Multiple sequence alignment - TraesCS5A01G021500

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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 TraesCS5A01G021500 chr5A 100.000 3350 0 0 1 3350 17569346 17572695 0.000000e+00 6187.0
1 TraesCS5A01G021500 chr5A 89.575 518 48 4 2609 3123 599249181 599248667 0.000000e+00 652.0
2 TraesCS5A01G021500 chr5A 89.796 245 20 4 3111 3350 599248756 599248512 3.250000e-80 309.0
3 TraesCS5A01G021500 chr5D 91.810 1685 84 16 638 2284 24332345 24334013 0.000000e+00 2298.0
4 TraesCS5A01G021500 chr5D 94.118 646 24 9 1 643 24331399 24332033 0.000000e+00 970.0
5 TraesCS5A01G021500 chr5D 95.946 74 3 0 2338 2411 24334042 24334115 1.630000e-23 121.0
6 TraesCS5A01G021500 chr5D 94.286 35 2 0 802 836 24332565 24332599 2.000000e-03 54.7
7 TraesCS5A01G021500 chr5B 87.449 1721 130 41 892 2551 17998241 17996546 0.000000e+00 1903.0
8 TraesCS5A01G021500 chr5B 98.182 55 1 0 698 752 17998407 17998353 2.750000e-16 97.1
9 TraesCS5A01G021500 chr7B 90.698 516 44 3 2609 3123 116074026 116073514 0.000000e+00 684.0
10 TraesCS5A01G021500 chr7B 88.934 244 21 4 3111 3350 116073600 116073359 2.530000e-76 296.0
11 TraesCS5A01G021500 chr4A 90.698 516 44 3 2609 3123 411877729 411877217 0.000000e+00 684.0
12 TraesCS5A01G021500 chr4A 88.571 245 18 7 3111 3350 23269992 23269753 4.230000e-74 289.0
13 TraesCS5A01G021500 chr4A 88.163 245 20 6 3111 3350 411877303 411877063 1.970000e-72 283.0
14 TraesCS5A01G021500 chr2A 90.347 518 41 7 2609 3123 73059982 73060493 0.000000e+00 671.0
15 TraesCS5A01G021500 chr2A 89.168 517 52 3 2609 3123 282884736 282884222 2.820000e-180 641.0
16 TraesCS5A01G021500 chr3B 89.942 517 47 4 2609 3123 711736613 711737126 0.000000e+00 662.0
17 TraesCS5A01G021500 chr3B 90.574 244 17 4 3111 3350 711737040 711737281 5.390000e-83 318.0
18 TraesCS5A01G021500 chr7A 89.788 519 46 6 2609 3123 676369105 676369620 0.000000e+00 658.0
19 TraesCS5A01G021500 chr7A 88.163 245 19 7 3111 3350 646503796 646503557 1.970000e-72 283.0
20 TraesCS5A01G021500 chr1A 89.768 518 47 5 2609 3123 529434153 529434667 0.000000e+00 658.0
21 TraesCS5A01G021500 chr1A 89.362 517 48 6 2609 3123 34918014 34918525 0.000000e+00 643.0
22 TraesCS5A01G021500 chr1A 88.571 245 18 8 3111 3350 34918439 34918678 4.230000e-74 289.0
23 TraesCS5A01G021500 chr7D 91.176 238 17 2 3117 3350 63303108 63303345 1.500000e-83 320.0
24 TraesCS5A01G021500 chr3A 88.571 245 19 7 3111 3350 632897876 632898116 4.230000e-74 289.0


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 TraesCS5A01G021500 chr5A 17569346 17572695 3349 False 6187.000 6187 100.0000 1 3350 1 chr5A.!!$F1 3349
1 TraesCS5A01G021500 chr5A 599248512 599249181 669 True 480.500 652 89.6855 2609 3350 2 chr5A.!!$R1 741
2 TraesCS5A01G021500 chr5D 24331399 24334115 2716 False 860.925 2298 94.0400 1 2411 4 chr5D.!!$F1 2410
3 TraesCS5A01G021500 chr5B 17996546 17998407 1861 True 1000.050 1903 92.8155 698 2551 2 chr5B.!!$R1 1853
4 TraesCS5A01G021500 chr7B 116073359 116074026 667 True 490.000 684 89.8160 2609 3350 2 chr7B.!!$R1 741
5 TraesCS5A01G021500 chr4A 411877063 411877729 666 True 483.500 684 89.4305 2609 3350 2 chr4A.!!$R2 741
6 TraesCS5A01G021500 chr2A 73059982 73060493 511 False 671.000 671 90.3470 2609 3123 1 chr2A.!!$F1 514
7 TraesCS5A01G021500 chr2A 282884222 282884736 514 True 641.000 641 89.1680 2609 3123 1 chr2A.!!$R1 514
8 TraesCS5A01G021500 chr3B 711736613 711737281 668 False 490.000 662 90.2580 2609 3350 2 chr3B.!!$F1 741
9 TraesCS5A01G021500 chr7A 676369105 676369620 515 False 658.000 658 89.7880 2609 3123 1 chr7A.!!$F1 514
10 TraesCS5A01G021500 chr1A 529434153 529434667 514 False 658.000 658 89.7680 2609 3123 1 chr1A.!!$F1 514
11 TraesCS5A01G021500 chr1A 34918014 34918678 664 False 466.000 643 88.9665 2609 3350 2 chr1A.!!$F2 741

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
883 1226 1.007502 TGTGGTGGTGCGTACGTAC 60.008 57.895 25.76 25.76 0.0 3.67 F
1224 1597 0.035036 TGGACGACTCTGACGACTCT 59.965 55.000 0.00 0.00 34.7 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2694 0.031716 TGGAGCTACCTGCAGGATCT 60.032 55.0 39.19 28.24 45.94 2.75 R
2959 3399 0.040942 TTGGCCCATATGCTTGTGGT 59.959 50.0 13.32 0.00 32.42 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
26 27 8.528044 TGAACTTCCCTTAGTTGTGTAATTTT 57.472 30.769 0.00 0.00 38.43 1.82
40 41 7.953005 TGTGTAATTTTATGACATCCATGGT 57.047 32.000 12.58 0.00 36.71 3.55
61 62 9.143631 CATGGTAAAAGATTTTTCCTCATGAAC 57.856 33.333 12.93 0.00 38.13 3.18
118 119 4.036262 GGGCATATACGCATCAAACTTCAA 59.964 41.667 0.00 0.00 0.00 2.69
247 248 7.621633 GCGTGTAACTATGTTTCTCCTTTCTTC 60.622 40.741 0.00 0.00 31.75 2.87
315 316 3.860754 GCGGGCACTTCTAAATGCTTTTT 60.861 43.478 2.59 0.00 41.74 1.94
316 317 3.674753 CGGGCACTTCTAAATGCTTTTTG 59.325 43.478 2.59 1.71 41.74 2.44
317 318 3.433274 GGGCACTTCTAAATGCTTTTTGC 59.567 43.478 2.59 6.53 41.74 3.68
318 319 3.121778 GGCACTTCTAAATGCTTTTTGCG 59.878 43.478 2.59 0.00 46.63 4.85
319 320 3.422214 GCACTTCTAAATGCTTTTTGCGC 60.422 43.478 0.00 0.00 46.63 6.09
320 321 3.983344 CACTTCTAAATGCTTTTTGCGCT 59.017 39.130 9.73 0.00 46.63 5.92
321 322 3.983344 ACTTCTAAATGCTTTTTGCGCTG 59.017 39.130 9.73 0.00 46.63 5.18
359 360 5.902681 TCTATCATCTTTGTAGGGTTCACG 58.097 41.667 0.00 0.00 0.00 4.35
361 362 4.188247 TCATCTTTGTAGGGTTCACGAG 57.812 45.455 0.00 0.00 0.00 4.18
366 367 5.617252 TCTTTGTAGGGTTCACGAGATTTT 58.383 37.500 0.00 0.00 0.00 1.82
370 371 5.232463 TGTAGGGTTCACGAGATTTTACAC 58.768 41.667 0.00 0.00 0.00 2.90
429 430 6.372937 GGCATAAAATATTCTACTCCCTCTGC 59.627 42.308 0.00 0.00 0.00 4.26
432 433 5.559148 AAATATTCTACTCCCTCTGCCTG 57.441 43.478 0.00 0.00 0.00 4.85
439 440 3.636153 ACTCCCTCTGCCTGAAAATAC 57.364 47.619 0.00 0.00 0.00 1.89
444 445 2.424956 CCTCTGCCTGAAAATACAAGGC 59.575 50.000 5.97 5.97 45.19 4.35
482 483 8.024865 GGTTAACCTATGATTTGTTTGGTACAC 58.975 37.037 17.83 0.00 39.29 2.90
495 496 7.893124 TGTTTGGTACACCCTTATTTTGTAA 57.107 32.000 0.00 0.00 39.29 2.41
496 497 7.942990 TGTTTGGTACACCCTTATTTTGTAAG 58.057 34.615 0.00 0.00 39.29 2.34
497 498 6.578163 TTGGTACACCCTTATTTTGTAAGC 57.422 37.500 0.00 0.00 39.29 3.09
498 499 5.632118 TGGTACACCCTTATTTTGTAAGCA 58.368 37.500 0.00 0.00 34.29 3.91
499 500 5.474189 TGGTACACCCTTATTTTGTAAGCAC 59.526 40.000 0.00 0.00 34.29 4.40
500 501 5.708697 GGTACACCCTTATTTTGTAAGCACT 59.291 40.000 0.00 0.00 0.00 4.40
501 502 6.208007 GGTACACCCTTATTTTGTAAGCACTT 59.792 38.462 0.00 0.00 0.00 3.16
502 503 7.391275 GGTACACCCTTATTTTGTAAGCACTTA 59.609 37.037 0.00 0.00 0.00 2.24
503 504 7.210718 ACACCCTTATTTTGTAAGCACTTAC 57.789 36.000 12.61 12.61 44.16 2.34
548 552 6.134535 TGGTAAATCAATAAGTGGTGGAGT 57.865 37.500 0.00 0.00 0.00 3.85
838 1181 1.336240 GGATTGTTTGGTGCAGTGCTC 60.336 52.381 17.60 13.00 0.00 4.26
867 1210 1.508632 CGACTCGGATTGTTTGGTGT 58.491 50.000 0.00 0.00 0.00 4.16
883 1226 1.007502 TGTGGTGGTGCGTACGTAC 60.008 57.895 25.76 25.76 0.00 3.67
987 1337 6.371595 ACTACTCTATATAGTACCGGCTGT 57.628 41.667 0.00 0.00 30.94 4.40
1055 1413 1.803519 GCGGAGTCACGAGAAGCAG 60.804 63.158 5.36 0.00 35.47 4.24
1170 1537 1.003718 GGACGACTGGGACAAAGGG 60.004 63.158 0.00 0.00 38.70 3.95
1181 1548 0.804989 GACAAAGGGTTCAGCATCCG 59.195 55.000 0.00 0.00 0.00 4.18
1224 1597 0.035036 TGGACGACTCTGACGACTCT 59.965 55.000 0.00 0.00 34.70 3.24
1293 1666 4.246206 CGTATCACCGAGGCGCGA 62.246 66.667 12.10 0.00 44.57 5.87
1348 1721 0.443869 CATCTTCGTCGCCAACAAGG 59.556 55.000 0.00 0.00 41.84 3.61
1355 1728 0.316689 GTCGCCAACAAGGAACAACG 60.317 55.000 0.00 0.00 41.22 4.10
1356 1729 1.657181 CGCCAACAAGGAACAACGC 60.657 57.895 0.00 0.00 41.22 4.84
1362 1735 2.032071 AAGGAACAACGCTCCCCG 59.968 61.111 0.00 0.00 44.21 5.73
1363 1736 4.699522 AGGAACAACGCTCCCCGC 62.700 66.667 0.00 0.00 41.76 6.13
1365 1738 3.423154 GAACAACGCTCCCCGCAG 61.423 66.667 0.00 0.00 41.76 5.18
1479 1859 3.499737 CGCGGCCGAAGCAAGAAT 61.500 61.111 33.48 0.00 42.56 2.40
1521 1904 0.387367 ACGAGAAGCTGTACACGCTG 60.387 55.000 17.01 9.46 37.87 5.18
1536 1919 0.314935 CGCTGGCAAAAGTTGACCAT 59.685 50.000 0.00 0.00 38.13 3.55
1541 1924 2.238521 GGCAAAAGTTGACCATGGAGA 58.761 47.619 21.47 0.13 30.38 3.71
1758 2141 3.133003 ACACCATATTCTTCTCCACGAGG 59.867 47.826 0.00 0.00 0.00 4.63
1848 2231 0.254178 ACTGGATGCTGCCTTTCGAT 59.746 50.000 0.00 0.00 0.00 3.59
1857 2240 1.299976 GCCTTTCGATGGTCAGGGT 59.700 57.895 6.80 0.00 0.00 4.34
2150 2539 1.870580 CGTGTTCGGCCTCAAGTACAA 60.871 52.381 0.00 0.00 0.00 2.41
2170 2559 4.008933 GTGACGGGGAGCTGCAGT 62.009 66.667 16.64 6.41 0.00 4.40
2193 2582 3.799755 GTCCGCCGCATCACCAAC 61.800 66.667 0.00 0.00 0.00 3.77
2257 2666 5.946942 AGCATTCTGGATGTAGAAGAAGA 57.053 39.130 0.00 0.00 39.81 2.87
2259 2668 6.347696 AGCATTCTGGATGTAGAAGAAGAAG 58.652 40.000 0.00 0.00 39.81 2.85
2262 2671 5.590530 TCTGGATGTAGAAGAAGAAGAGC 57.409 43.478 0.00 0.00 0.00 4.09
2263 2672 5.268387 TCTGGATGTAGAAGAAGAAGAGCT 58.732 41.667 0.00 0.00 0.00 4.09
2267 2676 5.301805 GGATGTAGAAGAAGAAGAGCTAGCT 59.698 44.000 19.45 19.45 0.00 3.32
2268 2677 6.488683 GGATGTAGAAGAAGAAGAGCTAGCTA 59.511 42.308 19.38 0.00 0.00 3.32
2269 2678 6.935741 TGTAGAAGAAGAAGAGCTAGCTAG 57.064 41.667 19.38 16.84 0.00 3.42
2270 2679 5.825679 TGTAGAAGAAGAAGAGCTAGCTAGG 59.174 44.000 19.38 4.48 0.00 3.02
2271 2680 4.867086 AGAAGAAGAAGAGCTAGCTAGGT 58.133 43.478 24.94 24.94 36.62 3.08
2273 2682 6.062095 AGAAGAAGAAGAGCTAGCTAGGTAG 58.938 44.000 24.74 22.09 33.58 3.18
2275 2684 6.008696 AGAAGAAGAGCTAGCTAGGTAGAA 57.991 41.667 28.81 0.00 33.58 2.10
2276 2685 6.062095 AGAAGAAGAGCTAGCTAGGTAGAAG 58.938 44.000 28.81 9.30 33.58 2.85
2279 2688 6.003950 AGAAGAGCTAGCTAGGTAGAAGATG 58.996 44.000 28.81 6.25 33.58 2.90
2281 2690 4.352595 AGAGCTAGCTAGGTAGAAGATGGA 59.647 45.833 28.81 0.00 33.58 3.41
2282 2691 5.015178 AGAGCTAGCTAGGTAGAAGATGGAT 59.985 44.000 28.81 3.03 33.58 3.41
2283 2692 6.216662 AGAGCTAGCTAGGTAGAAGATGGATA 59.783 42.308 28.81 0.00 33.58 2.59
2284 2693 6.184789 AGCTAGCTAGGTAGAAGATGGATAC 58.815 44.000 28.81 9.77 31.28 2.24
2285 2694 6.240321 AGCTAGCTAGGTAGAAGATGGATACA 60.240 42.308 28.81 0.00 41.56 2.29
2286 2695 8.016654 AGCTAGCTAGGTAGAAGATGGATACAG 61.017 44.444 28.81 3.94 40.90 2.74
2300 2709 3.311486 GATACAGATCCTGCAGGTAGC 57.689 52.381 31.58 20.40 45.96 3.58
2302 2711 1.118838 ACAGATCCTGCAGGTAGCTC 58.881 55.000 31.58 21.89 45.94 4.09
2303 2712 0.392336 CAGATCCTGCAGGTAGCTCC 59.608 60.000 31.58 14.88 45.94 4.70
2305 2714 0.392336 GATCCTGCAGGTAGCTCCAG 59.608 60.000 31.58 5.86 45.94 3.86
2306 2715 0.326048 ATCCTGCAGGTAGCTCCAGT 60.326 55.000 31.58 5.72 45.94 4.00
2307 2716 0.335019 TCCTGCAGGTAGCTCCAGTA 59.665 55.000 31.58 5.96 45.94 2.74
2308 2717 0.749649 CCTGCAGGTAGCTCCAGTAG 59.250 60.000 25.53 1.01 45.94 2.57
2309 2718 1.479709 CTGCAGGTAGCTCCAGTAGT 58.520 55.000 5.57 0.00 45.94 2.73
2310 2719 1.407258 CTGCAGGTAGCTCCAGTAGTC 59.593 57.143 5.57 0.00 45.94 2.59
2311 2720 0.382515 GCAGGTAGCTCCAGTAGTCG 59.617 60.000 0.00 0.00 41.15 4.18
2312 2721 1.025812 CAGGTAGCTCCAGTAGTCGG 58.974 60.000 0.00 0.00 39.02 4.79
2313 2722 0.752376 AGGTAGCTCCAGTAGTCGGC 60.752 60.000 0.00 0.00 39.02 5.54
2314 2723 1.734748 GTAGCTCCAGTAGTCGGCC 59.265 63.158 0.00 0.00 0.00 6.13
2317 2726 0.752376 AGCTCCAGTAGTCGGCCTAC 60.752 60.000 0.00 0.00 45.47 3.18
2331 2754 3.510753 TCGGCCTACAAGTGTGTATGTAA 59.489 43.478 0.00 0.00 39.51 2.41
2332 2755 4.160814 TCGGCCTACAAGTGTGTATGTAAT 59.839 41.667 0.00 0.00 39.51 1.89
2333 2756 5.360429 TCGGCCTACAAGTGTGTATGTAATA 59.640 40.000 0.00 0.00 39.51 0.98
2334 2757 6.041182 TCGGCCTACAAGTGTGTATGTAATAT 59.959 38.462 0.00 0.00 39.51 1.28
2335 2758 7.231115 TCGGCCTACAAGTGTGTATGTAATATA 59.769 37.037 0.00 0.00 39.51 0.86
2336 2759 8.033038 CGGCCTACAAGTGTGTATGTAATATAT 58.967 37.037 0.00 0.00 39.51 0.86
2402 2831 9.865484 GAAAGAAAAGAACTACTGACAATGTAC 57.135 33.333 0.00 0.00 0.00 2.90
2405 2834 7.381678 AGAAAAGAACTACTGACAATGTACGTC 59.618 37.037 0.00 0.00 0.00 4.34
2411 2840 6.427974 ACTACTGACAATGTACGTCGATATG 58.572 40.000 0.00 0.00 36.11 1.78
2412 2841 5.244785 ACTGACAATGTACGTCGATATGT 57.755 39.130 0.00 0.00 36.11 2.29
2413 2842 6.367686 ACTGACAATGTACGTCGATATGTA 57.632 37.500 0.00 0.00 36.11 2.29
2414 2843 6.788243 ACTGACAATGTACGTCGATATGTAA 58.212 36.000 0.00 0.00 36.11 2.41
2415 2844 7.423199 ACTGACAATGTACGTCGATATGTAAT 58.577 34.615 0.00 0.00 36.11 1.89
2416 2845 8.562052 ACTGACAATGTACGTCGATATGTAATA 58.438 33.333 0.00 0.00 36.11 0.98
2417 2846 8.718047 TGACAATGTACGTCGATATGTAATAC 57.282 34.615 0.00 0.00 36.11 1.89
2418 2847 7.531534 TGACAATGTACGTCGATATGTAATACG 59.468 37.037 0.00 0.00 36.11 3.06
2420 2849 8.495148 ACAATGTACGTCGATATGTAATACGTA 58.505 33.333 0.00 0.00 44.21 3.57
2480 2918 5.350504 TTTGAACAGGGCTCAAAATGAAA 57.649 34.783 0.00 0.00 39.28 2.69
2485 2923 3.321968 ACAGGGCTCAAAATGAAACTTCC 59.678 43.478 0.00 0.00 0.00 3.46
2491 2929 2.225491 TCAAAATGAAACTTCCGAGCCG 59.775 45.455 0.00 0.00 0.00 5.52
2505 2943 2.127383 GCCGCGTGCACTTACAAC 60.127 61.111 16.19 0.00 40.77 3.32
2514 2952 1.070134 TGCACTTACAACGCCTTCTCT 59.930 47.619 0.00 0.00 0.00 3.10
2515 2953 1.727335 GCACTTACAACGCCTTCTCTC 59.273 52.381 0.00 0.00 0.00 3.20
2517 2955 1.884579 ACTTACAACGCCTTCTCTCGA 59.115 47.619 0.00 0.00 0.00 4.04
2518 2956 2.095161 ACTTACAACGCCTTCTCTCGAG 60.095 50.000 5.93 5.93 0.00 4.04
2519 2957 0.170561 TACAACGCCTTCTCTCGAGC 59.829 55.000 7.81 0.00 0.00 5.03
2532 2970 4.318332 TCTCTCGAGCAACATCACAAAAT 58.682 39.130 7.81 0.00 0.00 1.82
2533 2971 4.389992 TCTCTCGAGCAACATCACAAAATC 59.610 41.667 7.81 0.00 0.00 2.17
2534 2972 3.436704 TCTCGAGCAACATCACAAAATCC 59.563 43.478 7.81 0.00 0.00 3.01
2551 2989 1.204146 TCCGAGCCTGCCTAAGAATT 58.796 50.000 0.00 0.00 0.00 2.17
2552 2990 2.394632 TCCGAGCCTGCCTAAGAATTA 58.605 47.619 0.00 0.00 0.00 1.40
2553 2991 2.972713 TCCGAGCCTGCCTAAGAATTAT 59.027 45.455 0.00 0.00 0.00 1.28
2554 2992 3.070018 CCGAGCCTGCCTAAGAATTATG 58.930 50.000 0.00 0.00 0.00 1.90
2555 2993 2.481952 CGAGCCTGCCTAAGAATTATGC 59.518 50.000 0.00 0.00 41.70 3.14
2565 3003 7.940850 TGCCTAAGAATTATGCAAAATACTCC 58.059 34.615 0.00 0.00 46.59 3.85
2566 3004 7.779798 TGCCTAAGAATTATGCAAAATACTCCT 59.220 33.333 0.00 0.00 46.59 3.69
2567 3005 8.633561 GCCTAAGAATTATGCAAAATACTCCTT 58.366 33.333 0.00 0.00 41.12 3.36
2571 3009 8.814038 AGAATTATGCAAAATACTCCTTCTGT 57.186 30.769 0.00 0.00 0.00 3.41
2572 3010 8.897752 AGAATTATGCAAAATACTCCTTCTGTC 58.102 33.333 0.00 0.00 0.00 3.51
2573 3011 7.573968 ATTATGCAAAATACTCCTTCTGTCC 57.426 36.000 0.00 0.00 0.00 4.02
2574 3012 3.334691 TGCAAAATACTCCTTCTGTCCG 58.665 45.455 0.00 0.00 0.00 4.79
2575 3013 3.007506 TGCAAAATACTCCTTCTGTCCGA 59.992 43.478 0.00 0.00 0.00 4.55
2576 3014 4.000988 GCAAAATACTCCTTCTGTCCGAA 58.999 43.478 0.00 0.00 0.00 4.30
2577 3015 4.454504 GCAAAATACTCCTTCTGTCCGAAA 59.545 41.667 0.00 0.00 0.00 3.46
2578 3016 5.048991 GCAAAATACTCCTTCTGTCCGAAAA 60.049 40.000 0.00 0.00 0.00 2.29
2579 3017 6.349363 GCAAAATACTCCTTCTGTCCGAAAAT 60.349 38.462 0.00 0.00 0.00 1.82
2580 3018 7.148306 GCAAAATACTCCTTCTGTCCGAAAATA 60.148 37.037 0.00 0.00 0.00 1.40
2581 3019 7.845066 AAATACTCCTTCTGTCCGAAAATAC 57.155 36.000 0.00 0.00 0.00 1.89
2582 3020 6.793505 ATACTCCTTCTGTCCGAAAATACT 57.206 37.500 0.00 0.00 0.00 2.12
2583 3021 5.485209 ACTCCTTCTGTCCGAAAATACTT 57.515 39.130 0.00 0.00 0.00 2.24
2584 3022 6.600882 ACTCCTTCTGTCCGAAAATACTTA 57.399 37.500 0.00 0.00 0.00 2.24
2585 3023 7.184067 ACTCCTTCTGTCCGAAAATACTTAT 57.816 36.000 0.00 0.00 0.00 1.73
2586 3024 7.266400 ACTCCTTCTGTCCGAAAATACTTATC 58.734 38.462 0.00 0.00 0.00 1.75
2587 3025 6.270815 TCCTTCTGTCCGAAAATACTTATCG 58.729 40.000 0.00 0.00 36.39 2.92
2588 3026 5.050972 CCTTCTGTCCGAAAATACTTATCGC 60.051 44.000 0.00 0.00 35.35 4.58
2589 3027 4.365723 TCTGTCCGAAAATACTTATCGCC 58.634 43.478 0.00 0.00 35.35 5.54
2590 3028 3.117794 TGTCCGAAAATACTTATCGCCG 58.882 45.455 0.00 0.00 35.35 6.46
2591 3029 3.181488 TGTCCGAAAATACTTATCGCCGA 60.181 43.478 0.00 0.00 35.35 5.54
2592 3030 3.798337 GTCCGAAAATACTTATCGCCGAA 59.202 43.478 0.00 0.00 35.35 4.30
2593 3031 4.268405 GTCCGAAAATACTTATCGCCGAAA 59.732 41.667 0.00 0.00 35.35 3.46
2594 3032 5.050567 GTCCGAAAATACTTATCGCCGAAAT 60.051 40.000 0.00 0.00 35.35 2.17
2595 3033 5.050634 TCCGAAAATACTTATCGCCGAAATG 60.051 40.000 0.00 0.00 35.35 2.32
2596 3034 5.137403 CGAAAATACTTATCGCCGAAATGG 58.863 41.667 0.00 0.00 42.50 3.16
2597 3035 5.050634 CGAAAATACTTATCGCCGAAATGGA 60.051 40.000 0.00 0.00 42.00 3.41
2598 3036 6.347402 CGAAAATACTTATCGCCGAAATGGAT 60.347 38.462 0.00 0.00 42.00 3.41
2599 3037 5.862924 AATACTTATCGCCGAAATGGATG 57.137 39.130 0.00 0.00 42.00 3.51
2600 3038 3.194005 ACTTATCGCCGAAATGGATGT 57.806 42.857 0.00 0.00 42.00 3.06
2601 3039 4.330944 ACTTATCGCCGAAATGGATGTA 57.669 40.909 0.00 0.00 42.00 2.29
2602 3040 4.894784 ACTTATCGCCGAAATGGATGTAT 58.105 39.130 0.00 0.00 42.00 2.29
2603 3041 4.929808 ACTTATCGCCGAAATGGATGTATC 59.070 41.667 0.00 0.00 42.00 2.24
2604 3042 3.685139 ATCGCCGAAATGGATGTATCT 57.315 42.857 0.00 0.00 42.00 1.98
2605 3043 3.469008 TCGCCGAAATGGATGTATCTT 57.531 42.857 0.00 0.00 42.00 2.40
2606 3044 4.594123 TCGCCGAAATGGATGTATCTTA 57.406 40.909 0.00 0.00 42.00 2.10
2607 3045 5.147330 TCGCCGAAATGGATGTATCTTAT 57.853 39.130 0.00 0.00 42.00 1.73
2677 3115 9.887406 ATTCGTCATTGTTTTCGTTTATTTACT 57.113 25.926 0.00 0.00 0.00 2.24
2771 3210 1.000739 CATGGCCACCCTTGACCAT 59.999 57.895 8.16 0.00 43.70 3.55
2848 3287 1.410517 CACGTAGGATCTGATGTGGCT 59.589 52.381 0.00 0.00 0.00 4.75
2884 3323 0.394080 TGCGATGACATGGATGCCAA 60.394 50.000 1.05 0.00 36.95 4.52
2894 3333 1.788229 TGGATGCCAAGTAGGATCGA 58.212 50.000 0.00 0.00 41.22 3.59
2959 3399 7.797062 AGCCCACTTTTAAATTTACTTTTGGA 58.203 30.769 13.24 0.00 0.00 3.53
2970 3410 6.909550 ATTTACTTTTGGACCACAAGCATA 57.090 33.333 18.44 3.63 40.82 3.14
2971 3411 6.909550 TTTACTTTTGGACCACAAGCATAT 57.090 33.333 18.44 3.81 40.82 1.78
3004 3444 3.228188 ACAAATCAGTTCTTGGGCTGA 57.772 42.857 0.00 0.00 44.55 4.26
3007 3447 0.034670 ATCAGTTCTTGGGCTGAGGC 60.035 55.000 0.00 0.00 43.81 4.70
3008 3448 1.073722 CAGTTCTTGGGCTGAGGCA 59.926 57.895 8.68 0.00 40.87 4.75
3028 3468 6.661777 AGGCATGCAACCCATTTATTTAATT 58.338 32.000 21.36 0.00 29.71 1.40
3032 3472 8.623030 GCATGCAACCCATTTATTTAATTCATT 58.377 29.630 14.21 0.00 29.71 2.57
3047 3487 8.900983 TTTAATTCATTATTAATTGGGCCAGC 57.099 30.769 6.23 0.00 38.24 4.85
3048 3488 4.953940 TTCATTATTAATTGGGCCAGCC 57.046 40.909 6.23 0.00 0.00 4.85
3049 3489 7.474079 TTAATTCATTATTAATTGGGCCAGCCC 60.474 37.037 21.38 21.38 43.04 5.19
3060 3500 1.610363 GGCCAGCCCTTTTATCTAGC 58.390 55.000 0.00 0.00 0.00 3.42
3061 3501 1.610363 GCCAGCCCTTTTATCTAGCC 58.390 55.000 0.00 0.00 0.00 3.93
3062 3502 1.133792 GCCAGCCCTTTTATCTAGCCA 60.134 52.381 0.00 0.00 0.00 4.75
3063 3503 2.686715 GCCAGCCCTTTTATCTAGCCAA 60.687 50.000 0.00 0.00 0.00 4.52
3064 3504 2.952310 CCAGCCCTTTTATCTAGCCAAC 59.048 50.000 0.00 0.00 0.00 3.77
3065 3505 3.620488 CAGCCCTTTTATCTAGCCAACA 58.380 45.455 0.00 0.00 0.00 3.33
3066 3506 4.016444 CAGCCCTTTTATCTAGCCAACAA 58.984 43.478 0.00 0.00 0.00 2.83
3067 3507 4.462483 CAGCCCTTTTATCTAGCCAACAAA 59.538 41.667 0.00 0.00 0.00 2.83
3068 3508 5.047377 CAGCCCTTTTATCTAGCCAACAAAA 60.047 40.000 0.00 0.00 0.00 2.44
3069 3509 5.542251 AGCCCTTTTATCTAGCCAACAAAAA 59.458 36.000 0.00 0.00 0.00 1.94
3070 3510 5.637810 GCCCTTTTATCTAGCCAACAAAAAC 59.362 40.000 0.00 0.00 0.00 2.43
3071 3511 6.740122 GCCCTTTTATCTAGCCAACAAAAACA 60.740 38.462 0.00 0.00 0.00 2.83
3072 3512 7.386059 CCCTTTTATCTAGCCAACAAAAACAT 58.614 34.615 0.00 0.00 0.00 2.71
3073 3513 7.877612 CCCTTTTATCTAGCCAACAAAAACATT 59.122 33.333 0.00 0.00 0.00 2.71
3074 3514 9.271828 CCTTTTATCTAGCCAACAAAAACATTT 57.728 29.630 0.00 0.00 0.00 2.32
3077 3517 9.823647 TTTATCTAGCCAACAAAAACATTTTGA 57.176 25.926 19.24 0.00 33.83 2.69
3078 3518 9.995003 TTATCTAGCCAACAAAAACATTTTGAT 57.005 25.926 19.24 7.40 33.83 2.57
3079 3519 8.907222 ATCTAGCCAACAAAAACATTTTGATT 57.093 26.923 19.24 9.09 33.83 2.57
3080 3520 8.729805 TCTAGCCAACAAAAACATTTTGATTT 57.270 26.923 19.24 4.60 33.83 2.17
3081 3521 9.171877 TCTAGCCAACAAAAACATTTTGATTTT 57.828 25.926 19.24 1.16 33.51 1.82
3082 3522 9.786105 CTAGCCAACAAAAACATTTTGATTTTT 57.214 25.926 19.24 4.09 38.28 1.94
3113 3553 3.915437 AACTGTATTGGCCTTGAAACG 57.085 42.857 3.32 0.00 0.00 3.60
3114 3554 2.159382 ACTGTATTGGCCTTGAAACGG 58.841 47.619 3.32 2.97 0.00 4.44
3115 3555 2.159382 CTGTATTGGCCTTGAAACGGT 58.841 47.619 3.32 0.00 0.00 4.83
3116 3556 2.156098 TGTATTGGCCTTGAAACGGTC 58.844 47.619 3.32 0.00 0.00 4.79
3117 3557 1.471287 GTATTGGCCTTGAAACGGTCC 59.529 52.381 3.32 0.00 0.00 4.46
3192 3637 5.437060 ACTATATTGGCATTGAAACGGTCT 58.563 37.500 0.00 0.00 0.00 3.85
3214 3659 4.634012 AGCCCACTCACACAATTTAGTA 57.366 40.909 0.00 0.00 0.00 1.82
3221 3666 8.023128 CCCACTCACACAATTTAGTATTTTCAG 58.977 37.037 0.00 0.00 0.00 3.02
3260 3705 1.203523 GTGACCAGCAACAACCAACAA 59.796 47.619 0.00 0.00 0.00 2.83
3266 3711 5.321102 ACCAGCAACAACCAACAATATCTA 58.679 37.500 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 7.308951 GGGTCGTTCATGAGGAAAAATCTTTTA 60.309 37.037 0.00 0.00 37.23 1.52
61 62 0.881118 CACCTTCCATGTTTGGGTCG 59.119 55.000 0.00 0.00 43.81 4.79
118 119 9.470399 AGGTTTTTCGGGTATATCAAATTTACT 57.530 29.630 0.00 0.00 0.00 2.24
219 220 5.148651 AGGAGAAACATAGTTACACGCTT 57.851 39.130 0.00 0.00 0.00 4.68
315 316 0.810648 GGATGGAATGAAACAGCGCA 59.189 50.000 11.47 0.00 0.00 6.09
316 317 0.101219 GGGATGGAATGAAACAGCGC 59.899 55.000 0.00 0.00 0.00 5.92
317 318 1.672881 GAGGGATGGAATGAAACAGCG 59.327 52.381 0.00 0.00 0.00 5.18
318 319 3.010200 AGAGGGATGGAATGAAACAGC 57.990 47.619 0.00 0.00 0.00 4.40
319 320 5.933617 TGATAGAGGGATGGAATGAAACAG 58.066 41.667 0.00 0.00 0.00 3.16
320 321 5.974156 TGATAGAGGGATGGAATGAAACA 57.026 39.130 0.00 0.00 0.00 2.83
321 322 6.777782 AGATGATAGAGGGATGGAATGAAAC 58.222 40.000 0.00 0.00 0.00 2.78
361 362 9.922305 GCAGTTATCTAGTGATTGTGTAAAATC 57.078 33.333 0.00 0.00 37.13 2.17
366 367 6.095021 ACGAGCAGTTATCTAGTGATTGTGTA 59.905 38.462 0.00 0.00 38.48 2.90
370 371 5.230936 CACACGAGCAGTTATCTAGTGATTG 59.769 44.000 9.56 0.00 38.79 2.67
453 454 7.438564 ACCAAACAAATCATAGGTTAACCAAC 58.561 34.615 26.26 0.00 38.89 3.77
454 455 7.604657 ACCAAACAAATCATAGGTTAACCAA 57.395 32.000 26.26 9.21 38.89 3.67
455 456 7.724506 TGTACCAAACAAATCATAGGTTAACCA 59.275 33.333 26.26 12.70 34.85 3.67
482 483 7.553044 AGCTAGTAAGTGCTTACAAAATAAGGG 59.447 37.037 20.14 4.81 45.79 3.95
548 552 8.558700 GGTATTTACTGAAAAACGGACAAACTA 58.441 33.333 0.00 0.00 0.00 2.24
587 591 6.596869 TTTTATTCCCTCCCATCTCTGATT 57.403 37.500 0.00 0.00 0.00 2.57
588 592 6.596869 TTTTTATTCCCTCCCATCTCTGAT 57.403 37.500 0.00 0.00 0.00 2.90
589 593 6.160282 TGATTTTTATTCCCTCCCATCTCTGA 59.840 38.462 0.00 0.00 0.00 3.27
590 594 6.367983 TGATTTTTATTCCCTCCCATCTCTG 58.632 40.000 0.00 0.00 0.00 3.35
594 598 7.047891 GGTTTTGATTTTTATTCCCTCCCATC 58.952 38.462 0.00 0.00 0.00 3.51
596 600 5.846714 TGGTTTTGATTTTTATTCCCTCCCA 59.153 36.000 0.00 0.00 0.00 4.37
599 603 8.122472 TCTCTGGTTTTGATTTTTATTCCCTC 57.878 34.615 0.00 0.00 0.00 4.30
600 604 7.950124 TCTCTCTGGTTTTGATTTTTATTCCCT 59.050 33.333 0.00 0.00 0.00 4.20
661 984 4.237976 ACCTCTCTCTTCACTCGGATTA 57.762 45.455 0.00 0.00 0.00 1.75
752 1084 4.754667 GTCGGGGGCGGTGAAGAC 62.755 72.222 0.00 0.00 0.00 3.01
775 1117 2.897846 CCGTTTGCCACACGTCCA 60.898 61.111 2.43 0.00 35.81 4.02
867 1210 2.254951 CGTACGTACGCACCACCA 59.745 61.111 32.36 0.00 43.14 4.17
888 1231 1.826385 CAATGGCGAGGAAAGGAAGT 58.174 50.000 0.00 0.00 0.00 3.01
1038 1388 1.803519 GCTGCTTCTCGTGACTCCG 60.804 63.158 0.00 0.00 0.00 4.63
1055 1413 3.554692 CCATCGTTGAGCCGACGC 61.555 66.667 9.37 0.00 40.63 5.19
1170 1537 1.427020 GAGCTTGCGGATGCTGAAC 59.573 57.895 21.78 4.23 43.34 3.18
1293 1666 1.115467 CGAAGAGCATAGGGGAGTGT 58.885 55.000 0.00 0.00 0.00 3.55
1374 1747 1.663379 CCGTGTCGTAGATGAGGGCA 61.663 60.000 0.00 0.00 40.67 5.36
1468 1848 2.160417 GTCCCTTGTCATTCTTGCTTCG 59.840 50.000 0.00 0.00 0.00 3.79
1469 1849 2.160417 CGTCCCTTGTCATTCTTGCTTC 59.840 50.000 0.00 0.00 0.00 3.86
1477 1857 4.345859 TGTACTTTCGTCCCTTGTCATT 57.654 40.909 0.00 0.00 0.00 2.57
1479 1859 3.460103 GTTGTACTTTCGTCCCTTGTCA 58.540 45.455 0.00 0.00 0.00 3.58
1495 1875 2.549329 TGTACAGCTTCTCGTCGTTGTA 59.451 45.455 0.00 0.00 0.00 2.41
1521 1904 2.029918 GTCTCCATGGTCAACTTTTGCC 60.030 50.000 12.58 0.00 0.00 4.52
1536 1919 2.093500 CGGGTGATTTGATCTGTCTCCA 60.093 50.000 12.42 0.00 0.00 3.86
1541 1924 1.740380 CGCTCGGGTGATTTGATCTGT 60.740 52.381 0.00 0.00 0.00 3.41
1736 2119 3.133003 CCTCGTGGAGAAGAATATGGTGT 59.867 47.826 0.00 0.00 34.57 4.16
1776 2159 1.449778 GAAAGAGTAGGTGCCCGCC 60.450 63.158 0.00 0.00 0.00 6.13
1791 2174 2.733218 CGCTGCTCCGTGTCGAAA 60.733 61.111 0.00 0.00 0.00 3.46
1830 2213 0.661552 CATCGAAAGGCAGCATCCAG 59.338 55.000 0.00 0.00 0.00 3.86
1834 2217 0.035152 TGACCATCGAAAGGCAGCAT 60.035 50.000 7.15 0.00 0.00 3.79
1848 2231 2.564062 CCTTTCGTAGTAACCCTGACCA 59.436 50.000 0.00 0.00 0.00 4.02
1857 2240 2.421424 GTCGAGCTCCCTTTCGTAGTAA 59.579 50.000 8.47 0.00 37.99 2.24
2185 2574 1.153901 CCGCGTACGAGTTGGTGAT 60.154 57.895 21.65 0.00 43.93 3.06
2193 2582 2.126618 TTGCAGACCGCGTACGAG 60.127 61.111 21.65 16.82 46.97 4.18
2255 2664 5.640158 TCTTCTACCTAGCTAGCTCTTCT 57.360 43.478 23.26 4.93 0.00 2.85
2257 2666 5.076873 CCATCTTCTACCTAGCTAGCTCTT 58.923 45.833 23.26 9.22 0.00 2.85
2259 2668 4.658063 TCCATCTTCTACCTAGCTAGCTC 58.342 47.826 23.26 0.00 0.00 4.09
2262 2671 7.398829 TCTGTATCCATCTTCTACCTAGCTAG 58.601 42.308 14.20 14.20 0.00 3.42
2263 2672 7.331089 TCTGTATCCATCTTCTACCTAGCTA 57.669 40.000 0.00 0.00 0.00 3.32
2279 2688 4.322340 AGCTACCTGCAGGATCTGTATCC 61.322 52.174 39.19 13.48 44.92 2.59
2281 2690 2.896685 GAGCTACCTGCAGGATCTGTAT 59.103 50.000 39.19 17.30 45.94 2.29
2282 2691 2.311463 GAGCTACCTGCAGGATCTGTA 58.689 52.381 39.19 18.99 45.94 2.74
2283 2692 1.118838 GAGCTACCTGCAGGATCTGT 58.881 55.000 39.19 18.87 45.94 3.41
2284 2693 0.392336 GGAGCTACCTGCAGGATCTG 59.608 60.000 39.19 23.43 45.94 2.90
2285 2694 0.031716 TGGAGCTACCTGCAGGATCT 60.032 55.000 39.19 28.24 45.94 2.75
2286 2695 2.521103 TGGAGCTACCTGCAGGATC 58.479 57.895 39.19 26.44 45.94 3.36
2287 2696 4.816109 TGGAGCTACCTGCAGGAT 57.184 55.556 39.19 24.04 45.94 3.24
2291 2700 1.475403 GACTACTGGAGCTACCTGCA 58.525 55.000 0.00 0.00 45.94 4.41
2292 2701 0.382515 CGACTACTGGAGCTACCTGC 59.617 60.000 0.00 0.00 40.59 4.85
2293 2702 1.025812 CCGACTACTGGAGCTACCTG 58.974 60.000 0.00 0.46 42.26 4.00
2294 2703 0.752376 GCCGACTACTGGAGCTACCT 60.752 60.000 0.00 0.00 39.86 3.08
2295 2704 1.734748 GCCGACTACTGGAGCTACC 59.265 63.158 0.00 0.00 39.54 3.18
2296 2705 0.752376 AGGCCGACTACTGGAGCTAC 60.752 60.000 0.00 0.00 0.00 3.58
2298 2707 0.752376 GTAGGCCGACTACTGGAGCT 60.752 60.000 9.01 0.00 46.89 4.09
2299 2708 1.734748 GTAGGCCGACTACTGGAGC 59.265 63.158 9.01 0.00 46.89 4.70
2306 2715 1.624336 ACACACTTGTAGGCCGACTA 58.376 50.000 17.46 8.78 32.60 2.59
2307 2716 1.624336 TACACACTTGTAGGCCGACT 58.376 50.000 17.46 0.00 37.15 4.18
2308 2717 2.268298 CATACACACTTGTAGGCCGAC 58.732 52.381 9.38 9.38 41.62 4.79
2309 2718 1.897133 ACATACACACTTGTAGGCCGA 59.103 47.619 0.00 0.00 42.61 5.54
2310 2719 2.380084 ACATACACACTTGTAGGCCG 57.620 50.000 0.00 0.00 42.61 6.13
2336 2759 9.725019 AGACAAGATGTTTCTGAATACATTGTA 57.275 29.630 15.95 0.00 35.24 2.41
2446 2876 7.039152 TGAGCCCTGTTCAAATATTTTGATCAA 60.039 33.333 3.38 3.38 30.54 2.57
2449 2879 6.855763 TGAGCCCTGTTCAAATATTTTGAT 57.144 33.333 0.00 0.00 0.00 2.57
2460 2890 3.960102 AGTTTCATTTTGAGCCCTGTTCA 59.040 39.130 0.00 0.00 0.00 3.18
2461 2891 4.590850 AGTTTCATTTTGAGCCCTGTTC 57.409 40.909 0.00 0.00 0.00 3.18
2468 2898 3.237628 GCTCGGAAGTTTCATTTTGAGC 58.762 45.455 0.00 0.00 40.50 4.26
2485 2923 3.838795 GTAAGTGCACGCGGCTCG 61.839 66.667 12.47 0.00 45.15 5.03
2505 2943 0.459237 ATGTTGCTCGAGAGAAGGCG 60.459 55.000 18.75 0.00 41.32 5.52
2514 2952 2.159430 CGGATTTTGTGATGTTGCTCGA 59.841 45.455 0.00 0.00 0.00 4.04
2515 2953 2.159430 TCGGATTTTGTGATGTTGCTCG 59.841 45.455 0.00 0.00 0.00 5.03
2517 2955 2.095059 GCTCGGATTTTGTGATGTTGCT 60.095 45.455 0.00 0.00 0.00 3.91
2518 2956 2.253603 GCTCGGATTTTGTGATGTTGC 58.746 47.619 0.00 0.00 0.00 4.17
2519 2957 2.489329 AGGCTCGGATTTTGTGATGTTG 59.511 45.455 0.00 0.00 0.00 3.33
2532 2970 1.204146 AATTCTTAGGCAGGCTCGGA 58.796 50.000 0.00 0.00 0.00 4.55
2533 2971 2.910688 TAATTCTTAGGCAGGCTCGG 57.089 50.000 0.00 0.00 0.00 4.63
2534 2972 2.481952 GCATAATTCTTAGGCAGGCTCG 59.518 50.000 0.00 0.00 42.12 5.03
2551 2989 5.105106 TCGGACAGAAGGAGTATTTTGCATA 60.105 40.000 0.00 0.00 0.00 3.14
2552 2990 3.941483 CGGACAGAAGGAGTATTTTGCAT 59.059 43.478 0.00 0.00 0.00 3.96
2553 2991 3.007506 TCGGACAGAAGGAGTATTTTGCA 59.992 43.478 0.00 0.00 0.00 4.08
2554 2992 3.596214 TCGGACAGAAGGAGTATTTTGC 58.404 45.455 0.00 0.00 0.00 3.68
2555 2993 6.554334 TTTTCGGACAGAAGGAGTATTTTG 57.446 37.500 0.00 0.00 40.40 2.44
2556 2994 8.101419 AGTATTTTCGGACAGAAGGAGTATTTT 58.899 33.333 0.00 0.00 40.40 1.82
2557 2995 7.621796 AGTATTTTCGGACAGAAGGAGTATTT 58.378 34.615 0.00 0.00 40.40 1.40
2558 2996 7.184067 AGTATTTTCGGACAGAAGGAGTATT 57.816 36.000 0.00 0.00 40.40 1.89
2559 2997 6.793505 AGTATTTTCGGACAGAAGGAGTAT 57.206 37.500 0.00 0.00 40.40 2.12
2560 2998 6.600882 AAGTATTTTCGGACAGAAGGAGTA 57.399 37.500 0.00 0.00 40.40 2.59
2561 2999 5.485209 AAGTATTTTCGGACAGAAGGAGT 57.515 39.130 0.00 0.00 40.40 3.85
2562 3000 6.418226 CGATAAGTATTTTCGGACAGAAGGAG 59.582 42.308 0.00 0.00 44.05 3.69
2563 3001 6.270815 CGATAAGTATTTTCGGACAGAAGGA 58.729 40.000 0.00 0.00 44.05 3.36
2564 3002 6.512177 CGATAAGTATTTTCGGACAGAAGG 57.488 41.667 0.00 0.00 44.05 3.46
2574 3012 6.295039 TCCATTTCGGCGATAAGTATTTTC 57.705 37.500 11.76 0.00 33.14 2.29
2575 3013 6.262273 ACATCCATTTCGGCGATAAGTATTTT 59.738 34.615 11.76 0.00 33.14 1.82
2576 3014 5.763204 ACATCCATTTCGGCGATAAGTATTT 59.237 36.000 11.76 0.00 33.14 1.40
2577 3015 5.305585 ACATCCATTTCGGCGATAAGTATT 58.694 37.500 11.76 0.00 33.14 1.89
2578 3016 4.894784 ACATCCATTTCGGCGATAAGTAT 58.105 39.130 11.76 0.00 33.14 2.12
2579 3017 4.330944 ACATCCATTTCGGCGATAAGTA 57.669 40.909 11.76 0.00 33.14 2.24
2580 3018 3.194005 ACATCCATTTCGGCGATAAGT 57.806 42.857 11.76 0.00 33.14 2.24
2581 3019 5.171476 AGATACATCCATTTCGGCGATAAG 58.829 41.667 11.76 2.45 33.14 1.73
2582 3020 5.147330 AGATACATCCATTTCGGCGATAA 57.853 39.130 11.76 8.71 33.14 1.75
2583 3021 4.801330 AGATACATCCATTTCGGCGATA 57.199 40.909 11.76 6.43 33.14 2.92
2584 3022 3.685139 AGATACATCCATTTCGGCGAT 57.315 42.857 11.76 0.00 33.14 4.58
2585 3023 3.469008 AAGATACATCCATTTCGGCGA 57.531 42.857 4.99 4.99 33.14 5.54
2586 3024 5.862924 AATAAGATACATCCATTTCGGCG 57.137 39.130 0.00 0.00 33.14 6.46
2587 3025 7.667043 TGTAATAAGATACATCCATTTCGGC 57.333 36.000 0.00 0.00 31.03 5.54
2588 3026 9.489084 TCTTGTAATAAGATACATCCATTTCGG 57.511 33.333 0.00 0.00 35.80 4.30
2622 3060 8.258007 ACGACCAAAATAGAGAGTCATAATTGA 58.742 33.333 0.00 0.00 0.00 2.57
2635 3073 7.837202 ATGACGAATTAACGACCAAAATAGA 57.163 32.000 0.00 0.00 37.03 1.98
2729 3168 4.100963 ACCAAAATTCCAGAAAAGGTCACC 59.899 41.667 0.00 0.00 0.00 4.02
2738 3177 2.566724 GGCCATGACCAAAATTCCAGAA 59.433 45.455 0.00 0.00 0.00 3.02
2771 3210 7.309920 GGTCAAAGATTTAGCGACCAAAATTA 58.690 34.615 0.00 0.00 44.55 1.40
2810 3249 7.994911 TCCTACGTGATCTAGGTTCATTAGTAA 59.005 37.037 0.00 0.00 33.58 2.24
2827 3266 1.409064 GCCACATCAGATCCTACGTGA 59.591 52.381 0.00 0.00 0.00 4.35
2894 3333 6.013466 AGCCCATTAAAACAACTGATTTGGAT 60.013 34.615 0.00 0.00 39.84 3.41
2933 3373 8.925338 TCCAAAAGTAAATTTAAAAGTGGGCTA 58.075 29.630 14.55 0.00 28.67 3.93
2959 3399 0.040942 TTGGCCCATATGCTTGTGGT 59.959 50.000 13.32 0.00 32.42 4.16
2987 3427 1.615384 GCCTCAGCCCAAGAACTGATT 60.615 52.381 0.00 0.00 41.84 2.57
3004 3444 5.690464 TTAAATAAATGGGTTGCATGCCT 57.310 34.783 16.68 0.00 0.00 4.75
3045 3485 4.316025 TTGTTGGCTAGATAAAAGGGCT 57.684 40.909 0.00 0.00 0.00 5.19
3046 3486 5.400066 TTTTGTTGGCTAGATAAAAGGGC 57.600 39.130 0.00 0.00 0.00 5.19
3047 3487 6.754193 TGTTTTTGTTGGCTAGATAAAAGGG 58.246 36.000 0.00 0.00 0.00 3.95
3048 3488 8.831715 AATGTTTTTGTTGGCTAGATAAAAGG 57.168 30.769 0.00 0.00 0.00 3.11
3051 3491 9.823647 TCAAAATGTTTTTGTTGGCTAGATAAA 57.176 25.926 11.30 0.00 0.00 1.40
3052 3492 9.995003 ATCAAAATGTTTTTGTTGGCTAGATAA 57.005 25.926 11.30 0.00 0.00 1.75
3053 3493 9.995003 AATCAAAATGTTTTTGTTGGCTAGATA 57.005 25.926 11.30 0.00 0.00 1.98
3054 3494 8.907222 AATCAAAATGTTTTTGTTGGCTAGAT 57.093 26.923 11.30 0.00 0.00 1.98
3055 3495 8.729805 AAATCAAAATGTTTTTGTTGGCTAGA 57.270 26.923 11.30 0.00 0.00 2.43
3056 3496 9.786105 AAAAATCAAAATGTTTTTGTTGGCTAG 57.214 25.926 11.30 0.00 36.48 3.42
3090 3530 5.047188 CGTTTCAAGGCCAATACAGTTTTT 58.953 37.500 5.01 0.00 0.00 1.94
3091 3531 4.500716 CCGTTTCAAGGCCAATACAGTTTT 60.501 41.667 5.01 0.00 0.00 2.43
3092 3532 3.005367 CCGTTTCAAGGCCAATACAGTTT 59.995 43.478 5.01 0.00 0.00 2.66
3093 3533 2.556622 CCGTTTCAAGGCCAATACAGTT 59.443 45.455 5.01 0.00 0.00 3.16
3094 3534 2.159382 CCGTTTCAAGGCCAATACAGT 58.841 47.619 5.01 0.00 0.00 3.55
3095 3535 2.159382 ACCGTTTCAAGGCCAATACAG 58.841 47.619 5.01 0.00 0.00 2.74
3096 3536 2.156098 GACCGTTTCAAGGCCAATACA 58.844 47.619 5.01 0.00 0.00 2.29
3097 3537 1.471287 GGACCGTTTCAAGGCCAATAC 59.529 52.381 5.01 0.00 0.00 1.89
3098 3538 1.074084 TGGACCGTTTCAAGGCCAATA 59.926 47.619 5.01 0.00 33.95 1.90
3099 3539 0.178975 TGGACCGTTTCAAGGCCAAT 60.179 50.000 5.01 0.00 33.95 3.16
3100 3540 0.821711 CTGGACCGTTTCAAGGCCAA 60.822 55.000 5.01 0.00 35.58 4.52
3101 3541 1.228124 CTGGACCGTTTCAAGGCCA 60.228 57.895 5.01 0.00 35.04 5.36
3102 3542 2.626780 GCTGGACCGTTTCAAGGCC 61.627 63.158 0.00 0.00 0.00 5.19
3103 3543 2.626780 GGCTGGACCGTTTCAAGGC 61.627 63.158 0.00 0.00 43.38 4.35
3104 3544 1.971695 GGGCTGGACCGTTTCAAGG 60.972 63.158 0.00 0.00 40.62 3.61
3105 3545 0.537371 AAGGGCTGGACCGTTTCAAG 60.537 55.000 0.00 0.00 44.14 3.02
3106 3546 1.534697 AAGGGCTGGACCGTTTCAA 59.465 52.632 0.00 0.00 44.14 2.69
3107 3547 3.246687 AAGGGCTGGACCGTTTCA 58.753 55.556 0.00 0.00 44.14 2.69
3111 3551 1.286248 AGATAAAAGGGCTGGACCGT 58.714 50.000 0.00 0.00 40.62 4.83
3112 3552 2.484947 GGTAGATAAAAGGGCTGGACCG 60.485 54.545 0.00 0.00 40.62 4.79
3113 3553 2.158652 GGGTAGATAAAAGGGCTGGACC 60.159 54.545 0.00 0.00 37.93 4.46
3114 3554 2.508300 TGGGTAGATAAAAGGGCTGGAC 59.492 50.000 0.00 0.00 0.00 4.02
3115 3555 2.853430 TGGGTAGATAAAAGGGCTGGA 58.147 47.619 0.00 0.00 0.00 3.86
3116 3556 3.288092 GTTGGGTAGATAAAAGGGCTGG 58.712 50.000 0.00 0.00 0.00 4.85
3117 3557 3.963129 TGTTGGGTAGATAAAAGGGCTG 58.037 45.455 0.00 0.00 0.00 4.85
3171 3616 5.468746 GCTAGACCGTTTCAATGCCAATATA 59.531 40.000 0.00 0.00 0.00 0.86
3172 3617 4.275936 GCTAGACCGTTTCAATGCCAATAT 59.724 41.667 0.00 0.00 0.00 1.28
3173 3618 3.625764 GCTAGACCGTTTCAATGCCAATA 59.374 43.478 0.00 0.00 0.00 1.90
3174 3619 2.423538 GCTAGACCGTTTCAATGCCAAT 59.576 45.455 0.00 0.00 0.00 3.16
3180 3625 1.628846 AGTGGGCTAGACCGTTTCAAT 59.371 47.619 10.91 0.00 40.62 2.57
3192 3637 4.634012 ACTAAATTGTGTGAGTGGGCTA 57.366 40.909 0.00 0.00 0.00 3.93
3214 3659 4.934356 TCAATAAGGGCTGGACTGAAAAT 58.066 39.130 0.00 0.00 0.00 1.82
3272 3717 8.987890 ACTGCCAAATTGTGTAATGTATTTTTC 58.012 29.630 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.