Multiple sequence alignment - TraesCS1D01G428600

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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 TraesCS1D01G428600 chr1D 100.000 2900 0 0 1 2900 480762212 480759313 0.000000e+00 5356.0
1 TraesCS1D01G428600 chr1A 92.853 1651 87 18 466 2097 577276440 577274802 0.000000e+00 2366.0
2 TraesCS1D01G428600 chr1A 88.975 517 35 10 2390 2900 577273664 577273164 1.140000e-173 619.0
3 TraesCS1D01G428600 chr1A 85.106 188 16 6 66 246 577276864 577276682 6.380000e-42 182.0
4 TraesCS1D01G428600 chr1A 98.246 57 1 0 1 57 577276956 577276900 1.840000e-17 100.0
5 TraesCS1D01G428600 chr1B 90.377 1829 123 28 289 2092 669024117 669022317 0.000000e+00 2353.0
6 TraesCS1D01G428600 chr1B 92.857 126 8 1 2091 2215 669022283 669022158 6.380000e-42 182.0
7 TraesCS1D01G428600 chr1B 81.513 119 12 7 76 190 669024235 669024123 3.980000e-14 89.8
8 TraesCS1D01G428600 chrUn 85.830 247 28 7 2588 2832 135321360 135321601 3.710000e-64 255.0
9 TraesCS1D01G428600 chrUn 85.830 247 28 7 2588 2832 135354514 135354755 3.710000e-64 255.0
10 TraesCS1D01G428600 chrUn 85.830 247 28 7 2588 2832 239421966 239422207 3.710000e-64 255.0
11 TraesCS1D01G428600 chrUn 85.830 247 28 7 2588 2832 245489001 245489242 3.710000e-64 255.0
12 TraesCS1D01G428600 chrUn 85.830 247 28 7 2588 2832 367976957 367976716 3.710000e-64 255.0
13 TraesCS1D01G428600 chrUn 85.425 247 29 7 2588 2832 91000486 91000245 1.730000e-62 250.0
14 TraesCS1D01G428600 chrUn 85.425 247 29 7 2588 2832 91056893 91056652 1.730000e-62 250.0
15 TraesCS1D01G428600 chrUn 85.020 247 29 8 2588 2832 91107720 91107480 8.030000e-61 244.0
16 TraesCS1D01G428600 chr6D 91.837 49 0 3 360 405 25766525 25766572 6.710000e-07 65.8
17 TraesCS1D01G428600 chr6A 91.837 49 1 1 361 406 579814346 579814394 6.710000e-07 65.8
18 TraesCS1D01G428600 chr6B 93.333 45 0 1 360 401 14353814 14353770 2.410000e-06 63.9
19 TraesCS1D01G428600 chr6B 91.489 47 0 2 360 403 705385850 705385805 8.680000e-06 62.1
20 TraesCS1D01G428600 chr5B 93.333 45 0 1 360 401 383210916 383210872 2.410000e-06 63.9
21 TraesCS1D01G428600 chr2B 93.333 45 0 1 360 401 127141846 127141890 2.410000e-06 63.9
22 TraesCS1D01G428600 chr2A 93.333 45 0 1 360 401 758293717 758293673 2.410000e-06 63.9
23 TraesCS1D01G428600 chr2A 90.196 51 0 3 360 406 611312119 611312070 8.680000e-06 62.1
24 TraesCS1D01G428600 chr7A 90.000 50 2 1 360 406 309275452 309275403 8.680000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G428600 chr1D 480759313 480762212 2899 True 5356.000000 5356 100.000 1 2900 1 chr1D.!!$R1 2899
1 TraesCS1D01G428600 chr1A 577273164 577276956 3792 True 816.750000 2366 91.295 1 2900 4 chr1A.!!$R1 2899
2 TraesCS1D01G428600 chr1B 669022158 669024235 2077 True 874.933333 2353 88.249 76 2215 3 chr1B.!!$R1 2139

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
108 136 0.032912 TGGAGCCCATGCAATCATGT 60.033 50.0 0.0 0.0 46.64 3.21 F
978 1107 0.179103 GCTCCTGCTCTTCTCTGCTC 60.179 60.0 0.0 0.0 36.03 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1090 1222 1.442148 GGGACGGTGATACAGAGGC 59.558 63.158 0.00 0.0 0.0 4.70 R
2800 3845 0.380024 CACACGTGTGGCATGAACAA 59.620 50.000 35.65 0.0 42.1 2.83 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
57 58 1.139734 CCGAGACACATGGGACGAG 59.860 63.158 0.00 0.00 0.00 4.18
58 59 1.595993 CCGAGACACATGGGACGAGT 61.596 60.000 0.00 0.00 0.00 4.18
59 60 1.092348 CGAGACACATGGGACGAGTA 58.908 55.000 0.00 0.00 0.00 2.59
61 62 2.093106 GAGACACATGGGACGAGTAGT 58.907 52.381 0.00 0.00 0.00 2.73
62 63 3.276857 GAGACACATGGGACGAGTAGTA 58.723 50.000 0.00 0.00 0.00 1.82
63 64 3.884091 GAGACACATGGGACGAGTAGTAT 59.116 47.826 0.00 0.00 0.00 2.12
64 65 4.279145 AGACACATGGGACGAGTAGTATT 58.721 43.478 0.00 0.00 0.00 1.89
74 102 1.961394 CGAGTAGTATTAGGCTGGGCA 59.039 52.381 0.00 0.00 0.00 5.36
108 136 0.032912 TGGAGCCCATGCAATCATGT 60.033 50.000 0.00 0.00 46.64 3.21
109 137 0.672342 GGAGCCCATGCAATCATGTC 59.328 55.000 0.00 0.00 46.64 3.06
110 138 1.395635 GAGCCCATGCAATCATGTCA 58.604 50.000 0.00 0.00 46.64 3.58
111 139 1.961394 GAGCCCATGCAATCATGTCAT 59.039 47.619 0.00 0.00 46.64 3.06
112 140 1.686587 AGCCCATGCAATCATGTCATG 59.313 47.619 6.47 6.47 46.64 3.07
138 174 8.824781 GCTAATCAACTGGATATACATGCATAG 58.175 37.037 0.00 0.00 34.28 2.23
142 178 6.498303 TCAACTGGATATACATGCATAGTCCT 59.502 38.462 0.00 0.00 31.41 3.85
143 179 7.673926 TCAACTGGATATACATGCATAGTCCTA 59.326 37.037 0.00 0.00 31.41 2.94
144 180 7.652524 ACTGGATATACATGCATAGTCCTAG 57.347 40.000 0.00 6.06 31.41 3.02
186 222 4.161189 TGAAGATCTACTCCAGCTCCTTTG 59.839 45.833 0.00 0.00 0.00 2.77
196 232 5.428131 ACTCCAGCTCCTTTGAAGATCTTAT 59.572 40.000 8.25 0.00 0.00 1.73
204 240 7.452880 TCCTTTGAAGATCTTATGTTTGGTG 57.547 36.000 8.25 0.00 0.00 4.17
215 255 7.517614 TCTTATGTTTGGTGTATGCTTTTGA 57.482 32.000 0.00 0.00 0.00 2.69
228 268 7.012327 GTGTATGCTTTTGATTAGCCAGTATGA 59.988 37.037 0.00 0.00 37.85 2.15
231 271 4.261363 GCTTTTGATTAGCCAGTATGAGCC 60.261 45.833 0.00 0.00 39.69 4.70
236 276 2.159179 TAGCCAGTATGAGCCTGTCA 57.841 50.000 0.00 0.00 39.69 3.58
248 355 2.613133 GAGCCTGTCAAATGATGCTCTC 59.387 50.000 17.79 7.27 38.67 3.20
260 367 3.849911 TGATGCTCTCGTTGGTTTCTAG 58.150 45.455 0.00 0.00 0.00 2.43
263 370 5.127194 TGATGCTCTCGTTGGTTTCTAGTAT 59.873 40.000 0.00 0.00 0.00 2.12
267 377 6.810182 TGCTCTCGTTGGTTTCTAGTATTAAC 59.190 38.462 0.00 0.00 0.00 2.01
270 380 8.114331 TCTCGTTGGTTTCTAGTATTAACTGA 57.886 34.615 0.00 0.00 36.36 3.41
286 396 0.396278 CTGAAATTGGAGGAGGCCCC 60.396 60.000 0.00 0.00 0.00 5.80
302 412 3.832490 AGGCCCCTGTAATTTTCTCAAAC 59.168 43.478 0.00 0.00 0.00 2.93
307 417 6.202762 GCCCCTGTAATTTTCTCAAACAAAAG 59.797 38.462 0.00 0.00 0.00 2.27
351 461 8.880878 TCAAACTTAATTAAAGAAACCTTGCC 57.119 30.769 0.00 0.00 38.67 4.52
359 469 1.154035 GAAACCTTGCCGGCAATCG 60.154 57.895 40.03 32.34 35.20 3.34
361 471 1.460273 AAACCTTGCCGGCAATCGTT 61.460 50.000 40.03 35.83 35.20 3.85
362 472 0.606944 AACCTTGCCGGCAATCGTTA 60.607 50.000 40.03 19.29 35.20 3.18
363 473 0.606944 ACCTTGCCGGCAATCGTTAA 60.607 50.000 40.03 18.50 35.20 2.01
365 475 1.944024 CCTTGCCGGCAATCGTTAATA 59.056 47.619 40.03 16.90 35.20 0.98
366 476 2.286772 CCTTGCCGGCAATCGTTAATAC 60.287 50.000 40.03 0.46 35.20 1.89
367 477 2.025589 TGCCGGCAATCGTTAATACA 57.974 45.000 30.74 0.00 37.11 2.29
368 478 2.357075 TGCCGGCAATCGTTAATACAA 58.643 42.857 30.74 0.00 37.11 2.41
369 479 2.747989 TGCCGGCAATCGTTAATACAAA 59.252 40.909 30.74 0.00 37.11 2.83
370 480 3.181505 TGCCGGCAATCGTTAATACAAAG 60.182 43.478 30.74 0.00 37.11 2.77
371 481 3.181504 GCCGGCAATCGTTAATACAAAGT 60.182 43.478 24.80 0.00 37.11 2.66
372 482 4.673320 GCCGGCAATCGTTAATACAAAGTT 60.673 41.667 24.80 0.00 37.11 2.66
373 483 4.791163 CCGGCAATCGTTAATACAAAGTTG 59.209 41.667 0.00 0.00 37.11 3.16
374 484 4.791163 CGGCAATCGTTAATACAAAGTTGG 59.209 41.667 0.00 0.00 0.00 3.77
375 485 5.099575 GGCAATCGTTAATACAAAGTTGGG 58.900 41.667 0.00 0.00 0.00 4.12
376 486 5.336134 GGCAATCGTTAATACAAAGTTGGGT 60.336 40.000 0.00 0.00 0.00 4.51
377 487 5.798434 GCAATCGTTAATACAAAGTTGGGTC 59.202 40.000 0.00 0.00 0.00 4.46
380 490 6.730960 TCGTTAATACAAAGTTGGGTCATC 57.269 37.500 0.00 0.00 0.00 2.92
381 491 6.469410 TCGTTAATACAAAGTTGGGTCATCT 58.531 36.000 0.00 0.00 0.00 2.90
382 492 7.613585 TCGTTAATACAAAGTTGGGTCATCTA 58.386 34.615 0.00 0.00 0.00 1.98
383 493 8.262227 TCGTTAATACAAAGTTGGGTCATCTAT 58.738 33.333 0.00 0.00 0.00 1.98
384 494 8.889717 CGTTAATACAAAGTTGGGTCATCTATT 58.110 33.333 0.00 0.00 0.00 1.73
389 499 7.141100 ACAAAGTTGGGTCATCTATTTTACG 57.859 36.000 0.00 0.00 0.00 3.18
390 500 6.150474 ACAAAGTTGGGTCATCTATTTTACGG 59.850 38.462 0.00 0.00 0.00 4.02
393 503 4.682778 TGGGTCATCTATTTTACGGAGG 57.317 45.455 0.00 0.00 0.00 4.30
394 504 3.389983 TGGGTCATCTATTTTACGGAGGG 59.610 47.826 0.00 0.00 0.00 4.30
396 506 4.262506 GGGTCATCTATTTTACGGAGGGAG 60.263 50.000 0.00 0.00 0.00 4.30
397 507 4.344390 GGTCATCTATTTTACGGAGGGAGT 59.656 45.833 0.00 0.00 0.00 3.85
399 509 6.445475 GTCATCTATTTTACGGAGGGAGTAC 58.555 44.000 0.00 0.00 0.00 2.73
400 510 5.240183 TCATCTATTTTACGGAGGGAGTACG 59.760 44.000 0.00 0.00 0.00 3.67
403 513 5.829924 TCTATTTTACGGAGGGAGTACGATT 59.170 40.000 0.00 0.00 0.00 3.34
404 514 4.806640 TTTTACGGAGGGAGTACGATTT 57.193 40.909 0.00 0.00 0.00 2.17
405 515 5.913137 TTTTACGGAGGGAGTACGATTTA 57.087 39.130 0.00 0.00 0.00 1.40
406 516 4.900635 TTACGGAGGGAGTACGATTTAC 57.099 45.455 0.00 0.00 0.00 2.01
408 518 1.942657 CGGAGGGAGTACGATTTACGA 59.057 52.381 0.00 0.00 45.77 3.43
435 545 5.111989 TGAGCCAAGAATCTTATTGAGACG 58.888 41.667 0.00 0.00 37.17 4.18
456 573 0.328592 TCGCTGAGGACTAGTCACCT 59.671 55.000 23.91 13.79 39.41 4.00
459 576 1.474879 GCTGAGGACTAGTCACCTGAC 59.525 57.143 23.91 5.87 45.08 3.51
508 627 1.065551 GATGCAATGGCCGGTAGTTTC 59.934 52.381 1.90 0.00 40.13 2.78
546 665 1.033574 CGGTCCAGATACTCCACTCC 58.966 60.000 0.00 0.00 0.00 3.85
550 669 2.691011 GTCCAGATACTCCACTCCACTC 59.309 54.545 0.00 0.00 0.00 3.51
552 671 3.099905 CCAGATACTCCACTCCACTCAA 58.900 50.000 0.00 0.00 0.00 3.02
564 683 4.686554 CACTCCACTCAACTACTTACTTGC 59.313 45.833 0.00 0.00 0.00 4.01
573 692 4.803098 ACTACTTACTTGCCTTCACGAT 57.197 40.909 0.00 0.00 0.00 3.73
620 740 1.694150 AGCCTGGACGCATACATGTAT 59.306 47.619 12.75 12.75 0.00 2.29
621 741 2.897326 AGCCTGGACGCATACATGTATA 59.103 45.455 17.86 1.03 0.00 1.47
622 742 3.323691 AGCCTGGACGCATACATGTATAA 59.676 43.478 17.86 0.00 0.00 0.98
624 744 4.627058 CCTGGACGCATACATGTATAACA 58.373 43.478 17.86 11.15 0.00 2.41
626 746 5.700832 CCTGGACGCATACATGTATAACAAT 59.299 40.000 17.86 5.08 0.00 2.71
627 747 6.204688 CCTGGACGCATACATGTATAACAATT 59.795 38.462 17.86 0.36 0.00 2.32
631 751 7.738609 GGACGCATACATGTATAACAATTAACG 59.261 37.037 17.86 11.98 0.00 3.18
651 771 2.351738 CGAGACCAAGATTTTTGCCACC 60.352 50.000 0.00 0.00 0.00 4.61
654 774 3.070015 AGACCAAGATTTTTGCCACCAAG 59.930 43.478 0.00 0.00 31.52 3.61
656 776 2.485124 CCAAGATTTTTGCCACCAAGCA 60.485 45.455 0.00 0.00 42.17 3.91
681 801 3.550678 GGAATCGACACGGACAGATTAAC 59.449 47.826 0.00 0.00 33.95 2.01
700 820 1.408340 ACTCTGACATCGATCTGCTGG 59.592 52.381 0.00 0.00 0.00 4.85
701 821 1.408340 CTCTGACATCGATCTGCTGGT 59.592 52.381 0.00 0.00 0.00 4.00
937 1062 1.856539 ATCCCAACCTCCACTGCCTG 61.857 60.000 0.00 0.00 0.00 4.85
978 1107 0.179103 GCTCCTGCTCTTCTCTGCTC 60.179 60.000 0.00 0.00 36.03 4.26
985 1114 1.024271 CTCTTCTCTGCTCTCTCCGG 58.976 60.000 0.00 0.00 0.00 5.14
987 1116 2.015227 CTTCTCTGCTCTCTCCGGCC 62.015 65.000 0.00 0.00 0.00 6.13
988 1117 2.441901 CTCTGCTCTCTCCGGCCT 60.442 66.667 0.00 0.00 0.00 5.19
989 1118 2.757508 TCTGCTCTCTCCGGCCTG 60.758 66.667 0.00 0.00 0.00 4.85
1065 1197 1.138883 CACGTCCATCACCGTCGAT 59.861 57.895 0.00 0.00 34.59 3.59
1068 1200 0.866061 CGTCCATCACCGTCGATGAC 60.866 60.000 6.11 7.80 44.67 3.06
1069 1201 0.527817 GTCCATCACCGTCGATGACC 60.528 60.000 6.11 0.48 44.67 4.02
1101 1233 4.221422 GCCGGCGCCTCTGTATCA 62.221 66.667 26.68 0.00 0.00 2.15
1216 1348 2.045045 CCAAGGGCTTCCGCATCA 60.045 61.111 0.00 0.00 38.10 3.07
1910 2047 1.600636 CGGTTTGAGCCAGCAAGGA 60.601 57.895 0.00 0.00 41.22 3.36
2026 2163 3.435327 TGTAATTGATCCGCCATTATCGC 59.565 43.478 0.00 0.00 0.00 4.58
2028 2165 1.795768 TTGATCCGCCATTATCGCTC 58.204 50.000 0.00 0.00 0.00 5.03
2082 2219 0.248539 GCGGTCGCTACTCCTACAAG 60.249 60.000 8.20 0.00 38.26 3.16
2085 2222 1.817447 GGTCGCTACTCCTACAAGTGT 59.183 52.381 0.00 0.00 0.00 3.55
2165 2375 6.355638 CGATCTCAAATAATTGTAGAACGCC 58.644 40.000 8.51 0.00 35.08 5.68
2175 2385 3.040147 TGTAGAACGCCCAAGAGAAAG 57.960 47.619 0.00 0.00 0.00 2.62
2212 2423 8.499162 GTTCTATCGATCACTTTGATTTATGGG 58.501 37.037 0.00 0.00 37.20 4.00
2215 2426 4.576053 TCGATCACTTTGATTTATGGGCTG 59.424 41.667 0.00 0.00 37.20 4.85
2216 2427 4.614946 GATCACTTTGATTTATGGGCTGC 58.385 43.478 0.00 0.00 37.20 5.25
2219 2430 2.292455 ACTTTGATTTATGGGCTGCCCT 60.292 45.455 35.80 23.69 45.70 5.19
2220 2431 2.548464 TTGATTTATGGGCTGCCCTT 57.452 45.000 35.80 31.18 45.70 3.95
2221 2432 2.071778 TGATTTATGGGCTGCCCTTC 57.928 50.000 35.80 23.25 45.70 3.46
2222 2433 1.332195 GATTTATGGGCTGCCCTTCC 58.668 55.000 35.80 16.68 45.70 3.46
2223 2434 0.936691 ATTTATGGGCTGCCCTTCCT 59.063 50.000 35.80 20.52 45.70 3.36
2226 2437 0.258774 TATGGGCTGCCCTTCCTTTC 59.741 55.000 35.80 9.74 45.70 2.62
2227 2438 1.803453 ATGGGCTGCCCTTCCTTTCA 61.803 55.000 35.80 15.68 45.70 2.69
2228 2439 1.979155 GGGCTGCCCTTCCTTTCAC 60.979 63.158 30.42 0.00 41.34 3.18
2229 2440 2.335712 GGCTGCCCTTCCTTTCACG 61.336 63.158 7.66 0.00 0.00 4.35
2231 2442 0.678048 GCTGCCCTTCCTTTCACGAT 60.678 55.000 0.00 0.00 0.00 3.73
2232 2443 1.373570 CTGCCCTTCCTTTCACGATC 58.626 55.000 0.00 0.00 0.00 3.69
2247 2684 4.806330 TCACGATCAAAGTAGAACACCTC 58.194 43.478 0.00 0.00 0.00 3.85
2251 2688 4.559251 CGATCAAAGTAGAACACCTCTTCG 59.441 45.833 0.00 0.00 35.41 3.79
2255 2692 1.811359 AGTAGAACACCTCTTCGACCG 59.189 52.381 0.00 0.00 35.41 4.79
2262 3301 2.874780 CTCTTCGACCGTTCGGCG 60.875 66.667 11.32 14.69 45.90 6.46
2271 3310 2.474266 CGTTCGGCGTGAATGGTG 59.526 61.111 6.85 0.00 39.49 4.17
2280 3319 1.863454 GCGTGAATGGTGAGCTATCTG 59.137 52.381 0.00 0.00 0.00 2.90
2290 3329 4.701651 TGGTGAGCTATCTGAAAACAATGG 59.298 41.667 0.00 0.00 0.00 3.16
2297 3336 7.725251 AGCTATCTGAAAACAATGGACAAAAA 58.275 30.769 0.00 0.00 0.00 1.94
2335 3374 7.381139 GCATCTTTTCAAACGTTTTCTATGGAA 59.619 33.333 11.66 7.91 0.00 3.53
2336 3375 9.243637 CATCTTTTCAAACGTTTTCTATGGAAA 57.756 29.630 11.66 13.40 39.38 3.13
2357 3396 8.303876 TGGAAAAAGTAGGATCTAAATGTTTGC 58.696 33.333 0.00 0.00 0.00 3.68
2358 3397 7.484959 GGAAAAAGTAGGATCTAAATGTTTGCG 59.515 37.037 0.00 0.00 0.00 4.85
2359 3398 7.681939 AAAAGTAGGATCTAAATGTTTGCGA 57.318 32.000 0.00 0.00 0.00 5.10
2360 3399 7.681939 AAAGTAGGATCTAAATGTTTGCGAA 57.318 32.000 0.00 0.00 0.00 4.70
2361 3400 7.681939 AAGTAGGATCTAAATGTTTGCGAAA 57.318 32.000 0.00 0.00 0.00 3.46
2362 3401 7.865706 AGTAGGATCTAAATGTTTGCGAAAT 57.134 32.000 0.00 0.00 0.00 2.17
2363 3402 8.281212 AGTAGGATCTAAATGTTTGCGAAATT 57.719 30.769 0.00 0.00 0.00 1.82
2364 3403 8.739972 AGTAGGATCTAAATGTTTGCGAAATTT 58.260 29.630 0.00 0.00 0.00 1.82
2365 3404 9.353999 GTAGGATCTAAATGTTTGCGAAATTTT 57.646 29.630 10.26 6.35 0.00 1.82
2367 3406 9.353999 AGGATCTAAATGTTTGCGAAATTTTAC 57.646 29.630 10.26 0.00 0.00 2.01
2368 3407 9.134734 GGATCTAAATGTTTGCGAAATTTTACA 57.865 29.630 10.26 0.00 0.00 2.41
2369 3408 9.937577 GATCTAAATGTTTGCGAAATTTTACAC 57.062 29.630 10.26 0.00 0.00 2.90
2370 3409 8.858003 TCTAAATGTTTGCGAAATTTTACACA 57.142 26.923 10.26 0.00 0.00 3.72
2371 3410 9.469807 TCTAAATGTTTGCGAAATTTTACACAT 57.530 25.926 10.26 0.00 0.00 3.21
2373 3412 8.986039 AAATGTTTGCGAAATTTTACACATTC 57.014 26.923 2.80 0.00 33.52 2.67
2374 3413 7.706281 ATGTTTGCGAAATTTTACACATTCA 57.294 28.000 0.00 0.00 0.00 2.57
2375 3414 7.525688 TGTTTGCGAAATTTTACACATTCAA 57.474 28.000 0.00 0.00 0.00 2.69
2376 3415 7.616673 TGTTTGCGAAATTTTACACATTCAAG 58.383 30.769 0.00 0.00 0.00 3.02
2377 3416 7.276658 TGTTTGCGAAATTTTACACATTCAAGT 59.723 29.630 0.00 0.00 0.00 3.16
2378 3417 7.763172 TTGCGAAATTTTACACATTCAAGTT 57.237 28.000 0.00 0.00 0.00 2.66
2379 3418 7.159437 TGCGAAATTTTACACATTCAAGTTG 57.841 32.000 0.00 0.00 0.00 3.16
2380 3419 6.064525 GCGAAATTTTACACATTCAAGTTGC 58.935 36.000 0.00 0.00 0.00 4.17
2381 3420 6.074356 GCGAAATTTTACACATTCAAGTTGCT 60.074 34.615 0.00 0.00 0.00 3.91
2382 3421 7.516627 GCGAAATTTTACACATTCAAGTTGCTT 60.517 33.333 0.00 0.00 0.00 3.91
2383 3422 8.327429 CGAAATTTTACACATTCAAGTTGCTTT 58.673 29.630 0.00 0.00 0.00 3.51
2384 3423 9.424659 GAAATTTTACACATTCAAGTTGCTTTG 57.575 29.630 0.00 0.00 0.00 2.77
2385 3424 8.491331 AATTTTACACATTCAAGTTGCTTTGT 57.509 26.923 0.00 1.70 0.00 2.83
2386 3425 9.593134 AATTTTACACATTCAAGTTGCTTTGTA 57.407 25.926 0.00 0.78 0.00 2.41
2387 3426 8.627487 TTTTACACATTCAAGTTGCTTTGTAG 57.373 30.769 0.00 0.87 0.00 2.74
2388 3427 5.835113 ACACATTCAAGTTGCTTTGTAGT 57.165 34.783 0.00 1.39 0.00 2.73
2389 3428 5.581605 ACACATTCAAGTTGCTTTGTAGTG 58.418 37.500 0.00 3.03 34.57 2.74
2390 3429 5.125417 ACACATTCAAGTTGCTTTGTAGTGT 59.875 36.000 0.00 3.60 35.63 3.55
2391 3430 6.035843 CACATTCAAGTTGCTTTGTAGTGTT 58.964 36.000 0.00 0.00 0.00 3.32
2392 3431 6.197096 CACATTCAAGTTGCTTTGTAGTGTTC 59.803 38.462 0.00 0.00 0.00 3.18
2393 3432 5.888691 TTCAAGTTGCTTTGTAGTGTTCA 57.111 34.783 0.00 0.00 0.00 3.18
2394 3433 5.888691 TCAAGTTGCTTTGTAGTGTTCAA 57.111 34.783 0.00 0.00 0.00 2.69
2395 3434 6.449635 TCAAGTTGCTTTGTAGTGTTCAAT 57.550 33.333 0.00 0.00 0.00 2.57
2396 3435 6.494842 TCAAGTTGCTTTGTAGTGTTCAATC 58.505 36.000 0.00 0.00 0.00 2.67
2397 3436 5.438761 AGTTGCTTTGTAGTGTTCAATCC 57.561 39.130 0.00 0.00 0.00 3.01
2398 3437 5.133221 AGTTGCTTTGTAGTGTTCAATCCT 58.867 37.500 0.00 0.00 0.00 3.24
2446 3485 9.921637 TTGTGTTTTATATTCCACAGAAATTCC 57.078 29.630 0.00 0.00 38.86 3.01
2447 3486 9.308000 TGTGTTTTATATTCCACAGAAATTCCT 57.692 29.630 0.00 0.00 35.09 3.36
2463 3502 7.011482 CAGAAATTCCTACAAGTTCCTATTCCG 59.989 40.741 0.00 0.00 0.00 4.30
2551 3596 6.252995 ACAAATTTAGCCTTGTAGGATTGGA 58.747 36.000 0.00 0.00 37.67 3.53
2570 3615 2.756760 GGAGTGGACAATTGCATGACAT 59.243 45.455 5.05 0.00 0.00 3.06
2638 3683 1.281899 GTGATACGAAGCACTCTGGC 58.718 55.000 0.00 0.00 38.98 4.85
2645 3690 2.116983 GAAGCACTCTGGCCCTGACA 62.117 60.000 0.00 0.00 0.00 3.58
2676 3721 3.771216 ACTGAAGTTGCCATCAGGAAAT 58.229 40.909 7.59 0.00 45.80 2.17
2680 3725 6.267471 ACTGAAGTTGCCATCAGGAAATAAAA 59.733 34.615 7.59 0.00 45.80 1.52
2718 3763 5.523438 AAACTAAAACTTGCCATCCGAAA 57.477 34.783 0.00 0.00 0.00 3.46
2719 3764 4.766404 ACTAAAACTTGCCATCCGAAAG 57.234 40.909 0.00 0.00 0.00 2.62
2740 3785 6.610075 AAGGAAGTTGCCATATTTGACAAT 57.390 33.333 0.00 0.00 0.00 2.71
2768 3813 1.278238 CCATCCTCGCGTCACTAAAC 58.722 55.000 5.77 0.00 0.00 2.01
2770 3815 2.607187 CATCCTCGCGTCACTAAACTT 58.393 47.619 5.77 0.00 0.00 2.66
2771 3816 2.806608 TCCTCGCGTCACTAAACTTT 57.193 45.000 5.77 0.00 0.00 2.66
2772 3817 2.400399 TCCTCGCGTCACTAAACTTTG 58.600 47.619 5.77 0.00 0.00 2.77
2773 3818 2.132762 CCTCGCGTCACTAAACTTTGT 58.867 47.619 5.77 0.00 0.00 2.83
2774 3819 2.155155 CCTCGCGTCACTAAACTTTGTC 59.845 50.000 5.77 0.00 0.00 3.18
2775 3820 2.792674 CTCGCGTCACTAAACTTTGTCA 59.207 45.455 5.77 0.00 0.00 3.58
2776 3821 3.386486 TCGCGTCACTAAACTTTGTCAT 58.614 40.909 5.77 0.00 0.00 3.06
2777 3822 4.548494 TCGCGTCACTAAACTTTGTCATA 58.452 39.130 5.77 0.00 0.00 2.15
2832 3877 0.973632 ACGTGTGGCACTTATCAGGA 59.026 50.000 19.83 0.00 31.34 3.86
2834 3879 2.205074 CGTGTGGCACTTATCAGGATC 58.795 52.381 19.83 0.00 31.34 3.36
2841 3886 4.476846 TGGCACTTATCAGGATCCCTTTAA 59.523 41.667 8.55 3.06 0.00 1.52
2849 3894 5.388599 TCAGGATCCCTTTAATTTCCTCC 57.611 43.478 8.55 0.00 34.59 4.30
2850 3895 4.168088 TCAGGATCCCTTTAATTTCCTCCC 59.832 45.833 8.55 0.00 34.59 4.30
2872 3917 3.343617 CAAAAGTACCGACACCATGGAT 58.656 45.455 21.47 5.75 0.00 3.41
2880 3925 4.703897 ACCGACACCATGGATAGTAATTG 58.296 43.478 21.47 5.91 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.766496 TGGTGCCCAGCCTAATACTAC 59.234 52.381 0.00 0.00 0.00 2.73
58 59 2.184088 TGGTGCCCAGCCTAATACTA 57.816 50.000 0.00 0.00 0.00 1.82
59 60 1.295020 TTGGTGCCCAGCCTAATACT 58.705 50.000 0.00 0.00 33.81 2.12
61 62 2.909504 TTTTGGTGCCCAGCCTAATA 57.090 45.000 0.00 0.00 33.81 0.98
62 63 1.832998 CATTTTGGTGCCCAGCCTAAT 59.167 47.619 0.00 0.00 33.81 1.73
63 64 1.203112 TCATTTTGGTGCCCAGCCTAA 60.203 47.619 0.00 0.00 33.81 2.69
64 65 0.407528 TCATTTTGGTGCCCAGCCTA 59.592 50.000 0.00 0.00 33.81 3.93
74 102 2.231235 GGCTCCATTTCGTCATTTTGGT 59.769 45.455 0.00 0.00 0.00 3.67
108 136 7.335171 GCATGTATATCCAGTTGATTAGCATGA 59.665 37.037 0.00 0.00 36.99 3.07
109 137 7.120138 TGCATGTATATCCAGTTGATTAGCATG 59.880 37.037 0.00 0.00 37.39 4.06
110 138 7.170277 TGCATGTATATCCAGTTGATTAGCAT 58.830 34.615 0.00 0.00 34.76 3.79
111 139 6.532826 TGCATGTATATCCAGTTGATTAGCA 58.467 36.000 0.00 0.00 34.76 3.49
112 140 7.621428 ATGCATGTATATCCAGTTGATTAGC 57.379 36.000 0.00 0.00 34.76 3.09
138 174 5.290386 ACAAAGCTTGCGATATACTAGGAC 58.710 41.667 0.00 0.00 0.00 3.85
142 178 6.144078 TCAGACAAAGCTTGCGATATACTA 57.856 37.500 0.00 0.00 0.00 1.82
143 179 5.011090 TCAGACAAAGCTTGCGATATACT 57.989 39.130 0.00 0.00 0.00 2.12
144 180 5.520288 TCTTCAGACAAAGCTTGCGATATAC 59.480 40.000 0.00 0.00 0.00 1.47
151 187 4.934602 AGTAGATCTTCAGACAAAGCTTGC 59.065 41.667 0.00 0.00 0.00 4.01
186 222 7.559590 AGCATACACCAAACATAAGATCTTC 57.440 36.000 12.24 0.00 0.00 2.87
196 232 6.155827 GCTAATCAAAAGCATACACCAAACA 58.844 36.000 0.00 0.00 39.83 2.83
204 240 7.496529 TCATACTGGCTAATCAAAAGCATAC 57.503 36.000 0.00 0.00 41.93 2.39
215 255 3.041211 TGACAGGCTCATACTGGCTAAT 58.959 45.455 0.00 0.00 44.41 1.73
228 268 2.641305 GAGAGCATCATTTGACAGGCT 58.359 47.619 3.68 3.68 37.82 4.58
231 271 3.181513 CCAACGAGAGCATCATTTGACAG 60.182 47.826 0.00 0.00 37.82 3.51
236 276 4.074970 AGAAACCAACGAGAGCATCATTT 58.925 39.130 0.00 0.00 37.82 2.32
260 367 5.299531 GGCCTCCTCCAATTTCAGTTAATAC 59.700 44.000 0.00 0.00 0.00 1.89
263 370 3.563479 GGGCCTCCTCCAATTTCAGTTAA 60.563 47.826 0.84 0.00 0.00 2.01
267 377 0.396278 GGGGCCTCCTCCAATTTCAG 60.396 60.000 0.84 0.00 0.00 3.02
270 380 1.149133 ACAGGGGCCTCCTCCAATTT 61.149 55.000 9.65 0.00 46.12 1.82
274 384 0.253630 AATTACAGGGGCCTCCTCCA 60.254 55.000 9.65 0.00 46.12 3.86
276 386 2.242452 AGAAAATTACAGGGGCCTCCTC 59.758 50.000 9.65 0.00 46.12 3.71
326 436 7.650104 CGGCAAGGTTTCTTTAATTAAGTTTGA 59.350 33.333 0.00 0.00 35.28 2.69
351 461 4.791163 CCAACTTTGTATTAACGATTGCCG 59.209 41.667 0.00 0.00 45.44 5.69
363 473 8.889717 CGTAAAATAGATGACCCAACTTTGTAT 58.110 33.333 0.00 0.00 0.00 2.29
365 475 6.150474 CCGTAAAATAGATGACCCAACTTTGT 59.850 38.462 0.00 0.00 0.00 2.83
366 476 6.373216 TCCGTAAAATAGATGACCCAACTTTG 59.627 38.462 0.00 0.00 0.00 2.77
367 477 6.478129 TCCGTAAAATAGATGACCCAACTTT 58.522 36.000 0.00 0.00 0.00 2.66
368 478 6.057321 TCCGTAAAATAGATGACCCAACTT 57.943 37.500 0.00 0.00 0.00 2.66
369 479 5.396436 CCTCCGTAAAATAGATGACCCAACT 60.396 44.000 0.00 0.00 0.00 3.16
370 480 4.814771 CCTCCGTAAAATAGATGACCCAAC 59.185 45.833 0.00 0.00 0.00 3.77
371 481 4.141574 CCCTCCGTAAAATAGATGACCCAA 60.142 45.833 0.00 0.00 0.00 4.12
372 482 3.389983 CCCTCCGTAAAATAGATGACCCA 59.610 47.826 0.00 0.00 0.00 4.51
373 483 3.644738 TCCCTCCGTAAAATAGATGACCC 59.355 47.826 0.00 0.00 0.00 4.46
374 484 4.344390 ACTCCCTCCGTAAAATAGATGACC 59.656 45.833 0.00 0.00 0.00 4.02
375 485 5.532664 ACTCCCTCCGTAAAATAGATGAC 57.467 43.478 0.00 0.00 0.00 3.06
376 486 5.240183 CGTACTCCCTCCGTAAAATAGATGA 59.760 44.000 0.00 0.00 0.00 2.92
377 487 5.240183 TCGTACTCCCTCCGTAAAATAGATG 59.760 44.000 0.00 0.00 0.00 2.90
380 490 5.702349 ATCGTACTCCCTCCGTAAAATAG 57.298 43.478 0.00 0.00 0.00 1.73
381 491 6.469782 AAATCGTACTCCCTCCGTAAAATA 57.530 37.500 0.00 0.00 0.00 1.40
382 492 5.349061 AAATCGTACTCCCTCCGTAAAAT 57.651 39.130 0.00 0.00 0.00 1.82
383 493 4.806640 AAATCGTACTCCCTCCGTAAAA 57.193 40.909 0.00 0.00 0.00 1.52
384 494 4.201910 CGTAAATCGTACTCCCTCCGTAAA 60.202 45.833 0.00 0.00 34.52 2.01
386 496 2.872245 CGTAAATCGTACTCCCTCCGTA 59.128 50.000 0.00 0.00 34.52 4.02
387 497 1.672881 CGTAAATCGTACTCCCTCCGT 59.327 52.381 0.00 0.00 34.52 4.69
389 499 2.287487 GCTCGTAAATCGTACTCCCTCC 60.287 54.545 0.00 0.00 40.80 4.30
390 500 2.357009 TGCTCGTAAATCGTACTCCCTC 59.643 50.000 0.00 0.00 40.80 4.30
393 503 3.961182 TCATGCTCGTAAATCGTACTCC 58.039 45.455 0.00 0.00 40.80 3.85
394 504 3.422546 GCTCATGCTCGTAAATCGTACTC 59.577 47.826 0.00 0.00 40.80 2.59
396 506 2.471743 GGCTCATGCTCGTAAATCGTAC 59.528 50.000 0.00 0.00 39.59 3.67
397 507 2.100087 TGGCTCATGCTCGTAAATCGTA 59.900 45.455 0.00 0.00 39.59 3.43
399 509 1.570813 TGGCTCATGCTCGTAAATCG 58.429 50.000 0.00 0.00 39.59 3.34
400 510 3.198068 TCTTGGCTCATGCTCGTAAATC 58.802 45.455 0.00 0.00 39.59 2.17
403 513 2.760634 TTCTTGGCTCATGCTCGTAA 57.239 45.000 0.00 0.00 39.59 3.18
404 514 2.432146 AGATTCTTGGCTCATGCTCGTA 59.568 45.455 0.00 0.00 39.59 3.43
405 515 1.209019 AGATTCTTGGCTCATGCTCGT 59.791 47.619 0.00 0.00 39.59 4.18
406 516 1.950828 AGATTCTTGGCTCATGCTCG 58.049 50.000 0.00 0.00 39.59 5.03
407 517 5.530171 TCAATAAGATTCTTGGCTCATGCTC 59.470 40.000 9.22 0.00 39.59 4.26
408 518 5.443283 TCAATAAGATTCTTGGCTCATGCT 58.557 37.500 9.22 0.00 39.59 3.79
435 545 0.099791 GTGACTAGTCCTCAGCGAGC 59.900 60.000 20.11 0.00 0.00 5.03
456 573 3.979948 TCGACCACGAACTTATTTGTCA 58.020 40.909 0.00 0.00 45.74 3.58
527 646 1.033574 GGAGTGGAGTATCTGGACCG 58.966 60.000 0.00 0.00 33.73 4.79
529 648 2.691011 GAGTGGAGTGGAGTATCTGGAC 59.309 54.545 0.00 0.00 33.73 4.02
532 651 3.766591 AGTTGAGTGGAGTGGAGTATCTG 59.233 47.826 0.00 0.00 33.73 2.90
546 665 5.177696 GTGAAGGCAAGTAAGTAGTTGAGTG 59.822 44.000 9.59 0.00 38.57 3.51
550 669 4.304110 TCGTGAAGGCAAGTAAGTAGTTG 58.696 43.478 2.11 2.11 39.14 3.16
552 671 4.021368 ACATCGTGAAGGCAAGTAAGTAGT 60.021 41.667 0.00 0.00 0.00 2.73
564 683 3.262420 CCTCTGGTTTACATCGTGAAGG 58.738 50.000 0.00 0.00 0.00 3.46
573 692 1.765074 GGTGGGCCTCTGGTTTACA 59.235 57.895 4.53 0.00 0.00 2.41
609 729 9.793245 GTCTCGTTAATTGTTATACATGTATGC 57.207 33.333 25.48 18.27 0.00 3.14
620 740 9.672086 CAAAAATCTTGGTCTCGTTAATTGTTA 57.328 29.630 0.00 0.00 0.00 2.41
621 741 7.169140 GCAAAAATCTTGGTCTCGTTAATTGTT 59.831 33.333 0.00 0.00 0.00 2.83
622 742 6.640907 GCAAAAATCTTGGTCTCGTTAATTGT 59.359 34.615 0.00 0.00 0.00 2.71
624 744 6.156519 GGCAAAAATCTTGGTCTCGTTAATT 58.843 36.000 0.00 0.00 0.00 1.40
626 746 4.580995 TGGCAAAAATCTTGGTCTCGTTAA 59.419 37.500 0.00 0.00 0.00 2.01
627 747 4.023536 GTGGCAAAAATCTTGGTCTCGTTA 60.024 41.667 0.00 0.00 0.00 3.18
631 751 2.627699 TGGTGGCAAAAATCTTGGTCTC 59.372 45.455 0.00 0.00 0.00 3.36
651 771 0.443869 CGTGTCGATTCCCTTGCTTG 59.556 55.000 0.00 0.00 0.00 4.01
654 774 1.079405 TCCGTGTCGATTCCCTTGC 60.079 57.895 0.00 0.00 0.00 4.01
656 776 0.246635 CTGTCCGTGTCGATTCCCTT 59.753 55.000 0.00 0.00 0.00 3.95
657 777 0.611062 TCTGTCCGTGTCGATTCCCT 60.611 55.000 0.00 0.00 0.00 4.20
681 801 1.408340 ACCAGCAGATCGATGTCAGAG 59.592 52.381 0.54 0.00 0.00 3.35
700 820 0.890542 TTCTGCTGGTGTGCATCCAC 60.891 55.000 9.10 4.36 42.48 4.02
701 821 0.178995 TTTCTGCTGGTGTGCATCCA 60.179 50.000 11.98 11.98 42.48 3.41
970 1099 2.441164 GGCCGGAGAGAGCAGAGA 60.441 66.667 5.05 0.00 0.00 3.10
1026 1158 4.459089 GAGGAGGCAGCGGTGGAC 62.459 72.222 17.54 0.00 0.00 4.02
1035 1167 2.680352 GACGTGGAGGAGGAGGCA 60.680 66.667 0.00 0.00 0.00 4.75
1087 1219 2.279517 CGGTGATACAGAGGCGCC 60.280 66.667 21.89 21.89 0.00 6.53
1088 1220 1.589196 GACGGTGATACAGAGGCGC 60.589 63.158 0.00 0.00 0.00 6.53
1090 1222 1.442148 GGGACGGTGATACAGAGGC 59.558 63.158 0.00 0.00 0.00 4.70
1910 2047 3.493830 TTCGTGCGCTGTTCCGACT 62.494 57.895 9.73 0.00 0.00 4.18
2026 2163 8.980481 ATCCCATTACTTAATTAACCACTGAG 57.020 34.615 0.00 0.00 0.00 3.35
2052 2189 2.561885 CGACCGCTGACTCGTCTT 59.438 61.111 0.00 0.00 0.00 3.01
2082 2219 9.783256 ACTGTGAATTTACAAAGAAAACTACAC 57.217 29.630 4.47 0.00 0.00 2.90
2165 2375 1.801178 GGTCGTCTTGCTTTCTCTTGG 59.199 52.381 0.00 0.00 0.00 3.61
2175 2385 1.189403 CGATAGAACGGTCGTCTTGC 58.811 55.000 0.00 0.00 39.76 4.01
2212 2423 0.678048 ATCGTGAAAGGAAGGGCAGC 60.678 55.000 0.00 0.00 32.76 5.25
2215 2426 1.821216 TTGATCGTGAAAGGAAGGGC 58.179 50.000 0.00 0.00 32.76 5.19
2216 2427 3.412386 ACTTTGATCGTGAAAGGAAGGG 58.588 45.455 8.42 0.00 35.15 3.95
2219 2430 6.202188 GTGTTCTACTTTGATCGTGAAAGGAA 59.798 38.462 8.42 2.06 35.15 3.36
2220 2431 5.694910 GTGTTCTACTTTGATCGTGAAAGGA 59.305 40.000 8.42 0.13 35.15 3.36
2221 2432 5.107065 GGTGTTCTACTTTGATCGTGAAAGG 60.107 44.000 8.42 0.00 35.15 3.11
2222 2433 5.696724 AGGTGTTCTACTTTGATCGTGAAAG 59.303 40.000 3.18 3.18 36.63 2.62
2223 2434 5.607477 AGGTGTTCTACTTTGATCGTGAAA 58.393 37.500 0.00 0.00 0.00 2.69
2226 2437 4.810790 AGAGGTGTTCTACTTTGATCGTG 58.189 43.478 0.00 0.00 33.23 4.35
2227 2438 5.470047 AAGAGGTGTTCTACTTTGATCGT 57.530 39.130 0.00 0.00 34.14 3.73
2228 2439 4.559251 CGAAGAGGTGTTCTACTTTGATCG 59.441 45.833 0.00 0.00 34.14 3.69
2229 2440 5.573669 GTCGAAGAGGTGTTCTACTTTGATC 59.426 44.000 0.00 0.00 36.95 2.92
2231 2442 4.261909 GGTCGAAGAGGTGTTCTACTTTGA 60.262 45.833 0.00 0.00 36.95 2.69
2232 2443 3.988517 GGTCGAAGAGGTGTTCTACTTTG 59.011 47.826 0.00 0.00 36.95 2.77
2255 2692 1.787847 CTCACCATTCACGCCGAAC 59.212 57.895 0.00 0.00 36.12 3.95
2262 3301 5.412594 TGTTTTCAGATAGCTCACCATTCAC 59.587 40.000 0.00 0.00 0.00 3.18
2271 3310 6.500684 TTGTCCATTGTTTTCAGATAGCTC 57.499 37.500 0.00 0.00 0.00 4.09
2298 3337 6.918022 CGTTTGAAAAGATGCTCTACCTTTTT 59.082 34.615 0.00 0.00 39.40 1.94
2299 3338 6.039382 ACGTTTGAAAAGATGCTCTACCTTTT 59.961 34.615 0.00 0.00 41.25 2.27
2303 3342 5.358298 AACGTTTGAAAAGATGCTCTACC 57.642 39.130 0.00 0.00 0.00 3.18
2309 3348 6.861055 TCCATAGAAAACGTTTGAAAAGATGC 59.139 34.615 15.46 0.00 0.00 3.91
2335 3374 7.681939 TCGCAAACATTTAGATCCTACTTTT 57.318 32.000 0.00 0.00 0.00 2.27
2336 3375 7.681939 TTCGCAAACATTTAGATCCTACTTT 57.318 32.000 0.00 0.00 0.00 2.66
2338 3377 7.865706 ATTTCGCAAACATTTAGATCCTACT 57.134 32.000 0.00 0.00 0.00 2.57
2341 3380 9.353999 GTAAAATTTCGCAAACATTTAGATCCT 57.646 29.630 0.00 0.00 0.00 3.24
2343 3382 9.937577 GTGTAAAATTTCGCAAACATTTAGATC 57.062 29.630 0.00 0.00 0.00 2.75
2349 3388 8.136057 TGAATGTGTAAAATTTCGCAAACATT 57.864 26.923 12.37 12.37 0.00 2.71
2350 3389 7.706281 TGAATGTGTAAAATTTCGCAAACAT 57.294 28.000 0.00 0.00 0.00 2.71
2351 3390 7.276658 ACTTGAATGTGTAAAATTTCGCAAACA 59.723 29.630 0.00 0.00 0.00 2.83
2352 3391 7.617557 ACTTGAATGTGTAAAATTTCGCAAAC 58.382 30.769 0.00 0.00 0.00 2.93
2353 3392 7.763172 ACTTGAATGTGTAAAATTTCGCAAA 57.237 28.000 0.00 0.00 0.00 3.68
2354 3393 7.616673 CAACTTGAATGTGTAAAATTTCGCAA 58.383 30.769 0.00 0.00 0.00 4.85
2355 3394 6.292061 GCAACTTGAATGTGTAAAATTTCGCA 60.292 34.615 0.00 0.00 0.00 5.10
2356 3395 6.064525 GCAACTTGAATGTGTAAAATTTCGC 58.935 36.000 0.00 0.00 0.00 4.70
2357 3396 7.393551 AGCAACTTGAATGTGTAAAATTTCG 57.606 32.000 0.00 0.00 0.00 3.46
2358 3397 9.424659 CAAAGCAACTTGAATGTGTAAAATTTC 57.575 29.630 0.00 0.00 0.00 2.17
2359 3398 8.945057 ACAAAGCAACTTGAATGTGTAAAATTT 58.055 25.926 0.00 0.00 0.00 1.82
2360 3399 8.491331 ACAAAGCAACTTGAATGTGTAAAATT 57.509 26.923 0.00 0.00 0.00 1.82
2361 3400 9.248291 CTACAAAGCAACTTGAATGTGTAAAAT 57.752 29.630 0.00 0.00 0.00 1.82
2362 3401 8.247562 ACTACAAAGCAACTTGAATGTGTAAAA 58.752 29.630 0.00 0.00 0.00 1.52
2363 3402 7.700234 CACTACAAAGCAACTTGAATGTGTAAA 59.300 33.333 0.00 0.00 0.00 2.01
2364 3403 7.148154 ACACTACAAAGCAACTTGAATGTGTAA 60.148 33.333 14.57 0.00 36.65 2.41
2365 3404 6.317642 ACACTACAAAGCAACTTGAATGTGTA 59.682 34.615 14.57 0.00 36.65 2.90
2366 3405 5.125417 ACACTACAAAGCAACTTGAATGTGT 59.875 36.000 0.00 0.00 35.27 3.72
2367 3406 5.581605 ACACTACAAAGCAACTTGAATGTG 58.418 37.500 0.00 0.00 34.23 3.21
2368 3407 5.835113 ACACTACAAAGCAACTTGAATGT 57.165 34.783 0.00 0.00 0.00 2.71
2369 3408 6.264832 TGAACACTACAAAGCAACTTGAATG 58.735 36.000 0.00 0.00 0.00 2.67
2370 3409 6.449635 TGAACACTACAAAGCAACTTGAAT 57.550 33.333 0.00 0.00 0.00 2.57
2371 3410 5.888691 TGAACACTACAAAGCAACTTGAA 57.111 34.783 0.00 0.00 0.00 2.69
2372 3411 5.888691 TTGAACACTACAAAGCAACTTGA 57.111 34.783 0.00 0.00 0.00 3.02
2373 3412 5.687285 GGATTGAACACTACAAAGCAACTTG 59.313 40.000 0.00 0.00 0.00 3.16
2374 3413 5.594317 AGGATTGAACACTACAAAGCAACTT 59.406 36.000 0.00 0.00 0.00 2.66
2375 3414 5.133221 AGGATTGAACACTACAAAGCAACT 58.867 37.500 0.00 0.00 0.00 3.16
2376 3415 5.438761 AGGATTGAACACTACAAAGCAAC 57.561 39.130 0.00 0.00 0.00 4.17
2377 3416 6.530120 TCTAGGATTGAACACTACAAAGCAA 58.470 36.000 0.00 0.00 0.00 3.91
2378 3417 6.109156 TCTAGGATTGAACACTACAAAGCA 57.891 37.500 0.00 0.00 0.00 3.91
2379 3418 5.582665 CCTCTAGGATTGAACACTACAAAGC 59.417 44.000 0.00 0.00 37.39 3.51
2380 3419 6.936279 TCCTCTAGGATTGAACACTACAAAG 58.064 40.000 0.00 0.00 39.78 2.77
2381 3420 6.928348 TCCTCTAGGATTGAACACTACAAA 57.072 37.500 0.00 0.00 39.78 2.83
2396 3435 8.404000 CAAAAATCATGAGAACAATCCTCTAGG 58.596 37.037 0.09 0.00 0.00 3.02
2397 3436 8.954350 ACAAAAATCATGAGAACAATCCTCTAG 58.046 33.333 0.09 0.00 0.00 2.43
2398 3437 8.733458 CACAAAAATCATGAGAACAATCCTCTA 58.267 33.333 0.09 0.00 0.00 2.43
2439 3478 6.260271 CCGGAATAGGAACTTGTAGGAATTTC 59.740 42.308 0.00 0.00 41.75 2.17
2440 3479 6.069847 TCCGGAATAGGAACTTGTAGGAATTT 60.070 38.462 0.00 0.00 41.75 1.82
2441 3480 5.427481 TCCGGAATAGGAACTTGTAGGAATT 59.573 40.000 0.00 0.00 41.75 2.17
2442 3481 4.966805 TCCGGAATAGGAACTTGTAGGAAT 59.033 41.667 0.00 0.00 41.75 3.01
2443 3482 4.355549 TCCGGAATAGGAACTTGTAGGAA 58.644 43.478 0.00 0.00 41.75 3.36
2444 3483 3.985127 TCCGGAATAGGAACTTGTAGGA 58.015 45.455 0.00 0.00 41.75 2.94
2445 3484 4.748277 TTCCGGAATAGGAACTTGTAGG 57.252 45.455 14.35 0.00 44.66 3.18
2477 3516 5.582665 AGATTTGAGAGCACGGAAAGTATTC 59.417 40.000 0.00 0.00 34.66 1.75
2479 3518 5.091261 AGATTTGAGAGCACGGAAAGTAT 57.909 39.130 0.00 0.00 0.00 2.12
2480 3519 4.220821 AGAGATTTGAGAGCACGGAAAGTA 59.779 41.667 0.00 0.00 0.00 2.24
2481 3520 3.007398 AGAGATTTGAGAGCACGGAAAGT 59.993 43.478 0.00 0.00 0.00 2.66
2486 3525 1.396301 GCAAGAGATTTGAGAGCACGG 59.604 52.381 0.00 0.00 0.00 4.94
2488 3527 4.214971 TCTTTGCAAGAGATTTGAGAGCAC 59.785 41.667 0.00 0.00 32.71 4.40
2519 3564 9.353999 CCTACAAGGCTAAATTTGTACAAAATC 57.646 33.333 23.97 11.33 38.41 2.17
2551 3596 3.693807 AGATGTCATGCAATTGTCCACT 58.306 40.909 7.40 0.00 0.00 4.00
2608 3653 1.779061 CGTATCACACGTGTGGCAC 59.221 57.895 39.88 33.56 45.82 5.01
2625 3670 2.435586 CAGGGCCAGAGTGCTTCG 60.436 66.667 6.18 0.00 0.00 3.79
2693 3738 7.925043 TTCGGATGGCAAGTTTTAGTTTATA 57.075 32.000 0.00 0.00 0.00 0.98
2725 3770 6.593382 GGCAACTTTAATTGTCAAATATGGCA 59.407 34.615 0.00 0.00 40.01 4.92
2726 3771 6.593382 TGGCAACTTTAATTGTCAAATATGGC 59.407 34.615 0.00 0.00 41.11 4.40
2727 3772 8.721019 ATGGCAACTTTAATTGTCAAATATGG 57.279 30.769 0.54 0.00 46.62 2.74
2728 3773 8.819974 GGATGGCAACTTTAATTGTCAAATATG 58.180 33.333 0.54 0.00 46.62 1.78
2740 3785 1.083489 CGCGAGGATGGCAACTTTAA 58.917 50.000 0.00 0.00 41.24 1.52
2800 3845 0.380024 CACACGTGTGGCATGAACAA 59.620 50.000 35.65 0.00 42.10 2.83
2820 3865 7.255625 GGAAATTAAAGGGATCCTGATAAGTGC 60.256 40.741 12.58 6.32 32.13 4.40
2828 3873 4.474394 GGGAGGAAATTAAAGGGATCCTG 58.526 47.826 12.58 0.00 40.53 3.86
2832 3877 4.984642 TTGGGGAGGAAATTAAAGGGAT 57.015 40.909 0.00 0.00 0.00 3.85
2834 3879 4.844085 ACTTTTGGGGAGGAAATTAAAGGG 59.156 41.667 0.00 0.00 0.00 3.95
2841 3886 2.645797 TCGGTACTTTTGGGGAGGAAAT 59.354 45.455 0.00 0.00 0.00 2.17
2849 3894 1.810151 CATGGTGTCGGTACTTTTGGG 59.190 52.381 0.00 0.00 0.00 4.12
2850 3895 1.810151 CCATGGTGTCGGTACTTTTGG 59.190 52.381 2.57 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.