Multiple sequence alignment - TraesCS3D01G440000

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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 TraesCS3D01G440000 chr3D 100.000 3105 0 0 1 3105 550383904 550380800 0.000000e+00 5734.0
1 TraesCS3D01G440000 chr3D 77.753 454 83 17 2224 2667 30275580 30275135 2.370000e-66 263.0
2 TraesCS3D01G440000 chr3B 94.633 1323 56 2 767 2074 729922262 729920940 0.000000e+00 2036.0
3 TraesCS3D01G440000 chr3B 96.276 725 24 2 1 725 729922971 729922250 0.000000e+00 1186.0
4 TraesCS3D01G440000 chr3B 89.083 687 72 2 1460 2146 729804632 729805315 0.000000e+00 850.0
5 TraesCS3D01G440000 chr3B 87.102 628 66 11 767 1389 729907736 729907119 0.000000e+00 697.0
6 TraesCS3D01G440000 chr3B 83.016 736 108 12 1 725 729908453 729907724 0.000000e+00 651.0
7 TraesCS3D01G440000 chr3B 83.585 597 82 9 767 1361 729803931 729804513 2.110000e-151 545.0
8 TraesCS3D01G440000 chr3B 80.464 732 125 14 1 725 729803223 729803943 7.570000e-151 544.0
9 TraesCS3D01G440000 chr3B 85.586 222 19 8 1986 2194 729912038 729912259 1.450000e-53 220.0
10 TraesCS3D01G440000 chr3B 95.455 44 2 0 726 769 13759051 13759008 1.540000e-08 71.3
11 TraesCS3D01G440000 chr5A 95.707 629 25 2 2232 2859 264591519 264590892 0.000000e+00 1011.0
12 TraesCS3D01G440000 chr1A 94.958 595 26 3 2265 2859 558103637 558104227 0.000000e+00 929.0
13 TraesCS3D01G440000 chr3A 87.179 702 87 1 1460 2161 687205725 687206423 0.000000e+00 795.0
14 TraesCS3D01G440000 chr3A 85.008 627 77 14 767 1389 687224641 687224028 3.400000e-174 621.0
15 TraesCS3D01G440000 chr3A 83.279 616 73 17 765 1365 687204941 687205541 9.800000e-150 540.0
16 TraesCS3D01G440000 chr3A 82.648 438 55 8 1 419 687126919 687127354 4.890000e-98 368.0
17 TraesCS3D01G440000 chr3A 82.967 364 56 4 363 725 687224987 687224629 1.070000e-84 324.0
18 TraesCS3D01G440000 chr3A 80.243 329 53 6 405 725 687204631 687204955 1.440000e-58 237.0
19 TraesCS3D01G440000 chr3A 85.217 230 33 1 1 229 687140651 687140880 5.180000e-58 235.0
20 TraesCS3D01G440000 chr7B 88.907 622 66 1 1464 2082 40655438 40656059 0.000000e+00 763.0
21 TraesCS3D01G440000 chr7B 85.691 622 60 7 1464 2082 40887716 40888311 2.030000e-176 628.0
22 TraesCS3D01G440000 chr7B 84.630 540 72 9 826 1361 40654844 40655376 7.630000e-146 527.0
23 TraesCS3D01G440000 chr7B 84.066 546 69 12 826 1366 40887109 40887641 7.680000e-141 510.0
24 TraesCS3D01G440000 chr7B 77.710 655 126 15 8 652 40654073 40654717 1.750000e-102 383.0
25 TraesCS3D01G440000 chr7B 100.000 40 0 0 730 769 422973135 422973096 1.190000e-09 75.0
26 TraesCS3D01G440000 chr7B 93.617 47 3 0 728 774 232741319 232741273 1.540000e-08 71.3
27 TraesCS3D01G440000 chr7B 93.182 44 3 0 726 769 714418819 714418862 7.190000e-07 65.8
28 TraesCS3D01G440000 chr7A 88.264 622 70 1 1464 2082 91362518 91363139 0.000000e+00 741.0
29 TraesCS3D01G440000 chr7A 83.942 548 74 12 826 1366 91361885 91362425 2.140000e-141 512.0
30 TraesCS3D01G440000 chr7A 78.425 635 118 16 29 652 91361132 91361758 2.240000e-106 396.0
31 TraesCS3D01G440000 chr7A 95.455 176 6 2 2931 3104 680662428 680662603 2.360000e-71 279.0
32 TraesCS3D01G440000 chr7A 77.143 455 91 12 2219 2667 208552927 208552480 5.140000e-63 252.0
33 TraesCS3D01G440000 chr7D 88.103 622 71 1 1464 2082 89831568 89832189 0.000000e+00 736.0
34 TraesCS3D01G440000 chr7D 84.586 532 70 10 841 1366 89830886 89831411 4.590000e-143 518.0
35 TraesCS3D01G440000 chr7D 84.516 310 48 0 2235 2544 618336402 618336711 1.080000e-79 307.0
36 TraesCS3D01G440000 chr7D 81.731 312 54 1 1800 2108 89862710 89863021 1.100000e-64 257.0
37 TraesCS3D01G440000 chr7D 97.500 40 1 0 730 769 108354683 108354722 5.560000e-08 69.4
38 TraesCS3D01G440000 chr7D 97.500 40 1 0 730 769 108376202 108376241 5.560000e-08 69.4
39 TraesCS3D01G440000 chr5D 95.455 352 14 2 2220 2569 48653108 48653459 7.520000e-156 560.0
40 TraesCS3D01G440000 chr5D 78.358 536 109 6 1461 1992 22859996 22859464 1.070000e-89 340.0
41 TraesCS3D01G440000 chr5D 75.096 522 117 12 2217 2732 267756642 267756128 6.700000e-57 231.0
42 TraesCS3D01G440000 chr2D 97.024 168 4 1 2938 3104 602776613 602776446 6.560000e-72 281.0
43 TraesCS3D01G440000 chr2D 74.859 533 124 9 2224 2750 9662751 9662223 1.860000e-57 233.0
44 TraesCS3D01G440000 chr2D 97.674 43 1 0 726 768 128364639 128364597 1.190000e-09 75.0
45 TraesCS3D01G440000 chr5B 76.096 502 108 10 1480 1975 448839476 448838981 5.140000e-63 252.0
46 TraesCS3D01G440000 chr1D 77.635 389 82 5 2224 2609 488499371 488498985 6.700000e-57 231.0
47 TraesCS3D01G440000 chr1D 97.619 42 1 0 728 769 320171344 320171385 4.300000e-09 73.1
48 TraesCS3D01G440000 chr6A 95.455 44 2 0 726 769 495790102 495790059 1.540000e-08 71.3


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 TraesCS3D01G440000 chr3D 550380800 550383904 3104 True 5734.000000 5734 100.000000 1 3105 1 chr3D.!!$R2 3104
1 TraesCS3D01G440000 chr3B 729920940 729922971 2031 True 1611.000000 2036 95.454500 1 2074 2 chr3B.!!$R3 2073
2 TraesCS3D01G440000 chr3B 729907119 729908453 1334 True 674.000000 697 85.059000 1 1389 2 chr3B.!!$R2 1388
3 TraesCS3D01G440000 chr3B 729803223 729805315 2092 False 646.333333 850 84.377333 1 2146 3 chr3B.!!$F2 2145
4 TraesCS3D01G440000 chr5A 264590892 264591519 627 True 1011.000000 1011 95.707000 2232 2859 1 chr5A.!!$R1 627
5 TraesCS3D01G440000 chr1A 558103637 558104227 590 False 929.000000 929 94.958000 2265 2859 1 chr1A.!!$F1 594
6 TraesCS3D01G440000 chr3A 687204631 687206423 1792 False 524.000000 795 83.567000 405 2161 3 chr3A.!!$F3 1756
7 TraesCS3D01G440000 chr3A 687224028 687224987 959 True 472.500000 621 83.987500 363 1389 2 chr3A.!!$R1 1026
8 TraesCS3D01G440000 chr7B 40887109 40888311 1202 False 569.000000 628 84.878500 826 2082 2 chr7B.!!$F3 1256
9 TraesCS3D01G440000 chr7B 40654073 40656059 1986 False 557.666667 763 83.749000 8 2082 3 chr7B.!!$F2 2074
10 TraesCS3D01G440000 chr7A 91361132 91363139 2007 False 549.666667 741 83.543667 29 2082 3 chr7A.!!$F2 2053
11 TraesCS3D01G440000 chr7D 89830886 89832189 1303 False 627.000000 736 86.344500 841 2082 2 chr7D.!!$F5 1241
12 TraesCS3D01G440000 chr5D 22859464 22859996 532 True 340.000000 340 78.358000 1461 1992 1 chr5D.!!$R1 531
13 TraesCS3D01G440000 chr5D 267756128 267756642 514 True 231.000000 231 75.096000 2217 2732 1 chr5D.!!$R2 515
14 TraesCS3D01G440000 chr2D 9662223 9662751 528 True 233.000000 233 74.859000 2224 2750 1 chr2D.!!$R1 526

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
727 761 1.068055 CGTGGTAACGGTACTGCTTCT 60.068 52.381 11.05 0.0 46.25 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2152 2476 0.394216 TTGATTGCATCCCGTCCAGG 60.394 55.0 0.0 0.0 40.63 4.45 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
83 84 2.214181 CTCGACCAACTCCTCCACGG 62.214 65.000 0.00 0.00 0.00 4.94
243 244 2.866762 GTCCTACGTGATGATCAAAGGC 59.133 50.000 12.49 6.63 0.00 4.35
684 718 2.158475 TGCAGGTCAACCTCCAAATCTT 60.158 45.455 0.00 0.00 46.65 2.40
726 760 1.343506 CGTGGTAACGGTACTGCTTC 58.656 55.000 11.05 0.00 46.25 3.86
727 761 1.068055 CGTGGTAACGGTACTGCTTCT 60.068 52.381 11.05 0.00 46.25 2.85
728 762 2.608752 CGTGGTAACGGTACTGCTTCTT 60.609 50.000 11.05 0.00 46.25 2.52
729 763 3.396560 GTGGTAACGGTACTGCTTCTTT 58.603 45.455 11.05 0.00 42.51 2.52
730 764 3.185797 GTGGTAACGGTACTGCTTCTTTG 59.814 47.826 11.05 0.00 42.51 2.77
732 766 3.811497 GGTAACGGTACTGCTTCTTTGTT 59.189 43.478 11.05 0.00 0.00 2.83
733 767 4.274214 GGTAACGGTACTGCTTCTTTGTTT 59.726 41.667 11.05 0.00 0.00 2.83
734 768 4.976224 AACGGTACTGCTTCTTTGTTTT 57.024 36.364 0.23 0.00 0.00 2.43
735 769 6.018016 GGTAACGGTACTGCTTCTTTGTTTTA 60.018 38.462 11.05 0.00 0.00 1.52
736 770 6.628919 AACGGTACTGCTTCTTTGTTTTAT 57.371 33.333 0.23 0.00 0.00 1.40
737 771 7.733402 AACGGTACTGCTTCTTTGTTTTATA 57.267 32.000 0.23 0.00 0.00 0.98
738 772 7.916914 ACGGTACTGCTTCTTTGTTTTATAT 57.083 32.000 0.23 0.00 0.00 0.86
739 773 9.439500 AACGGTACTGCTTCTTTGTTTTATATA 57.561 29.630 0.23 0.00 0.00 0.86
740 774 9.609346 ACGGTACTGCTTCTTTGTTTTATATAT 57.391 29.630 0.23 0.00 0.00 0.86
755 789 8.718047 GTTTTATATATAAAACGGGGCGAAAG 57.282 34.615 30.91 0.00 46.69 2.62
756 790 6.901265 TTTATATATAAAACGGGGCGAAAGC 58.099 36.000 14.26 0.00 41.85 3.51
772 806 4.414999 GAAAGCCTTTTTCGATAACGGT 57.585 40.909 11.71 0.00 40.21 4.83
773 807 5.535043 GAAAGCCTTTTTCGATAACGGTA 57.465 39.130 11.71 0.00 40.21 4.02
774 808 4.934075 AAGCCTTTTTCGATAACGGTAC 57.066 40.909 11.71 0.00 40.21 3.34
775 809 4.198028 AGCCTTTTTCGATAACGGTACT 57.802 40.909 11.71 0.66 40.21 2.73
776 810 3.930848 AGCCTTTTTCGATAACGGTACTG 59.069 43.478 11.71 0.00 40.21 2.74
777 811 3.484721 GCCTTTTTCGATAACGGTACTGC 60.485 47.826 11.71 0.00 40.21 4.40
778 812 3.930848 CCTTTTTCGATAACGGTACTGCT 59.069 43.478 0.23 0.00 40.21 4.24
792 831 7.448748 ACGGTACTGCTGAATCTAAATTTTT 57.551 32.000 0.23 0.00 0.00 1.94
800 839 9.590088 CTGCTGAATCTAAATTTTTCTTTTTGC 57.410 29.630 0.00 0.00 0.00 3.68
801 840 9.107177 TGCTGAATCTAAATTTTTCTTTTTGCA 57.893 25.926 0.00 0.00 0.00 4.08
803 842 9.571804 CTGAATCTAAATTTTTCTTTTTGCACG 57.428 29.630 0.00 0.00 0.00 5.34
1035 1099 0.104304 CTAGGCAATTCCGCTACCGT 59.896 55.000 0.00 0.00 40.77 4.83
1039 1103 0.739813 GCAATTCCGCTACCGTGAGT 60.740 55.000 0.00 0.00 0.00 3.41
1050 1114 4.081030 CGTGAGTTGGCAGCTGCG 62.081 66.667 31.19 11.96 43.26 5.18
1132 1196 3.071747 AGGGTTCTTGAAGGACTTGAGAC 59.928 47.826 3.26 0.00 0.00 3.36
1339 1405 0.179059 TCACCGTGCAGACAATGTGT 60.179 50.000 0.00 0.00 33.47 3.72
1478 1773 5.036117 TGGTTACTTCAGGCATAAGATCC 57.964 43.478 5.93 5.70 0.00 3.36
1992 2313 1.751349 AACGTGCTACGGTTGGAGGT 61.751 55.000 12.18 3.93 39.21 3.85
2056 2377 1.202330 CTCTTCCCATGCCAGACTCT 58.798 55.000 0.00 0.00 0.00 3.24
2074 2398 1.107114 CTGATACGGGTCACAGCTCT 58.893 55.000 0.00 0.00 0.00 4.09
2086 2410 1.190833 ACAGCTCTAGCACCAGCACT 61.191 55.000 4.54 0.00 45.49 4.40
2092 2416 0.321034 CTAGCACCAGCACTGCTCAA 60.321 55.000 0.00 0.00 44.07 3.02
2126 2450 1.893808 CAGTGTGGTGTGTGGGCTC 60.894 63.158 0.00 0.00 0.00 4.70
2153 2477 4.421952 GGCACGCTAGTTCTAGCC 57.578 61.111 21.29 10.72 39.82 3.93
2161 2485 1.033574 CTAGTTCTAGCCTGGACGGG 58.966 60.000 0.00 0.00 0.00 5.28
2162 2486 0.627451 TAGTTCTAGCCTGGACGGGA 59.373 55.000 0.00 0.00 0.00 5.14
2163 2487 0.032017 AGTTCTAGCCTGGACGGGAT 60.032 55.000 0.00 0.00 0.00 3.85
2164 2488 0.105039 GTTCTAGCCTGGACGGGATG 59.895 60.000 0.00 0.00 0.00 3.51
2165 2489 1.686325 TTCTAGCCTGGACGGGATGC 61.686 60.000 0.00 0.00 0.00 3.91
2166 2490 2.364973 TAGCCTGGACGGGATGCA 60.365 61.111 0.00 0.00 0.00 3.96
2167 2491 1.971505 CTAGCCTGGACGGGATGCAA 61.972 60.000 0.00 0.00 0.00 4.08
2168 2492 1.344953 TAGCCTGGACGGGATGCAAT 61.345 55.000 0.00 0.00 0.00 3.56
2169 2493 2.189499 GCCTGGACGGGATGCAATC 61.189 63.158 0.00 0.00 44.55 2.67
2203 2527 9.701355 ATTTTTCTTTACAAACGAATGCAAAAG 57.299 25.926 0.00 2.30 32.23 2.27
2204 2528 8.467402 TTTTCTTTACAAACGAATGCAAAAGA 57.533 26.923 13.72 13.72 35.51 2.52
2205 2529 7.678194 TTCTTTACAAACGAATGCAAAAGAG 57.322 32.000 15.51 0.00 37.14 2.85
2206 2530 6.791303 TCTTTACAAACGAATGCAAAAGAGT 58.209 32.000 13.72 0.00 33.87 3.24
2207 2531 7.254852 TCTTTACAAACGAATGCAAAAGAGTT 58.745 30.769 13.72 0.00 33.87 3.01
2208 2532 6.804534 TTACAAACGAATGCAAAAGAGTTG 57.195 33.333 0.00 0.00 0.00 3.16
2209 2533 3.551485 ACAAACGAATGCAAAAGAGTTGC 59.449 39.130 4.12 4.12 45.11 4.17
2210 2534 2.422276 ACGAATGCAAAAGAGTTGCC 57.578 45.000 8.47 0.00 44.32 4.52
2211 2535 1.956477 ACGAATGCAAAAGAGTTGCCT 59.044 42.857 8.47 0.00 44.32 4.75
2212 2536 3.146066 ACGAATGCAAAAGAGTTGCCTA 58.854 40.909 8.47 0.00 44.32 3.93
2213 2537 3.568007 ACGAATGCAAAAGAGTTGCCTAA 59.432 39.130 8.47 0.00 44.32 2.69
2214 2538 4.218417 ACGAATGCAAAAGAGTTGCCTAAT 59.782 37.500 8.47 0.00 44.32 1.73
2215 2539 4.795278 CGAATGCAAAAGAGTTGCCTAATC 59.205 41.667 8.47 1.78 44.32 1.75
2216 2540 4.725790 ATGCAAAAGAGTTGCCTAATCC 57.274 40.909 8.47 0.00 44.32 3.01
2217 2541 3.495331 TGCAAAAGAGTTGCCTAATCCA 58.505 40.909 8.47 0.00 44.32 3.41
2218 2542 3.894427 TGCAAAAGAGTTGCCTAATCCAA 59.106 39.130 8.47 0.00 44.32 3.53
2219 2543 4.527816 TGCAAAAGAGTTGCCTAATCCAAT 59.472 37.500 8.47 0.00 44.32 3.16
2220 2544 5.011943 TGCAAAAGAGTTGCCTAATCCAATT 59.988 36.000 8.47 0.00 44.32 2.32
2221 2545 5.934043 GCAAAAGAGTTGCCTAATCCAATTT 59.066 36.000 0.00 0.00 39.38 1.82
2222 2546 7.096551 GCAAAAGAGTTGCCTAATCCAATTTA 58.903 34.615 0.00 0.00 39.38 1.40
2302 2627 5.324409 TCACAAGGTGGCTGATTAAGAAAT 58.676 37.500 0.00 0.00 33.87 2.17
2338 2663 7.317842 TCAGACCAACTTCTATCGTACTTAG 57.682 40.000 0.00 0.00 0.00 2.18
2487 2812 2.145536 CACCATTTCTTTTGGCCTTGC 58.854 47.619 3.32 0.00 37.81 4.01
2586 2912 0.590195 CTCGCATTGCCATAGCTTCC 59.410 55.000 2.41 0.00 40.80 3.46
2674 3000 1.675714 CCCGAATAACAGCAGCAGTCA 60.676 52.381 0.00 0.00 0.00 3.41
2725 3051 6.484308 TGATGCATCGACATTGAGTTTGATAT 59.516 34.615 21.34 0.00 0.00 1.63
2859 3185 2.705658 TGGACAAGAGTCATGGTGAGTT 59.294 45.455 0.00 0.00 46.80 3.01
2860 3186 3.070018 GGACAAGAGTCATGGTGAGTTG 58.930 50.000 0.00 0.00 46.80 3.16
2861 3187 2.481952 GACAAGAGTCATGGTGAGTTGC 59.518 50.000 0.00 0.00 44.34 4.17
2862 3188 2.105477 ACAAGAGTCATGGTGAGTTGCT 59.895 45.455 0.00 0.00 28.50 3.91
2863 3189 3.144506 CAAGAGTCATGGTGAGTTGCTT 58.855 45.455 0.00 0.00 28.50 3.91
2864 3190 4.202357 ACAAGAGTCATGGTGAGTTGCTTA 60.202 41.667 0.00 0.00 28.50 3.09
2865 3191 4.623932 AGAGTCATGGTGAGTTGCTTAA 57.376 40.909 0.00 0.00 28.50 1.85
2866 3192 5.171339 AGAGTCATGGTGAGTTGCTTAAT 57.829 39.130 0.00 0.00 28.50 1.40
2867 3193 5.181748 AGAGTCATGGTGAGTTGCTTAATC 58.818 41.667 0.00 0.00 28.50 1.75
2868 3194 4.265073 AGTCATGGTGAGTTGCTTAATCC 58.735 43.478 0.00 0.00 0.00 3.01
2869 3195 4.009675 GTCATGGTGAGTTGCTTAATCCA 58.990 43.478 0.00 0.00 0.00 3.41
2870 3196 4.641989 GTCATGGTGAGTTGCTTAATCCAT 59.358 41.667 0.00 0.00 35.02 3.41
2871 3197 5.126061 GTCATGGTGAGTTGCTTAATCCATT 59.874 40.000 0.00 0.00 32.81 3.16
2872 3198 5.125900 TCATGGTGAGTTGCTTAATCCATTG 59.874 40.000 0.00 0.00 32.81 2.82
2873 3199 4.661222 TGGTGAGTTGCTTAATCCATTGA 58.339 39.130 0.00 0.00 0.00 2.57
2874 3200 5.263599 TGGTGAGTTGCTTAATCCATTGAT 58.736 37.500 0.00 0.00 0.00 2.57
2875 3201 5.716228 TGGTGAGTTGCTTAATCCATTGATT 59.284 36.000 0.00 0.00 43.56 2.57
2876 3202 6.889177 TGGTGAGTTGCTTAATCCATTGATTA 59.111 34.615 0.00 0.00 41.44 1.75
2877 3203 7.395772 TGGTGAGTTGCTTAATCCATTGATTAA 59.604 33.333 10.60 10.60 46.29 1.40
2909 3235 9.057089 AGAGATTAATTAATGATCCAAACGACC 57.943 33.333 15.39 0.00 0.00 4.79
2910 3236 8.746052 AGATTAATTAATGATCCAAACGACCA 57.254 30.769 15.39 0.00 0.00 4.02
2911 3237 9.184523 AGATTAATTAATGATCCAAACGACCAA 57.815 29.630 15.39 0.00 0.00 3.67
2912 3238 9.796120 GATTAATTAATGATCCAAACGACCAAA 57.204 29.630 15.39 0.00 0.00 3.28
2914 3240 9.796120 TTAATTAATGATCCAAACGACCAAATC 57.204 29.630 0.00 0.00 0.00 2.17
2915 3241 6.825944 TTAATGATCCAAACGACCAAATCA 57.174 33.333 0.00 0.00 0.00 2.57
2916 3242 5.920193 AATGATCCAAACGACCAAATCAT 57.080 34.783 0.00 0.00 35.85 2.45
2917 3243 4.700268 TGATCCAAACGACCAAATCATG 57.300 40.909 0.00 0.00 0.00 3.07
2918 3244 3.119531 TGATCCAAACGACCAAATCATGC 60.120 43.478 0.00 0.00 0.00 4.06
2919 3245 2.234143 TCCAAACGACCAAATCATGCA 58.766 42.857 0.00 0.00 0.00 3.96
2920 3246 2.824936 TCCAAACGACCAAATCATGCAT 59.175 40.909 0.00 0.00 0.00 3.96
2921 3247 2.924926 CCAAACGACCAAATCATGCATG 59.075 45.455 21.07 21.07 0.00 4.06
2922 3248 2.924926 CAAACGACCAAATCATGCATGG 59.075 45.455 25.97 14.21 40.16 3.66
2923 3249 0.457035 ACGACCAAATCATGCATGGC 59.543 50.000 25.97 7.16 37.77 4.40
2924 3250 0.249155 CGACCAAATCATGCATGGCC 60.249 55.000 25.97 3.00 37.77 5.36
2925 3251 0.825410 GACCAAATCATGCATGGCCA 59.175 50.000 25.97 8.56 37.77 5.36
2926 3252 1.414919 GACCAAATCATGCATGGCCAT 59.585 47.619 25.97 14.09 37.77 4.40
2927 3253 2.629137 GACCAAATCATGCATGGCCATA 59.371 45.455 25.97 3.77 37.77 2.74
2928 3254 3.244582 ACCAAATCATGCATGGCCATAT 58.755 40.909 25.97 6.54 37.77 1.78
2929 3255 3.649023 ACCAAATCATGCATGGCCATATT 59.351 39.130 25.97 11.50 37.77 1.28
2930 3256 4.839550 ACCAAATCATGCATGGCCATATTA 59.160 37.500 25.97 8.11 37.77 0.98
2931 3257 5.307456 ACCAAATCATGCATGGCCATATTAA 59.693 36.000 25.97 4.50 37.77 1.40
2932 3258 6.183361 ACCAAATCATGCATGGCCATATTAAA 60.183 34.615 25.97 4.75 37.77 1.52
2933 3259 6.370442 CCAAATCATGCATGGCCATATTAAAG 59.630 38.462 25.97 5.96 0.00 1.85
2934 3260 6.921486 AATCATGCATGGCCATATTAAAGA 57.079 33.333 25.97 12.14 0.00 2.52
2935 3261 7.490657 AATCATGCATGGCCATATTAAAGAT 57.509 32.000 25.97 13.85 0.00 2.40
2936 3262 6.921486 TCATGCATGGCCATATTAAAGATT 57.079 33.333 25.97 0.00 0.00 2.40
2937 3263 8.598202 ATCATGCATGGCCATATTAAAGATTA 57.402 30.769 25.97 1.01 0.00 1.75
2938 3264 8.419922 TCATGCATGGCCATATTAAAGATTAA 57.580 30.769 25.97 0.00 0.00 1.40
2939 3265 8.306038 TCATGCATGGCCATATTAAAGATTAAC 58.694 33.333 25.97 0.00 0.00 2.01
2940 3266 6.991938 TGCATGGCCATATTAAAGATTAACC 58.008 36.000 20.30 0.00 0.00 2.85
2941 3267 6.092748 GCATGGCCATATTAAAGATTAACCG 58.907 40.000 20.30 0.63 0.00 4.44
2942 3268 6.620678 CATGGCCATATTAAAGATTAACCGG 58.379 40.000 20.30 0.00 0.00 5.28
2943 3269 5.942961 TGGCCATATTAAAGATTAACCGGA 58.057 37.500 9.46 0.00 0.00 5.14
2944 3270 6.366340 TGGCCATATTAAAGATTAACCGGAA 58.634 36.000 9.46 0.00 0.00 4.30
2945 3271 6.263617 TGGCCATATTAAAGATTAACCGGAAC 59.736 38.462 9.46 0.00 0.00 3.62
2946 3272 6.263617 GGCCATATTAAAGATTAACCGGAACA 59.736 38.462 9.46 0.00 0.00 3.18
2947 3273 7.201839 GGCCATATTAAAGATTAACCGGAACAA 60.202 37.037 9.46 0.00 0.00 2.83
2948 3274 8.357402 GCCATATTAAAGATTAACCGGAACAAT 58.643 33.333 9.46 3.78 0.00 2.71
2962 3288 7.889873 ACCGGAACAATTAATTAATGATCCA 57.110 32.000 23.42 0.00 0.00 3.41
2963 3289 8.299990 ACCGGAACAATTAATTAATGATCCAA 57.700 30.769 23.42 0.00 0.00 3.53
2964 3290 8.754080 ACCGGAACAATTAATTAATGATCCAAA 58.246 29.630 23.42 0.00 0.00 3.28
2965 3291 9.030301 CCGGAACAATTAATTAATGATCCAAAC 57.970 33.333 23.42 8.74 0.00 2.93
2966 3292 8.742188 CGGAACAATTAATTAATGATCCAAACG 58.258 33.333 23.42 13.91 0.00 3.60
2967 3293 9.796120 GGAACAATTAATTAATGATCCAAACGA 57.204 29.630 21.16 0.00 0.00 3.85
2976 3302 9.874205 AATTAATGATCCAAACGAACAAATCAT 57.126 25.926 0.00 0.00 35.85 2.45
2977 3303 8.686397 TTAATGATCCAAACGAACAAATCATG 57.314 30.769 0.00 0.00 34.87 3.07
2978 3304 4.484236 TGATCCAAACGAACAAATCATGC 58.516 39.130 0.00 0.00 0.00 4.06
2979 3305 3.998099 TCCAAACGAACAAATCATGCA 57.002 38.095 0.00 0.00 0.00 3.96
2980 3306 4.517952 TCCAAACGAACAAATCATGCAT 57.482 36.364 0.00 0.00 0.00 3.96
2981 3307 4.236147 TCCAAACGAACAAATCATGCATG 58.764 39.130 21.07 21.07 0.00 4.06
2982 3308 3.368539 CCAAACGAACAAATCATGCATGG 59.631 43.478 25.97 12.57 0.00 3.66
2983 3309 2.282701 ACGAACAAATCATGCATGGC 57.717 45.000 25.97 6.75 0.00 4.40
2984 3310 1.135024 ACGAACAAATCATGCATGGCC 60.135 47.619 25.97 0.00 0.00 5.36
2985 3311 1.135053 CGAACAAATCATGCATGGCCA 60.135 47.619 25.97 8.56 0.00 5.36
2986 3312 2.482316 CGAACAAATCATGCATGGCCAT 60.482 45.455 25.97 14.09 0.00 4.40
2987 3313 3.243468 CGAACAAATCATGCATGGCCATA 60.243 43.478 25.97 3.77 0.00 2.74
2988 3314 4.559906 CGAACAAATCATGCATGGCCATAT 60.560 41.667 25.97 6.54 0.00 1.78
2989 3315 4.967084 ACAAATCATGCATGGCCATATT 57.033 36.364 25.97 11.50 0.00 1.28
2990 3316 6.422344 AACAAATCATGCATGGCCATATTA 57.578 33.333 25.97 8.11 0.00 0.98
2991 3317 6.422344 ACAAATCATGCATGGCCATATTAA 57.578 33.333 25.97 4.50 0.00 1.40
2992 3318 6.828788 ACAAATCATGCATGGCCATATTAAA 58.171 32.000 25.97 4.75 0.00 1.52
2993 3319 6.932400 ACAAATCATGCATGGCCATATTAAAG 59.068 34.615 25.97 5.96 0.00 1.85
2994 3320 6.675413 AATCATGCATGGCCATATTAAAGT 57.325 33.333 25.97 0.50 0.00 2.66
2995 3321 7.779754 AATCATGCATGGCCATATTAAAGTA 57.220 32.000 25.97 4.66 0.00 2.24
2996 3322 7.966339 ATCATGCATGGCCATATTAAAGTAT 57.034 32.000 25.97 7.10 0.00 2.12
2997 3323 7.779754 TCATGCATGGCCATATTAAAGTATT 57.220 32.000 25.97 0.00 0.00 1.89
2998 3324 7.604549 TCATGCATGGCCATATTAAAGTATTG 58.395 34.615 25.97 3.79 0.00 1.90
2999 3325 6.343716 TGCATGGCCATATTAAAGTATTGG 57.656 37.500 20.30 1.84 0.00 3.16
3000 3326 6.073981 TGCATGGCCATATTAAAGTATTGGA 58.926 36.000 20.30 0.50 0.00 3.53
3001 3327 6.725369 TGCATGGCCATATTAAAGTATTGGAT 59.275 34.615 20.30 0.00 0.00 3.41
3002 3328 7.892771 TGCATGGCCATATTAAAGTATTGGATA 59.107 33.333 20.30 0.00 0.00 2.59
3003 3329 8.408601 GCATGGCCATATTAAAGTATTGGATAG 58.591 37.037 20.30 0.00 0.00 2.08
3004 3330 7.938140 TGGCCATATTAAAGTATTGGATAGC 57.062 36.000 0.00 0.00 0.00 2.97
3005 3331 7.698912 TGGCCATATTAAAGTATTGGATAGCT 58.301 34.615 0.00 0.00 0.00 3.32
3006 3332 7.829211 TGGCCATATTAAAGTATTGGATAGCTC 59.171 37.037 0.00 0.00 0.00 4.09
3007 3333 7.829211 GGCCATATTAAAGTATTGGATAGCTCA 59.171 37.037 0.00 0.00 0.00 4.26
3008 3334 9.401058 GCCATATTAAAGTATTGGATAGCTCAT 57.599 33.333 0.00 0.00 0.00 2.90
3011 3337 9.964354 ATATTAAAGTATTGGATAGCTCATGCA 57.036 29.630 0.00 0.00 42.74 3.96
3013 3339 8.518430 TTAAAGTATTGGATAGCTCATGCAAA 57.482 30.769 11.82 3.17 46.51 3.68
3014 3340 7.408756 AAAGTATTGGATAGCTCATGCAAAA 57.591 32.000 11.82 0.00 46.51 2.44
3015 3341 7.408756 AAGTATTGGATAGCTCATGCAAAAA 57.591 32.000 11.82 4.23 46.51 1.94
3038 3364 6.515272 AAAAAGTATTGGATGGCTACAGTG 57.485 37.500 0.00 0.00 0.00 3.66
3039 3365 3.199880 AGTATTGGATGGCTACAGTGC 57.800 47.619 0.00 0.00 0.00 4.40
3040 3366 2.774234 AGTATTGGATGGCTACAGTGCT 59.226 45.455 0.00 0.00 0.00 4.40
3041 3367 2.814805 ATTGGATGGCTACAGTGCTT 57.185 45.000 0.00 0.00 0.00 3.91
3042 3368 2.113860 TTGGATGGCTACAGTGCTTC 57.886 50.000 0.00 0.00 0.00 3.86
3043 3369 1.279496 TGGATGGCTACAGTGCTTCT 58.721 50.000 0.00 0.00 0.00 2.85
3045 3371 1.208052 GGATGGCTACAGTGCTTCTGA 59.792 52.381 14.40 0.97 46.27 3.27
3046 3372 2.275318 GATGGCTACAGTGCTTCTGAC 58.725 52.381 14.40 5.42 46.27 3.51
3047 3373 0.321671 TGGCTACAGTGCTTCTGACC 59.678 55.000 14.40 12.33 46.27 4.02
3048 3374 0.610687 GGCTACAGTGCTTCTGACCT 59.389 55.000 14.40 0.00 46.27 3.85
3049 3375 1.825474 GGCTACAGTGCTTCTGACCTA 59.175 52.381 14.40 0.00 46.27 3.08
3050 3376 2.417515 GGCTACAGTGCTTCTGACCTAC 60.418 54.545 14.40 0.00 46.27 3.18
3051 3377 2.732597 GCTACAGTGCTTCTGACCTACG 60.733 54.545 14.40 0.00 46.27 3.51
3052 3378 0.603569 ACAGTGCTTCTGACCTACGG 59.396 55.000 14.40 0.00 46.27 4.02
3053 3379 0.737715 CAGTGCTTCTGACCTACGGC 60.738 60.000 3.96 0.00 46.27 5.68
3054 3380 1.185618 AGTGCTTCTGACCTACGGCA 61.186 55.000 0.00 0.00 0.00 5.69
3055 3381 1.014564 GTGCTTCTGACCTACGGCAC 61.015 60.000 0.00 0.00 42.04 5.01
3056 3382 1.185618 TGCTTCTGACCTACGGCACT 61.186 55.000 0.00 0.00 0.00 4.40
3057 3383 0.458716 GCTTCTGACCTACGGCACTC 60.459 60.000 0.00 0.00 0.00 3.51
3058 3384 1.178276 CTTCTGACCTACGGCACTCT 58.822 55.000 0.00 0.00 0.00 3.24
3059 3385 0.888619 TTCTGACCTACGGCACTCTG 59.111 55.000 0.00 0.00 0.00 3.35
3060 3386 1.153745 CTGACCTACGGCACTCTGC 60.154 63.158 0.00 0.00 44.08 4.26
3061 3387 1.599606 CTGACCTACGGCACTCTGCT 61.600 60.000 0.00 0.00 44.28 4.24
3062 3388 0.323087 TGACCTACGGCACTCTGCTA 60.323 55.000 0.00 0.00 44.28 3.49
3063 3389 0.815734 GACCTACGGCACTCTGCTAA 59.184 55.000 0.00 0.00 44.28 3.09
3064 3390 1.409427 GACCTACGGCACTCTGCTAAT 59.591 52.381 0.00 0.00 44.28 1.73
3065 3391 1.409427 ACCTACGGCACTCTGCTAATC 59.591 52.381 0.00 0.00 44.28 1.75
3066 3392 1.683917 CCTACGGCACTCTGCTAATCT 59.316 52.381 0.00 0.00 44.28 2.40
3067 3393 2.544694 CCTACGGCACTCTGCTAATCTG 60.545 54.545 0.00 0.00 44.28 2.90
3068 3394 1.186200 ACGGCACTCTGCTAATCTGA 58.814 50.000 0.00 0.00 44.28 3.27
3069 3395 1.759445 ACGGCACTCTGCTAATCTGAT 59.241 47.619 0.00 0.00 44.28 2.90
3070 3396 2.133553 CGGCACTCTGCTAATCTGATG 58.866 52.381 0.00 0.00 44.28 3.07
3071 3397 2.492012 GGCACTCTGCTAATCTGATGG 58.508 52.381 0.00 0.00 44.28 3.51
3072 3398 2.492012 GCACTCTGCTAATCTGATGGG 58.508 52.381 0.00 0.00 40.96 4.00
3073 3399 2.492012 CACTCTGCTAATCTGATGGGC 58.508 52.381 7.77 7.77 0.00 5.36
3074 3400 2.104451 CACTCTGCTAATCTGATGGGCT 59.896 50.000 13.52 0.00 0.00 5.19
3075 3401 2.104451 ACTCTGCTAATCTGATGGGCTG 59.896 50.000 13.52 12.91 0.00 4.85
3076 3402 1.202734 TCTGCTAATCTGATGGGCTGC 60.203 52.381 13.52 0.00 0.00 5.25
3077 3403 0.179009 TGCTAATCTGATGGGCTGCC 60.179 55.000 11.05 11.05 0.00 4.85
3078 3404 0.892814 GCTAATCTGATGGGCTGCCC 60.893 60.000 30.97 30.97 45.71 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.092882 GCTGCCGTCGGTGTAGTTC 61.093 63.158 13.94 0.00 0.00 3.01
486 493 1.600107 GCCGTACATCACCTGGGAA 59.400 57.895 0.00 0.00 0.00 3.97
547 554 3.621268 TGTGCGATGTTATTAAGGCAGTC 59.379 43.478 0.00 0.00 0.00 3.51
732 766 6.901265 GCTTTCGCCCCGTTTTATATATAAA 58.099 36.000 12.90 12.90 0.00 1.40
733 767 6.484818 GCTTTCGCCCCGTTTTATATATAA 57.515 37.500 0.81 0.81 0.00 0.98
751 785 4.414999 ACCGTTATCGAAAAAGGCTTTC 57.585 40.909 13.76 0.41 39.71 2.62
752 786 4.999311 AGTACCGTTATCGAAAAAGGCTTT 59.001 37.500 6.68 6.68 39.71 3.51
753 787 4.390909 CAGTACCGTTATCGAAAAAGGCTT 59.609 41.667 0.00 0.00 39.71 4.35
754 788 3.930848 CAGTACCGTTATCGAAAAAGGCT 59.069 43.478 0.00 0.00 39.71 4.58
755 789 3.484721 GCAGTACCGTTATCGAAAAAGGC 60.485 47.826 0.00 0.00 39.71 4.35
756 790 3.930848 AGCAGTACCGTTATCGAAAAAGG 59.069 43.478 0.00 0.00 39.71 3.11
757 791 4.624024 TCAGCAGTACCGTTATCGAAAAAG 59.376 41.667 0.00 0.00 39.71 2.27
758 792 4.558178 TCAGCAGTACCGTTATCGAAAAA 58.442 39.130 0.00 0.00 39.71 1.94
759 793 4.177165 TCAGCAGTACCGTTATCGAAAA 57.823 40.909 0.00 0.00 39.71 2.29
760 794 3.853831 TCAGCAGTACCGTTATCGAAA 57.146 42.857 0.00 0.00 39.71 3.46
761 795 3.853831 TTCAGCAGTACCGTTATCGAA 57.146 42.857 0.00 0.00 39.71 3.71
762 796 3.630769 AGATTCAGCAGTACCGTTATCGA 59.369 43.478 0.00 0.00 39.71 3.59
763 797 3.966154 AGATTCAGCAGTACCGTTATCG 58.034 45.455 0.00 0.00 0.00 2.92
764 798 7.948278 ATTTAGATTCAGCAGTACCGTTATC 57.052 36.000 0.00 0.00 0.00 1.75
765 799 8.732746 AAATTTAGATTCAGCAGTACCGTTAT 57.267 30.769 0.00 0.00 0.00 1.89
766 800 8.556213 AAAATTTAGATTCAGCAGTACCGTTA 57.444 30.769 0.00 0.00 0.00 3.18
767 801 7.448748 AAAATTTAGATTCAGCAGTACCGTT 57.551 32.000 0.00 0.00 0.00 4.44
768 802 7.390718 AGAAAAATTTAGATTCAGCAGTACCGT 59.609 33.333 4.40 0.00 0.00 4.83
769 803 7.752695 AGAAAAATTTAGATTCAGCAGTACCG 58.247 34.615 4.40 0.00 0.00 4.02
770 804 9.914131 AAAGAAAAATTTAGATTCAGCAGTACC 57.086 29.630 4.40 0.00 0.00 3.34
774 808 9.590088 GCAAAAAGAAAAATTTAGATTCAGCAG 57.410 29.630 4.40 0.00 0.00 4.24
775 809 9.107177 TGCAAAAAGAAAAATTTAGATTCAGCA 57.893 25.926 4.40 0.00 0.00 4.41
776 810 9.373750 GTGCAAAAAGAAAAATTTAGATTCAGC 57.626 29.630 0.00 0.00 0.00 4.26
777 811 9.571804 CGTGCAAAAAGAAAAATTTAGATTCAG 57.428 29.630 0.00 0.00 0.00 3.02
778 812 9.092876 ACGTGCAAAAAGAAAAATTTAGATTCA 57.907 25.926 0.00 0.00 0.00 2.57
1035 1099 2.666190 GTCGCAGCTGCCAACTCA 60.666 61.111 32.07 7.05 37.91 3.41
1078 1142 1.834822 CAAACCCGCCTTCCCCAAA 60.835 57.895 0.00 0.00 0.00 3.28
1132 1196 3.450457 ACTCTCTTGATAGCCACCTCAAG 59.550 47.826 6.05 6.05 46.27 3.02
1339 1405 2.337879 GACCTGACTGGCCACCACAA 62.338 60.000 0.00 0.00 40.22 3.33
1478 1773 4.247380 GGAGCCGATCCCCAGCAG 62.247 72.222 0.00 0.00 43.01 4.24
1588 1883 1.079405 CCCGAAGTCGCCAAGCTTA 60.079 57.895 0.00 0.00 38.18 3.09
1795 2090 3.320879 CTGCGCCAGGTGGATCAGT 62.321 63.158 4.18 0.00 37.39 3.41
1937 2258 3.396570 CGGCCTTAGGTCCCGGTT 61.397 66.667 9.08 0.00 38.42 4.44
2056 2377 2.298610 CTAGAGCTGTGACCCGTATCA 58.701 52.381 0.00 0.00 0.00 2.15
2101 2425 2.161855 CACACACCACACTGCCATTAT 58.838 47.619 0.00 0.00 0.00 1.28
2108 2432 1.893808 GAGCCCACACACCACACTG 60.894 63.158 0.00 0.00 0.00 3.66
2110 2434 2.731691 ATCGAGCCCACACACCACAC 62.732 60.000 0.00 0.00 0.00 3.82
2115 2439 1.514678 TTGCAATCGAGCCCACACAC 61.515 55.000 0.00 0.00 0.00 3.82
2116 2440 1.228094 TTGCAATCGAGCCCACACA 60.228 52.632 0.00 0.00 0.00 3.72
2146 2470 1.686325 GCATCCCGTCCAGGCTAGAA 61.686 60.000 0.00 0.00 39.21 2.10
2148 2472 1.971505 TTGCATCCCGTCCAGGCTAG 61.972 60.000 0.00 0.00 39.21 3.42
2152 2476 0.394216 TTGATTGCATCCCGTCCAGG 60.394 55.000 0.00 0.00 40.63 4.45
2153 2477 1.402968 CTTTGATTGCATCCCGTCCAG 59.597 52.381 0.00 0.00 0.00 3.86
2177 2501 9.701355 CTTTTGCATTCGTTTGTAAAGAAAAAT 57.299 25.926 0.00 0.00 33.66 1.82
2178 2502 8.926710 TCTTTTGCATTCGTTTGTAAAGAAAAA 58.073 25.926 2.73 0.00 33.66 1.94
2179 2503 8.467402 TCTTTTGCATTCGTTTGTAAAGAAAA 57.533 26.923 2.73 0.00 33.66 2.29
2180 2504 7.757624 ACTCTTTTGCATTCGTTTGTAAAGAAA 59.242 29.630 6.05 0.00 33.66 2.52
2181 2505 7.254852 ACTCTTTTGCATTCGTTTGTAAAGAA 58.745 30.769 6.05 0.00 33.66 2.52
2182 2506 6.791303 ACTCTTTTGCATTCGTTTGTAAAGA 58.209 32.000 4.79 4.79 33.66 2.52
2183 2507 7.329582 CAACTCTTTTGCATTCGTTTGTAAAG 58.670 34.615 0.00 0.00 33.66 1.85
2184 2508 6.237701 GCAACTCTTTTGCATTCGTTTGTAAA 60.238 34.615 4.12 1.09 44.34 2.01
2185 2509 5.231147 GCAACTCTTTTGCATTCGTTTGTAA 59.769 36.000 4.12 0.00 44.34 2.41
2186 2510 4.737765 GCAACTCTTTTGCATTCGTTTGTA 59.262 37.500 4.12 0.00 44.34 2.41
2187 2511 3.551485 GCAACTCTTTTGCATTCGTTTGT 59.449 39.130 4.12 0.00 44.34 2.83
2188 2512 3.060339 GGCAACTCTTTTGCATTCGTTTG 60.060 43.478 10.90 0.00 46.58 2.93
2189 2513 3.123050 GGCAACTCTTTTGCATTCGTTT 58.877 40.909 10.90 0.00 46.58 3.60
2190 2514 2.742774 GGCAACTCTTTTGCATTCGTT 58.257 42.857 10.90 0.00 46.58 3.85
2191 2515 2.422276 GGCAACTCTTTTGCATTCGT 57.578 45.000 10.90 0.00 46.58 3.85
2302 2627 1.993391 GGTCTGATGAACCCCCGGA 60.993 63.158 0.73 0.00 0.00 5.14
2338 2663 7.647715 TGAGCTAGCAAAATTCAGTTTTTGTAC 59.352 33.333 18.83 0.00 44.62 2.90
2487 2812 4.945543 TCTCTGAACATGGTGAATCATTGG 59.054 41.667 0.00 0.00 0.00 3.16
2492 2817 4.272018 CCGATTCTCTGAACATGGTGAATC 59.728 45.833 10.19 10.19 38.24 2.52
2586 2912 3.564262 AGCAGATGTGGTGACCATG 57.436 52.632 7.94 2.58 35.28 3.66
2674 3000 1.835927 GCAGAGGAAGGCTCAGGTGT 61.836 60.000 0.00 0.00 0.00 4.16
2725 3051 0.395311 ACGAAGCCAGACCCGAGATA 60.395 55.000 0.00 0.00 0.00 1.98
2883 3209 9.057089 GGTCGTTTGGATCATTAATTAATCTCT 57.943 33.333 7.76 0.00 0.00 3.10
2884 3210 8.836413 TGGTCGTTTGGATCATTAATTAATCTC 58.164 33.333 7.76 7.94 28.38 2.75
2885 3211 8.746052 TGGTCGTTTGGATCATTAATTAATCT 57.254 30.769 7.76 0.00 28.38 2.40
2886 3212 9.796120 TTTGGTCGTTTGGATCATTAATTAATC 57.204 29.630 7.76 0.00 35.20 1.75
2888 3214 9.796120 GATTTGGTCGTTTGGATCATTAATTAA 57.204 29.630 0.00 0.00 35.20 1.40
2889 3215 8.961634 TGATTTGGTCGTTTGGATCATTAATTA 58.038 29.630 0.00 0.00 35.20 1.40
2890 3216 7.835822 TGATTTGGTCGTTTGGATCATTAATT 58.164 30.769 0.00 0.00 35.20 1.40
2891 3217 7.403312 TGATTTGGTCGTTTGGATCATTAAT 57.597 32.000 0.00 0.00 35.20 1.40
2892 3218 6.825944 TGATTTGGTCGTTTGGATCATTAA 57.174 33.333 0.00 0.00 35.20 1.40
2893 3219 6.680131 GCATGATTTGGTCGTTTGGATCATTA 60.680 38.462 0.00 0.00 35.20 1.90
2894 3220 5.653507 CATGATTTGGTCGTTTGGATCATT 58.346 37.500 0.00 0.00 35.20 2.57
2895 3221 4.440525 GCATGATTTGGTCGTTTGGATCAT 60.441 41.667 0.00 0.00 35.20 2.45
2896 3222 3.119531 GCATGATTTGGTCGTTTGGATCA 60.120 43.478 0.00 0.00 32.70 2.92
2897 3223 3.119531 TGCATGATTTGGTCGTTTGGATC 60.120 43.478 0.00 0.00 0.00 3.36
2898 3224 2.824936 TGCATGATTTGGTCGTTTGGAT 59.175 40.909 0.00 0.00 0.00 3.41
2899 3225 2.234143 TGCATGATTTGGTCGTTTGGA 58.766 42.857 0.00 0.00 0.00 3.53
2900 3226 2.721274 TGCATGATTTGGTCGTTTGG 57.279 45.000 0.00 0.00 0.00 3.28
2901 3227 2.924926 CCATGCATGATTTGGTCGTTTG 59.075 45.455 28.31 2.27 0.00 2.93
2902 3228 2.674747 GCCATGCATGATTTGGTCGTTT 60.675 45.455 28.31 0.00 32.90 3.60
2903 3229 1.135024 GCCATGCATGATTTGGTCGTT 60.135 47.619 28.31 0.00 32.90 3.85
2904 3230 0.457035 GCCATGCATGATTTGGTCGT 59.543 50.000 28.31 0.00 32.90 4.34
2905 3231 0.249155 GGCCATGCATGATTTGGTCG 60.249 55.000 28.31 9.48 32.90 4.79
2906 3232 0.825410 TGGCCATGCATGATTTGGTC 59.175 50.000 28.31 14.72 35.66 4.02
2907 3233 1.502690 ATGGCCATGCATGATTTGGT 58.497 45.000 28.31 5.91 32.90 3.67
2908 3234 3.973206 ATATGGCCATGCATGATTTGG 57.027 42.857 29.04 13.77 0.00 3.28
2909 3235 7.156000 TCTTTAATATGGCCATGCATGATTTG 58.844 34.615 29.04 12.10 0.00 2.32
2910 3236 7.305813 TCTTTAATATGGCCATGCATGATTT 57.694 32.000 29.04 11.73 0.00 2.17
2911 3237 6.921486 TCTTTAATATGGCCATGCATGATT 57.079 33.333 29.04 20.33 0.00 2.57
2912 3238 7.490657 AATCTTTAATATGGCCATGCATGAT 57.509 32.000 29.04 18.64 0.00 2.45
2913 3239 6.921486 AATCTTTAATATGGCCATGCATGA 57.079 33.333 29.04 17.33 0.00 3.07
2914 3240 7.546667 GGTTAATCTTTAATATGGCCATGCATG 59.453 37.037 29.04 20.19 0.00 4.06
2915 3241 7.577426 CGGTTAATCTTTAATATGGCCATGCAT 60.577 37.037 29.04 12.11 0.00 3.96
2916 3242 6.294453 CGGTTAATCTTTAATATGGCCATGCA 60.294 38.462 29.04 9.94 0.00 3.96
2917 3243 6.092748 CGGTTAATCTTTAATATGGCCATGC 58.907 40.000 29.04 0.00 0.00 4.06
2918 3244 6.432783 TCCGGTTAATCTTTAATATGGCCATG 59.567 38.462 29.04 10.43 0.00 3.66
2919 3245 6.548321 TCCGGTTAATCTTTAATATGGCCAT 58.452 36.000 24.45 24.45 0.00 4.40
2920 3246 5.942961 TCCGGTTAATCTTTAATATGGCCA 58.057 37.500 8.56 8.56 0.00 5.36
2921 3247 6.263617 TGTTCCGGTTAATCTTTAATATGGCC 59.736 38.462 0.00 0.00 0.00 5.36
2922 3248 7.266922 TGTTCCGGTTAATCTTTAATATGGC 57.733 36.000 0.00 0.00 0.00 4.40
2936 3262 9.409918 TGGATCATTAATTAATTGTTCCGGTTA 57.590 29.630 11.05 0.00 0.00 2.85
2937 3263 8.299990 TGGATCATTAATTAATTGTTCCGGTT 57.700 30.769 11.05 0.00 0.00 4.44
2938 3264 7.889873 TGGATCATTAATTAATTGTTCCGGT 57.110 32.000 11.05 0.00 0.00 5.28
2939 3265 9.030301 GTTTGGATCATTAATTAATTGTTCCGG 57.970 33.333 11.05 0.00 0.00 5.14
2940 3266 8.742188 CGTTTGGATCATTAATTAATTGTTCCG 58.258 33.333 11.05 0.00 0.00 4.30
2941 3267 9.796120 TCGTTTGGATCATTAATTAATTGTTCC 57.204 29.630 11.05 13.60 0.00 3.62
2950 3276 9.874205 ATGATTTGTTCGTTTGGATCATTAATT 57.126 25.926 0.00 0.00 32.06 1.40
2951 3277 9.304731 CATGATTTGTTCGTTTGGATCATTAAT 57.695 29.630 0.00 0.00 33.34 1.40
2952 3278 7.275341 GCATGATTTGTTCGTTTGGATCATTAA 59.725 33.333 0.00 0.00 33.34 1.40
2953 3279 6.751425 GCATGATTTGTTCGTTTGGATCATTA 59.249 34.615 0.00 0.00 33.34 1.90
2954 3280 5.577945 GCATGATTTGTTCGTTTGGATCATT 59.422 36.000 0.00 0.00 33.34 2.57
2955 3281 5.104374 GCATGATTTGTTCGTTTGGATCAT 58.896 37.500 0.00 0.00 35.31 2.45
2956 3282 4.022503 TGCATGATTTGTTCGTTTGGATCA 60.023 37.500 0.00 0.00 0.00 2.92
2957 3283 4.484236 TGCATGATTTGTTCGTTTGGATC 58.516 39.130 0.00 0.00 0.00 3.36
2958 3284 4.517952 TGCATGATTTGTTCGTTTGGAT 57.482 36.364 0.00 0.00 0.00 3.41
2959 3285 3.998099 TGCATGATTTGTTCGTTTGGA 57.002 38.095 0.00 0.00 0.00 3.53
2960 3286 3.368539 CCATGCATGATTTGTTCGTTTGG 59.631 43.478 28.31 3.32 0.00 3.28
2961 3287 3.181528 GCCATGCATGATTTGTTCGTTTG 60.182 43.478 28.31 7.28 0.00 2.93
2962 3288 2.995258 GCCATGCATGATTTGTTCGTTT 59.005 40.909 28.31 0.00 0.00 3.60
2963 3289 2.609350 GCCATGCATGATTTGTTCGTT 58.391 42.857 28.31 0.00 0.00 3.85
2964 3290 1.135024 GGCCATGCATGATTTGTTCGT 60.135 47.619 28.31 0.00 0.00 3.85
2965 3291 1.135053 TGGCCATGCATGATTTGTTCG 60.135 47.619 28.31 9.48 0.00 3.95
2966 3292 2.676632 TGGCCATGCATGATTTGTTC 57.323 45.000 28.31 9.08 0.00 3.18
2967 3293 4.967084 ATATGGCCATGCATGATTTGTT 57.033 36.364 29.04 9.70 0.00 2.83
2968 3294 4.967084 AATATGGCCATGCATGATTTGT 57.033 36.364 29.04 11.73 0.00 2.83
2969 3295 6.932400 ACTTTAATATGGCCATGCATGATTTG 59.068 34.615 29.04 12.10 0.00 2.32
2970 3296 7.069877 ACTTTAATATGGCCATGCATGATTT 57.930 32.000 29.04 11.73 0.00 2.17
2971 3297 6.675413 ACTTTAATATGGCCATGCATGATT 57.325 33.333 29.04 20.33 0.00 2.57
2972 3298 7.966339 ATACTTTAATATGGCCATGCATGAT 57.034 32.000 29.04 15.63 0.00 2.45
2973 3299 7.309928 CCAATACTTTAATATGGCCATGCATGA 60.310 37.037 29.04 8.21 0.00 3.07
2974 3300 6.814644 CCAATACTTTAATATGGCCATGCATG 59.185 38.462 29.04 20.19 0.00 4.06
2975 3301 6.725369 TCCAATACTTTAATATGGCCATGCAT 59.275 34.615 29.04 12.11 0.00 3.96
2976 3302 6.073981 TCCAATACTTTAATATGGCCATGCA 58.926 36.000 29.04 9.94 0.00 3.96
2977 3303 6.588719 TCCAATACTTTAATATGGCCATGC 57.411 37.500 29.04 0.00 0.00 4.06
2978 3304 8.408601 GCTATCCAATACTTTAATATGGCCATG 58.591 37.037 29.04 12.72 0.00 3.66
2979 3305 8.339247 AGCTATCCAATACTTTAATATGGCCAT 58.661 33.333 24.45 24.45 0.00 4.40
2980 3306 7.698912 AGCTATCCAATACTTTAATATGGCCA 58.301 34.615 8.56 8.56 0.00 5.36
2981 3307 7.829211 TGAGCTATCCAATACTTTAATATGGCC 59.171 37.037 0.00 0.00 0.00 5.36
2982 3308 8.792830 TGAGCTATCCAATACTTTAATATGGC 57.207 34.615 0.00 0.00 0.00 4.40
2985 3311 9.964354 TGCATGAGCTATCCAATACTTTAATAT 57.036 29.630 0.00 0.00 42.74 1.28
2986 3312 9.791801 TTGCATGAGCTATCCAATACTTTAATA 57.208 29.630 0.00 0.00 42.74 0.98
2987 3313 8.696043 TTGCATGAGCTATCCAATACTTTAAT 57.304 30.769 0.00 0.00 42.74 1.40
2988 3314 8.518430 TTTGCATGAGCTATCCAATACTTTAA 57.482 30.769 0.00 0.00 42.74 1.52
2989 3315 8.518430 TTTTGCATGAGCTATCCAATACTTTA 57.482 30.769 0.00 0.00 42.74 1.85
2990 3316 7.408756 TTTTGCATGAGCTATCCAATACTTT 57.591 32.000 0.00 0.00 42.74 2.66
2991 3317 7.408756 TTTTTGCATGAGCTATCCAATACTT 57.591 32.000 0.00 0.00 42.74 2.24
3015 3341 5.105756 GCACTGTAGCCATCCAATACTTTTT 60.106 40.000 0.00 0.00 0.00 1.94
3016 3342 4.399303 GCACTGTAGCCATCCAATACTTTT 59.601 41.667 0.00 0.00 0.00 2.27
3017 3343 3.947834 GCACTGTAGCCATCCAATACTTT 59.052 43.478 0.00 0.00 0.00 2.66
3018 3344 3.200825 AGCACTGTAGCCATCCAATACTT 59.799 43.478 0.00 0.00 34.23 2.24
3019 3345 2.774234 AGCACTGTAGCCATCCAATACT 59.226 45.455 0.00 0.00 34.23 2.12
3020 3346 3.199880 AGCACTGTAGCCATCCAATAC 57.800 47.619 0.00 0.00 34.23 1.89
3021 3347 3.455910 AGAAGCACTGTAGCCATCCAATA 59.544 43.478 0.00 0.00 34.23 1.90
3022 3348 2.240667 AGAAGCACTGTAGCCATCCAAT 59.759 45.455 0.00 0.00 34.23 3.16
3023 3349 1.630369 AGAAGCACTGTAGCCATCCAA 59.370 47.619 0.00 0.00 34.23 3.53
3024 3350 1.065926 CAGAAGCACTGTAGCCATCCA 60.066 52.381 3.29 0.00 41.30 3.41
3025 3351 1.208052 TCAGAAGCACTGTAGCCATCC 59.792 52.381 9.97 0.00 45.86 3.51
3026 3352 2.275318 GTCAGAAGCACTGTAGCCATC 58.725 52.381 9.97 0.00 45.86 3.51
3027 3353 1.065854 GGTCAGAAGCACTGTAGCCAT 60.066 52.381 9.97 0.00 45.86 4.40
3028 3354 0.321671 GGTCAGAAGCACTGTAGCCA 59.678 55.000 9.97 0.00 45.86 4.75
3029 3355 0.610687 AGGTCAGAAGCACTGTAGCC 59.389 55.000 9.97 10.43 45.86 3.93
3030 3356 2.732597 CGTAGGTCAGAAGCACTGTAGC 60.733 54.545 9.97 7.32 45.86 3.58
3031 3357 3.138205 CGTAGGTCAGAAGCACTGTAG 57.862 52.381 9.97 0.00 45.86 2.74
3047 3373 2.359214 TCAGATTAGCAGAGTGCCGTAG 59.641 50.000 0.00 0.00 46.52 3.51
3048 3374 2.375146 TCAGATTAGCAGAGTGCCGTA 58.625 47.619 0.00 0.00 46.52 4.02
3049 3375 1.186200 TCAGATTAGCAGAGTGCCGT 58.814 50.000 0.00 0.00 46.52 5.68
3050 3376 2.133553 CATCAGATTAGCAGAGTGCCG 58.866 52.381 0.00 0.00 46.52 5.69
3051 3377 2.492012 CCATCAGATTAGCAGAGTGCC 58.508 52.381 0.00 0.00 46.52 5.01
3052 3378 2.492012 CCCATCAGATTAGCAGAGTGC 58.508 52.381 0.00 0.00 45.46 4.40
3053 3379 2.104451 AGCCCATCAGATTAGCAGAGTG 59.896 50.000 4.58 0.00 0.00 3.51
3054 3380 2.104451 CAGCCCATCAGATTAGCAGAGT 59.896 50.000 4.58 0.00 0.00 3.24
3055 3381 2.768698 CAGCCCATCAGATTAGCAGAG 58.231 52.381 4.58 0.00 0.00 3.35
3056 3382 1.202734 GCAGCCCATCAGATTAGCAGA 60.203 52.381 4.58 0.00 0.00 4.26
3057 3383 1.236628 GCAGCCCATCAGATTAGCAG 58.763 55.000 4.58 0.00 0.00 4.24
3058 3384 0.179009 GGCAGCCCATCAGATTAGCA 60.179 55.000 0.00 0.00 0.00 3.49
3059 3385 0.892814 GGGCAGCCCATCAGATTAGC 60.893 60.000 27.33 0.00 44.65 3.09
3060 3386 0.604780 CGGGCAGCCCATCAGATTAG 60.605 60.000 30.86 6.55 45.83 1.73
3061 3387 1.344953 ACGGGCAGCCCATCAGATTA 61.345 55.000 30.86 0.00 45.83 1.75
3062 3388 2.194056 CGGGCAGCCCATCAGATT 59.806 61.111 30.86 0.00 45.83 2.40
3063 3389 2.215451 AAACGGGCAGCCCATCAGAT 62.215 55.000 30.86 5.61 45.83 2.90
3064 3390 2.424842 AAAACGGGCAGCCCATCAGA 62.425 55.000 30.86 0.00 45.83 3.27
3065 3391 1.535204 AAAAACGGGCAGCCCATCAG 61.535 55.000 30.86 16.26 45.83 2.90
3066 3392 1.532794 AAAAACGGGCAGCCCATCA 60.533 52.632 30.86 0.00 45.83 3.07
3067 3393 3.376546 AAAAACGGGCAGCCCATC 58.623 55.556 30.86 3.39 45.83 3.51


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

AutoCloner maintained by Alex Coulton.