Multiple sequence alignment - TraesCS6A01G280100

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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 TraesCS6A01G280100 chr6A 100.000 3449 0 0 1 3449 508332402 508335850 0.000000e+00 6370.0
1 TraesCS6A01G280100 chr6A 90.053 1327 110 15 1129 2438 508293846 508295167 0.000000e+00 1700.0
2 TraesCS6A01G280100 chr6A 89.125 1177 119 1 1271 2438 509562291 509561115 0.000000e+00 1456.0
3 TraesCS6A01G280100 chr6A 87.490 1271 114 20 1205 2438 509285860 509284598 0.000000e+00 1424.0
4 TraesCS6A01G280100 chr6A 89.308 159 14 2 2448 2603 508295401 508295559 2.720000e-46 196.0
5 TraesCS6A01G280100 chr6D 93.760 1811 82 14 798 2604 367875486 367877269 0.000000e+00 2689.0
6 TraesCS6A01G280100 chr6D 91.583 1200 90 8 1248 2438 367864886 367866083 0.000000e+00 1646.0
7 TraesCS6A01G280100 chr6D 90.059 1177 106 3 1272 2438 368372233 368371058 0.000000e+00 1515.0
8 TraesCS6A01G280100 chr6D 89.169 1191 116 3 1260 2438 368741035 368739846 0.000000e+00 1472.0
9 TraesCS6A01G280100 chr6D 93.354 632 42 0 2603 3234 367877463 367878094 0.000000e+00 935.0
10 TraesCS6A01G280100 chr6D 87.789 303 34 3 207 509 367873785 367874084 5.480000e-93 351.0
11 TraesCS6A01G280100 chr6D 86.957 207 25 2 1 206 367873545 367873750 7.440000e-57 231.0
12 TraesCS6A01G280100 chr6D 95.172 145 5 2 3280 3423 367884773 367884916 9.630000e-56 228.0
13 TraesCS6A01G280100 chr6D 90.116 172 14 3 2435 2603 367866305 367866476 1.610000e-53 220.0
14 TraesCS6A01G280100 chr6B 95.780 1564 49 8 1057 2604 554123961 554122399 0.000000e+00 2507.0
15 TraesCS6A01G280100 chr6B 89.898 1376 104 22 1083 2438 554165769 554164409 0.000000e+00 1738.0
16 TraesCS6A01G280100 chr6B 84.136 706 85 8 2626 3330 554122177 554121498 0.000000e+00 658.0
17 TraesCS6A01G280100 chr6B 83.934 361 18 13 736 1065 554125868 554125517 3.340000e-80 309.0
18 TraesCS6A01G280100 chr6B 85.782 211 26 2 210 417 554127699 554127490 1.610000e-53 220.0
19 TraesCS6A01G280100 chr6B 83.582 201 31 2 10 209 554127933 554127734 1.630000e-43 187.0
20 TraesCS6A01G280100 chr7D 77.285 383 66 10 2603 2983 509561592 509561229 4.510000e-49 206.0
21 TraesCS6A01G280100 chr7D 74.607 382 70 18 2610 2983 420766423 420766785 3.590000e-30 143.0
22 TraesCS6A01G280100 chr5A 80.687 233 38 5 2747 2977 120744618 120744845 1.270000e-39 174.0
23 TraesCS6A01G280100 chr4D 81.221 213 38 2 2772 2983 13309509 13309298 1.650000e-38 171.0
24 TraesCS6A01G280100 chr2D 80.328 244 31 16 2747 2984 477275140 477275372 5.920000e-38 169.0
25 TraesCS6A01G280100 chr5D 78.390 236 46 3 2745 2979 461043246 461043477 7.710000e-32 148.0
26 TraesCS6A01G280100 chr1B 82.659 173 24 4 2747 2918 328993618 328993451 7.710000e-32 148.0
27 TraesCS6A01G280100 chr2A 77.381 168 33 5 2818 2983 79399855 79400019 1.020000e-15 95.3


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 TraesCS6A01G280100 chr6A 508332402 508335850 3448 False 6370.0 6370 100.0000 1 3449 1 chr6A.!!$F1 3448
1 TraesCS6A01G280100 chr6A 509561115 509562291 1176 True 1456.0 1456 89.1250 1271 2438 1 chr6A.!!$R2 1167
2 TraesCS6A01G280100 chr6A 509284598 509285860 1262 True 1424.0 1424 87.4900 1205 2438 1 chr6A.!!$R1 1233
3 TraesCS6A01G280100 chr6A 508293846 508295559 1713 False 948.0 1700 89.6805 1129 2603 2 chr6A.!!$F2 1474
4 TraesCS6A01G280100 chr6D 368371058 368372233 1175 True 1515.0 1515 90.0590 1272 2438 1 chr6D.!!$R1 1166
5 TraesCS6A01G280100 chr6D 368739846 368741035 1189 True 1472.0 1472 89.1690 1260 2438 1 chr6D.!!$R2 1178
6 TraesCS6A01G280100 chr6D 367873545 367878094 4549 False 1051.5 2689 90.4650 1 3234 4 chr6D.!!$F3 3233
7 TraesCS6A01G280100 chr6D 367864886 367866476 1590 False 933.0 1646 90.8495 1248 2603 2 chr6D.!!$F2 1355
8 TraesCS6A01G280100 chr6B 554164409 554165769 1360 True 1738.0 1738 89.8980 1083 2438 1 chr6B.!!$R1 1355
9 TraesCS6A01G280100 chr6B 554121498 554127933 6435 True 776.2 2507 86.6428 10 3330 5 chr6B.!!$R2 3320

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
95 96 0.179215 GAATGACGCAGCAGGAAACG 60.179 55.0 0.00 0.00 0.0 3.60 F
777 2197 0.187361 ATAGGAGCTCGAGAAGGCCT 59.813 55.0 18.75 17.25 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1158 5323 1.089112 CAAGCAGATCGCCATGAACA 58.911 50.0 0.00 0.00 44.04 3.18 R
2519 6969 0.521867 CCAATGCAATGACAGACGCG 60.522 55.0 3.53 3.53 0.00 6.01 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
25 26 1.136305 GTCATAGCTACAACGGGAGCA 59.864 52.381 0.00 0.00 41.36 4.26
31 32 1.876416 GCTACAACGGGAGCAGACAAA 60.876 52.381 0.00 0.00 38.62 2.83
36 37 2.317609 CGGGAGCAGACAAACACGG 61.318 63.158 0.00 0.00 0.00 4.94
62 63 4.101448 GGCGCCAGGTCTGACCAT 62.101 66.667 27.48 10.84 41.95 3.55
68 69 1.866015 CCAGGTCTGACCATGTCCTA 58.134 55.000 27.48 0.00 41.95 2.94
75 76 5.192522 AGGTCTGACCATGTCCTATTTGATT 59.807 40.000 27.48 0.00 41.95 2.57
92 93 1.739466 GATTGAATGACGCAGCAGGAA 59.261 47.619 0.00 0.00 0.00 3.36
95 96 0.179215 GAATGACGCAGCAGGAAACG 60.179 55.000 0.00 0.00 0.00 3.60
96 97 1.577328 AATGACGCAGCAGGAAACGG 61.577 55.000 0.00 0.00 0.00 4.44
117 118 4.881850 CGGTACATATTTTGCTCCTTTCCT 59.118 41.667 0.00 0.00 0.00 3.36
119 120 6.018180 CGGTACATATTTTGCTCCTTTCCTAC 60.018 42.308 0.00 0.00 0.00 3.18
168 170 9.801873 AATCAATTACAATTAGTTGCATGTACC 57.198 29.630 0.00 0.00 38.96 3.34
183 185 5.181433 TGCATGTACCGTTAGTTTATTTGCA 59.819 36.000 0.00 0.00 0.00 4.08
189 191 6.178239 ACCGTTAGTTTATTTGCAGTCATC 57.822 37.500 0.00 0.00 0.00 2.92
206 208 8.623903 TGCAGTCATCATAATTTTAGGACAATC 58.376 33.333 0.00 0.00 0.00 2.67
216 252 9.713684 ATAATTTTAGGACAATCTCCCAAATGA 57.286 29.630 0.00 0.00 40.53 2.57
227 263 9.178758 ACAATCTCCCAAATGAACTATTACTTC 57.821 33.333 0.00 0.00 0.00 3.01
235 271 7.068226 CCAAATGAACTATTACTTCGGGGATTT 59.932 37.037 0.00 0.00 0.00 2.17
262 298 1.068895 TCCTACGTTTGAAGTTGGCGA 59.931 47.619 0.00 0.00 35.10 5.54
264 300 2.482721 CCTACGTTTGAAGTTGGCGAAT 59.517 45.455 0.00 0.00 0.00 3.34
298 334 5.294306 CCAAAAGGAAAAGAAAGGCAAAGAC 59.706 40.000 0.00 0.00 0.00 3.01
299 335 5.675684 AAAGGAAAAGAAAGGCAAAGACA 57.324 34.783 0.00 0.00 0.00 3.41
304 340 2.452600 AGAAAGGCAAAGACACCCAA 57.547 45.000 0.00 0.00 0.00 4.12
305 341 2.031870 AGAAAGGCAAAGACACCCAAC 58.968 47.619 0.00 0.00 0.00 3.77
307 343 0.395173 AAGGCAAAGACACCCAACGT 60.395 50.000 0.00 0.00 0.00 3.99
350 389 8.778059 ACAATATTTGAGGGTATCTTCTTGGTA 58.222 33.333 0.00 0.00 0.00 3.25
364 403 3.637769 TCTTGGTAAAAGCTTGGTTGGT 58.362 40.909 0.00 0.00 0.00 3.67
367 406 2.691011 TGGTAAAAGCTTGGTTGGTCAC 59.309 45.455 0.00 0.00 0.00 3.67
391 430 3.012518 GCATGGATCCTATATGTGGCAC 58.987 50.000 14.23 11.55 0.00 5.01
434 473 6.846350 AGTATTGAGAAAAGATTTGGAAGCG 58.154 36.000 0.00 0.00 0.00 4.68
449 488 4.068599 TGGAAGCGTTATCATGAACACAA 58.931 39.130 0.00 0.00 0.00 3.33
459 498 8.171196 CGTTATCATGAACACAAGGATATATGC 58.829 37.037 0.00 0.00 0.00 3.14
461 500 4.452114 TCATGAACACAAGGATATATGCGC 59.548 41.667 0.00 0.00 0.00 6.09
485 524 4.165950 AGCCACATCCTATCATTAACACCA 59.834 41.667 0.00 0.00 0.00 4.17
494 533 6.430925 TCCTATCATTAACACCAGCAATATGC 59.569 38.462 0.00 0.00 45.46 3.14
499 538 0.921896 ACACCAGCAATATGCCCTCT 59.078 50.000 0.00 0.00 46.52 3.69
500 539 1.133976 ACACCAGCAATATGCCCTCTC 60.134 52.381 0.00 0.00 46.52 3.20
501 540 1.142465 CACCAGCAATATGCCCTCTCT 59.858 52.381 0.00 0.00 46.52 3.10
503 542 1.698532 CCAGCAATATGCCCTCTCTCT 59.301 52.381 0.00 0.00 46.52 3.10
505 544 3.326006 CCAGCAATATGCCCTCTCTCTAA 59.674 47.826 0.00 0.00 46.52 2.10
506 545 4.314121 CAGCAATATGCCCTCTCTCTAAC 58.686 47.826 0.00 0.00 46.52 2.34
507 546 3.969976 AGCAATATGCCCTCTCTCTAACA 59.030 43.478 0.00 0.00 46.52 2.41
508 547 4.596643 AGCAATATGCCCTCTCTCTAACAT 59.403 41.667 0.00 0.00 46.52 2.71
509 548 5.072872 AGCAATATGCCCTCTCTCTAACATT 59.927 40.000 0.00 0.00 46.52 2.71
510 549 5.767168 GCAATATGCCCTCTCTCTAACATTT 59.233 40.000 0.00 0.00 37.42 2.32
512 551 7.201857 GCAATATGCCCTCTCTCTAACATTTTT 60.202 37.037 0.00 0.00 37.42 1.94
530 569 3.909651 TTTTTGCGGGGGCCCTCT 61.910 61.111 22.56 0.00 0.00 3.69
531 570 3.879180 TTTTTGCGGGGGCCCTCTC 62.879 63.158 22.56 13.88 0.00 3.20
535 574 4.541648 GCGGGGGCCCTCTCTCTA 62.542 72.222 22.56 0.00 0.00 2.43
536 575 2.282446 CGGGGGCCCTCTCTCTAA 59.718 66.667 22.56 0.00 0.00 2.10
537 576 2.134933 CGGGGGCCCTCTCTCTAAC 61.135 68.421 22.56 0.00 0.00 2.34
538 577 1.003051 GGGGGCCCTCTCTCTAACA 59.997 63.158 24.38 0.00 0.00 2.41
539 578 0.400670 GGGGGCCCTCTCTCTAACAT 60.401 60.000 24.38 0.00 0.00 2.71
540 579 1.512735 GGGGCCCTCTCTCTAACATT 58.487 55.000 24.38 0.00 0.00 2.71
541 580 1.141858 GGGGCCCTCTCTCTAACATTG 59.858 57.143 24.38 0.00 0.00 2.82
542 581 2.119495 GGGCCCTCTCTCTAACATTGA 58.881 52.381 17.04 0.00 0.00 2.57
543 582 2.158885 GGGCCCTCTCTCTAACATTGAC 60.159 54.545 17.04 0.00 0.00 3.18
544 583 2.482142 GGCCCTCTCTCTAACATTGACG 60.482 54.545 0.00 0.00 0.00 4.35
545 584 2.482142 GCCCTCTCTCTAACATTGACGG 60.482 54.545 0.00 0.00 0.00 4.79
546 585 2.761208 CCCTCTCTCTAACATTGACGGT 59.239 50.000 0.00 0.00 0.00 4.83
547 586 3.181485 CCCTCTCTCTAACATTGACGGTC 60.181 52.174 0.00 0.00 0.00 4.79
548 587 3.181485 CCTCTCTCTAACATTGACGGTCC 60.181 52.174 5.55 0.00 0.00 4.46
549 588 3.427573 TCTCTCTAACATTGACGGTCCA 58.572 45.455 5.55 0.00 0.00 4.02
550 589 4.023980 TCTCTCTAACATTGACGGTCCAT 58.976 43.478 5.55 0.00 0.00 3.41
551 590 4.098044 TCTCTCTAACATTGACGGTCCATC 59.902 45.833 5.55 0.00 0.00 3.51
552 591 4.023980 TCTCTAACATTGACGGTCCATCT 58.976 43.478 5.55 0.00 0.00 2.90
553 592 5.198207 TCTCTAACATTGACGGTCCATCTA 58.802 41.667 5.55 0.00 0.00 1.98
554 593 5.833667 TCTCTAACATTGACGGTCCATCTAT 59.166 40.000 5.55 0.00 0.00 1.98
577 616 4.705337 AGAGGAAGTGAACGAGTATGTC 57.295 45.455 0.00 0.00 0.00 3.06
589 628 3.833442 CGAGTATGTCGGCTATTATGCA 58.167 45.455 0.00 0.00 45.58 3.96
596 635 2.936498 GTCGGCTATTATGCACAAGTGT 59.064 45.455 1.79 0.00 34.04 3.55
610 649 3.670377 GTGTTTGGCCGCCCTCAC 61.670 66.667 7.03 9.65 0.00 3.51
613 652 4.659172 TTTGGCCGCCCTCACAGG 62.659 66.667 7.03 0.00 34.30 4.00
631 670 2.432510 CAGGGAGATAGGAGTGTCAACC 59.567 54.545 0.00 0.00 0.00 3.77
632 671 2.044492 AGGGAGATAGGAGTGTCAACCA 59.956 50.000 0.00 0.00 0.00 3.67
633 672 2.168728 GGGAGATAGGAGTGTCAACCAC 59.831 54.545 0.00 0.00 44.89 4.16
662 701 6.877236 AGTTGAATTGTTCCATTTTGTCACT 58.123 32.000 0.00 0.00 0.00 3.41
695 734 7.080353 GTGAACACCAAGTTGTAAGTTAAGT 57.920 36.000 1.45 0.00 41.51 2.24
696 735 6.964934 GTGAACACCAAGTTGTAAGTTAAGTG 59.035 38.462 1.45 2.92 41.51 3.16
699 738 7.316544 ACACCAAGTTGTAAGTTAAGTGAAG 57.683 36.000 15.68 0.00 32.94 3.02
711 750 6.693315 AGTTAAGTGAAGCAAGTTAGCAAA 57.307 33.333 0.00 0.00 36.85 3.68
717 756 5.067674 AGTGAAGCAAGTTAGCAAATTGTGA 59.932 36.000 9.59 0.00 36.85 3.58
725 764 6.670695 AGTTAGCAAATTGTGAGGGAAAAT 57.329 33.333 0.00 0.00 0.00 1.82
734 773 9.793252 CAAATTGTGAGGGAAAATATAGAGTTG 57.207 33.333 0.00 0.00 0.00 3.16
740 2160 7.713073 GTGAGGGAAAATATAGAGTTGGAGAAG 59.287 40.741 0.00 0.00 0.00 2.85
741 2161 7.623677 TGAGGGAAAATATAGAGTTGGAGAAGA 59.376 37.037 0.00 0.00 0.00 2.87
774 2194 5.067936 TGTCTTAAATAGGAGCTCGAGAAGG 59.932 44.000 18.75 0.00 0.00 3.46
775 2195 2.900716 AAATAGGAGCTCGAGAAGGC 57.099 50.000 18.75 0.33 0.00 4.35
776 2196 1.044611 AATAGGAGCTCGAGAAGGCC 58.955 55.000 18.75 10.72 0.00 5.19
777 2197 0.187361 ATAGGAGCTCGAGAAGGCCT 59.813 55.000 18.75 17.25 0.00 5.19
778 2198 0.466555 TAGGAGCTCGAGAAGGCCTC 60.467 60.000 18.75 12.36 38.55 4.70
779 2199 2.791868 GGAGCTCGAGAAGGCCTCC 61.792 68.421 18.75 17.65 38.71 4.30
780 2200 1.756561 GAGCTCGAGAAGGCCTCCT 60.757 63.158 18.75 0.00 38.71 3.69
781 2201 0.466555 GAGCTCGAGAAGGCCTCCTA 60.467 60.000 18.75 0.00 38.71 2.94
783 2203 0.466555 GCTCGAGAAGGCCTCCTAGA 60.467 60.000 18.75 2.80 38.71 2.43
784 2204 1.604604 CTCGAGAAGGCCTCCTAGAG 58.395 60.000 14.51 14.51 38.71 2.43
806 3376 6.712547 AGAGGCATAGTTACATGAATTTAGCC 59.287 38.462 0.00 4.68 37.52 3.93
832 3402 0.899019 TACATGTGAAGCCGCTGGTA 59.101 50.000 9.11 0.00 0.00 3.25
907 3480 1.213537 CCAAACTTGCCATGCCGAG 59.786 57.895 0.00 0.00 0.00 4.63
928 3501 1.628447 GCGTGCGTATGGAAACGGAA 61.628 55.000 0.00 0.00 44.91 4.30
937 3534 2.693285 GAAACGGAACCGATCGCG 59.307 61.111 20.14 10.50 42.83 5.87
979 3576 2.806945 ACCGTGGGATGATGATGTTT 57.193 45.000 0.00 0.00 0.00 2.83
1002 3599 3.945434 GTGGCGGCAGATGCGATG 61.945 66.667 13.91 0.00 43.26 3.84
1067 5228 3.556306 CCTCCACCACCACCGTGT 61.556 66.667 0.00 0.00 38.41 4.49
1158 5323 8.639761 AGTATAACCAACTTGCTAGATATCGTT 58.360 33.333 1.04 0.12 0.00 3.85
1168 5333 3.121944 GCTAGATATCGTTGTTCATGGCG 59.878 47.826 0.00 0.00 0.00 5.69
1178 5343 0.248377 GTTCATGGCGATCTGCTTGC 60.248 55.000 8.94 0.00 45.43 4.01
1184 5349 0.737219 GGCGATCTGCTTGCAGAATT 59.263 50.000 26.00 13.08 45.43 2.17
1463 5667 1.834263 CAAGTCCTTCTCCTACCTGGG 59.166 57.143 0.00 0.00 36.20 4.45
1783 6003 1.544825 CGTCCCCAAGCAGAAGGAGA 61.545 60.000 0.00 0.00 0.00 3.71
1854 6074 2.505777 CTCCTCGTCGTGCAGCTG 60.506 66.667 10.11 10.11 0.00 4.24
2015 6235 2.432628 CGTGTCCCTCGCCTTGTC 60.433 66.667 0.00 0.00 0.00 3.18
2393 6616 0.456221 AAGGAGTGCATCTACGTCCG 59.544 55.000 0.00 0.00 32.14 4.79
2519 6969 4.612536 GCCGTGTGTGCTGTGTGC 62.613 66.667 0.00 0.00 43.25 4.57
2607 7271 5.554822 TTATGGCGGAATAACTGAAACAC 57.445 39.130 0.00 0.00 0.00 3.32
2647 7316 2.361119 TCGAGATTCATAAGACCACCGG 59.639 50.000 0.00 0.00 0.00 5.28
2664 7333 1.021390 CGGACGACCACTACTACCGT 61.021 60.000 4.48 0.00 35.21 4.83
2681 7350 2.162716 GTCAAAACGAGCCGCTGAT 58.837 52.632 0.00 0.00 0.00 2.90
2693 7362 1.734117 CGCTGATGTGTCGCTGTCA 60.734 57.895 0.00 0.00 0.00 3.58
2707 7376 1.001120 TGTCATCGCTCCCCTACCA 59.999 57.895 0.00 0.00 0.00 3.25
2745 7414 1.201722 CGACGTCGACGACAACCAAA 61.202 55.000 41.52 0.00 43.02 3.28
2804 7473 2.733593 GAAGCCGCACTCGTCGTT 60.734 61.111 0.00 0.00 0.00 3.85
2815 7484 1.931172 ACTCGTCGTTGTTGAACCTTG 59.069 47.619 0.00 0.00 0.00 3.61
2832 7501 2.543012 CCTTGCATAGATCTGAAGCACG 59.457 50.000 15.33 13.75 34.56 5.34
2849 7518 3.052036 GCACGTGACATCAAATTTTGCT 58.948 40.909 22.23 0.00 0.00 3.91
2864 7533 2.787601 TTGCTACGTGACGAGAAACT 57.212 45.000 13.70 0.00 0.00 2.66
2911 7580 1.007154 GGAATCTACGCCGGAGCTC 60.007 63.158 5.05 4.71 36.60 4.09
2943 7612 3.914312 GTCCAGACGATCAAACTCAAGA 58.086 45.455 0.00 0.00 0.00 3.02
2956 7625 4.779993 AACTCAAGAAGGACCAGAGTTT 57.220 40.909 0.00 0.00 44.54 2.66
2978 7647 7.461182 TTTGGAAGACAAACTCAAAGAAGAA 57.539 32.000 0.00 0.00 43.81 2.52
2981 7650 5.917447 GGAAGACAAACTCAAAGAAGAATGC 59.083 40.000 0.00 0.00 0.00 3.56
3015 7684 0.323178 ATGCCCTGTTTCAGCTCTGG 60.323 55.000 0.00 0.00 0.00 3.86
3183 7852 0.778815 CAGTTTCGCGTCTGTCTGTC 59.221 55.000 5.77 0.00 0.00 3.51
3240 7909 6.740944 TCCTGGAAACTCCGATTATGAATA 57.259 37.500 0.00 0.00 40.17 1.75
3252 7921 4.564372 CGATTATGAATATGAGGACCAGCG 59.436 45.833 0.00 0.00 0.00 5.18
3253 7922 4.955811 TTATGAATATGAGGACCAGCGT 57.044 40.909 0.00 0.00 0.00 5.07
3269 7938 1.576421 CGTTTGGAGCCTCAACTGC 59.424 57.895 0.00 0.00 0.00 4.40
3271 7940 0.538287 GTTTGGAGCCTCAACTGCCT 60.538 55.000 0.00 0.00 0.00 4.75
3272 7941 0.538057 TTTGGAGCCTCAACTGCCTG 60.538 55.000 0.00 0.00 0.00 4.85
3273 7942 1.708993 TTGGAGCCTCAACTGCCTGT 61.709 55.000 0.00 0.00 0.00 4.00
3274 7943 1.376553 GGAGCCTCAACTGCCTGTC 60.377 63.158 0.00 0.00 0.00 3.51
3275 7944 1.676384 GAGCCTCAACTGCCTGTCT 59.324 57.895 0.00 0.00 0.00 3.41
3276 7945 0.036022 GAGCCTCAACTGCCTGTCTT 59.964 55.000 0.00 0.00 0.00 3.01
3277 7946 0.250640 AGCCTCAACTGCCTGTCTTG 60.251 55.000 0.00 0.00 0.00 3.02
3278 7947 1.860484 GCCTCAACTGCCTGTCTTGC 61.860 60.000 0.00 0.00 0.00 4.01
3279 7948 0.535780 CCTCAACTGCCTGTCTTGCA 60.536 55.000 0.00 0.00 37.17 4.08
3280 7949 1.311859 CTCAACTGCCTGTCTTGCAA 58.688 50.000 0.00 0.00 38.46 4.08
3281 7950 1.677576 CTCAACTGCCTGTCTTGCAAA 59.322 47.619 0.00 0.00 38.46 3.68
3282 7951 1.405105 TCAACTGCCTGTCTTGCAAAC 59.595 47.619 0.00 2.76 38.46 2.93
3283 7952 0.381801 AACTGCCTGTCTTGCAAACG 59.618 50.000 0.00 0.00 38.46 3.60
3284 7953 1.283793 CTGCCTGTCTTGCAAACGG 59.716 57.895 0.00 7.06 38.46 4.44
3323 7992 0.760567 ATCTCTCGCCCATGCCTGTA 60.761 55.000 0.00 0.00 0.00 2.74
3327 7996 0.681733 CTCGCCCATGCCTGTACTAT 59.318 55.000 0.00 0.00 0.00 2.12
3330 7999 0.890996 GCCCATGCCTGTACTATGCC 60.891 60.000 0.00 0.00 0.00 4.40
3331 8000 0.767375 CCCATGCCTGTACTATGCCT 59.233 55.000 0.00 0.00 0.00 4.75
3332 8001 1.977854 CCCATGCCTGTACTATGCCTA 59.022 52.381 0.00 0.00 0.00 3.93
3333 8002 2.371841 CCCATGCCTGTACTATGCCTAA 59.628 50.000 0.00 0.00 0.00 2.69
3334 8003 3.181445 CCCATGCCTGTACTATGCCTAAA 60.181 47.826 0.00 0.00 0.00 1.85
3335 8004 4.067896 CCATGCCTGTACTATGCCTAAAG 58.932 47.826 0.00 0.00 0.00 1.85
3336 8005 4.444876 CCATGCCTGTACTATGCCTAAAGT 60.445 45.833 0.00 0.00 0.00 2.66
3337 8006 4.837093 TGCCTGTACTATGCCTAAAGTT 57.163 40.909 0.00 0.00 0.00 2.66
3338 8007 4.513442 TGCCTGTACTATGCCTAAAGTTG 58.487 43.478 0.00 0.00 0.00 3.16
3339 8008 4.224147 TGCCTGTACTATGCCTAAAGTTGA 59.776 41.667 0.00 0.00 0.00 3.18
3340 8009 5.104527 TGCCTGTACTATGCCTAAAGTTGAT 60.105 40.000 0.00 0.00 0.00 2.57
3341 8010 5.237344 GCCTGTACTATGCCTAAAGTTGATG 59.763 44.000 0.00 0.00 0.00 3.07
3342 8011 6.349300 CCTGTACTATGCCTAAAGTTGATGT 58.651 40.000 0.00 0.00 0.00 3.06
3343 8012 6.258727 CCTGTACTATGCCTAAAGTTGATGTG 59.741 42.308 0.00 0.00 0.00 3.21
3344 8013 6.112734 TGTACTATGCCTAAAGTTGATGTGG 58.887 40.000 0.00 0.00 0.00 4.17
3345 8014 4.526970 ACTATGCCTAAAGTTGATGTGGG 58.473 43.478 0.00 0.00 0.00 4.61
3346 8015 2.969821 TGCCTAAAGTTGATGTGGGT 57.030 45.000 0.00 0.00 0.00 4.51
3347 8016 2.513753 TGCCTAAAGTTGATGTGGGTG 58.486 47.619 0.00 0.00 0.00 4.61
3348 8017 1.818674 GCCTAAAGTTGATGTGGGTGG 59.181 52.381 0.00 0.00 0.00 4.61
3349 8018 1.818674 CCTAAAGTTGATGTGGGTGGC 59.181 52.381 0.00 0.00 0.00 5.01
3350 8019 1.818674 CTAAAGTTGATGTGGGTGGCC 59.181 52.381 0.00 0.00 0.00 5.36
3351 8020 1.178534 AAAGTTGATGTGGGTGGCCG 61.179 55.000 0.00 0.00 0.00 6.13
3352 8021 3.061848 GTTGATGTGGGTGGCCGG 61.062 66.667 0.00 0.00 0.00 6.13
3353 8022 4.358841 TTGATGTGGGTGGCCGGG 62.359 66.667 2.18 0.00 0.00 5.73
3377 8046 3.090765 GGCACTCCCTTCCCATGT 58.909 61.111 0.00 0.00 0.00 3.21
3378 8047 1.379044 GGCACTCCCTTCCCATGTG 60.379 63.158 0.00 0.00 0.00 3.21
3379 8048 2.048603 GCACTCCCTTCCCATGTGC 61.049 63.158 0.00 0.00 45.23 4.57
3380 8049 1.379044 CACTCCCTTCCCATGTGCC 60.379 63.158 0.00 0.00 0.00 5.01
3381 8050 1.852157 ACTCCCTTCCCATGTGCCA 60.852 57.895 0.00 0.00 0.00 4.92
3382 8051 1.217057 ACTCCCTTCCCATGTGCCAT 61.217 55.000 0.00 0.00 0.00 4.40
3383 8052 0.754217 CTCCCTTCCCATGTGCCATG 60.754 60.000 7.88 7.88 0.00 3.66
3384 8053 1.759299 CCCTTCCCATGTGCCATGG 60.759 63.158 21.10 21.10 38.88 3.66
3389 8058 4.690849 CCATGTGCCATGGGTCAT 57.309 55.556 20.58 1.83 35.58 3.06
3390 8059 2.120765 CCATGTGCCATGGGTCATG 58.879 57.895 20.58 12.23 41.10 3.07
3399 8068 1.402787 CATGGGTCATGGGTAAAGGC 58.597 55.000 0.00 0.00 38.11 4.35
3400 8069 0.261696 ATGGGTCATGGGTAAAGGCC 59.738 55.000 0.00 0.00 0.00 5.19
3401 8070 1.143329 TGGGTCATGGGTAAAGGCCA 61.143 55.000 5.01 0.00 0.00 5.36
3402 8071 0.261696 GGGTCATGGGTAAAGGCCAT 59.738 55.000 5.01 0.00 0.00 4.40
3403 8072 1.497286 GGGTCATGGGTAAAGGCCATA 59.503 52.381 5.01 0.00 0.00 2.74
3404 8073 2.091555 GGGTCATGGGTAAAGGCCATAA 60.092 50.000 5.01 0.00 0.00 1.90
3405 8074 3.222603 GGTCATGGGTAAAGGCCATAAG 58.777 50.000 5.01 0.00 0.00 1.73
3406 8075 3.222603 GTCATGGGTAAAGGCCATAAGG 58.777 50.000 5.01 0.00 38.23 2.69
3407 8076 2.176798 TCATGGGTAAAGGCCATAAGGG 59.823 50.000 5.01 0.00 40.85 3.95
3418 8087 1.094785 CCATAAGGGCAACTCCAACG 58.905 55.000 0.00 0.00 36.21 4.10
3419 8088 0.451783 CATAAGGGCAACTCCAACGC 59.548 55.000 0.00 0.00 36.21 4.84
3420 8089 0.679960 ATAAGGGCAACTCCAACGCC 60.680 55.000 0.00 0.00 45.47 5.68
3424 8093 2.975799 GCAACTCCAACGCCGGAA 60.976 61.111 5.05 0.00 33.65 4.30
3425 8094 2.548295 GCAACTCCAACGCCGGAAA 61.548 57.895 5.05 0.00 33.65 3.13
3426 8095 1.862602 GCAACTCCAACGCCGGAAAT 61.863 55.000 5.05 0.00 33.65 2.17
3427 8096 1.444836 CAACTCCAACGCCGGAAATA 58.555 50.000 5.05 0.00 33.65 1.40
3428 8097 1.396996 CAACTCCAACGCCGGAAATAG 59.603 52.381 5.05 0.00 33.65 1.73
3429 8098 0.107848 ACTCCAACGCCGGAAATAGG 60.108 55.000 5.05 0.00 33.65 2.57
3430 8099 0.814010 CTCCAACGCCGGAAATAGGG 60.814 60.000 5.05 0.00 33.65 3.53
3431 8100 1.078001 CCAACGCCGGAAATAGGGT 60.078 57.895 5.05 0.00 0.00 4.34
3432 8101 1.373590 CCAACGCCGGAAATAGGGTG 61.374 60.000 5.05 0.00 39.70 4.61
3433 8102 1.078001 AACGCCGGAAATAGGGTGG 60.078 57.895 5.05 0.00 38.13 4.61
3434 8103 1.555477 AACGCCGGAAATAGGGTGGA 61.555 55.000 5.05 0.00 38.13 4.02
3435 8104 1.523032 CGCCGGAAATAGGGTGGAC 60.523 63.158 5.05 0.00 0.00 4.02
3436 8105 1.153025 GCCGGAAATAGGGTGGACC 60.153 63.158 5.05 0.00 40.67 4.46
3437 8106 1.145377 CCGGAAATAGGGTGGACCG 59.855 63.158 0.00 0.00 46.96 4.79
3438 8107 1.145377 CGGAAATAGGGTGGACCGG 59.855 63.158 0.00 0.00 46.96 5.28
3439 8108 1.332144 CGGAAATAGGGTGGACCGGA 61.332 60.000 9.46 0.00 46.96 5.14
3440 8109 0.179702 GGAAATAGGGTGGACCGGAC 59.820 60.000 9.46 0.00 46.96 4.79
3441 8110 0.179092 GAAATAGGGTGGACCGGACG 60.179 60.000 9.46 0.00 46.96 4.79
3442 8111 2.248086 AAATAGGGTGGACCGGACGC 62.248 60.000 9.46 7.25 46.96 5.19
3446 8115 4.629523 GGTGGACCGGACGCCAAA 62.630 66.667 22.55 0.00 38.37 3.28
3447 8116 3.351416 GTGGACCGGACGCCAAAC 61.351 66.667 9.46 0.00 35.63 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.409064 CTGCTCCCGTTGTAGCTATGA 59.591 52.381 0.00 0.00 39.53 2.15
7 8 1.409064 TCTGCTCCCGTTGTAGCTATG 59.591 52.381 0.00 0.00 39.53 2.23
8 9 1.409427 GTCTGCTCCCGTTGTAGCTAT 59.591 52.381 0.00 0.00 39.53 2.97
19 20 1.966451 CCCGTGTTTGTCTGCTCCC 60.966 63.158 0.00 0.00 0.00 4.30
25 26 2.972505 CGCTGCCCGTGTTTGTCT 60.973 61.111 0.00 0.00 0.00 3.41
51 52 4.104086 TCAAATAGGACATGGTCAGACCT 58.896 43.478 20.82 0.00 39.58 3.85
58 59 6.038603 CGTCATTCAATCAAATAGGACATGGT 59.961 38.462 0.00 0.00 0.00 3.55
62 63 4.940654 TGCGTCATTCAATCAAATAGGACA 59.059 37.500 0.00 0.00 0.00 4.02
68 69 3.428452 CCTGCTGCGTCATTCAATCAAAT 60.428 43.478 0.00 0.00 0.00 2.32
75 76 0.874390 GTTTCCTGCTGCGTCATTCA 59.126 50.000 0.00 0.00 0.00 2.57
92 93 5.124936 GGAAAGGAGCAAAATATGTACCGTT 59.875 40.000 0.00 0.00 33.75 4.44
95 96 6.262496 GGTAGGAAAGGAGCAAAATATGTACC 59.738 42.308 0.00 0.00 0.00 3.34
96 97 6.826741 TGGTAGGAAAGGAGCAAAATATGTAC 59.173 38.462 0.00 0.00 0.00 2.90
117 118 4.445557 TGGCATATGCAAGGTATTGGTA 57.554 40.909 28.07 0.00 44.36 3.25
119 120 4.281435 TCAATGGCATATGCAAGGTATTGG 59.719 41.667 28.07 13.42 44.36 3.16
164 166 6.470557 TGACTGCAAATAAACTAACGGTAC 57.529 37.500 0.00 0.00 0.00 3.34
168 170 9.935682 ATTATGATGACTGCAAATAAACTAACG 57.064 29.630 0.00 0.00 0.00 3.18
183 185 9.566432 GGAGATTGTCCTAAAATTATGATGACT 57.434 33.333 0.00 0.00 42.99 3.41
206 208 5.527582 CCCGAAGTAATAGTTCATTTGGGAG 59.472 44.000 11.02 0.00 44.41 4.30
216 252 9.470399 ACAATTTAAATCCCCGAAGTAATAGTT 57.530 29.630 0.10 0.00 0.00 2.24
227 263 4.193865 ACGTAGGACAATTTAAATCCCCG 58.806 43.478 0.10 7.59 34.95 5.73
235 271 6.513720 GCCAACTTCAAACGTAGGACAATTTA 60.514 38.462 0.00 0.00 0.00 1.40
298 334 1.616865 TCAGACCTCTTACGTTGGGTG 59.383 52.381 0.00 0.00 31.60 4.61
299 335 1.617357 GTCAGACCTCTTACGTTGGGT 59.383 52.381 0.00 0.00 34.45 4.51
304 340 3.572682 TGTGAATGTCAGACCTCTTACGT 59.427 43.478 0.00 0.00 0.00 3.57
305 341 4.174411 TGTGAATGTCAGACCTCTTACG 57.826 45.455 0.00 0.00 0.00 3.18
307 343 9.166173 CAAATATTGTGAATGTCAGACCTCTTA 57.834 33.333 0.00 0.00 0.00 2.10
350 389 2.418609 GCTTGTGACCAACCAAGCTTTT 60.419 45.455 15.10 0.00 44.52 2.27
364 403 5.513614 CCACATATAGGATCCATGCTTGTGA 60.514 44.000 24.58 0.00 36.94 3.58
367 406 3.693085 GCCACATATAGGATCCATGCTTG 59.307 47.826 15.82 7.30 0.00 4.01
391 430 2.223805 ACTTGCTTTCCTTTTTGCTCCG 60.224 45.455 0.00 0.00 0.00 4.63
400 439 7.823745 TCTTTTCTCAATACTTGCTTTCCTT 57.176 32.000 0.00 0.00 0.00 3.36
401 440 8.414629 AATCTTTTCTCAATACTTGCTTTCCT 57.585 30.769 0.00 0.00 0.00 3.36
404 443 8.641541 TCCAAATCTTTTCTCAATACTTGCTTT 58.358 29.630 0.00 0.00 0.00 3.51
417 456 6.817765 TGATAACGCTTCCAAATCTTTTCT 57.182 33.333 0.00 0.00 0.00 2.52
420 459 6.757897 TCATGATAACGCTTCCAAATCTTT 57.242 33.333 0.00 0.00 0.00 2.52
429 468 4.391830 TCCTTGTGTTCATGATAACGCTTC 59.608 41.667 11.34 0.00 39.92 3.86
434 473 8.171196 CGCATATATCCTTGTGTTCATGATAAC 58.829 37.037 0.00 0.00 0.00 1.89
449 488 0.686789 TGTGGCTGCGCATATATCCT 59.313 50.000 12.24 0.00 0.00 3.24
459 498 1.888215 AATGATAGGATGTGGCTGCG 58.112 50.000 0.00 0.00 0.00 5.18
461 500 4.516698 GGTGTTAATGATAGGATGTGGCTG 59.483 45.833 0.00 0.00 0.00 4.85
485 524 3.969976 TGTTAGAGAGAGGGCATATTGCT 59.030 43.478 0.00 0.00 44.28 3.91
513 552 3.879180 GAGAGGGCCCCCGCAAAAA 62.879 63.158 21.43 0.00 41.95 1.94
518 557 4.541648 TAGAGAGAGGGCCCCCGC 62.542 72.222 21.43 9.17 41.95 6.13
520 559 0.400670 ATGTTAGAGAGAGGGCCCCC 60.401 60.000 21.43 6.71 0.00 5.40
521 560 1.141858 CAATGTTAGAGAGAGGGCCCC 59.858 57.143 21.43 10.60 0.00 5.80
522 561 2.119495 TCAATGTTAGAGAGAGGGCCC 58.881 52.381 16.46 16.46 0.00 5.80
523 562 2.482142 CGTCAATGTTAGAGAGAGGGCC 60.482 54.545 0.00 0.00 0.00 5.80
524 563 2.482142 CCGTCAATGTTAGAGAGAGGGC 60.482 54.545 0.00 0.00 0.00 5.19
525 564 2.761208 ACCGTCAATGTTAGAGAGAGGG 59.239 50.000 0.00 0.00 39.46 4.30
526 565 3.181485 GGACCGTCAATGTTAGAGAGAGG 60.181 52.174 0.00 0.00 0.00 3.69
527 566 3.444034 TGGACCGTCAATGTTAGAGAGAG 59.556 47.826 0.00 0.00 0.00 3.20
528 567 3.427573 TGGACCGTCAATGTTAGAGAGA 58.572 45.455 0.00 0.00 0.00 3.10
529 568 3.868757 TGGACCGTCAATGTTAGAGAG 57.131 47.619 0.00 0.00 0.00 3.20
530 569 4.023980 AGATGGACCGTCAATGTTAGAGA 58.976 43.478 16.18 0.00 0.00 3.10
531 570 4.392921 AGATGGACCGTCAATGTTAGAG 57.607 45.455 16.18 0.00 0.00 2.43
532 571 7.504574 TCTTATAGATGGACCGTCAATGTTAGA 59.495 37.037 16.18 7.59 0.00 2.10
533 572 7.658261 TCTTATAGATGGACCGTCAATGTTAG 58.342 38.462 16.18 5.58 0.00 2.34
534 573 7.255836 CCTCTTATAGATGGACCGTCAATGTTA 60.256 40.741 16.18 0.00 0.00 2.41
535 574 6.463049 CCTCTTATAGATGGACCGTCAATGTT 60.463 42.308 16.18 0.00 0.00 2.71
536 575 5.011125 CCTCTTATAGATGGACCGTCAATGT 59.989 44.000 16.18 0.00 0.00 2.71
537 576 5.243954 TCCTCTTATAGATGGACCGTCAATG 59.756 44.000 16.18 3.94 0.00 2.82
538 577 5.394738 TCCTCTTATAGATGGACCGTCAAT 58.605 41.667 16.18 0.00 0.00 2.57
539 578 4.800023 TCCTCTTATAGATGGACCGTCAA 58.200 43.478 16.18 0.95 0.00 3.18
540 579 4.448720 TCCTCTTATAGATGGACCGTCA 57.551 45.455 16.18 2.68 0.00 4.35
541 580 4.828387 ACTTCCTCTTATAGATGGACCGTC 59.172 45.833 5.47 5.47 0.00 4.79
542 581 4.585162 CACTTCCTCTTATAGATGGACCGT 59.415 45.833 0.00 0.00 0.00 4.83
543 582 4.827835 TCACTTCCTCTTATAGATGGACCG 59.172 45.833 0.00 0.00 0.00 4.79
544 583 6.517605 GTTCACTTCCTCTTATAGATGGACC 58.482 44.000 0.00 0.00 0.00 4.46
545 584 6.039493 TCGTTCACTTCCTCTTATAGATGGAC 59.961 42.308 0.00 0.00 0.00 4.02
546 585 6.127101 TCGTTCACTTCCTCTTATAGATGGA 58.873 40.000 0.00 0.00 0.00 3.41
547 586 6.039941 ACTCGTTCACTTCCTCTTATAGATGG 59.960 42.308 0.00 0.00 0.00 3.51
548 587 7.033530 ACTCGTTCACTTCCTCTTATAGATG 57.966 40.000 0.00 0.00 0.00 2.90
549 588 8.788806 CATACTCGTTCACTTCCTCTTATAGAT 58.211 37.037 0.00 0.00 0.00 1.98
550 589 7.774157 ACATACTCGTTCACTTCCTCTTATAGA 59.226 37.037 0.00 0.00 0.00 1.98
551 590 7.932335 ACATACTCGTTCACTTCCTCTTATAG 58.068 38.462 0.00 0.00 0.00 1.31
552 591 7.254692 CGACATACTCGTTCACTTCCTCTTATA 60.255 40.741 0.00 0.00 37.64 0.98
553 592 6.458478 CGACATACTCGTTCACTTCCTCTTAT 60.458 42.308 0.00 0.00 37.64 1.73
554 593 5.163784 CGACATACTCGTTCACTTCCTCTTA 60.164 44.000 0.00 0.00 37.64 2.10
577 616 4.097714 CAAACACTTGTGCATAATAGCCG 58.902 43.478 0.00 0.00 0.00 5.52
587 626 2.658268 GCGGCCAAACACTTGTGC 60.658 61.111 2.24 0.00 0.00 4.57
588 627 2.027460 GGCGGCCAAACACTTGTG 59.973 61.111 15.62 0.00 0.00 3.33
589 628 3.223589 GGGCGGCCAAACACTTGT 61.224 61.111 25.33 0.00 0.00 3.16
596 635 4.659172 CCTGTGAGGGCGGCCAAA 62.659 66.667 31.59 15.11 0.00 3.28
610 649 2.432510 GGTTGACACTCCTATCTCCCTG 59.567 54.545 0.00 0.00 0.00 4.45
613 652 3.528597 GTGGTTGACACTCCTATCTCC 57.471 52.381 0.00 0.00 46.72 3.71
650 689 3.244700 ACCCTCTCTCAGTGACAAAATGG 60.245 47.826 0.00 0.00 0.00 3.16
662 701 1.694150 CTTGGTGTTCACCCTCTCTCA 59.306 52.381 17.78 0.00 0.00 3.27
686 725 7.795482 TTGCTAACTTGCTTCACTTAACTTA 57.205 32.000 0.00 0.00 0.00 2.24
689 728 7.435192 ACAATTTGCTAACTTGCTTCACTTAAC 59.565 33.333 0.00 0.00 0.00 2.01
695 734 5.507817 CCTCACAATTTGCTAACTTGCTTCA 60.508 40.000 0.00 0.00 0.00 3.02
696 735 4.919754 CCTCACAATTTGCTAACTTGCTTC 59.080 41.667 0.00 0.00 0.00 3.86
699 738 3.255642 TCCCTCACAATTTGCTAACTTGC 59.744 43.478 0.00 0.00 0.00 4.01
711 750 7.872138 TCCAACTCTATATTTTCCCTCACAAT 58.128 34.615 0.00 0.00 0.00 2.71
717 756 7.996758 TCTTCTCCAACTCTATATTTTCCCT 57.003 36.000 0.00 0.00 0.00 4.20
747 2167 5.594725 TCTCGAGCTCCTATTTAAGACACAT 59.405 40.000 7.81 0.00 0.00 3.21
760 2180 1.756561 GAGGCCTTCTCGAGCTCCT 60.757 63.158 6.77 10.64 32.18 3.69
776 2196 6.656632 TTCATGTAACTATGCCTCTAGGAG 57.343 41.667 0.00 0.00 37.39 3.69
777 2197 7.618019 AATTCATGTAACTATGCCTCTAGGA 57.382 36.000 0.00 0.00 37.39 2.94
778 2198 9.429359 CTAAATTCATGTAACTATGCCTCTAGG 57.571 37.037 0.00 0.00 38.53 3.02
779 2199 8.930760 GCTAAATTCATGTAACTATGCCTCTAG 58.069 37.037 0.00 0.00 0.00 2.43
780 2200 7.878127 GGCTAAATTCATGTAACTATGCCTCTA 59.122 37.037 0.00 0.00 33.45 2.43
781 2201 6.712547 GGCTAAATTCATGTAACTATGCCTCT 59.287 38.462 0.00 0.00 33.45 3.69
783 2203 6.605119 AGGCTAAATTCATGTAACTATGCCT 58.395 36.000 10.97 10.97 40.64 4.75
784 2204 6.884280 AGGCTAAATTCATGTAACTATGCC 57.116 37.500 0.00 0.00 36.11 4.40
786 2206 8.607441 TGCTAGGCTAAATTCATGTAACTATG 57.393 34.615 0.00 0.00 0.00 2.23
787 2207 8.432805 ACTGCTAGGCTAAATTCATGTAACTAT 58.567 33.333 0.00 0.00 0.00 2.12
788 2208 7.792032 ACTGCTAGGCTAAATTCATGTAACTA 58.208 34.615 0.00 0.00 0.00 2.24
790 2210 6.927294 ACTGCTAGGCTAAATTCATGTAAC 57.073 37.500 0.00 0.00 0.00 2.50
791 2211 7.561251 TGTACTGCTAGGCTAAATTCATGTAA 58.439 34.615 0.00 0.00 0.00 2.41
794 2214 6.484643 ACATGTACTGCTAGGCTAAATTCATG 59.515 38.462 0.00 15.59 35.45 3.07
806 3376 2.196749 CGGCTTCACATGTACTGCTAG 58.803 52.381 0.00 0.00 0.00 3.42
832 3402 3.074412 AGATTCTTTTTCGGATGCGTGT 58.926 40.909 6.49 0.00 0.00 4.49
889 3462 1.213537 CTCGGCATGGCAAGTTTGG 59.786 57.895 20.37 0.65 0.00 3.28
907 3480 2.276430 GTTTCCATACGCACGCGC 60.276 61.111 12.02 0.00 44.19 6.86
979 3576 3.321648 ATCTGCCGCCACCTGTCA 61.322 61.111 0.00 0.00 0.00 3.58
1002 3599 2.435234 TGGAACCGTGCATACCGC 60.435 61.111 0.00 0.00 42.89 5.68
1039 3636 4.100963 GTGGTGGTGGAGGAAAAGATTTTT 59.899 41.667 0.00 0.00 0.00 1.94
1158 5323 1.089112 CAAGCAGATCGCCATGAACA 58.911 50.000 0.00 0.00 44.04 3.18
1178 5343 9.424319 ACTGTATATTCTAACGGCATAATTCTG 57.576 33.333 0.00 0.00 0.00 3.02
1238 5421 1.159285 CGGTGGTCAGACAGTACGTA 58.841 55.000 2.17 0.00 0.00 3.57
1239 5422 1.521450 CCGGTGGTCAGACAGTACGT 61.521 60.000 2.17 0.00 0.00 3.57
1240 5423 1.211969 CCGGTGGTCAGACAGTACG 59.788 63.158 2.17 1.32 0.00 3.67
1419 5623 2.431601 GAGCGCTCGAAGCAGTGT 60.432 61.111 23.61 0.00 42.58 3.55
1626 5846 1.883732 CAGCGAGGAGTCGGAGAAA 59.116 57.895 0.00 0.00 46.91 2.52
1973 6193 4.907034 CGCCGACGTCCGAGATGG 62.907 72.222 10.58 5.21 41.76 3.51
2034 6254 3.182996 ACCACCCACCAGAACCCC 61.183 66.667 0.00 0.00 0.00 4.95
2519 6969 0.521867 CCAATGCAATGACAGACGCG 60.522 55.000 3.53 3.53 0.00 6.01
2620 7284 7.210873 GGTGGTCTTATGAATCTCGATTTACT 58.789 38.462 0.00 0.00 0.00 2.24
2621 7285 6.144080 CGGTGGTCTTATGAATCTCGATTTAC 59.856 42.308 0.00 0.00 0.00 2.01
2622 7286 6.213677 CGGTGGTCTTATGAATCTCGATTTA 58.786 40.000 0.00 0.00 0.00 1.40
2623 7287 5.050490 CGGTGGTCTTATGAATCTCGATTT 58.950 41.667 0.00 0.00 0.00 2.17
2624 7288 4.501571 CCGGTGGTCTTATGAATCTCGATT 60.502 45.833 0.00 0.00 0.00 3.34
2647 7316 1.442769 TGACGGTAGTAGTGGTCGTC 58.557 55.000 7.15 7.15 46.86 4.20
2664 7333 0.602638 ACATCAGCGGCTCGTTTTGA 60.603 50.000 0.00 0.00 0.00 2.69
2681 7350 1.444383 GAGCGATGACAGCGACACA 60.444 57.895 18.71 0.00 40.04 3.72
2693 7362 1.527370 GCTTTGGTAGGGGAGCGAT 59.473 57.895 0.00 0.00 0.00 4.58
2707 7376 2.955660 TCGTCAAGGTCAAATTGGCTTT 59.044 40.909 0.00 0.00 30.01 3.51
2725 7394 2.051882 GGTTGTCGTCGACGTCGT 60.052 61.111 34.40 0.00 40.80 4.34
2745 7414 0.928229 GTCACGTGCACGAAGACTTT 59.072 50.000 42.94 18.38 43.02 2.66
2796 7465 1.332904 GCAAGGTTCAACAACGACGAG 60.333 52.381 0.00 0.00 32.68 4.18
2804 7473 5.164620 TCAGATCTATGCAAGGTTCAACA 57.835 39.130 0.00 0.00 0.00 3.33
2815 7484 2.537625 GTCACGTGCTTCAGATCTATGC 59.462 50.000 11.67 0.64 0.00 3.14
2832 7501 5.339611 GTCACGTAGCAAAATTTGATGTCAC 59.660 40.000 10.26 0.00 0.00 3.67
2849 7518 5.179929 TGATGTTAGAGTTTCTCGTCACGTA 59.820 40.000 0.00 0.00 35.36 3.57
2864 7533 2.354704 CCTTTGGAGCGGTGATGTTAGA 60.355 50.000 0.00 0.00 0.00 2.10
2927 7596 3.680458 GGTCCTTCTTGAGTTTGATCGTC 59.320 47.826 0.00 0.00 0.00 4.20
2931 7600 4.349342 ACTCTGGTCCTTCTTGAGTTTGAT 59.651 41.667 0.00 0.00 34.78 2.57
2932 7601 3.711704 ACTCTGGTCCTTCTTGAGTTTGA 59.288 43.478 0.00 0.00 34.78 2.69
2934 7603 4.779993 AACTCTGGTCCTTCTTGAGTTT 57.220 40.909 0.00 0.00 42.93 2.66
2943 7612 2.777692 TGTCTTCCAAACTCTGGTCCTT 59.222 45.455 0.00 0.00 46.51 3.36
2955 7624 7.483307 CATTCTTCTTTGAGTTTGTCTTCCAA 58.517 34.615 0.00 0.00 0.00 3.53
2956 7625 6.460123 GCATTCTTCTTTGAGTTTGTCTTCCA 60.460 38.462 0.00 0.00 0.00 3.53
2978 7647 5.477984 AGGGCATAAATATCAATCAACGCAT 59.522 36.000 0.00 0.00 0.00 4.73
2981 7650 6.317789 ACAGGGCATAAATATCAATCAACG 57.682 37.500 0.00 0.00 0.00 4.10
3183 7852 1.899814 TGGTAGTTCCACTGTAGCCAG 59.100 52.381 0.00 0.00 41.93 4.85
3240 7909 0.036010 CTCCAAACGCTGGTCCTCAT 60.036 55.000 4.19 0.00 46.51 2.90
3252 7921 0.538287 AGGCAGTTGAGGCTCCAAAC 60.538 55.000 12.86 10.70 40.91 2.93
3253 7922 0.538057 CAGGCAGTTGAGGCTCCAAA 60.538 55.000 12.86 0.00 43.24 3.28
3260 7929 0.535780 TGCAAGACAGGCAGTTGAGG 60.536 55.000 0.00 0.00 36.11 3.86
3269 7938 0.040067 GCTTCCGTTTGCAAGACAGG 60.040 55.000 0.00 2.28 0.00 4.00
3271 7940 1.871039 GTAGCTTCCGTTTGCAAGACA 59.129 47.619 0.00 0.00 0.00 3.41
3272 7941 2.143925 AGTAGCTTCCGTTTGCAAGAC 58.856 47.619 0.00 0.49 0.00 3.01
3273 7942 2.543777 AGTAGCTTCCGTTTGCAAGA 57.456 45.000 0.00 0.00 0.00 3.02
3274 7943 3.123621 CAGTAGTAGCTTCCGTTTGCAAG 59.876 47.826 0.00 0.00 0.00 4.01
3275 7944 3.064207 CAGTAGTAGCTTCCGTTTGCAA 58.936 45.455 0.00 0.00 0.00 4.08
3276 7945 2.683968 CAGTAGTAGCTTCCGTTTGCA 58.316 47.619 0.00 0.00 0.00 4.08
3277 7946 1.393883 GCAGTAGTAGCTTCCGTTTGC 59.606 52.381 0.00 0.00 0.00 3.68
3278 7947 2.000447 GGCAGTAGTAGCTTCCGTTTG 59.000 52.381 0.00 0.00 0.00 2.93
3279 7948 1.403780 CGGCAGTAGTAGCTTCCGTTT 60.404 52.381 0.00 0.00 39.72 3.60
3280 7949 0.172803 CGGCAGTAGTAGCTTCCGTT 59.827 55.000 0.00 0.00 39.72 4.44
3281 7950 0.679002 TCGGCAGTAGTAGCTTCCGT 60.679 55.000 0.00 0.00 43.78 4.69
3282 7951 0.454600 TTCGGCAGTAGTAGCTTCCG 59.545 55.000 0.00 0.00 44.50 4.30
3283 7952 2.892784 ATTCGGCAGTAGTAGCTTCC 57.107 50.000 0.00 0.00 0.00 3.46
3284 7953 5.774630 AGATAATTCGGCAGTAGTAGCTTC 58.225 41.667 0.00 0.00 0.00 3.86
3299 7968 2.079925 GGCATGGGCGAGAGATAATTC 58.920 52.381 0.00 0.00 42.47 2.17
3323 7992 4.018415 ACCCACATCAACTTTAGGCATAGT 60.018 41.667 0.00 0.00 0.00 2.12
3327 7996 2.513753 CACCCACATCAACTTTAGGCA 58.486 47.619 0.00 0.00 0.00 4.75
3330 7999 1.818674 GGCCACCCACATCAACTTTAG 59.181 52.381 0.00 0.00 0.00 1.85
3331 8000 1.884497 CGGCCACCCACATCAACTTTA 60.884 52.381 2.24 0.00 0.00 1.85
3332 8001 1.178534 CGGCCACCCACATCAACTTT 61.179 55.000 2.24 0.00 0.00 2.66
3333 8002 1.603455 CGGCCACCCACATCAACTT 60.603 57.895 2.24 0.00 0.00 2.66
3334 8003 2.034066 CGGCCACCCACATCAACT 59.966 61.111 2.24 0.00 0.00 3.16
3335 8004 3.061848 CCGGCCACCCACATCAAC 61.062 66.667 2.24 0.00 0.00 3.18
3336 8005 4.358841 CCCGGCCACCCACATCAA 62.359 66.667 2.24 0.00 0.00 2.57
3360 8029 1.379044 CACATGGGAAGGGAGTGCC 60.379 63.158 0.00 0.00 0.00 5.01
3361 8030 4.326255 CACATGGGAAGGGAGTGC 57.674 61.111 0.00 0.00 0.00 4.40
3362 8031 1.379044 GGCACATGGGAAGGGAGTG 60.379 63.158 0.00 0.00 0.00 3.51
3363 8032 1.852157 TGGCACATGGGAAGGGAGT 60.852 57.895 0.00 0.00 0.00 3.85
3364 8033 3.089838 TGGCACATGGGAAGGGAG 58.910 61.111 0.00 0.00 0.00 4.30
3380 8049 1.402787 GCCTTTACCCATGACCCATG 58.597 55.000 0.00 0.00 41.10 3.66
3381 8050 0.261696 GGCCTTTACCCATGACCCAT 59.738 55.000 0.00 0.00 0.00 4.00
3382 8051 1.143329 TGGCCTTTACCCATGACCCA 61.143 55.000 3.32 0.00 0.00 4.51
3383 8052 0.261696 ATGGCCTTTACCCATGACCC 59.738 55.000 3.32 0.00 41.40 4.46
3384 8053 3.222603 CTTATGGCCTTTACCCATGACC 58.777 50.000 3.32 0.00 42.80 4.02
3385 8054 3.222603 CCTTATGGCCTTTACCCATGAC 58.777 50.000 3.32 0.00 42.80 3.06
3386 8055 2.176798 CCCTTATGGCCTTTACCCATGA 59.823 50.000 3.32 0.00 42.80 3.07
3387 8056 2.597455 CCCTTATGGCCTTTACCCATG 58.403 52.381 3.32 0.00 42.80 3.66
3399 8068 1.094785 CGTTGGAGTTGCCCTTATGG 58.905 55.000 0.00 0.00 34.97 2.74
3400 8069 0.451783 GCGTTGGAGTTGCCCTTATG 59.548 55.000 0.00 0.00 34.97 1.90
3401 8070 0.679960 GGCGTTGGAGTTGCCCTTAT 60.680 55.000 0.00 0.00 43.06 1.73
3402 8071 1.302993 GGCGTTGGAGTTGCCCTTA 60.303 57.895 0.00 0.00 43.06 2.69
3403 8072 2.597510 GGCGTTGGAGTTGCCCTT 60.598 61.111 0.00 0.00 43.06 3.95
3407 8076 1.862602 ATTTCCGGCGTTGGAGTTGC 61.863 55.000 6.01 0.00 39.72 4.17
3408 8077 1.396996 CTATTTCCGGCGTTGGAGTTG 59.603 52.381 6.01 0.00 39.72 3.16
3409 8078 1.677820 CCTATTTCCGGCGTTGGAGTT 60.678 52.381 6.01 0.00 39.72 3.01
3410 8079 0.107848 CCTATTTCCGGCGTTGGAGT 60.108 55.000 6.01 0.00 39.72 3.85
3411 8080 0.814010 CCCTATTTCCGGCGTTGGAG 60.814 60.000 6.01 0.00 39.72 3.86
3412 8081 1.222387 CCCTATTTCCGGCGTTGGA 59.778 57.895 6.01 0.00 35.83 3.53
3413 8082 1.078001 ACCCTATTTCCGGCGTTGG 60.078 57.895 6.01 0.00 0.00 3.77
3414 8083 1.373590 CCACCCTATTTCCGGCGTTG 61.374 60.000 6.01 0.00 0.00 4.10
3415 8084 1.078001 CCACCCTATTTCCGGCGTT 60.078 57.895 6.01 0.00 0.00 4.84
3416 8085 1.991167 TCCACCCTATTTCCGGCGT 60.991 57.895 6.01 0.00 0.00 5.68
3417 8086 1.523032 GTCCACCCTATTTCCGGCG 60.523 63.158 0.00 0.00 0.00 6.46
3418 8087 1.153025 GGTCCACCCTATTTCCGGC 60.153 63.158 0.00 0.00 0.00 6.13
3419 8088 1.145377 CGGTCCACCCTATTTCCGG 59.855 63.158 0.00 0.00 35.25 5.14
3420 8089 1.145377 CCGGTCCACCCTATTTCCG 59.855 63.158 0.00 0.00 38.05 4.30
3421 8090 0.179702 GTCCGGTCCACCCTATTTCC 59.820 60.000 0.00 0.00 0.00 3.13
3422 8091 0.179092 CGTCCGGTCCACCCTATTTC 60.179 60.000 0.00 0.00 0.00 2.17
3423 8092 1.902556 CGTCCGGTCCACCCTATTT 59.097 57.895 0.00 0.00 0.00 1.40
3424 8093 2.728435 GCGTCCGGTCCACCCTATT 61.728 63.158 0.00 0.00 0.00 1.73
3425 8094 3.152400 GCGTCCGGTCCACCCTAT 61.152 66.667 0.00 0.00 0.00 2.57
3429 8098 4.629523 TTTGGCGTCCGGTCCACC 62.630 66.667 0.00 0.00 30.97 4.61
3430 8099 3.351416 GTTTGGCGTCCGGTCCAC 61.351 66.667 0.00 0.00 30.97 4.02
3431 8100 4.973055 CGTTTGGCGTCCGGTCCA 62.973 66.667 0.00 4.94 35.54 4.02


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

AutoCloner maintained by Alex Coulton.