Multiple sequence alignment - TraesCS2B01G281100

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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 TraesCS2B01G281100 chr2B 100.000 5447 0 0 1 5447 388101951 388107397 0.000000e+00 10059.0
1 TraesCS2B01G281100 chr2B 81.517 211 34 5 1 209 199405635 199405428 9.380000e-38 169.0
2 TraesCS2B01G281100 chr2D 94.260 5192 182 50 2 5147 320157716 320162837 0.000000e+00 7830.0
3 TraesCS2B01G281100 chr2D 77.055 292 52 14 1 284 462260891 462260607 2.630000e-33 154.0
4 TraesCS2B01G281100 chr2A 94.218 4514 173 35 662 5147 411127072 411122619 0.000000e+00 6809.0
5 TraesCS2B01G281100 chr2A 89.634 164 12 5 5240 5399 411122613 411122451 2.570000e-48 204.0
6 TraesCS2B01G281100 chr3D 82.090 268 36 8 1 264 559262322 559262581 9.190000e-53 219.0
7 TraesCS2B01G281100 chr3B 79.868 303 44 13 43 336 655621855 655621561 7.150000e-49 206.0
8 TraesCS2B01G281100 chr3B 81.429 140 21 5 176 312 43048897 43048760 5.770000e-20 110.0
9 TraesCS2B01G281100 chr6B 82.203 236 30 10 50 280 19089996 19089768 5.570000e-45 193.0
10 TraesCS2B01G281100 chr3A 81.197 234 36 4 32 264 695778848 695779074 1.210000e-41 182.0
11 TraesCS2B01G281100 chr7B 81.308 214 29 8 1 209 490427299 490427506 4.370000e-36 163.0
12 TraesCS2B01G281100 chr7B 82.447 188 23 7 1 183 490428027 490428209 7.310000e-34 156.0
13 TraesCS2B01G281100 chr7D 82.857 140 18 5 174 308 68927862 68928000 2.660000e-23 121.0
14 TraesCS2B01G281100 chr5B 78.095 105 16 5 234 332 466987232 466987335 5.890000e-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 TraesCS2B01G281100 chr2B 388101951 388107397 5446 False 10059.0 10059 100.000 1 5447 1 chr2B.!!$F1 5446
1 TraesCS2B01G281100 chr2D 320157716 320162837 5121 False 7830.0 7830 94.260 2 5147 1 chr2D.!!$F1 5145
2 TraesCS2B01G281100 chr2A 411122451 411127072 4621 True 3506.5 6809 91.926 662 5399 2 chr2A.!!$R1 4737

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
597 625 0.804933 GGCCCAGTCGTACGCTTTAG 60.805 60.000 11.24 0.04 0.00 1.85 F
1346 1381 0.114954 TTGCTTCCTGCCCCTGATTT 59.885 50.000 0.00 0.00 42.00 2.17 F
2231 2269 0.398318 GCAGAGAAGGGGACACAAGT 59.602 55.000 0.00 0.00 0.00 3.16 F
2407 2445 1.210722 GAGATGGAGAGGACCCAAACC 59.789 57.143 0.00 0.00 37.22 3.27 F
2572 2610 1.774639 CACAAATGTGGAAGCTGCAC 58.225 50.000 1.02 0.00 42.10 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1854 0.250727 TTCCGTTTCCCCAGCTTGAG 60.251 55.000 0.00 0.00 0.00 3.02 R
2572 2610 0.392193 GTGACATCAGCACCTCTGGG 60.392 60.000 0.00 0.00 43.06 4.45 R
3657 3702 4.709397 AGTGGAGACCATCAACAACAAAAA 59.291 37.500 0.00 0.00 33.82 1.94 R
4236 4283 7.223387 GGAACAACATTCAGCATTAATGATTCC 59.777 37.037 19.73 9.27 37.30 3.01 R
4486 4533 1.880819 CTGCCATCCAACACAAGCCC 61.881 60.000 0.00 0.00 0.00 5.19 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
100 101 2.156697 ACAAACAACTTTTGCACGCAAC 59.843 40.909 3.45 0.00 35.46 4.17
154 155 8.663911 TGAAAACATGAACCTTGTTTGAAATTC 58.336 29.630 0.00 6.16 44.32 2.17
173 174 8.233190 TGAAATTCGCAAACAATTTTTGAAACT 58.767 25.926 13.72 0.40 34.30 2.66
217 218 6.090088 CCGAACAAAACTTGAAAACATGAACA 59.910 34.615 0.00 0.00 0.00 3.18
280 281 7.608308 TTTTTGAAACTCCCAAACAAGATTG 57.392 32.000 0.00 0.00 33.74 2.67
320 322 8.955061 TTTTGAAAATTTGCGAACAATTTTGA 57.045 23.077 13.78 6.18 38.62 2.69
321 323 8.955061 TTTGAAAATTTGCGAACAATTTTGAA 57.045 23.077 13.78 10.43 38.62 2.69
322 324 8.955061 TTGAAAATTTGCGAACAATTTTGAAA 57.045 23.077 13.78 7.95 38.62 2.69
323 325 8.955061 TGAAAATTTGCGAACAATTTTGAAAA 57.045 23.077 13.78 0.00 38.62 2.29
324 326 9.565213 TGAAAATTTGCGAACAATTTTGAAAAT 57.435 22.222 13.78 0.00 38.62 1.82
325 327 9.818343 GAAAATTTGCGAACAATTTTGAAAATG 57.182 25.926 3.62 1.85 38.62 2.32
326 328 6.973006 ATTTGCGAACAATTTTGAAAATGC 57.027 29.167 3.62 3.69 34.20 3.56
327 329 4.112793 TGCGAACAATTTTGAAAATGCG 57.887 36.364 3.62 7.34 0.00 4.73
328 330 3.798878 TGCGAACAATTTTGAAAATGCGA 59.201 34.783 3.62 0.00 0.00 5.10
329 331 4.268644 TGCGAACAATTTTGAAAATGCGAA 59.731 33.333 3.62 0.00 0.00 4.70
330 332 4.602740 GCGAACAATTTTGAAAATGCGAAC 59.397 37.500 3.62 0.00 0.00 3.95
331 333 5.722237 CGAACAATTTTGAAAATGCGAACA 58.278 33.333 3.62 0.00 0.00 3.18
332 334 6.354080 CGAACAATTTTGAAAATGCGAACAT 58.646 32.000 3.62 0.00 38.49 2.71
351 353 7.090173 CGAACATTTTTCTGTGTCCCAAATAT 58.910 34.615 0.00 0.00 0.00 1.28
397 399 7.769272 TTGAACAAGCACATAAAGAAAAAGG 57.231 32.000 0.00 0.00 0.00 3.11
399 401 6.097554 TGAACAAGCACATAAAGAAAAAGGGA 59.902 34.615 0.00 0.00 0.00 4.20
401 403 7.066307 ACAAGCACATAAAGAAAAAGGGAAT 57.934 32.000 0.00 0.00 0.00 3.01
493 505 4.143986 GGAACCTTCTAGATGGTTCCAG 57.856 50.000 46.66 23.93 40.55 3.86
523 535 0.853530 AGACCAGGGCTGAAACCTTT 59.146 50.000 0.00 0.00 35.78 3.11
526 538 0.961753 CCAGGGCTGAAACCTTTCAC 59.038 55.000 0.00 0.00 41.88 3.18
529 541 2.035066 CAGGGCTGAAACCTTTCACAAG 59.965 50.000 0.00 0.00 41.88 3.16
548 560 1.073923 AGGTTCTCAAAACCGGATGCT 59.926 47.619 9.46 0.00 44.82 3.79
551 563 4.163458 AGGTTCTCAAAACCGGATGCTATA 59.837 41.667 9.46 0.00 44.82 1.31
594 622 4.430765 CGGCCCAGTCGTACGCTT 62.431 66.667 11.24 0.00 0.00 4.68
597 625 0.804933 GGCCCAGTCGTACGCTTTAG 60.805 60.000 11.24 0.04 0.00 1.85
618 648 1.719780 GCGTTACCTCGACAGTTTGAG 59.280 52.381 0.00 0.00 33.35 3.02
647 679 5.992217 AGAGCGTCATATAGGAAATTCCAAC 59.008 40.000 15.21 1.90 39.61 3.77
655 687 8.564574 TCATATAGGAAATTCCAACGCAAATAC 58.435 33.333 15.21 0.00 39.61 1.89
665 697 5.968254 TCCAACGCAAATACATAGTACAGA 58.032 37.500 0.00 0.00 0.00 3.41
668 700 4.357142 ACGCAAATACATAGTACAGACCG 58.643 43.478 0.00 0.00 0.00 4.79
675 707 7.642082 AATACATAGTACAGACCGAACTCTT 57.358 36.000 0.00 0.00 0.00 2.85
677 709 5.952033 ACATAGTACAGACCGAACTCTTTC 58.048 41.667 0.00 0.00 0.00 2.62
697 729 9.617975 CTCTTTCTTTTAGACAAATTGGATCAC 57.382 33.333 0.00 0.00 0.00 3.06
725 757 7.946918 TTGATGCAATTTCGTTTATTCGTAG 57.053 32.000 0.00 0.00 0.00 3.51
778 812 1.161843 CAAACTCGTACGGCCCAATT 58.838 50.000 16.52 0.00 0.00 2.32
779 813 1.129811 CAAACTCGTACGGCCCAATTC 59.870 52.381 16.52 0.00 0.00 2.17
860 894 1.437573 CTAATCCAGGCAGCGACGA 59.562 57.895 0.00 0.00 0.00 4.20
861 895 0.872021 CTAATCCAGGCAGCGACGAC 60.872 60.000 0.00 0.00 0.00 4.34
862 896 2.607668 TAATCCAGGCAGCGACGACG 62.608 60.000 2.12 2.12 42.93 5.12
887 921 4.376176 CGCCCCCGAAACCACGTA 62.376 66.667 0.00 0.00 36.29 3.57
964 999 0.869880 TGATGCGCTCGGTGTATTCG 60.870 55.000 9.73 0.00 0.00 3.34
1008 1043 4.855298 AAAACTAGATCGGATGGGGAAA 57.145 40.909 0.00 0.00 0.00 3.13
1116 1151 2.184322 GATTCAGCCACGCCGAGA 59.816 61.111 0.00 0.00 0.00 4.04
1320 1355 3.641906 AGGGTTTATCCATCTGGTAGTCG 59.358 47.826 0.00 0.00 38.11 4.18
1346 1381 0.114954 TTGCTTCCTGCCCCTGATTT 59.885 50.000 0.00 0.00 42.00 2.17
1352 1387 0.901580 CCTGCCCCTGATTTGCACTT 60.902 55.000 0.00 0.00 0.00 3.16
1353 1388 0.971386 CTGCCCCTGATTTGCACTTT 59.029 50.000 0.00 0.00 0.00 2.66
1355 1390 1.260544 GCCCCTGATTTGCACTTTCT 58.739 50.000 0.00 0.00 0.00 2.52
1360 1395 3.181483 CCCTGATTTGCACTTTCTATGCC 60.181 47.826 0.00 0.00 42.69 4.40
1368 1403 4.081406 TGCACTTTCTATGCCAATCTGTT 58.919 39.130 0.00 0.00 42.69 3.16
1373 1408 5.928264 ACTTTCTATGCCAATCTGTTTTTGC 59.072 36.000 0.00 0.00 0.00 3.68
1534 1569 3.728474 CATCGGGTGCTGATGCTC 58.272 61.111 0.00 0.00 39.85 4.26
1554 1589 2.469516 CGCCACGGGTAAATCAGGC 61.470 63.158 0.00 0.00 38.73 4.85
1588 1623 2.426431 TGGGGAAGGTGTTCTAGGAA 57.574 50.000 0.00 0.00 32.72 3.36
1738 1773 3.133542 TGTACCAGGAGATGATGAAGCTG 59.866 47.826 0.00 0.00 0.00 4.24
1781 1816 2.843113 AGGATCTAGGCTTTTCTGCTGT 59.157 45.455 0.00 0.00 0.00 4.40
1988 2026 1.148027 TGGAGAGGGTCAAGACTGTCT 59.852 52.381 4.06 4.06 0.00 3.41
2140 2178 2.170166 GAAATGTTGGCACAGATGGGA 58.830 47.619 0.00 0.00 42.39 4.37
2144 2182 0.819582 GTTGGCACAGATGGGAATGG 59.180 55.000 0.00 0.00 42.39 3.16
2151 2189 3.355378 CACAGATGGGAATGGTGCTTTA 58.645 45.455 0.00 0.00 0.00 1.85
2185 2223 5.508200 AGTTAGTATGAGCACAGTAGAGC 57.492 43.478 0.00 0.00 0.00 4.09
2205 2243 2.321263 ATCCATGCTGTCCAGAGGCG 62.321 60.000 0.00 0.00 0.00 5.52
2229 2267 1.059584 TGGCAGAGAAGGGGACACAA 61.060 55.000 0.00 0.00 0.00 3.33
2231 2269 0.398318 GCAGAGAAGGGGACACAAGT 59.602 55.000 0.00 0.00 0.00 3.16
2407 2445 1.210722 GAGATGGAGAGGACCCAAACC 59.789 57.143 0.00 0.00 37.22 3.27
2545 2583 4.858850 TGTTGTGCCAGATAAATCAGGAT 58.141 39.130 5.64 0.00 35.67 3.24
2572 2610 1.774639 CACAAATGTGGAAGCTGCAC 58.225 50.000 1.02 0.00 42.10 4.57
2681 2719 8.797438 GGAGGAAAATAAAGTGAATGAAGACTT 58.203 33.333 0.00 0.00 33.75 3.01
2717 2755 8.157476 ACCTAAGCTCAAGAAACAGAAGAAATA 58.843 33.333 0.00 0.00 0.00 1.40
2897 2935 7.336931 TCCTGAGGTAAACATAGCTGAAAATTC 59.663 37.037 0.00 0.00 0.00 2.17
2925 2963 5.396436 GGAGGGAAAGAATGAGAATAACGGA 60.396 44.000 0.00 0.00 0.00 4.69
3508 3553 6.406370 TCTTCACTTGACATGATTTATCCGT 58.594 36.000 0.00 0.00 0.00 4.69
3657 3702 4.410228 TGCTACTTCTAATCTCTGGCCAAT 59.590 41.667 7.01 0.00 0.00 3.16
3704 3749 5.260424 TGGAGTATAATTGCAAGAAAGCCA 58.740 37.500 4.94 3.84 0.00 4.75
4082 4129 4.220693 TGTATGTGTTGATGCTAAGCCT 57.779 40.909 0.00 0.00 0.00 4.58
4236 4283 4.838681 TGCGTTACTGTTTTACATGTGTG 58.161 39.130 9.11 0.00 0.00 3.82
4507 4554 0.524862 GCTTGTGTTGGATGGCAGAG 59.475 55.000 0.00 0.00 0.00 3.35
4594 4641 4.099419 GGGGGTATTGGTGATTTGAACATC 59.901 45.833 0.00 0.00 0.00 3.06
4665 4715 1.134226 GGTGTTCACAAGGTCGTACG 58.866 55.000 9.53 9.53 0.00 3.67
4700 4752 5.759506 TGTACTTTGGTTACACATGTTGG 57.240 39.130 0.00 0.00 0.00 3.77
4730 4782 5.946377 GTCATTAGTCATTCTTTCCCCTGTT 59.054 40.000 0.00 0.00 0.00 3.16
4744 4796 3.655777 TCCCCTGTTTCAAGGATAACAGT 59.344 43.478 12.38 0.00 46.13 3.55
4798 4852 8.528044 AAAAGTTGGTCAAGTATGTTTAAGGA 57.472 30.769 0.00 0.00 0.00 3.36
4799 4853 8.706322 AAAGTTGGTCAAGTATGTTTAAGGAT 57.294 30.769 0.00 0.00 0.00 3.24
4800 4854 7.687941 AGTTGGTCAAGTATGTTTAAGGATG 57.312 36.000 0.00 0.00 0.00 3.51
4801 4855 7.231467 AGTTGGTCAAGTATGTTTAAGGATGT 58.769 34.615 0.00 0.00 0.00 3.06
4803 4857 9.005777 GTTGGTCAAGTATGTTTAAGGATGTTA 57.994 33.333 0.00 0.00 0.00 2.41
4873 4928 9.299963 TGTAATCTTTTCACATTTGTTGAACTG 57.700 29.630 0.00 0.00 0.00 3.16
4876 4931 8.856490 ATCTTTTCACATTTGTTGAACTGTAC 57.144 30.769 0.00 0.00 0.00 2.90
4877 4932 7.254852 TCTTTTCACATTTGTTGAACTGTACC 58.745 34.615 0.00 0.00 0.00 3.34
4878 4933 6.767524 TTTCACATTTGTTGAACTGTACCT 57.232 33.333 0.00 0.00 0.00 3.08
4894 4957 4.513442 TGTACCTCCAATGCTGTTGATAC 58.487 43.478 4.30 3.16 0.00 2.24
4958 5021 3.506067 GGTTGTTCTATGTTGGGACTTGG 59.494 47.826 0.00 0.00 0.00 3.61
4967 5030 3.486383 TGTTGGGACTTGGAATCTTGTC 58.514 45.455 0.00 0.00 0.00 3.18
4975 5038 4.451900 ACTTGGAATCTTGTCGACTTTGT 58.548 39.130 17.92 0.00 0.00 2.83
5002 5067 5.809562 CCAACATTTGTCTTGCTGTTTTGTA 59.190 36.000 0.00 0.00 29.74 2.41
5076 5141 0.723414 CACTCGCGAATGCTGTCATT 59.277 50.000 11.33 0.00 45.04 2.57
5079 5144 2.171567 CTCGCGAATGCTGTCATTTTG 58.828 47.619 11.33 0.00 42.60 2.44
5085 5150 3.609879 CGAATGCTGTCATTTTGTGAGCA 60.610 43.478 0.00 0.00 42.60 4.26
5086 5151 4.491676 GAATGCTGTCATTTTGTGAGCAT 58.508 39.130 0.00 0.00 45.41 3.79
5118 5183 4.022416 TGTCAATATGGTGGCAGTTTTGTC 60.022 41.667 0.00 0.00 0.00 3.18
5150 5215 9.632638 AGATGTGATTAGTAATAATTGTGCCTT 57.367 29.630 0.00 0.00 0.00 4.35
5151 5216 9.669353 GATGTGATTAGTAATAATTGTGCCTTG 57.331 33.333 0.00 0.00 0.00 3.61
5152 5217 7.479980 TGTGATTAGTAATAATTGTGCCTTGC 58.520 34.615 0.00 0.00 0.00 4.01
5153 5218 6.632834 GTGATTAGTAATAATTGTGCCTTGCG 59.367 38.462 0.00 0.00 0.00 4.85
5154 5219 5.493133 TTAGTAATAATTGTGCCTTGCGG 57.507 39.130 0.00 0.00 0.00 5.69
5155 5220 3.352648 AGTAATAATTGTGCCTTGCGGT 58.647 40.909 0.00 0.00 0.00 5.68
5156 5221 2.939460 AATAATTGTGCCTTGCGGTC 57.061 45.000 0.00 0.00 0.00 4.79
5157 5222 2.128771 ATAATTGTGCCTTGCGGTCT 57.871 45.000 0.00 0.00 0.00 3.85
5158 5223 1.904287 TAATTGTGCCTTGCGGTCTT 58.096 45.000 0.00 0.00 0.00 3.01
5159 5224 0.314935 AATTGTGCCTTGCGGTCTTG 59.685 50.000 0.00 0.00 0.00 3.02
5160 5225 0.823356 ATTGTGCCTTGCGGTCTTGT 60.823 50.000 0.00 0.00 0.00 3.16
5161 5226 1.723608 TTGTGCCTTGCGGTCTTGTG 61.724 55.000 0.00 0.00 0.00 3.33
5162 5227 3.286751 TGCCTTGCGGTCTTGTGC 61.287 61.111 0.00 0.00 0.00 4.57
5163 5228 4.389576 GCCTTGCGGTCTTGTGCG 62.390 66.667 0.00 0.00 0.00 5.34
5164 5229 2.664851 CCTTGCGGTCTTGTGCGA 60.665 61.111 0.00 0.00 0.00 5.10
5165 5230 2.250939 CCTTGCGGTCTTGTGCGAA 61.251 57.895 0.00 0.00 0.00 4.70
5166 5231 1.646540 CTTGCGGTCTTGTGCGAAA 59.353 52.632 0.00 0.00 0.00 3.46
5167 5232 0.657368 CTTGCGGTCTTGTGCGAAAC 60.657 55.000 0.00 0.00 0.00 2.78
5168 5233 1.092921 TTGCGGTCTTGTGCGAAACT 61.093 50.000 0.00 0.00 0.00 2.66
5169 5234 0.249531 TGCGGTCTTGTGCGAAACTA 60.250 50.000 0.00 0.00 0.00 2.24
5170 5235 0.863144 GCGGTCTTGTGCGAAACTAA 59.137 50.000 0.00 0.00 0.00 2.24
5171 5236 1.398071 GCGGTCTTGTGCGAAACTAAC 60.398 52.381 0.00 0.00 0.00 2.34
5172 5237 2.132762 CGGTCTTGTGCGAAACTAACT 58.867 47.619 0.00 0.00 0.00 2.24
5173 5238 2.096909 CGGTCTTGTGCGAAACTAACTG 60.097 50.000 0.00 0.00 0.00 3.16
5174 5239 2.223377 GGTCTTGTGCGAAACTAACTGG 59.777 50.000 0.00 0.00 0.00 4.00
5175 5240 1.871039 TCTTGTGCGAAACTAACTGGC 59.129 47.619 0.00 0.00 0.00 4.85
5176 5241 1.601903 CTTGTGCGAAACTAACTGGCA 59.398 47.619 0.00 0.00 0.00 4.92
5177 5242 1.890876 TGTGCGAAACTAACTGGCAT 58.109 45.000 0.00 0.00 35.88 4.40
5178 5243 2.226330 TGTGCGAAACTAACTGGCATT 58.774 42.857 0.00 0.00 35.88 3.56
5179 5244 2.031245 TGTGCGAAACTAACTGGCATTG 60.031 45.455 0.00 0.00 35.88 2.82
5180 5245 2.031157 GTGCGAAACTAACTGGCATTGT 60.031 45.455 0.00 0.00 35.88 2.71
5181 5246 2.621055 TGCGAAACTAACTGGCATTGTT 59.379 40.909 0.00 0.00 0.00 2.83
5182 5247 2.979813 GCGAAACTAACTGGCATTGTTG 59.020 45.455 2.65 0.00 0.00 3.33
5192 5257 3.518381 GCATTGTTGCCAAGATGCA 57.482 47.368 16.58 0.00 43.38 3.96
5193 5258 2.018542 GCATTGTTGCCAAGATGCAT 57.981 45.000 16.58 0.00 43.38 3.96
5194 5259 1.663643 GCATTGTTGCCAAGATGCATG 59.336 47.619 16.58 0.00 43.38 4.06
5195 5260 2.675603 GCATTGTTGCCAAGATGCATGA 60.676 45.455 16.58 0.00 43.38 3.07
5196 5261 3.591023 CATTGTTGCCAAGATGCATGAA 58.409 40.909 2.46 0.00 41.70 2.57
5197 5262 3.965379 TTGTTGCCAAGATGCATGAAT 57.035 38.095 2.46 0.00 41.70 2.57
5198 5263 3.239587 TGTTGCCAAGATGCATGAATG 57.760 42.857 2.46 0.00 41.70 2.67
5199 5264 2.826725 TGTTGCCAAGATGCATGAATGA 59.173 40.909 2.46 0.00 41.70 2.57
5200 5265 3.258622 TGTTGCCAAGATGCATGAATGAA 59.741 39.130 2.46 0.00 41.70 2.57
5201 5266 4.081365 TGTTGCCAAGATGCATGAATGAAT 60.081 37.500 2.46 0.00 41.70 2.57
5202 5267 4.053469 TGCCAAGATGCATGAATGAATG 57.947 40.909 2.46 0.00 36.04 2.67
5203 5268 3.449377 TGCCAAGATGCATGAATGAATGT 59.551 39.130 2.46 0.00 36.04 2.71
5204 5269 3.802139 GCCAAGATGCATGAATGAATGTG 59.198 43.478 2.46 0.00 0.00 3.21
5205 5270 4.679639 GCCAAGATGCATGAATGAATGTGT 60.680 41.667 2.46 0.00 0.00 3.72
5206 5271 5.450826 GCCAAGATGCATGAATGAATGTGTA 60.451 40.000 2.46 0.00 0.00 2.90
5207 5272 6.737622 GCCAAGATGCATGAATGAATGTGTAT 60.738 38.462 2.46 0.00 0.00 2.29
5208 5273 6.640907 CCAAGATGCATGAATGAATGTGTATG 59.359 38.462 2.46 0.00 0.00 2.39
5209 5274 6.954487 AGATGCATGAATGAATGTGTATGT 57.046 33.333 2.46 0.00 0.00 2.29
5210 5275 8.347035 CAAGATGCATGAATGAATGTGTATGTA 58.653 33.333 2.46 0.00 0.00 2.29
5211 5276 8.095937 AGATGCATGAATGAATGTGTATGTAG 57.904 34.615 2.46 0.00 0.00 2.74
5212 5277 7.718314 AGATGCATGAATGAATGTGTATGTAGT 59.282 33.333 2.46 0.00 0.00 2.73
5213 5278 7.250445 TGCATGAATGAATGTGTATGTAGTC 57.750 36.000 0.00 0.00 0.00 2.59
5214 5279 7.049754 TGCATGAATGAATGTGTATGTAGTCT 58.950 34.615 0.00 0.00 0.00 3.24
5215 5280 7.553760 TGCATGAATGAATGTGTATGTAGTCTT 59.446 33.333 0.00 0.00 0.00 3.01
5216 5281 7.854422 GCATGAATGAATGTGTATGTAGTCTTG 59.146 37.037 0.00 0.00 0.00 3.02
5217 5282 7.848223 TGAATGAATGTGTATGTAGTCTTGG 57.152 36.000 0.00 0.00 0.00 3.61
5218 5283 7.619965 TGAATGAATGTGTATGTAGTCTTGGA 58.380 34.615 0.00 0.00 0.00 3.53
5219 5284 8.267183 TGAATGAATGTGTATGTAGTCTTGGAT 58.733 33.333 0.00 0.00 0.00 3.41
5220 5285 8.442632 AATGAATGTGTATGTAGTCTTGGATG 57.557 34.615 0.00 0.00 0.00 3.51
5221 5286 6.348498 TGAATGTGTATGTAGTCTTGGATGG 58.652 40.000 0.00 0.00 0.00 3.51
5222 5287 6.156083 TGAATGTGTATGTAGTCTTGGATGGA 59.844 38.462 0.00 0.00 0.00 3.41
5223 5288 5.598416 TGTGTATGTAGTCTTGGATGGAG 57.402 43.478 0.00 0.00 0.00 3.86
5224 5289 4.141937 TGTGTATGTAGTCTTGGATGGAGC 60.142 45.833 0.00 0.00 0.00 4.70
5225 5290 4.030216 TGTATGTAGTCTTGGATGGAGCA 58.970 43.478 0.00 0.00 0.00 4.26
5226 5291 3.834489 ATGTAGTCTTGGATGGAGCAG 57.166 47.619 0.00 0.00 0.00 4.24
5227 5292 1.833630 TGTAGTCTTGGATGGAGCAGG 59.166 52.381 0.00 0.00 0.00 4.85
5228 5293 2.111384 GTAGTCTTGGATGGAGCAGGA 58.889 52.381 0.00 0.00 0.00 3.86
5229 5294 1.202330 AGTCTTGGATGGAGCAGGAG 58.798 55.000 0.00 0.00 0.00 3.69
5230 5295 0.179936 GTCTTGGATGGAGCAGGAGG 59.820 60.000 0.00 0.00 0.00 4.30
5231 5296 0.984961 TCTTGGATGGAGCAGGAGGG 60.985 60.000 0.00 0.00 0.00 4.30
5232 5297 1.992519 CTTGGATGGAGCAGGAGGGG 61.993 65.000 0.00 0.00 0.00 4.79
5233 5298 2.367512 GGATGGAGCAGGAGGGGT 60.368 66.667 0.00 0.00 0.00 4.95
5234 5299 1.074471 GGATGGAGCAGGAGGGGTA 60.074 63.158 0.00 0.00 0.00 3.69
5235 5300 0.694444 GGATGGAGCAGGAGGGGTAA 60.694 60.000 0.00 0.00 0.00 2.85
5236 5301 0.761802 GATGGAGCAGGAGGGGTAAG 59.238 60.000 0.00 0.00 0.00 2.34
5237 5302 0.044855 ATGGAGCAGGAGGGGTAAGT 59.955 55.000 0.00 0.00 0.00 2.24
5254 5319 4.034858 GGTAAGTGATGACATGACATGCAG 59.965 45.833 15.41 0.00 0.00 4.41
5255 5320 2.014857 AGTGATGACATGACATGCAGC 58.985 47.619 15.41 15.96 0.00 5.25
5276 5348 2.281070 CACTGGTGCCGAAGTGCT 60.281 61.111 0.00 0.00 37.58 4.40
5288 5360 2.693591 CCGAAGTGCTTATCCTGACCTA 59.306 50.000 0.00 0.00 0.00 3.08
5289 5361 3.322254 CCGAAGTGCTTATCCTGACCTAT 59.678 47.826 0.00 0.00 0.00 2.57
5290 5362 4.302455 CGAAGTGCTTATCCTGACCTATG 58.698 47.826 0.00 0.00 0.00 2.23
5291 5363 4.038042 CGAAGTGCTTATCCTGACCTATGA 59.962 45.833 0.00 0.00 0.00 2.15
5292 5364 4.946478 AGTGCTTATCCTGACCTATGAC 57.054 45.455 0.00 0.00 0.00 3.06
5293 5365 4.551671 AGTGCTTATCCTGACCTATGACT 58.448 43.478 0.00 0.00 0.00 3.41
5297 5369 5.425217 TGCTTATCCTGACCTATGACTTTGA 59.575 40.000 0.00 0.00 0.00 2.69
5298 5370 6.100279 TGCTTATCCTGACCTATGACTTTGAT 59.900 38.462 0.00 0.00 0.00 2.57
5299 5371 6.426328 GCTTATCCTGACCTATGACTTTGATG 59.574 42.308 0.00 0.00 0.00 3.07
5300 5372 5.965033 ATCCTGACCTATGACTTTGATGT 57.035 39.130 0.00 0.00 0.00 3.06
5301 5373 5.344743 TCCTGACCTATGACTTTGATGTC 57.655 43.478 0.00 0.00 37.47 3.06
5323 5395 2.280797 GCGGGTTGCAGAGTCACA 60.281 61.111 0.00 0.00 45.45 3.58
5334 5406 1.878088 CAGAGTCACAAGTTGCATGCT 59.122 47.619 20.33 0.00 0.00 3.79
5339 5411 4.641396 AGTCACAAGTTGCATGCTAAGTA 58.359 39.130 20.33 0.00 0.00 2.24
5340 5412 4.452455 AGTCACAAGTTGCATGCTAAGTAC 59.548 41.667 20.33 9.00 0.00 2.73
5342 5414 4.690748 TCACAAGTTGCATGCTAAGTACTC 59.309 41.667 20.33 0.00 0.00 2.59
5345 5417 3.512680 AGTTGCATGCTAAGTACTCGAC 58.487 45.455 20.33 0.00 0.00 4.20
5354 5426 3.301116 GCTAAGTACTCGACGAAAGCAAG 59.699 47.826 0.00 0.00 34.19 4.01
5355 5427 1.699343 AGTACTCGACGAAAGCAAGC 58.301 50.000 0.00 0.00 0.00 4.01
5356 5428 1.269998 AGTACTCGACGAAAGCAAGCT 59.730 47.619 0.00 0.00 0.00 3.74
5357 5429 1.649662 GTACTCGACGAAAGCAAGCTC 59.350 52.381 0.00 0.00 0.00 4.09
5358 5430 0.032130 ACTCGACGAAAGCAAGCTCA 59.968 50.000 0.00 0.00 0.00 4.26
5399 5472 1.159285 ACACTGTTGTGATGATGGCG 58.841 50.000 3.03 0.00 46.55 5.69
5400 5473 0.448990 CACTGTTGTGATGATGGCGG 59.551 55.000 0.00 0.00 46.55 6.13
5401 5474 0.324614 ACTGTTGTGATGATGGCGGA 59.675 50.000 0.00 0.00 0.00 5.54
5402 5475 1.012086 CTGTTGTGATGATGGCGGAG 58.988 55.000 0.00 0.00 0.00 4.63
5417 5490 2.447244 CGGAGCTTTTGTCTCTGTCT 57.553 50.000 0.00 0.00 33.41 3.41
5418 5491 2.333014 CGGAGCTTTTGTCTCTGTCTC 58.667 52.381 0.00 0.00 33.41 3.36
5419 5492 2.029470 CGGAGCTTTTGTCTCTGTCTCT 60.029 50.000 0.00 0.00 33.41 3.10
5420 5493 3.584834 GGAGCTTTTGTCTCTGTCTCTC 58.415 50.000 0.00 0.00 0.00 3.20
5421 5494 3.258123 GGAGCTTTTGTCTCTGTCTCTCT 59.742 47.826 0.00 0.00 0.00 3.10
5422 5495 4.485163 GAGCTTTTGTCTCTGTCTCTCTC 58.515 47.826 0.00 0.00 0.00 3.20
5423 5496 4.151883 AGCTTTTGTCTCTGTCTCTCTCT 58.848 43.478 0.00 0.00 0.00 3.10
5424 5497 4.218417 AGCTTTTGTCTCTGTCTCTCTCTC 59.782 45.833 0.00 0.00 0.00 3.20
5425 5498 4.218417 GCTTTTGTCTCTGTCTCTCTCTCT 59.782 45.833 0.00 0.00 0.00 3.10
5426 5499 5.414454 GCTTTTGTCTCTGTCTCTCTCTCTA 59.586 44.000 0.00 0.00 0.00 2.43
5427 5500 6.072175 GCTTTTGTCTCTGTCTCTCTCTCTAA 60.072 42.308 0.00 0.00 0.00 2.10
5428 5501 7.523052 GCTTTTGTCTCTGTCTCTCTCTCTAAA 60.523 40.741 0.00 0.00 0.00 1.85
5429 5502 7.825331 TTTGTCTCTGTCTCTCTCTCTAAAA 57.175 36.000 0.00 0.00 0.00 1.52
5430 5503 7.825331 TTGTCTCTGTCTCTCTCTCTAAAAA 57.175 36.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.773976 TTTGAAAAGTCATTCCTGTTCAGT 57.226 33.333 0.00 0.00 39.30 3.41
23 24 9.710900 ATGTTCCTATTTTTGAAAAGTCATTCC 57.289 29.630 0.00 0.00 32.48 3.01
61 62 9.025020 GTTGTTTGTGTTTCCAAATTTTGTTTT 57.975 25.926 8.26 0.00 36.75 2.43
124 125 8.383318 TCAAACAAGGTTCATGTTTTCAAAAA 57.617 26.923 2.14 0.00 45.97 1.94
125 126 7.969536 TCAAACAAGGTTCATGTTTTCAAAA 57.030 28.000 2.14 0.00 45.97 2.44
154 155 6.302615 TGTTCAGTTTCAAAAATTGTTTGCG 58.697 32.000 0.00 0.00 0.00 4.85
160 161 8.386606 TCGGAAAATGTTCAGTTTCAAAAATTG 58.613 29.630 21.25 7.25 35.80 2.32
173 174 2.550606 CGGGAGTTTCGGAAAATGTTCA 59.449 45.455 8.29 0.00 35.25 3.18
183 184 1.944709 AGTTTTGTTCGGGAGTTTCGG 59.055 47.619 0.00 0.00 0.00 4.30
322 324 8.570260 TTGGGACACAGAAAAATGTTCGCATT 62.570 38.462 0.00 0.00 44.45 3.56
323 325 3.305335 GGGACACAGAAAAATGTTCGCAT 60.305 43.478 0.00 0.00 40.03 4.73
324 326 2.034053 GGGACACAGAAAAATGTTCGCA 59.966 45.455 0.00 0.00 0.00 5.10
325 327 2.034053 TGGGACACAGAAAAATGTTCGC 59.966 45.455 0.00 0.00 0.00 4.70
326 328 3.980646 TGGGACACAGAAAAATGTTCG 57.019 42.857 0.00 0.00 0.00 3.95
327 329 8.831715 AATATTTGGGACACAGAAAAATGTTC 57.168 30.769 0.00 0.00 39.29 3.18
328 330 9.625747 AAAATATTTGGGACACAGAAAAATGTT 57.374 25.926 0.39 0.00 39.29 2.71
329 331 9.625747 AAAAATATTTGGGACACAGAAAAATGT 57.374 25.926 0.39 0.00 39.29 2.71
359 361 7.434897 TGTGCTTGTTCAATATTTCACAACTTC 59.565 33.333 5.45 1.15 31.31 3.01
360 362 7.264221 TGTGCTTGTTCAATATTTCACAACTT 58.736 30.769 5.45 0.00 31.31 2.66
492 504 3.076032 AGCCCTGGTCTTTATTGGTTTCT 59.924 43.478 0.00 0.00 0.00 2.52
493 505 3.193479 CAGCCCTGGTCTTTATTGGTTTC 59.807 47.826 0.00 0.00 0.00 2.78
523 535 2.092861 TCCGGTTTTGAGAACCTTGTGA 60.093 45.455 0.00 0.00 38.15 3.58
526 538 2.351738 GCATCCGGTTTTGAGAACCTTG 60.352 50.000 0.00 0.19 38.15 3.61
529 541 1.534729 AGCATCCGGTTTTGAGAACC 58.465 50.000 0.00 0.00 36.96 3.62
534 546 4.986034 CGTGTATATAGCATCCGGTTTTGA 59.014 41.667 0.00 0.00 0.00 2.69
548 560 9.110502 CCATCAGAGCTATCTAACGTGTATATA 57.889 37.037 0.00 0.00 33.22 0.86
551 563 5.184096 CCCATCAGAGCTATCTAACGTGTAT 59.816 44.000 0.00 0.00 33.22 2.29
597 625 0.788391 CAAACTGTCGAGGTAACGCC 59.212 55.000 0.00 0.00 46.39 5.68
608 636 3.391049 ACGCTCTTTACCTCAAACTGTC 58.609 45.455 0.00 0.00 0.00 3.51
618 648 7.117956 GGAATTTCCTATATGACGCTCTTTACC 59.882 40.741 8.25 0.00 32.53 2.85
620 650 7.732025 TGGAATTTCCTATATGACGCTCTTTA 58.268 34.615 16.25 0.00 37.46 1.85
647 679 4.603985 TCGGTCTGTACTATGTATTTGCG 58.396 43.478 0.00 0.00 0.00 4.85
655 687 6.197364 AGAAAGAGTTCGGTCTGTACTATG 57.803 41.667 0.00 0.00 38.90 2.23
665 697 7.803279 ATTTGTCTAAAAGAAAGAGTTCGGT 57.197 32.000 0.00 0.00 38.90 4.69
697 729 9.009327 ACGAATAAACGAAATTGCATCAATTAG 57.991 29.630 5.35 5.90 38.51 1.73
746 779 5.447683 CGTACGAGTTTGGCTGTACTATGTA 60.448 44.000 10.44 0.00 36.04 2.29
778 812 0.322456 ACGCAAAGCCCTGCTATTGA 60.322 50.000 6.11 0.00 38.25 2.57
779 813 0.179156 CACGCAAAGCCCTGCTATTG 60.179 55.000 6.11 0.00 38.25 1.90
874 908 3.484547 GCGCTACGTGGTTTCGGG 61.485 66.667 0.00 0.00 34.94 5.14
1235 1270 0.665835 GGACACACGCATTTTCACCA 59.334 50.000 0.00 0.00 0.00 4.17
1288 1323 1.629353 GGATAAACCCTAGGCCCTAGC 59.371 57.143 12.62 0.00 33.12 3.42
1289 1324 2.986050 TGGATAAACCCTAGGCCCTAG 58.014 52.381 11.08 11.08 38.00 3.02
1290 1325 3.146055 AGATGGATAAACCCTAGGCCCTA 59.854 47.826 2.05 0.00 38.00 3.53
1291 1326 2.089350 AGATGGATAAACCCTAGGCCCT 60.089 50.000 2.05 0.00 38.00 5.19
1292 1327 2.040412 CAGATGGATAAACCCTAGGCCC 59.960 54.545 2.05 0.00 38.00 5.80
1293 1328 2.040412 CCAGATGGATAAACCCTAGGCC 59.960 54.545 2.05 0.00 37.39 5.19
1294 1329 2.711547 ACCAGATGGATAAACCCTAGGC 59.288 50.000 2.05 0.00 38.94 3.93
1295 1330 5.155905 ACTACCAGATGGATAAACCCTAGG 58.844 45.833 5.72 0.06 38.94 3.02
1296 1331 5.047943 CGACTACCAGATGGATAAACCCTAG 60.048 48.000 5.72 0.00 38.94 3.02
1297 1332 4.831155 CGACTACCAGATGGATAAACCCTA 59.169 45.833 5.72 0.00 38.94 3.53
1298 1333 3.641906 CGACTACCAGATGGATAAACCCT 59.358 47.826 5.72 0.00 38.94 4.34
1346 1381 3.689347 ACAGATTGGCATAGAAAGTGCA 58.311 40.909 0.00 0.00 44.25 4.57
1352 1387 5.726980 AGCAAAAACAGATTGGCATAGAA 57.273 34.783 0.00 0.00 0.00 2.10
1353 1388 5.726980 AAGCAAAAACAGATTGGCATAGA 57.273 34.783 0.00 0.00 0.00 1.98
1355 1390 5.011943 AGGAAAGCAAAAACAGATTGGCATA 59.988 36.000 0.00 0.00 0.00 3.14
1360 1395 5.581874 ACACAAGGAAAGCAAAAACAGATTG 59.418 36.000 0.00 0.00 0.00 2.67
1368 1403 3.608316 AGCAACACAAGGAAAGCAAAA 57.392 38.095 0.00 0.00 0.00 2.44
1373 1408 2.951642 TCTCCAAGCAACACAAGGAAAG 59.048 45.455 0.00 0.00 0.00 2.62
1554 1589 0.812811 CCCCATCAGTGCAGTCATCG 60.813 60.000 0.00 0.00 0.00 3.84
1600 1635 9.533253 CTTCTTATTCCTTTTTCTTTTCTTGCA 57.467 29.630 0.00 0.00 0.00 4.08
1667 1702 4.261405 CGGATTTGTTTACCTCAACAGCAA 60.261 41.667 0.00 0.00 37.93 3.91
1738 1773 0.539986 TCATTTCTGGGACGCCTACC 59.460 55.000 0.00 0.00 0.00 3.18
1781 1816 5.414454 GGTACATCCTGTTCTGCAATGTTTA 59.586 40.000 3.45 0.00 32.56 2.01
1819 1854 0.250727 TTCCGTTTCCCCAGCTTGAG 60.251 55.000 0.00 0.00 0.00 3.02
1820 1855 0.404040 ATTCCGTTTCCCCAGCTTGA 59.596 50.000 0.00 0.00 0.00 3.02
1956 1994 1.918957 CCCTCTCCATTTCTGGGACTT 59.081 52.381 0.00 0.00 43.34 3.01
1988 2026 1.001068 TCGCCACAATGTTTACCTCGA 59.999 47.619 0.00 0.00 0.00 4.04
2140 2178 3.054139 TGAGCATCTCCTAAAGCACCATT 60.054 43.478 0.00 0.00 34.92 3.16
2144 2182 3.604582 ACTTGAGCATCTCCTAAAGCAC 58.395 45.455 0.00 0.00 34.92 4.40
2151 2189 6.403866 CTCATACTAACTTGAGCATCTCCT 57.596 41.667 0.00 0.00 33.56 3.69
2185 2223 0.818445 GCCTCTGGACAGCATGGATG 60.818 60.000 0.00 0.00 43.62 3.51
2205 2243 0.620556 TCCCCTTCTCTGCCATGTTC 59.379 55.000 0.00 0.00 0.00 3.18
2229 2267 2.613223 GGGCTTACGCTTCTTCTTCACT 60.613 50.000 0.00 0.00 36.09 3.41
2231 2269 1.346395 TGGGCTTACGCTTCTTCTTCA 59.654 47.619 0.00 0.00 36.09 3.02
2330 2368 4.512944 CACCATCACCATTCATACAGCTAC 59.487 45.833 0.00 0.00 0.00 3.58
2407 2445 0.808755 GCAATGTTTACCCCAGGACG 59.191 55.000 0.00 0.00 0.00 4.79
2470 2508 2.933056 GCTCCTGGTTCTTCTTCTTCCG 60.933 54.545 0.00 0.00 0.00 4.30
2572 2610 0.392193 GTGACATCAGCACCTCTGGG 60.392 60.000 0.00 0.00 43.06 4.45
2681 2719 3.458044 TGAGCTTAGGTTCCTGAGAGA 57.542 47.619 13.65 0.00 0.00 3.10
2717 2755 5.383476 CAGAAGGGGATTGATCTTGCTTAT 58.617 41.667 0.00 0.00 0.00 1.73
2897 2935 1.555075 TCTCATTCTTTCCCTCCACCG 59.445 52.381 0.00 0.00 0.00 4.94
2925 2963 2.354203 CCGCTTAGGCTTCTGAGAGTTT 60.354 50.000 0.00 0.00 36.09 2.66
3362 3400 9.317936 TCTTATGAAGACTGTTGCAATAGTATG 57.682 33.333 26.34 11.97 30.01 2.39
3508 3553 7.925043 TTAGAAAATTGGAATTAGCACCGTA 57.075 32.000 0.00 0.00 0.00 4.02
3657 3702 4.709397 AGTGGAGACCATCAACAACAAAAA 59.291 37.500 0.00 0.00 33.82 1.94
4236 4283 7.223387 GGAACAACATTCAGCATTAATGATTCC 59.777 37.037 19.73 9.27 37.30 3.01
4486 4533 1.880819 CTGCCATCCAACACAAGCCC 61.881 60.000 0.00 0.00 0.00 5.19
4594 4641 5.753921 AGACCGAAACAACAGAGAGTAAAAG 59.246 40.000 0.00 0.00 0.00 2.27
4700 4752 4.542662 AAGAATGACTAATGACGCATGC 57.457 40.909 7.91 7.91 0.00 4.06
4772 4826 8.973182 TCCTTAAACATACTTGACCAACTTTTT 58.027 29.630 0.00 0.00 0.00 1.94
4774 4828 8.576442 CATCCTTAAACATACTTGACCAACTTT 58.424 33.333 0.00 0.00 0.00 2.66
4793 4847 4.698304 CCGGCAAAACTCTTAACATCCTTA 59.302 41.667 0.00 0.00 0.00 2.69
4794 4848 3.506067 CCGGCAAAACTCTTAACATCCTT 59.494 43.478 0.00 0.00 0.00 3.36
4796 4850 2.415491 GCCGGCAAAACTCTTAACATCC 60.415 50.000 24.80 0.00 0.00 3.51
4798 4852 2.514803 AGCCGGCAAAACTCTTAACAT 58.485 42.857 31.54 0.00 0.00 2.71
4799 4853 1.975660 AGCCGGCAAAACTCTTAACA 58.024 45.000 31.54 0.00 0.00 2.41
4800 4854 2.034179 ACAAGCCGGCAAAACTCTTAAC 59.966 45.455 31.54 0.00 0.00 2.01
4801 4855 2.303175 ACAAGCCGGCAAAACTCTTAA 58.697 42.857 31.54 0.00 0.00 1.85
4803 4857 1.975660 TACAAGCCGGCAAAACTCTT 58.024 45.000 31.54 9.43 0.00 2.85
4873 4928 4.770795 AGTATCAACAGCATTGGAGGTAC 58.229 43.478 1.34 0.00 0.00 3.34
4876 4931 3.181493 GCAAGTATCAACAGCATTGGAGG 60.181 47.826 1.34 0.00 0.00 4.30
4877 4932 3.181493 GGCAAGTATCAACAGCATTGGAG 60.181 47.826 1.34 0.00 32.41 3.86
4878 4933 2.754552 GGCAAGTATCAACAGCATTGGA 59.245 45.455 1.34 0.00 32.41 3.53
4933 4996 4.142038 AGTCCCAACATAGAACAACCAAC 58.858 43.478 0.00 0.00 0.00 3.77
4958 5021 2.095718 GGGCACAAAGTCGACAAGATTC 60.096 50.000 19.50 2.39 0.00 2.52
4967 5030 2.126467 CAAATGTTGGGCACAAAGTCG 58.874 47.619 1.02 0.00 39.50 4.18
4975 5038 1.068895 CAGCAAGACAAATGTTGGGCA 59.931 47.619 0.00 0.00 34.12 5.36
5057 5122 0.723414 AATGACAGCATTCGCGAGTG 59.277 50.000 25.40 25.40 40.65 3.51
5058 5123 1.442769 AAATGACAGCATTCGCGAGT 58.557 45.000 9.59 2.59 43.71 4.18
5061 5126 1.645265 CACAAAATGACAGCATTCGCG 59.355 47.619 0.00 0.00 43.71 5.87
5079 5144 9.241317 CCATATTGACAAAGAAAATATGCTCAC 57.759 33.333 8.46 0.00 40.53 3.51
5085 5150 8.076910 TGCCACCATATTGACAAAGAAAATAT 57.923 30.769 0.00 0.00 0.00 1.28
5086 5151 7.178274 ACTGCCACCATATTGACAAAGAAAATA 59.822 33.333 0.00 0.00 0.00 1.40
5148 5213 0.657368 GTTTCGCACAAGACCGCAAG 60.657 55.000 0.00 0.00 0.00 4.01
5149 5214 1.092921 AGTTTCGCACAAGACCGCAA 61.093 50.000 0.00 0.00 0.00 4.85
5150 5215 0.249531 TAGTTTCGCACAAGACCGCA 60.250 50.000 0.00 0.00 0.00 5.69
5151 5216 0.863144 TTAGTTTCGCACAAGACCGC 59.137 50.000 0.00 0.00 0.00 5.68
5152 5217 2.096909 CAGTTAGTTTCGCACAAGACCG 60.097 50.000 0.00 0.00 0.00 4.79
5153 5218 2.223377 CCAGTTAGTTTCGCACAAGACC 59.777 50.000 0.00 0.00 0.00 3.85
5154 5219 2.349532 GCCAGTTAGTTTCGCACAAGAC 60.350 50.000 0.00 0.00 0.00 3.01
5155 5220 1.871039 GCCAGTTAGTTTCGCACAAGA 59.129 47.619 0.00 0.00 0.00 3.02
5156 5221 1.601903 TGCCAGTTAGTTTCGCACAAG 59.398 47.619 0.00 0.00 0.00 3.16
5157 5222 1.669604 TGCCAGTTAGTTTCGCACAA 58.330 45.000 0.00 0.00 0.00 3.33
5158 5223 1.890876 ATGCCAGTTAGTTTCGCACA 58.109 45.000 0.00 0.00 31.17 4.57
5159 5224 2.031157 ACAATGCCAGTTAGTTTCGCAC 60.031 45.455 0.00 0.00 31.17 5.34
5160 5225 2.226330 ACAATGCCAGTTAGTTTCGCA 58.774 42.857 0.00 0.00 0.00 5.10
5161 5226 2.979813 CAACAATGCCAGTTAGTTTCGC 59.020 45.455 0.00 0.00 0.00 4.70
5182 5247 3.802139 CACATTCATTCATGCATCTTGGC 59.198 43.478 0.00 0.00 0.00 4.52
5183 5248 5.006153 ACACATTCATTCATGCATCTTGG 57.994 39.130 0.00 0.00 0.00 3.61
5184 5249 7.200455 ACATACACATTCATTCATGCATCTTG 58.800 34.615 0.00 0.00 0.00 3.02
5185 5250 7.342769 ACATACACATTCATTCATGCATCTT 57.657 32.000 0.00 0.00 0.00 2.40
5186 5251 6.954487 ACATACACATTCATTCATGCATCT 57.046 33.333 0.00 0.00 0.00 2.90
5187 5252 7.868775 ACTACATACACATTCATTCATGCATC 58.131 34.615 0.00 0.00 0.00 3.91
5188 5253 7.718314 AGACTACATACACATTCATTCATGCAT 59.282 33.333 0.00 0.00 0.00 3.96
5189 5254 7.049754 AGACTACATACACATTCATTCATGCA 58.950 34.615 0.00 0.00 0.00 3.96
5190 5255 7.488187 AGACTACATACACATTCATTCATGC 57.512 36.000 0.00 0.00 0.00 4.06
5191 5256 8.340443 CCAAGACTACATACACATTCATTCATG 58.660 37.037 0.00 0.00 0.00 3.07
5192 5257 8.267183 TCCAAGACTACATACACATTCATTCAT 58.733 33.333 0.00 0.00 0.00 2.57
5193 5258 7.619965 TCCAAGACTACATACACATTCATTCA 58.380 34.615 0.00 0.00 0.00 2.57
5194 5259 8.554528 CATCCAAGACTACATACACATTCATTC 58.445 37.037 0.00 0.00 0.00 2.67
5195 5260 7.500227 CCATCCAAGACTACATACACATTCATT 59.500 37.037 0.00 0.00 0.00 2.57
5196 5261 6.994496 CCATCCAAGACTACATACACATTCAT 59.006 38.462 0.00 0.00 0.00 2.57
5197 5262 6.156083 TCCATCCAAGACTACATACACATTCA 59.844 38.462 0.00 0.00 0.00 2.57
5198 5263 6.582636 TCCATCCAAGACTACATACACATTC 58.417 40.000 0.00 0.00 0.00 2.67
5199 5264 6.560003 TCCATCCAAGACTACATACACATT 57.440 37.500 0.00 0.00 0.00 2.71
5200 5265 5.453903 GCTCCATCCAAGACTACATACACAT 60.454 44.000 0.00 0.00 0.00 3.21
5201 5266 4.141937 GCTCCATCCAAGACTACATACACA 60.142 45.833 0.00 0.00 0.00 3.72
5202 5267 4.141937 TGCTCCATCCAAGACTACATACAC 60.142 45.833 0.00 0.00 0.00 2.90
5203 5268 4.030216 TGCTCCATCCAAGACTACATACA 58.970 43.478 0.00 0.00 0.00 2.29
5204 5269 4.502259 CCTGCTCCATCCAAGACTACATAC 60.502 50.000 0.00 0.00 0.00 2.39
5205 5270 3.643320 CCTGCTCCATCCAAGACTACATA 59.357 47.826 0.00 0.00 0.00 2.29
5206 5271 2.437281 CCTGCTCCATCCAAGACTACAT 59.563 50.000 0.00 0.00 0.00 2.29
5207 5272 1.833630 CCTGCTCCATCCAAGACTACA 59.166 52.381 0.00 0.00 0.00 2.74
5208 5273 2.102252 CTCCTGCTCCATCCAAGACTAC 59.898 54.545 0.00 0.00 0.00 2.73
5209 5274 2.392662 CTCCTGCTCCATCCAAGACTA 58.607 52.381 0.00 0.00 0.00 2.59
5210 5275 1.202330 CTCCTGCTCCATCCAAGACT 58.798 55.000 0.00 0.00 0.00 3.24
5211 5276 0.179936 CCTCCTGCTCCATCCAAGAC 59.820 60.000 0.00 0.00 0.00 3.01
5212 5277 0.984961 CCCTCCTGCTCCATCCAAGA 60.985 60.000 0.00 0.00 0.00 3.02
5213 5278 1.530771 CCCTCCTGCTCCATCCAAG 59.469 63.158 0.00 0.00 0.00 3.61
5214 5279 2.002977 CCCCTCCTGCTCCATCCAA 61.003 63.158 0.00 0.00 0.00 3.53
5215 5280 1.897037 TACCCCTCCTGCTCCATCCA 61.897 60.000 0.00 0.00 0.00 3.41
5216 5281 0.694444 TTACCCCTCCTGCTCCATCC 60.694 60.000 0.00 0.00 0.00 3.51
5217 5282 0.761802 CTTACCCCTCCTGCTCCATC 59.238 60.000 0.00 0.00 0.00 3.51
5218 5283 0.044855 ACTTACCCCTCCTGCTCCAT 59.955 55.000 0.00 0.00 0.00 3.41
5219 5284 0.909610 CACTTACCCCTCCTGCTCCA 60.910 60.000 0.00 0.00 0.00 3.86
5220 5285 0.617820 TCACTTACCCCTCCTGCTCC 60.618 60.000 0.00 0.00 0.00 4.70
5221 5286 1.139853 CATCACTTACCCCTCCTGCTC 59.860 57.143 0.00 0.00 0.00 4.26
5222 5287 1.207791 CATCACTTACCCCTCCTGCT 58.792 55.000 0.00 0.00 0.00 4.24
5223 5288 1.134371 GTCATCACTTACCCCTCCTGC 60.134 57.143 0.00 0.00 0.00 4.85
5224 5289 2.187958 TGTCATCACTTACCCCTCCTG 58.812 52.381 0.00 0.00 0.00 3.86
5225 5290 2.642171 TGTCATCACTTACCCCTCCT 57.358 50.000 0.00 0.00 0.00 3.69
5226 5291 2.771943 TCATGTCATCACTTACCCCTCC 59.228 50.000 0.00 0.00 0.00 4.30
5227 5292 3.197766 TGTCATGTCATCACTTACCCCTC 59.802 47.826 0.00 0.00 0.00 4.30
5228 5293 3.181329 TGTCATGTCATCACTTACCCCT 58.819 45.455 0.00 0.00 0.00 4.79
5229 5294 3.627395 TGTCATGTCATCACTTACCCC 57.373 47.619 0.00 0.00 0.00 4.95
5230 5295 3.313526 GCATGTCATGTCATCACTTACCC 59.686 47.826 14.26 0.00 0.00 3.69
5231 5296 3.940852 TGCATGTCATGTCATCACTTACC 59.059 43.478 14.26 0.00 0.00 2.85
5232 5297 4.495349 GCTGCATGTCATGTCATCACTTAC 60.495 45.833 14.26 0.00 0.00 2.34
5233 5298 3.624410 GCTGCATGTCATGTCATCACTTA 59.376 43.478 14.26 0.00 0.00 2.24
5234 5299 2.422479 GCTGCATGTCATGTCATCACTT 59.578 45.455 14.26 0.00 0.00 3.16
5235 5300 2.014857 GCTGCATGTCATGTCATCACT 58.985 47.619 14.26 0.00 0.00 3.41
5236 5301 2.014857 AGCTGCATGTCATGTCATCAC 58.985 47.619 14.26 0.00 0.00 3.06
5237 5302 2.413310 AGCTGCATGTCATGTCATCA 57.587 45.000 14.26 3.08 0.00 3.07
5266 5338 1.291132 GTCAGGATAAGCACTTCGGC 58.709 55.000 0.00 0.00 0.00 5.54
5268 5340 2.969628 AGGTCAGGATAAGCACTTCG 57.030 50.000 0.00 0.00 0.00 3.79
5276 5348 7.125659 TGACATCAAAGTCATAGGTCAGGATAA 59.874 37.037 0.00 0.00 43.18 1.75
5288 5360 2.485426 CCGCACTTGACATCAAAGTCAT 59.515 45.455 0.00 0.00 46.90 3.06
5289 5361 1.872952 CCGCACTTGACATCAAAGTCA 59.127 47.619 0.00 0.00 46.12 3.41
5290 5362 1.197721 CCCGCACTTGACATCAAAGTC 59.802 52.381 0.00 0.00 38.99 3.01
5291 5363 1.238439 CCCGCACTTGACATCAAAGT 58.762 50.000 0.00 0.00 35.15 2.66
5292 5364 1.238439 ACCCGCACTTGACATCAAAG 58.762 50.000 0.00 0.00 35.15 2.77
5293 5365 1.336440 CAACCCGCACTTGACATCAAA 59.664 47.619 0.00 0.00 35.15 2.69
5297 5369 3.354678 GCAACCCGCACTTGACAT 58.645 55.556 0.00 0.00 41.79 3.06
5323 5395 3.927142 GTCGAGTACTTAGCATGCAACTT 59.073 43.478 21.98 0.61 0.00 2.66
5334 5406 3.057736 AGCTTGCTTTCGTCGAGTACTTA 60.058 43.478 0.00 0.00 0.00 2.24
5339 5411 0.032130 TGAGCTTGCTTTCGTCGAGT 59.968 50.000 0.00 0.00 0.00 4.18
5340 5412 0.436531 GTGAGCTTGCTTTCGTCGAG 59.563 55.000 0.00 0.00 0.00 4.04
5342 5414 0.162507 CTGTGAGCTTGCTTTCGTCG 59.837 55.000 0.00 0.00 0.00 5.12
5345 5417 4.834828 GCTGTGAGCTTGCTTTCG 57.165 55.556 0.00 0.00 38.45 3.46
5354 5426 3.819537 GTTGAAGATTTCAGCTGTGAGC 58.180 45.455 14.67 6.42 41.38 4.26
5399 5472 3.258123 AGAGAGACAGAGACAAAAGCTCC 59.742 47.826 0.00 0.00 32.82 4.70
5400 5473 4.218417 AGAGAGAGACAGAGACAAAAGCTC 59.782 45.833 0.00 0.00 0.00 4.09
5401 5474 4.151883 AGAGAGAGACAGAGACAAAAGCT 58.848 43.478 0.00 0.00 0.00 3.74
5402 5475 4.218417 AGAGAGAGAGACAGAGACAAAAGC 59.782 45.833 0.00 0.00 0.00 3.51
5403 5476 5.964958 AGAGAGAGAGACAGAGACAAAAG 57.035 43.478 0.00 0.00 0.00 2.27
5404 5477 7.825331 TTTAGAGAGAGAGACAGAGACAAAA 57.175 36.000 0.00 0.00 0.00 2.44
5405 5478 7.825331 TTTTAGAGAGAGAGACAGAGACAAA 57.175 36.000 0.00 0.00 0.00 2.83
5406 5479 7.825331 TTTTTAGAGAGAGAGACAGAGACAA 57.175 36.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.