Multiple sequence alignment - TraesCS4A01G132900

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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 TraesCS4A01G132900 chr4A 100.000 6112 0 0 1 6112 179146957 179140846 0.000000e+00 11287.0
1 TraesCS4A01G132900 chr4D 96.125 2761 83 15 1952 4699 301730412 301733161 0.000000e+00 4484.0
2 TraesCS4A01G132900 chr4D 94.671 1126 34 8 836 1957 301729009 301730112 0.000000e+00 1724.0
3 TraesCS4A01G132900 chr4D 90.122 1063 55 15 4696 5727 301733370 301734413 0.000000e+00 1336.0
4 TraesCS4A01G132900 chr4D 88.767 908 53 19 5216 6112 301733909 301734778 0.000000e+00 1066.0
5 TraesCS4A01G132900 chr4D 86.654 517 44 18 1 497 301725847 301726358 3.220000e-152 549.0
6 TraesCS4A01G132900 chr4D 88.197 305 25 8 506 804 101499102 101498803 2.710000e-93 353.0
7 TraesCS4A01G132900 chr4D 86.751 317 28 10 513 822 31054236 31054545 2.110000e-89 340.0
8 TraesCS4A01G132900 chr4B 96.536 2021 55 7 2683 4699 376137772 376139781 0.000000e+00 3330.0
9 TraesCS4A01G132900 chr4B 90.737 1900 75 24 836 2694 376135316 376137155 0.000000e+00 2440.0
10 TraesCS4A01G132900 chr4B 92.366 1454 60 23 4696 6112 376139990 376141429 0.000000e+00 2023.0
11 TraesCS4A01G132900 chr4B 84.321 523 44 24 1 497 376134740 376135250 1.540000e-130 477.0
12 TraesCS4A01G132900 chr1B 88.673 309 24 8 510 812 484457858 484457555 3.480000e-97 366.0
13 TraesCS4A01G132900 chr7D 87.948 307 26 8 512 812 49806894 49806593 9.750000e-93 351.0
14 TraesCS4A01G132900 chr7D 90.426 94 7 2 2958 3050 243706972 243707064 8.320000e-24 122.0
15 TraesCS4A01G132900 chr2B 87.025 316 30 8 511 819 105850052 105849741 4.530000e-91 346.0
16 TraesCS4A01G132900 chr6D 87.338 308 27 9 511 812 11913500 11913199 5.870000e-90 342.0
17 TraesCS4A01G132900 chr6D 93.258 89 5 1 2958 3045 190909272 190909360 4.970000e-26 130.0
18 TraesCS4A01G132900 chr6D 89.691 97 8 2 2951 3045 29740986 29741082 8.320000e-24 122.0
19 TraesCS4A01G132900 chr3B 87.338 308 28 6 512 813 31124689 31124991 5.870000e-90 342.0
20 TraesCS4A01G132900 chr3B 83.721 86 8 4 2431 2515 623154512 623154592 6.570000e-10 76.8
21 TraesCS4A01G132900 chr3B 77.778 135 16 11 2541 2664 368958409 368958540 3.060000e-08 71.3
22 TraesCS4A01G132900 chr1A 87.296 307 29 6 511 812 11647932 11648233 5.870000e-90 342.0
23 TraesCS4A01G132900 chr1A 89.899 99 7 3 2958 3054 378191285 378191188 2.310000e-24 124.0
24 TraesCS4A01G132900 chr2D 86.709 316 30 10 512 821 12301861 12302170 2.110000e-89 340.0
25 TraesCS4A01G132900 chr2D 92.135 89 6 1 2958 3045 525600396 525600484 2.310000e-24 124.0
26 TraesCS4A01G132900 chr2D 92.453 53 2 2 424 475 385573073 385573022 2.360000e-09 75.0
27 TraesCS4A01G132900 chr1D 90.426 94 7 2 2958 3050 329154064 329154156 8.320000e-24 122.0
28 TraesCS4A01G132900 chr5D 91.011 89 7 1 2958 3045 79602485 79602573 1.080000e-22 119.0
29 TraesCS4A01G132900 chr5D 80.255 157 27 4 2171 2326 102531584 102531431 1.390000e-21 115.0
30 TraesCS4A01G132900 chr3A 84.524 84 7 4 2431 2513 611706263 611706341 1.830000e-10 78.7
31 TraesCS4A01G132900 chr3D 79.646 113 14 7 2405 2515 469158951 469159056 8.500000e-09 73.1
32 TraesCS4A01G132900 chr6A 90.385 52 5 0 425 476 158923278 158923329 1.100000e-07 69.4
33 TraesCS4A01G132900 chr5B 86.154 65 7 2 420 483 578708278 578708341 1.100000e-07 69.4


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 TraesCS4A01G132900 chr4A 179140846 179146957 6111 True 11287.0 11287 100.0000 1 6112 1 chr4A.!!$R1 6111
1 TraesCS4A01G132900 chr4D 301725847 301734778 8931 False 1831.8 4484 91.2678 1 6112 5 chr4D.!!$F2 6111
2 TraesCS4A01G132900 chr4B 376134740 376141429 6689 False 2067.5 3330 90.9900 1 6112 4 chr4B.!!$F1 6111

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
716 2140 0.038159 CGGCTCAGTCTTTCGAAGGT 60.038 55.0 7.2 0.0 0.00 3.50 F
1315 3676 0.110486 GGTACGCCATCCATCCCATT 59.890 55.0 0.0 0.0 34.09 3.16 F
1320 3681 0.115745 GCCATCCATCCCATTCCCAT 59.884 55.0 0.0 0.0 0.00 4.00 F
2315 5011 0.321298 TCTCTTAAACCAGCCGCACC 60.321 55.0 0.0 0.0 0.00 5.01 F
2473 5169 0.538584 TGCTGGACTGAGCCACATAG 59.461 55.0 0.0 0.0 38.28 2.23 F
4052 7377 0.027063 GTTGTTCGGTTCGGTGTGTG 59.973 55.0 0.0 0.0 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 4679 0.105504 AAAAGAACAGGGGCAAGCCT 60.106 50.000 11.40 0.0 36.1 4.58 R
2369 5065 0.179000 GTGTCACTATCCCCAGCAGG 59.821 60.000 0.00 0.0 0.0 4.85 R
2478 5174 0.254747 TTCCGTTTCCCCATGGCTAG 59.745 55.000 6.09 0.0 0.0 3.42 R
3832 7157 1.276989 TCTGCCGTACCCTCGAAAAAT 59.723 47.619 0.00 0.0 0.0 1.82 R
4123 7448 2.131972 GGCCAAAACAATCAACGGAAC 58.868 47.619 0.00 0.0 0.0 3.62 R
5618 9200 1.612395 CCGCCTTCTTGGAGAGAGCT 61.612 60.000 0.00 0.0 37.9 4.09 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
87 88 6.049955 AGTATACACTAGGTTGTGCACAAT 57.950 37.500 33.16 21.47 41.30 2.71
97 98 6.100404 AGGTTGTGCACAATAATGTTCAAT 57.900 33.333 33.16 9.79 37.82 2.57
165 166 4.385358 AAATGGTCGCCAAAATATGTCC 57.615 40.909 2.68 0.00 36.95 4.02
230 232 5.712917 ACAGACAAACCAGTAAAAAGACCAA 59.287 36.000 0.00 0.00 0.00 3.67
273 276 8.220434 GCATTTTAAAGTAAATTGATGTGCGTT 58.780 29.630 6.76 0.00 33.25 4.84
287 291 3.302555 TGTGCGTTTCGTCAGTAGTAAG 58.697 45.455 0.00 0.00 0.00 2.34
290 294 4.088213 GTGCGTTTCGTCAGTAGTAAGAAG 59.912 45.833 0.00 0.00 0.00 2.85
291 295 3.607209 GCGTTTCGTCAGTAGTAAGAAGG 59.393 47.826 0.00 0.00 0.00 3.46
314 318 5.720520 GGGAAATTACTCCTCCGTCCTATAT 59.279 44.000 0.00 0.00 35.63 0.86
315 319 6.894103 GGGAAATTACTCCTCCGTCCTATATA 59.106 42.308 0.00 0.00 35.63 0.86
373 397 9.670442 TTGTTATGTTATATTAGAGAGAGGGGT 57.330 33.333 0.00 0.00 0.00 4.95
383 409 2.913617 AGAGAGAGGGGTGGGTTTTAAG 59.086 50.000 0.00 0.00 0.00 1.85
384 410 2.910977 GAGAGAGGGGTGGGTTTTAAGA 59.089 50.000 0.00 0.00 0.00 2.10
385 411 3.523972 GAGAGAGGGGTGGGTTTTAAGAT 59.476 47.826 0.00 0.00 0.00 2.40
422 448 4.448210 ACCGTGAAACACACTTTGTAGAT 58.552 39.130 0.00 0.00 46.24 1.98
427 453 4.275689 TGAAACACACTTTGTAGATGCTGG 59.724 41.667 0.00 0.00 37.51 4.85
497 525 7.509141 AATGTCATGAAACACAGATACACAA 57.491 32.000 0.00 0.00 30.55 3.33
498 526 6.299023 TGTCATGAAACACAGATACACAAC 57.701 37.500 0.00 0.00 0.00 3.32
499 527 6.054941 TGTCATGAAACACAGATACACAACT 58.945 36.000 0.00 0.00 0.00 3.16
500 528 7.213678 TGTCATGAAACACAGATACACAACTA 58.786 34.615 0.00 0.00 0.00 2.24
501 529 7.170828 TGTCATGAAACACAGATACACAACTAC 59.829 37.037 0.00 0.00 0.00 2.73
502 530 7.170828 GTCATGAAACACAGATACACAACTACA 59.829 37.037 0.00 0.00 0.00 2.74
503 531 6.838198 TGAAACACAGATACACAACTACAC 57.162 37.500 0.00 0.00 0.00 2.90
504 532 6.342111 TGAAACACAGATACACAACTACACA 58.658 36.000 0.00 0.00 0.00 3.72
505 533 6.819146 TGAAACACAGATACACAACTACACAA 59.181 34.615 0.00 0.00 0.00 3.33
506 534 7.334671 TGAAACACAGATACACAACTACACAAA 59.665 33.333 0.00 0.00 0.00 2.83
507 535 6.598753 ACACAGATACACAACTACACAAAC 57.401 37.500 0.00 0.00 0.00 2.93
508 536 5.233476 ACACAGATACACAACTACACAAACG 59.767 40.000 0.00 0.00 0.00 3.60
509 537 5.460748 CACAGATACACAACTACACAAACGA 59.539 40.000 0.00 0.00 0.00 3.85
512 540 3.602390 ACACAACTACACAAACGATGC 57.398 42.857 0.00 0.00 0.00 3.91
513 541 2.033236 ACACAACTACACAAACGATGCG 60.033 45.455 0.00 0.00 0.00 4.73
514 542 2.219903 CACAACTACACAAACGATGCGA 59.780 45.455 0.00 0.00 0.00 5.10
515 543 2.867368 ACAACTACACAAACGATGCGAA 59.133 40.909 0.00 0.00 0.00 4.70
516 544 3.215244 CAACTACACAAACGATGCGAAC 58.785 45.455 0.00 0.00 0.00 3.95
519 547 1.018148 ACACAAACGATGCGAACCAA 58.982 45.000 0.00 0.00 0.00 3.67
520 548 1.606668 ACACAAACGATGCGAACCAAT 59.393 42.857 0.00 0.00 0.00 3.16
521 549 2.809119 ACACAAACGATGCGAACCAATA 59.191 40.909 0.00 0.00 0.00 1.90
522 550 3.438781 ACACAAACGATGCGAACCAATAT 59.561 39.130 0.00 0.00 0.00 1.28
523 551 3.785521 CACAAACGATGCGAACCAATATG 59.214 43.478 0.00 0.00 0.00 1.78
524 552 3.438781 ACAAACGATGCGAACCAATATGT 59.561 39.130 0.00 0.00 0.00 2.29
525 553 3.673746 AACGATGCGAACCAATATGTG 57.326 42.857 0.00 0.00 0.00 3.21
541 569 6.572519 CAATATGTGGTTGGATGGTTAAAGG 58.427 40.000 0.00 0.00 0.00 3.11
542 570 2.883026 TGTGGTTGGATGGTTAAAGGG 58.117 47.619 0.00 0.00 0.00 3.95
543 571 2.447429 TGTGGTTGGATGGTTAAAGGGA 59.553 45.455 0.00 0.00 0.00 4.20
544 572 3.076785 TGTGGTTGGATGGTTAAAGGGAT 59.923 43.478 0.00 0.00 0.00 3.85
545 573 3.699538 GTGGTTGGATGGTTAAAGGGATC 59.300 47.826 0.00 0.00 0.00 3.36
546 574 2.949644 GGTTGGATGGTTAAAGGGATCG 59.050 50.000 0.00 0.00 0.00 3.69
547 575 3.617284 GTTGGATGGTTAAAGGGATCGT 58.383 45.455 0.00 0.00 0.00 3.73
548 576 3.275617 TGGATGGTTAAAGGGATCGTG 57.724 47.619 0.00 0.00 0.00 4.35
549 577 2.092646 TGGATGGTTAAAGGGATCGTGG 60.093 50.000 0.00 0.00 0.00 4.94
550 578 2.092592 GGATGGTTAAAGGGATCGTGGT 60.093 50.000 0.00 0.00 0.00 4.16
552 580 4.202430 GGATGGTTAAAGGGATCGTGGTAT 60.202 45.833 0.00 0.00 0.00 2.73
553 581 4.411256 TGGTTAAAGGGATCGTGGTATC 57.589 45.455 0.00 0.00 0.00 2.24
559 587 1.371558 GGATCGTGGTATCCCAGCC 59.628 63.158 0.00 0.00 42.94 4.85
560 588 1.371558 GATCGTGGTATCCCAGCCC 59.628 63.158 0.00 0.00 42.94 5.19
561 589 1.383943 ATCGTGGTATCCCAGCCCA 60.384 57.895 0.00 0.00 42.94 5.36
562 590 1.696097 ATCGTGGTATCCCAGCCCAC 61.696 60.000 0.00 0.00 42.94 4.61
563 591 2.595655 GTGGTATCCCAGCCCACC 59.404 66.667 0.00 0.00 42.94 4.61
564 592 2.126142 TGGTATCCCAGCCCACCA 59.874 61.111 0.00 0.00 38.72 4.17
565 593 2.000701 TGGTATCCCAGCCCACCAG 61.001 63.158 0.00 0.00 36.15 4.00
576 604 2.034687 CCACCAGGGTTCAGCCTG 59.965 66.667 16.82 16.82 37.43 4.85
579 607 2.034687 CCAGGGTTCAGCCTGGTG 59.965 66.667 29.15 10.61 46.01 4.17
580 608 2.674380 CAGGGTTCAGCCTGGTGC 60.674 66.667 16.10 0.00 41.71 5.01
589 617 3.903783 GCCTGGTGCTCGCATTTA 58.096 55.556 0.00 0.00 36.87 1.40
592 620 1.268743 GCCTGGTGCTCGCATTTATTC 60.269 52.381 0.00 0.00 36.87 1.75
594 622 2.292267 CTGGTGCTCGCATTTATTCCT 58.708 47.619 0.00 0.00 0.00 3.36
595 623 3.466836 CTGGTGCTCGCATTTATTCCTA 58.533 45.455 0.00 0.00 0.00 2.94
597 625 4.265893 TGGTGCTCGCATTTATTCCTAAA 58.734 39.130 0.00 0.00 0.00 1.85
598 626 4.887071 TGGTGCTCGCATTTATTCCTAAAT 59.113 37.500 0.00 0.00 37.92 1.40
599 627 5.359576 TGGTGCTCGCATTTATTCCTAAATT 59.640 36.000 0.00 0.00 35.77 1.82
600 628 6.127479 TGGTGCTCGCATTTATTCCTAAATTT 60.127 34.615 0.00 0.00 35.77 1.82
601 629 7.067615 TGGTGCTCGCATTTATTCCTAAATTTA 59.932 33.333 0.00 0.00 35.77 1.40
602 630 8.082242 GGTGCTCGCATTTATTCCTAAATTTAT 58.918 33.333 0.00 0.00 35.77 1.40
603 631 9.463443 GTGCTCGCATTTATTCCTAAATTTATT 57.537 29.630 0.00 0.00 35.77 1.40
617 645 8.194769 TCCTAAATTTATTTCAGGATTTTCGGC 58.805 33.333 3.00 0.00 31.13 5.54
618 646 6.885735 AAATTTATTTCAGGATTTTCGGCG 57.114 33.333 0.00 0.00 0.00 6.46
620 648 4.609691 TTATTTCAGGATTTTCGGCGAC 57.390 40.909 10.16 0.00 0.00 5.19
622 650 1.153353 TTCAGGATTTTCGGCGACAC 58.847 50.000 10.16 0.84 0.00 3.67
641 2065 2.158449 CACGCATTCAGTGAAAGGAGAC 59.842 50.000 10.14 0.00 41.83 3.36
646 2070 2.814280 TCAGTGAAAGGAGACGTTCC 57.186 50.000 8.26 8.26 46.58 3.62
666 2090 3.970721 TCGACGACGAGGTGCTTA 58.029 55.556 5.75 0.00 43.81 3.09
667 2091 1.792301 TCGACGACGAGGTGCTTAG 59.208 57.895 5.75 0.00 43.81 2.18
669 2093 1.881602 GACGACGAGGTGCTTAGGT 59.118 57.895 0.00 0.00 0.00 3.08
670 2094 0.456312 GACGACGAGGTGCTTAGGTG 60.456 60.000 0.00 0.00 0.00 4.00
671 2095 0.892358 ACGACGAGGTGCTTAGGTGA 60.892 55.000 0.00 0.00 0.00 4.02
672 2096 0.456312 CGACGAGGTGCTTAGGTGAC 60.456 60.000 0.00 0.00 0.00 3.67
674 2098 1.272769 GACGAGGTGCTTAGGTGACTT 59.727 52.381 0.00 0.00 43.67 3.01
677 2101 2.548067 CGAGGTGCTTAGGTGACTTTGT 60.548 50.000 0.00 0.00 43.67 2.83
679 2103 4.638304 GAGGTGCTTAGGTGACTTTGTAA 58.362 43.478 0.00 0.00 43.67 2.41
680 2104 5.043737 AGGTGCTTAGGTGACTTTGTAAA 57.956 39.130 0.00 0.00 43.67 2.01
681 2105 5.631119 AGGTGCTTAGGTGACTTTGTAAAT 58.369 37.500 0.00 0.00 43.67 1.40
682 2106 6.068670 AGGTGCTTAGGTGACTTTGTAAATT 58.931 36.000 0.00 0.00 43.67 1.82
683 2107 6.549736 AGGTGCTTAGGTGACTTTGTAAATTT 59.450 34.615 0.00 0.00 43.67 1.82
684 2108 6.861572 GGTGCTTAGGTGACTTTGTAAATTTC 59.138 38.462 0.00 0.00 43.67 2.17
685 2109 7.422399 GTGCTTAGGTGACTTTGTAAATTTCA 58.578 34.615 0.00 0.00 43.67 2.69
686 2110 7.918562 GTGCTTAGGTGACTTTGTAAATTTCAA 59.081 33.333 0.00 0.00 43.67 2.69
688 2112 8.349983 GCTTAGGTGACTTTGTAAATTTCAAGA 58.650 33.333 10.26 0.00 43.67 3.02
692 2116 9.082313 AGGTGACTTTGTAAATTTCAAGATGAT 57.918 29.630 10.26 0.00 37.44 2.45
698 2122 8.854979 TTTGTAAATTTCAAGATGATATGCCG 57.145 30.769 0.00 0.00 0.00 5.69
699 2123 6.969366 TGTAAATTTCAAGATGATATGCCGG 58.031 36.000 0.00 0.00 0.00 6.13
701 2125 2.936919 TTCAAGATGATATGCCGGCT 57.063 45.000 29.70 15.76 0.00 5.52
702 2126 2.462456 TCAAGATGATATGCCGGCTC 57.538 50.000 29.70 17.89 0.00 4.70
703 2127 1.693606 TCAAGATGATATGCCGGCTCA 59.306 47.619 29.70 23.34 0.00 4.26
705 2129 1.346062 AGATGATATGCCGGCTCAGT 58.654 50.000 29.70 13.44 0.00 3.41
706 2130 1.274728 AGATGATATGCCGGCTCAGTC 59.725 52.381 29.70 19.55 0.00 3.51
709 2133 1.486310 TGATATGCCGGCTCAGTCTTT 59.514 47.619 29.70 3.35 0.00 2.52
711 2135 0.179111 TATGCCGGCTCAGTCTTTCG 60.179 55.000 29.70 0.00 0.00 3.46
713 2137 1.374252 GCCGGCTCAGTCTTTCGAA 60.374 57.895 22.15 0.00 0.00 3.71
715 2139 0.737715 CCGGCTCAGTCTTTCGAAGG 60.738 60.000 0.00 0.00 0.00 3.46
716 2140 0.038159 CGGCTCAGTCTTTCGAAGGT 60.038 55.000 7.20 0.00 0.00 3.50
717 2141 1.433534 GGCTCAGTCTTTCGAAGGTG 58.566 55.000 7.20 0.00 0.00 4.00
718 2142 0.793250 GCTCAGTCTTTCGAAGGTGC 59.207 55.000 7.20 2.27 0.00 5.01
720 2144 2.333014 CTCAGTCTTTCGAAGGTGCTC 58.667 52.381 7.20 0.00 0.00 4.26
721 2145 1.686587 TCAGTCTTTCGAAGGTGCTCA 59.313 47.619 7.20 0.00 0.00 4.26
724 2148 3.862267 CAGTCTTTCGAAGGTGCTCATAG 59.138 47.826 7.20 0.00 0.00 2.23
727 2151 0.830648 TTCGAAGGTGCTCATAGGGG 59.169 55.000 0.00 0.00 0.00 4.79
728 2152 0.325296 TCGAAGGTGCTCATAGGGGT 60.325 55.000 0.00 0.00 0.00 4.95
731 2155 1.694696 GAAGGTGCTCATAGGGGTAGG 59.305 57.143 0.00 0.00 0.00 3.18
732 2156 0.941963 AGGTGCTCATAGGGGTAGGA 59.058 55.000 0.00 0.00 0.00 2.94
734 2158 1.625818 GGTGCTCATAGGGGTAGGATG 59.374 57.143 0.00 0.00 0.00 3.51
735 2159 2.330216 GTGCTCATAGGGGTAGGATGT 58.670 52.381 0.00 0.00 0.00 3.06
736 2160 2.037772 GTGCTCATAGGGGTAGGATGTG 59.962 54.545 0.00 0.00 0.00 3.21
737 2161 2.330216 GCTCATAGGGGTAGGATGTGT 58.670 52.381 0.00 0.00 0.00 3.72
738 2162 2.037772 GCTCATAGGGGTAGGATGTGTG 59.962 54.545 0.00 0.00 0.00 3.82
740 2164 4.480115 CTCATAGGGGTAGGATGTGTGTA 58.520 47.826 0.00 0.00 0.00 2.90
741 2165 5.087323 CTCATAGGGGTAGGATGTGTGTAT 58.913 45.833 0.00 0.00 0.00 2.29
743 2167 6.014647 TCATAGGGGTAGGATGTGTGTATAC 58.985 44.000 0.00 0.00 0.00 1.47
744 2168 4.274794 AGGGGTAGGATGTGTGTATACA 57.725 45.455 0.08 0.08 34.63 2.29
745 2169 4.827789 AGGGGTAGGATGTGTGTATACAT 58.172 43.478 9.18 0.00 43.61 2.29
746 2170 5.224441 AGGGGTAGGATGTGTGTATACATT 58.776 41.667 9.18 0.00 41.15 2.71
749 2769 7.516209 AGGGGTAGGATGTGTGTATACATTTAT 59.484 37.037 9.18 3.82 41.15 1.40
752 2772 9.871238 GGTAGGATGTGTGTATACATTTATAGG 57.129 37.037 9.18 0.00 41.15 2.57
755 2775 9.338968 AGGATGTGTGTATACATTTATAGGGAT 57.661 33.333 9.18 0.00 41.15 3.85
756 2776 9.383519 GGATGTGTGTATACATTTATAGGGATG 57.616 37.037 9.18 0.00 41.15 3.51
771 2791 9.448438 TTTATAGGGATGAATGTATGTATGCAC 57.552 33.333 0.00 0.00 0.00 4.57
772 2792 4.318332 AGGGATGAATGTATGTATGCACG 58.682 43.478 0.00 0.00 0.00 5.34
778 2798 7.544217 GGATGAATGTATGTATGCACGTGTATA 59.456 37.037 20.58 20.58 0.00 1.47
781 2801 8.085296 TGAATGTATGTATGCACGTGTATATGA 58.915 33.333 25.81 17.13 0.00 2.15
782 2802 8.466086 AATGTATGTATGCACGTGTATATGAG 57.534 34.615 25.81 0.00 0.00 2.90
784 2804 6.861055 TGTATGTATGCACGTGTATATGAGTG 59.139 38.462 25.81 0.00 37.63 3.51
789 2809 3.575858 CACGTGTATATGAGTGCTTGC 57.424 47.619 7.58 0.00 0.00 4.01
790 2810 2.034591 CACGTGTATATGAGTGCTTGCG 60.035 50.000 7.58 0.00 0.00 4.85
791 2811 2.193447 CGTGTATATGAGTGCTTGCGT 58.807 47.619 0.00 0.00 0.00 5.24
792 2812 2.603110 CGTGTATATGAGTGCTTGCGTT 59.397 45.455 0.00 0.00 0.00 4.84
793 2813 3.062099 CGTGTATATGAGTGCTTGCGTTT 59.938 43.478 0.00 0.00 0.00 3.60
794 2814 4.266739 CGTGTATATGAGTGCTTGCGTTTA 59.733 41.667 0.00 0.00 0.00 2.01
795 2815 5.051039 CGTGTATATGAGTGCTTGCGTTTAT 60.051 40.000 0.00 0.00 0.00 1.40
799 2819 4.864916 ATGAGTGCTTGCGTTTATACTG 57.135 40.909 0.00 0.00 0.00 2.74
800 2820 3.659786 TGAGTGCTTGCGTTTATACTGT 58.340 40.909 0.00 0.00 0.00 3.55
804 2824 4.992319 AGTGCTTGCGTTTATACTGTGTTA 59.008 37.500 0.00 0.00 0.00 2.41
805 2825 5.467399 AGTGCTTGCGTTTATACTGTGTTAA 59.533 36.000 0.00 0.00 0.00 2.01
806 2826 6.017770 AGTGCTTGCGTTTATACTGTGTTAAA 60.018 34.615 0.00 0.00 0.00 1.52
809 2829 8.504815 TGCTTGCGTTTATACTGTGTTAAATAA 58.495 29.630 0.00 0.00 0.00 1.40
810 2830 9.332301 GCTTGCGTTTATACTGTGTTAAATAAA 57.668 29.630 0.00 0.00 0.00 1.40
822 2842 7.853929 ACTGTGTTAAATAAAACTACACAAGCG 59.146 33.333 0.00 0.00 45.72 4.68
823 2843 7.917597 TGTGTTAAATAAAACTACACAAGCGA 58.082 30.769 0.00 0.00 44.15 4.93
859 3199 6.945938 TTGGTTCCGTAGATTTTTCAGAAA 57.054 33.333 0.00 0.00 0.00 2.52
860 3200 6.554334 TGGTTCCGTAGATTTTTCAGAAAG 57.446 37.500 0.00 0.00 0.00 2.62
867 3207 7.387948 TCCGTAGATTTTTCAGAAAGAAAGAGG 59.612 37.037 0.00 0.00 46.24 3.69
880 3220 0.793617 AAAGAGGGAGACAGAGGGGA 59.206 55.000 0.00 0.00 0.00 4.81
881 3221 0.793617 AAGAGGGAGACAGAGGGGAA 59.206 55.000 0.00 0.00 0.00 3.97
911 3251 4.284550 GGCAGGCCTGGTTCACCA 62.285 66.667 33.46 0.00 45.30 4.17
921 3261 2.226330 CTGGTTCACCAAATTGACGGA 58.774 47.619 0.00 0.00 46.97 4.69
989 3329 0.612174 CTTCCACGACCCTCTCCTCA 60.612 60.000 0.00 0.00 0.00 3.86
1315 3676 0.110486 GGTACGCCATCCATCCCATT 59.890 55.000 0.00 0.00 34.09 3.16
1316 3677 1.523758 GTACGCCATCCATCCCATTC 58.476 55.000 0.00 0.00 0.00 2.67
1317 3678 0.400213 TACGCCATCCATCCCATTCC 59.600 55.000 0.00 0.00 0.00 3.01
1318 3679 1.604593 CGCCATCCATCCCATTCCC 60.605 63.158 0.00 0.00 0.00 3.97
1319 3680 1.543184 GCCATCCATCCCATTCCCA 59.457 57.895 0.00 0.00 0.00 4.37
1320 3681 0.115745 GCCATCCATCCCATTCCCAT 59.884 55.000 0.00 0.00 0.00 4.00
1336 3697 1.377994 CATCCCATCCCAGCCTAGC 59.622 63.158 0.00 0.00 0.00 3.42
1373 3738 2.424793 TCCCTTGGTTGTTAAGAGGGT 58.575 47.619 6.63 0.00 45.86 4.34
1391 3759 7.885009 AGAGGGTCACTACTTTCTAGAATAC 57.115 40.000 5.89 0.00 0.00 1.89
1422 3790 4.424626 TCTGCTTCGTGCTTCTATAGTTG 58.575 43.478 0.00 0.00 43.37 3.16
1476 3845 3.482472 GTCACTCGTGTAATCATGCTACG 59.518 47.826 0.00 0.00 36.20 3.51
1487 3856 8.691727 GTGTAATCATGCTACGTGTTCTTATAG 58.308 37.037 0.00 0.00 0.00 1.31
1678 4048 3.710722 CTGGGCGTCCTGCTCCTT 61.711 66.667 7.97 0.00 46.64 3.36
1682 4052 4.704833 GCGTCCTGCTCCTTGGCA 62.705 66.667 0.00 0.00 41.73 4.92
1696 4066 2.028484 GGCACGTCGGTCAAGTCA 59.972 61.111 0.00 0.00 0.00 3.41
1707 4077 0.533755 GTCAAGTCACTGCACCTGCT 60.534 55.000 0.00 0.00 42.66 4.24
1726 4096 2.413765 GACGTCTCTCCGGCCATC 59.586 66.667 8.70 0.00 0.00 3.51
1778 4148 2.126596 TGTTGCTGGCACTTGTGGG 61.127 57.895 2.81 0.00 0.00 4.61
1909 4279 2.031516 GGGAGACGTCGACTCGTGA 61.032 63.158 14.70 0.00 44.21 4.35
1939 4309 2.426522 CTTGCAGCTTACCTTGTGCTA 58.573 47.619 0.00 0.00 36.84 3.49
1959 4646 1.116536 TGTCAACCCCGTGCTGTCTA 61.117 55.000 0.00 0.00 0.00 2.59
1992 4679 1.005450 GTAAACATTCTGCCCCCAGGA 59.995 52.381 0.00 0.00 39.61 3.86
2113 4808 2.159114 AGTGTTGCCGCATTTGTTTTCT 60.159 40.909 0.00 0.00 0.00 2.52
2114 4809 2.607180 GTGTTGCCGCATTTGTTTTCTT 59.393 40.909 0.00 0.00 0.00 2.52
2115 4810 3.799420 GTGTTGCCGCATTTGTTTTCTTA 59.201 39.130 0.00 0.00 0.00 2.10
2116 4811 4.447389 GTGTTGCCGCATTTGTTTTCTTAT 59.553 37.500 0.00 0.00 0.00 1.73
2157 4852 6.700520 GTGGAAACGAATACGGAAAGAGATAT 59.299 38.462 0.00 0.00 44.46 1.63
2225 4921 2.816712 GCCGGAACTAAAAGACCCCTTT 60.817 50.000 5.05 0.00 44.00 3.11
2228 4924 5.258841 CCGGAACTAAAAGACCCCTTTAAT 58.741 41.667 0.00 0.00 41.46 1.40
2300 4996 4.442375 ACAACGTCTTTCGATGATCTCT 57.558 40.909 4.72 0.00 43.34 3.10
2315 5011 0.321298 TCTCTTAAACCAGCCGCACC 60.321 55.000 0.00 0.00 0.00 5.01
2318 5014 2.182614 CTTAAACCAGCCGCACCACG 62.183 60.000 0.00 0.00 43.15 4.94
2369 5065 2.689034 AGGAGGGTGTAGGCTGGC 60.689 66.667 0.00 0.00 0.00 4.85
2473 5169 0.538584 TGCTGGACTGAGCCACATAG 59.461 55.000 0.00 0.00 38.28 2.23
2474 5170 0.539051 GCTGGACTGAGCCACATAGT 59.461 55.000 0.00 0.00 33.52 2.12
2475 5171 1.757118 GCTGGACTGAGCCACATAGTA 59.243 52.381 0.00 0.00 33.52 1.82
2476 5172 2.223923 GCTGGACTGAGCCACATAGTAG 60.224 54.545 0.00 0.00 33.52 2.57
2477 5173 1.757118 TGGACTGAGCCACATAGTAGC 59.243 52.381 0.00 0.00 31.66 3.58
2478 5174 1.069358 GGACTGAGCCACATAGTAGCC 59.931 57.143 0.00 0.00 0.00 3.93
2488 5184 2.027745 CACATAGTAGCCTAGCCATGGG 60.028 54.545 15.13 0.00 0.00 4.00
2570 5266 9.627765 CGTTCAGCGTAAGAAATTCCATTTCCA 62.628 40.741 5.73 0.00 41.43 3.53
2590 5286 7.976414 TTCCATTTCCATTCCACAATATTCT 57.024 32.000 0.00 0.00 0.00 2.40
2666 5362 3.267031 CCACTCCCTTTTCATCCCTAAGT 59.733 47.826 0.00 0.00 0.00 2.24
2870 6194 3.732721 GGCGTATTCCATTCGTACTACAC 59.267 47.826 0.00 0.00 0.00 2.90
2930 6254 7.713764 AAACATTTTGATGCTTTCAAGGTAC 57.286 32.000 3.47 0.00 44.90 3.34
2969 6293 6.843333 GGTAGAAGATAAGTAGTACCCCCTTT 59.157 42.308 0.00 0.00 0.00 3.11
3000 6324 2.208326 AAGACGTTTTTGCAAGCTGG 57.792 45.000 0.00 0.00 0.00 4.85
3394 6718 8.696374 CATAGTTCTCACCTCCTCATTAGTTTA 58.304 37.037 0.00 0.00 0.00 2.01
3426 6750 8.671384 TGATTAGTATGGTTTCTATTTTCCGG 57.329 34.615 0.00 0.00 0.00 5.14
3555 6880 9.751542 CACTACTACTTCATGGATTTTACTAGG 57.248 37.037 0.00 0.00 0.00 3.02
3644 6969 4.993705 TCTTGATTTGGTGGTCCTTACT 57.006 40.909 0.00 0.00 34.23 2.24
3757 7082 7.253905 AGACACCTTGGTTAGTATACACATT 57.746 36.000 5.50 0.00 0.00 2.71
3832 7157 0.770499 TCATTGCTGGTTGTGGGAGA 59.230 50.000 0.00 0.00 0.00 3.71
3972 7297 3.369546 AACAGGCCTTCATTTTTGACG 57.630 42.857 0.00 0.00 0.00 4.35
4045 7370 6.470557 TTCCTTAATTAGTTGTTCGGTTCG 57.529 37.500 0.00 0.00 0.00 3.95
4052 7377 0.027063 GTTGTTCGGTTCGGTGTGTG 59.973 55.000 0.00 0.00 0.00 3.82
4123 7448 4.218200 CCACTCTCTACATCCTCTATGCTG 59.782 50.000 0.00 0.00 39.39 4.41
4128 7453 2.898729 ACATCCTCTATGCTGTTCCG 57.101 50.000 0.00 0.00 39.39 4.30
4185 7510 9.130312 GTTATAGAAGATGACGTATGCTTTAGG 57.870 37.037 0.00 0.00 0.00 2.69
4223 7548 7.944061 TGTGAAAACATGAATTCTGAATGAGT 58.056 30.769 7.05 0.00 0.00 3.41
4388 7716 3.514645 CTTTGCCATTAACTCCATGTGC 58.485 45.455 0.00 0.00 0.00 4.57
4391 7719 1.093972 CCATTAACTCCATGTGCGCA 58.906 50.000 5.66 5.66 0.00 6.09
4417 7745 7.870445 ACCCAACAATAATTTGTGTTATGTGTC 59.130 33.333 6.22 0.00 45.30 3.67
4534 7862 1.476085 CTGACAGTCGAGCCAGAGAAT 59.524 52.381 0.00 0.00 0.00 2.40
4703 8244 6.448006 CCGCTAGTTACTATGCTTCTGTAAT 58.552 40.000 10.40 0.00 0.00 1.89
4825 8366 7.226059 AGGATACCTGGAAAGGTTGATAAAT 57.774 36.000 0.00 0.00 42.99 1.40
4836 8377 2.101917 GGTTGATAAATGCAGCTGCCAT 59.898 45.455 34.64 23.90 41.18 4.40
4882 8423 5.163703 TGCTTCTTGTTTTAAGTTTGCGAGA 60.164 36.000 0.00 0.00 0.00 4.04
4889 8430 5.205565 GTTTTAAGTTTGCGAGACCTCTTG 58.794 41.667 0.00 0.00 0.00 3.02
5049 8590 4.701765 AGTCCAGTCTGCTAATATGCTTG 58.298 43.478 0.00 0.00 0.00 4.01
5054 8595 4.993584 CAGTCTGCTAATATGCTTGGGTAG 59.006 45.833 0.00 0.00 0.00 3.18
5091 8632 6.648879 ACTGTTGTGGCATGTTAATTACTT 57.351 33.333 0.00 0.00 0.00 2.24
5093 8634 6.019779 TGTTGTGGCATGTTAATTACTTCC 57.980 37.500 0.00 0.00 0.00 3.46
5116 8657 6.015350 TCCGGTATGTTATTTCTTGGCAAAAA 60.015 34.615 0.00 5.78 0.00 1.94
5175 8718 6.381133 TGTGTATATCTGAAGTCTGTGATGGT 59.619 38.462 0.00 0.00 0.00 3.55
5176 8719 7.093333 TGTGTATATCTGAAGTCTGTGATGGTT 60.093 37.037 0.00 0.00 0.00 3.67
5295 8866 0.531974 TATCATTTCCCCGCTGACGC 60.532 55.000 0.00 0.00 38.22 5.19
5316 8887 3.056536 GCTGAGCGATATAATGGGAGTCA 60.057 47.826 0.00 0.00 0.00 3.41
5356 8935 0.034059 CGGAGTGAACTTGCTGGAGT 59.966 55.000 0.00 0.00 0.00 3.85
5390 8969 1.066303 CATTCTCGTCTCTTCTCCCCG 59.934 57.143 0.00 0.00 0.00 5.73
5392 8971 2.754658 TCGTCTCTTCTCCCCGGC 60.755 66.667 0.00 0.00 0.00 6.13
5498 9077 1.301479 GAACGGTCCGAAAGTGGCT 60.301 57.895 20.51 0.00 0.00 4.75
5499 9078 1.566018 GAACGGTCCGAAAGTGGCTG 61.566 60.000 20.51 0.00 0.00 4.85
5500 9079 3.423154 CGGTCCGAAAGTGGCTGC 61.423 66.667 4.91 0.00 0.00 5.25
5522 9101 2.107953 GGATCGCCTGGCTCACTC 59.892 66.667 17.92 7.52 0.00 3.51
5528 9107 2.936912 GCCTGGCTCACTCGTCTGT 61.937 63.158 12.43 0.00 0.00 3.41
5618 9200 3.251245 CCGTGTAACCAAACATGTGCTTA 59.749 43.478 0.00 0.00 35.08 3.09
5736 9318 2.358125 CCGGTGACATTGTGCGGA 60.358 61.111 0.00 0.00 0.00 5.54
5861 9443 4.201920 CGAGTGTCACATTCGAGGATCTTA 60.202 45.833 17.22 0.00 44.29 2.10
5936 9518 1.412453 TTTCCTGGTACGTGTGCCCT 61.412 55.000 0.00 0.00 34.17 5.19
6007 9600 4.449068 CGCATCCATGATTGTTACTCCTAC 59.551 45.833 0.00 0.00 0.00 3.18
6008 9601 5.615289 GCATCCATGATTGTTACTCCTACT 58.385 41.667 0.00 0.00 0.00 2.57
6009 9602 6.516693 CGCATCCATGATTGTTACTCCTACTA 60.517 42.308 0.00 0.00 0.00 1.82
6011 9604 8.531982 GCATCCATGATTGTTACTCCTACTATA 58.468 37.037 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 139 7.051623 ACATATTTTGGCGACCATTTAGACTA 58.948 34.615 0.00 0.00 31.53 2.59
149 150 3.490761 CCCATTGGACATATTTTGGCGAC 60.491 47.826 3.62 0.00 32.19 5.19
151 152 2.430332 ACCCATTGGACATATTTTGGCG 59.570 45.455 3.62 0.00 32.19 5.69
152 153 4.486125 AACCCATTGGACATATTTTGGC 57.514 40.909 3.62 0.00 34.81 4.52
165 166 3.809279 GGCTTTGAAAGTGAAACCCATTG 59.191 43.478 6.81 0.00 37.80 2.82
269 272 3.607209 CCTTCTTACTACTGACGAAACGC 59.393 47.826 0.00 0.00 0.00 4.84
273 276 6.600882 ATTTCCCTTCTTACTACTGACGAA 57.399 37.500 0.00 0.00 0.00 3.85
287 291 3.431905 GGACGGAGGAGTAATTTCCCTTC 60.432 52.174 0.00 0.00 38.02 3.46
290 294 2.117051 AGGACGGAGGAGTAATTTCCC 58.883 52.381 0.00 0.00 38.02 3.97
291 295 6.854091 ATATAGGACGGAGGAGTAATTTCC 57.146 41.667 0.00 0.00 37.52 3.13
346 370 9.930693 CCCCTCTCTCTAATATAACATAACAAC 57.069 37.037 0.00 0.00 0.00 3.32
347 371 9.670442 ACCCCTCTCTCTAATATAACATAACAA 57.330 33.333 0.00 0.00 0.00 2.83
360 384 2.735259 AAACCCACCCCTCTCTCTAA 57.265 50.000 0.00 0.00 0.00 2.10
364 388 2.999928 TCTTAAAACCCACCCCTCTCT 58.000 47.619 0.00 0.00 0.00 3.10
366 390 4.759793 AAATCTTAAAACCCACCCCTCT 57.240 40.909 0.00 0.00 0.00 3.69
367 391 5.818678 AAAAATCTTAAAACCCACCCCTC 57.181 39.130 0.00 0.00 0.00 4.30
422 448 9.962809 TCATGAATATATCAATTACATCCAGCA 57.037 29.630 0.00 0.00 42.54 4.41
497 525 1.796459 GGTTCGCATCGTTTGTGTAGT 59.204 47.619 2.55 0.00 37.14 2.73
498 526 1.795872 TGGTTCGCATCGTTTGTGTAG 59.204 47.619 2.55 0.00 37.14 2.74
499 527 1.867166 TGGTTCGCATCGTTTGTGTA 58.133 45.000 2.55 0.00 37.14 2.90
500 528 1.018148 TTGGTTCGCATCGTTTGTGT 58.982 45.000 2.55 0.00 37.14 3.72
501 529 2.330231 ATTGGTTCGCATCGTTTGTG 57.670 45.000 0.00 0.00 37.17 3.33
502 530 3.438781 ACATATTGGTTCGCATCGTTTGT 59.561 39.130 0.00 0.00 0.00 2.83
503 531 3.785521 CACATATTGGTTCGCATCGTTTG 59.214 43.478 0.00 0.00 0.00 2.93
504 532 3.181501 CCACATATTGGTTCGCATCGTTT 60.182 43.478 0.00 0.00 41.10 3.60
505 533 2.354510 CCACATATTGGTTCGCATCGTT 59.645 45.455 0.00 0.00 41.10 3.85
506 534 1.939934 CCACATATTGGTTCGCATCGT 59.060 47.619 0.00 0.00 41.10 3.73
507 535 2.668617 CCACATATTGGTTCGCATCG 57.331 50.000 0.00 0.00 41.10 3.84
519 547 5.043732 TCCCTTTAACCATCCAACCACATAT 60.044 40.000 0.00 0.00 0.00 1.78
520 548 4.292571 TCCCTTTAACCATCCAACCACATA 59.707 41.667 0.00 0.00 0.00 2.29
521 549 3.076785 TCCCTTTAACCATCCAACCACAT 59.923 43.478 0.00 0.00 0.00 3.21
522 550 2.447429 TCCCTTTAACCATCCAACCACA 59.553 45.455 0.00 0.00 0.00 4.17
523 551 3.163616 TCCCTTTAACCATCCAACCAC 57.836 47.619 0.00 0.00 0.00 4.16
524 552 3.623703 CGATCCCTTTAACCATCCAACCA 60.624 47.826 0.00 0.00 0.00 3.67
525 553 2.949644 CGATCCCTTTAACCATCCAACC 59.050 50.000 0.00 0.00 0.00 3.77
526 554 3.377172 CACGATCCCTTTAACCATCCAAC 59.623 47.826 0.00 0.00 0.00 3.77
528 556 2.092646 CCACGATCCCTTTAACCATCCA 60.093 50.000 0.00 0.00 0.00 3.41
532 560 3.135167 GGATACCACGATCCCTTTAACCA 59.865 47.826 0.00 0.00 39.74 3.67
549 577 2.919043 CCTGGTGGGCTGGGATAC 59.081 66.667 0.00 0.00 0.00 2.24
559 587 2.034687 CAGGCTGAACCCTGGTGG 59.965 66.667 9.42 0.00 46.93 4.61
572 600 0.740737 AATAAATGCGAGCACCAGGC 59.259 50.000 0.00 0.00 45.30 4.85
573 601 1.334869 GGAATAAATGCGAGCACCAGG 59.665 52.381 0.00 0.00 0.00 4.45
574 602 2.292267 AGGAATAAATGCGAGCACCAG 58.708 47.619 0.00 0.00 0.00 4.00
575 603 2.418368 AGGAATAAATGCGAGCACCA 57.582 45.000 0.00 0.00 0.00 4.17
576 604 4.893424 TTTAGGAATAAATGCGAGCACC 57.107 40.909 0.00 0.00 0.00 5.01
577 605 9.463443 AATAAATTTAGGAATAAATGCGAGCAC 57.537 29.630 0.00 0.00 30.77 4.40
592 620 7.167468 CGCCGAAAATCCTGAAATAAATTTAGG 59.833 37.037 3.94 0.94 0.00 2.69
594 622 7.698970 GTCGCCGAAAATCCTGAAATAAATTTA 59.301 33.333 0.00 0.00 0.00 1.40
595 623 6.530181 GTCGCCGAAAATCCTGAAATAAATTT 59.470 34.615 0.00 0.00 0.00 1.82
597 625 5.124776 TGTCGCCGAAAATCCTGAAATAAAT 59.875 36.000 0.00 0.00 0.00 1.40
598 626 4.456222 TGTCGCCGAAAATCCTGAAATAAA 59.544 37.500 0.00 0.00 0.00 1.40
599 627 4.004314 TGTCGCCGAAAATCCTGAAATAA 58.996 39.130 0.00 0.00 0.00 1.40
600 628 3.372822 GTGTCGCCGAAAATCCTGAAATA 59.627 43.478 0.00 0.00 0.00 1.40
601 629 2.161609 GTGTCGCCGAAAATCCTGAAAT 59.838 45.455 0.00 0.00 0.00 2.17
602 630 1.533731 GTGTCGCCGAAAATCCTGAAA 59.466 47.619 0.00 0.00 0.00 2.69
603 631 1.153353 GTGTCGCCGAAAATCCTGAA 58.847 50.000 0.00 0.00 0.00 3.02
604 632 1.011968 CGTGTCGCCGAAAATCCTGA 61.012 55.000 0.00 0.00 0.00 3.86
605 633 1.419922 CGTGTCGCCGAAAATCCTG 59.580 57.895 0.00 0.00 0.00 3.86
606 634 3.870606 CGTGTCGCCGAAAATCCT 58.129 55.556 0.00 0.00 0.00 3.24
617 645 1.136252 CCTTTCACTGAATGCGTGTCG 60.136 52.381 0.00 0.00 34.14 4.35
618 646 2.143122 TCCTTTCACTGAATGCGTGTC 58.857 47.619 0.00 0.00 34.14 3.67
620 648 2.158449 GTCTCCTTTCACTGAATGCGTG 59.842 50.000 0.00 0.00 0.00 5.34
622 650 1.391485 CGTCTCCTTTCACTGAATGCG 59.609 52.381 0.00 0.00 0.00 4.73
626 2050 2.224209 GGGAACGTCTCCTTTCACTGAA 60.224 50.000 13.94 0.00 44.68 3.02
627 2051 1.343465 GGGAACGTCTCCTTTCACTGA 59.657 52.381 13.94 0.00 44.68 3.41
628 2052 1.797025 GGGAACGTCTCCTTTCACTG 58.203 55.000 13.94 0.00 44.68 3.66
648 2072 0.520827 CTAAGCACCTCGTCGTCGAC 60.521 60.000 15.51 15.51 41.35 4.20
650 2074 1.226323 CCTAAGCACCTCGTCGTCG 60.226 63.158 0.00 0.00 38.55 5.12
652 2076 0.892358 TCACCTAAGCACCTCGTCGT 60.892 55.000 0.00 0.00 0.00 4.34
653 2077 0.456312 GTCACCTAAGCACCTCGTCG 60.456 60.000 0.00 0.00 0.00 5.12
654 2078 0.889306 AGTCACCTAAGCACCTCGTC 59.111 55.000 0.00 0.00 0.00 4.20
655 2079 1.339097 AAGTCACCTAAGCACCTCGT 58.661 50.000 0.00 0.00 0.00 4.18
657 2081 3.127425 ACAAAGTCACCTAAGCACCTC 57.873 47.619 0.00 0.00 0.00 3.85
662 2086 8.349983 TCTTGAAATTTACAAAGTCACCTAAGC 58.650 33.333 0.00 0.00 0.00 3.09
665 2089 9.567776 TCATCTTGAAATTTACAAAGTCACCTA 57.432 29.630 0.00 0.00 0.00 3.08
666 2090 8.463930 TCATCTTGAAATTTACAAAGTCACCT 57.536 30.769 0.00 0.00 0.00 4.00
671 2095 9.807649 GGCATATCATCTTGAAATTTACAAAGT 57.192 29.630 0.00 0.00 0.00 2.66
672 2096 8.961092 CGGCATATCATCTTGAAATTTACAAAG 58.039 33.333 0.00 0.00 0.00 2.77
674 2098 7.424803 CCGGCATATCATCTTGAAATTTACAA 58.575 34.615 0.00 0.00 0.00 2.41
677 2101 5.769662 AGCCGGCATATCATCTTGAAATTTA 59.230 36.000 31.54 0.00 0.00 1.40
679 2103 4.147321 AGCCGGCATATCATCTTGAAATT 58.853 39.130 31.54 0.00 0.00 1.82
680 2104 3.755378 GAGCCGGCATATCATCTTGAAAT 59.245 43.478 31.54 0.06 0.00 2.17
681 2105 3.141398 GAGCCGGCATATCATCTTGAAA 58.859 45.455 31.54 0.00 0.00 2.69
682 2106 2.104622 TGAGCCGGCATATCATCTTGAA 59.895 45.455 31.54 0.00 0.00 2.69
683 2107 1.693606 TGAGCCGGCATATCATCTTGA 59.306 47.619 31.54 0.00 0.00 3.02
684 2108 2.074576 CTGAGCCGGCATATCATCTTG 58.925 52.381 31.54 7.95 0.00 3.02
685 2109 1.696336 ACTGAGCCGGCATATCATCTT 59.304 47.619 31.54 3.33 0.00 2.40
686 2110 1.274728 GACTGAGCCGGCATATCATCT 59.725 52.381 31.54 11.40 0.00 2.90
688 2112 1.346062 AGACTGAGCCGGCATATCAT 58.654 50.000 31.54 13.17 0.00 2.45
689 2113 1.123077 AAGACTGAGCCGGCATATCA 58.877 50.000 31.54 22.44 0.00 2.15
690 2114 2.139118 GAAAGACTGAGCCGGCATATC 58.861 52.381 31.54 18.63 0.00 1.63
692 2116 0.179111 CGAAAGACTGAGCCGGCATA 60.179 55.000 31.54 16.21 0.00 3.14
695 2119 1.355066 CTTCGAAAGACTGAGCCGGC 61.355 60.000 21.89 21.89 41.84 6.13
696 2120 0.737715 CCTTCGAAAGACTGAGCCGG 60.738 60.000 0.00 0.00 41.84 6.13
698 2122 1.433534 CACCTTCGAAAGACTGAGCC 58.566 55.000 0.00 0.00 41.84 4.70
699 2123 0.793250 GCACCTTCGAAAGACTGAGC 59.207 55.000 0.00 0.00 41.84 4.26
701 2125 1.686587 TGAGCACCTTCGAAAGACTGA 59.313 47.619 0.00 0.00 41.84 3.41
702 2126 2.154854 TGAGCACCTTCGAAAGACTG 57.845 50.000 0.00 0.00 41.84 3.51
703 2127 3.118956 CCTATGAGCACCTTCGAAAGACT 60.119 47.826 0.00 0.00 41.84 3.24
705 2129 2.168521 CCCTATGAGCACCTTCGAAAGA 59.831 50.000 0.00 0.00 39.20 2.52
706 2130 2.555199 CCCTATGAGCACCTTCGAAAG 58.445 52.381 0.00 0.00 0.00 2.62
709 2133 0.325296 ACCCCTATGAGCACCTTCGA 60.325 55.000 0.00 0.00 0.00 3.71
711 2135 1.694696 CCTACCCCTATGAGCACCTTC 59.305 57.143 0.00 0.00 0.00 3.46
713 2137 0.941963 TCCTACCCCTATGAGCACCT 59.058 55.000 0.00 0.00 0.00 4.00
715 2139 2.037772 CACATCCTACCCCTATGAGCAC 59.962 54.545 0.00 0.00 0.00 4.40
716 2140 2.329267 CACATCCTACCCCTATGAGCA 58.671 52.381 0.00 0.00 0.00 4.26
717 2141 2.037772 CACACATCCTACCCCTATGAGC 59.962 54.545 0.00 0.00 0.00 4.26
718 2142 3.309296 ACACACATCCTACCCCTATGAG 58.691 50.000 0.00 0.00 0.00 2.90
720 2144 5.778241 TGTATACACACATCCTACCCCTATG 59.222 44.000 0.08 0.00 0.00 2.23
721 2145 5.972698 TGTATACACACATCCTACCCCTAT 58.027 41.667 0.08 0.00 0.00 2.57
724 2148 5.562298 AATGTATACACACATCCTACCCC 57.438 43.478 7.96 0.00 38.19 4.95
727 2151 9.871238 CCCTATAAATGTATACACACATCCTAC 57.129 37.037 7.96 0.00 38.19 3.18
728 2152 9.831682 TCCCTATAAATGTATACACACATCCTA 57.168 33.333 7.96 0.00 38.19 2.94
745 2169 9.448438 GTGCATACATACATTCATCCCTATAAA 57.552 33.333 0.00 0.00 0.00 1.40
746 2170 7.763985 CGTGCATACATACATTCATCCCTATAA 59.236 37.037 0.00 0.00 0.00 0.98
749 2769 5.011635 ACGTGCATACATACATTCATCCCTA 59.988 40.000 0.00 0.00 0.00 3.53
752 2772 4.511454 ACACGTGCATACATACATTCATCC 59.489 41.667 17.22 0.00 0.00 3.51
755 2775 8.085296 TCATATACACGTGCATACATACATTCA 58.915 33.333 17.22 0.00 0.00 2.57
756 2776 8.460831 TCATATACACGTGCATACATACATTC 57.539 34.615 17.22 0.00 0.00 2.67
760 2780 7.265693 CACTCATATACACGTGCATACATAC 57.734 40.000 17.22 0.00 0.00 2.39
771 2791 2.193447 ACGCAAGCACTCATATACACG 58.807 47.619 0.00 0.00 45.62 4.49
772 2792 4.600012 AAACGCAAGCACTCATATACAC 57.400 40.909 0.00 0.00 45.62 2.90
778 2798 4.093408 CACAGTATAAACGCAAGCACTCAT 59.907 41.667 0.00 0.00 45.62 2.90
781 2801 3.399330 ACACAGTATAAACGCAAGCACT 58.601 40.909 0.00 0.00 45.62 4.40
782 2802 3.806316 ACACAGTATAAACGCAAGCAC 57.194 42.857 0.00 0.00 45.62 4.40
784 2804 8.883789 TTATTTAACACAGTATAAACGCAAGC 57.116 30.769 0.00 0.00 45.62 4.01
799 2819 8.944212 ATCGCTTGTGTAGTTTTATTTAACAC 57.056 30.769 0.00 0.00 40.61 3.32
804 2824 6.456449 CGCCTATCGCTTGTGTAGTTTTATTT 60.456 38.462 0.00 0.00 34.21 1.40
805 2825 5.006358 CGCCTATCGCTTGTGTAGTTTTATT 59.994 40.000 0.00 0.00 34.21 1.40
806 2826 4.506654 CGCCTATCGCTTGTGTAGTTTTAT 59.493 41.667 0.00 0.00 34.21 1.40
809 2829 2.268298 CGCCTATCGCTTGTGTAGTTT 58.732 47.619 0.00 0.00 34.21 2.66
810 2830 1.922570 CGCCTATCGCTTGTGTAGTT 58.077 50.000 0.00 0.00 34.21 2.24
811 2831 3.642901 CGCCTATCGCTTGTGTAGT 57.357 52.632 0.00 0.00 34.21 2.73
821 2841 0.033504 ACCAATACAGGCGCCTATCG 59.966 55.000 32.30 20.37 42.12 2.92
822 2842 2.143925 GAACCAATACAGGCGCCTATC 58.856 52.381 32.30 13.04 0.00 2.08
823 2843 1.202770 GGAACCAATACAGGCGCCTAT 60.203 52.381 32.30 23.53 0.00 2.57
825 2845 1.077716 GGAACCAATACAGGCGCCT 60.078 57.895 27.08 27.08 0.00 5.52
826 2846 2.469516 CGGAACCAATACAGGCGCC 61.470 63.158 21.89 21.89 0.00 6.53
829 2849 2.973694 TCTACGGAACCAATACAGGC 57.026 50.000 0.00 0.00 0.00 4.85
830 2850 6.373216 TGAAAAATCTACGGAACCAATACAGG 59.627 38.462 0.00 0.00 0.00 4.00
832 2852 7.162761 TCTGAAAAATCTACGGAACCAATACA 58.837 34.615 0.00 0.00 0.00 2.29
859 3199 1.273552 CCCCTCTGTCTCCCTCTTTCT 60.274 57.143 0.00 0.00 0.00 2.52
860 3200 1.199615 CCCCTCTGTCTCCCTCTTTC 58.800 60.000 0.00 0.00 0.00 2.62
881 3221 1.000843 GGCCTGCCATCGTTTCTTTTT 59.999 47.619 2.58 0.00 35.81 1.94
886 3226 2.409870 CCAGGCCTGCCATCGTTTC 61.410 63.158 28.39 0.00 38.92 2.78
911 3251 4.202367 GGGATCCTCTGTATCCGTCAATTT 60.202 45.833 12.58 0.00 43.36 1.82
921 3261 2.695585 GGAACCAGGGATCCTCTGTAT 58.304 52.381 21.69 13.59 34.69 2.29
989 3329 3.249189 TGGAAGCAGGCCGGAAGT 61.249 61.111 5.05 0.00 0.00 3.01
1042 3382 2.498167 CCACCGGAATGATCTTCATCC 58.502 52.381 9.46 0.00 35.76 3.51
1315 3676 1.984253 TAGGCTGGGATGGGATGGGA 61.984 60.000 0.00 0.00 0.00 4.37
1316 3677 1.464001 TAGGCTGGGATGGGATGGG 60.464 63.158 0.00 0.00 0.00 4.00
1317 3678 2.073232 CTAGGCTGGGATGGGATGG 58.927 63.158 0.00 0.00 0.00 3.51
1318 3679 1.377994 GCTAGGCTGGGATGGGATG 59.622 63.158 0.00 0.00 0.00 3.51
1319 3680 0.698886 TTGCTAGGCTGGGATGGGAT 60.699 55.000 0.00 0.00 0.00 3.85
1320 3681 0.698886 ATTGCTAGGCTGGGATGGGA 60.699 55.000 0.00 0.00 0.00 4.37
1336 3697 3.545703 AGGGAAGTAAGCCGATGAATTG 58.454 45.455 0.00 0.00 0.00 2.32
1373 3738 7.681304 GCACATCCGTATTCTAGAAAGTAGTGA 60.681 40.741 9.71 2.63 0.00 3.41
1391 3759 1.446792 ACGAAGCAGAGCACATCCG 60.447 57.895 0.00 0.00 0.00 4.18
1422 3790 6.089417 GCAATTATACTGGTTTGTTCTGCAAC 59.911 38.462 0.00 0.00 36.72 4.17
1487 3856 8.547069 CATTTCTCCATCTCTATTTTCGAGTTC 58.453 37.037 0.00 0.00 0.00 3.01
1496 3866 7.876371 TCCTTTTCCATTTCTCCATCTCTATT 58.124 34.615 0.00 0.00 0.00 1.73
1678 4048 2.028484 GACTTGACCGACGTGCCA 59.972 61.111 0.00 0.00 0.00 4.92
1682 4052 1.299926 GCAGTGACTTGACCGACGT 60.300 57.895 0.00 0.00 0.00 4.34
1696 4066 3.521529 GACGTCCAGCAGGTGCAGT 62.522 63.158 3.51 0.00 45.16 4.40
1707 4077 3.957435 ATGGCCGGAGAGACGTCCA 62.957 63.158 13.01 0.00 36.23 4.02
1726 4096 2.100631 GTCAACCGATGCCTGACCG 61.101 63.158 0.00 0.00 34.63 4.79
1778 4148 2.100631 CCACACCGTTCGGATGCTC 61.101 63.158 18.28 0.00 0.00 4.26
1785 4155 2.591311 CGGAACACCACACCGTTCG 61.591 63.158 0.00 0.00 41.97 3.95
1909 4279 2.437359 GCTGCAAGGGCGATCAGT 60.437 61.111 0.00 0.00 45.35 3.41
1939 4309 1.302511 GACAGCACGGGGTTGACAT 60.303 57.895 0.00 0.00 0.00 3.06
1959 4646 7.043565 GCAGAATGTTTACATCATTTTGGGAT 58.956 34.615 9.83 0.00 37.64 3.85
1992 4679 0.105504 AAAAGAACAGGGGCAAGCCT 60.106 50.000 11.40 0.00 36.10 4.58
2085 4780 1.237285 ATGCGGCAACACTCAGTTCC 61.237 55.000 6.82 0.00 38.74 3.62
2157 4852 3.456280 GCACCGTATTCATTACCGGTAA 58.544 45.455 28.40 28.40 36.33 2.85
2225 4921 7.993821 TTGCTTGTGTTTTTCGAAATCATTA 57.006 28.000 12.12 5.65 0.00 1.90
2228 4924 5.866633 AGTTTGCTTGTGTTTTTCGAAATCA 59.133 32.000 12.12 11.28 0.00 2.57
2300 4996 2.255172 CGTGGTGCGGCTGGTTTAA 61.255 57.895 0.00 0.00 36.85 1.52
2318 5014 4.767255 CTGTCCAGGCGCCTCCAC 62.767 72.222 30.29 25.51 37.29 4.02
2369 5065 0.179000 GTGTCACTATCCCCAGCAGG 59.821 60.000 0.00 0.00 0.00 4.85
2473 5169 0.843984 TTTCCCCATGGCTAGGCTAC 59.156 55.000 18.18 0.00 0.00 3.58
2474 5170 0.843984 GTTTCCCCATGGCTAGGCTA 59.156 55.000 18.18 4.39 0.00 3.93
2475 5171 1.615262 GTTTCCCCATGGCTAGGCT 59.385 57.895 18.18 0.00 0.00 4.58
2476 5172 1.823899 CGTTTCCCCATGGCTAGGC 60.824 63.158 9.85 9.85 0.00 3.93
2477 5173 1.152963 CCGTTTCCCCATGGCTAGG 60.153 63.158 6.09 2.13 0.00 3.02
2478 5174 0.254747 TTCCGTTTCCCCATGGCTAG 59.745 55.000 6.09 0.00 0.00 3.42
2570 5266 8.260114 GGAAACAGAATATTGTGGAATGGAAAT 58.740 33.333 16.24 0.00 0.00 2.17
2590 5286 6.148811 GGTGATGAAGAAGAAATACGGAAACA 59.851 38.462 0.00 0.00 0.00 2.83
2608 5304 3.147553 TCCATGGAAAAACGGTGATGA 57.852 42.857 13.46 0.00 0.00 2.92
2651 5347 7.510549 TTCTGTTCAACTTAGGGATGAAAAG 57.489 36.000 7.90 7.90 38.98 2.27
2838 6162 6.018507 ACGAATGGAATACGCCAATTACTTAC 60.019 38.462 0.00 0.00 42.16 2.34
2870 6194 2.791417 TTTGTATTAGAAACGCCGCG 57.209 45.000 12.14 12.14 0.00 6.46
2872 6196 7.634817 CAGTCTTTATTTGTATTAGAAACGCCG 59.365 37.037 0.00 0.00 0.00 6.46
2930 6254 4.730966 TCTTCTACCTACTGCCAGATAGG 58.269 47.826 14.86 14.86 43.26 2.57
2969 6293 5.583495 CAAAAACGTCTTTATTGTGGGACA 58.417 37.500 0.00 0.00 0.00 4.02
3000 6324 9.586435 AATATAAGATGTTTTTGCAAGCTAACC 57.414 29.630 14.60 4.89 0.00 2.85
3034 6358 8.526667 TTTAGCACATATTGAGTACTCTCTCT 57.473 34.615 23.01 10.89 40.98 3.10
3170 6494 2.173356 CCACCAGCATGATCCCTAGAAA 59.827 50.000 0.00 0.00 39.69 2.52
3424 6748 5.773239 TCTTTTAAAGCTTACGTGATCCG 57.227 39.130 0.00 2.55 44.03 4.18
3490 6815 1.825090 TTCAAGCGGATGCACATCTT 58.175 45.000 10.30 0.00 46.23 2.40
3555 6880 7.156876 TCCAACACCATTCAAATCAGTAATC 57.843 36.000 0.00 0.00 0.00 1.75
3757 7082 9.851686 AACATGGAGAAGAGCAATTATTATGTA 57.148 29.630 0.00 0.00 0.00 2.29
3808 7133 1.682854 CCACAACCAGCAATGAACTGT 59.317 47.619 0.00 0.00 33.09 3.55
3832 7157 1.276989 TCTGCCGTACCCTCGAAAAAT 59.723 47.619 0.00 0.00 0.00 1.82
4045 7370 3.202906 ACACATGTAACAGACACACACC 58.797 45.455 0.00 0.00 42.17 4.16
4052 7377 5.176774 TCGATGTTGAACACATGTAACAGAC 59.823 40.000 15.15 11.25 46.96 3.51
4123 7448 2.131972 GGCCAAAACAATCAACGGAAC 58.868 47.619 0.00 0.00 0.00 3.62
4128 7453 3.751479 AAGGAGGCCAAAACAATCAAC 57.249 42.857 5.01 0.00 0.00 3.18
4185 7510 3.066621 TGTTTTCACATGCACTCCAGAAC 59.933 43.478 0.00 0.00 0.00 3.01
4417 7745 7.586714 TCTGTTCAAGCATATCATATTAGCG 57.413 36.000 0.00 0.00 0.00 4.26
4579 7907 0.109919 GAACCGTCGGTTGATTTGCC 60.110 55.000 33.41 13.71 46.95 4.52
4668 7996 2.781681 AACTAGCGGGTGTGCTTTAT 57.218 45.000 0.00 0.00 44.46 1.40
4703 8244 2.025155 ACCAAATGTGTGCCGTTTGTA 58.975 42.857 6.34 0.00 44.95 2.41
4825 8366 1.340308 ACAGTATGAATGGCAGCTGCA 60.340 47.619 37.63 24.48 40.55 4.41
4836 8377 2.168521 GCAGCAGGACCTACAGTATGAA 59.831 50.000 0.00 0.00 39.69 2.57
4882 8423 2.787994 CATCAGCCAACTTCAAGAGGT 58.212 47.619 0.00 0.00 0.00 3.85
4889 8430 4.082571 ACAATTACTGCATCAGCCAACTTC 60.083 41.667 0.00 0.00 41.13 3.01
5049 8590 4.278419 ACAGTTGTTTTCTGATTGCTACCC 59.722 41.667 0.00 0.00 36.81 3.69
5054 8595 4.268405 CCACAACAGTTGTTTTCTGATTGC 59.732 41.667 16.70 0.00 43.23 3.56
5091 8632 4.223556 TGCCAAGAAATAACATACCGGA 57.776 40.909 9.46 0.00 0.00 5.14
5145 8688 7.394641 TCACAGACTTCAGATATACACAAGACT 59.605 37.037 0.00 0.00 0.00 3.24
5175 8718 7.440198 TCATCAAATGTATGCAAGTTCCAAAA 58.560 30.769 0.00 0.00 0.00 2.44
5176 8719 6.990798 TCATCAAATGTATGCAAGTTCCAAA 58.009 32.000 0.00 0.00 0.00 3.28
5295 8866 4.790765 TGACTCCCATTATATCGCTCAG 57.209 45.455 0.00 0.00 0.00 3.35
5316 8887 2.616842 GTCCATTTTGTGTCGTGTCCTT 59.383 45.455 0.00 0.00 0.00 3.36
5356 8935 2.611971 CGAGAATGAAGGACGAACCCAA 60.612 50.000 0.00 0.00 40.05 4.12
5390 8969 1.808411 TGGTGAAGTCGAATTCTGCC 58.192 50.000 24.25 23.57 0.00 4.85
5392 8971 4.434725 CGTTCATGGTGAAGTCGAATTCTG 60.435 45.833 24.25 14.98 37.00 3.02
5504 9083 3.781770 GAGTGAGCCAGGCGATCCG 62.782 68.421 5.55 0.00 37.47 4.18
5515 9094 2.807045 CGCCACAGACGAGTGAGC 60.807 66.667 8.54 8.86 42.05 4.26
5516 9095 2.755542 AAGCGCCACAGACGAGTGAG 62.756 60.000 2.29 4.55 42.05 3.51
5522 9101 2.356313 ACAGAAGCGCCACAGACG 60.356 61.111 2.29 0.00 0.00 4.18
5618 9200 1.612395 CCGCCTTCTTGGAGAGAGCT 61.612 60.000 0.00 0.00 37.90 4.09
5756 9338 3.682292 CTACCCCTCAAGTGCCGCC 62.682 68.421 0.00 0.00 0.00 6.13
5861 9443 3.133365 AAGGCTGGCCACCGAGTTT 62.133 57.895 14.39 0.00 38.92 2.66
5950 9532 2.228138 AGTTTTGGTGCAGCAACATG 57.772 45.000 29.69 0.00 28.36 3.21


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

AutoCloner maintained by Alex Coulton.