Multiple sequence alignment - TraesCS7B01G047200

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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 TraesCS7B01G047200 chr7B 100.000 3007 0 0 1 3007 46889780 46886774 0.000000e+00 5553
1 TraesCS7B01G047200 chr7D 90.530 1246 62 31 243 1453 93686473 93685249 0.000000e+00 1596
2 TraesCS7B01G047200 chr7D 84.397 1128 83 45 1448 2493 93685217 93684101 0.000000e+00 1022
3 TraesCS7B01G047200 chr7D 90.808 359 24 6 2653 3007 93683948 93683595 3.510000e-129 472
4 TraesCS7B01G047200 chr7D 83.784 148 17 3 2541 2686 93684095 93683953 1.880000e-27 134
5 TraesCS7B01G047200 chr7A 85.379 1149 74 32 111 1197 96194013 96192897 0.000000e+00 1105
6 TraesCS7B01G047200 chr7A 83.527 1032 49 36 1252 2192 96192800 96191799 0.000000e+00 852
7 TraesCS7B01G047200 chr7A 92.308 195 12 1 2813 3007 96169703 96169512 1.060000e-69 274
8 TraesCS7B01G047200 chr3B 84.301 465 41 15 1589 2043 52788223 52787781 2.770000e-115 425


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 TraesCS7B01G047200 chr7B 46886774 46889780 3006 True 5553.0 5553 100.00000 1 3007 1 chr7B.!!$R1 3006
1 TraesCS7B01G047200 chr7D 93683595 93686473 2878 True 806.0 1596 87.37975 243 3007 4 chr7D.!!$R1 2764
2 TraesCS7B01G047200 chr7A 96191799 96194013 2214 True 978.5 1105 84.45300 111 2192 2 chr7A.!!$R2 2081

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
737 794 0.02577 CGGTTATAAAGGCGTGTGCG 59.974 55.0 0.0 0.0 44.1 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 2484 0.109272 CTTCTCCTAGCGACGTTGCA 60.109 55.0 28.83 14.07 37.31 4.08 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 3.486263 CTAGCGAAACCGGCCAAG 58.514 61.111 0.00 0.00 0.00 3.61
18 19 2.744709 TAGCGAAACCGGCCAAGC 60.745 61.111 0.00 2.29 0.00 4.01
29 30 3.050275 GCCAAGCCACCTCGTGTC 61.050 66.667 0.00 0.00 0.00 3.67
30 31 2.738521 CCAAGCCACCTCGTGTCG 60.739 66.667 0.00 0.00 0.00 4.35
31 32 2.029073 CAAGCCACCTCGTGTCGT 59.971 61.111 0.00 0.00 0.00 4.34
32 33 2.029073 AAGCCACCTCGTGTCGTG 59.971 61.111 0.00 0.00 0.00 4.35
33 34 2.792947 AAGCCACCTCGTGTCGTGT 61.793 57.895 0.00 0.00 0.00 4.49
34 35 2.694829 AAGCCACCTCGTGTCGTGTC 62.695 60.000 0.00 0.00 0.00 3.67
35 36 2.049433 CCACCTCGTGTCGTGTCC 60.049 66.667 0.00 0.00 0.00 4.02
36 37 2.428569 CACCTCGTGTCGTGTCCG 60.429 66.667 0.00 0.00 0.00 4.79
37 38 2.592574 ACCTCGTGTCGTGTCCGA 60.593 61.111 0.00 0.00 41.73 4.55
69 70 4.477975 CACCGCCCGTCTCGAGTC 62.478 72.222 13.13 5.89 0.00 3.36
72 73 4.517703 CGCCCGTCTCGAGTCGAC 62.518 72.222 29.20 20.06 0.00 4.20
76 77 3.835476 CGTCTCGAGTCGACGCGA 61.835 66.667 35.72 35.72 46.12 5.87
88 89 2.871133 TCGACGCGACAATTATCAAGT 58.129 42.857 15.93 0.00 0.00 3.16
89 90 2.850060 TCGACGCGACAATTATCAAGTC 59.150 45.455 15.93 0.00 0.00 3.01
96 97 4.756868 GACAATTATCAAGTCGACGGAC 57.243 45.455 10.46 0.00 43.76 4.79
105 106 1.418755 GTCGACGGACGCAAAATCC 59.581 57.895 0.00 0.00 42.26 3.01
106 107 1.738830 TCGACGGACGCAAAATCCC 60.739 57.895 0.00 0.00 42.26 3.85
107 108 2.782615 GACGGACGCAAAATCCCG 59.217 61.111 0.00 0.00 46.65 5.14
109 110 2.478746 CGGACGCAAAATCCCGTG 59.521 61.111 0.00 0.00 37.87 4.94
114 115 1.154035 CGCAAAATCCCGTGGAAGC 60.154 57.895 0.00 0.04 34.34 3.86
117 118 0.527565 CAAAATCCCGTGGAAGCCAG 59.472 55.000 0.00 0.00 34.34 4.85
132 133 4.379243 CAGAACGCTGCCGGGTCT 62.379 66.667 2.18 0.00 39.22 3.85
144 150 2.035783 GGGTCTGGACTTTGGGCC 59.964 66.667 0.00 0.00 0.00 5.80
167 173 1.638467 CGATAGCAACAAGGCGAGC 59.362 57.895 0.00 0.00 39.27 5.03
168 174 1.638467 GATAGCAACAAGGCGAGCG 59.362 57.895 0.00 0.00 39.27 5.03
169 175 2.366787 GATAGCAACAAGGCGAGCGC 62.367 60.000 6.27 6.27 39.27 5.92
206 212 1.226802 CACGTGATGAGAGCGAGGG 60.227 63.158 10.90 0.00 0.00 4.30
235 254 3.572539 CGTAATGGCGCGGCATGT 61.573 61.111 43.08 32.59 0.00 3.21
277 296 1.003718 CGGAAGCTTCCCGGAAAGT 60.004 57.895 34.54 0.00 44.67 2.66
296 315 0.609957 TGGCCTCGTCCTTCTCGTTA 60.610 55.000 3.32 0.00 0.00 3.18
298 317 0.100861 GCCTCGTCCTTCTCGTTAGG 59.899 60.000 0.00 0.00 0.00 2.69
327 348 2.612115 AGGGGTGGAGGAGCTTGG 60.612 66.667 0.00 0.00 0.00 3.61
329 350 4.785453 GGGTGGAGGAGCTTGGCG 62.785 72.222 0.00 0.00 0.00 5.69
346 367 2.125512 GCCGACGCATTCACTCCT 60.126 61.111 0.00 0.00 34.03 3.69
347 368 2.456119 GCCGACGCATTCACTCCTG 61.456 63.158 0.00 0.00 34.03 3.86
388 424 3.891049 AGGAAAGCTCCATGATTGTACC 58.109 45.455 0.00 0.00 45.24 3.34
434 470 0.805322 GCTCCGATCTCAGCACTGTG 60.805 60.000 2.76 2.76 35.56 3.66
482 522 2.030412 ATGTGACTGAACCGCGCA 59.970 55.556 8.75 0.00 0.00 6.09
538 582 1.613317 ATGGTTCAGTGCGGATCGGA 61.613 55.000 4.16 0.00 0.00 4.55
649 706 1.302511 ATAATGCGATCCCGGCCAC 60.303 57.895 2.24 0.00 36.06 5.01
732 789 1.067635 ACACGACGGTTATAAAGGCGT 60.068 47.619 14.96 14.96 0.00 5.68
734 791 1.067635 ACGACGGTTATAAAGGCGTGT 60.068 47.619 18.61 0.00 0.00 4.49
737 794 0.025770 CGGTTATAAAGGCGTGTGCG 59.974 55.000 0.00 0.00 44.10 5.34
741 798 0.818938 TATAAAGGCGTGTGCGAGGA 59.181 50.000 0.00 0.00 44.10 3.71
851 927 4.738998 CCATGGAGGCGCACCCAA 62.739 66.667 21.20 7.72 35.85 4.12
853 929 4.740822 ATGGAGGCGCACCCAACC 62.741 66.667 21.20 9.76 35.85 3.77
903 979 3.550431 GGCTAGATCCTGCGCCCA 61.550 66.667 4.18 0.00 36.56 5.36
909 985 0.322975 AGATCCTGCGCCCATATGAC 59.677 55.000 4.18 0.00 0.00 3.06
929 1005 2.048503 GTGCTCGCGGTTAGGTGT 60.049 61.111 6.13 0.00 0.00 4.16
957 1033 3.768922 GCTCGGAGCAGGCTCACT 61.769 66.667 24.42 0.00 44.40 3.41
973 1049 1.202325 TCACTTACGTGCACAGTCGTT 60.202 47.619 18.64 1.15 40.99 3.85
1119 1195 0.677098 TCTCGTTCTGCCTCTACGCT 60.677 55.000 0.00 0.00 35.40 5.07
1178 1254 0.034574 TCCGGCAACAAGGTATGCAT 60.035 50.000 3.79 3.79 44.32 3.96
1198 1278 1.007964 CGGCGAGCTTGATCGATCT 60.008 57.895 25.02 5.76 45.56 2.75
1219 1299 7.058580 CGATCTATCGTCTCGTAGATTGTTTTC 59.941 40.741 4.20 3.84 44.74 2.29
1230 1312 7.726079 TCGTAGATTGTTTTCTGTGTAATTCG 58.274 34.615 0.00 0.00 0.00 3.34
1237 1319 7.789273 TGTTTTCTGTGTAATTCGGAGTTTA 57.211 32.000 0.00 0.00 0.00 2.01
1241 1323 8.842358 TTTCTGTGTAATTCGGAGTTTAAGAT 57.158 30.769 0.00 0.00 0.00 2.40
1244 1326 5.353123 TGTGTAATTCGGAGTTTAAGATGGC 59.647 40.000 0.00 0.00 0.00 4.40
1377 1503 1.471287 CGACACCGTCATCAAGAGGTA 59.529 52.381 0.00 0.00 34.83 3.08
1398 1524 7.556844 AGGTAGTTAATCAAGTTGATCGATGT 58.443 34.615 18.52 5.60 35.76 3.06
1437 1564 3.531538 TCTTTTGTTCTGCTTCACTCGT 58.468 40.909 0.00 0.00 0.00 4.18
1440 1567 1.852942 TGTTCTGCTTCACTCGTCAC 58.147 50.000 0.00 0.00 0.00 3.67
1442 1569 2.055100 GTTCTGCTTCACTCGTCACTC 58.945 52.381 0.00 0.00 0.00 3.51
1443 1570 1.318576 TCTGCTTCACTCGTCACTCA 58.681 50.000 0.00 0.00 0.00 3.41
1445 1572 1.000827 CTGCTTCACTCGTCACTCAGT 60.001 52.381 0.00 0.00 0.00 3.41
1446 1573 1.269257 TGCTTCACTCGTCACTCAGTG 60.269 52.381 0.00 0.00 41.32 3.66
1852 2040 2.505982 CCGGGCCATCAGTTCGAT 59.494 61.111 4.39 0.00 33.27 3.59
1929 2145 2.030562 CCACGGCGAAGAACCACT 59.969 61.111 16.62 0.00 0.00 4.00
1930 2146 1.597027 CCACGGCGAAGAACCACTT 60.597 57.895 16.62 0.00 42.03 3.16
1931 2147 1.569493 CACGGCGAAGAACCACTTG 59.431 57.895 16.62 0.00 39.13 3.16
1932 2148 1.145377 ACGGCGAAGAACCACTTGT 59.855 52.632 16.62 0.00 39.13 3.16
1933 2149 0.390124 ACGGCGAAGAACCACTTGTA 59.610 50.000 16.62 0.00 39.13 2.41
2012 2233 1.676014 CGGCCGTGAAAGAAATCCTCT 60.676 52.381 19.50 0.00 35.13 3.69
2040 2263 2.800541 TTGCATGGTTTTGGGCGCA 61.801 52.632 10.83 0.00 0.00 6.09
2044 2267 1.608918 ATGGTTTTGGGCGCATCCA 60.609 52.632 10.83 19.21 36.21 3.41
2046 2269 2.275380 GGTTTTGGGCGCATCCACT 61.275 57.895 10.83 0.00 36.38 4.00
2047 2270 1.665442 GTTTTGGGCGCATCCACTT 59.335 52.632 10.83 0.00 36.38 3.16
2053 2276 2.817834 GCGCATCCACTTACGCCA 60.818 61.111 0.30 0.00 45.35 5.69
2093 2338 1.805428 ATGAGGTTGTGTTTGGCGGC 61.805 55.000 0.00 0.00 0.00 6.53
2094 2339 3.536498 GAGGTTGTGTTTGGCGGCG 62.536 63.158 0.51 0.51 0.00 6.46
2117 2379 1.964373 GTCGGTTGGCAATGTCCGT 60.964 57.895 22.18 0.00 42.95 4.69
2132 2394 1.802365 GTCCGTTGTGTTACACCATCC 59.198 52.381 13.29 0.00 32.73 3.51
2143 2411 1.221840 CACCATCCGGTCAAGAGGG 59.778 63.158 0.00 0.00 44.71 4.30
2148 2416 2.357154 CCATCCGGTCAAGAGGGAAAAT 60.357 50.000 0.00 0.00 37.37 1.82
2184 2452 4.743955 GCTTAGTTATAGCAAGGGTGGGAG 60.744 50.000 0.00 0.00 38.51 4.30
2187 2455 3.200165 AGTTATAGCAAGGGTGGGAGTTC 59.800 47.826 0.00 0.00 0.00 3.01
2192 2460 2.147387 AAGGGTGGGAGTTCGTGCT 61.147 57.895 0.00 0.00 0.00 4.40
2194 2462 0.617820 AGGGTGGGAGTTCGTGCTAT 60.618 55.000 0.00 0.00 0.00 2.97
2195 2463 0.252197 GGGTGGGAGTTCGTGCTATT 59.748 55.000 0.00 0.00 0.00 1.73
2196 2464 1.369625 GGTGGGAGTTCGTGCTATTG 58.630 55.000 0.00 0.00 0.00 1.90
2197 2465 1.338769 GGTGGGAGTTCGTGCTATTGT 60.339 52.381 0.00 0.00 0.00 2.71
2198 2466 1.732259 GTGGGAGTTCGTGCTATTGTG 59.268 52.381 0.00 0.00 0.00 3.33
2199 2467 1.338674 TGGGAGTTCGTGCTATTGTGG 60.339 52.381 0.00 0.00 0.00 4.17
2200 2468 1.369625 GGAGTTCGTGCTATTGTGGG 58.630 55.000 0.00 0.00 0.00 4.61
2201 2469 0.727398 GAGTTCGTGCTATTGTGGGC 59.273 55.000 0.00 0.00 0.00 5.36
2202 2470 0.036164 AGTTCGTGCTATTGTGGGCA 59.964 50.000 0.00 0.00 36.01 5.36
2203 2471 1.094785 GTTCGTGCTATTGTGGGCAT 58.905 50.000 0.00 0.00 40.66 4.40
2204 2472 1.064060 GTTCGTGCTATTGTGGGCATC 59.936 52.381 0.00 0.00 40.66 3.91
2205 2473 0.809636 TCGTGCTATTGTGGGCATCG 60.810 55.000 0.00 0.00 40.66 3.84
2206 2474 1.775039 CGTGCTATTGTGGGCATCGG 61.775 60.000 0.00 0.00 40.66 4.18
2207 2475 0.748005 GTGCTATTGTGGGCATCGGT 60.748 55.000 0.00 0.00 40.66 4.69
2208 2476 0.034574 TGCTATTGTGGGCATCGGTT 60.035 50.000 0.00 0.00 33.23 4.44
2209 2477 1.210722 TGCTATTGTGGGCATCGGTTA 59.789 47.619 0.00 0.00 33.23 2.85
2210 2478 1.602377 GCTATTGTGGGCATCGGTTAC 59.398 52.381 0.00 0.00 0.00 2.50
2211 2479 2.745152 GCTATTGTGGGCATCGGTTACT 60.745 50.000 0.00 0.00 0.00 2.24
2212 2480 2.038387 ATTGTGGGCATCGGTTACTC 57.962 50.000 0.00 0.00 0.00 2.59
2213 2481 0.390603 TTGTGGGCATCGGTTACTCG 60.391 55.000 0.00 0.00 0.00 4.18
2214 2482 1.217244 GTGGGCATCGGTTACTCGT 59.783 57.895 0.00 0.00 0.00 4.18
2215 2483 0.457035 GTGGGCATCGGTTACTCGTA 59.543 55.000 0.00 0.00 0.00 3.43
2216 2484 1.068127 GTGGGCATCGGTTACTCGTAT 59.932 52.381 0.00 0.00 0.00 3.06
2217 2485 1.067974 TGGGCATCGGTTACTCGTATG 59.932 52.381 0.00 0.00 0.00 2.39
2218 2486 1.137513 GGCATCGGTTACTCGTATGC 58.862 55.000 14.80 14.80 39.96 3.14
2219 2487 1.537348 GGCATCGGTTACTCGTATGCA 60.537 52.381 19.59 0.00 41.12 3.96
2220 2488 2.198406 GCATCGGTTACTCGTATGCAA 58.802 47.619 16.49 0.00 40.18 4.08
2221 2489 2.034001 GCATCGGTTACTCGTATGCAAC 60.034 50.000 16.49 0.00 40.18 4.17
2230 2498 2.204491 CGTATGCAACGTCGCTAGG 58.796 57.895 0.00 0.00 46.72 3.02
2231 2499 0.248336 CGTATGCAACGTCGCTAGGA 60.248 55.000 0.00 0.00 46.72 2.94
2232 2500 1.478137 GTATGCAACGTCGCTAGGAG 58.522 55.000 0.00 0.00 0.00 3.69
2233 2501 1.065102 GTATGCAACGTCGCTAGGAGA 59.935 52.381 0.00 0.00 0.00 3.71
2234 2502 0.530744 ATGCAACGTCGCTAGGAGAA 59.469 50.000 0.00 0.00 0.00 2.87
2238 2506 2.455032 CAACGTCGCTAGGAGAAGATG 58.545 52.381 0.00 0.00 0.00 2.90
2251 2519 2.286872 AGAAGATGATGCTTTCGCCAG 58.713 47.619 0.00 0.00 34.43 4.85
2330 2636 0.180406 ACTGAAGAAGGCGTGGTTGT 59.820 50.000 0.00 0.00 0.00 3.32
2340 2646 1.724582 GCGTGGTTGTTGCTGAACCT 61.725 55.000 11.72 0.00 43.00 3.50
2356 2662 3.869246 TGAACCTGACGAAACTGAAGAAC 59.131 43.478 0.00 0.00 0.00 3.01
2376 2682 5.365619 GAACAGAAAGGGTGTTCTACTTCA 58.634 41.667 8.40 0.00 46.88 3.02
2379 2685 5.589050 ACAGAAAGGGTGTTCTACTTCAAAC 59.411 40.000 0.00 0.00 35.63 2.93
2385 2691 2.097056 GTGTTCTACTTCAAACGGCGAC 60.097 50.000 16.62 0.00 0.00 5.19
2387 2693 2.512485 TCTACTTCAAACGGCGACAA 57.488 45.000 16.62 0.00 0.00 3.18
2391 2697 0.591170 CTTCAAACGGCGACAACCAT 59.409 50.000 16.62 0.00 0.00 3.55
2395 2701 0.600782 AAACGGCGACAACCATACGT 60.601 50.000 16.62 0.00 35.95 3.57
2399 2705 0.441145 GGCGACAACCATACGTGAAC 59.559 55.000 0.00 0.00 0.00 3.18
2412 2718 1.598130 GTGAACGAGGGCAAGCTGT 60.598 57.895 0.00 0.00 0.00 4.40
2470 2776 3.019564 GCACAAGTATGCTGGGAAAGAT 58.980 45.455 0.00 0.00 42.62 2.40
2471 2777 3.445096 GCACAAGTATGCTGGGAAAGATT 59.555 43.478 0.00 0.00 42.62 2.40
2474 2780 4.019174 CAAGTATGCTGGGAAAGATTGGT 58.981 43.478 0.00 0.00 0.00 3.67
2488 2794 4.553330 AGATTGGTTCACGTCATAAGGT 57.447 40.909 0.00 0.00 0.00 3.50
2493 2799 2.093128 GGTTCACGTCATAAGGTGGGAT 60.093 50.000 0.00 0.00 40.77 3.85
2494 2800 3.606687 GTTCACGTCATAAGGTGGGATT 58.393 45.455 0.00 0.00 40.77 3.01
2498 2804 3.554324 CACGTCATAAGGTGGGATTTACG 59.446 47.826 0.00 0.00 37.57 3.18
2500 2806 4.186159 CGTCATAAGGTGGGATTTACGTT 58.814 43.478 0.00 0.00 0.00 3.99
2502 2808 4.573607 GTCATAAGGTGGGATTTACGTTCC 59.426 45.833 0.00 0.00 0.00 3.62
2503 2809 4.472108 TCATAAGGTGGGATTTACGTTCCT 59.528 41.667 4.81 0.00 33.53 3.36
2504 2810 5.662208 TCATAAGGTGGGATTTACGTTCCTA 59.338 40.000 4.81 0.00 33.53 2.94
2505 2811 4.914177 AAGGTGGGATTTACGTTCCTAA 57.086 40.909 4.81 0.00 33.53 2.69
2506 2812 4.914177 AGGTGGGATTTACGTTCCTAAA 57.086 40.909 4.81 0.00 33.53 1.85
2507 2813 5.446260 AGGTGGGATTTACGTTCCTAAAT 57.554 39.130 4.81 0.00 33.53 1.40
2508 2814 6.564557 AGGTGGGATTTACGTTCCTAAATA 57.435 37.500 4.81 0.00 33.53 1.40
2509 2815 7.145474 AGGTGGGATTTACGTTCCTAAATAT 57.855 36.000 4.81 0.00 33.53 1.28
2510 2816 8.266363 AGGTGGGATTTACGTTCCTAAATATA 57.734 34.615 4.81 0.00 33.53 0.86
2511 2817 8.373220 AGGTGGGATTTACGTTCCTAAATATAG 58.627 37.037 4.81 0.00 33.53 1.31
2543 2849 7.776933 TGATAGTTCAAACATGAGAGTATGC 57.223 36.000 0.00 0.00 0.00 3.14
2544 2850 7.330262 TGATAGTTCAAACATGAGAGTATGCA 58.670 34.615 0.00 0.00 0.00 3.96
2545 2851 7.823799 TGATAGTTCAAACATGAGAGTATGCAA 59.176 33.333 0.00 0.00 0.00 4.08
2546 2852 6.492007 AGTTCAAACATGAGAGTATGCAAG 57.508 37.500 0.00 0.00 0.00 4.01
2547 2853 4.952262 TCAAACATGAGAGTATGCAAGC 57.048 40.909 0.00 0.00 0.00 4.01
2558 2864 7.882179 TGAGAGTATGCAAGCGAGTATAATTA 58.118 34.615 0.00 0.00 0.00 1.40
2559 2865 8.357402 TGAGAGTATGCAAGCGAGTATAATTAA 58.643 33.333 0.00 0.00 0.00 1.40
2571 2877 8.634444 AGCGAGTATAATTAATCCCTGCTATAG 58.366 37.037 0.00 0.00 0.00 1.31
2607 2913 0.764271 AGTGTTTTTGGGCATTGGGG 59.236 50.000 0.00 0.00 0.00 4.96
2616 2922 2.120909 GGCATTGGGGTGGATCGTG 61.121 63.158 0.00 0.00 0.00 4.35
2617 2923 1.077787 GCATTGGGGTGGATCGTGA 60.078 57.895 0.00 0.00 0.00 4.35
2629 2935 3.678548 GTGGATCGTGAAACTGTAGAACC 59.321 47.826 0.00 0.00 31.75 3.62
2632 2938 3.655276 TCGTGAAACTGTAGAACCCTC 57.345 47.619 0.00 0.00 31.75 4.30
2638 2944 4.141892 TGAAACTGTAGAACCCTCGAAACA 60.142 41.667 0.00 0.00 0.00 2.83
2639 2945 4.411256 AACTGTAGAACCCTCGAAACAA 57.589 40.909 0.00 0.00 0.00 2.83
2640 2946 4.411256 ACTGTAGAACCCTCGAAACAAA 57.589 40.909 0.00 0.00 0.00 2.83
2641 2947 4.969484 ACTGTAGAACCCTCGAAACAAAT 58.031 39.130 0.00 0.00 0.00 2.32
2642 2948 6.105397 ACTGTAGAACCCTCGAAACAAATA 57.895 37.500 0.00 0.00 0.00 1.40
2643 2949 6.164176 ACTGTAGAACCCTCGAAACAAATAG 58.836 40.000 0.00 0.00 0.00 1.73
2644 2950 5.484715 TGTAGAACCCTCGAAACAAATAGG 58.515 41.667 0.00 0.00 0.00 2.57
2646 2952 3.009143 AGAACCCTCGAAACAAATAGGCT 59.991 43.478 0.00 0.00 0.00 4.58
2648 2954 2.304761 ACCCTCGAAACAAATAGGCTCA 59.695 45.455 0.00 0.00 0.00 4.26
2650 2956 3.313526 CCCTCGAAACAAATAGGCTCATG 59.686 47.826 0.00 0.00 0.00 3.07
2651 2957 3.941483 CCTCGAAACAAATAGGCTCATGT 59.059 43.478 0.00 0.00 0.00 3.21
2662 3002 0.947244 GGCTCATGTCCCGCTTTATG 59.053 55.000 0.00 0.00 0.00 1.90
2664 3004 2.484770 GGCTCATGTCCCGCTTTATGTA 60.485 50.000 0.00 0.00 0.00 2.29
2666 3006 3.187227 GCTCATGTCCCGCTTTATGTATG 59.813 47.826 0.00 0.00 0.00 2.39
2674 3014 4.702612 TCCCGCTTTATGTATGAAGCAAAA 59.297 37.500 17.80 3.46 46.17 2.44
2678 3018 6.075415 CCGCTTTATGTATGAAGCAAAAATCG 60.075 38.462 17.80 3.77 46.17 3.34
2686 3026 4.145876 TGAAGCAAAAATCGCAGTACAG 57.854 40.909 0.00 0.00 0.00 2.74
2687 3027 3.563808 TGAAGCAAAAATCGCAGTACAGT 59.436 39.130 0.00 0.00 0.00 3.55
2688 3028 4.752604 TGAAGCAAAAATCGCAGTACAGTA 59.247 37.500 0.00 0.00 0.00 2.74
2690 3030 4.062293 AGCAAAAATCGCAGTACAGTACA 58.938 39.130 13.37 0.00 0.00 2.90
2691 3031 4.084013 AGCAAAAATCGCAGTACAGTACAC 60.084 41.667 13.37 3.82 0.00 2.90
2692 3032 4.382831 CAAAAATCGCAGTACAGTACACG 58.617 43.478 13.37 15.01 33.55 4.49
2714 3056 1.180029 TCGTGTAACTGTAGAGGCCC 58.820 55.000 0.00 0.00 31.75 5.80
2735 3078 2.155279 GAAAGGGCAAACCACTCTCTC 58.845 52.381 0.00 0.00 43.89 3.20
2795 3138 4.220602 TCTGAGATGTTGAGATGAACCGAA 59.779 41.667 0.00 0.00 0.00 4.30
2809 3152 4.346730 TGAACCGAACAAGTAGATCCCTA 58.653 43.478 0.00 0.00 0.00 3.53
2849 3192 2.478894 AGCACGTTTGTAACAAGGATCG 59.521 45.455 0.00 0.00 0.00 3.69
2892 3235 0.680061 GACTTCGTCACTCTTGGGGT 59.320 55.000 0.00 0.00 32.09 4.95
2895 3238 1.070134 CTTCGTCACTCTTGGGGTCAA 59.930 52.381 0.00 0.00 0.00 3.18
2905 3248 5.068987 CACTCTTGGGGTCAATTCTTTTTCA 59.931 40.000 0.00 0.00 31.75 2.69
2916 3259 9.358872 GGTCAATTCTTTTTCATAATCTTCCAC 57.641 33.333 0.00 0.00 0.00 4.02
2919 3262 9.880157 CAATTCTTTTTCATAATCTTCCACCAT 57.120 29.630 0.00 0.00 0.00 3.55
2921 3264 8.648698 TTCTTTTTCATAATCTTCCACCATCA 57.351 30.769 0.00 0.00 0.00 3.07
2933 3276 1.815003 CCACCATCAGCAAACTTCTCC 59.185 52.381 0.00 0.00 0.00 3.71
2939 3282 1.695242 TCAGCAAACTTCTCCCCGTAA 59.305 47.619 0.00 0.00 0.00 3.18
2947 3290 1.413077 CTTCTCCCCGTAAGCTTAGGG 59.587 57.143 30.14 30.14 44.67 3.53
2970 3313 4.577834 TTTCGTTCCCCAAAATGACTTC 57.422 40.909 0.00 0.00 0.00 3.01
2984 3327 1.004918 ACTTCAACTCTTCCGCCCG 60.005 57.895 0.00 0.00 0.00 6.13
2996 3339 2.103143 CGCCCGCACAAACAACAA 59.897 55.556 0.00 0.00 0.00 2.83
3002 3345 3.448686 CCCGCACAAACAACAATGTAAA 58.551 40.909 0.00 0.00 39.40 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.750888 GCTTGGCCGGTTTCGCTAG 61.751 63.158 1.90 0.00 34.56 3.42
1 2 2.744709 GCTTGGCCGGTTTCGCTA 60.745 61.111 1.90 0.00 34.56 4.26
12 13 3.050275 GACACGAGGTGGCTTGGC 61.050 66.667 0.42 0.00 38.75 4.52
13 14 2.738521 CGACACGAGGTGGCTTGG 60.739 66.667 0.00 0.00 39.83 3.61
14 15 2.029073 ACGACACGAGGTGGCTTG 59.971 61.111 0.00 0.00 39.83 4.01
15 16 2.029073 CACGACACGAGGTGGCTT 59.971 61.111 0.00 0.00 39.83 4.35
16 17 3.208884 GACACGACACGAGGTGGCT 62.209 63.158 0.00 0.00 39.83 4.75
17 18 2.733593 GACACGACACGAGGTGGC 60.734 66.667 0.42 0.00 38.37 5.01
18 19 2.049433 GGACACGACACGAGGTGG 60.049 66.667 0.42 0.00 37.94 4.61
19 20 2.428569 CGGACACGACACGAGGTG 60.429 66.667 0.00 0.00 44.60 4.00
20 21 2.592574 TCGGACACGACACGAGGT 60.593 61.111 0.00 0.00 45.59 3.85
52 53 4.477975 GACTCGAGACGGGCGGTG 62.478 72.222 21.68 0.00 0.00 4.94
55 56 4.517703 GTCGACTCGAGACGGGCG 62.518 72.222 30.94 19.26 36.23 6.13
68 69 2.850060 GACTTGATAATTGTCGCGTCGA 59.150 45.455 5.77 0.00 0.00 4.20
69 70 2.345470 CGACTTGATAATTGTCGCGTCG 60.345 50.000 21.90 21.90 45.00 5.12
70 71 3.206271 CGACTTGATAATTGTCGCGTC 57.794 47.619 5.77 0.00 45.00 5.19
75 76 3.239941 CGTCCGTCGACTTGATAATTGTC 59.760 47.826 14.70 0.00 42.86 3.18
76 77 3.176708 CGTCCGTCGACTTGATAATTGT 58.823 45.455 14.70 0.00 42.86 2.71
77 78 2.034842 GCGTCCGTCGACTTGATAATTG 60.035 50.000 14.70 0.00 42.86 2.32
78 79 2.190981 GCGTCCGTCGACTTGATAATT 58.809 47.619 14.70 0.00 42.86 1.40
79 80 1.133598 TGCGTCCGTCGACTTGATAAT 59.866 47.619 14.70 0.00 42.86 1.28
80 81 0.522626 TGCGTCCGTCGACTTGATAA 59.477 50.000 14.70 0.00 42.86 1.75
81 82 0.522626 TTGCGTCCGTCGACTTGATA 59.477 50.000 14.70 0.00 42.86 2.15
82 83 0.319211 TTTGCGTCCGTCGACTTGAT 60.319 50.000 14.70 0.00 42.86 2.57
83 84 0.528033 TTTTGCGTCCGTCGACTTGA 60.528 50.000 14.70 7.28 42.86 3.02
84 85 0.511221 ATTTTGCGTCCGTCGACTTG 59.489 50.000 14.70 4.76 42.86 3.16
85 86 0.788391 GATTTTGCGTCCGTCGACTT 59.212 50.000 14.70 0.00 42.86 3.01
86 87 1.012486 GGATTTTGCGTCCGTCGACT 61.012 55.000 14.70 0.00 42.86 4.18
87 88 1.418755 GGATTTTGCGTCCGTCGAC 59.581 57.895 5.18 5.18 42.86 4.20
88 89 1.738830 GGGATTTTGCGTCCGTCGA 60.739 57.895 0.00 0.00 42.86 4.20
89 90 2.782615 GGGATTTTGCGTCCGTCG 59.217 61.111 0.00 0.00 43.12 5.12
90 91 2.782615 CGGGATTTTGCGTCCGTC 59.217 61.111 0.00 0.00 37.92 4.79
92 93 2.478746 CACGGGATTTTGCGTCCG 59.521 61.111 0.00 0.00 46.95 4.79
93 94 1.238625 TTCCACGGGATTTTGCGTCC 61.239 55.000 0.00 0.00 34.92 4.79
94 95 0.168128 CTTCCACGGGATTTTGCGTC 59.832 55.000 0.00 0.00 0.00 5.19
95 96 1.862602 GCTTCCACGGGATTTTGCGT 61.863 55.000 0.00 0.00 0.00 5.24
96 97 1.154035 GCTTCCACGGGATTTTGCG 60.154 57.895 0.00 0.00 0.00 4.85
97 98 1.215382 GGCTTCCACGGGATTTTGC 59.785 57.895 0.00 0.00 0.00 3.68
98 99 0.527565 CTGGCTTCCACGGGATTTTG 59.472 55.000 0.00 0.00 0.00 2.44
99 100 0.404040 TCTGGCTTCCACGGGATTTT 59.596 50.000 0.00 0.00 0.00 1.82
100 101 0.404040 TTCTGGCTTCCACGGGATTT 59.596 50.000 0.00 0.00 0.00 2.17
101 102 0.322546 GTTCTGGCTTCCACGGGATT 60.323 55.000 0.00 0.00 0.00 3.01
102 103 1.299976 GTTCTGGCTTCCACGGGAT 59.700 57.895 0.00 0.00 0.00 3.85
103 104 2.747686 GTTCTGGCTTCCACGGGA 59.252 61.111 0.00 0.00 0.00 5.14
104 105 2.742372 CGTTCTGGCTTCCACGGG 60.742 66.667 0.00 0.00 0.00 5.28
105 106 3.423154 GCGTTCTGGCTTCCACGG 61.423 66.667 0.00 0.00 0.00 4.94
106 107 2.357517 AGCGTTCTGGCTTCCACG 60.358 61.111 0.00 0.00 41.39 4.94
107 108 2.970974 GCAGCGTTCTGGCTTCCAC 61.971 63.158 0.00 0.00 42.53 4.02
108 109 2.669569 GCAGCGTTCTGGCTTCCA 60.670 61.111 0.00 0.00 42.53 3.53
144 150 2.321060 CTTGTTGCTATCGCCGCG 59.679 61.111 6.39 6.39 34.43 6.46
178 184 4.344865 ATCACGTGCCCCACCACC 62.345 66.667 11.67 0.00 32.10 4.61
187 193 1.875813 CCTCGCTCTCATCACGTGC 60.876 63.158 11.67 0.00 0.00 5.34
190 196 2.279120 GCCCTCGCTCTCATCACG 60.279 66.667 0.00 0.00 0.00 4.35
191 197 2.279120 CGCCCTCGCTCTCATCAC 60.279 66.667 0.00 0.00 0.00 3.06
277 296 0.609957 TAACGAGAAGGACGAGGCCA 60.610 55.000 5.01 0.00 34.70 5.36
296 315 2.752238 CCCTGTCGAGTCGAGCCT 60.752 66.667 17.12 0.00 36.23 4.58
298 317 3.063084 ACCCCTGTCGAGTCGAGC 61.063 66.667 17.12 11.46 36.23 5.03
329 350 2.125512 AGGAGTGAATGCGTCGGC 60.126 61.111 0.00 0.00 40.52 5.54
346 367 0.820482 CCCATGCAAGCGATGATCCA 60.820 55.000 0.00 0.00 0.00 3.41
347 368 0.535780 TCCCATGCAAGCGATGATCC 60.536 55.000 0.00 0.00 0.00 3.36
434 470 1.160329 CCGGTTGATCGATTGGGAGC 61.160 60.000 0.00 0.00 0.00 4.70
440 476 2.040009 ATCGGCCCGGTTGATCGATT 62.040 55.000 1.90 0.00 37.28 3.34
482 522 1.959085 CCAAAACTGTCGCTGGCAT 59.041 52.632 0.00 0.00 0.00 4.40
649 706 2.510906 GATGGATGGTGACGGGGG 59.489 66.667 0.00 0.00 0.00 5.40
732 789 3.303135 AACGCTCCTCCTCGCACA 61.303 61.111 0.00 0.00 0.00 4.57
734 791 4.742201 GCAACGCTCCTCCTCGCA 62.742 66.667 0.00 0.00 0.00 5.10
737 794 2.024176 TATTTGCAACGCTCCTCCTC 57.976 50.000 0.00 0.00 0.00 3.71
741 798 1.202348 GGCTTTATTTGCAACGCTCCT 59.798 47.619 0.00 0.00 0.00 3.69
747 812 1.338674 GGGGGTGGCTTTATTTGCAAC 60.339 52.381 0.00 0.00 33.83 4.17
853 929 2.438434 ATTTGAGGAAGCGGGGCG 60.438 61.111 0.00 0.00 0.00 6.13
903 979 1.068083 CCGCGAGCACTGGTCATAT 59.932 57.895 8.23 0.00 0.00 1.78
909 985 2.509336 CCTAACCGCGAGCACTGG 60.509 66.667 8.23 0.00 0.00 4.00
957 1033 1.492319 GCCAACGACTGTGCACGTAA 61.492 55.000 13.13 0.00 41.87 3.18
1008 1084 1.525923 CTCCACTCCAGGGAGCATG 59.474 63.158 15.18 7.06 44.95 4.06
1104 1180 1.811679 GGCAGCGTAGAGGCAGAAC 60.812 63.158 0.00 0.00 34.64 3.01
1178 1254 3.430565 ATCGATCAAGCTCGCCGCA 62.431 57.895 0.00 0.00 42.61 5.69
1198 1278 6.745907 CACAGAAAACAATCTACGAGACGATA 59.254 38.462 0.00 0.00 0.00 2.92
1219 1299 6.456988 GCCATCTTAAACTCCGAATTACACAG 60.457 42.308 0.00 0.00 0.00 3.66
1230 1312 3.071479 TGTTCACGCCATCTTAAACTCC 58.929 45.455 0.00 0.00 0.00 3.85
1244 1326 0.094216 CTCTGCTGCGAATGTTCACG 59.906 55.000 0.00 0.00 0.00 4.35
1312 1438 0.178891 TCTGGTCCAGCCTCTCCTTT 60.179 55.000 14.64 0.00 38.35 3.11
1319 1445 1.130054 TTGAGCTTCTGGTCCAGCCT 61.130 55.000 14.64 9.82 39.75 4.58
1354 1480 1.447838 CTTGATGACGGTGTCGGGG 60.448 63.158 0.00 0.00 41.39 5.73
1377 1503 6.330278 TCGACATCGATCAACTTGATTAACT 58.670 36.000 5.73 0.00 44.22 2.24
1398 1524 6.147164 ACAAAAGAAAACGAATCTAGCATCGA 59.853 34.615 19.53 0.00 41.43 3.59
1405 1531 7.259290 AGCAGAACAAAAGAAAACGAATCTA 57.741 32.000 0.00 0.00 0.00 1.98
1440 1567 1.068541 TGTTCGACCGATCACACTGAG 60.069 52.381 0.00 0.00 0.00 3.35
1442 1569 1.060713 GTGTTCGACCGATCACACTG 58.939 55.000 21.59 0.00 41.73 3.66
1443 1570 0.959553 AGTGTTCGACCGATCACACT 59.040 50.000 25.67 22.25 43.46 3.55
1445 1572 1.336517 GGAAGTGTTCGACCGATCACA 60.337 52.381 25.67 12.67 43.46 3.58
1446 1573 1.347320 GGAAGTGTTCGACCGATCAC 58.653 55.000 19.90 19.90 42.17 3.06
1656 1822 2.022129 GAACTCGTCCAGGCACACG 61.022 63.158 0.00 0.00 37.36 4.49
1908 2124 4.090057 GTTCTTCGCCGTGGCAGC 62.090 66.667 12.06 0.00 42.06 5.25
1929 2145 3.138304 GGCGATGCATCCTACAATACAA 58.862 45.455 20.87 0.00 0.00 2.41
1930 2146 2.766313 GGCGATGCATCCTACAATACA 58.234 47.619 20.87 0.00 0.00 2.29
1931 2147 1.726791 CGGCGATGCATCCTACAATAC 59.273 52.381 20.87 2.01 0.00 1.89
1932 2148 1.337728 CCGGCGATGCATCCTACAATA 60.338 52.381 20.87 0.00 0.00 1.90
1933 2149 0.603707 CCGGCGATGCATCCTACAAT 60.604 55.000 20.87 0.00 0.00 2.71
2012 2233 2.741985 CCATGCAACTCGGCGACA 60.742 61.111 4.99 2.21 36.28 4.35
2040 2263 0.179056 CCGGAATGGCGTAAGTGGAT 60.179 55.000 0.00 0.00 41.68 3.41
2067 2312 0.250727 AACACAACCTCATCACCCCG 60.251 55.000 0.00 0.00 0.00 5.73
2070 2315 1.000274 GCCAAACACAACCTCATCACC 60.000 52.381 0.00 0.00 0.00 4.02
2071 2316 1.334960 CGCCAAACACAACCTCATCAC 60.335 52.381 0.00 0.00 0.00 3.06
2072 2317 0.950836 CGCCAAACACAACCTCATCA 59.049 50.000 0.00 0.00 0.00 3.07
2093 2338 2.265182 ATTGCCAACCGACAACCCG 61.265 57.895 0.00 0.00 0.00 5.28
2094 2339 1.288752 CATTGCCAACCGACAACCC 59.711 57.895 0.00 0.00 0.00 4.11
2132 2394 4.575885 TCTACAATTTTCCCTCTTGACCG 58.424 43.478 0.00 0.00 0.00 4.79
2184 2452 1.064060 GATGCCCACAATAGCACGAAC 59.936 52.381 0.00 0.00 42.84 3.95
2187 2455 1.643292 CGATGCCCACAATAGCACG 59.357 57.895 0.00 0.00 42.84 5.34
2192 2460 2.482316 CGAGTAACCGATGCCCACAATA 60.482 50.000 0.00 0.00 0.00 1.90
2194 2462 0.390603 CGAGTAACCGATGCCCACAA 60.391 55.000 0.00 0.00 0.00 3.33
2195 2463 1.216977 CGAGTAACCGATGCCCACA 59.783 57.895 0.00 0.00 0.00 4.17
2196 2464 0.457035 TACGAGTAACCGATGCCCAC 59.543 55.000 0.00 0.00 0.00 4.61
2197 2465 1.067974 CATACGAGTAACCGATGCCCA 59.932 52.381 0.00 0.00 0.00 5.36
2198 2466 1.779569 CATACGAGTAACCGATGCCC 58.220 55.000 0.00 0.00 0.00 5.36
2199 2467 1.137513 GCATACGAGTAACCGATGCC 58.862 55.000 0.00 0.00 37.24 4.40
2200 2468 1.847818 TGCATACGAGTAACCGATGC 58.152 50.000 0.00 0.00 40.25 3.91
2201 2469 3.836229 GTTGCATACGAGTAACCGATG 57.164 47.619 0.00 0.00 0.00 3.84
2213 2481 1.065102 TCTCCTAGCGACGTTGCATAC 59.935 52.381 28.83 0.00 37.31 2.39
2214 2482 1.385528 TCTCCTAGCGACGTTGCATA 58.614 50.000 28.83 16.41 37.31 3.14
2215 2483 0.530744 TTCTCCTAGCGACGTTGCAT 59.469 50.000 28.83 16.17 37.31 3.96
2216 2484 0.109272 CTTCTCCTAGCGACGTTGCA 60.109 55.000 28.83 14.07 37.31 4.08
2217 2485 0.170561 TCTTCTCCTAGCGACGTTGC 59.829 55.000 20.54 20.54 0.00 4.17
2218 2486 2.097629 TCATCTTCTCCTAGCGACGTTG 59.902 50.000 0.00 0.00 0.00 4.10
2219 2487 2.366533 TCATCTTCTCCTAGCGACGTT 58.633 47.619 0.00 0.00 0.00 3.99
2220 2488 2.039818 TCATCTTCTCCTAGCGACGT 57.960 50.000 0.00 0.00 0.00 4.34
2221 2489 2.920227 GCATCATCTTCTCCTAGCGACG 60.920 54.545 0.00 0.00 0.00 5.12
2222 2490 2.295909 AGCATCATCTTCTCCTAGCGAC 59.704 50.000 0.00 0.00 0.00 5.19
2223 2491 2.591923 AGCATCATCTTCTCCTAGCGA 58.408 47.619 0.00 0.00 0.00 4.93
2224 2492 3.383620 AAGCATCATCTTCTCCTAGCG 57.616 47.619 0.00 0.00 0.00 4.26
2225 2493 3.740321 CGAAAGCATCATCTTCTCCTAGC 59.260 47.826 0.00 0.00 0.00 3.42
2277 2547 3.793144 GCAGCCACGCCTTCTTCG 61.793 66.667 0.00 0.00 0.00 3.79
2296 2566 2.890808 TCAGTTTCGTCAGCTTCAGT 57.109 45.000 0.00 0.00 0.00 3.41
2330 2636 1.939934 CAGTTTCGTCAGGTTCAGCAA 59.060 47.619 0.00 0.00 0.00 3.91
2340 2646 4.570772 CCTTTCTGTTCTTCAGTTTCGTCA 59.429 41.667 0.00 0.00 43.97 4.35
2356 2662 5.277345 CGTTTGAAGTAGAACACCCTTTCTG 60.277 44.000 0.00 0.00 36.48 3.02
2359 2665 3.881089 CCGTTTGAAGTAGAACACCCTTT 59.119 43.478 0.00 0.00 0.00 3.11
2367 2673 2.512485 TGTCGCCGTTTGAAGTAGAA 57.488 45.000 0.00 0.00 0.00 2.10
2374 2680 1.149987 GTATGGTTGTCGCCGTTTGA 58.850 50.000 0.00 0.00 0.00 2.69
2376 2682 0.600782 ACGTATGGTTGTCGCCGTTT 60.601 50.000 0.00 0.00 0.00 3.60
2379 2685 1.009903 TTCACGTATGGTTGTCGCCG 61.010 55.000 0.00 0.00 0.00 6.46
2385 2691 1.355971 CCCTCGTTCACGTATGGTTG 58.644 55.000 0.00 0.00 40.80 3.77
2387 2693 1.217244 GCCCTCGTTCACGTATGGT 59.783 57.895 0.00 0.00 40.80 3.55
2391 2697 1.373748 GCTTGCCCTCGTTCACGTA 60.374 57.895 0.00 0.00 40.80 3.57
2395 2701 1.148273 AACAGCTTGCCCTCGTTCA 59.852 52.632 0.00 0.00 0.00 3.18
2399 2705 3.058160 CCCAACAGCTTGCCCTCG 61.058 66.667 0.00 0.00 0.00 4.63
2470 2776 2.551287 CCCACCTTATGACGTGAACCAA 60.551 50.000 0.00 0.00 31.36 3.67
2471 2777 1.002659 CCCACCTTATGACGTGAACCA 59.997 52.381 0.00 0.00 31.36 3.67
2474 2780 3.992943 AATCCCACCTTATGACGTGAA 57.007 42.857 0.00 0.00 31.36 3.18
2518 2824 7.823799 TGCATACTCTCATGTTTGAACTATCAA 59.176 33.333 0.00 0.00 43.70 2.57
2519 2825 7.330262 TGCATACTCTCATGTTTGAACTATCA 58.670 34.615 0.00 0.00 0.00 2.15
2520 2826 7.776933 TGCATACTCTCATGTTTGAACTATC 57.223 36.000 0.00 0.00 0.00 2.08
2521 2827 7.201679 GCTTGCATACTCTCATGTTTGAACTAT 60.202 37.037 0.00 0.00 0.00 2.12
2522 2828 6.092670 GCTTGCATACTCTCATGTTTGAACTA 59.907 38.462 0.00 0.00 0.00 2.24
2523 2829 5.106396 GCTTGCATACTCTCATGTTTGAACT 60.106 40.000 0.00 0.00 0.00 3.01
2524 2830 5.091431 GCTTGCATACTCTCATGTTTGAAC 58.909 41.667 0.00 0.00 0.00 3.18
2525 2831 4.142838 CGCTTGCATACTCTCATGTTTGAA 60.143 41.667 0.00 0.00 0.00 2.69
2526 2832 3.371898 CGCTTGCATACTCTCATGTTTGA 59.628 43.478 0.00 0.00 0.00 2.69
2527 2833 3.371898 TCGCTTGCATACTCTCATGTTTG 59.628 43.478 0.00 0.00 0.00 2.93
2528 2834 3.599343 TCGCTTGCATACTCTCATGTTT 58.401 40.909 0.00 0.00 0.00 2.83
2529 2835 3.193263 CTCGCTTGCATACTCTCATGTT 58.807 45.455 0.00 0.00 0.00 2.71
2530 2836 2.167281 ACTCGCTTGCATACTCTCATGT 59.833 45.455 0.00 0.00 0.00 3.21
2531 2837 2.819115 ACTCGCTTGCATACTCTCATG 58.181 47.619 0.00 0.00 0.00 3.07
2532 2838 4.862902 ATACTCGCTTGCATACTCTCAT 57.137 40.909 0.00 0.00 0.00 2.90
2533 2839 5.767816 TTATACTCGCTTGCATACTCTCA 57.232 39.130 0.00 0.00 0.00 3.27
2534 2840 8.744008 TTAATTATACTCGCTTGCATACTCTC 57.256 34.615 0.00 0.00 0.00 3.20
2535 2841 9.360093 GATTAATTATACTCGCTTGCATACTCT 57.640 33.333 0.00 0.00 0.00 3.24
2536 2842 8.596380 GGATTAATTATACTCGCTTGCATACTC 58.404 37.037 0.00 0.00 0.00 2.59
2537 2843 7.549488 GGGATTAATTATACTCGCTTGCATACT 59.451 37.037 0.00 0.00 0.00 2.12
2538 2844 7.549488 AGGGATTAATTATACTCGCTTGCATAC 59.451 37.037 0.00 0.00 32.36 2.39
2539 2845 7.549134 CAGGGATTAATTATACTCGCTTGCATA 59.451 37.037 0.00 0.00 33.51 3.14
2540 2846 6.372659 CAGGGATTAATTATACTCGCTTGCAT 59.627 38.462 0.00 0.00 33.51 3.96
2541 2847 5.700832 CAGGGATTAATTATACTCGCTTGCA 59.299 40.000 6.91 0.00 33.51 4.08
2542 2848 5.390991 GCAGGGATTAATTATACTCGCTTGC 60.391 44.000 6.91 9.39 33.51 4.01
2543 2849 5.934625 AGCAGGGATTAATTATACTCGCTTG 59.065 40.000 6.91 5.49 33.51 4.01
2544 2850 6.115448 AGCAGGGATTAATTATACTCGCTT 57.885 37.500 6.91 0.00 33.51 4.68
2545 2851 5.746990 AGCAGGGATTAATTATACTCGCT 57.253 39.130 0.00 4.80 35.31 4.93
2546 2852 8.630917 TCTATAGCAGGGATTAATTATACTCGC 58.369 37.037 0.00 0.00 0.00 5.03
2547 2853 9.953697 GTCTATAGCAGGGATTAATTATACTCG 57.046 37.037 0.00 0.00 0.00 4.18
2558 2864 3.831911 GAGCTCTGTCTATAGCAGGGATT 59.168 47.826 21.26 11.97 41.32 3.01
2559 2865 3.430453 GAGCTCTGTCTATAGCAGGGAT 58.570 50.000 21.26 17.20 41.32 3.85
2571 2877 1.216710 CTCAACGGGGAGCTCTGTC 59.783 63.158 14.64 3.76 0.00 3.51
2607 2913 3.678548 GGTTCTACAGTTTCACGATCCAC 59.321 47.826 0.00 0.00 0.00 4.02
2616 2922 4.374399 TGTTTCGAGGGTTCTACAGTTTC 58.626 43.478 0.00 0.00 0.00 2.78
2617 2923 4.411256 TGTTTCGAGGGTTCTACAGTTT 57.589 40.909 0.00 0.00 0.00 2.66
2629 2935 3.941483 ACATGAGCCTATTTGTTTCGAGG 59.059 43.478 0.00 0.00 0.00 4.63
2632 2938 3.065371 GGGACATGAGCCTATTTGTTTCG 59.935 47.826 0.00 0.00 0.00 3.46
2638 2944 0.839946 AGCGGGACATGAGCCTATTT 59.160 50.000 0.00 0.00 0.00 1.40
2639 2945 0.839946 AAGCGGGACATGAGCCTATT 59.160 50.000 0.00 0.00 0.00 1.73
2640 2946 0.839946 AAAGCGGGACATGAGCCTAT 59.160 50.000 0.00 0.00 0.00 2.57
2641 2947 1.491668 TAAAGCGGGACATGAGCCTA 58.508 50.000 0.00 0.00 0.00 3.93
2642 2948 0.839946 ATAAAGCGGGACATGAGCCT 59.160 50.000 0.00 0.00 0.00 4.58
2643 2949 0.947244 CATAAAGCGGGACATGAGCC 59.053 55.000 0.00 0.00 0.00 4.70
2644 2950 1.668419 ACATAAAGCGGGACATGAGC 58.332 50.000 0.00 0.00 0.00 4.26
2646 2952 4.681074 TCATACATAAAGCGGGACATGA 57.319 40.909 0.00 0.00 0.00 3.07
2648 2954 3.815401 GCTTCATACATAAAGCGGGACAT 59.185 43.478 0.00 0.00 38.60 3.06
2650 2956 3.879932 GCTTCATACATAAAGCGGGAC 57.120 47.619 0.00 0.00 38.60 4.46
2662 3002 5.627172 TGTACTGCGATTTTTGCTTCATAC 58.373 37.500 0.00 0.00 0.00 2.39
2664 3004 4.216257 ACTGTACTGCGATTTTTGCTTCAT 59.784 37.500 0.00 0.00 0.00 2.57
2666 3006 4.147219 ACTGTACTGCGATTTTTGCTTC 57.853 40.909 0.00 0.00 0.00 3.86
2674 3014 1.814394 TCCGTGTACTGTACTGCGATT 59.186 47.619 25.10 0.00 32.59 3.34
2678 3018 1.131883 ACGATCCGTGTACTGTACTGC 59.868 52.381 17.98 10.33 39.18 4.40
2690 3030 2.681848 CCTCTACAGTTACACGATCCGT 59.318 50.000 0.00 0.00 42.36 4.69
2691 3031 2.541178 GCCTCTACAGTTACACGATCCG 60.541 54.545 0.00 0.00 0.00 4.18
2692 3032 2.223758 GGCCTCTACAGTTACACGATCC 60.224 54.545 0.00 0.00 0.00 3.36
2700 3042 1.829222 CCTTTCGGGCCTCTACAGTTA 59.171 52.381 0.84 0.00 0.00 2.24
2714 3056 0.875059 GAGAGTGGTTTGCCCTTTCG 59.125 55.000 0.00 0.00 0.00 3.46
2735 3078 5.192722 AGAAAGGAGGAATTAAAGAGAGGGG 59.807 44.000 0.00 0.00 0.00 4.79
2768 3111 6.111382 GGTTCATCTCAACATCTCAGATTCA 58.889 40.000 0.00 0.00 0.00 2.57
2795 3138 4.528596 CGGGAATCATAGGGATCTACTTGT 59.471 45.833 0.00 0.00 34.28 3.16
2809 3152 2.485479 GCTACACCATCACGGGAATCAT 60.485 50.000 0.00 0.00 40.22 2.45
2849 3192 5.107065 CCACAAAGTTCTGTATTTCGGAGTC 60.107 44.000 0.00 0.00 32.56 3.36
2892 3235 9.087871 TGGTGGAAGATTATGAAAAAGAATTGA 57.912 29.630 0.00 0.00 0.00 2.57
2895 3238 9.258629 TGATGGTGGAAGATTATGAAAAAGAAT 57.741 29.630 0.00 0.00 0.00 2.40
2905 3248 5.513233 AGTTTGCTGATGGTGGAAGATTAT 58.487 37.500 0.00 0.00 0.00 1.28
2916 3259 1.467920 GGGGAGAAGTTTGCTGATGG 58.532 55.000 0.00 0.00 0.00 3.51
2919 3262 1.344065 TACGGGGAGAAGTTTGCTGA 58.656 50.000 0.00 0.00 0.00 4.26
2920 3263 2.076863 CTTACGGGGAGAAGTTTGCTG 58.923 52.381 0.00 0.00 0.00 4.41
2921 3264 1.610886 GCTTACGGGGAGAAGTTTGCT 60.611 52.381 0.00 0.00 0.00 3.91
2933 3276 2.004733 CGAAAACCCTAAGCTTACGGG 58.995 52.381 26.72 26.72 43.79 5.28
2939 3282 1.271762 GGGGAACGAAAACCCTAAGCT 60.272 52.381 0.00 0.00 44.97 3.74
2970 3313 3.423154 GTGCGGGCGGAAGAGTTG 61.423 66.667 0.00 0.00 0.00 3.16
2984 3327 5.315118 GCTCTTTACATTGTTGTTTGTGC 57.685 39.130 0.00 0.00 37.28 4.57


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

AutoCloner maintained by Alex Coulton.