Multiple sequence alignment - TraesCS5A01G400800

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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 TraesCS5A01G400800 chr5A 100.000 5419 0 0 1 5419 593467720 593462302 0.000000e+00 10008.0
1 TraesCS5A01G400800 chr5A 94.203 69 2 1 4447 4515 311673978 311673912 2.670000e-18 104.0
2 TraesCS5A01G400800 chr5B 92.178 3861 200 41 617 4430 581139913 581136108 0.000000e+00 5363.0
3 TraesCS5A01G400800 chr5B 82.319 526 21 25 4843 5355 581135814 581135348 1.830000e-104 390.0
4 TraesCS5A01G400800 chr5D 91.670 2509 200 3 1927 4432 474210910 474208408 0.000000e+00 3467.0
5 TraesCS5A01G400800 chr5D 92.063 1197 57 11 667 1835 474212094 474210908 0.000000e+00 1650.0
6 TraesCS5A01G400800 chr5D 90.489 368 16 6 5054 5419 474207528 474207178 8.220000e-128 468.0
7 TraesCS5A01G400800 chr5D 81.461 534 45 20 1 498 474212947 474212432 6.580000e-104 388.0
8 TraesCS5A01G400800 chr5D 85.714 84 5 2 4938 5021 474207610 474207534 1.250000e-11 82.4
9 TraesCS5A01G400800 chr2D 92.553 94 7 0 1830 1923 426927816 426927909 9.470000e-28 135.0
10 TraesCS5A01G400800 chr2D 96.667 60 2 0 565 624 268894469 268894410 3.450000e-17 100.0
11 TraesCS5A01G400800 chr2D 95.082 61 1 2 555 614 155831309 155831368 1.610000e-15 95.3
12 TraesCS5A01G400800 chr1D 93.590 78 3 1 4439 4514 366246212 366246135 1.230000e-21 115.0
13 TraesCS5A01G400800 chr3D 92.208 77 4 1 4439 4515 535916267 535916341 2.060000e-19 108.0
14 TraesCS5A01G400800 chr3D 98.333 60 1 0 565 624 467283663 467283604 7.420000e-19 106.0
15 TraesCS5A01G400800 chr2B 98.276 58 1 0 567 624 662911304 662911361 9.600000e-18 102.0
16 TraesCS5A01G400800 chr2B 81.905 105 9 7 4419 4515 428791772 428791874 4.500000e-11 80.5
17 TraesCS5A01G400800 chr7B 98.246 57 1 0 568 624 506378159 506378103 3.450000e-17 100.0
18 TraesCS5A01G400800 chr7B 90.667 75 5 1 4441 4515 4091569 4091497 1.240000e-16 99.0
19 TraesCS5A01G400800 chr2A 98.214 56 1 0 563 618 161944621 161944676 1.240000e-16 99.0
20 TraesCS5A01G400800 chr1A 98.214 56 1 0 569 624 223939578 223939633 1.240000e-16 99.0
21 TraesCS5A01G400800 chr1A 89.474 76 5 2 4441 4513 24561278 24561203 5.780000e-15 93.5
22 TraesCS5A01G400800 chr7A 90.000 80 1 2 4441 4515 68235971 68236048 4.470000e-16 97.1
23 TraesCS5A01G400800 chr6D 95.000 60 3 0 565 624 446086751 446086810 1.610000e-15 95.3
24 TraesCS5A01G400800 chr7D 89.333 75 6 1 4441 4515 36045225 36045297 5.780000e-15 93.5
25 TraesCS5A01G400800 chr4A 93.548 62 4 0 563 624 584667426 584667487 5.780000e-15 93.5
26 TraesCS5A01G400800 chr3A 89.041 73 5 2 4441 4510 635388232 635388304 2.690000e-13 87.9


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 TraesCS5A01G400800 chr5A 593462302 593467720 5418 True 10008.00 10008 100.0000 1 5419 1 chr5A.!!$R2 5418
1 TraesCS5A01G400800 chr5B 581135348 581139913 4565 True 2876.50 5363 87.2485 617 5355 2 chr5B.!!$R1 4738
2 TraesCS5A01G400800 chr5D 474207178 474212947 5769 True 1211.08 3467 88.2794 1 5419 5 chr5D.!!$R1 5418

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
358 394 0.119561 TGTTCCCCTAACCTGGCCTA 59.880 55.0 3.32 0.0 37.27 3.93 F
1166 1499 0.036022 GACCCTCTTCTGCTGTTGCT 59.964 55.0 0.00 0.0 40.48 3.91 F
2919 3258 0.178068 ATCAGGTGAAATCGACGGGG 59.822 55.0 0.00 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 2191 0.175760 TATCGCAGCAGTTCCTCCAC 59.824 55.000 0.0 0.0 0.0 4.02 R
3048 3387 2.039405 GCAGCAGAGTTGAGGGCAG 61.039 63.158 0.0 0.0 0.0 4.85 R
4875 5620 0.172352 CTCTCTTGTCTCCTCCGCAC 59.828 60.000 0.0 0.0 0.0 5.34 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
18 19 3.818787 CAAGCTGCCATGGACGCC 61.819 66.667 18.40 0.00 0.00 5.68
36 37 4.554036 GGCTGGGGAGCTTAGCGG 62.554 72.222 0.00 0.00 38.31 5.52
86 87 1.831736 GCAGGTCAAACCCTAGCTCTA 59.168 52.381 0.00 0.00 39.75 2.43
100 101 2.670939 AGCTCTAATGCCCCCATTTTC 58.329 47.619 0.00 0.00 41.68 2.29
105 106 1.360185 AATGCCCCCATTTTCTTGCA 58.640 45.000 0.00 0.00 38.49 4.08
106 107 1.360185 ATGCCCCCATTTTCTTGCAA 58.640 45.000 0.00 0.00 31.81 4.08
109 110 1.741528 CCCCCATTTTCTTGCAATGC 58.258 50.000 0.00 0.00 31.26 3.56
116 117 2.143008 TTTCTTGCAATGCAGCTGTG 57.857 45.000 16.64 7.03 40.61 3.66
117 118 1.034356 TTCTTGCAATGCAGCTGTGT 58.966 45.000 16.64 0.86 40.61 3.72
118 119 1.894881 TCTTGCAATGCAGCTGTGTA 58.105 45.000 16.64 2.22 40.61 2.90
120 121 0.238025 TTGCAATGCAGCTGTGTACG 59.762 50.000 16.64 1.78 40.61 3.67
186 191 1.075674 TGTGAGGCTGGGGCAAAAA 60.076 52.632 0.00 0.00 40.87 1.94
188 193 1.836604 TGAGGCTGGGGCAAAAACC 60.837 57.895 0.00 0.00 40.87 3.27
189 194 1.836604 GAGGCTGGGGCAAAAACCA 60.837 57.895 0.00 0.00 40.87 3.67
195 200 1.371183 GGGGCAAAAACCAGGAAGC 59.629 57.895 0.00 0.00 0.00 3.86
199 204 2.421388 GGGCAAAAACCAGGAAGCTTTT 60.421 45.455 0.00 0.00 0.00 2.27
201 206 3.530535 GCAAAAACCAGGAAGCTTTTGA 58.469 40.909 17.52 0.00 39.86 2.69
202 207 3.557185 GCAAAAACCAGGAAGCTTTTGAG 59.443 43.478 17.52 0.35 39.86 3.02
210 238 4.326826 CAGGAAGCTTTTGAGATGGTGTA 58.673 43.478 0.00 0.00 0.00 2.90
211 239 4.394300 CAGGAAGCTTTTGAGATGGTGTAG 59.606 45.833 0.00 0.00 0.00 2.74
213 241 5.248477 AGGAAGCTTTTGAGATGGTGTAGTA 59.752 40.000 0.00 0.00 0.00 1.82
214 242 6.069963 AGGAAGCTTTTGAGATGGTGTAGTAT 60.070 38.462 0.00 0.00 0.00 2.12
216 244 7.224949 GGAAGCTTTTGAGATGGTGTAGTATAC 59.775 40.741 0.00 0.00 43.42 1.47
264 300 3.190118 CAGTGCTCAGAAATCCTTGGAAC 59.810 47.826 0.00 0.00 0.00 3.62
275 311 1.007387 CTTGGAACTTTGGCACGGC 60.007 57.895 0.00 0.00 0.00 5.68
292 328 1.868498 CGGCCGTTAAAGTTCTTGTCA 59.132 47.619 19.50 0.00 0.00 3.58
334 370 1.225855 GTGTTTCAGATGCACGGTGA 58.774 50.000 13.29 0.00 0.00 4.02
335 371 1.806542 GTGTTTCAGATGCACGGTGAT 59.193 47.619 13.29 2.54 0.00 3.06
350 386 2.677037 CGGTGATCTGTGTTCCCCTAAC 60.677 54.545 0.00 0.00 38.67 2.34
353 389 2.571653 TGATCTGTGTTCCCCTAACCTG 59.428 50.000 0.00 0.00 37.27 4.00
354 390 1.358152 TCTGTGTTCCCCTAACCTGG 58.642 55.000 0.00 0.00 37.27 4.45
356 392 1.001269 GTGTTCCCCTAACCTGGCC 60.001 63.158 0.00 0.00 37.27 5.36
358 394 0.119561 TGTTCCCCTAACCTGGCCTA 59.880 55.000 3.32 0.00 37.27 3.93
359 395 0.837940 GTTCCCCTAACCTGGCCTAG 59.162 60.000 3.32 0.00 31.38 3.02
360 396 0.986550 TTCCCCTAACCTGGCCTAGC 60.987 60.000 3.32 0.00 0.00 3.42
361 397 1.692749 CCCCTAACCTGGCCTAGCA 60.693 63.158 3.32 0.00 0.00 3.49
362 398 1.062488 CCCCTAACCTGGCCTAGCAT 61.062 60.000 3.32 0.00 0.00 3.79
363 399 0.398318 CCCTAACCTGGCCTAGCATC 59.602 60.000 3.32 0.00 0.00 3.91
364 400 1.428869 CCTAACCTGGCCTAGCATCT 58.571 55.000 3.32 0.00 0.00 2.90
365 401 2.609747 CCTAACCTGGCCTAGCATCTA 58.390 52.381 3.32 0.00 0.00 1.98
366 402 2.300437 CCTAACCTGGCCTAGCATCTAC 59.700 54.545 3.32 0.00 0.00 2.59
367 403 2.182516 AACCTGGCCTAGCATCTACT 57.817 50.000 3.32 0.00 0.00 2.57
368 404 1.710816 ACCTGGCCTAGCATCTACTC 58.289 55.000 3.32 0.00 0.00 2.59
376 412 3.671971 GCCTAGCATCTACTCAGCATACG 60.672 52.174 0.00 0.00 0.00 3.06
392 428 4.389992 AGCATACGAATGTTGTCACTCTTG 59.610 41.667 0.00 0.00 35.38 3.02
417 453 0.465097 CTTGCCTATGGAGTGCCTGG 60.465 60.000 0.00 0.00 34.31 4.45
420 456 0.837272 GCCTATGGAGTGCCTGGTAA 59.163 55.000 0.00 0.00 34.31 2.85
426 462 4.796110 ATGGAGTGCCTGGTAATATTGT 57.204 40.909 0.00 0.00 34.31 2.71
429 465 4.141574 TGGAGTGCCTGGTAATATTGTACC 60.142 45.833 0.00 0.00 43.45 3.34
431 467 5.291905 AGTGCCTGGTAATATTGTACCTC 57.708 43.478 8.53 0.56 43.52 3.85
432 468 4.056050 GTGCCTGGTAATATTGTACCTCG 58.944 47.826 8.53 1.12 43.52 4.63
437 473 5.458041 TGGTAATATTGTACCTCGCTACC 57.542 43.478 8.53 0.46 43.52 3.18
493 529 7.989826 ACTACCTATGAGTGAATTGCATTTTC 58.010 34.615 0.00 0.00 0.00 2.29
497 533 8.370182 ACCTATGAGTGAATTGCATTTTCTTTT 58.630 29.630 10.27 0.00 0.00 2.27
500 536 7.945033 TGAGTGAATTGCATTTTCTTTTACC 57.055 32.000 10.27 0.00 0.00 2.85
501 537 6.928492 TGAGTGAATTGCATTTTCTTTTACCC 59.072 34.615 10.27 0.00 0.00 3.69
502 538 6.230472 AGTGAATTGCATTTTCTTTTACCCC 58.770 36.000 10.27 0.00 0.00 4.95
503 539 5.411361 GTGAATTGCATTTTCTTTTACCCCC 59.589 40.000 10.27 0.00 0.00 5.40
504 540 3.669251 TTGCATTTTCTTTTACCCCCG 57.331 42.857 0.00 0.00 0.00 5.73
505 541 1.273886 TGCATTTTCTTTTACCCCCGC 59.726 47.619 0.00 0.00 0.00 6.13
511 799 1.135068 TCTTTTACCCCCGCCTCCAA 61.135 55.000 0.00 0.00 0.00 3.53
513 801 1.717038 TTTTACCCCCGCCTCCAACA 61.717 55.000 0.00 0.00 0.00 3.33
529 817 1.681264 CAACAAAACTGGTCCACTCCC 59.319 52.381 0.00 0.00 0.00 4.30
546 834 2.669569 CGTGGCTGTTGTCTGGGG 60.670 66.667 0.00 0.00 0.00 4.96
550 838 1.600916 GGCTGTTGTCTGGGGTGAC 60.601 63.158 0.00 0.00 37.47 3.67
551 839 1.148273 GCTGTTGTCTGGGGTGACA 59.852 57.895 0.00 0.00 44.17 3.58
552 840 1.166531 GCTGTTGTCTGGGGTGACAC 61.167 60.000 0.00 0.00 45.32 3.67
553 841 0.180171 CTGTTGTCTGGGGTGACACA 59.820 55.000 8.08 0.00 45.32 3.72
560 848 3.743714 TGGGGTGACACATTTGAGG 57.256 52.632 8.08 0.00 40.38 3.86
561 849 0.539438 TGGGGTGACACATTTGAGGC 60.539 55.000 8.08 0.00 40.38 4.70
562 850 0.539438 GGGGTGACACATTTGAGGCA 60.539 55.000 8.08 0.00 0.00 4.75
563 851 1.549203 GGGTGACACATTTGAGGCAT 58.451 50.000 8.08 0.00 0.00 4.40
564 852 2.620367 GGGGTGACACATTTGAGGCATA 60.620 50.000 8.08 0.00 0.00 3.14
565 853 3.088532 GGGTGACACATTTGAGGCATAA 58.911 45.455 8.08 0.00 0.00 1.90
566 854 3.509575 GGGTGACACATTTGAGGCATAAA 59.490 43.478 8.08 0.00 0.00 1.40
567 855 4.021544 GGGTGACACATTTGAGGCATAAAA 60.022 41.667 8.08 0.00 0.00 1.52
568 856 5.510520 GGGTGACACATTTGAGGCATAAAAA 60.511 40.000 8.08 0.00 0.00 1.94
591 879 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
592 880 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
593 881 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
594 882 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
595 883 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
601 889 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
602 890 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
603 891 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
604 892 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
607 895 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
636 924 5.376625 GACCACATTGGAGGCATAAGATAA 58.623 41.667 0.00 0.00 40.96 1.75
647 935 9.693739 TGGAGGCATAAGATAAAAGTAAATTGA 57.306 29.630 0.00 0.00 0.00 2.57
745 1045 4.381079 CGGAGAAGAAAGGACTAGAACTGG 60.381 50.000 0.00 0.00 0.00 4.00
747 1047 5.246429 GGAGAAGAAAGGACTAGAACTGGAA 59.754 44.000 0.00 0.00 0.00 3.53
793 1094 3.576078 TCAAATGGTTCCAGAGTGTGT 57.424 42.857 0.00 0.00 0.00 3.72
849 1173 2.865119 TCACTGCCACTCATGTCATT 57.135 45.000 0.00 0.00 0.00 2.57
876 1200 7.241042 AGAAGGTAAAAAGGGGAATTTTAGC 57.759 36.000 11.09 11.09 44.78 3.09
940 1271 3.815401 GCTGTCTTGTGTTGGTCATTACT 59.185 43.478 0.00 0.00 0.00 2.24
941 1272 4.083802 GCTGTCTTGTGTTGGTCATTACTC 60.084 45.833 0.00 0.00 0.00 2.59
942 1273 5.029807 TGTCTTGTGTTGGTCATTACTCA 57.970 39.130 0.00 0.00 0.00 3.41
943 1274 5.620206 TGTCTTGTGTTGGTCATTACTCAT 58.380 37.500 0.00 0.00 0.00 2.90
944 1275 6.061441 TGTCTTGTGTTGGTCATTACTCATT 58.939 36.000 0.00 0.00 0.00 2.57
945 1276 7.220740 TGTCTTGTGTTGGTCATTACTCATTA 58.779 34.615 0.00 0.00 0.00 1.90
946 1277 7.172532 TGTCTTGTGTTGGTCATTACTCATTAC 59.827 37.037 0.00 0.00 0.00 1.89
1038 1369 5.163152 GGATCCTGGTCCTGTTGATAAATCT 60.163 44.000 3.84 0.00 35.32 2.40
1114 1445 7.935755 AGGTAACAGTTTAGAGGTTTTCCTTAC 59.064 37.037 0.00 0.00 46.79 2.34
1166 1499 0.036022 GACCCTCTTCTGCTGTTGCT 59.964 55.000 0.00 0.00 40.48 3.91
1240 1574 3.572255 GCACAAGACTTAACCAATGGGAA 59.428 43.478 3.55 0.00 38.05 3.97
1402 1736 1.743996 GGTTTGGAGAGATGGCTGTC 58.256 55.000 0.00 0.00 33.86 3.51
1462 1796 0.905357 ATGGTACTCCTGTGACTGGC 59.095 55.000 3.33 0.00 34.23 4.85
1549 1883 4.032960 AGGTGGTTCTATCAACATTGCA 57.967 40.909 0.00 0.00 0.00 4.08
1567 1901 4.764679 TGCATGGTTGTATGACACTTTC 57.235 40.909 0.00 0.00 0.00 2.62
1582 1916 4.130118 ACACTTTCAGTAACTTGCCAGAG 58.870 43.478 0.00 0.00 0.00 3.35
1585 1919 2.024176 TCAGTAACTTGCCAGAGGGA 57.976 50.000 0.00 0.00 35.59 4.20
1848 2182 1.034292 GTACTACCTCCGGTCCGCTT 61.034 60.000 5.50 0.00 37.09 4.68
1857 2191 1.733360 TCCGGTCCGCTTTAATTTTCG 59.267 47.619 5.50 0.00 0.00 3.46
1923 2257 5.403766 CGACAATTATTTCGGATCAGAGGAG 59.596 44.000 0.00 0.00 0.00 3.69
1925 2259 6.051717 ACAATTATTTCGGATCAGAGGAGTG 58.948 40.000 0.00 0.00 0.00 3.51
1951 2285 2.124151 CCCCAGCCATGCAGTACC 60.124 66.667 0.00 0.00 0.00 3.34
1955 2289 1.549203 CCAGCCATGCAGTACCTTTT 58.451 50.000 0.00 0.00 0.00 2.27
2049 2383 5.479306 CGTCCTGAAAGACTGGAGAATAAA 58.521 41.667 0.00 0.00 45.01 1.40
2256 2592 9.770097 ATAACAGATTGTCAGGTATGAATGTAG 57.230 33.333 0.00 0.00 37.14 2.74
2795 3134 7.872113 AGCTCTGGTAAGAATTTTAGAATGG 57.128 36.000 0.00 0.00 30.03 3.16
2796 3135 7.406104 AGCTCTGGTAAGAATTTTAGAATGGT 58.594 34.615 0.00 0.00 30.03 3.55
2919 3258 0.178068 ATCAGGTGAAATCGACGGGG 59.822 55.000 0.00 0.00 0.00 5.73
2942 3281 5.644206 GGAGAGGGTCAAAGAATCACTTAAC 59.356 44.000 0.00 0.00 37.93 2.01
2983 3322 8.868522 ATTACTTCTGAAATGGAGAAATCACA 57.131 30.769 0.00 0.00 0.00 3.58
2992 3331 5.886960 ATGGAGAAATCACAGTTTGCTAC 57.113 39.130 0.00 0.00 0.00 3.58
2993 3332 4.072131 TGGAGAAATCACAGTTTGCTACC 58.928 43.478 0.00 0.00 0.00 3.18
3048 3387 6.903883 ACTACACGAATCAACATATGGTTC 57.096 37.500 7.80 5.23 44.30 3.62
3061 3400 1.366319 ATGGTTCTGCCCTCAACTCT 58.634 50.000 0.00 0.00 36.04 3.24
3187 3526 1.972872 AAGCTGGAACAAGTCACTGG 58.027 50.000 0.00 0.00 38.70 4.00
3312 3651 1.078848 AACTGGAGCGAGGATGTGC 60.079 57.895 0.00 0.00 0.00 4.57
3313 3652 1.830587 AACTGGAGCGAGGATGTGCA 61.831 55.000 0.00 0.00 0.00 4.57
3314 3653 1.145598 CTGGAGCGAGGATGTGCAT 59.854 57.895 0.00 0.00 0.00 3.96
3500 3839 3.744530 GCCATCCGCTAACTTCCTATGTT 60.745 47.826 0.00 0.00 0.00 2.71
3518 3857 3.995199 TGTTCTCATTGAGACTGTGGAC 58.005 45.455 15.90 10.73 38.51 4.02
3634 3973 2.606725 GTGCAGATGAGGAGATTGTTCG 59.393 50.000 0.00 0.00 0.00 3.95
3637 3976 2.606725 CAGATGAGGAGATTGTTCGTGC 59.393 50.000 0.00 0.00 0.00 5.34
3699 4038 2.281070 ACAGCGTTGCAGGTCAGG 60.281 61.111 0.00 0.00 0.00 3.86
3719 4058 3.438087 AGGAAACTGTGAGCAAATCATCG 59.562 43.478 0.00 0.00 40.92 3.84
3743 4082 6.239317 CGGATGGTCCAGAATCTTACAAGATA 60.239 42.308 4.93 0.00 39.64 1.98
3749 4088 6.205658 GTCCAGAATCTTACAAGATATTGGGC 59.794 42.308 22.11 19.60 44.67 5.36
3753 4092 6.929606 AGAATCTTACAAGATATTGGGCGTAC 59.070 38.462 4.88 0.00 44.67 3.67
3779 4118 5.705902 TCACATGATGATCAACTGCAAAAG 58.294 37.500 0.00 0.00 29.99 2.27
3826 4165 5.356426 TGATATAGTTGATGACGTTGTGGG 58.644 41.667 0.00 0.00 0.00 4.61
3868 4207 3.727258 TCAGGGGGCGATTGGTGG 61.727 66.667 0.00 0.00 0.00 4.61
3915 4254 4.577875 AGAGAACTTGAATGCTTCTGAGG 58.422 43.478 0.00 0.00 0.00 3.86
3985 4324 3.272031 GGAAGAACCTGCTGCTGC 58.728 61.111 8.89 8.89 40.20 5.25
3986 4325 1.303155 GGAAGAACCTGCTGCTGCT 60.303 57.895 17.00 0.00 40.48 4.24
3987 4326 1.584380 GGAAGAACCTGCTGCTGCTG 61.584 60.000 17.00 15.58 40.48 4.41
4028 4367 2.161855 GAGGACCATGTTGTTGATGCA 58.838 47.619 0.00 0.00 0.00 3.96
4077 4416 3.963374 TGTTGATGACCAAATTGGGAACA 59.037 39.130 17.27 13.10 43.37 3.18
4087 4426 3.849064 TGGGAACAACGCTTTGGG 58.151 55.556 7.92 0.00 37.00 4.12
4119 4467 4.458642 TCTTGCATAAAAGTGCTGTGCATA 59.541 37.500 0.00 0.00 44.27 3.14
4127 4475 2.831333 AGTGCTGTGCATATCACTAGC 58.169 47.619 17.02 0.82 45.81 3.42
4144 4492 0.319641 AGCGTTGGAGAGAACCGTTC 60.320 55.000 2.81 2.81 0.00 3.95
4221 4569 5.958380 GGTGATGGGTATCCTGATGAGTATA 59.042 44.000 0.00 0.00 32.09 1.47
4224 4572 7.819900 GTGATGGGTATCCTGATGAGTATAAAC 59.180 40.741 0.00 0.00 32.09 2.01
4364 4715 1.454479 CGCCCAAGCCCAGATGATT 60.454 57.895 0.00 0.00 34.57 2.57
4391 4742 8.490355 GCATTCACAAGAAGGAAAACAAATAAG 58.510 33.333 0.00 0.00 37.74 1.73
4432 4783 1.216678 TCCCTGACTCCTGATCCTCTC 59.783 57.143 0.00 0.00 0.00 3.20
4438 4789 4.724399 TGACTCCTGATCCTCTCATCTAC 58.276 47.826 0.00 0.00 32.10 2.59
4441 4792 4.665009 ACTCCTGATCCTCTCATCTACTCT 59.335 45.833 0.00 0.00 32.10 3.24
4442 4793 5.221925 ACTCCTGATCCTCTCATCTACTCTC 60.222 48.000 0.00 0.00 32.10 3.20
4443 4794 4.042809 TCCTGATCCTCTCATCTACTCTCC 59.957 50.000 0.00 0.00 32.10 3.71
4445 4796 3.392947 TGATCCTCTCATCTACTCTCCGT 59.607 47.826 0.00 0.00 0.00 4.69
4447 4798 5.071923 TGATCCTCTCATCTACTCTCCGTAA 59.928 44.000 0.00 0.00 0.00 3.18
4448 4799 5.369409 TCCTCTCATCTACTCTCCGTAAA 57.631 43.478 0.00 0.00 0.00 2.01
4453 4804 7.013846 CCTCTCATCTACTCTCCGTAAAGAAAT 59.986 40.741 0.00 0.00 0.00 2.17
4454 4805 8.975663 TCTCATCTACTCTCCGTAAAGAAATA 57.024 34.615 0.00 0.00 0.00 1.40
4455 4806 9.575868 TCTCATCTACTCTCCGTAAAGAAATAT 57.424 33.333 0.00 0.00 0.00 1.28
4461 4812 9.615295 CTACTCTCCGTAAAGAAATATAAGAGC 57.385 37.037 0.00 0.00 32.82 4.09
4464 4815 7.486647 TCTCCGTAAAGAAATATAAGAGCGTT 58.513 34.615 0.00 0.00 0.00 4.84
4465 4816 7.977853 TCTCCGTAAAGAAATATAAGAGCGTTT 59.022 33.333 0.00 0.00 0.00 3.60
4466 4817 8.483307 TCCGTAAAGAAATATAAGAGCGTTTT 57.517 30.769 0.00 0.00 0.00 2.43
4479 5210 6.952935 AAGAGCGTTTTTAGATCACTAGTG 57.047 37.500 17.17 17.17 0.00 2.74
4513 5244 7.547370 CACTCTTACATTTCTTTACAGAGGGAG 59.453 40.741 0.00 0.00 32.92 4.30
4515 5246 7.386851 TCTTACATTTCTTTACAGAGGGAGTG 58.613 38.462 0.00 0.00 0.00 3.51
4529 5260 6.948309 ACAGAGGGAGTGTTTTATTAAGCAAT 59.052 34.615 0.00 0.00 0.00 3.56
4565 5296 4.709886 GGGCTGGTTTTCCTTATGTATGTT 59.290 41.667 0.00 0.00 41.38 2.71
4566 5297 5.394115 GGGCTGGTTTTCCTTATGTATGTTG 60.394 44.000 0.00 0.00 41.38 3.33
4567 5298 5.185056 GGCTGGTTTTCCTTATGTATGTTGT 59.815 40.000 0.00 0.00 41.38 3.32
4569 5300 6.586082 GCTGGTTTTCCTTATGTATGTTGTTG 59.414 38.462 0.00 0.00 41.38 3.33
4570 5301 7.589958 TGGTTTTCCTTATGTATGTTGTTGT 57.410 32.000 0.00 0.00 41.38 3.32
4571 5302 8.693120 TGGTTTTCCTTATGTATGTTGTTGTA 57.307 30.769 0.00 0.00 41.38 2.41
4573 5304 9.567848 GGTTTTCCTTATGTATGTTGTTGTATG 57.432 33.333 0.00 0.00 36.94 2.39
4574 5305 9.567848 GTTTTCCTTATGTATGTTGTTGTATGG 57.432 33.333 0.00 0.00 0.00 2.74
4595 5326 3.118531 GAGGATGGGCATACTGGGATAT 58.881 50.000 0.00 0.00 30.53 1.63
4608 5339 8.819974 GCATACTGGGATATGAAAAATTGTTTG 58.180 33.333 0.00 0.00 34.94 2.93
4626 5357 5.406649 TGTTTGTTGCCAACTTTGTAGAAG 58.593 37.500 9.30 0.00 0.00 2.85
4650 5381 9.860898 AAGTGGATATGAAAAATCTTTGCTTAC 57.139 29.630 0.00 0.00 0.00 2.34
4664 5402 7.817418 TCTTTGCTTACATGTTTTTAGGACT 57.183 32.000 2.30 0.00 0.00 3.85
4666 5404 6.952773 TTGCTTACATGTTTTTAGGACTGT 57.047 33.333 2.30 0.00 0.00 3.55
4696 5434 0.472471 TTTCCGGTCCTCTGCTTTGT 59.528 50.000 0.00 0.00 0.00 2.83
4762 5507 1.206371 GCTTCCTCATGCTTGCCATTT 59.794 47.619 0.00 0.00 29.71 2.32
4779 5524 7.205515 TGCCATTTAATTTCCCATTTGGTAT 57.794 32.000 0.00 0.00 34.77 2.73
4780 5525 7.637511 TGCCATTTAATTTCCCATTTGGTATT 58.362 30.769 0.00 0.00 34.77 1.89
4788 5533 8.442660 AATTTCCCATTTGGTATTAGAAACCA 57.557 30.769 0.00 0.00 45.26 3.67
4789 5534 8.622572 ATTTCCCATTTGGTATTAGAAACCAT 57.377 30.769 0.00 0.00 46.16 3.55
4799 5544 6.099341 GGTATTAGAAACCATGCACCTTTTG 58.901 40.000 0.00 0.00 36.96 2.44
4832 5577 7.604545 GCTCCTGATATAATGACCCTAAACTTC 59.395 40.741 0.00 0.00 0.00 3.01
4837 5582 9.391006 TGATATAATGACCCTAAACTTCAACAC 57.609 33.333 0.00 0.00 0.00 3.32
4839 5584 3.935818 TGACCCTAAACTTCAACACCA 57.064 42.857 0.00 0.00 0.00 4.17
4840 5585 3.815809 TGACCCTAAACTTCAACACCAG 58.184 45.455 0.00 0.00 0.00 4.00
4841 5586 3.146847 GACCCTAAACTTCAACACCAGG 58.853 50.000 0.00 0.00 0.00 4.45
4870 5615 3.191581 CACTAGTTCCAGATCACTCACGT 59.808 47.826 0.00 0.00 0.00 4.49
4874 5619 0.244721 TCCAGATCACTCACGTGCAG 59.755 55.000 11.67 11.75 40.99 4.41
4875 5620 0.738762 CCAGATCACTCACGTGCAGG 60.739 60.000 11.67 4.53 40.99 4.85
4876 5621 0.037882 CAGATCACTCACGTGCAGGT 60.038 55.000 11.67 6.15 40.99 4.00
4877 5622 0.037882 AGATCACTCACGTGCAGGTG 60.038 55.000 29.08 29.08 40.99 4.00
4878 5623 1.630244 GATCACTCACGTGCAGGTGC 61.630 60.000 29.89 14.23 40.99 5.01
4879 5624 3.705638 CACTCACGTGCAGGTGCG 61.706 66.667 29.89 26.76 45.83 5.34
4913 5658 1.139095 CGAGGGAGACGTTGTAGCC 59.861 63.158 0.00 0.00 0.00 3.93
4932 5677 2.358003 GAGCAAGACACGCCAGCT 60.358 61.111 0.00 0.00 38.43 4.24
4935 5680 0.951040 AGCAAGACACGCCAGCTAAC 60.951 55.000 0.00 0.00 33.06 2.34
4963 5708 1.895131 CACAAGGATTTTCCACCCCTG 59.105 52.381 0.00 0.00 39.61 4.45
4967 5712 2.037208 ATTTTCCACCCCTGGCCG 59.963 61.111 0.00 0.00 37.49 6.13
4968 5713 3.600410 ATTTTCCACCCCTGGCCGG 62.600 63.158 3.88 3.88 37.49 6.13
4986 5731 1.682451 GGTGGCGGTGGTGATAGCTA 61.682 60.000 0.00 0.00 0.00 3.32
4987 5732 0.393077 GTGGCGGTGGTGATAGCTAT 59.607 55.000 5.76 5.76 0.00 2.97
4988 5733 1.616865 GTGGCGGTGGTGATAGCTATA 59.383 52.381 6.13 0.00 0.00 1.31
5042 5802 1.655114 GCTCCCCTCCTCTCCTCTCT 61.655 65.000 0.00 0.00 0.00 3.10
5045 5805 1.620259 CCCTCCTCTCCTCTCTGCT 59.380 63.158 0.00 0.00 0.00 4.24
5046 5806 0.756442 CCCTCCTCTCCTCTCTGCTG 60.756 65.000 0.00 0.00 0.00 4.41
5049 5809 0.032316 TCCTCTCCTCTCTGCTGCAT 60.032 55.000 1.31 0.00 0.00 3.96
5050 5810 0.390124 CCTCTCCTCTCTGCTGCATC 59.610 60.000 1.31 0.00 0.00 3.91
5051 5811 0.031043 CTCTCCTCTCTGCTGCATCG 59.969 60.000 1.31 0.00 0.00 3.84
5148 5910 2.738521 GATGTGACCGTGCGTGCT 60.739 61.111 0.00 0.00 0.00 4.40
5149 5911 3.015293 GATGTGACCGTGCGTGCTG 62.015 63.158 0.00 0.00 0.00 4.41
5237 5999 3.953652 TCCCCAGCCTTCCCCTCA 61.954 66.667 0.00 0.00 0.00 3.86
5241 6003 2.674220 CCAGCCTTCCCCTCACTCC 61.674 68.421 0.00 0.00 0.00 3.85
5309 6071 2.031120 CGGGACATAAATGTTGCCCAT 58.969 47.619 16.17 0.00 42.18 4.00
5310 6072 2.034558 CGGGACATAAATGTTGCCCATC 59.965 50.000 16.17 0.00 42.18 3.51
5390 6152 2.598589 CATCGTCCCATTTTGTTGCAG 58.401 47.619 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.367202 TTCCCGCTAAGCTCCCCAG 61.367 63.158 0.00 0.00 0.00 4.45
25 26 1.144276 GAGGTTCCCGCTAAGCTCC 59.856 63.158 13.27 0.00 44.48 4.70
58 59 3.621805 TTTGACCTGCGCTCGGGA 61.622 61.111 8.99 4.24 41.45 5.14
86 87 1.360185 TGCAAGAAAATGGGGGCATT 58.640 45.000 0.00 0.00 0.00 3.56
100 101 1.726892 CGTACACAGCTGCATTGCAAG 60.727 52.381 15.27 8.16 38.41 4.01
105 106 4.701663 AGCGTACACAGCTGCATT 57.298 50.000 15.27 0.00 44.22 3.56
186 191 2.108952 ACCATCTCAAAAGCTTCCTGGT 59.891 45.455 0.00 4.21 0.00 4.00
188 193 3.152341 ACACCATCTCAAAAGCTTCCTG 58.848 45.455 0.00 0.18 0.00 3.86
189 194 3.515602 ACACCATCTCAAAAGCTTCCT 57.484 42.857 0.00 0.00 0.00 3.36
190 195 4.327680 ACTACACCATCTCAAAAGCTTCC 58.672 43.478 0.00 0.00 0.00 3.46
191 196 7.982354 AGTATACTACACCATCTCAAAAGCTTC 59.018 37.037 2.75 0.00 0.00 3.86
193 198 7.425224 AGTATACTACACCATCTCAAAAGCT 57.575 36.000 2.75 0.00 0.00 3.74
195 200 9.307121 CTCAAGTATACTACACCATCTCAAAAG 57.693 37.037 5.65 0.00 0.00 2.27
199 204 7.255625 GCATCTCAAGTATACTACACCATCTCA 60.256 40.741 5.65 0.00 0.00 3.27
201 206 6.551227 TGCATCTCAAGTATACTACACCATCT 59.449 38.462 5.65 0.00 0.00 2.90
202 207 6.749139 TGCATCTCAAGTATACTACACCATC 58.251 40.000 5.65 0.00 0.00 3.51
210 238 7.057264 TCTACACTCTGCATCTCAAGTATACT 58.943 38.462 0.00 0.00 0.00 2.12
211 239 7.265647 TCTACACTCTGCATCTCAAGTATAC 57.734 40.000 0.00 0.00 0.00 1.47
213 241 6.975196 ATCTACACTCTGCATCTCAAGTAT 57.025 37.500 0.00 0.00 0.00 2.12
214 242 6.605194 AGAATCTACACTCTGCATCTCAAGTA 59.395 38.462 0.00 0.00 0.00 2.24
216 244 5.904941 AGAATCTACACTCTGCATCTCAAG 58.095 41.667 0.00 0.00 0.00 3.02
275 311 2.222445 CCGGTGACAAGAACTTTAACGG 59.778 50.000 0.00 0.00 0.00 4.44
276 312 3.125316 TCCGGTGACAAGAACTTTAACG 58.875 45.455 0.00 0.00 0.00 3.18
281 317 0.759346 AGCTCCGGTGACAAGAACTT 59.241 50.000 7.92 0.00 0.00 2.66
292 328 1.679032 GCTTAACCATCAAGCTCCGGT 60.679 52.381 0.00 0.00 44.04 5.28
313 349 1.536766 CACCGTGCATCTGAAACACAT 59.463 47.619 12.16 0.00 33.89 3.21
314 350 0.943673 CACCGTGCATCTGAAACACA 59.056 50.000 12.16 0.00 33.89 3.72
320 356 0.897621 ACAGATCACCGTGCATCTGA 59.102 50.000 28.74 6.57 46.23 3.27
327 363 0.673644 GGGGAACACAGATCACCGTG 60.674 60.000 8.03 8.03 39.10 4.94
330 366 2.355818 GGTTAGGGGAACACAGATCACC 60.356 54.545 0.00 0.00 40.91 4.02
334 370 1.916181 CCAGGTTAGGGGAACACAGAT 59.084 52.381 0.00 0.00 40.09 2.90
335 371 1.358152 CCAGGTTAGGGGAACACAGA 58.642 55.000 0.00 0.00 40.09 3.41
350 386 1.617850 CTGAGTAGATGCTAGGCCAGG 59.382 57.143 5.01 0.00 0.00 4.45
353 389 1.043816 TGCTGAGTAGATGCTAGGCC 58.956 55.000 0.00 0.00 0.00 5.19
354 390 3.671971 CGTATGCTGAGTAGATGCTAGGC 60.672 52.174 0.00 0.00 0.00 3.93
356 392 5.363979 TTCGTATGCTGAGTAGATGCTAG 57.636 43.478 0.00 0.00 0.00 3.42
358 394 4.038522 ACATTCGTATGCTGAGTAGATGCT 59.961 41.667 1.46 0.00 35.03 3.79
359 395 4.302455 ACATTCGTATGCTGAGTAGATGC 58.698 43.478 1.46 0.00 35.03 3.91
360 396 5.750547 ACAACATTCGTATGCTGAGTAGATG 59.249 40.000 11.73 0.00 35.03 2.90
361 397 5.907207 ACAACATTCGTATGCTGAGTAGAT 58.093 37.500 11.73 0.00 35.03 1.98
362 398 5.105917 TGACAACATTCGTATGCTGAGTAGA 60.106 40.000 11.73 0.00 35.03 2.59
363 399 5.004821 GTGACAACATTCGTATGCTGAGTAG 59.995 44.000 11.73 0.00 35.03 2.57
364 400 4.862574 GTGACAACATTCGTATGCTGAGTA 59.137 41.667 11.73 0.00 35.03 2.59
365 401 3.679980 GTGACAACATTCGTATGCTGAGT 59.320 43.478 11.73 1.55 35.03 3.41
366 402 3.928992 AGTGACAACATTCGTATGCTGAG 59.071 43.478 11.73 0.00 35.03 3.35
367 403 3.925379 AGTGACAACATTCGTATGCTGA 58.075 40.909 11.73 0.00 35.03 4.26
368 404 3.928992 AGAGTGACAACATTCGTATGCTG 59.071 43.478 1.46 2.93 37.73 4.41
376 412 5.766222 AGAAATGCAAGAGTGACAACATTC 58.234 37.500 0.00 0.00 33.80 2.67
403 439 5.869579 ACAATATTACCAGGCACTCCATAG 58.130 41.667 0.00 0.00 34.60 2.23
405 441 4.796110 ACAATATTACCAGGCACTCCAT 57.204 40.909 0.00 0.00 34.60 3.41
417 453 8.429493 AAAAAGGTAGCGAGGTACAATATTAC 57.571 34.615 13.45 0.00 0.00 1.89
446 482 7.639113 AGTCAGGTACACATTTTCTCAAAAA 57.361 32.000 0.00 0.00 38.66 1.94
447 483 7.227910 GGTAGTCAGGTACACATTTTCTCAAAA 59.772 37.037 0.00 0.00 34.41 2.44
448 484 6.708949 GGTAGTCAGGTACACATTTTCTCAAA 59.291 38.462 0.00 0.00 0.00 2.69
449 485 6.042781 AGGTAGTCAGGTACACATTTTCTCAA 59.957 38.462 0.00 0.00 0.00 3.02
450 486 5.542635 AGGTAGTCAGGTACACATTTTCTCA 59.457 40.000 0.00 0.00 0.00 3.27
451 487 6.038997 AGGTAGTCAGGTACACATTTTCTC 57.961 41.667 0.00 0.00 0.00 2.87
456 492 6.096987 CACTCATAGGTAGTCAGGTACACATT 59.903 42.308 0.00 0.00 0.00 2.71
493 529 0.963856 GTTGGAGGCGGGGGTAAAAG 60.964 60.000 0.00 0.00 0.00 2.27
497 533 1.717038 TTTTGTTGGAGGCGGGGGTA 61.717 55.000 0.00 0.00 0.00 3.69
499 535 2.203567 TTTTGTTGGAGGCGGGGG 60.204 61.111 0.00 0.00 0.00 5.40
500 536 1.530655 AGTTTTGTTGGAGGCGGGG 60.531 57.895 0.00 0.00 0.00 5.73
501 537 1.659794 CAGTTTTGTTGGAGGCGGG 59.340 57.895 0.00 0.00 0.00 6.13
502 538 1.106944 ACCAGTTTTGTTGGAGGCGG 61.107 55.000 0.00 0.00 39.08 6.13
503 539 0.310854 GACCAGTTTTGTTGGAGGCG 59.689 55.000 0.00 0.00 39.08 5.52
504 540 0.673985 GGACCAGTTTTGTTGGAGGC 59.326 55.000 0.00 0.00 39.08 4.70
505 541 1.681264 GTGGACCAGTTTTGTTGGAGG 59.319 52.381 0.00 0.00 39.08 4.30
511 799 0.179029 CGGGAGTGGACCAGTTTTGT 60.179 55.000 2.58 0.00 0.00 2.83
513 801 2.227737 ACGGGAGTGGACCAGTTTT 58.772 52.632 2.58 0.00 44.82 2.43
529 817 2.669569 CCCCAGACAACAGCCACG 60.670 66.667 0.00 0.00 0.00 4.94
568 856 2.917227 CACCGGGCTGCCCTTTTT 60.917 61.111 33.39 13.23 42.67 1.94
574 862 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
575 863 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
576 864 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
577 865 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
578 866 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
579 867 2.203070 GGAGCTACATGCACCGGG 60.203 66.667 6.32 0.00 42.21 5.73
603 891 3.605749 AATGTGGTCGGACCCTGCG 62.606 63.158 23.81 0.00 37.50 5.18
604 892 2.040544 CAATGTGGTCGGACCCTGC 61.041 63.158 23.81 14.23 37.50 4.85
605 893 1.377202 CCAATGTGGTCGGACCCTG 60.377 63.158 23.81 14.77 37.50 4.45
606 894 1.537889 TCCAATGTGGTCGGACCCT 60.538 57.895 23.81 6.46 39.03 4.34
607 895 1.078426 CTCCAATGTGGTCGGACCC 60.078 63.158 23.81 15.29 39.03 4.46
608 896 1.078426 CCTCCAATGTGGTCGGACC 60.078 63.158 20.36 20.36 39.03 4.46
609 897 1.745489 GCCTCCAATGTGGTCGGAC 60.745 63.158 0.00 0.00 39.03 4.79
610 898 1.561769 ATGCCTCCAATGTGGTCGGA 61.562 55.000 8.80 0.00 39.03 4.55
611 899 0.180171 TATGCCTCCAATGTGGTCGG 59.820 55.000 0.00 0.00 39.03 4.79
612 900 1.942657 CTTATGCCTCCAATGTGGTCG 59.057 52.381 0.00 0.00 39.03 4.79
613 901 3.281727 TCTTATGCCTCCAATGTGGTC 57.718 47.619 0.00 0.00 39.03 4.02
614 902 3.959495 ATCTTATGCCTCCAATGTGGT 57.041 42.857 0.00 0.00 39.03 4.16
615 903 6.322201 ACTTTTATCTTATGCCTCCAATGTGG 59.678 38.462 0.00 0.00 39.43 4.17
698 995 9.503427 CCGTAAAGTTTCAGAAAATTATCCATC 57.497 33.333 8.94 0.00 0.00 3.51
717 1017 6.512342 TCTAGTCCTTTCTTCTCCGTAAAG 57.488 41.667 0.00 0.00 0.00 1.85
765 1066 8.906867 ACACTCTGGAACCATTTGATTATTATG 58.093 33.333 0.00 0.00 0.00 1.90
816 1117 3.266772 TGGCAGTGAATATTCTTCCAGGT 59.733 43.478 16.24 0.00 0.00 4.00
818 1119 4.521146 AGTGGCAGTGAATATTCTTCCAG 58.479 43.478 16.24 6.87 0.00 3.86
819 1120 4.019411 TGAGTGGCAGTGAATATTCTTCCA 60.019 41.667 16.24 13.55 0.00 3.53
821 1122 5.587844 ACATGAGTGGCAGTGAATATTCTTC 59.412 40.000 16.24 9.46 0.00 2.87
823 1124 5.108187 ACATGAGTGGCAGTGAATATTCT 57.892 39.130 16.24 0.00 0.00 2.40
825 1126 4.847198 TGACATGAGTGGCAGTGAATATT 58.153 39.130 0.00 0.00 38.84 1.28
826 1127 4.492494 TGACATGAGTGGCAGTGAATAT 57.508 40.909 0.00 0.00 38.84 1.28
940 1271 5.484715 CCTAACAAAGAAGGACGGTAATGA 58.515 41.667 0.00 0.00 34.58 2.57
941 1272 4.094442 GCCTAACAAAGAAGGACGGTAATG 59.906 45.833 0.00 0.00 34.58 1.90
942 1273 4.259356 GCCTAACAAAGAAGGACGGTAAT 58.741 43.478 0.00 0.00 34.58 1.89
943 1274 3.071312 TGCCTAACAAAGAAGGACGGTAA 59.929 43.478 0.00 0.00 34.58 2.85
944 1275 2.633967 TGCCTAACAAAGAAGGACGGTA 59.366 45.455 0.00 0.00 34.58 4.02
945 1276 1.418637 TGCCTAACAAAGAAGGACGGT 59.581 47.619 0.00 0.00 34.58 4.83
946 1277 2.178912 TGCCTAACAAAGAAGGACGG 57.821 50.000 0.00 0.00 34.58 4.79
1038 1369 2.751166 GCTCCTGCTCTACAAGAACA 57.249 50.000 0.00 0.00 36.03 3.18
1114 1445 7.653767 ACTGGAGTATCTTTACAGAAAAACG 57.346 36.000 0.00 0.00 33.73 3.60
1131 1462 4.031611 GAGGGTCAATACCTTACTGGAGT 58.968 47.826 0.00 0.00 45.95 3.85
1166 1499 2.562298 CCTGCATTTTTAGCCCAAGTGA 59.438 45.455 0.00 0.00 0.00 3.41
1240 1574 1.760192 GCATTCCCTCATGCTTCACT 58.240 50.000 0.00 0.00 45.35 3.41
1264 1598 2.267174 ATCCAGCTCGCTGCAATATT 57.733 45.000 13.25 0.00 45.94 1.28
1492 1826 4.161754 GGTTCTTGGCCTAGTAGCTCTAAA 59.838 45.833 14.12 0.00 0.00 1.85
1567 1901 1.677217 GCTCCCTCTGGCAAGTTACTG 60.677 57.143 0.00 0.00 0.00 2.74
1582 1916 6.412362 TCTATTTCTGACTGATTAGCTCCC 57.588 41.667 0.00 0.00 0.00 4.30
1585 1919 6.477053 TGCTCTATTTCTGACTGATTAGCT 57.523 37.500 0.00 0.00 0.00 3.32
1675 2009 4.003648 GTGCCAAGTATCTTAAGTGCACT 58.996 43.478 15.25 15.25 43.25 4.40
1848 2182 4.215399 CAGCAGTTCCTCCACGAAAATTAA 59.785 41.667 0.00 0.00 0.00 1.40
1857 2191 0.175760 TATCGCAGCAGTTCCTCCAC 59.824 55.000 0.00 0.00 0.00 4.02
1869 2203 3.499048 ACACGACTTTGTACTATCGCAG 58.501 45.455 0.00 0.00 38.12 5.18
1895 2229 5.006649 TCTGATCCGAAATAATTGTCGCAAG 59.993 40.000 0.00 0.00 35.93 4.01
1897 2231 4.438148 TCTGATCCGAAATAATTGTCGCA 58.562 39.130 0.00 0.00 35.93 5.10
1923 2257 3.157087 CATGGCTGGGGAAATATACCAC 58.843 50.000 0.00 0.00 0.00 4.16
1925 2259 2.171003 GCATGGCTGGGGAAATATACC 58.829 52.381 0.00 0.00 0.00 2.73
1951 2285 7.094805 TGCCATTAGTTGCTGTACTAAGAAAAG 60.095 37.037 10.74 0.00 42.20 2.27
1955 2289 5.414789 TGCCATTAGTTGCTGTACTAAGA 57.585 39.130 10.74 0.00 42.20 2.10
2049 2383 2.141535 GCTGATCGCCGTTTAGAGAT 57.858 50.000 0.00 0.00 0.00 2.75
2256 2592 7.617041 ACTATTTTGCAGTTATGAGAAGTCC 57.383 36.000 0.00 0.00 0.00 3.85
2795 3134 8.723942 AATACAGACAGGAAGATGACAAATAC 57.276 34.615 0.00 0.00 0.00 1.89
2835 3174 4.724399 ACCTGTTCATGGTCAAATACACA 58.276 39.130 0.00 0.00 31.03 3.72
2919 3258 5.348997 CGTTAAGTGATTCTTTGACCCTCTC 59.651 44.000 0.00 0.00 37.56 3.20
3048 3387 2.039405 GCAGCAGAGTTGAGGGCAG 61.039 63.158 0.00 0.00 0.00 4.85
3187 3526 2.857592 ATTTCGCTCCATGCAATCAC 57.142 45.000 0.00 0.00 43.06 3.06
3207 3546 3.448093 TTGGTCCAATTGTAGCATGGA 57.552 42.857 3.62 0.00 40.84 3.41
3279 3618 2.164422 TCCAGTTGCTAGTGTCATCTCG 59.836 50.000 2.31 0.00 0.00 4.04
3312 3651 7.661127 GAGGATCTTCTTTCTGATGATGATG 57.339 40.000 0.00 0.00 38.97 3.07
3500 3839 1.067565 GCGTCCACAGTCTCAATGAGA 60.068 52.381 9.18 9.18 36.22 3.27
3518 3857 2.125552 TCAACATCCTCCTGCGCG 60.126 61.111 0.00 0.00 0.00 6.86
3634 3973 3.676646 GCAATTGTCTTTCCTGAATGCAC 59.323 43.478 7.40 0.00 0.00 4.57
3637 3976 4.868171 CCATGCAATTGTCTTTCCTGAATG 59.132 41.667 7.40 0.00 0.00 2.67
3699 4038 3.436704 TCCGATGATTTGCTCACAGTTTC 59.563 43.478 0.00 0.00 36.48 2.78
3719 4058 5.359194 TCTTGTAAGATTCTGGACCATCC 57.641 43.478 0.00 0.00 36.96 3.51
3743 4082 1.280710 TCATGTGAAGGTACGCCCAAT 59.719 47.619 0.00 0.00 34.66 3.16
3749 4088 5.006068 CAGTTGATCATCATGTGAAGGTACG 59.994 44.000 6.55 0.00 40.97 3.67
3753 4092 3.692593 TGCAGTTGATCATCATGTGAAGG 59.307 43.478 6.55 0.00 40.97 3.46
3779 4118 1.195115 TCCCAGATGCACTAGTGACC 58.805 55.000 27.08 13.37 0.00 4.02
3826 4165 4.191544 TGTACTATTGCCTGTTCTCATGC 58.808 43.478 0.00 0.00 36.11 4.06
3841 4180 0.759436 CGCCCCCTGACCTGTACTAT 60.759 60.000 0.00 0.00 0.00 2.12
3868 4207 1.541588 GTCCAGTGGCATTGAAAGGTC 59.458 52.381 12.01 0.00 0.00 3.85
3915 4254 5.314923 TCTTGCATTGAACTTGGCTTATC 57.685 39.130 0.00 0.00 0.00 1.75
3985 4324 4.655647 ACCCTGGCACTGCAGCAG 62.656 66.667 21.54 21.54 37.52 4.24
3986 4325 4.960866 CACCCTGGCACTGCAGCA 62.961 66.667 15.27 2.62 35.83 4.41
4028 4367 2.636768 GCAAGATAAGGTTTTGCGCT 57.363 45.000 9.73 0.00 37.97 5.92
4077 4416 4.912395 TGCAGGGCCCAAAGCGTT 62.912 61.111 27.56 0.00 45.17 4.84
4119 4467 2.166664 GGTTCTCTCCAACGCTAGTGAT 59.833 50.000 10.99 0.00 0.00 3.06
4127 4475 2.228343 ACTAGAACGGTTCTCTCCAACG 59.772 50.000 25.51 9.79 41.14 4.10
4144 4492 4.237724 TGCTTCGACAGTGAATGAACTAG 58.762 43.478 0.00 0.00 0.00 2.57
4221 4569 9.945904 CACTTTCCTCCTTTTACTAGATAGTTT 57.054 33.333 0.00 0.00 37.73 2.66
4224 4572 6.987404 GCCACTTTCCTCCTTTTACTAGATAG 59.013 42.308 0.00 0.00 0.00 2.08
4271 4622 6.374417 TCTATTTTAGTATCTGGGGCATCC 57.626 41.667 0.00 0.00 0.00 3.51
4273 4624 5.251700 CCCTCTATTTTAGTATCTGGGGCAT 59.748 44.000 0.00 0.00 0.00 4.40
4274 4625 4.597507 CCCTCTATTTTAGTATCTGGGGCA 59.402 45.833 0.00 0.00 0.00 5.36
4364 4715 4.998671 TGTTTTCCTTCTTGTGAATGCA 57.001 36.364 0.00 0.00 0.00 3.96
4391 4742 3.604582 AGAAGACTGCATTACTTCTGCC 58.395 45.455 21.07 3.92 45.35 4.85
4438 4789 7.140048 ACGCTCTTATATTTCTTTACGGAGAG 58.860 38.462 0.00 0.00 33.16 3.20
4441 4792 8.483307 AAAACGCTCTTATATTTCTTTACGGA 57.517 30.769 0.00 0.00 0.00 4.69
4453 4804 9.731819 CACTAGTGATCTAAAAACGCTCTTATA 57.268 33.333 18.45 0.00 0.00 0.98
4454 4805 8.467598 TCACTAGTGATCTAAAAACGCTCTTAT 58.532 33.333 21.74 0.00 34.14 1.73
4455 4806 7.823665 TCACTAGTGATCTAAAAACGCTCTTA 58.176 34.615 21.74 0.00 34.14 2.10
4457 4808 6.268825 TCACTAGTGATCTAAAAACGCTCT 57.731 37.500 21.74 0.00 34.14 4.09
4471 4822 8.631480 TGTAAGAGTGTTTAGATCACTAGTGA 57.369 34.615 27.07 27.07 44.68 3.41
4472 4823 9.862371 AATGTAAGAGTGTTTAGATCACTAGTG 57.138 33.333 17.17 17.17 44.68 2.74
4488 5219 7.235812 ACTCCCTCTGTAAAGAAATGTAAGAGT 59.764 37.037 0.00 0.00 0.00 3.24
4495 5226 6.884280 AAACACTCCCTCTGTAAAGAAATG 57.116 37.500 0.00 0.00 0.00 2.32
4565 5296 1.294041 TGCCCATCCTCCATACAACA 58.706 50.000 0.00 0.00 0.00 3.33
4566 5297 2.664402 ATGCCCATCCTCCATACAAC 57.336 50.000 0.00 0.00 0.00 3.32
4567 5298 3.072915 CAGTATGCCCATCCTCCATACAA 59.927 47.826 11.24 0.00 42.19 2.41
4569 5300 2.026822 CCAGTATGCCCATCCTCCATAC 60.027 54.545 0.00 0.00 40.82 2.39
4570 5301 2.269023 CCAGTATGCCCATCCTCCATA 58.731 52.381 0.00 0.00 31.97 2.74
4571 5302 1.070604 CCAGTATGCCCATCCTCCAT 58.929 55.000 0.00 0.00 31.97 3.41
4573 5304 0.768221 TCCCAGTATGCCCATCCTCC 60.768 60.000 0.00 0.00 31.97 4.30
4574 5305 1.366319 ATCCCAGTATGCCCATCCTC 58.634 55.000 0.00 0.00 31.97 3.71
4608 5339 3.630312 TCCACTTCTACAAAGTTGGCAAC 59.370 43.478 22.48 22.48 0.00 4.17
4626 5357 9.807649 ATGTAAGCAAAGATTTTTCATATCCAC 57.192 29.630 0.00 0.00 0.00 4.02
4649 5380 8.567948 CACAGAAATACAGTCCTAAAAACATGT 58.432 33.333 0.00 0.00 0.00 3.21
4650 5381 8.567948 ACACAGAAATACAGTCCTAAAAACATG 58.432 33.333 0.00 0.00 0.00 3.21
4659 5390 4.755123 CGGAAAACACAGAAATACAGTCCT 59.245 41.667 0.00 0.00 0.00 3.85
4664 5402 3.816523 GGACCGGAAAACACAGAAATACA 59.183 43.478 9.46 0.00 0.00 2.29
4666 5404 4.041198 AGAGGACCGGAAAACACAGAAATA 59.959 41.667 9.46 0.00 0.00 1.40
4696 5434 9.378551 CTAAAACCACAGAAATGTAGTATGCTA 57.621 33.333 0.00 0.00 0.00 3.49
4762 5507 9.548631 TGGTTTCTAATACCAAATGGGAAATTA 57.451 29.630 4.17 4.64 42.50 1.40
4806 5551 7.010339 AGTTTAGGGTCATTATATCAGGAGC 57.990 40.000 0.00 0.00 0.00 4.70
4832 5577 1.302832 GTGGCTCCTCCTGGTGTTG 60.303 63.158 0.00 0.00 35.26 3.33
4837 5582 0.827368 GAACTAGTGGCTCCTCCTGG 59.173 60.000 0.00 0.00 35.26 4.45
4839 5584 0.413832 TGGAACTAGTGGCTCCTCCT 59.586 55.000 12.31 0.00 35.26 3.69
4840 5585 0.827368 CTGGAACTAGTGGCTCCTCC 59.173 60.000 12.31 7.67 0.00 4.30
4841 5586 1.853963 TCTGGAACTAGTGGCTCCTC 58.146 55.000 12.31 0.00 0.00 3.71
4870 5615 3.695606 GTCTCCTCCGCACCTGCA 61.696 66.667 0.00 0.00 42.21 4.41
4874 5619 1.216710 CTCTTGTCTCCTCCGCACC 59.783 63.158 0.00 0.00 0.00 5.01
4875 5620 0.172352 CTCTCTTGTCTCCTCCGCAC 59.828 60.000 0.00 0.00 0.00 5.34
4876 5621 1.599606 GCTCTCTTGTCTCCTCCGCA 61.600 60.000 0.00 0.00 0.00 5.69
4877 5622 1.140804 GCTCTCTTGTCTCCTCCGC 59.859 63.158 0.00 0.00 0.00 5.54
4878 5623 1.027255 TCGCTCTCTTGTCTCCTCCG 61.027 60.000 0.00 0.00 0.00 4.63
4879 5624 0.738389 CTCGCTCTCTTGTCTCCTCC 59.262 60.000 0.00 0.00 0.00 4.30
4913 5658 2.675056 GCTGGCGTGTCTTGCTCAG 61.675 63.158 0.00 0.00 35.26 3.35
4967 5712 1.682451 TAGCTATCACCACCGCCACC 61.682 60.000 0.00 0.00 0.00 4.61
4968 5713 0.393077 ATAGCTATCACCACCGCCAC 59.607 55.000 0.00 0.00 0.00 5.01
4969 5714 1.893137 CTATAGCTATCACCACCGCCA 59.107 52.381 10.16 0.00 0.00 5.69
4970 5715 1.404315 GCTATAGCTATCACCACCGCC 60.404 57.143 17.75 0.00 38.21 6.13
4971 5716 1.272490 TGCTATAGCTATCACCACCGC 59.728 52.381 24.61 3.83 42.66 5.68
4986 5731 2.359900 CAACGGAAGGAGCTTTGCTAT 58.640 47.619 0.00 0.00 39.88 2.97
4987 5732 1.610624 CCAACGGAAGGAGCTTTGCTA 60.611 52.381 0.00 0.00 39.88 3.49
4988 5733 0.890996 CCAACGGAAGGAGCTTTGCT 60.891 55.000 0.00 0.00 43.88 3.91
5028 5773 1.394266 GCAGCAGAGAGGAGAGGAGG 61.394 65.000 0.00 0.00 0.00 4.30
5051 5811 2.432628 CCAAGGACGGCGTCAGTC 60.433 66.667 37.13 22.28 37.86 3.51
5121 5883 3.503363 GTCACATCAGCGGCTGGC 61.503 66.667 28.18 2.30 44.05 4.85
5122 5884 2.821366 GGTCACATCAGCGGCTGG 60.821 66.667 28.18 16.33 31.51 4.85
5123 5885 3.190849 CGGTCACATCAGCGGCTG 61.191 66.667 23.72 23.72 33.59 4.85
5124 5886 3.695606 ACGGTCACATCAGCGGCT 61.696 61.111 0.00 0.00 41.63 5.52
5263 6025 2.380102 CATAAATGCAGCACTCGAGC 57.620 50.000 13.61 0.00 0.00 5.03
5309 6071 1.490490 GGCCAGAGAGAGAGAGAGAGA 59.510 57.143 0.00 0.00 0.00 3.10
5310 6072 1.492176 AGGCCAGAGAGAGAGAGAGAG 59.508 57.143 5.01 0.00 0.00 3.20
5390 6152 4.641989 ACCATGTTTATGACCAAGATGAGC 59.358 41.667 0.00 0.00 36.36 4.26


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

AutoCloner maintained by Alex Coulton.