Multiple sequence alignment - TraesCS5D01G256100

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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 TraesCS5D01G256100 chr5D 100.000 6236 0 0 1 6236 362397503 362403738 0.000000e+00 11516.0
1 TraesCS5D01G256100 chr5D 91.549 71 3 2 3748 3818 362401186 362401253 1.850000e-15 95.3
2 TraesCS5D01G256100 chr5D 91.549 71 3 2 3684 3751 362401250 362401320 1.850000e-15 95.3
3 TraesCS5D01G256100 chr5D 95.455 44 1 1 5958 6000 362403418 362403461 1.120000e-07 69.4
4 TraesCS5D01G256100 chr5D 95.455 44 1 1 5916 5959 362403460 362403502 1.120000e-07 69.4
5 TraesCS5D01G256100 chr5D 83.750 80 6 1 4106 4178 477307658 477307737 1.120000e-07 69.4
6 TraesCS5D01G256100 chr5D 92.857 42 3 0 4099 4140 76408532 76408573 1.880000e-05 62.1
7 TraesCS5D01G256100 chr5A 95.606 3482 114 22 1958 5424 463063632 463067089 0.000000e+00 5546.0
8 TraesCS5D01G256100 chr5A 94.001 1967 85 10 3 1963 463061664 463063603 0.000000e+00 2948.0
9 TraesCS5D01G256100 chr5A 89.910 446 21 13 5530 5954 463067088 463067530 2.540000e-153 553.0
10 TraesCS5D01G256100 chr5A 86.913 298 20 9 5958 6236 463067490 463067787 3.630000e-82 316.0
11 TraesCS5D01G256100 chr5A 94.643 112 5 1 5420 5531 366242799 366242689 8.310000e-39 172.0
12 TraesCS5D01G256100 chr5A 92.500 120 7 2 5419 5537 46619766 46619648 2.990000e-38 171.0
13 TraesCS5D01G256100 chr5A 95.588 68 3 0 3684 3751 463065423 463065490 6.610000e-20 110.0
14 TraesCS5D01G256100 chr5A 90.000 50 5 0 4150 4199 463065820 463065771 1.450000e-06 65.8
15 TraesCS5D01G256100 chr5B 94.170 1338 68 5 635 1963 428127009 428128345 0.000000e+00 2030.0
16 TraesCS5D01G256100 chr5B 95.004 1241 52 6 4186 5424 428130536 428131768 0.000000e+00 1940.0
17 TraesCS5D01G256100 chr5B 86.623 1525 106 37 1989 3477 428128405 428129867 0.000000e+00 1596.0
18 TraesCS5D01G256100 chr5B 89.809 471 28 5 162 630 428126337 428126789 2.500000e-163 586.0
19 TraesCS5D01G256100 chr5B 91.033 368 28 5 5530 5896 428131764 428132127 5.620000e-135 492.0
20 TraesCS5D01G256100 chr5B 89.313 262 12 8 5975 6236 428135211 428135456 1.300000e-81 315.0
21 TraesCS5D01G256100 chr5B 95.238 168 3 2 3 165 428125988 428126155 1.720000e-65 261.0
22 TraesCS5D01G256100 chr5B 92.437 119 7 2 5416 5534 51836923 51836807 1.080000e-37 169.0
23 TraesCS5D01G256100 chr5B 87.586 145 13 3 3747 3890 428130148 428130288 5.000000e-36 163.0
24 TraesCS5D01G256100 chr5B 100.000 49 0 0 5893 5941 428133839 428133887 2.390000e-14 91.6
25 TraesCS5D01G256100 chr5B 82.927 82 5 4 4115 4187 696183791 696183872 1.450000e-06 65.8
26 TraesCS5D01G256100 chr5B 95.000 40 2 0 4150 4189 629934813 629934852 5.220000e-06 63.9
27 TraesCS5D01G256100 chr7D 83.181 547 88 4 1249 1793 291521627 291521083 1.210000e-136 497.0
28 TraesCS5D01G256100 chr7D 93.103 116 6 2 5420 5535 185178053 185178166 1.080000e-37 169.0
29 TraesCS5D01G256100 chr7D 82.500 80 7 3 4115 4187 16713326 16713247 5.220000e-06 63.9
30 TraesCS5D01G256100 chr7B 83.743 529 82 4 1249 1775 361146341 361146867 1.210000e-136 497.0
31 TraesCS5D01G256100 chr7B 88.312 77 4 2 4109 4180 726617359 726617283 3.100000e-13 87.9
32 TraesCS5D01G256100 chr7B 95.000 40 2 0 4150 4189 43549623 43549584 5.220000e-06 63.9
33 TraesCS5D01G256100 chr7A 83.619 525 82 4 1252 1774 326046254 326045732 2.020000e-134 490.0
34 TraesCS5D01G256100 chr7A 97.368 38 1 0 4150 4187 31103460 31103423 1.450000e-06 65.8
35 TraesCS5D01G256100 chr7A 100.000 33 0 0 4107 4139 424927500 424927532 1.880000e-05 62.1
36 TraesCS5D01G256100 chr4D 92.683 123 5 4 5423 5544 122197865 122197746 2.310000e-39 174.0
37 TraesCS5D01G256100 chr4D 93.966 116 6 1 5416 5531 155576682 155576796 2.310000e-39 174.0
38 TraesCS5D01G256100 chr2A 93.162 117 7 1 5416 5532 746800236 746800121 2.990000e-38 171.0
39 TraesCS5D01G256100 chr6A 93.103 116 7 1 5426 5541 450094815 450094701 1.080000e-37 169.0
40 TraesCS5D01G256100 chr2D 92.500 120 6 3 5415 5534 73968170 73968054 1.080000e-37 169.0
41 TraesCS5D01G256100 chr2D 85.185 81 2 5 4110 4180 49386239 49386159 2.410000e-09 75.0
42 TraesCS5D01G256100 chr2D 97.143 35 1 0 4106 4140 109627154 109627120 6.750000e-05 60.2
43 TraesCS5D01G256100 chr6D 96.000 50 2 0 670 719 334250164 334250213 1.440000e-11 82.4
44 TraesCS5D01G256100 chr2B 93.878 49 3 0 6188 6236 690965385 690965433 2.410000e-09 75.0
45 TraesCS5D01G256100 chr1B 97.500 40 1 0 4150 4189 26851561 26851600 1.120000e-07 69.4
46 TraesCS5D01G256100 chr1D 97.143 35 1 0 4106 4140 397558898 397558864 6.750000e-05 60.2


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 TraesCS5D01G256100 chr5D 362397503 362403738 6235 False 2369.080000 11516 94.801600 1 6236 5 chr5D.!!$F3 6235
1 TraesCS5D01G256100 chr5A 463061664 463067787 6123 False 1894.600000 5546 92.403600 3 6236 5 chr5A.!!$F1 6233
2 TraesCS5D01G256100 chr5B 428125988 428135456 9468 False 830.511111 2030 92.086222 3 6236 9 chr5B.!!$F3 6233
3 TraesCS5D01G256100 chr7D 291521083 291521627 544 True 497.000000 497 83.181000 1249 1793 1 chr7D.!!$R2 544
4 TraesCS5D01G256100 chr7B 361146341 361146867 526 False 497.000000 497 83.743000 1249 1775 1 chr7B.!!$F1 526
5 TraesCS5D01G256100 chr7A 326045732 326046254 522 True 490.000000 490 83.619000 1252 1774 1 chr7A.!!$R2 522

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
713 1121 0.889186 GCACCAACACAGATTCCGGT 60.889 55.000 0.0 0.0 0.00 5.28 F
754 1162 0.961358 CGAGCCCTAGTATCTCCCGG 60.961 65.000 0.0 0.0 0.00 5.73 F
2161 2613 1.741706 CGATGCTTGCTTGGTCAGAAT 59.258 47.619 0.0 0.0 0.00 2.40 F
2889 3377 2.544267 GTGCAAGAGTGACGTTAAAGCT 59.456 45.455 0.0 0.0 0.00 3.74 F
3886 4458 1.952296 AGGATGAATCGAAGCCAATGC 59.048 47.619 0.0 0.0 37.95 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 2256 0.532115 GCCAAATTACCAGCCACCAG 59.468 55.000 0.0 0.0 0.00 4.00 R
2297 2750 1.890489 TGCACTACTCTAGTTTCGCCA 59.110 47.619 0.0 0.0 36.76 5.69 R
3879 4451 0.740737 AAGGCAGTTATCGCATTGGC 59.259 50.000 0.0 0.0 31.16 4.52 R
4146 4749 1.560505 TAAGTCGTTGGGGGAGTACC 58.439 55.000 0.0 0.0 39.11 3.34 R
5824 6459 0.034670 AGCAGATGTTGGAGGAAGGC 60.035 55.000 0.0 0.0 0.00 4.35 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
76 82 2.667470 GGTCATAGACTGTAGGCCTGA 58.333 52.381 17.99 0.00 32.47 3.86
87 93 1.410882 GTAGGCCTGACTCTCATCCAC 59.589 57.143 17.99 0.00 0.00 4.02
171 362 6.041069 AGTCTCCAAGGTGTTATAGTATCTGC 59.959 42.308 0.00 0.00 0.00 4.26
192 383 3.395639 CCATTGATTGTTTGCAAGCTGT 58.604 40.909 14.67 2.92 41.21 4.40
218 410 1.189752 TGGTTTTGCTGCAAGGACAA 58.810 45.000 23.25 14.96 29.42 3.18
272 465 2.731217 ACTCACGAAAATTGTTGCTGC 58.269 42.857 0.00 0.00 0.00 5.25
275 468 2.031245 TCACGAAAATTGTTGCTGCGAT 60.031 40.909 0.00 0.00 0.00 4.58
299 492 5.163426 TGCAGGTCATTTTGTTTCACTGATT 60.163 36.000 0.00 0.00 0.00 2.57
300 493 6.040278 TGCAGGTCATTTTGTTTCACTGATTA 59.960 34.615 0.00 0.00 0.00 1.75
358 551 3.924114 TTGTCCAAACTCTGGTCTTCA 57.076 42.857 0.00 0.00 46.51 3.02
420 613 4.050553 TCTTTGCAATGCTTAGTGTTTGC 58.949 39.130 6.82 8.28 43.60 3.68
503 696 2.228822 GTGGGAAATGTGTGCGATCTTT 59.771 45.455 0.00 0.00 0.00 2.52
550 743 1.613925 GGATCGTCCAATCCTCATCGA 59.386 52.381 0.00 0.00 41.78 3.59
605 798 2.420043 CACGTGTCGACCCCTTGT 59.580 61.111 14.12 1.22 0.00 3.16
608 801 1.068417 CGTGTCGACCCCTTGTTGA 59.932 57.895 14.12 0.00 34.87 3.18
684 1092 4.383861 CTCAGCTCAGCCGCACCA 62.384 66.667 0.00 0.00 0.00 4.17
713 1121 0.889186 GCACCAACACAGATTCCGGT 60.889 55.000 0.00 0.00 0.00 5.28
754 1162 0.961358 CGAGCCCTAGTATCTCCCGG 60.961 65.000 0.00 0.00 0.00 5.73
828 1238 4.758251 CGGACGCCCAGCACATGA 62.758 66.667 0.00 0.00 0.00 3.07
831 1241 3.899981 GACGCCCAGCACATGACCA 62.900 63.158 0.00 0.00 0.00 4.02
851 1261 3.228188 ACACATGTCAGTGGGTGAAAT 57.772 42.857 0.00 0.00 43.72 2.17
853 1263 3.148412 CACATGTCAGTGGGTGAAATCA 58.852 45.455 0.00 0.00 36.74 2.57
854 1264 3.760151 CACATGTCAGTGGGTGAAATCAT 59.240 43.478 0.00 0.00 36.74 2.45
984 1395 4.154347 GCCTCTGCTCCTGGACCG 62.154 72.222 0.00 0.00 33.53 4.79
2101 2553 4.640201 GTGTTAGCATGATTTTCCTAGGCA 59.360 41.667 2.96 0.00 0.00 4.75
2125 2577 7.370383 CACAATTAGTGCAAGAACCTGTAATT 58.630 34.615 0.00 0.00 42.15 1.40
2161 2613 1.741706 CGATGCTTGCTTGGTCAGAAT 59.258 47.619 0.00 0.00 0.00 2.40
2297 2750 8.405850 AGTATCCTATCAGTTGGAGGATTCTAT 58.594 37.037 16.54 2.50 45.94 1.98
2455 2917 7.826690 TGGTTGAAATATGAAACCTAAGCTTC 58.173 34.615 0.00 0.00 43.16 3.86
2547 3014 4.210331 CAGGCCAGCCATTTTAGTCTAAT 58.790 43.478 12.03 0.00 38.92 1.73
2690 3162 7.510675 AATAGATGGAGGTGTTAGGAAGAAA 57.489 36.000 0.00 0.00 0.00 2.52
2692 3164 5.094387 AGATGGAGGTGTTAGGAAGAAAGA 58.906 41.667 0.00 0.00 0.00 2.52
2693 3165 4.891992 TGGAGGTGTTAGGAAGAAAGAG 57.108 45.455 0.00 0.00 0.00 2.85
2694 3166 4.232091 TGGAGGTGTTAGGAAGAAAGAGT 58.768 43.478 0.00 0.00 0.00 3.24
2695 3167 4.040461 TGGAGGTGTTAGGAAGAAAGAGTG 59.960 45.833 0.00 0.00 0.00 3.51
2769 3241 7.094508 TGATTTCTTAAAACTGTTGTGCTCA 57.905 32.000 0.00 0.00 0.00 4.26
2806 3278 6.265649 CCTAGCAGGAAAGCTACTCAACTATA 59.734 42.308 0.00 0.00 44.50 1.31
2827 3299 8.796475 ACTATAAAGATTTTGCTTCTTGCTTGA 58.204 29.630 0.00 0.00 43.37 3.02
2847 3319 9.008965 TGCTTGAATGCTATCTTAACTAAACAA 57.991 29.630 0.00 0.00 0.00 2.83
2880 3368 3.871594 ACAAGTAACAGTGCAAGAGTGAC 59.128 43.478 0.00 0.00 0.00 3.67
2889 3377 2.544267 GTGCAAGAGTGACGTTAAAGCT 59.456 45.455 0.00 0.00 0.00 3.74
2994 3482 9.823647 ACTCTAATAAAGTTCATACATGACTGG 57.176 33.333 0.00 0.00 36.36 4.00
3027 3515 5.885230 TCATCCAGCATTTCTTACAACAG 57.115 39.130 0.00 0.00 0.00 3.16
3038 3526 9.722056 GCATTTCTTACAACAGAACTATTATGG 57.278 33.333 0.00 0.00 32.28 2.74
3041 3529 6.869695 TCTTACAACAGAACTATTATGGCGA 58.130 36.000 0.00 0.00 0.00 5.54
3044 3532 5.109903 ACAACAGAACTATTATGGCGACTC 58.890 41.667 0.00 0.00 0.00 3.36
3415 3903 6.753107 TTTTGGGTAAGCTTCTATGTTAGC 57.247 37.500 0.00 0.00 37.66 3.09
3486 4057 7.147983 TGTGGTGTCTTTTACTATGCTGTTTTT 60.148 33.333 0.00 0.00 0.00 1.94
3615 4186 6.640092 GGAACTCTTGCTTCAGAAAGAAATTG 59.360 38.462 0.00 0.00 39.12 2.32
3645 4216 2.621998 TGATAGGCGCCTAGTCAAGTAC 59.378 50.000 37.16 20.61 31.45 2.73
3659 4231 5.579718 AGTCAAGTACGACTGGAATAATCG 58.420 41.667 2.97 0.00 44.59 3.34
3879 4451 7.443575 ACATTTAATCTGGAGGATGAATCGAAG 59.556 37.037 0.00 0.00 34.45 3.79
3886 4458 1.952296 AGGATGAATCGAAGCCAATGC 59.048 47.619 0.00 0.00 37.95 3.56
3904 4505 5.238432 CCAATGCGATAACTGCCTTTGTATA 59.762 40.000 0.00 0.00 0.00 1.47
3937 4538 8.626526 GTTAAAACTTGTATCTCAGTCCCAAAA 58.373 33.333 0.00 0.00 0.00 2.44
3976 4579 5.512232 CCCATTTCTGCTCCTAATCCTACTC 60.512 48.000 0.00 0.00 0.00 2.59
4016 4619 2.432444 TCAAACGCCACCTTATTCTGG 58.568 47.619 0.00 0.00 0.00 3.86
4118 4721 5.888982 TCAGAATACCATTTACTCCCTCC 57.111 43.478 0.00 0.00 0.00 4.30
4119 4722 5.285401 TCAGAATACCATTTACTCCCTCCA 58.715 41.667 0.00 0.00 0.00 3.86
4146 4749 4.432980 AAATATAAGTCGTTGGGGGAGG 57.567 45.455 0.00 0.00 0.00 4.30
4147 4750 1.797320 TATAAGTCGTTGGGGGAGGG 58.203 55.000 0.00 0.00 0.00 4.30
4148 4751 0.253020 ATAAGTCGTTGGGGGAGGGT 60.253 55.000 0.00 0.00 0.00 4.34
4150 4753 1.196766 AAGTCGTTGGGGGAGGGTAC 61.197 60.000 0.00 0.00 0.00 3.34
4152 4755 1.305549 TCGTTGGGGGAGGGTACTC 60.306 63.158 0.00 0.00 43.20 2.59
4163 4766 4.125239 GGTACTCCCCCAACGACT 57.875 61.111 0.00 0.00 0.00 4.18
4164 4767 2.369654 GGTACTCCCCCAACGACTT 58.630 57.895 0.00 0.00 0.00 3.01
4165 4768 1.560505 GGTACTCCCCCAACGACTTA 58.439 55.000 0.00 0.00 0.00 2.24
4166 4769 2.113807 GGTACTCCCCCAACGACTTAT 58.886 52.381 0.00 0.00 0.00 1.73
4167 4770 3.299503 GGTACTCCCCCAACGACTTATA 58.700 50.000 0.00 0.00 0.00 0.98
4168 4771 3.899980 GGTACTCCCCCAACGACTTATAT 59.100 47.826 0.00 0.00 0.00 0.86
4169 4772 4.346127 GGTACTCCCCCAACGACTTATATT 59.654 45.833 0.00 0.00 0.00 1.28
4170 4773 5.163269 GGTACTCCCCCAACGACTTATATTT 60.163 44.000 0.00 0.00 0.00 1.40
4171 4774 6.041979 GGTACTCCCCCAACGACTTATATTTA 59.958 42.308 0.00 0.00 0.00 1.40
4172 4775 6.170846 ACTCCCCCAACGACTTATATTTAG 57.829 41.667 0.00 0.00 0.00 1.85
4290 4893 7.372714 TGCATAATCCATTTCACAATATCTGC 58.627 34.615 0.00 0.00 0.00 4.26
4298 4901 0.940126 CACAATATCTGCGCAGGGAC 59.060 55.000 35.36 0.00 0.00 4.46
4451 5054 4.221422 GCGATGGCCGGACAGCTA 62.221 66.667 25.57 0.00 39.04 3.32
4562 5165 2.834549 TCTTGAGGCCTCCTACTTCTTG 59.165 50.000 29.95 9.05 31.76 3.02
4812 5415 3.702330 CATTTGCATGTGGCTGTAGATG 58.298 45.455 0.00 0.00 45.15 2.90
4988 5592 2.223377 GGTCAGTAACCTGTTGCTTTCG 59.777 50.000 0.00 0.00 45.45 3.46
5106 5710 1.186200 GGTGGAAATTTCTGGGGCTC 58.814 55.000 17.42 0.22 0.00 4.70
5181 5785 0.768622 AACTGTCCATGGTTCCGGAA 59.231 50.000 14.35 14.35 31.67 4.30
5301 5906 7.171678 CCCATTTTATCTCTCGGAAATGTAGAC 59.828 40.741 0.00 0.00 37.64 2.59
5323 5928 0.312102 GAGCTGAACAGTTTGGTGCC 59.688 55.000 0.00 0.00 0.00 5.01
5424 6039 6.183360 GCATCTTTTCCTCCCCAAAATACTAC 60.183 42.308 0.00 0.00 0.00 2.73
5426 6041 6.718294 TCTTTTCCTCCCCAAAATACTACTC 58.282 40.000 0.00 0.00 0.00 2.59
5427 6042 5.446260 TTTCCTCCCCAAAATACTACTCC 57.554 43.478 0.00 0.00 0.00 3.85
5429 6044 3.014807 TCCTCCCCAAAATACTACTCCCT 59.985 47.826 0.00 0.00 0.00 4.20
5430 6045 3.391626 CCTCCCCAAAATACTACTCCCTC 59.608 52.174 0.00 0.00 0.00 4.30
5431 6046 4.299485 CTCCCCAAAATACTACTCCCTCT 58.701 47.826 0.00 0.00 0.00 3.69
5432 6047 4.296056 TCCCCAAAATACTACTCCCTCTC 58.704 47.826 0.00 0.00 0.00 3.20
5433 6048 3.069729 CCCCAAAATACTACTCCCTCTCG 59.930 52.174 0.00 0.00 0.00 4.04
5434 6049 3.705072 CCCAAAATACTACTCCCTCTCGT 59.295 47.826 0.00 0.00 0.00 4.18
5435 6050 4.161754 CCCAAAATACTACTCCCTCTCGTT 59.838 45.833 0.00 0.00 0.00 3.85
5436 6051 5.349809 CCAAAATACTACTCCCTCTCGTTC 58.650 45.833 0.00 0.00 0.00 3.95
5437 6052 5.105473 CCAAAATACTACTCCCTCTCGTTCA 60.105 44.000 0.00 0.00 0.00 3.18
5438 6053 5.579564 AAATACTACTCCCTCTCGTTCAC 57.420 43.478 0.00 0.00 0.00 3.18
5439 6054 2.883122 ACTACTCCCTCTCGTTCACT 57.117 50.000 0.00 0.00 0.00 3.41
5440 6055 3.157750 ACTACTCCCTCTCGTTCACTT 57.842 47.619 0.00 0.00 0.00 3.16
5441 6056 3.498334 ACTACTCCCTCTCGTTCACTTT 58.502 45.455 0.00 0.00 0.00 2.66
5442 6057 3.896272 ACTACTCCCTCTCGTTCACTTTT 59.104 43.478 0.00 0.00 0.00 2.27
5443 6058 3.113260 ACTCCCTCTCGTTCACTTTTG 57.887 47.619 0.00 0.00 0.00 2.44
5444 6059 2.434702 ACTCCCTCTCGTTCACTTTTGT 59.565 45.455 0.00 0.00 0.00 2.83
5445 6060 3.640029 ACTCCCTCTCGTTCACTTTTGTA 59.360 43.478 0.00 0.00 0.00 2.41
5446 6061 4.100498 ACTCCCTCTCGTTCACTTTTGTAA 59.900 41.667 0.00 0.00 0.00 2.41
5447 6062 4.628074 TCCCTCTCGTTCACTTTTGTAAG 58.372 43.478 0.00 0.00 37.40 2.34
5448 6063 4.342951 TCCCTCTCGTTCACTTTTGTAAGA 59.657 41.667 0.00 0.00 35.30 2.10
5449 6064 4.448060 CCCTCTCGTTCACTTTTGTAAGAC 59.552 45.833 0.00 0.00 35.30 3.01
5450 6065 4.448060 CCTCTCGTTCACTTTTGTAAGACC 59.552 45.833 0.00 0.00 35.30 3.85
5451 6066 5.272283 TCTCGTTCACTTTTGTAAGACCT 57.728 39.130 0.00 0.00 35.30 3.85
5452 6067 5.667466 TCTCGTTCACTTTTGTAAGACCTT 58.333 37.500 0.00 0.00 35.30 3.50
5453 6068 6.110707 TCTCGTTCACTTTTGTAAGACCTTT 58.889 36.000 0.00 0.00 35.30 3.11
5454 6069 6.596497 TCTCGTTCACTTTTGTAAGACCTTTT 59.404 34.615 0.00 0.00 35.30 2.27
5455 6070 7.765360 TCTCGTTCACTTTTGTAAGACCTTTTA 59.235 33.333 0.00 0.00 35.30 1.52
5456 6071 7.912383 TCGTTCACTTTTGTAAGACCTTTTAG 58.088 34.615 0.00 0.00 35.30 1.85
5457 6072 7.765360 TCGTTCACTTTTGTAAGACCTTTTAGA 59.235 33.333 0.00 0.00 35.30 2.10
5458 6073 7.849515 CGTTCACTTTTGTAAGACCTTTTAGAC 59.150 37.037 0.00 0.00 35.30 2.59
5459 6074 8.671028 GTTCACTTTTGTAAGACCTTTTAGACA 58.329 33.333 0.00 0.00 35.30 3.41
5460 6075 8.974060 TCACTTTTGTAAGACCTTTTAGACAT 57.026 30.769 0.00 0.00 35.30 3.06
5461 6076 9.403583 TCACTTTTGTAAGACCTTTTAGACATT 57.596 29.630 0.00 0.00 35.30 2.71
5467 6082 8.331730 TGTAAGACCTTTTAGACATTTAAGGC 57.668 34.615 0.00 0.00 40.63 4.35
5468 6083 7.940137 TGTAAGACCTTTTAGACATTTAAGGCA 59.060 33.333 0.00 0.00 40.63 4.75
5469 6084 7.454260 AAGACCTTTTAGACATTTAAGGCAG 57.546 36.000 0.00 0.00 40.63 4.85
5470 6085 5.416013 AGACCTTTTAGACATTTAAGGCAGC 59.584 40.000 0.00 0.00 40.63 5.25
5471 6086 5.076873 ACCTTTTAGACATTTAAGGCAGCA 58.923 37.500 0.00 0.00 40.63 4.41
5472 6087 5.716703 ACCTTTTAGACATTTAAGGCAGCAT 59.283 36.000 0.00 0.00 40.63 3.79
5473 6088 6.127619 ACCTTTTAGACATTTAAGGCAGCATC 60.128 38.462 0.00 0.00 40.63 3.91
5474 6089 6.096001 CCTTTTAGACATTTAAGGCAGCATCT 59.904 38.462 0.00 0.00 31.59 2.90
5475 6090 7.283127 CCTTTTAGACATTTAAGGCAGCATCTA 59.717 37.037 0.00 0.00 31.59 1.98
5476 6091 8.574251 TTTTAGACATTTAAGGCAGCATCTAA 57.426 30.769 0.00 0.00 0.00 2.10
5477 6092 8.574251 TTTAGACATTTAAGGCAGCATCTAAA 57.426 30.769 0.00 0.00 35.89 1.85
5478 6093 8.574251 TTAGACATTTAAGGCAGCATCTAAAA 57.426 30.769 0.00 0.00 0.00 1.52
5479 6094 6.856895 AGACATTTAAGGCAGCATCTAAAAC 58.143 36.000 0.00 0.00 0.00 2.43
5480 6095 6.434028 AGACATTTAAGGCAGCATCTAAAACA 59.566 34.615 0.00 0.00 0.00 2.83
5481 6096 6.624423 ACATTTAAGGCAGCATCTAAAACAG 58.376 36.000 0.00 0.00 0.00 3.16
5482 6097 6.209391 ACATTTAAGGCAGCATCTAAAACAGT 59.791 34.615 0.00 0.00 0.00 3.55
5483 6098 6.648879 TTTAAGGCAGCATCTAAAACAGTT 57.351 33.333 0.00 0.00 0.00 3.16
5484 6099 4.773323 AAGGCAGCATCTAAAACAGTTC 57.227 40.909 0.00 0.00 0.00 3.01
5485 6100 3.754965 AGGCAGCATCTAAAACAGTTCA 58.245 40.909 0.00 0.00 0.00 3.18
5486 6101 4.144297 AGGCAGCATCTAAAACAGTTCAA 58.856 39.130 0.00 0.00 0.00 2.69
5487 6102 4.768968 AGGCAGCATCTAAAACAGTTCAAT 59.231 37.500 0.00 0.00 0.00 2.57
5488 6103 5.244626 AGGCAGCATCTAAAACAGTTCAATT 59.755 36.000 0.00 0.00 0.00 2.32
5489 6104 5.928264 GGCAGCATCTAAAACAGTTCAATTT 59.072 36.000 0.00 0.00 0.00 1.82
5490 6105 6.089954 GGCAGCATCTAAAACAGTTCAATTTC 59.910 38.462 0.00 0.00 0.00 2.17
5491 6106 6.642131 GCAGCATCTAAAACAGTTCAATTTCA 59.358 34.615 0.00 0.00 0.00 2.69
5492 6107 7.148853 GCAGCATCTAAAACAGTTCAATTTCAG 60.149 37.037 0.00 0.00 0.00 3.02
5493 6108 6.865205 AGCATCTAAAACAGTTCAATTTCAGC 59.135 34.615 0.00 0.00 0.00 4.26
5494 6109 6.865205 GCATCTAAAACAGTTCAATTTCAGCT 59.135 34.615 0.00 0.00 0.00 4.24
5495 6110 7.148853 GCATCTAAAACAGTTCAATTTCAGCTG 60.149 37.037 7.63 7.63 0.00 4.24
5496 6111 7.333528 TCTAAAACAGTTCAATTTCAGCTGT 57.666 32.000 14.67 0.00 41.51 4.40
5497 6112 7.417612 TCTAAAACAGTTCAATTTCAGCTGTC 58.582 34.615 14.67 0.00 39.19 3.51
5498 6113 5.841957 AAACAGTTCAATTTCAGCTGTCT 57.158 34.783 14.67 0.00 39.19 3.41
5499 6114 5.841957 AACAGTTCAATTTCAGCTGTCTT 57.158 34.783 14.67 3.02 39.19 3.01
5500 6115 6.942532 AACAGTTCAATTTCAGCTGTCTTA 57.057 33.333 14.67 0.00 39.19 2.10
5501 6116 6.942532 ACAGTTCAATTTCAGCTGTCTTAA 57.057 33.333 14.67 4.81 35.78 1.85
5502 6117 7.333528 ACAGTTCAATTTCAGCTGTCTTAAA 57.666 32.000 14.67 7.20 35.78 1.52
5503 6118 7.196331 ACAGTTCAATTTCAGCTGTCTTAAAC 58.804 34.615 14.67 11.99 35.78 2.01
5504 6119 6.358030 CAGTTCAATTTCAGCTGTCTTAAACG 59.642 38.462 14.67 2.54 0.00 3.60
5505 6120 6.038271 AGTTCAATTTCAGCTGTCTTAAACGT 59.962 34.615 14.67 0.00 0.00 3.99
5506 6121 5.985781 TCAATTTCAGCTGTCTTAAACGTC 58.014 37.500 14.67 0.00 0.00 4.34
5507 6122 5.758296 TCAATTTCAGCTGTCTTAAACGTCT 59.242 36.000 14.67 0.00 0.00 4.18
5508 6123 6.260050 TCAATTTCAGCTGTCTTAAACGTCTT 59.740 34.615 14.67 0.00 0.00 3.01
5509 6124 7.439955 TCAATTTCAGCTGTCTTAAACGTCTTA 59.560 33.333 14.67 0.00 0.00 2.10
5510 6125 6.520792 TTTCAGCTGTCTTAAACGTCTTAC 57.479 37.500 14.67 0.00 0.00 2.34
5511 6126 5.190992 TCAGCTGTCTTAAACGTCTTACA 57.809 39.130 14.67 0.00 0.00 2.41
5512 6127 5.593968 TCAGCTGTCTTAAACGTCTTACAA 58.406 37.500 14.67 0.00 0.00 2.41
5513 6128 6.044046 TCAGCTGTCTTAAACGTCTTACAAA 58.956 36.000 14.67 0.00 0.00 2.83
5514 6129 6.535865 TCAGCTGTCTTAAACGTCTTACAAAA 59.464 34.615 14.67 0.00 0.00 2.44
5515 6130 6.846283 CAGCTGTCTTAAACGTCTTACAAAAG 59.154 38.462 5.25 0.00 0.00 2.27
5516 6131 6.537660 AGCTGTCTTAAACGTCTTACAAAAGT 59.462 34.615 0.00 0.00 34.13 2.66
5517 6132 6.627671 GCTGTCTTAAACGTCTTACAAAAGTG 59.372 38.462 0.00 0.00 34.13 3.16
5518 6133 7.464977 GCTGTCTTAAACGTCTTACAAAAGTGA 60.465 37.037 0.00 0.00 34.13 3.41
5519 6134 8.254178 TGTCTTAAACGTCTTACAAAAGTGAA 57.746 30.769 0.00 0.00 34.13 3.18
5520 6135 8.170553 TGTCTTAAACGTCTTACAAAAGTGAAC 58.829 33.333 0.00 0.00 34.13 3.18
5521 6136 8.170553 GTCTTAAACGTCTTACAAAAGTGAACA 58.829 33.333 0.00 0.00 34.13 3.18
5522 6137 8.719648 TCTTAAACGTCTTACAAAAGTGAACAA 58.280 29.630 0.00 0.00 34.13 2.83
5523 6138 9.332301 CTTAAACGTCTTACAAAAGTGAACAAA 57.668 29.630 0.00 0.00 34.13 2.83
5524 6139 7.790861 AAACGTCTTACAAAAGTGAACAAAG 57.209 32.000 0.00 0.00 34.13 2.77
5525 6140 5.875930 ACGTCTTACAAAAGTGAACAAAGG 58.124 37.500 0.00 0.00 34.13 3.11
5526 6141 5.163693 ACGTCTTACAAAAGTGAACAAAGGG 60.164 40.000 0.00 0.00 34.13 3.95
5527 6142 5.065474 CGTCTTACAAAAGTGAACAAAGGGA 59.935 40.000 0.00 0.00 34.13 4.20
5528 6143 6.495706 GTCTTACAAAAGTGAACAAAGGGAG 58.504 40.000 0.00 0.00 34.13 4.30
5543 6158 8.611051 AACAAAGGGAGTAGTATTATCTGAGT 57.389 34.615 0.00 0.00 0.00 3.41
5546 6161 8.356657 CAAAGGGAGTAGTATTATCTGAGTGAG 58.643 40.741 0.00 0.00 0.00 3.51
5698 6327 0.984230 TGATCTTCCACCCCTGTGTC 59.016 55.000 0.00 0.00 41.09 3.67
5752 6382 3.209429 GCATCAAGCGAATGTCACG 57.791 52.632 0.00 0.00 0.00 4.35
5812 6447 1.879380 CGGCAAAGAAGATCCACAACA 59.121 47.619 0.00 0.00 0.00 3.33
5820 6455 7.172019 GCAAAGAAGATCCACAACAAATTTCAT 59.828 33.333 0.00 0.00 0.00 2.57
5824 6459 5.797051 AGATCCACAACAAATTTCATTGGG 58.203 37.500 13.63 10.43 34.56 4.12
5858 6493 6.803154 ACATCTGCTGTAAAAACTACTTCC 57.197 37.500 0.00 0.00 35.91 3.46
5889 6524 0.892755 ATAACTGTCGCTCAACCGGA 59.107 50.000 9.46 0.00 0.00 5.14
5890 6525 0.038892 TAACTGTCGCTCAACCGGAC 60.039 55.000 9.46 0.00 0.00 4.79
5948 8297 8.956426 CATAAACATGCTTAAGTTAAGGGAAGA 58.044 33.333 21.36 0.00 36.31 2.87
5950 8299 7.833285 AACATGCTTAAGTTAAGGGAAGAAA 57.167 32.000 21.36 0.00 36.31 2.52
5972 8321 6.655078 AAAAAGGAGCACTGACATAAACAT 57.345 33.333 0.00 0.00 0.00 2.71
5973 8322 5.633830 AAAGGAGCACTGACATAAACATG 57.366 39.130 0.00 0.00 0.00 3.21
5975 8324 3.012518 GGAGCACTGACATAAACATGCT 58.987 45.455 0.00 0.00 45.70 3.79
5978 8327 5.123820 GGAGCACTGACATAAACATGCTTAA 59.876 40.000 0.00 0.00 43.20 1.85
5986 9620 8.856153 TGACATAAACATGCTTAAGTTAAGGA 57.144 30.769 21.36 19.66 40.45 3.36
6062 9703 4.314961 CACTGTACACCAGCATCTACAAA 58.685 43.478 0.00 0.00 45.68 2.83
6064 9705 5.412594 CACTGTACACCAGCATCTACAAAAT 59.587 40.000 0.00 0.00 45.68 1.82
6098 9747 0.036164 GACCTACACCACACATGCCA 59.964 55.000 0.00 0.00 0.00 4.92
6117 9768 4.344102 TGCCAATCTACACATCTACCTACC 59.656 45.833 0.00 0.00 0.00 3.18
6185 9836 0.244994 AACTCTCCGTGCTACTGCTG 59.755 55.000 0.00 0.00 40.48 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 82 1.066286 GCTGAAGCAGTGGATGAGAGT 60.066 52.381 0.00 0.00 41.59 3.24
171 362 3.395639 ACAGCTTGCAAACAATCAATGG 58.604 40.909 0.00 0.00 34.61 3.16
218 410 2.812011 GCTGTTACAACTTTCCGTGGAT 59.188 45.455 0.00 0.00 0.00 3.41
272 465 3.670055 GTGAAACAAAATGACCTGCATCG 59.330 43.478 0.00 0.00 33.99 3.84
275 468 3.698539 TCAGTGAAACAAAATGACCTGCA 59.301 39.130 0.00 0.00 41.43 4.41
358 551 3.554934 TCAAGCCAACAAAGAGTGTGAT 58.445 40.909 0.00 0.00 40.60 3.06
420 613 2.033141 CTGCCAGTGGACCACCTG 59.967 66.667 21.32 16.95 34.49 4.00
421 614 3.252284 CCTGCCAGTGGACCACCT 61.252 66.667 21.32 5.90 34.49 4.00
542 735 1.874019 CGTCTGCCGTTCGATGAGG 60.874 63.158 0.00 0.00 0.00 3.86
575 768 1.447838 CACGTGGCGCCAGTAGATT 60.448 57.895 33.73 7.53 0.00 2.40
602 795 1.595929 GGGAAGCGACGGTCAACAA 60.596 57.895 9.10 0.00 0.00 2.83
605 798 3.562779 GACGGGAAGCGACGGTCAA 62.563 63.158 9.10 0.00 37.88 3.18
608 801 2.647680 TTTTGACGGGAAGCGACGGT 62.648 55.000 0.00 0.00 0.00 4.83
754 1162 1.942223 GTGTCGCCCACGTTTTTGC 60.942 57.895 0.00 0.00 41.18 3.68
815 1225 3.434319 GTGGTCATGTGCTGGGCG 61.434 66.667 0.00 0.00 0.00 6.13
826 1236 3.704100 CCACTGACATGTGTGGTCA 57.296 52.632 21.68 5.73 46.18 4.02
831 1241 2.727123 TTTCACCCACTGACATGTGT 57.273 45.000 1.15 0.00 36.30 3.72
1838 2256 0.532115 GCCAAATTACCAGCCACCAG 59.468 55.000 0.00 0.00 0.00 4.00
1843 2261 2.944129 TCTATGGCCAAATTACCAGCC 58.056 47.619 10.96 0.00 45.96 4.85
2101 2553 7.448469 AGAATTACAGGTTCTTGCACTAATTGT 59.552 33.333 0.00 0.00 32.17 2.71
2125 2577 4.809673 AGCATCGATTTGACGCATATAGA 58.190 39.130 0.00 0.00 38.54 1.98
2297 2750 1.890489 TGCACTACTCTAGTTTCGCCA 59.110 47.619 0.00 0.00 36.76 5.69
2455 2917 4.843220 AGTAAACCCTACGATATGGACG 57.157 45.455 0.00 0.00 0.00 4.79
2547 3014 6.154021 ACCTGTAAATAGGCTCTAGACGAAAA 59.846 38.462 0.00 0.00 41.75 2.29
2580 3047 8.650714 CCAGTAAAACAAATACTCCGTACTTAC 58.349 37.037 0.00 0.00 31.33 2.34
2616 3083 4.678509 TTCTCCATGCACGAAATGTTAC 57.321 40.909 0.00 0.00 0.00 2.50
2690 3162 7.761249 GCATTGGTTTTATAATGAAAGCACTCT 59.239 33.333 5.38 0.00 42.21 3.24
2692 3164 6.818142 GGCATTGGTTTTATAATGAAAGCACT 59.182 34.615 5.38 0.00 42.21 4.40
2693 3165 6.593382 TGGCATTGGTTTTATAATGAAAGCAC 59.407 34.615 5.38 0.00 42.21 4.40
2694 3166 6.705302 TGGCATTGGTTTTATAATGAAAGCA 58.295 32.000 0.00 2.32 41.21 3.91
2695 3167 7.413988 GGTTGGCATTGGTTTTATAATGAAAGC 60.414 37.037 0.00 0.00 36.61 3.51
2759 3231 6.296026 AGGATAGTTAACTTTGAGCACAACA 58.704 36.000 14.49 0.00 35.63 3.33
2769 3241 6.824196 GCTTTCCTGCTAGGATAGTTAACTTT 59.176 38.462 14.49 5.76 45.34 2.66
2827 3299 9.084533 TGGGTTTTGTTTAGTTAAGATAGCATT 57.915 29.630 0.00 0.00 0.00 3.56
2847 3319 4.885325 CACTGTTACTTGTAGGTTGGGTTT 59.115 41.667 0.00 0.00 0.00 3.27
2880 3368 6.248631 GCCAGTAGATAAAACAGCTTTAACG 58.751 40.000 0.00 0.00 33.20 3.18
2941 3429 3.244875 ACTGCACATACCATGGAAGTTCA 60.245 43.478 21.47 12.66 33.60 3.18
2994 3482 9.538508 AAGAAATGCTGGATGAATTTAATTAGC 57.461 29.630 3.28 3.28 34.16 3.09
3027 3515 5.961395 TTTTCGAGTCGCCATAATAGTTC 57.039 39.130 7.92 0.00 0.00 3.01
3415 3903 7.233348 AGGTCAATATTATGGGGCACTTTATTG 59.767 37.037 0.00 0.00 0.00 1.90
3486 4057 6.882610 AATCTCAATCAACAGTGCAAACTA 57.117 33.333 0.00 0.00 0.00 2.24
3615 4186 4.814771 ACTAGGCGCCTATCAATTAAACAC 59.185 41.667 35.29 0.00 0.00 3.32
3645 4216 9.027129 TGAAATAAAGTACGATTATTCCAGTCG 57.973 33.333 15.54 0.00 40.91 4.18
3879 4451 0.740737 AAGGCAGTTATCGCATTGGC 59.259 50.000 0.00 0.00 31.16 4.52
3886 4458 8.612619 ACTTCAAATATACAAAGGCAGTTATCG 58.387 33.333 0.00 0.00 0.00 2.92
3913 4514 7.229907 GGTTTTGGGACTGAGATACAAGTTTTA 59.770 37.037 0.00 0.00 0.00 1.52
3937 4538 6.595682 CAGAAATGGGATATACTGAGTTGGT 58.404 40.000 0.00 0.00 0.00 3.67
3976 4579 6.573664 TTGAAATGAACATGTAGAACTGGG 57.426 37.500 0.00 0.00 0.00 4.45
4118 4721 6.430000 CCCCCAACGACTTATATTTAGGAATG 59.570 42.308 0.00 0.00 0.00 2.67
4119 4722 6.330778 TCCCCCAACGACTTATATTTAGGAAT 59.669 38.462 0.00 0.00 0.00 3.01
4146 4749 1.560505 TAAGTCGTTGGGGGAGTACC 58.439 55.000 0.00 0.00 39.11 3.34
4147 4750 5.541953 AATATAAGTCGTTGGGGGAGTAC 57.458 43.478 0.00 0.00 0.00 2.73
4148 4751 6.268387 CCTAAATATAAGTCGTTGGGGGAGTA 59.732 42.308 0.00 0.00 0.00 2.59
4150 4753 5.306160 TCCTAAATATAAGTCGTTGGGGGAG 59.694 44.000 0.00 0.00 0.00 4.30
4152 4755 5.556006 TCCTAAATATAAGTCGTTGGGGG 57.444 43.478 0.00 0.00 0.00 5.40
4153 4756 6.350906 TGTTCCTAAATATAAGTCGTTGGGG 58.649 40.000 0.00 0.00 0.00 4.96
4154 4757 7.270047 TCTGTTCCTAAATATAAGTCGTTGGG 58.730 38.462 0.00 0.00 0.00 4.12
4155 4758 8.765219 CATCTGTTCCTAAATATAAGTCGTTGG 58.235 37.037 0.00 0.00 0.00 3.77
4156 4759 8.765219 CCATCTGTTCCTAAATATAAGTCGTTG 58.235 37.037 0.00 0.00 0.00 4.10
4157 4760 8.701895 TCCATCTGTTCCTAAATATAAGTCGTT 58.298 33.333 0.00 0.00 0.00 3.85
4158 4761 8.246430 TCCATCTGTTCCTAAATATAAGTCGT 57.754 34.615 0.00 0.00 0.00 4.34
4159 4762 8.361139 ACTCCATCTGTTCCTAAATATAAGTCG 58.639 37.037 0.00 0.00 0.00 4.18
4165 4768 9.213777 TCTTGTACTCCATCTGTTCCTAAATAT 57.786 33.333 0.00 0.00 0.00 1.28
4166 4769 8.603898 TCTTGTACTCCATCTGTTCCTAAATA 57.396 34.615 0.00 0.00 0.00 1.40
4167 4770 7.496346 TCTTGTACTCCATCTGTTCCTAAAT 57.504 36.000 0.00 0.00 0.00 1.40
4168 4771 6.928348 TCTTGTACTCCATCTGTTCCTAAA 57.072 37.500 0.00 0.00 0.00 1.85
4169 4772 8.783660 ATATCTTGTACTCCATCTGTTCCTAA 57.216 34.615 0.00 0.00 0.00 2.69
4170 4773 8.783660 AATATCTTGTACTCCATCTGTTCCTA 57.216 34.615 0.00 0.00 0.00 2.94
4171 4774 7.682787 AATATCTTGTACTCCATCTGTTCCT 57.317 36.000 0.00 0.00 0.00 3.36
4172 4775 9.429359 CATAATATCTTGTACTCCATCTGTTCC 57.571 37.037 0.00 0.00 0.00 3.62
4290 4893 2.173669 CACCAATAGCGTCCCTGCG 61.174 63.158 0.00 0.00 40.67 5.18
4298 4901 5.348986 ACAACACTAGATACACCAATAGCG 58.651 41.667 0.00 0.00 0.00 4.26
4451 5054 2.878406 CGACACAATTCCAAGGTCTGTT 59.122 45.455 0.00 0.00 0.00 3.16
4562 5165 5.348986 TGACTCGCAAATAGATAGTGAACC 58.651 41.667 0.00 0.00 0.00 3.62
4812 5415 2.629051 CCTTTTCCGTCCTGTATGTCC 58.371 52.381 0.00 0.00 0.00 4.02
4953 5557 5.419542 GTTACTGACCATGTGAGCTAATCA 58.580 41.667 0.00 0.00 34.79 2.57
5019 5623 2.381911 ACAAAGCCCAGCCTGAATATG 58.618 47.619 0.00 0.00 0.00 1.78
5181 5785 3.331889 ACAGACCACCAAAGGAAGATCAT 59.668 43.478 0.00 0.00 0.00 2.45
5229 5833 3.540211 CCGAAGGCTTGACACAGAT 57.460 52.632 3.46 0.00 46.14 2.90
5301 5906 1.605710 CACCAAACTGTTCAGCTCTGG 59.394 52.381 5.39 5.39 0.00 3.86
5424 6039 3.113260 ACAAAAGTGAACGAGAGGGAG 57.887 47.619 0.00 0.00 0.00 4.30
5426 6041 4.448060 GTCTTACAAAAGTGAACGAGAGGG 59.552 45.833 0.00 0.00 34.13 4.30
5427 6042 4.448060 GGTCTTACAAAAGTGAACGAGAGG 59.552 45.833 0.00 0.00 34.13 3.69
5429 6044 5.272283 AGGTCTTACAAAAGTGAACGAGA 57.728 39.130 0.00 0.00 34.13 4.04
5430 6045 5.986004 AAGGTCTTACAAAAGTGAACGAG 57.014 39.130 0.00 0.00 34.13 4.18
5431 6046 6.746745 AAAAGGTCTTACAAAAGTGAACGA 57.253 33.333 0.00 0.00 34.13 3.85
5432 6047 7.849515 GTCTAAAAGGTCTTACAAAAGTGAACG 59.150 37.037 0.00 0.00 34.13 3.95
5433 6048 8.671028 TGTCTAAAAGGTCTTACAAAAGTGAAC 58.329 33.333 0.00 0.00 34.13 3.18
5434 6049 8.795842 TGTCTAAAAGGTCTTACAAAAGTGAA 57.204 30.769 0.00 0.00 34.13 3.18
5435 6050 8.974060 ATGTCTAAAAGGTCTTACAAAAGTGA 57.026 30.769 0.00 0.00 34.13 3.41
5441 6056 8.789762 GCCTTAAATGTCTAAAAGGTCTTACAA 58.210 33.333 0.00 0.00 40.55 2.41
5442 6057 7.940137 TGCCTTAAATGTCTAAAAGGTCTTACA 59.060 33.333 0.00 0.00 40.55 2.41
5443 6058 8.331730 TGCCTTAAATGTCTAAAAGGTCTTAC 57.668 34.615 0.00 0.00 40.55 2.34
5444 6059 7.120726 GCTGCCTTAAATGTCTAAAAGGTCTTA 59.879 37.037 0.00 0.00 40.55 2.10
5445 6060 6.071896 GCTGCCTTAAATGTCTAAAAGGTCTT 60.072 38.462 0.00 0.00 40.55 3.01
5446 6061 5.416013 GCTGCCTTAAATGTCTAAAAGGTCT 59.584 40.000 0.00 0.00 40.55 3.85
5447 6062 5.183140 TGCTGCCTTAAATGTCTAAAAGGTC 59.817 40.000 0.00 0.00 40.55 3.85
5448 6063 5.076873 TGCTGCCTTAAATGTCTAAAAGGT 58.923 37.500 0.00 0.00 40.55 3.50
5449 6064 5.643379 TGCTGCCTTAAATGTCTAAAAGG 57.357 39.130 0.00 0.00 41.23 3.11
5450 6065 7.093322 AGATGCTGCCTTAAATGTCTAAAAG 57.907 36.000 0.00 0.00 0.00 2.27
5451 6066 8.574251 TTAGATGCTGCCTTAAATGTCTAAAA 57.426 30.769 0.00 0.00 0.00 1.52
5452 6067 8.574251 TTTAGATGCTGCCTTAAATGTCTAAA 57.426 30.769 0.00 0.00 35.66 1.85
5453 6068 8.458843 GTTTTAGATGCTGCCTTAAATGTCTAA 58.541 33.333 0.00 0.00 0.00 2.10
5454 6069 7.609918 TGTTTTAGATGCTGCCTTAAATGTCTA 59.390 33.333 0.00 0.00 0.00 2.59
5455 6070 6.434028 TGTTTTAGATGCTGCCTTAAATGTCT 59.566 34.615 0.00 0.00 0.00 3.41
5456 6071 6.620678 TGTTTTAGATGCTGCCTTAAATGTC 58.379 36.000 0.00 0.00 0.00 3.06
5457 6072 6.209391 ACTGTTTTAGATGCTGCCTTAAATGT 59.791 34.615 0.00 0.00 0.00 2.71
5458 6073 6.624423 ACTGTTTTAGATGCTGCCTTAAATG 58.376 36.000 0.00 0.00 0.00 2.32
5459 6074 6.840780 ACTGTTTTAGATGCTGCCTTAAAT 57.159 33.333 0.00 0.00 0.00 1.40
5460 6075 6.264292 TGAACTGTTTTAGATGCTGCCTTAAA 59.736 34.615 0.00 0.00 0.00 1.52
5461 6076 5.767665 TGAACTGTTTTAGATGCTGCCTTAA 59.232 36.000 0.00 0.00 0.00 1.85
5462 6077 5.312895 TGAACTGTTTTAGATGCTGCCTTA 58.687 37.500 0.00 0.00 0.00 2.69
5463 6078 4.144297 TGAACTGTTTTAGATGCTGCCTT 58.856 39.130 0.00 0.00 0.00 4.35
5464 6079 3.754965 TGAACTGTTTTAGATGCTGCCT 58.245 40.909 0.00 0.00 0.00 4.75
5465 6080 4.503741 TTGAACTGTTTTAGATGCTGCC 57.496 40.909 0.00 0.00 0.00 4.85
5466 6081 6.642131 TGAAATTGAACTGTTTTAGATGCTGC 59.358 34.615 0.00 0.00 0.00 5.25
5467 6082 7.148853 GCTGAAATTGAACTGTTTTAGATGCTG 60.149 37.037 0.00 0.00 0.00 4.41
5468 6083 6.865205 GCTGAAATTGAACTGTTTTAGATGCT 59.135 34.615 0.00 0.00 0.00 3.79
5469 6084 6.865205 AGCTGAAATTGAACTGTTTTAGATGC 59.135 34.615 0.00 0.00 0.00 3.91
5470 6085 7.864379 ACAGCTGAAATTGAACTGTTTTAGATG 59.136 33.333 23.35 6.40 40.74 2.90
5471 6086 7.945134 ACAGCTGAAATTGAACTGTTTTAGAT 58.055 30.769 23.35 0.00 38.38 1.98
5472 6087 7.283127 AGACAGCTGAAATTGAACTGTTTTAGA 59.717 33.333 23.35 0.00 41.45 2.10
5473 6088 7.420800 AGACAGCTGAAATTGAACTGTTTTAG 58.579 34.615 23.35 0.00 41.45 1.85
5474 6089 7.333528 AGACAGCTGAAATTGAACTGTTTTA 57.666 32.000 23.35 0.00 41.45 1.52
5475 6090 6.212888 AGACAGCTGAAATTGAACTGTTTT 57.787 33.333 23.35 0.00 41.45 2.43
5476 6091 5.841957 AGACAGCTGAAATTGAACTGTTT 57.158 34.783 23.35 0.00 41.45 2.83
5477 6092 5.841957 AAGACAGCTGAAATTGAACTGTT 57.158 34.783 23.35 0.00 41.45 3.16
5478 6093 6.942532 TTAAGACAGCTGAAATTGAACTGT 57.057 33.333 23.35 0.00 43.93 3.55
5479 6094 6.358030 CGTTTAAGACAGCTGAAATTGAACTG 59.642 38.462 23.35 14.61 27.41 3.16
5480 6095 6.038271 ACGTTTAAGACAGCTGAAATTGAACT 59.962 34.615 23.35 10.82 27.41 3.01
5481 6096 6.199393 ACGTTTAAGACAGCTGAAATTGAAC 58.801 36.000 23.35 20.12 27.41 3.18
5482 6097 6.260050 AGACGTTTAAGACAGCTGAAATTGAA 59.740 34.615 23.35 11.43 27.41 2.69
5483 6098 5.758296 AGACGTTTAAGACAGCTGAAATTGA 59.242 36.000 23.35 5.74 27.41 2.57
5484 6099 5.990408 AGACGTTTAAGACAGCTGAAATTG 58.010 37.500 23.35 9.51 27.41 2.32
5485 6100 6.619801 AAGACGTTTAAGACAGCTGAAATT 57.380 33.333 23.35 13.76 27.41 1.82
5486 6101 6.704493 TGTAAGACGTTTAAGACAGCTGAAAT 59.296 34.615 23.35 7.92 27.41 2.17
5487 6102 6.044046 TGTAAGACGTTTAAGACAGCTGAAA 58.956 36.000 23.35 7.52 0.00 2.69
5488 6103 5.593968 TGTAAGACGTTTAAGACAGCTGAA 58.406 37.500 23.35 0.04 0.00 3.02
5489 6104 5.190992 TGTAAGACGTTTAAGACAGCTGA 57.809 39.130 23.35 0.00 0.00 4.26
5490 6105 5.900339 TTGTAAGACGTTTAAGACAGCTG 57.100 39.130 13.48 13.48 0.00 4.24
5491 6106 6.537660 ACTTTTGTAAGACGTTTAAGACAGCT 59.462 34.615 0.00 0.00 35.30 4.24
5492 6107 6.627671 CACTTTTGTAAGACGTTTAAGACAGC 59.372 38.462 0.00 0.00 35.30 4.40
5493 6108 7.902032 TCACTTTTGTAAGACGTTTAAGACAG 58.098 34.615 0.00 0.00 35.30 3.51
5494 6109 7.830940 TCACTTTTGTAAGACGTTTAAGACA 57.169 32.000 0.00 0.00 35.30 3.41
5495 6110 8.170553 TGTTCACTTTTGTAAGACGTTTAAGAC 58.829 33.333 0.00 0.00 35.30 3.01
5496 6111 8.254178 TGTTCACTTTTGTAAGACGTTTAAGA 57.746 30.769 0.00 0.00 35.30 2.10
5497 6112 8.883789 TTGTTCACTTTTGTAAGACGTTTAAG 57.116 30.769 0.00 0.00 35.30 1.85
5498 6113 9.332301 CTTTGTTCACTTTTGTAAGACGTTTAA 57.668 29.630 0.00 0.00 35.30 1.52
5499 6114 7.964011 CCTTTGTTCACTTTTGTAAGACGTTTA 59.036 33.333 0.00 0.00 35.30 2.01
5500 6115 6.804783 CCTTTGTTCACTTTTGTAAGACGTTT 59.195 34.615 0.00 0.00 35.30 3.60
5501 6116 6.319399 CCTTTGTTCACTTTTGTAAGACGTT 58.681 36.000 0.00 0.00 35.30 3.99
5502 6117 5.163693 CCCTTTGTTCACTTTTGTAAGACGT 60.164 40.000 0.00 0.00 35.30 4.34
5503 6118 5.065474 TCCCTTTGTTCACTTTTGTAAGACG 59.935 40.000 0.00 0.00 35.30 4.18
5504 6119 6.095021 ACTCCCTTTGTTCACTTTTGTAAGAC 59.905 38.462 0.00 0.00 35.30 3.01
5505 6120 6.184789 ACTCCCTTTGTTCACTTTTGTAAGA 58.815 36.000 0.00 0.00 35.30 2.10
5506 6121 6.451064 ACTCCCTTTGTTCACTTTTGTAAG 57.549 37.500 0.00 0.00 37.40 2.34
5507 6122 7.114095 ACTACTCCCTTTGTTCACTTTTGTAA 58.886 34.615 0.00 0.00 0.00 2.41
5508 6123 6.655930 ACTACTCCCTTTGTTCACTTTTGTA 58.344 36.000 0.00 0.00 0.00 2.41
5509 6124 5.506708 ACTACTCCCTTTGTTCACTTTTGT 58.493 37.500 0.00 0.00 0.00 2.83
5510 6125 7.745620 ATACTACTCCCTTTGTTCACTTTTG 57.254 36.000 0.00 0.00 0.00 2.44
5512 6127 9.668497 GATAATACTACTCCCTTTGTTCACTTT 57.332 33.333 0.00 0.00 0.00 2.66
5513 6128 9.047947 AGATAATACTACTCCCTTTGTTCACTT 57.952 33.333 0.00 0.00 0.00 3.16
5514 6129 8.478877 CAGATAATACTACTCCCTTTGTTCACT 58.521 37.037 0.00 0.00 0.00 3.41
5515 6130 8.475639 TCAGATAATACTACTCCCTTTGTTCAC 58.524 37.037 0.00 0.00 0.00 3.18
5516 6131 8.603898 TCAGATAATACTACTCCCTTTGTTCA 57.396 34.615 0.00 0.00 0.00 3.18
5517 6132 8.697292 ACTCAGATAATACTACTCCCTTTGTTC 58.303 37.037 0.00 0.00 0.00 3.18
5518 6133 8.478877 CACTCAGATAATACTACTCCCTTTGTT 58.521 37.037 0.00 0.00 0.00 2.83
5519 6134 7.839705 TCACTCAGATAATACTACTCCCTTTGT 59.160 37.037 0.00 0.00 0.00 2.83
5520 6135 8.239038 TCACTCAGATAATACTACTCCCTTTG 57.761 38.462 0.00 0.00 0.00 2.77
5521 6136 7.507616 CCTCACTCAGATAATACTACTCCCTTT 59.492 40.741 0.00 0.00 0.00 3.11
5522 6137 7.007723 CCTCACTCAGATAATACTACTCCCTT 58.992 42.308 0.00 0.00 0.00 3.95
5523 6138 6.333168 TCCTCACTCAGATAATACTACTCCCT 59.667 42.308 0.00 0.00 0.00 4.20
5524 6139 6.544650 TCCTCACTCAGATAATACTACTCCC 58.455 44.000 0.00 0.00 0.00 4.30
5525 6140 8.644374 ATTCCTCACTCAGATAATACTACTCC 57.356 38.462 0.00 0.00 0.00 3.85
5526 6141 8.447833 CGATTCCTCACTCAGATAATACTACTC 58.552 40.741 0.00 0.00 0.00 2.59
5527 6142 8.158132 TCGATTCCTCACTCAGATAATACTACT 58.842 37.037 0.00 0.00 0.00 2.57
5528 6143 8.325421 TCGATTCCTCACTCAGATAATACTAC 57.675 38.462 0.00 0.00 0.00 2.73
5543 6158 1.141881 GGAGCGCTTCGATTCCTCA 59.858 57.895 13.26 0.00 32.29 3.86
5546 6161 0.741221 ACTTGGAGCGCTTCGATTCC 60.741 55.000 13.26 7.93 34.41 3.01
5587 6202 5.857517 AGCTGCACATTTGTTTTTGTTTTTG 59.142 32.000 1.02 0.00 0.00 2.44
5698 6327 1.538634 CCTTTTGGGTGTGTGTGCATG 60.539 52.381 0.00 0.00 35.46 4.06
5709 6338 5.428184 TTGTGTGATTTTTCCTTTTGGGT 57.572 34.783 0.00 0.00 40.87 4.51
5710 6339 6.727215 CAATTGTGTGATTTTTCCTTTTGGG 58.273 36.000 0.00 0.00 40.87 4.12
5743 6373 1.726791 ACATCGCAGTTCGTGACATTC 59.273 47.619 0.00 0.00 36.83 2.67
5752 6382 1.600957 CATGGATGGACATCGCAGTTC 59.399 52.381 6.24 0.00 38.69 3.01
5812 6447 2.840038 GGAGGAAGGCCCAATGAAATTT 59.160 45.455 0.00 0.00 31.22 1.82
5820 6455 0.039618 GATGTTGGAGGAAGGCCCAA 59.960 55.000 0.00 0.00 39.88 4.12
5824 6459 0.034670 AGCAGATGTTGGAGGAAGGC 60.035 55.000 0.00 0.00 0.00 4.35
5858 6493 3.103738 CGACAGTTATTTACGGACGGAG 58.896 50.000 0.00 0.00 36.75 4.63
5889 6524 4.124970 GTTCAACCAAGAGAACCTTACGT 58.875 43.478 0.00 0.00 38.49 3.57
5890 6525 4.377897 AGTTCAACCAAGAGAACCTTACG 58.622 43.478 0.00 0.00 43.89 3.18
5950 8299 5.565439 GCATGTTTATGTCAGTGCTCCTTTT 60.565 40.000 0.00 0.00 36.65 2.27
5953 8302 3.012518 GCATGTTTATGTCAGTGCTCCT 58.987 45.455 0.00 0.00 36.65 3.69
5954 8303 3.012518 AGCATGTTTATGTCAGTGCTCC 58.987 45.455 0.00 0.00 38.43 4.70
5956 8305 5.707298 ACTTAAGCATGTTTATGTCAGTGCT 59.293 36.000 13.01 0.00 44.05 4.40
5957 8306 5.942872 ACTTAAGCATGTTTATGTCAGTGC 58.057 37.500 13.01 0.00 36.65 4.40
5959 8308 8.730680 CCTTAACTTAAGCATGTTTATGTCAGT 58.269 33.333 17.31 9.15 36.65 3.41
5961 8310 8.856153 TCCTTAACTTAAGCATGTTTATGTCA 57.144 30.769 17.31 4.65 36.65 3.58
6088 9737 3.943381 AGATGTGTAGATTGGCATGTGTG 59.057 43.478 0.00 0.00 0.00 3.82
6098 9747 6.485984 CACGTAGGTAGGTAGATGTGTAGATT 59.514 42.308 0.00 0.00 0.00 2.40
6179 9830 4.873810 TGTTGGCGGTGCAGCAGT 62.874 61.111 17.33 0.00 39.27 4.40


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

AutoCloner maintained by Alex Coulton.