Multiple sequence alignment - TraesCS5B01G519200

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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 TraesCS5B01G519200 chr5B 100.000 5867 0 0 1 5867 681964875 681959009 0.000000e+00 10835.0
1 TraesCS5B01G519200 chr5B 81.637 1356 120 64 3311 4591 682850941 682852242 0.000000e+00 1005.0
2 TraesCS5B01G519200 chr5B 79.820 1110 97 58 2264 3308 682849852 682850899 0.000000e+00 691.0
3 TraesCS5B01G519200 chr5B 86.849 403 43 6 1857 2257 682848846 682849240 5.400000e-120 442.0
4 TraesCS5B01G519200 chr5B 80.592 608 65 26 3320 3914 683975296 683974729 2.530000e-113 420.0
5 TraesCS5B01G519200 chr5B 81.481 513 90 5 2265 2775 682849296 682849805 3.270000e-112 416.0
6 TraesCS5B01G519200 chr5B 87.925 265 14 6 1045 1291 682848247 682848511 4.450000e-76 296.0
7 TraesCS5B01G519200 chr5B 88.482 191 19 3 1472 1661 683974717 683974529 1.640000e-55 228.0
8 TraesCS5B01G519200 chr5B 83.010 206 31 1 4732 4937 683973443 683973242 3.610000e-42 183.0
9 TraesCS5B01G519200 chr5B 92.661 109 8 0 5533 5641 681662858 681662966 2.190000e-34 158.0
10 TraesCS5B01G519200 chr5B 76.842 285 34 18 4116 4369 683973870 683973587 1.330000e-26 132.0
11 TraesCS5B01G519200 chr5B 93.750 48 3 0 1681 1728 683974417 683974370 8.160000e-09 73.1
12 TraesCS5B01G519200 chr4A 91.570 2076 105 35 2824 4869 628504934 628506969 0.000000e+00 2800.0
13 TraesCS5B01G519200 chr4A 95.022 904 32 6 4974 5867 628507068 628507968 0.000000e+00 1408.0
14 TraesCS5B01G519200 chr4A 93.875 702 26 8 891 1590 628502863 628503549 0.000000e+00 1042.0
15 TraesCS5B01G519200 chr4A 84.144 1110 110 33 2264 3314 627752638 627751536 0.000000e+00 1014.0
16 TraesCS5B01G519200 chr4A 89.851 739 68 4 55 791 628502053 628502786 0.000000e+00 942.0
17 TraesCS5B01G519200 chr4A 89.035 684 45 16 1637 2307 628503547 628504213 0.000000e+00 821.0
18 TraesCS5B01G519200 chr4A 77.654 358 41 27 5533 5860 628693523 628693871 1.300000e-41 182.0
19 TraesCS5B01G519200 chr4A 74.847 326 43 32 5560 5852 628936699 628937018 1.730000e-20 111.0
20 TraesCS5B01G519200 chr4A 95.455 44 2 0 2782 2825 628504875 628504918 2.930000e-08 71.3
21 TraesCS5B01G519200 chr5D 91.795 1889 95 24 2021 3874 539875029 539873166 0.000000e+00 2575.0
22 TraesCS5B01G519200 chr5D 91.988 1685 90 27 4221 5867 539872592 539870915 0.000000e+00 2322.0
23 TraesCS5B01G519200 chr5D 88.326 1953 132 34 55 1997 539876889 539875023 0.000000e+00 2255.0
24 TraesCS5B01G519200 chr5D 81.770 2430 208 115 2264 4588 540831379 540833678 0.000000e+00 1816.0
25 TraesCS5B01G519200 chr5D 82.551 1960 160 84 2728 4588 540587267 540589143 0.000000e+00 1557.0
26 TraesCS5B01G519200 chr5D 83.333 1806 154 68 2270 3994 541910544 541908805 0.000000e+00 1531.0
27 TraesCS5B01G519200 chr5D 85.638 1128 79 32 1151 2257 540585160 540586225 0.000000e+00 1109.0
28 TraesCS5B01G519200 chr5D 86.103 1029 70 25 1256 2257 540829785 540830767 0.000000e+00 1040.0
29 TraesCS5B01G519200 chr5D 82.643 1256 134 35 1036 2257 541809902 541808697 0.000000e+00 1035.0
30 TraesCS5B01G519200 chr5D 83.438 1111 116 36 2264 3315 540615405 540616506 0.000000e+00 970.0
31 TraesCS5B01G519200 chr5D 82.463 1072 116 28 1225 2263 541912190 541911158 0.000000e+00 872.0
32 TraesCS5B01G519200 chr5D 83.386 951 80 32 3071 3994 541807162 541806263 0.000000e+00 809.0
33 TraesCS5B01G519200 chr5D 84.857 733 65 23 2380 3076 541807907 541807185 0.000000e+00 697.0
34 TraesCS5B01G519200 chr5D 94.186 344 14 4 3871 4214 539873064 539872727 2.420000e-143 520.0
35 TraesCS5B01G519200 chr5D 83.757 511 82 1 2265 2775 540830823 540831332 3.180000e-132 483.0
36 TraesCS5B01G519200 chr5D 82.617 512 83 5 2268 2775 541808642 541808133 1.160000e-121 448.0
37 TraesCS5B01G519200 chr5D 82.171 516 88 3 2264 2775 541911112 541910597 1.940000e-119 440.0
38 TraesCS5B01G519200 chr5D 81.323 514 72 13 1754 2263 541911089 541910596 4.260000e-106 396.0
39 TraesCS5B01G519200 chr5D 80.868 507 76 9 1754 2260 540586303 540586788 4.290000e-101 379.0
40 TraesCS5B01G519200 chr5D 80.645 496 60 20 3992 4453 541806183 541805690 9.350000e-93 351.0
41 TraesCS5B01G519200 chr5D 80.483 497 58 21 3992 4452 541908718 541908225 1.570000e-90 344.0
42 TraesCS5B01G519200 chr5D 92.547 161 6 1 1024 1184 540829426 540829580 5.920000e-55 226.0
43 TraesCS5B01G519200 chr5D 84.951 206 26 2 4732 4937 541908137 541907937 2.770000e-48 204.0
44 TraesCS5B01G519200 chr5D 77.961 363 39 27 5536 5867 539725982 539725630 7.760000e-44 189.0
45 TraesCS5B01G519200 chr5D 84.021 194 21 6 4971 5154 541805230 541805037 1.680000e-40 178.0
46 TraesCS5B01G519200 chr5D 93.333 60 3 1 5222 5281 541907711 541907653 2.910000e-13 87.9
47 TraesCS5B01G519200 chr6B 90.698 430 33 4 5445 5867 713923350 713922921 3.070000e-157 566.0
48 TraesCS5B01G519200 chr7A 84.669 287 30 8 3991 4268 251805285 251805004 2.080000e-69 274.0
49 TraesCS5B01G519200 chr2B 87.773 229 25 3 3988 4216 615888605 615888830 1.250000e-66 265.0
50 TraesCS5B01G519200 chr6A 87.619 105 8 3 1200 1304 604174213 604174312 3.710000e-22 117.0


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 TraesCS5B01G519200 chr5B 681959009 681964875 5866 True 10835.000000 10835 100.000000 1 5867 1 chr5B.!!$R1 5866
1 TraesCS5B01G519200 chr5B 682848247 682852242 3995 False 570.000000 1005 83.542400 1045 4591 5 chr5B.!!$F2 3546
2 TraesCS5B01G519200 chr5B 683973242 683975296 2054 True 207.220000 420 84.535200 1472 4937 5 chr5B.!!$R2 3465
3 TraesCS5B01G519200 chr4A 628502053 628507968 5915 False 1180.716667 2800 92.468000 55 5867 6 chr4A.!!$F3 5812
4 TraesCS5B01G519200 chr4A 627751536 627752638 1102 True 1014.000000 1014 84.144000 2264 3314 1 chr4A.!!$R1 1050
5 TraesCS5B01G519200 chr5D 539870915 539876889 5974 True 1918.000000 2575 91.573750 55 5867 4 chr5D.!!$R2 5812
6 TraesCS5B01G519200 chr5D 540585160 540589143 3983 False 1015.000000 1557 83.019000 1151 4588 3 chr5D.!!$F2 3437
7 TraesCS5B01G519200 chr5D 540615405 540616506 1101 False 970.000000 970 83.438000 2264 3315 1 chr5D.!!$F1 1051
8 TraesCS5B01G519200 chr5D 540829426 540833678 4252 False 891.250000 1816 86.044250 1024 4588 4 chr5D.!!$F3 3564
9 TraesCS5B01G519200 chr5D 541805037 541809902 4865 True 586.333333 1035 83.028167 1036 5154 6 chr5D.!!$R3 4118
10 TraesCS5B01G519200 chr5D 541907653 541912190 4537 True 553.557143 1531 84.008143 1225 5281 7 chr5D.!!$R4 4056

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
947 973 0.821711 CTCTCCCACCACCGCAAAAA 60.822 55.0 0.00 0.0 0.00 1.94 F
1559 1755 0.107165 GTCCACCTCCCCATGCTTAC 60.107 60.0 0.00 0.0 0.00 2.34 F
2570 4052 0.453390 GCCTGCATAGACTTTGGTGC 59.547 55.0 0.00 0.0 38.05 5.01 F
3781 5451 0.405198 TTGAAAGGATGAGCCAGCCA 59.595 50.0 11.32 0.0 43.12 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 2323 0.107410 TAAGCCCGGTCATCGCATTT 60.107 50.000 0.00 0.0 37.59 2.32 R
3417 5066 2.499693 TGGTAGAAGATGCACATTCGGA 59.500 45.455 6.99 0.0 0.00 4.55 R
4472 6537 0.172803 AGCTACCGAAACGCTACAGG 59.827 55.000 0.00 0.0 31.12 4.00 R
4949 7089 0.181350 AATCTCCAGGAACGGATGCC 59.819 55.000 0.00 0.0 33.56 4.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.941609 CACCAGGAACTCCGGATG 57.058 61.111 3.57 0.00 42.08 3.51
18 19 2.286826 CACCAGGAACTCCGGATGA 58.713 57.895 3.57 0.00 42.08 2.92
34 35 6.280643 TCCGGATGAGTGAAGTAATATGTTG 58.719 40.000 0.00 0.00 0.00 3.33
35 36 6.097696 TCCGGATGAGTGAAGTAATATGTTGA 59.902 38.462 0.00 0.00 0.00 3.18
36 37 6.201044 CCGGATGAGTGAAGTAATATGTTGAC 59.799 42.308 0.00 0.00 0.00 3.18
38 39 7.439356 CGGATGAGTGAAGTAATATGTTGACAT 59.561 37.037 1.84 1.84 40.22 3.06
39 40 9.764363 GGATGAGTGAAGTAATATGTTGACATA 57.236 33.333 6.32 6.32 42.38 2.29
49 50 9.784531 AGTAATATGTTGACATAATCCTCTTGG 57.215 33.333 7.82 0.00 41.60 3.61
50 51 9.561069 GTAATATGTTGACATAATCCTCTTGGT 57.439 33.333 7.82 0.00 41.60 3.67
53 54 5.428253 TGTTGACATAATCCTCTTGGTAGC 58.572 41.667 0.00 0.00 34.23 3.58
76 77 2.162681 GGCACAACCTAAGCAACTGAT 58.837 47.619 0.00 0.00 34.51 2.90
244 245 8.812329 CATTAAGACATTCTTTCTCTACTTCCG 58.188 37.037 0.00 0.00 37.89 4.30
369 370 1.003928 TGCACTGAATCTCTGGCACAT 59.996 47.619 0.00 0.00 38.20 3.21
426 428 6.630444 AGCATAGTATCATCTGCAAAAAGG 57.370 37.500 0.00 0.00 37.09 3.11
489 491 3.181472 CCATCGATGTCACTTCCTCATGA 60.181 47.826 23.27 0.00 0.00 3.07
495 497 5.987953 CGATGTCACTTCCTCATGATGTAAT 59.012 40.000 0.00 0.00 30.69 1.89
497 499 7.115520 CGATGTCACTTCCTCATGATGTAATAC 59.884 40.741 0.00 0.00 30.69 1.89
506 508 7.337938 TCCTCATGATGTAATACACAACACAT 58.662 34.615 0.00 0.00 42.06 3.21
568 570 2.033194 CGAGTCGGCCAAAACTCCC 61.033 63.158 19.07 2.66 38.96 4.30
602 607 6.607198 CCACCATTAAAGATCACCAAGGTAAT 59.393 38.462 0.00 0.00 0.00 1.89
610 615 3.328382 TCACCAAGGTAATCAAGGTCG 57.672 47.619 0.00 0.00 0.00 4.79
655 663 5.178061 CAAACCTTGGGCTATTCCAATTTC 58.822 41.667 0.00 0.00 44.79 2.17
656 664 3.023832 ACCTTGGGCTATTCCAATTTCG 58.976 45.455 0.00 0.00 44.79 3.46
670 678 6.757897 TCCAATTTCGTTCATGATAGCTTT 57.242 33.333 0.00 0.00 0.00 3.51
674 682 4.864916 TTCGTTCATGATAGCTTTCAGC 57.135 40.909 12.51 2.80 42.84 4.26
700 708 3.817647 CTCCATTTTACTCTGGCATAGGC 59.182 47.826 4.82 0.00 40.13 3.93
728 736 6.972901 TCATCGTATCTAACTTAACTGCACAG 59.027 38.462 0.00 0.00 0.00 3.66
737 745 5.679734 ACTTAACTGCACAGTGAGAATTG 57.320 39.130 16.76 3.39 41.58 2.32
739 747 2.645838 ACTGCACAGTGAGAATTGGT 57.354 45.000 4.15 0.00 40.75 3.67
740 748 3.769739 ACTGCACAGTGAGAATTGGTA 57.230 42.857 4.15 0.00 40.75 3.25
775 783 9.443283 CTATGCTTAATAAAGTGCAGACATTTC 57.557 33.333 0.00 0.00 38.87 2.17
791 799 7.232300 CAGACATTTCTATGCGCATACTTATG 58.768 38.462 25.78 25.16 35.03 1.90
792 800 7.116805 CAGACATTTCTATGCGCATACTTATGA 59.883 37.037 29.16 21.86 33.99 2.15
823 836 9.618890 ATCCGTAATAAGCAGCATTATGATATT 57.381 29.630 0.00 0.00 29.85 1.28
826 839 9.855361 CGTAATAAGCAGCATTATGATATTAGC 57.145 33.333 0.00 0.00 29.85 3.09
828 841 8.812513 AATAAGCAGCATTATGATATTAGCCA 57.187 30.769 0.00 0.00 0.00 4.75
829 842 6.754702 AAGCAGCATTATGATATTAGCCAG 57.245 37.500 0.00 0.00 0.00 4.85
830 843 6.058553 AGCAGCATTATGATATTAGCCAGA 57.941 37.500 0.00 0.00 0.00 3.86
831 844 6.479006 AGCAGCATTATGATATTAGCCAGAA 58.521 36.000 0.00 0.00 0.00 3.02
832 845 6.944290 AGCAGCATTATGATATTAGCCAGAAA 59.056 34.615 0.00 0.00 0.00 2.52
833 846 7.120873 AGCAGCATTATGATATTAGCCAGAAAG 59.879 37.037 0.00 0.00 0.00 2.62
834 847 7.249147 CAGCATTATGATATTAGCCAGAAAGC 58.751 38.462 0.00 0.00 31.10 3.51
835 848 6.376581 AGCATTATGATATTAGCCAGAAAGCC 59.623 38.462 0.00 0.00 31.23 4.35
836 849 6.376581 GCATTATGATATTAGCCAGAAAGCCT 59.623 38.462 0.00 0.00 0.00 4.58
837 850 7.094032 GCATTATGATATTAGCCAGAAAGCCTT 60.094 37.037 0.00 0.00 0.00 4.35
838 851 8.800332 CATTATGATATTAGCCAGAAAGCCTTT 58.200 33.333 0.00 0.00 0.00 3.11
839 852 8.766994 TTATGATATTAGCCAGAAAGCCTTTT 57.233 30.769 0.00 0.00 0.00 2.27
840 853 7.666063 ATGATATTAGCCAGAAAGCCTTTTT 57.334 32.000 0.00 0.00 0.00 1.94
947 973 0.821711 CTCTCCCACCACCGCAAAAA 60.822 55.000 0.00 0.00 0.00 1.94
983 1013 1.295357 ACACACACACACACACACGG 61.295 55.000 0.00 0.00 0.00 4.94
984 1014 1.743623 ACACACACACACACACGGG 60.744 57.895 0.00 0.00 0.00 5.28
1051 1081 1.906824 TCTCGTCCACCTCCACCAC 60.907 63.158 0.00 0.00 0.00 4.16
1237 1293 3.711782 CCTCCCCCTCCTTCCCCT 61.712 72.222 0.00 0.00 0.00 4.79
1238 1294 2.461637 CTCCCCCTCCTTCCCCTT 59.538 66.667 0.00 0.00 0.00 3.95
1304 1483 3.130227 CTCGGATCGAAGGGACCC 58.870 66.667 0.59 0.59 34.74 4.46
1330 1509 1.229209 AGAGCGAGGGTTTCCTGGA 60.229 57.895 0.00 0.00 45.05 3.86
1559 1755 0.107165 GTCCACCTCCCCATGCTTAC 60.107 60.000 0.00 0.00 0.00 2.34
1564 1760 0.695803 CCTCCCCATGCTTACTCCCT 60.696 60.000 0.00 0.00 0.00 4.20
1574 1770 2.565391 TGCTTACTCCCTGTCGATTTCA 59.435 45.455 0.00 0.00 0.00 2.69
1742 2012 6.594744 TGTATCTGAACCTGATGTATGCATT 58.405 36.000 3.54 0.00 35.07 3.56
1743 2013 6.484308 TGTATCTGAACCTGATGTATGCATTG 59.516 38.462 3.54 0.00 35.07 2.82
1745 2015 5.687780 TCTGAACCTGATGTATGCATTGAT 58.312 37.500 3.54 0.00 35.07 2.57
1746 2016 6.829849 TCTGAACCTGATGTATGCATTGATA 58.170 36.000 3.54 0.00 35.07 2.15
1748 2018 5.999600 TGAACCTGATGTATGCATTGATAGG 59.000 40.000 3.54 9.60 35.07 2.57
1749 2019 5.573380 ACCTGATGTATGCATTGATAGGT 57.427 39.130 3.54 10.24 35.07 3.08
1750 2020 6.686484 ACCTGATGTATGCATTGATAGGTA 57.314 37.500 3.54 0.00 35.61 3.08
1751 2021 7.262990 ACCTGATGTATGCATTGATAGGTAT 57.737 36.000 3.54 0.00 35.61 2.73
1752 2022 8.379428 ACCTGATGTATGCATTGATAGGTATA 57.621 34.615 3.54 0.00 35.61 1.47
1768 2050 9.136323 TGATAGGTATATATGCACTGTATCTGG 57.864 37.037 3.10 0.00 0.00 3.86
1831 2274 4.111916 GTTTCCAGTGTCATGTTGTTTGG 58.888 43.478 0.00 0.00 0.00 3.28
1841 2284 5.163513 GTCATGTTGTTTGGGAATGATCAC 58.836 41.667 0.00 0.00 30.52 3.06
1847 2290 1.024046 TTGGGAATGATCACGTGCCG 61.024 55.000 11.67 0.00 31.51 5.69
1848 2291 1.449601 GGGAATGATCACGTGCCGT 60.450 57.895 11.67 3.59 42.36 5.68
1849 2292 1.024579 GGGAATGATCACGTGCCGTT 61.025 55.000 11.67 12.38 38.32 4.44
1850 2293 0.802494 GGAATGATCACGTGCCGTTT 59.198 50.000 11.67 1.88 38.32 3.60
1851 2294 1.199097 GGAATGATCACGTGCCGTTTT 59.801 47.619 11.67 0.35 38.32 2.43
1852 2295 2.241722 GAATGATCACGTGCCGTTTTG 58.758 47.619 11.67 0.00 38.32 2.44
1853 2296 1.518325 ATGATCACGTGCCGTTTTGA 58.482 45.000 11.67 0.00 38.32 2.69
1854 2297 1.300481 TGATCACGTGCCGTTTTGAA 58.700 45.000 11.67 0.00 38.32 2.69
1880 2323 7.727578 TTTGATGATTGGAGTAGTAGGTACA 57.272 36.000 0.00 0.00 33.55 2.90
1892 2335 3.793559 AGTAGGTACAAATGCGATGACC 58.206 45.455 0.00 0.00 0.00 4.02
2007 2465 0.625316 CATCACATCCACCTCCCCAA 59.375 55.000 0.00 0.00 0.00 4.12
2044 2502 2.681848 CTCTCACAATAGCCTGCAAAGG 59.318 50.000 0.00 0.00 0.00 3.11
2077 2536 3.493129 TGTTAGTGCTTCTGTTTACTGCG 59.507 43.478 0.00 0.00 0.00 5.18
2078 2537 2.526304 AGTGCTTCTGTTTACTGCGA 57.474 45.000 0.00 0.00 0.00 5.10
2206 2665 4.960938 TCTTGCGCCAGTAGATCATAAAT 58.039 39.130 4.18 0.00 0.00 1.40
2243 2703 6.701145 TTTAGGCACTTTGTAATGTTGTGA 57.299 33.333 0.00 0.00 41.75 3.58
2480 3961 0.693049 ATCCGCCTTCTTTGTGGAGT 59.307 50.000 0.00 0.00 45.00 3.85
2558 4039 0.921896 ACTCCCACAATAGCCTGCAT 59.078 50.000 0.00 0.00 0.00 3.96
2565 4047 4.202441 CCACAATAGCCTGCATAGACTTT 58.798 43.478 0.00 0.00 0.00 2.66
2570 4052 0.453390 GCCTGCATAGACTTTGGTGC 59.547 55.000 0.00 0.00 38.05 5.01
2656 4139 1.351850 TGGCAGGGCAGCATACCATA 61.352 55.000 0.00 0.00 35.83 2.74
2714 4222 6.785488 ATGTAGTGTTGTGCCATTATATCG 57.215 37.500 0.00 0.00 0.00 2.92
2715 4223 5.666462 TGTAGTGTTGTGCCATTATATCGT 58.334 37.500 0.00 0.00 0.00 3.73
2716 4224 6.807789 TGTAGTGTTGTGCCATTATATCGTA 58.192 36.000 0.00 0.00 0.00 3.43
2717 4225 7.266400 TGTAGTGTTGTGCCATTATATCGTAA 58.734 34.615 0.00 0.00 0.00 3.18
2718 4226 7.764901 TGTAGTGTTGTGCCATTATATCGTAAA 59.235 33.333 0.00 0.00 0.00 2.01
2719 4227 7.011828 AGTGTTGTGCCATTATATCGTAAAC 57.988 36.000 0.00 0.00 0.00 2.01
2720 4228 6.821665 AGTGTTGTGCCATTATATCGTAAACT 59.178 34.615 0.00 0.00 0.00 2.66
2721 4229 7.335924 AGTGTTGTGCCATTATATCGTAAACTT 59.664 33.333 0.00 0.00 0.00 2.66
2722 4230 8.605746 GTGTTGTGCCATTATATCGTAAACTTA 58.394 33.333 0.00 0.00 0.00 2.24
2723 4231 9.332502 TGTTGTGCCATTATATCGTAAACTTAT 57.667 29.630 0.00 0.00 0.00 1.73
2784 4323 8.960591 AGTTGATCATAAACTTACAAGGAATGG 58.039 33.333 0.00 0.00 34.16 3.16
2817 4356 8.424133 CGGTATGAAGGATGGATTCATATGATA 58.576 37.037 6.17 0.00 46.09 2.15
2867 4423 1.268079 GCCTTTCCTGTCTGACAAAGC 59.732 52.381 12.16 5.04 0.00 3.51
3009 4567 6.127619 ACAAAGTTTGAGAAGGAAAGGTGAAG 60.128 38.462 22.23 0.00 0.00 3.02
3039 4598 7.165318 CGAACTGTTTTACTTGCCTTTAACTTC 59.835 37.037 0.00 0.00 0.00 3.01
3069 4629 9.461312 TGTGTAGGAATACAAATTTCTGCTATT 57.539 29.630 0.00 0.00 35.08 1.73
3242 4834 5.835113 TCCAAAGAGGTTTTGAACTTCTG 57.165 39.130 6.27 0.00 45.78 3.02
3265 4857 6.935167 TGTTGATACAGTCATGTACATCAGT 58.065 36.000 5.07 4.96 44.51 3.41
3303 4895 5.163499 CCACAGTTTGGTTACCAGCTTTAAA 60.163 40.000 3.65 0.00 41.10 1.52
3306 4898 8.138712 CACAGTTTGGTTACCAGCTTTAAATTA 58.861 33.333 3.65 0.00 33.81 1.40
3417 5066 5.355910 ACACGTACAGAATTTCAAAGGTGTT 59.644 36.000 13.61 4.54 33.60 3.32
3672 5328 5.127845 TGCCAAACAGTATCCAAAGAAAACA 59.872 36.000 0.00 0.00 0.00 2.83
3673 5329 6.183360 TGCCAAACAGTATCCAAAGAAAACAT 60.183 34.615 0.00 0.00 0.00 2.71
3675 5331 7.226523 GCCAAACAGTATCCAAAGAAAACATTT 59.773 33.333 0.00 0.00 0.00 2.32
3676 5332 8.764287 CCAAACAGTATCCAAAGAAAACATTTC 58.236 33.333 0.00 0.00 0.00 2.17
3701 5361 4.665833 AACCTTTAAAGCTGGTTGAACC 57.334 40.909 7.57 7.57 41.87 3.62
3778 5448 4.796038 ATTGTTTGAAAGGATGAGCCAG 57.204 40.909 0.00 0.00 40.02 4.85
3779 5449 1.888512 TGTTTGAAAGGATGAGCCAGC 59.111 47.619 0.00 0.00 40.02 4.85
3780 5450 1.203287 GTTTGAAAGGATGAGCCAGCC 59.797 52.381 1.65 1.65 40.67 4.85
3781 5451 0.405198 TTGAAAGGATGAGCCAGCCA 59.595 50.000 11.32 0.00 43.12 4.75
3788 5458 2.305343 AGGATGAGCCAGCCAATATCTC 59.695 50.000 11.32 0.00 43.12 2.75
3829 5503 7.119846 GCATACTGAGACCTGAATTTGTAGTTT 59.880 37.037 0.00 0.00 0.00 2.66
3830 5504 8.660373 CATACTGAGACCTGAATTTGTAGTTTC 58.340 37.037 0.00 0.00 0.00 2.78
3831 5505 5.998363 ACTGAGACCTGAATTTGTAGTTTCC 59.002 40.000 0.00 0.00 0.00 3.13
3832 5506 6.183361 ACTGAGACCTGAATTTGTAGTTTCCT 60.183 38.462 0.00 0.00 0.00 3.36
3833 5507 6.231211 TGAGACCTGAATTTGTAGTTTCCTC 58.769 40.000 0.00 0.00 0.00 3.71
3834 5508 6.043243 TGAGACCTGAATTTGTAGTTTCCTCT 59.957 38.462 0.00 0.00 0.00 3.69
3835 5509 6.842676 AGACCTGAATTTGTAGTTTCCTCTT 58.157 36.000 0.00 0.00 0.00 2.85
3850 5524 2.093658 TCCTCTTTCCTGCCACGTAATC 60.094 50.000 0.00 0.00 0.00 1.75
3881 5660 7.972527 TCTCTGTTGTCGACTACTTACTTATC 58.027 38.462 26.27 2.24 0.00 1.75
3882 5661 7.823310 TCTCTGTTGTCGACTACTTACTTATCT 59.177 37.037 26.27 0.00 0.00 1.98
3883 5662 8.332996 TCTGTTGTCGACTACTTACTTATCTT 57.667 34.615 26.27 0.00 0.00 2.40
3884 5663 9.440773 TCTGTTGTCGACTACTTACTTATCTTA 57.559 33.333 26.27 5.25 0.00 2.10
3885 5664 9.488124 CTGTTGTCGACTACTTACTTATCTTAC 57.512 37.037 26.27 0.54 0.00 2.34
3895 5674 7.735326 ACTTACTTATCTTACCCACATGTCT 57.265 36.000 0.00 0.00 0.00 3.41
4042 5915 4.974368 TTAAACAGTTCTTGTGTGTGGG 57.026 40.909 0.00 0.00 40.74 4.61
4149 6026 4.037327 TCGGAGAAGATAACAGATGCAGAG 59.963 45.833 0.00 0.00 0.00 3.35
4187 6065 0.882042 AAGCAGGTCTGTTCAGCACG 60.882 55.000 0.00 0.00 0.00 5.34
4217 6098 0.465460 ACTTGAACCGCCTTTCTGCA 60.465 50.000 0.00 0.00 0.00 4.41
4247 6260 5.457799 GCTTTAACAGAGTTCGATGCGTATA 59.542 40.000 0.00 0.00 0.00 1.47
4248 6261 6.345093 GCTTTAACAGAGTTCGATGCGTATAG 60.345 42.308 0.00 0.00 0.00 1.31
4249 6262 4.634184 AACAGAGTTCGATGCGTATAGT 57.366 40.909 0.00 0.00 0.00 2.12
4250 6263 5.746307 AACAGAGTTCGATGCGTATAGTA 57.254 39.130 0.00 0.00 0.00 1.82
4257 6281 3.338249 TCGATGCGTATAGTAGGTACCC 58.662 50.000 8.74 0.00 0.00 3.69
4260 6284 3.582998 TGCGTATAGTAGGTACCCTGT 57.417 47.619 8.74 0.14 34.61 4.00
4265 6289 6.550854 TGCGTATAGTAGGTACCCTGTAATTT 59.449 38.462 8.74 0.00 34.61 1.82
4373 6419 1.296755 CGACGACGAGGAGGACTGAA 61.297 60.000 0.00 0.00 42.66 3.02
4558 6634 4.677378 CGTCTTTCAGATCGACATGGATAC 59.323 45.833 0.00 0.00 0.00 2.24
4565 6641 5.416013 TCAGATCGACATGGATACTGGTATC 59.584 44.000 11.14 11.14 40.83 2.24
4730 6814 0.385029 TTGCTTTCTTGCACGCACAT 59.615 45.000 0.00 0.00 43.20 3.21
4740 6824 1.925415 GCACGCACATCAGCCATTGA 61.925 55.000 0.00 0.00 40.85 2.57
4802 6886 3.456380 AATTCTTTAGCAGCCTTCCCA 57.544 42.857 0.00 0.00 0.00 4.37
4834 6927 6.039382 GGACCAACAACATTCAGTAAGAAACT 59.961 38.462 0.00 0.00 40.22 2.66
4891 7029 9.537192 GCAATTATATAATATTGGCATGCATGT 57.463 29.630 26.79 10.48 33.41 3.21
4896 7034 4.739587 AATATTGGCATGCATGTTGTCA 57.260 36.364 26.79 16.79 0.00 3.58
4897 7035 4.739587 ATATTGGCATGCATGTTGTCAA 57.260 36.364 26.79 22.84 42.34 3.18
4898 7036 2.151881 TTGGCATGCATGTTGTCAAC 57.848 45.000 26.79 8.86 33.99 3.18
4899 7037 1.330234 TGGCATGCATGTTGTCAACT 58.670 45.000 26.79 0.07 0.00 3.16
4900 7038 1.687660 TGGCATGCATGTTGTCAACTT 59.312 42.857 26.79 7.72 0.00 2.66
4901 7039 2.889678 TGGCATGCATGTTGTCAACTTA 59.110 40.909 26.79 0.00 0.00 2.24
4902 7040 3.320256 TGGCATGCATGTTGTCAACTTAA 59.680 39.130 26.79 3.50 0.00 1.85
4903 7041 4.202192 TGGCATGCATGTTGTCAACTTAAA 60.202 37.500 26.79 3.18 0.00 1.52
4904 7042 4.749099 GGCATGCATGTTGTCAACTTAAAA 59.251 37.500 26.79 0.00 0.00 1.52
4937 7077 5.895636 TTACATCCACTGCAAGGTTTATG 57.104 39.130 4.89 4.62 39.30 1.90
4949 7089 3.802948 AGGTTTATGAGCTACTCCACG 57.197 47.619 0.00 0.00 33.44 4.94
4981 7187 4.099573 TCCTGGAGATTGTAATCGGAAGAC 59.900 45.833 0.00 0.00 46.97 3.01
4984 7190 4.081862 TGGAGATTGTAATCGGAAGACGTT 60.082 41.667 0.00 0.00 46.97 3.99
4985 7191 4.267928 GGAGATTGTAATCGGAAGACGTTG 59.732 45.833 0.00 0.00 46.97 4.10
5182 7423 1.153147 GGCGAAGGATGAGGGTTCC 60.153 63.158 0.00 0.00 0.00 3.62
5329 7570 3.252284 CCCTGGTCACCCTGCAGT 61.252 66.667 13.81 0.00 0.00 4.40
5357 7598 4.790861 GACGCGGACGAACCTCCC 62.791 72.222 12.47 0.00 43.93 4.30
5781 8031 3.917760 GGGAGCGACGGGGAGATG 61.918 72.222 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.176680 CTCATCCGGAGTTCCTGGTG 59.823 60.000 11.34 0.00 38.90 4.17
1 2 2.596776 CTCATCCGGAGTTCCTGGT 58.403 57.895 11.34 0.00 38.90 4.00
10 11 6.097696 TCAACATATTACTTCACTCATCCGGA 59.902 38.462 6.61 6.61 0.00 5.14
11 12 6.201044 GTCAACATATTACTTCACTCATCCGG 59.799 42.308 0.00 0.00 0.00 5.14
12 13 6.756542 TGTCAACATATTACTTCACTCATCCG 59.243 38.462 0.00 0.00 0.00 4.18
23 24 9.784531 CCAAGAGGATTATGTCAACATATTACT 57.215 33.333 8.75 8.75 36.56 2.24
24 25 9.561069 ACCAAGAGGATTATGTCAACATATTAC 57.439 33.333 3.80 2.16 37.22 1.89
27 28 7.880195 GCTACCAAGAGGATTATGTCAACATAT 59.120 37.037 3.80 0.00 37.22 1.78
28 29 7.071196 AGCTACCAAGAGGATTATGTCAACATA 59.929 37.037 0.00 0.00 36.72 2.29
30 31 5.189736 AGCTACCAAGAGGATTATGTCAACA 59.810 40.000 0.00 0.00 38.69 3.33
34 35 5.059833 CCAAGCTACCAAGAGGATTATGTC 58.940 45.833 0.00 0.00 38.69 3.06
35 36 4.687219 GCCAAGCTACCAAGAGGATTATGT 60.687 45.833 0.00 0.00 38.69 2.29
36 37 3.817647 GCCAAGCTACCAAGAGGATTATG 59.182 47.826 0.00 0.00 38.69 1.90
38 39 2.843730 TGCCAAGCTACCAAGAGGATTA 59.156 45.455 0.00 0.00 38.69 1.75
39 40 1.635487 TGCCAAGCTACCAAGAGGATT 59.365 47.619 0.00 0.00 38.69 3.01
40 41 1.065126 GTGCCAAGCTACCAAGAGGAT 60.065 52.381 0.00 0.00 38.69 3.24
41 42 0.324943 GTGCCAAGCTACCAAGAGGA 59.675 55.000 0.00 0.00 38.69 3.71
43 44 1.537202 GTTGTGCCAAGCTACCAAGAG 59.463 52.381 0.00 0.00 0.00 2.85
44 45 1.604604 GTTGTGCCAAGCTACCAAGA 58.395 50.000 0.00 0.00 0.00 3.02
45 46 0.598065 GGTTGTGCCAAGCTACCAAG 59.402 55.000 9.10 0.00 37.17 3.61
47 48 1.060729 TAGGTTGTGCCAAGCTACCA 58.939 50.000 17.44 4.27 40.61 3.25
48 49 2.084546 CTTAGGTTGTGCCAAGCTACC 58.915 52.381 19.73 7.82 40.61 3.18
49 50 1.468914 GCTTAGGTTGTGCCAAGCTAC 59.531 52.381 19.73 10.55 42.62 3.58
50 51 1.073125 TGCTTAGGTTGTGCCAAGCTA 59.927 47.619 17.44 17.44 44.39 3.32
53 54 1.956477 AGTTGCTTAGGTTGTGCCAAG 59.044 47.619 0.00 0.00 40.61 3.61
76 77 5.600484 TGGCTGGGAAGAGATTTTAAACAAA 59.400 36.000 0.00 0.00 0.00 2.83
196 197 5.511363 TGACAAATATTTGGGATTACCGGT 58.489 37.500 27.43 13.98 44.64 5.28
226 227 6.478344 CAGATTCCGGAAGTAGAGAAAGAATG 59.522 42.308 23.47 2.44 0.00 2.67
401 402 8.159447 TCCTTTTTGCAGATGATACTATGCTAT 58.841 33.333 0.00 0.00 39.42 2.97
404 405 6.293845 CCTCCTTTTTGCAGATGATACTATGC 60.294 42.308 0.00 0.00 39.14 3.14
407 408 6.115446 CACCTCCTTTTTGCAGATGATACTA 58.885 40.000 0.00 0.00 0.00 1.82
419 421 6.320418 ACTTACTGTTAACCACCTCCTTTTTG 59.680 38.462 2.48 0.00 0.00 2.44
425 427 4.284234 TGGTACTTACTGTTAACCACCTCC 59.716 45.833 2.48 0.00 33.63 4.30
426 428 5.473066 TGGTACTTACTGTTAACCACCTC 57.527 43.478 2.48 0.00 33.63 3.85
489 491 6.480763 TGAAGGGATGTGTTGTGTATTACAT 58.519 36.000 0.00 0.00 39.48 2.29
495 497 2.371841 AGCTGAAGGGATGTGTTGTGTA 59.628 45.455 0.00 0.00 0.00 2.90
497 499 1.538512 CAGCTGAAGGGATGTGTTGTG 59.461 52.381 8.42 0.00 0.00 3.33
506 508 2.356173 TTTGCTGGCAGCTGAAGGGA 62.356 55.000 36.50 14.98 42.97 4.20
529 531 2.569404 GGGCCTCATATCTCCTTACCTG 59.431 54.545 0.84 0.00 0.00 4.00
560 562 0.106918 TGGCGTGTCAAGGGAGTTTT 60.107 50.000 0.00 0.00 0.00 2.43
568 570 2.811431 TCTTTAATGGTGGCGTGTCAAG 59.189 45.455 0.00 0.00 0.00 3.02
610 615 1.878734 GCAGCTCATCTTGAATAGGGC 59.121 52.381 0.00 0.00 0.00 5.19
646 654 6.757897 AAGCTATCATGAACGAAATTGGAA 57.242 33.333 0.00 0.00 0.00 3.53
670 678 5.734720 CCAGAGTAAAATGGAGTTAGCTGA 58.265 41.667 0.00 0.00 39.02 4.26
674 682 6.708054 CCTATGCCAGAGTAAAATGGAGTTAG 59.292 42.308 0.00 0.00 39.02 2.34
685 693 4.708177 GATGAAAGCCTATGCCAGAGTAA 58.292 43.478 0.00 0.00 38.69 2.24
700 708 8.321716 GTGCAGTTAAGTTAGATACGATGAAAG 58.678 37.037 0.00 0.00 0.00 2.62
728 736 8.233190 GCATAGAATAGCAATACCAATTCTCAC 58.767 37.037 0.01 0.00 39.01 3.51
775 783 8.854312 CGGATAATATCATAAGTATGCGCATAG 58.146 37.037 29.66 17.55 32.40 2.23
918 943 2.532715 TGGGAGAGGCTTGGGCTT 60.533 61.111 0.00 0.00 38.98 4.35
947 973 0.401395 TGTGTGAAGGGGAGAAGGGT 60.401 55.000 0.00 0.00 0.00 4.34
1043 1073 2.113139 GTGGTGGTGGTGGTGGAG 59.887 66.667 0.00 0.00 0.00 3.86
1428 1624 0.319900 TCTGCTTGAAGTCGCTGTCC 60.320 55.000 0.00 0.00 0.00 4.02
1559 1755 2.096496 GCATTGTGAAATCGACAGGGAG 59.904 50.000 0.00 0.00 0.00 4.30
1564 1760 4.152223 CACACTAGCATTGTGAAATCGACA 59.848 41.667 6.17 0.00 46.18 4.35
1574 1770 0.603707 ACTGCGCACACTAGCATTGT 60.604 50.000 5.66 0.00 42.95 2.71
1639 1841 3.319405 CACTCGTAGCCACTGAATCCTAT 59.681 47.826 0.00 0.00 0.00 2.57
1742 2012 9.136323 CCAGATACAGTGCATATATACCTATCA 57.864 37.037 0.00 0.00 0.00 2.15
1743 2013 9.355916 TCCAGATACAGTGCATATATACCTATC 57.644 37.037 0.00 0.00 0.00 2.08
1745 2015 9.715119 AATCCAGATACAGTGCATATATACCTA 57.285 33.333 0.00 0.00 0.00 3.08
1746 2016 8.615360 AATCCAGATACAGTGCATATATACCT 57.385 34.615 0.00 0.00 0.00 3.08
1750 2020 7.989741 GCCTAAATCCAGATACAGTGCATATAT 59.010 37.037 0.00 0.00 0.00 0.86
1751 2021 7.180946 AGCCTAAATCCAGATACAGTGCATATA 59.819 37.037 0.00 0.00 0.00 0.86
1752 2022 6.013032 AGCCTAAATCCAGATACAGTGCATAT 60.013 38.462 0.00 0.00 0.00 1.78
1754 2024 4.103785 AGCCTAAATCCAGATACAGTGCAT 59.896 41.667 0.00 0.00 0.00 3.96
1756 2026 4.078639 AGCCTAAATCCAGATACAGTGC 57.921 45.455 0.00 0.00 0.00 4.40
1757 2027 5.674525 TGAAGCCTAAATCCAGATACAGTG 58.325 41.667 0.00 0.00 0.00 3.66
1768 2050 4.479786 ACAGACTCCTGAAGCCTAAATC 57.520 45.455 0.00 0.00 43.02 2.17
1847 2290 9.696917 ACTACTCCAATCATCAAAATTCAAAAC 57.303 29.630 0.00 0.00 0.00 2.43
1850 2293 9.177608 CCTACTACTCCAATCATCAAAATTCAA 57.822 33.333 0.00 0.00 0.00 2.69
1851 2294 8.328758 ACCTACTACTCCAATCATCAAAATTCA 58.671 33.333 0.00 0.00 0.00 2.57
1852 2295 8.738645 ACCTACTACTCCAATCATCAAAATTC 57.261 34.615 0.00 0.00 0.00 2.17
1853 2296 9.614792 GTACCTACTACTCCAATCATCAAAATT 57.385 33.333 0.00 0.00 0.00 1.82
1854 2297 8.768397 TGTACCTACTACTCCAATCATCAAAAT 58.232 33.333 0.00 0.00 0.00 1.82
1880 2323 0.107410 TAAGCCCGGTCATCGCATTT 60.107 50.000 0.00 0.00 37.59 2.32
1892 2335 0.949105 ACGCAACACTTCTAAGCCCG 60.949 55.000 0.00 0.00 0.00 6.13
1974 2432 9.836864 GGTGGATGTGATGCATATATTAGATTA 57.163 33.333 0.00 0.00 38.06 1.75
1979 2437 6.352996 GGGAGGTGGATGTGATGCATATATTA 60.353 42.308 0.00 0.00 38.06 0.98
2007 2465 2.373169 TGAGAGTGAGCCAAGGACAAAT 59.627 45.455 0.00 0.00 0.00 2.32
2044 2502 3.081710 AGCACTAACATAACCCCCAAC 57.918 47.619 0.00 0.00 0.00 3.77
2206 2665 3.687698 GTGCCTAAAATGCCTCTTACGAA 59.312 43.478 0.00 0.00 0.00 3.85
2216 2676 6.423604 ACAACATTACAAAGTGCCTAAAATGC 59.576 34.615 0.00 0.00 0.00 3.56
2243 2703 8.862325 TGGTAAATGAGTTTATGATCAACTGT 57.138 30.769 0.00 0.00 34.49 3.55
2453 3934 5.163519 CCACAAAGAAGGCGGATAAATCATT 60.164 40.000 0.00 0.00 0.00 2.57
2558 4039 4.202419 ACAGTAACATGGCACCAAAGTCTA 60.202 41.667 0.00 0.00 0.00 2.59
2565 4047 3.222173 AGAAACAGTAACATGGCACCA 57.778 42.857 0.00 0.00 0.00 4.17
2570 4052 4.393062 CAGCAGGTAGAAACAGTAACATGG 59.607 45.833 0.00 0.00 0.00 3.66
2656 4139 4.330250 CAGTCATGACCAATCTGGAAACT 58.670 43.478 22.21 0.00 40.96 2.66
2730 4238 9.507280 CCACAGCATTATAAAGTGACTAAAATG 57.493 33.333 10.46 0.00 32.14 2.32
2784 4323 3.071023 TCCATCCTTCATACCGGAATGAC 59.929 47.826 9.46 0.00 35.63 3.06
2867 4423 5.065218 GTGTGCAATAGACATAACTTGGGAG 59.935 44.000 0.00 0.00 0.00 4.30
3009 4567 3.314357 AGGCAAGTAAAACAGTTCGGTTC 59.686 43.478 0.00 0.00 0.00 3.62
3039 4598 7.530010 CAGAAATTTGTATTCCTACACACAGG 58.470 38.462 0.00 0.00 37.58 4.00
3242 4834 7.834068 AACTGATGTACATGACTGTATCAAC 57.166 36.000 14.43 0.00 41.93 3.18
3303 4895 5.595542 ACCTTCACACTGCATTGCATATAAT 59.404 36.000 12.53 0.00 38.13 1.28
3306 4898 3.359033 ACCTTCACACTGCATTGCATAT 58.641 40.909 12.53 0.40 38.13 1.78
3417 5066 2.499693 TGGTAGAAGATGCACATTCGGA 59.500 45.455 6.99 0.00 0.00 4.55
3445 5094 9.486123 AGAGTGTATATATGCCATAGACTTCAT 57.514 33.333 0.00 0.00 33.85 2.57
3618 5273 1.915489 TCCTACATGTGTCAGGGCAAT 59.085 47.619 9.11 0.00 0.00 3.56
3672 5328 7.289084 TCAACCAGCTTTAAAGGTTAAGGAAAT 59.711 33.333 22.28 9.97 43.43 2.17
3673 5329 6.608002 TCAACCAGCTTTAAAGGTTAAGGAAA 59.392 34.615 22.28 9.23 43.43 3.13
3675 5331 5.697067 TCAACCAGCTTTAAAGGTTAAGGA 58.303 37.500 22.28 13.77 43.43 3.36
3676 5332 6.213677 GTTCAACCAGCTTTAAAGGTTAAGG 58.786 40.000 17.04 16.78 43.43 2.69
3701 5361 2.741122 TTTTCCGTAAACTGTGCACG 57.259 45.000 13.13 9.67 35.50 5.34
3716 5378 9.364989 TGTATTTAATAGCCAAGCACAATTTTC 57.635 29.630 0.00 0.00 0.00 2.29
3754 5419 6.024552 TGGCTCATCCTTTCAAACAATAAC 57.975 37.500 0.00 0.00 35.26 1.89
3778 5448 6.428159 CACAAGTATAACCTGGAGATATTGGC 59.572 42.308 0.00 0.00 0.00 4.52
3779 5449 6.428159 GCACAAGTATAACCTGGAGATATTGG 59.572 42.308 0.00 0.00 0.00 3.16
3780 5450 6.992123 TGCACAAGTATAACCTGGAGATATTG 59.008 38.462 0.00 0.96 0.00 1.90
3781 5451 7.136822 TGCACAAGTATAACCTGGAGATATT 57.863 36.000 0.00 0.00 0.00 1.28
3788 5458 5.670485 TCAGTATGCACAAGTATAACCTGG 58.330 41.667 0.00 0.00 34.76 4.45
3829 5503 1.344065 TTACGTGGCAGGAAAGAGGA 58.656 50.000 14.98 0.00 0.00 3.71
3830 5504 2.280628 GATTACGTGGCAGGAAAGAGG 58.719 52.381 14.98 0.00 0.00 3.69
3831 5505 2.972625 TGATTACGTGGCAGGAAAGAG 58.027 47.619 14.98 0.00 0.00 2.85
3832 5506 3.410631 TTGATTACGTGGCAGGAAAGA 57.589 42.857 14.98 0.00 0.00 2.52
3833 5507 3.689161 TCATTGATTACGTGGCAGGAAAG 59.311 43.478 14.98 0.00 0.00 2.62
3834 5508 3.680490 TCATTGATTACGTGGCAGGAAA 58.320 40.909 14.98 0.00 0.00 3.13
3835 5509 3.342377 TCATTGATTACGTGGCAGGAA 57.658 42.857 14.98 4.50 0.00 3.36
3850 5524 5.645624 AGTAGTCGACAACAGAGATCATTG 58.354 41.667 19.50 0.00 0.00 2.82
3895 5674 3.479489 TGAGAAAAGATCTGCAGCACAA 58.521 40.909 9.47 0.00 38.96 3.33
3986 5766 7.334421 TGACAGCAAAGATCTTTCCTACATAAC 59.666 37.037 17.91 4.21 0.00 1.89
4042 5915 9.377312 AGTATTTGAGTAAGAGCAAAGAATCTC 57.623 33.333 0.00 0.00 37.41 2.75
4149 6026 4.999950 TGCTTCAACTTCTTCAGAGATTCC 59.000 41.667 0.00 0.00 0.00 3.01
4187 6065 2.792542 GCGGTTCAAGTAATGATGCAGC 60.793 50.000 0.00 0.00 38.03 5.25
4217 6098 6.676456 GCATCGAACTCTGTTAAAGCAATGAT 60.676 38.462 0.00 0.00 0.00 2.45
4257 6281 7.661847 AGGGTTACTTGTCAGAGAAAATTACAG 59.338 37.037 0.00 0.00 0.00 2.74
4260 6284 7.444183 CACAGGGTTACTTGTCAGAGAAAATTA 59.556 37.037 0.00 0.00 0.00 1.40
4265 6289 3.709653 ACACAGGGTTACTTGTCAGAGAA 59.290 43.478 0.00 0.00 0.00 2.87
4472 6537 0.172803 AGCTACCGAAACGCTACAGG 59.827 55.000 0.00 0.00 31.12 4.00
4730 6814 3.889815 CCAGGAGTTTATCAATGGCTGA 58.110 45.455 0.00 0.00 38.81 4.26
4740 6824 0.831307 GAGGTCGGCCAGGAGTTTAT 59.169 55.000 9.71 0.00 37.19 1.40
4802 6886 2.999185 ATGTTGTTGGTCCAGGGATT 57.001 45.000 0.00 0.00 0.00 3.01
4864 7002 8.984764 CATGCATGCCAATATTATATAATTGCC 58.015 33.333 14.93 0.00 32.79 4.52
4872 7010 7.521871 TGACAACATGCATGCCAATATTATA 57.478 32.000 26.53 0.44 0.00 0.98
4873 7011 6.408107 TGACAACATGCATGCCAATATTAT 57.592 33.333 26.53 0.90 0.00 1.28
4874 7012 5.848833 TGACAACATGCATGCCAATATTA 57.151 34.783 26.53 3.19 0.00 0.98
4875 7013 4.739587 TGACAACATGCATGCCAATATT 57.260 36.364 26.53 9.32 0.00 1.28
4876 7014 4.160814 AGTTGACAACATGCATGCCAATAT 59.839 37.500 26.53 13.89 0.00 1.28
4877 7015 3.510753 AGTTGACAACATGCATGCCAATA 59.489 39.130 26.53 7.96 0.00 1.90
4878 7016 2.300723 AGTTGACAACATGCATGCCAAT 59.699 40.909 26.53 9.75 0.00 3.16
4879 7017 1.687660 AGTTGACAACATGCATGCCAA 59.312 42.857 26.53 20.02 0.00 4.52
4880 7018 1.330234 AGTTGACAACATGCATGCCA 58.670 45.000 26.53 15.65 0.00 4.92
4881 7019 2.443887 AAGTTGACAACATGCATGCC 57.556 45.000 26.53 13.32 0.00 4.40
4882 7020 5.903764 TTTTAAGTTGACAACATGCATGC 57.096 34.783 26.53 11.82 0.00 4.06
4883 7021 8.969121 TCTATTTTAAGTTGACAACATGCATG 57.031 30.769 25.09 25.09 0.00 4.06
4884 7022 9.979578 TTTCTATTTTAAGTTGACAACATGCAT 57.020 25.926 20.08 0.00 0.00 3.96
4885 7023 9.809096 TTTTCTATTTTAAGTTGACAACATGCA 57.191 25.926 20.08 0.00 0.00 3.96
4901 7039 8.088365 GCAGTGGATGTAAACCTTTTCTATTTT 58.912 33.333 0.00 0.00 0.00 1.82
4902 7040 7.232534 TGCAGTGGATGTAAACCTTTTCTATTT 59.767 33.333 0.00 0.00 0.00 1.40
4903 7041 6.719370 TGCAGTGGATGTAAACCTTTTCTATT 59.281 34.615 0.00 0.00 0.00 1.73
4904 7042 6.245408 TGCAGTGGATGTAAACCTTTTCTAT 58.755 36.000 0.00 0.00 0.00 1.98
4922 7060 4.256920 AGTAGCTCATAAACCTTGCAGTG 58.743 43.478 0.00 0.00 0.00 3.66
4937 7077 1.068250 GGATGCCGTGGAGTAGCTC 59.932 63.158 0.00 0.00 0.00 4.09
4949 7089 0.181350 AATCTCCAGGAACGGATGCC 59.819 55.000 0.00 0.00 33.56 4.40
4956 7098 4.402056 TCCGATTACAATCTCCAGGAAC 57.598 45.455 0.00 0.00 33.24 3.62
4998 7233 2.557805 GACGAGGCGACGTGTACA 59.442 61.111 16.05 0.00 46.52 2.90
5318 7559 4.687215 GCGAGCACTGCAGGGTGA 62.687 66.667 19.18 0.00 39.34 4.02
5447 7694 2.276853 TGGTACCGATCGCACCACA 61.277 57.895 26.73 12.78 37.42 4.17


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

AutoCloner maintained by Alex Coulton.