Multiple sequence alignment - TraesCS3A01G358900

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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 TraesCS3A01G358900 chr3A 100.000 3299 0 0 1 3299 606831598 606828300 0.000000e+00 6093.0
1 TraesCS3A01G358900 chr3A 87.612 557 59 6 1 552 80626067 80626618 3.590000e-179 638.0
2 TraesCS3A01G358900 chr3A 97.222 108 3 0 3116 3223 399421550 399421657 2.020000e-42 183.0
3 TraesCS3A01G358900 chr3D 93.124 2298 94 20 619 2907 463811867 463809625 0.000000e+00 3310.0
4 TraesCS3A01G358900 chr3D 92.562 121 9 0 3112 3232 433565991 433566111 1.220000e-39 174.0
5 TraesCS3A01G358900 chr3D 96.053 76 3 0 3224 3299 463809488 463809413 1.240000e-24 124.0
6 TraesCS3A01G358900 chr3B 90.971 2337 96 32 619 2940 617269219 617266983 0.000000e+00 3040.0
7 TraesCS3A01G358900 chr3B 96.154 78 3 0 3222 3299 617266826 617266749 9.610000e-26 128.0
8 TraesCS3A01G358900 chr4D 84.874 1190 100 34 1302 2488 42238308 42237196 0.000000e+00 1127.0
9 TraesCS3A01G358900 chr4D 85.536 560 67 12 1 551 10646540 10647094 1.030000e-159 573.0
10 TraesCS3A01G358900 chr4D 81.818 77 2 5 2653 2729 42237137 42237073 2.000000e-03 54.7
11 TraesCS3A01G358900 chr4A 84.351 1195 115 33 1302 2488 597458292 597457162 0.000000e+00 1105.0
12 TraesCS3A01G358900 chr4A 84.365 1196 113 36 1302 2488 597637168 597636038 0.000000e+00 1105.0
13 TraesCS3A01G358900 chr4A 84.017 1195 119 33 1302 2488 597590707 597589577 0.000000e+00 1083.0
14 TraesCS3A01G358900 chr4A 83.766 1195 122 38 1302 2488 597648545 597647415 0.000000e+00 1066.0
15 TraesCS3A01G358900 chr4A 85.305 558 69 6 1 553 27574521 27575070 6.180000e-157 564.0
16 TraesCS3A01G358900 chr4A 92.537 134 10 0 1302 1435 597617490 597617357 3.360000e-45 193.0
17 TraesCS3A01G358900 chr4A 100.000 28 0 0 2702 2729 597346546 597346519 6.000000e-03 52.8
18 TraesCS3A01G358900 chr1B 84.308 1026 130 20 1067 2087 511451794 511452793 0.000000e+00 974.0
19 TraesCS3A01G358900 chr1D 84.524 1008 127 18 1084 2087 381313996 381314978 0.000000e+00 970.0
20 TraesCS3A01G358900 chr1A 84.175 1030 124 26 1067 2087 481932980 481933979 0.000000e+00 963.0
21 TraesCS3A01G358900 chr1A 84.957 585 65 15 1 579 478366850 478367417 3.690000e-159 571.0
22 TraesCS3A01G358900 chr1A 98.165 109 2 0 3116 3224 366271045 366270937 1.210000e-44 191.0
23 TraesCS3A01G358900 chr1A 90.698 129 11 1 3102 3230 333348518 333348391 1.570000e-38 171.0
24 TraesCS3A01G358900 chr5A 86.786 560 59 11 1 553 510219089 510218538 7.830000e-171 610.0
25 TraesCS3A01G358900 chr5A 95.575 113 5 0 3114 3226 248535326 248535438 7.270000e-42 182.0
26 TraesCS3A01G358900 chr5A 94.118 119 6 1 3115 3232 505508840 505508722 2.620000e-41 180.0
27 TraesCS3A01G358900 chr5A 94.643 112 6 0 3112 3223 169309772 169309883 1.220000e-39 174.0
28 TraesCS3A01G358900 chr7D 87.476 511 49 13 51 551 593424197 593423692 2.860000e-160 575.0
29 TraesCS3A01G358900 chr7D 93.966 116 5 2 3110 3223 419562326 419562441 1.220000e-39 174.0
30 TraesCS3A01G358900 chr5D 84.641 599 63 15 5 584 282486579 282485991 1.330000e-158 569.0
31 TraesCS3A01G358900 chr5D 83.245 567 70 17 1 553 419270630 419270075 6.360000e-137 497.0
32 TraesCS3A01G358900 chr2A 86.535 505 52 15 58 551 740087698 740088197 2.900000e-150 542.0
33 TraesCS3A01G358900 chr2A 93.162 117 8 0 3109 3225 753570302 753570186 4.380000e-39 172.0
34 TraesCS3A01G358900 chr2B 92.446 278 13 2 2639 2916 737750965 737750696 1.110000e-104 390.0
35 TraesCS3A01G358900 chr4B 91.727 278 14 3 2639 2916 560558223 560557955 8.640000e-101 377.0


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 TraesCS3A01G358900 chr3A 606828300 606831598 3298 True 6093.00 6093 100.0000 1 3299 1 chr3A.!!$R1 3298
1 TraesCS3A01G358900 chr3A 80626067 80626618 551 False 638.00 638 87.6120 1 552 1 chr3A.!!$F1 551
2 TraesCS3A01G358900 chr3D 463809413 463811867 2454 True 1717.00 3310 94.5885 619 3299 2 chr3D.!!$R1 2680
3 TraesCS3A01G358900 chr3B 617266749 617269219 2470 True 1584.00 3040 93.5625 619 3299 2 chr3B.!!$R1 2680
4 TraesCS3A01G358900 chr4D 42237073 42238308 1235 True 590.85 1127 83.3460 1302 2729 2 chr4D.!!$R1 1427
5 TraesCS3A01G358900 chr4D 10646540 10647094 554 False 573.00 573 85.5360 1 551 1 chr4D.!!$F1 550
6 TraesCS3A01G358900 chr4A 597457162 597458292 1130 True 1105.00 1105 84.3510 1302 2488 1 chr4A.!!$R2 1186
7 TraesCS3A01G358900 chr4A 597636038 597637168 1130 True 1105.00 1105 84.3650 1302 2488 1 chr4A.!!$R5 1186
8 TraesCS3A01G358900 chr4A 597589577 597590707 1130 True 1083.00 1083 84.0170 1302 2488 1 chr4A.!!$R3 1186
9 TraesCS3A01G358900 chr4A 597647415 597648545 1130 True 1066.00 1066 83.7660 1302 2488 1 chr4A.!!$R6 1186
10 TraesCS3A01G358900 chr4A 27574521 27575070 549 False 564.00 564 85.3050 1 553 1 chr4A.!!$F1 552
11 TraesCS3A01G358900 chr1B 511451794 511452793 999 False 974.00 974 84.3080 1067 2087 1 chr1B.!!$F1 1020
12 TraesCS3A01G358900 chr1D 381313996 381314978 982 False 970.00 970 84.5240 1084 2087 1 chr1D.!!$F1 1003
13 TraesCS3A01G358900 chr1A 481932980 481933979 999 False 963.00 963 84.1750 1067 2087 1 chr1A.!!$F2 1020
14 TraesCS3A01G358900 chr1A 478366850 478367417 567 False 571.00 571 84.9570 1 579 1 chr1A.!!$F1 578
15 TraesCS3A01G358900 chr5A 510218538 510219089 551 True 610.00 610 86.7860 1 553 1 chr5A.!!$R2 552
16 TraesCS3A01G358900 chr7D 593423692 593424197 505 True 575.00 575 87.4760 51 551 1 chr7D.!!$R1 500
17 TraesCS3A01G358900 chr5D 282485991 282486579 588 True 569.00 569 84.6410 5 584 1 chr5D.!!$R1 579
18 TraesCS3A01G358900 chr5D 419270075 419270630 555 True 497.00 497 83.2450 1 553 1 chr5D.!!$R2 552

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
578 613 0.108424 GAGACACGGCTGAAGATGCT 60.108 55.0 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2393 2458 0.186873 CCCTCTCCCCAATCCAATGG 59.813 60.0 0.0 0.0 40.35 3.16 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
144 163 0.623723 ACGGGAGAGAGAGAGAGCTT 59.376 55.000 0.00 0.00 0.00 3.74
203 229 1.445582 GCTTATATAGCCGCGCCGT 60.446 57.895 0.00 0.00 44.48 5.68
397 427 1.533033 CCCTTTCCCGCCAAAACCT 60.533 57.895 0.00 0.00 0.00 3.50
440 470 4.379243 CTCAGTGCGCCGGGTTCT 62.379 66.667 4.18 0.00 0.00 3.01
463 495 2.750237 GGTCCGCCGGCTGATTTT 60.750 61.111 26.68 0.00 0.00 1.82
484 516 2.339556 CCAAGGCCGGCGAAAATCA 61.340 57.895 22.54 0.00 0.00 2.57
494 526 0.678048 GCGAAAATCAGGCTCCTGGT 60.678 55.000 15.32 5.95 43.75 4.00
504 537 4.379243 CTCCTGGTGACGCGGCTT 62.379 66.667 15.80 0.00 0.00 4.35
560 595 2.541466 GAAGAGGTCTTCCCTTCCTGA 58.459 52.381 8.34 0.00 46.51 3.86
561 596 2.246091 AGAGGTCTTCCCTTCCTGAG 57.754 55.000 0.00 0.00 46.51 3.35
562 597 1.719378 AGAGGTCTTCCCTTCCTGAGA 59.281 52.381 0.00 0.00 46.51 3.27
563 598 1.828595 GAGGTCTTCCCTTCCTGAGAC 59.171 57.143 0.00 0.00 46.51 3.36
564 599 1.150135 AGGTCTTCCCTTCCTGAGACA 59.850 52.381 4.93 0.00 42.73 3.41
565 600 1.276705 GGTCTTCCCTTCCTGAGACAC 59.723 57.143 4.93 0.00 40.13 3.67
566 601 1.067495 GTCTTCCCTTCCTGAGACACG 60.067 57.143 0.00 0.00 38.64 4.49
567 602 0.247736 CTTCCCTTCCTGAGACACGG 59.752 60.000 0.00 0.00 0.00 4.94
568 603 1.827399 TTCCCTTCCTGAGACACGGC 61.827 60.000 0.00 0.00 0.00 5.68
569 604 2.286523 CCCTTCCTGAGACACGGCT 61.287 63.158 0.00 0.00 0.00 5.52
570 605 1.079543 CCTTCCTGAGACACGGCTG 60.080 63.158 0.00 0.00 0.00 4.85
571 606 1.536073 CCTTCCTGAGACACGGCTGA 61.536 60.000 0.00 0.00 0.00 4.26
572 607 0.318441 CTTCCTGAGACACGGCTGAA 59.682 55.000 0.00 0.00 0.00 3.02
573 608 0.318441 TTCCTGAGACACGGCTGAAG 59.682 55.000 0.00 0.00 0.00 3.02
574 609 0.539669 TCCTGAGACACGGCTGAAGA 60.540 55.000 0.00 0.00 0.00 2.87
575 610 0.534412 CCTGAGACACGGCTGAAGAT 59.466 55.000 0.00 0.00 0.00 2.40
576 611 1.638133 CTGAGACACGGCTGAAGATG 58.362 55.000 0.00 0.00 0.00 2.90
577 612 0.390340 TGAGACACGGCTGAAGATGC 60.390 55.000 0.00 0.00 0.00 3.91
578 613 0.108424 GAGACACGGCTGAAGATGCT 60.108 55.000 0.00 0.00 0.00 3.79
579 614 0.322975 AGACACGGCTGAAGATGCTT 59.677 50.000 0.00 0.00 0.00 3.91
580 615 1.160137 GACACGGCTGAAGATGCTTT 58.840 50.000 0.00 0.00 0.00 3.51
581 616 1.537202 GACACGGCTGAAGATGCTTTT 59.463 47.619 0.00 0.00 0.00 2.27
582 617 2.742053 GACACGGCTGAAGATGCTTTTA 59.258 45.455 0.00 0.00 0.00 1.52
583 618 2.744202 ACACGGCTGAAGATGCTTTTAG 59.256 45.455 0.00 0.00 0.00 1.85
584 619 1.740025 ACGGCTGAAGATGCTTTTAGC 59.260 47.619 0.00 0.00 42.82 3.09
585 620 1.267732 CGGCTGAAGATGCTTTTAGCG 60.268 52.381 0.00 0.00 46.26 4.26
586 621 1.532713 GGCTGAAGATGCTTTTAGCGC 60.533 52.381 0.00 0.00 46.26 5.92
587 622 1.853646 GCTGAAGATGCTTTTAGCGCG 60.854 52.381 0.00 0.00 46.26 6.86
588 623 1.394917 CTGAAGATGCTTTTAGCGCGT 59.605 47.619 8.43 0.00 46.26 6.01
589 624 1.128507 TGAAGATGCTTTTAGCGCGTG 59.871 47.619 8.43 0.00 46.26 5.34
590 625 0.447801 AAGATGCTTTTAGCGCGTGG 59.552 50.000 8.43 0.00 46.26 4.94
591 626 1.583709 GATGCTTTTAGCGCGTGGC 60.584 57.895 8.43 4.30 46.26 5.01
611 646 4.410400 GTCCGGGGGCTGTTGGAG 62.410 72.222 0.00 0.00 0.00 3.86
612 647 4.649705 TCCGGGGGCTGTTGGAGA 62.650 66.667 0.00 0.00 0.00 3.71
613 648 3.411517 CCGGGGGCTGTTGGAGAT 61.412 66.667 0.00 0.00 0.00 2.75
614 649 2.124570 CGGGGGCTGTTGGAGATG 60.125 66.667 0.00 0.00 0.00 2.90
615 650 2.440980 GGGGGCTGTTGGAGATGC 60.441 66.667 0.00 0.00 0.00 3.91
616 651 2.679716 GGGGCTGTTGGAGATGCT 59.320 61.111 0.00 0.00 0.00 3.79
617 652 1.452833 GGGGCTGTTGGAGATGCTC 60.453 63.158 0.00 0.00 0.00 4.26
621 656 2.356125 GGGCTGTTGGAGATGCTCTAAA 60.356 50.000 0.00 0.00 33.06 1.85
627 662 5.376625 TGTTGGAGATGCTCTAAAACAGTT 58.623 37.500 0.00 0.00 33.06 3.16
792 833 3.350219 TCCTTCCATGGTAGACTTTGC 57.650 47.619 19.29 0.00 0.00 3.68
804 849 1.956620 GACTTTGCGAGCTGGCGTAC 61.957 60.000 16.33 2.25 35.06 3.67
944 990 2.047179 GTCACCTTCCTCCCGTGC 60.047 66.667 0.00 0.00 0.00 5.34
991 1037 1.294780 CACCTCACTCCACTCCAGC 59.705 63.158 0.00 0.00 0.00 4.85
992 1038 1.915769 ACCTCACTCCACTCCAGCC 60.916 63.158 0.00 0.00 0.00 4.85
1333 1382 2.124403 TCGAGTACCTCTCCCCGC 60.124 66.667 0.00 0.00 39.84 6.13
1761 1816 0.107703 GCATCACCATCTTCGTCCCA 60.108 55.000 0.00 0.00 0.00 4.37
2118 2176 1.823899 CATTAACCCCGGAGCTGCC 60.824 63.158 0.73 0.00 0.00 4.85
2139 2201 4.489771 CCTCCCGCCACCATGACC 62.490 72.222 0.00 0.00 0.00 4.02
2258 2321 0.877213 AACGCGAACTGGTGGTGTAC 60.877 55.000 15.93 0.00 0.00 2.90
2259 2322 1.300311 CGCGAACTGGTGGTGTACA 60.300 57.895 0.00 0.00 0.00 2.90
2260 2323 1.282248 CGCGAACTGGTGGTGTACAG 61.282 60.000 0.00 0.00 40.48 2.74
2261 2324 0.949105 GCGAACTGGTGGTGTACAGG 60.949 60.000 0.00 0.00 39.00 4.00
2262 2325 0.677288 CGAACTGGTGGTGTACAGGA 59.323 55.000 0.00 0.00 39.00 3.86
2263 2326 1.069513 CGAACTGGTGGTGTACAGGAA 59.930 52.381 0.00 0.00 39.00 3.36
2293 2356 2.308968 CTGCCTGCTCCTACCTCTGC 62.309 65.000 0.00 0.00 0.00 4.26
2311 2374 1.764723 TGCTATGAGATCCAGGTGGTG 59.235 52.381 0.00 0.00 36.34 4.17
2333 2398 3.686241 GCCTTGCATTCTCAATTTTTCCC 59.314 43.478 0.00 0.00 0.00 3.97
2342 2407 6.901081 TTCTCAATTTTTCCCTCTTCTTCC 57.099 37.500 0.00 0.00 0.00 3.46
2352 2417 2.310052 CCCTCTTCTTCCACCATTTCCT 59.690 50.000 0.00 0.00 0.00 3.36
2360 2425 1.825474 TCCACCATTTCCTCTCTCGTC 59.175 52.381 0.00 0.00 0.00 4.20
2385 2450 2.036217 TCGAAACCGAATGTGTACACCT 59.964 45.455 22.91 10.89 32.51 4.00
2386 2451 2.410730 CGAAACCGAATGTGTACACCTC 59.589 50.000 22.91 17.23 0.00 3.85
2388 2453 0.245539 ACCGAATGTGTACACCTCCG 59.754 55.000 22.91 20.08 0.00 4.63
2389 2454 0.459585 CCGAATGTGTACACCTCCGG 60.460 60.000 24.99 24.99 0.00 5.14
2391 2456 1.734707 CGAATGTGTACACCTCCGGTC 60.735 57.143 22.91 7.03 31.02 4.79
2393 2458 2.126189 GTGTACACCTCCGGTCGC 60.126 66.667 15.42 0.00 31.02 5.19
2394 2459 3.376078 TGTACACCTCCGGTCGCC 61.376 66.667 0.00 0.00 31.02 5.54
2412 2477 0.186873 CCATTGGATTGGGGAGAGGG 59.813 60.000 0.00 0.00 32.80 4.30
2435 2507 1.539065 CCGTAGAGGCCATTGTAGCAG 60.539 57.143 5.01 0.00 0.00 4.24
2436 2508 1.587547 GTAGAGGCCATTGTAGCAGC 58.412 55.000 5.01 0.00 0.00 5.25
2437 2509 1.134401 GTAGAGGCCATTGTAGCAGCA 60.134 52.381 5.01 0.00 0.00 4.41
2454 2526 5.059833 AGCAGCAGTAGTAGCCATTATTTC 58.940 41.667 0.00 0.00 0.00 2.17
2456 2528 5.178438 GCAGCAGTAGTAGCCATTATTTCTC 59.822 44.000 0.00 0.00 0.00 2.87
2527 2622 6.057533 TGTGTAGAAATCTATGCATTCCCTG 58.942 40.000 3.54 0.00 0.00 4.45
2551 2646 1.798223 TCAGTTCCGTTGATCTTTGCG 59.202 47.619 0.00 0.00 0.00 4.85
2558 2653 1.468520 CGTTGATCTTTGCGGTTCCAT 59.531 47.619 0.00 0.00 0.00 3.41
2582 2677 7.954666 TTTTCCAAATGGGGTAGAGAATTAG 57.045 36.000 0.00 0.00 37.22 1.73
2593 2688 4.934602 GGTAGAGAATTAGCATGGCAGATC 59.065 45.833 0.00 0.00 0.00 2.75
2611 2706 1.803334 TCGGTGTCATGTTTACCTGC 58.197 50.000 11.84 0.00 32.28 4.85
2621 2716 0.393402 GTTTACCTGCTTACCCGGGG 60.393 60.000 27.92 12.73 35.47 5.73
2638 2733 0.914902 GGGCTAGAAGGTGGGTTCCT 60.915 60.000 0.00 0.00 39.84 3.36
2644 2739 2.164393 AAGGTGGGTTCCTTCCCTG 58.836 57.895 3.40 0.00 43.44 4.45
2645 2740 1.435346 AAGGTGGGTTCCTTCCCTGG 61.435 60.000 3.40 0.00 43.44 4.45
2648 2743 4.593677 GGGTTCCTTCCCTGGGTA 57.406 61.111 13.56 1.39 43.85 3.69
2649 2744 1.996900 GGGTTCCTTCCCTGGGTAC 59.003 63.158 13.56 4.62 43.85 3.34
2691 2786 4.380945 GTGGGAATGGGCTGGCCA 62.381 66.667 26.08 26.08 37.98 5.36
2692 2787 4.064768 TGGGAATGGGCTGGCCAG 62.065 66.667 29.34 29.34 37.98 4.85
2788 2883 2.233654 GCTCTACTCATGGCGCACG 61.234 63.158 10.83 0.00 0.00 5.34
2802 2897 1.395573 GCGCACGCTGTAAATACGATC 60.396 52.381 7.96 0.00 38.26 3.69
2805 2900 2.098021 GCACGCTGTAAATACGATCGAC 60.098 50.000 24.34 9.65 0.00 4.20
2831 2926 1.070821 CTACCACATGTCAGTGCACG 58.929 55.000 12.01 6.78 38.18 5.34
2843 2938 2.434185 TGCACGCCGATCTTGACC 60.434 61.111 0.00 0.00 0.00 4.02
2862 2957 1.604593 ATGGTGCAGTGCAGGAACC 60.605 57.895 20.42 16.68 40.08 3.62
2918 3019 0.661020 AGGTTCAGACGCCAAAAACG 59.339 50.000 0.00 0.00 0.00 3.60
2920 3021 0.658897 GTTCAGACGCCAAAAACGGA 59.341 50.000 0.00 0.00 34.00 4.69
2923 3024 0.041312 CAGACGCCAAAAACGGACTG 60.041 55.000 0.00 0.00 34.68 3.51
2924 3025 0.179067 AGACGCCAAAAACGGACTGA 60.179 50.000 0.00 0.00 34.00 3.41
2925 3026 0.872388 GACGCCAAAAACGGACTGAT 59.128 50.000 0.00 0.00 34.00 2.90
2928 3029 1.001815 CGCCAAAAACGGACTGATTGT 60.002 47.619 0.00 0.00 0.00 2.71
2929 3030 2.393764 GCCAAAAACGGACTGATTGTG 58.606 47.619 0.00 0.00 0.00 3.33
2930 3031 2.223711 GCCAAAAACGGACTGATTGTGT 60.224 45.455 0.00 0.00 0.00 3.72
2931 3032 3.371168 CCAAAAACGGACTGATTGTGTG 58.629 45.455 0.00 0.00 0.00 3.82
2933 3034 4.261572 CCAAAAACGGACTGATTGTGTGAT 60.262 41.667 0.00 0.00 0.00 3.06
2934 3035 4.749245 AAAACGGACTGATTGTGTGATC 57.251 40.909 0.00 0.00 0.00 2.92
2935 3036 3.401033 AACGGACTGATTGTGTGATCA 57.599 42.857 0.00 0.00 34.96 2.92
2937 3038 4.736126 ACGGACTGATTGTGTGATCATA 57.264 40.909 0.00 0.00 35.62 2.15
2938 3039 5.282055 ACGGACTGATTGTGTGATCATAT 57.718 39.130 0.00 0.00 35.62 1.78
2939 3040 5.052481 ACGGACTGATTGTGTGATCATATG 58.948 41.667 0.00 0.00 35.62 1.78
2982 3112 9.507329 AGTAAGAAACTAAAATCTGATGCTTCA 57.493 29.630 1.92 1.92 36.36 3.02
2988 3118 9.899226 AAACTAAAATCTGATGCTTCAAGTTAC 57.101 29.630 12.72 0.00 29.59 2.50
2989 3119 8.045176 ACTAAAATCTGATGCTTCAAGTTACC 57.955 34.615 3.65 0.00 0.00 2.85
2990 3120 5.551760 AAATCTGATGCTTCAAGTTACCG 57.448 39.130 3.65 0.00 0.00 4.02
2993 3123 4.433615 TCTGATGCTTCAAGTTACCGATC 58.566 43.478 3.65 0.00 0.00 3.69
2994 3124 4.081697 TCTGATGCTTCAAGTTACCGATCA 60.082 41.667 3.65 0.00 0.00 2.92
2995 3125 4.769688 TGATGCTTCAAGTTACCGATCAT 58.230 39.130 0.00 0.00 0.00 2.45
2996 3126 5.912892 TGATGCTTCAAGTTACCGATCATA 58.087 37.500 0.00 0.00 0.00 2.15
2997 3127 6.524734 TGATGCTTCAAGTTACCGATCATAT 58.475 36.000 0.00 0.00 0.00 1.78
2998 3128 6.424812 TGATGCTTCAAGTTACCGATCATATG 59.575 38.462 0.00 0.00 0.00 1.78
2999 3129 5.912892 TGCTTCAAGTTACCGATCATATGA 58.087 37.500 8.10 8.10 0.00 2.15
3000 3130 5.753438 TGCTTCAAGTTACCGATCATATGAC 59.247 40.000 7.78 1.55 0.00 3.06
3001 3131 5.986135 GCTTCAAGTTACCGATCATATGACT 59.014 40.000 7.78 0.00 0.00 3.41
3002 3132 6.480320 GCTTCAAGTTACCGATCATATGACTT 59.520 38.462 7.78 2.77 0.00 3.01
3003 3133 7.652105 GCTTCAAGTTACCGATCATATGACTTA 59.348 37.037 7.78 0.00 0.00 2.24
3004 3134 8.867112 TTCAAGTTACCGATCATATGACTTAC 57.133 34.615 7.78 1.38 0.00 2.34
3005 3135 8.234136 TCAAGTTACCGATCATATGACTTACT 57.766 34.615 7.78 3.61 0.00 2.24
3006 3136 8.135529 TCAAGTTACCGATCATATGACTTACTG 58.864 37.037 7.78 0.08 0.00 2.74
3007 3137 7.584122 AGTTACCGATCATATGACTTACTGT 57.416 36.000 7.78 5.65 0.00 3.55
3008 3138 8.008513 AGTTACCGATCATATGACTTACTGTT 57.991 34.615 7.78 0.00 0.00 3.16
3009 3139 8.475639 AGTTACCGATCATATGACTTACTGTTT 58.524 33.333 7.78 0.00 0.00 2.83
3010 3140 8.540492 GTTACCGATCATATGACTTACTGTTTG 58.460 37.037 7.78 0.00 0.00 2.93
3011 3141 6.640518 ACCGATCATATGACTTACTGTTTGT 58.359 36.000 7.78 0.00 0.00 2.83
3012 3142 6.535150 ACCGATCATATGACTTACTGTTTGTG 59.465 38.462 7.78 0.00 0.00 3.33
3013 3143 6.414079 CGATCATATGACTTACTGTTTGTGC 58.586 40.000 7.78 0.00 0.00 4.57
3014 3144 5.778161 TCATATGACTTACTGTTTGTGCG 57.222 39.130 0.00 0.00 0.00 5.34
3015 3145 5.474825 TCATATGACTTACTGTTTGTGCGA 58.525 37.500 0.00 0.00 0.00 5.10
3016 3146 5.576774 TCATATGACTTACTGTTTGTGCGAG 59.423 40.000 0.00 0.00 0.00 5.03
3017 3147 3.173668 TGACTTACTGTTTGTGCGAGT 57.826 42.857 0.00 0.00 0.00 4.18
3018 3148 3.527533 TGACTTACTGTTTGTGCGAGTT 58.472 40.909 0.00 0.00 0.00 3.01
3019 3149 3.936453 TGACTTACTGTTTGTGCGAGTTT 59.064 39.130 0.00 0.00 0.00 2.66
3020 3150 4.201773 TGACTTACTGTTTGTGCGAGTTTG 60.202 41.667 0.00 0.00 0.00 2.93
3021 3151 3.687698 ACTTACTGTTTGTGCGAGTTTGT 59.312 39.130 0.00 0.00 0.00 2.83
3022 3152 2.542766 ACTGTTTGTGCGAGTTTGTG 57.457 45.000 0.00 0.00 0.00 3.33
3023 3153 2.080693 ACTGTTTGTGCGAGTTTGTGA 58.919 42.857 0.00 0.00 0.00 3.58
3024 3154 2.159572 ACTGTTTGTGCGAGTTTGTGAC 60.160 45.455 0.00 0.00 0.00 3.67
3025 3155 2.080693 TGTTTGTGCGAGTTTGTGACT 58.919 42.857 0.00 0.00 42.70 3.41
3033 3163 2.992089 AGTTTGTGACTCCGCACTG 58.008 52.632 0.00 0.00 39.49 3.66
3034 3164 1.160329 AGTTTGTGACTCCGCACTGC 61.160 55.000 0.00 0.00 39.49 4.40
3035 3165 1.146041 TTTGTGACTCCGCACTGCT 59.854 52.632 0.00 0.00 39.49 4.24
3036 3166 0.391228 TTTGTGACTCCGCACTGCTA 59.609 50.000 0.00 0.00 39.49 3.49
3037 3167 0.038251 TTGTGACTCCGCACTGCTAG 60.038 55.000 0.00 0.00 39.49 3.42
3038 3168 1.807573 GTGACTCCGCACTGCTAGC 60.808 63.158 8.10 8.10 35.91 3.42
3039 3169 2.275380 TGACTCCGCACTGCTAGCA 61.275 57.895 18.22 18.22 0.00 3.49
3040 3170 1.142748 GACTCCGCACTGCTAGCAT 59.857 57.895 19.72 5.84 0.00 3.79
3041 3171 0.460987 GACTCCGCACTGCTAGCATT 60.461 55.000 19.72 10.33 0.00 3.56
3042 3172 0.824109 ACTCCGCACTGCTAGCATTA 59.176 50.000 19.72 0.00 0.00 1.90
3043 3173 1.414181 ACTCCGCACTGCTAGCATTAT 59.586 47.619 19.72 4.00 0.00 1.28
3044 3174 1.797046 CTCCGCACTGCTAGCATTATG 59.203 52.381 19.72 17.32 0.00 1.90
3060 3190 2.683820 TATGTGCCTAGCAGCGCTCG 62.684 60.000 7.13 4.46 43.73 5.03
3068 3198 2.154798 TAGCAGCGCTCGTTTGGAGT 62.155 55.000 7.13 0.00 45.03 3.85
3085 3215 2.633488 GAGTACATCCTTCCTTGCCAC 58.367 52.381 0.00 0.00 0.00 5.01
3111 3241 5.064707 ACTGTATGAACACTTGACAACACAC 59.935 40.000 0.00 0.00 0.00 3.82
3117 3247 4.875544 ACACTTGACAACACACATGTAC 57.124 40.909 0.00 0.00 38.45 2.90
3119 3249 4.570772 ACACTTGACAACACACATGTACTC 59.429 41.667 0.00 0.00 38.45 2.59
3120 3250 4.024893 CACTTGACAACACACATGTACTCC 60.025 45.833 0.00 0.00 38.45 3.85
3121 3251 3.120321 TGACAACACACATGTACTCCC 57.880 47.619 0.00 0.00 38.45 4.30
3122 3252 2.703536 TGACAACACACATGTACTCCCT 59.296 45.455 0.00 0.00 38.45 4.20
3123 3253 3.244078 TGACAACACACATGTACTCCCTC 60.244 47.826 0.00 0.00 38.45 4.30
3124 3254 2.038557 ACAACACACATGTACTCCCTCC 59.961 50.000 0.00 0.00 38.45 4.30
3125 3255 0.895530 ACACACATGTACTCCCTCCG 59.104 55.000 0.00 0.00 37.26 4.63
3126 3256 0.895530 CACACATGTACTCCCTCCGT 59.104 55.000 0.00 0.00 0.00 4.69
3127 3257 1.275291 CACACATGTACTCCCTCCGTT 59.725 52.381 0.00 0.00 0.00 4.44
3128 3258 1.549170 ACACATGTACTCCCTCCGTTC 59.451 52.381 0.00 0.00 0.00 3.95
3129 3259 1.134788 CACATGTACTCCCTCCGTTCC 60.135 57.143 0.00 0.00 0.00 3.62
3130 3260 1.191535 CATGTACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
3131 3261 1.762957 CATGTACTCCCTCCGTTCCAT 59.237 52.381 0.00 0.00 0.00 3.41
3132 3262 2.832643 TGTACTCCCTCCGTTCCATA 57.167 50.000 0.00 0.00 0.00 2.74
3133 3263 3.323774 TGTACTCCCTCCGTTCCATAT 57.676 47.619 0.00 0.00 0.00 1.78
3134 3264 3.649843 TGTACTCCCTCCGTTCCATATT 58.350 45.455 0.00 0.00 0.00 1.28
3135 3265 4.806892 TGTACTCCCTCCGTTCCATATTA 58.193 43.478 0.00 0.00 0.00 0.98
3136 3266 4.586001 TGTACTCCCTCCGTTCCATATTAC 59.414 45.833 0.00 0.00 0.00 1.89
3137 3267 3.924922 ACTCCCTCCGTTCCATATTACT 58.075 45.455 0.00 0.00 0.00 2.24
3138 3268 3.896272 ACTCCCTCCGTTCCATATTACTC 59.104 47.826 0.00 0.00 0.00 2.59
3139 3269 2.889045 TCCCTCCGTTCCATATTACTCG 59.111 50.000 0.00 0.00 0.00 4.18
3140 3270 2.626743 CCCTCCGTTCCATATTACTCGT 59.373 50.000 0.00 0.00 0.00 4.18
3141 3271 3.305199 CCCTCCGTTCCATATTACTCGTC 60.305 52.174 0.00 0.00 0.00 4.20
3142 3272 3.552541 CTCCGTTCCATATTACTCGTCG 58.447 50.000 0.00 0.00 0.00 5.12
3143 3273 2.049228 CCGTTCCATATTACTCGTCGC 58.951 52.381 0.00 0.00 0.00 5.19
3144 3274 2.542205 CCGTTCCATATTACTCGTCGCA 60.542 50.000 0.00 0.00 0.00 5.10
3145 3275 2.719556 CGTTCCATATTACTCGTCGCAG 59.280 50.000 0.00 0.00 0.00 5.18
3146 3276 3.547413 CGTTCCATATTACTCGTCGCAGA 60.547 47.826 0.00 0.00 0.00 4.26
3147 3277 4.357142 GTTCCATATTACTCGTCGCAGAA 58.643 43.478 0.00 0.00 39.69 3.02
3148 3278 4.642445 TCCATATTACTCGTCGCAGAAA 57.358 40.909 0.00 0.00 39.69 2.52
3149 3279 5.196341 TCCATATTACTCGTCGCAGAAAT 57.804 39.130 0.00 0.00 39.69 2.17
3150 3280 4.982295 TCCATATTACTCGTCGCAGAAATG 59.018 41.667 0.00 0.00 39.69 2.32
3151 3281 4.150627 CCATATTACTCGTCGCAGAAATGG 59.849 45.833 0.00 0.00 39.69 3.16
3152 3282 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
3153 3283 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
3154 3284 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
3155 3285 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
3156 3286 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
3157 3287 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
3158 3288 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
3159 3289 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
3160 3290 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
3161 3291 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
3162 3292 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
3163 3293 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
3164 3294 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
3165 3295 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
3166 3296 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
3167 3297 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
3168 3298 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
3197 3327 9.900710 ACATCTAGATACATTCATTTCTACGAC 57.099 33.333 4.54 0.00 0.00 4.34
3198 3328 9.056306 CATCTAGATACATTCATTTCTACGACG 57.944 37.037 4.54 0.00 0.00 5.12
3199 3329 8.374327 TCTAGATACATTCATTTCTACGACGA 57.626 34.615 0.00 0.00 0.00 4.20
3200 3330 8.496751 TCTAGATACATTCATTTCTACGACGAG 58.503 37.037 0.00 0.00 0.00 4.18
3201 3331 7.028926 AGATACATTCATTTCTACGACGAGT 57.971 36.000 0.00 0.00 0.00 4.18
3202 3332 8.151141 AGATACATTCATTTCTACGACGAGTA 57.849 34.615 0.00 0.00 0.00 2.59
3203 3333 8.618677 AGATACATTCATTTCTACGACGAGTAA 58.381 33.333 0.00 0.00 34.45 2.24
3204 3334 9.395707 GATACATTCATTTCTACGACGAGTAAT 57.604 33.333 0.00 0.00 34.45 1.89
3205 3335 9.745880 ATACATTCATTTCTACGACGAGTAATT 57.254 29.630 0.00 0.00 34.45 1.40
3206 3336 8.116624 ACATTCATTTCTACGACGAGTAATTC 57.883 34.615 0.00 0.00 34.45 2.17
3287 3417 4.629200 GCTGTTCCTAACATTCAGTCAGAG 59.371 45.833 0.00 0.00 41.26 3.35
3288 3418 4.569943 TGTTCCTAACATTCAGTCAGAGC 58.430 43.478 0.00 0.00 36.25 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 110 3.015332 GCCTCCCTCTCCCTCTCCA 62.015 68.421 0.00 0.00 0.00 3.86
263 289 0.617935 TGCCATTGATTCCTCACGGA 59.382 50.000 0.00 0.00 37.60 4.69
299 328 0.684153 CGGGGAATCAATGGCAAGGT 60.684 55.000 0.00 0.00 0.00 3.50
328 357 3.703127 GTCTTCCCCCGACGCCTT 61.703 66.667 0.00 0.00 0.00 4.35
380 410 0.539669 AGAGGTTTTGGCGGGAAAGG 60.540 55.000 0.00 0.00 0.00 3.11
386 416 3.431725 GGCGAGAGGTTTTGGCGG 61.432 66.667 0.00 0.00 0.00 6.13
468 500 2.046285 CCTGATTTTCGCCGGCCTT 61.046 57.895 23.46 0.04 0.00 4.35
553 588 0.318441 TTCAGCCGTGTCTCAGGAAG 59.682 55.000 0.00 0.00 0.00 3.46
554 589 0.318441 CTTCAGCCGTGTCTCAGGAA 59.682 55.000 0.00 0.00 0.00 3.36
555 590 0.539669 TCTTCAGCCGTGTCTCAGGA 60.540 55.000 0.00 0.00 0.00 3.86
556 591 0.534412 ATCTTCAGCCGTGTCTCAGG 59.466 55.000 0.00 0.00 0.00 3.86
557 592 1.638133 CATCTTCAGCCGTGTCTCAG 58.362 55.000 0.00 0.00 0.00 3.35
558 593 0.390340 GCATCTTCAGCCGTGTCTCA 60.390 55.000 0.00 0.00 0.00 3.27
559 594 0.108424 AGCATCTTCAGCCGTGTCTC 60.108 55.000 0.00 0.00 0.00 3.36
560 595 0.322975 AAGCATCTTCAGCCGTGTCT 59.677 50.000 0.00 0.00 0.00 3.41
561 596 1.160137 AAAGCATCTTCAGCCGTGTC 58.840 50.000 0.00 0.00 0.00 3.67
562 597 1.609208 AAAAGCATCTTCAGCCGTGT 58.391 45.000 0.00 0.00 0.00 4.49
563 598 2.476854 GCTAAAAGCATCTTCAGCCGTG 60.477 50.000 0.00 0.00 41.89 4.94
564 599 1.740025 GCTAAAAGCATCTTCAGCCGT 59.260 47.619 0.00 0.00 41.89 5.68
565 600 1.267732 CGCTAAAAGCATCTTCAGCCG 60.268 52.381 0.00 0.00 42.58 5.52
566 601 1.532713 GCGCTAAAAGCATCTTCAGCC 60.533 52.381 0.00 0.26 42.58 4.85
567 602 1.820092 GCGCTAAAAGCATCTTCAGC 58.180 50.000 0.00 0.00 42.58 4.26
568 603 1.394917 ACGCGCTAAAAGCATCTTCAG 59.605 47.619 5.73 0.00 42.58 3.02
569 604 1.128507 CACGCGCTAAAAGCATCTTCA 59.871 47.619 5.73 0.00 42.58 3.02
570 605 1.529826 CCACGCGCTAAAAGCATCTTC 60.530 52.381 5.73 0.00 42.58 2.87
571 606 0.447801 CCACGCGCTAAAAGCATCTT 59.552 50.000 5.73 0.00 42.58 2.40
572 607 1.982073 GCCACGCGCTAAAAGCATCT 61.982 55.000 5.73 0.00 42.58 2.90
573 608 1.583709 GCCACGCGCTAAAAGCATC 60.584 57.895 5.73 0.00 42.58 3.91
574 609 2.485122 GCCACGCGCTAAAAGCAT 59.515 55.556 5.73 0.00 42.58 3.79
594 629 4.410400 CTCCAACAGCCCCCGGAC 62.410 72.222 0.73 0.00 0.00 4.79
595 630 3.943137 ATCTCCAACAGCCCCCGGA 62.943 63.158 0.73 0.00 0.00 5.14
596 631 3.411517 ATCTCCAACAGCCCCCGG 61.412 66.667 0.00 0.00 0.00 5.73
597 632 2.124570 CATCTCCAACAGCCCCCG 60.125 66.667 0.00 0.00 0.00 5.73
598 633 2.440980 GCATCTCCAACAGCCCCC 60.441 66.667 0.00 0.00 0.00 5.40
599 634 1.452833 GAGCATCTCCAACAGCCCC 60.453 63.158 0.00 0.00 0.00 5.80
600 635 4.232310 GAGCATCTCCAACAGCCC 57.768 61.111 0.00 0.00 0.00 5.19
611 646 8.420189 CGAAAAATGAAACTGTTTTAGAGCATC 58.580 33.333 7.28 1.55 0.00 3.91
612 647 7.096065 GCGAAAAATGAAACTGTTTTAGAGCAT 60.096 33.333 7.28 3.20 0.00 3.79
613 648 6.198216 GCGAAAAATGAAACTGTTTTAGAGCA 59.802 34.615 7.28 0.82 0.00 4.26
614 649 6.198216 TGCGAAAAATGAAACTGTTTTAGAGC 59.802 34.615 7.28 6.44 0.00 4.09
615 650 7.432252 ACTGCGAAAAATGAAACTGTTTTAGAG 59.568 33.333 7.28 0.00 0.00 2.43
616 651 7.219917 CACTGCGAAAAATGAAACTGTTTTAGA 59.780 33.333 7.28 0.00 0.00 2.10
617 652 7.329582 CACTGCGAAAAATGAAACTGTTTTAG 58.670 34.615 7.28 0.00 0.00 1.85
621 656 3.551485 GCACTGCGAAAAATGAAACTGTT 59.449 39.130 0.00 0.00 0.00 3.16
673 709 3.070076 TGCTCGACAGAATGATGGC 57.930 52.632 0.00 0.00 39.69 4.40
767 806 2.045885 AGTCTACCATGGAAGGAAGGGA 59.954 50.000 21.47 1.51 0.00 4.20
775 816 2.935238 GCTCGCAAAGTCTACCATGGAA 60.935 50.000 21.47 0.00 0.00 3.53
944 990 4.148825 CCGAGGAGTGAAGCGGGG 62.149 72.222 0.00 0.00 40.08 5.73
992 1038 2.136878 CCTCTCCCCATCCTCGTGG 61.137 68.421 0.00 0.00 39.05 4.94
1527 1582 1.079336 GTTGTACGGCTCCCTGGTC 60.079 63.158 0.00 0.00 0.00 4.02
1668 1723 3.423154 GAGGCGGCCACGTTGAAG 61.423 66.667 23.09 0.00 43.45 3.02
2127 2185 3.716195 TCTGGGGTCATGGTGGCG 61.716 66.667 0.00 0.00 0.00 5.69
2258 2321 2.441001 AGGCAGACCAATCCTATTCCTG 59.559 50.000 0.00 0.00 39.06 3.86
2259 2322 2.441001 CAGGCAGACCAATCCTATTCCT 59.559 50.000 0.00 0.00 39.06 3.36
2260 2323 2.856222 CAGGCAGACCAATCCTATTCC 58.144 52.381 0.00 0.00 39.06 3.01
2261 2324 2.158696 AGCAGGCAGACCAATCCTATTC 60.159 50.000 0.00 0.00 39.06 1.75
2262 2325 1.849039 AGCAGGCAGACCAATCCTATT 59.151 47.619 0.00 0.00 39.06 1.73
2263 2326 1.419387 GAGCAGGCAGACCAATCCTAT 59.581 52.381 0.00 0.00 39.06 2.57
2293 2356 1.071385 GGCACCACCTGGATCTCATAG 59.929 57.143 0.00 0.00 38.94 2.23
2311 2374 3.686241 GGGAAAAATTGAGAATGCAAGGC 59.314 43.478 0.00 0.00 0.00 4.35
2333 2398 4.224818 AGAGAGGAAATGGTGGAAGAAGAG 59.775 45.833 0.00 0.00 0.00 2.85
2342 2407 2.493675 TCAGACGAGAGAGGAAATGGTG 59.506 50.000 0.00 0.00 0.00 4.17
2352 2417 1.397343 CGGTTTCGATCAGACGAGAGA 59.603 52.381 0.00 0.00 43.04 3.10
2360 2425 3.924073 TGTACACATTCGGTTTCGATCAG 59.076 43.478 0.00 0.00 45.51 2.90
2385 2450 1.451207 CAATCCAATGGCGACCGGA 60.451 57.895 9.46 0.00 0.00 5.14
2386 2451 2.480610 CCAATCCAATGGCGACCGG 61.481 63.158 0.00 0.00 32.78 5.28
2388 2453 2.127232 CCCCAATCCAATGGCGACC 61.127 63.158 0.00 0.00 39.26 4.79
2389 2454 1.077068 TCCCCAATCCAATGGCGAC 60.077 57.895 0.00 0.00 39.26 5.19
2391 2456 0.820891 CTCTCCCCAATCCAATGGCG 60.821 60.000 0.00 0.00 39.26 5.69
2393 2458 0.186873 CCCTCTCCCCAATCCAATGG 59.813 60.000 0.00 0.00 40.35 3.16
2394 2459 0.929244 ACCCTCTCCCCAATCCAATG 59.071 55.000 0.00 0.00 0.00 2.82
2412 2477 2.822764 CTACAATGGCCTCTACGGAAC 58.177 52.381 3.32 0.00 33.16 3.62
2435 2507 5.290386 ACGAGAAATAATGGCTACTACTGC 58.710 41.667 0.00 0.00 0.00 4.40
2436 2508 7.707035 AGAAACGAGAAATAATGGCTACTACTG 59.293 37.037 0.00 0.00 0.00 2.74
2437 2509 7.783042 AGAAACGAGAAATAATGGCTACTACT 58.217 34.615 0.00 0.00 0.00 2.57
2454 2526 4.081642 TCCCTAATCAGGTGAAGAAACGAG 60.082 45.833 0.00 0.00 40.79 4.18
2456 2528 4.202245 TCCCTAATCAGGTGAAGAAACG 57.798 45.455 0.00 0.00 40.79 3.60
2527 2622 4.527564 CAAAGATCAACGGAACTGAACAC 58.472 43.478 0.00 0.00 0.00 3.32
2558 2653 6.379988 GCTAATTCTCTACCCCATTTGGAAAA 59.620 38.462 0.00 0.00 37.39 2.29
2582 2677 0.816825 ATGACACCGATCTGCCATGC 60.817 55.000 0.00 0.00 0.00 4.06
2593 2688 1.808411 AGCAGGTAAACATGACACCG 58.192 50.000 0.00 1.88 37.42 4.94
2611 2706 0.690077 ACCTTCTAGCCCCGGGTAAG 60.690 60.000 21.85 13.61 0.00 2.34
2641 2736 0.481567 TCTATCCCCTCGTACCCAGG 59.518 60.000 0.00 0.00 0.00 4.45
2642 2737 2.376695 TTCTATCCCCTCGTACCCAG 57.623 55.000 0.00 0.00 0.00 4.45
2644 2739 2.892215 CTCTTTCTATCCCCTCGTACCC 59.108 54.545 0.00 0.00 0.00 3.69
2645 2740 3.569277 GTCTCTTTCTATCCCCTCGTACC 59.431 52.174 0.00 0.00 0.00 3.34
2646 2741 4.205587 TGTCTCTTTCTATCCCCTCGTAC 58.794 47.826 0.00 0.00 0.00 3.67
2647 2742 4.462133 CTGTCTCTTTCTATCCCCTCGTA 58.538 47.826 0.00 0.00 0.00 3.43
2648 2743 3.292460 CTGTCTCTTTCTATCCCCTCGT 58.708 50.000 0.00 0.00 0.00 4.18
2649 2744 2.625790 CCTGTCTCTTTCTATCCCCTCG 59.374 54.545 0.00 0.00 0.00 4.63
2692 2787 2.433838 TTCGCAGCTCAGCTCAGC 60.434 61.111 0.00 0.00 36.40 4.26
2693 2788 2.442999 CGTTCGCAGCTCAGCTCAG 61.443 63.158 0.00 0.00 36.40 3.35
2694 2789 2.431430 CGTTCGCAGCTCAGCTCA 60.431 61.111 0.00 0.00 36.40 4.26
2695 2790 3.847709 GCGTTCGCAGCTCAGCTC 61.848 66.667 12.33 0.00 36.40 4.09
2788 2883 4.206609 GGTTCAGTCGATCGTATTTACAGC 59.793 45.833 15.94 0.94 0.00 4.40
2802 2897 1.275291 ACATGTGGTAGGGTTCAGTCG 59.725 52.381 0.00 0.00 0.00 4.18
2805 2900 2.303022 ACTGACATGTGGTAGGGTTCAG 59.697 50.000 1.15 3.29 0.00 3.02
2831 2926 1.718757 GCACCATGGTCAAGATCGGC 61.719 60.000 16.53 9.26 0.00 5.54
2843 2938 1.582968 GTTCCTGCACTGCACCATG 59.417 57.895 0.00 0.00 33.79 3.66
2918 3019 9.363763 CTATACATATGATCACACAATCAGTCC 57.636 37.037 10.38 0.00 38.96 3.85
2920 3021 9.702494 CACTATACATATGATCACACAATCAGT 57.298 33.333 10.38 0.00 38.96 3.41
2956 3086 9.507329 TGAAGCATCAGATTTTAGTTTCTTACT 57.493 29.630 0.00 0.00 41.04 2.24
2977 3107 5.986135 AGTCATATGATCGGTAACTTGAAGC 59.014 40.000 9.02 0.00 0.00 3.86
2980 3110 8.135529 CAGTAAGTCATATGATCGGTAACTTGA 58.864 37.037 9.02 0.00 0.00 3.02
2981 3111 7.921214 ACAGTAAGTCATATGATCGGTAACTTG 59.079 37.037 9.02 2.58 0.00 3.16
2982 3112 8.008513 ACAGTAAGTCATATGATCGGTAACTT 57.991 34.615 9.02 8.58 0.00 2.66
2988 3118 6.510157 GCACAAACAGTAAGTCATATGATCGG 60.510 42.308 9.02 4.19 0.00 4.18
2989 3119 6.414079 GCACAAACAGTAAGTCATATGATCG 58.586 40.000 9.02 0.00 0.00 3.69
2990 3120 6.255670 TCGCACAAACAGTAAGTCATATGATC 59.744 38.462 9.02 3.10 0.00 2.92
2993 3123 5.348724 ACTCGCACAAACAGTAAGTCATATG 59.651 40.000 0.00 0.00 0.00 1.78
2994 3124 5.479306 ACTCGCACAAACAGTAAGTCATAT 58.521 37.500 0.00 0.00 0.00 1.78
2995 3125 4.878439 ACTCGCACAAACAGTAAGTCATA 58.122 39.130 0.00 0.00 0.00 2.15
2996 3126 3.728845 ACTCGCACAAACAGTAAGTCAT 58.271 40.909 0.00 0.00 0.00 3.06
2997 3127 3.173668 ACTCGCACAAACAGTAAGTCA 57.826 42.857 0.00 0.00 0.00 3.41
2998 3128 4.201783 ACAAACTCGCACAAACAGTAAGTC 60.202 41.667 0.00 0.00 0.00 3.01
2999 3129 3.687698 ACAAACTCGCACAAACAGTAAGT 59.312 39.130 0.00 0.00 0.00 2.24
3000 3130 4.028383 CACAAACTCGCACAAACAGTAAG 58.972 43.478 0.00 0.00 0.00 2.34
3001 3131 3.685272 TCACAAACTCGCACAAACAGTAA 59.315 39.130 0.00 0.00 0.00 2.24
3002 3132 3.062909 GTCACAAACTCGCACAAACAGTA 59.937 43.478 0.00 0.00 0.00 2.74
3003 3133 2.080693 TCACAAACTCGCACAAACAGT 58.919 42.857 0.00 0.00 0.00 3.55
3004 3134 2.095853 AGTCACAAACTCGCACAAACAG 59.904 45.455 0.00 0.00 30.02 3.16
3005 3135 2.080693 AGTCACAAACTCGCACAAACA 58.919 42.857 0.00 0.00 30.02 2.83
3006 3136 2.705154 GAGTCACAAACTCGCACAAAC 58.295 47.619 0.00 0.00 44.79 2.93
3015 3145 1.160329 GCAGTGCGGAGTCACAAACT 61.160 55.000 0.00 0.00 42.42 2.66
3016 3146 1.160329 AGCAGTGCGGAGTCACAAAC 61.160 55.000 10.00 0.00 37.10 2.93
3017 3147 0.391228 TAGCAGTGCGGAGTCACAAA 59.609 50.000 10.00 0.00 37.10 2.83
3018 3148 0.038251 CTAGCAGTGCGGAGTCACAA 60.038 55.000 10.00 0.00 37.10 3.33
3019 3149 1.586541 CTAGCAGTGCGGAGTCACA 59.413 57.895 10.00 0.00 37.10 3.58
3020 3150 1.807573 GCTAGCAGTGCGGAGTCAC 60.808 63.158 10.63 2.39 35.42 3.67
3021 3151 1.607801 ATGCTAGCAGTGCGGAGTCA 61.608 55.000 23.89 16.04 0.00 3.41
3022 3152 0.460987 AATGCTAGCAGTGCGGAGTC 60.461 55.000 23.89 12.18 0.00 3.36
3023 3153 0.824109 TAATGCTAGCAGTGCGGAGT 59.176 50.000 26.91 2.34 0.00 3.85
3024 3154 1.797046 CATAATGCTAGCAGTGCGGAG 59.203 52.381 26.91 12.33 0.00 4.63
3025 3155 1.138859 ACATAATGCTAGCAGTGCGGA 59.861 47.619 26.91 7.91 0.00 5.54
3026 3156 1.262417 CACATAATGCTAGCAGTGCGG 59.738 52.381 26.91 17.33 0.00 5.69
3027 3157 2.657960 CACATAATGCTAGCAGTGCG 57.342 50.000 26.91 18.89 0.00 5.34
3038 3168 0.236711 GCGCTGCTAGGCACATAATG 59.763 55.000 0.00 0.00 33.79 1.90
3039 3169 0.107456 AGCGCTGCTAGGCACATAAT 59.893 50.000 10.39 0.00 36.99 1.28
3040 3170 0.530650 GAGCGCTGCTAGGCACATAA 60.531 55.000 18.48 0.00 39.88 1.90
3041 3171 1.068083 GAGCGCTGCTAGGCACATA 59.932 57.895 18.48 0.00 39.88 2.29
3042 3172 2.202987 GAGCGCTGCTAGGCACAT 60.203 61.111 18.48 0.00 39.88 3.21
3043 3173 4.801624 CGAGCGCTGCTAGGCACA 62.802 66.667 18.48 0.00 39.88 4.57
3044 3174 4.803426 ACGAGCGCTGCTAGGCAC 62.803 66.667 18.48 0.00 39.88 5.01
3068 3198 3.197766 CAGTAGTGGCAAGGAAGGATGTA 59.802 47.826 0.00 0.00 0.00 2.29
3080 3210 4.039852 TCAAGTGTTCATACAGTAGTGGCA 59.960 41.667 1.92 0.00 36.93 4.92
3082 3212 5.538118 TGTCAAGTGTTCATACAGTAGTGG 58.462 41.667 1.92 0.00 36.93 4.00
3085 3215 6.478673 TGTGTTGTCAAGTGTTCATACAGTAG 59.521 38.462 0.00 0.00 36.93 2.57
3111 3241 1.191535 TGGAACGGAGGGAGTACATG 58.808 55.000 0.00 0.00 0.00 3.21
3117 3247 3.057456 CGAGTAATATGGAACGGAGGGAG 60.057 52.174 0.00 0.00 0.00 4.30
3119 3249 2.626743 ACGAGTAATATGGAACGGAGGG 59.373 50.000 0.00 0.00 0.00 4.30
3120 3250 3.608707 CGACGAGTAATATGGAACGGAGG 60.609 52.174 0.00 0.00 0.00 4.30
3121 3251 3.552541 CGACGAGTAATATGGAACGGAG 58.447 50.000 0.00 0.00 0.00 4.63
3122 3252 2.287188 GCGACGAGTAATATGGAACGGA 60.287 50.000 0.00 0.00 0.00 4.69
3123 3253 2.049228 GCGACGAGTAATATGGAACGG 58.951 52.381 0.00 0.00 0.00 4.44
3124 3254 2.719556 CTGCGACGAGTAATATGGAACG 59.280 50.000 0.00 0.00 0.00 3.95
3125 3255 3.961182 TCTGCGACGAGTAATATGGAAC 58.039 45.455 0.00 0.00 0.00 3.62
3126 3256 4.642445 TTCTGCGACGAGTAATATGGAA 57.358 40.909 0.00 0.00 0.00 3.53
3127 3257 4.642445 TTTCTGCGACGAGTAATATGGA 57.358 40.909 0.00 0.00 0.00 3.41
3128 3258 4.150627 CCATTTCTGCGACGAGTAATATGG 59.849 45.833 0.00 0.05 0.00 2.74
3129 3259 4.982295 TCCATTTCTGCGACGAGTAATATG 59.018 41.667 0.00 0.00 0.00 1.78
3130 3260 5.196341 TCCATTTCTGCGACGAGTAATAT 57.804 39.130 0.00 0.00 0.00 1.28
3131 3261 4.642445 TCCATTTCTGCGACGAGTAATA 57.358 40.909 0.00 0.00 0.00 0.98
3132 3262 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
3133 3263 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
3134 3264 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
3135 3265 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
3136 3266 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
3137 3267 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
3138 3268 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
3139 3269 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
3140 3270 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
3141 3271 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
3142 3272 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
3171 3301 9.900710 GTCGTAGAAATGAATGTATCTAGATGT 57.099 33.333 15.79 0.00 39.69 3.06
3172 3302 9.056306 CGTCGTAGAAATGAATGTATCTAGATG 57.944 37.037 15.79 0.00 39.69 2.90
3173 3303 9.000486 TCGTCGTAGAAATGAATGTATCTAGAT 58.000 33.333 10.73 10.73 39.69 1.98
3174 3304 8.374327 TCGTCGTAGAAATGAATGTATCTAGA 57.626 34.615 0.00 0.00 39.69 2.43
3175 3305 8.283992 ACTCGTCGTAGAAATGAATGTATCTAG 58.716 37.037 0.00 0.00 39.69 2.43
3176 3306 8.151141 ACTCGTCGTAGAAATGAATGTATCTA 57.849 34.615 0.00 0.00 39.69 1.98
3177 3307 7.028926 ACTCGTCGTAGAAATGAATGTATCT 57.971 36.000 0.00 0.00 39.69 1.98
3178 3308 8.778141 TTACTCGTCGTAGAAATGAATGTATC 57.222 34.615 0.00 0.00 39.69 2.24
3179 3309 9.745880 AATTACTCGTCGTAGAAATGAATGTAT 57.254 29.630 0.00 0.00 39.69 2.29
3180 3310 9.229784 GAATTACTCGTCGTAGAAATGAATGTA 57.770 33.333 0.00 0.00 39.69 2.29
3181 3311 7.044249 CGAATTACTCGTCGTAGAAATGAATGT 60.044 37.037 0.00 0.00 42.89 2.71
3182 3312 7.267318 CGAATTACTCGTCGTAGAAATGAATG 58.733 38.462 0.00 0.00 42.89 2.67
3183 3313 6.417044 CCGAATTACTCGTCGTAGAAATGAAT 59.583 38.462 0.00 0.00 46.65 2.57
3184 3314 5.740569 CCGAATTACTCGTCGTAGAAATGAA 59.259 40.000 0.00 0.00 46.65 2.57
3185 3315 5.065090 TCCGAATTACTCGTCGTAGAAATGA 59.935 40.000 0.00 0.00 46.65 2.57
3186 3316 5.268544 TCCGAATTACTCGTCGTAGAAATG 58.731 41.667 0.00 0.00 46.65 2.32
3187 3317 5.490139 TCCGAATTACTCGTCGTAGAAAT 57.510 39.130 0.00 0.00 46.65 2.17
3188 3318 4.944962 TCCGAATTACTCGTCGTAGAAA 57.055 40.909 0.00 0.00 46.65 2.52
3189 3319 4.651994 GTTCCGAATTACTCGTCGTAGAA 58.348 43.478 0.00 0.00 46.65 2.10
3190 3320 3.242091 CGTTCCGAATTACTCGTCGTAGA 60.242 47.826 0.00 0.00 46.65 2.59
3191 3321 3.024991 CGTTCCGAATTACTCGTCGTAG 58.975 50.000 0.00 0.00 46.65 3.51
3192 3322 2.223021 CCGTTCCGAATTACTCGTCGTA 60.223 50.000 0.00 0.00 46.65 3.43
3193 3323 1.466360 CCGTTCCGAATTACTCGTCGT 60.466 52.381 0.00 0.00 46.65 4.34
3194 3324 1.186030 CCGTTCCGAATTACTCGTCG 58.814 55.000 0.00 0.00 46.65 5.12
3195 3325 2.448219 CTCCGTTCCGAATTACTCGTC 58.552 52.381 0.00 0.00 46.65 4.20
3196 3326 1.133790 CCTCCGTTCCGAATTACTCGT 59.866 52.381 0.00 0.00 46.65 4.18
3198 3328 1.753073 TCCCTCCGTTCCGAATTACTC 59.247 52.381 0.00 0.00 0.00 2.59
3199 3329 1.856629 TCCCTCCGTTCCGAATTACT 58.143 50.000 0.00 0.00 0.00 2.24
3200 3330 2.678471 TTCCCTCCGTTCCGAATTAC 57.322 50.000 0.00 0.00 0.00 1.89
3201 3331 3.962718 AGTATTCCCTCCGTTCCGAATTA 59.037 43.478 0.00 0.00 0.00 1.40
3202 3332 2.770232 AGTATTCCCTCCGTTCCGAATT 59.230 45.455 0.00 0.00 0.00 2.17
3203 3333 2.395619 AGTATTCCCTCCGTTCCGAAT 58.604 47.619 0.00 0.00 0.00 3.34
3204 3334 1.856629 AGTATTCCCTCCGTTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
3205 3335 2.092212 ACTAGTATTCCCTCCGTTCCGA 60.092 50.000 0.00 0.00 0.00 4.55
3206 3336 2.034305 CACTAGTATTCCCTCCGTTCCG 59.966 54.545 0.00 0.00 0.00 4.30
3207 3337 3.294214 TCACTAGTATTCCCTCCGTTCC 58.706 50.000 0.00 0.00 0.00 3.62
3208 3338 4.205587 TCTCACTAGTATTCCCTCCGTTC 58.794 47.826 0.00 0.00 0.00 3.95
3209 3339 4.079901 TCTCTCACTAGTATTCCCTCCGTT 60.080 45.833 0.00 0.00 0.00 4.44
3210 3340 3.458857 TCTCTCACTAGTATTCCCTCCGT 59.541 47.826 0.00 0.00 0.00 4.69
3211 3341 3.816523 GTCTCTCACTAGTATTCCCTCCG 59.183 52.174 0.00 0.00 0.00 4.63
3212 3342 4.146564 GGTCTCTCACTAGTATTCCCTCC 58.853 52.174 0.00 0.00 0.00 4.30
3213 3343 4.146564 GGGTCTCTCACTAGTATTCCCTC 58.853 52.174 0.00 0.00 0.00 4.30
3214 3344 3.117054 GGGGTCTCTCACTAGTATTCCCT 60.117 52.174 0.00 0.00 33.59 4.20
3215 3345 3.117054 AGGGGTCTCTCACTAGTATTCCC 60.117 52.174 0.00 2.39 0.00 3.97
3216 3346 3.892588 CAGGGGTCTCTCACTAGTATTCC 59.107 52.174 0.00 0.00 0.00 3.01
3217 3347 3.892588 CCAGGGGTCTCTCACTAGTATTC 59.107 52.174 0.00 0.00 0.00 1.75
3218 3348 3.272551 ACCAGGGGTCTCTCACTAGTATT 59.727 47.826 0.00 0.00 0.00 1.89
3219 3349 2.860041 ACCAGGGGTCTCTCACTAGTAT 59.140 50.000 0.00 0.00 0.00 2.12
3220 3350 2.285707 ACCAGGGGTCTCTCACTAGTA 58.714 52.381 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.