Multiple sequence alignment - TraesCS5A01G176600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G176600 chr5A 100.000 6222 0 0 1 6222 371033656 371039877 0.000000e+00 11490.0
1 TraesCS5A01G176600 chr5A 94.000 150 8 1 2104 2252 687682717 687682568 6.280000e-55 226.0
2 TraesCS5A01G176600 chr5D 96.694 3267 68 20 2235 5483 280779089 280775845 0.000000e+00 5398.0
3 TraesCS5A01G176600 chr5D 88.921 1047 53 21 567 1581 280780950 280779935 0.000000e+00 1232.0
4 TraesCS5A01G176600 chr5D 96.378 497 15 2 1610 2103 280779609 280779113 0.000000e+00 815.0
5 TraesCS5A01G176600 chr5D 92.070 454 35 1 5769 6222 280773973 280773521 6.800000e-179 638.0
6 TraesCS5A01G176600 chr5D 87.452 263 32 1 3 265 280781533 280781272 1.010000e-77 302.0
7 TraesCS5A01G176600 chr5D 94.505 182 8 2 5569 5749 280775671 280775491 4.750000e-71 279.0
8 TraesCS5A01G176600 chr5D 96.992 133 4 0 2104 2236 231475468 231475600 2.260000e-54 224.0
9 TraesCS5A01G176600 chr5B 94.935 2389 95 14 2339 4717 318396407 318394035 0.000000e+00 3718.0
10 TraesCS5A01G176600 chr5B 90.286 1575 81 22 556 2103 318398234 318396705 0.000000e+00 1995.0
11 TraesCS5A01G176600 chr5B 93.657 741 14 9 4754 5483 318394040 318393322 0.000000e+00 1077.0
12 TraesCS5A01G176600 chr5B 89.427 454 47 1 5769 6222 318391719 318391267 7.000000e-159 571.0
13 TraesCS5A01G176600 chr5B 89.811 265 22 4 3 265 318398895 318398634 9.990000e-88 335.0
14 TraesCS5A01G176600 chr5B 89.908 109 3 2 2241 2341 318396673 318396565 3.910000e-27 134.0
15 TraesCS5A01G176600 chr1D 95.172 145 6 1 2104 2247 196817811 196817667 1.740000e-55 228.0
16 TraesCS5A01G176600 chr1D 79.646 113 18 4 262 371 260571544 260571434 6.690000e-10 76.8
17 TraesCS5A01G176600 chr6D 97.015 134 4 0 2103 2236 361051175 361051308 6.280000e-55 226.0
18 TraesCS5A01G176600 chr2D 94.040 151 6 3 2096 2245 525230423 525230571 6.280000e-55 226.0
19 TraesCS5A01G176600 chr6B 96.324 136 5 0 2104 2239 240047026 240046891 2.260000e-54 224.0
20 TraesCS5A01G176600 chr1B 94.483 145 7 1 2104 2247 277450517 277450373 8.120000e-54 222.0
21 TraesCS5A01G176600 chr4D 90.683 161 11 3 2104 2262 70989735 70989893 1.760000e-50 211.0
22 TraesCS5A01G176600 chr2A 90.123 162 13 3 2104 2263 744795967 744796127 2.270000e-49 207.0


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 TraesCS5A01G176600 chr5A 371033656 371039877 6221 False 11490 11490 100.000000 1 6222 1 chr5A.!!$F1 6221
1 TraesCS5A01G176600 chr5D 280773521 280781533 8012 True 1444 5398 92.670000 3 6222 6 chr5D.!!$R1 6219
2 TraesCS5A01G176600 chr5B 318391267 318398895 7628 True 1305 3718 91.337333 3 6222 6 chr5B.!!$R1 6219

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
490 583 0.366871 GTGCTCACGTGCGTTCATAG 59.633 55.000 11.67 1.87 35.36 2.23 F
1259 1419 0.106819 GATGAGTGGCATCCAGGCTT 60.107 55.000 0.00 0.00 46.23 4.35 F
2103 2599 0.673985 CACTCCGTGACCTTCACTGA 59.326 55.000 4.87 2.96 44.85 3.41 F
2107 2603 1.202891 TCCGTGACCTTCACTGAGAGA 60.203 52.381 4.87 0.00 44.85 3.10 F
3826 4496 1.252904 TACAGCCACACCGGACCTAC 61.253 60.000 9.46 0.00 36.56 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 1490 2.305928 CACAACTCCACCAACCATCAA 58.694 47.619 0.0 0.0 0.00 2.57 R
2681 3347 2.243736 ACTTTCCTGGTCTTTGGGTTCA 59.756 45.455 0.0 0.0 0.00 3.18 R
3355 4023 2.268298 AGCTACAATACGCAGGAAACG 58.732 47.619 0.0 0.0 0.00 3.60 R
3849 4519 5.695363 CAGCATGACCATCTACAATGAGTAG 59.305 44.000 0.0 0.0 45.42 2.57 R
5590 6420 0.874390 CAGGTGTCCACGGTCATTTG 59.126 55.000 0.0 0.0 0.00 2.32 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
30 31 3.131709 ACAGTTCTAGTTGCTGCACAT 57.868 42.857 0.00 0.00 33.87 3.21
47 48 1.547372 ACATGTTGCTCCCTTCAATGC 59.453 47.619 0.00 0.00 0.00 3.56
48 49 1.134907 CATGTTGCTCCCTTCAATGCC 60.135 52.381 0.00 0.00 0.00 4.40
95 96 2.894126 CGGCTCTTAGGTATCCATGACT 59.106 50.000 0.00 0.00 0.00 3.41
97 98 3.643792 GGCTCTTAGGTATCCATGACTGT 59.356 47.826 0.00 0.00 0.00 3.55
98 99 4.502259 GGCTCTTAGGTATCCATGACTGTG 60.502 50.000 0.00 0.00 0.00 3.66
99 100 4.342378 GCTCTTAGGTATCCATGACTGTGA 59.658 45.833 0.00 0.00 0.00 3.58
186 187 1.683917 TGGTTGCCTTGTTTGCGTTAT 59.316 42.857 0.00 0.00 0.00 1.89
197 198 4.193090 TGTTTGCGTTATCATTACCGGAT 58.807 39.130 9.46 0.00 0.00 4.18
213 214 7.756395 TTACCGGATATAACCAAACAAAACA 57.244 32.000 9.46 0.00 0.00 2.83
243 244 4.058124 GTCTCACTACAGTTGCAATGTGA 58.942 43.478 18.73 17.12 34.04 3.58
253 254 5.163824 ACAGTTGCAATGTGATGTATTCTCG 60.164 40.000 16.33 0.00 0.00 4.04
256 257 6.763135 AGTTGCAATGTGATGTATTCTCGTAT 59.237 34.615 0.59 0.00 0.00 3.06
262 263 8.417928 CAATGTGATGTATTCTCGTATCGTTAC 58.582 37.037 0.00 0.00 0.00 2.50
265 345 6.577800 GTGATGTATTCTCGTATCGTTACCAG 59.422 42.308 0.00 0.00 0.00 4.00
308 388 3.427670 GTGGAACCAACACACCGG 58.572 61.111 0.00 0.00 38.67 5.28
315 395 1.896660 CCAACACACCGGGGTTCAG 60.897 63.158 6.62 0.00 0.00 3.02
321 401 2.928396 ACCGGGGTTCAGGTCCTG 60.928 66.667 13.21 13.21 35.50 3.86
335 415 2.443255 AGGTCCTGAATTTGACACTGGT 59.557 45.455 0.00 0.00 33.09 4.00
341 421 2.218603 GAATTTGACACTGGTGGTCGT 58.781 47.619 5.70 0.00 38.10 4.34
342 422 1.593196 ATTTGACACTGGTGGTCGTG 58.407 50.000 5.70 0.00 38.10 4.35
350 432 0.944386 CTGGTGGTCGTGTTTTCTGG 59.056 55.000 0.00 0.00 0.00 3.86
362 444 7.308348 GGTCGTGTTTTCTGGATTTATTTCAGA 60.308 37.037 0.00 0.00 35.95 3.27
364 446 7.227711 TCGTGTTTTCTGGATTTATTTCAGACA 59.772 33.333 0.00 0.00 37.28 3.41
374 456 6.967199 GGATTTATTTCAGACATTTCGGTGAC 59.033 38.462 0.00 0.00 0.00 3.67
388 470 1.705256 GGTGACGTGTATTCAGCGAA 58.295 50.000 0.00 0.00 32.21 4.70
407 489 3.669824 CGAAAGGAGATGTTCTCGTCGAA 60.670 47.826 13.90 0.00 44.28 3.71
422 504 5.521372 TCTCGTCGAACTATGAAATCGTCTA 59.479 40.000 0.00 0.00 37.79 2.59
461 544 1.089920 AAATGATGTGTCGGCTCAGC 58.910 50.000 0.00 0.00 0.00 4.26
478 561 1.467734 CAGCCTCTCAAATGTGCTCAC 59.532 52.381 0.00 0.00 0.00 3.51
479 562 0.445436 GCCTCTCAAATGTGCTCACG 59.555 55.000 0.00 0.00 0.00 4.35
480 563 1.800805 CCTCTCAAATGTGCTCACGT 58.199 50.000 0.00 0.00 0.00 4.49
482 565 0.867746 TCTCAAATGTGCTCACGTGC 59.132 50.000 11.67 0.00 0.00 5.34
490 583 0.366871 GTGCTCACGTGCGTTCATAG 59.633 55.000 11.67 1.87 35.36 2.23
514 607 7.977818 AGGGATGAATGTGTATGTGTATGTAT 58.022 34.615 0.00 0.00 0.00 2.29
516 609 7.877612 GGGATGAATGTGTATGTGTATGTATGA 59.122 37.037 0.00 0.00 0.00 2.15
517 610 8.712363 GGATGAATGTGTATGTGTATGTATGAC 58.288 37.037 0.00 0.00 0.00 3.06
518 611 8.607441 ATGAATGTGTATGTGTATGTATGACC 57.393 34.615 0.00 0.00 0.00 4.02
526 619 2.028763 GTGTATGTATGACCGTTGCGTG 59.971 50.000 0.00 0.00 0.00 5.34
528 621 1.075542 ATGTATGACCGTTGCGTGTG 58.924 50.000 0.00 0.00 0.00 3.82
681 837 5.123227 TGTAACCCTTCTGTTTGTTCTCAG 58.877 41.667 0.00 0.00 0.00 3.35
707 863 0.531532 CAGCGGCTCAGATAACCCAG 60.532 60.000 0.00 0.00 0.00 4.45
727 883 0.885879 CCGCTCAAACCCTTAAACCC 59.114 55.000 0.00 0.00 0.00 4.11
728 884 1.546998 CCGCTCAAACCCTTAAACCCT 60.547 52.381 0.00 0.00 0.00 4.34
795 951 1.874299 AAATACCCCTGCCACCCCAG 61.874 60.000 0.00 0.00 0.00 4.45
826 982 3.612241 CGCGATGTATTCACGGGGTATAA 60.612 47.826 0.00 0.00 36.59 0.98
993 1153 1.949847 GCTCCCTGTTCTAGCGCAGA 61.950 60.000 11.47 7.90 34.87 4.26
1184 1344 0.171455 ACGGTCTGAGCTTCGATGTC 59.829 55.000 5.23 0.00 0.00 3.06
1215 1375 0.968901 TTGGGTCGCATCTCGTAGGT 60.969 55.000 0.00 0.00 39.67 3.08
1242 1402 8.697507 ATTTCTAGAATTTTTAGGATGCGGAT 57.302 30.769 5.89 0.00 0.00 4.18
1245 1405 6.931281 TCTAGAATTTTTAGGATGCGGATGAG 59.069 38.462 0.00 0.00 0.00 2.90
1259 1419 0.106819 GATGAGTGGCATCCAGGCTT 60.107 55.000 0.00 0.00 46.23 4.35
1288 1448 1.070309 CGGCTGCAGATTATTCTTCGC 60.070 52.381 20.43 0.00 0.00 4.70
1301 1461 2.966309 CTTCGCCCGTGGTTTCTGC 61.966 63.158 0.00 0.00 0.00 4.26
1330 1490 6.240882 GGGGGAATTCAGGGATTTATTCCTAT 60.241 42.308 7.93 0.00 44.75 2.57
1362 1523 1.692411 GAGTTGTGGGTTTTGCTCCT 58.308 50.000 0.00 0.00 0.00 3.69
1384 1545 6.100569 TCCTAATCGAGGTTGGATTTTGGATA 59.899 38.462 0.00 0.00 46.76 2.59
1394 1555 6.238648 GGTTGGATTTTGGATACGTCATAAGG 60.239 42.308 0.00 0.00 42.51 2.69
1464 1642 7.629157 TGATGGTCTATGAGTTATGTTTTCCA 58.371 34.615 0.00 0.00 0.00 3.53
1470 1648 8.443937 GTCTATGAGTTATGTTTTCCAAGTGTC 58.556 37.037 0.00 0.00 0.00 3.67
1583 1762 9.469807 CCTAACTTCTACTATTAGAATGCACAG 57.530 37.037 3.27 0.00 42.35 3.66
1626 2102 6.261826 CAGATTCCAGAATCCCAGTTTATCAC 59.738 42.308 15.16 0.00 46.28 3.06
1696 2172 9.850628 AAGAATATGATTTGAATGTTGTGTCAG 57.149 29.630 0.00 0.00 0.00 3.51
1706 2182 6.345298 TGAATGTTGTGTCAGTTAACTCTGA 58.655 36.000 4.77 0.00 41.40 3.27
1740 2216 7.385778 TGTTAGAAATTAACATGGCCTACAC 57.614 36.000 3.32 0.00 33.05 2.90
1808 2285 8.731275 ATTATCGTGTCTATGAACAATCCAAA 57.269 30.769 0.00 0.00 0.00 3.28
1810 2287 5.301555 TCGTGTCTATGAACAATCCAAACA 58.698 37.500 0.00 0.00 0.00 2.83
1985 2470 7.488187 CTGATGTAAATATGCAGCAACTACT 57.512 36.000 0.00 0.00 37.12 2.57
2103 2599 0.673985 CACTCCGTGACCTTCACTGA 59.326 55.000 4.87 2.96 44.85 3.41
2104 2600 3.802613 CTCCGTGACCTTCACTGAG 57.197 57.895 11.74 11.74 46.71 3.35
2105 2601 3.432262 TCCGTGACCTTCACTGAGA 57.568 52.632 4.87 0.00 44.85 3.27
2106 2602 1.248486 TCCGTGACCTTCACTGAGAG 58.752 55.000 4.87 0.00 44.85 3.20
2107 2603 1.202891 TCCGTGACCTTCACTGAGAGA 60.203 52.381 4.87 0.00 44.85 3.10
2109 2605 2.232452 CCGTGACCTTCACTGAGAGATT 59.768 50.000 4.87 0.00 44.85 2.40
2110 2606 3.306364 CCGTGACCTTCACTGAGAGATTT 60.306 47.826 4.87 0.00 44.85 2.17
2111 2607 3.923461 CGTGACCTTCACTGAGAGATTTC 59.077 47.826 4.87 0.00 44.85 2.17
2112 2608 4.559502 CGTGACCTTCACTGAGAGATTTCA 60.560 45.833 4.87 0.00 44.85 2.69
2113 2609 5.300752 GTGACCTTCACTGAGAGATTTCAA 58.699 41.667 0.00 0.00 43.73 2.69
2114 2610 5.760253 GTGACCTTCACTGAGAGATTTCAAA 59.240 40.000 0.00 0.00 43.73 2.69
2116 2612 6.429078 TGACCTTCACTGAGAGATTTCAAATG 59.571 38.462 0.00 0.00 0.00 2.32
2117 2613 5.709164 ACCTTCACTGAGAGATTTCAAATGG 59.291 40.000 0.00 0.00 0.00 3.16
2118 2614 5.942236 CCTTCACTGAGAGATTTCAAATGGA 59.058 40.000 0.00 0.00 0.00 3.41
2120 2616 6.119240 TCACTGAGAGATTTCAAATGGACT 57.881 37.500 0.00 0.00 0.00 3.85
2121 2617 7.244886 TCACTGAGAGATTTCAAATGGACTA 57.755 36.000 0.00 0.00 0.00 2.59
2123 2619 6.314896 CACTGAGAGATTTCAAATGGACTACC 59.685 42.308 0.00 0.00 0.00 3.18
2136 2632 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
2137 2633 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
2138 2634 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
2139 2635 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
2140 2636 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
2141 2637 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
2142 2638 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
2143 2639 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
2144 2640 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
2145 2641 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
2147 2643 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
2178 2674 7.036220 AGTGTAGATTCACTCATTTTACTCCG 58.964 38.462 0.00 0.00 44.07 4.63
2179 2675 6.812160 GTGTAGATTCACTCATTTTACTCCGT 59.188 38.462 0.00 0.00 35.68 4.69
2180 2676 7.972277 GTGTAGATTCACTCATTTTACTCCGTA 59.028 37.037 0.00 0.00 35.68 4.02
2181 2677 8.692710 TGTAGATTCACTCATTTTACTCCGTAT 58.307 33.333 0.00 0.00 0.00 3.06
2182 2678 8.969267 GTAGATTCACTCATTTTACTCCGTATG 58.031 37.037 0.00 0.00 0.00 2.39
2183 2679 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
2184 2680 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
2185 2681 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
2186 2682 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
2187 2683 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
2188 2684 7.121611 TCACTCATTTTACTCCGTATGTAGTCA 59.878 37.037 0.00 0.00 0.00 3.41
2189 2685 7.220300 CACTCATTTTACTCCGTATGTAGTCAC 59.780 40.741 0.00 0.00 0.00 3.67
2190 2686 7.122353 ACTCATTTTACTCCGTATGTAGTCACT 59.878 37.037 0.00 0.00 0.00 3.41
2191 2687 7.833786 TCATTTTACTCCGTATGTAGTCACTT 58.166 34.615 0.00 0.00 0.00 3.16
2192 2688 7.758076 TCATTTTACTCCGTATGTAGTCACTTG 59.242 37.037 0.00 0.00 0.00 3.16
2193 2689 6.579666 TTTACTCCGTATGTAGTCACTTGT 57.420 37.500 0.00 0.00 0.00 3.16
2194 2690 6.579666 TTACTCCGTATGTAGTCACTTGTT 57.420 37.500 0.00 0.00 0.00 2.83
2195 2691 4.806330 ACTCCGTATGTAGTCACTTGTTG 58.194 43.478 0.00 0.00 0.00 3.33
2196 2692 4.521639 ACTCCGTATGTAGTCACTTGTTGA 59.478 41.667 0.00 0.00 0.00 3.18
2197 2693 5.055642 TCCGTATGTAGTCACTTGTTGAG 57.944 43.478 0.00 0.00 33.71 3.02
2198 2694 4.763279 TCCGTATGTAGTCACTTGTTGAGA 59.237 41.667 0.00 0.00 33.71 3.27
2199 2695 5.417894 TCCGTATGTAGTCACTTGTTGAGAT 59.582 40.000 0.00 0.00 33.71 2.75
2200 2696 5.744345 CCGTATGTAGTCACTTGTTGAGATC 59.256 44.000 0.00 0.00 33.71 2.75
2201 2697 6.404844 CCGTATGTAGTCACTTGTTGAGATCT 60.405 42.308 0.00 0.00 33.71 2.75
2202 2698 6.689241 CGTATGTAGTCACTTGTTGAGATCTC 59.311 42.308 16.21 16.21 33.71 2.75
2203 2699 6.849085 ATGTAGTCACTTGTTGAGATCTCT 57.151 37.500 22.95 0.00 33.71 3.10
2204 2700 7.946381 ATGTAGTCACTTGTTGAGATCTCTA 57.054 36.000 22.95 13.48 33.71 2.43
2205 2701 7.384439 TGTAGTCACTTGTTGAGATCTCTAG 57.616 40.000 22.95 15.91 33.71 2.43
2206 2702 7.168905 TGTAGTCACTTGTTGAGATCTCTAGA 58.831 38.462 22.95 11.92 33.71 2.43
2207 2703 7.665974 TGTAGTCACTTGTTGAGATCTCTAGAA 59.334 37.037 22.95 18.26 33.71 2.10
2208 2704 7.531857 AGTCACTTGTTGAGATCTCTAGAAA 57.468 36.000 22.95 11.89 33.71 2.52
2209 2705 7.601856 AGTCACTTGTTGAGATCTCTAGAAAG 58.398 38.462 22.95 20.75 33.71 2.62
2210 2706 7.450014 AGTCACTTGTTGAGATCTCTAGAAAGA 59.550 37.037 24.08 18.10 33.71 2.52
2211 2707 7.540745 GTCACTTGTTGAGATCTCTAGAAAGAC 59.459 40.741 24.08 22.55 33.71 3.01
2212 2708 7.231519 TCACTTGTTGAGATCTCTAGAAAGACA 59.768 37.037 24.08 15.11 0.00 3.41
2213 2709 7.869937 CACTTGTTGAGATCTCTAGAAAGACAA 59.130 37.037 24.08 19.02 0.00 3.18
2214 2710 8.424918 ACTTGTTGAGATCTCTAGAAAGACAAA 58.575 33.333 24.08 8.07 0.00 2.83
2215 2711 9.434420 CTTGTTGAGATCTCTAGAAAGACAAAT 57.566 33.333 22.95 0.00 0.00 2.32
2227 2723 9.667107 TCTAGAAAGACAAATATTTAGGTGTGG 57.333 33.333 0.00 0.00 0.00 4.17
2228 2724 9.667107 CTAGAAAGACAAATATTTAGGTGTGGA 57.333 33.333 0.00 0.00 0.00 4.02
2229 2725 8.567285 AGAAAGACAAATATTTAGGTGTGGAG 57.433 34.615 0.00 0.00 0.00 3.86
2230 2726 7.611855 AGAAAGACAAATATTTAGGTGTGGAGG 59.388 37.037 0.00 0.00 0.00 4.30
2231 2727 5.755849 AGACAAATATTTAGGTGTGGAGGG 58.244 41.667 0.00 0.00 0.00 4.30
2232 2728 5.491078 AGACAAATATTTAGGTGTGGAGGGA 59.509 40.000 0.00 0.00 0.00 4.20
2233 2729 5.755849 ACAAATATTTAGGTGTGGAGGGAG 58.244 41.667 0.00 0.00 0.00 4.30
2234 2730 5.253096 ACAAATATTTAGGTGTGGAGGGAGT 59.747 40.000 0.00 0.00 0.00 3.85
2235 2731 6.445786 ACAAATATTTAGGTGTGGAGGGAGTA 59.554 38.462 0.00 0.00 0.00 2.59
2236 2732 7.037153 ACAAATATTTAGGTGTGGAGGGAGTAA 60.037 37.037 0.00 0.00 0.00 2.24
2237 2733 7.707467 AATATTTAGGTGTGGAGGGAGTAAT 57.293 36.000 0.00 0.00 0.00 1.89
2238 2734 7.707467 ATATTTAGGTGTGGAGGGAGTAATT 57.293 36.000 0.00 0.00 0.00 1.40
2239 2735 5.853572 TTTAGGTGTGGAGGGAGTAATTT 57.146 39.130 0.00 0.00 0.00 1.82
2468 3133 3.895232 TCACTTAATGGGAGACTCTGC 57.105 47.619 1.74 0.00 0.00 4.26
2538 3203 2.858745 TGGGCTGTTTCTGTTTCTACC 58.141 47.619 0.00 0.00 0.00 3.18
2681 3347 7.557719 CCTCAACAAAATGATAAGGAGGTACAT 59.442 37.037 0.00 0.00 36.72 2.29
2788 3454 4.040461 TGAAAGACTTAAGTCCCCAGTCTG 59.960 45.833 28.05 0.00 45.35 3.51
3003 3669 2.270275 AGCGTGAATCTGAGAACTCG 57.730 50.000 9.03 9.03 0.00 4.18
3355 4023 8.129840 GCATGCTATTCATCAGAATATGATTCC 58.870 37.037 11.37 0.00 46.97 3.01
3397 4065 6.321181 AGCTTTTCTGTACCTGAATTTTGTCA 59.679 34.615 0.00 0.00 0.00 3.58
3534 4204 4.240096 GAGTCGAAAGGTTTGATCCGTTA 58.760 43.478 0.00 0.00 30.06 3.18
3675 4345 6.983307 TGTGTATGTTTTTCCCTGTTCAATTG 59.017 34.615 0.00 0.00 0.00 2.32
3723 4393 7.882271 AGAGTTCTTGAGTTTGATCTATTGCTT 59.118 33.333 0.00 0.00 0.00 3.91
3787 4457 4.839121 AGGCTTGTTTTACGGACATATGA 58.161 39.130 10.38 0.00 0.00 2.15
3826 4496 1.252904 TACAGCCACACCGGACCTAC 61.253 60.000 9.46 0.00 36.56 3.18
3849 4519 6.049790 ACCCGTCTAGAAATATGCTCTTTTC 58.950 40.000 0.00 0.00 33.08 2.29
4232 4909 6.986817 CCATATTCCCTGCTTTACCTATATCG 59.013 42.308 0.00 0.00 0.00 2.92
4256 4933 9.378551 TCGCTATCTTAGAAACAATGTTGTATT 57.621 29.630 0.00 0.00 41.31 1.89
4268 4945 8.821686 AACAATGTTGTATTGATATCCTTCCA 57.178 30.769 0.00 0.00 41.31 3.53
4479 5163 4.996122 GCCAAATGTTTGATTCAACCATCA 59.004 37.500 9.53 3.39 40.55 3.07
4537 5221 3.057315 CCCTGTAGGTTGTTTGCTCAATG 60.057 47.826 0.00 0.00 0.00 2.82
4561 5245 1.028905 TTCACAGCCGTTCCCTTTTG 58.971 50.000 0.00 0.00 0.00 2.44
4579 5263 5.105351 CCTTTTGGACTTTGAAAACCAGTCT 60.105 40.000 4.28 0.00 44.07 3.24
4695 5379 3.165071 CTCAACCCTTTGGCCATTAAGT 58.835 45.455 6.09 0.00 33.06 2.24
4712 5396 7.567571 CCATTAAGTTCAGATAGTTACGCATG 58.432 38.462 0.00 0.00 0.00 4.06
4788 5472 3.904136 AAGAAACGAGGCATGAACTTG 57.096 42.857 0.00 0.00 0.00 3.16
4884 5569 4.764823 AGGACAAATGGAGCGTTTTGAATA 59.235 37.500 9.59 0.00 36.54 1.75
5079 5774 2.778299 GGCAAAATTCTGTTTTCCCCC 58.222 47.619 0.00 0.00 0.00 5.40
5218 5913 3.710677 CTGAGGAGAAATCAGGTGGAGAT 59.289 47.826 0.00 0.00 40.44 2.75
5287 5982 1.891060 GCTGTTCCTGCTTGACGACG 61.891 60.000 0.00 0.00 0.00 5.12
5388 6083 6.165577 GCTTGTTGAAATCCCATTTGTATGT 58.834 36.000 0.00 0.00 31.47 2.29
5420 6115 4.943705 CACACCATTCCTTAGCAGTACAAT 59.056 41.667 0.00 0.00 0.00 2.71
5438 6133 5.200368 ACAATGTTTCGGAGAATTTTGCT 57.800 34.783 0.00 0.00 45.90 3.91
5446 6141 2.356069 CGGAGAATTTTGCTAGGGCTTC 59.644 50.000 0.00 0.00 39.59 3.86
5448 6143 3.270877 GAGAATTTTGCTAGGGCTTCGA 58.729 45.455 0.00 0.00 39.59 3.71
5517 6212 5.669798 AGGGCATTCCTAATAATGTTCCT 57.330 39.130 0.00 0.00 45.98 3.36
5518 6213 6.030727 AGGGCATTCCTAATAATGTTCCTT 57.969 37.500 0.00 0.00 45.98 3.36
5519 6214 7.161715 AGGGCATTCCTAATAATGTTCCTTA 57.838 36.000 0.00 0.00 45.98 2.69
5520 6215 7.234355 AGGGCATTCCTAATAATGTTCCTTAG 58.766 38.462 0.00 0.00 45.98 2.18
5521 6216 6.071896 GGGCATTCCTAATAATGTTCCTTAGC 60.072 42.308 0.00 0.00 38.78 3.09
5522 6217 6.490040 GGCATTCCTAATAATGTTCCTTAGCA 59.510 38.462 0.00 0.00 38.78 3.49
5523 6218 7.308830 GGCATTCCTAATAATGTTCCTTAGCAG 60.309 40.741 0.00 0.00 38.78 4.24
5524 6219 7.229506 GCATTCCTAATAATGTTCCTTAGCAGT 59.770 37.037 0.00 0.00 38.78 4.40
5525 6220 9.778741 CATTCCTAATAATGTTCCTTAGCAGTA 57.221 33.333 0.00 0.00 33.11 2.74
5526 6221 9.780186 ATTCCTAATAATGTTCCTTAGCAGTAC 57.220 33.333 0.00 0.00 0.00 2.73
5527 6222 8.313944 TCCTAATAATGTTCCTTAGCAGTACA 57.686 34.615 0.00 0.00 0.00 2.90
5528 6223 8.764558 TCCTAATAATGTTCCTTAGCAGTACAA 58.235 33.333 0.00 0.00 0.00 2.41
5529 6224 9.561069 CCTAATAATGTTCCTTAGCAGTACAAT 57.439 33.333 0.00 0.00 0.00 2.71
5531 6226 8.807948 AATAATGTTCCTTAGCAGTACAATGT 57.192 30.769 0.00 0.00 0.00 2.71
5532 6227 8.807948 ATAATGTTCCTTAGCAGTACAATGTT 57.192 30.769 0.00 0.00 0.00 2.71
5566 6262 6.432403 AAAAGTGAATTAGGGCATTCCAAA 57.568 33.333 0.00 0.00 38.24 3.28
5567 6263 6.625532 AAAGTGAATTAGGGCATTCCAAAT 57.374 33.333 0.00 0.00 38.24 2.32
5590 6420 0.250770 GTCACCAAACAGACTCCCCC 60.251 60.000 0.00 0.00 0.00 5.40
5606 6436 1.241315 CCCCAAATGACCGTGGACAC 61.241 60.000 0.00 0.00 37.03 3.67
5784 8126 3.248266 GCCTGCAATGAGAACATCAAAC 58.752 45.455 0.00 0.00 42.53 2.93
5804 8146 3.550561 ACGTTGCGTTATGACATTTGTG 58.449 40.909 0.00 0.00 36.35 3.33
5856 8198 2.236766 CGTCGGTAGGGTGAAGGATAT 58.763 52.381 0.00 0.00 0.00 1.63
5861 8203 2.492196 GGTAGGGTGAAGGATATCCGGA 60.492 54.545 16.21 6.61 42.08 5.14
5928 8270 1.494721 GCATGGATTCTAGGGGGTTCA 59.505 52.381 0.00 0.00 0.00 3.18
5981 8324 2.336809 GAGCGGTATCTGGGAGCG 59.663 66.667 0.00 0.00 40.65 5.03
6007 8350 7.365473 GCAAATATAGAGCCAAGGAGGATAGAT 60.365 40.741 0.00 0.00 41.22 1.98
6056 8400 0.825840 CCGTTTTGGGTGGGACATGT 60.826 55.000 0.00 0.00 44.52 3.21
6083 8427 1.482593 GAGACCGACATGGAGGATGTT 59.517 52.381 14.54 0.00 45.90 2.71
6132 8476 1.304134 GGTCGGCCTGGTGGAATTT 60.304 57.895 0.00 0.00 34.57 1.82
6136 8480 0.897863 CGGCCTGGTGGAATTTGGAA 60.898 55.000 0.00 0.00 34.57 3.53
6145 8489 2.882137 GTGGAATTTGGAAGTTCGGACA 59.118 45.455 0.00 0.00 0.00 4.02
6171 8515 2.432510 CAACTTGTTTTGGTTAGCCCCA 59.567 45.455 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.009829 CTAGAACTGTTGATGGCCGC 58.990 55.000 0.00 0.00 0.00 6.53
1 2 2.386661 ACTAGAACTGTTGATGGCCG 57.613 50.000 0.00 0.00 0.00 6.13
30 31 0.899717 GGGCATTGAAGGGAGCAACA 60.900 55.000 0.00 0.00 0.00 3.33
48 49 1.003718 GTCTCACGGTTGAAGGGGG 60.004 63.158 0.00 0.00 0.00 5.40
95 96 6.639563 TGATTCTCCTGATACGAATTTCACA 58.360 36.000 0.00 0.00 0.00 3.58
97 98 6.203530 GCATGATTCTCCTGATACGAATTTCA 59.796 38.462 0.00 0.00 0.00 2.69
98 99 6.597614 GCATGATTCTCCTGATACGAATTTC 58.402 40.000 0.00 0.00 0.00 2.17
99 100 5.178252 CGCATGATTCTCCTGATACGAATTT 59.822 40.000 0.00 0.00 0.00 1.82
123 124 0.175073 CTACAACTAGGGGTGGCGTC 59.825 60.000 0.00 0.00 0.00 5.19
186 187 8.460428 GTTTTGTTTGGTTATATCCGGTAATGA 58.540 33.333 0.00 0.00 0.00 2.57
243 244 6.872628 TCTGGTAACGATACGAGAATACAT 57.127 37.500 13.77 0.00 41.93 2.29
253 254 7.261829 ACTATCTGAGTTCTGGTAACGATAC 57.738 40.000 0.00 0.00 33.13 2.24
256 257 6.318144 CCTAACTATCTGAGTTCTGGTAACGA 59.682 42.308 0.00 0.00 45.81 3.85
262 263 6.936279 TGAAACCTAACTATCTGAGTTCTGG 58.064 40.000 0.00 1.38 45.81 3.86
265 345 7.708752 CCAGATGAAACCTAACTATCTGAGTTC 59.291 40.741 12.63 0.00 45.81 3.01
302 382 3.246880 GGACCTGAACCCCGGTGT 61.247 66.667 0.00 0.00 32.62 4.16
315 395 2.554032 CACCAGTGTCAAATTCAGGACC 59.446 50.000 0.00 0.00 33.09 4.46
321 401 2.032030 CACGACCACCAGTGTCAAATTC 60.032 50.000 0.00 0.00 33.97 2.17
335 415 6.263392 TGAAATAAATCCAGAAAACACGACCA 59.737 34.615 0.00 0.00 0.00 4.02
350 432 6.682863 CGTCACCGAAATGTCTGAAATAAATC 59.317 38.462 0.00 0.00 35.63 2.17
362 444 3.655486 TGAATACACGTCACCGAAATGT 58.345 40.909 0.00 0.00 37.88 2.71
364 446 2.671396 GCTGAATACACGTCACCGAAAT 59.329 45.455 0.00 0.00 37.88 2.17
374 456 2.876091 TCTCCTTTCGCTGAATACACG 58.124 47.619 0.00 0.00 0.00 4.49
378 460 5.344743 AGAACATCTCCTTTCGCTGAATA 57.655 39.130 0.00 0.00 0.00 1.75
385 467 2.159558 TCGACGAGAACATCTCCTTTCG 60.160 50.000 0.00 11.52 40.34 3.46
407 489 4.037565 TGTCGCCATAGACGATTTCATAGT 59.962 41.667 0.00 0.00 43.70 2.12
415 497 2.558359 TGATGATGTCGCCATAGACGAT 59.442 45.455 0.00 0.00 43.70 3.73
416 498 1.953686 TGATGATGTCGCCATAGACGA 59.046 47.619 0.00 0.00 43.70 4.20
422 504 6.487668 TCATTTAAGATTGATGATGTCGCCAT 59.512 34.615 0.00 0.00 0.00 4.40
433 515 5.824624 AGCCGACACATCATTTAAGATTGAT 59.175 36.000 0.00 0.00 32.87 2.57
441 523 2.279741 GCTGAGCCGACACATCATTTA 58.720 47.619 0.00 0.00 0.00 1.40
461 544 1.462283 CACGTGAGCACATTTGAGAGG 59.538 52.381 10.90 0.00 0.00 3.69
478 561 1.934589 TTCATCCCTATGAACGCACG 58.065 50.000 0.00 0.00 45.17 5.34
490 583 7.877612 TCATACATACACATACACATTCATCCC 59.122 37.037 0.00 0.00 0.00 3.85
499 592 5.276678 GCAACGGTCATACATACACATACAC 60.277 44.000 0.00 0.00 0.00 2.90
501 594 4.085261 CGCAACGGTCATACATACACATAC 60.085 45.833 0.00 0.00 0.00 2.39
506 599 2.263945 CACGCAACGGTCATACATACA 58.736 47.619 0.00 0.00 0.00 2.29
514 607 1.669502 GGTATACACACGCAACGGTCA 60.670 52.381 5.01 0.00 0.00 4.02
516 609 0.733566 CGGTATACACACGCAACGGT 60.734 55.000 5.01 0.00 0.00 4.83
517 610 0.733566 ACGGTATACACACGCAACGG 60.734 55.000 5.01 0.00 0.00 4.44
518 611 0.364180 CACGGTATACACACGCAACG 59.636 55.000 5.01 0.00 0.00 4.10
639 795 3.650139 ACAGCTGACGTCGTATCTTTTT 58.350 40.909 23.35 0.00 0.00 1.94
681 837 0.179062 ATCTGAGCCGCTGACATTCC 60.179 55.000 0.00 0.00 0.00 3.01
707 863 0.242825 GGTTTAAGGGTTTGAGCGGC 59.757 55.000 0.00 0.00 0.00 6.53
795 951 0.249489 AATACATCGCGAGACAGGGC 60.249 55.000 16.66 0.00 46.97 5.19
806 962 3.916172 CGTTATACCCCGTGAATACATCG 59.084 47.826 0.00 0.00 0.00 3.84
826 982 0.527817 GGATCGAAGCGAATGACCGT 60.528 55.000 0.00 0.00 39.99 4.83
980 1136 0.172127 CTCTGCTCTGCGCTAGAACA 59.828 55.000 9.73 10.49 40.11 3.18
993 1153 2.818132 GCGGCTACCATCTCTGCT 59.182 61.111 0.00 0.00 0.00 4.24
1165 1325 0.171455 GACATCGAAGCTCAGACCGT 59.829 55.000 0.00 0.00 0.00 4.83
1170 1330 1.205655 TGGAAGGACATCGAAGCTCAG 59.794 52.381 0.00 0.00 0.00 3.35
1184 1344 0.951558 CGACCCAAAACACTGGAAGG 59.048 55.000 0.00 0.00 38.96 3.46
1215 1375 7.773224 TCCGCATCCTAAAAATTCTAGAAATCA 59.227 33.333 9.71 0.00 0.00 2.57
1242 1402 1.001764 CAAGCCTGGATGCCACTCA 60.002 57.895 0.00 0.00 0.00 3.41
1245 1405 2.036256 ACCAAGCCTGGATGCCAC 59.964 61.111 8.77 0.00 46.92 5.01
1259 1419 2.410322 ATCTGCAGCCGGAAACACCA 62.410 55.000 9.47 0.00 38.90 4.17
1288 1448 2.742372 CCGAGCAGAAACCACGGG 60.742 66.667 0.00 0.00 39.92 5.28
1330 1490 2.305928 CACAACTCCACCAACCATCAA 58.694 47.619 0.00 0.00 0.00 2.57
1362 1523 5.756347 CGTATCCAAAATCCAACCTCGATTA 59.244 40.000 0.00 0.00 29.78 1.75
1384 1545 4.402793 AGACTTAGCATGACCTTATGACGT 59.597 41.667 0.00 0.00 0.00 4.34
1394 1555 4.113354 CCGAAACCTAGACTTAGCATGAC 58.887 47.826 0.00 0.00 0.00 3.06
1464 1642 2.374170 AGGGTTTTATGGTCCGACACTT 59.626 45.455 0.00 0.00 0.00 3.16
1470 1648 2.500392 TCCAAGGGTTTTATGGTCCG 57.500 50.000 0.00 0.00 35.66 4.79
1596 1775 5.934781 ACTGGGATTCTGGAATCTGTATTC 58.065 41.667 18.80 5.32 44.90 1.75
1597 1776 5.983333 ACTGGGATTCTGGAATCTGTATT 57.017 39.130 18.80 2.73 44.90 1.89
1601 1780 6.261826 GTGATAAACTGGGATTCTGGAATCTG 59.738 42.308 18.80 13.11 44.90 2.90
1626 2102 3.517602 TGCAGGCATAAGTACAAGTACG 58.482 45.455 4.85 0.00 40.80 3.67
1696 2172 8.289618 TCTAACAATGCACAAATCAGAGTTAAC 58.710 33.333 0.00 0.00 0.00 2.01
1740 2216 9.166173 TGAAATTATGGACTCAGATTAGTTGTG 57.834 33.333 0.00 0.00 0.00 3.33
1808 2285 5.624159 TCATTCTTTCATCCTGTTGACTGT 58.376 37.500 0.00 0.00 0.00 3.55
1810 2287 6.349944 GCAATCATTCTTTCATCCTGTTGACT 60.350 38.462 0.00 0.00 0.00 3.41
1985 2470 9.844790 CAGATGAGCAGATTAAATTTGTTTGTA 57.155 29.630 0.00 0.00 0.00 2.41
2046 2542 6.954487 TGCTCTACCAAGATATAAGAACGA 57.046 37.500 0.00 0.00 0.00 3.85
2103 2599 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
2104 2600 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
2105 2601 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
2106 2602 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
2107 2603 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
2109 2605 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
2110 2606 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
2111 2607 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
2112 2608 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
2113 2609 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
2114 2610 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
2116 2612 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
2117 2613 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
2118 2614 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
2121 2617 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
2154 2650 6.812160 ACGGAGTAAAATGAGTGAATCTACAC 59.188 38.462 0.00 0.00 41.94 2.90
2155 2651 6.931838 ACGGAGTAAAATGAGTGAATCTACA 58.068 36.000 0.00 0.00 41.94 2.74
2171 2667 7.574404 CTCAACAAGTGACTACATACGGAGTAA 60.574 40.741 0.00 0.00 38.23 2.24
2172 2668 6.128090 CTCAACAAGTGACTACATACGGAGTA 60.128 42.308 0.00 0.00 38.79 2.59
2173 2669 5.335740 CTCAACAAGTGACTACATACGGAGT 60.336 44.000 0.00 0.00 36.91 3.85
2174 2670 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2175 2671 4.763279 TCTCAACAAGTGACTACATACGGA 59.237 41.667 0.00 0.00 31.13 4.69
2176 2672 5.055642 TCTCAACAAGTGACTACATACGG 57.944 43.478 0.00 0.00 31.13 4.02
2177 2673 6.556212 AGATCTCAACAAGTGACTACATACG 58.444 40.000 0.00 0.00 31.13 3.06
2178 2674 7.767261 AGAGATCTCAACAAGTGACTACATAC 58.233 38.462 24.39 0.00 31.13 2.39
2179 2675 7.946381 AGAGATCTCAACAAGTGACTACATA 57.054 36.000 24.39 0.00 31.13 2.29
2180 2676 6.849085 AGAGATCTCAACAAGTGACTACAT 57.151 37.500 24.39 0.00 31.13 2.29
2181 2677 7.168905 TCTAGAGATCTCAACAAGTGACTACA 58.831 38.462 24.39 0.00 31.13 2.74
2182 2678 7.618502 TCTAGAGATCTCAACAAGTGACTAC 57.381 40.000 24.39 0.00 31.13 2.73
2183 2679 8.637196 TTTCTAGAGATCTCAACAAGTGACTA 57.363 34.615 24.39 3.48 31.13 2.59
2184 2680 7.450014 TCTTTCTAGAGATCTCAACAAGTGACT 59.550 37.037 24.39 2.42 31.13 3.41
2185 2681 7.540745 GTCTTTCTAGAGATCTCAACAAGTGAC 59.459 40.741 24.39 17.50 31.13 3.67
2186 2682 7.231519 TGTCTTTCTAGAGATCTCAACAAGTGA 59.768 37.037 24.39 10.90 34.17 3.41
2187 2683 7.374272 TGTCTTTCTAGAGATCTCAACAAGTG 58.626 38.462 24.39 8.91 0.00 3.16
2188 2684 7.531857 TGTCTTTCTAGAGATCTCAACAAGT 57.468 36.000 24.39 5.35 0.00 3.16
2189 2685 8.824159 TTTGTCTTTCTAGAGATCTCAACAAG 57.176 34.615 24.39 18.07 0.00 3.16
2201 2697 9.667107 CCACACCTAAATATTTGTCTTTCTAGA 57.333 33.333 11.05 0.00 0.00 2.43
2202 2698 9.667107 TCCACACCTAAATATTTGTCTTTCTAG 57.333 33.333 11.05 0.00 0.00 2.43
2203 2699 9.667107 CTCCACACCTAAATATTTGTCTTTCTA 57.333 33.333 11.05 0.00 0.00 2.10
2204 2700 7.611855 CCTCCACACCTAAATATTTGTCTTTCT 59.388 37.037 11.05 0.00 0.00 2.52
2205 2701 7.148069 CCCTCCACACCTAAATATTTGTCTTTC 60.148 40.741 11.05 0.00 0.00 2.62
2206 2702 6.663523 CCCTCCACACCTAAATATTTGTCTTT 59.336 38.462 11.05 0.00 0.00 2.52
2207 2703 6.011981 TCCCTCCACACCTAAATATTTGTCTT 60.012 38.462 11.05 0.00 0.00 3.01
2208 2704 5.491078 TCCCTCCACACCTAAATATTTGTCT 59.509 40.000 11.05 0.00 0.00 3.41
2209 2705 5.751586 TCCCTCCACACCTAAATATTTGTC 58.248 41.667 11.05 0.00 0.00 3.18
2210 2706 5.253096 ACTCCCTCCACACCTAAATATTTGT 59.747 40.000 11.05 0.00 0.00 2.83
2211 2707 5.755849 ACTCCCTCCACACCTAAATATTTG 58.244 41.667 11.05 0.00 0.00 2.32
2212 2708 7.519347 TTACTCCCTCCACACCTAAATATTT 57.481 36.000 5.89 5.89 0.00 1.40
2213 2709 7.707467 ATTACTCCCTCCACACCTAAATATT 57.293 36.000 0.00 0.00 0.00 1.28
2214 2710 7.707467 AATTACTCCCTCCACACCTAAATAT 57.293 36.000 0.00 0.00 0.00 1.28
2215 2711 7.519347 AAATTACTCCCTCCACACCTAAATA 57.481 36.000 0.00 0.00 0.00 1.40
2216 2712 6.402981 AAATTACTCCCTCCACACCTAAAT 57.597 37.500 0.00 0.00 0.00 1.40
2217 2713 5.853572 AAATTACTCCCTCCACACCTAAA 57.146 39.130 0.00 0.00 0.00 1.85
2218 2714 6.956102 TTAAATTACTCCCTCCACACCTAA 57.044 37.500 0.00 0.00 0.00 2.69
2219 2715 6.674861 TCATTAAATTACTCCCTCCACACCTA 59.325 38.462 0.00 0.00 0.00 3.08
2220 2716 5.491078 TCATTAAATTACTCCCTCCACACCT 59.509 40.000 0.00 0.00 0.00 4.00
2221 2717 5.751586 TCATTAAATTACTCCCTCCACACC 58.248 41.667 0.00 0.00 0.00 4.16
2222 2718 6.202954 CGATCATTAAATTACTCCCTCCACAC 59.797 42.308 0.00 0.00 0.00 3.82
2223 2719 6.099125 TCGATCATTAAATTACTCCCTCCACA 59.901 38.462 0.00 0.00 0.00 4.17
2224 2720 6.522054 TCGATCATTAAATTACTCCCTCCAC 58.478 40.000 0.00 0.00 0.00 4.02
2225 2721 6.740944 TCGATCATTAAATTACTCCCTCCA 57.259 37.500 0.00 0.00 0.00 3.86
2226 2722 8.622948 ATTTCGATCATTAAATTACTCCCTCC 57.377 34.615 0.00 0.00 0.00 4.30
2227 2723 8.722394 GGATTTCGATCATTAAATTACTCCCTC 58.278 37.037 0.00 0.00 0.00 4.30
2228 2724 8.440771 AGGATTTCGATCATTAAATTACTCCCT 58.559 33.333 0.00 0.00 0.00 4.20
2229 2725 8.622948 AGGATTTCGATCATTAAATTACTCCC 57.377 34.615 0.00 0.00 0.00 4.30
2468 3133 7.548196 TCAGGCGTTATCTAAACCAAATTAG 57.452 36.000 0.00 0.00 34.79 1.73
2681 3347 2.243736 ACTTTCCTGGTCTTTGGGTTCA 59.756 45.455 0.00 0.00 0.00 3.18
2788 3454 5.582665 GTCATTTAGTTCATCACCTCCTGAC 59.417 44.000 0.00 0.00 0.00 3.51
3107 3775 8.912658 CGATTAAGACGCTATAAGAAATAGCAA 58.087 33.333 15.22 4.22 45.32 3.91
3108 3776 8.080417 ACGATTAAGACGCTATAAGAAATAGCA 58.920 33.333 15.22 0.00 45.32 3.49
3355 4023 2.268298 AGCTACAATACGCAGGAAACG 58.732 47.619 0.00 0.00 0.00 3.60
3534 4204 7.500227 TGCTTATCAGGATCGAATTTCTCATTT 59.500 33.333 0.00 0.00 0.00 2.32
3651 4321 7.206687 TCAATTGAACAGGGAAAAACATACAC 58.793 34.615 5.45 0.00 0.00 2.90
3675 4345 9.232473 ACTCTAAGAACCAACCATTTTAGATTC 57.768 33.333 0.00 0.00 0.00 2.52
3826 4496 6.284459 AGAAAAGAGCATATTTCTAGACGGG 58.716 40.000 8.36 0.00 42.47 5.28
3849 4519 5.695363 CAGCATGACCATCTACAATGAGTAG 59.305 44.000 0.00 0.00 45.42 2.57
4256 4933 4.111577 ACTGGGAAGTTGGAAGGATATCA 58.888 43.478 4.83 0.00 0.00 2.15
4268 4945 2.635427 GTCAAGGAGAGACTGGGAAGTT 59.365 50.000 0.00 0.00 33.29 2.66
4463 5147 5.409214 CCCACAATTGATGGTTGAATCAAAC 59.591 40.000 13.59 3.69 46.66 2.93
4479 5163 1.575419 TCGCTACCCTACCCACAATT 58.425 50.000 0.00 0.00 0.00 2.32
4537 5221 2.919228 AGGGAACGGCTGTGAATATTC 58.081 47.619 8.60 8.60 0.00 1.75
4561 5245 4.983671 AACAGACTGGTTTTCAAAGTCC 57.016 40.909 7.51 0.00 41.02 3.85
4610 5294 0.685097 TAGGTGCACAGGGAGTTCAC 59.315 55.000 20.43 0.00 42.63 3.18
4618 5302 1.098050 GAAAGCCATAGGTGCACAGG 58.902 55.000 20.43 15.04 0.00 4.00
4695 5379 2.484770 GCCCCATGCGTAACTATCTGAA 60.485 50.000 0.00 0.00 0.00 3.02
4712 5396 1.209747 AGTGAGACGGATAAAAGCCCC 59.790 52.381 0.00 0.00 0.00 5.80
4884 5569 3.503365 AGCTGCCCACATAAATATGCAT 58.497 40.909 3.79 3.79 37.19 3.96
5079 5774 4.463515 CAGGAAATCATGCATACGTCAG 57.536 45.455 0.00 0.00 0.00 3.51
5287 5982 1.065928 CGCTGATGAGGTACCGGTC 59.934 63.158 12.40 2.31 0.00 4.79
5420 6115 3.756434 CCCTAGCAAAATTCTCCGAAACA 59.244 43.478 0.00 0.00 0.00 2.83
5438 6133 5.895534 TCTTATTAAGGTCTTCGAAGCCCTA 59.104 40.000 26.87 13.79 0.00 3.53
5494 6189 6.780198 AGGAACATTATTAGGAATGCCCTA 57.220 37.500 8.18 0.00 45.48 3.53
5496 6191 6.071896 GCTAAGGAACATTATTAGGAATGCCC 60.072 42.308 0.00 0.00 39.94 5.36
5497 6192 6.490040 TGCTAAGGAACATTATTAGGAATGCC 59.510 38.462 0.00 0.00 39.94 4.40
5498 6193 7.229506 ACTGCTAAGGAACATTATTAGGAATGC 59.770 37.037 0.00 0.00 39.94 3.56
5499 6194 8.682936 ACTGCTAAGGAACATTATTAGGAATG 57.317 34.615 0.00 0.00 41.69 2.67
5500 6195 9.780186 GTACTGCTAAGGAACATTATTAGGAAT 57.220 33.333 0.00 0.00 0.00 3.01
5501 6196 8.764558 TGTACTGCTAAGGAACATTATTAGGAA 58.235 33.333 0.00 0.00 0.00 3.36
5502 6197 8.313944 TGTACTGCTAAGGAACATTATTAGGA 57.686 34.615 0.00 0.00 0.00 2.94
5503 6198 8.958119 TTGTACTGCTAAGGAACATTATTAGG 57.042 34.615 0.00 0.00 0.00 2.69
5505 6200 9.899661 ACATTGTACTGCTAAGGAACATTATTA 57.100 29.630 0.00 0.00 0.00 0.98
5506 6201 8.807948 ACATTGTACTGCTAAGGAACATTATT 57.192 30.769 0.00 0.00 0.00 1.40
5507 6202 8.807948 AACATTGTACTGCTAAGGAACATTAT 57.192 30.769 0.00 0.00 0.00 1.28
5508 6203 8.630054 AAACATTGTACTGCTAAGGAACATTA 57.370 30.769 0.00 0.00 0.00 1.90
5509 6204 7.448469 AGAAACATTGTACTGCTAAGGAACATT 59.552 33.333 0.00 0.00 0.00 2.71
5510 6205 6.942576 AGAAACATTGTACTGCTAAGGAACAT 59.057 34.615 0.00 0.00 0.00 2.71
5511 6206 6.296026 AGAAACATTGTACTGCTAAGGAACA 58.704 36.000 0.00 0.00 0.00 3.18
5512 6207 6.651225 AGAGAAACATTGTACTGCTAAGGAAC 59.349 38.462 0.00 0.00 0.00 3.62
5513 6208 6.769512 AGAGAAACATTGTACTGCTAAGGAA 58.230 36.000 0.00 0.00 0.00 3.36
5514 6209 6.360370 AGAGAAACATTGTACTGCTAAGGA 57.640 37.500 0.00 0.00 0.00 3.36
5515 6210 6.650807 TCAAGAGAAACATTGTACTGCTAAGG 59.349 38.462 0.00 0.00 0.00 2.69
5516 6211 7.658179 TCAAGAGAAACATTGTACTGCTAAG 57.342 36.000 0.00 0.00 0.00 2.18
5517 6212 8.445275 TTTCAAGAGAAACATTGTACTGCTAA 57.555 30.769 0.00 0.00 38.76 3.09
5518 6213 8.445275 TTTTCAAGAGAAACATTGTACTGCTA 57.555 30.769 0.00 0.00 43.09 3.49
5519 6214 6.942532 TTTCAAGAGAAACATTGTACTGCT 57.057 33.333 0.00 0.00 38.76 4.24
5520 6215 7.985634 TTTTTCAAGAGAAACATTGTACTGC 57.014 32.000 0.00 0.00 43.09 4.40
5566 6262 4.506802 GGGGAGTCTGTTTGGTGACTTAAT 60.507 45.833 0.00 0.00 42.79 1.40
5567 6263 3.181448 GGGGAGTCTGTTTGGTGACTTAA 60.181 47.826 0.00 0.00 42.79 1.85
5590 6420 0.874390 CAGGTGTCCACGGTCATTTG 59.126 55.000 0.00 0.00 0.00 2.32
5606 6436 1.898574 GTCATTATGCCCGGCCAGG 60.899 63.158 7.03 0.29 40.63 4.45
5735 6572 2.068519 CTGCGTGCAACTAGAACATGA 58.931 47.619 0.00 0.00 31.75 3.07
5784 8126 2.338228 GCACAAATGTCATAACGCAACG 59.662 45.455 0.00 0.00 0.00 4.10
5804 8146 1.274798 CGCACCCGACAAATGTTTGC 61.275 55.000 5.44 0.00 41.79 3.68
5847 8189 0.949397 CGTCGTCCGGATATCCTTCA 59.051 55.000 19.61 0.21 0.00 3.02
5856 8198 0.169672 GAATTCAGTCGTCGTCCGGA 59.830 55.000 0.00 0.00 37.11 5.14
5861 8203 0.389948 GCCCTGAATTCAGTCGTCGT 60.390 55.000 29.03 0.00 42.27 4.34
5891 8233 2.713967 GCATGCCTTGCCGGATGTT 61.714 57.895 5.05 0.00 46.15 2.71
5914 8256 1.566231 CCTTGCTGAACCCCCTAGAAT 59.434 52.381 0.00 0.00 0.00 2.40
5964 8306 2.336809 CGCTCCCAGATACCGCTC 59.663 66.667 0.00 0.00 0.00 5.03
5971 8313 3.618507 GCTCTATATTTGCGCTCCCAGAT 60.619 47.826 9.73 0.00 0.00 2.90
5974 8316 1.270839 GGCTCTATATTTGCGCTCCCA 60.271 52.381 9.73 0.00 0.00 4.37
5975 8317 1.270839 TGGCTCTATATTTGCGCTCCC 60.271 52.381 9.73 0.00 0.00 4.30
5981 8324 4.357918 TCCTCCTTGGCTCTATATTTGC 57.642 45.455 0.00 0.00 35.26 3.68
6022 8366 1.802553 AACGGTACTGGAGCCCATAT 58.197 50.000 6.65 0.00 30.82 1.78
6023 8367 1.575419 AAACGGTACTGGAGCCCATA 58.425 50.000 6.65 0.00 30.82 2.74
6024 8368 0.696501 AAAACGGTACTGGAGCCCAT 59.303 50.000 6.65 0.00 30.82 4.00
6038 8382 0.313672 CACATGTCCCACCCAAAACG 59.686 55.000 0.00 0.00 0.00 3.60
6083 8427 0.106619 GGAGCTCTAAGGGAGTCCGA 60.107 60.000 14.64 0.00 43.62 4.55
6171 8515 3.068590 CCAAACACTTTGAGCACTCCAAT 59.931 43.478 0.00 0.00 43.26 3.16


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

AutoCloner maintained by Alex Coulton.