Multiple sequence alignment - TraesCS2D01G155200

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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 TraesCS2D01G155200 chr2D 100.000 4805 0 0 666 5470 98903645 98908449 0.000000e+00 8874.0
1 TraesCS2D01G155200 chr2D 100.000 285 0 0 1 285 98902980 98903264 1.350000e-145 527.0
2 TraesCS2D01G155200 chr2A 94.704 3059 106 27 666 3693 97840769 97843802 0.000000e+00 4700.0
3 TraesCS2D01G155200 chr2A 92.185 1625 69 25 3760 5349 97843807 97845408 0.000000e+00 2244.0
4 TraesCS2D01G155200 chr2A 90.043 231 19 3 1 227 97840400 97840630 4.140000e-76 296.0
5 TraesCS2D01G155200 chr2A 90.909 88 7 1 4743 4830 364478313 364478399 3.460000e-22 117.0
6 TraesCS2D01G155200 chr2B 91.779 2068 93 28 3288 5306 150598453 150600492 0.000000e+00 2806.0
7 TraesCS2D01G155200 chr2B 96.225 1404 39 4 1900 3291 150597009 150598410 0.000000e+00 2287.0
8 TraesCS2D01G155200 chr2B 92.857 980 37 10 929 1903 150595802 150596753 0.000000e+00 1391.0
9 TraesCS2D01G155200 chr2B 91.667 240 16 2 666 901 150595303 150595542 4.080000e-86 329.0
10 TraesCS2D01G155200 chr2B 95.652 115 3 1 1 113 150585046 150585160 3.370000e-42 183.0
11 TraesCS2D01G155200 chr2B 87.179 117 12 2 5350 5463 675291828 675291944 4.450000e-26 130.0
12 TraesCS2D01G155200 chr3D 77.200 1193 155 51 1725 2889 608300355 608299252 6.100000e-164 588.0
13 TraesCS2D01G155200 chr3D 89.773 88 8 1 4743 4830 13182039 13182125 1.610000e-20 111.0
14 TraesCS2D01G155200 chr5A 83.916 572 81 7 1888 2457 3316399 3316961 2.240000e-148 536.0
15 TraesCS2D01G155200 chr5A 87.931 174 16 3 2367 2540 3316970 3317138 3.340000e-47 200.0
16 TraesCS2D01G155200 chr5D 83.649 581 77 12 1891 2468 9918652 9918087 1.040000e-146 531.0
17 TraesCS2D01G155200 chr1D 78.120 681 107 23 1752 2428 392565223 392564581 1.430000e-105 394.0
18 TraesCS2D01G155200 chr1D 81.265 427 52 11 2477 2889 392564574 392564162 2.460000e-83 320.0
19 TraesCS2D01G155200 chr1D 89.344 122 13 0 5349 5470 307837729 307837850 2.640000e-33 154.0
20 TraesCS2D01G155200 chr7A 86.782 174 17 4 2367 2540 165002152 165001985 7.230000e-44 189.0
21 TraesCS2D01G155200 chr7A 90.909 88 7 1 4743 4830 573432705 573432791 3.460000e-22 117.0
22 TraesCS2D01G155200 chr7D 92.623 122 8 1 5350 5470 384054793 384054914 2.030000e-39 174.0
23 TraesCS2D01G155200 chr7D 89.773 88 8 1 4743 4830 506006952 506007038 1.610000e-20 111.0
24 TraesCS2D01G155200 chr1B 86.179 123 16 1 5349 5470 483963011 483962889 1.240000e-26 132.0
25 TraesCS2D01G155200 chr6B 85.714 126 14 2 5349 5470 641277899 641277774 4.450000e-26 130.0
26 TraesCS2D01G155200 chr6B 90.909 88 7 1 4743 4830 284652753 284652667 3.460000e-22 117.0
27 TraesCS2D01G155200 chr6B 83.036 112 15 4 5354 5462 688043678 688043568 1.250000e-16 99.0
28 TraesCS2D01G155200 chr6B 82.456 114 17 3 5349 5459 679248527 679248640 4.510000e-16 97.1
29 TraesCS2D01G155200 chr4B 86.607 112 13 2 5350 5459 534272951 534272840 7.440000e-24 122.0
30 TraesCS2D01G155200 chr6D 89.888 89 8 1 4742 4830 7414613 7414526 4.480000e-21 113.0
31 TraesCS2D01G155200 chr7B 90.476 84 8 0 4743 4826 533775230 533775313 1.610000e-20 111.0
32 TraesCS2D01G155200 chr3B 81.197 117 20 2 5349 5465 622749974 622749860 5.830000e-15 93.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G155200 chr2D 98902980 98908449 5469 False 4700.500000 8874 100.000000 1 5470 2 chr2D.!!$F1 5469
1 TraesCS2D01G155200 chr2A 97840400 97845408 5008 False 2413.333333 4700 92.310667 1 5349 3 chr2A.!!$F2 5348
2 TraesCS2D01G155200 chr2B 150595303 150600492 5189 False 1703.250000 2806 93.132000 666 5306 4 chr2B.!!$F3 4640
3 TraesCS2D01G155200 chr3D 608299252 608300355 1103 True 588.000000 588 77.200000 1725 2889 1 chr3D.!!$R1 1164
4 TraesCS2D01G155200 chr5A 3316399 3317138 739 False 368.000000 536 85.923500 1888 2540 2 chr5A.!!$F1 652
5 TraesCS2D01G155200 chr5D 9918087 9918652 565 True 531.000000 531 83.649000 1891 2468 1 chr5D.!!$R1 577
6 TraesCS2D01G155200 chr1D 392564162 392565223 1061 True 357.000000 394 79.692500 1752 2889 2 chr1D.!!$R1 1137

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
687 692 1.395045 AAGCTCATCCGCGATCTGGA 61.395 55.000 8.23 6.07 40.46 3.86 F
1390 1640 0.593128 GACATGTTTTGGTGAGCGCT 59.407 50.000 11.27 11.27 0.00 5.92 F
2184 2702 0.685785 TGGCTTTGGGAGTGCAACAA 60.686 50.000 0.00 0.00 41.43 2.83 F
2232 2750 0.695803 AGCTTCCCCCAGGATTCGAT 60.696 55.000 0.00 0.00 43.54 3.59 F
3743 4444 1.201414 CGCCAGTTATTGTCCAAACCC 59.799 52.381 0.00 0.00 0.00 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 2597 0.179108 CGTCCCGATTCCTCACTTCC 60.179 60.000 0.0 0.0 0.00 3.46 R
2232 2750 0.613260 CAAGGAACCCGTGGATCTCA 59.387 55.000 0.0 0.0 29.60 3.27 R
3755 4456 0.679505 AGTTAGGCACTGAACTCGCA 59.320 50.000 0.0 0.0 41.52 5.10 R
3756 4457 2.531206 CTAGTTAGGCACTGAACTCGC 58.469 52.381 0.0 0.0 41.52 5.03 R
5429 6187 0.109723 AGCCCTTTGACGGTAGCAAA 59.890 50.000 0.0 0.0 34.40 3.68 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
28 29 4.327357 CGTAGAATGCACCTTGAAGTAGTG 59.673 45.833 0.00 0.00 34.58 2.74
50 51 4.097741 TGGCAAAATTCTCATTGATACGGG 59.902 41.667 0.00 0.00 0.00 5.28
52 53 4.610945 CAAAATTCTCATTGATACGGGCC 58.389 43.478 0.00 0.00 0.00 5.80
70 71 5.479027 ACGGGCCTTATTGTAAAACAGATTT 59.521 36.000 0.84 0.00 34.92 2.17
113 117 9.492973 TTCATAGAATGCATCTTGAATTATCGA 57.507 29.630 0.00 0.00 39.71 3.59
114 118 9.662947 TCATAGAATGCATCTTGAATTATCGAT 57.337 29.630 0.00 2.16 39.71 3.59
133 137 6.313744 TCGATGAAATTCTAGCAGATACGA 57.686 37.500 0.00 0.00 0.00 3.43
143 147 4.974275 TCTAGCAGATACGAACGTTATTGC 59.026 41.667 0.00 12.01 0.00 3.56
148 152 5.737290 GCAGATACGAACGTTATTGCAAAAT 59.263 36.000 1.71 0.00 0.00 1.82
154 158 7.719689 ACGAACGTTATTGCAAAATAGATTG 57.280 32.000 1.71 0.00 0.00 2.67
186 190 5.420409 GGTGACCAAGTTCATAGAACCTAG 58.580 45.833 0.00 0.00 0.00 3.02
216 221 6.771267 ACCTAGACGGTTTTTCTTTCAAGAAT 59.229 34.615 2.83 0.00 46.37 2.40
222 227 7.712797 ACGGTTTTTCTTTCAAGAATGTACAT 58.287 30.769 1.41 1.41 43.92 2.29
231 236 9.897744 TCTTTCAAGAATGTACATTGATTGAAC 57.102 29.630 33.06 18.79 39.81 3.18
271 276 7.813852 ATATATTCCGTATTTGCGAAGAGAC 57.186 36.000 0.00 0.00 0.00 3.36
277 282 6.798482 TCCGTATTTGCGAAGAGACTAATTA 58.202 36.000 0.00 0.00 0.00 1.40
279 284 6.916387 CCGTATTTGCGAAGAGACTAATTAGA 59.084 38.462 19.38 0.00 0.00 2.10
283 288 8.723942 ATTTGCGAAGAGACTAATTAGACATT 57.276 30.769 19.38 11.36 0.00 2.71
687 692 1.395045 AAGCTCATCCGCGATCTGGA 61.395 55.000 8.23 6.07 40.46 3.86
698 703 3.382803 GATCTGGACCAGCTGCGCT 62.383 63.158 17.33 0.00 40.77 5.92
699 704 2.021068 GATCTGGACCAGCTGCGCTA 62.021 60.000 17.33 0.00 36.40 4.26
921 935 1.507141 CGCCTTAATTAGCCGCCTGG 61.507 60.000 0.00 0.00 38.77 4.45
1243 1489 2.190578 CCGCCATCCTCAAGGTCC 59.809 66.667 0.00 0.00 36.34 4.46
1244 1490 2.370445 CCGCCATCCTCAAGGTCCT 61.370 63.158 0.00 0.00 36.34 3.85
1340 1590 1.648467 GCCGTTGTCCTTGATGGCTC 61.648 60.000 0.00 0.00 43.17 4.70
1342 1592 0.670546 CGTTGTCCTTGATGGCTCGT 60.671 55.000 0.00 0.00 35.26 4.18
1380 1630 4.379394 CCCGTCGATGATTTGACATGTTTT 60.379 41.667 6.11 0.00 36.21 2.43
1390 1640 0.593128 GACATGTTTTGGTGAGCGCT 59.407 50.000 11.27 11.27 0.00 5.92
1425 1676 1.684248 GCTTGCTTGGGGAGATGATGT 60.684 52.381 0.00 0.00 0.00 3.06
1444 1695 6.472016 TGATGTTTTTGCTGTCTGTATCCTA 58.528 36.000 0.00 0.00 0.00 2.94
1448 1699 8.856153 TGTTTTTGCTGTCTGTATCCTAATTA 57.144 30.769 0.00 0.00 0.00 1.40
1449 1700 9.461312 TGTTTTTGCTGTCTGTATCCTAATTAT 57.539 29.630 0.00 0.00 0.00 1.28
1497 1752 6.262273 GGATCATTTTAAAAGGTCAGCGGATA 59.738 38.462 11.96 0.00 0.00 2.59
1524 1779 6.534475 TTGGTATATCTCCGTGTTTACTGT 57.466 37.500 0.00 0.00 0.00 3.55
1525 1780 6.534475 TGGTATATCTCCGTGTTTACTGTT 57.466 37.500 0.00 0.00 0.00 3.16
1526 1781 7.643569 TGGTATATCTCCGTGTTTACTGTTA 57.356 36.000 0.00 0.00 0.00 2.41
1527 1782 7.709947 TGGTATATCTCCGTGTTTACTGTTAG 58.290 38.462 0.00 0.00 0.00 2.34
1528 1783 7.144000 GGTATATCTCCGTGTTTACTGTTAGG 58.856 42.308 0.00 0.00 0.00 2.69
1529 1784 7.013655 GGTATATCTCCGTGTTTACTGTTAGGA 59.986 40.741 0.00 0.00 0.00 2.94
1530 1785 5.733620 ATCTCCGTGTTTACTGTTAGGAA 57.266 39.130 0.00 0.00 0.00 3.36
1557 1812 1.710013 TCGATTCGGTGTCAGCTTTC 58.290 50.000 6.18 0.00 0.00 2.62
1590 1845 4.371855 TCGAATGCGAAGAAGATACTGT 57.628 40.909 0.00 0.00 44.78 3.55
1591 1846 5.494632 TCGAATGCGAAGAAGATACTGTA 57.505 39.130 0.00 0.00 44.78 2.74
1592 1847 5.271625 TCGAATGCGAAGAAGATACTGTAC 58.728 41.667 0.00 0.00 44.78 2.90
1593 1848 5.066117 TCGAATGCGAAGAAGATACTGTACT 59.934 40.000 0.00 0.00 44.78 2.73
1594 1849 6.259387 TCGAATGCGAAGAAGATACTGTACTA 59.741 38.462 0.00 0.00 44.78 1.82
1671 1928 4.141620 ACTCTTGAGTGACCAACTGATGTT 60.142 41.667 2.11 0.00 40.07 2.71
1712 1969 8.397148 TCCTTTTTCATTTTCACTTCAATTTGC 58.603 29.630 0.00 0.00 0.00 3.68
1789 2046 3.699038 TCTTGCTTGCCAACTTGTTTACT 59.301 39.130 0.00 0.00 0.00 2.24
1790 2047 4.159506 TCTTGCTTGCCAACTTGTTTACTT 59.840 37.500 0.00 0.00 0.00 2.24
1791 2048 4.464069 TGCTTGCCAACTTGTTTACTTT 57.536 36.364 0.00 0.00 0.00 2.66
1940 2458 8.795786 TTCATTGAATAGTAAATATTTGCCGC 57.204 30.769 11.05 0.66 34.10 6.53
1941 2459 7.367285 TCATTGAATAGTAAATATTTGCCGCC 58.633 34.615 11.05 0.83 34.10 6.13
1977 2495 4.018960 ACAGCTGGATTTACTGATTCCTGT 60.019 41.667 19.93 0.00 35.38 4.00
1985 2503 6.127897 GGATTTACTGATTCCTGTCAAACTGG 60.128 42.308 0.00 0.00 38.41 4.00
2160 2678 1.673626 CGGCACAATAACGTGGTACCT 60.674 52.381 14.36 0.00 37.37 3.08
2184 2702 0.685785 TGGCTTTGGGAGTGCAACAA 60.686 50.000 0.00 0.00 41.43 2.83
2232 2750 0.695803 AGCTTCCCCCAGGATTCGAT 60.696 55.000 0.00 0.00 43.54 3.59
2971 3625 7.865875 TTTTCGTGGATTAAATCATGTGTTG 57.134 32.000 0.00 0.00 0.00 3.33
3069 3723 1.686052 TGGCCTCATTTGTTGTTGTCC 59.314 47.619 3.32 0.00 0.00 4.02
3071 3725 2.365293 GGCCTCATTTGTTGTTGTCCTT 59.635 45.455 0.00 0.00 0.00 3.36
3132 3786 3.808174 CACATCGCATCTTCATCTCATGT 59.192 43.478 0.00 0.00 0.00 3.21
3327 4027 8.904099 AAGAGTACACAAGCAGTTACTAAAAT 57.096 30.769 0.00 0.00 29.91 1.82
3333 4033 7.312899 ACACAAGCAGTTACTAAAATATTGCC 58.687 34.615 0.00 0.00 0.00 4.52
3436 4136 2.163211 GCTTCTGAACCTTTCTCCATGC 59.837 50.000 0.00 0.00 0.00 4.06
3456 4156 5.537300 TGCATATGAACCTCTCTACCTTC 57.463 43.478 6.97 0.00 0.00 3.46
3460 4160 2.821437 TGAACCTCTCTACCTTCCCAG 58.179 52.381 0.00 0.00 0.00 4.45
3529 4230 6.086785 ACTTCTACCGATACCTATCTTTGC 57.913 41.667 0.00 0.00 0.00 3.68
3717 4418 2.889045 CCATTCTAGGGCATGTCCATTG 59.111 50.000 20.74 8.02 36.21 2.82
3734 4435 3.919804 CCATTGTTCAACGCCAGTTATTG 59.080 43.478 0.00 0.00 38.79 1.90
3736 4437 3.889196 TGTTCAACGCCAGTTATTGTC 57.111 42.857 0.00 0.00 38.79 3.18
3737 4438 2.550606 TGTTCAACGCCAGTTATTGTCC 59.449 45.455 0.00 0.00 38.79 4.02
3738 4439 2.550606 GTTCAACGCCAGTTATTGTCCA 59.449 45.455 0.00 0.00 38.79 4.02
3739 4440 2.852449 TCAACGCCAGTTATTGTCCAA 58.148 42.857 0.00 0.00 38.79 3.53
3741 4442 3.003897 TCAACGCCAGTTATTGTCCAAAC 59.996 43.478 0.00 0.00 38.79 2.93
3742 4443 1.883926 ACGCCAGTTATTGTCCAAACC 59.116 47.619 0.00 0.00 0.00 3.27
3743 4444 1.201414 CGCCAGTTATTGTCCAAACCC 59.799 52.381 0.00 0.00 0.00 4.11
3744 4445 2.243810 GCCAGTTATTGTCCAAACCCA 58.756 47.619 0.00 0.00 0.00 4.51
3745 4446 2.630580 GCCAGTTATTGTCCAAACCCAA 59.369 45.455 0.00 0.00 0.00 4.12
3747 4448 4.627058 CCAGTTATTGTCCAAACCCAAAC 58.373 43.478 0.00 0.00 0.00 2.93
3748 4449 4.100189 CCAGTTATTGTCCAAACCCAAACA 59.900 41.667 0.00 0.00 0.00 2.83
3749 4450 5.047188 CAGTTATTGTCCAAACCCAAACAC 58.953 41.667 0.00 0.00 0.00 3.32
3751 4452 1.938585 TTGTCCAAACCCAAACACCA 58.061 45.000 0.00 0.00 0.00 4.17
3752 4453 1.938585 TGTCCAAACCCAAACACCAA 58.061 45.000 0.00 0.00 0.00 3.67
3754 4455 2.840651 TGTCCAAACCCAAACACCAATT 59.159 40.909 0.00 0.00 0.00 2.32
3755 4456 3.264450 TGTCCAAACCCAAACACCAATTT 59.736 39.130 0.00 0.00 0.00 1.82
3756 4457 3.625313 GTCCAAACCCAAACACCAATTTG 59.375 43.478 0.00 0.00 38.96 2.32
3757 4458 2.357323 CCAAACCCAAACACCAATTTGC 59.643 45.455 0.00 0.00 38.10 3.68
3758 4459 1.946745 AACCCAAACACCAATTTGCG 58.053 45.000 0.00 0.00 38.10 4.85
3763 4464 2.794350 CCAAACACCAATTTGCGAGTTC 59.206 45.455 0.00 0.00 38.10 3.01
3885 4586 6.704493 TGTCATTACTGTCACTAAAACTGGAC 59.296 38.462 0.00 0.00 0.00 4.02
3956 4657 7.509318 TCTTCTTATGCTAGAAGCTATAACCCA 59.491 37.037 14.87 0.00 46.91 4.51
4047 4748 5.260140 GTCGTTTGAGTTCATTGTTTCGAA 58.740 37.500 0.00 0.00 0.00 3.71
4306 5007 2.493675 TGCTAATCTCTCAGCGTGAACT 59.506 45.455 0.00 0.00 40.79 3.01
4325 5026 7.062138 CGTGAACTTTGGATAATTTGTCAATGG 59.938 37.037 0.00 0.00 0.00 3.16
4338 5039 8.831715 AATTTGTCAATGGTTACCTGAATTTC 57.168 30.769 2.07 0.00 0.00 2.17
4346 5047 7.587037 ATGGTTACCTGAATTTCCATGTATG 57.413 36.000 2.07 0.00 34.88 2.39
4369 5070 4.934001 GTCTTTCTGCTTCTGTCATCATGA 59.066 41.667 0.00 0.00 0.00 3.07
4370 5071 5.585445 GTCTTTCTGCTTCTGTCATCATGAT 59.415 40.000 1.18 1.18 0.00 2.45
4439 5140 1.939838 GCTTACCTCCACTTGTCACGG 60.940 57.143 0.00 0.00 0.00 4.94
4520 5221 9.515226 TTCTGTAATTAGGTTGCTCTTGTTATT 57.485 29.630 0.00 0.00 0.00 1.40
4521 5222 9.515226 TCTGTAATTAGGTTGCTCTTGTTATTT 57.485 29.630 0.00 0.00 0.00 1.40
4579 5280 3.802132 TCAAGGGCCAGCCATATATAGA 58.198 45.455 11.50 0.00 37.98 1.98
4580 5281 4.175172 TCAAGGGCCAGCCATATATAGAA 58.825 43.478 11.50 0.00 37.98 2.10
4669 5370 2.556189 TGGCATTGTTGTTCGTAAGCAT 59.444 40.909 0.00 0.00 37.18 3.79
4828 5529 8.924511 AATAACATCTTGTATTATGGGACTGG 57.075 34.615 0.00 0.00 0.00 4.00
4829 5530 6.575244 AACATCTTGTATTATGGGACTGGA 57.425 37.500 0.00 0.00 0.00 3.86
4830 5531 6.575244 ACATCTTGTATTATGGGACTGGAA 57.425 37.500 0.00 0.00 0.00 3.53
4831 5532 6.595682 ACATCTTGTATTATGGGACTGGAAG 58.404 40.000 0.00 0.00 42.29 3.46
4909 5655 6.203338 CACCCTGATCTGTTTTCAAATTTTGG 59.797 38.462 9.18 0.00 0.00 3.28
4911 5657 6.424812 CCCTGATCTGTTTTCAAATTTTGGTC 59.575 38.462 9.18 0.00 0.00 4.02
4924 5670 6.928492 TCAAATTTTGGTCACTTTTGATAGCC 59.072 34.615 9.18 0.00 32.88 3.93
5090 5839 2.927553 AAATGTCGCTTCCAATCAGC 57.072 45.000 0.00 0.00 0.00 4.26
5100 5849 0.321564 TCCAATCAGCAGGTCGTTGG 60.322 55.000 6.29 6.29 40.45 3.77
5190 5948 0.668535 CGTGCTCGATATGAGGTGGA 59.331 55.000 1.00 0.00 45.38 4.02
5249 6007 1.534235 AACAGACCAGACGAGGCCT 60.534 57.895 3.86 3.86 0.00 5.19
5250 6008 1.122019 AACAGACCAGACGAGGCCTT 61.122 55.000 6.77 0.00 0.00 4.35
5251 6009 1.216710 CAGACCAGACGAGGCCTTC 59.783 63.158 6.77 0.07 0.00 3.46
5307 6065 2.828520 CTCGATAGCCCCACATCTACAT 59.171 50.000 0.00 0.00 0.00 2.29
5308 6066 2.562738 TCGATAGCCCCACATCTACATG 59.437 50.000 0.00 0.00 35.92 3.21
5325 6083 0.249073 ATGTGTATCGTCGCAGCTCC 60.249 55.000 0.00 0.00 0.00 4.70
5349 6107 1.745141 GCTAGGAGCCTTCCACACATG 60.745 57.143 0.00 0.00 46.64 3.21
5350 6108 0.911769 TAGGAGCCTTCCACACATGG 59.088 55.000 0.00 0.00 46.64 3.66
5351 6109 2.048603 GGAGCCTTCCACACATGGC 61.049 63.158 0.00 0.00 46.80 4.40
5352 6110 2.036256 AGCCTTCCACACATGGCC 59.964 61.111 0.00 0.00 46.80 5.36
5353 6111 2.283101 GCCTTCCACACATGGCCA 60.283 61.111 8.56 8.56 46.80 5.36
5354 6112 1.907807 GCCTTCCACACATGGCCAA 60.908 57.895 10.96 0.00 46.80 4.52
5355 6113 1.470996 GCCTTCCACACATGGCCAAA 61.471 55.000 10.96 0.00 46.80 3.28
5356 6114 1.269012 CCTTCCACACATGGCCAAAT 58.731 50.000 10.96 0.00 46.80 2.32
5357 6115 1.624813 CCTTCCACACATGGCCAAATT 59.375 47.619 10.96 0.00 46.80 1.82
5358 6116 2.038820 CCTTCCACACATGGCCAAATTT 59.961 45.455 10.96 0.00 46.80 1.82
5359 6117 3.328505 CTTCCACACATGGCCAAATTTC 58.671 45.455 10.96 0.00 46.80 2.17
5360 6118 1.271934 TCCACACATGGCCAAATTTCG 59.728 47.619 10.96 0.00 46.80 3.46
5361 6119 1.000731 CCACACATGGCCAAATTTCGT 59.999 47.619 10.96 0.00 39.82 3.85
5362 6120 2.060284 CACACATGGCCAAATTTCGTG 58.940 47.619 10.96 12.90 0.00 4.35
5363 6121 1.686052 ACACATGGCCAAATTTCGTGT 59.314 42.857 10.96 13.56 0.00 4.49
5364 6122 2.102252 ACACATGGCCAAATTTCGTGTT 59.898 40.909 10.96 0.00 32.49 3.32
5365 6123 3.129871 CACATGGCCAAATTTCGTGTTT 58.870 40.909 10.96 0.00 0.00 2.83
5366 6124 3.559242 CACATGGCCAAATTTCGTGTTTT 59.441 39.130 10.96 0.00 0.00 2.43
5367 6125 3.559242 ACATGGCCAAATTTCGTGTTTTG 59.441 39.130 10.96 0.01 33.58 2.44
5368 6126 3.526931 TGGCCAAATTTCGTGTTTTGA 57.473 38.095 0.61 0.00 35.34 2.69
5369 6127 3.190874 TGGCCAAATTTCGTGTTTTGAC 58.809 40.909 0.61 0.00 35.34 3.18
5370 6128 2.542178 GGCCAAATTTCGTGTTTTGACC 59.458 45.455 0.00 3.43 35.34 4.02
5371 6129 2.542178 GCCAAATTTCGTGTTTTGACCC 59.458 45.455 7.82 0.00 35.34 4.46
5372 6130 3.739830 GCCAAATTTCGTGTTTTGACCCT 60.740 43.478 7.82 0.00 35.34 4.34
5373 6131 4.438148 CCAAATTTCGTGTTTTGACCCTT 58.562 39.130 7.82 0.00 35.34 3.95
5374 6132 4.873259 CCAAATTTCGTGTTTTGACCCTTT 59.127 37.500 7.82 0.00 35.34 3.11
5375 6133 5.220567 CCAAATTTCGTGTTTTGACCCTTTG 60.221 40.000 7.82 0.00 35.34 2.77
5376 6134 3.512033 TTTCGTGTTTTGACCCTTTGG 57.488 42.857 0.00 0.00 37.80 3.28
5389 6147 4.053469 ACCCTTTGGTCAAACAAAATCG 57.947 40.909 0.00 0.00 43.06 3.34
5390 6148 3.181470 ACCCTTTGGTCAAACAAAATCGG 60.181 43.478 0.00 0.00 43.06 4.18
5391 6149 3.389221 CCTTTGGTCAAACAAAATCGGG 58.611 45.455 0.00 0.00 39.60 5.14
5392 6150 3.068873 CCTTTGGTCAAACAAAATCGGGA 59.931 43.478 0.00 0.00 39.60 5.14
5393 6151 4.262420 CCTTTGGTCAAACAAAATCGGGAT 60.262 41.667 0.00 0.00 39.60 3.85
5394 6152 4.513198 TTGGTCAAACAAAATCGGGATC 57.487 40.909 0.00 0.00 0.00 3.36
5395 6153 3.761897 TGGTCAAACAAAATCGGGATCT 58.238 40.909 0.00 0.00 0.00 2.75
5396 6154 3.505680 TGGTCAAACAAAATCGGGATCTG 59.494 43.478 0.00 0.00 0.00 2.90
5397 6155 3.756434 GGTCAAACAAAATCGGGATCTGA 59.244 43.478 0.00 0.00 0.00 3.27
5398 6156 4.379499 GGTCAAACAAAATCGGGATCTGAC 60.379 45.833 0.00 0.00 0.00 3.51
5399 6157 3.756434 TCAAACAAAATCGGGATCTGACC 59.244 43.478 0.00 0.00 0.00 4.02
5400 6158 2.420058 ACAAAATCGGGATCTGACCC 57.580 50.000 0.00 0.00 45.92 4.46
5401 6159 1.064685 ACAAAATCGGGATCTGACCCC 60.065 52.381 0.00 0.00 46.62 4.95
5402 6160 0.551396 AAAATCGGGATCTGACCCCC 59.449 55.000 0.09 4.19 46.62 5.40
5403 6161 0.327576 AAATCGGGATCTGACCCCCT 60.328 55.000 0.09 0.00 46.62 4.79
5404 6162 0.327576 AATCGGGATCTGACCCCCTT 60.328 55.000 0.09 0.00 46.62 3.95
5405 6163 1.056700 ATCGGGATCTGACCCCCTTG 61.057 60.000 0.09 0.00 46.62 3.61
5406 6164 1.995626 CGGGATCTGACCCCCTTGT 60.996 63.158 0.09 0.00 46.62 3.16
5407 6165 0.689745 CGGGATCTGACCCCCTTGTA 60.690 60.000 0.09 0.00 46.62 2.41
5408 6166 1.591768 GGGATCTGACCCCCTTGTAA 58.408 55.000 0.00 0.00 43.81 2.41
5409 6167 2.136026 GGGATCTGACCCCCTTGTAAT 58.864 52.381 0.00 0.00 43.81 1.89
5410 6168 2.514160 GGGATCTGACCCCCTTGTAATT 59.486 50.000 0.00 0.00 43.81 1.40
5411 6169 3.052869 GGGATCTGACCCCCTTGTAATTT 60.053 47.826 0.00 0.00 43.81 1.82
5412 6170 4.572007 GGGATCTGACCCCCTTGTAATTTT 60.572 45.833 0.00 0.00 43.81 1.82
5413 6171 5.023452 GGATCTGACCCCCTTGTAATTTTT 58.977 41.667 0.00 0.00 0.00 1.94
5433 6191 4.320608 TTTTGACATCTGACCCTTTTGC 57.679 40.909 0.00 0.00 0.00 3.68
5434 6192 2.957402 TGACATCTGACCCTTTTGCT 57.043 45.000 0.00 0.00 0.00 3.91
5435 6193 4.365514 TTGACATCTGACCCTTTTGCTA 57.634 40.909 0.00 0.00 0.00 3.49
5436 6194 3.674997 TGACATCTGACCCTTTTGCTAC 58.325 45.455 0.00 0.00 0.00 3.58
5437 6195 3.010420 GACATCTGACCCTTTTGCTACC 58.990 50.000 0.00 0.00 0.00 3.18
5438 6196 2.009774 CATCTGACCCTTTTGCTACCG 58.990 52.381 0.00 0.00 0.00 4.02
5439 6197 1.053424 TCTGACCCTTTTGCTACCGT 58.947 50.000 0.00 0.00 0.00 4.83
5440 6198 1.001633 TCTGACCCTTTTGCTACCGTC 59.998 52.381 0.00 0.00 0.00 4.79
5441 6199 0.759959 TGACCCTTTTGCTACCGTCA 59.240 50.000 0.00 0.00 0.00 4.35
5442 6200 1.141254 TGACCCTTTTGCTACCGTCAA 59.859 47.619 0.00 0.00 0.00 3.18
5443 6201 2.223745 GACCCTTTTGCTACCGTCAAA 58.776 47.619 0.00 0.00 0.00 2.69
5444 6202 2.225727 GACCCTTTTGCTACCGTCAAAG 59.774 50.000 0.00 0.00 35.21 2.77
5445 6203 1.539827 CCCTTTTGCTACCGTCAAAGG 59.460 52.381 3.00 3.00 35.21 3.11
5446 6204 1.539827 CCTTTTGCTACCGTCAAAGGG 59.460 52.381 2.14 2.94 41.87 3.95
5447 6205 0.955905 TTTTGCTACCGTCAAAGGGC 59.044 50.000 0.00 0.00 35.21 5.19
5448 6206 0.109723 TTTGCTACCGTCAAAGGGCT 59.890 50.000 0.00 0.00 35.02 5.19
5449 6207 0.321298 TTGCTACCGTCAAAGGGCTC 60.321 55.000 0.00 0.00 35.02 4.70
5450 6208 1.810030 GCTACCGTCAAAGGGCTCG 60.810 63.158 0.00 0.00 35.02 5.03
5451 6209 1.153628 CTACCGTCAAAGGGCTCGG 60.154 63.158 0.00 0.00 46.98 4.63
5452 6210 3.305177 TACCGTCAAAGGGCTCGGC 62.305 63.158 0.00 0.00 45.76 5.54
5453 6211 4.394712 CCGTCAAAGGGCTCGGCT 62.395 66.667 0.00 0.00 36.68 5.52
5454 6212 3.121030 CGTCAAAGGGCTCGGCTG 61.121 66.667 0.00 0.00 0.00 4.85
5455 6213 2.032681 GTCAAAGGGCTCGGCTGT 59.967 61.111 0.00 0.00 0.00 4.40
5456 6214 1.295423 GTCAAAGGGCTCGGCTGTA 59.705 57.895 0.00 0.00 0.00 2.74
5457 6215 0.741221 GTCAAAGGGCTCGGCTGTAG 60.741 60.000 0.00 0.00 0.00 2.74
5458 6216 1.450312 CAAAGGGCTCGGCTGTAGG 60.450 63.158 0.00 0.00 0.00 3.18
5459 6217 2.670148 AAAGGGCTCGGCTGTAGGG 61.670 63.158 0.00 0.00 0.00 3.53
5460 6218 3.925914 AAGGGCTCGGCTGTAGGGT 62.926 63.158 0.00 0.00 0.00 4.34
5461 6219 3.851128 GGGCTCGGCTGTAGGGTC 61.851 72.222 0.00 0.00 0.00 4.46
5462 6220 3.075005 GGCTCGGCTGTAGGGTCA 61.075 66.667 0.00 0.00 0.00 4.02
5463 6221 2.184579 GCTCGGCTGTAGGGTCAC 59.815 66.667 0.00 0.00 0.00 3.67
5464 6222 2.490217 CTCGGCTGTAGGGTCACG 59.510 66.667 0.00 0.00 0.00 4.35
5465 6223 3.064987 CTCGGCTGTAGGGTCACGG 62.065 68.421 0.00 0.00 0.00 4.94
5466 6224 3.066190 CGGCTGTAGGGTCACGGA 61.066 66.667 0.00 0.00 0.00 4.69
5467 6225 2.893398 GGCTGTAGGGTCACGGAG 59.107 66.667 0.00 0.00 0.00 4.63
5468 6226 2.722201 GGCTGTAGGGTCACGGAGG 61.722 68.421 0.00 0.00 0.00 4.30
5469 6227 2.893398 CTGTAGGGTCACGGAGGC 59.107 66.667 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.327357 CACTACTTCAAGGTGCATTCTACG 59.673 45.833 0.00 0.00 0.00 3.51
7 8 4.832248 CCACTACTTCAAGGTGCATTCTA 58.168 43.478 0.00 0.00 0.00 2.10
11 12 1.073763 TGCCACTACTTCAAGGTGCAT 59.926 47.619 0.00 0.00 0.00 3.96
28 29 4.610945 CCCGTATCAATGAGAATTTTGCC 58.389 43.478 0.00 0.00 0.00 4.52
50 51 5.861787 ACGCAAATCTGTTTTACAATAAGGC 59.138 36.000 0.00 0.00 0.00 4.35
52 53 8.500837 TTCACGCAAATCTGTTTTACAATAAG 57.499 30.769 0.00 0.00 0.00 1.73
70 71 5.874261 TCTATGAACTTGATCATTTCACGCA 59.126 36.000 18.00 9.02 40.44 5.24
110 114 6.313744 TCGTATCTGCTAGAATTTCATCGA 57.686 37.500 0.00 0.00 0.00 3.59
113 117 6.273825 ACGTTCGTATCTGCTAGAATTTCAT 58.726 36.000 0.00 0.00 0.00 2.57
114 118 5.647589 ACGTTCGTATCTGCTAGAATTTCA 58.352 37.500 0.00 0.00 0.00 2.69
124 128 3.918258 TGCAATAACGTTCGTATCTGC 57.082 42.857 2.82 6.65 0.00 4.26
130 134 7.480542 GTCAATCTATTTTGCAATAACGTTCGT 59.519 33.333 2.82 0.00 0.00 3.85
133 137 7.270365 CGTGTCAATCTATTTTGCAATAACGTT 59.730 33.333 5.88 5.88 0.00 3.99
143 147 5.411361 TCACCCTTCGTGTCAATCTATTTTG 59.589 40.000 0.00 0.00 43.51 2.44
148 152 2.232941 GGTCACCCTTCGTGTCAATCTA 59.767 50.000 0.00 0.00 43.51 1.98
154 158 0.106149 ACTTGGTCACCCTTCGTGTC 59.894 55.000 0.00 0.00 43.51 3.67
239 244 9.911138 TCGCAAATACGGAATATATTTACTGTA 57.089 29.630 0.00 4.18 32.27 2.74
240 245 8.821147 TCGCAAATACGGAATATATTTACTGT 57.179 30.769 0.00 2.05 32.27 3.55
241 246 9.741168 CTTCGCAAATACGGAATATATTTACTG 57.259 33.333 0.00 0.00 32.27 2.74
242 247 9.701098 TCTTCGCAAATACGGAATATATTTACT 57.299 29.630 0.00 0.00 32.27 2.24
243 248 9.953825 CTCTTCGCAAATACGGAATATATTTAC 57.046 33.333 0.00 0.00 32.27 2.01
244 249 9.917129 TCTCTTCGCAAATACGGAATATATTTA 57.083 29.630 0.00 0.00 32.27 1.40
245 250 8.709646 GTCTCTTCGCAAATACGGAATATATTT 58.290 33.333 0.00 0.00 33.45 1.40
246 251 8.088981 AGTCTCTTCGCAAATACGGAATATATT 58.911 33.333 0.00 0.00 0.00 1.28
247 252 7.603651 AGTCTCTTCGCAAATACGGAATATAT 58.396 34.615 0.00 0.00 0.00 0.86
248 253 6.978338 AGTCTCTTCGCAAATACGGAATATA 58.022 36.000 0.00 0.00 0.00 0.86
249 254 5.844004 AGTCTCTTCGCAAATACGGAATAT 58.156 37.500 0.00 0.00 0.00 1.28
250 255 5.258456 AGTCTCTTCGCAAATACGGAATA 57.742 39.130 0.00 0.00 0.00 1.75
251 256 4.124851 AGTCTCTTCGCAAATACGGAAT 57.875 40.909 0.00 0.00 0.00 3.01
252 257 3.587797 AGTCTCTTCGCAAATACGGAA 57.412 42.857 0.00 0.00 0.00 4.30
253 258 4.707030 TTAGTCTCTTCGCAAATACGGA 57.293 40.909 0.00 0.00 0.00 4.69
254 259 5.968387 AATTAGTCTCTTCGCAAATACGG 57.032 39.130 0.00 0.00 0.00 4.02
255 260 7.431376 TGTCTAATTAGTCTCTTCGCAAATACG 59.569 37.037 12.19 0.00 0.00 3.06
256 261 8.630278 TGTCTAATTAGTCTCTTCGCAAATAC 57.370 34.615 12.19 0.00 0.00 1.89
257 262 9.817809 AATGTCTAATTAGTCTCTTCGCAAATA 57.182 29.630 12.19 0.00 0.00 1.40
258 263 8.723942 AATGTCTAATTAGTCTCTTCGCAAAT 57.276 30.769 12.19 0.00 0.00 2.32
676 681 3.842923 AGCTGGTCCAGATCGCGG 61.843 66.667 23.77 0.00 32.44 6.46
698 703 1.537814 ATCGGTTCTGTGTGCGGGTA 61.538 55.000 0.00 0.00 0.00 3.69
699 704 2.391724 AATCGGTTCTGTGTGCGGGT 62.392 55.000 0.00 0.00 0.00 5.28
833 847 1.997669 CCGGCGATTTATAGAGGAGC 58.002 55.000 9.30 0.00 0.00 4.70
1340 1590 3.323243 ACGGGACAGACTGATAAAAACG 58.677 45.455 10.08 6.24 0.00 3.60
1342 1592 3.256383 TCGACGGGACAGACTGATAAAAA 59.744 43.478 10.08 0.00 0.00 1.94
1380 1630 1.069296 CGAAAAATTGAGCGCTCACCA 60.069 47.619 38.36 26.00 39.66 4.17
1390 1640 2.294233 AGCAAGCAGAGCGAAAAATTGA 59.706 40.909 0.00 0.00 37.01 2.57
1448 1699 7.724506 TCCCGAGAAAACATACTAGTCAGATAT 59.275 37.037 0.00 0.00 0.00 1.63
1449 1700 7.058525 TCCCGAGAAAACATACTAGTCAGATA 58.941 38.462 0.00 0.00 0.00 1.98
1450 1701 5.892119 TCCCGAGAAAACATACTAGTCAGAT 59.108 40.000 0.00 0.00 0.00 2.90
1454 1705 6.145338 TGATCCCGAGAAAACATACTAGTC 57.855 41.667 0.00 0.00 0.00 2.59
1497 1752 8.889717 CAGTAAACACGGAGATATACCAAAAAT 58.110 33.333 0.00 0.00 0.00 1.82
1524 1779 6.183360 ACACCGAATCGAATCCTAATTCCTAA 60.183 38.462 3.36 0.00 38.46 2.69
1525 1780 5.303589 ACACCGAATCGAATCCTAATTCCTA 59.696 40.000 3.36 0.00 38.46 2.94
1526 1781 4.101119 ACACCGAATCGAATCCTAATTCCT 59.899 41.667 3.36 0.00 38.46 3.36
1527 1782 4.377897 ACACCGAATCGAATCCTAATTCC 58.622 43.478 3.36 0.00 38.46 3.01
1528 1783 5.047847 TGACACCGAATCGAATCCTAATTC 58.952 41.667 3.36 0.00 38.34 2.17
1529 1784 5.018539 TGACACCGAATCGAATCCTAATT 57.981 39.130 3.36 0.00 0.00 1.40
1530 1785 4.621991 CTGACACCGAATCGAATCCTAAT 58.378 43.478 3.36 0.00 0.00 1.73
1557 1812 0.657840 GCATTCGAAATCCCCTGACG 59.342 55.000 0.00 0.00 0.00 4.35
1590 1845 4.377762 AGGTACTGACACAGTGGTAGTA 57.622 45.455 13.62 9.88 45.01 1.82
1591 1846 3.240310 AGGTACTGACACAGTGGTAGT 57.760 47.619 13.62 14.23 45.01 2.73
1592 1847 5.010314 TGTTTAGGTACTGACACAGTGGTAG 59.990 44.000 13.62 5.19 45.01 3.18
1593 1848 4.894705 TGTTTAGGTACTGACACAGTGGTA 59.105 41.667 13.62 0.00 45.01 3.25
1594 1849 3.707611 TGTTTAGGTACTGACACAGTGGT 59.292 43.478 13.62 0.00 45.01 4.16
1712 1969 8.642908 TCTACGATAACTTTACATGTTGATGG 57.357 34.615 2.30 0.00 33.39 3.51
1748 2005 4.359434 AGAGTCTTCAAAAGTTCCTCCC 57.641 45.455 0.00 0.00 0.00 4.30
1948 2466 5.738619 TCAGTAAATCCAGCTGTGAGTTA 57.261 39.130 13.81 15.29 0.00 2.24
1977 2495 1.133513 ACACAAGGATGCCCAGTTTGA 60.134 47.619 0.00 0.00 33.88 2.69
1985 2503 0.962356 CAGTCCCACACAAGGATGCC 60.962 60.000 0.00 0.00 35.38 4.40
2079 2597 0.179108 CGTCCCGATTCCTCACTTCC 60.179 60.000 0.00 0.00 0.00 3.46
2160 2678 1.912731 TGCACTCCCAAAGCCATAGTA 59.087 47.619 0.00 0.00 0.00 1.82
2184 2702 3.689649 AGCTGAACTGTTCGTTTTTCAGT 59.310 39.130 15.18 0.00 44.54 3.41
2232 2750 0.613260 CAAGGAACCCGTGGATCTCA 59.387 55.000 0.00 0.00 29.60 3.27
2350 2876 8.027524 AGATTTAGGATAGAATGACAAGAGCA 57.972 34.615 0.00 0.00 0.00 4.26
2629 3283 9.767684 TTTGATACAGAATTTACACATTAAGCG 57.232 29.630 0.00 0.00 0.00 4.68
2663 3317 8.988934 TCTAACAATTAGCACTCAACTTAAGTG 58.011 33.333 9.34 3.91 45.57 3.16
2692 3346 5.614887 GCAAGTCGGTCTAATTCAGAACAAC 60.615 44.000 0.00 0.00 41.52 3.32
2971 3625 0.746659 AACAAAGAGGTGCTGTTGCC 59.253 50.000 0.00 0.00 38.71 4.52
3132 3786 5.877564 GGGAATTTTTCACCAGTTCAAACAA 59.122 36.000 0.00 0.00 0.00 2.83
3436 4136 4.901849 TGGGAAGGTAGAGAGGTTCATATG 59.098 45.833 0.00 0.00 0.00 1.78
3456 4156 4.142182 ACACTTGTGTTTCATTTCACTGGG 60.142 41.667 0.00 0.00 35.82 4.45
3460 4160 6.519419 GCAAAAACACTTGTGTTTCATTTCAC 59.481 34.615 25.67 11.61 40.67 3.18
3514 4215 7.959651 GCTAAATTCATGCAAAGATAGGTATCG 59.040 37.037 0.00 0.00 37.76 2.92
3529 4230 3.867055 ACGCGAGATGCTAAATTCATG 57.133 42.857 15.93 0.00 43.27 3.07
3717 4418 2.550606 TGGACAATAACTGGCGTTGAAC 59.449 45.455 5.24 0.00 31.39 3.18
3734 4435 3.552132 AATTGGTGTTTGGGTTTGGAC 57.448 42.857 0.00 0.00 0.00 4.02
3736 4437 2.357323 GCAAATTGGTGTTTGGGTTTGG 59.643 45.455 0.00 0.00 39.03 3.28
3737 4438 2.031437 CGCAAATTGGTGTTTGGGTTTG 59.969 45.455 7.88 0.00 43.17 2.93
3738 4439 2.093447 TCGCAAATTGGTGTTTGGGTTT 60.093 40.909 13.60 0.00 46.21 3.27
3739 4440 1.482593 TCGCAAATTGGTGTTTGGGTT 59.517 42.857 13.60 0.00 46.21 4.11
3741 4442 1.068434 ACTCGCAAATTGGTGTTTGGG 59.932 47.619 9.33 9.33 46.97 4.12
3742 4443 2.507339 ACTCGCAAATTGGTGTTTGG 57.493 45.000 0.00 0.00 39.03 3.28
3743 4444 3.443037 TGAACTCGCAAATTGGTGTTTG 58.557 40.909 0.00 0.00 41.02 2.93
3744 4445 3.130340 ACTGAACTCGCAAATTGGTGTTT 59.870 39.130 0.00 0.00 0.00 2.83
3745 4446 2.687935 ACTGAACTCGCAAATTGGTGTT 59.312 40.909 0.00 0.00 0.00 3.32
3747 4448 2.653890 CACTGAACTCGCAAATTGGTG 58.346 47.619 0.00 0.00 0.00 4.17
3748 4449 1.001378 GCACTGAACTCGCAAATTGGT 60.001 47.619 0.00 0.00 0.00 3.67
3749 4450 1.666888 GGCACTGAACTCGCAAATTGG 60.667 52.381 0.00 0.00 0.00 3.16
3751 4452 1.609208 AGGCACTGAACTCGCAAATT 58.391 45.000 0.00 0.00 37.18 1.82
3752 4453 2.472695 TAGGCACTGAACTCGCAAAT 57.527 45.000 0.00 0.00 41.52 2.32
3754 4455 1.070134 AGTTAGGCACTGAACTCGCAA 59.930 47.619 0.00 0.00 41.52 4.85
3755 4456 0.679505 AGTTAGGCACTGAACTCGCA 59.320 50.000 0.00 0.00 41.52 5.10
3756 4457 2.531206 CTAGTTAGGCACTGAACTCGC 58.469 52.381 0.00 0.00 41.52 5.03
3757 4458 2.753452 TCCTAGTTAGGCACTGAACTCG 59.247 50.000 0.07 0.00 43.31 4.18
3758 4459 3.510360 TGTCCTAGTTAGGCACTGAACTC 59.490 47.826 0.07 0.00 43.31 3.01
3763 4464 6.823689 ACAATAAATGTCCTAGTTAGGCACTG 59.176 38.462 0.07 0.00 43.31 3.66
3885 4586 6.057533 TGATATCTAGCACTTTGACAATGGG 58.942 40.000 3.98 2.74 0.00 4.00
3956 4657 7.770897 GGTCTCATATGTTCCACAAATCTTAGT 59.229 37.037 1.90 0.00 0.00 2.24
4047 4748 3.087031 CCTTCATCACTGACCTGCATTT 58.913 45.455 0.00 0.00 0.00 2.32
4162 4863 2.709397 ACCATACCCAGCCATAGTTACC 59.291 50.000 0.00 0.00 0.00 2.85
4306 5007 8.310382 CAGGTAACCATTGACAAATTATCCAAA 58.690 33.333 0.00 0.00 37.17 3.28
4325 5026 7.865706 AGACATACATGGAAATTCAGGTAAC 57.134 36.000 0.00 0.00 37.44 2.50
4338 5039 4.940046 ACAGAAGCAGAAAGACATACATGG 59.060 41.667 0.00 0.00 0.00 3.66
4346 5047 4.934001 TCATGATGACAGAAGCAGAAAGAC 59.066 41.667 0.00 0.00 0.00 3.01
4369 5070 6.093219 GCAAGAATGATCAGCCGAATACATAT 59.907 38.462 0.09 0.00 0.00 1.78
4370 5071 5.409520 GCAAGAATGATCAGCCGAATACATA 59.590 40.000 0.09 0.00 0.00 2.29
4439 5140 2.043852 TCCTCCGAGTCTCCCAGC 60.044 66.667 0.00 0.00 0.00 4.85
4521 5222 8.682710 GCAAACCAGAACAAGGATTACAATATA 58.317 33.333 0.00 0.00 0.00 0.86
4522 5223 7.178274 TGCAAACCAGAACAAGGATTACAATAT 59.822 33.333 0.00 0.00 0.00 1.28
4523 5224 6.491745 TGCAAACCAGAACAAGGATTACAATA 59.508 34.615 0.00 0.00 0.00 1.90
4738 5439 1.315690 TAGGACGGAGGCAGTAATCG 58.684 55.000 0.00 0.00 0.00 3.34
4814 5515 9.654663 GATATACAACTTCCAGTCCCATAATAC 57.345 37.037 0.00 0.00 0.00 1.89
4822 5523 7.171678 GCATACAAGATATACAACTTCCAGTCC 59.828 40.741 0.00 0.00 0.00 3.85
4826 5527 6.101150 AGGGCATACAAGATATACAACTTCCA 59.899 38.462 0.00 0.00 0.00 3.53
4828 5529 6.073003 GCAGGGCATACAAGATATACAACTTC 60.073 42.308 0.00 0.00 0.00 3.01
4829 5530 5.765182 GCAGGGCATACAAGATATACAACTT 59.235 40.000 0.00 0.00 0.00 2.66
4830 5531 5.163205 TGCAGGGCATACAAGATATACAACT 60.163 40.000 0.00 0.00 31.71 3.16
4831 5532 5.049405 GTGCAGGGCATACAAGATATACAAC 60.049 44.000 0.00 0.00 41.91 3.32
4832 5533 5.063204 GTGCAGGGCATACAAGATATACAA 58.937 41.667 0.00 0.00 41.91 2.41
4833 5534 4.641396 GTGCAGGGCATACAAGATATACA 58.359 43.478 0.00 0.00 41.91 2.29
4834 5535 3.679980 CGTGCAGGGCATACAAGATATAC 59.320 47.826 0.00 0.00 41.91 1.47
4835 5536 3.864540 GCGTGCAGGGCATACAAGATATA 60.865 47.826 8.72 0.00 41.91 0.86
4836 5537 2.771089 CGTGCAGGGCATACAAGATAT 58.229 47.619 0.00 0.00 41.91 1.63
4837 5538 1.810031 GCGTGCAGGGCATACAAGATA 60.810 52.381 8.72 0.00 41.91 1.98
4909 5655 4.319177 AGTGACAGGCTATCAAAAGTGAC 58.681 43.478 0.00 0.00 36.31 3.67
4911 5657 4.154918 GGAAGTGACAGGCTATCAAAAGTG 59.845 45.833 0.00 0.00 0.00 3.16
4924 5670 3.902881 AAGGCAGATAGGAAGTGACAG 57.097 47.619 0.00 0.00 0.00 3.51
4991 5740 3.688673 CAGGAAATGAGAAGACTTCCAGC 59.311 47.826 11.67 2.85 39.91 4.85
5003 5752 6.071896 GGGAAAAGTAGGAAACAGGAAATGAG 60.072 42.308 0.00 0.00 0.00 2.90
5090 5839 0.323629 TTAGAAGGGCCAACGACCTG 59.676 55.000 6.18 0.00 37.13 4.00
5100 5849 5.432645 AGTGAGCTTTCTTATTAGAAGGGC 58.567 41.667 5.83 8.84 41.25 5.19
5190 5948 1.885157 CCTGCAACGCCACATTCAT 59.115 52.632 0.00 0.00 0.00 2.57
5249 6007 3.056107 AGAATCTGAATTCCGACCACGAA 60.056 43.478 2.27 0.00 41.97 3.85
5250 6008 2.496070 AGAATCTGAATTCCGACCACGA 59.504 45.455 2.27 0.00 41.97 4.35
5251 6009 2.860735 GAGAATCTGAATTCCGACCACG 59.139 50.000 2.27 0.00 41.97 4.94
5307 6065 1.138883 GGAGCTGCGACGATACACA 59.861 57.895 0.00 0.00 0.00 3.72
5308 6066 1.589196 GGGAGCTGCGACGATACAC 60.589 63.158 0.00 0.00 0.00 2.90
5349 6107 3.852471 GTCAAAACACGAAATTTGGCC 57.148 42.857 0.00 0.00 35.62 5.36
5350 6108 2.542178 GGGTCAAAACACGAAATTTGGC 59.458 45.455 0.00 0.00 39.72 4.52
5351 6109 4.053469 AGGGTCAAAACACGAAATTTGG 57.947 40.909 0.00 0.00 37.19 3.28
5352 6110 5.220567 CCAAAGGGTCAAAACACGAAATTTG 60.221 40.000 0.00 0.00 37.77 2.32
5353 6111 4.873259 CCAAAGGGTCAAAACACGAAATTT 59.127 37.500 0.00 0.00 32.44 1.82
5354 6112 4.438148 CCAAAGGGTCAAAACACGAAATT 58.562 39.130 0.00 0.00 32.44 1.82
5355 6113 4.053469 CCAAAGGGTCAAAACACGAAAT 57.947 40.909 0.00 0.00 32.44 2.17
5356 6114 3.512033 CCAAAGGGTCAAAACACGAAA 57.488 42.857 0.00 0.00 32.44 3.46
5369 6127 3.389221 CCGATTTTGTTTGACCAAAGGG 58.611 45.455 0.00 0.00 35.85 3.95
5370 6128 3.068873 TCCCGATTTTGTTTGACCAAAGG 59.931 43.478 0.00 0.00 35.85 3.11
5371 6129 4.314740 TCCCGATTTTGTTTGACCAAAG 57.685 40.909 0.00 0.00 35.85 2.77
5372 6130 4.586841 AGATCCCGATTTTGTTTGACCAAA 59.413 37.500 0.00 0.00 32.70 3.28
5373 6131 4.022416 CAGATCCCGATTTTGTTTGACCAA 60.022 41.667 0.00 0.00 0.00 3.67
5374 6132 3.505680 CAGATCCCGATTTTGTTTGACCA 59.494 43.478 0.00 0.00 0.00 4.02
5375 6133 3.756434 TCAGATCCCGATTTTGTTTGACC 59.244 43.478 0.00 0.00 0.00 4.02
5376 6134 4.379499 GGTCAGATCCCGATTTTGTTTGAC 60.379 45.833 0.00 0.00 33.51 3.18
5377 6135 3.756434 GGTCAGATCCCGATTTTGTTTGA 59.244 43.478 0.00 0.00 0.00 2.69
5378 6136 3.119495 GGGTCAGATCCCGATTTTGTTTG 60.119 47.826 0.00 0.00 37.93 2.93
5379 6137 3.089284 GGGTCAGATCCCGATTTTGTTT 58.911 45.455 0.00 0.00 37.93 2.83
5380 6138 2.723273 GGGTCAGATCCCGATTTTGTT 58.277 47.619 0.00 0.00 37.93 2.83
5381 6139 2.420058 GGGTCAGATCCCGATTTTGT 57.580 50.000 0.00 0.00 37.93 2.83
5389 6147 1.591768 TTACAAGGGGGTCAGATCCC 58.408 55.000 10.90 10.90 46.31 3.85
5390 6148 3.953542 AATTACAAGGGGGTCAGATCC 57.046 47.619 0.00 0.00 0.00 3.36
5411 6169 4.405358 AGCAAAAGGGTCAGATGTCAAAAA 59.595 37.500 0.00 0.00 0.00 1.94
5412 6170 3.960102 AGCAAAAGGGTCAGATGTCAAAA 59.040 39.130 0.00 0.00 0.00 2.44
5413 6171 3.565307 AGCAAAAGGGTCAGATGTCAAA 58.435 40.909 0.00 0.00 0.00 2.69
5414 6172 3.228188 AGCAAAAGGGTCAGATGTCAA 57.772 42.857 0.00 0.00 0.00 3.18
5415 6173 2.957402 AGCAAAAGGGTCAGATGTCA 57.043 45.000 0.00 0.00 0.00 3.58
5416 6174 3.010420 GGTAGCAAAAGGGTCAGATGTC 58.990 50.000 0.00 0.00 0.00 3.06
5417 6175 2.615493 CGGTAGCAAAAGGGTCAGATGT 60.615 50.000 0.00 0.00 0.00 3.06
5418 6176 2.009774 CGGTAGCAAAAGGGTCAGATG 58.990 52.381 0.00 0.00 0.00 2.90
5419 6177 1.628846 ACGGTAGCAAAAGGGTCAGAT 59.371 47.619 0.00 0.00 0.00 2.90
5420 6178 1.001633 GACGGTAGCAAAAGGGTCAGA 59.998 52.381 0.00 0.00 0.00 3.27
5421 6179 1.270625 TGACGGTAGCAAAAGGGTCAG 60.271 52.381 0.00 0.00 31.45 3.51
5422 6180 0.759959 TGACGGTAGCAAAAGGGTCA 59.240 50.000 0.00 0.00 32.51 4.02
5423 6181 1.886886 TTGACGGTAGCAAAAGGGTC 58.113 50.000 0.00 0.00 0.00 4.46
5424 6182 2.227194 CTTTGACGGTAGCAAAAGGGT 58.773 47.619 0.00 0.00 35.09 4.34
5425 6183 1.539827 CCTTTGACGGTAGCAAAAGGG 59.460 52.381 17.11 4.63 35.09 3.95
5426 6184 1.539827 CCCTTTGACGGTAGCAAAAGG 59.460 52.381 17.61 17.61 35.09 3.11
5427 6185 1.068541 GCCCTTTGACGGTAGCAAAAG 60.069 52.381 0.00 0.00 35.09 2.27
5428 6186 0.955905 GCCCTTTGACGGTAGCAAAA 59.044 50.000 0.00 0.00 35.09 2.44
5429 6187 0.109723 AGCCCTTTGACGGTAGCAAA 59.890 50.000 0.00 0.00 34.40 3.68
5430 6188 0.321298 GAGCCCTTTGACGGTAGCAA 60.321 55.000 0.00 0.00 0.00 3.91
5431 6189 1.295423 GAGCCCTTTGACGGTAGCA 59.705 57.895 0.00 0.00 0.00 3.49
5432 6190 1.810030 CGAGCCCTTTGACGGTAGC 60.810 63.158 0.00 0.00 0.00 3.58
5433 6191 1.153628 CCGAGCCCTTTGACGGTAG 60.154 63.158 0.00 0.00 40.42 3.18
5434 6192 2.975536 CCGAGCCCTTTGACGGTA 59.024 61.111 0.00 0.00 40.42 4.02
5435 6193 4.699522 GCCGAGCCCTTTGACGGT 62.700 66.667 0.00 0.00 45.91 4.83
5436 6194 4.394712 AGCCGAGCCCTTTGACGG 62.395 66.667 0.00 0.00 46.74 4.79
5437 6195 2.501223 TACAGCCGAGCCCTTTGACG 62.501 60.000 0.00 0.00 0.00 4.35
5438 6196 0.741221 CTACAGCCGAGCCCTTTGAC 60.741 60.000 0.00 0.00 0.00 3.18
5439 6197 1.596934 CTACAGCCGAGCCCTTTGA 59.403 57.895 0.00 0.00 0.00 2.69
5440 6198 1.450312 CCTACAGCCGAGCCCTTTG 60.450 63.158 0.00 0.00 0.00 2.77
5441 6199 2.670148 CCCTACAGCCGAGCCCTTT 61.670 63.158 0.00 0.00 0.00 3.11
5442 6200 3.083997 CCCTACAGCCGAGCCCTT 61.084 66.667 0.00 0.00 0.00 3.95
5443 6201 4.400251 ACCCTACAGCCGAGCCCT 62.400 66.667 0.00 0.00 0.00 5.19
5444 6202 3.851128 GACCCTACAGCCGAGCCC 61.851 72.222 0.00 0.00 0.00 5.19
5445 6203 3.075005 TGACCCTACAGCCGAGCC 61.075 66.667 0.00 0.00 0.00 4.70
5446 6204 2.184579 GTGACCCTACAGCCGAGC 59.815 66.667 0.00 0.00 0.00 5.03
5447 6205 2.490217 CGTGACCCTACAGCCGAG 59.510 66.667 0.00 0.00 0.00 4.63
5448 6206 3.066190 CCGTGACCCTACAGCCGA 61.066 66.667 0.00 0.00 0.00 5.54
5449 6207 3.064987 CTCCGTGACCCTACAGCCG 62.065 68.421 0.00 0.00 0.00 5.52
5450 6208 2.722201 CCTCCGTGACCCTACAGCC 61.722 68.421 0.00 0.00 0.00 4.85
5451 6209 2.893398 CCTCCGTGACCCTACAGC 59.107 66.667 0.00 0.00 0.00 4.40
5452 6210 2.893398 GCCTCCGTGACCCTACAG 59.107 66.667 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.