Multiple sequence alignment - TraesCS5D01G198100

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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 TraesCS5D01G198100 chr5D 100.000 4020 0 0 1 4020 301109494 301113513 0.000000e+00 7424
1 TraesCS5D01G198100 chr5A 94.892 3093 124 18 943 4020 398278158 398281231 0.000000e+00 4806
2 TraesCS5D01G198100 chr5A 76.292 329 45 17 347 654 398277577 398277893 1.160000e-30 145
3 TraesCS5D01G198100 chr5B 88.451 3273 228 84 72 3268 344307141 344310339 0.000000e+00 3812
4 TraesCS5D01G198100 chr5B 93.141 729 34 10 3294 4019 344310325 344311040 0.000000e+00 1055


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 TraesCS5D01G198100 chr5D 301109494 301113513 4019 False 7424.0 7424 100.000 1 4020 1 chr5D.!!$F1 4019
1 TraesCS5D01G198100 chr5A 398277577 398281231 3654 False 2475.5 4806 85.592 347 4020 2 chr5A.!!$F1 3673
2 TraesCS5D01G198100 chr5B 344307141 344311040 3899 False 2433.5 3812 90.796 72 4019 2 chr5B.!!$F1 3947

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
533 566 0.035458 CCGCCATGATTAGTCCCCTC 59.965 60.0 0.00 0.0 0.00 4.30 F
1329 1427 0.250338 AAGTGGACAGTTTCTCGCCC 60.250 55.0 0.00 0.0 0.00 6.13 F
1761 1859 0.899717 GCAAGGATGGCTGTGGGAAA 60.900 55.0 0.00 0.0 26.77 3.13 F
2704 2807 0.763652 CATATGCCTCCAGCTCAGGT 59.236 55.0 9.58 0.0 44.23 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1778 0.804989 GAGTGGGTTTTGGCAGATCG 59.195 55.000 0.00 0.0 0.00 3.69 R
2242 2342 0.879090 CAGTCAACTTTTACCCGGGC 59.121 55.000 24.08 0.0 0.00 6.13 R
2886 2989 1.210204 TCCAGCCAAGGAGCAATCCT 61.210 55.000 0.00 0.0 43.04 3.24 R
3988 4104 3.055530 ACTTCTTGGATCTGCGTCATCTT 60.056 43.478 0.00 0.0 0.00 2.40 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 1.710339 GTAAGAAGAGGCGCTTGCG 59.290 57.895 8.61 10.90 40.46 4.85
19 20 2.100631 TAAGAAGAGGCGCTTGCGC 61.101 57.895 28.67 28.67 40.46 6.09
20 21 2.507110 TAAGAAGAGGCGCTTGCGCT 62.507 55.000 33.22 21.76 40.46 5.92
21 22 3.426568 GAAGAGGCGCTTGCGCTT 61.427 61.111 33.22 28.74 40.46 4.68
22 23 3.657835 GAAGAGGCGCTTGCGCTTG 62.658 63.158 33.22 1.85 40.46 4.01
35 36 2.254051 GCTTGCGCGCCTAACAAA 59.746 55.556 30.77 14.13 0.00 2.83
36 37 1.371145 GCTTGCGCGCCTAACAAAA 60.371 52.632 30.77 13.32 0.00 2.44
37 38 0.937231 GCTTGCGCGCCTAACAAAAA 60.937 50.000 30.77 12.51 0.00 1.94
38 39 1.696988 CTTGCGCGCCTAACAAAAAT 58.303 45.000 30.77 0.00 0.00 1.82
39 40 1.386412 CTTGCGCGCCTAACAAAAATG 59.614 47.619 30.77 4.64 0.00 2.32
40 41 0.593618 TGCGCGCCTAACAAAAATGA 59.406 45.000 30.77 0.71 0.00 2.57
41 42 0.981956 GCGCGCCTAACAAAAATGAC 59.018 50.000 23.24 0.00 0.00 3.06
42 43 1.246970 CGCGCCTAACAAAAATGACG 58.753 50.000 0.00 0.00 0.00 4.35
43 44 1.136197 CGCGCCTAACAAAAATGACGA 60.136 47.619 0.00 0.00 0.00 4.20
44 45 2.505866 GCGCCTAACAAAAATGACGAG 58.494 47.619 0.00 0.00 0.00 4.18
45 46 2.158841 GCGCCTAACAAAAATGACGAGA 59.841 45.455 0.00 0.00 0.00 4.04
46 47 3.364565 GCGCCTAACAAAAATGACGAGAA 60.365 43.478 0.00 0.00 0.00 2.87
47 48 4.778904 CGCCTAACAAAAATGACGAGAAA 58.221 39.130 0.00 0.00 0.00 2.52
48 49 5.209240 CGCCTAACAAAAATGACGAGAAAA 58.791 37.500 0.00 0.00 0.00 2.29
49 50 5.856455 CGCCTAACAAAAATGACGAGAAAAT 59.144 36.000 0.00 0.00 0.00 1.82
50 51 6.362283 CGCCTAACAAAAATGACGAGAAAATT 59.638 34.615 0.00 0.00 0.00 1.82
51 52 7.096230 CGCCTAACAAAAATGACGAGAAAATTT 60.096 33.333 0.00 0.00 0.00 1.82
52 53 8.547894 GCCTAACAAAAATGACGAGAAAATTTT 58.452 29.630 2.28 2.28 35.55 1.82
111 112 0.400213 TTGCGTCTGATTGTTCCCCT 59.600 50.000 0.00 0.00 0.00 4.79
137 138 2.542020 TGCTTTCACGTCATTCTCCA 57.458 45.000 0.00 0.00 0.00 3.86
161 166 1.370900 GGCAGACAAGCAACGCAAG 60.371 57.895 0.00 0.00 39.18 4.01
162 167 1.648720 GCAGACAAGCAACGCAAGA 59.351 52.632 0.00 0.00 43.62 3.02
163 168 0.385223 GCAGACAAGCAACGCAAGAG 60.385 55.000 0.00 0.00 43.62 2.85
165 170 1.070309 CAGACAAGCAACGCAAGAGAC 60.070 52.381 0.00 0.00 43.62 3.36
166 171 0.235926 GACAAGCAACGCAAGAGACC 59.764 55.000 0.00 0.00 43.62 3.85
167 172 0.179045 ACAAGCAACGCAAGAGACCT 60.179 50.000 0.00 0.00 43.62 3.85
168 173 0.514691 CAAGCAACGCAAGAGACCTC 59.485 55.000 0.00 0.00 43.62 3.85
169 174 0.603975 AAGCAACGCAAGAGACCTCC 60.604 55.000 0.00 0.00 43.62 4.30
170 175 2.035442 GCAACGCAAGAGACCTCCC 61.035 63.158 0.00 0.00 43.62 4.30
171 176 1.738099 CAACGCAAGAGACCTCCCG 60.738 63.158 0.00 0.00 43.62 5.14
225 239 3.987501 TCCCCCTTCTCCATTTATTAGGG 59.012 47.826 0.00 0.00 41.63 3.53
227 241 3.767711 CCCTTCTCCATTTATTAGGGGC 58.232 50.000 0.00 0.00 38.92 5.80
228 242 3.140144 CCCTTCTCCATTTATTAGGGGCA 59.860 47.826 0.00 0.00 38.92 5.36
229 243 4.145052 CCTTCTCCATTTATTAGGGGCAC 58.855 47.826 0.00 0.00 0.00 5.01
230 244 3.485463 TCTCCATTTATTAGGGGCACG 57.515 47.619 0.00 0.00 0.00 5.34
231 245 2.775384 TCTCCATTTATTAGGGGCACGT 59.225 45.455 0.00 0.00 0.00 4.49
232 246 3.201266 TCTCCATTTATTAGGGGCACGTT 59.799 43.478 0.00 0.00 0.00 3.99
233 247 3.547746 TCCATTTATTAGGGGCACGTTC 58.452 45.455 0.00 0.00 0.00 3.95
247 261 2.349817 GCACGTTCACTTGTTGATCCAG 60.350 50.000 0.00 0.00 32.84 3.86
248 262 1.873591 ACGTTCACTTGTTGATCCAGC 59.126 47.619 0.00 0.00 32.84 4.85
249 263 2.146342 CGTTCACTTGTTGATCCAGCT 58.854 47.619 0.00 0.00 32.84 4.24
251 265 3.123621 CGTTCACTTGTTGATCCAGCTAC 59.876 47.826 0.00 0.00 32.84 3.58
252 266 4.319177 GTTCACTTGTTGATCCAGCTACT 58.681 43.478 0.00 0.00 32.84 2.57
259 273 3.327757 TGTTGATCCAGCTACTTCACCTT 59.672 43.478 0.00 0.00 0.00 3.50
260 274 3.616956 TGATCCAGCTACTTCACCTTG 57.383 47.619 0.00 0.00 0.00 3.61
261 275 2.284190 GATCCAGCTACTTCACCTTGC 58.716 52.381 0.00 0.00 0.00 4.01
262 276 1.352083 TCCAGCTACTTCACCTTGCT 58.648 50.000 0.00 0.00 0.00 3.91
263 277 2.536066 TCCAGCTACTTCACCTTGCTA 58.464 47.619 0.00 0.00 32.29 3.49
264 278 2.497675 TCCAGCTACTTCACCTTGCTAG 59.502 50.000 0.00 0.00 32.29 3.42
265 279 2.275318 CAGCTACTTCACCTTGCTAGC 58.725 52.381 8.10 8.10 32.29 3.42
266 280 2.093764 CAGCTACTTCACCTTGCTAGCT 60.094 50.000 17.23 0.00 40.64 3.32
268 282 2.898705 CTACTTCACCTTGCTAGCTGG 58.101 52.381 17.23 19.24 0.00 4.85
269 283 0.326264 ACTTCACCTTGCTAGCTGGG 59.674 55.000 24.10 22.02 0.00 4.45
271 285 0.840288 TTCACCTTGCTAGCTGGGGA 60.840 55.000 22.46 22.46 0.00 4.81
272 286 0.621571 TCACCTTGCTAGCTGGGGAT 60.622 55.000 22.46 6.15 0.00 3.85
273 287 0.179034 CACCTTGCTAGCTGGGGATC 60.179 60.000 24.10 0.00 0.00 3.36
275 289 1.070445 CTTGCTAGCTGGGGATCGG 59.930 63.158 17.23 0.00 0.00 4.18
281 295 4.593864 GCTGGGGATCGGCGTCTC 62.594 72.222 6.85 3.62 38.09 3.36
282 296 3.917760 CTGGGGATCGGCGTCTCC 61.918 72.222 17.80 17.80 39.34 3.71
287 312 3.607661 GATCGGCGTCTCCCCTCC 61.608 72.222 6.85 0.00 0.00 4.30
324 350 2.417516 GCGCCTGGCTCGAATCTA 59.582 61.111 17.92 0.00 39.11 1.98
326 352 1.736586 CGCCTGGCTCGAATCTACT 59.263 57.895 17.92 0.00 0.00 2.57
329 355 1.137086 GCCTGGCTCGAATCTACTTCA 59.863 52.381 12.43 0.00 33.10 3.02
354 380 4.554036 GGGGCTCGCTCATCCCAC 62.554 72.222 0.00 0.00 41.85 4.61
359 385 3.144120 CTCGCTCATCCCACCTCCG 62.144 68.421 0.00 0.00 0.00 4.63
366 392 0.745845 CATCCCACCTCCGCTTCTTG 60.746 60.000 0.00 0.00 0.00 3.02
367 393 2.543067 ATCCCACCTCCGCTTCTTGC 62.543 60.000 0.00 0.00 38.57 4.01
368 394 2.747855 CCACCTCCGCTTCTTGCC 60.748 66.667 0.00 0.00 38.78 4.52
409 435 3.989817 CCTTCGCCTGAAAATTTTCTTGG 59.010 43.478 26.73 26.04 38.02 3.61
410 436 3.658757 TCGCCTGAAAATTTTCTTGGG 57.341 42.857 28.11 25.15 38.02 4.12
411 437 3.226777 TCGCCTGAAAATTTTCTTGGGA 58.773 40.909 28.11 25.72 38.02 4.37
412 438 3.831911 TCGCCTGAAAATTTTCTTGGGAT 59.168 39.130 28.11 1.20 38.02 3.85
413 439 3.928375 CGCCTGAAAATTTTCTTGGGATG 59.072 43.478 28.11 19.73 38.02 3.51
414 440 4.561326 CGCCTGAAAATTTTCTTGGGATGT 60.561 41.667 28.11 0.00 38.02 3.06
415 441 4.931601 GCCTGAAAATTTTCTTGGGATGTC 59.068 41.667 28.11 16.51 38.02 3.06
416 442 5.163513 CCTGAAAATTTTCTTGGGATGTCG 58.836 41.667 26.73 6.44 38.02 4.35
419 445 5.300539 TGAAAATTTTCTTGGGATGTCGTCA 59.699 36.000 26.73 4.25 38.02 4.35
439 468 3.065648 TCAATGATTGTCCATGTCATGCG 59.934 43.478 7.35 1.48 33.19 4.73
442 471 3.281158 TGATTGTCCATGTCATGCGATT 58.719 40.909 7.35 0.00 0.00 3.34
447 476 5.422666 TGTCCATGTCATGCGATTATTTC 57.577 39.130 7.35 0.00 0.00 2.17
454 483 4.023792 TGTCATGCGATTATTTCATGGAGC 60.024 41.667 0.00 0.00 38.41 4.70
459 488 3.393800 CGATTATTTCATGGAGCCGAGT 58.606 45.455 0.00 0.00 0.00 4.18
463 492 5.560966 TTATTTCATGGAGCCGAGTTTTC 57.439 39.130 0.00 0.00 0.00 2.29
464 493 2.859165 TTCATGGAGCCGAGTTTTCT 57.141 45.000 0.00 0.00 0.00 2.52
465 494 2.859165 TCATGGAGCCGAGTTTTCTT 57.141 45.000 0.00 0.00 0.00 2.52
490 523 5.758784 GGAATTAAACAAGATAGGAGTCCGG 59.241 44.000 2.76 0.00 0.00 5.14
493 526 0.325296 ACAAGATAGGAGTCCGGGCA 60.325 55.000 9.71 0.00 0.00 5.36
525 558 1.059098 AGATCCAGCCGCCATGATTA 58.941 50.000 0.00 0.00 0.00 1.75
526 559 1.002888 AGATCCAGCCGCCATGATTAG 59.997 52.381 0.00 0.00 0.00 1.73
529 562 0.886490 CCAGCCGCCATGATTAGTCC 60.886 60.000 0.00 0.00 0.00 3.85
530 563 0.886490 CAGCCGCCATGATTAGTCCC 60.886 60.000 0.00 0.00 0.00 4.46
533 566 0.035458 CCGCCATGATTAGTCCCCTC 59.965 60.000 0.00 0.00 0.00 4.30
534 567 0.758734 CGCCATGATTAGTCCCCTCA 59.241 55.000 0.00 0.00 0.00 3.86
537 570 2.224402 GCCATGATTAGTCCCCTCACTC 60.224 54.545 0.00 0.00 0.00 3.51
539 572 1.776662 TGATTAGTCCCCTCACTCGG 58.223 55.000 0.00 0.00 0.00 4.63
588 629 6.413235 GGTACTCGCGTAATCTTTTACTACTG 59.587 42.308 5.77 0.00 36.37 2.74
604 652 2.755952 ACTGCTTCCCTTCCAAAGTT 57.244 45.000 0.00 0.00 0.00 2.66
605 653 2.310538 ACTGCTTCCCTTCCAAAGTTG 58.689 47.619 0.00 0.00 0.00 3.16
613 661 0.593128 CTTCCAAAGTTGCACTCCCG 59.407 55.000 0.00 0.00 0.00 5.14
621 669 1.377202 TTGCACTCCCGCTGGAATC 60.377 57.895 0.00 0.00 41.17 2.52
627 675 1.115467 CTCCCGCTGGAATCAGTAGT 58.885 55.000 0.00 0.00 41.17 2.73
630 678 3.305720 TCCCGCTGGAATCAGTAGTAAT 58.694 45.455 0.00 0.00 42.78 1.89
635 683 4.271049 CGCTGGAATCAGTAGTAATGGTTG 59.729 45.833 0.00 0.00 42.78 3.77
637 685 4.523083 TGGAATCAGTAGTAATGGTTGCC 58.477 43.478 11.82 8.35 28.84 4.52
654 703 1.953231 GCCTTCTTCTTGGCCATGGC 61.953 60.000 29.47 29.47 43.11 4.40
676 725 1.203052 CATGGGTGGACATTTCTGTGC 59.797 52.381 0.00 0.00 43.48 4.57
677 726 0.478072 TGGGTGGACATTTCTGTGCT 59.522 50.000 0.00 0.00 43.56 4.40
678 727 1.133513 TGGGTGGACATTTCTGTGCTT 60.134 47.619 0.00 0.00 43.56 3.91
679 728 1.541588 GGGTGGACATTTCTGTGCTTC 59.458 52.381 0.00 0.00 43.56 3.86
680 729 2.229792 GGTGGACATTTCTGTGCTTCA 58.770 47.619 0.00 0.00 43.56 3.02
681 730 2.622942 GGTGGACATTTCTGTGCTTCAA 59.377 45.455 0.00 0.00 43.56 2.69
682 731 3.550842 GGTGGACATTTCTGTGCTTCAAC 60.551 47.826 0.00 0.00 43.56 3.18
683 732 2.290367 TGGACATTTCTGTGCTTCAACG 59.710 45.455 0.00 0.00 43.56 4.10
684 733 2.290641 GGACATTTCTGTGCTTCAACGT 59.709 45.455 0.00 0.00 40.31 3.99
687 736 2.187351 TTTCTGTGCTTCAACGTTGC 57.813 45.000 23.47 12.65 0.00 4.17
694 743 0.848305 GCTTCAACGTTGCTTGCTTG 59.152 50.000 23.47 8.58 0.00 4.01
698 747 0.573521 CAACGTTGCTTGCTTGCTTG 59.426 50.000 16.51 0.00 0.00 4.01
699 748 1.147557 AACGTTGCTTGCTTGCTTGC 61.148 50.000 0.00 0.00 0.00 4.01
700 749 1.299620 CGTTGCTTGCTTGCTTGCT 60.300 52.632 10.35 0.00 0.00 3.91
701 750 0.872881 CGTTGCTTGCTTGCTTGCTT 60.873 50.000 10.35 0.00 0.00 3.91
702 751 0.580104 GTTGCTTGCTTGCTTGCTTG 59.420 50.000 10.35 0.00 0.00 4.01
722 774 2.691409 CTTTGGGGAAGCGACATAGA 57.309 50.000 0.00 0.00 0.00 1.98
725 785 4.310769 CTTTGGGGAAGCGACATAGATAG 58.689 47.826 0.00 0.00 0.00 2.08
727 787 2.628178 TGGGGAAGCGACATAGATAGTG 59.372 50.000 0.00 0.00 0.00 2.74
735 795 7.201741 GGAAGCGACATAGATAGTGCTATCATA 60.202 40.741 18.15 9.90 43.27 2.15
739 799 8.779303 GCGACATAGATAGTGCTATCATATACT 58.221 37.037 18.15 2.90 43.27 2.12
742 802 9.413734 ACATAGATAGTGCTATCATATACTGCA 57.586 33.333 18.15 0.00 43.27 4.41
746 806 3.914312 GTGCTATCATATACTGCACCGT 58.086 45.455 0.00 0.00 45.52 4.83
747 807 5.055642 GTGCTATCATATACTGCACCGTA 57.944 43.478 0.00 0.00 45.52 4.02
748 808 5.096169 GTGCTATCATATACTGCACCGTAG 58.904 45.833 0.00 0.00 45.52 3.51
749 809 4.106197 GCTATCATATACTGCACCGTAGC 58.894 47.826 0.00 0.00 0.00 3.58
750 810 4.380550 GCTATCATATACTGCACCGTAGCA 60.381 45.833 0.00 0.00 43.35 3.49
782 848 8.099537 ACTGTCCTATATCTGGCATCTAAATTG 58.900 37.037 0.00 0.00 0.00 2.32
783 849 7.977818 TGTCCTATATCTGGCATCTAAATTGT 58.022 34.615 0.00 0.00 0.00 2.71
785 851 8.940952 GTCCTATATCTGGCATCTAAATTGTTC 58.059 37.037 0.00 0.00 0.00 3.18
786 852 8.103305 TCCTATATCTGGCATCTAAATTGTTCC 58.897 37.037 0.00 0.00 0.00 3.62
787 853 8.105829 CCTATATCTGGCATCTAAATTGTTCCT 58.894 37.037 0.00 0.00 0.00 3.36
793 859 4.142381 GGCATCTAAATTGTTCCTGACACC 60.142 45.833 0.00 0.00 38.18 4.16
797 863 5.690865 TCTAAATTGTTCCTGACACCAAGT 58.309 37.500 0.00 0.00 38.18 3.16
799 865 7.284074 TCTAAATTGTTCCTGACACCAAGTAA 58.716 34.615 0.00 0.00 38.18 2.24
800 866 6.783708 AAATTGTTCCTGACACCAAGTAAA 57.216 33.333 0.00 0.00 38.18 2.01
802 868 6.976934 ATTGTTCCTGACACCAAGTAAATT 57.023 33.333 0.00 0.00 38.18 1.82
804 870 7.883391 TTGTTCCTGACACCAAGTAAATTAA 57.117 32.000 0.00 0.00 38.18 1.40
806 872 8.106247 TGTTCCTGACACCAAGTAAATTAATC 57.894 34.615 0.00 0.00 32.00 1.75
807 873 7.721842 TGTTCCTGACACCAAGTAAATTAATCA 59.278 33.333 0.00 0.00 32.00 2.57
808 874 8.739972 GTTCCTGACACCAAGTAAATTAATCAT 58.260 33.333 0.00 0.00 0.00 2.45
828 894 3.428746 TGGACGTTTGTGAATGGTTTG 57.571 42.857 0.00 0.00 0.00 2.93
848 934 6.128035 GGTTTGTCCAATAATTTTGGGAATGC 60.128 38.462 15.15 7.20 39.96 3.56
855 941 6.654161 CCAATAATTTTGGGAATGCTTGTGAA 59.346 34.615 10.04 0.00 35.96 3.18
860 946 8.866970 AATTTTGGGAATGCTTGTGAATTATT 57.133 26.923 0.00 0.00 0.00 1.40
861 947 9.956640 AATTTTGGGAATGCTTGTGAATTATTA 57.043 25.926 0.00 0.00 0.00 0.98
863 949 8.945481 TTTGGGAATGCTTGTGAATTATTATG 57.055 30.769 0.00 0.00 0.00 1.90
864 950 6.514947 TGGGAATGCTTGTGAATTATTATGC 58.485 36.000 0.00 0.00 0.00 3.14
865 951 6.097981 TGGGAATGCTTGTGAATTATTATGCA 59.902 34.615 0.00 0.00 0.00 3.96
867 953 7.117236 GGGAATGCTTGTGAATTATTATGCATG 59.883 37.037 10.16 0.00 39.42 4.06
869 955 8.951787 AATGCTTGTGAATTATTATGCATGTT 57.048 26.923 10.16 0.00 39.42 2.71
892 978 3.449018 ACGTTGTGGCTCTCATCTCTTAT 59.551 43.478 0.00 0.00 0.00 1.73
894 980 5.303078 ACGTTGTGGCTCTCATCTCTTATAT 59.697 40.000 0.00 0.00 0.00 0.86
895 981 6.490381 ACGTTGTGGCTCTCATCTCTTATATA 59.510 38.462 0.00 0.00 0.00 0.86
896 982 7.177568 ACGTTGTGGCTCTCATCTCTTATATAT 59.822 37.037 0.00 0.00 0.00 0.86
897 983 8.678199 CGTTGTGGCTCTCATCTCTTATATATA 58.322 37.037 0.00 0.00 0.00 0.86
899 985 9.981460 TTGTGGCTCTCATCTCTTATATATAGA 57.019 33.333 0.00 0.00 0.00 1.98
920 1006 4.926238 AGAGAGAACGTTTTGCTGATACTG 59.074 41.667 0.46 0.00 0.00 2.74
930 1021 6.140737 CGTTTTGCTGATACTGTTTTCACTTC 59.859 38.462 0.00 0.00 0.00 3.01
938 1029 7.406553 TGATACTGTTTTCACTTCGAAACAAG 58.593 34.615 0.00 0.00 43.35 3.16
941 1032 6.540205 ACTGTTTTCACTTCGAAACAAGTAC 58.460 36.000 0.00 0.00 43.35 2.73
968 1062 4.708726 GCTAATGCTGATGGTCAACTTT 57.291 40.909 0.00 0.00 36.03 2.66
975 1069 3.128242 GCTGATGGTCAACTTTCTGATGG 59.872 47.826 0.00 0.00 0.00 3.51
976 1070 4.330250 CTGATGGTCAACTTTCTGATGGT 58.670 43.478 0.00 0.00 0.00 3.55
1074 1172 2.795231 TTCAGGAGGATGCAAAGAGG 57.205 50.000 0.00 0.00 0.00 3.69
1080 1178 1.821332 GGATGCAAAGAGGGCTCCG 60.821 63.158 0.00 0.00 0.00 4.63
1164 1262 2.981302 CGAGACTGCCACATCCCA 59.019 61.111 0.00 0.00 0.00 4.37
1167 1265 1.168714 GAGACTGCCACATCCCAAAC 58.831 55.000 0.00 0.00 0.00 2.93
1177 1275 3.429822 CCACATCCCAAACTTCATGCATC 60.430 47.826 0.00 0.00 0.00 3.91
1218 1316 1.073964 CCAATCAGCCGATAGATGCG 58.926 55.000 0.00 0.00 39.76 4.73
1329 1427 0.250338 AAGTGGACAGTTTCTCGCCC 60.250 55.000 0.00 0.00 0.00 6.13
1383 1481 2.125350 GAGTGCCCTTCTGAGCCG 60.125 66.667 0.00 0.00 0.00 5.52
1518 1616 8.107196 AGGATAAAGAGGTTATGGACTTCAAT 57.893 34.615 0.00 0.00 36.86 2.57
1527 1625 8.336801 AGGTTATGGACTTCAATACTTTTGAC 57.663 34.615 0.00 0.00 0.00 3.18
1680 1778 2.780065 TGCAGCACATTGAGAACAAC 57.220 45.000 0.00 0.00 38.90 3.32
1742 1840 3.120580 GCAAAATTGAACGGCCATGAAAG 60.121 43.478 2.24 0.00 0.00 2.62
1761 1859 0.899717 GCAAGGATGGCTGTGGGAAA 60.900 55.000 0.00 0.00 26.77 3.13
1954 2052 8.380099 TCATAACCATCAAAACTACAACTAGGT 58.620 33.333 0.00 0.00 0.00 3.08
1956 2054 5.937111 ACCATCAAAACTACAACTAGGTGT 58.063 37.500 19.20 19.20 35.43 4.16
1975 2075 3.440522 GTGTCCTCCTTTGTAGATTTGCC 59.559 47.826 0.00 0.00 0.00 4.52
1983 2083 2.949177 TGTAGATTTGCCCGCCATAT 57.051 45.000 0.00 0.00 0.00 1.78
2098 2198 6.294508 GCTGAAATTAAAGGAACAGGCTGTTA 60.295 38.462 31.24 16.13 41.28 2.41
2103 2203 9.845740 AAATTAAAGGAACAGGCTGTTAATTTT 57.154 25.926 30.88 28.22 41.28 1.82
2123 2223 7.678947 ATTTTGCTCCAGTCTGTATATATGC 57.321 36.000 0.00 0.00 0.00 3.14
2269 2369 7.081976 CCGGGTAAAAGTTGACTGAATTTAAG 58.918 38.462 0.00 0.00 0.00 1.85
2355 2458 6.713762 TTATGTTATTCCTGGAAATGCCTG 57.286 37.500 14.03 0.00 37.63 4.85
2370 2473 1.770324 CCTGAGGTGCCCTTTCCTT 59.230 57.895 0.00 0.00 31.76 3.36
2469 2572 8.031864 CAGGATTCATATAGTAGTGGTGATCAC 58.968 40.741 17.91 17.91 46.39 3.06
2704 2807 0.763652 CATATGCCTCCAGCTCAGGT 59.236 55.000 9.58 0.00 44.23 4.00
2771 2874 2.192263 GGTGATGAAGGAGGAGAAGGT 58.808 52.381 0.00 0.00 0.00 3.50
2775 2878 1.645710 TGAAGGAGGAGAAGGTGGAC 58.354 55.000 0.00 0.00 0.00 4.02
2886 2989 1.739929 CGTAGGCATCGTTGGTGCA 60.740 57.895 4.25 0.00 44.25 4.57
2985 3095 2.644060 AGGTGGTAGGTAAAGCTCCT 57.356 50.000 0.00 0.00 36.34 3.69
3039 3149 8.655935 AAATGATGGAATTCTTAGAACCACTT 57.344 30.769 6.48 0.00 33.38 3.16
3072 3186 2.702478 CCTTGCTGGTGATATCTCTCCA 59.298 50.000 3.98 9.01 41.57 3.86
3133 3248 7.415206 GGGTTTTAGTGTACATATTTGCCAGAG 60.415 40.741 0.00 0.00 0.00 3.35
3307 3422 7.040755 ACTGCAAGCATATGTAACTTTGTTGTA 60.041 33.333 4.29 0.00 37.60 2.41
3350 3465 0.970640 TTAGTCGCTGGTTGGTAGCA 59.029 50.000 0.00 0.00 41.18 3.49
3484 3599 6.687958 GTGGCAATTTCATCTTTTTGTTGTTG 59.312 34.615 0.00 0.00 0.00 3.33
3493 3608 7.961855 TCATCTTTTTGTTGTTGTTGTTGATG 58.038 30.769 0.00 0.00 0.00 3.07
3494 3609 7.816513 TCATCTTTTTGTTGTTGTTGTTGATGA 59.183 29.630 0.00 0.00 34.87 2.92
3495 3610 8.605746 CATCTTTTTGTTGTTGTTGTTGATGAT 58.394 29.630 0.00 0.00 31.18 2.45
3652 3767 6.049955 TCGAAACCTCCAACAGAATATCTT 57.950 37.500 0.00 0.00 0.00 2.40
3653 3768 6.472887 TCGAAACCTCCAACAGAATATCTTT 58.527 36.000 0.00 0.00 0.00 2.52
3691 3806 5.749462 ACAAAGAATCTATCCTTGTCAGGG 58.251 41.667 0.00 0.00 38.08 4.45
3716 3831 4.380531 TCATTCCACAGACTGAAGTGAAC 58.619 43.478 10.08 0.00 37.97 3.18
3717 3832 4.101585 TCATTCCACAGACTGAAGTGAACT 59.898 41.667 10.08 0.00 37.97 3.01
3718 3833 3.459232 TCCACAGACTGAAGTGAACTG 57.541 47.619 10.08 0.00 37.97 3.16
3719 3834 3.031013 TCCACAGACTGAAGTGAACTGA 58.969 45.455 10.08 0.00 37.97 3.41
3720 3835 3.643320 TCCACAGACTGAAGTGAACTGAT 59.357 43.478 10.08 0.00 37.97 2.90
3724 3839 5.861251 CACAGACTGAAGTGAACTGATACTC 59.139 44.000 10.08 0.00 37.97 2.59
3744 3859 3.433343 TCGTATTACAACAGTGAGGGGA 58.567 45.455 0.00 0.00 0.00 4.81
3856 3972 2.109799 CTATCCAGGCCACGGCAG 59.890 66.667 10.83 1.91 44.11 4.85
3880 3996 4.166888 GCGCAGAGATGGCTCCCA 62.167 66.667 0.30 0.00 42.30 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.710339 CGCAAGCGCCTCTTCTTAC 59.290 57.895 2.29 0.00 31.27 2.34
1 2 4.185413 CGCAAGCGCCTCTTCTTA 57.815 55.556 2.29 0.00 31.27 2.10
19 20 1.386412 CATTTTTGTTAGGCGCGCAAG 59.614 47.619 34.42 1.18 43.44 4.01
20 21 1.001268 TCATTTTTGTTAGGCGCGCAA 60.001 42.857 34.42 17.36 0.00 4.85
21 22 0.593618 TCATTTTTGTTAGGCGCGCA 59.406 45.000 34.42 10.96 0.00 6.09
22 23 0.981956 GTCATTTTTGTTAGGCGCGC 59.018 50.000 25.94 25.94 0.00 6.86
23 24 1.136197 TCGTCATTTTTGTTAGGCGCG 60.136 47.619 0.00 0.00 0.00 6.86
24 25 2.158841 TCTCGTCATTTTTGTTAGGCGC 59.841 45.455 0.00 0.00 0.00 6.53
25 26 4.398549 TTCTCGTCATTTTTGTTAGGCG 57.601 40.909 0.00 0.00 0.00 5.52
26 27 7.637709 AATTTTCTCGTCATTTTTGTTAGGC 57.362 32.000 0.00 0.00 0.00 3.93
88 89 2.749621 GGGAACAATCAGACGCAAAGAT 59.250 45.455 0.00 0.00 0.00 2.40
111 112 2.929531 TGACGTGAAAGCAAAGCAAA 57.070 40.000 0.00 0.00 0.00 3.68
137 138 2.156098 TTGCTTGTCTGCCCCCTCT 61.156 57.895 0.00 0.00 0.00 3.69
161 166 1.834822 CAGGGGATCGGGAGGTCTC 60.835 68.421 0.00 0.00 40.72 3.36
162 167 2.283809 CAGGGGATCGGGAGGTCT 59.716 66.667 0.00 0.00 40.70 3.85
163 168 3.551407 GCAGGGGATCGGGAGGTC 61.551 72.222 0.00 0.00 39.96 3.85
200 214 5.833667 CCTAATAAATGGAGAAGGGGGAAAC 59.166 44.000 0.00 0.00 0.00 2.78
201 215 5.103258 CCCTAATAAATGGAGAAGGGGGAAA 60.103 44.000 0.00 0.00 40.07 3.13
202 216 4.418863 CCCTAATAAATGGAGAAGGGGGAA 59.581 45.833 0.00 0.00 40.07 3.97
203 217 3.987501 CCCTAATAAATGGAGAAGGGGGA 59.012 47.826 0.00 0.00 40.07 4.81
225 239 1.069227 GGATCAACAAGTGAACGTGCC 60.069 52.381 0.00 0.00 40.50 5.01
226 240 1.601903 TGGATCAACAAGTGAACGTGC 59.398 47.619 0.00 0.00 40.50 5.34
227 241 2.349817 GCTGGATCAACAAGTGAACGTG 60.350 50.000 0.00 0.00 40.50 4.49
228 242 1.873591 GCTGGATCAACAAGTGAACGT 59.126 47.619 0.00 0.00 40.50 3.99
229 243 2.146342 AGCTGGATCAACAAGTGAACG 58.854 47.619 0.00 0.00 40.50 3.95
230 244 4.319177 AGTAGCTGGATCAACAAGTGAAC 58.681 43.478 0.00 0.00 40.50 3.18
231 245 4.623932 AGTAGCTGGATCAACAAGTGAA 57.376 40.909 0.00 0.00 40.50 3.18
232 246 4.040339 TGAAGTAGCTGGATCAACAAGTGA 59.960 41.667 0.00 0.00 41.67 3.41
233 247 4.153117 GTGAAGTAGCTGGATCAACAAGTG 59.847 45.833 0.00 0.00 0.00 3.16
247 261 2.682155 AGCTAGCAAGGTGAAGTAGC 57.318 50.000 18.83 0.00 37.05 3.58
259 273 3.550431 GCCGATCCCCAGCTAGCA 61.550 66.667 18.83 0.00 0.00 3.49
260 274 4.671569 CGCCGATCCCCAGCTAGC 62.672 72.222 6.62 6.62 0.00 3.42
261 275 3.214250 GACGCCGATCCCCAGCTAG 62.214 68.421 0.00 0.00 0.00 3.42
262 276 3.224324 GACGCCGATCCCCAGCTA 61.224 66.667 0.00 0.00 0.00 3.32
264 278 4.593864 GAGACGCCGATCCCCAGC 62.594 72.222 0.00 0.00 0.00 4.85
265 279 3.917760 GGAGACGCCGATCCCCAG 61.918 72.222 0.00 0.00 0.00 4.45
269 283 3.607661 GAGGGGAGACGCCGATCC 61.608 72.222 0.00 0.00 46.15 3.36
271 285 4.144727 AGGAGGGGAGACGCCGAT 62.145 66.667 0.00 0.00 46.15 4.18
272 286 4.816984 GAGGAGGGGAGACGCCGA 62.817 72.222 0.00 0.00 46.15 5.54
282 296 4.521062 CTTGAGCGGCGAGGAGGG 62.521 72.222 12.98 0.00 0.00 4.30
287 312 1.227999 TTGGAAACTTGAGCGGCGAG 61.228 55.000 12.98 0.20 0.00 5.03
324 350 4.265056 GCCCCACCCACGTGAAGT 62.265 66.667 19.30 11.43 43.14 3.01
326 352 3.948719 GAGCCCCACCCACGTGAA 61.949 66.667 19.30 0.00 43.14 3.18
344 370 2.932130 GAAGCGGAGGTGGGATGAGC 62.932 65.000 0.00 0.00 39.47 4.26
348 374 1.604378 CAAGAAGCGGAGGTGGGAT 59.396 57.895 0.00 0.00 39.47 3.85
359 385 3.577313 GGATCGGCGGCAAGAAGC 61.577 66.667 10.53 0.00 44.65 3.86
366 392 4.467084 TTGACCTGGATCGGCGGC 62.467 66.667 7.21 0.00 0.00 6.53
367 393 2.202932 CTTGACCTGGATCGGCGG 60.203 66.667 7.21 0.00 0.00 6.13
368 394 2.892425 GCTTGACCTGGATCGGCG 60.892 66.667 0.00 0.00 0.00 6.46
389 415 3.639094 TCCCAAGAAAATTTTCAGGCGAA 59.361 39.130 28.00 15.61 39.61 4.70
409 435 3.270027 TGGACAATCATTGACGACATCC 58.730 45.455 3.79 0.00 0.00 3.51
410 436 4.333649 ACATGGACAATCATTGACGACATC 59.666 41.667 3.79 0.00 0.00 3.06
411 437 4.264253 ACATGGACAATCATTGACGACAT 58.736 39.130 3.79 0.19 0.00 3.06
412 438 3.673902 ACATGGACAATCATTGACGACA 58.326 40.909 3.79 0.00 0.00 4.35
413 439 3.684305 TGACATGGACAATCATTGACGAC 59.316 43.478 3.79 0.00 0.00 4.34
414 440 3.936564 TGACATGGACAATCATTGACGA 58.063 40.909 3.79 0.00 0.00 4.20
415 441 4.594136 CATGACATGGACAATCATTGACG 58.406 43.478 3.79 0.00 30.58 4.35
416 442 4.357142 GCATGACATGGACAATCATTGAC 58.643 43.478 17.03 0.00 30.58 3.18
419 445 3.281158 TCGCATGACATGGACAATCATT 58.719 40.909 17.03 0.00 30.58 2.57
439 468 5.757850 AAACTCGGCTCCATGAAATAATC 57.242 39.130 0.00 0.00 0.00 1.75
442 471 4.843728 AGAAAACTCGGCTCCATGAAATA 58.156 39.130 0.00 0.00 0.00 1.40
447 476 1.470098 CCAAGAAAACTCGGCTCCATG 59.530 52.381 0.00 0.00 0.00 3.66
454 483 7.422399 TCTTGTTTAATTCCAAGAAAACTCGG 58.578 34.615 10.87 0.00 42.92 4.63
463 492 7.011482 CGGACTCCTATCTTGTTTAATTCCAAG 59.989 40.741 6.23 6.23 39.50 3.61
464 493 6.821665 CGGACTCCTATCTTGTTTAATTCCAA 59.178 38.462 0.00 0.00 0.00 3.53
465 494 6.346096 CGGACTCCTATCTTGTTTAATTCCA 58.654 40.000 0.00 0.00 0.00 3.53
467 496 5.758784 CCCGGACTCCTATCTTGTTTAATTC 59.241 44.000 0.73 0.00 0.00 2.17
468 497 5.681639 CCCGGACTCCTATCTTGTTTAATT 58.318 41.667 0.73 0.00 0.00 1.40
470 499 3.118519 GCCCGGACTCCTATCTTGTTTAA 60.119 47.826 0.73 0.00 0.00 1.52
471 500 2.433239 GCCCGGACTCCTATCTTGTTTA 59.567 50.000 0.73 0.00 0.00 2.01
472 501 1.209747 GCCCGGACTCCTATCTTGTTT 59.790 52.381 0.73 0.00 0.00 2.83
473 502 0.831307 GCCCGGACTCCTATCTTGTT 59.169 55.000 0.73 0.00 0.00 2.83
474 503 0.325296 TGCCCGGACTCCTATCTTGT 60.325 55.000 0.73 0.00 0.00 3.16
475 504 0.390860 CTGCCCGGACTCCTATCTTG 59.609 60.000 0.73 0.00 0.00 3.02
478 507 0.389757 GAACTGCCCGGACTCCTATC 59.610 60.000 0.73 0.00 0.00 2.08
480 509 1.684734 GGAACTGCCCGGACTCCTA 60.685 63.158 0.73 0.00 0.00 2.94
493 526 3.090532 GATCTGGCCCGGGGAACT 61.091 66.667 25.28 0.00 0.00 3.01
514 547 0.035458 GAGGGGACTAATCATGGCGG 59.965 60.000 0.00 0.00 44.43 6.13
526 559 3.936535 CCTACCGAGTGAGGGGAC 58.063 66.667 0.00 0.00 35.02 4.46
530 563 2.119655 CGACCCCTACCGAGTGAGG 61.120 68.421 0.00 0.00 37.30 3.86
533 566 3.145551 CCCGACCCCTACCGAGTG 61.146 72.222 0.00 0.00 0.00 3.51
534 567 4.453892 CCCCGACCCCTACCGAGT 62.454 72.222 0.00 0.00 0.00 4.18
588 629 1.039856 TGCAACTTTGGAAGGGAAGC 58.960 50.000 0.00 0.00 0.00 3.86
604 652 2.268920 GATTCCAGCGGGAGTGCA 59.731 61.111 5.45 0.00 46.01 4.57
605 653 1.817099 CTGATTCCAGCGGGAGTGC 60.817 63.158 5.45 0.32 46.01 4.40
613 661 4.035675 GCAACCATTACTACTGATTCCAGC 59.964 45.833 0.00 0.00 44.16 4.85
621 669 5.491982 AGAAGAAGGCAACCATTACTACTG 58.508 41.667 0.00 0.00 37.17 2.74
649 698 2.442643 GTCCACCCATGGGCCATG 60.443 66.667 34.76 34.76 45.80 3.66
656 705 1.203052 GCACAGAAATGTCCACCCATG 59.797 52.381 0.00 0.00 0.00 3.66
657 706 1.076024 AGCACAGAAATGTCCACCCAT 59.924 47.619 0.00 0.00 0.00 4.00
658 707 0.478072 AGCACAGAAATGTCCACCCA 59.522 50.000 0.00 0.00 0.00 4.51
659 708 1.541588 GAAGCACAGAAATGTCCACCC 59.458 52.381 0.00 0.00 0.00 4.61
660 709 2.229792 TGAAGCACAGAAATGTCCACC 58.770 47.619 0.00 0.00 0.00 4.61
661 710 3.632189 GTTGAAGCACAGAAATGTCCAC 58.368 45.455 0.00 0.00 0.00 4.02
662 711 2.290367 CGTTGAAGCACAGAAATGTCCA 59.710 45.455 0.00 0.00 0.00 4.02
664 713 3.609103 ACGTTGAAGCACAGAAATGTC 57.391 42.857 0.00 0.00 0.00 3.06
666 715 2.468777 GCAACGTTGAAGCACAGAAATG 59.531 45.455 31.62 0.68 0.00 2.32
667 716 2.358898 AGCAACGTTGAAGCACAGAAAT 59.641 40.909 31.62 0.00 0.00 2.17
668 717 1.742831 AGCAACGTTGAAGCACAGAAA 59.257 42.857 31.62 0.00 0.00 2.52
669 718 1.378531 AGCAACGTTGAAGCACAGAA 58.621 45.000 31.62 0.00 0.00 3.02
670 719 1.063912 CAAGCAACGTTGAAGCACAGA 59.936 47.619 31.62 0.00 0.00 3.41
671 720 1.469917 CAAGCAACGTTGAAGCACAG 58.530 50.000 31.62 9.32 0.00 3.66
672 721 0.525242 GCAAGCAACGTTGAAGCACA 60.525 50.000 31.62 0.00 0.00 4.57
673 722 0.248621 AGCAAGCAACGTTGAAGCAC 60.249 50.000 31.62 13.28 0.00 4.40
674 723 0.455410 AAGCAAGCAACGTTGAAGCA 59.545 45.000 31.62 0.00 0.00 3.91
675 724 0.848305 CAAGCAAGCAACGTTGAAGC 59.152 50.000 31.62 26.91 0.00 3.86
676 725 0.848305 GCAAGCAAGCAACGTTGAAG 59.152 50.000 31.62 19.39 0.00 3.02
677 726 0.455410 AGCAAGCAAGCAACGTTGAA 59.545 45.000 31.62 0.00 36.85 2.69
678 727 0.455410 AAGCAAGCAAGCAACGTTGA 59.545 45.000 31.62 0.00 36.85 3.18
679 728 0.573521 CAAGCAAGCAAGCAACGTTG 59.426 50.000 23.90 23.90 36.85 4.10
680 729 1.147557 GCAAGCAAGCAAGCAACGTT 61.148 50.000 0.00 0.00 36.85 3.99
681 730 1.589727 GCAAGCAAGCAAGCAACGT 60.590 52.632 3.19 0.00 36.85 3.99
682 731 0.872881 AAGCAAGCAAGCAAGCAACG 60.873 50.000 10.52 0.00 36.85 4.10
683 732 0.580104 CAAGCAAGCAAGCAAGCAAC 59.420 50.000 10.52 0.00 36.85 4.17
684 733 1.155424 GCAAGCAAGCAAGCAAGCAA 61.155 50.000 10.52 0.00 36.81 3.91
687 736 1.260561 CAAAGCAAGCAAGCAAGCAAG 59.739 47.619 10.52 0.00 36.85 4.01
694 743 0.320160 CTTCCCCAAAGCAAGCAAGC 60.320 55.000 0.00 0.00 0.00 4.01
715 764 9.891828 GCAGTATATGATAGCACTATCTATGTC 57.108 37.037 16.50 6.83 41.80 3.06
716 765 9.413734 TGCAGTATATGATAGCACTATCTATGT 57.586 33.333 16.50 10.15 41.80 2.29
727 787 4.106197 GCTACGGTGCAGTATATGATAGC 58.894 47.826 0.00 0.00 0.00 2.97
739 799 3.934962 TGCCACTGCTACGGTGCA 61.935 61.111 0.88 4.63 39.22 4.57
742 802 2.343758 CAGTGCCACTGCTACGGT 59.656 61.111 12.63 0.00 39.62 4.83
750 810 2.968574 CCAGATATAGGACAGTGCCACT 59.031 50.000 0.00 0.00 0.00 4.00
751 811 2.548920 GCCAGATATAGGACAGTGCCAC 60.549 54.545 6.40 0.00 0.00 5.01
752 812 1.694150 GCCAGATATAGGACAGTGCCA 59.306 52.381 6.40 0.00 0.00 4.92
753 813 1.694150 TGCCAGATATAGGACAGTGCC 59.306 52.381 0.00 0.00 0.00 5.01
782 848 8.106247 TGATTAATTTACTTGGTGTCAGGAAC 57.894 34.615 0.00 0.00 0.00 3.62
783 849 8.739039 CATGATTAATTTACTTGGTGTCAGGAA 58.261 33.333 0.00 0.00 0.00 3.36
785 851 7.339212 TCCATGATTAATTTACTTGGTGTCAGG 59.661 37.037 0.00 0.00 32.88 3.86
786 852 8.184192 GTCCATGATTAATTTACTTGGTGTCAG 58.816 37.037 0.00 0.00 32.88 3.51
787 853 7.148323 CGTCCATGATTAATTTACTTGGTGTCA 60.148 37.037 0.00 0.00 32.88 3.58
793 859 8.849490 CACAAACGTCCATGATTAATTTACTTG 58.151 33.333 0.00 0.00 0.00 3.16
797 863 9.566530 CATTCACAAACGTCCATGATTAATTTA 57.433 29.630 0.00 0.00 0.00 1.40
799 865 7.035004 CCATTCACAAACGTCCATGATTAATT 58.965 34.615 0.00 0.00 0.00 1.40
800 866 6.152661 ACCATTCACAAACGTCCATGATTAAT 59.847 34.615 0.00 0.00 0.00 1.40
802 868 5.007034 ACCATTCACAAACGTCCATGATTA 58.993 37.500 0.00 0.00 0.00 1.75
804 870 3.420893 ACCATTCACAAACGTCCATGAT 58.579 40.909 0.00 0.00 0.00 2.45
806 872 3.641437 AACCATTCACAAACGTCCATG 57.359 42.857 0.00 0.00 0.00 3.66
807 873 3.383185 ACAAACCATTCACAAACGTCCAT 59.617 39.130 0.00 0.00 0.00 3.41
808 874 2.755655 ACAAACCATTCACAAACGTCCA 59.244 40.909 0.00 0.00 0.00 4.02
828 894 6.092533 CACAAGCATTCCCAAAATTATTGGAC 59.907 38.462 16.38 5.36 42.06 4.02
848 934 9.502145 AACGTAACATGCATAATAATTCACAAG 57.498 29.630 0.00 0.00 0.00 3.16
855 941 6.039270 AGCCACAACGTAACATGCATAATAAT 59.961 34.615 0.00 0.00 0.00 1.28
860 946 2.675844 GAGCCACAACGTAACATGCATA 59.324 45.455 0.00 0.00 0.00 3.14
861 947 1.468520 GAGCCACAACGTAACATGCAT 59.531 47.619 0.00 0.00 0.00 3.96
862 948 0.871722 GAGCCACAACGTAACATGCA 59.128 50.000 0.00 0.00 0.00 3.96
863 949 1.128692 GAGAGCCACAACGTAACATGC 59.871 52.381 0.00 0.00 0.00 4.06
864 950 2.412870 TGAGAGCCACAACGTAACATG 58.587 47.619 0.00 0.00 0.00 3.21
865 951 2.831685 TGAGAGCCACAACGTAACAT 57.168 45.000 0.00 0.00 0.00 2.71
867 953 2.924290 GAGATGAGAGCCACAACGTAAC 59.076 50.000 0.00 0.00 0.00 2.50
869 955 2.447443 AGAGATGAGAGCCACAACGTA 58.553 47.619 0.00 0.00 0.00 3.57
870 956 1.261480 AGAGATGAGAGCCACAACGT 58.739 50.000 0.00 0.00 0.00 3.99
892 978 9.894783 GTATCAGCAAAACGTTCTCTCTATATA 57.105 33.333 0.00 0.00 0.00 0.86
894 980 7.915923 CAGTATCAGCAAAACGTTCTCTCTATA 59.084 37.037 0.00 0.00 0.00 1.31
895 981 6.754209 CAGTATCAGCAAAACGTTCTCTCTAT 59.246 38.462 0.00 0.00 0.00 1.98
896 982 6.093404 CAGTATCAGCAAAACGTTCTCTCTA 58.907 40.000 0.00 0.00 0.00 2.43
897 983 4.926238 CAGTATCAGCAAAACGTTCTCTCT 59.074 41.667 0.00 0.00 0.00 3.10
898 984 4.686554 ACAGTATCAGCAAAACGTTCTCTC 59.313 41.667 0.00 0.00 0.00 3.20
899 985 4.632153 ACAGTATCAGCAAAACGTTCTCT 58.368 39.130 0.00 0.00 0.00 3.10
930 1021 6.641062 GCATTAGCTCATAGTACTTGTTTCG 58.359 40.000 0.00 0.00 37.91 3.46
975 1069 2.159184 TCTCGCATGTCAAGGATCTGAC 60.159 50.000 7.90 7.90 45.01 3.51
976 1070 2.102578 TCTCGCATGTCAAGGATCTGA 58.897 47.619 0.00 0.00 0.00 3.27
980 1074 1.827344 TCAGTCTCGCATGTCAAGGAT 59.173 47.619 0.00 0.00 0.00 3.24
981 1075 1.256812 TCAGTCTCGCATGTCAAGGA 58.743 50.000 0.00 0.00 0.00 3.36
982 1076 1.931841 CATCAGTCTCGCATGTCAAGG 59.068 52.381 0.00 0.00 0.00 3.61
1051 1149 4.820716 CCTCTTTGCATCCTCCTGAAATAG 59.179 45.833 0.00 0.00 0.00 1.73
1074 1172 2.747855 CAGGCCAGTTTCGGAGCC 60.748 66.667 5.01 0.00 46.13 4.70
1080 1178 1.228245 TGGACAGCAGGCCAGTTTC 60.228 57.895 5.01 0.00 0.00 2.78
1164 1262 4.401022 TCCAGTTCAGATGCATGAAGTTT 58.599 39.130 2.46 0.00 40.14 2.66
1167 1265 3.128242 GGTTCCAGTTCAGATGCATGAAG 59.872 47.826 2.46 0.00 39.78 3.02
1177 1275 2.076863 GTTCATCGGGTTCCAGTTCAG 58.923 52.381 0.00 0.00 0.00 3.02
1218 1316 0.039708 GCTGCAGCTGAAGAAACCAC 60.040 55.000 31.33 2.11 38.21 4.16
1304 1402 4.119862 CGAGAAACTGTCCACTTTCTTCA 58.880 43.478 4.24 0.00 36.95 3.02
1305 1403 3.059529 GCGAGAAACTGTCCACTTTCTTC 60.060 47.826 0.00 0.00 36.95 2.87
1395 1493 5.978919 TGTTTGCTTCATAAAAGCTGTTGAG 59.021 36.000 10.75 0.00 43.38 3.02
1398 1496 6.643770 CAGATGTTTGCTTCATAAAAGCTGTT 59.356 34.615 10.75 0.00 43.38 3.16
1401 1499 6.579666 TCAGATGTTTGCTTCATAAAAGCT 57.420 33.333 10.75 0.00 43.38 3.74
1518 1616 4.525024 TCGGAAACAAAGGGTCAAAAGTA 58.475 39.130 0.00 0.00 0.00 2.24
1680 1778 0.804989 GAGTGGGTTTTGGCAGATCG 59.195 55.000 0.00 0.00 0.00 3.69
1742 1840 0.899717 TTTCCCACAGCCATCCTTGC 60.900 55.000 0.00 0.00 0.00 4.01
1761 1859 8.088463 ACTCTTTACCAGAAGAAGATGATGAT 57.912 34.615 0.00 0.00 35.38 2.45
1954 2052 3.561313 GGGCAAATCTACAAAGGAGGACA 60.561 47.826 0.00 0.00 0.00 4.02
1956 2054 2.355716 CGGGCAAATCTACAAAGGAGGA 60.356 50.000 0.00 0.00 0.00 3.71
1975 2075 6.436843 AAGAAAAGAAAGTACATATGGCGG 57.563 37.500 7.80 0.00 0.00 6.13
2098 2198 7.720957 TGCATATATACAGACTGGAGCAAAATT 59.279 33.333 7.51 0.00 0.00 1.82
2103 2203 4.835056 ACTGCATATATACAGACTGGAGCA 59.165 41.667 18.11 2.90 37.35 4.26
2123 2223 4.533919 AAGGACTGACAGAGATTCACTG 57.466 45.455 10.08 9.25 40.68 3.66
2242 2342 0.879090 CAGTCAACTTTTACCCGGGC 59.121 55.000 24.08 0.00 0.00 6.13
2269 2369 7.763528 TGGACATGATGCCAAATTACATTAAAC 59.236 33.333 0.00 0.00 0.00 2.01
2704 2807 3.875727 GCTGCTATCTGATGCTCTTTCAA 59.124 43.478 0.00 0.00 0.00 2.69
2886 2989 1.210204 TCCAGCCAAGGAGCAATCCT 61.210 55.000 0.00 0.00 43.04 3.24
2985 3095 4.962362 TCCTACTCCACAAAGCAGATATCA 59.038 41.667 5.32 0.00 0.00 2.15
3039 3149 2.170166 CCAGCAAGGCTTCCAAATACA 58.830 47.619 0.00 0.00 36.40 2.29
3133 3248 2.024414 GGTGTGCCAGAAATACCCATC 58.976 52.381 0.00 0.00 34.09 3.51
3350 3465 3.073946 ACAGCCCAGGTTTACATGTAGTT 59.926 43.478 5.56 0.00 0.00 2.24
3410 3525 5.934625 CACCAAGCTGAGTAATACAACTTCT 59.065 40.000 0.00 0.00 0.00 2.85
3585 3700 9.703892 TGTTTCACATATGTTAATTTTTGGAGG 57.296 29.630 5.37 0.00 0.00 4.30
3652 3767 8.912988 AGATTCTTTGTAAATGTCCTTGTTCAA 58.087 29.630 0.00 0.00 0.00 2.69
3653 3768 8.463930 AGATTCTTTGTAAATGTCCTTGTTCA 57.536 30.769 0.00 0.00 0.00 3.18
3691 3806 5.240891 TCACTTCAGTCTGTGGAATGATTC 58.759 41.667 0.00 0.00 44.33 2.52
3701 3816 5.335269 CGAGTATCAGTTCACTTCAGTCTGT 60.335 44.000 0.00 0.00 33.17 3.41
3711 3826 7.754027 ACTGTTGTAATACGAGTATCAGTTCAC 59.246 37.037 8.03 0.00 31.02 3.18
3716 3831 6.913132 CCTCACTGTTGTAATACGAGTATCAG 59.087 42.308 0.00 2.59 33.17 2.90
3717 3832 6.183360 CCCTCACTGTTGTAATACGAGTATCA 60.183 42.308 0.00 0.00 33.17 2.15
3718 3833 6.207213 CCCTCACTGTTGTAATACGAGTATC 58.793 44.000 0.00 0.00 0.00 2.24
3719 3834 5.068723 CCCCTCACTGTTGTAATACGAGTAT 59.931 44.000 0.00 0.00 0.00 2.12
3720 3835 4.400251 CCCCTCACTGTTGTAATACGAGTA 59.600 45.833 0.00 0.00 0.00 2.59
3724 3839 3.880047 TCCCCTCACTGTTGTAATACG 57.120 47.619 0.00 0.00 0.00 3.06
3744 3859 6.183360 TGGAGTGCGAAACTGTATTTCTTTTT 60.183 34.615 0.00 0.00 40.07 1.94
3880 3996 3.524789 TGGTGGATGTCATCTCTGGATTT 59.475 43.478 12.54 0.00 0.00 2.17
3988 4104 3.055530 ACTTCTTGGATCTGCGTCATCTT 60.056 43.478 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.