Multiple sequence alignment - TraesCS2B01G341800

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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 TraesCS2B01G341800 chr2B 100.000 8051 0 0 1 8051 487238830 487230780 0.000000e+00 14868.0
1 TraesCS2B01G341800 chr2B 82.167 1200 208 5 5840 7036 746321791 746322987 0.000000e+00 1026.0
2 TraesCS2B01G341800 chr2B 88.129 497 37 8 2 496 646418376 646417900 9.060000e-159 571.0
3 TraesCS2B01G341800 chr2D 95.225 4042 133 22 827 4832 413957763 413953746 0.000000e+00 6340.0
4 TraesCS2B01G341800 chr2D 95.232 2454 78 19 4892 7330 413953746 413951317 0.000000e+00 3847.0
5 TraesCS2B01G341800 chr2D 82.068 1199 211 4 5840 7036 611897416 611898612 0.000000e+00 1020.0
6 TraesCS2B01G341800 chr2D 90.766 509 36 3 1 500 620297370 620296864 0.000000e+00 669.0
7 TraesCS2B01G341800 chr2D 89.634 492 46 5 7338 7826 413949837 413949348 8.870000e-174 621.0
8 TraesCS2B01G341800 chr2D 88.720 461 51 1 1 460 248488852 248489312 5.460000e-156 562.0
9 TraesCS2B01G341800 chr2D 89.614 337 19 13 496 827 413959037 413958712 1.620000e-111 414.0
10 TraesCS2B01G341800 chr2D 89.933 149 12 3 7904 8051 413946086 413945940 1.070000e-43 189.0
11 TraesCS2B01G341800 chr2A 94.121 3963 164 33 815 4734 581170445 581166509 0.000000e+00 5963.0
12 TraesCS2B01G341800 chr2A 94.097 2626 87 28 4743 7330 581166471 581163876 0.000000e+00 3928.0
13 TraesCS2B01G341800 chr2A 82.421 1206 203 8 5835 7036 744330845 744332045 0.000000e+00 1044.0
14 TraesCS2B01G341800 chr2A 89.593 221 19 3 496 715 581171343 581171126 2.210000e-70 278.0
15 TraesCS2B01G341800 chr2A 83.333 306 30 3 7369 7672 581151928 581151642 6.200000e-66 263.0
16 TraesCS2B01G341800 chr2A 97.222 36 1 0 4746 4781 692641996 692642031 2.430000e-05 62.1
17 TraesCS2B01G341800 chr6B 90.141 497 45 2 1 496 64690761 64690268 1.890000e-180 643.0
18 TraesCS2B01G341800 chr3B 89.157 498 49 3 3 496 235971447 235971943 4.130000e-172 616.0
19 TraesCS2B01G341800 chr6A 88.755 498 53 3 1 496 73787683 73787187 2.480000e-169 606.0
20 TraesCS2B01G341800 chr6A 97.436 39 1 0 4748 4786 33259118 33259080 5.210000e-07 67.6
21 TraesCS2B01G341800 chr1A 88.163 490 53 5 1 490 578244784 578245268 5.420000e-161 579.0
22 TraesCS2B01G341800 chr1A 97.619 42 1 0 4746 4787 296923110 296923069 1.120000e-08 73.1
23 TraesCS2B01G341800 chr7D 89.552 402 41 1 96 496 563051320 563051721 7.210000e-140 508.0
24 TraesCS2B01G341800 chr7D 80.000 280 48 8 6716 6991 298512597 298512872 4.930000e-47 200.0
25 TraesCS2B01G341800 chr1B 84.279 458 65 5 1 453 63173504 63173049 2.670000e-119 440.0
26 TraesCS2B01G341800 chr7A 84.390 205 30 2 6722 6925 325711845 325711642 4.930000e-47 200.0
27 TraesCS2B01G341800 chr1D 97.619 42 1 0 4746 4787 228806369 228806328 1.120000e-08 73.1
28 TraesCS2B01G341800 chr1D 97.368 38 1 0 4746 4783 124343562 124343599 1.880000e-06 65.8
29 TraesCS2B01G341800 chr6D 97.436 39 1 0 4748 4786 29145619 29145657 5.210000e-07 67.6
30 TraesCS2B01G341800 chr3A 88.679 53 4 2 4746 4797 15804182 15804131 6.750000e-06 63.9


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G341800 chr2B 487230780 487238830 8050 True 14868.000000 14868 100.000000 1 8051 1 chr2B.!!$R1 8050
1 TraesCS2B01G341800 chr2B 746321791 746322987 1196 False 1026.000000 1026 82.167000 5840 7036 1 chr2B.!!$F1 1196
2 TraesCS2B01G341800 chr2D 413945940 413959037 13097 True 2282.200000 6340 91.927600 496 8051 5 chr2D.!!$R2 7555
3 TraesCS2B01G341800 chr2D 611897416 611898612 1196 False 1020.000000 1020 82.068000 5840 7036 1 chr2D.!!$F2 1196
4 TraesCS2B01G341800 chr2D 620296864 620297370 506 True 669.000000 669 90.766000 1 500 1 chr2D.!!$R1 499
5 TraesCS2B01G341800 chr2A 581163876 581171343 7467 True 3389.666667 5963 92.603667 496 7330 3 chr2A.!!$R2 6834
6 TraesCS2B01G341800 chr2A 744330845 744332045 1200 False 1044.000000 1044 82.421000 5835 7036 1 chr2A.!!$F2 1201

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
158 159 0.115745 TTGAGGAACCCTAGGACCGT 59.884 55.0 11.48 0.0 31.76 4.83 F
1327 2925 0.103937 CATCCTTCCTCTCTGCGGTC 59.896 60.0 0.00 0.0 0.00 4.79 F
1774 3397 0.178935 ATAGCTCTGGCCTCCTCCTC 60.179 60.0 3.32 0.0 39.73 3.71 F
2088 3711 0.250901 TGGTGGGAGAAGAAAGCTGC 60.251 55.0 0.00 0.0 0.00 5.25 F
3204 4827 0.185901 AAGAACCTGCCCTCTTTGCA 59.814 50.0 0.00 0.0 37.17 4.08 F
5120 6805 0.034186 AATTCCGGCCAGATGCTTCA 60.034 50.0 2.24 0.0 40.92 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 2952 0.108424 GGCAGTCAGATTGAGCGTCT 60.108 55.0 0.00 0.00 0.00 4.18 R
2617 4240 0.806102 CTTACAGGCCACCGACGATG 60.806 60.0 5.01 0.00 0.00 3.84 R
2872 4495 0.824759 ACGGATAGCTGAAGGACACC 59.175 55.0 0.00 0.00 0.00 4.16 R
3896 5529 0.173708 AGCGAGATGACCGGTTCTTC 59.826 55.0 9.42 9.91 33.72 2.87 R
5146 6831 0.248134 CGGCGAGTGCTGTAGTAGTC 60.248 60.0 0.00 0.00 42.79 2.59 R
7098 8816 0.966370 AAAGCTCGCCTCGGTCTACT 60.966 55.0 0.00 0.00 0.00 2.57 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
42 43 1.758936 TTCAGCAATCTCCAGGCATG 58.241 50.000 0.00 0.00 0.00 4.06
44 45 1.493446 TCAGCAATCTCCAGGCATGAT 59.507 47.619 0.00 0.00 0.00 2.45
61 62 2.891941 GATGCGCCCATGGGAGTTCA 62.892 60.000 36.00 24.41 37.40 3.18
62 63 2.124151 GCGCCCATGGGAGTTCAT 60.124 61.111 36.00 0.00 37.40 2.57
111 112 2.169352 CCGACCAGATCAAGAAGGACAT 59.831 50.000 0.00 0.00 0.00 3.06
113 114 3.368843 CGACCAGATCAAGAAGGACATGT 60.369 47.826 0.00 0.00 0.00 3.21
119 120 3.407424 TCAAGAAGGACATGTGTCAGG 57.593 47.619 1.15 0.00 46.47 3.86
130 131 0.969149 TGTGTCAGGCAGATCTTCGT 59.031 50.000 0.00 0.00 0.00 3.85
158 159 0.115745 TTGAGGAACCCTAGGACCGT 59.884 55.000 11.48 0.00 31.76 4.83
165 167 0.261109 ACCCTAGGACCGTCCCTTAG 59.739 60.000 11.48 9.97 37.19 2.18
217 219 1.453669 GGCACCCCAGATCAGATCC 59.546 63.158 6.80 0.00 0.00 3.36
222 224 2.341543 CCAGATCAGATCCGGGCG 59.658 66.667 6.80 0.00 0.00 6.13
395 397 4.186433 CGCCGCGAGAGAGAGCTT 62.186 66.667 8.23 0.00 0.00 3.74
440 442 4.893601 GCTTAGCCCGGTCGCCTC 62.894 72.222 0.00 0.00 0.00 4.70
441 443 4.222847 CTTAGCCCGGTCGCCTCC 62.223 72.222 0.00 0.00 0.00 4.30
442 444 4.772231 TTAGCCCGGTCGCCTCCT 62.772 66.667 0.00 0.00 0.00 3.69
464 466 3.606662 CGACGGCGAGGGGATGAT 61.607 66.667 16.62 0.00 40.82 2.45
465 467 2.029666 GACGGCGAGGGGATGATG 59.970 66.667 16.62 0.00 0.00 3.07
466 468 3.521529 GACGGCGAGGGGATGATGG 62.522 68.421 16.62 0.00 0.00 3.51
467 469 3.233980 CGGCGAGGGGATGATGGA 61.234 66.667 0.00 0.00 0.00 3.41
468 470 2.746359 GGCGAGGGGATGATGGAG 59.254 66.667 0.00 0.00 0.00 3.86
469 471 2.746359 GCGAGGGGATGATGGAGG 59.254 66.667 0.00 0.00 0.00 4.30
470 472 2.888447 GCGAGGGGATGATGGAGGG 61.888 68.421 0.00 0.00 0.00 4.30
471 473 2.219875 CGAGGGGATGATGGAGGGG 61.220 68.421 0.00 0.00 0.00 4.79
472 474 1.240129 GAGGGGATGATGGAGGGGA 59.760 63.158 0.00 0.00 0.00 4.81
473 475 0.839853 GAGGGGATGATGGAGGGGAG 60.840 65.000 0.00 0.00 0.00 4.30
474 476 1.849823 GGGGATGATGGAGGGGAGG 60.850 68.421 0.00 0.00 0.00 4.30
475 477 1.849823 GGGATGATGGAGGGGAGGG 60.850 68.421 0.00 0.00 0.00 4.30
476 478 1.849823 GGATGATGGAGGGGAGGGG 60.850 68.421 0.00 0.00 0.00 4.79
477 479 2.451294 ATGATGGAGGGGAGGGGC 60.451 66.667 0.00 0.00 0.00 5.80
478 480 2.998668 GATGATGGAGGGGAGGGGCT 62.999 65.000 0.00 0.00 0.00 5.19
479 481 2.368878 GATGGAGGGGAGGGGCTT 60.369 66.667 0.00 0.00 0.00 4.35
480 482 2.697644 ATGGAGGGGAGGGGCTTG 60.698 66.667 0.00 0.00 0.00 4.01
481 483 3.287954 ATGGAGGGGAGGGGCTTGA 62.288 63.158 0.00 0.00 0.00 3.02
482 484 3.093172 GGAGGGGAGGGGCTTGAG 61.093 72.222 0.00 0.00 0.00 3.02
483 485 3.093172 GAGGGGAGGGGCTTGAGG 61.093 72.222 0.00 0.00 0.00 3.86
484 486 3.952799 GAGGGGAGGGGCTTGAGGT 62.953 68.421 0.00 0.00 0.00 3.85
485 487 3.732849 GGGGAGGGGCTTGAGGTG 61.733 72.222 0.00 0.00 0.00 4.00
486 488 3.732849 GGGAGGGGCTTGAGGTGG 61.733 72.222 0.00 0.00 0.00 4.61
487 489 4.432741 GGAGGGGCTTGAGGTGGC 62.433 72.222 0.00 0.00 0.00 5.01
521 523 7.527796 AGATAGCTCTTAACCTACCATCACTA 58.472 38.462 0.00 0.00 0.00 2.74
560 563 8.021396 GTCAAGCGAACTTTACATTTAGGAAAT 58.979 33.333 0.00 0.00 32.29 2.17
563 566 9.444600 AAGCGAACTTTACATTTAGGAAATAGA 57.555 29.630 0.00 0.00 29.41 1.98
720 1336 0.180406 AGCCGTATTTGTAGCCCTGG 59.820 55.000 0.00 0.00 0.00 4.45
727 1343 1.906105 TTTGTAGCCCTGGCCTACCG 61.906 60.000 11.91 0.00 43.17 4.02
745 1361 3.258225 GTGTCATCGCGAGTGCTAT 57.742 52.632 16.66 0.00 39.65 2.97
760 1397 5.244785 AGTGCTATTGCTCACATTTGATG 57.755 39.130 0.00 0.00 40.48 3.07
770 1407 0.631212 ACATTTGATGTCCCCCTCCC 59.369 55.000 0.00 0.00 39.92 4.30
786 1423 1.211709 CCCCGAAAAGCGCGATTTT 59.788 52.632 32.47 32.47 39.11 1.82
816 1453 0.845985 TACCCAAGTACCCAACCCCC 60.846 60.000 0.00 0.00 0.00 5.40
947 2545 2.933878 GATCCAATGCCACGGCGGTA 62.934 60.000 13.24 0.00 45.51 4.02
948 2546 2.940890 ATCCAATGCCACGGCGGTAG 62.941 60.000 13.24 0.00 45.51 3.18
1327 2925 0.103937 CATCCTTCCTCTCTGCGGTC 59.896 60.000 0.00 0.00 0.00 4.79
1354 2952 5.830000 TTTCTATGCTCGCTCTAGTTACA 57.170 39.130 0.00 0.00 0.00 2.41
1381 2987 2.902486 TCAATCTGACTGCCTCACTCTT 59.098 45.455 0.00 0.00 0.00 2.85
1403 3009 0.309302 CGCTGCAGTACTCGCTCTAT 59.691 55.000 16.64 0.00 0.00 1.98
1748 3371 1.935327 GAAGGTCTCTAGCGCACCGT 61.935 60.000 11.47 6.01 35.13 4.83
1774 3397 0.178935 ATAGCTCTGGCCTCCTCCTC 60.179 60.000 3.32 0.00 39.73 3.71
1778 3401 2.445654 CTGGCCTCCTCCTCCTCC 60.446 72.222 3.32 0.00 0.00 4.30
1779 3402 4.095400 TGGCCTCCTCCTCCTCCC 62.095 72.222 3.32 0.00 0.00 4.30
1780 3403 3.773154 GGCCTCCTCCTCCTCCCT 61.773 72.222 0.00 0.00 0.00 4.20
1781 3404 2.445654 GCCTCCTCCTCCTCCCTG 60.446 72.222 0.00 0.00 0.00 4.45
1782 3405 2.445654 CCTCCTCCTCCTCCCTGC 60.446 72.222 0.00 0.00 0.00 4.85
1805 3428 1.344942 GACTGACGACGGACACATGC 61.345 60.000 0.00 0.00 0.00 4.06
1861 3484 4.020617 TTCCTGGCAGGGCTCGTG 62.021 66.667 32.23 6.00 35.59 4.35
1951 3574 2.103736 GGGCTCTACGCGTACACC 59.896 66.667 16.41 15.97 40.44 4.16
2027 3650 2.803492 GCCGAGCAGGTACTATTTCTGG 60.803 54.545 0.00 0.00 43.70 3.86
2087 3710 1.528129 GTGGTGGGAGAAGAAAGCTG 58.472 55.000 0.00 0.00 0.00 4.24
2088 3711 0.250901 TGGTGGGAGAAGAAAGCTGC 60.251 55.000 0.00 0.00 0.00 5.25
2098 3721 1.968540 GAAAGCTGCGTGGGCTCTT 60.969 57.895 0.00 0.00 39.30 2.85
2186 3809 2.491693 TCATTTTGGATTTCTGCCGGTC 59.508 45.455 1.90 0.00 0.00 4.79
2231 3854 4.637483 TTTCCGATGGATGATTTCTTGC 57.363 40.909 0.00 0.00 0.00 4.01
2233 3856 3.470709 TCCGATGGATGATTTCTTGCTC 58.529 45.455 0.00 0.00 0.00 4.26
2296 3919 6.525628 GTCAAATGTCAATCATGCTGTACTTG 59.474 38.462 0.00 0.00 36.81 3.16
2297 3920 6.207221 TCAAATGTCAATCATGCTGTACTTGT 59.793 34.615 0.00 0.00 36.81 3.16
2298 3921 6.579666 AATGTCAATCATGCTGTACTTGTT 57.420 33.333 0.00 0.00 36.81 2.83
2332 3955 7.759433 CCCGATTTTGTTTCATGTAAATAAGCT 59.241 33.333 0.00 0.00 30.92 3.74
2554 4177 1.004918 GCTGGTGTTCTGGTACGCT 60.005 57.895 0.00 0.00 0.00 5.07
2572 4195 2.264794 GGCGTGTTCATCCGGAGT 59.735 61.111 11.34 0.00 0.00 3.85
2617 4240 4.162690 ACGGCCATCTTCTCCGCC 62.163 66.667 2.24 0.00 46.49 6.13
2681 4304 2.126580 CTGCAGCTTGCTTTCGGC 60.127 61.111 0.00 0.00 45.31 5.54
2691 4314 3.363341 TTGCTTTCGGCGAGAAAATTT 57.637 38.095 10.46 0.00 46.98 1.82
2702 4325 5.474825 GGCGAGAAAATTTACCCAAATTCA 58.525 37.500 0.00 0.00 42.29 2.57
2872 4495 2.886523 TGGCAACATTGAGTTCAAGGAG 59.113 45.455 12.83 6.48 46.17 3.69
3192 4815 3.909732 TGGTTTGGTGAATCAAGAACCT 58.090 40.909 18.19 0.00 34.90 3.50
3201 4824 3.181429 TGAATCAAGAACCTGCCCTCTTT 60.181 43.478 0.00 0.00 29.29 2.52
3204 4827 0.185901 AAGAACCTGCCCTCTTTGCA 59.814 50.000 0.00 0.00 37.17 4.08
3360 4988 8.125448 GGTTGTACTCTCAATTGCAATCTTATC 58.875 37.037 13.38 0.36 0.00 1.75
3400 5032 8.539770 TTTTGTGATTTGATCTGACTAGAGTC 57.460 34.615 0.00 2.56 44.97 3.36
3436 5068 4.851639 ACTTCTGACCAGGCTAATTGAT 57.148 40.909 0.00 0.00 0.00 2.57
3450 5082 9.806203 CAGGCTAATTGATTTTTGAATCATGTA 57.194 29.630 2.98 0.00 38.79 2.29
3489 5122 6.596497 TCGTGTCTATGGTCTTTTTATTTCCC 59.404 38.462 0.00 0.00 0.00 3.97
3566 5199 4.641645 CAGCTGTCCGGTGGCCAA 62.642 66.667 7.24 0.00 37.47 4.52
3656 5289 1.350351 AGTGCTCTTGATGCTGGTTCT 59.650 47.619 0.00 0.00 0.00 3.01
3800 5433 3.096852 TGTTGAGACCGGTACTCATGAT 58.903 45.455 26.72 0.00 42.68 2.45
3872 5505 0.984230 AGGAGATGGCAAGAAACCGA 59.016 50.000 0.00 0.00 0.00 4.69
4163 5796 0.611618 TCATTGGCCCGACATTTGCT 60.612 50.000 0.00 0.00 0.00 3.91
4295 5928 1.878522 CGCGTACCTGATCCAGCAC 60.879 63.158 0.00 0.00 0.00 4.40
4359 5992 1.022735 GAGGATGATGCTTGCAGGTG 58.977 55.000 0.87 0.00 0.00 4.00
4368 6007 1.798735 CTTGCAGGTGATTCGCAGG 59.201 57.895 0.00 0.00 36.91 4.85
4376 6015 0.179215 GTGATTCGCAGGCTTGTTCG 60.179 55.000 0.00 0.00 0.00 3.95
4377 6016 1.298157 TGATTCGCAGGCTTGTTCGG 61.298 55.000 0.00 0.00 0.00 4.30
4389 6032 3.119955 GGCTTGTTCGGTTGTTCCTATTC 60.120 47.826 0.00 0.00 0.00 1.75
4402 6045 7.416777 GGTTGTTCCTATTCTTTTCCATGATCC 60.417 40.741 0.00 0.00 0.00 3.36
4413 6060 2.415624 TCCATGATCCCTGCAGAGAAT 58.584 47.619 17.39 5.15 0.00 2.40
4626 6273 0.036010 CGCTCCTGGTGTCCTTCATT 60.036 55.000 0.00 0.00 0.00 2.57
4653 6300 0.180171 TCATCATCGAATGGCGGGTT 59.820 50.000 0.00 0.00 41.33 4.11
4692 6339 1.199615 CCTTCCCTCTCCTTGTCCTC 58.800 60.000 0.00 0.00 0.00 3.71
4712 6359 1.812571 CGCCAACTTTGCTCAGGTAAT 59.187 47.619 0.00 0.00 0.00 1.89
4740 6388 8.311836 ACCCAATTGACATATATTACTACCTCG 58.688 37.037 7.12 0.00 0.00 4.63
4741 6389 7.764443 CCCAATTGACATATATTACTACCTCGG 59.236 40.741 7.12 0.00 0.00 4.63
4742 6390 8.311836 CCAATTGACATATATTACTACCTCGGT 58.688 37.037 7.12 0.00 0.00 4.69
4743 6391 9.706691 CAATTGACATATATTACTACCTCGGTT 57.293 33.333 0.00 0.00 0.00 4.44
4744 6392 9.924650 AATTGACATATATTACTACCTCGGTTC 57.075 33.333 0.00 0.00 0.00 3.62
4745 6393 8.701908 TTGACATATATTACTACCTCGGTTCT 57.298 34.615 0.00 0.00 0.00 3.01
4758 6434 3.497262 CCTCGGTTCTGAACTAAAACCAC 59.503 47.826 19.05 0.49 42.09 4.16
4787 6467 1.631405 TTCCGAACCGAGGGAGTAAA 58.369 50.000 0.00 0.00 33.01 2.01
4831 6511 1.472904 GGAGAAAACGCCTAGGTAGCC 60.473 57.143 11.31 0.00 0.00 3.93
5086 6771 3.918544 GAGCTCGCTCTCCACTCT 58.081 61.111 11.49 0.00 39.80 3.24
5120 6805 0.034186 AATTCCGGCCAGATGCTTCA 60.034 50.000 2.24 0.00 40.92 3.02
5126 6811 0.035630 GGCCAGATGCTTCACACTCT 60.036 55.000 0.00 0.00 40.92 3.24
5133 6818 1.372683 GCTTCACACTCTCTGGCCA 59.627 57.895 4.71 4.71 0.00 5.36
5141 6826 0.901124 ACTCTCTGGCCAGTGTCATC 59.099 55.000 31.58 0.00 0.00 2.92
5142 6827 1.193323 CTCTCTGGCCAGTGTCATCT 58.807 55.000 31.58 0.00 0.00 2.90
5143 6828 2.291865 ACTCTCTGGCCAGTGTCATCTA 60.292 50.000 31.58 11.59 0.00 1.98
5144 6829 2.100584 CTCTCTGGCCAGTGTCATCTAC 59.899 54.545 31.58 0.00 0.00 2.59
5145 6830 1.827344 CTCTGGCCAGTGTCATCTACA 59.173 52.381 31.58 7.96 35.06 2.74
5146 6831 1.827344 TCTGGCCAGTGTCATCTACAG 59.173 52.381 31.58 2.78 39.29 2.74
5147 6832 1.827344 CTGGCCAGTGTCATCTACAGA 59.173 52.381 25.53 0.00 39.29 3.41
5148 6833 1.550524 TGGCCAGTGTCATCTACAGAC 59.449 52.381 0.00 0.00 39.29 3.51
5149 6834 1.827969 GGCCAGTGTCATCTACAGACT 59.172 52.381 0.00 0.00 39.29 3.24
5150 6835 3.024547 GGCCAGTGTCATCTACAGACTA 58.975 50.000 0.00 0.00 39.29 2.59
5160 6845 5.587043 GTCATCTACAGACTACTACAGCACT 59.413 44.000 0.00 0.00 33.29 4.40
5243 6928 1.568612 CGATGCTTTGTCGCACCAGT 61.569 55.000 0.00 0.00 43.61 4.00
5256 6944 0.320247 CACCAGTCGCTGCTTCTTCT 60.320 55.000 0.00 0.00 0.00 2.85
5257 6945 1.067565 CACCAGTCGCTGCTTCTTCTA 60.068 52.381 0.00 0.00 0.00 2.10
5280 6968 3.377573 TGTGGATGAGATGAGATGGTCA 58.622 45.455 0.00 0.00 40.38 4.02
5314 7003 1.893808 CTGTTGCTGCTCGTTGGGT 60.894 57.895 0.00 0.00 0.00 4.51
5626 7332 1.642037 CGTGCATGAAGCCTGTCAGG 61.642 60.000 15.15 15.15 44.83 3.86
5633 7340 0.952984 GAAGCCTGTCAGGTGTCAGC 60.953 60.000 20.24 4.64 37.80 4.26
5698 7405 2.212652 GCCACGCATCATCACTCATTA 58.787 47.619 0.00 0.00 0.00 1.90
5711 7418 7.710896 TCATCACTCATTACTCATCACTAGTG 58.289 38.462 17.17 17.17 35.54 2.74
5712 7419 7.557719 TCATCACTCATTACTCATCACTAGTGA 59.442 37.037 27.07 27.07 44.25 3.41
5786 7502 4.645762 TTTGCATGTGTTGTTTCTGCTA 57.354 36.364 0.00 0.00 34.02 3.49
5787 7503 3.624326 TGCATGTGTTGTTTCTGCTAC 57.376 42.857 0.00 0.00 34.02 3.58
5788 7504 3.213506 TGCATGTGTTGTTTCTGCTACT 58.786 40.909 0.00 0.00 34.02 2.57
5789 7505 4.384940 TGCATGTGTTGTTTCTGCTACTA 58.615 39.130 0.00 0.00 34.02 1.82
6156 7872 1.986378 GTCATCAAGGTCTTCGTCGTG 59.014 52.381 0.00 0.00 0.00 4.35
6315 8031 2.342648 GTGGAGAAGGTTCGCGGT 59.657 61.111 6.13 0.00 0.00 5.68
6642 8358 3.379445 GGCGTGACGGAGGAGGAA 61.379 66.667 7.25 0.00 0.00 3.36
6717 8433 2.125793 GGTTACAGGACGCCCGTC 60.126 66.667 12.07 12.07 43.87 4.79
7142 8860 0.036952 ACACTCCGATGAGCAACAGG 60.037 55.000 0.00 0.00 42.74 4.00
7266 8990 5.809562 TGTTACATTTTGTTCCAACTTGCAG 59.190 36.000 0.00 0.00 0.00 4.41
7267 8991 3.795877 ACATTTTGTTCCAACTTGCAGG 58.204 40.909 0.00 0.00 0.00 4.85
7275 8999 1.702401 TCCAACTTGCAGGTATGTCCA 59.298 47.619 0.22 0.00 39.02 4.02
7330 9054 1.808945 TCGTTCTCCTCGTTGTCTACC 59.191 52.381 0.00 0.00 0.00 3.18
7331 9055 1.538512 CGTTCTCCTCGTTGTCTACCA 59.461 52.381 0.00 0.00 0.00 3.25
7334 9058 3.081710 TCTCCTCGTTGTCTACCATGA 57.918 47.619 0.00 0.00 0.00 3.07
7335 9059 3.427573 TCTCCTCGTTGTCTACCATGAA 58.572 45.455 0.00 0.00 0.00 2.57
7336 9060 3.192844 TCTCCTCGTTGTCTACCATGAAC 59.807 47.826 0.00 0.00 0.00 3.18
7349 10545 4.419522 ACCATGAACGAGTATGTTTTGC 57.580 40.909 0.00 0.00 30.75 3.68
7380 10576 1.160137 ACTGCCATGAACGAGAAAGC 58.840 50.000 0.00 0.00 0.00 3.51
7381 10577 1.271054 ACTGCCATGAACGAGAAAGCT 60.271 47.619 0.00 0.00 0.00 3.74
7448 10645 1.500396 GATTTTCGGTGCGGTGTCC 59.500 57.895 0.00 0.00 0.00 4.02
7463 10660 2.622436 GTGTCCTTCCTTCAATCTCCG 58.378 52.381 0.00 0.00 0.00 4.63
7482 10679 0.579630 GTTGCAATGTGTGACGACGA 59.420 50.000 0.59 0.00 0.00 4.20
7489 10686 2.050714 TGTGACGACGACCTTCGC 60.051 61.111 0.00 0.00 45.12 4.70
7515 10712 2.187946 GCCCCTGATGACGACCAG 59.812 66.667 0.00 0.00 0.00 4.00
7544 10741 1.129251 CGGCTCAACTACATGCTTGTG 59.871 52.381 15.08 7.81 36.53 3.33
7545 10742 1.135575 GGCTCAACTACATGCTTGTGC 60.136 52.381 15.08 8.43 36.53 4.57
7564 10761 4.091424 GTGCGAGTATGATTTTCACTTGC 58.909 43.478 6.29 6.29 45.87 4.01
7580 10777 1.830587 TTGCGTGGCATCTCACCTCT 61.831 55.000 0.00 0.00 38.76 3.69
7631 10829 4.153475 ACCGTGGAAAGTTATTGTGAATCG 59.847 41.667 0.00 0.00 0.00 3.34
7637 10835 6.072230 TGGAAAGTTATTGTGAATCGCATGAA 60.072 34.615 0.00 0.00 0.00 2.57
7650 10848 3.673902 TCGCATGAAGACTTGGATTTGA 58.326 40.909 0.00 0.00 0.00 2.69
7651 10849 3.436704 TCGCATGAAGACTTGGATTTGAC 59.563 43.478 0.00 0.00 0.00 3.18
7682 10880 2.519771 AGCATTGATTTGGAGCTCCA 57.480 45.000 32.00 32.00 45.94 3.86
7696 10894 0.250338 GCTCCAGGGTGAAAACTCGT 60.250 55.000 0.00 0.00 0.00 4.18
7703 10901 1.202604 GGGTGAAAACTCGTGGTCTGA 60.203 52.381 0.00 0.00 0.00 3.27
7728 10927 7.403312 CCCATTTGGTTATATTTGACACTGA 57.597 36.000 0.00 0.00 0.00 3.41
7746 10945 4.671964 CACTGATGATGTTTTTGTGTCGTG 59.328 41.667 0.00 0.00 0.00 4.35
7755 10954 4.454847 TGTTTTTGTGTCGTGTCCTTGTTA 59.545 37.500 0.00 0.00 0.00 2.41
7769 10968 2.031157 CCTTGTTAAAGGCACTGTTCGG 60.031 50.000 0.00 0.00 46.50 4.30
7770 10969 1.600023 TGTTAAAGGCACTGTTCGGG 58.400 50.000 0.00 0.00 40.86 5.14
7771 10970 1.134037 TGTTAAAGGCACTGTTCGGGT 60.134 47.619 0.00 0.00 40.86 5.28
7775 10974 0.822121 AAGGCACTGTTCGGGTTTCC 60.822 55.000 0.00 0.00 40.86 3.13
7792 10991 4.584743 GGTTTCCTTGGACTTGTTCTTCAT 59.415 41.667 0.00 0.00 0.00 2.57
7794 10993 4.705110 TCCTTGGACTTGTTCTTCATGA 57.295 40.909 0.00 0.00 0.00 3.07
7795 10994 4.389374 TCCTTGGACTTGTTCTTCATGAC 58.611 43.478 0.00 0.00 0.00 3.06
7796 10995 4.136796 CCTTGGACTTGTTCTTCATGACA 58.863 43.478 0.00 0.00 0.00 3.58
7803 11002 7.492020 TGGACTTGTTCTTCATGACAAAAATTG 59.508 33.333 0.00 0.00 0.00 2.32
7805 11004 8.411318 ACTTGTTCTTCATGACAAAAATTGAC 57.589 30.769 0.00 0.00 0.00 3.18
7822 11021 2.766313 TGACGATCTGACCTTTGGTTG 58.234 47.619 0.00 0.00 35.25 3.77
7824 11023 3.139077 GACGATCTGACCTTTGGTTGTT 58.861 45.455 0.00 0.00 35.25 2.83
7826 11025 4.315803 ACGATCTGACCTTTGGTTGTTAG 58.684 43.478 0.00 0.00 35.25 2.34
7828 11027 4.389077 CGATCTGACCTTTGGTTGTTAGAC 59.611 45.833 0.00 0.00 35.25 2.59
7830 11029 3.146847 CTGACCTTTGGTTGTTAGACCC 58.853 50.000 0.00 0.00 39.01 4.46
7831 11030 2.148768 GACCTTTGGTTGTTAGACCCG 58.851 52.381 0.00 0.00 39.01 5.28
7832 11031 1.770061 ACCTTTGGTTGTTAGACCCGA 59.230 47.619 0.00 0.00 39.01 5.14
7833 11032 2.148768 CCTTTGGTTGTTAGACCCGAC 58.851 52.381 0.00 0.00 39.01 4.79
7834 11033 1.796459 CTTTGGTTGTTAGACCCGACG 59.204 52.381 0.00 0.00 39.01 5.12
7835 11034 1.039068 TTGGTTGTTAGACCCGACGA 58.961 50.000 0.00 0.00 39.01 4.20
7836 11035 0.314935 TGGTTGTTAGACCCGACGAC 59.685 55.000 0.00 0.00 39.01 4.34
7837 11036 0.314935 GGTTGTTAGACCCGACGACA 59.685 55.000 0.00 0.00 32.86 4.35
7838 11037 1.269726 GGTTGTTAGACCCGACGACAA 60.270 52.381 0.00 0.00 32.86 3.18
7839 11038 1.788886 GTTGTTAGACCCGACGACAAC 59.211 52.381 10.85 10.85 41.95 3.32
7840 11039 0.040157 TGTTAGACCCGACGACAACG 60.040 55.000 0.00 0.00 45.75 4.10
7848 11047 3.033764 GACGACAACGGCGCTTCA 61.034 61.111 6.90 0.00 44.46 3.02
7849 11048 2.586635 ACGACAACGGCGCTTCAA 60.587 55.556 6.90 0.00 44.46 2.69
7850 11049 2.170985 CGACAACGGCGCTTCAAG 59.829 61.111 6.90 0.00 35.72 3.02
7851 11050 2.556287 GACAACGGCGCTTCAAGG 59.444 61.111 6.90 0.00 0.00 3.61
7852 11051 2.203153 ACAACGGCGCTTCAAGGT 60.203 55.556 6.90 0.00 0.00 3.50
7853 11052 1.782028 GACAACGGCGCTTCAAGGTT 61.782 55.000 6.90 0.00 0.00 3.50
7854 11053 1.370414 CAACGGCGCTTCAAGGTTG 60.370 57.895 6.90 8.73 32.99 3.77
7855 11054 1.822186 AACGGCGCTTCAAGGTTGT 60.822 52.632 6.90 0.00 0.00 3.32
7856 11055 1.381165 AACGGCGCTTCAAGGTTGTT 61.381 50.000 6.90 0.00 0.00 2.83
7857 11056 1.082104 CGGCGCTTCAAGGTTGTTC 60.082 57.895 7.64 0.00 0.00 3.18
7858 11057 1.285950 GGCGCTTCAAGGTTGTTCC 59.714 57.895 7.64 0.00 0.00 3.62
7859 11058 1.285950 GCGCTTCAAGGTTGTTCCC 59.714 57.895 0.00 0.00 36.75 3.97
7860 11059 1.956802 CGCTTCAAGGTTGTTCCCC 59.043 57.895 0.00 0.00 36.75 4.81
7861 11060 0.537371 CGCTTCAAGGTTGTTCCCCT 60.537 55.000 0.00 0.00 36.75 4.79
7862 11061 1.704641 GCTTCAAGGTTGTTCCCCTT 58.295 50.000 0.00 0.00 43.11 3.95
7863 11062 2.039418 GCTTCAAGGTTGTTCCCCTTT 58.961 47.619 0.00 0.00 40.35 3.11
7864 11063 2.434336 GCTTCAAGGTTGTTCCCCTTTT 59.566 45.455 0.00 0.00 40.35 2.27
7865 11064 3.639561 GCTTCAAGGTTGTTCCCCTTTTA 59.360 43.478 0.00 0.00 40.35 1.52
7866 11065 4.100344 GCTTCAAGGTTGTTCCCCTTTTAA 59.900 41.667 0.00 0.00 40.35 1.52
7867 11066 5.395879 GCTTCAAGGTTGTTCCCCTTTTAAA 60.396 40.000 0.00 0.00 40.35 1.52
7870 11069 7.916077 TCAAGGTTGTTCCCCTTTTAAATTA 57.084 32.000 0.00 0.00 40.35 1.40
7889 11088 7.681939 AAATTAAAGCATCCTTCTCGTTGTA 57.318 32.000 0.00 0.00 0.00 2.41
7890 11089 6.663944 ATTAAAGCATCCTTCTCGTTGTAC 57.336 37.500 0.00 0.00 0.00 2.90
7891 11090 3.963428 AAGCATCCTTCTCGTTGTACT 57.037 42.857 0.00 0.00 0.00 2.73
7892 11091 5.401531 AAAGCATCCTTCTCGTTGTACTA 57.598 39.130 0.00 0.00 0.00 1.82
7910 11109 9.216117 GTTGTACTAGTGATGTTAAAAGATGGT 57.784 33.333 5.39 0.00 0.00 3.55
7914 14330 7.048512 ACTAGTGATGTTAAAAGATGGTAGGC 58.951 38.462 0.00 0.00 0.00 3.93
7920 14336 4.573201 TGTTAAAAGATGGTAGGCGCATAC 59.427 41.667 23.23 23.23 0.00 2.39
7925 14341 0.764890 ATGGTAGGCGCATACATGGT 59.235 50.000 30.57 12.32 0.00 3.55
7941 14357 7.975616 GCATACATGGTTGTTGATGTAGATTTT 59.024 33.333 0.00 0.00 38.21 1.82
8029 14446 8.986847 TGTTTGATTTTATTATTTGCTGGTGTG 58.013 29.630 0.00 0.00 0.00 3.82
8030 14447 8.442384 GTTTGATTTTATTATTTGCTGGTGTGG 58.558 33.333 0.00 0.00 0.00 4.17
8040 14457 2.660572 TGCTGGTGTGGTTTTATGTGT 58.339 42.857 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.107214 TTGCTGAATCGGGTGGGATC 60.107 55.000 0.00 0.00 0.00 3.36
24 25 0.913924 TCATGCCTGGAGATTGCTGA 59.086 50.000 0.00 0.00 0.00 4.26
42 43 2.124151 AACTCCCATGGGCGCATC 60.124 61.111 27.41 0.40 34.68 3.91
44 45 2.891941 GATGAACTCCCATGGGCGCA 62.892 60.000 27.41 19.61 34.68 6.09
111 112 0.969149 ACGAAGATCTGCCTGACACA 59.031 50.000 0.00 0.00 0.00 3.72
113 114 1.550327 AGACGAAGATCTGCCTGACA 58.450 50.000 0.00 0.00 0.00 3.58
119 120 2.953020 AGTGACAAGACGAAGATCTGC 58.047 47.619 0.00 0.00 0.00 4.26
130 131 2.408565 AGGGTTCCTCAAGTGACAAGA 58.591 47.619 0.00 0.00 0.00 3.02
158 159 1.115930 GCTCGGCCTGATCTAAGGGA 61.116 60.000 0.00 0.00 37.84 4.20
207 209 2.123251 ACCGCCCGGATCTGATCT 60.123 61.111 14.44 0.00 38.96 2.75
264 266 4.035102 GGCGAGGCACCCTTTCCT 62.035 66.667 0.00 0.00 31.76 3.36
384 386 2.498726 CGGGGCAAGCTCTCTCTC 59.501 66.667 0.00 0.00 0.00 3.20
447 449 3.606662 ATCATCCCCTCGCCGTCG 61.607 66.667 0.00 0.00 0.00 5.12
448 450 2.029666 CATCATCCCCTCGCCGTC 59.970 66.667 0.00 0.00 0.00 4.79
449 451 3.550431 CCATCATCCCCTCGCCGT 61.550 66.667 0.00 0.00 0.00 5.68
450 452 3.231889 CTCCATCATCCCCTCGCCG 62.232 68.421 0.00 0.00 0.00 6.46
451 453 2.746359 CTCCATCATCCCCTCGCC 59.254 66.667 0.00 0.00 0.00 5.54
452 454 2.746359 CCTCCATCATCCCCTCGC 59.254 66.667 0.00 0.00 0.00 5.03
453 455 2.219875 CCCCTCCATCATCCCCTCG 61.220 68.421 0.00 0.00 0.00 4.63
454 456 0.839853 CTCCCCTCCATCATCCCCTC 60.840 65.000 0.00 0.00 0.00 4.30
455 457 1.241327 CTCCCCTCCATCATCCCCT 59.759 63.158 0.00 0.00 0.00 4.79
456 458 1.849823 CCTCCCCTCCATCATCCCC 60.850 68.421 0.00 0.00 0.00 4.81
457 459 1.849823 CCCTCCCCTCCATCATCCC 60.850 68.421 0.00 0.00 0.00 3.85
458 460 1.849823 CCCCTCCCCTCCATCATCC 60.850 68.421 0.00 0.00 0.00 3.51
459 461 2.533463 GCCCCTCCCCTCCATCATC 61.533 68.421 0.00 0.00 0.00 2.92
460 462 2.451294 GCCCCTCCCCTCCATCAT 60.451 66.667 0.00 0.00 0.00 2.45
461 463 3.287954 AAGCCCCTCCCCTCCATCA 62.288 63.158 0.00 0.00 0.00 3.07
462 464 2.368878 AAGCCCCTCCCCTCCATC 60.369 66.667 0.00 0.00 0.00 3.51
463 465 2.697644 CAAGCCCCTCCCCTCCAT 60.698 66.667 0.00 0.00 0.00 3.41
464 466 3.950861 CTCAAGCCCCTCCCCTCCA 62.951 68.421 0.00 0.00 0.00 3.86
465 467 3.093172 CTCAAGCCCCTCCCCTCC 61.093 72.222 0.00 0.00 0.00 4.30
466 468 3.093172 CCTCAAGCCCCTCCCCTC 61.093 72.222 0.00 0.00 0.00 4.30
467 469 3.960313 ACCTCAAGCCCCTCCCCT 61.960 66.667 0.00 0.00 0.00 4.79
468 470 3.732849 CACCTCAAGCCCCTCCCC 61.733 72.222 0.00 0.00 0.00 4.81
469 471 3.732849 CCACCTCAAGCCCCTCCC 61.733 72.222 0.00 0.00 0.00 4.30
470 472 4.432741 GCCACCTCAAGCCCCTCC 62.433 72.222 0.00 0.00 0.00 4.30
471 473 4.432741 GGCCACCTCAAGCCCCTC 62.433 72.222 0.00 0.00 43.76 4.30
494 496 7.668052 AGTGATGGTAGGTTAAGAGCTATCTAG 59.332 40.741 0.00 0.00 37.75 2.43
495 497 7.527796 AGTGATGGTAGGTTAAGAGCTATCTA 58.472 38.462 0.00 0.00 37.75 1.98
496 498 6.377912 AGTGATGGTAGGTTAAGAGCTATCT 58.622 40.000 0.00 0.00 37.75 1.98
497 499 6.658188 AGTGATGGTAGGTTAAGAGCTATC 57.342 41.667 0.00 0.00 38.09 2.08
498 500 8.548880 TTTAGTGATGGTAGGTTAAGAGCTAT 57.451 34.615 0.00 0.00 38.09 2.97
499 501 7.837689 TCTTTAGTGATGGTAGGTTAAGAGCTA 59.162 37.037 0.00 0.00 34.88 3.32
500 502 6.668283 TCTTTAGTGATGGTAGGTTAAGAGCT 59.332 38.462 0.00 0.00 37.40 4.09
511 513 8.525316 TGACTTTTACGATCTTTAGTGATGGTA 58.475 33.333 0.00 0.00 36.86 3.25
513 515 7.827819 TGACTTTTACGATCTTTAGTGATGG 57.172 36.000 0.00 0.00 0.00 3.51
521 523 5.465724 AGTTCGCTTGACTTTTACGATCTTT 59.534 36.000 0.00 0.00 30.90 2.52
560 563 7.966246 TTCAAAACACGGCTAAAATACTCTA 57.034 32.000 0.00 0.00 0.00 2.43
659 663 7.222872 TCGGTTACCCTATTTTGAAGTGTTAA 58.777 34.615 0.00 0.00 0.00 2.01
683 687 1.012841 CTCGGCATTTGGAGAAGCTC 58.987 55.000 0.00 0.00 31.90 4.09
720 1336 2.954868 CGCGATGACACGGTAGGC 60.955 66.667 0.00 0.00 0.00 3.93
727 1343 1.256376 CAATAGCACTCGCGATGACAC 59.744 52.381 10.36 0.00 45.49 3.67
742 1358 4.037208 GGGGACATCAAATGTGAGCAATAG 59.963 45.833 0.00 0.00 45.03 1.73
745 1361 2.170166 GGGGACATCAAATGTGAGCAA 58.830 47.619 0.00 0.00 45.03 3.91
760 1397 2.675371 CTTTTCGGGGAGGGGGAC 59.325 66.667 0.00 0.00 0.00 4.46
786 1423 4.525100 GGGTACTTGGGTATGCTTGAAAAA 59.475 41.667 0.00 0.00 0.00 1.94
796 1433 1.301916 GGGGTTGGGTACTTGGGTAT 58.698 55.000 0.00 0.00 0.00 2.73
798 1435 2.164967 GGGGGTTGGGTACTTGGGT 61.165 63.158 0.00 0.00 0.00 4.51
816 1453 3.004629 TGTTGCAGTGTGCTAATTTCTGG 59.995 43.478 0.00 0.00 45.31 3.86
947 2545 1.529244 GCAACCACAAGAGCACCCT 60.529 57.895 0.00 0.00 0.00 4.34
948 2546 2.908073 CGCAACCACAAGAGCACCC 61.908 63.158 0.00 0.00 0.00 4.61
1327 2925 0.510359 GAGCGAGCATAGAAATGGCG 59.490 55.000 0.00 0.00 33.38 5.69
1354 2952 0.108424 GGCAGTCAGATTGAGCGTCT 60.108 55.000 0.00 0.00 0.00 4.18
1403 3009 1.651240 CGAGGCCGAGGTAGACGAAA 61.651 60.000 0.00 0.00 38.22 3.46
1672 3278 2.563614 GACGCTGAATACGACGTCC 58.436 57.895 10.58 0.00 46.84 4.79
1681 3287 1.215647 GTCCGTGGAGACGCTGAAT 59.784 57.895 0.00 0.00 44.68 2.57
1774 3397 1.294780 GTCAGTCACAGCAGGGAGG 59.705 63.158 0.00 0.00 0.00 4.30
1778 3401 1.730902 CGTCGTCAGTCACAGCAGG 60.731 63.158 0.00 0.00 0.00 4.85
1779 3402 1.730902 CCGTCGTCAGTCACAGCAG 60.731 63.158 0.00 0.00 0.00 4.24
1780 3403 2.190841 TCCGTCGTCAGTCACAGCA 61.191 57.895 0.00 0.00 0.00 4.41
1781 3404 1.729838 GTCCGTCGTCAGTCACAGC 60.730 63.158 0.00 0.00 0.00 4.40
1782 3405 0.660595 GTGTCCGTCGTCAGTCACAG 60.661 60.000 0.00 0.00 0.00 3.66
1894 3517 1.066422 GATGACGGCGATGCTGAGA 59.934 57.895 16.62 0.00 38.46 3.27
1939 3562 1.138247 GGTGAGGGTGTACGCGTAG 59.862 63.158 21.25 0.00 0.00 3.51
1951 3574 3.775654 GAGGTGAGCCCGGTGAGG 61.776 72.222 0.00 0.00 38.74 3.86
2027 3650 1.160137 GTGGGATGATAATGGCGCTC 58.840 55.000 7.64 0.00 0.00 5.03
2066 3689 0.110486 GCTTTCTTCTCCCACCACCA 59.890 55.000 0.00 0.00 0.00 4.17
2072 3695 0.603707 CACGCAGCTTTCTTCTCCCA 60.604 55.000 0.00 0.00 0.00 4.37
2075 3698 1.916697 GCCCACGCAGCTTTCTTCTC 61.917 60.000 0.00 0.00 34.03 2.87
2088 3711 4.069232 TCCGAGCAAGAGCCCACG 62.069 66.667 0.00 0.00 43.56 4.94
2332 3955 5.010314 ACACTTGGTCGTCAGAATTACACTA 59.990 40.000 0.00 0.00 0.00 2.74
2554 4177 2.264480 CTCCGGATGAACACGCCA 59.736 61.111 3.57 0.00 0.00 5.69
2572 4195 3.625897 CCACCGTCTGTCTGGCCA 61.626 66.667 4.71 4.71 0.00 5.36
2617 4240 0.806102 CTTACAGGCCACCGACGATG 60.806 60.000 5.01 0.00 0.00 3.84
2681 4304 8.755696 TTCATGAATTTGGGTAAATTTTCTCG 57.244 30.769 3.38 0.00 44.35 4.04
2689 4312 6.013898 TCCTGCAATTCATGAATTTGGGTAAA 60.014 34.615 27.30 12.76 38.84 2.01
2691 4314 5.022122 TCCTGCAATTCATGAATTTGGGTA 58.978 37.500 27.30 16.32 38.84 3.69
2702 4325 1.006281 TCCAAGGCTCCTGCAATTCAT 59.994 47.619 0.00 0.00 41.91 2.57
2767 4390 1.493022 ACCTCCAACAGCTTGTAACCA 59.507 47.619 0.00 0.00 0.00 3.67
2803 4426 4.523173 TCAGTTGAGTCTTGGACTATCGTT 59.477 41.667 0.00 0.00 43.53 3.85
2806 4429 5.355596 CCATCAGTTGAGTCTTGGACTATC 58.644 45.833 0.00 0.00 43.53 2.08
2872 4495 0.824759 ACGGATAGCTGAAGGACACC 59.175 55.000 0.00 0.00 0.00 4.16
3192 4815 1.832167 GGTGGTTGCAAAGAGGGCA 60.832 57.895 0.00 0.00 40.00 5.36
3201 4824 1.992538 TGTCAATGATGGTGGTTGCA 58.007 45.000 0.00 0.00 0.00 4.08
3204 4827 7.722949 AAGAATATTGTCAATGATGGTGGTT 57.277 32.000 8.39 0.00 0.00 3.67
3360 4988 5.351233 TCACAAAATACAGGCTGTAAACG 57.649 39.130 29.35 19.61 36.31 3.60
3405 5037 5.426833 AGCCTGGTCAGAAGTATGAACTAAT 59.573 40.000 0.00 0.00 37.79 1.73
3411 5043 5.425217 TCAATTAGCCTGGTCAGAAGTATGA 59.575 40.000 0.00 0.00 0.00 2.15
3450 5082 9.754382 ACCATAGACACGATAAAATTTATACGT 57.246 29.630 13.38 13.38 34.40 3.57
3483 5115 6.245890 TGGATTCAACAAGTTTTGGGAAAT 57.754 33.333 3.48 0.00 33.74 2.17
3484 5116 5.683876 TGGATTCAACAAGTTTTGGGAAA 57.316 34.783 3.48 0.00 33.74 3.13
3597 5230 5.316987 GAGAAGGATCTTTGGGTTCTTCAA 58.683 41.667 0.00 0.00 35.54 2.69
3656 5289 4.284490 AGTGCCTCTTGAACAATACTCTCA 59.716 41.667 0.00 0.00 0.00 3.27
3896 5529 0.173708 AGCGAGATGACCGGTTCTTC 59.826 55.000 9.42 9.91 33.72 2.87
3956 5589 1.627834 CTCAGGTTCCTCAAGCTTCCT 59.372 52.381 0.00 0.00 38.33 3.36
4163 5796 5.358922 TCAATCATGTTGCTCATCACGATA 58.641 37.500 0.00 0.00 34.09 2.92
4295 5928 2.877168 GCCCATGATGCTGAAGAAGTAG 59.123 50.000 0.00 0.00 0.00 2.57
4359 5992 1.298859 ACCGAACAAGCCTGCGAATC 61.299 55.000 0.00 0.00 0.00 2.52
4368 6007 3.751698 AGAATAGGAACAACCGAACAAGC 59.248 43.478 0.00 0.00 44.74 4.01
4376 6015 6.834168 TCATGGAAAAGAATAGGAACAACC 57.166 37.500 0.00 0.00 39.35 3.77
4377 6016 7.416777 GGGATCATGGAAAAGAATAGGAACAAC 60.417 40.741 0.00 0.00 0.00 3.32
4389 6032 2.950309 CTCTGCAGGGATCATGGAAAAG 59.050 50.000 8.28 0.00 0.00 2.27
4413 6060 3.321396 TGCCTCAGATCAAACAATGCAAA 59.679 39.130 0.00 0.00 0.00 3.68
4626 6273 2.204237 CATTCGATGATGAAGCCGACA 58.796 47.619 0.00 0.00 0.00 4.35
4653 6300 0.687427 TGACGAGGATGAGGATGGCA 60.687 55.000 0.00 0.00 0.00 4.92
4692 6339 1.234821 TTACCTGAGCAAAGTTGGCG 58.765 50.000 0.00 0.00 36.08 5.69
4734 6382 4.344679 TGGTTTTAGTTCAGAACCGAGGTA 59.655 41.667 9.85 0.00 44.49 3.08
4735 6383 3.135167 TGGTTTTAGTTCAGAACCGAGGT 59.865 43.478 9.85 0.00 44.49 3.85
4739 6387 2.867975 ACGTGGTTTTAGTTCAGAACCG 59.132 45.455 9.85 6.27 44.49 4.44
4740 6388 3.872771 TGACGTGGTTTTAGTTCAGAACC 59.127 43.478 9.85 0.00 42.44 3.62
4741 6389 4.569564 ACTGACGTGGTTTTAGTTCAGAAC 59.430 41.667 5.00 5.00 0.00 3.01
4742 6390 4.761975 ACTGACGTGGTTTTAGTTCAGAA 58.238 39.130 0.00 0.00 0.00 3.02
4743 6391 4.395959 ACTGACGTGGTTTTAGTTCAGA 57.604 40.909 0.00 0.00 0.00 3.27
4744 6392 6.780706 ATAACTGACGTGGTTTTAGTTCAG 57.219 37.500 0.00 0.00 33.93 3.02
4745 6393 7.254863 GGAAATAACTGACGTGGTTTTAGTTCA 60.255 37.037 0.00 0.00 31.54 3.18
4758 6434 2.597305 CTCGGTTCGGAAATAACTGACG 59.403 50.000 0.00 0.00 37.32 4.35
4787 6467 6.349243 TCATCCAGCAAACATCTCAAAAAT 57.651 33.333 0.00 0.00 0.00 1.82
4831 6511 3.169733 GCTTACCGTGAAGAACTACTCG 58.830 50.000 0.00 0.00 0.00 4.18
5086 6771 4.523083 CCGGAATTAAACAAGGGATCAGA 58.477 43.478 0.00 0.00 0.00 3.27
5120 6805 4.302622 ACACTGGCCAGAGAGTGT 57.697 55.556 39.19 28.60 46.35 3.55
5126 6811 1.827344 CTGTAGATGACACTGGCCAGA 59.173 52.381 39.19 17.61 33.31 3.86
5133 6818 5.587043 GCTGTAGTAGTCTGTAGATGACACT 59.413 44.000 0.00 0.00 36.94 3.55
5141 6826 3.242478 GCGAGTGCTGTAGTAGTCTGTAG 60.242 52.174 3.84 0.00 38.39 2.74
5142 6827 2.676839 GCGAGTGCTGTAGTAGTCTGTA 59.323 50.000 3.84 0.00 38.39 2.74
5143 6828 1.469308 GCGAGTGCTGTAGTAGTCTGT 59.531 52.381 3.84 0.00 38.39 3.41
5144 6829 1.202200 GGCGAGTGCTGTAGTAGTCTG 60.202 57.143 3.84 0.00 42.25 3.51
5145 6830 1.096416 GGCGAGTGCTGTAGTAGTCT 58.904 55.000 3.84 0.00 42.25 3.24
5146 6831 0.248134 CGGCGAGTGCTGTAGTAGTC 60.248 60.000 0.00 0.00 42.79 2.59
5147 6832 1.801332 CGGCGAGTGCTGTAGTAGT 59.199 57.895 0.00 0.00 42.79 2.73
5148 6833 4.692129 CGGCGAGTGCTGTAGTAG 57.308 61.111 0.00 0.00 42.79 2.57
5160 6845 0.320073 CTGGGAGTTGTTTACGGCGA 60.320 55.000 16.62 0.00 0.00 5.54
5243 6928 2.233676 TCCACAATAGAAGAAGCAGCGA 59.766 45.455 0.00 0.00 0.00 4.93
5256 6944 5.603813 TGACCATCTCATCTCATCCACAATA 59.396 40.000 0.00 0.00 0.00 1.90
5257 6945 4.411212 TGACCATCTCATCTCATCCACAAT 59.589 41.667 0.00 0.00 0.00 2.71
5377 7066 2.238701 AAAGGCCCCAGATTCCCGT 61.239 57.895 0.00 0.00 0.00 5.28
5378 7067 1.754234 CAAAGGCCCCAGATTCCCG 60.754 63.158 0.00 0.00 0.00 5.14
5652 7359 1.406069 CCGTTCCAGTATGCAAGAGCT 60.406 52.381 0.00 0.00 42.74 4.09
5667 7374 0.944311 ATGCGTGGCGATATCCGTTC 60.944 55.000 0.00 0.00 41.15 3.95
5712 7419 9.829507 ACAATCTCATTACTACTACGTAGTACT 57.170 33.333 27.51 21.23 46.86 2.73
5744 7460 7.893824 GCAAATCGCAACAACAATGAATAATA 58.106 30.769 0.00 0.00 41.79 0.98
5787 7503 6.916401 TTGAATTGAACAGTACGTACGTAG 57.084 37.500 27.48 18.92 0.00 3.51
5788 7504 7.060979 GTCATTGAATTGAACAGTACGTACGTA 59.939 37.037 23.60 23.60 0.00 3.57
5789 7505 5.921976 TCATTGAATTGAACAGTACGTACGT 59.078 36.000 25.98 25.98 0.00 3.57
6156 7872 2.434185 TTGGCGGTGATGACGAGC 60.434 61.111 0.00 0.00 0.00 5.03
6438 8154 1.901085 GATGACGGTGCTCTTCCCT 59.099 57.895 0.00 0.00 0.00 4.20
6702 8418 3.751246 CCGACGGGCGTCCTGTAA 61.751 66.667 5.81 0.00 44.10 2.41
7056 8772 1.153086 GAGCAGGACGCCAATCCAT 60.153 57.895 0.00 0.00 44.04 3.41
7098 8816 0.966370 AAAGCTCGCCTCGGTCTACT 60.966 55.000 0.00 0.00 0.00 2.57
7142 8860 1.429423 GCCGCACTACAGCAAATCC 59.571 57.895 0.00 0.00 0.00 3.01
7167 8885 3.632145 GGCTAACACCTATCACCATTTGG 59.368 47.826 0.00 0.00 42.17 3.28
7266 8990 0.811616 CTGCCGAAGCTGGACATACC 60.812 60.000 0.00 0.00 40.80 2.73
7267 8991 0.175760 TCTGCCGAAGCTGGACATAC 59.824 55.000 0.00 0.00 40.80 2.39
7275 8999 3.057245 GGAAAAGAAATTCTGCCGAAGCT 60.057 43.478 0.00 0.00 40.80 3.74
7330 9054 5.106948 ACTCAGCAAAACATACTCGTTCATG 60.107 40.000 0.00 0.00 0.00 3.07
7331 9055 4.997395 ACTCAGCAAAACATACTCGTTCAT 59.003 37.500 0.00 0.00 0.00 2.57
7334 9058 4.377021 TCACTCAGCAAAACATACTCGTT 58.623 39.130 0.00 0.00 0.00 3.85
7335 9059 3.990092 TCACTCAGCAAAACATACTCGT 58.010 40.909 0.00 0.00 0.00 4.18
7336 9060 5.349817 AGAATCACTCAGCAAAACATACTCG 59.650 40.000 0.00 0.00 0.00 4.18
7349 10545 4.397481 TCATGGCAGTAGAATCACTCAG 57.603 45.455 0.00 0.00 0.00 3.35
7380 10576 2.110967 CCGCACCCTCATGCTTCAG 61.111 63.158 0.00 0.00 43.80 3.02
7381 10577 2.046023 CCGCACCCTCATGCTTCA 60.046 61.111 0.00 0.00 43.80 3.02
7422 10618 1.693083 GCACCGAAAATCCCGAGTCG 61.693 60.000 5.29 5.29 0.00 4.18
7423 10619 1.693083 CGCACCGAAAATCCCGAGTC 61.693 60.000 0.00 0.00 0.00 3.36
7435 10631 3.998672 GGAAGGACACCGCACCGA 61.999 66.667 0.00 0.00 0.00 4.69
7448 10645 2.426522 TGCAACGGAGATTGAAGGAAG 58.573 47.619 0.00 0.00 0.00 3.46
7463 10660 0.579630 TCGTCGTCACACATTGCAAC 59.420 50.000 0.00 0.00 0.00 4.17
7482 10679 4.443266 GCTCCGAGCAGCGAAGGT 62.443 66.667 15.78 0.00 44.57 3.50
7489 10686 3.160047 ATCAGGGGCTCCGAGCAG 61.160 66.667 21.76 8.58 44.75 4.24
7502 10699 0.036952 ACAAGGCTGGTCGTCATCAG 60.037 55.000 0.00 0.00 0.00 2.90
7523 10720 0.097674 CAAGCATGTAGTTGAGCCGC 59.902 55.000 0.00 0.00 0.00 6.53
7544 10741 3.345714 CGCAAGTGAAAATCATACTCGC 58.654 45.455 0.00 0.00 0.00 5.03
7564 10761 2.898729 ATTAGAGGTGAGATGCCACG 57.101 50.000 0.00 0.00 37.91 4.94
7608 10805 4.153475 CGATTCACAATAACTTTCCACGGT 59.847 41.667 0.00 0.00 0.00 4.83
7609 10806 4.647964 CGATTCACAATAACTTTCCACGG 58.352 43.478 0.00 0.00 0.00 4.94
7631 10829 3.426695 CCGTCAAATCCAAGTCTTCATGC 60.427 47.826 0.00 0.00 0.00 4.06
7637 10835 1.072331 AGCACCGTCAAATCCAAGTCT 59.928 47.619 0.00 0.00 0.00 3.24
7670 10868 1.075601 TTCACCCTGGAGCTCCAAAT 58.924 50.000 34.30 20.31 46.97 2.32
7672 10870 0.850100 TTTTCACCCTGGAGCTCCAA 59.150 50.000 34.30 18.17 46.97 3.53
7674 10872 0.402121 AGTTTTCACCCTGGAGCTCC 59.598 55.000 26.78 26.78 0.00 4.70
7680 10878 0.179029 ACCACGAGTTTTCACCCTGG 60.179 55.000 0.00 0.00 0.00 4.45
7682 10880 1.129058 AGACCACGAGTTTTCACCCT 58.871 50.000 0.00 0.00 0.00 4.34
7722 10921 4.335315 ACGACACAAAAACATCATCAGTGT 59.665 37.500 0.00 0.00 40.96 3.55
7725 10924 4.847633 ACACGACACAAAAACATCATCAG 58.152 39.130 0.00 0.00 0.00 2.90
7728 10927 3.882888 AGGACACGACACAAAAACATCAT 59.117 39.130 0.00 0.00 0.00 2.45
7755 10954 1.029681 GAAACCCGAACAGTGCCTTT 58.970 50.000 0.00 0.00 0.00 3.11
7764 10963 1.607148 CAAGTCCAAGGAAACCCGAAC 59.393 52.381 0.00 0.00 0.00 3.95
7769 10968 3.951680 TGAAGAACAAGTCCAAGGAAACC 59.048 43.478 0.00 0.00 0.00 3.27
7770 10969 5.299279 TCATGAAGAACAAGTCCAAGGAAAC 59.701 40.000 0.00 0.00 0.00 2.78
7771 10970 5.299279 GTCATGAAGAACAAGTCCAAGGAAA 59.701 40.000 0.00 0.00 0.00 3.13
7775 10974 5.756195 TTGTCATGAAGAACAAGTCCAAG 57.244 39.130 0.00 0.00 0.00 3.61
7792 10991 5.063204 AGGTCAGATCGTCAATTTTTGTCA 58.937 37.500 0.00 0.00 0.00 3.58
7794 10993 6.208644 CAAAGGTCAGATCGTCAATTTTTGT 58.791 36.000 0.00 0.00 0.00 2.83
7795 10994 5.630680 CCAAAGGTCAGATCGTCAATTTTTG 59.369 40.000 0.00 0.00 0.00 2.44
7796 10995 5.301805 ACCAAAGGTCAGATCGTCAATTTTT 59.698 36.000 0.00 0.00 0.00 1.94
7803 11002 2.767505 ACAACCAAAGGTCAGATCGTC 58.232 47.619 0.00 0.00 33.12 4.20
7805 11004 4.389077 GTCTAACAACCAAAGGTCAGATCG 59.611 45.833 0.00 0.00 33.12 3.69
7822 11021 0.730494 CCGTTGTCGTCGGGTCTAAC 60.730 60.000 0.00 0.00 43.68 2.34
7824 11023 2.981560 GCCGTTGTCGTCGGGTCTA 61.982 63.158 6.50 0.00 46.90 2.59
7830 11029 4.117372 GAAGCGCCGTTGTCGTCG 62.117 66.667 2.29 0.00 41.33 5.12
7831 11030 2.480426 CTTGAAGCGCCGTTGTCGTC 62.480 60.000 2.29 0.00 35.01 4.20
7832 11031 2.586635 TTGAAGCGCCGTTGTCGT 60.587 55.556 2.29 0.00 35.01 4.34
7833 11032 2.170985 CTTGAAGCGCCGTTGTCG 59.829 61.111 2.29 0.00 0.00 4.35
7834 11033 1.782028 AACCTTGAAGCGCCGTTGTC 61.782 55.000 2.29 0.00 0.00 3.18
7835 11034 1.822186 AACCTTGAAGCGCCGTTGT 60.822 52.632 2.29 0.00 0.00 3.32
7836 11035 1.370414 CAACCTTGAAGCGCCGTTG 60.370 57.895 2.29 3.75 0.00 4.10
7837 11036 1.381165 AACAACCTTGAAGCGCCGTT 61.381 50.000 2.29 0.00 0.00 4.44
7838 11037 1.782028 GAACAACCTTGAAGCGCCGT 61.782 55.000 2.29 0.00 0.00 5.68
7839 11038 1.082104 GAACAACCTTGAAGCGCCG 60.082 57.895 2.29 0.00 0.00 6.46
7840 11039 1.285950 GGAACAACCTTGAAGCGCC 59.714 57.895 2.29 0.00 35.41 6.53
7841 11040 1.285950 GGGAACAACCTTGAAGCGC 59.714 57.895 0.00 0.00 38.98 5.92
7842 11041 0.537371 AGGGGAACAACCTTGAAGCG 60.537 55.000 0.00 0.00 33.64 4.68
7843 11042 1.704641 AAGGGGAACAACCTTGAAGC 58.295 50.000 0.00 0.00 46.21 3.86
7849 11048 7.147461 TGCTTTAATTTAAAAGGGGAACAACCT 60.147 33.333 3.37 0.00 40.96 3.50
7850 11049 6.993308 TGCTTTAATTTAAAAGGGGAACAACC 59.007 34.615 3.37 0.00 37.03 3.77
7851 11050 8.615878 ATGCTTTAATTTAAAAGGGGAACAAC 57.384 30.769 3.37 0.00 37.03 3.32
7852 11051 7.880713 GGATGCTTTAATTTAAAAGGGGAACAA 59.119 33.333 3.37 0.00 37.03 2.83
7853 11052 7.236640 AGGATGCTTTAATTTAAAAGGGGAACA 59.763 33.333 3.37 0.00 37.03 3.18
7854 11053 7.620880 AGGATGCTTTAATTTAAAAGGGGAAC 58.379 34.615 3.37 0.00 37.03 3.62
7855 11054 7.806680 AGGATGCTTTAATTTAAAAGGGGAA 57.193 32.000 3.37 0.00 37.03 3.97
7856 11055 7.678171 AGAAGGATGCTTTAATTTAAAAGGGGA 59.322 33.333 0.00 0.00 37.03 4.81
7857 11056 7.851228 AGAAGGATGCTTTAATTTAAAAGGGG 58.149 34.615 0.00 0.00 37.03 4.79
7858 11057 7.702348 CGAGAAGGATGCTTTAATTTAAAAGGG 59.298 37.037 0.00 0.00 37.03 3.95
7859 11058 8.244113 ACGAGAAGGATGCTTTAATTTAAAAGG 58.756 33.333 0.00 0.00 37.03 3.11
7860 11059 9.626045 AACGAGAAGGATGCTTTAATTTAAAAG 57.374 29.630 0.00 0.00 39.10 2.27
7861 11060 9.405587 CAACGAGAAGGATGCTTTAATTTAAAA 57.594 29.630 0.00 0.00 0.00 1.52
7862 11061 8.573035 ACAACGAGAAGGATGCTTTAATTTAAA 58.427 29.630 0.00 1.85 0.00 1.52
7863 11062 8.106247 ACAACGAGAAGGATGCTTTAATTTAA 57.894 30.769 0.00 0.00 0.00 1.52
7864 11063 7.681939 ACAACGAGAAGGATGCTTTAATTTA 57.318 32.000 0.00 0.00 0.00 1.40
7865 11064 6.575162 ACAACGAGAAGGATGCTTTAATTT 57.425 33.333 0.00 0.00 0.00 1.82
7866 11065 6.879458 AGTACAACGAGAAGGATGCTTTAATT 59.121 34.615 0.00 0.00 0.00 1.40
7867 11066 6.407202 AGTACAACGAGAAGGATGCTTTAAT 58.593 36.000 0.00 0.00 0.00 1.40
7870 11069 4.273148 AGTACAACGAGAAGGATGCTTT 57.727 40.909 0.00 0.00 0.00 3.51
7889 11088 7.048512 GCCTACCATCTTTTAACATCACTAGT 58.951 38.462 0.00 0.00 0.00 2.57
7890 11089 6.201044 CGCCTACCATCTTTTAACATCACTAG 59.799 42.308 0.00 0.00 0.00 2.57
7891 11090 6.046593 CGCCTACCATCTTTTAACATCACTA 58.953 40.000 0.00 0.00 0.00 2.74
7892 11091 4.876107 CGCCTACCATCTTTTAACATCACT 59.124 41.667 0.00 0.00 0.00 3.41
7910 11109 2.013400 CAACAACCATGTATGCGCCTA 58.987 47.619 4.18 0.00 39.40 3.93
7911 11110 0.810648 CAACAACCATGTATGCGCCT 59.189 50.000 4.18 0.00 39.40 5.52
7914 14330 3.763097 ACATCAACAACCATGTATGCG 57.237 42.857 0.00 0.00 39.40 4.73
8018 14435 3.449018 ACACATAAAACCACACCAGCAAA 59.551 39.130 0.00 0.00 0.00 3.68
8024 14441 1.928595 GCGCACACATAAAACCACACC 60.929 52.381 0.30 0.00 0.00 4.16
8029 14446 1.065031 CAGCGCGCACACATAAAACC 61.065 55.000 35.10 0.00 0.00 3.27
8030 14447 0.110419 TCAGCGCGCACACATAAAAC 60.110 50.000 35.10 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.