Multiple sequence alignment - TraesCS5A01G255300

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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 TraesCS5A01G255300 chr5A 100.000 4313 0 0 1 4313 470999216 470994904 0.000000e+00 7965.0
1 TraesCS5A01G255300 chr5B 89.434 2281 147 36 2077 4313 436465266 436467496 0.000000e+00 2791.0
2 TraesCS5A01G255300 chr5B 92.791 1401 50 25 709 2078 436463805 436465185 0.000000e+00 1980.0
3 TraesCS5A01G255300 chr5B 91.776 535 43 1 1 535 436462051 436462584 0.000000e+00 743.0
4 TraesCS5A01G255300 chr4D 93.333 45 3 0 11 55 364538079 364538123 2.780000e-07 67.6


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 TraesCS5A01G255300 chr5A 470994904 470999216 4312 True 7965 7965 100.000000 1 4313 1 chr5A.!!$R1 4312
1 TraesCS5A01G255300 chr5B 436462051 436467496 5445 False 1838 2791 91.333667 1 4313 3 chr5B.!!$F1 4312

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
115 116 0.104304 GTGGTATGCGACTAGGGGTG 59.896 60.0 0.00 0.0 0.00 4.61 F
1021 2069 0.038310 GGGGTTTGACAGGAAGGAGG 59.962 60.0 0.00 0.0 0.00 4.30 F
1065 2128 0.403271 AGGTGAAGTGGCTGAAGCAT 59.597 50.0 4.43 0.0 44.36 3.79 F
2997 4159 0.386731 GGCATGAACCGTGTTTTCCG 60.387 55.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 2488 0.176680 AGGCAGGCTGACAGTATTCG 59.823 55.000 24.81 0.00 0.00 3.34 R
2997 4159 0.877071 CCATGCCATCGATGCTAACC 59.123 55.000 20.25 5.72 0.00 2.85 R
3051 4213 0.245266 CAATGCTGCACAATGGCTGA 59.755 50.000 3.57 0.00 35.02 4.26 R
4284 5487 1.001815 AGACCAACATTGTTTTCGCCG 60.002 47.619 0.00 0.00 0.00 6.46 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
45 46 1.549203 CAATAGCCTTGTGCCCTTGT 58.451 50.000 0.00 0.00 42.71 3.16
65 66 2.340328 GGTCATCAACGGGGTTGGC 61.340 63.158 8.47 0.00 42.99 4.52
68 69 1.603455 CATCAACGGGGTTGGCTGT 60.603 57.895 8.47 0.00 42.99 4.40
73 74 1.671901 AACGGGGTTGGCTGTTGTTG 61.672 55.000 0.00 0.00 0.00 3.33
81 82 2.028043 GCTGTTGTTGGTGGCTGC 59.972 61.111 0.00 0.00 0.00 5.25
106 107 0.970427 TCTGCTCTGGTGGTATGCGA 60.970 55.000 0.00 0.00 0.00 5.10
115 116 0.104304 GTGGTATGCGACTAGGGGTG 59.896 60.000 0.00 0.00 0.00 4.61
122 123 3.155167 GACTAGGGGTGGGCTCCG 61.155 72.222 0.00 0.00 41.22 4.63
127 128 2.866523 TAGGGGTGGGCTCCGTAGTG 62.867 65.000 0.00 0.00 41.22 2.74
149 150 1.473965 CGTGGTTGGGATGGATCTCAG 60.474 57.143 0.00 0.00 38.75 3.35
168 169 2.228711 CCATGAGTGGCTGGATCCT 58.771 57.895 14.23 0.00 39.01 3.24
171 172 0.106819 ATGAGTGGCTGGATCCTTGC 60.107 55.000 14.23 16.52 0.00 4.01
209 210 2.304831 TGATGGGTGCCGGGAATCA 61.305 57.895 2.18 3.80 0.00 2.57
219 220 1.705002 CCGGGAATCATGGCCTGGTA 61.705 60.000 3.32 0.00 44.26 3.25
221 222 1.140312 GGGAATCATGGCCTGGTAGA 58.860 55.000 3.32 0.00 0.00 2.59
233 234 0.976641 CTGGTAGACAGCACAAGGGA 59.023 55.000 0.00 0.00 40.97 4.20
248 249 2.904866 GGAGGTTGTTGTGCGGCA 60.905 61.111 0.00 0.00 0.00 5.69
270 271 0.171007 GATGGTGATGGTTGTTGGCG 59.829 55.000 0.00 0.00 0.00 5.69
317 318 2.739913 CTCGGTTTGAACGAATAGCCAA 59.260 45.455 0.00 0.00 40.16 4.52
343 344 1.054231 TGCAACATTTTGGGCATGGA 58.946 45.000 0.00 0.00 32.81 3.41
383 384 1.078759 CCACCGACTTCAGCGATGAC 61.079 60.000 1.08 0.00 0.00 3.06
384 385 0.388520 CACCGACTTCAGCGATGACA 60.389 55.000 1.08 0.00 0.00 3.58
412 413 1.170290 GGGTGTCGTTCCCCTTGTTG 61.170 60.000 0.00 0.00 39.08 3.33
455 456 3.808984 CCTCCCTAGGCATTTGGAC 57.191 57.895 2.05 0.00 35.64 4.02
464 465 3.525800 AGGCATTTGGACCTACAACTT 57.474 42.857 0.00 0.00 33.38 2.66
471 472 1.154197 GGACCTACAACTTTCCACGC 58.846 55.000 0.00 0.00 0.00 5.34
486 487 1.136057 CCACGCGAAAACCTAAGCTTC 60.136 52.381 15.93 0.00 0.00 3.86
489 490 1.128692 CGCGAAAACCTAAGCTTCAGG 59.871 52.381 0.00 11.09 39.25 3.86
490 491 1.135660 GCGAAAACCTAAGCTTCAGGC 60.136 52.381 17.07 3.61 36.57 4.85
510 511 4.742201 GGCTGAAGCAGGCGACGA 62.742 66.667 0.00 0.00 46.35 4.20
512 513 2.049156 CTGAAGCAGGCGACGACA 60.049 61.111 2.19 0.00 0.00 4.35
531 532 2.019249 CATCGTTCACATTGCATCCCT 58.981 47.619 0.00 0.00 0.00 4.20
532 533 1.737838 TCGTTCACATTGCATCCCTC 58.262 50.000 0.00 0.00 0.00 4.30
536 537 3.084039 GTTCACATTGCATCCCTCTTGA 58.916 45.455 0.00 0.00 0.00 3.02
537 538 3.657398 TCACATTGCATCCCTCTTGAT 57.343 42.857 0.00 0.00 0.00 2.57
541 542 0.332293 TTGCATCCCTCTTGATGGCA 59.668 50.000 0.00 0.00 41.96 4.92
545 546 1.071228 CATCCCTCTTGATGGCATCGA 59.929 52.381 21.65 19.03 38.76 3.59
546 547 0.755079 TCCCTCTTGATGGCATCGAG 59.245 55.000 30.88 30.88 41.32 4.04
548 549 1.688735 CCCTCTTGATGGCATCGAGTA 59.311 52.381 33.36 22.68 40.87 2.59
549 550 2.546795 CCCTCTTGATGGCATCGAGTAC 60.547 54.545 33.36 9.28 40.87 2.73
550 551 2.101415 CCTCTTGATGGCATCGAGTACA 59.899 50.000 33.36 19.78 40.87 2.90
552 553 3.521560 TCTTGATGGCATCGAGTACAAC 58.478 45.455 33.36 7.26 40.87 3.32
553 554 3.195610 TCTTGATGGCATCGAGTACAACT 59.804 43.478 33.36 0.00 40.87 3.16
554 555 3.165058 TGATGGCATCGAGTACAACTC 57.835 47.619 21.65 0.00 41.71 3.01
555 556 2.760650 TGATGGCATCGAGTACAACTCT 59.239 45.455 21.65 0.00 42.92 3.24
557 558 4.584743 TGATGGCATCGAGTACAACTCTAT 59.415 41.667 21.65 0.00 42.92 1.98
559 560 6.264518 TGATGGCATCGAGTACAACTCTATAA 59.735 38.462 21.65 0.00 42.92 0.98
561 562 5.358725 TGGCATCGAGTACAACTCTATAACA 59.641 40.000 5.59 1.01 42.92 2.41
563 564 6.459848 GGCATCGAGTACAACTCTATAACACT 60.460 42.308 5.59 0.00 42.92 3.55
564 565 7.255035 GGCATCGAGTACAACTCTATAACACTA 60.255 40.741 5.59 0.00 42.92 2.74
565 566 8.291032 GCATCGAGTACAACTCTATAACACTAT 58.709 37.037 5.59 0.00 42.92 2.12
566 567 9.600646 CATCGAGTACAACTCTATAACACTATG 57.399 37.037 5.59 0.00 42.92 2.23
569 570 7.376336 CGAGTACAACTCTATAACACTATGCAC 59.624 40.741 5.59 0.00 42.92 4.57
570 571 8.294954 AGTACAACTCTATAACACTATGCACT 57.705 34.615 0.00 0.00 0.00 4.40
571 572 9.404848 AGTACAACTCTATAACACTATGCACTA 57.595 33.333 0.00 0.00 0.00 2.74
574 575 8.696374 ACAACTCTATAACACTATGCACTATGT 58.304 33.333 0.00 0.00 0.00 2.29
624 1539 8.635328 TCATATCTTATTGTAAGTCCGCACTTA 58.365 33.333 0.00 0.00 41.39 2.24
637 1552 2.228822 CCGCACTTAAGGCAAAATGAGT 59.771 45.455 7.53 0.00 0.00 3.41
648 1563 6.927294 AGGCAAAATGAGTATACAAGCTAC 57.073 37.500 5.50 0.00 0.00 3.58
650 1565 7.056635 AGGCAAAATGAGTATACAAGCTACAT 58.943 34.615 5.50 0.00 0.00 2.29
657 1572 7.360113 TGAGTATACAAGCTACATCAATCCA 57.640 36.000 5.50 0.00 0.00 3.41
660 1575 8.438676 AGTATACAAGCTACATCAATCCAAAC 57.561 34.615 5.50 0.00 0.00 2.93
661 1576 8.046708 AGTATACAAGCTACATCAATCCAAACA 58.953 33.333 5.50 0.00 0.00 2.83
669 1584 9.995003 AGCTACATCAATCCAAACAATTTAAAA 57.005 25.926 0.00 0.00 0.00 1.52
707 1710 6.387465 TCGATACAACTCTAGAACACTTTGG 58.613 40.000 0.00 0.00 0.00 3.28
708 1711 6.208007 TCGATACAACTCTAGAACACTTTGGA 59.792 38.462 0.00 0.00 0.00 3.53
709 1712 6.308282 CGATACAACTCTAGAACACTTTGGAC 59.692 42.308 0.00 0.00 0.00 4.02
710 1713 5.615925 ACAACTCTAGAACACTTTGGACT 57.384 39.130 0.00 0.00 0.00 3.85
711 1714 6.726490 ACAACTCTAGAACACTTTGGACTA 57.274 37.500 0.00 0.00 0.00 2.59
712 1715 7.304497 ACAACTCTAGAACACTTTGGACTAT 57.696 36.000 0.00 0.00 0.00 2.12
713 1716 7.155328 ACAACTCTAGAACACTTTGGACTATG 58.845 38.462 0.00 0.00 0.00 2.23
715 1718 6.926313 ACTCTAGAACACTTTGGACTATGAC 58.074 40.000 0.00 0.00 0.00 3.06
716 1719 6.722129 ACTCTAGAACACTTTGGACTATGACT 59.278 38.462 0.00 0.00 0.00 3.41
717 1720 7.889073 ACTCTAGAACACTTTGGACTATGACTA 59.111 37.037 0.00 0.00 0.00 2.59
718 1721 8.053026 TCTAGAACACTTTGGACTATGACTAC 57.947 38.462 0.00 0.00 0.00 2.73
721 1724 4.806330 ACACTTTGGACTATGACTACGTG 58.194 43.478 0.00 0.00 0.00 4.49
722 1725 4.521639 ACACTTTGGACTATGACTACGTGA 59.478 41.667 0.00 0.00 0.00 4.35
971 2019 1.699656 CGTCGATTGCTGCCAAGGAG 61.700 60.000 0.00 0.00 33.80 3.69
972 2020 1.078214 TCGATTGCTGCCAAGGAGG 60.078 57.895 0.00 0.00 41.84 4.30
1012 2060 1.303236 CAGGCGATGGGGTTTGACA 60.303 57.895 0.00 0.00 0.00 3.58
1013 2061 1.002134 AGGCGATGGGGTTTGACAG 60.002 57.895 0.00 0.00 0.00 3.51
1021 2069 0.038310 GGGGTTTGACAGGAAGGAGG 59.962 60.000 0.00 0.00 0.00 4.30
1065 2128 0.403271 AGGTGAAGTGGCTGAAGCAT 59.597 50.000 4.43 0.00 44.36 3.79
1078 2141 1.134367 TGAAGCATTACTCCTCGACGG 59.866 52.381 0.00 0.00 0.00 4.79
1171 2234 4.988716 ACCTCGTCGCCACCTCCA 62.989 66.667 0.00 0.00 0.00 3.86
1252 2318 1.129879 CGCGATGCAAACTCACATGC 61.130 55.000 0.00 0.00 42.86 4.06
1272 2338 2.379005 CCCCTCCCTTGTTAAATGCTC 58.621 52.381 0.00 0.00 0.00 4.26
1286 2362 8.126871 TGTTAAATGCTCGCACTAAATAGTAG 57.873 34.615 0.00 0.00 34.13 2.57
1287 2363 7.762615 TGTTAAATGCTCGCACTAAATAGTAGT 59.237 33.333 0.00 0.00 34.13 2.73
1290 2366 5.179045 TGCTCGCACTAAATAGTAGTACC 57.821 43.478 0.00 0.00 34.13 3.34
1339 2416 4.743493 TGGCCTTTAATTTGCGATTTCTC 58.257 39.130 3.32 0.00 0.00 2.87
1396 2473 6.688385 CGGTGAATCATTGTGAACATTCATAC 59.312 38.462 0.00 0.00 39.73 2.39
1397 2474 7.537715 GGTGAATCATTGTGAACATTCATACA 58.462 34.615 0.00 0.00 39.73 2.29
1398 2475 7.699391 GGTGAATCATTGTGAACATTCATACAG 59.301 37.037 0.00 0.00 39.73 2.74
1399 2476 8.239314 GTGAATCATTGTGAACATTCATACAGT 58.761 33.333 0.00 0.00 39.73 3.55
1400 2477 9.447157 TGAATCATTGTGAACATTCATACAGTA 57.553 29.630 0.00 0.00 39.73 2.74
1411 2488 8.970691 AACATTCATACAGTATTCAGCAAAAC 57.029 30.769 0.00 0.00 0.00 2.43
1427 2504 3.667960 GCAAAACGAATACTGTCAGCCTG 60.668 47.826 0.00 0.00 0.00 4.85
1435 2512 1.504912 ACTGTCAGCCTGCCTCATAT 58.495 50.000 0.00 0.00 0.00 1.78
1460 2537 5.589831 AGTGCCCCTTTTTACCTTCATAAT 58.410 37.500 0.00 0.00 0.00 1.28
1484 2562 6.970484 TGAACCTTTTTATGTCAGCTTCTTC 58.030 36.000 0.00 0.00 0.00 2.87
1496 2574 5.880332 TGTCAGCTTCTTCAGTAAAAGTTGT 59.120 36.000 0.00 0.00 34.20 3.32
1571 2649 7.382218 GCTGCTGCTTAACTTAAAATCTCAAAA 59.618 33.333 8.53 0.00 36.03 2.44
1603 2681 9.173939 GATAATGCTTTTAGGATTTTGTGATCG 57.826 33.333 0.00 0.00 37.45 3.69
1606 2684 7.441890 TGCTTTTAGGATTTTGTGATCGTTA 57.558 32.000 0.00 0.00 0.00 3.18
1610 2688 9.289303 CTTTTAGGATTTTGTGATCGTTATTGG 57.711 33.333 0.00 0.00 0.00 3.16
1771 2849 5.887598 TGCCAATACTATGAAGCTTCACAAT 59.112 36.000 30.66 19.84 40.49 2.71
1807 2885 1.518929 CGCTTCGATCGGATTGTCTTC 59.481 52.381 16.41 0.00 0.00 2.87
1845 2923 3.004419 GGGTTCAAAGGAAAAGAAGACCG 59.996 47.826 0.00 0.00 34.13 4.79
1898 2976 7.362662 TCTTTGTTAGTTGCTGCTAGATTTTG 58.637 34.615 0.00 0.00 0.00 2.44
1948 3026 9.747898 TGGTTGTACCATTAAATGTATCTTCTT 57.252 29.630 0.00 0.00 44.79 2.52
1983 3061 6.438259 TCTCAGAGTTAGTTGAGTATTCCG 57.562 41.667 0.00 0.00 41.21 4.30
2002 3080 3.047796 CCGAAGGCACGTATGTATGTAC 58.952 50.000 0.00 0.00 46.14 2.90
2054 3132 7.492352 TCTTTTAGAAAACCTGTAAGCAGAC 57.508 36.000 0.00 0.00 45.28 3.51
2069 3147 2.095567 AGCAGACGCAAATGACATTGAC 60.096 45.455 0.34 0.00 42.27 3.18
2160 3320 7.064016 CACTACTGAACTTATTTTGAGCTCTCC 59.936 40.741 16.19 0.00 0.00 3.71
2172 3332 2.620585 TGAGCTCTCCATCGTCACATAG 59.379 50.000 16.19 0.00 0.00 2.23
2181 3341 5.597806 TCCATCGTCACATAGTTCCATAAC 58.402 41.667 0.00 0.00 35.72 1.89
2184 3344 5.006153 TCGTCACATAGTTCCATAACTGG 57.994 43.478 1.11 0.00 45.63 4.00
2201 3361 3.228453 ACTGGAAACGAACTGTAGGAGA 58.772 45.455 0.00 0.00 0.00 3.71
2210 3370 5.425630 ACGAACTGTAGGAGAAGTTTGTTT 58.574 37.500 3.18 0.00 44.86 2.83
2217 3377 9.628500 ACTGTAGGAGAAGTTTGTTTAATTCTT 57.372 29.630 0.00 0.00 32.31 2.52
2236 3396 4.523083 TCTTGTACATTTGCATCTACCCC 58.477 43.478 0.00 0.00 0.00 4.95
2239 3399 4.929479 TGTACATTTGCATCTACCCCTTT 58.071 39.130 0.00 0.00 0.00 3.11
2240 3400 5.329399 TGTACATTTGCATCTACCCCTTTT 58.671 37.500 0.00 0.00 0.00 2.27
2284 3444 2.571653 TGCTAGTTTCTATGTGCCCACT 59.428 45.455 0.00 0.00 0.00 4.00
2285 3445 3.198872 GCTAGTTTCTATGTGCCCACTC 58.801 50.000 0.00 0.00 0.00 3.51
2286 3446 3.118592 GCTAGTTTCTATGTGCCCACTCT 60.119 47.826 0.00 0.00 0.00 3.24
2287 3447 3.618690 AGTTTCTATGTGCCCACTCTC 57.381 47.619 0.00 0.00 0.00 3.20
2288 3448 3.177228 AGTTTCTATGTGCCCACTCTCT 58.823 45.455 0.00 0.00 0.00 3.10
2289 3449 4.353777 AGTTTCTATGTGCCCACTCTCTA 58.646 43.478 0.00 0.00 0.00 2.43
2290 3450 4.404073 AGTTTCTATGTGCCCACTCTCTAG 59.596 45.833 0.00 0.00 0.00 2.43
2298 3458 2.576648 TGCCCACTCTCTAGTCTCTACA 59.423 50.000 0.00 0.00 31.97 2.74
2427 3587 6.545666 TCTTAAATTTCTTCTGACAGTGCCAA 59.454 34.615 1.59 0.00 0.00 4.52
2443 3603 5.065218 CAGTGCCAATAAAGTAGTTAGCTGG 59.935 44.000 0.00 1.73 34.09 4.85
2456 3616 6.879458 AGTAGTTAGCTGGTGGTTTCTTATTG 59.121 38.462 0.00 0.00 0.00 1.90
2458 3618 5.473504 AGTTAGCTGGTGGTTTCTTATTGTG 59.526 40.000 0.00 0.00 0.00 3.33
2560 3722 4.772624 ACTTGATACTGACCTTCTGTGCTA 59.227 41.667 0.00 0.00 31.00 3.49
2741 3903 8.934023 ATTAAGGTTGATCAAGTTAGTTTCCA 57.066 30.769 8.80 0.00 0.00 3.53
2742 3904 8.754991 TTAAGGTTGATCAAGTTAGTTTCCAA 57.245 30.769 8.80 0.00 0.00 3.53
2846 4008 7.092079 TGCACATTCAAATTTTGTATCAGAGG 58.908 34.615 8.89 0.00 0.00 3.69
2864 4026 3.056891 AGAGGCTCGAAGAAACTGAAGAG 60.057 47.826 9.22 0.00 34.09 2.85
2867 4029 2.156697 GCTCGAAGAAACTGAAGAGTGC 59.843 50.000 0.00 0.00 34.09 4.40
2974 4136 2.891580 CCTTACAGCCTCGGATTAGCTA 59.108 50.000 0.00 0.00 34.38 3.32
2997 4159 0.386731 GGCATGAACCGTGTTTTCCG 60.387 55.000 0.00 0.00 0.00 4.30
3008 4170 2.070783 GTGTTTTCCGGTTAGCATCGA 58.929 47.619 0.00 0.00 0.00 3.59
3038 4200 2.284190 GGCTTCTCCTTCCTTTGATCG 58.716 52.381 0.00 0.00 0.00 3.69
3046 4208 0.623194 TTCCTTTGATCGGCATGGGA 59.377 50.000 0.00 0.00 0.00 4.37
3051 4213 1.496060 TTGATCGGCATGGGACTAGT 58.504 50.000 0.00 0.00 0.00 2.57
3052 4214 1.040646 TGATCGGCATGGGACTAGTC 58.959 55.000 14.87 14.87 0.00 2.59
3054 4216 1.000283 GATCGGCATGGGACTAGTCAG 60.000 57.143 23.91 11.50 0.00 3.51
3081 4243 2.876581 CAGCATTGCAGGGTCATCA 58.123 52.632 11.91 0.00 0.00 3.07
3083 4245 0.330604 AGCATTGCAGGGTCATCACT 59.669 50.000 11.91 0.00 0.00 3.41
3195 4357 1.805945 CGGCGGCTACTCACACTTC 60.806 63.158 7.61 0.00 0.00 3.01
3210 4372 1.065418 CACTTCGCCTGGGAATACCTT 60.065 52.381 0.00 0.00 41.11 3.50
3211 4373 1.209747 ACTTCGCCTGGGAATACCTTC 59.790 52.381 0.00 0.00 41.11 3.46
3217 4379 1.413077 CCTGGGAATACCTTCGGAGTC 59.587 57.143 0.00 0.00 41.11 3.36
3240 4402 1.069823 CTCAGGGAGTATGAAGCGCAT 59.930 52.381 11.47 0.00 41.08 4.73
3251 4413 1.401552 TGAAGCGCATAGGCAAATGAC 59.598 47.619 11.47 0.00 41.24 3.06
3301 4463 3.498774 ACTCTGTCTTGCTGGAACATT 57.501 42.857 0.00 0.00 38.20 2.71
3310 4472 1.251251 GCTGGAACATTGCTTCAGGT 58.749 50.000 0.00 0.00 38.20 4.00
3350 4512 2.241479 CTCCAGGAGTGGCTGCAGAG 62.241 65.000 20.43 0.00 44.60 3.35
3351 4513 2.288778 CCAGGAGTGGCTGCAGAGA 61.289 63.158 20.43 0.00 36.89 3.10
3366 4528 1.160329 AGAGAGCGGTTGTGTTGCAC 61.160 55.000 0.00 0.00 34.56 4.57
3387 4549 1.135199 GGTAGACGTTGAAGGATCGCA 60.135 52.381 0.00 0.00 0.00 5.10
3388 4550 2.481449 GGTAGACGTTGAAGGATCGCAT 60.481 50.000 0.00 0.00 0.00 4.73
3403 4565 3.728076 TCGCATGGAGGTATAAGTGTC 57.272 47.619 0.00 0.00 0.00 3.67
3429 4591 9.469807 CTGTGTTGTAAGGATCACTAGATATTC 57.530 37.037 0.00 0.00 33.72 1.75
3439 4601 7.512058 AGGATCACTAGATATTCCAAGATGTGT 59.488 37.037 0.00 0.00 33.72 3.72
3440 4602 8.153550 GGATCACTAGATATTCCAAGATGTGTT 58.846 37.037 0.00 0.00 33.72 3.32
3449 4611 3.411446 TCCAAGATGTGTTGTGTCATCC 58.589 45.455 0.00 0.00 40.63 3.51
3450 4612 2.160219 CCAAGATGTGTTGTGTCATCCG 59.840 50.000 0.00 0.00 40.63 4.18
3451 4613 2.099141 AGATGTGTTGTGTCATCCGG 57.901 50.000 0.00 0.00 40.63 5.14
3455 4617 2.967362 TGTGTTGTGTCATCCGGTATC 58.033 47.619 0.00 0.00 0.00 2.24
3507 4670 0.596082 ACGCAGGGCATTTTGTGTAC 59.404 50.000 0.00 0.00 36.36 2.90
3523 4686 3.957497 TGTGTACTGGGAATGCTGTTTTT 59.043 39.130 0.00 0.00 0.00 1.94
3629 4792 9.823647 CTTGTTATCTCAATTATCACTGGTACT 57.176 33.333 0.00 0.00 0.00 2.73
3648 4811 0.179094 TGCGCCTAAGATGTAACCGG 60.179 55.000 4.18 0.00 0.00 5.28
3659 4822 0.249120 TGTAACCGGATCAGGCAGTG 59.751 55.000 9.46 0.00 33.69 3.66
3660 4823 0.535335 GTAACCGGATCAGGCAGTGA 59.465 55.000 9.46 0.00 40.38 3.41
3662 4825 0.620556 AACCGGATCAGGCAGTGATT 59.379 50.000 9.46 0.00 46.64 2.57
3663 4826 0.620556 ACCGGATCAGGCAGTGATTT 59.379 50.000 9.46 0.00 46.64 2.17
3664 4827 1.004745 ACCGGATCAGGCAGTGATTTT 59.995 47.619 9.46 0.00 46.64 1.82
3665 4828 2.094675 CCGGATCAGGCAGTGATTTTT 58.905 47.619 0.00 0.00 46.64 1.94
3683 4846 4.268720 TTTTTGCGGGAAGGCAGT 57.731 50.000 0.00 0.00 44.94 4.40
3691 4854 1.475034 GCGGGAAGGCAGTGATTGATA 60.475 52.381 0.00 0.00 0.00 2.15
3698 4861 3.689347 AGGCAGTGATTGATACTTGCAA 58.311 40.909 0.00 0.00 0.00 4.08
3700 4863 4.082571 AGGCAGTGATTGATACTTGCAAAC 60.083 41.667 0.00 0.00 0.00 2.93
3703 4866 5.287752 GCAGTGATTGATACTTGCAAACATG 59.712 40.000 0.00 0.00 32.06 3.21
3734 4897 6.230472 TCGAACAGGATCAATCTCTTTTTGA 58.770 36.000 0.00 0.00 37.49 2.69
3737 4900 8.025445 CGAACAGGATCAATCTCTTTTTGAATT 58.975 33.333 0.00 0.00 36.72 2.17
3774 4937 5.576563 TTCTTCCCTGGTGACTGATTTTA 57.423 39.130 0.00 0.00 0.00 1.52
3852 5030 7.379529 GTCAACCATGTTGTATTTCTTGTTCAG 59.620 37.037 6.83 0.00 0.00 3.02
3877 5055 1.753649 GAACGACTAGAAGGTACCCCC 59.246 57.143 8.74 0.00 0.00 5.40
3885 5063 3.801620 AGGTACCCCCTTGTGACG 58.198 61.111 8.74 0.00 42.73 4.35
3888 5066 1.373812 GTACCCCCTTGTGACGCTT 59.626 57.895 0.00 0.00 0.00 4.68
3889 5067 0.953960 GTACCCCCTTGTGACGCTTG 60.954 60.000 0.00 0.00 0.00 4.01
3890 5068 2.741486 TACCCCCTTGTGACGCTTGC 62.741 60.000 0.00 0.00 0.00 4.01
3891 5069 3.365265 CCCCTTGTGACGCTTGCC 61.365 66.667 0.00 0.00 0.00 4.52
3892 5070 3.365265 CCCTTGTGACGCTTGCCC 61.365 66.667 0.00 0.00 0.00 5.36
3893 5071 2.594303 CCTTGTGACGCTTGCCCA 60.594 61.111 0.00 0.00 0.00 5.36
3894 5072 2.620112 CCTTGTGACGCTTGCCCAG 61.620 63.158 0.00 0.00 0.00 4.45
3895 5073 2.594303 TTGTGACGCTTGCCCAGG 60.594 61.111 0.00 0.00 0.00 4.45
3896 5074 4.641645 TGTGACGCTTGCCCAGGG 62.642 66.667 0.00 0.00 41.39 4.45
3924 5102 2.175811 GTGCAAAACCTAGCGCCG 59.824 61.111 2.29 0.00 35.33 6.46
3926 5104 4.476410 GCAAAACCTAGCGCCGCC 62.476 66.667 4.98 0.00 0.00 6.13
3927 5105 3.053291 CAAAACCTAGCGCCGCCA 61.053 61.111 4.98 0.00 0.00 5.69
3952 5131 0.678048 CTACCAAGCCACTGCCTTCC 60.678 60.000 0.00 0.00 38.69 3.46
3963 5142 2.354343 GCCTTCCCTTCTGCTGCT 59.646 61.111 0.00 0.00 0.00 4.24
3964 5143 2.045131 GCCTTCCCTTCTGCTGCTG 61.045 63.158 0.00 0.00 0.00 4.41
4138 5341 0.738975 CGTTCTCTAGCGATGGTGGA 59.261 55.000 0.00 0.00 0.00 4.02
4141 5344 0.395724 TCTCTAGCGATGGTGGAGCA 60.396 55.000 4.72 0.00 38.28 4.26
4230 5433 2.362120 GAGGGGTCGACGAGGGAA 60.362 66.667 9.92 0.00 0.00 3.97
4238 5441 2.185608 GACGAGGGAAGCAGGCTC 59.814 66.667 0.00 0.00 0.00 4.70
4249 5452 4.335647 CAGGCTCCCTGTTGGCGT 62.336 66.667 3.09 0.00 45.82 5.68
4251 5454 2.597510 GGCTCCCTGTTGGCGTTT 60.598 61.111 0.00 0.00 0.00 3.60
4252 5455 2.200337 GGCTCCCTGTTGGCGTTTT 61.200 57.895 0.00 0.00 0.00 2.43
4255 5458 2.028925 CCCTGTTGGCGTTTTGGC 59.971 61.111 0.00 0.00 45.12 4.52
4263 5466 3.879159 GCGTTTTGGCGGCTACTA 58.121 55.556 11.43 0.00 0.00 1.82
4269 5472 2.380084 TTTGGCGGCTACTAGTTCAG 57.620 50.000 11.43 0.00 0.00 3.02
4273 5476 2.295885 GGCGGCTACTAGTTCAGAGTA 58.704 52.381 0.00 0.00 0.00 2.59
4276 5479 3.364167 GCGGCTACTAGTTCAGAGTATCG 60.364 52.174 0.00 0.34 42.67 2.92
4284 5487 2.939103 AGTTCAGAGTATCGCAATTGCC 59.061 45.455 24.24 10.42 42.67 4.52
4287 5490 1.160329 AGAGTATCGCAATTGCCGGC 61.160 55.000 22.73 22.73 42.67 6.13
4294 5497 1.663074 GCAATTGCCGGCGAAAACA 60.663 52.632 22.97 0.00 34.31 2.83
4295 5498 1.218230 GCAATTGCCGGCGAAAACAA 61.218 50.000 22.97 9.06 34.31 2.83
4301 5504 1.281566 GCCGGCGAAAACAATGTTGG 61.282 55.000 12.58 0.00 0.00 3.77
4303 5506 1.404477 CGGCGAAAACAATGTTGGTC 58.596 50.000 0.00 0.00 0.00 4.02
4305 5508 2.661594 GGCGAAAACAATGTTGGTCTC 58.338 47.619 0.00 0.00 0.00 3.36
4307 5510 2.916111 CGAAAACAATGTTGGTCTCGG 58.084 47.619 0.00 0.00 0.00 4.63
4308 5511 2.289547 CGAAAACAATGTTGGTCTCGGT 59.710 45.455 0.00 0.00 0.00 4.69
4309 5512 3.606153 CGAAAACAATGTTGGTCTCGGTC 60.606 47.826 0.00 0.00 0.00 4.79
4310 5513 2.631160 AACAATGTTGGTCTCGGTCA 57.369 45.000 0.00 0.00 0.00 4.02
4311 5514 2.859165 ACAATGTTGGTCTCGGTCAT 57.141 45.000 0.00 0.00 0.00 3.06
4312 5515 2.426522 ACAATGTTGGTCTCGGTCATG 58.573 47.619 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 0.826062 GGGCACAAGGCTATTGCATT 59.174 50.000 18.79 0.00 44.53 3.56
45 46 0.616371 CCAACCCCGTTGATGACCTA 59.384 55.000 6.09 0.00 45.28 3.08
65 66 1.518056 ATCGCAGCCACCAACAACAG 61.518 55.000 0.00 0.00 0.00 3.16
68 69 2.267351 CCATCGCAGCCACCAACAA 61.267 57.895 0.00 0.00 0.00 2.83
73 74 2.821366 CAGACCATCGCAGCCACC 60.821 66.667 0.00 0.00 0.00 4.61
81 82 1.153489 CCACCAGAGCAGACCATCG 60.153 63.158 0.00 0.00 0.00 3.84
106 107 2.584873 CTACGGAGCCCACCCCTAGT 62.585 65.000 0.00 0.00 0.00 2.57
115 116 2.181021 CACGACACTACGGAGCCC 59.819 66.667 0.00 0.00 37.61 5.19
122 123 1.674817 CCATCCCAACCACGACACTAC 60.675 57.143 0.00 0.00 0.00 2.73
127 128 0.541863 AGATCCATCCCAACCACGAC 59.458 55.000 0.00 0.00 0.00 4.34
152 153 0.106819 GCAAGGATCCAGCCACTCAT 60.107 55.000 15.82 0.00 0.00 2.90
193 194 1.152694 CATGATTCCCGGCACCCAT 60.153 57.895 0.00 0.00 0.00 4.00
209 210 1.200760 TGTGCTGTCTACCAGGCCAT 61.201 55.000 5.01 0.00 41.81 4.40
219 220 0.109342 CAACCTCCCTTGTGCTGTCT 59.891 55.000 0.00 0.00 0.00 3.41
221 222 0.258774 AACAACCTCCCTTGTGCTGT 59.741 50.000 0.00 0.00 34.50 4.40
233 234 3.595758 GCTGCCGCACAACAACCT 61.596 61.111 0.00 0.00 35.78 3.50
248 249 1.167851 CAACAACCATCACCATCGCT 58.832 50.000 0.00 0.00 0.00 4.93
252 253 1.250154 CCGCCAACAACCATCACCAT 61.250 55.000 0.00 0.00 0.00 3.55
256 257 3.361158 CGCCGCCAACAACCATCA 61.361 61.111 0.00 0.00 0.00 3.07
258 259 1.531739 AAATCGCCGCCAACAACCAT 61.532 50.000 0.00 0.00 0.00 3.55
270 271 2.258286 GTGCCCACACAAATCGCC 59.742 61.111 0.00 0.00 46.61 5.54
292 293 3.001330 GCTATTCGTTCAAACCGAGATGG 59.999 47.826 0.00 0.00 46.41 3.51
303 304 5.101628 GCATCAAATTTGGCTATTCGTTCA 58.898 37.500 17.90 0.00 0.00 3.18
309 310 7.690952 AAATGTTGCATCAAATTTGGCTATT 57.309 28.000 17.90 12.37 0.00 1.73
317 318 4.142790 TGCCCAAAATGTTGCATCAAATT 58.857 34.783 0.75 0.00 33.01 1.82
343 344 1.201429 AGGCATTCACCCGGAGTTCT 61.201 55.000 0.73 0.00 0.00 3.01
383 384 2.618053 GAACGACACCCTAGGATGTTG 58.382 52.381 20.86 20.86 36.45 3.33
384 385 1.553704 GGAACGACACCCTAGGATGTT 59.446 52.381 11.09 6.98 0.00 2.71
412 413 2.109126 GCTCCACAACGATGCCTCC 61.109 63.158 0.00 0.00 0.00 4.30
455 456 1.504359 TTCGCGTGGAAAGTTGTAGG 58.496 50.000 5.77 0.00 0.00 3.18
464 465 0.869730 GCTTAGGTTTTCGCGTGGAA 59.130 50.000 5.77 0.00 0.00 3.53
471 472 2.902065 GCCTGAAGCTTAGGTTTTCG 57.098 50.000 17.77 0.00 37.64 3.46
490 491 2.359107 TCGCCTGCTTCAGCCAAG 60.359 61.111 0.00 0.00 41.18 3.61
496 497 1.446099 GATGTCGTCGCCTGCTTCA 60.446 57.895 0.00 0.00 0.00 3.02
510 511 1.745087 GGGATGCAATGTGAACGATGT 59.255 47.619 0.00 0.00 0.00 3.06
512 513 2.092753 AGAGGGATGCAATGTGAACGAT 60.093 45.455 0.00 0.00 0.00 3.73
531 532 3.195610 AGTTGTACTCGATGCCATCAAGA 59.804 43.478 5.40 0.00 0.00 3.02
532 533 3.525537 AGTTGTACTCGATGCCATCAAG 58.474 45.455 5.40 0.00 0.00 3.02
545 546 8.294954 AGTGCATAGTGTTATAGAGTTGTACT 57.705 34.615 0.00 0.00 0.00 2.73
548 549 8.696374 ACATAGTGCATAGTGTTATAGAGTTGT 58.304 33.333 0.00 0.00 0.00 3.32
557 558 9.803507 AGTACCTATACATAGTGCATAGTGTTA 57.196 33.333 6.21 0.70 33.30 2.41
559 560 9.803507 TTAGTACCTATACATAGTGCATAGTGT 57.196 33.333 0.00 0.00 33.30 3.55
593 1503 7.096023 GCGGACTTACAATAAGATATGACACTG 60.096 40.741 2.65 0.00 0.00 3.66
604 1514 5.220605 GCCTTAAGTGCGGACTTACAATAAG 60.221 44.000 26.64 21.50 43.09 1.73
609 1519 1.345089 TGCCTTAAGTGCGGACTTACA 59.655 47.619 26.64 18.97 43.09 2.41
610 1520 2.088950 TGCCTTAAGTGCGGACTTAC 57.911 50.000 26.64 16.81 43.09 2.34
624 1539 6.884295 TGTAGCTTGTATACTCATTTTGCCTT 59.116 34.615 4.17 0.00 0.00 4.35
637 1552 8.800370 TTGTTTGGATTGATGTAGCTTGTATA 57.200 30.769 0.00 0.00 0.00 1.47
685 1600 7.379750 AGTCCAAAGTGTTCTAGAGTTGTATC 58.620 38.462 0.00 0.00 0.00 2.24
687 1602 6.726490 AGTCCAAAGTGTTCTAGAGTTGTA 57.274 37.500 0.00 0.00 0.00 2.41
688 1603 5.615925 AGTCCAAAGTGTTCTAGAGTTGT 57.384 39.130 0.00 0.00 0.00 3.32
689 1604 7.329717 GTCATAGTCCAAAGTGTTCTAGAGTTG 59.670 40.741 0.00 0.00 0.00 3.16
698 1701 5.010314 TCACGTAGTCATAGTCCAAAGTGTT 59.990 40.000 0.00 0.00 41.61 3.32
707 1710 5.911615 CGTCTTTTCACGTAGTCATAGTC 57.088 43.478 0.00 0.00 41.61 2.59
718 1721 0.654472 GCAGCACACGTCTTTTCACG 60.654 55.000 0.00 0.00 45.65 4.35
721 1724 3.148823 GTGCAGCACACGTCTTTTC 57.851 52.632 21.22 0.00 40.07 2.29
796 1843 2.358247 CGGTTCTTGTCCACCCGG 60.358 66.667 0.00 0.00 35.11 5.73
833 1880 0.380378 TGCCAACTTTTGTGAGCGTC 59.620 50.000 0.00 0.00 34.96 5.19
842 1889 1.111277 GTGGTGACCTGCCAACTTTT 58.889 50.000 2.11 0.00 37.81 2.27
843 1890 0.033601 TGTGGTGACCTGCCAACTTT 60.034 50.000 2.11 0.00 37.81 2.66
1033 2081 3.151022 CACCTCCTCCTCCTCCGC 61.151 72.222 0.00 0.00 0.00 5.54
1037 2085 0.252467 CCACTTCACCTCCTCCTCCT 60.252 60.000 0.00 0.00 0.00 3.69
1040 2088 1.159664 AGCCACTTCACCTCCTCCT 59.840 57.895 0.00 0.00 0.00 3.69
1078 2141 1.523095 GCCGACGATCAGTATGCTTTC 59.477 52.381 0.00 0.00 34.76 2.62
1171 2234 3.632333 TGAACAGACCATAGGAGTCGAT 58.368 45.455 0.00 0.00 39.31 3.59
1252 2318 2.379005 GAGCATTTAACAAGGGAGGGG 58.621 52.381 0.00 0.00 0.00 4.79
1272 2338 8.400947 TCTTTACTGGTACTACTATTTAGTGCG 58.599 37.037 0.45 0.00 37.10 5.34
1286 2362 3.118884 TCATCCGGCTTCTTTACTGGTAC 60.119 47.826 0.00 0.00 33.74 3.34
1287 2363 3.101437 TCATCCGGCTTCTTTACTGGTA 58.899 45.455 0.00 0.00 33.74 3.25
1290 2366 2.289002 GCATCATCCGGCTTCTTTACTG 59.711 50.000 0.00 0.00 0.00 2.74
1324 2401 4.447290 TCCCATCGAGAAATCGCAAATTA 58.553 39.130 0.00 0.00 0.00 1.40
1339 2416 1.787155 CTAAATCTCGCGTTCCCATCG 59.213 52.381 5.77 0.00 0.00 3.84
1349 2426 5.401674 CCGTTCTTGTATACCTAAATCTCGC 59.598 44.000 0.00 0.00 0.00 5.03
1399 2476 6.402118 GCTGACAGTATTCGTTTTGCTGAATA 60.402 38.462 3.99 0.00 36.32 1.75
1400 2477 5.617751 GCTGACAGTATTCGTTTTGCTGAAT 60.618 40.000 3.99 0.00 38.34 2.57
1411 2488 0.176680 AGGCAGGCTGACAGTATTCG 59.823 55.000 24.81 0.00 0.00 3.34
1418 2495 3.041211 ACTTATATGAGGCAGGCTGACA 58.959 45.455 24.81 16.48 0.00 3.58
1419 2496 3.397482 CACTTATATGAGGCAGGCTGAC 58.603 50.000 20.86 17.58 0.00 3.51
1427 2504 2.959465 AAGGGGCACTTATATGAGGC 57.041 50.000 0.00 0.16 37.74 4.70
1435 2512 4.456662 TGAAGGTAAAAAGGGGCACTTA 57.543 40.909 0.50 0.00 38.85 2.24
1460 2537 6.545666 TGAAGAAGCTGACATAAAAAGGTTCA 59.454 34.615 14.16 0.00 46.08 3.18
1484 2562 7.083875 TCCTGAAAGACAACAACTTTTACTG 57.916 36.000 0.00 0.00 37.64 2.74
1571 2649 9.603921 CAAAATCCTAAAAGCATTATCACCAAT 57.396 29.630 0.00 0.00 0.00 3.16
1575 2653 9.807649 ATCACAAAATCCTAAAAGCATTATCAC 57.192 29.630 0.00 0.00 0.00 3.06
1584 2662 9.289303 CCAATAACGATCACAAAATCCTAAAAG 57.711 33.333 0.00 0.00 0.00 2.27
1642 2720 0.918983 CTGGCCAAGAGGATTACCCA 59.081 55.000 7.01 0.00 36.89 4.51
1665 2743 5.737635 GCTTTGCTATACTTCCTCGTCAGAT 60.738 44.000 0.00 0.00 0.00 2.90
1673 2751 4.141824 GGACTCTGCTTTGCTATACTTCCT 60.142 45.833 0.00 0.00 0.00 3.36
1681 2759 7.775093 ACAAATATATTGGACTCTGCTTTGCTA 59.225 33.333 6.86 0.00 0.00 3.49
1771 2849 1.550327 AGCGTCTCATCTTCAGGTCA 58.450 50.000 0.00 0.00 0.00 4.02
1807 2885 3.258872 TGAACCCAGCATGAGGAAAATTG 59.741 43.478 0.00 0.00 39.69 2.32
1845 2923 4.556104 GCACATACTTGATCACATCCATGC 60.556 45.833 0.00 0.00 0.00 4.06
1898 2976 7.376866 CCAATACACATGACAAGCGAATTATTC 59.623 37.037 0.00 0.00 0.00 1.75
1904 2982 3.407698 ACCAATACACATGACAAGCGAA 58.592 40.909 0.00 0.00 0.00 4.70
1950 3028 9.567776 CTCAACTAACTCTGAGATAAGGAGATA 57.432 37.037 12.44 0.00 41.38 1.98
1951 3029 8.058847 ACTCAACTAACTCTGAGATAAGGAGAT 58.941 37.037 12.44 0.99 41.38 2.75
1973 3051 0.892755 ACGTGCCTTCGGAATACTCA 59.107 50.000 0.00 0.00 34.94 3.41
1991 3069 6.898189 GCAAAACTAGCAACGTACATACATAC 59.102 38.462 0.00 0.00 0.00 2.39
1994 3072 4.992319 AGCAAAACTAGCAACGTACATACA 59.008 37.500 0.00 0.00 0.00 2.29
1995 3073 5.107220 ACAGCAAAACTAGCAACGTACATAC 60.107 40.000 0.00 0.00 0.00 2.39
1996 3074 4.992319 ACAGCAAAACTAGCAACGTACATA 59.008 37.500 0.00 0.00 0.00 2.29
1997 3075 3.813166 ACAGCAAAACTAGCAACGTACAT 59.187 39.130 0.00 0.00 0.00 2.29
1998 3076 3.199677 ACAGCAAAACTAGCAACGTACA 58.800 40.909 0.00 0.00 0.00 2.90
1999 3077 3.872560 ACAGCAAAACTAGCAACGTAC 57.127 42.857 0.00 0.00 0.00 3.67
2002 3080 4.152402 AGTGATACAGCAAAACTAGCAACG 59.848 41.667 0.00 0.00 0.00 4.10
2003 3081 5.049405 ACAGTGATACAGCAAAACTAGCAAC 60.049 40.000 0.00 0.00 0.00 4.17
2004 3082 5.063204 ACAGTGATACAGCAAAACTAGCAA 58.937 37.500 0.00 0.00 0.00 3.91
2005 3083 4.641396 ACAGTGATACAGCAAAACTAGCA 58.359 39.130 0.00 0.00 0.00 3.49
2006 3084 4.932200 AGACAGTGATACAGCAAAACTAGC 59.068 41.667 0.00 0.00 0.00 3.42
2007 3085 6.870965 AGAAGACAGTGATACAGCAAAACTAG 59.129 38.462 0.00 0.00 0.00 2.57
2110 3270 5.009610 GGACAACTGTGGCTAGAATCAAAAA 59.990 40.000 0.00 0.00 31.06 1.94
2160 3320 6.516478 CAGTTATGGAACTATGTGACGATG 57.484 41.667 0.00 0.00 44.39 3.84
2181 3341 3.936372 TCTCCTACAGTTCGTTTCCAG 57.064 47.619 0.00 0.00 0.00 3.86
2184 3344 5.522824 ACAAACTTCTCCTACAGTTCGTTTC 59.477 40.000 0.00 0.00 31.79 2.78
2210 3370 7.284489 GGGGTAGATGCAAATGTACAAGAATTA 59.716 37.037 0.00 0.00 0.00 1.40
2217 3377 4.584638 AAGGGGTAGATGCAAATGTACA 57.415 40.909 0.00 0.00 0.00 2.90
2221 3381 5.151297 ACAAAAAGGGGTAGATGCAAATG 57.849 39.130 0.00 0.00 0.00 2.32
2236 3396 7.440523 AGTTACCATGAAGAGCTACAAAAAG 57.559 36.000 0.00 0.00 0.00 2.27
2239 3399 7.648142 CAAAAGTTACCATGAAGAGCTACAAA 58.352 34.615 0.00 0.00 0.00 2.83
2240 3400 6.293955 GCAAAAGTTACCATGAAGAGCTACAA 60.294 38.462 0.00 0.00 0.00 2.41
2284 3444 7.175797 TGTCTTCCATTTGTAGAGACTAGAGA 58.824 38.462 0.00 0.00 38.02 3.10
2285 3445 7.397892 TGTCTTCCATTTGTAGAGACTAGAG 57.602 40.000 0.00 0.00 38.02 2.43
2286 3446 7.962995 ATGTCTTCCATTTGTAGAGACTAGA 57.037 36.000 0.00 0.00 38.02 2.43
2287 3447 8.474025 AGAATGTCTTCCATTTGTAGAGACTAG 58.526 37.037 0.00 0.00 43.87 2.57
2288 3448 8.367660 AGAATGTCTTCCATTTGTAGAGACTA 57.632 34.615 0.00 0.00 43.87 2.59
2289 3449 7.251321 AGAATGTCTTCCATTTGTAGAGACT 57.749 36.000 0.00 0.00 43.87 3.24
2290 3450 7.913674 AAGAATGTCTTCCATTTGTAGAGAC 57.086 36.000 0.00 0.00 43.87 3.36
2298 3458 6.265196 TGCTGTTGTAAGAATGTCTTCCATTT 59.735 34.615 0.00 0.00 43.87 2.32
2362 3522 8.328758 ACCAATTCATCTTCTTTCATAGGTACA 58.671 33.333 0.00 0.00 0.00 2.90
2367 3527 9.565213 GTCAAACCAATTCATCTTCTTTCATAG 57.435 33.333 0.00 0.00 0.00 2.23
2408 3568 6.491403 ACTTTATTGGCACTGTCAGAAGAAAT 59.509 34.615 6.91 4.20 0.00 2.17
2411 3571 4.973168 ACTTTATTGGCACTGTCAGAAGA 58.027 39.130 6.91 0.00 0.00 2.87
2412 3572 5.934625 ACTACTTTATTGGCACTGTCAGAAG 59.065 40.000 6.91 0.00 0.00 2.85
2413 3573 5.865085 ACTACTTTATTGGCACTGTCAGAA 58.135 37.500 6.91 0.00 0.00 3.02
2427 3587 7.017319 AGAAACCACCAGCTAACTACTTTAT 57.983 36.000 0.00 0.00 0.00 1.40
2443 3603 5.897050 TGACCAAACACAATAAGAAACCAC 58.103 37.500 0.00 0.00 0.00 4.16
2495 3656 7.362660 GGCCCTAAAACAACAGACCTTTATAAG 60.363 40.741 0.00 0.00 0.00 1.73
2560 3722 0.878416 TGCGCGCTAAAGGTTCAATT 59.122 45.000 33.29 0.00 0.00 2.32
2697 3859 6.432472 CCTTAATAAGAGAAGATCCCAATGCC 59.568 42.308 0.83 0.00 0.00 4.40
2741 3903 5.544682 TGTACCCAGGGTAATCCTCTATTT 58.455 41.667 21.00 0.00 46.12 1.40
2742 3904 5.166013 TGTACCCAGGGTAATCCTCTATT 57.834 43.478 21.00 0.00 46.12 1.73
2826 3988 6.599244 TCGAGCCTCTGATACAAAATTTGAAT 59.401 34.615 13.19 0.00 0.00 2.57
2846 4008 2.156697 GCACTCTTCAGTTTCTTCGAGC 59.843 50.000 0.00 0.00 0.00 5.03
2864 4026 2.336554 AATCATGTTTCTGTGCGCAC 57.663 45.000 33.11 33.11 0.00 5.34
2867 4029 3.155998 GACGAAATCATGTTTCTGTGCG 58.844 45.455 14.59 0.00 0.00 5.34
2959 4121 2.485657 GCCTTTTAGCTAATCCGAGGCT 60.486 50.000 26.83 0.00 43.62 4.58
2974 4136 3.453424 GAAAACACGGTTCATGCCTTTT 58.547 40.909 0.00 0.00 0.00 2.27
2997 4159 0.877071 CCATGCCATCGATGCTAACC 59.123 55.000 20.25 5.72 0.00 2.85
3001 4163 1.527611 CCACCATGCCATCGATGCT 60.528 57.895 20.25 3.77 0.00 3.79
3008 4170 1.076485 GGAGAAGCCACCATGCCAT 60.076 57.895 0.00 0.00 36.34 4.40
3038 4200 1.147153 GGCTGACTAGTCCCATGCC 59.853 63.158 20.11 21.11 0.00 4.40
3046 4208 1.947678 GCTGCACAATGGCTGACTAGT 60.948 52.381 0.00 0.00 35.02 2.57
3051 4213 0.245266 CAATGCTGCACAATGGCTGA 59.755 50.000 3.57 0.00 35.02 4.26
3052 4214 2.749541 CAATGCTGCACAATGGCTG 58.250 52.632 3.57 0.00 36.01 4.85
3081 4243 0.179062 GGATCGGCAGAGCATTCAGT 60.179 55.000 4.14 0.00 33.76 3.41
3083 4245 0.543277 AAGGATCGGCAGAGCATTCA 59.457 50.000 4.14 0.00 30.47 2.57
3179 4341 2.445438 GCGAAGTGTGAGTAGCCGC 61.445 63.158 0.00 0.00 0.00 6.53
3195 4357 4.438346 CGAAGGTATTCCCAGGCG 57.562 61.111 0.00 0.00 34.66 5.52
3210 4372 1.379176 CTCCCTGAGCAGACTCCGA 60.379 63.158 0.00 0.00 42.74 4.55
3211 4373 0.394488 TACTCCCTGAGCAGACTCCG 60.394 60.000 0.00 0.00 42.74 4.63
3217 4379 1.537776 CGCTTCATACTCCCTGAGCAG 60.538 57.143 0.00 0.00 32.04 4.24
3251 4413 4.082523 TTGCTCTTCCTCCGGGCG 62.083 66.667 0.00 0.00 0.00 6.13
3260 4422 4.631813 AGTAATTCACATCGGTTGCTCTTC 59.368 41.667 0.00 0.00 0.00 2.87
3271 4433 5.064452 CCAGCAAGACAGAGTAATTCACATC 59.936 44.000 0.00 0.00 0.00 3.06
3301 4463 2.016318 CGCAATGGATTACCTGAAGCA 58.984 47.619 0.00 0.00 37.04 3.91
3310 4472 1.640210 AACGCGCACGCAATGGATTA 61.640 50.000 16.04 0.00 45.53 1.75
3350 4512 2.052237 CGTGCAACACAACCGCTC 60.052 61.111 0.00 0.00 35.74 5.03
3351 4513 2.926901 TACCGTGCAACACAACCGCT 62.927 55.000 0.00 0.00 35.74 5.52
3366 4528 1.823828 CGATCCTTCAACGTCTACCG 58.176 55.000 0.00 0.00 44.03 4.02
3387 4549 5.248477 ACAACACAGACACTTATACCTCCAT 59.752 40.000 0.00 0.00 0.00 3.41
3388 4550 4.591498 ACAACACAGACACTTATACCTCCA 59.409 41.667 0.00 0.00 0.00 3.86
3403 4565 9.469807 GAATATCTAGTGATCCTTACAACACAG 57.530 37.037 0.00 0.00 35.97 3.66
3429 4591 2.160219 CGGATGACACAACACATCTTGG 59.840 50.000 0.00 0.00 41.50 3.61
3439 4601 2.027653 TGCAAGATACCGGATGACACAA 60.028 45.455 9.46 0.00 0.00 3.33
3440 4602 1.552792 TGCAAGATACCGGATGACACA 59.447 47.619 9.46 0.00 0.00 3.72
3449 4611 6.258727 ACAAAGAGAACATATGCAAGATACCG 59.741 38.462 1.58 0.00 0.00 4.02
3450 4612 7.066284 ACACAAAGAGAACATATGCAAGATACC 59.934 37.037 1.58 0.00 0.00 2.73
3451 4613 7.978982 ACACAAAGAGAACATATGCAAGATAC 58.021 34.615 1.58 0.00 0.00 2.24
3455 4617 5.181811 TGGACACAAAGAGAACATATGCAAG 59.818 40.000 1.58 0.00 0.00 4.01
3537 4700 7.498239 ACTCTTGTCCAGGTTTACTTCTTTAAC 59.502 37.037 0.00 0.00 0.00 2.01
3538 4701 7.571025 ACTCTTGTCCAGGTTTACTTCTTTAA 58.429 34.615 0.00 0.00 0.00 1.52
3545 4708 4.039366 GTGAGACTCTTGTCCAGGTTTACT 59.961 45.833 3.68 0.00 43.91 2.24
3550 4713 2.390225 AGTGAGACTCTTGTCCAGGT 57.610 50.000 3.68 0.00 43.91 4.00
3629 4792 0.179094 CCGGTTACATCTTAGGCGCA 60.179 55.000 10.83 0.00 0.00 6.09
3666 4829 0.753479 TCACTGCCTTCCCGCAAAAA 60.753 50.000 0.00 0.00 38.56 1.94
3667 4830 0.539438 ATCACTGCCTTCCCGCAAAA 60.539 50.000 0.00 0.00 38.56 2.44
3668 4831 0.539438 AATCACTGCCTTCCCGCAAA 60.539 50.000 0.00 0.00 38.56 3.68
3669 4832 1.074775 AATCACTGCCTTCCCGCAA 59.925 52.632 0.00 0.00 38.56 4.85
3670 4833 1.675310 CAATCACTGCCTTCCCGCA 60.675 57.895 0.00 0.00 37.19 5.69
3671 4834 0.749454 ATCAATCACTGCCTTCCCGC 60.749 55.000 0.00 0.00 0.00 6.13
3672 4835 2.158900 AGTATCAATCACTGCCTTCCCG 60.159 50.000 0.00 0.00 0.00 5.14
3673 4836 3.567478 AGTATCAATCACTGCCTTCCC 57.433 47.619 0.00 0.00 0.00 3.97
3674 4837 3.065925 GCAAGTATCAATCACTGCCTTCC 59.934 47.826 0.00 0.00 0.00 3.46
3675 4838 3.691118 TGCAAGTATCAATCACTGCCTTC 59.309 43.478 0.00 0.00 0.00 3.46
3676 4839 3.689347 TGCAAGTATCAATCACTGCCTT 58.311 40.909 0.00 0.00 0.00 4.35
3677 4840 3.354948 TGCAAGTATCAATCACTGCCT 57.645 42.857 0.00 0.00 0.00 4.75
3678 4841 4.168760 GTTTGCAAGTATCAATCACTGCC 58.831 43.478 0.00 0.00 0.00 4.85
3679 4842 4.797471 TGTTTGCAAGTATCAATCACTGC 58.203 39.130 0.00 0.00 0.00 4.40
3680 4843 6.384224 ACATGTTTGCAAGTATCAATCACTG 58.616 36.000 0.00 0.00 0.00 3.66
3681 4844 6.579666 ACATGTTTGCAAGTATCAATCACT 57.420 33.333 0.00 0.00 0.00 3.41
3682 4845 7.359431 CCAAACATGTTTGCAAGTATCAATCAC 60.359 37.037 35.57 0.00 46.25 3.06
3683 4846 6.645827 CCAAACATGTTTGCAAGTATCAATCA 59.354 34.615 35.57 0.00 46.25 2.57
3691 4854 3.119316 TCGAACCAAACATGTTTGCAAGT 60.119 39.130 35.57 27.29 46.25 3.16
3698 4861 3.283751 TCCTGTTCGAACCAAACATGTT 58.716 40.909 24.78 4.92 36.14 2.71
3700 4863 3.501828 TGATCCTGTTCGAACCAAACATG 59.498 43.478 24.78 4.59 36.14 3.21
3703 4866 4.455877 AGATTGATCCTGTTCGAACCAAAC 59.544 41.667 24.78 17.84 0.00 2.93
3716 4879 9.305555 TCTTCAATTCAAAAAGAGATTGATCCT 57.694 29.630 0.00 0.00 36.72 3.24
3734 4897 5.896106 GGAAGAAATCCCCTGATCTTCAATT 59.104 40.000 14.23 0.00 43.00 2.32
3737 4900 4.510167 GGAAGAAATCCCCTGATCTTCA 57.490 45.455 14.23 0.00 43.00 3.02
3825 4988 6.959639 ACAAGAAATACAACATGGTTGACT 57.040 33.333 15.35 0.15 0.00 3.41
3852 5030 5.172460 GGTACCTTCTAGTCGTTCTGATC 57.828 47.826 4.06 0.00 0.00 2.92
3877 5055 2.620112 CCTGGGCAAGCGTCACAAG 61.620 63.158 0.00 0.00 0.00 3.16
3879 5057 4.641645 CCCTGGGCAAGCGTCACA 62.642 66.667 0.00 0.00 0.00 3.58
3898 5076 4.662961 GTTTTGCACCCTGGCGGC 62.663 66.667 0.00 0.00 36.28 6.53
3899 5077 3.989787 GGTTTTGCACCCTGGCGG 61.990 66.667 0.00 0.00 40.19 6.13
3910 5088 3.039202 CTGGCGGCGCTAGGTTTTG 62.039 63.158 33.85 11.39 33.47 2.44
3924 5102 3.136791 GCTTGGTAGGCTGCTGGC 61.137 66.667 9.27 9.27 40.90 4.85
3926 5104 2.042831 GTGGCTTGGTAGGCTGCTG 61.043 63.158 1.79 0.00 46.59 4.41
3927 5105 2.227036 AGTGGCTTGGTAGGCTGCT 61.227 57.895 1.79 0.00 46.59 4.24
3997 5176 4.351054 CCCGGCTCCTTTGGCACT 62.351 66.667 0.00 0.00 0.00 4.40
4147 5350 3.928779 TGATCCAGATCCGCGGCC 61.929 66.667 23.51 15.11 37.02 6.13
4171 5374 1.696832 GGCAAAGCCGACGACAGATC 61.697 60.000 0.00 0.00 39.62 2.75
4205 5408 3.458163 TCGACCCCTCATCACGCC 61.458 66.667 0.00 0.00 0.00 5.68
4206 5409 2.202756 GTCGACCCCTCATCACGC 60.203 66.667 3.51 0.00 0.00 5.34
4209 5412 1.753078 CCTCGTCGACCCCTCATCA 60.753 63.158 10.58 0.00 0.00 3.07
4238 5441 2.028925 GCCAAAACGCCAACAGGG 59.971 61.111 0.00 0.00 40.85 4.45
4243 5446 2.594882 TAGCCGCCAAAACGCCAA 60.595 55.556 0.00 0.00 0.00 4.52
4244 5447 2.451928 TAGTAGCCGCCAAAACGCCA 62.452 55.000 0.00 0.00 0.00 5.69
4249 5452 2.300723 TCTGAACTAGTAGCCGCCAAAA 59.699 45.455 0.00 0.00 0.00 2.44
4251 5454 1.476891 CTCTGAACTAGTAGCCGCCAA 59.523 52.381 0.00 0.00 0.00 4.52
4252 5455 1.103803 CTCTGAACTAGTAGCCGCCA 58.896 55.000 0.00 0.00 0.00 5.69
4255 5458 3.364167 GCGATACTCTGAACTAGTAGCCG 60.364 52.174 0.00 0.00 33.33 5.52
4256 5459 3.564644 TGCGATACTCTGAACTAGTAGCC 59.435 47.826 0.00 0.00 33.33 3.93
4258 5461 6.143118 GCAATTGCGATACTCTGAACTAGTAG 59.857 42.308 15.87 0.00 33.15 2.57
4260 5463 4.806247 GCAATTGCGATACTCTGAACTAGT 59.194 41.667 15.87 0.00 0.00 2.57
4263 5466 2.939103 GGCAATTGCGATACTCTGAACT 59.061 45.455 23.48 0.00 43.26 3.01
4269 5472 1.279840 GCCGGCAATTGCGATACTC 59.720 57.895 24.80 8.10 43.26 2.59
4276 5479 1.218230 TTGTTTTCGCCGGCAATTGC 61.218 50.000 28.98 22.47 41.14 3.56
4284 5487 1.001815 AGACCAACATTGTTTTCGCCG 60.002 47.619 0.00 0.00 0.00 6.46
4287 5490 2.289547 ACCGAGACCAACATTGTTTTCG 59.710 45.455 0.00 7.27 0.00 3.46


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

AutoCloner maintained by Alex Coulton.