Multiple sequence alignment - TraesCS5D01G147900

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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 TraesCS5D01G147900 chr5D 100.000 2870 0 0 1 2870 234144877 234147746 0.000000e+00 5301.0
1 TraesCS5D01G147900 chr5D 93.313 329 20 2 2524 2852 220857467 220857141 4.300000e-133 484.0
2 TraesCS5D01G147900 chr5B 93.792 2400 104 19 159 2525 270438993 270436606 0.000000e+00 3565.0
3 TraesCS5D01G147900 chr5B 96.067 178 6 1 1 178 270440044 270439868 3.620000e-74 289.0
4 TraesCS5D01G147900 chr5B 82.305 243 31 6 2217 2448 529963620 529963861 1.740000e-47 200.0
5 TraesCS5D01G147900 chr5A 92.601 2230 113 19 329 2525 320214245 320212035 0.000000e+00 3157.0
6 TraesCS5D01G147900 chr5A 94.030 201 5 3 137 330 320214604 320214404 6.010000e-77 298.0
7 TraesCS5D01G147900 chr5A 94.245 139 6 2 1 139 320214834 320214698 8.060000e-51 211.0
8 TraesCS5D01G147900 chr7B 85.325 661 64 16 838 1467 531655025 531655683 0.000000e+00 652.0
9 TraesCS5D01G147900 chr7B 84.838 587 76 10 1512 2091 531655918 531656498 1.920000e-161 579.0
10 TraesCS5D01G147900 chr7B 87.500 128 11 2 332 458 531650594 531650717 2.980000e-30 143.0
11 TraesCS5D01G147900 chr7D 85.045 662 65 16 838 1467 502873690 502874349 0.000000e+00 643.0
12 TraesCS5D01G147900 chr7D 84.854 581 72 10 1520 2094 502874618 502875188 3.210000e-159 571.0
13 TraesCS5D01G147900 chr7D 92.816 348 20 5 2523 2869 6794964 6795307 1.540000e-137 499.0
14 TraesCS5D01G147900 chr7D 81.590 239 34 9 2217 2447 442203287 442203523 3.770000e-44 189.0
15 TraesCS5D01G147900 chr7D 87.413 143 13 4 427 567 502872661 502872800 2.960000e-35 159.0
16 TraesCS5D01G147900 chr7D 86.957 69 8 1 2457 2525 502875340 502875407 3.070000e-10 76.8
17 TraesCS5D01G147900 chr7A 85.500 600 60 12 889 1467 570113205 570113798 4.090000e-168 601.0
18 TraesCS5D01G147900 chr7A 91.254 343 26 4 2511 2852 75619620 75619281 5.600000e-127 464.0
19 TraesCS5D01G147900 chr7A 82.296 514 67 11 1512 2020 570114179 570114673 9.510000e-115 424.0
20 TraesCS5D01G147900 chr7A 89.634 164 10 6 572 729 15631503 15631341 4.850000e-48 202.0
21 TraesCS5D01G147900 chr7A 86.982 169 15 4 332 498 570111919 570112082 1.760000e-42 183.0
22 TraesCS5D01G147900 chr7A 89.167 120 12 1 449 567 570112188 570112307 6.410000e-32 148.0
23 TraesCS5D01G147900 chr7A 100.000 41 0 0 2830 2870 75619284 75619244 3.070000e-10 76.8
24 TraesCS5D01G147900 chr6D 94.984 319 14 2 2524 2842 61020348 61020664 1.540000e-137 499.0
25 TraesCS5D01G147900 chr6D 84.541 207 30 2 2213 2418 382617308 382617513 1.350000e-48 204.0
26 TraesCS5D01G147900 chr4B 94.357 319 15 3 2524 2842 144684529 144684844 1.200000e-133 486.0
27 TraesCS5D01G147900 chr4B 84.426 244 27 6 2218 2451 183525224 183524982 2.220000e-56 230.0
28 TraesCS5D01G147900 chr1D 93.478 322 20 1 2521 2842 213336432 213336752 7.190000e-131 477.0
29 TraesCS5D01G147900 chr1D 93.189 323 20 2 2520 2842 457136828 457136508 9.310000e-130 473.0
30 TraesCS5D01G147900 chr2D 93.458 321 20 1 2522 2842 125736036 125736355 2.590000e-130 475.0
31 TraesCS5D01G147900 chr2D 91.964 336 24 3 2518 2852 318252706 318252373 4.330000e-128 468.0
32 TraesCS5D01G147900 chr2D 92.138 318 22 3 2522 2838 53967152 53967467 2.030000e-121 446.0
33 TraesCS5D01G147900 chr2D 87.187 359 36 9 2506 2857 623445848 623446203 1.600000e-107 399.0
34 TraesCS5D01G147900 chr2D 89.506 162 13 3 572 729 336892542 336892381 4.850000e-48 202.0
35 TraesCS5D01G147900 chr2D 92.188 64 5 0 1617 1680 321239517 321239454 1.100000e-14 91.6
36 TraesCS5D01G147900 chr1B 86.174 311 38 4 2524 2834 687183002 687183307 5.930000e-87 331.0
37 TraesCS5D01G147900 chr3D 84.298 242 26 5 2217 2449 282930575 282930813 2.880000e-55 226.0
38 TraesCS5D01G147900 chr3A 85.022 227 24 7 2231 2447 701176874 701177100 3.720000e-54 222.0
39 TraesCS5D01G147900 chr1A 83.784 222 27 5 2233 2446 362190268 362190488 4.850000e-48 202.0
40 TraesCS5D01G147900 chr2B 90.722 97 8 1 2511 2606 419289875 419289971 8.350000e-26 128.0
41 TraesCS5D01G147900 chr6B 97.059 34 1 0 2416 2449 655267153 655267186 1.110000e-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 TraesCS5D01G147900 chr5D 234144877 234147746 2869 False 5301.00 5301 100.000000 1 2870 1 chr5D.!!$F1 2869
1 TraesCS5D01G147900 chr5B 270436606 270440044 3438 True 1927.00 3565 94.929500 1 2525 2 chr5B.!!$R1 2524
2 TraesCS5D01G147900 chr5A 320212035 320214834 2799 True 1222.00 3157 93.625333 1 2525 3 chr5A.!!$R1 2524
3 TraesCS5D01G147900 chr7B 531655025 531656498 1473 False 615.50 652 85.081500 838 2091 2 chr7B.!!$F2 1253
4 TraesCS5D01G147900 chr7D 502872661 502875407 2746 False 362.45 643 86.067250 427 2525 4 chr7D.!!$F3 2098
5 TraesCS5D01G147900 chr7A 570111919 570114673 2754 False 339.00 601 85.986250 332 2020 4 chr7A.!!$F1 1688

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
738 2062 0.673644 GCCGCCGCTGATTACCATAT 60.674 55.0 0.0 0.0 0.0 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2648 5188 0.110147 TACGTTTGAATTTGCCGCGG 60.11 50.0 24.05 24.05 0.0 6.46 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
36 37 4.567159 GTCAAGTCTATCCAGCTTTAACCG 59.433 45.833 0.00 0.00 0.00 4.44
43 44 7.233757 AGTCTATCCAGCTTTAACCGAAGATAT 59.766 37.037 0.00 0.00 0.00 1.63
52 53 8.099537 AGCTTTAACCGAAGATATGATCATGAT 58.900 33.333 18.72 8.25 0.00 2.45
63 64 7.879070 AGATATGATCATGATTTTTCGGGTTG 58.121 34.615 18.72 0.00 0.00 3.77
201 1193 8.940952 AGACTTTGAAATGTAAGAAGCACTATC 58.059 33.333 0.00 0.00 0.00 2.08
202 1194 8.854614 ACTTTGAAATGTAAGAAGCACTATCT 57.145 30.769 0.00 0.00 0.00 1.98
446 1612 9.393249 TCACTGAAAATCTTTATAAACGCTTTG 57.607 29.630 0.00 0.00 0.00 2.77
536 1858 2.094390 CCAAGGGTGATTGCACATGAAG 60.094 50.000 0.00 0.00 46.96 3.02
596 1918 2.546899 AGCTACATGTAACCTGTGGGA 58.453 47.619 7.06 0.00 36.25 4.37
738 2062 0.673644 GCCGCCGCTGATTACCATAT 60.674 55.000 0.00 0.00 0.00 1.78
780 2105 9.753674 TCCTATCTGGATAACTTCAATTTTGTT 57.246 29.630 0.00 0.00 40.56 2.83
851 2969 6.688073 ATTTTAGTCCTCAGTTTCTCTCCA 57.312 37.500 0.00 0.00 0.00 3.86
852 2970 5.730296 TTTAGTCCTCAGTTTCTCTCCAG 57.270 43.478 0.00 0.00 0.00 3.86
1083 3215 0.250793 TTGACCGCCGGTTCACATAT 59.749 50.000 11.54 0.00 35.25 1.78
1396 3535 3.065786 CAGTGGGCACTTGCATATACTTG 59.934 47.826 3.15 0.00 44.36 3.16
1403 3555 5.446709 GCACTTGCATATACTTGCTGTATG 58.553 41.667 11.41 0.03 43.18 2.39
1479 3633 2.030946 GCTCATTACGCATGTCCACTTC 59.969 50.000 0.00 0.00 34.06 3.01
1602 4115 2.938956 ATAGGCTCTTCCATTTCGGG 57.061 50.000 0.00 0.00 37.29 5.14
1638 4151 7.202526 CCGTTTTGGCATCTCAATTATTATGT 58.797 34.615 0.00 0.00 0.00 2.29
1741 4254 3.119602 TCTGTAGAACCGATCCACTTTCG 60.120 47.826 0.00 0.00 36.38 3.46
1924 4439 4.197750 AGATATTGAACAGCAAGAGCCAG 58.802 43.478 0.00 0.00 43.56 4.85
1954 4469 8.717821 ACGAAACTTTATCGAGAATGAAATGAA 58.282 29.630 12.07 0.00 42.76 2.57
2195 4732 2.645730 TTGTTCTGCTTTGCGTGTTT 57.354 40.000 0.00 0.00 0.00 2.83
2202 4739 5.530519 TCTGCTTTGCGTGTTTAAGATAG 57.469 39.130 0.00 0.00 0.00 2.08
2210 4747 9.849607 CTTTGCGTGTTTAAGATAGTACATATG 57.150 33.333 0.00 0.00 0.00 1.78
2224 4763 3.317455 ACATATGACCCCGTACTACCA 57.683 47.619 10.38 0.00 0.00 3.25
2238 4777 1.620323 ACTACCACGGTCCTGGTTTAC 59.380 52.381 15.56 0.00 42.29 2.01
2243 4782 1.134228 ACGGTCCTGGTTTACTGGTT 58.866 50.000 0.00 0.00 39.12 3.67
2245 4784 1.346722 CGGTCCTGGTTTACTGGTTCT 59.653 52.381 0.00 0.00 39.12 3.01
2249 4788 4.445879 GGTCCTGGTTTACTGGTTCTCTTT 60.446 45.833 0.00 0.00 39.12 2.52
2260 4799 8.514330 TTACTGGTTCTCTTTGTATTTTGTGT 57.486 30.769 0.00 0.00 0.00 3.72
2264 4804 7.831753 TGGTTCTCTTTGTATTTTGTGTCAAA 58.168 30.769 0.00 0.00 0.00 2.69
2286 4826 6.642707 AATTTGACCGTAGATTTGACCAAA 57.357 33.333 0.00 0.00 34.46 3.28
2454 4994 4.210331 TGGACGGAGGTAGTACTTTATCC 58.790 47.826 0.00 5.31 0.00 2.59
2525 5065 8.293699 TGCTGATACTTGAACTGTATCTAAGA 57.706 34.615 12.94 0.00 43.79 2.10
2526 5066 8.409371 TGCTGATACTTGAACTGTATCTAAGAG 58.591 37.037 12.94 5.51 43.79 2.85
2527 5067 7.381139 GCTGATACTTGAACTGTATCTAAGAGC 59.619 40.741 12.94 10.11 43.79 4.09
2528 5068 8.293699 TGATACTTGAACTGTATCTAAGAGCA 57.706 34.615 12.94 0.00 43.79 4.26
2529 5069 8.918116 TGATACTTGAACTGTATCTAAGAGCAT 58.082 33.333 12.94 0.00 43.79 3.79
2530 5070 9.405587 GATACTTGAACTGTATCTAAGAGCATC 57.594 37.037 0.00 0.00 41.58 3.91
2542 5082 3.143675 GAGCATCTTCAGCCGTTCA 57.856 52.632 0.00 0.00 0.00 3.18
2543 5083 1.005340 GAGCATCTTCAGCCGTTCAG 58.995 55.000 0.00 0.00 0.00 3.02
2544 5084 1.023513 AGCATCTTCAGCCGTTCAGC 61.024 55.000 0.00 0.00 0.00 4.26
2545 5085 1.986575 GCATCTTCAGCCGTTCAGCC 61.987 60.000 0.00 0.00 0.00 4.85
2546 5086 1.078143 ATCTTCAGCCGTTCAGCCC 60.078 57.895 0.00 0.00 0.00 5.19
2547 5087 2.543067 ATCTTCAGCCGTTCAGCCCC 62.543 60.000 0.00 0.00 0.00 5.80
2548 5088 4.344865 TTCAGCCGTTCAGCCCCC 62.345 66.667 0.00 0.00 0.00 5.40
2562 5102 4.293671 CCCCCAGGGTGCCGAAAA 62.294 66.667 4.22 0.00 38.25 2.29
2563 5103 2.203567 CCCCAGGGTGCCGAAAAA 60.204 61.111 4.22 0.00 0.00 1.94
2564 5104 2.275380 CCCCAGGGTGCCGAAAAAG 61.275 63.158 4.22 0.00 0.00 2.27
2565 5105 1.228429 CCCAGGGTGCCGAAAAAGA 60.228 57.895 0.00 0.00 0.00 2.52
2566 5106 1.244019 CCCAGGGTGCCGAAAAAGAG 61.244 60.000 0.00 0.00 0.00 2.85
2567 5107 1.581447 CAGGGTGCCGAAAAAGAGC 59.419 57.895 0.00 0.00 0.00 4.09
2568 5108 1.966451 AGGGTGCCGAAAAAGAGCG 60.966 57.895 0.00 0.00 0.00 5.03
2573 5113 2.870372 CCGAAAAAGAGCGGCCTG 59.130 61.111 0.00 0.00 41.17 4.85
2574 5114 2.690778 CCGAAAAAGAGCGGCCTGG 61.691 63.158 0.00 0.00 41.17 4.45
2575 5115 2.690778 CGAAAAAGAGCGGCCTGGG 61.691 63.158 0.00 0.00 0.00 4.45
2576 5116 2.283173 AAAAAGAGCGGCCTGGGG 60.283 61.111 0.00 0.00 0.00 4.96
2577 5117 3.886550 AAAAAGAGCGGCCTGGGGG 62.887 63.158 0.00 0.00 0.00 5.40
2595 5135 3.309675 CGAACCGGCGCTAGATTG 58.690 61.111 7.64 0.00 0.00 2.67
2596 5136 2.237751 CGAACCGGCGCTAGATTGG 61.238 63.158 7.64 2.50 0.00 3.16
2597 5137 2.513897 AACCGGCGCTAGATTGGC 60.514 61.111 7.64 0.00 0.00 4.52
2598 5138 4.547367 ACCGGCGCTAGATTGGCC 62.547 66.667 7.64 0.00 43.42 5.36
2601 5141 3.878667 GGCGCTAGATTGGCCCCT 61.879 66.667 7.64 0.00 41.01 4.79
2602 5142 2.592861 GCGCTAGATTGGCCCCTG 60.593 66.667 0.00 0.00 0.00 4.45
2603 5143 2.111878 CGCTAGATTGGCCCCTGG 59.888 66.667 0.00 0.00 0.00 4.45
2604 5144 2.517919 GCTAGATTGGCCCCTGGG 59.482 66.667 5.50 5.50 38.57 4.45
2622 5162 3.851128 GGCGACCTACCTCCCAGC 61.851 72.222 0.00 0.00 0.00 4.85
2623 5163 3.851128 GCGACCTACCTCCCAGCC 61.851 72.222 0.00 0.00 0.00 4.85
2624 5164 2.363795 CGACCTACCTCCCAGCCA 60.364 66.667 0.00 0.00 0.00 4.75
2625 5165 2.722201 CGACCTACCTCCCAGCCAC 61.722 68.421 0.00 0.00 0.00 5.01
2626 5166 2.683933 ACCTACCTCCCAGCCACG 60.684 66.667 0.00 0.00 0.00 4.94
2627 5167 4.162690 CCTACCTCCCAGCCACGC 62.163 72.222 0.00 0.00 0.00 5.34
2628 5168 4.162690 CTACCTCCCAGCCACGCC 62.163 72.222 0.00 0.00 0.00 5.68
2660 5200 4.536687 CTCGGCCGCGGCAAATTC 62.537 66.667 46.88 30.03 44.11 2.17
2662 5202 4.412270 CGGCCGCGGCAAATTCAA 62.412 61.111 46.88 0.00 44.11 2.69
2663 5203 2.048690 GGCCGCGGCAAATTCAAA 60.049 55.556 46.88 0.00 44.11 2.69
2664 5204 2.379634 GGCCGCGGCAAATTCAAAC 61.380 57.895 46.88 25.44 44.11 2.93
2665 5205 2.715849 GCCGCGGCAAATTCAAACG 61.716 57.895 43.55 5.41 41.49 3.60
2666 5206 1.371145 CCGCGGCAAATTCAAACGT 60.371 52.632 14.67 0.00 0.00 3.99
2667 5207 0.110147 CCGCGGCAAATTCAAACGTA 60.110 50.000 14.67 0.00 0.00 3.57
2668 5208 1.246970 CGCGGCAAATTCAAACGTAG 58.753 50.000 0.00 0.00 0.00 3.51
2670 5210 2.239201 GCGGCAAATTCAAACGTAGTC 58.761 47.619 0.00 0.00 45.00 2.59
2671 5211 2.350007 GCGGCAAATTCAAACGTAGTCA 60.350 45.455 0.00 0.00 45.00 3.41
2672 5212 3.669557 GCGGCAAATTCAAACGTAGTCAT 60.670 43.478 0.00 0.00 45.00 3.06
2673 5213 4.472286 CGGCAAATTCAAACGTAGTCATT 58.528 39.130 0.00 0.00 45.00 2.57
2674 5214 4.553429 CGGCAAATTCAAACGTAGTCATTC 59.447 41.667 0.00 0.00 45.00 2.67
2675 5215 4.857037 GGCAAATTCAAACGTAGTCATTCC 59.143 41.667 0.00 0.00 45.00 3.01
2676 5216 4.857037 GCAAATTCAAACGTAGTCATTCCC 59.143 41.667 0.00 0.00 45.00 3.97
2677 5217 4.939509 AATTCAAACGTAGTCATTCCCG 57.060 40.909 0.00 0.00 45.00 5.14
2678 5218 1.717194 TCAAACGTAGTCATTCCCGC 58.283 50.000 0.00 0.00 45.00 6.13
2679 5219 1.274167 TCAAACGTAGTCATTCCCGCT 59.726 47.619 0.00 0.00 45.00 5.52
2680 5220 1.659098 CAAACGTAGTCATTCCCGCTC 59.341 52.381 0.00 0.00 45.00 5.03
2681 5221 0.892755 AACGTAGTCATTCCCGCTCA 59.107 50.000 0.00 0.00 45.00 4.26
2682 5222 0.172803 ACGTAGTCATTCCCGCTCAC 59.827 55.000 0.00 0.00 29.74 3.51
2683 5223 0.172578 CGTAGTCATTCCCGCTCACA 59.827 55.000 0.00 0.00 0.00 3.58
2684 5224 1.403647 CGTAGTCATTCCCGCTCACAA 60.404 52.381 0.00 0.00 0.00 3.33
2685 5225 2.695359 GTAGTCATTCCCGCTCACAAA 58.305 47.619 0.00 0.00 0.00 2.83
2686 5226 2.270352 AGTCATTCCCGCTCACAAAA 57.730 45.000 0.00 0.00 0.00 2.44
2687 5227 2.795329 AGTCATTCCCGCTCACAAAAT 58.205 42.857 0.00 0.00 0.00 1.82
2688 5228 3.950397 AGTCATTCCCGCTCACAAAATA 58.050 40.909 0.00 0.00 0.00 1.40
2689 5229 3.941483 AGTCATTCCCGCTCACAAAATAG 59.059 43.478 0.00 0.00 0.00 1.73
2690 5230 3.938963 GTCATTCCCGCTCACAAAATAGA 59.061 43.478 0.00 0.00 0.00 1.98
2691 5231 3.938963 TCATTCCCGCTCACAAAATAGAC 59.061 43.478 0.00 0.00 0.00 2.59
2692 5232 2.004583 TCCCGCTCACAAAATAGACG 57.995 50.000 0.00 0.00 0.00 4.18
2693 5233 1.274167 TCCCGCTCACAAAATAGACGT 59.726 47.619 0.00 0.00 0.00 4.34
2694 5234 1.659098 CCCGCTCACAAAATAGACGTC 59.341 52.381 7.70 7.70 0.00 4.34
2695 5235 2.333926 CCGCTCACAAAATAGACGTCA 58.666 47.619 19.50 4.13 0.00 4.35
2696 5236 2.092211 CCGCTCACAAAATAGACGTCAC 59.908 50.000 19.50 0.00 0.00 3.67
2697 5237 2.729360 CGCTCACAAAATAGACGTCACA 59.271 45.455 19.50 5.22 0.00 3.58
2698 5238 3.183574 CGCTCACAAAATAGACGTCACAA 59.816 43.478 19.50 2.77 0.00 3.33
2699 5239 4.318475 CGCTCACAAAATAGACGTCACAAA 60.318 41.667 19.50 0.00 0.00 2.83
2700 5240 5.614668 CGCTCACAAAATAGACGTCACAAAT 60.615 40.000 19.50 2.61 0.00 2.32
2701 5241 5.790495 GCTCACAAAATAGACGTCACAAATC 59.210 40.000 19.50 0.00 0.00 2.17
2702 5242 6.236017 TCACAAAATAGACGTCACAAATCC 57.764 37.500 19.50 0.00 0.00 3.01
2703 5243 5.079406 CACAAAATAGACGTCACAAATCCG 58.921 41.667 19.50 1.46 0.00 4.18
2704 5244 4.153475 ACAAAATAGACGTCACAAATCCGG 59.847 41.667 19.50 0.00 0.00 5.14
2705 5245 1.935933 ATAGACGTCACAAATCCGGC 58.064 50.000 19.50 0.00 0.00 6.13
2706 5246 0.457166 TAGACGTCACAAATCCGGCG 60.457 55.000 19.50 0.00 34.03 6.46
2707 5247 1.735198 GACGTCACAAATCCGGCGA 60.735 57.895 9.30 0.00 0.00 5.54
2708 5248 1.079405 ACGTCACAAATCCGGCGAT 60.079 52.632 9.30 0.00 0.00 4.58
2709 5249 1.082117 ACGTCACAAATCCGGCGATC 61.082 55.000 9.30 0.00 0.00 3.69
2710 5250 1.081556 CGTCACAAATCCGGCGATCA 61.082 55.000 9.30 0.00 0.00 2.92
2711 5251 1.083489 GTCACAAATCCGGCGATCAA 58.917 50.000 9.30 0.00 0.00 2.57
2712 5252 1.062587 GTCACAAATCCGGCGATCAAG 59.937 52.381 9.30 0.00 0.00 3.02
2713 5253 0.248215 CACAAATCCGGCGATCAAGC 60.248 55.000 9.30 0.00 0.00 4.01
2714 5254 1.010797 CAAATCCGGCGATCAAGCG 60.011 57.895 9.30 0.00 38.18 4.68
2715 5255 2.180204 AAATCCGGCGATCAAGCGG 61.180 57.895 9.30 0.00 38.18 5.52
2721 5261 3.794270 GCGATCAAGCGGCTACAA 58.206 55.556 1.35 0.00 0.00 2.41
2722 5262 1.638467 GCGATCAAGCGGCTACAAG 59.362 57.895 1.35 0.00 0.00 3.16
2723 5263 1.084370 GCGATCAAGCGGCTACAAGT 61.084 55.000 1.35 0.00 0.00 3.16
2724 5264 1.359848 CGATCAAGCGGCTACAAGTT 58.640 50.000 1.35 0.00 0.00 2.66
2725 5265 1.324736 CGATCAAGCGGCTACAAGTTC 59.675 52.381 1.35 0.00 0.00 3.01
2726 5266 1.324736 GATCAAGCGGCTACAAGTTCG 59.675 52.381 1.35 0.00 0.00 3.95
2727 5267 0.669318 TCAAGCGGCTACAAGTTCGG 60.669 55.000 1.35 0.00 0.00 4.30
2728 5268 0.949105 CAAGCGGCTACAAGTTCGGT 60.949 55.000 1.35 0.00 34.77 4.69
2729 5269 0.949105 AAGCGGCTACAAGTTCGGTG 60.949 55.000 1.35 0.00 33.58 4.94
2730 5270 1.373748 GCGGCTACAAGTTCGGTGA 60.374 57.895 0.00 0.00 0.00 4.02
2731 5271 0.739813 GCGGCTACAAGTTCGGTGAT 60.740 55.000 0.00 0.00 0.00 3.06
2732 5272 1.278238 CGGCTACAAGTTCGGTGATC 58.722 55.000 0.00 0.00 0.00 2.92
2733 5273 1.278238 GGCTACAAGTTCGGTGATCG 58.722 55.000 0.00 0.00 40.90 3.69
2745 5285 4.921470 TCGGTGATCGAATGAAAAGTTC 57.079 40.909 0.00 0.00 45.86 3.01
2746 5286 3.366724 TCGGTGATCGAATGAAAAGTTCG 59.633 43.478 0.00 2.15 45.86 3.95
2747 5287 3.483574 CGGTGATCGAATGAAAAGTTCGG 60.484 47.826 8.19 0.00 46.14 4.30
2748 5288 3.417185 GTGATCGAATGAAAAGTTCGGC 58.583 45.455 8.19 2.80 46.14 5.54
2749 5289 2.093625 TGATCGAATGAAAAGTTCGGCG 59.906 45.455 0.00 0.00 46.14 6.46
2750 5290 1.504359 TCGAATGAAAAGTTCGGCGT 58.496 45.000 6.85 0.00 46.14 5.68
2751 5291 2.674954 TCGAATGAAAAGTTCGGCGTA 58.325 42.857 6.85 0.00 46.14 4.42
2752 5292 2.409378 TCGAATGAAAAGTTCGGCGTAC 59.591 45.455 8.72 8.72 46.14 3.67
2753 5293 2.156117 CGAATGAAAAGTTCGGCGTACA 59.844 45.455 18.71 0.00 43.36 2.90
2754 5294 3.363182 CGAATGAAAAGTTCGGCGTACAA 60.363 43.478 18.71 0.00 43.36 2.41
2755 5295 4.529446 GAATGAAAAGTTCGGCGTACAAA 58.471 39.130 18.71 0.00 0.00 2.83
2756 5296 4.555348 ATGAAAAGTTCGGCGTACAAAA 57.445 36.364 18.71 0.00 0.00 2.44
2757 5297 4.555348 TGAAAAGTTCGGCGTACAAAAT 57.445 36.364 18.71 2.03 0.00 1.82
2758 5298 4.283678 TGAAAAGTTCGGCGTACAAAATG 58.716 39.130 18.71 0.00 0.00 2.32
2759 5299 2.325509 AAGTTCGGCGTACAAAATGC 57.674 45.000 18.71 0.00 39.58 3.56
2760 5300 1.231221 AGTTCGGCGTACAAAATGCA 58.769 45.000 18.71 0.00 42.33 3.96
2761 5301 1.196808 AGTTCGGCGTACAAAATGCAG 59.803 47.619 18.71 0.00 42.33 4.41
2762 5302 1.195900 GTTCGGCGTACAAAATGCAGA 59.804 47.619 11.92 0.00 41.74 4.26
2763 5303 1.514003 TCGGCGTACAAAATGCAGAA 58.486 45.000 6.85 0.00 40.71 3.02
2764 5304 1.874231 TCGGCGTACAAAATGCAGAAA 59.126 42.857 6.85 0.00 40.71 2.52
2765 5305 2.290916 TCGGCGTACAAAATGCAGAAAA 59.709 40.909 6.85 0.00 40.71 2.29
2766 5306 2.656422 CGGCGTACAAAATGCAGAAAAG 59.344 45.455 0.00 0.00 42.33 2.27
2767 5307 2.986479 GGCGTACAAAATGCAGAAAAGG 59.014 45.455 0.00 0.00 42.33 3.11
2768 5308 2.986479 GCGTACAAAATGCAGAAAAGGG 59.014 45.455 0.00 0.00 40.09 3.95
2769 5309 2.986479 CGTACAAAATGCAGAAAAGGGC 59.014 45.455 0.00 0.00 0.00 5.19
2770 5310 2.153366 ACAAAATGCAGAAAAGGGCG 57.847 45.000 0.00 0.00 0.00 6.13
2771 5311 0.792031 CAAAATGCAGAAAAGGGCGC 59.208 50.000 0.00 0.00 0.00 6.53
2772 5312 0.667184 AAAATGCAGAAAAGGGCGCG 60.667 50.000 0.00 0.00 0.00 6.86
2773 5313 1.805428 AAATGCAGAAAAGGGCGCGT 61.805 50.000 8.43 0.00 0.00 6.01
2774 5314 2.476534 AATGCAGAAAAGGGCGCGTG 62.477 55.000 8.43 0.00 0.00 5.34
2775 5315 3.660111 GCAGAAAAGGGCGCGTGT 61.660 61.111 8.43 0.00 0.00 4.49
2776 5316 2.252260 CAGAAAAGGGCGCGTGTG 59.748 61.111 8.43 0.00 0.00 3.82
2777 5317 3.660111 AGAAAAGGGCGCGTGTGC 61.660 61.111 8.43 0.00 37.91 4.57
2789 5329 4.152625 GTGTGCGCATCAGACGGC 62.153 66.667 15.91 0.00 0.00 5.68
2795 5335 2.583593 GCATCAGACGGCGAGGTC 60.584 66.667 16.62 0.00 37.19 3.85
2796 5336 2.278206 CATCAGACGGCGAGGTCG 60.278 66.667 16.62 0.00 41.81 4.79
2797 5337 3.518998 ATCAGACGGCGAGGTCGG 61.519 66.667 16.62 1.12 41.81 4.79
2856 5396 3.414700 GTCGGCGTGGCTTCTGTG 61.415 66.667 6.85 0.00 0.00 3.66
2859 5399 3.730761 GGCGTGGCTTCTGTGCTG 61.731 66.667 0.00 0.00 0.00 4.41
2860 5400 4.395583 GCGTGGCTTCTGTGCTGC 62.396 66.667 0.00 0.00 0.00 5.25
2861 5401 4.081030 CGTGGCTTCTGTGCTGCG 62.081 66.667 0.00 0.00 0.00 5.18
2862 5402 3.730761 GTGGCTTCTGTGCTGCGG 61.731 66.667 0.00 0.00 0.00 5.69
2865 5405 4.704833 GCTTCTGTGCTGCGGGGA 62.705 66.667 0.00 0.00 0.00 4.81
2866 5406 2.435586 CTTCTGTGCTGCGGGGAG 60.436 66.667 0.00 0.00 0.00 4.30
2867 5407 3.241530 TTCTGTGCTGCGGGGAGT 61.242 61.111 0.00 0.00 0.00 3.85
2868 5408 3.240134 TTCTGTGCTGCGGGGAGTC 62.240 63.158 0.00 0.00 0.00 3.36
2869 5409 3.699894 CTGTGCTGCGGGGAGTCT 61.700 66.667 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 8.103948 ACCCGAAAAATCATGATCATATCTTC 57.896 34.615 9.06 6.51 0.00 2.87
43 44 3.509184 TGCAACCCGAAAAATCATGATCA 59.491 39.130 9.06 0.00 0.00 2.92
52 53 6.203723 CCTTTTCATAAATGCAACCCGAAAAA 59.796 34.615 12.46 6.56 32.36 1.94
201 1193 9.268268 TGTACACAACCTGTAGAAAATAGAAAG 57.732 33.333 0.00 0.00 35.93 2.62
202 1194 9.616156 TTGTACACAACCTGTAGAAAATAGAAA 57.384 29.630 0.00 0.00 36.05 2.52
536 1858 5.419542 TGCTTGATAGTGGACATTAGACAC 58.580 41.667 0.00 0.00 35.43 3.67
738 2062 8.569596 TCCAGATAGGAGGCTATCTAAATATGA 58.430 37.037 0.00 0.00 42.78 2.15
791 2116 5.741388 AAGCACTTAAACAGTCAAGACAG 57.259 39.130 2.72 0.00 30.92 3.51
831 2939 4.090090 CCTGGAGAGAAACTGAGGACTAA 58.910 47.826 0.00 0.00 30.37 2.24
851 2969 5.896963 AGGAAACAGAGAAATTCCATTCCT 58.103 37.500 6.55 8.56 44.08 3.36
852 2970 6.209391 TGAAGGAAACAGAGAAATTCCATTCC 59.791 38.462 6.55 0.00 44.08 3.01
973 3105 4.726416 CAGTATCAGCATTGGAAACACAC 58.274 43.478 0.00 0.00 42.67 3.82
1183 3315 0.401738 CCCTCCATGTGACCTGTGTT 59.598 55.000 0.00 0.00 0.00 3.32
1184 3316 0.768221 ACCCTCCATGTGACCTGTGT 60.768 55.000 0.00 0.00 0.00 3.72
1355 3494 7.628580 GCCCACTGTTTTTACAGGAATATTCTC 60.629 40.741 14.95 5.73 41.76 2.87
1356 3495 6.152831 GCCCACTGTTTTTACAGGAATATTCT 59.847 38.462 14.95 0.00 41.76 2.40
1396 3535 4.362279 CAAATGGCCATTGTACATACAGC 58.638 43.478 31.28 0.00 37.52 4.40
1403 3555 3.119029 AGTGATGCAAATGGCCATTGTAC 60.119 43.478 31.28 22.14 43.89 2.90
1602 4115 1.212455 CCAAAACGGGCTTGTTTCGC 61.212 55.000 8.44 0.00 41.01 4.70
1638 4151 8.575649 AAGAGTAGGAAAAGTTCTGTTTTCAA 57.424 30.769 10.37 0.00 44.81 2.69
1722 4235 3.498927 TCGAAAGTGGATCGGTTCTAC 57.501 47.619 0.00 0.00 40.59 2.59
1741 4254 7.732664 ACACGTAAAAACCATATACTCGTTTC 58.267 34.615 0.00 0.00 0.00 2.78
1780 4295 6.299141 GGGTCTCATAAAATCCTGCATAAGA 58.701 40.000 0.00 0.00 0.00 2.10
2184 4721 9.849607 CATATGTACTATCTTAAACACGCAAAG 57.150 33.333 0.00 0.00 0.00 2.77
2195 4732 7.693132 AGTACGGGGTCATATGTACTATCTTA 58.307 38.462 1.90 0.00 44.08 2.10
2202 4739 4.022849 GTGGTAGTACGGGGTCATATGTAC 60.023 50.000 1.90 0.00 37.93 2.90
2224 4763 1.071228 GAACCAGTAAACCAGGACCGT 59.929 52.381 0.00 0.00 0.00 4.83
2238 4777 7.026631 TGACACAAAATACAAAGAGAACCAG 57.973 36.000 0.00 0.00 0.00 4.00
2260 4799 5.765677 TGGTCAAATCTACGGTCAAATTTGA 59.234 36.000 16.91 16.91 42.66 2.69
2264 4804 6.642707 TTTTGGTCAAATCTACGGTCAAAT 57.357 33.333 0.00 0.00 0.00 2.32
2432 4972 4.210331 GGATAAAGTACTACCTCCGTCCA 58.790 47.826 0.00 0.00 0.00 4.02
2454 4994 4.318332 TGATGCAACTGACAGAAACTAGG 58.682 43.478 10.08 0.00 0.00 3.02
2525 5065 1.023513 GCTGAACGGCTGAAGATGCT 61.024 55.000 0.00 0.00 0.00 3.79
2526 5066 1.427020 GCTGAACGGCTGAAGATGC 59.573 57.895 0.00 0.00 0.00 3.91
2527 5067 1.372087 GGGCTGAACGGCTGAAGATG 61.372 60.000 0.00 0.00 38.46 2.90
2528 5068 1.078143 GGGCTGAACGGCTGAAGAT 60.078 57.895 0.00 0.00 38.46 2.40
2529 5069 2.347490 GGGCTGAACGGCTGAAGA 59.653 61.111 0.00 0.00 38.46 2.87
2530 5070 2.747855 GGGGCTGAACGGCTGAAG 60.748 66.667 0.00 0.00 38.46 3.02
2531 5071 4.344865 GGGGGCTGAACGGCTGAA 62.345 66.667 0.00 0.00 38.46 3.02
2546 5086 2.203567 TTTTTCGGCACCCTGGGG 60.204 61.111 18.88 7.87 42.03 4.96
2547 5087 1.228429 TCTTTTTCGGCACCCTGGG 60.228 57.895 12.28 12.28 0.00 4.45
2548 5088 1.866853 GCTCTTTTTCGGCACCCTGG 61.867 60.000 0.00 0.00 0.00 4.45
2549 5089 1.581447 GCTCTTTTTCGGCACCCTG 59.419 57.895 0.00 0.00 0.00 4.45
2550 5090 1.966451 CGCTCTTTTTCGGCACCCT 60.966 57.895 0.00 0.00 0.00 4.34
2551 5091 2.561373 CGCTCTTTTTCGGCACCC 59.439 61.111 0.00 0.00 0.00 4.61
2552 5092 2.561373 CCGCTCTTTTTCGGCACC 59.439 61.111 0.00 0.00 39.14 5.01
2557 5097 2.690778 CCCAGGCCGCTCTTTTTCG 61.691 63.158 0.00 0.00 0.00 3.46
2558 5098 2.343426 CCCCAGGCCGCTCTTTTTC 61.343 63.158 0.00 0.00 0.00 2.29
2559 5099 2.283173 CCCCAGGCCGCTCTTTTT 60.283 61.111 0.00 0.00 0.00 1.94
2560 5100 4.366684 CCCCCAGGCCGCTCTTTT 62.367 66.667 0.00 0.00 0.00 2.27
2578 5118 2.237751 CCAATCTAGCGCCGGTTCG 61.238 63.158 2.29 0.00 0.00 3.95
2579 5119 2.534903 GCCAATCTAGCGCCGGTTC 61.535 63.158 2.29 0.00 0.00 3.62
2580 5120 2.513897 GCCAATCTAGCGCCGGTT 60.514 61.111 2.29 0.00 0.00 4.44
2581 5121 4.547367 GGCCAATCTAGCGCCGGT 62.547 66.667 2.29 0.00 31.92 5.28
2585 5125 2.592861 CAGGGGCCAATCTAGCGC 60.593 66.667 4.39 0.00 42.07 5.92
2586 5126 2.111878 CCAGGGGCCAATCTAGCG 59.888 66.667 4.39 0.00 0.00 4.26
2587 5127 2.517919 CCCAGGGGCCAATCTAGC 59.482 66.667 4.39 0.00 0.00 3.42
2588 5128 3.255032 CCCCAGGGGCCAATCTAG 58.745 66.667 13.35 0.00 35.35 2.43
2599 5139 4.798682 AGGTAGGTCGCCCCCAGG 62.799 72.222 5.44 0.00 0.00 4.45
2600 5140 3.155167 GAGGTAGGTCGCCCCCAG 61.155 72.222 5.44 0.00 0.00 4.45
2601 5141 4.791069 GGAGGTAGGTCGCCCCCA 62.791 72.222 5.44 0.00 0.00 4.96
2603 5143 4.791069 TGGGAGGTAGGTCGCCCC 62.791 72.222 0.00 0.00 39.93 5.80
2604 5144 3.155167 CTGGGAGGTAGGTCGCCC 61.155 72.222 0.00 0.00 41.08 6.13
2605 5145 3.851128 GCTGGGAGGTAGGTCGCC 61.851 72.222 0.00 0.00 0.00 5.54
2606 5146 3.851128 GGCTGGGAGGTAGGTCGC 61.851 72.222 0.00 0.00 0.00 5.19
2607 5147 2.363795 TGGCTGGGAGGTAGGTCG 60.364 66.667 0.00 0.00 0.00 4.79
2608 5148 2.722201 CGTGGCTGGGAGGTAGGTC 61.722 68.421 0.00 0.00 0.00 3.85
2609 5149 2.683933 CGTGGCTGGGAGGTAGGT 60.684 66.667 0.00 0.00 0.00 3.08
2610 5150 4.162690 GCGTGGCTGGGAGGTAGG 62.163 72.222 0.00 0.00 0.00 3.18
2611 5151 4.162690 GGCGTGGCTGGGAGGTAG 62.163 72.222 0.00 0.00 0.00 3.18
2643 5183 4.536687 GAATTTGCCGCGGCCGAG 62.537 66.667 44.42 28.06 41.09 4.63
2645 5185 3.905705 TTTGAATTTGCCGCGGCCG 62.906 57.895 44.42 24.05 41.09 6.13
2646 5186 2.048690 TTTGAATTTGCCGCGGCC 60.049 55.556 44.42 29.66 41.09 6.13
2647 5187 2.715849 CGTTTGAATTTGCCGCGGC 61.716 57.895 42.35 42.35 42.35 6.53
2648 5188 0.110147 TACGTTTGAATTTGCCGCGG 60.110 50.000 24.05 24.05 0.00 6.46
2649 5189 1.246970 CTACGTTTGAATTTGCCGCG 58.753 50.000 0.00 0.00 0.00 6.46
2650 5190 2.239201 GACTACGTTTGAATTTGCCGC 58.761 47.619 0.00 0.00 0.00 6.53
2651 5191 3.529634 TGACTACGTTTGAATTTGCCG 57.470 42.857 0.00 0.00 0.00 5.69
2652 5192 4.857037 GGAATGACTACGTTTGAATTTGCC 59.143 41.667 0.00 0.00 0.00 4.52
2653 5193 4.857037 GGGAATGACTACGTTTGAATTTGC 59.143 41.667 0.00 0.00 0.00 3.68
2654 5194 5.086058 CGGGAATGACTACGTTTGAATTTG 58.914 41.667 0.00 0.00 0.00 2.32
2655 5195 4.379082 GCGGGAATGACTACGTTTGAATTT 60.379 41.667 0.00 0.00 0.00 1.82
2656 5196 3.126343 GCGGGAATGACTACGTTTGAATT 59.874 43.478 0.00 0.00 0.00 2.17
2657 5197 2.676342 GCGGGAATGACTACGTTTGAAT 59.324 45.455 0.00 0.00 0.00 2.57
2658 5198 2.070783 GCGGGAATGACTACGTTTGAA 58.929 47.619 0.00 0.00 0.00 2.69
2659 5199 1.274167 AGCGGGAATGACTACGTTTGA 59.726 47.619 0.00 0.00 0.00 2.69
2660 5200 1.659098 GAGCGGGAATGACTACGTTTG 59.341 52.381 0.00 0.00 0.00 2.93
2661 5201 1.274167 TGAGCGGGAATGACTACGTTT 59.726 47.619 0.00 0.00 0.00 3.60
2662 5202 0.892755 TGAGCGGGAATGACTACGTT 59.107 50.000 0.00 0.00 0.00 3.99
2663 5203 0.172803 GTGAGCGGGAATGACTACGT 59.827 55.000 0.00 0.00 0.00 3.57
2664 5204 0.172578 TGTGAGCGGGAATGACTACG 59.827 55.000 0.00 0.00 0.00 3.51
2665 5205 2.380084 TTGTGAGCGGGAATGACTAC 57.620 50.000 0.00 0.00 0.00 2.73
2666 5206 3.410631 TTTTGTGAGCGGGAATGACTA 57.589 42.857 0.00 0.00 0.00 2.59
2667 5207 2.270352 TTTTGTGAGCGGGAATGACT 57.730 45.000 0.00 0.00 0.00 3.41
2668 5208 3.938963 TCTATTTTGTGAGCGGGAATGAC 59.061 43.478 0.00 0.00 0.00 3.06
2669 5209 3.938963 GTCTATTTTGTGAGCGGGAATGA 59.061 43.478 0.00 0.00 0.00 2.57
2670 5210 3.242413 CGTCTATTTTGTGAGCGGGAATG 60.242 47.826 0.00 0.00 0.00 2.67
2671 5211 2.936498 CGTCTATTTTGTGAGCGGGAAT 59.064 45.455 0.00 0.00 0.00 3.01
2672 5212 2.289195 ACGTCTATTTTGTGAGCGGGAA 60.289 45.455 0.00 0.00 0.00 3.97
2673 5213 1.274167 ACGTCTATTTTGTGAGCGGGA 59.726 47.619 0.00 0.00 0.00 5.14
2674 5214 1.659098 GACGTCTATTTTGTGAGCGGG 59.341 52.381 8.70 0.00 0.00 6.13
2675 5215 2.092211 GTGACGTCTATTTTGTGAGCGG 59.908 50.000 17.92 0.00 0.00 5.52
2676 5216 2.729360 TGTGACGTCTATTTTGTGAGCG 59.271 45.455 17.92 0.00 0.00 5.03
2677 5217 4.725556 TTGTGACGTCTATTTTGTGAGC 57.274 40.909 17.92 0.00 0.00 4.26
2678 5218 6.307155 GGATTTGTGACGTCTATTTTGTGAG 58.693 40.000 17.92 0.00 0.00 3.51
2679 5219 5.107259 CGGATTTGTGACGTCTATTTTGTGA 60.107 40.000 17.92 0.00 0.00 3.58
2680 5220 5.079406 CGGATTTGTGACGTCTATTTTGTG 58.921 41.667 17.92 0.00 0.00 3.33
2681 5221 4.153475 CCGGATTTGTGACGTCTATTTTGT 59.847 41.667 17.92 0.00 0.00 2.83
2682 5222 4.647964 CCGGATTTGTGACGTCTATTTTG 58.352 43.478 17.92 0.05 0.00 2.44
2683 5223 3.126343 GCCGGATTTGTGACGTCTATTTT 59.874 43.478 17.92 0.00 0.00 1.82
2684 5224 2.676342 GCCGGATTTGTGACGTCTATTT 59.324 45.455 17.92 0.00 0.00 1.40
2685 5225 2.277084 GCCGGATTTGTGACGTCTATT 58.723 47.619 17.92 0.00 0.00 1.73
2686 5226 1.801395 CGCCGGATTTGTGACGTCTAT 60.801 52.381 17.92 5.02 0.00 1.98
2687 5227 0.457166 CGCCGGATTTGTGACGTCTA 60.457 55.000 17.92 2.84 0.00 2.59
2688 5228 1.736645 CGCCGGATTTGTGACGTCT 60.737 57.895 17.92 0.00 0.00 4.18
2689 5229 1.082117 ATCGCCGGATTTGTGACGTC 61.082 55.000 5.05 9.11 0.00 4.34
2690 5230 1.079405 ATCGCCGGATTTGTGACGT 60.079 52.632 5.05 0.00 0.00 4.34
2691 5231 1.081556 TGATCGCCGGATTTGTGACG 61.082 55.000 5.05 0.00 31.51 4.35
2692 5232 1.062587 CTTGATCGCCGGATTTGTGAC 59.937 52.381 5.05 0.00 31.51 3.67
2693 5233 1.368641 CTTGATCGCCGGATTTGTGA 58.631 50.000 5.05 0.00 31.51 3.58
2694 5234 0.248215 GCTTGATCGCCGGATTTGTG 60.248 55.000 5.05 0.00 31.51 3.33
2695 5235 1.705337 CGCTTGATCGCCGGATTTGT 61.705 55.000 5.05 0.00 31.51 2.83
2696 5236 1.010797 CGCTTGATCGCCGGATTTG 60.011 57.895 5.05 0.00 31.51 2.32
2697 5237 2.180204 CCGCTTGATCGCCGGATTT 61.180 57.895 5.05 0.00 44.55 2.17
2698 5238 2.588877 CCGCTTGATCGCCGGATT 60.589 61.111 5.05 0.00 44.55 3.01
2701 5241 4.585526 TAGCCGCTTGATCGCCGG 62.586 66.667 12.50 12.50 44.58 6.13
2702 5242 3.330853 GTAGCCGCTTGATCGCCG 61.331 66.667 0.00 0.00 0.00 6.46
2703 5243 1.766143 CTTGTAGCCGCTTGATCGCC 61.766 60.000 0.00 0.00 0.00 5.54
2704 5244 1.084370 ACTTGTAGCCGCTTGATCGC 61.084 55.000 0.00 0.00 0.00 4.58
2705 5245 1.324736 GAACTTGTAGCCGCTTGATCG 59.675 52.381 0.00 0.00 0.00 3.69
2706 5246 1.324736 CGAACTTGTAGCCGCTTGATC 59.675 52.381 0.00 0.00 0.00 2.92
2707 5247 1.359848 CGAACTTGTAGCCGCTTGAT 58.640 50.000 0.00 0.00 0.00 2.57
2708 5248 0.669318 CCGAACTTGTAGCCGCTTGA 60.669 55.000 0.00 0.00 0.00 3.02
2709 5249 0.949105 ACCGAACTTGTAGCCGCTTG 60.949 55.000 0.00 0.00 0.00 4.01
2710 5250 0.949105 CACCGAACTTGTAGCCGCTT 60.949 55.000 0.00 0.00 0.00 4.68
2711 5251 1.374252 CACCGAACTTGTAGCCGCT 60.374 57.895 0.00 0.00 0.00 5.52
2712 5252 0.739813 ATCACCGAACTTGTAGCCGC 60.740 55.000 0.00 0.00 0.00 6.53
2713 5253 1.278238 GATCACCGAACTTGTAGCCG 58.722 55.000 0.00 0.00 0.00 5.52
2714 5254 1.135199 TCGATCACCGAACTTGTAGCC 60.135 52.381 0.00 0.00 45.43 3.93
2715 5255 2.273370 TCGATCACCGAACTTGTAGC 57.727 50.000 0.00 0.00 45.43 3.58
2724 5264 4.921470 GAACTTTTCATTCGATCACCGA 57.079 40.909 0.00 0.00 46.94 4.69
2732 5272 2.156117 TGTACGCCGAACTTTTCATTCG 59.844 45.455 0.00 0.26 46.67 3.34
2733 5273 3.799137 TGTACGCCGAACTTTTCATTC 57.201 42.857 0.00 0.00 0.00 2.67
2734 5274 4.555348 TTTGTACGCCGAACTTTTCATT 57.445 36.364 0.00 0.00 0.00 2.57
2735 5275 4.555348 TTTTGTACGCCGAACTTTTCAT 57.445 36.364 0.00 0.00 0.00 2.57
2736 5276 4.283678 CATTTTGTACGCCGAACTTTTCA 58.716 39.130 0.00 0.00 0.00 2.69
2737 5277 3.118972 GCATTTTGTACGCCGAACTTTTC 59.881 43.478 0.00 0.00 0.00 2.29
2738 5278 3.047093 GCATTTTGTACGCCGAACTTTT 58.953 40.909 0.00 0.00 0.00 2.27
2739 5279 2.033550 TGCATTTTGTACGCCGAACTTT 59.966 40.909 0.00 0.00 0.00 2.66
2740 5280 1.604755 TGCATTTTGTACGCCGAACTT 59.395 42.857 0.00 0.00 0.00 2.66
2741 5281 1.196808 CTGCATTTTGTACGCCGAACT 59.803 47.619 0.00 0.00 0.00 3.01
2742 5282 1.195900 TCTGCATTTTGTACGCCGAAC 59.804 47.619 0.00 0.00 0.00 3.95
2743 5283 1.514003 TCTGCATTTTGTACGCCGAA 58.486 45.000 0.00 0.00 0.00 4.30
2744 5284 1.514003 TTCTGCATTTTGTACGCCGA 58.486 45.000 0.00 0.00 0.00 5.54
2745 5285 2.323939 TTTCTGCATTTTGTACGCCG 57.676 45.000 0.00 0.00 0.00 6.46
2746 5286 2.986479 CCTTTTCTGCATTTTGTACGCC 59.014 45.455 0.00 0.00 0.00 5.68
2747 5287 2.986479 CCCTTTTCTGCATTTTGTACGC 59.014 45.455 0.00 0.00 0.00 4.42
2748 5288 2.986479 GCCCTTTTCTGCATTTTGTACG 59.014 45.455 0.00 0.00 0.00 3.67
2749 5289 2.986479 CGCCCTTTTCTGCATTTTGTAC 59.014 45.455 0.00 0.00 0.00 2.90
2750 5290 2.609244 GCGCCCTTTTCTGCATTTTGTA 60.609 45.455 0.00 0.00 0.00 2.41
2751 5291 1.873486 GCGCCCTTTTCTGCATTTTGT 60.873 47.619 0.00 0.00 0.00 2.83
2752 5292 0.792031 GCGCCCTTTTCTGCATTTTG 59.208 50.000 0.00 0.00 0.00 2.44
2753 5293 0.667184 CGCGCCCTTTTCTGCATTTT 60.667 50.000 0.00 0.00 0.00 1.82
2754 5294 1.080569 CGCGCCCTTTTCTGCATTT 60.081 52.632 0.00 0.00 0.00 2.32
2755 5295 2.268076 ACGCGCCCTTTTCTGCATT 61.268 52.632 5.73 0.00 0.00 3.56
2756 5296 2.672996 ACGCGCCCTTTTCTGCAT 60.673 55.556 5.73 0.00 0.00 3.96
2757 5297 3.659092 CACGCGCCCTTTTCTGCA 61.659 61.111 5.73 0.00 0.00 4.41
2758 5298 3.660111 ACACGCGCCCTTTTCTGC 61.660 61.111 5.73 0.00 0.00 4.26
2759 5299 2.252260 CACACGCGCCCTTTTCTG 59.748 61.111 5.73 0.00 0.00 3.02
2760 5300 3.660111 GCACACGCGCCCTTTTCT 61.660 61.111 5.73 0.00 0.00 2.52
2771 5311 3.842126 CCGTCTGATGCGCACACG 61.842 66.667 14.90 18.51 38.43 4.49
2772 5312 4.152625 GCCGTCTGATGCGCACAC 62.153 66.667 14.90 11.26 0.00 3.82
2778 5318 2.583593 GACCTCGCCGTCTGATGC 60.584 66.667 0.00 0.00 0.00 3.91
2779 5319 2.278206 CGACCTCGCCGTCTGATG 60.278 66.667 1.10 0.00 0.00 3.07
2780 5320 3.518998 CCGACCTCGCCGTCTGAT 61.519 66.667 0.00 0.00 38.18 2.90
2839 5379 3.414700 CACAGAAGCCACGCCGAC 61.415 66.667 0.00 0.00 0.00 4.79
2842 5382 3.730761 CAGCACAGAAGCCACGCC 61.731 66.667 0.00 0.00 34.23 5.68
2843 5383 4.395583 GCAGCACAGAAGCCACGC 62.396 66.667 0.00 0.00 34.23 5.34
2844 5384 4.081030 CGCAGCACAGAAGCCACG 62.081 66.667 0.00 0.00 34.23 4.94
2845 5385 3.730761 CCGCAGCACAGAAGCCAC 61.731 66.667 0.00 0.00 34.23 5.01
2848 5388 4.704833 TCCCCGCAGCACAGAAGC 62.705 66.667 0.00 0.00 0.00 3.86
2849 5389 2.435586 CTCCCCGCAGCACAGAAG 60.436 66.667 0.00 0.00 0.00 2.85
2850 5390 3.240134 GACTCCCCGCAGCACAGAA 62.240 63.158 0.00 0.00 0.00 3.02
2851 5391 3.695606 GACTCCCCGCAGCACAGA 61.696 66.667 0.00 0.00 0.00 3.41
2852 5392 3.699894 AGACTCCCCGCAGCACAG 61.700 66.667 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.