Multiple sequence alignment - TraesCS5A01G332000

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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 TraesCS5A01G332000 chr5A 100.000 2210 0 0 987 3196 540594903 540592694 0.000000e+00 4082.0
1 TraesCS5A01G332000 chr5A 100.000 565 0 0 1 565 540595889 540595325 0.000000e+00 1044.0
2 TraesCS5A01G332000 chr5A 84.091 88 12 1 2646 2733 617128295 617128210 2.040000e-12 84.2
3 TraesCS5A01G332000 chr5B 88.473 1631 82 48 990 2584 516464513 516462953 0.000000e+00 1873.0
4 TraesCS5A01G332000 chr5B 87.175 538 31 19 8 542 516465190 516464688 7.690000e-161 577.0
5 TraesCS5A01G332000 chr5B 86.869 297 23 10 2735 3016 516462883 516462588 5.140000e-83 318.0
6 TraesCS5A01G332000 chr5B 92.708 96 5 2 3100 3194 229512129 229512223 1.550000e-28 137.0
7 TraesCS5A01G332000 chr5B 89.041 73 8 0 2573 2645 289565430 289565502 1.220000e-14 91.6
8 TraesCS5A01G332000 chr5D 87.452 1570 88 50 987 2497 426458184 426456665 0.000000e+00 1707.0
9 TraesCS5A01G332000 chr5D 84.843 574 44 24 4 565 426458868 426458326 3.630000e-149 538.0
10 TraesCS5A01G332000 chr5D 85.816 282 20 11 2735 3010 426456608 426456341 6.750000e-72 281.0
11 TraesCS5A01G332000 chr5D 84.694 98 13 1 2625 2720 388039466 388039369 2.620000e-16 97.1
12 TraesCS5A01G332000 chr5D 89.189 74 6 2 2573 2645 381777156 381777228 1.220000e-14 91.6
13 TraesCS5A01G332000 chr5D 87.671 73 9 0 2573 2645 42040505 42040577 5.680000e-13 86.1
14 TraesCS5A01G332000 chr5D 85.714 77 10 1 2652 2728 503136634 503136559 2.640000e-11 80.5
15 TraesCS5A01G332000 chr4A 95.699 93 2 2 3103 3194 297079900 297079991 7.140000e-32 148.0
16 TraesCS5A01G332000 chr4A 97.143 35 1 0 3051 3085 3108761 3108727 3.440000e-05 60.2
17 TraesCS5A01G332000 chr2D 94.624 93 3 2 3103 3194 411533474 411533383 3.320000e-30 143.0
18 TraesCS5A01G332000 chr2D 91.667 72 6 0 2572 2643 495786049 495785978 2.030000e-17 100.0
19 TraesCS5A01G332000 chr2D 92.647 68 5 0 2576 2643 628898544 628898477 7.300000e-17 99.0
20 TraesCS5A01G332000 chr2D 89.041 73 8 0 2573 2645 93661784 93661712 1.220000e-14 91.6
21 TraesCS5A01G332000 chr2A 94.624 93 3 2 3103 3194 154095672 154095763 3.320000e-30 143.0
22 TraesCS5A01G332000 chr2A 90.278 72 6 1 2573 2643 4144019 4144090 3.390000e-15 93.5
23 TraesCS5A01G332000 chr1B 93.750 96 4 2 3100 3194 326870198 326870292 3.320000e-30 143.0
24 TraesCS5A01G332000 chr4D 93.548 93 4 2 3103 3194 29232635 29232544 1.550000e-28 137.0
25 TraesCS5A01G332000 chr3B 92.708 96 5 2 3100 3194 656760905 656760999 1.550000e-28 137.0
26 TraesCS5A01G332000 chr3A 92.784 97 4 3 3099 3194 482445327 482445421 1.550000e-28 137.0
27 TraesCS5A01G332000 chr2B 93.548 93 4 2 3103 3194 89354130 89354221 1.550000e-28 137.0
28 TraesCS5A01G332000 chr2B 87.500 72 9 0 2646 2717 248148893 248148822 2.040000e-12 84.2
29 TraesCS5A01G332000 chr2B 94.737 38 1 1 3051 3088 556701592 556701628 1.240000e-04 58.4
30 TraesCS5A01G332000 chr6D 92.958 71 5 0 2573 2643 455718016 455718086 1.570000e-18 104.0
31 TraesCS5A01G332000 chr6D 94.231 52 3 0 3034 3085 117346623 117346572 2.640000e-11 80.5
32 TraesCS5A01G332000 chr6B 88.732 71 8 0 2573 2643 155979901 155979971 1.580000e-13 87.9
33 TraesCS5A01G332000 chr6B 88.571 70 8 0 2648 2717 560706108 560706177 5.680000e-13 86.1
34 TraesCS5A01G332000 chr6B 88.571 70 8 0 2648 2717 560745559 560745628 5.680000e-13 86.1
35 TraesCS5A01G332000 chr7D 86.842 76 10 0 2648 2723 350100552 350100477 5.680000e-13 86.1
36 TraesCS5A01G332000 chr7D 84.810 79 12 0 2646 2724 25009498 25009576 2.640000e-11 80.5
37 TraesCS5A01G332000 chr1A 85.897 78 11 0 2646 2723 522970077 522970000 2.040000e-12 84.2
38 TraesCS5A01G332000 chr1A 97.143 35 1 0 3051 3085 98606944 98606910 3.440000e-05 60.2
39 TraesCS5A01G332000 chr1A 94.595 37 2 0 1464 1500 466897345 466897381 1.240000e-04 58.4
40 TraesCS5A01G332000 chrUn 97.143 35 1 0 3051 3085 28403086 28403120 3.440000e-05 60.2
41 TraesCS5A01G332000 chr6A 97.143 35 1 0 3051 3085 101719996 101720030 3.440000e-05 60.2
42 TraesCS5A01G332000 chr4B 94.872 39 1 1 3051 3089 672964428 672964465 3.440000e-05 60.2
43 TraesCS5A01G332000 chr3D 97.143 35 1 0 3051 3085 39615893 39615927 3.440000e-05 60.2
44 TraesCS5A01G332000 chr7B 94.737 38 1 1 3051 3088 312383929 312383965 1.240000e-04 58.4


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 TraesCS5A01G332000 chr5A 540592694 540595889 3195 True 2563.000000 4082 100.000000 1 3196 2 chr5A.!!$R2 3195
1 TraesCS5A01G332000 chr5B 516462588 516465190 2602 True 922.666667 1873 87.505667 8 3016 3 chr5B.!!$R1 3008
2 TraesCS5A01G332000 chr5D 426456341 426458868 2527 True 842.000000 1707 86.037000 4 3010 3 chr5D.!!$R3 3006

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
41 42 0.967662 TGTCACGAATAACCCACGGA 59.032 50.0 0.0 0.0 0.0 4.69 F
1786 1830 0.107459 GCGCCCTTCTGATCCTTCTT 60.107 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 1843 1.760268 CTGCTTGCTTCGATCTCGGC 61.76 60.0 0.0 0.0 40.29 5.54 R
3030 3145 0.100325 CTCTGCTGTGGCTAGTCTCG 59.90 60.0 0.0 0.0 39.59 4.04 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 4.090066 CACGATCCGTTTACAGAAGAAGTG 59.910 45.833 0.00 0.00 38.32 3.16
26 27 4.659111 TCCGTTTACAGAAGAAGTGTCA 57.341 40.909 0.00 0.00 0.00 3.58
41 42 0.967662 TGTCACGAATAACCCACGGA 59.032 50.000 0.00 0.00 0.00 4.69
54 55 1.156736 CCACGGAAGCAAACCTACAG 58.843 55.000 0.00 0.00 0.00 2.74
55 56 1.156736 CACGGAAGCAAACCTACAGG 58.843 55.000 0.00 0.00 42.17 4.00
210 219 3.276091 TTTGACCAGTGCCACGCG 61.276 61.111 3.53 3.53 0.00 6.01
236 245 4.320456 CACACACCGGGCAGAGCT 62.320 66.667 6.32 0.00 0.00 4.09
453 470 4.056125 CCACGGAGCGAGCAGTGA 62.056 66.667 15.80 0.00 36.79 3.41
454 471 2.505777 CACGGAGCGAGCAGTGAG 60.506 66.667 11.01 0.00 36.79 3.51
457 474 4.828925 GGAGCGAGCAGTGAGGGC 62.829 72.222 0.00 0.00 0.00 5.19
462 479 4.767255 GAGCAGTGAGGGCGGGTG 62.767 72.222 0.00 0.00 36.08 4.61
516 533 2.513204 CCAGGCACCAGCTCGATG 60.513 66.667 0.00 0.00 41.70 3.84
538 555 1.153862 CTCTCGCTGTCTGGTGAGC 60.154 63.158 0.00 0.00 41.85 4.26
1015 1032 3.485431 CACGAGCGAGCCAAGCTG 61.485 66.667 2.79 0.00 46.13 4.24
1031 1048 4.262207 CCAAGCTGAGATACATACGGACAT 60.262 45.833 0.00 0.00 0.00 3.06
1033 1050 4.145052 AGCTGAGATACATACGGACATCA 58.855 43.478 0.00 0.00 0.00 3.07
1316 1343 1.341581 CCGACCTCCTTCTTCTCCTCT 60.342 57.143 0.00 0.00 0.00 3.69
1660 1704 0.835276 ATTCCTGGCCGTACCTAACC 59.165 55.000 0.00 0.00 40.22 2.85
1748 1792 2.432628 GTGCCGGTGAGGAAGACG 60.433 66.667 1.90 0.00 45.00 4.18
1785 1829 1.524482 GCGCCCTTCTGATCCTTCT 59.476 57.895 0.00 0.00 0.00 2.85
1786 1830 0.107459 GCGCCCTTCTGATCCTTCTT 60.107 55.000 0.00 0.00 0.00 2.52
1787 1831 1.946745 CGCCCTTCTGATCCTTCTTC 58.053 55.000 0.00 0.00 0.00 2.87
1790 1834 2.240921 GCCCTTCTGATCCTTCTTCCTT 59.759 50.000 0.00 0.00 0.00 3.36
1792 1836 3.118075 CCCTTCTGATCCTTCTTCCTTCC 60.118 52.174 0.00 0.00 0.00 3.46
1799 1843 1.627297 CCTTCTTCCTTCCCGAGGGG 61.627 65.000 8.53 0.00 46.31 4.79
1800 1844 2.258748 CTTCTTCCTTCCCGAGGGGC 62.259 65.000 8.53 0.00 46.31 5.80
1810 1854 3.217017 CGAGGGGCCGAGATCGAA 61.217 66.667 12.03 0.00 43.02 3.71
1813 1857 3.849951 GGGGCCGAGATCGAAGCA 61.850 66.667 3.31 0.00 43.02 3.91
1814 1858 2.186903 GGGCCGAGATCGAAGCAA 59.813 61.111 3.31 0.00 43.02 3.91
1900 1944 8.844244 GCTAGCACTTACTAGTAACTATTACCA 58.156 37.037 10.63 0.00 41.49 3.25
1904 1948 8.844244 GCACTTACTAGTAACTATTACCAGCTA 58.156 37.037 11.38 0.00 36.81 3.32
1913 1969 6.874288 AACTATTACCAGCTACTACTACGG 57.126 41.667 0.00 0.00 0.00 4.02
1964 2020 6.910191 TCCATATGGATGTTATTGTGTTCCT 58.090 36.000 20.98 0.00 39.78 3.36
1966 2022 6.207417 CCATATGGATGTTATTGTGTTCCTCC 59.793 42.308 17.49 0.00 37.39 4.30
2028 2086 5.437060 TCTTTTTGGTCACTCAGCTAAACT 58.563 37.500 0.00 0.00 28.71 2.66
2045 2103 2.511373 TAGAGGTGGCAATGCGCG 60.511 61.111 0.00 0.00 43.84 6.86
2063 2121 1.276705 GCGAGGAAAGGGAAGAAGACT 59.723 52.381 0.00 0.00 0.00 3.24
2121 2187 8.504409 ACCAGTAGTAGAACTCCTAGTAATCAT 58.496 37.037 0.00 0.00 35.61 2.45
2226 2292 9.683870 ACTTACTGTTAGTTCTAGTGCTAGTAT 57.316 33.333 6.18 0.00 34.84 2.12
2403 2486 1.515521 CTTCGGGTGACAAGTTGCCC 61.516 60.000 1.81 4.87 37.79 5.36
2454 2537 2.730672 CGCTCTGTTTTCTCCGCCG 61.731 63.158 0.00 0.00 0.00 6.46
2455 2538 2.391389 GCTCTGTTTTCTCCGCCGG 61.391 63.158 0.00 0.00 0.00 6.13
2456 2539 2.358247 TCTGTTTTCTCCGCCGGC 60.358 61.111 19.07 19.07 0.00 6.13
2457 2540 3.431725 CTGTTTTCTCCGCCGGCC 61.432 66.667 23.46 4.19 0.00 6.13
2535 2624 6.356186 TCCCCTCTTCTTTTTAGTAGACAC 57.644 41.667 0.00 0.00 0.00 3.67
2538 2627 7.676893 TCCCCTCTTCTTTTTAGTAGACACATA 59.323 37.037 0.00 0.00 0.00 2.29
2553 2642 9.332502 AGTAGACACATAGACATTGTAGAGTAG 57.667 37.037 0.00 0.00 0.00 2.57
2576 2665 9.392021 GTAGTAGTACAAAGTTGACACTTACTC 57.608 37.037 2.52 0.00 42.89 2.59
2581 2670 4.409247 ACAAAGTTGACACTTACTCCCTCT 59.591 41.667 0.00 0.00 42.89 3.69
2584 2673 3.574826 AGTTGACACTTACTCCCTCTGTC 59.425 47.826 0.00 0.00 33.30 3.51
2585 2674 3.527507 TGACACTTACTCCCTCTGTCT 57.472 47.619 0.00 0.00 33.75 3.41
2586 2675 3.422796 TGACACTTACTCCCTCTGTCTC 58.577 50.000 0.00 0.00 33.75 3.36
2587 2676 3.181433 TGACACTTACTCCCTCTGTCTCA 60.181 47.826 0.00 0.00 33.75 3.27
2588 2677 4.020543 GACACTTACTCCCTCTGTCTCAT 58.979 47.826 0.00 0.00 0.00 2.90
2589 2678 5.194432 GACACTTACTCCCTCTGTCTCATA 58.806 45.833 0.00 0.00 0.00 2.15
2590 2679 5.580998 ACACTTACTCCCTCTGTCTCATAA 58.419 41.667 0.00 0.00 0.00 1.90
2591 2680 6.198639 ACACTTACTCCCTCTGTCTCATAAT 58.801 40.000 0.00 0.00 0.00 1.28
2592 2681 7.355101 ACACTTACTCCCTCTGTCTCATAATA 58.645 38.462 0.00 0.00 0.00 0.98
2593 2682 8.007742 ACACTTACTCCCTCTGTCTCATAATAT 58.992 37.037 0.00 0.00 0.00 1.28
2594 2683 9.521841 CACTTACTCCCTCTGTCTCATAATATA 57.478 37.037 0.00 0.00 0.00 0.86
2595 2684 9.523168 ACTTACTCCCTCTGTCTCATAATATAC 57.477 37.037 0.00 0.00 0.00 1.47
2596 2685 8.563123 TTACTCCCTCTGTCTCATAATATACG 57.437 38.462 0.00 0.00 0.00 3.06
2597 2686 6.780901 ACTCCCTCTGTCTCATAATATACGA 58.219 40.000 0.00 0.00 0.00 3.43
2598 2687 6.882140 ACTCCCTCTGTCTCATAATATACGAG 59.118 42.308 0.00 0.00 0.00 4.18
2599 2688 5.648526 TCCCTCTGTCTCATAATATACGAGC 59.351 44.000 0.00 0.00 0.00 5.03
2600 2689 5.447954 CCCTCTGTCTCATAATATACGAGCG 60.448 48.000 0.00 0.00 0.00 5.03
2601 2690 5.122554 CCTCTGTCTCATAATATACGAGCGT 59.877 44.000 0.00 0.00 0.00 5.07
2602 2691 6.348622 CCTCTGTCTCATAATATACGAGCGTT 60.349 42.308 0.00 0.00 0.00 4.84
2603 2692 6.967135 TCTGTCTCATAATATACGAGCGTTT 58.033 36.000 0.00 0.00 0.00 3.60
2604 2693 7.076362 TCTGTCTCATAATATACGAGCGTTTC 58.924 38.462 0.00 0.00 0.00 2.78
2605 2694 6.967135 TGTCTCATAATATACGAGCGTTTCT 58.033 36.000 0.00 0.00 0.00 2.52
2606 2695 6.856426 TGTCTCATAATATACGAGCGTTTCTG 59.144 38.462 0.00 0.00 0.00 3.02
2607 2696 7.076362 GTCTCATAATATACGAGCGTTTCTGA 58.924 38.462 0.00 0.00 0.00 3.27
2608 2697 7.059716 GTCTCATAATATACGAGCGTTTCTGAC 59.940 40.741 0.00 0.00 0.00 3.51
2609 2698 6.731164 TCATAATATACGAGCGTTTCTGACA 58.269 36.000 0.00 0.00 0.00 3.58
2610 2699 7.368059 TCATAATATACGAGCGTTTCTGACAT 58.632 34.615 0.00 0.00 0.00 3.06
2611 2700 7.865889 TCATAATATACGAGCGTTTCTGACATT 59.134 33.333 0.00 0.00 0.00 2.71
2612 2701 9.124807 CATAATATACGAGCGTTTCTGACATTA 57.875 33.333 0.00 0.00 0.00 1.90
2613 2702 6.988109 ATATACGAGCGTTTCTGACATTAC 57.012 37.500 0.00 0.00 0.00 1.89
2614 2703 3.299340 ACGAGCGTTTCTGACATTACT 57.701 42.857 0.00 0.00 0.00 2.24
2615 2704 4.430137 ACGAGCGTTTCTGACATTACTA 57.570 40.909 0.00 0.00 0.00 1.82
2616 2705 4.995124 ACGAGCGTTTCTGACATTACTAT 58.005 39.130 0.00 0.00 0.00 2.12
2617 2706 6.127810 ACGAGCGTTTCTGACATTACTATA 57.872 37.500 0.00 0.00 0.00 1.31
2618 2707 6.200100 ACGAGCGTTTCTGACATTACTATAG 58.800 40.000 0.00 0.00 0.00 1.31
2619 2708 6.183360 ACGAGCGTTTCTGACATTACTATAGT 60.183 38.462 10.87 10.87 0.00 2.12
2620 2709 6.140895 CGAGCGTTTCTGACATTACTATAGTG 59.859 42.308 15.90 1.43 0.00 2.74
2621 2710 6.864342 AGCGTTTCTGACATTACTATAGTGT 58.136 36.000 15.90 4.91 0.00 3.55
2622 2711 7.993101 AGCGTTTCTGACATTACTATAGTGTA 58.007 34.615 15.90 3.92 0.00 2.90
2623 2712 8.464404 AGCGTTTCTGACATTACTATAGTGTAA 58.536 33.333 15.90 3.05 36.92 2.41
2624 2713 9.079833 GCGTTTCTGACATTACTATAGTGTAAA 57.920 33.333 15.90 2.29 36.22 2.01
2650 2739 9.601217 AAAACGTTCTTATATTATGAGCTGTCT 57.399 29.630 0.00 0.00 0.00 3.41
2651 2740 8.804688 AACGTTCTTATATTATGAGCTGTCTC 57.195 34.615 0.00 0.00 39.78 3.36
2666 2755 4.456222 AGCTGTCTCATAATATACGAGCGT 59.544 41.667 0.00 0.00 0.00 5.07
2667 2756 5.048643 AGCTGTCTCATAATATACGAGCGTT 60.049 40.000 0.00 0.00 0.00 4.84
2668 2757 5.629849 GCTGTCTCATAATATACGAGCGTTT 59.370 40.000 0.00 0.00 0.00 3.60
2672 2761 7.076362 GTCTCATAATATACGAGCGTTTCTGA 58.924 38.462 0.00 0.00 0.00 3.27
2674 2763 8.943002 TCTCATAATATACGAGCGTTTCTGATA 58.057 33.333 0.00 0.00 0.00 2.15
2683 2772 7.624706 ACGAGCGTTTCTGATATTATTGTAG 57.375 36.000 0.00 0.00 0.00 2.74
2685 2774 8.347771 ACGAGCGTTTCTGATATTATTGTAGTA 58.652 33.333 0.00 0.00 0.00 1.82
2686 2775 9.343103 CGAGCGTTTCTGATATTATTGTAGTAT 57.657 33.333 0.00 0.00 0.00 2.12
2717 2806 6.183360 ACGTTTTTATATTATGGGACGGAGGA 60.183 38.462 0.00 0.00 33.95 3.71
2720 2809 7.621006 TTTTATATTATGGGACGGAGGAAGA 57.379 36.000 0.00 0.00 0.00 2.87
2733 2822 7.499895 GGGACGGAGGAAGAAGAGTATATATAG 59.500 44.444 0.00 0.00 0.00 1.31
2776 2877 1.008194 CACGTCGGTGTCGGAAAGA 60.008 57.895 0.00 0.00 39.38 2.52
2862 2966 0.538746 TCCCTTTGGCCTTTCCGTTC 60.539 55.000 3.32 0.00 37.80 3.95
2872 2976 6.052405 TGGCCTTTCCGTTCTACTAATAAA 57.948 37.500 3.32 0.00 37.80 1.40
2874 2978 7.114095 TGGCCTTTCCGTTCTACTAATAAATT 58.886 34.615 3.32 0.00 37.80 1.82
2875 2979 8.266473 TGGCCTTTCCGTTCTACTAATAAATTA 58.734 33.333 3.32 0.00 37.80 1.40
2876 2980 8.771766 GGCCTTTCCGTTCTACTAATAAATTAG 58.228 37.037 7.96 7.96 44.07 1.73
2905 3009 4.551388 TGAAAACACGAAACAAAACTGCT 58.449 34.783 0.00 0.00 0.00 4.24
2922 3026 2.046023 TGAGTCCAGCAATGGCCG 60.046 61.111 0.00 0.00 42.56 6.13
2938 3050 2.176546 CGCGCCCATTGTCTGTTG 59.823 61.111 0.00 0.00 0.00 3.33
2958 3070 6.591935 TGTTGACAAGAGAAAAGTCAGGTAT 58.408 36.000 0.00 0.00 42.54 2.73
2960 3072 7.226720 TGTTGACAAGAGAAAAGTCAGGTATTC 59.773 37.037 0.00 0.00 42.54 1.75
2969 3081 3.322191 AGTCAGGTATTCCTCCTCCTC 57.678 52.381 0.00 0.00 43.07 3.71
2996 3111 0.179043 TTGCTTAGACCACGCCACAA 60.179 50.000 0.00 0.00 0.00 3.33
3046 3161 2.573869 GCGAGACTAGCCACAGCA 59.426 61.111 0.00 0.00 43.56 4.41
3047 3162 1.518133 GCGAGACTAGCCACAGCAG 60.518 63.158 0.00 0.00 43.56 4.24
3048 3163 1.938657 GCGAGACTAGCCACAGCAGA 61.939 60.000 0.00 0.00 43.56 4.26
3049 3164 0.100325 CGAGACTAGCCACAGCAGAG 59.900 60.000 0.00 0.00 43.56 3.35
3050 3165 1.468985 GAGACTAGCCACAGCAGAGA 58.531 55.000 0.00 0.00 43.56 3.10
3051 3166 1.405105 GAGACTAGCCACAGCAGAGAG 59.595 57.143 0.00 0.00 43.56 3.20
3052 3167 1.181786 GACTAGCCACAGCAGAGAGT 58.818 55.000 0.00 0.00 43.56 3.24
3053 3168 2.025793 AGACTAGCCACAGCAGAGAGTA 60.026 50.000 0.00 0.00 43.56 2.59
3054 3169 2.755655 GACTAGCCACAGCAGAGAGTAA 59.244 50.000 0.00 0.00 43.56 2.24
3055 3170 3.370104 ACTAGCCACAGCAGAGAGTAAT 58.630 45.455 0.00 0.00 43.56 1.89
3056 3171 4.537751 ACTAGCCACAGCAGAGAGTAATA 58.462 43.478 0.00 0.00 43.56 0.98
3057 3172 5.144100 ACTAGCCACAGCAGAGAGTAATAT 58.856 41.667 0.00 0.00 43.56 1.28
3058 3173 6.307776 ACTAGCCACAGCAGAGAGTAATATA 58.692 40.000 0.00 0.00 43.56 0.86
3059 3174 5.461032 AGCCACAGCAGAGAGTAATATAC 57.539 43.478 0.00 0.00 43.56 1.47
3060 3175 4.895889 AGCCACAGCAGAGAGTAATATACA 59.104 41.667 0.00 0.00 43.56 2.29
3061 3176 4.985409 GCCACAGCAGAGAGTAATATACAC 59.015 45.833 0.00 0.00 39.53 2.90
3062 3177 5.451937 GCCACAGCAGAGAGTAATATACACA 60.452 44.000 0.00 0.00 39.53 3.72
3063 3178 6.739843 GCCACAGCAGAGAGTAATATACACAT 60.740 42.308 0.00 0.00 39.53 3.21
3064 3179 7.523873 GCCACAGCAGAGAGTAATATACACATA 60.524 40.741 0.00 0.00 39.53 2.29
3065 3180 8.526978 CCACAGCAGAGAGTAATATACACATAT 58.473 37.037 0.00 0.00 0.00 1.78
3066 3181 9.920133 CACAGCAGAGAGTAATATACACATATT 57.080 33.333 0.00 0.00 39.95 1.28
3068 3183 9.579768 CAGCAGAGAGTAATATACACATATTCC 57.420 37.037 0.00 0.00 38.17 3.01
3069 3184 9.540538 AGCAGAGAGTAATATACACATATTCCT 57.459 33.333 0.00 0.00 38.17 3.36
3096 3211 8.697292 AGACTATGTTATTACTCTCTTTGGTCC 58.303 37.037 0.00 0.00 0.00 4.46
3097 3212 8.611051 ACTATGTTATTACTCTCTTTGGTCCT 57.389 34.615 0.00 0.00 0.00 3.85
3098 3213 9.047947 ACTATGTTATTACTCTCTTTGGTCCTT 57.952 33.333 0.00 0.00 0.00 3.36
3099 3214 9.892130 CTATGTTATTACTCTCTTTGGTCCTTT 57.108 33.333 0.00 0.00 0.00 3.11
3101 3216 8.990163 TGTTATTACTCTCTTTGGTCCTTTTT 57.010 30.769 0.00 0.00 0.00 1.94
3104 3219 9.734984 TTATTACTCTCTTTGGTCCTTTTTAGG 57.265 33.333 0.00 0.00 0.00 2.69
3105 3220 4.986783 ACTCTCTTTGGTCCTTTTTAGGG 58.013 43.478 0.00 0.00 0.00 3.53
3106 3221 4.202577 ACTCTCTTTGGTCCTTTTTAGGGG 60.203 45.833 0.00 0.00 0.00 4.79
3107 3222 3.725267 TCTCTTTGGTCCTTTTTAGGGGT 59.275 43.478 0.00 0.00 0.00 4.95
3108 3223 4.169264 TCTCTTTGGTCCTTTTTAGGGGTT 59.831 41.667 0.00 0.00 0.00 4.11
3109 3224 4.219919 TCTTTGGTCCTTTTTAGGGGTTG 58.780 43.478 0.00 0.00 0.00 3.77
3110 3225 3.691698 TTGGTCCTTTTTAGGGGTTGT 57.308 42.857 0.00 0.00 0.00 3.32
3111 3226 3.691698 TGGTCCTTTTTAGGGGTTGTT 57.308 42.857 0.00 0.00 0.00 2.83
3112 3227 3.996957 TGGTCCTTTTTAGGGGTTGTTT 58.003 40.909 0.00 0.00 0.00 2.83
3113 3228 3.707102 TGGTCCTTTTTAGGGGTTGTTTG 59.293 43.478 0.00 0.00 0.00 2.93
3114 3229 3.070446 GGTCCTTTTTAGGGGTTGTTTGG 59.930 47.826 0.00 0.00 0.00 3.28
3115 3230 3.707611 GTCCTTTTTAGGGGTTGTTTGGT 59.292 43.478 0.00 0.00 0.00 3.67
3116 3231 4.162698 GTCCTTTTTAGGGGTTGTTTGGTT 59.837 41.667 0.00 0.00 0.00 3.67
3117 3232 4.406326 TCCTTTTTAGGGGTTGTTTGGTTC 59.594 41.667 0.00 0.00 0.00 3.62
3118 3233 4.407621 CCTTTTTAGGGGTTGTTTGGTTCT 59.592 41.667 0.00 0.00 0.00 3.01
3119 3234 5.599242 CCTTTTTAGGGGTTGTTTGGTTCTA 59.401 40.000 0.00 0.00 0.00 2.10
3120 3235 6.239204 CCTTTTTAGGGGTTGTTTGGTTCTAG 60.239 42.308 0.00 0.00 0.00 2.43
3121 3236 2.971901 AGGGGTTGTTTGGTTCTAGG 57.028 50.000 0.00 0.00 0.00 3.02
3122 3237 2.424793 AGGGGTTGTTTGGTTCTAGGA 58.575 47.619 0.00 0.00 0.00 2.94
3123 3238 2.107726 AGGGGTTGTTTGGTTCTAGGAC 59.892 50.000 0.00 0.00 0.00 3.85
3124 3239 2.107726 GGGGTTGTTTGGTTCTAGGACT 59.892 50.000 0.01 0.00 0.00 3.85
3125 3240 3.328637 GGGGTTGTTTGGTTCTAGGACTA 59.671 47.826 0.01 0.00 0.00 2.59
3126 3241 4.565028 GGGGTTGTTTGGTTCTAGGACTAG 60.565 50.000 0.01 0.00 34.56 2.57
3127 3242 4.001652 GGTTGTTTGGTTCTAGGACTAGC 58.998 47.826 0.01 0.00 33.32 3.42
3128 3243 4.504340 GGTTGTTTGGTTCTAGGACTAGCA 60.504 45.833 0.01 0.00 33.32 3.49
3129 3244 5.246307 GTTGTTTGGTTCTAGGACTAGCAT 58.754 41.667 0.01 0.00 33.32 3.79
3130 3245 5.499004 TGTTTGGTTCTAGGACTAGCATT 57.501 39.130 0.01 0.00 33.32 3.56
3131 3246 5.245531 TGTTTGGTTCTAGGACTAGCATTG 58.754 41.667 0.01 0.00 33.32 2.82
3132 3247 3.543680 TGGTTCTAGGACTAGCATTGC 57.456 47.619 0.01 0.00 33.32 3.56
3133 3248 2.170607 TGGTTCTAGGACTAGCATTGCC 59.829 50.000 4.70 0.00 33.32 4.52
3134 3249 2.170607 GGTTCTAGGACTAGCATTGCCA 59.829 50.000 4.70 0.00 33.32 4.92
3135 3250 3.181450 GGTTCTAGGACTAGCATTGCCAT 60.181 47.826 4.70 0.00 33.32 4.40
3136 3251 4.040461 GGTTCTAGGACTAGCATTGCCATA 59.960 45.833 4.70 0.00 33.32 2.74
3137 3252 4.873746 TCTAGGACTAGCATTGCCATAC 57.126 45.455 4.70 0.00 33.32 2.39
3138 3253 4.483950 TCTAGGACTAGCATTGCCATACT 58.516 43.478 4.70 0.00 33.32 2.12
3139 3254 4.901849 TCTAGGACTAGCATTGCCATACTT 59.098 41.667 4.70 0.00 33.32 2.24
3140 3255 4.510167 AGGACTAGCATTGCCATACTTT 57.490 40.909 4.70 0.00 0.00 2.66
3141 3256 4.202441 AGGACTAGCATTGCCATACTTTG 58.798 43.478 4.70 0.00 0.00 2.77
3142 3257 3.243201 GGACTAGCATTGCCATACTTTGC 60.243 47.826 4.70 0.00 0.00 3.68
3143 3258 2.689983 ACTAGCATTGCCATACTTTGCC 59.310 45.455 4.70 0.00 33.85 4.52
3144 3259 1.559368 AGCATTGCCATACTTTGCCA 58.441 45.000 4.70 0.00 33.85 4.92
3145 3260 1.205417 AGCATTGCCATACTTTGCCAC 59.795 47.619 4.70 0.00 33.85 5.01
3146 3261 1.067000 GCATTGCCATACTTTGCCACA 60.067 47.619 0.00 0.00 0.00 4.17
3147 3262 2.609350 CATTGCCATACTTTGCCACAC 58.391 47.619 0.00 0.00 0.00 3.82
3148 3263 1.697284 TTGCCATACTTTGCCACACA 58.303 45.000 0.00 0.00 0.00 3.72
3149 3264 1.921982 TGCCATACTTTGCCACACAT 58.078 45.000 0.00 0.00 0.00 3.21
3150 3265 2.246469 TGCCATACTTTGCCACACATT 58.754 42.857 0.00 0.00 0.00 2.71
3151 3266 2.632028 TGCCATACTTTGCCACACATTT 59.368 40.909 0.00 0.00 0.00 2.32
3152 3267 3.070734 TGCCATACTTTGCCACACATTTT 59.929 39.130 0.00 0.00 0.00 1.82
3153 3268 4.064388 GCCATACTTTGCCACACATTTTT 58.936 39.130 0.00 0.00 0.00 1.94
3154 3269 4.083908 GCCATACTTTGCCACACATTTTTG 60.084 41.667 0.00 0.00 0.00 2.44
3155 3270 5.055812 CCATACTTTGCCACACATTTTTGT 58.944 37.500 0.00 0.00 0.00 2.83
3156 3271 5.177327 CCATACTTTGCCACACATTTTTGTC 59.823 40.000 0.00 0.00 0.00 3.18
3157 3272 4.199432 ACTTTGCCACACATTTTTGTCA 57.801 36.364 0.00 0.00 0.00 3.58
3158 3273 4.573900 ACTTTGCCACACATTTTTGTCAA 58.426 34.783 0.00 0.00 0.00 3.18
3159 3274 4.630940 ACTTTGCCACACATTTTTGTCAAG 59.369 37.500 0.00 0.00 0.00 3.02
3160 3275 2.548875 TGCCACACATTTTTGTCAAGC 58.451 42.857 0.00 0.00 0.00 4.01
3161 3276 2.168106 TGCCACACATTTTTGTCAAGCT 59.832 40.909 0.00 0.00 0.00 3.74
3162 3277 3.197265 GCCACACATTTTTGTCAAGCTT 58.803 40.909 0.00 0.00 0.00 3.74
3163 3278 3.001533 GCCACACATTTTTGTCAAGCTTG 59.998 43.478 20.81 20.81 0.00 4.01
3164 3279 3.001533 CCACACATTTTTGTCAAGCTTGC 59.998 43.478 21.99 16.43 0.00 4.01
3165 3280 3.001533 CACACATTTTTGTCAAGCTTGCC 59.998 43.478 21.99 11.57 0.00 4.52
3166 3281 3.118665 ACACATTTTTGTCAAGCTTGCCT 60.119 39.130 21.99 0.00 0.00 4.75
3167 3282 4.099266 ACACATTTTTGTCAAGCTTGCCTA 59.901 37.500 21.99 4.29 0.00 3.93
3168 3283 5.049167 CACATTTTTGTCAAGCTTGCCTAA 58.951 37.500 21.99 11.00 0.00 2.69
3169 3284 5.176223 CACATTTTTGTCAAGCTTGCCTAAG 59.824 40.000 21.99 4.89 36.97 2.18
3170 3285 4.320608 TTTTTGTCAAGCTTGCCTAAGG 57.679 40.909 21.99 0.00 34.40 2.69
3171 3286 2.656947 TTGTCAAGCTTGCCTAAGGT 57.343 45.000 21.99 0.00 45.98 3.50
3178 3293 2.973945 AGCTTGCCTAAGGTTAGTTCG 58.026 47.619 0.00 0.00 41.61 3.95
3179 3294 2.565834 AGCTTGCCTAAGGTTAGTTCGA 59.434 45.455 0.00 0.00 41.61 3.71
3180 3295 3.197983 AGCTTGCCTAAGGTTAGTTCGAT 59.802 43.478 0.00 0.00 41.61 3.59
3181 3296 4.404715 AGCTTGCCTAAGGTTAGTTCGATA 59.595 41.667 0.00 0.00 41.61 2.92
3182 3297 5.105064 AGCTTGCCTAAGGTTAGTTCGATAA 60.105 40.000 0.00 0.00 41.61 1.75
3183 3298 5.583457 GCTTGCCTAAGGTTAGTTCGATAAA 59.417 40.000 0.00 0.00 34.40 1.40
3184 3299 6.093082 GCTTGCCTAAGGTTAGTTCGATAAAA 59.907 38.462 0.00 0.00 34.40 1.52
3185 3300 7.201705 GCTTGCCTAAGGTTAGTTCGATAAAAT 60.202 37.037 0.00 0.00 34.40 1.82
3186 3301 7.548196 TGCCTAAGGTTAGTTCGATAAAATG 57.452 36.000 0.00 0.00 0.00 2.32
3187 3302 7.332557 TGCCTAAGGTTAGTTCGATAAAATGA 58.667 34.615 0.00 0.00 0.00 2.57
3188 3303 7.494625 TGCCTAAGGTTAGTTCGATAAAATGAG 59.505 37.037 0.00 0.00 0.00 2.90
3189 3304 7.709613 GCCTAAGGTTAGTTCGATAAAATGAGA 59.290 37.037 0.00 0.00 0.00 3.27
3190 3305 9.250624 CCTAAGGTTAGTTCGATAAAATGAGAG 57.749 37.037 0.00 0.00 0.00 3.20
3191 3306 7.541122 AAGGTTAGTTCGATAAAATGAGAGC 57.459 36.000 0.00 0.00 0.00 4.09
3192 3307 6.049790 AGGTTAGTTCGATAAAATGAGAGCC 58.950 40.000 0.00 0.00 0.00 4.70
3193 3308 5.815740 GGTTAGTTCGATAAAATGAGAGCCA 59.184 40.000 0.00 0.00 0.00 4.75
3194 3309 6.483640 GGTTAGTTCGATAAAATGAGAGCCAT 59.516 38.462 0.00 0.00 36.99 4.40
3195 3310 7.656137 GGTTAGTTCGATAAAATGAGAGCCATA 59.344 37.037 0.00 0.00 34.45 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.090066 CACTTCTTCTGTAAACGGATCGTG 59.910 45.833 0.00 0.00 39.99 4.35
1 2 4.235360 CACTTCTTCTGTAAACGGATCGT 58.765 43.478 0.00 0.00 43.97 3.73
2 3 4.235360 ACACTTCTTCTGTAAACGGATCG 58.765 43.478 0.00 0.00 0.00 3.69
23 24 1.997606 CTTCCGTGGGTTATTCGTGAC 59.002 52.381 0.00 0.00 0.00 3.67
26 27 0.322322 TGCTTCCGTGGGTTATTCGT 59.678 50.000 0.00 0.00 0.00 3.85
54 55 4.264460 AGATCATTTCCAGATCGCTACC 57.736 45.455 0.00 0.00 45.05 3.18
55 56 6.072175 ACTCTAGATCATTTCCAGATCGCTAC 60.072 42.308 0.00 0.00 45.05 3.58
216 225 3.460672 CTCTGCCCGGTGTGTGTGT 62.461 63.158 0.00 0.00 0.00 3.72
220 229 4.320456 CAGCTCTGCCCGGTGTGT 62.320 66.667 0.00 0.00 0.00 3.72
226 235 3.978723 CTGTCGACAGCTCTGCCCG 62.979 68.421 31.00 6.94 37.15 6.13
228 237 2.125753 CCTGTCGACAGCTCTGCC 60.126 66.667 35.09 0.00 42.47 4.85
230 239 2.125753 GCCCTGTCGACAGCTCTG 60.126 66.667 35.09 22.76 42.47 3.35
416 429 4.731612 AGAGACAGCCAGTGCGCG 62.732 66.667 0.00 0.00 44.33 6.86
417 430 3.117171 CAGAGACAGCCAGTGCGC 61.117 66.667 0.00 0.00 44.33 6.09
418 431 2.433838 CCAGAGACAGCCAGTGCG 60.434 66.667 0.00 0.00 44.33 5.34
419 432 2.745492 GCCAGAGACAGCCAGTGC 60.745 66.667 0.00 0.00 37.95 4.40
430 447 4.504916 CTCGCTCCGTGGCCAGAG 62.505 72.222 15.97 15.97 0.00 3.35
1014 1031 3.572682 GGGTGATGTCCGTATGTATCTCA 59.427 47.826 0.00 0.00 0.00 3.27
1015 1032 3.056749 GGGGTGATGTCCGTATGTATCTC 60.057 52.174 0.00 0.00 0.00 2.75
1049 1066 3.486685 ATGGCCATGGCTCGCTCT 61.487 61.111 34.70 11.46 41.60 4.09
1618 1662 3.010767 CGAGAGACGGAGAGAGCG 58.989 66.667 0.00 0.00 38.46 5.03
1660 1704 2.136878 CCATGGAGGAGAGGGACGG 61.137 68.421 5.56 0.00 41.22 4.79
1718 1762 4.699522 GGCACCGACACCTCCACC 62.700 72.222 0.00 0.00 0.00 4.61
1799 1843 1.760268 CTGCTTGCTTCGATCTCGGC 61.760 60.000 0.00 0.00 40.29 5.54
1800 1844 1.760268 GCTGCTTGCTTCGATCTCGG 61.760 60.000 0.00 0.00 38.15 4.63
1827 1871 2.652095 TAGTAGTGGCGGTGGTGGC 61.652 63.158 0.00 0.00 0.00 5.01
1833 1877 2.290514 TGTGAGTAGTAGTAGTGGCGGT 60.291 50.000 0.00 0.00 0.00 5.68
1838 1882 8.145767 ACTCTAGCTATGTGAGTAGTAGTAGTG 58.854 40.741 11.36 0.00 39.02 2.74
1900 1944 4.073549 GGATGATCACCGTAGTAGTAGCT 58.926 47.826 0.00 0.00 0.00 3.32
1904 1948 4.470602 TGATGGATGATCACCGTAGTAGT 58.529 43.478 0.00 0.00 36.06 2.73
1913 1969 2.301296 AGGGACGATGATGGATGATCAC 59.699 50.000 0.00 0.00 44.12 3.06
1957 2013 4.887655 TGAAAGAAGGAAAAGGAGGAACAC 59.112 41.667 0.00 0.00 0.00 3.32
1963 2019 4.697828 GCCTAGTGAAAGAAGGAAAAGGAG 59.302 45.833 0.00 0.00 31.64 3.69
1964 2020 4.506802 GGCCTAGTGAAAGAAGGAAAAGGA 60.507 45.833 0.00 0.00 31.64 3.36
1966 2022 3.437049 CGGCCTAGTGAAAGAAGGAAAAG 59.563 47.826 0.00 0.00 31.64 2.27
1996 2053 5.885352 TGAGTGACCAAAAAGATTGAGACAA 59.115 36.000 0.00 0.00 0.00 3.18
1998 2055 5.561725 GCTGAGTGACCAAAAAGATTGAGAC 60.562 44.000 0.00 0.00 0.00 3.36
2028 2086 2.511373 CGCGCATTGCCACCTCTA 60.511 61.111 8.75 0.00 42.08 2.43
2045 2103 3.618752 GCTGAGTCTTCTTCCCTTTCCTC 60.619 52.174 0.00 0.00 0.00 3.71
2063 2121 3.525537 GCTGTACAGATTAAGCTGCTGA 58.474 45.455 27.08 3.66 39.51 4.26
2107 2173 4.894114 ACAACGGCTATGATTACTAGGAGT 59.106 41.667 0.00 0.00 0.00 3.85
2115 2181 4.994852 GCTAATCCACAACGGCTATGATTA 59.005 41.667 0.00 0.00 33.14 1.75
2119 2185 1.873591 GGCTAATCCACAACGGCTATG 59.126 52.381 0.00 0.00 34.01 2.23
2121 2187 0.906066 TGGCTAATCCACAACGGCTA 59.094 50.000 0.00 0.00 40.72 3.93
2200 2266 7.999450 ACTAGCACTAGAACTAACAGTAAGT 57.001 36.000 11.59 0.00 36.97 2.24
2225 2291 9.492973 ACGGTAACTAACAACAGTAATAACAAT 57.507 29.630 0.00 0.00 0.00 2.71
2226 2292 8.763356 CACGGTAACTAACAACAGTAATAACAA 58.237 33.333 0.00 0.00 0.00 2.83
2228 2294 8.519492 TCACGGTAACTAACAACAGTAATAAC 57.481 34.615 0.00 0.00 0.00 1.89
2240 2309 8.082852 ACAGATCATATCATCACGGTAACTAAC 58.917 37.037 0.00 0.00 0.00 2.34
2501 2584 4.864483 AGAAGAGGGGAAAGGGTAAATC 57.136 45.455 0.00 0.00 0.00 2.17
2515 2604 9.575783 GTCTATGTGTCTACTAAAAAGAAGAGG 57.424 37.037 0.00 0.00 0.00 3.69
2538 2627 9.517868 ACTTTGTACTACTACTCTACAATGTCT 57.482 33.333 0.00 0.00 35.47 3.41
2543 2632 9.123902 TGTCAACTTTGTACTACTACTCTACAA 57.876 33.333 0.00 0.00 0.00 2.41
2550 2639 9.392021 GAGTAAGTGTCAACTTTGTACTACTAC 57.608 37.037 0.00 4.02 44.47 2.73
2553 2642 6.644181 GGGAGTAAGTGTCAACTTTGTACTAC 59.356 42.308 0.00 0.00 44.47 2.73
2576 2665 5.447954 CGCTCGTATATTATGAGACAGAGGG 60.448 48.000 7.73 0.00 43.02 4.30
2581 2670 6.856426 CAGAAACGCTCGTATATTATGAGACA 59.144 38.462 7.73 0.00 43.02 3.41
2584 2673 6.856426 TGTCAGAAACGCTCGTATATTATGAG 59.144 38.462 0.00 0.35 43.19 2.90
2585 2674 6.731164 TGTCAGAAACGCTCGTATATTATGA 58.269 36.000 0.00 0.00 0.00 2.15
2586 2675 6.986424 TGTCAGAAACGCTCGTATATTATG 57.014 37.500 0.00 0.00 0.00 1.90
2587 2676 9.125906 GTAATGTCAGAAACGCTCGTATATTAT 57.874 33.333 0.00 0.00 0.00 1.28
2588 2677 8.347771 AGTAATGTCAGAAACGCTCGTATATTA 58.652 33.333 0.00 0.00 0.00 0.98
2589 2678 7.201145 AGTAATGTCAGAAACGCTCGTATATT 58.799 34.615 0.00 0.00 0.00 1.28
2590 2679 6.736123 AGTAATGTCAGAAACGCTCGTATAT 58.264 36.000 0.00 0.00 0.00 0.86
2591 2680 6.127810 AGTAATGTCAGAAACGCTCGTATA 57.872 37.500 0.00 0.00 0.00 1.47
2592 2681 4.995124 AGTAATGTCAGAAACGCTCGTAT 58.005 39.130 0.00 0.00 0.00 3.06
2593 2682 4.430137 AGTAATGTCAGAAACGCTCGTA 57.570 40.909 0.00 0.00 0.00 3.43
2594 2683 3.299340 AGTAATGTCAGAAACGCTCGT 57.701 42.857 0.00 0.00 0.00 4.18
2595 2684 6.140895 CACTATAGTAATGTCAGAAACGCTCG 59.859 42.308 4.74 0.00 0.00 5.03
2596 2685 6.973474 ACACTATAGTAATGTCAGAAACGCTC 59.027 38.462 4.74 0.00 0.00 5.03
2597 2686 6.864342 ACACTATAGTAATGTCAGAAACGCT 58.136 36.000 4.74 0.00 0.00 5.07
2598 2687 8.624701 TTACACTATAGTAATGTCAGAAACGC 57.375 34.615 4.74 0.00 0.00 4.84
2624 2713 9.601217 AGACAGCTCATAATATAAGAACGTTTT 57.399 29.630 0.46 0.00 0.00 2.43
2625 2714 9.250624 GAGACAGCTCATAATATAAGAACGTTT 57.749 33.333 0.46 0.00 40.96 3.60
2626 2715 8.414003 TGAGACAGCTCATAATATAAGAACGTT 58.586 33.333 0.00 0.00 45.88 3.99
2627 2716 7.941919 TGAGACAGCTCATAATATAAGAACGT 58.058 34.615 0.00 0.00 45.88 3.99
2642 2731 5.025190 CGCTCGTATATTATGAGACAGCTC 58.975 45.833 7.73 0.00 43.02 4.09
2643 2732 4.456222 ACGCTCGTATATTATGAGACAGCT 59.544 41.667 7.73 0.00 43.02 4.24
2644 2733 4.724303 ACGCTCGTATATTATGAGACAGC 58.276 43.478 7.73 0.00 43.02 4.40
2645 2734 7.060059 CAGAAACGCTCGTATATTATGAGACAG 59.940 40.741 7.73 1.99 43.02 3.51
2646 2735 6.856426 CAGAAACGCTCGTATATTATGAGACA 59.144 38.462 7.73 0.00 43.02 3.41
2647 2736 7.076362 TCAGAAACGCTCGTATATTATGAGAC 58.924 38.462 7.73 0.11 43.02 3.36
2648 2737 7.198306 TCAGAAACGCTCGTATATTATGAGA 57.802 36.000 7.73 0.00 43.02 3.27
2649 2738 9.723447 ATATCAGAAACGCTCGTATATTATGAG 57.277 33.333 8.10 0.35 43.19 2.90
2657 2746 9.343103 CTACAATAATATCAGAAACGCTCGTAT 57.657 33.333 0.00 0.00 0.00 3.06
2660 2749 7.624706 ACTACAATAATATCAGAAACGCTCG 57.375 36.000 0.00 0.00 0.00 5.03
2686 2775 9.557338 CGTCCCATAATATAAAAACGTTTTTGA 57.443 29.630 36.92 27.73 40.33 2.69
2687 2776 8.800031 CCGTCCCATAATATAAAAACGTTTTTG 58.200 33.333 36.92 24.07 40.33 2.44
2688 2777 8.738106 TCCGTCCCATAATATAAAAACGTTTTT 58.262 29.630 33.94 33.94 42.51 1.94
2690 2779 7.012610 CCTCCGTCCCATAATATAAAAACGTTT 59.987 37.037 7.96 7.96 0.00 3.60
2692 2781 5.993441 CCTCCGTCCCATAATATAAAAACGT 59.007 40.000 0.00 0.00 0.00 3.99
2693 2782 6.225318 TCCTCCGTCCCATAATATAAAAACG 58.775 40.000 0.00 0.00 0.00 3.60
2694 2783 7.935210 TCTTCCTCCGTCCCATAATATAAAAAC 59.065 37.037 0.00 0.00 0.00 2.43
2695 2784 8.036585 TCTTCCTCCGTCCCATAATATAAAAA 57.963 34.615 0.00 0.00 0.00 1.94
2696 2785 7.621006 TCTTCCTCCGTCCCATAATATAAAA 57.379 36.000 0.00 0.00 0.00 1.52
2698 2787 7.014449 TCTTCTTCCTCCGTCCCATAATATAA 58.986 38.462 0.00 0.00 0.00 0.98
2702 2791 3.643792 CTCTTCTTCCTCCGTCCCATAAT 59.356 47.826 0.00 0.00 0.00 1.28
2707 2796 2.140839 TACTCTTCTTCCTCCGTCCC 57.859 55.000 0.00 0.00 0.00 4.46
2709 2798 9.669887 TTCTATATATACTCTTCTTCCTCCGTC 57.330 37.037 0.00 0.00 0.00 4.79
2711 2800 8.895737 GGTTCTATATATACTCTTCTTCCTCCG 58.104 40.741 0.00 0.00 0.00 4.63
2720 2809 8.968969 GGGATCGTTGGTTCTATATATACTCTT 58.031 37.037 0.00 0.00 0.00 2.85
2733 2822 0.958876 AAAGCCGGGATCGTTGGTTC 60.959 55.000 2.18 0.00 33.95 3.62
2776 2877 0.381089 CGGATAGAAAGACGGCGTCT 59.619 55.000 34.91 34.91 45.64 4.18
2879 2983 6.641062 CAGTTTTGTTTCGTGTTTTCAAACA 58.359 32.000 0.79 0.79 45.88 2.83
2922 3026 1.210155 GTCAACAGACAATGGGCGC 59.790 57.895 0.00 0.00 32.50 6.53
2932 3036 5.118990 CCTGACTTTTCTCTTGTCAACAGA 58.881 41.667 0.00 0.00 39.74 3.41
2934 3038 4.843728 ACCTGACTTTTCTCTTGTCAACA 58.156 39.130 0.00 0.00 39.74 3.33
2935 3039 7.308049 GGAATACCTGACTTTTCTCTTGTCAAC 60.308 40.741 0.00 0.00 39.74 3.18
2938 3050 6.468543 AGGAATACCTGACTTTTCTCTTGTC 58.531 40.000 0.00 0.00 45.92 3.18
2958 3070 3.173965 CAAACAGTAGGAGGAGGAGGAA 58.826 50.000 0.00 0.00 0.00 3.36
2960 3072 1.208293 GCAAACAGTAGGAGGAGGAGG 59.792 57.143 0.00 0.00 0.00 4.30
2969 3081 2.993899 CGTGGTCTAAGCAAACAGTAGG 59.006 50.000 0.00 0.00 0.00 3.18
3029 3144 1.518133 CTGCTGTGGCTAGTCTCGC 60.518 63.158 0.00 1.31 39.59 5.03
3030 3145 0.100325 CTCTGCTGTGGCTAGTCTCG 59.900 60.000 0.00 0.00 39.59 4.04
3031 3146 1.405105 CTCTCTGCTGTGGCTAGTCTC 59.595 57.143 0.00 0.00 39.59 3.36
3032 3147 1.272425 ACTCTCTGCTGTGGCTAGTCT 60.272 52.381 0.00 0.00 39.59 3.24
3033 3148 1.181786 ACTCTCTGCTGTGGCTAGTC 58.818 55.000 0.00 0.00 39.59 2.59
3034 3149 2.516227 TACTCTCTGCTGTGGCTAGT 57.484 50.000 0.00 0.00 39.59 2.57
3035 3150 5.720371 ATATTACTCTCTGCTGTGGCTAG 57.280 43.478 0.00 0.00 39.59 3.42
3036 3151 6.016192 GTGTATATTACTCTCTGCTGTGGCTA 60.016 42.308 0.00 0.00 39.59 3.93
3037 3152 4.895889 TGTATATTACTCTCTGCTGTGGCT 59.104 41.667 0.00 0.00 39.59 4.75
3038 3153 4.985409 GTGTATATTACTCTCTGCTGTGGC 59.015 45.833 0.00 0.00 39.26 5.01
3039 3154 6.149129 TGTGTATATTACTCTCTGCTGTGG 57.851 41.667 0.00 0.00 0.00 4.17
3040 3155 9.920133 AATATGTGTATATTACTCTCTGCTGTG 57.080 33.333 0.00 0.00 37.64 3.66
3042 3157 9.579768 GGAATATGTGTATATTACTCTCTGCTG 57.420 37.037 0.00 0.00 39.10 4.41
3043 3158 9.540538 AGGAATATGTGTATATTACTCTCTGCT 57.459 33.333 0.00 0.00 43.82 4.24
3070 3185 8.697292 GGACCAAAGAGAGTAATAACATAGTCT 58.303 37.037 0.00 0.00 38.09 3.24
3071 3186 8.697292 AGGACCAAAGAGAGTAATAACATAGTC 58.303 37.037 0.00 0.00 0.00 2.59
3072 3187 8.611051 AGGACCAAAGAGAGTAATAACATAGT 57.389 34.615 0.00 0.00 0.00 2.12
3073 3188 9.892130 AAAGGACCAAAGAGAGTAATAACATAG 57.108 33.333 0.00 0.00 0.00 2.23
3075 3190 9.588096 AAAAAGGACCAAAGAGAGTAATAACAT 57.412 29.630 0.00 0.00 0.00 2.71
3076 3191 8.990163 AAAAAGGACCAAAGAGAGTAATAACA 57.010 30.769 0.00 0.00 0.00 2.41
3078 3193 9.734984 CCTAAAAAGGACCAAAGAGAGTAATAA 57.265 33.333 0.00 0.00 0.00 1.40
3079 3194 8.326529 CCCTAAAAAGGACCAAAGAGAGTAATA 58.673 37.037 0.00 0.00 0.00 0.98
3080 3195 7.175797 CCCTAAAAAGGACCAAAGAGAGTAAT 58.824 38.462 0.00 0.00 0.00 1.89
3081 3196 6.466759 CCCCTAAAAAGGACCAAAGAGAGTAA 60.467 42.308 0.00 0.00 0.00 2.24
3082 3197 5.013808 CCCCTAAAAAGGACCAAAGAGAGTA 59.986 44.000 0.00 0.00 0.00 2.59
3083 3198 4.202577 CCCCTAAAAAGGACCAAAGAGAGT 60.203 45.833 0.00 0.00 0.00 3.24
3084 3199 4.202577 ACCCCTAAAAAGGACCAAAGAGAG 60.203 45.833 0.00 0.00 0.00 3.20
3085 3200 3.725267 ACCCCTAAAAAGGACCAAAGAGA 59.275 43.478 0.00 0.00 0.00 3.10
3086 3201 4.114015 ACCCCTAAAAAGGACCAAAGAG 57.886 45.455 0.00 0.00 0.00 2.85
3087 3202 4.219919 CAACCCCTAAAAAGGACCAAAGA 58.780 43.478 0.00 0.00 0.00 2.52
3088 3203 3.964688 ACAACCCCTAAAAAGGACCAAAG 59.035 43.478 0.00 0.00 0.00 2.77
3089 3204 3.996957 ACAACCCCTAAAAAGGACCAAA 58.003 40.909 0.00 0.00 0.00 3.28
3090 3205 3.691698 ACAACCCCTAAAAAGGACCAA 57.308 42.857 0.00 0.00 0.00 3.67
3091 3206 3.691698 AACAACCCCTAAAAAGGACCA 57.308 42.857 0.00 0.00 0.00 4.02
3092 3207 3.070446 CCAAACAACCCCTAAAAAGGACC 59.930 47.826 0.00 0.00 0.00 4.46
3093 3208 3.707611 ACCAAACAACCCCTAAAAAGGAC 59.292 43.478 0.00 0.00 0.00 3.85
3094 3209 3.996957 ACCAAACAACCCCTAAAAAGGA 58.003 40.909 0.00 0.00 0.00 3.36
3095 3210 4.407621 AGAACCAAACAACCCCTAAAAAGG 59.592 41.667 0.00 0.00 0.00 3.11
3096 3211 5.607939 AGAACCAAACAACCCCTAAAAAG 57.392 39.130 0.00 0.00 0.00 2.27
3097 3212 5.599242 CCTAGAACCAAACAACCCCTAAAAA 59.401 40.000 0.00 0.00 0.00 1.94
3098 3213 5.103601 TCCTAGAACCAAACAACCCCTAAAA 60.104 40.000 0.00 0.00 0.00 1.52
3099 3214 4.416179 TCCTAGAACCAAACAACCCCTAAA 59.584 41.667 0.00 0.00 0.00 1.85
3100 3215 3.982052 TCCTAGAACCAAACAACCCCTAA 59.018 43.478 0.00 0.00 0.00 2.69
3101 3216 3.328637 GTCCTAGAACCAAACAACCCCTA 59.671 47.826 0.00 0.00 0.00 3.53
3102 3217 2.107726 GTCCTAGAACCAAACAACCCCT 59.892 50.000 0.00 0.00 0.00 4.79
3103 3218 2.107726 AGTCCTAGAACCAAACAACCCC 59.892 50.000 0.00 0.00 0.00 4.95
3104 3219 3.503800 AGTCCTAGAACCAAACAACCC 57.496 47.619 0.00 0.00 0.00 4.11
3105 3220 4.001652 GCTAGTCCTAGAACCAAACAACC 58.998 47.826 5.52 0.00 35.21 3.77
3106 3221 4.638304 TGCTAGTCCTAGAACCAAACAAC 58.362 43.478 5.52 0.00 35.21 3.32
3107 3222 4.967084 TGCTAGTCCTAGAACCAAACAA 57.033 40.909 5.52 0.00 35.21 2.83
3108 3223 5.245531 CAATGCTAGTCCTAGAACCAAACA 58.754 41.667 5.52 0.00 35.21 2.83
3109 3224 4.095036 GCAATGCTAGTCCTAGAACCAAAC 59.905 45.833 5.52 0.00 35.21 2.93
3110 3225 4.261801 GCAATGCTAGTCCTAGAACCAAA 58.738 43.478 5.52 0.00 35.21 3.28
3111 3226 3.370527 GGCAATGCTAGTCCTAGAACCAA 60.371 47.826 4.82 0.00 35.21 3.67
3112 3227 2.170607 GGCAATGCTAGTCCTAGAACCA 59.829 50.000 4.82 0.00 35.21 3.67
3113 3228 2.170607 TGGCAATGCTAGTCCTAGAACC 59.829 50.000 4.82 0.00 35.21 3.62
3114 3229 3.543680 TGGCAATGCTAGTCCTAGAAC 57.456 47.619 4.82 0.00 35.21 3.01
3115 3230 4.901849 AGTATGGCAATGCTAGTCCTAGAA 59.098 41.667 4.82 0.00 35.21 2.10
3116 3231 4.483950 AGTATGGCAATGCTAGTCCTAGA 58.516 43.478 4.82 0.00 35.21 2.43
3117 3232 4.881019 AGTATGGCAATGCTAGTCCTAG 57.119 45.455 4.82 0.00 36.29 3.02
3118 3233 5.368145 CAAAGTATGGCAATGCTAGTCCTA 58.632 41.667 4.82 0.00 0.00 2.94
3119 3234 4.202441 CAAAGTATGGCAATGCTAGTCCT 58.798 43.478 4.82 0.00 0.00 3.85
3120 3235 3.243201 GCAAAGTATGGCAATGCTAGTCC 60.243 47.826 4.82 0.00 34.29 3.85
3121 3236 3.957468 GCAAAGTATGGCAATGCTAGTC 58.043 45.455 4.82 0.00 34.29 2.59
3132 3247 5.055812 ACAAAAATGTGTGGCAAAGTATGG 58.944 37.500 0.00 0.00 0.00 2.74
3133 3248 5.752472 TGACAAAAATGTGTGGCAAAGTATG 59.248 36.000 0.00 0.00 26.90 2.39
3134 3249 5.911752 TGACAAAAATGTGTGGCAAAGTAT 58.088 33.333 0.00 0.00 26.90 2.12
3135 3250 5.330455 TGACAAAAATGTGTGGCAAAGTA 57.670 34.783 0.00 0.00 26.90 2.24
3136 3251 4.199432 TGACAAAAATGTGTGGCAAAGT 57.801 36.364 0.00 0.00 26.90 2.66
3137 3252 4.494526 GCTTGACAAAAATGTGTGGCAAAG 60.495 41.667 0.00 0.00 42.11 2.77
3138 3253 3.373439 GCTTGACAAAAATGTGTGGCAAA 59.627 39.130 0.00 0.00 42.11 3.68
3139 3254 2.935201 GCTTGACAAAAATGTGTGGCAA 59.065 40.909 0.00 0.00 40.47 4.52
3140 3255 2.168106 AGCTTGACAAAAATGTGTGGCA 59.832 40.909 0.00 0.00 0.00 4.92
3141 3256 2.825205 AGCTTGACAAAAATGTGTGGC 58.175 42.857 0.00 0.00 0.00 5.01
3142 3257 3.001533 GCAAGCTTGACAAAAATGTGTGG 59.998 43.478 30.39 0.00 0.00 4.17
3143 3258 3.001533 GGCAAGCTTGACAAAAATGTGTG 59.998 43.478 30.39 0.00 35.83 3.82
3144 3259 3.118665 AGGCAAGCTTGACAAAAATGTGT 60.119 39.130 33.20 7.10 39.18 3.72
3145 3260 3.460103 AGGCAAGCTTGACAAAAATGTG 58.540 40.909 33.20 1.84 39.18 3.21
3146 3261 3.825143 AGGCAAGCTTGACAAAAATGT 57.175 38.095 33.20 8.70 39.18 2.71
3147 3262 4.687483 CCTTAGGCAAGCTTGACAAAAATG 59.313 41.667 33.20 16.65 39.18 2.32
3148 3263 4.344968 ACCTTAGGCAAGCTTGACAAAAAT 59.655 37.500 33.20 15.37 39.18 1.82
3149 3264 3.704061 ACCTTAGGCAAGCTTGACAAAAA 59.296 39.130 33.20 21.63 39.18 1.94
3150 3265 3.295973 ACCTTAGGCAAGCTTGACAAAA 58.704 40.909 33.20 23.97 39.18 2.44
3151 3266 2.944129 ACCTTAGGCAAGCTTGACAAA 58.056 42.857 33.20 18.55 39.18 2.83
3152 3267 2.656947 ACCTTAGGCAAGCTTGACAA 57.343 45.000 33.20 22.35 39.18 3.18
3153 3268 2.656947 AACCTTAGGCAAGCTTGACA 57.343 45.000 33.20 16.86 39.18 3.58
3154 3269 3.676093 ACTAACCTTAGGCAAGCTTGAC 58.324 45.455 30.39 28.05 35.08 3.18
3155 3270 4.324267 GAACTAACCTTAGGCAAGCTTGA 58.676 43.478 30.39 6.42 35.08 3.02
3156 3271 3.125316 CGAACTAACCTTAGGCAAGCTTG 59.875 47.826 22.44 22.44 35.08 4.01
3157 3272 3.007614 TCGAACTAACCTTAGGCAAGCTT 59.992 43.478 0.00 0.00 35.08 3.74
3158 3273 2.565834 TCGAACTAACCTTAGGCAAGCT 59.434 45.455 0.00 0.00 35.08 3.74
3159 3274 2.968675 TCGAACTAACCTTAGGCAAGC 58.031 47.619 0.00 0.00 35.08 4.01
3160 3275 7.605410 TTTTATCGAACTAACCTTAGGCAAG 57.395 36.000 0.00 0.00 35.08 4.01
3161 3276 7.825270 TCATTTTATCGAACTAACCTTAGGCAA 59.175 33.333 0.00 0.00 35.08 4.52
3162 3277 7.332557 TCATTTTATCGAACTAACCTTAGGCA 58.667 34.615 0.00 0.00 35.08 4.75
3163 3278 7.709613 TCTCATTTTATCGAACTAACCTTAGGC 59.290 37.037 0.00 0.00 35.08 3.93
3164 3279 9.250624 CTCTCATTTTATCGAACTAACCTTAGG 57.749 37.037 0.00 0.00 35.08 2.69
3165 3280 8.756864 GCTCTCATTTTATCGAACTAACCTTAG 58.243 37.037 0.00 0.00 36.82 2.18
3166 3281 7.709613 GGCTCTCATTTTATCGAACTAACCTTA 59.290 37.037 0.00 0.00 0.00 2.69
3167 3282 6.539103 GGCTCTCATTTTATCGAACTAACCTT 59.461 38.462 0.00 0.00 0.00 3.50
3168 3283 6.049790 GGCTCTCATTTTATCGAACTAACCT 58.950 40.000 0.00 0.00 0.00 3.50
3169 3284 5.815740 TGGCTCTCATTTTATCGAACTAACC 59.184 40.000 0.00 0.00 0.00 2.85
3170 3285 6.903883 TGGCTCTCATTTTATCGAACTAAC 57.096 37.500 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.