Multiple sequence alignment - TraesCS7D01G008800

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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 TraesCS7D01G008800 chr7D 100.000 4964 0 0 1 4964 4271738 4266775 0.000000e+00 9167.0
1 TraesCS7D01G008800 chr7D 91.787 1181 79 10 1744 2911 29550728 29551903 0.000000e+00 1628.0
2 TraesCS7D01G008800 chr7D 92.355 968 63 5 3004 3971 29551936 29552892 0.000000e+00 1367.0
3 TraesCS7D01G008800 chr7D 87.374 895 104 7 1973 2861 4201397 4200506 0.000000e+00 1018.0
4 TraesCS7D01G008800 chr7D 86.456 886 111 6 3007 3890 4199504 4198626 0.000000e+00 963.0
5 TraesCS7D01G008800 chr7D 80.754 743 69 37 965 1659 29549951 29550667 3.430000e-141 512.0
6 TraesCS7D01G008800 chr7D 82.927 287 27 12 1322 1596 4201804 4201528 6.420000e-59 239.0
7 TraesCS7D01G008800 chr7D 89.908 109 10 1 4261 4368 29554168 29554276 6.700000e-29 139.0
8 TraesCS7D01G008800 chr7D 93.506 77 5 0 769 845 29538200 29538276 1.130000e-21 115.0
9 TraesCS7D01G008800 chr7A 90.872 3637 216 51 826 4390 4017430 4013838 0.000000e+00 4771.0
10 TraesCS7D01G008800 chr7A 85.329 2004 188 62 965 2911 29784033 29785987 0.000000e+00 1975.0
11 TraesCS7D01G008800 chr7A 91.039 1049 75 10 3004 4044 29786034 29787071 0.000000e+00 1399.0
12 TraesCS7D01G008800 chr7A 86.176 897 112 10 1973 2861 3985847 3984955 0.000000e+00 959.0
13 TraesCS7D01G008800 chr7A 86.020 887 113 8 3007 3890 3983867 3982989 0.000000e+00 941.0
14 TraesCS7D01G008800 chr7A 90.487 431 30 6 5 431 4018743 4018320 4.340000e-155 558.0
15 TraesCS7D01G008800 chr7A 89.504 343 30 4 436 773 4017890 4017549 3.550000e-116 429.0
16 TraesCS7D01G008800 chr7A 84.223 431 25 8 4411 4816 4013765 4013353 3.630000e-101 379.0
17 TraesCS7D01G008800 chr7A 76.498 634 139 9 3050 3678 4430731 4430103 2.210000e-88 337.0
18 TraesCS7D01G008800 chr7A 77.823 487 104 4 1978 2462 4254334 4253850 1.040000e-76 298.0
19 TraesCS7D01G008800 chr7A 79.946 369 59 7 968 1325 3986666 3986302 1.770000e-64 257.0
20 TraesCS7D01G008800 chr7A 85.616 146 10 8 4599 4742 4001599 4001463 5.180000e-30 143.0
21 TraesCS7D01G008800 chr7A 88.073 109 12 1 4261 4368 29787776 29787884 1.450000e-25 128.0
22 TraesCS7D01G008800 chr7A 92.208 77 6 0 769 845 29782034 29782110 5.250000e-20 110.0
23 TraesCS7D01G008800 chr7A 93.617 47 2 1 1 47 4012818 4012773 8.920000e-08 69.4
24 TraesCS7D01G008800 chr7A 85.075 67 8 2 370 435 642249807 642249872 3.210000e-07 67.6
25 TraesCS7D01G008800 chr7A 90.698 43 4 0 4760 4802 29791245 29791287 1.930000e-04 58.4
26 TraesCS7D01G008800 chr4A 94.406 1001 55 1 1908 2908 739311248 739312247 0.000000e+00 1537.0
27 TraesCS7D01G008800 chr4A 92.337 1057 66 6 3009 4065 739312943 739313984 0.000000e+00 1489.0
28 TraesCS7D01G008800 chr4A 87.054 896 106 8 1973 2861 739416099 739416991 0.000000e+00 1003.0
29 TraesCS7D01G008800 chr4A 86.230 886 113 5 3007 3890 739418007 739418885 0.000000e+00 952.0
30 TraesCS7D01G008800 chr4A 83.582 871 74 29 965 1783 739310212 739311065 0.000000e+00 752.0
31 TraesCS7D01G008800 chr4A 76.289 679 149 10 3017 3689 739067388 739068060 7.910000e-93 351.0
32 TraesCS7D01G008800 chr4A 79.098 488 96 6 1978 2462 739130019 739130503 1.030000e-86 331.0
33 TraesCS7D01G008800 chr4A 87.000 300 32 6 437 733 739309403 739309698 1.030000e-86 331.0
34 TraesCS7D01G008800 chr4A 86.429 280 28 4 1322 1592 739415718 739415996 1.040000e-76 298.0
35 TraesCS7D01G008800 chr4A 87.568 185 14 6 45 226 739308602 739308780 6.510000e-49 206.0
36 TraesCS7D01G008800 chr4A 95.745 47 2 0 727 773 739309939 739309985 5.330000e-10 76.8
37 TraesCS7D01G008800 chr6A 82.353 119 18 3 4097 4214 570863439 570863555 3.160000e-17 100.0
38 TraesCS7D01G008800 chr6A 88.235 68 4 3 369 432 587855033 587855100 1.480000e-10 78.7
39 TraesCS7D01G008800 chr2A 89.855 69 2 5 367 431 764857713 764857780 3.180000e-12 84.2
40 TraesCS7D01G008800 chr1D 90.698 43 2 2 394 434 480809794 480809752 6.940000e-04 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G008800 chr7D 4266775 4271738 4963 True 9167.000000 9167 100.000000 1 4964 1 chr7D.!!$R1 4963
1 TraesCS7D01G008800 chr7D 29549951 29554276 4325 False 911.500000 1628 88.701000 965 4368 4 chr7D.!!$F2 3403
2 TraesCS7D01G008800 chr7D 4198626 4201804 3178 True 740.000000 1018 85.585667 1322 3890 3 chr7D.!!$R2 2568
3 TraesCS7D01G008800 chr7A 4012773 4018743 5970 True 1241.280000 4771 89.740600 1 4816 5 chr7A.!!$R5 4815
4 TraesCS7D01G008800 chr7A 29782034 29791287 9253 False 734.080000 1975 89.469400 769 4802 5 chr7A.!!$F2 4033
5 TraesCS7D01G008800 chr7A 3982989 3986666 3677 True 719.000000 959 84.047333 968 3890 3 chr7A.!!$R4 2922
6 TraesCS7D01G008800 chr7A 4430103 4430731 628 True 337.000000 337 76.498000 3050 3678 1 chr7A.!!$R3 628
7 TraesCS7D01G008800 chr4A 739415718 739418885 3167 False 751.000000 1003 86.571000 1322 3890 3 chr4A.!!$F4 2568
8 TraesCS7D01G008800 chr4A 739308602 739313984 5382 False 731.966667 1537 90.106333 45 4065 6 chr4A.!!$F3 4020
9 TraesCS7D01G008800 chr4A 739067388 739068060 672 False 351.000000 351 76.289000 3017 3689 1 chr4A.!!$F1 672

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
334 376 0.685131 ATGGCCCATCACATGTGTGG 60.685 55.000 27.24 27.24 45.65 4.17 F
1025 3898 0.460311 ATCCGTCGGCGAGAAAGAAT 59.540 50.000 12.93 0.00 41.33 2.40 F
2918 6107 1.154413 CGTCATTTGCTGCACCGTC 60.154 57.895 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 4448 1.092348 GGATCAAAGTAACCACGCCC 58.908 55.0 0.00 0.0 0.00 6.13 R
3003 6215 0.239613 GCACACACAACACACACACA 59.760 50.0 0.00 0.0 0.00 3.72 R
4615 10929 0.537143 TGGCATCAAGTGACCACACC 60.537 55.0 2.78 0.0 46.99 4.16 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
178 179 5.533533 TGCATTATTGTTGCTGATTTTGC 57.466 34.783 0.00 0.00 40.77 3.68
213 214 1.798234 TTGTGCTGCTCCACATGTGC 61.798 55.000 20.81 10.03 44.44 4.57
214 215 1.970114 GTGCTGCTCCACATGTGCT 60.970 57.895 20.81 0.00 35.80 4.40
215 216 1.969589 TGCTGCTCCACATGTGCTG 60.970 57.895 20.81 14.97 36.03 4.41
216 217 2.875485 CTGCTCCACATGTGCTGC 59.125 61.111 24.81 24.81 34.56 5.25
249 281 4.819761 ATCGGAGCACGCACGCAT 62.820 61.111 0.00 0.00 43.86 4.73
275 315 1.137479 CTCGCCAGTTTAATCCCGGTA 59.863 52.381 0.00 0.00 0.00 4.02
289 329 4.157120 GGTAGGTGGCCGTCGCAT 62.157 66.667 0.00 0.00 36.38 4.73
291 331 2.171725 GTAGGTGGCCGTCGCATTC 61.172 63.158 0.00 0.00 36.38 2.67
292 332 2.651105 TAGGTGGCCGTCGCATTCA 61.651 57.895 0.00 0.00 36.38 2.57
293 333 1.966901 TAGGTGGCCGTCGCATTCAT 61.967 55.000 0.00 0.00 36.38 2.57
334 376 0.685131 ATGGCCCATCACATGTGTGG 60.685 55.000 27.24 27.24 45.65 4.17
352 403 6.844254 TGTGTGGTTTTTAAACTCTGTACAC 58.156 36.000 5.43 11.60 38.89 2.90
355 406 6.316890 TGTGGTTTTTAAACTCTGTACACTCC 59.683 38.462 5.43 0.00 38.89 3.85
369 420 6.040209 TGTACACTCCGTTTATATGGTGTT 57.960 37.500 0.00 0.00 35.50 3.32
395 446 7.919313 TTTCTAACACAGTACAGACGTAAAG 57.081 36.000 0.00 0.00 0.00 1.85
403 454 5.035443 CAGTACAGACGTAAAGGCTCATAC 58.965 45.833 0.00 0.00 34.57 2.39
404 455 4.703575 AGTACAGACGTAAAGGCTCATACA 59.296 41.667 10.04 0.00 34.57 2.29
409 460 3.378339 ACGTAAAGGCTCATACATACGC 58.622 45.455 10.04 0.00 39.60 4.42
415 466 1.654105 GGCTCATACATACGCGCATAC 59.346 52.381 5.73 0.00 0.00 2.39
419 470 3.972403 TCATACATACGCGCATACACTT 58.028 40.909 5.73 0.00 0.00 3.16
421 472 5.705902 TCATACATACGCGCATACACTTAT 58.294 37.500 5.73 0.00 0.00 1.73
422 473 5.798434 TCATACATACGCGCATACACTTATC 59.202 40.000 5.73 0.00 0.00 1.75
424 475 3.005472 ACATACGCGCATACACTTATCCT 59.995 43.478 5.73 0.00 0.00 3.24
425 476 4.216902 ACATACGCGCATACACTTATCCTA 59.783 41.667 5.73 0.00 0.00 2.94
426 477 3.936372 ACGCGCATACACTTATCCTAT 57.064 42.857 5.73 0.00 0.00 2.57
427 478 3.575630 ACGCGCATACACTTATCCTATG 58.424 45.455 5.73 0.00 0.00 2.23
428 479 3.254903 ACGCGCATACACTTATCCTATGA 59.745 43.478 5.73 0.00 0.00 2.15
430 481 4.090066 CGCGCATACACTTATCCTATGAAC 59.910 45.833 8.75 0.00 0.00 3.18
431 482 4.988540 GCGCATACACTTATCCTATGAACA 59.011 41.667 0.30 0.00 0.00 3.18
432 483 5.107453 GCGCATACACTTATCCTATGAACAC 60.107 44.000 0.30 0.00 0.00 3.32
433 484 5.983118 CGCATACACTTATCCTATGAACACA 59.017 40.000 0.00 0.00 0.00 3.72
434 485 6.646653 CGCATACACTTATCCTATGAACACAT 59.353 38.462 0.00 0.00 0.00 3.21
500 1220 2.770164 AGGATTGTCCAGCACTACAC 57.230 50.000 0.00 0.00 39.61 2.90
502 1222 1.279271 GGATTGTCCAGCACTACACCT 59.721 52.381 0.00 0.00 36.28 4.00
541 1261 3.209410 CCAACAGAGAGGACAATATGGC 58.791 50.000 0.00 0.00 0.00 4.40
562 1282 1.425428 CGGTCGCCTTTTGCATCTC 59.575 57.895 0.00 0.00 41.33 2.75
565 1285 0.881118 GTCGCCTTTTGCATCTCCAA 59.119 50.000 0.00 0.00 41.33 3.53
568 1288 0.893447 GCCTTTTGCATCTCCAAGCT 59.107 50.000 0.00 0.00 40.77 3.74
577 1297 1.140652 CATCTCCAAGCTCTCCCTTCC 59.859 57.143 0.00 0.00 0.00 3.46
591 1311 4.141135 TCTCCCTTCCACAAACAACCATTA 60.141 41.667 0.00 0.00 0.00 1.90
622 1342 5.518847 TCTTAACAAACTCGGCGATAATCTG 59.481 40.000 11.27 6.56 0.00 2.90
653 1373 3.383825 GCAATCTCCAAAAGGCAGATGAT 59.616 43.478 0.00 0.00 0.00 2.45
654 1374 4.581824 GCAATCTCCAAAAGGCAGATGATA 59.418 41.667 0.00 0.00 0.00 2.15
783 1795 1.266718 GCACAAAAGTGATTCTGCCGA 59.733 47.619 0.00 0.00 0.00 5.54
845 1880 1.661341 CCAAGAGCAATCCCTTCTCG 58.339 55.000 0.00 0.00 32.42 4.04
856 1891 5.531287 GCAATCCCTTCTCGTTACCATTAAT 59.469 40.000 0.00 0.00 0.00 1.40
857 1892 6.039382 GCAATCCCTTCTCGTTACCATTAATT 59.961 38.462 0.00 0.00 0.00 1.40
858 1893 7.227910 GCAATCCCTTCTCGTTACCATTAATTA 59.772 37.037 0.00 0.00 0.00 1.40
859 1894 9.116067 CAATCCCTTCTCGTTACCATTAATTAA 57.884 33.333 0.00 0.00 0.00 1.40
900 1935 5.606505 TGTGTGCAACTAATCTAAGTGTGA 58.393 37.500 0.00 0.00 38.04 3.58
937 3729 8.533569 TCCCCATTAAAATTCTCATCTTTACC 57.466 34.615 0.00 0.00 0.00 2.85
938 3730 8.119246 TCCCCATTAAAATTCTCATCTTTACCA 58.881 33.333 0.00 0.00 0.00 3.25
985 3854 3.827302 TCTGTATAAATCTCCCTCGCTCC 59.173 47.826 0.00 0.00 0.00 4.70
1025 3898 0.460311 ATCCGTCGGCGAGAAAGAAT 59.540 50.000 12.93 0.00 41.33 2.40
1333 4282 4.250305 GGCGTGTCCGGGGCATAT 62.250 66.667 3.85 0.00 33.68 1.78
1337 4286 1.837090 GTGTCCGGGGCATATTCCT 59.163 57.895 3.85 0.00 0.00 3.36
1340 4289 1.846124 TCCGGGGCATATTCCTCCC 60.846 63.158 0.00 0.00 39.33 4.30
1473 4426 8.873830 GTTCGATTAAATCTTCAGATTCAGACA 58.126 33.333 2.47 0.00 43.41 3.41
1475 4428 8.034804 TCGATTAAATCTTCAGATTCAGACACA 58.965 33.333 2.47 0.00 43.41 3.72
1489 4448 7.645340 AGATTCAGACACAATTTTGTTTTCTCG 59.355 33.333 0.00 0.00 39.91 4.04
1930 5054 7.929785 GGATTTTAATGTTCATCCAGATGCATT 59.070 33.333 0.00 14.10 38.65 3.56
1932 5056 8.481974 TTTTAATGTTCATCCAGATGCATTTG 57.518 30.769 10.22 10.22 38.65 2.32
1940 5064 2.026542 TCCAGATGCATTTGAGCTCAGT 60.027 45.455 18.32 7.20 34.99 3.41
1944 5068 5.505819 CCAGATGCATTTGAGCTCAGTATTG 60.506 44.000 18.32 13.47 34.99 1.90
2496 5623 2.185093 GGGTACTTGTACCGCGGG 59.815 66.667 31.76 13.93 40.98 6.13
2817 5944 1.377463 CGAGACCGACTCCTGGAGT 60.377 63.158 28.70 28.70 46.42 3.85
2823 5950 2.418910 CGACTCCTGGAGTGCCGAT 61.419 63.158 32.86 8.09 43.53 4.18
2826 5953 4.147449 TCCTGGAGTGCCGATGCG 62.147 66.667 0.00 0.00 41.78 4.73
2869 6002 3.117926 TCAGGTAACCATCATGGACATGG 60.118 47.826 11.90 9.76 45.74 3.66
2918 6107 1.154413 CGTCATTTGCTGCACCGTC 60.154 57.895 0.00 0.00 0.00 4.79
2919 6108 1.840630 CGTCATTTGCTGCACCGTCA 61.841 55.000 0.00 0.00 0.00 4.35
2989 6201 1.421410 CGTGCAGCACTATTCCGACC 61.421 60.000 23.15 0.00 31.34 4.79
2991 6203 1.883084 GCAGCACTATTCCGACCCG 60.883 63.158 0.00 0.00 0.00 5.28
2992 6204 1.813859 CAGCACTATTCCGACCCGA 59.186 57.895 0.00 0.00 0.00 5.14
2996 6208 2.897969 AGCACTATTCCGACCCGATATT 59.102 45.455 0.00 0.00 0.00 1.28
3000 6212 5.291128 GCACTATTCCGACCCGATATTATTG 59.709 44.000 0.00 0.00 0.00 1.90
3003 6215 5.740290 ATTCCGACCCGATATTATTGAGT 57.260 39.130 0.00 0.00 0.00 3.41
3018 7320 2.177394 TGAGTGTGTGTGTGTTGTGT 57.823 45.000 0.00 0.00 0.00 3.72
3066 7368 0.824595 TTGACGAGAAGACCCGGACA 60.825 55.000 0.73 0.00 0.00 4.02
3332 7634 3.909258 TTCTCGTCCTCGCCAACGC 62.909 63.158 0.00 0.00 38.72 4.84
3396 7701 2.175078 CTCGACGGCGTTCTTCGA 59.825 61.111 16.19 17.51 42.86 3.71
3540 7845 1.416813 CCATCGTGCAGAGCTTCGTC 61.417 60.000 0.00 0.00 0.00 4.20
3660 7965 0.610174 TCACCGCTGAGAAGCTCATT 59.390 50.000 0.00 0.00 39.92 2.57
3747 8055 9.856488 GATTAGACTGATCACTTACAACAAGTA 57.144 33.333 2.45 0.00 0.00 2.24
3771 8081 3.739167 TTTTTGCTCGGTCCGTGG 58.261 55.556 11.88 6.89 0.00 4.94
3772 8082 1.146485 TTTTTGCTCGGTCCGTGGA 59.854 52.632 11.88 7.39 0.00 4.02
3783 8093 1.002773 GGTCCGTGGAGCTTCCTTTTA 59.997 52.381 10.76 0.00 37.46 1.52
3796 8106 6.488715 AGCTTCCTTTTATCTTGGACAGATT 58.511 36.000 0.00 0.00 39.47 2.40
3797 8107 6.950619 AGCTTCCTTTTATCTTGGACAGATTT 59.049 34.615 0.00 0.00 39.47 2.17
3798 8108 7.452813 AGCTTCCTTTTATCTTGGACAGATTTT 59.547 33.333 0.00 0.00 39.47 1.82
3799 8109 8.090831 GCTTCCTTTTATCTTGGACAGATTTTT 58.909 33.333 0.00 0.00 39.47 1.94
3827 8137 0.322975 AGCACCAGCAAGTCTACCTG 59.677 55.000 0.00 0.00 45.49 4.00
3845 8155 9.167311 GTCTACCTGTCATCTTGATTTATGTTT 57.833 33.333 0.00 0.00 0.00 2.83
3895 8205 6.769822 AGATGAATTAGATGATGTTGGTCACC 59.230 38.462 0.00 0.00 0.00 4.02
4038 8735 4.703379 TTTTTGGGGAAAGCAATCATGT 57.297 36.364 0.00 0.00 0.00 3.21
4044 8741 4.776837 TGGGGAAAGCAATCATGTTGTATT 59.223 37.500 8.97 5.55 0.00 1.89
4046 8743 6.172630 GGGGAAAGCAATCATGTTGTATTTT 58.827 36.000 8.97 7.75 0.00 1.82
4048 8745 7.148423 GGGGAAAGCAATCATGTTGTATTTTTC 60.148 37.037 8.97 11.52 0.00 2.29
4094 9274 7.354751 AGAATAGAAAGTAGACTCCCATCAC 57.645 40.000 0.00 0.00 0.00 3.06
4112 9292 4.115401 TCACACATGCATCACTACTCTC 57.885 45.455 0.00 0.00 0.00 3.20
4114 9294 2.159184 ACACATGCATCACTACTCTCCG 60.159 50.000 0.00 0.00 0.00 4.63
4122 9302 4.678309 GCATCACTACTCTCCGCTTTAACT 60.678 45.833 0.00 0.00 0.00 2.24
4139 9319 7.998212 CGCTTTAACTTTTTCAACTTTATGCAG 59.002 33.333 0.00 0.00 0.00 4.41
4146 9326 3.138884 TCAACTTTATGCAGCTGACCA 57.861 42.857 20.43 7.27 0.00 4.02
4206 9387 2.607282 CCGCTACATCATCCGAACCTAC 60.607 54.545 0.00 0.00 0.00 3.18
4212 9393 5.422214 ACATCATCCGAACCTACTTTTCT 57.578 39.130 0.00 0.00 0.00 2.52
4214 9395 5.643777 ACATCATCCGAACCTACTTTTCTTG 59.356 40.000 0.00 0.00 0.00 3.02
4218 9399 7.039882 TCATCCGAACCTACTTTTCTTGATAC 58.960 38.462 0.00 0.00 0.00 2.24
4220 9401 4.874396 CCGAACCTACTTTTCTTGATACCC 59.126 45.833 0.00 0.00 0.00 3.69
4232 9413 3.832490 TCTTGATACCCGATCCTACATGG 59.168 47.826 0.00 0.00 33.07 3.66
4247 9428 3.330192 TGGCTTACGGGGCATCAT 58.670 55.556 0.00 0.00 36.85 2.45
4253 9434 1.276421 CTTACGGGGCATCATCCTAGG 59.724 57.143 0.82 0.82 0.00 3.02
4295 9629 6.985117 ACCTGACGTAATCAAAGTACAGTTA 58.015 36.000 0.00 0.00 36.69 2.24
4296 9630 6.865205 ACCTGACGTAATCAAAGTACAGTTAC 59.135 38.462 0.00 0.00 36.69 2.50
4297 9631 6.864685 CCTGACGTAATCAAAGTACAGTTACA 59.135 38.462 0.00 0.00 36.69 2.41
4317 9651 3.891366 ACATGGCTCCCATAACTAAATGC 59.109 43.478 0.00 0.00 43.15 3.56
4356 9690 8.623310 TTCCGAAAAGAAAATACTTGACAAAC 57.377 30.769 0.00 0.00 0.00 2.93
4401 9950 1.005924 AGAACGGGCCCTGATTTTCAT 59.994 47.619 22.43 2.44 0.00 2.57
4404 9953 3.094484 ACGGGCCCTGATTTTCATTAA 57.906 42.857 22.43 0.00 0.00 1.40
4405 9954 3.023832 ACGGGCCCTGATTTTCATTAAG 58.976 45.455 22.43 0.39 0.00 1.85
4434 9983 1.404851 GCAGTCTGACTGGCTAGAACC 60.405 57.143 32.28 14.13 46.01 3.62
4448 9997 1.700955 AGAACCGACTACACACCACT 58.299 50.000 0.00 0.00 0.00 4.00
4463 10012 0.955919 CCACTTGAACCTCCCGAAGC 60.956 60.000 0.00 0.00 0.00 3.86
4470 10019 1.915078 AACCTCCCGAAGCATCAGGG 61.915 60.000 11.19 11.19 46.40 4.45
4489 10041 3.031736 GGGACTAGATCTACCAGCACAA 58.968 50.000 10.66 0.00 0.00 3.33
4500 10052 1.064017 ACCAGCACAAAGGAACAGGAA 60.064 47.619 0.00 0.00 0.00 3.36
4549 10107 3.624300 CGCAGCCGCAGAATCTCG 61.624 66.667 0.00 0.00 38.40 4.04
4557 10115 0.029967 CGCAGAATCTCGCAGCTCTA 59.970 55.000 5.75 0.00 0.00 2.43
4615 10929 4.201891 GCAGCAGATCTGTTTGTATGAAGG 60.202 45.833 23.38 4.22 44.66 3.46
4652 10966 4.144297 TGCCATAATATCAAGGTCAAGCC 58.856 43.478 0.00 0.00 37.58 4.35
4680 10994 2.925162 ATTAGCCTCTCCGCCGTTGC 62.925 60.000 0.00 0.00 0.00 4.17
4693 11007 1.247567 CCGTTGCTGTCCCTTTCAAT 58.752 50.000 0.00 0.00 0.00 2.57
4694 11008 1.613437 CCGTTGCTGTCCCTTTCAATT 59.387 47.619 0.00 0.00 0.00 2.32
4695 11009 2.351738 CCGTTGCTGTCCCTTTCAATTC 60.352 50.000 0.00 0.00 0.00 2.17
4747 12197 1.302033 CCCACAGCCACAGTCAGAC 60.302 63.158 0.00 0.00 0.00 3.51
4789 13107 2.968574 GAGGGTCTCCAGCTCAATCATA 59.031 50.000 0.00 0.00 34.83 2.15
4820 13174 3.689224 CAGTGTTGCATGCACTAGC 57.311 52.632 22.58 11.56 44.43 3.42
4822 13176 2.349590 CAGTGTTGCATGCACTAGCTA 58.650 47.619 22.58 0.52 44.43 3.32
4823 13177 2.350804 CAGTGTTGCATGCACTAGCTAG 59.649 50.000 22.58 19.44 44.43 3.42
4824 13178 1.667724 GTGTTGCATGCACTAGCTAGG 59.332 52.381 22.58 14.10 42.74 3.02
4826 13180 2.290260 TGTTGCATGCACTAGCTAGGTT 60.290 45.455 22.58 1.58 42.74 3.50
4828 13182 3.904800 TGCATGCACTAGCTAGGTTTA 57.095 42.857 24.35 8.48 42.74 2.01
4829 13183 4.422073 TGCATGCACTAGCTAGGTTTAT 57.578 40.909 24.35 10.31 42.74 1.40
4830 13184 5.545063 TGCATGCACTAGCTAGGTTTATA 57.455 39.130 24.35 5.44 42.74 0.98
4831 13185 6.114187 TGCATGCACTAGCTAGGTTTATAT 57.886 37.500 24.35 7.39 42.74 0.86
4858 13266 0.522495 AAACAAACGTGCGAGCACAC 60.522 50.000 25.18 3.06 46.47 3.82
4864 13272 0.173481 ACGTGCGAGCACACATCTAT 59.827 50.000 25.18 1.68 46.47 1.98
4865 13273 1.404035 ACGTGCGAGCACACATCTATA 59.596 47.619 25.18 0.00 46.47 1.31
4866 13274 2.047040 CGTGCGAGCACACATCTATAG 58.953 52.381 25.18 4.59 46.47 1.31
4867 13275 2.287009 CGTGCGAGCACACATCTATAGA 60.287 50.000 25.18 4.57 46.47 1.98
4917 13369 1.961793 TATATTTGCACCTCCCACGC 58.038 50.000 0.00 0.00 0.00 5.34
4933 13385 4.802051 GCCTTGGCCTCGGCATCA 62.802 66.667 25.07 0.00 45.59 3.07
4934 13386 2.045045 CCTTGGCCTCGGCATCAA 60.045 61.111 10.51 5.00 44.11 2.57
4935 13387 2.117156 CCTTGGCCTCGGCATCAAG 61.117 63.158 15.67 15.67 44.11 3.02
4936 13388 2.045045 TTGGCCTCGGCATCAAGG 60.045 61.111 10.51 0.00 44.11 3.61
4937 13389 2.826777 CTTGGCCTCGGCATCAAGGT 62.827 60.000 10.51 0.00 44.11 3.50
4939 13391 2.409870 GGCCTCGGCATCAAGGTTG 61.410 63.158 10.51 0.00 44.11 3.77
4940 13392 1.377202 GCCTCGGCATCAAGGTTGA 60.377 57.895 2.41 0.00 42.14 3.18
4941 13393 1.648467 GCCTCGGCATCAAGGTTGAC 61.648 60.000 2.41 0.00 40.49 3.18
4943 13395 1.970917 CTCGGCATCAAGGTTGACGC 61.971 60.000 2.17 2.17 45.22 5.19
4944 13396 2.480555 GGCATCAAGGTTGACGCG 59.519 61.111 3.53 3.53 46.38 6.01
4945 13397 2.325082 GGCATCAAGGTTGACGCGT 61.325 57.895 13.85 13.85 46.38 6.01
4946 13398 1.132640 GCATCAAGGTTGACGCGTC 59.867 57.895 31.66 31.66 36.63 5.19
4948 13400 1.006571 ATCAAGGTTGACGCGTCGT 60.007 52.632 31.88 15.23 45.10 4.34
4949 13401 0.241749 ATCAAGGTTGACGCGTCGTA 59.758 50.000 31.88 20.74 41.37 3.43
4950 13402 0.030504 TCAAGGTTGACGCGTCGTAA 59.969 50.000 31.88 20.10 41.37 3.18
4952 13404 1.458064 CAAGGTTGACGCGTCGTAAAT 59.542 47.619 31.88 16.58 41.37 1.40
4953 13405 1.787012 AGGTTGACGCGTCGTAAATT 58.213 45.000 31.88 13.88 41.37 1.82
4954 13406 1.458064 AGGTTGACGCGTCGTAAATTG 59.542 47.619 31.88 0.00 41.37 2.32
4955 13407 1.456544 GGTTGACGCGTCGTAAATTGA 59.543 47.619 31.88 11.12 41.37 2.57
4956 13408 2.479328 GTTGACGCGTCGTAAATTGAC 58.521 47.619 31.88 16.17 41.37 3.18
4958 13410 2.125685 TGACGCGTCGTAAATTGACAA 58.874 42.857 31.88 9.04 41.37 3.18
4959 13411 2.154198 TGACGCGTCGTAAATTGACAAG 59.846 45.455 31.88 0.00 41.37 3.16
4960 13412 2.129607 ACGCGTCGTAAATTGACAAGT 58.870 42.857 5.58 0.00 38.73 3.16
4961 13413 2.154389 ACGCGTCGTAAATTGACAAGTC 59.846 45.455 5.58 0.00 38.73 3.01
4962 13414 2.743172 GCGTCGTAAATTGACAAGTCG 58.257 47.619 0.00 0.00 36.11 4.18
4963 13415 2.406024 GCGTCGTAAATTGACAAGTCGA 59.594 45.455 0.00 0.00 36.11 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.272146 GGTCACATGGTGGCGGAT 59.728 61.111 0.00 0.00 39.27 4.18
1 2 4.028490 GGGTCACATGGTGGCGGA 62.028 66.667 0.00 0.00 39.27 5.54
4 5 4.344865 ACGGGGTCACATGGTGGC 62.345 66.667 0.00 0.00 37.44 5.01
5 6 2.359850 CACGGGGTCACATGGTGG 60.360 66.667 0.00 0.00 33.87 4.61
6 7 2.359850 CCACGGGGTCACATGGTG 60.360 66.667 0.00 0.00 34.45 4.17
7 8 2.528127 TCCACGGGGTCACATGGT 60.528 61.111 2.12 0.00 33.67 3.55
8 9 2.046314 GTCCACGGGGTCACATGG 60.046 66.667 2.12 0.00 34.93 3.66
9 10 2.046314 GGTCCACGGGGTCACATG 60.046 66.667 2.12 0.00 34.93 3.21
178 179 1.938577 CACAATGCCGAGAGATCCAAG 59.061 52.381 0.00 0.00 0.00 3.61
213 214 2.433838 ACGTAGCAGCAGCAGCAG 60.434 61.111 12.92 5.55 45.49 4.24
214 215 2.511545 ATCACGTAGCAGCAGCAGCA 62.512 55.000 12.92 0.00 45.49 4.41
215 216 1.760268 GATCACGTAGCAGCAGCAGC 61.760 60.000 3.17 0.46 45.49 5.25
216 217 1.477826 CGATCACGTAGCAGCAGCAG 61.478 60.000 3.17 0.00 37.76 4.24
249 281 3.945285 GGGATTAAACTGGCGAGATTGAA 59.055 43.478 1.44 0.00 0.00 2.69
275 315 3.329542 ATGAATGCGACGGCCACCT 62.330 57.895 2.24 0.00 38.85 4.00
287 327 4.570772 ACTTTTCGTACCCATCGATGAATG 59.429 41.667 26.86 15.98 37.18 2.67
288 328 4.766375 ACTTTTCGTACCCATCGATGAAT 58.234 39.130 26.86 15.72 37.18 2.57
289 329 4.196626 ACTTTTCGTACCCATCGATGAA 57.803 40.909 26.86 8.86 37.18 2.57
291 331 4.269363 GGTTACTTTTCGTACCCATCGATG 59.731 45.833 18.76 18.76 37.18 3.84
292 332 4.081531 TGGTTACTTTTCGTACCCATCGAT 60.082 41.667 0.00 0.00 35.93 3.59
293 333 3.257873 TGGTTACTTTTCGTACCCATCGA 59.742 43.478 0.00 0.00 35.93 3.59
334 376 6.594284 ACGGAGTGTACAGAGTTTAAAAAC 57.406 37.500 0.00 0.00 42.51 2.43
369 420 8.700722 TTTACGTCTGTACTGTGTTAGAAAAA 57.299 30.769 0.00 0.00 0.00 1.94
374 425 4.620184 GCCTTTACGTCTGTACTGTGTTAG 59.380 45.833 0.00 0.30 0.00 2.34
378 429 3.243336 GAGCCTTTACGTCTGTACTGTG 58.757 50.000 0.00 0.00 0.00 3.66
379 430 2.889045 TGAGCCTTTACGTCTGTACTGT 59.111 45.455 0.00 0.00 0.00 3.55
380 431 3.570926 TGAGCCTTTACGTCTGTACTG 57.429 47.619 0.00 0.00 0.00 2.74
391 442 2.223852 TGCGCGTATGTATGAGCCTTTA 60.224 45.455 8.43 0.00 37.23 1.85
395 446 1.654105 GTATGCGCGTATGTATGAGCC 59.346 52.381 20.45 0.00 37.23 4.70
403 454 3.575630 AGGATAAGTGTATGCGCGTATG 58.424 45.455 20.45 0.00 33.48 2.39
404 455 3.936372 AGGATAAGTGTATGCGCGTAT 57.064 42.857 15.52 15.52 33.48 3.06
409 460 5.983118 TGTGTTCATAGGATAAGTGTATGCG 59.017 40.000 0.00 0.00 33.48 4.73
415 466 7.062722 CGATAGCATGTGTTCATAGGATAAGTG 59.937 40.741 0.00 0.00 32.47 3.16
419 470 6.350194 GGACGATAGCATGTGTTCATAGGATA 60.350 42.308 0.00 0.00 42.67 2.59
421 472 4.262036 GGACGATAGCATGTGTTCATAGGA 60.262 45.833 0.00 0.00 42.67 2.94
422 473 3.990469 GGACGATAGCATGTGTTCATAGG 59.010 47.826 0.00 0.00 42.67 2.57
424 475 4.368315 GTGGACGATAGCATGTGTTCATA 58.632 43.478 0.00 0.00 42.67 2.15
425 476 3.198068 GTGGACGATAGCATGTGTTCAT 58.802 45.455 0.00 0.00 42.67 2.57
426 477 2.616960 GTGGACGATAGCATGTGTTCA 58.383 47.619 0.00 0.00 42.67 3.18
427 478 1.933853 GGTGGACGATAGCATGTGTTC 59.066 52.381 0.00 0.00 42.67 3.18
428 479 1.406887 GGGTGGACGATAGCATGTGTT 60.407 52.381 0.00 0.00 42.67 3.32
430 481 0.177836 TGGGTGGACGATAGCATGTG 59.822 55.000 0.00 0.00 42.67 3.21
431 482 1.131638 ATGGGTGGACGATAGCATGT 58.868 50.000 0.00 0.00 42.67 3.21
432 483 2.146342 GAATGGGTGGACGATAGCATG 58.854 52.381 0.00 0.00 42.67 4.06
433 484 2.037772 GAGAATGGGTGGACGATAGCAT 59.962 50.000 0.00 0.00 42.67 3.79
434 485 1.412710 GAGAATGGGTGGACGATAGCA 59.587 52.381 0.00 0.00 42.67 3.49
500 1220 2.482333 CCGTCCGAGGAGCTACAGG 61.482 68.421 0.00 0.49 0.00 4.00
502 1222 2.439701 CCCGTCCGAGGAGCTACA 60.440 66.667 0.00 0.00 0.00 2.74
510 1230 3.649277 CTCTGTTGGCCCGTCCGAG 62.649 68.421 0.00 0.00 37.80 4.63
562 1282 0.401738 TTGTGGAAGGGAGAGCTTGG 59.598 55.000 0.00 0.00 0.00 3.61
565 1285 1.140312 TGTTTGTGGAAGGGAGAGCT 58.860 50.000 0.00 0.00 0.00 4.09
568 1288 1.566703 TGGTTGTTTGTGGAAGGGAGA 59.433 47.619 0.00 0.00 0.00 3.71
577 1297 9.757227 TTAAGAAGGAAATAATGGTTGTTTGTG 57.243 29.630 0.00 0.00 0.00 3.33
591 1311 4.083484 CGCCGAGTTTGTTAAGAAGGAAAT 60.083 41.667 0.00 0.00 0.00 2.17
622 1342 0.605319 TTGGAGATTGCGTGTCCCAC 60.605 55.000 3.14 0.00 39.52 4.61
741 1710 5.049828 GCCATGTGTTAAAAAGCAAGTTCT 58.950 37.500 0.00 0.00 0.00 3.01
770 1782 0.603569 AAGACGTCGGCAGAATCACT 59.396 50.000 10.46 0.00 0.00 3.41
776 1788 0.387929 AGAAACAAGACGTCGGCAGA 59.612 50.000 10.46 0.00 0.00 4.26
856 1891 8.397906 CACACATTCTCTTTCTTCTTGTGTTAA 58.602 33.333 3.26 0.00 42.39 2.01
857 1892 7.467267 GCACACATTCTCTTTCTTCTTGTGTTA 60.467 37.037 3.26 0.00 42.39 2.41
858 1893 6.678900 GCACACATTCTCTTTCTTCTTGTGTT 60.679 38.462 3.26 0.00 42.39 3.32
859 1894 5.220931 GCACACATTCTCTTTCTTCTTGTGT 60.221 40.000 0.00 0.00 44.95 3.72
875 1910 6.710295 TCACACTTAGATTAGTTGCACACATT 59.290 34.615 0.00 0.00 0.00 2.71
900 1935 4.430388 TGGGGAAACACCTCACCT 57.570 55.556 0.00 0.00 45.39 4.00
937 3729 2.758423 GGTTTATAGCTGGGGTTTGGTG 59.242 50.000 0.00 0.00 0.00 4.17
938 3730 2.652857 AGGTTTATAGCTGGGGTTTGGT 59.347 45.455 0.00 0.00 0.00 3.67
985 3854 3.579302 TGCTGGGTTCAGTGGGGG 61.579 66.667 0.00 0.00 42.78 5.40
1015 3888 7.715249 TGGGAATTTGGTAGATATTCTTTCTCG 59.285 37.037 0.00 0.00 0.00 4.04
1025 3898 3.386063 TCCCGTGGGAATTTGGTAGATA 58.614 45.455 4.80 0.00 42.05 1.98
1078 3967 1.953138 GATGAGGATGCCGCGTGAG 60.953 63.158 4.92 0.00 0.00 3.51
1473 4426 2.100087 ACGCCCGAGAAAACAAAATTGT 59.900 40.909 0.00 0.00 44.72 2.71
1475 4428 2.544903 CCACGCCCGAGAAAACAAAATT 60.545 45.455 0.00 0.00 0.00 1.82
1489 4448 1.092348 GGATCAAAGTAACCACGCCC 58.908 55.000 0.00 0.00 0.00 6.13
1794 4909 2.380064 TTTGTGGAGGCCTGACAAAT 57.620 45.000 25.78 0.00 35.26 2.32
1922 5046 4.579340 CCAATACTGAGCTCAAATGCATCT 59.421 41.667 18.85 0.00 34.99 2.90
1930 5054 3.866651 GCTCTTCCAATACTGAGCTCAA 58.133 45.455 18.85 3.88 45.78 3.02
1940 5064 3.002791 CAGCGAAAGTGCTCTTCCAATA 58.997 45.455 0.74 0.00 45.23 1.90
1944 5068 1.512926 TTCAGCGAAAGTGCTCTTCC 58.487 50.000 0.74 0.00 45.23 3.46
2770 5897 4.933064 CCAGACGATCCGCCGCTC 62.933 72.222 0.00 0.00 0.00 5.03
2869 6002 7.013529 CGGTGATAACTGTAAAGTAAAACAGC 58.986 38.462 2.52 0.00 45.65 4.40
2918 6107 1.444836 CCACCCAGCATGCAAAATTG 58.555 50.000 21.98 8.77 31.97 2.32
2919 6108 0.325602 CCCACCCAGCATGCAAAATT 59.674 50.000 21.98 0.00 31.97 1.82
2989 6201 5.580691 ACACACACACACTCAATAATATCGG 59.419 40.000 0.00 0.00 0.00 4.18
2991 6203 7.746034 CACAACACACACACACTCAATAATATC 59.254 37.037 0.00 0.00 0.00 1.63
2992 6204 7.228507 ACACAACACACACACACTCAATAATAT 59.771 33.333 0.00 0.00 0.00 1.28
2996 6208 4.094146 CACACAACACACACACACTCAATA 59.906 41.667 0.00 0.00 0.00 1.90
3000 6212 1.804151 ACACACAACACACACACACTC 59.196 47.619 0.00 0.00 0.00 3.51
3003 6215 0.239613 GCACACACAACACACACACA 59.760 50.000 0.00 0.00 0.00 3.72
3018 7320 0.601057 TTCTCGGAATCGACTGCACA 59.399 50.000 0.00 0.00 40.88 4.57
3066 7368 0.684153 CCGGCCATTGGATGAGGTTT 60.684 55.000 6.95 0.00 0.00 3.27
3332 7634 1.374758 GTCTGTTCTGTCAGGGCGG 60.375 63.158 0.00 0.00 36.25 6.13
3389 7694 0.859232 GCAGAAGTGCGTTCGAAGAA 59.141 50.000 0.00 0.00 40.73 2.52
3540 7845 2.111878 GTCATCCTCCCGCCCATG 59.888 66.667 0.00 0.00 0.00 3.66
3638 7943 3.805267 GCTTCTCAGCGGTGATGG 58.195 61.111 18.98 7.68 35.91 3.51
3660 7965 2.454921 CGAATCCATGTCGTGCACA 58.545 52.632 18.64 0.81 40.18 4.57
3767 8077 3.375299 CCAAGATAAAAGGAAGCTCCACG 59.625 47.826 5.21 0.00 39.61 4.94
3771 8081 5.491982 TCTGTCCAAGATAAAAGGAAGCTC 58.508 41.667 0.00 0.00 32.30 4.09
3772 8082 5.505181 TCTGTCCAAGATAAAAGGAAGCT 57.495 39.130 0.00 0.00 32.30 3.74
3796 8106 4.390048 GGTGCTCCACCGCTAAAA 57.610 55.556 0.00 0.00 44.95 1.52
3817 8127 8.543774 ACATAAATCAAGATGACAGGTAGACTT 58.456 33.333 0.00 0.00 0.00 3.01
3827 8137 8.925700 GGAACCAAAAACATAAATCAAGATGAC 58.074 33.333 0.00 0.00 0.00 3.06
3845 8155 3.697619 AAAACCAAAACCGGAACCAAA 57.302 38.095 9.46 0.00 0.00 3.28
3937 8247 9.747898 TTGAAATAGTCACTTATATTTGGTGGT 57.252 29.630 0.00 0.00 35.39 4.16
4038 8735 8.194769 GTGTTTCCCTTCTGAAGAAAAATACAA 58.805 33.333 23.22 10.43 33.07 2.41
4044 8741 4.266714 ACGTGTTTCCCTTCTGAAGAAAA 58.733 39.130 18.68 14.40 33.07 2.29
4046 8743 3.118555 TGACGTGTTTCCCTTCTGAAGAA 60.119 43.478 18.68 3.61 0.00 2.52
4048 8745 2.833794 TGACGTGTTTCCCTTCTGAAG 58.166 47.619 10.46 10.46 0.00 3.02
4094 9274 2.467838 CGGAGAGTAGTGATGCATGTG 58.532 52.381 2.46 0.00 0.00 3.21
4112 9292 7.043059 TGCATAAAGTTGAAAAAGTTAAAGCGG 60.043 33.333 0.00 0.00 0.00 5.52
4114 9294 7.793888 GCTGCATAAAGTTGAAAAAGTTAAAGC 59.206 33.333 0.00 0.00 0.00 3.51
4122 9302 5.163468 TGGTCAGCTGCATAAAGTTGAAAAA 60.163 36.000 9.47 0.00 38.85 1.94
4139 9319 5.703876 CTTAGGAAGAAAAATGTGGTCAGC 58.296 41.667 0.00 0.00 0.00 4.26
4146 9326 3.506067 CGGGTGCTTAGGAAGAAAAATGT 59.494 43.478 0.00 0.00 0.00 2.71
4206 9387 5.914033 TGTAGGATCGGGTATCAAGAAAAG 58.086 41.667 0.00 0.00 36.20 2.27
4212 9393 2.301870 GCCATGTAGGATCGGGTATCAA 59.698 50.000 0.00 0.00 41.22 2.57
4214 9395 2.180276 AGCCATGTAGGATCGGGTATC 58.820 52.381 0.00 0.00 41.22 2.24
4218 9399 1.336887 CGTAAGCCATGTAGGATCGGG 60.337 57.143 0.00 0.00 41.22 5.14
4220 9401 1.336887 CCCGTAAGCCATGTAGGATCG 60.337 57.143 0.00 0.00 41.22 3.69
4232 9413 0.685097 TAGGATGATGCCCCGTAAGC 59.315 55.000 0.00 0.00 0.00 3.09
4295 9629 3.891366 GCATTTAGTTATGGGAGCCATGT 59.109 43.478 0.00 0.00 44.84 3.21
4296 9630 3.256631 GGCATTTAGTTATGGGAGCCATG 59.743 47.826 0.00 0.00 44.84 3.66
4297 9631 3.500343 GGCATTTAGTTATGGGAGCCAT 58.500 45.455 0.00 0.00 46.99 4.40
4401 9950 5.296780 CAGTCAGACTGCTTGGTTTTCTTAA 59.703 40.000 17.77 0.00 39.62 1.85
4404 9953 3.209410 CAGTCAGACTGCTTGGTTTTCT 58.791 45.455 17.77 0.00 39.62 2.52
4405 9954 2.291741 CCAGTCAGACTGCTTGGTTTTC 59.708 50.000 23.46 0.00 44.63 2.29
4434 9983 2.132762 GGTTCAAGTGGTGTGTAGTCG 58.867 52.381 0.00 0.00 0.00 4.18
4448 9997 0.690192 TGATGCTTCGGGAGGTTCAA 59.310 50.000 0.00 0.00 0.00 2.69
4463 10012 3.509575 GCTGGTAGATCTAGTCCCTGATG 59.490 52.174 15.05 4.02 0.00 3.07
4470 10019 4.402793 TCCTTTGTGCTGGTAGATCTAGTC 59.597 45.833 1.64 0.00 0.00 2.59
4489 10041 1.826385 CAGGCGATTTCCTGTTCCTT 58.174 50.000 1.80 0.00 46.59 3.36
4557 10115 3.044156 TCTCCCTCATCTTTGCAGCTAT 58.956 45.455 0.00 0.00 0.00 2.97
4615 10929 0.537143 TGGCATCAAGTGACCACACC 60.537 55.000 2.78 0.00 46.99 4.16
4652 10966 3.388308 CGGAGAGGCTAATTCATCTGTG 58.612 50.000 0.00 0.00 0.00 3.66
4680 10994 4.098960 CCATGGATGAATTGAAAGGGACAG 59.901 45.833 5.56 0.00 0.00 3.51
4693 11007 2.234586 GGAGGAGCCCATGGATGAA 58.765 57.895 15.22 0.00 0.00 2.57
4694 11008 3.992406 GGAGGAGCCCATGGATGA 58.008 61.111 15.22 0.00 0.00 2.92
4789 13107 1.198408 CAACACTGCATCTGCGTGAAT 59.802 47.619 23.72 14.19 45.83 2.57
4822 13176 8.301002 ACGTTTGTTTGTTGCATATATAAACCT 58.699 29.630 6.74 0.00 31.96 3.50
4823 13177 8.369588 CACGTTTGTTTGTTGCATATATAAACC 58.630 33.333 6.74 0.00 31.96 3.27
4824 13178 7.890717 GCACGTTTGTTTGTTGCATATATAAAC 59.109 33.333 3.14 3.14 33.20 2.01
4826 13180 6.249471 CGCACGTTTGTTTGTTGCATATATAA 59.751 34.615 0.00 0.00 0.00 0.98
4828 13182 4.556912 CGCACGTTTGTTTGTTGCATATAT 59.443 37.500 0.00 0.00 0.00 0.86
4829 13183 3.908978 CGCACGTTTGTTTGTTGCATATA 59.091 39.130 0.00 0.00 0.00 0.86
4830 13184 2.723658 CGCACGTTTGTTTGTTGCATAT 59.276 40.909 0.00 0.00 0.00 1.78
4831 13185 2.112522 CGCACGTTTGTTTGTTGCATA 58.887 42.857 0.00 0.00 0.00 3.14
4892 13303 5.354234 CGTGGGAGGTGCAAATATATATTCC 59.646 44.000 8.42 5.75 0.00 3.01
4894 13305 4.700213 GCGTGGGAGGTGCAAATATATATT 59.300 41.667 1.91 1.91 0.00 1.28
4903 13314 3.884774 AAGGCGTGGGAGGTGCAA 61.885 61.111 0.00 0.00 0.00 4.08
4917 13369 2.045045 TTGATGCCGAGGCCAAGG 60.045 61.111 12.05 9.14 41.09 3.61
4930 13382 0.241749 TACGACGCGTCAACCTTGAT 59.758 50.000 35.71 14.10 41.54 2.57
4933 13385 1.787012 ATTTACGACGCGTCAACCTT 58.213 45.000 35.71 16.42 41.54 3.50
4934 13386 1.458064 CAATTTACGACGCGTCAACCT 59.542 47.619 35.71 18.37 41.54 3.50
4935 13387 1.456544 TCAATTTACGACGCGTCAACC 59.543 47.619 35.71 12.83 41.54 3.77
4936 13388 2.097299 TGTCAATTTACGACGCGTCAAC 60.097 45.455 35.71 19.65 41.54 3.18
4937 13389 2.125685 TGTCAATTTACGACGCGTCAA 58.874 42.857 35.71 23.99 41.54 3.18
4939 13391 2.154389 ACTTGTCAATTTACGACGCGTC 59.846 45.455 28.96 28.96 41.54 5.19
4940 13392 2.129607 ACTTGTCAATTTACGACGCGT 58.870 42.857 13.85 13.85 44.35 6.01
4941 13393 2.743172 GACTTGTCAATTTACGACGCG 58.257 47.619 3.53 3.53 36.11 6.01


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

AutoCloner maintained by Alex Coulton.