Multiple sequence alignment - TraesCS5A01G031500

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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 TraesCS5A01G031500 chr5A 100.000 4710 0 0 1 4710 29127533 29122824 0.000000e+00 8698.0
1 TraesCS5A01G031500 chr5A 87.574 1175 108 23 1613 2772 28698038 28699189 0.000000e+00 1327.0
2 TraesCS5A01G031500 chr5A 90.823 632 47 8 997 1618 28697286 28697916 0.000000e+00 835.0
3 TraesCS5A01G031500 chr5A 80.964 788 114 17 1646 2418 29119037 29119803 4.060000e-165 592.0
4 TraesCS5A01G031500 chr5A 80.564 638 93 14 970 1584 29118269 29118898 3.320000e-126 462.0
5 TraesCS5A01G031500 chr5A 83.333 420 59 8 3297 3711 28699938 28700351 1.240000e-100 377.0
6 TraesCS5A01G031500 chr5A 87.429 175 19 2 2921 3095 28699493 28699664 1.030000e-46 198.0
7 TraesCS5A01G031500 chr5A 77.239 268 31 18 4342 4607 28702190 28702429 3.820000e-26 130.0
8 TraesCS5A01G031500 chr5B 92.683 1476 70 12 2261 3712 34766644 34765183 0.000000e+00 2093.0
9 TraesCS5A01G031500 chr5B 94.083 1014 48 8 1616 2624 34767650 34766644 0.000000e+00 1530.0
10 TraesCS5A01G031500 chr5B 87.169 1169 121 21 1613 2772 34039364 34040512 0.000000e+00 1301.0
11 TraesCS5A01G031500 chr5B 86.142 1169 104 32 1613 2772 34250403 34251522 0.000000e+00 1208.0
12 TraesCS5A01G031500 chr5B 91.383 824 36 11 799 1609 34768570 34767769 0.000000e+00 1096.0
13 TraesCS5A01G031500 chr5B 91.763 607 39 6 1022 1618 34249682 34250287 0.000000e+00 833.0
14 TraesCS5A01G031500 chr5B 91.540 591 39 8 1029 1609 34038674 34039263 0.000000e+00 804.0
15 TraesCS5A01G031500 chr5B 80.982 815 119 16 1619 2418 34743428 34744221 8.660000e-172 614.0
16 TraesCS5A01G031500 chr5B 85.238 420 54 7 3297 3711 34041300 34041716 4.360000e-115 425.0
17 TraesCS5A01G031500 chr5B 93.488 215 13 1 169 382 34769134 34768920 7.610000e-83 318.0
18 TraesCS5A01G031500 chr5B 82.836 268 27 10 2921 3188 34040800 34041048 6.130000e-54 222.0
19 TraesCS5A01G031500 chr5B 81.181 271 24 10 4342 4610 34253442 34253687 4.810000e-45 193.0
20 TraesCS5A01G031500 chr5B 90.714 140 4 3 4580 4710 34747619 34747480 1.350000e-40 178.0
21 TraesCS5A01G031500 chr5B 88.095 126 9 5 732 852 34038522 34038646 1.370000e-30 145.0
22 TraesCS5A01G031500 chr5B 92.708 96 7 0 4390 4485 34764401 34764306 6.360000e-29 139.0
23 TraesCS5A01G031500 chr5B 86.000 100 10 3 3781 3878 34558134 34558037 2.320000e-18 104.0
24 TraesCS5A01G031500 chr5B 100.000 33 0 0 3268 3300 545083458 545083490 1.420000e-05 62.1
25 TraesCS5A01G031500 chr5D 95.427 1006 42 2 1619 2620 40922786 40921781 0.000000e+00 1600.0
26 TraesCS5A01G031500 chr5D 93.449 977 42 9 2752 3711 40921774 40920803 0.000000e+00 1430.0
27 TraesCS5A01G031500 chr5D 88.130 1171 106 22 1613 2772 40716472 40717620 0.000000e+00 1362.0
28 TraesCS5A01G031500 chr5D 91.632 717 39 7 909 1609 40923619 40922908 0.000000e+00 972.0
29 TraesCS5A01G031500 chr5D 90.333 631 52 6 997 1618 40715720 40716350 0.000000e+00 819.0
30 TraesCS5A01G031500 chr5D 95.056 445 17 3 4269 4710 40920274 40919832 0.000000e+00 695.0
31 TraesCS5A01G031500 chr5D 81.081 814 116 19 1619 2416 40915735 40916526 2.410000e-172 616.0
32 TraesCS5A01G031500 chr5D 95.300 383 15 3 1 382 40925734 40925354 5.210000e-169 604.0
33 TraesCS5A01G031500 chr5D 80.818 636 93 14 970 1583 40914953 40915581 5.520000e-129 472.0
34 TraesCS5A01G031500 chr5D 91.259 286 13 3 3711 3993 40920590 40920314 3.440000e-101 379.0
35 TraesCS5A01G031500 chr5D 83.212 274 27 8 2921 3188 40717909 40718169 2.830000e-57 233.0
36 TraesCS5A01G031500 chr5D 79.817 327 45 11 3711 4030 40718953 40719265 7.940000e-53 219.0
37 TraesCS5A01G031500 chr5D 79.336 271 29 11 4342 4610 40720683 40720928 1.050000e-36 165.0
38 TraesCS5A01G031500 chr5D 94.545 110 1 1 799 908 40924037 40923933 1.050000e-36 165.0
39 TraesCS5A01G031500 chr5D 94.253 87 4 1 465 551 40925355 40925270 1.060000e-26 132.0
40 TraesCS5A01G031500 chr5D 91.781 73 3 3 3967 4037 40767035 40766964 1.080000e-16 99.0
41 TraesCS5A01G031500 chr5D 85.227 88 11 2 4211 4297 491878524 491878610 6.490000e-14 89.8
42 TraesCS5A01G031500 chr5D 94.000 50 0 3 4005 4054 40920322 40920276 6.540000e-09 73.1
43 TraesCS5A01G031500 chr5D 100.000 29 0 0 709 737 40925053 40925025 2.000000e-03 54.7
44 TraesCS5A01G031500 chr3B 89.293 934 66 13 2550 3463 754379483 754380402 0.000000e+00 1140.0
45 TraesCS5A01G031500 chr3B 90.500 400 30 3 2154 2551 754378574 754378967 5.400000e-144 521.0
46 TraesCS5A01G031500 chr3B 93.939 66 4 0 4046 4111 655849231 655849296 3.000000e-17 100.0
47 TraesCS5A01G031500 chr3B 90.411 73 6 1 4046 4118 125572613 125572684 1.400000e-15 95.3
48 TraesCS5A01G031500 chr4B 80.186 646 85 21 970 1583 628579207 628578573 1.200000e-120 444.0
49 TraesCS5A01G031500 chr4B 84.906 265 23 6 2361 2620 628583287 628583539 7.820000e-63 252.0
50 TraesCS5A01G031500 chr4B 90.805 87 8 0 97 183 628582593 628582679 2.980000e-22 117.0
51 TraesCS5A01G031500 chr4A 88.421 95 9 2 374 468 742557422 742557514 3.850000e-21 113.0
52 TraesCS5A01G031500 chr4A 100.000 28 0 0 380 407 723602532 723602505 9.000000e-03 52.8
53 TraesCS5A01G031500 chr6D 89.773 88 7 2 4211 4297 385564667 385564581 1.390000e-20 111.0
54 TraesCS5A01G031500 chr2A 96.774 62 2 0 4046 4107 16527049 16526988 2.320000e-18 104.0
55 TraesCS5A01G031500 chr2A 97.222 36 1 0 2994 3029 705588650 705588615 1.420000e-05 62.1
56 TraesCS5A01G031500 chr7D 95.161 62 3 0 4046 4107 600490447 600490386 1.080000e-16 99.0
57 TraesCS5A01G031500 chr7D 93.750 64 2 2 4046 4108 59867613 59867551 1.400000e-15 95.3
58 TraesCS5A01G031500 chr7A 95.161 62 3 0 4046 4107 24673626 24673687 1.080000e-16 99.0
59 TraesCS5A01G031500 chr7A 95.161 62 3 0 4046 4107 24692875 24692936 1.080000e-16 99.0
60 TraesCS5A01G031500 chr1D 95.161 62 3 0 4046 4107 437855316 437855377 1.080000e-16 99.0
61 TraesCS5A01G031500 chr6B 80.597 134 18 6 4201 4332 504564812 504564939 3.880000e-16 97.1
62 TraesCS5A01G031500 chr6B 100.000 28 0 0 380 407 692573016 692573043 9.000000e-03 52.8
63 TraesCS5A01G031500 chr1B 93.651 63 4 0 4046 4108 345303744 345303806 1.400000e-15 95.3
64 TraesCS5A01G031500 chr1B 100.000 33 0 0 434 466 5955748 5955780 1.420000e-05 62.1
65 TraesCS5A01G031500 chr6A 90.476 63 6 0 4196 4258 4831774 4831712 3.020000e-12 84.2
66 TraesCS5A01G031500 chr3A 100.000 33 0 0 3269 3301 602889107 602889139 1.420000e-05 62.1
67 TraesCS5A01G031500 chr2B 97.222 36 1 0 2994 3029 677015810 677015775 1.420000e-05 62.1
68 TraesCS5A01G031500 chr2D 97.143 35 1 0 2995 3029 565147667 565147633 5.090000e-05 60.2
69 TraesCS5A01G031500 chr2D 100.000 30 0 0 380 409 387192251 387192280 6.580000e-04 56.5
70 TraesCS5A01G031500 chr2D 94.444 36 1 1 373 407 382954861 382954826 2.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G031500 chr5A 29122824 29127533 4709 True 8698.000000 8698 100.0000 1 4710 1 chr5A.!!$R1 4709
1 TraesCS5A01G031500 chr5A 28697286 28702429 5143 False 573.400000 1327 85.2796 997 4607 5 chr5A.!!$F1 3610
2 TraesCS5A01G031500 chr5A 29118269 29119803 1534 False 527.000000 592 80.7640 970 2418 2 chr5A.!!$F2 1448
3 TraesCS5A01G031500 chr5B 34764306 34769134 4828 True 1035.200000 2093 92.8690 169 4485 5 chr5B.!!$R3 4316
4 TraesCS5A01G031500 chr5B 34249682 34253687 4005 False 744.666667 1208 86.3620 1022 4610 3 chr5B.!!$F4 3588
5 TraesCS5A01G031500 chr5B 34743428 34744221 793 False 614.000000 614 80.9820 1619 2418 1 chr5B.!!$F1 799
6 TraesCS5A01G031500 chr5B 34038522 34041716 3194 False 579.400000 1301 86.9756 732 3711 5 chr5B.!!$F3 2979
7 TraesCS5A01G031500 chr5D 40919832 40925734 5902 True 610.480000 1600 94.4921 1 4710 10 chr5D.!!$R2 4709
8 TraesCS5A01G031500 chr5D 40715720 40720928 5208 False 559.600000 1362 84.1656 997 4610 5 chr5D.!!$F2 3613
9 TraesCS5A01G031500 chr5D 40914953 40916526 1573 False 544.000000 616 80.9495 970 2416 2 chr5D.!!$F3 1446
10 TraesCS5A01G031500 chr3B 754378574 754380402 1828 False 830.500000 1140 89.8965 2154 3463 2 chr3B.!!$F3 1309
11 TraesCS5A01G031500 chr4B 628578573 628579207 634 True 444.000000 444 80.1860 970 1583 1 chr4B.!!$R1 613

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
793 1800 0.106149 GTAGGTTTCCATCCCGCGAT 59.894 55.000 8.23 0.00 0.0 4.58 F
2135 3663 0.390472 GGAAGCCTCAAGTCCTGTCG 60.390 60.000 0.00 0.00 0.0 4.35 F
2879 5441 1.129251 CATGTCATCTGCGGTGTGAAC 59.871 52.381 5.22 2.37 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2790 5348 0.322816 AGCAGGTGTGGCATTCGAAT 60.323 50.0 4.39 4.39 0.0 3.34 R
3550 6488 0.947180 CGTTGTTGTACACCTCCCGG 60.947 60.0 0.00 0.00 0.0 5.73 R
4234 9150 0.249280 TCTGCGTTCGTGTCATGTGT 60.249 50.0 0.00 0.00 0.0 3.72 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
30 31 1.536284 GGACGTCTTATCTGCGGAAGG 60.536 57.143 16.46 0.00 0.00 3.46
34 35 2.098607 CGTCTTATCTGCGGAAGGTACA 59.901 50.000 0.00 0.00 0.00 2.90
36 37 2.100916 TCTTATCTGCGGAAGGTACAGC 59.899 50.000 0.00 0.00 0.00 4.40
92 93 3.731867 CGGCTGAAACAGGATTGTATTGC 60.732 47.826 0.00 0.00 36.23 3.56
102 103 5.245751 ACAGGATTGTATTGCAACCAATTCA 59.754 36.000 23.84 4.42 41.68 2.57
150 151 2.005451 CAAGAAGGTGGAAGATCAGCG 58.995 52.381 0.00 0.00 39.81 5.18
210 211 4.900635 AGTTTGTGTAGCTGTTTTCCAG 57.099 40.909 0.00 0.00 44.53 3.86
250 251 6.554419 TGTAATGTTGTTGCTCATATGCTTC 58.446 36.000 0.00 0.00 0.00 3.86
273 274 0.603065 GTGGCTTGATGAACCAACCC 59.397 55.000 0.00 0.00 34.63 4.11
327 328 8.883789 TGTAACTCGTGTCAAAGTTTTAAAAG 57.116 30.769 0.00 0.00 37.02 2.27
328 329 8.719648 TGTAACTCGTGTCAAAGTTTTAAAAGA 58.280 29.630 0.00 0.00 37.02 2.52
382 385 8.948631 TCAATGGTGAACTCTTTATCTCATAC 57.051 34.615 0.00 0.00 0.00 2.39
383 386 8.762645 TCAATGGTGAACTCTTTATCTCATACT 58.237 33.333 0.00 0.00 0.00 2.12
384 387 9.039870 CAATGGTGAACTCTTTATCTCATACTC 57.960 37.037 0.00 0.00 0.00 2.59
385 388 7.113658 TGGTGAACTCTTTATCTCATACTCC 57.886 40.000 0.00 0.00 0.00 3.85
386 389 6.098409 TGGTGAACTCTTTATCTCATACTCCC 59.902 42.308 0.00 0.00 0.00 4.30
387 390 6.325286 GGTGAACTCTTTATCTCATACTCCCT 59.675 42.308 0.00 0.00 0.00 4.20
388 391 7.430441 GTGAACTCTTTATCTCATACTCCCTC 58.570 42.308 0.00 0.00 0.00 4.30
389 392 6.551601 TGAACTCTTTATCTCATACTCCCTCC 59.448 42.308 0.00 0.00 0.00 4.30
390 393 5.074115 ACTCTTTATCTCATACTCCCTCCG 58.926 45.833 0.00 0.00 0.00 4.63
391 394 5.063017 TCTTTATCTCATACTCCCTCCGT 57.937 43.478 0.00 0.00 0.00 4.69
392 395 5.455872 TCTTTATCTCATACTCCCTCCGTT 58.544 41.667 0.00 0.00 0.00 4.44
393 396 5.535406 TCTTTATCTCATACTCCCTCCGTTC 59.465 44.000 0.00 0.00 0.00 3.95
394 397 2.068834 TCTCATACTCCCTCCGTTCC 57.931 55.000 0.00 0.00 0.00 3.62
395 398 1.286849 TCTCATACTCCCTCCGTTCCA 59.713 52.381 0.00 0.00 0.00 3.53
396 399 2.091278 TCTCATACTCCCTCCGTTCCAT 60.091 50.000 0.00 0.00 0.00 3.41
397 400 3.139584 TCTCATACTCCCTCCGTTCCATA 59.860 47.826 0.00 0.00 0.00 2.74
398 401 3.895656 CTCATACTCCCTCCGTTCCATAA 59.104 47.826 0.00 0.00 0.00 1.90
399 402 4.489737 TCATACTCCCTCCGTTCCATAAT 58.510 43.478 0.00 0.00 0.00 1.28
400 403 4.283467 TCATACTCCCTCCGTTCCATAATG 59.717 45.833 0.00 0.00 0.00 1.90
401 404 2.478292 ACTCCCTCCGTTCCATAATGT 58.522 47.619 0.00 0.00 0.00 2.71
402 405 3.649843 ACTCCCTCCGTTCCATAATGTA 58.350 45.455 0.00 0.00 0.00 2.29
403 406 4.035112 ACTCCCTCCGTTCCATAATGTAA 58.965 43.478 0.00 0.00 0.00 2.41
404 407 4.658901 ACTCCCTCCGTTCCATAATGTAAT 59.341 41.667 0.00 0.00 0.00 1.89
405 408 4.968259 TCCCTCCGTTCCATAATGTAATG 58.032 43.478 0.00 0.00 0.00 1.90
406 409 3.502211 CCCTCCGTTCCATAATGTAATGC 59.498 47.826 0.00 0.00 0.00 3.56
407 410 3.186409 CCTCCGTTCCATAATGTAATGCG 59.814 47.826 0.00 0.00 0.00 4.73
408 411 3.799366 TCCGTTCCATAATGTAATGCGT 58.201 40.909 0.00 0.00 0.00 5.24
409 412 4.193090 TCCGTTCCATAATGTAATGCGTT 58.807 39.130 0.00 0.00 0.00 4.84
410 413 4.636648 TCCGTTCCATAATGTAATGCGTTT 59.363 37.500 0.00 0.00 0.00 3.60
411 414 5.124138 TCCGTTCCATAATGTAATGCGTTTT 59.876 36.000 0.00 0.00 0.00 2.43
412 415 5.802956 CCGTTCCATAATGTAATGCGTTTTT 59.197 36.000 0.00 0.00 0.00 1.94
558 592 5.118286 CAAGCACCCTCAATTTCAAAACTT 58.882 37.500 0.00 0.00 0.00 2.66
602 636 8.833493 ACCTATTAATACGGATGCTTTTGTAAC 58.167 33.333 14.32 0.00 0.00 2.50
774 1781 1.244019 CGGCCCAAAGAAGGAACAGG 61.244 60.000 0.00 0.00 0.00 4.00
775 1782 0.178961 GGCCCAAAGAAGGAACAGGT 60.179 55.000 0.00 0.00 0.00 4.00
776 1783 1.074889 GGCCCAAAGAAGGAACAGGTA 59.925 52.381 0.00 0.00 0.00 3.08
777 1784 2.437413 GCCCAAAGAAGGAACAGGTAG 58.563 52.381 0.00 0.00 0.00 3.18
778 1785 2.880167 GCCCAAAGAAGGAACAGGTAGG 60.880 54.545 0.00 0.00 0.00 3.18
779 1786 2.375509 CCCAAAGAAGGAACAGGTAGGT 59.624 50.000 0.00 0.00 0.00 3.08
780 1787 3.181433 CCCAAAGAAGGAACAGGTAGGTT 60.181 47.826 0.00 0.00 0.00 3.50
782 1789 4.519350 CCAAAGAAGGAACAGGTAGGTTTC 59.481 45.833 0.00 0.00 0.00 2.78
783 1790 4.368565 AAGAAGGAACAGGTAGGTTTCC 57.631 45.455 0.00 0.00 0.00 3.13
784 1791 3.323775 AGAAGGAACAGGTAGGTTTCCA 58.676 45.455 2.61 0.00 0.00 3.53
785 1792 3.916989 AGAAGGAACAGGTAGGTTTCCAT 59.083 43.478 2.61 0.00 0.00 3.41
786 1793 4.019231 AGAAGGAACAGGTAGGTTTCCATC 60.019 45.833 2.61 0.19 0.00 3.51
787 1794 2.576648 AGGAACAGGTAGGTTTCCATCC 59.423 50.000 2.61 0.00 0.00 3.51
788 1795 2.356844 GGAACAGGTAGGTTTCCATCCC 60.357 54.545 0.00 0.00 0.00 3.85
789 1796 0.909623 ACAGGTAGGTTTCCATCCCG 59.090 55.000 0.00 0.00 0.00 5.14
790 1797 0.463833 CAGGTAGGTTTCCATCCCGC 60.464 60.000 0.00 0.00 0.00 6.13
791 1798 1.523032 GGTAGGTTTCCATCCCGCG 60.523 63.158 0.00 0.00 0.00 6.46
792 1799 1.518774 GTAGGTTTCCATCCCGCGA 59.481 57.895 8.23 0.00 0.00 5.87
793 1800 0.106149 GTAGGTTTCCATCCCGCGAT 59.894 55.000 8.23 0.00 0.00 4.58
794 1801 1.342174 GTAGGTTTCCATCCCGCGATA 59.658 52.381 8.23 0.00 0.00 2.92
795 1802 0.393077 AGGTTTCCATCCCGCGATAG 59.607 55.000 8.23 0.00 0.00 2.08
796 1803 0.391597 GGTTTCCATCCCGCGATAGA 59.608 55.000 8.23 0.84 39.76 1.98
797 1804 1.202604 GGTTTCCATCCCGCGATAGAA 60.203 52.381 8.23 0.00 39.76 2.10
1164 2514 2.047844 GTCAAGCTGCTCGCCTCA 60.048 61.111 1.00 0.00 40.39 3.86
1191 2541 0.665835 ATCTGCTACGCTTCCTCGAG 59.334 55.000 5.13 5.13 0.00 4.04
1413 2790 4.144703 GAAGCCGACCCCCTCGTC 62.145 72.222 0.00 0.00 41.18 4.20
1598 2975 4.821589 CACCCTCGAGAAGGCCGC 62.822 72.222 15.71 0.00 44.71 6.53
1674 3187 1.683917 CACTAAGGCGAGTGCTCCTAT 59.316 52.381 9.23 0.00 40.42 2.57
1703 3216 0.392998 ATGGTTTCTACCTGCAGGCG 60.393 55.000 33.06 23.10 45.27 5.52
1945 3458 0.994247 TTCCTCTGCACCCATGACAT 59.006 50.000 0.00 0.00 0.00 3.06
2014 3527 3.357079 CTTGGCCGCGACAAAGCT 61.357 61.111 8.23 0.00 26.41 3.74
2106 3622 1.210204 TGCCCAAGCAGGATTCCTCT 61.210 55.000 0.98 0.63 46.52 3.69
2135 3663 0.390472 GGAAGCCTCAAGTCCTGTCG 60.390 60.000 0.00 0.00 0.00 4.35
2460 3992 3.251004 ACATCAAGAAAAAGCCACTCGAC 59.749 43.478 0.00 0.00 0.00 4.20
2481 4013 1.815003 CAAAACAGCTGATGGACCTCC 59.185 52.381 23.35 0.00 0.00 4.30
2577 4995 4.218417 GGCCTACTTGATCAAAACATGTGT 59.782 41.667 9.88 4.66 0.00 3.72
2595 5017 1.133945 TGTTGGAACTTGCTGCTACCA 60.134 47.619 0.00 0.76 0.00 3.25
2652 5077 3.515630 CTGCTTCTTGTGATAAGCTCGA 58.484 45.455 8.36 0.00 46.57 4.04
2729 5154 1.944709 ACCGTGTAAACAGAGTTTGGC 59.055 47.619 5.45 0.08 0.00 4.52
2730 5155 2.218603 CCGTGTAAACAGAGTTTGGCT 58.781 47.619 5.45 0.00 0.00 4.75
2775 5200 8.712285 ATTTATTTCAGTGCATGATTTGGAAG 57.288 30.769 0.00 0.00 37.89 3.46
2788 5346 7.147742 GCATGATTTGGAAGTTCCCCTTAATTA 60.148 37.037 19.42 10.26 35.03 1.40
2789 5347 8.927411 CATGATTTGGAAGTTCCCCTTAATTAT 58.073 33.333 19.42 11.80 35.03 1.28
2879 5441 1.129251 CATGTCATCTGCGGTGTGAAC 59.871 52.381 5.22 2.37 0.00 3.18
2894 5456 3.741344 GTGTGAACATATCCGTATCTGGC 59.259 47.826 0.00 0.00 0.00 4.85
3124 5752 9.057089 CCCGCTCTTATGTTTAAGATAAGATTT 57.943 33.333 20.02 0.00 42.22 2.17
3229 6129 9.528018 GAATCTTACTTCTGAAGTCAAGATAGG 57.472 37.037 29.75 16.78 41.77 2.57
3235 6135 8.602472 ACTTCTGAAGTCAAGATAGGAAGTAT 57.398 34.615 17.00 0.00 39.81 2.12
3380 6318 3.512680 AGTGCGTGTAAATCTCTGCTAC 58.487 45.455 0.00 0.00 0.00 3.58
3550 6488 7.380431 AGATCTATATGACAACGGCTACTAC 57.620 40.000 0.00 0.00 0.00 2.73
3570 6508 0.947180 CGGGAGGTGTACAACAACGG 60.947 60.000 14.58 5.89 41.63 4.44
3596 6534 7.434307 GCCGCATTCTAAGTAATAGCGATTATA 59.566 37.037 5.41 0.00 37.97 0.98
3712 7393 5.336055 GGATGATTATGGAGACGAGTAGTGG 60.336 48.000 0.00 0.00 0.00 4.00
3713 7394 4.533815 TGATTATGGAGACGAGTAGTGGT 58.466 43.478 0.00 0.00 0.00 4.16
3857 7789 2.107378 TGCAGGTGATACCAGGTTTTCA 59.893 45.455 0.00 0.00 41.95 2.69
3905 7839 1.078759 CGATCACTCACAGCGGGTTC 61.079 60.000 0.00 0.00 0.00 3.62
3911 7845 4.760047 CACAGCGGGTTCCCCTCG 62.760 72.222 1.93 0.00 42.67 4.63
3931 7865 2.022764 GCTCTCTGCCTCTCTTTTCC 57.977 55.000 0.00 0.00 35.15 3.13
3935 7869 4.190772 CTCTCTGCCTCTCTTTTCCATTC 58.809 47.826 0.00 0.00 0.00 2.67
3947 7881 2.673775 TTCCATTCCCAGTTTGCTGA 57.326 45.000 0.00 0.00 45.28 4.26
4013 7947 2.820197 GGTTAGCCCAGTTGGAAAAGAG 59.180 50.000 0.00 0.00 37.39 2.85
4014 7948 2.820197 GTTAGCCCAGTTGGAAAAGAGG 59.180 50.000 0.00 0.00 37.39 3.69
4054 7988 2.549754 GGAATCTGTTGGCATCCGTATG 59.450 50.000 0.00 0.00 36.09 2.39
4055 7989 3.206150 GAATCTGTTGGCATCCGTATGT 58.794 45.455 0.00 0.00 35.38 2.29
4056 7990 4.377021 GAATCTGTTGGCATCCGTATGTA 58.623 43.478 0.00 0.00 35.38 2.29
4061 7995 1.783071 TGGCATCCGTATGTAGTCCA 58.217 50.000 0.00 0.00 35.38 4.02
4062 7996 2.325484 TGGCATCCGTATGTAGTCCAT 58.675 47.619 0.00 0.00 35.38 3.41
4066 8000 5.717654 TGGCATCCGTATGTAGTCCATATTA 59.282 40.000 0.00 0.00 38.29 0.98
4067 8001 6.211785 TGGCATCCGTATGTAGTCCATATTAA 59.788 38.462 0.00 0.00 38.29 1.40
4068 8002 7.101054 GGCATCCGTATGTAGTCCATATTAAA 58.899 38.462 0.00 0.00 38.29 1.52
4069 8003 7.604927 GGCATCCGTATGTAGTCCATATTAAAA 59.395 37.037 0.00 0.00 38.29 1.52
4100 8034 8.934507 AGAAAGACTTGTATTTAGAATCGGAG 57.065 34.615 0.00 0.00 0.00 4.63
4101 8035 7.982354 AGAAAGACTTGTATTTAGAATCGGAGG 59.018 37.037 0.00 0.00 0.00 4.30
4102 8036 6.163135 AGACTTGTATTTAGAATCGGAGGG 57.837 41.667 0.00 0.00 0.00 4.30
4104 8038 6.041069 AGACTTGTATTTAGAATCGGAGGGAG 59.959 42.308 0.00 0.00 0.00 4.30
4105 8039 5.661759 ACTTGTATTTAGAATCGGAGGGAGT 59.338 40.000 0.00 0.00 0.00 3.85
4107 8041 7.509659 ACTTGTATTTAGAATCGGAGGGAGTAT 59.490 37.037 0.00 0.00 0.00 2.12
4108 8042 7.850935 TGTATTTAGAATCGGAGGGAGTATT 57.149 36.000 0.00 0.00 0.00 1.89
4110 8044 9.370930 TGTATTTAGAATCGGAGGGAGTATTAA 57.629 33.333 0.00 0.00 0.00 1.40
4111 8045 9.857957 GTATTTAGAATCGGAGGGAGTATTAAG 57.142 37.037 0.00 0.00 0.00 1.85
4123 8187 6.694611 AGGGAGTATTAAGTTACAGAGGGAT 58.305 40.000 0.00 0.00 0.00 3.85
4126 8190 9.102453 GGGAGTATTAAGTTACAGAGGGATTAT 57.898 37.037 0.00 0.00 0.00 1.28
4127 8191 9.930693 GGAGTATTAAGTTACAGAGGGATTATG 57.069 37.037 0.00 0.00 0.00 1.90
4132 8196 8.849543 TTAAGTTACAGAGGGATTATGTAGGT 57.150 34.615 0.00 0.00 35.12 3.08
4134 8198 8.849543 AAGTTACAGAGGGATTATGTAGGTTA 57.150 34.615 0.00 0.00 35.12 2.85
4135 8199 8.849543 AGTTACAGAGGGATTATGTAGGTTAA 57.150 34.615 0.00 0.00 35.12 2.01
4136 8200 9.275572 AGTTACAGAGGGATTATGTAGGTTAAA 57.724 33.333 0.00 0.00 35.12 1.52
4140 8204 9.448587 ACAGAGGGATTATGTAGGTTAAATACT 57.551 33.333 1.95 0.00 27.16 2.12
4141 8205 9.712305 CAGAGGGATTATGTAGGTTAAATACTG 57.288 37.037 0.00 0.00 0.00 2.74
4142 8206 9.670442 AGAGGGATTATGTAGGTTAAATACTGA 57.330 33.333 1.95 0.00 0.00 3.41
4152 8216 9.344772 TGTAGGTTAAATACTGATGTTGTTTGT 57.655 29.630 1.95 0.00 0.00 2.83
4183 9099 5.455056 AAAAAGGTGTGTGTGTGTGTAAA 57.545 34.783 0.00 0.00 0.00 2.01
4184 9100 5.652994 AAAAGGTGTGTGTGTGTGTAAAT 57.347 34.783 0.00 0.00 0.00 1.40
4185 9101 4.893424 AAGGTGTGTGTGTGTGTAAATC 57.107 40.909 0.00 0.00 0.00 2.17
4186 9102 4.150897 AGGTGTGTGTGTGTGTAAATCT 57.849 40.909 0.00 0.00 0.00 2.40
4187 9103 4.127171 AGGTGTGTGTGTGTGTAAATCTC 58.873 43.478 0.00 0.00 0.00 2.75
4188 9104 4.127171 GGTGTGTGTGTGTGTAAATCTCT 58.873 43.478 0.00 0.00 0.00 3.10
4189 9105 4.024893 GGTGTGTGTGTGTGTAAATCTCTG 60.025 45.833 0.00 0.00 0.00 3.35
4190 9106 3.559655 TGTGTGTGTGTGTAAATCTCTGC 59.440 43.478 0.00 0.00 0.00 4.26
4191 9107 3.809832 GTGTGTGTGTGTAAATCTCTGCT 59.190 43.478 0.00 0.00 0.00 4.24
4192 9108 4.988540 GTGTGTGTGTGTAAATCTCTGCTA 59.011 41.667 0.00 0.00 0.00 3.49
4194 9110 5.639082 TGTGTGTGTGTAAATCTCTGCTATG 59.361 40.000 0.00 0.00 0.00 2.23
4195 9111 5.639506 GTGTGTGTGTAAATCTCTGCTATGT 59.360 40.000 0.00 0.00 0.00 2.29
4197 9113 6.710295 TGTGTGTGTAAATCTCTGCTATGTTT 59.290 34.615 0.00 0.00 0.00 2.83
4198 9114 7.875554 TGTGTGTGTAAATCTCTGCTATGTTTA 59.124 33.333 0.00 0.00 0.00 2.01
4211 9127 9.474920 CTCTGCTATGTTTAATAGAGGAAAGAG 57.525 37.037 0.00 0.00 0.00 2.85
4212 9128 9.201989 TCTGCTATGTTTAATAGAGGAAAGAGA 57.798 33.333 0.00 0.00 0.00 3.10
4213 9129 9.823647 CTGCTATGTTTAATAGAGGAAAGAGAA 57.176 33.333 0.00 0.00 0.00 2.87
4226 9142 8.423906 AGAGGAAAGAGAATTAGTACAAGTGA 57.576 34.615 0.00 0.00 0.00 3.41
4227 9143 8.527810 AGAGGAAAGAGAATTAGTACAAGTGAG 58.472 37.037 0.00 0.00 0.00 3.51
4228 9144 7.616313 AGGAAAGAGAATTAGTACAAGTGAGG 58.384 38.462 0.00 0.00 0.00 3.86
4229 9145 7.455008 AGGAAAGAGAATTAGTACAAGTGAGGA 59.545 37.037 0.00 0.00 0.00 3.71
4230 9146 8.261522 GGAAAGAGAATTAGTACAAGTGAGGAT 58.738 37.037 0.00 0.00 0.00 3.24
4234 9150 9.256228 AGAGAATTAGTACAAGTGAGGATACAA 57.744 33.333 0.00 0.00 41.41 2.41
4235 9151 9.303537 GAGAATTAGTACAAGTGAGGATACAAC 57.696 37.037 0.00 0.00 41.41 3.32
4236 9152 8.812972 AGAATTAGTACAAGTGAGGATACAACA 58.187 33.333 0.00 0.00 41.41 3.33
4237 9153 8.773404 AATTAGTACAAGTGAGGATACAACAC 57.227 34.615 0.00 0.00 43.22 3.32
4238 9154 5.801531 AGTACAAGTGAGGATACAACACA 57.198 39.130 7.77 0.00 44.57 3.72
4239 9155 6.360370 AGTACAAGTGAGGATACAACACAT 57.640 37.500 7.77 0.00 44.57 3.21
4240 9156 6.166279 AGTACAAGTGAGGATACAACACATG 58.834 40.000 7.77 8.05 44.57 3.21
4241 9157 5.227569 ACAAGTGAGGATACAACACATGA 57.772 39.130 14.30 0.00 42.71 3.07
4242 9158 4.997395 ACAAGTGAGGATACAACACATGAC 59.003 41.667 14.30 0.00 42.71 3.06
4244 9160 4.569943 AGTGAGGATACAACACATGACAC 58.430 43.478 0.00 0.00 44.57 3.67
4245 9161 3.367932 GTGAGGATACAACACATGACACG 59.632 47.826 0.00 0.00 42.71 4.49
4247 9163 4.242475 GAGGATACAACACATGACACGAA 58.758 43.478 0.00 0.00 41.41 3.85
4249 9165 3.181534 GGATACAACACATGACACGAACG 60.182 47.826 0.00 0.00 0.00 3.95
4250 9166 0.303493 ACAACACATGACACGAACGC 59.697 50.000 0.00 0.00 0.00 4.84
4251 9167 0.303191 CAACACATGACACGAACGCA 59.697 50.000 0.00 0.00 0.00 5.24
4252 9168 0.581529 AACACATGACACGAACGCAG 59.418 50.000 0.00 0.00 0.00 5.18
4253 9169 0.249280 ACACATGACACGAACGCAGA 60.249 50.000 0.00 0.00 0.00 4.26
4254 9170 0.858583 CACATGACACGAACGCAGAA 59.141 50.000 0.00 0.00 0.00 3.02
4258 9174 2.665185 ACACGAACGCAGAAGGGC 60.665 61.111 0.00 0.00 0.00 5.19
4266 9182 3.987404 GCAGAAGGGCGTGAACAT 58.013 55.556 0.00 0.00 0.00 2.71
4267 9183 1.503542 GCAGAAGGGCGTGAACATG 59.496 57.895 0.00 0.00 0.00 3.21
4269 9185 0.606401 CAGAAGGGCGTGAACATGGT 60.606 55.000 0.00 0.00 0.00 3.55
4270 9186 0.606401 AGAAGGGCGTGAACATGGTG 60.606 55.000 0.00 0.00 0.00 4.17
4271 9187 2.200170 GAAGGGCGTGAACATGGTGC 62.200 60.000 0.00 0.00 0.00 5.01
4272 9188 3.747976 GGGCGTGAACATGGTGCC 61.748 66.667 1.91 1.91 44.98 5.01
4273 9189 3.747976 GGCGTGAACATGGTGCCC 61.748 66.667 0.00 0.00 39.83 5.36
4274 9190 4.101790 GCGTGAACATGGTGCCCG 62.102 66.667 0.00 0.00 0.00 6.13
4275 9191 3.430862 CGTGAACATGGTGCCCGG 61.431 66.667 0.00 0.00 0.00 5.73
4276 9192 3.747976 GTGAACATGGTGCCCGGC 61.748 66.667 1.04 1.04 0.00 6.13
4320 9236 9.874215 GCTTGACCGAAATAAGGTAATAATAAC 57.126 33.333 0.00 0.00 43.01 1.89
4371 9654 2.844946 TGCTCACGAGAAATGTGGAAA 58.155 42.857 0.00 0.00 37.91 3.13
4450 9735 2.548178 ACAGCGCTTGTCCTGATTG 58.452 52.632 7.50 0.00 33.87 2.67
4695 9983 8.617761 AATGTTTTTGTAGCTTGCAAAATTTG 57.382 26.923 21.46 0.57 42.85 2.32
4700 9988 7.966246 TTTGTAGCTTGCAAAATTTGATCAT 57.034 28.000 10.26 0.00 33.51 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.855349 CGCAGATAAGACGTCCATGC 59.145 55.000 13.01 13.92 0.00 4.06
8 9 1.399714 TCCGCAGATAAGACGTCCAT 58.600 50.000 13.01 5.90 0.00 3.41
30 31 2.229302 AGACCGAGTTTCAGAGCTGTAC 59.771 50.000 0.00 0.00 0.00 2.90
34 35 2.490115 CTGTAGACCGAGTTTCAGAGCT 59.510 50.000 0.00 0.00 0.00 4.09
36 37 4.230657 CAACTGTAGACCGAGTTTCAGAG 58.769 47.826 0.00 0.00 29.73 3.35
92 93 7.492020 TGAAATCTGAGTTGTTTGAATTGGTTG 59.508 33.333 0.00 0.00 0.00 3.77
102 103 6.208007 TGATGCTCATGAAATCTGAGTTGTTT 59.792 34.615 15.52 0.00 41.77 2.83
137 138 0.749454 AATGCCCGCTGATCTTCCAC 60.749 55.000 0.00 0.00 0.00 4.02
150 151 2.443390 ATGGCTGCAGGAATGCCC 60.443 61.111 17.12 7.37 45.56 5.36
250 251 0.321564 TGGTTCATCAAGCCACTCCG 60.322 55.000 0.00 0.00 0.00 4.63
382 385 4.682778 TTACATTATGGAACGGAGGGAG 57.317 45.455 0.00 0.00 0.00 4.30
383 386 4.745478 GCATTACATTATGGAACGGAGGGA 60.745 45.833 0.00 0.00 0.00 4.20
384 387 3.502211 GCATTACATTATGGAACGGAGGG 59.498 47.826 0.00 0.00 0.00 4.30
385 388 3.186409 CGCATTACATTATGGAACGGAGG 59.814 47.826 0.00 0.00 0.00 4.30
386 389 3.807622 ACGCATTACATTATGGAACGGAG 59.192 43.478 5.41 0.41 0.00 4.63
387 390 3.799366 ACGCATTACATTATGGAACGGA 58.201 40.909 5.41 0.00 0.00 4.69
388 391 4.545823 AACGCATTACATTATGGAACGG 57.454 40.909 5.41 0.00 0.00 4.44
389 392 6.862944 AAAAACGCATTACATTATGGAACG 57.137 33.333 0.00 0.00 0.00 3.95
433 436 9.401058 CTCTGTCCCATAATCTAAGATGTTTTT 57.599 33.333 0.00 0.00 0.00 1.94
434 437 7.995488 CCTCTGTCCCATAATCTAAGATGTTTT 59.005 37.037 0.00 0.00 0.00 2.43
435 438 7.420680 CCCTCTGTCCCATAATCTAAGATGTTT 60.421 40.741 0.00 0.00 0.00 2.83
436 439 6.043706 CCCTCTGTCCCATAATCTAAGATGTT 59.956 42.308 0.00 0.00 0.00 2.71
437 440 5.545723 CCCTCTGTCCCATAATCTAAGATGT 59.454 44.000 0.00 0.00 0.00 3.06
438 441 5.782331 TCCCTCTGTCCCATAATCTAAGATG 59.218 44.000 0.00 0.00 0.00 2.90
439 442 5.982391 TCCCTCTGTCCCATAATCTAAGAT 58.018 41.667 0.00 0.00 0.00 2.40
440 443 5.103043 ACTCCCTCTGTCCCATAATCTAAGA 60.103 44.000 0.00 0.00 0.00 2.10
441 444 5.151454 ACTCCCTCTGTCCCATAATCTAAG 58.849 45.833 0.00 0.00 0.00 2.18
442 445 5.157770 ACTCCCTCTGTCCCATAATCTAA 57.842 43.478 0.00 0.00 0.00 2.10
443 446 4.834406 ACTCCCTCTGTCCCATAATCTA 57.166 45.455 0.00 0.00 0.00 1.98
444 447 3.715648 ACTCCCTCTGTCCCATAATCT 57.284 47.619 0.00 0.00 0.00 2.40
445 448 7.554959 TTTATACTCCCTCTGTCCCATAATC 57.445 40.000 0.00 0.00 0.00 1.75
446 449 7.794683 TCTTTTATACTCCCTCTGTCCCATAAT 59.205 37.037 0.00 0.00 0.00 1.28
447 450 7.136885 TCTTTTATACTCCCTCTGTCCCATAA 58.863 38.462 0.00 0.00 0.00 1.90
448 451 6.689561 TCTTTTATACTCCCTCTGTCCCATA 58.310 40.000 0.00 0.00 0.00 2.74
449 452 5.538877 TCTTTTATACTCCCTCTGTCCCAT 58.461 41.667 0.00 0.00 0.00 4.00
450 453 4.955335 TCTTTTATACTCCCTCTGTCCCA 58.045 43.478 0.00 0.00 0.00 4.37
451 454 5.952347 TTCTTTTATACTCCCTCTGTCCC 57.048 43.478 0.00 0.00 0.00 4.46
452 455 8.047310 TCATTTTCTTTTATACTCCCTCTGTCC 58.953 37.037 0.00 0.00 0.00 4.02
453 456 9.620259 ATCATTTTCTTTTATACTCCCTCTGTC 57.380 33.333 0.00 0.00 0.00 3.51
499 502 0.255890 ACAGATAAGTGGGCGCCAAT 59.744 50.000 30.85 12.90 34.18 3.16
558 592 7.701539 AATAGGTGTGAGCACATTTAATTCA 57.298 32.000 6.59 0.00 46.95 2.57
571 605 5.784177 AGCATCCGTATTAATAGGTGTGAG 58.216 41.667 12.80 0.00 0.00 3.51
602 636 9.214957 TCATAAGTACCATGTAAACAGAAAGTG 57.785 33.333 5.28 0.00 0.00 3.16
684 718 7.094805 GGCCTAAAATGAAATTCTTTTTGTCCC 60.095 37.037 22.03 16.34 33.67 4.46
694 730 2.798145 CGGCCGGCCTAAAATGAAATTC 60.798 50.000 41.01 11.70 33.67 2.17
737 801 0.535335 CGGCCCACTAGCTCACTTTA 59.465 55.000 0.00 0.00 0.00 1.85
774 1781 0.106149 ATCGCGGGATGGAAACCTAC 59.894 55.000 14.93 0.00 0.00 3.18
775 1782 1.616865 CTATCGCGGGATGGAAACCTA 59.383 52.381 23.88 1.34 33.27 3.08
776 1783 0.393077 CTATCGCGGGATGGAAACCT 59.607 55.000 23.88 0.00 33.27 3.50
777 1784 0.391597 TCTATCGCGGGATGGAAACC 59.608 55.000 23.24 0.00 37.24 3.27
778 1785 2.234300 TTCTATCGCGGGATGGAAAC 57.766 50.000 30.22 0.00 44.22 2.78
782 1789 1.726853 GGAATTCTATCGCGGGATGG 58.273 55.000 23.88 20.96 34.00 3.51
783 1790 1.336887 ACGGAATTCTATCGCGGGATG 60.337 52.381 23.88 13.89 34.00 3.51
784 1791 0.966920 ACGGAATTCTATCGCGGGAT 59.033 50.000 19.59 19.59 36.65 3.85
785 1792 0.313043 GACGGAATTCTATCGCGGGA 59.687 55.000 6.13 4.03 0.00 5.14
786 1793 0.666577 GGACGGAATTCTATCGCGGG 60.667 60.000 6.13 0.00 0.00 6.13
787 1794 0.666577 GGGACGGAATTCTATCGCGG 60.667 60.000 6.13 0.00 0.00 6.46
788 1795 0.031585 TGGGACGGAATTCTATCGCG 59.968 55.000 0.00 0.00 0.00 5.87
789 1796 2.234300 TTGGGACGGAATTCTATCGC 57.766 50.000 5.23 11.52 0.00 4.58
790 1797 3.746492 GGATTTGGGACGGAATTCTATCG 59.254 47.826 5.23 3.22 0.00 2.92
791 1798 4.072839 GGGATTTGGGACGGAATTCTATC 58.927 47.826 5.23 3.35 0.00 2.08
792 1799 3.181433 GGGGATTTGGGACGGAATTCTAT 60.181 47.826 5.23 0.00 0.00 1.98
793 1800 2.173996 GGGGATTTGGGACGGAATTCTA 59.826 50.000 5.23 0.00 0.00 2.10
794 1801 1.063942 GGGGATTTGGGACGGAATTCT 60.064 52.381 5.23 0.00 0.00 2.40
795 1802 1.399714 GGGGATTTGGGACGGAATTC 58.600 55.000 0.00 0.00 0.00 2.17
796 1803 0.032515 GGGGGATTTGGGACGGAATT 60.033 55.000 0.00 0.00 0.00 2.17
797 1804 1.218439 TGGGGGATTTGGGACGGAAT 61.218 55.000 0.00 0.00 0.00 3.01
1164 2514 3.207354 CGTAGCAGATCGGGGTGT 58.793 61.111 0.00 0.00 0.00 4.16
1598 2975 4.521062 CCGCCGAGAGCAAGGAGG 62.521 72.222 0.00 0.00 44.04 4.30
1828 3341 1.347707 GACTCAGTGGTGGGAATGTGA 59.652 52.381 0.00 0.00 0.00 3.58
1904 3417 5.413309 AAGAGACAAGTCCATACAAGGAG 57.587 43.478 0.00 0.00 38.64 3.69
1945 3458 3.949842 CCTGATCGGCATTGAGATCTA 57.050 47.619 17.51 8.24 42.62 1.98
2014 3527 2.591429 CCTGAACACCGCTGCACA 60.591 61.111 0.00 0.00 0.00 4.57
2027 3540 3.136443 TGAAGGCTTCTTGTTCTTCCTGA 59.864 43.478 26.26 0.00 35.91 3.86
2106 3622 0.401356 TGAGGCTTCCAGCATGAACA 59.599 50.000 0.00 0.00 44.75 3.18
2135 3663 1.602311 CCCCATTATCTGTCAGCAGC 58.398 55.000 0.00 0.00 42.29 5.25
2201 3729 5.048224 AGTGGAATTGAAAGCAGATGACAAG 60.048 40.000 0.00 0.00 0.00 3.16
2282 3813 1.812922 GCGTCCCTCTGACATGCTG 60.813 63.158 0.00 0.00 44.71 4.41
2460 3992 1.815003 GAGGTCCATCAGCTGTTTTGG 59.185 52.381 14.67 18.15 30.88 3.28
2577 4995 1.953686 GTTGGTAGCAGCAAGTTCCAA 59.046 47.619 3.69 0.00 36.14 3.53
2595 5017 3.744530 GCTAATAAGCGTCCATGGAGGTT 60.745 47.826 29.85 26.06 39.39 3.50
2750 5175 8.316214 ACTTCCAAATCATGCACTGAAATAAAT 58.684 29.630 0.00 0.00 37.44 1.40
2754 5179 5.733620 ACTTCCAAATCATGCACTGAAAT 57.266 34.783 0.00 0.00 37.44 2.17
2775 5200 7.175990 TGGCATTCGAATATAATTAAGGGGAAC 59.824 37.037 10.97 0.00 0.00 3.62
2788 5346 1.949525 GCAGGTGTGGCATTCGAATAT 59.050 47.619 10.97 0.00 0.00 1.28
2789 5347 1.065491 AGCAGGTGTGGCATTCGAATA 60.065 47.619 10.97 0.00 0.00 1.75
2790 5348 0.322816 AGCAGGTGTGGCATTCGAAT 60.323 50.000 4.39 4.39 0.00 3.34
2791 5349 1.073025 AGCAGGTGTGGCATTCGAA 59.927 52.632 0.00 0.00 0.00 3.71
2792 5350 1.672030 CAGCAGGTGTGGCATTCGA 60.672 57.895 0.00 0.00 0.00 3.71
2879 5441 1.544246 TCACGGCCAGATACGGATATG 59.456 52.381 2.24 0.00 0.00 1.78
2894 5456 0.941542 TTTTTCGCTTCCAGTCACGG 59.058 50.000 0.00 0.00 0.00 4.94
3235 6135 8.752187 ACGTCTTACATTAAGTTACATAGGGAA 58.248 33.333 0.00 0.00 37.10 3.97
3380 6318 5.991328 ATGCAGACCACAATTAGTAATCG 57.009 39.130 0.00 0.00 0.00 3.34
3550 6488 0.947180 CGTTGTTGTACACCTCCCGG 60.947 60.000 0.00 0.00 0.00 5.73
3570 6508 3.314553 TCGCTATTACTTAGAATGCGGC 58.685 45.455 0.00 0.00 37.16 6.53
3596 6534 3.492656 CCATCGTGGATCCAGTTCGTAAT 60.493 47.826 16.81 3.21 40.96 1.89
3712 7393 1.277557 AGACTCCTTGATCACCAGCAC 59.722 52.381 0.00 0.00 0.00 4.40
3713 7394 1.649321 AGACTCCTTGATCACCAGCA 58.351 50.000 0.00 0.00 0.00 4.41
3871 7805 4.769688 AGTGATCGCCATCAAACTATCAA 58.230 39.130 1.76 0.00 40.90 2.57
3872 7806 4.141959 TGAGTGATCGCCATCAAACTATCA 60.142 41.667 1.76 0.00 40.90 2.15
3873 7807 4.210120 GTGAGTGATCGCCATCAAACTATC 59.790 45.833 1.76 0.00 40.90 2.08
3874 7808 4.122776 GTGAGTGATCGCCATCAAACTAT 58.877 43.478 1.76 0.00 40.90 2.12
3875 7809 3.056179 TGTGAGTGATCGCCATCAAACTA 60.056 43.478 1.76 0.00 40.90 2.24
3876 7810 2.289631 TGTGAGTGATCGCCATCAAACT 60.290 45.455 1.76 0.00 40.90 2.66
3877 7811 2.076100 TGTGAGTGATCGCCATCAAAC 58.924 47.619 1.76 0.00 40.90 2.93
3878 7812 2.349590 CTGTGAGTGATCGCCATCAAA 58.650 47.619 1.76 0.00 40.90 2.69
3931 7865 3.508793 ACAAGATCAGCAAACTGGGAATG 59.491 43.478 0.00 0.00 44.59 2.67
3935 7869 4.326826 TCTTACAAGATCAGCAAACTGGG 58.673 43.478 0.00 0.00 44.59 4.45
4001 7935 6.014584 ACAAACAGTTTTCCTCTTTTCCAACT 60.015 34.615 0.00 0.00 0.00 3.16
4075 8009 7.982354 CCTCCGATTCTAAATACAAGTCTTTCT 59.018 37.037 0.00 0.00 0.00 2.52
4076 8010 7.224949 CCCTCCGATTCTAAATACAAGTCTTTC 59.775 40.741 0.00 0.00 0.00 2.62
4078 8012 6.383147 TCCCTCCGATTCTAAATACAAGTCTT 59.617 38.462 0.00 0.00 0.00 3.01
4082 8016 6.163135 ACTCCCTCCGATTCTAAATACAAG 57.837 41.667 0.00 0.00 0.00 3.16
4083 8017 7.850935 ATACTCCCTCCGATTCTAAATACAA 57.149 36.000 0.00 0.00 0.00 2.41
4085 8019 9.857957 CTTAATACTCCCTCCGATTCTAAATAC 57.142 37.037 0.00 0.00 0.00 1.89
4086 8020 9.597681 ACTTAATACTCCCTCCGATTCTAAATA 57.402 33.333 0.00 0.00 0.00 1.40
4088 8022 7.909485 ACTTAATACTCCCTCCGATTCTAAA 57.091 36.000 0.00 0.00 0.00 1.85
4089 8023 7.909485 AACTTAATACTCCCTCCGATTCTAA 57.091 36.000 0.00 0.00 0.00 2.10
4090 8024 8.000709 TGTAACTTAATACTCCCTCCGATTCTA 58.999 37.037 0.00 0.00 0.00 2.10
4091 8025 6.837568 TGTAACTTAATACTCCCTCCGATTCT 59.162 38.462 0.00 0.00 0.00 2.40
4092 8026 7.014038 TCTGTAACTTAATACTCCCTCCGATTC 59.986 40.741 0.00 0.00 0.00 2.52
4093 8027 6.837568 TCTGTAACTTAATACTCCCTCCGATT 59.162 38.462 0.00 0.00 0.00 3.34
4094 8028 6.371278 TCTGTAACTTAATACTCCCTCCGAT 58.629 40.000 0.00 0.00 0.00 4.18
4096 8030 5.009811 CCTCTGTAACTTAATACTCCCTCCG 59.990 48.000 0.00 0.00 0.00 4.63
4098 8032 6.134754 TCCCTCTGTAACTTAATACTCCCTC 58.865 44.000 0.00 0.00 0.00 4.30
4099 8033 6.101274 TCCCTCTGTAACTTAATACTCCCT 57.899 41.667 0.00 0.00 0.00 4.20
4100 8034 6.997942 ATCCCTCTGTAACTTAATACTCCC 57.002 41.667 0.00 0.00 0.00 4.30
4101 8035 9.930693 CATAATCCCTCTGTAACTTAATACTCC 57.069 37.037 0.00 0.00 0.00 3.85
4107 8041 8.849543 ACCTACATAATCCCTCTGTAACTTAA 57.150 34.615 0.00 0.00 0.00 1.85
4108 8042 8.849543 AACCTACATAATCCCTCTGTAACTTA 57.150 34.615 0.00 0.00 0.00 2.24
4110 8044 8.849543 TTAACCTACATAATCCCTCTGTAACT 57.150 34.615 0.00 0.00 0.00 2.24
4126 8190 9.344772 ACAAACAACATCAGTATTTAACCTACA 57.655 29.630 0.00 0.00 0.00 2.74
4171 9087 5.639506 ACATAGCAGAGATTTACACACACAC 59.360 40.000 0.00 0.00 0.00 3.82
4172 9088 5.793817 ACATAGCAGAGATTTACACACACA 58.206 37.500 0.00 0.00 0.00 3.72
4173 9089 6.727824 AACATAGCAGAGATTTACACACAC 57.272 37.500 0.00 0.00 0.00 3.82
4174 9090 8.840833 TTAAACATAGCAGAGATTTACACACA 57.159 30.769 0.00 0.00 0.00 3.72
4183 9099 9.995003 CTTTCCTCTATTAAACATAGCAGAGAT 57.005 33.333 0.00 0.00 32.98 2.75
4184 9100 9.201989 TCTTTCCTCTATTAAACATAGCAGAGA 57.798 33.333 0.00 0.00 32.98 3.10
4185 9101 9.474920 CTCTTTCCTCTATTAAACATAGCAGAG 57.525 37.037 0.00 0.00 0.00 3.35
4186 9102 9.201989 TCTCTTTCCTCTATTAAACATAGCAGA 57.798 33.333 0.00 0.00 0.00 4.26
4187 9103 9.823647 TTCTCTTTCCTCTATTAAACATAGCAG 57.176 33.333 0.00 0.00 0.00 4.24
4201 9117 8.423906 TCACTTGTACTAATTCTCTTTCCTCT 57.576 34.615 0.00 0.00 0.00 3.69
4202 9118 7.762159 CCTCACTTGTACTAATTCTCTTTCCTC 59.238 40.741 0.00 0.00 0.00 3.71
4203 9119 7.455008 TCCTCACTTGTACTAATTCTCTTTCCT 59.545 37.037 0.00 0.00 0.00 3.36
4207 9123 9.256228 TGTATCCTCACTTGTACTAATTCTCTT 57.744 33.333 0.00 0.00 0.00 2.85
4208 9124 8.824756 TGTATCCTCACTTGTACTAATTCTCT 57.175 34.615 0.00 0.00 0.00 3.10
4211 9127 8.870879 GTGTTGTATCCTCACTTGTACTAATTC 58.129 37.037 0.00 0.00 0.00 2.17
4212 9128 8.372459 TGTGTTGTATCCTCACTTGTACTAATT 58.628 33.333 0.00 0.00 33.82 1.40
4213 9129 7.903145 TGTGTTGTATCCTCACTTGTACTAAT 58.097 34.615 0.00 0.00 33.82 1.73
4214 9130 7.292713 TGTGTTGTATCCTCACTTGTACTAA 57.707 36.000 0.00 0.00 33.82 2.24
4215 9131 6.904463 TGTGTTGTATCCTCACTTGTACTA 57.096 37.500 0.00 0.00 33.82 1.82
4216 9132 5.801531 TGTGTTGTATCCTCACTTGTACT 57.198 39.130 0.00 0.00 33.82 2.73
4217 9133 6.090898 GTCATGTGTTGTATCCTCACTTGTAC 59.909 42.308 0.00 0.00 37.96 2.90
4218 9134 6.163476 GTCATGTGTTGTATCCTCACTTGTA 58.837 40.000 0.00 0.00 37.96 2.41
4219 9135 4.997395 GTCATGTGTTGTATCCTCACTTGT 59.003 41.667 0.00 0.00 37.96 3.16
4220 9136 4.996758 TGTCATGTGTTGTATCCTCACTTG 59.003 41.667 0.00 0.00 38.05 3.16
4221 9137 4.997395 GTGTCATGTGTTGTATCCTCACTT 59.003 41.667 0.00 0.00 33.82 3.16
4222 9138 4.569943 GTGTCATGTGTTGTATCCTCACT 58.430 43.478 0.00 0.00 33.82 3.41
4223 9139 3.367932 CGTGTCATGTGTTGTATCCTCAC 59.632 47.826 0.00 0.00 0.00 3.51
4225 9141 3.845178 TCGTGTCATGTGTTGTATCCTC 58.155 45.455 0.00 0.00 0.00 3.71
4226 9142 3.953712 TCGTGTCATGTGTTGTATCCT 57.046 42.857 0.00 0.00 0.00 3.24
4227 9143 3.181534 CGTTCGTGTCATGTGTTGTATCC 60.182 47.826 0.00 0.00 0.00 2.59
4228 9144 3.720920 GCGTTCGTGTCATGTGTTGTATC 60.721 47.826 0.00 0.00 0.00 2.24
4229 9145 2.156891 GCGTTCGTGTCATGTGTTGTAT 59.843 45.455 0.00 0.00 0.00 2.29
4230 9146 1.523515 GCGTTCGTGTCATGTGTTGTA 59.476 47.619 0.00 0.00 0.00 2.41
4232 9148 0.303191 TGCGTTCGTGTCATGTGTTG 59.697 50.000 0.00 0.00 0.00 3.33
4234 9150 0.249280 TCTGCGTTCGTGTCATGTGT 60.249 50.000 0.00 0.00 0.00 3.72
4235 9151 0.858583 TTCTGCGTTCGTGTCATGTG 59.141 50.000 0.00 0.00 0.00 3.21
4236 9152 1.139989 CTTCTGCGTTCGTGTCATGT 58.860 50.000 0.00 0.00 0.00 3.21
4237 9153 0.439985 CCTTCTGCGTTCGTGTCATG 59.560 55.000 0.00 0.00 0.00 3.07
4238 9154 0.670546 CCCTTCTGCGTTCGTGTCAT 60.671 55.000 0.00 0.00 0.00 3.06
4239 9155 1.300620 CCCTTCTGCGTTCGTGTCA 60.301 57.895 0.00 0.00 0.00 3.58
4240 9156 2.668280 GCCCTTCTGCGTTCGTGTC 61.668 63.158 0.00 0.00 0.00 3.67
4241 9157 2.665185 GCCCTTCTGCGTTCGTGT 60.665 61.111 0.00 0.00 0.00 4.49
4249 9165 1.503542 CATGTTCACGCCCTTCTGC 59.496 57.895 0.00 0.00 0.00 4.26
4250 9166 0.606401 ACCATGTTCACGCCCTTCTG 60.606 55.000 0.00 0.00 0.00 3.02
4251 9167 0.606401 CACCATGTTCACGCCCTTCT 60.606 55.000 0.00 0.00 0.00 2.85
4252 9168 1.875963 CACCATGTTCACGCCCTTC 59.124 57.895 0.00 0.00 0.00 3.46
4253 9169 2.268076 GCACCATGTTCACGCCCTT 61.268 57.895 0.00 0.00 0.00 3.95
4254 9170 2.672996 GCACCATGTTCACGCCCT 60.673 61.111 0.00 0.00 0.00 5.19
4269 9185 2.281484 GTCTTTCTGTGCCGGGCA 60.281 61.111 19.77 19.77 35.60 5.36
4270 9186 1.675641 ATGTCTTTCTGTGCCGGGC 60.676 57.895 13.32 13.32 0.00 6.13
4271 9187 1.308069 CCATGTCTTTCTGTGCCGGG 61.308 60.000 2.18 0.00 0.00 5.73
4272 9188 1.308069 CCCATGTCTTTCTGTGCCGG 61.308 60.000 0.00 0.00 0.00 6.13
4273 9189 0.321564 TCCCATGTCTTTCTGTGCCG 60.322 55.000 0.00 0.00 0.00 5.69
4274 9190 1.747355 CATCCCATGTCTTTCTGTGCC 59.253 52.381 0.00 0.00 0.00 5.01
4275 9191 1.133790 GCATCCCATGTCTTTCTGTGC 59.866 52.381 0.00 0.00 0.00 4.57
4276 9192 2.719739 AGCATCCCATGTCTTTCTGTG 58.280 47.619 0.00 0.00 0.00 3.66
4336 9609 4.838152 GCAATCTCCCGCCTCGCA 62.838 66.667 0.00 0.00 0.00 5.10
4338 9611 2.279784 GAGCAATCTCCCGCCTCG 60.280 66.667 0.00 0.00 33.19 4.63
4371 9654 2.807676 CAAAGGGGTGCTCCAATTAGT 58.192 47.619 7.20 0.00 37.22 2.24
4450 9735 3.877508 AGTTTCAGTCTTGTAGCCACAAC 59.122 43.478 0.00 0.00 39.75 3.32
4514 9799 6.490040 TCTGGGATTTTCTCATTTCGTTTCTT 59.510 34.615 0.00 0.00 0.00 2.52
4564 9849 2.367567 GCCAATCCGGTCCAGAATACTA 59.632 50.000 0.00 0.00 36.97 1.82


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

AutoCloner maintained by Alex Coulton.