Multiple sequence alignment - TraesCS7D01G298800

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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 TraesCS7D01G298800 chr7D 100.000 5823 0 0 1 5823 378487132 378492954 0.000000e+00 10754.0
1 TraesCS7D01G298800 chr7D 81.496 254 32 6 7 258 378403100 378403340 1.660000e-45 195.0
2 TraesCS7D01G298800 chr7D 96.364 110 4 0 4087 4196 20083041 20082932 1.290000e-41 182.0
3 TraesCS7D01G298800 chr7D 100.000 47 0 0 4333 4379 378491418 378491464 2.890000e-13 87.9
4 TraesCS7D01G298800 chr7D 100.000 47 0 0 4287 4333 378491464 378491510 2.890000e-13 87.9
5 TraesCS7D01G298800 chr7B 95.414 3794 87 23 363 4085 373171627 373175404 0.000000e+00 5962.0
6 TraesCS7D01G298800 chr7B 95.116 1249 47 9 4196 5434 373175402 373176646 0.000000e+00 1956.0
7 TraesCS7D01G298800 chr7B 85.246 488 71 1 2 489 373170695 373171181 8.710000e-138 501.0
8 TraesCS7D01G298800 chr7B 81.538 260 33 5 7 264 373169428 373169674 3.560000e-47 200.0
9 TraesCS7D01G298800 chr7B 95.745 47 2 0 4287 4333 373175539 373175585 6.260000e-10 76.8
10 TraesCS7D01G298800 chr7A 93.713 3881 122 46 1 3802 426795533 426799370 0.000000e+00 5703.0
11 TraesCS7D01G298800 chr7A 97.736 1237 21 6 4196 5427 426799616 426800850 0.000000e+00 2122.0
12 TraesCS7D01G298800 chr7A 96.011 351 10 2 5476 5823 426800853 426801202 8.470000e-158 568.0
13 TraesCS7D01G298800 chr7A 86.141 469 63 2 1 468 426794841 426795308 6.730000e-139 505.0
14 TraesCS7D01G298800 chr7A 83.624 458 68 6 11 468 426794154 426794604 1.940000e-114 424.0
15 TraesCS7D01G298800 chr7A 95.257 253 9 3 3835 4085 426799367 426799618 1.180000e-106 398.0
16 TraesCS7D01G298800 chr7A 78.462 260 31 10 7 264 426793585 426793821 4.700000e-31 147.0
17 TraesCS7D01G298800 chr7A 97.872 47 0 1 4333 4379 426799707 426799752 4.840000e-11 80.5
18 TraesCS7D01G298800 chr5D 99.130 115 1 0 4086 4200 542576437 542576323 2.130000e-49 207.0
19 TraesCS7D01G298800 chr3D 100.000 111 0 0 4086 4196 363329802 363329692 7.650000e-49 206.0
20 TraesCS7D01G298800 chr3D 95.041 121 4 2 4086 4206 348544402 348544520 7.700000e-44 189.0
21 TraesCS7D01G298800 chr2D 99.115 113 1 0 4086 4198 414957668 414957780 2.750000e-48 204.0
22 TraesCS7D01G298800 chr2D 92.241 116 9 0 4086 4201 453702372 453702487 1.300000e-36 165.0
23 TraesCS7D01G298800 chr4D 96.522 115 4 0 4086 4200 362783378 362783264 2.140000e-44 191.0
24 TraesCS7D01G298800 chr4D 92.920 113 8 0 4086 4198 462619373 462619485 1.300000e-36 165.0
25 TraesCS7D01G298800 chr6D 95.495 111 5 0 4086 4196 427339620 427339510 1.670000e-40 178.0
26 TraesCS7D01G298800 chr6D 84.043 94 15 0 2459 2552 10699137 10699230 2.230000e-14 91.6
27 TraesCS7D01G298800 chr6B 84.043 94 15 0 2459 2552 20011492 20011585 2.230000e-14 91.6
28 TraesCS7D01G298800 chr6B 96.154 52 1 1 3794 3845 713975890 713975940 3.740000e-12 84.2
29 TraesCS7D01G298800 chr5A 100.000 47 0 0 3792 3838 659866870 659866916 2.890000e-13 87.9
30 TraesCS7D01G298800 chr5B 90.769 65 3 3 3793 3855 261247942 261248005 3.740000e-12 84.2
31 TraesCS7D01G298800 chr5B 86.154 65 8 1 3869 3933 658446662 658446599 1.050000e-07 69.4
32 TraesCS7D01G298800 chr2B 91.667 60 3 2 3797 3855 185025781 185025723 1.340000e-11 82.4
33 TraesCS7D01G298800 chr2A 97.826 46 1 0 3792 3837 766900089 766900044 4.840000e-11 80.5
34 TraesCS7D01G298800 chr2A 95.745 47 2 0 3792 3838 391898700 391898746 6.260000e-10 76.8
35 TraesCS7D01G298800 chr1B 89.231 65 4 3 3793 3855 534709018 534709081 1.740000e-10 78.7
36 TraesCS7D01G298800 chr4B 97.674 43 1 0 3796 3838 447450510 447450552 2.250000e-09 75.0
37 TraesCS7D01G298800 chr4B 81.188 101 10 8 3869 3966 554561657 554561751 8.090000e-09 73.1
38 TraesCS7D01G298800 chr4B 95.000 40 1 1 3869 3908 671618197 671618159 1.750000e-05 62.1


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 TraesCS7D01G298800 chr7D 378487132 378492954 5822 False 3643.266667 10754 100.0000 1 5823 3 chr7D.!!$F2 5822
1 TraesCS7D01G298800 chr7B 373169428 373176646 7218 False 1739.160000 5962 90.6118 2 5434 5 chr7B.!!$F1 5432
2 TraesCS7D01G298800 chr7A 426793585 426801202 7617 False 1243.437500 5703 91.1020 1 5823 8 chr7A.!!$F1 5822

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
295 2281 0.179103 ATCATCGCACTGCATCGACA 60.179 50.000 7.80 0.22 37.55 4.35 F
692 2689 0.523072 CGCAACACCCTCCAAATCTG 59.477 55.000 0.00 0.00 0.00 2.90 F
1266 3283 1.072331 TCCTCTTTCTCCAAGTGTGCC 59.928 52.381 0.00 0.00 33.66 5.01 F
1269 3286 1.202806 TCTTTCTCCAAGTGTGCCTGG 60.203 52.381 0.00 0.00 33.66 4.45 F
1901 3935 2.038557 GGAGGTACAGCTCAAGGTGAAA 59.961 50.000 15.60 1.23 45.66 2.69 F
3305 5356 0.804364 TCTTGTCGCATGGCATGTTC 59.196 50.000 26.94 17.48 0.00 3.18 F
4091 6199 1.000496 GGAGGGAGTATTAACGGCTCG 60.000 57.143 0.00 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1251 3268 0.178992 CCCAGGCACACTTGGAGAAA 60.179 55.000 0.00 0.0 33.86 2.52 R
1609 3643 0.313043 CAAGCACACAAAGAGGCCAG 59.687 55.000 5.01 0.0 0.00 4.85 R
2331 4366 2.036217 CTGAACTGGCAATGCTGGAAAA 59.964 45.455 4.82 0.0 0.00 2.29 R
2649 4685 2.040278 AGTCAGGTAAGGCAAAGCATCA 59.960 45.455 0.00 0.0 0.00 3.07 R
3388 5441 3.222603 AGCCTGACGGAAAGAAACATTT 58.777 40.909 0.00 0.0 0.00 2.32 R
4146 6254 0.178961 GAGTTGGGGAGCTGGGTTTT 60.179 55.000 0.00 0.0 0.00 2.43 R
5435 7556 1.617850 TCCAATGTTCATGCAACCCAC 59.382 47.619 0.00 0.0 33.51 4.61 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
28 1306 3.381908 GTGTGATGAGGGACGAAGATAGT 59.618 47.826 0.00 0.00 0.00 2.12
59 1337 4.441792 ACCCAAGTAAAGCAAAGCAAAAG 58.558 39.130 0.00 0.00 0.00 2.27
66 1344 6.348498 AGTAAAGCAAAGCAAAAGACCATTT 58.652 32.000 0.00 0.00 0.00 2.32
73 1351 2.948979 AGCAAAAGACCATTTCGTCACA 59.051 40.909 0.00 0.00 35.07 3.58
205 2191 4.357142 GCTTCTTTCCACGTCGATATACA 58.643 43.478 0.00 0.00 0.00 2.29
209 2195 5.898174 TCTTTCCACGTCGATATACAATGT 58.102 37.500 0.00 0.00 0.00 2.71
243 2229 2.152016 TGACACAAACACGACAAACCA 58.848 42.857 0.00 0.00 0.00 3.67
294 2280 0.231534 CATCATCGCACTGCATCGAC 59.768 55.000 7.80 0.00 37.55 4.20
295 2281 0.179103 ATCATCGCACTGCATCGACA 60.179 50.000 7.80 0.22 37.55 4.35
307 2293 1.354040 CATCGACAGAGCAAGGACAC 58.646 55.000 0.00 0.00 0.00 3.67
309 2295 1.170290 TCGACAGAGCAAGGACACGA 61.170 55.000 0.00 0.00 0.00 4.35
345 2331 1.885850 AAACCGCACGTCCACACTC 60.886 57.895 0.00 0.00 0.00 3.51
349 2335 2.108157 GCACGTCCACACTCCACA 59.892 61.111 0.00 0.00 0.00 4.17
367 2353 1.351017 ACACCATCCCACGAGAAACAT 59.649 47.619 0.00 0.00 0.00 2.71
414 2400 7.655732 CAGAAAACATACCAAACCCCTAAAAAG 59.344 37.037 0.00 0.00 0.00 2.27
421 2407 6.502074 ACCAAACCCCTAAAAAGCAAAATA 57.498 33.333 0.00 0.00 0.00 1.40
495 2482 3.161866 GCCCCCTAAATTTGACAGTCAA 58.838 45.455 12.24 12.24 34.03 3.18
550 2540 6.709397 TGTTACCGTGATCTTATCGTAGAGAT 59.291 38.462 0.00 0.00 43.63 2.75
551 2541 7.874528 TGTTACCGTGATCTTATCGTAGAGATA 59.125 37.037 0.00 0.00 43.63 1.98
552 2542 6.724694 ACCGTGATCTTATCGTAGAGATAC 57.275 41.667 0.00 0.00 43.63 2.24
692 2689 0.523072 CGCAACACCCTCCAAATCTG 59.477 55.000 0.00 0.00 0.00 2.90
726 2723 7.054124 CACTGCCCCTATATAAACTGAAAAGA 58.946 38.462 0.00 0.00 0.00 2.52
749 2746 1.220493 AGGAAAGAAAGGCAAAGGGGT 59.780 47.619 0.00 0.00 0.00 4.95
750 2747 1.618837 GGAAAGAAAGGCAAAGGGGTC 59.381 52.381 0.00 0.00 0.00 4.46
751 2748 2.598565 GAAAGAAAGGCAAAGGGGTCT 58.401 47.619 0.00 0.00 0.00 3.85
907 2908 4.767255 GCTCCACCCGTCAGCCTG 62.767 72.222 0.00 0.00 0.00 4.85
963 2977 1.152355 AGAGGGGGCTAGCAGCTAG 60.152 63.158 23.40 23.40 41.99 3.42
1251 3268 2.835431 CGCGGGTCATCCTCCTCT 60.835 66.667 0.00 0.00 0.00 3.69
1263 3280 2.977808 TCCTCCTCTTTCTCCAAGTGT 58.022 47.619 0.00 0.00 33.66 3.55
1266 3283 1.072331 TCCTCTTTCTCCAAGTGTGCC 59.928 52.381 0.00 0.00 33.66 5.01
1269 3286 1.202806 TCTTTCTCCAAGTGTGCCTGG 60.203 52.381 0.00 0.00 33.66 4.45
1308 3342 3.606662 GCCTAGGAGATCGCCGCA 61.607 66.667 14.75 1.33 0.00 5.69
1341 3375 2.812619 GCCTAGGATTCCCAGCGCT 61.813 63.158 14.75 2.64 33.88 5.92
1344 3378 2.315781 CTAGGATTCCCAGCGCTGCA 62.316 60.000 31.96 17.38 33.88 4.41
1400 3434 2.202797 CGCCGGATCACTCACTGG 60.203 66.667 5.05 0.00 35.81 4.00
1609 3643 4.378253 GCTTTTCTTCTGCTGATGTGACTC 60.378 45.833 6.41 0.00 0.00 3.36
1813 3847 9.974750 GAGGTTCTGTTCTTCTAATATTTTTCG 57.025 33.333 0.00 0.00 0.00 3.46
1901 3935 2.038557 GGAGGTACAGCTCAAGGTGAAA 59.961 50.000 15.60 1.23 45.66 2.69
1931 3965 5.277857 ACAATAGCTACAGGGTATGTGTC 57.722 43.478 0.00 0.00 43.80 3.67
1971 4005 4.574828 GGTGAAAATCTAAGCCGCTATTCA 59.425 41.667 0.00 0.00 0.00 2.57
1974 4008 7.291567 GTGAAAATCTAAGCCGCTATTCATAC 58.708 38.462 0.00 0.00 0.00 2.39
2000 4034 5.737860 TGAAATGAGAGCTTAGCATGAAGA 58.262 37.500 7.07 0.00 0.00 2.87
2094 4128 8.294690 AGTACTCTTTTAGGGGGAATACTATCA 58.705 37.037 0.00 0.00 0.00 2.15
2168 4202 9.113838 AGTTGTTTTGCAGATATAGATGTTAGG 57.886 33.333 0.00 0.00 0.00 2.69
2331 4366 3.499202 GGTCATGGCTATGGAATGGATGT 60.499 47.826 10.47 0.00 34.97 3.06
2442 4477 7.453393 TCTGAAAGATAAACTGACAGGTCAAT 58.547 34.615 7.51 0.00 38.67 2.57
2603 4639 9.504708 TTTTTCTTAATGGTGATTCATTGCATT 57.495 25.926 0.00 0.00 37.82 3.56
2613 4649 6.857964 GGTGATTCATTGCATTTTAGTATCGG 59.142 38.462 0.00 0.00 0.00 4.18
2623 4659 6.017440 TGCATTTTAGTATCGGCCAGTATTTC 60.017 38.462 2.24 0.00 0.00 2.17
2636 4672 5.009410 GGCCAGTATTTCCATCTCTCATTTG 59.991 44.000 0.00 0.00 0.00 2.32
2637 4673 5.824624 GCCAGTATTTCCATCTCTCATTTGA 59.175 40.000 0.00 0.00 0.00 2.69
2638 4674 6.319658 GCCAGTATTTCCATCTCTCATTTGAA 59.680 38.462 0.00 0.00 0.00 2.69
2639 4675 7.468357 GCCAGTATTTCCATCTCTCATTTGAAG 60.468 40.741 0.00 0.00 0.00 3.02
2640 4676 7.013083 CCAGTATTTCCATCTCTCATTTGAAGG 59.987 40.741 0.00 0.00 0.00 3.46
2641 4677 7.013083 CAGTATTTCCATCTCTCATTTGAAGGG 59.987 40.741 0.00 0.00 0.00 3.95
2642 4678 3.939740 TCCATCTCTCATTTGAAGGGG 57.060 47.619 0.00 0.00 0.00 4.79
2643 4679 3.463825 TCCATCTCTCATTTGAAGGGGA 58.536 45.455 0.00 0.00 0.00 4.81
2644 4680 4.050037 TCCATCTCTCATTTGAAGGGGAT 58.950 43.478 0.00 0.00 0.00 3.85
2645 4681 5.226803 TCCATCTCTCATTTGAAGGGGATA 58.773 41.667 0.00 0.00 0.00 2.59
2646 4682 5.853922 TCCATCTCTCATTTGAAGGGGATAT 59.146 40.000 0.00 0.00 0.00 1.63
2647 4683 6.333702 TCCATCTCTCATTTGAAGGGGATATT 59.666 38.462 0.00 0.00 0.00 1.28
2648 4684 7.517254 TCCATCTCTCATTTGAAGGGGATATTA 59.483 37.037 0.00 0.00 0.00 0.98
2649 4685 8.334734 CCATCTCTCATTTGAAGGGGATATTAT 58.665 37.037 0.00 0.00 0.00 1.28
2690 4740 9.831737 CCTGACTAAAAGATAACAACAATTCTG 57.168 33.333 0.00 0.00 0.00 3.02
2803 4853 8.557592 ACTCATTATGCATATAATCACCAGTG 57.442 34.615 7.36 0.00 37.38 3.66
3156 5206 8.593945 AATACATTTTGATAGAGAAGGGCAAA 57.406 30.769 0.00 0.00 0.00 3.68
3305 5356 0.804364 TCTTGTCGCATGGCATGTTC 59.196 50.000 26.94 17.48 0.00 3.18
3485 5538 3.490348 CTGTTGTGTCCCATCCTCTTTT 58.510 45.455 0.00 0.00 0.00 2.27
3689 5770 2.368011 CGTTCCCCCTCCTCTTCCC 61.368 68.421 0.00 0.00 0.00 3.97
4082 6190 5.911178 TGTAATCTGGAATGGAGGGAGTATT 59.089 40.000 0.00 0.00 0.00 1.89
4083 6191 7.079700 TGTAATCTGGAATGGAGGGAGTATTA 58.920 38.462 0.00 0.00 0.00 0.98
4084 6192 7.570982 TGTAATCTGGAATGGAGGGAGTATTAA 59.429 37.037 0.00 0.00 0.00 1.40
4085 6193 5.888982 TCTGGAATGGAGGGAGTATTAAC 57.111 43.478 0.00 0.00 0.00 2.01
4086 6194 4.344102 TCTGGAATGGAGGGAGTATTAACG 59.656 45.833 0.00 0.00 0.00 3.18
4087 6195 3.389983 TGGAATGGAGGGAGTATTAACGG 59.610 47.826 0.00 0.00 0.00 4.44
4088 6196 3.400255 GAATGGAGGGAGTATTAACGGC 58.600 50.000 0.00 0.00 0.00 5.68
4089 6197 2.170012 TGGAGGGAGTATTAACGGCT 57.830 50.000 0.00 0.00 0.00 5.52
4090 6198 2.037144 TGGAGGGAGTATTAACGGCTC 58.963 52.381 0.00 0.00 0.00 4.70
4091 6199 1.000496 GGAGGGAGTATTAACGGCTCG 60.000 57.143 0.00 0.00 0.00 5.03
4092 6200 1.680207 GAGGGAGTATTAACGGCTCGT 59.320 52.381 0.00 0.00 43.97 4.18
4101 6209 4.565531 ACGGCTCGTTTAACTCCG 57.434 55.556 14.92 14.92 45.04 4.63
4102 6210 1.735559 ACGGCTCGTTTAACTCCGC 60.736 57.895 15.91 6.07 43.50 5.54
4103 6211 1.445582 CGGCTCGTTTAACTCCGCT 60.446 57.895 7.19 0.00 33.36 5.52
4104 6212 1.411493 CGGCTCGTTTAACTCCGCTC 61.411 60.000 7.19 0.00 33.36 5.03
4105 6213 1.082679 GGCTCGTTTAACTCCGCTCC 61.083 60.000 0.00 0.00 0.00 4.70
4106 6214 1.411493 GCTCGTTTAACTCCGCTCCG 61.411 60.000 0.00 0.00 0.00 4.63
4118 6226 3.775654 GCTCCGGGAGTGGACCAG 61.776 72.222 24.30 0.00 33.48 4.00
4119 6227 2.037367 CTCCGGGAGTGGACCAGA 59.963 66.667 16.15 0.00 33.48 3.86
4120 6228 2.283676 TCCGGGAGTGGACCAGAC 60.284 66.667 0.00 0.00 31.53 3.51
4121 6229 2.283966 CCGGGAGTGGACCAGACT 60.284 66.667 0.00 0.00 0.00 3.24
4122 6230 1.913762 CCGGGAGTGGACCAGACTT 60.914 63.158 0.00 0.00 0.00 3.01
4123 6231 1.481056 CCGGGAGTGGACCAGACTTT 61.481 60.000 0.00 0.00 0.00 2.66
4124 6232 1.263356 CGGGAGTGGACCAGACTTTA 58.737 55.000 0.00 0.00 0.00 1.85
4125 6233 1.204941 CGGGAGTGGACCAGACTTTAG 59.795 57.143 0.00 0.00 0.00 1.85
4126 6234 1.066071 GGGAGTGGACCAGACTTTAGC 60.066 57.143 0.00 0.00 0.00 3.09
4127 6235 1.903183 GGAGTGGACCAGACTTTAGCT 59.097 52.381 0.00 0.00 0.00 3.32
4128 6236 2.303311 GGAGTGGACCAGACTTTAGCTT 59.697 50.000 0.00 0.00 0.00 3.74
4129 6237 3.514309 GGAGTGGACCAGACTTTAGCTTA 59.486 47.826 0.00 0.00 0.00 3.09
4130 6238 4.020485 GGAGTGGACCAGACTTTAGCTTAA 60.020 45.833 0.00 0.00 0.00 1.85
4131 6239 5.338463 GGAGTGGACCAGACTTTAGCTTAAT 60.338 44.000 0.00 0.00 0.00 1.40
4132 6240 6.128138 AGTGGACCAGACTTTAGCTTAATT 57.872 37.500 0.00 0.00 0.00 1.40
4133 6241 6.543735 AGTGGACCAGACTTTAGCTTAATTT 58.456 36.000 0.00 0.00 0.00 1.82
4134 6242 7.004691 AGTGGACCAGACTTTAGCTTAATTTT 58.995 34.615 0.00 0.00 0.00 1.82
4135 6243 8.161425 AGTGGACCAGACTTTAGCTTAATTTTA 58.839 33.333 0.00 0.00 0.00 1.52
4136 6244 8.957466 GTGGACCAGACTTTAGCTTAATTTTAT 58.043 33.333 0.00 0.00 0.00 1.40
4137 6245 8.956426 TGGACCAGACTTTAGCTTAATTTTATG 58.044 33.333 0.00 0.00 0.00 1.90
4138 6246 8.406297 GGACCAGACTTTAGCTTAATTTTATGG 58.594 37.037 0.00 0.00 0.00 2.74
4139 6247 9.174166 GACCAGACTTTAGCTTAATTTTATGGA 57.826 33.333 0.00 0.00 0.00 3.41
4140 6248 9.178758 ACCAGACTTTAGCTTAATTTTATGGAG 57.821 33.333 0.00 0.00 0.00 3.86
4141 6249 8.131731 CCAGACTTTAGCTTAATTTTATGGAGC 58.868 37.037 0.00 0.00 0.00 4.70
4142 6250 8.897752 CAGACTTTAGCTTAATTTTATGGAGCT 58.102 33.333 0.00 1.58 45.01 4.09
4143 6251 8.897752 AGACTTTAGCTTAATTTTATGGAGCTG 58.102 33.333 6.44 0.00 43.06 4.24
4144 6252 7.484140 ACTTTAGCTTAATTTTATGGAGCTGC 58.516 34.615 0.00 0.00 43.06 5.25
4145 6253 4.926140 AGCTTAATTTTATGGAGCTGCC 57.074 40.909 1.53 0.00 41.75 4.85
4153 6261 2.605873 TGGAGCTGCCAAAACCCA 59.394 55.556 1.53 0.00 45.87 4.51
4154 6262 1.531365 TGGAGCTGCCAAAACCCAG 60.531 57.895 1.53 0.00 45.87 4.45
4158 6266 3.369921 CTGCCAAAACCCAGCTCC 58.630 61.111 0.00 0.00 0.00 4.70
4159 6267 2.203625 TGCCAAAACCCAGCTCCC 60.204 61.111 0.00 0.00 0.00 4.30
4160 6268 2.997315 GCCAAAACCCAGCTCCCC 60.997 66.667 0.00 0.00 0.00 4.81
4161 6269 2.525592 CCAAAACCCAGCTCCCCA 59.474 61.111 0.00 0.00 0.00 4.96
4162 6270 1.152355 CCAAAACCCAGCTCCCCAA 60.152 57.895 0.00 0.00 0.00 4.12
4163 6271 1.471829 CCAAAACCCAGCTCCCCAAC 61.472 60.000 0.00 0.00 0.00 3.77
4164 6272 0.469892 CAAAACCCAGCTCCCCAACT 60.470 55.000 0.00 0.00 0.00 3.16
4165 6273 0.178961 AAAACCCAGCTCCCCAACTC 60.179 55.000 0.00 0.00 0.00 3.01
4166 6274 2.081585 AAACCCAGCTCCCCAACTCC 62.082 60.000 0.00 0.00 0.00 3.85
4167 6275 4.101448 CCCAGCTCCCCAACTCCG 62.101 72.222 0.00 0.00 0.00 4.63
4168 6276 4.785453 CCAGCTCCCCAACTCCGC 62.785 72.222 0.00 0.00 0.00 5.54
4172 6280 4.148825 CTCCCCAACTCCGCGGAG 62.149 72.222 45.26 45.26 46.91 4.63
4191 6299 3.668386 GGGCAAGTTCCGAACAGG 58.332 61.111 13.69 6.01 42.97 4.00
4192 6300 1.971695 GGGCAAGTTCCGAACAGGG 60.972 63.158 13.69 3.68 41.52 4.45
4193 6301 2.626780 GGCAAGTTCCGAACAGGGC 61.627 63.158 13.69 12.31 41.52 5.19
4194 6302 2.626780 GCAAGTTCCGAACAGGGCC 61.627 63.158 13.69 0.00 41.52 5.80
4249 6357 8.088981 TGAAGGATAGACTAGTTTTGTCTTCAC 58.911 37.037 18.96 7.19 41.45 3.18
4294 6403 8.314143 CATGATGTGCTAAATTTTCCTGTTTT 57.686 30.769 0.00 0.00 0.00 2.43
4393 6502 7.994425 TTATCTAGATTGGTTTTTCTGTGCA 57.006 32.000 11.25 0.00 0.00 4.57
4488 6597 7.174080 GGCAATTATCTTGACTTCCCTTCTATC 59.826 40.741 0.00 0.00 0.00 2.08
4833 6943 0.729690 GGAGCTTGAAATGGAGACGC 59.270 55.000 0.00 0.00 0.00 5.19
5068 7181 3.493524 GGGCTAGATGAACTTAGGACTGC 60.494 52.174 0.00 0.00 0.00 4.40
5080 7193 1.446016 AGGACTGCAAGGGGTAGTTT 58.554 50.000 0.00 0.00 42.98 2.66
5154 7267 7.795431 AATCAAACATGCAAAGTTGTATACG 57.205 32.000 8.45 0.00 32.12 3.06
5265 7379 2.100631 GTCGGTCAATCCTGTGCCG 61.101 63.158 0.00 0.00 40.73 5.69
5272 7386 0.664166 CAATCCTGTGCCGTGTTTGC 60.664 55.000 0.00 0.00 0.00 3.68
5434 7555 6.936900 TCCTAGCACAAATATAGGATTGAAGC 59.063 38.462 0.00 6.37 40.09 3.86
5435 7556 5.679734 AGCACAAATATAGGATTGAAGCG 57.320 39.130 3.50 0.00 36.75 4.68
5436 7557 5.126067 AGCACAAATATAGGATTGAAGCGT 58.874 37.500 3.50 0.00 36.75 5.07
5437 7558 5.008019 AGCACAAATATAGGATTGAAGCGTG 59.992 40.000 3.50 0.00 36.75 5.34
5438 7559 5.751680 CACAAATATAGGATTGAAGCGTGG 58.248 41.667 3.50 0.00 0.00 4.94
5439 7560 4.821805 ACAAATATAGGATTGAAGCGTGGG 59.178 41.667 3.50 0.00 0.00 4.61
5440 7561 4.706842 AATATAGGATTGAAGCGTGGGT 57.293 40.909 0.00 0.00 0.00 4.51
5441 7562 4.706842 ATATAGGATTGAAGCGTGGGTT 57.293 40.909 0.00 0.00 0.00 4.11
5442 7563 2.107950 TAGGATTGAAGCGTGGGTTG 57.892 50.000 0.00 0.00 0.00 3.77
5443 7564 1.212751 GGATTGAAGCGTGGGTTGC 59.787 57.895 0.00 0.00 0.00 4.17
5444 7565 1.523154 GGATTGAAGCGTGGGTTGCA 61.523 55.000 0.00 0.00 33.85 4.08
5445 7566 0.527565 GATTGAAGCGTGGGTTGCAT 59.472 50.000 0.00 0.00 33.85 3.96
5446 7567 0.244450 ATTGAAGCGTGGGTTGCATG 59.756 50.000 0.00 0.00 33.85 4.06
5447 7568 0.821301 TTGAAGCGTGGGTTGCATGA 60.821 50.000 0.00 0.00 33.85 3.07
5448 7569 0.821301 TGAAGCGTGGGTTGCATGAA 60.821 50.000 0.00 0.00 33.85 2.57
5449 7570 0.387239 GAAGCGTGGGTTGCATGAAC 60.387 55.000 0.00 0.00 33.85 3.18
5450 7571 1.106351 AAGCGTGGGTTGCATGAACA 61.106 50.000 0.00 0.00 36.12 3.18
5451 7572 0.895100 AGCGTGGGTTGCATGAACAT 60.895 50.000 0.00 0.00 36.12 2.71
5452 7573 0.038343 GCGTGGGTTGCATGAACATT 60.038 50.000 0.00 0.00 36.12 2.71
5453 7574 1.700523 CGTGGGTTGCATGAACATTG 58.299 50.000 0.00 0.00 36.12 2.82
5454 7575 1.669502 CGTGGGTTGCATGAACATTGG 60.670 52.381 0.00 0.00 36.12 3.16
5455 7576 1.617850 GTGGGTTGCATGAACATTGGA 59.382 47.619 0.00 0.00 36.12 3.53
5456 7577 2.234414 GTGGGTTGCATGAACATTGGAT 59.766 45.455 0.00 0.00 36.12 3.41
5457 7578 3.446873 GTGGGTTGCATGAACATTGGATA 59.553 43.478 0.00 0.00 36.12 2.59
5458 7579 4.099881 GTGGGTTGCATGAACATTGGATAT 59.900 41.667 0.00 0.00 36.12 1.63
5459 7580 4.715792 TGGGTTGCATGAACATTGGATATT 59.284 37.500 0.00 0.00 36.12 1.28
5460 7581 5.189342 TGGGTTGCATGAACATTGGATATTT 59.811 36.000 0.00 0.00 36.12 1.40
5461 7582 5.524646 GGGTTGCATGAACATTGGATATTTG 59.475 40.000 0.00 0.00 36.12 2.32
5462 7583 5.524646 GGTTGCATGAACATTGGATATTTGG 59.475 40.000 0.00 0.00 36.12 3.28
5463 7584 5.936187 TGCATGAACATTGGATATTTGGT 57.064 34.783 0.00 0.00 0.00 3.67
5464 7585 5.662456 TGCATGAACATTGGATATTTGGTG 58.338 37.500 0.00 0.00 0.00 4.17
5465 7586 5.051816 GCATGAACATTGGATATTTGGTGG 58.948 41.667 0.00 0.00 0.00 4.61
5466 7587 5.603596 CATGAACATTGGATATTTGGTGGG 58.396 41.667 0.00 0.00 0.00 4.61
5467 7588 4.682563 TGAACATTGGATATTTGGTGGGT 58.317 39.130 0.00 0.00 0.00 4.51
5468 7589 4.709397 TGAACATTGGATATTTGGTGGGTC 59.291 41.667 0.00 0.00 0.00 4.46
5469 7590 3.642141 ACATTGGATATTTGGTGGGTCC 58.358 45.455 0.00 0.00 0.00 4.46
5470 7591 3.012274 ACATTGGATATTTGGTGGGTCCA 59.988 43.478 0.00 0.00 45.60 4.02
5496 7617 7.569111 ACCTCTATATTAGATGGTGGTTCACTT 59.431 37.037 0.00 0.00 36.02 3.16
5511 7632 5.067283 TGGTTCACTTTTGTCCTCTTTTAGC 59.933 40.000 0.00 0.00 0.00 3.09
5662 7786 6.804677 TGCATGTATATTTTCCGCTTCATTT 58.195 32.000 0.00 0.00 0.00 2.32
5673 7797 8.696410 TTTTCCGCTTCATTTAAATGGTTATC 57.304 30.769 24.40 10.92 37.03 1.75
5701 7825 0.602905 GAGTTGGTTGAGGTCCCACG 60.603 60.000 0.00 0.00 0.00 4.94
5760 7884 4.717877 TGTGACCAGACAAATTGATCACT 58.282 39.130 0.00 0.00 36.72 3.41
5765 7889 6.065976 ACCAGACAAATTGATCACTATGGA 57.934 37.500 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.404181 CGTCCCTCATCACACGTCAAT 60.404 52.381 0.00 0.00 0.00 2.57
2 3 0.891904 TCGTCCCTCATCACACGTCA 60.892 55.000 0.00 0.00 33.89 4.35
3 4 0.242825 TTCGTCCCTCATCACACGTC 59.757 55.000 0.00 0.00 33.89 4.34
4 5 0.243907 CTTCGTCCCTCATCACACGT 59.756 55.000 0.00 0.00 33.89 4.49
5 6 0.526211 TCTTCGTCCCTCATCACACG 59.474 55.000 0.00 0.00 0.00 4.49
14 1292 2.101582 GTCATGCACTATCTTCGTCCCT 59.898 50.000 0.00 0.00 0.00 4.20
28 1306 2.295909 GCTTTACTTGGGTTGTCATGCA 59.704 45.455 0.00 0.00 0.00 3.96
59 1337 4.497473 TGGAAATTGTGACGAAATGGTC 57.503 40.909 0.00 0.00 37.45 4.02
66 1344 8.335532 AGAGATAAAAATGGAAATTGTGACGA 57.664 30.769 0.00 0.00 0.00 4.20
98 2084 7.208777 TGCACATCACTAAATTGAACACAAAT 58.791 30.769 0.00 0.00 0.00 2.32
205 2191 0.726827 CATTAGCCGTGCACGACATT 59.273 50.000 39.10 22.21 43.02 2.71
209 2195 1.011968 GTGTCATTAGCCGTGCACGA 61.012 55.000 39.10 20.77 43.02 4.35
243 2229 6.594937 TCTTTACGTGGCGGTTTATCTTTTAT 59.405 34.615 0.00 0.00 0.00 1.40
294 2280 0.032678 ACACTCGTGTCCTTGCTCTG 59.967 55.000 0.00 0.00 40.24 3.35
295 2281 1.617322 TACACTCGTGTCCTTGCTCT 58.383 50.000 5.89 0.00 43.74 4.09
307 2293 4.777140 TTGATCGCATGAAATACACTCG 57.223 40.909 0.00 0.00 0.00 4.18
309 2295 4.201812 CGGTTTGATCGCATGAAATACACT 60.202 41.667 0.00 0.00 0.00 3.55
345 2331 0.036164 TTTCTCGTGGGATGGTGTGG 59.964 55.000 0.00 0.00 0.00 4.17
349 2335 2.879103 AATGTTTCTCGTGGGATGGT 57.121 45.000 0.00 0.00 0.00 3.55
367 2353 9.938280 TTTCTGTTATTCTTTCGAAGGAGATAA 57.062 29.630 10.08 13.04 31.60 1.75
431 2417 7.918076 TCAAATGGATAAGAGTTAAGACCTGT 58.082 34.615 0.00 0.00 0.00 4.00
447 2433 5.045432 AGGGACATGCAAATTTCAAATGGAT 60.045 36.000 0.00 0.00 0.00 3.41
448 2435 4.286549 AGGGACATGCAAATTTCAAATGGA 59.713 37.500 0.00 0.00 0.00 3.41
577 2567 2.221055 CACTTTCTAAGCACACGTGGAC 59.779 50.000 21.57 11.32 0.00 4.02
692 2689 1.050988 TAGGGGCAGTGGAGATGAGC 61.051 60.000 0.00 0.00 0.00 4.26
726 2723 3.136443 CCCCTTTGCCTTTCTTTCCTTTT 59.864 43.478 0.00 0.00 0.00 2.27
907 2908 1.794116 CTCTAGTCTCTACTACGCGGC 59.206 57.143 12.47 0.00 37.15 6.53
963 2977 2.418060 CCCTTTCCTTCTCTTCTCTCGC 60.418 54.545 0.00 0.00 0.00 5.03
964 2978 2.418060 GCCCTTTCCTTCTCTTCTCTCG 60.418 54.545 0.00 0.00 0.00 4.04
1251 3268 0.178992 CCCAGGCACACTTGGAGAAA 60.179 55.000 0.00 0.00 33.86 2.52
1294 3328 3.592814 CCGTGCGGCGATCTCCTA 61.593 66.667 12.98 0.00 44.77 2.94
1396 3430 0.824759 GCACGTAGATCTTCCCCAGT 59.175 55.000 0.00 0.00 0.00 4.00
1400 3434 1.146358 GCACGCACGTAGATCTTCCC 61.146 60.000 0.00 0.00 0.00 3.97
1609 3643 0.313043 CAAGCACACAAAGAGGCCAG 59.687 55.000 5.01 0.00 0.00 4.85
1813 3847 0.611062 GCCTGTAAACCCCCAAGACC 60.611 60.000 0.00 0.00 0.00 3.85
1901 3935 5.468658 ACCCTGTAGCTATTGTATTCCTCT 58.531 41.667 0.00 0.00 0.00 3.69
1971 4005 7.772292 TCATGCTAAGCTCTCATTTCAAAGTAT 59.228 33.333 0.00 0.00 0.00 2.12
1974 4008 6.432607 TCATGCTAAGCTCTCATTTCAAAG 57.567 37.500 0.00 0.00 0.00 2.77
1986 4020 2.573369 CAGCCATCTTCATGCTAAGCT 58.427 47.619 0.00 0.00 0.00 3.74
2000 4034 1.338973 CTCAAACACACTTGCAGCCAT 59.661 47.619 0.00 0.00 0.00 4.40
2101 4135 7.872993 CAGGTACATCTTTCACTTTGTAGAAGA 59.127 37.037 0.00 0.00 0.00 2.87
2168 4202 2.542595 CAGTACACGGTTCTCCACAAAC 59.457 50.000 0.00 0.00 0.00 2.93
2331 4366 2.036217 CTGAACTGGCAATGCTGGAAAA 59.964 45.455 4.82 0.00 0.00 2.29
2442 4477 7.782644 AGCCAGGCCTGTTAAACATAATATAAA 59.217 33.333 30.63 0.00 0.00 1.40
2447 4482 3.701040 CAGCCAGGCCTGTTAAACATAAT 59.299 43.478 30.63 1.69 0.00 1.28
2603 4639 5.617528 TGGAAATACTGGCCGATACTAAA 57.382 39.130 0.00 0.00 0.00 1.85
2613 4649 5.824624 TCAAATGAGAGATGGAAATACTGGC 59.175 40.000 0.00 0.00 0.00 4.85
2623 4659 3.939740 TCCCCTTCAAATGAGAGATGG 57.060 47.619 0.00 0.00 0.00 3.51
2636 4672 5.105595 GGCAAAGCATCATAATATCCCCTTC 60.106 44.000 0.00 0.00 0.00 3.46
2637 4673 4.774200 GGCAAAGCATCATAATATCCCCTT 59.226 41.667 0.00 0.00 0.00 3.95
2638 4674 4.045079 AGGCAAAGCATCATAATATCCCCT 59.955 41.667 0.00 0.00 0.00 4.79
2639 4675 4.347607 AGGCAAAGCATCATAATATCCCC 58.652 43.478 0.00 0.00 0.00 4.81
2640 4676 5.990120 AAGGCAAAGCATCATAATATCCC 57.010 39.130 0.00 0.00 0.00 3.85
2641 4677 6.660949 AGGTAAGGCAAAGCATCATAATATCC 59.339 38.462 0.00 0.00 0.00 2.59
2642 4678 7.391554 TCAGGTAAGGCAAAGCATCATAATATC 59.608 37.037 0.00 0.00 0.00 1.63
2643 4679 7.175641 GTCAGGTAAGGCAAAGCATCATAATAT 59.824 37.037 0.00 0.00 0.00 1.28
2644 4680 6.486657 GTCAGGTAAGGCAAAGCATCATAATA 59.513 38.462 0.00 0.00 0.00 0.98
2645 4681 5.300286 GTCAGGTAAGGCAAAGCATCATAAT 59.700 40.000 0.00 0.00 0.00 1.28
2646 4682 4.640201 GTCAGGTAAGGCAAAGCATCATAA 59.360 41.667 0.00 0.00 0.00 1.90
2647 4683 4.080356 AGTCAGGTAAGGCAAAGCATCATA 60.080 41.667 0.00 0.00 0.00 2.15
2648 4684 3.019564 GTCAGGTAAGGCAAAGCATCAT 58.980 45.455 0.00 0.00 0.00 2.45
2649 4685 2.040278 AGTCAGGTAAGGCAAAGCATCA 59.960 45.455 0.00 0.00 0.00 3.07
2690 4740 6.884836 AGGTGGATAAACAGGTATTGAAGAAC 59.115 38.462 0.00 0.00 0.00 3.01
2795 4845 6.094881 CCAAAAAGAACTAACTTCACTGGTGA 59.905 38.462 0.00 0.00 37.91 4.02
2803 4853 7.254421 CCAAATGCACCAAAAAGAACTAACTTC 60.254 37.037 0.00 0.00 0.00 3.01
3305 5356 4.679373 AGTAGAAGTCATATGGTGCCTG 57.321 45.455 2.13 0.00 0.00 4.85
3388 5441 3.222603 AGCCTGACGGAAAGAAACATTT 58.777 40.909 0.00 0.00 0.00 2.32
3689 5770 6.080009 AGATGGGAGGGGATAAATCAAAATG 58.920 40.000 0.00 0.00 0.00 2.32
4084 6192 1.735559 GCGGAGTTAAACGAGCCGT 60.736 57.895 0.00 0.00 43.61 5.68
4085 6193 1.411493 GAGCGGAGTTAAACGAGCCG 61.411 60.000 0.00 0.00 44.47 5.52
4086 6194 1.082679 GGAGCGGAGTTAAACGAGCC 61.083 60.000 0.00 0.00 0.00 4.70
4087 6195 1.411493 CGGAGCGGAGTTAAACGAGC 61.411 60.000 0.00 0.00 0.00 5.03
4088 6196 2.650163 CGGAGCGGAGTTAAACGAG 58.350 57.895 0.00 0.00 0.00 4.18
4089 6197 4.874534 CGGAGCGGAGTTAAACGA 57.125 55.556 0.00 0.00 0.00 3.85
4102 6210 2.037367 TCTGGTCCACTCCCGGAG 59.963 66.667 13.31 13.31 35.10 4.63
4103 6211 2.283676 GTCTGGTCCACTCCCGGA 60.284 66.667 0.73 0.00 34.95 5.14
4104 6212 1.481056 AAAGTCTGGTCCACTCCCGG 61.481 60.000 0.00 0.00 0.00 5.73
4105 6213 1.204941 CTAAAGTCTGGTCCACTCCCG 59.795 57.143 0.00 0.00 0.00 5.14
4106 6214 1.066071 GCTAAAGTCTGGTCCACTCCC 60.066 57.143 0.00 0.00 0.00 4.30
4107 6215 1.903183 AGCTAAAGTCTGGTCCACTCC 59.097 52.381 0.00 0.00 0.00 3.85
4108 6216 3.686916 AAGCTAAAGTCTGGTCCACTC 57.313 47.619 0.00 0.00 0.00 3.51
4109 6217 5.763876 ATTAAGCTAAAGTCTGGTCCACT 57.236 39.130 0.00 0.00 0.00 4.00
4110 6218 6.819397 AAATTAAGCTAAAGTCTGGTCCAC 57.181 37.500 0.00 0.00 0.00 4.02
4111 6219 8.956426 CATAAAATTAAGCTAAAGTCTGGTCCA 58.044 33.333 0.00 0.00 0.00 4.02
4112 6220 8.406297 CCATAAAATTAAGCTAAAGTCTGGTCC 58.594 37.037 0.00 0.00 0.00 4.46
4113 6221 9.174166 TCCATAAAATTAAGCTAAAGTCTGGTC 57.826 33.333 0.00 0.00 0.00 4.02
4114 6222 9.178758 CTCCATAAAATTAAGCTAAAGTCTGGT 57.821 33.333 0.00 0.00 0.00 4.00
4115 6223 8.131731 GCTCCATAAAATTAAGCTAAAGTCTGG 58.868 37.037 0.00 0.00 0.00 3.86
4116 6224 8.897752 AGCTCCATAAAATTAAGCTAAAGTCTG 58.102 33.333 0.00 0.00 41.32 3.51
4117 6225 8.897752 CAGCTCCATAAAATTAAGCTAAAGTCT 58.102 33.333 0.00 0.00 41.19 3.24
4118 6226 7.645735 GCAGCTCCATAAAATTAAGCTAAAGTC 59.354 37.037 0.00 0.00 41.19 3.01
4119 6227 7.416777 GGCAGCTCCATAAAATTAAGCTAAAGT 60.417 37.037 0.00 0.00 41.19 2.66
4120 6228 6.920210 GGCAGCTCCATAAAATTAAGCTAAAG 59.080 38.462 0.00 0.00 41.19 1.85
4121 6229 6.379703 TGGCAGCTCCATAAAATTAAGCTAAA 59.620 34.615 1.25 0.00 41.19 1.85
4122 6230 5.890985 TGGCAGCTCCATAAAATTAAGCTAA 59.109 36.000 1.25 0.00 41.19 3.09
4123 6231 5.445069 TGGCAGCTCCATAAAATTAAGCTA 58.555 37.500 1.25 0.00 41.19 3.32
4124 6232 4.280819 TGGCAGCTCCATAAAATTAAGCT 58.719 39.130 1.25 0.00 43.81 3.74
4125 6233 4.654091 TGGCAGCTCCATAAAATTAAGC 57.346 40.909 1.25 0.00 40.72 3.09
4126 6234 6.313658 GGTTTTGGCAGCTCCATAAAATTAAG 59.686 38.462 5.83 0.00 46.04 1.85
4127 6235 6.169800 GGTTTTGGCAGCTCCATAAAATTAA 58.830 36.000 5.83 0.00 46.04 1.40
4128 6236 5.337975 GGGTTTTGGCAGCTCCATAAAATTA 60.338 40.000 5.83 0.00 46.04 1.40
4129 6237 4.565444 GGGTTTTGGCAGCTCCATAAAATT 60.565 41.667 5.83 0.00 46.04 1.82
4130 6238 3.055167 GGGTTTTGGCAGCTCCATAAAAT 60.055 43.478 5.83 0.00 46.04 1.82
4131 6239 2.301583 GGGTTTTGGCAGCTCCATAAAA 59.698 45.455 5.83 2.91 46.04 1.52
4132 6240 1.899142 GGGTTTTGGCAGCTCCATAAA 59.101 47.619 5.83 6.94 46.04 1.40
4133 6241 1.203112 TGGGTTTTGGCAGCTCCATAA 60.203 47.619 5.83 5.22 46.04 1.90
4134 6242 0.407528 TGGGTTTTGGCAGCTCCATA 59.592 50.000 5.83 0.00 46.04 2.74
4135 6243 0.901580 CTGGGTTTTGGCAGCTCCAT 60.902 55.000 5.83 0.00 46.04 3.41
4136 6244 1.531365 CTGGGTTTTGGCAGCTCCA 60.531 57.895 1.25 1.25 44.85 3.86
4137 6245 2.935740 GCTGGGTTTTGGCAGCTCC 61.936 63.158 0.00 0.00 37.66 4.70
4138 6246 1.905354 AGCTGGGTTTTGGCAGCTC 60.905 57.895 0.00 0.00 46.74 4.09
4139 6247 2.199535 AGCTGGGTTTTGGCAGCT 59.800 55.556 0.00 0.00 45.07 4.24
4140 6248 2.653115 GAGCTGGGTTTTGGCAGC 59.347 61.111 0.00 0.00 40.66 5.25
4141 6249 2.278330 GGGAGCTGGGTTTTGGCAG 61.278 63.158 0.00 0.00 0.00 4.85
4142 6250 2.203625 GGGAGCTGGGTTTTGGCA 60.204 61.111 0.00 0.00 0.00 4.92
4143 6251 2.997315 GGGGAGCTGGGTTTTGGC 60.997 66.667 0.00 0.00 0.00 4.52
4144 6252 1.152355 TTGGGGAGCTGGGTTTTGG 60.152 57.895 0.00 0.00 0.00 3.28
4145 6253 0.469892 AGTTGGGGAGCTGGGTTTTG 60.470 55.000 0.00 0.00 0.00 2.44
4146 6254 0.178961 GAGTTGGGGAGCTGGGTTTT 60.179 55.000 0.00 0.00 0.00 2.43
4147 6255 1.460699 GAGTTGGGGAGCTGGGTTT 59.539 57.895 0.00 0.00 0.00 3.27
4148 6256 2.539081 GGAGTTGGGGAGCTGGGTT 61.539 63.158 0.00 0.00 0.00 4.11
4149 6257 2.936032 GGAGTTGGGGAGCTGGGT 60.936 66.667 0.00 0.00 0.00 4.51
4150 6258 4.101448 CGGAGTTGGGGAGCTGGG 62.101 72.222 0.00 0.00 0.00 4.45
4151 6259 4.785453 GCGGAGTTGGGGAGCTGG 62.785 72.222 0.00 0.00 0.00 4.85
4169 6277 3.894547 TTCGGAACTTGCCCGCTCC 62.895 63.158 0.00 0.00 46.10 4.70
4170 6278 2.358247 TTCGGAACTTGCCCGCTC 60.358 61.111 0.00 0.00 46.10 5.03
4171 6279 2.668550 GTTCGGAACTTGCCCGCT 60.669 61.111 13.49 0.00 46.10 5.52
4172 6280 2.966309 CTGTTCGGAACTTGCCCGC 61.966 63.158 20.53 0.00 46.10 6.13
4174 6282 1.971695 CCCTGTTCGGAACTTGCCC 60.972 63.158 20.53 0.00 33.16 5.36
4175 6283 2.626780 GCCCTGTTCGGAACTTGCC 61.627 63.158 20.53 4.79 33.16 4.52
4176 6284 2.626780 GGCCCTGTTCGGAACTTGC 61.627 63.158 20.53 18.04 33.16 4.01
4177 6285 0.323629 TAGGCCCTGTTCGGAACTTG 59.676 55.000 20.53 13.22 33.16 3.16
4178 6286 1.061546 TTAGGCCCTGTTCGGAACTT 58.938 50.000 20.53 3.85 33.16 2.66
4179 6287 1.061546 TTTAGGCCCTGTTCGGAACT 58.938 50.000 20.53 3.18 33.16 3.01
4180 6288 2.124277 ATTTAGGCCCTGTTCGGAAC 57.876 50.000 13.86 13.86 33.16 3.62
4181 6289 3.815809 CATATTTAGGCCCTGTTCGGAA 58.184 45.455 0.00 0.00 33.16 4.30
4182 6290 2.486548 GCATATTTAGGCCCTGTTCGGA 60.487 50.000 0.00 0.00 33.16 4.55
4183 6291 1.880027 GCATATTTAGGCCCTGTTCGG 59.120 52.381 0.00 0.00 0.00 4.30
4184 6292 2.571212 TGCATATTTAGGCCCTGTTCG 58.429 47.619 0.00 0.00 30.87 3.95
4185 6293 5.535753 ATTTGCATATTTAGGCCCTGTTC 57.464 39.130 0.00 0.00 30.87 3.18
4186 6294 6.782000 TGATATTTGCATATTTAGGCCCTGTT 59.218 34.615 0.00 0.00 30.87 3.16
4187 6295 6.314120 TGATATTTGCATATTTAGGCCCTGT 58.686 36.000 0.00 0.00 30.87 4.00
4188 6296 6.839124 TGATATTTGCATATTTAGGCCCTG 57.161 37.500 0.00 0.00 30.87 4.45
4189 6297 6.211384 GGTTGATATTTGCATATTTAGGCCCT 59.789 38.462 0.00 0.00 30.87 5.19
4190 6298 6.398095 GGTTGATATTTGCATATTTAGGCCC 58.602 40.000 0.00 0.00 30.87 5.80
4191 6299 6.014669 TGGGTTGATATTTGCATATTTAGGCC 60.015 38.462 0.00 0.00 30.87 5.19
4192 6300 6.991938 TGGGTTGATATTTGCATATTTAGGC 58.008 36.000 0.00 0.00 0.00 3.93
4193 6301 7.599998 GCTTGGGTTGATATTTGCATATTTAGG 59.400 37.037 0.00 0.00 0.00 2.69
4194 6302 8.362639 AGCTTGGGTTGATATTTGCATATTTAG 58.637 33.333 0.00 0.00 0.00 1.85
4249 6357 4.508461 TGCCAAGATCAAATGTGAACTG 57.492 40.909 0.00 0.00 37.01 3.16
4393 6502 2.012673 GGCGAGAATGCTCACTTGATT 58.987 47.619 0.51 0.00 41.36 2.57
4488 6597 6.992715 CCAACATAACCCTCAAAGACCTATAG 59.007 42.308 0.00 0.00 0.00 1.31
4833 6943 3.508793 GGGCAATGTTCATATGATGGGAG 59.491 47.826 6.17 0.00 0.00 4.30
4836 6946 6.785337 ATATGGGCAATGTTCATATGATGG 57.215 37.500 6.17 0.00 34.11 3.51
4973 7084 2.038863 ACCCTCAACCTGACACCATA 57.961 50.000 0.00 0.00 0.00 2.74
5154 7267 1.620822 AATTGGCAGGGTCACAGTTC 58.379 50.000 0.00 0.00 0.00 3.01
5265 7379 6.555315 CAATCCATAACTTCTAGGCAAACAC 58.445 40.000 0.00 0.00 0.00 3.32
5434 7555 1.669502 CCAATGTTCATGCAACCCACG 60.670 52.381 0.00 0.00 33.51 4.94
5435 7556 1.617850 TCCAATGTTCATGCAACCCAC 59.382 47.619 0.00 0.00 33.51 4.61
5436 7557 2.006805 TCCAATGTTCATGCAACCCA 57.993 45.000 0.00 0.00 33.51 4.51
5437 7558 4.942761 ATATCCAATGTTCATGCAACCC 57.057 40.909 0.00 0.00 33.51 4.11
5438 7559 5.524646 CCAAATATCCAATGTTCATGCAACC 59.475 40.000 0.00 0.00 33.51 3.77
5439 7560 6.036300 CACCAAATATCCAATGTTCATGCAAC 59.964 38.462 0.00 0.00 35.28 4.17
5440 7561 6.107343 CACCAAATATCCAATGTTCATGCAA 58.893 36.000 0.00 0.00 0.00 4.08
5441 7562 5.395435 CCACCAAATATCCAATGTTCATGCA 60.395 40.000 0.00 0.00 0.00 3.96
5442 7563 5.051816 CCACCAAATATCCAATGTTCATGC 58.948 41.667 0.00 0.00 0.00 4.06
5443 7564 5.129155 ACCCACCAAATATCCAATGTTCATG 59.871 40.000 0.00 0.00 0.00 3.07
5444 7565 5.279685 ACCCACCAAATATCCAATGTTCAT 58.720 37.500 0.00 0.00 0.00 2.57
5445 7566 4.682563 ACCCACCAAATATCCAATGTTCA 58.317 39.130 0.00 0.00 0.00 3.18
5446 7567 4.099419 GGACCCACCAAATATCCAATGTTC 59.901 45.833 0.00 0.00 38.79 3.18
5447 7568 4.030216 GGACCCACCAAATATCCAATGTT 58.970 43.478 0.00 0.00 38.79 2.71
5448 7569 3.012274 TGGACCCACCAAATATCCAATGT 59.988 43.478 0.00 0.00 46.75 2.71
5449 7570 3.641046 TGGACCCACCAAATATCCAATG 58.359 45.455 0.00 0.00 46.75 2.82
5462 7583 5.187967 CCATCTAATATAGAGGTGGACCCAC 59.812 48.000 10.61 10.61 37.21 4.61
5463 7584 5.162760 ACCATCTAATATAGAGGTGGACCCA 60.163 44.000 19.24 0.00 37.21 4.51
5464 7585 5.187967 CACCATCTAATATAGAGGTGGACCC 59.812 48.000 19.24 0.00 43.12 4.46
5465 7586 6.287589 CACCATCTAATATAGAGGTGGACC 57.712 45.833 19.24 0.00 43.12 4.46
5469 7590 7.015682 AGTGAACCACCATCTAATATAGAGGTG 59.984 40.741 18.82 18.82 44.58 4.00
5470 7591 7.076446 AGTGAACCACCATCTAATATAGAGGT 58.924 38.462 0.00 1.92 37.03 3.85
5471 7592 7.546250 AGTGAACCACCATCTAATATAGAGG 57.454 40.000 0.00 0.00 34.95 3.69
5472 7593 9.838339 AAAAGTGAACCACCATCTAATATAGAG 57.162 33.333 0.00 0.00 34.95 2.43
5473 7594 9.613428 CAAAAGTGAACCACCATCTAATATAGA 57.387 33.333 0.00 0.00 35.56 1.98
5474 7595 9.396022 ACAAAAGTGAACCACCATCTAATATAG 57.604 33.333 0.00 0.00 34.49 1.31
5496 7617 7.765695 ATGAAATCAGCTAAAAGAGGACAAA 57.234 32.000 0.00 0.00 0.00 2.83
5547 7668 6.270000 TCTTCCAATTCTCTCAACTAAGGACA 59.730 38.462 0.00 0.00 0.00 4.02
5551 7672 7.659390 ACAACTCTTCCAATTCTCTCAACTAAG 59.341 37.037 0.00 0.00 0.00 2.18
5662 7786 8.141909 CCAACTCTCGAGTATGATAACCATTTA 58.858 37.037 13.13 0.00 41.58 1.40
5673 7797 3.193691 ACCTCAACCAACTCTCGAGTATG 59.806 47.826 13.13 9.75 41.58 2.39
5701 7825 3.366781 GGATTTGCAGAGCTTCCAACTTC 60.367 47.826 0.00 0.00 0.00 3.01
5760 7884 6.944096 TCACATTGGCAAATGAAATTCCATA 58.056 32.000 20.90 0.00 45.17 2.74
5765 7889 8.505625 GTTATGTTCACATTGGCAAATGAAATT 58.494 29.630 23.79 18.06 45.17 1.82
5772 7896 3.570125 TCCGTTATGTTCACATTGGCAAA 59.430 39.130 3.01 0.00 37.76 3.68


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

AutoCloner maintained by Alex Coulton.