Multiple sequence alignment - TraesCS6D01G161000

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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 TraesCS6D01G161000 chr6D 100.000 5317 0 0 1824 7140 139314600 139309284 0.000000e+00 9819.0
1 TraesCS6D01G161000 chr6D 100.000 1574 0 0 1 1574 139316423 139314850 0.000000e+00 2907.0
2 TraesCS6D01G161000 chr6B 96.020 2739 65 21 3114 5816 239288391 239285661 0.000000e+00 4414.0
3 TraesCS6D01G161000 chr6B 96.472 1304 25 7 5843 7139 239285664 239284375 0.000000e+00 2134.0
4 TraesCS6D01G161000 chr6B 84.814 1475 78 47 149 1572 239291294 239289915 0.000000e+00 1349.0
5 TraesCS6D01G161000 chr6B 96.822 535 6 3 2520 3052 239289156 239288631 0.000000e+00 883.0
6 TraesCS6D01G161000 chr6B 92.222 630 30 5 1824 2434 239289847 239289218 0.000000e+00 874.0
7 TraesCS6D01G161000 chr6B 98.936 94 1 0 2427 2520 239289130 239289223 1.230000e-37 169.0
8 TraesCS6D01G161000 chr6A 97.235 1736 42 5 3998 5729 181898723 181896990 0.000000e+00 2935.0
9 TraesCS6D01G161000 chr6A 95.284 1442 41 9 5724 7140 181896775 181895336 0.000000e+00 2261.0
10 TraesCS6D01G161000 chr6A 91.721 1232 43 20 387 1572 181902477 181901259 0.000000e+00 1655.0
11 TraesCS6D01G161000 chr6A 96.588 850 24 2 3110 3959 181899755 181898911 0.000000e+00 1404.0
12 TraesCS6D01G161000 chr6A 92.540 630 27 6 1824 2434 181901193 181900565 0.000000e+00 885.0
13 TraesCS6D01G161000 chr6A 96.318 516 17 2 2520 3035 181900503 181899990 0.000000e+00 846.0
14 TraesCS6D01G161000 chr6A 95.082 122 6 0 1 122 181902744 181902623 7.310000e-45 193.0
15 TraesCS6D01G161000 chr6A 97.872 94 2 0 2427 2520 181900477 181900570 5.730000e-36 163.0
16 TraesCS6D01G161000 chr7A 75.882 510 102 12 4716 5208 566540880 566541385 2.570000e-59 241.0
17 TraesCS6D01G161000 chr7A 87.755 147 18 0 5290 5436 566541485 566541631 9.520000e-39 172.0
18 TraesCS6D01G161000 chr7A 89.744 117 12 0 4228 4344 566540640 566540756 4.460000e-32 150.0
19 TraesCS6D01G161000 chr7D 75.000 512 102 16 4716 5208 500629657 500630161 5.610000e-51 213.0
20 TraesCS6D01G161000 chr7D 88.435 147 17 0 5290 5436 500630263 500630409 2.050000e-40 178.0
21 TraesCS6D01G161000 chr7D 81.818 187 31 3 4161 4344 500629362 500629548 3.450000e-33 154.0
22 TraesCS6D01G161000 chr7B 85.714 147 21 0 5290 5436 528766987 528767133 9.590000e-34 156.0
23 TraesCS6D01G161000 chr7B 80.749 187 33 3 4160 4343 528766046 528766232 7.470000e-30 143.0
24 TraesCS6D01G161000 chr5B 100.000 28 0 0 2386 2413 44985705 44985678 1.300000e-02 52.8


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 TraesCS6D01G161000 chr6D 139309284 139316423 7139 True 6363.000000 9819 100.000000 1 7140 2 chr6D.!!$R1 7139
1 TraesCS6D01G161000 chr6B 239284375 239291294 6919 True 1930.800000 4414 93.270000 149 7139 5 chr6B.!!$R1 6990
2 TraesCS6D01G161000 chr6A 181895336 181902744 7408 True 1454.142857 2935 94.966857 1 7140 7 chr6A.!!$R1 7139

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
381 387 0.039472 TGGGGCGTACTGTACCTGTA 59.961 55.0 12.08 0.0 0.00 2.74 F
382 388 0.457443 GGGGCGTACTGTACCTGTAC 59.543 60.0 12.08 13.2 36.10 2.90 F
408 438 0.555769 AAAGCCTGTGTGGAAAGGGA 59.444 50.0 0.00 0.0 38.35 4.20 F
672 720 0.727970 TAAGACGCGAGCAGAGAGAC 59.272 55.0 15.93 0.0 0.00 3.36 F
2283 2408 0.813184 CTTCTTCCGCAACATGGCAT 59.187 50.0 0.00 0.0 0.00 4.40 F
3068 3196 0.035739 TCCCAGAACGCTTTACACCC 59.964 55.0 0.00 0.0 0.00 4.61 F
3092 3220 0.179081 GCCCCGAACTGTAGGCTTAG 60.179 60.0 0.00 0.0 42.34 2.18 F
4258 4713 0.250295 CTTCCCTCCAAGTTGCGACA 60.250 55.0 6.90 0.0 0.00 4.35 F
5191 5654 1.463674 CTGCCTTGACACCCAATACC 58.536 55.0 0.00 0.0 33.68 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1429 1.228063 GGCATGCGAGGATGGATGT 60.228 57.895 12.44 0.0 39.59 3.06 R
2012 2115 1.332375 CCGAAAAAGTTGCGAGGAACA 59.668 47.619 9.97 0.0 0.00 3.18 R
2267 2392 1.667236 TAGATGCCATGTTGCGGAAG 58.333 50.000 0.00 0.0 0.00 3.46 R
2479 2605 0.043940 AGAGAGCACCCATCCCTTCT 59.956 55.000 0.00 0.0 0.00 2.85 R
3857 4163 1.034838 AGTGCCGTGCCTCAAAAACA 61.035 50.000 0.00 0.0 0.00 2.83 R
3975 4281 2.442087 CGAAATTGGGGAGGGGGC 60.442 66.667 0.00 0.0 0.00 5.80 R
4404 4862 6.055588 CCCACGAATTGAGGTTTATGAGTAT 58.944 40.000 0.00 0.0 0.00 2.12 R
5496 5960 0.814457 ACTGCAACAGCCGTTCAAAA 59.186 45.000 0.00 0.0 34.37 2.44 R
7004 7746 1.214589 CCTCCAAGGTACACGACGG 59.785 63.158 0.00 0.0 0.00 4.79 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
36 37 1.743394 GAACACGGCCTGGAATTTAGG 59.257 52.381 0.00 5.55 38.39 2.69
38 39 1.065418 ACACGGCCTGGAATTTAGGAG 60.065 52.381 12.46 8.29 37.52 3.69
127 128 2.579201 CGCAAGTGGGTCGGATCT 59.421 61.111 0.00 0.00 0.00 2.75
128 129 1.811266 CGCAAGTGGGTCGGATCTG 60.811 63.158 0.00 0.00 0.00 2.90
129 130 1.596934 GCAAGTGGGTCGGATCTGA 59.403 57.895 0.00 0.00 0.00 3.27
130 131 0.179000 GCAAGTGGGTCGGATCTGAT 59.821 55.000 7.68 0.00 0.00 2.90
131 132 1.808133 GCAAGTGGGTCGGATCTGATC 60.808 57.143 7.68 6.92 0.00 2.92
132 133 0.747255 AAGTGGGTCGGATCTGATCG 59.253 55.000 7.68 7.24 0.00 3.69
133 134 1.109920 AGTGGGTCGGATCTGATCGG 61.110 60.000 16.52 16.52 0.00 4.18
134 135 1.107538 GTGGGTCGGATCTGATCGGA 61.108 60.000 20.05 20.05 36.44 4.55
135 136 0.178961 TGGGTCGGATCTGATCGGAT 60.179 55.000 24.68 17.16 40.14 4.18
136 137 0.528470 GGGTCGGATCTGATCGGATC 59.472 60.000 29.36 29.36 40.14 3.36
137 138 0.169230 GGTCGGATCTGATCGGATCG 59.831 60.000 29.69 24.93 41.99 3.69
138 139 1.157585 GTCGGATCTGATCGGATCGA 58.842 55.000 29.69 26.29 41.99 3.59
139 140 1.129624 GTCGGATCTGATCGGATCGAG 59.870 57.143 29.69 25.89 41.99 4.04
140 141 0.179176 CGGATCTGATCGGATCGAGC 60.179 60.000 29.69 19.04 42.86 5.03
141 142 0.172352 GGATCTGATCGGATCGAGCC 59.828 60.000 29.69 21.87 41.81 4.70
142 143 0.884514 GATCTGATCGGATCGAGCCA 59.115 55.000 25.10 7.43 41.81 4.75
143 144 0.600557 ATCTGATCGGATCGAGCCAC 59.399 55.000 21.44 10.82 41.81 5.01
144 145 0.751643 TCTGATCGGATCGAGCCACA 60.752 55.000 21.44 14.79 41.81 4.17
145 146 0.316522 CTGATCGGATCGAGCCACAT 59.683 55.000 21.44 10.83 41.81 3.21
146 147 0.752658 TGATCGGATCGAGCCACATT 59.247 50.000 21.44 0.00 41.81 2.71
147 148 1.143305 GATCGGATCGAGCCACATTG 58.857 55.000 21.44 2.50 39.91 2.82
156 157 1.376609 GAGCCACATTGGTTAGCCGG 61.377 60.000 0.00 0.00 40.46 6.13
177 178 1.080638 TGGGCCCACCTTAACTCATT 58.919 50.000 24.45 0.00 41.11 2.57
181 182 3.699538 GGGCCCACCTTAACTCATTTTAG 59.300 47.826 19.95 0.00 35.85 1.85
207 211 2.744202 CAGCAATAGTCAACCCAGTGTC 59.256 50.000 0.00 0.00 0.00 3.67
208 212 2.084546 GCAATAGTCAACCCAGTGTCC 58.915 52.381 0.00 0.00 0.00 4.02
223 227 0.254462 TGTCCACAAGTGAAGCACCA 59.746 50.000 0.94 0.00 34.49 4.17
244 248 5.215160 CCAATCTCAACGGTTCTGAAAAAG 58.785 41.667 0.00 0.00 0.00 2.27
248 252 4.131596 CTCAACGGTTCTGAAAAAGGGTA 58.868 43.478 0.00 0.00 0.00 3.69
255 259 5.564063 CGGTTCTGAAAAAGGGTAAACCATC 60.564 44.000 0.81 0.00 43.89 3.51
258 262 5.650283 TCTGAAAAAGGGTAAACCATCCAT 58.350 37.500 0.81 0.00 43.89 3.41
260 264 5.398236 TGAAAAAGGGTAAACCATCCATCA 58.602 37.500 0.81 0.00 43.89 3.07
270 274 6.071391 GGTAAACCATCCATCAACAATGAACT 60.071 38.462 0.00 0.00 36.01 3.01
272 276 5.649782 ACCATCCATCAACAATGAACTTC 57.350 39.130 0.00 0.00 39.49 3.01
273 277 5.078949 ACCATCCATCAACAATGAACTTCA 58.921 37.500 0.00 0.00 39.49 3.02
279 284 7.874940 TCCATCAACAATGAACTTCAAACTAG 58.125 34.615 0.00 0.00 39.49 2.57
292 298 9.914131 GAACTTCAAACTAGATTAGCCATTTTT 57.086 29.630 0.00 0.00 0.00 1.94
316 322 4.641094 TCACAAACAAAGTAATCAACGGGT 59.359 37.500 0.00 0.00 0.00 5.28
317 323 5.125739 TCACAAACAAAGTAATCAACGGGTT 59.874 36.000 0.00 0.00 0.00 4.11
319 325 6.415573 CACAAACAAAGTAATCAACGGGTTAC 59.584 38.462 0.00 0.00 0.00 2.50
320 326 6.319405 ACAAACAAAGTAATCAACGGGTTACT 59.681 34.615 0.00 0.00 41.54 2.24
322 328 6.308371 ACAAAGTAATCAACGGGTTACTTG 57.692 37.500 12.39 9.69 45.46 3.16
323 329 5.239963 ACAAAGTAATCAACGGGTTACTTGG 59.760 40.000 12.39 11.97 45.46 3.61
324 330 3.340928 AGTAATCAACGGGTTACTTGGC 58.659 45.455 0.00 0.00 37.77 4.52
325 331 2.279935 AATCAACGGGTTACTTGGCA 57.720 45.000 0.00 0.00 0.00 4.92
326 332 2.507407 ATCAACGGGTTACTTGGCAT 57.493 45.000 0.00 0.00 0.00 4.40
327 333 3.637911 ATCAACGGGTTACTTGGCATA 57.362 42.857 0.00 0.00 0.00 3.14
328 334 3.637911 TCAACGGGTTACTTGGCATAT 57.362 42.857 0.00 0.00 0.00 1.78
329 335 3.275143 TCAACGGGTTACTTGGCATATG 58.725 45.455 0.00 0.00 0.00 1.78
330 336 2.341846 ACGGGTTACTTGGCATATGG 57.658 50.000 4.56 0.00 0.00 2.74
362 368 2.335316 TGTTGTGGTTAACGAAGGCT 57.665 45.000 0.00 0.00 33.28 4.58
372 378 3.771160 CGAAGGCTGGGGCGTACT 61.771 66.667 0.00 0.00 39.81 2.73
377 383 2.186125 GCTGGGGCGTACTGTACC 59.814 66.667 12.08 5.34 0.00 3.34
378 384 2.356780 GCTGGGGCGTACTGTACCT 61.357 63.158 12.08 0.00 0.00 3.08
379 385 1.515954 CTGGGGCGTACTGTACCTG 59.484 63.158 12.08 0.86 0.00 4.00
380 386 1.228956 TGGGGCGTACTGTACCTGT 60.229 57.895 12.08 0.00 0.00 4.00
381 387 0.039472 TGGGGCGTACTGTACCTGTA 59.961 55.000 12.08 0.00 0.00 2.74
382 388 0.457443 GGGGCGTACTGTACCTGTAC 59.543 60.000 12.08 13.20 36.10 2.90
408 438 0.555769 AAAGCCTGTGTGGAAAGGGA 59.444 50.000 0.00 0.00 38.35 4.20
411 441 1.303643 CCTGTGTGGAAAGGGAGCC 60.304 63.158 0.00 0.00 38.35 4.70
440 470 3.201290 CGGAAGGATCTCATTTGACCAG 58.799 50.000 0.00 0.00 0.00 4.00
452 482 8.375493 TCTCATTTGACCAGGTTAACTACTAT 57.625 34.615 5.42 0.00 0.00 2.12
496 526 6.542370 ACAAAGCACAAAATCACTGTAGTACT 59.458 34.615 0.00 0.00 0.00 2.73
497 527 7.713507 ACAAAGCACAAAATCACTGTAGTACTA 59.286 33.333 0.00 0.00 0.00 1.82
498 528 8.721478 CAAAGCACAAAATCACTGTAGTACTAT 58.279 33.333 5.75 0.00 0.00 2.12
672 720 0.727970 TAAGACGCGAGCAGAGAGAC 59.272 55.000 15.93 0.00 0.00 3.36
673 721 1.237954 AAGACGCGAGCAGAGAGACA 61.238 55.000 15.93 0.00 0.00 3.41
674 722 1.226267 GACGCGAGCAGAGAGACAG 60.226 63.158 15.93 0.00 0.00 3.51
675 723 1.640210 GACGCGAGCAGAGAGACAGA 61.640 60.000 15.93 0.00 0.00 3.41
680 728 2.355197 CGAGCAGAGAGACAGAGAGAA 58.645 52.381 0.00 0.00 0.00 2.87
682 730 3.190327 CGAGCAGAGAGACAGAGAGAAAA 59.810 47.826 0.00 0.00 0.00 2.29
702 753 3.320673 AAGAGAGTTAAGTCTTGCCGG 57.679 47.619 14.03 0.00 31.63 6.13
777 839 1.153469 CTCCTCTTTCCGCTGCCTC 60.153 63.158 0.00 0.00 0.00 4.70
812 874 3.179265 CGCACGTTAGCTGGACCG 61.179 66.667 0.00 0.00 0.00 4.79
1167 1269 2.286025 GTCGGTGGGCGTGATAATTAAC 59.714 50.000 0.00 0.00 0.00 2.01
1327 1429 1.158434 GGGCGTCACCGAAATGTAAA 58.842 50.000 0.00 0.00 40.62 2.01
1348 1450 2.446142 ATCCATCCTCGCATGCCTCG 62.446 60.000 13.15 0.00 0.00 4.63
1449 1552 3.943381 TCTCATATCCAACAGCAAGCTTG 59.057 43.478 22.44 22.44 0.00 4.01
1460 1563 3.570212 AAGCTTGCGGGGACAGGT 61.570 61.111 0.00 0.00 0.00 4.00
1496 1599 1.000717 GGCTACGAGCTCTCCAATCTC 60.001 57.143 12.85 0.00 41.99 2.75
1523 1626 4.274214 TCACTCAAAACATTGTGAGAGCTG 59.726 41.667 17.03 6.67 43.32 4.24
1572 1675 4.997905 TTCTTCTTCTCTTTGTGCATCG 57.002 40.909 0.00 0.00 0.00 3.84
2035 2138 1.600485 TCCTCGCAACTTTTTCGGTTC 59.400 47.619 0.00 0.00 0.00 3.62
2046 2149 4.331717 ACTTTTTCGGTTCTATATGCACGG 59.668 41.667 0.00 0.00 0.00 4.94
2047 2150 2.519377 TTCGGTTCTATATGCACGGG 57.481 50.000 0.00 0.00 0.00 5.28
2049 2152 1.067974 TCGGTTCTATATGCACGGGTG 59.932 52.381 0.00 0.00 0.00 4.61
2222 2329 7.693969 ACTCTGCTCTTTATTTGCAAACTAT 57.306 32.000 15.41 0.94 36.22 2.12
2223 2330 7.533426 ACTCTGCTCTTTATTTGCAAACTATG 58.467 34.615 15.41 7.82 36.22 2.23
2225 2332 8.109705 TCTGCTCTTTATTTGCAAACTATGAA 57.890 30.769 15.41 1.15 36.22 2.57
2226 2333 8.742777 TCTGCTCTTTATTTGCAAACTATGAAT 58.257 29.630 15.41 0.00 36.22 2.57
2227 2334 9.362539 CTGCTCTTTATTTGCAAACTATGAATT 57.637 29.630 15.41 0.00 36.22 2.17
2228 2335 9.709495 TGCTCTTTATTTGCAAACTATGAATTT 57.291 25.926 15.41 0.00 33.48 1.82
2229 2336 9.962759 GCTCTTTATTTGCAAACTATGAATTTG 57.037 29.630 15.41 3.28 39.57 2.32
2250 2375 3.190327 TGTAGGCAATTTTGTCATCCACG 59.810 43.478 0.00 0.00 34.61 4.94
2258 2383 2.772568 TTGTCATCCACGCACTTTTG 57.227 45.000 0.00 0.00 0.00 2.44
2267 2392 2.161609 CCACGCACTTTTGGGATACTTC 59.838 50.000 0.00 0.00 39.02 3.01
2272 2397 3.127030 GCACTTTTGGGATACTTCTTCCG 59.873 47.826 0.00 0.00 33.82 4.30
2277 2402 1.626321 TGGGATACTTCTTCCGCAACA 59.374 47.619 0.00 0.00 33.82 3.33
2283 2408 0.813184 CTTCTTCCGCAACATGGCAT 59.187 50.000 0.00 0.00 0.00 4.40
2416 2542 4.631234 TCCACCAATAACTCCCATAGTCT 58.369 43.478 0.00 0.00 37.50 3.24
2430 2556 3.327172 CCATAGTCTCATCTCCCAGCATT 59.673 47.826 0.00 0.00 0.00 3.56
2434 2560 3.265221 AGTCTCATCTCCCAGCATTTCAA 59.735 43.478 0.00 0.00 0.00 2.69
2435 2561 4.012374 GTCTCATCTCCCAGCATTTCAAA 58.988 43.478 0.00 0.00 0.00 2.69
2436 2562 4.460382 GTCTCATCTCCCAGCATTTCAAAA 59.540 41.667 0.00 0.00 0.00 2.44
2438 2564 4.151121 TCATCTCCCAGCATTTCAAAACA 58.849 39.130 0.00 0.00 0.00 2.83
2439 2565 4.219070 TCATCTCCCAGCATTTCAAAACAG 59.781 41.667 0.00 0.00 0.00 3.16
2440 2566 3.831323 TCTCCCAGCATTTCAAAACAGA 58.169 40.909 0.00 0.00 0.00 3.41
2441 2567 3.822735 TCTCCCAGCATTTCAAAACAGAG 59.177 43.478 0.00 0.00 0.00 3.35
2442 2568 3.822735 CTCCCAGCATTTCAAAACAGAGA 59.177 43.478 0.00 0.00 0.00 3.10
2445 2571 4.219070 CCCAGCATTTCAAAACAGAGATGA 59.781 41.667 0.00 0.00 33.30 2.92
2446 2572 5.105473 CCCAGCATTTCAAAACAGAGATGAT 60.105 40.000 0.00 0.00 33.30 2.45
2447 2573 6.395629 CCAGCATTTCAAAACAGAGATGATT 58.604 36.000 0.00 0.00 33.30 2.57
2448 2574 7.363181 CCCAGCATTTCAAAACAGAGATGATTA 60.363 37.037 0.00 0.00 33.30 1.75
2449 2575 7.701078 CCAGCATTTCAAAACAGAGATGATTAG 59.299 37.037 0.00 0.00 33.30 1.73
2451 2577 7.395489 AGCATTTCAAAACAGAGATGATTAGGT 59.605 33.333 0.00 0.00 33.30 3.08
2452 2578 8.677300 GCATTTCAAAACAGAGATGATTAGGTA 58.323 33.333 0.00 0.00 33.30 3.08
2454 2580 9.965902 ATTTCAAAACAGAGATGATTAGGTAGT 57.034 29.630 0.00 0.00 0.00 2.73
2457 2583 8.696374 TCAAAACAGAGATGATTAGGTAGTAGG 58.304 37.037 0.00 0.00 0.00 3.18
2458 2584 7.604657 AAACAGAGATGATTAGGTAGTAGGG 57.395 40.000 0.00 0.00 0.00 3.53
2459 2585 5.646215 ACAGAGATGATTAGGTAGTAGGGG 58.354 45.833 0.00 0.00 0.00 4.79
2460 2586 5.136392 ACAGAGATGATTAGGTAGTAGGGGT 59.864 44.000 0.00 0.00 0.00 4.95
2461 2587 6.334774 ACAGAGATGATTAGGTAGTAGGGGTA 59.665 42.308 0.00 0.00 0.00 3.69
2462 2588 6.887545 CAGAGATGATTAGGTAGTAGGGGTAG 59.112 46.154 0.00 0.00 0.00 3.18
2463 2589 6.567260 AGAGATGATTAGGTAGTAGGGGTAGT 59.433 42.308 0.00 0.00 0.00 2.73
2464 2590 6.553857 AGATGATTAGGTAGTAGGGGTAGTG 58.446 44.000 0.00 0.00 0.00 2.74
2465 2591 5.999987 TGATTAGGTAGTAGGGGTAGTGA 57.000 43.478 0.00 0.00 0.00 3.41
2466 2592 6.345646 TGATTAGGTAGTAGGGGTAGTGAA 57.654 41.667 0.00 0.00 0.00 3.18
2467 2593 6.744822 TGATTAGGTAGTAGGGGTAGTGAAA 58.255 40.000 0.00 0.00 0.00 2.69
2468 2594 6.837568 TGATTAGGTAGTAGGGGTAGTGAAAG 59.162 42.308 0.00 0.00 0.00 2.62
2469 2595 3.991683 AGGTAGTAGGGGTAGTGAAAGG 58.008 50.000 0.00 0.00 0.00 3.11
2471 2597 4.234693 AGGTAGTAGGGGTAGTGAAAGGAT 59.765 45.833 0.00 0.00 0.00 3.24
2473 2599 5.163332 GGTAGTAGGGGTAGTGAAAGGATTG 60.163 48.000 0.00 0.00 0.00 2.67
2474 2600 4.436079 AGTAGGGGTAGTGAAAGGATTGT 58.564 43.478 0.00 0.00 0.00 2.71
2476 2602 4.838904 AGGGGTAGTGAAAGGATTGTAC 57.161 45.455 0.00 0.00 0.00 2.90
2478 2604 4.225267 AGGGGTAGTGAAAGGATTGTACTG 59.775 45.833 0.00 0.00 0.00 2.74
2479 2605 4.224370 GGGGTAGTGAAAGGATTGTACTGA 59.776 45.833 0.00 0.00 0.00 3.41
2480 2606 5.420409 GGGTAGTGAAAGGATTGTACTGAG 58.580 45.833 0.00 0.00 0.00 3.35
2481 2607 5.187186 GGGTAGTGAAAGGATTGTACTGAGA 59.813 44.000 0.00 0.00 0.00 3.27
2482 2608 6.295688 GGGTAGTGAAAGGATTGTACTGAGAA 60.296 42.308 0.00 0.00 0.00 2.87
2483 2609 6.814146 GGTAGTGAAAGGATTGTACTGAGAAG 59.186 42.308 0.00 0.00 0.00 2.85
2484 2610 5.799213 AGTGAAAGGATTGTACTGAGAAGG 58.201 41.667 0.00 0.00 0.00 3.46
2485 2611 4.938226 GTGAAAGGATTGTACTGAGAAGGG 59.062 45.833 0.00 0.00 0.00 3.95
2486 2612 4.844085 TGAAAGGATTGTACTGAGAAGGGA 59.156 41.667 0.00 0.00 0.00 4.20
2487 2613 5.488919 TGAAAGGATTGTACTGAGAAGGGAT 59.511 40.000 0.00 0.00 0.00 3.85
2488 2614 5.365021 AAGGATTGTACTGAGAAGGGATG 57.635 43.478 0.00 0.00 0.00 3.51
2489 2615 3.713764 AGGATTGTACTGAGAAGGGATGG 59.286 47.826 0.00 0.00 0.00 3.51
2490 2616 3.181450 GGATTGTACTGAGAAGGGATGGG 60.181 52.174 0.00 0.00 0.00 4.00
2491 2617 2.642171 TGTACTGAGAAGGGATGGGT 57.358 50.000 0.00 0.00 0.00 4.51
2492 2618 2.187958 TGTACTGAGAAGGGATGGGTG 58.812 52.381 0.00 0.00 0.00 4.61
2493 2619 1.134371 GTACTGAGAAGGGATGGGTGC 60.134 57.143 0.00 0.00 0.00 5.01
2494 2620 0.548682 ACTGAGAAGGGATGGGTGCT 60.549 55.000 0.00 0.00 0.00 4.40
2495 2621 0.179936 CTGAGAAGGGATGGGTGCTC 59.820 60.000 0.00 0.00 0.00 4.26
2496 2622 0.252881 TGAGAAGGGATGGGTGCTCT 60.253 55.000 0.00 0.00 0.00 4.09
2497 2623 0.467804 GAGAAGGGATGGGTGCTCTC 59.532 60.000 0.00 0.00 0.00 3.20
2498 2624 0.043940 AGAAGGGATGGGTGCTCTCT 59.956 55.000 0.00 0.00 0.00 3.10
2499 2625 0.179936 GAAGGGATGGGTGCTCTCTG 59.820 60.000 0.00 0.00 0.00 3.35
2500 2626 0.548682 AAGGGATGGGTGCTCTCTGT 60.549 55.000 0.00 0.00 0.00 3.41
2501 2627 1.222936 GGGATGGGTGCTCTCTGTG 59.777 63.158 0.00 0.00 0.00 3.66
2502 2628 1.267574 GGGATGGGTGCTCTCTGTGA 61.268 60.000 0.00 0.00 0.00 3.58
2503 2629 0.107945 GGATGGGTGCTCTCTGTGAC 60.108 60.000 0.00 0.00 0.00 3.67
2504 2630 0.610174 GATGGGTGCTCTCTGTGACA 59.390 55.000 0.00 0.00 0.00 3.58
2505 2631 0.612229 ATGGGTGCTCTCTGTGACAG 59.388 55.000 6.18 6.18 0.00 3.51
2506 2632 1.294780 GGGTGCTCTCTGTGACAGG 59.705 63.158 13.33 3.77 31.51 4.00
2507 2633 1.294780 GGTGCTCTCTGTGACAGGG 59.705 63.158 13.33 9.91 32.35 4.45
2508 2634 1.476007 GGTGCTCTCTGTGACAGGGT 61.476 60.000 12.89 0.00 33.01 4.34
2509 2635 0.320247 GTGCTCTCTGTGACAGGGTG 60.320 60.000 12.89 11.37 33.01 4.61
2510 2636 1.294780 GCTCTCTGTGACAGGGTGG 59.705 63.158 12.89 7.97 33.01 4.61
2511 2637 1.978473 CTCTCTGTGACAGGGTGGG 59.022 63.158 12.89 0.00 33.01 4.61
2512 2638 0.542938 CTCTCTGTGACAGGGTGGGA 60.543 60.000 12.89 3.23 33.01 4.37
2513 2639 0.105194 TCTCTGTGACAGGGTGGGAA 60.105 55.000 12.89 0.00 33.01 3.97
2514 2640 0.987294 CTCTGTGACAGGGTGGGAAT 59.013 55.000 13.33 0.00 31.51 3.01
2515 2641 0.692476 TCTGTGACAGGGTGGGAATG 59.308 55.000 13.33 0.00 31.51 2.67
2516 2642 0.692476 CTGTGACAGGGTGGGAATGA 59.308 55.000 4.28 0.00 0.00 2.57
2517 2643 0.692476 TGTGACAGGGTGGGAATGAG 59.308 55.000 0.00 0.00 0.00 2.90
2518 2644 0.984230 GTGACAGGGTGGGAATGAGA 59.016 55.000 0.00 0.00 0.00 3.27
2532 2658 7.102346 GTGGGAATGAGATACCTAATCATCTG 58.898 42.308 0.00 0.00 37.03 2.90
2778 2904 8.023128 TCTTAAGAGCACAATTTGACTTTATGC 58.977 33.333 0.00 1.46 0.00 3.14
2898 3024 2.223758 CCTTACTACCCTGTAAGCGAGC 60.224 54.545 8.42 0.00 44.66 5.03
2907 3033 1.014044 TGTAAGCGAGCTTTCAGGCG 61.014 55.000 15.90 0.00 37.47 5.52
3052 3180 1.202533 CCCAGACGTGATGTATGTCCC 60.203 57.143 0.00 0.00 44.76 4.46
3053 3181 1.480545 CCAGACGTGATGTATGTCCCA 59.519 52.381 0.00 0.00 44.76 4.37
3054 3182 2.481969 CCAGACGTGATGTATGTCCCAG 60.482 54.545 0.00 0.00 44.76 4.45
3055 3183 2.427095 CAGACGTGATGTATGTCCCAGA 59.573 50.000 0.00 0.00 44.76 3.86
3056 3184 3.096852 AGACGTGATGTATGTCCCAGAA 58.903 45.455 0.00 0.00 44.76 3.02
3057 3185 3.119101 AGACGTGATGTATGTCCCAGAAC 60.119 47.826 0.00 0.00 44.76 3.01
3058 3186 2.193447 CGTGATGTATGTCCCAGAACG 58.807 52.381 0.00 0.00 0.00 3.95
3059 3187 1.933853 GTGATGTATGTCCCAGAACGC 59.066 52.381 0.00 0.00 0.00 4.84
3060 3188 1.831106 TGATGTATGTCCCAGAACGCT 59.169 47.619 0.00 0.00 0.00 5.07
3061 3189 2.236146 TGATGTATGTCCCAGAACGCTT 59.764 45.455 0.00 0.00 0.00 4.68
3062 3190 2.851263 TGTATGTCCCAGAACGCTTT 57.149 45.000 0.00 0.00 0.00 3.51
3063 3191 3.965379 TGTATGTCCCAGAACGCTTTA 57.035 42.857 0.00 0.00 0.00 1.85
3064 3192 3.592059 TGTATGTCCCAGAACGCTTTAC 58.408 45.455 0.00 0.00 0.00 2.01
3065 3193 2.851263 ATGTCCCAGAACGCTTTACA 57.149 45.000 0.00 0.00 0.00 2.41
3066 3194 1.873698 TGTCCCAGAACGCTTTACAC 58.126 50.000 0.00 0.00 0.00 2.90
3067 3195 1.154197 GTCCCAGAACGCTTTACACC 58.846 55.000 0.00 0.00 0.00 4.16
3068 3196 0.035739 TCCCAGAACGCTTTACACCC 59.964 55.000 0.00 0.00 0.00 4.61
3069 3197 0.958876 CCCAGAACGCTTTACACCCC 60.959 60.000 0.00 0.00 0.00 4.95
3070 3198 0.958876 CCAGAACGCTTTACACCCCC 60.959 60.000 0.00 0.00 0.00 5.40
3086 3214 4.157120 CCCCGCCCCGAACTGTAG 62.157 72.222 0.00 0.00 0.00 2.74
3087 3215 4.157120 CCCGCCCCGAACTGTAGG 62.157 72.222 0.00 0.00 0.00 3.18
3088 3216 4.832608 CCGCCCCGAACTGTAGGC 62.833 72.222 0.00 0.00 42.18 3.93
3089 3217 3.771160 CGCCCCGAACTGTAGGCT 61.771 66.667 0.00 0.00 43.48 4.58
3090 3218 2.669240 GCCCCGAACTGTAGGCTT 59.331 61.111 0.00 0.00 42.34 4.35
3091 3219 1.902556 GCCCCGAACTGTAGGCTTA 59.097 57.895 0.00 0.00 42.34 3.09
3092 3220 0.179081 GCCCCGAACTGTAGGCTTAG 60.179 60.000 0.00 0.00 42.34 2.18
3093 3221 1.192428 CCCCGAACTGTAGGCTTAGT 58.808 55.000 0.00 0.00 0.00 2.24
3094 3222 2.381911 CCCCGAACTGTAGGCTTAGTA 58.618 52.381 0.00 0.00 0.00 1.82
3095 3223 2.361438 CCCCGAACTGTAGGCTTAGTAG 59.639 54.545 0.00 0.00 0.00 2.57
3096 3224 3.285484 CCCGAACTGTAGGCTTAGTAGA 58.715 50.000 0.00 0.00 0.00 2.59
3097 3225 3.890147 CCCGAACTGTAGGCTTAGTAGAT 59.110 47.826 0.00 0.00 0.00 1.98
3098 3226 5.068636 CCCGAACTGTAGGCTTAGTAGATA 58.931 45.833 0.00 0.00 0.00 1.98
3099 3227 5.711036 CCCGAACTGTAGGCTTAGTAGATAT 59.289 44.000 0.00 0.00 0.00 1.63
3100 3228 6.127952 CCCGAACTGTAGGCTTAGTAGATATC 60.128 46.154 0.00 0.00 0.00 1.63
3101 3229 6.127952 CCGAACTGTAGGCTTAGTAGATATCC 60.128 46.154 0.00 0.00 0.00 2.59
3102 3230 6.655848 CGAACTGTAGGCTTAGTAGATATCCT 59.344 42.308 0.00 0.00 0.00 3.24
3103 3231 7.148373 CGAACTGTAGGCTTAGTAGATATCCTC 60.148 44.444 0.00 0.00 0.00 3.71
3104 3232 6.174760 ACTGTAGGCTTAGTAGATATCCTCG 58.825 44.000 0.00 0.00 0.00 4.63
3105 3233 6.124316 TGTAGGCTTAGTAGATATCCTCGT 57.876 41.667 0.00 0.00 0.00 4.18
3106 3234 6.540995 TGTAGGCTTAGTAGATATCCTCGTT 58.459 40.000 0.00 0.00 0.00 3.85
3107 3235 7.683578 TGTAGGCTTAGTAGATATCCTCGTTA 58.316 38.462 0.00 0.00 0.00 3.18
3108 3236 8.159447 TGTAGGCTTAGTAGATATCCTCGTTAA 58.841 37.037 0.00 0.00 0.00 2.01
3321 3627 0.982704 ATGGTCTGCAGACAGCTTCT 59.017 50.000 39.71 19.06 46.47 2.85
3346 3652 3.096092 GTGGGGATAATTGTTGGCTCAA 58.904 45.455 0.00 0.00 0.00 3.02
3829 4135 3.877508 GGTAGCACATTACTAGCCTTTGG 59.122 47.826 0.00 0.00 33.09 3.28
3849 4155 6.500684 TTGGCATCAAGATCAGTTTAGTTC 57.499 37.500 0.00 0.00 0.00 3.01
3857 4163 6.767902 TCAAGATCAGTTTAGTTCTGCAACTT 59.232 34.615 0.00 0.00 40.16 2.66
3975 4281 1.971695 GCAAACCCTGTTCCCCTCG 60.972 63.158 0.00 0.00 0.00 4.63
3976 4282 1.971695 CAAACCCTGTTCCCCTCGC 60.972 63.158 0.00 0.00 0.00 5.03
4258 4713 0.250295 CTTCCCTCCAAGTTGCGACA 60.250 55.000 6.90 0.00 0.00 4.35
4381 4837 9.659830 CGTTTTAAATGAGTTATATAACCCTGC 57.340 33.333 19.74 9.39 36.88 4.85
4403 4861 9.299397 CCTGCTGGAATTTAACAAGTCCTTGTT 62.299 40.741 24.14 24.14 45.84 2.83
4657 5120 4.828072 ACATACACCCTCTTCCTCTTTC 57.172 45.455 0.00 0.00 0.00 2.62
4709 5172 4.766373 TGAATTCTATGCCACTTTTGCAGA 59.234 37.500 7.05 0.00 42.92 4.26
5191 5654 1.463674 CTGCCTTGACACCCAATACC 58.536 55.000 0.00 0.00 33.68 2.73
5301 5764 2.825861 TGTCGTTCCAGGTTTCTACC 57.174 50.000 0.00 0.00 45.39 3.18
5575 6039 3.482156 ACGCCTCAGCTTCATGATATT 57.518 42.857 0.00 0.00 36.60 1.28
5638 6102 1.270907 ACCCTGCGAAATCACTCTCT 58.729 50.000 0.00 0.00 0.00 3.10
5665 6129 3.062323 GCAGACATAATTGCACTCTGC 57.938 47.619 11.25 11.25 45.11 4.26
5677 6141 0.317160 CACTCTGCGTTCAGGTACCA 59.683 55.000 15.94 0.00 40.69 3.25
5691 6155 4.540099 TCAGGTACCATCTTTCTTTGGGAT 59.460 41.667 15.94 0.00 37.32 3.85
5697 6161 7.878644 GGTACCATCTTTCTTTGGGATAGATAC 59.121 40.741 7.15 0.00 39.54 2.24
5708 6197 8.861086 TCTTTGGGATAGATACTCAGTTGTATC 58.139 37.037 6.56 6.56 45.38 2.24
5722 6211 9.464714 ACTCAGTTGTATCGTAGCATTTAATAG 57.535 33.333 0.00 0.00 0.00 1.73
5761 6473 5.622770 AAACAGCCCTAATAGTTTGTTCG 57.377 39.130 0.00 0.00 33.35 3.95
5896 6608 6.764308 TCCTGGCTCATCTCTTAAAATTTG 57.236 37.500 0.00 0.00 0.00 2.32
5943 6655 9.875460 ATGTATTTCATGTCAGGGGCATATCCC 62.875 44.444 0.00 2.48 44.00 3.85
6010 6722 1.682323 GAGTTCCGTCCTCCTATGTCC 59.318 57.143 0.00 0.00 0.00 4.02
6169 6881 6.219417 TCTTCAATGGCAAAAGTGAAAAGA 57.781 33.333 0.00 0.00 30.03 2.52
6474 7194 1.421410 GCACTGCGTTCCATCCTACG 61.421 60.000 0.00 0.00 40.55 3.51
6614 7340 7.923888 GCGATACCTCGGTATATGAACTATAA 58.076 38.462 8.53 0.00 45.15 0.98
7004 7746 3.470562 GTCGAAGAATGCGTTGAAGAAC 58.529 45.455 0.00 0.00 39.14 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.432444 CTAAATTCCAGGCCGTGTTCA 58.568 47.619 0.00 0.00 0.00 3.18
16 17 1.743394 CCTAAATTCCAGGCCGTGTTC 59.257 52.381 0.00 0.00 0.00 3.18
36 37 0.318784 AAACACACGTCTCTCGCCTC 60.319 55.000 0.00 0.00 44.19 4.70
38 39 0.507358 GAAAACACACGTCTCTCGCC 59.493 55.000 0.00 0.00 44.19 5.54
119 120 1.129624 CTCGATCCGATCAGATCCGAC 59.870 57.143 12.37 0.00 39.67 4.79
121 122 0.179176 GCTCGATCCGATCAGATCCG 60.179 60.000 12.37 8.36 39.67 4.18
122 123 0.172352 GGCTCGATCCGATCAGATCC 59.828 60.000 12.37 7.90 39.67 3.36
123 124 0.884514 TGGCTCGATCCGATCAGATC 59.115 55.000 8.64 8.64 39.47 2.75
124 125 0.600557 GTGGCTCGATCCGATCAGAT 59.399 55.000 9.07 0.00 34.61 2.90
125 126 0.751643 TGTGGCTCGATCCGATCAGA 60.752 55.000 9.07 6.09 34.61 3.27
126 127 0.316522 ATGTGGCTCGATCCGATCAG 59.683 55.000 9.07 6.38 34.61 2.90
127 128 0.752658 AATGTGGCTCGATCCGATCA 59.247 50.000 9.07 0.85 34.61 2.92
128 129 1.143305 CAATGTGGCTCGATCCGATC 58.857 55.000 0.03 0.00 34.61 3.69
129 130 0.250038 CCAATGTGGCTCGATCCGAT 60.250 55.000 0.03 0.00 34.61 4.18
130 131 1.143838 CCAATGTGGCTCGATCCGA 59.856 57.895 0.03 0.00 0.00 4.55
131 132 0.744414 AACCAATGTGGCTCGATCCG 60.744 55.000 0.03 0.00 42.67 4.18
132 133 2.213499 CTAACCAATGTGGCTCGATCC 58.787 52.381 0.00 0.00 42.67 3.36
133 134 1.599542 GCTAACCAATGTGGCTCGATC 59.400 52.381 0.00 0.00 42.67 3.69
134 135 1.668419 GCTAACCAATGTGGCTCGAT 58.332 50.000 0.00 0.00 42.67 3.59
135 136 0.392461 GGCTAACCAATGTGGCTCGA 60.392 55.000 0.00 0.00 42.67 4.04
136 137 1.705337 CGGCTAACCAATGTGGCTCG 61.705 60.000 0.00 0.00 42.67 5.03
137 138 1.376609 CCGGCTAACCAATGTGGCTC 61.377 60.000 0.00 0.00 42.67 4.70
138 139 1.378514 CCGGCTAACCAATGTGGCT 60.379 57.895 0.00 0.00 42.67 4.75
139 140 2.414785 CCCGGCTAACCAATGTGGC 61.415 63.158 0.00 0.00 42.67 5.01
140 141 1.001393 ACCCGGCTAACCAATGTGG 60.001 57.895 0.00 0.00 45.02 4.17
141 142 1.312371 CCACCCGGCTAACCAATGTG 61.312 60.000 0.00 0.00 34.57 3.21
142 143 1.001393 CCACCCGGCTAACCAATGT 60.001 57.895 0.00 0.00 34.57 2.71
143 144 1.752694 CCCACCCGGCTAACCAATG 60.753 63.158 0.00 0.00 34.57 2.82
144 145 2.680965 CCCACCCGGCTAACCAAT 59.319 61.111 0.00 0.00 34.57 3.16
166 167 5.412594 TGCTGTCAGCTAAAATGAGTTAAGG 59.587 40.000 24.76 0.00 42.97 2.69
171 172 6.176183 ACTATTGCTGTCAGCTAAAATGAGT 58.824 36.000 24.76 15.35 42.97 3.41
172 173 6.314648 TGACTATTGCTGTCAGCTAAAATGAG 59.685 38.462 24.76 14.87 42.97 2.90
177 178 4.695455 GGTTGACTATTGCTGTCAGCTAAA 59.305 41.667 24.76 12.73 43.98 1.85
181 182 1.740025 GGGTTGACTATTGCTGTCAGC 59.260 52.381 18.32 18.32 43.98 4.26
207 211 2.227388 GAGATTGGTGCTTCACTTGTGG 59.773 50.000 0.64 0.00 34.40 4.17
208 212 2.880268 TGAGATTGGTGCTTCACTTGTG 59.120 45.455 0.00 0.00 34.40 3.33
223 227 4.278419 CCCTTTTTCAGAACCGTTGAGATT 59.722 41.667 0.00 0.00 0.00 2.40
244 248 4.709397 TCATTGTTGATGGATGGTTTACCC 59.291 41.667 0.00 0.00 36.37 3.69
248 252 6.041865 TGAAGTTCATTGTTGATGGATGGTTT 59.958 34.615 0.08 0.00 36.37 3.27
255 259 7.874940 TCTAGTTTGAAGTTCATTGTTGATGG 58.125 34.615 6.36 0.00 36.37 3.51
260 264 8.515414 GGCTAATCTAGTTTGAAGTTCATTGTT 58.485 33.333 6.36 0.00 0.00 2.83
292 298 5.125739 ACCCGTTGATTACTTTGTTTGTGAA 59.874 36.000 0.00 0.00 0.00 3.18
297 303 6.947644 AGTAACCCGTTGATTACTTTGTTT 57.052 33.333 0.00 0.00 38.23 2.83
306 312 2.279935 TGCCAAGTAACCCGTTGATT 57.720 45.000 0.00 0.00 0.00 2.57
309 315 2.357637 CCATATGCCAAGTAACCCGTTG 59.642 50.000 0.00 0.00 0.00 4.10
316 322 5.949354 AGTTACAAAGCCATATGCCAAGTAA 59.051 36.000 0.00 0.32 42.71 2.24
317 323 5.505780 AGTTACAAAGCCATATGCCAAGTA 58.494 37.500 0.00 0.00 42.71 2.24
319 325 4.989279 AGTTACAAAGCCATATGCCAAG 57.011 40.909 0.00 0.00 42.71 3.61
320 326 5.736951 AAAGTTACAAAGCCATATGCCAA 57.263 34.783 0.00 0.00 42.71 4.52
321 327 5.011533 ACAAAAGTTACAAAGCCATATGCCA 59.988 36.000 0.00 0.00 42.71 4.92
322 328 5.478407 ACAAAAGTTACAAAGCCATATGCC 58.522 37.500 0.00 0.00 42.71 4.40
323 329 6.423604 ACAACAAAAGTTACAAAGCCATATGC 59.576 34.615 0.00 0.00 41.71 3.14
324 330 7.095691 CCACAACAAAAGTTACAAAGCCATATG 60.096 37.037 0.00 0.00 0.00 1.78
325 331 6.928492 CCACAACAAAAGTTACAAAGCCATAT 59.072 34.615 0.00 0.00 0.00 1.78
326 332 6.127310 ACCACAACAAAAGTTACAAAGCCATA 60.127 34.615 0.00 0.00 0.00 2.74
327 333 5.115480 CCACAACAAAAGTTACAAAGCCAT 58.885 37.500 0.00 0.00 0.00 4.40
328 334 4.021016 ACCACAACAAAAGTTACAAAGCCA 60.021 37.500 0.00 0.00 0.00 4.75
329 335 4.500127 ACCACAACAAAAGTTACAAAGCC 58.500 39.130 0.00 0.00 0.00 4.35
330 336 7.449827 GTTAACCACAACAAAAGTTACAAAGC 58.550 34.615 0.00 0.00 0.00 3.51
362 368 0.039472 TACAGGTACAGTACGCCCCA 59.961 55.000 4.58 0.00 0.00 4.96
372 378 3.319755 GCTTTACTTGCGTACAGGTACA 58.680 45.455 9.97 0.00 38.01 2.90
377 383 2.157668 CACAGGCTTTACTTGCGTACAG 59.842 50.000 0.00 0.00 0.00 2.74
378 384 2.139917 CACAGGCTTTACTTGCGTACA 58.860 47.619 0.00 0.00 0.00 2.90
379 385 2.096417 CACACAGGCTTTACTTGCGTAC 60.096 50.000 0.00 0.00 0.00 3.67
380 386 2.139917 CACACAGGCTTTACTTGCGTA 58.860 47.619 0.00 0.00 0.00 4.42
381 387 0.944386 CACACAGGCTTTACTTGCGT 59.056 50.000 0.00 0.00 0.00 5.24
382 388 0.238289 CCACACAGGCTTTACTTGCG 59.762 55.000 0.00 0.00 0.00 4.85
384 390 3.004734 CCTTTCCACACAGGCTTTACTTG 59.995 47.826 0.00 0.00 37.29 3.16
411 441 1.281899 GAGATCCTTCCGTTGCTTCG 58.718 55.000 0.00 0.00 0.00 3.79
425 455 7.331791 AGTAGTTAACCTGGTCAAATGAGATC 58.668 38.462 0.00 0.00 0.00 2.75
440 470 4.407945 TGAGGAGGCCAATAGTAGTTAACC 59.592 45.833 5.01 0.00 0.00 2.85
452 482 0.843309 TGTTTGACTGAGGAGGCCAA 59.157 50.000 5.01 0.00 0.00 4.52
672 720 8.977505 CAAGACTTAACTCTCTTTTTCTCTCTG 58.022 37.037 0.00 0.00 0.00 3.35
673 721 7.655732 GCAAGACTTAACTCTCTTTTTCTCTCT 59.344 37.037 0.00 0.00 0.00 3.10
674 722 7.095397 GGCAAGACTTAACTCTCTTTTTCTCTC 60.095 40.741 0.00 0.00 0.00 3.20
675 723 6.708502 GGCAAGACTTAACTCTCTTTTTCTCT 59.291 38.462 0.00 0.00 0.00 3.10
680 728 4.065789 CCGGCAAGACTTAACTCTCTTTT 58.934 43.478 0.00 0.00 0.00 2.27
682 730 2.613223 GCCGGCAAGACTTAACTCTCTT 60.613 50.000 24.80 0.00 0.00 2.85
1093 1195 3.900892 GATCGGAAGCGGAGGCGA 61.901 66.667 0.00 0.00 46.35 5.54
1096 1198 4.286320 CGGGATCGGAAGCGGAGG 62.286 72.222 0.00 0.00 0.00 4.30
1124 1226 1.341802 CGCGCGAGAGATCAACAAC 59.658 57.895 28.94 0.00 0.00 3.32
1125 1227 1.080772 ACGCGCGAGAGATCAACAA 60.081 52.632 39.36 0.00 33.96 2.83
1157 1259 4.431416 ACCCAGGCATCGTTAATTATCA 57.569 40.909 0.00 0.00 0.00 2.15
1327 1429 1.228063 GGCATGCGAGGATGGATGT 60.228 57.895 12.44 0.00 39.59 3.06
1348 1450 6.507299 CGAAAAGAAAAACAAATCAACGGGTC 60.507 38.462 0.00 0.00 0.00 4.46
1449 1552 2.047179 GTTCAGACCTGTCCCCGC 60.047 66.667 0.00 0.00 0.00 6.13
1451 1554 2.663196 CCGTTCAGACCTGTCCCC 59.337 66.667 0.00 0.00 0.00 4.81
1460 1563 2.650116 GCCCAGAGAGCCGTTCAGA 61.650 63.158 0.00 0.00 0.00 3.27
1523 1626 1.961277 CAGTGGGCGAGTTGTGGTC 60.961 63.158 0.00 0.00 0.00 4.02
2012 2115 1.332375 CCGAAAAAGTTGCGAGGAACA 59.668 47.619 9.97 0.00 0.00 3.18
2035 2138 3.466836 ACATTCACACCCGTGCATATAG 58.533 45.455 0.00 0.00 43.28 1.31
2222 2329 6.873076 GGATGACAAAATTGCCTACAAATTCA 59.127 34.615 0.00 0.00 39.77 2.57
2223 2330 6.873076 TGGATGACAAAATTGCCTACAAATTC 59.127 34.615 0.00 0.00 39.77 2.17
2225 2332 6.165577 GTGGATGACAAAATTGCCTACAAAT 58.834 36.000 0.00 0.00 39.77 2.32
2226 2333 5.537188 GTGGATGACAAAATTGCCTACAAA 58.463 37.500 0.00 0.00 39.77 2.83
2227 2334 4.320861 CGTGGATGACAAAATTGCCTACAA 60.321 41.667 0.00 0.00 40.87 2.41
2228 2335 3.190327 CGTGGATGACAAAATTGCCTACA 59.810 43.478 0.00 0.00 0.00 2.74
2229 2336 3.758300 CGTGGATGACAAAATTGCCTAC 58.242 45.455 0.00 0.00 0.00 3.18
2250 2375 3.127030 CGGAAGAAGTATCCCAAAAGTGC 59.873 47.826 0.00 0.00 33.13 4.40
2258 2383 2.396590 TGTTGCGGAAGAAGTATCCC 57.603 50.000 0.00 0.00 33.13 3.85
2267 2392 1.667236 TAGATGCCATGTTGCGGAAG 58.333 50.000 0.00 0.00 0.00 3.46
2272 2397 3.881688 AGAAGACATAGATGCCATGTTGC 59.118 43.478 0.00 0.00 36.76 4.17
2277 2402 4.445448 GGTTCCAGAAGACATAGATGCCAT 60.445 45.833 0.00 0.00 0.00 4.40
2283 2408 8.783660 ACTATATTGGTTCCAGAAGACATAGA 57.216 34.615 0.00 0.00 0.00 1.98
2416 2542 4.151121 TGTTTTGAAATGCTGGGAGATGA 58.849 39.130 0.00 0.00 0.00 2.92
2434 2560 6.555360 CCCCTACTACCTAATCATCTCTGTTT 59.445 42.308 0.00 0.00 0.00 2.83
2435 2561 6.078664 CCCCTACTACCTAATCATCTCTGTT 58.921 44.000 0.00 0.00 0.00 3.16
2436 2562 5.136392 ACCCCTACTACCTAATCATCTCTGT 59.864 44.000 0.00 0.00 0.00 3.41
2438 2564 5.952161 ACCCCTACTACCTAATCATCTCT 57.048 43.478 0.00 0.00 0.00 3.10
2439 2565 6.660094 CACTACCCCTACTACCTAATCATCTC 59.340 46.154 0.00 0.00 0.00 2.75
2440 2566 6.334774 TCACTACCCCTACTACCTAATCATCT 59.665 42.308 0.00 0.00 0.00 2.90
2441 2567 6.550163 TCACTACCCCTACTACCTAATCATC 58.450 44.000 0.00 0.00 0.00 2.92
2442 2568 6.541264 TCACTACCCCTACTACCTAATCAT 57.459 41.667 0.00 0.00 0.00 2.45
2445 2571 6.068021 TCCTTTCACTACCCCTACTACCTAAT 60.068 42.308 0.00 0.00 0.00 1.73
2446 2572 5.256152 TCCTTTCACTACCCCTACTACCTAA 59.744 44.000 0.00 0.00 0.00 2.69
2447 2573 4.795714 TCCTTTCACTACCCCTACTACCTA 59.204 45.833 0.00 0.00 0.00 3.08
2448 2574 3.599698 TCCTTTCACTACCCCTACTACCT 59.400 47.826 0.00 0.00 0.00 3.08
2449 2575 3.986435 TCCTTTCACTACCCCTACTACC 58.014 50.000 0.00 0.00 0.00 3.18
2451 2577 5.596763 ACAATCCTTTCACTACCCCTACTA 58.403 41.667 0.00 0.00 0.00 1.82
2452 2578 4.436079 ACAATCCTTTCACTACCCCTACT 58.564 43.478 0.00 0.00 0.00 2.57
2454 2580 5.424252 CAGTACAATCCTTTCACTACCCCTA 59.576 44.000 0.00 0.00 0.00 3.53
2455 2581 4.225267 CAGTACAATCCTTTCACTACCCCT 59.775 45.833 0.00 0.00 0.00 4.79
2456 2582 4.224370 TCAGTACAATCCTTTCACTACCCC 59.776 45.833 0.00 0.00 0.00 4.95
2457 2583 5.187186 TCTCAGTACAATCCTTTCACTACCC 59.813 44.000 0.00 0.00 0.00 3.69
2458 2584 6.282199 TCTCAGTACAATCCTTTCACTACC 57.718 41.667 0.00 0.00 0.00 3.18
2459 2585 6.814146 CCTTCTCAGTACAATCCTTTCACTAC 59.186 42.308 0.00 0.00 0.00 2.73
2460 2586 6.070767 CCCTTCTCAGTACAATCCTTTCACTA 60.071 42.308 0.00 0.00 0.00 2.74
2461 2587 5.280215 CCCTTCTCAGTACAATCCTTTCACT 60.280 44.000 0.00 0.00 0.00 3.41
2462 2588 4.938226 CCCTTCTCAGTACAATCCTTTCAC 59.062 45.833 0.00 0.00 0.00 3.18
2463 2589 4.844085 TCCCTTCTCAGTACAATCCTTTCA 59.156 41.667 0.00 0.00 0.00 2.69
2464 2590 5.422214 TCCCTTCTCAGTACAATCCTTTC 57.578 43.478 0.00 0.00 0.00 2.62
2465 2591 5.339530 CCATCCCTTCTCAGTACAATCCTTT 60.340 44.000 0.00 0.00 0.00 3.11
2466 2592 4.164988 CCATCCCTTCTCAGTACAATCCTT 59.835 45.833 0.00 0.00 0.00 3.36
2467 2593 3.713764 CCATCCCTTCTCAGTACAATCCT 59.286 47.826 0.00 0.00 0.00 3.24
2468 2594 3.181450 CCCATCCCTTCTCAGTACAATCC 60.181 52.174 0.00 0.00 0.00 3.01
2469 2595 3.456277 ACCCATCCCTTCTCAGTACAATC 59.544 47.826 0.00 0.00 0.00 2.67
2471 2597 2.571653 CACCCATCCCTTCTCAGTACAA 59.428 50.000 0.00 0.00 0.00 2.41
2473 2599 1.134371 GCACCCATCCCTTCTCAGTAC 60.134 57.143 0.00 0.00 0.00 2.73
2474 2600 1.204146 GCACCCATCCCTTCTCAGTA 58.796 55.000 0.00 0.00 0.00 2.74
2476 2602 0.179936 GAGCACCCATCCCTTCTCAG 59.820 60.000 0.00 0.00 0.00 3.35
2478 2604 0.467804 GAGAGCACCCATCCCTTCTC 59.532 60.000 0.00 0.00 0.00 2.87
2479 2605 0.043940 AGAGAGCACCCATCCCTTCT 59.956 55.000 0.00 0.00 0.00 2.85
2480 2606 0.179936 CAGAGAGCACCCATCCCTTC 59.820 60.000 0.00 0.00 0.00 3.46
2481 2607 0.548682 ACAGAGAGCACCCATCCCTT 60.549 55.000 0.00 0.00 0.00 3.95
2482 2608 1.081833 ACAGAGAGCACCCATCCCT 59.918 57.895 0.00 0.00 0.00 4.20
2483 2609 1.222936 CACAGAGAGCACCCATCCC 59.777 63.158 0.00 0.00 0.00 3.85
2484 2610 0.107945 GTCACAGAGAGCACCCATCC 60.108 60.000 0.00 0.00 0.00 3.51
2485 2611 0.610174 TGTCACAGAGAGCACCCATC 59.390 55.000 0.00 0.00 0.00 3.51
2486 2612 0.612229 CTGTCACAGAGAGCACCCAT 59.388 55.000 0.00 0.00 32.44 4.00
2487 2613 1.475169 CCTGTCACAGAGAGCACCCA 61.475 60.000 6.30 0.00 32.44 4.51
2488 2614 1.294780 CCTGTCACAGAGAGCACCC 59.705 63.158 6.30 0.00 32.44 4.61
2489 2615 1.294780 CCCTGTCACAGAGAGCACC 59.705 63.158 6.30 0.00 32.44 5.01
2490 2616 0.320247 CACCCTGTCACAGAGAGCAC 60.320 60.000 6.30 0.00 32.44 4.40
2491 2617 1.475169 CCACCCTGTCACAGAGAGCA 61.475 60.000 6.30 0.00 32.44 4.26
2492 2618 1.294780 CCACCCTGTCACAGAGAGC 59.705 63.158 6.30 0.00 32.44 4.09
2493 2619 0.542938 TCCCACCCTGTCACAGAGAG 60.543 60.000 6.30 0.00 32.44 3.20
2494 2620 0.105194 TTCCCACCCTGTCACAGAGA 60.105 55.000 6.30 0.00 32.44 3.10
2495 2621 0.987294 ATTCCCACCCTGTCACAGAG 59.013 55.000 6.30 0.00 32.44 3.35
2496 2622 0.692476 CATTCCCACCCTGTCACAGA 59.308 55.000 6.30 0.00 32.44 3.41
2497 2623 0.692476 TCATTCCCACCCTGTCACAG 59.308 55.000 0.00 0.00 0.00 3.66
2498 2624 0.692476 CTCATTCCCACCCTGTCACA 59.308 55.000 0.00 0.00 0.00 3.58
2499 2625 0.984230 TCTCATTCCCACCCTGTCAC 59.016 55.000 0.00 0.00 0.00 3.67
2500 2626 1.971149 ATCTCATTCCCACCCTGTCA 58.029 50.000 0.00 0.00 0.00 3.58
2501 2627 2.104963 GGTATCTCATTCCCACCCTGTC 59.895 54.545 0.00 0.00 0.00 3.51
2502 2628 2.127708 GGTATCTCATTCCCACCCTGT 58.872 52.381 0.00 0.00 0.00 4.00
2503 2629 2.412591 AGGTATCTCATTCCCACCCTG 58.587 52.381 0.00 0.00 0.00 4.45
2504 2630 2.897823 AGGTATCTCATTCCCACCCT 57.102 50.000 0.00 0.00 0.00 4.34
2505 2631 4.597507 TGATTAGGTATCTCATTCCCACCC 59.402 45.833 0.00 0.00 34.17 4.61
2506 2632 5.825593 TGATTAGGTATCTCATTCCCACC 57.174 43.478 0.00 0.00 34.17 4.61
2507 2633 7.102346 CAGATGATTAGGTATCTCATTCCCAC 58.898 42.308 0.00 0.00 34.17 4.61
2508 2634 6.789457 ACAGATGATTAGGTATCTCATTCCCA 59.211 38.462 0.00 0.00 34.17 4.37
2509 2635 7.102346 CACAGATGATTAGGTATCTCATTCCC 58.898 42.308 0.00 0.00 34.17 3.97
2510 2636 7.675062 ACACAGATGATTAGGTATCTCATTCC 58.325 38.462 0.00 0.00 34.17 3.01
2511 2637 9.553064 AAACACAGATGATTAGGTATCTCATTC 57.447 33.333 0.00 0.00 34.17 2.67
2512 2638 9.911788 AAAACACAGATGATTAGGTATCTCATT 57.088 29.630 0.00 0.00 34.17 2.57
2513 2639 9.334947 CAAAACACAGATGATTAGGTATCTCAT 57.665 33.333 0.00 0.00 34.17 2.90
2514 2640 8.539544 TCAAAACACAGATGATTAGGTATCTCA 58.460 33.333 0.00 0.00 34.17 3.27
2515 2641 8.948631 TCAAAACACAGATGATTAGGTATCTC 57.051 34.615 0.00 0.00 34.17 2.75
2516 2642 9.739276 TTTCAAAACACAGATGATTAGGTATCT 57.261 29.630 0.00 0.00 34.17 1.98
2532 2658 4.506288 GGGTACAAGTGCATTTCAAAACAC 59.494 41.667 0.00 0.00 0.00 3.32
2778 2904 3.552890 GCAACCAGGGCTAAAAAGTTGAG 60.553 47.826 4.96 0.00 37.39 3.02
2898 3024 3.575965 AGTTAAATTGCCGCCTGAAAG 57.424 42.857 0.00 0.00 0.00 2.62
2907 3033 9.736023 CAGGATGAGTTAAATAGTTAAATTGCC 57.264 33.333 0.00 0.45 39.69 4.52
3052 3180 2.551644 GGGGGTGTAAAGCGTTCTG 58.448 57.895 0.00 0.00 0.00 3.02
3069 3197 4.157120 CTACAGTTCGGGGCGGGG 62.157 72.222 0.00 0.00 0.00 5.73
3070 3198 4.157120 CCTACAGTTCGGGGCGGG 62.157 72.222 0.00 0.00 0.00 6.13
3071 3199 4.832608 GCCTACAGTTCGGGGCGG 62.833 72.222 0.00 0.00 35.08 6.13
3073 3201 0.179081 CTAAGCCTACAGTTCGGGGC 60.179 60.000 0.00 0.00 44.38 5.80
3074 3202 1.192428 ACTAAGCCTACAGTTCGGGG 58.808 55.000 0.00 0.00 0.00 5.73
3075 3203 3.285484 TCTACTAAGCCTACAGTTCGGG 58.715 50.000 0.00 0.00 0.00 5.14
3076 3204 6.127952 GGATATCTACTAAGCCTACAGTTCGG 60.128 46.154 2.05 0.00 0.00 4.30
3077 3205 6.655848 AGGATATCTACTAAGCCTACAGTTCG 59.344 42.308 2.05 0.00 0.00 3.95
3078 3206 7.148373 CGAGGATATCTACTAAGCCTACAGTTC 60.148 44.444 2.05 0.00 0.00 3.01
3079 3207 6.655848 CGAGGATATCTACTAAGCCTACAGTT 59.344 42.308 2.05 0.00 0.00 3.16
3080 3208 6.174760 CGAGGATATCTACTAAGCCTACAGT 58.825 44.000 2.05 0.00 0.00 3.55
3081 3209 6.174760 ACGAGGATATCTACTAAGCCTACAG 58.825 44.000 2.05 0.00 0.00 2.74
3082 3210 6.124316 ACGAGGATATCTACTAAGCCTACA 57.876 41.667 2.05 0.00 0.00 2.74
3083 3211 8.558973 TTAACGAGGATATCTACTAAGCCTAC 57.441 38.462 2.05 0.00 0.00 3.18
3084 3212 9.578576 TTTTAACGAGGATATCTACTAAGCCTA 57.421 33.333 2.05 0.00 0.00 3.93
3085 3213 8.358895 GTTTTAACGAGGATATCTACTAAGCCT 58.641 37.037 2.05 0.00 0.00 4.58
3086 3214 8.139989 TGTTTTAACGAGGATATCTACTAAGCC 58.860 37.037 2.05 0.00 0.00 4.35
3087 3215 9.694137 ATGTTTTAACGAGGATATCTACTAAGC 57.306 33.333 2.05 0.00 0.00 3.09
3321 3627 3.096092 GCCAACAATTATCCCCACAAGA 58.904 45.455 0.00 0.00 0.00 3.02
3346 3652 2.287788 GCACACACAAAGCAGCAAGTAT 60.288 45.455 0.00 0.00 0.00 2.12
3692 3998 7.710907 CGGATGGTCAGAACTCAATTATCTTAA 59.289 37.037 0.00 0.00 0.00 1.85
3787 4093 1.236616 TTGTGCTGGAGGTTGCATCG 61.237 55.000 0.00 0.00 41.45 3.84
3829 4135 5.122869 TGCAGAACTAAACTGATCTTGATGC 59.877 40.000 0.00 0.00 37.54 3.91
3849 4155 2.604462 GTGCCTCAAAAACAAGTTGCAG 59.396 45.455 1.81 0.00 0.00 4.41
3857 4163 1.034838 AGTGCCGTGCCTCAAAAACA 61.035 50.000 0.00 0.00 0.00 2.83
3943 4249 3.387699 AGGGTTTGCAGTTTTTATGTGCT 59.612 39.130 0.00 0.00 38.09 4.40
3975 4281 2.442087 CGAAATTGGGGAGGGGGC 60.442 66.667 0.00 0.00 0.00 5.80
3976 4282 2.442087 GCGAAATTGGGGAGGGGG 60.442 66.667 0.00 0.00 0.00 5.40
4258 4713 6.072199 AGGGAATCTTGACAGAAGCTATTT 57.928 37.500 0.00 0.00 30.76 1.40
4403 4861 7.147620 ACCCACGAATTGAGGTTTATGAGTATA 60.148 37.037 0.00 0.00 0.00 1.47
4404 4862 6.055588 CCCACGAATTGAGGTTTATGAGTAT 58.944 40.000 0.00 0.00 0.00 2.12
4709 5172 7.092846 ACTGTCTACCTTCTTAACAGCCATAAT 60.093 37.037 0.00 0.00 40.74 1.28
5037 5500 6.320551 ACAAATGTTTGGAAAACGTTAACG 57.679 33.333 25.68 25.68 42.34 3.18
5191 5654 2.164422 TGTGATACTTGCCTGTCTCTCG 59.836 50.000 0.00 0.00 0.00 4.04
5301 5764 1.068333 CCAAATGAGCCAACCACTTCG 60.068 52.381 0.00 0.00 0.00 3.79
5496 5960 0.814457 ACTGCAACAGCCGTTCAAAA 59.186 45.000 0.00 0.00 34.37 2.44
5501 5965 1.070134 TCTAGAACTGCAACAGCCGTT 59.930 47.619 0.00 0.00 38.21 4.44
5575 6039 5.559770 TCAACCATCTTAGAAAGTGCATCA 58.440 37.500 0.00 0.00 0.00 3.07
5638 6102 2.487372 TGCAATTATGTCTGCAAAGCGA 59.513 40.909 0.00 0.00 45.25 4.93
5665 6129 4.154195 CCAAAGAAAGATGGTACCTGAACG 59.846 45.833 14.36 0.00 31.84 3.95
5677 6141 8.560124 ACTGAGTATCTATCCCAAAGAAAGAT 57.440 34.615 0.00 0.00 34.92 2.40
5691 6155 7.981102 ATGCTACGATACAACTGAGTATCTA 57.019 36.000 16.65 10.51 45.15 1.98
5697 6161 9.464714 ACTATTAAATGCTACGATACAACTGAG 57.535 33.333 0.00 0.00 0.00 3.35
5746 6455 6.093495 TGCAAGAATCCGAACAAACTATTAGG 59.907 38.462 0.00 0.00 0.00 2.69
5749 6458 5.957842 TGCAAGAATCCGAACAAACTATT 57.042 34.783 0.00 0.00 0.00 1.73
5761 6473 3.487544 GCCACGTTAGATTGCAAGAATCC 60.488 47.826 4.94 0.00 0.00 3.01
5819 6531 6.414408 AATCGAAGCAACTCAAACATAGAG 57.586 37.500 0.00 0.00 39.04 2.43
6169 6881 4.597507 TCTTGTATTTGACCCTCAGACCTT 59.402 41.667 0.00 0.00 0.00 3.50
6474 7194 9.595823 TTTTAGCCTATACAGTAAGAACATGAC 57.404 33.333 0.00 0.00 0.00 3.06
6503 7224 7.226720 ACTTACAAAAGGTCGCATAATCATAGG 59.773 37.037 0.00 0.00 37.01 2.57
6614 7340 3.557595 GCTGCTGCTACGTTATTGAGATT 59.442 43.478 8.53 0.00 36.03 2.40
6917 7659 2.434428 CTGCCTGAGCTCTTGATGTTT 58.566 47.619 16.19 0.00 40.80 2.83
7004 7746 1.214589 CCTCCAAGGTACACGACGG 59.785 63.158 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.