Multiple sequence alignment - TraesCS7D01G478500

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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 TraesCS7D01G478500 chr7D 100.000 5258 0 0 1 5258 589321289 589316032 0.000000e+00 9710.0
1 TraesCS7D01G478500 chr7D 81.879 149 17 6 4566 4704 31379475 31379623 3.330000e-22 117.0
2 TraesCS7D01G478500 chr7A 93.609 4256 189 35 292 4501 680578834 680574616 0.000000e+00 6276.0
3 TraesCS7D01G478500 chr7A 90.793 391 33 1 3599 3989 680579494 680579881 2.170000e-143 520.0
4 TraesCS7D01G478500 chr7A 91.691 337 15 5 3985 4311 680594142 680594475 6.210000e-124 455.0
5 TraesCS7D01G478500 chr7A 85.484 310 33 7 1 299 680579168 680578860 3.950000e-81 313.0
6 TraesCS7D01G478500 chr7A 83.030 330 34 8 4562 4882 432967832 432967516 4.010000e-71 279.0
7 TraesCS7D01G478500 chr7A 84.615 247 25 8 4565 4798 206014511 206014265 3.170000e-57 233.0
8 TraesCS7D01G478500 chr7A 85.586 222 12 9 5041 5258 432966891 432966686 1.150000e-51 215.0
9 TraesCS7D01G478500 chr7A 88.415 164 11 6 5096 5258 701213800 701213956 1.930000e-44 191.0
10 TraesCS7D01G478500 chr7A 89.262 149 13 3 5110 5257 603520425 603520279 3.230000e-42 183.0
11 TraesCS7D01G478500 chr7A 96.386 83 3 0 4946 5028 432967273 432967355 2.550000e-28 137.0
12 TraesCS7D01G478500 chr7A 93.056 72 3 1 4878 4947 432967477 432967406 2.590000e-18 104.0
13 TraesCS7D01G478500 chr7B 93.565 3947 150 48 642 4539 663486015 663489906 0.000000e+00 5786.0
14 TraesCS7D01G478500 chr7B 87.500 216 16 4 398 605 663485805 663486017 6.810000e-59 239.0
15 TraesCS7D01G478500 chr4A 74.257 1414 287 65 2895 4263 598147710 598146329 1.680000e-144 523.0
16 TraesCS7D01G478500 chr4D 73.944 1397 296 55 2895 4256 5525414 5526777 7.860000e-138 501.0
17 TraesCS7D01G478500 chr4B 73.707 1411 287 69 2895 4256 9516544 9515169 1.710000e-129 473.0
18 TraesCS7D01G478500 chr4B 85.542 249 22 7 4561 4798 616805601 616805846 1.130000e-61 248.0
19 TraesCS7D01G478500 chr4B 94.667 75 2 1 4875 4947 37570828 37570902 1.200000e-21 115.0
20 TraesCS7D01G478500 chr4B 97.619 42 1 0 5044 5085 616640281 616640240 7.300000e-09 73.1
21 TraesCS7D01G478500 chr3A 92.661 218 14 2 5042 5258 155960698 155960482 3.950000e-81 313.0
22 TraesCS7D01G478500 chr3A 83.735 332 25 15 4566 4882 155961459 155961142 2.400000e-73 287.0
23 TraesCS7D01G478500 chr3A 95.238 84 3 1 4946 5028 155960898 155960981 1.190000e-26 132.0
24 TraesCS7D01G478500 chr1B 84.366 339 29 10 4563 4882 525826492 525826825 1.420000e-80 311.0
25 TraesCS7D01G478500 chr1B 89.655 145 13 2 5115 5258 525828847 525828990 3.230000e-42 183.0
26 TraesCS7D01G478500 chr1B 96.591 88 3 0 5042 5129 525827273 525827360 4.240000e-31 147.0
27 TraesCS7D01G478500 chr1B 89.855 69 5 2 4557 4623 610895272 610895340 2.610000e-13 87.9
28 TraesCS7D01G478500 chr1B 86.076 79 5 1 4875 4947 525826862 525826940 4.360000e-11 80.5
29 TraesCS7D01G478500 chr5A 84.226 336 29 10 4566 4882 401150180 401149850 6.620000e-79 305.0
30 TraesCS7D01G478500 chr5A 97.590 83 2 0 4946 5028 401149611 401149693 5.490000e-30 143.0
31 TraesCS7D01G478500 chr5B 84.478 335 23 9 4563 4882 606281457 606281777 2.380000e-78 303.0
32 TraesCS7D01G478500 chr5B 95.349 86 4 0 4946 5031 606282016 606281931 2.550000e-28 137.0
33 TraesCS7D01G478500 chr5B 95.349 86 4 0 4946 5031 637257792 637257707 2.550000e-28 137.0
34 TraesCS7D01G478500 chr5B 94.366 71 3 1 4875 4944 637257585 637257655 2.000000e-19 108.0
35 TraesCS7D01G478500 chr5B 94.286 70 2 1 4878 4947 606281816 606281883 7.200000e-19 106.0
36 TraesCS7D01G478500 chr6B 82.996 247 29 8 4564 4798 641951663 641951418 1.480000e-50 211.0
37 TraesCS7D01G478500 chr6B 80.392 204 31 4 4564 4758 717562260 717562057 4.240000e-31 147.0
38 TraesCS7D01G478500 chr6B 74.855 346 69 14 3094 3424 502793036 502792694 1.970000e-29 141.0
39 TraesCS7D01G478500 chr2D 82.988 241 31 7 4564 4795 493086493 493086254 5.340000e-50 209.0
40 TraesCS7D01G478500 chr2D 88.889 153 15 2 5106 5257 671310 671461 2.500000e-43 187.0
41 TraesCS7D01G478500 chr3D 87.117 163 18 3 5097 5258 609148860 609149020 1.160000e-41 182.0
42 TraesCS7D01G478500 chr1D 86.420 162 22 0 5097 5258 83694186 83694347 1.500000e-40 178.0
43 TraesCS7D01G478500 chr3B 85.119 168 22 2 5091 5258 449204296 449204460 9.060000e-38 169.0
44 TraesCS7D01G478500 chr3B 83.099 142 12 8 4562 4693 28310876 28310737 9.250000e-23 119.0
45 TraesCS7D01G478500 chr3B 86.486 74 10 0 4564 4637 452980087 452980160 1.210000e-11 82.4
46 TraesCS7D01G478500 chr6A 73.789 454 90 23 3095 3529 457618515 457618958 9.120000e-33 152.0
47 TraesCS7D01G478500 chr6A 86.585 82 10 1 4556 4637 2061301 2061221 7.250000e-14 89.8
48 TraesCS7D01G478500 chr6D 75.072 345 68 14 3095 3424 320113231 320113572 1.530000e-30 145.0
49 TraesCS7D01G478500 chr1A 90.123 81 7 1 4557 4637 372892432 372892353 2.590000e-18 104.0
50 TraesCS7D01G478500 chrUn 80.000 125 22 3 3115 3239 22436838 22436959 7.250000e-14 89.8
51 TraesCS7D01G478500 chr2B 85.542 83 12 0 4564 4646 199168716 199168634 2.610000e-13 87.9
52 TraesCS7D01G478500 chr2B 78.788 132 22 5 3115 3243 795756441 795756313 3.370000e-12 84.2
53 TraesCS7D01G478500 chr2A 78.358 134 29 0 3115 3248 761897462 761897329 2.610000e-13 87.9


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 TraesCS7D01G478500 chr7D 589316032 589321289 5257 True 9710.0 9710 100.0000 1 5258 1 chr7D.!!$R1 5257
1 TraesCS7D01G478500 chr7A 680574616 680579168 4552 True 3294.5 6276 89.5465 1 4501 2 chr7A.!!$R4 4500
2 TraesCS7D01G478500 chr7B 663485805 663489906 4101 False 3012.5 5786 90.5325 398 4539 2 chr7B.!!$F1 4141
3 TraesCS7D01G478500 chr4A 598146329 598147710 1381 True 523.0 523 74.2570 2895 4263 1 chr4A.!!$R1 1368
4 TraesCS7D01G478500 chr4D 5525414 5526777 1363 False 501.0 501 73.9440 2895 4256 1 chr4D.!!$F1 1361
5 TraesCS7D01G478500 chr4B 9515169 9516544 1375 True 473.0 473 73.7070 2895 4256 1 chr4B.!!$R1 1361
6 TraesCS7D01G478500 chr3A 155960482 155961459 977 True 300.0 313 88.1980 4566 5258 2 chr3A.!!$R1 692

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
615 675 0.041663 CCGATTCTCTCGCTCGAGTC 60.042 60.0 15.13 5.54 46.25 3.36 F
616 676 0.382515 CGATTCTCTCGCTCGAGTCG 60.383 60.0 15.13 17.39 41.14 4.18 F
953 1039 0.543749 CTCGCTTTCCCTTCCCATCT 59.456 55.0 0.00 0.00 0.00 2.90 F
2601 2708 0.037232 GCGTCAAGGTTCAGCTAGGT 60.037 55.0 0.00 0.00 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1781 1.096967 TCATGTGGCCGTGCATCATC 61.097 55.000 0.00 0.0 0.00 2.92 R
1836 1943 1.449601 AGGCGGGTACATTTCTGCG 60.450 57.895 0.00 0.0 36.21 5.18 R
2808 2915 0.248661 ATCTTGACGCGACGATCTGG 60.249 55.000 15.93 0.0 0.00 3.86 R
4539 4687 0.693622 TAAACCGGAGCAACCCATGA 59.306 50.000 9.46 0.0 34.64 3.07 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
22 23 1.576356 GCCGGATTTGTTGTTTGCAA 58.424 45.000 5.05 0.00 0.00 4.08
72 77 3.165559 CGATCGATCGTCCAAGGAC 57.834 57.895 33.95 9.22 44.74 3.85
106 111 1.687494 GCTACGCTTTCAGGCTCGTG 61.687 60.000 8.27 1.00 36.50 4.35
174 179 2.566529 GGGTGGCGCTTTTGTAGC 59.433 61.111 7.64 0.00 46.83 3.58
239 250 0.460811 CCTGCTCTGCGCACTATCAA 60.461 55.000 5.66 0.00 45.47 2.57
243 254 1.565305 CTCTGCGCACTATCAACTCC 58.435 55.000 5.66 0.00 0.00 3.85
244 255 0.175760 TCTGCGCACTATCAACTCCC 59.824 55.000 5.66 0.00 0.00 4.30
245 256 1.148157 CTGCGCACTATCAACTCCCG 61.148 60.000 5.66 0.00 0.00 5.14
246 257 2.526120 GCGCACTATCAACTCCCGC 61.526 63.158 0.30 0.00 0.00 6.13
247 258 1.153647 CGCACTATCAACTCCCGCA 60.154 57.895 0.00 0.00 0.00 5.69
248 259 0.530650 CGCACTATCAACTCCCGCAT 60.531 55.000 0.00 0.00 0.00 4.73
249 260 1.221414 GCACTATCAACTCCCGCATC 58.779 55.000 0.00 0.00 0.00 3.91
250 261 1.871080 CACTATCAACTCCCGCATCC 58.129 55.000 0.00 0.00 0.00 3.51
285 296 2.552315 TGAAGCCGGATTTCACTTTCAC 59.448 45.455 6.32 0.00 30.03 3.18
294 305 5.560953 CGGATTTCACTTTCACAAGGAGTTC 60.561 44.000 0.00 0.00 33.82 3.01
299 310 2.224305 ACTTTCACAAGGAGTTCTCCCG 60.224 50.000 14.40 9.24 33.82 5.14
300 311 1.712056 TTCACAAGGAGTTCTCCCGA 58.288 50.000 14.40 4.89 0.00 5.14
366 410 0.165079 AAATGAAGTTACCGCACGCG 59.835 50.000 3.53 3.53 39.44 6.01
388 432 0.170116 CGCGCCATAGAAAAAGCCAA 59.830 50.000 0.00 0.00 0.00 4.52
443 487 1.973138 CAGAATCCGCAACAGCAAAG 58.027 50.000 0.00 0.00 0.00 2.77
460 504 3.726517 GCACATCACCAAGCGCGT 61.727 61.111 8.43 0.00 0.00 6.01
461 505 2.387445 GCACATCACCAAGCGCGTA 61.387 57.895 8.43 0.00 0.00 4.42
464 508 2.508439 ATCACCAAGCGCGTACGG 60.508 61.111 18.39 8.21 40.57 4.02
478 522 2.938511 TACGGCCCCTCTCCTCCAA 61.939 63.158 0.00 0.00 0.00 3.53
488 540 3.080319 CCTCTCCTCCAAAGAAAAGCAG 58.920 50.000 0.00 0.00 0.00 4.24
515 567 1.410517 GACAGATGAGATTCTGCGGGA 59.589 52.381 1.51 0.00 45.75 5.14
562 621 2.871096 AGCAACCAACCTCCGAATAA 57.129 45.000 0.00 0.00 0.00 1.40
563 622 3.366052 AGCAACCAACCTCCGAATAAT 57.634 42.857 0.00 0.00 0.00 1.28
564 623 4.497291 AGCAACCAACCTCCGAATAATA 57.503 40.909 0.00 0.00 0.00 0.98
606 666 3.472652 TCACTCTAGCTCCGATTCTCTC 58.527 50.000 0.00 0.00 0.00 3.20
613 673 0.234625 CTCCGATTCTCTCGCTCGAG 59.765 60.000 8.45 8.45 46.25 4.04
614 674 0.462225 TCCGATTCTCTCGCTCGAGT 60.462 55.000 15.13 0.00 46.25 4.18
615 675 0.041663 CCGATTCTCTCGCTCGAGTC 60.042 60.000 15.13 5.54 46.25 3.36
616 676 0.382515 CGATTCTCTCGCTCGAGTCG 60.383 60.000 15.13 17.39 41.14 4.18
617 677 0.931702 GATTCTCTCGCTCGAGTCGA 59.068 55.000 23.67 23.67 42.49 4.20
626 686 1.442857 CTCGAGTCGAGCACACCAC 60.443 63.158 28.13 0.00 46.75 4.16
627 687 2.430921 CGAGTCGAGCACACCACC 60.431 66.667 6.73 0.00 0.00 4.61
628 688 2.734591 GAGTCGAGCACACCACCA 59.265 61.111 0.00 0.00 0.00 4.17
629 689 1.373497 GAGTCGAGCACACCACCAG 60.373 63.158 0.00 0.00 0.00 4.00
630 690 3.044305 GTCGAGCACACCACCAGC 61.044 66.667 0.00 0.00 0.00 4.85
631 691 3.233980 TCGAGCACACCACCAGCT 61.234 61.111 0.00 0.00 42.17 4.24
645 722 2.681778 AGCTGCCTACGTGCTCCT 60.682 61.111 0.00 0.00 30.41 3.69
677 754 2.086610 AGCATTTGGAAACCACCACT 57.913 45.000 0.00 0.00 39.85 4.00
680 757 2.890945 GCATTTGGAAACCACCACTACT 59.109 45.455 0.00 0.00 39.85 2.57
858 936 1.031571 AGCTCCTCTCTCACTGCTCG 61.032 60.000 0.00 0.00 0.00 5.03
880 958 3.641648 CTCCAAAAGCAAAAGCATTCGA 58.358 40.909 0.00 0.00 0.00 3.71
881 959 4.240096 CTCCAAAAGCAAAAGCATTCGAT 58.760 39.130 0.00 0.00 0.00 3.59
882 960 4.236935 TCCAAAAGCAAAAGCATTCGATC 58.763 39.130 0.00 0.00 0.00 3.69
883 961 3.059834 CCAAAAGCAAAAGCATTCGATCG 59.940 43.478 9.36 9.36 0.00 3.69
895 973 0.682852 TTCGATCGGAAACCACCACT 59.317 50.000 16.41 0.00 0.00 4.00
905 983 2.529136 CCACCACTCCCCTCCACA 60.529 66.667 0.00 0.00 0.00 4.17
933 1019 5.732331 AGGAACCCTATTCCATTTCATCA 57.268 39.130 8.35 0.00 41.00 3.07
953 1039 0.543749 CTCGCTTTCCCTTCCCATCT 59.456 55.000 0.00 0.00 0.00 2.90
959 1045 1.204786 TTCCCTTCCCATCTTCGGCA 61.205 55.000 0.00 0.00 0.00 5.69
1563 1670 2.040278 CTCCCACCTGAGCTCCCT 59.960 66.667 12.15 0.00 0.00 4.20
2304 2411 4.477975 GACCTCTCCGACGTGCCG 62.478 72.222 0.00 0.00 0.00 5.69
2490 2597 2.666862 CGCGCCAAGGTGTACCAA 60.667 61.111 0.00 0.00 38.89 3.67
2598 2705 1.736645 GCGCGTCAAGGTTCAGCTA 60.737 57.895 8.43 0.00 0.00 3.32
2601 2708 0.037232 GCGTCAAGGTTCAGCTAGGT 60.037 55.000 0.00 0.00 0.00 3.08
2718 2825 4.386413 GACACCCTTGTCCTGCTG 57.614 61.111 0.00 0.00 45.77 4.41
2748 2855 0.250081 GGTCGATGATCAAGGAGCCC 60.250 60.000 14.33 4.51 0.00 5.19
2891 2998 0.615331 GGAGATCAGCAGGGACAACA 59.385 55.000 0.00 0.00 0.00 3.33
2989 3096 2.826277 CATGTGTGCAGCGACTACA 58.174 52.632 0.00 0.00 0.00 2.74
4266 4391 1.489649 AGGATGCTCTGAGATTGGTGG 59.510 52.381 9.28 0.00 0.00 4.61
4284 4412 0.735471 GGCGGCTCCAATCTTCTTTC 59.265 55.000 0.00 0.00 34.01 2.62
4310 4452 2.096220 TTCCGTTGCCGCAATAAGTA 57.904 45.000 9.46 0.00 0.00 2.24
4325 4467 6.822506 GCAATAAGTATGCGATAGGAAGTTC 58.177 40.000 0.00 0.00 42.54 3.01
4344 4487 7.340999 GGAAGTTCCTATATATCTGGGAGAGAC 59.659 44.444 15.09 0.00 30.45 3.36
4347 4490 7.672239 AGTTCCTATATATCTGGGAGAGACAAC 59.328 40.741 0.00 0.00 31.75 3.32
4464 4611 4.211389 GCATAATTTACATTCGCCTCGTG 58.789 43.478 0.00 0.00 0.00 4.35
4478 4625 2.860735 GCCTCGTGTTCATAGCTACAAG 59.139 50.000 0.00 0.00 0.00 3.16
4504 4651 2.435059 GGTGAAGGACTCCGCTGC 60.435 66.667 0.00 0.00 0.00 5.25
4510 4657 1.936547 GAAGGACTCCGCTGCTAATTG 59.063 52.381 0.00 0.00 0.00 2.32
4525 4673 4.756642 TGCTAATTGTATCTGCTATGGTGC 59.243 41.667 0.00 0.00 0.00 5.01
4530 4678 2.158769 TGTATCTGCTATGGTGCCAAGG 60.159 50.000 0.00 0.00 0.00 3.61
4531 4679 0.921896 ATCTGCTATGGTGCCAAGGT 59.078 50.000 0.00 0.00 0.00 3.50
4539 4687 4.342092 GCTATGGTGCCAAGGTTATGATTT 59.658 41.667 0.00 0.00 0.00 2.17
4540 4688 5.507985 GCTATGGTGCCAAGGTTATGATTTC 60.508 44.000 0.00 0.00 0.00 2.17
4541 4689 3.772387 TGGTGCCAAGGTTATGATTTCA 58.228 40.909 0.00 0.00 0.00 2.69
4542 4690 4.352009 TGGTGCCAAGGTTATGATTTCAT 58.648 39.130 0.00 0.00 40.22 2.57
4543 4691 4.160065 TGGTGCCAAGGTTATGATTTCATG 59.840 41.667 3.30 0.00 37.15 3.07
4544 4692 4.441913 GGTGCCAAGGTTATGATTTCATGG 60.442 45.833 3.30 0.00 37.15 3.66
4545 4693 3.705579 TGCCAAGGTTATGATTTCATGGG 59.294 43.478 3.30 0.00 37.15 4.00
4546 4694 3.706086 GCCAAGGTTATGATTTCATGGGT 59.294 43.478 3.30 0.00 37.15 4.51
4547 4695 4.162131 GCCAAGGTTATGATTTCATGGGTT 59.838 41.667 3.30 0.00 37.15 4.11
4548 4696 5.663456 CCAAGGTTATGATTTCATGGGTTG 58.337 41.667 3.30 2.71 37.15 3.77
4549 4697 5.111293 CAAGGTTATGATTTCATGGGTTGC 58.889 41.667 3.30 0.00 37.15 4.17
4550 4698 4.613437 AGGTTATGATTTCATGGGTTGCT 58.387 39.130 3.30 0.00 37.15 3.91
4551 4699 4.646492 AGGTTATGATTTCATGGGTTGCTC 59.354 41.667 3.30 0.00 37.15 4.26
4552 4700 4.202151 GGTTATGATTTCATGGGTTGCTCC 60.202 45.833 3.30 0.00 37.15 4.70
4553 4701 1.462616 TGATTTCATGGGTTGCTCCG 58.537 50.000 0.00 0.00 37.00 4.63
4554 4702 0.740737 GATTTCATGGGTTGCTCCGG 59.259 55.000 0.00 0.00 37.00 5.14
4555 4703 0.039618 ATTTCATGGGTTGCTCCGGT 59.960 50.000 0.00 0.00 37.00 5.28
4556 4704 0.178975 TTTCATGGGTTGCTCCGGTT 60.179 50.000 0.00 0.00 37.00 4.44
4557 4705 0.178975 TTCATGGGTTGCTCCGGTTT 60.179 50.000 0.00 0.00 37.00 3.27
4558 4706 0.693622 TCATGGGTTGCTCCGGTTTA 59.306 50.000 0.00 0.00 37.00 2.01
4559 4707 1.074084 TCATGGGTTGCTCCGGTTTAA 59.926 47.619 0.00 0.00 37.00 1.52
4560 4708 1.472480 CATGGGTTGCTCCGGTTTAAG 59.528 52.381 0.00 0.00 37.00 1.85
4561 4709 0.766131 TGGGTTGCTCCGGTTTAAGA 59.234 50.000 0.00 0.00 37.00 2.10
4562 4710 1.143277 TGGGTTGCTCCGGTTTAAGAA 59.857 47.619 0.00 0.00 37.00 2.52
4563 4711 1.810755 GGGTTGCTCCGGTTTAAGAAG 59.189 52.381 0.00 0.00 37.00 2.85
4564 4712 1.810755 GGTTGCTCCGGTTTAAGAAGG 59.189 52.381 0.00 0.00 0.00 3.46
4632 4780 2.952116 ACCCCAAACTTCAAATTCCGA 58.048 42.857 0.00 0.00 0.00 4.55
4639 4787 6.481644 CCCAAACTTCAAATTCCGAAAATCAA 59.518 34.615 0.00 0.00 0.00 2.57
4648 4796 2.773487 TCCGAAAATCAACACACCGAT 58.227 42.857 0.00 0.00 0.00 4.18
4650 4798 2.159572 CCGAAAATCAACACACCGATCC 60.160 50.000 0.00 0.00 0.00 3.36
4652 4800 2.577606 AAATCAACACACCGATCCCA 57.422 45.000 0.00 0.00 0.00 4.37
4662 4819 3.871594 CACACCGATCCCAGTCTATTTTC 59.128 47.826 0.00 0.00 0.00 2.29
4669 4826 6.346096 CGATCCCAGTCTATTTTCAACCTTA 58.654 40.000 0.00 0.00 0.00 2.69
4688 4845 4.445735 CCTTAAGTGAGTTCCCAAACAGGA 60.446 45.833 0.97 0.00 41.22 3.86
4695 4852 0.965439 TTCCCAAACAGGAATTGGCG 59.035 50.000 0.00 0.00 44.87 5.69
4697 4854 1.185315 CCCAAACAGGAATTGGCGAT 58.815 50.000 0.00 0.00 44.87 4.58
4698 4855 1.135024 CCCAAACAGGAATTGGCGATG 60.135 52.381 0.00 0.00 44.87 3.84
4701 4858 1.176527 AACAGGAATTGGCGATGTGG 58.823 50.000 0.00 0.00 0.00 4.17
4745 4902 4.436998 GTGGACTCGACTGGGCCG 62.437 72.222 0.00 0.00 0.00 6.13
4799 4962 7.148733 TCTTAACACGTGACGTAAAAAGTAC 57.851 36.000 25.01 0.00 38.32 2.73
4801 4964 5.379757 AACACGTGACGTAAAAAGTACTG 57.620 39.130 25.01 0.00 38.32 2.74
4802 4965 4.423732 ACACGTGACGTAAAAAGTACTGT 58.576 39.130 25.01 0.00 38.32 3.55
4803 4966 5.577835 ACACGTGACGTAAAAAGTACTGTA 58.422 37.500 25.01 0.00 38.32 2.74
4805 4968 6.697019 ACACGTGACGTAAAAAGTACTGTATT 59.303 34.615 25.01 0.00 38.32 1.89
4806 4969 7.222611 ACACGTGACGTAAAAAGTACTGTATTT 59.777 33.333 25.01 1.53 38.32 1.40
4808 4971 7.649306 ACGTGACGTAAAAAGTACTGTATTTCT 59.351 33.333 9.69 0.00 38.73 2.52
4809 4972 8.482429 CGTGACGTAAAAAGTACTGTATTTCTT 58.518 33.333 0.00 0.00 0.00 2.52
4810 4973 9.789029 GTGACGTAAAAAGTACTGTATTTCTTC 57.211 33.333 0.00 0.00 0.00 2.87
4811 4974 9.754382 TGACGTAAAAAGTACTGTATTTCTTCT 57.246 29.630 0.00 0.00 0.00 2.85
4813 4976 9.978044 ACGTAAAAAGTACTGTATTTCTTCTCT 57.022 29.630 0.00 0.00 0.00 3.10
4824 4987 7.332182 ACTGTATTTCTTCTCTTCCTTAAAGCG 59.668 37.037 0.00 0.00 34.76 4.68
4837 5000 2.587612 TAAAGCGCGATGTGACAAAC 57.412 45.000 12.10 0.00 0.00 2.93
4838 5001 0.944386 AAAGCGCGATGTGACAAACT 59.056 45.000 12.10 0.00 0.00 2.66
4839 5002 0.235665 AAGCGCGATGTGACAAACTG 59.764 50.000 12.10 0.00 0.00 3.16
4840 5003 0.599991 AGCGCGATGTGACAAACTGA 60.600 50.000 12.10 0.00 0.00 3.41
4841 5004 0.451135 GCGCGATGTGACAAACTGAC 60.451 55.000 12.10 0.00 0.00 3.51
4842 5005 0.858583 CGCGATGTGACAAACTGACA 59.141 50.000 0.00 0.00 0.00 3.58
4847 5010 4.027702 GCGATGTGACAAACTGACAAAAAC 60.028 41.667 0.00 0.00 0.00 2.43
4879 5042 0.526211 GTCGAATTTGGAACCTGGCC 59.474 55.000 0.00 0.00 0.00 5.36
4902 5112 6.461509 GCCGACATTTCCAAATTTATCAGGAT 60.462 38.462 0.00 0.00 0.00 3.24
4913 5123 3.820425 TCAGGATGAAACCGGCCT 58.180 55.556 0.00 0.00 45.97 5.19
4919 5129 0.827368 GATGAAACCGGCCTCTCTCT 59.173 55.000 0.00 0.00 0.00 3.10
4920 5130 2.032620 GATGAAACCGGCCTCTCTCTA 58.967 52.381 0.00 0.00 0.00 2.43
4949 5159 2.867472 GCATGTGTGGCGTGTACC 59.133 61.111 0.00 0.00 36.50 3.34
4950 5160 1.671054 GCATGTGTGGCGTGTACCT 60.671 57.895 0.00 0.00 36.50 3.08
4951 5161 1.911293 GCATGTGTGGCGTGTACCTG 61.911 60.000 0.00 0.00 36.50 4.00
4952 5162 1.003839 ATGTGTGGCGTGTACCTGG 60.004 57.895 0.00 0.00 0.00 4.45
4953 5163 2.358247 GTGTGGCGTGTACCTGGG 60.358 66.667 0.00 0.00 0.00 4.45
4954 5164 4.323477 TGTGGCGTGTACCTGGGC 62.323 66.667 0.00 0.00 0.00 5.36
4955 5165 4.323477 GTGGCGTGTACCTGGGCA 62.323 66.667 0.00 0.00 0.00 5.36
4956 5166 4.015406 TGGCGTGTACCTGGGCAG 62.015 66.667 0.00 0.00 0.00 4.85
4959 5169 4.373116 CGTGTACCTGGGCAGCGT 62.373 66.667 0.00 0.00 0.00 5.07
4960 5170 2.032071 GTGTACCTGGGCAGCGTT 59.968 61.111 0.00 0.00 0.00 4.84
4961 5171 2.031919 TGTACCTGGGCAGCGTTG 59.968 61.111 0.00 0.00 0.00 4.10
4964 5174 2.824880 TACCTGGGCAGCGTTGGTT 61.825 57.895 0.16 0.00 32.74 3.67
4966 5176 3.365265 CTGGGCAGCGTTGGTTCC 61.365 66.667 0.16 0.00 0.00 3.62
4967 5177 4.196778 TGGGCAGCGTTGGTTCCA 62.197 61.111 0.16 0.00 0.00 3.53
4968 5178 3.670377 GGGCAGCGTTGGTTCCAC 61.670 66.667 0.16 0.00 0.00 4.02
4969 5179 4.025401 GGCAGCGTTGGTTCCACG 62.025 66.667 0.16 8.59 0.00 4.94
4970 5180 4.025401 GCAGCGTTGGTTCCACGG 62.025 66.667 0.16 1.56 0.00 4.94
4971 5181 4.025401 CAGCGTTGGTTCCACGGC 62.025 66.667 12.70 9.43 0.00 5.68
4988 5198 4.362476 CCGGCCAAAAGCAGCACC 62.362 66.667 2.24 0.00 46.50 5.01
4989 5199 4.362476 CGGCCAAAAGCAGCACCC 62.362 66.667 2.24 0.00 46.50 4.61
4990 5200 3.233231 GGCCAAAAGCAGCACCCA 61.233 61.111 0.00 0.00 46.50 4.51
4993 5203 2.355009 CAAAAGCAGCACCCACGC 60.355 61.111 0.00 0.00 0.00 5.34
4994 5204 2.832661 AAAAGCAGCACCCACGCA 60.833 55.556 0.00 0.00 0.00 5.24
4995 5205 2.422231 AAAAGCAGCACCCACGCAA 61.422 52.632 0.00 0.00 0.00 4.85
5013 5223 2.126228 CGGCGCCGAGAACAAGTA 60.126 61.111 44.86 0.00 42.83 2.24
5014 5224 1.735198 CGGCGCCGAGAACAAGTAA 60.735 57.895 44.86 0.00 42.83 2.24
5016 5226 1.084289 GGCGCCGAGAACAAGTAATT 58.916 50.000 12.58 0.00 0.00 1.40
5018 5228 2.674357 GGCGCCGAGAACAAGTAATTTA 59.326 45.455 12.58 0.00 0.00 1.40
5019 5229 3.242316 GGCGCCGAGAACAAGTAATTTAG 60.242 47.826 12.58 0.00 0.00 1.85
5020 5230 3.784525 GCGCCGAGAACAAGTAATTTAGC 60.785 47.826 0.00 0.00 0.00 3.09
5022 5232 3.687698 GCCGAGAACAAGTAATTTAGCCA 59.312 43.478 0.00 0.00 0.00 4.75
5026 5236 5.291128 CGAGAACAAGTAATTTAGCCATCGT 59.709 40.000 0.00 0.00 0.00 3.73
5028 5238 6.170506 AGAACAAGTAATTTAGCCATCGTCA 58.829 36.000 0.00 0.00 0.00 4.35
5029 5239 5.796350 ACAAGTAATTTAGCCATCGTCAC 57.204 39.130 0.00 0.00 0.00 3.67
5030 5240 4.634443 ACAAGTAATTTAGCCATCGTCACC 59.366 41.667 0.00 0.00 0.00 4.02
5031 5241 3.805207 AGTAATTTAGCCATCGTCACCC 58.195 45.455 0.00 0.00 0.00 4.61
5033 5243 0.182775 ATTTAGCCATCGTCACCCCC 59.817 55.000 0.00 0.00 0.00 5.40
5141 5590 9.868160 ATAATAAGAGGCCCCATATATTTAAGC 57.132 33.333 0.00 0.00 0.00 3.09
5147 5596 4.772100 GGCCCCATATATTTAAGCACACAT 59.228 41.667 0.00 0.00 0.00 3.21
5149 5598 5.105756 GCCCCATATATTTAAGCACACATCC 60.106 44.000 0.00 0.00 0.00 3.51
5150 5599 5.123820 CCCCATATATTTAAGCACACATCCG 59.876 44.000 0.00 0.00 0.00 4.18
5154 5603 2.177394 TTTAAGCACACATCCGAGCA 57.823 45.000 0.00 0.00 0.00 4.26
5161 5610 2.079158 CACACATCCGAGCATTGAACT 58.921 47.619 0.00 0.00 0.00 3.01
5166 5615 3.820467 ACATCCGAGCATTGAACTTTGAA 59.180 39.130 0.00 0.00 0.00 2.69
5243 5692 7.658167 TGTCCGAACATTTTATAAAGTGTGAGA 59.342 33.333 22.48 16.95 38.60 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.543670 CGCAATTGCAAACAACAAATCC 58.456 40.909 28.77 0.00 38.99 3.01
41 46 1.872388 TCGATCGGAAGCAAACACAA 58.128 45.000 16.41 0.00 0.00 3.33
91 96 2.048222 TCCACGAGCCTGAAAGCG 60.048 61.111 0.00 0.00 38.01 4.68
97 102 1.638388 TACGTACGTCCACGAGCCTG 61.638 60.000 26.53 0.00 44.69 4.85
146 151 3.917760 GCCACCCGATCCCTCTCG 61.918 72.222 0.00 0.00 38.37 4.04
154 159 1.003112 TACAAAAGCGCCACCCGAT 60.003 52.632 2.29 0.00 40.02 4.18
157 162 2.566529 GCTACAAAAGCGCCACCC 59.433 61.111 2.29 0.00 42.53 4.61
166 171 0.407528 TCCTGGCCATGGCTACAAAA 59.592 50.000 34.70 13.58 41.60 2.44
174 179 1.389609 GCAGTTCATCCTGGCCATGG 61.390 60.000 5.51 7.63 32.92 3.66
175 180 2.112898 GCAGTTCATCCTGGCCATG 58.887 57.895 5.51 2.84 32.92 3.66
176 181 4.672251 GCAGTTCATCCTGGCCAT 57.328 55.556 5.51 0.00 32.92 4.40
234 245 1.415672 GGGGGATGCGGGAGTTGATA 61.416 60.000 0.00 0.00 0.00 2.15
256 267 3.941483 TGAAATCCGGCTTCAGAAAGATC 59.059 43.478 13.11 0.00 34.14 2.75
271 282 5.532779 AGAACTCCTTGTGAAAGTGAAATCC 59.467 40.000 0.00 0.00 0.00 3.01
285 296 3.873952 GATGAAATCGGGAGAACTCCTTG 59.126 47.826 18.54 12.36 45.37 3.61
294 305 1.539065 CCTGACGGATGAAATCGGGAG 60.539 57.143 0.00 0.00 46.86 4.30
366 410 1.934476 CTTTTTCTATGGCGCGCGC 60.934 57.895 44.40 44.40 41.06 6.86
388 432 1.764571 TTAGTTCACACTGGCCGCCT 61.765 55.000 11.61 0.00 34.06 5.52
394 438 1.060713 CGCTCGTTAGTTCACACTGG 58.939 55.000 0.00 0.00 34.06 4.00
443 487 2.387445 TACGCGCTTGGTGATGTGC 61.387 57.895 5.73 0.00 36.47 4.57
460 504 2.465010 TTTGGAGGAGAGGGGCCGTA 62.465 60.000 0.00 0.00 0.00 4.02
461 505 3.864983 TTTGGAGGAGAGGGGCCGT 62.865 63.158 0.00 0.00 0.00 5.68
464 508 0.698818 TTTCTTTGGAGGAGAGGGGC 59.301 55.000 0.00 0.00 0.00 5.80
465 509 2.881816 GCTTTTCTTTGGAGGAGAGGGG 60.882 54.545 0.00 0.00 0.00 4.79
467 511 3.080319 CTGCTTTTCTTTGGAGGAGAGG 58.920 50.000 0.00 0.00 31.36 3.69
468 512 3.080319 CCTGCTTTTCTTTGGAGGAGAG 58.920 50.000 0.00 0.00 43.26 3.20
469 513 2.815589 GCCTGCTTTTCTTTGGAGGAGA 60.816 50.000 4.75 0.00 43.26 3.71
470 514 1.543358 GCCTGCTTTTCTTTGGAGGAG 59.457 52.381 4.75 0.00 43.26 3.69
471 515 1.620822 GCCTGCTTTTCTTTGGAGGA 58.379 50.000 4.75 0.00 43.26 3.71
474 518 1.805428 GCCGCCTGCTTTTCTTTGGA 61.805 55.000 0.00 0.00 36.87 3.53
478 522 1.228245 TCTGCCGCCTGCTTTTCTT 60.228 52.632 0.00 0.00 42.00 2.52
488 540 0.179062 AATCTCATCTGTCTGCCGCC 60.179 55.000 0.00 0.00 0.00 6.13
562 621 2.569404 GCGAGGGAGGAAGATGGATTAT 59.431 50.000 0.00 0.00 0.00 1.28
563 622 1.971357 GCGAGGGAGGAAGATGGATTA 59.029 52.381 0.00 0.00 0.00 1.75
564 623 0.761802 GCGAGGGAGGAAGATGGATT 59.238 55.000 0.00 0.00 0.00 3.01
613 673 3.044305 GCTGGTGGTGTGCTCGAC 61.044 66.667 0.00 0.00 0.00 4.20
614 674 3.233980 AGCTGGTGGTGTGCTCGA 61.234 61.111 0.00 0.00 30.41 4.04
615 675 3.046087 CAGCTGGTGGTGTGCTCG 61.046 66.667 5.57 0.00 36.97 5.03
616 676 3.360340 GCAGCTGGTGGTGTGCTC 61.360 66.667 17.12 0.00 43.05 4.26
617 677 4.962836 GGCAGCTGGTGGTGTGCT 62.963 66.667 17.12 0.00 43.05 4.40
618 678 3.551496 TAGGCAGCTGGTGGTGTGC 62.551 63.158 17.12 0.00 43.05 4.57
620 680 2.750350 GTAGGCAGCTGGTGGTGT 59.250 61.111 17.12 0.00 43.05 4.16
624 684 3.121030 GCACGTAGGCAGCTGGTG 61.121 66.667 17.12 15.12 0.00 4.17
626 686 2.510238 GAGCACGTAGGCAGCTGG 60.510 66.667 17.12 0.00 39.02 4.85
627 687 2.510238 GGAGCACGTAGGCAGCTG 60.510 66.667 10.11 10.11 39.02 4.24
628 688 2.232298 GAAGGAGCACGTAGGCAGCT 62.232 60.000 0.00 0.00 42.17 4.24
629 689 1.811679 GAAGGAGCACGTAGGCAGC 60.812 63.158 0.36 0.00 35.83 5.25
630 690 1.153549 GGAAGGAGCACGTAGGCAG 60.154 63.158 0.36 0.00 35.83 4.85
631 691 1.476845 TTGGAAGGAGCACGTAGGCA 61.477 55.000 0.36 0.00 35.83 4.75
677 754 3.882515 TCCATATGGTGTTGACGGGAGTA 60.883 47.826 21.28 0.00 39.03 2.59
680 757 1.574263 TCCATATGGTGTTGACGGGA 58.426 50.000 21.28 0.00 36.34 5.14
880 958 1.683441 GGGAGTGGTGGTTTCCGAT 59.317 57.895 0.00 0.00 31.59 4.18
881 959 2.522367 GGGGAGTGGTGGTTTCCGA 61.522 63.158 0.00 0.00 31.59 4.55
882 960 2.033602 GGGGAGTGGTGGTTTCCG 59.966 66.667 0.00 0.00 31.59 4.30
883 961 1.379146 GAGGGGAGTGGTGGTTTCC 59.621 63.158 0.00 0.00 0.00 3.13
895 973 0.419865 TCCTTATGGTGTGGAGGGGA 59.580 55.000 0.00 0.00 34.23 4.81
905 983 6.068498 TGAAATGGAATAGGGTTCCTTATGGT 60.068 38.462 8.17 0.00 39.31 3.55
933 1019 0.253327 GATGGGAAGGGAAAGCGAGT 59.747 55.000 0.00 0.00 0.00 4.18
1674 1781 1.096967 TCATGTGGCCGTGCATCATC 61.097 55.000 0.00 0.00 0.00 2.92
1833 1940 1.743623 CGGGTACATTTCTGCGCCA 60.744 57.895 4.18 0.00 0.00 5.69
1836 1943 1.449601 AGGCGGGTACATTTCTGCG 60.450 57.895 0.00 0.00 36.21 5.18
2265 2372 4.514577 CAGACGCCGCCGAGGAAT 62.515 66.667 0.00 0.00 45.00 3.01
2709 2816 2.204034 TCCTCCACCAGCAGGACA 59.796 61.111 0.35 0.00 38.69 4.02
2718 2825 2.758737 ATCGACCGGTCCTCCACC 60.759 66.667 28.52 2.75 42.69 4.61
2763 2870 3.716195 CTCACGGGGATGGTGGCA 61.716 66.667 0.00 0.00 36.09 4.92
2808 2915 0.248661 ATCTTGACGCGACGATCTGG 60.249 55.000 15.93 0.00 0.00 3.86
2891 2998 2.285442 AGTAGAAGCCCGGCCCTT 60.285 61.111 5.55 0.00 0.00 3.95
2901 3008 1.142748 CAGCCTGCCCGAGTAGAAG 59.857 63.158 0.00 0.00 0.00 2.85
3276 3392 3.792053 GATGCGGTAGTCCTGGCGG 62.792 68.421 0.00 0.00 0.00 6.13
4050 4175 3.775654 GGGTCCCTCCAGCTGACG 61.776 72.222 17.39 5.18 38.11 4.35
4080 4205 2.508891 GCAGACGCCGACGAAGATG 61.509 63.158 0.00 0.00 43.93 2.90
4266 4391 1.743996 AGAAAGAAGATTGGAGCCGC 58.256 50.000 0.00 0.00 0.00 6.53
4322 4464 7.362229 CGTTGTCTCTCCCAGATATATAGGAAC 60.362 44.444 5.46 0.74 32.08 3.62
4323 4465 6.659668 CGTTGTCTCTCCCAGATATATAGGAA 59.340 42.308 5.46 0.00 32.08 3.36
4325 4467 5.946972 ACGTTGTCTCTCCCAGATATATAGG 59.053 44.000 0.00 0.00 32.08 2.57
4328 4470 5.141182 ACACGTTGTCTCTCCCAGATATAT 58.859 41.667 0.00 0.00 32.08 0.86
4344 4487 8.227119 TCATCATTGTGTTATTTCTACACGTTG 58.773 33.333 0.00 0.00 46.85 4.10
4347 4490 9.213819 CAATCATCATTGTGTTATTTCTACACG 57.786 33.333 0.00 0.00 46.85 4.49
4456 4603 1.202256 TGTAGCTATGAACACGAGGCG 60.202 52.381 0.00 0.00 0.00 5.52
4478 4625 2.147150 GAGTCCTTCACCACAAGCTTC 58.853 52.381 0.00 0.00 0.00 3.86
4487 4634 1.605058 TAGCAGCGGAGTCCTTCACC 61.605 60.000 7.77 0.00 0.00 4.02
4504 4651 5.308014 TGGCACCATAGCAGATACAATTAG 58.692 41.667 0.00 0.00 35.83 1.73
4510 4657 2.158755 ACCTTGGCACCATAGCAGATAC 60.159 50.000 0.00 0.00 35.83 2.24
4525 4673 5.663456 CAACCCATGAAATCATAACCTTGG 58.337 41.667 0.00 0.00 34.26 3.61
4530 4678 4.498009 CGGAGCAACCCATGAAATCATAAC 60.498 45.833 0.00 0.00 34.71 1.89
4531 4679 3.631686 CGGAGCAACCCATGAAATCATAA 59.368 43.478 0.00 0.00 34.71 1.90
4539 4687 0.693622 TAAACCGGAGCAACCCATGA 59.306 50.000 9.46 0.00 34.64 3.07
4540 4688 1.472480 CTTAAACCGGAGCAACCCATG 59.528 52.381 9.46 0.00 34.64 3.66
4541 4689 1.353022 TCTTAAACCGGAGCAACCCAT 59.647 47.619 9.46 0.00 34.64 4.00
4542 4690 0.766131 TCTTAAACCGGAGCAACCCA 59.234 50.000 9.46 0.00 34.64 4.51
4543 4691 1.810755 CTTCTTAAACCGGAGCAACCC 59.189 52.381 9.46 0.00 34.64 4.11
4544 4692 1.810755 CCTTCTTAAACCGGAGCAACC 59.189 52.381 9.46 0.00 0.00 3.77
4545 4693 2.774687 TCCTTCTTAAACCGGAGCAAC 58.225 47.619 9.46 0.00 0.00 4.17
4546 4694 3.495434 TTCCTTCTTAAACCGGAGCAA 57.505 42.857 9.46 0.00 0.00 3.91
4547 4695 3.495434 TTTCCTTCTTAAACCGGAGCA 57.505 42.857 9.46 0.00 0.00 4.26
4548 4696 4.277672 ACTTTTTCCTTCTTAAACCGGAGC 59.722 41.667 9.46 0.00 0.00 4.70
4549 4697 5.763698 AGACTTTTTCCTTCTTAAACCGGAG 59.236 40.000 9.46 0.00 0.00 4.63
4550 4698 5.687780 AGACTTTTTCCTTCTTAAACCGGA 58.312 37.500 9.46 0.00 0.00 5.14
4551 4699 7.500720 TTAGACTTTTTCCTTCTTAAACCGG 57.499 36.000 0.00 0.00 0.00 5.28
4552 4700 9.961265 ATTTTAGACTTTTTCCTTCTTAAACCG 57.039 29.630 0.00 0.00 0.00 4.44
4587 4735 8.496751 GTTTGATTTAGCTTTCGTCTAGAAGTT 58.503 33.333 5.55 0.00 40.40 2.66
4592 4740 5.064834 GGGGTTTGATTTAGCTTTCGTCTAG 59.935 44.000 0.00 0.00 0.00 2.43
4597 4745 4.513198 TTGGGGTTTGATTTAGCTTTCG 57.487 40.909 0.00 0.00 0.00 3.46
4632 4780 2.819608 CTGGGATCGGTGTGTTGATTTT 59.180 45.455 0.00 0.00 0.00 1.82
4639 4787 2.160721 ATAGACTGGGATCGGTGTGT 57.839 50.000 0.00 0.00 31.54 3.72
4648 4796 6.940298 CACTTAAGGTTGAAAATAGACTGGGA 59.060 38.462 7.53 0.00 0.00 4.37
4650 4798 7.661847 ACTCACTTAAGGTTGAAAATAGACTGG 59.338 37.037 7.53 0.00 0.00 4.00
4652 4800 9.274206 GAACTCACTTAAGGTTGAAAATAGACT 57.726 33.333 7.53 0.00 0.00 3.24
4662 4819 4.642885 TGTTTGGGAACTCACTTAAGGTTG 59.357 41.667 7.53 0.00 36.70 3.77
4669 4826 3.662759 TTCCTGTTTGGGAACTCACTT 57.337 42.857 0.00 0.00 40.08 3.16
4688 4845 0.896923 AACATGCCACATCGCCAATT 59.103 45.000 0.00 0.00 0.00 2.32
4693 4850 2.543653 GGGATTTAACATGCCACATCGC 60.544 50.000 0.00 0.00 0.00 4.58
4695 4852 2.034558 CCGGGATTTAACATGCCACATC 59.965 50.000 0.00 0.00 0.00 3.06
4697 4854 1.468985 CCGGGATTTAACATGCCACA 58.531 50.000 0.00 0.00 0.00 4.17
4698 4855 0.744281 CCCGGGATTTAACATGCCAC 59.256 55.000 18.48 0.00 0.00 5.01
4701 4858 2.693074 ACAATCCCGGGATTTAACATGC 59.307 45.455 40.51 0.00 42.30 4.06
4747 4904 2.588877 CGCTCCGTGCCTAATGGG 60.589 66.667 0.00 0.00 38.78 4.00
4752 4909 0.034337 AAAAACTCGCTCCGTGCCTA 59.966 50.000 0.00 0.00 38.78 3.93
4782 4945 7.649306 AGAAATACAGTACTTTTTACGTCACGT 59.351 33.333 8.49 8.49 44.35 4.49
4799 4962 7.675170 GCGCTTTAAGGAAGAGAAGAAATACAG 60.675 40.741 0.00 0.00 37.35 2.74
4801 4964 6.479436 GCGCTTTAAGGAAGAGAAGAAATAC 58.521 40.000 0.00 0.00 37.35 1.89
4802 4965 5.291128 CGCGCTTTAAGGAAGAGAAGAAATA 59.709 40.000 5.56 0.00 37.35 1.40
4803 4966 4.093556 CGCGCTTTAAGGAAGAGAAGAAAT 59.906 41.667 5.56 0.00 37.35 2.17
4805 4968 2.993899 CGCGCTTTAAGGAAGAGAAGAA 59.006 45.455 5.56 0.00 37.35 2.52
4806 4969 2.230508 TCGCGCTTTAAGGAAGAGAAGA 59.769 45.455 5.56 0.00 37.35 2.87
4808 4971 2.736144 TCGCGCTTTAAGGAAGAGAA 57.264 45.000 5.56 0.00 37.35 2.87
4809 4972 2.094182 ACATCGCGCTTTAAGGAAGAGA 60.094 45.455 5.56 0.00 37.35 3.10
4810 4973 2.029728 CACATCGCGCTTTAAGGAAGAG 59.970 50.000 5.56 0.00 37.57 2.85
4811 4974 1.999735 CACATCGCGCTTTAAGGAAGA 59.000 47.619 5.56 0.00 37.57 2.87
4812 4975 1.999735 TCACATCGCGCTTTAAGGAAG 59.000 47.619 5.56 0.00 38.45 3.46
4813 4976 1.730064 GTCACATCGCGCTTTAAGGAA 59.270 47.619 5.56 0.00 0.00 3.36
4824 4987 3.332761 TTTGTCAGTTTGTCACATCGC 57.667 42.857 0.00 0.00 0.00 4.58
4837 5000 2.480419 CTGCCCGAGTAGTTTTTGTCAG 59.520 50.000 0.00 0.00 0.00 3.51
4838 5001 2.103432 TCTGCCCGAGTAGTTTTTGTCA 59.897 45.455 0.00 0.00 0.00 3.58
4839 5002 2.737252 CTCTGCCCGAGTAGTTTTTGTC 59.263 50.000 0.00 0.00 34.95 3.18
4840 5003 2.767505 CTCTGCCCGAGTAGTTTTTGT 58.232 47.619 0.00 0.00 34.95 2.83
4862 5025 0.958382 TCGGCCAGGTTCCAAATTCG 60.958 55.000 2.24 0.00 0.00 3.34
4879 5042 7.706159 TCATCCTGATAAATTTGGAAATGTCG 58.294 34.615 0.00 0.00 31.87 4.35
4902 5112 2.160721 ATAGAGAGAGGCCGGTTTCA 57.839 50.000 1.90 0.00 0.00 2.69
4913 5123 9.343539 ACACATGCGCTTATATATATAGAGAGA 57.656 33.333 9.73 0.00 0.00 3.10
4919 5129 5.689961 CGCCACACATGCGCTTATATATATA 59.310 40.000 9.73 0.00 46.01 0.86
4920 5130 4.507756 CGCCACACATGCGCTTATATATAT 59.492 41.667 9.73 0.00 46.01 0.86
4947 5157 4.204028 AACCAACGCTGCCCAGGT 62.204 61.111 0.00 0.00 0.00 4.00
4949 5159 3.365265 GGAACCAACGCTGCCCAG 61.365 66.667 0.00 0.00 0.00 4.45
4950 5160 4.196778 TGGAACCAACGCTGCCCA 62.197 61.111 0.00 0.00 0.00 5.36
4951 5161 3.670377 GTGGAACCAACGCTGCCC 61.670 66.667 0.00 0.00 0.00 5.36
4952 5162 4.025401 CGTGGAACCAACGCTGCC 62.025 66.667 0.00 0.00 0.00 4.85
4953 5163 4.025401 CCGTGGAACCAACGCTGC 62.025 66.667 0.00 0.00 0.00 5.25
4954 5164 4.025401 GCCGTGGAACCAACGCTG 62.025 66.667 0.00 0.00 0.00 5.18
4971 5181 4.362476 GGTGCTGCTTTTGGCCGG 62.362 66.667 0.00 0.00 40.92 6.13
4973 5183 3.233231 TGGGTGCTGCTTTTGGCC 61.233 61.111 0.00 0.00 40.92 5.36
4975 5185 2.336088 CGTGGGTGCTGCTTTTGG 59.664 61.111 0.00 0.00 0.00 3.28
4976 5186 2.355009 GCGTGGGTGCTGCTTTTG 60.355 61.111 0.00 0.00 0.00 2.44
4977 5187 2.422231 TTGCGTGGGTGCTGCTTTT 61.422 52.632 0.00 0.00 35.36 2.27
4993 5203 3.295228 CTTGTTCTCGGCGCCGTTG 62.295 63.158 44.16 35.47 40.74 4.10
4994 5204 2.424705 TACTTGTTCTCGGCGCCGTT 62.425 55.000 44.16 22.23 40.74 4.44
4995 5205 2.424705 TTACTTGTTCTCGGCGCCGT 62.425 55.000 44.16 27.05 40.74 5.68
4998 5208 2.894307 AAATTACTTGTTCTCGGCGC 57.106 45.000 0.00 0.00 0.00 6.53
5001 5211 5.276868 CGATGGCTAAATTACTTGTTCTCGG 60.277 44.000 0.00 0.00 0.00 4.63
5002 5212 5.291128 ACGATGGCTAAATTACTTGTTCTCG 59.709 40.000 0.00 0.00 0.00 4.04
5004 5214 6.092259 GTGACGATGGCTAAATTACTTGTTCT 59.908 38.462 0.00 0.00 0.00 3.01
5005 5215 6.248631 GTGACGATGGCTAAATTACTTGTTC 58.751 40.000 0.00 0.00 0.00 3.18
5006 5216 5.123344 GGTGACGATGGCTAAATTACTTGTT 59.877 40.000 0.00 0.00 0.00 2.83
5008 5218 4.035208 GGGTGACGATGGCTAAATTACTTG 59.965 45.833 0.00 0.00 0.00 3.16
5010 5220 3.433173 GGGGTGACGATGGCTAAATTACT 60.433 47.826 0.00 0.00 0.00 2.24
5011 5221 2.876550 GGGGTGACGATGGCTAAATTAC 59.123 50.000 0.00 0.00 0.00 1.89
5012 5222 2.158726 GGGGGTGACGATGGCTAAATTA 60.159 50.000 0.00 0.00 0.00 1.40
5013 5223 1.409661 GGGGGTGACGATGGCTAAATT 60.410 52.381 0.00 0.00 0.00 1.82
5014 5224 0.182775 GGGGGTGACGATGGCTAAAT 59.817 55.000 0.00 0.00 0.00 1.40
5016 5226 3.316029 GGGGGTGACGATGGCTAA 58.684 61.111 0.00 0.00 0.00 3.09
5038 5248 8.511321 TCTACGACAAATCAACATGCTATTTTT 58.489 29.630 0.00 0.00 0.00 1.94
5039 5249 8.039603 TCTACGACAAATCAACATGCTATTTT 57.960 30.769 0.00 0.00 0.00 1.82
5040 5250 7.609760 TCTACGACAAATCAACATGCTATTT 57.390 32.000 0.00 0.00 0.00 1.40
5056 5505 4.134563 TCTCCATCGATCAATCTACGACA 58.865 43.478 0.00 0.00 38.79 4.35
5057 5506 4.750952 TCTCCATCGATCAATCTACGAC 57.249 45.455 0.00 0.00 38.79 4.34
5141 5590 2.079158 AGTTCAATGCTCGGATGTGTG 58.921 47.619 0.00 0.00 0.00 3.82
5147 5596 3.004315 GGTTTCAAAGTTCAATGCTCGGA 59.996 43.478 0.00 0.00 0.00 4.55
5149 5598 3.963665 TGGTTTCAAAGTTCAATGCTCG 58.036 40.909 0.00 0.00 0.00 5.03
5150 5599 6.849588 AAATGGTTTCAAAGTTCAATGCTC 57.150 33.333 0.00 0.00 0.00 4.26
5177 5626 4.282195 TGTTTTGAATATTTGTTCGGCCCT 59.718 37.500 0.00 0.00 0.00 5.19
5220 5669 8.504005 AGTTCTCACACTTTATAAAATGTTCGG 58.496 33.333 9.49 0.16 0.00 4.30


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

AutoCloner maintained by Alex Coulton.