Multiple sequence alignment - TraesCS1A01G287500

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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 TraesCS1A01G287500 chr1A 100.000 2906 0 0 1 2906 484997886 485000791 0.000000e+00 5367
1 TraesCS1A01G287500 chr1A 100.000 191 0 0 3184 3374 485001069 485001259 1.490000e-93 353
2 TraesCS1A01G287500 chr1B 96.116 2137 65 7 755 2886 516947894 516950017 0.000000e+00 3470
3 TraesCS1A01G287500 chr1B 91.071 168 15 0 87 254 516920733 516920900 9.420000e-56 228
4 TraesCS1A01G287500 chr1D 96.028 2140 61 11 755 2886 384831897 384834020 0.000000e+00 3459
5 TraesCS1A01G287500 chr1D 89.447 199 14 3 87 285 384829937 384830128 9.350000e-61 244
6 TraesCS1A01G287500 chr1D 92.523 107 6 2 3269 3374 384834751 384834856 5.830000e-33 152
7 TraesCS1A01G287500 chr3D 78.038 1366 245 33 1025 2375 460252146 460250821 0.000000e+00 809
8 TraesCS1A01G287500 chr3D 96.591 88 3 0 1 88 210668520 210668607 2.710000e-31 147
9 TraesCS1A01G287500 chr3D 96.591 88 3 0 1 88 438223988 438223901 2.710000e-31 147
10 TraesCS1A01G287500 chr3B 77.900 1362 247 32 1028 2375 610178847 610177526 0.000000e+00 798
11 TraesCS1A01G287500 chr3A 77.820 1321 249 28 1068 2375 602241501 602240212 0.000000e+00 776
12 TraesCS1A01G287500 chr5A 96.739 92 3 0 1 92 704874286 704874195 1.620000e-33 154
13 TraesCS1A01G287500 chrUn 96.667 90 3 0 1 90 28763986 28764075 2.100000e-32 150
14 TraesCS1A01G287500 chrUn 96.591 88 3 0 1 88 28757164 28757251 2.710000e-31 147
15 TraesCS1A01G287500 chr6A 96.591 88 3 0 1 88 136602705 136602618 2.710000e-31 147
16 TraesCS1A01G287500 chr6A 96.591 88 3 0 1 88 456845861 456845774 2.710000e-31 147
17 TraesCS1A01G287500 chr5D 96.591 88 3 0 1 88 112240602 112240689 2.710000e-31 147
18 TraesCS1A01G287500 chr7B 95.604 91 3 1 1 91 661902345 661902434 9.760000e-31 145


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 TraesCS1A01G287500 chr1A 484997886 485001259 3373 False 2860 5367 100.000 1 3374 2 chr1A.!!$F1 3373
1 TraesCS1A01G287500 chr1B 516947894 516950017 2123 False 3470 3470 96.116 755 2886 1 chr1B.!!$F2 2131
2 TraesCS1A01G287500 chr1D 384829937 384834856 4919 False 1285 3459 92.666 87 3374 3 chr1D.!!$F1 3287
3 TraesCS1A01G287500 chr3D 460250821 460252146 1325 True 809 809 78.038 1025 2375 1 chr3D.!!$R2 1350
4 TraesCS1A01G287500 chr3B 610177526 610178847 1321 True 798 798 77.900 1028 2375 1 chr3B.!!$R1 1347
5 TraesCS1A01G287500 chr3A 602240212 602241501 1289 True 776 776 77.820 1068 2375 1 chr3A.!!$R1 1307

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
23 24 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.0 3.79 3.79 38.76 3.96 F
460 1540 0.112606 TATGGGTAGGCGAGAGAGGG 59.887 60.0 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1233 2548 1.153804 GTCGGCGAGGAGGAAGAAC 60.154 63.158 11.20 0.0 0.00 3.01 R
2414 3732 1.744798 CGCCAAGAGAGCAATCATGGA 60.745 52.381 14.48 0.0 39.85 3.41 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
17 18 2.445614 TCTCCCCCTCTCGTTGCT 59.554 61.111 0.00 0.00 0.00 3.91
18 19 1.695465 TCTCCCCCTCTCGTTGCTA 59.305 57.895 0.00 0.00 0.00 3.49
19 20 0.261991 TCTCCCCCTCTCGTTGCTAT 59.738 55.000 0.00 0.00 0.00 2.97
20 21 0.390860 CTCCCCCTCTCGTTGCTATG 59.609 60.000 0.00 0.00 0.00 2.23
21 22 1.227674 CCCCCTCTCGTTGCTATGC 60.228 63.158 0.00 0.00 0.00 3.14
22 23 1.522092 CCCCTCTCGTTGCTATGCA 59.478 57.895 0.00 0.00 36.47 3.96
23 24 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.000 3.79 3.79 38.76 3.96
24 25 1.506493 CCCTCTCGTTGCTATGCATC 58.494 55.000 0.19 0.00 38.76 3.91
25 26 1.069823 CCCTCTCGTTGCTATGCATCT 59.930 52.381 0.19 0.00 38.76 2.90
26 27 2.484417 CCCTCTCGTTGCTATGCATCTT 60.484 50.000 0.19 0.00 38.76 2.40
27 28 2.799412 CCTCTCGTTGCTATGCATCTTC 59.201 50.000 0.19 0.00 38.76 2.87
28 29 3.492309 CCTCTCGTTGCTATGCATCTTCT 60.492 47.826 0.19 0.00 38.76 2.85
29 30 4.261783 CCTCTCGTTGCTATGCATCTTCTA 60.262 45.833 0.19 0.00 38.76 2.10
30 31 4.864633 TCTCGTTGCTATGCATCTTCTAG 58.135 43.478 0.19 0.00 38.76 2.43
31 32 4.580580 TCTCGTTGCTATGCATCTTCTAGA 59.419 41.667 0.19 0.00 38.76 2.43
32 33 5.242615 TCTCGTTGCTATGCATCTTCTAGAT 59.757 40.000 0.19 0.00 38.76 1.98
33 34 6.431234 TCTCGTTGCTATGCATCTTCTAGATA 59.569 38.462 0.19 0.00 38.76 1.98
34 35 6.616017 TCGTTGCTATGCATCTTCTAGATAG 58.384 40.000 0.19 0.00 38.76 2.08
35 36 6.431234 TCGTTGCTATGCATCTTCTAGATAGA 59.569 38.462 0.19 0.11 38.76 1.98
36 37 7.121907 TCGTTGCTATGCATCTTCTAGATAGAT 59.878 37.037 0.19 10.06 38.76 1.98
37 38 7.431960 CGTTGCTATGCATCTTCTAGATAGATC 59.568 40.741 0.19 9.17 38.76 2.75
38 39 8.469200 GTTGCTATGCATCTTCTAGATAGATCT 58.531 37.037 0.19 0.00 38.76 2.75
39 40 8.592529 TGCTATGCATCTTCTAGATAGATCTT 57.407 34.615 0.19 0.00 32.12 2.40
40 41 8.468399 TGCTATGCATCTTCTAGATAGATCTTG 58.532 37.037 0.19 0.00 32.12 3.02
41 42 7.436080 GCTATGCATCTTCTAGATAGATCTTGC 59.564 40.741 0.19 13.69 38.32 4.01
42 43 5.707931 TGCATCTTCTAGATAGATCTTGCG 58.292 41.667 0.00 5.35 38.32 4.85
43 44 5.242615 TGCATCTTCTAGATAGATCTTGCGT 59.757 40.000 0.00 0.00 38.32 5.24
44 45 5.572511 GCATCTTCTAGATAGATCTTGCGTG 59.427 44.000 0.00 5.42 38.32 5.34
45 46 6.569418 GCATCTTCTAGATAGATCTTGCGTGA 60.569 42.308 0.00 0.00 38.32 4.35
46 47 6.552859 TCTTCTAGATAGATCTTGCGTGAG 57.447 41.667 0.00 0.00 38.32 3.51
65 66 7.790861 CGTGAGCGTAGGAAATTTTTAAAAT 57.209 32.000 0.55 0.00 0.00 1.82
66 67 8.222984 CGTGAGCGTAGGAAATTTTTAAAATT 57.777 30.769 9.58 9.58 0.00 1.82
67 68 8.153411 CGTGAGCGTAGGAAATTTTTAAAATTG 58.847 33.333 15.24 4.46 0.00 2.32
68 69 7.949962 GTGAGCGTAGGAAATTTTTAAAATTGC 59.050 33.333 15.24 13.40 0.00 3.56
69 70 7.653713 TGAGCGTAGGAAATTTTTAAAATTGCA 59.346 29.630 19.29 1.32 0.00 4.08
70 71 8.546597 AGCGTAGGAAATTTTTAAAATTGCAT 57.453 26.923 19.29 15.81 0.00 3.96
71 72 8.442384 AGCGTAGGAAATTTTTAAAATTGCATG 58.558 29.630 19.29 9.00 0.00 4.06
72 73 7.216130 GCGTAGGAAATTTTTAAAATTGCATGC 59.784 33.333 19.29 11.82 0.00 4.06
73 74 8.442384 CGTAGGAAATTTTTAAAATTGCATGCT 58.558 29.630 20.33 14.61 0.00 3.79
76 77 8.442384 AGGAAATTTTTAAAATTGCATGCTACG 58.558 29.630 20.33 0.00 0.00 3.51
77 78 8.227119 GGAAATTTTTAAAATTGCATGCTACGT 58.773 29.630 20.33 0.00 0.00 3.57
78 79 9.592720 GAAATTTTTAAAATTGCATGCTACGTT 57.407 25.926 20.33 11.27 0.00 3.99
79 80 9.592720 AAATTTTTAAAATTGCATGCTACGTTC 57.407 25.926 20.33 0.00 0.00 3.95
80 81 6.698359 TTTTAAAATTGCATGCTACGTTCC 57.302 33.333 20.33 0.00 0.00 3.62
81 82 2.939460 AAATTGCATGCTACGTTCCC 57.061 45.000 20.33 0.00 0.00 3.97
82 83 2.128771 AATTGCATGCTACGTTCCCT 57.871 45.000 20.33 0.00 0.00 4.20
83 84 3.275617 AATTGCATGCTACGTTCCCTA 57.724 42.857 20.33 0.00 0.00 3.53
84 85 2.772077 TTGCATGCTACGTTCCCTAA 57.228 45.000 20.33 0.00 0.00 2.69
85 86 2.018542 TGCATGCTACGTTCCCTAAC 57.981 50.000 20.33 0.00 0.00 2.34
109 110 5.803967 CAGAATTAGCAAAATCAAGGCACTC 59.196 40.000 0.00 0.00 38.49 3.51
120 121 5.690464 ATCAAGGCACTCAGATTACTCTT 57.310 39.130 0.00 0.00 38.49 2.85
121 122 5.489792 TCAAGGCACTCAGATTACTCTTT 57.510 39.130 0.00 0.00 38.49 2.52
144 145 4.235079 TCCACCAAGGACATGATAAAGG 57.765 45.455 0.00 0.00 43.07 3.11
145 146 3.591527 TCCACCAAGGACATGATAAAGGT 59.408 43.478 0.00 0.00 43.07 3.50
146 147 4.785914 TCCACCAAGGACATGATAAAGGTA 59.214 41.667 0.00 0.00 43.07 3.08
147 148 5.431731 TCCACCAAGGACATGATAAAGGTAT 59.568 40.000 0.00 0.00 43.07 2.73
152 153 8.723365 ACCAAGGACATGATAAAGGTATATTCA 58.277 33.333 0.00 0.00 0.00 2.57
178 179 3.006110 TCACACGAAACTACGAGGGAAAT 59.994 43.478 0.00 0.00 33.97 2.17
210 211 2.430332 CCTGCAAAGAACCAAAGACCAA 59.570 45.455 0.00 0.00 0.00 3.67
216 217 2.031870 AGAACCAAAGACCAAAGCACC 58.968 47.619 0.00 0.00 0.00 5.01
229 230 1.256812 AAGCACCAATAGCCAACCAC 58.743 50.000 0.00 0.00 0.00 4.16
230 231 0.960364 AGCACCAATAGCCAACCACG 60.960 55.000 0.00 0.00 0.00 4.94
231 232 1.506262 CACCAATAGCCAACCACGC 59.494 57.895 0.00 0.00 0.00 5.34
232 233 1.074072 ACCAATAGCCAACCACGCA 59.926 52.632 0.00 0.00 0.00 5.24
233 234 0.538516 ACCAATAGCCAACCACGCAA 60.539 50.000 0.00 0.00 0.00 4.85
234 235 0.817013 CCAATAGCCAACCACGCAAT 59.183 50.000 0.00 0.00 0.00 3.56
235 236 1.202290 CCAATAGCCAACCACGCAATC 60.202 52.381 0.00 0.00 0.00 2.67
254 255 5.293079 GCAATCAAGCCAAACAAACACTTTA 59.707 36.000 0.00 0.00 0.00 1.85
255 256 6.509997 GCAATCAAGCCAAACAAACACTTTAG 60.510 38.462 0.00 0.00 0.00 1.85
261 262 6.745116 AGCCAAACAAACACTTTAGATAACC 58.255 36.000 0.00 0.00 0.00 2.85
269 270 8.962679 ACAAACACTTTAGATAACCTGTTTTCA 58.037 29.630 3.84 0.00 31.16 2.69
270 271 9.233232 CAAACACTTTAGATAACCTGTTTTCAC 57.767 33.333 3.84 0.00 31.16 3.18
279 280 6.828785 AGATAACCTGTTTTCACTTTCACACT 59.171 34.615 3.84 0.00 0.00 3.55
308 1388 2.482374 GAAGTGACATGGCAGCGC 59.518 61.111 0.00 0.00 0.00 5.92
309 1389 2.281692 AAGTGACATGGCAGCGCA 60.282 55.556 11.47 0.00 0.00 6.09
310 1390 2.518836 GAAGTGACATGGCAGCGCAC 62.519 60.000 11.47 0.00 0.00 5.34
311 1391 4.450122 GTGACATGGCAGCGCACG 62.450 66.667 11.47 0.01 0.00 5.34
323 1403 0.320073 AGCGCACGGTACTTTTAGCA 60.320 50.000 11.47 0.00 0.00 3.49
335 1415 5.983720 GGTACTTTTAGCATAGATGAAGCGA 59.016 40.000 0.00 0.00 0.00 4.93
341 1421 2.965831 AGCATAGATGAAGCGAGGGTTA 59.034 45.455 0.00 0.00 0.00 2.85
351 1431 4.996122 TGAAGCGAGGGTTATTTTTCGTTA 59.004 37.500 0.00 0.00 35.61 3.18
352 1432 5.121142 TGAAGCGAGGGTTATTTTTCGTTAG 59.879 40.000 0.00 0.00 35.61 2.34
379 1459 3.432592 GCCGACTTACTTCAAAACCTCTC 59.567 47.826 0.00 0.00 0.00 3.20
386 1466 7.339482 ACTTACTTCAAAACCTCTCTGAAACT 58.661 34.615 0.00 0.00 0.00 2.66
387 1467 8.483758 ACTTACTTCAAAACCTCTCTGAAACTA 58.516 33.333 0.00 0.00 0.00 2.24
396 1476 6.099159 ACCTCTCTGAAACTAGGTACAAAC 57.901 41.667 0.00 0.00 40.57 2.93
411 1491 4.405036 GGTACAAACCTTAAAACCACCCAA 59.595 41.667 0.00 0.00 43.08 4.12
416 1496 6.156429 ACAAACCTTAAAACCACCCAATTGTA 59.844 34.615 4.43 0.00 0.00 2.41
418 1498 6.599356 ACCTTAAAACCACCCAATTGTATC 57.401 37.500 4.43 0.00 0.00 2.24
425 1505 4.199310 ACCACCCAATTGTATCGAATCAG 58.801 43.478 4.43 0.00 0.00 2.90
431 1511 4.024556 CCAATTGTATCGAATCAGAGCCAC 60.025 45.833 4.43 0.00 0.00 5.01
435 1515 0.817654 ATCGAATCAGAGCCACGTGA 59.182 50.000 19.30 0.00 0.00 4.35
447 1527 1.475403 CCACGTGAGAGAGTATGGGT 58.525 55.000 19.30 0.00 0.00 4.51
456 1536 2.156098 GAGAGTATGGGTAGGCGAGAG 58.844 57.143 0.00 0.00 0.00 3.20
460 1540 0.112606 TATGGGTAGGCGAGAGAGGG 59.887 60.000 0.00 0.00 0.00 4.30
470 1550 3.001414 GGCGAGAGAGGGTTTCTTAAAC 58.999 50.000 0.00 0.00 40.65 2.01
472 1552 4.081807 GGCGAGAGAGGGTTTCTTAAACTA 60.082 45.833 2.84 0.00 41.14 2.24
513 1593 9.681062 CTCCATTTTGTTTATTAGTCCCTCTTA 57.319 33.333 0.00 0.00 0.00 2.10
589 1670 6.028146 TGCTACAAAAGTAGTACCATCGAA 57.972 37.500 0.00 0.00 0.00 3.71
590 1671 6.457355 TGCTACAAAAGTAGTACCATCGAAA 58.543 36.000 0.00 0.00 0.00 3.46
591 1672 6.930164 TGCTACAAAAGTAGTACCATCGAAAA 59.070 34.615 0.00 0.00 0.00 2.29
593 1674 6.549912 ACAAAAGTAGTACCATCGAAAACC 57.450 37.500 0.00 0.00 0.00 3.27
594 1675 6.056884 ACAAAAGTAGTACCATCGAAAACCA 58.943 36.000 0.00 0.00 0.00 3.67
595 1676 6.017687 ACAAAAGTAGTACCATCGAAAACCAC 60.018 38.462 0.00 0.00 0.00 4.16
596 1677 4.877378 AGTAGTACCATCGAAAACCACA 57.123 40.909 0.00 0.00 0.00 4.17
597 1678 5.416271 AGTAGTACCATCGAAAACCACAT 57.584 39.130 0.00 0.00 0.00 3.21
598 1679 5.801380 AGTAGTACCATCGAAAACCACATT 58.199 37.500 0.00 0.00 0.00 2.71
673 1754 6.638610 TGTCAAATCTGTGGTCAAAATTTGT 58.361 32.000 5.56 0.00 38.10 2.83
674 1755 7.102346 TGTCAAATCTGTGGTCAAAATTTGTT 58.898 30.769 5.56 0.00 38.10 2.83
701 1782 7.573968 AAAATATGAAGAGCACCAGTAATCC 57.426 36.000 0.00 0.00 0.00 3.01
704 1785 2.237143 TGAAGAGCACCAGTAATCCCAG 59.763 50.000 0.00 0.00 0.00 4.45
711 1792 2.496070 CACCAGTAATCCCAGACGAAGA 59.504 50.000 0.00 0.00 0.00 2.87
723 1830 6.182627 TCCCAGACGAAGATAGTACTACAAA 58.817 40.000 4.31 0.00 0.00 2.83
725 1832 6.973474 CCCAGACGAAGATAGTACTACAAAAG 59.027 42.308 4.31 0.15 0.00 2.27
731 1838 9.672673 ACGAAGATAGTACTACAAAAGTAGGTA 57.327 33.333 4.31 0.00 41.42 3.08
753 1860 9.574516 AGGTAGATGTAAAAAGAAATGACACTT 57.425 29.630 0.00 0.00 0.00 3.16
769 2084 1.272490 CACTTAGCCGTTCAGTCCTCA 59.728 52.381 0.00 0.00 0.00 3.86
772 2087 0.738975 TAGCCGTTCAGTCCTCATCG 59.261 55.000 0.00 0.00 0.00 3.84
831 2146 3.799753 TCGGCTACGACCTACGAC 58.200 61.111 0.00 0.00 45.59 4.34
1161 2476 2.436824 GGCTTCTCCAAGACCGGC 60.437 66.667 0.00 0.00 30.14 6.13
1164 2479 4.735132 TTCTCCAAGACCGGCGCG 62.735 66.667 0.00 0.00 0.00 6.86
1233 2548 2.190578 GACCCCAAGCAGATCGGG 59.809 66.667 0.00 0.00 41.71 5.14
1722 3040 2.026945 GCCTGCTCTACTGCCTCTCC 62.027 65.000 0.00 0.00 0.00 3.71
1744 3062 2.490217 CCGAGGACCAGCACTACG 59.510 66.667 0.00 0.00 0.00 3.51
1996 3314 1.408822 GGGTGACATGGAACCAGATCC 60.409 57.143 17.85 0.48 38.27 3.36
2001 3319 1.211457 ACATGGAACCAGATCCTGCTC 59.789 52.381 0.00 0.00 40.35 4.26
2325 3643 1.069924 TCTCTCTCGACGACGACGAC 61.070 60.000 17.84 7.02 43.81 4.34
2374 3692 3.490761 GGAAGAGGAATTCGAGCTCTGAG 60.491 52.174 12.85 0.00 0.00 3.35
2392 3710 3.497118 TGAGCATTTGTAATTTTCCGCG 58.503 40.909 0.00 0.00 0.00 6.46
2414 3732 0.604578 AATGCCGTGAGCTGCAATTT 59.395 45.000 1.02 0.00 44.23 1.82
2530 3850 6.885952 ATAGCTCATCGTCTTGTATGTACT 57.114 37.500 0.00 0.00 0.00 2.73
2540 3860 1.275666 TGTATGTACTGCAGGGCTGT 58.724 50.000 19.93 0.00 42.86 4.40
2541 3861 2.462723 TGTATGTACTGCAGGGCTGTA 58.537 47.619 19.93 0.00 40.85 2.74
2628 3948 2.002586 CTGGATACGTGCAAAGAGGTG 58.997 52.381 0.00 0.00 42.51 4.00
2713 4034 1.937278 TGCTGCAATTTTGTGTGGTG 58.063 45.000 0.00 0.00 0.00 4.17
2739 4060 8.812513 ATCAGTCATTTCATTCTTTGACCATA 57.187 30.769 0.00 0.00 39.39 2.74
2740 4061 8.812513 TCAGTCATTTCATTCTTTGACCATAT 57.187 30.769 0.00 0.00 39.39 1.78
2743 4064 9.028284 AGTCATTTCATTCTTTGACCATATTGT 57.972 29.630 0.00 0.00 39.39 2.71
2752 4073 8.421249 TTCTTTGACCATATTGTTGATCCTTT 57.579 30.769 0.00 0.00 0.00 3.11
2770 4091 5.632959 TCCTTTTGTTTGTCTGTTAACACG 58.367 37.500 3.59 1.56 34.25 4.49
2774 4095 5.459110 TTGTTTGTCTGTTAACACGACTC 57.541 39.130 25.19 19.02 34.25 3.36
2784 4105 3.959478 ACACGACTCGATGTGTTGT 57.041 47.368 5.20 2.01 46.61 3.32
2785 4106 1.767289 ACACGACTCGATGTGTTGTC 58.233 50.000 5.20 1.96 46.61 3.18
2810 4134 7.041848 TCGTATCTTATGATTTGCCACTCATTG 60.042 37.037 0.00 0.00 34.14 2.82
2818 4142 0.821301 TGCCACTCATTGCAACGGAA 60.821 50.000 0.00 0.00 33.87 4.30
2821 4145 2.867429 CCACTCATTGCAACGGAAATC 58.133 47.619 0.00 0.00 0.00 2.17
2825 4149 1.543802 TCATTGCAACGGAAATCCCAC 59.456 47.619 0.00 0.00 34.14 4.61
3204 4533 4.749048 AAATGGAAGGGAAAAGAGGTCT 57.251 40.909 0.00 0.00 0.00 3.85
3205 4534 5.860648 AAATGGAAGGGAAAAGAGGTCTA 57.139 39.130 0.00 0.00 0.00 2.59
3206 4535 4.846168 ATGGAAGGGAAAAGAGGTCTAC 57.154 45.455 0.00 0.00 0.00 2.59
3207 4536 3.870559 TGGAAGGGAAAAGAGGTCTACT 58.129 45.455 0.00 0.00 0.00 2.57
3208 4537 4.240323 TGGAAGGGAAAAGAGGTCTACTT 58.760 43.478 0.00 0.00 0.00 2.24
3209 4538 4.041691 TGGAAGGGAAAAGAGGTCTACTTG 59.958 45.833 0.00 0.00 0.00 3.16
3210 4539 4.286291 GGAAGGGAAAAGAGGTCTACTTGA 59.714 45.833 0.00 0.00 0.00 3.02
3211 4540 5.221864 GGAAGGGAAAAGAGGTCTACTTGAA 60.222 44.000 0.00 0.00 0.00 2.69
3212 4541 5.491323 AGGGAAAAGAGGTCTACTTGAAG 57.509 43.478 0.00 0.00 0.00 3.02
3213 4542 5.155905 AGGGAAAAGAGGTCTACTTGAAGA 58.844 41.667 0.00 0.00 0.00 2.87
3214 4543 5.247337 AGGGAAAAGAGGTCTACTTGAAGAG 59.753 44.000 0.00 0.00 0.00 2.85
3215 4544 5.483811 GGAAAAGAGGTCTACTTGAAGAGG 58.516 45.833 0.00 0.00 0.00 3.69
3216 4545 5.246429 GGAAAAGAGGTCTACTTGAAGAGGA 59.754 44.000 0.00 0.00 0.00 3.71
3217 4546 6.239629 GGAAAAGAGGTCTACTTGAAGAGGAA 60.240 42.308 0.00 0.00 0.00 3.36
3218 4547 6.749036 AAAGAGGTCTACTTGAAGAGGAAA 57.251 37.500 0.00 0.00 0.00 3.13
3219 4548 6.749036 AAGAGGTCTACTTGAAGAGGAAAA 57.251 37.500 0.00 0.00 0.00 2.29
3220 4549 6.353404 AGAGGTCTACTTGAAGAGGAAAAG 57.647 41.667 0.00 0.00 0.00 2.27
3221 4550 4.900684 AGGTCTACTTGAAGAGGAAAAGC 58.099 43.478 0.00 0.00 0.00 3.51
3222 4551 4.004314 GGTCTACTTGAAGAGGAAAAGCC 58.996 47.826 0.00 0.00 0.00 4.35
3223 4552 4.505039 GGTCTACTTGAAGAGGAAAAGCCA 60.505 45.833 0.00 0.00 40.02 4.75
3224 4553 4.693095 GTCTACTTGAAGAGGAAAAGCCAG 59.307 45.833 0.00 0.00 40.02 4.85
3225 4554 2.868899 ACTTGAAGAGGAAAAGCCAGG 58.131 47.619 0.00 0.00 40.02 4.45
3226 4555 2.175715 ACTTGAAGAGGAAAAGCCAGGT 59.824 45.455 0.00 0.00 40.02 4.00
3227 4556 2.276732 TGAAGAGGAAAAGCCAGGTG 57.723 50.000 0.00 0.00 40.02 4.00
3228 4557 1.494721 TGAAGAGGAAAAGCCAGGTGT 59.505 47.619 0.00 0.00 40.02 4.16
3229 4558 2.155279 GAAGAGGAAAAGCCAGGTGTC 58.845 52.381 0.00 0.00 40.02 3.67
3230 4559 1.439543 AGAGGAAAAGCCAGGTGTCT 58.560 50.000 0.00 0.00 40.02 3.41
3231 4560 2.621070 AGAGGAAAAGCCAGGTGTCTA 58.379 47.619 0.00 0.00 40.02 2.59
3232 4561 2.979678 AGAGGAAAAGCCAGGTGTCTAA 59.020 45.455 0.00 0.00 40.02 2.10
3233 4562 3.394606 AGAGGAAAAGCCAGGTGTCTAAA 59.605 43.478 0.00 0.00 40.02 1.85
3234 4563 3.487372 AGGAAAAGCCAGGTGTCTAAAC 58.513 45.455 0.00 0.00 40.02 2.01
3235 4564 3.138468 AGGAAAAGCCAGGTGTCTAAACT 59.862 43.478 0.00 0.00 40.02 2.66
3236 4565 4.349930 AGGAAAAGCCAGGTGTCTAAACTA 59.650 41.667 0.00 0.00 40.02 2.24
3237 4566 4.695928 GGAAAAGCCAGGTGTCTAAACTAG 59.304 45.833 0.00 0.00 36.34 2.57
3238 4567 3.336138 AAGCCAGGTGTCTAAACTAGC 57.664 47.619 0.00 0.00 0.00 3.42
3239 4568 2.541466 AGCCAGGTGTCTAAACTAGCT 58.459 47.619 0.00 0.00 0.00 3.32
3240 4569 2.498078 AGCCAGGTGTCTAAACTAGCTC 59.502 50.000 0.00 0.00 0.00 4.09
3241 4570 2.418884 GCCAGGTGTCTAAACTAGCTCC 60.419 54.545 0.00 0.00 0.00 4.70
3242 4571 2.832129 CCAGGTGTCTAAACTAGCTCCA 59.168 50.000 0.00 0.00 0.00 3.86
3243 4572 3.452627 CCAGGTGTCTAAACTAGCTCCAT 59.547 47.826 0.00 0.00 0.00 3.41
3244 4573 4.437239 CAGGTGTCTAAACTAGCTCCATG 58.563 47.826 0.00 0.00 0.00 3.66
3245 4574 4.160439 CAGGTGTCTAAACTAGCTCCATGA 59.840 45.833 0.00 0.00 0.00 3.07
3246 4575 4.777896 AGGTGTCTAAACTAGCTCCATGAA 59.222 41.667 0.00 0.00 0.00 2.57
3247 4576 5.105146 AGGTGTCTAAACTAGCTCCATGAAG 60.105 44.000 0.00 0.00 0.00 3.02
3252 4581 6.536941 GTCTAAACTAGCTCCATGAAGAAAGG 59.463 42.308 0.00 0.00 0.00 3.11
3257 4586 2.641815 AGCTCCATGAAGAAAGGTCTGT 59.358 45.455 0.00 0.00 33.05 3.41
3263 4592 4.217118 CCATGAAGAAAGGTCTGTTCAAGG 59.783 45.833 0.00 0.00 33.05 3.61
3264 4593 4.771114 TGAAGAAAGGTCTGTTCAAGGA 57.229 40.909 0.00 0.00 33.05 3.36
3265 4594 4.708177 TGAAGAAAGGTCTGTTCAAGGAG 58.292 43.478 0.00 0.00 33.05 3.69
3266 4595 4.408921 TGAAGAAAGGTCTGTTCAAGGAGA 59.591 41.667 0.00 0.00 33.05 3.71
3267 4596 5.104527 TGAAGAAAGGTCTGTTCAAGGAGAA 60.105 40.000 0.00 0.00 33.05 2.87
3288 5224 1.068352 AGTCCTTTTCCCCAGTGCCT 61.068 55.000 0.00 0.00 0.00 4.75
3368 5305 4.346730 TCTGATTGGGCATTGTTTGAGAT 58.653 39.130 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.261991 ATAGCAACGAGAGGGGGAGA 59.738 55.000 0.00 0.00 0.00 3.71
2 3 1.686325 GCATAGCAACGAGAGGGGGA 61.686 60.000 0.00 0.00 0.00 4.81
5 6 1.069823 AGATGCATAGCAACGAGAGGG 59.930 52.381 0.00 0.00 43.62 4.30
6 7 2.522836 AGATGCATAGCAACGAGAGG 57.477 50.000 0.00 0.00 43.62 3.69
7 8 3.715495 AGAAGATGCATAGCAACGAGAG 58.285 45.455 0.00 0.00 43.62 3.20
8 9 3.808466 AGAAGATGCATAGCAACGAGA 57.192 42.857 0.00 0.00 43.62 4.04
9 10 4.864633 TCTAGAAGATGCATAGCAACGAG 58.135 43.478 0.00 0.00 43.62 4.18
10 11 4.918810 TCTAGAAGATGCATAGCAACGA 57.081 40.909 0.00 0.00 43.62 3.85
11 12 6.616017 TCTATCTAGAAGATGCATAGCAACG 58.384 40.000 0.00 0.00 43.62 4.10
12 13 8.469200 AGATCTATCTAGAAGATGCATAGCAAC 58.531 37.037 17.03 0.00 37.77 4.17
13 14 8.592529 AGATCTATCTAGAAGATGCATAGCAA 57.407 34.615 17.03 0.00 37.77 3.91
14 15 8.468399 CAAGATCTATCTAGAAGATGCATAGCA 58.532 37.037 17.03 0.00 38.57 3.49
15 16 7.436080 GCAAGATCTATCTAGAAGATGCATAGC 59.564 40.741 17.03 11.67 37.63 2.97
16 17 7.644945 CGCAAGATCTATCTAGAAGATGCATAG 59.355 40.741 17.03 5.41 37.60 2.23
17 18 7.121907 ACGCAAGATCTATCTAGAAGATGCATA 59.878 37.037 17.03 0.00 37.60 3.14
18 19 6.071447 ACGCAAGATCTATCTAGAAGATGCAT 60.071 38.462 17.03 0.00 37.60 3.96
19 20 5.242615 ACGCAAGATCTATCTAGAAGATGCA 59.757 40.000 17.03 0.00 37.60 3.96
20 21 5.572511 CACGCAAGATCTATCTAGAAGATGC 59.427 44.000 17.03 15.04 36.70 3.91
21 22 6.907741 TCACGCAAGATCTATCTAGAAGATG 58.092 40.000 17.03 9.37 36.70 2.90
22 23 6.349280 GCTCACGCAAGATCTATCTAGAAGAT 60.349 42.308 13.81 13.81 38.77 2.40
23 24 5.049060 GCTCACGCAAGATCTATCTAGAAGA 60.049 44.000 0.00 1.80 43.62 2.87
24 25 5.153513 GCTCACGCAAGATCTATCTAGAAG 58.846 45.833 0.00 0.00 43.62 2.85
25 26 4.319839 CGCTCACGCAAGATCTATCTAGAA 60.320 45.833 0.00 0.00 43.62 2.10
26 27 3.187432 CGCTCACGCAAGATCTATCTAGA 59.813 47.826 0.00 0.00 43.62 2.43
27 28 3.058570 ACGCTCACGCAAGATCTATCTAG 60.059 47.826 0.00 0.00 45.53 2.43
28 29 2.879026 ACGCTCACGCAAGATCTATCTA 59.121 45.455 0.00 0.00 45.53 1.98
29 30 1.678627 ACGCTCACGCAAGATCTATCT 59.321 47.619 0.00 0.00 45.53 1.98
30 31 2.126914 ACGCTCACGCAAGATCTATC 57.873 50.000 0.00 0.00 45.53 2.08
31 32 2.030717 CCTACGCTCACGCAAGATCTAT 60.031 50.000 0.00 0.00 45.53 1.98
32 33 1.333931 CCTACGCTCACGCAAGATCTA 59.666 52.381 0.00 0.00 45.53 1.98
33 34 0.101399 CCTACGCTCACGCAAGATCT 59.899 55.000 0.00 0.00 45.53 2.75
34 35 0.100682 TCCTACGCTCACGCAAGATC 59.899 55.000 0.00 0.00 45.53 2.75
35 36 0.530744 TTCCTACGCTCACGCAAGAT 59.469 50.000 0.00 0.00 45.53 2.40
36 37 0.315886 TTTCCTACGCTCACGCAAGA 59.684 50.000 0.00 0.00 45.53 3.02
37 38 1.359848 ATTTCCTACGCTCACGCAAG 58.640 50.000 0.00 0.00 45.53 4.01
38 39 1.803334 AATTTCCTACGCTCACGCAA 58.197 45.000 0.00 0.00 45.53 4.85
39 40 1.803334 AAATTTCCTACGCTCACGCA 58.197 45.000 0.00 0.00 45.53 5.24
40 41 2.894307 AAAATTTCCTACGCTCACGC 57.106 45.000 0.00 0.00 45.53 5.34
42 43 7.949962 GCAATTTTAAAAATTTCCTACGCTCAC 59.050 33.333 4.44 0.00 0.00 3.51
43 44 7.653713 TGCAATTTTAAAAATTTCCTACGCTCA 59.346 29.630 4.44 0.00 0.00 4.26
44 45 8.013236 TGCAATTTTAAAAATTTCCTACGCTC 57.987 30.769 4.44 0.00 0.00 5.03
45 46 7.954788 TGCAATTTTAAAAATTTCCTACGCT 57.045 28.000 4.44 0.00 0.00 5.07
46 47 7.216130 GCATGCAATTTTAAAAATTTCCTACGC 59.784 33.333 14.21 0.00 0.00 4.42
47 48 8.442384 AGCATGCAATTTTAAAAATTTCCTACG 58.558 29.630 21.98 0.00 0.00 3.51
50 51 8.442384 CGTAGCATGCAATTTTAAAAATTTCCT 58.558 29.630 21.98 0.00 0.00 3.36
51 52 8.227119 ACGTAGCATGCAATTTTAAAAATTTCC 58.773 29.630 21.98 0.00 0.00 3.13
52 53 9.592720 AACGTAGCATGCAATTTTAAAAATTTC 57.407 25.926 21.98 0.00 0.00 2.17
53 54 9.592720 GAACGTAGCATGCAATTTTAAAAATTT 57.407 25.926 21.98 0.00 0.00 1.82
54 55 8.227119 GGAACGTAGCATGCAATTTTAAAAATT 58.773 29.630 21.98 0.00 0.00 1.82
55 56 7.148490 GGGAACGTAGCATGCAATTTTAAAAAT 60.148 33.333 21.98 0.00 0.00 1.82
56 57 6.146347 GGGAACGTAGCATGCAATTTTAAAAA 59.854 34.615 21.98 0.00 0.00 1.94
57 58 5.635700 GGGAACGTAGCATGCAATTTTAAAA 59.364 36.000 21.98 2.51 0.00 1.52
58 59 5.047660 AGGGAACGTAGCATGCAATTTTAAA 60.048 36.000 21.98 0.00 0.00 1.52
59 60 4.461081 AGGGAACGTAGCATGCAATTTTAA 59.539 37.500 21.98 0.00 0.00 1.52
60 61 4.013728 AGGGAACGTAGCATGCAATTTTA 58.986 39.130 21.98 0.00 0.00 1.52
61 62 2.825532 AGGGAACGTAGCATGCAATTTT 59.174 40.909 21.98 7.41 0.00 1.82
62 63 2.446435 AGGGAACGTAGCATGCAATTT 58.554 42.857 21.98 7.02 0.00 1.82
63 64 2.128771 AGGGAACGTAGCATGCAATT 57.871 45.000 21.98 7.96 0.00 2.32
64 65 2.943033 GTTAGGGAACGTAGCATGCAAT 59.057 45.455 21.98 1.90 30.48 3.56
65 66 2.289756 TGTTAGGGAACGTAGCATGCAA 60.290 45.455 21.98 0.00 35.19 4.08
66 67 1.276705 TGTTAGGGAACGTAGCATGCA 59.723 47.619 21.98 2.77 35.19 3.96
67 68 1.933853 CTGTTAGGGAACGTAGCATGC 59.066 52.381 10.51 10.51 39.01 4.06
68 69 3.520290 TCTGTTAGGGAACGTAGCATG 57.480 47.619 0.00 0.00 39.01 4.06
69 70 4.755266 ATTCTGTTAGGGAACGTAGCAT 57.245 40.909 0.00 0.00 39.01 3.79
70 71 4.546829 AATTCTGTTAGGGAACGTAGCA 57.453 40.909 0.00 0.00 37.56 3.49
71 72 4.507021 GCTAATTCTGTTAGGGAACGTAGC 59.493 45.833 0.00 0.00 38.51 3.58
72 73 5.657474 TGCTAATTCTGTTAGGGAACGTAG 58.343 41.667 0.00 0.00 38.51 3.51
73 74 5.664294 TGCTAATTCTGTTAGGGAACGTA 57.336 39.130 0.00 0.00 38.51 3.57
74 75 4.546829 TGCTAATTCTGTTAGGGAACGT 57.453 40.909 0.00 0.00 38.51 3.99
75 76 5.873179 TTTGCTAATTCTGTTAGGGAACG 57.127 39.130 0.00 0.00 38.51 3.95
76 77 7.826690 TGATTTTGCTAATTCTGTTAGGGAAC 58.173 34.615 4.80 0.00 36.00 3.62
77 78 8.415950 TTGATTTTGCTAATTCTGTTAGGGAA 57.584 30.769 4.80 0.00 0.00 3.97
78 79 7.122650 CCTTGATTTTGCTAATTCTGTTAGGGA 59.877 37.037 4.80 0.00 0.00 4.20
79 80 7.260603 CCTTGATTTTGCTAATTCTGTTAGGG 58.739 38.462 4.80 0.00 0.00 3.53
80 81 6.753744 GCCTTGATTTTGCTAATTCTGTTAGG 59.246 38.462 4.80 0.00 0.00 2.69
81 82 7.274250 GTGCCTTGATTTTGCTAATTCTGTTAG 59.726 37.037 4.80 0.00 0.00 2.34
82 83 7.039784 AGTGCCTTGATTTTGCTAATTCTGTTA 60.040 33.333 4.80 0.00 0.00 2.41
83 84 5.928264 GTGCCTTGATTTTGCTAATTCTGTT 59.072 36.000 4.80 0.00 0.00 3.16
84 85 5.244626 AGTGCCTTGATTTTGCTAATTCTGT 59.755 36.000 4.80 0.00 0.00 3.41
85 86 5.717119 AGTGCCTTGATTTTGCTAATTCTG 58.283 37.500 4.80 0.00 0.00 3.02
109 110 4.697352 CCTTGGTGGACAAAGAGTAATCTG 59.303 45.833 0.00 0.00 38.91 2.90
142 143 4.937201 TCGTGTGAGCATGAATATACCT 57.063 40.909 0.00 0.00 37.67 3.08
144 145 6.589830 AGTTTCGTGTGAGCATGAATATAC 57.410 37.500 0.00 0.54 44.07 1.47
145 146 6.416750 CGTAGTTTCGTGTGAGCATGAATATA 59.583 38.462 0.00 0.00 44.07 0.86
146 147 5.232202 CGTAGTTTCGTGTGAGCATGAATAT 59.768 40.000 0.00 0.00 44.07 1.28
147 148 4.561213 CGTAGTTTCGTGTGAGCATGAATA 59.439 41.667 0.00 0.00 44.07 1.75
152 153 2.596452 CTCGTAGTTTCGTGTGAGCAT 58.404 47.619 0.00 0.00 0.00 3.79
178 179 4.566907 GGTTCTTTGCAGGGATAAGGTACA 60.567 45.833 0.00 0.00 0.00 2.90
210 211 1.256812 GTGGTTGGCTATTGGTGCTT 58.743 50.000 0.00 0.00 0.00 3.91
216 217 1.472082 TGATTGCGTGGTTGGCTATTG 59.528 47.619 0.00 0.00 0.00 1.90
229 230 2.033832 GTGTTTGTTTGGCTTGATTGCG 60.034 45.455 0.00 0.00 0.00 4.85
230 231 3.197265 AGTGTTTGTTTGGCTTGATTGC 58.803 40.909 0.00 0.00 0.00 3.56
231 232 5.799681 AAAGTGTTTGTTTGGCTTGATTG 57.200 34.783 0.00 0.00 0.00 2.67
232 233 6.872920 TCTAAAGTGTTTGTTTGGCTTGATT 58.127 32.000 0.00 0.00 0.00 2.57
233 234 6.463995 TCTAAAGTGTTTGTTTGGCTTGAT 57.536 33.333 0.00 0.00 0.00 2.57
234 235 5.906113 TCTAAAGTGTTTGTTTGGCTTGA 57.094 34.783 0.00 0.00 0.00 3.02
235 236 7.169140 GGTTATCTAAAGTGTTTGTTTGGCTTG 59.831 37.037 0.00 0.00 0.00 4.01
254 255 6.828785 AGTGTGAAAGTGAAAACAGGTTATCT 59.171 34.615 0.00 0.00 0.00 1.98
255 256 6.912591 CAGTGTGAAAGTGAAAACAGGTTATC 59.087 38.462 0.00 0.00 0.00 1.75
261 262 8.909708 TTTTATCAGTGTGAAAGTGAAAACAG 57.090 30.769 0.00 0.00 41.61 3.16
297 1377 4.386951 TACCGTGCGCTGCCATGT 62.387 61.111 9.73 0.00 0.00 3.21
298 1378 3.864686 GTACCGTGCGCTGCCATG 61.865 66.667 9.73 0.00 0.00 3.66
299 1379 3.605749 AAGTACCGTGCGCTGCCAT 62.606 57.895 9.73 0.00 0.00 4.40
308 1388 6.292381 GCTTCATCTATGCTAAAAGTACCGTG 60.292 42.308 0.00 0.00 0.00 4.94
309 1389 5.753921 GCTTCATCTATGCTAAAAGTACCGT 59.246 40.000 0.00 0.00 0.00 4.83
310 1390 5.107837 CGCTTCATCTATGCTAAAAGTACCG 60.108 44.000 0.00 0.00 0.00 4.02
311 1391 5.983720 TCGCTTCATCTATGCTAAAAGTACC 59.016 40.000 0.00 0.00 0.00 3.34
323 1403 6.202954 CGAAAAATAACCCTCGCTTCATCTAT 59.797 38.462 0.00 0.00 0.00 1.98
335 1415 4.628766 GCGAGACTAACGAAAAATAACCCT 59.371 41.667 0.00 0.00 0.00 4.34
341 1421 2.665052 GTCGGCGAGACTAACGAAAAAT 59.335 45.455 11.20 0.00 46.13 1.82
368 1448 5.888982 ACCTAGTTTCAGAGAGGTTTTGA 57.111 39.130 0.00 0.00 39.32 2.69
396 1476 5.416326 TCGATACAATTGGGTGGTTTTAAGG 59.584 40.000 10.83 0.00 0.00 2.69
401 1481 5.013547 TGATTCGATACAATTGGGTGGTTT 58.986 37.500 10.83 0.00 0.00 3.27
411 1491 3.181475 ACGTGGCTCTGATTCGATACAAT 60.181 43.478 0.00 0.00 0.00 2.71
416 1496 0.817654 TCACGTGGCTCTGATTCGAT 59.182 50.000 17.00 0.00 0.00 3.59
418 1498 0.171231 TCTCACGTGGCTCTGATTCG 59.829 55.000 17.00 0.00 0.00 3.34
425 1505 1.066303 CCATACTCTCTCACGTGGCTC 59.934 57.143 17.00 0.00 0.00 4.70
431 1511 1.609555 GCCTACCCATACTCTCTCACG 59.390 57.143 0.00 0.00 0.00 4.35
435 1515 1.775459 TCTCGCCTACCCATACTCTCT 59.225 52.381 0.00 0.00 0.00 3.10
447 1527 2.233305 AAGAAACCCTCTCTCGCCTA 57.767 50.000 0.00 0.00 31.02 3.93
569 1650 7.171337 GTGGTTTTCGATGGTACTACTTTTGTA 59.829 37.037 0.00 0.00 0.00 2.41
576 1657 5.640357 TGAATGTGGTTTTCGATGGTACTAC 59.360 40.000 0.00 0.00 0.00 2.73
582 1663 7.257003 TCATATTTGAATGTGGTTTTCGATGG 58.743 34.615 0.00 0.00 0.00 3.51
687 1768 1.471676 CGTCTGGGATTACTGGTGCTC 60.472 57.143 0.00 0.00 0.00 4.26
688 1769 0.537188 CGTCTGGGATTACTGGTGCT 59.463 55.000 0.00 0.00 0.00 4.40
690 1771 2.496070 TCTTCGTCTGGGATTACTGGTG 59.504 50.000 0.00 0.00 0.00 4.17
691 1772 2.816411 TCTTCGTCTGGGATTACTGGT 58.184 47.619 0.00 0.00 0.00 4.00
699 1780 5.363562 TGTAGTACTATCTTCGTCTGGGA 57.636 43.478 5.75 0.00 0.00 4.37
701 1782 7.536855 ACTTTTGTAGTACTATCTTCGTCTGG 58.463 38.462 5.75 0.00 34.56 3.86
731 1838 8.515414 GGCTAAGTGTCATTTCTTTTTACATCT 58.485 33.333 0.00 0.00 0.00 2.90
746 1853 1.000506 GGACTGAACGGCTAAGTGTCA 59.999 52.381 0.00 0.00 0.00 3.58
747 1854 1.272769 AGGACTGAACGGCTAAGTGTC 59.727 52.381 0.00 0.00 0.00 3.67
748 1855 1.272769 GAGGACTGAACGGCTAAGTGT 59.727 52.381 0.00 0.00 0.00 3.55
749 1856 1.272490 TGAGGACTGAACGGCTAAGTG 59.728 52.381 0.00 0.00 0.00 3.16
750 1857 1.629043 TGAGGACTGAACGGCTAAGT 58.371 50.000 0.00 0.00 0.00 2.24
751 1858 2.796383 CGATGAGGACTGAACGGCTAAG 60.796 54.545 0.00 0.00 0.00 2.18
753 1860 0.738975 CGATGAGGACTGAACGGCTA 59.261 55.000 0.00 0.00 0.00 3.93
772 2087 0.320160 GTACACTTCGGGGTCACACC 60.320 60.000 0.00 0.00 37.60 4.16
830 2145 1.062488 AGGAGGTTGACTTGGGCAGT 61.062 55.000 0.00 0.00 39.07 4.40
831 2146 0.984230 TAGGAGGTTGACTTGGGCAG 59.016 55.000 0.00 0.00 0.00 4.85
1164 2479 1.369321 GGAGAGGATGATGCGGACC 59.631 63.158 0.00 0.00 0.00 4.46
1233 2548 1.153804 GTCGGCGAGGAGGAAGAAC 60.154 63.158 11.20 0.00 0.00 3.01
1393 2708 2.354729 CCCGCCCTCCATGTCAAA 59.645 61.111 0.00 0.00 0.00 2.69
1394 2709 4.424711 GCCCGCCCTCCATGTCAA 62.425 66.667 0.00 0.00 0.00 3.18
1623 2941 3.372554 GAGCGTGAGGTAGGCCCAC 62.373 68.421 0.00 0.00 45.11 4.61
1996 3314 1.859564 CGACGTCGACGAAGAGCAG 60.860 63.158 41.52 19.85 43.02 4.24
2374 3692 3.238441 TGTCGCGGAAAATTACAAATGC 58.762 40.909 6.13 0.00 0.00 3.56
2392 3710 1.855213 TTGCAGCTCACGGCATTGTC 61.855 55.000 0.00 0.00 46.55 3.18
2414 3732 1.744798 CGCCAAGAGAGCAATCATGGA 60.745 52.381 14.48 0.00 39.85 3.41
2530 3850 8.163408 ACAAATATAATCTTATACAGCCCTGCA 58.837 33.333 0.00 0.00 0.00 4.41
2564 3884 4.558496 CGGCAAAATTTGAAGCTACAAGGA 60.558 41.667 10.26 0.00 0.00 3.36
2628 3948 1.589779 GTGTGCACTTTTCAAGCAAGC 59.410 47.619 19.41 0.00 40.35 4.01
2646 3966 3.440173 ACACCTGCTCAATTAATTCCGTG 59.560 43.478 0.00 1.91 0.00 4.94
2648 3968 4.701956 AACACCTGCTCAATTAATTCCG 57.298 40.909 0.00 0.00 0.00 4.30
2713 4034 7.149569 TGGTCAAAGAATGAAATGACTGATC 57.850 36.000 4.94 0.00 40.50 2.92
2739 4060 6.877236 ACAGACAAACAAAAGGATCAACAAT 58.123 32.000 0.00 0.00 0.00 2.71
2740 4061 6.279513 ACAGACAAACAAAAGGATCAACAA 57.720 33.333 0.00 0.00 0.00 2.83
2743 4064 7.757624 GTGTTAACAGACAAACAAAAGGATCAA 59.242 33.333 8.98 0.00 37.35 2.57
2752 4073 4.031991 CGAGTCGTGTTAACAGACAAACAA 59.968 41.667 26.08 0.00 37.35 2.83
2770 4091 4.017380 AGATACGACAACACATCGAGTC 57.983 45.455 0.78 0.00 42.25 3.36
2774 4095 6.993175 ATCATAAGATACGACAACACATCG 57.007 37.500 0.00 0.00 45.17 3.84
2781 4102 6.112734 AGTGGCAAATCATAAGATACGACAA 58.887 36.000 0.00 0.00 33.08 3.18
2783 4104 5.753438 TGAGTGGCAAATCATAAGATACGAC 59.247 40.000 0.00 0.00 33.08 4.34
2784 4105 5.912892 TGAGTGGCAAATCATAAGATACGA 58.087 37.500 0.00 0.00 33.08 3.43
2785 4106 6.791887 ATGAGTGGCAAATCATAAGATACG 57.208 37.500 1.22 0.00 34.42 3.06
2810 4134 3.013921 TGAATAGTGGGATTTCCGTTGC 58.986 45.455 0.00 0.00 38.76 4.17
2821 4145 8.971073 GGATAATCCCATAAAATGAATAGTGGG 58.029 37.037 1.82 1.82 46.05 4.61
3183 4512 4.749048 AGACCTCTTTTCCCTTCCATTT 57.251 40.909 0.00 0.00 0.00 2.32
3184 4513 4.852697 AGTAGACCTCTTTTCCCTTCCATT 59.147 41.667 0.00 0.00 0.00 3.16
3185 4514 4.439860 AGTAGACCTCTTTTCCCTTCCAT 58.560 43.478 0.00 0.00 0.00 3.41
3186 4515 3.870559 AGTAGACCTCTTTTCCCTTCCA 58.129 45.455 0.00 0.00 0.00 3.53
3187 4516 4.286291 TCAAGTAGACCTCTTTTCCCTTCC 59.714 45.833 0.00 0.00 0.00 3.46
3188 4517 5.485209 TCAAGTAGACCTCTTTTCCCTTC 57.515 43.478 0.00 0.00 0.00 3.46
3189 4518 5.607171 TCTTCAAGTAGACCTCTTTTCCCTT 59.393 40.000 0.00 0.00 0.00 3.95
3190 4519 5.155905 TCTTCAAGTAGACCTCTTTTCCCT 58.844 41.667 0.00 0.00 0.00 4.20
3191 4520 5.483811 CTCTTCAAGTAGACCTCTTTTCCC 58.516 45.833 0.00 0.00 0.00 3.97
3192 4521 5.246429 TCCTCTTCAAGTAGACCTCTTTTCC 59.754 44.000 0.00 0.00 0.00 3.13
3193 4522 6.347859 TCCTCTTCAAGTAGACCTCTTTTC 57.652 41.667 0.00 0.00 0.00 2.29
3194 4523 6.749036 TTCCTCTTCAAGTAGACCTCTTTT 57.251 37.500 0.00 0.00 0.00 2.27
3195 4524 6.749036 TTTCCTCTTCAAGTAGACCTCTTT 57.251 37.500 0.00 0.00 0.00 2.52
3196 4525 6.742926 GCTTTTCCTCTTCAAGTAGACCTCTT 60.743 42.308 0.00 0.00 0.00 2.85
3197 4526 5.279758 GCTTTTCCTCTTCAAGTAGACCTCT 60.280 44.000 0.00 0.00 0.00 3.69
3198 4527 4.932799 GCTTTTCCTCTTCAAGTAGACCTC 59.067 45.833 0.00 0.00 0.00 3.85
3199 4528 4.263112 GGCTTTTCCTCTTCAAGTAGACCT 60.263 45.833 0.00 0.00 0.00 3.85
3200 4529 4.004314 GGCTTTTCCTCTTCAAGTAGACC 58.996 47.826 0.00 0.00 0.00 3.85
3201 4530 4.642429 TGGCTTTTCCTCTTCAAGTAGAC 58.358 43.478 0.00 0.00 35.26 2.59
3202 4531 4.263068 CCTGGCTTTTCCTCTTCAAGTAGA 60.263 45.833 0.00 0.00 35.26 2.59
3203 4532 4.006319 CCTGGCTTTTCCTCTTCAAGTAG 58.994 47.826 0.00 0.00 35.26 2.57
3204 4533 3.394606 ACCTGGCTTTTCCTCTTCAAGTA 59.605 43.478 0.00 0.00 35.26 2.24
3205 4534 2.175715 ACCTGGCTTTTCCTCTTCAAGT 59.824 45.455 0.00 0.00 35.26 3.16
3206 4535 2.555757 CACCTGGCTTTTCCTCTTCAAG 59.444 50.000 0.00 0.00 35.26 3.02
3207 4536 2.091885 ACACCTGGCTTTTCCTCTTCAA 60.092 45.455 0.00 0.00 35.26 2.69
3208 4537 1.494721 ACACCTGGCTTTTCCTCTTCA 59.505 47.619 0.00 0.00 35.26 3.02
3209 4538 2.155279 GACACCTGGCTTTTCCTCTTC 58.845 52.381 0.00 0.00 35.26 2.87
3210 4539 1.777272 AGACACCTGGCTTTTCCTCTT 59.223 47.619 0.00 0.00 35.26 2.85
3211 4540 1.439543 AGACACCTGGCTTTTCCTCT 58.560 50.000 0.00 0.00 35.26 3.69
3212 4541 3.418684 TTAGACACCTGGCTTTTCCTC 57.581 47.619 0.00 0.00 33.72 3.71
3213 4542 3.138468 AGTTTAGACACCTGGCTTTTCCT 59.862 43.478 0.00 0.00 33.72 3.36
3214 4543 3.487372 AGTTTAGACACCTGGCTTTTCC 58.513 45.455 0.00 0.00 33.72 3.13
3215 4544 4.154375 GCTAGTTTAGACACCTGGCTTTTC 59.846 45.833 0.00 0.00 33.72 2.29
3216 4545 4.072839 GCTAGTTTAGACACCTGGCTTTT 58.927 43.478 0.00 0.00 33.72 2.27
3217 4546 3.328050 AGCTAGTTTAGACACCTGGCTTT 59.672 43.478 0.00 0.00 39.64 3.51
3218 4547 2.907042 AGCTAGTTTAGACACCTGGCTT 59.093 45.455 0.00 0.00 39.64 4.35
3219 4548 2.498078 GAGCTAGTTTAGACACCTGGCT 59.502 50.000 0.00 0.00 44.42 4.75
3220 4549 2.418884 GGAGCTAGTTTAGACACCTGGC 60.419 54.545 0.00 0.00 33.39 4.85
3221 4550 2.832129 TGGAGCTAGTTTAGACACCTGG 59.168 50.000 0.00 0.00 0.00 4.45
3222 4551 4.160439 TCATGGAGCTAGTTTAGACACCTG 59.840 45.833 0.00 0.00 0.00 4.00
3223 4552 4.353777 TCATGGAGCTAGTTTAGACACCT 58.646 43.478 0.00 0.00 0.00 4.00
3224 4553 4.737855 TCATGGAGCTAGTTTAGACACC 57.262 45.455 0.00 0.00 0.00 4.16
3225 4554 5.967088 TCTTCATGGAGCTAGTTTAGACAC 58.033 41.667 0.00 0.00 0.00 3.67
3226 4555 6.605471 TTCTTCATGGAGCTAGTTTAGACA 57.395 37.500 0.00 0.00 0.00 3.41
3227 4556 6.536941 CCTTTCTTCATGGAGCTAGTTTAGAC 59.463 42.308 0.00 0.00 0.00 2.59
3228 4557 6.213600 ACCTTTCTTCATGGAGCTAGTTTAGA 59.786 38.462 0.00 0.00 0.00 2.10
3229 4558 6.410540 ACCTTTCTTCATGGAGCTAGTTTAG 58.589 40.000 0.00 0.00 0.00 1.85
3230 4559 6.213600 AGACCTTTCTTCATGGAGCTAGTTTA 59.786 38.462 0.00 0.00 0.00 2.01
3231 4560 5.013599 AGACCTTTCTTCATGGAGCTAGTTT 59.986 40.000 0.00 0.00 0.00 2.66
3232 4561 4.534103 AGACCTTTCTTCATGGAGCTAGTT 59.466 41.667 0.00 0.00 0.00 2.24
3233 4562 4.081198 CAGACCTTTCTTCATGGAGCTAGT 60.081 45.833 0.00 0.00 0.00 2.57
3234 4563 4.081198 ACAGACCTTTCTTCATGGAGCTAG 60.081 45.833 0.00 0.00 0.00 3.42
3235 4564 3.840666 ACAGACCTTTCTTCATGGAGCTA 59.159 43.478 0.00 0.00 0.00 3.32
3236 4565 2.641815 ACAGACCTTTCTTCATGGAGCT 59.358 45.455 0.00 0.00 0.00 4.09
3237 4566 3.064900 ACAGACCTTTCTTCATGGAGC 57.935 47.619 0.00 0.00 0.00 4.70
3238 4567 4.645535 TGAACAGACCTTTCTTCATGGAG 58.354 43.478 0.00 0.00 0.00 3.86
3239 4568 4.705110 TGAACAGACCTTTCTTCATGGA 57.295 40.909 0.00 0.00 0.00 3.41
3240 4569 4.217118 CCTTGAACAGACCTTTCTTCATGG 59.783 45.833 0.00 0.00 32.03 3.66
3241 4570 5.065914 TCCTTGAACAGACCTTTCTTCATG 58.934 41.667 0.00 0.00 0.00 3.07
3242 4571 5.072329 TCTCCTTGAACAGACCTTTCTTCAT 59.928 40.000 0.00 0.00 0.00 2.57
3243 4572 4.408921 TCTCCTTGAACAGACCTTTCTTCA 59.591 41.667 0.00 0.00 0.00 3.02
3244 4573 4.962155 TCTCCTTGAACAGACCTTTCTTC 58.038 43.478 0.00 0.00 0.00 2.87
3245 4574 5.373812 TTCTCCTTGAACAGACCTTTCTT 57.626 39.130 0.00 0.00 0.00 2.52
3263 4592 2.106684 ACTGGGGAAAAGGACTGTTCTC 59.893 50.000 2.52 0.00 0.00 2.87
3264 4593 2.136026 ACTGGGGAAAAGGACTGTTCT 58.864 47.619 2.52 0.00 0.00 3.01
3265 4594 2.230660 CACTGGGGAAAAGGACTGTTC 58.769 52.381 0.00 0.00 0.00 3.18
3266 4595 1.754201 GCACTGGGGAAAAGGACTGTT 60.754 52.381 0.00 0.00 0.00 3.16
3267 4596 0.178990 GCACTGGGGAAAAGGACTGT 60.179 55.000 0.00 0.00 0.00 3.55
3268 4597 0.895559 GGCACTGGGGAAAAGGACTG 60.896 60.000 0.00 0.00 0.00 3.51
3269 4598 1.068352 AGGCACTGGGGAAAAGGACT 61.068 55.000 0.00 0.00 37.18 3.85
3270 4599 0.178961 AAGGCACTGGGGAAAAGGAC 60.179 55.000 0.00 0.00 40.86 3.85
3271 4600 0.178964 CAAGGCACTGGGGAAAAGGA 60.179 55.000 0.00 0.00 40.86 3.36
3272 4601 0.178964 TCAAGGCACTGGGGAAAAGG 60.179 55.000 0.00 0.00 40.86 3.11
3273 4602 1.703411 TTCAAGGCACTGGGGAAAAG 58.297 50.000 0.00 0.00 40.86 2.27
3274 4603 1.760029 GTTTCAAGGCACTGGGGAAAA 59.240 47.619 0.00 0.00 40.86 2.29
3276 4605 0.260230 TGTTTCAAGGCACTGGGGAA 59.740 50.000 0.00 0.00 40.86 3.97
3278 4607 0.890683 GATGTTTCAAGGCACTGGGG 59.109 55.000 0.00 0.00 40.86 4.96
3279 4608 1.915141 AGATGTTTCAAGGCACTGGG 58.085 50.000 0.00 0.00 40.86 4.45
3288 5224 9.177608 CATTAACCTATCCAGAAGATGTTTCAA 57.822 33.333 0.00 0.00 36.33 2.69
3347 5284 4.441079 GGATCTCAAACAATGCCCAATCAG 60.441 45.833 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.