Multiple sequence alignment - TraesCS2B01G326400

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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 TraesCS2B01G326400 chr2B 100.000 5917 0 0 615 6531 466195071 466189155 0.000000e+00 10927.0
1 TraesCS2B01G326400 chr2B 83.520 625 67 15 2904 3517 671352627 671353226 9.570000e-153 551.0
2 TraesCS2B01G326400 chr2B 100.000 253 0 0 1 253 466195685 466195433 9.920000e-128 468.0
3 TraesCS2B01G326400 chr2B 84.940 166 15 8 2898 3062 209135574 209135730 6.780000e-35 159.0
4 TraesCS2B01G326400 chr2B 100.000 33 0 0 2864 2896 466192854 466192822 1.970000e-05 62.1
5 TraesCS2B01G326400 chr2D 94.740 3612 105 37 2864 6461 394539137 394535597 0.000000e+00 5539.0
6 TraesCS2B01G326400 chr2D 93.057 2319 87 16 615 2864 394541418 394539105 0.000000e+00 3323.0
7 TraesCS2B01G326400 chr2D 87.703 431 41 4 2429 2850 30416829 30417256 5.880000e-135 492.0
8 TraesCS2B01G326400 chr2D 86.902 397 47 2 2473 2864 463922370 463922766 2.160000e-119 440.0
9 TraesCS2B01G326400 chr2D 86.842 342 41 4 2390 2727 29684358 29684699 4.780000e-101 379.0
10 TraesCS2B01G326400 chr2D 93.923 181 6 4 76 251 394541632 394541452 1.080000e-67 268.0
11 TraesCS2B01G326400 chr2A 95.639 3302 94 19 2864 6163 532494496 532491243 0.000000e+00 5254.0
12 TraesCS2B01G326400 chr2A 92.335 1670 69 28 741 2375 532496723 532495078 0.000000e+00 2320.0
13 TraesCS2B01G326400 chr2A 96.755 493 16 0 2372 2864 532494956 532494464 0.000000e+00 822.0
14 TraesCS2B01G326400 chr2A 84.903 616 66 13 2904 3517 702297895 702298485 1.210000e-166 597.0
15 TraesCS2B01G326400 chr2A 90.000 350 30 4 6164 6508 532488491 532488142 1.290000e-121 448.0
16 TraesCS2B01G326400 chr2A 83.673 245 9 9 1 234 532497464 532497240 1.110000e-47 202.0
17 TraesCS2B01G326400 chr5B 87.196 453 56 2 2411 2863 493087897 493087447 1.260000e-141 514.0
18 TraesCS2B01G326400 chr5B 84.848 396 55 3 2473 2864 430286104 430285710 1.710000e-105 394.0
19 TraesCS2B01G326400 chr5B 89.375 160 13 4 2905 3063 493087448 493087292 1.440000e-46 198.0
20 TraesCS2B01G326400 chr5A 85.774 478 62 2 2388 2864 194768581 194768109 9.780000e-138 501.0
21 TraesCS2B01G326400 chr5A 86.875 160 17 3 2904 3063 154481889 154481734 6.730000e-40 176.0
22 TraesCS2B01G326400 chr6A 88.579 359 40 1 2507 2864 97749424 97749066 1.010000e-117 435.0
23 TraesCS2B01G326400 chr3A 86.650 397 48 2 2473 2864 155050378 155049982 1.010000e-117 435.0
24 TraesCS2B01G326400 chr7A 85.583 326 45 2 2411 2735 55158353 55158677 2.260000e-89 340.0
25 TraesCS2B01G326400 chr4A 85.583 326 45 2 2411 2735 94766878 94767202 2.260000e-89 340.0
26 TraesCS2B01G326400 chr6D 84.577 201 17 6 2864 3062 446714894 446714706 3.110000e-43 187.0
27 TraesCS2B01G326400 chr6B 83.523 176 22 6 2898 3072 109073447 109073278 2.440000e-34 158.0


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 TraesCS2B01G326400 chr2B 466189155 466195685 6530 True 3819.033333 10927 100.000000 1 6531 3 chr2B.!!$R1 6530
1 TraesCS2B01G326400 chr2B 671352627 671353226 599 False 551.000000 551 83.520000 2904 3517 1 chr2B.!!$F2 613
2 TraesCS2B01G326400 chr2D 394535597 394541632 6035 True 3043.333333 5539 93.906667 76 6461 3 chr2D.!!$R1 6385
3 TraesCS2B01G326400 chr2A 532488142 532497464 9322 True 1809.200000 5254 91.680400 1 6508 5 chr2A.!!$R1 6507
4 TraesCS2B01G326400 chr2A 702297895 702298485 590 False 597.000000 597 84.903000 2904 3517 1 chr2A.!!$F1 613
5 TraesCS2B01G326400 chr5B 493087292 493087897 605 True 356.000000 514 88.285500 2411 3063 2 chr5B.!!$R2 652

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
63 68 0.035458 CAAAACAGGGGAGACTCGCT 59.965 55.000 18.01 3.06 34.16 4.93 F
64 69 0.321996 AAAACAGGGGAGACTCGCTC 59.678 55.000 18.01 9.17 43.17 5.03 F
679 691 0.462789 GCATCCAAATCCCAAGCCAG 59.537 55.000 0.00 0.00 0.00 4.85 F
1493 1591 0.716108 CGAAGCGTGATCCAGTCAAC 59.284 55.000 0.00 0.00 38.90 3.18 F
2123 2234 0.541392 TCCTATGCAGCGTGGTCAAT 59.459 50.000 0.00 0.00 0.00 2.57 F
2856 3092 0.034337 TTTAAGCTTCCCGTCGCTGT 59.966 50.000 0.00 0.00 36.45 4.40 F
2864 3100 0.242825 TCCCGTCGCTGTGTTCTTAG 59.757 55.000 0.00 0.00 0.00 2.18 F
3381 3631 0.674581 TGCATCTTGGAGTCCTTGCG 60.675 55.000 11.33 0.00 32.90 4.85 F
4305 4560 1.076777 ACCATGGGAATTGGAGCCG 60.077 57.895 18.09 0.00 37.69 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 1860 0.250467 GAACAGGAACAGCAGAGGCA 60.250 55.000 0.00 0.00 44.61 4.75 R
1828 1935 1.599667 CGGAATAGTGCGTCGCTACAT 60.600 52.381 19.50 5.53 33.27 2.29 R
2123 2234 0.965866 CACTGACCCGGAGCTCTACA 60.966 60.000 14.64 6.23 0.00 2.74 R
2837 3073 0.034337 ACAGCGACGGGAAGCTTAAA 59.966 50.000 0.00 0.00 42.52 1.52 R
3381 3631 0.106819 AGATTGCATGGGAGGCTGTC 60.107 55.000 0.00 0.00 0.00 3.51 R
4162 4416 0.517316 GCACCACTAAAAGCACTCCG 59.483 55.000 0.00 0.00 0.00 4.63 R
4356 4611 1.201429 ATGAAGCTGGAAGTCGGGGT 61.201 55.000 0.00 0.00 35.30 4.95 R
5297 5552 0.171679 CTGCATCCATTCGCAAGCAA 59.828 50.000 0.00 0.00 37.76 3.91 R
6131 6390 0.038166 TTAAAGGCAGGCTCCCAGTG 59.962 55.000 0.00 0.00 0.00 3.66 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
54 59 1.681486 AAACACGGGCAAAACAGGGG 61.681 55.000 0.00 0.00 0.00 4.79
55 60 2.203422 CACGGGCAAAACAGGGGA 60.203 61.111 0.00 0.00 0.00 4.81
56 61 2.115266 ACGGGCAAAACAGGGGAG 59.885 61.111 0.00 0.00 0.00 4.30
57 62 2.434331 CGGGCAAAACAGGGGAGA 59.566 61.111 0.00 0.00 0.00 3.71
58 63 1.971695 CGGGCAAAACAGGGGAGAC 60.972 63.158 0.00 0.00 0.00 3.36
59 64 1.460699 GGGCAAAACAGGGGAGACT 59.539 57.895 0.00 0.00 0.00 3.24
60 65 0.609406 GGGCAAAACAGGGGAGACTC 60.609 60.000 0.00 0.00 0.00 3.36
61 66 0.955919 GGCAAAACAGGGGAGACTCG 60.956 60.000 0.00 0.00 34.16 4.18
62 67 1.578206 GCAAAACAGGGGAGACTCGC 61.578 60.000 10.97 10.97 34.16 5.03
63 68 0.035458 CAAAACAGGGGAGACTCGCT 59.965 55.000 18.01 3.06 34.16 4.93
64 69 0.321996 AAAACAGGGGAGACTCGCTC 59.678 55.000 18.01 9.17 43.17 5.03
125 130 1.762460 CTATCCGCCCAGACCCACT 60.762 63.158 0.00 0.00 0.00 4.00
133 138 4.394712 CAGACCCACTGCCGACCC 62.395 72.222 0.00 0.00 39.86 4.46
247 259 2.623431 AGCTCCCCTCTCCCCTCT 60.623 66.667 0.00 0.00 0.00 3.69
251 263 1.550374 TCCCCTCTCCCCTCTCCTT 60.550 63.158 0.00 0.00 0.00 3.36
252 264 1.074850 CCCCTCTCCCCTCTCCTTC 60.075 68.421 0.00 0.00 0.00 3.46
636 648 1.398958 GCTGTCAAAACCCAGCCCAA 61.399 55.000 0.24 0.00 46.55 4.12
679 691 0.462789 GCATCCAAATCCCAAGCCAG 59.537 55.000 0.00 0.00 0.00 4.85
737 768 4.787280 CACCTCCTCCCCGGCTCT 62.787 72.222 0.00 0.00 0.00 4.09
770 801 2.364317 CCCTTCCCCGAGAGCAGA 60.364 66.667 0.00 0.00 0.00 4.26
1056 1099 1.449601 TTCGATTTGCCGCCCTCTC 60.450 57.895 0.00 0.00 0.00 3.20
1066 1109 2.817396 GCCCTCTCTTGTCGCAGC 60.817 66.667 0.00 0.00 0.00 5.25
1075 1118 1.621301 CTTGTCGCAGCTTCCGTCTG 61.621 60.000 3.74 0.00 34.79 3.51
1141 1184 3.835978 TCCGGTTTCTCTCTCATGGTAAA 59.164 43.478 0.00 0.00 0.00 2.01
1148 1191 5.201713 TCTCTCTCATGGTAAATTAGGCG 57.798 43.478 0.00 0.00 0.00 5.52
1273 1362 7.216494 CCTGTCCATTTTGTTTCCAGTATTTT 58.784 34.615 0.00 0.00 0.00 1.82
1327 1416 5.871396 TCGCCCTCTATTCAAAGTAATCT 57.129 39.130 0.00 0.00 0.00 2.40
1354 1443 5.685841 TGTTTGCGCAATTTTCTCTAGTAC 58.314 37.500 25.64 14.48 0.00 2.73
1393 1488 0.908198 AGTGATGGGTTGCTCTCTCC 59.092 55.000 0.00 0.00 0.00 3.71
1467 1562 9.317936 GAATTGTGATTCACTTCCTTTCTTTTT 57.682 29.630 17.26 0.00 41.10 1.94
1493 1591 0.716108 CGAAGCGTGATCCAGTCAAC 59.284 55.000 0.00 0.00 38.90 3.18
1564 1662 9.793252 GTTAATATGCTTGATCTGTGTTGAATT 57.207 29.630 0.00 0.00 0.00 2.17
1582 1680 5.167121 TGAATTCGTATGGTGGCAAATTTG 58.833 37.500 14.03 14.03 0.00 2.32
1661 1760 3.883489 AGTTGGGTAGAGTTTTGTGCTTC 59.117 43.478 0.00 0.00 0.00 3.86
1679 1778 9.897744 TTGTGCTTCAACTTTTCTAATTATGAG 57.102 29.630 0.00 0.00 0.00 2.90
1734 1833 7.482654 TGACAATCGGATATTTAGAAAGCAG 57.517 36.000 0.00 0.00 0.00 4.24
1757 1859 5.706369 AGATAGTGTCGTACCATGTATCCTC 59.294 44.000 0.00 0.00 0.00 3.71
1758 1860 3.899726 AGTGTCGTACCATGTATCCTCT 58.100 45.455 0.00 0.00 0.00 3.69
1779 1881 1.805869 CCTCTGCTGTTCCTGTTCTG 58.194 55.000 0.00 0.00 0.00 3.02
1786 1888 2.064762 CTGTTCCTGTTCTGAAGCTCG 58.935 52.381 0.00 0.00 0.00 5.03
2123 2234 0.541392 TCCTATGCAGCGTGGTCAAT 59.459 50.000 0.00 0.00 0.00 2.57
2148 2259 0.670854 GCTCCGGGTCAGTGTCTTTC 60.671 60.000 0.00 0.00 0.00 2.62
2186 2297 2.224378 CCTCTTTGCTTGGAGTGTCTGA 60.224 50.000 0.00 0.00 0.00 3.27
2202 2313 5.071788 AGTGTCTGAGAAATGGTTGGTCTAA 59.928 40.000 0.00 0.00 0.00 2.10
2403 2639 1.787012 CCCTTTTCATGTTGCAGTGC 58.213 50.000 8.58 8.58 0.00 4.40
2427 2663 7.549842 TGCACAGTACTTTGTTAGTTCAGTTTA 59.450 33.333 10.59 0.00 38.33 2.01
2618 2854 4.159321 TCTGTTCTTAGGAGACATGCTGAG 59.841 45.833 0.00 0.00 32.51 3.35
2658 2894 6.260870 TGGTTAGCATCGAAAGCATTTTTA 57.739 33.333 14.53 0.00 39.27 1.52
2671 2907 8.020819 CGAAAGCATTTTTAACTCCAGTTGATA 58.979 33.333 2.01 0.00 39.27 2.15
2690 2926 7.497249 AGTTGATATCTACACAATTTCTGGCTC 59.503 37.037 17.69 0.00 0.00 4.70
2836 3072 1.514553 GCATTCAGCTTGAAGCCCC 59.485 57.895 14.45 0.00 43.77 5.80
2837 3073 0.969409 GCATTCAGCTTGAAGCCCCT 60.969 55.000 14.45 0.00 43.77 4.79
2838 3074 1.553706 CATTCAGCTTGAAGCCCCTT 58.446 50.000 14.45 0.00 43.77 3.95
2839 3075 1.897802 CATTCAGCTTGAAGCCCCTTT 59.102 47.619 14.45 0.00 43.77 3.11
2840 3076 2.969821 TTCAGCTTGAAGCCCCTTTA 57.030 45.000 14.45 0.00 43.77 1.85
2841 3077 2.969821 TCAGCTTGAAGCCCCTTTAA 57.030 45.000 14.45 0.00 43.77 1.52
2842 3078 2.795329 TCAGCTTGAAGCCCCTTTAAG 58.205 47.619 14.45 5.44 43.77 1.85
2848 3084 3.691820 AAGCCCCTTTAAGCTTCCC 57.308 52.632 0.00 0.00 46.11 3.97
2849 3085 0.323451 AAGCCCCTTTAAGCTTCCCG 60.323 55.000 0.00 0.00 46.11 5.14
2850 3086 1.001269 GCCCCTTTAAGCTTCCCGT 60.001 57.895 0.00 0.00 0.00 5.28
2851 3087 1.030488 GCCCCTTTAAGCTTCCCGTC 61.030 60.000 0.00 0.00 0.00 4.79
2852 3088 0.743345 CCCCTTTAAGCTTCCCGTCG 60.743 60.000 0.00 0.00 0.00 5.12
2853 3089 1.366854 CCCTTTAAGCTTCCCGTCGC 61.367 60.000 0.00 0.00 0.00 5.19
2854 3090 0.391263 CCTTTAAGCTTCCCGTCGCT 60.391 55.000 0.00 0.00 38.30 4.93
2855 3091 0.721718 CTTTAAGCTTCCCGTCGCTG 59.278 55.000 0.00 0.00 36.45 5.18
2856 3092 0.034337 TTTAAGCTTCCCGTCGCTGT 59.966 50.000 0.00 0.00 36.45 4.40
2857 3093 0.669318 TTAAGCTTCCCGTCGCTGTG 60.669 55.000 0.00 0.00 36.45 3.66
2858 3094 1.812686 TAAGCTTCCCGTCGCTGTGT 61.813 55.000 0.00 0.00 36.45 3.72
2859 3095 2.660258 AAGCTTCCCGTCGCTGTGTT 62.660 55.000 0.00 0.00 36.45 3.32
2860 3096 2.668280 GCTTCCCGTCGCTGTGTTC 61.668 63.158 0.00 0.00 0.00 3.18
2861 3097 1.006102 CTTCCCGTCGCTGTGTTCT 60.006 57.895 0.00 0.00 0.00 3.01
2862 3098 0.600255 CTTCCCGTCGCTGTGTTCTT 60.600 55.000 0.00 0.00 0.00 2.52
2863 3099 0.675083 TTCCCGTCGCTGTGTTCTTA 59.325 50.000 0.00 0.00 0.00 2.10
2864 3100 0.242825 TCCCGTCGCTGTGTTCTTAG 59.757 55.000 0.00 0.00 0.00 2.18
3015 3255 5.565509 TGACTATGTGTGAACTCTCTCTCT 58.434 41.667 0.00 0.00 0.00 3.10
3016 3256 5.645929 TGACTATGTGTGAACTCTCTCTCTC 59.354 44.000 0.00 0.00 0.00 3.20
3171 3419 6.904463 TCTGAGGTACACAACACAATACTA 57.096 37.500 0.00 0.00 0.00 1.82
3185 3433 5.983720 ACACAATACTATAATCCTGTCACGC 59.016 40.000 0.00 0.00 0.00 5.34
3213 3463 5.106987 GGCAGTTTTTATGCATTTTCACCTG 60.107 40.000 3.54 6.09 45.68 4.00
3215 3465 6.018016 GCAGTTTTTATGCATTTTCACCTGTT 60.018 34.615 3.54 0.00 43.31 3.16
3225 3475 5.682212 GCATTTTCACCTGTTTCCTGTCTTT 60.682 40.000 0.00 0.00 0.00 2.52
3318 3568 4.199002 TGGAGTAAGGAGGCATATGAGA 57.801 45.455 6.97 0.00 0.00 3.27
3381 3631 0.674581 TGCATCTTGGAGTCCTTGCG 60.675 55.000 11.33 0.00 32.90 4.85
3469 3720 5.531659 TCAACCAGTTTTCGCCTTTGTTATA 59.468 36.000 0.00 0.00 0.00 0.98
3481 3732 1.080298 TTGTTATACCCGTTGCTGCG 58.920 50.000 0.00 0.00 0.00 5.18
3483 3734 1.081094 GTTATACCCGTTGCTGCGTT 58.919 50.000 0.00 0.00 0.00 4.84
3578 3829 6.822667 TGCTATGGCAATTCCTTATGTATG 57.177 37.500 0.00 0.00 46.36 2.39
3579 3830 6.306199 TGCTATGGCAATTCCTTATGTATGT 58.694 36.000 0.00 0.00 46.36 2.29
3580 3831 6.777091 TGCTATGGCAATTCCTTATGTATGTT 59.223 34.615 0.00 0.00 46.36 2.71
3581 3832 7.287466 TGCTATGGCAATTCCTTATGTATGTTT 59.713 33.333 0.00 0.00 46.36 2.83
3582 3833 8.143835 GCTATGGCAATTCCTTATGTATGTTTT 58.856 33.333 0.00 0.00 38.54 2.43
3634 3885 6.491714 ACATTCTGCTTAGGTGTGAGATAT 57.508 37.500 0.00 0.00 0.00 1.63
3724 3978 6.097554 TGTTTCTTTTTGCTTAACTGGGATGA 59.902 34.615 0.00 0.00 0.00 2.92
3735 3989 3.744940 ACTGGGATGACATCATGGTTT 57.255 42.857 17.08 0.00 36.57 3.27
3736 3990 3.624777 ACTGGGATGACATCATGGTTTC 58.375 45.455 17.08 0.00 36.57 2.78
3738 3992 2.582172 TGGGATGACATCATGGTTTCCT 59.418 45.455 17.08 0.00 36.57 3.36
3954 4208 3.977999 TCTTGAAAGAAGGTAACCTGGGA 59.022 43.478 0.00 0.00 32.13 4.37
3970 4224 3.321682 CCTGGGATTGCTTTTGACAAGAA 59.678 43.478 0.00 0.00 0.00 2.52
4017 4271 7.861629 TCTAGGTGGATATGACAAACATTTCT 58.138 34.615 0.00 0.00 40.07 2.52
4064 4318 2.130821 TTGGTATTGGGAGCACGCCA 62.131 55.000 0.00 0.00 0.00 5.69
4068 4322 2.173758 TATTGGGAGCACGCCAACGA 62.174 55.000 6.31 0.00 43.93 3.85
4206 4461 7.148373 GCATTATCATGTTTCCATGTTTGCTTT 60.148 33.333 2.91 0.00 46.99 3.51
4305 4560 1.076777 ACCATGGGAATTGGAGCCG 60.077 57.895 18.09 0.00 37.69 5.52
4356 4611 2.832129 ACCTCCACTGAGAAATAAGCGA 59.168 45.455 0.00 0.00 41.42 4.93
4375 4630 1.201429 ACCCCGACTTCCAGCTTCAT 61.201 55.000 0.00 0.00 0.00 2.57
4765 5020 5.047377 ACTGTTGAAAGAAAGCTTGAACCAA 60.047 36.000 0.00 0.00 33.79 3.67
5027 5282 5.522456 TGTCACATTTTGAAGATGCTCAAC 58.478 37.500 0.00 0.00 35.39 3.18
5036 5291 8.721019 TTTTGAAGATGCTCAACTTTCAATTT 57.279 26.923 0.00 0.00 35.07 1.82
5233 5488 5.195001 TCAAGAAATGGCAGGTTGTTTAC 57.805 39.130 0.00 0.00 0.00 2.01
5269 5524 4.458256 TGATATGATGCTTGTTGGGGAT 57.542 40.909 0.00 0.00 0.00 3.85
5286 5541 3.318313 GGGATGATCCTTGGGAGTAAGA 58.682 50.000 11.87 0.00 36.57 2.10
5297 5552 5.132816 CCTTGGGAGTAAGAACCCTTATCAT 59.867 44.000 0.00 0.00 45.74 2.45
5300 5555 4.822350 GGGAGTAAGAACCCTTATCATTGC 59.178 45.833 0.00 0.00 42.56 3.56
5301 5556 5.398012 GGGAGTAAGAACCCTTATCATTGCT 60.398 44.000 0.00 0.00 42.56 3.91
5304 5559 4.725790 AAGAACCCTTATCATTGCTTGC 57.274 40.909 0.00 0.00 0.00 4.01
5392 5647 2.090760 TGCAGCATGGCGAAAAGAATA 58.909 42.857 0.00 0.00 35.86 1.75
5497 5752 1.881903 CTCCGCAGAGTGGCTCAGAA 61.882 60.000 0.00 0.00 35.21 3.02
5583 5838 5.474876 ACGCTCTTTCTTCCTTTGATCATTT 59.525 36.000 0.00 0.00 0.00 2.32
5588 5843 3.099141 TCTTCCTTTGATCATTTGGGGC 58.901 45.455 0.00 0.00 0.00 5.80
5591 5846 3.246301 TCCTTTGATCATTTGGGGCAAA 58.754 40.909 0.00 0.00 37.75 3.68
5624 5879 1.919654 TCCACTCTACTCAGGAGAGCT 59.080 52.381 14.59 0.00 46.09 4.09
5627 5882 3.118038 CCACTCTACTCAGGAGAGCTACT 60.118 52.174 14.59 0.00 46.09 2.57
5628 5883 4.127171 CACTCTACTCAGGAGAGCTACTC 58.873 52.174 14.59 0.00 46.09 2.59
5629 5884 3.181469 ACTCTACTCAGGAGAGCTACTCG 60.181 52.174 14.59 0.00 46.09 4.18
5672 5927 1.100463 ATTGTGTGCGTTGCTGTGGA 61.100 50.000 0.00 0.00 0.00 4.02
5673 5928 1.987704 TTGTGTGCGTTGCTGTGGAC 61.988 55.000 0.00 0.00 0.00 4.02
5674 5929 2.180204 GTGTGCGTTGCTGTGGACT 61.180 57.895 0.00 0.00 0.00 3.85
5675 5930 2.179547 TGTGCGTTGCTGTGGACTG 61.180 57.895 0.00 0.00 0.00 3.51
5676 5931 2.180204 GTGCGTTGCTGTGGACTGT 61.180 57.895 0.00 0.00 0.00 3.55
5677 5932 2.179547 TGCGTTGCTGTGGACTGTG 61.180 57.895 0.00 0.00 0.00 3.66
5678 5933 2.896801 GCGTTGCTGTGGACTGTGG 61.897 63.158 0.00 0.00 0.00 4.17
5814 6069 1.810030 CCGTAGACCTTGCCTTCGC 60.810 63.158 0.00 0.00 0.00 4.70
5934 6189 0.763035 ACCTTTTCGCTAGTGGTGGT 59.237 50.000 2.90 4.31 0.00 4.16
5935 6190 1.156736 CCTTTTCGCTAGTGGTGGTG 58.843 55.000 2.90 0.00 0.00 4.17
5936 6191 1.542547 CCTTTTCGCTAGTGGTGGTGT 60.543 52.381 2.90 0.00 0.00 4.16
5937 6192 2.218603 CTTTTCGCTAGTGGTGGTGTT 58.781 47.619 2.90 0.00 0.00 3.32
5938 6193 1.588674 TTTCGCTAGTGGTGGTGTTG 58.411 50.000 2.90 0.00 0.00 3.33
5939 6194 0.250124 TTCGCTAGTGGTGGTGTTGG 60.250 55.000 2.90 0.00 0.00 3.77
5940 6195 1.070786 CGCTAGTGGTGGTGTTGGT 59.929 57.895 0.00 0.00 0.00 3.67
6198 9210 2.941720 GCAGGAATGTCTCTTCCATGAC 59.058 50.000 5.70 0.00 46.02 3.06
6203 9215 0.904865 TGTCTCTTCCATGACGGGCT 60.905 55.000 0.00 0.00 36.10 5.19
6222 9234 3.832490 GGCTTCTTTTGGGTTGTAGGAAT 59.168 43.478 0.00 0.00 0.00 3.01
6225 9237 6.014925 GGCTTCTTTTGGGTTGTAGGAATTTA 60.015 38.462 0.00 0.00 0.00 1.40
6290 9302 5.482163 TTGGATCATAGGATTGCGATACA 57.518 39.130 0.00 0.00 32.67 2.29
6323 9337 1.059913 ATCCTTTCCTATGCCTCCCG 58.940 55.000 0.00 0.00 0.00 5.14
6368 9382 6.882678 ACATAAGCTCAAACCGTATTTTACCT 59.117 34.615 0.00 0.00 0.00 3.08
6437 9451 8.712363 TCTCTCGTCAATACTTGAAATTTTCTG 58.288 33.333 10.33 6.06 42.15 3.02
6439 9453 8.836413 TCTCGTCAATACTTGAAATTTTCTGTT 58.164 29.630 10.33 0.00 42.15 3.16
6441 9455 9.232082 TCGTCAATACTTGAAATTTTCTGTTTG 57.768 29.630 10.33 13.21 42.15 2.93
6450 9464 9.801714 CTTGAAATTTTCTGTTTGTCATTATGC 57.198 29.630 10.33 0.00 0.00 3.14
6451 9465 8.883954 TGAAATTTTCTGTTTGTCATTATGCA 57.116 26.923 10.33 0.00 0.00 3.96
6452 9466 9.491675 TGAAATTTTCTGTTTGTCATTATGCAT 57.508 25.926 3.79 3.79 0.00 3.96
6461 9478 6.812656 TGTTTGTCATTATGCATCATCCAAAC 59.187 34.615 23.43 23.43 39.48 2.93
6466 9483 1.175654 ATGCATCATCCAAACGCACA 58.824 45.000 0.00 0.00 35.02 4.57
6491 9508 9.027129 CATGTTGCATAATTCCTGTATTTTCAG 57.973 33.333 0.00 0.00 35.45 3.02
6509 9527 7.429636 TTTTCAGTTTAGTAGGATTTCACCG 57.570 36.000 0.00 0.00 34.73 4.94
6510 9528 5.733620 TCAGTTTAGTAGGATTTCACCGT 57.266 39.130 0.00 0.00 34.73 4.83
6511 9529 6.839124 TCAGTTTAGTAGGATTTCACCGTA 57.161 37.500 0.00 0.00 34.73 4.02
6512 9530 6.624423 TCAGTTTAGTAGGATTTCACCGTAC 58.376 40.000 0.00 0.00 34.73 3.67
6513 9531 6.209192 TCAGTTTAGTAGGATTTCACCGTACA 59.791 38.462 0.00 0.00 34.73 2.90
6514 9532 7.039882 CAGTTTAGTAGGATTTCACCGTACAT 58.960 38.462 0.00 0.00 34.73 2.29
6515 9533 7.010183 CAGTTTAGTAGGATTTCACCGTACATG 59.990 40.741 0.00 0.00 34.73 3.21
6516 9534 6.778834 TTAGTAGGATTTCACCGTACATGA 57.221 37.500 0.00 0.00 34.73 3.07
6517 9535 5.007385 AGTAGGATTTCACCGTACATGAC 57.993 43.478 0.00 0.00 34.73 3.06
6518 9536 3.973206 AGGATTTCACCGTACATGACA 57.027 42.857 0.00 0.00 34.73 3.58
6519 9537 4.487714 AGGATTTCACCGTACATGACAT 57.512 40.909 0.00 0.00 34.73 3.06
6520 9538 4.442706 AGGATTTCACCGTACATGACATC 58.557 43.478 0.00 12.00 34.08 3.06
6521 9539 3.560068 GGATTTCACCGTACATGACATCC 59.440 47.826 19.18 19.18 42.97 3.51
6522 9540 2.684001 TTCACCGTACATGACATCCC 57.316 50.000 0.00 0.00 0.00 3.85
6523 9541 1.562783 TCACCGTACATGACATCCCA 58.437 50.000 0.00 0.00 0.00 4.37
6524 9542 1.206132 TCACCGTACATGACATCCCAC 59.794 52.381 0.00 0.00 0.00 4.61
6525 9543 1.207089 CACCGTACATGACATCCCACT 59.793 52.381 0.00 0.00 0.00 4.00
6526 9544 1.480954 ACCGTACATGACATCCCACTC 59.519 52.381 0.00 0.00 0.00 3.51
6527 9545 1.202533 CCGTACATGACATCCCACTCC 60.203 57.143 0.00 0.00 0.00 3.85
6528 9546 1.757118 CGTACATGACATCCCACTCCT 59.243 52.381 0.00 0.00 0.00 3.69
6529 9547 2.956333 CGTACATGACATCCCACTCCTA 59.044 50.000 0.00 0.00 0.00 2.94
6530 9548 3.243434 CGTACATGACATCCCACTCCTAC 60.243 52.174 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.370584 TGTATGGTCTTGGATCCATCTTGAT 59.629 40.000 17.06 8.16 42.56 2.57
54 59 2.341101 TTCCACCGGAGCGAGTCTC 61.341 63.158 9.46 0.00 41.15 3.36
55 60 2.282958 TTCCACCGGAGCGAGTCT 60.283 61.111 9.46 0.00 31.21 3.24
56 61 2.126031 GTTCCACCGGAGCGAGTC 60.126 66.667 9.46 0.00 31.21 3.36
57 62 3.692406 GGTTCCACCGGAGCGAGT 61.692 66.667 9.46 0.00 33.63 4.18
58 63 2.725203 TTTGGTTCCACCGGAGCGAG 62.725 60.000 9.46 0.00 42.58 5.03
59 64 2.725203 CTTTGGTTCCACCGGAGCGA 62.725 60.000 9.46 0.00 42.58 4.93
60 65 2.281208 TTTGGTTCCACCGGAGCG 60.281 61.111 9.46 0.00 42.58 5.03
61 66 2.626780 GCTTTGGTTCCACCGGAGC 61.627 63.158 9.46 0.00 42.58 4.70
62 67 1.228124 TGCTTTGGTTCCACCGGAG 60.228 57.895 9.46 0.00 42.58 4.63
63 68 1.527380 GTGCTTTGGTTCCACCGGA 60.527 57.895 9.46 0.00 42.58 5.14
64 69 2.903547 CGTGCTTTGGTTCCACCGG 61.904 63.158 0.00 0.00 42.58 5.28
65 70 2.637025 CGTGCTTTGGTTCCACCG 59.363 61.111 0.00 0.00 42.58 4.94
66 71 2.561037 CCCGTGCTTTGGTTCCACC 61.561 63.158 0.00 0.00 39.22 4.61
67 72 3.039134 CCCGTGCTTTGGTTCCAC 58.961 61.111 0.00 0.00 0.00 4.02
70 75 2.335011 GTGCCCGTGCTTTGGTTC 59.665 61.111 0.00 0.00 38.71 3.62
74 79 2.098426 ATTTGGGTGCCCGTGCTTTG 62.098 55.000 2.44 0.00 39.42 2.77
636 648 1.240256 GACTGAGTCGACTGGTCTGT 58.760 55.000 25.58 18.09 0.00 3.41
679 691 2.032681 GGAGGGTGAGGTGTGTGC 59.967 66.667 0.00 0.00 0.00 4.57
913 956 2.104928 CGCGATGTGCTAGCCTCA 59.895 61.111 13.29 12.04 43.27 3.86
956 999 2.162408 CCAAACGGCAAGAGAATTCTCC 59.838 50.000 28.01 14.98 43.88 3.71
996 1039 3.814615 ATTCGCCATCGCCATCGCT 62.815 57.895 0.00 0.00 35.26 4.93
1056 1099 1.373497 AGACGGAAGCTGCGACAAG 60.373 57.895 4.30 0.00 34.49 3.16
1148 1191 0.818040 ACCGACTCAGTTTGGGCAAC 60.818 55.000 2.38 0.00 35.32 4.17
1154 1197 6.645415 ACTTAATCAACTACCGACTCAGTTTG 59.355 38.462 0.00 0.00 32.72 2.93
1213 1278 7.324178 ACTCAAGTTAGATGAAGTTTCGCTAT 58.676 34.615 0.00 0.00 0.00 2.97
1273 1362 1.001487 CAACAAGAGCGATTGCAACCA 60.001 47.619 7.90 0.00 46.23 3.67
1327 1416 3.005684 AGAGAAAATTGCGCAAACATGGA 59.994 39.130 28.81 1.57 0.00 3.41
1354 1443 3.383825 ACTCCATAAGGTGCGGTACTAAG 59.616 47.826 0.00 0.00 35.89 2.18
1393 1488 1.136891 TCACATCACAGGCATCGGTAG 59.863 52.381 0.00 0.00 0.00 3.18
1493 1591 9.994432 GTCACAAGAATATCCATACTTTTTCAG 57.006 33.333 0.00 0.00 0.00 3.02
1564 1662 1.203523 GCCAAATTTGCCACCATACGA 59.796 47.619 12.92 0.00 0.00 3.43
1582 1680 5.261209 TCAATAAAATACTGCCATGTGCC 57.739 39.130 4.07 0.00 40.16 5.01
1710 1809 7.272244 TCTGCTTTCTAAATATCCGATTGTCA 58.728 34.615 0.00 0.00 0.00 3.58
1721 1820 8.133627 GGTACGACACTATCTGCTTTCTAAATA 58.866 37.037 0.00 0.00 0.00 1.40
1734 1833 5.706369 AGAGGATACATGGTACGACACTATC 59.294 44.000 0.00 0.00 41.41 2.08
1757 1859 0.250640 AACAGGAACAGCAGAGGCAG 60.251 55.000 0.00 0.00 44.61 4.85
1758 1860 0.250467 GAACAGGAACAGCAGAGGCA 60.250 55.000 0.00 0.00 44.61 4.75
1779 1881 5.542779 ACAATATTAGGTGATCCGAGCTTC 58.457 41.667 0.00 0.00 39.05 3.86
1828 1935 1.599667 CGGAATAGTGCGTCGCTACAT 60.600 52.381 19.50 5.53 33.27 2.29
2032 2143 5.869649 TGTAGATGCCTCAAGCTATACAA 57.130 39.130 0.00 0.00 44.23 2.41
2123 2234 0.965866 CACTGACCCGGAGCTCTACA 60.966 60.000 14.64 6.23 0.00 2.74
2186 2297 5.815581 TGCATAGTTAGACCAACCATTTCT 58.184 37.500 0.00 0.00 37.93 2.52
2202 2313 8.970859 AAGAATAACATTTCTAGCTGCATAGT 57.029 30.769 1.02 0.00 34.89 2.12
2645 2881 6.205784 TCAACTGGAGTTAAAAATGCTTTCG 58.794 36.000 0.00 0.00 36.32 3.46
2658 2894 9.167311 GAAATTGTGTAGATATCAACTGGAGTT 57.833 33.333 5.32 0.00 39.12 3.01
2671 2907 6.182627 TCAATGAGCCAGAAATTGTGTAGAT 58.817 36.000 0.00 0.00 33.84 1.98
2690 2926 3.181497 CGAAGCAACCCTACCATTCAATG 60.181 47.826 0.00 0.00 0.00 2.82
2833 3069 0.743345 CGACGGGAAGCTTAAAGGGG 60.743 60.000 0.00 0.00 0.00 4.79
2834 3070 1.366854 GCGACGGGAAGCTTAAAGGG 61.367 60.000 0.00 0.00 0.00 3.95
2835 3071 0.391263 AGCGACGGGAAGCTTAAAGG 60.391 55.000 0.00 0.00 41.52 3.11
2836 3072 0.721718 CAGCGACGGGAAGCTTAAAG 59.278 55.000 0.00 0.00 42.52 1.85
2837 3073 0.034337 ACAGCGACGGGAAGCTTAAA 59.966 50.000 0.00 0.00 42.52 1.52
2838 3074 0.669318 CACAGCGACGGGAAGCTTAA 60.669 55.000 0.00 0.00 42.52 1.85
2839 3075 1.080093 CACAGCGACGGGAAGCTTA 60.080 57.895 0.00 0.00 42.52 3.09
2840 3076 2.357517 CACAGCGACGGGAAGCTT 60.358 61.111 0.00 0.00 42.52 3.74
2841 3077 3.165160 AACACAGCGACGGGAAGCT 62.165 57.895 0.00 0.00 45.74 3.74
2842 3078 2.665185 AACACAGCGACGGGAAGC 60.665 61.111 0.00 0.00 0.00 3.86
2843 3079 0.600255 AAGAACACAGCGACGGGAAG 60.600 55.000 0.00 0.00 0.00 3.46
2844 3080 0.675083 TAAGAACACAGCGACGGGAA 59.325 50.000 0.00 0.00 0.00 3.97
2845 3081 0.242825 CTAAGAACACAGCGACGGGA 59.757 55.000 0.00 0.00 0.00 5.14
2846 3082 1.352156 GCTAAGAACACAGCGACGGG 61.352 60.000 0.00 0.00 0.00 5.28
2847 3083 1.352156 GGCTAAGAACACAGCGACGG 61.352 60.000 0.00 0.00 38.73 4.79
2848 3084 1.352156 GGGCTAAGAACACAGCGACG 61.352 60.000 0.00 0.00 38.73 5.12
2849 3085 1.019805 GGGGCTAAGAACACAGCGAC 61.020 60.000 0.00 0.00 38.73 5.19
2850 3086 1.192146 AGGGGCTAAGAACACAGCGA 61.192 55.000 0.00 0.00 38.73 4.93
2851 3087 0.321653 AAGGGGCTAAGAACACAGCG 60.322 55.000 0.00 0.00 38.73 5.18
2852 3088 1.911057 AAAGGGGCTAAGAACACAGC 58.089 50.000 0.00 0.00 37.05 4.40
2853 3089 3.440522 GCTTAAAGGGGCTAAGAACACAG 59.559 47.826 0.00 0.00 0.00 3.66
2854 3090 3.073946 AGCTTAAAGGGGCTAAGAACACA 59.926 43.478 0.00 0.00 37.00 3.72
2855 3091 3.687125 AGCTTAAAGGGGCTAAGAACAC 58.313 45.455 0.00 0.00 37.00 3.32
2856 3092 4.332828 GAAGCTTAAAGGGGCTAAGAACA 58.667 43.478 0.00 0.00 37.87 3.18
2857 3093 3.695060 GGAAGCTTAAAGGGGCTAAGAAC 59.305 47.826 0.00 0.00 37.87 3.01
2858 3094 3.308904 GGGAAGCTTAAAGGGGCTAAGAA 60.309 47.826 0.00 0.00 37.87 2.52
2859 3095 2.241430 GGGAAGCTTAAAGGGGCTAAGA 59.759 50.000 0.00 0.00 37.87 2.10
2860 3096 2.656002 GGGAAGCTTAAAGGGGCTAAG 58.344 52.381 0.00 0.00 37.87 2.18
2861 3097 1.064979 CGGGAAGCTTAAAGGGGCTAA 60.065 52.381 0.00 0.00 37.87 3.09
2862 3098 0.544697 CGGGAAGCTTAAAGGGGCTA 59.455 55.000 0.00 0.00 37.87 3.93
2863 3099 1.303282 CGGGAAGCTTAAAGGGGCT 59.697 57.895 0.00 0.00 40.85 5.19
2864 3100 1.001269 ACGGGAAGCTTAAAGGGGC 60.001 57.895 0.00 0.00 0.00 5.80
3015 3255 3.269643 TGAGATAGAACCAGACAGAGGGA 59.730 47.826 0.00 0.00 0.00 4.20
3016 3256 3.636679 TGAGATAGAACCAGACAGAGGG 58.363 50.000 0.00 0.00 0.00 4.30
3171 3419 0.389391 CCTCCGCGTGACAGGATTAT 59.611 55.000 4.92 0.00 35.75 1.28
3185 3433 3.508744 AATGCATAAAAACTGCCTCCG 57.491 42.857 0.00 0.00 38.89 4.63
3213 3463 7.435192 CACCAGAATTAAACAAAGACAGGAAAC 59.565 37.037 0.00 0.00 0.00 2.78
3215 3465 6.831353 TCACCAGAATTAAACAAAGACAGGAA 59.169 34.615 0.00 0.00 0.00 3.36
3318 3568 7.340232 ACAGATGATGGCATGTTATTTACTTGT 59.660 33.333 3.81 0.00 34.11 3.16
3381 3631 0.106819 AGATTGCATGGGAGGCTGTC 60.107 55.000 0.00 0.00 0.00 3.51
3469 3720 0.887387 ATTACAACGCAGCAACGGGT 60.887 50.000 3.39 3.80 37.37 5.28
3481 3732 5.867174 GGTTGCCAGAAATAACCATTACAAC 59.133 40.000 0.00 0.00 33.86 3.32
3483 3734 5.080337 TGGTTGCCAGAAATAACCATTACA 58.920 37.500 4.10 0.00 38.48 2.41
3537 3788 6.472163 CCATAGCAATTAAGTAAAAACTGCGG 59.528 38.462 0.00 0.00 33.61 5.69
3581 3832 5.873179 ACATAAGGAATTCTCGCGAAAAA 57.127 34.783 11.33 8.26 31.91 1.94
3582 3833 6.537301 ACATACATAAGGAATTCTCGCGAAAA 59.463 34.615 11.33 2.82 31.91 2.29
3583 3834 6.046593 ACATACATAAGGAATTCTCGCGAAA 58.953 36.000 11.33 8.23 31.91 3.46
3584 3835 5.597806 ACATACATAAGGAATTCTCGCGAA 58.402 37.500 11.33 0.00 0.00 4.70
3585 3836 5.196341 ACATACATAAGGAATTCTCGCGA 57.804 39.130 9.26 9.26 0.00 5.87
3586 3837 5.234329 ACAACATACATAAGGAATTCTCGCG 59.766 40.000 0.00 0.00 0.00 5.87
3587 3838 6.604735 ACAACATACATAAGGAATTCTCGC 57.395 37.500 5.23 0.00 0.00 5.03
3588 3839 8.642908 TGTACAACATACATAAGGAATTCTCG 57.357 34.615 5.23 0.00 0.00 4.04
3593 3844 8.840321 GCAGAATGTACAACATACATAAGGAAT 58.160 33.333 0.00 0.00 37.97 3.01
3594 3845 8.046708 AGCAGAATGTACAACATACATAAGGAA 58.953 33.333 0.00 0.00 37.97 3.36
3595 3846 7.564793 AGCAGAATGTACAACATACATAAGGA 58.435 34.615 0.00 0.00 37.97 3.36
3596 3847 7.792374 AGCAGAATGTACAACATACATAAGG 57.208 36.000 0.00 0.00 37.97 2.69
3598 3849 9.325198 CCTAAGCAGAATGTACAACATACATAA 57.675 33.333 0.00 0.00 37.97 1.90
3599 3850 8.482943 ACCTAAGCAGAATGTACAACATACATA 58.517 33.333 0.00 0.00 37.97 2.29
3600 3851 7.280876 CACCTAAGCAGAATGTACAACATACAT 59.719 37.037 0.00 0.00 37.97 2.29
3601 3852 6.593770 CACCTAAGCAGAATGTACAACATACA 59.406 38.462 0.00 0.00 37.97 2.29
3602 3853 6.594159 ACACCTAAGCAGAATGTACAACATAC 59.406 38.462 0.00 0.00 37.97 2.39
3603 3854 6.593770 CACACCTAAGCAGAATGTACAACATA 59.406 38.462 0.00 0.00 37.97 2.29
3604 3855 5.412594 CACACCTAAGCAGAATGTACAACAT 59.587 40.000 0.00 0.00 41.31 2.71
3605 3856 4.754618 CACACCTAAGCAGAATGTACAACA 59.245 41.667 0.00 0.00 39.31 3.33
3670 3921 4.160065 TGGGTGAATTCTCGGACGTAAATA 59.840 41.667 7.05 0.00 0.00 1.40
3735 3989 9.967451 TCACCAATTGTTAATACTCATTAAGGA 57.033 29.630 4.43 0.00 37.30 3.36
3783 4037 1.415289 GCCCGGTAAGCCTTATACACT 59.585 52.381 0.00 0.00 0.00 3.55
3954 4208 5.007921 GCCAACATTTCTTGTCAAAAGCAAT 59.992 36.000 0.00 0.00 37.68 3.56
4017 4271 2.684943 TCCACTGAACCTGTAACCAGA 58.315 47.619 0.00 0.00 41.50 3.86
4068 4322 1.285667 TGCCCATGGAGATGTTGACAT 59.714 47.619 15.22 0.00 39.70 3.06
4081 4335 2.940158 TCCAATCAGAATCTGCCCATG 58.060 47.619 5.18 1.93 0.00 3.66
4162 4416 0.517316 GCACCACTAAAAGCACTCCG 59.483 55.000 0.00 0.00 0.00 4.63
4356 4611 1.201429 ATGAAGCTGGAAGTCGGGGT 61.201 55.000 0.00 0.00 35.30 4.95
4507 4762 9.535878 GTAAAACTCAAGGATAATGGACTAGAG 57.464 37.037 0.00 0.00 0.00 2.43
4776 5031 9.894783 CTTATCTCAATTCCAAATAATCTGCAG 57.105 33.333 7.63 7.63 0.00 4.41
5027 5282 5.402270 CCCTGAACGCTACAAAAATTGAAAG 59.598 40.000 0.00 0.00 0.00 2.62
5036 5291 6.232692 ACTTAATTACCCTGAACGCTACAAA 58.767 36.000 0.00 0.00 0.00 2.83
5233 5488 3.119352 TCATATCATCCTCTTCATCCGCG 60.119 47.826 0.00 0.00 0.00 6.46
5269 5524 2.844348 GGGTTCTTACTCCCAAGGATCA 59.156 50.000 0.00 0.00 42.95 2.92
5286 5541 2.722094 TCGCAAGCAATGATAAGGGTT 58.278 42.857 0.00 0.00 37.18 4.11
5297 5552 0.171679 CTGCATCCATTCGCAAGCAA 59.828 50.000 0.00 0.00 37.76 3.91
5300 5555 2.642139 AAACTGCATCCATTCGCAAG 57.358 45.000 0.00 0.00 37.76 4.01
5301 5556 2.352617 GGAAAACTGCATCCATTCGCAA 60.353 45.455 0.00 0.00 37.76 4.85
5304 5559 6.128172 GGATATAGGAAAACTGCATCCATTCG 60.128 42.308 6.83 0.00 39.17 3.34
5342 5597 5.163864 CGCTGCAACAACATGAATTAGAGTA 60.164 40.000 0.00 0.00 0.00 2.59
5376 5631 8.970691 ATAAATGTATATTCTTTTCGCCATGC 57.029 30.769 0.00 0.00 0.00 4.06
5392 5647 8.392631 TGGCCTCCTCATATGTATAAATGTAT 57.607 34.615 3.32 0.00 0.00 2.29
5497 5752 0.546122 TGGCAAACGAGGCTGGATAT 59.454 50.000 2.65 0.00 34.73 1.63
5553 5808 7.972832 TCAAAGGAAGAAAGAGCGTAATTAA 57.027 32.000 0.00 0.00 0.00 1.40
5588 5843 2.963101 AGTGGATGATCATGGGCATTTG 59.037 45.455 14.30 0.00 0.00 2.32
5591 5846 2.063425 AGAGTGGATGATCATGGGCAT 58.937 47.619 14.30 0.00 0.00 4.40
5672 5927 1.229076 GGACCAAACCCACCACAGT 59.771 57.895 0.00 0.00 0.00 3.55
5673 5928 0.823356 CAGGACCAAACCCACCACAG 60.823 60.000 0.00 0.00 0.00 3.66
5674 5929 1.228793 CAGGACCAAACCCACCACA 59.771 57.895 0.00 0.00 0.00 4.17
5675 5930 1.106944 CACAGGACCAAACCCACCAC 61.107 60.000 0.00 0.00 0.00 4.16
5676 5931 1.228793 CACAGGACCAAACCCACCA 59.771 57.895 0.00 0.00 0.00 4.17
5677 5932 0.822121 GACACAGGACCAAACCCACC 60.822 60.000 0.00 0.00 0.00 4.61
5678 5933 0.106918 TGACACAGGACCAAACCCAC 60.107 55.000 0.00 0.00 0.00 4.61
5814 6069 5.463724 GCCTATTTACTACTGTAGCAAGCAG 59.536 44.000 14.55 8.65 39.67 4.24
5934 6189 4.440826 AACATACTAACCACCACCAACA 57.559 40.909 0.00 0.00 0.00 3.33
5935 6190 4.216902 GGAAACATACTAACCACCACCAAC 59.783 45.833 0.00 0.00 0.00 3.77
5936 6191 4.105057 AGGAAACATACTAACCACCACCAA 59.895 41.667 0.00 0.00 0.00 3.67
5937 6192 3.653836 AGGAAACATACTAACCACCACCA 59.346 43.478 0.00 0.00 0.00 4.17
5938 6193 4.296621 AGGAAACATACTAACCACCACC 57.703 45.455 0.00 0.00 0.00 4.61
5939 6194 5.067954 ACAAGGAAACATACTAACCACCAC 58.932 41.667 0.00 0.00 0.00 4.16
5940 6195 5.313280 ACAAGGAAACATACTAACCACCA 57.687 39.130 0.00 0.00 0.00 4.17
6054 6311 5.134339 ACAGATGCCCAATCCCTAAAAGATA 59.866 40.000 0.00 0.00 35.72 1.98
6055 6312 4.078980 ACAGATGCCCAATCCCTAAAAGAT 60.079 41.667 0.00 0.00 35.72 2.40
6131 6390 0.038166 TTAAAGGCAGGCTCCCAGTG 59.962 55.000 0.00 0.00 0.00 3.66
6132 6391 0.777446 TTTAAAGGCAGGCTCCCAGT 59.223 50.000 0.00 0.00 0.00 4.00
6133 6392 1.177401 GTTTAAAGGCAGGCTCCCAG 58.823 55.000 0.00 0.00 0.00 4.45
6134 6393 0.251608 GGTTTAAAGGCAGGCTCCCA 60.252 55.000 0.00 0.00 0.00 4.37
6135 6394 0.251608 TGGTTTAAAGGCAGGCTCCC 60.252 55.000 0.00 0.00 0.00 4.30
6198 9210 1.539827 CTACAACCCAAAAGAAGCCCG 59.460 52.381 0.00 0.00 0.00 6.13
6203 9215 7.299134 TCCTAAATTCCTACAACCCAAAAGAA 58.701 34.615 0.00 0.00 0.00 2.52
6264 9276 4.971939 TCGCAATCCTATGATCCAAATGA 58.028 39.130 0.00 0.00 0.00 2.57
6437 9451 6.020440 CGTTTGGATGATGCATAATGACAAAC 60.020 38.462 26.45 26.45 40.76 2.93
6439 9453 5.580661 CGTTTGGATGATGCATAATGACAA 58.419 37.500 0.00 4.08 0.00 3.18
6441 9455 3.976942 GCGTTTGGATGATGCATAATGAC 59.023 43.478 0.00 0.00 0.00 3.06
6443 9457 3.732219 GTGCGTTTGGATGATGCATAATG 59.268 43.478 0.00 0.00 40.74 1.90
6444 9458 3.380954 TGTGCGTTTGGATGATGCATAAT 59.619 39.130 0.00 0.00 40.74 1.28
6445 9459 2.751806 TGTGCGTTTGGATGATGCATAA 59.248 40.909 0.00 0.00 40.74 1.90
6446 9460 2.363683 TGTGCGTTTGGATGATGCATA 58.636 42.857 0.00 0.00 40.74 3.14
6447 9461 1.175654 TGTGCGTTTGGATGATGCAT 58.824 45.000 0.00 0.00 40.74 3.96
6448 9462 1.135344 CATGTGCGTTTGGATGATGCA 60.135 47.619 0.00 0.00 36.73 3.96
6449 9463 1.135315 ACATGTGCGTTTGGATGATGC 60.135 47.619 0.00 0.00 0.00 3.91
6450 9464 2.918600 CAACATGTGCGTTTGGATGATG 59.081 45.455 0.00 0.00 0.00 3.07
6451 9465 2.671914 GCAACATGTGCGTTTGGATGAT 60.672 45.455 0.00 0.00 45.10 2.45
6452 9466 1.335780 GCAACATGTGCGTTTGGATGA 60.336 47.619 0.00 0.00 45.10 2.92
6466 9483 8.752187 ACTGAAAATACAGGAATTATGCAACAT 58.248 29.630 0.00 0.00 41.59 2.71
6487 9504 6.105397 ACGGTGAAATCCTACTAAACTGAA 57.895 37.500 0.00 0.00 0.00 3.02
6491 9508 7.009907 GTCATGTACGGTGAAATCCTACTAAAC 59.990 40.741 2.70 0.00 0.00 2.01
6508 9526 1.757118 AGGAGTGGGATGTCATGTACG 59.243 52.381 0.00 0.00 0.00 3.67
6509 9527 4.323553 GTAGGAGTGGGATGTCATGTAC 57.676 50.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.