Multiple sequence alignment - TraesCS6B01G141300

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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 TraesCS6B01G141300 chr6B 100.000 8859 0 0 1 8859 140605670 140596812 0.000000e+00 16360.0
1 TraesCS6B01G141300 chr6D 96.035 6406 188 35 2482 8859 65503881 65497514 0.000000e+00 10362.0
2 TraesCS6B01G141300 chr6D 91.092 2234 139 44 152 2370 65506169 65503981 0.000000e+00 2968.0
3 TraesCS6B01G141300 chr6D 80.380 316 54 8 7071 7380 63762205 63761892 5.350000e-57 233.0
4 TraesCS6B01G141300 chr6D 85.526 228 26 7 7158 7380 63733717 63733492 1.920000e-56 231.0
5 TraesCS6B01G141300 chr6A 95.526 6437 179 37 2477 8859 83252982 83259363 0.000000e+00 10190.0
6 TraesCS6B01G141300 chr6A 89.871 2399 151 50 5 2365 83250525 83252869 0.000000e+00 3000.0
7 TraesCS6B01G141300 chr6A 83.475 236 32 7 7131 7362 80884813 80884581 6.970000e-51 213.0
8 TraesCS6B01G141300 chr7D 88.571 140 14 1 1171 1310 528141631 528141494 1.530000e-37 169.0
9 TraesCS6B01G141300 chr7D 87.736 106 13 0 1206 1311 112046617 112046722 3.360000e-24 124.0
10 TraesCS6B01G141300 chr7B 87.857 140 15 1 1171 1310 565916615 565916478 7.120000e-36 163.0
11 TraesCS6B01G141300 chr7A 89.600 125 13 0 1186 1310 608406043 608405919 9.210000e-35 159.0
12 TraesCS6B01G141300 chr2D 87.619 105 13 0 1206 1310 589973874 589973978 1.210000e-23 122.0
13 TraesCS6B01G141300 chr2A 86.916 107 12 2 1206 1311 724297748 724297853 1.560000e-22 119.0
14 TraesCS6B01G141300 chr2B 83.000 100 17 0 1211 1310 766557990 766558089 3.410000e-14 91.6
15 TraesCS6B01G141300 chr5D 95.122 41 2 0 1 41 526752542 526752502 2.060000e-06 65.8


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 TraesCS6B01G141300 chr6B 140596812 140605670 8858 True 16360 16360 100.0000 1 8859 1 chr6B.!!$R1 8858
1 TraesCS6B01G141300 chr6D 65497514 65506169 8655 True 6665 10362 93.5635 152 8859 2 chr6D.!!$R3 8707
2 TraesCS6B01G141300 chr6A 83250525 83259363 8838 False 6595 10190 92.6985 5 8859 2 chr6A.!!$F1 8854

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
905 940 0.107848 ACCCATACCGCGAAAAGGAG 60.108 55.000 8.23 1.44 0.00 3.69 F
2587 2693 0.463833 GCTACCCCAACCTTCCATCG 60.464 60.000 0.00 0.00 0.00 3.84 F
2659 2766 0.320374 CTGCCCCTACTGTTCGACAA 59.680 55.000 0.00 0.00 0.00 3.18 F
2668 2775 0.586319 CTGTTCGACAAACACGGCAT 59.414 50.000 0.00 0.00 42.95 4.40 F
3639 3749 1.757118 AGCGACAGTATGCACATAGGT 59.243 47.619 0.00 0.00 42.53 3.08 F
4856 4995 2.113243 GACCCTCAAACCCAGAGCGT 62.113 60.000 0.00 0.00 0.00 5.07 F
4949 5088 0.744874 GCCATGCAGTCCGAGTACTA 59.255 55.000 0.00 0.00 0.00 1.82 F
5124 5263 1.135859 GCAGCACTTCCGTTGAATCAG 60.136 52.381 0.00 0.00 0.00 2.90 F
5493 5635 2.290367 TCAGCAAACACAATTGTCCGAG 59.710 45.455 8.48 0.00 33.55 4.63 F
5835 5986 2.368311 TCCCCAAAACTGGTAACACC 57.632 50.000 0.00 0.00 46.17 4.16 F
7385 7544 2.360801 TGCCTTTCTGCCTGTGTTTAAC 59.639 45.455 0.00 0.00 0.00 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2640 2746 0.320374 TTGTCGAACAGTAGGGGCAG 59.680 55.000 0.00 0.00 0.00 4.85 R
4219 4353 1.755179 CAAGCGGTTCAATCTCCCAT 58.245 50.000 0.00 0.00 0.00 4.00 R
4437 4576 2.362077 ACCAAAAGCAGTCAATCACCAC 59.638 45.455 0.00 0.00 0.00 4.16 R
4620 4759 5.588246 TCAATCTACTGTTTGCAAGACAACA 59.412 36.000 13.10 8.27 38.23 3.33 R
4949 5088 0.683504 AGGGTTACTCGCTGATCGGT 60.684 55.000 2.89 0.00 37.93 4.69 R
6706 6858 0.247460 GTGGAGGGGCTTCATTTTGC 59.753 55.000 0.00 0.00 0.00 3.68 R
6708 6860 1.428912 TCAGTGGAGGGGCTTCATTTT 59.571 47.619 0.00 0.00 0.00 1.82 R
7042 7200 1.564348 GAGGGCCCTGATTTCCAACTA 59.436 52.381 34.59 0.00 0.00 2.24 R
7287 7446 2.230508 TGTGTAGACTAGCTTCCAACCG 59.769 50.000 0.00 0.00 0.00 4.44 R
7834 7994 0.182537 CGAATTGGTCATAGGGGCCA 59.817 55.000 4.39 0.00 0.00 5.36 R
8644 8808 1.736126 CGTCAATGCTGCTTGAGACAT 59.264 47.619 12.60 0.00 35.88 3.06 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
34 35 7.925483 AGATGAATAGATCAGAAGTTTTCTCGG 59.075 37.037 0.00 0.00 42.53 4.63
39 40 8.848474 ATAGATCAGAAGTTTTCTCGGAAAAA 57.152 30.769 11.69 3.31 38.11 1.94
74 76 1.790755 TTCTCAGTTTACACGCGCAT 58.209 45.000 5.73 0.00 0.00 4.73
75 77 1.067693 TCTCAGTTTACACGCGCATG 58.932 50.000 5.73 4.48 0.00 4.06
95 97 9.424659 GCGCATGAAAAATATTTATTCCTTTTG 57.575 29.630 0.30 5.24 0.00 2.44
106 108 6.499234 TTTATTCCTTTTGTACTAACCGGC 57.501 37.500 0.00 0.00 0.00 6.13
112 114 0.813184 TTGTACTAACCGGCCTCTCG 59.187 55.000 0.00 0.00 0.00 4.04
113 115 1.065436 GTACTAACCGGCCTCTCGC 59.935 63.158 0.00 0.00 0.00 5.03
124 126 2.169789 CCTCTCGCAATGCCAGTCG 61.170 63.158 0.00 0.00 0.00 4.18
129 131 2.644418 GCAATGCCAGTCGTGCAA 59.356 55.556 0.00 0.00 42.92 4.08
138 145 1.200020 CCAGTCGTGCAATTTCCTTCC 59.800 52.381 0.00 0.00 0.00 3.46
156 163 6.074648 TCCTTCCTTTTGGCTTCTTTGATTA 58.925 36.000 0.00 0.00 40.12 1.75
161 168 9.747898 TTCCTTTTGGCTTCTTTGATTAGTATA 57.252 29.630 0.00 0.00 40.12 1.47
229 237 3.004839 GCCATCTTCGATGCTACTACTCA 59.995 47.826 0.00 0.00 0.00 3.41
236 244 3.630769 TCGATGCTACTACTCATCCGTTT 59.369 43.478 0.00 0.00 36.60 3.60
237 245 4.818005 TCGATGCTACTACTCATCCGTTTA 59.182 41.667 0.00 0.00 36.60 2.01
272 280 9.241919 TGTCATGGTTTTAGTTCACATGATATT 57.758 29.630 0.00 0.00 46.41 1.28
278 286 9.965824 GGTTTTAGTTCACATGATATTTATGGG 57.034 33.333 0.00 2.44 0.00 4.00
307 315 1.272490 TCTTCGCATGAGGTTCGAGTT 59.728 47.619 0.00 0.00 33.56 3.01
348 356 9.547279 AATACACCAAAATTCCCTTAGAAATCT 57.453 29.630 0.00 0.00 38.21 2.40
352 360 8.802267 CACCAAAATTCCCTTAGAAATCTGTTA 58.198 33.333 0.00 0.00 38.21 2.41
479 487 2.126149 CGAGCTGAGCTGAAGCGT 60.126 61.111 13.71 0.00 45.59 5.07
493 501 0.382515 AAGCGTAGATGAGCTCGGAC 59.617 55.000 9.64 2.87 43.78 4.79
494 502 1.369448 GCGTAGATGAGCTCGGACG 60.369 63.158 19.23 19.23 39.59 4.79
495 503 1.280142 CGTAGATGAGCTCGGACGG 59.720 63.158 16.99 0.19 35.62 4.79
496 504 1.158484 CGTAGATGAGCTCGGACGGA 61.158 60.000 16.99 0.00 35.62 4.69
497 505 0.589223 GTAGATGAGCTCGGACGGAG 59.411 60.000 9.64 5.68 46.06 4.63
569 594 3.819564 TCGAAGAGGAGAGAGAGAGAG 57.180 52.381 0.00 0.00 0.00 3.20
570 595 3.371034 TCGAAGAGGAGAGAGAGAGAGA 58.629 50.000 0.00 0.00 0.00 3.10
571 596 3.384789 TCGAAGAGGAGAGAGAGAGAGAG 59.615 52.174 0.00 0.00 0.00 3.20
572 597 3.384789 CGAAGAGGAGAGAGAGAGAGAGA 59.615 52.174 0.00 0.00 0.00 3.10
573 598 4.500545 CGAAGAGGAGAGAGAGAGAGAGAG 60.501 54.167 0.00 0.00 0.00 3.20
574 599 4.271807 AGAGGAGAGAGAGAGAGAGAGA 57.728 50.000 0.00 0.00 0.00 3.10
575 600 4.222336 AGAGGAGAGAGAGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
576 601 4.078922 AGAGGAGAGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
593 618 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
712 741 1.830477 GCTCACAACTCTCATCCCTCT 59.170 52.381 0.00 0.00 0.00 3.69
746 775 3.495100 GCTCCCTCTCTCTCTCTCTAGTG 60.495 56.522 0.00 0.00 0.00 2.74
894 929 2.738938 GGTGACCGGGACCCATACC 61.739 68.421 12.15 8.90 0.00 2.73
905 940 0.107848 ACCCATACCGCGAAAAGGAG 60.108 55.000 8.23 1.44 0.00 3.69
974 1009 4.214327 GAGCCGCCGAAGCTAGCT 62.214 66.667 12.68 12.68 45.69 3.32
991 1026 1.506718 CTAGCTTCCGCGTGTGAGA 59.493 57.895 4.92 0.00 42.32 3.27
1121 1156 3.812019 GCTTCGACGAGGCGGAGA 61.812 66.667 16.49 0.00 39.23 3.71
1329 1364 4.475381 AGGTGAGTGAGTGAGACCTATCTA 59.525 45.833 0.00 0.00 35.19 1.98
1330 1365 4.577283 GGTGAGTGAGTGAGACCTATCTAC 59.423 50.000 0.00 0.00 34.34 2.59
1332 1367 5.295787 GTGAGTGAGTGAGACCTATCTACTG 59.704 48.000 0.00 0.00 34.34 2.74
1335 1370 2.550606 GAGTGAGACCTATCTACTGGCG 59.449 54.545 0.00 0.00 34.34 5.69
1354 1389 1.228245 AGTGCCATTTCCGCAGTGT 60.228 52.632 0.00 0.00 38.46 3.55
1370 1405 1.899814 AGTGTTCGTTCTATGCTCCCA 59.100 47.619 0.00 0.00 0.00 4.37
1371 1406 2.000447 GTGTTCGTTCTATGCTCCCAC 59.000 52.381 0.00 0.00 0.00 4.61
1385 1420 2.498167 CTCCCACTGGTTCTGTTCTTG 58.502 52.381 0.00 0.00 0.00 3.02
1386 1421 2.104792 CTCCCACTGGTTCTGTTCTTGA 59.895 50.000 0.00 0.00 0.00 3.02
1387 1422 2.507886 TCCCACTGGTTCTGTTCTTGAA 59.492 45.455 0.00 0.00 0.00 2.69
1395 1430 6.774656 ACTGGTTCTGTTCTTGAAGAATGATT 59.225 34.615 11.20 0.00 36.50 2.57
1407 1442 5.480710 TGAAGAATGATTATCTCCCCTCCT 58.519 41.667 0.00 0.00 0.00 3.69
1541 1577 3.570125 CCTTTGAAGTTCAAGAGGGTTCC 59.430 47.826 24.61 0.00 37.70 3.62
1550 1586 3.256704 TCAAGAGGGTTCCTAACATGGT 58.743 45.455 0.00 0.00 31.76 3.55
1558 1594 5.189934 AGGGTTCCTAACATGGTCTTCTTAG 59.810 44.000 0.00 0.00 28.47 2.18
1559 1595 5.429130 GGTTCCTAACATGGTCTTCTTAGG 58.571 45.833 10.05 10.05 37.61 2.69
1560 1596 5.429130 GTTCCTAACATGGTCTTCTTAGGG 58.571 45.833 14.36 1.45 37.10 3.53
1562 1598 3.136626 CCTAACATGGTCTTCTTAGGGGG 59.863 52.174 8.88 0.00 34.09 5.40
1567 1603 4.107311 ACATGGTCTTCTTAGGGGGAAAAA 59.893 41.667 0.00 0.00 0.00 1.94
1610 1648 5.163513 GCATTTTCAGTAGTTGTGATTGGG 58.836 41.667 0.00 0.00 0.00 4.12
1613 1651 2.626785 TCAGTAGTTGTGATTGGGGGA 58.373 47.619 0.00 0.00 0.00 4.81
1639 1680 8.421784 ACTATACTTGCTTGCTACTAATTGCTA 58.578 33.333 0.00 0.00 0.00 3.49
1739 1785 1.068264 GCTTTTGGTGCCTTGTAGAGC 60.068 52.381 0.00 0.00 0.00 4.09
1804 1853 4.482386 CATGCATCCATGTATAGCTTTGC 58.518 43.478 0.00 0.00 43.07 3.68
1834 1883 5.263599 TGCATTTATGGTCCTGATTTCTGT 58.736 37.500 0.00 0.00 0.00 3.41
1860 1909 2.082231 CTTCCACTGATTCTGCACTGG 58.918 52.381 0.00 0.00 0.00 4.00
2210 2270 6.449698 CATGTTTGAATGCTTGTACTTCCTT 58.550 36.000 0.00 0.00 0.00 3.36
2462 2568 5.560966 TTTTCTTTTGCGAGTGAACTTCT 57.439 34.783 0.00 0.00 0.00 2.85
2463 2569 4.795970 TTCTTTTGCGAGTGAACTTCTC 57.204 40.909 0.00 0.00 0.00 2.87
2464 2570 4.060038 TCTTTTGCGAGTGAACTTCTCT 57.940 40.909 0.00 0.00 0.00 3.10
2465 2571 4.442706 TCTTTTGCGAGTGAACTTCTCTT 58.557 39.130 0.00 0.00 0.00 2.85
2466 2572 4.876107 TCTTTTGCGAGTGAACTTCTCTTT 59.124 37.500 0.00 0.00 0.00 2.52
2467 2573 6.046593 TCTTTTGCGAGTGAACTTCTCTTTA 58.953 36.000 0.00 0.00 0.00 1.85
2468 2574 6.706270 TCTTTTGCGAGTGAACTTCTCTTTAT 59.294 34.615 0.00 0.00 0.00 1.40
2469 2575 6.467723 TTTGCGAGTGAACTTCTCTTTATC 57.532 37.500 0.00 0.00 0.00 1.75
2470 2576 5.392767 TGCGAGTGAACTTCTCTTTATCT 57.607 39.130 0.00 0.00 0.00 1.98
2471 2577 5.784177 TGCGAGTGAACTTCTCTTTATCTT 58.216 37.500 0.00 0.00 0.00 2.40
2472 2578 5.864474 TGCGAGTGAACTTCTCTTTATCTTC 59.136 40.000 0.00 0.00 0.00 2.87
2473 2579 5.864474 GCGAGTGAACTTCTCTTTATCTTCA 59.136 40.000 0.00 0.00 0.00 3.02
2474 2580 6.366332 GCGAGTGAACTTCTCTTTATCTTCAA 59.634 38.462 0.00 0.00 0.00 2.69
2475 2581 7.095607 GCGAGTGAACTTCTCTTTATCTTCAAA 60.096 37.037 0.00 0.00 0.00 2.69
2557 2663 1.603456 TGCAAAAGGATGTCGAAGCA 58.397 45.000 0.00 0.00 0.00 3.91
2584 2690 1.550130 CGAGCTACCCCAACCTTCCA 61.550 60.000 0.00 0.00 0.00 3.53
2587 2693 0.463833 GCTACCCCAACCTTCCATCG 60.464 60.000 0.00 0.00 0.00 3.84
2636 2742 6.145534 CGTCACTTTGCAAGTAATCTAACAGA 59.854 38.462 0.00 0.00 40.46 3.41
2639 2745 6.204688 CACTTTGCAAGTAATCTAACAGACCA 59.795 38.462 0.00 0.00 40.46 4.02
2640 2746 6.204882 ACTTTGCAAGTAATCTAACAGACCAC 59.795 38.462 0.00 0.00 40.69 4.16
2646 2753 0.912486 ATCTAACAGACCACTGCCCC 59.088 55.000 0.00 0.00 46.95 5.80
2659 2766 0.320374 CTGCCCCTACTGTTCGACAA 59.680 55.000 0.00 0.00 0.00 3.18
2660 2767 0.759959 TGCCCCTACTGTTCGACAAA 59.240 50.000 0.00 0.00 0.00 2.83
2661 2768 1.154197 GCCCCTACTGTTCGACAAAC 58.846 55.000 0.00 0.00 38.43 2.93
2662 2769 1.541670 GCCCCTACTGTTCGACAAACA 60.542 52.381 0.00 0.00 45.60 2.83
2663 2770 2.140717 CCCCTACTGTTCGACAAACAC 58.859 52.381 0.00 0.00 42.95 3.32
2664 2771 1.790623 CCCTACTGTTCGACAAACACG 59.209 52.381 0.00 0.00 42.95 4.49
2665 2772 1.790623 CCTACTGTTCGACAAACACGG 59.209 52.381 0.00 0.00 42.95 4.94
2666 2773 1.191647 CTACTGTTCGACAAACACGGC 59.808 52.381 0.00 0.00 42.95 5.68
2667 2774 0.741574 ACTGTTCGACAAACACGGCA 60.742 50.000 0.00 0.00 42.95 5.69
2668 2775 0.586319 CTGTTCGACAAACACGGCAT 59.414 50.000 0.00 0.00 42.95 4.40
2709 2817 7.308469 GCTCTGAAAGATGTTGTCTCTTGATTT 60.308 37.037 0.00 0.00 45.62 2.17
2710 2818 8.455903 TCTGAAAGATGTTGTCTCTTGATTTT 57.544 30.769 0.00 0.00 38.67 1.82
2711 2819 8.906867 TCTGAAAGATGTTGTCTCTTGATTTTT 58.093 29.630 0.00 0.00 38.67 1.94
2831 2939 6.628185 AGAATTTCTCTGCATGTTTCCAATC 58.372 36.000 0.00 0.00 31.12 2.67
2841 2949 4.651045 GCATGTTTCCAATCCCTTAATCCT 59.349 41.667 0.00 0.00 0.00 3.24
3069 3177 2.290641 CCAGGTCTTTTCCACGACAAAG 59.709 50.000 0.00 0.00 31.88 2.77
3070 3178 1.947456 AGGTCTTTTCCACGACAAAGC 59.053 47.619 0.00 0.00 31.15 3.51
3071 3179 1.947456 GGTCTTTTCCACGACAAAGCT 59.053 47.619 0.00 0.00 31.15 3.74
3072 3180 2.031944 GGTCTTTTCCACGACAAAGCTC 60.032 50.000 0.00 0.00 31.15 4.09
3073 3181 1.864711 TCTTTTCCACGACAAAGCTCG 59.135 47.619 0.00 0.00 39.68 5.03
3232 3342 8.665685 GGTACAGAAAATGTAGTACAATTGAGG 58.334 37.037 13.59 1.51 45.06 3.86
3426 3536 2.636830 CATGCTTCCGTCCATCTTCTT 58.363 47.619 0.00 0.00 0.00 2.52
3427 3537 2.859165 TGCTTCCGTCCATCTTCTTT 57.141 45.000 0.00 0.00 0.00 2.52
3435 3545 6.174720 TCCGTCCATCTTCTTTAAGCATAT 57.825 37.500 0.00 0.00 32.36 1.78
3534 3644 7.148656 GCCACATTTTCGTTTTATTTGCTACAT 60.149 33.333 0.00 0.00 0.00 2.29
3639 3749 1.757118 AGCGACAGTATGCACATAGGT 59.243 47.619 0.00 0.00 42.53 3.08
3841 3961 5.671493 AGTCCTACTGAATTTGTTATCCCG 58.329 41.667 0.00 0.00 0.00 5.14
3981 4101 3.904339 ACTCTTACCTCTGAAGCTCCAAA 59.096 43.478 0.00 0.00 0.00 3.28
4101 4221 5.048991 AGCTTACAGGTTGGATTTACAAACG 60.049 40.000 0.00 0.00 42.75 3.60
4219 4353 7.661847 GGAGAAAGAAGGAACAGAGTTTCAATA 59.338 37.037 0.00 0.00 0.00 1.90
4273 4407 3.152341 CATATGTCCCCAGCCATTCTTC 58.848 50.000 0.00 0.00 0.00 2.87
4327 4461 7.122353 ACGTCTGGTATAAGTATGACAAAGACT 59.878 37.037 0.00 0.00 0.00 3.24
4406 4545 6.948309 GCATGTATGGGGGTAAAGATCTTAAT 59.052 38.462 8.75 0.00 0.00 1.40
4437 4576 8.012957 AGATACATAAAGACTACTTGGTGGAG 57.987 38.462 0.00 0.00 36.39 3.86
4454 4593 2.158623 TGGAGTGGTGATTGACTGCTTT 60.159 45.455 0.00 0.00 32.15 3.51
4581 4720 7.095774 CGTAGTTTATGTGCCATACAGATAACC 60.096 40.741 0.00 0.00 42.44 2.85
4737 4876 5.900865 TGTCTGATAATTTGCATGCTTCA 57.099 34.783 20.33 10.70 0.00 3.02
4792 4931 7.911651 TGAGTCATTAGAGATGGAAAGTCTTT 58.088 34.615 0.00 0.00 0.00 2.52
4856 4995 2.113243 GACCCTCAAACCCAGAGCGT 62.113 60.000 0.00 0.00 0.00 5.07
4948 5087 0.972983 AGCCATGCAGTCCGAGTACT 60.973 55.000 0.00 0.00 0.00 2.73
4949 5088 0.744874 GCCATGCAGTCCGAGTACTA 59.255 55.000 0.00 0.00 0.00 1.82
5124 5263 1.135859 GCAGCACTTCCGTTGAATCAG 60.136 52.381 0.00 0.00 0.00 2.90
5218 5357 4.512914 CCCTAAGCCAGGCCCAGC 62.513 72.222 8.22 6.49 43.98 4.85
5231 5370 3.012934 GGCCCAGCCTCAAACTAATAA 57.987 47.619 0.00 0.00 46.69 1.40
5292 5431 2.734079 ACAACAGCAACAAAAACAACCG 59.266 40.909 0.00 0.00 0.00 4.44
5490 5632 3.715628 AGTCAGCAAACACAATTGTCC 57.284 42.857 8.48 0.00 33.55 4.02
5493 5635 2.290367 TCAGCAAACACAATTGTCCGAG 59.710 45.455 8.48 0.00 33.55 4.63
5569 5711 3.244078 ACAATCCGCAGTTACACTCTCAA 60.244 43.478 0.00 0.00 0.00 3.02
5835 5986 2.368311 TCCCCAAAACTGGTAACACC 57.632 50.000 0.00 0.00 46.17 4.16
5962 6113 3.118920 TGGCAGGAATGATCATTGCAAAG 60.119 43.478 33.08 24.46 40.94 2.77
6678 6830 9.257651 AGTACGATTTTTAAGGCAGTATATGTC 57.742 33.333 0.00 0.00 0.00 3.06
6706 6858 8.372459 TGTGGTGCCTATATTACCAAATAGTAG 58.628 37.037 0.00 0.00 45.30 2.57
6707 6859 7.333672 GTGGTGCCTATATTACCAAATAGTAGC 59.666 40.741 0.00 0.00 45.30 3.58
6708 6860 7.016760 TGGTGCCTATATTACCAAATAGTAGCA 59.983 37.037 0.00 0.00 41.25 3.49
6849 7001 4.121317 AGGAATGCACACAACAACAATTG 58.879 39.130 3.24 3.24 35.59 2.32
7022 7180 3.452264 TCACACATAGGCACATAGAGCTT 59.548 43.478 0.00 0.00 0.00 3.74
7054 7212 7.470841 GCTTGTTAAAGGGTTAGTTGGAAATCA 60.471 37.037 0.00 0.00 33.68 2.57
7287 7446 4.181309 ACTTGAAGACCGACAGAGAATC 57.819 45.455 0.00 0.00 0.00 2.52
7385 7544 2.360801 TGCCTTTCTGCCTGTGTTTAAC 59.639 45.455 0.00 0.00 0.00 2.01
7505 7664 8.604035 ACGCTGACATAACTGAAACATAAATAG 58.396 33.333 0.00 0.00 0.00 1.73
7510 7669 8.980481 ACATAACTGAAACATAAATAGGGGAG 57.020 34.615 0.00 0.00 0.00 4.30
7887 8047 3.819564 AGAGGCGCATTCACATAGTTA 57.180 42.857 10.83 0.00 0.00 2.24
7958 8118 4.817318 TGGATTCATGTGTACTACAGCA 57.183 40.909 0.00 0.00 43.80 4.41
8052 8212 8.650143 AAAAATGCTCCTCAGATTAGGTTTTA 57.350 30.769 0.00 0.00 37.91 1.52
8091 8251 8.068893 TGTAGTTTTATCAGTTGAAACGAGTC 57.931 34.615 0.00 0.00 38.09 3.36
8150 8310 2.165437 GAGACCTGAGACAGTTAGGCAG 59.835 54.545 0.00 0.00 34.93 4.85
8219 8379 1.436326 TGGGTTGTGTGTAGCCCTTA 58.564 50.000 0.00 0.00 41.33 2.69
8288 8451 6.749923 AATGAAACTGAGATAACAAGCCTC 57.250 37.500 0.00 0.00 0.00 4.70
8348 8511 7.382218 CCATATGAAATTTGGTTCTAAATCCGC 59.618 37.037 3.65 0.00 40.13 5.54
8362 8525 0.039618 ATCCGCCAAATGGACCTGTT 59.960 50.000 2.98 0.00 38.60 3.16
8364 8527 0.893270 CCGCCAAATGGACCTGTTGA 60.893 55.000 2.98 0.00 37.39 3.18
8571 8734 6.232692 AGGCAAAATTTTAACATGACAGCAT 58.767 32.000 2.44 0.00 34.29 3.79
8644 8808 8.939929 TCAAGTTTAATTTGTTTCACATGCAAA 58.060 25.926 0.00 0.00 36.68 3.68
8685 8849 3.983344 CGGATCCAAAAAGCACAGAAAAG 59.017 43.478 13.41 0.00 0.00 2.27
8725 8889 2.418976 TCGAGTCTATGGTCGTCACAAG 59.581 50.000 0.00 0.00 37.46 3.16
8776 8940 4.320494 GGTTGATGGCAATCCGATGAATAC 60.320 45.833 0.00 0.00 36.22 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 6.107901 ACTGAGAAATCAGTCTTGCTAGTT 57.892 37.500 5.09 0.00 46.96 2.24
53 55 2.139917 TGCGCGTGTAAACTGAGAAAT 58.860 42.857 8.43 0.00 0.00 2.17
57 59 1.067693 TCATGCGCGTGTAAACTGAG 58.932 50.000 27.72 0.22 0.00 3.35
95 97 1.065436 GCGAGAGGCCGGTTAGTAC 59.935 63.158 1.90 0.00 34.80 2.73
96 98 0.966875 TTGCGAGAGGCCGGTTAGTA 60.967 55.000 1.90 0.00 42.61 1.82
106 108 2.169789 CGACTGGCATTGCGAGAGG 61.170 63.158 24.95 12.93 36.50 3.69
112 114 0.388907 AATTGCACGACTGGCATTGC 60.389 50.000 0.00 0.00 41.58 3.56
113 115 1.987770 GAAATTGCACGACTGGCATTG 59.012 47.619 0.00 0.00 41.58 2.82
124 126 2.807967 GCCAAAAGGAAGGAAATTGCAC 59.192 45.455 0.00 0.00 0.00 4.57
129 131 5.366477 TCAAAGAAGCCAAAAGGAAGGAAAT 59.634 36.000 0.00 0.00 0.00 2.17
208 216 4.837896 TGAGTAGTAGCATCGAAGATGG 57.162 45.455 11.41 0.00 45.12 3.51
216 224 7.766219 TTTTAAACGGATGAGTAGTAGCATC 57.234 36.000 0.00 0.00 40.05 3.91
229 237 9.936759 AACCATGACAATAATTTTTAAACGGAT 57.063 25.926 0.00 0.00 0.00 4.18
272 280 3.128349 GCGAAGAATTCTACGCCCATAA 58.872 45.455 8.75 0.00 44.75 1.90
273 281 2.750948 GCGAAGAATTCTACGCCCATA 58.249 47.619 8.75 0.00 44.75 2.74
274 282 1.583054 GCGAAGAATTCTACGCCCAT 58.417 50.000 8.75 0.00 44.75 4.00
275 283 3.059603 GCGAAGAATTCTACGCCCA 57.940 52.632 8.75 0.00 44.75 5.36
278 286 2.219674 CCTCATGCGAAGAATTCTACGC 59.780 50.000 8.75 10.37 44.75 4.42
338 346 8.978539 GCCTTTTTGGTTTAACAGATTTCTAAG 58.021 33.333 0.00 0.00 38.35 2.18
348 356 2.838202 TGTGGGCCTTTTTGGTTTAACA 59.162 40.909 4.53 0.00 38.35 2.41
352 360 3.286353 CATTTGTGGGCCTTTTTGGTTT 58.714 40.909 4.53 0.00 38.35 3.27
355 363 1.545204 CCCATTTGTGGGCCTTTTTGG 60.545 52.381 4.53 5.62 42.99 3.28
356 364 1.894881 CCCATTTGTGGGCCTTTTTG 58.105 50.000 4.53 0.00 42.99 2.44
467 475 1.202348 GCTCATCTACGCTTCAGCTCA 60.202 52.381 0.00 0.00 39.32 4.26
479 487 3.008141 CTCCGTCCGAGCTCATCTA 57.992 57.895 15.40 0.00 0.00 1.98
557 582 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
558 583 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
559 584 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
560 585 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
561 586 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
562 587 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
563 588 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
564 589 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
565 590 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
566 591 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
567 592 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
568 593 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
569 594 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
570 595 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
571 596 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
572 597 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
573 598 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
574 599 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
575 600 5.596361 TCTTCTCTCTCTCTCTCTCTCTCTC 59.404 48.000 0.00 0.00 0.00 3.20
576 601 5.523588 TCTTCTCTCTCTCTCTCTCTCTCT 58.476 45.833 0.00 0.00 0.00 3.10
593 618 2.067414 AAACCGAGACGCTTCTTCTC 57.933 50.000 0.00 0.00 36.85 2.87
647 672 1.081840 GCTTTGCTGTCGCTGGTTC 60.082 57.895 0.00 0.00 36.97 3.62
691 716 1.830477 GAGGGATGAGAGTTGTGAGCT 59.170 52.381 0.00 0.00 0.00 4.09
712 741 2.972713 GAGAGGGAGCTAGAGAGAGAGA 59.027 54.545 0.00 0.00 0.00 3.10
746 775 3.108292 GACCCCGTCTAGTCCTACC 57.892 63.158 0.00 0.00 0.00 3.18
905 940 1.721804 CGCCGAGTTCTTCTTTTTCGC 60.722 52.381 0.00 0.00 0.00 4.70
931 966 1.253593 ATGAGTCACAGAGGAGCGCA 61.254 55.000 11.47 0.00 0.00 6.09
1044 1079 0.250295 AGCAGCAAGTACCTTCGCAA 60.250 50.000 0.00 0.00 0.00 4.85
1121 1156 4.783227 TCCTTCCTTTTCTAGCTGTACCAT 59.217 41.667 0.00 0.00 0.00 3.55
1132 1167 2.157926 AGAGACCCCTCCTTCCTTTTCT 60.158 50.000 0.00 0.00 40.30 2.52
1335 1370 1.237285 ACACTGCGGAAATGGCACTC 61.237 55.000 0.00 0.00 36.24 3.51
1346 1381 0.370273 GCATAGAACGAACACTGCGG 59.630 55.000 0.00 0.00 0.00 5.69
1354 1389 1.207089 CCAGTGGGAGCATAGAACGAA 59.793 52.381 0.00 0.00 35.59 3.85
1370 1405 5.684704 TCATTCTTCAAGAACAGAACCAGT 58.315 37.500 0.68 0.00 37.00 4.00
1371 1406 6.814506 ATCATTCTTCAAGAACAGAACCAG 57.185 37.500 0.68 0.00 37.00 4.00
1385 1420 6.446909 AAGGAGGGGAGATAATCATTCTTC 57.553 41.667 0.00 0.00 0.00 2.87
1386 1421 6.855375 AAAGGAGGGGAGATAATCATTCTT 57.145 37.500 0.00 0.00 0.00 2.52
1387 1422 6.855375 AAAAGGAGGGGAGATAATCATTCT 57.145 37.500 0.00 0.00 0.00 2.40
1417 1452 4.991687 GGGAATCGATTTAGTTGGCTAGAG 59.008 45.833 12.81 0.00 0.00 2.43
1541 1577 4.037927 TCCCCCTAAGAAGACCATGTTAG 58.962 47.826 0.00 0.00 0.00 2.34
1567 1603 5.648178 TGCAACATGTTTGATAGCATCTT 57.352 34.783 14.52 0.00 0.00 2.40
1579 1615 6.476380 CACAACTACTGAAAATGCAACATGTT 59.524 34.615 4.92 4.92 0.00 2.71
1580 1616 5.978919 CACAACTACTGAAAATGCAACATGT 59.021 36.000 0.00 0.00 0.00 3.21
1581 1617 6.207928 TCACAACTACTGAAAATGCAACATG 58.792 36.000 0.00 0.00 0.00 3.21
1610 1648 4.674281 AGTAGCAAGCAAGTATAGTCCC 57.326 45.455 0.00 0.00 0.00 4.46
1613 1651 7.275920 AGCAATTAGTAGCAAGCAAGTATAGT 58.724 34.615 0.00 0.00 0.00 2.12
1639 1680 4.521146 CAAGAATACCACTGGCTTGAGAT 58.479 43.478 7.16 0.00 38.50 2.75
1739 1785 9.653287 TGATAACAAGAAAACAGTACTCCTATG 57.347 33.333 0.00 0.00 0.00 2.23
1804 1853 4.116961 CAGGACCATAAATGCAAGCAATG 58.883 43.478 0.00 0.00 0.00 2.82
1834 1883 2.507484 CAGAATCAGTGGAAGGTGCAA 58.493 47.619 0.00 0.00 0.00 4.08
1860 1909 3.715628 TCTGAAAGCAGGCTGTTTTTC 57.284 42.857 26.59 26.24 42.53 2.29
2170 2230 6.616947 TCAAACATGCTTCCCTTTTTATACG 58.383 36.000 0.00 0.00 0.00 3.06
2439 2545 5.949735 AGAAGTTCACTCGCAAAAGAAAAA 58.050 33.333 5.50 0.00 0.00 1.94
2440 2546 5.354234 AGAGAAGTTCACTCGCAAAAGAAAA 59.646 36.000 5.50 0.00 39.12 2.29
2441 2547 4.876107 AGAGAAGTTCACTCGCAAAAGAAA 59.124 37.500 5.50 0.00 39.12 2.52
2442 2548 4.442706 AGAGAAGTTCACTCGCAAAAGAA 58.557 39.130 5.50 0.00 39.12 2.52
2443 2549 4.060038 AGAGAAGTTCACTCGCAAAAGA 57.940 40.909 5.50 0.00 39.12 2.52
2444 2550 4.802876 AAGAGAAGTTCACTCGCAAAAG 57.197 40.909 5.50 0.00 39.12 2.27
2445 2551 6.706270 AGATAAAGAGAAGTTCACTCGCAAAA 59.294 34.615 5.50 0.00 39.12 2.44
2446 2552 6.223852 AGATAAAGAGAAGTTCACTCGCAAA 58.776 36.000 5.50 0.00 39.12 3.68
2447 2553 5.784177 AGATAAAGAGAAGTTCACTCGCAA 58.216 37.500 5.50 0.00 39.12 4.85
2448 2554 5.392767 AGATAAAGAGAAGTTCACTCGCA 57.607 39.130 5.50 0.00 39.12 5.10
2449 2555 5.864474 TGAAGATAAAGAGAAGTTCACTCGC 59.136 40.000 5.50 0.00 39.12 5.03
2450 2556 7.875316 TTGAAGATAAAGAGAAGTTCACTCG 57.125 36.000 5.50 0.00 39.12 4.18
2452 2558 9.784531 TGATTTGAAGATAAAGAGAAGTTCACT 57.215 29.630 5.50 0.64 0.00 3.41
2584 2690 5.521735 GTGCAGAAGACATATCAACTTCGAT 59.478 40.000 0.00 0.00 42.95 3.59
2587 2693 5.447010 GCTGTGCAGAAGACATATCAACTTC 60.447 44.000 3.02 0.00 39.87 3.01
2636 2742 1.827399 CGAACAGTAGGGGCAGTGGT 61.827 60.000 0.00 0.00 0.00 4.16
2639 2745 0.830444 TGTCGAACAGTAGGGGCAGT 60.830 55.000 0.00 0.00 0.00 4.40
2640 2746 0.320374 TTGTCGAACAGTAGGGGCAG 59.680 55.000 0.00 0.00 0.00 4.85
2659 2766 3.697439 ATAGCGGGCATGCCGTGTT 62.697 57.895 29.90 23.43 36.85 3.32
2660 2767 3.697439 AATAGCGGGCATGCCGTGT 62.697 57.895 29.90 18.33 36.85 4.49
2661 2768 2.901840 AATAGCGGGCATGCCGTG 60.902 61.111 29.90 24.60 36.85 4.94
2662 2769 2.901840 CAATAGCGGGCATGCCGT 60.902 61.111 29.90 19.05 36.85 5.68
2663 2770 4.332637 GCAATAGCGGGCATGCCG 62.333 66.667 29.90 24.35 36.85 5.69
2664 2771 2.688526 CTTGCAATAGCGGGCATGCC 62.689 60.000 29.47 29.47 46.23 4.40
2665 2772 1.299620 CTTGCAATAGCGGGCATGC 60.300 57.895 9.90 9.90 46.23 4.06
2666 2773 1.299620 GCTTGCAATAGCGGGCATG 60.300 57.895 0.00 0.00 46.23 4.06
2667 2774 1.450531 GAGCTTGCAATAGCGGGCAT 61.451 55.000 0.00 0.00 45.82 4.40
2668 2775 2.045045 AGCTTGCAATAGCGGGCA 60.045 55.556 0.00 0.00 45.82 5.36
2675 2782 5.474532 ACAACATCTTTCAGAGCTTGCAATA 59.525 36.000 0.00 0.00 0.00 1.90
2711 2819 0.404040 ATCCGGGTCTGCCTGAAAAA 59.596 50.000 0.00 0.00 43.97 1.94
2712 2820 1.065709 GTATCCGGGTCTGCCTGAAAA 60.066 52.381 0.00 0.00 43.97 2.29
2831 2939 2.755103 GGAGCAACACAAGGATTAAGGG 59.245 50.000 0.00 0.00 0.00 3.95
2841 2949 2.815503 CACATGATCAGGAGCAACACAA 59.184 45.455 15.42 0.00 0.00 3.33
2911 3019 1.739562 CTGTGGCCTCGCTTGTCTC 60.740 63.158 3.32 0.00 0.00 3.36
3069 3177 2.743938 CCATGATACTGGTACACGAGC 58.256 52.381 0.00 0.00 0.00 5.03
3232 3342 0.036577 TGCAGCAGAAGGAAGCTCTC 60.037 55.000 0.00 0.00 39.50 3.20
3426 3536 8.589701 TCTAGGATGAACCGATATATGCTTAA 57.410 34.615 0.00 0.00 44.74 1.85
3427 3537 7.834681 ACTCTAGGATGAACCGATATATGCTTA 59.165 37.037 0.00 0.00 44.74 3.09
3435 3545 4.800023 TGGAACTCTAGGATGAACCGATA 58.200 43.478 0.00 0.00 44.74 2.92
3516 3626 7.389330 TCTCTGGAATGTAGCAAATAAAACGAA 59.611 33.333 0.00 0.00 0.00 3.85
3534 3644 3.144657 TGCTGCTTTTCATCTCTGGAA 57.855 42.857 0.00 0.00 0.00 3.53
3795 3915 2.815589 GCCCTGAAAGTCCACAGTTCAT 60.816 50.000 0.00 0.00 31.21 2.57
3841 3961 2.959516 GCCTTCTGGTATTTGGCAAAC 58.040 47.619 16.00 3.94 42.79 2.93
4064 4184 2.889606 TAAGCTGCGCCACTGGGAA 61.890 57.895 4.18 0.00 35.59 3.97
4101 4221 1.978454 AGAGCTGCAATTAGGATGGC 58.022 50.000 1.02 0.00 32.47 4.40
4219 4353 1.755179 CAAGCGGTTCAATCTCCCAT 58.245 50.000 0.00 0.00 0.00 4.00
4273 4407 2.509336 CTAGGGCGCTTCACACCG 60.509 66.667 9.23 0.00 0.00 4.94
4302 4436 7.432545 CAGTCTTTGTCATACTTATACCAGACG 59.567 40.741 0.00 0.00 32.04 4.18
4350 4486 8.408043 ACATAGTGATTTGAAGAAATTCACCA 57.592 30.769 0.00 0.00 34.02 4.17
4406 4545 8.946085 CCAAGTAGTCTTTATGTATCTTTGCAA 58.054 33.333 0.00 0.00 0.00 4.08
4437 4576 2.362077 ACCAAAAGCAGTCAATCACCAC 59.638 45.455 0.00 0.00 0.00 4.16
4454 4593 9.635404 TCCAGAAAAGAAGATAAAAAGTACCAA 57.365 29.630 0.00 0.00 0.00 3.67
4581 4720 7.495606 TGTTGGTATGTTAAGATATGCAGACAG 59.504 37.037 0.00 0.00 0.00 3.51
4620 4759 5.588246 TCAATCTACTGTTTGCAAGACAACA 59.412 36.000 13.10 8.27 38.23 3.33
4773 4912 9.447157 CTCTTCAAAAGACTTTCCATCTCTAAT 57.553 33.333 0.00 0.00 33.12 1.73
4776 4915 7.072263 TCTCTTCAAAAGACTTTCCATCTCT 57.928 36.000 0.00 0.00 33.12 3.10
4792 4931 2.165167 CCAAGGCATTGCTCTCTTCAA 58.835 47.619 5.36 0.00 34.91 2.69
4856 4995 0.698238 ACTCAGGCCAGGCATTGTAA 59.302 50.000 15.19 0.00 0.00 2.41
4948 5087 1.027357 GGGTTACTCGCTGATCGGTA 58.973 55.000 2.89 0.00 39.05 4.02
4949 5088 0.683504 AGGGTTACTCGCTGATCGGT 60.684 55.000 2.89 0.00 37.93 4.69
5124 5263 2.615912 GTGATTTCTGATGGCACCTAGC 59.384 50.000 0.00 0.00 44.65 3.42
5218 5357 5.066505 GTGCCTGGACATTATTAGTTTGAGG 59.933 44.000 0.00 0.00 0.00 3.86
5231 5370 4.265073 GAGAATTACTTGTGCCTGGACAT 58.735 43.478 0.00 0.00 0.00 3.06
5292 5431 1.327303 TTTGAGTTGGTGATGGTGGC 58.673 50.000 0.00 0.00 0.00 5.01
5323 5462 3.957586 CAGGTGCTGGCCACTGGA 61.958 66.667 0.00 0.00 44.08 3.86
5391 5530 6.183360 GCTGTAACTGTTGGTGAAGTAAAAGT 60.183 38.462 2.69 0.00 0.00 2.66
5490 5632 1.294659 GCAAGTGGAGTTCCTGCTCG 61.295 60.000 0.00 0.00 36.41 5.03
5493 5635 1.860484 GCTGCAAGTGGAGTTCCTGC 61.860 60.000 1.62 2.15 35.85 4.85
5569 5711 5.767168 GCTGCTCTTGGATTATTGGTAATCT 59.233 40.000 7.78 0.00 43.68 2.40
5835 5986 1.586422 CAGCACCCGGAACTATCATG 58.414 55.000 0.73 0.00 0.00 3.07
6678 6830 3.462483 TGGTAATATAGGCACCACACG 57.538 47.619 0.00 0.00 37.42 4.49
6706 6858 0.247460 GTGGAGGGGCTTCATTTTGC 59.753 55.000 0.00 0.00 0.00 3.68
6707 6859 1.547372 CAGTGGAGGGGCTTCATTTTG 59.453 52.381 0.00 0.00 0.00 2.44
6708 6860 1.428912 TCAGTGGAGGGGCTTCATTTT 59.571 47.619 0.00 0.00 0.00 1.82
6713 6865 1.794714 TATCTCAGTGGAGGGGCTTC 58.205 55.000 0.00 0.00 41.69 3.86
6912 7066 3.570540 TGAACCATCAACCACCATTTCA 58.429 40.909 0.00 0.00 30.99 2.69
7022 7180 8.198778 CCAACTAACCCTTTAACAAGCTTTTAA 58.801 33.333 0.00 3.14 0.00 1.52
7042 7200 1.564348 GAGGGCCCTGATTTCCAACTA 59.436 52.381 34.59 0.00 0.00 2.24
7287 7446 2.230508 TGTGTAGACTAGCTTCCAACCG 59.769 50.000 0.00 0.00 0.00 4.44
7385 7544 5.122396 CAGACCGGGAAGTTTAGAAATTCAG 59.878 44.000 6.32 0.00 0.00 3.02
7607 7766 3.190327 AGCGATGGATAGAATCTCTCACG 59.810 47.826 0.00 2.51 0.00 4.35
7834 7994 0.182537 CGAATTGGTCATAGGGGCCA 59.817 55.000 4.39 0.00 0.00 5.36
7887 8047 8.635765 ACAACTAACCAAGATGTTAACATGAT 57.364 30.769 25.42 11.06 37.95 2.45
7958 8118 6.348213 GCATTTCTTTTGCAGCTTTGATGATT 60.348 34.615 0.00 0.00 39.90 2.57
8027 8187 7.544804 AAAACCTAATCTGAGGAGCATTTTT 57.455 32.000 0.00 0.00 39.15 1.94
8091 8251 4.822026 AGTTTTCAGTTCTCATCCCTACG 58.178 43.478 0.00 0.00 0.00 3.51
8150 8310 7.957002 TCCCAAGAACATACTATCTTCAGATC 58.043 38.462 0.00 0.00 33.73 2.75
8219 8379 4.625225 ATTTGGGGATGGTGACCTTAAT 57.375 40.909 2.11 0.00 0.00 1.40
8286 8449 5.794894 ACCAAACAGTAGAACTACATGGAG 58.205 41.667 21.09 2.41 38.48 3.86
8288 8451 5.794894 AGACCAAACAGTAGAACTACATGG 58.205 41.667 13.34 15.29 38.48 3.66
8348 8511 2.292828 AGGTCAACAGGTCCATTTGG 57.707 50.000 0.00 0.00 0.00 3.28
8362 8525 2.575735 TCCAGTATGCCATGAAAGGTCA 59.424 45.455 0.00 0.00 33.91 4.02
8364 8527 3.737559 TTCCAGTATGCCATGAAAGGT 57.262 42.857 0.00 0.00 31.97 3.50
8439 8602 2.608268 GGGTAGAGAAAGTCGTGCTTC 58.392 52.381 0.00 0.00 36.17 3.86
8443 8606 5.340439 AATAAGGGGTAGAGAAAGTCGTG 57.660 43.478 0.00 0.00 0.00 4.35
8571 8734 2.038295 CCCTTTTGCCTGTTTTGCCATA 59.962 45.455 0.00 0.00 0.00 2.74
8644 8808 1.736126 CGTCAATGCTGCTTGAGACAT 59.264 47.619 12.60 0.00 35.88 3.06
8685 8849 2.978489 CGAGGTGTTCAAGTCTACGTTC 59.022 50.000 0.00 0.00 0.00 3.95
8776 8940 9.941664 CAGCTCTAATGTGAATTGTAAATAAGG 57.058 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.