Multiple sequence alignment - TraesCS4D01G295300

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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 TraesCS4D01G295300 chr4D 100.000 3043 0 0 1 3043 465353010 465349968 0.000000e+00 5620.0
1 TraesCS4D01G295300 chr4D 86.234 632 62 17 1415 2041 465161504 465160893 0.000000e+00 662.0
2 TraesCS4D01G295300 chr4D 92.987 385 27 0 1007 1391 465185724 465185340 2.050000e-156 562.0
3 TraesCS4D01G295300 chr4D 91.948 385 31 0 1007 1391 465161965 465161581 9.600000e-150 540.0
4 TraesCS4D01G295300 chr4D 86.965 491 45 13 1546 2034 465157833 465157360 4.470000e-148 534.0
5 TraesCS4D01G295300 chr4D 93.493 292 19 0 1754 2045 465183709 465183418 4.660000e-118 435.0
6 TraesCS4D01G295300 chr4D 83.984 487 23 24 2067 2537 465182962 465182515 1.690000e-112 416.0
7 TraesCS4D01G295300 chr4D 93.443 61 4 0 79 139 465352846 465352786 1.160000e-14 91.6
8 TraesCS4D01G295300 chr4D 93.443 61 4 0 165 225 465352932 465352872 1.160000e-14 91.6
9 TraesCS4D01G295300 chr4A 90.248 1692 94 30 714 2357 5121948 5123616 0.000000e+00 2145.0
10 TraesCS4D01G295300 chr4A 84.735 642 55 23 1411 2042 5200222 5200830 1.210000e-168 603.0
11 TraesCS4D01G295300 chr4A 92.839 391 28 0 1001 1391 5193110 5193500 4.400000e-158 568.0
12 TraesCS4D01G295300 chr4A 89.223 399 32 9 2643 3035 656755238 656754845 3.530000e-134 488.0
13 TraesCS4D01G295300 chr4A 96.063 127 5 0 2401 2527 5123620 5123746 1.110000e-49 207.0
14 TraesCS4D01G295300 chr4A 96.667 60 2 0 658 717 5120026 5120085 1.930000e-17 100.0
15 TraesCS4D01G295300 chr4B 89.274 951 41 28 1429 2357 582023202 582022291 0.000000e+00 1134.0
16 TraesCS4D01G295300 chr4B 92.967 782 38 8 622 1394 582024069 582023296 0.000000e+00 1123.0
17 TraesCS4D01G295300 chr4B 85.470 234 18 5 1415 1645 581955669 581955449 2.360000e-56 230.0
18 TraesCS4D01G295300 chr5A 95.341 558 13 5 67 623 485729238 485728693 0.000000e+00 874.0
19 TraesCS4D01G295300 chr5A 96.078 51 2 0 79 129 485729139 485729089 1.940000e-12 84.2
20 TraesCS4D01G295300 chr7A 94.014 568 19 5 67 632 709577011 709577565 0.000000e+00 846.0
21 TraesCS4D01G295300 chr7A 92.523 214 13 2 411 624 75606813 75607023 1.370000e-78 303.0
22 TraesCS4D01G295300 chr7A 92.523 214 13 2 411 624 75608116 75608326 1.370000e-78 303.0
23 TraesCS4D01G295300 chr7A 92.523 214 13 2 411 624 75609419 75609629 1.370000e-78 303.0
24 TraesCS4D01G295300 chr7A 92.093 215 14 2 411 625 75601605 75601816 1.770000e-77 300.0
25 TraesCS4D01G295300 chr7A 92.453 212 13 2 411 622 75610722 75610930 1.770000e-77 300.0
26 TraesCS4D01G295300 chr7A 92.268 194 15 0 222 415 43041144 43040951 2.990000e-70 276.0
27 TraesCS4D01G295300 chr7A 92.147 191 15 0 222 412 75597704 75597894 1.390000e-68 270.0
28 TraesCS4D01G295300 chr7A 91.803 61 5 0 165 225 709577024 709577084 5.410000e-13 86.1
29 TraesCS4D01G295300 chr7A 94.118 51 3 0 79 129 709577110 709577160 9.050000e-11 78.7
30 TraesCS4D01G295300 chr2A 92.969 512 24 4 114 625 69762971 69762472 0.000000e+00 736.0
31 TraesCS4D01G295300 chr3A 84.605 708 70 22 918 1600 569890772 569891465 0.000000e+00 667.0
32 TraesCS4D01G295300 chr3A 87.945 506 47 8 888 1391 570113937 570114430 4.370000e-163 584.0
33 TraesCS4D01G295300 chr3A 92.517 147 11 0 1454 1600 570114583 570114729 8.550000e-51 211.0
34 TraesCS4D01G295300 chr3D 90.239 461 32 8 933 1392 432513097 432513545 9.400000e-165 590.0
35 TraesCS4D01G295300 chr3D 93.750 144 9 0 1457 1600 432513641 432513784 1.840000e-52 217.0
36 TraesCS4D01G295300 chr3B 88.129 497 45 8 898 1392 564759046 564759530 2.030000e-161 579.0
37 TraesCS4D01G295300 chr3B 85.496 393 48 8 1726 2118 564759826 564760209 4.730000e-108 401.0
38 TraesCS4D01G295300 chr3B 93.377 151 9 1 1450 1600 564759615 564759764 3.950000e-54 222.0
39 TraesCS4D01G295300 chr1B 88.107 412 42 6 2637 3043 507550200 507549791 1.640000e-132 483.0
40 TraesCS4D01G295300 chr1B 85.759 323 31 10 2651 2961 170008528 170008209 8.130000e-86 327.0
41 TraesCS4D01G295300 chr1B 85.666 293 26 11 2651 2931 170007916 170008204 8.250000e-76 294.0
42 TraesCS4D01G295300 chrUn 92.093 215 14 2 411 625 338575481 338575692 1.770000e-77 300.0
43 TraesCS4D01G295300 chrUn 91.710 193 16 0 223 415 1184786 1184594 5.000000e-68 268.0
44 TraesCS4D01G295300 chr1D 93.194 191 12 1 222 412 468026389 468026578 2.310000e-71 279.0
45 TraesCS4D01G295300 chr6A 92.568 148 10 1 1454 1600 166114878 166115025 8.550000e-51 211.0
46 TraesCS4D01G295300 chr1A 76.210 248 38 13 2633 2863 531328342 531328585 8.920000e-21 111.0


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 TraesCS4D01G295300 chr4D 465349968 465353010 3042 True 1934.400000 5620 95.628667 1 3043 3 chr4D.!!$R3 3042
1 TraesCS4D01G295300 chr4D 465157360 465161965 4605 True 578.666667 662 88.382333 1007 2041 3 chr4D.!!$R1 1034
2 TraesCS4D01G295300 chr4D 465182515 465185724 3209 True 471.000000 562 90.154667 1007 2537 3 chr4D.!!$R2 1530
3 TraesCS4D01G295300 chr4A 5120026 5123746 3720 False 817.333333 2145 94.326000 658 2527 3 chr4A.!!$F3 1869
4 TraesCS4D01G295300 chr4A 5200222 5200830 608 False 603.000000 603 84.735000 1411 2042 1 chr4A.!!$F2 631
5 TraesCS4D01G295300 chr4B 582022291 582024069 1778 True 1128.500000 1134 91.120500 622 2357 2 chr4B.!!$R2 1735
6 TraesCS4D01G295300 chr5A 485728693 485729238 545 True 479.100000 874 95.709500 67 623 2 chr5A.!!$R1 556
7 TraesCS4D01G295300 chr7A 709577011 709577565 554 False 336.933333 846 93.311667 67 632 3 chr7A.!!$F3 565
8 TraesCS4D01G295300 chr7A 75606813 75610930 4117 False 302.250000 303 92.505500 411 624 4 chr7A.!!$F2 213
9 TraesCS4D01G295300 chr7A 75597704 75601816 4112 False 285.000000 300 92.120000 222 625 2 chr7A.!!$F1 403
10 TraesCS4D01G295300 chr3A 569890772 569891465 693 False 667.000000 667 84.605000 918 1600 1 chr3A.!!$F1 682
11 TraesCS4D01G295300 chr3A 570113937 570114729 792 False 397.500000 584 90.231000 888 1600 2 chr3A.!!$F2 712
12 TraesCS4D01G295300 chr3D 432513097 432513784 687 False 403.500000 590 91.994500 933 1600 2 chr3D.!!$F1 667
13 TraesCS4D01G295300 chr3B 564759046 564760209 1163 False 400.666667 579 89.000667 898 2118 3 chr3B.!!$F1 1220

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
966 6574 0.388134 GCTAACGACAAGCACGGAGA 60.388 55.0 0.0 0.0 39.83 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2621 13607 0.035458 AGCTCTCCGTTTCAAGGGTG 59.965 55.0 0.0 0.0 35.51 4.61 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
218 219 4.722361 ACCGTTAAACTGCCAAAAGAAA 57.278 36.364 0.00 0.00 0.00 2.52
310 311 7.024340 ACATGTTCTGAATATGATCACTTGC 57.976 36.000 27.05 0.00 34.51 4.01
492 4205 9.944376 AGATTTTTCTCTTGTACTAGCATGTAA 57.056 29.630 0.00 0.00 0.00 2.41
519 4232 7.092716 TCCTTGAGAAATTTGTACTACCGTAC 58.907 38.462 0.00 0.00 44.95 3.67
636 4350 4.514577 CCTGGCGGCTACGGACTG 62.515 72.222 11.43 0.00 41.36 3.51
653 4374 3.359654 GACTGGTGCACTTGTTTAAACG 58.640 45.455 17.98 3.03 0.00 3.60
695 4416 0.801251 GAAGCTAGCCAACTGCACAG 59.199 55.000 12.13 0.00 44.83 3.66
747 6335 8.870879 GTGCGTATATTCTTTCCATATAAGTCC 58.129 37.037 0.00 0.00 0.00 3.85
831 6428 6.471976 TCGCATACATGATTATTCAAGCTC 57.528 37.500 0.00 0.00 34.96 4.09
876 6477 3.384668 CTGATCGATGATAGTTTGCGGT 58.615 45.455 0.54 0.00 0.00 5.68
877 6478 3.792401 TGATCGATGATAGTTTGCGGTT 58.208 40.909 0.54 0.00 0.00 4.44
878 6479 3.555547 TGATCGATGATAGTTTGCGGTTG 59.444 43.478 0.54 0.00 0.00 3.77
879 6480 1.663643 TCGATGATAGTTTGCGGTTGC 59.336 47.619 0.00 0.00 43.20 4.17
924 6525 2.479837 TCATAAATCTAACAGCGCCCG 58.520 47.619 2.29 0.00 0.00 6.13
965 6573 0.388649 AGCTAACGACAAGCACGGAG 60.389 55.000 10.17 0.00 42.62 4.63
966 6574 0.388134 GCTAACGACAAGCACGGAGA 60.388 55.000 0.00 0.00 39.83 3.71
994 6603 3.587933 GTCGCAAAACCCCACGCA 61.588 61.111 0.00 0.00 0.00 5.24
1226 6835 1.897225 CTGCTGGACCTCCTGGAGTG 61.897 65.000 21.70 15.18 44.43 3.51
1394 7010 0.110373 GTGCTTGAAAAGGTACGCCG 60.110 55.000 0.00 0.00 46.35 6.46
1413 7101 1.320555 CGTCGAATCTGCAAAGGTACG 59.679 52.381 0.00 0.00 0.00 3.67
1518 8492 3.198872 GGAGTTTAAGCCTCAAGATCCG 58.801 50.000 6.57 0.00 0.00 4.18
1690 8674 3.072330 TGGGAAGCTGTACACTGATTGAA 59.928 43.478 0.00 0.00 0.00 2.69
1818 8811 0.528470 GTTCGTGGAGGACCTGAGAG 59.472 60.000 0.00 0.00 37.04 3.20
1964 12497 2.818274 AAGGAAATCGACGGCGCC 60.818 61.111 19.07 19.07 37.46 6.53
2034 12567 1.002142 CCGACATCGCCGTCAAGTATA 60.002 52.381 0.00 0.00 35.54 1.47
2057 12590 0.177836 CCTGACGATATGGTGTGGCA 59.822 55.000 0.00 0.00 0.00 4.92
2105 13075 6.942976 TCTTTACCTTTGATGATACGGTCTT 58.057 36.000 0.00 0.00 0.00 3.01
2148 13118 0.823460 TGTCAGTGCTGTCTGTGTCA 59.177 50.000 0.00 0.00 36.85 3.58
2149 13119 1.202452 TGTCAGTGCTGTCTGTGTCAG 60.202 52.381 0.00 0.00 36.85 3.51
2151 13121 1.067669 TCAGTGCTGTCTGTGTCAGTC 59.932 52.381 0.00 0.00 36.85 3.51
2164 13134 2.295349 GTGTCAGTCTCCGACCTTTGTA 59.705 50.000 0.00 0.00 32.18 2.41
2165 13135 2.557056 TGTCAGTCTCCGACCTTTGTAG 59.443 50.000 0.00 0.00 32.18 2.74
2166 13136 2.557490 GTCAGTCTCCGACCTTTGTAGT 59.443 50.000 0.00 0.00 32.18 2.73
2167 13137 3.755378 GTCAGTCTCCGACCTTTGTAGTA 59.245 47.826 0.00 0.00 32.18 1.82
2168 13138 3.755378 TCAGTCTCCGACCTTTGTAGTAC 59.245 47.826 0.00 0.00 32.18 2.73
2169 13139 3.504906 CAGTCTCCGACCTTTGTAGTACA 59.495 47.826 0.00 0.00 32.18 2.90
2170 13140 3.757493 AGTCTCCGACCTTTGTAGTACAG 59.243 47.826 2.68 0.00 32.18 2.74
2173 13145 4.697352 TCTCCGACCTTTGTAGTACAGTAC 59.303 45.833 2.05 2.05 0.00 2.73
2196 13168 7.038154 ACTGATCTATCTACTGCTCTTGTTC 57.962 40.000 0.00 0.00 0.00 3.18
2197 13169 6.605194 ACTGATCTATCTACTGCTCTTGTTCA 59.395 38.462 0.00 0.00 0.00 3.18
2198 13170 7.287466 ACTGATCTATCTACTGCTCTTGTTCAT 59.713 37.037 0.00 0.00 0.00 2.57
2199 13171 7.432059 TGATCTATCTACTGCTCTTGTTCATG 58.568 38.462 0.00 0.00 0.00 3.07
2200 13172 6.154203 TCTATCTACTGCTCTTGTTCATGG 57.846 41.667 0.00 0.00 0.00 3.66
2201 13173 4.833478 ATCTACTGCTCTTGTTCATGGT 57.167 40.909 0.00 0.00 0.00 3.55
2263 13249 6.642707 TTTGTTGTCGATTGGATAGGTTTT 57.357 33.333 0.00 0.00 0.00 2.43
2264 13250 5.621197 TGTTGTCGATTGGATAGGTTTTG 57.379 39.130 0.00 0.00 0.00 2.44
2265 13251 5.309638 TGTTGTCGATTGGATAGGTTTTGA 58.690 37.500 0.00 0.00 0.00 2.69
2271 13257 6.747280 GTCGATTGGATAGGTTTTGAATGTTG 59.253 38.462 0.00 0.00 0.00 3.33
2306 13292 4.732285 TCGCACTCAATTTCAGAAAGAC 57.268 40.909 1.28 0.00 0.00 3.01
2381 13367 2.271944 GGTGAGCACCTACTGGTTTT 57.728 50.000 12.30 0.00 46.05 2.43
2382 13368 2.583143 GGTGAGCACCTACTGGTTTTT 58.417 47.619 12.30 0.00 46.05 1.94
2479 13465 1.501604 AGGGGAGGGAGAGATACAGAC 59.498 57.143 0.00 0.00 0.00 3.51
2509 13495 5.221742 GGGGAAATGGTCTAGTTCTATCTGG 60.222 48.000 0.00 0.00 33.99 3.86
2527 13513 4.560128 TCTGGAAACTCGACATTCTTCAG 58.440 43.478 5.65 5.76 0.00 3.02
2531 13517 0.108615 ACTCGACATTCTTCAGGCCG 60.109 55.000 0.00 0.00 0.00 6.13
2533 13519 0.108804 TCGACATTCTTCAGGCCGTC 60.109 55.000 0.00 0.00 0.00 4.79
2537 13523 1.347707 ACATTCTTCAGGCCGTCTTCA 59.652 47.619 0.00 0.00 0.00 3.02
2538 13524 1.734465 CATTCTTCAGGCCGTCTTCAC 59.266 52.381 0.00 0.00 0.00 3.18
2539 13525 0.319555 TTCTTCAGGCCGTCTTCACG 60.320 55.000 0.00 0.00 46.29 4.35
2540 13526 2.357034 TTCAGGCCGTCTTCACGC 60.357 61.111 0.00 0.00 45.29 5.34
2541 13527 3.876589 TTCAGGCCGTCTTCACGCC 62.877 63.158 0.00 0.00 45.29 5.68
2542 13528 4.680237 CAGGCCGTCTTCACGCCA 62.680 66.667 0.00 0.00 45.29 5.69
2543 13529 3.706373 AGGCCGTCTTCACGCCAT 61.706 61.111 0.00 0.00 45.29 4.40
2544 13530 3.195698 GGCCGTCTTCACGCCATC 61.196 66.667 0.00 0.00 45.29 3.51
2545 13531 2.125512 GCCGTCTTCACGCCATCT 60.126 61.111 0.00 0.00 45.29 2.90
2546 13532 1.741770 GCCGTCTTCACGCCATCTT 60.742 57.895 0.00 0.00 45.29 2.40
2547 13533 1.696832 GCCGTCTTCACGCCATCTTC 61.697 60.000 0.00 0.00 45.29 2.87
2548 13534 0.108615 CCGTCTTCACGCCATCTTCT 60.109 55.000 0.00 0.00 45.29 2.85
2549 13535 0.994995 CGTCTTCACGCCATCTTCTG 59.005 55.000 0.00 0.00 39.69 3.02
2550 13536 1.670087 CGTCTTCACGCCATCTTCTGT 60.670 52.381 0.00 0.00 39.69 3.41
2551 13537 1.996191 GTCTTCACGCCATCTTCTGTC 59.004 52.381 0.00 0.00 0.00 3.51
2552 13538 1.895798 TCTTCACGCCATCTTCTGTCT 59.104 47.619 0.00 0.00 0.00 3.41
2553 13539 1.998315 CTTCACGCCATCTTCTGTCTG 59.002 52.381 0.00 0.00 0.00 3.51
2554 13540 0.247460 TCACGCCATCTTCTGTCTGG 59.753 55.000 0.00 0.00 0.00 3.86
2555 13541 0.742281 CACGCCATCTTCTGTCTGGG 60.742 60.000 0.00 0.00 0.00 4.45
2556 13542 1.817099 CGCCATCTTCTGTCTGGGC 60.817 63.158 0.00 0.00 38.04 5.36
2557 13543 1.452833 GCCATCTTCTGTCTGGGCC 60.453 63.158 0.00 0.00 35.42 5.80
2558 13544 1.919600 GCCATCTTCTGTCTGGGCCT 61.920 60.000 4.53 0.00 35.42 5.19
2559 13545 0.179936 CCATCTTCTGTCTGGGCCTC 59.820 60.000 4.53 0.00 0.00 4.70
2560 13546 0.179936 CATCTTCTGTCTGGGCCTCC 59.820 60.000 4.53 0.00 0.00 4.30
2561 13547 0.252881 ATCTTCTGTCTGGGCCTCCA 60.253 55.000 4.53 0.00 41.58 3.86
2569 13555 4.480480 TGGGCCTCCAGTTCCTAG 57.520 61.111 4.53 0.00 38.32 3.02
2570 13556 1.306997 TGGGCCTCCAGTTCCTAGG 60.307 63.158 4.53 0.82 38.32 3.02
2571 13557 1.307084 GGGCCTCCAGTTCCTAGGT 60.307 63.158 9.08 0.00 32.67 3.08
2572 13558 1.338890 GGGCCTCCAGTTCCTAGGTC 61.339 65.000 9.08 3.65 34.11 3.85
2573 13559 0.325765 GGCCTCCAGTTCCTAGGTCT 60.326 60.000 9.08 6.06 32.07 3.85
2574 13560 0.827368 GCCTCCAGTTCCTAGGTCTG 59.173 60.000 21.28 21.28 32.67 3.51
2575 13561 1.490574 CCTCCAGTTCCTAGGTCTGG 58.509 60.000 31.26 31.26 46.94 3.86
2576 13562 0.827368 CTCCAGTTCCTAGGTCTGGC 59.173 60.000 31.79 13.53 45.67 4.85
2577 13563 0.970937 TCCAGTTCCTAGGTCTGGCG 60.971 60.000 31.79 19.62 45.67 5.69
2578 13564 1.153549 CAGTTCCTAGGTCTGGCGC 60.154 63.158 20.81 0.00 0.00 6.53
2579 13565 2.187163 GTTCCTAGGTCTGGCGCC 59.813 66.667 22.73 22.73 0.00 6.53
2580 13566 2.038975 TTCCTAGGTCTGGCGCCT 59.961 61.111 29.70 9.54 40.00 5.52
2581 13567 1.612442 TTCCTAGGTCTGGCGCCTT 60.612 57.895 29.70 10.42 37.54 4.35
2582 13568 1.899437 TTCCTAGGTCTGGCGCCTTG 61.899 60.000 29.70 20.24 37.54 3.61
2583 13569 2.187946 CTAGGTCTGGCGCCTTGG 59.812 66.667 29.70 17.48 37.54 3.61
2584 13570 3.391665 CTAGGTCTGGCGCCTTGGG 62.392 68.421 29.70 14.88 37.54 4.12
2598 13584 3.731547 TGGGCTGATGTCCAGGAG 58.268 61.111 0.00 0.00 44.07 3.69
2599 13585 1.229625 TGGGCTGATGTCCAGGAGT 60.230 57.895 0.00 0.00 44.07 3.85
2600 13586 1.222936 GGGCTGATGTCCAGGAGTG 59.777 63.158 0.00 0.00 43.13 3.51
2601 13587 1.222936 GGCTGATGTCCAGGAGTGG 59.777 63.158 0.00 0.00 46.63 4.00
2602 13588 1.222936 GCTGATGTCCAGGAGTGGG 59.777 63.158 0.00 0.00 45.11 4.61
2607 13593 3.721706 GTCCAGGAGTGGGCCAGG 61.722 72.222 6.40 3.96 43.45 4.45
2608 13594 4.270153 TCCAGGAGTGGGCCAGGT 62.270 66.667 6.40 0.00 45.11 4.00
2609 13595 3.721706 CCAGGAGTGGGCCAGGTC 61.722 72.222 6.40 6.91 40.67 3.85
2610 13596 2.930019 CAGGAGTGGGCCAGGTCA 60.930 66.667 6.40 0.00 0.00 4.02
2611 13597 2.125912 AGGAGTGGGCCAGGTCAT 59.874 61.111 6.40 0.79 0.00 3.06
2612 13598 2.273449 GGAGTGGGCCAGGTCATG 59.727 66.667 6.40 0.00 0.00 3.07
2613 13599 2.300967 GGAGTGGGCCAGGTCATGA 61.301 63.158 6.40 0.00 0.00 3.07
2614 13600 1.078143 GAGTGGGCCAGGTCATGAC 60.078 63.158 17.91 17.91 0.00 3.06
2615 13601 1.841302 GAGTGGGCCAGGTCATGACA 61.841 60.000 26.47 1.84 0.00 3.58
2616 13602 1.675641 GTGGGCCAGGTCATGACAC 60.676 63.158 26.47 15.79 0.00 3.67
2617 13603 1.847506 TGGGCCAGGTCATGACACT 60.848 57.895 26.47 17.67 0.00 3.55
2618 13604 1.078143 GGGCCAGGTCATGACACTC 60.078 63.158 26.47 10.13 0.00 3.51
2619 13605 1.448540 GGCCAGGTCATGACACTCG 60.449 63.158 26.47 14.58 0.00 4.18
2620 13606 2.103042 GCCAGGTCATGACACTCGC 61.103 63.158 26.47 19.62 0.00 5.03
2621 13607 1.448540 CCAGGTCATGACACTCGCC 60.449 63.158 26.47 8.88 0.00 5.54
2622 13608 1.293179 CAGGTCATGACACTCGCCA 59.707 57.895 26.47 0.00 0.00 5.69
2623 13609 1.016130 CAGGTCATGACACTCGCCAC 61.016 60.000 26.47 7.23 0.00 5.01
2624 13610 1.741770 GGTCATGACACTCGCCACC 60.742 63.158 26.47 3.39 0.00 4.61
2625 13611 1.741770 GTCATGACACTCGCCACCC 60.742 63.158 21.07 0.00 0.00 4.61
2626 13612 1.913262 TCATGACACTCGCCACCCT 60.913 57.895 0.00 0.00 0.00 4.34
2627 13613 1.003355 CATGACACTCGCCACCCTT 60.003 57.895 0.00 0.00 0.00 3.95
2628 13614 1.003355 ATGACACTCGCCACCCTTG 60.003 57.895 0.00 0.00 0.00 3.61
2629 13615 1.480212 ATGACACTCGCCACCCTTGA 61.480 55.000 0.00 0.00 0.00 3.02
2630 13616 1.070786 GACACTCGCCACCCTTGAA 59.929 57.895 0.00 0.00 0.00 2.69
2631 13617 0.534203 GACACTCGCCACCCTTGAAA 60.534 55.000 0.00 0.00 0.00 2.69
2632 13618 0.818040 ACACTCGCCACCCTTGAAAC 60.818 55.000 0.00 0.00 0.00 2.78
2633 13619 1.597027 ACTCGCCACCCTTGAAACG 60.597 57.895 0.00 0.00 0.00 3.60
2634 13620 2.281208 TCGCCACCCTTGAAACGG 60.281 61.111 0.00 0.00 0.00 4.44
2635 13621 2.281208 CGCCACCCTTGAAACGGA 60.281 61.111 0.00 0.00 0.00 4.69
2636 13622 2.325082 CGCCACCCTTGAAACGGAG 61.325 63.158 0.00 0.00 0.00 4.63
2637 13623 1.072505 GCCACCCTTGAAACGGAGA 59.927 57.895 0.00 0.00 0.00 3.71
2638 13624 0.955919 GCCACCCTTGAAACGGAGAG 60.956 60.000 0.00 0.00 0.00 3.20
2639 13625 0.955919 CCACCCTTGAAACGGAGAGC 60.956 60.000 0.00 0.00 0.00 4.09
2640 13626 0.035458 CACCCTTGAAACGGAGAGCT 59.965 55.000 0.00 0.00 0.00 4.09
2641 13627 0.321996 ACCCTTGAAACGGAGAGCTC 59.678 55.000 5.27 5.27 0.00 4.09
2642 13628 0.391793 CCCTTGAAACGGAGAGCTCC 60.392 60.000 10.93 6.46 46.18 4.70
2650 13636 2.809010 GGAGAGCTCCTGTACGGC 59.191 66.667 10.93 0.00 46.16 5.68
2651 13637 2.409651 GAGAGCTCCTGTACGGCG 59.590 66.667 10.93 4.80 0.00 6.46
2652 13638 3.759766 GAGAGCTCCTGTACGGCGC 62.760 68.421 10.93 0.00 43.98 6.53
2653 13639 4.874977 GAGCTCCTGTACGGCGCC 62.875 72.222 19.07 19.07 44.75 6.53
2656 13642 4.208686 CTCCTGTACGGCGCCCTC 62.209 72.222 23.46 12.06 0.00 4.30
2657 13643 4.753662 TCCTGTACGGCGCCCTCT 62.754 66.667 23.46 5.94 0.00 3.69
2658 13644 4.514577 CCTGTACGGCGCCCTCTG 62.515 72.222 23.46 9.53 0.00 3.35
2669 13655 4.785453 CCCTCTGCGCCCTGGAAC 62.785 72.222 4.18 0.00 0.00 3.62
2671 13657 4.069232 CTCTGCGCCCTGGAACGA 62.069 66.667 4.18 0.00 0.00 3.85
2672 13658 3.589654 CTCTGCGCCCTGGAACGAA 62.590 63.158 4.18 1.81 0.00 3.85
2673 13659 3.423154 CTGCGCCCTGGAACGAAC 61.423 66.667 4.18 0.00 0.00 3.95
2674 13660 3.883744 CTGCGCCCTGGAACGAACT 62.884 63.158 4.18 0.00 0.00 3.01
2675 13661 3.423154 GCGCCCTGGAACGAACTG 61.423 66.667 12.38 0.00 0.00 3.16
2676 13662 2.742372 CGCCCTGGAACGAACTGG 60.742 66.667 0.00 0.00 0.00 4.00
2677 13663 3.056328 GCCCTGGAACGAACTGGC 61.056 66.667 0.00 0.00 0.00 4.85
2678 13664 2.742372 CCCTGGAACGAACTGGCG 60.742 66.667 0.00 0.00 37.29 5.69
2679 13665 3.423154 CCTGGAACGAACTGGCGC 61.423 66.667 0.00 0.00 33.86 6.53
2680 13666 2.357517 CTGGAACGAACTGGCGCT 60.358 61.111 7.64 0.00 33.86 5.92
2681 13667 2.357034 TGGAACGAACTGGCGCTC 60.357 61.111 7.64 0.00 33.86 5.03
2682 13668 2.357034 GGAACGAACTGGCGCTCA 60.357 61.111 7.64 2.39 33.86 4.26
2683 13669 2.668280 GGAACGAACTGGCGCTCAC 61.668 63.158 7.64 0.00 33.86 3.51
2684 13670 3.000080 GAACGAACTGGCGCTCACG 62.000 63.158 7.64 9.26 44.07 4.35
2726 13712 3.828885 GCAACGCGCTTTTCTTCC 58.171 55.556 5.73 0.00 37.77 3.46
2727 13713 1.282875 GCAACGCGCTTTTCTTCCT 59.717 52.632 5.73 0.00 37.77 3.36
2728 13714 0.726118 GCAACGCGCTTTTCTTCCTC 60.726 55.000 5.73 0.00 37.77 3.71
2729 13715 0.110192 CAACGCGCTTTTCTTCCTCC 60.110 55.000 5.73 0.00 0.00 4.30
2730 13716 1.566018 AACGCGCTTTTCTTCCTCCG 61.566 55.000 5.73 0.00 0.00 4.63
2731 13717 2.027625 CGCGCTTTTCTTCCTCCGT 61.028 57.895 5.56 0.00 0.00 4.69
2732 13718 1.566018 CGCGCTTTTCTTCCTCCGTT 61.566 55.000 5.56 0.00 0.00 4.44
2733 13719 0.110192 GCGCTTTTCTTCCTCCGTTG 60.110 55.000 0.00 0.00 0.00 4.10
2734 13720 0.517316 CGCTTTTCTTCCTCCGTTGG 59.483 55.000 0.00 0.00 0.00 3.77
2735 13721 0.881796 GCTTTTCTTCCTCCGTTGGG 59.118 55.000 0.00 0.00 0.00 4.12
2736 13722 1.818131 GCTTTTCTTCCTCCGTTGGGT 60.818 52.381 0.00 0.00 33.83 4.51
2737 13723 2.583143 CTTTTCTTCCTCCGTTGGGTT 58.417 47.619 0.00 0.00 33.83 4.11
2738 13724 2.265589 TTTCTTCCTCCGTTGGGTTC 57.734 50.000 0.00 0.00 33.83 3.62
2739 13725 0.399075 TTCTTCCTCCGTTGGGTTCC 59.601 55.000 0.00 0.00 33.83 3.62
2740 13726 0.765135 TCTTCCTCCGTTGGGTTCCA 60.765 55.000 0.00 0.00 33.83 3.53
2741 13727 0.321653 CTTCCTCCGTTGGGTTCCAG 60.322 60.000 0.00 0.00 33.81 3.86
2742 13728 1.057851 TTCCTCCGTTGGGTTCCAGT 61.058 55.000 0.00 0.00 33.81 4.00
2743 13729 1.057851 TCCTCCGTTGGGTTCCAGTT 61.058 55.000 0.00 0.00 33.81 3.16
2744 13730 0.889186 CCTCCGTTGGGTTCCAGTTG 60.889 60.000 0.00 0.00 33.81 3.16
2745 13731 1.515521 CTCCGTTGGGTTCCAGTTGC 61.516 60.000 0.00 0.00 33.81 4.17
2746 13732 1.826054 CCGTTGGGTTCCAGTTGCA 60.826 57.895 0.00 0.00 33.81 4.08
2747 13733 1.358759 CGTTGGGTTCCAGTTGCAC 59.641 57.895 0.00 0.00 33.81 4.57
2748 13734 1.358759 GTTGGGTTCCAGTTGCACG 59.641 57.895 0.00 0.00 33.81 5.34
2749 13735 2.485795 TTGGGTTCCAGTTGCACGC 61.486 57.895 0.00 0.00 33.81 5.34
2750 13736 3.670377 GGGTTCCAGTTGCACGCC 61.670 66.667 0.00 0.00 0.00 5.68
2751 13737 3.670377 GGTTCCAGTTGCACGCCC 61.670 66.667 0.00 0.00 0.00 6.13
2752 13738 4.025401 GTTCCAGTTGCACGCCCG 62.025 66.667 0.00 0.00 0.00 6.13
2777 13763 3.127533 GCTCGCTCGGCCACATTT 61.128 61.111 2.24 0.00 0.00 2.32
2778 13764 2.690778 GCTCGCTCGGCCACATTTT 61.691 57.895 2.24 0.00 0.00 1.82
2779 13765 1.875963 CTCGCTCGGCCACATTTTT 59.124 52.632 2.24 0.00 0.00 1.94
2802 13788 6.804534 TTTTCTCGTATTTGTTTGCAGTTG 57.195 33.333 0.00 0.00 0.00 3.16
2803 13789 4.481930 TCTCGTATTTGTTTGCAGTTGG 57.518 40.909 0.00 0.00 0.00 3.77
2804 13790 2.979813 CTCGTATTTGTTTGCAGTTGGC 59.020 45.455 0.00 0.00 45.13 4.52
2805 13791 2.058057 CGTATTTGTTTGCAGTTGGCC 58.942 47.619 0.00 0.00 43.89 5.36
2806 13792 2.288152 CGTATTTGTTTGCAGTTGGCCT 60.288 45.455 3.32 0.00 43.89 5.19
2807 13793 2.243602 ATTTGTTTGCAGTTGGCCTG 57.756 45.000 3.32 0.00 43.89 4.85
2808 13794 0.177604 TTTGTTTGCAGTTGGCCTGG 59.822 50.000 3.32 0.00 43.89 4.45
2809 13795 0.975040 TTGTTTGCAGTTGGCCTGGT 60.975 50.000 3.32 0.00 43.89 4.00
2810 13796 1.363807 GTTTGCAGTTGGCCTGGTC 59.636 57.895 3.32 0.00 43.89 4.02
2811 13797 2.192861 TTTGCAGTTGGCCTGGTCG 61.193 57.895 3.32 0.00 43.89 4.79
2812 13798 2.616797 TTTGCAGTTGGCCTGGTCGA 62.617 55.000 3.32 0.00 43.89 4.20
2813 13799 2.281484 GCAGTTGGCCTGGTCGAA 60.281 61.111 3.32 0.00 41.81 3.71
2814 13800 1.896660 GCAGTTGGCCTGGTCGAAA 60.897 57.895 3.32 0.00 41.81 3.46
2815 13801 1.452145 GCAGTTGGCCTGGTCGAAAA 61.452 55.000 3.32 0.00 41.81 2.29
2816 13802 1.028905 CAGTTGGCCTGGTCGAAAAA 58.971 50.000 3.32 0.00 37.54 1.94
2865 13851 9.617523 ATGGAAAATTGTGAAATCAGAAAAGTT 57.382 25.926 0.00 0.00 32.73 2.66
2866 13852 9.097257 TGGAAAATTGTGAAATCAGAAAAGTTC 57.903 29.630 0.00 2.48 32.73 3.01
2867 13853 9.097257 GGAAAATTGTGAAATCAGAAAAGTTCA 57.903 29.630 0.00 0.00 32.73 3.18
2870 13856 8.822652 AATTGTGAAATCAGAAAAGTTCATCC 57.177 30.769 0.00 0.00 32.73 3.51
2871 13857 6.957920 TGTGAAATCAGAAAAGTTCATCCA 57.042 33.333 0.00 0.00 32.93 3.41
2872 13858 7.528996 TGTGAAATCAGAAAAGTTCATCCAT 57.471 32.000 0.00 0.00 32.93 3.41
2873 13859 7.954835 TGTGAAATCAGAAAAGTTCATCCATT 58.045 30.769 0.00 0.00 32.93 3.16
2874 13860 8.423349 TGTGAAATCAGAAAAGTTCATCCATTT 58.577 29.630 0.00 0.00 32.93 2.32
2875 13861 8.706035 GTGAAATCAGAAAAGTTCATCCATTTG 58.294 33.333 0.00 0.00 32.93 2.32
2876 13862 7.385752 TGAAATCAGAAAAGTTCATCCATTTGC 59.614 33.333 0.00 0.00 0.00 3.68
2877 13863 5.787953 TCAGAAAAGTTCATCCATTTGCA 57.212 34.783 0.00 0.00 0.00 4.08
2878 13864 5.775686 TCAGAAAAGTTCATCCATTTGCAG 58.224 37.500 0.00 0.00 0.00 4.41
2879 13865 5.535783 TCAGAAAAGTTCATCCATTTGCAGA 59.464 36.000 0.00 0.00 0.00 4.26
2880 13866 6.040729 TCAGAAAAGTTCATCCATTTGCAGAA 59.959 34.615 0.00 0.00 0.00 3.02
2881 13867 6.702723 CAGAAAAGTTCATCCATTTGCAGAAA 59.297 34.615 0.00 0.00 0.00 2.52
2882 13868 7.225145 CAGAAAAGTTCATCCATTTGCAGAAAA 59.775 33.333 0.00 0.00 0.00 2.29
2883 13869 7.769970 AGAAAAGTTCATCCATTTGCAGAAAAA 59.230 29.630 0.00 0.00 0.00 1.94
2953 13939 8.926715 AATGTAAAAACTGAGAAAAGTTCACC 57.073 30.769 0.00 0.00 39.48 4.02
2954 13940 7.455641 TGTAAAAACTGAGAAAAGTTCACCA 57.544 32.000 0.00 0.00 39.48 4.17
2955 13941 7.887381 TGTAAAAACTGAGAAAAGTTCACCAA 58.113 30.769 0.00 0.00 39.48 3.67
2956 13942 8.361139 TGTAAAAACTGAGAAAAGTTCACCAAA 58.639 29.630 0.00 0.00 39.48 3.28
2957 13943 9.198837 GTAAAAACTGAGAAAAGTTCACCAAAA 57.801 29.630 0.00 0.00 39.48 2.44
2958 13944 8.846943 AAAAACTGAGAAAAGTTCACCAAAAT 57.153 26.923 0.00 0.00 39.48 1.82
2959 13945 8.846943 AAAACTGAGAAAAGTTCACCAAAATT 57.153 26.923 0.00 0.00 39.48 1.82
2960 13946 7.832503 AACTGAGAAAAGTTCACCAAAATTG 57.167 32.000 0.00 0.00 35.44 2.32
2961 13947 6.818142 AACTGAGAAAAGTTCACCAAAATTGG 59.182 34.615 10.61 10.61 44.22 3.16
2962 13948 7.310361 AACTGAGAAAAGTTCACCAAAATTGGA 60.310 33.333 18.71 0.00 42.61 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 219 6.744056 GCCCAATCATTAAAACCCTCACTTTT 60.744 38.462 0.00 0.00 0.00 2.27
310 311 3.302480 GCAACCGTAGACGCAAATCATAG 60.302 47.826 0.00 0.00 38.18 2.23
416 4129 7.338449 TCTTTTACTCTTTTAGCCAAAGTGTGT 59.662 33.333 17.69 12.02 44.97 3.72
482 4195 9.512435 CAAATTTCTCAAGGAATTACATGCTAG 57.488 33.333 0.00 0.00 33.53 3.42
492 4205 7.166167 ACGGTAGTACAAATTTCTCAAGGAAT 58.834 34.615 2.06 0.00 33.53 3.01
636 4350 2.356695 ACTCCGTTTAAACAAGTGCACC 59.643 45.455 14.63 0.00 0.00 5.01
653 4374 0.034616 AGTTGCTCAGCACTCACTCC 59.965 55.000 0.00 0.00 38.71 3.85
809 6397 6.232139 TGAGCTTGAATAATCATGTATGCG 57.768 37.500 0.00 0.00 34.96 4.73
831 6428 0.031314 ATCACGTGCTAGCGAGGATG 59.969 55.000 11.67 6.01 36.17 3.51
879 6480 3.127533 CTTGAAGCTTCGGGCCCG 61.128 66.667 39.13 39.13 43.05 6.13
880 6481 1.746991 CTCTTGAAGCTTCGGGCCC 60.747 63.158 21.11 13.57 43.05 5.80
881 6482 3.896479 CTCTTGAAGCTTCGGGCC 58.104 61.111 21.11 0.00 43.05 5.80
924 6525 1.087501 GGCTCCGATGTCAAAACCTC 58.912 55.000 0.00 0.00 0.00 3.85
965 6573 4.035684 GGTTTTGCGACTGTTTCTCTTTC 58.964 43.478 0.00 0.00 0.00 2.62
966 6574 3.181490 GGGTTTTGCGACTGTTTCTCTTT 60.181 43.478 0.00 0.00 0.00 2.52
994 6603 1.524002 CCTCCATCTCCATGTGCGT 59.476 57.895 0.00 0.00 0.00 5.24
1341 6950 1.077501 CCTGTGGTCCGGCATGAAT 60.078 57.895 0.00 0.00 0.00 2.57
1394 7010 1.060698 GCGTACCTTTGCAGATTCGAC 59.939 52.381 0.00 0.00 0.00 4.20
1431 8385 5.358442 AGATCGAGCAAACACTCAGTAGTAT 59.642 40.000 2.38 0.00 36.42 2.12
1441 8395 5.560378 CGAACTTTTTAGATCGAGCAAACAC 59.440 40.000 2.38 0.00 36.42 3.32
1518 8492 0.107459 CAGTAGGAAGCTTGCCCTCC 60.107 60.000 15.04 3.53 34.11 4.30
1818 8811 2.398554 CCGTGTATGGTGGCTGCAC 61.399 63.158 0.50 0.00 0.00 4.57
1964 12497 1.206578 GAACAACGCCATGTGGTCG 59.793 57.895 12.19 12.19 31.82 4.79
2034 12567 1.327690 ACACCATATCGTCAGGCGGT 61.328 55.000 0.00 0.00 41.72 5.68
2105 13075 2.297315 TCACAAATTAATGCCGGCAACA 59.703 40.909 36.33 21.70 0.00 3.33
2151 13121 4.699257 AGTACTGTACTACAAAGGTCGGAG 59.301 45.833 18.42 0.00 37.23 4.63
2164 13134 7.741785 AGCAGTAGATAGATCAGTACTGTACT 58.258 38.462 21.99 21.37 42.87 2.73
2165 13135 7.876068 AGAGCAGTAGATAGATCAGTACTGTAC 59.124 40.741 21.99 14.48 42.87 2.90
2166 13136 7.969004 AGAGCAGTAGATAGATCAGTACTGTA 58.031 38.462 21.99 8.35 42.87 2.74
2167 13137 6.837312 AGAGCAGTAGATAGATCAGTACTGT 58.163 40.000 21.99 9.95 42.87 3.55
2168 13138 7.228507 ACAAGAGCAGTAGATAGATCAGTACTG 59.771 40.741 17.17 17.17 43.49 2.74
2169 13139 7.287061 ACAAGAGCAGTAGATAGATCAGTACT 58.713 38.462 0.00 0.00 0.00 2.73
2170 13140 7.504924 ACAAGAGCAGTAGATAGATCAGTAC 57.495 40.000 0.00 0.00 0.00 2.73
2173 13145 7.036996 TGAACAAGAGCAGTAGATAGATCAG 57.963 40.000 0.00 0.00 0.00 2.90
2196 13168 1.703411 AGGGACAAAACACCACCATG 58.297 50.000 0.00 0.00 0.00 3.66
2197 13169 2.470057 AAGGGACAAAACACCACCAT 57.530 45.000 0.00 0.00 0.00 3.55
2198 13170 2.104170 GAAAGGGACAAAACACCACCA 58.896 47.619 0.00 0.00 0.00 4.17
2199 13171 2.104170 TGAAAGGGACAAAACACCACC 58.896 47.619 0.00 0.00 0.00 4.61
2200 13172 4.400529 AATGAAAGGGACAAAACACCAC 57.599 40.909 0.00 0.00 0.00 4.16
2201 13173 5.600484 ACATAATGAAAGGGACAAAACACCA 59.400 36.000 0.00 0.00 0.00 4.17
2254 13240 4.394920 TCTCGGCAACATTCAAAACCTATC 59.605 41.667 0.00 0.00 0.00 2.08
2255 13241 4.156008 GTCTCGGCAACATTCAAAACCTAT 59.844 41.667 0.00 0.00 0.00 2.57
2256 13242 3.500680 GTCTCGGCAACATTCAAAACCTA 59.499 43.478 0.00 0.00 0.00 3.08
2257 13243 2.293399 GTCTCGGCAACATTCAAAACCT 59.707 45.455 0.00 0.00 0.00 3.50
2259 13245 3.626028 AGTCTCGGCAACATTCAAAAC 57.374 42.857 0.00 0.00 0.00 2.43
2263 13249 5.462068 CGATATAAAGTCTCGGCAACATTCA 59.538 40.000 0.00 0.00 0.00 2.57
2264 13250 5.612709 GCGATATAAAGTCTCGGCAACATTC 60.613 44.000 0.00 0.00 33.17 2.67
2265 13251 4.211374 GCGATATAAAGTCTCGGCAACATT 59.789 41.667 0.00 0.00 33.17 2.71
2271 13257 2.981140 GAGTGCGATATAAAGTCTCGGC 59.019 50.000 0.00 0.00 33.17 5.54
2395 13381 6.326229 GTGCATCACAACAACCAGTAGGTG 62.326 50.000 0.00 0.00 39.90 4.00
2396 13382 4.303805 GTGCATCACAACAACCAGTAGGT 61.304 47.826 0.00 0.00 41.50 3.08
2397 13383 2.226437 GTGCATCACAACAACCAGTAGG 59.774 50.000 0.00 0.00 36.14 3.18
2398 13384 3.141398 AGTGCATCACAACAACCAGTAG 58.859 45.455 0.00 0.00 36.74 2.57
2399 13385 3.138304 GAGTGCATCACAACAACCAGTA 58.862 45.455 0.00 0.00 36.74 2.74
2400 13386 1.949525 GAGTGCATCACAACAACCAGT 59.050 47.619 0.00 0.00 36.74 4.00
2401 13387 1.948834 TGAGTGCATCACAACAACCAG 59.051 47.619 0.00 0.00 36.74 4.00
2402 13388 1.948834 CTGAGTGCATCACAACAACCA 59.051 47.619 0.00 0.00 36.74 3.67
2403 13389 1.335324 GCTGAGTGCATCACAACAACC 60.335 52.381 0.00 0.00 42.31 3.77
2479 13465 1.139058 CTAGACCATTTCCCCCGTCTG 59.861 57.143 0.00 0.00 36.31 3.51
2509 13495 2.416893 GGCCTGAAGAATGTCGAGTTTC 59.583 50.000 0.00 0.00 0.00 2.78
2531 13517 1.996191 GACAGAAGATGGCGTGAAGAC 59.004 52.381 0.00 0.00 0.00 3.01
2533 13519 1.998315 CAGACAGAAGATGGCGTGAAG 59.002 52.381 0.00 0.00 44.27 3.02
2537 13523 1.599047 CCCAGACAGAAGATGGCGT 59.401 57.895 0.00 0.00 44.27 5.68
2538 13524 1.817099 GCCCAGACAGAAGATGGCG 60.817 63.158 0.00 0.00 44.27 5.69
2539 13525 1.452833 GGCCCAGACAGAAGATGGC 60.453 63.158 0.00 0.00 37.09 4.40
2540 13526 0.179936 GAGGCCCAGACAGAAGATGG 59.820 60.000 0.00 0.00 0.00 3.51
2541 13527 0.179936 GGAGGCCCAGACAGAAGATG 59.820 60.000 0.00 0.00 0.00 2.90
2542 13528 0.252881 TGGAGGCCCAGACAGAAGAT 60.253 55.000 0.00 0.00 37.58 2.40
2543 13529 1.158466 TGGAGGCCCAGACAGAAGA 59.842 57.895 0.00 0.00 37.58 2.87
2544 13530 3.811702 TGGAGGCCCAGACAGAAG 58.188 61.111 0.00 0.00 37.58 2.85
2552 13538 1.306997 CCTAGGAACTGGAGGCCCA 60.307 63.158 1.05 0.00 40.33 5.36
2553 13539 1.307084 ACCTAGGAACTGGAGGCCC 60.307 63.158 17.98 0.00 40.33 5.80
2554 13540 0.325765 AGACCTAGGAACTGGAGGCC 60.326 60.000 17.98 0.00 40.33 5.19
2555 13541 0.827368 CAGACCTAGGAACTGGAGGC 59.173 60.000 17.98 0.00 40.33 4.70
2560 13546 1.153549 GCGCCAGACCTAGGAACTG 60.154 63.158 17.98 21.71 41.52 3.16
2561 13547 2.359967 GGCGCCAGACCTAGGAACT 61.360 63.158 24.80 11.50 46.37 3.01
2562 13548 1.900545 AAGGCGCCAGACCTAGGAAC 61.901 60.000 31.54 9.20 36.14 3.62
2563 13549 1.612442 AAGGCGCCAGACCTAGGAA 60.612 57.895 31.54 0.00 36.14 3.36
2564 13550 2.038975 AAGGCGCCAGACCTAGGA 59.961 61.111 31.54 0.00 36.14 2.94
2565 13551 2.187946 CAAGGCGCCAGACCTAGG 59.812 66.667 31.54 7.41 36.14 3.02
2566 13552 2.187946 CCAAGGCGCCAGACCTAG 59.812 66.667 31.54 9.41 36.14 3.02
2567 13553 3.399181 CCCAAGGCGCCAGACCTA 61.399 66.667 31.54 0.00 36.14 3.08
2578 13564 1.077212 CCTGGACATCAGCCCAAGG 60.077 63.158 0.00 0.00 42.05 3.61
2579 13565 0.107312 CTCCTGGACATCAGCCCAAG 60.107 60.000 0.00 0.00 42.05 3.61
2580 13566 0.842030 ACTCCTGGACATCAGCCCAA 60.842 55.000 0.00 0.00 42.05 4.12
2581 13567 1.229625 ACTCCTGGACATCAGCCCA 60.230 57.895 0.00 0.00 42.05 5.36
2582 13568 1.222936 CACTCCTGGACATCAGCCC 59.777 63.158 0.00 0.00 42.05 5.19
2583 13569 1.222936 CCACTCCTGGACATCAGCC 59.777 63.158 0.00 0.00 40.55 4.85
2584 13570 1.222936 CCCACTCCTGGACATCAGC 59.777 63.158 0.00 0.00 40.55 4.26
2585 13571 1.222936 GCCCACTCCTGGACATCAG 59.777 63.158 0.00 0.00 40.55 2.90
2586 13572 2.300967 GGCCCACTCCTGGACATCA 61.301 63.158 0.00 0.00 40.55 3.07
2587 13573 2.262774 CTGGCCCACTCCTGGACATC 62.263 65.000 0.00 0.00 40.55 3.06
2588 13574 2.204136 TGGCCCACTCCTGGACAT 60.204 61.111 0.00 0.00 40.55 3.06
2589 13575 2.930019 CTGGCCCACTCCTGGACA 60.930 66.667 0.00 0.00 40.55 4.02
2590 13576 3.721706 CCTGGCCCACTCCTGGAC 61.722 72.222 0.00 0.00 45.12 4.02
2591 13577 4.270153 ACCTGGCCCACTCCTGGA 62.270 66.667 0.00 0.00 45.12 3.86
2592 13578 3.721706 GACCTGGCCCACTCCTGG 61.722 72.222 0.00 4.46 46.93 4.45
2593 13579 2.304056 ATGACCTGGCCCACTCCTG 61.304 63.158 0.00 0.00 0.00 3.86
2594 13580 2.125912 ATGACCTGGCCCACTCCT 59.874 61.111 0.00 0.00 0.00 3.69
2595 13581 2.273449 CATGACCTGGCCCACTCC 59.727 66.667 0.00 0.00 0.00 3.85
2596 13582 1.078143 GTCATGACCTGGCCCACTC 60.078 63.158 15.31 0.00 0.00 3.51
2597 13583 1.847506 TGTCATGACCTGGCCCACT 60.848 57.895 22.85 0.00 0.00 4.00
2598 13584 1.675641 GTGTCATGACCTGGCCCAC 60.676 63.158 22.85 8.85 0.00 4.61
2599 13585 1.841302 GAGTGTCATGACCTGGCCCA 61.841 60.000 22.85 0.00 0.00 5.36
2600 13586 1.078143 GAGTGTCATGACCTGGCCC 60.078 63.158 22.85 4.59 0.00 5.80
2601 13587 1.448540 CGAGTGTCATGACCTGGCC 60.449 63.158 22.85 0.00 0.00 5.36
2602 13588 2.103042 GCGAGTGTCATGACCTGGC 61.103 63.158 24.29 24.29 0.00 4.85
2603 13589 1.448540 GGCGAGTGTCATGACCTGG 60.449 63.158 22.85 19.08 0.00 4.45
2604 13590 1.016130 GTGGCGAGTGTCATGACCTG 61.016 60.000 22.85 10.77 28.63 4.00
2605 13591 1.293498 GTGGCGAGTGTCATGACCT 59.707 57.895 22.85 18.18 28.63 3.85
2606 13592 1.741770 GGTGGCGAGTGTCATGACC 60.742 63.158 22.85 13.88 28.63 4.02
2607 13593 1.741770 GGGTGGCGAGTGTCATGAC 60.742 63.158 19.27 19.27 28.63 3.06
2608 13594 1.480212 AAGGGTGGCGAGTGTCATGA 61.480 55.000 0.00 0.00 28.63 3.07
2609 13595 1.003355 AAGGGTGGCGAGTGTCATG 60.003 57.895 0.00 0.00 28.63 3.07
2610 13596 1.003355 CAAGGGTGGCGAGTGTCAT 60.003 57.895 0.00 0.00 28.63 3.06
2611 13597 1.691195 TTCAAGGGTGGCGAGTGTCA 61.691 55.000 0.00 0.00 0.00 3.58
2612 13598 0.534203 TTTCAAGGGTGGCGAGTGTC 60.534 55.000 0.00 0.00 0.00 3.67
2613 13599 0.818040 GTTTCAAGGGTGGCGAGTGT 60.818 55.000 0.00 0.00 0.00 3.55
2614 13600 1.841663 CGTTTCAAGGGTGGCGAGTG 61.842 60.000 0.00 0.00 0.00 3.51
2615 13601 1.597027 CGTTTCAAGGGTGGCGAGT 60.597 57.895 0.00 0.00 0.00 4.18
2616 13602 2.325082 CCGTTTCAAGGGTGGCGAG 61.325 63.158 0.00 0.00 0.00 5.03
2617 13603 2.281208 CCGTTTCAAGGGTGGCGA 60.281 61.111 0.00 0.00 0.00 5.54
2618 13604 2.281208 TCCGTTTCAAGGGTGGCG 60.281 61.111 0.00 0.00 35.51 5.69
2619 13605 0.955919 CTCTCCGTTTCAAGGGTGGC 60.956 60.000 0.00 0.00 35.51 5.01
2620 13606 0.955919 GCTCTCCGTTTCAAGGGTGG 60.956 60.000 0.00 0.00 35.51 4.61
2621 13607 0.035458 AGCTCTCCGTTTCAAGGGTG 59.965 55.000 0.00 0.00 35.51 4.61
2622 13608 0.321996 GAGCTCTCCGTTTCAAGGGT 59.678 55.000 6.43 0.00 35.51 4.34
2623 13609 0.391793 GGAGCTCTCCGTTTCAAGGG 60.392 60.000 14.64 0.00 40.36 3.95
2624 13610 3.145228 GGAGCTCTCCGTTTCAAGG 57.855 57.895 14.64 0.00 40.36 3.61
2634 13620 2.409651 CGCCGTACAGGAGCTCTC 59.590 66.667 14.64 3.76 45.00 3.20
2639 13625 4.208686 GAGGGCGCCGTACAGGAG 62.209 72.222 23.69 5.69 45.00 3.69
2640 13626 4.753662 AGAGGGCGCCGTACAGGA 62.754 66.667 23.69 0.00 45.00 3.86
2641 13627 4.514577 CAGAGGGCGCCGTACAGG 62.515 72.222 23.69 7.99 44.97 4.00
2652 13638 4.785453 GTTCCAGGGCGCAGAGGG 62.785 72.222 10.83 4.85 0.00 4.30
2654 13640 3.589654 TTCGTTCCAGGGCGCAGAG 62.590 63.158 10.83 0.00 0.00 3.35
2655 13641 3.621805 TTCGTTCCAGGGCGCAGA 61.622 61.111 10.83 0.00 0.00 4.26
2656 13642 3.423154 GTTCGTTCCAGGGCGCAG 61.423 66.667 10.83 0.00 0.00 5.18
2657 13643 3.936203 AGTTCGTTCCAGGGCGCA 61.936 61.111 10.83 0.00 0.00 6.09
2658 13644 3.423154 CAGTTCGTTCCAGGGCGC 61.423 66.667 0.00 0.00 0.00 6.53
2659 13645 2.742372 CCAGTTCGTTCCAGGGCG 60.742 66.667 0.00 0.00 0.00 6.13
2660 13646 3.056328 GCCAGTTCGTTCCAGGGC 61.056 66.667 0.00 0.00 0.00 5.19
2661 13647 2.742372 CGCCAGTTCGTTCCAGGG 60.742 66.667 0.00 0.00 0.00 4.45
2662 13648 3.423154 GCGCCAGTTCGTTCCAGG 61.423 66.667 0.00 0.00 0.00 4.45
2663 13649 2.357517 AGCGCCAGTTCGTTCCAG 60.358 61.111 2.29 0.00 0.00 3.86
2664 13650 2.357034 GAGCGCCAGTTCGTTCCA 60.357 61.111 2.29 0.00 34.34 3.53
2665 13651 2.357034 TGAGCGCCAGTTCGTTCC 60.357 61.111 2.29 0.00 38.62 3.62
2666 13652 2.853914 GTGAGCGCCAGTTCGTTC 59.146 61.111 2.29 0.00 39.59 3.95
2667 13653 3.036084 CGTGAGCGCCAGTTCGTT 61.036 61.111 2.29 0.00 0.00 3.85
2709 13695 0.726118 GAGGAAGAAAAGCGCGTTGC 60.726 55.000 9.90 7.82 46.98 4.17
2710 13696 0.110192 GGAGGAAGAAAAGCGCGTTG 60.110 55.000 9.90 0.00 0.00 4.10
2711 13697 1.566018 CGGAGGAAGAAAAGCGCGTT 61.566 55.000 8.43 1.67 0.00 4.84
2712 13698 2.027625 CGGAGGAAGAAAAGCGCGT 61.028 57.895 8.43 0.00 0.00 6.01
2713 13699 1.566018 AACGGAGGAAGAAAAGCGCG 61.566 55.000 0.00 0.00 0.00 6.86
2714 13700 0.110192 CAACGGAGGAAGAAAAGCGC 60.110 55.000 0.00 0.00 0.00 5.92
2715 13701 0.517316 CCAACGGAGGAAGAAAAGCG 59.483 55.000 0.00 0.00 0.00 4.68
2716 13702 0.881796 CCCAACGGAGGAAGAAAAGC 59.118 55.000 0.00 0.00 0.00 3.51
2717 13703 2.271944 ACCCAACGGAGGAAGAAAAG 57.728 50.000 0.00 0.00 0.00 2.27
2718 13704 2.578786 GAACCCAACGGAGGAAGAAAA 58.421 47.619 0.00 0.00 0.00 2.29
2719 13705 1.202842 GGAACCCAACGGAGGAAGAAA 60.203 52.381 0.00 0.00 0.00 2.52
2720 13706 0.399075 GGAACCCAACGGAGGAAGAA 59.601 55.000 0.00 0.00 0.00 2.52
2721 13707 0.765135 TGGAACCCAACGGAGGAAGA 60.765 55.000 0.00 0.00 0.00 2.87
2722 13708 0.321653 CTGGAACCCAACGGAGGAAG 60.322 60.000 0.00 0.00 30.80 3.46
2723 13709 1.057851 ACTGGAACCCAACGGAGGAA 61.058 55.000 0.00 0.00 30.80 3.36
2724 13710 1.057851 AACTGGAACCCAACGGAGGA 61.058 55.000 0.00 0.00 30.80 3.71
2725 13711 0.889186 CAACTGGAACCCAACGGAGG 60.889 60.000 0.00 0.00 30.80 4.30
2726 13712 1.515521 GCAACTGGAACCCAACGGAG 61.516 60.000 0.00 0.00 30.80 4.63
2727 13713 1.527380 GCAACTGGAACCCAACGGA 60.527 57.895 0.00 0.00 30.80 4.69
2728 13714 1.826054 TGCAACTGGAACCCAACGG 60.826 57.895 0.00 0.00 30.80 4.44
2729 13715 1.358759 GTGCAACTGGAACCCAACG 59.641 57.895 0.00 0.00 30.80 4.10
2730 13716 1.358759 CGTGCAACTGGAACCCAAC 59.641 57.895 0.00 0.00 30.80 3.77
2731 13717 2.485795 GCGTGCAACTGGAACCCAA 61.486 57.895 0.00 0.00 30.80 4.12
2732 13718 2.904866 GCGTGCAACTGGAACCCA 60.905 61.111 0.00 0.00 31.75 4.51
2733 13719 3.670377 GGCGTGCAACTGGAACCC 61.670 66.667 0.00 0.00 31.75 4.11
2734 13720 3.670377 GGGCGTGCAACTGGAACC 61.670 66.667 0.00 0.00 31.75 3.62
2735 13721 4.025401 CGGGCGTGCAACTGGAAC 62.025 66.667 0.00 0.00 31.75 3.62
2760 13746 2.200170 AAAAATGTGGCCGAGCGAGC 62.200 55.000 0.00 0.00 0.00 5.03
2761 13747 1.875963 AAAAATGTGGCCGAGCGAG 59.124 52.632 0.00 0.00 0.00 5.03
2762 13748 4.073052 AAAAATGTGGCCGAGCGA 57.927 50.000 0.00 0.00 0.00 4.93
2778 13764 6.254589 CCAACTGCAAACAAATACGAGAAAAA 59.745 34.615 0.00 0.00 0.00 1.94
2779 13765 5.746245 CCAACTGCAAACAAATACGAGAAAA 59.254 36.000 0.00 0.00 0.00 2.29
2780 13766 5.277825 CCAACTGCAAACAAATACGAGAAA 58.722 37.500 0.00 0.00 0.00 2.52
2781 13767 4.791411 GCCAACTGCAAACAAATACGAGAA 60.791 41.667 0.00 0.00 40.77 2.87
2782 13768 3.304391 GCCAACTGCAAACAAATACGAGA 60.304 43.478 0.00 0.00 40.77 4.04
2783 13769 2.979813 GCCAACTGCAAACAAATACGAG 59.020 45.455 0.00 0.00 40.77 4.18
2784 13770 2.287909 GGCCAACTGCAAACAAATACGA 60.288 45.455 0.00 0.00 43.89 3.43
2785 13771 2.058057 GGCCAACTGCAAACAAATACG 58.942 47.619 0.00 0.00 43.89 3.06
2786 13772 3.059166 CAGGCCAACTGCAAACAAATAC 58.941 45.455 5.01 0.00 43.89 1.89
2787 13773 2.036992 CCAGGCCAACTGCAAACAAATA 59.963 45.455 5.01 0.00 46.14 1.40
2788 13774 1.202675 CCAGGCCAACTGCAAACAAAT 60.203 47.619 5.01 0.00 46.14 2.32
2789 13775 0.177604 CCAGGCCAACTGCAAACAAA 59.822 50.000 5.01 0.00 46.14 2.83
2790 13776 0.975040 ACCAGGCCAACTGCAAACAA 60.975 50.000 5.01 0.00 46.14 2.83
2791 13777 1.381056 ACCAGGCCAACTGCAAACA 60.381 52.632 5.01 0.00 46.14 2.83
2792 13778 1.363807 GACCAGGCCAACTGCAAAC 59.636 57.895 5.01 0.00 46.14 2.93
2793 13779 2.192861 CGACCAGGCCAACTGCAAA 61.193 57.895 5.01 0.00 46.14 3.68
2794 13780 2.594303 CGACCAGGCCAACTGCAA 60.594 61.111 5.01 0.00 46.14 4.08
2795 13781 2.616797 TTTCGACCAGGCCAACTGCA 62.617 55.000 5.01 0.00 46.14 4.41
2796 13782 1.452145 TTTTCGACCAGGCCAACTGC 61.452 55.000 5.01 0.00 46.14 4.40
2798 13784 3.505835 TTTTTCGACCAGGCCAACT 57.494 47.368 5.01 0.00 0.00 3.16
2839 13825 9.617523 AACTTTTCTGATTTCACAATTTTCCAT 57.382 25.926 0.00 0.00 0.00 3.41
2840 13826 9.097257 GAACTTTTCTGATTTCACAATTTTCCA 57.903 29.630 0.00 0.00 0.00 3.53
2841 13827 9.097257 TGAACTTTTCTGATTTCACAATTTTCC 57.903 29.630 0.00 0.00 0.00 3.13
2844 13830 9.264719 GGATGAACTTTTCTGATTTCACAATTT 57.735 29.630 0.00 0.00 30.99 1.82
2845 13831 8.423349 TGGATGAACTTTTCTGATTTCACAATT 58.577 29.630 0.00 0.00 30.99 2.32
2846 13832 7.954835 TGGATGAACTTTTCTGATTTCACAAT 58.045 30.769 0.00 0.00 30.99 2.71
2847 13833 7.345422 TGGATGAACTTTTCTGATTTCACAA 57.655 32.000 0.00 0.00 30.99 3.33
2848 13834 6.957920 TGGATGAACTTTTCTGATTTCACA 57.042 33.333 0.00 0.00 30.99 3.58
2849 13835 8.706035 CAAATGGATGAACTTTTCTGATTTCAC 58.294 33.333 0.00 0.00 30.99 3.18
2850 13836 7.385752 GCAAATGGATGAACTTTTCTGATTTCA 59.614 33.333 0.00 0.00 32.71 2.69
2851 13837 7.385752 TGCAAATGGATGAACTTTTCTGATTTC 59.614 33.333 0.00 0.00 0.00 2.17
2852 13838 7.218614 TGCAAATGGATGAACTTTTCTGATTT 58.781 30.769 0.00 0.00 0.00 2.17
2853 13839 6.761312 TGCAAATGGATGAACTTTTCTGATT 58.239 32.000 0.00 0.00 0.00 2.57
2854 13840 6.209986 TCTGCAAATGGATGAACTTTTCTGAT 59.790 34.615 0.00 0.00 0.00 2.90
2855 13841 5.535783 TCTGCAAATGGATGAACTTTTCTGA 59.464 36.000 0.00 0.00 0.00 3.27
2856 13842 5.775686 TCTGCAAATGGATGAACTTTTCTG 58.224 37.500 0.00 0.00 0.00 3.02
2857 13843 6.409524 TTCTGCAAATGGATGAACTTTTCT 57.590 33.333 0.00 0.00 0.00 2.52
2858 13844 7.481275 TTTTCTGCAAATGGATGAACTTTTC 57.519 32.000 0.00 0.00 0.00 2.29
2859 13845 7.862512 TTTTTCTGCAAATGGATGAACTTTT 57.137 28.000 0.00 0.00 0.00 2.27
2927 13913 9.366216 GGTGAACTTTTCTCAGTTTTTACATTT 57.634 29.630 0.00 0.00 37.11 2.32
2928 13914 8.527810 TGGTGAACTTTTCTCAGTTTTTACATT 58.472 29.630 0.00 0.00 37.11 2.71
2929 13915 8.062065 TGGTGAACTTTTCTCAGTTTTTACAT 57.938 30.769 0.00 0.00 37.11 2.29
2930 13916 7.455641 TGGTGAACTTTTCTCAGTTTTTACA 57.544 32.000 0.00 0.00 37.11 2.41
2931 13917 8.751302 TTTGGTGAACTTTTCTCAGTTTTTAC 57.249 30.769 0.00 0.00 37.11 2.01
2932 13918 9.936759 ATTTTGGTGAACTTTTCTCAGTTTTTA 57.063 25.926 0.00 0.00 37.11 1.52
2933 13919 8.846943 ATTTTGGTGAACTTTTCTCAGTTTTT 57.153 26.923 0.00 0.00 37.11 1.94
2934 13920 8.720562 CAATTTTGGTGAACTTTTCTCAGTTTT 58.279 29.630 0.00 0.00 37.11 2.43
2935 13921 7.334171 CCAATTTTGGTGAACTTTTCTCAGTTT 59.666 33.333 0.95 0.00 43.43 2.66
2936 13922 6.818142 CCAATTTTGGTGAACTTTTCTCAGTT 59.182 34.615 0.95 0.00 43.43 3.16
2937 13923 6.340522 CCAATTTTGGTGAACTTTTCTCAGT 58.659 36.000 0.95 0.00 43.43 3.41
2938 13924 6.833342 CCAATTTTGGTGAACTTTTCTCAG 57.167 37.500 0.95 0.00 43.43 3.35


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

AutoCloner maintained by Alex Coulton.