Multiple sequence alignment - TraesCS1B01G035500

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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 TraesCS1B01G035500 chr1B 100.000 4846 0 0 1 4846 16855400 16860245 0.000000e+00 8949.0
1 TraesCS1B01G035500 chr1B 96.100 3308 59 14 589 3879 16925398 16928652 0.000000e+00 5330.0
2 TraesCS1B01G035500 chr1B 86.895 2274 281 13 2571 4841 17017316 17015057 0.000000e+00 2532.0
3 TraesCS1B01G035500 chr1B 84.501 2555 346 33 2296 4841 16891522 16894035 0.000000e+00 2479.0
4 TraesCS1B01G035500 chr1B 100.000 1187 0 0 5119 6305 16860518 16861704 0.000000e+00 2193.0
5 TraesCS1B01G035500 chr1B 90.535 1289 112 6 998 2279 16530027 16531312 0.000000e+00 1696.0
6 TraesCS1B01G035500 chr1B 87.234 893 102 8 998 1886 17018935 17018051 0.000000e+00 1007.0
7 TraesCS1B01G035500 chr1B 84.758 866 113 9 983 1840 16518229 16519083 0.000000e+00 850.0
8 TraesCS1B01G035500 chr1B 91.711 567 39 5 1718 2279 16545670 16546233 0.000000e+00 780.0
9 TraesCS1B01G035500 chr1B 88.323 471 46 4 2276 2745 16531379 16531841 1.990000e-154 556.0
10 TraesCS1B01G035500 chr1B 88.323 471 46 4 2276 2745 16546300 16546762 1.990000e-154 556.0
11 TraesCS1B01G035500 chr1B 91.081 370 25 5 1915 2279 16519090 16519456 1.580000e-135 494.0
12 TraesCS1B01G035500 chr1B 87.185 437 33 7 118 550 16924855 16925272 5.720000e-130 475.0
13 TraesCS1B01G035500 chr1B 93.478 92 6 0 6 97 16924639 16924730 3.070000e-28 137.0
14 TraesCS1B01G035500 chr1B 100.000 33 0 0 562 594 16925325 16925357 1.900000e-05 62.1
15 TraesCS1B01G035500 chr1A 88.452 2520 260 18 2318 4833 22614737 22612245 0.000000e+00 3013.0
16 TraesCS1B01G035500 chr1A 88.079 2441 259 18 2403 4835 13665245 13667661 0.000000e+00 2867.0
17 TraesCS1B01G035500 chr1A 87.607 2461 286 12 2380 4836 13454430 13456875 0.000000e+00 2837.0
18 TraesCS1B01G035500 chr1A 85.899 2546 320 29 2310 4844 12589445 12586928 0.000000e+00 2676.0
19 TraesCS1B01G035500 chr1A 87.468 1165 119 13 998 2147 13453277 13454429 0.000000e+00 1317.0
20 TraesCS1B01G035500 chr1A 85.823 917 117 9 995 1905 13569528 13570437 0.000000e+00 961.0
21 TraesCS1B01G035500 chr1A 80.891 1235 185 35 998 2206 13314117 13315326 0.000000e+00 926.0
22 TraesCS1B01G035500 chr1A 95.962 520 19 2 5783 6301 12586040 12585522 0.000000e+00 843.0
23 TraesCS1B01G035500 chr1A 77.435 421 60 18 5871 6264 13318845 13319257 1.060000e-52 219.0
24 TraesCS1B01G035500 chr1A 79.679 187 28 7 5471 5655 13457130 13457308 6.640000e-25 126.0
25 TraesCS1B01G035500 chr1A 82.075 106 11 3 5294 5398 13417953 13418051 4.050000e-12 84.2
26 TraesCS1B01G035500 chr1A 80.189 106 13 3 5294 5398 13667788 13667886 8.770000e-09 73.1
27 TraesCS1B01G035500 chr1D 86.872 2468 308 11 2380 4841 11178192 11180649 0.000000e+00 2748.0
28 TraesCS1B01G035500 chr1D 88.480 2118 233 8 2676 4789 11495881 11497991 0.000000e+00 2549.0
29 TraesCS1B01G035500 chr1D 87.276 1171 115 16 998 2153 11177047 11178198 0.000000e+00 1306.0
30 TraesCS1B01G035500 chr1D 86.087 920 118 7 995 1911 11273109 11274021 0.000000e+00 981.0
31 TraesCS1B01G035500 chr1D 86.456 886 96 13 999 1875 11494273 11495143 0.000000e+00 950.0
32 TraesCS1B01G035500 chr1D 79.186 1057 156 33 5287 6301 11321942 11322976 0.000000e+00 675.0
33 TraesCS1B01G035500 chr1D 79.092 617 81 26 5150 5746 11276813 11277401 1.280000e-101 381.0
34 TraesCS1B01G035500 chr1D 87.829 304 35 2 5999 6301 11181657 11181959 7.770000e-94 355.0
35 TraesCS1B01G035500 chr1D 89.209 278 28 2 5783 6059 11181386 11181662 4.680000e-91 346.0
36 TraesCS1B01G035500 chr1D 76.724 464 74 23 5296 5743 11180789 11181234 1.770000e-55 228.0
37 TraesCS1B01G035500 chr1D 85.217 115 14 3 6138 6250 11280564 11280677 1.440000e-21 115.0
38 TraesCS1B01G035500 chrUn 88.031 2097 241 6 2752 4844 2472476 2470386 0.000000e+00 2473.0
39 TraesCS1B01G035500 chrUn 88.061 2094 240 6 2752 4841 345524787 345526874 0.000000e+00 2473.0
40 TraesCS1B01G035500 chrUn 81.743 241 34 3 2039 2279 317004341 317004111 6.450000e-45 193.0
41 TraesCS1B01G035500 chrUn 81.743 241 34 3 2039 2279 317984141 317983911 6.450000e-45 193.0
42 TraesCS1B01G035500 chr2B 88.618 123 12 2 277 397 422983951 422983829 1.420000e-31 148.0
43 TraesCS1B01G035500 chr2B 87.500 128 10 5 274 397 53029634 53029509 6.590000e-30 143.0
44 TraesCS1B01G035500 chr3B 86.290 124 15 1 277 398 202578929 202579052 3.970000e-27 134.0
45 TraesCS1B01G035500 chr3D 88.288 111 9 3 290 397 140773493 140773602 5.130000e-26 130.0
46 TraesCS1B01G035500 chr4A 85.600 125 14 4 276 397 76010694 76010571 1.840000e-25 128.0
47 TraesCS1B01G035500 chr3A 85.156 128 16 3 274 398 158472049 158472176 1.840000e-25 128.0
48 TraesCS1B01G035500 chr2A 86.066 122 9 1 276 397 745064442 745064555 2.390000e-24 124.0
49 TraesCS1B01G035500 chr7A 84.800 125 10 2 274 397 558722437 558722553 3.990000e-22 117.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G035500 chr1B 16855400 16861704 6304 False 5571.000000 8949 100.000000 1 6305 2 chr1B.!!$F5 6304
1 TraesCS1B01G035500 chr1B 16891522 16894035 2513 False 2479.000000 2479 84.501000 2296 4841 1 chr1B.!!$F1 2545
2 TraesCS1B01G035500 chr1B 17015057 17018935 3878 True 1769.500000 2532 87.064500 998 4841 2 chr1B.!!$R1 3843
3 TraesCS1B01G035500 chr1B 16924639 16928652 4013 False 1501.025000 5330 94.190750 6 3879 4 chr1B.!!$F6 3873
4 TraesCS1B01G035500 chr1B 16530027 16531841 1814 False 1126.000000 1696 89.429000 998 2745 2 chr1B.!!$F3 1747
5 TraesCS1B01G035500 chr1B 16518229 16519456 1227 False 672.000000 850 87.919500 983 2279 2 chr1B.!!$F2 1296
6 TraesCS1B01G035500 chr1B 16545670 16546762 1092 False 668.000000 780 90.017000 1718 2745 2 chr1B.!!$F4 1027
7 TraesCS1B01G035500 chr1A 22612245 22614737 2492 True 3013.000000 3013 88.452000 2318 4833 1 chr1A.!!$R1 2515
8 TraesCS1B01G035500 chr1A 12585522 12589445 3923 True 1759.500000 2676 90.930500 2310 6301 2 chr1A.!!$R2 3991
9 TraesCS1B01G035500 chr1A 13665245 13667886 2641 False 1470.050000 2867 84.134000 2403 5398 2 chr1A.!!$F5 2995
10 TraesCS1B01G035500 chr1A 13453277 13457308 4031 False 1426.666667 2837 84.918000 998 5655 3 chr1A.!!$F4 4657
11 TraesCS1B01G035500 chr1A 13569528 13570437 909 False 961.000000 961 85.823000 995 1905 1 chr1A.!!$F2 910
12 TraesCS1B01G035500 chr1A 13314117 13319257 5140 False 572.500000 926 79.163000 998 6264 2 chr1A.!!$F3 5266
13 TraesCS1B01G035500 chr1D 11494273 11497991 3718 False 1749.500000 2549 87.468000 999 4789 2 chr1D.!!$F4 3790
14 TraesCS1B01G035500 chr1D 11177047 11181959 4912 False 996.600000 2748 85.582000 998 6301 5 chr1D.!!$F2 5303
15 TraesCS1B01G035500 chr1D 11321942 11322976 1034 False 675.000000 675 79.186000 5287 6301 1 chr1D.!!$F1 1014
16 TraesCS1B01G035500 chr1D 11273109 11280677 7568 False 492.333333 981 83.465333 995 6250 3 chr1D.!!$F3 5255
17 TraesCS1B01G035500 chrUn 2470386 2472476 2090 True 2473.000000 2473 88.031000 2752 4844 1 chrUn.!!$R1 2092
18 TraesCS1B01G035500 chrUn 345524787 345526874 2087 False 2473.000000 2473 88.061000 2752 4841 1 chrUn.!!$F1 2089

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
396 505 0.036306 ACCCTGCCTAACCGAACAAG 59.964 55.000 0.00 0.00 0.00 3.16 F
400 509 0.037590 TGCCTAACCGAACAAGCCAT 59.962 50.000 0.00 0.00 0.00 4.40 F
1428 1651 0.040067 GGCGTGAAAGGAACAAGCTG 60.040 55.000 0.00 0.00 41.09 4.24 F
2666 3404 2.486982 AGGATCATAATGCATGCTTCGC 59.513 45.455 20.33 0.18 34.35 4.70 F
4433 5221 0.110486 ACGTGGATATCATTGGGGGC 59.890 55.000 4.83 0.00 0.00 5.80 F
5145 5945 0.039437 ACTCGTGCACGTACTCCTTG 60.039 55.000 35.74 18.72 40.80 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2518 0.801251 GTCATTGCACTCACTCTGGC 59.199 55.000 0.00 0.00 0.00 4.85 R
2431 3085 2.106511 CCTCTTGGAGACCCACTCAAAA 59.893 50.000 0.00 0.00 46.54 2.44 R
3146 3929 1.518367 TTGGTTTCACCTCCTGACCT 58.482 50.000 0.00 0.00 39.58 3.85 R
4537 5326 0.310543 TTGCGTTGCTGATCCACAAC 59.689 50.000 14.77 14.77 42.15 3.32 R
5284 6102 0.035458 CAGTTCTCCACCAGGTCCAC 59.965 60.000 0.00 0.00 35.89 4.02 R
6078 7348 1.275291 CCACCGCCTCTTTTCTACTGA 59.725 52.381 0.00 0.00 0.00 3.41 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
33 34 6.334102 AGAGGCTAGTGTACTGTATTATGC 57.666 41.667 0.00 0.00 0.00 3.14
85 86 1.001282 GGGGTGGTGGGGTTGTATTA 58.999 55.000 0.00 0.00 0.00 0.98
90 91 3.469739 GTGGTGGGGTTGTATTATACCG 58.530 50.000 0.00 0.00 35.19 4.02
97 98 4.514066 GGGGTTGTATTATACCGAAGCAAG 59.486 45.833 0.00 0.00 35.19 4.01
99 100 5.235831 GGGTTGTATTATACCGAAGCAAGTC 59.764 44.000 0.00 0.00 35.19 3.01
101 102 6.314400 GGTTGTATTATACCGAAGCAAGTCAA 59.686 38.462 0.00 0.00 0.00 3.18
102 103 7.148373 GGTTGTATTATACCGAAGCAAGTCAAA 60.148 37.037 0.00 0.00 0.00 2.69
103 104 7.908827 TGTATTATACCGAAGCAAGTCAAAA 57.091 32.000 0.00 0.00 0.00 2.44
111 190 7.308782 ACCGAAGCAAGTCAAAATAGATAAG 57.691 36.000 0.00 0.00 0.00 1.73
132 237 5.499004 AGTATTTGTCCTCTGCTTTACCA 57.501 39.130 0.00 0.00 0.00 3.25
193 298 3.993736 AGCAAAAGCAACGTGTTTTCTTT 59.006 34.783 0.00 4.73 29.43 2.52
226 331 1.004044 ACCCAACAGGAAGCATCTCAG 59.996 52.381 0.00 0.00 39.89 3.35
255 364 2.878406 CCACCATCTCAACGTGTTTTCT 59.122 45.455 0.00 0.00 0.00 2.52
262 371 5.464965 TCTCAACGTGTTTTCTCTTTCAC 57.535 39.130 0.00 0.00 0.00 3.18
263 372 4.331717 TCTCAACGTGTTTTCTCTTTCACC 59.668 41.667 0.00 0.00 0.00 4.02
269 378 4.033129 CGTGTTTTCTCTTTCACCGTAACA 59.967 41.667 0.00 0.00 0.00 2.41
288 397 2.037511 ACAACGTCGTTAATCCCCTCAA 59.962 45.455 10.86 0.00 0.00 3.02
289 398 2.375173 ACGTCGTTAATCCCCTCAAC 57.625 50.000 0.00 0.00 0.00 3.18
324 433 3.245264 GGGGATTGGAGAGGTTTGAAGAA 60.245 47.826 0.00 0.00 0.00 2.52
325 434 4.013050 GGGATTGGAGAGGTTTGAAGAAG 58.987 47.826 0.00 0.00 0.00 2.85
349 458 7.734942 AGATTTTGACTTGCAAGGGATTTAAA 58.265 30.769 29.18 18.55 37.87 1.52
350 459 8.377799 AGATTTTGACTTGCAAGGGATTTAAAT 58.622 29.630 29.18 21.57 37.87 1.40
351 460 9.651913 GATTTTGACTTGCAAGGGATTTAAATA 57.348 29.630 29.18 4.33 37.87 1.40
372 481 6.731292 ATATTTAATCCCTTGCAAACCTCC 57.269 37.500 0.00 0.00 0.00 4.30
384 493 2.673027 AAACCTCCCCAAACCCTGCC 62.673 60.000 0.00 0.00 0.00 4.85
385 494 3.268032 CCTCCCCAAACCCTGCCT 61.268 66.667 0.00 0.00 0.00 4.75
386 495 1.928567 CCTCCCCAAACCCTGCCTA 60.929 63.158 0.00 0.00 0.00 3.93
387 496 1.506028 CCTCCCCAAACCCTGCCTAA 61.506 60.000 0.00 0.00 0.00 2.69
388 497 0.323451 CTCCCCAAACCCTGCCTAAC 60.323 60.000 0.00 0.00 0.00 2.34
389 498 1.304962 CCCCAAACCCTGCCTAACC 60.305 63.158 0.00 0.00 0.00 2.85
390 499 1.677633 CCCAAACCCTGCCTAACCG 60.678 63.158 0.00 0.00 0.00 4.44
392 501 0.250989 CCAAACCCTGCCTAACCGAA 60.251 55.000 0.00 0.00 0.00 4.30
393 502 0.879090 CAAACCCTGCCTAACCGAAC 59.121 55.000 0.00 0.00 0.00 3.95
394 503 0.475044 AAACCCTGCCTAACCGAACA 59.525 50.000 0.00 0.00 0.00 3.18
396 505 0.036306 ACCCTGCCTAACCGAACAAG 59.964 55.000 0.00 0.00 0.00 3.16
397 506 1.305930 CCCTGCCTAACCGAACAAGC 61.306 60.000 0.00 0.00 0.00 4.01
398 507 1.305930 CCTGCCTAACCGAACAAGCC 61.306 60.000 0.00 0.00 0.00 4.35
399 508 0.605319 CTGCCTAACCGAACAAGCCA 60.605 55.000 0.00 0.00 0.00 4.75
400 509 0.037590 TGCCTAACCGAACAAGCCAT 59.962 50.000 0.00 0.00 0.00 4.40
401 510 0.733150 GCCTAACCGAACAAGCCATC 59.267 55.000 0.00 0.00 0.00 3.51
402 511 1.379527 CCTAACCGAACAAGCCATCC 58.620 55.000 0.00 0.00 0.00 3.51
421 530 2.546368 TCCGTGTGTATGCAGTTGAAAC 59.454 45.455 0.00 0.00 0.00 2.78
423 532 2.033236 CGTGTGTATGCAGTTGAAACGT 60.033 45.455 0.00 0.00 0.00 3.99
430 539 5.864474 TGTATGCAGTTGAAACGTTTTTGTT 59.136 32.000 15.89 0.00 0.00 2.83
431 540 5.854431 ATGCAGTTGAAACGTTTTTGTTT 57.146 30.435 15.89 0.00 44.36 2.83
432 541 5.011451 TGCAGTTGAAACGTTTTTGTTTG 57.989 34.783 15.89 11.14 41.89 2.93
433 542 4.508124 TGCAGTTGAAACGTTTTTGTTTGT 59.492 33.333 15.89 0.00 41.89 2.83
454 563 2.297033 TCTTCCAAATGGCTTCACTTGC 59.703 45.455 0.00 0.00 34.44 4.01
456 565 1.614903 TCCAAATGGCTTCACTTGCTG 59.385 47.619 0.00 0.00 34.44 4.41
485 594 3.895656 TGGGACATGTATAGAGTACCAGC 59.104 47.826 0.00 0.00 41.24 4.85
492 601 8.534954 ACATGTATAGAGTACCAGCTTTTCTA 57.465 34.615 0.00 0.00 0.00 2.10
497 606 7.906199 ATAGAGTACCAGCTTTTCTATCAGT 57.094 36.000 0.00 0.00 0.00 3.41
501 610 3.679389 ACCAGCTTTTCTATCAGTGTGG 58.321 45.455 0.00 0.00 0.00 4.17
519 628 6.016527 CAGTGTGGATGATTTTCTATCATGGG 60.017 42.308 5.07 0.00 38.73 4.00
524 633 6.183361 TGGATGATTTTCTATCATGGGGCTTA 60.183 38.462 5.07 0.00 38.73 3.09
691 887 1.047002 CCACCCACCAAAAGCATTCA 58.953 50.000 0.00 0.00 0.00 2.57
722 918 3.470645 ACCACTCTTTGTACACTCACC 57.529 47.619 0.00 0.00 0.00 4.02
763 959 4.785453 CCAAGGCCCAGCGACCTC 62.785 72.222 0.00 0.00 34.31 3.85
764 960 4.785453 CAAGGCCCAGCGACCTCC 62.785 72.222 0.00 0.00 34.31 4.30
769 965 3.625897 CCCAGCGACCTCCACACA 61.626 66.667 0.00 0.00 0.00 3.72
770 966 2.357517 CCAGCGACCTCCACACAC 60.358 66.667 0.00 0.00 0.00 3.82
771 967 2.421314 CAGCGACCTCCACACACA 59.579 61.111 0.00 0.00 0.00 3.72
772 968 1.956170 CAGCGACCTCCACACACAC 60.956 63.158 0.00 0.00 0.00 3.82
773 969 2.665185 GCGACCTCCACACACACC 60.665 66.667 0.00 0.00 0.00 4.16
774 970 2.818841 CGACCTCCACACACACCA 59.181 61.111 0.00 0.00 0.00 4.17
791 988 2.203640 AGTCTCCCCTGTCGTGCA 60.204 61.111 0.00 0.00 0.00 4.57
797 994 2.579657 CCCCTGTCGTGCACCACTA 61.580 63.158 15.75 1.84 31.34 2.74
811 1008 2.300152 CACCACTACTTCCTCTGCTTCA 59.700 50.000 0.00 0.00 0.00 3.02
846 1043 1.083657 CGCCGTGTTCTGTTGTTCG 60.084 57.895 0.00 0.00 0.00 3.95
919 1116 2.565841 AGTTCAGAGCTTCACACAACC 58.434 47.619 0.00 0.00 0.00 3.77
921 1118 2.245159 TCAGAGCTTCACACAACCTG 57.755 50.000 0.00 0.00 0.00 4.00
973 1170 2.923035 CCAGAGGTGGTGACGGGT 60.923 66.667 0.00 0.00 39.30 5.28
976 1173 1.908793 AGAGGTGGTGACGGGTGAG 60.909 63.158 0.00 0.00 0.00 3.51
981 1178 0.106149 GTGGTGACGGGTGAGAAAGT 59.894 55.000 0.00 0.00 0.00 2.66
1372 1595 0.388649 CCGGATAGCTGACGCCATAC 60.389 60.000 0.00 0.00 36.60 2.39
1428 1651 0.040067 GGCGTGAAAGGAACAAGCTG 60.040 55.000 0.00 0.00 41.09 4.24
2159 2518 9.763465 AAATCCATCTAAACATTTTACGTTACG 57.237 29.630 2.19 2.19 0.00 3.18
2666 3404 2.486982 AGGATCATAATGCATGCTTCGC 59.513 45.455 20.33 0.18 34.35 4.70
2787 3570 5.220739 GGTCATCAGCTTTGTGATATGTGTC 60.221 44.000 0.00 0.00 35.30 3.67
2807 3590 4.164796 TGTCGACCTTACCCTGATACTCTA 59.835 45.833 14.12 0.00 0.00 2.43
3012 3795 6.071051 ACCTCTTTCTAAAGATGACTCCAGAC 60.071 42.308 12.76 0.00 43.52 3.51
3149 3932 1.208293 GCTAGTGCTTTGGCTAGAGGT 59.792 52.381 0.00 0.00 37.47 3.85
3846 4632 2.112279 TCACCTGAGGTACCTTGGTT 57.888 50.000 27.80 16.06 32.11 3.67
4050 4838 5.466058 CAGAATCTGACATCCATAGAAGTGC 59.534 44.000 3.77 0.00 32.44 4.40
4076 4864 2.192263 GGGGTCTTGGTCTCTCTGAAT 58.808 52.381 0.00 0.00 0.00 2.57
4131 4919 1.340405 TGAGGGAGCTTCAGATTTGCC 60.340 52.381 0.00 0.00 0.00 4.52
4140 4928 3.446516 GCTTCAGATTTGCCTCAAGGATT 59.553 43.478 0.00 0.00 37.39 3.01
4189 4977 2.288213 TGAAGTCTCTGTGCAACCTACG 60.288 50.000 0.00 0.00 34.36 3.51
4206 4994 4.201990 ACCTACGTCACATCGAAATCCTAC 60.202 45.833 0.00 0.00 34.70 3.18
4214 5002 7.169140 CGTCACATCGAAATCCTACATATTGAA 59.831 37.037 0.00 0.00 0.00 2.69
4246 5034 7.590279 TCCGGAGAAATTTATTTTGAACTGAC 58.410 34.615 0.00 0.00 0.00 3.51
4258 5046 2.525368 TGAACTGACGGATCTCTTGGA 58.475 47.619 0.00 0.00 0.00 3.53
4269 5057 0.320771 TCTCTTGGAAGAACGCTGGC 60.321 55.000 0.00 0.00 34.03 4.85
4291 5079 0.387202 CCTCCTGTACATCTCCGCAG 59.613 60.000 0.00 0.00 0.00 5.18
4300 5088 2.783135 ACATCTCCGCAGATTTGTGTT 58.217 42.857 0.00 0.00 37.25 3.32
4310 5098 3.491356 CAGATTTGTGTTGTACATGCCG 58.509 45.455 0.00 0.00 39.48 5.69
4353 5141 2.478292 GGTGGATAAAGAGAGACCCCA 58.522 52.381 0.00 0.00 0.00 4.96
4354 5142 3.049344 GGTGGATAAAGAGAGACCCCAT 58.951 50.000 0.00 0.00 0.00 4.00
4412 5200 0.694771 TGAAGGAAGTGCAGCAGGAT 59.305 50.000 0.00 0.00 0.00 3.24
4433 5221 0.110486 ACGTGGATATCATTGGGGGC 59.890 55.000 4.83 0.00 0.00 5.80
4456 5245 2.272918 CTGTCCCTTCGCCGTCTCTC 62.273 65.000 0.00 0.00 0.00 3.20
4520 5309 1.747206 GCAGATGGGTTCCGCTGTATT 60.747 52.381 0.00 0.00 33.20 1.89
4537 5326 7.201444 CCGCTGTATTGTAGACTTTAACTTGAG 60.201 40.741 0.00 0.00 0.00 3.02
4613 5402 1.142870 TCAGTTGGGTTCAGTCTTGGG 59.857 52.381 0.00 0.00 0.00 4.12
4646 5435 2.789409 AAGAGGATGGTAACTGTGGC 57.211 50.000 0.00 0.00 37.61 5.01
4653 5442 0.753867 TGGTAACTGTGGCTTCGACA 59.246 50.000 0.00 0.00 37.61 4.35
4659 5448 2.045926 GTGGCTTCGACATGGGCT 60.046 61.111 0.00 0.00 0.00 5.19
4704 5493 0.043310 GCGGCGTGTCGATGTTAATC 60.043 55.000 9.37 0.00 0.00 1.75
4715 5504 5.293324 TGTCGATGTTAATCTGTATTGTGGC 59.707 40.000 0.00 0.00 0.00 5.01
4773 5562 4.273257 TGAGGCACGCGTTCGACA 62.273 61.111 10.22 5.71 39.41 4.35
4789 5578 0.625849 GACACCCATCCCAACCATCT 59.374 55.000 0.00 0.00 0.00 2.90
4791 5580 0.396139 CACCCATCCCAACCATCTGG 60.396 60.000 0.00 0.00 42.17 3.86
4792 5581 0.552367 ACCCATCCCAACCATCTGGA 60.552 55.000 2.55 0.00 38.96 3.86
4798 5587 2.278245 TCCCAACCATCTGGAGATTGT 58.722 47.619 2.55 0.00 38.96 2.71
4802 5591 4.581824 CCCAACCATCTGGAGATTGTAATG 59.418 45.833 2.55 0.00 38.96 1.90
4804 5593 5.653769 CCAACCATCTGGAGATTGTAATGTT 59.346 40.000 2.55 0.00 38.96 2.71
4811 5600 8.830580 CATCTGGAGATTGTAATGTTTACGAAT 58.169 33.333 0.00 0.00 31.21 3.34
5144 5944 1.527034 TACTCGTGCACGTACTCCTT 58.473 50.000 35.74 16.59 40.80 3.36
5145 5945 0.039437 ACTCGTGCACGTACTCCTTG 60.039 55.000 35.74 18.72 40.80 3.61
5146 5946 0.732880 CTCGTGCACGTACTCCTTGG 60.733 60.000 35.74 13.40 40.80 3.61
5147 5947 1.736645 CGTGCACGTACTCCTTGGG 60.737 63.158 30.50 0.00 34.11 4.12
5149 5949 3.990034 CGTGCACGTACTCCTTGGGAG 62.990 61.905 30.50 11.57 43.86 4.30
5189 6002 2.074576 GACCGCCTGACCTTTTTACTC 58.925 52.381 0.00 0.00 0.00 2.59
5203 6018 6.151817 ACCTTTTTACTCTCTGCATGGATTTC 59.848 38.462 0.00 0.00 0.00 2.17
5223 6038 6.891306 TTTCATCTCTAAATCTCCCAAGGA 57.109 37.500 0.00 0.00 0.00 3.36
5235 6050 4.428294 CTCCCAAGGAGCTAATGATGAA 57.572 45.455 0.00 0.00 43.29 2.57
5257 6075 2.455674 TTTGTGTGAGGACGAGATGG 57.544 50.000 0.00 0.00 0.00 3.51
5261 6079 1.751351 GTGTGAGGACGAGATGGATGA 59.249 52.381 0.00 0.00 0.00 2.92
5265 6083 4.649218 TGTGAGGACGAGATGGATGATAAA 59.351 41.667 0.00 0.00 0.00 1.40
5266 6084 5.128663 TGTGAGGACGAGATGGATGATAAAA 59.871 40.000 0.00 0.00 0.00 1.52
5267 6085 5.694006 GTGAGGACGAGATGGATGATAAAAG 59.306 44.000 0.00 0.00 0.00 2.27
5271 6089 6.540189 AGGACGAGATGGATGATAAAAGTTTG 59.460 38.462 0.00 0.00 0.00 2.93
5273 6091 7.494625 GGACGAGATGGATGATAAAAGTTTGTA 59.505 37.037 0.00 0.00 0.00 2.41
5275 6093 9.046296 ACGAGATGGATGATAAAAGTTTGTATC 57.954 33.333 0.00 0.66 0.00 2.24
5276 6094 9.045223 CGAGATGGATGATAAAAGTTTGTATCA 57.955 33.333 16.15 16.15 40.17 2.15
5278 6096 9.911788 AGATGGATGATAAAAGTTTGTATCAGT 57.088 29.630 17.59 10.81 39.46 3.41
5279 6097 9.941664 GATGGATGATAAAAGTTTGTATCAGTG 57.058 33.333 17.59 0.00 39.46 3.66
5280 6098 7.761409 TGGATGATAAAAGTTTGTATCAGTGC 58.239 34.615 17.59 13.58 39.46 4.40
5281 6099 7.148086 TGGATGATAAAAGTTTGTATCAGTGCC 60.148 37.037 17.59 17.28 39.46 5.01
5282 6100 7.067494 GGATGATAAAAGTTTGTATCAGTGCCT 59.933 37.037 17.59 7.76 39.46 4.75
5283 6101 7.144722 TGATAAAAGTTTGTATCAGTGCCTG 57.855 36.000 12.54 0.00 32.94 4.85
5284 6102 4.853924 AAAAGTTTGTATCAGTGCCTGG 57.146 40.909 2.86 0.00 31.51 4.45
5285 6103 3.508845 AAGTTTGTATCAGTGCCTGGT 57.491 42.857 0.00 0.00 31.51 4.00
5290 6108 0.107654 GTATCAGTGCCTGGTGGACC 60.108 60.000 0.00 0.00 34.57 4.46
5291 6109 0.252696 TATCAGTGCCTGGTGGACCT 60.253 55.000 0.00 0.00 36.82 3.85
5314 6132 5.005740 TGGTGGAGAACTGATTTTCTGATG 58.994 41.667 0.00 0.00 35.90 3.07
5320 6138 5.558818 AGAACTGATTTTCTGATGCAGAGT 58.441 37.500 0.00 0.00 41.75 3.24
5321 6139 6.705302 AGAACTGATTTTCTGATGCAGAGTA 58.295 36.000 0.00 0.00 41.75 2.59
5344 6162 2.385013 TACATTGCGTCAGATGTGCT 57.615 45.000 0.00 0.00 37.12 4.40
5345 6163 1.081892 ACATTGCGTCAGATGTGCTC 58.918 50.000 0.00 0.00 35.31 4.26
5346 6164 1.338484 ACATTGCGTCAGATGTGCTCT 60.338 47.619 0.00 0.00 35.31 4.09
5347 6165 1.326852 CATTGCGTCAGATGTGCTCTC 59.673 52.381 0.00 0.00 29.16 3.20
5348 6166 0.318120 TTGCGTCAGATGTGCTCTCA 59.682 50.000 0.00 0.00 29.16 3.27
5349 6167 0.108945 TGCGTCAGATGTGCTCTCAG 60.109 55.000 0.00 0.00 29.16 3.35
5406 6229 4.826274 TTCCATCTTTCTCCATCGTCTT 57.174 40.909 0.00 0.00 0.00 3.01
5411 6234 6.098266 TCCATCTTTCTCCATCGTCTTGAATA 59.902 38.462 0.00 0.00 0.00 1.75
5412 6235 6.933521 CCATCTTTCTCCATCGTCTTGAATAT 59.066 38.462 0.00 0.00 0.00 1.28
5413 6236 7.117523 CCATCTTTCTCCATCGTCTTGAATATC 59.882 40.741 0.00 0.00 0.00 1.63
5416 6239 6.715347 TTCTCCATCGTCTTGAATATCTCA 57.285 37.500 0.00 0.00 0.00 3.27
5515 6342 5.423886 AGGCATAAGTCTCTAAGCAGAAAC 58.576 41.667 0.00 0.00 0.00 2.78
5553 6381 4.265893 TGTAGTGTGGAACTTGCTCAAAA 58.734 39.130 0.00 0.00 40.56 2.44
5576 6404 4.524328 ACTAATTTTTGTCAAGGGGCTGAG 59.476 41.667 0.00 0.00 0.00 3.35
5595 6423 6.238869 GGCTGAGGAAAGCTAAGGATTATTTG 60.239 42.308 0.00 0.00 43.06 2.32
5613 6444 7.993821 TTATTTGAGTGCAATTTTGTCGAAA 57.006 28.000 0.00 0.00 33.25 3.46
5630 6461 3.118884 TCGAAAGATAGTTGGTAGTGGGC 60.119 47.826 0.00 0.00 33.31 5.36
5634 6465 4.222124 AGATAGTTGGTAGTGGGCAAAG 57.778 45.455 0.00 0.00 0.00 2.77
5636 6467 4.288626 AGATAGTTGGTAGTGGGCAAAGAA 59.711 41.667 0.00 0.00 0.00 2.52
5637 6468 3.306472 AGTTGGTAGTGGGCAAAGAAA 57.694 42.857 0.00 0.00 0.00 2.52
5697 6538 9.059260 GTTTTAATTAGGTGACAAGTACTCCAA 57.941 33.333 0.00 0.00 0.00 3.53
5706 6778 6.398918 GTGACAAGTACTCCAAGTCATACAT 58.601 40.000 17.65 0.00 40.80 2.29
5746 6826 5.463286 CATATCTCTGAAGCTAGAGTGCTG 58.537 45.833 12.28 5.79 43.24 4.41
5790 6992 8.669946 TTAGTTGTTGATTATGGCATCGATTA 57.330 30.769 1.65 0.00 0.00 1.75
5801 7003 4.702831 TGGCATCGATTACTTGCTGATTA 58.297 39.130 7.79 0.00 36.62 1.75
5805 7007 6.093219 GGCATCGATTACTTGCTGATTATGAT 59.907 38.462 7.79 0.00 36.62 2.45
5840 7043 5.698104 TGGGAATGAGCAAGATTCATGTAT 58.302 37.500 0.00 0.00 35.54 2.29
6114 10141 5.721960 AGGCGGTGGATTATATCTTCTGTAT 59.278 40.000 0.00 0.00 0.00 2.29
6135 10162 7.941919 TGTATGTGTTTGGTTGCTTGTTATAA 58.058 30.769 0.00 0.00 0.00 0.98
6229 10279 8.686334 GGTAAAGATAGGAATCTGAATTTTGCA 58.314 33.333 0.00 0.00 41.81 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.809395 ACAGTACACTAGCCTCTTTGATATATA 57.191 33.333 0.00 0.00 0.00 0.86
1 2 8.713708 ACAGTACACTAGCCTCTTTGATATAT 57.286 34.615 0.00 0.00 0.00 0.86
2 3 9.809395 ATACAGTACACTAGCCTCTTTGATATA 57.191 33.333 0.00 0.00 0.00 0.86
3 4 8.713708 ATACAGTACACTAGCCTCTTTGATAT 57.286 34.615 0.00 0.00 0.00 1.63
4 5 8.534954 AATACAGTACACTAGCCTCTTTGATA 57.465 34.615 0.00 0.00 0.00 2.15
54 55 3.506398 CCACCACCCCTACTTCAAATTT 58.494 45.455 0.00 0.00 0.00 1.82
60 61 1.138228 AACCCCACCACCCCTACTTC 61.138 60.000 0.00 0.00 0.00 3.01
65 66 0.778479 AATACAACCCCACCACCCCT 60.778 55.000 0.00 0.00 0.00 4.79
85 86 8.958119 TTATCTATTTTGACTTGCTTCGGTAT 57.042 30.769 0.00 0.00 0.00 2.73
111 190 6.569179 TTTGGTAAAGCAGAGGACAAATAC 57.431 37.500 0.00 0.00 0.00 1.89
123 228 2.235016 AGATGCGGTTTTGGTAAAGCA 58.765 42.857 0.00 0.00 40.83 3.91
132 237 5.003804 ACAATCACTAGAAGATGCGGTTTT 58.996 37.500 0.00 0.00 0.00 2.43
193 298 3.498481 CCTGTTGGGTGGAGATCAAAAGA 60.498 47.826 0.00 0.00 29.62 2.52
226 331 0.899717 TTGAGATGGTGGGCAAAGGC 60.900 55.000 0.00 0.00 40.13 4.35
269 378 2.037511 TGTTGAGGGGATTAACGACGTT 59.962 45.455 18.47 18.47 0.00 3.99
288 397 3.444029 CAATCCCCTTCAATCCCTTTGT 58.556 45.455 0.00 0.00 36.65 2.83
289 398 2.767960 CCAATCCCCTTCAATCCCTTTG 59.232 50.000 0.00 0.00 36.61 2.77
302 411 2.308866 TCTTCAAACCTCTCCAATCCCC 59.691 50.000 0.00 0.00 0.00 4.81
324 433 5.813513 AAATCCCTTGCAAGTCAAAATCT 57.186 34.783 24.35 0.00 33.65 2.40
325 434 7.961325 TTTAAATCCCTTGCAAGTCAAAATC 57.039 32.000 24.35 0.00 33.65 2.17
349 458 5.602561 GGGAGGTTTGCAAGGGATTAAATAT 59.397 40.000 0.00 0.00 0.00 1.28
350 459 4.959839 GGGAGGTTTGCAAGGGATTAAATA 59.040 41.667 0.00 0.00 0.00 1.40
351 460 3.774766 GGGAGGTTTGCAAGGGATTAAAT 59.225 43.478 0.00 0.00 0.00 1.40
352 461 3.169908 GGGAGGTTTGCAAGGGATTAAA 58.830 45.455 0.00 0.00 0.00 1.52
353 462 2.558800 GGGGAGGTTTGCAAGGGATTAA 60.559 50.000 0.00 0.00 0.00 1.40
354 463 1.006639 GGGGAGGTTTGCAAGGGATTA 59.993 52.381 0.00 0.00 0.00 1.75
355 464 0.252239 GGGGAGGTTTGCAAGGGATT 60.252 55.000 0.00 0.00 0.00 3.01
356 465 1.388133 GGGGAGGTTTGCAAGGGAT 59.612 57.895 0.00 0.00 0.00 3.85
363 472 1.152333 AGGGTTTGGGGAGGTTTGC 60.152 57.895 0.00 0.00 0.00 3.68
367 476 2.723334 TAGGCAGGGTTTGGGGAGGT 62.723 60.000 0.00 0.00 0.00 3.85
372 481 1.677633 CGGTTAGGCAGGGTTTGGG 60.678 63.158 0.00 0.00 0.00 4.12
384 493 1.006832 CGGATGGCTTGTTCGGTTAG 58.993 55.000 0.00 0.00 0.00 2.34
385 494 0.322322 ACGGATGGCTTGTTCGGTTA 59.678 50.000 0.00 0.00 0.00 2.85
386 495 1.072505 ACGGATGGCTTGTTCGGTT 59.927 52.632 0.00 0.00 0.00 4.44
387 496 1.671054 CACGGATGGCTTGTTCGGT 60.671 57.895 0.00 0.00 0.00 4.69
388 497 1.671054 ACACGGATGGCTTGTTCGG 60.671 57.895 0.00 0.00 0.00 4.30
389 498 1.227999 ACACACGGATGGCTTGTTCG 61.228 55.000 0.00 0.00 0.00 3.95
390 499 1.803334 TACACACGGATGGCTTGTTC 58.197 50.000 0.00 0.00 0.00 3.18
392 501 1.737838 CATACACACGGATGGCTTGT 58.262 50.000 0.00 0.00 0.00 3.16
393 502 0.378257 GCATACACACGGATGGCTTG 59.622 55.000 0.00 0.00 0.00 4.01
394 503 0.035534 TGCATACACACGGATGGCTT 60.036 50.000 0.00 0.00 0.00 4.35
396 505 0.744414 ACTGCATACACACGGATGGC 60.744 55.000 0.00 0.00 0.00 4.40
397 506 1.398041 CAACTGCATACACACGGATGG 59.602 52.381 0.00 0.00 0.00 3.51
398 507 2.345876 TCAACTGCATACACACGGATG 58.654 47.619 0.00 0.00 0.00 3.51
399 508 2.760634 TCAACTGCATACACACGGAT 57.239 45.000 0.00 0.00 0.00 4.18
400 509 2.535012 TTCAACTGCATACACACGGA 57.465 45.000 0.00 0.00 0.00 4.69
401 510 2.661709 CGTTTCAACTGCATACACACGG 60.662 50.000 0.00 0.00 0.00 4.94
402 511 2.033236 ACGTTTCAACTGCATACACACG 60.033 45.455 0.00 0.00 0.00 4.49
430 539 3.565307 AGTGAAGCCATTTGGAAGACAA 58.435 40.909 0.00 0.00 37.39 3.18
431 540 3.228188 AGTGAAGCCATTTGGAAGACA 57.772 42.857 0.00 0.00 37.39 3.41
432 541 3.858503 GCAAGTGAAGCCATTTGGAAGAC 60.859 47.826 0.00 0.00 39.50 3.01
433 542 2.297033 GCAAGTGAAGCCATTTGGAAGA 59.703 45.455 0.00 0.00 39.50 2.87
476 585 5.578727 CACACTGATAGAAAAGCTGGTACTC 59.421 44.000 0.00 0.00 0.00 2.59
485 594 8.954350 AGAAAATCATCCACACTGATAGAAAAG 58.046 33.333 0.00 0.00 33.08 2.27
492 601 7.447545 CCATGATAGAAAATCATCCACACTGAT 59.552 37.037 0.00 0.00 36.69 2.90
497 606 5.387788 CCCCATGATAGAAAATCATCCACA 58.612 41.667 0.00 0.00 36.69 4.17
501 610 6.716628 TGTAAGCCCCATGATAGAAAATCATC 59.283 38.462 0.00 0.00 36.69 2.92
513 622 1.367346 TTCAGGTGTAAGCCCCATGA 58.633 50.000 0.00 0.00 32.25 3.07
519 628 8.063200 ACCTATTAAAATTTCAGGTGTAAGCC 57.937 34.615 11.04 0.00 38.20 4.35
524 633 8.576442 CACTCAACCTATTAAAATTTCAGGTGT 58.424 33.333 12.06 6.01 39.54 4.16
610 806 5.349061 TGATCATGACAAGCACTACAGAT 57.651 39.130 0.00 0.00 0.00 2.90
653 849 1.546029 GGGTGTGGAAAGAAGGAATGC 59.454 52.381 0.00 0.00 0.00 3.56
691 887 5.061721 ACAAAGAGTGGTAAAGGGAACAT 57.938 39.130 0.00 0.00 0.00 2.71
722 918 2.226330 TGGAAGAAAATGGGTGTGACG 58.774 47.619 0.00 0.00 0.00 4.35
763 959 1.071471 GGGAGACTGGTGTGTGTGG 59.929 63.158 0.00 0.00 0.00 4.17
764 960 1.071471 GGGGAGACTGGTGTGTGTG 59.929 63.158 0.00 0.00 0.00 3.82
765 961 1.074471 AGGGGAGACTGGTGTGTGT 60.074 57.895 0.00 0.00 0.00 3.72
766 962 1.372683 CAGGGGAGACTGGTGTGTG 59.627 63.158 0.00 0.00 34.84 3.82
767 963 1.074471 ACAGGGGAGACTGGTGTGT 60.074 57.895 0.00 0.00 42.75 3.72
768 964 1.674057 GACAGGGGAGACTGGTGTG 59.326 63.158 0.00 0.00 42.75 3.82
769 965 1.908793 CGACAGGGGAGACTGGTGT 60.909 63.158 0.00 0.00 42.75 4.16
770 966 1.908793 ACGACAGGGGAGACTGGTG 60.909 63.158 0.00 0.00 42.75 4.17
771 967 1.908793 CACGACAGGGGAGACTGGT 60.909 63.158 0.00 0.00 42.75 4.00
772 968 2.973899 CACGACAGGGGAGACTGG 59.026 66.667 0.00 0.00 42.75 4.00
773 969 2.262915 GCACGACAGGGGAGACTG 59.737 66.667 0.00 0.00 44.03 3.51
774 970 2.203640 TGCACGACAGGGGAGACT 60.204 61.111 0.00 0.00 0.00 3.24
791 988 2.300437 GTGAAGCAGAGGAAGTAGTGGT 59.700 50.000 0.00 0.00 0.00 4.16
797 994 1.980765 TGGATGTGAAGCAGAGGAAGT 59.019 47.619 0.00 0.00 0.00 3.01
811 1008 4.101448 GGCTGCGGGACTGGATGT 62.101 66.667 0.00 0.00 0.00 3.06
840 1037 2.144078 TCCTGGTGGAGGCGAACAA 61.144 57.895 0.00 0.00 42.47 2.83
846 1043 3.316573 CTTCGGTCCTGGTGGAGGC 62.317 68.421 0.00 0.00 44.16 4.70
907 1104 1.537202 GTGATCCAGGTTGTGTGAAGC 59.463 52.381 0.00 0.00 0.00 3.86
919 1116 3.310774 CGGAGCTGTAAATTGTGATCCAG 59.689 47.826 0.00 0.00 0.00 3.86
921 1118 3.531538 TCGGAGCTGTAAATTGTGATCC 58.468 45.455 0.00 0.00 0.00 3.36
973 1170 3.117888 AGGAGTTGGAGCAAACTTTCTCA 60.118 43.478 1.61 0.00 40.48 3.27
976 1173 4.390264 AGTAGGAGTTGGAGCAAACTTTC 58.610 43.478 1.61 0.00 40.48 2.62
981 1178 3.307691 CCATGAGTAGGAGTTGGAGCAAA 60.308 47.826 0.00 0.00 0.00 3.68
1317 1540 5.509670 GCCTTTCTTGAACAAGCCTAACATT 60.510 40.000 9.38 0.00 38.28 2.71
1372 1595 2.751806 GGAGTTGCTCCTTGATTTCCTG 59.248 50.000 7.86 0.00 46.41 3.86
1428 1651 4.566488 CCAGGATTAGGAGCAATACCATCC 60.566 50.000 0.00 0.00 33.10 3.51
1746 1971 1.748493 GAGTGAGAGTTGCCGAGATCT 59.252 52.381 0.00 0.00 0.00 2.75
1821 2046 4.772624 AGTAGTGCATACCTCTTGTTCTCA 59.227 41.667 0.00 0.00 34.67 3.27
1925 2239 2.094597 CCCTTCCGTGTGACGTACAATA 60.095 50.000 0.00 0.00 41.89 1.90
2086 2444 4.057432 AGCCATTGTAACAAATGCAACAC 58.943 39.130 0.00 0.00 36.41 3.32
2159 2518 0.801251 GTCATTGCACTCACTCTGGC 59.199 55.000 0.00 0.00 0.00 4.85
2431 3085 2.106511 CCTCTTGGAGACCCACTCAAAA 59.893 50.000 0.00 0.00 46.54 2.44
2666 3404 6.600350 TCTTAAACTCGATAATCCGATCTCG 58.400 40.000 6.88 6.88 37.96 4.04
2787 3570 5.593502 AGTTTAGAGTATCAGGGTAAGGTCG 59.406 44.000 0.00 0.00 37.82 4.79
3146 3929 1.518367 TTGGTTTCACCTCCTGACCT 58.482 50.000 0.00 0.00 39.58 3.85
3149 3932 2.777692 ACTCTTTGGTTTCACCTCCTGA 59.222 45.455 0.00 0.00 39.58 3.86
3274 4057 8.200792 GGTACAATAGACAAGTTCTCAGATGAT 58.799 37.037 0.00 0.00 35.55 2.45
3846 4632 9.601217 GAGTTTTCTTATTCCAGTATCTGCTAA 57.399 33.333 0.00 0.00 0.00 3.09
3908 4694 6.406177 GCTCATAATTGCTTCCAAGATCCAAA 60.406 38.462 0.00 0.00 33.80 3.28
4076 4864 4.015764 TGCCAAGCTCTTGTGCAATAATA 58.984 39.130 17.29 1.39 40.81 0.98
4131 4919 6.102663 ACAGATCGAAACTACAATCCTTGAG 58.897 40.000 0.00 0.00 0.00 3.02
4140 4928 6.525578 ACCTTCATACAGATCGAAACTACA 57.474 37.500 0.00 0.00 0.00 2.74
4148 4936 4.421058 TCACGAAACCTTCATACAGATCG 58.579 43.478 0.00 0.00 35.36 3.69
4152 4940 5.230942 AGACTTCACGAAACCTTCATACAG 58.769 41.667 0.00 0.00 0.00 2.74
4189 4977 7.946655 TCAATATGTAGGATTTCGATGTGAC 57.053 36.000 0.00 0.00 0.00 3.67
4206 4994 5.694231 TCTCCGGAATTGCATTCAATATG 57.306 39.130 5.23 0.00 41.77 1.78
4214 5002 8.040132 TCAAAATAAATTTCTCCGGAATTGCAT 58.960 29.630 5.23 0.00 0.00 3.96
4231 5019 7.094805 CCAAGAGATCCGTCAGTTCAAAATAAA 60.095 37.037 0.00 0.00 0.00 1.40
4234 5022 4.697352 CCAAGAGATCCGTCAGTTCAAAAT 59.303 41.667 0.00 0.00 0.00 1.82
4246 5034 1.134965 AGCGTTCTTCCAAGAGATCCG 60.135 52.381 0.00 0.00 36.22 4.18
4269 5057 0.387202 CGGAGATGTACAGGAGGCAG 59.613 60.000 0.33 0.00 0.00 4.85
4291 5079 3.747193 CTCGGCATGTACAACACAAATC 58.253 45.455 0.00 0.00 41.55 2.17
4300 5088 0.391130 GAGTTGGCTCGGCATGTACA 60.391 55.000 0.00 0.00 31.39 2.90
4310 5098 1.297456 GCAGTGCAGAGAGTTGGCTC 61.297 60.000 11.09 0.00 41.94 4.70
4353 5141 1.686052 GGAGAGGTTCGAGAGATGCAT 59.314 52.381 0.00 0.00 41.60 3.96
4354 5142 1.107114 GGAGAGGTTCGAGAGATGCA 58.893 55.000 0.00 0.00 41.60 3.96
4412 5200 1.419762 CCCCCAATGATATCCACGTCA 59.580 52.381 0.00 0.00 0.00 4.35
4433 5221 3.121030 CGGCGAAGGGACAGCAAG 61.121 66.667 0.00 0.00 0.00 4.01
4520 5309 6.880484 TCCACAACTCAAGTTAAAGTCTACA 58.120 36.000 0.00 0.00 36.32 2.74
4537 5326 0.310543 TTGCGTTGCTGATCCACAAC 59.689 50.000 14.77 14.77 42.15 3.32
4588 5377 2.711009 AGACTGAACCCAACTGATTCCA 59.289 45.455 0.00 0.00 0.00 3.53
4646 5435 1.651240 CCTGCAAGCCCATGTCGAAG 61.651 60.000 0.00 0.00 0.00 3.79
4653 5442 2.037847 GTTCCCCTGCAAGCCCAT 59.962 61.111 0.00 0.00 0.00 4.00
4695 5484 4.814234 TCCGCCACAATACAGATTAACATC 59.186 41.667 0.00 0.00 0.00 3.06
4697 5486 4.188462 CTCCGCCACAATACAGATTAACA 58.812 43.478 0.00 0.00 0.00 2.41
4704 5493 1.148157 CTCGCTCCGCCACAATACAG 61.148 60.000 0.00 0.00 0.00 2.74
4746 5535 2.740055 GTGCCTCACCGCAGACTG 60.740 66.667 0.00 0.00 40.05 3.51
4767 5556 1.377229 GGTTGGGATGGGTGTCGAA 59.623 57.895 0.00 0.00 0.00 3.71
4773 5562 0.552367 TCCAGATGGTTGGGATGGGT 60.552 55.000 0.00 0.00 38.81 4.51
4789 5578 6.256975 CGGATTCGTAAACATTACAATCTCCA 59.743 38.462 16.12 0.00 0.00 3.86
4791 5580 6.127403 GCGGATTCGTAAACATTACAATCTC 58.873 40.000 0.00 10.50 38.89 2.75
4792 5581 5.583061 TGCGGATTCGTAAACATTACAATCT 59.417 36.000 0.00 0.00 38.89 2.40
4798 5587 6.869388 TGCTATATGCGGATTCGTAAACATTA 59.131 34.615 0.00 0.00 46.63 1.90
5118 5918 5.172771 GGAGTACGTGCACGAGTAATTAATC 59.827 44.000 42.94 28.93 43.02 1.75
5119 5919 5.039333 GGAGTACGTGCACGAGTAATTAAT 58.961 41.667 42.94 23.63 43.02 1.40
5120 5920 4.156556 AGGAGTACGTGCACGAGTAATTAA 59.843 41.667 42.94 15.51 43.02 1.40
5144 5944 8.010697 TCATGAGAAAATAGATAGGTACTCCCA 58.989 37.037 0.00 0.00 41.75 4.37
5145 5945 8.308207 GTCATGAGAAAATAGATAGGTACTCCC 58.692 40.741 0.00 0.00 41.75 4.30
5146 5946 8.308207 GGTCATGAGAAAATAGATAGGTACTCC 58.692 40.741 0.00 0.00 41.75 3.85
5147 5947 8.024285 CGGTCATGAGAAAATAGATAGGTACTC 58.976 40.741 0.00 0.00 41.75 2.59
5149 5949 6.586844 GCGGTCATGAGAAAATAGATAGGTAC 59.413 42.308 0.00 0.00 0.00 3.34
5150 5950 6.295123 GGCGGTCATGAGAAAATAGATAGGTA 60.295 42.308 0.00 0.00 0.00 3.08
5151 5951 5.511545 GGCGGTCATGAGAAAATAGATAGGT 60.512 44.000 0.00 0.00 0.00 3.08
5154 5954 5.304357 TCAGGCGGTCATGAGAAAATAGATA 59.696 40.000 0.00 0.00 0.00 1.98
5155 5955 4.101585 TCAGGCGGTCATGAGAAAATAGAT 59.898 41.667 0.00 0.00 0.00 1.98
5156 5956 3.450817 TCAGGCGGTCATGAGAAAATAGA 59.549 43.478 0.00 0.00 0.00 1.98
5157 5957 3.557595 GTCAGGCGGTCATGAGAAAATAG 59.442 47.826 0.00 0.00 0.00 1.73
5223 6038 6.318144 CCTCACACAAATCTTCATCATTAGCT 59.682 38.462 0.00 0.00 0.00 3.32
5227 6042 5.122869 CGTCCTCACACAAATCTTCATCATT 59.877 40.000 0.00 0.00 0.00 2.57
5235 6050 3.368843 CCATCTCGTCCTCACACAAATCT 60.369 47.826 0.00 0.00 0.00 2.40
5257 6075 7.989826 AGGCACTGATACAAACTTTTATCATC 58.010 34.615 0.11 0.00 37.18 2.92
5276 6094 3.252284 CCAGGTCCACCAGGCACT 61.252 66.667 0.00 0.00 35.82 4.40
5277 6095 3.570212 ACCAGGTCCACCAGGCAC 61.570 66.667 7.09 0.00 45.71 5.01
5278 6096 3.569210 CACCAGGTCCACCAGGCA 61.569 66.667 7.09 0.00 45.71 4.75
5279 6097 4.351054 CCACCAGGTCCACCAGGC 62.351 72.222 7.09 0.00 45.71 4.85
5281 6099 1.127567 TTCTCCACCAGGTCCACCAG 61.128 60.000 0.00 0.00 38.89 4.00
5282 6100 1.074090 TTCTCCACCAGGTCCACCA 60.074 57.895 0.00 0.00 38.89 4.17
5283 6101 1.128188 AGTTCTCCACCAGGTCCACC 61.128 60.000 0.00 0.00 35.89 4.61
5284 6102 0.035458 CAGTTCTCCACCAGGTCCAC 59.965 60.000 0.00 0.00 35.89 4.02
5285 6103 0.105194 TCAGTTCTCCACCAGGTCCA 60.105 55.000 0.00 0.00 35.89 4.02
5290 6108 4.645535 TCAGAAAATCAGTTCTCCACCAG 58.354 43.478 0.00 0.00 35.63 4.00
5291 6109 4.705110 TCAGAAAATCAGTTCTCCACCA 57.295 40.909 0.00 0.00 35.63 4.17
5294 6112 4.654915 TGCATCAGAAAATCAGTTCTCCA 58.345 39.130 0.00 0.00 35.63 3.86
5314 6132 4.112634 TGACGCAATGTAAGATACTCTGC 58.887 43.478 0.00 0.00 35.23 4.26
5320 6138 4.507756 GCACATCTGACGCAATGTAAGATA 59.492 41.667 0.00 0.00 45.59 1.98
5325 6143 2.094026 AGAGCACATCTGACGCAATGTA 60.094 45.455 0.00 0.00 36.69 2.29
5333 6151 2.491298 TGAGACTGAGAGCACATCTGAC 59.509 50.000 0.00 0.00 38.84 3.51
5344 6162 5.105023 ACGTACTACATACCTGAGACTGAGA 60.105 44.000 0.00 0.00 0.00 3.27
5345 6163 5.117584 ACGTACTACATACCTGAGACTGAG 58.882 45.833 0.00 0.00 0.00 3.35
5346 6164 5.095145 ACGTACTACATACCTGAGACTGA 57.905 43.478 0.00 0.00 0.00 3.41
5347 6165 7.493743 AATACGTACTACATACCTGAGACTG 57.506 40.000 0.00 0.00 0.00 3.51
5348 6166 7.468357 GCAAATACGTACTACATACCTGAGACT 60.468 40.741 0.00 0.00 0.00 3.24
5349 6167 6.636044 GCAAATACGTACTACATACCTGAGAC 59.364 42.308 0.00 0.00 0.00 3.36
5411 6234 7.040617 GCATGGTTGATCAATAGAATGTGAGAT 60.041 37.037 12.12 0.00 0.00 2.75
5412 6235 6.261603 GCATGGTTGATCAATAGAATGTGAGA 59.738 38.462 12.12 0.00 0.00 3.27
5413 6236 6.262496 AGCATGGTTGATCAATAGAATGTGAG 59.738 38.462 12.12 0.00 0.00 3.51
5416 6239 6.363065 AGAGCATGGTTGATCAATAGAATGT 58.637 36.000 12.12 4.94 40.79 2.71
5433 6259 5.411831 TTCCATATAGCCAGTAGAGCATG 57.588 43.478 0.00 0.00 0.00 4.06
5502 6329 4.745125 TCAAGTTCACGTTTCTGCTTAGAG 59.255 41.667 0.00 0.00 0.00 2.43
5506 6333 3.006940 TGTCAAGTTCACGTTTCTGCTT 58.993 40.909 0.00 0.00 0.00 3.91
5508 6335 3.609103 ATGTCAAGTTCACGTTTCTGC 57.391 42.857 0.00 0.00 0.00 4.26
5515 6342 6.401047 CCACACTACATTATGTCAAGTTCACG 60.401 42.308 0.00 0.00 0.00 4.35
5553 6381 4.479158 TCAGCCCCTTGACAAAAATTAGT 58.521 39.130 0.00 0.00 0.00 2.24
5564 6392 1.136329 AGCTTTCCTCAGCCCCTTGA 61.136 55.000 0.00 0.00 41.12 3.02
5569 6397 0.912486 TCCTTAGCTTTCCTCAGCCC 59.088 55.000 0.00 0.00 41.12 5.19
5576 6404 6.095440 TGCACTCAAATAATCCTTAGCTTTCC 59.905 38.462 0.00 0.00 0.00 3.13
5595 6423 6.603095 ACTATCTTTCGACAAAATTGCACTC 58.397 36.000 0.00 0.00 0.00 3.51
5613 6444 3.844211 TCTTTGCCCACTACCAACTATCT 59.156 43.478 0.00 0.00 0.00 1.98
5657 6497 4.601406 ATTAAAACAGCACCCCCTATCA 57.399 40.909 0.00 0.00 0.00 2.15
5660 6500 4.292836 ACCTAATTAAAACAGCACCCCCTA 59.707 41.667 0.00 0.00 0.00 3.53
5733 6813 5.683876 TCTAAATTCCAGCACTCTAGCTT 57.316 39.130 0.00 0.00 43.70 3.74
5766 6873 7.931407 AGTAATCGATGCCATAATCAACAACTA 59.069 33.333 0.00 0.00 0.00 2.24
5767 6874 6.767902 AGTAATCGATGCCATAATCAACAACT 59.232 34.615 0.00 0.00 0.00 3.16
5769 6876 7.416817 CAAGTAATCGATGCCATAATCAACAA 58.583 34.615 0.00 0.00 0.00 2.83
5772 6879 5.764686 AGCAAGTAATCGATGCCATAATCAA 59.235 36.000 0.00 0.00 40.93 2.57
5773 6880 5.179929 CAGCAAGTAATCGATGCCATAATCA 59.820 40.000 0.00 0.00 40.93 2.57
5774 6881 5.409520 TCAGCAAGTAATCGATGCCATAATC 59.590 40.000 0.00 0.00 40.93 1.75
5775 6882 5.308014 TCAGCAAGTAATCGATGCCATAAT 58.692 37.500 0.00 0.00 40.93 1.28
5790 6992 7.944729 ACTAAAACCATCATAATCAGCAAGT 57.055 32.000 0.00 0.00 0.00 3.16
5801 7003 7.014615 GCTCATTCCCAATACTAAAACCATCAT 59.985 37.037 0.00 0.00 0.00 2.45
5805 7007 5.575157 TGCTCATTCCCAATACTAAAACCA 58.425 37.500 0.00 0.00 0.00 3.67
5815 7017 4.960469 ACATGAATCTTGCTCATTCCCAAT 59.040 37.500 0.00 0.00 30.99 3.16
5859 7062 9.727627 CTTCTCTAAAAGCCATTTACATGAATC 57.272 33.333 0.00 0.00 31.07 2.52
5868 7071 6.950619 ACTCCATTCTTCTCTAAAAGCCATTT 59.049 34.615 0.00 0.00 34.92 2.32
6078 7348 1.275291 CCACCGCCTCTTTTCTACTGA 59.725 52.381 0.00 0.00 0.00 3.41
6092 7362 6.311445 CACATACAGAAGATATAATCCACCGC 59.689 42.308 0.00 0.00 0.00 5.68
6114 10141 6.201806 GCAATTATAACAAGCAACCAAACACA 59.798 34.615 0.00 0.00 0.00 3.72
6161 10210 4.671831 TCACAAAATCCCTCCATGCTAAA 58.328 39.130 0.00 0.00 0.00 1.85
6229 10279 3.638592 AATAACAGCCGCCGCCCTT 62.639 57.895 0.00 0.00 34.57 3.95


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

AutoCloner maintained by Alex Coulton.