Multiple sequence alignment - TraesCS4B01G081900

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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 TraesCS4B01G081900 chr4B 100.000 3519 0 0 1 3519 80592574 80596092 0.000000e+00 6499.0
1 TraesCS4B01G081900 chr4B 83.472 1319 143 54 2195 3465 68730183 68728892 0.000000e+00 1158.0
2 TraesCS4B01G081900 chr4B 81.446 927 107 41 2560 3447 68959248 68958348 0.000000e+00 699.0
3 TraesCS4B01G081900 chr4B 88.521 514 53 3 1219 1726 80557164 80557677 4.990000e-173 617.0
4 TraesCS4B01G081900 chr4B 88.521 514 53 3 1219 1726 80585834 80586347 4.990000e-173 617.0
5 TraesCS4B01G081900 chr4B 90.489 368 32 1 1223 1590 68961542 68961178 1.900000e-132 483.0
6 TraesCS4B01G081900 chr4B 87.879 264 16 6 176 430 68962440 68962184 2.660000e-76 296.0
7 TraesCS4B01G081900 chr4B 84.387 269 34 5 2195 2457 68959814 68959548 1.250000e-64 257.0
8 TraesCS4B01G081900 chr4B 89.474 190 11 4 207 393 68730562 68730379 7.600000e-57 231.0
9 TraesCS4B01G081900 chr4B 75.641 390 69 18 2255 2641 80559198 80559564 1.680000e-38 171.0
10 TraesCS4B01G081900 chr4B 75.641 390 69 18 2255 2641 80587868 80588234 1.680000e-38 171.0
11 TraesCS4B01G081900 chr4B 83.085 201 19 7 920 1114 80556912 80557103 6.040000e-38 169.0
12 TraesCS4B01G081900 chr4B 83.085 201 19 7 920 1114 80585582 80585773 6.040000e-38 169.0
13 TraesCS4B01G081900 chr4D 88.831 1737 112 39 1809 3517 54475629 54477311 0.000000e+00 2058.0
14 TraesCS4B01G081900 chr4D 89.990 1029 63 22 2149 3156 54605416 54606425 0.000000e+00 1293.0
15 TraesCS4B01G081900 chr4D 83.948 1302 135 46 2195 3447 47334689 47333413 0.000000e+00 1179.0
16 TraesCS4B01G081900 chr4D 85.232 948 85 29 749 1690 54604112 54605010 0.000000e+00 924.0
17 TraesCS4B01G081900 chr4D 89.258 512 49 2 1198 1706 47336600 47336092 1.380000e-178 636.0
18 TraesCS4B01G081900 chr4D 88.212 509 53 4 1223 1727 54475103 54475608 5.030000e-168 601.0
19 TraesCS4B01G081900 chr4D 91.477 352 25 3 2767 3113 54479578 54479929 2.460000e-131 479.0
20 TraesCS4B01G081900 chr4D 90.305 361 31 2 1794 2151 54605026 54605385 1.480000e-128 470.0
21 TraesCS4B01G081900 chr4D 85.470 351 38 8 799 1149 47336952 47336615 1.550000e-93 353.0
22 TraesCS4B01G081900 chr4D 87.379 309 28 5 802 1107 54474744 54475044 9.350000e-91 344.0
23 TraesCS4B01G081900 chr4D 91.053 190 12 4 522 710 54603942 54604127 5.830000e-63 252.0
24 TraesCS4B01G081900 chr4D 90.155 193 10 7 522 710 54474513 54474700 3.510000e-60 243.0
25 TraesCS4B01G081900 chr4D 86.099 223 16 7 214 430 54603691 54603904 3.530000e-55 226.0
26 TraesCS4B01G081900 chr4D 83.268 257 29 10 902 1146 54446470 54446724 1.270000e-54 224.0
27 TraesCS4B01G081900 chr4D 83.019 265 21 8 169 430 47337550 47337307 5.910000e-53 219.0
28 TraesCS4B01G081900 chr4D 80.508 236 39 7 1906 2138 54448332 54448563 1.300000e-39 174.0
29 TraesCS4B01G081900 chr4A 87.256 1538 116 25 1821 3339 542532786 542531310 0.000000e+00 1681.0
30 TraesCS4B01G081900 chr4A 84.115 1322 134 42 2195 3465 551133542 551134838 0.000000e+00 1208.0
31 TraesCS4B01G081900 chr4A 92.829 516 34 1 1215 1727 542533310 542532795 0.000000e+00 745.0
32 TraesCS4B01G081900 chr4A 89.020 510 49 3 1223 1728 542555714 542555208 2.980000e-175 625.0
33 TraesCS4B01G081900 chr4A 88.732 497 50 2 1210 1703 551132596 551133089 1.400000e-168 603.0
34 TraesCS4B01G081900 chr4A 86.686 353 34 7 799 1146 551132228 551132572 2.560000e-101 379.0
35 TraesCS4B01G081900 chr4A 85.196 358 36 9 802 1149 542533688 542533338 5.590000e-93 351.0
36 TraesCS4B01G081900 chr4A 80.171 469 41 17 2 430 542534404 542533948 1.590000e-78 303.0
37 TraesCS4B01G081900 chr4A 88.136 236 10 6 207 430 551131718 551131947 7.490000e-67 265.0
38 TraesCS4B01G081900 chr4A 83.922 255 30 7 902 1146 542556013 542555760 2.110000e-57 233.0
39 TraesCS4B01G081900 chr4A 90.756 119 9 1 592 710 551132027 551132143 1.310000e-34 158.0
40 TraesCS4B01G081900 chr6D 81.928 83 7 3 1725 1804 72021739 72021816 2.930000e-06 63.9
41 TraesCS4B01G081900 chr3D 97.143 35 1 0 593 627 91709462 91709428 3.790000e-05 60.2
42 TraesCS4B01G081900 chr6A 80.723 83 8 3 1725 1804 88767598 88767675 1.360000e-04 58.4
43 TraesCS4B01G081900 chr5B 100.000 30 0 0 1767 1796 290819768 290819797 4.910000e-04 56.5


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 TraesCS4B01G081900 chr4B 80592574 80596092 3518 False 6499.00 6499 100.000000 1 3519 1 chr4B.!!$F1 3518
1 TraesCS4B01G081900 chr4B 68728892 68730562 1670 True 694.50 1158 86.473000 207 3465 2 chr4B.!!$R1 3258
2 TraesCS4B01G081900 chr4B 68958348 68962440 4092 True 433.75 699 86.050250 176 3447 4 chr4B.!!$R2 3271
3 TraesCS4B01G081900 chr4B 80556912 80559564 2652 False 319.00 617 82.415667 920 2641 3 chr4B.!!$F2 1721
4 TraesCS4B01G081900 chr4B 80585582 80588234 2652 False 319.00 617 82.415667 920 2641 3 chr4B.!!$F3 1721
5 TraesCS4B01G081900 chr4D 54474513 54479929 5416 False 745.00 2058 89.210800 522 3517 5 chr4D.!!$F2 2995
6 TraesCS4B01G081900 chr4D 54603691 54606425 2734 False 633.00 1293 88.535800 214 3156 5 chr4D.!!$F3 2942
7 TraesCS4B01G081900 chr4D 47333413 47337550 4137 True 596.75 1179 85.423750 169 3447 4 chr4D.!!$R1 3278
8 TraesCS4B01G081900 chr4A 542531310 542534404 3094 True 770.00 1681 86.363000 2 3339 4 chr4A.!!$R1 3337
9 TraesCS4B01G081900 chr4A 551131718 551134838 3120 False 522.60 1208 87.685000 207 3465 5 chr4A.!!$F1 3258
10 TraesCS4B01G081900 chr4A 542555208 542556013 805 True 429.00 625 86.471000 902 1728 2 chr4A.!!$R2 826

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
796 961 0.105224 TCGTTCCCGCTCTGTTCAAA 59.895 50.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2618 4145 0.320374 TGCCCACAGTTCTACTTCCG 59.68 55.0 0.0 0.0 0.0 4.3 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
64 65 8.457238 AAAAGTTGTCTTTGCTCTAAGAATCT 57.543 30.769 0.00 0.00 42.26 2.40
73 74 7.716998 TCTTTGCTCTAAGAATCTGAAACAAGT 59.283 33.333 0.00 0.00 31.45 3.16
77 78 8.367911 TGCTCTAAGAATCTGAAACAAGTCTTA 58.632 33.333 0.00 0.00 0.00 2.10
89 90 9.775854 CTGAAACAAGTCTTATATGGATCTGAT 57.224 33.333 0.00 0.00 0.00 2.90
120 125 5.277857 AGATAAATCCAACACCCTACTCG 57.722 43.478 0.00 0.00 0.00 4.18
145 150 3.353836 CGAACCGGTGGTGCCAAG 61.354 66.667 8.52 0.00 35.34 3.61
151 156 1.515521 CCGGTGGTGCCAAGTTTCTC 61.516 60.000 0.00 0.00 36.97 2.87
184 206 2.162338 TTGTCCAAGACGGGCCTACG 62.162 60.000 0.84 0.00 39.41 3.51
204 226 3.316588 ACGAGTCTATGATACAGTGGCAG 59.683 47.826 0.00 0.00 0.00 4.85
205 227 3.304996 CGAGTCTATGATACAGTGGCAGG 60.305 52.174 0.00 0.00 0.00 4.85
230 271 1.333177 GCCGTAGAGTCCCATCAGAT 58.667 55.000 0.00 0.00 0.00 2.90
272 314 1.203100 GGGCAAATCAGGGCATCCTAT 60.203 52.381 0.00 0.00 42.67 2.57
281 323 0.685097 GGGCATCCTATAGGCGTTCA 59.315 55.000 14.50 0.00 35.10 3.18
317 361 0.109086 TCCGCTTGCTTCTTCTCTCG 60.109 55.000 0.00 0.00 0.00 4.04
396 440 2.755650 CGTTGTGAGCCTTGAGTACTT 58.244 47.619 0.00 0.00 0.00 2.24
439 509 0.528017 GTCCTTGGCTAGCCTTTTGC 59.472 55.000 33.07 17.08 41.71 3.68
454 524 6.220579 GCCTTTTGCTTCTTTTCTTTCATC 57.779 37.500 0.00 0.00 36.87 2.92
456 526 5.698089 CCTTTTGCTTCTTTTCTTTCATCCC 59.302 40.000 0.00 0.00 0.00 3.85
457 527 6.463472 CCTTTTGCTTCTTTTCTTTCATCCCT 60.463 38.462 0.00 0.00 0.00 4.20
458 528 7.255942 CCTTTTGCTTCTTTTCTTTCATCCCTA 60.256 37.037 0.00 0.00 0.00 3.53
459 529 6.575162 TTGCTTCTTTTCTTTCATCCCTAC 57.425 37.500 0.00 0.00 0.00 3.18
460 530 5.630121 TGCTTCTTTTCTTTCATCCCTACA 58.370 37.500 0.00 0.00 0.00 2.74
461 531 6.248433 TGCTTCTTTTCTTTCATCCCTACAT 58.752 36.000 0.00 0.00 0.00 2.29
462 532 6.151648 TGCTTCTTTTCTTTCATCCCTACATG 59.848 38.462 0.00 0.00 0.00 3.21
463 533 6.151817 GCTTCTTTTCTTTCATCCCTACATGT 59.848 38.462 2.69 2.69 0.00 3.21
464 534 7.452880 TTCTTTTCTTTCATCCCTACATGTG 57.547 36.000 9.11 0.00 0.00 3.21
465 535 5.415701 TCTTTTCTTTCATCCCTACATGTGC 59.584 40.000 9.11 0.00 0.00 4.57
466 536 3.998913 TCTTTCATCCCTACATGTGCA 57.001 42.857 9.11 0.00 0.00 4.57
467 537 4.508551 TCTTTCATCCCTACATGTGCAT 57.491 40.909 9.11 0.00 0.00 3.96
468 538 4.858850 TCTTTCATCCCTACATGTGCATT 58.141 39.130 9.11 0.00 0.00 3.56
469 539 4.641541 TCTTTCATCCCTACATGTGCATTG 59.358 41.667 9.11 0.09 0.00 2.82
470 540 3.929955 TCATCCCTACATGTGCATTGA 57.070 42.857 9.11 2.59 0.00 2.57
471 541 3.812262 TCATCCCTACATGTGCATTGAG 58.188 45.455 9.11 0.00 0.00 3.02
472 542 3.455543 TCATCCCTACATGTGCATTGAGA 59.544 43.478 9.11 0.00 0.00 3.27
473 543 3.998913 TCCCTACATGTGCATTGAGAA 57.001 42.857 9.11 0.00 0.00 2.87
474 544 3.609853 TCCCTACATGTGCATTGAGAAC 58.390 45.455 9.11 0.00 0.00 3.01
475 545 3.264193 TCCCTACATGTGCATTGAGAACT 59.736 43.478 9.11 0.00 0.00 3.01
476 546 4.012374 CCCTACATGTGCATTGAGAACTT 58.988 43.478 9.11 0.00 0.00 2.66
477 547 4.460382 CCCTACATGTGCATTGAGAACTTT 59.540 41.667 9.11 0.00 0.00 2.66
478 548 5.392380 CCCTACATGTGCATTGAGAACTTTC 60.392 44.000 9.11 0.00 0.00 2.62
479 549 4.510038 ACATGTGCATTGAGAACTTTCC 57.490 40.909 0.00 0.00 0.00 3.13
480 550 3.058016 ACATGTGCATTGAGAACTTTCCG 60.058 43.478 0.00 0.00 0.00 4.30
481 551 2.844946 TGTGCATTGAGAACTTTCCGA 58.155 42.857 0.00 0.00 0.00 4.55
482 552 2.548057 TGTGCATTGAGAACTTTCCGAC 59.452 45.455 0.00 0.00 0.00 4.79
483 553 1.798223 TGCATTGAGAACTTTCCGACG 59.202 47.619 0.00 0.00 0.00 5.12
484 554 1.128692 GCATTGAGAACTTTCCGACGG 59.871 52.381 7.84 7.84 0.00 4.79
485 555 1.732259 CATTGAGAACTTTCCGACGGG 59.268 52.381 15.25 0.00 0.00 5.28
486 556 0.754472 TTGAGAACTTTCCGACGGGT 59.246 50.000 15.25 0.52 33.83 5.28
487 557 1.619654 TGAGAACTTTCCGACGGGTA 58.380 50.000 15.25 0.00 33.83 3.69
488 558 1.270550 TGAGAACTTTCCGACGGGTAC 59.729 52.381 15.25 0.51 33.83 3.34
502 572 1.666580 GGTACCAGATAGGCCGAGC 59.333 63.158 7.15 0.00 43.14 5.03
503 573 0.828343 GGTACCAGATAGGCCGAGCT 60.828 60.000 7.15 0.00 43.14 4.09
504 574 1.547223 GGTACCAGATAGGCCGAGCTA 60.547 57.143 7.15 0.00 43.14 3.32
505 575 1.813786 GTACCAGATAGGCCGAGCTAG 59.186 57.143 2.37 0.00 43.14 3.42
506 576 0.540830 ACCAGATAGGCCGAGCTAGG 60.541 60.000 8.78 8.78 43.14 3.02
507 577 0.251386 CCAGATAGGCCGAGCTAGGA 60.251 60.000 18.16 0.00 0.00 2.94
508 578 1.621992 CAGATAGGCCGAGCTAGGAA 58.378 55.000 18.16 1.07 0.00 3.36
509 579 1.543802 CAGATAGGCCGAGCTAGGAAG 59.456 57.143 18.16 0.00 0.00 3.46
510 580 0.892063 GATAGGCCGAGCTAGGAAGG 59.108 60.000 18.16 2.16 0.00 3.46
511 581 0.483328 ATAGGCCGAGCTAGGAAGGA 59.517 55.000 18.16 0.00 0.00 3.36
512 582 0.260816 TAGGCCGAGCTAGGAAGGAA 59.739 55.000 18.16 0.00 0.00 3.36
513 583 1.144276 GGCCGAGCTAGGAAGGAAC 59.856 63.158 18.16 0.00 0.00 3.62
540 610 6.050432 TCAGATGTGCATTTTGCTTCTTTTT 58.950 32.000 0.00 0.00 45.31 1.94
547 617 7.066043 TGTGCATTTTGCTTCTTTTTCTTTCAT 59.934 29.630 0.00 0.00 45.31 2.57
549 619 7.280428 TGCATTTTGCTTCTTTTTCTTTCATCA 59.720 29.630 0.75 0.00 45.31 3.07
643 714 8.379331 AGAAGCTCTATACAGGTTTCTTTCTTT 58.621 33.333 0.00 0.00 34.21 2.52
645 716 8.329203 AGCTCTATACAGGTTTCTTTCTTTTG 57.671 34.615 0.00 0.00 0.00 2.44
736 810 3.399234 AAAAAGGAGGAATGCCCCC 57.601 52.632 0.00 0.00 34.66 5.40
737 811 0.614697 AAAAAGGAGGAATGCCCCCG 60.615 55.000 0.00 0.00 34.66 5.73
738 812 2.514516 AAAAGGAGGAATGCCCCCGG 62.515 60.000 0.00 0.00 34.66 5.73
751 825 4.809496 CCCGGCCTCTGCATGCTT 62.809 66.667 20.33 0.00 40.13 3.91
752 826 3.515286 CCGGCCTCTGCATGCTTG 61.515 66.667 20.33 11.88 40.13 4.01
792 957 2.342648 GGTCGTTCCCGCTCTGTT 59.657 61.111 0.00 0.00 0.00 3.16
793 958 1.737008 GGTCGTTCCCGCTCTGTTC 60.737 63.158 0.00 0.00 0.00 3.18
794 959 1.006571 GTCGTTCCCGCTCTGTTCA 60.007 57.895 0.00 0.00 0.00 3.18
795 960 0.599204 GTCGTTCCCGCTCTGTTCAA 60.599 55.000 0.00 0.00 0.00 2.69
796 961 0.105224 TCGTTCCCGCTCTGTTCAAA 59.895 50.000 0.00 0.00 0.00 2.69
797 962 1.156736 CGTTCCCGCTCTGTTCAAAT 58.843 50.000 0.00 0.00 0.00 2.32
874 1047 2.503061 CTCCTGCATGACTCGGGG 59.497 66.667 0.00 0.00 0.00 5.73
918 1091 3.441922 TGCAGTGTAAAACAAAGTGCTGA 59.558 39.130 10.06 0.00 34.50 4.26
936 1109 4.516698 TGCTGAAGAGGACAACAAGATTTC 59.483 41.667 0.00 0.00 0.00 2.17
949 1122 4.154942 ACAAGATTTCCTTTCACTGCCAT 58.845 39.130 0.00 0.00 31.42 4.40
953 1138 1.538047 TTCCTTTCACTGCCATCAGC 58.462 50.000 0.00 0.00 44.10 4.26
981 1172 6.599244 TGATCTATGTTTTTCTGCTTACAGGG 59.401 38.462 0.00 0.00 44.59 4.45
1008 1199 0.821517 TAGGCGGCGAGATGAGAAAA 59.178 50.000 12.98 0.00 0.00 2.29
1011 1202 1.576356 GCGGCGAGATGAGAAAATCT 58.424 50.000 12.98 0.00 39.66 2.40
1045 1236 5.046376 TGCAAGAGATACTGGACTCATTTGA 60.046 40.000 0.00 0.00 35.83 2.69
1108 1299 2.303022 TCTAGGCATAGCATGGTAAGCC 59.697 50.000 33.24 33.24 42.31 4.35
1151 1350 9.494271 TCATTGAATCAGTAGCAATAATACTCC 57.506 33.333 0.00 0.00 31.05 3.85
1152 1351 8.725148 CATTGAATCAGTAGCAATAATACTCCC 58.275 37.037 0.00 0.00 31.05 4.30
1155 1354 6.613153 ATCAGTAGCAATAATACTCCCTCC 57.387 41.667 0.00 0.00 31.05 4.30
1164 1363 6.775629 GCAATAATACTCCCTCCATACCAAAA 59.224 38.462 0.00 0.00 0.00 2.44
1169 1368 7.947782 ATACTCCCTCCATACCAAAATAAGA 57.052 36.000 0.00 0.00 0.00 2.10
1170 1369 6.253946 ACTCCCTCCATACCAAAATAAGAG 57.746 41.667 0.00 0.00 0.00 2.85
1172 1371 6.126739 ACTCCCTCCATACCAAAATAAGAGTC 60.127 42.308 0.00 0.00 0.00 3.36
1173 1372 5.057149 CCCTCCATACCAAAATAAGAGTCG 58.943 45.833 0.00 0.00 0.00 4.18
1174 1373 4.511826 CCTCCATACCAAAATAAGAGTCGC 59.488 45.833 0.00 0.00 0.00 5.19
1175 1374 5.353394 TCCATACCAAAATAAGAGTCGCT 57.647 39.130 0.00 0.00 0.00 4.93
1176 1375 5.116180 TCCATACCAAAATAAGAGTCGCTG 58.884 41.667 0.00 0.00 0.00 5.18
1177 1376 5.105106 TCCATACCAAAATAAGAGTCGCTGA 60.105 40.000 0.00 0.00 0.00 4.26
1178 1377 5.760253 CCATACCAAAATAAGAGTCGCTGAT 59.240 40.000 0.00 0.00 0.00 2.90
1179 1378 6.260936 CCATACCAAAATAAGAGTCGCTGATT 59.739 38.462 0.00 0.00 0.00 2.57
1180 1379 7.201732 CCATACCAAAATAAGAGTCGCTGATTT 60.202 37.037 0.00 0.00 39.00 2.17
1181 1380 8.826710 CATACCAAAATAAGAGTCGCTGATTTA 58.173 33.333 0.00 0.00 36.78 1.40
1182 1381 7.308782 ACCAAAATAAGAGTCGCTGATTTAG 57.691 36.000 0.00 0.00 36.78 1.85
1183 1382 6.879458 ACCAAAATAAGAGTCGCTGATTTAGT 59.121 34.615 0.00 0.00 36.78 2.24
1184 1383 8.038944 ACCAAAATAAGAGTCGCTGATTTAGTA 58.961 33.333 0.00 0.00 36.78 1.82
1185 1384 8.543774 CCAAAATAAGAGTCGCTGATTTAGTAG 58.456 37.037 0.00 0.00 36.78 2.57
1186 1385 9.088512 CAAAATAAGAGTCGCTGATTTAGTAGT 57.911 33.333 0.00 0.00 36.78 2.73
1187 1386 9.654663 AAAATAAGAGTCGCTGATTTAGTAGTT 57.345 29.630 0.00 0.00 36.78 2.24
1189 1388 9.953697 AATAAGAGTCGCTGATTTAGTAGTTAG 57.046 33.333 0.00 0.00 0.00 2.34
1190 1389 7.393841 AAGAGTCGCTGATTTAGTAGTTAGT 57.606 36.000 0.00 0.00 0.00 2.24
1191 1390 8.503458 AAGAGTCGCTGATTTAGTAGTTAGTA 57.497 34.615 0.00 0.00 0.00 1.82
1192 1391 7.918643 AGAGTCGCTGATTTAGTAGTTAGTAC 58.081 38.462 0.00 0.00 0.00 2.73
1193 1392 7.551974 AGAGTCGCTGATTTAGTAGTTAGTACA 59.448 37.037 0.00 0.00 33.55 2.90
1194 1393 8.048534 AGTCGCTGATTTAGTAGTTAGTACAA 57.951 34.615 0.00 0.00 33.55 2.41
1195 1394 8.517878 AGTCGCTGATTTAGTAGTTAGTACAAA 58.482 33.333 0.00 0.00 33.55 2.83
1196 1395 8.796278 GTCGCTGATTTAGTAGTTAGTACAAAG 58.204 37.037 0.00 0.00 33.55 2.77
1313 1515 2.517980 AGCCCCCAATGGTAATGTGTAT 59.482 45.455 0.00 0.00 0.00 2.29
1392 1594 4.605354 CGTTTGTCGACGCCAATCATATAC 60.605 45.833 11.62 0.00 42.86 1.47
1401 1603 5.853936 ACGCCAATCATATACTAGAAAGCA 58.146 37.500 0.00 0.00 0.00 3.91
1482 1684 1.065551 GTGGTTGTGAGAAAGTGGTGC 59.934 52.381 0.00 0.00 0.00 5.01
1505 1713 1.405463 TGTACTGCTCGCATACAGAGG 59.595 52.381 4.06 0.00 37.35 3.69
1524 1732 8.905660 ACAGAGGAATATCAATGATCAAGAAG 57.094 34.615 0.00 0.00 0.00 2.85
1546 1754 4.023707 AGCAAGCACAAATTCTACAGACAC 60.024 41.667 0.00 0.00 0.00 3.67
1551 1759 5.468072 AGCACAAATTCTACAGACACTTCAG 59.532 40.000 0.00 0.00 0.00 3.02
1555 1763 3.386768 TTCTACAGACACTTCAGCCAC 57.613 47.619 0.00 0.00 0.00 5.01
1556 1764 2.316108 TCTACAGACACTTCAGCCACA 58.684 47.619 0.00 0.00 0.00 4.17
1747 1959 9.940166 ATGGTAAAAAGTGTAAGACGTTTTAAG 57.060 29.630 0.00 0.00 44.70 1.85
1748 1960 8.945057 TGGTAAAAAGTGTAAGACGTTTTAAGT 58.055 29.630 0.00 0.00 44.70 2.24
1749 1961 9.425893 GGTAAAAAGTGTAAGACGTTTTAAGTC 57.574 33.333 0.00 0.00 44.70 3.01
1750 1962 9.971744 GTAAAAAGTGTAAGACGTTTTAAGTCA 57.028 29.630 0.00 0.00 44.70 3.41
1751 1963 8.885302 AAAAAGTGTAAGACGTTTTAAGTCAC 57.115 30.769 0.00 5.26 42.31 3.67
1752 1964 7.838771 AAAGTGTAAGACGTTTTAAGTCACT 57.161 32.000 12.19 12.19 40.84 3.41
1753 1965 8.931385 AAAGTGTAAGACGTTTTAAGTCACTA 57.069 30.769 16.11 0.00 40.84 2.74
1754 1966 7.920908 AGTGTAAGACGTTTTAAGTCACTAC 57.079 36.000 14.90 0.00 40.84 2.73
1755 1967 7.710896 AGTGTAAGACGTTTTAAGTCACTACT 58.289 34.615 14.90 4.46 40.84 2.57
1757 1969 8.811378 GTGTAAGACGTTTTAAGTCACTACTTT 58.189 33.333 0.00 0.00 43.60 2.66
1775 1987 8.803201 ACTACTTTAGTGACCTAACGTTTTAC 57.197 34.615 5.91 0.00 37.04 2.01
1776 1988 8.413229 ACTACTTTAGTGACCTAACGTTTTACA 58.587 33.333 5.91 0.00 37.04 2.41
1777 1989 9.415544 CTACTTTAGTGACCTAACGTTTTACAT 57.584 33.333 5.91 0.00 37.04 2.29
1778 1990 8.667076 ACTTTAGTGACCTAACGTTTTACATT 57.333 30.769 5.91 2.29 33.26 2.71
1779 1991 9.112725 ACTTTAGTGACCTAACGTTTTACATTT 57.887 29.630 5.91 0.00 33.26 2.32
1780 1992 9.377383 CTTTAGTGACCTAACGTTTTACATTTG 57.623 33.333 5.91 0.00 32.91 2.32
1781 1993 6.930667 AGTGACCTAACGTTTTACATTTGT 57.069 33.333 5.91 0.00 0.00 2.83
1782 1994 7.324354 AGTGACCTAACGTTTTACATTTGTT 57.676 32.000 5.91 0.00 0.00 2.83
1783 1995 7.764331 AGTGACCTAACGTTTTACATTTGTTT 58.236 30.769 5.91 0.00 0.00 2.83
1784 1996 8.891720 AGTGACCTAACGTTTTACATTTGTTTA 58.108 29.630 5.91 0.00 0.00 2.01
1785 1997 8.946935 GTGACCTAACGTTTTACATTTGTTTAC 58.053 33.333 5.91 0.00 0.00 2.01
1786 1998 8.671921 TGACCTAACGTTTTACATTTGTTTACA 58.328 29.630 5.91 0.00 0.00 2.41
1787 1999 9.161684 GACCTAACGTTTTACATTTGTTTACAG 57.838 33.333 5.91 0.00 0.00 2.74
1788 2000 8.891720 ACCTAACGTTTTACATTTGTTTACAGA 58.108 29.630 5.91 0.00 0.00 3.41
1789 2001 9.377383 CCTAACGTTTTACATTTGTTTACAGAG 57.623 33.333 5.91 0.00 0.00 3.35
1790 2002 9.377383 CTAACGTTTTACATTTGTTTACAGAGG 57.623 33.333 5.91 0.00 0.00 3.69
1791 2003 6.731164 ACGTTTTACATTTGTTTACAGAGGG 58.269 36.000 0.00 0.00 0.00 4.30
1792 2004 6.543100 ACGTTTTACATTTGTTTACAGAGGGA 59.457 34.615 0.00 0.00 0.00 4.20
1806 2028 7.563724 TTACAGAGGGAGTACCATTTTACTT 57.436 36.000 0.00 0.00 43.89 2.24
1807 2029 6.449830 ACAGAGGGAGTACCATTTTACTTT 57.550 37.500 0.00 0.00 43.89 2.66
1833 2055 2.107726 ACCCACCCTTACTCTTGAAACC 59.892 50.000 0.00 0.00 0.00 3.27
1877 2102 2.493278 TGAGCACGAGTCATCTGAATCA 59.507 45.455 8.21 0.00 38.92 2.57
1886 2782 7.538334 CACGAGTCATCTGAATCAGAAGATATC 59.462 40.741 19.24 17.75 44.04 1.63
1922 3070 2.042464 ACACCCGAGCATGATGATACT 58.958 47.619 0.00 0.00 0.00 2.12
2041 3189 2.094182 ACGTCGCAGTTATGACCAAGAT 60.094 45.455 0.00 0.00 0.00 2.40
2054 3202 2.416547 GACCAAGATCAATGTCCGTGTG 59.583 50.000 0.00 0.00 0.00 3.82
2162 3352 3.709587 ACTATGCTACTACCGCCCATAT 58.290 45.455 0.00 0.00 0.00 1.78
2184 3396 1.133407 TGTTTCGCCACAGTTGTTTCC 59.867 47.619 0.00 0.00 0.00 3.13
2202 3514 3.342377 TCCGCAACAGTCCATAATTGA 57.658 42.857 0.00 0.00 0.00 2.57
2244 3568 5.973651 ATATGTTGAGTATTCTGCGTGTG 57.026 39.130 0.00 0.00 0.00 3.82
2314 3638 2.295602 GGGGAGCCGGAGTTTGGTA 61.296 63.158 5.05 0.00 0.00 3.25
2334 3658 1.444933 TTTCAGGCAGAGGGGAAGAA 58.555 50.000 0.00 0.00 0.00 2.52
2409 3733 1.039856 GGCTGGACTTCTTTTGCCAA 58.960 50.000 0.00 0.00 40.04 4.52
2425 3749 1.021202 CCAAAGACAACAACCTGCGA 58.979 50.000 0.00 0.00 0.00 5.10
2567 4088 2.703007 AGAGAGGTTCTGCTCTTTGTGT 59.297 45.455 0.00 0.00 38.26 3.72
2576 4097 3.054878 CTGCTCTTTGTGTTGCCATTTC 58.945 45.455 0.00 0.00 0.00 2.17
2587 4108 3.753797 TGTTGCCATTTCGTATGTTGCTA 59.246 39.130 0.00 0.00 0.00 3.49
2618 4145 3.572584 CTCTTTGCTGCTTTTGTGATCC 58.427 45.455 0.00 0.00 0.00 3.36
2745 4302 5.177511 GCCTTATTTTGTGGCAAGAAGTTTC 59.822 40.000 0.00 0.00 45.46 2.78
2826 4387 4.584029 AGTTTAATGAACTCGTGATGCG 57.416 40.909 0.00 0.00 45.40 4.73
2841 4402 4.258899 CGTGATGCGTAGTTTCTTAGTTCG 60.259 45.833 0.00 0.00 35.54 3.95
2865 4427 3.522759 TGTGTACTTCCCTGGGTTGATA 58.477 45.455 13.56 0.00 0.00 2.15
2945 4512 3.679980 CCAGGAATTAGTGAGACAACGTG 59.320 47.826 0.00 0.00 0.00 4.49
2953 4526 1.261619 GTGAGACAACGTGCAAGAAGG 59.738 52.381 6.65 0.00 0.00 3.46
2955 4528 1.527311 GAGACAACGTGCAAGAAGGAC 59.473 52.381 6.65 0.00 34.85 3.85
3056 4636 8.532186 TGGCCTAAACATATACAACATCAAAT 57.468 30.769 3.32 0.00 0.00 2.32
3058 4638 7.803189 GGCCTAAACATATACAACATCAAATCG 59.197 37.037 0.00 0.00 0.00 3.34
3060 4640 7.803189 CCTAAACATATACAACATCAAATCGGC 59.197 37.037 0.00 0.00 0.00 5.54
3067 4649 3.127548 ACAACATCAAATCGGCATGAGAC 59.872 43.478 0.00 0.00 0.00 3.36
3072 4654 2.499693 TCAAATCGGCATGAGACCTGTA 59.500 45.455 0.00 0.00 0.00 2.74
3073 4655 3.055458 TCAAATCGGCATGAGACCTGTAA 60.055 43.478 0.00 0.00 0.00 2.41
3079 4661 3.555956 CGGCATGAGACCTGTAACATAAC 59.444 47.826 0.00 0.00 0.00 1.89
3093 4675 8.268850 CTGTAACATAACAGGCTTATGAAACT 57.731 34.615 12.08 0.00 42.63 2.66
3166 4758 8.540388 TCAACTATATTAGGATAAGGCACCATC 58.460 37.037 0.00 0.00 0.00 3.51
3174 4766 4.891756 AGGATAAGGCACCATCATTTTGAG 59.108 41.667 0.00 0.00 0.00 3.02
3223 4818 2.086610 AAACAATTGGGCTGTCTGGT 57.913 45.000 10.83 0.00 0.00 4.00
3230 4826 1.859302 TGGGCTGTCTGGTTTTTGTT 58.141 45.000 0.00 0.00 0.00 2.83
3247 4843 7.430211 GGTTTTTGTTACGTAGAAACCTTTCAG 59.570 37.037 23.36 0.00 43.57 3.02
3248 4844 6.607735 TTTGTTACGTAGAAACCTTTCAGG 57.392 37.500 0.00 0.00 42.49 3.86
3467 5067 4.527509 TCTCATGGTCTTCACTTCTCAC 57.472 45.455 0.00 0.00 0.00 3.51
3471 5071 5.684704 TCATGGTCTTCACTTCTCACTTTT 58.315 37.500 0.00 0.00 0.00 2.27
3517 5118 1.329292 TGGTTCGTTTGTTTCTCGCAG 59.671 47.619 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 8.907885 AGATTCTTAGAGCAAAGACAACTTTTT 58.092 29.630 0.00 0.00 43.41 1.94
41 42 7.220030 TCAGATTCTTAGAGCAAAGACAACTT 58.780 34.615 0.00 0.00 35.25 2.66
62 63 8.981659 TCAGATCCATATAAGACTTGTTTCAGA 58.018 33.333 0.00 0.00 0.00 3.27
96 97 6.113411 CGAGTAGGGTGTTGGATTTATCTTT 58.887 40.000 0.00 0.00 0.00 2.52
97 98 5.671493 CGAGTAGGGTGTTGGATTTATCTT 58.329 41.667 0.00 0.00 0.00 2.40
98 99 4.443034 GCGAGTAGGGTGTTGGATTTATCT 60.443 45.833 0.00 0.00 0.00 1.98
99 100 3.808174 GCGAGTAGGGTGTTGGATTTATC 59.192 47.826 0.00 0.00 0.00 1.75
101 102 2.568062 TGCGAGTAGGGTGTTGGATTTA 59.432 45.455 0.00 0.00 0.00 1.40
139 144 3.883830 TTGCAAAAGAGAAACTTGGCA 57.116 38.095 0.00 0.00 43.15 4.92
145 150 7.015289 GGACAAAAAGTTTGCAAAAGAGAAAC 58.985 34.615 14.67 0.00 0.00 2.78
151 156 6.306397 GTCTTGGACAAAAAGTTTGCAAAAG 58.694 36.000 14.67 3.11 32.09 2.27
184 206 3.553922 GCCTGCCACTGTATCATAGACTC 60.554 52.174 0.00 0.00 0.00 3.36
205 227 2.201708 GGGACTCTACGGCCCTAGC 61.202 68.421 0.00 0.00 38.85 3.42
230 271 4.322574 CCTCTCATTCTTTGTCTCTGCTGA 60.323 45.833 0.00 0.00 0.00 4.26
272 314 2.126228 CGCCGAACTGAACGCCTA 60.126 61.111 0.00 0.00 0.00 3.93
292 334 1.507141 AAGAAGCAAGCGGAACCACG 61.507 55.000 0.00 0.00 0.00 4.94
293 335 0.238553 GAAGAAGCAAGCGGAACCAC 59.761 55.000 0.00 0.00 0.00 4.16
297 339 1.670087 CGAGAGAAGAAGCAAGCGGAA 60.670 52.381 0.00 0.00 0.00 4.30
301 343 0.998669 GAGCGAGAGAAGAAGCAAGC 59.001 55.000 0.00 0.00 0.00 4.01
396 440 2.123248 TGCAATGCAGACCGGAAGGA 62.123 55.000 9.46 0.00 44.28 3.36
439 509 7.533426 CACATGTAGGGATGAAAGAAAAGAAG 58.467 38.462 0.00 0.00 0.00 2.85
442 512 5.183713 TGCACATGTAGGGATGAAAGAAAAG 59.816 40.000 0.00 0.00 0.00 2.27
444 514 4.661222 TGCACATGTAGGGATGAAAGAAA 58.339 39.130 0.00 0.00 0.00 2.52
446 516 3.998913 TGCACATGTAGGGATGAAAGA 57.001 42.857 0.00 0.00 0.00 2.52
452 522 4.080129 AGTTCTCAATGCACATGTAGGGAT 60.080 41.667 0.00 0.00 0.00 3.85
454 524 3.614092 AGTTCTCAATGCACATGTAGGG 58.386 45.455 0.00 0.00 0.00 3.53
456 526 5.634896 GGAAAGTTCTCAATGCACATGTAG 58.365 41.667 0.00 0.00 0.00 2.74
457 527 4.154015 CGGAAAGTTCTCAATGCACATGTA 59.846 41.667 0.00 0.00 0.00 2.29
458 528 3.058016 CGGAAAGTTCTCAATGCACATGT 60.058 43.478 0.00 0.00 0.00 3.21
459 529 3.189080 TCGGAAAGTTCTCAATGCACATG 59.811 43.478 0.00 0.00 0.00 3.21
460 530 3.189287 GTCGGAAAGTTCTCAATGCACAT 59.811 43.478 0.00 0.00 0.00 3.21
461 531 2.548057 GTCGGAAAGTTCTCAATGCACA 59.452 45.455 0.00 0.00 0.00 4.57
462 532 2.411547 CGTCGGAAAGTTCTCAATGCAC 60.412 50.000 0.00 0.00 0.00 4.57
463 533 1.798223 CGTCGGAAAGTTCTCAATGCA 59.202 47.619 0.00 0.00 0.00 3.96
464 534 1.128692 CCGTCGGAAAGTTCTCAATGC 59.871 52.381 4.91 0.00 0.00 3.56
465 535 1.732259 CCCGTCGGAAAGTTCTCAATG 59.268 52.381 14.39 0.00 0.00 2.82
466 536 1.346722 ACCCGTCGGAAAGTTCTCAAT 59.653 47.619 14.39 0.00 0.00 2.57
467 537 0.754472 ACCCGTCGGAAAGTTCTCAA 59.246 50.000 14.39 0.00 0.00 3.02
468 538 1.270550 GTACCCGTCGGAAAGTTCTCA 59.729 52.381 14.39 0.00 0.00 3.27
469 539 1.403382 GGTACCCGTCGGAAAGTTCTC 60.403 57.143 14.39 0.00 0.00 2.87
470 540 0.605083 GGTACCCGTCGGAAAGTTCT 59.395 55.000 14.39 0.00 0.00 3.01
471 541 0.318120 TGGTACCCGTCGGAAAGTTC 59.682 55.000 14.39 0.00 0.00 3.01
472 542 0.319405 CTGGTACCCGTCGGAAAGTT 59.681 55.000 14.39 0.00 0.00 2.66
473 543 0.540365 TCTGGTACCCGTCGGAAAGT 60.540 55.000 14.39 4.74 0.00 2.66
474 544 0.822164 ATCTGGTACCCGTCGGAAAG 59.178 55.000 14.39 0.00 0.00 2.62
475 545 2.026641 CTATCTGGTACCCGTCGGAAA 58.973 52.381 14.39 0.00 0.00 3.13
476 546 1.683943 CTATCTGGTACCCGTCGGAA 58.316 55.000 14.39 0.00 0.00 4.30
477 547 0.179009 CCTATCTGGTACCCGTCGGA 60.179 60.000 14.39 0.40 0.00 4.55
478 548 1.803366 GCCTATCTGGTACCCGTCGG 61.803 65.000 10.07 3.60 38.35 4.79
479 549 1.658673 GCCTATCTGGTACCCGTCG 59.341 63.158 10.07 0.00 38.35 5.12
480 550 1.803366 CGGCCTATCTGGTACCCGTC 61.803 65.000 10.07 0.00 35.26 4.79
481 551 1.831286 CGGCCTATCTGGTACCCGT 60.831 63.158 10.07 0.00 35.26 5.28
482 552 1.524863 CTCGGCCTATCTGGTACCCG 61.525 65.000 10.07 2.49 39.38 5.28
483 553 1.817911 GCTCGGCCTATCTGGTACCC 61.818 65.000 10.07 0.00 38.35 3.69
484 554 0.828343 AGCTCGGCCTATCTGGTACC 60.828 60.000 4.43 4.43 38.35 3.34
485 555 1.813786 CTAGCTCGGCCTATCTGGTAC 59.186 57.143 0.00 0.00 38.35 3.34
486 556 1.271982 CCTAGCTCGGCCTATCTGGTA 60.272 57.143 0.00 0.00 38.35 3.25
487 557 0.540830 CCTAGCTCGGCCTATCTGGT 60.541 60.000 0.00 0.00 38.35 4.00
488 558 0.251386 TCCTAGCTCGGCCTATCTGG 60.251 60.000 0.00 0.00 39.35 3.86
489 559 1.543802 CTTCCTAGCTCGGCCTATCTG 59.456 57.143 0.00 0.00 0.00 2.90
490 560 1.549037 CCTTCCTAGCTCGGCCTATCT 60.549 57.143 0.00 0.00 0.00 1.98
491 561 0.892063 CCTTCCTAGCTCGGCCTATC 59.108 60.000 0.00 0.00 0.00 2.08
492 562 0.483328 TCCTTCCTAGCTCGGCCTAT 59.517 55.000 0.00 0.00 0.00 2.57
493 563 0.260816 TTCCTTCCTAGCTCGGCCTA 59.739 55.000 0.00 0.00 0.00 3.93
494 564 1.001760 TTCCTTCCTAGCTCGGCCT 59.998 57.895 0.00 0.00 0.00 5.19
495 565 1.144276 GTTCCTTCCTAGCTCGGCC 59.856 63.158 0.00 0.00 0.00 6.13
496 566 0.537653 AAGTTCCTTCCTAGCTCGGC 59.462 55.000 0.00 0.00 0.00 5.54
497 567 2.233922 TGAAAGTTCCTTCCTAGCTCGG 59.766 50.000 0.00 0.00 0.00 4.63
498 568 3.193691 TCTGAAAGTTCCTTCCTAGCTCG 59.806 47.826 0.00 0.00 33.76 5.03
499 569 4.810191 TCTGAAAGTTCCTTCCTAGCTC 57.190 45.455 0.00 0.00 33.76 4.09
500 570 4.534103 ACATCTGAAAGTTCCTTCCTAGCT 59.466 41.667 0.00 0.00 33.76 3.32
501 571 4.633565 CACATCTGAAAGTTCCTTCCTAGC 59.366 45.833 0.00 0.00 33.76 3.42
502 572 4.633565 GCACATCTGAAAGTTCCTTCCTAG 59.366 45.833 0.00 0.00 33.76 3.02
503 573 4.041567 TGCACATCTGAAAGTTCCTTCCTA 59.958 41.667 0.00 0.00 33.76 2.94
504 574 3.181440 TGCACATCTGAAAGTTCCTTCCT 60.181 43.478 0.00 0.00 33.76 3.36
505 575 3.149196 TGCACATCTGAAAGTTCCTTCC 58.851 45.455 0.00 0.00 33.76 3.46
506 576 5.382618 AATGCACATCTGAAAGTTCCTTC 57.617 39.130 0.00 0.00 33.76 3.46
507 577 5.796424 AAATGCACATCTGAAAGTTCCTT 57.204 34.783 0.00 0.00 33.76 3.36
508 578 5.535333 CAAAATGCACATCTGAAAGTTCCT 58.465 37.500 0.00 0.00 33.76 3.36
509 579 4.151157 GCAAAATGCACATCTGAAAGTTCC 59.849 41.667 0.00 0.00 44.26 3.62
510 580 5.260027 GCAAAATGCACATCTGAAAGTTC 57.740 39.130 0.00 0.00 44.26 3.01
540 610 3.960102 AGCCCAACAAAAGTGATGAAAGA 59.040 39.130 0.00 0.00 29.21 2.52
547 617 1.032014 GCTGAGCCCAACAAAAGTGA 58.968 50.000 0.00 0.00 0.00 3.41
549 619 1.410153 CTTGCTGAGCCCAACAAAAGT 59.590 47.619 0.23 0.00 29.11 2.66
622 693 7.883311 TCCCAAAAGAAAGAAACCTGTATAGAG 59.117 37.037 0.00 0.00 0.00 2.43
623 694 7.751646 TCCCAAAAGAAAGAAACCTGTATAGA 58.248 34.615 0.00 0.00 0.00 1.98
643 714 4.080356 CCATCAAGTTACCTGATCTCCCAA 60.080 45.833 0.00 0.00 0.00 4.12
645 716 3.181450 CCCATCAAGTTACCTGATCTCCC 60.181 52.174 0.00 0.00 0.00 4.30
734 808 4.809496 AAGCATGCAGAGGCCGGG 62.809 66.667 21.98 0.00 40.13 5.73
735 809 3.515286 CAAGCATGCAGAGGCCGG 61.515 66.667 21.98 0.00 40.13 6.13
753 827 4.174009 CAGCCAGAGATGAAGCAAAATTG 58.826 43.478 0.00 0.00 0.00 2.32
754 828 3.194968 CCAGCCAGAGATGAAGCAAAATT 59.805 43.478 0.00 0.00 0.00 1.82
755 829 2.758979 CCAGCCAGAGATGAAGCAAAAT 59.241 45.455 0.00 0.00 0.00 1.82
756 830 2.165167 CCAGCCAGAGATGAAGCAAAA 58.835 47.619 0.00 0.00 0.00 2.44
757 831 1.074405 ACCAGCCAGAGATGAAGCAAA 59.926 47.619 0.00 0.00 0.00 3.68
758 832 0.694771 ACCAGCCAGAGATGAAGCAA 59.305 50.000 0.00 0.00 0.00 3.91
764 838 0.460987 GGAACGACCAGCCAGAGATG 60.461 60.000 0.00 0.00 38.79 2.90
792 957 6.126409 ACAAAGTACAGGGAGTTTGATTTGA 58.874 36.000 16.67 0.00 40.67 2.69
793 958 6.391227 ACAAAGTACAGGGAGTTTGATTTG 57.609 37.500 16.67 3.08 40.67 2.32
794 959 7.342026 AGAAACAAAGTACAGGGAGTTTGATTT 59.658 33.333 16.67 12.71 40.67 2.17
795 960 6.833933 AGAAACAAAGTACAGGGAGTTTGATT 59.166 34.615 16.67 11.72 40.67 2.57
796 961 6.365520 AGAAACAAAGTACAGGGAGTTTGAT 58.634 36.000 16.67 4.12 40.67 2.57
797 962 5.751586 AGAAACAAAGTACAGGGAGTTTGA 58.248 37.500 16.67 0.00 40.67 2.69
834 999 7.819900 GGAGGACTGCTTGTGGTATATTATAAG 59.180 40.741 0.00 0.00 0.00 1.73
883 1056 8.339714 TGTTTTACACTGCAACTACTCATAAAC 58.660 33.333 0.00 0.00 0.00 2.01
886 1059 8.439993 TTTGTTTTACACTGCAACTACTCATA 57.560 30.769 0.00 0.00 0.00 2.15
918 1091 6.039829 GTGAAAGGAAATCTTGTTGTCCTCTT 59.960 38.462 0.00 0.00 39.65 2.85
936 1109 0.609957 TGGCTGATGGCAGTGAAAGG 60.610 55.000 0.00 0.00 44.10 3.11
949 1122 5.066893 GCAGAAAAACATAGATCATGGCTGA 59.933 40.000 0.00 0.00 39.13 4.26
953 1138 7.988737 TGTAAGCAGAAAAACATAGATCATGG 58.011 34.615 0.00 0.00 39.13 3.66
981 1172 0.666913 TCTCGCCGCCTACTAATGTC 59.333 55.000 0.00 0.00 0.00 3.06
1008 1199 2.038164 TCTCTTGCAGCACTCACAAGAT 59.962 45.455 11.22 0.00 46.28 2.40
1011 1202 2.556144 ATCTCTTGCAGCACTCACAA 57.444 45.000 0.00 0.00 0.00 3.33
1045 1236 5.221048 CGAAGAAACACTTGACCTTTCCATT 60.221 40.000 0.00 0.00 39.13 3.16
1108 1299 0.251297 TGATCAAGGCAACCCACTGG 60.251 55.000 0.00 0.00 37.80 4.00
1146 1345 6.906901 ACTCTTATTTTGGTATGGAGGGAGTA 59.093 38.462 0.00 0.00 0.00 2.59
1149 1348 5.163343 CGACTCTTATTTTGGTATGGAGGGA 60.163 44.000 0.00 0.00 0.00 4.20
1150 1349 5.057149 CGACTCTTATTTTGGTATGGAGGG 58.943 45.833 0.00 0.00 0.00 4.30
1151 1350 4.511826 GCGACTCTTATTTTGGTATGGAGG 59.488 45.833 0.00 0.00 0.00 4.30
1152 1351 5.235186 CAGCGACTCTTATTTTGGTATGGAG 59.765 44.000 0.00 0.00 0.00 3.86
1155 1354 6.851222 ATCAGCGACTCTTATTTTGGTATG 57.149 37.500 0.00 0.00 0.00 2.39
1164 1363 9.122779 ACTAACTACTAAATCAGCGACTCTTAT 57.877 33.333 0.00 0.00 0.00 1.73
1168 1367 7.692088 TGTACTAACTACTAAATCAGCGACTC 58.308 38.462 0.00 0.00 0.00 3.36
1169 1368 7.621428 TGTACTAACTACTAAATCAGCGACT 57.379 36.000 0.00 0.00 0.00 4.18
1170 1369 8.679288 TTTGTACTAACTACTAAATCAGCGAC 57.321 34.615 0.00 0.00 0.00 5.19
1172 1371 8.684973 ACTTTGTACTAACTACTAAATCAGCG 57.315 34.615 0.00 0.00 0.00 5.18
1208 1407 5.460646 ACCTGCAAAATTGTGAATCGTTAG 58.539 37.500 0.00 0.00 0.00 2.34
1221 1423 4.521146 CTCTCTGGTATGACCTGCAAAAT 58.479 43.478 0.00 0.00 39.58 1.82
1313 1515 2.165641 ACGCTCAGTAATTCCGACATCA 59.834 45.455 0.00 0.00 0.00 3.07
1392 1594 5.389935 GGAACATCAACGAGTTGCTTTCTAG 60.390 44.000 10.83 0.00 40.24 2.43
1401 1603 3.518590 GGTATCGGAACATCAACGAGTT 58.481 45.455 0.00 0.00 40.21 3.01
1482 1684 2.130395 CTGTATGCGAGCAGTACATGG 58.870 52.381 15.31 6.65 0.00 3.66
1505 1713 7.378995 GTGCTTGCTTCTTGATCATTGATATTC 59.621 37.037 0.00 0.00 0.00 1.75
1524 1732 4.023707 AGTGTCTGTAGAATTTGTGCTTGC 60.024 41.667 0.00 0.00 0.00 4.01
1546 1754 2.422479 CCATCACTGAATGTGGCTGAAG 59.578 50.000 0.00 0.00 46.20 3.02
1551 1759 1.026182 TCGCCATCACTGAATGTGGC 61.026 55.000 10.92 10.92 46.20 5.01
1555 1763 3.721035 TGAGTATCGCCATCACTGAATG 58.279 45.455 0.00 0.00 38.61 2.67
1556 1764 4.613925 ATGAGTATCGCCATCACTGAAT 57.386 40.909 0.00 0.00 38.61 2.57
1728 1940 7.838771 AGTGACTTAAAACGTCTTACACTTT 57.161 32.000 0.00 0.00 33.29 2.66
1729 1941 8.193438 AGTAGTGACTTAAAACGTCTTACACTT 58.807 33.333 8.22 0.00 37.31 3.16
1730 1942 7.710896 AGTAGTGACTTAAAACGTCTTACACT 58.289 34.615 8.06 8.06 39.03 3.55
1731 1943 7.920908 AGTAGTGACTTAAAACGTCTTACAC 57.079 36.000 0.00 0.00 28.61 2.90
1732 1944 8.931385 AAAGTAGTGACTTAAAACGTCTTACA 57.069 30.769 0.00 0.00 45.50 2.41
1750 1962 8.413229 TGTAAAACGTTAGGTCACTAAAGTAGT 58.587 33.333 0.00 2.08 46.46 2.73
1751 1963 8.801715 TGTAAAACGTTAGGTCACTAAAGTAG 57.198 34.615 0.00 0.00 46.46 2.57
1752 1964 9.762933 AATGTAAAACGTTAGGTCACTAAAGTA 57.237 29.630 0.00 0.00 46.46 2.24
1754 1966 9.377383 CAAATGTAAAACGTTAGGTCACTAAAG 57.623 33.333 0.00 0.00 40.66 1.85
1755 1967 8.891720 ACAAATGTAAAACGTTAGGTCACTAAA 58.108 29.630 0.00 0.00 40.66 1.85
1756 1968 8.436046 ACAAATGTAAAACGTTAGGTCACTAA 57.564 30.769 0.00 0.00 36.86 2.24
1757 1969 8.436046 AACAAATGTAAAACGTTAGGTCACTA 57.564 30.769 0.00 0.00 0.00 2.74
1758 1970 6.930667 ACAAATGTAAAACGTTAGGTCACT 57.069 33.333 0.00 0.00 0.00 3.41
1759 1971 7.974243 AAACAAATGTAAAACGTTAGGTCAC 57.026 32.000 0.00 0.00 0.00 3.67
1760 1972 8.671921 TGTAAACAAATGTAAAACGTTAGGTCA 58.328 29.630 0.00 0.00 0.00 4.02
1761 1973 9.161684 CTGTAAACAAATGTAAAACGTTAGGTC 57.838 33.333 0.00 0.00 0.00 3.85
1762 1974 8.891720 TCTGTAAACAAATGTAAAACGTTAGGT 58.108 29.630 0.00 0.00 0.00 3.08
1763 1975 9.377383 CTCTGTAAACAAATGTAAAACGTTAGG 57.623 33.333 0.00 0.00 0.00 2.69
1764 1976 9.377383 CCTCTGTAAACAAATGTAAAACGTTAG 57.623 33.333 0.00 0.00 0.00 2.34
1765 1977 8.344098 CCCTCTGTAAACAAATGTAAAACGTTA 58.656 33.333 0.00 0.00 0.00 3.18
1766 1978 7.067251 TCCCTCTGTAAACAAATGTAAAACGTT 59.933 33.333 0.00 0.00 0.00 3.99
1767 1979 6.543100 TCCCTCTGTAAACAAATGTAAAACGT 59.457 34.615 0.00 0.00 0.00 3.99
1768 1980 6.961576 TCCCTCTGTAAACAAATGTAAAACG 58.038 36.000 0.00 0.00 0.00 3.60
1769 1981 7.937649 ACTCCCTCTGTAAACAAATGTAAAAC 58.062 34.615 0.00 0.00 0.00 2.43
1770 1982 9.059260 GTACTCCCTCTGTAAACAAATGTAAAA 57.941 33.333 0.00 0.00 0.00 1.52
1771 1983 7.662669 GGTACTCCCTCTGTAAACAAATGTAAA 59.337 37.037 0.00 0.00 0.00 2.01
1772 1984 7.163441 GGTACTCCCTCTGTAAACAAATGTAA 58.837 38.462 0.00 0.00 0.00 2.41
1773 1985 6.270463 TGGTACTCCCTCTGTAAACAAATGTA 59.730 38.462 0.00 0.00 0.00 2.29
1774 1986 5.072600 TGGTACTCCCTCTGTAAACAAATGT 59.927 40.000 0.00 0.00 0.00 2.71
1775 1987 5.556915 TGGTACTCCCTCTGTAAACAAATG 58.443 41.667 0.00 0.00 0.00 2.32
1776 1988 5.836024 TGGTACTCCCTCTGTAAACAAAT 57.164 39.130 0.00 0.00 0.00 2.32
1777 1989 5.836024 ATGGTACTCCCTCTGTAAACAAA 57.164 39.130 0.00 0.00 0.00 2.83
1778 1990 5.836024 AATGGTACTCCCTCTGTAAACAA 57.164 39.130 0.00 0.00 0.00 2.83
1779 1991 5.836024 AAATGGTACTCCCTCTGTAAACA 57.164 39.130 0.00 0.00 0.00 2.83
1780 1992 7.392418 AGTAAAATGGTACTCCCTCTGTAAAC 58.608 38.462 0.00 0.00 27.56 2.01
1781 1993 7.563724 AGTAAAATGGTACTCCCTCTGTAAA 57.436 36.000 0.00 0.00 27.56 2.01
1782 1994 7.563724 AAGTAAAATGGTACTCCCTCTGTAA 57.436 36.000 0.00 0.00 33.05 2.41
1783 1995 7.563724 AAAGTAAAATGGTACTCCCTCTGTA 57.436 36.000 0.00 0.00 33.05 2.74
1784 1996 6.449830 AAAGTAAAATGGTACTCCCTCTGT 57.550 37.500 0.00 0.00 33.05 3.41
1785 1997 7.621796 ACTAAAGTAAAATGGTACTCCCTCTG 58.378 38.462 0.00 0.00 33.05 3.35
1786 1998 7.809880 ACTAAAGTAAAATGGTACTCCCTCT 57.190 36.000 0.00 0.00 33.05 3.69
1787 1999 9.376075 GTAACTAAAGTAAAATGGTACTCCCTC 57.624 37.037 0.00 0.00 33.05 4.30
1788 2000 8.324306 GGTAACTAAAGTAAAATGGTACTCCCT 58.676 37.037 0.00 0.00 33.05 4.20
1789 2001 7.554118 GGGTAACTAAAGTAAAATGGTACTCCC 59.446 40.741 0.00 0.00 33.05 4.30
1790 2002 8.102676 TGGGTAACTAAAGTAAAATGGTACTCC 58.897 37.037 0.00 0.00 33.05 3.85
1791 2003 8.939929 GTGGGTAACTAAAGTAAAATGGTACTC 58.060 37.037 0.00 0.00 33.05 2.59
1792 2004 7.884877 GGTGGGTAACTAAAGTAAAATGGTACT 59.115 37.037 0.00 0.00 35.80 2.73
1806 2028 5.405279 TCAAGAGTAAGGGTGGGTAACTAA 58.595 41.667 0.00 0.00 0.00 2.24
1807 2029 5.014534 TCAAGAGTAAGGGTGGGTAACTA 57.985 43.478 0.00 0.00 0.00 2.24
1833 2055 8.722480 TCATATGGACTGTCTTCTGTAAAATG 57.278 34.615 7.85 0.67 0.00 2.32
1886 2782 6.509039 GCTCGGGTGTTAATCTAATACGTTTG 60.509 42.308 0.00 0.00 31.46 2.93
1896 2792 3.134623 TCATCATGCTCGGGTGTTAATCT 59.865 43.478 0.00 0.00 0.00 2.40
1964 3112 5.878406 TCTCCAGAACTTTCTTCTTCTGT 57.122 39.130 6.64 0.00 41.22 3.41
2016 3164 2.159476 TGGTCATAACTGCGACGTAGAC 60.159 50.000 20.16 6.83 32.74 2.59
2030 3178 4.081142 ACACGGACATTGATCTTGGTCATA 60.081 41.667 11.45 0.00 32.00 2.15
2041 3189 1.195442 TAGGGCCACACGGACATTGA 61.195 55.000 6.18 0.00 45.55 2.57
2054 3202 4.534797 TCTAGACAAGACTTACTAGGGCC 58.465 47.826 19.47 0.00 34.80 5.80
2155 3338 1.203523 TGTGGCGAAACAAATATGGGC 59.796 47.619 0.00 0.00 0.00 5.36
2162 3352 3.246619 GAAACAACTGTGGCGAAACAAA 58.753 40.909 0.00 0.00 0.00 2.83
2184 3396 5.046910 ACTTTCAATTATGGACTGTTGCG 57.953 39.130 0.00 0.00 0.00 4.85
2229 3553 4.862574 TGTTCATACACACGCAGAATACTC 59.137 41.667 0.00 0.00 0.00 2.59
2244 3568 4.037446 TGGCAAAGGTCTGTTTGTTCATAC 59.963 41.667 0.00 0.00 39.27 2.39
2314 3638 1.673767 TCTTCCCCTCTGCCTGAAAT 58.326 50.000 0.00 0.00 0.00 2.17
2334 3658 0.968901 CTCACCATGCCATTGCTGGT 60.969 55.000 6.97 6.97 44.55 4.00
2362 3686 2.297698 TCCTCAGGGAACGACTGTTA 57.702 50.000 0.00 0.00 38.78 2.41
2367 3691 2.159085 CCACTTATCCTCAGGGAACGAC 60.159 54.545 0.00 0.00 45.78 4.34
2409 3733 1.541233 CCTCTCGCAGGTTGTTGTCTT 60.541 52.381 0.00 0.00 37.53 3.01
2425 3749 1.383803 GAGGCAGATGTCCCCCTCT 60.384 63.158 8.50 0.00 40.51 3.69
2567 4088 4.006989 ACTAGCAACATACGAAATGGCAA 58.993 39.130 0.00 0.00 0.00 4.52
2576 4097 4.621991 AGCTCCATTACTAGCAACATACG 58.378 43.478 0.00 0.00 41.32 3.06
2618 4145 0.320374 TGCCCACAGTTCTACTTCCG 59.680 55.000 0.00 0.00 0.00 4.30
2745 4302 5.464965 AACTTCGTCAACACAACTAGTTG 57.535 39.130 29.76 29.76 45.82 3.16
2826 4387 5.902051 ACACAAGCGAACTAAGAAACTAC 57.098 39.130 0.00 0.00 0.00 2.73
2841 4402 0.400594 ACCCAGGGAAGTACACAAGC 59.599 55.000 14.54 0.00 0.00 4.01
2865 4427 9.740239 GTACATTCTGATATGCAATGAATTTGT 57.260 29.630 0.00 0.00 37.65 2.83
2945 4512 2.160417 CCATCTTTCACGTCCTTCTTGC 59.840 50.000 0.00 0.00 0.00 4.01
2953 4526 1.270625 TGTCCCACCATCTTTCACGTC 60.271 52.381 0.00 0.00 0.00 4.34
2955 4528 1.890876 TTGTCCCACCATCTTTCACG 58.109 50.000 0.00 0.00 0.00 4.35
2959 4532 5.543405 TCAAATGAATTGTCCCACCATCTTT 59.457 36.000 0.00 0.00 40.11 2.52
3056 4636 1.262417 TGTTACAGGTCTCATGCCGA 58.738 50.000 0.00 0.00 0.00 5.54
3058 4638 4.513442 TGTTATGTTACAGGTCTCATGCC 58.487 43.478 0.00 0.00 0.00 4.40
3079 4661 9.561069 AGGTACATTAATAGTTTCATAAGCCTG 57.439 33.333 0.00 0.00 0.00 4.85
3156 4748 5.750352 AAATCTCAAAATGATGGTGCCTT 57.250 34.783 0.00 0.00 0.00 4.35
3325 4921 7.801752 TGGTGATTTGTTTTGAAACTTGAAAC 58.198 30.769 7.97 0.00 39.59 2.78
3434 5034 8.610896 GTGAAGACCATGAGATTTTCTGAATAG 58.389 37.037 0.00 0.00 0.00 1.73
3436 5036 7.173722 AGTGAAGACCATGAGATTTTCTGAAT 58.826 34.615 0.00 0.00 0.00 2.57
3447 5047 4.533919 AGTGAGAAGTGAAGACCATGAG 57.466 45.455 0.00 0.00 0.00 2.90
3467 5067 9.554395 AAAAAGTACAATAAACCATGGGAAAAG 57.446 29.630 18.09 3.75 0.00 2.27
3471 5071 6.042093 TGCAAAAAGTACAATAAACCATGGGA 59.958 34.615 18.09 0.54 0.00 4.37


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

AutoCloner maintained by Alex Coulton.