474 109053863 109053648 4.320000e-74 289.0
5 TraesCS4D01G099700 chr4B 97.368 76 2 0 840 915 109053299 109053224 2.770000e-26 130.0
6 TraesCS4D01G099700 chr4A 96.007 1728 66 1 937 2664 511036913 511038637 0.000000e+00 2806.0
7 TraesCS4D01G099700 chr4A 92.550 698 31 4 2726 3422 511038638 511039315 0.000000e+00 981.0
8 TraesCS4D01G099700 chr4A 90.672 268 18 6 47 311 511035584 511035847 1.950000e-92 350.0
9 TraesCS4D01G099700 chr4A 93.571 140 9 0 335 474 511035841 511035980 3.460000e-50 209.0
10 TraesCS4D01G099700 chr5B 87.898 314 32 4 542 849 230244472 230244785 6.980000e-97 364.0
11 TraesCS4D01G099700 chr7D 88.274 307 30 4 542 843 117216055 117215750 2.510000e-96 363.0
12 TraesCS4D01G099700 chr7D 88.274 307 31 3 542 843 257272870 257272564 2.510000e-96 363.0
13 TraesCS4D01G099700 chr6D 88.667 300 29 3 542 836 414504412 414504711 9.030000e-96 361.0
14 TraesCS4D01G099700 chr6D 87.869 305 32 3 542 841 358330435 358330131 1.510000e-93 353.0
15 TraesCS4D01G099700 chrUn 88.197 305 30 4 542 841 126990717 126990414 3.250000e-95 359.0
16 TraesCS4D01G099700 chr7B 87.908 306 30 5 542 841 74736277 74735973 1.510000e-93 353.0
17 TraesCS4D01G099700 chr7B 89.820 167 14 2 3256 3422 316408357 316408194 9.620000e-51 211.0
18 TraesCS4D01G099700 chr5A 87.500 304 33 3 543 841 306895257 306894954 2.530000e-91 346.0
19 TraesCS4D01G099700 chr1D 93.478 46 3 0 291 336 263868150 263868195 6.130000e-08 69.4
20 TraesCS4D01G099700 chr2D 88.636 44 5 0 2643 2686 410416717 410416674 2.000000e-03 54.7


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 TraesCS4D01G099700 chr4D 77015873 77019294 3421 False 6320.000000 6320 100.000000 1 3422 1 chr4D.!!$F1 3421
1 TraesCS4D01G099700 chr4D 76623234 76625059 1825 True 2918.000000 2918 95.512000 932 2758 1 chr4D.!!$R1 1826
2 TraesCS4D01G099700 chr4B 109051290 109053863 2573 True 1113.666667 2922 94.481667 259 2758 3 chr4B.!!$R1 2499
3 TraesCS4D01G099700 chr4A 511035584 511039315 3731 False 1086.500000 2806 93.200000 47 3422 4 chr4A.!!$F1 3375

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
28 29 0.038067 TGGTCGTTGTACCATGGACG 60.038 55.0 21.47 17.98 44.68 4.79 F
663 1474 0.039256 CCGCCTCATGGTGTTGTTTG 60.039 55.0 0.00 0.00 42.08 2.93 F
664 1475 0.039256 CGCCTCATGGTGTTGTTTGG 60.039 55.0 0.00 0.00 38.95 3.28 F
665 1476 1.039856 GCCTCATGGTGTTGTTTGGT 58.960 50.0 0.00 0.00 35.27 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 2656 0.884704 GCCCAAGAACGCTGTGAAGA 60.885 55.000 0.0 0.0 0.00 2.87 R
1762 2658 1.153066 TGCCCAAGAACGCTGTGAA 60.153 52.632 0.0 0.0 0.00 3.18 R
2136 3032 1.402194 GGCATCCGCTCTATCTTCTCG 60.402 57.143 0.0 0.0 38.60 4.04 R
2664 3571 6.312672 ACACTACTTTGGTGCAAACAAAATTC 59.687 34.615 15.9 0.0 37.37 2.17 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
18 19 2.282887 GGGGGCAATGGTCGTTGT 60.283 61.111 5.03 0.00 0.00 3.32
19 20 1.001887 GGGGGCAATGGTCGTTGTA 60.002 57.895 5.03 0.00 0.00 2.41
20 21 1.310216 GGGGGCAATGGTCGTTGTAC 61.310 60.000 5.03 0.00 0.00 2.90
21 22 1.310216 GGGGCAATGGTCGTTGTACC 61.310 60.000 5.03 7.28 40.19 3.34
27 28 3.919163 TGGTCGTTGTACCATGGAC 57.081 52.632 21.47 12.84 44.68 4.02
28 29 0.038067 TGGTCGTTGTACCATGGACG 60.038 55.000 21.47 17.98 44.68 4.79
29 30 0.738412 GGTCGTTGTACCATGGACGG 60.738 60.000 21.47 6.20 39.50 4.79
30 31 0.738412 GTCGTTGTACCATGGACGGG 60.738 60.000 21.47 2.29 36.27 5.28
31 32 2.104253 CGTTGTACCATGGACGGGC 61.104 63.158 21.47 4.55 32.29 6.13
32 33 2.104253 GTTGTACCATGGACGGGCG 61.104 63.158 21.47 0.00 0.00 6.13
33 34 3.318006 TTGTACCATGGACGGGCGG 62.318 63.158 21.47 0.00 0.00 6.13
34 35 3.777910 GTACCATGGACGGGCGGT 61.778 66.667 21.47 0.00 35.46 5.68
35 36 3.463585 TACCATGGACGGGCGGTC 61.464 66.667 21.47 16.08 45.31 4.79
44 45 4.452733 CGGGCGGTCAGGGAGAAC 62.453 72.222 0.00 0.00 0.00 3.01
45 46 3.319198 GGGCGGTCAGGGAGAACA 61.319 66.667 0.00 0.00 31.63 3.18
46 47 2.747686 GGCGGTCAGGGAGAACAA 59.252 61.111 0.00 0.00 31.63 2.83
47 48 1.376037 GGCGGTCAGGGAGAACAAG 60.376 63.158 0.00 0.00 31.63 3.16
48 49 1.376037 GCGGTCAGGGAGAACAAGG 60.376 63.158 0.00 0.00 31.63 3.61
49 50 1.296715 CGGTCAGGGAGAACAAGGG 59.703 63.158 0.00 0.00 31.63 3.95
50 51 1.192146 CGGTCAGGGAGAACAAGGGA 61.192 60.000 0.00 0.00 31.63 4.20
51 52 0.615850 GGTCAGGGAGAACAAGGGAG 59.384 60.000 0.00 0.00 32.78 4.30
111 112 4.141733 CCAAATTAGGGCCGAAAATGGATT 60.142 41.667 21.49 2.17 0.00 3.01
150 151 6.925610 TGGACATATGTCTGTTTAATCAGC 57.074 37.500 29.87 12.91 44.20 4.26
151 152 5.523552 TGGACATATGTCTGTTTAATCAGCG 59.476 40.000 29.87 0.00 44.20 5.18
152 153 5.409643 ACATATGTCTGTTTAATCAGCGC 57.590 39.130 1.41 0.00 35.63 5.92
153 154 4.875536 ACATATGTCTGTTTAATCAGCGCA 59.124 37.500 11.47 9.77 35.63 6.09
154 155 5.528690 ACATATGTCTGTTTAATCAGCGCAT 59.471 36.000 11.47 18.51 36.09 4.73
156 157 7.226523 ACATATGTCTGTTTAATCAGCGCATTA 59.773 33.333 11.47 2.67 34.94 1.90
158 159 5.175127 TGTCTGTTTAATCAGCGCATTAGA 58.825 37.500 11.47 1.66 35.63 2.10
159 160 5.063438 TGTCTGTTTAATCAGCGCATTAGAC 59.937 40.000 11.47 11.73 35.63 2.59
161 162 3.308595 TGTTTAATCAGCGCATTAGACCG 59.691 43.478 11.47 0.00 0.00 4.79
162 163 2.882927 TAATCAGCGCATTAGACCGT 57.117 45.000 11.47 0.00 0.00 4.83
163 164 1.290203 AATCAGCGCATTAGACCGTG 58.710 50.000 11.47 0.00 0.00 4.94
194 195 3.136763 CAGCGCAGATCCAAATAGACAT 58.863 45.455 11.47 0.00 0.00 3.06
199 200 3.824133 CAGATCCAAATAGACATGGGCA 58.176 45.455 0.00 0.00 37.31 5.36
209 210 0.099436 GACATGGGCAGACGAAATGC 59.901 55.000 0.00 0.00 43.09 3.56
227 228 3.350219 TGCATCCTTAGGTTGGAGTTC 57.650 47.619 10.90 0.00 36.99 3.01
252 253 0.250640 AGCTCCTGCACACTTTCCTG 60.251 55.000 0.00 0.00 42.74 3.86
255 256 1.071385 CTCCTGCACACTTTCCTGAGT 59.929 52.381 0.00 0.00 0.00 3.41
265 266 2.103263 ACTTTCCTGAGTTGCTCTCGTT 59.897 45.455 5.36 0.00 45.46 3.85
286 287 5.450274 CGTTATGTGATGCATCCAAATCCAA 60.450 40.000 23.67 6.20 38.94 3.53
307 308 5.219633 CAACTGAAATCCCTGTTTTTACCG 58.780 41.667 0.00 0.00 0.00 4.02
313 314 3.967203 TCCCTGTTTTTACCGTTTTCG 57.033 42.857 0.00 0.00 43.67 3.46
431 432 3.985925 CCTAGACACGTCAAACTTACCAC 59.014 47.826 0.00 0.00 0.00 4.16
460 461 9.574458 TTTCTTCTTTGACTAGATAAGTGATCG 57.426 33.333 0.00 0.00 39.07 3.69
477 478 2.127534 GTGGGCACGCGTTAAACG 60.128 61.111 10.22 0.00 45.88 3.60
503 775 4.032104 ACAAGACGTGACGTTTGTTCTTAC 59.968 41.667 22.93 6.29 41.37 2.34
504 776 4.037858 AGACGTGACGTTTGTTCTTACT 57.962 40.909 13.44 0.00 41.37 2.24
517 789 2.472695 TCTTACTGCAGAAACGCCAT 57.527 45.000 23.35 0.00 0.00 4.40
518 790 2.778299 TCTTACTGCAGAAACGCCATT 58.222 42.857 23.35 0.00 0.00 3.16
536 808 4.495844 GCCATTGGCTATAGTGTTTTCGAC 60.496 45.833 20.66 0.00 46.69 4.20
537 809 4.035208 CCATTGGCTATAGTGTTTTCGACC 59.965 45.833 0.84 0.00 0.00 4.79
538 810 4.546829 TTGGCTATAGTGTTTTCGACCT 57.453 40.909 0.84 0.00 0.00 3.85
540 812 5.664294 TGGCTATAGTGTTTTCGACCTAA 57.336 39.130 0.84 0.00 0.00 2.69
541 813 6.040209 TGGCTATAGTGTTTTCGACCTAAA 57.960 37.500 0.84 0.00 0.00 1.85
542 814 5.870978 TGGCTATAGTGTTTTCGACCTAAAC 59.129 40.000 0.84 4.58 36.32 2.01
543 815 6.104665 GGCTATAGTGTTTTCGACCTAAACT 58.895 40.000 11.38 3.27 36.64 2.66
544 816 7.093814 TGGCTATAGTGTTTTCGACCTAAACTA 60.094 37.037 11.38 5.11 36.64 2.24
566 1377 7.441836 ACTAGGGATTAAAAGTTGCTTTTTGG 58.558 34.615 11.39 0.00 40.23 3.28
567 1378 6.493189 AGGGATTAAAAGTTGCTTTTTGGA 57.507 33.333 11.39 1.27 40.23 3.53
568 1379 6.894682 AGGGATTAAAAGTTGCTTTTTGGAA 58.105 32.000 11.39 2.35 40.23 3.53
569 1380 6.765989 AGGGATTAAAAGTTGCTTTTTGGAAC 59.234 34.615 11.39 0.00 40.23 3.62
581 1392 8.542953 GTTGCTTTTTGGAACTAAATGAAGAAG 58.457 33.333 0.00 0.00 42.63 2.85
583 1394 8.641541 TGCTTTTTGGAACTAAATGAAGAAGAT 58.358 29.630 0.00 0.00 0.00 2.40
584 1395 9.481340 GCTTTTTGGAACTAAATGAAGAAGATT 57.519 29.630 0.00 0.00 0.00 2.40
598 1409 9.571816 AATGAAGAAGATTCTCAAAGAGTCTTT 57.428 29.630 12.50 12.50 46.82 2.52
600 1411 9.401058 TGAAGAAGATTCTCAAAGAGTCTTTTT 57.599 29.630 15.60 13.86 46.82 1.94
620 1431 5.809719 TTTTGGGACTTTTTCAACAATGC 57.190 34.783 0.00 0.00 0.00 3.56
621 1432 3.467374 TGGGACTTTTTCAACAATGCC 57.533 42.857 0.00 0.00 0.00 4.40
622 1433 2.103941 TGGGACTTTTTCAACAATGCCC 59.896 45.455 0.00 0.00 0.00 5.36
623 1434 2.549992 GGGACTTTTTCAACAATGCCCC 60.550 50.000 0.00 0.00 0.00 5.80
624 1435 2.368548 GGACTTTTTCAACAATGCCCCT 59.631 45.455 0.00 0.00 0.00 4.79
625 1436 3.554960 GGACTTTTTCAACAATGCCCCTC 60.555 47.826 0.00 0.00 0.00 4.30
626 1437 2.368548 ACTTTTTCAACAATGCCCCTCC 59.631 45.455 0.00 0.00 0.00 4.30
627 1438 1.347062 TTTTCAACAATGCCCCTCCC 58.653 50.000 0.00 0.00 0.00 4.30
628 1439 0.486879 TTTCAACAATGCCCCTCCCT 59.513 50.000 0.00 0.00 0.00 4.20
629 1440 0.251742 TTCAACAATGCCCCTCCCTG 60.252 55.000 0.00 0.00 0.00 4.45
630 1441 2.037847 AACAATGCCCCTCCCTGC 59.962 61.111 0.00 0.00 0.00 4.85
631 1442 2.855770 AACAATGCCCCTCCCTGCA 61.856 57.895 0.00 0.00 42.52 4.41
632 1443 2.757099 CAATGCCCCTCCCTGCAC 60.757 66.667 0.00 0.00 40.88 4.57
633 1444 4.066139 AATGCCCCTCCCTGCACC 62.066 66.667 0.00 0.00 40.88 5.01
637 1448 3.350163 CCCCTCCCTGCACCCATT 61.350 66.667 0.00 0.00 0.00 3.16
638 1449 2.043652 CCCTCCCTGCACCCATTG 60.044 66.667 0.00 0.00 0.00 2.82
659 1470 3.803082 CGCCGCCTCATGGTGTTG 61.803 66.667 0.00 0.00 42.08 3.33
660 1471 2.672996 GCCGCCTCATGGTGTTGT 60.673 61.111 0.00 0.00 42.08 3.32
661 1472 2.268076 GCCGCCTCATGGTGTTGTT 61.268 57.895 0.00 0.00 42.08 2.83
662 1473 1.805428 GCCGCCTCATGGTGTTGTTT 61.805 55.000 0.00 0.00 42.08 2.83
663 1474 0.039256 CCGCCTCATGGTGTTGTTTG 60.039 55.000 0.00 0.00 42.08 2.93
664 1475 0.039256 CGCCTCATGGTGTTGTTTGG 60.039 55.000 0.00 0.00 38.95 3.28
665 1476 1.039856 GCCTCATGGTGTTGTTTGGT 58.960 50.000 0.00 0.00 35.27 3.67
666 1477 1.412343 GCCTCATGGTGTTGTTTGGTT 59.588 47.619 0.00 0.00 35.27 3.67
667 1478 2.802774 GCCTCATGGTGTTGTTTGGTTG 60.803 50.000 0.00 0.00 35.27 3.77
668 1479 2.430332 CCTCATGGTGTTGTTTGGTTGT 59.570 45.455 0.00 0.00 0.00 3.32
669 1480 3.118811 CCTCATGGTGTTGTTTGGTTGTT 60.119 43.478 0.00 0.00 0.00 2.83
670 1481 4.098654 CCTCATGGTGTTGTTTGGTTGTTA 59.901 41.667 0.00 0.00 0.00 2.41
671 1482 5.221422 CCTCATGGTGTTGTTTGGTTGTTAT 60.221 40.000 0.00 0.00 0.00 1.89
672 1483 6.227298 TCATGGTGTTGTTTGGTTGTTATT 57.773 33.333 0.00 0.00 0.00 1.40
673 1484 6.644347 TCATGGTGTTGTTTGGTTGTTATTT 58.356 32.000 0.00 0.00 0.00 1.40
674 1485 7.106239 TCATGGTGTTGTTTGGTTGTTATTTT 58.894 30.769 0.00 0.00 0.00 1.82
675 1486 7.607991 TCATGGTGTTGTTTGGTTGTTATTTTT 59.392 29.630 0.00 0.00 0.00 1.94
676 1487 7.365840 TGGTGTTGTTTGGTTGTTATTTTTC 57.634 32.000 0.00 0.00 0.00 2.29
677 1488 7.162082 TGGTGTTGTTTGGTTGTTATTTTTCT 58.838 30.769 0.00 0.00 0.00 2.52
678 1489 7.118390 TGGTGTTGTTTGGTTGTTATTTTTCTG 59.882 33.333 0.00 0.00 0.00 3.02
679 1490 7.118535 GGTGTTGTTTGGTTGTTATTTTTCTGT 59.881 33.333 0.00 0.00 0.00 3.41
680 1491 9.141400 GTGTTGTTTGGTTGTTATTTTTCTGTA 57.859 29.630 0.00 0.00 0.00 2.74
681 1492 9.877178 TGTTGTTTGGTTGTTATTTTTCTGTAT 57.123 25.926 0.00 0.00 0.00 2.29
699 1510 9.880157 TTTCTGTATACTAAAGGTAACATGGTC 57.120 33.333 4.17 0.00 41.41 4.02
700 1511 8.834004 TCTGTATACTAAAGGTAACATGGTCT 57.166 34.615 4.17 0.00 41.41 3.85
701 1512 9.263446 TCTGTATACTAAAGGTAACATGGTCTT 57.737 33.333 4.17 0.00 41.41 3.01
702 1513 9.886132 CTGTATACTAAAGGTAACATGGTCTTT 57.114 33.333 4.17 0.00 41.41 2.52
743 1554 5.900865 CTTAGGAAGGAACTAGAGACGTT 57.099 43.478 0.00 0.00 38.49 3.99
744 1555 6.270156 CTTAGGAAGGAACTAGAGACGTTT 57.730 41.667 0.00 0.00 38.49 3.60
745 1556 6.661304 TTAGGAAGGAACTAGAGACGTTTT 57.339 37.500 0.00 0.00 38.49 2.43
746 1557 7.765695 TTAGGAAGGAACTAGAGACGTTTTA 57.234 36.000 0.00 0.00 38.49 1.52
747 1558 6.270156 AGGAAGGAACTAGAGACGTTTTAG 57.730 41.667 0.00 0.00 38.49 1.85
748 1559 5.774184 AGGAAGGAACTAGAGACGTTTTAGT 59.226 40.000 0.00 0.00 38.49 2.24
749 1560 6.072008 AGGAAGGAACTAGAGACGTTTTAGTC 60.072 42.308 0.00 0.00 38.49 2.59
760 1571 5.978934 GACGTTTTAGTCTCTGAAAACCA 57.021 39.130 0.00 0.00 40.75 3.67
761 1572 6.354039 GACGTTTTAGTCTCTGAAAACCAA 57.646 37.500 0.00 0.00 40.75 3.67
762 1573 6.937436 ACGTTTTAGTCTCTGAAAACCAAT 57.063 33.333 5.02 0.00 40.75 3.16
763 1574 8.080083 GACGTTTTAGTCTCTGAAAACCAATA 57.920 34.615 0.00 0.00 40.75 1.90
764 1575 8.441312 ACGTTTTAGTCTCTGAAAACCAATAA 57.559 30.769 5.02 0.00 40.75 1.40
765 1576 8.557029 ACGTTTTAGTCTCTGAAAACCAATAAG 58.443 33.333 5.02 0.00 40.75 1.73
766 1577 8.015658 CGTTTTAGTCTCTGAAAACCAATAAGG 58.984 37.037 5.02 0.00 40.75 2.69
767 1578 9.063615 GTTTTAGTCTCTGAAAACCAATAAGGA 57.936 33.333 0.00 0.00 38.86 3.36
768 1579 8.848474 TTTAGTCTCTGAAAACCAATAAGGAG 57.152 34.615 0.00 0.00 41.22 3.69
769 1580 5.810095 AGTCTCTGAAAACCAATAAGGAGG 58.190 41.667 0.00 0.00 41.22 4.30
770 1581 4.944317 GTCTCTGAAAACCAATAAGGAGGG 59.056 45.833 0.00 0.00 41.22 4.30
771 1582 4.849810 TCTCTGAAAACCAATAAGGAGGGA 59.150 41.667 0.00 0.00 41.22 4.20
772 1583 4.918588 TCTGAAAACCAATAAGGAGGGAC 58.081 43.478 0.00 0.00 41.22 4.46
773 1584 4.017126 CTGAAAACCAATAAGGAGGGACC 58.983 47.826 0.00 0.00 41.22 4.46
787 1598 5.100344 GGAGGGACCTTTTAAAGACTAGG 57.900 47.826 6.24 2.66 35.41 3.02
788 1599 4.080469 GGAGGGACCTTTTAAAGACTAGGG 60.080 50.000 6.24 0.00 35.41 3.53
789 1600 4.771338 AGGGACCTTTTAAAGACTAGGGA 58.229 43.478 6.24 0.00 31.91 4.20
790 1601 4.535294 AGGGACCTTTTAAAGACTAGGGAC 59.465 45.833 6.24 2.90 31.91 4.46
791 1602 4.535294 GGGACCTTTTAAAGACTAGGGACT 59.465 45.833 6.24 0.00 46.37 3.85
792 1603 5.013913 GGGACCTTTTAAAGACTAGGGACTT 59.986 44.000 6.24 0.00 41.75 3.01
793 1604 6.466904 GGGACCTTTTAAAGACTAGGGACTTT 60.467 42.308 6.24 13.38 41.75 2.66
794 1605 7.002879 GGACCTTTTAAAGACTAGGGACTTTT 58.997 38.462 6.24 2.35 41.75 2.27
795 1606 7.504911 GGACCTTTTAAAGACTAGGGACTTTTT 59.495 37.037 6.24 0.00 41.75 1.94
796 1607 9.565090 GACCTTTTAAAGACTAGGGACTTTTTA 57.435 33.333 6.24 4.55 41.75 1.52
797 1608 9.925545 ACCTTTTAAAGACTAGGGACTTTTTAA 57.074 29.630 6.24 8.56 41.75 1.52
825 1636 8.986929 AGGAATAGGAAAAATCATAGGACTTG 57.013 34.615 0.00 0.00 0.00 3.16
826 1637 8.781951 AGGAATAGGAAAAATCATAGGACTTGA 58.218 33.333 0.00 0.00 0.00 3.02
827 1638 9.408648 GGAATAGGAAAAATCATAGGACTTGAA 57.591 33.333 0.00 0.00 0.00 2.69
829 1640 8.753497 ATAGGAAAAATCATAGGACTTGAACC 57.247 34.615 0.00 0.00 0.00 3.62
830 1641 6.552008 AGGAAAAATCATAGGACTTGAACCA 58.448 36.000 0.00 0.00 0.00 3.67
831 1642 7.010160 AGGAAAAATCATAGGACTTGAACCAA 58.990 34.615 0.00 0.00 0.00 3.67
832 1643 7.508977 AGGAAAAATCATAGGACTTGAACCAAA 59.491 33.333 0.00 0.00 0.00 3.28
833 1644 7.598869 GGAAAAATCATAGGACTTGAACCAAAC 59.401 37.037 0.00 0.00 0.00 2.93
834 1645 7.595819 AAAATCATAGGACTTGAACCAAACA 57.404 32.000 0.00 0.00 0.00 2.83
835 1646 6.824305 AATCATAGGACTTGAACCAAACAG 57.176 37.500 0.00 0.00 0.00 3.16
836 1647 5.560722 TCATAGGACTTGAACCAAACAGA 57.439 39.130 0.00 0.00 0.00 3.41
837 1648 5.551233 TCATAGGACTTGAACCAAACAGAG 58.449 41.667 0.00 0.00 0.00 3.35
838 1649 2.576615 AGGACTTGAACCAAACAGAGC 58.423 47.619 0.00 0.00 0.00 4.09
920 1731 8.417273 AGGTTAAATTGTGCTAAAGTTACCAT 57.583 30.769 0.00 0.00 0.00 3.55
1152 2048 1.607612 CGCCACCTTCCCCTACAAT 59.392 57.895 0.00 0.00 0.00 2.71
1324 2220 2.930019 CCACCAGGGCTCTCCACA 60.930 66.667 0.00 0.00 38.24 4.17
1394 2290 1.381191 TCGTCAGCTCCTATGGCCA 60.381 57.895 8.56 8.56 0.00 5.36
1577 2473 1.133407 GACGACACTCATCTCTGGGTC 59.867 57.143 0.00 0.00 32.17 4.46
1744 2640 2.089936 GCCGTTCACGCGTATGTCA 61.090 57.895 13.44 0.00 38.18 3.58
1760 2656 1.271325 TGTCATTCGGCATGAGGTTGT 60.271 47.619 0.00 0.00 42.98 3.32
1762 2658 1.278985 TCATTCGGCATGAGGTTGTCT 59.721 47.619 0.00 0.00 36.94 3.41
1820 2716 1.340991 TGGGAAGTATGGGAAGCTTGC 60.341 52.381 9.87 9.87 0.00 4.01
1840 2736 2.701073 CTGTTGCAGGAGAGCTTTTG 57.299 50.000 0.00 0.00 34.99 2.44
1876 2772 2.537143 AGGAGGTCTGTACGTGGAATT 58.463 47.619 0.00 0.00 0.00 2.17
2136 3032 0.668535 GCCGTTTTATGGAGGCCATC 59.331 55.000 5.01 0.00 40.74 3.51
2433 3329 5.932303 TGCCATTACTTGACTAGAGTTTGTC 59.068 40.000 0.00 0.00 0.00 3.18
2474 3370 2.806244 CTGGGACTACCGTTTGTTTCTG 59.194 50.000 0.00 0.00 44.64 3.02
2515 3415 8.706322 AGGAAAATACTAAACCACATCTTGTT 57.294 30.769 0.00 0.00 0.00 2.83
2516 3416 8.576442 AGGAAAATACTAAACCACATCTTGTTG 58.424 33.333 0.00 0.00 0.00 3.33
2517 3417 8.357402 GGAAAATACTAAACCACATCTTGTTGT 58.643 33.333 0.00 0.00 0.00 3.32
2658 3565 5.804639 TGTAGTGGCATGTCTACTCAAAAT 58.195 37.500 18.19 0.00 37.67 1.82
2664 3571 8.147058 AGTGGCATGTCTACTCAAAATCTATAG 58.853 37.037 0.00 0.00 29.79 1.31
2786 3693 2.680370 GCTCCCGGGAATTGGAGGT 61.680 63.158 26.68 0.00 46.79 3.85
2793 3700 0.548510 GGGAATTGGAGGTCTGGGAG 59.451 60.000 0.00 0.00 0.00 4.30
2794 3701 0.106967 GGAATTGGAGGTCTGGGAGC 60.107 60.000 0.00 0.00 0.00 4.70
2795 3702 0.620556 GAATTGGAGGTCTGGGAGCA 59.379 55.000 0.00 0.00 31.89 4.26
2796 3703 0.329596 AATTGGAGGTCTGGGAGCAC 59.670 55.000 0.00 0.00 31.89 4.40
2797 3704 0.548682 ATTGGAGGTCTGGGAGCACT 60.549 55.000 0.00 0.00 31.89 4.40
2798 3705 1.194781 TTGGAGGTCTGGGAGCACTC 61.195 60.000 0.00 0.00 31.89 3.51
2817 3724 0.520412 CCGTGTATTTTTCGCTGGCG 60.520 55.000 8.80 8.80 41.35 5.69
2842 3749 0.909623 CGGTTGTAAGGGGGAGATGT 59.090 55.000 0.00 0.00 0.00 3.06
2933 3840 1.323412 TCGTTTCATGGTGGTTTGGG 58.677 50.000 0.00 0.00 0.00 4.12
2937 3844 0.755686 TTCATGGTGGTTTGGGTTGC 59.244 50.000 0.00 0.00 0.00 4.17
2957 3864 1.289800 GGTCGTGTCTTCTTTCCGCC 61.290 60.000 0.00 0.00 0.00 6.13
2975 3882 2.883828 CGGCCCTTGTGAGTCTGGT 61.884 63.158 0.00 0.00 0.00 4.00
3018 3925 2.983592 GGGGTGAAGTGGTTGGCG 60.984 66.667 0.00 0.00 0.00 5.69
3042 3949 2.303600 TGTAGTTTCGGCAGGGTTGTAT 59.696 45.455 0.00 0.00 0.00 2.29
3067 3974 2.606519 TGGAAGACGAGGGTGGGG 60.607 66.667 0.00 0.00 0.00 4.96
3132 4039 1.113517 GGCTGCTACGATAGGGTGGA 61.114 60.000 0.00 0.00 43.77 4.02
3136 4043 1.105759 GCTACGATAGGGTGGACGGT 61.106 60.000 0.00 0.00 43.77 4.83
3155 4062 2.126965 CGGTCGTCGTCGCTCTTT 60.127 61.111 0.00 0.00 36.96 2.52
3272 4179 5.410067 TCTTTCTTTCTTTGTGCCTTTGTG 58.590 37.500 0.00 0.00 0.00 3.33
3273 4180 3.799281 TCTTTCTTTGTGCCTTTGTGG 57.201 42.857 0.00 0.00 39.35 4.17
3274 4181 3.096092 TCTTTCTTTGTGCCTTTGTGGT 58.904 40.909 0.00 0.00 38.35 4.16
3275 4182 2.957491 TTCTTTGTGCCTTTGTGGTG 57.043 45.000 0.00 0.00 38.35 4.17
3276 4183 1.846007 TCTTTGTGCCTTTGTGGTGT 58.154 45.000 0.00 0.00 38.35 4.16
3277 4184 2.175202 TCTTTGTGCCTTTGTGGTGTT 58.825 42.857 0.00 0.00 38.35 3.32
3278 4185 2.094286 TCTTTGTGCCTTTGTGGTGTTG 60.094 45.455 0.00 0.00 38.35 3.33
3279 4186 1.261480 TTGTGCCTTTGTGGTGTTGT 58.739 45.000 0.00 0.00 38.35 3.32
3280 4187 1.261480 TGTGCCTTTGTGGTGTTGTT 58.739 45.000 0.00 0.00 38.35 2.83
3281 4188 1.620819 TGTGCCTTTGTGGTGTTGTTT 59.379 42.857 0.00 0.00 38.35 2.83
3282 4189 2.267426 GTGCCTTTGTGGTGTTGTTTC 58.733 47.619 0.00 0.00 38.35 2.78
3283 4190 1.205893 TGCCTTTGTGGTGTTGTTTCC 59.794 47.619 0.00 0.00 38.35 3.13
3284 4191 1.480545 GCCTTTGTGGTGTTGTTTCCT 59.519 47.619 0.00 0.00 38.35 3.36
3285 4192 2.093711 GCCTTTGTGGTGTTGTTTCCTT 60.094 45.455 0.00 0.00 38.35 3.36
3286 4193 3.520569 CCTTTGTGGTGTTGTTTCCTTG 58.479 45.455 0.00 0.00 0.00 3.61
3287 4194 2.663826 TTGTGGTGTTGTTTCCTTGC 57.336 45.000 0.00 0.00 0.00 4.01
3306 4213 1.334960 GCCGGTGCCGATTGATATTTG 60.335 52.381 12.71 0.00 42.83 2.32
3328 4235 3.660111 GCTTGTTTCGGCTGCGGT 61.660 61.111 7.10 0.00 0.00 5.68
3380 4287 1.145571 TGGATTACATGGTAGGGGCC 58.854 55.000 0.00 0.00 0.00 5.80
3381 4288 0.036306 GGATTACATGGTAGGGGCCG 59.964 60.000 0.00 0.00 0.00 6.13
3382 4289 0.763035 GATTACATGGTAGGGGCCGT 59.237 55.000 3.37 3.37 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.728279 GACCGCCCGTCCATGGTAC 62.728 68.421 12.58 7.90 35.23 3.34
18 19 3.463585 GACCGCCCGTCCATGGTA 61.464 66.667 12.58 0.00 35.23 3.25
20 21 4.838152 CTGACCGCCCGTCCATGG 62.838 72.222 4.97 4.97 41.18 3.66
21 22 4.838152 CCTGACCGCCCGTCCATG 62.838 72.222 0.00 0.00 41.18 3.66
27 28 4.452733 GTTCTCCCTGACCGCCCG 62.453 72.222 0.00 0.00 0.00 6.13
28 29 2.804828 CTTGTTCTCCCTGACCGCCC 62.805 65.000 0.00 0.00 0.00 6.13
29 30 1.376037 CTTGTTCTCCCTGACCGCC 60.376 63.158 0.00 0.00 0.00 6.13
30 31 1.376037 CCTTGTTCTCCCTGACCGC 60.376 63.158 0.00 0.00 0.00 5.68
31 32 1.192146 TCCCTTGTTCTCCCTGACCG 61.192 60.000 0.00 0.00 0.00 4.79
32 33 0.615850 CTCCCTTGTTCTCCCTGACC 59.384 60.000 0.00 0.00 0.00 4.02
33 34 0.615850 CCTCCCTTGTTCTCCCTGAC 59.384 60.000 0.00 0.00 0.00 3.51
34 35 0.547712 CCCTCCCTTGTTCTCCCTGA 60.548 60.000 0.00 0.00 0.00 3.86
35 36 1.994463 CCCTCCCTTGTTCTCCCTG 59.006 63.158 0.00 0.00 0.00 4.45
36 37 1.925972 GCCCTCCCTTGTTCTCCCT 60.926 63.158 0.00 0.00 0.00 4.20
37 38 2.677848 GCCCTCCCTTGTTCTCCC 59.322 66.667 0.00 0.00 0.00 4.30
38 39 2.269241 CGCCCTCCCTTGTTCTCC 59.731 66.667 0.00 0.00 0.00 3.71
39 40 1.079057 GACGCCCTCCCTTGTTCTC 60.079 63.158 0.00 0.00 0.00 2.87
40 41 2.943978 CGACGCCCTCCCTTGTTCT 61.944 63.158 0.00 0.00 0.00 3.01
41 42 2.434359 CGACGCCCTCCCTTGTTC 60.434 66.667 0.00 0.00 0.00 3.18
42 43 4.699522 GCGACGCCCTCCCTTGTT 62.700 66.667 9.14 0.00 0.00 2.83
129 130 5.006649 TGCGCTGATTAAACAGACATATGTC 59.993 40.000 25.47 25.47 45.08 3.06
134 135 4.970662 AATGCGCTGATTAAACAGACAT 57.029 36.364 16.23 14.24 39.94 3.06
144 145 1.290203 CACGGTCTAATGCGCTGATT 58.710 50.000 9.73 3.18 0.00 2.57
146 147 0.037697 AACACGGTCTAATGCGCTGA 60.038 50.000 9.73 0.00 0.00 4.26
147 148 0.796312 AAACACGGTCTAATGCGCTG 59.204 50.000 9.73 0.00 0.00 5.18
148 149 1.519408 AAAACACGGTCTAATGCGCT 58.481 45.000 9.73 0.00 0.00 5.92
179 180 3.718434 TCTGCCCATGTCTATTTGGATCT 59.282 43.478 0.00 0.00 34.81 2.75
181 182 3.745480 CGTCTGCCCATGTCTATTTGGAT 60.745 47.826 0.00 0.00 34.81 3.41
194 195 1.031571 GGATGCATTTCGTCTGCCCA 61.032 55.000 0.00 0.00 38.89 5.36
199 200 3.914426 ACCTAAGGATGCATTTCGTCT 57.086 42.857 0.00 0.00 0.00 4.18
209 210 2.280628 GCGAACTCCAACCTAAGGATG 58.719 52.381 0.00 0.00 33.99 3.51
227 228 2.103042 GTGTGCAGGAGCTAAGGCG 61.103 63.158 0.00 0.00 44.37 5.52
252 253 3.000724 GCATCACATAACGAGAGCAACTC 59.999 47.826 0.00 1.59 41.79 3.01
255 256 2.971307 TGCATCACATAACGAGAGCAA 58.029 42.857 0.00 0.00 0.00 3.91
265 266 5.068067 CAGTTGGATTTGGATGCATCACATA 59.932 40.000 27.25 17.09 39.84 2.29
286 287 4.466827 ACGGTAAAAACAGGGATTTCAGT 58.533 39.130 0.00 0.00 0.00 3.41
307 308 7.432838 TCATTTTGTGCTAAAGTTACCGAAAAC 59.567 33.333 0.00 0.00 0.00 2.43
313 314 9.908152 AATAGTTCATTTTGTGCTAAAGTTACC 57.092 29.630 0.00 0.00 0.00 2.85
355 356 9.919416 TTATCATTTATCAAAAGGGTCAGATCA 57.081 29.630 0.00 0.00 0.00 2.92
397 398 5.889853 TGACGTGTCTAGGTAGGACATAAAT 59.110 40.000 0.00 0.00 44.04 1.40
431 432 9.698309 TCACTTATCTAGTCAAAGAAGAAACAG 57.302 33.333 7.98 0.00 33.85 3.16
460 461 2.127534 CGTTTAACGCGTGCCCAC 60.128 61.111 14.98 6.79 33.65 4.61
480 481 2.613691 AGAACAAACGTCACGTCTTGT 58.386 42.857 18.92 18.92 39.99 3.16
503 775 1.444895 GCCAATGGCGTTTCTGCAG 60.445 57.895 9.14 7.63 39.62 4.41
504 776 2.650196 GCCAATGGCGTTTCTGCA 59.350 55.556 9.14 0.00 39.62 4.41
517 789 4.546829 AGGTCGAAAACACTATAGCCAA 57.453 40.909 0.00 0.00 0.00 4.52
518 790 5.664294 TTAGGTCGAAAACACTATAGCCA 57.336 39.130 0.00 0.00 0.00 4.75
522 794 7.615365 TCCCTAGTTTAGGTCGAAAACACTATA 59.385 37.037 12.41 0.00 44.73 1.31
527 799 5.750352 ATCCCTAGTTTAGGTCGAAAACA 57.250 39.130 12.41 0.60 44.73 2.83
532 804 7.486407 ACTTTTAATCCCTAGTTTAGGTCGA 57.514 36.000 1.76 0.00 44.73 4.20
536 808 7.939784 AGCAACTTTTAATCCCTAGTTTAGG 57.060 36.000 0.00 0.00 45.81 2.69
540 812 7.931407 CCAAAAAGCAACTTTTAATCCCTAGTT 59.069 33.333 5.79 0.00 41.98 2.24
541 813 7.289084 TCCAAAAAGCAACTTTTAATCCCTAGT 59.711 33.333 5.79 0.00 41.98 2.57
542 814 7.666623 TCCAAAAAGCAACTTTTAATCCCTAG 58.333 34.615 5.79 0.00 41.98 3.02
543 815 7.604657 TCCAAAAAGCAACTTTTAATCCCTA 57.395 32.000 5.79 0.00 41.98 3.53
544 816 6.493189 TCCAAAAAGCAACTTTTAATCCCT 57.507 33.333 5.79 0.00 41.98 4.20
546 818 7.786178 AGTTCCAAAAAGCAACTTTTAATCC 57.214 32.000 5.79 0.00 41.98 3.01
550 822 9.877178 TCATTTAGTTCCAAAAAGCAACTTTTA 57.123 25.926 5.79 0.00 41.98 1.52
558 1369 9.481340 AATCTTCTTCATTTAGTTCCAAAAAGC 57.519 29.630 0.00 0.00 0.00 3.51
574 1385 8.970859 AAAAGACTCTTTGAGAATCTTCTTCA 57.029 30.769 4.75 0.00 37.73 3.02
597 1408 5.124617 GGCATTGTTGAAAAAGTCCCAAAAA 59.875 36.000 0.00 0.00 0.00 1.94
598 1409 4.637977 GGCATTGTTGAAAAAGTCCCAAAA 59.362 37.500 0.00 0.00 0.00 2.44
600 1411 3.432890 GGGCATTGTTGAAAAAGTCCCAA 60.433 43.478 3.40 0.00 0.00 4.12
601 1412 2.103941 GGGCATTGTTGAAAAAGTCCCA 59.896 45.455 3.40 0.00 0.00 4.37
602 1413 2.549992 GGGGCATTGTTGAAAAAGTCCC 60.550 50.000 0.00 0.00 0.00 4.46
604 1415 3.554960 GGAGGGGCATTGTTGAAAAAGTC 60.555 47.826 0.00 0.00 0.00 3.01
605 1416 2.368548 GGAGGGGCATTGTTGAAAAAGT 59.631 45.455 0.00 0.00 0.00 2.66
606 1417 2.289631 GGGAGGGGCATTGTTGAAAAAG 60.290 50.000 0.00 0.00 0.00 2.27
607 1418 1.696884 GGGAGGGGCATTGTTGAAAAA 59.303 47.619 0.00 0.00 0.00 1.94
609 1420 0.486879 AGGGAGGGGCATTGTTGAAA 59.513 50.000 0.00 0.00 0.00 2.69
610 1421 0.251742 CAGGGAGGGGCATTGTTGAA 60.252 55.000 0.00 0.00 0.00 2.69
612 1423 2.353610 GCAGGGAGGGGCATTGTTG 61.354 63.158 0.00 0.00 0.00 3.33
615 1426 2.757099 GTGCAGGGAGGGGCATTG 60.757 66.667 0.00 0.00 42.75 2.82
616 1427 4.066139 GGTGCAGGGAGGGGCATT 62.066 66.667 0.00 0.00 42.75 3.56
620 1431 3.350163 AATGGGTGCAGGGAGGGG 61.350 66.667 0.00 0.00 0.00 4.79
621 1432 2.043652 CAATGGGTGCAGGGAGGG 60.044 66.667 0.00 0.00 0.00 4.30
642 1453 3.803082 CAACACCATGAGGCGGCG 61.803 66.667 0.51 0.51 39.06 6.46
643 1454 1.805428 AAACAACACCATGAGGCGGC 61.805 55.000 0.00 0.00 39.06 6.53
644 1455 0.039256 CAAACAACACCATGAGGCGG 60.039 55.000 0.00 0.00 39.06 6.13
645 1456 0.039256 CCAAACAACACCATGAGGCG 60.039 55.000 0.00 0.00 39.06 5.52
646 1457 1.039856 ACCAAACAACACCATGAGGC 58.960 50.000 0.00 0.00 39.06 4.70
647 1458 2.430332 ACAACCAAACAACACCATGAGG 59.570 45.455 0.00 0.00 42.21 3.86
648 1459 3.799281 ACAACCAAACAACACCATGAG 57.201 42.857 0.00 0.00 0.00 2.90
649 1460 5.860941 ATAACAACCAAACAACACCATGA 57.139 34.783 0.00 0.00 0.00 3.07
650 1461 6.917217 AAATAACAACCAAACAACACCATG 57.083 33.333 0.00 0.00 0.00 3.66
651 1462 7.826744 AGAAAAATAACAACCAAACAACACCAT 59.173 29.630 0.00 0.00 0.00 3.55
652 1463 7.118390 CAGAAAAATAACAACCAAACAACACCA 59.882 33.333 0.00 0.00 0.00 4.17
653 1464 7.118535 ACAGAAAAATAACAACCAAACAACACC 59.881 33.333 0.00 0.00 0.00 4.16
654 1465 8.024146 ACAGAAAAATAACAACCAAACAACAC 57.976 30.769 0.00 0.00 0.00 3.32
655 1466 9.877178 ATACAGAAAAATAACAACCAAACAACA 57.123 25.926 0.00 0.00 0.00 3.33
673 1484 9.880157 GACCATGTTACCTTTAGTATACAGAAA 57.120 33.333 5.50 4.43 30.65 2.52
674 1485 9.263446 AGACCATGTTACCTTTAGTATACAGAA 57.737 33.333 5.50 0.00 30.65 3.02
675 1486 8.834004 AGACCATGTTACCTTTAGTATACAGA 57.166 34.615 5.50 0.00 30.65 3.41
676 1487 9.886132 AAAGACCATGTTACCTTTAGTATACAG 57.114 33.333 5.50 0.00 30.65 2.74
682 1493 9.010029 CATGTAAAAGACCATGTTACCTTTAGT 57.990 33.333 0.00 0.00 34.97 2.24
721 1532 5.900865 AACGTCTCTAGTTCCTTCCTAAG 57.099 43.478 0.00 0.00 0.00 2.18
722 1533 6.661304 AAAACGTCTCTAGTTCCTTCCTAA 57.339 37.500 0.00 0.00 0.00 2.69
723 1534 6.944862 ACTAAAACGTCTCTAGTTCCTTCCTA 59.055 38.462 0.00 0.00 0.00 2.94
724 1535 5.774184 ACTAAAACGTCTCTAGTTCCTTCCT 59.226 40.000 0.00 0.00 0.00 3.36
725 1536 6.023357 ACTAAAACGTCTCTAGTTCCTTCC 57.977 41.667 0.00 0.00 0.00 3.46
726 1537 6.912082 AGACTAAAACGTCTCTAGTTCCTTC 58.088 40.000 0.00 0.00 40.04 3.46
727 1538 6.897706 AGACTAAAACGTCTCTAGTTCCTT 57.102 37.500 0.00 0.00 40.04 3.36
737 1548 5.667466 TGGTTTTCAGAGACTAAAACGTCT 58.333 37.500 0.00 0.00 46.39 4.18
738 1549 5.978934 TGGTTTTCAGAGACTAAAACGTC 57.021 39.130 0.00 0.00 43.36 4.34
739 1550 6.937436 ATTGGTTTTCAGAGACTAAAACGT 57.063 33.333 0.00 0.00 43.36 3.99
740 1551 8.015658 CCTTATTGGTTTTCAGAGACTAAAACG 58.984 37.037 0.00 0.00 43.36 3.60
741 1552 9.063615 TCCTTATTGGTTTTCAGAGACTAAAAC 57.936 33.333 4.21 4.21 42.28 2.43
742 1553 9.284968 CTCCTTATTGGTTTTCAGAGACTAAAA 57.715 33.333 0.00 0.00 37.07 1.52
743 1554 7.883311 CCTCCTTATTGGTTTTCAGAGACTAAA 59.117 37.037 0.00 0.00 37.07 1.85
744 1555 7.394816 CCTCCTTATTGGTTTTCAGAGACTAA 58.605 38.462 0.00 0.00 37.07 2.24
745 1556 6.070194 CCCTCCTTATTGGTTTTCAGAGACTA 60.070 42.308 0.00 0.00 37.07 2.59
746 1557 5.280727 CCCTCCTTATTGGTTTTCAGAGACT 60.281 44.000 0.00 0.00 37.07 3.24
747 1558 4.944317 CCCTCCTTATTGGTTTTCAGAGAC 59.056 45.833 0.00 0.00 37.07 3.36
748 1559 4.849810 TCCCTCCTTATTGGTTTTCAGAGA 59.150 41.667 0.00 0.00 37.07 3.10
749 1560 4.944317 GTCCCTCCTTATTGGTTTTCAGAG 59.056 45.833 0.00 0.00 37.07 3.35
750 1561 4.263771 GGTCCCTCCTTATTGGTTTTCAGA 60.264 45.833 0.00 0.00 37.07 3.27
751 1562 4.017126 GGTCCCTCCTTATTGGTTTTCAG 58.983 47.826 0.00 0.00 37.07 3.02
752 1563 3.660669 AGGTCCCTCCTTATTGGTTTTCA 59.339 43.478 0.00 0.00 45.67 2.69
753 1564 4.317530 AGGTCCCTCCTTATTGGTTTTC 57.682 45.455 0.00 0.00 45.67 2.29
765 1576 4.080469 CCCTAGTCTTTAAAAGGTCCCTCC 60.080 50.000 3.55 0.00 0.00 4.30
766 1577 4.781621 TCCCTAGTCTTTAAAAGGTCCCTC 59.218 45.833 3.55 0.00 0.00 4.30
767 1578 4.535294 GTCCCTAGTCTTTAAAAGGTCCCT 59.465 45.833 3.55 0.00 0.00 4.20
768 1579 4.535294 AGTCCCTAGTCTTTAAAAGGTCCC 59.465 45.833 3.55 0.00 0.00 4.46
769 1580 5.758790 AGTCCCTAGTCTTTAAAAGGTCC 57.241 43.478 3.55 0.00 0.00 4.46
770 1581 8.461249 AAAAAGTCCCTAGTCTTTAAAAGGTC 57.539 34.615 3.55 0.00 32.14 3.85
771 1582 9.925545 TTAAAAAGTCCCTAGTCTTTAAAAGGT 57.074 29.630 3.55 0.00 32.14 3.50
800 1611 8.781951 TCAAGTCCTATGATTTTTCCTATTCCT 58.218 33.333 0.00 0.00 0.00 3.36
801 1612 8.980481 TCAAGTCCTATGATTTTTCCTATTCC 57.020 34.615 0.00 0.00 0.00 3.01
803 1614 9.190317 GGTTCAAGTCCTATGATTTTTCCTATT 57.810 33.333 0.00 0.00 0.00 1.73
804 1615 8.336235 TGGTTCAAGTCCTATGATTTTTCCTAT 58.664 33.333 0.00 0.00 0.00 2.57
805 1616 7.695055 TGGTTCAAGTCCTATGATTTTTCCTA 58.305 34.615 0.00 0.00 0.00 2.94
806 1617 6.552008 TGGTTCAAGTCCTATGATTTTTCCT 58.448 36.000 0.00 0.00 0.00 3.36
807 1618 6.834168 TGGTTCAAGTCCTATGATTTTTCC 57.166 37.500 0.00 0.00 0.00 3.13
808 1619 8.141268 TGTTTGGTTCAAGTCCTATGATTTTTC 58.859 33.333 0.00 0.00 0.00 2.29
809 1620 8.017418 TGTTTGGTTCAAGTCCTATGATTTTT 57.983 30.769 0.00 0.00 0.00 1.94
810 1621 7.505585 TCTGTTTGGTTCAAGTCCTATGATTTT 59.494 33.333 0.00 0.00 0.00 1.82
811 1622 7.004086 TCTGTTTGGTTCAAGTCCTATGATTT 58.996 34.615 0.00 0.00 0.00 2.17
812 1623 6.542821 TCTGTTTGGTTCAAGTCCTATGATT 58.457 36.000 0.00 0.00 0.00 2.57
813 1624 6.126863 TCTGTTTGGTTCAAGTCCTATGAT 57.873 37.500 0.00 0.00 0.00 2.45
814 1625 5.551233 CTCTGTTTGGTTCAAGTCCTATGA 58.449 41.667 0.00 0.00 0.00 2.15
815 1626 4.154918 GCTCTGTTTGGTTCAAGTCCTATG 59.845 45.833 0.00 0.00 0.00 2.23
816 1627 4.327680 GCTCTGTTTGGTTCAAGTCCTAT 58.672 43.478 0.00 0.00 0.00 2.57
817 1628 3.496160 GGCTCTGTTTGGTTCAAGTCCTA 60.496 47.826 0.00 0.00 0.00 2.94
818 1629 2.576615 GCTCTGTTTGGTTCAAGTCCT 58.423 47.619 0.00 0.00 0.00 3.85
819 1630 1.609072 GGCTCTGTTTGGTTCAAGTCC 59.391 52.381 0.00 0.00 0.00 3.85
820 1631 2.576615 AGGCTCTGTTTGGTTCAAGTC 58.423 47.619 0.00 0.00 0.00 3.01
821 1632 2.736670 AGGCTCTGTTTGGTTCAAGT 57.263 45.000 0.00 0.00 0.00 3.16
822 1633 3.253432 GGTAAGGCTCTGTTTGGTTCAAG 59.747 47.826 0.00 0.00 0.00 3.02
823 1634 3.117663 AGGTAAGGCTCTGTTTGGTTCAA 60.118 43.478 0.00 0.00 0.00 2.69
824 1635 2.441750 AGGTAAGGCTCTGTTTGGTTCA 59.558 45.455 0.00 0.00 0.00 3.18
825 1636 2.814336 CAGGTAAGGCTCTGTTTGGTTC 59.186 50.000 0.00 0.00 0.00 3.62
826 1637 2.863809 CAGGTAAGGCTCTGTTTGGTT 58.136 47.619 0.00 0.00 0.00 3.67
827 1638 1.545651 GCAGGTAAGGCTCTGTTTGGT 60.546 52.381 3.93 0.00 33.81 3.67
828 1639 1.168714 GCAGGTAAGGCTCTGTTTGG 58.831 55.000 3.93 0.00 33.81 3.28
829 1640 0.798776 CGCAGGTAAGGCTCTGTTTG 59.201 55.000 3.93 0.00 33.81 2.93
830 1641 0.396811 ACGCAGGTAAGGCTCTGTTT 59.603 50.000 3.93 0.00 33.81 2.83
831 1642 0.396811 AACGCAGGTAAGGCTCTGTT 59.603 50.000 3.93 0.00 33.81 3.16
832 1643 0.320771 CAACGCAGGTAAGGCTCTGT 60.321 55.000 3.93 0.00 33.81 3.41
833 1644 1.639298 GCAACGCAGGTAAGGCTCTG 61.639 60.000 0.00 0.00 0.00 3.35
834 1645 1.376037 GCAACGCAGGTAAGGCTCT 60.376 57.895 0.00 0.00 0.00 4.09
835 1646 2.740714 CGCAACGCAGGTAAGGCTC 61.741 63.158 0.00 0.00 0.00 4.70
836 1647 2.742372 CGCAACGCAGGTAAGGCT 60.742 61.111 0.00 0.00 0.00 4.58
837 1648 2.613506 AACGCAACGCAGGTAAGGC 61.614 57.895 0.00 0.00 0.00 4.35
838 1649 1.206578 CAACGCAACGCAGGTAAGG 59.793 57.895 0.00 0.00 0.00 2.69
895 1706 7.826918 TGGTAACTTTAGCACAATTTAACCT 57.173 32.000 0.00 0.00 36.35 3.50
929 1825 2.159296 GCCGGCGGTAAAAATCAAATCT 60.159 45.455 28.82 0.00 0.00 2.40
1152 2048 1.380246 GTGGGCATGGATGAGGCAA 60.380 57.895 0.00 0.00 30.95 4.52
1577 2473 1.097547 GTGGCACCCATTCCTCGATG 61.098 60.000 6.29 0.00 35.28 3.84
1663 2559 2.505777 CGAGAGCACGCTGACCAG 60.506 66.667 0.00 0.00 0.00 4.00
1689 2585 1.308069 CCTCGGCACCATCCAAGTTG 61.308 60.000 0.00 0.00 0.00 3.16
1737 2633 2.838736 ACCTCATGCCGAATGACATAC 58.161 47.619 0.00 0.00 40.50 2.39
1744 2640 2.290260 TGAAGACAACCTCATGCCGAAT 60.290 45.455 0.00 0.00 0.00 3.34
1760 2656 0.884704 GCCCAAGAACGCTGTGAAGA 60.885 55.000 0.00 0.00 0.00 2.87
1762 2658 1.153066 TGCCCAAGAACGCTGTGAA 60.153 52.632 0.00 0.00 0.00 3.18
1785 2681 5.296151 ACTTCCCATACATGTCGATCAAT 57.704 39.130 0.00 0.00 0.00 2.57
1840 2736 3.068873 ACCTCCTTCTCGCATACAATCTC 59.931 47.826 0.00 0.00 0.00 2.75
2136 3032 1.402194 GGCATCCGCTCTATCTTCTCG 60.402 57.143 0.00 0.00 38.60 4.04
2474 3370 9.668497 AGTATTTTCCTAAAGGTACAAGTCATC 57.332 33.333 0.00 0.00 36.34 2.92
2658 3565 8.637986 ACTTTGGTGCAAACAAAATTCTATAGA 58.362 29.630 15.90 0.00 37.37 1.98
2664 3571 6.312672 ACACTACTTTGGTGCAAACAAAATTC 59.687 34.615 15.90 0.00 37.37 2.17
2796 3703 1.202031 GCCAGCGAAAAATACACGGAG 60.202 52.381 0.00 0.00 0.00 4.63
2797 3704 0.800012 GCCAGCGAAAAATACACGGA 59.200 50.000 0.00 0.00 0.00 4.69
2798 3705 0.520412 CGCCAGCGAAAAATACACGG 60.520 55.000 6.06 0.00 42.83 4.94
2799 3706 0.520412 CCGCCAGCGAAAAATACACG 60.520 55.000 14.67 0.00 42.83 4.49
2800 3707 0.179174 CCCGCCAGCGAAAAATACAC 60.179 55.000 14.67 0.00 42.83 2.90
2801 3708 0.606944 ACCCGCCAGCGAAAAATACA 60.607 50.000 14.67 0.00 42.83 2.29
2802 3709 0.098200 GACCCGCCAGCGAAAAATAC 59.902 55.000 14.67 0.00 42.83 1.89
2803 3710 1.027792 GGACCCGCCAGCGAAAAATA 61.028 55.000 14.67 0.00 42.83 1.40
2804 3711 2.340328 GGACCCGCCAGCGAAAAAT 61.340 57.895 14.67 0.00 42.83 1.82
2817 3724 2.672908 CCCTTACAACCGGGACCC 59.327 66.667 6.32 0.00 43.44 4.46
2904 3811 1.795872 CCATGAAACGAACACGCTACA 59.204 47.619 0.00 0.00 0.00 2.74
2907 3814 0.586319 CACCATGAAACGAACACGCT 59.414 50.000 0.00 0.00 0.00 5.07
2933 3840 0.935196 AAAGAAGACACGACCGCAAC 59.065 50.000 0.00 0.00 0.00 4.17
2937 3844 1.615107 GCGGAAAGAAGACACGACCG 61.615 60.000 0.00 0.00 41.44 4.79
2957 3864 2.046892 CCAGACTCACAAGGGCCG 60.047 66.667 0.00 0.00 0.00 6.13
2975 3882 5.251468 TCTCTGAATGAAGAATCCCCTTTGA 59.749 40.000 0.00 0.00 0.00 2.69
3018 3925 1.745489 CCCTGCCGAAACTACAGCC 60.745 63.158 0.00 0.00 0.00 4.85
3042 3949 2.989253 TCGTCTTCCAGCCGCTCA 60.989 61.111 0.00 0.00 0.00 4.26
3058 3965 3.330720 CCCAGTGACCCCACCCTC 61.331 72.222 0.00 0.00 44.22 4.30
3067 3974 2.040544 CCGCCAATCACCCAGTGAC 61.041 63.158 0.00 0.00 45.65 3.67
3112 4019 1.007271 CACCCTATCGTAGCAGCCG 60.007 63.158 0.00 0.00 0.00 5.52
3113 4020 1.113517 TCCACCCTATCGTAGCAGCC 61.114 60.000 0.00 0.00 0.00 4.85
3121 4028 2.106332 GCACCGTCCACCCTATCG 59.894 66.667 0.00 0.00 0.00 2.92
3142 4049 0.291989 CGAATCAAAGAGCGACGACG 59.708 55.000 2.12 2.12 42.93 5.12
3176 4083 0.527385 GCAGCAGCCGAAACAAAACA 60.527 50.000 0.00 0.00 33.58 2.83
3272 4179 1.362355 CCGGCAAGGAAACAACACC 59.638 57.895 0.00 0.00 45.00 4.16
3273 4180 0.248866 CACCGGCAAGGAAACAACAC 60.249 55.000 0.00 0.00 45.00 3.32
3274 4181 2.010582 GCACCGGCAAGGAAACAACA 62.011 55.000 0.00 0.00 45.00 3.33
3275 4182 1.299850 GCACCGGCAAGGAAACAAC 60.300 57.895 0.00 0.00 45.00 3.32
3276 4183 2.494530 GGCACCGGCAAGGAAACAA 61.495 57.895 0.00 0.00 45.00 2.83
3277 4184 2.909965 GGCACCGGCAAGGAAACA 60.910 61.111 0.00 0.00 45.00 2.83
3278 4185 4.038080 CGGCACCGGCAAGGAAAC 62.038 66.667 0.00 0.00 45.00 2.78
3279 4186 3.561120 ATCGGCACCGGCAAGGAAA 62.561 57.895 9.58 0.00 45.00 3.13
3280 4187 3.561120 AATCGGCACCGGCAAGGAA 62.561 57.895 9.58 0.00 45.00 3.36
3281 4188 4.028490 AATCGGCACCGGCAAGGA 62.028 61.111 9.58 0.00 45.00 3.36
3283 4190 0.813610 TATCAATCGGCACCGGCAAG 60.814 55.000 9.58 0.00 43.71 4.01
3284 4191 0.179032 ATATCAATCGGCACCGGCAA 60.179 50.000 9.58 0.00 43.71 4.52
3285 4192 0.179032 AATATCAATCGGCACCGGCA 60.179 50.000 9.58 0.00 43.71 5.69
3286 4193 0.951558 AAATATCAATCGGCACCGGC 59.048 50.000 9.58 0.00 40.25 6.13
3287 4194 2.032030 GTCAAATATCAATCGGCACCGG 60.032 50.000 9.58 0.00 40.25 5.28
3306 4213 1.576421 CAGCCGAAACAAGCCTGTC 59.424 57.895 0.00 0.00 33.45 3.51
3380 4287 3.065575 GGAAGCATCCACCACTACG 57.934 57.895 2.32 0.00 45.79 3.51


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

AutoCloner maintained by Alex Coulton.