Multiple sequence alignment - TraesCS6A01G091700

Loading Multiple Alignment...

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 TraesCS6A01G091700 chr6A 100.000 5779 0 0 1 5779 60227705 60221927 0.000000e+00 10672
1 TraesCS6A01G091700 chr6A 82.533 1729 272 26 3089 4798 530122346 530124063 0.000000e+00 1493
2 TraesCS6A01G091700 chr6A 79.688 256 39 9 2623 2871 530121893 530122142 7.700000e-39 172
3 TraesCS6A01G091700 chr6A 88.764 89 6 2 169 254 530119526 530119613 7.920000e-19 106
4 TraesCS6A01G091700 chr6B 93.689 2868 120 27 2309 5142 114510086 114507246 0.000000e+00 4237
5 TraesCS6A01G091700 chr6B 91.086 2109 110 43 84 2152 114512189 114510119 0.000000e+00 2782
6 TraesCS6A01G091700 chr6B 82.139 1730 276 24 3089 4798 576017681 576019397 0.000000e+00 1452
7 TraesCS6A01G091700 chr6B 79.688 256 39 9 2623 2871 576017228 576017477 7.700000e-39 172
8 TraesCS6A01G091700 chr6B 95.238 84 4 0 4 87 114512304 114512221 3.630000e-27 134
9 TraesCS6A01G091700 chr6B 88.764 89 6 3 169 254 576014603 576014690 7.920000e-19 106
10 TraesCS6A01G091700 chr6D 94.146 2306 108 14 2872 5161 46051050 46048756 0.000000e+00 3485
11 TraesCS6A01G091700 chr6D 94.204 1294 40 18 1536 2806 46052339 46051058 0.000000e+00 1941
12 TraesCS6A01G091700 chr6D 82.649 1729 270 26 3089 4798 385663879 385665596 0.000000e+00 1504
13 TraesCS6A01G091700 chr6D 90.449 869 52 20 669 1525 46053253 46052404 0.000000e+00 1116
14 TraesCS6A01G091700 chr6D 93.409 531 22 5 85 610 46053776 46053254 0.000000e+00 774
15 TraesCS6A01G091700 chr6D 91.949 472 33 4 5151 5619 46046154 46045685 0.000000e+00 656
16 TraesCS6A01G091700 chr5A 94.643 168 5 1 5616 5779 323384983 323385150 2.070000e-64 257
17 TraesCS6A01G091700 chr5A 94.479 163 9 0 5617 5779 656496467 656496629 9.610000e-63 252
18 TraesCS6A01G091700 chr3A 95.625 160 7 0 5620 5779 90142547 90142706 2.070000e-64 257
19 TraesCS6A01G091700 chr3A 95.062 162 6 2 5619 5779 17703410 17703570 2.670000e-63 254
20 TraesCS6A01G091700 chr2A 94.012 167 8 2 5614 5779 694055027 694055192 9.610000e-63 252
21 TraesCS6A01G091700 chr1A 95.000 160 8 0 5620 5779 55760157 55759998 9.610000e-63 252
22 TraesCS6A01G091700 chr1A 95.031 161 7 1 5620 5779 56480344 56480184 9.610000e-63 252
23 TraesCS6A01G091700 chr5B 93.902 164 10 0 5616 5779 198132992 198132829 1.240000e-61 248
24 TraesCS6A01G091700 chr4A 93.452 168 10 1 5613 5779 179809540 179809707 1.240000e-61 248


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 TraesCS6A01G091700 chr6A 60221927 60227705 5778 True 10672.000000 10672 100.000000 1 5779 1 chr6A.!!$R1 5778
1 TraesCS6A01G091700 chr6A 530119526 530124063 4537 False 590.333333 1493 83.661667 169 4798 3 chr6A.!!$F1 4629
2 TraesCS6A01G091700 chr6B 114507246 114512304 5058 True 2384.333333 4237 93.337667 4 5142 3 chr6B.!!$R1 5138
3 TraesCS6A01G091700 chr6B 576014603 576019397 4794 False 576.666667 1452 83.530333 169 4798 3 chr6B.!!$F1 4629
4 TraesCS6A01G091700 chr6D 46045685 46053776 8091 True 1594.400000 3485 92.831400 85 5619 5 chr6D.!!$R1 5534
5 TraesCS6A01G091700 chr6D 385663879 385665596 1717 False 1504.000000 1504 82.649000 3089 4798 1 chr6D.!!$F1 1709

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
576 868 0.241749 ACGTATCCTTTGTCGACGCA 59.758 50.000 11.62 0.0 37.02 5.24 F
2251 3491 0.235665 AAGAAAGTCATGCACGCACG 59.764 50.000 0.00 0.0 0.00 5.34 F
2328 3568 0.606604 ACTTGCGGACGTTCTGGTAT 59.393 50.000 0.00 0.0 0.00 2.73 F
3241 4518 2.224769 ACCCATCCAACAAGTCGATGTT 60.225 45.455 0.00 0.0 44.08 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2328 3568 1.482177 CCCCCAATTCCACACTTCCAA 60.482 52.381 0.00 0.0 0.0 3.53 R
3307 4584 0.238289 CGTTCTTTGCGGCATCAACT 59.762 50.000 2.28 0.0 0.0 3.16 R
3491 4768 1.694048 CCTACCCTCTCTGGCCTTCAT 60.694 57.143 3.32 0.0 0.0 2.57 R
5226 9138 0.033894 GGGCGTGGATTAAAAGGGGA 60.034 55.000 0.00 0.0 0.0 4.81 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
60 61 4.953940 ACCAGCTTCCAAAATGCTAAAA 57.046 36.364 0.00 0.00 35.05 1.52
63 64 6.298361 ACCAGCTTCCAAAATGCTAAAATTT 58.702 32.000 0.00 0.00 35.05 1.82
69 70 7.622048 GCTTCCAAAATGCTAAAATTTCTTCCG 60.622 37.037 0.00 0.00 0.00 4.30
109 147 5.986004 AACTAACGGCTAAATGCATCTAC 57.014 39.130 0.00 0.00 45.15 2.59
228 268 2.765807 CCTCCTGGGCTCGATGGT 60.766 66.667 0.00 0.00 0.00 3.55
233 273 1.883084 CTGGGCTCGATGGTTACGC 60.883 63.158 0.00 0.00 0.00 4.42
263 303 2.126189 GGTGACGGACGGCTGTAC 60.126 66.667 0.45 0.00 32.58 2.90
317 359 3.001330 CGAAGGAACGCTCATGGAAATAC 59.999 47.826 0.00 0.00 0.00 1.89
371 422 1.348538 CGTACGCTGCCATCGAACAA 61.349 55.000 0.52 0.00 0.00 2.83
377 428 1.401539 GCTGCCATCGAACAAAAGACC 60.402 52.381 0.00 0.00 0.00 3.85
405 456 1.012486 GTCCGGTCGCGTTGATTTCT 61.012 55.000 5.77 0.00 0.00 2.52
415 466 3.125316 CGCGTTGATTTCTAGCTCCTTTT 59.875 43.478 0.00 0.00 0.00 2.27
417 468 5.089411 GCGTTGATTTCTAGCTCCTTTTTC 58.911 41.667 0.00 0.00 0.00 2.29
418 469 5.631992 CGTTGATTTCTAGCTCCTTTTTCC 58.368 41.667 0.00 0.00 0.00 3.13
419 470 5.631992 GTTGATTTCTAGCTCCTTTTTCCG 58.368 41.667 0.00 0.00 0.00 4.30
420 471 4.261801 TGATTTCTAGCTCCTTTTTCCGG 58.738 43.478 0.00 0.00 0.00 5.14
421 472 3.782656 TTTCTAGCTCCTTTTTCCGGT 57.217 42.857 0.00 0.00 0.00 5.28
422 473 3.329929 TTCTAGCTCCTTTTTCCGGTC 57.670 47.619 0.00 0.00 0.00 4.79
423 474 2.253610 TCTAGCTCCTTTTTCCGGTCA 58.746 47.619 0.00 0.00 0.00 4.02
424 475 2.838202 TCTAGCTCCTTTTTCCGGTCAT 59.162 45.455 0.00 0.00 0.00 3.06
576 868 0.241749 ACGTATCCTTTGTCGACGCA 59.758 50.000 11.62 0.00 37.02 5.24
633 941 8.552034 GCTGGTATGTACACTGAAATTAATCTC 58.448 37.037 0.00 0.00 0.00 2.75
634 942 9.823647 CTGGTATGTACACTGAAATTAATCTCT 57.176 33.333 0.00 0.00 0.00 3.10
697 1007 3.560902 TGCGCTACTAGCTTAGCTATG 57.439 47.619 14.78 11.01 42.12 2.23
745 1055 2.689766 GCGCATTCTGTCGTCGTC 59.310 61.111 0.30 0.00 0.00 4.20
769 1080 5.297547 TGGCACCGCAATTGTTTTATTTTA 58.702 33.333 7.40 0.00 0.00 1.52
806 1117 1.992667 TCGCAGCAATTTCTCTACGTG 59.007 47.619 0.00 0.00 0.00 4.49
808 1119 2.346803 GCAGCAATTTCTCTACGTGGA 58.653 47.619 0.34 0.34 0.00 4.02
865 1211 2.018644 GCATTCCTTTCGAGCATCCCA 61.019 52.381 0.00 0.00 0.00 4.37
885 1233 3.393970 CCTCTGGCGCCTCCTTCA 61.394 66.667 29.70 4.55 35.26 3.02
900 1257 2.117865 CCTTCATGCTTCTCTCTCCCT 58.882 52.381 0.00 0.00 0.00 4.20
901 1258 2.158928 CCTTCATGCTTCTCTCTCCCTG 60.159 54.545 0.00 0.00 0.00 4.45
902 1259 0.829333 TCATGCTTCTCTCTCCCTGC 59.171 55.000 0.00 0.00 0.00 4.85
903 1260 0.831966 CATGCTTCTCTCTCCCTGCT 59.168 55.000 0.00 0.00 0.00 4.24
904 1261 1.209990 CATGCTTCTCTCTCCCTGCTT 59.790 52.381 0.00 0.00 0.00 3.91
905 1262 1.356124 TGCTTCTCTCTCCCTGCTTT 58.644 50.000 0.00 0.00 0.00 3.51
915 1272 1.211457 CTCCCTGCTTTCTACCTGCAT 59.789 52.381 0.00 0.00 36.07 3.96
960 1323 1.066908 CTAGCTCTTCGGCTCTTCCTG 59.933 57.143 0.00 0.00 42.97 3.86
961 1324 1.153469 GCTCTTCGGCTCTTCCTGG 60.153 63.158 0.00 0.00 0.00 4.45
969 1332 0.609406 GGCTCTTCCTGGTGGTTTCC 60.609 60.000 0.00 0.00 34.23 3.13
1134 1512 5.804692 TCAGATCGTTAGTCTCTTCACTC 57.195 43.478 0.00 0.00 0.00 3.51
1212 1590 3.631250 TGGTGGCTTGACTTCTTTCTTT 58.369 40.909 0.00 0.00 0.00 2.52
1240 1619 6.961554 GCTAGCAACTACATATGTGTTTGTTC 59.038 38.462 18.81 8.99 39.77 3.18
1340 1720 3.629398 AGATTTGATCAGCCGATTGTTCC 59.371 43.478 0.00 0.00 29.66 3.62
1481 2444 8.567948 TCAACTCTTGTAAAACTGATGAAATCC 58.432 33.333 0.00 0.00 44.73 3.01
1497 2460 8.830580 TGATGAAATCCGATTTTAGATTCACTC 58.169 33.333 7.78 0.00 44.73 3.51
1526 2580 7.093858 ACCCAAGCTAGTTTGTAGTAGTAAGAG 60.094 40.741 16.87 0.00 31.14 2.85
1529 2583 9.130312 CAAGCTAGTTTGTAGTAGTAAGAGTTG 57.870 37.037 10.90 0.00 31.14 3.16
1678 2792 5.932619 ACTTTGTATATGCCTTTTTCCCC 57.067 39.130 0.00 0.00 0.00 4.81
1679 2793 5.337788 ACTTTGTATATGCCTTTTTCCCCA 58.662 37.500 0.00 0.00 0.00 4.96
1680 2794 5.782845 ACTTTGTATATGCCTTTTTCCCCAA 59.217 36.000 0.00 0.00 0.00 4.12
1827 2943 7.162082 GGTGGTAAGATTCAGAACCCTATATG 58.838 42.308 0.00 0.00 0.00 1.78
1861 2980 7.927048 TCTCACTTTGTTTAGCCTACTTTTTC 58.073 34.615 0.00 0.00 0.00 2.29
1902 3025 8.131455 ACGCACTAAATCAACTTCTACATATG 57.869 34.615 0.00 0.00 0.00 1.78
1905 3028 7.012327 GCACTAAATCAACTTCTACATATGGCA 59.988 37.037 7.80 0.00 0.00 4.92
2095 3328 7.040132 ACAAATCACAACAAACCACCAAATTTT 60.040 29.630 0.00 0.00 0.00 1.82
2096 3329 7.459795 AATCACAACAAACCACCAAATTTTT 57.540 28.000 0.00 0.00 0.00 1.94
2122 3355 5.968528 TGCCCGTTAATAGTTGAATTGTT 57.031 34.783 0.00 0.00 0.00 2.83
2123 3356 7.201750 GGATGCCCGTTAATAGTTGAATTGTTA 60.202 37.037 0.00 0.00 0.00 2.41
2248 3488 2.721090 GTGAAAAGAAAGTCATGCACGC 59.279 45.455 0.00 0.00 0.00 5.34
2251 3491 0.235665 AAGAAAGTCATGCACGCACG 59.764 50.000 0.00 0.00 0.00 5.34
2328 3568 0.606604 ACTTGCGGACGTTCTGGTAT 59.393 50.000 0.00 0.00 0.00 2.73
2338 3578 3.399330 ACGTTCTGGTATTGGAAGTGTG 58.601 45.455 0.00 0.00 0.00 3.82
2343 3583 5.255397 TCTGGTATTGGAAGTGTGGAATT 57.745 39.130 0.00 0.00 0.00 2.17
2558 3799 3.553511 CACGGTAGCATGAAAAGAGCTAG 59.446 47.826 0.00 0.00 41.11 3.42
2732 3982 7.986085 AGACTGCAATGTTTAAGTGTCTATT 57.014 32.000 0.00 0.00 32.64 1.73
2783 4033 7.430502 GGAAATTCAGAACATCTTTTATCAGCG 59.569 37.037 0.00 0.00 0.00 5.18
2963 4216 7.120285 GTCAATACATGCAGCCATATTCTACAT 59.880 37.037 0.00 0.00 0.00 2.29
2992 4245 7.678947 ATAGGTTGCAACATATTCATAGAGC 57.321 36.000 26.52 8.01 32.52 4.09
3069 4336 8.451908 AAGCAACACTCTATTACTTTTTGAGT 57.548 30.769 0.00 0.00 42.55 3.41
3072 4339 7.530861 GCAACACTCTATTACTTTTTGAGTTCG 59.469 37.037 0.00 0.00 39.86 3.95
3219 4496 5.350504 TCATTCATCAGGTCTCTTCCTTC 57.649 43.478 0.00 0.00 35.37 3.46
3241 4518 2.224769 ACCCATCCAACAAGTCGATGTT 60.225 45.455 0.00 0.00 44.08 2.71
3307 4584 3.745975 CGATCTTCACCAACAACAAGCTA 59.254 43.478 0.00 0.00 0.00 3.32
3436 4713 4.024670 AGGTACTTGTCCTAGATGGTGAC 58.975 47.826 0.00 0.00 27.25 3.67
3491 4768 1.592064 TCAGTTCAACGCTGCAATCA 58.408 45.000 0.00 0.00 34.21 2.57
3571 4848 2.664402 ACAATCAAGGAGTGGCTGTT 57.336 45.000 0.00 0.00 31.53 3.16
3715 4992 3.681897 GCTTCACAGTGAAAGATCATCGT 59.318 43.478 16.85 0.00 35.73 3.73
3729 5006 3.786516 TCATCGTGGCGAATGTAAGTA 57.213 42.857 0.00 0.00 39.99 2.24
3804 5083 4.106029 TCATGACTACACGTAGCCTTTC 57.894 45.455 4.10 0.00 36.66 2.62
3808 5089 3.243336 GACTACACGTAGCCTTTCTGTG 58.757 50.000 4.10 0.00 36.66 3.66
3815 5096 2.338500 GTAGCCTTTCTGTGAGTTCCG 58.662 52.381 0.00 0.00 0.00 4.30
3834 5115 3.967326 TCCGCCATATCATATTCCCTAGG 59.033 47.826 0.06 0.06 0.00 3.02
3837 5118 5.512060 CCGCCATATCATATTCCCTAGGATG 60.512 48.000 11.48 6.07 33.17 3.51
3840 5121 7.445945 GCCATATCATATTCCCTAGGATGTAC 58.554 42.308 11.48 0.00 33.17 2.90
3924 5207 4.017130 AGAAGCATTACCCTCCAATCCTTT 60.017 41.667 0.00 0.00 0.00 3.11
3926 5209 2.959030 GCATTACCCTCCAATCCTTTCC 59.041 50.000 0.00 0.00 0.00 3.13
4031 5314 3.871594 AGGACTTCTTGAAACTTCACACG 59.128 43.478 0.00 0.00 36.83 4.49
4163 5455 1.194218 TGTCAGATCGGCAATGGAGA 58.806 50.000 0.00 0.00 0.00 3.71
4208 5500 3.134081 CGTGTAGTATGGGAGGGAAATGT 59.866 47.826 0.00 0.00 0.00 2.71
4340 5632 7.120923 ACATAAGGTACATCATCCGTAAAGT 57.879 36.000 0.00 0.00 0.00 2.66
4357 5653 6.255215 CGTAAAGTAGTTTGTGGCAATATGG 58.745 40.000 5.77 0.00 0.00 2.74
4409 5708 1.109323 AACTGCAGGCCCAAGTGAAC 61.109 55.000 19.93 0.00 0.00 3.18
4505 5804 5.163764 TGCATATGAAGGTTTGACGTCATTC 60.164 40.000 20.80 19.34 39.63 2.67
4565 5864 3.965292 AATGAAAGCATGATCAGCTCG 57.035 42.857 16.64 1.01 42.53 5.03
4596 5895 1.982660 TGCCGAGTATCTAGACAGGG 58.017 55.000 0.00 0.00 0.00 4.45
4955 6255 4.373156 AGAACACCCTAAATGCAGTCTT 57.627 40.909 0.00 0.00 0.00 3.01
4991 6291 9.212593 AGGTATGGAATTTTATTTGCAAGGTAT 57.787 29.630 0.00 0.00 30.43 2.73
4992 6292 9.830975 GGTATGGAATTTTATTTGCAAGGTATT 57.169 29.630 0.00 0.00 30.43 1.89
5024 6324 9.705103 ATGATTAAAGGAAGATGGATCAGAAAA 57.295 29.630 0.00 0.00 0.00 2.29
5047 6347 4.191033 TGAGATTTACTTCGGCGGTTAA 57.809 40.909 7.21 0.00 0.00 2.01
5145 6445 4.336433 ACGAAGTCCATGCCAATTATTCAG 59.664 41.667 0.00 0.00 29.74 3.02
5193 9105 1.683917 CTCCTTGCCTCGCTAGTGTAT 59.316 52.381 2.66 0.00 30.04 2.29
5205 9117 6.978659 CCTCGCTAGTGTATAAATTCTCACAA 59.021 38.462 2.66 0.00 33.84 3.33
5226 9138 5.301805 ACAAGCAAACTTAATTAGTGGCACT 59.698 36.000 25.34 25.34 39.30 4.40
5233 9145 4.044191 ACTTAATTAGTGGCACTCCCCTTT 59.956 41.667 25.80 13.41 35.19 3.11
5237 9149 4.668138 TTAGTGGCACTCCCCTTTTAAT 57.332 40.909 25.80 0.00 0.00 1.40
5238 9150 3.087370 AGTGGCACTCCCCTTTTAATC 57.913 47.619 15.88 0.00 0.00 1.75
5274 9189 1.196012 TTTTCCCAAAAAGCGGTGGT 58.804 45.000 0.00 0.00 32.60 4.16
5280 9195 2.791868 AAAAAGCGGTGGTGTGGGC 61.792 57.895 0.00 0.00 0.00 5.36
5313 9228 4.789095 GTGTGTCTACATTTTCACACGT 57.211 40.909 10.62 0.00 46.50 4.49
5328 9243 1.438651 CACGTCATAAGTGTGTGGGG 58.561 55.000 0.00 0.00 35.08 4.96
5338 9253 1.149627 TGTGTGGGGCCAAGTGTAC 59.850 57.895 4.39 0.00 0.00 2.90
5345 9260 0.321653 GGGCCAAGTGTACTGGTCAG 60.322 60.000 4.39 0.00 0.00 3.51
5357 9272 3.268023 ACTGGTCAGGCATAAGTTAGC 57.732 47.619 2.87 0.00 0.00 3.09
5363 9278 1.672881 CAGGCATAAGTTAGCAGTGGC 59.327 52.381 0.00 0.69 41.61 5.01
5386 9301 1.996292 TCAGCGATGTTGTCACTAGC 58.004 50.000 0.00 0.00 0.00 3.42
5422 9337 2.508439 CACCAATCCCGACGTCCG 60.508 66.667 10.58 3.03 38.18 4.79
5480 9395 2.369394 GATGCAAGAGGAATTTCCCGT 58.631 47.619 11.92 0.00 37.19 5.28
5483 9398 1.751437 CAAGAGGAATTTCCCGTCCC 58.249 55.000 11.92 0.00 37.19 4.46
5484 9399 1.282157 CAAGAGGAATTTCCCGTCCCT 59.718 52.381 11.92 0.00 37.19 4.20
5485 9400 1.205055 AGAGGAATTTCCCGTCCCTC 58.795 55.000 11.92 0.00 42.73 4.30
5486 9401 0.909623 GAGGAATTTCCCGTCCCTCA 59.090 55.000 11.92 0.00 42.15 3.86
5487 9402 1.490910 GAGGAATTTCCCGTCCCTCAT 59.509 52.381 11.92 0.00 42.15 2.90
5488 9403 2.704065 GAGGAATTTCCCGTCCCTCATA 59.296 50.000 11.92 0.00 42.15 2.15
5499 9414 2.677037 CGTCCCTCATACCAACTCAACC 60.677 54.545 0.00 0.00 0.00 3.77
5524 9439 2.082231 CACTCGTTCCTCGACCTTCTA 58.918 52.381 0.00 0.00 44.01 2.10
5558 9473 1.374252 CCGACGAGTGGGTTTCCAG 60.374 63.158 0.00 0.00 45.05 3.86
5571 9486 3.279434 GGTTTCCAGGCATAAACTCGAT 58.721 45.455 8.57 0.00 36.17 3.59
5574 9489 5.355910 GGTTTCCAGGCATAAACTCGATTTA 59.644 40.000 8.57 0.00 37.18 1.40
5601 9516 3.570550 GGCACTCTCGATCACTATAAGGT 59.429 47.826 0.00 0.00 0.00 3.50
5612 9527 3.889538 TCACTATAAGGTGAGATGGGTCG 59.110 47.826 0.00 0.00 40.72 4.79
5619 9534 1.009829 GTGAGATGGGTCGTTCATGC 58.990 55.000 0.00 0.00 0.00 4.06
5620 9535 0.612744 TGAGATGGGTCGTTCATGCA 59.387 50.000 0.00 0.00 0.00 3.96
5621 9536 1.009829 GAGATGGGTCGTTCATGCAC 58.990 55.000 0.00 0.00 0.00 4.57
5622 9537 0.615331 AGATGGGTCGTTCATGCACT 59.385 50.000 0.00 0.00 0.00 4.40
5623 9538 1.831106 AGATGGGTCGTTCATGCACTA 59.169 47.619 0.00 0.00 0.00 2.74
5624 9539 2.159043 AGATGGGTCGTTCATGCACTAG 60.159 50.000 0.00 0.00 0.00 2.57
5625 9540 0.973632 TGGGTCGTTCATGCACTAGT 59.026 50.000 0.00 0.00 0.00 2.57
5626 9541 1.337728 TGGGTCGTTCATGCACTAGTG 60.338 52.381 18.93 18.93 0.00 2.74
5636 9551 4.598257 CACTAGTGCAGAACCGGG 57.402 61.111 10.54 0.00 0.00 5.73
5637 9552 1.741770 CACTAGTGCAGAACCGGGC 60.742 63.158 10.54 0.00 0.00 6.13
5638 9553 1.913762 ACTAGTGCAGAACCGGGCT 60.914 57.895 6.32 0.00 0.00 5.19
5639 9554 0.613853 ACTAGTGCAGAACCGGGCTA 60.614 55.000 6.32 0.00 0.00 3.93
5640 9555 0.753262 CTAGTGCAGAACCGGGCTAT 59.247 55.000 6.32 0.00 0.00 2.97
5641 9556 1.961394 CTAGTGCAGAACCGGGCTATA 59.039 52.381 6.32 0.00 0.00 1.31
5642 9557 0.753262 AGTGCAGAACCGGGCTATAG 59.247 55.000 6.32 0.00 0.00 1.31
5643 9558 0.880718 GTGCAGAACCGGGCTATAGC 60.881 60.000 16.78 16.78 41.14 2.97
5644 9559 1.334384 TGCAGAACCGGGCTATAGCA 61.334 55.000 25.53 6.20 44.36 3.49
5645 9560 0.880718 GCAGAACCGGGCTATAGCAC 60.881 60.000 25.53 21.77 44.36 4.40
5646 9561 0.249911 CAGAACCGGGCTATAGCACC 60.250 60.000 25.53 21.08 42.67 5.01
5647 9562 1.300697 GAACCGGGCTATAGCACCG 60.301 63.158 31.50 31.50 46.81 4.94
5650 9565 2.819550 CGGGCTATAGCACCGGTT 59.180 61.111 31.12 0.00 44.99 4.44
5651 9566 1.145377 CGGGCTATAGCACCGGTTT 59.855 57.895 31.12 0.00 44.99 3.27
5652 9567 1.157870 CGGGCTATAGCACCGGTTTG 61.158 60.000 31.12 12.97 44.99 2.93
5653 9568 0.107361 GGGCTATAGCACCGGTTTGT 60.107 55.000 25.53 0.00 44.36 2.83
5654 9569 1.139455 GGGCTATAGCACCGGTTTGTA 59.861 52.381 25.53 0.00 44.36 2.41
5655 9570 2.420408 GGGCTATAGCACCGGTTTGTAA 60.420 50.000 25.53 0.00 44.36 2.41
5656 9571 2.870411 GGCTATAGCACCGGTTTGTAAG 59.130 50.000 25.53 0.90 44.36 2.34
5657 9572 2.870411 GCTATAGCACCGGTTTGTAAGG 59.130 50.000 20.01 0.00 41.59 2.69
5658 9573 1.746470 ATAGCACCGGTTTGTAAGGC 58.254 50.000 2.97 2.83 0.00 4.35
5659 9574 0.397187 TAGCACCGGTTTGTAAGGCA 59.603 50.000 2.97 0.00 0.00 4.75
5660 9575 1.170290 AGCACCGGTTTGTAAGGCAC 61.170 55.000 2.97 0.00 0.00 5.01
5677 9592 2.144482 CACTTTAGTGTCGGTTCGGT 57.856 50.000 1.69 0.00 40.96 4.69
5678 9593 3.287312 CACTTTAGTGTCGGTTCGGTA 57.713 47.619 1.69 0.00 40.96 4.02
5679 9594 3.641648 CACTTTAGTGTCGGTTCGGTAA 58.358 45.455 1.69 0.00 40.96 2.85
5680 9595 3.426525 CACTTTAGTGTCGGTTCGGTAAC 59.573 47.826 1.69 0.00 40.96 2.50
5681 9596 5.608262 CACTTTAGTGTCGGTTCGGTAACC 61.608 50.000 1.69 0.00 44.53 2.85
5692 9607 3.520187 CGGTAACCGGCACTAAAGT 57.480 52.632 0.00 0.00 44.15 2.66
5693 9608 1.073177 CGGTAACCGGCACTAAAGTG 58.927 55.000 0.00 5.73 44.15 3.16
5694 9609 1.606224 CGGTAACCGGCACTAAAGTGT 60.606 52.381 0.00 0.00 44.15 3.55
5695 9610 3.745341 CGGTAACCGGCACTAAAGTGTG 61.745 54.545 0.00 5.04 44.15 3.82
5706 9621 4.324267 CACTAAAGTGTGGGGACTAAAGG 58.676 47.826 1.81 0.00 40.96 3.11
5707 9622 3.978672 ACTAAAGTGTGGGGACTAAAGGT 59.021 43.478 0.00 0.00 0.00 3.50
5708 9623 3.503800 AAAGTGTGGGGACTAAAGGTC 57.496 47.619 0.00 0.00 43.79 3.85
5729 9644 0.543277 CCCCCTTTAGTACCGGTTCC 59.457 60.000 15.04 3.66 0.00 3.62
5730 9645 0.176449 CCCCTTTAGTACCGGTTCCG 59.824 60.000 15.04 4.08 0.00 4.30
5731 9646 0.460811 CCCTTTAGTACCGGTTCCGC 60.461 60.000 15.04 0.59 0.00 5.54
5732 9647 0.247185 CCTTTAGTACCGGTTCCGCA 59.753 55.000 15.04 0.00 0.00 5.69
5733 9648 1.353076 CTTTAGTACCGGTTCCGCAC 58.647 55.000 15.04 3.84 0.00 5.34
5734 9649 0.388391 TTTAGTACCGGTTCCGCACG 60.388 55.000 15.04 0.00 0.00 5.34
5735 9650 1.240641 TTAGTACCGGTTCCGCACGA 61.241 55.000 15.04 0.00 0.00 4.35
5736 9651 1.240641 TAGTACCGGTTCCGCACGAA 61.241 55.000 15.04 0.00 0.00 3.85
5742 9657 3.708734 GTTCCGCACGAACCGGTG 61.709 66.667 8.52 0.00 44.46 4.94
5749 9664 2.159181 CACGAACCGGTGCTAAAGG 58.841 57.895 8.52 0.00 0.00 3.11
5750 9665 1.004200 ACGAACCGGTGCTAAAGGG 60.004 57.895 8.52 0.00 0.00 3.95
5751 9666 2.396157 CGAACCGGTGCTAAAGGGC 61.396 63.158 8.52 0.00 0.00 5.19
5752 9667 1.302993 GAACCGGTGCTAAAGGGCA 60.303 57.895 8.52 0.00 40.15 5.36
5753 9668 0.891904 GAACCGGTGCTAAAGGGCAA 60.892 55.000 8.52 0.00 44.18 4.52
5754 9669 1.176619 AACCGGTGCTAAAGGGCAAC 61.177 55.000 8.52 0.00 45.46 4.17
5767 9682 4.012895 GCAACCACGTGGCACGAG 62.013 66.667 42.65 34.61 46.05 4.18
5768 9683 2.587753 CAACCACGTGGCACGAGT 60.588 61.111 42.65 33.51 46.05 4.18
5769 9684 2.279918 AACCACGTGGCACGAGTC 60.280 61.111 42.65 4.23 46.05 3.36
5770 9685 3.083848 AACCACGTGGCACGAGTCA 62.084 57.895 42.65 0.00 46.05 3.41
5771 9686 2.734723 CCACGTGGCACGAGTCAG 60.735 66.667 42.65 25.00 46.05 3.51
5772 9687 3.406361 CACGTGGCACGAGTCAGC 61.406 66.667 42.65 1.70 46.05 4.26
5773 9688 3.606662 ACGTGGCACGAGTCAGCT 61.607 61.111 42.65 18.80 46.05 4.24
5774 9689 2.807045 CGTGGCACGAGTCAGCTC 60.807 66.667 34.85 0.00 46.05 4.09
5775 9690 2.433318 GTGGCACGAGTCAGCTCC 60.433 66.667 0.00 0.00 38.49 4.70
5776 9691 4.056125 TGGCACGAGTCAGCTCCG 62.056 66.667 4.76 0.00 38.49 4.63
5777 9692 4.803426 GGCACGAGTCAGCTCCGG 62.803 72.222 0.00 0.00 38.49 5.14
5778 9693 4.803426 GCACGAGTCAGCTCCGGG 62.803 72.222 0.00 0.00 38.49 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.992829 TGTCGTTTTCTATGCACCTTCTTAA 59.007 36.000 0.00 0.00 0.00 1.85
1 2 5.543714 TGTCGTTTTCTATGCACCTTCTTA 58.456 37.500 0.00 0.00 0.00 2.10
2 3 4.385825 TGTCGTTTTCTATGCACCTTCTT 58.614 39.130 0.00 0.00 0.00 2.52
69 70 2.362717 AGTTTAGCTAGCTGGATCGACC 59.637 50.000 27.68 6.22 39.54 4.79
109 147 2.456989 TCGAAATTACGGCTAGCTTCG 58.543 47.619 21.76 21.76 37.57 3.79
263 303 3.325135 AGAAATTAGGGACAGCTATCGGG 59.675 47.826 0.00 0.00 0.00 5.14
387 438 0.527113 TAGAAATCAACGCGACCGGA 59.473 50.000 15.93 4.49 39.22 5.14
405 456 2.355716 CCATGACCGGAAAAAGGAGCTA 60.356 50.000 9.46 0.00 0.00 3.32
415 466 0.899720 GTACCAGACCATGACCGGAA 59.100 55.000 9.46 0.00 0.00 4.30
417 468 1.141019 CGTACCAGACCATGACCGG 59.859 63.158 0.00 0.00 0.00 5.28
418 469 1.518572 GCGTACCAGACCATGACCG 60.519 63.158 0.00 0.00 0.00 4.79
419 470 1.518572 CGCGTACCAGACCATGACC 60.519 63.158 0.00 0.00 0.00 4.02
420 471 0.452987 TACGCGTACCAGACCATGAC 59.547 55.000 16.41 0.00 0.00 3.06
421 472 1.066454 CATACGCGTACCAGACCATGA 59.934 52.381 23.19 0.00 0.00 3.07
422 473 1.202371 ACATACGCGTACCAGACCATG 60.202 52.381 23.19 16.45 0.00 3.66
423 474 1.108776 ACATACGCGTACCAGACCAT 58.891 50.000 23.19 0.13 0.00 3.55
424 475 1.401552 GTACATACGCGTACCAGACCA 59.598 52.381 23.19 0.00 36.54 4.02
482 680 2.693069 CCATGACGAAGAAGACTTGCT 58.307 47.619 0.00 0.00 36.39 3.91
563 855 2.243957 TGCTGTGCGTCGACAAAGG 61.244 57.895 17.16 0.00 0.00 3.11
633 941 4.389374 AGCAAGCTAGCTCTAGTCTCTAG 58.611 47.826 19.65 9.66 42.18 2.43
634 942 4.431416 AGCAAGCTAGCTCTAGTCTCTA 57.569 45.455 19.65 0.00 42.18 2.43
635 943 3.297134 AGCAAGCTAGCTCTAGTCTCT 57.703 47.619 19.65 4.76 42.18 3.10
662 970 2.080700 CGCATCGCACTGTTCATCA 58.919 52.632 0.00 0.00 0.00 3.07
745 1055 2.430546 TAAAACAATTGCGGTGCCAG 57.569 45.000 5.05 0.00 0.00 4.85
769 1080 1.060713 CGAGCTTTTGTCGTCGACAT 58.939 50.000 27.42 13.25 42.40 3.06
819 1130 5.344066 CCTGAAGCCGTATATATAGTGCTG 58.656 45.833 13.85 5.16 0.00 4.41
822 1133 5.344066 CAGCCTGAAGCCGTATATATAGTG 58.656 45.833 0.00 0.00 45.47 2.74
823 1134 4.142138 GCAGCCTGAAGCCGTATATATAGT 60.142 45.833 0.00 0.00 45.47 2.12
885 1233 1.582389 AAGCAGGGAGAGAGAAGCAT 58.418 50.000 0.00 0.00 0.00 3.79
900 1257 2.768527 AGCTAGATGCAGGTAGAAAGCA 59.231 45.455 8.90 0.00 45.94 3.91
901 1258 3.467374 AGCTAGATGCAGGTAGAAAGC 57.533 47.619 8.90 3.27 45.94 3.51
902 1259 4.038522 TGCTAGCTAGATGCAGGTAGAAAG 59.961 45.833 25.15 7.90 45.40 2.62
903 1260 3.960755 TGCTAGCTAGATGCAGGTAGAAA 59.039 43.478 25.15 0.00 45.40 2.52
904 1261 3.566351 TGCTAGCTAGATGCAGGTAGAA 58.434 45.455 25.15 1.01 45.40 2.10
905 1262 3.153130 CTGCTAGCTAGATGCAGGTAGA 58.847 50.000 25.15 0.00 45.40 2.59
938 1297 1.394618 GAAGAGCCGAAGAGCTAGGA 58.605 55.000 0.00 0.00 45.15 2.94
939 1298 0.387565 GGAAGAGCCGAAGAGCTAGG 59.612 60.000 0.00 0.00 45.15 3.02
969 1332 8.073768 GTCTAGATCTCTAACGATCAAAAGAGG 58.926 40.741 0.00 1.12 41.74 3.69
1023 1390 0.456995 CCTGCTCGTCGTCTTCTTCC 60.457 60.000 0.00 0.00 0.00 3.46
1212 1590 7.822334 ACAAACACATATGTAGTTGCTAGCTAA 59.178 33.333 21.88 5.90 38.45 3.09
1231 1610 3.801114 AAGGAAGCAAGGAACAAACAC 57.199 42.857 0.00 0.00 0.00 3.32
1240 1619 1.740025 GTCGATCCAAAGGAAGCAAGG 59.260 52.381 0.00 0.00 34.34 3.61
1312 1692 2.123342 CGGCTGATCAAATCTCTCGTC 58.877 52.381 0.00 0.00 0.00 4.20
1317 1697 4.260948 GGAACAATCGGCTGATCAAATCTC 60.261 45.833 8.88 0.58 32.24 2.75
1340 1720 6.263168 AGGTATCGATTCAGCAAATAAAAGGG 59.737 38.462 1.71 0.00 0.00 3.95
1387 1769 7.706607 TCATGTAGTATTTTCATCTCTTGACCG 59.293 37.037 0.00 0.00 32.84 4.79
1481 2444 6.494893 TGGGTTTGAGTGAATCTAAAATCG 57.505 37.500 0.00 0.00 30.25 3.34
1526 2580 6.879400 ACAGAGATCTTAGATGGGTTACAAC 58.121 40.000 0.00 0.00 0.00 3.32
1529 2583 6.969993 AGACAGAGATCTTAGATGGGTTAC 57.030 41.667 0.00 0.00 0.00 2.50
1714 2830 1.970917 GACGCTGCAAAGATGGTCCG 61.971 60.000 0.00 0.00 0.00 4.79
1790 2906 6.381994 TGAATCTTACCACCCTACGAATAACT 59.618 38.462 0.00 0.00 0.00 2.24
1827 2943 9.000486 AGGCTAAACAAAGTGAGAACTAAATAC 58.000 33.333 0.00 0.00 0.00 1.89
1845 2964 9.613957 GATTCTTCAAGAAAAAGTAGGCTAAAC 57.386 33.333 3.35 0.00 37.82 2.01
1849 2968 7.823745 TTGATTCTTCAAGAAAAAGTAGGCT 57.176 32.000 3.35 0.00 37.82 4.58
1861 2980 8.948853 TTTAGTGCGTTATTTGATTCTTCAAG 57.051 30.769 0.00 0.00 42.60 3.02
1876 2995 8.604035 CATATGTAGAAGTTGATTTAGTGCGTT 58.396 33.333 0.00 0.00 0.00 4.84
1878 2997 7.567571 CCATATGTAGAAGTTGATTTAGTGCG 58.432 38.462 1.24 0.00 0.00 5.34
2095 3328 4.223556 TCAACTATTAACGGGCATCCAA 57.776 40.909 0.00 0.00 0.00 3.53
2096 3329 3.916359 TCAACTATTAACGGGCATCCA 57.084 42.857 0.00 0.00 0.00 3.41
2122 3355 5.596763 ACTGTTATTCCTCCCCTTGTAGTA 58.403 41.667 0.00 0.00 0.00 1.82
2123 3356 4.436079 ACTGTTATTCCTCCCCTTGTAGT 58.564 43.478 0.00 0.00 0.00 2.73
2248 3488 4.854399 TCTCTACCAAAATTTTGCACGTG 58.146 39.130 22.90 12.28 36.86 4.49
2251 3491 8.349983 TCTTACTTCTCTACCAAAATTTTGCAC 58.650 33.333 22.90 0.00 36.86 4.57
2283 3523 7.279615 TGCAGTATGTACTTTGCCACTAATAT 58.720 34.615 0.00 0.00 39.31 1.28
2284 3524 6.645306 TGCAGTATGTACTTTGCCACTAATA 58.355 36.000 0.00 0.00 39.31 0.98
2285 3525 5.496556 TGCAGTATGTACTTTGCCACTAAT 58.503 37.500 0.00 0.00 39.31 1.73
2286 3526 4.900684 TGCAGTATGTACTTTGCCACTAA 58.099 39.130 0.00 0.00 39.31 2.24
2287 3527 4.545208 TGCAGTATGTACTTTGCCACTA 57.455 40.909 0.00 0.00 39.31 2.74
2328 3568 1.482177 CCCCCAATTCCACACTTCCAA 60.482 52.381 0.00 0.00 0.00 3.53
2362 3602 3.673809 GTGTGTACACTCTTTCCGTGATC 59.326 47.826 25.60 0.00 43.25 2.92
2390 3630 4.883585 TGTCATTTTTCTCTGCACTTCTGT 59.116 37.500 0.00 0.00 0.00 3.41
2558 3799 3.248043 TGCAAGAGTGTATGCACCC 57.752 52.632 10.59 0.00 46.87 4.61
2596 3837 9.460019 TGATCAATATTTGTGTAAATGGACTGA 57.540 29.630 0.00 0.00 37.12 3.41
2651 3895 6.853279 AACGAAATACATCAGAAATTTGCG 57.147 33.333 0.00 0.00 0.00 4.85
2732 3982 6.709281 TCCCGTACCTAAATGTTAACATGAA 58.291 36.000 21.46 11.61 36.56 2.57
2824 4074 8.847196 TGAATACTAGTAGCTCACGATGTAATT 58.153 33.333 8.85 0.00 0.00 1.40
2825 4075 8.392372 TGAATACTAGTAGCTCACGATGTAAT 57.608 34.615 8.85 0.00 0.00 1.89
2826 4076 7.498239 ACTGAATACTAGTAGCTCACGATGTAA 59.502 37.037 8.85 0.00 0.00 2.41
2934 4185 2.495155 TGGCTGCATGTATTGACTGT 57.505 45.000 0.50 0.00 0.00 3.55
3026 4286 9.065871 GTGTTGCTTCTTAATATGTGATGTTTC 57.934 33.333 0.00 0.00 0.00 2.78
3030 4290 8.206325 AGAGTGTTGCTTCTTAATATGTGATG 57.794 34.615 0.00 0.00 0.00 3.07
3062 4329 4.377839 TTTCCAATGTGCGAACTCAAAA 57.622 36.364 0.00 0.00 0.00 2.44
3150 4426 3.900601 TGCAACCCAATACCACTGAATTT 59.099 39.130 0.00 0.00 0.00 1.82
3151 4427 3.505386 TGCAACCCAATACCACTGAATT 58.495 40.909 0.00 0.00 0.00 2.17
3152 4428 3.168035 TGCAACCCAATACCACTGAAT 57.832 42.857 0.00 0.00 0.00 2.57
3156 4432 5.129368 AGATATTGCAACCCAATACCACT 57.871 39.130 0.00 0.00 46.21 4.00
3219 4496 1.739466 CATCGACTTGTTGGATGGGTG 59.261 52.381 0.00 0.00 36.92 4.61
3241 4518 0.690762 AAAGCTTCAACCTAGGCGGA 59.309 50.000 9.30 3.44 36.31 5.54
3307 4584 0.238289 CGTTCTTTGCGGCATCAACT 59.762 50.000 2.28 0.00 0.00 3.16
3491 4768 1.694048 CCTACCCTCTCTGGCCTTCAT 60.694 57.143 3.32 0.00 0.00 2.57
3715 4992 6.161855 AGAGAATCATACTTACATTCGCCA 57.838 37.500 0.00 0.00 37.82 5.69
3760 5037 6.762187 TGAAACTGACGTTCAACATAAACCTA 59.238 34.615 0.00 0.00 31.66 3.08
3778 5057 3.612860 GGCTACGTGTAGTCATGAAACTG 59.387 47.826 6.76 0.00 37.70 3.16
3804 5083 2.602257 TGATATGGCGGAACTCACAG 57.398 50.000 0.00 0.00 0.00 3.66
3808 5089 4.080863 AGGGAATATGATATGGCGGAACTC 60.081 45.833 0.00 0.00 0.00 3.01
3815 5096 6.506538 ACATCCTAGGGAATATGATATGGC 57.493 41.667 9.46 0.00 34.34 4.40
3875 5158 8.314143 TGTACACTAGTAAACAAGGTAAATGC 57.686 34.615 6.94 0.00 30.67 3.56
3924 5207 3.506398 TGAGCCTCCATATATTGTCGGA 58.494 45.455 0.00 0.00 0.00 4.55
3926 5209 6.038161 TGTTTTTGAGCCTCCATATATTGTCG 59.962 38.462 0.00 0.00 0.00 4.35
4114 5404 5.010012 ACGAGCTGAAAATTTGGAACAGATT 59.990 36.000 14.60 5.99 45.38 2.40
4163 5455 5.005586 CGTTTTTGCATGATTGAGTGTTGTT 59.994 36.000 0.00 0.00 0.00 2.83
4208 5500 7.286546 TCACACCCTTCAGATTTGAAAACATAA 59.713 33.333 0.00 0.00 42.48 1.90
4340 5632 4.704540 CCAAGTCCATATTGCCACAAACTA 59.295 41.667 0.00 0.00 0.00 2.24
4357 5653 4.378874 GCAAAGCTAAGTGATGACCAAGTC 60.379 45.833 0.00 0.00 0.00 3.01
4505 5804 2.678190 CGAACTAGGCTTTTCCTCAGGG 60.678 54.545 0.00 0.00 43.20 4.45
4565 5864 0.322546 ACTCGGCATTTTGAGACCCC 60.323 55.000 0.00 0.00 36.11 4.95
4596 5895 2.152016 GGTTGCTGTTCTAGAACCCAC 58.848 52.381 28.43 19.05 40.46 4.61
4803 6102 4.620982 TGGATCACGAGCATACAACATAG 58.379 43.478 0.00 0.00 0.00 2.23
4922 6222 8.750298 CATTTAGGGTGTTCTTAGAGTAGAGAA 58.250 37.037 0.00 0.00 0.00 2.87
4923 6223 7.147880 GCATTTAGGGTGTTCTTAGAGTAGAGA 60.148 40.741 0.00 0.00 0.00 3.10
4928 6228 5.013183 ACTGCATTTAGGGTGTTCTTAGAGT 59.987 40.000 0.00 0.00 0.00 3.24
5024 6324 3.261981 ACCGCCGAAGTAAATCTCATT 57.738 42.857 0.00 0.00 0.00 2.57
5027 6327 5.729974 ATTTAACCGCCGAAGTAAATCTC 57.270 39.130 0.00 0.00 0.00 2.75
5047 6347 2.888834 AAGACTTTGCGCCAACAATT 57.111 40.000 4.18 0.00 0.00 2.32
5090 6390 0.394565 AGAGGGATATGTGCGCCTTC 59.605 55.000 4.18 0.00 0.00 3.46
5100 6400 3.602922 TGTCCTAGGCCATAGAGGGATAT 59.397 47.826 5.01 0.00 38.09 1.63
5145 6445 5.236047 GGTTGCTTCATGTGATGATCTACTC 59.764 44.000 0.00 0.00 39.39 2.59
5205 9117 4.459337 GGAGTGCCACTAATTAAGTTTGCT 59.541 41.667 0.00 0.00 35.76 3.91
5226 9138 0.033894 GGGCGTGGATTAAAAGGGGA 60.034 55.000 0.00 0.00 0.00 4.81
5233 9145 2.279935 AACTTGTGGGCGTGGATTAA 57.720 45.000 0.00 0.00 0.00 1.40
5237 9149 2.889200 AAAAACTTGTGGGCGTGGA 58.111 47.368 0.00 0.00 0.00 4.02
5259 9171 1.067250 CACACCACCGCTTTTTGGG 59.933 57.895 0.00 0.00 37.18 4.12
5271 9186 2.428187 CAGTAACCGCCCACACCA 59.572 61.111 0.00 0.00 0.00 4.17
5274 9189 2.428187 CACCAGTAACCGCCCACA 59.572 61.111 0.00 0.00 0.00 4.17
5280 9195 0.391597 AGACACACCACCAGTAACCG 59.608 55.000 0.00 0.00 0.00 4.44
5313 9228 0.774276 TTGGCCCCACACACTTATGA 59.226 50.000 0.00 0.00 0.00 2.15
5328 9243 0.955919 GCCTGACCAGTACACTTGGC 60.956 60.000 0.00 0.00 0.00 4.52
5338 9253 3.201290 CTGCTAACTTATGCCTGACCAG 58.799 50.000 0.00 0.00 0.00 4.00
5345 9260 0.657840 CGCCACTGCTAACTTATGCC 59.342 55.000 0.00 0.00 34.43 4.40
5372 9287 1.002366 CCAGCGCTAGTGACAACATC 58.998 55.000 10.99 0.00 0.00 3.06
5376 9291 0.599991 CACACCAGCGCTAGTGACAA 60.600 55.000 36.78 0.00 37.43 3.18
5406 9321 2.993264 ACGGACGTCGGGATTGGT 60.993 61.111 24.65 2.22 44.45 3.67
5429 9344 1.976132 ATGGGGATCAGTGAGTGCCG 61.976 60.000 0.00 0.00 0.00 5.69
5431 9346 1.386533 CAATGGGGATCAGTGAGTGC 58.613 55.000 0.00 0.00 43.46 4.40
5461 9376 2.369394 GACGGGAAATTCCTCTTGCAT 58.631 47.619 12.28 0.00 36.57 3.96
5480 9395 2.571653 CAGGTTGAGTTGGTATGAGGGA 59.428 50.000 0.00 0.00 0.00 4.20
5483 9398 3.007940 TGTCCAGGTTGAGTTGGTATGAG 59.992 47.826 0.00 0.00 35.89 2.90
5484 9399 2.976185 TGTCCAGGTTGAGTTGGTATGA 59.024 45.455 0.00 0.00 35.89 2.15
5485 9400 3.074412 GTGTCCAGGTTGAGTTGGTATG 58.926 50.000 0.00 0.00 35.89 2.39
5486 9401 2.979678 AGTGTCCAGGTTGAGTTGGTAT 59.020 45.455 0.00 0.00 35.89 2.73
5487 9402 2.367567 GAGTGTCCAGGTTGAGTTGGTA 59.632 50.000 0.00 0.00 35.89 3.25
5488 9403 1.141053 GAGTGTCCAGGTTGAGTTGGT 59.859 52.381 0.00 0.00 35.89 3.67
5499 9414 2.254471 TCGAGGAACGAGTGTCCAG 58.746 57.895 0.00 0.00 46.45 3.86
5524 9439 2.735444 CGTCGGAGATAACATGTGCACT 60.735 50.000 19.41 0.00 40.67 4.40
5571 9486 0.464036 ATCGAGAGTGCCGCCATAAA 59.536 50.000 0.00 0.00 0.00 1.40
5574 9489 2.419198 GATCGAGAGTGCCGCCAT 59.581 61.111 0.00 0.00 0.00 4.40
5601 9516 0.612744 TGCATGAACGACCCATCTCA 59.387 50.000 0.00 0.00 0.00 3.27
5619 9534 1.741770 GCCCGGTTCTGCACTAGTG 60.742 63.158 18.93 18.93 0.00 2.74
5620 9535 0.613853 TAGCCCGGTTCTGCACTAGT 60.614 55.000 0.00 0.00 0.00 2.57
5621 9536 0.753262 ATAGCCCGGTTCTGCACTAG 59.247 55.000 0.00 0.00 0.00 2.57
5622 9537 1.961394 CTATAGCCCGGTTCTGCACTA 59.039 52.381 0.00 0.00 0.00 2.74
5623 9538 0.753262 CTATAGCCCGGTTCTGCACT 59.247 55.000 0.00 0.00 0.00 4.40
5624 9539 0.880718 GCTATAGCCCGGTTCTGCAC 60.881 60.000 14.13 0.00 34.31 4.57
5625 9540 1.334384 TGCTATAGCCCGGTTCTGCA 61.334 55.000 21.84 0.00 41.18 4.41
5626 9541 0.880718 GTGCTATAGCCCGGTTCTGC 60.881 60.000 21.84 0.00 41.18 4.26
5627 9542 0.249911 GGTGCTATAGCCCGGTTCTG 60.250 60.000 21.84 0.00 41.18 3.02
5628 9543 1.745320 CGGTGCTATAGCCCGGTTCT 61.745 60.000 31.12 0.00 44.99 3.01
5629 9544 1.300697 CGGTGCTATAGCCCGGTTC 60.301 63.158 31.12 13.98 44.99 3.62
5630 9545 2.819550 CGGTGCTATAGCCCGGTT 59.180 61.111 31.12 0.00 44.99 4.44
5633 9548 1.145377 AAACCGGTGCTATAGCCCG 59.855 57.895 31.50 31.50 46.81 6.13
5634 9549 0.107361 ACAAACCGGTGCTATAGCCC 60.107 55.000 21.84 19.43 41.18 5.19
5635 9550 2.607631 TACAAACCGGTGCTATAGCC 57.392 50.000 21.84 12.70 41.18 3.93
5636 9551 2.870411 CCTTACAAACCGGTGCTATAGC 59.130 50.000 18.18 18.18 42.50 2.97
5637 9552 2.870411 GCCTTACAAACCGGTGCTATAG 59.130 50.000 8.52 3.38 0.00 1.31
5638 9553 2.236644 TGCCTTACAAACCGGTGCTATA 59.763 45.455 8.52 0.00 0.00 1.31
5639 9554 1.003812 TGCCTTACAAACCGGTGCTAT 59.996 47.619 8.52 0.00 0.00 2.97
5640 9555 0.397187 TGCCTTACAAACCGGTGCTA 59.603 50.000 8.52 0.00 0.00 3.49
5641 9556 1.149627 TGCCTTACAAACCGGTGCT 59.850 52.632 8.52 0.00 0.00 4.40
5642 9557 1.170290 AGTGCCTTACAAACCGGTGC 61.170 55.000 8.52 5.73 0.00 5.01
5643 9558 1.314730 AAGTGCCTTACAAACCGGTG 58.685 50.000 8.52 0.00 0.00 4.94
5644 9559 2.061509 AAAGTGCCTTACAAACCGGT 57.938 45.000 0.00 0.00 0.00 5.28
5645 9560 3.058501 CACTAAAGTGCCTTACAAACCGG 60.059 47.826 0.00 0.00 39.39 5.28
5646 9561 4.141855 CACTAAAGTGCCTTACAAACCG 57.858 45.455 0.00 0.00 39.39 4.44
5658 9573 5.608262 GGTTACCGAACCGACACTAAAGTG 61.608 50.000 8.56 8.56 45.73 3.16
5659 9574 3.552890 GGTTACCGAACCGACACTAAAGT 60.553 47.826 0.00 0.00 45.73 2.66
5660 9575 2.989166 GGTTACCGAACCGACACTAAAG 59.011 50.000 0.00 0.00 45.73 1.85
5661 9576 3.025287 GGTTACCGAACCGACACTAAA 57.975 47.619 0.00 0.00 45.73 1.85
5662 9577 2.723124 GGTTACCGAACCGACACTAA 57.277 50.000 0.00 0.00 45.73 2.24
5671 9586 4.945824 CACTTTAGTGCCGGTTACCGAAC 61.946 52.174 26.59 21.33 43.81 3.95
5672 9587 2.867251 CACTTTAGTGCCGGTTACCGAA 60.867 50.000 26.59 10.31 43.81 4.30
5673 9588 1.337074 CACTTTAGTGCCGGTTACCGA 60.337 52.381 26.59 2.64 43.81 4.69
5674 9589 1.073177 CACTTTAGTGCCGGTTACCG 58.927 55.000 17.88 17.88 40.97 4.02
5684 9599 6.029729 GACCTTTAGTCCCCACACTTTAGTG 61.030 48.000 8.29 8.29 44.47 2.74
5685 9600 3.978672 ACCTTTAGTCCCCACACTTTAGT 59.021 43.478 0.00 0.00 0.00 2.24
5686 9601 4.576879 GACCTTTAGTCCCCACACTTTAG 58.423 47.826 0.00 0.00 39.84 1.85
5687 9602 4.628963 GACCTTTAGTCCCCACACTTTA 57.371 45.455 0.00 0.00 39.84 1.85
5688 9603 3.503800 GACCTTTAGTCCCCACACTTT 57.496 47.619 0.00 0.00 39.84 2.66
5710 9625 0.543277 GGAACCGGTACTAAAGGGGG 59.457 60.000 8.00 0.00 0.00 5.40
5711 9626 0.176449 CGGAACCGGTACTAAAGGGG 59.824 60.000 8.00 0.00 35.56 4.79
5712 9627 0.460811 GCGGAACCGGTACTAAAGGG 60.461 60.000 8.00 0.00 40.19 3.95
5713 9628 0.247185 TGCGGAACCGGTACTAAAGG 59.753 55.000 8.00 0.00 40.19 3.11
5714 9629 1.353076 GTGCGGAACCGGTACTAAAG 58.647 55.000 8.00 0.00 40.19 1.85
5715 9630 0.388391 CGTGCGGAACCGGTACTAAA 60.388 55.000 8.00 0.00 40.19 1.85
5716 9631 1.212490 CGTGCGGAACCGGTACTAA 59.788 57.895 8.00 0.00 40.19 2.24
5717 9632 1.240641 TTCGTGCGGAACCGGTACTA 61.241 55.000 8.00 0.00 40.19 1.82
5718 9633 2.563798 TTCGTGCGGAACCGGTACT 61.564 57.895 8.00 0.00 40.19 2.73
5719 9634 2.049248 TTCGTGCGGAACCGGTAC 60.049 61.111 8.00 2.70 40.19 3.34
5731 9646 1.296056 CCCTTTAGCACCGGTTCGTG 61.296 60.000 2.97 0.00 36.80 4.35
5732 9647 1.004200 CCCTTTAGCACCGGTTCGT 60.004 57.895 2.97 0.00 0.00 3.85
5733 9648 2.396157 GCCCTTTAGCACCGGTTCG 61.396 63.158 2.97 0.00 0.00 3.95
5734 9649 0.891904 TTGCCCTTTAGCACCGGTTC 60.892 55.000 2.97 0.00 43.97 3.62
5735 9650 1.151908 TTGCCCTTTAGCACCGGTT 59.848 52.632 2.97 0.00 43.97 4.44
5736 9651 1.602605 GTTGCCCTTTAGCACCGGT 60.603 57.895 0.00 0.00 43.97 5.28
5737 9652 2.340328 GGTTGCCCTTTAGCACCGG 61.340 63.158 0.00 0.00 43.97 5.28
5738 9653 1.602323 TGGTTGCCCTTTAGCACCG 60.602 57.895 0.00 0.00 43.97 4.94
5739 9654 1.862602 CGTGGTTGCCCTTTAGCACC 61.863 60.000 0.00 0.00 43.97 5.01
5740 9655 1.170290 ACGTGGTTGCCCTTTAGCAC 61.170 55.000 0.00 0.00 43.97 4.40
5741 9656 1.149627 ACGTGGTTGCCCTTTAGCA 59.850 52.632 0.00 0.00 42.17 3.49
5742 9657 1.579429 CACGTGGTTGCCCTTTAGC 59.421 57.895 7.95 0.00 0.00 3.09
5743 9658 1.862602 GCCACGTGGTTGCCCTTTAG 61.863 60.000 33.92 6.07 37.57 1.85
5744 9659 1.899534 GCCACGTGGTTGCCCTTTA 60.900 57.895 33.92 0.00 37.57 1.85
5745 9660 3.223589 GCCACGTGGTTGCCCTTT 61.224 61.111 33.92 0.00 37.57 3.11
5746 9661 4.514585 TGCCACGTGGTTGCCCTT 62.515 61.111 33.92 0.00 37.57 3.95
5750 9665 4.012895 CTCGTGCCACGTGGTTGC 62.013 66.667 33.92 20.95 43.14 4.17
5751 9666 2.587753 ACTCGTGCCACGTGGTTG 60.588 61.111 33.92 23.28 43.14 3.77
5752 9667 2.279918 GACTCGTGCCACGTGGTT 60.280 61.111 33.92 12.83 43.14 3.67
5753 9668 3.499929 CTGACTCGTGCCACGTGGT 62.500 63.158 33.92 14.84 43.14 4.16
5754 9669 2.734723 CTGACTCGTGCCACGTGG 60.735 66.667 30.66 30.66 43.14 4.94
5755 9670 3.406361 GCTGACTCGTGCCACGTG 61.406 66.667 17.83 17.30 43.14 4.49
5756 9671 3.559657 GAGCTGACTCGTGCCACGT 62.560 63.158 17.83 0.00 43.14 4.49
5757 9672 2.807045 GAGCTGACTCGTGCCACG 60.807 66.667 11.80 11.80 44.19 4.94
5758 9673 2.433318 GGAGCTGACTCGTGCCAC 60.433 66.667 0.00 0.00 44.48 5.01
5759 9674 4.056125 CGGAGCTGACTCGTGCCA 62.056 66.667 0.00 0.00 44.48 4.92
5760 9675 4.803426 CCGGAGCTGACTCGTGCC 62.803 72.222 0.00 0.00 44.48 5.01
5761 9676 4.803426 CCCGGAGCTGACTCGTGC 62.803 72.222 0.73 0.00 44.48 5.34


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

AutoCloner maintained by Alex Coulton.