Multiple sequence alignment - TraesCS2A01G050400

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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 TraesCS2A01G050400 chr2A 100.000 3773 0 0 1 3773 19445872 19449644 0.000000e+00 6968.0
1 TraesCS2A01G050400 chr2A 91.003 389 26 6 3246 3632 732561175 732561556 2.010000e-142 516.0
2 TraesCS2A01G050400 chr2A 100.000 28 0 0 3194 3221 630289088 630289061 7.000000e-03 52.8
3 TraesCS2A01G050400 chr2D 90.966 2236 123 24 707 2902 18302772 18304968 0.000000e+00 2937.0
4 TraesCS2A01G050400 chr2D 93.113 1510 89 7 1062 2565 487360888 487362388 0.000000e+00 2198.0
5 TraesCS2A01G050400 chr2D 88.864 880 48 18 2902 3771 18305003 18305842 0.000000e+00 1037.0
6 TraesCS2A01G050400 chr2D 84.691 712 75 16 28 711 18300944 18301649 0.000000e+00 680.0
7 TraesCS2A01G050400 chr2D 82.028 434 42 11 2067 2473 43463152 43463576 1.680000e-88 337.0
8 TraesCS2A01G050400 chr2B 89.137 2191 119 51 777 2902 30429409 30431545 0.000000e+00 2617.0
9 TraesCS2A01G050400 chr2B 90.254 236 12 7 2990 3221 30431621 30431849 7.920000e-77 298.0
10 TraesCS2A01G050400 chr5A 81.912 774 87 24 1746 2478 119031164 119031925 4.170000e-169 604.0
11 TraesCS2A01G050400 chr4B 81.677 775 87 24 1746 2478 334214431 334213670 9.020000e-166 593.0
12 TraesCS2A01G050400 chr4B 100.000 29 0 0 2591 2619 18925076 18925048 2.000000e-03 54.7
13 TraesCS2A01G050400 chrUn 81.481 729 110 11 994 1720 16338351 16337646 3.270000e-160 575.0
14 TraesCS2A01G050400 chrUn 80.132 453 60 14 1272 1720 16378485 16378911 1.020000e-80 311.0
15 TraesCS2A01G050400 chrUn 87.624 202 25 0 1716 1917 16337093 16336892 6.300000e-58 235.0
16 TraesCS2A01G050400 chrUn 84.716 229 32 3 1716 1941 16379526 16379754 3.790000e-55 226.0
17 TraesCS2A01G050400 chrUn 96.875 32 1 0 2588 2619 151389332 151389363 2.000000e-03 54.7
18 TraesCS2A01G050400 chrUn 100.000 29 0 0 2591 2619 205004942 205004914 2.000000e-03 54.7
19 TraesCS2A01G050400 chrUn 96.875 32 1 0 2588 2619 210540883 210540914 2.000000e-03 54.7
20 TraesCS2A01G050400 chr5D 90.196 408 30 7 3229 3632 362192532 362192933 1.200000e-144 523.0
21 TraesCS2A01G050400 chr5D 88.517 418 29 14 3220 3632 540195681 540196084 4.380000e-134 488.0
22 TraesCS2A01G050400 chr7D 89.681 407 28 10 3229 3631 48707163 48707559 1.210000e-139 507.0
23 TraesCS2A01G050400 chr7D 89.461 408 26 13 3229 3631 48751068 48751463 2.020000e-137 499.0
24 TraesCS2A01G050400 chr7D 100.000 28 0 0 3194 3221 57715050 57715077 7.000000e-03 52.8
25 TraesCS2A01G050400 chr7D 100.000 28 0 0 3194 3221 538141724 538141697 7.000000e-03 52.8
26 TraesCS2A01G050400 chr1A 89.538 411 28 9 3229 3632 161668216 161668618 1.210000e-139 507.0
27 TraesCS2A01G050400 chr1A 100.000 28 0 0 3194 3221 542765906 542765933 7.000000e-03 52.8
28 TraesCS2A01G050400 chr7A 89.216 408 34 7 3229 3632 548333411 548333010 5.630000e-138 501.0
29 TraesCS2A01G050400 chr7A 89.078 412 31 8 3229 3634 85029176 85028773 2.020000e-137 499.0
30 TraesCS2A01G050400 chr4D 82.488 434 40 13 2067 2473 478731751 478732175 7.760000e-92 348.0
31 TraesCS2A01G050400 chr1B 80.594 438 46 16 2033 2443 635817001 635816576 6.120000e-78 302.0
32 TraesCS2A01G050400 chr7B 100.000 28 0 0 3194 3221 87167551 87167524 7.000000e-03 52.8
33 TraesCS2A01G050400 chr6D 100.000 28 0 0 3194 3221 32658560 32658587 7.000000e-03 52.8
34 TraesCS2A01G050400 chr6B 100.000 28 0 0 3194 3221 405057595 405057568 7.000000e-03 52.8


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 TraesCS2A01G050400 chr2A 19445872 19449644 3772 False 6968.000000 6968 100.000000 1 3773 1 chr2A.!!$F1 3772
1 TraesCS2A01G050400 chr2D 487360888 487362388 1500 False 2198.000000 2198 93.113000 1062 2565 1 chr2D.!!$F2 1503
2 TraesCS2A01G050400 chr2D 18300944 18305842 4898 False 1551.333333 2937 88.173667 28 3771 3 chr2D.!!$F3 3743
3 TraesCS2A01G050400 chr2B 30429409 30431849 2440 False 1457.500000 2617 89.695500 777 3221 2 chr2B.!!$F1 2444
4 TraesCS2A01G050400 chr5A 119031164 119031925 761 False 604.000000 604 81.912000 1746 2478 1 chr5A.!!$F1 732
5 TraesCS2A01G050400 chr4B 334213670 334214431 761 True 593.000000 593 81.677000 1746 2478 1 chr4B.!!$R2 732
6 TraesCS2A01G050400 chrUn 16336892 16338351 1459 True 405.000000 575 84.552500 994 1917 2 chrUn.!!$R2 923
7 TraesCS2A01G050400 chrUn 16378485 16379754 1269 False 268.500000 311 82.424000 1272 1941 2 chrUn.!!$F3 669

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
334 356 0.035725 GGTCCTAAACCCACTTCCGG 60.036 60.0 0.00 0.0 42.85 5.14 F
879 2044 0.178995 TGCCAACAACAGAGCATCCA 60.179 50.0 0.00 0.0 33.66 3.41 F
1637 2822 0.036732 TCCGAGCATTGCTTTCCAGT 59.963 50.0 13.35 0.0 39.88 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 2598 0.687427 AGAAGCTCTCCCTCTCCTGC 60.687 60.0 0.0 0.0 0.0 4.85 R
2604 4494 1.020333 CGTCGTCCTCCTCGTCTTCT 61.020 60.0 0.0 0.0 0.0 2.85 R
3161 5090 1.183549 GCCCTTACCACTCTCTTCGA 58.816 55.0 0.0 0.0 0.0 3.71 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
20 21 3.154827 AGGGTACTTGGTCAATGGTTG 57.845 47.619 0.00 0.00 0.00 3.77
21 22 2.445525 AGGGTACTTGGTCAATGGTTGT 59.554 45.455 0.00 0.00 0.00 3.32
22 23 2.556622 GGGTACTTGGTCAATGGTTGTG 59.443 50.000 0.00 0.00 0.00 3.33
23 24 2.556622 GGTACTTGGTCAATGGTTGTGG 59.443 50.000 0.00 0.00 0.00 4.17
24 25 1.039856 ACTTGGTCAATGGTTGTGGC 58.960 50.000 0.00 0.00 0.00 5.01
25 26 1.331214 CTTGGTCAATGGTTGTGGCT 58.669 50.000 0.00 0.00 0.00 4.75
26 27 1.000060 CTTGGTCAATGGTTGTGGCTG 60.000 52.381 0.00 0.00 0.00 4.85
27 28 0.827089 TGGTCAATGGTTGTGGCTGG 60.827 55.000 0.00 0.00 0.00 4.85
28 29 1.535204 GGTCAATGGTTGTGGCTGGG 61.535 60.000 0.00 0.00 0.00 4.45
29 30 1.228831 TCAATGGTTGTGGCTGGGG 60.229 57.895 0.00 0.00 0.00 4.96
30 31 1.533753 CAATGGTTGTGGCTGGGGT 60.534 57.895 0.00 0.00 0.00 4.95
31 32 1.533753 AATGGTTGTGGCTGGGGTG 60.534 57.895 0.00 0.00 0.00 4.61
32 33 4.912395 TGGTTGTGGCTGGGGTGC 62.912 66.667 0.00 0.00 0.00 5.01
33 34 4.603535 GGTTGTGGCTGGGGTGCT 62.604 66.667 0.00 0.00 0.00 4.40
34 35 2.521708 GTTGTGGCTGGGGTGCTT 60.522 61.111 0.00 0.00 0.00 3.91
35 36 2.133641 GTTGTGGCTGGGGTGCTTT 61.134 57.895 0.00 0.00 0.00 3.51
36 37 1.832167 TTGTGGCTGGGGTGCTTTC 60.832 57.895 0.00 0.00 0.00 2.62
37 38 2.116125 GTGGCTGGGGTGCTTTCT 59.884 61.111 0.00 0.00 0.00 2.52
38 39 1.531602 GTGGCTGGGGTGCTTTCTT 60.532 57.895 0.00 0.00 0.00 2.52
46 47 2.291540 TGGGGTGCTTTCTTTCCCATAG 60.292 50.000 0.00 0.00 42.21 2.23
48 49 1.401905 GGTGCTTTCTTTCCCATAGCG 59.598 52.381 0.00 0.00 34.65 4.26
49 50 2.084546 GTGCTTTCTTTCCCATAGCGT 58.915 47.619 0.00 0.00 34.65 5.07
102 103 0.605860 CATAGAGGCTGCCATGGAGC 60.606 60.000 22.65 20.27 35.57 4.70
103 104 2.109517 ATAGAGGCTGCCATGGAGCG 62.110 60.000 22.65 3.22 37.32 5.03
158 172 1.383803 CTCCTCCCCCTCCCTTCTG 60.384 68.421 0.00 0.00 0.00 3.02
173 187 0.242825 TTCTGTTGGGACTAGCGACG 59.757 55.000 0.00 0.00 0.00 5.12
177 191 1.604308 TTGGGACTAGCGACGGTGA 60.604 57.895 10.33 0.00 0.00 4.02
193 207 1.383523 GTGATAGTTGGGCTCTTGGC 58.616 55.000 0.00 0.00 40.90 4.52
205 219 2.046314 CTTGGCCCGTTGGTCGAT 60.046 61.111 0.00 0.00 40.01 3.59
228 242 1.139520 GCATTTGGGCATGGACGAC 59.860 57.895 0.00 0.00 0.00 4.34
239 253 2.742372 GGACGACGTGCCTGCAAT 60.742 61.111 4.58 0.00 0.00 3.56
242 256 3.049674 CGACGTGCCTGCAATGGT 61.050 61.111 0.00 0.00 0.00 3.55
243 257 2.562912 GACGTGCCTGCAATGGTG 59.437 61.111 0.00 0.00 0.00 4.17
251 265 1.856629 CCTGCAATGGTGGATCCTTT 58.143 50.000 14.23 0.00 37.07 3.11
269 283 2.125225 GTCCACCCTCCCTCCCTT 59.875 66.667 0.00 0.00 0.00 3.95
270 284 1.541620 GTCCACCCTCCCTCCCTTT 60.542 63.158 0.00 0.00 0.00 3.11
271 285 1.541368 TCCACCCTCCCTCCCTTTG 60.541 63.158 0.00 0.00 0.00 2.77
280 302 1.299648 CCTCCCTTTGCCGATGACA 59.700 57.895 0.00 0.00 0.00 3.58
288 310 0.911769 TTGCCGATGACAGGAATCCT 59.088 50.000 0.00 0.00 0.00 3.24
334 356 0.035725 GGTCCTAAACCCACTTCCGG 60.036 60.000 0.00 0.00 42.85 5.14
345 367 1.666872 ACTTCCGGCGTTTTCTCCG 60.667 57.895 6.01 0.00 46.34 4.63
353 375 1.070105 CGTTTTCTCCGGTGGGACA 59.930 57.895 0.00 0.00 37.43 4.02
387 410 2.224159 ACCCAACGCCAGGATCTGT 61.224 57.895 0.00 0.00 0.00 3.41
388 411 1.450312 CCCAACGCCAGGATCTGTC 60.450 63.158 0.00 0.00 0.00 3.51
400 423 4.187694 CAGGATCTGTCTAACAAGAAGGC 58.812 47.826 0.00 0.00 0.00 4.35
409 432 3.793144 CAAGAAGGCGCGAGGTGC 61.793 66.667 12.10 0.00 41.47 5.01
413 436 3.064987 GAAGGCGCGAGGTGCTAGA 62.065 63.158 12.10 0.00 43.27 2.43
416 439 2.025441 GCGCGAGGTGCTAGAGAG 59.975 66.667 12.10 0.00 43.27 3.20
429 452 2.544685 CTAGAGAGGTTGCCGACAATG 58.455 52.381 0.00 0.00 38.27 2.82
442 465 1.336440 CGACAATGGTGGCTTCAACAA 59.664 47.619 0.00 0.00 41.96 2.83
448 471 3.006112 TGGTGGCTTCAACAACAAGTA 57.994 42.857 0.00 0.00 34.76 2.24
450 473 4.720046 TGGTGGCTTCAACAACAAGTATA 58.280 39.130 0.00 0.00 34.76 1.47
461 484 7.802738 TCAACAACAAGTATACAAATTCTCCG 58.197 34.615 5.50 0.00 0.00 4.63
465 488 7.065803 ACAACAAGTATACAAATTCTCCGGATG 59.934 37.037 3.57 1.65 0.00 3.51
466 489 6.055588 ACAAGTATACAAATTCTCCGGATGG 58.944 40.000 3.57 0.00 0.00 3.51
469 492 6.895782 AGTATACAAATTCTCCGGATGGAAA 58.104 36.000 3.57 0.00 45.87 3.13
479 502 1.143684 CCGGATGGAAACCCATGATCT 59.856 52.381 0.00 0.00 44.15 2.75
492 515 2.222678 CCATGATCTCGCCTTCGATTTG 59.777 50.000 0.00 0.00 44.56 2.32
494 517 3.459232 TGATCTCGCCTTCGATTTGAT 57.541 42.857 0.00 0.00 44.56 2.57
501 524 3.118920 TCGCCTTCGATTTGATTGACCTA 60.119 43.478 0.00 0.00 40.21 3.08
502 525 3.621268 CGCCTTCGATTTGATTGACCTAA 59.379 43.478 0.00 0.00 38.10 2.69
503 526 4.260375 CGCCTTCGATTTGATTGACCTAAG 60.260 45.833 0.00 0.00 38.10 2.18
504 527 4.876107 GCCTTCGATTTGATTGACCTAAGA 59.124 41.667 0.00 0.00 0.00 2.10
505 528 5.220681 GCCTTCGATTTGATTGACCTAAGAC 60.221 44.000 0.00 0.00 0.00 3.01
509 532 7.596749 TCGATTTGATTGACCTAAGACTTTC 57.403 36.000 0.00 0.00 0.00 2.62
510 533 7.386851 TCGATTTGATTGACCTAAGACTTTCT 58.613 34.615 0.00 0.00 0.00 2.52
511 534 8.528643 TCGATTTGATTGACCTAAGACTTTCTA 58.471 33.333 0.00 0.00 0.00 2.10
512 535 9.151471 CGATTTGATTGACCTAAGACTTTCTAA 57.849 33.333 0.00 0.00 0.00 2.10
546 569 1.712401 CAATTGGTTGGGCATTGACG 58.288 50.000 0.00 0.00 30.66 4.35
591 614 1.195115 TATGGATGCGGAGATAGGGC 58.805 55.000 0.00 0.00 0.00 5.19
608 633 7.519057 AGATAGGGCTATCCTCCTTTAAAAAC 58.481 38.462 0.00 0.00 44.06 2.43
614 639 7.258441 GGCTATCCTCCTTTAAAAACACAATC 58.742 38.462 0.00 0.00 0.00 2.67
643 670 0.387202 TTGTCCACGGGTTTGCATTG 59.613 50.000 0.00 0.00 0.00 2.82
645 672 0.887933 GTCCACGGGTTTGCATTGAT 59.112 50.000 0.00 0.00 0.00 2.57
656 683 2.634982 TGCATTGATCTGTTTTCGCC 57.365 45.000 0.00 0.00 0.00 5.54
667 694 0.843872 GTTTTCGCCGTGTTTCAAGC 59.156 50.000 0.00 0.00 0.00 4.01
668 695 0.452184 TTTTCGCCGTGTTTCAAGCA 59.548 45.000 0.00 0.00 0.00 3.91
683 710 0.393077 AAGCAGTGTACTTCGGCAGT 59.607 50.000 13.38 0.00 39.87 4.40
715 1869 0.179702 GAGGGATGGGTTTACCGACC 59.820 60.000 0.00 0.00 44.64 4.79
726 1880 2.198827 TTACCGACCTCGTAAGGACA 57.801 50.000 0.00 0.00 46.67 4.02
741 1895 0.521735 GGACACCCTTGACGAAATGC 59.478 55.000 0.00 0.00 0.00 3.56
879 2044 0.178995 TGCCAACAACAGAGCATCCA 60.179 50.000 0.00 0.00 33.66 3.41
883 2048 1.068055 CAACAACAGAGCATCCAAGGC 60.068 52.381 0.00 0.00 33.66 4.35
884 2049 0.957395 ACAACAGAGCATCCAAGGCG 60.957 55.000 0.00 0.00 33.66 5.52
885 2050 1.377725 AACAGAGCATCCAAGGCGG 60.378 57.895 0.00 0.00 33.66 6.13
989 2171 2.265182 GGCGGAGATCGAGGAGGAG 61.265 68.421 0.00 0.00 42.43 3.69
992 2174 0.179015 CGGAGATCGAGGAGGAGGAA 60.179 60.000 0.00 0.00 42.43 3.36
1413 2598 3.058363 GTGCTTCTTGCTTTCTTCTGGAG 60.058 47.826 0.00 0.00 43.37 3.86
1424 2609 0.325110 CTTCTGGAGCAGGAGAGGGA 60.325 60.000 0.00 0.00 39.34 4.20
1435 2620 0.177836 GGAGAGGGAGAGCTTCTTGC 59.822 60.000 0.00 0.00 43.29 4.01
1463 2648 3.047877 GGAGGTGTTCGCCGTTGG 61.048 66.667 0.00 0.00 0.00 3.77
1518 2703 2.922162 CTACCTGAGCACTGGGGAT 58.078 57.895 11.55 0.00 39.06 3.85
1578 2763 3.149196 TCAGGAGAAAAATGTGGTCTGC 58.851 45.455 0.00 0.00 0.00 4.26
1611 2796 2.821991 AGGCTCCGGAATCTTTATCG 57.178 50.000 5.23 0.00 0.00 2.92
1620 2805 4.745620 CCGGAATCTTTATCGTCTTCTTCC 59.254 45.833 0.00 0.00 0.00 3.46
1632 2817 2.485814 GTCTTCTTCCGAGCATTGCTTT 59.514 45.455 13.35 0.00 39.88 3.51
1633 2818 2.744202 TCTTCTTCCGAGCATTGCTTTC 59.256 45.455 13.35 0.00 39.88 2.62
1634 2819 1.453155 TCTTCCGAGCATTGCTTTCC 58.547 50.000 13.35 0.00 39.88 3.13
1635 2820 1.167851 CTTCCGAGCATTGCTTTCCA 58.832 50.000 13.35 0.00 39.88 3.53
1636 2821 1.131883 CTTCCGAGCATTGCTTTCCAG 59.868 52.381 13.35 3.78 39.88 3.86
1637 2822 0.036732 TCCGAGCATTGCTTTCCAGT 59.963 50.000 13.35 0.00 39.88 4.00
1659 2850 1.340308 CCAGGTGAGACATTCATGCCA 60.340 52.381 0.00 0.00 38.29 4.92
1662 2853 2.840038 AGGTGAGACATTCATGCCAGTA 59.160 45.455 0.00 0.00 38.29 2.74
1679 2870 2.028130 AGTACCAGAGATGGAAGAGCG 58.972 52.381 0.31 0.00 0.00 5.03
1701 2901 4.881273 CGGGAGAAATCCATCAACAATGTA 59.119 41.667 0.00 0.00 33.13 2.29
1702 2902 5.220854 CGGGAGAAATCCATCAACAATGTAC 60.221 44.000 0.00 0.00 33.13 2.90
1703 2903 5.652014 GGGAGAAATCCATCAACAATGTACA 59.348 40.000 0.00 0.00 33.13 2.90
1704 2904 6.183360 GGGAGAAATCCATCAACAATGTACAG 60.183 42.308 0.33 0.00 33.13 2.74
1705 2905 6.599244 GGAGAAATCCATCAACAATGTACAGA 59.401 38.462 0.33 0.00 33.13 3.41
1706 2906 7.201679 GGAGAAATCCATCAACAATGTACAGAG 60.202 40.741 0.33 0.00 33.13 3.35
1707 2907 7.170965 AGAAATCCATCAACAATGTACAGAGT 58.829 34.615 0.33 0.00 33.13 3.24
1708 2908 6.748333 AATCCATCAACAATGTACAGAGTG 57.252 37.500 0.33 2.06 33.13 3.51
1709 2909 5.227569 TCCATCAACAATGTACAGAGTGT 57.772 39.130 0.33 2.73 33.13 3.55
1744 3570 4.018597 AGAGAAAGGGATTCAGCAGTGATT 60.019 41.667 0.00 0.00 40.72 2.57
1819 3645 1.004918 AAGAAACCTGAGCGGGTCG 60.005 57.895 0.66 0.00 38.87 4.79
1865 3692 2.624838 AGCGAATAAGGCAATGGGAATG 59.375 45.455 0.00 0.00 0.00 2.67
1873 3700 1.839354 GGCAATGGGAATGTGGGAATT 59.161 47.619 0.00 0.00 0.00 2.17
1931 3764 4.082733 GGTGGAAATCTTTTTCGAGAAGGG 60.083 45.833 9.79 0.00 41.84 3.95
2072 3920 6.112058 AGCTTGTAGATGTCAAGGAAGAATC 58.888 40.000 7.58 0.00 41.50 2.52
2184 4032 2.450619 GCAAGAACAGAGGAGCGAC 58.549 57.895 0.00 0.00 0.00 5.19
2262 4110 2.125229 CAGCCTGCGTCAGAGCAT 60.125 61.111 16.19 5.54 46.97 3.79
2443 4321 4.717629 TCAAGGTCTGCCGCGACG 62.718 66.667 8.23 0.00 40.50 5.12
2585 4475 1.804748 GGCGAAAGAAGAATCCGTTGT 59.195 47.619 0.00 0.00 0.00 3.32
2589 4479 3.181543 CGAAAGAAGAATCCGTTGTCGAC 60.182 47.826 9.11 9.11 39.71 4.20
2602 4492 1.820481 GTCGACGAGGAGGAGGAGG 60.820 68.421 0.00 0.00 0.00 4.30
2603 4493 1.993948 TCGACGAGGAGGAGGAGGA 60.994 63.158 0.00 0.00 0.00 3.71
2604 4494 1.077644 CGACGAGGAGGAGGAGGAA 60.078 63.158 0.00 0.00 0.00 3.36
2622 4512 1.130938 GAAGAAGACGAGGAGGACGAC 59.869 57.143 0.00 0.00 34.70 4.34
2685 4575 1.472878 TCGACGAGGAAGATGAACCTG 59.527 52.381 0.00 0.00 36.57 4.00
2688 4578 0.462759 CGAGGAAGATGAACCTGGGC 60.463 60.000 0.00 0.00 36.57 5.36
2868 4758 6.418819 AGTGTGTTCAGTTTGTGTATACGTAC 59.581 38.462 0.00 0.00 0.00 3.67
2902 4793 9.349713 TGAAATATATATGGGTCTGTTTGGTTC 57.650 33.333 0.00 0.00 0.00 3.62
2903 4794 9.349713 GAAATATATATGGGTCTGTTTGGTTCA 57.650 33.333 0.00 0.00 0.00 3.18
2904 4795 8.924511 AATATATATGGGTCTGTTTGGTTCAG 57.075 34.615 0.00 0.00 0.00 3.02
2905 4796 1.620822 ATGGGTCTGTTTGGTTCAGC 58.379 50.000 0.00 0.00 33.48 4.26
2924 4849 5.904941 TCAGCCTATGCCAAATAATTTGTG 58.095 37.500 0.00 0.00 38.98 3.33
2930 4855 7.010091 GCCTATGCCAAATAATTTGTGTGTTAC 59.990 37.037 0.00 0.00 38.98 2.50
2932 4857 7.887996 ATGCCAAATAATTTGTGTGTTACTG 57.112 32.000 0.00 0.00 38.98 2.74
2933 4858 6.810911 TGCCAAATAATTTGTGTGTTACTGT 58.189 32.000 0.00 0.00 38.98 3.55
2942 4867 8.865590 AATTTGTGTGTTACTGTATTTGGTTC 57.134 30.769 0.00 0.00 0.00 3.62
2943 4868 5.660629 TGTGTGTTACTGTATTTGGTTCG 57.339 39.130 0.00 0.00 0.00 3.95
2957 4882 3.404224 TGGTTCGTGCCAAATACTACA 57.596 42.857 0.00 0.00 35.25 2.74
2959 4884 4.135306 TGGTTCGTGCCAAATACTACAAA 58.865 39.130 0.00 0.00 35.25 2.83
2960 4885 4.214545 TGGTTCGTGCCAAATACTACAAAG 59.785 41.667 0.00 0.00 35.25 2.77
2963 4888 6.203647 GTTCGTGCCAAATACTACAAAGTTT 58.796 36.000 0.00 0.00 37.15 2.66
2966 4891 5.108027 CGTGCCAAATACTACAAAGTTTTGC 60.108 40.000 4.58 0.00 41.79 3.68
2967 4892 5.983118 GTGCCAAATACTACAAAGTTTTGCT 59.017 36.000 4.58 0.00 41.79 3.91
2971 4896 7.115805 GCCAAATACTACAAAGTTTTGCTAACC 59.884 37.037 4.58 0.00 41.79 2.85
2973 4898 9.744468 CAAATACTACAAAGTTTTGCTAACCTT 57.256 29.630 4.58 0.00 41.79 3.50
2975 4900 9.961265 AATACTACAAAGTTTTGCTAACCTTTC 57.039 29.630 0.70 0.00 41.79 2.62
2976 4901 7.399245 ACTACAAAGTTTTGCTAACCTTTCA 57.601 32.000 0.70 0.00 41.79 2.69
2977 4902 8.007405 ACTACAAAGTTTTGCTAACCTTTCAT 57.993 30.769 0.70 0.00 41.79 2.57
2978 4903 9.127277 ACTACAAAGTTTTGCTAACCTTTCATA 57.873 29.630 0.70 0.00 41.79 2.15
2985 4910 6.374417 TTTGCTAACCTTTCATACTCCTCT 57.626 37.500 0.00 0.00 0.00 3.69
2997 4922 5.150715 TCATACTCCTCTGCATGTAATCCT 58.849 41.667 0.00 0.00 0.00 3.24
3010 4935 2.034685 TGTAATCCTTCGGAGCATCTCG 59.965 50.000 0.00 0.00 34.05 4.04
3090 5016 0.402121 ACCAAAGCTCTGTTCCTCCC 59.598 55.000 0.00 0.00 0.00 4.30
3122 5048 0.325602 TTACGCCGGAAATCCAAGGT 59.674 50.000 5.05 0.00 35.14 3.50
3232 5161 1.601914 GCCAATTGCGGAGAAAAACGT 60.602 47.619 0.00 0.00 0.00 3.99
3235 5164 3.060607 CCAATTGCGGAGAAAAACGTTTG 60.061 43.478 15.46 1.63 0.00 2.93
3237 5166 1.096416 TGCGGAGAAAAACGTTTGGT 58.904 45.000 15.46 5.69 0.00 3.67
3254 5183 5.121142 CGTTTGGTTTCCGAGTACATATGTT 59.879 40.000 14.77 0.00 0.00 2.71
3262 5191 9.924650 GTTTCCGAGTACATATGTTTCCTATAT 57.075 33.333 14.77 0.00 0.00 0.86
3352 5282 7.656137 TGACCTTTCATTGTACTAGTGAGAAAC 59.344 37.037 5.39 0.00 0.00 2.78
3356 5286 8.428186 TTTCATTGTACTAGTGAGAAACGTTT 57.572 30.769 14.57 14.57 0.00 3.60
3370 5300 7.007995 GTGAGAAACGTTTCACGAAAAGAAAAT 59.992 33.333 35.29 15.33 46.05 1.82
3371 5301 7.539366 TGAGAAACGTTTCACGAAAAGAAAATT 59.461 29.630 35.29 14.93 46.05 1.82
3441 5372 8.123639 AGCATGAATAGTGACCTATAATACGT 57.876 34.615 0.00 0.00 32.57 3.57
3442 5373 9.239551 AGCATGAATAGTGACCTATAATACGTA 57.760 33.333 0.00 0.00 32.57 3.57
3443 5374 9.504710 GCATGAATAGTGACCTATAATACGTAG 57.495 37.037 0.08 0.00 32.57 3.51
3444 5375 9.504710 CATGAATAGTGACCTATAATACGTAGC 57.495 37.037 0.08 0.00 32.57 3.58
3445 5376 8.625786 TGAATAGTGACCTATAATACGTAGCA 57.374 34.615 0.08 0.00 32.57 3.49
3446 5377 9.070179 TGAATAGTGACCTATAATACGTAGCAA 57.930 33.333 0.08 0.00 32.57 3.91
3447 5378 9.903682 GAATAGTGACCTATAATACGTAGCAAA 57.096 33.333 0.08 0.00 32.57 3.68
3478 5409 4.029043 GTCTTTTTCGCTGTGAAGTCAAC 58.971 43.478 3.65 0.00 37.99 3.18
3678 5609 6.516693 CGTTGCCATGTTATATGGAGAGAGTA 60.517 42.308 12.25 0.00 41.64 2.59
3719 5652 9.160496 CTCTATCACTCCCTTCATATTTATTGC 57.840 37.037 0.00 0.00 0.00 3.56
3771 5704 1.818674 AGCCCTCAGCCGTTATTTTTG 59.181 47.619 0.00 0.00 45.47 2.44
3772 5705 1.816224 GCCCTCAGCCGTTATTTTTGA 59.184 47.619 0.00 0.00 34.35 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.445525 ACAACCATTGACCAAGTACCCT 59.554 45.455 0.00 0.00 0.00 4.34
3 4 2.030274 GCCACAACCATTGACCAAGTAC 60.030 50.000 0.00 0.00 0.00 2.73
5 6 1.039856 GCCACAACCATTGACCAAGT 58.960 50.000 0.00 0.00 0.00 3.16
6 7 1.000060 CAGCCACAACCATTGACCAAG 60.000 52.381 0.00 0.00 0.00 3.61
9 10 1.535204 CCCAGCCACAACCATTGACC 61.535 60.000 0.00 0.00 0.00 4.02
10 11 1.535204 CCCCAGCCACAACCATTGAC 61.535 60.000 0.00 0.00 0.00 3.18
12 13 1.533753 ACCCCAGCCACAACCATTG 60.534 57.895 0.00 0.00 0.00 2.82
13 14 1.533753 CACCCCAGCCACAACCATT 60.534 57.895 0.00 0.00 0.00 3.16
14 15 2.118076 CACCCCAGCCACAACCAT 59.882 61.111 0.00 0.00 0.00 3.55
15 16 4.912395 GCACCCCAGCCACAACCA 62.912 66.667 0.00 0.00 0.00 3.67
16 17 4.603535 AGCACCCCAGCCACAACC 62.604 66.667 0.00 0.00 34.23 3.77
17 18 2.087462 GAAAGCACCCCAGCCACAAC 62.087 60.000 0.00 0.00 34.23 3.32
18 19 1.832167 GAAAGCACCCCAGCCACAA 60.832 57.895 0.00 0.00 34.23 3.33
19 20 2.203480 GAAAGCACCCCAGCCACA 60.203 61.111 0.00 0.00 34.23 4.17
20 21 1.115326 AAAGAAAGCACCCCAGCCAC 61.115 55.000 0.00 0.00 34.23 5.01
21 22 0.827507 GAAAGAAAGCACCCCAGCCA 60.828 55.000 0.00 0.00 34.23 4.75
22 23 1.536073 GGAAAGAAAGCACCCCAGCC 61.536 60.000 0.00 0.00 34.23 4.85
23 24 1.536073 GGGAAAGAAAGCACCCCAGC 61.536 60.000 0.00 0.00 37.04 4.85
24 25 0.178964 TGGGAAAGAAAGCACCCCAG 60.179 55.000 0.00 0.00 41.78 4.45
25 26 1.934410 TGGGAAAGAAAGCACCCCA 59.066 52.632 0.00 0.00 44.21 4.96
26 27 2.379005 CTATGGGAAAGAAAGCACCCC 58.621 52.381 0.00 0.00 41.44 4.95
27 28 1.751351 GCTATGGGAAAGAAAGCACCC 59.249 52.381 0.00 0.00 42.37 4.61
28 29 1.401905 CGCTATGGGAAAGAAAGCACC 59.598 52.381 0.00 0.00 32.69 5.01
29 30 2.084546 ACGCTATGGGAAAGAAAGCAC 58.915 47.619 0.00 0.00 32.69 4.40
30 31 2.083774 CACGCTATGGGAAAGAAAGCA 58.916 47.619 0.00 0.00 32.69 3.91
31 32 1.401905 CCACGCTATGGGAAAGAAAGC 59.598 52.381 0.00 0.00 45.95 3.51
46 47 1.298859 GATCAAGACCACCACCACGC 61.299 60.000 0.00 0.00 0.00 5.34
48 49 0.673644 CCGATCAAGACCACCACCAC 60.674 60.000 0.00 0.00 0.00 4.16
49 50 1.125093 ACCGATCAAGACCACCACCA 61.125 55.000 0.00 0.00 0.00 4.17
84 85 1.759881 GCTCCATGGCAGCCTCTAT 59.240 57.895 19.68 0.00 0.00 1.98
118 119 2.038837 GGCGGTGACTACAAAGGCC 61.039 63.158 0.00 0.00 33.28 5.19
119 120 0.676782 ATGGCGGTGACTACAAAGGC 60.677 55.000 0.00 0.00 0.00 4.35
122 123 0.981183 AGGATGGCGGTGACTACAAA 59.019 50.000 0.00 0.00 0.00 2.83
124 125 1.327690 GGAGGATGGCGGTGACTACA 61.328 60.000 0.00 0.00 0.00 2.74
158 172 1.445582 CACCGTCGCTAGTCCCAAC 60.446 63.158 0.00 0.00 0.00 3.77
173 187 2.019156 GCCAAGAGCCCAACTATCACC 61.019 57.143 0.00 0.00 34.35 4.02
193 207 0.461163 TGCATACATCGACCAACGGG 60.461 55.000 0.00 0.00 42.82 5.28
225 239 3.049674 ACCATTGCAGGCACGTCG 61.050 61.111 0.00 0.00 0.00 5.12
228 242 1.996786 GATCCACCATTGCAGGCACG 61.997 60.000 0.00 0.00 0.00 5.34
232 246 1.479323 CAAAGGATCCACCATTGCAGG 59.521 52.381 15.82 0.00 39.83 4.85
242 256 0.991920 GAGGGTGGACAAAGGATCCA 59.008 55.000 15.82 0.00 44.20 3.41
243 257 0.256177 GGAGGGTGGACAAAGGATCC 59.744 60.000 2.48 2.48 36.70 3.36
251 265 2.355484 AAAGGGAGGGAGGGTGGACA 62.355 60.000 0.00 0.00 0.00 4.02
269 283 0.911769 AGGATTCCTGTCATCGGCAA 59.088 50.000 3.86 0.00 29.57 4.52
270 284 0.178767 CAGGATTCCTGTCATCGGCA 59.821 55.000 22.45 0.00 45.82 5.69
271 285 2.997899 CAGGATTCCTGTCATCGGC 58.002 57.895 22.45 0.00 45.82 5.54
280 302 2.043526 ACCCAAGCATTTCAGGATTCCT 59.956 45.455 0.00 0.00 0.00 3.36
288 310 2.036217 CTCTTTGCACCCAAGCATTTCA 59.964 45.455 0.00 0.00 45.19 2.69
289 311 2.611224 CCTCTTTGCACCCAAGCATTTC 60.611 50.000 0.00 0.00 45.19 2.17
294 316 2.935740 GCCCTCTTTGCACCCAAGC 61.936 63.158 0.00 0.00 31.52 4.01
295 317 2.629656 CGCCCTCTTTGCACCCAAG 61.630 63.158 0.00 0.00 31.52 3.61
296 318 2.597217 CGCCCTCTTTGCACCCAA 60.597 61.111 0.00 0.00 0.00 4.12
325 347 1.574702 GGAGAAAACGCCGGAAGTGG 61.575 60.000 5.05 0.00 0.00 4.00
334 356 2.031465 TCCCACCGGAGAAAACGC 59.969 61.111 9.46 0.00 32.86 4.84
387 410 0.108804 CCTCGCGCCTTCTTGTTAGA 60.109 55.000 0.00 0.00 0.00 2.10
388 411 0.389948 ACCTCGCGCCTTCTTGTTAG 60.390 55.000 0.00 0.00 0.00 2.34
409 432 2.544685 CATTGTCGGCAACCTCTCTAG 58.455 52.381 3.66 0.00 37.44 2.43
413 436 0.606401 CACCATTGTCGGCAACCTCT 60.606 55.000 3.66 0.00 37.44 3.69
416 439 2.961768 CCACCATTGTCGGCAACC 59.038 61.111 3.66 0.00 37.44 3.77
429 452 4.517453 TGTATACTTGTTGTTGAAGCCACC 59.483 41.667 4.17 0.00 0.00 4.61
442 465 6.055588 CCATCCGGAGAATTTGTATACTTGT 58.944 40.000 11.34 0.00 0.00 3.16
448 471 4.887655 GGTTTCCATCCGGAGAATTTGTAT 59.112 41.667 11.34 0.00 44.10 2.29
450 473 3.089284 GGTTTCCATCCGGAGAATTTGT 58.911 45.455 11.34 0.00 44.10 2.83
465 488 0.181350 AGGCGAGATCATGGGTTTCC 59.819 55.000 0.00 0.00 0.00 3.13
466 489 1.943340 GAAGGCGAGATCATGGGTTTC 59.057 52.381 0.00 0.00 0.00 2.78
469 492 1.043116 TCGAAGGCGAGATCATGGGT 61.043 55.000 0.00 0.00 42.51 4.51
512 535 9.176460 CCCAACCAATTGCTTCATAATTTAATT 57.824 29.630 0.00 0.00 34.17 1.40
513 536 7.282901 GCCCAACCAATTGCTTCATAATTTAAT 59.717 33.333 0.00 0.00 34.17 1.40
514 537 6.597280 GCCCAACCAATTGCTTCATAATTTAA 59.403 34.615 0.00 0.00 34.17 1.52
515 538 6.112058 GCCCAACCAATTGCTTCATAATTTA 58.888 36.000 0.00 0.00 34.17 1.40
517 540 4.019501 TGCCCAACCAATTGCTTCATAATT 60.020 37.500 0.00 0.00 34.17 1.40
519 542 2.902486 TGCCCAACCAATTGCTTCATAA 59.098 40.909 0.00 0.00 34.17 1.90
520 543 2.533916 TGCCCAACCAATTGCTTCATA 58.466 42.857 0.00 0.00 34.17 2.15
521 544 1.350071 TGCCCAACCAATTGCTTCAT 58.650 45.000 0.00 0.00 34.17 2.57
522 545 1.350071 ATGCCCAACCAATTGCTTCA 58.650 45.000 0.00 0.00 34.17 3.02
523 546 2.078392 CAATGCCCAACCAATTGCTTC 58.922 47.619 0.00 0.00 34.17 3.86
524 547 1.698532 TCAATGCCCAACCAATTGCTT 59.301 42.857 0.00 0.00 34.17 3.91
525 548 1.002315 GTCAATGCCCAACCAATTGCT 59.998 47.619 0.00 0.00 34.17 3.91
526 549 1.441738 GTCAATGCCCAACCAATTGC 58.558 50.000 0.00 0.00 34.17 3.56
608 633 8.236586 CCCGTGGACAAATATATATTGATTGTG 58.763 37.037 13.52 8.59 0.00 3.33
614 639 6.861055 GCAAACCCGTGGACAAATATATATTG 59.139 38.462 8.74 6.15 0.00 1.90
643 670 2.032377 TGAAACACGGCGAAAACAGATC 60.032 45.455 16.62 1.19 0.00 2.75
645 672 1.370609 TGAAACACGGCGAAAACAGA 58.629 45.000 16.62 0.00 0.00 3.41
656 683 3.601586 CGAAGTACACTGCTTGAAACACG 60.602 47.826 0.00 0.00 0.00 4.49
667 694 1.139989 CACACTGCCGAAGTACACTG 58.860 55.000 0.00 0.00 36.83 3.66
668 695 1.037493 TCACACTGCCGAAGTACACT 58.963 50.000 0.00 0.00 36.83 3.55
683 710 2.113807 CATCCCTCTGGAGTGATCACA 58.886 52.381 27.02 6.47 46.08 3.58
699 726 0.179092 CGAGGTCGGTAAACCCATCC 60.179 60.000 0.00 0.00 40.42 3.51
726 1880 1.298859 GAGCGCATTTCGTCAAGGGT 61.299 55.000 11.47 0.00 41.07 4.34
747 1901 2.180769 CACCTACGCGCTGCAGTA 59.819 61.111 16.64 0.00 0.00 2.74
989 2171 4.179579 GCGCCATTGTCGCCTTCC 62.180 66.667 0.00 0.00 46.18 3.46
1309 2494 4.527583 GGAGCAGAGCTGGCCGAG 62.528 72.222 0.00 0.00 39.88 4.63
1413 2598 0.687427 AGAAGCTCTCCCTCTCCTGC 60.687 60.000 0.00 0.00 0.00 4.85
1424 2609 2.046507 CGGCAGGCAAGAAGCTCT 60.047 61.111 0.00 0.00 44.79 4.09
1502 2687 0.779997 AAAATCCCCAGTGCTCAGGT 59.220 50.000 0.00 0.00 0.00 4.00
1511 2696 8.389366 AGATATCCTCTTCATAAAAATCCCCAG 58.611 37.037 0.00 0.00 0.00 4.45
1578 2763 1.068434 GGAGCCTTCTTCAGATCCTCG 59.932 57.143 0.00 0.00 0.00 4.63
1611 2796 1.731720 AGCAATGCTCGGAAGAAGAC 58.268 50.000 0.00 0.00 41.32 3.01
1620 2805 1.135575 GGAACTGGAAAGCAATGCTCG 60.136 52.381 8.71 0.00 38.25 5.03
1634 2819 3.407424 TGAATGTCTCACCTGGAACTG 57.593 47.619 0.00 0.00 0.00 3.16
1635 2820 3.871463 GCATGAATGTCTCACCTGGAACT 60.871 47.826 0.00 0.00 36.69 3.01
1636 2821 2.421424 GCATGAATGTCTCACCTGGAAC 59.579 50.000 0.00 0.00 36.69 3.62
1637 2822 2.618816 GGCATGAATGTCTCACCTGGAA 60.619 50.000 0.00 0.00 36.69 3.53
1659 2850 2.028130 CGCTCTTCCATCTCTGGTACT 58.972 52.381 0.00 0.00 43.61 2.73
1662 2853 1.333636 CCCGCTCTTCCATCTCTGGT 61.334 60.000 0.00 0.00 43.61 4.00
1679 2870 5.652014 TGTACATTGTTGATGGATTTCTCCC 59.348 40.000 0.00 0.00 41.29 4.30
1701 2901 1.694150 TCTGGCAAGCTTACACTCTGT 59.306 47.619 0.00 0.00 0.00 3.41
1702 2902 2.028658 TCTCTGGCAAGCTTACACTCTG 60.029 50.000 0.00 0.00 0.00 3.35
1703 2903 2.233431 CTCTCTGGCAAGCTTACACTCT 59.767 50.000 0.00 0.00 0.00 3.24
1704 2904 2.232452 TCTCTCTGGCAAGCTTACACTC 59.768 50.000 0.00 0.00 0.00 3.51
1705 2905 2.251818 TCTCTCTGGCAAGCTTACACT 58.748 47.619 0.00 0.00 0.00 3.55
1706 2906 2.751166 TCTCTCTGGCAAGCTTACAC 57.249 50.000 0.00 0.00 0.00 2.90
1707 2907 3.557898 CCTTTCTCTCTGGCAAGCTTACA 60.558 47.826 0.00 0.13 0.00 2.41
1708 2908 3.006247 CCTTTCTCTCTGGCAAGCTTAC 58.994 50.000 0.00 0.00 0.00 2.34
1709 2909 2.026822 CCCTTTCTCTCTGGCAAGCTTA 60.027 50.000 0.00 0.00 0.00 3.09
1744 3570 1.618837 CAACCTCTTCTCCTCAACCGA 59.381 52.381 0.00 0.00 0.00 4.69
1819 3645 1.098050 ATCGAAGAATGTGGCTTGCC 58.902 50.000 4.43 4.43 43.58 4.52
1865 3692 3.767711 AGAACTCCCTTCAAATTCCCAC 58.232 45.455 0.00 0.00 0.00 4.61
1873 3700 5.412594 CGATTTCATCAAGAACTCCCTTCAA 59.587 40.000 0.00 0.00 35.56 2.69
1931 3764 2.168521 TCCTCCACGACCTTGAATGATC 59.831 50.000 0.00 0.00 0.00 2.92
2184 4032 4.717629 TCTTCGGCCTGCACGTCG 62.718 66.667 0.00 3.14 0.00 5.12
2275 4150 2.685380 CGACCTCAGGGGGCTCTT 60.685 66.667 0.00 0.00 42.26 2.85
2585 4475 1.559965 TTCCTCCTCCTCCTCGTCGA 61.560 60.000 0.00 0.00 0.00 4.20
2589 4479 1.064314 TCTTCTTCCTCCTCCTCCTCG 60.064 57.143 0.00 0.00 0.00 4.63
2602 4492 1.130938 GTCGTCCTCCTCGTCTTCTTC 59.869 57.143 0.00 0.00 0.00 2.87
2603 4493 1.166989 GTCGTCCTCCTCGTCTTCTT 58.833 55.000 0.00 0.00 0.00 2.52
2604 4494 1.020333 CGTCGTCCTCCTCGTCTTCT 61.020 60.000 0.00 0.00 0.00 2.85
2902 4793 5.521010 CACACAAATTATTTGGCATAGGCTG 59.479 40.000 20.00 9.95 44.81 4.85
2903 4794 5.187576 ACACACAAATTATTTGGCATAGGCT 59.812 36.000 20.00 0.00 44.81 4.58
2904 4795 5.418676 ACACACAAATTATTTGGCATAGGC 58.581 37.500 20.00 0.00 44.81 3.93
2905 4796 8.250332 AGTAACACACAAATTATTTGGCATAGG 58.750 33.333 20.00 7.33 44.81 2.57
2924 4849 4.460505 GCACGAACCAAATACAGTAACAC 58.539 43.478 0.00 0.00 0.00 3.32
2939 4864 5.352643 ACTTTGTAGTATTTGGCACGAAC 57.647 39.130 0.00 0.00 31.21 3.95
2940 4865 6.380095 AAACTTTGTAGTATTTGGCACGAA 57.620 33.333 0.00 0.00 33.17 3.85
2941 4866 6.202937 CAAAACTTTGTAGTATTTGGCACGA 58.797 36.000 0.00 0.00 33.54 4.35
2942 4867 5.108027 GCAAAACTTTGTAGTATTTGGCACG 60.108 40.000 4.23 0.00 40.24 5.34
2943 4868 5.983118 AGCAAAACTTTGTAGTATTTGGCAC 59.017 36.000 4.23 0.00 40.24 5.01
2959 4884 6.543735 AGGAGTATGAAAGGTTAGCAAAACT 58.456 36.000 2.48 0.00 32.55 2.66
2960 4885 6.655425 AGAGGAGTATGAAAGGTTAGCAAAAC 59.345 38.462 0.00 0.00 0.00 2.43
2963 4888 5.734720 CAGAGGAGTATGAAAGGTTAGCAA 58.265 41.667 0.00 0.00 0.00 3.91
2966 4891 5.344743 TGCAGAGGAGTATGAAAGGTTAG 57.655 43.478 0.00 0.00 0.00 2.34
2967 4892 5.189736 ACATGCAGAGGAGTATGAAAGGTTA 59.810 40.000 0.00 0.00 35.51 2.85
2971 4896 6.426328 GGATTACATGCAGAGGAGTATGAAAG 59.574 42.308 0.00 0.00 35.51 2.62
2973 4898 5.604231 AGGATTACATGCAGAGGAGTATGAA 59.396 40.000 0.00 0.00 35.51 2.57
2974 4899 5.150715 AGGATTACATGCAGAGGAGTATGA 58.849 41.667 0.00 0.00 35.51 2.15
2975 4900 5.480642 AGGATTACATGCAGAGGAGTATG 57.519 43.478 0.00 0.00 37.58 2.39
2976 4901 5.279206 CGAAGGATTACATGCAGAGGAGTAT 60.279 44.000 0.00 0.00 0.00 2.12
2977 4902 4.038042 CGAAGGATTACATGCAGAGGAGTA 59.962 45.833 0.00 0.00 0.00 2.59
2978 4903 3.181471 CGAAGGATTACATGCAGAGGAGT 60.181 47.826 0.00 0.00 0.00 3.85
2997 4922 1.996292 CAACTTCGAGATGCTCCGAA 58.004 50.000 0.00 0.00 41.71 4.30
3010 4935 2.663119 GCCGTTGAATCATTGCAACTTC 59.337 45.455 0.00 6.29 41.56 3.01
3013 4938 1.987770 CTGCCGTTGAATCATTGCAAC 59.012 47.619 0.00 0.00 40.62 4.17
3090 5016 2.140717 CGGCGTAATTAAAGCTAGGGG 58.859 52.381 0.00 0.00 0.00 4.79
3122 5048 4.072131 CCCTGTTGATCCTCGAAAGAAAA 58.928 43.478 0.00 0.00 41.32 2.29
3161 5090 1.183549 GCCCTTACCACTCTCTTCGA 58.816 55.000 0.00 0.00 0.00 3.71
3223 5152 3.441222 ACTCGGAAACCAAACGTTTTTCT 59.559 39.130 11.66 0.00 44.88 2.52
3225 5154 3.853831 ACTCGGAAACCAAACGTTTTT 57.146 38.095 11.66 3.18 44.88 1.94
3226 5155 3.688673 TGTACTCGGAAACCAAACGTTTT 59.311 39.130 11.66 0.00 44.88 2.43
3232 5161 6.149807 GGAAACATATGTACTCGGAAACCAAA 59.850 38.462 9.21 0.00 0.00 3.28
3235 5164 5.425630 AGGAAACATATGTACTCGGAAACC 58.574 41.667 9.21 3.08 0.00 3.27
3237 5166 9.923143 CATATAGGAAACATATGTACTCGGAAA 57.077 33.333 9.21 0.00 33.51 3.13
3325 5255 7.482169 TCTCACTAGTACAATGAAAGGTCAT 57.518 36.000 0.00 0.00 46.91 3.06
3395 5326 5.240623 TGCTATTTTGACCGAACATTTGTCT 59.759 36.000 0.00 0.00 0.00 3.41
3403 5334 6.907212 CACTATTCATGCTATTTTGACCGAAC 59.093 38.462 0.00 0.00 0.00 3.95
3439 5370 9.498433 CGAAAAAGACAAAATTTATTTGCTACG 57.502 29.630 0.00 0.00 32.93 3.51
3440 5371 9.301606 GCGAAAAAGACAAAATTTATTTGCTAC 57.698 29.630 0.00 0.00 32.93 3.58
3441 5372 9.255304 AGCGAAAAAGACAAAATTTATTTGCTA 57.745 25.926 0.00 0.00 32.93 3.49
3442 5373 8.063630 CAGCGAAAAAGACAAAATTTATTTGCT 58.936 29.630 0.00 0.00 32.93 3.91
3443 5374 7.850492 ACAGCGAAAAAGACAAAATTTATTTGC 59.150 29.630 0.00 0.00 32.93 3.68
3444 5375 9.146270 CACAGCGAAAAAGACAAAATTTATTTG 57.854 29.630 0.00 0.00 35.64 2.32
3445 5376 9.092876 TCACAGCGAAAAAGACAAAATTTATTT 57.907 25.926 0.00 0.00 0.00 1.40
3446 5377 8.641499 TCACAGCGAAAAAGACAAAATTTATT 57.359 26.923 0.00 0.00 0.00 1.40
3447 5378 8.641499 TTCACAGCGAAAAAGACAAAATTTAT 57.359 26.923 0.00 0.00 0.00 1.40
3448 5379 7.757624 ACTTCACAGCGAAAAAGACAAAATTTA 59.242 29.630 0.00 0.00 31.71 1.40
3449 5380 6.589907 ACTTCACAGCGAAAAAGACAAAATTT 59.410 30.769 0.00 0.00 31.71 1.82
3450 5381 6.099341 ACTTCACAGCGAAAAAGACAAAATT 58.901 32.000 0.00 0.00 31.71 1.82
3451 5382 5.650543 ACTTCACAGCGAAAAAGACAAAAT 58.349 33.333 0.00 0.00 31.71 1.82
3452 5383 5.054390 ACTTCACAGCGAAAAAGACAAAA 57.946 34.783 0.00 0.00 31.71 2.44
3453 5384 4.155099 TGACTTCACAGCGAAAAAGACAAA 59.845 37.500 0.00 0.00 31.71 2.83
3454 5385 3.687212 TGACTTCACAGCGAAAAAGACAA 59.313 39.130 0.00 0.00 31.71 3.18
3455 5386 3.266636 TGACTTCACAGCGAAAAAGACA 58.733 40.909 0.00 0.00 31.71 3.41
3456 5387 3.944422 TGACTTCACAGCGAAAAAGAC 57.056 42.857 0.00 0.00 31.71 3.01
3457 5388 3.242284 CGTTGACTTCACAGCGAAAAAGA 60.242 43.478 0.00 0.00 44.63 2.52
3458 5389 3.029074 CGTTGACTTCACAGCGAAAAAG 58.971 45.455 0.00 0.00 44.63 2.27
3459 5390 2.417239 ACGTTGACTTCACAGCGAAAAA 59.583 40.909 11.22 0.00 44.63 1.94
3685 5618 7.155442 TGAAGGGAGTGATAGAGAGAAGATA 57.845 40.000 0.00 0.00 0.00 1.98
3698 5631 7.520798 AGATGCAATAAATATGAAGGGAGTGA 58.479 34.615 0.00 0.00 0.00 3.41
3703 5636 6.149308 TGCGTAGATGCAATAAATATGAAGGG 59.851 38.462 0.00 0.00 43.02 3.95
3719 5652 8.082852 ACAAGAACCTAGTTATATGCGTAGATG 58.917 37.037 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.