Multiple sequence alignment - TraesCS2B01G433200

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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 TraesCS2B01G433200 chr2B 100.000 3206 0 0 1 3206 622655952 622659157 0.000000e+00 5921.0
1 TraesCS2B01G433200 chr2B 97.222 180 5 0 2176 2355 622658307 622658486 4.020000e-79 305.0
2 TraesCS2B01G433200 chr2B 74.728 368 84 8 170 531 47814766 47815130 4.280000e-34 156.0
3 TraesCS2B01G433200 chr2A 90.519 2215 141 29 1 2176 671281128 671283312 0.000000e+00 2863.0
4 TraesCS2B01G433200 chr2D 93.257 1572 53 21 619 2174 526344801 526346335 0.000000e+00 2266.0
5 TraesCS2B01G433200 chr2D 86.897 580 63 5 21 588 526343867 526344445 3.490000e-179 638.0
6 TraesCS2B01G433200 chr2D 77.126 341 69 8 214 547 186635368 186635706 4.220000e-44 189.0
7 TraesCS2B01G433200 chr2D 79.661 236 36 9 392 625 639967166 639967391 3.310000e-35 159.0
8 TraesCS2B01G433200 chr2D 76.489 319 57 12 318 624 525408540 525408228 1.190000e-34 158.0
9 TraesCS2B01G433200 chr2D 74.933 375 74 20 14 379 596575666 596576029 1.540000e-33 154.0
10 TraesCS2B01G433200 chr2D 72.578 547 107 34 20 546 513098222 513097699 4.310000e-29 139.0
11 TraesCS2B01G433200 chr2D 77.714 175 29 10 19 189 555857516 555857684 7.320000e-17 99.0
12 TraesCS2B01G433200 chr7A 98.825 851 10 0 2356 3206 635097548 635098398 0.000000e+00 1517.0
13 TraesCS2B01G433200 chr7A 98.476 853 11 2 2355 3206 75213988 75213137 0.000000e+00 1502.0
14 TraesCS2B01G433200 chr7A 98.239 852 15 0 2355 3206 518158911 518158060 0.000000e+00 1491.0
15 TraesCS2B01G433200 chr7A 97.790 181 4 0 2175 2355 635097547 635097727 2.400000e-81 313.0
16 TraesCS2B01G433200 chr7A 97.222 180 5 0 2176 2355 75213987 75213808 4.020000e-79 305.0
17 TraesCS2B01G433200 chr7A 96.667 180 6 0 2176 2355 518158910 518158731 1.870000e-77 300.0
18 TraesCS2B01G433200 chr7A 85.252 278 41 0 1688 1965 484525275 484525552 1.460000e-73 287.0
19 TraesCS2B01G433200 chr7A 73.288 584 126 22 51 623 80568518 80569082 1.520000e-43 187.0
20 TraesCS2B01G433200 chr7A 71.024 635 158 19 14 633 149029468 149028845 2.600000e-26 130.0
21 TraesCS2B01G433200 chr1B 98.709 852 11 0 2355 3206 417413814 417414665 0.000000e+00 1513.0
22 TraesCS2B01G433200 chr1B 71.603 574 137 22 23 578 588332171 588332736 2.010000e-27 134.0
23 TraesCS2B01G433200 chr1A 98.595 854 12 0 2353 3206 86132524 86133377 0.000000e+00 1511.0
24 TraesCS2B01G433200 chr1A 97.222 180 5 0 2176 2355 86132527 86132706 4.020000e-79 305.0
25 TraesCS2B01G433200 chr1A 73.197 638 136 28 5 625 556085900 556086519 7.020000e-47 198.0
26 TraesCS2B01G433200 chr3B 98.592 852 12 0 2355 3206 690455390 690454539 0.000000e+00 1507.0
27 TraesCS2B01G433200 chr3B 96.703 182 6 0 2173 2354 51223297 51223478 1.450000e-78 303.0
28 TraesCS2B01G433200 chr3B 80.435 276 46 6 1695 1966 826725618 826725889 1.510000e-48 204.0
29 TraesCS2B01G433200 chr6A 98.590 851 12 0 2356 3206 513105384 513106234 0.000000e+00 1506.0
30 TraesCS2B01G433200 chr6A 90.909 374 31 2 1647 2017 464538478 464538851 1.720000e-137 499.0
31 TraesCS2B01G433200 chr6A 90.226 133 13 0 1094 1226 464537913 464538045 1.180000e-39 174.0
32 TraesCS2B01G433200 chr4A 98.361 854 14 0 2353 3206 721824310 721825163 0.000000e+00 1500.0
33 TraesCS2B01G433200 chr4A 97.222 180 5 0 2176 2355 721824313 721824492 4.020000e-79 305.0
34 TraesCS2B01G433200 chr6B 98.355 851 14 0 2356 3206 516869819 516870669 0.000000e+00 1495.0
35 TraesCS2B01G433200 chr6B 83.219 727 101 13 1297 2020 497216539 497215831 0.000000e+00 647.0
36 TraesCS2B01G433200 chr6B 96.685 181 6 0 2175 2355 516869818 516869998 5.200000e-78 302.0
37 TraesCS2B01G433200 chr6D 84.828 725 87 15 1297 2017 325755903 325756608 0.000000e+00 708.0
38 TraesCS2B01G433200 chr6D 73.927 629 137 22 14 628 121158998 121158383 8.950000e-56 228.0
39 TraesCS2B01G433200 chr6D 74.024 589 125 19 51 625 454064714 454064140 6.970000e-52 215.0
40 TraesCS2B01G433200 chr6D 73.466 603 107 35 39 625 467150410 467149845 9.140000e-41 178.0
41 TraesCS2B01G433200 chr6D 73.154 596 109 37 45 624 61601374 61600814 1.980000e-37 167.0
42 TraesCS2B01G433200 chr6D 88.722 133 15 0 1094 1226 325755666 325755798 2.560000e-36 163.0
43 TraesCS2B01G433200 chr6D 78.970 233 44 4 393 625 13074848 13075075 1.540000e-33 154.0
44 TraesCS2B01G433200 chr6D 76.144 306 61 9 328 625 460272500 460272199 1.990000e-32 150.0
45 TraesCS2B01G433200 chr6D 75.316 316 64 10 328 635 5735732 5735423 4.310000e-29 139.0
46 TraesCS2B01G433200 chrUn 94.150 359 20 1 2175 2532 433954279 433953921 2.170000e-151 545.0
47 TraesCS2B01G433200 chrUn 73.743 537 100 27 23 546 443024879 443025387 4.250000e-39 172.0
48 TraesCS2B01G433200 chrUn 73.455 550 105 30 39 577 51394101 51393582 5.500000e-38 169.0
49 TraesCS2B01G433200 chrUn 73.796 519 97 28 39 546 278334614 278335104 5.500000e-38 169.0
50 TraesCS2B01G433200 chrUn 73.524 525 101 27 48 563 273858576 273858081 7.120000e-37 165.0
51 TraesCS2B01G433200 chrUn 73.140 551 105 30 39 577 35558332 35558851 1.190000e-34 158.0
52 TraesCS2B01G433200 chrUn 72.801 614 112 34 26 625 143907059 143907631 1.190000e-34 158.0
53 TraesCS2B01G433200 chrUn 78.571 224 44 4 402 625 99838213 99837994 9.270000e-31 145.0
54 TraesCS2B01G433200 chrUn 72.373 590 118 31 48 625 257412207 257411651 9.270000e-31 145.0
55 TraesCS2B01G433200 chrUn 71.986 589 126 26 45 624 21234246 21234804 1.550000e-28 137.0
56 TraesCS2B01G433200 chrUn 75.079 317 65 9 318 624 32936614 32936302 5.580000e-28 135.0
57 TraesCS2B01G433200 chrUn 82.468 154 27 0 393 546 33277977 33277824 5.580000e-28 135.0
58 TraesCS2B01G433200 chrUn 82.468 154 27 0 393 546 400230557 400230710 5.580000e-28 135.0
59 TraesCS2B01G433200 chrUn 76.891 238 48 4 393 630 60959896 60959666 9.340000e-26 128.0
60 TraesCS2B01G433200 chr7D 85.507 276 40 0 1690 1965 433876570 433876845 4.050000e-74 289.0
61 TraesCS2B01G433200 chr7D 73.885 628 132 20 14 625 475154786 475155397 4.160000e-54 222.0
62 TraesCS2B01G433200 chr7D 76.708 322 57 11 318 628 7568125 7568439 2.560000e-36 163.0
63 TraesCS2B01G433200 chr7D 73.797 374 80 16 214 577 43881981 43882346 7.220000e-27 132.0
64 TraesCS2B01G433200 chr7B 84.483 290 45 0 1690 1979 451289912 451290201 1.460000e-73 287.0
65 TraesCS2B01G433200 chr7B 73.565 575 110 28 62 625 721070528 721071071 7.060000e-42 182.0
66 TraesCS2B01G433200 chr1D 75.258 582 95 32 20 585 431763614 431764162 6.920000e-57 231.0
67 TraesCS2B01G433200 chr1D 74.320 588 124 17 51 625 466406552 466407125 1.160000e-54 224.0
68 TraesCS2B01G433200 chr1D 73.301 618 137 25 21 624 418405418 418404815 5.420000e-48 202.0
69 TraesCS2B01G433200 chr1D 73.473 573 116 24 63 628 491722015 491721472 1.960000e-42 183.0
70 TraesCS2B01G433200 chr3D 74.450 591 118 27 51 625 300618140 300618713 1.160000e-54 224.0
71 TraesCS2B01G433200 chr3D 74.204 597 116 28 45 624 49458665 49459240 6.970000e-52 215.0
72 TraesCS2B01G433200 chr3D 80.444 225 41 3 402 626 526190285 526190506 5.500000e-38 169.0
73 TraesCS2B01G433200 chr3D 79.574 235 39 7 393 625 24641228 24641455 3.310000e-35 159.0
74 TraesCS2B01G433200 chr3D 72.488 418 88 23 20 422 590232273 590232678 3.380000e-20 110.0
75 TraesCS2B01G433200 chr3D 72.727 187 46 5 74 256 577778325 577778510 1.240000e-04 58.4
76 TraesCS2B01G433200 chr4D 73.642 626 125 29 20 624 19338410 19339016 4.190000e-49 206.0
77 TraesCS2B01G433200 chr4D 74.245 563 97 33 39 585 69656501 69657031 3.260000e-45 193.0
78 TraesCS2B01G433200 chr4D 72.884 579 116 32 44 612 319083612 319084159 9.200000e-36 161.0
79 TraesCS2B01G433200 chr4D 72.712 590 121 31 39 622 450150602 450150047 9.200000e-36 161.0
80 TraesCS2B01G433200 chr3A 74.732 467 92 17 172 624 644817072 644817526 5.460000e-43 185.0
81 TraesCS2B01G433200 chr3A 77.987 159 34 1 229 386 121316019 121315861 7.320000e-17 99.0
82 TraesCS2B01G433200 chr5A 73.230 579 117 26 66 628 547713820 547713264 3.290000e-40 176.0
83 TraesCS2B01G433200 chr5A 73.333 510 103 26 44 531 443586483 443586981 1.190000e-34 158.0
84 TraesCS2B01G433200 chr5A 71.511 523 109 26 105 613 684708401 684708897 1.570000e-18 104.0
85 TraesCS2B01G433200 chr5D 77.303 304 51 10 332 625 539226255 539225960 2.560000e-36 163.0
86 TraesCS2B01G433200 chr5D 71.927 545 125 23 20 546 476718522 476717988 2.010000e-27 134.0
87 TraesCS2B01G433200 chr4B 76.871 294 58 10 284 575 52403915 52404200 1.190000e-34 158.0


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 TraesCS2B01G433200 chr2B 622655952 622659157 3205 False 3113.0 5921 98.6110 1 3206 2 chr2B.!!$F2 3205
1 TraesCS2B01G433200 chr2A 671281128 671283312 2184 False 2863.0 2863 90.5190 1 2176 1 chr2A.!!$F1 2175
2 TraesCS2B01G433200 chr2D 526343867 526346335 2468 False 1452.0 2266 90.0770 21 2174 2 chr2D.!!$F5 2153
3 TraesCS2B01G433200 chr7A 635097547 635098398 851 False 915.0 1517 98.3075 2175 3206 2 chr7A.!!$F3 1031
4 TraesCS2B01G433200 chr7A 75213137 75213988 851 True 903.5 1502 97.8490 2176 3206 2 chr7A.!!$R2 1030
5 TraesCS2B01G433200 chr7A 518158060 518158911 851 True 895.5 1491 97.4530 2176 3206 2 chr7A.!!$R3 1030
6 TraesCS2B01G433200 chr1B 417413814 417414665 851 False 1513.0 1513 98.7090 2355 3206 1 chr1B.!!$F1 851
7 TraesCS2B01G433200 chr1A 86132524 86133377 853 False 908.0 1511 97.9085 2176 3206 2 chr1A.!!$F2 1030
8 TraesCS2B01G433200 chr3B 690454539 690455390 851 True 1507.0 1507 98.5920 2355 3206 1 chr3B.!!$R1 851
9 TraesCS2B01G433200 chr6A 513105384 513106234 850 False 1506.0 1506 98.5900 2356 3206 1 chr6A.!!$F1 850
10 TraesCS2B01G433200 chr6A 464537913 464538851 938 False 336.5 499 90.5675 1094 2017 2 chr6A.!!$F2 923
11 TraesCS2B01G433200 chr4A 721824310 721825163 853 False 902.5 1500 97.7915 2176 3206 2 chr4A.!!$F1 1030
12 TraesCS2B01G433200 chr6B 516869818 516870669 851 False 898.5 1495 97.5200 2175 3206 2 chr6B.!!$F1 1031
13 TraesCS2B01G433200 chr6B 497215831 497216539 708 True 647.0 647 83.2190 1297 2020 1 chr6B.!!$R1 723
14 TraesCS2B01G433200 chr6D 325755666 325756608 942 False 435.5 708 86.7750 1094 2017 2 chr6D.!!$F2 923
15 TraesCS2B01G433200 chr6D 121158383 121158998 615 True 228.0 228 73.9270 14 628 1 chr6D.!!$R3 614
16 TraesCS2B01G433200 chr6D 454064140 454064714 574 True 215.0 215 74.0240 51 625 1 chr6D.!!$R4 574
17 TraesCS2B01G433200 chr7D 475154786 475155397 611 False 222.0 222 73.8850 14 625 1 chr7D.!!$F4 611
18 TraesCS2B01G433200 chr1D 431763614 431764162 548 False 231.0 231 75.2580 20 585 1 chr1D.!!$F1 565
19 TraesCS2B01G433200 chr1D 466406552 466407125 573 False 224.0 224 74.3200 51 625 1 chr1D.!!$F2 574
20 TraesCS2B01G433200 chr1D 418404815 418405418 603 True 202.0 202 73.3010 21 624 1 chr1D.!!$R1 603
21 TraesCS2B01G433200 chr3D 300618140 300618713 573 False 224.0 224 74.4500 51 625 1 chr3D.!!$F3 574
22 TraesCS2B01G433200 chr3D 49458665 49459240 575 False 215.0 215 74.2040 45 624 1 chr3D.!!$F2 579
23 TraesCS2B01G433200 chr4D 19338410 19339016 606 False 206.0 206 73.6420 20 624 1 chr4D.!!$F1 604


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
500 519 0.168348 GACACGTCTTCAGCTCGCTA 59.832 55.0 0.00 0.0 0.0 4.26 F
1544 1965 0.179020 CCTCCTGCAGTTTGTCACCA 60.179 55.0 13.81 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 2698 0.180171 TGGGACTAATCATGCGGTGG 59.820 55.000 0.00 0.0 0.0 4.61 R
2494 2945 7.023575 GTCAGTCAATGTAAATTGCTAAGTGG 58.976 38.462 0.22 0.0 0.0 4.00 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
17 18 4.572571 GTTGTCACACCCCCGCCA 62.573 66.667 0.00 0.00 0.00 5.69
18 19 4.263572 TTGTCACACCCCCGCCAG 62.264 66.667 0.00 0.00 0.00 4.85
37 38 1.142748 CGATCTGCCTCGCCTCTTT 59.857 57.895 0.00 0.00 0.00 2.52
72 73 2.204291 AGGGCTGGTGGATCCCAA 60.204 61.111 9.90 0.00 42.52 4.12
103 105 0.179034 GGGAGGGCTCTTGCTATGTG 60.179 60.000 0.00 0.00 39.59 3.21
261 268 0.386985 GAGGTGTGTCTCCGACGAAC 60.387 60.000 0.00 0.00 34.95 3.95
265 272 0.250858 TGTGTCTCCGACGAACCCTA 60.251 55.000 0.00 0.00 34.95 3.53
449 467 9.856488 GTGTCTGTCTACTACAATAAGATTTGA 57.144 33.333 0.00 0.00 37.74 2.69
482 501 2.276116 GGAGGGGCGATGATAGCGA 61.276 63.158 0.00 0.00 35.00 4.93
492 511 2.538939 CGATGATAGCGACACGTCTTCA 60.539 50.000 0.00 0.00 0.00 3.02
500 519 0.168348 GACACGTCTTCAGCTCGCTA 59.832 55.000 0.00 0.00 0.00 4.26
566 590 8.773404 TGTAAGGTTTCTCTTACTTCTATTGC 57.227 34.615 13.60 0.00 45.51 3.56
578 602 8.035394 TCTTACTTCTATTGCTCTTTGTACTGG 58.965 37.037 0.00 0.00 0.00 4.00
596 620 4.142790 ACTGGGATGATGCTTGATGAATC 58.857 43.478 0.00 0.00 0.00 2.52
606 630 6.915843 TGATGCTTGATGAATCGATCAAAATG 59.084 34.615 0.00 0.00 40.89 2.32
614 638 8.306038 TGATGAATCGATCAAAATGTTTTCCTT 58.694 29.630 0.00 0.00 42.54 3.36
615 639 7.872163 TGAATCGATCAAAATGTTTTCCTTG 57.128 32.000 0.00 0.00 34.30 3.61
616 640 6.867816 TGAATCGATCAAAATGTTTTCCTTGG 59.132 34.615 0.00 0.00 34.30 3.61
678 1027 8.007405 TGATCTCACCTAATTTCAATAGACGA 57.993 34.615 0.00 0.00 0.00 4.20
790 1140 5.931724 CACTGTCTTGTGGTGTATCATAACA 59.068 40.000 0.00 0.00 34.56 2.41
949 1317 4.073052 TGCGTGTTTTAGGCAGGG 57.927 55.556 0.00 0.00 44.54 4.45
950 1318 2.265182 TGCGTGTTTTAGGCAGGGC 61.265 57.895 0.00 0.00 44.54 5.19
951 1319 2.265182 GCGTGTTTTAGGCAGGGCA 61.265 57.895 0.00 0.00 39.88 5.36
979 1347 1.676916 CCATCAGTGCCATCTCACGTT 60.677 52.381 0.00 0.00 41.61 3.99
987 1355 6.092122 TCAGTGCCATCTCACGTTTATAAAAG 59.908 38.462 9.27 9.27 41.61 2.27
999 1367 5.235831 ACGTTTATAAAAGGAGCGCCTAATC 59.764 40.000 10.31 0.00 46.28 1.75
1010 1378 1.123928 CGCCTAATCAGAGGGAAGGT 58.876 55.000 0.00 0.00 37.06 3.50
1070 1438 2.926838 CTCTTTAGCTTGAAGACCTCGC 59.073 50.000 0.00 0.00 0.00 5.03
1088 1459 2.551032 TCGCTGAGAAAACAGTCGAGTA 59.449 45.455 0.00 0.00 39.41 2.59
1226 1597 1.369625 GCCATTTCCTACGGTGAGTG 58.630 55.000 0.00 0.00 0.00 3.51
1249 1620 0.532417 CCTGCTAGCTGGTGATCTGC 60.532 60.000 27.73 0.00 40.14 4.26
1277 1652 1.195115 TCTGGCTTACTCCATCGCTT 58.805 50.000 0.00 0.00 35.22 4.68
1288 1663 1.209504 TCCATCGCTTACCAAAGAGGG 59.790 52.381 0.00 0.00 43.89 4.30
1309 1730 1.419762 TCTTCTTGTGCAGGGCAACTA 59.580 47.619 0.00 0.00 41.47 2.24
1544 1965 0.179020 CCTCCTGCAGTTTGTCACCA 60.179 55.000 13.81 0.00 0.00 4.17
1576 1999 2.158871 TGGCGTTCAACTCAGTACCTTT 60.159 45.455 0.00 0.00 0.00 3.11
1602 2026 4.351192 GAACACGTCTGCAACAAATCTTT 58.649 39.130 0.00 0.00 0.00 2.52
1643 2078 6.374565 AGTACTTACTGGCTTCTATGTACG 57.625 41.667 0.00 0.00 34.72 3.67
1712 2150 0.384309 GCGTGGTGATGGAGATCGTA 59.616 55.000 0.00 0.00 0.00 3.43
1931 2369 3.315949 GTGTACTGGGTCGGGCCA 61.316 66.667 4.39 0.00 39.65 5.36
2046 2484 1.069358 GGATCCGAACCTAGCTTCCTG 59.931 57.143 0.00 0.00 0.00 3.86
2047 2485 1.069358 GATCCGAACCTAGCTTCCTGG 59.931 57.143 0.00 0.00 0.00 4.45
2048 2486 0.976073 TCCGAACCTAGCTTCCTGGG 60.976 60.000 0.00 0.00 44.74 4.45
2049 2487 1.153349 CGAACCTAGCTTCCTGGGC 60.153 63.158 0.00 0.00 43.12 5.36
2050 2488 1.617947 CGAACCTAGCTTCCTGGGCT 61.618 60.000 0.00 2.98 43.12 5.19
2179 2630 5.642063 TCTGCGTTTTTCCGAAATCTTCTAT 59.358 36.000 0.00 0.00 0.00 1.98
2180 2631 6.814644 TCTGCGTTTTTCCGAAATCTTCTATA 59.185 34.615 0.00 0.00 0.00 1.31
2181 2632 6.768078 TGCGTTTTTCCGAAATCTTCTATAC 58.232 36.000 0.00 0.00 0.00 1.47
2182 2633 6.592607 TGCGTTTTTCCGAAATCTTCTATACT 59.407 34.615 0.00 0.00 0.00 2.12
2183 2634 7.760794 TGCGTTTTTCCGAAATCTTCTATACTA 59.239 33.333 0.00 0.00 0.00 1.82
2184 2635 8.054819 GCGTTTTTCCGAAATCTTCTATACTAC 58.945 37.037 0.00 0.00 0.00 2.73
2185 2636 9.298774 CGTTTTTCCGAAATCTTCTATACTACT 57.701 33.333 0.00 0.00 0.00 2.57
2232 2683 5.968528 TTTAAGTGCATCCCATAAAACGT 57.031 34.783 0.00 0.00 0.00 3.99
2233 2684 7.450124 TTTTAAGTGCATCCCATAAAACGTA 57.550 32.000 0.00 0.00 0.00 3.57
2234 2685 4.957759 AAGTGCATCCCATAAAACGTAC 57.042 40.909 0.00 0.00 0.00 3.67
2235 2686 3.945346 AGTGCATCCCATAAAACGTACA 58.055 40.909 0.00 0.00 0.00 2.90
2236 2687 3.687698 AGTGCATCCCATAAAACGTACAC 59.312 43.478 0.00 0.00 0.00 2.90
2237 2688 2.673862 TGCATCCCATAAAACGTACACG 59.326 45.455 0.00 0.00 46.33 4.49
2238 2689 2.031191 GCATCCCATAAAACGTACACGG 59.969 50.000 6.72 0.00 44.95 4.94
2239 2690 3.523547 CATCCCATAAAACGTACACGGA 58.476 45.455 6.72 0.00 44.95 4.69
2240 2691 3.891422 TCCCATAAAACGTACACGGAT 57.109 42.857 6.72 0.00 44.95 4.18
2241 2692 4.998671 TCCCATAAAACGTACACGGATA 57.001 40.909 6.72 0.00 44.95 2.59
2242 2693 4.681744 TCCCATAAAACGTACACGGATAC 58.318 43.478 6.72 0.00 44.95 2.24
2243 2694 4.159321 TCCCATAAAACGTACACGGATACA 59.841 41.667 6.72 0.00 44.95 2.29
2244 2695 5.051816 CCCATAAAACGTACACGGATACAT 58.948 41.667 6.72 0.00 44.95 2.29
2245 2696 5.524646 CCCATAAAACGTACACGGATACATT 59.475 40.000 6.72 0.00 44.95 2.71
2246 2697 6.700960 CCCATAAAACGTACACGGATACATTA 59.299 38.462 6.72 0.00 44.95 1.90
2247 2698 7.306749 CCCATAAAACGTACACGGATACATTAC 60.307 40.741 6.72 0.00 44.95 1.89
2248 2699 7.306749 CCATAAAACGTACACGGATACATTACC 60.307 40.741 6.72 0.00 44.95 2.85
2249 2700 4.717233 AACGTACACGGATACATTACCA 57.283 40.909 6.72 0.00 44.95 3.25
2250 2701 4.032703 ACGTACACGGATACATTACCAC 57.967 45.455 6.72 0.00 44.95 4.16
2251 2702 3.181487 ACGTACACGGATACATTACCACC 60.181 47.826 6.72 0.00 44.95 4.61
2253 2704 1.214367 CACGGATACATTACCACCGC 58.786 55.000 0.00 0.00 46.18 5.68
2254 2705 0.825410 ACGGATACATTACCACCGCA 59.175 50.000 0.00 0.00 46.18 5.69
2255 2706 1.414919 ACGGATACATTACCACCGCAT 59.585 47.619 0.00 0.00 46.18 4.73
2256 2707 1.798223 CGGATACATTACCACCGCATG 59.202 52.381 0.00 0.00 37.32 4.06
2257 2708 2.547007 CGGATACATTACCACCGCATGA 60.547 50.000 0.00 0.00 37.32 3.07
2258 2709 3.674997 GGATACATTACCACCGCATGAT 58.325 45.455 0.00 0.00 0.00 2.45
2259 2710 4.072131 GGATACATTACCACCGCATGATT 58.928 43.478 0.00 0.00 0.00 2.57
2260 2711 5.242434 GGATACATTACCACCGCATGATTA 58.758 41.667 0.00 0.00 0.00 1.75
2261 2712 5.351465 GGATACATTACCACCGCATGATTAG 59.649 44.000 0.00 0.00 0.00 1.73
2262 2713 4.150897 ACATTACCACCGCATGATTAGT 57.849 40.909 0.00 0.00 0.00 2.24
2263 2714 4.127171 ACATTACCACCGCATGATTAGTC 58.873 43.478 0.00 0.00 0.00 2.59
2264 2715 2.902705 TACCACCGCATGATTAGTCC 57.097 50.000 0.00 0.00 0.00 3.85
2265 2716 0.180406 ACCACCGCATGATTAGTCCC 59.820 55.000 0.00 0.00 0.00 4.46
2266 2717 0.180171 CCACCGCATGATTAGTCCCA 59.820 55.000 0.00 0.00 0.00 4.37
2267 2718 1.299541 CACCGCATGATTAGTCCCAC 58.700 55.000 0.00 0.00 0.00 4.61
2268 2719 1.134401 CACCGCATGATTAGTCCCACT 60.134 52.381 0.00 0.00 0.00 4.00
2269 2720 2.102420 CACCGCATGATTAGTCCCACTA 59.898 50.000 0.00 0.00 0.00 2.74
2270 2721 2.769663 ACCGCATGATTAGTCCCACTAA 59.230 45.455 0.00 0.00 43.95 2.24
2271 2722 3.199071 ACCGCATGATTAGTCCCACTAAA 59.801 43.478 0.00 0.00 43.16 1.85
2272 2723 3.560068 CCGCATGATTAGTCCCACTAAAC 59.440 47.826 0.00 0.00 43.16 2.01
2273 2724 4.442706 CGCATGATTAGTCCCACTAAACT 58.557 43.478 0.00 0.00 43.16 2.66
2274 2725 4.876107 CGCATGATTAGTCCCACTAAACTT 59.124 41.667 0.00 0.00 43.16 2.66
2275 2726 6.046593 CGCATGATTAGTCCCACTAAACTTA 58.953 40.000 0.00 0.00 43.16 2.24
2276 2727 6.537301 CGCATGATTAGTCCCACTAAACTTAA 59.463 38.462 0.00 0.00 43.16 1.85
2277 2728 7.226720 CGCATGATTAGTCCCACTAAACTTAAT 59.773 37.037 0.00 0.00 43.16 1.40
2278 2729 8.560374 GCATGATTAGTCCCACTAAACTTAATC 58.440 37.037 0.00 0.00 43.16 1.75
2279 2730 9.838339 CATGATTAGTCCCACTAAACTTAATCT 57.162 33.333 0.37 0.00 43.16 2.40
2283 2734 9.813446 ATTAGTCCCACTAAACTTAATCTAACG 57.187 33.333 0.37 0.00 43.16 3.18
2284 2735 6.637657 AGTCCCACTAAACTTAATCTAACGG 58.362 40.000 0.00 0.00 0.00 4.44
2285 2736 5.292834 GTCCCACTAAACTTAATCTAACGGC 59.707 44.000 0.00 0.00 0.00 5.68
2286 2737 5.188359 TCCCACTAAACTTAATCTAACGGCT 59.812 40.000 0.00 0.00 0.00 5.52
2287 2738 6.380846 TCCCACTAAACTTAATCTAACGGCTA 59.619 38.462 0.00 0.00 0.00 3.93
2288 2739 6.700520 CCCACTAAACTTAATCTAACGGCTAG 59.299 42.308 0.00 0.00 0.00 3.42
2289 2740 6.200475 CCACTAAACTTAATCTAACGGCTAGC 59.800 42.308 6.04 6.04 0.00 3.42
2290 2741 6.200475 CACTAAACTTAATCTAACGGCTAGCC 59.800 42.308 24.75 24.75 0.00 3.93
2291 2742 5.354842 AAACTTAATCTAACGGCTAGCCT 57.645 39.130 30.55 16.25 0.00 4.58
2292 2743 5.354842 AACTTAATCTAACGGCTAGCCTT 57.645 39.130 30.55 23.63 0.00 4.35
2293 2744 6.475596 AACTTAATCTAACGGCTAGCCTTA 57.524 37.500 30.55 23.50 0.00 2.69
2294 2745 6.475596 ACTTAATCTAACGGCTAGCCTTAA 57.524 37.500 30.55 23.07 0.00 1.85
2295 2746 6.279123 ACTTAATCTAACGGCTAGCCTTAAC 58.721 40.000 30.55 4.97 0.00 2.01
2296 2747 3.747854 ATCTAACGGCTAGCCTTAACC 57.252 47.619 30.55 4.19 0.00 2.85
2297 2748 2.743553 TCTAACGGCTAGCCTTAACCT 58.256 47.619 30.55 9.72 0.00 3.50
2298 2749 3.902218 TCTAACGGCTAGCCTTAACCTA 58.098 45.455 30.55 10.37 0.00 3.08
2299 2750 4.280819 TCTAACGGCTAGCCTTAACCTAA 58.719 43.478 30.55 6.51 0.00 2.69
2300 2751 4.897670 TCTAACGGCTAGCCTTAACCTAAT 59.102 41.667 30.55 7.85 0.00 1.73
2301 2752 6.070656 TCTAACGGCTAGCCTTAACCTAATA 58.929 40.000 30.55 8.60 0.00 0.98
2302 2753 5.820404 AACGGCTAGCCTTAACCTAATAT 57.180 39.130 30.55 0.55 0.00 1.28
2303 2754 5.148651 ACGGCTAGCCTTAACCTAATATG 57.851 43.478 30.55 12.97 0.00 1.78
2304 2755 4.591924 ACGGCTAGCCTTAACCTAATATGT 59.408 41.667 30.55 13.62 0.00 2.29
2305 2756 5.071384 ACGGCTAGCCTTAACCTAATATGTT 59.929 40.000 30.55 0.00 0.00 2.71
2306 2757 5.638234 CGGCTAGCCTTAACCTAATATGTTC 59.362 44.000 30.55 0.00 0.00 3.18
2307 2758 6.518537 CGGCTAGCCTTAACCTAATATGTTCT 60.519 42.308 30.55 0.00 0.00 3.01
2308 2759 6.874664 GGCTAGCCTTAACCTAATATGTTCTC 59.125 42.308 27.17 0.00 0.00 2.87
2309 2760 7.256368 GGCTAGCCTTAACCTAATATGTTCTCT 60.256 40.741 27.17 0.00 0.00 3.10
2310 2761 7.600752 GCTAGCCTTAACCTAATATGTTCTCTG 59.399 40.741 2.29 0.00 0.00 3.35
2311 2762 7.439108 AGCCTTAACCTAATATGTTCTCTGT 57.561 36.000 0.00 0.00 0.00 3.41
2312 2763 7.275920 AGCCTTAACCTAATATGTTCTCTGTG 58.724 38.462 0.00 0.00 0.00 3.66
2313 2764 7.048512 GCCTTAACCTAATATGTTCTCTGTGT 58.951 38.462 0.00 0.00 0.00 3.72
2314 2765 7.011482 GCCTTAACCTAATATGTTCTCTGTGTG 59.989 40.741 0.00 0.00 0.00 3.82
2315 2766 7.011482 CCTTAACCTAATATGTTCTCTGTGTGC 59.989 40.741 0.00 0.00 0.00 4.57
2316 2767 5.420725 ACCTAATATGTTCTCTGTGTGCA 57.579 39.130 0.00 0.00 0.00 4.57
2317 2768 5.178797 ACCTAATATGTTCTCTGTGTGCAC 58.821 41.667 10.75 10.75 0.00 4.57
2318 2769 5.046304 ACCTAATATGTTCTCTGTGTGCACT 60.046 40.000 19.41 0.00 0.00 4.40
2319 2770 5.877012 CCTAATATGTTCTCTGTGTGCACTT 59.123 40.000 19.41 1.31 0.00 3.16
2320 2771 7.041721 CCTAATATGTTCTCTGTGTGCACTTA 58.958 38.462 19.41 5.91 0.00 2.24
2321 2772 6.974932 AATATGTTCTCTGTGTGCACTTAG 57.025 37.500 19.41 15.55 0.00 2.18
2322 2773 2.483876 TGTTCTCTGTGTGCACTTAGC 58.516 47.619 19.41 6.38 45.96 3.09
2337 2788 6.859715 GCACTTAGCAATTTACATTGACTG 57.140 37.500 5.78 0.00 42.35 3.51
2338 2789 6.611381 GCACTTAGCAATTTACATTGACTGA 58.389 36.000 5.78 0.00 42.35 3.41
2339 2790 6.524586 GCACTTAGCAATTTACATTGACTGAC 59.475 38.462 5.78 0.00 42.35 3.51
2340 2791 7.023575 CACTTAGCAATTTACATTGACTGACC 58.976 38.462 5.78 0.00 42.35 4.02
2341 2792 4.685169 AGCAATTTACATTGACTGACCG 57.315 40.909 5.78 0.00 42.35 4.79
2342 2793 4.072131 AGCAATTTACATTGACTGACCGT 58.928 39.130 5.78 0.00 42.35 4.83
2343 2794 5.242434 AGCAATTTACATTGACTGACCGTA 58.758 37.500 5.78 0.00 42.35 4.02
2344 2795 5.880332 AGCAATTTACATTGACTGACCGTAT 59.120 36.000 5.78 0.00 42.35 3.06
2345 2796 6.374333 AGCAATTTACATTGACTGACCGTATT 59.626 34.615 5.78 0.00 42.35 1.89
2346 2797 6.687105 GCAATTTACATTGACTGACCGTATTC 59.313 38.462 5.78 0.00 42.35 1.75
2347 2798 6.920569 ATTTACATTGACTGACCGTATTCC 57.079 37.500 0.00 0.00 0.00 3.01
2348 2799 3.973206 ACATTGACTGACCGTATTCCA 57.027 42.857 0.00 0.00 0.00 3.53
2349 2800 3.596214 ACATTGACTGACCGTATTCCAC 58.404 45.455 0.00 0.00 0.00 4.02
2350 2801 2.754946 TTGACTGACCGTATTCCACC 57.245 50.000 0.00 0.00 0.00 4.61
2351 2802 0.528924 TGACTGACCGTATTCCACCG 59.471 55.000 0.00 0.00 0.00 4.94
2352 2803 0.529378 GACTGACCGTATTCCACCGT 59.471 55.000 0.00 0.00 0.00 4.83
2353 2804 0.245539 ACTGACCGTATTCCACCGTG 59.754 55.000 0.00 0.00 0.00 4.94
2494 2945 7.224949 GCCTTAACCTAATATGTTCTCTGTGTC 59.775 40.741 0.00 0.00 0.00 3.67
2925 3377 1.107114 GGAGACATGCGAAGAGGAGA 58.893 55.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 3.260100 CCTCCCACCAGCAAGGGT 61.260 66.667 0.00 0.00 45.64 4.34
127 131 3.998913 TCATGAGCAGGATACAAACCA 57.001 42.857 0.00 0.00 41.41 3.67
261 268 6.495872 ACAATCATTCATCAAATCCCATAGGG 59.504 38.462 0.00 0.00 46.11 3.53
265 272 7.469594 CGAAGACAATCATTCATCAAATCCCAT 60.470 37.037 0.00 0.00 0.00 4.00
282 289 4.443457 CCATACAGATCCACCGAAGACAAT 60.443 45.833 0.00 0.00 0.00 2.71
409 426 1.014352 AGACACGAAGTTGTTGTGCC 58.986 50.000 0.00 0.00 41.61 5.01
423 441 9.856488 TCAAATCTTATTGTAGTAGACAGACAC 57.144 33.333 0.00 0.00 39.88 3.67
424 442 9.856488 GTCAAATCTTATTGTAGTAGACAGACA 57.144 33.333 0.00 0.00 39.88 3.41
482 501 0.811915 ATAGCGAGCTGAAGACGTGT 59.188 50.000 7.99 0.00 0.00 4.49
492 511 2.952978 ACTACAAGCACTATAGCGAGCT 59.047 45.455 8.62 8.62 40.15 4.09
500 519 1.743958 AGCGACGACTACAAGCACTAT 59.256 47.619 0.00 0.00 0.00 2.12
566 590 4.148128 AGCATCATCCCAGTACAAAGAG 57.852 45.455 0.00 0.00 0.00 2.85
578 602 4.694037 TGATCGATTCATCAAGCATCATCC 59.306 41.667 0.00 0.00 29.41 3.51
596 620 7.475771 TTTTCCAAGGAAAACATTTTGATCG 57.524 32.000 20.08 0.00 45.59 3.69
678 1027 7.558444 TGTTTTCTATGTAAGGTTGTGTCCTTT 59.442 33.333 3.31 0.00 44.36 3.11
949 1317 1.530013 GCACTGATGGCCCCATATGC 61.530 60.000 0.00 7.96 36.70 3.14
950 1318 0.896940 GGCACTGATGGCCCCATATG 60.897 60.000 0.00 0.00 45.87 1.78
951 1319 1.462035 GGCACTGATGGCCCCATAT 59.538 57.895 0.00 0.00 45.87 1.78
979 1347 6.169557 TCTGATTAGGCGCTCCTTTTATAA 57.830 37.500 7.64 0.00 40.66 0.98
987 1355 1.115930 TCCCTCTGATTAGGCGCTCC 61.116 60.000 7.64 0.00 35.09 4.70
995 1363 4.007581 TGGATGACCTTCCCTCTGATTA 57.992 45.455 0.00 0.00 34.67 1.75
999 1367 2.104451 CTGATGGATGACCTTCCCTCTG 59.896 54.545 0.00 5.03 38.91 3.35
1058 1426 3.131396 GTTTTCTCAGCGAGGTCTTCAA 58.869 45.455 5.87 0.00 0.00 2.69
1070 1438 5.520632 TCTTGTACTCGACTGTTTTCTCAG 58.479 41.667 0.00 0.00 40.80 3.35
1088 1459 1.985473 TGCAAGCTTCACCATCTTGT 58.015 45.000 0.00 0.00 39.36 3.16
1136 1507 0.669077 ATAGGATCTGACGGACGTGC 59.331 55.000 0.53 0.00 0.00 5.34
1226 1597 1.068434 GATCACCAGCTAGCAGGAGAC 59.932 57.143 30.85 18.13 0.00 3.36
1277 1652 3.496160 GCACAAGAAGACCCTCTTTGGTA 60.496 47.826 0.00 0.00 39.24 3.25
1288 1663 0.312102 GTTGCCCTGCACAAGAAGAC 59.688 55.000 0.00 0.00 38.71 3.01
1348 1769 3.289834 GCATGGGCGATGGCGATT 61.290 61.111 11.58 0.00 41.24 3.34
1559 1980 6.256321 TGTTCGTAAAAGGTACTGAGTTGAAC 59.744 38.462 0.00 0.00 40.86 3.18
1607 2031 5.051240 CCAGTAAGTACTTTTCACGTGTGAC 60.051 44.000 14.49 1.57 35.17 3.67
1626 2054 2.100252 GCACCGTACATAGAAGCCAGTA 59.900 50.000 0.00 0.00 0.00 2.74
2046 2484 3.435186 GCAACGAGCCAAGAGCCC 61.435 66.667 0.00 0.00 45.47 5.19
2208 2659 6.750148 ACGTTTTATGGGATGCACTTAAAAA 58.250 32.000 0.00 0.00 32.69 1.94
2209 2660 6.334102 ACGTTTTATGGGATGCACTTAAAA 57.666 33.333 0.00 0.00 0.00 1.52
2210 2661 5.968528 ACGTTTTATGGGATGCACTTAAA 57.031 34.783 0.00 0.00 0.00 1.52
2211 2662 5.938710 TGTACGTTTTATGGGATGCACTTAA 59.061 36.000 0.00 0.00 0.00 1.85
2212 2663 5.352016 GTGTACGTTTTATGGGATGCACTTA 59.648 40.000 0.00 0.00 0.00 2.24
2213 2664 4.155280 GTGTACGTTTTATGGGATGCACTT 59.845 41.667 0.00 0.00 0.00 3.16
2214 2665 3.687698 GTGTACGTTTTATGGGATGCACT 59.312 43.478 0.00 0.00 0.00 4.40
2215 2666 3.484557 CGTGTACGTTTTATGGGATGCAC 60.485 47.826 0.00 0.00 34.11 4.57
2216 2667 2.673862 CGTGTACGTTTTATGGGATGCA 59.326 45.455 0.00 0.00 34.11 3.96
2217 2668 2.031191 CCGTGTACGTTTTATGGGATGC 59.969 50.000 0.00 0.00 37.74 3.91
2218 2669 3.523547 TCCGTGTACGTTTTATGGGATG 58.476 45.455 0.00 0.00 37.74 3.51
2219 2670 3.891422 TCCGTGTACGTTTTATGGGAT 57.109 42.857 0.00 0.00 37.74 3.85
2220 2671 3.891422 ATCCGTGTACGTTTTATGGGA 57.109 42.857 0.00 0.00 37.74 4.37
2221 2672 4.431809 TGTATCCGTGTACGTTTTATGGG 58.568 43.478 0.00 0.00 37.74 4.00
2222 2673 6.592798 AATGTATCCGTGTACGTTTTATGG 57.407 37.500 0.00 0.00 37.74 2.74
2223 2674 7.222417 TGGTAATGTATCCGTGTACGTTTTATG 59.778 37.037 0.00 0.00 35.84 1.90
2224 2675 7.222611 GTGGTAATGTATCCGTGTACGTTTTAT 59.777 37.037 0.00 0.00 35.84 1.40
2225 2676 6.529829 GTGGTAATGTATCCGTGTACGTTTTA 59.470 38.462 0.00 0.00 35.84 1.52
2226 2677 5.348451 GTGGTAATGTATCCGTGTACGTTTT 59.652 40.000 0.00 0.00 35.84 2.43
2227 2678 4.864247 GTGGTAATGTATCCGTGTACGTTT 59.136 41.667 0.00 0.00 35.84 3.60
2228 2679 4.423732 GTGGTAATGTATCCGTGTACGTT 58.576 43.478 0.00 6.98 37.51 3.99
2229 2680 3.181487 GGTGGTAATGTATCCGTGTACGT 60.181 47.826 3.57 0.00 37.74 3.57
2230 2681 3.374745 GGTGGTAATGTATCCGTGTACG 58.625 50.000 0.00 0.00 39.44 3.67
2231 2682 3.374745 CGGTGGTAATGTATCCGTGTAC 58.625 50.000 0.00 0.00 36.99 2.90
2232 2683 2.223782 GCGGTGGTAATGTATCCGTGTA 60.224 50.000 0.00 0.00 42.62 2.90
2233 2684 1.472026 GCGGTGGTAATGTATCCGTGT 60.472 52.381 0.00 0.00 42.62 4.49
2234 2685 1.214367 GCGGTGGTAATGTATCCGTG 58.786 55.000 0.00 0.00 42.62 4.94
2235 2686 0.825410 TGCGGTGGTAATGTATCCGT 59.175 50.000 0.00 0.00 42.62 4.69
2236 2687 1.798223 CATGCGGTGGTAATGTATCCG 59.202 52.381 0.00 0.00 43.37 4.18
2237 2688 3.120321 TCATGCGGTGGTAATGTATCC 57.880 47.619 0.00 0.00 0.00 2.59
2238 2689 5.932303 ACTAATCATGCGGTGGTAATGTATC 59.068 40.000 0.00 0.00 0.00 2.24
2239 2690 5.865085 ACTAATCATGCGGTGGTAATGTAT 58.135 37.500 0.00 0.00 0.00 2.29
2240 2691 5.284861 ACTAATCATGCGGTGGTAATGTA 57.715 39.130 0.00 0.00 0.00 2.29
2241 2692 4.127171 GACTAATCATGCGGTGGTAATGT 58.873 43.478 0.00 0.00 0.00 2.71
2242 2693 3.498397 GGACTAATCATGCGGTGGTAATG 59.502 47.826 0.00 0.00 0.00 1.90
2243 2694 3.496160 GGGACTAATCATGCGGTGGTAAT 60.496 47.826 0.00 0.00 0.00 1.89
2244 2695 2.158871 GGGACTAATCATGCGGTGGTAA 60.159 50.000 0.00 0.00 0.00 2.85
2245 2696 1.414919 GGGACTAATCATGCGGTGGTA 59.585 52.381 0.00 0.00 0.00 3.25
2246 2697 0.180406 GGGACTAATCATGCGGTGGT 59.820 55.000 0.00 0.00 0.00 4.16
2247 2698 0.180171 TGGGACTAATCATGCGGTGG 59.820 55.000 0.00 0.00 0.00 4.61
2248 2699 1.134401 AGTGGGACTAATCATGCGGTG 60.134 52.381 0.00 0.00 0.00 4.94
2249 2700 1.204146 AGTGGGACTAATCATGCGGT 58.796 50.000 0.00 0.00 0.00 5.68
2250 2701 3.469008 TTAGTGGGACTAATCATGCGG 57.531 47.619 0.00 0.00 35.89 5.69
2251 2702 4.442706 AGTTTAGTGGGACTAATCATGCG 58.557 43.478 0.00 0.00 40.08 4.73
2252 2703 7.859325 TTAAGTTTAGTGGGACTAATCATGC 57.141 36.000 0.00 0.00 40.08 4.06
2253 2704 9.838339 AGATTAAGTTTAGTGGGACTAATCATG 57.162 33.333 0.00 0.00 40.08 3.07
2257 2708 9.813446 CGTTAGATTAAGTTTAGTGGGACTAAT 57.187 33.333 0.00 0.00 40.08 1.73
2258 2709 8.253113 CCGTTAGATTAAGTTTAGTGGGACTAA 58.747 37.037 0.00 0.00 38.79 2.24
2259 2710 7.631377 GCCGTTAGATTAAGTTTAGTGGGACTA 60.631 40.741 0.00 0.00 0.00 2.59
2260 2711 6.637657 CCGTTAGATTAAGTTTAGTGGGACT 58.362 40.000 0.00 0.00 0.00 3.85
2261 2712 5.292834 GCCGTTAGATTAAGTTTAGTGGGAC 59.707 44.000 0.00 0.00 0.00 4.46
2262 2713 5.188359 AGCCGTTAGATTAAGTTTAGTGGGA 59.812 40.000 0.00 0.00 0.00 4.37
2263 2714 5.425630 AGCCGTTAGATTAAGTTTAGTGGG 58.574 41.667 0.00 0.00 0.00 4.61
2264 2715 6.200475 GCTAGCCGTTAGATTAAGTTTAGTGG 59.800 42.308 2.29 0.00 0.00 4.00
2265 2716 6.200475 GGCTAGCCGTTAGATTAAGTTTAGTG 59.800 42.308 20.16 0.00 0.00 2.74
2266 2717 6.097981 AGGCTAGCCGTTAGATTAAGTTTAGT 59.902 38.462 27.83 0.51 41.95 2.24
2267 2718 6.514063 AGGCTAGCCGTTAGATTAAGTTTAG 58.486 40.000 27.83 0.00 41.95 1.85
2268 2719 6.475596 AGGCTAGCCGTTAGATTAAGTTTA 57.524 37.500 27.83 0.00 41.95 2.01
2269 2720 5.354842 AGGCTAGCCGTTAGATTAAGTTT 57.645 39.130 27.83 2.04 41.95 2.66
2270 2721 5.354842 AAGGCTAGCCGTTAGATTAAGTT 57.645 39.130 27.83 9.30 41.95 2.66
2271 2722 6.279123 GTTAAGGCTAGCCGTTAGATTAAGT 58.721 40.000 27.50 2.40 41.95 2.24
2272 2723 5.695363 GGTTAAGGCTAGCCGTTAGATTAAG 59.305 44.000 27.50 0.00 41.95 1.85
2273 2724 5.364735 AGGTTAAGGCTAGCCGTTAGATTAA 59.635 40.000 27.50 20.71 41.95 1.40
2274 2725 4.897670 AGGTTAAGGCTAGCCGTTAGATTA 59.102 41.667 27.50 16.17 41.95 1.75
2275 2726 3.710165 AGGTTAAGGCTAGCCGTTAGATT 59.290 43.478 27.50 17.21 41.95 2.40
2276 2727 3.306613 AGGTTAAGGCTAGCCGTTAGAT 58.693 45.455 27.50 11.35 41.95 1.98
2277 2728 2.743553 AGGTTAAGGCTAGCCGTTAGA 58.256 47.619 27.50 11.29 41.95 2.10
2278 2729 4.660789 TTAGGTTAAGGCTAGCCGTTAG 57.339 45.455 27.50 0.00 41.95 2.34
2279 2730 6.268387 ACATATTAGGTTAAGGCTAGCCGTTA 59.732 38.462 27.50 21.22 41.95 3.18
2280 2731 5.071384 ACATATTAGGTTAAGGCTAGCCGTT 59.929 40.000 27.50 22.19 41.95 4.44
2281 2732 4.591924 ACATATTAGGTTAAGGCTAGCCGT 59.408 41.667 27.83 26.74 41.95 5.68
2282 2733 5.148651 ACATATTAGGTTAAGGCTAGCCG 57.851 43.478 27.83 11.21 41.95 5.52
2283 2734 6.770542 AGAACATATTAGGTTAAGGCTAGCC 58.229 40.000 27.19 27.19 0.00 3.93
2284 2735 7.600752 CAGAGAACATATTAGGTTAAGGCTAGC 59.399 40.741 6.04 6.04 0.00 3.42
2285 2736 8.643324 ACAGAGAACATATTAGGTTAAGGCTAG 58.357 37.037 0.00 0.00 0.00 3.42
2286 2737 8.421784 CACAGAGAACATATTAGGTTAAGGCTA 58.578 37.037 0.00 0.00 0.00 3.93
2287 2738 7.092846 ACACAGAGAACATATTAGGTTAAGGCT 60.093 37.037 0.00 0.00 0.00 4.58
2288 2739 7.011482 CACACAGAGAACATATTAGGTTAAGGC 59.989 40.741 0.00 0.00 0.00 4.35
2289 2740 7.011482 GCACACAGAGAACATATTAGGTTAAGG 59.989 40.741 0.00 0.00 0.00 2.69
2290 2741 7.549134 TGCACACAGAGAACATATTAGGTTAAG 59.451 37.037 0.00 0.00 0.00 1.85
2291 2742 7.333423 GTGCACACAGAGAACATATTAGGTTAA 59.667 37.037 13.17 0.00 0.00 2.01
2292 2743 6.816640 GTGCACACAGAGAACATATTAGGTTA 59.183 38.462 13.17 0.00 0.00 2.85
2293 2744 5.643777 GTGCACACAGAGAACATATTAGGTT 59.356 40.000 13.17 0.00 0.00 3.50
2294 2745 5.046304 AGTGCACACAGAGAACATATTAGGT 60.046 40.000 21.04 0.00 0.00 3.08
2295 2746 5.423015 AGTGCACACAGAGAACATATTAGG 58.577 41.667 21.04 0.00 0.00 2.69
2296 2747 6.974932 AAGTGCACACAGAGAACATATTAG 57.025 37.500 21.04 0.00 0.00 1.73
2297 2748 6.535150 GCTAAGTGCACACAGAGAACATATTA 59.465 38.462 21.04 3.04 42.31 0.98
2298 2749 5.352569 GCTAAGTGCACACAGAGAACATATT 59.647 40.000 21.04 1.88 42.31 1.28
2299 2750 4.872691 GCTAAGTGCACACAGAGAACATAT 59.127 41.667 21.04 0.00 42.31 1.78
2300 2751 4.245660 GCTAAGTGCACACAGAGAACATA 58.754 43.478 21.04 0.00 42.31 2.29
2301 2752 3.070018 GCTAAGTGCACACAGAGAACAT 58.930 45.455 21.04 0.00 42.31 2.71
2302 2753 2.483876 GCTAAGTGCACACAGAGAACA 58.516 47.619 21.04 0.00 42.31 3.18
2314 2765 6.524586 GTCAGTCAATGTAAATTGCTAAGTGC 59.475 38.462 0.22 0.00 43.25 4.40
2315 2766 7.023575 GGTCAGTCAATGTAAATTGCTAAGTG 58.976 38.462 0.22 0.00 0.00 3.16
2316 2767 6.128282 CGGTCAGTCAATGTAAATTGCTAAGT 60.128 38.462 0.22 0.00 0.00 2.24
2317 2768 6.128282 ACGGTCAGTCAATGTAAATTGCTAAG 60.128 38.462 0.22 0.00 0.00 2.18
2318 2769 5.703592 ACGGTCAGTCAATGTAAATTGCTAA 59.296 36.000 0.22 0.00 0.00 3.09
2319 2770 5.242434 ACGGTCAGTCAATGTAAATTGCTA 58.758 37.500 0.22 0.00 0.00 3.49
2320 2771 4.072131 ACGGTCAGTCAATGTAAATTGCT 58.928 39.130 0.22 0.00 0.00 3.91
2321 2772 4.419522 ACGGTCAGTCAATGTAAATTGC 57.580 40.909 0.22 0.00 0.00 3.56
2322 2773 7.148323 TGGAATACGGTCAGTCAATGTAAATTG 60.148 37.037 0.00 0.00 0.00 2.32
2323 2774 6.882140 TGGAATACGGTCAGTCAATGTAAATT 59.118 34.615 0.00 0.00 0.00 1.82
2324 2775 6.315393 GTGGAATACGGTCAGTCAATGTAAAT 59.685 38.462 0.00 0.00 0.00 1.40
2325 2776 5.640357 GTGGAATACGGTCAGTCAATGTAAA 59.360 40.000 0.00 0.00 0.00 2.01
2326 2777 5.172934 GTGGAATACGGTCAGTCAATGTAA 58.827 41.667 0.00 0.00 0.00 2.41
2327 2778 4.382254 GGTGGAATACGGTCAGTCAATGTA 60.382 45.833 0.00 0.00 0.00 2.29
2328 2779 3.596214 GTGGAATACGGTCAGTCAATGT 58.404 45.455 0.00 0.00 0.00 2.71
2329 2780 2.936498 GGTGGAATACGGTCAGTCAATG 59.064 50.000 0.00 0.00 0.00 2.82
2330 2781 2.418197 CGGTGGAATACGGTCAGTCAAT 60.418 50.000 0.00 0.00 0.00 2.57
2331 2782 1.067425 CGGTGGAATACGGTCAGTCAA 60.067 52.381 0.00 0.00 0.00 3.18
2332 2783 0.528924 CGGTGGAATACGGTCAGTCA 59.471 55.000 0.00 0.00 0.00 3.41
2333 2784 0.529378 ACGGTGGAATACGGTCAGTC 59.471 55.000 0.00 0.00 38.30 3.51
2334 2785 0.245539 CACGGTGGAATACGGTCAGT 59.754 55.000 0.00 0.00 40.42 3.41
2335 2786 0.528924 TCACGGTGGAATACGGTCAG 59.471 55.000 8.50 0.00 40.42 3.51
2336 2787 1.135527 GATCACGGTGGAATACGGTCA 59.864 52.381 8.50 0.00 40.42 4.02
2337 2788 1.407979 AGATCACGGTGGAATACGGTC 59.592 52.381 8.50 0.00 40.42 4.79
2338 2789 1.481871 AGATCACGGTGGAATACGGT 58.518 50.000 8.50 0.00 42.80 4.83
2339 2790 3.936372 ATAGATCACGGTGGAATACGG 57.064 47.619 8.50 0.00 35.86 4.02
2340 2791 5.624344 AGTATAGATCACGGTGGAATACG 57.376 43.478 8.50 0.00 0.00 3.06
2341 2792 7.684937 AGTAGTATAGATCACGGTGGAATAC 57.315 40.000 8.50 10.52 0.00 1.89
2342 2793 9.970553 ATAAGTAGTATAGATCACGGTGGAATA 57.029 33.333 8.50 0.00 0.00 1.75
2343 2794 8.880991 ATAAGTAGTATAGATCACGGTGGAAT 57.119 34.615 8.50 0.00 0.00 3.01
2344 2795 9.797642 TTATAAGTAGTATAGATCACGGTGGAA 57.202 33.333 8.50 0.00 0.00 3.53
2345 2796 9.797642 TTTATAAGTAGTATAGATCACGGTGGA 57.202 33.333 8.50 0.00 0.00 4.02
2494 2945 7.023575 GTCAGTCAATGTAAATTGCTAAGTGG 58.976 38.462 0.22 0.00 0.00 4.00
2703 3155 7.665559 TGATTAATTTCCTAATAGGATGCGCTT 59.334 33.333 10.21 0.55 45.34 4.68



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

AutoCloner maintained by Alex Coulton.