Multiple sequence alignment - TraesCS1A01G220200

Loading Multiple Alignment...

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 TraesCS1A01G220200 chr1A 100.000 4786 0 0 1 4786 389060591 389065376 0.000000e+00 8839.0
1 TraesCS1A01G220200 chr1A 93.443 61 3 1 2943 3003 95850333 95850274 6.600000e-14 89.8
2 TraesCS1A01G220200 chr1D 96.036 2195 53 20 663 2848 309565182 309567351 0.000000e+00 3541.0
3 TraesCS1A01G220200 chr1D 93.619 1144 47 15 2825 3942 309567355 309568498 0.000000e+00 1685.0
4 TraesCS1A01G220200 chr1D 92.092 784 28 9 4023 4785 309568496 309569266 0.000000e+00 1074.0
5 TraesCS1A01G220200 chr1D 94.737 95 3 2 3934 4027 275947616 275947709 3.860000e-31 147.0
6 TraesCS1A01G220200 chr1B 92.567 2314 94 20 663 2935 419200873 419203149 0.000000e+00 3249.0
7 TraesCS1A01G220200 chr1B 95.032 946 38 3 2999 3942 419203148 419204086 0.000000e+00 1478.0
8 TraesCS1A01G220200 chr1B 82.656 738 79 25 4023 4728 419204084 419204804 4.100000e-170 608.0
9 TraesCS1A01G220200 chr1B 90.000 70 3 4 2942 3010 151463456 151463390 2.370000e-13 87.9
10 TraesCS1A01G220200 chr1B 93.220 59 3 1 2942 3000 598882773 598882716 8.530000e-13 86.1
11 TraesCS1A01G220200 chr3D 92.832 837 49 7 2019 2851 188627693 188626864 0.000000e+00 1203.0
12 TraesCS1A01G220200 chr3D 91.452 854 57 9 1075 1921 188628540 188627696 0.000000e+00 1158.0
13 TraesCS1A01G220200 chr3D 94.776 670 32 3 1661 2327 73325952 73325283 0.000000e+00 1040.0
14 TraesCS1A01G220200 chr3D 91.282 195 15 2 1075 1268 73326144 73325951 1.020000e-66 265.0
15 TraesCS1A01G220200 chr3D 91.743 109 9 0 2825 2933 188626863 188626755 8.300000e-33 152.0
16 TraesCS1A01G220200 chr3D 91.346 104 7 2 3929 4031 302930483 302930381 1.800000e-29 141.0
17 TraesCS1A01G220200 chr3D 93.333 60 3 1 2943 3002 420463239 420463297 2.370000e-13 87.9
18 TraesCS1A01G220200 chr7D 83.910 578 72 12 19 594 549721902 549721344 2.540000e-147 532.0
19 TraesCS1A01G220200 chr7D 87.912 273 18 4 7 272 49665091 49665355 1.670000e-79 307.0
20 TraesCS1A01G220200 chr7D 93.478 92 6 0 3934 4025 498229832 498229923 2.320000e-28 137.0
21 TraesCS1A01G220200 chr4D 80.399 602 98 7 9 600 481055721 481056312 1.580000e-119 440.0
22 TraesCS1A01G220200 chr5D 79.139 604 87 14 8 600 495379932 495379357 9.720000e-102 381.0
23 TraesCS1A01G220200 chr2D 77.143 595 99 20 19 594 621499756 621500332 1.290000e-80 311.0
24 TraesCS1A01G220200 chr2D 97.727 88 2 0 3940 4027 612817262 612817349 8.300000e-33 152.0
25 TraesCS1A01G220200 chr2D 92.188 64 2 3 2939 3001 573891838 573891899 2.370000e-13 87.9
26 TraesCS1A01G220200 chr2D 89.706 68 5 2 2939 3006 631487251 631487316 8.530000e-13 86.1
27 TraesCS1A01G220200 chr3B 76.420 581 110 14 34 600 775077377 775077944 6.060000e-74 289.0
28 TraesCS1A01G220200 chr7A 76.014 567 108 18 22 574 646094604 646095156 7.900000e-68 268.0
29 TraesCS1A01G220200 chr7A 93.548 62 3 1 2942 3003 692919246 692919186 1.830000e-14 91.6
30 TraesCS1A01G220200 chr3A 75.309 567 111 17 22 574 121465120 121465671 1.330000e-60 244.0
31 TraesCS1A01G220200 chr3A 75.393 573 101 26 22 574 221939038 221939590 1.720000e-59 241.0
32 TraesCS1A01G220200 chr3A 93.878 98 3 3 3937 4033 692055444 692055349 1.390000e-30 145.0
33 TraesCS1A01G220200 chr4A 73.862 593 114 27 22 594 387058350 387057779 1.050000e-46 198.0
34 TraesCS1A01G220200 chr4A 93.878 98 4 2 3940 4037 428159973 428159878 3.860000e-31 147.0
35 TraesCS1A01G220200 chr4B 96.739 92 3 0 3937 4028 418517473 418517382 2.310000e-33 154.0
36 TraesCS1A01G220200 chr7B 92.079 101 5 3 3924 4024 622831026 622831123 6.460000e-29 139.0
37 TraesCS1A01G220200 chr7B 95.294 85 4 0 3940 4024 107127399 107127483 8.350000e-28 135.0
38 TraesCS1A01G220200 chr7B 92.424 66 3 2 2942 3007 680211579 680211516 5.100000e-15 93.5
39 TraesCS1A01G220200 chr7B 90.698 43 4 0 4477 4519 55758697 55758739 1.860000e-04 58.4
40 TraesCS1A01G220200 chr5B 90.769 65 5 1 2939 3003 36765422 36765485 8.530000e-13 86.1
41 TraesCS1A01G220200 chr5A 95.000 40 2 0 4482 4521 632201758 632201797 4.000000e-06 63.9


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G220200 chr1A 389060591 389065376 4785 False 8839.000000 8839 100.000000 1 4786 1 chr1A.!!$F1 4785
1 TraesCS1A01G220200 chr1D 309565182 309569266 4084 False 2100.000000 3541 93.915667 663 4785 3 chr1D.!!$F2 4122
2 TraesCS1A01G220200 chr1B 419200873 419204804 3931 False 1778.333333 3249 90.085000 663 4728 3 chr1B.!!$F1 4065
3 TraesCS1A01G220200 chr3D 188626755 188628540 1785 True 837.666667 1203 92.009000 1075 2933 3 chr3D.!!$R3 1858
4 TraesCS1A01G220200 chr3D 73325283 73326144 861 True 652.500000 1040 93.029000 1075 2327 2 chr3D.!!$R2 1252
5 TraesCS1A01G220200 chr7D 549721344 549721902 558 True 532.000000 532 83.910000 19 594 1 chr7D.!!$R1 575
6 TraesCS1A01G220200 chr4D 481055721 481056312 591 False 440.000000 440 80.399000 9 600 1 chr4D.!!$F1 591
7 TraesCS1A01G220200 chr5D 495379357 495379932 575 True 381.000000 381 79.139000 8 600 1 chr5D.!!$R1 592
8 TraesCS1A01G220200 chr2D 621499756 621500332 576 False 311.000000 311 77.143000 19 594 1 chr2D.!!$F3 575
9 TraesCS1A01G220200 chr3B 775077377 775077944 567 False 289.000000 289 76.420000 34 600 1 chr3B.!!$F1 566
10 TraesCS1A01G220200 chr7A 646094604 646095156 552 False 268.000000 268 76.014000 22 574 1 chr7A.!!$F1 552
11 TraesCS1A01G220200 chr3A 121465120 121465671 551 False 244.000000 244 75.309000 22 574 1 chr3A.!!$F1 552
12 TraesCS1A01G220200 chr3A 221939038 221939590 552 False 241.000000 241 75.393000 22 574 1 chr3A.!!$F2 552

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
918 932 0.030603 AACCCATCCTCCTCCTCCTC 60.031 60.0 0.00 0.0 0.0 3.71 F
925 939 0.105709 CCTCCTCCTCCTCCTTCTCC 60.106 65.0 0.00 0.0 0.0 3.71 F
1233 1262 0.815615 GTGGGGCGTCTGATTGATCC 60.816 60.0 0.00 0.0 0.0 3.36 F
2621 2668 0.603569 CTCCACGTGTCTGGCTTACT 59.396 55.0 15.65 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2152 2191 0.107703 TGTCATCATCCGGCTGTTCC 60.108 55.000 5.0 0.0 0.00 3.62 R
2156 2195 1.671979 ATGTTGTCATCATCCGGCTG 58.328 50.000 0.0 0.0 0.00 4.85 R
2883 2957 2.029739 TCACGAATGCCGACTTACTGAA 60.030 45.455 0.0 0.0 41.76 3.02 R
4220 4337 0.537653 TCCAGACGAACCAACACACA 59.462 50.000 0.0 0.0 0.00 3.72 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
95 97 2.044650 TGGCCCTCAGCATCTTGC 60.045 61.111 0.00 0.00 46.50 4.01
96 98 2.832201 GGCCCTCAGCATCTTGCC 60.832 66.667 0.00 0.00 46.52 4.52
97 99 2.832201 GCCCTCAGCATCTTGCCC 60.832 66.667 0.00 0.00 46.52 5.36
98 100 2.123982 CCCTCAGCATCTTGCCCC 60.124 66.667 0.00 0.00 46.52 5.80
99 101 2.123982 CCTCAGCATCTTGCCCCC 60.124 66.667 0.00 0.00 46.52 5.40
187 189 2.034939 CCACATGCTGAAAAGCTCACAA 59.965 45.455 0.00 0.00 35.49 3.33
188 190 3.305813 CCACATGCTGAAAAGCTCACAAT 60.306 43.478 0.00 0.00 35.49 2.71
226 237 1.541588 CTCAAAGGTAGCTTGGTTGCC 59.458 52.381 8.16 0.00 0.00 4.52
233 244 2.037121 GGTAGCTTGGTTGCCACAATTT 59.963 45.455 0.00 0.00 30.78 1.82
267 278 3.181445 ACATATGGCCGCTAATCCAAAGA 60.181 43.478 7.80 0.00 35.75 2.52
278 289 6.458342 CCGCTAATCCAAAGATGTAAAACCTC 60.458 42.308 0.00 0.00 31.29 3.85
312 323 5.480422 GGGAGGAAAACATAACACCAAGAAT 59.520 40.000 0.00 0.00 0.00 2.40
313 324 6.014584 GGGAGGAAAACATAACACCAAGAATT 60.015 38.462 0.00 0.00 0.00 2.17
314 325 7.441836 GGAGGAAAACATAACACCAAGAATTT 58.558 34.615 0.00 0.00 0.00 1.82
316 327 9.325198 GAGGAAAACATAACACCAAGAATTTTT 57.675 29.630 0.00 0.00 0.00 1.94
390 402 4.160626 GTCCTCCAAACACTCTAGCTACAT 59.839 45.833 0.00 0.00 0.00 2.29
400 412 7.353414 ACACTCTAGCTACATGACATGTAAT 57.647 36.000 24.68 19.04 44.44 1.89
428 440 5.761205 AGGTGCTTAGAAGTCTCTCTATCA 58.239 41.667 0.00 0.00 32.70 2.15
445 457 3.687572 ATCATTGCAGAACGAGCATTC 57.312 42.857 0.00 0.00 42.33 2.67
446 458 2.703416 TCATTGCAGAACGAGCATTCT 58.297 42.857 0.00 0.00 42.33 2.40
500 513 4.008074 TCTCTTGTCAAGACAACATCCC 57.992 45.455 11.36 0.00 45.42 3.85
520 533 2.420022 CCGAAACAGTTGCCATAGGAAG 59.580 50.000 0.00 0.00 0.00 3.46
550 563 8.147704 TGGATTTTAAGAAGGATTTTCGCTTTT 58.852 29.630 0.00 0.00 0.00 2.27
595 608 6.126361 ACCCAGCAATATTTCTCTCAAGGTAT 60.126 38.462 0.00 0.00 0.00 2.73
600 613 9.638176 AGCAATATTTCTCTCAAGGTATTCATT 57.362 29.630 0.00 0.00 0.00 2.57
640 653 8.408601 CCTCAAGGTATTCATAAACTGATTTGG 58.591 37.037 0.00 0.00 32.72 3.28
641 654 8.877864 TCAAGGTATTCATAAACTGATTTGGT 57.122 30.769 0.00 0.00 32.72 3.67
642 655 9.308000 TCAAGGTATTCATAAACTGATTTGGTT 57.692 29.630 0.00 0.00 32.72 3.67
643 656 9.357652 CAAGGTATTCATAAACTGATTTGGTTG 57.642 33.333 0.00 0.00 32.72 3.77
644 657 8.650143 AGGTATTCATAAACTGATTTGGTTGT 57.350 30.769 0.00 0.00 32.72 3.32
645 658 8.522830 AGGTATTCATAAACTGATTTGGTTGTG 58.477 33.333 0.00 0.00 32.72 3.33
646 659 7.275560 GGTATTCATAAACTGATTTGGTTGTGC 59.724 37.037 0.00 0.00 32.72 4.57
647 660 5.132897 TCATAAACTGATTTGGTTGTGCC 57.867 39.130 0.00 0.00 37.90 5.01
648 661 4.832266 TCATAAACTGATTTGGTTGTGCCT 59.168 37.500 0.00 0.00 38.35 4.75
649 662 5.304101 TCATAAACTGATTTGGTTGTGCCTT 59.696 36.000 0.00 0.00 38.35 4.35
650 663 3.457610 AACTGATTTGGTTGTGCCTTG 57.542 42.857 0.00 0.00 38.35 3.61
651 664 1.688197 ACTGATTTGGTTGTGCCTTGG 59.312 47.619 0.00 0.00 38.35 3.61
652 665 1.001181 CTGATTTGGTTGTGCCTTGGG 59.999 52.381 0.00 0.00 38.35 4.12
706 719 2.709397 GCCAGGGCCTATAAACTAAGGA 59.291 50.000 5.28 0.00 34.58 3.36
748 761 1.756561 AACCAGGCAACCACCACAC 60.757 57.895 0.00 0.00 37.17 3.82
830 844 1.598701 AACTCCGGTGGCGTACTACC 61.599 60.000 8.63 0.00 0.00 3.18
918 932 0.030603 AACCCATCCTCCTCCTCCTC 60.031 60.000 0.00 0.00 0.00 3.71
920 934 1.673928 CCCATCCTCCTCCTCCTCCT 61.674 65.000 0.00 0.00 0.00 3.69
921 935 0.267356 CCATCCTCCTCCTCCTCCTT 59.733 60.000 0.00 0.00 0.00 3.36
922 936 1.715785 CATCCTCCTCCTCCTCCTTC 58.284 60.000 0.00 0.00 0.00 3.46
923 937 1.220236 CATCCTCCTCCTCCTCCTTCT 59.780 57.143 0.00 0.00 0.00 2.85
924 938 0.930726 TCCTCCTCCTCCTCCTTCTC 59.069 60.000 0.00 0.00 0.00 2.87
925 939 0.105709 CCTCCTCCTCCTCCTTCTCC 60.106 65.000 0.00 0.00 0.00 3.71
926 940 0.933700 CTCCTCCTCCTCCTTCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
929 943 0.105709 CTCCTCCTCCTTCTCCTCCC 60.106 65.000 0.00 0.00 0.00 4.30
954 968 3.703127 ACGCTTCCCCCTTCGTCC 61.703 66.667 0.00 0.00 0.00 4.79
1198 1212 1.890174 CGGTTCAGGGATTTTGGGC 59.110 57.895 0.00 0.00 0.00 5.36
1200 1214 1.604147 GGTTCAGGGATTTTGGGCGG 61.604 60.000 0.00 0.00 0.00 6.13
1205 1219 0.902984 AGGGATTTTGGGCGGTTTCC 60.903 55.000 0.00 0.00 0.00 3.13
1233 1262 0.815615 GTGGGGCGTCTGATTGATCC 60.816 60.000 0.00 0.00 0.00 3.36
1294 1323 2.303549 ATCCGAGCAAGAGGAAGCCG 62.304 60.000 0.00 0.00 40.32 5.52
1369 1399 3.239026 CGAATTGAATTGCGTCAAGATGC 59.761 43.478 7.31 7.31 40.72 3.91
1432 1465 1.793258 CTGCGCTGGAGGATAGAATG 58.207 55.000 9.73 0.00 0.00 2.67
1505 1539 7.549134 TGTTTGTCTAGGCATATTTCTGTACTG 59.451 37.037 0.00 0.00 0.00 2.74
1512 1546 5.363868 AGGCATATTTCTGTACTGCTAGTCA 59.636 40.000 0.00 0.00 33.43 3.41
1542 1576 7.843490 AATTGGCTGATGAATGAAAAAGATG 57.157 32.000 0.00 0.00 0.00 2.90
1639 1675 7.506328 ACAAGTGTACTCCTAAATTTGGTTC 57.494 36.000 0.00 0.00 0.00 3.62
1780 1816 3.005155 GCTGCAAGGTTGATTTCTCAGTT 59.995 43.478 0.00 0.00 31.68 3.16
1806 1842 2.127251 GCTGCTTTGTTTTACACTGCC 58.873 47.619 0.00 0.00 0.00 4.85
1809 1845 2.223386 TGCTTTGTTTTACACTGCCGAC 60.223 45.455 0.00 0.00 0.00 4.79
1878 1914 4.757594 CATCAGAGTCAAAAGAGGAGGAG 58.242 47.826 0.00 0.00 0.00 3.69
1887 1923 3.491766 AAAGAGGAGGAGGACATACCA 57.508 47.619 0.00 0.00 42.04 3.25
1935 1971 7.713073 GGGAAAGTCGAAGAGATCAAATCTATT 59.287 37.037 0.00 0.00 42.99 1.73
2084 2123 4.689612 AGGCTGACAAAGTTCAGAACTA 57.310 40.909 16.46 0.00 45.19 2.24
2152 2191 2.351418 TCAGCCTTCATATTTTGTCGCG 59.649 45.455 0.00 0.00 0.00 5.87
2156 2195 3.680789 CCTTCATATTTTGTCGCGGAAC 58.319 45.455 6.13 0.00 0.00 3.62
2182 2221 4.034858 CCGGATGATGACAACATTCTTCTG 59.965 45.833 0.00 0.00 36.82 3.02
2253 2293 8.515414 GCTGTGTATTTTGATTTAACTCTTCCT 58.485 33.333 0.00 0.00 0.00 3.36
2321 2364 4.872691 TCTGTACTAGTCGTAGCTACAACC 59.127 45.833 23.21 10.05 29.76 3.77
2336 2379 4.157656 GCTACAACCATGCATAAGTGGAAA 59.842 41.667 11.04 0.00 38.86 3.13
2337 2380 5.336372 GCTACAACCATGCATAAGTGGAAAA 60.336 40.000 11.04 0.00 38.86 2.29
2621 2668 0.603569 CTCCACGTGTCTGGCTTACT 59.396 55.000 15.65 0.00 0.00 2.24
2724 2771 8.427774 GCTAAACTTGATGTGCTTTATTTGTTC 58.572 33.333 0.00 0.00 0.00 3.18
2883 2957 6.525629 ACGCAGATAGCTAATTTATTCCACT 58.474 36.000 0.00 0.00 42.61 4.00
2899 2973 2.301870 TCCACTTCAGTAAGTCGGCATT 59.698 45.455 0.00 0.00 44.28 3.56
2942 3016 7.965107 GCCATGCTTATAATTTCTAAAGGATCG 59.035 37.037 0.00 0.00 28.89 3.69
2943 3017 9.003658 CCATGCTTATAATTTCTAAAGGATCGT 57.996 33.333 0.00 0.00 28.89 3.73
3022 3121 6.942163 ACATAGCCTCCAGTGTCATATAAT 57.058 37.500 0.00 0.00 0.00 1.28
3051 3150 5.357878 TGCATATTAACCCAAAGAAGCAGAG 59.642 40.000 0.00 0.00 0.00 3.35
3135 3234 7.383102 TCCAGAATTTCTGCTATCTTTCAAC 57.617 36.000 19.04 0.00 42.98 3.18
3169 3268 9.892130 CTTTAGAGTCCAGATATTAGGTTTTGT 57.108 33.333 0.00 0.00 0.00 2.83
3195 3294 5.008619 TCTGTTTCATGCATGTTGTGTTT 57.991 34.783 25.43 0.00 0.00 2.83
3271 3370 7.407393 TGTGAATCATGATAAGCCAATGAAA 57.593 32.000 9.04 0.00 0.00 2.69
3368 3467 3.128068 TCTCTTGCTCGCGTAGTTTATCA 59.872 43.478 5.77 0.00 0.00 2.15
3474 3573 1.409427 CTATCGAAGACCACCCTCACC 59.591 57.143 0.00 0.00 42.51 4.02
3591 3690 7.441157 CACCAGAAGTTGACAAGTAATGTTCTA 59.559 37.037 0.00 0.00 44.12 2.10
3805 3911 0.663153 GTCGCCCATTGAAGGTATGC 59.337 55.000 0.00 0.00 0.00 3.14
3806 3912 0.465460 TCGCCCATTGAAGGTATGCC 60.465 55.000 0.00 0.00 0.00 4.40
3807 3913 0.751277 CGCCCATTGAAGGTATGCCA 60.751 55.000 1.54 0.00 37.19 4.92
3808 3914 1.484038 GCCCATTGAAGGTATGCCAA 58.516 50.000 1.54 0.00 37.19 4.52
3809 3915 1.136891 GCCCATTGAAGGTATGCCAAC 59.863 52.381 1.54 0.00 37.19 3.77
3810 3916 2.455557 CCCATTGAAGGTATGCCAACA 58.544 47.619 1.54 0.00 37.19 3.33
3811 3917 2.428171 CCCATTGAAGGTATGCCAACAG 59.572 50.000 1.54 0.00 37.19 3.16
3897 4005 4.991056 GTGCTTGTTCAGACATCAGAACTA 59.009 41.667 15.52 9.08 41.24 2.24
3906 4014 5.092105 CAGACATCAGAACTAACTCGAGTG 58.908 45.833 20.85 10.28 0.00 3.51
3913 4021 5.886474 TCAGAACTAACTCGAGTGACCATAT 59.114 40.000 20.85 3.61 0.00 1.78
3945 4053 6.714278 TCTTCAAAACTGTATAACTACCCCC 58.286 40.000 0.00 0.00 0.00 5.40
3946 4054 6.502863 TCTTCAAAACTGTATAACTACCCCCT 59.497 38.462 0.00 0.00 0.00 4.79
3947 4055 6.303903 TCAAAACTGTATAACTACCCCCTC 57.696 41.667 0.00 0.00 0.00 4.30
3951 4059 5.739143 ACTGTATAACTACCCCCTCTGTA 57.261 43.478 0.00 0.00 0.00 2.74
3952 4060 6.096164 ACTGTATAACTACCCCCTCTGTAA 57.904 41.667 0.00 0.00 0.00 2.41
3953 4061 6.505754 ACTGTATAACTACCCCCTCTGTAAA 58.494 40.000 0.00 0.00 0.00 2.01
3954 4062 6.382282 ACTGTATAACTACCCCCTCTGTAAAC 59.618 42.308 0.00 0.00 0.00 2.01
3956 4064 6.730038 TGTATAACTACCCCCTCTGTAAACAA 59.270 38.462 0.00 0.00 0.00 2.83
3957 4065 6.707273 ATAACTACCCCCTCTGTAAACAAA 57.293 37.500 0.00 0.00 0.00 2.83
3958 4066 5.594199 AACTACCCCCTCTGTAAACAAAT 57.406 39.130 0.00 0.00 0.00 2.32
3959 4067 6.707273 AACTACCCCCTCTGTAAACAAATA 57.293 37.500 0.00 0.00 0.00 1.40
3960 4068 6.903340 ACTACCCCCTCTGTAAACAAATAT 57.097 37.500 0.00 0.00 0.00 1.28
3961 4069 8.396619 AACTACCCCCTCTGTAAACAAATATA 57.603 34.615 0.00 0.00 0.00 0.86
3962 4070 8.396619 ACTACCCCCTCTGTAAACAAATATAA 57.603 34.615 0.00 0.00 0.00 0.98
3963 4071 8.491958 ACTACCCCCTCTGTAAACAAATATAAG 58.508 37.037 0.00 0.00 0.00 1.73
3964 4072 7.519347 ACCCCCTCTGTAAACAAATATAAGA 57.481 36.000 0.00 0.00 0.00 2.10
3965 4073 7.574607 ACCCCCTCTGTAAACAAATATAAGAG 58.425 38.462 0.00 0.00 0.00 2.85
3966 4074 6.486993 CCCCCTCTGTAAACAAATATAAGAGC 59.513 42.308 0.00 0.00 0.00 4.09
3967 4075 6.202954 CCCCTCTGTAAACAAATATAAGAGCG 59.797 42.308 0.00 0.00 0.00 5.03
3968 4076 6.761714 CCCTCTGTAAACAAATATAAGAGCGT 59.238 38.462 0.00 0.00 0.00 5.07
3969 4077 7.280205 CCCTCTGTAAACAAATATAAGAGCGTT 59.720 37.037 0.00 0.00 0.00 4.84
3970 4078 8.665685 CCTCTGTAAACAAATATAAGAGCGTTT 58.334 33.333 0.00 0.00 0.00 3.60
3978 4086 9.601217 AACAAATATAAGAGCGTTTAGATCACT 57.399 29.630 0.00 0.00 37.82 3.41
4015 4123 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
4016 4124 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
4017 4125 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
4018 4126 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
4019 4127 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
4020 4128 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
4021 4129 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
4022 4130 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
4023 4131 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
4024 4132 8.854117 TCTTATATTTCTTTACGGAGGGAGTAC 58.146 37.037 0.00 0.00 0.00 2.73
4025 4133 8.537728 TTATATTTCTTTACGGAGGGAGTACA 57.462 34.615 0.00 0.00 0.00 2.90
4026 4134 5.952347 ATTTCTTTACGGAGGGAGTACAT 57.048 39.130 0.00 0.00 0.00 2.29
4027 4135 4.996788 TTCTTTACGGAGGGAGTACATC 57.003 45.455 0.00 0.00 0.00 3.06
4028 4136 3.972133 TCTTTACGGAGGGAGTACATCA 58.028 45.455 0.00 0.00 0.00 3.07
4036 4144 4.003648 GGAGGGAGTACATCAGTTGTTTG 58.996 47.826 0.00 0.00 39.87 2.93
4161 4278 1.580845 CCAAGAAGGCAAGCTGGTCG 61.581 60.000 0.00 0.00 0.00 4.79
4219 4336 1.013596 ACATTGTGTCCGTGTGTGTG 58.986 50.000 0.00 0.00 0.00 3.82
4220 4337 1.013596 CATTGTGTCCGTGTGTGTGT 58.986 50.000 0.00 0.00 0.00 3.72
4221 4338 1.013596 ATTGTGTCCGTGTGTGTGTG 58.986 50.000 0.00 0.00 0.00 3.82
4222 4339 0.320858 TTGTGTCCGTGTGTGTGTGT 60.321 50.000 0.00 0.00 0.00 3.72
4223 4340 1.016653 TGTGTCCGTGTGTGTGTGTG 61.017 55.000 0.00 0.00 0.00 3.82
4224 4341 1.017177 GTGTCCGTGTGTGTGTGTGT 61.017 55.000 0.00 0.00 0.00 3.72
4225 4342 1.016653 TGTCCGTGTGTGTGTGTGTG 61.017 55.000 0.00 0.00 0.00 3.82
4226 4343 1.017177 GTCCGTGTGTGTGTGTGTGT 61.017 55.000 0.00 0.00 0.00 3.72
4394 4521 4.137543 GGATAGTAAAATCCCTGCACTGG 58.862 47.826 0.00 0.00 39.74 4.00
4411 4538 4.171005 CACTGGCATGACATTTGTGATTC 58.829 43.478 12.90 0.00 0.00 2.52
4452 4579 0.824759 GCCCGGTCTTCAGTCATACT 59.175 55.000 0.00 0.00 0.00 2.12
4454 4581 1.137086 CCCGGTCTTCAGTCATACTGG 59.863 57.143 0.00 0.00 45.94 4.00
4455 4582 1.825474 CCGGTCTTCAGTCATACTGGT 59.175 52.381 7.18 0.00 45.94 4.00
4456 4583 2.417379 CCGGTCTTCAGTCATACTGGTG 60.417 54.545 7.18 1.56 45.94 4.17
4457 4584 2.417379 CGGTCTTCAGTCATACTGGTGG 60.417 54.545 7.18 0.00 45.94 4.61
4458 4585 2.567615 GGTCTTCAGTCATACTGGTGGT 59.432 50.000 7.18 0.00 45.94 4.16
4459 4586 3.008049 GGTCTTCAGTCATACTGGTGGTT 59.992 47.826 7.18 0.00 45.94 3.67
4460 4587 4.246458 GTCTTCAGTCATACTGGTGGTTC 58.754 47.826 7.18 0.00 45.94 3.62
4461 4588 3.056821 TCTTCAGTCATACTGGTGGTTCG 60.057 47.826 7.18 0.00 45.94 3.95
4468 4605 8.459621 CAGTCATACTGGTGGTTCGAAACCTA 62.460 46.154 17.65 5.73 45.76 3.08
4510 4647 2.283532 CCAATGCCGACCCCCAAA 60.284 61.111 0.00 0.00 0.00 3.28
4550 4687 2.565841 GTGGACATGGATACTGAAGCC 58.434 52.381 0.00 0.00 37.61 4.35
4564 4702 0.744771 GAAGCCGGTCCTCCAACATC 60.745 60.000 1.90 0.00 0.00 3.06
4616 4754 4.637276 TCTTAACTCCGCATCAGTGAAAA 58.363 39.130 0.00 0.00 0.00 2.29
4665 4803 8.465273 AGGAGTTTAGATATTAAAATGCCACC 57.535 34.615 0.00 0.00 0.00 4.61
4746 4886 9.463443 AAACTTGATGTTTCTTTCTTAAATCGG 57.537 29.630 0.00 0.00 44.81 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.289819 TGGGGATCTCGGTTGTTGTAAC 60.290 50.000 0.00 0.00 0.00 2.50
1 2 1.979308 TGGGGATCTCGGTTGTTGTAA 59.021 47.619 0.00 0.00 0.00 2.41
2 3 1.646912 TGGGGATCTCGGTTGTTGTA 58.353 50.000 0.00 0.00 0.00 2.41
3 4 0.991920 ATGGGGATCTCGGTTGTTGT 59.008 50.000 0.00 0.00 0.00 3.32
4 5 1.065491 TGATGGGGATCTCGGTTGTTG 60.065 52.381 0.00 0.00 0.00 3.33
5 6 1.210478 CTGATGGGGATCTCGGTTGTT 59.790 52.381 0.00 0.00 0.00 2.83
6 7 0.833287 CTGATGGGGATCTCGGTTGT 59.167 55.000 0.00 0.00 0.00 3.32
49 51 1.315690 CCATGATGAGGATTTGCGCT 58.684 50.000 9.73 0.00 0.00 5.92
226 237 5.692613 ATGTTGGGCAATTTGAAATTGTG 57.307 34.783 25.98 8.54 0.00 3.33
267 278 4.324563 CCCTGATGGTGAGAGGTTTTACAT 60.325 45.833 0.00 0.00 0.00 2.29
278 289 2.040278 TGTTTTCCTCCCTGATGGTGAG 59.960 50.000 0.00 0.00 34.77 3.51
316 327 5.201713 TGTCCGAACAATATTTGGCAAAA 57.798 34.783 17.70 7.00 30.70 2.44
317 328 4.855715 TGTCCGAACAATATTTGGCAAA 57.144 36.364 16.01 16.01 30.70 3.68
365 376 1.544691 GCTAGAGTGTTTGGAGGACGA 59.455 52.381 0.00 0.00 0.00 4.20
390 402 6.939730 TCTAAGCACCTTTTCATTACATGTCA 59.060 34.615 0.00 0.00 0.00 3.58
400 412 5.305644 AGAGAGACTTCTAAGCACCTTTTCA 59.694 40.000 0.00 0.00 32.53 2.69
416 428 4.642437 TCGTTCTGCAATGATAGAGAGACT 59.358 41.667 0.00 0.00 0.00 3.24
460 473 2.363680 AGATGTCATGAGTAGAAGGCGG 59.636 50.000 0.00 0.00 0.00 6.13
500 513 3.334691 TCTTCCTATGGCAACTGTTTCG 58.665 45.455 0.00 0.00 37.61 3.46
520 533 8.595533 GCGAAAATCCTTCTTAAAATCCAAATC 58.404 33.333 0.00 0.00 0.00 2.17
550 563 7.429374 TGGGTGCAATTATAAATGGATTTGA 57.571 32.000 2.79 0.00 0.00 2.69
609 622 7.606456 TCAGTTTATGAATACCTTGAGGTTGTC 59.394 37.037 8.18 6.88 41.49 3.18
610 623 7.458397 TCAGTTTATGAATACCTTGAGGTTGT 58.542 34.615 8.18 0.00 41.49 3.32
611 624 7.921786 TCAGTTTATGAATACCTTGAGGTTG 57.078 36.000 8.18 0.00 41.49 3.77
612 625 9.533831 AAATCAGTTTATGAATACCTTGAGGTT 57.466 29.630 8.18 0.00 43.67 3.50
613 626 8.960591 CAAATCAGTTTATGAATACCTTGAGGT 58.039 33.333 7.95 7.95 46.24 3.85
614 627 8.408601 CCAAATCAGTTTATGAATACCTTGAGG 58.591 37.037 0.00 0.00 42.53 3.86
615 628 8.960591 ACCAAATCAGTTTATGAATACCTTGAG 58.039 33.333 0.00 0.00 42.53 3.02
616 629 8.877864 ACCAAATCAGTTTATGAATACCTTGA 57.122 30.769 0.00 0.00 42.53 3.02
617 630 9.357652 CAACCAAATCAGTTTATGAATACCTTG 57.642 33.333 0.00 0.00 42.53 3.61
618 631 9.088987 ACAACCAAATCAGTTTATGAATACCTT 57.911 29.630 0.00 0.00 42.53 3.50
619 632 8.522830 CACAACCAAATCAGTTTATGAATACCT 58.477 33.333 0.00 0.00 42.53 3.08
620 633 7.275560 GCACAACCAAATCAGTTTATGAATACC 59.724 37.037 0.00 0.00 42.53 2.73
621 634 7.275560 GGCACAACCAAATCAGTTTATGAATAC 59.724 37.037 0.00 0.00 39.08 1.89
622 635 7.178274 AGGCACAACCAAATCAGTTTATGAATA 59.822 33.333 0.00 0.00 40.94 1.75
623 636 6.014327 AGGCACAACCAAATCAGTTTATGAAT 60.014 34.615 0.00 0.00 40.94 2.57
624 637 5.304101 AGGCACAACCAAATCAGTTTATGAA 59.696 36.000 0.00 0.00 40.94 2.57
625 638 4.832266 AGGCACAACCAAATCAGTTTATGA 59.168 37.500 0.00 0.00 43.14 2.15
626 639 5.138125 AGGCACAACCAAATCAGTTTATG 57.862 39.130 0.00 0.00 43.14 1.90
627 640 5.511202 CCAAGGCACAACCAAATCAGTTTAT 60.511 40.000 0.00 0.00 43.14 1.40
628 641 4.202202 CCAAGGCACAACCAAATCAGTTTA 60.202 41.667 0.00 0.00 43.14 2.01
629 642 3.432046 CCAAGGCACAACCAAATCAGTTT 60.432 43.478 0.00 0.00 43.14 2.66
630 643 2.102925 CCAAGGCACAACCAAATCAGTT 59.897 45.455 0.00 0.00 43.14 3.16
631 644 1.688197 CCAAGGCACAACCAAATCAGT 59.312 47.619 0.00 0.00 43.14 3.41
632 645 1.001181 CCCAAGGCACAACCAAATCAG 59.999 52.381 0.00 0.00 43.14 2.90
633 646 1.047002 CCCAAGGCACAACCAAATCA 58.953 50.000 0.00 0.00 43.14 2.57
634 647 3.912899 CCCAAGGCACAACCAAATC 57.087 52.632 0.00 0.00 43.14 2.17
646 659 0.040204 AGGTTTCAGGATGCCCAAGG 59.960 55.000 0.00 0.00 34.76 3.61
647 660 2.369394 GTAGGTTTCAGGATGCCCAAG 58.631 52.381 0.00 0.00 34.76 3.61
648 661 1.339631 CGTAGGTTTCAGGATGCCCAA 60.340 52.381 0.00 0.00 34.76 4.12
649 662 0.251916 CGTAGGTTTCAGGATGCCCA 59.748 55.000 0.00 0.00 34.76 5.36
650 663 0.252197 ACGTAGGTTTCAGGATGCCC 59.748 55.000 0.00 0.00 34.76 5.36
651 664 1.653151 GACGTAGGTTTCAGGATGCC 58.347 55.000 0.00 0.00 34.76 4.40
652 665 1.278238 CGACGTAGGTTTCAGGATGC 58.722 55.000 0.00 0.00 34.76 3.91
653 666 1.475280 TCCGACGTAGGTTTCAGGATG 59.525 52.381 14.76 0.00 37.54 3.51
654 667 1.843368 TCCGACGTAGGTTTCAGGAT 58.157 50.000 14.76 0.00 0.00 3.24
655 668 1.747355 GATCCGACGTAGGTTTCAGGA 59.253 52.381 14.76 1.79 0.00 3.86
656 669 1.749634 AGATCCGACGTAGGTTTCAGG 59.250 52.381 14.76 0.00 0.00 3.86
657 670 2.479730 CCAGATCCGACGTAGGTTTCAG 60.480 54.545 14.76 9.53 0.00 3.02
658 671 1.475280 CCAGATCCGACGTAGGTTTCA 59.525 52.381 14.76 0.00 0.00 2.69
659 672 1.202382 CCCAGATCCGACGTAGGTTTC 60.202 57.143 14.76 12.38 0.00 2.78
660 673 0.822164 CCCAGATCCGACGTAGGTTT 59.178 55.000 14.76 3.68 0.00 3.27
661 674 1.673808 GCCCAGATCCGACGTAGGTT 61.674 60.000 14.76 6.27 0.00 3.50
748 761 2.365105 TAGGAGTTGGAGCCGGGG 60.365 66.667 2.18 0.00 0.00 5.73
830 844 0.514691 GCCGTCTCTGCTGTTTTCTG 59.485 55.000 0.00 0.00 0.00 3.02
918 932 1.074850 GGGAGAGGGGAGGAGAAGG 60.075 68.421 0.00 0.00 0.00 3.46
920 934 1.392534 GTGGGAGAGGGGAGGAGAA 59.607 63.158 0.00 0.00 0.00 2.87
921 935 2.997584 CGTGGGAGAGGGGAGGAGA 61.998 68.421 0.00 0.00 0.00 3.71
922 936 2.443016 CGTGGGAGAGGGGAGGAG 60.443 72.222 0.00 0.00 0.00 3.69
923 937 4.779733 GCGTGGGAGAGGGGAGGA 62.780 72.222 0.00 0.00 0.00 3.71
924 938 4.787280 AGCGTGGGAGAGGGGAGG 62.787 72.222 0.00 0.00 0.00 4.30
925 939 2.685380 AAGCGTGGGAGAGGGGAG 60.685 66.667 0.00 0.00 0.00 4.30
926 940 2.683933 GAAGCGTGGGAGAGGGGA 60.684 66.667 0.00 0.00 0.00 4.81
929 943 3.787001 GGGGAAGCGTGGGAGAGG 61.787 72.222 0.00 0.00 0.00 3.69
954 968 2.027625 GTTGCTTCCTGTCGACGGG 61.028 63.158 33.73 33.73 43.86 5.28
1137 1151 2.282462 CAGGTGGGGCACTTGGAC 60.282 66.667 0.00 0.00 37.72 4.02
1200 1214 4.671590 CCACCCCCACCCGGAAAC 62.672 72.222 0.73 0.00 0.00 2.78
1233 1262 0.320421 AGACACCCACCAAACGATCG 60.320 55.000 14.88 14.88 0.00 3.69
1294 1323 0.967662 GCTTATCGGAGGGGAGGTAC 59.032 60.000 0.00 0.00 0.00 3.34
1369 1399 7.455641 AATACTAGACAGGAAGTATGGATCG 57.544 40.000 0.00 0.00 38.58 3.69
1432 1465 5.586243 CCATCGATACATGGGGATAACAATC 59.414 44.000 0.00 0.00 39.95 2.67
1505 1539 5.818136 TCAGCCAATTATGTTTGACTAGC 57.182 39.130 0.00 0.00 0.00 3.42
1512 1546 9.504708 TTTTTCATTCATCAGCCAATTATGTTT 57.495 25.926 0.00 0.00 0.00 2.83
1542 1576 6.796072 CCGTTCTACTAACTATGTCGCTATTC 59.204 42.308 0.00 0.00 0.00 1.75
1622 1658 5.475564 GCCAACAGAACCAAATTTAGGAGTA 59.524 40.000 11.98 0.00 0.00 2.59
1780 1816 5.519566 CAGTGTAAAACAAAGCAGCATTGAA 59.480 36.000 17.11 0.00 0.00 2.69
1806 1842 1.478510 AGAGTTCAGCCCATACAGTCG 59.521 52.381 0.00 0.00 0.00 4.18
1887 1923 7.199048 TCCCTATGTCCAATGTATCCATAGAT 58.801 38.462 0.00 0.00 38.01 1.98
1935 1971 0.320374 CAGCACCAAAGTACGAGGGA 59.680 55.000 6.72 0.00 0.00 4.20
1941 1977 3.795488 GCTTTTCACCAGCACCAAAGTAC 60.795 47.826 0.00 0.00 37.22 2.73
2084 2123 5.722021 AAGGCAAAACAGGAATCGTTAAT 57.278 34.783 0.00 0.00 0.00 1.40
2152 2191 0.107703 TGTCATCATCCGGCTGTTCC 60.108 55.000 5.00 0.00 0.00 3.62
2156 2195 1.671979 ATGTTGTCATCATCCGGCTG 58.328 50.000 0.00 0.00 0.00 4.85
2161 2200 5.065731 GGTCAGAAGAATGTTGTCATCATCC 59.934 44.000 0.00 0.00 32.56 3.51
2182 2221 4.445453 TGCTGACATCATATGTTCTGGTC 58.555 43.478 1.90 5.54 45.03 4.02
2253 2293 8.086143 ACTAGGCACTATCACTAACCAATTAA 57.914 34.615 0.00 0.00 41.70 1.40
2321 2364 9.153721 ACACATAAATTTTTCCACTTATGCATG 57.846 29.630 10.16 0.00 35.90 4.06
2336 2379 7.312899 CCGGCTTTAGAAGAACACATAAATTT 58.687 34.615 0.00 0.00 0.00 1.82
2337 2380 6.625081 GCCGGCTTTAGAAGAACACATAAATT 60.625 38.462 22.15 0.00 0.00 1.82
2451 2498 7.888021 TGAACTATGGTAATCCTTCAACACAAT 59.112 33.333 0.00 0.00 34.23 2.71
2621 2668 7.498900 CACAAATACTTTACCTCATCATAGCCA 59.501 37.037 0.00 0.00 0.00 4.75
2883 2957 2.029739 TCACGAATGCCGACTTACTGAA 60.030 45.455 0.00 0.00 41.76 3.02
2899 2973 4.693283 CATGGCTATTAAGGAAGTCACGA 58.307 43.478 0.00 0.00 28.44 4.35
2935 3009 8.968969 ACTACTTTAGTGATCTAAACGATCCTT 58.031 33.333 0.00 0.00 46.52 3.36
2936 3010 8.522542 ACTACTTTAGTGATCTAAACGATCCT 57.477 34.615 0.00 0.00 46.52 3.24
3022 3121 6.094881 GCTTCTTTGGGTTAATATGCACAGTA 59.905 38.462 0.00 0.00 0.00 2.74
3051 3150 5.051841 GCCGAGTATTTTCTAAAGTACGCTC 60.052 44.000 9.10 0.00 36.55 5.03
3135 3234 3.861840 TCTGGACTCTAAAGCCGAAATG 58.138 45.455 0.00 0.00 0.00 2.32
3169 3268 3.384146 ACAACATGCATGAAACAGAACCA 59.616 39.130 32.75 0.00 0.00 3.67
3195 3294 6.430925 CACAACTTGAATAACAGGATGGAGAA 59.569 38.462 0.00 0.00 43.62 2.87
3271 3370 4.299978 GAAACTCTTACACTGAAGACGCT 58.700 43.478 0.00 0.00 32.05 5.07
3368 3467 0.252835 AAGGGGGCATGGAAATGCTT 60.253 50.000 10.27 0.00 46.22 3.91
3387 3486 5.404466 CAATGCCAATTGTAGGAAAAGGA 57.596 39.130 4.43 0.00 38.72 3.36
3474 3573 1.291877 GCGTGCTGTCCCACTAACAG 61.292 60.000 0.00 0.00 45.57 3.16
3805 3911 6.199719 GTGAAAAGAAGAGATTTTGCTGTTGG 59.800 38.462 0.00 0.00 30.22 3.77
3806 3912 6.753279 TGTGAAAAGAAGAGATTTTGCTGTTG 59.247 34.615 0.00 0.00 30.22 3.33
3807 3913 6.866480 TGTGAAAAGAAGAGATTTTGCTGTT 58.134 32.000 0.00 0.00 30.22 3.16
3808 3914 6.455360 TGTGAAAAGAAGAGATTTTGCTGT 57.545 33.333 0.00 0.00 30.22 4.40
3809 3915 7.114529 GTCATGTGAAAAGAAGAGATTTTGCTG 59.885 37.037 0.00 0.00 30.22 4.41
3810 3916 7.144000 GTCATGTGAAAAGAAGAGATTTTGCT 58.856 34.615 0.00 0.00 30.22 3.91
3811 3917 6.919662 TGTCATGTGAAAAGAAGAGATTTTGC 59.080 34.615 0.00 0.00 30.22 3.68
3821 3927 2.680339 TGTGCGTGTCATGTGAAAAGAA 59.320 40.909 0.00 0.00 0.00 2.52
3927 4035 5.347978 ACAGAGGGGGTAGTTATACAGTTT 58.652 41.667 0.00 0.00 33.21 2.66
3942 4050 6.202954 CGCTCTTATATTTGTTTACAGAGGGG 59.797 42.308 0.00 0.00 32.58 4.79
3943 4051 6.761714 ACGCTCTTATATTTGTTTACAGAGGG 59.238 38.462 8.36 8.36 38.95 4.30
3952 4060 9.601217 AGTGATCTAAACGCTCTTATATTTGTT 57.399 29.630 0.00 0.00 0.00 2.83
3989 4097 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
3990 4098 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
3991 4099 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
3992 4100 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
3993 4101 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
3994 4102 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
3995 4103 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
3996 4104 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
3997 4105 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
3998 4106 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
3999 4107 8.636213 TGTACTCCCTCCGTAAAGAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
4000 4108 8.537728 TGTACTCCCTCCGTAAAGAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
4001 4109 8.716674 ATGTACTCCCTCCGTAAAGAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
4002 4110 7.289317 TGATGTACTCCCTCCGTAAAGAAATAT 59.711 37.037 0.00 0.00 0.00 1.28
4003 4111 6.608405 TGATGTACTCCCTCCGTAAAGAAATA 59.392 38.462 0.00 0.00 0.00 1.40
4004 4112 5.424252 TGATGTACTCCCTCCGTAAAGAAAT 59.576 40.000 0.00 0.00 0.00 2.17
4005 4113 4.773674 TGATGTACTCCCTCCGTAAAGAAA 59.226 41.667 0.00 0.00 0.00 2.52
4006 4114 4.346730 TGATGTACTCCCTCCGTAAAGAA 58.653 43.478 0.00 0.00 0.00 2.52
4007 4115 3.952323 CTGATGTACTCCCTCCGTAAAGA 59.048 47.826 0.00 0.00 0.00 2.52
4008 4116 3.700038 ACTGATGTACTCCCTCCGTAAAG 59.300 47.826 0.00 0.00 0.00 1.85
4009 4117 3.705051 ACTGATGTACTCCCTCCGTAAA 58.295 45.455 0.00 0.00 0.00 2.01
4010 4118 3.377253 ACTGATGTACTCCCTCCGTAA 57.623 47.619 0.00 0.00 0.00 3.18
4011 4119 3.021695 CAACTGATGTACTCCCTCCGTA 58.978 50.000 0.00 0.00 0.00 4.02
4012 4120 1.825474 CAACTGATGTACTCCCTCCGT 59.175 52.381 0.00 0.00 0.00 4.69
4013 4121 1.825474 ACAACTGATGTACTCCCTCCG 59.175 52.381 0.00 0.00 41.63 4.63
4014 4122 3.983044 AACAACTGATGTACTCCCTCC 57.017 47.619 0.00 0.00 42.99 4.30
4015 4123 4.642429 ACAAACAACTGATGTACTCCCTC 58.358 43.478 0.00 0.00 42.99 4.30
4016 4124 4.706842 ACAAACAACTGATGTACTCCCT 57.293 40.909 0.00 0.00 42.99 4.20
4017 4125 5.638234 GTCTACAAACAACTGATGTACTCCC 59.362 44.000 0.00 0.00 42.99 4.30
4018 4126 6.220930 TGTCTACAAACAACTGATGTACTCC 58.779 40.000 0.00 0.00 42.99 3.85
4019 4127 7.145985 TCTGTCTACAAACAACTGATGTACTC 58.854 38.462 0.00 0.00 42.99 2.59
4020 4128 7.014326 TCTCTGTCTACAAACAACTGATGTACT 59.986 37.037 0.00 0.00 42.99 2.73
4021 4129 7.145985 TCTCTGTCTACAAACAACTGATGTAC 58.854 38.462 0.00 0.00 42.99 2.90
4022 4130 7.230712 TCTCTCTGTCTACAAACAACTGATGTA 59.769 37.037 0.00 0.00 42.99 2.29
4023 4131 6.040955 TCTCTCTGTCTACAAACAACTGATGT 59.959 38.462 0.00 0.00 46.82 3.06
4024 4132 6.450545 TCTCTCTGTCTACAAACAACTGATG 58.549 40.000 0.00 0.00 0.00 3.07
4025 4133 6.656632 TCTCTCTGTCTACAAACAACTGAT 57.343 37.500 0.00 0.00 0.00 2.90
4026 4134 6.127451 TGTTCTCTCTGTCTACAAACAACTGA 60.127 38.462 0.00 0.00 0.00 3.41
4027 4135 6.019479 GTGTTCTCTCTGTCTACAAACAACTG 60.019 42.308 0.28 0.00 0.00 3.16
4028 4136 6.043411 GTGTTCTCTCTGTCTACAAACAACT 58.957 40.000 0.28 0.00 0.00 3.16
4036 4144 8.462811 TGAGATAAATGTGTTCTCTCTGTCTAC 58.537 37.037 0.00 0.00 37.40 2.59
4078 4188 4.473196 TCTGACCATCTCTCTCAGTCTACT 59.527 45.833 0.00 0.00 34.26 2.57
4161 4278 2.440501 CAGCAATTATTCGGCGACAAC 58.559 47.619 10.16 0.00 0.00 3.32
4219 4336 0.655733 CCAGACGAACCAACACACAC 59.344 55.000 0.00 0.00 0.00 3.82
4220 4337 0.537653 TCCAGACGAACCAACACACA 59.462 50.000 0.00 0.00 0.00 3.72
4221 4338 1.658994 TTCCAGACGAACCAACACAC 58.341 50.000 0.00 0.00 0.00 3.82
4222 4339 2.404923 TTTCCAGACGAACCAACACA 57.595 45.000 0.00 0.00 0.00 3.72
4223 4340 2.875933 TCATTTCCAGACGAACCAACAC 59.124 45.455 0.00 0.00 0.00 3.32
4224 4341 3.201353 TCATTTCCAGACGAACCAACA 57.799 42.857 0.00 0.00 0.00 3.33
4225 4342 3.564225 AGTTCATTTCCAGACGAACCAAC 59.436 43.478 0.00 0.00 38.80 3.77
4226 4343 3.815809 AGTTCATTTCCAGACGAACCAA 58.184 40.909 0.00 0.00 38.80 3.67
4394 4521 4.433283 GCAAACGAATCACAAATGTCATGC 60.433 41.667 0.00 0.00 0.00 4.06
4457 4584 5.006068 ACGAACTGACTTTTAGGTTTCGAAC 59.994 40.000 0.00 0.00 0.00 3.95
4458 4585 5.111293 ACGAACTGACTTTTAGGTTTCGAA 58.889 37.500 7.73 0.00 0.00 3.71
4459 4586 4.685924 ACGAACTGACTTTTAGGTTTCGA 58.314 39.130 7.73 0.00 0.00 3.71
4460 4587 5.399604 AACGAACTGACTTTTAGGTTTCG 57.600 39.130 0.00 0.00 0.00 3.46
4461 4588 7.350467 CCTAAACGAACTGACTTTTAGGTTTC 58.650 38.462 17.10 0.00 42.03 2.78
4468 4605 3.547746 TGCCCTAAACGAACTGACTTTT 58.452 40.909 0.00 0.00 0.00 2.27
4475 4612 1.906574 TGGAGATGCCCTAAACGAACT 59.093 47.619 0.00 0.00 34.97 3.01
4510 4647 2.955660 ACCGACAAACAATGTGTCCATT 59.044 40.909 0.00 0.00 44.12 3.16
4544 4681 1.488705 ATGTTGGAGGACCGGCTTCA 61.489 55.000 0.00 0.00 39.42 3.02
4550 4687 1.522569 GGGAGATGTTGGAGGACCG 59.477 63.158 0.00 0.00 39.42 4.79
4564 4702 0.541863 AGTGCGGACATTTAGGGGAG 59.458 55.000 10.52 0.00 0.00 4.30
4592 4730 3.585862 TCACTGATGCGGAGTTAAGAAC 58.414 45.455 0.00 0.00 0.00 3.01
4745 4885 6.748198 GCTACTATATTATTCTGAGCGTCACC 59.252 42.308 0.00 0.00 0.00 4.02
4746 4886 7.306213 TGCTACTATATTATTCTGAGCGTCAC 58.694 38.462 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.