Multiple sequence alignment - TraesCS1A01G325700

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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 TraesCS1A01G325700 chr1A 100.000 2805 0 0 1 2805 516453410 516456214 0.000000e+00 5180.0
1 TraesCS1A01G325700 chr1B 89.699 1427 79 29 756 2147 566720617 566722010 0.000000e+00 1759.0
2 TraesCS1A01G325700 chr1D 87.255 1530 117 45 856 2352 419601851 419603335 0.000000e+00 1674.0
3 TraesCS1A01G325700 chr1D 84.961 645 65 14 17 649 464275697 464275073 2.370000e-175 625.0
4 TraesCS1A01G325700 chr1D 84.674 261 30 4 2500 2750 419603326 419603586 4.640000e-63 252.0
5 TraesCS1A01G325700 chr1D 94.059 101 5 1 756 855 419601776 419601876 4.840000e-33 152.0
6 TraesCS1A01G325700 chr7A 85.973 663 80 9 1 653 636699170 636699829 0.000000e+00 697.0
7 TraesCS1A01G325700 chr7A 97.059 34 1 0 2207 2240 375896532 375896565 1.090000e-04 58.4
8 TraesCS1A01G325700 chr7D 85.800 669 70 11 18 678 477205176 477205827 0.000000e+00 686.0
9 TraesCS1A01G325700 chrUn 85.015 674 73 11 17 680 61000840 61000185 0.000000e+00 660.0
10 TraesCS1A01G325700 chrUn 85.015 674 73 11 17 680 330691663 330692318 0.000000e+00 660.0
11 TraesCS1A01G325700 chrUn 86.173 405 37 8 17 420 60997337 60996951 1.200000e-113 420.0
12 TraesCS1A01G325700 chr6D 84.460 695 75 12 1 680 32249649 32248973 0.000000e+00 654.0
13 TraesCS1A01G325700 chr6D 85.161 620 66 12 71 680 7156200 7156803 1.850000e-171 612.0
14 TraesCS1A01G325700 chr5D 83.885 695 72 20 1 680 386101705 386101036 6.600000e-176 627.0
15 TraesCS1A01G325700 chr5D 83.306 599 66 21 93 677 33670546 33671124 3.200000e-144 521.0
16 TraesCS1A01G325700 chr5D 86.885 61 5 3 2324 2381 514030214 514030154 6.490000e-07 65.8
17 TraesCS1A01G325700 chr7B 83.852 675 78 15 17 680 207903798 207903144 5.140000e-172 614.0
18 TraesCS1A01G325700 chr5B 84.848 594 63 12 93 677 600363799 600364374 8.720000e-160 573.0
19 TraesCS1A01G325700 chr3A 84.168 619 69 14 71 680 52204265 52203667 8.720000e-160 573.0
20 TraesCS1A01G325700 chr3A 83.601 622 66 19 71 677 16019018 16018418 4.080000e-153 551.0
21 TraesCS1A01G325700 chr5A 82.256 665 93 15 1 660 445423283 445422639 4.080000e-153 551.0
22 TraesCS1A01G325700 chr6A 83.333 618 73 17 71 680 158425181 158424586 6.830000e-151 544.0


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 TraesCS1A01G325700 chr1A 516453410 516456214 2804 False 5180.000000 5180 100.000000 1 2805 1 chr1A.!!$F1 2804
1 TraesCS1A01G325700 chr1B 566720617 566722010 1393 False 1759.000000 1759 89.699000 756 2147 1 chr1B.!!$F1 1391
2 TraesCS1A01G325700 chr1D 419601776 419603586 1810 False 692.666667 1674 88.662667 756 2750 3 chr1D.!!$F1 1994
3 TraesCS1A01G325700 chr1D 464275073 464275697 624 True 625.000000 625 84.961000 17 649 1 chr1D.!!$R1 632
4 TraesCS1A01G325700 chr7A 636699170 636699829 659 False 697.000000 697 85.973000 1 653 1 chr7A.!!$F2 652
5 TraesCS1A01G325700 chr7D 477205176 477205827 651 False 686.000000 686 85.800000 18 678 1 chr7D.!!$F1 660
6 TraesCS1A01G325700 chrUn 330691663 330692318 655 False 660.000000 660 85.015000 17 680 1 chrUn.!!$F1 663
7 TraesCS1A01G325700 chrUn 60996951 61000840 3889 True 540.000000 660 85.594000 17 680 2 chrUn.!!$R1 663
8 TraesCS1A01G325700 chr6D 32248973 32249649 676 True 654.000000 654 84.460000 1 680 1 chr6D.!!$R1 679
9 TraesCS1A01G325700 chr6D 7156200 7156803 603 False 612.000000 612 85.161000 71 680 1 chr6D.!!$F1 609
10 TraesCS1A01G325700 chr5D 386101036 386101705 669 True 627.000000 627 83.885000 1 680 1 chr5D.!!$R1 679
11 TraesCS1A01G325700 chr5D 33670546 33671124 578 False 521.000000 521 83.306000 93 677 1 chr5D.!!$F1 584
12 TraesCS1A01G325700 chr7B 207903144 207903798 654 True 614.000000 614 83.852000 17 680 1 chr7B.!!$R1 663
13 TraesCS1A01G325700 chr5B 600363799 600364374 575 False 573.000000 573 84.848000 93 677 1 chr5B.!!$F1 584
14 TraesCS1A01G325700 chr3A 52203667 52204265 598 True 573.000000 573 84.168000 71 680 1 chr3A.!!$R2 609
15 TraesCS1A01G325700 chr3A 16018418 16019018 600 True 551.000000 551 83.601000 71 677 1 chr3A.!!$R1 606
16 TraesCS1A01G325700 chr5A 445422639 445423283 644 True 551.000000 551 82.256000 1 660 1 chr5A.!!$R1 659
17 TraesCS1A01G325700 chr6A 158424586 158425181 595 True 544.000000 544 83.333000 71 680 1 chr6A.!!$R1 609

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
709 1336 0.108585 TTCCCAACCTGCTGTCTCAC 59.891 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2401 4754 0.109873 GTCCGTACGTCAGTCCAGTG 60.11 60.0 15.21 0.0 0.0 3.66 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
59 61 1.082038 CTGCGACTTCGTGACGACT 60.082 57.895 7.39 0.00 42.22 4.18
63 65 1.866982 CGACTTCGTGACGACTACAG 58.133 55.000 7.39 4.86 34.89 2.74
65 67 0.949397 ACTTCGTGACGACTACAGCA 59.051 50.000 7.39 0.00 34.89 4.41
66 68 1.069159 ACTTCGTGACGACTACAGCAG 60.069 52.381 7.39 2.78 34.89 4.24
129 133 6.418057 TTGAAGGTTTTTGCTACATCCATT 57.582 33.333 0.00 0.00 0.00 3.16
154 158 0.179116 CGGAGCTGTGACCTCATGAG 60.179 60.000 16.24 16.24 0.00 2.90
177 181 1.274476 GCGACGACGTTTTTGCTGA 59.726 52.632 9.33 0.00 41.98 4.26
210 218 4.250464 TGATTTTGCTACTACCGGTGAAG 58.750 43.478 19.93 10.55 0.00 3.02
253 264 2.032634 GGCGTTGATTGACTGGCGA 61.033 57.895 0.00 0.00 0.00 5.54
317 334 2.820037 GGCGGCAGAGCTACAACC 60.820 66.667 3.07 0.00 37.29 3.77
319 336 2.571757 CGGCAGAGCTACAACCGA 59.428 61.111 10.51 0.00 46.71 4.69
352 369 1.963338 GCCGTCAAGAGCTGCAACT 60.963 57.895 1.02 0.00 0.00 3.16
382 399 2.359850 GTTGCATGGGTCGAGGCA 60.360 61.111 0.00 0.00 0.00 4.75
387 404 1.315257 GCATGGGTCGAGGCAACAAT 61.315 55.000 0.00 0.00 41.41 2.71
392 409 1.026718 GGTCGAGGCAACAATGAGGG 61.027 60.000 0.00 0.00 41.41 4.30
465 487 4.493747 GACGAGGAAGACCGGCGG 62.494 72.222 27.06 27.06 40.88 6.13
496 519 1.592400 GACGATGAGGACGACCACCA 61.592 60.000 6.71 4.12 38.94 4.17
548 574 2.588877 CGGGACATGCGGATCCAC 60.589 66.667 13.41 1.81 36.65 4.02
559 586 4.530857 GATCCACCCCGACTGCCG 62.531 72.222 0.00 0.00 38.18 5.69
611 1226 0.800683 CTGAATCTAACGGTCGCGCA 60.801 55.000 8.75 0.00 0.00 6.09
632 1254 1.983972 CTCATATCGAACGGCCTAGC 58.016 55.000 0.00 0.00 0.00 3.42
660 1287 4.097863 CGAAACTTTCGCCCGGCC 62.098 66.667 10.83 0.00 46.97 6.13
695 1322 3.857157 AGCGCTTATAGGATTTTCCCA 57.143 42.857 2.64 0.00 37.19 4.37
696 1323 4.164843 AGCGCTTATAGGATTTTCCCAA 57.835 40.909 2.64 0.00 37.19 4.12
697 1324 3.883489 AGCGCTTATAGGATTTTCCCAAC 59.117 43.478 2.64 0.00 37.19 3.77
698 1325 3.004419 GCGCTTATAGGATTTTCCCAACC 59.996 47.826 0.00 0.00 37.19 3.77
699 1326 4.461198 CGCTTATAGGATTTTCCCAACCT 58.539 43.478 0.00 0.00 37.19 3.50
700 1327 4.275936 CGCTTATAGGATTTTCCCAACCTG 59.724 45.833 0.00 0.00 37.19 4.00
701 1328 4.038042 GCTTATAGGATTTTCCCAACCTGC 59.962 45.833 0.00 0.00 37.19 4.85
702 1329 5.449553 CTTATAGGATTTTCCCAACCTGCT 58.550 41.667 0.00 0.00 37.19 4.24
703 1330 1.928868 AGGATTTTCCCAACCTGCTG 58.071 50.000 0.00 0.00 37.19 4.41
704 1331 1.147817 AGGATTTTCCCAACCTGCTGT 59.852 47.619 0.00 0.00 37.19 4.40
705 1332 1.546029 GGATTTTCCCAACCTGCTGTC 59.454 52.381 0.00 0.00 0.00 3.51
706 1333 2.519013 GATTTTCCCAACCTGCTGTCT 58.481 47.619 0.00 0.00 0.00 3.41
707 1334 1.981256 TTTTCCCAACCTGCTGTCTC 58.019 50.000 0.00 0.00 0.00 3.36
708 1335 0.843309 TTTCCCAACCTGCTGTCTCA 59.157 50.000 0.00 0.00 0.00 3.27
709 1336 0.108585 TTCCCAACCTGCTGTCTCAC 59.891 55.000 0.00 0.00 0.00 3.51
710 1337 1.302832 CCCAACCTGCTGTCTCACC 60.303 63.158 0.00 0.00 0.00 4.02
711 1338 1.302832 CCAACCTGCTGTCTCACCC 60.303 63.158 0.00 0.00 0.00 4.61
712 1339 1.302832 CAACCTGCTGTCTCACCCC 60.303 63.158 0.00 0.00 0.00 4.95
713 1340 2.883828 AACCTGCTGTCTCACCCCG 61.884 63.158 0.00 0.00 0.00 5.73
714 1341 2.997315 CCTGCTGTCTCACCCCGA 60.997 66.667 0.00 0.00 0.00 5.14
715 1342 2.262915 CTGCTGTCTCACCCCGAC 59.737 66.667 0.00 0.00 0.00 4.79
716 1343 2.523168 TGCTGTCTCACCCCGACA 60.523 61.111 0.00 0.00 38.94 4.35
717 1344 1.892819 CTGCTGTCTCACCCCGACAT 61.893 60.000 0.00 0.00 40.30 3.06
718 1345 1.448540 GCTGTCTCACCCCGACATG 60.449 63.158 0.00 0.00 40.30 3.21
719 1346 1.219124 CTGTCTCACCCCGACATGG 59.781 63.158 0.00 0.00 40.30 3.66
766 1393 5.834204 ACCTGGGCTAGTACTATTTGACTAG 59.166 44.000 2.33 1.62 45.33 2.57
777 1404 5.819059 ACTATTTGACTAGTCGTCGATTCC 58.181 41.667 17.85 0.00 45.87 3.01
783 1410 4.094090 ACTAGTCGTCGATTCCAAACTC 57.906 45.455 0.00 0.00 0.00 3.01
789 1416 5.050295 AGTCGTCGATTCCAAACTCTTTTTC 60.050 40.000 0.00 0.00 0.00 2.29
792 1419 6.037830 TCGTCGATTCCAAACTCTTTTTCTTT 59.962 34.615 0.00 0.00 0.00 2.52
809 1440 8.488651 TTTTTCTTTCTTGACTAGTCGTCTTT 57.511 30.769 17.85 0.00 43.25 2.52
869 1500 6.493115 TCTGATCTTCTGATTCTATCCACTCC 59.507 42.308 0.00 0.00 32.19 3.85
887 1518 1.388065 CCTCTGATCTTCTCCCGCGT 61.388 60.000 4.92 0.00 0.00 6.01
916 1547 5.699458 AGGTGGTTGAGTAGTTAAAACGATG 59.301 40.000 0.00 0.00 0.00 3.84
973 1604 0.978146 AGAGGCGCCACCATAAGAGT 60.978 55.000 31.54 2.38 43.14 3.24
977 1608 1.982073 GCGCCACCATAAGAGTGTGC 61.982 60.000 0.00 0.00 33.20 4.57
993 1624 4.779696 AGTGTGCCATTTGTTCCAAAAAT 58.220 34.783 0.00 0.00 0.00 1.82
1020 1659 6.980416 ACCATAAGAGAGTTACATCCTACC 57.020 41.667 0.00 0.00 0.00 3.18
1021 1660 6.441222 ACCATAAGAGAGTTACATCCTACCA 58.559 40.000 0.00 0.00 0.00 3.25
1039 1678 5.306678 CCTACCAATTAGCTCTCCAGAGAAT 59.693 44.000 7.84 0.00 44.74 2.40
1207 1853 6.683861 GCCTCCAAATCCCATTTATTTCACTC 60.684 42.308 0.00 0.00 0.00 3.51
1236 1882 5.541101 ACATTACATATGCATGGCCATTTCT 59.459 36.000 17.92 5.67 36.39 2.52
1254 1900 5.695851 TTTCTTCTTCTGCTGGTTCATTC 57.304 39.130 0.00 0.00 0.00 2.67
1255 1901 4.356405 TCTTCTTCTGCTGGTTCATTCA 57.644 40.909 0.00 0.00 0.00 2.57
1256 1902 4.914983 TCTTCTTCTGCTGGTTCATTCAT 58.085 39.130 0.00 0.00 0.00 2.57
1257 1903 4.698780 TCTTCTTCTGCTGGTTCATTCATG 59.301 41.667 0.00 0.00 0.00 3.07
1259 1905 4.259356 TCTTCTGCTGGTTCATTCATGAG 58.741 43.478 0.00 0.00 38.19 2.90
1292 1938 1.001974 TCGTGTGAGGCTATGCAAGTT 59.998 47.619 0.00 0.00 0.00 2.66
1304 1952 5.467063 GGCTATGCAAGTTACCTACTGATTC 59.533 44.000 0.00 0.00 37.12 2.52
1330 1978 3.000041 TGTGGACGATCTGTAAATGTGC 59.000 45.455 0.00 0.00 0.00 4.57
1350 2135 1.300620 CCCGTGTTCTTCAGACGCA 60.301 57.895 0.00 0.00 0.00 5.24
1392 3508 2.033194 GTACGTGCCCTTCTGCCAC 61.033 63.158 0.00 0.00 0.00 5.01
1464 3580 2.434428 CGTCTACAGGAGTACAGGTGT 58.566 52.381 0.00 0.00 0.00 4.16
1545 3661 2.224867 CCTCCACCTCCACTGAAAACAT 60.225 50.000 0.00 0.00 0.00 2.71
1546 3662 3.077359 CTCCACCTCCACTGAAAACATC 58.923 50.000 0.00 0.00 0.00 3.06
1567 3690 1.332686 CCACGACCGTCTCGATATTCA 59.667 52.381 6.73 0.00 46.14 2.57
1595 3722 2.169769 CGGCAGGAATTACCCACTAGAA 59.830 50.000 0.00 0.00 40.05 2.10
1597 3724 3.945921 GGCAGGAATTACCCACTAGAAAC 59.054 47.826 0.00 0.00 40.05 2.78
1665 3815 1.137872 AGCAGCAGCAGATGTAGTACC 59.862 52.381 3.17 0.00 45.49 3.34
1670 3820 7.949035 GCAGCAGCAGATGTAGTACCTACAG 62.949 52.000 9.67 0.00 44.07 2.74
1902 4250 0.535102 AACAGGTTTCCGCTGGAGTG 60.535 55.000 0.00 0.00 31.21 3.51
1914 4262 2.084546 GCTGGAGTGGGTACATGAAAC 58.915 52.381 0.00 0.00 0.00 2.78
1981 4333 8.598075 GTCAATTCAAGATTAATCATTTGTGCC 58.402 33.333 17.56 0.00 0.00 5.01
2003 4355 8.040727 GTGCCTATTGTTTTCCCTCAAAATTAT 58.959 33.333 0.00 0.00 36.35 1.28
2049 4401 6.218746 ACACTCAAAAGAAAAATCTGATGGC 58.781 36.000 0.00 0.00 0.00 4.40
2111 4464 6.672357 GCAGATGAACATCCTACGTGTAAAAC 60.672 42.308 10.63 0.00 38.58 2.43
2127 4480 7.148035 ACGTGTAAAACTTAAACCCTCAAACAT 60.148 33.333 0.00 0.00 0.00 2.71
2141 4494 6.725834 ACCCTCAAACATACATTTCTGGAATT 59.274 34.615 0.00 0.00 0.00 2.17
2182 4535 8.995027 TTATACTCATGCCCTTGTGATAAAAT 57.005 30.769 0.00 0.00 0.00 1.82
2193 4546 7.382759 GCCCTTGTGATAAAATAAACGTTTCAA 59.617 33.333 18.42 10.81 0.00 2.69
2200 4553 8.973378 TGATAAAATAAACGTTTCAAAAGCCAG 58.027 29.630 18.42 0.00 0.00 4.85
2226 4579 2.280457 GCATCTACAGCCGGGCTC 60.280 66.667 20.97 1.62 36.40 4.70
2227 4580 2.801631 GCATCTACAGCCGGGCTCT 61.802 63.158 20.97 10.88 36.40 4.09
2233 4586 0.321298 TACAGCCGGGCTCTTCAAAC 60.321 55.000 20.97 0.00 36.40 2.93
2247 4600 2.922740 TCAAACGCCCCCTATATGTC 57.077 50.000 0.00 0.00 0.00 3.06
2249 4602 3.578978 TCAAACGCCCCCTATATGTCTA 58.421 45.455 0.00 0.00 0.00 2.59
2255 4608 2.100989 CCCCCTATATGTCTAGACGGC 58.899 57.143 17.85 0.00 0.00 5.68
2261 4614 0.826256 TATGTCTAGACGGCCGGCAT 60.826 55.000 36.60 20.48 0.00 4.40
2263 4616 2.758327 TCTAGACGGCCGGCATGT 60.758 61.111 36.60 25.96 0.00 3.21
2267 4620 1.038681 TAGACGGCCGGCATGTTCTA 61.039 55.000 36.60 24.01 0.00 2.10
2273 4626 0.463654 GCCGGCATGTTCTATGACCA 60.464 55.000 24.80 0.00 0.00 4.02
2287 4640 6.558771 TCTATGACCAGTCACAAAAATGTG 57.441 37.500 1.88 2.60 43.11 3.21
2297 4650 2.865551 CACAAAAATGTGACCCAAGCAC 59.134 45.455 2.88 0.00 42.02 4.40
2309 4662 1.338020 CCCAAGCACACTTCTCAAACC 59.662 52.381 0.00 0.00 32.29 3.27
2313 4666 1.949257 CACACTTCTCAAACCGGCC 59.051 57.895 0.00 0.00 0.00 6.13
2322 4675 2.168936 TCTCAAACCGGCCATATACGTT 59.831 45.455 0.00 0.00 0.00 3.99
2323 4676 2.542595 CTCAAACCGGCCATATACGTTC 59.457 50.000 0.00 0.00 0.00 3.95
2332 4685 2.394708 CCATATACGTTCGGCTGACAG 58.605 52.381 0.00 0.00 0.00 3.51
2338 4691 3.241530 TTCGGCTGACAGGCACCT 61.242 61.111 26.64 0.00 41.44 4.00
2339 4692 3.240134 TTCGGCTGACAGGCACCTC 62.240 63.158 26.64 0.00 41.44 3.85
2340 4693 3.699894 CGGCTGACAGGCACCTCT 61.700 66.667 26.64 0.00 41.44 3.69
2341 4694 2.267324 GGCTGACAGGCACCTCTC 59.733 66.667 23.18 0.00 40.97 3.20
2342 4695 2.587247 GGCTGACAGGCACCTCTCA 61.587 63.158 23.18 0.00 40.97 3.27
2343 4696 1.601171 GCTGACAGGCACCTCTCAT 59.399 57.895 4.26 0.00 0.00 2.90
2344 4697 0.826715 GCTGACAGGCACCTCTCATA 59.173 55.000 4.26 0.00 0.00 2.15
2345 4698 1.415659 GCTGACAGGCACCTCTCATAT 59.584 52.381 4.26 0.00 0.00 1.78
2346 4699 2.158842 GCTGACAGGCACCTCTCATATT 60.159 50.000 4.26 0.00 0.00 1.28
2347 4700 3.683847 GCTGACAGGCACCTCTCATATTT 60.684 47.826 4.26 0.00 0.00 1.40
2348 4701 4.443457 GCTGACAGGCACCTCTCATATTTA 60.443 45.833 4.26 0.00 0.00 1.40
2349 4702 5.282055 TGACAGGCACCTCTCATATTTAG 57.718 43.478 0.00 0.00 0.00 1.85
2350 4703 4.061596 GACAGGCACCTCTCATATTTAGC 58.938 47.826 0.00 0.00 0.00 3.09
2351 4704 3.181450 ACAGGCACCTCTCATATTTAGCC 60.181 47.826 0.00 0.00 41.08 3.93
2352 4705 2.373502 AGGCACCTCTCATATTTAGCCC 59.626 50.000 0.00 0.00 41.69 5.19
2353 4706 2.106511 GGCACCTCTCATATTTAGCCCA 59.893 50.000 0.00 0.00 34.94 5.36
2354 4707 3.435026 GGCACCTCTCATATTTAGCCCAA 60.435 47.826 0.00 0.00 34.94 4.12
2355 4708 4.207165 GCACCTCTCATATTTAGCCCAAA 58.793 43.478 0.00 0.00 0.00 3.28
2356 4709 4.829492 GCACCTCTCATATTTAGCCCAAAT 59.171 41.667 0.17 0.17 40.10 2.32
2357 4710 5.048434 GCACCTCTCATATTTAGCCCAAATC 60.048 44.000 0.00 0.00 37.93 2.17
2358 4711 6.302269 CACCTCTCATATTTAGCCCAAATCT 58.698 40.000 0.00 0.00 37.93 2.40
2359 4712 6.206243 CACCTCTCATATTTAGCCCAAATCTG 59.794 42.308 0.00 0.17 37.93 2.90
2360 4713 5.709164 CCTCTCATATTTAGCCCAAATCTGG 59.291 44.000 0.00 0.00 43.10 3.86
2379 4732 2.280186 GCGAATACGAGGCCCAGG 60.280 66.667 0.00 0.00 42.66 4.45
2380 4733 2.280186 CGAATACGAGGCCCAGGC 60.280 66.667 0.00 0.00 42.66 4.85
2382 4735 3.081409 AATACGAGGCCCAGGCGT 61.081 61.111 13.75 13.75 43.06 5.68
2383 4736 3.385749 AATACGAGGCCCAGGCGTG 62.386 63.158 17.41 0.00 43.06 5.34
2399 4752 2.747460 TGCTCAAGCGCATCCACC 60.747 61.111 11.47 0.00 45.83 4.61
2400 4753 2.747460 GCTCAAGCGCATCCACCA 60.747 61.111 11.47 0.00 0.00 4.17
2401 4754 3.044059 GCTCAAGCGCATCCACCAC 62.044 63.158 11.47 0.00 0.00 4.16
2403 4756 1.915614 CTCAAGCGCATCCACCACAC 61.916 60.000 11.47 0.00 0.00 3.82
2404 4757 1.968017 CAAGCGCATCCACCACACT 60.968 57.895 11.47 0.00 0.00 3.55
2405 4758 1.968017 AAGCGCATCCACCACACTG 60.968 57.895 11.47 0.00 0.00 3.66
2406 4759 3.434319 GCGCATCCACCACACTGG 61.434 66.667 0.30 0.00 45.02 4.00
2407 4760 2.347114 CGCATCCACCACACTGGA 59.653 61.111 0.00 0.00 44.72 3.86
2408 4761 2.034879 CGCATCCACCACACTGGAC 61.035 63.158 0.00 0.00 43.38 4.02
2409 4762 1.376466 GCATCCACCACACTGGACT 59.624 57.895 0.00 0.00 43.38 3.85
2410 4763 0.957395 GCATCCACCACACTGGACTG 60.957 60.000 0.00 0.00 43.38 3.51
2411 4764 0.686789 CATCCACCACACTGGACTGA 59.313 55.000 0.00 0.00 43.38 3.41
2412 4765 0.687354 ATCCACCACACTGGACTGAC 59.313 55.000 0.00 0.00 43.38 3.51
2413 4766 1.300931 CCACCACACTGGACTGACG 60.301 63.158 0.00 0.00 40.96 4.35
2414 4767 1.441729 CACCACACTGGACTGACGT 59.558 57.895 0.00 0.00 40.96 4.34
2415 4768 0.671796 CACCACACTGGACTGACGTA 59.328 55.000 0.00 0.00 40.96 3.57
2416 4769 0.672342 ACCACACTGGACTGACGTAC 59.328 55.000 0.00 0.00 40.96 3.67
2417 4770 0.386858 CCACACTGGACTGACGTACG 60.387 60.000 15.01 15.01 40.96 3.67
2418 4771 0.386858 CACACTGGACTGACGTACGG 60.387 60.000 21.06 4.19 36.36 4.02
2419 4772 0.535780 ACACTGGACTGACGTACGGA 60.536 55.000 21.06 4.56 33.76 4.69
2420 4773 0.109873 CACTGGACTGACGTACGGAC 60.110 60.000 21.06 13.48 33.76 4.79
2421 4774 1.239968 ACTGGACTGACGTACGGACC 61.240 60.000 21.06 11.87 39.49 4.46
2422 4775 1.930908 CTGGACTGACGTACGGACCC 61.931 65.000 21.06 12.90 38.57 4.46
2423 4776 2.482374 GACTGACGTACGGACCCG 59.518 66.667 21.06 6.94 46.03 5.28
2424 4777 3.673867 GACTGACGTACGGACCCGC 62.674 68.421 21.06 0.33 44.19 6.13
2425 4778 4.824166 CTGACGTACGGACCCGCG 62.824 72.222 21.06 0.00 44.19 6.46
2441 4794 2.666862 CGTGGGCAGCGGTTGTTA 60.667 61.111 0.00 0.00 0.00 2.41
2442 4795 2.951458 GTGGGCAGCGGTTGTTAC 59.049 61.111 0.00 0.00 0.00 2.50
2443 4796 2.281900 TGGGCAGCGGTTGTTACC 60.282 61.111 0.00 0.00 41.33 2.85
2444 4797 2.033602 GGGCAGCGGTTGTTACCT 59.966 61.111 0.00 0.00 42.66 3.08
2445 4798 1.297364 GGGCAGCGGTTGTTACCTA 59.703 57.895 0.00 0.00 42.66 3.08
2446 4799 0.743345 GGGCAGCGGTTGTTACCTAG 60.743 60.000 0.00 0.00 42.66 3.02
2447 4800 1.366854 GGCAGCGGTTGTTACCTAGC 61.367 60.000 0.00 0.00 42.66 3.42
2448 4801 0.672401 GCAGCGGTTGTTACCTAGCA 60.672 55.000 0.00 0.00 42.66 3.49
2449 4802 1.359848 CAGCGGTTGTTACCTAGCAG 58.640 55.000 0.00 0.00 42.66 4.24
2450 4803 0.974383 AGCGGTTGTTACCTAGCAGT 59.026 50.000 0.00 0.00 42.66 4.40
2451 4804 1.067071 AGCGGTTGTTACCTAGCAGTC 60.067 52.381 0.00 0.00 42.66 3.51
2452 4805 2.005560 GCGGTTGTTACCTAGCAGTCC 61.006 57.143 0.00 0.00 42.66 3.85
2453 4806 1.734707 CGGTTGTTACCTAGCAGTCCG 60.735 57.143 0.00 0.00 42.66 4.79
2454 4807 1.547372 GGTTGTTACCTAGCAGTCCGA 59.453 52.381 0.00 0.00 41.53 4.55
2455 4808 2.603953 GTTGTTACCTAGCAGTCCGAC 58.396 52.381 0.00 0.00 0.00 4.79
2456 4809 1.913778 TGTTACCTAGCAGTCCGACA 58.086 50.000 0.40 0.00 0.00 4.35
2457 4810 2.241160 TGTTACCTAGCAGTCCGACAA 58.759 47.619 0.40 0.00 0.00 3.18
2458 4811 2.230508 TGTTACCTAGCAGTCCGACAAG 59.769 50.000 0.40 0.00 0.00 3.16
2459 4812 1.471119 TACCTAGCAGTCCGACAAGG 58.529 55.000 0.40 4.75 42.97 3.61
2467 4820 2.915659 TCCGACAAGGACACCGCT 60.916 61.111 0.00 0.00 45.98 5.52
2468 4821 2.432628 CCGACAAGGACACCGCTC 60.433 66.667 0.00 0.00 45.00 5.03
2469 4822 2.432628 CGACAAGGACACCGCTCC 60.433 66.667 0.00 0.00 0.00 4.70
2470 4823 2.432628 GACAAGGACACCGCTCCG 60.433 66.667 0.00 0.00 35.20 4.63
2493 4846 2.046314 CCGCCCGAGGTGACAAAT 60.046 61.111 5.20 0.00 34.74 2.32
2494 4847 2.106683 CCGCCCGAGGTGACAAATC 61.107 63.158 5.20 0.00 34.74 2.17
2495 4848 2.106683 CGCCCGAGGTGACAAATCC 61.107 63.158 0.00 0.00 34.74 3.01
2496 4849 2.106683 GCCCGAGGTGACAAATCCG 61.107 63.158 0.00 0.00 0.00 4.18
2497 4850 1.449601 CCCGAGGTGACAAATCCGG 60.450 63.158 0.00 0.00 36.98 5.14
2498 4851 2.106683 CCGAGGTGACAAATCCGGC 61.107 63.158 0.00 0.00 0.00 6.13
2503 4856 3.491964 CGAGGTGACAAATCCGGCTATTA 60.492 47.826 0.00 0.00 0.00 0.98
2531 4884 4.642542 GCGACCCCCGATCGTAGC 62.643 72.222 15.09 3.53 41.68 3.58
2532 4885 3.214123 CGACCCCCGATCGTAGCA 61.214 66.667 15.09 0.00 41.76 3.49
2534 4887 1.746517 GACCCCCGATCGTAGCAAT 59.253 57.895 15.09 0.00 0.00 3.56
2546 4899 4.067972 TCGTAGCAATAGTCCCATTTCC 57.932 45.455 0.00 0.00 0.00 3.13
2555 4908 1.359130 AGTCCCATTTCCCTCCCTTTG 59.641 52.381 0.00 0.00 0.00 2.77
2556 4909 0.709992 TCCCATTTCCCTCCCTTTGG 59.290 55.000 0.00 0.00 0.00 3.28
2557 4910 0.977627 CCCATTTCCCTCCCTTTGGC 60.978 60.000 0.00 0.00 0.00 4.52
2614 4967 3.391665 CTTGTAGCTCTGGCCCGGG 62.392 68.421 19.09 19.09 39.73 5.73
2622 4975 2.844362 CTGGCCCGGGAGCAGATA 60.844 66.667 29.31 0.00 0.00 1.98
2632 4985 2.755650 GGGAGCAGATAACCATGTACG 58.244 52.381 0.00 0.00 0.00 3.67
2633 4986 2.364324 GGGAGCAGATAACCATGTACGA 59.636 50.000 0.00 0.00 0.00 3.43
2634 4987 3.381949 GGAGCAGATAACCATGTACGAC 58.618 50.000 0.00 0.00 0.00 4.34
2653 5008 3.443925 CTCACTCCAGAGCGCCGA 61.444 66.667 2.29 0.00 0.00 5.54
2657 5012 2.185350 CTCCAGAGCGCCGATTGT 59.815 61.111 2.29 0.00 0.00 2.71
2659 5014 0.596083 CTCCAGAGCGCCGATTGTAG 60.596 60.000 2.29 0.00 0.00 2.74
2682 5037 1.814772 CTAGAGCAGATCTGGGCCCG 61.815 65.000 23.89 12.57 39.20 6.13
2683 5038 2.298335 TAGAGCAGATCTGGGCCCGA 62.298 60.000 23.89 17.96 39.20 5.14
2703 5058 3.889227 TGCCACTCGCATTGTAGC 58.111 55.556 0.00 0.00 44.64 3.58
2716 5079 0.835971 TTGTAGCTGACCTGCCTCCA 60.836 55.000 0.00 0.00 0.00 3.86
2730 5093 1.979155 CTCCAGACTCTCCGGTGCA 60.979 63.158 0.00 0.00 0.00 4.57
2750 5113 1.292941 TGAGGAGGAGGAGGAGGAGG 61.293 65.000 0.00 0.00 0.00 4.30
2751 5114 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
2752 5115 0.556380 AGGAGGAGGAGGAGGAGGAA 60.556 60.000 0.00 0.00 0.00 3.36
2753 5116 0.565674 GGAGGAGGAGGAGGAGGAAT 59.434 60.000 0.00 0.00 0.00 3.01
2754 5117 1.715785 GAGGAGGAGGAGGAGGAATG 58.284 60.000 0.00 0.00 0.00 2.67
2755 5118 0.267356 AGGAGGAGGAGGAGGAATGG 59.733 60.000 0.00 0.00 0.00 3.16
2756 5119 0.766288 GGAGGAGGAGGAGGAATGGG 60.766 65.000 0.00 0.00 0.00 4.00
2757 5120 0.266152 GAGGAGGAGGAGGAATGGGA 59.734 60.000 0.00 0.00 0.00 4.37
2758 5121 0.725133 AGGAGGAGGAGGAATGGGAA 59.275 55.000 0.00 0.00 0.00 3.97
2759 5122 1.135960 GGAGGAGGAGGAATGGGAAG 58.864 60.000 0.00 0.00 0.00 3.46
2760 5123 1.135960 GAGGAGGAGGAATGGGAAGG 58.864 60.000 0.00 0.00 0.00 3.46
2761 5124 0.990818 AGGAGGAGGAATGGGAAGGC 60.991 60.000 0.00 0.00 0.00 4.35
2762 5125 1.147153 GAGGAGGAATGGGAAGGCG 59.853 63.158 0.00 0.00 0.00 5.52
2763 5126 1.306997 AGGAGGAATGGGAAGGCGA 60.307 57.895 0.00 0.00 0.00 5.54
2764 5127 1.147153 GGAGGAATGGGAAGGCGAG 59.853 63.158 0.00 0.00 0.00 5.03
2765 5128 1.147153 GAGGAATGGGAAGGCGAGG 59.853 63.158 0.00 0.00 0.00 4.63
2766 5129 2.517166 GGAATGGGAAGGCGAGGC 60.517 66.667 0.00 0.00 0.00 4.70
2785 5148 4.699522 GGGTCGGCGCTTCCAGTT 62.700 66.667 7.64 0.00 34.01 3.16
2786 5149 3.423154 GGTCGGCGCTTCCAGTTG 61.423 66.667 7.64 0.00 34.01 3.16
2787 5150 4.090057 GTCGGCGCTTCCAGTTGC 62.090 66.667 7.64 0.00 34.01 4.17
2790 5153 3.741476 GGCGCTTCCAGTTGCCAG 61.741 66.667 7.64 0.00 46.76 4.85
2791 5154 2.669569 GCGCTTCCAGTTGCCAGA 60.670 61.111 0.00 0.00 0.00 3.86
2792 5155 2.042831 GCGCTTCCAGTTGCCAGAT 61.043 57.895 0.00 0.00 0.00 2.90
2793 5156 1.589716 GCGCTTCCAGTTGCCAGATT 61.590 55.000 0.00 0.00 0.00 2.40
2794 5157 0.449388 CGCTTCCAGTTGCCAGATTC 59.551 55.000 0.00 0.00 0.00 2.52
2795 5158 0.449388 GCTTCCAGTTGCCAGATTCG 59.551 55.000 0.00 0.00 0.00 3.34
2796 5159 1.089920 CTTCCAGTTGCCAGATTCGG 58.910 55.000 0.00 0.00 0.00 4.30
2797 5160 0.400213 TTCCAGTTGCCAGATTCGGT 59.600 50.000 0.00 0.00 0.00 4.69
2798 5161 1.271856 TCCAGTTGCCAGATTCGGTA 58.728 50.000 0.00 0.00 0.00 4.02
2799 5162 1.837439 TCCAGTTGCCAGATTCGGTAT 59.163 47.619 0.00 0.00 0.00 2.73
2800 5163 1.942657 CCAGTTGCCAGATTCGGTATG 59.057 52.381 0.00 0.00 0.00 2.39
2801 5164 1.942657 CAGTTGCCAGATTCGGTATGG 59.057 52.381 0.00 0.00 42.29 2.74
2802 5165 1.134098 AGTTGCCAGATTCGGTATGGG 60.134 52.381 4.89 0.00 39.67 4.00
2803 5166 0.465460 TTGCCAGATTCGGTATGGGC 60.465 55.000 0.00 0.00 39.67 5.36
2804 5167 1.148273 GCCAGATTCGGTATGGGCA 59.852 57.895 0.00 0.00 39.67 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 50 0.386858 GCTGCTGTAGTCGTCACGAA 60.387 55.000 0.00 0.00 37.72 3.85
65 67 1.081242 CGGTTGCAGCAAAATCGCT 60.081 52.632 10.11 0.00 45.21 4.93
66 68 0.109964 TACGGTTGCAGCAAAATCGC 60.110 50.000 10.11 0.00 0.00 4.58
129 133 1.192146 AGGTCACAGCTCCGCCTTAA 61.192 55.000 0.00 0.00 0.00 1.85
177 181 7.122204 GGTAGTAGCAAAATCAAACTATGGGTT 59.878 37.037 0.00 0.00 40.28 4.11
306 322 1.067495 GTTGCTCTCGGTTGTAGCTCT 60.067 52.381 0.00 0.00 37.16 4.09
317 334 3.147294 CGACGGTTGTTGCTCTCG 58.853 61.111 0.00 0.00 0.00 4.04
352 369 1.077140 TGCAACAGGTCCACTTGCA 60.077 52.632 17.95 17.95 46.15 4.08
356 373 1.075482 CCCATGCAACAGGTCCACT 59.925 57.895 0.00 0.00 0.00 4.00
362 379 1.746615 CCTCGACCCATGCAACAGG 60.747 63.158 0.00 0.00 0.00 4.00
382 399 2.677228 CCTCCCGCCCTCATTGTT 59.323 61.111 0.00 0.00 0.00 2.83
465 487 0.970937 TCATCGTCAGTCCTCACCCC 60.971 60.000 0.00 0.00 0.00 4.95
471 493 0.035343 TCGTCCTCATCGTCAGTCCT 60.035 55.000 0.00 0.00 0.00 3.85
559 586 1.925972 ACCCCCAGCTTCTTCCTCC 60.926 63.158 0.00 0.00 0.00 4.30
599 1213 1.995646 TATGAGCTGCGCGACCGTTA 61.996 55.000 12.10 0.00 36.67 3.18
605 1219 0.934901 GTTCGATATGAGCTGCGCGA 60.935 55.000 12.10 0.00 0.00 5.87
611 1226 1.542030 CTAGGCCGTTCGATATGAGCT 59.458 52.381 0.00 0.00 0.00 4.09
632 1254 3.546714 AAGTTTCGGCCGGTCCAGG 62.547 63.158 27.83 0.00 34.01 4.45
680 1307 5.200483 CAGCAGGTTGGGAAAATCCTATAA 58.800 41.667 0.00 0.00 36.57 0.98
681 1308 4.229582 ACAGCAGGTTGGGAAAATCCTATA 59.770 41.667 0.00 0.00 36.57 1.31
682 1309 3.011708 ACAGCAGGTTGGGAAAATCCTAT 59.988 43.478 0.00 0.00 36.57 2.57
684 1311 1.147817 ACAGCAGGTTGGGAAAATCCT 59.852 47.619 0.00 0.00 36.57 3.24
685 1312 1.546029 GACAGCAGGTTGGGAAAATCC 59.454 52.381 0.00 0.00 35.23 3.01
686 1313 2.489722 GAGACAGCAGGTTGGGAAAATC 59.510 50.000 0.00 0.00 0.00 2.17
687 1314 2.158475 TGAGACAGCAGGTTGGGAAAAT 60.158 45.455 0.00 0.00 0.00 1.82
688 1315 1.214175 TGAGACAGCAGGTTGGGAAAA 59.786 47.619 0.00 0.00 0.00 2.29
689 1316 0.843309 TGAGACAGCAGGTTGGGAAA 59.157 50.000 0.00 0.00 0.00 3.13
690 1317 0.108585 GTGAGACAGCAGGTTGGGAA 59.891 55.000 0.00 0.00 0.00 3.97
691 1318 1.754745 GTGAGACAGCAGGTTGGGA 59.245 57.895 0.00 0.00 0.00 4.37
692 1319 1.302832 GGTGAGACAGCAGGTTGGG 60.303 63.158 0.00 0.00 0.00 4.12
693 1320 1.302832 GGGTGAGACAGCAGGTTGG 60.303 63.158 0.00 0.00 33.07 3.77
695 1322 2.883828 CGGGGTGAGACAGCAGGTT 61.884 63.158 0.00 0.00 33.07 3.50
696 1323 3.314331 CGGGGTGAGACAGCAGGT 61.314 66.667 0.00 0.00 33.07 4.00
697 1324 2.997315 TCGGGGTGAGACAGCAGG 60.997 66.667 0.00 0.00 33.07 4.85
698 1325 2.262915 GTCGGGGTGAGACAGCAG 59.737 66.667 0.00 0.00 38.42 4.24
699 1326 2.523168 TGTCGGGGTGAGACAGCA 60.523 61.111 0.00 0.00 42.91 4.41
740 1367 3.709653 TCAAATAGTACTAGCCCAGGTGG 59.290 47.826 8.85 0.00 37.09 4.61
741 1368 4.406003 AGTCAAATAGTACTAGCCCAGGTG 59.594 45.833 8.85 0.00 0.00 4.00
742 1369 4.621769 AGTCAAATAGTACTAGCCCAGGT 58.378 43.478 8.85 0.00 0.00 4.00
743 1370 5.834204 ACTAGTCAAATAGTACTAGCCCAGG 59.166 44.000 8.85 0.00 45.99 4.45
744 1371 6.293516 CGACTAGTCAAATAGTACTAGCCCAG 60.294 46.154 22.37 2.24 45.99 4.45
745 1372 5.530171 CGACTAGTCAAATAGTACTAGCCCA 59.470 44.000 22.37 0.00 45.99 5.36
746 1373 5.530543 ACGACTAGTCAAATAGTACTAGCCC 59.469 44.000 22.37 2.31 45.99 5.19
747 1374 6.616774 ACGACTAGTCAAATAGTACTAGCC 57.383 41.667 22.37 0.00 45.99 3.93
766 1393 4.727235 AAAAGAGTTTGGAATCGACGAC 57.273 40.909 0.00 0.00 0.00 4.34
777 1404 9.709600 GACTAGTCAAGAAAGAAAAAGAGTTTG 57.290 33.333 18.20 0.00 0.00 2.93
809 1440 1.065199 CCTGCTAGATCAAGGTGCCAA 60.065 52.381 0.00 0.00 0.00 4.52
869 1500 0.030101 GACGCGGGAGAAGATCAGAG 59.970 60.000 12.47 0.00 0.00 3.35
887 1518 0.830444 ACTACTCAACCACCTGCGGA 60.830 55.000 0.00 0.00 0.00 5.54
916 1547 3.798548 GCGAGAGAATGAAGGATCTGTCC 60.799 52.174 0.00 0.00 45.45 4.02
1010 1646 5.464069 TGGAGAGCTAATTGGTAGGATGTA 58.536 41.667 0.00 0.00 0.00 2.29
1020 1659 4.038522 TCGGATTCTCTGGAGAGCTAATTG 59.961 45.833 0.00 0.00 41.80 2.32
1021 1660 4.219115 TCGGATTCTCTGGAGAGCTAATT 58.781 43.478 0.00 0.00 41.80 1.40
1026 1665 1.535015 CGTTCGGATTCTCTGGAGAGC 60.535 57.143 0.00 0.00 41.80 4.09
1039 1678 0.396695 ATTAGCTCCTCCCGTTCGGA 60.397 55.000 13.08 0.00 38.83 4.55
1067 1706 1.299468 GGACAGATCGGTAGCTGCG 60.299 63.158 0.00 0.00 43.10 5.18
1207 1853 5.241285 TGGCCATGCATATGTAATGTAACAG 59.759 40.000 0.00 5.27 31.70 3.16
1221 1867 3.132289 CAGAAGAAGAAATGGCCATGCAT 59.868 43.478 21.63 9.00 0.00 3.96
1222 1868 2.494471 CAGAAGAAGAAATGGCCATGCA 59.506 45.455 21.63 0.00 0.00 3.96
1223 1869 2.737679 GCAGAAGAAGAAATGGCCATGC 60.738 50.000 21.63 14.92 0.00 4.06
1224 1870 2.758979 AGCAGAAGAAGAAATGGCCATG 59.241 45.455 21.63 4.98 0.00 3.66
1236 1882 4.654915 TCATGAATGAACCAGCAGAAGAA 58.345 39.130 0.00 0.00 33.08 2.52
1254 1900 7.088905 TCACACGATCTCATCATATTCTCATG 58.911 38.462 0.00 0.00 0.00 3.07
1255 1901 7.224522 TCACACGATCTCATCATATTCTCAT 57.775 36.000 0.00 0.00 0.00 2.90
1256 1902 6.294397 CCTCACACGATCTCATCATATTCTCA 60.294 42.308 0.00 0.00 0.00 3.27
1257 1903 6.092092 CCTCACACGATCTCATCATATTCTC 58.908 44.000 0.00 0.00 0.00 2.87
1259 1905 4.624882 GCCTCACACGATCTCATCATATTC 59.375 45.833 0.00 0.00 0.00 1.75
1292 1938 4.097437 GTCCACACATCGAATCAGTAGGTA 59.903 45.833 0.00 0.00 0.00 3.08
1304 1952 2.844122 TACAGATCGTCCACACATCG 57.156 50.000 0.00 0.00 0.00 3.84
1330 1978 2.372690 CGTCTGAAGAACACGGGCG 61.373 63.158 0.00 0.00 35.54 6.13
1350 2135 1.717032 TCCTGTACTTGCACACCTCT 58.283 50.000 0.00 0.00 0.00 3.69
1464 3580 1.451504 CTTGATGCCGCCCCTGATA 59.548 57.895 0.00 0.00 0.00 2.15
1567 3690 1.209747 GGTAATTCCTGCCGGAGAAGT 59.790 52.381 5.05 6.57 41.25 3.01
1595 3722 6.494666 TTATGAGACAAGGGATTATCGGTT 57.505 37.500 0.00 0.00 0.00 4.44
1597 3724 5.701290 GGTTTATGAGACAAGGGATTATCGG 59.299 44.000 0.00 0.00 0.00 4.18
1643 3793 3.006323 GGTACTACATCTGCTGCTGCTAT 59.994 47.826 17.00 7.56 40.48 2.97
1805 4153 9.725019 TTAGGAAGCTACCATCATGTAATTATG 57.275 33.333 0.00 0.00 0.00 1.90
1806 4154 9.726438 GTTAGGAAGCTACCATCATGTAATTAT 57.274 33.333 0.00 0.00 0.00 1.28
1823 4171 2.352960 CTGAGCATTTCGGTTAGGAAGC 59.647 50.000 0.00 0.00 0.00 3.86
1826 4174 3.973206 TTCTGAGCATTTCGGTTAGGA 57.027 42.857 0.00 0.00 33.64 2.94
1902 4250 4.117685 GACATCCGTAGTTTCATGTACCC 58.882 47.826 0.00 0.00 29.43 3.69
1914 4262 2.356695 TGTGACATACCGACATCCGTAG 59.643 50.000 0.00 0.00 36.31 3.51
1975 4325 3.838565 TGAGGGAAAACAATAGGCACAA 58.161 40.909 0.00 0.00 0.00 3.33
2003 4355 9.287373 AGTGTATAGACCCGAAAAATTTGTTAA 57.713 29.630 0.00 0.00 0.00 2.01
2012 4364 6.761312 TCTTTTGAGTGTATAGACCCGAAAA 58.239 36.000 0.00 0.09 0.00 2.29
2017 4369 9.232473 AGATTTTTCTTTTGAGTGTATAGACCC 57.768 33.333 0.00 0.00 0.00 4.46
2111 4464 8.028938 CCAGAAATGTATGTTTGAGGGTTTAAG 58.971 37.037 0.00 0.00 0.00 1.85
2153 4506 4.130118 CACAAGGGCATGAGTATAAGACC 58.870 47.826 0.00 0.00 0.00 3.85
2182 4535 5.570234 ACTTCTGGCTTTTGAAACGTTTA 57.430 34.783 14.65 0.00 0.00 2.01
2193 4546 4.566426 AGATGCTCTAACTTCTGGCTTT 57.434 40.909 0.00 0.00 0.00 3.51
2195 4548 4.026744 TGTAGATGCTCTAACTTCTGGCT 58.973 43.478 0.00 0.00 29.58 4.75
2200 4553 3.376540 CGGCTGTAGATGCTCTAACTTC 58.623 50.000 0.00 0.00 29.58 3.01
2226 4579 3.139077 GACATATAGGGGGCGTTTGAAG 58.861 50.000 0.00 0.00 0.00 3.02
2227 4580 2.775384 AGACATATAGGGGGCGTTTGAA 59.225 45.455 0.00 0.00 0.00 2.69
2233 4586 1.743958 CGTCTAGACATATAGGGGGCG 59.256 57.143 22.37 0.25 0.00 6.13
2237 4590 1.743958 CGGCCGTCTAGACATATAGGG 59.256 57.143 19.50 14.51 0.00 3.53
2247 4600 1.883084 GAACATGCCGGCCGTCTAG 60.883 63.158 26.77 13.72 0.00 2.43
2249 4602 1.686325 ATAGAACATGCCGGCCGTCT 61.686 55.000 26.77 20.70 0.00 4.18
2255 4608 1.134401 ACTGGTCATAGAACATGCCGG 60.134 52.381 0.00 0.00 0.00 6.13
2261 4614 6.545666 ACATTTTTGTGACTGGTCATAGAACA 59.454 34.615 6.71 0.00 42.18 3.18
2263 4616 6.770303 TCACATTTTTGTGACTGGTCATAGAA 59.230 34.615 6.71 3.41 43.09 2.10
2287 4640 1.967319 TTGAGAAGTGTGCTTGGGTC 58.033 50.000 0.00 0.00 34.61 4.46
2293 4646 1.166531 GCCGGTTTGAGAAGTGTGCT 61.167 55.000 1.90 0.00 0.00 4.40
2297 4650 2.107950 TATGGCCGGTTTGAGAAGTG 57.892 50.000 1.90 0.00 0.00 3.16
2301 4654 1.758280 ACGTATATGGCCGGTTTGAGA 59.242 47.619 1.90 0.00 0.00 3.27
2309 4662 3.545911 GCCGAACGTATATGGCCG 58.454 61.111 0.00 0.00 41.70 6.13
2313 4666 2.394708 CCTGTCAGCCGAACGTATATG 58.605 52.381 0.00 0.00 0.00 1.78
2322 4675 3.695606 GAGGTGCCTGTCAGCCGA 61.696 66.667 0.00 0.00 43.95 5.54
2323 4676 3.655810 GAGAGGTGCCTGTCAGCCG 62.656 68.421 10.11 0.00 43.95 5.52
2332 4685 2.106511 TGGGCTAAATATGAGAGGTGCC 59.893 50.000 0.00 0.00 38.49 5.01
2351 4704 0.944386 CGTATTCGCCCCAGATTTGG 59.056 55.000 0.00 0.00 44.60 3.28
2352 4705 1.867233 CTCGTATTCGCCCCAGATTTG 59.133 52.381 0.00 0.00 36.96 2.32
2353 4706 1.202651 CCTCGTATTCGCCCCAGATTT 60.203 52.381 0.00 0.00 36.96 2.17
2354 4707 0.393077 CCTCGTATTCGCCCCAGATT 59.607 55.000 0.00 0.00 36.96 2.40
2355 4708 2.050269 CCTCGTATTCGCCCCAGAT 58.950 57.895 0.00 0.00 36.96 2.90
2356 4709 2.792947 GCCTCGTATTCGCCCCAGA 61.793 63.158 0.00 0.00 36.96 3.86
2357 4710 2.280186 GCCTCGTATTCGCCCCAG 60.280 66.667 0.00 0.00 36.96 4.45
2358 4711 3.857038 GGCCTCGTATTCGCCCCA 61.857 66.667 0.00 0.00 36.63 4.96
2366 4719 3.849951 CACGCCTGGGCCTCGTAT 61.850 66.667 16.02 0.00 37.98 3.06
2383 4736 2.747460 TGGTGGATGCGCTTGAGC 60.747 61.111 9.73 1.49 37.78 4.26
2384 4737 1.672030 TGTGGTGGATGCGCTTGAG 60.672 57.895 9.73 0.00 0.00 3.02
2385 4738 1.965930 GTGTGGTGGATGCGCTTGA 60.966 57.895 9.73 0.00 0.00 3.02
2386 4739 1.968017 AGTGTGGTGGATGCGCTTG 60.968 57.895 9.73 0.00 0.00 4.01
2387 4740 1.968017 CAGTGTGGTGGATGCGCTT 60.968 57.895 9.73 0.55 0.00 4.68
2388 4741 2.359107 CAGTGTGGTGGATGCGCT 60.359 61.111 9.73 0.00 0.00 5.92
2389 4742 3.434319 CCAGTGTGGTGGATGCGC 61.434 66.667 0.00 0.00 40.44 6.09
2394 4747 1.744320 CGTCAGTCCAGTGTGGTGGA 61.744 60.000 0.00 0.00 44.82 4.02
2395 4748 1.300931 CGTCAGTCCAGTGTGGTGG 60.301 63.158 0.00 0.00 39.03 4.61
2396 4749 0.671796 TACGTCAGTCCAGTGTGGTG 59.328 55.000 0.00 0.00 39.03 4.17
2397 4750 0.672342 GTACGTCAGTCCAGTGTGGT 59.328 55.000 0.00 0.00 39.03 4.16
2398 4751 0.386858 CGTACGTCAGTCCAGTGTGG 60.387 60.000 7.22 0.00 39.43 4.17
2399 4752 0.386858 CCGTACGTCAGTCCAGTGTG 60.387 60.000 15.21 0.00 0.00 3.82
2400 4753 0.535780 TCCGTACGTCAGTCCAGTGT 60.536 55.000 15.21 0.00 0.00 3.55
2401 4754 0.109873 GTCCGTACGTCAGTCCAGTG 60.110 60.000 15.21 0.00 0.00 3.66
2403 4756 1.505353 GGTCCGTACGTCAGTCCAG 59.495 63.158 15.21 0.00 0.00 3.86
2404 4757 1.973281 GGGTCCGTACGTCAGTCCA 60.973 63.158 15.21 0.00 0.00 4.02
2405 4758 2.880648 GGGTCCGTACGTCAGTCC 59.119 66.667 15.21 6.16 0.00 3.85
2406 4759 2.482374 CGGGTCCGTACGTCAGTC 59.518 66.667 15.21 0.00 34.35 3.51
2407 4760 3.741476 GCGGGTCCGTACGTCAGT 61.741 66.667 15.21 0.00 42.09 3.41
2408 4761 4.824166 CGCGGGTCCGTACGTCAG 62.824 72.222 15.21 5.51 42.09 3.51
2424 4777 2.666862 TAACAACCGCTGCCCACG 60.667 61.111 0.00 0.00 0.00 4.94
2425 4778 2.622962 GGTAACAACCGCTGCCCAC 61.623 63.158 0.00 0.00 0.00 4.61
2426 4779 1.481901 TAGGTAACAACCGCTGCCCA 61.482 55.000 0.00 0.00 41.41 5.36
2427 4780 0.743345 CTAGGTAACAACCGCTGCCC 60.743 60.000 0.00 0.00 41.41 5.36
2428 4781 1.366854 GCTAGGTAACAACCGCTGCC 61.367 60.000 0.00 0.00 41.41 4.85
2429 4782 0.672401 TGCTAGGTAACAACCGCTGC 60.672 55.000 0.00 0.00 41.41 5.25
2430 4783 1.337823 ACTGCTAGGTAACAACCGCTG 60.338 52.381 0.00 0.00 41.41 5.18
2431 4784 0.974383 ACTGCTAGGTAACAACCGCT 59.026 50.000 0.00 0.00 41.41 5.52
2432 4785 1.356938 GACTGCTAGGTAACAACCGC 58.643 55.000 0.00 0.00 41.41 5.68
2433 4786 1.734707 CGGACTGCTAGGTAACAACCG 60.735 57.143 0.00 0.00 41.41 4.44
2434 4787 1.547372 TCGGACTGCTAGGTAACAACC 59.453 52.381 0.00 0.00 41.41 3.77
2435 4788 2.029649 TGTCGGACTGCTAGGTAACAAC 60.030 50.000 9.88 0.00 41.41 3.32
2436 4789 2.241160 TGTCGGACTGCTAGGTAACAA 58.759 47.619 9.88 0.00 41.41 2.83
2437 4790 1.913778 TGTCGGACTGCTAGGTAACA 58.086 50.000 9.88 0.00 41.41 2.41
2438 4791 2.416972 CCTTGTCGGACTGCTAGGTAAC 60.417 54.545 9.88 0.00 33.16 2.50
2439 4792 1.822990 CCTTGTCGGACTGCTAGGTAA 59.177 52.381 9.88 0.00 33.16 2.85
2440 4793 1.005097 TCCTTGTCGGACTGCTAGGTA 59.995 52.381 9.88 0.35 36.69 3.08
2441 4794 0.251653 TCCTTGTCGGACTGCTAGGT 60.252 55.000 9.88 0.00 36.69 3.08
2442 4795 2.579878 TCCTTGTCGGACTGCTAGG 58.420 57.895 9.88 10.41 36.69 3.02
2450 4803 2.915659 AGCGGTGTCCTTGTCGGA 60.916 61.111 0.00 0.00 40.30 4.55
2451 4804 2.432628 GAGCGGTGTCCTTGTCGG 60.433 66.667 0.00 0.00 0.00 4.79
2452 4805 2.432628 GGAGCGGTGTCCTTGTCG 60.433 66.667 0.00 0.00 33.30 4.35
2453 4806 2.432628 CGGAGCGGTGTCCTTGTC 60.433 66.667 0.00 0.00 34.00 3.18
2454 4807 4.003788 CCGGAGCGGTGTCCTTGT 62.004 66.667 0.00 0.00 42.73 3.16
2476 4829 2.046314 ATTTGTCACCTCGGGCGG 60.046 61.111 0.00 0.00 0.00 6.13
2477 4830 2.106683 GGATTTGTCACCTCGGGCG 61.107 63.158 0.00 0.00 0.00 6.13
2478 4831 2.106683 CGGATTTGTCACCTCGGGC 61.107 63.158 0.00 0.00 0.00 6.13
2479 4832 1.449601 CCGGATTTGTCACCTCGGG 60.450 63.158 0.00 0.00 34.54 5.14
2480 4833 2.106683 GCCGGATTTGTCACCTCGG 61.107 63.158 5.05 0.00 40.33 4.63
2481 4834 0.174845 TAGCCGGATTTGTCACCTCG 59.825 55.000 5.05 0.00 0.00 4.63
2482 4835 2.622064 ATAGCCGGATTTGTCACCTC 57.378 50.000 5.05 0.00 0.00 3.85
2483 4836 4.497291 TTAATAGCCGGATTTGTCACCT 57.503 40.909 5.05 0.00 0.00 4.00
2484 4837 4.497507 GCTTTAATAGCCGGATTTGTCACC 60.498 45.833 5.05 0.00 44.48 4.02
2485 4838 4.598062 GCTTTAATAGCCGGATTTGTCAC 58.402 43.478 5.05 0.00 44.48 3.67
2486 4839 4.893424 GCTTTAATAGCCGGATTTGTCA 57.107 40.909 5.05 0.00 44.48 3.58
2516 4869 0.963962 TATTGCTACGATCGGGGGTC 59.036 55.000 20.98 4.25 0.00 4.46
2523 4876 4.691216 GGAAATGGGACTATTGCTACGATC 59.309 45.833 0.00 0.00 0.00 3.69
2525 4878 3.181458 GGGAAATGGGACTATTGCTACGA 60.181 47.826 0.00 0.00 0.00 3.43
2527 4880 4.390264 GAGGGAAATGGGACTATTGCTAC 58.610 47.826 0.00 0.00 0.00 3.58
2531 4884 2.785857 AGGGAGGGAAATGGGACTATTG 59.214 50.000 0.00 0.00 0.00 1.90
2532 4885 3.166636 AGGGAGGGAAATGGGACTATT 57.833 47.619 0.00 0.00 0.00 1.73
2534 4887 2.580783 CAAAGGGAGGGAAATGGGACTA 59.419 50.000 0.00 0.00 0.00 2.59
2614 4967 3.043586 CGTCGTACATGGTTATCTGCTC 58.956 50.000 0.00 0.00 0.00 4.26
2618 4971 2.686405 TGAGCGTCGTACATGGTTATCT 59.314 45.455 0.00 0.00 0.00 1.98
2622 4975 0.601558 AGTGAGCGTCGTACATGGTT 59.398 50.000 0.00 0.00 0.00 3.67
2669 5024 1.227764 CACATCGGGCCCAGATCTG 60.228 63.158 24.92 18.16 0.00 2.90
2695 5050 1.661341 GAGGCAGGTCAGCTACAATG 58.339 55.000 0.00 0.00 34.17 2.82
2698 5053 1.229177 TGGAGGCAGGTCAGCTACA 60.229 57.895 0.00 0.00 34.17 2.74
2701 5056 2.121385 TCTGGAGGCAGGTCAGCT 59.879 61.111 0.00 0.00 34.17 4.24
2703 5058 0.614415 AGAGTCTGGAGGCAGGTCAG 60.614 60.000 0.00 0.00 0.00 3.51
2716 5079 1.326213 CCTCATGCACCGGAGAGTCT 61.326 60.000 9.46 0.00 32.87 3.24
2730 5093 0.859760 CTCCTCCTCCTCCTCCTCAT 59.140 60.000 0.00 0.00 0.00 2.90
2750 5113 2.517166 GGCCTCGCCTTCCCATTC 60.517 66.667 0.00 0.00 46.69 2.67
2768 5131 4.699522 AACTGGAAGCGCCGACCC 62.700 66.667 2.29 0.14 40.66 4.46
2769 5132 3.423154 CAACTGGAAGCGCCGACC 61.423 66.667 2.29 5.91 40.66 4.79
2770 5133 4.090057 GCAACTGGAAGCGCCGAC 62.090 66.667 2.29 0.00 40.66 4.79
2774 5137 1.589716 AATCTGGCAACTGGAAGCGC 61.590 55.000 0.00 0.00 37.60 5.92
2775 5138 0.449388 GAATCTGGCAACTGGAAGCG 59.551 55.000 0.00 0.00 37.60 4.68
2776 5139 0.449388 CGAATCTGGCAACTGGAAGC 59.551 55.000 0.00 0.00 37.60 3.86
2777 5140 1.089920 CCGAATCTGGCAACTGGAAG 58.910 55.000 0.00 0.00 42.29 3.46
2778 5141 0.400213 ACCGAATCTGGCAACTGGAA 59.600 50.000 0.00 0.00 35.97 3.53
2779 5142 1.271856 TACCGAATCTGGCAACTGGA 58.728 50.000 0.00 0.00 35.97 3.86
2780 5143 1.942657 CATACCGAATCTGGCAACTGG 59.057 52.381 0.00 0.00 35.97 4.00
2781 5144 1.942657 CCATACCGAATCTGGCAACTG 59.057 52.381 0.00 0.00 37.61 3.16
2782 5145 1.134098 CCCATACCGAATCTGGCAACT 60.134 52.381 0.00 0.00 37.61 3.16
2783 5146 1.308998 CCCATACCGAATCTGGCAAC 58.691 55.000 0.00 0.00 0.00 4.17
2784 5147 0.465460 GCCCATACCGAATCTGGCAA 60.465 55.000 0.00 0.00 38.73 4.52
2785 5148 1.148273 GCCCATACCGAATCTGGCA 59.852 57.895 0.00 0.00 38.73 4.92
2786 5149 1.148273 TGCCCATACCGAATCTGGC 59.852 57.895 0.00 0.00 39.33 4.85


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

AutoCloner maintained by Alex Coulton.