Multiple sequence alignment - TraesCS1A01G159600

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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 TraesCS1A01G159600 chr1A 100.000 3391 0 0 2465 5855 286008002 286011392 0.000000e+00 6263.0
1 TraesCS1A01G159600 chr1A 100.000 1396 0 0 832 2227 286006369 286007764 0.000000e+00 2579.0
2 TraesCS1A01G159600 chr1A 100.000 536 0 0 1 536 286005538 286006073 0.000000e+00 990.0
3 TraesCS1A01G159600 chr1A 80.506 395 69 7 5464 5852 391947683 391947291 4.440000e-76 296.0
4 TraesCS1A01G159600 chr1D 96.859 1560 37 9 2856 4410 221122132 221123684 0.000000e+00 2599.0
5 TraesCS1A01G159600 chr1D 96.943 1374 31 4 832 2200 221120408 221121775 0.000000e+00 2294.0
6 TraesCS1A01G159600 chr1D 95.577 1379 56 5 4480 5855 221123683 221125059 0.000000e+00 2204.0
7 TraesCS1A01G159600 chr1D 90.590 542 20 14 1 536 221119899 221120415 0.000000e+00 689.0
8 TraesCS1A01G159600 chr1D 100.000 307 0 0 2465 2771 221121824 221122130 8.510000e-158 568.0
9 TraesCS1A01G159600 chr1D 86.424 302 36 4 5464 5761 365430514 365430214 5.660000e-85 326.0
10 TraesCS1A01G159600 chr1B 95.524 1564 63 5 2854 4410 317441172 317442735 0.000000e+00 2494.0
11 TraesCS1A01G159600 chr1B 96.011 1404 45 4 832 2227 317439432 317440832 0.000000e+00 2272.0
12 TraesCS1A01G159600 chr1B 97.841 741 16 0 4480 5220 317442734 317443474 0.000000e+00 1280.0
13 TraesCS1A01G159600 chr1B 94.424 538 7 10 1 536 317438923 317439439 0.000000e+00 806.0
14 TraesCS1A01G159600 chr1B 86.702 564 46 6 5293 5852 317444456 317444994 3.020000e-167 599.0
15 TraesCS1A01G159600 chr1B 99.668 301 1 0 2465 2765 317440870 317441170 8.580000e-153 551.0
16 TraesCS1A01G159600 chr1B 95.000 100 5 0 5203 5302 317443535 317443634 2.180000e-34 158.0
17 TraesCS1A01G159600 chr1B 96.774 93 3 0 2771 2863 604705772 604705680 7.860000e-34 156.0
18 TraesCS1A01G159600 chr1B 83.178 107 4 5 4386 4481 476025036 476025139 1.050000e-12 86.1
19 TraesCS1A01G159600 chr3B 82.785 395 64 4 5464 5855 98024142 98023749 3.360000e-92 350.0
20 TraesCS1A01G159600 chr3B 97.802 91 1 1 2771 2860 2308912 2309002 7.860000e-34 156.0
21 TraesCS1A01G159600 chr3B 90.265 113 10 1 2771 2883 805351690 805351579 4.730000e-31 147.0
22 TraesCS1A01G159600 chr3B 89.796 49 3 2 4389 4436 349890861 349890814 1.760000e-05 62.1
23 TraesCS1A01G159600 chr5D 81.772 395 66 5 5464 5853 348500063 348499670 5.660000e-85 326.0
24 TraesCS1A01G159600 chr5D 100.000 86 0 0 2770 2855 37920307 37920392 6.070000e-35 159.0
25 TraesCS1A01G159600 chr5D 97.727 88 2 0 2771 2858 383306973 383306886 1.020000e-32 152.0
26 TraesCS1A01G159600 chr5D 97.368 76 0 2 4408 4481 418873985 418874060 1.710000e-25 128.0
27 TraesCS1A01G159600 chr4D 82.199 382 64 4 5473 5851 484062566 484062946 5.660000e-85 326.0
28 TraesCS1A01G159600 chr4D 94.059 101 6 0 2770 2870 26481865 26481765 2.830000e-33 154.0
29 TraesCS1A01G159600 chr7D 81.108 397 68 6 5462 5855 199487160 199487552 1.580000e-80 311.0
30 TraesCS1A01G159600 chr3D 79.337 392 77 3 5465 5852 374035979 374036370 7.480000e-69 272.0
31 TraesCS1A01G159600 chr3D 97.368 76 1 1 4408 4482 120008618 120008693 1.710000e-25 128.0
32 TraesCS1A01G159600 chr6B 98.851 87 1 0 2771 2857 632889449 632889535 7.860000e-34 156.0
33 TraesCS1A01G159600 chr6B 87.500 56 5 2 4389 4442 6880298 6880353 4.900000e-06 63.9
34 TraesCS1A01G159600 chr5B 90.654 107 9 1 2750 2856 103572159 103572054 2.200000e-29 141.0
35 TraesCS1A01G159600 chr5B 96.154 78 2 1 4405 4481 605314121 605314198 6.160000e-25 126.0
36 TraesCS1A01G159600 chr5B 84.906 106 4 4 4385 4481 60588733 60588631 4.830000e-16 97.1
37 TraesCS1A01G159600 chr5B 89.796 49 3 2 4389 4436 588318287 588318334 1.760000e-05 62.1
38 TraesCS1A01G159600 chr4A 88.889 117 10 2 2761 2877 38077737 38077624 2.200000e-29 141.0
39 TraesCS1A01G159600 chr4A 83.019 106 4 3 4389 4481 38740426 38740530 3.760000e-12 84.2
40 TraesCS1A01G159600 chr2D 97.500 80 0 2 4409 4487 120560096 120560018 1.020000e-27 135.0
41 TraesCS1A01G159600 chr2B 98.684 76 0 1 4407 4481 754965172 754965247 3.680000e-27 134.0
42 TraesCS1A01G159600 chr2B 98.361 61 1 0 956 1016 705883054 705883114 2.230000e-19 108.0
43 TraesCS1A01G159600 chrUn 98.630 73 0 1 4409 4481 27084473 27084544 1.710000e-25 128.0
44 TraesCS1A01G159600 chr6A 94.048 84 4 1 4406 4488 235083782 235083865 6.160000e-25 126.0
45 TraesCS1A01G159600 chr6A 91.860 86 5 2 4405 4488 494440777 494440862 1.030000e-22 119.0
46 TraesCS1A01G159600 chr4B 96.154 78 1 2 4406 4481 612401508 612401585 6.160000e-25 126.0
47 TraesCS1A01G159600 chr4B 81.443 97 2 9 4399 4481 657304940 657304846 1.360000e-06 65.8
48 TraesCS1A01G159600 chr7A 88.421 95 6 5 4392 4481 206709751 206709845 6.200000e-20 110.0
49 TraesCS1A01G159600 chr7B 88.000 50 4 2 4388 4436 330340592 330340544 2.280000e-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 TraesCS1A01G159600 chr1A 286005538 286011392 5854 False 3277.333333 6263 100.000000 1 5855 3 chr1A.!!$F1 5854
1 TraesCS1A01G159600 chr1D 221119899 221125059 5160 False 1670.800000 2599 95.993800 1 5855 5 chr1D.!!$F1 5854
2 TraesCS1A01G159600 chr1B 317438923 317444994 6071 False 1165.714286 2494 95.024286 1 5852 7 chr1B.!!$F2 5851

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
986 1009 1.649664 CAGCCTCCAAGAATCACTCG 58.350 55.0 0.00 0.00 0.00 4.18 F
1251 1274 0.179161 CGTCTCTAGGCAAGGTGACG 60.179 60.0 14.67 14.67 41.91 4.35 F
2202 2230 0.034089 AATGTGGAGCAGGTAAGCCC 60.034 55.0 0.00 0.00 34.57 5.19 F
2776 2804 0.035458 AAGCTGTGTGTGCTACTCCC 59.965 55.0 0.00 0.00 40.22 4.30 F
2782 2810 0.038599 TGTGTGCTACTCCCTCCGTA 59.961 55.0 0.00 0.00 0.00 4.02 F
4668 4706 0.826715 ATCGCCACATAGCTGACACT 59.173 50.0 0.00 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 2096 0.178938 TTGCAGGGAAGGCAATGGAA 60.179 50.000 0.0 0.0 45.57 3.53 R
3107 3137 0.188587 AGGGACTATCTCATGCCCGA 59.811 55.000 0.0 0.0 43.64 5.14 R
3464 3494 2.557869 ACCCACTCCATAGTAAAGGCA 58.442 47.619 0.0 0.0 33.48 4.75 R
4683 4721 1.407258 GCCAAGTACTGTTTTGCACCA 59.593 47.619 0.0 0.0 0.00 4.17 R
4832 4870 1.203050 AGCTTGCATAAACCCCAGTGT 60.203 47.619 0.0 0.0 0.00 3.55 R
5554 6506 0.169672 GCAGTAGCGGTCGTTCAGTA 59.830 55.000 0.0 0.0 0.00 2.74 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
31 34 6.143118 GTCTACTTGCATGTCATCGATCTTAC 59.857 42.308 8.74 0.00 0.00 2.34
32 35 5.016051 ACTTGCATGTCATCGATCTTACT 57.984 39.130 0.00 0.00 0.00 2.24
33 36 6.149129 ACTTGCATGTCATCGATCTTACTA 57.851 37.500 0.00 0.00 0.00 1.82
34 37 5.980116 ACTTGCATGTCATCGATCTTACTAC 59.020 40.000 0.00 0.00 0.00 2.73
127 130 5.441718 AAAGTGGGAGCTGATGAAATAGA 57.558 39.130 0.00 0.00 0.00 1.98
128 131 5.441718 AAGTGGGAGCTGATGAAATAGAA 57.558 39.130 0.00 0.00 0.00 2.10
129 132 5.643421 AGTGGGAGCTGATGAAATAGAAT 57.357 39.130 0.00 0.00 0.00 2.40
130 133 5.619220 AGTGGGAGCTGATGAAATAGAATC 58.381 41.667 0.00 0.00 0.00 2.52
131 134 5.131642 AGTGGGAGCTGATGAAATAGAATCA 59.868 40.000 0.00 0.00 0.00 2.57
132 135 5.238214 GTGGGAGCTGATGAAATAGAATCAC 59.762 44.000 0.00 0.00 0.00 3.06
305 316 3.023832 TGTGTGTGTGTGAGAGAGAGAA 58.976 45.455 0.00 0.00 0.00 2.87
349 360 3.620488 GAAGATCACATGGTGGCCTTTA 58.380 45.455 3.32 0.00 33.87 1.85
396 407 6.149640 CCCTTTAGTCTTTTAGTGCTTCCTTC 59.850 42.308 0.00 0.00 0.00 3.46
397 408 6.149640 CCTTTAGTCTTTTAGTGCTTCCTTCC 59.850 42.308 0.00 0.00 0.00 3.46
398 409 4.984146 AGTCTTTTAGTGCTTCCTTCCT 57.016 40.909 0.00 0.00 0.00 3.36
399 410 5.311844 AGTCTTTTAGTGCTTCCTTCCTT 57.688 39.130 0.00 0.00 0.00 3.36
522 533 4.521146 TGCTCATCCCTTTCTTCTTCATC 58.479 43.478 0.00 0.00 0.00 2.92
528 539 4.114597 TCCCTTTCTTCTTCATCCATCCT 58.885 43.478 0.00 0.00 0.00 3.24
529 540 4.164988 TCCCTTTCTTCTTCATCCATCCTC 59.835 45.833 0.00 0.00 0.00 3.71
530 541 4.165758 CCCTTTCTTCTTCATCCATCCTCT 59.834 45.833 0.00 0.00 0.00 3.69
531 542 5.367302 CCTTTCTTCTTCATCCATCCTCTC 58.633 45.833 0.00 0.00 0.00 3.20
532 543 5.130809 CCTTTCTTCTTCATCCATCCTCTCT 59.869 44.000 0.00 0.00 0.00 3.10
533 544 5.867903 TTCTTCTTCATCCATCCTCTCTC 57.132 43.478 0.00 0.00 0.00 3.20
534 545 5.141455 TCTTCTTCATCCATCCTCTCTCT 57.859 43.478 0.00 0.00 0.00 3.10
535 546 5.139727 TCTTCTTCATCCATCCTCTCTCTC 58.860 45.833 0.00 0.00 0.00 3.20
928 939 3.196901 TCCACAATAGCAATACACCTCGT 59.803 43.478 0.00 0.00 0.00 4.18
986 1009 1.649664 CAGCCTCCAAGAATCACTCG 58.350 55.000 0.00 0.00 0.00 4.18
1146 1169 3.112709 GCGTCCAGTGACTTCGGC 61.113 66.667 0.00 0.00 39.47 5.54
1251 1274 0.179161 CGTCTCTAGGCAAGGTGACG 60.179 60.000 14.67 14.67 41.91 4.35
1328 1351 1.028330 ATTGTGGTGGAGATGCGCTG 61.028 55.000 9.73 0.00 0.00 5.18
1355 1378 1.136500 TGCTGAGATAGAGCTGCACAG 59.864 52.381 1.02 0.00 37.35 3.66
1653 1677 2.936032 GGCCCTGTCTCCCTTGGT 60.936 66.667 0.00 0.00 0.00 3.67
1706 1730 6.022163 AGATTTTGTGCTCCTCTTTGATTG 57.978 37.500 0.00 0.00 0.00 2.67
1846 1870 4.870991 GGAAGCTCCACAGAAAGTATGTAC 59.129 45.833 0.00 0.00 36.28 2.90
1860 1884 0.245539 ATGTACGCAGCGTTACACCT 59.754 50.000 28.31 8.58 41.54 4.00
1878 1902 5.542779 ACACCTGTCTTGTTCTCATTAGTC 58.457 41.667 0.00 0.00 0.00 2.59
2068 2096 0.390860 AACAGTCGCTTCACAGCTCT 59.609 50.000 0.00 0.00 44.85 4.09
2074 2102 1.002430 TCGCTTCACAGCTCTTCCATT 59.998 47.619 0.00 0.00 44.85 3.16
2174 2202 1.136529 CGGTTCATGATTATCAGCGCG 60.137 52.381 0.00 0.00 0.00 6.86
2175 2203 1.867233 GGTTCATGATTATCAGCGCGT 59.133 47.619 8.43 0.00 0.00 6.01
2201 2229 1.098050 CAATGTGGAGCAGGTAAGCC 58.902 55.000 0.00 0.00 34.23 4.35
2202 2230 0.034089 AATGTGGAGCAGGTAAGCCC 60.034 55.000 0.00 0.00 34.57 5.19
2771 2799 3.069586 AGACAAGTAAGCTGTGTGTGCTA 59.930 43.478 0.00 0.00 40.22 3.49
2772 2800 3.131396 ACAAGTAAGCTGTGTGTGCTAC 58.869 45.455 0.00 0.00 40.22 3.58
2773 2801 3.181465 ACAAGTAAGCTGTGTGTGCTACT 60.181 43.478 0.00 0.00 40.22 2.57
2774 2802 3.305398 AGTAAGCTGTGTGTGCTACTC 57.695 47.619 0.00 0.00 40.22 2.59
2775 2803 2.028930 AGTAAGCTGTGTGTGCTACTCC 60.029 50.000 0.00 0.00 40.22 3.85
2776 2804 0.035458 AAGCTGTGTGTGCTACTCCC 59.965 55.000 0.00 0.00 40.22 4.30
2777 2805 0.833834 AGCTGTGTGTGCTACTCCCT 60.834 55.000 0.00 0.00 39.21 4.20
2778 2806 0.390472 GCTGTGTGTGCTACTCCCTC 60.390 60.000 0.00 0.00 0.00 4.30
2779 2807 0.247736 CTGTGTGTGCTACTCCCTCC 59.752 60.000 0.00 0.00 0.00 4.30
2780 2808 1.215647 GTGTGTGCTACTCCCTCCG 59.784 63.158 0.00 0.00 0.00 4.63
2781 2809 1.228769 TGTGTGCTACTCCCTCCGT 60.229 57.895 0.00 0.00 0.00 4.69
2782 2810 0.038599 TGTGTGCTACTCCCTCCGTA 59.961 55.000 0.00 0.00 0.00 4.02
2783 2811 1.180029 GTGTGCTACTCCCTCCGTAA 58.820 55.000 0.00 0.00 0.00 3.18
2784 2812 1.547372 GTGTGCTACTCCCTCCGTAAA 59.453 52.381 0.00 0.00 0.00 2.01
2785 2813 1.547372 TGTGCTACTCCCTCCGTAAAC 59.453 52.381 0.00 0.00 0.00 2.01
2786 2814 1.823610 GTGCTACTCCCTCCGTAAACT 59.176 52.381 0.00 0.00 0.00 2.66
2787 2815 3.019564 GTGCTACTCCCTCCGTAAACTA 58.980 50.000 0.00 0.00 0.00 2.24
2788 2816 3.445096 GTGCTACTCCCTCCGTAAACTAA 59.555 47.826 0.00 0.00 0.00 2.24
2789 2817 4.099113 GTGCTACTCCCTCCGTAAACTAAT 59.901 45.833 0.00 0.00 0.00 1.73
2790 2818 5.300286 GTGCTACTCCCTCCGTAAACTAATA 59.700 44.000 0.00 0.00 0.00 0.98
2791 2819 6.015603 GTGCTACTCCCTCCGTAAACTAATAT 60.016 42.308 0.00 0.00 0.00 1.28
2792 2820 7.175641 GTGCTACTCCCTCCGTAAACTAATATA 59.824 40.741 0.00 0.00 0.00 0.86
2793 2821 7.725397 TGCTACTCCCTCCGTAAACTAATATAA 59.275 37.037 0.00 0.00 0.00 0.98
2794 2822 8.242739 GCTACTCCCTCCGTAAACTAATATAAG 58.757 40.741 0.00 0.00 0.00 1.73
2795 2823 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
2796 2824 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2797 2825 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2798 2826 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2799 2827 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2800 2828 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2801 2829 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2802 2830 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2803 2831 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2804 2832 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2832 2860 9.654663 AACTATTTTAGTGATCTAAACGCTCTT 57.345 29.630 0.00 0.00 43.20 2.85
2849 2877 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2850 2878 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2851 2879 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2852 2880 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2870 2898 3.002348 GGGAGTACTAATCAACGCAATGC 59.998 47.826 0.00 0.00 0.00 3.56
2878 2906 2.917701 TCAACGCAATGCATTGTAGG 57.082 45.000 33.67 25.72 39.88 3.18
2914 2942 3.589542 CAACTTGGGGCTGGGGGA 61.590 66.667 0.00 0.00 0.00 4.81
2931 2959 3.454375 GGGGACACATCAATACGTGTAG 58.546 50.000 0.00 0.00 46.06 2.74
2999 3027 1.654137 GTTTGTGACCGCTGCGTTG 60.654 57.895 21.59 9.06 0.00 4.10
3107 3137 5.926663 TGAGAATTAATCAGCTCTGCTCAT 58.073 37.500 11.73 0.00 36.40 2.90
3243 3273 2.486796 GGCACCATTCTGCTCTTCC 58.513 57.895 0.00 0.00 37.33 3.46
3244 3274 1.034292 GGCACCATTCTGCTCTTCCC 61.034 60.000 0.00 0.00 37.33 3.97
3370 3400 9.059260 TGATAAATGATGTGTGATGTATCCTTG 57.941 33.333 0.00 0.00 0.00 3.61
3543 3573 2.822561 ACATTGGACACAACACACACAA 59.177 40.909 0.00 0.00 39.87 3.33
3801 3834 6.748333 TGAGTGGCATCTTCTTTATTTGAG 57.252 37.500 0.00 0.00 0.00 3.02
3963 3997 8.477256 ACAATGCATTATAAACAATAACTGCCT 58.523 29.630 12.53 0.00 35.70 4.75
4064 4098 5.369685 TGATGCATAACGTTGTTCACAAT 57.630 34.783 11.99 0.00 38.24 2.71
4069 4103 4.086524 GCATAACGTTGTTCACAATTCACG 59.913 41.667 11.99 0.00 38.24 4.35
4218 4252 7.112122 TGATTGAGCCTTAGCAAAAGATCTAA 58.888 34.615 0.00 0.00 43.56 2.10
4408 4446 3.390311 TGATCTGGCAGTTGCTGAGATAT 59.610 43.478 15.27 0.00 39.00 1.63
4409 4447 4.590222 TGATCTGGCAGTTGCTGAGATATA 59.410 41.667 15.27 8.13 39.00 0.86
4410 4448 4.327982 TCTGGCAGTTGCTGAGATATAC 57.672 45.455 15.27 0.00 41.70 1.47
4411 4449 3.963374 TCTGGCAGTTGCTGAGATATACT 59.037 43.478 15.27 0.00 41.70 2.12
4412 4450 4.038522 TCTGGCAGTTGCTGAGATATACTC 59.961 45.833 15.27 0.00 40.77 2.59
4413 4451 3.070159 TGGCAGTTGCTGAGATATACTCC 59.930 47.826 3.88 0.00 40.18 3.85
4414 4452 3.556004 GGCAGTTGCTGAGATATACTCCC 60.556 52.174 3.88 0.00 40.18 4.30
4415 4453 3.323403 GCAGTTGCTGAGATATACTCCCT 59.677 47.826 0.00 0.00 44.34 4.20
4416 4454 4.560513 GCAGTTGCTGAGATATACTCCCTC 60.561 50.000 0.00 0.00 44.34 4.30
4417 4455 4.021544 CAGTTGCTGAGATATACTCCCTCC 60.022 50.000 0.00 0.00 44.34 4.30
4418 4456 2.796557 TGCTGAGATATACTCCCTCCG 58.203 52.381 0.00 0.00 44.34 4.63
4419 4457 2.108425 TGCTGAGATATACTCCCTCCGT 59.892 50.000 0.00 0.00 44.34 4.69
4420 4458 3.158676 GCTGAGATATACTCCCTCCGTT 58.841 50.000 0.00 0.00 44.34 4.44
4421 4459 3.191791 GCTGAGATATACTCCCTCCGTTC 59.808 52.174 0.00 0.00 44.34 3.95
4422 4460 3.759618 CTGAGATATACTCCCTCCGTTCC 59.240 52.174 0.00 0.00 44.34 3.62
4423 4461 3.139584 TGAGATATACTCCCTCCGTTCCA 59.860 47.826 0.00 0.00 44.34 3.53
4424 4462 4.150359 GAGATATACTCCCTCCGTTCCAA 58.850 47.826 0.00 0.00 39.53 3.53
4425 4463 4.553678 AGATATACTCCCTCCGTTCCAAA 58.446 43.478 0.00 0.00 0.00 3.28
4426 4464 4.966805 AGATATACTCCCTCCGTTCCAAAA 59.033 41.667 0.00 0.00 0.00 2.44
4427 4465 5.607171 AGATATACTCCCTCCGTTCCAAAAT 59.393 40.000 0.00 0.00 0.00 1.82
4428 4466 6.785963 AGATATACTCCCTCCGTTCCAAAATA 59.214 38.462 0.00 0.00 0.00 1.40
4429 4467 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
4430 4468 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
4431 4469 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
4432 4470 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
4433 4471 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
4434 4472 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
4435 4473 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
4436 4474 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
4437 4475 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
4438 4476 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
4439 4477 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
4440 4478 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
4441 4479 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
4442 4480 6.373216 CGTTCCAAAATAGATGACCCAACTTA 59.627 38.462 0.00 0.00 0.00 2.24
4443 4481 7.067008 CGTTCCAAAATAGATGACCCAACTTAT 59.933 37.037 0.00 0.00 0.00 1.73
4444 4482 9.403583 GTTCCAAAATAGATGACCCAACTTATA 57.596 33.333 0.00 0.00 0.00 0.98
4445 4483 8.974060 TCCAAAATAGATGACCCAACTTATAC 57.026 34.615 0.00 0.00 0.00 1.47
4446 4484 8.553153 TCCAAAATAGATGACCCAACTTATACA 58.447 33.333 0.00 0.00 0.00 2.29
4447 4485 9.184523 CCAAAATAGATGACCCAACTTATACAA 57.815 33.333 0.00 0.00 0.00 2.41
4450 4488 9.975218 AAATAGATGACCCAACTTATACAAAGT 57.025 29.630 0.00 0.00 0.00 2.66
4451 4489 9.975218 AATAGATGACCCAACTTATACAAAGTT 57.025 29.630 0.00 0.00 40.80 2.66
4463 4501 9.975218 AACTTATACAAAGTTGGGTCATCTATT 57.025 29.630 2.49 0.00 38.88 1.73
4464 4502 9.975218 ACTTATACAAAGTTGGGTCATCTATTT 57.025 29.630 0.00 0.00 0.00 1.40
4467 4505 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
4468 4506 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
4469 4507 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
4470 4508 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
4471 4509 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
4472 4510 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
4473 4511 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
4474 4512 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
4475 4513 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
4476 4514 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
4477 4515 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
4478 4516 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
4668 4706 0.826715 ATCGCCACATAGCTGACACT 59.173 50.000 0.00 0.00 0.00 3.55
4683 4721 4.704833 ACTGCCGGAGTGCGCATT 62.705 61.111 15.91 10.23 33.78 3.56
4832 4870 2.509243 AGGTATATTCCCCAAGGGCAA 58.491 47.619 0.00 0.00 43.94 4.52
4864 4902 1.320507 TGCAAGCTGACAGCATGAAA 58.679 45.000 31.12 17.81 42.02 2.69
4869 4907 4.552355 CAAGCTGACAGCATGAAATTTCA 58.448 39.130 28.43 22.52 42.02 2.69
4956 4994 2.298163 TCTTTCGTAGCTCTTTTCGGGT 59.702 45.455 0.00 0.00 0.00 5.28
5013 5051 0.549902 ATGGTGGTGGTGGATCCTGA 60.550 55.000 14.23 0.00 37.07 3.86
5274 5390 5.128205 TCAGAACCCAAGATGATATGCTTG 58.872 41.667 0.00 0.00 40.81 4.01
5288 5404 2.900122 TGCTTGCGAATTTACAGAGC 57.100 45.000 0.00 0.00 0.00 4.09
5291 5407 2.784665 GCTTGCGAATTTACAGAGCGAC 60.785 50.000 0.00 0.00 0.00 5.19
5342 6289 6.245890 TGTGAATCATACACCATGTCCATA 57.754 37.500 0.00 0.00 37.45 2.74
5358 6305 9.334947 CCATGTCCATATGATATTCTTATCACC 57.665 37.037 3.65 0.00 45.29 4.02
5409 6356 5.120399 TGTTTAGTTCATTGTGACCGACTT 58.880 37.500 0.00 0.00 0.00 3.01
5554 6506 8.641498 ACAAATTACATCAAGATTCCAAGACT 57.359 30.769 0.00 0.00 0.00 3.24
5660 6612 1.423584 TGACAGGCAGGAAGTCTTCA 58.576 50.000 14.49 0.00 33.56 3.02
5680 6632 2.955881 GCACGTGCCCCTAAGGACT 61.956 63.158 30.12 0.00 38.24 3.85
5684 6636 1.327690 CGTGCCCCTAAGGACTAGCA 61.328 60.000 0.00 0.00 38.24 3.49
5696 6648 1.000019 ACTAGCACCTGGAGCCGTA 60.000 57.895 12.66 0.00 0.00 4.02
5699 6651 0.613853 TAGCACCTGGAGCCGTAGTT 60.614 55.000 12.66 0.00 0.00 2.24
5717 6669 1.407618 GTTGTCGCCTTTGAACCCTTT 59.592 47.619 0.00 0.00 0.00 3.11
5761 6713 1.731709 CAAATCTCGCCACATGACGAA 59.268 47.619 0.00 0.00 37.94 3.85
5807 6759 1.696336 AGATGGCAGGAATCTACGCAT 59.304 47.619 0.00 0.00 32.54 4.73
5814 6766 4.372656 GCAGGAATCTACGCATAAGTTCT 58.627 43.478 0.00 0.00 0.00 3.01
5842 6794 1.604023 AGCCAGACGGACGAACTCT 60.604 57.895 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 34 6.340537 ACCATGCGTTCGTTAAATAAGTAG 57.659 37.500 0.00 0.00 0.00 2.57
32 35 7.824704 TTACCATGCGTTCGTTAAATAAGTA 57.175 32.000 0.00 0.00 0.00 2.24
33 36 6.724694 TTACCATGCGTTCGTTAAATAAGT 57.275 33.333 0.00 0.00 0.00 2.24
34 37 7.627340 AGATTACCATGCGTTCGTTAAATAAG 58.373 34.615 0.00 0.00 0.00 1.73
74 77 5.221106 CCTCAATTTTCAAGTGCTGTCAAGA 60.221 40.000 0.00 0.00 0.00 3.02
127 130 3.693085 GTCAGCTCCATGTGATTGTGATT 59.307 43.478 0.00 0.00 0.00 2.57
128 131 3.054582 AGTCAGCTCCATGTGATTGTGAT 60.055 43.478 0.00 0.00 0.00 3.06
129 132 2.303890 AGTCAGCTCCATGTGATTGTGA 59.696 45.455 0.00 0.00 0.00 3.58
130 133 2.708051 AGTCAGCTCCATGTGATTGTG 58.292 47.619 0.00 0.00 0.00 3.33
131 134 3.430042 AAGTCAGCTCCATGTGATTGT 57.570 42.857 0.00 0.00 0.00 2.71
132 135 4.940046 ACTTAAGTCAGCTCCATGTGATTG 59.060 41.667 1.12 0.00 0.00 2.67
284 287 2.654863 TCTCTCTCTCACACACACACA 58.345 47.619 0.00 0.00 0.00 3.72
349 360 4.265073 GAGAAGCTGTCACATACCCAAAT 58.735 43.478 0.00 0.00 0.00 2.32
928 939 2.024868 GCGTGCGTGTGTATCACCA 61.025 57.895 0.00 0.00 43.51 4.17
941 952 3.181169 AAGAAAGGCGTGTGCGTGC 62.181 57.895 0.00 0.00 44.10 5.34
942 953 1.082756 GAAGAAAGGCGTGTGCGTG 60.083 57.895 0.00 0.00 44.10 5.34
943 954 0.814010 AAGAAGAAAGGCGTGTGCGT 60.814 50.000 0.00 0.00 44.10 5.24
1146 1169 1.127343 GGGAGTGGAAGAGGATCCTG 58.873 60.000 22.02 0.00 40.35 3.86
1328 1351 1.868469 CTCTATCTCAGCAGGCAAGC 58.132 55.000 0.00 0.00 0.00 4.01
1355 1378 3.133901 GGAAACATCTCCTTCTCCTCCTC 59.866 52.174 0.00 0.00 32.21 3.71
1639 1663 0.764890 TGTTGACCAAGGGAGACAGG 59.235 55.000 0.00 0.00 0.00 4.00
1706 1730 2.363172 GGTCTCTCCCCTGCCTGTC 61.363 68.421 0.00 0.00 0.00 3.51
1846 1870 0.944311 AAGACAGGTGTAACGCTGCG 60.944 55.000 21.91 21.91 38.26 5.18
1860 1884 7.526142 ACACTAGACTAATGAGAACAAGACA 57.474 36.000 0.00 0.00 0.00 3.41
2068 2096 0.178938 TTGCAGGGAAGGCAATGGAA 60.179 50.000 0.00 0.00 45.57 3.53
2074 2102 1.287442 TCCATATTTGCAGGGAAGGCA 59.713 47.619 0.00 0.00 40.00 4.75
2174 2202 2.684881 CCTGCTCCACATTGGTATTCAC 59.315 50.000 0.00 0.00 39.03 3.18
2175 2203 2.308570 ACCTGCTCCACATTGGTATTCA 59.691 45.455 0.00 0.00 39.03 2.57
2771 2799 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
2772 2800 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
2773 2801 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
2774 2802 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2775 2803 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2776 2804 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2777 2805 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2778 2806 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2806 2834 9.654663 AAGAGCGTTTAGATCACTAAAATAGTT 57.345 29.630 0.00 0.00 45.97 2.24
2823 2851 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2824 2852 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2825 2853 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2826 2854 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2827 2855 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2835 2863 9.710818 TGATTAGTACTCCCTCTGTAAACTAAT 57.289 33.333 0.00 4.90 32.62 1.73
2836 2864 9.537852 TTGATTAGTACTCCCTCTGTAAACTAA 57.462 33.333 0.00 0.00 0.00 2.24
2837 2865 8.964772 GTTGATTAGTACTCCCTCTGTAAACTA 58.035 37.037 0.00 0.00 0.00 2.24
2838 2866 7.362747 CGTTGATTAGTACTCCCTCTGTAAACT 60.363 40.741 0.00 0.00 0.00 2.66
2839 2867 6.750963 CGTTGATTAGTACTCCCTCTGTAAAC 59.249 42.308 0.00 0.00 0.00 2.01
2840 2868 6.626623 GCGTTGATTAGTACTCCCTCTGTAAA 60.627 42.308 0.00 0.00 0.00 2.01
2841 2869 5.163581 GCGTTGATTAGTACTCCCTCTGTAA 60.164 44.000 0.00 0.00 0.00 2.41
2842 2870 4.337555 GCGTTGATTAGTACTCCCTCTGTA 59.662 45.833 0.00 0.00 0.00 2.74
2843 2871 3.130693 GCGTTGATTAGTACTCCCTCTGT 59.869 47.826 0.00 0.00 0.00 3.41
2844 2872 3.130516 TGCGTTGATTAGTACTCCCTCTG 59.869 47.826 0.00 0.00 0.00 3.35
2845 2873 3.362706 TGCGTTGATTAGTACTCCCTCT 58.637 45.455 0.00 0.00 0.00 3.69
2846 2874 3.795623 TGCGTTGATTAGTACTCCCTC 57.204 47.619 0.00 0.00 0.00 4.30
2847 2875 4.442706 CATTGCGTTGATTAGTACTCCCT 58.557 43.478 0.00 0.00 0.00 4.20
2848 2876 3.002348 GCATTGCGTTGATTAGTACTCCC 59.998 47.826 0.00 0.00 0.00 4.30
2849 2877 3.621268 TGCATTGCGTTGATTAGTACTCC 59.379 43.478 0.00 0.00 0.00 3.85
2850 2878 4.857871 TGCATTGCGTTGATTAGTACTC 57.142 40.909 0.00 0.00 0.00 2.59
2851 2879 5.818136 AATGCATTGCGTTGATTAGTACT 57.182 34.783 12.09 0.00 36.34 2.73
2896 2924 3.589542 CCCCCAGCCCCAAGTTGA 61.590 66.667 3.87 0.00 0.00 3.18
2967 2995 5.967088 CGGTCACAAACAAGGTTAGTTAAAC 59.033 40.000 0.00 0.00 37.36 2.01
3020 3048 1.021390 ATGCGGAGAAAGGCTTGTCG 61.021 55.000 0.00 4.04 0.00 4.35
3063 3092 8.256611 TCTCAGCACTTTGATTACATAGAAAC 57.743 34.615 0.00 0.00 0.00 2.78
3107 3137 0.188587 AGGGACTATCTCATGCCCGA 59.811 55.000 0.00 0.00 43.64 5.14
3289 3319 8.364894 ACAATATACTGTACAAGAGAACACACA 58.635 33.333 0.00 0.00 0.00 3.72
3464 3494 2.557869 ACCCACTCCATAGTAAAGGCA 58.442 47.619 0.00 0.00 33.48 4.75
3801 3834 5.379187 TCCCTGTACTTAACAAAGGTTTCC 58.621 41.667 0.00 0.00 37.74 3.13
3937 3971 8.477256 AGGCAGTTATTGTTTATAATGCATTGT 58.523 29.630 22.27 17.77 36.28 2.71
3963 3997 3.890756 ACATGCTGATGTTTGAACTGGAA 59.109 39.130 0.00 0.00 40.05 3.53
3969 4003 5.005740 AGAGCTTACATGCTGATGTTTGAA 58.994 37.500 0.00 0.00 44.17 2.69
4038 4072 5.008118 TGTGAACAACGTTATGCATCAAAGA 59.992 36.000 0.19 0.00 0.00 2.52
4064 4098 7.866729 TCTTAAAAACATACAGAATGCGTGAA 58.133 30.769 0.00 0.00 42.53 3.18
4363 4401 5.560722 TGACCTGGATAAGAACACAAGAA 57.439 39.130 0.00 0.00 0.00 2.52
4408 4446 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
4409 4447 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
4410 4448 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
4411 4449 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
4412 4450 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
4413 4451 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
4414 4452 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
4415 4453 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
4416 4454 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
4417 4455 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
4418 4456 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
4419 4457 9.403583 GTATAAGTTGGGTCATCTATTTTGGAA 57.596 33.333 0.00 0.00 0.00 3.53
4420 4458 8.553153 TGTATAAGTTGGGTCATCTATTTTGGA 58.447 33.333 0.00 0.00 0.00 3.53
4421 4459 8.746052 TGTATAAGTTGGGTCATCTATTTTGG 57.254 34.615 0.00 0.00 0.00 3.28
4424 4462 9.975218 ACTTTGTATAAGTTGGGTCATCTATTT 57.025 29.630 0.00 0.00 0.00 1.40
4425 4463 9.975218 AACTTTGTATAAGTTGGGTCATCTATT 57.025 29.630 2.36 0.00 38.88 1.73
4437 4475 9.975218 AATAGATGACCCAACTTTGTATAAGTT 57.025 29.630 0.00 0.00 40.80 2.66
4438 4476 9.975218 AAATAGATGACCCAACTTTGTATAAGT 57.025 29.630 0.00 0.00 0.00 2.24
4441 4479 9.184523 CCAAAATAGATGACCCAACTTTGTATA 57.815 33.333 0.00 0.00 0.00 1.47
4442 4480 7.893302 TCCAAAATAGATGACCCAACTTTGTAT 59.107 33.333 0.00 0.00 0.00 2.29
4443 4481 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
4444 4482 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
4445 4483 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
4446 4484 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
4447 4485 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
4448 4486 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
4449 4487 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
4450 4488 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
4451 4489 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
4452 4490 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
4453 4491 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
4454 4492 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
4455 4493 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
4456 4494 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
4457 4495 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
4458 4496 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
4459 4497 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
4460 4498 4.717778 TGATACTCCCTCCGTTCCAAAATA 59.282 41.667 0.00 0.00 0.00 1.40
4461 4499 3.521937 TGATACTCCCTCCGTTCCAAAAT 59.478 43.478 0.00 0.00 0.00 1.82
4462 4500 2.907696 TGATACTCCCTCCGTTCCAAAA 59.092 45.455 0.00 0.00 0.00 2.44
4463 4501 2.542550 TGATACTCCCTCCGTTCCAAA 58.457 47.619 0.00 0.00 0.00 3.28
4464 4502 2.241281 TGATACTCCCTCCGTTCCAA 57.759 50.000 0.00 0.00 0.00 3.53
4465 4503 2.471815 ATGATACTCCCTCCGTTCCA 57.528 50.000 0.00 0.00 0.00 3.53
4466 4504 3.840124 AAATGATACTCCCTCCGTTCC 57.160 47.619 0.00 0.00 0.00 3.62
4467 4505 5.753921 CAGTTAAATGATACTCCCTCCGTTC 59.246 44.000 0.00 0.00 0.00 3.95
4468 4506 5.189145 ACAGTTAAATGATACTCCCTCCGTT 59.811 40.000 10.35 0.00 0.00 4.44
4469 4507 4.715297 ACAGTTAAATGATACTCCCTCCGT 59.285 41.667 10.35 0.00 0.00 4.69
4470 4508 5.277857 ACAGTTAAATGATACTCCCTCCG 57.722 43.478 10.35 0.00 0.00 4.63
4471 4509 7.793036 AGTAACAGTTAAATGATACTCCCTCC 58.207 38.462 17.03 0.00 34.72 4.30
4472 4510 8.874744 GAGTAACAGTTAAATGATACTCCCTC 57.125 38.462 28.74 14.43 43.99 4.30
4683 4721 1.407258 GCCAAGTACTGTTTTGCACCA 59.593 47.619 0.00 0.00 0.00 4.17
4832 4870 1.203050 AGCTTGCATAAACCCCAGTGT 60.203 47.619 0.00 0.00 0.00 3.55
4864 4902 2.363038 CACCGATGAATGGCCATGAAAT 59.637 45.455 21.63 13.33 0.00 2.17
4869 4907 0.843309 TACCACCGATGAATGGCCAT 59.157 50.000 14.09 14.09 39.84 4.40
4870 4908 0.621082 TTACCACCGATGAATGGCCA 59.379 50.000 8.56 8.56 39.84 5.36
4956 4994 3.641437 CTCAAAATGCCGAGGAAACAA 57.359 42.857 0.00 0.00 0.00 2.83
5013 5051 6.440647 TGGTATTCATAACCACTGAGTTCTCT 59.559 38.462 1.53 0.00 42.10 3.10
5029 5067 5.588845 TCCAAAATTCCCAGTGGTATTCAT 58.411 37.500 8.74 0.00 31.05 2.57
5201 5239 1.685302 CCGAAAGCACAAATGAACCG 58.315 50.000 0.00 0.00 0.00 4.44
5274 5390 1.641577 AGGTCGCTCTGTAAATTCGC 58.358 50.000 0.00 0.00 0.00 4.70
5288 5404 7.761704 TGATTTTAGAAGAATCTCAGAAGGTCG 59.238 37.037 0.00 0.00 37.10 4.79
5318 6265 4.916183 TGGACATGGTGTATGATTCACAA 58.084 39.130 4.61 0.00 39.21 3.33
5326 6273 9.676861 AAGAATATCATATGGACATGGTGTATG 57.323 33.333 2.13 0.89 42.68 2.39
5358 6305 4.576053 TCAGACCAACATCAGACAAAAGTG 59.424 41.667 0.00 0.00 0.00 3.16
5409 6356 2.840651 TGGCCCTGTTTGGAAAAGAAAA 59.159 40.909 0.00 0.00 38.35 2.29
5530 6482 9.994432 GTAGTCTTGGAATCTTGATGTAATTTG 57.006 33.333 0.00 0.00 0.00 2.32
5541 6493 5.471257 GTCGTTCAGTAGTCTTGGAATCTT 58.529 41.667 0.00 0.00 0.00 2.40
5554 6506 0.169672 GCAGTAGCGGTCGTTCAGTA 59.830 55.000 0.00 0.00 0.00 2.74
5660 6612 2.272146 CCTTAGGGGCACGTGCAT 59.728 61.111 38.60 26.23 44.36 3.96
5680 6632 0.613853 AACTACGGCTCCAGGTGCTA 60.614 55.000 13.24 0.00 0.00 3.49
5684 6636 1.874345 CGACAACTACGGCTCCAGGT 61.874 60.000 0.00 0.00 0.00 4.00
5696 6648 0.182775 AGGGTTCAAAGGCGACAACT 59.817 50.000 0.00 0.00 0.00 3.16
5699 6651 1.314730 GAAAGGGTTCAAAGGCGACA 58.685 50.000 0.00 0.00 33.61 4.35
5717 6669 5.221402 GGTGTCAGATGCTTCAGATCTATGA 60.221 44.000 0.00 0.00 0.00 2.15
5761 6713 0.952010 AGCGGCGGTGTTACGATTTT 60.952 50.000 12.25 0.00 35.47 1.82
5814 6766 0.317160 CCGTCTGGCTGTAGTCAACA 59.683 55.000 0.00 0.00 36.42 3.33


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

AutoCloner maintained by Alex Coulton.