Multiple sequence alignment - TraesCS6A01G070800

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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 TraesCS6A01G070800 chr6A 100.000 3110 0 0 1 3110 38683607 38686716 0.000000e+00 5744.0
1 TraesCS6A01G070800 chr6A 87.660 1248 112 15 903 2129 38723638 38724864 0.000000e+00 1413.0
2 TraesCS6A01G070800 chr6A 83.132 1405 148 51 893 2258 38741713 38743067 0.000000e+00 1199.0
3 TraesCS6A01G070800 chr6B 92.000 2175 119 25 109 2262 71197051 71199191 0.000000e+00 3001.0
4 TraesCS6A01G070800 chr6B 86.347 1399 119 32 903 2263 71226594 71227958 0.000000e+00 1459.0
5 TraesCS6A01G070800 chr6B 82.653 1372 158 45 893 2229 71262061 71263387 0.000000e+00 1142.0
6 TraesCS6A01G070800 chr6B 96.471 255 9 0 2856 3110 71199447 71199701 3.710000e-114 422.0
7 TraesCS6A01G070800 chr6B 90.441 272 23 2 2590 2861 356337191 356337459 3.810000e-94 355.0
8 TraesCS6A01G070800 chr6B 85.542 166 8 5 2441 2590 71199284 71199449 3.210000e-35 159.0
9 TraesCS6A01G070800 chr6B 89.412 85 4 2 2321 2401 71199200 71199283 5.490000e-18 102.0
10 TraesCS6A01G070800 chr6D 90.076 1975 120 31 411 2350 34430151 34432084 0.000000e+00 2492.0
11 TraesCS6A01G070800 chr6D 85.818 1375 119 23 903 2254 34501988 34503309 0.000000e+00 1389.0
12 TraesCS6A01G070800 chr6D 80.540 1408 175 57 893 2258 34508025 34509375 0.000000e+00 990.0
13 TraesCS6A01G070800 chr6D 90.588 255 23 1 2856 3110 34434038 34434291 1.380000e-88 337.0
14 TraesCS6A01G070800 chr6D 89.844 256 24 2 2856 3110 34432937 34433191 8.320000e-86 327.0
15 TraesCS6A01G070800 chr6D 87.170 265 26 6 27 288 34428904 34429163 8.430000e-76 294.0
16 TraesCS6A01G070800 chr6D 92.553 94 7 0 2349 2442 34432345 34432438 5.410000e-28 135.0
17 TraesCS6A01G070800 chr6D 86.316 95 4 3 279 373 34430066 34430151 9.180000e-16 95.3
18 TraesCS6A01G070800 chr7B 80.562 818 113 24 997 1805 592701588 592700808 3.450000e-164 588.0
19 TraesCS6A01G070800 chr7B 79.375 800 115 25 998 1787 592777349 592776590 4.600000e-143 518.0
20 TraesCS6A01G070800 chr7A 81.172 717 100 18 998 1707 634446678 634445990 7.590000e-151 544.0
21 TraesCS6A01G070800 chr7A 78.822 798 125 22 997 1787 634455099 634454339 5.990000e-137 497.0
22 TraesCS6A01G070800 chr7D 79.474 799 120 22 1014 1805 549128024 549127263 7.640000e-146 527.0
23 TraesCS6A01G070800 chr7D 90.037 271 23 3 2586 2856 496965411 496965145 6.380000e-92 348.0
24 TraesCS6A01G070800 chr7D 90.262 267 23 2 2590 2856 439023370 439023633 2.300000e-91 346.0
25 TraesCS6A01G070800 chr5A 93.258 267 15 3 2590 2856 666292385 666292122 1.050000e-104 390.0
26 TraesCS6A01G070800 chr4B 91.386 267 20 2 2590 2856 38369674 38369411 2.280000e-96 363.0
27 TraesCS6A01G070800 chr1B 90.545 275 23 2 2582 2856 401987678 401987949 8.200000e-96 361.0
28 TraesCS6A01G070800 chr2B 91.011 267 21 2 2590 2856 3268134 3268397 1.060000e-94 357.0
29 TraesCS6A01G070800 chr2B 90.637 267 22 2 2590 2856 534638802 534639065 4.930000e-93 351.0
30 TraesCS6A01G070800 chr2B 93.750 48 1 1 3 48 234830767 234830814 1.550000e-08 71.3
31 TraesCS6A01G070800 chr4D 90.000 270 24 2 2590 2859 350977589 350977323 2.300000e-91 346.0
32 TraesCS6A01G070800 chr3A 90.000 60 3 3 1 58 341285109 341285167 1.200000e-09 75.0
33 TraesCS6A01G070800 chr3A 100.000 40 0 0 1 40 490165896 490165935 1.200000e-09 75.0
34 TraesCS6A01G070800 chr3A 95.455 44 1 1 1 44 207777442 207777400 5.570000e-08 69.4
35 TraesCS6A01G070800 chr5D 95.556 45 2 0 2 46 486284850 486284806 4.300000e-09 73.1
36 TraesCS6A01G070800 chr5D 93.478 46 1 2 3 48 175637008 175636965 2.000000e-07 67.6
37 TraesCS6A01G070800 chr1A 100.000 39 0 0 1 39 22660335 22660297 4.300000e-09 73.1
38 TraesCS6A01G070800 chr5B 95.556 45 0 2 1 44 506528120 506528077 1.550000e-08 71.3
39 TraesCS6A01G070800 chr3B 90.909 55 1 3 2 56 771981245 771981295 1.550000e-08 71.3


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 TraesCS6A01G070800 chr6A 38683607 38686716 3109 False 5744.000000 5744 100.00000 1 3110 1 chr6A.!!$F1 3109
1 TraesCS6A01G070800 chr6A 38723638 38724864 1226 False 1413.000000 1413 87.66000 903 2129 1 chr6A.!!$F2 1226
2 TraesCS6A01G070800 chr6A 38741713 38743067 1354 False 1199.000000 1199 83.13200 893 2258 1 chr6A.!!$F3 1365
3 TraesCS6A01G070800 chr6B 71226594 71227958 1364 False 1459.000000 1459 86.34700 903 2263 1 chr6B.!!$F1 1360
4 TraesCS6A01G070800 chr6B 71262061 71263387 1326 False 1142.000000 1142 82.65300 893 2229 1 chr6B.!!$F2 1336
5 TraesCS6A01G070800 chr6B 71197051 71199701 2650 False 921.000000 3001 90.85625 109 3110 4 chr6B.!!$F4 3001
6 TraesCS6A01G070800 chr6D 34501988 34503309 1321 False 1389.000000 1389 85.81800 903 2254 1 chr6D.!!$F1 1351
7 TraesCS6A01G070800 chr6D 34508025 34509375 1350 False 990.000000 990 80.54000 893 2258 1 chr6D.!!$F2 1365
8 TraesCS6A01G070800 chr6D 34428904 34434291 5387 False 613.383333 2492 89.42450 27 3110 6 chr6D.!!$F3 3083
9 TraesCS6A01G070800 chr7B 592700808 592701588 780 True 588.000000 588 80.56200 997 1805 1 chr7B.!!$R1 808
10 TraesCS6A01G070800 chr7B 592776590 592777349 759 True 518.000000 518 79.37500 998 1787 1 chr7B.!!$R2 789
11 TraesCS6A01G070800 chr7A 634445990 634446678 688 True 544.000000 544 81.17200 998 1707 1 chr7A.!!$R1 709
12 TraesCS6A01G070800 chr7A 634454339 634455099 760 True 497.000000 497 78.82200 997 1787 1 chr7A.!!$R2 790
13 TraesCS6A01G070800 chr7D 549127263 549128024 761 True 527.000000 527 79.47400 1014 1805 1 chr7D.!!$R2 791

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
80 82 0.672342 TAGAAGCGTATTCCGAGCCC 59.328 55.000 0.0 0.0 39.56 5.19 F
510 1429 0.764890 AGGCAGACTTGTAAGCACCA 59.235 50.000 0.0 0.0 0.00 4.17 F
1005 1939 1.227380 CTCGTAGCCAGCCATGTCC 60.227 63.158 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1064 1998 0.386113 GATGACTAGACGACCCAGGC 59.614 60.000 0.0 0.0 0.0 4.85 R
1749 2724 2.025155 GACATCTCCTTCCAGCTCGTA 58.975 52.381 0.0 0.0 0.0 3.43 R
2838 5627 0.042581 TGAGGCTGGTCATAGTGGGA 59.957 55.000 0.0 0.0 0.0 4.37 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
65 66 8.418597 AAGTGTTGGATACTGTAAGACTAGAA 57.581 34.615 0.00 0.00 37.43 2.10
67 68 6.752815 GTGTTGGATACTGTAAGACTAGAAGC 59.247 42.308 0.00 0.00 37.43 3.86
68 69 5.752892 TGGATACTGTAAGACTAGAAGCG 57.247 43.478 0.00 0.00 37.43 4.68
80 82 0.672342 TAGAAGCGTATTCCGAGCCC 59.328 55.000 0.00 0.00 39.56 5.19
85 87 1.145803 GCGTATTCCGAGCCCAATAC 58.854 55.000 0.00 0.00 39.56 1.89
161 164 4.583871 AGAAAGCAACCTTAGTCCTCATG 58.416 43.478 0.00 0.00 0.00 3.07
177 180 3.009473 CCTCATGAGACCCTTCCAAAAGA 59.991 47.826 24.62 0.00 34.14 2.52
193 196 4.437930 CCAAAAGAGTGAATCATTCGGCTC 60.438 45.833 11.72 11.72 35.74 4.70
195 198 3.834489 AGAGTGAATCATTCGGCTCAT 57.166 42.857 18.39 6.36 37.02 2.90
243 246 8.668510 AGAATGTAGATACTTGTTAGGCAATG 57.331 34.615 0.00 0.00 36.36 2.82
254 257 5.247507 TGTTAGGCAATGAATGTATGCAC 57.752 39.130 0.00 0.00 41.80 4.57
263 266 2.840038 TGAATGTATGCACACTCCCTCT 59.160 45.455 0.00 0.00 37.54 3.69
266 269 5.045942 TGAATGTATGCACACTCCCTCTTTA 60.046 40.000 0.00 0.00 37.54 1.85
327 1242 8.062065 ACACTTGTTTTTAATCTCCAAGTTCA 57.938 30.769 0.00 0.00 42.09 3.18
376 1291 4.663120 TGGCCTACACATAATATCCCACTT 59.337 41.667 3.32 0.00 0.00 3.16
377 1292 5.847265 TGGCCTACACATAATATCCCACTTA 59.153 40.000 3.32 0.00 0.00 2.24
378 1293 6.330514 TGGCCTACACATAATATCCCACTTAA 59.669 38.462 3.32 0.00 0.00 1.85
379 1294 7.018149 TGGCCTACACATAATATCCCACTTAAT 59.982 37.037 3.32 0.00 0.00 1.40
380 1295 7.553044 GGCCTACACATAATATCCCACTTAATC 59.447 40.741 0.00 0.00 0.00 1.75
381 1296 8.100791 GCCTACACATAATATCCCACTTAATCA 58.899 37.037 0.00 0.00 0.00 2.57
382 1297 9.658799 CCTACACATAATATCCCACTTAATCAG 57.341 37.037 0.00 0.00 0.00 2.90
509 1428 2.762535 TAGGCAGACTTGTAAGCACC 57.237 50.000 0.00 0.00 0.00 5.01
510 1429 0.764890 AGGCAGACTTGTAAGCACCA 59.235 50.000 0.00 0.00 0.00 4.17
533 1452 6.407202 CAAGTTTACAAGTATCAGCCTACCT 58.593 40.000 0.00 0.00 0.00 3.08
535 1454 5.720041 AGTTTACAAGTATCAGCCTACCTCA 59.280 40.000 0.00 0.00 0.00 3.86
536 1455 6.384305 AGTTTACAAGTATCAGCCTACCTCAT 59.616 38.462 0.00 0.00 0.00 2.90
662 1582 6.961554 CCTTAGATAACGAAACAATTGTCTGC 59.038 38.462 12.39 3.52 30.10 4.26
666 1586 4.836125 AACGAAACAATTGTCTGCAGAT 57.164 36.364 21.47 0.00 0.00 2.90
790 1714 7.046033 AGAAATTGCAAAGGATGATCCATTTC 58.954 34.615 14.90 16.84 39.61 2.17
791 1715 5.943349 ATTGCAAAGGATGATCCATTTCA 57.057 34.783 14.90 5.94 39.61 2.69
794 1718 5.481105 TGCAAAGGATGATCCATTTCAAAC 58.519 37.500 14.90 2.54 39.61 2.93
795 1719 4.872124 GCAAAGGATGATCCATTTCAAACC 59.128 41.667 14.90 0.00 39.61 3.27
797 1721 4.335735 AGGATGATCCATTTCAAACCCA 57.664 40.909 14.90 0.00 39.61 4.51
798 1722 4.026052 AGGATGATCCATTTCAAACCCAC 58.974 43.478 14.90 0.00 39.61 4.61
800 1724 3.541242 TGATCCATTTCAAACCCACCT 57.459 42.857 0.00 0.00 0.00 4.00
801 1725 4.666412 TGATCCATTTCAAACCCACCTA 57.334 40.909 0.00 0.00 0.00 3.08
802 1726 4.599041 TGATCCATTTCAAACCCACCTAG 58.401 43.478 0.00 0.00 0.00 3.02
803 1727 4.290985 TGATCCATTTCAAACCCACCTAGA 59.709 41.667 0.00 0.00 0.00 2.43
804 1728 4.733077 TCCATTTCAAACCCACCTAGAA 57.267 40.909 0.00 0.00 0.00 2.10
805 1729 4.662278 TCCATTTCAAACCCACCTAGAAG 58.338 43.478 0.00 0.00 0.00 2.85
806 1730 3.193479 CCATTTCAAACCCACCTAGAAGC 59.807 47.826 0.00 0.00 0.00 3.86
807 1731 2.178912 TTCAAACCCACCTAGAAGCG 57.821 50.000 0.00 0.00 0.00 4.68
831 1755 4.630069 GCTACCATACAAGACAACACGAAT 59.370 41.667 0.00 0.00 0.00 3.34
837 1761 3.926616 ACAAGACAACACGAATCTAGGG 58.073 45.455 0.00 0.00 0.00 3.53
841 1765 5.223449 AGACAACACGAATCTAGGGAAAA 57.777 39.130 0.00 0.00 0.00 2.29
842 1766 5.805728 AGACAACACGAATCTAGGGAAAAT 58.194 37.500 0.00 0.00 0.00 1.82
847 1771 3.877508 CACGAATCTAGGGAAAATGGGTC 59.122 47.826 0.00 0.00 0.00 4.46
848 1772 3.780850 ACGAATCTAGGGAAAATGGGTCT 59.219 43.478 0.00 0.00 0.00 3.85
876 1800 4.631377 ACAAGAAAAGCAAGCTCCAAAAAC 59.369 37.500 0.00 0.00 0.00 2.43
877 1801 4.470334 AGAAAAGCAAGCTCCAAAAACA 57.530 36.364 0.00 0.00 0.00 2.83
878 1802 4.831107 AGAAAAGCAAGCTCCAAAAACAA 58.169 34.783 0.00 0.00 0.00 2.83
879 1803 5.244755 AGAAAAGCAAGCTCCAAAAACAAA 58.755 33.333 0.00 0.00 0.00 2.83
880 1804 5.704978 AGAAAAGCAAGCTCCAAAAACAAAA 59.295 32.000 0.00 0.00 0.00 2.44
935 1863 2.513753 TCGCCATTGAAAACTCACCAT 58.486 42.857 0.00 0.00 0.00 3.55
936 1864 2.487762 TCGCCATTGAAAACTCACCATC 59.512 45.455 0.00 0.00 0.00 3.51
963 1897 5.534654 CAGACCCCTCTTTACACAATCAAAA 59.465 40.000 0.00 0.00 0.00 2.44
965 1899 4.832823 ACCCCTCTTTACACAATCAAAAGG 59.167 41.667 0.00 0.00 32.33 3.11
966 1900 4.321974 CCCCTCTTTACACAATCAAAAGGC 60.322 45.833 0.00 0.00 32.33 4.35
1005 1939 1.227380 CTCGTAGCCAGCCATGTCC 60.227 63.158 0.00 0.00 0.00 4.02
1017 1951 3.675086 CATGTCCTCCATGGTCTCG 57.325 57.895 12.58 0.00 46.03 4.04
1041 1975 3.275088 CACGGAGTAGTGGACGCT 58.725 61.111 0.00 0.00 41.61 5.07
1118 2052 4.521062 CCTCGAGGCGGGCTTCAG 62.521 72.222 20.67 4.67 0.00 3.02
1336 2290 2.190313 GGATCAGCCCGCACATGA 59.810 61.111 0.00 0.00 0.00 3.07
1633 2602 3.596066 GAGCTGAGGCGCTTGGTGA 62.596 63.158 7.64 0.00 41.08 4.02
1737 2712 1.445410 CGACAGCGATTCCCACGAA 60.445 57.895 0.00 0.00 40.82 3.85
1749 2724 2.579201 CACGAAGACCTGCCGGAT 59.421 61.111 5.05 0.00 0.00 4.18
1769 2750 0.820871 ACGAGCTGGAAGGAGATGTC 59.179 55.000 1.44 0.00 0.00 3.06
1869 2856 4.253685 TCCTCGATGAGTTGAAATGGTTC 58.746 43.478 0.00 0.00 0.00 3.62
1892 2885 3.667497 TGGATCCGCAAGATACTCATC 57.333 47.619 7.39 0.00 36.67 2.92
2130 3186 2.586792 GCCGGTCATCCTTGCTCT 59.413 61.111 1.90 0.00 0.00 4.09
2148 3204 3.487544 GCTCTGTTTGTTCACTTTCGCTT 60.488 43.478 0.00 0.00 0.00 4.68
2278 3343 6.500910 CACTTCACCGTGCTACTATATGTAA 58.499 40.000 0.00 0.00 0.00 2.41
2282 3347 7.940178 TCACCGTGCTACTATATGTAAATTG 57.060 36.000 0.00 0.00 0.00 2.32
2301 3370 5.571784 ATTGTACAAGATCCATGTTGCTG 57.428 39.130 14.65 0.00 34.72 4.41
2313 3382 5.263599 TCCATGTTGCTGATCCACTTTATT 58.736 37.500 0.00 0.00 0.00 1.40
2357 3688 7.884816 TTTGTGCATAACAGTTAGAGTAGAC 57.115 36.000 0.00 0.00 40.74 2.59
2364 3695 8.133627 GCATAACAGTTAGAGTAGACGGAATAA 58.866 37.037 0.00 0.00 0.00 1.40
2404 3739 3.827302 TCGTCTTCCCTAAGATCCTATGC 59.173 47.826 0.00 0.00 43.50 3.14
2445 3780 7.872993 ACAATAAATATGGACTACTCATCACCG 59.127 37.037 0.00 0.00 0.00 4.94
2511 4183 4.814294 GCAACGGAGGGCGATCGT 62.814 66.667 17.81 0.00 38.89 3.73
2522 4194 1.080093 GCGATCGTCCACCTGAACA 60.080 57.895 17.81 0.00 0.00 3.18
2536 4208 8.034804 GTCCACCTGAACATAATTGCTTAATTT 58.965 33.333 0.00 0.00 0.00 1.82
2537 4209 8.250332 TCCACCTGAACATAATTGCTTAATTTC 58.750 33.333 0.00 0.00 0.00 2.17
2539 4211 7.492344 CACCTGAACATAATTGCTTAATTTCCC 59.508 37.037 0.00 0.00 0.00 3.97
2581 5370 7.345691 TCTTTATTCTCCATCTTATTGCACCA 58.654 34.615 0.00 0.00 0.00 4.17
2587 5376 6.189859 TCTCCATCTTATTGCACCATTTCTT 58.810 36.000 0.00 0.00 0.00 2.52
2588 5377 6.319658 TCTCCATCTTATTGCACCATTTCTTC 59.680 38.462 0.00 0.00 0.00 2.87
2589 5378 5.951148 TCCATCTTATTGCACCATTTCTTCA 59.049 36.000 0.00 0.00 0.00 3.02
2590 5379 6.095860 TCCATCTTATTGCACCATTTCTTCAG 59.904 38.462 0.00 0.00 0.00 3.02
2591 5380 5.902613 TCTTATTGCACCATTTCTTCAGG 57.097 39.130 0.00 0.00 0.00 3.86
2592 5381 4.158394 TCTTATTGCACCATTTCTTCAGGC 59.842 41.667 0.00 0.00 0.00 4.85
2593 5382 1.999648 TTGCACCATTTCTTCAGGCT 58.000 45.000 0.00 0.00 0.00 4.58
2594 5383 2.877097 TGCACCATTTCTTCAGGCTA 57.123 45.000 0.00 0.00 0.00 3.93
2595 5384 2.715046 TGCACCATTTCTTCAGGCTAG 58.285 47.619 0.00 0.00 0.00 3.42
2596 5385 2.040278 TGCACCATTTCTTCAGGCTAGT 59.960 45.455 0.00 0.00 0.00 2.57
2597 5386 2.680339 GCACCATTTCTTCAGGCTAGTC 59.320 50.000 0.00 0.00 0.00 2.59
2598 5387 3.869912 GCACCATTTCTTCAGGCTAGTCA 60.870 47.826 0.00 0.00 0.00 3.41
2599 5388 3.686726 CACCATTTCTTCAGGCTAGTCAC 59.313 47.826 0.00 0.00 0.00 3.67
2600 5389 3.327757 ACCATTTCTTCAGGCTAGTCACA 59.672 43.478 0.00 0.00 0.00 3.58
2601 5390 3.937706 CCATTTCTTCAGGCTAGTCACAG 59.062 47.826 0.00 0.00 0.00 3.66
2602 5391 4.564406 CCATTTCTTCAGGCTAGTCACAGT 60.564 45.833 0.00 0.00 0.00 3.55
2603 5392 3.667497 TTCTTCAGGCTAGTCACAGTG 57.333 47.619 0.00 0.00 0.00 3.66
2604 5393 1.895798 TCTTCAGGCTAGTCACAGTGG 59.104 52.381 0.00 0.00 0.00 4.00
2605 5394 0.976641 TTCAGGCTAGTCACAGTGGG 59.023 55.000 0.00 0.00 0.00 4.61
2606 5395 0.114364 TCAGGCTAGTCACAGTGGGA 59.886 55.000 0.00 0.00 0.00 4.37
2607 5396 0.534412 CAGGCTAGTCACAGTGGGAG 59.466 60.000 0.00 0.00 0.00 4.30
2608 5397 0.115349 AGGCTAGTCACAGTGGGAGT 59.885 55.000 8.06 8.06 0.00 3.85
2609 5398 1.358103 AGGCTAGTCACAGTGGGAGTA 59.642 52.381 9.60 9.60 0.00 2.59
2610 5399 2.176889 GGCTAGTCACAGTGGGAGTAA 58.823 52.381 11.10 0.00 0.00 2.24
2611 5400 2.094130 GGCTAGTCACAGTGGGAGTAAC 60.094 54.545 11.10 6.73 0.00 2.50
2612 5401 2.826725 GCTAGTCACAGTGGGAGTAACT 59.173 50.000 11.10 0.68 0.00 2.24
2613 5402 3.258622 GCTAGTCACAGTGGGAGTAACTT 59.741 47.826 11.10 0.00 0.00 2.66
2614 5403 4.461781 GCTAGTCACAGTGGGAGTAACTTA 59.538 45.833 11.10 0.00 0.00 2.24
2615 5404 5.393243 GCTAGTCACAGTGGGAGTAACTTAG 60.393 48.000 11.10 2.33 0.00 2.18
2616 5405 3.833070 AGTCACAGTGGGAGTAACTTAGG 59.167 47.826 0.00 0.00 0.00 2.69
2617 5406 3.577415 GTCACAGTGGGAGTAACTTAGGT 59.423 47.826 0.00 0.00 0.00 3.08
2618 5407 4.768968 GTCACAGTGGGAGTAACTTAGGTA 59.231 45.833 0.00 0.00 0.00 3.08
2619 5408 5.014858 TCACAGTGGGAGTAACTTAGGTAG 58.985 45.833 0.00 0.00 0.00 3.18
2620 5409 4.771054 CACAGTGGGAGTAACTTAGGTAGT 59.229 45.833 0.00 0.00 39.32 2.73
2621 5410 5.948162 CACAGTGGGAGTAACTTAGGTAGTA 59.052 44.000 0.00 0.00 35.54 1.82
2622 5411 6.435277 CACAGTGGGAGTAACTTAGGTAGTAA 59.565 42.308 0.00 0.00 35.54 2.24
2623 5412 6.435591 ACAGTGGGAGTAACTTAGGTAGTAAC 59.564 42.308 0.00 0.00 35.54 2.50
2624 5413 6.435277 CAGTGGGAGTAACTTAGGTAGTAACA 59.565 42.308 0.00 0.00 35.54 2.41
2625 5414 7.123847 CAGTGGGAGTAACTTAGGTAGTAACAT 59.876 40.741 0.00 0.00 35.54 2.71
2626 5415 8.339247 AGTGGGAGTAACTTAGGTAGTAACATA 58.661 37.037 0.00 0.00 35.54 2.29
2627 5416 8.971073 GTGGGAGTAACTTAGGTAGTAACATAA 58.029 37.037 0.00 0.00 35.54 1.90
2628 5417 8.971073 TGGGAGTAACTTAGGTAGTAACATAAC 58.029 37.037 0.00 0.00 35.54 1.89
2629 5418 8.131731 GGGAGTAACTTAGGTAGTAACATAACG 58.868 40.741 0.00 0.00 35.54 3.18
2630 5419 7.645735 GGAGTAACTTAGGTAGTAACATAACGC 59.354 40.741 0.00 0.00 35.54 4.84
2631 5420 8.055279 AGTAACTTAGGTAGTAACATAACGCA 57.945 34.615 0.00 0.00 35.54 5.24
2632 5421 7.970614 AGTAACTTAGGTAGTAACATAACGCAC 59.029 37.037 0.00 0.00 35.54 5.34
2633 5422 6.521151 ACTTAGGTAGTAACATAACGCACT 57.479 37.500 0.00 0.00 34.56 4.40
2634 5423 6.928520 ACTTAGGTAGTAACATAACGCACTT 58.071 36.000 0.00 0.00 34.56 3.16
2635 5424 7.031975 ACTTAGGTAGTAACATAACGCACTTC 58.968 38.462 0.00 0.00 34.56 3.01
2636 5425 5.395682 AGGTAGTAACATAACGCACTTCA 57.604 39.130 0.00 0.00 0.00 3.02
2637 5426 5.786311 AGGTAGTAACATAACGCACTTCAA 58.214 37.500 0.00 0.00 0.00 2.69
2638 5427 5.867716 AGGTAGTAACATAACGCACTTCAAG 59.132 40.000 0.00 0.00 0.00 3.02
2639 5428 5.865552 GGTAGTAACATAACGCACTTCAAGA 59.134 40.000 0.00 0.00 0.00 3.02
2640 5429 6.366877 GGTAGTAACATAACGCACTTCAAGAA 59.633 38.462 0.00 0.00 0.00 2.52
2641 5430 6.854496 AGTAACATAACGCACTTCAAGAAA 57.146 33.333 0.00 0.00 0.00 2.52
2642 5431 7.435068 AGTAACATAACGCACTTCAAGAAAT 57.565 32.000 0.00 0.00 0.00 2.17
2643 5432 7.298122 AGTAACATAACGCACTTCAAGAAATG 58.702 34.615 0.00 0.00 0.00 2.32
2644 5433 5.689383 ACATAACGCACTTCAAGAAATGT 57.311 34.783 0.00 0.00 0.00 2.71
2645 5434 6.072112 ACATAACGCACTTCAAGAAATGTT 57.928 33.333 0.00 0.00 0.00 2.71
2646 5435 6.503524 ACATAACGCACTTCAAGAAATGTTT 58.496 32.000 0.00 0.00 0.00 2.83
2647 5436 6.417635 ACATAACGCACTTCAAGAAATGTTTG 59.582 34.615 0.00 0.00 0.00 2.93
2648 5437 3.115554 ACGCACTTCAAGAAATGTTTGC 58.884 40.909 0.00 0.00 0.00 3.68
2649 5438 3.181487 ACGCACTTCAAGAAATGTTTGCT 60.181 39.130 0.00 0.00 31.35 3.91
2650 5439 3.798337 CGCACTTCAAGAAATGTTTGCTT 59.202 39.130 0.00 0.00 31.35 3.91
2651 5440 4.975502 CGCACTTCAAGAAATGTTTGCTTA 59.024 37.500 0.00 0.00 31.35 3.09
2652 5441 5.108254 CGCACTTCAAGAAATGTTTGCTTAC 60.108 40.000 0.00 0.00 31.35 2.34
2653 5442 5.108254 GCACTTCAAGAAATGTTTGCTTACG 60.108 40.000 0.00 0.00 0.00 3.18
2654 5443 5.971202 CACTTCAAGAAATGTTTGCTTACGT 59.029 36.000 0.00 0.00 0.00 3.57
2655 5444 5.971202 ACTTCAAGAAATGTTTGCTTACGTG 59.029 36.000 0.00 0.00 0.00 4.49
2656 5445 5.743026 TCAAGAAATGTTTGCTTACGTGA 57.257 34.783 0.00 0.00 0.00 4.35
2657 5446 5.507077 TCAAGAAATGTTTGCTTACGTGAC 58.493 37.500 0.00 0.00 0.00 3.67
2658 5447 5.065346 TCAAGAAATGTTTGCTTACGTGACA 59.935 36.000 0.00 0.00 0.00 3.58
2659 5448 5.493133 AGAAATGTTTGCTTACGTGACAA 57.507 34.783 0.00 0.00 0.00 3.18
2660 5449 5.510671 AGAAATGTTTGCTTACGTGACAAG 58.489 37.500 0.00 0.00 0.00 3.16
2661 5450 4.893424 AATGTTTGCTTACGTGACAAGT 57.107 36.364 0.00 0.00 0.00 3.16
2662 5451 5.994887 AATGTTTGCTTACGTGACAAGTA 57.005 34.783 0.00 0.00 0.00 2.24
2663 5452 5.591643 ATGTTTGCTTACGTGACAAGTAG 57.408 39.130 0.00 0.00 0.00 2.57
2664 5453 4.435425 TGTTTGCTTACGTGACAAGTAGT 58.565 39.130 0.00 0.00 0.00 2.73
2665 5454 4.871557 TGTTTGCTTACGTGACAAGTAGTT 59.128 37.500 0.00 0.00 0.00 2.24
2666 5455 6.041511 TGTTTGCTTACGTGACAAGTAGTTA 58.958 36.000 0.00 0.00 0.00 2.24
2667 5456 6.534436 TGTTTGCTTACGTGACAAGTAGTTAA 59.466 34.615 0.00 0.00 0.00 2.01
2668 5457 7.225145 TGTTTGCTTACGTGACAAGTAGTTAAT 59.775 33.333 0.00 0.00 0.00 1.40
2669 5458 6.699895 TGCTTACGTGACAAGTAGTTAATG 57.300 37.500 0.00 0.00 0.00 1.90
2670 5459 6.448852 TGCTTACGTGACAAGTAGTTAATGA 58.551 36.000 0.00 0.00 0.00 2.57
2671 5460 6.924612 TGCTTACGTGACAAGTAGTTAATGAA 59.075 34.615 0.00 0.00 0.00 2.57
2672 5461 7.438757 TGCTTACGTGACAAGTAGTTAATGAAA 59.561 33.333 0.00 0.00 0.00 2.69
2673 5462 7.950496 GCTTACGTGACAAGTAGTTAATGAAAG 59.050 37.037 0.00 0.00 0.00 2.62
2674 5463 6.780706 ACGTGACAAGTAGTTAATGAAAGG 57.219 37.500 0.00 0.00 0.00 3.11
2675 5464 6.285990 ACGTGACAAGTAGTTAATGAAAGGT 58.714 36.000 0.00 0.00 0.00 3.50
2676 5465 6.202188 ACGTGACAAGTAGTTAATGAAAGGTG 59.798 38.462 0.00 0.00 0.00 4.00
2677 5466 6.347402 CGTGACAAGTAGTTAATGAAAGGTGG 60.347 42.308 0.00 0.00 0.00 4.61
2678 5467 6.485648 GTGACAAGTAGTTAATGAAAGGTGGT 59.514 38.462 0.00 0.00 0.00 4.16
2679 5468 7.658575 GTGACAAGTAGTTAATGAAAGGTGGTA 59.341 37.037 0.00 0.00 0.00 3.25
2680 5469 8.212312 TGACAAGTAGTTAATGAAAGGTGGTAA 58.788 33.333 0.00 0.00 0.00 2.85
2681 5470 8.387190 ACAAGTAGTTAATGAAAGGTGGTAAC 57.613 34.615 0.00 0.00 0.00 2.50
2710 5499 4.178540 TGTTACTGTAACATAGCGCTTCC 58.821 43.478 25.14 0.00 43.23 3.46
2711 5500 2.311124 ACTGTAACATAGCGCTTCCC 57.689 50.000 18.68 0.00 0.00 3.97
2712 5501 1.209128 CTGTAACATAGCGCTTCCCG 58.791 55.000 18.68 4.15 40.75 5.14
2713 5502 0.818938 TGTAACATAGCGCTTCCCGA 59.181 50.000 18.68 0.00 40.02 5.14
2714 5503 1.202371 TGTAACATAGCGCTTCCCGAG 60.202 52.381 18.68 1.79 40.02 4.63
2715 5504 1.066605 GTAACATAGCGCTTCCCGAGA 59.933 52.381 18.68 0.00 40.02 4.04
2716 5505 0.179108 AACATAGCGCTTCCCGAGAC 60.179 55.000 18.68 0.00 40.02 3.36
2717 5506 1.320344 ACATAGCGCTTCCCGAGACA 61.320 55.000 18.68 0.00 40.02 3.41
2718 5507 0.179111 CATAGCGCTTCCCGAGACAA 60.179 55.000 18.68 0.00 40.02 3.18
2719 5508 0.103208 ATAGCGCTTCCCGAGACAAG 59.897 55.000 18.68 0.00 40.02 3.16
2720 5509 0.963856 TAGCGCTTCCCGAGACAAGA 60.964 55.000 18.68 0.00 40.02 3.02
2721 5510 1.153549 GCGCTTCCCGAGACAAGAT 60.154 57.895 0.00 0.00 40.02 2.40
2722 5511 1.424493 GCGCTTCCCGAGACAAGATG 61.424 60.000 0.00 0.00 40.02 2.90
2723 5512 0.173481 CGCTTCCCGAGACAAGATGA 59.827 55.000 0.00 0.00 40.02 2.92
2724 5513 1.800655 CGCTTCCCGAGACAAGATGAG 60.801 57.143 0.00 0.00 40.02 2.90
2725 5514 1.205893 GCTTCCCGAGACAAGATGAGT 59.794 52.381 0.00 0.00 0.00 3.41
2726 5515 2.427453 GCTTCCCGAGACAAGATGAGTA 59.573 50.000 0.00 0.00 0.00 2.59
2727 5516 3.068873 GCTTCCCGAGACAAGATGAGTAT 59.931 47.826 0.00 0.00 0.00 2.12
2728 5517 4.278669 GCTTCCCGAGACAAGATGAGTATA 59.721 45.833 0.00 0.00 0.00 1.47
2729 5518 5.764131 CTTCCCGAGACAAGATGAGTATAC 58.236 45.833 0.00 0.00 0.00 1.47
2730 5519 4.788679 TCCCGAGACAAGATGAGTATACA 58.211 43.478 5.50 0.00 0.00 2.29
2731 5520 5.198207 TCCCGAGACAAGATGAGTATACAA 58.802 41.667 5.50 0.00 0.00 2.41
2732 5521 5.299531 TCCCGAGACAAGATGAGTATACAAG 59.700 44.000 5.50 0.00 0.00 3.16
2733 5522 5.067936 CCCGAGACAAGATGAGTATACAAGT 59.932 44.000 5.50 0.00 0.00 3.16
2734 5523 6.405953 CCCGAGACAAGATGAGTATACAAGTT 60.406 42.308 5.50 0.00 0.00 2.66
2735 5524 7.201794 CCCGAGACAAGATGAGTATACAAGTTA 60.202 40.741 5.50 0.00 0.00 2.24
2736 5525 8.188799 CCGAGACAAGATGAGTATACAAGTTAA 58.811 37.037 5.50 0.00 0.00 2.01
2737 5526 9.737427 CGAGACAAGATGAGTATACAAGTTAAT 57.263 33.333 5.50 0.00 0.00 1.40
2789 5578 9.060347 ACTATTATGTCACTTTGCATTATGAGG 57.940 33.333 0.00 0.00 0.00 3.86
2790 5579 6.698008 TTATGTCACTTTGCATTATGAGGG 57.302 37.500 0.00 0.00 0.00 4.30
2791 5580 4.032960 TGTCACTTTGCATTATGAGGGT 57.967 40.909 0.00 0.00 0.00 4.34
2792 5581 5.172687 TGTCACTTTGCATTATGAGGGTA 57.827 39.130 0.00 0.00 0.00 3.69
2793 5582 5.185454 TGTCACTTTGCATTATGAGGGTAG 58.815 41.667 0.00 0.00 0.00 3.18
2794 5583 5.186198 GTCACTTTGCATTATGAGGGTAGT 58.814 41.667 0.00 0.00 0.00 2.73
2795 5584 6.070481 TGTCACTTTGCATTATGAGGGTAGTA 60.070 38.462 0.00 0.00 0.00 1.82
2796 5585 6.821665 GTCACTTTGCATTATGAGGGTAGTAA 59.178 38.462 0.00 0.00 0.00 2.24
2797 5586 6.821665 TCACTTTGCATTATGAGGGTAGTAAC 59.178 38.462 0.00 0.00 0.00 2.50
2798 5587 6.823689 CACTTTGCATTATGAGGGTAGTAACT 59.176 38.462 0.00 0.00 0.00 2.24
2799 5588 7.336931 CACTTTGCATTATGAGGGTAGTAACTT 59.663 37.037 0.00 0.00 0.00 2.66
2800 5589 8.545472 ACTTTGCATTATGAGGGTAGTAACTTA 58.455 33.333 0.00 0.00 0.00 2.24
2801 5590 8.958119 TTTGCATTATGAGGGTAGTAACTTAG 57.042 34.615 0.00 0.00 0.00 2.18
2802 5591 7.907841 TGCATTATGAGGGTAGTAACTTAGA 57.092 36.000 0.00 0.00 0.00 2.10
2803 5592 7.723324 TGCATTATGAGGGTAGTAACTTAGAC 58.277 38.462 0.00 0.00 0.00 2.59
2804 5593 7.563924 TGCATTATGAGGGTAGTAACTTAGACT 59.436 37.037 0.00 0.00 0.00 3.24
2805 5594 9.075678 GCATTATGAGGGTAGTAACTTAGACTA 57.924 37.037 0.00 0.00 0.00 2.59
2810 5599 8.517062 TGAGGGTAGTAACTTAGACTAATGTC 57.483 38.462 0.00 0.00 43.22 3.06
2811 5600 8.111545 TGAGGGTAGTAACTTAGACTAATGTCA 58.888 37.037 0.00 0.00 45.20 3.58
2812 5601 9.134055 GAGGGTAGTAACTTAGACTAATGTCAT 57.866 37.037 0.00 0.00 45.20 3.06
2844 5633 9.317827 TGATACTAGTTTAAGTTACTTCCCACT 57.682 33.333 0.00 5.08 0.00 4.00
2848 5637 9.317827 ACTAGTTTAAGTTACTTCCCACTATGA 57.682 33.333 0.00 0.00 0.00 2.15
2849 5638 9.583765 CTAGTTTAAGTTACTTCCCACTATGAC 57.416 37.037 0.00 0.00 0.00 3.06
2850 5639 7.392418 AGTTTAAGTTACTTCCCACTATGACC 58.608 38.462 0.00 0.00 0.00 4.02
2851 5640 6.938698 TTAAGTTACTTCCCACTATGACCA 57.061 37.500 0.00 0.00 0.00 4.02
2852 5641 5.422214 AAGTTACTTCCCACTATGACCAG 57.578 43.478 0.00 0.00 0.00 4.00
2853 5642 3.197983 AGTTACTTCCCACTATGACCAGC 59.802 47.826 0.00 0.00 0.00 4.85
2854 5643 0.912486 ACTTCCCACTATGACCAGCC 59.088 55.000 0.00 0.00 0.00 4.85
2908 5698 7.432869 TGACCGATGACAAATTCTGAAAATTT 58.567 30.769 0.00 0.00 0.00 1.82
2909 5699 8.572185 TGACCGATGACAAATTCTGAAAATTTA 58.428 29.630 0.00 0.00 0.00 1.40
3022 5812 2.814805 ATCCTCCACCAATTCCACTG 57.185 50.000 0.00 0.00 0.00 3.66
3061 5851 5.339008 TTCGCTATGGTTCTGTCACTAAT 57.661 39.130 0.00 0.00 0.00 1.73
3066 5856 5.698545 GCTATGGTTCTGTCACTAATCCATC 59.301 44.000 0.00 0.00 36.01 3.51
3094 5884 1.248101 GCCACACCAGCCCGTAAATT 61.248 55.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 8.982723 AGTCTTACAGTATCCAACACTTCATAT 58.017 33.333 0.00 0.00 0.00 1.78
39 40 8.053026 TCTAGTCTTACAGTATCCAACACTTC 57.947 38.462 0.00 0.00 0.00 3.01
59 60 1.337387 GGCTCGGAATACGCTTCTAGT 59.663 52.381 0.00 0.00 43.86 2.57
65 66 1.045407 TATTGGGCTCGGAATACGCT 58.955 50.000 0.00 0.00 43.86 5.07
67 68 1.607251 GGGTATTGGGCTCGGAATACG 60.607 57.143 1.82 0.00 46.11 3.06
68 69 1.697982 AGGGTATTGGGCTCGGAATAC 59.302 52.381 0.00 0.00 35.25 1.89
80 82 1.280998 ACTCGGTTTGGGAGGGTATTG 59.719 52.381 0.00 0.00 35.82 1.90
85 87 2.351276 CCACTCGGTTTGGGAGGG 59.649 66.667 0.00 0.00 35.82 4.30
161 164 3.771577 TCACTCTTTTGGAAGGGTCTC 57.228 47.619 0.00 0.00 43.08 3.36
177 180 2.171237 TGGATGAGCCGAATGATTCACT 59.829 45.455 5.95 1.75 40.66 3.41
237 240 3.489738 GGAGTGTGCATACATTCATTGCC 60.490 47.826 16.44 0.63 43.19 4.52
243 246 3.550437 AGAGGGAGTGTGCATACATTC 57.450 47.619 16.44 5.37 41.36 2.67
286 1201 9.541143 AAAACAAGTGTTTGATTAGTAAATGGG 57.459 29.630 10.05 0.00 46.47 4.00
327 1242 2.545810 CCAATGGGGTTTGGGTATTGT 58.454 47.619 0.00 0.00 42.09 2.71
509 1428 6.407202 AGGTAGGCTGATACTTGTAAACTTG 58.593 40.000 0.00 0.00 0.00 3.16
510 1429 6.212791 TGAGGTAGGCTGATACTTGTAAACTT 59.787 38.462 0.00 0.00 0.00 2.66
540 1460 2.760092 TGTTGGAAGGGCAAGATTATGC 59.240 45.455 0.00 0.00 45.67 3.14
648 1568 9.282247 CTATGTTAATCTGCAGACAATTGTTTC 57.718 33.333 20.97 0.37 0.00 2.78
790 1714 1.305930 GCCGCTTCTAGGTGGGTTTG 61.306 60.000 1.42 0.00 37.35 2.93
791 1715 1.002502 GCCGCTTCTAGGTGGGTTT 60.003 57.895 1.42 0.00 37.35 3.27
794 1718 1.442148 GTAGCCGCTTCTAGGTGGG 59.558 63.158 0.00 0.00 37.35 4.61
795 1719 1.327690 TGGTAGCCGCTTCTAGGTGG 61.328 60.000 0.00 0.00 39.64 4.61
797 1721 1.962100 GTATGGTAGCCGCTTCTAGGT 59.038 52.381 0.00 0.00 0.00 3.08
798 1722 1.961394 TGTATGGTAGCCGCTTCTAGG 59.039 52.381 0.00 0.00 0.00 3.02
800 1724 3.067742 GTCTTGTATGGTAGCCGCTTCTA 59.932 47.826 0.00 0.00 0.00 2.10
801 1725 2.108168 TCTTGTATGGTAGCCGCTTCT 58.892 47.619 0.00 0.00 0.00 2.85
802 1726 2.202566 GTCTTGTATGGTAGCCGCTTC 58.797 52.381 0.00 0.00 0.00 3.86
803 1727 1.553248 TGTCTTGTATGGTAGCCGCTT 59.447 47.619 0.00 0.00 0.00 4.68
804 1728 1.191535 TGTCTTGTATGGTAGCCGCT 58.808 50.000 0.00 0.00 0.00 5.52
805 1729 1.664151 GTTGTCTTGTATGGTAGCCGC 59.336 52.381 0.00 0.00 0.00 6.53
806 1730 2.671396 GTGTTGTCTTGTATGGTAGCCG 59.329 50.000 0.00 0.00 0.00 5.52
807 1731 2.671396 CGTGTTGTCTTGTATGGTAGCC 59.329 50.000 0.00 0.00 0.00 3.93
831 1755 2.116238 CGGAGACCCATTTTCCCTAGA 58.884 52.381 0.00 0.00 0.00 2.43
837 1761 3.934068 TCTTGTACGGAGACCCATTTTC 58.066 45.455 0.00 0.00 0.00 2.29
841 1765 3.868754 GCTTTTCTTGTACGGAGACCCAT 60.869 47.826 0.00 0.00 0.00 4.00
842 1766 2.549349 GCTTTTCTTGTACGGAGACCCA 60.549 50.000 0.00 0.00 0.00 4.51
847 1771 2.808543 AGCTTGCTTTTCTTGTACGGAG 59.191 45.455 0.00 0.00 0.00 4.63
848 1772 2.806244 GAGCTTGCTTTTCTTGTACGGA 59.194 45.455 0.00 0.00 0.00 4.69
878 1802 5.652014 TGACGAAGCCCTGAATGATATTTTT 59.348 36.000 0.00 0.00 0.00 1.94
879 1803 5.192927 TGACGAAGCCCTGAATGATATTTT 58.807 37.500 0.00 0.00 0.00 1.82
880 1804 4.780815 TGACGAAGCCCTGAATGATATTT 58.219 39.130 0.00 0.00 0.00 1.40
935 1863 1.975680 GTGTAAAGAGGGGTCTGGTGA 59.024 52.381 0.00 0.00 0.00 4.02
936 1864 1.697432 TGTGTAAAGAGGGGTCTGGTG 59.303 52.381 0.00 0.00 0.00 4.17
1005 1939 2.765807 AGGGGCGAGACCATGGAG 60.766 66.667 21.47 7.81 42.05 3.86
1064 1998 0.386113 GATGACTAGACGACCCAGGC 59.614 60.000 0.00 0.00 0.00 4.85
1737 2712 2.491022 GCTCGTATCCGGCAGGTCT 61.491 63.158 1.81 0.00 39.05 3.85
1749 2724 2.025155 GACATCTCCTTCCAGCTCGTA 58.975 52.381 0.00 0.00 0.00 3.43
1869 2856 3.797039 TGAGTATCTTGCGGATCCAAAG 58.203 45.455 13.41 14.49 35.98 2.77
1892 2885 4.463879 CCACCGGCAGCTCCTCAG 62.464 72.222 0.00 0.00 0.00 3.35
2061 3081 3.942439 GGGGAGTGGATAGCGCCC 61.942 72.222 2.29 0.00 43.94 6.13
2130 3186 2.750166 TGGAAGCGAAAGTGAACAAACA 59.250 40.909 0.00 0.00 0.00 2.83
2202 3260 2.610433 TGTGATCGATGAACAGACAGC 58.390 47.619 0.54 0.00 0.00 4.40
2278 3343 5.711506 TCAGCAACATGGATCTTGTACAATT 59.288 36.000 9.13 0.00 0.00 2.32
2282 3347 4.274459 GGATCAGCAACATGGATCTTGTAC 59.726 45.833 0.00 0.00 37.99 2.90
2291 3360 5.587388 AATAAAGTGGATCAGCAACATGG 57.413 39.130 0.00 0.00 0.00 3.66
2301 3370 7.126398 GCACGAATGTTCTAATAAAGTGGATC 58.874 38.462 0.00 0.00 0.00 3.36
2384 3719 3.262151 GGGCATAGGATCTTAGGGAAGAC 59.738 52.174 0.00 0.00 44.50 3.01
2445 3780 8.635877 AATGAAGTCGAGTATGAAACATACTC 57.364 34.615 27.74 27.74 44.19 2.59
2511 4183 7.716799 AATTAAGCAATTATGTTCAGGTGGA 57.283 32.000 0.00 0.00 32.46 4.02
2522 4194 6.546034 ACGCTACAGGGAAATTAAGCAATTAT 59.454 34.615 0.00 0.00 33.09 1.28
2564 5353 6.095860 TGAAGAAATGGTGCAATAAGATGGAG 59.904 38.462 0.00 0.00 0.00 3.86
2581 5370 4.564406 CCACTGTGACTAGCCTGAAGAAAT 60.564 45.833 9.86 0.00 0.00 2.17
2587 5376 0.114364 TCCCACTGTGACTAGCCTGA 59.886 55.000 9.86 0.00 0.00 3.86
2588 5377 0.534412 CTCCCACTGTGACTAGCCTG 59.466 60.000 9.86 0.00 0.00 4.85
2589 5378 0.115349 ACTCCCACTGTGACTAGCCT 59.885 55.000 9.86 0.00 0.00 4.58
2590 5379 1.848652 TACTCCCACTGTGACTAGCC 58.151 55.000 9.86 0.00 0.00 3.93
2591 5380 2.826725 AGTTACTCCCACTGTGACTAGC 59.173 50.000 9.86 0.00 33.46 3.42
2592 5381 5.125739 CCTAAGTTACTCCCACTGTGACTAG 59.874 48.000 9.86 5.97 33.98 2.57
2593 5382 5.014858 CCTAAGTTACTCCCACTGTGACTA 58.985 45.833 9.86 0.00 33.98 2.59
2594 5383 3.833070 CCTAAGTTACTCCCACTGTGACT 59.167 47.826 9.86 0.30 36.11 3.41
2595 5384 3.577415 ACCTAAGTTACTCCCACTGTGAC 59.423 47.826 9.86 0.00 0.00 3.67
2596 5385 3.853207 ACCTAAGTTACTCCCACTGTGA 58.147 45.455 9.86 0.00 0.00 3.58
2597 5386 4.771054 ACTACCTAAGTTACTCCCACTGTG 59.229 45.833 0.00 0.00 33.35 3.66
2598 5387 5.008165 ACTACCTAAGTTACTCCCACTGT 57.992 43.478 0.00 0.00 33.35 3.55
2599 5388 6.435277 TGTTACTACCTAAGTTACTCCCACTG 59.565 42.308 0.00 0.00 38.33 3.66
2600 5389 6.555711 TGTTACTACCTAAGTTACTCCCACT 58.444 40.000 0.00 0.00 38.33 4.00
2601 5390 6.840780 TGTTACTACCTAAGTTACTCCCAC 57.159 41.667 0.00 0.00 38.33 4.61
2602 5391 8.971073 GTTATGTTACTACCTAAGTTACTCCCA 58.029 37.037 0.00 0.00 38.33 4.37
2603 5392 8.131731 CGTTATGTTACTACCTAAGTTACTCCC 58.868 40.741 0.00 0.00 38.33 4.30
2604 5393 7.645735 GCGTTATGTTACTACCTAAGTTACTCC 59.354 40.741 0.00 0.00 38.33 3.85
2605 5394 8.184192 TGCGTTATGTTACTACCTAAGTTACTC 58.816 37.037 0.00 0.00 38.33 2.59
2606 5395 7.970614 GTGCGTTATGTTACTACCTAAGTTACT 59.029 37.037 0.00 0.00 38.33 2.24
2607 5396 7.970614 AGTGCGTTATGTTACTACCTAAGTTAC 59.029 37.037 0.00 0.00 39.80 2.50
2608 5397 8.055279 AGTGCGTTATGTTACTACCTAAGTTA 57.945 34.615 0.00 0.00 39.80 2.24
2609 5398 6.928520 AGTGCGTTATGTTACTACCTAAGTT 58.071 36.000 0.00 0.00 39.80 2.66
2610 5399 6.521151 AGTGCGTTATGTTACTACCTAAGT 57.479 37.500 0.00 0.00 42.62 2.24
2611 5400 7.031372 TGAAGTGCGTTATGTTACTACCTAAG 58.969 38.462 0.00 0.00 0.00 2.18
2612 5401 6.923012 TGAAGTGCGTTATGTTACTACCTAA 58.077 36.000 0.00 0.00 0.00 2.69
2613 5402 6.513806 TGAAGTGCGTTATGTTACTACCTA 57.486 37.500 0.00 0.00 0.00 3.08
2614 5403 5.395682 TGAAGTGCGTTATGTTACTACCT 57.604 39.130 0.00 0.00 0.00 3.08
2615 5404 5.865552 TCTTGAAGTGCGTTATGTTACTACC 59.134 40.000 0.00 0.00 0.00 3.18
2616 5405 6.939551 TCTTGAAGTGCGTTATGTTACTAC 57.060 37.500 0.00 0.00 0.00 2.73
2617 5406 7.949903 TTTCTTGAAGTGCGTTATGTTACTA 57.050 32.000 0.00 0.00 0.00 1.82
2618 5407 6.854496 TTTCTTGAAGTGCGTTATGTTACT 57.146 33.333 0.00 0.00 0.00 2.24
2619 5408 7.075741 ACATTTCTTGAAGTGCGTTATGTTAC 58.924 34.615 5.90 0.00 0.00 2.50
2620 5409 7.197071 ACATTTCTTGAAGTGCGTTATGTTA 57.803 32.000 5.90 0.00 0.00 2.41
2621 5410 6.072112 ACATTTCTTGAAGTGCGTTATGTT 57.928 33.333 5.90 0.00 0.00 2.71
2622 5411 5.689383 ACATTTCTTGAAGTGCGTTATGT 57.311 34.783 5.90 0.00 0.00 2.29
2623 5412 6.614162 GCAAACATTTCTTGAAGTGCGTTATG 60.614 38.462 5.90 0.00 0.00 1.90
2624 5413 5.402270 GCAAACATTTCTTGAAGTGCGTTAT 59.598 36.000 5.90 0.00 0.00 1.89
2625 5414 4.737765 GCAAACATTTCTTGAAGTGCGTTA 59.262 37.500 5.90 0.00 0.00 3.18
2626 5415 3.551485 GCAAACATTTCTTGAAGTGCGTT 59.449 39.130 5.90 0.00 0.00 4.84
2627 5416 3.115554 GCAAACATTTCTTGAAGTGCGT 58.884 40.909 5.90 0.00 0.00 5.24
2628 5417 3.374745 AGCAAACATTTCTTGAAGTGCG 58.625 40.909 5.90 0.00 36.05 5.34
2629 5418 5.108254 CGTAAGCAAACATTTCTTGAAGTGC 60.108 40.000 5.90 0.00 33.23 4.40
2630 5419 5.971202 ACGTAAGCAAACATTTCTTGAAGTG 59.029 36.000 4.65 4.65 45.62 3.16
2631 5420 5.971202 CACGTAAGCAAACATTTCTTGAAGT 59.029 36.000 0.00 0.00 45.62 3.01
2632 5421 6.140737 GTCACGTAAGCAAACATTTCTTGAAG 59.859 38.462 0.00 0.00 45.62 3.02
2633 5422 5.968848 GTCACGTAAGCAAACATTTCTTGAA 59.031 36.000 0.00 0.00 45.62 2.69
2634 5423 5.065346 TGTCACGTAAGCAAACATTTCTTGA 59.935 36.000 0.00 0.00 45.62 3.02
2635 5424 5.270083 TGTCACGTAAGCAAACATTTCTTG 58.730 37.500 0.00 0.00 45.62 3.02
2636 5425 5.493133 TGTCACGTAAGCAAACATTTCTT 57.507 34.783 0.00 0.00 45.62 2.52
2637 5426 5.065988 ACTTGTCACGTAAGCAAACATTTCT 59.934 36.000 0.00 0.00 45.62 2.52
2638 5427 5.270853 ACTTGTCACGTAAGCAAACATTTC 58.729 37.500 0.00 0.00 45.62 2.17
2639 5428 5.243426 ACTTGTCACGTAAGCAAACATTT 57.757 34.783 0.00 0.00 45.62 2.32
2640 5429 4.893424 ACTTGTCACGTAAGCAAACATT 57.107 36.364 0.00 0.00 45.62 2.71
2641 5430 5.054477 ACTACTTGTCACGTAAGCAAACAT 58.946 37.500 0.00 0.00 45.62 2.71
2642 5431 4.435425 ACTACTTGTCACGTAAGCAAACA 58.565 39.130 0.00 0.00 45.62 2.83
2643 5432 5.399604 AACTACTTGTCACGTAAGCAAAC 57.600 39.130 0.00 0.00 45.62 2.93
2644 5433 7.438757 TCATTAACTACTTGTCACGTAAGCAAA 59.561 33.333 0.00 0.00 45.62 3.68
2645 5434 6.924612 TCATTAACTACTTGTCACGTAAGCAA 59.075 34.615 0.00 0.00 45.62 3.91
2646 5435 6.448852 TCATTAACTACTTGTCACGTAAGCA 58.551 36.000 0.00 0.00 45.62 3.91
2647 5436 6.939551 TCATTAACTACTTGTCACGTAAGC 57.060 37.500 0.00 0.00 45.62 3.09
2649 5438 7.927629 ACCTTTCATTAACTACTTGTCACGTAA 59.072 33.333 0.00 0.00 0.00 3.18
2650 5439 7.383029 CACCTTTCATTAACTACTTGTCACGTA 59.617 37.037 0.00 0.00 0.00 3.57
2651 5440 6.202188 CACCTTTCATTAACTACTTGTCACGT 59.798 38.462 0.00 0.00 0.00 4.49
2652 5441 6.347402 CCACCTTTCATTAACTACTTGTCACG 60.347 42.308 0.00 0.00 0.00 4.35
2653 5442 6.485648 ACCACCTTTCATTAACTACTTGTCAC 59.514 38.462 0.00 0.00 0.00 3.67
2654 5443 6.597562 ACCACCTTTCATTAACTACTTGTCA 58.402 36.000 0.00 0.00 0.00 3.58
2655 5444 8.501580 GTTACCACCTTTCATTAACTACTTGTC 58.498 37.037 0.00 0.00 0.00 3.18
2656 5445 7.994334 TGTTACCACCTTTCATTAACTACTTGT 59.006 33.333 0.00 0.00 0.00 3.16
2657 5446 8.385898 TGTTACCACCTTTCATTAACTACTTG 57.614 34.615 0.00 0.00 0.00 3.16
2689 5478 3.554731 GGGAAGCGCTATGTTACAGTAAC 59.445 47.826 12.05 15.58 39.11 2.50
2690 5479 3.735820 CGGGAAGCGCTATGTTACAGTAA 60.736 47.826 12.05 0.00 0.00 2.24
2691 5480 2.223641 CGGGAAGCGCTATGTTACAGTA 60.224 50.000 12.05 0.00 0.00 2.74
2692 5481 1.470979 CGGGAAGCGCTATGTTACAGT 60.471 52.381 12.05 0.00 0.00 3.55
2693 5482 1.202371 TCGGGAAGCGCTATGTTACAG 60.202 52.381 12.05 0.00 0.00 2.74
2694 5483 0.818938 TCGGGAAGCGCTATGTTACA 59.181 50.000 12.05 0.00 0.00 2.41
2695 5484 1.066605 TCTCGGGAAGCGCTATGTTAC 59.933 52.381 12.05 0.00 0.00 2.50
2696 5485 1.066605 GTCTCGGGAAGCGCTATGTTA 59.933 52.381 12.05 0.00 0.00 2.41
2697 5486 0.179108 GTCTCGGGAAGCGCTATGTT 60.179 55.000 12.05 0.00 0.00 2.71
2698 5487 1.320344 TGTCTCGGGAAGCGCTATGT 61.320 55.000 12.05 0.00 0.00 2.29
2699 5488 0.179111 TTGTCTCGGGAAGCGCTATG 60.179 55.000 12.05 0.24 0.00 2.23
2700 5489 0.103208 CTTGTCTCGGGAAGCGCTAT 59.897 55.000 12.05 0.00 0.00 2.97
2701 5490 0.963856 TCTTGTCTCGGGAAGCGCTA 60.964 55.000 12.05 0.00 0.00 4.26
2702 5491 1.608717 ATCTTGTCTCGGGAAGCGCT 61.609 55.000 2.64 2.64 0.00 5.92
2703 5492 1.153549 ATCTTGTCTCGGGAAGCGC 60.154 57.895 0.00 0.00 0.00 5.92
2704 5493 0.173481 TCATCTTGTCTCGGGAAGCG 59.827 55.000 0.00 0.00 0.00 4.68
2705 5494 1.205893 ACTCATCTTGTCTCGGGAAGC 59.794 52.381 0.00 0.00 0.00 3.86
2706 5495 4.927978 ATACTCATCTTGTCTCGGGAAG 57.072 45.455 0.00 0.00 0.00 3.46
2707 5496 5.198207 TGTATACTCATCTTGTCTCGGGAA 58.802 41.667 4.17 0.00 0.00 3.97
2708 5497 4.788679 TGTATACTCATCTTGTCTCGGGA 58.211 43.478 4.17 0.00 0.00 5.14
2709 5498 5.067936 ACTTGTATACTCATCTTGTCTCGGG 59.932 44.000 4.17 0.00 0.00 5.14
2710 5499 6.137794 ACTTGTATACTCATCTTGTCTCGG 57.862 41.667 4.17 0.00 0.00 4.63
2711 5500 9.737427 ATTAACTTGTATACTCATCTTGTCTCG 57.263 33.333 4.17 0.00 0.00 4.04
2763 5552 9.060347 CCTCATAATGCAAAGTGACATAATAGT 57.940 33.333 0.00 0.00 0.00 2.12
2764 5553 8.509690 CCCTCATAATGCAAAGTGACATAATAG 58.490 37.037 0.00 0.00 0.00 1.73
2765 5554 7.998383 ACCCTCATAATGCAAAGTGACATAATA 59.002 33.333 0.00 0.00 0.00 0.98
2766 5555 6.835488 ACCCTCATAATGCAAAGTGACATAAT 59.165 34.615 0.00 0.00 0.00 1.28
2767 5556 6.186957 ACCCTCATAATGCAAAGTGACATAA 58.813 36.000 0.00 0.00 0.00 1.90
2768 5557 5.754782 ACCCTCATAATGCAAAGTGACATA 58.245 37.500 0.00 0.00 0.00 2.29
2769 5558 4.603131 ACCCTCATAATGCAAAGTGACAT 58.397 39.130 0.00 0.00 0.00 3.06
2770 5559 4.032960 ACCCTCATAATGCAAAGTGACA 57.967 40.909 0.00 0.00 0.00 3.58
2771 5560 5.186198 ACTACCCTCATAATGCAAAGTGAC 58.814 41.667 0.00 0.00 0.00 3.67
2772 5561 5.435686 ACTACCCTCATAATGCAAAGTGA 57.564 39.130 0.00 0.00 0.00 3.41
2773 5562 6.823689 AGTTACTACCCTCATAATGCAAAGTG 59.176 38.462 0.00 0.00 0.00 3.16
2774 5563 6.958767 AGTTACTACCCTCATAATGCAAAGT 58.041 36.000 0.00 0.00 0.00 2.66
2775 5564 7.865706 AAGTTACTACCCTCATAATGCAAAG 57.134 36.000 0.00 0.00 0.00 2.77
2776 5565 8.764558 TCTAAGTTACTACCCTCATAATGCAAA 58.235 33.333 0.00 0.00 0.00 3.68
2777 5566 8.202137 GTCTAAGTTACTACCCTCATAATGCAA 58.798 37.037 0.00 0.00 0.00 4.08
2778 5567 7.563924 AGTCTAAGTTACTACCCTCATAATGCA 59.436 37.037 0.00 0.00 0.00 3.96
2779 5568 7.953752 AGTCTAAGTTACTACCCTCATAATGC 58.046 38.462 0.00 0.00 0.00 3.56
2784 5573 9.134055 GACATTAGTCTAAGTTACTACCCTCAT 57.866 37.037 0.00 0.00 41.64 2.90
2785 5574 8.111545 TGACATTAGTCTAAGTTACTACCCTCA 58.888 37.037 0.00 0.00 45.20 3.86
2786 5575 8.517062 TGACATTAGTCTAAGTTACTACCCTC 57.483 38.462 0.00 0.00 45.20 4.30
2818 5607 9.317827 AGTGGGAAGTAACTTAAACTAGTATCA 57.682 33.333 0.00 0.00 0.00 2.15
2822 5611 9.317827 TCATAGTGGGAAGTAACTTAAACTAGT 57.682 33.333 0.00 0.00 0.00 2.57
2823 5612 9.583765 GTCATAGTGGGAAGTAACTTAAACTAG 57.416 37.037 0.00 0.00 0.00 2.57
2824 5613 8.534496 GGTCATAGTGGGAAGTAACTTAAACTA 58.466 37.037 0.00 0.00 0.00 2.24
2825 5614 7.016858 TGGTCATAGTGGGAAGTAACTTAAACT 59.983 37.037 0.00 0.00 0.00 2.66
2826 5615 7.163441 TGGTCATAGTGGGAAGTAACTTAAAC 58.837 38.462 0.00 0.00 0.00 2.01
2827 5616 7.319052 TGGTCATAGTGGGAAGTAACTTAAA 57.681 36.000 0.00 0.00 0.00 1.52
2828 5617 6.575649 GCTGGTCATAGTGGGAAGTAACTTAA 60.576 42.308 0.00 0.00 0.00 1.85
2829 5618 5.105064 GCTGGTCATAGTGGGAAGTAACTTA 60.105 44.000 0.00 0.00 0.00 2.24
2830 5619 4.323562 GCTGGTCATAGTGGGAAGTAACTT 60.324 45.833 0.00 0.00 0.00 2.66
2831 5620 3.197983 GCTGGTCATAGTGGGAAGTAACT 59.802 47.826 0.00 0.00 0.00 2.24
2832 5621 3.532542 GCTGGTCATAGTGGGAAGTAAC 58.467 50.000 0.00 0.00 0.00 2.50
2833 5622 2.504175 GGCTGGTCATAGTGGGAAGTAA 59.496 50.000 0.00 0.00 0.00 2.24
2834 5623 2.116238 GGCTGGTCATAGTGGGAAGTA 58.884 52.381 0.00 0.00 0.00 2.24
2835 5624 0.912486 GGCTGGTCATAGTGGGAAGT 59.088 55.000 0.00 0.00 0.00 3.01
2836 5625 1.139853 GAGGCTGGTCATAGTGGGAAG 59.860 57.143 0.00 0.00 0.00 3.46
2837 5626 1.204146 GAGGCTGGTCATAGTGGGAA 58.796 55.000 0.00 0.00 0.00 3.97
2838 5627 0.042581 TGAGGCTGGTCATAGTGGGA 59.957 55.000 0.00 0.00 0.00 4.37
2839 5628 1.135094 ATGAGGCTGGTCATAGTGGG 58.865 55.000 0.00 0.00 35.30 4.61
2840 5629 3.674528 CTATGAGGCTGGTCATAGTGG 57.325 52.381 16.73 1.45 46.23 4.00
2844 5633 4.226384 ACACATCTATGAGGCTGGTCATA 58.774 43.478 0.00 0.00 38.21 2.15
2845 5634 3.044156 ACACATCTATGAGGCTGGTCAT 58.956 45.455 0.00 0.00 40.40 3.06
2846 5635 2.470990 ACACATCTATGAGGCTGGTCA 58.529 47.619 0.00 0.00 0.00 4.02
2847 5636 3.118629 TCAACACATCTATGAGGCTGGTC 60.119 47.826 0.00 0.00 0.00 4.02
2848 5637 2.840038 TCAACACATCTATGAGGCTGGT 59.160 45.455 0.00 0.00 0.00 4.00
2849 5638 3.118482 AGTCAACACATCTATGAGGCTGG 60.118 47.826 0.00 0.00 0.00 4.85
2850 5639 4.134379 AGTCAACACATCTATGAGGCTG 57.866 45.455 0.00 0.00 0.00 4.85
2851 5640 4.833478 AAGTCAACACATCTATGAGGCT 57.167 40.909 0.00 0.00 0.00 4.58
2852 5641 4.033358 CGAAAGTCAACACATCTATGAGGC 59.967 45.833 0.00 0.00 0.00 4.70
2853 5642 4.568359 CCGAAAGTCAACACATCTATGAGG 59.432 45.833 0.00 0.00 0.00 3.86
2854 5643 4.033358 GCCGAAAGTCAACACATCTATGAG 59.967 45.833 0.00 0.00 0.00 2.90
2908 5698 7.558604 ACGGAGCAGGTTGTAGTTTTATAATA 58.441 34.615 0.00 0.00 0.00 0.98
2909 5699 6.412214 ACGGAGCAGGTTGTAGTTTTATAAT 58.588 36.000 0.00 0.00 0.00 1.28
3022 5812 2.480802 GCGAAAGTCAAGAGGAAAGGTC 59.519 50.000 0.00 0.00 0.00 3.85
3066 5856 4.758251 TGGTGTGGCGCCATCTCG 62.758 66.667 35.23 0.00 39.28 4.04


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

AutoCloner maintained by Alex Coulton.