Multiple sequence alignment - TraesCS3A01G185400

Loading Multiple Alignment...

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 TraesCS3A01G185400 chr3A 100.000 4586 0 0 1 4586 217816489 217821074 0.000000e+00 8469.0
1 TraesCS3A01G185400 chr3B 95.087 1669 55 6 2443 4094 256196056 256197714 0.000000e+00 2603.0
2 TraesCS3A01G185400 chr3B 94.701 1170 29 5 903 2050 256188891 256190049 0.000000e+00 1786.0
3 TraesCS3A01G185400 chr3B 95.418 502 19 2 4086 4583 256199061 256199562 0.000000e+00 797.0
4 TraesCS3A01G185400 chr3B 97.633 338 8 0 2046 2383 256195724 256196061 8.550000e-162 580.0
5 TraesCS3A01G185400 chr3D 95.282 1611 49 11 785 2383 177040376 177041971 0.000000e+00 2529.0
6 TraesCS3A01G185400 chr3D 94.368 1669 47 13 2443 4083 177041966 177043615 0.000000e+00 2518.0
7 TraesCS3A01G185400 chr3D 91.523 755 58 5 34 785 177039574 177040325 0.000000e+00 1035.0
8 TraesCS3A01G185400 chr3D 96.457 508 18 0 4079 4586 177057344 177057851 0.000000e+00 839.0
9 TraesCS3A01G185400 chr3D 81.769 373 43 13 2030 2383 604538797 604538431 5.810000e-74 289.0
10 TraesCS3A01G185400 chr3D 84.892 139 20 1 2245 2383 87735195 87735058 6.190000e-29 139.0
11 TraesCS3A01G185400 chr3D 92.958 71 2 3 2374 2443 2253297 2253365 2.920000e-17 100.0
12 TraesCS3A01G185400 chr3D 92.754 69 2 3 2379 2446 441190902 441190836 3.780000e-16 97.1
13 TraesCS3A01G185400 chr4B 84.772 394 48 8 1993 2383 9670291 9669907 7.200000e-103 385.0
14 TraesCS3A01G185400 chrUn 83.455 411 44 10 1991 2383 306222555 306222151 1.210000e-95 361.0
15 TraesCS3A01G185400 chr7D 84.184 392 41 12 1992 2383 5162976 5162606 1.210000e-95 361.0
16 TraesCS3A01G185400 chr7D 82.767 412 47 10 1990 2383 601899411 601899816 3.400000e-91 346.0
17 TraesCS3A01G185400 chr2D 82.767 412 44 12 1991 2383 329946888 329946485 4.390000e-90 342.0
18 TraesCS3A01G185400 chr1B 91.765 85 7 0 3650 3734 56061711 56061795 8.060000e-23 119.0
19 TraesCS3A01G185400 chr1B 94.030 67 3 1 2378 2443 122964607 122964541 2.920000e-17 100.0
20 TraesCS3A01G185400 chr4A 90.476 84 8 0 3650 3733 697388796 697388879 1.350000e-20 111.0
21 TraesCS3A01G185400 chr4A 87.912 91 11 0 3656 3746 662286415 662286505 1.740000e-19 108.0
22 TraesCS3A01G185400 chr4A 94.030 67 1 3 2377 2443 352509925 352509862 1.050000e-16 99.0
23 TraesCS3A01G185400 chr2B 89.535 86 9 0 3659 3744 247368538 247368623 4.850000e-20 110.0
24 TraesCS3A01G185400 chr2B 91.139 79 7 0 3658 3736 247368623 247368545 1.740000e-19 108.0
25 TraesCS3A01G185400 chr5D 98.387 62 0 1 2374 2434 58683248 58683187 1.740000e-19 108.0
26 TraesCS3A01G185400 chr5D 88.372 86 10 0 3659 3744 421531409 421531324 2.260000e-18 104.0
27 TraesCS3A01G185400 chr5D 96.774 62 0 2 2382 2443 24091178 24091119 8.120000e-18 102.0
28 TraesCS3A01G185400 chr5A 88.764 89 8 1 3657 3745 3397703 3397789 1.740000e-19 108.0
29 TraesCS3A01G185400 chr1D 96.825 63 1 1 2378 2440 128509172 128509233 2.260000e-18 104.0
30 TraesCS3A01G185400 chr1D 98.305 59 1 0 2382 2440 149688474 149688532 2.260000e-18 104.0
31 TraesCS3A01G185400 chr7A 92.857 70 1 4 2376 2443 402046978 402046911 1.050000e-16 99.0


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 TraesCS3A01G185400 chr3A 217816489 217821074 4585 False 8469.000000 8469 100.000000 1 4586 1 chr3A.!!$F1 4585
1 TraesCS3A01G185400 chr3B 256188891 256190049 1158 False 1786.000000 1786 94.701000 903 2050 1 chr3B.!!$F1 1147
2 TraesCS3A01G185400 chr3B 256195724 256199562 3838 False 1326.666667 2603 96.046000 2046 4583 3 chr3B.!!$F2 2537
3 TraesCS3A01G185400 chr3D 177039574 177043615 4041 False 2027.333333 2529 93.724333 34 4083 3 chr3D.!!$F3 4049
4 TraesCS3A01G185400 chr3D 177057344 177057851 507 False 839.000000 839 96.457000 4079 4586 1 chr3D.!!$F2 507

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
193 195 0.106335 TTACGACGCCTTCACCCAAA 59.894 50.0 0.0 0.0 0.00 3.28 F
541 544 0.257039 CCTGGAGTAAGCCATTGCCT 59.743 55.0 0.0 0.0 37.30 4.75 F
824 879 0.469331 ATCGGTATCCTTCGGGCTGA 60.469 55.0 0.0 0.0 34.44 4.26 F
2444 2544 0.609131 CCCGAGCCACAAACATCCTT 60.609 55.0 0.0 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 1778 2.151202 CCAGCAACGGTTACTGAACAT 58.849 47.619 20.10 0.0 37.29 2.71 R
2425 2525 0.609131 AAGGATGTTTGTGGCTCGGG 60.609 55.000 0.00 0.0 0.00 5.14 R
2667 2767 0.316442 CAATGATCGGCGCACATGAC 60.316 55.000 10.83 0.0 0.00 3.06 R
4313 5798 0.924090 GCGTCGATCTAAGCAAGGTG 59.076 55.000 0.00 0.0 0.00 4.00 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 4.494811 CGTGTCTTGCGAGGCATA 57.505 55.556 12.35 0.00 40.15 3.14
18 19 2.749541 CGTGTCTTGCGAGGCATAA 58.250 52.632 12.35 0.00 40.15 1.90
19 20 1.290203 CGTGTCTTGCGAGGCATAAT 58.710 50.000 12.35 0.00 40.15 1.28
20 21 2.469826 CGTGTCTTGCGAGGCATAATA 58.530 47.619 12.35 0.00 40.15 0.98
21 22 2.218759 CGTGTCTTGCGAGGCATAATAC 59.781 50.000 12.35 0.00 40.15 1.89
22 23 2.544267 GTGTCTTGCGAGGCATAATACC 59.456 50.000 12.35 0.00 40.15 2.73
23 24 1.792949 GTCTTGCGAGGCATAATACCG 59.207 52.381 0.00 0.00 38.76 4.02
24 25 1.148310 CTTGCGAGGCATAATACCGG 58.852 55.000 0.00 0.00 38.76 5.28
25 26 0.753867 TTGCGAGGCATAATACCGGA 59.246 50.000 9.46 0.00 38.76 5.14
26 27 0.973632 TGCGAGGCATAATACCGGAT 59.026 50.000 9.46 0.00 31.71 4.18
27 28 1.337728 TGCGAGGCATAATACCGGATG 60.338 52.381 9.46 1.59 31.71 3.51
28 29 1.067142 GCGAGGCATAATACCGGATGA 60.067 52.381 9.46 0.00 0.00 2.92
29 30 2.611971 GCGAGGCATAATACCGGATGAA 60.612 50.000 9.46 0.00 0.00 2.57
30 31 3.861840 CGAGGCATAATACCGGATGAAT 58.138 45.455 9.46 0.00 0.00 2.57
31 32 3.618594 CGAGGCATAATACCGGATGAATG 59.381 47.826 9.46 7.86 0.00 2.67
32 33 3.347216 AGGCATAATACCGGATGAATGC 58.653 45.455 9.46 17.29 37.17 3.56
37 38 3.845781 AATACCGGATGAATGCACTCT 57.154 42.857 9.46 0.00 0.00 3.24
89 90 2.115595 TGCAAAATTTGTCAAGCGACG 58.884 42.857 7.60 0.00 45.80 5.12
91 92 2.856720 GCAAAATTTGTCAAGCGACGGA 60.857 45.455 7.60 0.00 45.80 4.69
111 113 4.002316 GGATGAGGATTTAGAGCATGCTC 58.998 47.826 35.57 35.57 43.03 4.26
131 133 5.471116 TGCTCTTATTCATTATTCGCATGCT 59.529 36.000 17.13 0.00 0.00 3.79
132 134 5.793952 GCTCTTATTCATTATTCGCATGCTG 59.206 40.000 17.13 9.63 0.00 4.41
147 149 1.691196 TGCTGAGTGTTTTTGGGAGG 58.309 50.000 0.00 0.00 0.00 4.30
154 156 0.469144 TGTTTTTGGGAGGAGGCACC 60.469 55.000 0.00 0.00 39.35 5.01
178 180 8.836413 ACCTATGTTGATGGACATAAAATTACG 58.164 33.333 0.00 0.00 40.80 3.18
185 187 4.255301 TGGACATAAAATTACGACGCCTT 58.745 39.130 0.00 0.00 0.00 4.35
193 195 0.106335 TTACGACGCCTTCACCCAAA 59.894 50.000 0.00 0.00 0.00 3.28
217 219 2.099141 TGGGCGAGAGACATTTCTTG 57.901 50.000 0.00 0.00 45.40 3.02
246 248 6.966632 TCACATGTTTTCAAAAGAAGAACGAG 59.033 34.615 0.00 0.00 0.00 4.18
252 254 4.330944 TCAAAAGAAGAACGAGCCACTA 57.669 40.909 0.00 0.00 0.00 2.74
257 259 4.744795 AGAAGAACGAGCCACTATCATT 57.255 40.909 0.00 0.00 0.00 2.57
258 260 5.854010 AGAAGAACGAGCCACTATCATTA 57.146 39.130 0.00 0.00 0.00 1.90
259 261 5.593010 AGAAGAACGAGCCACTATCATTAC 58.407 41.667 0.00 0.00 0.00 1.89
260 262 3.966154 AGAACGAGCCACTATCATTACG 58.034 45.455 0.00 0.00 0.00 3.18
266 268 3.990469 GAGCCACTATCATTACGGTGATG 59.010 47.826 6.56 6.56 39.13 3.07
277 279 5.540719 TCATTACGGTGATGTGGTCCATATA 59.459 40.000 11.98 0.00 32.56 0.86
286 288 2.038426 TGTGGTCCATATAGCATTCCCG 59.962 50.000 0.00 0.00 0.00 5.14
317 319 4.977739 TGGACCCATGATAAGGAGAAGATT 59.022 41.667 0.00 0.00 0.00 2.40
336 338 6.150396 AGATTGACCCGATAAAGTCTGTAG 57.850 41.667 0.00 0.00 34.02 2.74
342 344 4.960469 ACCCGATAAAGTCTGTAGGATTGA 59.040 41.667 0.00 0.00 0.00 2.57
352 354 5.777732 AGTCTGTAGGATTGACAAGAGAAGT 59.222 40.000 0.00 0.00 33.56 3.01
377 379 3.964688 TGGCTCTTTTGGATATACCTCGA 59.035 43.478 0.00 0.00 39.86 4.04
378 380 4.202223 TGGCTCTTTTGGATATACCTCGAC 60.202 45.833 0.00 0.00 39.86 4.20
430 432 1.302511 GCCCGCCCGAACATGATAT 60.303 57.895 0.00 0.00 0.00 1.63
470 472 9.593565 ACTGATATAACTATTGACAGAGATGGA 57.406 33.333 0.00 0.00 0.00 3.41
476 479 4.648762 ACTATTGACAGAGATGGAGTCTGG 59.351 45.833 5.18 0.00 44.96 3.86
477 480 2.907458 TGACAGAGATGGAGTCTGGA 57.093 50.000 5.18 0.00 44.96 3.86
485 488 0.994247 ATGGAGTCTGGATGGTGCAA 59.006 50.000 0.00 0.00 0.00 4.08
511 514 2.836154 GCCAGGTCCCACAACTCA 59.164 61.111 0.00 0.00 0.00 3.41
538 541 1.673168 GAGCCTGGAGTAAGCCATTG 58.327 55.000 0.00 0.00 37.30 2.82
541 544 0.257039 CCTGGAGTAAGCCATTGCCT 59.743 55.000 0.00 0.00 37.30 4.75
543 546 0.991146 TGGAGTAAGCCATTGCCTGA 59.009 50.000 0.00 0.00 38.69 3.86
551 554 2.806434 AGCCATTGCCTGATGTTACAA 58.194 42.857 0.00 0.00 38.69 2.41
564 567 6.016777 CCTGATGTTACAAATCCCTTGATAGC 60.017 42.308 0.00 0.00 38.50 2.97
616 619 1.442769 TTGCAGCACTTCGAGGATTC 58.557 50.000 0.00 0.00 0.00 2.52
630 633 3.058914 CGAGGATTCAACAAAGTGGTCAC 60.059 47.826 0.00 0.00 0.00 3.67
644 647 3.514777 GTCACTGAGACCGATTGCA 57.485 52.632 0.00 0.00 41.56 4.08
649 652 1.278985 ACTGAGACCGATTGCATGGAA 59.721 47.619 0.79 0.79 0.00 3.53
661 664 1.702401 TGCATGGAAGTGGTGAACCTA 59.298 47.619 0.37 0.00 36.82 3.08
663 666 3.521531 TGCATGGAAGTGGTGAACCTATA 59.478 43.478 0.37 0.00 36.82 1.31
672 675 5.235516 AGTGGTGAACCTATAAAACACTCG 58.764 41.667 0.37 0.00 33.04 4.18
673 676 4.992951 GTGGTGAACCTATAAAACACTCGT 59.007 41.667 0.37 0.00 36.82 4.18
700 703 2.425312 CTCTCGTTCAGTAGTGGCATCT 59.575 50.000 0.00 0.00 0.00 2.90
713 717 8.514594 CAGTAGTGGCATCTATTTTTCAGAAAA 58.485 33.333 4.06 4.06 38.96 2.29
745 749 9.243105 AGCTAGCCAATAGTTTTGATTTCTTTA 57.757 29.630 12.13 0.00 33.65 1.85
785 789 4.039092 AGCCAATGGTCCAGCGCT 62.039 61.111 2.64 2.64 0.00 5.92
786 790 3.818787 GCCAATGGTCCAGCGCTG 61.819 66.667 30.52 30.52 0.00 5.18
804 859 2.159114 GCTGGAGACTCTTAGCTTCCTG 60.159 54.545 18.78 0.00 33.53 3.86
806 861 3.960102 CTGGAGACTCTTAGCTTCCTGAT 59.040 47.826 1.74 0.00 0.00 2.90
808 863 3.004315 GGAGACTCTTAGCTTCCTGATCG 59.996 52.174 1.74 0.00 0.00 3.69
812 867 4.475345 ACTCTTAGCTTCCTGATCGGTAT 58.525 43.478 0.00 0.00 0.00 2.73
818 873 2.608261 GCTTCCTGATCGGTATCCTTCG 60.608 54.545 0.00 0.00 0.00 3.79
824 879 0.469331 ATCGGTATCCTTCGGGCTGA 60.469 55.000 0.00 0.00 34.44 4.26
843 898 1.541588 GATTGCTCAGCGAACCCTTTT 59.458 47.619 0.00 0.00 0.00 2.27
847 902 1.335051 GCTCAGCGAACCCTTTTGTTC 60.335 52.381 0.00 0.00 40.96 3.18
862 917 6.127897 CCCTTTTGTTCGAATAAAGCTCTCAT 60.128 38.462 17.75 0.00 0.00 2.90
868 923 9.988350 TTGTTCGAATAAAGCTCTCATAATTTC 57.012 29.630 4.71 0.00 0.00 2.17
872 927 8.204160 TCGAATAAAGCTCTCATAATTTCCTGA 58.796 33.333 0.00 0.00 0.00 3.86
1190 1283 1.821061 CGTGTCTTGCTCCCTCCTGT 61.821 60.000 0.00 0.00 0.00 4.00
1443 1542 1.218875 CGCGTTGACAGGTGTGCTTA 61.219 55.000 0.00 0.00 0.00 3.09
1593 1692 2.124736 CCAGGTATGGGCACACCG 60.125 66.667 0.00 0.00 43.54 4.94
1594 1693 2.824041 CAGGTATGGGCACACCGC 60.824 66.667 0.00 0.00 44.64 5.68
1595 1694 3.326578 AGGTATGGGCACACCGCA 61.327 61.111 0.00 0.00 45.17 5.69
1709 1809 0.946221 CCGTTGCTGGTGTCTGACTC 60.946 60.000 9.51 5.31 0.00 3.36
1731 1831 6.772716 ACTCTGATATTGTGGTGTCTTTGTTT 59.227 34.615 0.00 0.00 0.00 2.83
1750 1850 2.928801 TTCTTGCAGGAACTACAGCA 57.071 45.000 7.24 0.00 36.02 4.41
1759 1859 5.709631 TGCAGGAACTACAGCATTTATTGAA 59.290 36.000 0.00 0.00 36.02 2.69
2101 2201 5.931441 AAGCAGTGTGATCTAGTTCAAAC 57.069 39.130 14.09 14.09 34.59 2.93
2108 2208 6.926272 AGTGTGATCTAGTTCAAACTCAGTTC 59.074 38.462 17.56 0.00 39.50 3.01
2208 2308 4.381411 GTTCTGTTAGTGACTTCTTGCCT 58.619 43.478 0.00 0.00 0.00 4.75
2216 2316 4.273318 AGTGACTTCTTGCCTTCTGTTTT 58.727 39.130 0.00 0.00 0.00 2.43
2384 2484 9.597170 CCTAAGGTTTGTTACTCTTCTTATACC 57.403 37.037 0.00 0.00 0.00 2.73
2385 2485 9.298774 CTAAGGTTTGTTACTCTTCTTATACCG 57.701 37.037 0.00 0.00 0.00 4.02
2386 2486 7.472334 AGGTTTGTTACTCTTCTTATACCGA 57.528 36.000 0.00 0.00 0.00 4.69
2387 2487 7.899973 AGGTTTGTTACTCTTCTTATACCGAA 58.100 34.615 0.00 0.00 0.00 4.30
2388 2488 8.370182 AGGTTTGTTACTCTTCTTATACCGAAA 58.630 33.333 0.00 0.00 0.00 3.46
2389 2489 8.992073 GGTTTGTTACTCTTCTTATACCGAAAA 58.008 33.333 0.00 0.00 0.00 2.29
2392 2492 8.767478 TGTTACTCTTCTTATACCGAAAAAGG 57.233 34.615 0.00 0.00 37.30 3.11
2393 2493 7.332678 TGTTACTCTTCTTATACCGAAAAAGGC 59.667 37.037 0.00 0.00 33.69 4.35
2394 2494 6.051179 ACTCTTCTTATACCGAAAAAGGCT 57.949 37.500 0.00 0.00 33.69 4.58
2395 2495 6.473758 ACTCTTCTTATACCGAAAAAGGCTT 58.526 36.000 0.00 0.00 33.69 4.35
2396 2496 6.940867 ACTCTTCTTATACCGAAAAAGGCTTT 59.059 34.615 6.68 6.68 33.69 3.51
2397 2497 7.119407 ACTCTTCTTATACCGAAAAAGGCTTTC 59.881 37.037 13.76 0.41 33.69 2.62
2399 2499 2.913777 ATACCGAAAAAGGCTTTCGC 57.086 45.000 13.76 7.41 46.89 4.70
2409 2509 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
2410 2510 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
2411 2511 1.235724 GCTTTCGCCCCGCTTTATAT 58.764 50.000 0.00 0.00 0.00 0.86
2412 2512 2.419667 GCTTTCGCCCCGCTTTATATA 58.580 47.619 0.00 0.00 0.00 0.86
2413 2513 3.007635 GCTTTCGCCCCGCTTTATATAT 58.992 45.455 0.00 0.00 0.00 0.86
2414 2514 4.186159 GCTTTCGCCCCGCTTTATATATA 58.814 43.478 0.00 0.00 0.00 0.86
2415 2515 4.632688 GCTTTCGCCCCGCTTTATATATAA 59.367 41.667 0.81 0.81 0.00 0.98
2416 2516 5.122711 GCTTTCGCCCCGCTTTATATATAAA 59.877 40.000 15.47 15.47 0.00 1.40
2428 2528 5.866335 TTATATATAAAGCAAACCGCCCG 57.134 39.130 2.56 0.00 44.04 6.13
2429 2529 2.335316 ATATAAAGCAAACCGCCCGA 57.665 45.000 0.00 0.00 44.04 5.14
2430 2530 1.658994 TATAAAGCAAACCGCCCGAG 58.341 50.000 0.00 0.00 44.04 4.63
2431 2531 1.654023 ATAAAGCAAACCGCCCGAGC 61.654 55.000 0.00 0.00 44.04 5.03
2436 2536 4.572571 AAACCGCCCGAGCCACAA 62.573 61.111 0.00 0.00 34.57 3.33
2437 2537 4.572571 AACCGCCCGAGCCACAAA 62.573 61.111 0.00 0.00 34.57 2.83
2440 2540 3.055719 CGCCCGAGCCACAAACAT 61.056 61.111 0.00 0.00 34.57 2.71
2441 2541 2.877691 GCCCGAGCCACAAACATC 59.122 61.111 0.00 0.00 0.00 3.06
2442 2542 2.700773 GCCCGAGCCACAAACATCC 61.701 63.158 0.00 0.00 0.00 3.51
2443 2543 1.002134 CCCGAGCCACAAACATCCT 60.002 57.895 0.00 0.00 0.00 3.24
2444 2544 0.609131 CCCGAGCCACAAACATCCTT 60.609 55.000 0.00 0.00 0.00 3.36
2445 2545 1.339631 CCCGAGCCACAAACATCCTTA 60.340 52.381 0.00 0.00 0.00 2.69
2446 2546 2.643551 CCGAGCCACAAACATCCTTAT 58.356 47.619 0.00 0.00 0.00 1.73
2447 2547 3.433031 CCCGAGCCACAAACATCCTTATA 60.433 47.826 0.00 0.00 0.00 0.98
2448 2548 4.389374 CCGAGCCACAAACATCCTTATAT 58.611 43.478 0.00 0.00 0.00 0.86
2449 2549 4.214119 CCGAGCCACAAACATCCTTATATG 59.786 45.833 0.00 0.00 0.00 1.78
2450 2550 4.319766 CGAGCCACAAACATCCTTATATGC 60.320 45.833 0.00 0.00 0.00 3.14
2451 2551 3.891366 AGCCACAAACATCCTTATATGCC 59.109 43.478 0.00 0.00 0.00 4.40
2452 2552 3.891366 GCCACAAACATCCTTATATGCCT 59.109 43.478 0.00 0.00 0.00 4.75
2540 2640 4.405116 TGGCATTTCAATAAAGATGCCC 57.595 40.909 19.93 6.31 44.74 5.36
2543 2643 5.104444 TGGCATTTCAATAAAGATGCCCAAT 60.104 36.000 19.93 0.00 44.74 3.16
2666 2766 3.033764 CGTGTCGGTGGGTTCGTG 61.034 66.667 0.00 0.00 0.00 4.35
2667 2767 2.663852 GTGTCGGTGGGTTCGTGG 60.664 66.667 0.00 0.00 0.00 4.94
2702 2802 0.329596 ATTGCAACCCAGGAGACCTC 59.670 55.000 0.00 0.00 0.00 3.85
2771 2872 3.084786 GAGTGAAGAAATCTGGGTTGGG 58.915 50.000 0.00 0.00 0.00 4.12
2807 2908 2.174854 GGATTAGGTTGGGGTGCTATGT 59.825 50.000 0.00 0.00 0.00 2.29
2818 2919 3.181450 GGGGTGCTATGTTCTAAGCTGAT 60.181 47.826 0.00 0.00 39.53 2.90
2845 2946 7.148188 GGCAGTAATGAATCAAATCTGAGTTCA 60.148 37.037 13.11 0.00 35.48 3.18
2977 3078 9.214957 CTAATTGTAGACTTAACATGACACCAA 57.785 33.333 0.00 0.00 0.00 3.67
3049 3163 1.473278 CCCTTCTACGTCTGTCAGGAC 59.527 57.143 0.00 0.00 0.00 3.85
3152 3266 7.831753 TCTTACAATTTTCCAAGTCACAACAA 58.168 30.769 0.00 0.00 0.00 2.83
3272 3386 5.798132 TGATGTGCTCTCTGTGTATTTCTT 58.202 37.500 0.00 0.00 0.00 2.52
3315 3429 7.192913 CACTGAGCAAACAAACTAATTACACA 58.807 34.615 0.00 0.00 0.00 3.72
3316 3430 7.862372 CACTGAGCAAACAAACTAATTACACAT 59.138 33.333 0.00 0.00 0.00 3.21
3317 3431 9.062524 ACTGAGCAAACAAACTAATTACACATA 57.937 29.630 0.00 0.00 0.00 2.29
3321 3435 9.554724 AGCAAACAAACTAATTACACATATTCG 57.445 29.630 0.00 0.00 0.00 3.34
3322 3436 8.794406 GCAAACAAACTAATTACACATATTCGG 58.206 33.333 0.00 0.00 0.00 4.30
3336 3450 6.267699 ACACATATTCGGATATTCCTCACAGA 59.732 38.462 0.00 0.00 33.30 3.41
3398 3512 4.654091 ATTTAATTGAATGACCCGCTGG 57.346 40.909 0.00 0.00 37.80 4.85
3420 3534 5.462068 TGGAAAATGAGTAGATGATAACGCG 59.538 40.000 3.53 3.53 0.00 6.01
3562 3679 3.709987 CTGAAGCAAGAAACCAACTTGG 58.290 45.455 6.24 6.24 43.12 3.61
3721 3838 8.609478 TCAAATTGAAGTACAAAAACGTCTTC 57.391 30.769 0.00 4.45 42.03 2.87
3740 3857 8.308931 ACGTCTTCTATTTTGGTACAGATGTAA 58.691 33.333 0.00 0.00 42.39 2.41
3991 4108 2.416202 ACACGTCATATGCATGTGTGTG 59.584 45.455 30.16 30.16 44.00 3.82
4041 4167 6.544931 CAGCTGAATTATCCAGGAGAAATGAA 59.455 38.462 8.42 0.00 32.51 2.57
4044 4170 7.067981 GCTGAATTATCCAGGAGAAATGAAAGT 59.932 37.037 0.00 0.00 32.51 2.66
4050 4176 3.192212 CCAGGAGAAATGAAAGTGGCTTC 59.808 47.826 0.00 0.00 0.00 3.86
4134 5616 9.249457 CTGTATTGGTACTGTACATGTATCTTG 57.751 37.037 18.79 2.76 31.16 3.02
4178 5663 4.343811 CGATAAACGGGCACAACATTAA 57.656 40.909 0.00 0.00 38.46 1.40
4224 5709 1.836166 AGCAGCCTCATAGCTTTGAGA 59.164 47.619 29.16 6.37 44.88 3.27
4309 5794 2.184322 GATGAACTCGCCGGCTGA 59.816 61.111 26.68 21.48 0.00 4.26
4313 5798 1.590259 GAACTCGCCGGCTGAGATC 60.590 63.158 37.37 32.68 36.93 2.75
4403 5888 1.039233 CATTCCCTGATGCGCCCTTT 61.039 55.000 4.18 0.00 0.00 3.11
4500 5985 4.967036 TGGTTGATCACATACAAGTGTCA 58.033 39.130 0.00 0.00 40.37 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.290203 ATTATGCCTCGCAAGACACG 58.710 50.000 0.00 0.00 43.62 4.49
1 2 2.544267 GGTATTATGCCTCGCAAGACAC 59.456 50.000 0.00 0.00 43.62 3.67
2 3 2.801699 CGGTATTATGCCTCGCAAGACA 60.802 50.000 0.00 0.00 43.62 3.41
3 4 1.792949 CGGTATTATGCCTCGCAAGAC 59.207 52.381 0.00 0.00 43.62 3.01
4 5 1.270094 CCGGTATTATGCCTCGCAAGA 60.270 52.381 0.00 0.00 43.62 3.02
5 6 1.148310 CCGGTATTATGCCTCGCAAG 58.852 55.000 0.00 0.00 43.62 4.01
6 7 0.753867 TCCGGTATTATGCCTCGCAA 59.246 50.000 0.00 0.00 43.62 4.85
7 8 0.973632 ATCCGGTATTATGCCTCGCA 59.026 50.000 0.00 0.00 44.86 5.10
8 9 1.067142 TCATCCGGTATTATGCCTCGC 60.067 52.381 0.00 0.00 0.00 5.03
9 10 3.313012 TTCATCCGGTATTATGCCTCG 57.687 47.619 0.00 0.00 0.00 4.63
10 11 3.375299 GCATTCATCCGGTATTATGCCTC 59.625 47.826 17.51 0.00 33.96 4.70
11 12 3.244875 TGCATTCATCCGGTATTATGCCT 60.245 43.478 22.13 2.15 38.02 4.75
12 13 3.081061 TGCATTCATCCGGTATTATGCC 58.919 45.455 22.13 11.31 38.02 4.40
13 14 3.753272 AGTGCATTCATCCGGTATTATGC 59.247 43.478 19.88 19.88 38.97 3.14
14 15 5.240891 AGAGTGCATTCATCCGGTATTATG 58.759 41.667 12.16 0.00 0.00 1.90
15 16 5.489792 AGAGTGCATTCATCCGGTATTAT 57.510 39.130 12.16 0.00 0.00 1.28
16 17 4.955811 AGAGTGCATTCATCCGGTATTA 57.044 40.909 12.16 0.00 0.00 0.98
17 18 3.845781 AGAGTGCATTCATCCGGTATT 57.154 42.857 12.16 0.00 0.00 1.89
18 19 4.588951 TCTTAGAGTGCATTCATCCGGTAT 59.411 41.667 12.16 0.00 0.00 2.73
19 20 3.958147 TCTTAGAGTGCATTCATCCGGTA 59.042 43.478 12.16 0.00 0.00 4.02
20 21 2.766263 TCTTAGAGTGCATTCATCCGGT 59.234 45.455 12.16 0.00 0.00 5.28
21 22 3.459232 TCTTAGAGTGCATTCATCCGG 57.541 47.619 12.16 0.00 0.00 5.14
22 23 6.018589 TCTATCTTAGAGTGCATTCATCCG 57.981 41.667 12.16 0.00 0.00 4.18
37 38 7.277405 TCCTCTCTGATATGCCTCTATCTTA 57.723 40.000 0.00 0.00 0.00 2.10
89 90 4.002316 GAGCATGCTCTAAATCCTCATCC 58.998 47.826 35.26 8.85 39.80 3.51
111 113 6.795593 CACTCAGCATGCGAATAATGAATAAG 59.204 38.462 13.01 0.36 34.76 1.73
131 133 1.478654 GCCTCCTCCCAAAAACACTCA 60.479 52.381 0.00 0.00 0.00 3.41
132 134 1.248486 GCCTCCTCCCAAAAACACTC 58.752 55.000 0.00 0.00 0.00 3.51
147 149 2.092968 TGTCCATCAACATAGGTGCCTC 60.093 50.000 0.00 0.00 0.00 4.70
154 156 9.864034 GTCGTAATTTTATGTCCATCAACATAG 57.136 33.333 0.00 0.00 41.73 2.23
162 164 4.448210 AGGCGTCGTAATTTTATGTCCAT 58.552 39.130 0.00 0.00 0.00 3.41
178 180 0.818040 AGTGTTTGGGTGAAGGCGTC 60.818 55.000 0.00 0.00 0.00 5.19
193 195 0.687354 AATGTCTCTCGCCCAAGTGT 59.313 50.000 0.00 0.00 0.00 3.55
217 219 8.534778 GTTCTTCTTTTGAAAACATGTGATCAC 58.465 33.333 19.27 19.27 38.07 3.06
246 248 3.494626 CACATCACCGTAATGATAGTGGC 59.505 47.826 0.00 0.00 37.20 5.01
252 254 2.503765 TGGACCACATCACCGTAATGAT 59.496 45.455 0.00 0.00 40.03 2.45
257 259 3.257375 GCTATATGGACCACATCACCGTA 59.743 47.826 0.00 0.00 41.03 4.02
258 260 2.037251 GCTATATGGACCACATCACCGT 59.963 50.000 0.00 0.00 41.03 4.83
259 261 2.037121 TGCTATATGGACCACATCACCG 59.963 50.000 0.00 0.00 41.03 4.94
260 262 3.769739 TGCTATATGGACCACATCACC 57.230 47.619 0.00 0.00 41.03 4.02
266 268 2.615493 CCGGGAATGCTATATGGACCAC 60.615 54.545 0.00 0.00 0.00 4.16
277 279 0.250467 CCATCGATTCCGGGAATGCT 60.250 55.000 26.29 3.80 31.89 3.79
286 288 2.867109 ATCATGGGTCCATCGATTCC 57.133 50.000 0.00 0.00 33.90 3.01
317 319 3.972133 TCCTACAGACTTTATCGGGTCA 58.028 45.455 0.00 0.00 35.18 4.02
336 338 3.438434 GCCAGAACTTCTCTTGTCAATCC 59.562 47.826 0.00 0.00 29.07 3.01
342 344 4.429854 AAAGAGCCAGAACTTCTCTTGT 57.570 40.909 13.13 5.47 43.92 3.16
352 354 5.453339 CGAGGTATATCCAAAAGAGCCAGAA 60.453 44.000 0.00 0.00 39.02 3.02
416 418 3.876914 TCTTGACAATATCATGTTCGGGC 59.123 43.478 0.00 0.00 37.11 6.13
450 452 7.015098 CCAGACTCCATCTCTGTCAATAGTTAT 59.985 40.741 0.00 0.00 34.41 1.89
461 463 2.102757 CACCATCCAGACTCCATCTCTG 59.897 54.545 0.00 0.00 34.41 3.35
470 472 1.687612 CCCTTGCACCATCCAGACT 59.312 57.895 0.00 0.00 0.00 3.24
476 479 1.166531 GCGATACCCCTTGCACCATC 61.167 60.000 0.00 0.00 0.00 3.51
477 480 1.152963 GCGATACCCCTTGCACCAT 60.153 57.895 0.00 0.00 0.00 3.55
485 488 2.446036 GGACCTGGCGATACCCCT 60.446 66.667 0.00 0.00 37.83 4.79
511 514 3.181439 GCTTACTCCAGGCTCCCATAAAT 60.181 47.826 0.00 0.00 0.00 1.40
538 541 4.016444 TCAAGGGATTTGTAACATCAGGC 58.984 43.478 0.00 0.00 38.01 4.85
541 544 5.527214 CGCTATCAAGGGATTTGTAACATCA 59.473 40.000 0.00 0.00 37.88 3.07
543 546 4.821805 CCGCTATCAAGGGATTTGTAACAT 59.178 41.667 0.00 0.00 37.88 2.71
551 554 1.490490 TGCTTCCGCTATCAAGGGATT 59.510 47.619 0.00 0.00 37.88 3.01
564 567 5.862924 TTCTTGAATAGAAGTTGCTTCCG 57.137 39.130 5.38 0.00 40.98 4.30
578 581 6.870439 GCTGCAAAAATAACTCCTTCTTGAAT 59.130 34.615 0.00 0.00 0.00 2.57
581 584 5.403466 GTGCTGCAAAAATAACTCCTTCTTG 59.597 40.000 2.77 0.00 0.00 3.02
582 585 5.302823 AGTGCTGCAAAAATAACTCCTTCTT 59.697 36.000 2.77 0.00 0.00 2.52
587 590 3.914364 CGAAGTGCTGCAAAAATAACTCC 59.086 43.478 2.77 0.00 0.00 3.85
616 619 3.951979 GTCTCAGTGACCACTTTGTTG 57.048 47.619 0.00 0.00 40.20 3.33
630 633 1.938577 CTTCCATGCAATCGGTCTCAG 59.061 52.381 0.00 0.00 0.00 3.35
644 647 6.433093 GTGTTTTATAGGTTCACCACTTCCAT 59.567 38.462 0.00 0.00 38.89 3.41
649 652 5.221581 ACGAGTGTTTTATAGGTTCACCACT 60.222 40.000 0.00 0.00 38.89 4.00
661 664 4.680110 CGAGAGTTGTGACGAGTGTTTTAT 59.320 41.667 0.00 0.00 0.00 1.40
663 666 2.858344 CGAGAGTTGTGACGAGTGTTTT 59.142 45.455 0.00 0.00 0.00 2.43
713 717 6.476378 TCAAAACTATTGGCTAGCTCTCTTT 58.524 36.000 15.72 2.65 0.00 2.52
715 719 5.683876 TCAAAACTATTGGCTAGCTCTCT 57.316 39.130 15.72 0.00 0.00 3.10
745 749 7.138736 GCTGACCGCAATACATGTTAAATTAT 58.861 34.615 2.30 0.00 38.92 1.28
751 755 2.285083 GGCTGACCGCAATACATGTTA 58.715 47.619 2.30 0.00 41.67 2.41
785 789 3.458044 TCAGGAAGCTAAGAGTCTCCA 57.542 47.619 0.00 0.00 0.00 3.86
786 790 3.004315 CGATCAGGAAGCTAAGAGTCTCC 59.996 52.174 0.00 0.00 0.00 3.71
794 849 3.845860 AGGATACCGATCAGGAAGCTAA 58.154 45.455 10.05 0.00 45.00 3.09
824 879 1.270550 CAAAAGGGTTCGCTGAGCAAT 59.729 47.619 4.88 0.00 0.00 3.56
837 892 5.181245 TGAGAGCTTTATTCGAACAAAAGGG 59.819 40.000 24.95 8.84 32.14 3.95
838 893 6.241207 TGAGAGCTTTATTCGAACAAAAGG 57.759 37.500 24.95 12.84 32.14 3.11
843 898 8.612619 GGAAATTATGAGAGCTTTATTCGAACA 58.387 33.333 0.00 0.00 0.00 3.18
847 902 8.370493 TCAGGAAATTATGAGAGCTTTATTCG 57.630 34.615 0.00 0.00 0.00 3.34
895 973 2.610374 GAGACGAGACCAGCTACTACTG 59.390 54.545 0.00 0.00 37.42 2.74
897 975 1.593933 CGAGACGAGACCAGCTACTAC 59.406 57.143 0.00 0.00 0.00 2.73
898 976 1.472904 CCGAGACGAGACCAGCTACTA 60.473 57.143 0.00 0.00 0.00 1.82
899 977 0.745128 CCGAGACGAGACCAGCTACT 60.745 60.000 0.00 0.00 0.00 2.57
900 978 1.722677 CCGAGACGAGACCAGCTAC 59.277 63.158 0.00 0.00 0.00 3.58
901 979 2.113433 GCCGAGACGAGACCAGCTA 61.113 63.158 0.00 0.00 0.00 3.32
1061 1139 4.041762 GGGCGTTCATGGGGTGGA 62.042 66.667 0.00 0.00 0.00 4.02
1122 1215 4.760047 GAGAAGAAGGCCGCGGCA 62.760 66.667 46.88 0.00 44.11 5.69
1443 1542 3.974401 CGTGAAAACGTGAATGAATGCTT 59.026 39.130 0.00 0.00 0.00 3.91
1668 1767 5.063060 CGGTTACTGAACATAACTAACTGCC 59.937 44.000 0.00 0.00 37.29 4.85
1676 1775 4.378046 CCAGCAACGGTTACTGAACATAAC 60.378 45.833 20.10 0.00 37.29 1.89
1677 1776 3.749088 CCAGCAACGGTTACTGAACATAA 59.251 43.478 20.10 0.00 37.29 1.90
1678 1777 3.244284 ACCAGCAACGGTTACTGAACATA 60.244 43.478 20.10 0.00 34.91 2.29
1679 1778 2.151202 CCAGCAACGGTTACTGAACAT 58.849 47.619 20.10 0.00 37.29 2.71
1709 1809 7.651808 AGAAAACAAAGACACCACAATATCAG 58.348 34.615 0.00 0.00 0.00 2.90
1731 1831 2.928801 TGCTGTAGTTCCTGCAAGAA 57.071 45.000 0.00 0.00 36.52 2.52
1750 1850 9.710900 GGAAATGGACTTGACTTTTCAATAAAT 57.289 29.630 0.00 0.00 41.05 1.40
1759 1859 5.200483 TCAGTTGGAAATGGACTTGACTTT 58.800 37.500 0.00 0.00 0.00 2.66
1884 1984 3.947612 ATCCAATGGCATGACTTCTCT 57.052 42.857 0.00 0.00 0.00 3.10
1923 2023 5.171339 AGTGAGCAATGTAATCCTCAACT 57.829 39.130 0.00 0.00 36.23 3.16
2108 2208 8.607459 ACTAGATTCTATCAAGTTCAAATTGCG 58.393 33.333 0.00 0.00 0.00 4.85
2177 2277 8.305317 AGAAGTCACTAACAGAACCTACATTAC 58.695 37.037 0.00 0.00 0.00 1.89
2216 2316 8.925447 TCCACCATCCCTAAATATACATCATA 57.075 34.615 0.00 0.00 0.00 2.15
2393 2493 6.730960 TTTATATATAAAGCGGGGCGAAAG 57.269 37.500 12.90 0.00 0.00 2.62
2394 2494 6.730960 CTTTATATATAAAGCGGGGCGAAA 57.269 37.500 25.10 1.66 41.69 3.46
2405 2505 5.996513 TCGGGCGGTTTGCTTTATATATAAA 59.003 36.000 15.47 15.47 45.43 1.40
2406 2506 5.549347 TCGGGCGGTTTGCTTTATATATAA 58.451 37.500 0.81 0.81 45.43 0.98
2407 2507 5.149973 TCGGGCGGTTTGCTTTATATATA 57.850 39.130 0.00 0.00 45.43 0.86
2408 2508 4.000988 CTCGGGCGGTTTGCTTTATATAT 58.999 43.478 0.00 0.00 45.43 0.86
2409 2509 3.395639 CTCGGGCGGTTTGCTTTATATA 58.604 45.455 0.00 0.00 45.43 0.86
2410 2510 2.218603 CTCGGGCGGTTTGCTTTATAT 58.781 47.619 0.00 0.00 45.43 0.86
2411 2511 1.658994 CTCGGGCGGTTTGCTTTATA 58.341 50.000 0.00 0.00 45.43 0.98
2412 2512 1.654023 GCTCGGGCGGTTTGCTTTAT 61.654 55.000 0.00 0.00 45.43 1.40
2413 2513 2.329614 GCTCGGGCGGTTTGCTTTA 61.330 57.895 0.00 0.00 45.43 1.85
2414 2514 3.670377 GCTCGGGCGGTTTGCTTT 61.670 61.111 0.00 0.00 45.43 3.51
2419 2519 4.572571 TTGTGGCTCGGGCGGTTT 62.573 61.111 0.00 0.00 39.81 3.27
2420 2520 4.572571 TTTGTGGCTCGGGCGGTT 62.573 61.111 0.00 0.00 39.81 4.44
2423 2523 3.039202 GATGTTTGTGGCTCGGGCG 62.039 63.158 0.00 0.00 39.81 6.13
2424 2524 2.700773 GGATGTTTGTGGCTCGGGC 61.701 63.158 0.00 0.00 37.82 6.13
2425 2525 0.609131 AAGGATGTTTGTGGCTCGGG 60.609 55.000 0.00 0.00 0.00 5.14
2426 2526 2.107950 TAAGGATGTTTGTGGCTCGG 57.892 50.000 0.00 0.00 0.00 4.63
2427 2527 4.319766 GCATATAAGGATGTTTGTGGCTCG 60.320 45.833 0.00 0.00 0.00 5.03
2428 2528 4.022849 GGCATATAAGGATGTTTGTGGCTC 60.023 45.833 0.00 0.00 0.00 4.70
2429 2529 3.891366 GGCATATAAGGATGTTTGTGGCT 59.109 43.478 0.00 0.00 0.00 4.75
2430 2530 3.891366 AGGCATATAAGGATGTTTGTGGC 59.109 43.478 0.00 0.00 0.00 5.01
2431 2531 5.829924 AGAAGGCATATAAGGATGTTTGTGG 59.170 40.000 0.00 0.00 0.00 4.17
2432 2532 6.543465 TGAGAAGGCATATAAGGATGTTTGTG 59.457 38.462 0.00 0.00 0.00 3.33
2433 2533 6.662755 TGAGAAGGCATATAAGGATGTTTGT 58.337 36.000 0.00 0.00 0.00 2.83
2434 2534 7.756395 ATGAGAAGGCATATAAGGATGTTTG 57.244 36.000 0.00 0.00 0.00 2.93
2435 2535 8.773033 AAATGAGAAGGCATATAAGGATGTTT 57.227 30.769 0.00 0.00 0.00 2.83
2436 2536 9.289782 GTAAATGAGAAGGCATATAAGGATGTT 57.710 33.333 0.00 0.00 0.00 2.71
2437 2537 8.439971 TGTAAATGAGAAGGCATATAAGGATGT 58.560 33.333 0.00 0.00 0.00 3.06
2438 2538 8.853077 TGTAAATGAGAAGGCATATAAGGATG 57.147 34.615 0.00 0.00 0.00 3.51
2439 2539 8.884323 TCTGTAAATGAGAAGGCATATAAGGAT 58.116 33.333 0.00 0.00 0.00 3.24
2440 2540 8.262601 TCTGTAAATGAGAAGGCATATAAGGA 57.737 34.615 0.00 0.00 0.00 3.36
2441 2541 8.908786 TTCTGTAAATGAGAAGGCATATAAGG 57.091 34.615 0.00 0.00 0.00 2.69
2444 2544 9.905713 AGTTTTCTGTAAATGAGAAGGCATATA 57.094 29.630 0.00 0.00 31.17 0.86
2445 2545 8.680903 CAGTTTTCTGTAAATGAGAAGGCATAT 58.319 33.333 0.00 0.00 42.48 1.78
2446 2546 7.121168 CCAGTTTTCTGTAAATGAGAAGGCATA 59.879 37.037 0.00 0.00 45.68 3.14
2447 2547 6.071728 CCAGTTTTCTGTAAATGAGAAGGCAT 60.072 38.462 0.00 0.00 45.68 4.40
2448 2548 5.241506 CCAGTTTTCTGTAAATGAGAAGGCA 59.758 40.000 0.00 0.00 45.68 4.75
2449 2549 5.241728 ACCAGTTTTCTGTAAATGAGAAGGC 59.758 40.000 0.00 0.00 45.68 4.35
2450 2550 6.884280 ACCAGTTTTCTGTAAATGAGAAGG 57.116 37.500 0.00 0.00 45.68 3.46
2451 2551 8.833231 TCTACCAGTTTTCTGTAAATGAGAAG 57.167 34.615 0.00 0.00 45.68 2.85
2452 2552 9.621629 TTTCTACCAGTTTTCTGTAAATGAGAA 57.378 29.630 0.00 0.00 45.68 2.87
2588 2688 9.091220 GGACTCAATACTTACCCTGTTATCTAT 57.909 37.037 0.00 0.00 0.00 1.98
2666 2766 1.439353 AATGATCGGCGCACATGACC 61.439 55.000 10.83 0.00 0.00 4.02
2667 2767 0.316442 CAATGATCGGCGCACATGAC 60.316 55.000 10.83 0.00 0.00 3.06
2771 2872 8.734386 CCAACCTAATCCAATGATATCTAAAGC 58.266 37.037 3.98 0.00 0.00 3.51
2807 2908 5.357742 TCATTACTGCCATCAGCTTAGAA 57.642 39.130 0.00 0.00 44.10 2.10
2818 2919 6.182627 ACTCAGATTTGATTCATTACTGCCA 58.817 36.000 0.00 0.00 31.68 4.92
2845 2946 4.151883 ACCACAGTAGCAATCAATTGGTT 58.848 39.130 12.18 0.78 45.24 3.67
2894 2995 4.099727 CAGATGAGGAGAGAGAAATGCTCA 59.900 45.833 0.00 0.00 46.07 4.26
3002 3116 9.586435 TCATAAGATAACTATTATGATGCGGTG 57.414 33.333 4.04 0.00 41.28 4.94
3133 3247 8.474025 TGACTTATTGTTGTGACTTGGAAAATT 58.526 29.630 0.00 0.00 0.00 1.82
3290 3404 7.192913 TGTGTAATTAGTTTGTTTGCTCAGTG 58.807 34.615 0.00 0.00 0.00 3.66
3315 3429 5.780282 TGGTCTGTGAGGAATATCCGAATAT 59.220 40.000 0.00 0.00 42.75 1.28
3316 3430 5.144832 TGGTCTGTGAGGAATATCCGAATA 58.855 41.667 0.00 0.00 42.75 1.75
3317 3431 3.967326 TGGTCTGTGAGGAATATCCGAAT 59.033 43.478 0.00 0.00 42.75 3.34
3318 3432 3.371034 TGGTCTGTGAGGAATATCCGAA 58.629 45.455 0.00 0.00 42.75 4.30
3319 3433 2.959030 CTGGTCTGTGAGGAATATCCGA 59.041 50.000 0.00 0.00 42.75 4.55
3320 3434 2.546795 GCTGGTCTGTGAGGAATATCCG 60.547 54.545 0.00 0.00 42.75 4.18
3321 3435 2.703007 AGCTGGTCTGTGAGGAATATCC 59.297 50.000 0.00 0.00 36.58 2.59
3322 3436 5.537300 TTAGCTGGTCTGTGAGGAATATC 57.463 43.478 0.00 0.00 0.00 1.63
3336 3450 6.187682 ACTAGCCAAAACATATTTAGCTGGT 58.812 36.000 0.00 5.05 40.83 4.00
3376 3490 5.441500 TCCAGCGGGTCATTCAATTAAATA 58.558 37.500 1.81 0.00 34.93 1.40
3398 3512 6.512177 ACGCGTTATCATCTACTCATTTTC 57.488 37.500 5.58 0.00 0.00 2.29
3420 3534 9.086336 TCAAAACATCAATGAACTGAAGAAAAC 57.914 29.630 0.00 0.00 0.00 2.43
3562 3679 4.672251 AGGCATCCCTGTCAATGC 57.328 55.556 0.10 0.10 45.96 3.56
3991 4108 9.044150 TGTTAAACCTGTTGTACACTATGTAAC 57.956 33.333 0.00 0.19 34.21 2.50
4041 4167 5.357742 AAAAAGGACATTTGAAGCCACTT 57.642 34.783 0.00 0.00 0.00 3.16
4111 5593 7.709182 GCACAAGATACATGTACAGTACCAATA 59.291 37.037 7.96 0.00 0.00 1.90
4134 5616 1.003839 TCGTGATCCCCTGTTGCAC 60.004 57.895 0.00 0.00 0.00 4.57
4158 5643 5.554822 TCTTAATGTTGTGCCCGTTTATC 57.445 39.130 0.00 0.00 0.00 1.75
4178 5663 5.730296 AGTGCTGTTACTCTGTAACATCT 57.270 39.130 19.34 15.36 36.90 2.90
4224 5709 2.431942 CAAGGTTACCGCGAGCGT 60.432 61.111 8.23 0.00 37.81 5.07
4309 5794 3.243234 CGTCGATCTAAGCAAGGTGATCT 60.243 47.826 0.00 0.00 34.75 2.75
4313 5798 0.924090 GCGTCGATCTAAGCAAGGTG 59.076 55.000 0.00 0.00 0.00 4.00
4403 5888 2.123769 GGTGGCTGCCCATATGCA 60.124 61.111 17.53 0.00 44.51 3.96
4430 5915 1.529948 TGTCGTGGACTCCTCCGTT 60.530 57.895 0.00 0.00 39.88 4.44
4471 5956 6.716628 ACTTGTATGTGATCAACCATGTTCTT 59.283 34.615 8.65 0.00 0.00 2.52
4500 5985 9.863650 AAAATGGTGATTCAGATCTTATCATCT 57.136 29.630 20.57 9.73 32.04 2.90
4535 6021 4.929211 TGAGATACTGAACAAACCATCACG 59.071 41.667 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.