Multiple sequence alignment - TraesCS5D01G393200

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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 TraesCS5D01G393200 chr5D 100.000 3306 0 0 1 3306 461441998 461438693 0.000000e+00 6106.0
1 TraesCS5D01G393200 chr5D 87.500 112 10 3 2785 2894 367482372 367482263 3.460000e-25 126.0
2 TraesCS5D01G393200 chr5A 93.260 2730 112 34 25 2728 581489278 581486595 0.000000e+00 3956.0
3 TraesCS5D01G393200 chr5A 83.636 440 41 18 2888 3306 581486561 581486132 5.180000e-103 385.0
4 TraesCS5D01G393200 chr4A 81.739 230 40 2 1153 1381 19622533 19622305 1.210000e-44 191.0
5 TraesCS5D01G393200 chr4A 90.099 101 4 5 2792 2889 639988787 639988884 3.460000e-25 126.0
6 TraesCS5D01G393200 chr1B 81.818 231 38 4 1150 1378 627929091 627928863 1.210000e-44 191.0
7 TraesCS5D01G393200 chr1A 81.818 231 38 4 1150 1378 550314240 550314012 1.210000e-44 191.0
8 TraesCS5D01G393200 chr1A 87.179 117 7 8 2783 2895 492431639 492431527 3.460000e-25 126.0
9 TraesCS5D01G393200 chr1D 80.952 231 40 4 1150 1378 457852091 457851863 2.620000e-41 180.0
10 TraesCS5D01G393200 chr2D 93.000 100 7 0 2792 2891 590075915 590076014 2.660000e-31 147.0
11 TraesCS5D01G393200 chr7A 90.099 101 6 2 2790 2888 365238264 365238166 9.630000e-26 128.0
12 TraesCS5D01G393200 chr4B 90.196 102 4 5 2791 2889 300941616 300941714 9.630000e-26 128.0
13 TraesCS5D01G393200 chr3B 88.073 109 9 4 2782 2888 238110213 238110319 3.460000e-25 126.0
14 TraesCS5D01G393200 chr3B 80.233 172 26 7 1204 1371 799860562 799860395 4.480000e-24 122.0
15 TraesCS5D01G393200 chr6D 89.320 103 6 3 2787 2888 389646570 389646668 1.250000e-24 124.0
16 TraesCS5D01G393200 chr4D 87.273 110 8 3 2785 2891 306239507 306239613 1.610000e-23 121.0
17 TraesCS5D01G393200 chr3D 77.778 189 40 2 1191 1378 388534452 388534265 7.500000e-22 115.0
18 TraesCS5D01G393200 chr3A 77.249 189 41 2 1191 1378 509798927 509798740 3.490000e-20 110.0
19 TraesCS5D01G393200 chr3A 76.536 179 36 4 1191 1366 640951902 640952077 3.510000e-15 93.5


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 TraesCS5D01G393200 chr5D 461438693 461441998 3305 True 6106.0 6106 100.000 1 3306 1 chr5D.!!$R2 3305
1 TraesCS5D01G393200 chr5A 581486132 581489278 3146 True 2170.5 3956 88.448 25 3306 2 chr5A.!!$R1 3281

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
611 619 0.036199 CTCCTCTTGCAGCTGCTTCT 60.036 55.000 36.61 0.0 42.66 2.85 F
1409 1420 1.007502 TGCACGCATTGTTCTTGCC 60.008 52.632 0.00 0.0 36.75 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 1536 0.030504 CCTGCGATGCAACACAAACA 59.969 50.0 0.00 0.00 38.41 2.83 R
3136 3173 0.031585 ACAAAGTAGACGCAGCGTGA 59.968 50.0 28.57 10.47 41.37 4.35 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
23 24 4.849329 CGTGCGTACGCCCTCCTC 62.849 72.222 35.11 17.35 44.11 3.71
28 29 3.834799 GTACGCCCTCCTCACCCG 61.835 72.222 0.00 0.00 0.00 5.28
96 97 2.632544 CGACCACGGCCACTGTAGA 61.633 63.158 2.24 0.00 35.72 2.59
105 106 1.153842 CCACTGTAGACGCATCGCA 60.154 57.895 0.00 0.00 0.00 5.10
244 245 1.986698 TAAGCGGCTACTTGTTCGAC 58.013 50.000 1.35 0.00 0.00 4.20
265 266 2.893682 CTTCCAGAACCATCGCCCCC 62.894 65.000 0.00 0.00 0.00 5.40
284 285 3.665675 CTCCGGGCCTTCCAGAACG 62.666 68.421 0.84 0.00 34.36 3.95
291 292 2.269241 CTTCCAGAACGCTCCCCC 59.731 66.667 0.00 0.00 0.00 5.40
306 307 4.082523 CCCGCCACGTCACAGGAT 62.083 66.667 0.00 0.00 0.00 3.24
314 321 0.617820 ACGTCACAGGATAAGCCCCT 60.618 55.000 0.00 0.00 37.37 4.79
315 322 0.105039 CGTCACAGGATAAGCCCCTC 59.895 60.000 0.00 0.00 37.37 4.30
368 375 0.451783 CTTTCGGAATTGGAAGCCCG 59.548 55.000 0.00 0.00 43.02 6.13
371 378 2.359011 GGAATTGGAAGCCCGGGT 59.641 61.111 24.63 1.57 34.29 5.28
453 461 2.453638 GCGCCTCAAGTACGAAGCC 61.454 63.158 0.00 0.00 0.00 4.35
455 463 0.454600 CGCCTCAAGTACGAAGCCTA 59.545 55.000 0.00 0.00 0.00 3.93
456 464 1.534175 CGCCTCAAGTACGAAGCCTAG 60.534 57.143 0.00 0.00 0.00 3.02
496 504 1.341581 CCTCTCCCTTCTTCTCCGTCT 60.342 57.143 0.00 0.00 0.00 4.18
497 505 1.748493 CTCTCCCTTCTTCTCCGTCTG 59.252 57.143 0.00 0.00 0.00 3.51
499 507 1.153745 CCCTTCTTCTCCGTCTGCG 60.154 63.158 0.00 0.00 37.95 5.18
515 523 2.262915 CGGTCTGGTCTGGTCTGC 59.737 66.667 0.00 0.00 0.00 4.26
543 551 2.558795 TCTTCTCTCTCCGTCCTTGTTG 59.441 50.000 0.00 0.00 0.00 3.33
579 587 6.978343 TGTACTCTCCGATTTTACATTTGG 57.022 37.500 0.00 0.00 0.00 3.28
588 596 3.534357 TTTTACATTTGGCCTCCTCCA 57.466 42.857 3.32 0.00 0.00 3.86
611 619 0.036199 CTCCTCTTGCAGCTGCTTCT 60.036 55.000 36.61 0.00 42.66 2.85
645 653 2.171448 GGAGCTCTGCCATTTTAGGAGA 59.829 50.000 14.64 0.00 0.00 3.71
671 679 3.117360 GGAGATCCCCTGAATTGGTCAAT 60.117 47.826 0.00 0.00 35.22 2.57
687 697 5.069318 TGGTCAATCAGCATTGTTAGTTCA 58.931 37.500 0.00 0.00 40.47 3.18
713 723 6.220930 ACGATTGCTCAAACTTTGACTACTA 58.779 36.000 0.00 0.00 35.46 1.82
731 741 7.017254 TGACTACTACAGATTCTTTTCCCCTTT 59.983 37.037 0.00 0.00 0.00 3.11
742 752 5.293560 TCTTTTCCCCTTTATTTTGCAACG 58.706 37.500 0.00 0.00 0.00 4.10
748 758 4.502431 CCCCTTTATTTTGCAACGACCTTT 60.502 41.667 0.00 0.00 0.00 3.11
772 782 3.746492 GGTAGCCCGTAATTGATTGCTAG 59.254 47.826 0.00 0.00 32.47 3.42
778 788 4.876107 CCCGTAATTGATTGCTAGTCTTGT 59.124 41.667 0.00 0.00 0.00 3.16
804 814 9.103861 TGGTTCTGAATTTTGTTTTTGGTATTC 57.896 29.630 0.00 0.00 0.00 1.75
828 838 3.430333 TTCAGAAACTTTCGGGTTTGC 57.570 42.857 6.76 0.00 39.20 3.68
844 854 2.276732 TTGCTTCTTTGGAGTCTGGG 57.723 50.000 0.00 0.00 0.00 4.45
879 890 2.209838 TCTAGCAAAGATCGCCTTCG 57.790 50.000 0.00 0.00 33.02 3.79
885 896 2.354821 GCAAAGATCGCCTTCGGTTAAT 59.645 45.455 0.00 0.00 33.02 1.40
938 949 3.007635 GTTTTCCTTGGTCCGATCGATT 58.992 45.455 18.66 0.00 0.00 3.34
1005 1016 4.078537 TGTTTGGTCGTTTGATCATGGAT 58.921 39.130 0.00 0.00 34.53 3.41
1038 1049 4.142293 GGCATTGTGAAAGAGGAGGAATTC 60.142 45.833 0.00 0.00 0.00 2.17
1052 1063 1.753468 GAATTCGACTTCGCCGGAGC 61.753 60.000 5.05 0.00 39.60 4.70
1056 1067 4.742201 GACTTCGCCGGAGCTGCA 62.742 66.667 5.05 0.00 36.60 4.41
1333 1344 1.296715 CCCCGCTACTTCAAGCACT 59.703 57.895 0.00 0.00 42.91 4.40
1388 1399 4.508124 CACCTATGTAAGTTTCTGCCGATC 59.492 45.833 0.00 0.00 0.00 3.69
1389 1400 4.161565 ACCTATGTAAGTTTCTGCCGATCA 59.838 41.667 0.00 0.00 0.00 2.92
1393 1404 1.160137 AAGTTTCTGCCGATCAGTGC 58.840 50.000 0.00 0.00 43.32 4.40
1409 1420 1.007502 TGCACGCATTGTTCTTGCC 60.008 52.632 0.00 0.00 36.75 4.52
1418 1429 1.588674 TTGTTCTTGCCGTACCAGTG 58.411 50.000 0.00 0.00 0.00 3.66
1448 1459 2.905736 TCCATCTATCCATGGCGATTGA 59.094 45.455 6.96 7.42 42.97 2.57
1472 1483 4.496360 TGGCAAAATGTGATGCAATGTAG 58.504 39.130 0.00 0.00 44.32 2.74
1473 1484 3.307782 GGCAAAATGTGATGCAATGTAGC 59.692 43.478 0.00 0.00 44.32 3.58
1480 1491 1.926510 TGATGCAATGTAGCTCGAACG 59.073 47.619 0.00 0.00 34.99 3.95
1487 1498 1.825090 TGTAGCTCGAACGGAACCTA 58.175 50.000 0.00 0.00 0.00 3.08
1633 1644 2.520904 GCTGAAGACGATCAGGCGC 61.521 63.158 0.00 0.00 45.60 6.53
1636 1647 4.514577 AAGACGATCAGGCGCCGG 62.515 66.667 23.20 22.36 33.86 6.13
1657 1668 3.432588 CCTCAGTCGTCGCCGTCT 61.433 66.667 0.00 0.00 32.66 4.18
2040 2051 3.114616 CAACGGCGAGACCAGCAG 61.115 66.667 16.62 0.00 39.03 4.24
2185 2196 2.841988 GAGAGGCATCGGGAGGCT 60.842 66.667 5.25 0.00 45.38 4.58
2281 2295 2.427245 CCTCTACCACCTCAGCCCG 61.427 68.421 0.00 0.00 0.00 6.13
2311 2325 0.109342 ACAGCCACCAGTGAAGGAAG 59.891 55.000 0.00 0.00 0.00 3.46
2315 2329 1.476833 GCCACCAGTGAAGGAAGAACA 60.477 52.381 0.00 0.00 0.00 3.18
2316 2330 2.498167 CCACCAGTGAAGGAAGAACAG 58.502 52.381 0.00 0.00 0.00 3.16
2317 2331 2.104792 CCACCAGTGAAGGAAGAACAGA 59.895 50.000 0.00 0.00 0.00 3.41
2318 2332 3.433598 CCACCAGTGAAGGAAGAACAGAA 60.434 47.826 0.00 0.00 0.00 3.02
2319 2333 3.812053 CACCAGTGAAGGAAGAACAGAAG 59.188 47.826 0.00 0.00 0.00 2.85
2320 2334 3.711704 ACCAGTGAAGGAAGAACAGAAGA 59.288 43.478 0.00 0.00 0.00 2.87
2321 2335 4.061596 CCAGTGAAGGAAGAACAGAAGAC 58.938 47.826 0.00 0.00 0.00 3.01
2322 2336 4.443457 CCAGTGAAGGAAGAACAGAAGACA 60.443 45.833 0.00 0.00 0.00 3.41
2357 2371 2.216898 GAGAAATATCTGCTGCCGCTT 58.783 47.619 0.70 0.00 35.54 4.68
2369 2383 2.251642 GCCGCTTGGAGAACAACGT 61.252 57.895 0.00 0.00 34.76 3.99
2370 2384 0.947180 GCCGCTTGGAGAACAACGTA 60.947 55.000 0.00 0.00 34.76 3.57
2390 2404 3.730761 GCCGCAGCCTGACAAGTG 61.731 66.667 0.00 0.00 0.00 3.16
2391 2405 2.031012 CCGCAGCCTGACAAGTGA 59.969 61.111 0.00 0.00 0.00 3.41
2392 2406 2.320587 CCGCAGCCTGACAAGTGAC 61.321 63.158 0.00 0.00 0.00 3.67
2393 2407 1.595109 CGCAGCCTGACAAGTGACA 60.595 57.895 0.00 0.00 0.00 3.58
2394 2408 1.159713 CGCAGCCTGACAAGTGACAA 61.160 55.000 0.00 0.00 0.00 3.18
2395 2409 0.308993 GCAGCCTGACAAGTGACAAC 59.691 55.000 0.00 0.00 0.00 3.32
2396 2410 0.947244 CAGCCTGACAAGTGACAACC 59.053 55.000 0.00 0.00 0.00 3.77
2494 2508 2.345760 CCGTAGGCGTAGTGGTGGT 61.346 63.158 0.00 0.00 46.14 4.16
2498 2512 1.537814 TAGGCGTAGTGGTGGTGGTG 61.538 60.000 0.00 0.00 0.00 4.17
2500 2514 3.144285 CGTAGTGGTGGTGGTGGT 58.856 61.111 0.00 0.00 0.00 4.16
2501 2515 1.818959 GCGTAGTGGTGGTGGTGGTA 61.819 60.000 0.00 0.00 0.00 3.25
2503 2517 0.036671 GTAGTGGTGGTGGTGGTAGC 60.037 60.000 0.00 0.00 0.00 3.58
2507 2521 2.285024 GGTGGTGGTGGTAGCGGTA 61.285 63.158 0.00 0.00 0.00 4.02
2508 2522 1.217244 GTGGTGGTGGTAGCGGTAG 59.783 63.158 0.00 0.00 0.00 3.18
2509 2523 1.228956 TGGTGGTGGTAGCGGTAGT 60.229 57.895 0.00 0.00 0.00 2.73
2510 2524 1.217244 GGTGGTGGTAGCGGTAGTG 59.783 63.158 0.00 0.00 0.00 2.74
2511 2525 1.447314 GTGGTGGTAGCGGTAGTGC 60.447 63.158 0.00 0.00 0.00 4.40
2513 2527 1.153628 GGTGGTAGCGGTAGTGCTG 60.154 63.158 0.00 0.00 46.70 4.41
2514 2528 1.810030 GTGGTAGCGGTAGTGCTGC 60.810 63.158 3.47 3.47 46.70 5.25
2554 2574 2.116125 GGGGCTGGTCTGCTTTGT 59.884 61.111 0.24 0.00 0.00 2.83
2662 2686 4.362476 GCCTTTTGCCTGGCGTGG 62.362 66.667 14.98 13.54 39.71 4.94
2685 2709 3.135712 TGGAATAATGCTCCGAGGCTTTA 59.864 43.478 0.00 9.12 36.66 1.85
2718 2742 2.163815 ACTCCAAGTTGGACGTAGATCG 59.836 50.000 21.05 10.86 42.67 3.69
2722 2746 3.372954 CAAGTTGGACGTAGATCGATCC 58.627 50.000 21.66 7.68 42.86 3.36
2724 2748 3.223435 AGTTGGACGTAGATCGATCCAT 58.777 45.455 21.66 7.09 43.40 3.41
2728 2752 2.755655 GGACGTAGATCGATCCATCCAT 59.244 50.000 21.66 4.83 42.86 3.41
2729 2753 3.181495 GGACGTAGATCGATCCATCCATC 60.181 52.174 21.66 11.63 42.86 3.51
2730 2754 2.755655 ACGTAGATCGATCCATCCATCC 59.244 50.000 21.66 0.00 42.86 3.51
2731 2755 3.020274 CGTAGATCGATCCATCCATCCT 58.980 50.000 21.66 2.60 42.86 3.24
2733 2757 2.186243 AGATCGATCCATCCATCCTGG 58.814 52.381 21.66 0.00 39.43 4.45
2734 2758 1.905215 GATCGATCCATCCATCCTGGT 59.095 52.381 14.76 0.00 39.03 4.00
2735 2759 1.806496 TCGATCCATCCATCCTGGTT 58.194 50.000 0.00 0.00 39.03 3.67
2736 2760 1.694150 TCGATCCATCCATCCTGGTTC 59.306 52.381 0.00 0.00 39.03 3.62
2737 2761 1.606480 CGATCCATCCATCCTGGTTCG 60.606 57.143 8.02 8.02 44.72 3.95
2738 2762 1.417890 GATCCATCCATCCTGGTTCGT 59.582 52.381 0.00 0.00 39.03 3.85
2739 2763 1.285280 TCCATCCATCCTGGTTCGTT 58.715 50.000 0.00 0.00 39.03 3.85
2740 2764 1.209504 TCCATCCATCCTGGTTCGTTC 59.790 52.381 0.00 0.00 39.03 3.95
2741 2765 1.668419 CATCCATCCTGGTTCGTTCC 58.332 55.000 0.00 0.00 39.03 3.62
2742 2766 0.546598 ATCCATCCTGGTTCGTTCCC 59.453 55.000 0.00 0.00 39.03 3.97
2743 2767 1.449601 CCATCCTGGTTCGTTCCCG 60.450 63.158 0.00 0.00 31.35 5.14
2744 2768 1.594833 CATCCTGGTTCGTTCCCGA 59.405 57.895 0.00 0.00 42.41 5.14
2745 2769 0.739813 CATCCTGGTTCGTTCCCGAC 60.740 60.000 0.00 0.00 44.13 4.79
2746 2770 1.896122 ATCCTGGTTCGTTCCCGACC 61.896 60.000 0.00 0.00 44.13 4.79
2747 2771 2.431942 CTGGTTCGTTCCCGACCG 60.432 66.667 0.00 0.00 44.13 4.79
2748 2772 2.911509 TGGTTCGTTCCCGACCGA 60.912 61.111 0.00 0.00 44.13 4.69
2749 2773 2.431430 GGTTCGTTCCCGACCGAC 60.431 66.667 0.00 0.00 44.13 4.79
2750 2774 2.802414 GTTCGTTCCCGACCGACG 60.802 66.667 0.00 0.00 44.13 5.12
2751 2775 2.977456 TTCGTTCCCGACCGACGA 60.977 61.111 0.00 1.63 44.13 4.20
2752 2776 2.969806 TTCGTTCCCGACCGACGAG 61.970 63.158 0.00 0.00 45.18 4.18
2753 2777 4.471726 CGTTCCCGACCGACGAGG 62.472 72.222 0.00 0.00 45.77 4.63
2754 2778 4.790861 GTTCCCGACCGACGAGGC 62.791 72.222 0.00 0.00 46.52 4.70
2758 2782 4.873129 CCGACCGACGAGGCCATG 62.873 72.222 5.01 0.00 46.52 3.66
2759 2783 4.873129 CGACCGACGAGGCCATGG 62.873 72.222 7.63 7.63 46.52 3.66
2760 2784 3.458163 GACCGACGAGGCCATGGA 61.458 66.667 18.40 0.00 46.52 3.41
2761 2785 3.000819 ACCGACGAGGCCATGGAA 61.001 61.111 18.40 0.00 46.52 3.53
2762 2786 2.202932 CCGACGAGGCCATGGAAG 60.203 66.667 18.40 5.25 0.00 3.46
2763 2787 2.202932 CGACGAGGCCATGGAAGG 60.203 66.667 18.40 3.26 0.00 3.46
2771 2795 4.039042 CCATGGAAGGGGCAAAGG 57.961 61.111 5.56 0.00 31.11 3.11
2796 2820 3.817148 GCGAGTGCTAGTAGATACTCC 57.183 52.381 20.43 13.61 36.97 3.85
2797 2821 2.485038 GCGAGTGCTAGTAGATACTCCC 59.515 54.545 20.43 13.04 36.97 4.30
2798 2822 3.807913 GCGAGTGCTAGTAGATACTCCCT 60.808 52.174 20.43 0.00 36.97 4.20
2799 2823 3.998341 CGAGTGCTAGTAGATACTCCCTC 59.002 52.174 20.43 3.15 36.97 4.30
2800 2824 4.329392 GAGTGCTAGTAGATACTCCCTCC 58.671 52.174 17.66 1.55 37.73 4.30
2801 2825 3.075884 GTGCTAGTAGATACTCCCTCCG 58.924 54.545 0.00 0.00 37.73 4.63
2802 2826 2.709934 TGCTAGTAGATACTCCCTCCGT 59.290 50.000 0.00 0.00 37.73 4.69
2803 2827 3.137913 TGCTAGTAGATACTCCCTCCGTT 59.862 47.826 0.00 0.00 37.73 4.44
2804 2828 4.143543 GCTAGTAGATACTCCCTCCGTTT 58.856 47.826 0.00 0.00 37.73 3.60
2805 2829 4.583907 GCTAGTAGATACTCCCTCCGTTTT 59.416 45.833 0.00 0.00 37.73 2.43
2806 2830 5.767168 GCTAGTAGATACTCCCTCCGTTTTA 59.233 44.000 0.00 0.00 37.73 1.52
2807 2831 6.264067 GCTAGTAGATACTCCCTCCGTTTTAA 59.736 42.308 0.00 0.00 37.73 1.52
2808 2832 7.201857 GCTAGTAGATACTCCCTCCGTTTTAAA 60.202 40.741 0.00 0.00 37.73 1.52
2809 2833 7.486407 AGTAGATACTCCCTCCGTTTTAAAA 57.514 36.000 0.00 0.00 0.00 1.52
2810 2834 8.087303 AGTAGATACTCCCTCCGTTTTAAAAT 57.913 34.615 3.52 0.00 0.00 1.82
2811 2835 9.205513 AGTAGATACTCCCTCCGTTTTAAAATA 57.794 33.333 3.52 0.00 0.00 1.40
2812 2836 9.473640 GTAGATACTCCCTCCGTTTTAAAATAG 57.526 37.037 3.52 1.99 0.00 1.73
2813 2837 8.315220 AGATACTCCCTCCGTTTTAAAATAGA 57.685 34.615 3.52 3.61 0.00 1.98
2814 2838 8.935741 AGATACTCCCTCCGTTTTAAAATAGAT 58.064 33.333 3.52 0.00 0.00 1.98
2815 2839 8.904099 ATACTCCCTCCGTTTTAAAATAGATG 57.096 34.615 3.52 2.01 0.00 2.90
2816 2840 6.954232 ACTCCCTCCGTTTTAAAATAGATGA 58.046 36.000 3.52 3.96 0.00 2.92
2817 2841 7.574607 ACTCCCTCCGTTTTAAAATAGATGAT 58.425 34.615 3.52 0.00 0.00 2.45
2818 2842 8.053355 ACTCCCTCCGTTTTAAAATAGATGATT 58.947 33.333 3.52 0.00 0.00 2.57
2819 2843 8.446599 TCCCTCCGTTTTAAAATAGATGATTC 57.553 34.615 3.52 0.00 0.00 2.52
2820 2844 8.050325 TCCCTCCGTTTTAAAATAGATGATTCA 58.950 33.333 3.52 0.00 0.00 2.57
2821 2845 8.682710 CCCTCCGTTTTAAAATAGATGATTCAA 58.317 33.333 3.52 0.00 0.00 2.69
2822 2846 9.503427 CCTCCGTTTTAAAATAGATGATTCAAC 57.497 33.333 3.52 0.00 0.00 3.18
2866 2890 9.227777 ACAAAGTTAGTATAAAGTTGGGTCATC 57.772 33.333 0.00 0.00 0.00 2.92
2867 2891 9.449719 CAAAGTTAGTATAAAGTTGGGTCATCT 57.550 33.333 0.00 0.00 0.00 2.90
2874 2898 9.408648 AGTATAAAGTTGGGTCATCTATTTTGG 57.591 33.333 0.00 0.00 0.00 3.28
2875 2899 9.403583 GTATAAAGTTGGGTCATCTATTTTGGA 57.596 33.333 0.00 0.00 0.00 3.53
2876 2900 8.893563 ATAAAGTTGGGTCATCTATTTTGGAA 57.106 30.769 0.00 0.00 0.00 3.53
2877 2901 7.797121 AAAGTTGGGTCATCTATTTTGGAAT 57.203 32.000 0.00 0.00 0.00 3.01
2878 2902 6.780457 AGTTGGGTCATCTATTTTGGAATG 57.220 37.500 0.00 0.00 0.00 2.67
2879 2903 5.658190 AGTTGGGTCATCTATTTTGGAATGG 59.342 40.000 0.00 0.00 0.00 3.16
2880 2904 5.464588 TGGGTCATCTATTTTGGAATGGA 57.535 39.130 0.00 0.00 37.20 3.41
2881 2905 5.448654 TGGGTCATCTATTTTGGAATGGAG 58.551 41.667 0.00 0.00 36.39 3.86
2882 2906 5.193527 TGGGTCATCTATTTTGGAATGGAGA 59.806 40.000 0.00 0.00 36.39 3.71
2883 2907 5.767168 GGGTCATCTATTTTGGAATGGAGAG 59.233 44.000 0.00 0.00 36.39 3.20
2884 2908 6.409695 GGGTCATCTATTTTGGAATGGAGAGA 60.410 42.308 0.00 0.00 36.39 3.10
2885 2909 6.709846 GGTCATCTATTTTGGAATGGAGAGAG 59.290 42.308 0.00 0.00 36.39 3.20
2886 2910 7.278875 GTCATCTATTTTGGAATGGAGAGAGT 58.721 38.462 0.00 0.00 36.39 3.24
2887 2911 8.424918 GTCATCTATTTTGGAATGGAGAGAGTA 58.575 37.037 0.00 0.00 36.39 2.59
2888 2912 8.646004 TCATCTATTTTGGAATGGAGAGAGTAG 58.354 37.037 0.00 0.00 36.39 2.57
2889 2913 8.646004 CATCTATTTTGGAATGGAGAGAGTAGA 58.354 37.037 0.00 0.00 36.39 2.59
2890 2914 8.789767 TCTATTTTGGAATGGAGAGAGTAGAT 57.210 34.615 0.00 0.00 30.37 1.98
2945 2969 0.038435 TCGGCGTTTTCATGGTCGTA 60.038 50.000 6.85 0.00 0.00 3.43
2979 3003 3.828451 TCTGGAATGAAAAGGAAAGGCTG 59.172 43.478 0.00 0.00 0.00 4.85
2983 3007 2.086610 TGAAAAGGAAAGGCTGGCTT 57.913 45.000 11.07 11.07 0.00 4.35
2990 3014 0.449388 GAAAGGCTGGCTTGTCATCG 59.551 55.000 17.73 0.00 0.00 3.84
2995 3019 1.975363 GCTGGCTTGTCATCGTCAGC 61.975 60.000 11.85 11.85 40.30 4.26
2998 3022 2.456119 GCTTGTCATCGTCAGCGGG 61.456 63.158 0.00 0.00 38.89 6.13
3005 3029 1.086696 CATCGTCAGCGGGTTTGATT 58.913 50.000 0.00 0.00 38.89 2.57
3009 3033 1.401018 CGTCAGCGGGTTTGATTTTCC 60.401 52.381 0.00 0.00 0.00 3.13
3010 3034 1.067846 GTCAGCGGGTTTGATTTTCCC 60.068 52.381 0.00 0.00 37.98 3.97
3011 3035 0.246360 CAGCGGGTTTGATTTTCCCC 59.754 55.000 0.00 0.00 38.09 4.81
3012 3036 0.178947 AGCGGGTTTGATTTTCCCCA 60.179 50.000 0.00 0.00 38.09 4.96
3013 3037 0.901827 GCGGGTTTGATTTTCCCCAT 59.098 50.000 0.00 0.00 38.09 4.00
3043 3071 2.809601 CCGGCGGTTCTCGTTCAG 60.810 66.667 19.97 0.00 41.72 3.02
3055 3083 3.782244 GTTCAGACTGCGCCGCTG 61.782 66.667 14.66 14.66 0.00 5.18
3077 3107 1.679032 CCCGTTCATCCTCCCTTTCAC 60.679 57.143 0.00 0.00 0.00 3.18
3079 3109 1.679032 CGTTCATCCTCCCTTTCACCC 60.679 57.143 0.00 0.00 0.00 4.61
3083 3120 1.214992 ATCCTCCCTTTCACCCACCC 61.215 60.000 0.00 0.00 0.00 4.61
3109 3146 0.030908 CGCTCGATTCTACTGGGTCC 59.969 60.000 0.00 0.00 0.00 4.46
3151 3188 1.081376 GTGTCACGCTGCGTCTACT 60.081 57.895 26.49 0.00 38.32 2.57
3152 3189 0.663568 GTGTCACGCTGCGTCTACTT 60.664 55.000 26.49 0.00 38.32 2.24
3153 3190 0.031585 TGTCACGCTGCGTCTACTTT 59.968 50.000 26.49 0.00 38.32 2.66
3154 3191 0.435008 GTCACGCTGCGTCTACTTTG 59.565 55.000 26.49 12.44 38.32 2.77
3159 3196 1.398451 CGCTGCGTCTACTTTGTTTGG 60.398 52.381 14.93 0.00 0.00 3.28
3160 3197 1.871039 GCTGCGTCTACTTTGTTTGGA 59.129 47.619 0.00 0.00 0.00 3.53
3161 3198 2.484264 GCTGCGTCTACTTTGTTTGGAT 59.516 45.455 0.00 0.00 0.00 3.41
3173 3210 0.174162 GTTTGGATGGATGCAGTGGC 59.826 55.000 0.00 0.00 41.68 5.01
3178 3215 2.324014 GATGGATGCAGTGGCGGGTA 62.324 60.000 0.00 0.00 45.35 3.69
3192 3234 1.373590 CGGGTAGGTTGGATTTGGCG 61.374 60.000 0.00 0.00 0.00 5.69
3198 3240 0.603065 GGTTGGATTTGGCGAGCTTT 59.397 50.000 0.00 0.00 0.00 3.51
3199 3241 1.402852 GGTTGGATTTGGCGAGCTTTC 60.403 52.381 0.00 0.00 0.00 2.62
3200 3242 1.269448 GTTGGATTTGGCGAGCTTTCA 59.731 47.619 0.00 0.00 0.00 2.69
3201 3243 0.881118 TGGATTTGGCGAGCTTTCAC 59.119 50.000 0.00 0.00 0.00 3.18
3203 3245 0.171231 GATTTGGCGAGCTTTCACCC 59.829 55.000 0.00 0.00 0.00 4.61
3204 3246 0.539438 ATTTGGCGAGCTTTCACCCA 60.539 50.000 0.00 0.00 0.00 4.51
3207 3249 3.056328 GCGAGCTTTCACCCACCC 61.056 66.667 0.00 0.00 0.00 4.61
3208 3250 2.359975 CGAGCTTTCACCCACCCC 60.360 66.667 0.00 0.00 0.00 4.95
3209 3251 2.895424 CGAGCTTTCACCCACCCCT 61.895 63.158 0.00 0.00 0.00 4.79
3210 3252 1.002011 GAGCTTTCACCCACCCCTC 60.002 63.158 0.00 0.00 0.00 4.30
3211 3253 1.464198 AGCTTTCACCCACCCCTCT 60.464 57.895 0.00 0.00 0.00 3.69
3214 3256 0.615850 CTTTCACCCACCCCTCTCTC 59.384 60.000 0.00 0.00 0.00 3.20
3217 3259 1.687493 CACCCACCCCTCTCTCTCC 60.687 68.421 0.00 0.00 0.00 3.71
3218 3260 2.443016 CCCACCCCTCTCTCTCCG 60.443 72.222 0.00 0.00 0.00 4.63
3249 3294 2.165319 AACGTCTAGGCCACTGTTTC 57.835 50.000 5.01 0.00 0.00 2.78
3250 3295 0.038526 ACGTCTAGGCCACTGTTTCG 60.039 55.000 5.01 2.74 0.00 3.46
3267 3312 4.998033 TGTTTCGTTGTACCATTGCTGATA 59.002 37.500 0.00 0.00 0.00 2.15
3283 3328 2.165641 CTGATACCACGGCAACAGACTA 59.834 50.000 0.00 0.00 0.00 2.59
3284 3329 2.165641 TGATACCACGGCAACAGACTAG 59.834 50.000 0.00 0.00 0.00 2.57
3285 3330 1.624336 TACCACGGCAACAGACTAGT 58.376 50.000 0.00 0.00 0.00 2.57
3286 3331 1.624336 ACCACGGCAACAGACTAGTA 58.376 50.000 0.00 0.00 0.00 1.82
3287 3332 1.271656 ACCACGGCAACAGACTAGTAC 59.728 52.381 0.00 0.00 0.00 2.73
3292 3337 1.467035 GGCAACAGACTAGTACGTCGG 60.467 57.143 0.00 0.79 38.90 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.755628 TGAGGAGGGCGTACGCAC 61.756 66.667 37.99 36.35 46.56 5.34
8 9 3.755628 GTGAGGAGGGCGTACGCA 61.756 66.667 37.99 16.10 44.11 5.24
9 10 4.509737 GGTGAGGAGGGCGTACGC 62.510 72.222 31.54 31.54 41.06 4.42
10 11 3.834799 GGGTGAGGAGGGCGTACG 61.835 72.222 11.84 11.84 0.00 3.67
11 12 3.834799 CGGGTGAGGAGGGCGTAC 61.835 72.222 0.00 0.00 0.00 3.67
212 213 2.158755 AGCCGCTTATCTTATTGCAGGT 60.159 45.455 0.00 0.00 0.00 4.00
244 245 1.452108 GGCGATGGTTCTGGAAGGG 60.452 63.158 0.00 0.00 0.00 3.95
291 292 1.421410 GCTTATCCTGTGACGTGGCG 61.421 60.000 0.00 0.00 0.00 5.69
303 304 1.128188 ACCATCCGAGGGGCTTATCC 61.128 60.000 3.73 0.00 0.00 2.59
304 305 0.765510 AACCATCCGAGGGGCTTATC 59.234 55.000 3.73 0.00 0.00 1.75
305 306 0.765510 GAACCATCCGAGGGGCTTAT 59.234 55.000 3.73 0.00 0.00 1.73
306 307 1.342672 GGAACCATCCGAGGGGCTTA 61.343 60.000 3.73 0.00 35.59 3.09
368 375 4.037760 CCCGTACCAACCCCACCC 62.038 72.222 0.00 0.00 0.00 4.61
371 378 3.642503 CAGCCCGTACCAACCCCA 61.643 66.667 0.00 0.00 0.00 4.96
375 382 3.562557 CCATTTATACAGCCCGTACCAAC 59.437 47.826 0.00 0.00 31.27 3.77
377 384 2.105134 CCCATTTATACAGCCCGTACCA 59.895 50.000 0.00 0.00 31.27 3.25
379 386 2.148768 GCCCATTTATACAGCCCGTAC 58.851 52.381 0.00 0.00 31.27 3.67
380 387 1.270412 CGCCCATTTATACAGCCCGTA 60.270 52.381 0.00 0.00 0.00 4.02
381 388 0.534203 CGCCCATTTATACAGCCCGT 60.534 55.000 0.00 0.00 0.00 5.28
382 389 1.234615 CCGCCCATTTATACAGCCCG 61.235 60.000 0.00 0.00 0.00 6.13
453 461 7.519927 AGGAAAGTACAGTACTATCCCTCTAG 58.480 42.308 13.87 0.00 38.26 2.43
455 463 6.160814 AGAGGAAAGTACAGTACTATCCCTCT 59.839 42.308 30.27 30.27 44.75 3.69
456 464 6.367161 AGAGGAAAGTACAGTACTATCCCTC 58.633 44.000 28.26 28.26 42.59 4.30
496 504 2.203640 AGACCAGACCAGACCGCA 60.204 61.111 0.00 0.00 0.00 5.69
497 505 2.262915 CAGACCAGACCAGACCGC 59.737 66.667 0.00 0.00 0.00 5.68
499 507 0.902516 AGAGCAGACCAGACCAGACC 60.903 60.000 0.00 0.00 0.00 3.85
500 508 0.246086 CAGAGCAGACCAGACCAGAC 59.754 60.000 0.00 0.00 0.00 3.51
501 509 1.539560 GCAGAGCAGACCAGACCAGA 61.540 60.000 0.00 0.00 0.00 3.86
502 510 1.079266 GCAGAGCAGACCAGACCAG 60.079 63.158 0.00 0.00 0.00 4.00
503 511 1.123861 AAGCAGAGCAGACCAGACCA 61.124 55.000 0.00 0.00 0.00 4.02
515 523 2.091541 ACGGAGAGAGAAGAAGCAGAG 58.908 52.381 0.00 0.00 0.00 3.35
543 551 4.438200 CGGAGAGTACAAGAAGAGAGAAGC 60.438 50.000 0.00 0.00 0.00 3.86
579 587 2.285743 AGGAGGGTTGGAGGAGGC 60.286 66.667 0.00 0.00 0.00 4.70
588 596 1.377994 CAGCTGCAAGAGGAGGGTT 59.622 57.895 0.00 0.00 34.07 4.11
611 619 4.424711 GCTCCCCATTGACGCCCA 62.425 66.667 0.00 0.00 0.00 5.36
671 679 4.251543 TCGTCTGAACTAACAATGCTGA 57.748 40.909 0.00 0.00 0.00 4.26
687 697 4.130118 AGTCAAAGTTTGAGCAATCGTCT 58.870 39.130 18.56 6.88 41.01 4.18
713 723 7.161404 GCAAAATAAAGGGGAAAAGAATCTGT 58.839 34.615 0.00 0.00 0.00 3.41
731 741 2.959707 ACCCAAAGGTCGTTGCAAAATA 59.040 40.909 0.00 0.00 46.45 1.40
742 752 0.614812 TTACGGGCTACCCAAAGGTC 59.385 55.000 3.08 0.00 46.45 3.85
748 758 2.925724 CAATCAATTACGGGCTACCCA 58.074 47.619 3.08 0.00 45.83 4.51
758 768 6.743575 ACCACAAGACTAGCAATCAATTAC 57.256 37.500 0.00 0.00 0.00 1.89
760 770 6.006449 AGAACCACAAGACTAGCAATCAATT 58.994 36.000 0.00 0.00 0.00 2.32
772 782 7.595311 AAAACAAAATTCAGAACCACAAGAC 57.405 32.000 0.00 0.00 0.00 3.01
778 788 9.103861 GAATACCAAAAACAAAATTCAGAACCA 57.896 29.630 0.00 0.00 0.00 3.67
804 814 5.215160 CAAACCCGAAAGTTTCTGAATCAG 58.785 41.667 13.56 3.38 37.87 2.90
828 838 3.965888 CCCCCAGACTCCAAAGAAG 57.034 57.895 0.00 0.00 0.00 2.85
859 870 2.540515 CGAAGGCGATCTTTGCTAGAA 58.459 47.619 0.00 0.00 40.82 2.10
879 890 3.006003 TCAAGAACCGGCCAAAATTAACC 59.994 43.478 0.00 0.00 0.00 2.85
885 896 2.593026 AGAATCAAGAACCGGCCAAAA 58.407 42.857 0.00 0.00 0.00 2.44
938 949 1.117150 GGGATTACTGAGCACCGGTA 58.883 55.000 6.87 0.00 35.60 4.02
1065 1076 1.433879 CCAGGAAGACGGCGAGTAG 59.566 63.158 16.62 0.00 0.00 2.57
1115 1126 4.489771 CGCCGGCCCAGGAAGATT 62.490 66.667 23.46 0.00 0.00 2.40
1188 1199 0.250295 TCTTGTTCAGGAAGGGCGTG 60.250 55.000 0.00 0.00 0.00 5.34
1191 1202 0.250338 ACGTCTTGTTCAGGAAGGGC 60.250 55.000 3.56 0.00 0.00 5.19
1194 1205 3.235195 CTCGTACGTCTTGTTCAGGAAG 58.765 50.000 16.05 0.00 0.00 3.46
1271 1282 3.041940 CGTCCCACACCACGAAGC 61.042 66.667 0.00 0.00 38.32 3.86
1333 1344 0.106708 ACGAAGCTGGAGAAGTTGCA 59.893 50.000 0.00 0.00 0.00 4.08
1388 1399 1.401530 CAAGAACAATGCGTGCACTG 58.598 50.000 16.19 8.82 0.00 3.66
1389 1400 0.318107 GCAAGAACAATGCGTGCACT 60.318 50.000 16.19 0.00 39.89 4.40
1393 1404 0.515127 TACGGCAAGAACAATGCGTG 59.485 50.000 0.00 0.00 44.75 5.34
1409 1420 1.202533 GGATGGATGGACACTGGTACG 60.203 57.143 0.00 0.00 0.00 3.67
1418 1429 4.384978 CCATGGATAGATGGATGGATGGAC 60.385 50.000 5.56 0.00 45.24 4.02
1448 1459 4.328536 ACATTGCATCACATTTTGCCAAT 58.671 34.783 0.00 0.00 38.08 3.16
1472 1483 1.664151 CCAATTAGGTTCCGTTCGAGC 59.336 52.381 0.00 0.00 0.00 5.03
1480 1491 6.184789 TCTGGAACAATACCAATTAGGTTCC 58.815 40.000 13.01 13.01 45.27 3.62
1487 1498 8.017418 TGAGTTTTTCTGGAACAATACCAATT 57.983 30.769 0.00 0.00 38.70 2.32
1494 1505 4.202111 CGGGTTGAGTTTTTCTGGAACAAT 60.202 41.667 0.00 0.00 38.70 2.71
1525 1536 0.030504 CCTGCGATGCAACACAAACA 59.969 50.000 0.00 0.00 38.41 2.83
1603 1614 0.612229 TCTTCAGCAGCTCCTTCTGG 59.388 55.000 0.00 0.00 34.74 3.86
1819 1830 1.227586 CATCTCCTGCATCTGCGCT 60.228 57.895 9.73 0.00 45.83 5.92
2292 2306 0.109342 CTTCCTTCACTGGTGGCTGT 59.891 55.000 0.70 0.00 0.00 4.40
2297 2311 3.475566 TCTGTTCTTCCTTCACTGGTG 57.524 47.619 0.00 0.00 0.00 4.17
2311 2325 6.334102 TCTAGAACCTTCTGTCTTCTGTTC 57.666 41.667 0.00 0.00 38.19 3.18
2315 2329 3.442273 CGCTCTAGAACCTTCTGTCTTCT 59.558 47.826 0.00 0.00 38.19 2.85
2316 2330 3.440872 TCGCTCTAGAACCTTCTGTCTTC 59.559 47.826 0.00 0.00 38.19 2.87
2317 2331 3.422796 TCGCTCTAGAACCTTCTGTCTT 58.577 45.455 0.00 0.00 38.19 3.01
2318 2332 3.013921 CTCGCTCTAGAACCTTCTGTCT 58.986 50.000 0.00 0.00 38.19 3.41
2319 2333 3.011119 TCTCGCTCTAGAACCTTCTGTC 58.989 50.000 0.00 0.00 38.19 3.51
2320 2334 3.074675 TCTCGCTCTAGAACCTTCTGT 57.925 47.619 0.00 0.00 38.19 3.41
2321 2335 4.442375 TTTCTCGCTCTAGAACCTTCTG 57.558 45.455 0.00 0.00 38.19 3.02
2322 2336 6.775629 AGATATTTCTCGCTCTAGAACCTTCT 59.224 38.462 0.00 0.00 41.24 2.85
2357 2371 1.675219 GGCCCTACGTTGTTCTCCA 59.325 57.895 0.00 0.00 0.00 3.86
2387 2401 1.149174 CACTGCTGGGGTTGTCACT 59.851 57.895 0.00 0.00 0.00 3.41
2388 2402 0.886490 CTCACTGCTGGGGTTGTCAC 60.886 60.000 0.00 0.00 0.00 3.67
2389 2403 1.451504 CTCACTGCTGGGGTTGTCA 59.548 57.895 0.00 0.00 0.00 3.58
2390 2404 1.968540 GCTCACTGCTGGGGTTGTC 60.969 63.158 0.00 0.00 38.95 3.18
2391 2405 2.113986 GCTCACTGCTGGGGTTGT 59.886 61.111 0.00 0.00 38.95 3.32
2392 2406 3.052082 CGCTCACTGCTGGGGTTG 61.052 66.667 0.00 0.00 40.11 3.77
2393 2407 2.337879 TTTCGCTCACTGCTGGGGTT 62.338 55.000 0.00 0.00 40.11 4.11
2394 2408 2.738213 CTTTCGCTCACTGCTGGGGT 62.738 60.000 0.00 0.00 40.11 4.95
2395 2409 2.032528 TTTCGCTCACTGCTGGGG 59.967 61.111 0.00 0.00 40.11 4.96
2396 2410 0.603707 TTCTTTCGCTCACTGCTGGG 60.604 55.000 0.00 0.00 40.11 4.45
2419 2433 7.499563 GGAAACTTCTTGTTCTAGAACCTTCTT 59.500 37.037 28.43 14.47 40.46 2.52
2420 2434 6.993308 GGAAACTTCTTGTTCTAGAACCTTCT 59.007 38.462 28.43 8.53 40.46 2.85
2464 2478 1.077501 CCTACGGTCTACCCCACGA 60.078 63.158 0.00 0.00 0.00 4.35
2492 2506 1.217244 CACTACCGCTACCACCACC 59.783 63.158 0.00 0.00 0.00 4.61
2494 2508 1.608336 AGCACTACCGCTACCACCA 60.608 57.895 0.00 0.00 41.55 4.17
2498 2512 2.202892 GGCAGCACTACCGCTACC 60.203 66.667 0.00 0.00 41.38 3.18
2500 2514 2.423898 GGAGGCAGCACTACCGCTA 61.424 63.158 0.00 0.00 41.38 4.26
2501 2515 3.775654 GGAGGCAGCACTACCGCT 61.776 66.667 0.00 0.00 45.21 5.52
2503 2517 1.522355 CATGGAGGCAGCACTACCG 60.522 63.158 0.00 0.00 0.00 4.02
2507 2521 4.437587 GGGCATGGAGGCAGCACT 62.438 66.667 0.00 0.00 46.44 4.40
2511 2525 3.829226 ATGGGGGCATGGAGGCAG 61.829 66.667 0.00 0.00 46.44 4.85
2512 2526 4.146156 CATGGGGGCATGGAGGCA 62.146 66.667 0.00 0.00 46.44 4.75
2541 2561 5.192327 AGAAAATGAACAAAGCAGACCAG 57.808 39.130 0.00 0.00 0.00 4.00
2662 2686 1.202698 AGCCTCGGAGCATTATTCCAC 60.203 52.381 0.00 0.00 34.24 4.02
2685 2709 4.323257 CCAACTTGGAGTACTTAATCCGGT 60.323 45.833 0.00 0.00 43.04 5.28
2737 2761 4.790861 GCCTCGTCGGTCGGGAAC 62.791 72.222 0.00 0.00 43.64 3.62
2741 2765 4.873129 CATGGCCTCGTCGGTCGG 62.873 72.222 3.32 0.00 41.63 4.79
2742 2766 4.873129 CCATGGCCTCGTCGGTCG 62.873 72.222 3.32 0.00 41.63 4.79
2743 2767 2.907897 CTTCCATGGCCTCGTCGGTC 62.908 65.000 6.96 0.00 38.12 4.79
2744 2768 3.000819 TTCCATGGCCTCGTCGGT 61.001 61.111 6.96 0.00 34.25 4.69
2745 2769 2.202932 CTTCCATGGCCTCGTCGG 60.203 66.667 6.96 0.00 0.00 4.79
2746 2770 2.202932 CCTTCCATGGCCTCGTCG 60.203 66.667 6.96 0.00 0.00 5.12
2747 2771 2.190578 CCCTTCCATGGCCTCGTC 59.809 66.667 6.96 0.00 0.00 4.20
2748 2772 3.411517 CCCCTTCCATGGCCTCGT 61.412 66.667 6.96 0.00 0.00 4.18
2749 2773 4.883354 GCCCCTTCCATGGCCTCG 62.883 72.222 6.96 0.00 41.97 4.63
2754 2778 2.361567 GCCTTTGCCCCTTCCATGG 61.362 63.158 4.97 4.97 0.00 3.66
2755 2779 1.193462 TTGCCTTTGCCCCTTCCATG 61.193 55.000 0.00 0.00 36.33 3.66
2756 2780 0.473501 TTTGCCTTTGCCCCTTCCAT 60.474 50.000 0.00 0.00 36.33 3.41
2757 2781 1.074926 TTTGCCTTTGCCCCTTCCA 60.075 52.632 0.00 0.00 36.33 3.53
2758 2782 1.673477 CTTTGCCTTTGCCCCTTCC 59.327 57.895 0.00 0.00 36.33 3.46
2759 2783 1.004560 GCTTTGCCTTTGCCCCTTC 60.005 57.895 0.00 0.00 36.33 3.46
2760 2784 2.871253 CGCTTTGCCTTTGCCCCTT 61.871 57.895 0.00 0.00 36.33 3.95
2761 2785 3.305516 CGCTTTGCCTTTGCCCCT 61.306 61.111 0.00 0.00 36.33 4.79
2762 2786 3.286915 CTCGCTTTGCCTTTGCCCC 62.287 63.158 0.00 0.00 36.33 5.80
2763 2787 2.259511 CTCGCTTTGCCTTTGCCC 59.740 61.111 0.00 0.00 36.33 5.36
2787 2811 9.425248 TCTATTTTAAAACGGAGGGAGTATCTA 57.575 33.333 1.97 0.00 33.73 1.98
2792 2816 6.954232 TCATCTATTTTAAAACGGAGGGAGT 58.046 36.000 1.97 0.00 0.00 3.85
2793 2817 8.451908 AATCATCTATTTTAAAACGGAGGGAG 57.548 34.615 1.97 0.00 0.00 4.30
2794 2818 8.050325 TGAATCATCTATTTTAAAACGGAGGGA 58.950 33.333 1.97 7.05 0.00 4.20
2795 2819 8.220755 TGAATCATCTATTTTAAAACGGAGGG 57.779 34.615 1.97 2.46 0.00 4.30
2796 2820 9.503427 GTTGAATCATCTATTTTAAAACGGAGG 57.497 33.333 1.97 6.55 0.00 4.30
2840 2864 9.227777 GATGACCCAACTTTATACTAACTTTGT 57.772 33.333 0.00 0.00 0.00 2.83
2841 2865 9.449719 AGATGACCCAACTTTATACTAACTTTG 57.550 33.333 0.00 0.00 0.00 2.77
2848 2872 9.408648 CCAAAATAGATGACCCAACTTTATACT 57.591 33.333 0.00 0.00 0.00 2.12
2849 2873 9.403583 TCCAAAATAGATGACCCAACTTTATAC 57.596 33.333 0.00 0.00 0.00 1.47
2850 2874 9.983024 TTCCAAAATAGATGACCCAACTTTATA 57.017 29.630 0.00 0.00 0.00 0.98
2851 2875 8.893563 TTCCAAAATAGATGACCCAACTTTAT 57.106 30.769 0.00 0.00 0.00 1.40
2852 2876 8.748412 CATTCCAAAATAGATGACCCAACTTTA 58.252 33.333 0.00 0.00 0.00 1.85
2853 2877 7.310609 CCATTCCAAAATAGATGACCCAACTTT 60.311 37.037 0.00 0.00 0.00 2.66
2854 2878 6.155049 CCATTCCAAAATAGATGACCCAACTT 59.845 38.462 0.00 0.00 0.00 2.66
2855 2879 5.658190 CCATTCCAAAATAGATGACCCAACT 59.342 40.000 0.00 0.00 0.00 3.16
2856 2880 5.656416 TCCATTCCAAAATAGATGACCCAAC 59.344 40.000 0.00 0.00 0.00 3.77
2857 2881 5.836705 TCCATTCCAAAATAGATGACCCAA 58.163 37.500 0.00 0.00 0.00 4.12
2858 2882 5.193527 TCTCCATTCCAAAATAGATGACCCA 59.806 40.000 0.00 0.00 0.00 4.51
2859 2883 5.694995 TCTCCATTCCAAAATAGATGACCC 58.305 41.667 0.00 0.00 0.00 4.46
2860 2884 6.595682 TCTCTCCATTCCAAAATAGATGACC 58.404 40.000 0.00 0.00 0.00 4.02
2861 2885 7.278875 ACTCTCTCCATTCCAAAATAGATGAC 58.721 38.462 0.00 0.00 0.00 3.06
2862 2886 7.443302 ACTCTCTCCATTCCAAAATAGATGA 57.557 36.000 0.00 0.00 0.00 2.92
2863 2887 8.646004 TCTACTCTCTCCATTCCAAAATAGATG 58.354 37.037 0.00 0.00 0.00 2.90
2864 2888 8.789767 TCTACTCTCTCCATTCCAAAATAGAT 57.210 34.615 0.00 0.00 0.00 1.98
2865 2889 8.789767 ATCTACTCTCTCCATTCCAAAATAGA 57.210 34.615 0.00 0.00 0.00 1.98
2866 2890 9.270640 CAATCTACTCTCTCCATTCCAAAATAG 57.729 37.037 0.00 0.00 0.00 1.73
2867 2891 7.716998 GCAATCTACTCTCTCCATTCCAAAATA 59.283 37.037 0.00 0.00 0.00 1.40
2868 2892 6.545298 GCAATCTACTCTCTCCATTCCAAAAT 59.455 38.462 0.00 0.00 0.00 1.82
2869 2893 5.882557 GCAATCTACTCTCTCCATTCCAAAA 59.117 40.000 0.00 0.00 0.00 2.44
2870 2894 5.045651 TGCAATCTACTCTCTCCATTCCAAA 60.046 40.000 0.00 0.00 0.00 3.28
2871 2895 4.471025 TGCAATCTACTCTCTCCATTCCAA 59.529 41.667 0.00 0.00 0.00 3.53
2872 2896 4.033009 TGCAATCTACTCTCTCCATTCCA 58.967 43.478 0.00 0.00 0.00 3.53
2873 2897 4.630111 CTGCAATCTACTCTCTCCATTCC 58.370 47.826 0.00 0.00 0.00 3.01
2874 2898 4.057432 GCTGCAATCTACTCTCTCCATTC 58.943 47.826 0.00 0.00 0.00 2.67
2875 2899 3.453717 TGCTGCAATCTACTCTCTCCATT 59.546 43.478 0.00 0.00 0.00 3.16
2876 2900 3.036819 TGCTGCAATCTACTCTCTCCAT 58.963 45.455 0.00 0.00 0.00 3.41
2877 2901 2.429971 CTGCTGCAATCTACTCTCTCCA 59.570 50.000 3.02 0.00 0.00 3.86
2878 2902 2.692557 TCTGCTGCAATCTACTCTCTCC 59.307 50.000 3.02 0.00 0.00 3.71
2879 2903 4.142182 ACTTCTGCTGCAATCTACTCTCTC 60.142 45.833 3.02 0.00 0.00 3.20
2880 2904 3.768757 ACTTCTGCTGCAATCTACTCTCT 59.231 43.478 3.02 0.00 0.00 3.10
2881 2905 4.122143 ACTTCTGCTGCAATCTACTCTC 57.878 45.455 3.02 0.00 0.00 3.20
2882 2906 4.550076 AACTTCTGCTGCAATCTACTCT 57.450 40.909 3.02 0.00 0.00 3.24
2883 2907 5.062809 GTGTAACTTCTGCTGCAATCTACTC 59.937 44.000 3.02 0.00 0.00 2.59
2884 2908 4.932200 GTGTAACTTCTGCTGCAATCTACT 59.068 41.667 3.02 0.00 0.00 2.57
2885 2909 4.201628 CGTGTAACTTCTGCTGCAATCTAC 60.202 45.833 3.02 2.42 31.75 2.59
2886 2910 3.926527 CGTGTAACTTCTGCTGCAATCTA 59.073 43.478 3.02 0.00 31.75 1.98
2887 2911 2.738846 CGTGTAACTTCTGCTGCAATCT 59.261 45.455 3.02 0.00 31.75 2.40
2888 2912 2.736721 TCGTGTAACTTCTGCTGCAATC 59.263 45.455 3.02 0.00 31.75 2.67
2889 2913 2.766313 TCGTGTAACTTCTGCTGCAAT 58.234 42.857 3.02 0.00 31.75 3.56
2890 2914 2.232756 TCGTGTAACTTCTGCTGCAA 57.767 45.000 3.02 0.00 31.75 4.08
2945 2969 2.637872 TCATTCCAGACTTTCTTCCCGT 59.362 45.455 0.00 0.00 0.00 5.28
2979 3003 2.456119 CCGCTGACGATGACAAGCC 61.456 63.158 0.00 0.00 43.93 4.35
2983 3007 0.948623 CAAACCCGCTGACGATGACA 60.949 55.000 0.00 0.00 43.93 3.58
2990 3014 1.067846 GGGAAAATCAAACCCGCTGAC 60.068 52.381 0.00 0.00 34.03 3.51
2995 3019 1.405391 GCATGGGGAAAATCAAACCCG 60.405 52.381 0.00 0.00 46.38 5.28
2998 3022 1.358877 GCGCATGGGGAAAATCAAAC 58.641 50.000 12.19 0.00 0.00 2.93
3030 3058 1.337817 CGCAGTCTGAACGAGAACCG 61.338 60.000 3.32 0.00 45.44 4.44
3032 3060 1.618640 GGCGCAGTCTGAACGAGAAC 61.619 60.000 10.83 0.00 30.26 3.01
3055 3083 2.211468 AAAGGGAGGATGAACGGGGC 62.211 60.000 0.00 0.00 0.00 5.80
3059 3087 1.679032 GGGTGAAAGGGAGGATGAACG 60.679 57.143 0.00 0.00 0.00 3.95
3061 3089 1.354368 GTGGGTGAAAGGGAGGATGAA 59.646 52.381 0.00 0.00 0.00 2.57
3062 3090 0.991920 GTGGGTGAAAGGGAGGATGA 59.008 55.000 0.00 0.00 0.00 2.92
3064 3092 1.214992 GGGTGGGTGAAAGGGAGGAT 61.215 60.000 0.00 0.00 0.00 3.24
3083 3120 0.594110 GTAGAATCGAGCGGGAGAGG 59.406 60.000 0.00 0.00 0.00 3.69
3096 3133 0.108329 CAACGCGGACCCAGTAGAAT 60.108 55.000 12.47 0.00 0.00 2.40
3131 3168 2.265904 TAGACGCAGCGTGACACCT 61.266 57.895 28.57 18.04 41.37 4.00
3136 3173 0.031585 ACAAAGTAGACGCAGCGTGA 59.968 50.000 28.57 10.47 41.37 4.35
3141 3178 3.120199 CCATCCAAACAAAGTAGACGCAG 60.120 47.826 0.00 0.00 0.00 5.18
3151 3188 2.299582 CCACTGCATCCATCCAAACAAA 59.700 45.455 0.00 0.00 0.00 2.83
3152 3189 1.894466 CCACTGCATCCATCCAAACAA 59.106 47.619 0.00 0.00 0.00 2.83
3153 3190 1.548081 CCACTGCATCCATCCAAACA 58.452 50.000 0.00 0.00 0.00 2.83
3154 3191 0.174162 GCCACTGCATCCATCCAAAC 59.826 55.000 0.00 0.00 37.47 2.93
3159 3196 2.324014 TACCCGCCACTGCATCCATC 62.324 60.000 0.00 0.00 37.32 3.51
3160 3197 2.329539 CTACCCGCCACTGCATCCAT 62.330 60.000 0.00 0.00 37.32 3.41
3161 3198 3.006133 TACCCGCCACTGCATCCA 61.006 61.111 0.00 0.00 37.32 3.41
3173 3210 1.373590 CGCCAAATCCAACCTACCCG 61.374 60.000 0.00 0.00 0.00 5.28
3178 3215 0.251341 AAGCTCGCCAAATCCAACCT 60.251 50.000 0.00 0.00 0.00 3.50
3192 3234 1.002011 GAGGGGTGGGTGAAAGCTC 60.002 63.158 0.00 0.00 0.00 4.09
3198 3240 1.388531 GAGAGAGAGGGGTGGGTGA 59.611 63.158 0.00 0.00 0.00 4.02
3199 3241 1.687493 GGAGAGAGAGGGGTGGGTG 60.687 68.421 0.00 0.00 0.00 4.61
3200 3242 2.781406 GGAGAGAGAGGGGTGGGT 59.219 66.667 0.00 0.00 0.00 4.51
3201 3243 2.443016 CGGAGAGAGAGGGGTGGG 60.443 72.222 0.00 0.00 0.00 4.61
3203 3245 2.443016 CCCGGAGAGAGAGGGGTG 60.443 72.222 0.73 0.00 41.43 4.61
3223 3268 1.875364 GGCCTAGACGTTAACGCGG 60.875 63.158 27.07 21.12 44.43 6.46
3224 3269 1.153978 TGGCCTAGACGTTAACGCG 60.154 57.895 27.07 3.53 44.43 6.01
3267 3312 1.271656 GTACTAGTCTGTTGCCGTGGT 59.728 52.381 0.00 0.00 0.00 4.16
3277 3322 3.181512 GGTCTTTCCGACGTACTAGTCTG 60.182 52.174 0.00 0.00 43.79 3.51
3283 3328 1.271656 CTTGGGTCTTTCCGACGTACT 59.728 52.381 0.00 0.00 43.79 2.73
3284 3329 1.000171 ACTTGGGTCTTTCCGACGTAC 60.000 52.381 0.00 0.00 43.79 3.67
3285 3330 1.000060 CACTTGGGTCTTTCCGACGTA 60.000 52.381 0.00 0.00 43.79 3.57
3286 3331 0.249741 CACTTGGGTCTTTCCGACGT 60.250 55.000 0.00 0.00 43.79 4.34
3287 3332 2.528797 CACTTGGGTCTTTCCGACG 58.471 57.895 0.00 0.00 43.79 5.12


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

AutoCloner maintained by Alex Coulton.