Multiple sequence alignment - TraesCS7B01G413200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G413200 chr7B 100.000 3041 0 0 1 3041 681555282 681558322 0.000000e+00 5616.0
1 TraesCS7B01G413200 chr7B 78.602 472 97 4 1412 1882 558318557 558319025 2.940000e-80 309.0
2 TraesCS7B01G413200 chr2D 86.139 1717 132 35 804 2462 30471317 30469649 0.000000e+00 1755.0
3 TraesCS7B01G413200 chr2D 90.538 539 43 4 2500 3033 30469652 30469117 0.000000e+00 706.0
4 TraesCS7B01G413200 chr2D 86.667 525 56 8 1 523 21830428 21830940 1.220000e-158 569.0
5 TraesCS7B01G413200 chr2D 77.371 601 114 16 1417 2013 30462558 30461976 1.350000e-88 337.0
6 TraesCS7B01G413200 chr2D 90.805 174 16 0 576 749 21830943 21831116 1.820000e-57 233.0
7 TraesCS7B01G413200 chr2D 83.333 66 5 6 753 815 486758691 486758629 4.240000e-04 56.5
8 TraesCS7B01G413200 chr5A 88.813 1323 99 16 981 2259 71462724 71461407 0.000000e+00 1578.0
9 TraesCS7B01G413200 chr5A 86.757 808 51 21 2264 3033 71461360 71460571 0.000000e+00 848.0
10 TraesCS7B01G413200 chr5B 86.745 762 82 8 995 1737 84714010 84713249 0.000000e+00 830.0
11 TraesCS7B01G413200 chr5B 88.837 645 42 14 2408 3027 84669491 84668852 0.000000e+00 765.0
12 TraesCS7B01G413200 chr5B 88.385 551 39 13 1733 2259 84692826 84692277 9.190000e-180 640.0
13 TraesCS7B01G413200 chr5B 77.262 862 164 19 1171 2007 652097637 652098491 7.630000e-131 477.0
14 TraesCS7B01G413200 chr5B 75.155 805 169 18 1228 2007 652093065 652093863 1.730000e-92 350.0
15 TraesCS7B01G413200 chr5B 77.922 308 62 6 1703 2007 652367216 652367520 1.440000e-43 187.0
16 TraesCS7B01G413200 chr5B 83.626 171 8 5 2262 2412 84692227 84692057 3.160000e-30 143.0
17 TraesCS7B01G413200 chr2A 81.121 821 133 16 1417 2219 14750135 14750951 3.310000e-179 638.0
18 TraesCS7B01G413200 chr2A 89.671 426 31 3 2043 2462 32493069 32492651 5.770000e-147 531.0
19 TraesCS7B01G413200 chr2A 86.551 461 31 9 2576 3033 32492634 32492202 2.120000e-131 479.0
20 TraesCS7B01G413200 chr7D 77.893 484 98 8 1412 1892 523195830 523196307 2.970000e-75 292.0
21 TraesCS7B01G413200 chr7D 82.353 68 7 4 718 783 597680294 597680230 2.000000e-03 54.7
22 TraesCS7B01G413200 chr1A 85.629 167 12 5 2832 2990 98575127 98575289 6.750000e-37 165.0
23 TraesCS7B01G413200 chr1A 81.579 114 21 0 1769 1882 555088575 555088688 8.980000e-16 95.3
24 TraesCS7B01G413200 chr6D 81.944 144 23 3 1224 1365 438456970 438457112 5.330000e-23 119.0
25 TraesCS7B01G413200 chr5D 86.441 59 5 2 725 781 360943227 360943170 9.100000e-06 62.1
26 TraesCS7B01G413200 chr3D 84.848 66 5 4 718 781 545547857 545547795 9.100000e-06 62.1
27 TraesCS7B01G413200 chr3D 83.333 66 6 5 753 815 420386482 420386419 4.240000e-04 56.5
28 TraesCS7B01G413200 chr3D 81.333 75 6 8 753 823 83028129 83028059 2.000000e-03 54.7
29 TraesCS7B01G413200 chr7A 85.965 57 7 1 728 783 159986889 159986945 3.270000e-05 60.2
30 TraesCS7B01G413200 chr4D 81.818 77 7 6 718 790 455894173 455894246 1.180000e-04 58.4
31 TraesCS7B01G413200 chr4D 100.000 29 0 0 753 781 24923030 24923058 2.000000e-03 54.7
32 TraesCS7B01G413200 chr4D 82.090 67 9 3 717 781 350724122 350724187 2.000000e-03 54.7
33 TraesCS7B01G413200 chr1B 86.792 53 6 1 3 54 279189698 279189646 1.180000e-04 58.4
34 TraesCS7B01G413200 chr2B 82.609 69 6 6 752 817 20933723 20933658 4.240000e-04 56.5
35 TraesCS7B01G413200 chr2B 82.353 68 7 4 718 783 21211547 21211483 2.000000e-03 54.7
36 TraesCS7B01G413200 chr3B 83.077 65 6 4 718 780 190160942 190161003 2.000000e-03 54.7


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 TraesCS7B01G413200 chr7B 681555282 681558322 3040 False 5616.0 5616 100.0000 1 3041 1 chr7B.!!$F2 3040
1 TraesCS7B01G413200 chr2D 30469117 30471317 2200 True 1230.5 1755 88.3385 804 3033 2 chr2D.!!$R3 2229
2 TraesCS7B01G413200 chr2D 21830428 21831116 688 False 401.0 569 88.7360 1 749 2 chr2D.!!$F1 748
3 TraesCS7B01G413200 chr2D 30461976 30462558 582 True 337.0 337 77.3710 1417 2013 1 chr2D.!!$R1 596
4 TraesCS7B01G413200 chr5A 71460571 71462724 2153 True 1213.0 1578 87.7850 981 3033 2 chr5A.!!$R1 2052
5 TraesCS7B01G413200 chr5B 84713249 84714010 761 True 830.0 830 86.7450 995 1737 1 chr5B.!!$R2 742
6 TraesCS7B01G413200 chr5B 84668852 84669491 639 True 765.0 765 88.8370 2408 3027 1 chr5B.!!$R1 619
7 TraesCS7B01G413200 chr5B 652093065 652098491 5426 False 413.5 477 76.2085 1171 2007 2 chr5B.!!$F2 836
8 TraesCS7B01G413200 chr5B 84692057 84692826 769 True 391.5 640 86.0055 1733 2412 2 chr5B.!!$R3 679
9 TraesCS7B01G413200 chr2A 14750135 14750951 816 False 638.0 638 81.1210 1417 2219 1 chr2A.!!$F1 802
10 TraesCS7B01G413200 chr2A 32492202 32493069 867 True 505.0 531 88.1110 2043 3033 2 chr2A.!!$R1 990

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
559 562 0.036306 TCGAAAACCTCAAGGAGCCC 59.964 55.0 2.3 0.0 38.94 5.19 F
560 563 0.036875 CGAAAACCTCAAGGAGCCCT 59.963 55.0 2.3 0.0 38.94 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 6544 1.611491 GTCTCCGATCTCCAGGACATC 59.389 57.143 0.0 0.0 32.33 3.06 R
2070 6660 2.356125 GCACTCTCTTTTATCCCAGCCA 60.356 50.000 0.0 0.0 0.00 4.75 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
52 53 2.289444 ACAAAGTCCATGGACCACGTAG 60.289 50.000 36.09 23.14 45.59 3.51
78 79 2.805845 TCTATTAGCACCGAAACGAGC 58.194 47.619 0.00 0.00 0.00 5.03
87 88 0.600255 CCGAAACGAGCTGAAGGTGT 60.600 55.000 0.00 0.00 0.00 4.16
110 111 2.292192 CCACCAACATTACCCATCCCTT 60.292 50.000 0.00 0.00 0.00 3.95
114 115 3.563261 CCAACATTACCCATCCCTTGTCA 60.563 47.826 0.00 0.00 0.00 3.58
154 155 4.179926 TGTAGCTGACAATCAGTGAGTC 57.820 45.455 7.62 2.17 45.94 3.36
157 159 4.348863 AGCTGACAATCAGTGAGTCTTT 57.651 40.909 12.30 0.00 45.94 2.52
160 162 4.152045 GCTGACAATCAGTGAGTCTTTGAG 59.848 45.833 10.44 3.23 45.94 3.02
164 166 6.047511 ACAATCAGTGAGTCTTTGAGCTAT 57.952 37.500 10.44 0.00 0.00 2.97
170 172 0.548510 AGTCTTTGAGCTATGGCCCC 59.451 55.000 0.00 0.00 39.73 5.80
171 173 0.255890 GTCTTTGAGCTATGGCCCCA 59.744 55.000 0.00 0.00 39.73 4.96
188 190 2.211806 CCCAATTTGCCAACACACAAG 58.788 47.619 0.00 0.00 0.00 3.16
193 195 3.883830 TTTGCCAACACACAAGAACAT 57.116 38.095 0.00 0.00 0.00 2.71
199 201 1.593196 ACACACAAGAACATGACCCG 58.407 50.000 0.00 0.00 0.00 5.28
208 210 2.282110 CATGACCCGTGGCCAACA 60.282 61.111 7.24 3.46 0.00 3.33
224 226 4.218417 GGCCAACAAAGAGAAGCAAAGATA 59.782 41.667 0.00 0.00 0.00 1.98
226 228 5.860716 GCCAACAAAGAGAAGCAAAGATAAG 59.139 40.000 0.00 0.00 0.00 1.73
227 229 6.385033 CCAACAAAGAGAAGCAAAGATAAGG 58.615 40.000 0.00 0.00 0.00 2.69
228 230 6.207417 CCAACAAAGAGAAGCAAAGATAAGGA 59.793 38.462 0.00 0.00 0.00 3.36
229 231 7.303998 CAACAAAGAGAAGCAAAGATAAGGAG 58.696 38.462 0.00 0.00 0.00 3.69
230 232 5.942826 ACAAAGAGAAGCAAAGATAAGGAGG 59.057 40.000 0.00 0.00 0.00 4.30
231 233 6.176183 CAAAGAGAAGCAAAGATAAGGAGGA 58.824 40.000 0.00 0.00 0.00 3.71
232 234 5.351948 AGAGAAGCAAAGATAAGGAGGAC 57.648 43.478 0.00 0.00 0.00 3.85
233 235 4.163268 AGAGAAGCAAAGATAAGGAGGACC 59.837 45.833 0.00 0.00 0.00 4.46
234 236 3.846588 AGAAGCAAAGATAAGGAGGACCA 59.153 43.478 0.00 0.00 38.94 4.02
235 237 3.636153 AGCAAAGATAAGGAGGACCAC 57.364 47.619 0.00 0.00 38.94 4.16
236 238 2.912956 AGCAAAGATAAGGAGGACCACA 59.087 45.455 0.00 0.00 38.94 4.17
237 239 3.010420 GCAAAGATAAGGAGGACCACAC 58.990 50.000 0.00 0.00 38.94 3.82
238 240 3.610911 CAAAGATAAGGAGGACCACACC 58.389 50.000 0.00 0.00 38.94 4.16
239 241 2.950990 AGATAAGGAGGACCACACCT 57.049 50.000 0.00 0.00 43.64 4.00
240 242 2.472029 AGATAAGGAGGACCACACCTG 58.528 52.381 5.81 0.00 40.73 4.00
241 243 0.912486 ATAAGGAGGACCACACCTGC 59.088 55.000 5.81 0.00 46.42 4.85
248 250 1.355210 GACCACACCTGCAAACACG 59.645 57.895 0.00 0.00 0.00 4.49
267 269 0.671796 GCCAACAACCACTAACACCC 59.328 55.000 0.00 0.00 0.00 4.61
273 275 3.253220 ACAACCACTAACACCCTATGGA 58.747 45.455 0.00 0.00 34.38 3.41
296 298 2.892852 CCATGATCCGCCATAAACCAAT 59.107 45.455 0.00 0.00 0.00 3.16
297 299 3.305539 CCATGATCCGCCATAAACCAATG 60.306 47.826 0.00 0.00 0.00 2.82
320 322 6.349300 TGCCAACTAGTTCCAAATAGATCTC 58.651 40.000 4.77 0.00 31.50 2.75
323 325 7.554476 GCCAACTAGTTCCAAATAGATCTCTTT 59.446 37.037 4.77 0.00 31.50 2.52
324 326 8.887717 CCAACTAGTTCCAAATAGATCTCTTTG 58.112 37.037 21.01 21.01 31.50 2.77
325 327 9.442047 CAACTAGTTCCAAATAGATCTCTTTGT 57.558 33.333 24.10 13.19 31.83 2.83
329 331 7.461749 AGTTCCAAATAGATCTCTTTGTTGGA 58.538 34.615 24.10 19.88 31.83 3.53
334 336 3.045601 AGATCTCTTTGTTGGACCACG 57.954 47.619 0.00 0.00 0.00 4.94
345 347 2.279918 GACCACGCACCTTCACGT 60.280 61.111 0.00 0.00 44.75 4.49
353 355 0.389948 GCACCTTCACGTACCCTCAG 60.390 60.000 0.00 0.00 0.00 3.35
354 356 0.966920 CACCTTCACGTACCCTCAGT 59.033 55.000 0.00 0.00 0.00 3.41
357 359 1.162698 CTTCACGTACCCTCAGTCGA 58.837 55.000 0.00 0.00 0.00 4.20
358 360 1.743958 CTTCACGTACCCTCAGTCGAT 59.256 52.381 0.00 0.00 0.00 3.59
359 361 1.092348 TCACGTACCCTCAGTCGATG 58.908 55.000 0.00 0.00 0.00 3.84
366 368 3.377253 ACCCTCAGTCGATGTTAGGTA 57.623 47.619 0.00 0.00 0.00 3.08
368 370 3.021695 CCCTCAGTCGATGTTAGGTACA 58.978 50.000 0.00 0.00 41.97 2.90
377 379 1.140375 GTTAGGTACACCGCCGGAG 59.860 63.158 11.71 3.87 42.08 4.63
396 398 1.961277 CGGTGGCAAGGCGGATATC 60.961 63.158 0.00 0.00 0.00 1.63
420 422 5.022122 TCATTATTCCAACTTGGGATGCAA 58.978 37.500 11.53 0.00 36.15 4.08
430 432 2.892425 GGATGCAACCGCCTCGAG 60.892 66.667 5.13 5.13 37.32 4.04
435 437 3.197790 CAACCGCCTCGAGCATGG 61.198 66.667 6.99 10.47 44.04 3.66
436 438 4.473520 AACCGCCTCGAGCATGGG 62.474 66.667 6.99 7.30 44.04 4.00
439 441 4.147449 CGCCTCGAGCATGGGACA 62.147 66.667 6.99 0.00 44.04 4.02
477 480 4.871993 AAATGAGAACGCTAATGCTGAG 57.128 40.909 0.00 0.00 36.97 3.35
484 487 0.683973 CGCTAATGCTGAGGAGGGAT 59.316 55.000 0.00 0.00 36.97 3.85
486 489 1.337635 GCTAATGCTGAGGAGGGATCG 60.338 57.143 0.00 0.00 36.03 3.69
510 513 2.202892 GCCGACCCTCTAAAGCCG 60.203 66.667 0.00 0.00 0.00 5.52
512 515 2.029307 GCCGACCCTCTAAAGCCGAT 62.029 60.000 0.00 0.00 0.00 4.18
525 528 3.207677 GCCGATAGCTCCATCACAG 57.792 57.895 0.00 0.00 38.99 3.66
526 529 0.676184 GCCGATAGCTCCATCACAGA 59.324 55.000 0.00 0.00 38.99 3.41
527 530 1.336702 GCCGATAGCTCCATCACAGAG 60.337 57.143 0.00 0.00 38.99 3.35
528 531 2.234143 CCGATAGCTCCATCACAGAGA 58.766 52.381 0.00 0.00 32.86 3.10
529 532 2.228582 CCGATAGCTCCATCACAGAGAG 59.771 54.545 0.00 0.00 32.86 3.20
530 533 2.228582 CGATAGCTCCATCACAGAGAGG 59.771 54.545 0.00 0.00 32.86 3.69
534 537 2.914289 CCATCACAGAGAGGGGGC 59.086 66.667 0.00 0.00 44.44 5.80
535 538 2.503061 CATCACAGAGAGGGGGCG 59.497 66.667 0.00 0.00 0.00 6.13
536 539 2.060383 CATCACAGAGAGGGGGCGA 61.060 63.158 0.00 0.00 0.00 5.54
537 540 2.060980 ATCACAGAGAGGGGGCGAC 61.061 63.158 0.00 0.00 0.00 5.19
548 551 3.417224 GGGCGACCGTCGAAAACC 61.417 66.667 24.78 14.92 43.74 3.27
549 552 2.356673 GGCGACCGTCGAAAACCT 60.357 61.111 24.78 0.00 43.74 3.50
550 553 2.378084 GGCGACCGTCGAAAACCTC 61.378 63.158 24.78 4.60 43.74 3.85
551 554 1.662446 GCGACCGTCGAAAACCTCA 60.662 57.895 24.78 0.00 43.74 3.86
552 555 1.216941 GCGACCGTCGAAAACCTCAA 61.217 55.000 24.78 0.00 43.74 3.02
553 556 0.782384 CGACCGTCGAAAACCTCAAG 59.218 55.000 16.03 0.00 43.74 3.02
554 557 1.145803 GACCGTCGAAAACCTCAAGG 58.854 55.000 0.00 0.00 42.17 3.61
555 558 0.754472 ACCGTCGAAAACCTCAAGGA 59.246 50.000 2.30 0.00 38.94 3.36
556 559 1.270147 ACCGTCGAAAACCTCAAGGAG 60.270 52.381 2.30 0.00 38.94 3.69
557 560 0.790814 CGTCGAAAACCTCAAGGAGC 59.209 55.000 2.30 0.00 38.94 4.70
558 561 1.157585 GTCGAAAACCTCAAGGAGCC 58.842 55.000 2.30 0.00 38.94 4.70
559 562 0.036306 TCGAAAACCTCAAGGAGCCC 59.964 55.000 2.30 0.00 38.94 5.19
560 563 0.036875 CGAAAACCTCAAGGAGCCCT 59.963 55.000 2.30 0.00 38.94 5.19
561 564 1.539157 GAAAACCTCAAGGAGCCCTG 58.461 55.000 2.30 0.00 38.94 4.45
562 565 0.853530 AAAACCTCAAGGAGCCCTGT 59.146 50.000 2.30 0.00 38.94 4.00
563 566 0.111253 AAACCTCAAGGAGCCCTGTG 59.889 55.000 2.30 0.00 38.94 3.66
564 567 1.062488 AACCTCAAGGAGCCCTGTGT 61.062 55.000 2.30 0.00 38.94 3.72
565 568 1.298014 CCTCAAGGAGCCCTGTGTC 59.702 63.158 0.00 0.00 37.39 3.67
566 569 1.079543 CTCAAGGAGCCCTGTGTCG 60.080 63.158 0.00 0.00 32.13 4.35
567 570 1.821061 CTCAAGGAGCCCTGTGTCGT 61.821 60.000 0.00 0.00 32.13 4.34
568 571 1.669115 CAAGGAGCCCTGTGTCGTG 60.669 63.158 0.00 0.00 32.13 4.35
569 572 2.883828 AAGGAGCCCTGTGTCGTGG 61.884 63.158 0.00 0.00 32.13 4.94
570 573 4.394712 GGAGCCCTGTGTCGTGGG 62.395 72.222 0.00 0.00 46.00 4.61
660 663 2.167693 TGGATGAGTAAGGTACAAGCGG 59.832 50.000 0.00 0.00 0.00 5.52
662 665 0.108992 TGAGTAAGGTACAAGCGGCG 60.109 55.000 0.51 0.51 0.00 6.46
714 717 2.041686 GGACGACACCTCGCTCTCT 61.042 63.158 0.00 0.00 44.33 3.10
716 719 0.179184 GACGACACCTCGCTCTCTTC 60.179 60.000 0.00 0.00 44.33 2.87
717 720 0.889638 ACGACACCTCGCTCTCTTCA 60.890 55.000 0.00 0.00 44.33 3.02
718 721 0.241213 CGACACCTCGCTCTCTTCAA 59.759 55.000 0.00 0.00 31.91 2.69
753 756 4.920640 AGGATTAGTGTAGTGATGTCCG 57.079 45.455 0.00 0.00 0.00 4.79
754 757 4.279145 AGGATTAGTGTAGTGATGTCCGT 58.721 43.478 0.00 0.00 0.00 4.69
755 758 4.710375 AGGATTAGTGTAGTGATGTCCGTT 59.290 41.667 0.00 0.00 0.00 4.44
756 759 5.041940 GGATTAGTGTAGTGATGTCCGTTC 58.958 45.833 0.00 0.00 0.00 3.95
757 760 5.163540 GGATTAGTGTAGTGATGTCCGTTCT 60.164 44.000 0.00 0.00 0.00 3.01
758 761 5.717078 TTAGTGTAGTGATGTCCGTTCTT 57.283 39.130 0.00 0.00 0.00 2.52
759 762 6.822667 TTAGTGTAGTGATGTCCGTTCTTA 57.177 37.500 0.00 0.00 0.00 2.10
760 763 5.916661 AGTGTAGTGATGTCCGTTCTTAT 57.083 39.130 0.00 0.00 0.00 1.73
761 764 8.510243 TTAGTGTAGTGATGTCCGTTCTTATA 57.490 34.615 0.00 0.00 0.00 0.98
762 765 7.584122 AGTGTAGTGATGTCCGTTCTTATAT 57.416 36.000 0.00 0.00 0.00 0.86
763 766 8.008513 AGTGTAGTGATGTCCGTTCTTATATT 57.991 34.615 0.00 0.00 0.00 1.28
764 767 9.128404 AGTGTAGTGATGTCCGTTCTTATATTA 57.872 33.333 0.00 0.00 0.00 0.98
765 768 9.909644 GTGTAGTGATGTCCGTTCTTATATTAT 57.090 33.333 0.00 0.00 0.00 1.28
766 769 9.908152 TGTAGTGATGTCCGTTCTTATATTATG 57.092 33.333 0.00 0.00 0.00 1.90
767 770 9.355215 GTAGTGATGTCCGTTCTTATATTATGG 57.645 37.037 0.00 0.00 0.00 2.74
768 771 7.386851 AGTGATGTCCGTTCTTATATTATGGG 58.613 38.462 0.00 0.00 0.00 4.00
769 772 7.234782 AGTGATGTCCGTTCTTATATTATGGGA 59.765 37.037 0.00 0.00 0.00 4.37
770 773 7.331193 GTGATGTCCGTTCTTATATTATGGGAC 59.669 40.741 0.00 0.00 42.28 4.46
771 774 5.775686 TGTCCGTTCTTATATTATGGGACG 58.224 41.667 0.00 5.74 44.29 4.79
772 775 5.166398 GTCCGTTCTTATATTATGGGACGG 58.834 45.833 17.79 17.79 34.09 4.79
773 776 5.047802 GTCCGTTCTTATATTATGGGACGGA 60.048 44.000 20.43 20.43 42.60 4.69
774 777 5.184479 TCCGTTCTTATATTATGGGACGGAG 59.816 44.000 20.43 6.28 40.45 4.63
775 778 5.408356 CGTTCTTATATTATGGGACGGAGG 58.592 45.833 0.00 0.00 0.00 4.30
776 779 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
777 780 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
778 781 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
779 782 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
780 783 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
781 784 3.562108 ATTATGGGACGGAGGGAGTAT 57.438 47.619 0.00 0.00 0.00 2.12
782 785 4.687262 ATTATGGGACGGAGGGAGTATA 57.313 45.455 0.00 0.00 0.00 1.47
783 786 2.305858 ATGGGACGGAGGGAGTATAC 57.694 55.000 0.00 0.00 0.00 1.47
784 787 0.928505 TGGGACGGAGGGAGTATACA 59.071 55.000 5.50 0.00 0.00 2.29
785 788 1.288633 TGGGACGGAGGGAGTATACAA 59.711 52.381 5.50 0.00 0.00 2.41
786 789 2.292389 TGGGACGGAGGGAGTATACAAA 60.292 50.000 5.50 0.00 0.00 2.83
787 790 2.364647 GGGACGGAGGGAGTATACAAAG 59.635 54.545 5.50 0.00 0.00 2.77
788 791 3.294214 GGACGGAGGGAGTATACAAAGA 58.706 50.000 5.50 0.00 0.00 2.52
789 792 3.318557 GGACGGAGGGAGTATACAAAGAG 59.681 52.174 5.50 0.00 0.00 2.85
790 793 3.952967 GACGGAGGGAGTATACAAAGAGT 59.047 47.826 5.50 0.00 0.00 3.24
791 794 4.351127 ACGGAGGGAGTATACAAAGAGTT 58.649 43.478 5.50 0.00 0.00 3.01
792 795 5.513233 ACGGAGGGAGTATACAAAGAGTTA 58.487 41.667 5.50 0.00 0.00 2.24
793 796 6.134754 ACGGAGGGAGTATACAAAGAGTTAT 58.865 40.000 5.50 0.00 0.00 1.89
794 797 6.610425 ACGGAGGGAGTATACAAAGAGTTATT 59.390 38.462 5.50 0.00 0.00 1.40
795 798 7.781693 ACGGAGGGAGTATACAAAGAGTTATTA 59.218 37.037 5.50 0.00 0.00 0.98
796 799 8.298140 CGGAGGGAGTATACAAAGAGTTATTAG 58.702 40.741 5.50 0.00 0.00 1.73
797 800 9.145442 GGAGGGAGTATACAAAGAGTTATTAGT 57.855 37.037 5.50 0.00 0.00 2.24
849 852 5.453567 AAAGGAACAAATTAGTGACCAGC 57.546 39.130 0.00 0.00 0.00 4.85
850 853 3.421844 AGGAACAAATTAGTGACCAGCC 58.578 45.455 0.00 0.00 0.00 4.85
851 854 3.153919 GGAACAAATTAGTGACCAGCCA 58.846 45.455 0.00 0.00 0.00 4.75
852 855 3.763897 GGAACAAATTAGTGACCAGCCAT 59.236 43.478 0.00 0.00 0.00 4.40
856 859 4.943705 ACAAATTAGTGACCAGCCATAGTG 59.056 41.667 0.00 0.00 0.00 2.74
864 867 3.580895 TGACCAGCCATAGTGACAAACTA 59.419 43.478 0.00 0.00 45.47 2.24
871 874 3.270877 CATAGTGACAAACTAGTGGGCC 58.729 50.000 0.00 0.00 44.61 5.80
891 894 3.864540 GCCCTGAATTTGGCCAAACTAAC 60.865 47.826 32.62 21.82 41.97 2.34
892 895 3.574614 CCTGAATTTGGCCAAACTAACG 58.425 45.455 32.62 18.60 32.51 3.18
893 896 2.986479 CTGAATTTGGCCAAACTAACGC 59.014 45.455 32.62 17.40 32.51 4.84
895 898 3.068873 TGAATTTGGCCAAACTAACGCTT 59.931 39.130 32.62 20.49 32.51 4.68
896 899 3.744238 ATTTGGCCAAACTAACGCTTT 57.256 38.095 32.62 11.20 32.51 3.51
897 900 3.528597 TTTGGCCAAACTAACGCTTTT 57.471 38.095 27.13 0.00 0.00 2.27
898 901 3.528597 TTGGCCAAACTAACGCTTTTT 57.471 38.095 17.98 0.00 0.00 1.94
919 922 7.946655 TTTTTAGACACAGTCACAGTCATAG 57.053 36.000 0.00 0.00 34.60 2.23
920 923 6.894339 TTTAGACACAGTCACAGTCATAGA 57.106 37.500 0.00 0.00 34.60 1.98
921 924 4.775058 AGACACAGTCACAGTCATAGAC 57.225 45.455 0.00 0.00 34.60 2.59
922 925 3.189495 AGACACAGTCACAGTCATAGACG 59.811 47.826 0.00 0.00 37.36 4.18
923 926 2.229062 ACACAGTCACAGTCATAGACGG 59.771 50.000 0.00 0.00 37.67 4.79
924 927 2.488153 CACAGTCACAGTCATAGACGGA 59.512 50.000 4.38 0.00 37.67 4.69
934 937 0.528924 CATAGACGGACACGGACCAA 59.471 55.000 0.00 0.00 46.48 3.67
937 940 1.447314 GACGGACACGGACCAATCC 60.447 63.158 0.00 0.00 46.48 3.01
950 953 1.340991 ACCAATCCCCCATTTCACTCG 60.341 52.381 0.00 0.00 0.00 4.18
952 955 0.395724 AATCCCCCATTTCACTCGCC 60.396 55.000 0.00 0.00 0.00 5.54
953 956 1.570857 ATCCCCCATTTCACTCGCCA 61.571 55.000 0.00 0.00 0.00 5.69
960 963 0.737715 ATTTCACTCGCCACTCGCTC 60.738 55.000 0.00 0.00 38.27 5.03
961 964 2.082629 TTTCACTCGCCACTCGCTCA 62.083 55.000 0.00 0.00 38.27 4.26
962 965 2.749110 TTCACTCGCCACTCGCTCAC 62.749 60.000 0.00 0.00 38.27 3.51
963 966 4.406173 ACTCGCCACTCGCTCACG 62.406 66.667 0.00 0.00 42.01 4.35
974 977 2.253513 CGCTCACGAACCCCAAAAT 58.746 52.632 0.00 0.00 43.93 1.82
976 979 1.534729 GCTCACGAACCCCAAAATCT 58.465 50.000 0.00 0.00 0.00 2.40
979 982 0.802494 CACGAACCCCAAAATCTCCG 59.198 55.000 0.00 0.00 0.00 4.63
990 993 1.550130 AAATCTCCGAACCCTCGCCA 61.550 55.000 0.00 0.00 44.04 5.69
1027 1030 3.351416 GGACGCCGTTCACCAACC 61.351 66.667 0.00 0.00 0.00 3.77
1081 1084 4.452733 GCTTCGACCCCCACGAGG 62.453 72.222 0.00 0.00 40.72 4.63
1117 1120 0.813210 GCAGCTGCTCACCTACATCC 60.813 60.000 31.33 0.00 38.21 3.51
1239 5775 3.138798 AGCGCCGACCGTATCAGT 61.139 61.111 2.29 0.00 39.71 3.41
1374 5911 0.387202 CCTCATCGACGCATTCCTCT 59.613 55.000 0.00 0.00 0.00 3.69
1383 5932 2.409870 GCATTCCTCTGGCCCAACG 61.410 63.158 0.00 0.00 0.00 4.10
1414 5974 2.434884 CGCAACCGTCTCCTGCAT 60.435 61.111 0.00 0.00 35.78 3.96
1415 5975 2.456119 CGCAACCGTCTCCTGCATC 61.456 63.158 0.00 0.00 35.78 3.91
1424 5984 4.731853 TCCTGCATCCCCGGGACA 62.732 66.667 26.32 13.70 35.36 4.02
1542 6102 2.911484 CGTCCTCGTCAACCGACCA 61.911 63.158 0.00 0.00 41.60 4.02
1686 6252 3.260483 GAGCTCGGCATCTGCACG 61.260 66.667 0.00 5.71 44.36 5.34
1704 6270 2.660064 GGTCGTGATGGAGCAGGGT 61.660 63.158 0.00 0.00 34.64 4.34
1918 6484 1.221021 GCTAGTGGCCTGTGTACCC 59.779 63.158 3.32 0.00 34.27 3.69
1924 6490 4.091939 GCCTGTGTACCCGGGTCC 62.092 72.222 34.27 21.88 33.07 4.46
1953 6519 0.929244 ATGCCCCCAAGCTACATTCT 59.071 50.000 0.00 0.00 0.00 2.40
1978 6544 2.692041 GGATTCTTGGAGCCAGGAAATG 59.308 50.000 16.53 0.00 43.44 2.32
2000 6566 1.272480 TGTCCTGGAGATCGGAGACAA 60.272 52.381 0.00 0.00 42.51 3.18
2022 6588 4.945246 ACGTCATAATGGTGAGTATCCAC 58.055 43.478 0.00 0.00 37.81 4.02
2070 6660 9.546428 CTTTGTTCTTAAATTGGGTGAATTTCT 57.454 29.630 0.00 0.00 42.27 2.52
2083 6673 4.466015 GGTGAATTTCTGGCTGGGATAAAA 59.534 41.667 0.00 0.00 0.00 1.52
2112 6702 2.502510 CACCATTGTCGCAAGCGC 60.503 61.111 9.97 0.00 39.59 5.92
2125 6715 1.472376 GCAAGCGCTAAGATCCTGAGT 60.472 52.381 12.05 0.00 34.30 3.41
2197 6787 6.183361 TGTTCCTTAAATGCTTTCCCAATGTT 60.183 34.615 0.00 0.00 0.00 2.71
2323 7008 7.693951 GGTCTTTCAAGTCATTTATTCATCACG 59.306 37.037 0.00 0.00 0.00 4.35
2324 7009 8.443160 GTCTTTCAAGTCATTTATTCATCACGA 58.557 33.333 0.00 0.00 0.00 4.35
2335 7034 6.844696 TTATTCATCACGACTCTTTATGGC 57.155 37.500 0.00 0.00 0.00 4.40
2376 7081 2.159393 CCACATGTTAAGGTGCCATTCG 60.159 50.000 0.00 0.00 36.76 3.34
2471 7176 4.276678 TCTGCTTATGCTATGACATTTGGC 59.723 41.667 0.00 0.00 40.48 4.52
2476 7181 7.039574 TGCTTATGCTATGACATTTGGCAATAT 60.040 33.333 0.00 0.00 36.97 1.28
2509 7216 9.096823 TCCGGTGGTACAATTTCTATTATATCT 57.903 33.333 0.00 0.00 44.16 1.98
2510 7217 9.151471 CCGGTGGTACAATTTCTATTATATCTG 57.849 37.037 0.00 0.00 44.16 2.90
2550 7258 7.041848 GCTTTGTTTCTTAAATTCTGGCATGTT 60.042 33.333 0.00 0.00 0.00 2.71
2551 7259 8.729805 TTTGTTTCTTAAATTCTGGCATGTTT 57.270 26.923 0.00 0.00 0.00 2.83
2565 7273 4.344679 TGGCATGTTTGGATCTTTTTCTGT 59.655 37.500 0.00 0.00 0.00 3.41
2570 7278 7.599998 GCATGTTTGGATCTTTTTCTGTAACAT 59.400 33.333 0.00 0.00 34.93 2.71
2611 7319 7.253420 CGTTTGCTTATTTTACACTGATGCATC 60.253 37.037 20.14 20.14 0.00 3.91
2778 7489 0.451383 CAATTCCATTTCGCGGCAGA 59.549 50.000 6.13 0.00 0.00 4.26
2781 7492 2.031258 TTCCATTTCGCGGCAGATTA 57.969 45.000 6.13 0.00 0.00 1.75
2784 7495 2.146342 CCATTTCGCGGCAGATTATCT 58.854 47.619 6.13 0.00 0.00 1.98
2822 7548 0.029433 GCCGCTAAGCCATTTAGTGC 59.971 55.000 2.74 0.30 44.76 4.40
2845 7571 4.271049 CCAGCTAGTACATGGACATTTTCG 59.729 45.833 11.55 0.00 36.09 3.46
2860 7586 1.460273 TTTCGGCAGGAAAACAGGGC 61.460 55.000 0.21 0.00 41.55 5.19
2883 7609 2.276732 TTCAGCAGGAAAACAGAGGG 57.723 50.000 0.00 0.00 30.98 4.30
2896 7622 6.998673 GGAAAACAGAGGGTTGCAGTATATAT 59.001 38.462 0.00 0.00 40.35 0.86
2943 7672 7.598493 GCATCACCAATTACAACTTACAAACAT 59.402 33.333 0.00 0.00 0.00 2.71
2951 7680 4.536065 ACAACTTACAAACATGCATCACG 58.464 39.130 0.00 0.00 0.00 4.35
2952 7681 4.274705 ACAACTTACAAACATGCATCACGA 59.725 37.500 0.00 0.00 0.00 4.35
2953 7682 4.668576 ACTTACAAACATGCATCACGAG 57.331 40.909 0.00 0.00 0.00 4.18
3011 7740 6.706295 TGTTCTGGTTCCAAATGAAAACTTT 58.294 32.000 0.00 0.00 33.94 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 2.417339 TCGGTGCTAATAGATGTCGC 57.583 50.000 0.00 0.00 0.00 5.19
87 88 1.618345 GGATGGGTAATGTTGGTGGCA 60.618 52.381 0.00 0.00 0.00 4.92
100 101 1.566298 GCCTCTGACAAGGGATGGGT 61.566 60.000 6.01 0.00 36.88 4.51
110 111 4.397420 ACAATGTTTACATGCCTCTGACA 58.603 39.130 0.00 0.00 36.56 3.58
114 115 5.106157 GCTACAACAATGTTTACATGCCTCT 60.106 40.000 0.00 0.00 41.05 3.69
154 155 2.077687 ATTGGGGCCATAGCTCAAAG 57.922 50.000 4.39 0.00 43.51 2.77
157 159 1.779221 CAAATTGGGGCCATAGCTCA 58.221 50.000 4.39 0.00 43.51 4.26
170 172 3.931468 TGTTCTTGTGTGTTGGCAAATTG 59.069 39.130 0.00 0.00 0.00 2.32
171 173 4.199432 TGTTCTTGTGTGTTGGCAAATT 57.801 36.364 0.00 0.00 0.00 1.82
188 190 1.602323 TTGGCCACGGGTCATGTTC 60.602 57.895 3.88 0.00 37.08 3.18
193 195 1.826054 CTTTGTTGGCCACGGGTCA 60.826 57.895 3.88 0.00 34.47 4.02
199 201 1.032014 TGCTTCTCTTTGTTGGCCAC 58.968 50.000 3.88 0.75 0.00 5.01
208 210 6.176896 GTCCTCCTTATCTTTGCTTCTCTTT 58.823 40.000 0.00 0.00 0.00 2.52
224 226 1.352622 TTGCAGGTGTGGTCCTCCTT 61.353 55.000 0.00 0.00 35.37 3.36
226 228 1.150536 TTTGCAGGTGTGGTCCTCC 59.849 57.895 0.00 0.00 35.37 4.30
227 229 0.465460 TGTTTGCAGGTGTGGTCCTC 60.465 55.000 0.00 0.00 35.37 3.71
228 230 0.751643 GTGTTTGCAGGTGTGGTCCT 60.752 55.000 0.00 0.00 38.51 3.85
229 231 1.733526 GTGTTTGCAGGTGTGGTCC 59.266 57.895 0.00 0.00 0.00 4.46
230 232 1.355210 CGTGTTTGCAGGTGTGGTC 59.645 57.895 0.00 0.00 0.00 4.02
231 233 2.770589 GCGTGTTTGCAGGTGTGGT 61.771 57.895 0.00 0.00 33.42 4.16
232 234 2.026014 GCGTGTTTGCAGGTGTGG 59.974 61.111 0.00 0.00 33.42 4.17
233 235 2.026014 GGCGTGTTTGCAGGTGTG 59.974 61.111 0.00 0.00 36.28 3.82
234 236 2.049185 TTGGCGTGTTTGCAGGTGT 61.049 52.632 0.00 0.00 36.28 4.16
235 237 1.588667 GTTGGCGTGTTTGCAGGTG 60.589 57.895 0.00 0.00 36.28 4.00
236 238 1.599606 TTGTTGGCGTGTTTGCAGGT 61.600 50.000 0.00 0.00 36.28 4.00
237 239 1.140589 TTGTTGGCGTGTTTGCAGG 59.859 52.632 0.00 0.00 36.28 4.85
238 240 1.145162 GGTTGTTGGCGTGTTTGCAG 61.145 55.000 0.00 0.00 36.28 4.41
239 241 1.153745 GGTTGTTGGCGTGTTTGCA 60.154 52.632 0.00 0.00 36.28 4.08
240 242 1.153745 TGGTTGTTGGCGTGTTTGC 60.154 52.632 0.00 0.00 0.00 3.68
241 243 0.172352 AGTGGTTGTTGGCGTGTTTG 59.828 50.000 0.00 0.00 0.00 2.93
248 250 0.671796 GGGTGTTAGTGGTTGTTGGC 59.328 55.000 0.00 0.00 0.00 4.52
273 275 2.108075 TGGTTTATGGCGGATCATGGAT 59.892 45.455 0.00 0.00 0.00 3.41
288 290 4.730966 TGGAACTAGTTGGCATTGGTTTA 58.269 39.130 14.14 0.00 0.00 2.01
296 298 6.156949 AGAGATCTATTTGGAACTAGTTGGCA 59.843 38.462 14.14 0.00 0.00 4.92
297 299 6.587273 AGAGATCTATTTGGAACTAGTTGGC 58.413 40.000 14.14 0.00 0.00 4.52
320 322 1.101049 AGGTGCGTGGTCCAACAAAG 61.101 55.000 0.00 0.00 0.00 2.77
323 325 1.525077 GAAGGTGCGTGGTCCAACA 60.525 57.895 0.00 0.00 0.00 3.33
324 326 1.525077 TGAAGGTGCGTGGTCCAAC 60.525 57.895 0.00 0.00 0.00 3.77
325 327 1.525077 GTGAAGGTGCGTGGTCCAA 60.525 57.895 0.00 0.00 0.00 3.53
326 328 2.110213 GTGAAGGTGCGTGGTCCA 59.890 61.111 0.00 0.00 0.00 4.02
329 331 1.300388 GTACGTGAAGGTGCGTGGT 60.300 57.895 0.00 0.00 41.68 4.16
334 336 0.389948 CTGAGGGTACGTGAAGGTGC 60.390 60.000 0.00 0.00 0.00 5.01
345 347 3.377253 ACCTAACATCGACTGAGGGTA 57.623 47.619 8.79 0.00 0.00 3.69
357 359 0.971959 TCCGGCGGTGTACCTAACAT 60.972 55.000 27.32 0.00 41.10 2.71
358 360 1.597797 CTCCGGCGGTGTACCTAACA 61.598 60.000 27.32 0.43 35.06 2.41
359 361 1.140375 CTCCGGCGGTGTACCTAAC 59.860 63.158 27.32 0.00 0.00 2.34
377 379 4.849310 TATCCGCCTTGCCACCGC 62.849 66.667 0.00 0.00 0.00 5.68
388 390 6.128172 CCAAGTTGGAATAATGAGATATCCGC 60.128 42.308 17.60 0.00 40.96 5.54
389 391 6.372659 CCCAAGTTGGAATAATGAGATATCCG 59.627 42.308 24.06 0.00 40.96 4.18
393 395 6.716628 GCATCCCAAGTTGGAATAATGAGATA 59.283 38.462 24.06 0.00 40.96 1.98
396 398 4.646040 TGCATCCCAAGTTGGAATAATGAG 59.354 41.667 24.06 3.83 40.96 2.90
430 432 8.770438 TTATTTAGTTTTGATTTGTCCCATGC 57.230 30.769 0.00 0.00 0.00 4.06
469 472 0.399091 TCCGATCCCTCCTCAGCATT 60.399 55.000 0.00 0.00 0.00 3.56
470 473 0.831288 CTCCGATCCCTCCTCAGCAT 60.831 60.000 0.00 0.00 0.00 3.79
486 489 3.711059 TAGAGGGTCGGCGGACTCC 62.711 68.421 19.74 18.87 45.26 3.85
495 498 1.336056 GCTATCGGCTTTAGAGGGTCG 60.336 57.143 0.00 0.00 38.06 4.79
510 513 2.562298 CCCTCTCTGTGATGGAGCTATC 59.438 54.545 0.00 0.00 32.98 2.08
512 515 1.412217 CCCCTCTCTGTGATGGAGCTA 60.412 57.143 3.07 0.00 32.98 3.32
529 532 4.685467 TTTTCGACGGTCGCCCCC 62.685 66.667 24.76 0.00 40.21 5.40
530 533 3.417224 GTTTTCGACGGTCGCCCC 61.417 66.667 24.76 9.22 40.21 5.80
531 534 3.417224 GGTTTTCGACGGTCGCCC 61.417 66.667 24.76 16.72 40.21 6.13
532 535 2.356673 AGGTTTTCGACGGTCGCC 60.357 61.111 24.76 19.13 40.21 5.54
533 536 1.216941 TTGAGGTTTTCGACGGTCGC 61.217 55.000 24.76 11.12 40.21 5.19
534 537 0.782384 CTTGAGGTTTTCGACGGTCG 59.218 55.000 23.73 23.73 42.10 4.79
535 538 1.145803 CCTTGAGGTTTTCGACGGTC 58.854 55.000 0.00 0.00 0.00 4.79
536 539 0.754472 TCCTTGAGGTTTTCGACGGT 59.246 50.000 0.00 0.00 36.34 4.83
537 540 1.429463 CTCCTTGAGGTTTTCGACGG 58.571 55.000 0.00 0.00 36.34 4.79
538 541 0.790814 GCTCCTTGAGGTTTTCGACG 59.209 55.000 0.00 0.00 36.34 5.12
539 542 1.157585 GGCTCCTTGAGGTTTTCGAC 58.842 55.000 0.00 0.00 36.34 4.20
540 543 0.036306 GGGCTCCTTGAGGTTTTCGA 59.964 55.000 0.00 0.00 36.34 3.71
541 544 0.036875 AGGGCTCCTTGAGGTTTTCG 59.963 55.000 0.00 0.00 36.34 3.46
542 545 1.202940 ACAGGGCTCCTTGAGGTTTTC 60.203 52.381 4.97 0.00 36.34 2.29
543 546 0.853530 ACAGGGCTCCTTGAGGTTTT 59.146 50.000 4.97 0.00 36.34 2.43
544 547 0.111253 CACAGGGCTCCTTGAGGTTT 59.889 55.000 4.97 0.00 36.34 3.27
545 548 1.062488 ACACAGGGCTCCTTGAGGTT 61.062 55.000 4.97 0.00 36.34 3.50
546 549 1.462238 ACACAGGGCTCCTTGAGGT 60.462 57.895 4.97 0.44 36.34 3.85
547 550 1.298014 GACACAGGGCTCCTTGAGG 59.702 63.158 4.97 0.00 0.00 3.86
548 551 1.079543 CGACACAGGGCTCCTTGAG 60.080 63.158 4.97 0.00 0.00 3.02
549 552 1.837051 ACGACACAGGGCTCCTTGA 60.837 57.895 4.97 0.00 0.00 3.02
550 553 1.669115 CACGACACAGGGCTCCTTG 60.669 63.158 0.00 0.00 0.00 3.61
551 554 2.743718 CACGACACAGGGCTCCTT 59.256 61.111 0.00 0.00 0.00 3.36
552 555 3.314331 CCACGACACAGGGCTCCT 61.314 66.667 0.00 0.00 0.00 3.69
553 556 4.394712 CCCACGACACAGGGCTCC 62.395 72.222 0.00 0.00 38.44 4.70
559 562 3.907260 ATGGCAGCCCACGACACAG 62.907 63.158 9.64 0.00 45.77 3.66
560 563 3.899981 GATGGCAGCCCACGACACA 62.900 63.158 9.64 0.00 45.77 3.72
561 564 2.238847 TAGATGGCAGCCCACGACAC 62.239 60.000 9.64 0.00 45.77 3.67
562 565 1.549243 TTAGATGGCAGCCCACGACA 61.549 55.000 9.64 0.00 45.77 4.35
563 566 1.090052 GTTAGATGGCAGCCCACGAC 61.090 60.000 9.64 4.19 45.77 4.34
564 567 1.220749 GTTAGATGGCAGCCCACGA 59.779 57.895 9.64 0.00 45.77 4.35
565 568 0.464373 ATGTTAGATGGCAGCCCACG 60.464 55.000 9.64 0.00 45.77 4.94
566 569 1.027357 CATGTTAGATGGCAGCCCAC 58.973 55.000 9.64 2.58 45.77 4.61
568 571 2.638480 TACATGTTAGATGGCAGCCC 57.362 50.000 9.64 0.00 0.00 5.19
569 572 4.136796 TCATTACATGTTAGATGGCAGCC 58.863 43.478 2.30 3.66 0.00 4.85
570 573 5.297776 ACTTCATTACATGTTAGATGGCAGC 59.702 40.000 2.30 0.00 0.00 5.25
571 574 6.932356 ACTTCATTACATGTTAGATGGCAG 57.068 37.500 2.30 8.77 0.00 4.85
572 575 7.701539 AAACTTCATTACATGTTAGATGGCA 57.298 32.000 2.30 0.00 0.00 4.92
617 620 7.067421 TCCAGTACTATCTATGCACCTAAGTT 58.933 38.462 0.00 0.00 0.00 2.66
624 627 6.582677 ACTCATCCAGTACTATCTATGCAC 57.417 41.667 0.00 0.00 31.37 4.57
626 629 7.394923 ACCTTACTCATCCAGTACTATCTATGC 59.605 40.741 0.00 0.00 37.32 3.14
640 643 2.822764 CCGCTTGTACCTTACTCATCC 58.177 52.381 0.00 0.00 0.00 3.51
662 665 9.722056 ATCATTTCTCTTGTGCGTATATTTTTC 57.278 29.630 0.00 0.00 0.00 2.29
703 706 2.490115 CACTACTTGAAGAGAGCGAGGT 59.510 50.000 0.00 0.00 0.00 3.85
730 733 5.889853 ACGGACATCACTACACTAATCCTAA 59.110 40.000 0.00 0.00 0.00 2.69
738 741 5.916661 ATAAGAACGGACATCACTACACT 57.083 39.130 0.00 0.00 0.00 3.55
740 743 9.908152 CATAATATAAGAACGGACATCACTACA 57.092 33.333 0.00 0.00 0.00 2.74
749 752 5.047802 TCCGTCCCATAATATAAGAACGGAC 60.048 44.000 9.04 0.00 40.45 4.79
750 753 5.078949 TCCGTCCCATAATATAAGAACGGA 58.921 41.667 9.04 9.04 42.60 4.69
751 754 5.395682 TCCGTCCCATAATATAAGAACGG 57.604 43.478 4.33 4.33 38.24 4.44
752 755 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
753 756 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
754 757 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
755 758 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
756 759 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
757 760 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
758 761 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
759 762 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
760 763 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
761 764 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
762 765 3.140707 TGTATACTCCCTCCGTCCCATAA 59.859 47.826 4.17 0.00 0.00 1.90
763 766 2.718062 TGTATACTCCCTCCGTCCCATA 59.282 50.000 4.17 0.00 0.00 2.74
764 767 1.502039 TGTATACTCCCTCCGTCCCAT 59.498 52.381 4.17 0.00 0.00 4.00
765 768 0.928505 TGTATACTCCCTCCGTCCCA 59.071 55.000 4.17 0.00 0.00 4.37
766 769 2.077687 TTGTATACTCCCTCCGTCCC 57.922 55.000 4.17 0.00 0.00 4.46
767 770 3.294214 TCTTTGTATACTCCCTCCGTCC 58.706 50.000 4.17 0.00 0.00 4.79
768 771 3.952967 ACTCTTTGTATACTCCCTCCGTC 59.047 47.826 4.17 0.00 0.00 4.79
769 772 3.978610 ACTCTTTGTATACTCCCTCCGT 58.021 45.455 4.17 0.00 0.00 4.69
770 773 6.651975 ATAACTCTTTGTATACTCCCTCCG 57.348 41.667 4.17 0.00 0.00 4.63
771 774 9.145442 ACTAATAACTCTTTGTATACTCCCTCC 57.855 37.037 4.17 0.00 0.00 4.30
826 829 5.221441 GGCTGGTCACTAATTTGTTCCTTTT 60.221 40.000 10.54 0.00 0.00 2.27
830 833 3.153919 TGGCTGGTCACTAATTTGTTCC 58.846 45.455 0.00 0.00 0.00 3.62
831 834 5.648092 ACTATGGCTGGTCACTAATTTGTTC 59.352 40.000 0.00 0.00 0.00 3.18
843 846 3.059352 AGTTTGTCACTATGGCTGGTC 57.941 47.619 0.00 0.00 31.97 4.02
844 847 3.583086 ACTAGTTTGTCACTATGGCTGGT 59.417 43.478 0.00 0.00 37.36 4.00
846 849 3.935203 CCACTAGTTTGTCACTATGGCTG 59.065 47.826 0.00 0.00 37.36 4.85
847 850 3.055094 CCCACTAGTTTGTCACTATGGCT 60.055 47.826 0.00 0.00 37.36 4.75
848 851 3.270877 CCCACTAGTTTGTCACTATGGC 58.729 50.000 0.00 0.00 37.36 4.40
849 852 3.270877 GCCCACTAGTTTGTCACTATGG 58.729 50.000 0.00 0.00 37.36 2.74
850 853 3.270877 GGCCCACTAGTTTGTCACTATG 58.729 50.000 0.00 0.00 37.36 2.23
851 854 2.238898 GGGCCCACTAGTTTGTCACTAT 59.761 50.000 19.95 0.00 37.36 2.12
852 855 1.626825 GGGCCCACTAGTTTGTCACTA 59.373 52.381 19.95 0.00 36.88 2.74
856 859 0.690762 TCAGGGCCCACTAGTTTGTC 59.309 55.000 27.56 0.00 0.00 3.18
864 867 1.610379 GCCAAATTCAGGGCCCACT 60.610 57.895 27.56 0.00 44.53 4.00
871 874 3.574614 CGTTAGTTTGGCCAAATTCAGG 58.425 45.455 32.52 20.94 32.36 3.86
895 898 7.652105 GTCTATGACTGTGACTGTGTCTAAAAA 59.348 37.037 0.00 0.00 33.15 1.94
896 899 7.145985 GTCTATGACTGTGACTGTGTCTAAAA 58.854 38.462 0.00 0.00 33.15 1.52
897 900 6.567891 CGTCTATGACTGTGACTGTGTCTAAA 60.568 42.308 0.00 0.00 33.15 1.85
898 901 5.106673 CGTCTATGACTGTGACTGTGTCTAA 60.107 44.000 0.00 0.00 33.15 2.10
899 902 4.392138 CGTCTATGACTGTGACTGTGTCTA 59.608 45.833 0.00 0.00 33.15 2.59
900 903 3.189495 CGTCTATGACTGTGACTGTGTCT 59.811 47.826 0.00 0.00 33.15 3.41
901 904 3.493272 CGTCTATGACTGTGACTGTGTC 58.507 50.000 0.00 0.00 0.00 3.67
902 905 2.229062 CCGTCTATGACTGTGACTGTGT 59.771 50.000 0.00 0.00 0.00 3.72
904 907 2.488545 GTCCGTCTATGACTGTGACTGT 59.511 50.000 0.00 0.00 0.00 3.55
905 908 2.488153 TGTCCGTCTATGACTGTGACTG 59.512 50.000 0.00 0.00 33.83 3.51
906 909 2.488545 GTGTCCGTCTATGACTGTGACT 59.511 50.000 0.00 0.00 33.83 3.41
907 910 2.728225 CGTGTCCGTCTATGACTGTGAC 60.728 54.545 0.00 0.00 33.83 3.67
908 911 1.467342 CGTGTCCGTCTATGACTGTGA 59.533 52.381 0.00 0.00 33.83 3.58
909 912 1.467543 CCGTGTCCGTCTATGACTGTG 60.468 57.143 0.00 0.00 33.83 3.66
910 913 0.809385 CCGTGTCCGTCTATGACTGT 59.191 55.000 0.00 0.00 33.83 3.55
911 914 1.092348 TCCGTGTCCGTCTATGACTG 58.908 55.000 0.00 0.00 33.83 3.51
912 915 1.093159 GTCCGTGTCCGTCTATGACT 58.907 55.000 0.00 0.00 33.83 3.41
913 916 0.100146 GGTCCGTGTCCGTCTATGAC 59.900 60.000 0.00 0.00 0.00 3.06
914 917 0.322726 TGGTCCGTGTCCGTCTATGA 60.323 55.000 0.00 0.00 0.00 2.15
915 918 0.528924 TTGGTCCGTGTCCGTCTATG 59.471 55.000 0.00 0.00 0.00 2.23
916 919 1.407979 GATTGGTCCGTGTCCGTCTAT 59.592 52.381 0.00 0.00 0.00 1.98
917 920 0.813184 GATTGGTCCGTGTCCGTCTA 59.187 55.000 0.00 0.00 0.00 2.59
918 921 1.590147 GATTGGTCCGTGTCCGTCT 59.410 57.895 0.00 0.00 0.00 4.18
919 922 1.447314 GGATTGGTCCGTGTCCGTC 60.447 63.158 0.00 0.00 34.13 4.79
920 923 2.660802 GGATTGGTCCGTGTCCGT 59.339 61.111 0.00 0.00 34.13 4.69
921 924 2.125269 GGGATTGGTCCGTGTCCG 60.125 66.667 2.07 0.00 46.09 4.79
922 925 2.271173 GGGGATTGGTCCGTGTCC 59.729 66.667 0.00 0.00 46.09 4.02
923 926 1.921869 ATGGGGGATTGGTCCGTGTC 61.922 60.000 0.00 0.00 46.09 3.67
924 927 1.506028 AATGGGGGATTGGTCCGTGT 61.506 55.000 0.00 0.00 46.09 4.49
934 937 1.227383 GGCGAGTGAAATGGGGGAT 59.773 57.895 0.00 0.00 0.00 3.85
937 940 1.002134 AGTGGCGAGTGAAATGGGG 60.002 57.895 0.00 0.00 0.00 4.96
960 963 0.802494 CGGAGATTTTGGGGTTCGTG 59.198 55.000 0.00 0.00 0.00 4.35
961 964 0.688487 TCGGAGATTTTGGGGTTCGT 59.312 50.000 0.00 0.00 0.00 3.85
962 965 1.467342 GTTCGGAGATTTTGGGGTTCG 59.533 52.381 0.00 0.00 35.04 3.95
963 966 1.816835 GGTTCGGAGATTTTGGGGTTC 59.183 52.381 0.00 0.00 35.04 3.62
964 967 1.549265 GGGTTCGGAGATTTTGGGGTT 60.549 52.381 0.00 0.00 35.04 4.11
965 968 0.039180 GGGTTCGGAGATTTTGGGGT 59.961 55.000 0.00 0.00 35.04 4.95
966 969 0.331616 AGGGTTCGGAGATTTTGGGG 59.668 55.000 0.00 0.00 35.04 4.96
967 970 1.751437 GAGGGTTCGGAGATTTTGGG 58.249 55.000 0.00 0.00 35.04 4.12
968 971 1.369625 CGAGGGTTCGGAGATTTTGG 58.630 55.000 0.00 0.00 43.05 3.28
969 972 0.727398 GCGAGGGTTCGGAGATTTTG 59.273 55.000 0.00 0.00 46.76 2.44
970 973 0.392595 GGCGAGGGTTCGGAGATTTT 60.393 55.000 0.00 0.00 46.76 1.82
974 977 3.379445 GTGGCGAGGGTTCGGAGA 61.379 66.667 0.00 0.00 46.76 3.71
1011 1014 2.280592 AGGTTGGTGAACGGCGTC 60.281 61.111 15.17 7.82 32.28 5.19
1158 1167 2.510238 GAGAAGATGCTGCGCGGT 60.510 61.111 19.23 0.00 0.00 5.68
1233 5769 0.750546 CGTCGGGGAGGACACTGATA 60.751 60.000 0.00 0.00 37.15 2.15
1400 5949 2.670148 GGGGATGCAGGAGACGGTT 61.670 63.158 0.00 0.00 0.00 4.44
1401 5950 3.083997 GGGGATGCAGGAGACGGT 61.084 66.667 0.00 0.00 0.00 4.83
1560 6120 4.400961 AAGAGCGTGGCAGGGAGC 62.401 66.667 9.49 2.77 44.65 4.70
1653 6219 3.952628 CTCGCGGAGGTTGGGGAAC 62.953 68.421 6.13 0.00 0.00 3.62
1686 6252 2.187946 CCCTGCTCCATCACGACC 59.812 66.667 0.00 0.00 0.00 4.79
1780 6346 4.457496 CTGGCTCACCACGCGGAT 62.457 66.667 12.47 0.00 42.67 4.18
1918 6484 2.202878 ATCACGAATGCGGACCCG 60.203 61.111 3.73 3.73 43.17 5.28
1953 6519 2.109834 TCCTGGCTCCAAGAATCCAAAA 59.890 45.455 0.00 0.00 0.00 2.44
1978 6544 1.611491 GTCTCCGATCTCCAGGACATC 59.389 57.143 0.00 0.00 32.33 3.06
2000 6566 4.649674 AGTGGATACTCACCATTATGACGT 59.350 41.667 0.00 0.00 39.69 4.34
2070 6660 2.356125 GCACTCTCTTTTATCCCAGCCA 60.356 50.000 0.00 0.00 0.00 4.75
2083 6673 2.596851 AATGGTGGCCGCACTCTCT 61.597 57.895 19.98 0.00 0.00 3.10
2112 6702 6.313905 ACGCACATTTAAACTCAGGATCTTAG 59.686 38.462 0.00 0.00 0.00 2.18
2125 6715 4.500035 GGGACTCCAAAACGCACATTTAAA 60.500 41.667 0.00 0.00 0.00 1.52
2266 6951 9.247126 CATTCAATCAGAACACACAACATTTAA 57.753 29.630 0.00 0.00 39.49 1.52
2273 6958 4.915158 TGCATTCAATCAGAACACACAA 57.085 36.364 0.00 0.00 39.49 3.33
2323 7008 3.198068 TCAGCATTCGCCATAAAGAGTC 58.802 45.455 0.00 0.00 39.83 3.36
2324 7009 3.266510 TCAGCATTCGCCATAAAGAGT 57.733 42.857 0.00 0.00 39.83 3.24
2335 7034 7.420184 TGTGGTACATAATTATCAGCATTCG 57.580 36.000 10.21 0.00 44.52 3.34
2485 7192 9.706691 ACAGATATAATAGAAATTGTACCACCG 57.293 33.333 0.00 0.00 0.00 4.94
2530 7238 7.060383 TCCAAACATGCCAGAATTTAAGAAA 57.940 32.000 0.00 0.00 0.00 2.52
2536 7244 5.750352 AAGATCCAAACATGCCAGAATTT 57.250 34.783 0.00 0.00 0.00 1.82
2582 7290 7.201266 GCATCAGTGTAAAATAAGCAAACGAAG 60.201 37.037 0.00 0.00 0.00 3.79
2598 7306 2.498885 ACAGCTCAGATGCATCAGTGTA 59.501 45.455 27.81 4.24 34.99 2.90
2740 7451 8.825745 TGGAATTGCACTTGATTTAAAACTTTC 58.174 29.630 0.00 0.00 0.00 2.62
2755 7466 0.171007 CCGCGAAATGGAATTGCACT 59.829 50.000 8.23 0.00 36.10 4.40
2757 7468 1.153862 GCCGCGAAATGGAATTGCA 60.154 52.632 8.23 0.79 36.10 4.08
2778 7489 1.745232 TTGCGGGCGTTTCAGATAAT 58.255 45.000 0.00 0.00 0.00 1.28
2781 7492 1.299541 CTATTGCGGGCGTTTCAGAT 58.700 50.000 0.00 0.00 0.00 2.90
2784 7495 3.183259 GCTATTGCGGGCGTTTCA 58.817 55.556 0.00 0.00 0.00 2.69
2822 7548 4.271049 CGAAAATGTCCATGTACTAGCTGG 59.729 45.833 0.00 0.00 0.00 4.85
2845 7571 0.686789 AAATGCCCTGTTTTCCTGCC 59.313 50.000 0.00 0.00 0.00 4.85
2896 7622 6.214191 TGCTTGTTTCAGTTTATGTCCAAA 57.786 33.333 0.00 0.00 0.00 3.28
2943 7672 3.378911 TTGTGAACTACTCGTGATGCA 57.621 42.857 0.00 0.00 0.00 3.96
2951 7680 4.275196 GGTTCCCTTGTTTGTGAACTACTC 59.725 45.833 0.00 0.00 37.74 2.59
2952 7681 4.204799 GGTTCCCTTGTTTGTGAACTACT 58.795 43.478 0.00 0.00 37.74 2.57
2953 7682 3.949113 TGGTTCCCTTGTTTGTGAACTAC 59.051 43.478 0.00 0.00 37.74 2.73


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

AutoCloner maintained by Alex Coulton.