Multiple sequence alignment - TraesCS6B01G366700

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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 TraesCS6B01G366700 chr6B 100.000 3431 0 0 1 3431 639535769 639532339 0.000000e+00 6336
1 TraesCS6B01G366700 chr6B 92.989 542 22 9 3 534 225554241 225553706 0.000000e+00 776
2 TraesCS6B01G366700 chr6B 97.333 300 6 2 3 302 715194285 715193988 3.050000e-140 508
3 TraesCS6B01G366700 chr6B 96.207 290 10 1 232 521 506705269 506705557 1.110000e-129 473
4 TraesCS6B01G366700 chr6B 95.960 198 7 1 3234 3431 639984046 639983850 1.540000e-83 320
5 TraesCS6B01G366700 chr6D 95.379 2099 51 19 711 2779 423817016 423814934 0.000000e+00 3297
6 TraesCS6B01G366700 chr6D 89.978 459 21 13 2782 3234 423814899 423814460 1.380000e-158 569
7 TraesCS6B01G366700 chr6D 98.925 186 2 0 528 713 423817228 423817043 1.970000e-87 333
8 TraesCS6B01G366700 chr6A 94.688 2052 56 13 714 2739 568518082 568516058 0.000000e+00 3136
9 TraesCS6B01G366700 chr6A 90.652 460 23 10 2780 3234 568515971 568515527 8.200000e-166 593
10 TraesCS6B01G366700 chr6A 96.316 190 6 1 525 713 568519702 568519513 9.250000e-81 311
11 TraesCS6B01G366700 chr7B 94.518 529 19 6 3 521 510630524 510629996 0.000000e+00 808
12 TraesCS6B01G366700 chr7B 97.306 297 7 1 3 298 467536114 467535818 1.420000e-138 503
13 TraesCS6B01G366700 chr7B 91.667 144 12 0 1377 1520 76904322 76904465 2.090000e-47 200
14 TraesCS6B01G366700 chr7B 81.026 195 23 10 1026 1214 76903937 76904123 3.570000e-30 143
15 TraesCS6B01G366700 chr5B 92.279 531 30 4 3 522 506764955 506765485 0.000000e+00 743
16 TraesCS6B01G366700 chr5B 92.405 474 24 6 4 477 461544006 461543545 0.000000e+00 665
17 TraesCS6B01G366700 chr4B 92.352 523 25 5 3 523 2616764 2617273 0.000000e+00 730
18 TraesCS6B01G366700 chr4B 91.236 445 26 7 6 438 642091160 642090717 8.200000e-166 593
19 TraesCS6B01G366700 chr1B 89.847 522 25 14 5 522 279500818 279500321 0.000000e+00 645
20 TraesCS6B01G366700 chr1B 96.447 197 7 0 3235 3431 305284871 305284675 3.300000e-85 326
21 TraesCS6B01G366700 chr2B 96.885 321 10 0 3 323 395740701 395740381 3.900000e-149 538
22 TraesCS6B01G366700 chr3B 94.237 295 17 0 228 522 107773507 107773213 5.220000e-123 451
23 TraesCS6B01G366700 chr5A 97.970 197 4 0 3235 3431 481684405 481684601 3.280000e-90 342
24 TraesCS6B01G366700 chr4D 96.429 196 7 0 3236 3431 481841718 481841913 1.190000e-84 324
25 TraesCS6B01G366700 chr4D 95.939 197 8 0 3235 3431 170665333 170665529 1.540000e-83 320
26 TraesCS6B01G366700 chr4D 95.897 195 8 0 3237 3431 506212633 506212439 1.990000e-82 316
27 TraesCS6B01G366700 chr5D 95.960 198 8 0 3234 3431 342525684 342525881 4.270000e-84 322
28 TraesCS6B01G366700 chr5D 95.939 197 8 0 3235 3431 524004702 524004898 1.540000e-83 320
29 TraesCS6B01G366700 chr1D 95.939 197 8 0 3235 3431 250741386 250741190 1.540000e-83 320
30 TraesCS6B01G366700 chr7D 94.444 144 8 0 1377 1520 117133156 117133299 4.460000e-54 222
31 TraesCS6B01G366700 chr7D 80.541 185 27 7 1036 1214 117132790 117132971 2.150000e-27 134
32 TraesCS6B01G366700 chr7A 93.750 144 9 0 1377 1520 121056642 121056785 2.070000e-52 217
33 TraesCS6B01G366700 chr7A 78.774 212 32 9 1039 1239 121056270 121056479 2.780000e-26 130


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 TraesCS6B01G366700 chr6B 639532339 639535769 3430 True 6336.000000 6336 100.000000 1 3431 1 chr6B.!!$R2 3430
1 TraesCS6B01G366700 chr6B 225553706 225554241 535 True 776.000000 776 92.989000 3 534 1 chr6B.!!$R1 531
2 TraesCS6B01G366700 chr6D 423814460 423817228 2768 True 1399.666667 3297 94.760667 528 3234 3 chr6D.!!$R1 2706
3 TraesCS6B01G366700 chr6A 568515527 568519702 4175 True 1346.666667 3136 93.885333 525 3234 3 chr6A.!!$R1 2709
4 TraesCS6B01G366700 chr7B 510629996 510630524 528 True 808.000000 808 94.518000 3 521 1 chr7B.!!$R2 518
5 TraesCS6B01G366700 chr5B 506764955 506765485 530 False 743.000000 743 92.279000 3 522 1 chr5B.!!$F1 519
6 TraesCS6B01G366700 chr4B 2616764 2617273 509 False 730.000000 730 92.352000 3 523 1 chr4B.!!$F1 520

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
312 353 1.294138 CCCGCCTCGGTTTGTTCTA 59.706 57.895 4.47 0.0 46.80 2.10 F
1261 2742 0.031585 TGTCCGTGTCTTCTTCACCG 59.968 55.000 0.00 0.0 32.86 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 2839 0.393808 CGAACCCCATCCCGAAACAT 60.394 55.0 0.0 0.0 0.0 2.71 R
2719 4246 0.102481 AACATAGTAGCCTCGCCACG 59.898 55.0 0.0 0.0 0.0 4.94 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
312 353 1.294138 CCCGCCTCGGTTTGTTCTA 59.706 57.895 4.47 0.00 46.80 2.10
343 384 2.046023 CAGCGGTGCCTCCAATCA 60.046 61.111 0.00 0.00 35.57 2.57
426 467 2.005370 ACAAACAGGTAGGGACTCGA 57.995 50.000 0.00 0.00 41.75 4.04
515 556 7.923414 GTCCTAGGACTTATGAAACAAACAT 57.077 36.000 31.12 0.00 41.57 2.71
523 564 5.772672 ACTTATGAAACAAACATGGCCTACA 59.227 36.000 3.32 0.00 0.00 2.74
728 2200 2.163601 AACGTTAGCGGACCCTCCAC 62.164 60.000 0.00 0.00 43.45 4.02
899 2377 1.811965 CATCGCCATTCTCAACAACCA 59.188 47.619 0.00 0.00 0.00 3.67
938 2416 2.978010 CCGTGCCTCACAACCACC 60.978 66.667 0.00 0.00 33.40 4.61
1247 2728 2.860293 ACGTACGTACCGTGTCCG 59.140 61.111 21.41 8.88 41.39 4.79
1248 2729 1.959226 ACGTACGTACCGTGTCCGT 60.959 57.895 21.41 9.53 41.39 4.69
1249 2730 1.509787 CGTACGTACCGTGTCCGTG 60.510 63.158 19.67 0.00 41.39 4.94
1250 2731 1.574428 GTACGTACCGTGTCCGTGT 59.426 57.895 15.00 0.00 41.39 4.49
1251 2732 0.452784 GTACGTACCGTGTCCGTGTC 60.453 60.000 15.00 0.00 41.39 3.67
1261 2742 0.031585 TGTCCGTGTCTTCTTCACCG 59.968 55.000 0.00 0.00 32.86 4.94
1270 2751 4.807304 GTGTCTTCTTCACCGACTTGTTTA 59.193 41.667 0.00 0.00 0.00 2.01
1307 2788 2.202388 CGACCTTGCTTGCATGCG 60.202 61.111 18.54 8.04 35.36 4.73
1309 2790 1.286880 GACCTTGCTTGCATGCGTT 59.713 52.632 18.54 3.77 35.36 4.84
1345 2830 0.514255 CTCGTGATGGTGTTGCAGTG 59.486 55.000 0.00 0.00 0.00 3.66
1354 2839 4.284550 GTTGCAGTGGGCTGGGGA 62.285 66.667 0.00 0.00 45.15 4.81
1357 2842 4.052518 GCAGTGGGCTGGGGATGT 62.053 66.667 0.00 0.00 42.78 3.06
1360 2845 0.967380 CAGTGGGCTGGGGATGTTTC 60.967 60.000 0.00 0.00 39.01 2.78
1363 2848 2.440247 GGCTGGGGATGTTTCGGG 60.440 66.667 0.00 0.00 0.00 5.14
1676 3161 2.913578 ACACGACGCCCTACCACA 60.914 61.111 0.00 0.00 0.00 4.17
1909 3394 1.972223 CTCCTCCGACGTCACCACT 60.972 63.158 17.16 0.00 0.00 4.00
1942 3439 3.591835 CACCACCAACACCACGCC 61.592 66.667 0.00 0.00 0.00 5.68
2031 3528 4.821589 GTCGCTCTTCCCCGGCTG 62.822 72.222 0.00 0.00 0.00 4.85
2364 3870 3.648009 ACGTTCAGCTCTTCTTCTCTTG 58.352 45.455 0.00 0.00 0.00 3.02
2454 3966 1.129058 AAGTCCCAACGAGACCAAGT 58.871 50.000 0.00 0.00 34.67 3.16
2488 4000 2.516227 AGAGACCATCTCCACGAAGA 57.484 50.000 2.18 0.00 44.42 2.87
2628 4154 0.037160 TTGAAAGGCCGGAACCTACC 59.963 55.000 5.05 0.00 39.93 3.18
2629 4155 0.838987 TGAAAGGCCGGAACCTACCT 60.839 55.000 5.05 0.00 39.93 3.08
2630 4156 1.197812 GAAAGGCCGGAACCTACCTA 58.802 55.000 5.05 0.00 39.93 3.08
2631 4157 0.907486 AAAGGCCGGAACCTACCTAC 59.093 55.000 5.05 0.00 39.93 3.18
2719 4246 1.447317 ATTTCCGCGACATCCATGGC 61.447 55.000 8.23 0.00 0.00 4.40
2796 4370 8.606040 ATTTTCTTAGATGAGATGCTAGCTTC 57.394 34.615 20.13 20.13 0.00 3.86
2799 4373 2.591923 AGATGAGATGCTAGCTTCCGA 58.408 47.619 23.07 12.74 0.00 4.55
2800 4374 2.557924 AGATGAGATGCTAGCTTCCGAG 59.442 50.000 23.07 0.00 0.00 4.63
2822 4396 3.081993 GCTAAGCCGAGCGTGTTC 58.918 61.111 0.00 0.00 31.57 3.18
2852 4426 7.823745 AGCTAATGTCCTTTTTCTTTTCTCA 57.176 32.000 0.00 0.00 0.00 3.27
2856 4430 9.334693 CTAATGTCCTTTTTCTTTTCTCATTCG 57.665 33.333 0.00 0.00 0.00 3.34
2871 4445 3.365472 TCATTCGGATTCCTCTGTGAGA 58.635 45.455 0.30 0.00 0.00 3.27
2908 4482 2.027469 TGTCACATCTGCTGATTCTGCT 60.027 45.455 15.38 0.00 0.00 4.24
2975 4551 4.836825 TCAGCAGCTTTACTTTATGCTCT 58.163 39.130 0.00 0.00 45.03 4.09
2992 4568 1.326245 CTCTCTGAGACGCTCGTACAG 59.674 57.143 16.82 16.82 35.52 2.74
3032 4608 3.039011 ACAGTACTCCAACTTGGTCACT 58.961 45.455 7.72 6.76 39.03 3.41
3034 4610 3.069586 CAGTACTCCAACTTGGTCACTCA 59.930 47.826 7.72 0.00 39.03 3.41
3035 4611 2.622064 ACTCCAACTTGGTCACTCAC 57.378 50.000 7.72 0.00 39.03 3.51
3036 4612 1.837439 ACTCCAACTTGGTCACTCACA 59.163 47.619 7.72 0.00 39.03 3.58
3037 4613 2.213499 CTCCAACTTGGTCACTCACAC 58.787 52.381 7.72 0.00 39.03 3.82
3039 4615 1.408127 CCAACTTGGTCACTCACACCA 60.408 52.381 0.00 0.00 42.48 4.17
3041 4617 2.260844 ACTTGGTCACTCACACCATG 57.739 50.000 3.79 3.79 43.66 3.66
3042 4618 0.877071 CTTGGTCACTCACACCATGC 59.123 55.000 0.00 0.00 43.66 4.06
3043 4619 0.537143 TTGGTCACTCACACCATGCC 60.537 55.000 0.00 0.00 43.66 4.40
3044 4620 1.376466 GGTCACTCACACCATGCCT 59.624 57.895 0.00 0.00 33.63 4.75
3045 4621 0.674895 GGTCACTCACACCATGCCTC 60.675 60.000 0.00 0.00 33.63 4.70
3046 4622 0.322975 GTCACTCACACCATGCCTCT 59.677 55.000 0.00 0.00 0.00 3.69
3047 4623 0.322648 TCACTCACACCATGCCTCTG 59.677 55.000 0.00 0.00 0.00 3.35
3056 4632 3.457380 ACACCATGCCTCTGATGATAAGT 59.543 43.478 0.00 0.00 0.00 2.24
3062 4638 4.953667 TGCCTCTGATGATAAGTGCTAAG 58.046 43.478 0.00 0.00 0.00 2.18
3117 4693 0.671472 GGCATGGTCTTTGCTTTGCC 60.671 55.000 0.00 0.00 42.40 4.52
3162 4743 3.242478 CGCTCTCTAGTCTCTACCGTTTG 60.242 52.174 0.00 0.00 0.00 2.93
3212 4793 2.758736 AGAGCTAGGTTTCAGTGCTG 57.241 50.000 0.00 0.00 33.83 4.41
3234 4815 2.034879 ACGCTGCATTCCAAGTCCG 61.035 57.895 0.00 0.00 0.00 4.79
3235 4816 2.753966 CGCTGCATTCCAAGTCCGG 61.754 63.158 0.00 0.00 0.00 5.14
3236 4817 3.056313 GCTGCATTCCAAGTCCGGC 62.056 63.158 0.00 0.00 0.00 6.13
3237 4818 1.675310 CTGCATTCCAAGTCCGGCA 60.675 57.895 0.00 0.00 0.00 5.69
3238 4819 1.228398 TGCATTCCAAGTCCGGCAA 60.228 52.632 0.00 0.00 0.00 4.52
3239 4820 0.825425 TGCATTCCAAGTCCGGCAAA 60.825 50.000 0.00 0.00 0.00 3.68
3240 4821 0.316841 GCATTCCAAGTCCGGCAAAA 59.683 50.000 0.00 0.00 0.00 2.44
3241 4822 1.066929 GCATTCCAAGTCCGGCAAAAT 60.067 47.619 0.00 0.00 0.00 1.82
3242 4823 2.612721 GCATTCCAAGTCCGGCAAAATT 60.613 45.455 0.00 0.00 0.00 1.82
3243 4824 2.810439 TTCCAAGTCCGGCAAAATTG 57.190 45.000 0.00 0.00 0.00 2.32
3244 4825 1.988293 TCCAAGTCCGGCAAAATTGA 58.012 45.000 0.00 0.00 0.00 2.57
3245 4826 2.524306 TCCAAGTCCGGCAAAATTGAT 58.476 42.857 0.00 0.00 0.00 2.57
3246 4827 3.691575 TCCAAGTCCGGCAAAATTGATA 58.308 40.909 0.00 0.00 0.00 2.15
3247 4828 4.082845 TCCAAGTCCGGCAAAATTGATAA 58.917 39.130 0.00 0.00 0.00 1.75
3248 4829 4.524714 TCCAAGTCCGGCAAAATTGATAAA 59.475 37.500 0.00 0.00 0.00 1.40
3249 4830 5.186797 TCCAAGTCCGGCAAAATTGATAAAT 59.813 36.000 0.00 0.00 0.00 1.40
3250 4831 5.874261 CCAAGTCCGGCAAAATTGATAAATT 59.126 36.000 0.00 0.00 0.00 1.82
3251 4832 6.371271 CCAAGTCCGGCAAAATTGATAAATTT 59.629 34.615 0.00 0.00 34.09 1.82
3252 4833 6.966435 AGTCCGGCAAAATTGATAAATTTG 57.034 33.333 1.29 0.00 37.17 2.32
3253 4834 6.696411 AGTCCGGCAAAATTGATAAATTTGA 58.304 32.000 1.29 0.00 36.41 2.69
3254 4835 6.589907 AGTCCGGCAAAATTGATAAATTTGAC 59.410 34.615 1.29 4.92 38.43 3.18
3255 4836 5.872070 TCCGGCAAAATTGATAAATTTGACC 59.128 36.000 1.29 5.81 38.55 4.02
3256 4837 5.874261 CCGGCAAAATTGATAAATTTGACCT 59.126 36.000 13.98 0.00 38.55 3.85
3257 4838 7.038659 CCGGCAAAATTGATAAATTTGACCTA 58.961 34.615 13.98 0.00 38.55 3.08
3258 4839 7.710475 CCGGCAAAATTGATAAATTTGACCTAT 59.290 33.333 13.98 0.00 38.55 2.57
3259 4840 8.542132 CGGCAAAATTGATAAATTTGACCTATG 58.458 33.333 13.98 5.22 38.55 2.23
3260 4841 8.829612 GGCAAAATTGATAAATTTGACCTATGG 58.170 33.333 1.29 0.00 36.32 2.74
3261 4842 9.598517 GCAAAATTGATAAATTTGACCTATGGA 57.401 29.630 1.29 0.00 36.41 3.41
3263 4844 9.801873 AAAATTGATAAATTTGACCTATGGACG 57.198 29.630 1.29 0.00 33.08 4.79
3264 4845 8.746052 AATTGATAAATTTGACCTATGGACGA 57.254 30.769 0.00 0.00 0.00 4.20
3265 4846 8.746052 ATTGATAAATTTGACCTATGGACGAA 57.254 30.769 0.00 0.00 0.00 3.85
3266 4847 8.568676 TTGATAAATTTGACCTATGGACGAAA 57.431 30.769 0.00 0.00 0.00 3.46
3267 4848 8.746052 TGATAAATTTGACCTATGGACGAAAT 57.254 30.769 0.00 0.00 0.00 2.17
3268 4849 8.836413 TGATAAATTTGACCTATGGACGAAATC 58.164 33.333 0.00 0.00 0.00 2.17
3269 4850 8.746052 ATAAATTTGACCTATGGACGAAATCA 57.254 30.769 0.00 0.00 0.00 2.57
3270 4851 7.461182 AAATTTGACCTATGGACGAAATCAA 57.539 32.000 0.00 0.00 0.00 2.57
3271 4852 7.461182 AATTTGACCTATGGACGAAATCAAA 57.539 32.000 0.00 0.00 38.52 2.69
3272 4853 7.645058 ATTTGACCTATGGACGAAATCAAAT 57.355 32.000 0.00 0.00 39.34 2.32
3273 4854 6.677781 TTGACCTATGGACGAAATCAAATC 57.322 37.500 0.00 0.00 0.00 2.17
3274 4855 5.739959 TGACCTATGGACGAAATCAAATCA 58.260 37.500 0.00 0.00 0.00 2.57
3275 4856 5.584649 TGACCTATGGACGAAATCAAATCAC 59.415 40.000 0.00 0.00 0.00 3.06
3276 4857 5.496556 ACCTATGGACGAAATCAAATCACA 58.503 37.500 0.00 0.00 0.00 3.58
3277 4858 5.586243 ACCTATGGACGAAATCAAATCACAG 59.414 40.000 0.00 0.00 0.00 3.66
3278 4859 5.817296 CCTATGGACGAAATCAAATCACAGA 59.183 40.000 0.00 0.00 0.00 3.41
3279 4860 6.316140 CCTATGGACGAAATCAAATCACAGAA 59.684 38.462 0.00 0.00 0.00 3.02
3280 4861 6.764308 ATGGACGAAATCAAATCACAGAAT 57.236 33.333 0.00 0.00 0.00 2.40
3281 4862 5.941733 TGGACGAAATCAAATCACAGAATG 58.058 37.500 0.00 0.00 46.00 2.67
3282 4863 5.704978 TGGACGAAATCAAATCACAGAATGA 59.295 36.000 0.00 0.00 43.13 2.57
3283 4864 6.206438 TGGACGAAATCAAATCACAGAATGAA 59.794 34.615 0.00 0.00 41.93 2.57
3284 4865 6.524586 GGACGAAATCAAATCACAGAATGAAC 59.475 38.462 0.00 0.00 41.93 3.18
3285 4866 7.206981 ACGAAATCAAATCACAGAATGAACT 57.793 32.000 0.00 0.00 41.93 3.01
3286 4867 7.080099 ACGAAATCAAATCACAGAATGAACTG 58.920 34.615 0.00 0.00 41.93 3.16
3287 4868 6.033196 CGAAATCAAATCACAGAATGAACTGC 59.967 38.462 0.00 0.00 41.93 4.40
3288 4869 4.771590 TCAAATCACAGAATGAACTGCC 57.228 40.909 0.00 0.00 41.93 4.85
3289 4870 3.189080 TCAAATCACAGAATGAACTGCCG 59.811 43.478 0.00 0.00 41.93 5.69
3290 4871 1.742761 ATCACAGAATGAACTGCCGG 58.257 50.000 0.00 0.00 41.93 6.13
3291 4872 0.396435 TCACAGAATGAACTGCCGGT 59.604 50.000 1.90 0.00 39.69 5.28
3292 4873 0.518636 CACAGAATGAACTGCCGGTG 59.481 55.000 1.90 0.00 39.69 4.94
3293 4874 0.396435 ACAGAATGAACTGCCGGTGA 59.604 50.000 1.90 0.00 39.69 4.02
3294 4875 1.202758 ACAGAATGAACTGCCGGTGAA 60.203 47.619 1.90 0.00 39.69 3.18
3295 4876 1.879380 CAGAATGAACTGCCGGTGAAA 59.121 47.619 1.90 0.00 39.69 2.69
3296 4877 2.489329 CAGAATGAACTGCCGGTGAAAT 59.511 45.455 1.90 0.00 39.69 2.17
3297 4878 3.057315 CAGAATGAACTGCCGGTGAAATT 60.057 43.478 1.90 0.00 39.69 1.82
3298 4879 4.155826 CAGAATGAACTGCCGGTGAAATTA 59.844 41.667 1.90 0.00 39.69 1.40
3299 4880 4.949856 AGAATGAACTGCCGGTGAAATTAT 59.050 37.500 1.90 0.00 0.00 1.28
3300 4881 5.418840 AGAATGAACTGCCGGTGAAATTATT 59.581 36.000 1.90 0.00 0.00 1.40
3301 4882 5.659440 ATGAACTGCCGGTGAAATTATTT 57.341 34.783 1.90 0.00 0.00 1.40
3302 4883 5.054390 TGAACTGCCGGTGAAATTATTTC 57.946 39.130 10.47 10.47 40.08 2.17
3303 4884 4.520874 TGAACTGCCGGTGAAATTATTTCA 59.479 37.500 15.46 15.46 46.68 2.69
3311 4892 3.129852 TGAAATTATTTCACGCGGCTG 57.870 42.857 15.46 0.00 44.21 4.85
3312 4893 2.744741 TGAAATTATTTCACGCGGCTGA 59.255 40.909 15.46 2.44 44.21 4.26
3313 4894 2.825086 AATTATTTCACGCGGCTGAC 57.175 45.000 12.47 0.00 0.00 3.51
3314 4895 1.014352 ATTATTTCACGCGGCTGACC 58.986 50.000 12.47 0.00 0.00 4.02
3315 4896 0.036765 TTATTTCACGCGGCTGACCT 60.037 50.000 12.47 0.00 0.00 3.85
3316 4897 0.036765 TATTTCACGCGGCTGACCTT 60.037 50.000 12.47 0.00 0.00 3.50
3317 4898 0.889186 ATTTCACGCGGCTGACCTTT 60.889 50.000 12.47 0.00 0.00 3.11
3318 4899 1.098712 TTTCACGCGGCTGACCTTTT 61.099 50.000 12.47 0.00 0.00 2.27
3319 4900 1.098712 TTCACGCGGCTGACCTTTTT 61.099 50.000 12.47 0.00 0.00 1.94
3320 4901 1.370414 CACGCGGCTGACCTTTTTG 60.370 57.895 12.47 0.00 0.00 2.44
3321 4902 1.822186 ACGCGGCTGACCTTTTTGT 60.822 52.632 12.47 0.00 0.00 2.83
3322 4903 1.370414 CGCGGCTGACCTTTTTGTG 60.370 57.895 0.00 0.00 0.00 3.33
3323 4904 1.733526 GCGGCTGACCTTTTTGTGT 59.266 52.632 0.00 0.00 0.00 3.72
3324 4905 0.594796 GCGGCTGACCTTTTTGTGTG 60.595 55.000 0.00 0.00 0.00 3.82
3325 4906 1.021202 CGGCTGACCTTTTTGTGTGA 58.979 50.000 0.00 0.00 0.00 3.58
3326 4907 1.268539 CGGCTGACCTTTTTGTGTGAC 60.269 52.381 0.00 0.00 0.00 3.67
3327 4908 1.268539 GGCTGACCTTTTTGTGTGACG 60.269 52.381 0.00 0.00 0.00 4.35
3328 4909 1.859998 GCTGACCTTTTTGTGTGACGC 60.860 52.381 0.00 0.00 0.00 5.19
3329 4910 0.736053 TGACCTTTTTGTGTGACGCC 59.264 50.000 0.00 0.00 0.00 5.68
3330 4911 0.030235 GACCTTTTTGTGTGACGCCC 59.970 55.000 0.00 0.00 0.00 6.13
3331 4912 1.008995 CCTTTTTGTGTGACGCCCG 60.009 57.895 0.00 0.00 0.00 6.13
3332 4913 1.440938 CCTTTTTGTGTGACGCCCGA 61.441 55.000 0.00 0.00 0.00 5.14
3333 4914 0.316689 CTTTTTGTGTGACGCCCGAC 60.317 55.000 0.00 0.00 0.00 4.79
3334 4915 1.025113 TTTTTGTGTGACGCCCGACA 61.025 50.000 0.00 0.00 0.00 4.35
3335 4916 1.707239 TTTTGTGTGACGCCCGACAC 61.707 55.000 14.47 14.47 42.40 3.67
3336 4917 4.934942 TGTGTGACGCCCGACACG 62.935 66.667 15.80 0.00 44.55 4.49
3337 4918 4.634133 GTGTGACGCCCGACACGA 62.634 66.667 15.80 5.46 42.06 4.35
3338 4919 3.902086 TGTGACGCCCGACACGAA 61.902 61.111 15.80 0.31 42.06 3.85
3339 4920 3.103911 GTGACGCCCGACACGAAG 61.104 66.667 7.43 0.00 32.16 3.79
3340 4921 4.351938 TGACGCCCGACACGAAGG 62.352 66.667 0.00 0.00 0.00 3.46
3348 4929 3.712881 GACACGAAGGCGCCACAC 61.713 66.667 31.54 17.81 42.48 3.82
3349 4930 4.235762 ACACGAAGGCGCCACACT 62.236 61.111 31.54 9.96 42.48 3.55
3350 4931 2.048597 CACGAAGGCGCCACACTA 60.049 61.111 31.54 0.00 42.48 2.74
3351 4932 2.048503 ACGAAGGCGCCACACTAC 60.049 61.111 31.54 11.50 42.48 2.73
3352 4933 2.048597 CGAAGGCGCCACACTACA 60.049 61.111 31.54 0.00 0.00 2.74
3353 4934 2.380410 CGAAGGCGCCACACTACAC 61.380 63.158 31.54 8.98 0.00 2.90
3354 4935 1.004918 GAAGGCGCCACACTACACT 60.005 57.895 31.54 0.00 0.00 3.55
3355 4936 1.291877 GAAGGCGCCACACTACACTG 61.292 60.000 31.54 0.00 0.00 3.66
3356 4937 2.030562 GGCGCCACACTACACTGT 59.969 61.111 24.80 0.00 0.00 3.55
3357 4938 2.317609 GGCGCCACACTACACTGTG 61.318 63.158 24.80 6.19 41.19 3.66
3358 4939 2.954753 GCGCCACACTACACTGTGC 61.955 63.158 7.90 0.00 40.33 4.57
3359 4940 1.594021 CGCCACACTACACTGTGCA 60.594 57.895 7.90 0.00 40.33 4.57
3360 4941 1.157257 CGCCACACTACACTGTGCAA 61.157 55.000 7.90 0.00 40.33 4.08
3361 4942 0.307760 GCCACACTACACTGTGCAAC 59.692 55.000 7.90 0.00 40.33 4.17
3362 4943 0.581529 CCACACTACACTGTGCAACG 59.418 55.000 7.90 0.00 42.39 4.10
3363 4944 0.042188 CACACTACACTGTGCAACGC 60.042 55.000 7.90 0.00 42.39 4.84
3364 4945 1.157870 ACACTACACTGTGCAACGCC 61.158 55.000 7.90 0.00 42.39 5.68
3365 4946 0.880278 CACTACACTGTGCAACGCCT 60.880 55.000 7.90 0.00 42.39 5.52
3366 4947 0.600255 ACTACACTGTGCAACGCCTC 60.600 55.000 7.90 0.00 42.39 4.70
3367 4948 1.617755 CTACACTGTGCAACGCCTCG 61.618 60.000 7.90 0.00 42.39 4.63
3368 4949 4.374702 CACTGTGCAACGCCTCGC 62.375 66.667 0.00 0.00 42.39 5.03
3369 4950 4.908687 ACTGTGCAACGCCTCGCA 62.909 61.111 0.00 0.00 42.39 5.10
3370 4951 4.081030 CTGTGCAACGCCTCGCAG 62.081 66.667 0.00 0.00 42.39 5.18
3371 4952 4.600576 TGTGCAACGCCTCGCAGA 62.601 61.111 0.00 0.00 42.39 4.26
3372 4953 3.121030 GTGCAACGCCTCGCAGAT 61.121 61.111 0.00 0.00 39.20 2.90
3373 4954 1.809619 GTGCAACGCCTCGCAGATA 60.810 57.895 0.00 0.00 39.20 1.98
3374 4955 1.519234 TGCAACGCCTCGCAGATAG 60.519 57.895 0.00 0.00 33.89 2.08
3375 4956 2.240500 GCAACGCCTCGCAGATAGG 61.241 63.158 0.00 0.00 33.89 2.57
3385 4966 1.065928 GCAGATAGGCGCTACACGT 59.934 57.895 7.64 0.00 46.11 4.49
3391 4972 2.506438 GGCGCTACACGTCTGACC 60.506 66.667 7.64 0.00 45.03 4.02
3392 4973 2.257371 GCGCTACACGTCTGACCA 59.743 61.111 0.00 0.00 46.11 4.02
3393 4974 1.801913 GCGCTACACGTCTGACCAG 60.802 63.158 0.00 0.00 46.11 4.00
3394 4975 1.801913 CGCTACACGTCTGACCAGC 60.802 63.158 1.55 5.43 36.87 4.85
3395 4976 1.801913 GCTACACGTCTGACCAGCG 60.802 63.158 1.55 10.59 35.30 5.18
3396 4977 1.579932 CTACACGTCTGACCAGCGT 59.420 57.895 1.55 11.57 40.07 5.07
3397 4978 0.039437 CTACACGTCTGACCAGCGTT 60.039 55.000 13.69 9.75 38.44 4.84
3398 4979 0.318360 TACACGTCTGACCAGCGTTG 60.318 55.000 13.69 0.00 38.44 4.10
3399 4980 2.661866 ACGTCTGACCAGCGTTGC 60.662 61.111 1.55 0.00 37.71 4.17
3400 4981 2.661537 CGTCTGACCAGCGTTGCA 60.662 61.111 1.55 0.00 0.00 4.08
3401 4982 2.939022 GTCTGACCAGCGTTGCAC 59.061 61.111 0.00 0.00 0.00 4.57
3402 4983 2.280797 TCTGACCAGCGTTGCACC 60.281 61.111 0.00 0.00 0.00 5.01
3403 4984 3.357079 CTGACCAGCGTTGCACCC 61.357 66.667 0.00 0.00 0.00 4.61
3408 4989 4.312231 CAGCGTTGCACCCGTGTG 62.312 66.667 6.80 0.00 45.65 3.82
3409 4990 4.539083 AGCGTTGCACCCGTGTGA 62.539 61.111 0.90 0.00 45.76 3.58
3410 4991 3.353836 GCGTTGCACCCGTGTGAT 61.354 61.111 0.90 0.00 45.76 3.06
3411 4992 2.860293 CGTTGCACCCGTGTGATC 59.140 61.111 0.90 0.00 45.76 2.92
3412 4993 2.677003 CGTTGCACCCGTGTGATCC 61.677 63.158 0.90 0.00 45.76 3.36
3413 4994 2.358125 TTGCACCCGTGTGATCCG 60.358 61.111 0.90 0.00 45.76 4.18
3414 4995 2.873525 TTGCACCCGTGTGATCCGA 61.874 57.895 0.90 0.00 45.76 4.55
3415 4996 2.047655 GCACCCGTGTGATCCGAA 60.048 61.111 0.90 0.00 45.76 4.30
3416 4997 1.669760 GCACCCGTGTGATCCGAAA 60.670 57.895 0.90 0.00 45.76 3.46
3417 4998 1.231958 GCACCCGTGTGATCCGAAAA 61.232 55.000 0.90 0.00 45.76 2.29
3418 4999 1.448985 CACCCGTGTGATCCGAAAAT 58.551 50.000 0.00 0.00 45.76 1.82
3419 5000 1.810151 CACCCGTGTGATCCGAAAATT 59.190 47.619 0.00 0.00 45.76 1.82
3420 5001 3.004171 CACCCGTGTGATCCGAAAATTA 58.996 45.455 0.00 0.00 45.76 1.40
3421 5002 3.004862 ACCCGTGTGATCCGAAAATTAC 58.995 45.455 0.00 0.00 0.00 1.89
3422 5003 3.267483 CCCGTGTGATCCGAAAATTACT 58.733 45.455 0.00 0.00 0.00 2.24
3423 5004 4.081531 ACCCGTGTGATCCGAAAATTACTA 60.082 41.667 0.00 0.00 0.00 1.82
3424 5005 4.871557 CCCGTGTGATCCGAAAATTACTAA 59.128 41.667 0.00 0.00 0.00 2.24
3425 5006 5.006358 CCCGTGTGATCCGAAAATTACTAAG 59.994 44.000 0.00 0.00 0.00 2.18
3426 5007 5.579511 CCGTGTGATCCGAAAATTACTAAGT 59.420 40.000 0.00 0.00 0.00 2.24
3427 5008 6.237755 CCGTGTGATCCGAAAATTACTAAGTC 60.238 42.308 0.00 0.00 0.00 3.01
3428 5009 6.309494 CGTGTGATCCGAAAATTACTAAGTCA 59.691 38.462 0.00 0.00 0.00 3.41
3429 5010 7.462856 CGTGTGATCCGAAAATTACTAAGTCAG 60.463 40.741 0.00 0.00 0.00 3.51
3430 5011 7.331193 GTGTGATCCGAAAATTACTAAGTCAGT 59.669 37.037 0.00 0.00 41.62 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.675552 CTGGAAACAAACACCCTCGT 58.324 50.000 0.00 0.00 42.06 4.18
1 2 0.951558 CCTGGAAACAAACACCCTCG 59.048 55.000 0.00 0.00 42.06 4.63
51 52 6.272792 TGTTTGGTTTAGGTGGGACTTATAGA 59.727 38.462 0.00 0.00 0.00 1.98
306 347 1.603678 GCAACGAACCGAGGTAGAACA 60.604 52.381 0.00 0.00 0.00 3.18
312 353 2.665185 GCTGCAACGAACCGAGGT 60.665 61.111 0.00 0.00 0.00 3.85
361 402 4.139420 CCGCTGCAACGAAGCTCG 62.139 66.667 11.83 4.36 46.93 5.03
515 556 3.719268 ACTTTGTCATCATGTAGGCCA 57.281 42.857 5.01 0.00 0.00 5.36
523 564 4.397420 TGCAACCTGTACTTTGTCATCAT 58.603 39.130 0.00 0.00 0.00 2.45
899 2377 3.215597 TTGGCGATCGACGTGGTGT 62.216 57.895 21.57 0.00 44.60 4.16
1246 2727 1.787155 CAAGTCGGTGAAGAAGACACG 59.213 52.381 0.00 0.00 38.90 4.49
1247 2728 2.822764 ACAAGTCGGTGAAGAAGACAC 58.177 47.619 0.00 0.00 37.36 3.67
1248 2729 3.536956 AACAAGTCGGTGAAGAAGACA 57.463 42.857 0.00 0.00 37.36 3.41
1249 2730 5.048507 AGTAAACAAGTCGGTGAAGAAGAC 58.951 41.667 0.00 0.00 35.30 3.01
1250 2731 5.272283 AGTAAACAAGTCGGTGAAGAAGA 57.728 39.130 0.00 0.00 0.00 2.87
1251 2732 5.986004 AAGTAAACAAGTCGGTGAAGAAG 57.014 39.130 0.00 0.00 0.00 2.85
1261 2742 6.978080 TGGAAGCAAATCAAAGTAAACAAGTC 59.022 34.615 0.00 0.00 0.00 3.01
1270 2751 3.820467 TCGACATGGAAGCAAATCAAAGT 59.180 39.130 0.00 0.00 0.00 2.66
1307 2788 4.913924 ACGAGTCAGTATCAACACGTAAAC 59.086 41.667 0.00 0.00 40.13 2.01
1309 2790 4.213906 TCACGAGTCAGTATCAACACGTAA 59.786 41.667 0.00 0.00 39.97 3.18
1345 2830 2.440247 CCGAAACATCCCCAGCCC 60.440 66.667 0.00 0.00 0.00 5.19
1354 2839 0.393808 CGAACCCCATCCCGAAACAT 60.394 55.000 0.00 0.00 0.00 2.71
1357 2842 2.672295 CCGAACCCCATCCCGAAA 59.328 61.111 0.00 0.00 0.00 3.46
1363 2848 4.104183 TTCCGGCCGAACCCCATC 62.104 66.667 30.73 0.00 33.26 3.51
1417 2902 2.664851 CGCCACTTCTTGCCGTCA 60.665 61.111 0.00 0.00 0.00 4.35
1909 3394 2.040359 TGGTGGTGGTCCCTGTCA 60.040 61.111 0.00 0.00 0.00 3.58
1960 3457 1.285023 CTGCTTGAACTGCCACTGC 59.715 57.895 0.00 0.00 38.26 4.40
2033 3530 3.729698 GTTGTTGCCGTACCCGCC 61.730 66.667 0.00 0.00 0.00 6.13
2034 3531 4.079748 CGTTGTTGCCGTACCCGC 62.080 66.667 0.00 0.00 0.00 6.13
2035 3532 4.079748 GCGTTGTTGCCGTACCCG 62.080 66.667 0.00 0.00 0.00 5.28
2036 3533 4.079748 CGCGTTGTTGCCGTACCC 62.080 66.667 0.00 0.00 0.00 3.69
2037 3534 4.079748 CCGCGTTGTTGCCGTACC 62.080 66.667 4.92 0.00 0.00 3.34
2038 3535 4.729798 GCCGCGTTGTTGCCGTAC 62.730 66.667 4.92 0.00 0.00 3.67
2343 3849 3.648009 CAAGAGAAGAAGAGCTGAACGT 58.352 45.455 0.00 0.00 0.00 3.99
2344 3850 2.411409 GCAAGAGAAGAAGAGCTGAACG 59.589 50.000 0.00 0.00 0.00 3.95
2345 3851 3.186205 GTGCAAGAGAAGAAGAGCTGAAC 59.814 47.826 0.00 0.00 0.00 3.18
2346 3852 3.070734 AGTGCAAGAGAAGAAGAGCTGAA 59.929 43.478 0.00 0.00 0.00 3.02
2364 3870 5.629079 ACTAATGGCTAGTTTCAAAGTGC 57.371 39.130 0.00 0.00 37.61 4.40
2391 3900 0.883833 AAAGCGAACCATTGAGCCAG 59.116 50.000 0.00 0.00 0.00 4.85
2454 3966 0.879090 TCTCTCGTTGCAGCTTCGTA 59.121 50.000 0.00 0.80 0.00 3.43
2486 3998 1.081641 CTCCGTACGTGCGTGTTCT 60.082 57.895 24.09 0.00 0.00 3.01
2487 3999 2.713894 GCTCCGTACGTGCGTGTTC 61.714 63.158 24.09 7.12 0.00 3.18
2488 4000 2.732094 GCTCCGTACGTGCGTGTT 60.732 61.111 24.09 0.00 0.00 3.32
2554 4069 0.117340 AGGTAGCTGGTCCAGGTCTT 59.883 55.000 26.62 12.13 41.50 3.01
2628 4154 8.425577 AGAAATGAAAATGATGGTCGTAGTAG 57.574 34.615 0.00 0.00 0.00 2.57
2629 4155 8.786826 AAGAAATGAAAATGATGGTCGTAGTA 57.213 30.769 0.00 0.00 0.00 1.82
2630 4156 7.607991 AGAAGAAATGAAAATGATGGTCGTAGT 59.392 33.333 0.00 0.00 0.00 2.73
2631 4157 7.978982 AGAAGAAATGAAAATGATGGTCGTAG 58.021 34.615 0.00 0.00 0.00 3.51
2719 4246 0.102481 AACATAGTAGCCTCGCCACG 59.898 55.000 0.00 0.00 0.00 4.94
2796 4370 2.279120 CGGCTTAGCTCAGCTCGG 60.279 66.667 18.91 0.00 40.44 4.63
2799 4373 2.498726 GCTCGGCTTAGCTCAGCT 59.501 61.111 18.91 3.60 43.41 4.24
2800 4374 2.959071 CGCTCGGCTTAGCTCAGC 60.959 66.667 11.60 11.60 40.49 4.26
2801 4375 1.875813 CACGCTCGGCTTAGCTCAG 60.876 63.158 3.59 1.31 40.49 3.35
2802 4376 2.154798 AACACGCTCGGCTTAGCTCA 62.155 55.000 3.59 0.00 40.49 4.26
2803 4377 1.414527 GAACACGCTCGGCTTAGCTC 61.415 60.000 3.59 0.00 40.49 4.09
2830 4404 9.334693 CGAATGAGAAAAGAAAAAGGACATTAG 57.665 33.333 0.00 0.00 0.00 1.73
2852 4426 3.131933 CAGTCTCACAGAGGAATCCGAAT 59.868 47.826 0.00 0.00 0.00 3.34
2856 4430 3.096092 AGACAGTCTCACAGAGGAATCC 58.904 50.000 0.00 0.00 0.00 3.01
2871 4445 3.134623 TGTGACAAACCATCTCAGACAGT 59.865 43.478 0.00 0.00 0.00 3.55
2929 4503 2.051804 GAGCAGTGTGTGTGTGGTGC 62.052 60.000 0.00 0.00 0.00 5.01
2975 4551 0.321387 ACCTGTACGAGCGTCTCAGA 60.321 55.000 20.95 0.00 34.55 3.27
3018 4594 1.134220 GGTGTGAGTGACCAAGTTGGA 60.134 52.381 28.80 3.77 40.96 3.53
3032 4608 1.278537 TCATCAGAGGCATGGTGTGA 58.721 50.000 0.00 0.00 32.88 3.58
3034 4610 3.457380 ACTTATCATCAGAGGCATGGTGT 59.543 43.478 0.00 0.00 32.88 4.16
3035 4611 3.813724 CACTTATCATCAGAGGCATGGTG 59.186 47.826 0.00 0.00 32.28 4.17
3036 4612 3.746751 GCACTTATCATCAGAGGCATGGT 60.747 47.826 0.00 0.00 0.00 3.55
3037 4613 2.812591 GCACTTATCATCAGAGGCATGG 59.187 50.000 0.00 0.00 0.00 3.66
3039 4615 5.549347 CTTAGCACTTATCATCAGAGGCAT 58.451 41.667 0.00 0.00 0.00 4.40
3041 4617 3.745458 GCTTAGCACTTATCATCAGAGGC 59.255 47.826 0.00 0.00 0.00 4.70
3042 4618 4.953667 TGCTTAGCACTTATCATCAGAGG 58.046 43.478 1.39 0.00 31.71 3.69
3043 4619 7.328982 CAGTATGCTTAGCACTTATCATCAGAG 59.671 40.741 9.82 0.00 43.04 3.35
3044 4620 7.150640 CAGTATGCTTAGCACTTATCATCAGA 58.849 38.462 9.82 0.00 43.04 3.27
3045 4621 6.927936 ACAGTATGCTTAGCACTTATCATCAG 59.072 38.462 9.82 0.00 43.04 2.90
3046 4622 6.820335 ACAGTATGCTTAGCACTTATCATCA 58.180 36.000 9.82 0.00 43.04 3.07
3047 4623 7.721286 AACAGTATGCTTAGCACTTATCATC 57.279 36.000 9.82 0.00 43.04 2.92
3056 4632 6.940298 AGGAAAAAGTAACAGTATGCTTAGCA 59.060 34.615 10.09 10.09 42.53 3.49
3062 4638 5.390567 CGTGGAGGAAAAAGTAACAGTATGC 60.391 44.000 0.00 0.00 42.53 3.14
3225 4806 1.988293 TCAATTTTGCCGGACTTGGA 58.012 45.000 5.05 0.00 0.00 3.53
3226 4807 4.448537 TTATCAATTTTGCCGGACTTGG 57.551 40.909 5.05 0.00 0.00 3.61
3234 4815 8.829612 CCATAGGTCAAATTTATCAATTTTGCC 58.170 33.333 0.00 1.90 40.09 4.52
3235 4816 9.598517 TCCATAGGTCAAATTTATCAATTTTGC 57.401 29.630 0.00 0.00 40.09 3.68
3237 4818 9.801873 CGTCCATAGGTCAAATTTATCAATTTT 57.198 29.630 0.00 0.00 40.09 1.82
3238 4819 9.184523 TCGTCCATAGGTCAAATTTATCAATTT 57.815 29.630 0.00 0.00 42.37 1.82
3239 4820 8.746052 TCGTCCATAGGTCAAATTTATCAATT 57.254 30.769 0.00 0.00 33.72 2.32
3240 4821 8.746052 TTCGTCCATAGGTCAAATTTATCAAT 57.254 30.769 0.00 0.00 0.00 2.57
3241 4822 8.568676 TTTCGTCCATAGGTCAAATTTATCAA 57.431 30.769 0.00 0.00 0.00 2.57
3242 4823 8.746052 ATTTCGTCCATAGGTCAAATTTATCA 57.254 30.769 0.00 0.00 0.00 2.15
3243 4824 8.836413 TGATTTCGTCCATAGGTCAAATTTATC 58.164 33.333 0.00 0.00 0.00 1.75
3244 4825 8.746052 TGATTTCGTCCATAGGTCAAATTTAT 57.254 30.769 0.00 0.00 0.00 1.40
3245 4826 8.568676 TTGATTTCGTCCATAGGTCAAATTTA 57.431 30.769 0.00 0.00 0.00 1.40
3246 4827 7.461182 TTGATTTCGTCCATAGGTCAAATTT 57.539 32.000 0.00 0.00 0.00 1.82
3247 4828 7.461182 TTTGATTTCGTCCATAGGTCAAATT 57.539 32.000 0.00 0.00 31.46 1.82
3248 4829 7.339212 TGATTTGATTTCGTCCATAGGTCAAAT 59.661 33.333 9.41 9.41 43.48 2.32
3249 4830 6.657117 TGATTTGATTTCGTCCATAGGTCAAA 59.343 34.615 0.00 0.00 38.14 2.69
3250 4831 6.093495 GTGATTTGATTTCGTCCATAGGTCAA 59.907 38.462 0.00 0.00 0.00 3.18
3251 4832 5.584649 GTGATTTGATTTCGTCCATAGGTCA 59.415 40.000 0.00 0.00 0.00 4.02
3252 4833 5.584649 TGTGATTTGATTTCGTCCATAGGTC 59.415 40.000 0.00 0.00 0.00 3.85
3253 4834 5.496556 TGTGATTTGATTTCGTCCATAGGT 58.503 37.500 0.00 0.00 0.00 3.08
3254 4835 5.817296 TCTGTGATTTGATTTCGTCCATAGG 59.183 40.000 0.00 0.00 0.00 2.57
3255 4836 6.908870 TCTGTGATTTGATTTCGTCCATAG 57.091 37.500 0.00 0.00 0.00 2.23
3256 4837 7.552330 TCATTCTGTGATTTGATTTCGTCCATA 59.448 33.333 0.00 0.00 0.00 2.74
3257 4838 6.375174 TCATTCTGTGATTTGATTTCGTCCAT 59.625 34.615 0.00 0.00 0.00 3.41
3258 4839 5.704978 TCATTCTGTGATTTGATTTCGTCCA 59.295 36.000 0.00 0.00 0.00 4.02
3259 4840 6.182039 TCATTCTGTGATTTGATTTCGTCC 57.818 37.500 0.00 0.00 0.00 4.79
3260 4841 7.269937 CAGTTCATTCTGTGATTTGATTTCGTC 59.730 37.037 0.00 0.00 36.54 4.20
3261 4842 7.080099 CAGTTCATTCTGTGATTTGATTTCGT 58.920 34.615 0.00 0.00 36.54 3.85
3262 4843 6.033196 GCAGTTCATTCTGTGATTTGATTTCG 59.967 38.462 0.00 0.00 36.54 3.46
3263 4844 6.309737 GGCAGTTCATTCTGTGATTTGATTTC 59.690 38.462 0.00 0.00 36.54 2.17
3264 4845 6.161381 GGCAGTTCATTCTGTGATTTGATTT 58.839 36.000 0.00 0.00 36.54 2.17
3265 4846 5.620654 CGGCAGTTCATTCTGTGATTTGATT 60.621 40.000 0.00 0.00 36.54 2.57
3266 4847 4.142534 CGGCAGTTCATTCTGTGATTTGAT 60.143 41.667 0.00 0.00 36.54 2.57
3267 4848 3.189080 CGGCAGTTCATTCTGTGATTTGA 59.811 43.478 0.00 0.00 36.54 2.69
3268 4849 3.495193 CGGCAGTTCATTCTGTGATTTG 58.505 45.455 0.00 0.00 36.54 2.32
3269 4850 2.489329 CCGGCAGTTCATTCTGTGATTT 59.511 45.455 0.00 0.00 36.54 2.17
3270 4851 2.086869 CCGGCAGTTCATTCTGTGATT 58.913 47.619 0.00 0.00 36.54 2.57
3271 4852 1.003580 ACCGGCAGTTCATTCTGTGAT 59.996 47.619 0.00 0.00 36.54 3.06
3272 4853 0.396435 ACCGGCAGTTCATTCTGTGA 59.604 50.000 0.00 0.00 37.70 3.58
3273 4854 0.518636 CACCGGCAGTTCATTCTGTG 59.481 55.000 0.00 0.00 37.70 3.66
3274 4855 0.396435 TCACCGGCAGTTCATTCTGT 59.604 50.000 0.00 0.00 37.70 3.41
3275 4856 1.522668 TTCACCGGCAGTTCATTCTG 58.477 50.000 0.00 0.00 38.35 3.02
3276 4857 2.270352 TTTCACCGGCAGTTCATTCT 57.730 45.000 0.00 0.00 0.00 2.40
3277 4858 3.575965 AATTTCACCGGCAGTTCATTC 57.424 42.857 0.00 0.00 0.00 2.67
3278 4859 5.659440 AATAATTTCACCGGCAGTTCATT 57.341 34.783 0.00 0.00 0.00 2.57
3279 4860 5.184864 TGAAATAATTTCACCGGCAGTTCAT 59.815 36.000 0.00 0.00 44.21 2.57
3280 4861 4.520874 TGAAATAATTTCACCGGCAGTTCA 59.479 37.500 0.00 0.00 44.21 3.18
3281 4862 5.054390 TGAAATAATTTCACCGGCAGTTC 57.946 39.130 0.00 0.00 44.21 3.01
3291 4872 2.744741 TCAGCCGCGTGAAATAATTTCA 59.255 40.909 4.92 0.00 46.68 2.69
3292 4873 3.098636 GTCAGCCGCGTGAAATAATTTC 58.901 45.455 4.92 0.00 40.08 2.17
3293 4874 2.159435 GGTCAGCCGCGTGAAATAATTT 60.159 45.455 4.92 0.00 0.00 1.82
3294 4875 1.400494 GGTCAGCCGCGTGAAATAATT 59.600 47.619 4.92 0.00 0.00 1.40
3295 4876 1.014352 GGTCAGCCGCGTGAAATAAT 58.986 50.000 4.92 0.00 0.00 1.28
3296 4877 0.036765 AGGTCAGCCGCGTGAAATAA 60.037 50.000 4.92 0.00 40.50 1.40
3297 4878 0.036765 AAGGTCAGCCGCGTGAAATA 60.037 50.000 4.92 0.00 40.50 1.40
3298 4879 0.889186 AAAGGTCAGCCGCGTGAAAT 60.889 50.000 4.92 0.00 40.50 2.17
3299 4880 1.098712 AAAAGGTCAGCCGCGTGAAA 61.099 50.000 4.92 0.00 40.50 2.69
3300 4881 1.098712 AAAAAGGTCAGCCGCGTGAA 61.099 50.000 4.92 0.00 40.50 3.18
3301 4882 1.525077 AAAAAGGTCAGCCGCGTGA 60.525 52.632 4.92 0.00 40.50 4.35
3302 4883 1.370414 CAAAAAGGTCAGCCGCGTG 60.370 57.895 4.92 0.00 40.50 5.34
3303 4884 1.822186 ACAAAAAGGTCAGCCGCGT 60.822 52.632 4.92 0.00 40.50 6.01
3304 4885 1.370414 CACAAAAAGGTCAGCCGCG 60.370 57.895 0.00 0.00 40.50 6.46
3305 4886 0.594796 CACACAAAAAGGTCAGCCGC 60.595 55.000 0.00 0.00 40.50 6.53
3306 4887 1.021202 TCACACAAAAAGGTCAGCCG 58.979 50.000 0.00 0.00 40.50 5.52
3307 4888 1.268539 CGTCACACAAAAAGGTCAGCC 60.269 52.381 0.00 0.00 0.00 4.85
3308 4889 1.859998 GCGTCACACAAAAAGGTCAGC 60.860 52.381 0.00 0.00 0.00 4.26
3309 4890 1.268539 GGCGTCACACAAAAAGGTCAG 60.269 52.381 0.00 0.00 0.00 3.51
3310 4891 0.736053 GGCGTCACACAAAAAGGTCA 59.264 50.000 0.00 0.00 0.00 4.02
3311 4892 0.030235 GGGCGTCACACAAAAAGGTC 59.970 55.000 0.00 0.00 0.00 3.85
3312 4893 1.720694 CGGGCGTCACACAAAAAGGT 61.721 55.000 0.00 0.00 0.00 3.50
3313 4894 1.008995 CGGGCGTCACACAAAAAGG 60.009 57.895 0.00 0.00 0.00 3.11
3314 4895 0.316689 GTCGGGCGTCACACAAAAAG 60.317 55.000 0.00 0.00 0.00 2.27
3315 4896 1.025113 TGTCGGGCGTCACACAAAAA 61.025 50.000 0.00 0.00 0.00 1.94
3316 4897 1.449778 TGTCGGGCGTCACACAAAA 60.450 52.632 0.00 0.00 0.00 2.44
3317 4898 2.174969 GTGTCGGGCGTCACACAAA 61.175 57.895 5.81 0.00 42.20 2.83
3318 4899 2.586635 GTGTCGGGCGTCACACAA 60.587 61.111 5.81 0.00 42.20 3.33
3319 4900 4.934942 CGTGTCGGGCGTCACACA 62.935 66.667 10.72 0.00 42.67 3.72
3320 4901 4.634133 TCGTGTCGGGCGTCACAC 62.634 66.667 0.75 0.75 39.70 3.82
3321 4902 3.834447 CTTCGTGTCGGGCGTCACA 62.834 63.158 0.00 0.00 34.69 3.58
3322 4903 3.103911 CTTCGTGTCGGGCGTCAC 61.104 66.667 0.00 0.00 0.00 3.67
3323 4904 4.351938 CCTTCGTGTCGGGCGTCA 62.352 66.667 0.00 0.00 0.00 4.35
3331 4912 2.758770 TAGTGTGGCGCCTTCGTGTC 62.759 60.000 29.70 10.72 38.14 3.67
3332 4913 2.863346 TAGTGTGGCGCCTTCGTGT 61.863 57.895 29.70 9.85 38.14 4.49
3333 4914 2.048597 TAGTGTGGCGCCTTCGTG 60.049 61.111 29.70 0.00 38.14 4.35
3334 4915 2.048503 GTAGTGTGGCGCCTTCGT 60.049 61.111 29.70 12.53 38.14 3.85
3335 4916 2.048597 TGTAGTGTGGCGCCTTCG 60.049 61.111 29.70 0.00 39.07 3.79
3336 4917 1.004918 AGTGTAGTGTGGCGCCTTC 60.005 57.895 29.70 20.58 0.00 3.46
3337 4918 1.301716 CAGTGTAGTGTGGCGCCTT 60.302 57.895 29.70 13.03 0.00 4.35
3338 4919 2.343758 CAGTGTAGTGTGGCGCCT 59.656 61.111 29.70 9.99 0.00 5.52
3339 4920 2.030562 ACAGTGTAGTGTGGCGCC 59.969 61.111 22.73 22.73 0.00 6.53
3340 4921 2.954753 GCACAGTGTAGTGTGGCGC 61.955 63.158 18.52 0.00 46.73 6.53
3341 4922 1.157257 TTGCACAGTGTAGTGTGGCG 61.157 55.000 18.52 0.00 46.73 5.69
3342 4923 0.307760 GTTGCACAGTGTAGTGTGGC 59.692 55.000 18.52 12.34 46.73 5.01
3343 4924 0.581529 CGTTGCACAGTGTAGTGTGG 59.418 55.000 18.52 1.81 46.73 4.17
3345 4926 1.157870 GGCGTTGCACAGTGTAGTGT 61.158 55.000 1.61 0.00 41.52 3.55
3346 4927 0.880278 AGGCGTTGCACAGTGTAGTG 60.880 55.000 1.61 0.00 42.37 2.74
3347 4928 0.600255 GAGGCGTTGCACAGTGTAGT 60.600 55.000 1.61 0.00 0.00 2.73
3348 4929 1.617755 CGAGGCGTTGCACAGTGTAG 61.618 60.000 1.61 0.00 0.00 2.74
3349 4930 1.663388 CGAGGCGTTGCACAGTGTA 60.663 57.895 1.61 0.00 0.00 2.90
3350 4931 2.967076 CGAGGCGTTGCACAGTGT 60.967 61.111 1.61 0.00 0.00 3.55
3351 4932 4.374702 GCGAGGCGTTGCACAGTG 62.375 66.667 13.75 0.00 32.59 3.66
3352 4933 4.908687 TGCGAGGCGTTGCACAGT 62.909 61.111 17.22 0.00 38.24 3.55
3353 4934 4.081030 CTGCGAGGCGTTGCACAG 62.081 66.667 17.22 5.41 38.24 3.66
3354 4935 2.499756 TATCTGCGAGGCGTTGCACA 62.500 55.000 17.22 8.16 38.24 4.57
3355 4936 1.756375 CTATCTGCGAGGCGTTGCAC 61.756 60.000 17.22 0.00 38.24 4.57
3356 4937 1.519234 CTATCTGCGAGGCGTTGCA 60.519 57.895 19.70 19.70 41.13 4.08
3357 4938 2.240500 CCTATCTGCGAGGCGTTGC 61.241 63.158 11.80 11.80 0.00 4.17
3358 4939 4.018609 CCTATCTGCGAGGCGTTG 57.981 61.111 0.00 0.00 0.00 4.10
3367 4948 0.935366 GACGTGTAGCGCCTATCTGC 60.935 60.000 2.29 0.00 46.11 4.26
3368 4949 0.663688 AGACGTGTAGCGCCTATCTG 59.336 55.000 2.29 0.00 46.11 2.90
3369 4950 0.663688 CAGACGTGTAGCGCCTATCT 59.336 55.000 2.29 0.00 46.11 1.98
3370 4951 0.661552 TCAGACGTGTAGCGCCTATC 59.338 55.000 2.29 0.00 46.11 2.08
3371 4952 0.381089 GTCAGACGTGTAGCGCCTAT 59.619 55.000 2.29 0.00 46.11 2.57
3372 4953 1.651240 GGTCAGACGTGTAGCGCCTA 61.651 60.000 2.29 0.00 46.11 3.93
3373 4954 2.567049 GTCAGACGTGTAGCGCCT 59.433 61.111 2.29 0.00 46.11 5.52
3374 4955 2.506438 GGTCAGACGTGTAGCGCC 60.506 66.667 2.29 0.00 46.11 6.53
3375 4956 1.801913 CTGGTCAGACGTGTAGCGC 60.802 63.158 0.00 0.00 46.11 5.92
3377 4958 1.801913 CGCTGGTCAGACGTGTAGC 60.802 63.158 0.00 0.00 0.00 3.58
3378 4959 0.039437 AACGCTGGTCAGACGTGTAG 60.039 55.000 16.41 0.00 39.64 2.74
3379 4960 0.318360 CAACGCTGGTCAGACGTGTA 60.318 55.000 16.41 0.00 39.64 2.90
3380 4961 1.591594 CAACGCTGGTCAGACGTGT 60.592 57.895 16.41 0.00 39.64 4.49
3381 4962 2.943345 GCAACGCTGGTCAGACGTG 61.943 63.158 16.41 12.76 39.64 4.49
3382 4963 2.661866 GCAACGCTGGTCAGACGT 60.662 61.111 12.17 12.17 40.75 4.34
3383 4964 2.661537 TGCAACGCTGGTCAGACG 60.662 61.111 1.65 7.55 35.30 4.18
3384 4965 2.607892 GGTGCAACGCTGGTCAGAC 61.608 63.158 1.65 0.00 38.12 3.51
3385 4966 2.280797 GGTGCAACGCTGGTCAGA 60.281 61.111 1.65 0.00 38.12 3.27
3394 4975 2.677003 GGATCACACGGGTGCAACG 61.677 63.158 14.50 10.16 44.87 4.10
3395 4976 2.677003 CGGATCACACGGGTGCAAC 61.677 63.158 14.50 6.54 44.87 4.17
3396 4977 2.358125 CGGATCACACGGGTGCAA 60.358 61.111 14.50 0.00 44.87 4.08
3397 4978 2.384653 TTTCGGATCACACGGGTGCA 62.385 55.000 14.50 2.22 44.87 4.57
3398 4979 1.231958 TTTTCGGATCACACGGGTGC 61.232 55.000 14.50 0.00 44.87 5.01
3399 4980 1.448985 ATTTTCGGATCACACGGGTG 58.551 50.000 12.84 12.84 46.66 4.61
3400 4981 2.194201 AATTTTCGGATCACACGGGT 57.806 45.000 0.00 0.00 0.00 5.28
3401 4982 3.267483 AGTAATTTTCGGATCACACGGG 58.733 45.455 0.00 0.00 0.00 5.28
3402 4983 5.579511 ACTTAGTAATTTTCGGATCACACGG 59.420 40.000 0.00 0.00 0.00 4.94
3403 4984 6.309494 TGACTTAGTAATTTTCGGATCACACG 59.691 38.462 0.00 0.00 0.00 4.49
3404 4985 7.331193 ACTGACTTAGTAATTTTCGGATCACAC 59.669 37.037 0.00 0.00 38.04 3.82
3405 4986 7.383687 ACTGACTTAGTAATTTTCGGATCACA 58.616 34.615 0.00 0.00 38.04 3.58
3406 4987 7.829378 ACTGACTTAGTAATTTTCGGATCAC 57.171 36.000 0.00 0.00 38.04 3.06


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

AutoCloner maintained by Alex Coulton.