Multiple sequence alignment - TraesCS1A01G372100

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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 TraesCS1A01G372100 chr1A 100.000 3329 0 0 1 3329 548732372 548735700 0.000000e+00 6148.0
1 TraesCS1A01G372100 chr1A 90.664 1371 104 11 961 2325 548772380 548773732 0.000000e+00 1801.0
2 TraesCS1A01G372100 chr1A 89.608 1251 105 13 939 2172 548789270 548790512 0.000000e+00 1567.0
3 TraesCS1A01G372100 chr1A 78.916 498 57 28 71 523 548771392 548771886 9.030000e-76 294.0
4 TraesCS1A01G372100 chr1A 82.609 299 32 11 71 353 548787837 548788131 2.570000e-61 246.0
5 TraesCS1A01G372100 chr1A 77.273 198 43 2 2411 2607 62453427 62453623 7.550000e-22 115.0
6 TraesCS1A01G372100 chr1A 97.143 35 1 0 794 828 482962056 482962090 3.590000e-05 60.2
7 TraesCS1A01G372100 chr1D 91.268 1672 89 20 929 2563 454493881 454492230 0.000000e+00 2226.0
8 TraesCS1A01G372100 chr1D 90.151 1391 111 11 945 2326 454769049 454770422 0.000000e+00 1786.0
9 TraesCS1A01G372100 chr1D 89.557 1398 106 14 960 2346 454458460 454457092 0.000000e+00 1736.0
10 TraesCS1A01G372100 chr1D 90.320 1188 97 7 997 2172 454812763 454813944 0.000000e+00 1541.0
11 TraesCS1A01G372100 chr1D 92.464 491 25 9 20 502 454495067 454494581 0.000000e+00 691.0
12 TraesCS1A01G372100 chr1D 91.772 316 26 0 540 855 454494507 454494192 1.100000e-119 440.0
13 TraesCS1A01G372100 chr1D 82.727 330 36 14 216 525 454459297 454458969 1.180000e-69 274.0
14 TraesCS1A01G372100 chr1D 93.064 173 11 1 2929 3100 409539764 409539936 5.510000e-63 252.0
15 TraesCS1A01G372100 chr1D 88.050 159 17 2 3092 3249 454491427 454491270 1.580000e-43 187.0
16 TraesCS1A01G372100 chr1D 84.049 163 19 6 82 238 454768143 454768304 2.070000e-32 150.0
17 TraesCS1A01G372100 chr1D 74.194 403 58 32 285 667 454768308 454768684 3.490000e-25 126.0
18 TraesCS1A01G372100 chr1D 92.308 78 4 2 520 596 454494585 454494509 3.510000e-20 110.0
19 TraesCS1A01G372100 chr1D 83.486 109 9 8 476 584 454812336 454812435 3.540000e-15 93.5
20 TraesCS1A01G372100 chr1D 100.000 32 0 0 852 883 454493966 454493935 3.590000e-05 60.2
21 TraesCS1A01G372100 chr1B 89.873 1412 116 11 945 2347 625082546 625083939 0.000000e+00 1790.0
22 TraesCS1A01G372100 chr1B 89.607 1424 104 20 935 2346 624970770 624972161 0.000000e+00 1770.0
23 TraesCS1A01G372100 chr1B 89.297 1252 104 17 939 2172 625145165 625146404 0.000000e+00 1543.0
24 TraesCS1A01G372100 chr1B 82.901 848 107 19 1946 2769 625051984 625052817 0.000000e+00 728.0
25 TraesCS1A01G372100 chr1B 88.068 528 39 9 68 578 624969690 624970210 3.670000e-169 604.0
26 TraesCS1A01G372100 chr1B 84.731 334 35 14 71 389 625081586 625081918 1.490000e-83 320.0
27 TraesCS1A01G372100 chr1B 79.901 403 48 25 65 438 625143189 625143587 7.080000e-67 265.0
28 TraesCS1A01G372100 chr1B 81.395 215 27 10 71 274 625045877 625046089 2.660000e-36 163.0
29 TraesCS1A01G372100 chr1B 92.500 80 6 0 273 352 625046172 625046251 7.550000e-22 115.0
30 TraesCS1A01G372100 chr1B 100.000 33 0 0 2901 2933 625055008 625055040 9.970000e-06 62.1
31 TraesCS1A01G372100 chr5A 93.605 172 9 2 2930 3100 362179181 362179011 4.260000e-64 255.0
32 TraesCS1A01G372100 chr6A 93.023 172 11 1 2930 3100 153669712 153669883 1.980000e-62 250.0
33 TraesCS1A01G372100 chr7D 93.939 165 9 1 2930 3093 500255327 500255163 7.130000e-62 248.0
34 TraesCS1A01G372100 chr7D 78.771 179 31 5 595 773 8963453 8963282 2.710000e-21 113.0
35 TraesCS1A01G372100 chr4A 92.090 177 12 2 2926 3101 732790023 732790198 7.130000e-62 248.0
36 TraesCS1A01G372100 chr4A 83.562 73 8 3 3 73 26887907 26887977 7.710000e-07 65.8
37 TraesCS1A01G372100 chr4A 100.000 33 0 0 2901 2933 138261060 138261092 9.970000e-06 62.1
38 TraesCS1A01G372100 chr3A 89.447 199 17 3 2914 3111 596110572 596110377 7.130000e-62 248.0
39 TraesCS1A01G372100 chr6D 91.620 179 14 1 2927 3104 452949627 452949805 2.570000e-61 246.0
40 TraesCS1A01G372100 chr6D 84.615 65 10 0 10 74 20246483 20246419 7.710000e-07 65.8
41 TraesCS1A01G372100 chr6B 92.045 176 12 2 2926 3100 276259264 276259090 2.570000e-61 246.0
42 TraesCS1A01G372100 chr5B 90.426 188 17 1 2929 3115 6397054 6397241 2.570000e-61 246.0
43 TraesCS1A01G372100 chr5B 90.667 75 7 0 1 75 549977107 549977033 2.110000e-17 100.0
44 TraesCS1A01G372100 chr4D 83.333 186 17 9 596 773 15690893 15690714 3.440000e-35 159.0
45 TraesCS1A01G372100 chr2D 86.508 126 16 1 648 773 589286140 589286264 1.610000e-28 137.0
46 TraesCS1A01G372100 chr7B 79.503 161 28 3 592 751 738672206 738672362 3.510000e-20 110.0
47 TraesCS1A01G372100 chr4B 79.825 114 19 4 628 738 26787580 26787468 2.750000e-11 80.5
48 TraesCS1A01G372100 chr4B 97.222 36 1 0 796 831 637736598 637736633 9.970000e-06 62.1


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 TraesCS1A01G372100 chr1A 548732372 548735700 3328 False 6148.000000 6148 100.000000 1 3329 1 chr1A.!!$F3 3328
1 TraesCS1A01G372100 chr1A 548771392 548773732 2340 False 1047.500000 1801 84.790000 71 2325 2 chr1A.!!$F4 2254
2 TraesCS1A01G372100 chr1A 548787837 548790512 2675 False 906.500000 1567 86.108500 71 2172 2 chr1A.!!$F5 2101
3 TraesCS1A01G372100 chr1D 454457092 454459297 2205 True 1005.000000 1736 86.142000 216 2346 2 chr1D.!!$R1 2130
4 TraesCS1A01G372100 chr1D 454812336 454813944 1608 False 817.250000 1541 86.903000 476 2172 2 chr1D.!!$F3 1696
5 TraesCS1A01G372100 chr1D 454768143 454770422 2279 False 687.333333 1786 82.798000 82 2326 3 chr1D.!!$F2 2244
6 TraesCS1A01G372100 chr1D 454491270 454495067 3797 True 619.033333 2226 92.643667 20 3249 6 chr1D.!!$R2 3229
7 TraesCS1A01G372100 chr1B 624969690 624972161 2471 False 1187.000000 1770 88.837500 68 2346 2 chr1B.!!$F1 2278
8 TraesCS1A01G372100 chr1B 625081586 625083939 2353 False 1055.000000 1790 87.302000 71 2347 2 chr1B.!!$F4 2276
9 TraesCS1A01G372100 chr1B 625143189 625146404 3215 False 904.000000 1543 84.599000 65 2172 2 chr1B.!!$F5 2107
10 TraesCS1A01G372100 chr1B 625051984 625055040 3056 False 395.050000 728 91.450500 1946 2933 2 chr1B.!!$F3 987

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
881 3393 0.178992 CTCCAGCTCCTCTCCTCGAT 60.179 60.0 0.0 0.0 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2506 5235 0.396974 ACAAGGTTTGCCCAGCTTCA 60.397 50.0 0.0 0.0 32.01 3.02 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
23 24 4.210328 TGCGTGTATGCGTTTATAAGGATG 59.790 41.667 0.00 0.00 37.81 3.51
25 26 5.050634 GCGTGTATGCGTTTATAAGGATGAA 60.051 40.000 0.00 0.00 0.00 2.57
31 32 9.973246 GTATGCGTTTATAAGGATGAATGTATG 57.027 33.333 0.00 0.00 0.00 2.39
39 40 2.995939 AGGATGAATGTATGCGCGTATG 59.004 45.455 20.45 0.00 0.00 2.39
42 43 4.201589 GGATGAATGTATGCGCGTATGTAC 60.202 45.833 20.45 11.39 0.00 2.90
43 44 3.972403 TGAATGTATGCGCGTATGTACT 58.028 40.909 20.45 1.67 0.00 2.73
44 45 5.110940 TGAATGTATGCGCGTATGTACTA 57.889 39.130 20.45 0.00 0.00 1.82
46 47 5.400188 TGAATGTATGCGCGTATGTACTAAC 59.600 40.000 20.45 9.16 0.00 2.34
47 48 4.290104 TGTATGCGCGTATGTACTAACA 57.710 40.909 20.45 11.76 40.69 2.41
53 56 3.242155 GCGCGTATGTACTAACATTTGCA 60.242 43.478 8.43 0.00 44.07 4.08
222 263 2.866351 AGGCGTTAGTAGGAGGAGATC 58.134 52.381 0.00 0.00 0.00 2.75
223 264 1.536331 GGCGTTAGTAGGAGGAGATCG 59.464 57.143 0.00 0.00 0.00 3.69
254 302 3.139077 CGTGCCACTACTTTTCTTCCTT 58.861 45.455 0.00 0.00 0.00 3.36
348 396 1.564622 CATACCATACTGCGTGCGC 59.435 57.895 9.85 9.85 42.35 6.09
417 500 7.470935 TCTTCCATGGATGCCATAAAATATG 57.529 36.000 17.06 0.00 43.15 1.78
497 1976 6.173339 TCAGAATGGAATCCTGTGTCTAAAC 58.827 40.000 0.00 0.00 36.16 2.01
596 2643 9.950680 AATAAAAAGAAACATCAGTACAGTGTG 57.049 29.630 5.88 0.00 0.00 3.82
599 2646 5.276461 AGAAACATCAGTACAGTGTGTGA 57.724 39.130 5.88 9.25 0.00 3.58
601 2648 3.386768 ACATCAGTACAGTGTGTGACC 57.613 47.619 5.88 0.00 0.00 4.02
608 2765 3.451178 AGTACAGTGTGTGACCAAGTCTT 59.549 43.478 5.88 0.00 33.15 3.01
615 2772 4.270325 GTGTGTGACCAAGTCTTAGTTGAC 59.730 45.833 0.00 0.00 37.23 3.18
619 2776 4.745620 GTGACCAAGTCTTAGTTGACTGAC 59.254 45.833 0.00 0.00 45.49 3.51
626 2783 7.657761 CCAAGTCTTAGTTGACTGACACTTAAT 59.342 37.037 0.00 0.00 45.49 1.40
641 2798 7.272244 TGACACTTAATCAAGTCTCAGTCAAA 58.728 34.615 0.00 0.00 43.30 2.69
732 2889 9.314321 GATCAAAGGAATAAAGTATCGACTGAA 57.686 33.333 0.00 0.00 35.52 3.02
736 2893 9.449719 AAAGGAATAAAGTATCGACTGAAACAT 57.550 29.630 0.00 0.00 35.52 2.71
754 2911 4.343811 ACATAACGAAGTCTCAGTCGAG 57.656 45.455 0.00 0.00 45.00 4.04
775 2938 7.116519 GTCGAGTAAGACTTAGCAAAACTGATT 59.883 37.037 0.00 0.00 38.09 2.57
784 2947 9.846248 GACTTAGCAAAACTGATTGAACAATAT 57.154 29.630 0.00 0.00 31.84 1.28
830 2993 1.327303 AAGATCGTTTTGCCAGCCAA 58.673 45.000 0.00 0.00 0.00 4.52
881 3393 0.178992 CTCCAGCTCCTCTCCTCGAT 60.179 60.000 0.00 0.00 0.00 3.59
882 3394 0.179004 TCCAGCTCCTCTCCTCGATC 60.179 60.000 0.00 0.00 0.00 3.69
883 3395 1.514678 CCAGCTCCTCTCCTCGATCG 61.515 65.000 9.36 9.36 0.00 3.69
884 3396 1.228124 AGCTCCTCTCCTCGATCGG 60.228 63.158 16.41 5.93 0.00 4.18
885 3397 2.914908 GCTCCTCTCCTCGATCGGC 61.915 68.421 16.41 3.21 0.00 5.54
886 3398 1.228124 CTCCTCTCCTCGATCGGCT 60.228 63.158 16.41 0.00 0.00 5.52
887 3399 1.228003 TCCTCTCCTCGATCGGCTC 60.228 63.158 16.41 0.00 0.00 4.70
888 3400 2.265182 CCTCTCCTCGATCGGCTCC 61.265 68.421 16.41 0.00 0.00 4.70
889 3401 1.228124 CTCTCCTCGATCGGCTCCT 60.228 63.158 16.41 0.00 0.00 3.69
890 3402 1.228003 TCTCCTCGATCGGCTCCTC 60.228 63.158 16.41 0.00 0.00 3.71
891 3403 2.592001 TCCTCGATCGGCTCCTCG 60.592 66.667 16.41 0.00 36.25 4.63
892 3404 2.592001 CCTCGATCGGCTCCTCGA 60.592 66.667 16.41 5.27 43.61 4.04
900 3412 2.110901 TCGGCTCCTCGATCCTATAC 57.889 55.000 0.00 0.00 33.92 1.47
926 3441 1.376424 GCACTTGCCTCTGCTGCTA 60.376 57.895 0.00 0.00 38.71 3.49
969 3606 6.999705 AGCTACTACTCTACCTAGCTAAGA 57.000 41.667 0.00 0.00 40.13 2.10
1029 3688 3.644719 AGGAGCTGCCTCATGGAG 58.355 61.111 0.00 0.00 46.97 3.86
1903 4577 2.113139 CCTCGGGCAACAACCAGT 59.887 61.111 0.00 0.00 39.74 4.00
2028 4720 2.963371 GGCGTCGACCTTCTCACT 59.037 61.111 10.58 0.00 0.00 3.41
2175 4876 4.159244 AGACTTCTCGCTGACCTATAGT 57.841 45.455 0.00 0.00 0.00 2.12
2201 4902 2.357517 CACCTCACAGTGCCCGAC 60.358 66.667 0.00 0.00 0.00 4.79
2224 4925 5.477291 ACGTCAAGAGATCAACTAGAAGGAA 59.523 40.000 0.00 0.00 0.00 3.36
2253 4954 2.012673 GCAGGGAGTACATTTGCTCTG 58.987 52.381 0.00 0.00 34.96 3.35
2254 4955 2.012673 CAGGGAGTACATTTGCTCTGC 58.987 52.381 0.00 0.00 34.96 4.26
2297 5001 0.035458 AGTGCCCGAGGTCAAAAGAG 59.965 55.000 0.00 0.00 0.00 2.85
2348 5052 1.269166 CCGACTCACATTCACGTAGC 58.731 55.000 0.00 0.00 0.00 3.58
2351 5055 2.263077 GACTCACATTCACGTAGCAGG 58.737 52.381 0.00 0.00 0.00 4.85
2438 5167 5.296283 AGAAATTGCATGCAGTCTCATAGAC 59.704 40.000 21.50 6.39 45.38 2.59
2441 5170 2.236893 TGCATGCAGTCTCATAGACCAA 59.763 45.455 18.46 0.00 46.18 3.67
2466 5195 5.682943 AGCAACGACTACAAGCATTAAAA 57.317 34.783 0.00 0.00 0.00 1.52
2473 5202 6.598064 ACGACTACAAGCATTAAAATAAGCCT 59.402 34.615 0.00 0.00 0.00 4.58
2501 5230 0.895530 TCGCCGTCATCTCTCCTTTT 59.104 50.000 0.00 0.00 0.00 2.27
2524 5253 0.752054 TTGAAGCTGGGCAAACCTTG 59.248 50.000 0.00 0.00 41.11 3.61
2565 5294 1.376812 CGTTGTCCTAAGGCCCCAC 60.377 63.158 0.00 0.00 0.00 4.61
2567 5296 2.598787 TTGTCCTAAGGCCCCACCG 61.599 63.158 0.00 0.00 46.52 4.94
2578 5307 3.061848 CCCACCGGACCAATGCAC 61.062 66.667 9.46 0.00 0.00 4.57
2590 5332 3.230134 ACCAATGCACCAGTACAACAAT 58.770 40.909 0.00 0.00 0.00 2.71
2599 5341 2.412870 CAGTACAACAATGGTCGCTGA 58.587 47.619 0.00 0.00 0.00 4.26
2617 5359 4.317698 CGCTGACGAAGAGAAGCATAAATC 60.318 45.833 0.00 0.00 43.93 2.17
2618 5360 4.025313 GCTGACGAAGAGAAGCATAAATCC 60.025 45.833 0.00 0.00 34.69 3.01
2619 5361 4.442706 TGACGAAGAGAAGCATAAATCCC 58.557 43.478 0.00 0.00 0.00 3.85
2620 5362 3.458189 ACGAAGAGAAGCATAAATCCCG 58.542 45.455 0.00 0.00 0.00 5.14
2621 5363 2.221981 CGAAGAGAAGCATAAATCCCGC 59.778 50.000 0.00 0.00 0.00 6.13
2623 5365 1.412710 AGAGAAGCATAAATCCCGCGA 59.587 47.619 8.23 0.00 0.00 5.87
2640 5806 2.284457 CGCGAATGTAGACACATGAACG 60.284 50.000 0.00 0.00 44.83 3.95
2641 5807 2.534939 GCGAATGTAGACACATGAACGC 60.535 50.000 0.00 15.49 44.83 4.84
2672 5838 3.485463 AGGTCGAATCCAAGTTGAACA 57.515 42.857 3.87 0.00 0.00 3.18
2677 5843 2.289547 CGAATCCAAGTTGAACAACCGT 59.710 45.455 13.07 0.72 42.06 4.83
2689 5855 5.008619 TGAACAACCGTAGACAAACACTA 57.991 39.130 0.00 0.00 0.00 2.74
2692 5858 5.014808 ACAACCGTAGACAAACACTAACT 57.985 39.130 0.00 0.00 0.00 2.24
2698 5864 6.870439 ACCGTAGACAAACACTAACTAAATCC 59.130 38.462 0.00 0.00 0.00 3.01
2719 5885 1.809869 CGAGATCCGCCAGAGACAA 59.190 57.895 0.00 0.00 0.00 3.18
2722 5888 1.205893 GAGATCCGCCAGAGACAAACT 59.794 52.381 0.00 0.00 0.00 2.66
2738 5904 2.549754 CAAACTTGCACAACTCTCCGAT 59.450 45.455 0.00 0.00 0.00 4.18
2770 8059 2.685534 CCGGGATGGGGGTTAAGCA 61.686 63.158 7.03 0.00 0.00 3.91
2778 8067 0.107165 GGGGGTTAAGCAGCGAGAAT 60.107 55.000 7.03 0.00 0.00 2.40
2792 8081 5.238214 GCAGCGAGAATCTTATTCCATCTTT 59.762 40.000 0.00 0.00 0.00 2.52
2801 8090 4.474651 TCTTATTCCATCTTTGAGGGAGCA 59.525 41.667 1.31 0.00 43.48 4.26
2806 8095 1.210204 ATCTTTGAGGGAGCAGGGCA 61.210 55.000 0.00 0.00 0.00 5.36
2835 8124 1.203001 TCTTTCCGGGCAGGTCAAAAT 60.203 47.619 0.00 0.00 41.99 1.82
2838 8127 1.304052 CCGGGCAGGTCAAAATCCA 60.304 57.895 0.00 0.00 34.51 3.41
2847 8136 4.501229 GCAGGTCAAAATCCAAATCACACA 60.501 41.667 0.00 0.00 0.00 3.72
2859 8148 6.169094 TCCAAATCACACACAACAAAACATT 58.831 32.000 0.00 0.00 0.00 2.71
2897 8186 3.939837 CTTCCGCGAGCCTTGCTGA 62.940 63.158 8.23 0.00 39.88 4.26
2899 8188 4.441695 CCGCGAGCCTTGCTGAGA 62.442 66.667 8.23 0.00 39.88 3.27
2933 8222 8.929746 GGTGTTTACTCCAACTATTAGTTACAC 58.070 37.037 19.17 19.17 36.03 2.90
2934 8223 8.929746 GTGTTTACTCCAACTATTAGTTACACC 58.070 37.037 17.76 7.27 36.03 4.16
2935 8224 8.096414 TGTTTACTCCAACTATTAGTTACACCC 58.904 37.037 8.71 0.00 36.03 4.61
2936 8225 8.316946 GTTTACTCCAACTATTAGTTACACCCT 58.683 37.037 8.71 0.00 36.03 4.34
2937 8226 6.541934 ACTCCAACTATTAGTTACACCCTC 57.458 41.667 8.71 0.00 36.03 4.30
2938 8227 6.262207 ACTCCAACTATTAGTTACACCCTCT 58.738 40.000 8.71 0.00 36.03 3.69
2939 8228 6.154706 ACTCCAACTATTAGTTACACCCTCTG 59.845 42.308 8.71 0.00 36.03 3.35
2940 8229 6.021030 TCCAACTATTAGTTACACCCTCTGT 58.979 40.000 8.71 0.00 36.03 3.41
2941 8230 6.499350 TCCAACTATTAGTTACACCCTCTGTT 59.501 38.462 8.71 0.00 36.03 3.16
2942 8231 6.817140 CCAACTATTAGTTACACCCTCTGTTC 59.183 42.308 8.71 0.00 36.03 3.18
2943 8232 6.541934 ACTATTAGTTACACCCTCTGTTCC 57.458 41.667 0.00 0.00 33.91 3.62
2944 8233 6.262207 ACTATTAGTTACACCCTCTGTTCCT 58.738 40.000 0.00 0.00 33.91 3.36
2945 8234 7.416731 ACTATTAGTTACACCCTCTGTTCCTA 58.583 38.462 0.00 0.00 33.91 2.94
2946 8235 7.897565 ACTATTAGTTACACCCTCTGTTCCTAA 59.102 37.037 0.00 0.00 33.91 2.69
2947 8236 6.999705 TTAGTTACACCCTCTGTTCCTAAA 57.000 37.500 0.00 0.00 33.91 1.85
2948 8237 7.563724 TTAGTTACACCCTCTGTTCCTAAAT 57.436 36.000 0.00 0.00 33.91 1.40
2949 8238 8.669055 TTAGTTACACCCTCTGTTCCTAAATA 57.331 34.615 0.00 0.00 33.91 1.40
2950 8239 7.750947 AGTTACACCCTCTGTTCCTAAATAT 57.249 36.000 0.00 0.00 33.91 1.28
2951 8240 8.159229 AGTTACACCCTCTGTTCCTAAATATT 57.841 34.615 0.00 0.00 33.91 1.28
2952 8241 8.612145 AGTTACACCCTCTGTTCCTAAATATTT 58.388 33.333 5.89 5.89 33.91 1.40
2953 8242 8.674607 GTTACACCCTCTGTTCCTAAATATTTG 58.325 37.037 11.05 1.40 33.91 2.32
2954 8243 6.790319 ACACCCTCTGTTCCTAAATATTTGT 58.210 36.000 11.05 0.00 0.00 2.83
2955 8244 6.884836 ACACCCTCTGTTCCTAAATATTTGTC 59.115 38.462 11.05 0.00 0.00 3.18
2956 8245 7.112779 CACCCTCTGTTCCTAAATATTTGTCT 58.887 38.462 11.05 0.00 0.00 3.41
2957 8246 7.611855 CACCCTCTGTTCCTAAATATTTGTCTT 59.388 37.037 11.05 0.00 0.00 3.01
2958 8247 8.170730 ACCCTCTGTTCCTAAATATTTGTCTTT 58.829 33.333 11.05 0.00 0.00 2.52
2959 8248 8.678199 CCCTCTGTTCCTAAATATTTGTCTTTC 58.322 37.037 11.05 0.00 0.00 2.62
2960 8249 9.454859 CCTCTGTTCCTAAATATTTGTCTTTCT 57.545 33.333 11.05 0.00 0.00 2.52
2987 8276 9.355215 AGAGATTTTAACAAGTGACTACATACG 57.645 33.333 0.00 0.00 0.00 3.06
2988 8277 8.475331 AGATTTTAACAAGTGACTACATACGG 57.525 34.615 0.00 0.00 0.00 4.02
2989 8278 8.308931 AGATTTTAACAAGTGACTACATACGGA 58.691 33.333 0.00 0.00 0.00 4.69
2990 8279 7.878477 TTTTAACAAGTGACTACATACGGAG 57.122 36.000 0.00 0.00 0.00 4.63
3053 8342 7.297936 ACATCCGTATATGGTAGTCATTTGA 57.702 36.000 10.85 0.00 37.30 2.69
3054 8343 7.732025 ACATCCGTATATGGTAGTCATTTGAA 58.268 34.615 10.85 0.00 37.30 2.69
3055 8344 8.208224 ACATCCGTATATGGTAGTCATTTGAAA 58.792 33.333 10.85 0.00 37.30 2.69
3056 8345 9.219603 CATCCGTATATGGTAGTCATTTGAAAT 57.780 33.333 10.85 0.00 37.30 2.17
3057 8346 9.793259 ATCCGTATATGGTAGTCATTTGAAATT 57.207 29.630 10.85 0.00 37.30 1.82
3058 8347 9.621629 TCCGTATATGGTAGTCATTTGAAATTT 57.378 29.630 10.85 0.00 37.30 1.82
3087 8376 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
3088 8377 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3089 8378 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3090 8379 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3091 8380 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3092 8381 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3093 8382 6.416631 AATATTTAGGAACGGAGGGAGTAC 57.583 41.667 0.00 0.00 0.00 2.73
3094 8383 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
3095 8384 3.393426 TTAGGAACGGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
3096 8385 1.486211 AGGAACGGAGGGAGTACATG 58.514 55.000 0.00 0.00 0.00 3.21
3099 8388 1.822990 GAACGGAGGGAGTACATGACA 59.177 52.381 0.00 0.00 0.00 3.58
3107 8396 3.703556 AGGGAGTACATGACAGTGATCTG 59.296 47.826 0.00 0.00 46.18 2.90
3110 8399 4.400884 GGAGTACATGACAGTGATCTGACT 59.599 45.833 0.00 0.00 43.76 3.41
3113 8402 4.998671 ACATGACAGTGATCTGACTAGG 57.001 45.455 0.00 0.00 43.76 3.02
3114 8403 4.604156 ACATGACAGTGATCTGACTAGGA 58.396 43.478 0.00 0.00 43.76 2.94
3136 8426 1.406539 CCCTGATGCATACCAACTTGC 59.593 52.381 0.00 0.00 39.33 4.01
3141 8431 3.944650 TGATGCATACCAACTTGCGTATT 59.055 39.130 0.00 0.00 41.80 1.89
3217 8507 9.624373 AGCATTTTCATAGTAGATTGTCAAGAT 57.376 29.630 0.00 0.00 0.00 2.40
3224 8514 8.851145 TCATAGTAGATTGTCAAGATAGTGTCC 58.149 37.037 0.00 0.00 0.00 4.02
3226 8516 7.482169 AGTAGATTGTCAAGATAGTGTCCAA 57.518 36.000 0.00 0.00 0.00 3.53
3230 8520 2.028476 TGTCAAGATAGTGTCCAACCGG 60.028 50.000 0.00 0.00 0.00 5.28
3243 8533 4.884668 TCCAACCGGGAGAATATCATAC 57.115 45.455 6.32 0.00 42.15 2.39
3249 8539 5.295152 ACCGGGAGAATATCATACGAAAAC 58.705 41.667 6.32 0.00 0.00 2.43
3250 8540 4.689345 CCGGGAGAATATCATACGAAAACC 59.311 45.833 0.00 0.00 0.00 3.27
3251 8541 5.510861 CCGGGAGAATATCATACGAAAACCT 60.511 44.000 0.00 0.00 0.00 3.50
3252 8542 5.989777 CGGGAGAATATCATACGAAAACCTT 59.010 40.000 0.00 0.00 0.00 3.50
3253 8543 6.145696 CGGGAGAATATCATACGAAAACCTTC 59.854 42.308 0.00 0.00 0.00 3.46
3254 8544 7.217906 GGGAGAATATCATACGAAAACCTTCT 58.782 38.462 0.00 0.00 0.00 2.85
3255 8545 8.365647 GGGAGAATATCATACGAAAACCTTCTA 58.634 37.037 0.00 0.00 0.00 2.10
3256 8546 9.760077 GGAGAATATCATACGAAAACCTTCTAA 57.240 33.333 0.00 0.00 0.00 2.10
3278 8568 4.729227 AAAAACTTCGTGGAAACCATGT 57.271 36.364 9.39 0.00 41.03 3.21
3279 8569 4.729227 AAAACTTCGTGGAAACCATGTT 57.271 36.364 9.39 3.73 41.03 2.71
3280 8570 5.838531 AAAACTTCGTGGAAACCATGTTA 57.161 34.783 9.39 0.41 41.03 2.41
3281 8571 5.432885 AAACTTCGTGGAAACCATGTTAG 57.567 39.130 9.39 10.13 41.03 2.34
3282 8572 4.345859 ACTTCGTGGAAACCATGTTAGA 57.654 40.909 9.39 0.00 41.03 2.10
3283 8573 4.315803 ACTTCGTGGAAACCATGTTAGAG 58.684 43.478 9.39 6.81 41.03 2.43
3284 8574 4.039973 ACTTCGTGGAAACCATGTTAGAGA 59.960 41.667 9.39 0.00 41.03 3.10
3285 8575 4.610605 TCGTGGAAACCATGTTAGAGAA 57.389 40.909 9.39 0.00 41.03 2.87
3286 8576 5.160607 TCGTGGAAACCATGTTAGAGAAT 57.839 39.130 9.39 0.00 41.03 2.40
3287 8577 5.556915 TCGTGGAAACCATGTTAGAGAATT 58.443 37.500 9.39 0.00 41.03 2.17
3288 8578 5.642063 TCGTGGAAACCATGTTAGAGAATTC 59.358 40.000 9.39 0.00 41.03 2.17
3289 8579 5.163754 CGTGGAAACCATGTTAGAGAATTCC 60.164 44.000 0.65 0.00 35.92 3.01
3290 8580 5.710099 GTGGAAACCATGTTAGAGAATTCCA 59.290 40.000 0.65 0.00 41.89 3.53
3291 8581 6.208599 GTGGAAACCATGTTAGAGAATTCCAA 59.791 38.462 0.65 0.00 44.62 3.53
3292 8582 6.780031 TGGAAACCATGTTAGAGAATTCCAAA 59.220 34.615 0.65 0.00 41.37 3.28
3293 8583 7.288852 TGGAAACCATGTTAGAGAATTCCAAAA 59.711 33.333 0.65 0.00 41.37 2.44
3294 8584 8.147704 GGAAACCATGTTAGAGAATTCCAAAAA 58.852 33.333 0.65 0.00 36.09 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.783191 TCCTTATAAACGCATACACGCA 58.217 40.909 0.00 0.00 36.19 5.24
1 2 4.446385 TCATCCTTATAAACGCATACACGC 59.554 41.667 0.00 0.00 36.19 5.34
2 3 6.519353 TTCATCCTTATAAACGCATACACG 57.481 37.500 0.00 0.00 39.50 4.49
3 4 7.861630 ACATTCATCCTTATAAACGCATACAC 58.138 34.615 0.00 0.00 0.00 2.90
4 5 9.719355 ATACATTCATCCTTATAAACGCATACA 57.281 29.630 0.00 0.00 0.00 2.29
5 6 9.973246 CATACATTCATCCTTATAAACGCATAC 57.027 33.333 0.00 0.00 0.00 2.39
6 7 8.664798 GCATACATTCATCCTTATAAACGCATA 58.335 33.333 0.00 0.00 0.00 3.14
7 8 7.530010 GCATACATTCATCCTTATAAACGCAT 58.470 34.615 0.00 0.00 0.00 4.73
8 9 6.347321 CGCATACATTCATCCTTATAAACGCA 60.347 38.462 0.00 0.00 0.00 5.24
9 10 6.015504 CGCATACATTCATCCTTATAAACGC 58.984 40.000 0.00 0.00 0.00 4.84
10 11 6.015504 GCGCATACATTCATCCTTATAAACG 58.984 40.000 0.30 0.00 0.00 3.60
11 12 6.015504 CGCGCATACATTCATCCTTATAAAC 58.984 40.000 8.75 0.00 0.00 2.01
12 13 5.699001 ACGCGCATACATTCATCCTTATAAA 59.301 36.000 5.73 0.00 0.00 1.40
13 14 5.234752 ACGCGCATACATTCATCCTTATAA 58.765 37.500 5.73 0.00 0.00 0.98
14 15 4.816392 ACGCGCATACATTCATCCTTATA 58.184 39.130 5.73 0.00 0.00 0.98
15 16 3.664107 ACGCGCATACATTCATCCTTAT 58.336 40.909 5.73 0.00 0.00 1.73
16 17 3.106242 ACGCGCATACATTCATCCTTA 57.894 42.857 5.73 0.00 0.00 2.69
17 18 1.953559 ACGCGCATACATTCATCCTT 58.046 45.000 5.73 0.00 0.00 3.36
18 19 2.812358 TACGCGCATACATTCATCCT 57.188 45.000 5.73 0.00 0.00 3.24
23 24 5.400188 TGTTAGTACATACGCGCATACATTC 59.600 40.000 5.73 0.00 0.00 2.67
25 26 4.862350 TGTTAGTACATACGCGCATACAT 58.138 39.130 5.73 0.00 0.00 2.29
31 32 3.242155 TGCAAATGTTAGTACATACGCGC 60.242 43.478 5.73 0.00 44.14 6.86
39 40 9.314321 ACATAGTACAGATGCAAATGTTAGTAC 57.686 33.333 11.86 8.19 0.00 2.73
76 80 2.669569 ACGCTGATGGTGCCACAC 60.670 61.111 0.00 0.00 0.00 3.82
222 263 2.666862 TGGCACGCCAAGTAACCG 60.667 61.111 8.67 0.00 44.12 4.44
348 396 3.072468 CACCCCTTGGCCATGCTG 61.072 66.667 6.09 5.13 33.59 4.41
360 408 0.947244 GATGATGATGAACGCACCCC 59.053 55.000 0.00 0.00 0.00 4.95
417 500 6.225318 TGTGTTGGTGTAGGTCAACTATTAC 58.775 40.000 0.00 0.00 42.48 1.89
584 2430 2.764010 ACTTGGTCACACACTGTACTGA 59.236 45.455 6.77 0.00 0.00 3.41
592 2639 4.270325 GTCAACTAAGACTTGGTCACACAC 59.730 45.833 4.51 0.00 34.60 3.82
593 2640 4.161565 AGTCAACTAAGACTTGGTCACACA 59.838 41.667 4.51 0.00 46.26 3.72
594 2641 4.508124 CAGTCAACTAAGACTTGGTCACAC 59.492 45.833 4.51 2.72 46.26 3.82
595 2642 4.404394 TCAGTCAACTAAGACTTGGTCACA 59.596 41.667 4.51 0.00 46.26 3.58
596 2643 4.745620 GTCAGTCAACTAAGACTTGGTCAC 59.254 45.833 4.51 5.34 46.26 3.67
599 2646 4.406003 AGTGTCAGTCAACTAAGACTTGGT 59.594 41.667 0.00 0.00 46.26 3.67
601 2648 8.594881 ATTAAGTGTCAGTCAACTAAGACTTG 57.405 34.615 6.18 0.00 46.26 3.16
608 2765 7.952671 AGACTTGATTAAGTGTCAGTCAACTA 58.047 34.615 7.73 0.00 46.79 2.24
619 2776 8.226448 GTCATTTGACTGAGACTTGATTAAGTG 58.774 37.037 7.73 0.00 42.94 3.16
626 2783 6.997655 ACTATGTCATTTGACTGAGACTTGA 58.002 36.000 11.67 0.00 44.99 3.02
722 2879 6.849502 AGACTTCGTTATGTTTCAGTCGATA 58.150 36.000 0.00 0.00 36.56 2.92
732 2889 4.215827 ACTCGACTGAGACTTCGTTATGTT 59.784 41.667 0.00 0.00 45.57 2.71
736 2893 5.119898 GTCTTACTCGACTGAGACTTCGTTA 59.880 44.000 8.96 0.00 45.57 3.18
754 2911 8.342634 TGTTCAATCAGTTTTGCTAAGTCTTAC 58.657 33.333 0.00 0.00 0.00 2.34
775 2938 9.778741 GATGAAGGGACTACATTATATTGTTCA 57.221 33.333 5.64 2.93 38.49 3.18
830 2993 5.785423 TGAGTATGGGTATGGCTAAGCTAAT 59.215 40.000 0.00 0.00 0.00 1.73
881 3393 1.350019 TGTATAGGATCGAGGAGCCGA 59.650 52.381 0.00 0.00 43.66 5.54
882 3394 1.822506 TGTATAGGATCGAGGAGCCG 58.177 55.000 0.00 0.00 43.66 5.52
883 3395 2.891580 TGTTGTATAGGATCGAGGAGCC 59.108 50.000 0.00 0.00 38.56 4.70
884 3396 3.318275 TGTGTTGTATAGGATCGAGGAGC 59.682 47.826 0.00 0.00 0.00 4.70
885 3397 4.554919 CGTGTGTTGTATAGGATCGAGGAG 60.555 50.000 0.00 0.00 0.00 3.69
886 3398 3.314357 CGTGTGTTGTATAGGATCGAGGA 59.686 47.826 0.00 0.00 0.00 3.71
887 3399 3.629058 CGTGTGTTGTATAGGATCGAGG 58.371 50.000 0.00 0.00 0.00 4.63
888 3400 3.043586 GCGTGTGTTGTATAGGATCGAG 58.956 50.000 0.00 0.00 0.00 4.04
889 3401 2.424246 TGCGTGTGTTGTATAGGATCGA 59.576 45.455 0.00 0.00 0.00 3.59
890 3402 2.534349 GTGCGTGTGTTGTATAGGATCG 59.466 50.000 0.00 0.00 0.00 3.69
891 3403 3.782046 AGTGCGTGTGTTGTATAGGATC 58.218 45.455 0.00 0.00 0.00 3.36
892 3404 3.887621 AGTGCGTGTGTTGTATAGGAT 57.112 42.857 0.00 0.00 0.00 3.24
900 3412 1.009675 GAGGCAAGTGCGTGTGTTG 60.010 57.895 2.75 0.00 43.26 3.33
988 3627 1.628340 ACTTTCCATCCGATCACCACA 59.372 47.619 0.00 0.00 0.00 4.17
1730 4404 1.363744 GTCATCGAAGTTGAGCAGGG 58.636 55.000 0.00 0.00 0.00 4.45
1731 4405 0.994995 CGTCATCGAAGTTGAGCAGG 59.005 55.000 0.00 0.00 39.71 4.85
1903 4577 3.262420 GGAGCTTGCAGTCGATAAAGAA 58.738 45.455 0.00 0.00 0.00 2.52
2175 4876 1.376086 CTGTGAGGTGGTGGCATGA 59.624 57.895 0.00 0.00 0.00 3.07
2201 4902 5.568685 TCCTTCTAGTTGATCTCTTGACG 57.431 43.478 0.00 0.00 0.00 4.35
2224 4925 2.187958 TGTACTCCCTGCTGCTTGTAT 58.812 47.619 0.00 0.00 0.00 2.29
2403 5129 6.210796 TGCATGCAATTTCTATTACTGATGC 58.789 36.000 20.30 0.00 34.43 3.91
2413 5142 6.481313 GTCTATGAGACTGCATGCAATTTCTA 59.519 38.462 22.88 7.92 41.88 2.10
2438 5167 2.412089 GCTTGTAGTCGTTGCTAGTTGG 59.588 50.000 0.00 0.00 0.00 3.77
2441 5170 3.594603 ATGCTTGTAGTCGTTGCTAGT 57.405 42.857 0.00 0.00 0.00 2.57
2466 5195 1.543429 GGCGATGCACCTTAGGCTTAT 60.543 52.381 0.00 0.00 0.00 1.73
2473 5202 0.529773 GATGACGGCGATGCACCTTA 60.530 55.000 16.62 0.00 0.00 2.69
2501 5230 3.238597 AGGTTTGCCCAGCTTCAATAAA 58.761 40.909 0.00 0.00 34.66 1.40
2506 5235 0.396974 ACAAGGTTTGCCCAGCTTCA 60.397 50.000 0.00 0.00 32.01 3.02
2524 5253 1.475682 CTCCCGGTTGTCTACTACCAC 59.524 57.143 13.00 0.00 40.94 4.16
2538 5267 1.252904 TTAGGACAACGACCTCCCGG 61.253 60.000 0.00 0.00 38.76 5.73
2550 5279 3.006728 CGGTGGGGCCTTAGGACA 61.007 66.667 6.40 0.00 27.52 4.02
2565 5294 1.024579 GTACTGGTGCATTGGTCCGG 61.025 60.000 0.00 0.00 0.00 5.14
2567 5296 1.539827 GTTGTACTGGTGCATTGGTCC 59.460 52.381 0.00 0.00 0.00 4.46
2574 5303 2.226330 GACCATTGTTGTACTGGTGCA 58.774 47.619 8.37 0.00 43.23 4.57
2578 5307 1.464608 CAGCGACCATTGTTGTACTGG 59.535 52.381 0.00 0.00 36.09 4.00
2599 5341 3.458189 CGGGATTTATGCTTCTCTTCGT 58.542 45.455 0.00 0.00 0.00 3.85
2617 5359 0.930310 CATGTGTCTACATTCGCGGG 59.070 55.000 6.13 0.00 45.01 6.13
2618 5360 1.921243 TCATGTGTCTACATTCGCGG 58.079 50.000 6.13 0.00 45.01 6.46
2619 5361 2.284457 CGTTCATGTGTCTACATTCGCG 60.284 50.000 0.00 0.00 45.01 5.87
2620 5362 2.534939 GCGTTCATGTGTCTACATTCGC 60.535 50.000 13.83 13.83 45.01 4.70
2621 5363 2.666022 TGCGTTCATGTGTCTACATTCG 59.334 45.455 0.00 0.00 45.01 3.34
2623 5365 4.267690 CGTATGCGTTCATGTGTCTACATT 59.732 41.667 0.00 0.00 45.01 2.71
2635 5801 2.927477 GACCTTCATTCGTATGCGTTCA 59.073 45.455 2.37 0.00 39.49 3.18
2640 5806 3.184581 GGATTCGACCTTCATTCGTATGC 59.815 47.826 0.00 0.00 37.73 3.14
2641 5807 4.368315 TGGATTCGACCTTCATTCGTATG 58.632 43.478 0.00 0.00 37.73 2.39
2672 5838 7.386025 GGATTTAGTTAGTGTTTGTCTACGGTT 59.614 37.037 0.00 0.00 0.00 4.44
2677 5843 6.588756 CGCAGGATTTAGTTAGTGTTTGTCTA 59.411 38.462 0.00 0.00 0.00 2.59
2689 5855 3.099267 CGGATCTCGCAGGATTTAGTT 57.901 47.619 0.00 0.00 0.00 2.24
2719 5885 2.146342 CATCGGAGAGTTGTGCAAGTT 58.854 47.619 0.00 0.00 43.63 2.66
2722 5888 1.618343 TCTCATCGGAGAGTTGTGCAA 59.382 47.619 0.00 0.00 45.12 4.08
2738 5904 2.490148 CCCGGCGATGCTACTCTCA 61.490 63.158 9.30 0.00 0.00 3.27
2743 5909 2.357517 CCATCCCGGCGATGCTAC 60.358 66.667 21.14 0.00 46.17 3.58
2764 5930 5.670485 TGGAATAAGATTCTCGCTGCTTAA 58.330 37.500 0.00 0.00 0.00 1.85
2770 8059 6.586344 TCAAAGATGGAATAAGATTCTCGCT 58.414 36.000 0.00 0.00 0.00 4.93
2778 8067 4.474651 TGCTCCCTCAAAGATGGAATAAGA 59.525 41.667 0.00 0.00 0.00 2.10
2792 8081 3.473647 CGATGCCCTGCTCCCTCA 61.474 66.667 0.00 0.00 0.00 3.86
2806 8095 2.029307 GCCCGGAAAGACTAGGCGAT 62.029 60.000 0.73 0.00 33.18 4.58
2835 8124 5.139435 TGTTTTGTTGTGTGTGATTTGGA 57.861 34.783 0.00 0.00 0.00 3.53
2847 8136 9.824534 CTGCTTTCTTTTTAAATGTTTTGTTGT 57.175 25.926 0.00 0.00 0.00 3.32
2859 8148 3.844640 AGGGCTCCTGCTTTCTTTTTAA 58.155 40.909 0.00 0.00 39.59 1.52
2866 8155 1.746991 CGGAAGGGCTCCTGCTTTC 60.747 63.158 0.00 0.00 42.85 2.62
2883 8172 2.884685 CTCTCAGCAAGGCTCGCG 60.885 66.667 0.00 0.00 36.40 5.87
2886 8175 0.604780 TGCAACTCTCAGCAAGGCTC 60.605 55.000 0.00 0.00 36.40 4.70
2887 8176 0.037877 ATGCAACTCTCAGCAAGGCT 59.962 50.000 0.00 0.00 44.88 4.58
2897 8186 3.181445 TGGAGTAAACACCATGCAACTCT 60.181 43.478 9.97 0.00 34.99 3.24
2899 8188 3.222173 TGGAGTAAACACCATGCAACT 57.778 42.857 0.00 0.00 31.62 3.16
2933 8222 8.581253 AAAGACAAATATTTAGGAACAGAGGG 57.419 34.615 0.00 0.00 0.00 4.30
2934 8223 9.454859 AGAAAGACAAATATTTAGGAACAGAGG 57.545 33.333 0.00 0.00 0.00 3.69
2961 8250 9.355215 CGTATGTAGTCACTTGTTAAAATCTCT 57.645 33.333 0.00 0.00 0.00 3.10
2962 8251 8.592998 CCGTATGTAGTCACTTGTTAAAATCTC 58.407 37.037 0.00 0.00 0.00 2.75
2963 8252 8.308931 TCCGTATGTAGTCACTTGTTAAAATCT 58.691 33.333 0.00 0.00 0.00 2.40
2964 8253 8.470040 TCCGTATGTAGTCACTTGTTAAAATC 57.530 34.615 0.00 0.00 0.00 2.17
2965 8254 8.092687 ACTCCGTATGTAGTCACTTGTTAAAAT 58.907 33.333 0.00 0.00 0.00 1.82
2966 8255 7.436118 ACTCCGTATGTAGTCACTTGTTAAAA 58.564 34.615 0.00 0.00 0.00 1.52
2967 8256 6.985117 ACTCCGTATGTAGTCACTTGTTAAA 58.015 36.000 0.00 0.00 0.00 1.52
2968 8257 6.579666 ACTCCGTATGTAGTCACTTGTTAA 57.420 37.500 0.00 0.00 0.00 2.01
2969 8258 7.686438 TTACTCCGTATGTAGTCACTTGTTA 57.314 36.000 0.00 0.00 0.00 2.41
2970 8259 6.579666 TTACTCCGTATGTAGTCACTTGTT 57.420 37.500 0.00 0.00 0.00 2.83
2971 8260 6.579666 TTTACTCCGTATGTAGTCACTTGT 57.420 37.500 0.00 0.00 0.00 3.16
2972 8261 9.577110 TTATTTTACTCCGTATGTAGTCACTTG 57.423 33.333 0.00 0.00 0.00 3.16
2973 8262 9.798994 CTTATTTTACTCCGTATGTAGTCACTT 57.201 33.333 0.00 0.00 0.00 3.16
2974 8263 8.964772 ACTTATTTTACTCCGTATGTAGTCACT 58.035 33.333 0.00 0.00 0.00 3.41
2975 8264 9.017669 CACTTATTTTACTCCGTATGTAGTCAC 57.982 37.037 0.00 0.00 0.00 3.67
2976 8265 8.959548 TCACTTATTTTACTCCGTATGTAGTCA 58.040 33.333 0.00 0.00 0.00 3.41
2977 8266 9.793252 TTCACTTATTTTACTCCGTATGTAGTC 57.207 33.333 0.00 0.00 0.00 2.59
3027 8316 9.031537 TCAAATGACTACCATATACGGATGTAT 57.968 33.333 0.00 0.00 43.62 2.29
3028 8317 8.411991 TCAAATGACTACCATATACGGATGTA 57.588 34.615 0.00 0.00 34.45 2.29
3029 8318 7.297936 TCAAATGACTACCATATACGGATGT 57.702 36.000 0.00 0.00 34.45 3.06
3030 8319 8.601845 TTTCAAATGACTACCATATACGGATG 57.398 34.615 0.00 0.00 34.45 3.51
3031 8320 9.793259 AATTTCAAATGACTACCATATACGGAT 57.207 29.630 0.00 0.00 34.45 4.18
3032 8321 9.621629 AAATTTCAAATGACTACCATATACGGA 57.378 29.630 0.00 0.00 34.45 4.69
3061 8350 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
3062 8351 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
3063 8352 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3064 8353 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3065 8354 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3066 8355 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3067 8356 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3068 8357 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3069 8358 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3070 8359 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
3071 8360 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
3072 8361 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
3073 8362 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
3074 8363 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
3075 8364 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
3076 8365 2.242965 TCATGTACTCCCTCCGTTCCTA 59.757 50.000 0.00 0.00 0.00 2.94
3077 8366 1.006758 TCATGTACTCCCTCCGTTCCT 59.993 52.381 0.00 0.00 0.00 3.36
3078 8367 1.136500 GTCATGTACTCCCTCCGTTCC 59.864 57.143 0.00 0.00 0.00 3.62
3079 8368 1.822990 TGTCATGTACTCCCTCCGTTC 59.177 52.381 0.00 0.00 0.00 3.95
3080 8369 1.825474 CTGTCATGTACTCCCTCCGTT 59.175 52.381 0.00 0.00 0.00 4.44
3081 8370 1.272536 ACTGTCATGTACTCCCTCCGT 60.273 52.381 0.00 0.00 0.00 4.69
3082 8371 1.135139 CACTGTCATGTACTCCCTCCG 59.865 57.143 0.00 0.00 0.00 4.63
3083 8372 2.457598 TCACTGTCATGTACTCCCTCC 58.542 52.381 0.00 0.00 0.00 4.30
3084 8373 3.957497 AGATCACTGTCATGTACTCCCTC 59.043 47.826 0.00 0.00 0.00 4.30
3085 8374 3.703556 CAGATCACTGTCATGTACTCCCT 59.296 47.826 0.00 0.00 39.11 4.20
3086 8375 3.701542 TCAGATCACTGTCATGTACTCCC 59.298 47.826 0.00 0.00 43.81 4.30
3087 8376 4.400884 AGTCAGATCACTGTCATGTACTCC 59.599 45.833 0.00 0.00 43.81 3.85
3088 8377 5.574891 AGTCAGATCACTGTCATGTACTC 57.425 43.478 0.00 0.00 43.81 2.59
3089 8378 5.592282 CCTAGTCAGATCACTGTCATGTACT 59.408 44.000 0.00 0.00 43.81 2.73
3090 8379 5.590663 TCCTAGTCAGATCACTGTCATGTAC 59.409 44.000 0.00 0.00 43.81 2.90
3091 8380 5.755849 TCCTAGTCAGATCACTGTCATGTA 58.244 41.667 0.00 0.00 43.81 2.29
3092 8381 4.604156 TCCTAGTCAGATCACTGTCATGT 58.396 43.478 0.00 0.00 43.81 3.21
3093 8382 4.499526 GCTCCTAGTCAGATCACTGTCATG 60.500 50.000 0.00 0.00 43.81 3.07
3094 8383 3.636300 GCTCCTAGTCAGATCACTGTCAT 59.364 47.826 0.00 0.00 43.81 3.06
3095 8384 3.020274 GCTCCTAGTCAGATCACTGTCA 58.980 50.000 0.00 0.00 43.81 3.58
3096 8385 2.360801 GGCTCCTAGTCAGATCACTGTC 59.639 54.545 0.00 0.00 43.81 3.51
3099 8388 1.573376 AGGGCTCCTAGTCAGATCACT 59.427 52.381 0.00 0.00 28.47 3.41
3107 8396 1.055040 ATGCATCAGGGCTCCTAGTC 58.945 55.000 0.00 0.00 29.64 2.59
3110 8399 1.352083 GGTATGCATCAGGGCTCCTA 58.648 55.000 0.19 0.00 29.64 2.94
3113 8402 1.133976 AGTTGGTATGCATCAGGGCTC 60.134 52.381 0.19 0.00 34.04 4.70
3114 8403 0.921896 AGTTGGTATGCATCAGGGCT 59.078 50.000 0.19 0.00 34.04 5.19
3170 8460 8.588290 ATGCTGGTTAATATTTGGTTTACTGA 57.412 30.769 0.00 0.00 0.00 3.41
3171 8461 9.651913 AAATGCTGGTTAATATTTGGTTTACTG 57.348 29.630 0.00 0.00 0.00 2.74
3198 8488 8.851145 GGACACTATCTTGACAATCTACTATGA 58.149 37.037 0.00 0.00 0.00 2.15
3217 8507 1.946984 ATTCTCCCGGTTGGACACTA 58.053 50.000 0.00 0.00 38.61 2.74
3224 8514 4.514781 TCGTATGATATTCTCCCGGTTG 57.485 45.455 0.00 0.00 0.00 3.77
3226 8516 5.295152 GTTTTCGTATGATATTCTCCCGGT 58.705 41.667 0.00 0.00 0.00 5.28
3230 8520 9.760077 TTAGAAGGTTTTCGTATGATATTCTCC 57.240 33.333 0.00 0.00 38.38 3.71
3257 8547 4.729227 ACATGGTTTCCACGAAGTTTTT 57.271 36.364 0.00 0.00 41.61 1.94
3258 8548 4.729227 AACATGGTTTCCACGAAGTTTT 57.271 36.364 0.00 0.00 41.61 2.43
3259 8549 5.127491 TCTAACATGGTTTCCACGAAGTTT 58.873 37.500 0.00 0.00 41.61 2.66
3260 8550 4.710324 TCTAACATGGTTTCCACGAAGTT 58.290 39.130 0.00 0.00 41.61 2.66
3262 8552 4.566004 TCTCTAACATGGTTTCCACGAAG 58.434 43.478 0.00 0.00 35.80 3.79
3263 8553 4.610605 TCTCTAACATGGTTTCCACGAA 57.389 40.909 0.00 0.00 35.80 3.85
3264 8554 4.610605 TTCTCTAACATGGTTTCCACGA 57.389 40.909 0.00 0.00 35.80 4.35
3265 8555 5.163754 GGAATTCTCTAACATGGTTTCCACG 60.164 44.000 5.23 0.00 35.80 4.94
3266 8556 5.710099 TGGAATTCTCTAACATGGTTTCCAC 59.290 40.000 8.02 0.00 37.15 4.02
3267 8557 5.886609 TGGAATTCTCTAACATGGTTTCCA 58.113 37.500 8.02 8.02 39.12 3.53
3268 8558 6.834168 TTGGAATTCTCTAACATGGTTTCC 57.166 37.500 5.23 3.13 33.58 3.13


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

AutoCloner maintained by Alex Coulton.