Multiple sequence alignment - TraesCS2D01G489800

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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 TraesCS2D01G489800 chr2D 100.000 3622 0 0 1 3622 588734915 588738536 0.000000e+00 6689.0
1 TraesCS2D01G489800 chr2D 79.277 1134 192 36 1059 2166 588498579 588499695 0.000000e+00 752.0
2 TraesCS2D01G489800 chr2D 82.368 794 102 26 19 789 588497473 588498251 0.000000e+00 656.0
3 TraesCS2D01G489800 chr2D 79.548 841 121 30 1 795 588540145 588540980 1.470000e-153 553.0
4 TraesCS2D01G489800 chr2D 85.612 417 57 2 1085 1501 573952358 573951945 5.550000e-118 435.0
5 TraesCS2D01G489800 chr2D 77.302 467 99 6 1547 2008 573951932 573951468 5.960000e-68 268.0
6 TraesCS2D01G489800 chr2D 79.618 314 53 9 40 344 589188484 589188795 7.880000e-52 215.0
7 TraesCS2D01G489800 chr2D 82.888 187 27 5 2648 2832 39419742 39419559 2.890000e-36 163.0
8 TraesCS2D01G489800 chr2B 92.050 2566 133 36 4 2538 712359137 712361662 0.000000e+00 3542.0
9 TraesCS2D01G489800 chr2B 78.369 1202 222 31 981 2166 712002361 712003540 0.000000e+00 745.0
10 TraesCS2D01G489800 chr2B 81.416 791 117 22 19 789 712001320 712002100 1.430000e-173 619.0
11 TraesCS2D01G489800 chr2B 79.117 929 169 14 1085 2008 689777646 689776738 5.140000e-173 617.0
12 TraesCS2D01G489800 chr2B 84.673 398 53 6 402 795 712076945 712077338 1.220000e-104 390.0
13 TraesCS2D01G489800 chr2B 84.383 397 56 4 401 794 712050588 712050981 5.670000e-103 385.0
14 TraesCS2D01G489800 chr2B 83.920 398 61 1 397 794 712008129 712008523 9.490000e-101 377.0
15 TraesCS2D01G489800 chr2B 79.108 426 78 11 1082 1500 712641974 712642395 2.130000e-72 283.0
16 TraesCS2D01G489800 chr2A 95.249 842 39 1 1730 2571 723512455 723513295 0.000000e+00 1332.0
17 TraesCS2D01G489800 chr2A 92.084 859 31 4 4 855 723511075 723511903 0.000000e+00 1175.0
18 TraesCS2D01G489800 chr2A 96.053 532 19 2 979 1510 723511932 723512461 0.000000e+00 865.0
19 TraesCS2D01G489800 chr2A 78.130 1198 203 47 981 2166 723101387 723102537 0.000000e+00 706.0
20 TraesCS2D01G489800 chr2A 82.828 792 103 25 18 789 723100364 723101142 0.000000e+00 678.0
21 TraesCS2D01G489800 chr2A 86.600 403 51 2 1082 1484 712539266 712538867 3.320000e-120 442.0
22 TraesCS2D01G489800 chr2A 85.112 403 51 7 397 794 723159800 723160198 1.570000e-108 403.0
23 TraesCS2D01G489800 chr2A 84.140 372 53 4 426 794 723133749 723134117 4.450000e-94 355.0
24 TraesCS2D01G489800 chr2A 74.149 793 153 36 39 788 723578351 723579134 7.660000e-72 281.0
25 TraesCS2D01G489800 chr2A 76.790 405 84 10 1613 2012 712538776 712538377 6.090000e-53 219.0
26 TraesCS2D01G489800 chr6B 83.626 513 66 14 3116 3622 716311478 716310978 1.970000e-127 466.0
27 TraesCS2D01G489800 chr6B 90.572 297 26 1 2648 2944 716312083 716311789 3.390000e-105 392.0
28 TraesCS2D01G489800 chr6B 91.463 164 13 1 2959 3121 716311723 716311560 1.310000e-54 224.0
29 TraesCS2D01G489800 chr5D 85.938 320 36 5 3305 3622 534577025 534576713 2.080000e-87 333.0
30 TraesCS2D01G489800 chr5D 82.680 306 47 6 2648 2951 548192215 548191914 2.140000e-67 267.0
31 TraesCS2D01G489800 chr5D 77.778 297 45 16 3113 3393 562711472 562711763 2.890000e-36 163.0
32 TraesCS2D01G489800 chr5D 81.967 183 32 1 2648 2829 534576644 534576826 1.740000e-33 154.0
33 TraesCS2D01G489800 chr4A 86.447 273 34 3 2648 2918 108513745 108514016 2.730000e-76 296.0
34 TraesCS2D01G489800 chr4A 87.273 55 5 2 3542 3595 611978917 611978864 1.090000e-05 62.1
35 TraesCS2D01G489800 chr6D 78.596 285 38 9 3116 3377 389590668 389590384 2.240000e-37 167.0
36 TraesCS2D01G489800 chr3D 83.237 173 29 0 2647 2819 94477291 94477119 3.740000e-35 159.0
37 TraesCS2D01G489800 chr3D 83.333 174 23 6 2644 2813 209674723 209674894 4.840000e-34 156.0
38 TraesCS2D01G489800 chr1B 83.333 174 26 3 2651 2823 636794878 636794707 1.350000e-34 158.0
39 TraesCS2D01G489800 chr1B 80.682 176 24 8 3454 3622 645279151 645279323 1.060000e-25 128.0
40 TraesCS2D01G489800 chr5A 81.868 182 32 1 2648 2828 42679599 42679418 6.260000e-33 152.0
41 TraesCS2D01G489800 chr7A 86.957 115 14 1 3506 3620 403189225 403189338 1.060000e-25 128.0
42 TraesCS2D01G489800 chr7A 76.404 267 39 15 3113 3356 488030849 488031114 4.910000e-24 122.0
43 TraesCS2D01G489800 chr1A 80.576 139 26 1 3481 3619 570235493 570235630 4.950000e-19 106.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G489800 chr2D 588734915 588738536 3621 False 6689.000000 6689 100.000000 1 3622 1 chr2D.!!$F2 3621
1 TraesCS2D01G489800 chr2D 588497473 588499695 2222 False 704.000000 752 80.822500 19 2166 2 chr2D.!!$F4 2147
2 TraesCS2D01G489800 chr2D 588540145 588540980 835 False 553.000000 553 79.548000 1 795 1 chr2D.!!$F1 794
3 TraesCS2D01G489800 chr2D 573951468 573952358 890 True 351.500000 435 81.457000 1085 2008 2 chr2D.!!$R2 923
4 TraesCS2D01G489800 chr2B 712359137 712361662 2525 False 3542.000000 3542 92.050000 4 2538 1 chr2B.!!$F4 2534
5 TraesCS2D01G489800 chr2B 712001320 712003540 2220 False 682.000000 745 79.892500 19 2166 2 chr2B.!!$F6 2147
6 TraesCS2D01G489800 chr2B 689776738 689777646 908 True 617.000000 617 79.117000 1085 2008 1 chr2B.!!$R1 923
7 TraesCS2D01G489800 chr2A 723511075 723513295 2220 False 1124.000000 1332 94.462000 4 2571 3 chr2A.!!$F5 2567
8 TraesCS2D01G489800 chr2A 723100364 723102537 2173 False 692.000000 706 80.479000 18 2166 2 chr2A.!!$F4 2148
9 TraesCS2D01G489800 chr2A 712538377 712539266 889 True 330.500000 442 81.695000 1082 2012 2 chr2A.!!$R1 930
10 TraesCS2D01G489800 chr2A 723578351 723579134 783 False 281.000000 281 74.149000 39 788 1 chr2A.!!$F3 749
11 TraesCS2D01G489800 chr6B 716310978 716312083 1105 True 360.666667 466 88.553667 2648 3622 3 chr6B.!!$R1 974

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
951 1107 0.455005 GCTCGTTTAGTCGGTAGCCT 59.545 55.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2829 3062 0.246635 AACGCCATCTAACGTGAGCT 59.753 50.0 0.0 0.0 42.68 4.09 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 172 2.883253 GAGCTCCTTGACGCTCGC 60.883 66.667 0.87 0.00 42.62 5.03
856 993 4.193826 TCTCGATGCCTGCCTATTTATC 57.806 45.455 0.00 0.00 0.00 1.75
863 1000 3.256879 TGCCTGCCTATTTATCTCTCTCG 59.743 47.826 0.00 0.00 0.00 4.04
870 1007 6.653740 TGCCTATTTATCTCTCTCGTCGATAA 59.346 38.462 0.00 0.00 0.00 1.75
878 1015 5.426504 TCTCTCTCGTCGATAAGTTAACCT 58.573 41.667 0.88 0.00 0.00 3.50
881 1018 7.009568 TCTCTCGTCGATAAGTTAACCTAAC 57.990 40.000 0.88 0.00 38.94 2.34
882 1019 6.595326 TCTCTCGTCGATAAGTTAACCTAACA 59.405 38.462 0.88 0.00 41.07 2.41
883 1020 7.119699 TCTCTCGTCGATAAGTTAACCTAACAA 59.880 37.037 0.88 0.00 41.07 2.83
886 1023 8.176814 TCGTCGATAAGTTAACCTAACAATTG 57.823 34.615 3.24 3.24 41.07 2.32
888 1025 9.075519 CGTCGATAAGTTAACCTAACAATTGTA 57.924 33.333 12.39 0.00 41.07 2.41
915 1071 4.091509 CGATTCTTAAGTCGGTTCCAACTG 59.908 45.833 1.63 0.00 34.39 3.16
949 1105 1.469912 GCGCTCGTTTAGTCGGTAGC 61.470 60.000 0.00 0.00 0.00 3.58
951 1107 0.455005 GCTCGTTTAGTCGGTAGCCT 59.545 55.000 0.00 0.00 0.00 4.58
952 1108 1.135170 GCTCGTTTAGTCGGTAGCCTT 60.135 52.381 0.00 0.00 0.00 4.35
954 1110 2.422832 CTCGTTTAGTCGGTAGCCTTCT 59.577 50.000 0.00 0.00 0.00 2.85
956 1112 4.009675 TCGTTTAGTCGGTAGCCTTCTTA 58.990 43.478 0.00 0.00 0.00 2.10
957 1113 4.641989 TCGTTTAGTCGGTAGCCTTCTTAT 59.358 41.667 0.00 0.00 0.00 1.73
958 1114 4.974888 CGTTTAGTCGGTAGCCTTCTTATC 59.025 45.833 0.00 0.00 0.00 1.75
959 1115 5.221009 CGTTTAGTCGGTAGCCTTCTTATCT 60.221 44.000 0.00 0.00 0.00 1.98
960 1116 6.017605 CGTTTAGTCGGTAGCCTTCTTATCTA 60.018 42.308 0.00 0.00 0.00 1.98
961 1117 6.874288 TTAGTCGGTAGCCTTCTTATCTAC 57.126 41.667 0.00 0.00 33.72 2.59
962 1118 3.814283 AGTCGGTAGCCTTCTTATCTACG 59.186 47.826 0.00 0.00 34.92 3.51
963 1119 3.058363 GTCGGTAGCCTTCTTATCTACGG 60.058 52.174 0.00 0.00 34.92 4.02
964 1120 3.144506 CGGTAGCCTTCTTATCTACGGA 58.855 50.000 0.00 0.00 36.41 4.69
965 1121 3.188873 CGGTAGCCTTCTTATCTACGGAG 59.811 52.174 0.00 0.00 36.41 4.63
967 1123 5.312079 GGTAGCCTTCTTATCTACGGAGTA 58.688 45.833 0.00 0.00 45.11 2.59
1387 1593 4.771356 TCCGCTTCGCCTTCGACG 62.771 66.667 0.00 0.00 45.43 5.12
1550 1768 1.205893 CGAGGAAGAAGAAGAGGTGGG 59.794 57.143 0.00 0.00 0.00 4.61
1608 1829 1.292541 GAAGTGGAGACCGTGGTCC 59.707 63.158 15.28 7.13 45.59 4.46
1686 1907 1.895707 CTGCCGGATGAATCTGCCC 60.896 63.158 5.05 0.00 31.76 5.36
1716 1937 2.202492 CTGCCGTTCCTCGAGACG 60.202 66.667 15.71 16.59 42.86 4.18
1781 2002 2.813901 GCTGATCTCGAGCTGCCT 59.186 61.111 7.81 0.00 35.98 4.75
1880 2101 3.506096 CATCCGCTGCTGCCACAG 61.506 66.667 10.24 0.00 40.80 3.66
2022 2243 3.241530 TGCCAAGCACCGTCCTCT 61.242 61.111 0.00 0.00 31.71 3.69
2026 2247 1.668294 CAAGCACCGTCCTCTGAGT 59.332 57.895 3.66 0.00 0.00 3.41
2028 2249 0.827925 AAGCACCGTCCTCTGAGTCA 60.828 55.000 3.66 0.00 0.00 3.41
2046 2279 3.470567 GAGCGCGACAGGTTCACG 61.471 66.667 12.10 0.00 32.66 4.35
2172 2405 2.434884 GCGCTGCAAGGTGCTCTA 60.435 61.111 0.00 0.00 45.31 2.43
2186 2419 3.214250 CTCTACTGATCCCCGGCGC 62.214 68.421 0.00 0.00 0.00 6.53
2248 2481 0.390866 CACGCTGCTCATGGAGTTCT 60.391 55.000 0.00 0.00 33.91 3.01
2340 2573 4.946157 GTGAAGGAGATCAACATGGTTCAT 59.054 41.667 0.00 0.00 0.00 2.57
2452 2685 1.058748 CCGTTCGCGTTGCAGTATG 59.941 57.895 5.77 0.00 39.32 2.39
2526 2759 2.554370 TCCTTTGATCGGTCGGTTTT 57.446 45.000 0.00 0.00 0.00 2.43
2528 2761 1.877443 CCTTTGATCGGTCGGTTTTGT 59.123 47.619 0.00 0.00 0.00 2.83
2538 2771 3.002965 CGGTCGGTTTTGTTTTAGCTTCT 59.997 43.478 0.00 0.00 0.00 2.85
2555 2788 4.214971 AGCTTCTATGGAATAATTGCGCTG 59.785 41.667 9.73 0.00 0.00 5.18
2559 2792 3.904136 ATGGAATAATTGCGCTGTAGC 57.096 42.857 9.73 0.00 37.78 3.58
2571 2804 2.613696 TGTAGCCCCATGCCCACT 60.614 61.111 0.00 0.00 42.71 4.00
2572 2805 2.215451 CTGTAGCCCCATGCCCACTT 62.215 60.000 0.00 0.00 42.71 3.16
2573 2806 1.000359 GTAGCCCCATGCCCACTTT 60.000 57.895 0.00 0.00 42.71 2.66
2574 2807 0.257616 GTAGCCCCATGCCCACTTTA 59.742 55.000 0.00 0.00 42.71 1.85
2575 2808 1.133482 GTAGCCCCATGCCCACTTTAT 60.133 52.381 0.00 0.00 42.71 1.40
2576 2809 0.397535 AGCCCCATGCCCACTTTATG 60.398 55.000 0.00 0.00 42.71 1.90
2577 2810 0.687427 GCCCCATGCCCACTTTATGT 60.687 55.000 0.00 0.00 0.00 2.29
2578 2811 1.113788 CCCCATGCCCACTTTATGTG 58.886 55.000 0.00 0.00 45.80 3.21
2579 2812 1.619432 CCCCATGCCCACTTTATGTGT 60.619 52.381 0.00 0.00 44.81 3.72
2580 2813 2.178580 CCCATGCCCACTTTATGTGTT 58.821 47.619 0.00 0.00 44.81 3.32
2581 2814 2.094078 CCCATGCCCACTTTATGTGTTG 60.094 50.000 0.00 0.00 44.81 3.33
2582 2815 2.609350 CATGCCCACTTTATGTGTTGC 58.391 47.619 0.00 1.36 44.81 4.17
2583 2816 0.965439 TGCCCACTTTATGTGTTGCC 59.035 50.000 7.25 0.00 44.81 4.52
2584 2817 0.109319 GCCCACTTTATGTGTTGCCG 60.109 55.000 0.00 0.00 44.81 5.69
2585 2818 1.529226 CCCACTTTATGTGTTGCCGA 58.471 50.000 0.00 0.00 44.81 5.54
2586 2819 1.468520 CCCACTTTATGTGTTGCCGAG 59.531 52.381 0.00 0.00 44.81 4.63
2587 2820 2.422597 CCACTTTATGTGTTGCCGAGA 58.577 47.619 0.00 0.00 44.81 4.04
2588 2821 2.811431 CCACTTTATGTGTTGCCGAGAA 59.189 45.455 0.00 0.00 44.81 2.87
2589 2822 3.252215 CCACTTTATGTGTTGCCGAGAAA 59.748 43.478 0.00 0.00 44.81 2.52
2590 2823 4.082787 CCACTTTATGTGTTGCCGAGAAAT 60.083 41.667 0.00 0.00 44.81 2.17
2591 2824 5.460646 CACTTTATGTGTTGCCGAGAAATT 58.539 37.500 0.00 0.00 41.53 1.82
2592 2825 5.343058 CACTTTATGTGTTGCCGAGAAATTG 59.657 40.000 0.00 0.00 41.53 2.32
2593 2826 2.352503 ATGTGTTGCCGAGAAATTGC 57.647 45.000 0.00 0.00 0.00 3.56
2594 2827 1.317613 TGTGTTGCCGAGAAATTGCT 58.682 45.000 0.00 0.00 0.00 3.91
2595 2828 1.680735 TGTGTTGCCGAGAAATTGCTT 59.319 42.857 0.00 0.00 0.00 3.91
2596 2829 2.100584 TGTGTTGCCGAGAAATTGCTTT 59.899 40.909 0.00 0.00 0.00 3.51
2597 2830 3.123050 GTGTTGCCGAGAAATTGCTTTT 58.877 40.909 0.00 0.00 0.00 2.27
2598 2831 3.060339 GTGTTGCCGAGAAATTGCTTTTG 60.060 43.478 0.00 0.00 0.00 2.44
2599 2832 2.437200 TGCCGAGAAATTGCTTTTGG 57.563 45.000 0.00 0.00 0.00 3.28
2600 2833 1.686052 TGCCGAGAAATTGCTTTTGGT 59.314 42.857 0.00 0.00 0.00 3.67
2601 2834 2.102252 TGCCGAGAAATTGCTTTTGGTT 59.898 40.909 0.00 0.00 0.00 3.67
2602 2835 3.319405 TGCCGAGAAATTGCTTTTGGTTA 59.681 39.130 0.00 0.00 0.00 2.85
2603 2836 4.202161 TGCCGAGAAATTGCTTTTGGTTAA 60.202 37.500 0.00 0.00 0.00 2.01
2604 2837 4.929211 GCCGAGAAATTGCTTTTGGTTAAT 59.071 37.500 0.00 0.00 0.00 1.40
2605 2838 6.096695 GCCGAGAAATTGCTTTTGGTTAATA 58.903 36.000 0.00 0.00 0.00 0.98
2606 2839 6.588373 GCCGAGAAATTGCTTTTGGTTAATAA 59.412 34.615 0.00 0.00 0.00 1.40
2607 2840 7.117092 GCCGAGAAATTGCTTTTGGTTAATAAA 59.883 33.333 0.00 0.00 0.00 1.40
2608 2841 8.983724 CCGAGAAATTGCTTTTGGTTAATAAAA 58.016 29.630 0.00 2.08 0.00 1.52
2614 2847 8.972458 ATTGCTTTTGGTTAATAAAAACAGGT 57.028 26.923 0.00 0.00 28.55 4.00
2615 2848 8.794335 TTGCTTTTGGTTAATAAAAACAGGTT 57.206 26.923 0.00 0.00 28.55 3.50
2616 2849 8.426881 TGCTTTTGGTTAATAAAAACAGGTTC 57.573 30.769 0.00 0.00 0.00 3.62
2617 2850 7.222999 TGCTTTTGGTTAATAAAAACAGGTTCG 59.777 33.333 0.00 0.00 0.00 3.95
2618 2851 7.306925 GCTTTTGGTTAATAAAAACAGGTTCGG 60.307 37.037 3.29 0.00 0.00 4.30
2619 2852 6.712179 TTGGTTAATAAAAACAGGTTCGGT 57.288 33.333 0.00 0.00 0.00 4.69
2620 2853 6.712179 TGGTTAATAAAAACAGGTTCGGTT 57.288 33.333 0.00 0.00 0.00 4.44
2621 2854 6.505272 TGGTTAATAAAAACAGGTTCGGTTG 58.495 36.000 0.00 0.00 0.00 3.77
2622 2855 6.096564 TGGTTAATAAAAACAGGTTCGGTTGT 59.903 34.615 0.00 0.00 0.00 3.32
2623 2856 6.418523 GGTTAATAAAAACAGGTTCGGTTGTG 59.581 38.462 0.00 0.00 0.00 3.33
2624 2857 5.838531 AATAAAAACAGGTTCGGTTGTGA 57.161 34.783 0.00 0.00 0.00 3.58
2625 2858 6.399639 AATAAAAACAGGTTCGGTTGTGAT 57.600 33.333 0.00 0.00 0.00 3.06
2626 2859 7.513371 AATAAAAACAGGTTCGGTTGTGATA 57.487 32.000 0.00 0.00 0.00 2.15
2627 2860 7.696992 ATAAAAACAGGTTCGGTTGTGATAT 57.303 32.000 0.00 0.00 0.00 1.63
2628 2861 5.371115 AAAACAGGTTCGGTTGTGATATG 57.629 39.130 0.00 0.00 0.00 1.78
2629 2862 3.973206 ACAGGTTCGGTTGTGATATGA 57.027 42.857 0.00 0.00 0.00 2.15
2630 2863 3.861840 ACAGGTTCGGTTGTGATATGAG 58.138 45.455 0.00 0.00 0.00 2.90
2631 2864 3.260884 ACAGGTTCGGTTGTGATATGAGT 59.739 43.478 0.00 0.00 0.00 3.41
2632 2865 4.253685 CAGGTTCGGTTGTGATATGAGTT 58.746 43.478 0.00 0.00 0.00 3.01
2633 2866 4.695455 CAGGTTCGGTTGTGATATGAGTTT 59.305 41.667 0.00 0.00 0.00 2.66
2634 2867 5.181245 CAGGTTCGGTTGTGATATGAGTTTT 59.819 40.000 0.00 0.00 0.00 2.43
2635 2868 6.370442 CAGGTTCGGTTGTGATATGAGTTTTA 59.630 38.462 0.00 0.00 0.00 1.52
2636 2869 6.370718 AGGTTCGGTTGTGATATGAGTTTTAC 59.629 38.462 0.00 0.00 0.00 2.01
2637 2870 6.148150 GGTTCGGTTGTGATATGAGTTTTACA 59.852 38.462 0.00 0.00 0.00 2.41
2638 2871 6.715344 TCGGTTGTGATATGAGTTTTACAC 57.285 37.500 0.00 0.00 0.00 2.90
2639 2872 6.224584 TCGGTTGTGATATGAGTTTTACACA 58.775 36.000 0.00 0.00 36.66 3.72
2640 2873 6.876789 TCGGTTGTGATATGAGTTTTACACAT 59.123 34.615 0.00 0.00 37.91 3.21
2641 2874 7.389330 TCGGTTGTGATATGAGTTTTACACATT 59.611 33.333 0.00 0.00 37.91 2.71
2642 2875 8.661257 CGGTTGTGATATGAGTTTTACACATTA 58.339 33.333 0.00 0.00 37.91 1.90
2658 2891 9.715123 TTTACACATTATATTGAGTGAATTGCG 57.285 29.630 7.65 0.00 35.97 4.85
2682 2915 2.418368 ACCACCACATTGACGCATAT 57.582 45.000 0.00 0.00 0.00 1.78
2690 2923 3.544682 CACATTGACGCATATGTTTGCAG 59.455 43.478 4.29 0.00 42.91 4.41
2705 2938 5.121071 GTTTGCAGAAAACAACGGTTTAC 57.879 39.130 0.00 0.00 46.20 2.01
2706 2939 4.436242 TTGCAGAAAACAACGGTTTACA 57.564 36.364 0.00 0.00 46.20 2.41
2722 2955 7.382898 ACGGTTTACAAATTTATGGCAGAAAT 58.617 30.769 13.98 13.98 0.00 2.17
2727 2960 8.984891 TTACAAATTTATGGCAGAAATCACTG 57.015 30.769 19.31 17.53 40.43 3.66
2741 2974 6.259608 CAGAAATCACTGATTCTCGGCTTAAT 59.740 38.462 4.70 0.00 39.94 1.40
2774 3007 5.432885 AAACACTAACTGATCGTTTTGGG 57.567 39.130 7.96 6.21 37.05 4.12
2786 3019 4.674281 TCGTTTTGGGCATTTTAACCTT 57.326 36.364 0.00 0.00 0.00 3.50
2802 3035 7.403312 TTTAACCTTGATTATGACATGTGGG 57.597 36.000 1.15 0.00 0.00 4.61
2804 3037 3.527253 ACCTTGATTATGACATGTGGGGA 59.473 43.478 1.15 0.00 0.00 4.81
2823 3056 1.326548 GACCGTATTTGATGACGTGGC 59.673 52.381 0.00 0.00 37.36 5.01
2828 3061 3.540744 CGTATTTGATGACGTGGCGTAAC 60.541 47.826 0.00 0.00 41.37 2.50
2829 3062 1.867166 TTTGATGACGTGGCGTAACA 58.133 45.000 0.00 0.00 41.37 2.41
2834 3067 1.372499 GACGTGGCGTAACAGCTCA 60.372 57.895 0.00 0.00 41.37 4.26
2864 3097 7.224297 AGATGGCGTTTGGTCTAATATTACAT 58.776 34.615 0.00 0.00 0.00 2.29
2923 3156 7.209471 ACCATAAAGTGAAAACGCAATTAGA 57.791 32.000 0.00 0.00 0.00 2.10
2928 3161 4.079253 AGTGAAAACGCAATTAGACCCAT 58.921 39.130 0.00 0.00 0.00 4.00
2929 3162 4.082787 AGTGAAAACGCAATTAGACCCATG 60.083 41.667 0.00 0.00 0.00 3.66
2932 3165 1.094785 ACGCAATTAGACCCATGTGC 58.905 50.000 0.00 0.00 0.00 4.57
2935 3168 1.202177 GCAATTAGACCCATGTGCACG 60.202 52.381 13.13 0.00 32.29 5.34
2944 3177 1.302431 CATGTGCACGGAACCTCCA 60.302 57.895 13.13 0.00 35.91 3.86
2945 3178 0.888736 CATGTGCACGGAACCTCCAA 60.889 55.000 13.13 0.00 35.91 3.53
2948 3181 1.525077 TGCACGGAACCTCCAACAC 60.525 57.895 0.00 0.00 35.91 3.32
2951 3184 2.424302 CGGAACCTCCAACACGGT 59.576 61.111 0.00 0.00 35.91 4.83
2956 3189 3.953775 CCTCCAACACGGTGGGCT 61.954 66.667 13.48 0.00 43.69 5.19
2957 3190 2.358737 CTCCAACACGGTGGGCTC 60.359 66.667 13.48 0.00 39.34 4.70
3047 3331 4.749310 CCTGCAGCGAAGGCGAGT 62.749 66.667 8.66 0.00 46.35 4.18
3048 3332 2.181777 CTGCAGCGAAGGCGAGTA 59.818 61.111 0.00 0.00 46.35 2.59
3126 3498 4.541020 GCTCCACGCTGCTTTTTC 57.459 55.556 0.00 0.00 35.14 2.29
3141 3513 4.689549 TTCTCTCGGCCACGGGGA 62.690 66.667 8.67 0.00 42.10 4.81
3161 3533 1.520342 GGACATGACCTGCTCGAGC 60.520 63.158 30.42 30.42 42.50 5.03
3172 3544 4.363990 CTCGAGCACCACGGCAGT 62.364 66.667 0.00 0.00 35.83 4.40
3185 3557 3.986006 GCAGTGGACGTGGTCGGA 61.986 66.667 0.00 0.00 41.85 4.55
3186 3558 2.049433 CAGTGGACGTGGTCGGAC 60.049 66.667 0.00 0.00 41.85 4.79
3187 3559 3.300765 AGTGGACGTGGTCGGACC 61.301 66.667 20.36 20.36 41.85 4.46
3188 3560 4.712425 GTGGACGTGGTCGGACCG 62.712 72.222 21.52 7.84 42.58 4.79
3189 3561 4.953010 TGGACGTGGTCGGACCGA 62.953 66.667 21.52 13.88 42.58 4.69
3212 3584 3.391382 CCTTCCGTCCTTCGCCCT 61.391 66.667 0.00 0.00 38.35 5.19
3365 3753 2.280552 CCGGGAGAACGAGGGACAA 61.281 63.158 0.00 0.00 35.47 3.18
3374 3762 3.134081 AGAACGAGGGACAAAGAAGAACA 59.866 43.478 0.00 0.00 0.00 3.18
3377 3765 3.118371 ACGAGGGACAAAGAAGAACAAGT 60.118 43.478 0.00 0.00 0.00 3.16
3386 3774 2.519013 AGAAGAACAAGTTGGGCATCC 58.481 47.619 7.96 0.00 0.00 3.51
3390 3778 2.170166 GAACAAGTTGGGCATCCATCA 58.830 47.619 7.96 0.00 43.63 3.07
3401 3789 4.266962 TCCATCAGGAGCGAGAGG 57.733 61.111 0.00 0.00 39.61 3.69
3430 3818 4.182744 CGATCCGGATCAGGGAGT 57.817 61.111 36.89 7.50 36.91 3.85
3435 3823 0.106469 TCCGGATCAGGGAGTGAGAG 60.106 60.000 12.28 0.00 39.07 3.20
3436 3824 1.112315 CCGGATCAGGGAGTGAGAGG 61.112 65.000 3.59 0.00 39.07 3.69
3437 3825 1.112315 CGGATCAGGGAGTGAGAGGG 61.112 65.000 0.00 0.00 39.07 4.30
3438 3826 0.263172 GGATCAGGGAGTGAGAGGGA 59.737 60.000 0.00 0.00 39.07 4.20
3439 3827 1.132881 GGATCAGGGAGTGAGAGGGAT 60.133 57.143 0.00 0.00 39.07 3.85
3440 3828 2.688477 GATCAGGGAGTGAGAGGGATT 58.312 52.381 0.00 0.00 39.07 3.01
3441 3829 3.438668 GGATCAGGGAGTGAGAGGGATTA 60.439 52.174 0.00 0.00 39.07 1.75
3442 3830 3.776731 TCAGGGAGTGAGAGGGATTAA 57.223 47.619 0.00 0.00 0.00 1.40
3443 3831 4.286813 TCAGGGAGTGAGAGGGATTAAT 57.713 45.455 0.00 0.00 0.00 1.40
3444 3832 4.227197 TCAGGGAGTGAGAGGGATTAATC 58.773 47.826 6.93 6.93 0.00 1.75
3445 3833 3.006323 CAGGGAGTGAGAGGGATTAATCG 59.994 52.174 9.32 0.00 0.00 3.34
3455 3843 9.110502 GTGAGAGGGATTAATCGTTTTTAGAAT 57.889 33.333 9.32 0.00 0.00 2.40
3459 3847 7.351166 AGGGATTAATCGTTTTTAGAATGGGA 58.649 34.615 9.32 0.00 0.00 4.37
3492 3880 4.237724 GGCAAAAAGACCTTGTCTAATGC 58.762 43.478 15.01 15.01 42.59 3.56
3502 3890 4.634443 ACCTTGTCTAATGCCGTTTATCAC 59.366 41.667 0.00 0.00 0.00 3.06
3523 3911 1.296056 AACCGTTACGCCACATCAGC 61.296 55.000 0.00 0.00 0.00 4.26
3551 3939 2.733552 CGGGCTTCATCTGTCATAATCG 59.266 50.000 0.00 0.00 0.00 3.34
3557 3945 5.693555 GCTTCATCTGTCATAATCGTCATCA 59.306 40.000 0.00 0.00 0.00 3.07
3563 3951 5.290885 TCTGTCATAATCGTCATCAAAACGG 59.709 40.000 0.00 0.00 40.45 4.44
3569 3957 8.547894 TCATAATCGTCATCAAAACGGATAAAG 58.452 33.333 0.00 0.00 40.45 1.85
3572 3960 3.126171 CGTCATCAAAACGGATAAAGCCA 59.874 43.478 0.00 0.00 36.51 4.75
3577 3965 5.054390 TCAAAACGGATAAAGCCATCAAC 57.946 39.130 0.00 0.00 0.00 3.18
3584 3972 4.876107 CGGATAAAGCCATCAACTAGTGTT 59.124 41.667 0.00 0.00 36.75 3.32
3610 3998 9.513727 TTTTTGCAAAAGATTAAGCCAAAAATC 57.486 25.926 22.78 0.00 31.45 2.17
3614 4002 7.041916 TGCAAAAGATTAAGCCAAAAATCAGTG 60.042 33.333 0.00 0.00 35.07 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 8 0.861866 CGTTCATCGTCGTCGCAGAT 60.862 55.000 0.00 0.00 34.70 2.90
170 172 4.803426 GCCGACCTGAGGAGTGCG 62.803 72.222 4.99 3.10 0.00 5.34
359 374 2.359848 CGATTCCTGGATGTACACCGTA 59.640 50.000 0.00 0.00 0.00 4.02
431 497 2.348685 CGACATCGATCTCAGGTACGAC 60.349 54.545 0.00 0.00 43.02 4.34
856 993 5.738118 AGGTTAACTTATCGACGAGAGAG 57.262 43.478 15.47 9.79 0.00 3.20
870 1007 9.933723 AATCGTAGTACAATTGTTAGGTTAACT 57.066 29.630 17.78 14.00 39.38 2.24
881 1018 7.487189 ACCGACTTAAGAATCGTAGTACAATTG 59.513 37.037 10.09 3.24 36.60 2.32
882 1019 7.542025 ACCGACTTAAGAATCGTAGTACAATT 58.458 34.615 10.09 0.00 36.60 2.32
883 1020 7.093322 ACCGACTTAAGAATCGTAGTACAAT 57.907 36.000 10.09 0.00 36.60 2.71
886 1023 5.968261 GGAACCGACTTAAGAATCGTAGTAC 59.032 44.000 10.09 0.00 36.60 2.73
888 1025 4.460382 TGGAACCGACTTAAGAATCGTAGT 59.540 41.667 10.09 0.95 36.60 2.73
889 1026 4.990257 TGGAACCGACTTAAGAATCGTAG 58.010 43.478 10.09 0.34 36.60 3.51
891 1028 3.947910 TGGAACCGACTTAAGAATCGT 57.052 42.857 10.09 0.00 36.60 3.73
956 1112 9.642327 CTGCGACTATATATATACTCCGTAGAT 57.358 37.037 17.22 0.00 0.00 1.98
957 1113 8.854117 TCTGCGACTATATATATACTCCGTAGA 58.146 37.037 18.97 18.97 0.00 2.59
958 1114 9.642327 ATCTGCGACTATATATATACTCCGTAG 57.358 37.037 16.62 16.62 0.00 3.51
959 1115 9.636879 GATCTGCGACTATATATATACTCCGTA 57.363 37.037 0.00 2.54 0.00 4.02
960 1116 7.328982 CGATCTGCGACTATATATATACTCCGT 59.671 40.741 0.00 0.00 44.57 4.69
961 1117 7.541437 TCGATCTGCGACTATATATATACTCCG 59.459 40.741 0.00 4.42 45.59 4.63
962 1118 8.760103 TCGATCTGCGACTATATATATACTCC 57.240 38.462 0.00 0.00 45.59 3.85
1387 1593 1.961277 CGTTCCAGTGGTGGCAGTC 60.961 63.158 9.54 0.00 44.60 3.51
1513 1722 4.944372 GCCCCCGTAGCGATCACG 62.944 72.222 0.00 0.00 42.93 4.35
1520 1732 4.222847 CTTCCTCGCCCCCGTAGC 62.223 72.222 0.00 0.00 35.54 3.58
1581 1799 0.246910 GTCTCCACTTCCTCCGTTCC 59.753 60.000 0.00 0.00 0.00 3.62
1585 1803 1.977544 ACGGTCTCCACTTCCTCCG 60.978 63.158 0.00 0.00 42.94 4.63
1686 1907 2.811317 GGCAGCTCGACGGTCTTG 60.811 66.667 6.57 0.00 0.00 3.02
1781 2002 4.710167 TCAGGTCGACGAGGCGGA 62.710 66.667 9.92 0.00 0.00 5.54
1880 2101 2.579684 GATGTGGACGGTCCTCAGGC 62.580 65.000 29.11 21.64 42.50 4.85
2022 2243 2.563427 CTGTCGCGCTCTGACTCA 59.437 61.111 5.56 0.00 37.26 3.41
2026 2247 2.258591 GAACCTGTCGCGCTCTGA 59.741 61.111 5.56 0.00 0.00 3.27
2028 2249 2.049063 GTGAACCTGTCGCGCTCT 60.049 61.111 5.56 0.00 0.00 4.09
2033 2254 1.282930 GAACCTCGTGAACCTGTCGC 61.283 60.000 0.00 0.00 0.00 5.19
2046 2279 4.740334 GCAGAGATCTTCTCCATGAACCTC 60.740 50.000 0.00 0.00 44.42 3.85
2340 2573 1.078497 CAGCGCATCACCCTGGTAA 60.078 57.895 11.47 0.00 0.00 2.85
2403 2636 1.869574 CACGACGCACATCCTCTCG 60.870 63.158 0.00 0.00 0.00 4.04
2452 2685 1.115467 TCGATCTCCTTCTTGAGCCC 58.885 55.000 0.00 0.00 32.22 5.19
2518 2751 6.072893 TCCATAGAAGCTAAAACAAAACCGAC 60.073 38.462 0.00 0.00 0.00 4.79
2526 2759 8.128582 CGCAATTATTCCATAGAAGCTAAAACA 58.871 33.333 0.00 0.00 34.86 2.83
2528 2761 7.013274 AGCGCAATTATTCCATAGAAGCTAAAA 59.987 33.333 11.47 0.00 34.86 1.52
2538 2771 3.751175 GGCTACAGCGCAATTATTCCATA 59.249 43.478 11.47 0.00 43.26 2.74
2559 2792 1.113788 CACATAAAGTGGGCATGGGG 58.886 55.000 0.00 0.00 44.69 4.96
2571 2804 4.022416 AGCAATTTCTCGGCAACACATAAA 60.022 37.500 0.00 0.00 0.00 1.40
2572 2805 3.505680 AGCAATTTCTCGGCAACACATAA 59.494 39.130 0.00 0.00 0.00 1.90
2573 2806 3.081061 AGCAATTTCTCGGCAACACATA 58.919 40.909 0.00 0.00 0.00 2.29
2574 2807 1.888512 AGCAATTTCTCGGCAACACAT 59.111 42.857 0.00 0.00 0.00 3.21
2575 2808 1.317613 AGCAATTTCTCGGCAACACA 58.682 45.000 0.00 0.00 0.00 3.72
2576 2809 2.422276 AAGCAATTTCTCGGCAACAC 57.578 45.000 0.00 0.00 0.00 3.32
2577 2810 3.122297 CAAAAGCAATTTCTCGGCAACA 58.878 40.909 0.00 0.00 0.00 3.33
2578 2811 2.476241 CCAAAAGCAATTTCTCGGCAAC 59.524 45.455 0.00 0.00 0.00 4.17
2579 2812 2.102252 ACCAAAAGCAATTTCTCGGCAA 59.898 40.909 0.00 0.00 0.00 4.52
2580 2813 1.686052 ACCAAAAGCAATTTCTCGGCA 59.314 42.857 0.00 0.00 0.00 5.69
2581 2814 2.438868 ACCAAAAGCAATTTCTCGGC 57.561 45.000 0.00 0.00 0.00 5.54
2582 2815 8.527567 TTTATTAACCAAAAGCAATTTCTCGG 57.472 30.769 0.00 0.00 0.00 4.63
2588 2821 9.402320 ACCTGTTTTTATTAACCAAAAGCAATT 57.598 25.926 11.95 3.51 36.22 2.32
2589 2822 8.972458 ACCTGTTTTTATTAACCAAAAGCAAT 57.028 26.923 11.95 4.58 36.22 3.56
2590 2823 8.794335 AACCTGTTTTTATTAACCAAAAGCAA 57.206 26.923 11.95 1.98 36.22 3.91
2591 2824 7.222999 CGAACCTGTTTTTATTAACCAAAAGCA 59.777 33.333 10.95 10.95 35.61 3.91
2592 2825 7.306925 CCGAACCTGTTTTTATTAACCAAAAGC 60.307 37.037 0.00 4.81 0.00 3.51
2593 2826 7.707464 ACCGAACCTGTTTTTATTAACCAAAAG 59.293 33.333 0.00 0.00 0.00 2.27
2594 2827 7.554211 ACCGAACCTGTTTTTATTAACCAAAA 58.446 30.769 0.00 0.00 0.00 2.44
2595 2828 7.110043 ACCGAACCTGTTTTTATTAACCAAA 57.890 32.000 0.00 0.00 0.00 3.28
2596 2829 6.712179 ACCGAACCTGTTTTTATTAACCAA 57.288 33.333 0.00 0.00 0.00 3.67
2597 2830 6.096564 ACAACCGAACCTGTTTTTATTAACCA 59.903 34.615 0.00 0.00 0.00 3.67
2598 2831 6.418523 CACAACCGAACCTGTTTTTATTAACC 59.581 38.462 0.00 0.00 0.00 2.85
2599 2832 7.194962 TCACAACCGAACCTGTTTTTATTAAC 58.805 34.615 0.00 0.00 0.00 2.01
2600 2833 7.330900 TCACAACCGAACCTGTTTTTATTAA 57.669 32.000 0.00 0.00 0.00 1.40
2601 2834 6.939132 TCACAACCGAACCTGTTTTTATTA 57.061 33.333 0.00 0.00 0.00 0.98
2602 2835 5.838531 TCACAACCGAACCTGTTTTTATT 57.161 34.783 0.00 0.00 0.00 1.40
2603 2836 7.392113 TCATATCACAACCGAACCTGTTTTTAT 59.608 33.333 0.00 0.00 0.00 1.40
2604 2837 6.711194 TCATATCACAACCGAACCTGTTTTTA 59.289 34.615 0.00 0.00 0.00 1.52
2605 2838 5.533154 TCATATCACAACCGAACCTGTTTTT 59.467 36.000 0.00 0.00 0.00 1.94
2606 2839 5.067273 TCATATCACAACCGAACCTGTTTT 58.933 37.500 0.00 0.00 0.00 2.43
2607 2840 4.647611 TCATATCACAACCGAACCTGTTT 58.352 39.130 0.00 0.00 0.00 2.83
2608 2841 4.253685 CTCATATCACAACCGAACCTGTT 58.746 43.478 0.00 0.00 0.00 3.16
2609 2842 3.260884 ACTCATATCACAACCGAACCTGT 59.739 43.478 0.00 0.00 0.00 4.00
2610 2843 3.861840 ACTCATATCACAACCGAACCTG 58.138 45.455 0.00 0.00 0.00 4.00
2611 2844 4.553330 AACTCATATCACAACCGAACCT 57.447 40.909 0.00 0.00 0.00 3.50
2612 2845 5.622770 AAAACTCATATCACAACCGAACC 57.377 39.130 0.00 0.00 0.00 3.62
2613 2846 7.013529 GTGTAAAACTCATATCACAACCGAAC 58.986 38.462 0.00 0.00 0.00 3.95
2614 2847 6.706716 TGTGTAAAACTCATATCACAACCGAA 59.293 34.615 0.00 0.00 33.81 4.30
2615 2848 6.224584 TGTGTAAAACTCATATCACAACCGA 58.775 36.000 0.00 0.00 33.81 4.69
2616 2849 6.474819 TGTGTAAAACTCATATCACAACCG 57.525 37.500 0.00 0.00 33.81 4.44
2632 2865 9.715123 CGCAATTCACTCAATATAATGTGTAAA 57.285 29.630 0.00 0.00 0.00 2.01
2633 2866 9.103861 TCGCAATTCACTCAATATAATGTGTAA 57.896 29.630 0.00 0.00 0.00 2.41
2634 2867 8.655651 TCGCAATTCACTCAATATAATGTGTA 57.344 30.769 0.00 0.00 0.00 2.90
2635 2868 7.552458 TCGCAATTCACTCAATATAATGTGT 57.448 32.000 0.00 0.00 0.00 3.72
2636 2869 8.839947 TTTCGCAATTCACTCAATATAATGTG 57.160 30.769 0.00 0.00 0.00 3.21
2637 2870 9.853555 TTTTTCGCAATTCACTCAATATAATGT 57.146 25.926 0.00 0.00 0.00 2.71
2639 2872 9.301153 GGTTTTTCGCAATTCACTCAATATAAT 57.699 29.630 0.00 0.00 0.00 1.28
2640 2873 8.300286 TGGTTTTTCGCAATTCACTCAATATAA 58.700 29.630 0.00 0.00 0.00 0.98
2641 2874 7.753132 GTGGTTTTTCGCAATTCACTCAATATA 59.247 33.333 0.00 0.00 0.00 0.86
2642 2875 6.586082 GTGGTTTTTCGCAATTCACTCAATAT 59.414 34.615 0.00 0.00 0.00 1.28
2643 2876 5.918011 GTGGTTTTTCGCAATTCACTCAATA 59.082 36.000 0.00 0.00 0.00 1.90
2644 2877 4.744631 GTGGTTTTTCGCAATTCACTCAAT 59.255 37.500 0.00 0.00 0.00 2.57
2645 2878 4.109050 GTGGTTTTTCGCAATTCACTCAA 58.891 39.130 0.00 0.00 0.00 3.02
2646 2879 3.490078 GGTGGTTTTTCGCAATTCACTCA 60.490 43.478 0.00 0.00 0.00 3.41
2658 2891 2.124122 GCGTCAATGTGGTGGTTTTTC 58.876 47.619 0.00 0.00 0.00 2.29
2690 2923 7.794810 GCCATAAATTTGTAAACCGTTGTTTTC 59.205 33.333 0.00 0.00 41.92 2.29
2698 2931 7.543868 TGATTTCTGCCATAAATTTGTAAACCG 59.456 33.333 0.00 0.00 0.00 4.44
2699 2932 8.655970 GTGATTTCTGCCATAAATTTGTAAACC 58.344 33.333 0.00 0.00 0.00 3.27
2700 2933 9.423061 AGTGATTTCTGCCATAAATTTGTAAAC 57.577 29.630 0.00 0.00 0.00 2.01
2702 2935 8.801299 TCAGTGATTTCTGCCATAAATTTGTAA 58.199 29.630 0.00 0.00 35.63 2.41
2704 2937 7.230849 TCAGTGATTTCTGCCATAAATTTGT 57.769 32.000 0.00 0.00 35.63 2.83
2705 2938 8.712285 AATCAGTGATTTCTGCCATAAATTTG 57.288 30.769 12.75 0.00 35.63 2.32
2706 2939 8.755977 AGAATCAGTGATTTCTGCCATAAATTT 58.244 29.630 19.19 0.00 31.89 1.82
2722 2955 5.344743 AAGATTAAGCCGAGAATCAGTGA 57.655 39.130 0.00 0.00 35.00 3.41
2727 2960 5.235305 TGCAAAAGATTAAGCCGAGAATC 57.765 39.130 0.00 0.00 33.11 2.52
2762 2995 4.282195 AGGTTAAAATGCCCAAAACGATCA 59.718 37.500 0.00 0.00 0.00 2.92
2768 3001 8.378565 TCATAATCAAGGTTAAAATGCCCAAAA 58.621 29.630 0.00 0.00 0.00 2.44
2774 3007 8.810427 CACATGTCATAATCAAGGTTAAAATGC 58.190 33.333 0.00 0.00 0.00 3.56
2786 3019 2.158827 CGGTCCCCACATGTCATAATCA 60.159 50.000 0.00 0.00 0.00 2.57
2802 3035 1.931172 CCACGTCATCAAATACGGTCC 59.069 52.381 0.00 0.00 43.25 4.46
2804 3037 1.365699 GCCACGTCATCAAATACGGT 58.634 50.000 0.00 0.00 43.25 4.83
2806 3039 0.996462 ACGCCACGTCATCAAATACG 59.004 50.000 0.00 0.00 44.47 3.06
2823 3056 2.852413 CCATCTAACGTGAGCTGTTACG 59.148 50.000 11.78 11.78 45.19 3.18
2828 3061 0.458543 ACGCCATCTAACGTGAGCTG 60.459 55.000 0.00 0.00 41.76 4.24
2829 3062 0.246635 AACGCCATCTAACGTGAGCT 59.753 50.000 0.00 0.00 42.68 4.09
2834 3067 1.001633 AGACCAAACGCCATCTAACGT 59.998 47.619 0.00 0.00 46.07 3.99
2888 3121 3.081804 CACTTTATGGTTGAGGGGTGTC 58.918 50.000 0.00 0.00 0.00 3.67
2923 3156 2.282180 GGTTCCGTGCACATGGGT 60.282 61.111 18.64 0.00 38.05 4.51
2928 3161 1.525077 GTTGGAGGTTCCGTGCACA 60.525 57.895 18.64 0.00 40.17 4.57
2929 3162 1.525077 TGTTGGAGGTTCCGTGCAC 60.525 57.895 6.82 6.82 40.17 4.57
2932 3165 1.959226 CCGTGTTGGAGGTTCCGTG 60.959 63.158 0.00 0.00 40.17 4.94
2935 3168 1.599797 CCACCGTGTTGGAGGTTCC 60.600 63.158 0.00 0.00 43.10 3.62
2944 3177 2.915659 TCGAGAGCCCACCGTGTT 60.916 61.111 0.00 0.00 0.00 3.32
2945 3178 3.374402 CTCGAGAGCCCACCGTGT 61.374 66.667 6.58 0.00 0.00 4.49
2956 3189 3.385384 CCTGCCTGGTGCTCGAGA 61.385 66.667 18.75 0.00 42.00 4.04
2957 3190 4.463879 CCCTGCCTGGTGCTCGAG 62.464 72.222 8.45 8.45 42.00 4.04
2971 3255 0.033405 TACGCAGTTCTCCTAGCCCT 60.033 55.000 0.00 0.00 37.78 5.19
2976 3260 0.750850 GGGCATACGCAGTTCTCCTA 59.249 55.000 0.00 0.00 37.78 2.94
3057 3341 4.778415 CGTGGACCTGCTCGTCGG 62.778 72.222 0.00 0.00 33.30 4.79
3061 3345 2.811317 GAAGCGTGGACCTGCTCG 60.811 66.667 11.51 3.97 41.46 5.03
3096 3380 0.809241 GTGGAGCTCGAGCAAGGATG 60.809 60.000 36.87 0.00 45.16 3.51
3097 3381 1.519719 GTGGAGCTCGAGCAAGGAT 59.480 57.895 36.87 18.07 45.16 3.24
3125 3497 4.689549 TTCCCCGTGGCCGAGAGA 62.690 66.667 0.00 0.00 35.63 3.10
3126 3498 4.148825 CTTCCCCGTGGCCGAGAG 62.149 72.222 0.00 0.00 35.63 3.20
3141 3513 0.534412 CTCGAGCAGGTCATGTCCTT 59.466 55.000 8.95 0.00 35.37 3.36
3165 3537 4.295119 GACCACGTCCACTGCCGT 62.295 66.667 0.00 0.00 37.90 5.68
3168 3540 3.986006 TCCGACCACGTCCACTGC 61.986 66.667 0.00 0.00 37.88 4.40
3169 3541 2.049433 GTCCGACCACGTCCACTG 60.049 66.667 0.00 0.00 37.88 3.66
3170 3542 3.300765 GGTCCGACCACGTCCACT 61.301 66.667 13.05 0.00 38.42 4.00
3172 3544 4.953010 TCGGTCCGACCACGTCCA 62.953 66.667 17.87 0.00 38.47 4.02
3282 3670 4.290622 ACAAGCCTGGCCACCCTG 62.291 66.667 16.57 7.83 0.00 4.45
3346 3734 4.144703 GTCCCTCGTTCTCCCGGC 62.145 72.222 0.00 0.00 0.00 6.13
3365 3753 2.893489 GGATGCCCAACTTGTTCTTCTT 59.107 45.455 0.00 0.00 0.00 2.52
3386 3774 1.047002 AATCCCTCTCGCTCCTGATG 58.953 55.000 0.00 0.00 0.00 3.07
3390 3778 0.325671 TCCAAATCCCTCTCGCTCCT 60.326 55.000 0.00 0.00 0.00 3.69
3418 3806 1.112315 CCCTCTCACTCCCTGATCCG 61.112 65.000 0.00 0.00 0.00 4.18
3430 3818 9.109393 CATTCTAAAAACGATTAATCCCTCTCA 57.891 33.333 9.87 0.00 0.00 3.27
3435 3823 7.576861 TCCCATTCTAAAAACGATTAATCCC 57.423 36.000 9.87 0.00 0.00 3.85
3436 3824 8.135529 CCTTCCCATTCTAAAAACGATTAATCC 58.864 37.037 9.87 0.00 0.00 3.01
3437 3825 8.899771 TCCTTCCCATTCTAAAAACGATTAATC 58.100 33.333 5.30 5.30 0.00 1.75
3438 3826 8.817092 TCCTTCCCATTCTAAAAACGATTAAT 57.183 30.769 0.00 0.00 0.00 1.40
3439 3827 7.886446 ACTCCTTCCCATTCTAAAAACGATTAA 59.114 33.333 0.00 0.00 0.00 1.40
3440 3828 7.399634 ACTCCTTCCCATTCTAAAAACGATTA 58.600 34.615 0.00 0.00 0.00 1.75
3441 3829 6.246163 ACTCCTTCCCATTCTAAAAACGATT 58.754 36.000 0.00 0.00 0.00 3.34
3442 3830 5.816682 ACTCCTTCCCATTCTAAAAACGAT 58.183 37.500 0.00 0.00 0.00 3.73
3443 3831 5.237236 ACTCCTTCCCATTCTAAAAACGA 57.763 39.130 0.00 0.00 0.00 3.85
3444 3832 5.959618 AACTCCTTCCCATTCTAAAAACG 57.040 39.130 0.00 0.00 0.00 3.60
3445 3833 7.441157 CCAAAAACTCCTTCCCATTCTAAAAAC 59.559 37.037 0.00 0.00 0.00 2.43
3455 3843 2.166907 TTGCCAAAAACTCCTTCCCA 57.833 45.000 0.00 0.00 0.00 4.37
3459 3847 4.225042 AGGTCTTTTTGCCAAAAACTCCTT 59.775 37.500 19.49 10.19 36.15 3.36
3502 3890 1.009903 TGATGTGGCGTAACGGTTCG 61.010 55.000 0.00 0.00 0.00 3.95
3523 3911 1.376424 AGATGAAGCCCGCTGTGTG 60.376 57.895 0.00 0.00 0.00 3.82
3531 3919 3.733337 ACGATTATGACAGATGAAGCCC 58.267 45.455 0.00 0.00 0.00 5.19
3536 3924 7.254084 CGTTTTGATGACGATTATGACAGATGA 60.254 37.037 0.00 0.00 42.82 2.92
3551 3939 4.695217 TGGCTTTATCCGTTTTGATGAC 57.305 40.909 0.00 0.00 0.00 3.06
3557 3945 5.944007 ACTAGTTGATGGCTTTATCCGTTTT 59.056 36.000 0.00 0.00 0.00 2.43
3584 3972 9.513727 GATTTTTGGCTTAATCTTTTGCAAAAA 57.486 25.926 23.92 15.47 36.79 1.94
3589 3977 7.293018 CACTGATTTTTGGCTTAATCTTTTGC 58.707 34.615 0.00 0.00 33.08 3.68
3590 3978 7.442062 ACCACTGATTTTTGGCTTAATCTTTTG 59.558 33.333 0.00 0.00 36.20 2.44
3591 3979 7.508687 ACCACTGATTTTTGGCTTAATCTTTT 58.491 30.769 0.00 0.00 36.20 2.27


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

AutoCloner maintained by Alex Coulton.