Multiple sequence alignment - TraesCS7A01G075500

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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 TraesCS7A01G075500 chr7A 100.000 3686 0 0 1411 5096 41435858 41439543 0.000000e+00 6807.0
1 TraesCS7A01G075500 chr7A 100.000 1013 0 0 1 1013 41434448 41435460 0.000000e+00 1871.0
2 TraesCS7A01G075500 chr7A 95.820 646 24 2 2 644 732058306 732058951 0.000000e+00 1040.0
3 TraesCS7A01G075500 chr7A 95.238 651 30 1 1 650 276128280 276127630 0.000000e+00 1029.0
4 TraesCS7A01G075500 chr7D 90.669 1436 90 13 2568 3979 41771962 41773377 0.000000e+00 1869.0
5 TraesCS7A01G075500 chr7D 91.309 1024 63 13 3994 5001 41773582 41774595 0.000000e+00 1375.0
6 TraesCS7A01G075500 chr7D 87.889 867 56 23 1411 2251 41770919 41771762 0.000000e+00 974.0
7 TraesCS7A01G075500 chr7D 89.130 138 6 5 758 889 41770631 41770765 4.080000e-36 163.0
8 TraesCS7A01G075500 chr7D 98.485 66 1 0 5031 5096 41774688 41774753 3.220000e-22 117.0
9 TraesCS7A01G075500 chr7D 90.110 91 8 1 2480 2569 602187762 602187852 3.220000e-22 117.0
10 TraesCS7A01G075500 chr4A 88.454 1481 98 31 3222 4636 648892328 648893801 0.000000e+00 1720.0
11 TraesCS7A01G075500 chr4A 93.401 591 33 4 2568 3152 648891712 648892302 0.000000e+00 870.0
12 TraesCS7A01G075500 chr4A 87.113 807 49 20 1411 2186 648890674 648891456 0.000000e+00 863.0
13 TraesCS7A01G075500 chr4A 89.418 189 14 2 2304 2486 648891525 648891713 3.070000e-57 233.0
14 TraesCS7A01G075500 chr4A 76.883 385 29 29 677 1013 648890303 648890675 4.080000e-36 163.0
15 TraesCS7A01G075500 chr4A 98.529 68 1 0 5029 5096 648894402 648894469 2.490000e-23 121.0
16 TraesCS7A01G075500 chr4A 89.412 85 9 0 2485 2569 594380336 594380252 1.940000e-19 108.0
17 TraesCS7A01G075500 chr3A 95.820 646 25 2 1 644 649849184 649848539 0.000000e+00 1042.0
18 TraesCS7A01G075500 chr2A 95.552 652 28 1 1 651 319017593 319016942 0.000000e+00 1042.0
19 TraesCS7A01G075500 chr2A 95.532 649 25 4 1 648 202221810 202221165 0.000000e+00 1035.0
20 TraesCS7A01G075500 chr2A 95.659 645 26 2 1 644 769032003 769032646 0.000000e+00 1035.0
21 TraesCS7A01G075500 chr2A 88.235 85 10 0 2485 2569 34328129 34328213 9.030000e-18 102.0
22 TraesCS7A01G075500 chr1B 95.820 646 25 2 1 644 26840426 26839781 0.000000e+00 1042.0
23 TraesCS7A01G075500 chr6B 95.538 650 26 3 1 649 711427728 711428375 0.000000e+00 1037.0
24 TraesCS7A01G075500 chr6B 90.000 400 32 5 1854 2251 52702337 52702730 1.270000e-140 510.0
25 TraesCS7A01G075500 chr6B 90.025 401 31 6 1854 2251 52714811 52715205 1.270000e-140 510.0
26 TraesCS7A01G075500 chr6B 78.454 427 37 25 1411 1805 52701920 52702323 1.430000e-55 228.0
27 TraesCS7A01G075500 chr6B 78.454 427 37 25 1411 1805 52714394 52714797 1.430000e-55 228.0
28 TraesCS7A01G075500 chr6B 94.545 55 3 0 2645 2699 116357102 116357048 9.090000e-13 86.1
29 TraesCS7A01G075500 chr2B 95.659 645 26 2 1 644 2070175 2070818 0.000000e+00 1035.0
30 TraesCS7A01G075500 chr2D 91.195 159 12 1 2645 2801 559462359 559462201 1.110000e-51 215.0
31 TraesCS7A01G075500 chr2D 91.195 159 12 1 2645 2801 559602586 559602428 1.110000e-51 215.0
32 TraesCS7A01G075500 chr2D 96.364 55 2 0 2645 2699 573801629 573801575 1.950000e-14 91.6
33 TraesCS7A01G075500 chr1D 91.860 86 7 0 2484 2569 325484493 325484578 2.490000e-23 121.0
34 TraesCS7A01G075500 chr1A 89.888 89 9 0 2484 2572 419033925 419033837 1.160000e-21 115.0
35 TraesCS7A01G075500 chr1A 94.545 55 3 0 2645 2699 37143036 37143090 9.090000e-13 86.1
36 TraesCS7A01G075500 chr6A 87.059 85 7 2 2485 2569 530600115 530600195 5.430000e-15 93.5
37 TraesCS7A01G075500 chr7B 96.364 55 2 0 2645 2699 467541764 467541710 1.950000e-14 91.6
38 TraesCS7A01G075500 chr3D 96.364 55 2 0 2645 2699 586214697 586214751 1.950000e-14 91.6
39 TraesCS7A01G075500 chr3B 85.227 88 13 0 2482 2569 256197277 256197364 1.950000e-14 91.6
40 TraesCS7A01G075500 chr3B 82.353 102 16 2 2471 2572 490598013 490598112 2.530000e-13 87.9
41 TraesCS7A01G075500 chr5D 84.043 94 13 2 2478 2569 546651447 546651540 7.030000e-14 89.8


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 TraesCS7A01G075500 chr7A 41434448 41439543 5095 False 4339.000000 6807 100.000000 1 5096 2 chr7A.!!$F2 5095
1 TraesCS7A01G075500 chr7A 732058306 732058951 645 False 1040.000000 1040 95.820000 2 644 1 chr7A.!!$F1 642
2 TraesCS7A01G075500 chr7A 276127630 276128280 650 True 1029.000000 1029 95.238000 1 650 1 chr7A.!!$R1 649
3 TraesCS7A01G075500 chr7D 41770631 41774753 4122 False 899.600000 1869 91.496400 758 5096 5 chr7D.!!$F2 4338
4 TraesCS7A01G075500 chr4A 648890303 648894469 4166 False 661.666667 1720 88.966333 677 5096 6 chr4A.!!$F1 4419
5 TraesCS7A01G075500 chr3A 649848539 649849184 645 True 1042.000000 1042 95.820000 1 644 1 chr3A.!!$R1 643
6 TraesCS7A01G075500 chr2A 319016942 319017593 651 True 1042.000000 1042 95.552000 1 651 1 chr2A.!!$R2 650
7 TraesCS7A01G075500 chr2A 202221165 202221810 645 True 1035.000000 1035 95.532000 1 648 1 chr2A.!!$R1 647
8 TraesCS7A01G075500 chr2A 769032003 769032646 643 False 1035.000000 1035 95.659000 1 644 1 chr2A.!!$F2 643
9 TraesCS7A01G075500 chr1B 26839781 26840426 645 True 1042.000000 1042 95.820000 1 644 1 chr1B.!!$R1 643
10 TraesCS7A01G075500 chr6B 711427728 711428375 647 False 1037.000000 1037 95.538000 1 649 1 chr6B.!!$F1 648
11 TraesCS7A01G075500 chr6B 52701920 52702730 810 False 369.000000 510 84.227000 1411 2251 2 chr6B.!!$F2 840
12 TraesCS7A01G075500 chr6B 52714394 52715205 811 False 369.000000 510 84.239500 1411 2251 2 chr6B.!!$F3 840
13 TraesCS7A01G075500 chr2B 2070175 2070818 643 False 1035.000000 1035 95.659000 1 644 1 chr2B.!!$F1 643

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
746 758 1.134946 GGATTCCCTGCGGTGAAAATG 59.865 52.381 0.00 0.0 0.00 2.32 F
1583 1679 0.406361 TGTTAACCCCCTGGCGATTT 59.594 50.000 2.48 0.0 33.59 2.17 F
2411 2557 0.460811 CTCAGTGCTTAGATGCGCCA 60.461 55.000 4.18 0.0 43.73 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 1888 0.532573 GTGGAGATCTGGACGCAGAA 59.467 55.0 0.0 0.0 34.56 3.02 R
3191 3344 0.039618 TCTTCAGCACCCATTTCCCC 59.960 55.0 0.0 0.0 0.00 4.81 R
4279 4669 0.886490 CGAGCAACAAGAAGCACCCT 60.886 55.0 0.0 0.0 0.00 4.34 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
173 175 1.697284 CTCCTCATCCGAGTCCATCA 58.303 55.000 0.00 0.00 37.59 3.07
280 283 1.228644 AAATGCCCAGCTGCTGTGA 60.229 52.632 26.41 11.33 0.00 3.58
373 376 2.636830 GTCGCCGGGATATAGCTAGTA 58.363 52.381 2.18 0.00 0.00 1.82
493 498 2.677875 CCCAACTGCTTCCCAGCC 60.678 66.667 0.00 0.00 46.74 4.85
570 576 2.188469 GTTCTGGGGGCGCGATTA 59.812 61.111 12.10 0.00 0.00 1.75
614 622 1.543429 CGAAAAAGTGGCCTGAGGAGT 60.543 52.381 0.65 0.00 0.00 3.85
651 659 2.036604 GCTGGAGATGCCCTTAGTAGTC 59.963 54.545 0.00 0.00 34.97 2.59
652 660 3.571590 CTGGAGATGCCCTTAGTAGTCT 58.428 50.000 0.00 0.00 34.97 3.24
653 661 3.964031 CTGGAGATGCCCTTAGTAGTCTT 59.036 47.826 0.00 0.00 34.97 3.01
654 662 3.706594 TGGAGATGCCCTTAGTAGTCTTG 59.293 47.826 0.00 0.00 34.97 3.02
655 663 3.070302 GGAGATGCCCTTAGTAGTCTTGG 59.930 52.174 0.00 0.00 0.00 3.61
656 664 3.961408 GAGATGCCCTTAGTAGTCTTGGA 59.039 47.826 0.00 0.00 0.00 3.53
657 665 4.362677 AGATGCCCTTAGTAGTCTTGGAA 58.637 43.478 0.00 0.00 0.00 3.53
658 666 4.783227 AGATGCCCTTAGTAGTCTTGGAAA 59.217 41.667 0.00 0.00 0.00 3.13
660 668 3.908103 TGCCCTTAGTAGTCTTGGAAAGT 59.092 43.478 0.00 0.00 46.34 2.66
661 669 5.088730 TGCCCTTAGTAGTCTTGGAAAGTA 58.911 41.667 0.00 0.00 46.34 2.24
662 670 5.544948 TGCCCTTAGTAGTCTTGGAAAGTAA 59.455 40.000 0.00 0.00 46.34 2.24
663 671 6.043474 TGCCCTTAGTAGTCTTGGAAAGTAAA 59.957 38.462 0.00 0.00 46.34 2.01
664 672 7.110810 GCCCTTAGTAGTCTTGGAAAGTAAAT 58.889 38.462 0.00 0.00 46.34 1.40
665 673 7.280428 GCCCTTAGTAGTCTTGGAAAGTAAATC 59.720 40.741 0.00 0.00 46.34 2.17
666 674 7.769507 CCCTTAGTAGTCTTGGAAAGTAAATCC 59.230 40.741 0.00 0.00 46.34 3.01
667 675 8.319146 CCTTAGTAGTCTTGGAAAGTAAATCCA 58.681 37.037 0.00 0.00 46.34 3.41
691 699 2.753452 TGTAAAACACGCTTTCACCCAA 59.247 40.909 0.00 0.00 0.00 4.12
695 703 1.757682 ACACGCTTTCACCCAAAAGA 58.242 45.000 0.75 0.00 38.30 2.52
726 738 4.161976 TCGAGAGGAAGCGACGCG 62.162 66.667 15.18 3.53 0.00 6.01
745 757 1.474330 GGATTCCCTGCGGTGAAAAT 58.526 50.000 0.00 0.00 0.00 1.82
746 758 1.134946 GGATTCCCTGCGGTGAAAATG 59.865 52.381 0.00 0.00 0.00 2.32
747 759 1.818674 GATTCCCTGCGGTGAAAATGT 59.181 47.619 0.00 0.00 0.00 2.71
748 760 1.698506 TTCCCTGCGGTGAAAATGTT 58.301 45.000 0.00 0.00 0.00 2.71
750 762 1.202879 TCCCTGCGGTGAAAATGTTCT 60.203 47.619 0.00 0.00 34.60 3.01
756 768 2.412847 GCGGTGAAAATGTTCTTCTCGG 60.413 50.000 0.00 0.00 34.60 4.63
819 835 2.914908 CGCCCCTTTCCACCGTTTG 61.915 63.158 0.00 0.00 0.00 2.93
880 911 4.193334 CGCGCATCGGGTCTCTCA 62.193 66.667 8.75 0.00 35.14 3.27
882 913 2.279120 CGCATCGGGTCTCTCAGC 60.279 66.667 0.00 0.00 0.00 4.26
884 915 2.775856 GCATCGGGTCTCTCAGCGA 61.776 63.158 0.00 0.00 0.00 4.93
885 916 2.037053 CATCGGGTCTCTCAGCGAT 58.963 57.895 0.00 0.00 0.00 4.58
1011 1098 0.526524 CAGGCGAGATGGTCTTCGTC 60.527 60.000 0.00 0.00 0.00 4.20
1012 1099 0.681564 AGGCGAGATGGTCTTCGTCT 60.682 55.000 0.00 0.00 43.97 4.18
1438 1525 1.514443 GCCTTCTTCCTCGTCGTCG 60.514 63.158 0.00 0.00 38.55 5.12
1508 1599 3.800863 GTCTCGTCTCCGCTCGCA 61.801 66.667 0.00 0.00 0.00 5.10
1583 1679 0.406361 TGTTAACCCCCTGGCGATTT 59.594 50.000 2.48 0.00 33.59 2.17
1693 1800 1.997928 GCGGATTTGGAGCTTCTGGC 61.998 60.000 0.00 0.00 42.19 4.85
1744 1870 3.797546 GCGTCTTCTGCTGCTGGC 61.798 66.667 6.69 0.00 42.22 4.85
1840 1968 3.281395 CCCGGCAACCGTCGTTTT 61.281 61.111 5.17 0.00 46.80 2.43
2025 2161 4.958509 TGTTCACCAAATGTGCAATCAAT 58.041 34.783 0.00 0.00 45.03 2.57
2084 2220 2.613977 CCCTCTGTCCTGCTACTTGTTG 60.614 54.545 0.00 0.00 0.00 3.33
2112 2248 9.278011 TCTATCATGATACCTCTAGAGATCAGA 57.722 37.037 21.76 18.42 32.12 3.27
2118 2255 6.658816 TGATACCTCTAGAGATCAGAATCAGC 59.341 42.308 21.76 0.00 34.07 4.26
2166 2303 2.030540 TCTTTGCAGCTTGCTTGATGTC 60.031 45.455 9.12 0.00 45.31 3.06
2173 2310 5.662447 GCAGCTTGCTTGATGTCAAACATC 61.662 45.833 12.12 12.12 46.09 3.06
2260 2398 7.885399 AGCTTTTGTACTACTTTGATTCATCCT 59.115 33.333 0.00 0.00 0.00 3.24
2261 2399 8.178313 GCTTTTGTACTACTTTGATTCATCCTC 58.822 37.037 0.00 0.00 0.00 3.71
2262 2400 9.442047 CTTTTGTACTACTTTGATTCATCCTCT 57.558 33.333 0.00 0.00 0.00 3.69
2263 2401 8.777865 TTTGTACTACTTTGATTCATCCTCTG 57.222 34.615 0.00 0.00 0.00 3.35
2264 2402 6.878317 TGTACTACTTTGATTCATCCTCTGG 58.122 40.000 0.00 0.00 0.00 3.86
2265 2403 6.667848 TGTACTACTTTGATTCATCCTCTGGA 59.332 38.462 0.00 0.00 35.55 3.86
2266 2404 6.627087 ACTACTTTGATTCATCCTCTGGAA 57.373 37.500 0.00 0.00 34.34 3.53
2267 2405 7.205515 ACTACTTTGATTCATCCTCTGGAAT 57.794 36.000 0.00 0.00 34.34 3.01
2268 2406 7.052873 ACTACTTTGATTCATCCTCTGGAATG 58.947 38.462 0.00 0.00 34.34 2.67
2269 2407 6.070951 ACTTTGATTCATCCTCTGGAATGA 57.929 37.500 0.00 0.00 34.34 2.57
2270 2408 6.487828 ACTTTGATTCATCCTCTGGAATGAA 58.512 36.000 11.10 11.10 35.47 2.57
2271 2409 7.124052 ACTTTGATTCATCCTCTGGAATGAAT 58.876 34.615 16.48 16.48 39.81 2.57
2272 2410 8.277197 ACTTTGATTCATCCTCTGGAATGAATA 58.723 33.333 16.49 6.94 38.61 1.75
2273 2411 9.128404 CTTTGATTCATCCTCTGGAATGAATAA 57.872 33.333 16.49 11.15 38.61 1.40
2274 2412 9.478238 TTTGATTCATCCTCTGGAATGAATAAA 57.522 29.630 16.49 14.39 38.61 1.40
2275 2413 8.455903 TGATTCATCCTCTGGAATGAATAAAC 57.544 34.615 16.49 10.09 38.61 2.01
2276 2414 8.054572 TGATTCATCCTCTGGAATGAATAAACA 58.945 33.333 16.49 11.55 38.61 2.83
2277 2415 7.870509 TTCATCCTCTGGAATGAATAAACAG 57.129 36.000 0.00 0.00 34.34 3.16
2278 2416 7.199167 TCATCCTCTGGAATGAATAAACAGA 57.801 36.000 0.00 0.00 34.34 3.41
2283 2421 6.874278 TCTGGAATGAATAAACAGAGGAGA 57.126 37.500 0.00 0.00 33.62 3.71
2284 2422 7.443302 TCTGGAATGAATAAACAGAGGAGAT 57.557 36.000 0.00 0.00 33.62 2.75
2285 2423 7.278135 TCTGGAATGAATAAACAGAGGAGATG 58.722 38.462 0.00 0.00 33.62 2.90
2286 2424 6.962182 TGGAATGAATAAACAGAGGAGATGT 58.038 36.000 0.00 0.00 0.00 3.06
2287 2425 7.405292 TGGAATGAATAAACAGAGGAGATGTT 58.595 34.615 0.00 0.00 42.55 2.71
2294 2432 4.899352 AACAGAGGAGATGTTTGCTACT 57.101 40.909 0.00 0.00 37.61 2.57
2295 2433 4.199432 ACAGAGGAGATGTTTGCTACTG 57.801 45.455 0.00 0.00 0.00 2.74
2296 2434 3.580458 ACAGAGGAGATGTTTGCTACTGT 59.420 43.478 0.00 0.00 0.00 3.55
2297 2435 4.772624 ACAGAGGAGATGTTTGCTACTGTA 59.227 41.667 0.00 0.00 34.95 2.74
2298 2436 5.423610 ACAGAGGAGATGTTTGCTACTGTAT 59.576 40.000 0.00 0.00 34.95 2.29
2299 2437 6.070538 ACAGAGGAGATGTTTGCTACTGTATT 60.071 38.462 0.00 0.00 34.95 1.89
2326 2467 9.629878 TTCTTTTGTTACTGTATACTTTTCCCA 57.370 29.630 4.17 0.00 0.00 4.37
2327 2468 9.629878 TCTTTTGTTACTGTATACTTTTCCCAA 57.370 29.630 4.17 0.00 0.00 4.12
2346 2487 4.144297 CCAACTCCATTTTCTGTCTTCCA 58.856 43.478 0.00 0.00 0.00 3.53
2395 2541 2.289694 GGTTCTAGCTGCAACTTCCTCA 60.290 50.000 1.02 0.00 0.00 3.86
2411 2557 0.460811 CTCAGTGCTTAGATGCGCCA 60.461 55.000 4.18 0.00 43.73 5.69
2464 2611 9.057089 ACTAGTTTTGATTTTCTTGTAGGACAG 57.943 33.333 0.00 0.00 0.00 3.51
2472 2619 4.891992 TTCTTGTAGGACAGAGGGAAAG 57.108 45.455 0.00 0.00 0.00 2.62
2484 2631 7.515514 AGGACAGAGGGAAAGTCATTGATATAT 59.484 37.037 0.00 0.00 34.04 0.86
2485 2632 8.816894 GGACAGAGGGAAAGTCATTGATATATA 58.183 37.037 0.00 0.00 34.04 0.86
2486 2633 9.646427 GACAGAGGGAAAGTCATTGATATATAC 57.354 37.037 0.00 0.00 32.68 1.47
2487 2634 9.386122 ACAGAGGGAAAGTCATTGATATATACT 57.614 33.333 0.00 0.00 0.00 2.12
2491 2638 9.845214 AGGGAAAGTCATTGATATATACTACCT 57.155 33.333 0.00 0.00 0.00 3.08
2523 2670 9.624697 TCACAATATAAGATGTTTTTGCAGTTC 57.375 29.630 0.00 0.00 0.00 3.01
2524 2671 9.409312 CACAATATAAGATGTTTTTGCAGTTCA 57.591 29.630 0.00 0.00 0.00 3.18
2525 2672 9.979578 ACAATATAAGATGTTTTTGCAGTTCAA 57.020 25.926 0.00 0.00 0.00 2.69
2536 2683 9.049523 TGTTTTTGCAGTTCAAATTATATTGCA 57.950 25.926 0.00 0.00 43.53 4.08
2537 2684 9.875675 GTTTTTGCAGTTCAAATTATATTGCAA 57.124 25.926 0.00 0.00 45.12 4.08
2541 2688 9.875675 TTGCAGTTCAAATTATATTGCAAAAAC 57.124 25.926 1.71 0.00 44.22 2.43
2542 2689 8.219769 TGCAGTTCAAATTATATTGCAAAAACG 58.780 29.630 1.71 0.00 37.17 3.60
2543 2690 8.220434 GCAGTTCAAATTATATTGCAAAAACGT 58.780 29.630 1.71 0.00 0.00 3.99
2544 2691 9.726034 CAGTTCAAATTATATTGCAAAAACGTC 57.274 29.630 1.71 0.00 0.00 4.34
2545 2692 9.691362 AGTTCAAATTATATTGCAAAAACGTCT 57.309 25.926 1.71 0.00 0.00 4.18
2559 2706 9.268255 TGCAAAAACGTCTTATATTTTGATACG 57.732 29.630 19.73 0.00 42.48 3.06
2560 2707 8.730427 GCAAAAACGTCTTATATTTTGATACGG 58.270 33.333 19.73 0.00 42.48 4.02
2561 2708 9.976255 CAAAAACGTCTTATATTTTGATACGGA 57.024 29.630 13.15 0.00 42.48 4.69
2564 2711 7.941795 ACGTCTTATATTTTGATACGGAAGG 57.058 36.000 0.00 0.00 33.44 3.46
2565 2712 7.719483 ACGTCTTATATTTTGATACGGAAGGA 58.281 34.615 0.00 0.00 33.44 3.36
2566 2713 7.866393 ACGTCTTATATTTTGATACGGAAGGAG 59.134 37.037 0.00 0.00 33.44 3.69
2592 2739 4.797800 TCCATTGATTTTGATTGCCGAA 57.202 36.364 0.00 0.00 0.00 4.30
2596 2743 4.925061 TTGATTTTGATTGCCGAATTGC 57.075 36.364 0.00 0.00 0.00 3.56
2626 2773 8.568794 GGCATTTAGTATTTCCTAATGTTCCTC 58.431 37.037 0.00 0.00 0.00 3.71
2634 2781 9.931210 GTATTTCCTAATGTTCCTCATTAAACG 57.069 33.333 0.00 0.00 44.95 3.60
2640 2787 9.326413 CCTAATGTTCCTCATTAAACGTAGAAT 57.674 33.333 0.00 0.00 44.95 2.40
2716 2863 1.442526 GGTGGAATCTGCATGGCTCG 61.443 60.000 0.00 0.00 0.00 5.03
2731 2878 5.220854 GCATGGCTCGTTACTCATGTTTAAT 60.221 40.000 0.00 0.00 39.17 1.40
2789 2941 7.011482 CCAGAAAGTTATTCTTATTCCTGACGG 59.989 40.741 0.00 0.00 35.02 4.79
2981 3133 4.134563 CTGCCCCAATGGTGTACTATAAC 58.865 47.826 0.00 0.00 36.04 1.89
3022 3174 5.376625 TCTTGTCTTCTGTTTGCCTTACAT 58.623 37.500 0.00 0.00 0.00 2.29
3189 3342 7.174599 ACATGAGAATTGAGAACCAGAAGAAAG 59.825 37.037 0.00 0.00 0.00 2.62
3191 3344 6.484643 TGAGAATTGAGAACCAGAAGAAAGTG 59.515 38.462 0.00 0.00 0.00 3.16
3198 3351 3.903530 ACCAGAAGAAAGTGGGGAAAT 57.096 42.857 0.00 0.00 38.25 2.17
3294 3454 0.980423 ACCCAAGTCTTCTCCTGCTC 59.020 55.000 0.00 0.00 0.00 4.26
3394 3556 6.169557 ACGATATTTGGATGCACCTAAGTA 57.830 37.500 0.00 0.00 36.89 2.24
3417 3585 6.144078 ACTGTGCTACAATATCGTCATGTA 57.856 37.500 0.00 0.00 0.00 2.29
3496 3668 2.158623 TCACTGGTTGGAATCACAAGCT 60.159 45.455 12.35 0.00 46.11 3.74
3515 3687 3.674528 CTGCTAGGCATATACAGCTGT 57.325 47.619 25.12 25.12 38.13 4.40
3557 3729 0.179037 GGCCATACATGCTCTGCAGA 60.179 55.000 17.19 17.19 43.65 4.26
3560 3732 2.550423 GCCATACATGCTCTGCAGAGAT 60.550 50.000 41.20 28.24 43.65 2.75
3574 3746 5.243507 TCTGCAGAGATGCTAAGAATAGGAG 59.756 44.000 13.74 0.00 32.57 3.69
3582 3754 3.519510 TGCTAAGAATAGGAGTTGCACCT 59.480 43.478 0.00 0.00 41.05 4.00
3629 3805 5.779241 ATATTGACTTTGGGACTTCAGGA 57.221 39.130 0.00 0.00 0.00 3.86
3671 3853 0.579630 TCGCGCACTTACTGTTTGTG 59.420 50.000 8.75 8.01 35.08 3.33
3683 3865 7.334421 CACTTACTGTTTGTGCTACCTGAATAT 59.666 37.037 0.00 0.00 0.00 1.28
3687 3869 6.942576 ACTGTTTGTGCTACCTGAATATCTTT 59.057 34.615 0.00 0.00 0.00 2.52
3712 3894 1.955778 CCACAACACATGGTGTCACAT 59.044 47.619 0.00 0.00 43.59 3.21
3719 3907 5.435686 ACACATGGTGTCACATATAACCT 57.564 39.130 5.12 0.00 43.92 3.50
3762 3950 7.661536 ACTCATGATTAGCTCTACTTGGTTA 57.338 36.000 0.00 0.00 0.00 2.85
3766 3954 6.716934 TGATTAGCTCTACTTGGTTAGGAG 57.283 41.667 0.00 0.00 35.99 3.69
3769 3957 3.792515 AGCTCTACTTGGTTAGGAGGTT 58.207 45.455 0.00 0.00 35.31 3.50
3804 3992 0.889994 TGCATGTGCCATTCTTGGTC 59.110 50.000 2.07 0.00 45.57 4.02
3817 4005 5.296780 CCATTCTTGGTCTTATATGTTGCGT 59.703 40.000 0.00 0.00 38.30 5.24
3848 4039 2.956333 ACCTTTTGTCTTTGCAGGTACC 59.044 45.455 2.73 2.73 36.02 3.34
3853 4044 0.602905 GTCTTTGCAGGTACCAGCGT 60.603 55.000 22.64 0.00 32.30 5.07
3979 4170 6.485313 TGTCCTTGTTCTGGTAAACATAACAG 59.515 38.462 0.00 0.00 43.97 3.16
3984 4181 7.667043 TGTTCTGGTAAACATAACAGACATC 57.333 36.000 3.19 0.00 40.10 3.06
4028 4409 2.140065 GCAACCAGCAAAGAAGGAAC 57.860 50.000 0.00 0.00 44.79 3.62
4033 4414 5.567423 GCAACCAGCAAAGAAGGAACATAAT 60.567 40.000 0.00 0.00 44.79 1.28
4034 4415 6.458210 CAACCAGCAAAGAAGGAACATAATT 58.542 36.000 0.00 0.00 0.00 1.40
4129 4517 2.234908 ACTGTGATAGCTCAACCTGGTC 59.765 50.000 0.00 0.00 31.85 4.02
4158 4546 4.919754 GCCATTAGTTAGGTATTACGACGG 59.080 45.833 0.00 0.00 0.00 4.79
4159 4547 5.507985 GCCATTAGTTAGGTATTACGACGGT 60.508 44.000 0.00 0.00 0.00 4.83
4239 4629 7.399634 CCTTTTGGATAACTTTAGGGTGTCTA 58.600 38.462 0.00 0.00 44.07 2.59
4279 4669 1.582968 GGCGAAGACTACGTGTCCA 59.417 57.895 12.53 0.00 46.46 4.02
4280 4670 0.456312 GGCGAAGACTACGTGTCCAG 60.456 60.000 12.53 0.00 46.46 3.86
4287 4677 1.119574 ACTACGTGTCCAGGGTGCTT 61.120 55.000 0.00 0.00 0.00 3.91
4288 4678 0.389948 CTACGTGTCCAGGGTGCTTC 60.390 60.000 0.00 0.00 0.00 3.86
4363 4753 8.295175 TAACATGTAAGTTAGGAGCCACTCCG 62.295 46.154 0.00 0.00 42.55 4.63
4432 4826 1.138661 ACCCAACTGTGCATGGTTTTG 59.861 47.619 3.47 2.29 34.79 2.44
4435 4829 2.608546 CCAACTGTGCATGGTTTTGTTG 59.391 45.455 0.00 0.00 34.79 3.33
4436 4830 2.600470 ACTGTGCATGGTTTTGTTGG 57.400 45.000 0.00 0.00 0.00 3.77
4437 4832 2.106566 ACTGTGCATGGTTTTGTTGGA 58.893 42.857 0.00 0.00 0.00 3.53
4440 4835 2.499289 TGTGCATGGTTTTGTTGGAACT 59.501 40.909 0.00 0.00 0.00 3.01
4482 4878 2.098934 TGCCTTGCACCTTTATAATGCG 59.901 45.455 5.35 0.00 42.44 4.73
4557 4981 0.603569 CAGAGTAGGCACTGTCGGTT 59.396 55.000 0.00 0.00 41.52 4.44
4587 5011 6.985188 TCAGTTGATTGATAAGTACCAAGC 57.015 37.500 0.00 0.00 0.00 4.01
4768 5578 0.460311 CGGGTAGAGAACGCTTGGAT 59.540 55.000 0.00 0.00 38.85 3.41
4817 5627 2.015736 AGCAGCACCATAAGAACTCG 57.984 50.000 0.00 0.00 0.00 4.18
4843 5653 2.038295 CCATCTCCCTTCAGACCTATGC 59.962 54.545 0.00 0.00 0.00 3.14
4849 5659 2.286872 CCTTCAGACCTATGCAGCAAG 58.713 52.381 0.00 0.00 0.00 4.01
4987 5797 1.198637 GCCTCAGAACACAGAACATGC 59.801 52.381 0.00 0.00 0.00 4.06
5003 5820 2.809446 CATGCAGCATGTGGAAAGATG 58.191 47.619 25.12 0.00 39.31 2.90
5011 5828 4.080129 AGCATGTGGAAAGATGACTATGGT 60.080 41.667 0.00 0.00 0.00 3.55
5017 5834 3.430929 GGAAAGATGACTATGGTGTCGCT 60.431 47.826 0.00 0.00 39.64 4.93
5018 5835 3.444703 AAGATGACTATGGTGTCGCTC 57.555 47.619 0.00 0.00 39.64 5.03
5020 5837 0.249073 ATGACTATGGTGTCGCTCGC 60.249 55.000 0.00 0.00 39.64 5.03
5021 5838 1.589196 GACTATGGTGTCGCTCGCC 60.589 63.158 0.00 3.64 46.12 5.54
5026 5843 4.664677 GGTGTCGCTCGCCACTGT 62.665 66.667 3.52 0.00 45.32 3.55
5057 5937 0.323302 TGTATTTGGCCAGACGCTCA 59.677 50.000 5.11 0.00 37.74 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 175 2.251642 GCGTTTTGCCTGTCTCGGT 61.252 57.895 0.00 0.00 37.76 4.69
651 659 7.519032 TTTACACCTGGATTTACTTTCCAAG 57.481 36.000 0.00 0.00 42.56 3.61
652 660 7.342284 TGTTTTACACCTGGATTTACTTTCCAA 59.658 33.333 0.00 0.00 42.56 3.53
653 661 6.834451 TGTTTTACACCTGGATTTACTTTCCA 59.166 34.615 0.00 0.00 40.96 3.53
654 662 7.143340 GTGTTTTACACCTGGATTTACTTTCC 58.857 38.462 0.00 0.00 43.05 3.13
655 663 6.854381 CGTGTTTTACACCTGGATTTACTTTC 59.146 38.462 0.00 0.00 45.93 2.62
656 664 6.731164 CGTGTTTTACACCTGGATTTACTTT 58.269 36.000 0.00 0.00 45.93 2.66
657 665 5.278120 GCGTGTTTTACACCTGGATTTACTT 60.278 40.000 0.00 0.00 45.93 2.24
658 666 4.214758 GCGTGTTTTACACCTGGATTTACT 59.785 41.667 0.00 0.00 45.93 2.24
659 667 4.214758 AGCGTGTTTTACACCTGGATTTAC 59.785 41.667 0.00 0.00 45.93 2.01
660 668 4.391155 AGCGTGTTTTACACCTGGATTTA 58.609 39.130 0.00 0.00 45.93 1.40
661 669 3.219281 AGCGTGTTTTACACCTGGATTT 58.781 40.909 0.00 0.00 45.93 2.17
662 670 2.858745 AGCGTGTTTTACACCTGGATT 58.141 42.857 0.00 0.00 45.93 3.01
663 671 2.561478 AGCGTGTTTTACACCTGGAT 57.439 45.000 0.00 0.00 45.93 3.41
664 672 2.335316 AAGCGTGTTTTACACCTGGA 57.665 45.000 0.00 0.00 45.93 3.86
665 673 2.356382 TGAAAGCGTGTTTTACACCTGG 59.644 45.455 4.52 0.00 45.93 4.45
666 674 3.359654 GTGAAAGCGTGTTTTACACCTG 58.640 45.455 4.52 0.00 45.93 4.00
667 675 2.356695 GGTGAAAGCGTGTTTTACACCT 59.643 45.455 16.06 0.85 45.93 4.00
668 676 2.542205 GGGTGAAAGCGTGTTTTACACC 60.542 50.000 15.51 15.51 45.93 4.16
669 677 2.097791 TGGGTGAAAGCGTGTTTTACAC 59.902 45.455 8.72 0.00 45.26 2.90
670 678 2.366533 TGGGTGAAAGCGTGTTTTACA 58.633 42.857 8.72 0.00 33.03 2.41
671 679 3.423996 TTGGGTGAAAGCGTGTTTTAC 57.576 42.857 0.00 0.00 33.03 2.01
672 680 4.158025 TCTTTTGGGTGAAAGCGTGTTTTA 59.842 37.500 0.00 0.00 36.73 1.52
673 681 3.056465 TCTTTTGGGTGAAAGCGTGTTTT 60.056 39.130 0.00 0.00 36.73 2.43
674 682 2.494073 TCTTTTGGGTGAAAGCGTGTTT 59.506 40.909 0.00 0.00 36.73 2.83
675 683 2.096248 TCTTTTGGGTGAAAGCGTGTT 58.904 42.857 0.00 0.00 36.73 3.32
685 693 2.005451 CAGATCTCGCTCTTTTGGGTG 58.995 52.381 0.00 0.00 0.00 4.61
691 699 0.463620 GAGGGCAGATCTCGCTCTTT 59.536 55.000 17.21 1.08 41.37 2.52
712 724 2.615262 GAATCCGCGTCGCTTCCTCT 62.615 60.000 16.36 0.00 0.00 3.69
715 727 3.262686 GGAATCCGCGTCGCTTCC 61.263 66.667 17.72 17.72 32.94 3.46
745 757 2.733218 CGTGCGCCGAGAAGAACA 60.733 61.111 4.18 0.00 39.56 3.18
746 758 4.135493 GCGTGCGCCGAGAAGAAC 62.135 66.667 20.06 1.41 39.56 3.01
747 759 4.656117 TGCGTGCGCCGAGAAGAA 62.656 61.111 20.06 0.00 41.09 2.52
777 789 0.104671 GAGATGGGACTGAGCTGAGC 59.895 60.000 0.00 0.00 0.00 4.26
779 791 2.037901 GATGAGATGGGACTGAGCTGA 58.962 52.381 0.00 0.00 0.00 4.26
780 792 2.036217 GAGATGAGATGGGACTGAGCTG 59.964 54.545 0.00 0.00 0.00 4.24
781 793 2.318908 GAGATGAGATGGGACTGAGCT 58.681 52.381 0.00 0.00 0.00 4.09
789 801 1.414061 AAGGGGCGAGATGAGATGGG 61.414 60.000 0.00 0.00 0.00 4.00
819 835 1.967597 GCGAGGCCGAAACTTACTGC 61.968 60.000 0.00 0.00 38.22 4.40
864 895 2.279120 CTGAGAGACCCGATGCGC 60.279 66.667 0.00 0.00 0.00 6.09
1438 1525 3.611792 GACGAGCACGATGAGCGC 61.612 66.667 11.40 0.00 46.04 5.92
1513 1604 4.208686 GCTCCGTACAGCCCGAGG 62.209 72.222 0.00 0.00 32.76 4.63
1583 1679 1.544724 CCTTCCCAAAATCTCGCCAA 58.455 50.000 0.00 0.00 0.00 4.52
1762 1888 0.532573 GTGGAGATCTGGACGCAGAA 59.467 55.000 0.00 0.00 34.56 3.02
1840 1968 5.308014 TGATTTTCAGAGCTGCAAGACTAA 58.692 37.500 1.02 0.00 34.07 2.24
1929 2059 7.652300 TTTACTGAACATACTGTGTGCTAAG 57.348 36.000 4.33 0.00 41.14 2.18
1960 2096 5.987347 CCTTCAGTACGACCTTACAAAAAGA 59.013 40.000 0.00 0.00 0.00 2.52
1961 2097 5.756833 ACCTTCAGTACGACCTTACAAAAAG 59.243 40.000 0.00 0.00 0.00 2.27
1963 2099 5.280654 ACCTTCAGTACGACCTTACAAAA 57.719 39.130 0.00 0.00 0.00 2.44
1967 2103 5.052481 ACAAAACCTTCAGTACGACCTTAC 58.948 41.667 0.00 0.00 0.00 2.34
2025 2161 0.550914 ACCAAACTGGGACAAGAGCA 59.449 50.000 0.00 0.00 43.37 4.26
2084 2220 8.271458 TGATCTCTAGAGGTATCATGATAGACC 58.729 40.741 19.67 16.42 0.00 3.85
2112 2248 7.806180 AGTTTATAACCATCCACTAGCTGATT 58.194 34.615 0.00 0.00 0.00 2.57
2187 2324 4.837093 AAGATCAGAAACCATTACCCGA 57.163 40.909 0.00 0.00 0.00 5.14
2248 2386 9.478238 TTTATTCATTCCAGAGGATGAATCAAA 57.522 29.630 11.86 9.01 38.94 2.69
2251 2389 8.455903 TGTTTATTCATTCCAGAGGATGAATC 57.544 34.615 11.86 1.45 38.94 2.52
2252 2390 8.277197 TCTGTTTATTCATTCCAGAGGATGAAT 58.723 33.333 12.85 12.85 40.03 2.57
2253 2391 7.632861 TCTGTTTATTCATTCCAGAGGATGAA 58.367 34.615 0.00 0.00 35.47 2.57
2254 2392 7.199167 TCTGTTTATTCATTCCAGAGGATGA 57.801 36.000 0.00 0.00 0.00 2.92
2260 2398 6.874278 TCTCCTCTGTTTATTCATTCCAGA 57.126 37.500 0.00 0.00 0.00 3.86
2261 2399 7.052873 ACATCTCCTCTGTTTATTCATTCCAG 58.947 38.462 0.00 0.00 0.00 3.86
2262 2400 6.962182 ACATCTCCTCTGTTTATTCATTCCA 58.038 36.000 0.00 0.00 0.00 3.53
2263 2401 7.872113 AACATCTCCTCTGTTTATTCATTCC 57.128 36.000 0.00 0.00 33.10 3.01
2264 2402 7.699812 GCAAACATCTCCTCTGTTTATTCATTC 59.300 37.037 1.51 0.00 43.15 2.67
2265 2403 7.395489 AGCAAACATCTCCTCTGTTTATTCATT 59.605 33.333 1.51 0.00 43.15 2.57
2266 2404 6.888632 AGCAAACATCTCCTCTGTTTATTCAT 59.111 34.615 1.51 0.00 43.15 2.57
2267 2405 6.240894 AGCAAACATCTCCTCTGTTTATTCA 58.759 36.000 1.51 0.00 43.15 2.57
2268 2406 6.749923 AGCAAACATCTCCTCTGTTTATTC 57.250 37.500 1.51 0.00 43.15 1.75
2269 2407 7.335422 CAGTAGCAAACATCTCCTCTGTTTATT 59.665 37.037 1.51 0.00 43.15 1.40
2270 2408 6.820656 CAGTAGCAAACATCTCCTCTGTTTAT 59.179 38.462 1.51 0.00 43.15 1.40
2271 2409 6.166279 CAGTAGCAAACATCTCCTCTGTTTA 58.834 40.000 1.51 0.00 43.15 2.01
2272 2410 4.999950 CAGTAGCAAACATCTCCTCTGTTT 59.000 41.667 0.00 0.00 45.23 2.83
2273 2411 4.040952 ACAGTAGCAAACATCTCCTCTGTT 59.959 41.667 0.00 0.00 38.44 3.16
2274 2412 3.580458 ACAGTAGCAAACATCTCCTCTGT 59.420 43.478 0.00 0.00 0.00 3.41
2275 2413 4.199432 ACAGTAGCAAACATCTCCTCTG 57.801 45.455 0.00 0.00 0.00 3.35
2276 2414 6.552445 AATACAGTAGCAAACATCTCCTCT 57.448 37.500 0.00 0.00 0.00 3.69
2277 2415 7.550906 AGAAAATACAGTAGCAAACATCTCCTC 59.449 37.037 0.00 0.00 0.00 3.71
2278 2416 7.398024 AGAAAATACAGTAGCAAACATCTCCT 58.602 34.615 0.00 0.00 0.00 3.69
2279 2417 7.617041 AGAAAATACAGTAGCAAACATCTCC 57.383 36.000 0.00 0.00 0.00 3.71
2280 2418 9.899226 AAAAGAAAATACAGTAGCAAACATCTC 57.101 29.630 0.00 0.00 0.00 2.75
2281 2419 9.683069 CAAAAGAAAATACAGTAGCAAACATCT 57.317 29.630 0.00 0.00 0.00 2.90
2282 2420 9.463443 ACAAAAGAAAATACAGTAGCAAACATC 57.537 29.630 0.00 0.00 0.00 3.06
2283 2421 9.816354 AACAAAAGAAAATACAGTAGCAAACAT 57.184 25.926 0.00 0.00 0.00 2.71
2287 2425 9.944663 CAGTAACAAAAGAAAATACAGTAGCAA 57.055 29.630 0.00 0.00 0.00 3.91
2288 2426 9.116067 ACAGTAACAAAAGAAAATACAGTAGCA 57.884 29.630 0.00 0.00 0.00 3.49
2326 2467 8.112183 AGATAATGGAAGACAGAAAATGGAGTT 58.888 33.333 0.00 0.00 0.00 3.01
2327 2468 7.637511 AGATAATGGAAGACAGAAAATGGAGT 58.362 34.615 0.00 0.00 0.00 3.85
2346 2487 9.838339 ACAATACAGTAGCAAAAGCTAGATAAT 57.162 29.630 0.00 0.00 0.00 1.28
2361 2502 5.292101 GCAGCTAGAACCAACAATACAGTAG 59.708 44.000 0.00 0.00 0.00 2.57
2395 2541 1.303309 GAATGGCGCATCTAAGCACT 58.697 50.000 10.83 0.00 34.54 4.40
2411 2557 5.068723 GCTGAAATGTTCATCTCCCATGAAT 59.931 40.000 0.00 0.00 39.80 2.57
2497 2644 9.624697 GAACTGCAAAAACATCTTATATTGTGA 57.375 29.630 0.00 0.00 0.00 3.58
2498 2645 9.409312 TGAACTGCAAAAACATCTTATATTGTG 57.591 29.630 0.00 0.00 0.00 3.33
2499 2646 9.979578 TTGAACTGCAAAAACATCTTATATTGT 57.020 25.926 0.00 0.00 32.46 2.71
2515 2662 9.875675 GTTTTTGCAATATAATTTGAACTGCAA 57.124 25.926 0.00 2.65 44.16 4.08
2516 2663 8.219769 CGTTTTTGCAATATAATTTGAACTGCA 58.780 29.630 0.00 0.00 36.60 4.41
2517 2664 8.220434 ACGTTTTTGCAATATAATTTGAACTGC 58.780 29.630 0.00 0.00 0.00 4.40
2518 2665 9.726034 GACGTTTTTGCAATATAATTTGAACTG 57.274 29.630 0.00 0.00 0.00 3.16
2519 2666 9.691362 AGACGTTTTTGCAATATAATTTGAACT 57.309 25.926 0.00 0.00 0.00 3.01
2533 2680 9.268255 CGTATCAAAATATAAGACGTTTTTGCA 57.732 29.630 13.47 6.02 38.38 4.08
2534 2681 8.730427 CCGTATCAAAATATAAGACGTTTTTGC 58.270 33.333 13.47 2.95 38.38 3.68
2535 2682 9.976255 TCCGTATCAAAATATAAGACGTTTTTG 57.024 29.630 12.50 12.50 39.33 2.44
2538 2685 8.823818 CCTTCCGTATCAAAATATAAGACGTTT 58.176 33.333 0.00 0.00 0.00 3.60
2539 2686 8.199449 TCCTTCCGTATCAAAATATAAGACGTT 58.801 33.333 0.00 0.00 0.00 3.99
2540 2687 7.719483 TCCTTCCGTATCAAAATATAAGACGT 58.281 34.615 0.00 0.00 0.00 4.34
2541 2688 7.866393 ACTCCTTCCGTATCAAAATATAAGACG 59.134 37.037 0.00 0.00 0.00 4.18
2547 2694 9.503399 GGAAATACTCCTTCCGTATCAAAATAT 57.497 33.333 0.00 0.00 41.61 1.28
2548 2695 8.487848 TGGAAATACTCCTTCCGTATCAAAATA 58.512 33.333 0.00 0.00 44.61 1.40
2549 2696 7.343357 TGGAAATACTCCTTCCGTATCAAAAT 58.657 34.615 0.00 0.00 44.61 1.82
2550 2697 6.713276 TGGAAATACTCCTTCCGTATCAAAA 58.287 36.000 0.00 0.00 44.61 2.44
2551 2698 6.302535 TGGAAATACTCCTTCCGTATCAAA 57.697 37.500 0.00 0.00 44.61 2.69
2552 2699 5.943349 TGGAAATACTCCTTCCGTATCAA 57.057 39.130 0.00 0.00 44.61 2.57
2553 2700 6.099125 TCAATGGAAATACTCCTTCCGTATCA 59.901 38.462 0.00 0.00 44.61 2.15
2554 2701 6.522054 TCAATGGAAATACTCCTTCCGTATC 58.478 40.000 0.00 0.00 44.61 2.24
2555 2702 6.494666 TCAATGGAAATACTCCTTCCGTAT 57.505 37.500 0.00 0.00 44.61 3.06
2556 2703 5.943349 TCAATGGAAATACTCCTTCCGTA 57.057 39.130 0.00 0.00 44.61 4.02
2557 2704 4.837093 TCAATGGAAATACTCCTTCCGT 57.163 40.909 0.00 0.00 44.61 4.69
2558 2705 6.699575 AAATCAATGGAAATACTCCTTCCG 57.300 37.500 0.00 0.00 44.61 4.30
2559 2706 8.066612 TCAAAATCAATGGAAATACTCCTTCC 57.933 34.615 0.00 0.00 45.64 3.46
2561 2708 9.880157 CAATCAAAATCAATGGAAATACTCCTT 57.120 29.630 0.00 0.00 45.64 3.36
2562 2709 7.983484 GCAATCAAAATCAATGGAAATACTCCT 59.017 33.333 0.00 0.00 45.64 3.69
2563 2710 7.225341 GGCAATCAAAATCAATGGAAATACTCC 59.775 37.037 0.00 0.00 45.64 3.85
2564 2711 7.043192 CGGCAATCAAAATCAATGGAAATACTC 60.043 37.037 0.00 0.00 0.00 2.59
2565 2712 6.757947 CGGCAATCAAAATCAATGGAAATACT 59.242 34.615 0.00 0.00 0.00 2.12
2566 2713 6.756074 TCGGCAATCAAAATCAATGGAAATAC 59.244 34.615 0.00 0.00 0.00 1.89
2570 2717 4.797800 TCGGCAATCAAAATCAATGGAA 57.202 36.364 0.00 0.00 0.00 3.53
2626 2773 9.878599 AAAAACAGTCAGATTCTACGTTTAATG 57.121 29.630 0.00 0.00 0.00 1.90
2634 2781 9.173939 CATGAAACAAAAACAGTCAGATTCTAC 57.826 33.333 0.00 0.00 0.00 2.59
2640 2787 6.507958 TCACATGAAACAAAAACAGTCAGA 57.492 33.333 0.00 0.00 0.00 3.27
2747 2896 8.738645 AACTTTCTGGCTAATCTTACTTATGG 57.261 34.615 0.00 0.00 0.00 2.74
3032 3185 6.920758 CACAGCTTAGAGTAACCATATCAGTC 59.079 42.308 0.00 0.00 0.00 3.51
3045 3198 6.381420 ACAATATACTGACCACAGCTTAGAGT 59.619 38.462 0.00 0.00 46.95 3.24
3051 3204 8.046708 TCAATAAACAATATACTGACCACAGCT 58.953 33.333 0.00 0.00 46.95 4.24
3157 3310 8.539544 TCTGGTTCTCAATTCTCATGTACAATA 58.460 33.333 0.00 0.00 0.00 1.90
3160 3313 6.358974 TCTGGTTCTCAATTCTCATGTACA 57.641 37.500 0.00 0.00 0.00 2.90
3161 3314 7.099764 TCTTCTGGTTCTCAATTCTCATGTAC 58.900 38.462 0.00 0.00 0.00 2.90
3165 3318 7.174599 CACTTTCTTCTGGTTCTCAATTCTCAT 59.825 37.037 0.00 0.00 0.00 2.90
3172 3325 3.435026 CCCCACTTTCTTCTGGTTCTCAA 60.435 47.826 0.00 0.00 0.00 3.02
3189 3342 0.541764 TTCAGCACCCATTTCCCCAC 60.542 55.000 0.00 0.00 0.00 4.61
3191 3344 0.039618 TCTTCAGCACCCATTTCCCC 59.960 55.000 0.00 0.00 0.00 4.81
3198 3351 2.256306 TGTATCAGTCTTCAGCACCCA 58.744 47.619 0.00 0.00 0.00 4.51
3267 3427 4.034410 GGAGAAGACTTGGGTCCTTATCT 58.966 47.826 0.00 0.00 43.05 1.98
3294 3454 8.999431 ACATTATGTGTAAAGTACAAAGACTGG 58.001 33.333 0.00 0.00 40.93 4.00
3372 3534 6.146184 CAGTACTTAGGTGCATCCAAATATCG 59.854 42.308 0.00 0.00 39.02 2.92
3394 3556 5.011090 ACATGACGATATTGTAGCACAGT 57.989 39.130 0.00 0.00 0.00 3.55
3417 3585 6.183360 CCTTTCAGAGATTTTCACACCAACTT 60.183 38.462 0.00 0.00 0.00 2.66
3496 3668 5.545063 TTTACAGCTGTATATGCCTAGCA 57.455 39.130 26.54 5.46 44.86 3.49
3557 3729 5.363939 GTGCAACTCCTATTCTTAGCATCT 58.636 41.667 0.00 0.00 32.98 2.90
3560 3732 3.519510 AGGTGCAACTCCTATTCTTAGCA 59.480 43.478 0.00 0.00 36.74 3.49
3574 3746 6.603237 AAAGCAGAATTTTAAAGGTGCAAC 57.397 33.333 0.00 0.00 33.24 4.17
3730 3918 9.678260 AGTAGAGCTAATCATGAGTTCAAAAAT 57.322 29.630 0.00 0.00 0.00 1.82
3744 3932 5.599242 ACCTCCTAACCAAGTAGAGCTAATC 59.401 44.000 0.00 0.00 0.00 1.75
3762 3950 1.428869 ACTTGCAGTGAGAACCTCCT 58.571 50.000 0.00 0.00 0.00 3.69
3766 3954 2.860136 GCAAAAACTTGCAGTGAGAACC 59.140 45.455 5.01 0.00 46.60 3.62
3804 3992 9.472361 AGGTTACACTTATACGCAACATATAAG 57.528 33.333 9.27 9.27 43.66 1.73
3817 4005 8.453238 TGCAAAGACAAAAGGTTACACTTATA 57.547 30.769 0.00 0.00 0.00 0.98
3848 4039 2.816958 AAGATGCTGCCGACGCTG 60.817 61.111 0.00 0.00 37.03 5.18
3853 4044 2.229675 CATCTACAAGATGCTGCCGA 57.770 50.000 4.10 0.00 44.69 5.54
3979 4170 6.962686 TGCAGTGATTATAGCAAATGATGTC 58.037 36.000 0.00 0.00 33.48 3.06
4028 4409 4.860907 GCACAGAAACAAGAGGCAATTATG 59.139 41.667 0.00 0.00 0.00 1.90
4033 4414 2.057137 AGCACAGAAACAAGAGGCAA 57.943 45.000 0.00 0.00 0.00 4.52
4034 4415 1.677576 CAAGCACAGAAACAAGAGGCA 59.322 47.619 0.00 0.00 0.00 4.75
4129 4517 2.717639 ACCTAACTAATGGCTGCAGG 57.282 50.000 17.12 0.00 0.00 4.85
4226 4615 5.640189 TCGTTTCTCTAGACACCCTAAAG 57.360 43.478 0.00 0.00 0.00 1.85
4239 4629 2.462456 TCTGCTTGCATCGTTTCTCT 57.538 45.000 0.00 0.00 0.00 3.10
4279 4669 0.886490 CGAGCAACAAGAAGCACCCT 60.886 55.000 0.00 0.00 0.00 4.34
4280 4670 1.576421 CGAGCAACAAGAAGCACCC 59.424 57.895 0.00 0.00 0.00 4.61
4363 4753 5.985781 ACGGATGCACGATCAAATAAATAC 58.014 37.500 3.48 0.00 37.61 1.89
4365 4755 5.065859 TGAACGGATGCACGATCAAATAAAT 59.934 36.000 7.13 0.00 41.59 1.40
4440 4835 8.079201 AGGCAACACAAGACATGAAAATGTCA 62.079 38.462 18.29 0.00 46.35 3.58
4454 4849 4.736165 GGTGCAAGGCAACACAAG 57.264 55.556 0.59 0.00 46.68 3.16
4482 4878 4.394920 ACCACGACATCAACATAATCAACC 59.605 41.667 0.00 0.00 0.00 3.77
4510 4906 6.550481 TGCATACCCATCAATCAACAATACAT 59.450 34.615 0.00 0.00 0.00 2.29
4557 4981 8.946085 GGTACTTATCAATCAACTGAAACATGA 58.054 33.333 0.00 0.00 0.00 3.07
4587 5011 8.729756 TGCATCCATAAATGAAAATCTATACCG 58.270 33.333 0.00 0.00 0.00 4.02
4643 5444 1.335964 TGCTCTTCTGACGAGTTTCGG 60.336 52.381 12.10 0.00 45.59 4.30
4689 5490 1.467342 GGCCGATTAGTGGTGTGTTTC 59.533 52.381 0.00 0.00 0.00 2.78
4843 5653 0.608582 AAGAAGGAGCCTGCTTGCTG 60.609 55.000 9.01 0.00 40.27 4.41
4849 5659 1.902938 ACTGAAAAGAAGGAGCCTGC 58.097 50.000 0.00 0.00 0.00 4.85
4851 5661 2.573915 CCCTACTGAAAAGAAGGAGCCT 59.426 50.000 0.00 0.00 0.00 4.58
4854 5664 3.369997 GGAGCCCTACTGAAAAGAAGGAG 60.370 52.174 0.00 0.00 0.00 3.69
4855 5665 2.572104 GGAGCCCTACTGAAAAGAAGGA 59.428 50.000 0.00 0.00 0.00 3.36
4856 5666 2.305927 TGGAGCCCTACTGAAAAGAAGG 59.694 50.000 0.00 0.00 0.00 3.46
4952 5762 0.520847 GAGGCTTCTTGCTTGTGCTC 59.479 55.000 0.00 0.00 42.39 4.26
4959 5769 1.141657 TGTGTTCTGAGGCTTCTTGCT 59.858 47.619 0.00 0.00 42.39 3.91
4960 5770 1.534595 CTGTGTTCTGAGGCTTCTTGC 59.465 52.381 0.00 0.00 41.94 4.01
4961 5771 3.117491 TCTGTGTTCTGAGGCTTCTTG 57.883 47.619 0.00 0.00 0.00 3.02
4987 5797 4.275196 CCATAGTCATCTTTCCACATGCTG 59.725 45.833 0.00 0.00 0.00 4.41
5003 5820 1.589196 GGCGAGCGACACCATAGTC 60.589 63.158 0.00 0.00 35.19 2.59
5011 5828 1.029681 ATATACAGTGGCGAGCGACA 58.970 50.000 12.43 0.79 0.00 4.35
5017 5834 2.953453 ACCAGGTATATACAGTGGCGA 58.047 47.619 23.92 0.00 36.05 5.54
5018 5835 3.181469 ACAACCAGGTATATACAGTGGCG 60.181 47.826 23.92 19.36 36.05 5.69
5020 5837 7.444183 CCAAATACAACCAGGTATATACAGTGG 59.556 40.741 22.99 22.99 37.67 4.00
5021 5838 7.041372 GCCAAATACAACCAGGTATATACAGTG 60.041 40.741 14.70 10.57 32.95 3.66
5022 5839 6.996282 GCCAAATACAACCAGGTATATACAGT 59.004 38.462 14.70 6.00 32.95 3.55
5023 5840 6.430000 GGCCAAATACAACCAGGTATATACAG 59.570 42.308 14.70 6.42 32.95 2.74
5024 5841 6.126449 TGGCCAAATACAACCAGGTATATACA 60.126 38.462 14.70 0.00 32.95 2.29
5025 5842 6.300703 TGGCCAAATACAACCAGGTATATAC 58.699 40.000 0.61 4.14 32.95 1.47
5026 5843 6.517013 TGGCCAAATACAACCAGGTATATA 57.483 37.500 0.61 0.00 32.95 0.86
5057 5937 2.686835 GGAGCTCCCTGCAGGTCT 60.687 66.667 30.63 22.84 45.94 3.85


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

AutoCloner maintained by Alex Coulton.