Multiple sequence alignment - TraesCS6B01G393800

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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 TraesCS6B01G393800 chr6B 100.000 4004 0 0 1 4004 668779663 668775660 0.000000e+00 7395.0
1 TraesCS6B01G393800 chr6D 96.725 2412 58 11 997 3402 444138373 444135977 0.000000e+00 3997.0
2 TraesCS6B01G393800 chr6D 86.203 790 67 18 194 949 444139335 444138554 0.000000e+00 817.0
3 TraesCS6B01G393800 chr6D 74.555 1179 273 23 1829 2995 375029269 375030432 1.290000e-134 490.0
4 TraesCS6B01G393800 chr6D 83.491 527 55 21 274 778 444140830 444140314 2.820000e-126 462.0
5 TraesCS6B01G393800 chr6D 88.716 257 11 6 3749 4004 444135650 444135411 8.410000e-77 298.0
6 TraesCS6B01G393800 chr6D 87.500 256 24 3 23 277 444141208 444140960 5.060000e-74 289.0
7 TraesCS6B01G393800 chr6D 93.333 195 12 1 1 195 444139807 444139614 1.820000e-73 287.0
8 TraesCS6B01G393800 chr6D 88.333 240 15 10 3544 3783 444135980 444135754 3.940000e-70 276.0
9 TraesCS6B01G393800 chr6A 95.658 2349 63 23 1090 3418 591733881 591731552 0.000000e+00 3736.0
10 TraesCS6B01G393800 chr6A 89.694 359 34 2 1 356 591734995 591734637 4.720000e-124 455.0
11 TraesCS6B01G393800 chr6A 83.333 198 18 12 681 875 591734492 591734307 6.880000e-38 169.0
12 TraesCS6B01G393800 chr2D 74.407 1180 286 14 1814 2985 593219471 593220642 3.600000e-135 492.0
13 TraesCS6B01G393800 chr2D 96.063 127 5 0 3417 3543 450745509 450745635 1.460000e-49 207.0
14 TraesCS6B01G393800 chr2D 76.011 371 76 10 1076 1438 593218727 593219092 3.180000e-41 180.0
15 TraesCS6B01G393800 chr2A 74.293 1202 287 17 1812 3002 727957648 727958838 4.650000e-134 488.0
16 TraesCS6B01G393800 chr2A 74.656 363 73 16 1076 1427 727956900 727957254 4.170000e-30 143.0
17 TraesCS6B01G393800 chr2B 74.389 1187 278 24 1812 2985 719473162 719474335 6.020000e-133 484.0
18 TraesCS6B01G393800 chr2B 94.118 136 7 1 3409 3544 550044046 550044180 5.250000e-49 206.0
19 TraesCS6B01G393800 chr2B 75.714 350 76 7 1084 1427 719472419 719472765 2.480000e-37 167.0
20 TraesCS6B01G393800 chr7B 92.237 219 13 3 1254 1471 609643669 609643884 1.400000e-79 307.0
21 TraesCS6B01G393800 chr7B 90.476 147 10 3 3406 3552 227053651 227053793 1.470000e-44 191.0
22 TraesCS6B01G393800 chr5B 93.720 207 10 2 3213 3418 22519803 22519599 1.400000e-79 307.0
23 TraesCS6B01G393800 chr5B 92.893 197 9 4 3587 3783 22519539 22519348 8.470000e-72 281.0
24 TraesCS6B01G393800 chr5B 95.349 129 6 0 3415 3543 96879071 96878943 5.250000e-49 206.0
25 TraesCS6B01G393800 chr5B 90.909 55 1 3 3749 3803 22519254 22519204 2.000000e-08 71.3
26 TraesCS6B01G393800 chr5B 97.436 39 0 1 3542 3579 22519600 22519562 9.290000e-07 65.8
27 TraesCS6B01G393800 chr3A 92.271 207 13 2 3213 3418 235363388 235363592 1.410000e-74 291.0
28 TraesCS6B01G393800 chr3A 86.466 133 8 5 3542 3667 235363591 235363720 1.940000e-28 137.0
29 TraesCS6B01G393800 chr1A 92.271 207 13 2 3213 3418 562930731 562930527 1.410000e-74 291.0
30 TraesCS6B01G393800 chr1A 93.333 135 9 0 3417 3551 574666552 574666418 2.440000e-47 200.0
31 TraesCS6B01G393800 chr1A 86.466 133 8 4 3542 3667 562930528 562930399 1.940000e-28 137.0
32 TraesCS6B01G393800 chr4A 91.457 199 14 2 3221 3418 720301123 720300927 1.830000e-68 270.0
33 TraesCS6B01G393800 chr4A 85.659 258 19 12 3176 3418 418180216 418179962 5.140000e-64 255.0
34 TraesCS6B01G393800 chr4A 87.310 197 21 2 3579 3775 720300875 720300683 5.210000e-54 222.0
35 TraesCS6B01G393800 chr4A 94.697 132 7 0 3416 3547 675518274 675518143 5.250000e-49 206.0
36 TraesCS6B01G393800 chr4A 100.000 44 0 0 3749 3792 720300583 720300540 9.220000e-12 82.4
37 TraesCS6B01G393800 chr3B 95.349 129 4 2 3416 3543 544781551 544781424 1.890000e-48 204.0
38 TraesCS6B01G393800 chr3B 93.750 128 8 0 3416 3543 666705043 666705170 4.080000e-45 193.0
39 TraesCS6B01G393800 chr5D 94.574 129 7 0 3415 3543 455608057 455607929 2.440000e-47 200.0


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 TraesCS6B01G393800 chr6B 668775660 668779663 4003 True 7395.000000 7395 100.000000 1 4004 1 chr6B.!!$R1 4003
1 TraesCS6B01G393800 chr6D 444135411 444141208 5797 True 918.000000 3997 89.185857 1 4004 7 chr6D.!!$R1 4003
2 TraesCS6B01G393800 chr6D 375029269 375030432 1163 False 490.000000 490 74.555000 1829 2995 1 chr6D.!!$F1 1166
3 TraesCS6B01G393800 chr6A 591731552 591734995 3443 True 1453.333333 3736 89.561667 1 3418 3 chr6A.!!$R1 3417
4 TraesCS6B01G393800 chr2D 593218727 593220642 1915 False 336.000000 492 75.209000 1076 2985 2 chr2D.!!$F2 1909
5 TraesCS6B01G393800 chr2A 727956900 727958838 1938 False 315.500000 488 74.474500 1076 3002 2 chr2A.!!$F1 1926
6 TraesCS6B01G393800 chr2B 719472419 719474335 1916 False 325.500000 484 75.051500 1084 2985 2 chr2B.!!$F2 1901

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
561 2264 0.168568 GACGACTCTCCGGTCAAGTC 59.831 60.000 17.87 17.87 36.12 3.01 F
661 2364 0.321919 TCCATCCAAGCTCACACTGC 60.322 55.000 0.00 0.00 0.00 4.40 F
811 2527 1.066858 GTTCTCCGTCTCCAATCTGCA 60.067 52.381 0.00 0.00 0.00 4.41 F
1734 3714 1.335132 GGGCCCTCAAGATGTACGGA 61.335 60.000 17.04 0.00 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2316 4302 0.913451 AGAAGCAGGCTGTCCTCCAT 60.913 55.000 17.16 0.0 41.93 3.41 R
2553 4542 1.255667 GCCAGGACGGGTACTTCTGA 61.256 60.000 0.00 0.0 34.06 3.27 R
2784 4773 1.214853 GGACCCGGACGAGAAGAAC 59.785 63.158 0.73 0.0 0.00 3.01 R
3526 5538 0.548031 ACATACTACCTCCGTCCGGA 59.452 55.000 0.00 0.0 42.90 5.14 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
133 1535 6.495181 TCCAATAGTAGAAACCCATTTGCAAA 59.505 34.615 15.44 15.44 0.00 3.68
185 1587 7.056006 TCATTATGAGAAGCTAAATCCTTGCA 58.944 34.615 0.00 0.00 0.00 4.08
212 1894 7.419634 GGAGCTCTCACCTAAAAAGATATCCTT 60.420 40.741 14.64 0.00 36.47 3.36
220 1902 7.340487 CACCTAAAAAGATATCCTTGAGGCTTT 59.660 37.037 14.71 0.00 35.24 3.51
243 1925 9.106070 CTTTGGGTAACTTATGTAGATACAACC 57.894 37.037 0.00 0.00 39.99 3.77
244 1926 7.128234 TGGGTAACTTATGTAGATACAACCC 57.872 40.000 16.42 16.42 44.38 4.11
252 1934 5.945144 ATGTAGATACAACCCCGTAACTT 57.055 39.130 0.00 0.00 39.99 2.66
255 1937 5.163663 TGTAGATACAACCCCGTAACTTACG 60.164 44.000 13.44 13.44 41.45 3.18
302 1987 2.605818 TCTTTTCACGTGAACGACAAGG 59.394 45.455 29.74 15.50 43.02 3.61
320 2005 7.175990 ACGACAAGGTACCATTTTGAACAATAT 59.824 33.333 15.94 0.00 0.00 1.28
322 2007 8.415950 ACAAGGTACCATTTTGAACAATATCA 57.584 30.769 15.94 0.00 0.00 2.15
343 2028 4.892345 TCATCTTTCACCATGGTTGTTTGA 59.108 37.500 16.84 10.90 0.00 2.69
356 2041 1.225376 TGTTTGATGACCACGCCGAC 61.225 55.000 0.00 0.00 0.00 4.79
357 2042 1.069935 TTTGATGACCACGCCGACA 59.930 52.632 0.00 0.00 0.00 4.35
358 2043 0.533085 TTTGATGACCACGCCGACAA 60.533 50.000 0.00 0.00 0.00 3.18
359 2044 0.948623 TTGATGACCACGCCGACAAG 60.949 55.000 0.00 0.00 0.00 3.16
370 2073 2.288729 ACGCCGACAAGTTACTTTTTCC 59.711 45.455 0.00 0.00 0.00 3.13
379 2082 6.807789 ACAAGTTACTTTTTCCGCCAATAAA 58.192 32.000 0.00 0.00 0.00 1.40
389 2092 8.888579 TTTTTCCGCCAATAAAAGAATAAACA 57.111 26.923 0.00 0.00 0.00 2.83
413 2116 8.974408 ACAAAGGTTATTTGAAAAGTAATTCGC 58.026 29.630 7.30 0.00 30.57 4.70
428 2131 1.934589 TTCGCCAATCACCATACTCG 58.065 50.000 0.00 0.00 0.00 4.18
443 2146 2.930826 ACTCGGTTGGAATGTGAAGT 57.069 45.000 0.00 0.00 0.00 3.01
445 2148 1.197721 CTCGGTTGGAATGTGAAGTGC 59.802 52.381 0.00 0.00 0.00 4.40
447 2150 0.951558 GGTTGGAATGTGAAGTGCGT 59.048 50.000 0.00 0.00 0.00 5.24
467 2170 2.095252 GCTGGCTTCGAGTCGTTCC 61.095 63.158 13.12 12.16 0.00 3.62
484 2187 3.119602 CGTTCCGTCTGACCTCTATTTCA 60.120 47.826 1.55 0.00 0.00 2.69
485 2188 4.425520 GTTCCGTCTGACCTCTATTTCAG 58.574 47.826 1.55 0.00 40.65 3.02
486 2189 3.024547 TCCGTCTGACCTCTATTTCAGG 58.975 50.000 1.55 0.00 39.86 3.86
489 2192 3.368427 CGTCTGACCTCTATTTCAGGCAA 60.368 47.826 1.55 0.00 43.42 4.52
490 2193 3.935828 GTCTGACCTCTATTTCAGGCAAC 59.064 47.826 0.00 0.00 42.88 4.17
505 2208 2.007608 GGCAACCGTGAAACTCTATCC 58.992 52.381 0.00 0.00 31.75 2.59
507 2210 1.659098 CAACCGTGAAACTCTATCCGC 59.341 52.381 0.00 0.00 31.75 5.54
531 2234 1.320507 GGGTTAACGGTTTTCAGCCA 58.679 50.000 0.00 0.00 0.00 4.75
538 2241 2.548295 GGTTTTCAGCCACCGCGAA 61.548 57.895 8.23 0.00 41.18 4.70
561 2264 0.168568 GACGACTCTCCGGTCAAGTC 59.831 60.000 17.87 17.87 36.12 3.01
563 2266 1.002888 ACGACTCTCCGGTCAAGTCTA 59.997 52.381 22.21 0.00 37.79 2.59
603 2306 5.568747 TTTTCCGCAAGAAAATAAAAGCG 57.431 34.783 7.39 0.00 47.00 4.68
604 2307 5.282510 TTTTCCGCAAGAAAATAAAAGCGA 58.717 33.333 6.16 0.00 47.00 4.93
605 2308 5.174216 TTTTCCGCAAGAAAATAAAAGCGAC 59.826 36.000 6.16 0.00 47.00 5.19
610 2313 4.143618 GCAAGAAAATAAAAGCGACGTTGG 60.144 41.667 4.64 0.00 0.00 3.77
633 2336 0.666374 GTTGAACCTTGAACCCACGG 59.334 55.000 0.00 0.00 37.68 4.94
636 2339 1.064611 TGAACCTTGAACCCACGGAAA 60.065 47.619 0.00 0.00 35.45 3.13
639 2342 0.666374 CCTTGAACCCACGGAAACAC 59.334 55.000 0.00 0.00 33.86 3.32
655 2358 2.957402 ACACTTTCCATCCAAGCTCA 57.043 45.000 0.00 0.00 0.00 4.26
656 2359 2.508526 ACACTTTCCATCCAAGCTCAC 58.491 47.619 0.00 0.00 0.00 3.51
657 2360 2.158623 ACACTTTCCATCCAAGCTCACA 60.159 45.455 0.00 0.00 0.00 3.58
658 2361 2.227388 CACTTTCCATCCAAGCTCACAC 59.773 50.000 0.00 0.00 0.00 3.82
659 2362 2.107204 ACTTTCCATCCAAGCTCACACT 59.893 45.455 0.00 0.00 0.00 3.55
660 2363 2.189594 TTCCATCCAAGCTCACACTG 57.810 50.000 0.00 0.00 0.00 3.66
661 2364 0.321919 TCCATCCAAGCTCACACTGC 60.322 55.000 0.00 0.00 0.00 4.40
692 2398 3.321396 TGGTTTAACCCGGATTTTTGTCC 59.679 43.478 12.02 0.00 37.50 4.02
785 2501 2.282816 CACCCCCGGCACAATTCA 60.283 61.111 0.00 0.00 0.00 2.57
797 2513 2.159517 GCACAATTCATCCACGTTCTCC 60.160 50.000 0.00 0.00 0.00 3.71
798 2514 2.094258 CACAATTCATCCACGTTCTCCG 59.906 50.000 0.00 0.00 44.03 4.63
809 2525 1.914634 CGTTCTCCGTCTCCAATCTG 58.085 55.000 0.00 0.00 0.00 2.90
810 2526 1.646189 GTTCTCCGTCTCCAATCTGC 58.354 55.000 0.00 0.00 0.00 4.26
811 2527 1.066858 GTTCTCCGTCTCCAATCTGCA 60.067 52.381 0.00 0.00 0.00 4.41
812 2528 1.489481 TCTCCGTCTCCAATCTGCAT 58.511 50.000 0.00 0.00 0.00 3.96
813 2529 1.410517 TCTCCGTCTCCAATCTGCATC 59.589 52.381 0.00 0.00 0.00 3.91
905 2701 3.551407 GCGTCCCCCTCCATCTCC 61.551 72.222 0.00 0.00 0.00 3.71
906 2702 3.227276 CGTCCCCCTCCATCTCCG 61.227 72.222 0.00 0.00 0.00 4.63
907 2703 3.551407 GTCCCCCTCCATCTCCGC 61.551 72.222 0.00 0.00 0.00 5.54
908 2704 4.880426 TCCCCCTCCATCTCCGCC 62.880 72.222 0.00 0.00 0.00 6.13
988 2784 3.099170 CCCCACCCCCAGATCCAG 61.099 72.222 0.00 0.00 0.00 3.86
989 2785 2.042762 CCCACCCCCAGATCCAGA 59.957 66.667 0.00 0.00 0.00 3.86
990 2786 1.386485 CCCACCCCCAGATCCAGAT 60.386 63.158 0.00 0.00 0.00 2.90
991 2787 1.422161 CCCACCCCCAGATCCAGATC 61.422 65.000 0.00 0.00 38.09 2.75
992 2788 1.422161 CCACCCCCAGATCCAGATCC 61.422 65.000 4.01 0.00 38.58 3.36
993 2789 1.460305 ACCCCCAGATCCAGATCCG 60.460 63.158 4.01 0.00 38.58 4.18
994 2790 2.219875 CCCCCAGATCCAGATCCGG 61.220 68.421 0.00 0.00 38.58 5.14
995 2791 2.746359 CCCAGATCCAGATCCGGC 59.254 66.667 0.00 0.00 38.58 6.13
1298 3254 2.105128 CTCGCCCTACCGCTTCAG 59.895 66.667 0.00 0.00 0.00 3.02
1734 3714 1.335132 GGGCCCTCAAGATGTACGGA 61.335 60.000 17.04 0.00 0.00 4.69
2316 4302 2.197324 GGCTGGGTGGGTGTTTCA 59.803 61.111 0.00 0.00 0.00 2.69
2403 4389 4.785453 GGAAGCCAGAGCACCGGG 62.785 72.222 6.32 0.00 43.56 5.73
2475 4461 1.617755 CTGTGCCGCTTACACTCGTG 61.618 60.000 0.00 0.00 38.86 4.35
2478 4464 2.654877 CCGCTTACACTCGTGGGT 59.345 61.111 0.00 0.00 34.19 4.51
2553 4542 3.842923 CCGCGTGAGATCCCTGCT 61.843 66.667 4.92 0.00 0.00 4.24
2784 4773 0.602905 GGAAGTGGTGGTGGAAGTCG 60.603 60.000 0.00 0.00 0.00 4.18
3013 5002 1.486726 AGGCCGATTAAGTTCCTCCTG 59.513 52.381 0.00 0.00 0.00 3.86
3091 5082 7.362401 GCATTGGAAAGAGTTTGTAGTCATCAT 60.362 37.037 0.00 0.00 0.00 2.45
3092 5083 7.672983 TTGGAAAGAGTTTGTAGTCATCATC 57.327 36.000 0.00 0.00 0.00 2.92
3093 5084 6.768483 TGGAAAGAGTTTGTAGTCATCATCA 58.232 36.000 0.00 0.00 0.00 3.07
3094 5085 6.650807 TGGAAAGAGTTTGTAGTCATCATCAC 59.349 38.462 0.00 0.00 0.00 3.06
3095 5086 6.650807 GGAAAGAGTTTGTAGTCATCATCACA 59.349 38.462 0.00 0.00 0.00 3.58
3097 5088 6.352016 AGAGTTTGTAGTCATCATCACAGT 57.648 37.500 0.00 0.00 0.00 3.55
3098 5089 6.393990 AGAGTTTGTAGTCATCATCACAGTC 58.606 40.000 0.00 0.00 0.00 3.51
3099 5090 5.482908 AGTTTGTAGTCATCATCACAGTCC 58.517 41.667 0.00 0.00 0.00 3.85
3100 5091 5.247110 AGTTTGTAGTCATCATCACAGTCCT 59.753 40.000 0.00 0.00 0.00 3.85
3101 5092 6.437477 AGTTTGTAGTCATCATCACAGTCCTA 59.563 38.462 0.00 0.00 0.00 2.94
3102 5093 6.456795 TTGTAGTCATCATCACAGTCCTAG 57.543 41.667 0.00 0.00 0.00 3.02
3103 5094 5.510430 TGTAGTCATCATCACAGTCCTAGT 58.490 41.667 0.00 0.00 0.00 2.57
3104 5095 5.952347 TGTAGTCATCATCACAGTCCTAGTT 59.048 40.000 0.00 0.00 0.00 2.24
3105 5096 5.590530 AGTCATCATCACAGTCCTAGTTC 57.409 43.478 0.00 0.00 0.00 3.01
3106 5097 5.019470 AGTCATCATCACAGTCCTAGTTCA 58.981 41.667 0.00 0.00 0.00 3.18
3173 5164 0.672342 TCTAAGTAGGATTCGCCCGC 59.328 55.000 0.00 0.00 37.37 6.13
3174 5165 0.663568 CTAAGTAGGATTCGCCCGCG 60.664 60.000 0.00 0.00 37.37 6.46
3393 5405 1.201647 TGCTAGTTAGTGCCGACTGTC 59.798 52.381 0.00 0.00 33.21 3.51
3400 5412 0.610174 AGTGCCGACTGTCATGATGT 59.390 50.000 8.73 0.81 0.00 3.06
3415 5427 9.738832 CTGTCATGATGTTAAATTGATATTGCA 57.261 29.630 0.00 0.00 0.00 4.08
3422 5434 9.846248 GATGTTAAATTGATATTGCATACTCCC 57.154 33.333 0.00 0.00 0.00 4.30
3423 5435 8.995027 TGTTAAATTGATATTGCATACTCCCT 57.005 30.769 0.00 0.00 0.00 4.20
3424 5436 9.066892 TGTTAAATTGATATTGCATACTCCCTC 57.933 33.333 0.00 0.00 0.00 4.30
3425 5437 8.515414 GTTAAATTGATATTGCATACTCCCTCC 58.485 37.037 0.00 0.00 0.00 4.30
3426 5438 3.961480 TGATATTGCATACTCCCTCCG 57.039 47.619 0.00 0.00 0.00 4.63
3427 5439 3.239449 TGATATTGCATACTCCCTCCGT 58.761 45.455 0.00 0.00 0.00 4.69
3428 5440 4.412843 TGATATTGCATACTCCCTCCGTA 58.587 43.478 0.00 0.00 0.00 4.02
3429 5441 4.219944 TGATATTGCATACTCCCTCCGTAC 59.780 45.833 0.00 0.00 0.00 3.67
3430 5442 1.855295 TTGCATACTCCCTCCGTACA 58.145 50.000 0.00 0.00 0.00 2.90
3431 5443 1.855295 TGCATACTCCCTCCGTACAA 58.145 50.000 0.00 0.00 0.00 2.41
3432 5444 2.181125 TGCATACTCCCTCCGTACAAA 58.819 47.619 0.00 0.00 0.00 2.83
3433 5445 2.568062 TGCATACTCCCTCCGTACAAAA 59.432 45.455 0.00 0.00 0.00 2.44
3434 5446 3.008157 TGCATACTCCCTCCGTACAAAAA 59.992 43.478 0.00 0.00 0.00 1.94
3435 5447 4.196971 GCATACTCCCTCCGTACAAAAAT 58.803 43.478 0.00 0.00 0.00 1.82
3436 5448 5.104859 TGCATACTCCCTCCGTACAAAAATA 60.105 40.000 0.00 0.00 0.00 1.40
3437 5449 5.235831 GCATACTCCCTCCGTACAAAAATAC 59.764 44.000 0.00 0.00 0.00 1.89
3438 5450 6.579865 CATACTCCCTCCGTACAAAAATACT 58.420 40.000 0.00 0.00 0.00 2.12
3439 5451 5.494390 ACTCCCTCCGTACAAAAATACTT 57.506 39.130 0.00 0.00 0.00 2.24
3440 5452 5.243207 ACTCCCTCCGTACAAAAATACTTG 58.757 41.667 0.00 0.00 0.00 3.16
3441 5453 5.221783 ACTCCCTCCGTACAAAAATACTTGT 60.222 40.000 0.00 0.00 42.20 3.16
3442 5454 4.998672 TCCCTCCGTACAAAAATACTTGTG 59.001 41.667 0.00 0.00 39.81 3.33
3443 5455 4.998672 CCCTCCGTACAAAAATACTTGTGA 59.001 41.667 0.00 0.00 39.81 3.58
3444 5456 5.646360 CCCTCCGTACAAAAATACTTGTGAT 59.354 40.000 0.00 0.00 39.81 3.06
3445 5457 6.183360 CCCTCCGTACAAAAATACTTGTGATC 60.183 42.308 0.00 0.00 39.81 2.92
3446 5458 6.397831 TCCGTACAAAAATACTTGTGATCG 57.602 37.500 0.00 2.62 39.81 3.69
3447 5459 6.157904 TCCGTACAAAAATACTTGTGATCGA 58.842 36.000 0.00 0.00 39.81 3.59
3448 5460 6.814644 TCCGTACAAAAATACTTGTGATCGAT 59.185 34.615 0.00 0.00 39.81 3.59
3449 5461 7.975058 TCCGTACAAAAATACTTGTGATCGATA 59.025 33.333 0.00 0.00 39.81 2.92
3450 5462 8.761497 CCGTACAAAAATACTTGTGATCGATAT 58.239 33.333 0.00 0.00 39.81 1.63
3451 5463 9.567917 CGTACAAAAATACTTGTGATCGATATG 57.432 33.333 0.00 0.00 39.81 1.78
3452 5464 9.864034 GTACAAAAATACTTGTGATCGATATGG 57.136 33.333 0.00 0.00 39.81 2.74
3453 5465 8.731275 ACAAAAATACTTGTGATCGATATGGA 57.269 30.769 0.00 0.00 38.12 3.41
3454 5466 9.342308 ACAAAAATACTTGTGATCGATATGGAT 57.658 29.630 0.00 0.00 38.12 3.41
3461 5473 8.383318 ACTTGTGATCGATATGGATAAAAAGG 57.617 34.615 15.86 1.98 0.00 3.11
3462 5474 7.445402 ACTTGTGATCGATATGGATAAAAAGGG 59.555 37.037 15.86 0.00 0.00 3.95
3463 5475 7.073457 TGTGATCGATATGGATAAAAAGGGA 57.927 36.000 0.00 0.00 0.00 4.20
3464 5476 7.689299 TGTGATCGATATGGATAAAAAGGGAT 58.311 34.615 0.00 0.00 0.00 3.85
3465 5477 7.607607 TGTGATCGATATGGATAAAAAGGGATG 59.392 37.037 0.00 0.00 0.00 3.51
3466 5478 7.607991 GTGATCGATATGGATAAAAAGGGATGT 59.392 37.037 0.00 0.00 0.00 3.06
3467 5479 8.821817 TGATCGATATGGATAAAAAGGGATGTA 58.178 33.333 0.00 0.00 0.00 2.29
3468 5480 9.838339 GATCGATATGGATAAAAAGGGATGTAT 57.162 33.333 0.00 0.00 0.00 2.29
3469 5481 9.838339 ATCGATATGGATAAAAAGGGATGTATC 57.162 33.333 0.00 0.00 0.00 2.24
3470 5482 9.046846 TCGATATGGATAAAAAGGGATGTATCT 57.953 33.333 0.00 0.00 0.00 1.98
3476 5488 9.225682 TGGATAAAAAGGGATGTATCTAGAACT 57.774 33.333 0.00 0.00 0.00 3.01
3508 5520 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
3514 5526 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
3517 5529 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
3518 5530 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
3519 5531 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
3520 5532 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
3521 5533 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
3522 5534 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
3529 5541 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
3530 5542 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
3531 5543 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
3532 5544 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
3533 5545 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
3534 5546 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
3535 5547 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
3536 5548 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
3537 5549 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3538 5550 1.206371 CAAGTATTTCCGGACGGAGGT 59.794 52.381 13.64 9.03 46.06 3.85
3539 5551 2.428171 CAAGTATTTCCGGACGGAGGTA 59.572 50.000 13.64 8.09 46.06 3.08
3540 5552 2.305009 AGTATTTCCGGACGGAGGTAG 58.695 52.381 13.64 0.00 46.06 3.18
3541 5553 2.027385 GTATTTCCGGACGGAGGTAGT 58.973 52.381 13.64 0.00 46.06 2.73
3542 5554 2.442236 ATTTCCGGACGGAGGTAGTA 57.558 50.000 13.64 0.00 46.06 1.82
3576 5588 3.392947 TCAGAACCATTGGTTAGGACACA 59.607 43.478 20.85 0.00 46.95 3.72
3577 5589 3.502211 CAGAACCATTGGTTAGGACACAC 59.498 47.826 20.85 6.32 46.95 3.82
3585 5597 4.595762 TGGTTAGGACACACTAGTTGTC 57.404 45.455 20.73 20.73 35.67 3.18
3596 5608 4.923871 CACACTAGTTGTCACAGTATGTCC 59.076 45.833 0.00 0.00 41.23 4.02
3597 5609 5.508994 CACACTAGTTGTCACAGTATGTCCA 60.509 44.000 0.00 0.00 41.23 4.02
3598 5610 7.280573 CACACTAGTTGTCACAGTATGTCCAG 61.281 46.154 0.00 0.00 41.23 3.86
3621 5633 5.012561 AGAGAGTGTGACAGATTAGGCTTTT 59.987 40.000 0.00 0.00 0.00 2.27
3630 5642 6.015180 TGACAGATTAGGCTTTTGATGCTTTT 60.015 34.615 0.00 0.00 0.00 2.27
3634 5646 1.273327 AGGCTTTTGATGCTTTTCCCG 59.727 47.619 0.00 0.00 0.00 5.14
3641 5653 0.179153 GATGCTTTTCCCGCTTCTGC 60.179 55.000 0.00 0.00 0.00 4.26
3642 5654 1.598701 ATGCTTTTCCCGCTTCTGCC 61.599 55.000 0.00 0.00 35.36 4.85
3643 5655 1.973812 GCTTTTCCCGCTTCTGCCT 60.974 57.895 0.00 0.00 35.36 4.75
3645 5657 1.821216 CTTTTCCCGCTTCTGCCTTA 58.179 50.000 0.00 0.00 35.36 2.69
3646 5658 1.740025 CTTTTCCCGCTTCTGCCTTAG 59.260 52.381 0.00 0.00 35.36 2.18
3647 5659 0.981183 TTTCCCGCTTCTGCCTTAGA 59.019 50.000 0.00 0.00 35.36 2.10
3648 5660 1.204146 TTCCCGCTTCTGCCTTAGAT 58.796 50.000 0.00 0.00 34.80 1.98
3649 5661 2.082140 TCCCGCTTCTGCCTTAGATA 57.918 50.000 0.00 0.00 34.80 1.98
3650 5662 2.609747 TCCCGCTTCTGCCTTAGATAT 58.390 47.619 0.00 0.00 34.80 1.63
3651 5663 2.300152 TCCCGCTTCTGCCTTAGATATG 59.700 50.000 0.00 0.00 34.80 1.78
3652 5664 2.037772 CCCGCTTCTGCCTTAGATATGT 59.962 50.000 0.00 0.00 34.80 2.29
3676 5688 8.836413 TGTTCAAATACAAGAGTAAAACTCCAG 58.164 33.333 3.49 0.02 46.18 3.86
3716 5728 2.897969 GTTGTCCTTCACTACAGGAGGA 59.102 50.000 0.00 0.00 41.36 3.71
3718 5730 2.526432 GTCCTTCACTACAGGAGGACA 58.474 52.381 14.96 0.00 41.36 4.02
3722 5734 3.306364 CCTTCACTACAGGAGGACACAAG 60.306 52.174 0.00 0.00 32.41 3.16
3729 5741 1.824230 CAGGAGGACACAAGAGGAGAG 59.176 57.143 0.00 0.00 0.00 3.20
3730 5742 0.534873 GGAGGACACAAGAGGAGAGC 59.465 60.000 0.00 0.00 0.00 4.09
3733 5745 0.172352 GGACACAAGAGGAGAGCTCG 59.828 60.000 8.37 0.00 0.00 5.03
3739 5751 1.132262 CAAGAGGAGAGCTCGAGTGTC 59.868 57.143 15.13 11.30 0.00 3.67
3783 5795 3.648339 ATGTTTCTTTGCGCAGATGTT 57.352 38.095 11.31 0.00 0.00 2.71
3784 5796 2.998772 TGTTTCTTTGCGCAGATGTTC 58.001 42.857 11.31 2.43 0.00 3.18
3849 5999 5.312120 AGTAGTATGTCCAAAGTGTCTCG 57.688 43.478 0.00 0.00 0.00 4.04
3896 6046 0.678950 TGTGCACTGGAGTCGATTCA 59.321 50.000 19.41 0.00 0.00 2.57
3903 6053 4.248859 CACTGGAGTCGATTCATCAGTTT 58.751 43.478 14.30 0.00 33.80 2.66
3904 6054 4.692625 CACTGGAGTCGATTCATCAGTTTT 59.307 41.667 14.30 0.00 33.80 2.43
3905 6055 5.869344 CACTGGAGTCGATTCATCAGTTTTA 59.131 40.000 14.30 0.00 33.80 1.52
3906 6056 5.869888 ACTGGAGTCGATTCATCAGTTTTAC 59.130 40.000 10.32 0.00 32.34 2.01
3907 6057 6.037786 TGGAGTCGATTCATCAGTTTTACT 57.962 37.500 10.32 0.00 0.00 2.24
3908 6058 7.093902 ACTGGAGTCGATTCATCAGTTTTACTA 60.094 37.037 10.32 0.00 32.34 1.82
3909 6059 7.258441 TGGAGTCGATTCATCAGTTTTACTAG 58.742 38.462 10.32 0.00 0.00 2.57
3910 6060 7.093902 TGGAGTCGATTCATCAGTTTTACTAGT 60.094 37.037 10.32 0.00 0.00 2.57
3911 6061 8.404000 GGAGTCGATTCATCAGTTTTACTAGTA 58.596 37.037 10.32 0.00 0.00 1.82
3912 6062 9.224058 GAGTCGATTCATCAGTTTTACTAGTAC 57.776 37.037 0.91 0.00 0.00 2.73
3913 6063 8.958506 AGTCGATTCATCAGTTTTACTAGTACT 58.041 33.333 0.91 0.00 0.00 2.73
3942 6092 5.772825 AGTACTAGTCGGTACAAACAACA 57.227 39.130 0.00 0.00 43.01 3.33
3952 6102 4.041723 GGTACAAACAACACTTGTCATGC 58.958 43.478 0.00 0.00 44.59 4.06
3985 6136 5.126061 GCCCATAATTCTGTTGATCAACTGT 59.874 40.000 32.57 20.85 41.67 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 1418 9.534565 TGTGTAATCAATAGAAGACTTCATAGC 57.465 33.333 17.34 0.26 0.00 2.97
91 1493 1.065564 TGGATCACATGCACCAATCGA 60.066 47.619 0.00 0.00 0.00 3.59
133 1535 4.098914 TGTCCTAGCAAATTGAGTTGGT 57.901 40.909 0.00 1.52 41.80 3.67
185 1587 6.042666 GGATATCTTTTTAGGTGAGAGCTCCT 59.957 42.308 10.93 3.13 40.85 3.69
212 1894 4.650972 ACATAAGTTACCCAAAGCCTCA 57.349 40.909 0.00 0.00 0.00 3.86
220 1902 6.100134 GGGGTTGTATCTACATAAGTTACCCA 59.900 42.308 19.80 0.00 45.23 4.51
266 1951 5.411361 CGTGAAAAGAATTGGTGGAGTCATA 59.589 40.000 0.00 0.00 0.00 2.15
320 2005 4.892345 TCAAACAACCATGGTGAAAGATGA 59.108 37.500 20.60 15.08 0.00 2.92
322 2007 5.539574 TCATCAAACAACCATGGTGAAAGAT 59.460 36.000 20.60 15.11 33.91 2.40
329 2014 2.627699 GTGGTCATCAAACAACCATGGT 59.372 45.455 13.00 13.00 44.44 3.55
343 2028 0.319083 TAACTTGTCGGCGTGGTCAT 59.681 50.000 6.85 0.00 0.00 3.06
356 2041 7.650104 TCTTTTATTGGCGGAAAAAGTAACTTG 59.350 33.333 13.95 0.00 39.86 3.16
357 2042 7.718525 TCTTTTATTGGCGGAAAAAGTAACTT 58.281 30.769 13.95 0.00 39.86 2.66
358 2043 7.279750 TCTTTTATTGGCGGAAAAAGTAACT 57.720 32.000 13.95 0.00 39.86 2.24
359 2044 7.933728 TTCTTTTATTGGCGGAAAAAGTAAC 57.066 32.000 13.95 0.00 39.86 2.50
370 2073 7.883229 ACCTTTGTTTATTCTTTTATTGGCG 57.117 32.000 0.00 0.00 0.00 5.69
389 2092 8.145122 TGGCGAATTACTTTTCAAATAACCTTT 58.855 29.630 0.00 0.00 0.00 3.11
413 2116 2.093181 TCCAACCGAGTATGGTGATTGG 60.093 50.000 0.00 0.00 42.89 3.16
428 2131 0.951558 ACGCACTTCACATTCCAACC 59.048 50.000 0.00 0.00 0.00 3.77
445 2148 2.811317 GACTCGAAGCCAGCCACG 60.811 66.667 0.00 0.00 0.00 4.94
447 2150 2.765250 GAACGACTCGAAGCCAGCCA 62.765 60.000 5.20 0.00 0.00 4.75
467 2170 2.166459 TGCCTGAAATAGAGGTCAGACG 59.834 50.000 2.28 0.00 43.32 4.18
484 2187 2.354805 GGATAGAGTTTCACGGTTGCCT 60.355 50.000 0.00 0.00 0.00 4.75
485 2188 2.007608 GGATAGAGTTTCACGGTTGCC 58.992 52.381 0.00 0.00 0.00 4.52
486 2189 1.659098 CGGATAGAGTTTCACGGTTGC 59.341 52.381 0.00 0.00 0.00 4.17
489 2192 0.179145 CGCGGATAGAGTTTCACGGT 60.179 55.000 0.00 0.00 0.00 4.83
490 2193 0.179145 ACGCGGATAGAGTTTCACGG 60.179 55.000 12.47 0.00 0.00 4.94
507 2210 0.384601 GAAAACCGTTAACCCGCACG 60.385 55.000 0.00 0.00 36.12 5.34
514 2217 2.410785 GGTGGCTGAAAACCGTTAAC 57.589 50.000 0.00 0.00 0.00 2.01
531 2234 3.886329 GAGTCGTCGGTTTCGCGGT 62.886 63.158 6.13 0.00 36.87 5.68
561 2264 1.227263 CGTTGGACCAGCCCGATAG 60.227 63.158 2.33 0.00 34.97 2.08
563 2266 4.096003 CCGTTGGACCAGCCCGAT 62.096 66.667 2.33 0.00 34.97 4.18
596 2299 0.249405 ACCGTCCAACGTCGCTTTTA 60.249 50.000 0.00 0.00 40.58 1.52
603 2306 0.531311 AGGTTCAACCGTCCAACGTC 60.531 55.000 0.00 0.00 44.90 4.34
604 2307 0.107557 AAGGTTCAACCGTCCAACGT 60.108 50.000 0.00 0.00 44.90 3.99
605 2308 0.306533 CAAGGTTCAACCGTCCAACG 59.693 55.000 0.00 0.00 44.90 4.10
610 2313 0.949397 GGGTTCAAGGTTCAACCGTC 59.051 55.000 0.00 0.00 44.90 4.79
633 2336 3.569701 TGAGCTTGGATGGAAAGTGTTTC 59.430 43.478 0.00 0.00 38.94 2.78
636 2339 2.158623 TGTGAGCTTGGATGGAAAGTGT 60.159 45.455 0.00 0.00 0.00 3.55
639 2342 2.486982 CAGTGTGAGCTTGGATGGAAAG 59.513 50.000 0.00 0.00 0.00 2.62
658 2361 2.111932 TTAAACCACAGCGCACGCAG 62.112 55.000 18.24 12.05 44.88 5.18
659 2362 2.180862 TTAAACCACAGCGCACGCA 61.181 52.632 18.24 0.00 44.88 5.24
660 2363 1.724581 GTTAAACCACAGCGCACGC 60.725 57.895 11.47 6.99 42.33 5.34
661 2364 1.082366 GGTTAAACCACAGCGCACG 60.082 57.895 11.47 1.85 38.42 5.34
668 2374 3.705072 ACAAAAATCCGGGTTAAACCACA 59.295 39.130 10.88 0.00 41.02 4.17
692 2398 5.275881 GCACAAGTTTTTGATCACGTTTCTG 60.276 40.000 0.00 0.00 37.73 3.02
749 2458 3.123620 CGGTGCTGCTCCTCTTGC 61.124 66.667 17.64 0.00 0.00 4.01
797 2513 1.137675 TGGAGATGCAGATTGGAGACG 59.862 52.381 0.00 0.00 0.00 4.18
798 2514 2.996249 TGGAGATGCAGATTGGAGAC 57.004 50.000 0.00 0.00 0.00 3.36
799 2515 2.371179 GGATGGAGATGCAGATTGGAGA 59.629 50.000 0.00 0.00 0.00 3.71
800 2516 2.552591 GGGATGGAGATGCAGATTGGAG 60.553 54.545 0.00 0.00 0.00 3.86
801 2517 1.422781 GGGATGGAGATGCAGATTGGA 59.577 52.381 0.00 0.00 0.00 3.53
802 2518 1.547223 GGGGATGGAGATGCAGATTGG 60.547 57.143 0.00 0.00 0.00 3.16
803 2519 1.144298 TGGGGATGGAGATGCAGATTG 59.856 52.381 0.00 0.00 0.00 2.67
804 2520 1.526315 TGGGGATGGAGATGCAGATT 58.474 50.000 0.00 0.00 0.00 2.40
805 2521 1.424302 CTTGGGGATGGAGATGCAGAT 59.576 52.381 0.00 0.00 0.00 2.90
806 2522 0.841961 CTTGGGGATGGAGATGCAGA 59.158 55.000 0.00 0.00 0.00 4.26
807 2523 0.822532 GCTTGGGGATGGAGATGCAG 60.823 60.000 0.00 0.00 0.00 4.41
808 2524 1.228228 GCTTGGGGATGGAGATGCA 59.772 57.895 0.00 0.00 0.00 3.96
809 2525 0.822532 CTGCTTGGGGATGGAGATGC 60.823 60.000 0.00 0.00 0.00 3.91
810 2526 0.841961 TCTGCTTGGGGATGGAGATG 59.158 55.000 0.00 0.00 0.00 2.90
811 2527 1.138568 CTCTGCTTGGGGATGGAGAT 58.861 55.000 0.00 0.00 30.65 2.75
812 2528 1.630126 GCTCTGCTTGGGGATGGAGA 61.630 60.000 0.00 0.00 0.00 3.71
813 2529 1.153005 GCTCTGCTTGGGGATGGAG 60.153 63.158 0.00 0.00 0.00 3.86
971 2767 2.940421 ATCTGGATCTGGGGGTGGGG 62.940 65.000 0.00 0.00 0.00 4.96
972 2768 1.386485 ATCTGGATCTGGGGGTGGG 60.386 63.158 0.00 0.00 0.00 4.61
973 2769 1.422161 GGATCTGGATCTGGGGGTGG 61.422 65.000 9.96 0.00 37.92 4.61
974 2770 1.762522 CGGATCTGGATCTGGGGGTG 61.763 65.000 10.63 0.00 39.85 4.61
975 2771 1.460305 CGGATCTGGATCTGGGGGT 60.460 63.158 10.63 0.00 39.85 4.95
976 2772 3.476386 CGGATCTGGATCTGGGGG 58.524 66.667 10.63 0.00 39.85 5.40
980 2776 2.341543 CCGCCGGATCTGGATCTG 59.658 66.667 25.54 9.87 42.45 2.90
981 2777 3.620785 GCCGCCGGATCTGGATCT 61.621 66.667 25.54 0.00 37.92 2.75
982 2778 4.688966 GGCCGCCGGATCTGGATC 62.689 72.222 25.54 11.24 37.11 3.36
1298 3254 2.740714 GACTCGTTGGCGTGCATCC 61.741 63.158 0.00 0.00 39.49 3.51
1734 3714 4.020839 CACTTGATCTTGCTGGGGAATTTT 60.021 41.667 0.00 0.00 0.00 1.82
2316 4302 0.913451 AGAAGCAGGCTGTCCTCCAT 60.913 55.000 17.16 0.00 41.93 3.41
2403 4389 3.483869 AGCGAGAAGGGGATGGCC 61.484 66.667 0.00 0.00 0.00 5.36
2475 4461 4.717313 GCACCGAGGAACCCACCC 62.717 72.222 0.00 0.00 0.00 4.61
2478 4464 3.172106 TTGGCACCGAGGAACCCA 61.172 61.111 0.00 0.00 0.00 4.51
2553 4542 1.255667 GCCAGGACGGGTACTTCTGA 61.256 60.000 0.00 0.00 34.06 3.27
2784 4773 1.214853 GGACCCGGACGAGAAGAAC 59.785 63.158 0.73 0.00 0.00 3.01
2934 4923 4.404098 ATGAACCCGACCGTGCCC 62.404 66.667 0.00 0.00 0.00 5.36
3025 5014 3.599343 TCACCTCTCAATTCAATGGTCG 58.401 45.455 0.00 0.00 0.00 4.79
3091 5082 3.706594 GGATGGATGAACTAGGACTGTGA 59.293 47.826 0.00 0.00 0.00 3.58
3092 5083 3.181461 GGGATGGATGAACTAGGACTGTG 60.181 52.174 0.00 0.00 0.00 3.66
3093 5084 3.041946 GGGATGGATGAACTAGGACTGT 58.958 50.000 0.00 0.00 0.00 3.55
3094 5085 3.041211 TGGGATGGATGAACTAGGACTG 58.959 50.000 0.00 0.00 0.00 3.51
3095 5086 3.421394 TGGGATGGATGAACTAGGACT 57.579 47.619 0.00 0.00 0.00 3.85
3097 5088 3.736094 AGTTGGGATGGATGAACTAGGA 58.264 45.455 0.00 0.00 0.00 2.94
3098 5089 4.510167 AAGTTGGGATGGATGAACTAGG 57.490 45.455 0.00 0.00 0.00 3.02
3099 5090 6.199937 CAAAAGTTGGGATGGATGAACTAG 57.800 41.667 0.00 0.00 0.00 2.57
3158 5149 3.912907 CCGCGGGCGAATCCTACT 61.913 66.667 20.10 0.00 42.83 2.57
3173 5164 1.134098 ACCTCATCATAAAGCCCACCG 60.134 52.381 0.00 0.00 0.00 4.94
3174 5165 2.301346 CACCTCATCATAAAGCCCACC 58.699 52.381 0.00 0.00 0.00 4.61
3287 5279 4.003648 ACCACTACTAAGCTTGCACATTC 58.996 43.478 9.86 0.00 0.00 2.67
3326 5335 8.181904 ACAACTTGACCTATGACATTTCAAAT 57.818 30.769 0.00 0.00 34.61 2.32
3400 5412 7.390440 CGGAGGGAGTATGCAATATCAATTTAA 59.610 37.037 0.00 0.00 0.00 1.52
3415 5427 6.803366 AGTATTTTTGTACGGAGGGAGTAT 57.197 37.500 0.00 0.00 0.00 2.12
3418 5430 5.121768 CACAAGTATTTTTGTACGGAGGGAG 59.878 44.000 0.00 0.00 39.17 4.30
3419 5431 4.998672 CACAAGTATTTTTGTACGGAGGGA 59.001 41.667 0.00 0.00 39.17 4.20
3420 5432 4.998672 TCACAAGTATTTTTGTACGGAGGG 59.001 41.667 0.00 0.00 39.17 4.30
3421 5433 6.455113 CGATCACAAGTATTTTTGTACGGAGG 60.455 42.308 0.00 0.00 39.17 4.30
3422 5434 6.309494 TCGATCACAAGTATTTTTGTACGGAG 59.691 38.462 0.00 0.00 39.17 4.63
3423 5435 6.157904 TCGATCACAAGTATTTTTGTACGGA 58.842 36.000 0.00 0.00 39.17 4.69
3424 5436 6.397831 TCGATCACAAGTATTTTTGTACGG 57.602 37.500 0.00 0.00 39.17 4.02
3425 5437 9.567917 CATATCGATCACAAGTATTTTTGTACG 57.432 33.333 0.00 0.00 39.17 3.67
3426 5438 9.864034 CCATATCGATCACAAGTATTTTTGTAC 57.136 33.333 0.00 0.00 39.17 2.90
3427 5439 9.825109 TCCATATCGATCACAAGTATTTTTGTA 57.175 29.630 0.00 0.00 39.17 2.41
3428 5440 8.731275 TCCATATCGATCACAAGTATTTTTGT 57.269 30.769 0.00 0.00 41.77 2.83
3435 5447 9.489084 CCTTTTTATCCATATCGATCACAAGTA 57.511 33.333 0.00 0.00 0.00 2.24
3436 5448 7.445402 CCCTTTTTATCCATATCGATCACAAGT 59.555 37.037 0.00 0.00 0.00 3.16
3437 5449 7.661437 TCCCTTTTTATCCATATCGATCACAAG 59.339 37.037 0.00 0.00 0.00 3.16
3438 5450 7.513856 TCCCTTTTTATCCATATCGATCACAA 58.486 34.615 0.00 0.00 0.00 3.33
3439 5451 7.073457 TCCCTTTTTATCCATATCGATCACA 57.927 36.000 0.00 0.00 0.00 3.58
3440 5452 7.607991 ACATCCCTTTTTATCCATATCGATCAC 59.392 37.037 0.00 0.00 0.00 3.06
3441 5453 7.689299 ACATCCCTTTTTATCCATATCGATCA 58.311 34.615 0.00 0.00 0.00 2.92
3442 5454 9.838339 ATACATCCCTTTTTATCCATATCGATC 57.162 33.333 0.00 0.00 0.00 3.69
3443 5455 9.838339 GATACATCCCTTTTTATCCATATCGAT 57.162 33.333 2.16 2.16 0.00 3.59
3444 5456 9.046846 AGATACATCCCTTTTTATCCATATCGA 57.953 33.333 0.00 0.00 0.00 3.59
3450 5462 9.225682 AGTTCTAGATACATCCCTTTTTATCCA 57.774 33.333 0.00 0.00 0.00 3.41
3482 5494 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
3488 5500 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
3491 5503 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
3492 5504 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
3493 5505 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
3494 5506 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
3495 5507 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
3496 5508 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
3504 5516 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
3505 5517 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
3506 5518 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
3507 5519 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
3508 5520 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
3509 5521 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
3510 5522 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
3511 5523 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
3512 5524 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
3513 5525 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
3514 5526 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
3515 5527 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
3516 5528 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3517 5529 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3518 5530 1.206371 ACCTCCGTCCGGAAATACTTG 59.794 52.381 5.23 0.00 44.66 3.16
3519 5531 1.565067 ACCTCCGTCCGGAAATACTT 58.435 50.000 5.23 0.00 44.66 2.24
3520 5532 2.305009 CTACCTCCGTCCGGAAATACT 58.695 52.381 5.23 0.00 44.66 2.12
3521 5533 2.027385 ACTACCTCCGTCCGGAAATAC 58.973 52.381 5.23 0.00 44.66 1.89
3522 5534 2.442236 ACTACCTCCGTCCGGAAATA 57.558 50.000 5.23 4.45 44.66 1.40
3523 5535 2.442236 TACTACCTCCGTCCGGAAAT 57.558 50.000 5.23 3.48 44.66 2.17
3524 5536 2.026641 CATACTACCTCCGTCCGGAAA 58.973 52.381 5.23 0.00 44.66 3.13
3525 5537 1.064463 ACATACTACCTCCGTCCGGAA 60.064 52.381 5.23 0.00 44.66 4.30
3526 5538 0.548031 ACATACTACCTCCGTCCGGA 59.452 55.000 0.00 0.00 42.90 5.14
3527 5539 1.396653 AACATACTACCTCCGTCCGG 58.603 55.000 0.00 0.00 0.00 5.14
3528 5540 2.686915 AGAAACATACTACCTCCGTCCG 59.313 50.000 0.00 0.00 0.00 4.79
3529 5541 4.732672 AAGAAACATACTACCTCCGTCC 57.267 45.455 0.00 0.00 0.00 4.79
3530 5542 4.329256 GCAAAGAAACATACTACCTCCGTC 59.671 45.833 0.00 0.00 0.00 4.79
3531 5543 4.020485 AGCAAAGAAACATACTACCTCCGT 60.020 41.667 0.00 0.00 0.00 4.69
3532 5544 4.504858 AGCAAAGAAACATACTACCTCCG 58.495 43.478 0.00 0.00 0.00 4.63
3533 5545 5.488341 TGAGCAAAGAAACATACTACCTCC 58.512 41.667 0.00 0.00 0.00 4.30
3534 5546 6.398918 TCTGAGCAAAGAAACATACTACCTC 58.601 40.000 0.00 0.00 0.00 3.85
3535 5547 6.360370 TCTGAGCAAAGAAACATACTACCT 57.640 37.500 0.00 0.00 0.00 3.08
3536 5548 6.128254 GGTTCTGAGCAAAGAAACATACTACC 60.128 42.308 10.62 0.42 42.43 3.18
3537 5549 6.426937 TGGTTCTGAGCAAAGAAACATACTAC 59.573 38.462 13.43 0.00 46.44 2.73
3538 5550 6.530120 TGGTTCTGAGCAAAGAAACATACTA 58.470 36.000 13.43 0.00 46.44 1.82
3539 5551 5.376625 TGGTTCTGAGCAAAGAAACATACT 58.623 37.500 13.43 0.00 46.44 2.12
3540 5552 5.689383 TGGTTCTGAGCAAAGAAACATAC 57.311 39.130 13.43 0.00 46.44 2.39
3576 5588 5.077564 TCTGGACATACTGTGACAACTAGT 58.922 41.667 0.00 0.00 0.00 2.57
3577 5589 5.416013 TCTCTGGACATACTGTGACAACTAG 59.584 44.000 0.00 0.00 0.00 2.57
3585 5597 3.507622 TCACACTCTCTGGACATACTGTG 59.492 47.826 0.00 0.00 0.00 3.66
3596 5608 3.446873 AGCCTAATCTGTCACACTCTCTG 59.553 47.826 0.00 0.00 0.00 3.35
3597 5609 3.707316 AGCCTAATCTGTCACACTCTCT 58.293 45.455 0.00 0.00 0.00 3.10
3598 5610 4.464069 AAGCCTAATCTGTCACACTCTC 57.536 45.455 0.00 0.00 0.00 3.20
3621 5633 1.167851 CAGAAGCGGGAAAAGCATCA 58.832 50.000 0.00 0.00 35.09 3.07
3630 5642 2.082140 TATCTAAGGCAGAAGCGGGA 57.918 50.000 0.00 0.00 43.41 5.14
3634 5646 6.683974 TTTGAACATATCTAAGGCAGAAGC 57.316 37.500 0.00 0.00 36.67 3.86
3649 5661 9.349713 TGGAGTTTTACTCTTGTATTTGAACAT 57.650 29.630 6.77 0.00 44.46 2.71
3650 5662 8.740123 TGGAGTTTTACTCTTGTATTTGAACA 57.260 30.769 6.77 0.00 44.46 3.18
3651 5663 8.837389 ACTGGAGTTTTACTCTTGTATTTGAAC 58.163 33.333 6.77 0.00 44.46 3.18
3652 5664 8.836413 CACTGGAGTTTTACTCTTGTATTTGAA 58.164 33.333 6.77 0.00 44.46 2.69
3703 5715 3.157881 CTCTTGTGTCCTCCTGTAGTGA 58.842 50.000 0.00 0.00 0.00 3.41
3704 5716 2.232452 CCTCTTGTGTCCTCCTGTAGTG 59.768 54.545 0.00 0.00 0.00 2.74
3716 5728 1.173043 CTCGAGCTCTCCTCTTGTGT 58.827 55.000 12.85 0.00 38.49 3.72
3718 5730 1.173043 CACTCGAGCTCTCCTCTTGT 58.827 55.000 13.61 0.00 38.49 3.16
3722 5734 1.381165 GGGACACTCGAGCTCTCCTC 61.381 65.000 13.61 4.67 37.22 3.71
3729 5741 1.079750 GTCTTGGGGACACTCGAGC 60.080 63.158 13.61 0.00 43.94 5.03
3739 5751 3.763360 TGCACTATCAATTTGTCTTGGGG 59.237 43.478 0.00 0.00 0.00 4.96
3783 5795 6.491383 ACATCTAGTGTCCTAACTAACCAGA 58.509 40.000 0.00 0.00 35.77 3.86
3784 5796 6.777213 ACATCTAGTGTCCTAACTAACCAG 57.223 41.667 0.00 0.00 35.77 4.00
3826 5976 5.163683 GCGAGACACTTTGGACATACTACTA 60.164 44.000 0.00 0.00 0.00 1.82
3828 5978 3.858238 GCGAGACACTTTGGACATACTAC 59.142 47.826 0.00 0.00 0.00 2.73
3829 5979 3.508402 TGCGAGACACTTTGGACATACTA 59.492 43.478 0.00 0.00 0.00 1.82
3830 5980 2.299013 TGCGAGACACTTTGGACATACT 59.701 45.455 0.00 0.00 0.00 2.12
3831 5981 2.668457 CTGCGAGACACTTTGGACATAC 59.332 50.000 0.00 0.00 0.00 2.39
3834 5984 0.750249 TCTGCGAGACACTTTGGACA 59.250 50.000 0.00 0.00 0.00 4.02
3849 5999 3.861689 GCAAACATCAAAGCCTAATCTGC 59.138 43.478 0.00 0.00 0.00 4.26
3913 6063 8.528643 TGTTTGTACCGACTAGTACTAGTACTA 58.471 37.037 31.39 31.39 45.63 1.82
3914 6064 7.386851 TGTTTGTACCGACTAGTACTAGTACT 58.613 38.462 32.39 32.39 45.63 2.73
3915 6065 7.596749 TGTTTGTACCGACTAGTACTAGTAC 57.403 40.000 30.80 24.79 45.63 2.73
3916 6066 7.659799 TGTTGTTTGTACCGACTAGTACTAGTA 59.340 37.037 30.80 15.83 45.63 1.82
3922 6072 5.772825 AGTGTTGTTTGTACCGACTAGTA 57.227 39.130 0.00 0.00 0.00 1.82
3952 6102 2.033801 CAGAATTATGGGCAGGCGAAAG 59.966 50.000 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.