Multiple sequence alignment - TraesCS4D01G156600

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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 TraesCS4D01G156600 chr4D 100.000 5961 0 0 1420 7380 211389386 211383426 0.000000e+00 11008.0
1 TraesCS4D01G156600 chr4D 100.000 1054 0 0 1 1054 211390805 211389752 0.000000e+00 1947.0
2 TraesCS4D01G156600 chr4D 87.850 321 39 0 2469 2789 75046291 75046611 1.940000e-100 377.0
3 TraesCS4D01G156600 chr4D 94.186 86 5 0 2163 2248 270678549 270678634 1.670000e-26 132.0
4 TraesCS4D01G156600 chr4D 95.082 61 3 0 4799 4859 1371532 1371472 6.090000e-16 97.1
5 TraesCS4D01G156600 chr4B 96.461 3984 97 13 1420 5370 282887719 282883747 0.000000e+00 6536.0
6 TraesCS4D01G156600 chr4B 92.610 1881 51 22 5474 7330 282883748 282881932 0.000000e+00 2623.0
7 TraesCS4D01G156600 chr4B 90.446 471 36 2 362 823 282895113 282894643 4.890000e-171 612.0
8 TraesCS4D01G156600 chr4B 98.842 259 3 0 796 1054 282888079 282887821 5.220000e-126 462.0
9 TraesCS4D01G156600 chr4B 90.578 329 21 4 1 329 283047782 283047464 1.900000e-115 427.0
10 TraesCS4D01G156600 chr4B 88.438 320 36 1 2468 2787 107453013 107453331 1.160000e-102 385.0
11 TraesCS4D01G156600 chr4A 95.146 1813 63 7 2733 4520 204961505 204963317 0.000000e+00 2837.0
12 TraesCS4D01G156600 chr4A 94.743 1769 58 16 5474 7221 204964525 204966279 0.000000e+00 2719.0
13 TraesCS4D01G156600 chr4A 90.659 1092 62 8 1 1054 204956159 204957248 0.000000e+00 1415.0
14 TraesCS4D01G156600 chr4A 97.503 721 16 2 1420 2139 204957350 204958069 0.000000e+00 1230.0
15 TraesCS4D01G156600 chr4A 94.279 402 14 1 4958 5359 204964128 204964520 2.280000e-169 606.0
16 TraesCS4D01G156600 chr4A 93.899 377 13 6 4537 4908 204963466 204963837 1.800000e-155 560.0
17 TraesCS4D01G156600 chr4A 90.031 321 32 0 2469 2789 512543504 512543184 4.120000e-112 416.0
18 TraesCS4D01G156600 chr4A 83.333 138 18 3 1 137 385069586 385069719 1.010000e-23 122.0
19 TraesCS4D01G156600 chr4A 90.909 77 7 0 2213 2289 204961428 204961504 3.640000e-18 104.0
20 TraesCS4D01G156600 chr4A 97.959 49 1 0 2122 2170 204961380 204961428 1.320000e-12 86.1
21 TraesCS4D01G156600 chr6B 89.841 315 29 3 2474 2788 26227683 26227994 1.150000e-107 401.0
22 TraesCS4D01G156600 chr6B 88.924 316 34 1 2474 2789 26012970 26012656 8.980000e-104 388.0
23 TraesCS4D01G156600 chr5D 89.776 313 31 1 2474 2786 114976363 114976674 4.150000e-107 399.0
24 TraesCS4D01G156600 chr5D 96.471 85 3 0 2163 2247 318879332 318879416 2.780000e-29 141.0
25 TraesCS4D01G156600 chr5D 80.000 160 13 12 5834 5992 280380902 280381043 4.710000e-17 100.0
26 TraesCS4D01G156600 chr1A 88.365 318 33 4 2472 2789 412467082 412466769 5.400000e-101 379.0
27 TraesCS4D01G156600 chr1A 98.276 116 1 1 5360 5475 343396688 343396802 1.260000e-47 202.0
28 TraesCS4D01G156600 chr7D 87.195 328 41 1 2464 2791 104883725 104883399 9.040000e-99 372.0
29 TraesCS4D01G156600 chr7D 87.864 206 21 4 96 299 166884946 166885149 9.570000e-59 239.0
30 TraesCS4D01G156600 chr7D 87.879 132 11 5 4677 4806 484423865 484423993 4.610000e-32 150.0
31 TraesCS4D01G156600 chr7D 94.915 59 3 0 348 406 196125282 196125224 7.880000e-15 93.5
32 TraesCS4D01G156600 chr2A 97.561 123 3 0 5363 5485 187955809 187955931 2.090000e-50 211.0
33 TraesCS4D01G156600 chr2A 98.246 114 1 1 5362 5475 28208316 28208204 1.620000e-46 198.0
34 TraesCS4D01G156600 chr2A 92.553 94 6 1 2154 2247 509051635 509051727 4.650000e-27 134.0
35 TraesCS4D01G156600 chr5A 98.291 117 2 0 5366 5482 492896370 492896254 9.710000e-49 206.0
36 TraesCS4D01G156600 chr5A 81.675 191 21 9 4678 4858 109953097 109953283 5.970000e-31 147.0
37 TraesCS4D01G156600 chr1B 97.479 119 1 1 5360 5476 687254060 687253942 1.260000e-47 202.0
38 TraesCS4D01G156600 chr1B 96.639 119 2 1 5360 5476 651523580 651523698 5.840000e-46 196.0
39 TraesCS4D01G156600 chr1B 84.868 152 14 4 1 152 17740475 17740333 2.150000e-30 145.0
40 TraesCS4D01G156600 chr1B 87.500 112 13 1 2140 2250 447815472 447815361 2.160000e-25 128.0
41 TraesCS4D01G156600 chr3D 86.559 186 19 4 4677 4861 540237422 540237242 4.520000e-47 200.0
42 TraesCS4D01G156600 chr3D 84.153 183 25 2 4676 4858 126947003 126947181 2.740000e-39 174.0
43 TraesCS4D01G156600 chr3B 100.000 107 0 0 5369 5475 12156967 12156861 1.620000e-46 198.0
44 TraesCS4D01G156600 chr3B 85.326 184 20 4 4676 4858 181286734 181286911 4.550000e-42 183.0
45 TraesCS4D01G156600 chr3B 90.909 99 8 1 2150 2247 406868780 406868878 1.670000e-26 132.0
46 TraesCS4D01G156600 chr3B 81.250 176 21 3 1 176 553475275 553475438 1.670000e-26 132.0
47 TraesCS4D01G156600 chr1D 86.022 186 23 3 4678 4861 211688916 211688732 5.840000e-46 196.0
48 TraesCS4D01G156600 chr1D 94.318 88 5 0 2162 2249 338394563 338394476 1.290000e-27 135.0
49 TraesCS4D01G156600 chr3A 96.610 118 3 1 5358 5475 46169091 46169207 2.100000e-45 195.0
50 TraesCS4D01G156600 chr3A 98.198 111 2 0 5366 5476 336604532 336604642 2.100000e-45 195.0
51 TraesCS4D01G156600 chr3A 86.022 186 20 4 4677 4861 675330789 675330609 2.100000e-45 195.0
52 TraesCS4D01G156600 chr7A 94.382 89 5 0 2160 2248 608509126 608509214 3.590000e-28 137.0
53 TraesCS4D01G156600 chr7A 86.000 100 13 1 4762 4861 126583796 126583698 1.010000e-18 106.0
54 TraesCS4D01G156600 chr5B 94.382 89 5 0 2160 2248 26770502 26770414 3.590000e-28 137.0
55 TraesCS4D01G156600 chr5B 86.792 106 13 1 5883 5987 74996065 74996170 4.680000e-22 117.0
56 TraesCS4D01G156600 chr2B 80.447 179 20 5 1 177 441493026 441493191 1.010000e-23 122.0
57 TraesCS4D01G156600 chr2B 80.503 159 22 5 5834 5991 220904687 220904537 6.050000e-21 113.0
58 TraesCS4D01G156600 chr2B 81.250 144 18 4 4 147 425093448 425093314 2.820000e-19 108.0
59 TraesCS4D01G156600 chr7B 91.463 82 6 1 326 406 160473233 160473152 2.180000e-20 111.0
60 TraesCS4D01G156600 chr2D 85.714 56 7 1 582 637 606205195 606205141 2.880000e-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 TraesCS4D01G156600 chr4D 211383426 211390805 7379 True 6477.5000 11008 100.000000 1 7380 2 chr4D.!!$R2 7379
1 TraesCS4D01G156600 chr4B 282881932 282888079 6147 True 3207.0000 6536 95.971000 796 7330 3 chr4B.!!$R3 6534
2 TraesCS4D01G156600 chr4A 204956159 204966279 10120 False 1194.6375 2837 94.387125 1 7221 8 chr4A.!!$F2 7220

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
345 346 0.179145 CCTGGTACTTGTAGCCGTCG 60.179 60.000 7.40 0.0 0.0 5.12 F
642 643 0.320946 TAAGTTTTCGGGCTGGGTCG 60.321 55.000 0.00 0.0 0.0 4.79 F
1437 1476 1.373497 ACTGTTCCTTCGCTCGCTG 60.373 57.895 0.00 0.0 0.0 5.18 F
3124 6506 0.095245 CTAAGTGCATGCGTTGTCCG 59.905 55.000 14.09 0.0 40.4 4.79 F
4760 8288 0.912486 ATAGCAACACCTCCCCTCAC 59.088 55.000 0.00 0.0 0.0 3.51 F
5383 9170 0.108945 GTGTTACTCCCTCCGTTCCG 60.109 60.000 0.00 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1476 1.929169 GCACGTAAATTCTACGGTCCC 59.071 52.381 18.04 5.95 44.38 4.46 R
2604 5972 0.037447 TCCCGTGCATGGTTGAATGA 59.963 50.000 23.39 9.55 0.00 2.57 R
3415 6797 0.886563 CCTAGACCGACCAACGAGTT 59.113 55.000 0.00 0.00 45.77 3.01 R
4878 8423 1.451504 CTCACACCTGACTTGGGCA 59.548 57.895 0.00 0.00 0.00 5.36 R
5879 9672 0.040067 CGCTTTGGTCAGGAAAGTGC 60.040 55.000 0.00 0.00 34.96 4.40 R
7028 10836 0.594796 GCGTGCAAAGGTGAAACAGG 60.595 55.000 0.00 0.00 39.98 4.00 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
26 27 3.859627 GCTCATTTGCATACATGGCATCC 60.860 47.826 0.00 0.00 41.58 3.51
31 32 1.063792 TGCATACATGGCATCCCACTT 60.064 47.619 0.00 0.00 45.77 3.16
47 48 1.476085 CACTTTGGTGGTTTGACAGCA 59.524 47.619 0.00 0.00 46.02 4.41
51 52 1.827789 GGTGGTTTGACAGCAGGCA 60.828 57.895 0.00 0.00 38.65 4.75
99 100 2.325661 ACTGGGAGAAAAATTGGGGG 57.674 50.000 0.00 0.00 0.00 5.40
102 103 3.247162 CTGGGAGAAAAATTGGGGGAAA 58.753 45.455 0.00 0.00 0.00 3.13
111 112 2.268796 ATTGGGGGAAATTTGAGGGG 57.731 50.000 0.00 0.00 0.00 4.79
124 125 4.617595 AGGGGGAAGGGTGGTGCT 62.618 66.667 0.00 0.00 0.00 4.40
127 128 2.283173 GGGAAGGGTGGTGCTTGG 60.283 66.667 0.00 0.00 0.00 3.61
153 154 5.766670 TCTGTATACCAGATGTTAGGTACCG 59.233 44.000 6.18 0.00 45.34 4.02
169 170 9.352191 GTTAGGTACCGGATATATCTATCACAT 57.648 37.037 9.46 6.58 36.27 3.21
186 187 5.113502 TCACATGATCTATAGCACTCACG 57.886 43.478 0.00 0.00 0.00 4.35
247 248 4.583489 GGATACACGAATGTAGAGGAAGGA 59.417 45.833 0.00 0.00 44.51 3.36
250 251 3.024547 CACGAATGTAGAGGAAGGAGGA 58.975 50.000 0.00 0.00 0.00 3.71
260 261 2.178106 GAGGAAGGAGGATGGAGGTAGA 59.822 54.545 0.00 0.00 0.00 2.59
276 277 4.672899 AGGTAGAAGAAGAACAGAGAGCT 58.327 43.478 0.00 0.00 0.00 4.09
302 303 0.798776 GCCAAGTTCGTGATCCACTG 59.201 55.000 0.00 0.00 31.34 3.66
314 315 1.122019 ATCCACTGGATACCTCGCCC 61.122 60.000 9.00 0.00 41.16 6.13
345 346 0.179145 CCTGGTACTTGTAGCCGTCG 60.179 60.000 7.40 0.00 0.00 5.12
357 358 2.183555 CCGTCGGGGTTGTAGCTC 59.816 66.667 2.34 0.00 0.00 4.09
401 402 0.616679 TAGCCCATACCTATCGGCCC 60.617 60.000 0.00 0.00 40.32 5.80
407 408 1.482593 CATACCTATCGGCCCAGGATC 59.517 57.143 17.46 0.00 35.76 3.36
411 412 1.152419 TATCGGCCCAGGATCGGAA 60.152 57.895 0.00 0.00 0.00 4.30
413 414 4.241555 CGGCCCAGGATCGGAAGG 62.242 72.222 0.00 0.00 0.00 3.46
417 418 1.072159 CCCAGGATCGGAAGGATGC 59.928 63.158 0.00 0.00 43.29 3.91
449 450 3.257873 TGGACCGTCGGTAAGTTTTATCA 59.742 43.478 18.88 2.31 35.25 2.15
461 462 5.373981 AAGTTTTATCAGACGACGACTCT 57.626 39.130 0.00 0.00 0.00 3.24
470 471 2.683867 AGACGACGACTCTAAATCAGGG 59.316 50.000 0.00 0.00 0.00 4.45
473 474 2.539142 CGACGACTCTAAATCAGGGACG 60.539 54.545 0.00 0.00 46.53 4.79
474 475 1.749634 ACGACTCTAAATCAGGGACGG 59.250 52.381 0.00 0.00 45.59 4.79
475 476 2.022195 CGACTCTAAATCAGGGACGGA 58.978 52.381 0.00 0.00 38.95 4.69
508 509 3.411517 CCGGGACAATGGCTCCCT 61.412 66.667 7.83 0.00 45.00 4.20
512 513 0.694444 GGGACAATGGCTCCCTCCTA 60.694 60.000 2.37 0.00 43.93 2.94
513 514 0.470341 GGACAATGGCTCCCTCCTAC 59.530 60.000 0.00 0.00 0.00 3.18
527 528 6.262056 TCCCTCCTACAGTTTTTCTTCTTT 57.738 37.500 0.00 0.00 0.00 2.52
532 533 9.338622 CCTCCTACAGTTTTTCTTCTTTTTCTA 57.661 33.333 0.00 0.00 0.00 2.10
547 548 6.311735 TCTTTTTCTAAAAGCACCCCTACAT 58.688 36.000 6.96 0.00 0.00 2.29
583 584 2.734079 GCTCTAAATCTATGTGCTCGCC 59.266 50.000 0.00 0.00 0.00 5.54
596 597 0.678048 GCTCGCCTCCCTTGATGTTT 60.678 55.000 0.00 0.00 0.00 2.83
642 643 0.320946 TAAGTTTTCGGGCTGGGTCG 60.321 55.000 0.00 0.00 0.00 4.79
788 794 1.691196 TTGCAAGTGAGACCCAAAGG 58.309 50.000 0.00 0.00 40.04 3.11
806 812 3.320673 AGGCCGAAACAAACAAACAAA 57.679 38.095 0.00 0.00 0.00 2.83
1437 1476 1.373497 ACTGTTCCTTCGCTCGCTG 60.373 57.895 0.00 0.00 0.00 5.18
1479 1518 3.480470 TGTTTTTCTTGGCTCTCAGGAG 58.520 45.455 0.00 0.00 42.18 3.69
1603 1642 8.855952 AGATAGATCCAAGGATTAGATACTCCT 58.144 37.037 2.62 0.00 43.86 3.69
2170 5538 8.915057 ATTTTCATGTTCTGATATACTCCCTG 57.085 34.615 0.00 0.00 32.72 4.45
2260 5628 2.233922 AGGGAGTATATTCGATTGGCCG 59.766 50.000 0.00 0.00 0.00 6.13
2303 5671 9.918630 AAAAGAATTTCTAATGGTTGATCACTG 57.081 29.630 0.00 0.00 37.28 3.66
2365 5733 5.405935 AATTTTAGTTTAGGCAGGCTTGG 57.594 39.130 0.00 0.00 0.00 3.61
2425 5793 4.234550 AGTTATATCCCTCATGCCACAGA 58.765 43.478 0.00 0.00 0.00 3.41
2604 5972 4.892002 GGAAAAGACCCACCACGT 57.108 55.556 0.00 0.00 0.00 4.49
2632 6000 2.103941 ACCATGCACGGGAAAATGTTTT 59.896 40.909 12.94 0.00 0.00 2.43
2633 6001 2.736192 CCATGCACGGGAAAATGTTTTC 59.264 45.455 9.22 9.22 44.38 2.29
2634 6002 3.554752 CCATGCACGGGAAAATGTTTTCT 60.555 43.478 15.49 0.00 44.49 2.52
2760 6128 5.221702 CCCAAATTTTCATCAACCAACTCCT 60.222 40.000 0.00 0.00 0.00 3.69
2841 6209 3.523606 CAGAGATAGTGTGCTGCTCTT 57.476 47.619 0.00 0.00 36.41 2.85
3001 6382 3.749609 GCCGACTTAGCCTTTTCTTGTTA 59.250 43.478 0.00 0.00 0.00 2.41
3044 6426 5.579047 ACAAATTGGTCACAAGGATGGATA 58.421 37.500 0.00 0.00 40.49 2.59
3089 6471 6.675026 TCTTTGATTCACTGCTTTCATGAAG 58.325 36.000 8.41 4.57 35.89 3.02
3124 6506 0.095245 CTAAGTGCATGCGTTGTCCG 59.905 55.000 14.09 0.00 40.40 4.79
3185 6567 4.158764 AGCAACTAATCTACTCAACGAGCT 59.841 41.667 0.00 0.00 32.04 4.09
3216 6598 5.119694 CACCTCTAAGGAAGCTAAATGTCC 58.880 45.833 0.00 0.00 37.67 4.02
3263 6645 5.388890 GCACATCTTGAGTCAAGTTAACTCG 60.389 44.000 27.83 12.82 44.96 4.18
3368 6750 5.895928 ACATATAGGCTAGACATGTATGCG 58.104 41.667 14.19 0.00 0.00 4.73
3375 6757 2.121116 AGACATGTATGCGCGTAGAC 57.879 50.000 15.23 15.23 0.00 2.59
3414 6796 2.364002 TGTTGTCAACGATGGTCTGAGA 59.636 45.455 11.03 0.00 0.00 3.27
3415 6797 3.181470 TGTTGTCAACGATGGTCTGAGAA 60.181 43.478 11.03 0.00 0.00 2.87
3705 7087 4.212716 CATGAACCTGATTGTGGATCCAT 58.787 43.478 19.62 0.75 33.60 3.41
3736 7118 1.418637 TGGTCTTGGTAACTGTGGACC 59.581 52.381 0.00 0.00 39.73 4.46
3772 7156 3.574396 TCAAGTCGTTCTCTTCTGTGGAT 59.426 43.478 0.00 0.00 0.00 3.41
3855 7239 8.991026 CACATTTCATTATGTGTTGACCAAAAT 58.009 29.630 8.24 0.00 46.53 1.82
3867 7251 7.496920 TGTGTTGACCAAAATCATTTATTTGCA 59.503 29.630 0.00 0.00 37.85 4.08
4020 7405 3.751479 TGTAACACTGCATGACTCACT 57.249 42.857 0.00 0.00 0.00 3.41
4125 7510 5.535783 TGGGCATCATGTACCAAAATATGAG 59.464 40.000 1.15 0.00 33.53 2.90
4306 7698 4.792513 TGGGTGTTTGGAAGGTTAGTAA 57.207 40.909 0.00 0.00 0.00 2.24
4366 7758 3.579709 AGCACTTCAGACACGTGATTAG 58.420 45.455 25.01 13.43 0.00 1.73
4479 7871 3.920446 ACCACCGAAATTATTTGTTGCC 58.080 40.909 0.00 0.00 0.00 4.52
4641 8169 7.333323 TGTATGTATGATAGCCAGATGGAATG 58.667 38.462 2.18 0.00 37.39 2.67
4661 8189 4.746535 TGTCGTTTATCTATTCAGGGCA 57.253 40.909 0.00 0.00 0.00 5.36
4760 8288 0.912486 ATAGCAACACCTCCCCTCAC 59.088 55.000 0.00 0.00 0.00 3.51
4858 8403 1.568504 AATGCGGGGACTGAGACTTA 58.431 50.000 0.00 0.00 36.31 2.24
4878 8423 5.312443 ACTTAAAGGGGGTTGTTGTATCTCT 59.688 40.000 0.00 0.00 0.00 3.10
4916 8462 0.404040 GGGAGGTGTTGGTCATTCCA 59.596 55.000 0.00 0.00 45.60 3.53
4921 8467 4.137543 GAGGTGTTGGTCATTCCATATCC 58.862 47.826 0.00 0.00 46.60 2.59
4925 8471 2.254546 TGGTCATTCCATATCCACGC 57.745 50.000 0.00 0.00 41.93 5.34
5062 8849 6.341316 TCAACTAATCTCAGTAGAACATGCC 58.659 40.000 0.00 0.00 34.73 4.40
5189 8976 4.501400 GGTGGTTTGGAATTGGTTGAAGAG 60.501 45.833 0.00 0.00 0.00 2.85
5267 9054 5.163395 GGGTTGTGTTGAGAATTTTTGGGTA 60.163 40.000 0.00 0.00 0.00 3.69
5274 9061 9.010029 GTGTTGAGAATTTTTGGGTAGAGAATA 57.990 33.333 0.00 0.00 0.00 1.75
5275 9062 9.581289 TGTTGAGAATTTTTGGGTAGAGAATAA 57.419 29.630 0.00 0.00 0.00 1.40
5368 9155 2.014128 CCTGTGGTCGAAAACAGTGTT 58.986 47.619 21.12 1.64 41.85 3.32
5369 9156 3.199677 CCTGTGGTCGAAAACAGTGTTA 58.800 45.455 21.12 0.00 41.85 2.41
5370 9157 3.001939 CCTGTGGTCGAAAACAGTGTTAC 59.998 47.826 21.12 3.44 41.85 2.50
5371 9158 3.864243 TGTGGTCGAAAACAGTGTTACT 58.136 40.909 9.37 0.00 0.00 2.24
5372 9159 3.866910 TGTGGTCGAAAACAGTGTTACTC 59.133 43.478 9.37 8.30 0.00 2.59
5373 9160 3.246936 GTGGTCGAAAACAGTGTTACTCC 59.753 47.826 9.37 11.42 0.00 3.85
5374 9161 2.804527 GGTCGAAAACAGTGTTACTCCC 59.195 50.000 9.37 2.67 0.00 4.30
5375 9162 3.493873 GGTCGAAAACAGTGTTACTCCCT 60.494 47.826 9.37 0.00 0.00 4.20
5376 9163 3.739810 GTCGAAAACAGTGTTACTCCCTC 59.260 47.826 9.37 0.00 0.00 4.30
5377 9164 3.064931 CGAAAACAGTGTTACTCCCTCC 58.935 50.000 9.37 0.00 0.00 4.30
5378 9165 2.833631 AAACAGTGTTACTCCCTCCG 57.166 50.000 9.37 0.00 0.00 4.63
5379 9166 1.713297 AACAGTGTTACTCCCTCCGT 58.287 50.000 6.75 0.00 0.00 4.69
5380 9167 1.713297 ACAGTGTTACTCCCTCCGTT 58.287 50.000 0.00 0.00 0.00 4.44
5381 9168 1.617357 ACAGTGTTACTCCCTCCGTTC 59.383 52.381 0.00 0.00 0.00 3.95
5382 9169 1.067071 CAGTGTTACTCCCTCCGTTCC 60.067 57.143 0.00 0.00 0.00 3.62
5383 9170 0.108945 GTGTTACTCCCTCCGTTCCG 60.109 60.000 0.00 0.00 0.00 4.30
5384 9171 0.251297 TGTTACTCCCTCCGTTCCGA 60.251 55.000 0.00 0.00 0.00 4.55
5385 9172 0.890683 GTTACTCCCTCCGTTCCGAA 59.109 55.000 0.00 0.00 0.00 4.30
5386 9173 1.479730 GTTACTCCCTCCGTTCCGAAT 59.520 52.381 0.00 0.00 0.00 3.34
5387 9174 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
5388 9175 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
5389 9176 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
5390 9177 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
5391 9178 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
5392 9179 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
5393 9180 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
5394 9181 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
5395 9182 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
5396 9183 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
5397 9184 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
5398 9185 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
5399 9186 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85
5400 9187 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00
5401 9188 2.492881 TCCGAATTACTTGTCGCAGGTA 59.507 45.455 0.00 0.00 35.93 3.08
5402 9189 3.131577 TCCGAATTACTTGTCGCAGGTAT 59.868 43.478 3.46 0.00 35.93 2.73
5403 9190 3.245284 CCGAATTACTTGTCGCAGGTATG 59.755 47.826 3.46 0.00 35.93 2.39
5404 9191 3.245284 CGAATTACTTGTCGCAGGTATGG 59.755 47.826 3.46 0.00 0.00 2.74
5405 9192 4.439057 GAATTACTTGTCGCAGGTATGGA 58.561 43.478 3.46 0.00 0.00 3.41
5406 9193 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
5407 9194 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
5408 9195 1.555075 ACTTGTCGCAGGTATGGATGT 59.445 47.619 0.00 0.00 0.00 3.06
5409 9196 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
5410 9197 3.388024 ACTTGTCGCAGGTATGGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
5411 9198 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
5412 9199 3.230976 TGTCGCAGGTATGGATGTATCT 58.769 45.455 0.00 0.00 0.00 1.98
5413 9200 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
5414 9201 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
5415 9202 4.700692 GTCGCAGGTATGGATGTATCTAGA 59.299 45.833 0.00 0.00 0.00 2.43
5416 9203 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
5417 9204 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
5418 9205 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
5419 9206 6.318900 CGCAGGTATGGATGTATCTAGATGTA 59.681 42.308 15.79 4.44 0.00 2.29
5420 9207 7.013750 CGCAGGTATGGATGTATCTAGATGTAT 59.986 40.741 15.79 9.11 0.00 2.29
5421 9208 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
5447 9234 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
5448 9235 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
5449 9236 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
5450 9237 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
5451 9238 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
5452 9239 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
5453 9240 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
5454 9241 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
5455 9242 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
5456 9243 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
5457 9244 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
5458 9245 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
5459 9246 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
5460 9247 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
5461 9248 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
5462 9249 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
5463 9250 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
5464 9251 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
5465 9252 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
5466 9253 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
5467 9254 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
5468 9255 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
5469 9256 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
5470 9257 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
5471 9258 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
5472 9259 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
5556 9349 3.081061 ACCTGAATCGTTTATGCTTGCA 58.919 40.909 0.00 0.00 0.00 4.08
5707 9500 8.856153 TTTCTTAAACTACATGTGCCAGATAA 57.144 30.769 9.11 3.43 0.00 1.75
5843 9636 4.547532 TCGAAGTTGAAGAAGTGCTAGAC 58.452 43.478 0.00 0.00 0.00 2.59
5874 9667 0.390209 ATTTTGCCATCGCCTTGCAC 60.390 50.000 0.00 0.00 34.16 4.57
5875 9668 1.742324 TTTTGCCATCGCCTTGCACA 61.742 50.000 0.00 0.00 34.16 4.57
5876 9669 2.144833 TTTGCCATCGCCTTGCACAG 62.145 55.000 0.00 0.00 34.16 3.66
5877 9670 3.058160 GCCATCGCCTTGCACAGT 61.058 61.111 0.00 0.00 0.00 3.55
5878 9671 2.629656 GCCATCGCCTTGCACAGTT 61.630 57.895 0.00 0.00 0.00 3.16
5879 9672 1.210931 CCATCGCCTTGCACAGTTG 59.789 57.895 0.00 0.00 0.00 3.16
6214 10008 0.829182 CCTTTTTGCCTCTGGGTGCT 60.829 55.000 0.00 0.00 34.45 4.40
6459 10253 9.826574 TGGTATCTGTACTAAAGCGAAATTTAT 57.173 29.630 0.00 0.00 0.00 1.40
6607 10402 6.381133 TCTCTTCTGCTTACCATGTCTGATTA 59.619 38.462 0.00 0.00 0.00 1.75
6697 10492 9.495754 GATAAATAGCTGTGAGATTTGTTGTTC 57.504 33.333 0.00 0.00 0.00 3.18
6713 10508 2.920524 TGTTCGGTTTAGCTGGTTGAA 58.079 42.857 0.00 0.00 0.00 2.69
6913 10721 2.751806 GCTCATCCTCCCAAGACAAAAG 59.248 50.000 0.00 0.00 0.00 2.27
6939 10747 8.610896 GCAATTATGTGCCAAATTATTTGCTTA 58.389 29.630 11.82 0.00 39.31 3.09
7028 10836 4.023107 TCGCTGAGTATGGTGCTCTTATAC 60.023 45.833 0.00 0.00 34.30 1.47
7048 10856 0.594796 CTGTTTCACCTTTGCACGCC 60.595 55.000 0.00 0.00 0.00 5.68
7120 10928 1.444553 GTGAACCAGAGCGAGACCG 60.445 63.158 0.00 0.00 39.16 4.79
7226 11042 0.813610 CACCCGACACAGCTTGTTCA 60.814 55.000 3.56 0.00 39.17 3.18
7227 11043 0.107410 ACCCGACACAGCTTGTTCAA 60.107 50.000 3.56 0.00 39.17 2.69
7228 11044 0.588252 CCCGACACAGCTTGTTCAAG 59.412 55.000 8.04 8.04 39.17 3.02
7270 11086 1.591863 GCCCGTCCTCGAAGTATGC 60.592 63.158 0.00 0.00 39.71 3.14
7305 11121 0.108585 CTTATATGTGCCGGCTGGGT 59.891 55.000 29.70 13.43 38.44 4.51
7330 11146 0.383949 GTCCATCTCACGAGCTCCTC 59.616 60.000 8.47 0.00 0.00 3.71
7331 11147 0.257328 TCCATCTCACGAGCTCCTCT 59.743 55.000 8.47 0.00 0.00 3.69
7332 11148 1.490910 TCCATCTCACGAGCTCCTCTA 59.509 52.381 8.47 0.00 0.00 2.43
7333 11149 1.879380 CCATCTCACGAGCTCCTCTAG 59.121 57.143 8.47 0.91 0.00 2.43
7334 11150 2.571212 CATCTCACGAGCTCCTCTAGT 58.429 52.381 8.47 0.00 0.00 2.57
7335 11151 2.791347 TCTCACGAGCTCCTCTAGTT 57.209 50.000 8.47 0.00 0.00 2.24
7336 11152 2.634600 TCTCACGAGCTCCTCTAGTTC 58.365 52.381 8.47 0.00 32.38 3.01
7337 11153 1.673920 CTCACGAGCTCCTCTAGTTCC 59.326 57.143 8.47 0.00 32.05 3.62
7338 11154 1.282447 TCACGAGCTCCTCTAGTTCCT 59.718 52.381 8.47 0.00 32.05 3.36
7339 11155 1.673920 CACGAGCTCCTCTAGTTCCTC 59.326 57.143 8.47 0.00 32.05 3.71
7340 11156 1.314730 CGAGCTCCTCTAGTTCCTCC 58.685 60.000 8.47 0.00 32.05 4.30
7341 11157 1.133915 CGAGCTCCTCTAGTTCCTCCT 60.134 57.143 8.47 0.00 32.05 3.69
7342 11158 2.306847 GAGCTCCTCTAGTTCCTCCTG 58.693 57.143 0.87 0.00 29.55 3.86
7343 11159 1.643811 AGCTCCTCTAGTTCCTCCTGT 59.356 52.381 0.00 0.00 0.00 4.00
7344 11160 2.853707 AGCTCCTCTAGTTCCTCCTGTA 59.146 50.000 0.00 0.00 0.00 2.74
7345 11161 2.953648 GCTCCTCTAGTTCCTCCTGTAC 59.046 54.545 0.00 0.00 0.00 2.90
7346 11162 3.372241 GCTCCTCTAGTTCCTCCTGTACT 60.372 52.174 0.00 0.00 0.00 2.73
7347 11163 4.862371 CTCCTCTAGTTCCTCCTGTACTT 58.138 47.826 0.00 0.00 0.00 2.24
7348 11164 5.265989 CTCCTCTAGTTCCTCCTGTACTTT 58.734 45.833 0.00 0.00 0.00 2.66
7349 11165 5.262804 TCCTCTAGTTCCTCCTGTACTTTC 58.737 45.833 0.00 0.00 0.00 2.62
7350 11166 4.403113 CCTCTAGTTCCTCCTGTACTTTCC 59.597 50.000 0.00 0.00 0.00 3.13
7351 11167 5.265989 CTCTAGTTCCTCCTGTACTTTCCT 58.734 45.833 0.00 0.00 0.00 3.36
7352 11168 5.017490 TCTAGTTCCTCCTGTACTTTCCTG 58.983 45.833 0.00 0.00 0.00 3.86
7353 11169 2.907042 AGTTCCTCCTGTACTTTCCTGG 59.093 50.000 0.00 0.00 0.00 4.45
7354 11170 1.276622 TCCTCCTGTACTTTCCTGGC 58.723 55.000 0.00 0.00 0.00 4.85
7355 11171 0.984230 CCTCCTGTACTTTCCTGGCA 59.016 55.000 0.00 0.00 0.00 4.92
7356 11172 1.561542 CCTCCTGTACTTTCCTGGCAT 59.438 52.381 0.00 0.00 0.00 4.40
7357 11173 2.636830 CTCCTGTACTTTCCTGGCATG 58.363 52.381 0.00 0.00 0.00 4.06
7358 11174 2.237143 CTCCTGTACTTTCCTGGCATGA 59.763 50.000 0.00 0.00 0.00 3.07
7359 11175 2.846206 TCCTGTACTTTCCTGGCATGAT 59.154 45.455 0.00 0.00 0.00 2.45
7360 11176 3.266772 TCCTGTACTTTCCTGGCATGATT 59.733 43.478 0.00 0.00 0.00 2.57
7361 11177 3.629398 CCTGTACTTTCCTGGCATGATTC 59.371 47.826 0.00 0.00 0.00 2.52
7362 11178 3.270027 TGTACTTTCCTGGCATGATTCG 58.730 45.455 0.00 0.00 0.00 3.34
7363 11179 1.098050 ACTTTCCTGGCATGATTCGC 58.902 50.000 0.00 0.00 0.00 4.70
7371 11187 2.036556 GGCATGATTCGCCGTTATTG 57.963 50.000 0.00 0.00 40.35 1.90
7372 11188 1.398595 GCATGATTCGCCGTTATTGC 58.601 50.000 0.00 0.00 0.00 3.56
7373 11189 1.268488 GCATGATTCGCCGTTATTGCA 60.268 47.619 0.00 0.00 0.00 4.08
7374 11190 2.605338 GCATGATTCGCCGTTATTGCAT 60.605 45.455 0.00 0.00 0.00 3.96
7375 11191 2.753989 TGATTCGCCGTTATTGCATG 57.246 45.000 0.00 0.00 0.00 4.06
7376 11192 2.013400 TGATTCGCCGTTATTGCATGT 58.987 42.857 0.00 0.00 0.00 3.21
7377 11193 3.198872 TGATTCGCCGTTATTGCATGTA 58.801 40.909 0.00 0.00 0.00 2.29
7378 11194 3.812609 TGATTCGCCGTTATTGCATGTAT 59.187 39.130 0.00 0.00 0.00 2.29
7379 11195 4.991687 TGATTCGCCGTTATTGCATGTATA 59.008 37.500 0.00 0.00 0.00 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.629137 GGGATGCCATGTATGCAAATGA 59.371 45.455 0.00 0.00 42.92 2.57
11 12 0.552363 AGTGGGATGCCATGTATGCA 59.448 50.000 10.01 0.00 43.97 3.96
15 16 1.357420 ACCAAAGTGGGATGCCATGTA 59.643 47.619 10.01 0.00 43.37 2.29
31 32 1.391157 GCCTGCTGTCAAACCACCAA 61.391 55.000 0.00 0.00 0.00 3.67
47 48 4.760047 GGTGACGACGCCATGCCT 62.760 66.667 12.66 0.00 45.14 4.75
66 67 2.243221 CTCCCAGTTCCTCCAATTCCAT 59.757 50.000 0.00 0.00 0.00 3.41
99 100 2.179427 CACCCTTCCCCCTCAAATTTC 58.821 52.381 0.00 0.00 0.00 2.17
102 103 0.780090 ACCACCCTTCCCCCTCAAAT 60.780 55.000 0.00 0.00 0.00 2.32
111 112 2.991540 GCCAAGCACCACCCTTCC 60.992 66.667 0.00 0.00 0.00 3.46
169 170 3.305608 CCATGCGTGAGTGCTATAGATCA 60.306 47.826 7.72 1.34 35.36 2.92
186 187 3.559242 GCTACTGAGACAAGAATCCATGC 59.441 47.826 0.00 0.00 0.00 4.06
238 239 1.022903 ACCTCCATCCTCCTTCCTCT 58.977 55.000 0.00 0.00 0.00 3.69
247 248 4.689062 TGTTCTTCTTCTACCTCCATCCT 58.311 43.478 0.00 0.00 0.00 3.24
250 251 5.584913 TCTCTGTTCTTCTTCTACCTCCAT 58.415 41.667 0.00 0.00 0.00 3.41
260 261 1.337635 CGGCAGCTCTCTGTTCTTCTT 60.338 52.381 0.00 0.00 42.29 2.52
286 287 3.118738 GGTATCCAGTGGATCACGAACTT 60.119 47.826 28.15 4.58 42.11 2.66
302 303 1.526225 GGCTTTGGGCGAGGTATCC 60.526 63.158 0.00 0.00 42.94 2.59
314 315 0.391263 GTACCAGGACCGAGGCTTTG 60.391 60.000 5.98 0.00 0.00 2.77
324 325 0.893447 ACGGCTACAAGTACCAGGAC 59.107 55.000 0.00 0.00 0.00 3.85
345 346 0.036875 ACTGCAAGAGCTACAACCCC 59.963 55.000 0.00 0.00 42.74 4.95
401 402 2.103094 TGTTAGCATCCTTCCGATCCTG 59.897 50.000 0.00 0.00 0.00 3.86
407 408 3.388308 CAGATCTGTTAGCATCCTTCCG 58.612 50.000 14.95 0.00 0.00 4.30
411 412 2.703007 GGTCCAGATCTGTTAGCATCCT 59.297 50.000 21.11 0.00 0.00 3.24
413 414 2.101582 ACGGTCCAGATCTGTTAGCATC 59.898 50.000 21.11 3.29 0.00 3.91
417 418 1.065701 CCGACGGTCCAGATCTGTTAG 59.934 57.143 21.11 11.61 0.00 2.34
419 420 0.898789 ACCGACGGTCCAGATCTGTT 60.899 55.000 21.11 0.16 0.00 3.16
449 450 2.683867 CCCTGATTTAGAGTCGTCGTCT 59.316 50.000 0.00 0.00 0.00 4.18
461 462 0.830648 CTGGCTCCGTCCCTGATTTA 59.169 55.000 0.00 0.00 0.00 1.40
486 487 2.516225 GCCATTGTCCCGGCCTAC 60.516 66.667 0.00 0.00 42.82 3.18
494 495 0.470341 GTAGGAGGGAGCCATTGTCC 59.530 60.000 0.00 0.00 0.00 4.02
495 496 1.139853 CTGTAGGAGGGAGCCATTGTC 59.860 57.143 0.00 0.00 0.00 3.18
498 499 1.972588 AACTGTAGGAGGGAGCCATT 58.027 50.000 0.00 0.00 0.00 3.16
512 513 9.705290 TGCTTTTAGAAAAAGAAGAAAAACTGT 57.295 25.926 14.63 0.00 0.00 3.55
513 514 9.958285 GTGCTTTTAGAAAAAGAAGAAAAACTG 57.042 29.630 14.63 0.00 0.00 3.16
527 528 5.390387 ACAATGTAGGGGTGCTTTTAGAAA 58.610 37.500 0.00 0.00 0.00 2.52
532 533 5.144832 AGTAAACAATGTAGGGGTGCTTTT 58.855 37.500 0.00 0.00 0.00 2.27
583 584 4.392138 GGAAGACGTAAAACATCAAGGGAG 59.608 45.833 0.00 0.00 0.00 4.30
596 597 0.034863 GGGGCCAATGGAAGACGTAA 60.035 55.000 2.05 0.00 0.00 3.18
620 621 3.743269 CGACCCAGCCCGAAAACTTATAT 60.743 47.826 0.00 0.00 0.00 0.86
632 633 2.180159 TTAGAGCAACGACCCAGCCC 62.180 60.000 0.00 0.00 0.00 5.19
634 635 1.739067 ATTTAGAGCAACGACCCAGC 58.261 50.000 0.00 0.00 0.00 4.85
642 643 5.362556 TTCTCACAGCAATTTAGAGCAAC 57.637 39.130 0.00 0.00 0.00 4.17
732 735 7.391620 TCGGTTCCAGATTAGTTGTATTTCTT 58.608 34.615 0.00 0.00 0.00 2.52
740 746 4.158764 ACTCTCTCGGTTCCAGATTAGTTG 59.841 45.833 0.00 0.00 0.00 3.16
750 756 3.866327 GCAATTCTTACTCTCTCGGTTCC 59.134 47.826 0.00 0.00 0.00 3.62
755 761 5.164233 TCACTTGCAATTCTTACTCTCTCG 58.836 41.667 0.00 0.00 0.00 4.04
788 794 5.463499 AGATTTTGTTTGTTTGTTTCGGC 57.537 34.783 0.00 0.00 0.00 5.54
806 812 4.525912 GTCCTGCATTTGACCAAAGATT 57.474 40.909 1.57 0.00 33.32 2.40
1437 1476 1.929169 GCACGTAAATTCTACGGTCCC 59.071 52.381 18.04 5.95 44.38 4.46
2260 5628 3.192001 TCTTTTGCTCAATCAGGCATCAC 59.808 43.478 0.00 0.00 38.30 3.06
2303 5671 9.178758 AGAATATTTTCAGATGAGTAAACACCC 57.821 33.333 0.00 0.00 34.08 4.61
2414 5782 5.887598 ACATAAGCTAAAATCTGTGGCATGA 59.112 36.000 0.00 0.00 0.00 3.07
2604 5972 0.037447 TCCCGTGCATGGTTGAATGA 59.963 50.000 23.39 9.55 0.00 2.57
2760 6128 0.959867 ATACACCGCATGTTGCTGCA 60.960 50.000 0.00 0.00 42.25 4.41
2841 6209 3.128589 GGTGTGAGAAGCAACTTCAACAA 59.871 43.478 13.91 1.83 42.37 2.83
3027 6409 6.213397 CCTGTATATATCCATCCTTGTGACCA 59.787 42.308 0.00 0.00 0.00 4.02
3044 6426 6.299805 AGATGTTGTGTGTGTCCTGTATAT 57.700 37.500 0.00 0.00 0.00 0.86
3124 6506 3.131933 AGTGTGCATCCATGAGTCTACTC 59.868 47.826 3.08 3.08 43.15 2.59
3158 6540 4.627467 CGTTGAGTAGATTAGTTGCTTGCT 59.373 41.667 0.00 0.00 0.00 3.91
3185 6567 5.331069 AGCTTCCTTAGAGGTGTAACAGTA 58.669 41.667 0.00 0.00 39.98 2.74
3368 6750 1.520787 CCAATCCCGGTGTCTACGC 60.521 63.158 0.00 0.00 0.00 4.42
3375 6757 1.037030 CATCAACCCCAATCCCGGTG 61.037 60.000 0.00 0.00 30.96 4.94
3402 6784 2.638556 ACGAGTTTCTCAGACCATCG 57.361 50.000 0.00 1.06 35.00 3.84
3414 6796 1.271656 CCTAGACCGACCAACGAGTTT 59.728 52.381 0.00 0.00 45.77 2.66
3415 6797 0.886563 CCTAGACCGACCAACGAGTT 59.113 55.000 0.00 0.00 45.77 3.01
3705 7087 6.429692 CAGTTACCAAGACCAATGTCAATGTA 59.570 38.462 0.00 0.00 44.33 2.29
3736 7118 2.786027 CGACTTGATGTATGAGCGACTG 59.214 50.000 0.00 0.00 0.00 3.51
3867 7251 8.076910 TCAATTTTACCATGGAGCAAACATAT 57.923 30.769 21.47 3.83 0.00 1.78
3990 7375 6.953189 GTCATGCAGTGTTACAAAACAAAAAC 59.047 34.615 0.00 0.00 46.84 2.43
4020 7405 2.044793 ACCCAAGGGAATCAGACTGA 57.955 50.000 13.15 7.80 38.96 3.41
4032 7417 7.721399 AGAAGCATATATTTCTTGTACCCAAGG 59.279 37.037 2.88 0.00 46.65 3.61
4125 7510 2.736144 TCACGTGGACAATGAGGTAC 57.264 50.000 17.00 0.00 0.00 3.34
4190 7582 9.823647 TTAAATGGTTCAAAAACTGCAAAGATA 57.176 25.926 0.00 0.00 35.61 1.98
4306 7698 6.127619 GCAGATTCTGGCTTAACCTGTTATTT 60.128 38.462 15.28 0.00 40.22 1.40
4366 7758 7.023575 CCAATGTATTGAGCTGTAGAACAAAC 58.976 38.462 6.18 0.00 40.14 2.93
4479 7871 5.366460 ACAATGAGAATATGGCACTGAGAG 58.634 41.667 0.00 0.00 0.00 3.20
4594 8122 6.476378 ACATAACTGAGACCAATACAAGCTT 58.524 36.000 0.00 0.00 0.00 3.74
4641 8169 4.508124 CAGTGCCCTGAATAGATAAACGAC 59.492 45.833 0.00 0.00 41.50 4.34
4760 8288 2.680312 ATCCACGTCAGATGTGAAGG 57.320 50.000 22.47 7.70 37.29 3.46
4858 8403 3.814316 GCAGAGATACAACAACCCCCTTT 60.814 47.826 0.00 0.00 0.00 3.11
4878 8423 1.451504 CTCACACCTGACTTGGGCA 59.548 57.895 0.00 0.00 0.00 5.36
4916 8462 2.224378 CCTTCACATCTGGCGTGGATAT 60.224 50.000 0.00 0.00 35.03 1.63
4921 8467 1.746615 CCCCTTCACATCTGGCGTG 60.747 63.158 0.00 0.00 35.63 5.34
4956 8502 4.060038 TCTATCCAAAAGACCGATCTGC 57.940 45.455 0.00 0.00 34.48 4.26
5062 8849 6.183360 ACAGAATCTCACTGTTGTTTGACAAG 60.183 38.462 0.00 0.00 44.69 3.16
5189 8976 2.897326 ACCCAAAGCCAAACTGTTATCC 59.103 45.455 0.00 0.00 0.00 2.59
5267 9054 8.526147 CATGGGTTGAACTTGAAATTATTCTCT 58.474 33.333 0.00 0.00 36.48 3.10
5274 9061 4.622260 CCCATGGGTTGAACTTGAAATT 57.378 40.909 23.93 0.00 0.00 1.82
5378 9165 2.093783 CCTGCGACAAGTAATTCGGAAC 59.906 50.000 0.00 0.00 35.02 3.62
5379 9166 2.289195 ACCTGCGACAAGTAATTCGGAA 60.289 45.455 0.00 0.00 35.02 4.30
5380 9167 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.00 0.00 35.73 4.55
5381 9168 1.722011 ACCTGCGACAAGTAATTCGG 58.278 50.000 0.00 0.00 35.73 4.30
5382 9169 3.245284 CCATACCTGCGACAAGTAATTCG 59.755 47.826 0.00 0.00 38.31 3.34
5383 9170 4.439057 TCCATACCTGCGACAAGTAATTC 58.561 43.478 0.00 0.00 0.00 2.17
5384 9171 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
5385 9172 4.141711 ACATCCATACCTGCGACAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
5386 9173 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
5387 9174 2.764010 ACATCCATACCTGCGACAAGTA 59.236 45.455 0.00 0.00 0.00 2.24
5388 9175 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
5389 9176 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
5390 9177 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
5391 9178 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
5392 9179 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
5393 9180 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
5394 9181 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
5395 9182 6.537453 ACATCTAGATACATCCATACCTGC 57.463 41.667 4.54 0.00 0.00 4.85
5421 9208 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
5422 9209 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
5423 9210 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
5424 9211 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
5425 9212 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
5426 9213 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
5427 9214 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
5428 9215 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
5429 9216 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
5430 9217 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
5431 9218 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
5432 9219 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
5433 9220 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
5434 9221 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
5435 9222 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
5436 9223 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
5437 9224 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
5438 9225 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
5439 9226 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
5440 9227 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
5441 9228 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
5442 9229 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
5443 9230 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
5444 9231 2.222508 CGTTCCAAATTACTCGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
5445 9232 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
5446 9233 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
5447 9234 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
5448 9235 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
5449 9236 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
5450 9237 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
5451 9238 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
5452 9239 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
5453 9240 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
5454 9241 3.118519 GCTACTCCCTCCGTTCCAAATTA 60.119 47.826 0.00 0.00 0.00 1.40
5455 9242 2.355818 GCTACTCCCTCCGTTCCAAATT 60.356 50.000 0.00 0.00 0.00 1.82
5456 9243 1.209747 GCTACTCCCTCCGTTCCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
5457 9244 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
5458 9245 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
5459 9246 0.970937 CAGCTACTCCCTCCGTTCCA 60.971 60.000 0.00 0.00 0.00 3.53
5460 9247 1.817209 CAGCTACTCCCTCCGTTCC 59.183 63.158 0.00 0.00 0.00 3.62
5461 9248 1.142097 GCAGCTACTCCCTCCGTTC 59.858 63.158 0.00 0.00 0.00 3.95
5462 9249 2.359967 GGCAGCTACTCCCTCCGTT 61.360 63.158 0.00 0.00 0.00 4.44
5463 9250 2.760385 GGCAGCTACTCCCTCCGT 60.760 66.667 0.00 0.00 0.00 4.69
5464 9251 2.136878 ATGGCAGCTACTCCCTCCG 61.137 63.158 0.00 0.00 0.00 4.63
5465 9252 1.449353 CATGGCAGCTACTCCCTCC 59.551 63.158 0.00 0.00 0.00 4.30
5466 9253 1.449353 CCATGGCAGCTACTCCCTC 59.551 63.158 0.00 0.00 0.00 4.30
5467 9254 2.750657 GCCATGGCAGCTACTCCCT 61.751 63.158 32.08 0.00 41.49 4.20
5468 9255 2.203266 GCCATGGCAGCTACTCCC 60.203 66.667 32.08 0.00 41.49 4.30
5680 9473 7.575414 TCTGGCACATGTAGTTTAAGAAAAA 57.425 32.000 0.00 0.00 38.20 1.94
5707 9500 3.963428 CCAAAGGCAGTAGTAGTGTCT 57.037 47.619 6.27 6.27 34.41 3.41
5876 9669 2.799562 GCTTTGGTCAGGAAAGTGCAAC 60.800 50.000 0.00 0.00 33.66 4.17
5877 9670 1.408702 GCTTTGGTCAGGAAAGTGCAA 59.591 47.619 0.00 0.00 33.66 4.08
5878 9671 1.032014 GCTTTGGTCAGGAAAGTGCA 58.968 50.000 0.00 0.00 33.66 4.57
5879 9672 0.040067 CGCTTTGGTCAGGAAAGTGC 60.040 55.000 0.00 0.00 34.96 4.40
5880 9673 0.040067 GCGCTTTGGTCAGGAAAGTG 60.040 55.000 0.00 0.00 41.72 3.16
5881 9674 0.465460 TGCGCTTTGGTCAGGAAAGT 60.465 50.000 9.73 0.00 33.66 2.66
5979 9772 9.566432 AGCATGGATTTTTACCATTGTTAAAAA 57.434 25.926 12.43 12.43 44.51 1.94
6214 10008 3.439825 TGTTATTGACTAGGCGTCGTGTA 59.560 43.478 0.00 0.00 45.87 2.90
6414 10208 4.828829 ACCATCCTCCAAGTAGTAAAACG 58.171 43.478 0.00 0.00 0.00 3.60
6421 10215 6.071984 AGTACAGATACCATCCTCCAAGTAG 58.928 44.000 0.00 0.00 30.88 2.57
6607 10402 6.926313 AGAGTTAGCGACAACTTCTCTATTT 58.074 36.000 3.91 0.00 38.86 1.40
6622 10417 3.535561 ACATTGAATGGGAGAGTTAGCG 58.464 45.455 10.27 0.00 33.60 4.26
6697 10492 4.226761 GTCAATTTCAACCAGCTAAACCG 58.773 43.478 0.00 0.00 0.00 4.44
6816 10623 4.451096 TCAGAATTTAGGAACGTTGACTGC 59.549 41.667 5.00 0.00 0.00 4.40
6825 10632 5.689383 TGCACAACTCAGAATTTAGGAAC 57.311 39.130 0.00 0.00 0.00 3.62
6913 10721 7.018635 AGCAAATAATTTGGCACATAATTGC 57.981 32.000 16.63 16.63 40.94 3.56
7028 10836 0.594796 GCGTGCAAAGGTGAAACAGG 60.595 55.000 0.00 0.00 39.98 4.00
7048 10856 3.737850 GGACTGCCTGGAGATAATTGAG 58.262 50.000 0.00 0.00 0.00 3.02
7183 10999 2.483876 CTGAGAACTTGGTTTCGCTCA 58.516 47.619 0.00 0.00 0.00 4.26
7270 11086 7.465111 GCACATATAAGATGAATACGGATGCAG 60.465 40.741 0.00 0.00 0.00 4.41
7330 11146 4.160626 CCAGGAAAGTACAGGAGGAACTAG 59.839 50.000 0.00 0.00 41.55 2.57
7331 11147 4.094476 CCAGGAAAGTACAGGAGGAACTA 58.906 47.826 0.00 0.00 41.55 2.24
7333 11149 2.615747 GCCAGGAAAGTACAGGAGGAAC 60.616 54.545 0.00 0.00 0.00 3.62
7334 11150 1.628846 GCCAGGAAAGTACAGGAGGAA 59.371 52.381 0.00 0.00 0.00 3.36
7335 11151 1.276622 GCCAGGAAAGTACAGGAGGA 58.723 55.000 0.00 0.00 0.00 3.71
7336 11152 0.984230 TGCCAGGAAAGTACAGGAGG 59.016 55.000 0.00 0.00 0.00 4.30
7337 11153 2.237143 TCATGCCAGGAAAGTACAGGAG 59.763 50.000 0.00 0.00 0.00 3.69
7338 11154 2.265367 TCATGCCAGGAAAGTACAGGA 58.735 47.619 0.00 0.00 0.00 3.86
7339 11155 2.787473 TCATGCCAGGAAAGTACAGG 57.213 50.000 0.00 0.00 0.00 4.00
7340 11156 3.310774 CGAATCATGCCAGGAAAGTACAG 59.689 47.826 0.00 0.00 0.00 2.74
7341 11157 3.270027 CGAATCATGCCAGGAAAGTACA 58.730 45.455 0.00 0.00 0.00 2.90
7342 11158 2.032178 GCGAATCATGCCAGGAAAGTAC 59.968 50.000 0.00 0.00 0.00 2.73
7343 11159 2.288666 GCGAATCATGCCAGGAAAGTA 58.711 47.619 0.00 0.00 0.00 2.24
7344 11160 1.098050 GCGAATCATGCCAGGAAAGT 58.902 50.000 0.00 0.00 0.00 2.66
7345 11161 3.932459 GCGAATCATGCCAGGAAAG 57.068 52.632 0.00 0.00 0.00 2.62
7353 11169 1.268488 TGCAATAACGGCGAATCATGC 60.268 47.619 16.62 17.10 0.00 4.06
7354 11170 2.753989 TGCAATAACGGCGAATCATG 57.246 45.000 16.62 7.00 0.00 3.07
7355 11171 2.618241 ACATGCAATAACGGCGAATCAT 59.382 40.909 16.62 4.77 0.00 2.45
7356 11172 2.013400 ACATGCAATAACGGCGAATCA 58.987 42.857 16.62 2.44 0.00 2.57
7357 11173 2.755836 ACATGCAATAACGGCGAATC 57.244 45.000 16.62 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.