Multiple sequence alignment - TraesCS1D01G009200

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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 TraesCS1D01G009200 chr1D 100.000 4562 0 0 1 4562 4878853 4874292 0.000000e+00 8425.0
1 TraesCS1D01G009200 chr1D 84.520 1615 205 25 4 1609 5134260 5132682 0.000000e+00 1555.0
2 TraesCS1D01G009200 chr1D 81.579 1140 169 27 4 1136 4867893 4866788 0.000000e+00 904.0
3 TraesCS1D01G009200 chr1D 82.729 828 106 18 2 807 3176919 3177731 0.000000e+00 702.0
4 TraesCS1D01G009200 chr1D 80.103 774 132 13 2137 2907 4928544 4927790 1.430000e-154 556.0
5 TraesCS1D01G009200 chr1D 80.500 200 36 2 1783 1979 3178904 3179103 2.840000e-32 150.0
6 TraesCS1D01G009200 chr1D 100.000 35 0 0 445 479 4878341 4878307 1.060000e-06 65.8
7 TraesCS1D01G009200 chr1A 96.903 2422 62 5 1649 4068 5647499 5645089 0.000000e+00 4045.0
8 TraesCS1D01G009200 chr1A 95.229 1614 58 9 1 1609 5649102 5647503 0.000000e+00 2536.0
9 TraesCS1D01G009200 chr1A 83.807 1618 214 32 4 1609 5505031 5503450 0.000000e+00 1493.0
10 TraesCS1D01G009200 chr1A 83.118 1623 219 34 4 1609 6340300 6338716 0.000000e+00 1428.0
11 TraesCS1D01G009200 chr1A 81.280 1250 179 39 1 1236 4498719 4499927 0.000000e+00 961.0
12 TraesCS1D01G009200 chr1A 78.392 1430 239 35 1652 3040 4552863 4554263 0.000000e+00 865.0
13 TraesCS1D01G009200 chr1A 93.382 272 8 1 4291 4562 5644454 5644193 1.190000e-105 394.0
14 TraesCS1D01G009200 chr1A 77.707 628 123 13 2460 3077 4215583 4216203 7.210000e-98 368.0
15 TraesCS1D01G009200 chr1A 92.958 71 3 2 3099 3169 5645861 5645793 8.070000e-18 102.0
16 TraesCS1D01G009200 chr1A 97.917 48 1 0 4186 4233 5644496 5644449 2.920000e-12 84.2
17 TraesCS1D01G009200 chr1A 76.224 143 19 6 681 808 5525404 5525262 1.370000e-05 62.1
18 TraesCS1D01G009200 chr1B 83.364 1617 228 25 1 1609 5695890 5697473 0.000000e+00 1458.0
19 TraesCS1D01G009200 chr1B 83.066 1618 232 28 4 1615 7256011 7254430 0.000000e+00 1432.0
20 TraesCS1D01G009200 chr1B 83.025 1620 226 31 4 1609 6486787 6485203 0.000000e+00 1423.0
21 TraesCS1D01G009200 chr1B 82.528 1614 234 29 4 1609 29908074 29906501 0.000000e+00 1375.0
22 TraesCS1D01G009200 chr1B 82.426 1616 228 31 1 1609 6061440 6063006 0.000000e+00 1360.0
23 TraesCS1D01G009200 chr1B 77.425 2268 394 60 1005 3173 7292068 7294316 0.000000e+00 1243.0
24 TraesCS1D01G009200 chr1B 82.921 1335 197 24 537 1861 29937968 29936655 0.000000e+00 1173.0
25 TraesCS1D01G009200 chr1B 86.031 766 105 1 846 1609 7338983 7339748 0.000000e+00 821.0
26 TraesCS1D01G009200 chr1B 76.644 1490 269 42 1648 3078 5854340 5855809 0.000000e+00 750.0
27 TraesCS1D01G009200 chr1B 82.981 852 107 18 1 834 7291011 7291842 0.000000e+00 736.0
28 TraesCS1D01G009200 chr1B 83.133 830 96 24 1 806 5986889 5987698 0.000000e+00 717.0
29 TraesCS1D01G009200 chr1B 82.510 749 112 8 1 748 6848616 6847886 1.380000e-179 640.0
30 TraesCS1D01G009200 chr1B 77.018 1140 205 23 1984 3076 5698025 5699154 6.530000e-168 601.0
31 TraesCS1D01G009200 chr1B 75.793 1293 252 31 1789 3028 5954362 5955646 8.450000e-167 597.0
32 TraesCS1D01G009200 chr1B 75.439 1083 209 26 1984 3051 5747401 5748441 1.490000e-129 473.0
33 TraesCS1D01G009200 chr1B 80.077 261 40 6 1726 1980 6197061 6197315 2.800000e-42 183.0
34 TraesCS1D01G009200 chr1B 80.420 143 12 10 3288 3425 22720942 22720811 1.350000e-15 95.3
35 TraesCS1D01G009200 chrUn 83.018 1637 204 40 4 1609 117299603 117298010 0.000000e+00 1415.0


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 TraesCS1D01G009200 chr1D 4874292 4878853 4561 True 4245.40 8425 100.0000 1 4562 2 chr1D.!!$R4 4561
1 TraesCS1D01G009200 chr1D 5132682 5134260 1578 True 1555.00 1555 84.5200 4 1609 1 chr1D.!!$R3 1605
2 TraesCS1D01G009200 chr1D 4866788 4867893 1105 True 904.00 904 81.5790 4 1136 1 chr1D.!!$R1 1132
3 TraesCS1D01G009200 chr1D 4927790 4928544 754 True 556.00 556 80.1030 2137 2907 1 chr1D.!!$R2 770
4 TraesCS1D01G009200 chr1D 3176919 3179103 2184 False 426.00 702 81.6145 2 1979 2 chr1D.!!$F1 1977
5 TraesCS1D01G009200 chr1A 5503450 5505031 1581 True 1493.00 1493 83.8070 4 1609 1 chr1A.!!$R1 1605
6 TraesCS1D01G009200 chr1A 5644193 5649102 4909 True 1432.24 4045 95.2778 1 4562 5 chr1A.!!$R4 4561
7 TraesCS1D01G009200 chr1A 6338716 6340300 1584 True 1428.00 1428 83.1180 4 1609 1 chr1A.!!$R3 1605
8 TraesCS1D01G009200 chr1A 4498719 4499927 1208 False 961.00 961 81.2800 1 1236 1 chr1A.!!$F2 1235
9 TraesCS1D01G009200 chr1A 4552863 4554263 1400 False 865.00 865 78.3920 1652 3040 1 chr1A.!!$F3 1388
10 TraesCS1D01G009200 chr1A 4215583 4216203 620 False 368.00 368 77.7070 2460 3077 1 chr1A.!!$F1 617
11 TraesCS1D01G009200 chr1B 7254430 7256011 1581 True 1432.00 1432 83.0660 4 1615 1 chr1B.!!$R3 1611
12 TraesCS1D01G009200 chr1B 6485203 6486787 1584 True 1423.00 1423 83.0250 4 1609 1 chr1B.!!$R1 1605
13 TraesCS1D01G009200 chr1B 29906501 29908074 1573 True 1375.00 1375 82.5280 4 1609 1 chr1B.!!$R5 1605
14 TraesCS1D01G009200 chr1B 6061440 6063006 1566 False 1360.00 1360 82.4260 1 1609 1 chr1B.!!$F5 1608
15 TraesCS1D01G009200 chr1B 29936655 29937968 1313 True 1173.00 1173 82.9210 537 1861 1 chr1B.!!$R6 1324
16 TraesCS1D01G009200 chr1B 5695890 5699154 3264 False 1029.50 1458 80.1910 1 3076 2 chr1B.!!$F8 3075
17 TraesCS1D01G009200 chr1B 7291011 7294316 3305 False 989.50 1243 80.2030 1 3173 2 chr1B.!!$F9 3172
18 TraesCS1D01G009200 chr1B 7338983 7339748 765 False 821.00 821 86.0310 846 1609 1 chr1B.!!$F7 763
19 TraesCS1D01G009200 chr1B 5854340 5855809 1469 False 750.00 750 76.6440 1648 3078 1 chr1B.!!$F2 1430
20 TraesCS1D01G009200 chr1B 5986889 5987698 809 False 717.00 717 83.1330 1 806 1 chr1B.!!$F4 805
21 TraesCS1D01G009200 chr1B 6847886 6848616 730 True 640.00 640 82.5100 1 748 1 chr1B.!!$R2 747
22 TraesCS1D01G009200 chr1B 5954362 5955646 1284 False 597.00 597 75.7930 1789 3028 1 chr1B.!!$F3 1239
23 TraesCS1D01G009200 chr1B 5747401 5748441 1040 False 473.00 473 75.4390 1984 3051 1 chr1B.!!$F1 1067
24 TraesCS1D01G009200 chrUn 117298010 117299603 1593 True 1415.00 1415 83.0180 4 1609 1 chrUn.!!$R1 1605

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
978 1026 1.528129 GGACCTTTCCAACTGCTCAG 58.472 55.0 0.00 0.00 42.30 3.35 F
1616 1802 1.168407 CCTGAGGCACCACAGTTGTG 61.168 60.0 12.31 5.28 45.23 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2932 3734 0.901124 GGGAGCTTCTTCAGAGCAGA 59.099 55.0 0.00 0.0 0.0 4.26 R
3593 4408 1.026182 TTGACCAGCTAGCATTGCCG 61.026 55.0 18.83 0.0 0.0 5.69 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
31 35 8.169977 TCCTGAAATTATGGATGCAAATAGAC 57.830 34.615 0.00 0.00 0.00 2.59
443 449 8.040132 AGAGGAAGAAGATAGTCTTGAAACATG 58.960 37.037 0.00 0.00 36.73 3.21
444 450 7.108847 AGGAAGAAGATAGTCTTGAAACATGG 58.891 38.462 0.00 0.00 36.73 3.66
445 451 7.038017 AGGAAGAAGATAGTCTTGAAACATGGA 60.038 37.037 0.00 0.00 36.73 3.41
446 452 7.607991 GGAAGAAGATAGTCTTGAAACATGGAA 59.392 37.037 0.00 0.00 36.73 3.53
449 455 9.007901 AGAAGATAGTCTTGAAACATGGAAAAG 57.992 33.333 0.00 0.00 36.73 2.27
450 456 8.697507 AAGATAGTCTTGAAACATGGAAAAGT 57.302 30.769 0.00 0.00 34.98 2.66
451 457 9.793259 AAGATAGTCTTGAAACATGGAAAAGTA 57.207 29.630 0.00 0.00 34.98 2.24
455 461 8.519799 AGTCTTGAAACATGGAAAAGTAAAGA 57.480 30.769 0.00 0.00 0.00 2.52
457 463 9.185192 GTCTTGAAACATGGAAAAGTAAAGATG 57.815 33.333 0.00 0.00 0.00 2.90
458 464 8.912988 TCTTGAAACATGGAAAAGTAAAGATGT 58.087 29.630 0.00 0.00 0.00 3.06
459 465 9.185192 CTTGAAACATGGAAAAGTAAAGATGTC 57.815 33.333 0.00 0.00 0.00 3.06
460 466 8.463930 TGAAACATGGAAAAGTAAAGATGTCT 57.536 30.769 0.00 0.00 0.00 3.41
461 467 8.567948 TGAAACATGGAAAAGTAAAGATGTCTC 58.432 33.333 0.00 0.00 0.00 3.36
462 468 6.727824 ACATGGAAAAGTAAAGATGTCTCG 57.272 37.500 0.00 0.00 0.00 4.04
463 469 5.643777 ACATGGAAAAGTAAAGATGTCTCGG 59.356 40.000 0.00 0.00 0.00 4.63
464 470 4.575885 TGGAAAAGTAAAGATGTCTCGGG 58.424 43.478 0.00 0.00 0.00 5.14
465 471 3.939592 GGAAAAGTAAAGATGTCTCGGGG 59.060 47.826 0.00 0.00 0.00 5.73
466 472 4.565028 GGAAAAGTAAAGATGTCTCGGGGT 60.565 45.833 0.00 0.00 0.00 4.95
467 473 5.337813 GGAAAAGTAAAGATGTCTCGGGGTA 60.338 44.000 0.00 0.00 0.00 3.69
468 474 5.952347 AAAGTAAAGATGTCTCGGGGTAT 57.048 39.130 0.00 0.00 0.00 2.73
469 475 5.952347 AAGTAAAGATGTCTCGGGGTATT 57.048 39.130 0.00 0.00 0.00 1.89
470 476 7.427989 AAAGTAAAGATGTCTCGGGGTATTA 57.572 36.000 0.00 0.00 0.00 0.98
474 480 5.485209 AAGATGTCTCGGGGTATTATTCC 57.515 43.478 0.00 0.00 0.00 3.01
658 691 5.209318 ACCAAGTGGCTTCCAGATACTGG 62.209 52.174 11.10 11.10 45.43 4.00
689 722 9.353999 CATTTATTTTTGCTAGGTGAAGTAACC 57.646 33.333 0.00 0.00 40.85 2.85
810 858 6.695429 CATGCCTTGAAGCTCTGTATAGATA 58.305 40.000 0.00 0.00 31.21 1.98
812 860 8.473219 CATGCCTTGAAGCTCTGTATAGATATA 58.527 37.037 0.00 0.00 31.21 0.86
931 979 2.960384 TCGACACACTTCCTGAAGGTAA 59.040 45.455 11.34 0.00 42.53 2.85
978 1026 1.528129 GGACCTTTCCAACTGCTCAG 58.472 55.000 0.00 0.00 42.30 3.35
1086 1219 1.608283 CCAGGACTCGGAAAACTCACC 60.608 57.143 0.00 0.00 0.00 4.02
1616 1802 1.168407 CCTGAGGCACCACAGTTGTG 61.168 60.000 12.31 5.28 45.23 3.33
1621 1807 3.071747 TGAGGCACCACAGTTGTGTATTA 59.928 43.478 11.02 0.00 44.21 0.98
1622 1808 4.069304 GAGGCACCACAGTTGTGTATTAA 58.931 43.478 11.02 0.00 44.21 1.40
1635 1821 9.743057 CAGTTGTGTATTAAGAAATGTGGAAAA 57.257 29.630 0.00 0.00 0.00 2.29
1638 1824 9.743057 TTGTGTATTAAGAAATGTGGAAAACTG 57.257 29.630 0.00 0.00 0.00 3.16
1646 1832 5.416952 AGAAATGTGGAAAACTGATAGCAGG 59.583 40.000 13.45 0.00 46.60 4.85
1649 1835 3.327757 TGTGGAAAACTGATAGCAGGACT 59.672 43.478 13.45 0.00 46.60 3.85
2164 2863 3.445096 AGAGAAAGTGTTGCAAAGCTTGT 59.555 39.130 14.87 7.83 0.00 3.16
2206 2905 8.632679 TGAAGATTGTAAACTGCAGAAATCTTT 58.367 29.630 26.76 18.62 41.82 2.52
2333 3057 3.458163 TGACGTCCCGGCATCTCC 61.458 66.667 14.12 0.00 41.22 3.71
2453 3177 2.359981 ATCATGCCTGCAGCTGTATT 57.640 45.000 16.64 0.00 44.23 1.89
2522 3291 9.216117 GTTACTTGATTGTGATAGTTTACCAGT 57.784 33.333 0.00 0.00 0.00 4.00
2853 3655 6.345096 TCATTGGAATCCCTTTTTCTTGAC 57.655 37.500 0.00 0.00 0.00 3.18
2932 3734 5.751990 CGATACCTTCGTATTAAAGGCTGTT 59.248 40.000 1.87 0.00 46.03 3.16
3000 3808 6.452872 GCAGCATTTACTTCAAACAAATAGCG 60.453 38.462 0.00 0.00 0.00 4.26
3036 3849 4.026804 GGTATGTTGCACGTCTTTCTATCG 60.027 45.833 0.00 0.00 0.00 2.92
3040 3853 3.021269 TGCACGTCTTTCTATCGTTGT 57.979 42.857 0.00 0.00 35.62 3.32
3219 4032 5.124457 GCATGACTTACAATCTTCACCACAT 59.876 40.000 0.00 0.00 0.00 3.21
3228 4041 6.748132 ACAATCTTCACCACATTTAACCAAG 58.252 36.000 0.00 0.00 0.00 3.61
3452 4267 1.377725 AGCCTGCTGAAACCGATGG 60.378 57.895 0.00 0.00 0.00 3.51
3488 4303 4.890581 CACTGACTTAGAGGGTATGCTAGT 59.109 45.833 0.00 0.00 0.00 2.57
3489 4304 5.361285 CACTGACTTAGAGGGTATGCTAGTT 59.639 44.000 0.00 0.00 0.00 2.24
3490 4305 5.361285 ACTGACTTAGAGGGTATGCTAGTTG 59.639 44.000 0.00 0.00 0.00 3.16
3491 4306 4.099573 TGACTTAGAGGGTATGCTAGTTGC 59.900 45.833 0.00 0.00 43.25 4.17
3492 4307 4.290942 ACTTAGAGGGTATGCTAGTTGCT 58.709 43.478 0.00 0.00 43.37 3.91
3493 4308 5.455872 ACTTAGAGGGTATGCTAGTTGCTA 58.544 41.667 0.00 0.00 43.37 3.49
3494 4309 5.536916 ACTTAGAGGGTATGCTAGTTGCTAG 59.463 44.000 0.00 0.00 43.37 3.42
3551 4366 1.079127 GGCCGCTAGCTTGTTCAGA 60.079 57.895 13.93 0.00 43.05 3.27
3593 4408 2.203209 CCCCTTGGATGCTACGCC 60.203 66.667 0.00 0.00 0.00 5.68
3668 4483 2.754552 CCTGGTGCTTGCTTTGCTTATA 59.245 45.455 0.00 0.00 0.00 0.98
3681 4496 5.371526 CTTTGCTTATATGGGCAGAGAAGA 58.628 41.667 13.29 0.00 41.30 2.87
3682 4497 5.372343 TTGCTTATATGGGCAGAGAAGAA 57.628 39.130 0.00 0.00 39.68 2.52
3683 4498 5.573380 TGCTTATATGGGCAGAGAAGAAT 57.427 39.130 0.00 0.00 34.22 2.40
3742 4557 6.997655 TGAGGTATATGTAATGCTCCTTCTG 58.002 40.000 0.00 0.00 0.00 3.02
3755 4570 1.975407 CTTCTGCTGTTGGGCTGGG 60.975 63.158 0.00 0.00 33.09 4.45
3757 4572 2.005606 TTCTGCTGTTGGGCTGGGAA 62.006 55.000 0.00 0.00 33.09 3.97
3758 4573 1.304713 CTGCTGTTGGGCTGGGAAT 60.305 57.895 0.00 0.00 0.00 3.01
3760 4575 0.407528 TGCTGTTGGGCTGGGAATAA 59.592 50.000 0.00 0.00 0.00 1.40
3761 4576 0.817654 GCTGTTGGGCTGGGAATAAC 59.182 55.000 0.00 0.00 0.00 1.89
3762 4577 1.616994 GCTGTTGGGCTGGGAATAACT 60.617 52.381 0.00 0.00 0.00 2.24
3763 4578 2.094675 CTGTTGGGCTGGGAATAACTG 58.905 52.381 0.00 0.00 0.00 3.16
3771 4586 3.010420 GCTGGGAATAACTGTCCTTGTC 58.990 50.000 0.00 0.00 35.33 3.18
3775 4590 3.370633 GGGAATAACTGTCCTTGTCTCCC 60.371 52.174 0.00 0.00 35.33 4.30
3806 4621 1.012486 GTCGAGTGTTTAGGTGGCGG 61.012 60.000 0.00 0.00 0.00 6.13
3814 4629 2.359531 TGTTTAGGTGGCGGTTTTCTTG 59.640 45.455 0.00 0.00 0.00 3.02
3856 4671 5.541845 TGACATAATTCCTCATGGATCGAC 58.458 41.667 0.00 0.00 42.81 4.20
3864 4679 3.634910 TCCTCATGGATCGACGAAATACA 59.365 43.478 0.00 0.00 37.46 2.29
3873 4688 5.107453 GGATCGACGAAATACATGAATGTCC 60.107 44.000 0.00 0.00 41.97 4.02
3920 4735 0.457443 TACTCAGACTGCCTGCATCG 59.543 55.000 0.00 0.00 42.62 3.84
3959 4774 2.398588 TGGTAGAGTGCTAGGGGAATG 58.601 52.381 0.00 0.00 0.00 2.67
4053 4869 1.588239 TGCCTGGAATCACTCATCCT 58.412 50.000 0.00 0.00 36.64 3.24
4058 4874 2.038295 CTGGAATCACTCATCCTAGCCC 59.962 54.545 0.00 0.00 36.64 5.19
4068 4884 2.569218 ATCCTAGCCCGAGACGGTGT 62.569 60.000 9.28 0.00 46.80 4.16
4070 4886 1.749638 CTAGCCCGAGACGGTGTCT 60.750 63.158 9.28 0.00 46.80 3.41
4071 4887 1.994507 CTAGCCCGAGACGGTGTCTG 61.995 65.000 3.85 0.00 46.80 3.51
4073 4889 4.436998 CCCGAGACGGTGTCTGCC 62.437 72.222 3.85 0.00 46.80 4.85
4074 4890 4.436998 CCGAGACGGTGTCTGCCC 62.437 72.222 3.85 0.00 43.53 5.36
4075 4891 3.374402 CGAGACGGTGTCTGCCCT 61.374 66.667 3.85 0.00 43.53 5.19
4076 4892 2.044555 CGAGACGGTGTCTGCCCTA 61.045 63.158 3.85 0.00 43.53 3.53
4077 4893 1.384989 CGAGACGGTGTCTGCCCTAT 61.385 60.000 3.85 0.00 43.53 2.57
4078 4894 0.824759 GAGACGGTGTCTGCCCTATT 59.175 55.000 3.85 0.00 43.53 1.73
4079 4895 0.824759 AGACGGTGTCTGCCCTATTC 59.175 55.000 0.00 0.00 41.76 1.75
4080 4896 0.824759 GACGGTGTCTGCCCTATTCT 59.175 55.000 0.00 0.00 0.00 2.40
4081 4897 0.537188 ACGGTGTCTGCCCTATTCTG 59.463 55.000 0.00 0.00 0.00 3.02
4082 4898 0.824109 CGGTGTCTGCCCTATTCTGA 59.176 55.000 0.00 0.00 0.00 3.27
4083 4899 1.414181 CGGTGTCTGCCCTATTCTGAT 59.586 52.381 0.00 0.00 0.00 2.90
4084 4900 2.804572 CGGTGTCTGCCCTATTCTGATG 60.805 54.545 0.00 0.00 0.00 3.07
4085 4901 2.171448 GGTGTCTGCCCTATTCTGATGT 59.829 50.000 0.00 0.00 0.00 3.06
4086 4902 3.388024 GGTGTCTGCCCTATTCTGATGTA 59.612 47.826 0.00 0.00 0.00 2.29
4087 4903 4.372656 GTGTCTGCCCTATTCTGATGTAC 58.627 47.826 0.00 0.00 0.00 2.90
4088 4904 4.100189 GTGTCTGCCCTATTCTGATGTACT 59.900 45.833 0.00 0.00 0.00 2.73
4089 4905 5.302059 GTGTCTGCCCTATTCTGATGTACTA 59.698 44.000 0.00 0.00 0.00 1.82
4090 4906 6.015010 GTGTCTGCCCTATTCTGATGTACTAT 60.015 42.308 0.00 0.00 0.00 2.12
4091 4907 6.554982 TGTCTGCCCTATTCTGATGTACTATT 59.445 38.462 0.00 0.00 0.00 1.73
4092 4908 7.071196 TGTCTGCCCTATTCTGATGTACTATTT 59.929 37.037 0.00 0.00 0.00 1.40
4093 4909 7.386299 GTCTGCCCTATTCTGATGTACTATTTG 59.614 40.741 0.00 0.00 0.00 2.32
4094 4910 6.533730 TGCCCTATTCTGATGTACTATTTGG 58.466 40.000 0.00 0.00 0.00 3.28
4095 4911 6.328934 TGCCCTATTCTGATGTACTATTTGGA 59.671 38.462 0.00 0.00 0.00 3.53
4096 4912 7.147391 TGCCCTATTCTGATGTACTATTTGGAA 60.147 37.037 0.00 0.00 0.00 3.53
4097 4913 7.719633 GCCCTATTCTGATGTACTATTTGGAAA 59.280 37.037 0.00 0.00 0.00 3.13
4098 4914 9.277783 CCCTATTCTGATGTACTATTTGGAAAG 57.722 37.037 0.00 0.00 0.00 2.62
4099 4915 8.778358 CCTATTCTGATGTACTATTTGGAAAGC 58.222 37.037 0.00 0.00 0.00 3.51
4100 4916 9.553064 CTATTCTGATGTACTATTTGGAAAGCT 57.447 33.333 0.00 0.00 0.00 3.74
4101 4917 8.814038 ATTCTGATGTACTATTTGGAAAGCTT 57.186 30.769 0.00 0.00 0.00 3.74
4102 4918 9.905713 ATTCTGATGTACTATTTGGAAAGCTTA 57.094 29.630 0.00 0.00 0.00 3.09
4103 4919 8.718102 TCTGATGTACTATTTGGAAAGCTTAC 57.282 34.615 0.00 0.00 0.00 2.34
4104 4920 7.491372 TCTGATGTACTATTTGGAAAGCTTACG 59.509 37.037 0.00 0.00 0.00 3.18
4105 4921 7.101054 TGATGTACTATTTGGAAAGCTTACGT 58.899 34.615 0.00 0.00 0.00 3.57
4106 4922 6.715344 TGTACTATTTGGAAAGCTTACGTG 57.285 37.500 0.00 0.00 0.00 4.49
4107 4923 5.640357 TGTACTATTTGGAAAGCTTACGTGG 59.360 40.000 0.00 0.00 0.00 4.94
4108 4924 4.007659 ACTATTTGGAAAGCTTACGTGGG 58.992 43.478 0.00 0.00 0.00 4.61
4121 4937 0.893727 ACGTGGGCATTCAGTTTCCC 60.894 55.000 0.00 0.00 39.22 3.97
4166 4983 4.491409 GAGAAGAAGGGGGCCGGC 62.491 72.222 21.18 21.18 0.00 6.13
4182 4999 2.280119 GCGACGGAGCCATATGCA 60.280 61.111 0.00 0.00 44.83 3.96
4184 5001 1.363807 CGACGGAGCCATATGCAGA 59.636 57.895 0.00 0.00 44.83 4.26
4216 5546 2.562296 TCCTTTGGCCAGAGGAACTAT 58.438 47.619 36.53 0.00 41.55 2.12
4234 5564 9.530633 AGGAACTATTAAAGCTATAACTTGTCG 57.469 33.333 0.00 0.00 36.02 4.35
4235 5565 9.525409 GGAACTATTAAAGCTATAACTTGTCGA 57.475 33.333 0.00 0.00 0.00 4.20
4241 5571 9.654663 ATTAAAGCTATAACTTGTCGAGAAACT 57.345 29.630 0.00 0.00 0.00 2.66
4242 5572 7.964604 AAAGCTATAACTTGTCGAGAAACTT 57.035 32.000 0.00 0.00 0.00 2.66
4244 5574 9.485206 AAAGCTATAACTTGTCGAGAAACTTAA 57.515 29.630 0.00 0.00 0.00 1.85
4245 5575 8.463456 AGCTATAACTTGTCGAGAAACTTAAC 57.537 34.615 0.00 0.00 0.00 2.01
4246 5576 8.305317 AGCTATAACTTGTCGAGAAACTTAACT 58.695 33.333 0.00 0.00 0.00 2.24
4247 5577 8.373992 GCTATAACTTGTCGAGAAACTTAACTG 58.626 37.037 0.00 0.00 0.00 3.16
4248 5578 5.405331 AACTTGTCGAGAAACTTAACTGC 57.595 39.130 0.00 0.00 0.00 4.40
4249 5579 4.439057 ACTTGTCGAGAAACTTAACTGCA 58.561 39.130 0.00 0.00 0.00 4.41
4250 5580 4.873827 ACTTGTCGAGAAACTTAACTGCAA 59.126 37.500 0.00 0.00 0.00 4.08
4251 5581 5.527582 ACTTGTCGAGAAACTTAACTGCAAT 59.472 36.000 0.00 0.00 0.00 3.56
4252 5582 5.591643 TGTCGAGAAACTTAACTGCAATC 57.408 39.130 0.00 0.00 0.00 2.67
4253 5583 5.297547 TGTCGAGAAACTTAACTGCAATCT 58.702 37.500 0.00 0.00 0.00 2.40
4254 5584 5.177511 TGTCGAGAAACTTAACTGCAATCTG 59.822 40.000 0.00 0.00 0.00 2.90
4255 5585 5.177696 GTCGAGAAACTTAACTGCAATCTGT 59.822 40.000 0.00 0.00 0.00 3.41
4256 5586 6.365247 GTCGAGAAACTTAACTGCAATCTGTA 59.635 38.462 0.00 0.00 0.00 2.74
4257 5587 7.063544 GTCGAGAAACTTAACTGCAATCTGTAT 59.936 37.037 0.00 0.00 0.00 2.29
4258 5588 7.063426 TCGAGAAACTTAACTGCAATCTGTATG 59.937 37.037 0.00 0.00 0.00 2.39
4259 5589 7.148573 CGAGAAACTTAACTGCAATCTGTATGT 60.149 37.037 0.00 0.00 0.00 2.29
4260 5590 9.151471 GAGAAACTTAACTGCAATCTGTATGTA 57.849 33.333 0.00 0.00 0.00 2.29
4261 5591 9.155975 AGAAACTTAACTGCAATCTGTATGTAG 57.844 33.333 0.00 0.00 36.68 2.74
4262 5592 7.849804 AACTTAACTGCAATCTGTATGTAGG 57.150 36.000 0.00 0.00 35.17 3.18
4263 5593 5.817816 ACTTAACTGCAATCTGTATGTAGGC 59.182 40.000 0.00 0.00 35.17 3.93
4264 5594 4.494091 AACTGCAATCTGTATGTAGGCT 57.506 40.909 0.00 0.00 35.17 4.58
4265 5595 3.801698 ACTGCAATCTGTATGTAGGCTG 58.198 45.455 0.00 0.00 35.17 4.85
4266 5596 3.136763 CTGCAATCTGTATGTAGGCTGG 58.863 50.000 0.00 0.00 0.00 4.85
4267 5597 2.771372 TGCAATCTGTATGTAGGCTGGA 59.229 45.455 0.00 0.00 0.00 3.86
4268 5598 3.181462 TGCAATCTGTATGTAGGCTGGAG 60.181 47.826 0.00 0.00 0.00 3.86
4269 5599 3.397482 CAATCTGTATGTAGGCTGGAGC 58.603 50.000 0.00 0.00 41.14 4.70
4286 5616 3.915575 CCATGCAGAAGGCTGGTC 58.084 61.111 0.00 0.00 45.15 4.02
4287 5617 1.302285 CCATGCAGAAGGCTGGTCT 59.698 57.895 0.00 0.00 45.15 3.85
4288 5618 1.030488 CCATGCAGAAGGCTGGTCTG 61.030 60.000 11.12 11.12 44.48 3.51
4289 5619 0.322277 CATGCAGAAGGCTGGTCTGT 60.322 55.000 15.63 0.00 43.71 3.41
4290 5620 1.065926 CATGCAGAAGGCTGGTCTGTA 60.066 52.381 15.63 12.47 43.71 2.74
4291 5621 0.321671 TGCAGAAGGCTGGTCTGTAC 59.678 55.000 15.63 3.32 43.71 2.90
4292 5622 0.610687 GCAGAAGGCTGGTCTGTACT 59.389 55.000 15.63 0.00 43.71 2.73
4293 5623 1.825474 GCAGAAGGCTGGTCTGTACTA 59.175 52.381 15.63 0.00 43.71 1.82
4341 5671 3.326297 GCCCCTATCTTGCTCAGATACTT 59.674 47.826 2.91 0.00 40.85 2.24
4345 5675 6.042093 CCCCTATCTTGCTCAGATACTTGTAA 59.958 42.308 2.91 0.00 40.85 2.41
4381 5711 6.374613 CCTGAATTTCCCAGGTTTAGTAGAAC 59.625 42.308 3.93 0.00 44.66 3.01
4391 5721 7.919091 CCCAGGTTTAGTAGAACAAACTTTTTC 59.081 37.037 0.00 0.00 35.45 2.29
4454 5784 1.282157 GTGCTGGTTACTGGGGAGATT 59.718 52.381 0.00 0.00 0.00 2.40
4461 5791 1.789523 TACTGGGGAGATTTCGAGGG 58.210 55.000 0.00 0.00 0.00 4.30
4462 5792 1.147153 CTGGGGAGATTTCGAGGGC 59.853 63.158 0.00 0.00 0.00 5.19
4463 5793 1.615124 TGGGGAGATTTCGAGGGCA 60.615 57.895 0.00 0.00 0.00 5.36
4464 5794 1.204786 TGGGGAGATTTCGAGGGCAA 61.205 55.000 0.00 0.00 0.00 4.52
4465 5795 0.183731 GGGGAGATTTCGAGGGCAAT 59.816 55.000 0.00 0.00 0.00 3.56
4466 5796 1.312815 GGGAGATTTCGAGGGCAATG 58.687 55.000 0.00 0.00 0.00 2.82
4467 5797 0.665298 GGAGATTTCGAGGGCAATGC 59.335 55.000 0.00 0.00 0.00 3.56
4540 5870 3.955859 GGAACTTTCCAGCACTCTGCAC 61.956 54.545 2.93 0.00 46.76 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.373493 GGTCTATTTGCATCCATAATTTCAGG 58.627 38.462 0.00 0.00 0.00 3.86
31 35 2.420129 CCAAAGGACCGAGATTGTAGGG 60.420 54.545 0.00 0.00 0.00 3.53
126 131 5.425196 TCACAATCTGATCAACCATCTCA 57.575 39.130 0.00 0.00 31.92 3.27
443 449 3.939592 CCCCGAGACATCTTTACTTTTCC 59.060 47.826 0.00 0.00 0.00 3.13
444 450 4.576879 ACCCCGAGACATCTTTACTTTTC 58.423 43.478 0.00 0.00 0.00 2.29
445 451 4.635699 ACCCCGAGACATCTTTACTTTT 57.364 40.909 0.00 0.00 0.00 2.27
446 452 5.952347 ATACCCCGAGACATCTTTACTTT 57.048 39.130 0.00 0.00 0.00 2.66
449 455 6.872547 GGAATAATACCCCGAGACATCTTTAC 59.127 42.308 0.00 0.00 0.00 2.01
450 456 6.555738 TGGAATAATACCCCGAGACATCTTTA 59.444 38.462 0.00 0.00 0.00 1.85
451 457 5.368523 TGGAATAATACCCCGAGACATCTTT 59.631 40.000 0.00 0.00 0.00 2.52
453 459 4.489737 TGGAATAATACCCCGAGACATCT 58.510 43.478 0.00 0.00 0.00 2.90
454 460 4.884668 TGGAATAATACCCCGAGACATC 57.115 45.455 0.00 0.00 0.00 3.06
455 461 4.844085 TCATGGAATAATACCCCGAGACAT 59.156 41.667 0.00 0.00 0.00 3.06
457 463 4.822026 CTCATGGAATAATACCCCGAGAC 58.178 47.826 0.00 0.00 30.96 3.36
458 464 3.260884 GCTCATGGAATAATACCCCGAGA 59.739 47.826 0.00 0.00 30.96 4.04
459 465 3.261897 AGCTCATGGAATAATACCCCGAG 59.738 47.826 0.00 0.00 0.00 4.63
460 466 3.248024 AGCTCATGGAATAATACCCCGA 58.752 45.455 0.00 0.00 0.00 5.14
461 467 3.703001 AGCTCATGGAATAATACCCCG 57.297 47.619 0.00 0.00 0.00 5.73
462 468 3.507622 GCAAGCTCATGGAATAATACCCC 59.492 47.826 0.00 0.00 0.00 4.95
463 469 3.507622 GGCAAGCTCATGGAATAATACCC 59.492 47.826 0.00 0.00 0.00 3.69
464 470 4.401925 AGGCAAGCTCATGGAATAATACC 58.598 43.478 0.00 0.00 0.00 2.73
465 471 4.153117 CGAGGCAAGCTCATGGAATAATAC 59.847 45.833 0.00 0.00 0.00 1.89
466 472 4.040339 TCGAGGCAAGCTCATGGAATAATA 59.960 41.667 0.00 0.00 0.00 0.98
467 473 3.144506 CGAGGCAAGCTCATGGAATAAT 58.855 45.455 0.00 0.00 0.00 1.28
468 474 2.170397 TCGAGGCAAGCTCATGGAATAA 59.830 45.455 0.00 0.00 0.00 1.40
469 475 1.762370 TCGAGGCAAGCTCATGGAATA 59.238 47.619 0.00 0.00 0.00 1.75
470 476 0.543277 TCGAGGCAAGCTCATGGAAT 59.457 50.000 0.00 0.00 0.00 3.01
474 480 0.809241 GACCTCGAGGCAAGCTCATG 60.809 60.000 31.56 3.82 39.32 3.07
658 691 3.123050 CCTAGCAAAAATAAATGCCGCC 58.877 45.455 0.00 0.00 43.57 6.13
659 692 3.551485 CACCTAGCAAAAATAAATGCCGC 59.449 43.478 0.00 0.00 43.57 6.53
725 758 5.396884 GGATAGAAGTGTTTGGATAGCAGGT 60.397 44.000 0.00 0.00 0.00 4.00
824 872 5.705441 TGATGTTGTCTCTAATGGTTTCACC 59.295 40.000 0.00 0.00 39.22 4.02
931 979 9.609346 ACGTTTGCAGGTTATATAGAATACTTT 57.391 29.630 0.00 0.00 0.00 2.66
978 1026 1.202313 CCTCGGAAGTCGGTCAAGATC 60.202 57.143 0.00 0.00 39.77 2.75
1086 1219 2.277969 CATGTAAGAGTCTGCAGCCTG 58.722 52.381 9.47 0.00 0.00 4.85
1621 1807 6.071728 CCTGCTATCAGTTTTCCACATTTCTT 60.072 38.462 0.00 0.00 38.66 2.52
1622 1808 5.416952 CCTGCTATCAGTTTTCCACATTTCT 59.583 40.000 0.00 0.00 38.66 2.52
1635 1821 2.568956 TGCTTCAAGTCCTGCTATCAGT 59.431 45.455 0.00 0.00 38.66 3.41
1638 1824 2.284190 GGTGCTTCAAGTCCTGCTATC 58.716 52.381 0.00 0.00 0.00 2.08
1645 1831 1.594331 AGAAACGGTGCTTCAAGTCC 58.406 50.000 0.00 0.00 0.00 3.85
1646 1832 2.612212 TGAAGAAACGGTGCTTCAAGTC 59.388 45.455 21.95 0.00 45.26 3.01
1894 2563 5.488919 TGTCTACCCAATGGAAGATCTCTTT 59.511 40.000 0.00 0.00 36.11 2.52
2164 2863 8.884124 ACAATCTTCAATTTCCTCAAGGATAA 57.116 30.769 0.00 0.00 44.98 1.75
2206 2905 3.027412 GAGGAGCTTCTGTGTATCCAGA 58.973 50.000 0.00 0.00 39.65 3.86
2333 3057 8.896744 TGCACTTAGAAATATTCATTCTCTTGG 58.103 33.333 0.00 0.00 38.13 3.61
2353 3077 4.336889 TGTACTCAAGCTTACTGCACTT 57.663 40.909 0.00 0.00 45.94 3.16
2396 3120 3.519913 AGACCCTTGGAATAACTCTGACC 59.480 47.826 0.00 0.00 0.00 4.02
2453 3177 5.360714 GGGCAAAAATGATTCATGGACTCTA 59.639 40.000 0.00 0.00 0.00 2.43
2522 3291 2.940514 TGGAGGGAGATGTAGAACCA 57.059 50.000 0.00 0.00 0.00 3.67
2853 3655 1.630126 ATGCCAGGGTCCTACAGCTG 61.630 60.000 13.48 13.48 0.00 4.24
2932 3734 0.901124 GGGAGCTTCTTCAGAGCAGA 59.099 55.000 0.00 0.00 0.00 4.26
3000 3808 3.005791 GCAACATACCTTCATAATGGGCC 59.994 47.826 0.00 0.00 0.00 5.80
3036 3849 8.635877 TGTATTTGTTGGTTAAATGTGACAAC 57.364 30.769 0.00 0.00 41.18 3.32
3040 3853 6.040955 TGGCTGTATTTGTTGGTTAAATGTGA 59.959 34.615 0.00 0.00 0.00 3.58
3219 4032 5.376625 AGATGACTGCAGTTCTTGGTTAAA 58.623 37.500 22.65 0.00 0.00 1.52
3228 4041 5.221402 TGGATGAGATAGATGACTGCAGTTC 60.221 44.000 22.65 15.66 0.00 3.01
3452 4267 2.183679 AGTCAGTGGGAGATTCAGGAC 58.816 52.381 0.00 0.00 0.00 3.85
3488 4303 7.520451 TCTTCGGTATAATAGCTTCTAGCAA 57.480 36.000 0.00 0.00 45.56 3.91
3489 4304 7.704578 ATCTTCGGTATAATAGCTTCTAGCA 57.295 36.000 0.00 0.00 45.56 3.49
3490 4305 8.895737 AGTATCTTCGGTATAATAGCTTCTAGC 58.104 37.037 0.00 0.00 42.84 3.42
3593 4408 1.026182 TTGACCAGCTAGCATTGCCG 61.026 55.000 18.83 0.00 0.00 5.69
3668 4483 4.581309 TTCAGAATTCTTCTCTGCCCAT 57.419 40.909 4.86 0.00 40.18 4.00
3712 4527 6.406400 GGAGCATTACATATACCTCAGCCTAG 60.406 46.154 0.00 0.00 0.00 3.02
3742 4557 0.817654 GTTATTCCCAGCCCAACAGC 59.182 55.000 0.00 0.00 0.00 4.40
3755 4570 4.828072 AGGGAGACAAGGACAGTTATTC 57.172 45.455 0.00 0.00 0.00 1.75
3757 4572 6.697641 TTTTAGGGAGACAAGGACAGTTAT 57.302 37.500 0.00 0.00 0.00 1.89
3758 4573 6.271391 TCATTTTAGGGAGACAAGGACAGTTA 59.729 38.462 0.00 0.00 0.00 2.24
3760 4575 4.597507 TCATTTTAGGGAGACAAGGACAGT 59.402 41.667 0.00 0.00 0.00 3.55
3761 4576 4.938226 GTCATTTTAGGGAGACAAGGACAG 59.062 45.833 0.00 0.00 0.00 3.51
3762 4577 4.597507 AGTCATTTTAGGGAGACAAGGACA 59.402 41.667 0.00 0.00 33.56 4.02
3763 4578 5.167303 AGTCATTTTAGGGAGACAAGGAC 57.833 43.478 0.00 0.00 33.56 3.85
3771 4586 4.627467 CACTCGACAAGTCATTTTAGGGAG 59.373 45.833 0.72 0.00 35.45 4.30
3775 4590 7.170998 ACCTAAACACTCGACAAGTCATTTTAG 59.829 37.037 0.72 5.46 35.45 1.85
3806 4621 2.865551 CACCAATGCCACACAAGAAAAC 59.134 45.455 0.00 0.00 0.00 2.43
3814 4629 0.968405 ATGAACCACCAATGCCACAC 59.032 50.000 0.00 0.00 0.00 3.82
3929 4744 1.537202 GCACTCTACCAAAGCAACCAG 59.463 52.381 0.00 0.00 0.00 4.00
4058 4874 1.384989 ATAGGGCAGACACCGTCTCG 61.385 60.000 0.00 0.00 41.37 4.04
4068 4884 7.445121 CAAATAGTACATCAGAATAGGGCAGA 58.555 38.462 0.00 0.00 0.00 4.26
4070 4886 6.328934 TCCAAATAGTACATCAGAATAGGGCA 59.671 38.462 0.00 0.00 0.00 5.36
4071 4887 6.769512 TCCAAATAGTACATCAGAATAGGGC 58.230 40.000 0.00 0.00 0.00 5.19
4072 4888 9.277783 CTTTCCAAATAGTACATCAGAATAGGG 57.722 37.037 0.00 0.00 0.00 3.53
4073 4889 8.778358 GCTTTCCAAATAGTACATCAGAATAGG 58.222 37.037 0.00 0.00 0.00 2.57
4074 4890 9.553064 AGCTTTCCAAATAGTACATCAGAATAG 57.447 33.333 0.00 0.00 0.00 1.73
4075 4891 9.905713 AAGCTTTCCAAATAGTACATCAGAATA 57.094 29.630 0.00 0.00 0.00 1.75
4076 4892 8.814038 AAGCTTTCCAAATAGTACATCAGAAT 57.186 30.769 0.00 0.00 0.00 2.40
4077 4893 9.162764 GTAAGCTTTCCAAATAGTACATCAGAA 57.837 33.333 3.20 0.00 0.00 3.02
4078 4894 7.491372 CGTAAGCTTTCCAAATAGTACATCAGA 59.509 37.037 3.20 0.00 0.00 3.27
4079 4895 7.277981 ACGTAAGCTTTCCAAATAGTACATCAG 59.722 37.037 3.20 0.00 45.62 2.90
4080 4896 7.064134 CACGTAAGCTTTCCAAATAGTACATCA 59.936 37.037 3.20 0.00 45.62 3.07
4081 4897 7.399523 CACGTAAGCTTTCCAAATAGTACATC 58.600 38.462 3.20 0.00 45.62 3.06
4082 4898 6.315393 CCACGTAAGCTTTCCAAATAGTACAT 59.685 38.462 3.20 0.00 45.62 2.29
4083 4899 5.640357 CCACGTAAGCTTTCCAAATAGTACA 59.360 40.000 3.20 0.00 45.62 2.90
4084 4900 5.064325 CCCACGTAAGCTTTCCAAATAGTAC 59.936 44.000 3.20 0.00 45.62 2.73
4085 4901 5.180271 CCCACGTAAGCTTTCCAAATAGTA 58.820 41.667 3.20 0.00 45.62 1.82
4086 4902 4.007659 CCCACGTAAGCTTTCCAAATAGT 58.992 43.478 3.20 0.00 45.62 2.12
4087 4903 3.181500 GCCCACGTAAGCTTTCCAAATAG 60.181 47.826 3.20 0.00 45.62 1.73
4088 4904 2.750712 GCCCACGTAAGCTTTCCAAATA 59.249 45.455 3.20 0.00 45.62 1.40
4089 4905 1.544246 GCCCACGTAAGCTTTCCAAAT 59.456 47.619 3.20 0.00 45.62 2.32
4090 4906 0.955905 GCCCACGTAAGCTTTCCAAA 59.044 50.000 3.20 0.00 45.62 3.28
4091 4907 0.179015 TGCCCACGTAAGCTTTCCAA 60.179 50.000 3.20 0.00 45.62 3.53
4092 4908 0.037590 ATGCCCACGTAAGCTTTCCA 59.962 50.000 3.20 0.00 45.62 3.53
4093 4909 1.132453 GAATGCCCACGTAAGCTTTCC 59.868 52.381 19.03 0.00 45.62 3.13
4094 4910 1.810151 TGAATGCCCACGTAAGCTTTC 59.190 47.619 21.24 21.24 41.22 2.62
4095 4911 1.812571 CTGAATGCCCACGTAAGCTTT 59.187 47.619 3.20 9.53 45.62 3.51
4096 4912 1.271379 ACTGAATGCCCACGTAAGCTT 60.271 47.619 3.48 3.48 45.62 3.74
4097 4913 0.324943 ACTGAATGCCCACGTAAGCT 59.675 50.000 10.02 0.00 45.62 3.74
4098 4914 1.165270 AACTGAATGCCCACGTAAGC 58.835 50.000 2.15 2.15 45.62 3.09
4099 4915 4.972271 GGGAAACTGAATGCCCACGTAAG 61.972 52.174 0.00 0.00 40.39 2.34
4100 4916 2.156098 GGAAACTGAATGCCCACGTAA 58.844 47.619 0.00 0.00 0.00 3.18
4101 4917 1.612199 GGGAAACTGAATGCCCACGTA 60.612 52.381 0.00 0.00 40.39 3.57
4102 4918 0.893727 GGGAAACTGAATGCCCACGT 60.894 55.000 0.00 0.00 40.39 4.49
4103 4919 1.883021 GGGAAACTGAATGCCCACG 59.117 57.895 0.00 0.00 40.39 4.94
4104 4920 0.893727 ACGGGAAACTGAATGCCCAC 60.894 55.000 0.00 0.00 40.71 4.61
4105 4921 0.608035 GACGGGAAACTGAATGCCCA 60.608 55.000 0.00 0.00 40.71 5.36
4106 4922 0.322546 AGACGGGAAACTGAATGCCC 60.323 55.000 0.00 0.00 41.09 5.36
4107 4923 0.804989 CAGACGGGAAACTGAATGCC 59.195 55.000 0.00 0.00 41.09 4.40
4108 4924 0.804989 CCAGACGGGAAACTGAATGC 59.195 55.000 0.00 0.00 40.01 3.56
4166 4983 0.249447 TTCTGCATATGGCTCCGTCG 60.249 55.000 4.56 0.00 45.15 5.12
4167 4984 1.802960 CATTCTGCATATGGCTCCGTC 59.197 52.381 4.56 0.00 45.15 4.79
4168 4985 1.141657 ACATTCTGCATATGGCTCCGT 59.858 47.619 4.56 0.00 45.15 4.69
4169 4986 1.888215 ACATTCTGCATATGGCTCCG 58.112 50.000 4.56 0.00 45.15 4.63
4171 4988 4.906065 TTCAACATTCTGCATATGGCTC 57.094 40.909 4.56 0.00 45.15 4.70
4172 4989 4.891168 TGATTCAACATTCTGCATATGGCT 59.109 37.500 4.56 0.00 45.15 4.75
4173 4990 5.190992 TGATTCAACATTCTGCATATGGC 57.809 39.130 4.56 0.00 45.13 4.40
4174 4991 6.208797 AGGATGATTCAACATTCTGCATATGG 59.791 38.462 4.56 0.00 35.11 2.74
4175 4992 7.215719 AGGATGATTCAACATTCTGCATATG 57.784 36.000 0.00 0.00 35.11 1.78
4176 4993 7.834881 AAGGATGATTCAACATTCTGCATAT 57.165 32.000 0.00 0.00 36.38 1.78
4177 4994 7.417003 CCAAAGGATGATTCAACATTCTGCATA 60.417 37.037 0.00 0.00 36.38 3.14
4178 4995 6.338146 CAAAGGATGATTCAACATTCTGCAT 58.662 36.000 0.00 0.00 36.38 3.96
4179 4996 5.336929 CCAAAGGATGATTCAACATTCTGCA 60.337 40.000 0.00 0.00 36.38 4.41
4180 4997 5.107133 CCAAAGGATGATTCAACATTCTGC 58.893 41.667 0.00 0.00 36.38 4.26
4182 4999 4.161001 GGCCAAAGGATGATTCAACATTCT 59.839 41.667 0.00 0.00 37.68 2.40
4184 5001 3.839490 TGGCCAAAGGATGATTCAACATT 59.161 39.130 0.61 0.00 0.00 2.71
4216 5546 9.485206 AAGTTTCTCGACAAGTTATAGCTTTAA 57.515 29.630 0.00 0.00 0.00 1.52
4231 5561 5.177696 ACAGATTGCAGTTAAGTTTCTCGAC 59.822 40.000 0.00 0.00 0.00 4.20
4232 5562 5.297547 ACAGATTGCAGTTAAGTTTCTCGA 58.702 37.500 0.00 0.00 0.00 4.04
4233 5563 5.597813 ACAGATTGCAGTTAAGTTTCTCG 57.402 39.130 0.00 0.00 0.00 4.04
4234 5564 8.034058 ACATACAGATTGCAGTTAAGTTTCTC 57.966 34.615 0.00 0.00 0.00 2.87
4235 5565 7.986085 ACATACAGATTGCAGTTAAGTTTCT 57.014 32.000 0.00 0.00 0.00 2.52
4236 5566 8.391106 CCTACATACAGATTGCAGTTAAGTTTC 58.609 37.037 0.00 0.00 0.00 2.78
4237 5567 7.148239 GCCTACATACAGATTGCAGTTAAGTTT 60.148 37.037 0.00 0.00 0.00 2.66
4238 5568 6.316390 GCCTACATACAGATTGCAGTTAAGTT 59.684 38.462 0.00 0.00 0.00 2.66
4239 5569 5.817816 GCCTACATACAGATTGCAGTTAAGT 59.182 40.000 0.00 0.00 0.00 2.24
4240 5570 6.018425 CAGCCTACATACAGATTGCAGTTAAG 60.018 42.308 0.00 0.00 0.00 1.85
4241 5571 5.817296 CAGCCTACATACAGATTGCAGTTAA 59.183 40.000 0.00 0.00 0.00 2.01
4242 5572 5.359756 CAGCCTACATACAGATTGCAGTTA 58.640 41.667 0.00 0.00 0.00 2.24
4243 5573 4.194640 CAGCCTACATACAGATTGCAGTT 58.805 43.478 0.00 0.00 0.00 3.16
4244 5574 3.432749 CCAGCCTACATACAGATTGCAGT 60.433 47.826 0.00 0.00 0.00 4.40
4245 5575 3.136763 CCAGCCTACATACAGATTGCAG 58.863 50.000 0.00 0.00 0.00 4.41
4246 5576 2.771372 TCCAGCCTACATACAGATTGCA 59.229 45.455 0.00 0.00 0.00 4.08
4247 5577 3.397482 CTCCAGCCTACATACAGATTGC 58.603 50.000 0.00 0.00 0.00 3.56
4248 5578 3.397482 GCTCCAGCCTACATACAGATTG 58.603 50.000 0.00 0.00 34.31 2.67
4249 5579 3.760580 GCTCCAGCCTACATACAGATT 57.239 47.619 0.00 0.00 34.31 2.40
4262 5592 2.119655 CCTTCTGCATGGCTCCAGC 61.120 63.158 0.00 0.00 41.14 4.85
4263 5593 2.119655 GCCTTCTGCATGGCTCCAG 61.120 63.158 15.50 0.00 45.26 3.86
4264 5594 2.044650 GCCTTCTGCATGGCTCCA 60.045 61.111 15.50 0.00 45.26 3.86
4269 5599 1.030488 CAGACCAGCCTTCTGCATGG 61.030 60.000 0.11 0.11 44.83 3.66
4270 5600 0.322277 ACAGACCAGCCTTCTGCATG 60.322 55.000 6.71 0.00 43.79 4.06
4271 5601 1.065854 GTACAGACCAGCCTTCTGCAT 60.066 52.381 6.71 0.00 43.79 3.96
4272 5602 0.321671 GTACAGACCAGCCTTCTGCA 59.678 55.000 6.71 0.00 43.79 4.41
4273 5603 0.610687 AGTACAGACCAGCCTTCTGC 59.389 55.000 6.71 0.00 43.79 4.26
4274 5604 3.093057 ACTAGTACAGACCAGCCTTCTG 58.907 50.000 0.00 5.49 45.21 3.02
4275 5605 3.459710 ACTAGTACAGACCAGCCTTCT 57.540 47.619 0.00 0.00 0.00 2.85
4276 5606 4.098196 CCTAACTAGTACAGACCAGCCTTC 59.902 50.000 0.00 0.00 0.00 3.46
4277 5607 4.024670 CCTAACTAGTACAGACCAGCCTT 58.975 47.826 0.00 0.00 0.00 4.35
4278 5608 3.627747 CCCTAACTAGTACAGACCAGCCT 60.628 52.174 0.00 0.00 0.00 4.58
4279 5609 2.694109 CCCTAACTAGTACAGACCAGCC 59.306 54.545 0.00 0.00 0.00 4.85
4280 5610 3.629087 TCCCTAACTAGTACAGACCAGC 58.371 50.000 0.00 0.00 0.00 4.85
4281 5611 5.446860 TGATCCCTAACTAGTACAGACCAG 58.553 45.833 0.00 0.00 0.00 4.00
4282 5612 5.461516 TGATCCCTAACTAGTACAGACCA 57.538 43.478 0.00 0.00 0.00 4.02
4283 5613 5.477637 GGATGATCCCTAACTAGTACAGACC 59.522 48.000 0.00 0.00 0.00 3.85
4284 5614 6.207810 CAGGATGATCCCTAACTAGTACAGAC 59.792 46.154 8.08 0.00 39.69 3.51
4285 5615 6.102762 TCAGGATGATCCCTAACTAGTACAGA 59.897 42.308 8.08 0.00 42.56 3.41
4286 5616 6.307776 TCAGGATGATCCCTAACTAGTACAG 58.692 44.000 8.08 0.00 42.56 2.74
4287 5617 6.275692 TCAGGATGATCCCTAACTAGTACA 57.724 41.667 8.08 0.00 42.56 2.90
4341 5671 3.394674 TTCAGGTTCACTCGCATTACA 57.605 42.857 0.00 0.00 0.00 2.41
4345 5675 2.749621 GGAAATTCAGGTTCACTCGCAT 59.250 45.455 0.00 0.00 0.00 4.73
4381 5711 5.861222 AAAACCACAGCTGAAAAAGTTTG 57.139 34.783 23.35 5.12 0.00 2.93
4391 5721 1.453155 AGCGGATAAAACCACAGCTG 58.547 50.000 13.48 13.48 31.76 4.24
4461 5791 2.202919 GATTTGGCGGGGCATTGC 60.203 61.111 0.00 0.00 0.00 3.56
4462 5792 0.249573 GATGATTTGGCGGGGCATTG 60.250 55.000 0.00 0.00 0.00 2.82
4463 5793 1.402107 GGATGATTTGGCGGGGCATT 61.402 55.000 0.00 0.00 0.00 3.56
4464 5794 1.833934 GGATGATTTGGCGGGGCAT 60.834 57.895 0.00 0.00 0.00 4.40
4465 5795 2.441901 GGATGATTTGGCGGGGCA 60.442 61.111 0.00 0.00 0.00 5.36
4466 5796 1.809567 GATGGATGATTTGGCGGGGC 61.810 60.000 0.00 0.00 0.00 5.80
4467 5797 0.178981 AGATGGATGATTTGGCGGGG 60.179 55.000 0.00 0.00 0.00 5.73
4468 5798 1.242076 GAGATGGATGATTTGGCGGG 58.758 55.000 0.00 0.00 0.00 6.13
4469 5799 0.870393 CGAGATGGATGATTTGGCGG 59.130 55.000 0.00 0.00 0.00 6.13
4470 5800 0.236711 GCGAGATGGATGATTTGGCG 59.763 55.000 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.