Multiple sequence alignment - TraesCS1A01G313500

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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 TraesCS1A01G313500 chr1A 100.000 5425 0 0 1 5425 505287202 505281778 0.000000e+00 10019.0
1 TraesCS1A01G313500 chr1A 89.851 335 20 6 238 559 49147751 49148084 8.400000e-113 418.0
2 TraesCS1A01G313500 chr1A 81.312 503 79 8 3715 4214 505283725 505283235 1.420000e-105 394.0
3 TraesCS1A01G313500 chr1A 87.786 262 23 3 609 861 49148164 49148425 1.140000e-76 298.0
4 TraesCS1A01G313500 chr1A 74.611 386 64 13 2048 2407 576213166 576212789 7.330000e-29 139.0
5 TraesCS1A01G313500 chr1A 74.611 386 58 20 2147 2515 576215817 576215455 3.410000e-27 134.0
6 TraesCS1A01G313500 chr1A 74.541 381 60 22 2147 2514 576217859 576217503 1.230000e-26 132.0
7 TraesCS1A01G313500 chr1A 81.132 159 17 12 2509 2661 549605281 549605432 1.230000e-21 115.0
8 TraesCS1A01G313500 chr1D 96.312 3796 89 19 1671 5425 409070071 409066286 0.000000e+00 6187.0
9 TraesCS1A01G313500 chr1D 90.922 727 41 7 971 1684 409070809 409070095 0.000000e+00 953.0
10 TraesCS1A01G313500 chr1D 81.511 503 78 7 3715 4214 409068241 409067751 3.040000e-107 399.0
11 TraesCS1A01G313500 chr1D 81.119 143 26 1 2147 2289 479769376 479769235 4.440000e-21 113.0
12 TraesCS1A01G313500 chr1B 93.573 3999 161 38 891 4823 551035847 551031879 0.000000e+00 5873.0
13 TraesCS1A01G313500 chr1B 91.785 633 25 12 4820 5425 551031767 551031135 0.000000e+00 856.0
14 TraesCS1A01G313500 chr1B 84.110 365 38 12 242 589 57505130 57505491 8.710000e-88 335.0
15 TraesCS1A01G313500 chr1B 84.078 358 33 11 239 573 113878039 113877683 1.880000e-84 324.0
16 TraesCS1A01G313500 chr1B 86.641 262 24 5 612 862 113877593 113877332 4.140000e-71 279.0
17 TraesCS1A01G313500 chr1B 79.012 324 51 7 268 589 638819814 638820122 7.120000e-49 206.0
18 TraesCS1A01G313500 chr3B 84.130 1235 167 14 2709 3927 747746086 747744865 0.000000e+00 1168.0
19 TraesCS1A01G313500 chrUn 81.811 1281 160 39 2718 3968 108328176 108329413 0.000000e+00 1007.0
20 TraesCS1A01G313500 chrUn 88.208 653 75 2 3046 3696 134246288 134245636 0.000000e+00 778.0
21 TraesCS1A01G313500 chrUn 88.055 653 76 2 3046 3696 65140588 65139936 0.000000e+00 773.0
22 TraesCS1A01G313500 chrUn 84.615 637 86 5 3717 4353 108328928 108329552 1.660000e-174 623.0
23 TraesCS1A01G313500 chrUn 78.388 819 104 35 4630 5416 134245176 134244399 1.060000e-126 464.0
24 TraesCS1A01G313500 chrUn 84.233 463 73 0 3967 4429 134245851 134245389 8.290000e-123 451.0
25 TraesCS1A01G313500 chrUn 83.766 462 75 0 3967 4428 65140151 65139690 6.450000e-119 438.0
26 TraesCS1A01G313500 chrUn 81.124 498 39 24 4540 4996 108329743 108330226 1.120000e-91 348.0
27 TraesCS1A01G313500 chrUn 83.471 363 43 12 238 585 343337592 343337952 6.780000e-84 322.0
28 TraesCS1A01G313500 chrUn 80.909 440 55 14 2151 2573 134246857 134246430 2.440000e-83 320.0
29 TraesCS1A01G313500 chrUn 86.809 235 28 3 3715 3949 134245854 134245623 5.390000e-65 259.0
30 TraesCS1A01G313500 chrUn 86.383 235 29 3 3715 3949 65140154 65139923 2.510000e-63 254.0
31 TraesCS1A01G313500 chrUn 83.871 217 17 8 4630 4837 65139480 65139273 1.990000e-44 191.0
32 TraesCS1A01G313500 chrUn 87.342 158 11 8 2854 3010 134246435 134246286 7.220000e-39 172.0
33 TraesCS1A01G313500 chrUn 78.544 261 27 15 985 1222 108327197 108327451 1.570000e-30 145.0
34 TraesCS1A01G313500 chr4B 85.476 778 103 9 2792 3565 625962302 625963073 0.000000e+00 802.0
35 TraesCS1A01G313500 chr4B 82.492 891 122 21 3728 4611 625996489 625997352 0.000000e+00 750.0
36 TraesCS1A01G313500 chr4B 82.307 763 112 7 3020 3771 665915456 665914706 1.650000e-179 640.0
37 TraesCS1A01G313500 chr4B 84.013 638 77 9 3047 3682 666572874 666572260 1.680000e-164 590.0
38 TraesCS1A01G313500 chr4B 83.512 467 75 2 3967 4432 666572461 666571996 8.350000e-118 435.0
39 TraesCS1A01G313500 chr4B 82.495 497 79 7 3476 3968 625996475 625996967 3.880000e-116 429.0
40 TraesCS1A01G313500 chr4B 83.005 406 53 8 3315 3720 625995987 625996376 2.400000e-93 353.0
41 TraesCS1A01G313500 chr4B 81.004 458 53 18 4630 5061 666571804 666571355 3.130000e-87 333.0
42 TraesCS1A01G313500 chr4B 81.395 430 38 19 2157 2566 666573430 666573023 4.080000e-81 313.0
43 TraesCS1A01G313500 chr4B 77.207 623 80 38 970 1569 666574573 666573990 1.900000e-79 307.0
44 TraesCS1A01G313500 chr4B 82.866 321 35 10 4699 5004 625997590 625997905 2.490000e-68 270.0
45 TraesCS1A01G313500 chr4B 84.404 218 26 7 2830 3046 665915669 665915459 1.980000e-49 207.0
46 TraesCS1A01G313500 chr4B 80.565 283 40 12 2903 3173 666745789 666746068 2.560000e-48 204.0
47 TraesCS1A01G313500 chr4B 76.455 378 56 24 1239 1591 666760265 666760634 2.010000e-39 174.0
48 TraesCS1A01G313500 chr4B 84.211 152 17 6 2857 3008 666573020 666572876 2.040000e-29 141.0
49 TraesCS1A01G313500 chr4B 81.679 131 19 2 4773 4903 665961641 665961516 2.670000e-18 104.0
50 TraesCS1A01G313500 chr5A 87.549 514 61 2 3020 3530 705897366 705896853 4.680000e-165 592.0
51 TraesCS1A01G313500 chr5A 90.365 384 22 4 240 610 353610989 353611370 1.760000e-134 490.0
52 TraesCS1A01G313500 chr5A 90.691 333 16 7 240 559 616360456 616360786 3.880000e-116 429.0
53 TraesCS1A01G313500 chr5A 86.735 392 32 9 237 610 672344055 672344444 8.400000e-113 418.0
54 TraesCS1A01G313500 chr5A 89.615 260 16 5 609 859 353611437 353611694 2.440000e-83 320.0
55 TraesCS1A01G313500 chr5A 83.607 366 32 12 238 585 346097994 346098349 8.770000e-83 318.0
56 TraesCS1A01G313500 chr5A 86.667 255 24 4 609 855 616360866 616361118 1.930000e-69 274.0
57 TraesCS1A01G313500 chr5A 84.674 261 24 8 609 859 672344511 672344765 4.200000e-61 246.0
58 TraesCS1A01G313500 chr5A 76.301 346 56 17 1012 1340 705902419 705902083 1.560000e-35 161.0
59 TraesCS1A01G313500 chr6D 78.341 651 126 14 3286 3930 915574 914933 1.820000e-109 407.0
60 TraesCS1A01G313500 chr2B 84.973 366 32 16 242 589 499165524 499165164 3.110000e-92 350.0
61 TraesCS1A01G313500 chr2B 85.057 261 28 5 609 859 523091664 523091923 6.970000e-64 255.0
62 TraesCS1A01G313500 chr2B 83.117 231 29 3 641 862 109355928 109355699 9.210000e-48 202.0
63 TraesCS1A01G313500 chr2B 78.731 268 37 9 612 864 9286493 9286755 1.560000e-35 161.0
64 TraesCS1A01G313500 chr2B 77.368 190 21 15 680 862 109337230 109337056 5.790000e-15 93.5
65 TraesCS1A01G313500 chr6B 84.916 358 32 12 237 575 396920597 396920951 5.200000e-90 342.0
66 TraesCS1A01G313500 chr6B 83.459 266 28 8 609 864 681230637 681230896 3.270000e-57 233.0
67 TraesCS1A01G313500 chr5D 84.282 369 32 12 238 585 492176470 492176833 2.420000e-88 337.0
68 TraesCS1A01G313500 chr5D 80.056 356 56 7 237 578 394993087 394993441 3.240000e-62 250.0
69 TraesCS1A01G313500 chr3D 86.719 256 25 6 609 855 537905798 537906053 5.350000e-70 276.0
70 TraesCS1A01G313500 chr4A 87.200 250 18 7 1 237 119307308 119307556 6.920000e-69 272.0
71 TraesCS1A01G313500 chr4A 85.771 253 22 5 1 240 360969158 360968907 6.970000e-64 255.0
72 TraesCS1A01G313500 chr4A 86.000 250 21 7 1 237 432796976 432797224 6.970000e-64 255.0
73 TraesCS1A01G313500 chr7D 81.073 354 50 11 241 584 578840201 578839855 3.220000e-67 267.0
74 TraesCS1A01G313500 chr7D 80.791 354 51 11 241 584 579045234 579044888 1.500000e-65 261.0
75 TraesCS1A01G313500 chr3A 86.747 249 20 7 1 237 109973121 109972874 1.160000e-66 265.0
76 TraesCS1A01G313500 chr3A 86.454 251 19 7 1 237 564766516 564766267 1.500000e-65 261.0
77 TraesCS1A01G313500 chr2A 86.561 253 19 9 1 240 507108782 507108532 1.160000e-66 265.0
78 TraesCS1A01G313500 chr2A 86.111 252 19 7 1 237 678301679 678301929 1.940000e-64 257.0
79 TraesCS1A01G313500 chr7A 86.400 250 20 7 1 237 567641685 567641933 1.500000e-65 261.0
80 TraesCS1A01G313500 chr7A 85.057 261 27 6 609 859 308635729 308635987 6.970000e-64 255.0
81 TraesCS1A01G313500 chr7A 84.942 259 31 2 609 859 663743113 663743371 6.970000e-64 255.0
82 TraesCS1A01G313500 chr6A 86.345 249 20 6 1 237 298485469 298485223 5.390000e-65 259.0
83 TraesCS1A01G313500 chr6A 95.238 42 2 0 4782 4823 50357026 50356985 3.510000e-07 67.6
84 TraesCS1A01G313500 chr4D 100.000 28 0 0 1184 1211 312759590 312759617 1.000000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G313500 chr1A 505281778 505287202 5424 True 5206.500000 10019 90.656000 1 5425 2 chr1A.!!$R1 5424
1 TraesCS1A01G313500 chr1A 49147751 49148425 674 False 358.000000 418 88.818500 238 861 2 chr1A.!!$F2 623
2 TraesCS1A01G313500 chr1D 409066286 409070809 4523 True 2513.000000 6187 89.581667 971 5425 3 chr1D.!!$R2 4454
3 TraesCS1A01G313500 chr1B 551031135 551035847 4712 True 3364.500000 5873 92.679000 891 5425 2 chr1B.!!$R2 4534
4 TraesCS1A01G313500 chr1B 113877332 113878039 707 True 301.500000 324 85.359500 239 862 2 chr1B.!!$R1 623
5 TraesCS1A01G313500 chr3B 747744865 747746086 1221 True 1168.000000 1168 84.130000 2709 3927 1 chr3B.!!$R1 1218
6 TraesCS1A01G313500 chrUn 108327197 108330226 3029 False 530.750000 1007 81.523500 985 4996 4 chrUn.!!$F2 4011
7 TraesCS1A01G313500 chrUn 65139273 65140588 1315 True 414.000000 773 85.518750 3046 4837 4 chrUn.!!$R1 1791
8 TraesCS1A01G313500 chrUn 134244399 134246857 2458 True 407.333333 778 84.314833 2151 5416 6 chrUn.!!$R2 3265
9 TraesCS1A01G313500 chr4B 625962302 625963073 771 False 802.000000 802 85.476000 2792 3565 1 chr4B.!!$F1 773
10 TraesCS1A01G313500 chr4B 625995987 625997905 1918 False 450.500000 750 82.714500 3315 5004 4 chr4B.!!$F4 1689
11 TraesCS1A01G313500 chr4B 665914706 665915669 963 True 423.500000 640 83.355500 2830 3771 2 chr4B.!!$R2 941
12 TraesCS1A01G313500 chr4B 666571355 666574573 3218 True 353.166667 590 81.890333 970 5061 6 chr4B.!!$R3 4091
13 TraesCS1A01G313500 chr5A 705896853 705897366 513 True 592.000000 592 87.549000 3020 3530 1 chr5A.!!$R1 510
14 TraesCS1A01G313500 chr5A 353610989 353611694 705 False 405.000000 490 89.990000 240 859 2 chr5A.!!$F2 619
15 TraesCS1A01G313500 chr5A 616360456 616361118 662 False 351.500000 429 88.679000 240 855 2 chr5A.!!$F3 615
16 TraesCS1A01G313500 chr5A 672344055 672344765 710 False 332.000000 418 85.704500 237 859 2 chr5A.!!$F4 622
17 TraesCS1A01G313500 chr6D 914933 915574 641 True 407.000000 407 78.341000 3286 3930 1 chr6D.!!$R1 644

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
967 1078 0.035458 CCAACACTCTCCCACTCCAC 59.965 60.000 0.00 0.0 0.00 4.02 F
1659 1883 0.255604 CATTTCCCCATTTTGGCCCC 59.744 55.000 0.00 0.0 35.79 5.80 F
1675 1900 1.214305 CCCCTCCATTTGGGTCAGGA 61.214 60.000 4.74 0.0 43.09 3.86 F
1760 2026 1.519408 TCTAGAACAAAGCGCCCAAC 58.481 50.000 2.29 0.0 0.00 3.77 F
2601 3232 4.249638 TGCTGGCCAAAGATATAAAGGT 57.750 40.909 7.01 0.0 0.00 3.50 F
4253 5555 1.587547 GGAAGGAGGTCATTGATCGC 58.412 55.000 0.00 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2128 2406 1.751924 CCTCACTAGTCACCTGCTACC 59.248 57.143 0.00 0.00 0.00 3.18 R
2566 3075 2.070783 GCCAGCAAAATGTCACAATGG 58.929 47.619 0.00 0.00 0.00 3.16 R
2567 3076 2.070783 GGCCAGCAAAATGTCACAATG 58.929 47.619 0.00 0.00 0.00 2.82 R
2632 3263 3.592427 ACCCTACTAGAGACTGAGACCAA 59.408 47.826 0.00 0.00 0.00 3.67 R
4377 5679 0.107410 AGAACAAGGGTGCACGAACA 60.107 50.000 11.45 0.00 0.00 3.18 R
5300 7008 2.670414 GCGTCTCCTGATTTCAGTCAAG 59.330 50.000 6.81 2.19 42.27 3.02 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
36 37 4.356405 AAATTCCTTTGAAGCCCTTTGG 57.644 40.909 0.00 0.00 33.05 3.28
37 38 2.470057 TTCCTTTGAAGCCCTTTGGT 57.530 45.000 0.00 0.00 0.00 3.67
38 39 2.470057 TCCTTTGAAGCCCTTTGGTT 57.530 45.000 0.00 0.00 37.39 3.67
39 40 2.758130 TCCTTTGAAGCCCTTTGGTTT 58.242 42.857 0.00 0.00 37.85 3.27
40 41 2.433970 TCCTTTGAAGCCCTTTGGTTTG 59.566 45.455 0.00 0.00 34.87 2.93
41 42 2.170397 CCTTTGAAGCCCTTTGGTTTGT 59.830 45.455 0.00 0.00 34.87 2.83
42 43 3.386402 CCTTTGAAGCCCTTTGGTTTGTA 59.614 43.478 0.00 0.00 34.87 2.41
43 44 4.501400 CCTTTGAAGCCCTTTGGTTTGTAG 60.501 45.833 0.00 0.00 34.87 2.74
44 45 3.586470 TGAAGCCCTTTGGTTTGTAGA 57.414 42.857 0.00 0.00 34.87 2.59
45 46 3.904717 TGAAGCCCTTTGGTTTGTAGAA 58.095 40.909 0.00 0.00 34.87 2.10
46 47 4.282496 TGAAGCCCTTTGGTTTGTAGAAA 58.718 39.130 0.00 0.00 34.87 2.52
47 48 4.898861 TGAAGCCCTTTGGTTTGTAGAAAT 59.101 37.500 0.00 0.00 34.87 2.17
48 49 4.871933 AGCCCTTTGGTTTGTAGAAATG 57.128 40.909 0.00 0.00 0.00 2.32
49 50 3.578282 AGCCCTTTGGTTTGTAGAAATGG 59.422 43.478 0.00 0.00 0.00 3.16
50 51 3.576550 GCCCTTTGGTTTGTAGAAATGGA 59.423 43.478 0.00 0.00 0.00 3.41
51 52 4.222810 GCCCTTTGGTTTGTAGAAATGGAT 59.777 41.667 0.00 0.00 0.00 3.41
52 53 5.279960 GCCCTTTGGTTTGTAGAAATGGATT 60.280 40.000 0.00 0.00 0.00 3.01
53 54 6.398095 CCCTTTGGTTTGTAGAAATGGATTC 58.602 40.000 0.00 0.00 38.39 2.52
54 55 6.398095 CCTTTGGTTTGTAGAAATGGATTCC 58.602 40.000 0.00 0.00 38.94 3.01
55 56 6.211384 CCTTTGGTTTGTAGAAATGGATTCCT 59.789 38.462 3.95 0.00 38.94 3.36
56 57 7.396055 CCTTTGGTTTGTAGAAATGGATTCCTA 59.604 37.037 3.95 0.00 38.94 2.94
57 58 8.893563 TTTGGTTTGTAGAAATGGATTCCTAT 57.106 30.769 3.95 0.00 38.94 2.57
58 59 8.893563 TTGGTTTGTAGAAATGGATTCCTATT 57.106 30.769 3.95 0.00 38.94 1.73
59 60 8.519799 TGGTTTGTAGAAATGGATTCCTATTC 57.480 34.615 3.95 8.33 38.94 1.75
60 61 7.559897 TGGTTTGTAGAAATGGATTCCTATTCC 59.440 37.037 13.88 4.81 38.94 3.01
61 62 7.780271 GGTTTGTAGAAATGGATTCCTATTCCT 59.220 37.037 13.88 5.21 38.94 3.36
62 63 9.847224 GTTTGTAGAAATGGATTCCTATTCCTA 57.153 33.333 13.88 4.47 38.94 2.94
65 66 9.170890 TGTAGAAATGGATTCCTATTCCTATGT 57.829 33.333 13.88 2.98 38.94 2.29
68 69 9.621239 AGAAATGGATTCCTATTCCTATGTAGA 57.379 33.333 13.88 0.00 38.94 2.59
123 124 8.635765 AAAAACATTAGCCTAGACTCAATGAA 57.364 30.769 12.01 0.00 32.29 2.57
124 125 8.635765 AAAACATTAGCCTAGACTCAATGAAA 57.364 30.769 12.01 0.00 32.29 2.69
125 126 8.635765 AAACATTAGCCTAGACTCAATGAAAA 57.364 30.769 12.01 0.00 32.29 2.29
126 127 8.635765 AACATTAGCCTAGACTCAATGAAAAA 57.364 30.769 12.01 0.00 32.29 1.94
167 168 9.288576 ACATCAAATGACATTTCTTTCTCTACA 57.711 29.630 10.52 0.00 0.00 2.74
168 169 9.770503 CATCAAATGACATTTCTTTCTCTACAG 57.229 33.333 10.52 0.00 0.00 2.74
169 170 8.327941 TCAAATGACATTTCTTTCTCTACAGG 57.672 34.615 10.52 0.00 0.00 4.00
170 171 7.939039 TCAAATGACATTTCTTTCTCTACAGGT 59.061 33.333 10.52 0.00 0.00 4.00
171 172 9.219603 CAAATGACATTTCTTTCTCTACAGGTA 57.780 33.333 10.52 0.00 0.00 3.08
172 173 9.965902 AAATGACATTTCTTTCTCTACAGGTAT 57.034 29.630 7.62 0.00 0.00 2.73
173 174 9.606631 AATGACATTTCTTTCTCTACAGGTATC 57.393 33.333 0.00 0.00 0.00 2.24
174 175 8.134202 TGACATTTCTTTCTCTACAGGTATCA 57.866 34.615 0.00 0.00 0.00 2.15
175 176 8.593679 TGACATTTCTTTCTCTACAGGTATCAA 58.406 33.333 0.00 0.00 0.00 2.57
176 177 9.606631 GACATTTCTTTCTCTACAGGTATCAAT 57.393 33.333 0.00 0.00 0.00 2.57
177 178 9.606631 ACATTTCTTTCTCTACAGGTATCAATC 57.393 33.333 0.00 0.00 0.00 2.67
178 179 9.829507 CATTTCTTTCTCTACAGGTATCAATCT 57.170 33.333 0.00 0.00 0.00 2.40
180 181 8.595362 TTCTTTCTCTACAGGTATCAATCTCA 57.405 34.615 0.00 0.00 0.00 3.27
181 182 8.001881 TCTTTCTCTACAGGTATCAATCTCAC 57.998 38.462 0.00 0.00 0.00 3.51
182 183 7.836685 TCTTTCTCTACAGGTATCAATCTCACT 59.163 37.037 0.00 0.00 0.00 3.41
183 184 7.962995 TTCTCTACAGGTATCAATCTCACTT 57.037 36.000 0.00 0.00 0.00 3.16
184 185 7.575414 TCTCTACAGGTATCAATCTCACTTC 57.425 40.000 0.00 0.00 0.00 3.01
185 186 7.119387 TCTCTACAGGTATCAATCTCACTTCA 58.881 38.462 0.00 0.00 0.00 3.02
186 187 7.782168 TCTCTACAGGTATCAATCTCACTTCAT 59.218 37.037 0.00 0.00 0.00 2.57
187 188 8.996651 TCTACAGGTATCAATCTCACTTCATA 57.003 34.615 0.00 0.00 0.00 2.15
188 189 9.593565 TCTACAGGTATCAATCTCACTTCATAT 57.406 33.333 0.00 0.00 0.00 1.78
189 190 9.636879 CTACAGGTATCAATCTCACTTCATATG 57.363 37.037 0.00 0.00 0.00 1.78
190 191 8.255111 ACAGGTATCAATCTCACTTCATATGA 57.745 34.615 0.00 0.00 0.00 2.15
191 192 8.878211 ACAGGTATCAATCTCACTTCATATGAT 58.122 33.333 6.17 0.00 0.00 2.45
192 193 9.722184 CAGGTATCAATCTCACTTCATATGATT 57.278 33.333 6.17 0.00 0.00 2.57
198 199 9.465199 TCAATCTCACTTCATATGATTTTTCCA 57.535 29.630 6.17 0.00 0.00 3.53
202 203 8.192774 TCTCACTTCATATGATTTTTCCATTGC 58.807 33.333 6.17 0.00 0.00 3.56
203 204 8.070034 TCACTTCATATGATTTTTCCATTGCT 57.930 30.769 6.17 0.00 0.00 3.91
204 205 9.187996 TCACTTCATATGATTTTTCCATTGCTA 57.812 29.630 6.17 0.00 0.00 3.49
205 206 9.976511 CACTTCATATGATTTTTCCATTGCTAT 57.023 29.630 6.17 0.00 0.00 2.97
219 220 9.881773 TTTCCATTGCTATAAAATTCCTATCCT 57.118 29.630 0.00 0.00 0.00 3.24
221 222 9.959721 TCCATTGCTATAAAATTCCTATCCTAC 57.040 33.333 0.00 0.00 0.00 3.18
222 223 9.739276 CCATTGCTATAAAATTCCTATCCTACA 57.261 33.333 0.00 0.00 0.00 2.74
226 227 9.569122 TGCTATAAAATTCCTATCCTACAAACC 57.431 33.333 0.00 0.00 0.00 3.27
227 228 9.569122 GCTATAAAATTCCTATCCTACAAACCA 57.431 33.333 0.00 0.00 0.00 3.67
232 233 9.996554 AAAATTCCTATCCTACAAACCAAAAAG 57.003 29.630 0.00 0.00 0.00 2.27
233 234 8.950007 AATTCCTATCCTACAAACCAAAAAGA 57.050 30.769 0.00 0.00 0.00 2.52
234 235 7.996098 TTCCTATCCTACAAACCAAAAAGAG 57.004 36.000 0.00 0.00 0.00 2.85
235 236 6.481643 TCCTATCCTACAAACCAAAAAGAGG 58.518 40.000 0.00 0.00 0.00 3.69
236 237 5.125578 CCTATCCTACAAACCAAAAAGAGGC 59.874 44.000 0.00 0.00 0.00 4.70
321 322 6.422333 TCAATAGATGGGCAACAAATACTCA 58.578 36.000 0.00 0.00 39.74 3.41
327 328 6.719370 AGATGGGCAACAAATACTCAAGTTTA 59.281 34.615 0.00 0.00 39.74 2.01
392 395 2.210424 TGGCAACTGGCAGCTTTTT 58.790 47.368 15.89 0.00 46.12 1.94
425 432 2.946329 TGGTTTGCACAGATTGTTACGT 59.054 40.909 0.00 0.00 0.00 3.57
483 498 0.179121 TGTGCTAATCGCCACCGTAG 60.179 55.000 0.00 0.00 38.05 3.51
484 499 1.227147 TGCTAATCGCCACCGTAGC 60.227 57.895 0.00 0.00 38.67 3.58
485 500 1.067582 GCTAATCGCCACCGTAGCT 59.932 57.895 0.00 0.00 36.61 3.32
486 501 0.529992 GCTAATCGCCACCGTAGCTT 60.530 55.000 0.00 0.00 36.61 3.74
488 503 2.800629 GCTAATCGCCACCGTAGCTTTA 60.801 50.000 0.00 0.00 36.61 1.85
707 805 2.294449 AAGGTCTGGGCCTCTTTTTC 57.706 50.000 4.53 0.00 38.03 2.29
717 815 7.389053 GTCTGGGCCTCTTTTTCATATACTATG 59.611 40.741 4.53 0.00 0.00 2.23
742 842 9.287373 TGAAAATACCACCGTTTTAAAGATACT 57.713 29.630 0.00 0.00 0.00 2.12
746 846 6.024552 ACCACCGTTTTAAAGATACTACGA 57.975 37.500 8.93 0.00 0.00 3.43
750 850 9.086336 CCACCGTTTTAAAGATACTACGATTTA 57.914 33.333 8.93 0.00 0.00 1.40
802 903 7.383687 ACGACTCAAAGTATTGAATACCAAGA 58.616 34.615 11.47 6.42 44.64 3.02
862 973 1.611519 CTCCCAAACGCACCCTAAAA 58.388 50.000 0.00 0.00 0.00 1.52
863 974 1.539827 CTCCCAAACGCACCCTAAAAG 59.460 52.381 0.00 0.00 0.00 2.27
864 975 0.038618 CCCAAACGCACCCTAAAAGC 60.039 55.000 0.00 0.00 0.00 3.51
865 976 0.038618 CCAAACGCACCCTAAAAGCC 60.039 55.000 0.00 0.00 0.00 4.35
866 977 0.386731 CAAACGCACCCTAAAAGCCG 60.387 55.000 0.00 0.00 0.00 5.52
867 978 0.820482 AAACGCACCCTAAAAGCCGT 60.820 50.000 0.00 0.00 0.00 5.68
868 979 1.232621 AACGCACCCTAAAAGCCGTC 61.233 55.000 0.00 0.00 0.00 4.79
869 980 2.736682 CGCACCCTAAAAGCCGTCG 61.737 63.158 0.00 0.00 0.00 5.12
870 981 2.396157 GCACCCTAAAAGCCGTCGG 61.396 63.158 6.99 6.99 0.00 4.79
887 998 4.367023 GCGGCGGCGGGATATACA 62.367 66.667 33.02 0.00 0.00 2.29
888 999 2.126071 CGGCGGCGGGATATACAG 60.126 66.667 25.36 0.00 0.00 2.74
889 1000 2.632544 CGGCGGCGGGATATACAGA 61.633 63.158 25.36 0.00 0.00 3.41
894 1005 1.248785 GGCGGGATATACAGAGCCGA 61.249 60.000 0.00 0.00 34.94 5.54
910 1021 2.039084 AGCCGAATCAGTCAAAGAGGTT 59.961 45.455 0.00 0.00 0.00 3.50
930 1041 2.856988 TTCCCCACCCTTCCGCTT 60.857 61.111 0.00 0.00 0.00 4.68
931 1042 2.821679 CTTCCCCACCCTTCCGCTTC 62.822 65.000 0.00 0.00 0.00 3.86
932 1043 4.778143 CCCCACCCTTCCGCTTCG 62.778 72.222 0.00 0.00 0.00 3.79
933 1044 4.016706 CCCACCCTTCCGCTTCGT 62.017 66.667 0.00 0.00 0.00 3.85
953 1064 2.283809 CACCCCCAAACCCCAACA 59.716 61.111 0.00 0.00 0.00 3.33
957 1068 1.541672 CCCCAAACCCCAACACTCT 59.458 57.895 0.00 0.00 0.00 3.24
960 1071 0.539669 CCAAACCCCAACACTCTCCC 60.540 60.000 0.00 0.00 0.00 4.30
961 1072 0.184933 CAAACCCCAACACTCTCCCA 59.815 55.000 0.00 0.00 0.00 4.37
962 1073 0.185175 AAACCCCAACACTCTCCCAC 59.815 55.000 0.00 0.00 0.00 4.61
963 1074 0.697854 AACCCCAACACTCTCCCACT 60.698 55.000 0.00 0.00 0.00 4.00
964 1075 1.128188 ACCCCAACACTCTCCCACTC 61.128 60.000 0.00 0.00 0.00 3.51
965 1076 1.679898 CCCAACACTCTCCCACTCC 59.320 63.158 0.00 0.00 0.00 3.85
966 1077 1.127567 CCCAACACTCTCCCACTCCA 61.128 60.000 0.00 0.00 0.00 3.86
967 1078 0.035458 CCAACACTCTCCCACTCCAC 59.965 60.000 0.00 0.00 0.00 4.02
968 1079 0.319900 CAACACTCTCCCACTCCACG 60.320 60.000 0.00 0.00 0.00 4.94
969 1080 2.100879 AACACTCTCCCACTCCACGC 62.101 60.000 0.00 0.00 0.00 5.34
976 1087 4.394712 CCACTCCACGCACCCTCC 62.395 72.222 0.00 0.00 0.00 4.30
1047 1166 2.203070 CCAAATCCCCTCCTCGCG 60.203 66.667 0.00 0.00 0.00 5.87
1108 1237 4.954118 ACCCCAGTCTCGCCCACA 62.954 66.667 0.00 0.00 0.00 4.17
1109 1238 4.394712 CCCCAGTCTCGCCCACAC 62.395 72.222 0.00 0.00 0.00 3.82
1110 1239 4.742201 CCCAGTCTCGCCCACACG 62.742 72.222 0.00 0.00 0.00 4.49
1111 1240 4.742201 CCAGTCTCGCCCACACGG 62.742 72.222 0.00 0.00 0.00 4.94
1181 1334 0.521735 CGAAAGCGAGGGGGAAAAAG 59.478 55.000 0.00 0.00 40.82 2.27
1433 1600 1.623311 GGGTTTCTGTCAATTTGGGGG 59.377 52.381 0.00 0.00 0.00 5.40
1438 1605 2.235016 TCTGTCAATTTGGGGGTTTCG 58.765 47.619 0.00 0.00 0.00 3.46
1459 1628 7.624360 TTCGTAAATAATCATGGCTTGTTCT 57.376 32.000 0.00 0.00 0.00 3.01
1627 1824 4.491676 CTTGCTTTGAATGATCTGGGTTG 58.508 43.478 0.00 0.00 0.00 3.77
1649 1872 3.054508 GGAAAATTGGCATCATTTCCCCA 60.055 43.478 20.15 0.00 43.14 4.96
1657 1881 2.921821 CATCATTTCCCCATTTTGGCC 58.078 47.619 0.00 0.00 35.79 5.36
1659 1883 0.255604 CATTTCCCCATTTTGGCCCC 59.744 55.000 0.00 0.00 35.79 5.80
1675 1900 1.214305 CCCCTCCATTTGGGTCAGGA 61.214 60.000 4.74 0.00 43.09 3.86
1692 1954 6.294843 GGGTCAGGAAGTTATCTATGTAGCTC 60.295 46.154 0.00 0.00 0.00 4.09
1707 1973 4.686972 TGTAGCTCTATGATGTGCTCAAC 58.313 43.478 0.00 0.00 37.44 3.18
1733 1999 5.393461 GCAATTTGGTTGTCCATTAGGAGAG 60.393 44.000 0.00 0.00 46.92 3.20
1760 2026 1.519408 TCTAGAACAAAGCGCCCAAC 58.481 50.000 2.29 0.00 0.00 3.77
1919 2192 6.713762 AACATCAGTTCCACATCTGAAAAA 57.286 33.333 0.00 0.00 42.67 1.94
1935 2208 5.360714 TCTGAAAAACAATCTGTCCAGCTTT 59.639 36.000 0.00 0.00 0.00 3.51
2054 2332 8.745149 AAAACCATTAATTAGGGGTTAGGTTT 57.255 30.769 18.01 12.71 45.64 3.27
2306 2776 7.551035 TGATTTTGCTGTAAACAATTTTGCT 57.449 28.000 0.00 0.00 0.00 3.91
2436 2943 4.870636 TCCCTGATGAATTAACCTTGCAT 58.129 39.130 0.00 0.00 0.00 3.96
2566 3075 7.319646 TGGCCAGTCAATCATTTAATTTACAC 58.680 34.615 0.00 0.00 0.00 2.90
2567 3076 6.756542 GGCCAGTCAATCATTTAATTTACACC 59.243 38.462 0.00 0.00 0.00 4.16
2601 3232 4.249638 TGCTGGCCAAAGATATAAAGGT 57.750 40.909 7.01 0.00 0.00 3.50
2632 3263 4.827692 TGAATCGTATACAGCTGTTGGTT 58.172 39.130 27.06 14.78 0.00 3.67
2672 3303 4.332428 GGGTCTACCTGCATATAACGTT 57.668 45.455 5.88 5.88 35.85 3.99
2685 3316 6.912051 TGCATATAACGTTTGATCTTGAATGC 59.088 34.615 5.91 7.37 36.32 3.56
2767 3406 6.482524 CATCATAGATGGGGTTGATCTCATT 58.517 40.000 0.00 0.00 32.32 2.57
2789 3428 8.417106 TCATTAGACTTGTCAGATCTTATGACC 58.583 37.037 10.19 0.00 45.24 4.02
2869 3511 7.979786 AAAGGACTAATCTGTAGGATTCTCA 57.020 36.000 0.00 0.00 42.96 3.27
2944 3598 8.658609 ACTTGATTTTCTCAAAACATTGTTGTG 58.341 29.630 12.69 12.69 43.20 3.33
2945 3599 8.545229 TTGATTTTCTCAAAACATTGTTGTGT 57.455 26.923 17.23 0.00 40.92 3.72
2976 3633 3.826524 TGACTGACAACATAGCCCAAAA 58.173 40.909 0.00 0.00 0.00 2.44
3302 4017 9.429359 CACTGTTTAAAGACTATCACTCTTGAT 57.571 33.333 0.00 0.00 45.04 2.57
3551 4267 5.430089 GGTTGGGGGAGAAGATAGCATATAT 59.570 44.000 0.00 0.00 0.00 0.86
3932 4987 4.759693 TGTACCATTCATCTTGTGGTGTTC 59.240 41.667 6.53 0.00 45.38 3.18
4037 5092 5.128008 GGCTGAGGGAGAAGATACCATATAC 59.872 48.000 0.00 0.00 0.00 1.47
4253 5555 1.587547 GGAAGGAGGTCATTGATCGC 58.412 55.000 0.00 0.00 0.00 4.58
4266 5568 3.487104 GATCGCGCGTTTAAGCCCG 62.487 63.158 30.98 0.00 39.48 6.13
4492 5814 3.986277 TCGGTAGAGGTTGAGTTTGAAC 58.014 45.455 0.00 0.00 0.00 3.18
4493 5815 3.640029 TCGGTAGAGGTTGAGTTTGAACT 59.360 43.478 0.00 0.00 43.16 3.01
4494 5816 4.100498 TCGGTAGAGGTTGAGTTTGAACTT 59.900 41.667 0.00 0.00 39.88 2.66
4495 5817 4.814771 CGGTAGAGGTTGAGTTTGAACTTT 59.185 41.667 0.00 0.00 39.88 2.66
4496 5818 5.277345 CGGTAGAGGTTGAGTTTGAACTTTG 60.277 44.000 0.00 0.00 39.88 2.77
4497 5819 5.820947 GGTAGAGGTTGAGTTTGAACTTTGA 59.179 40.000 0.00 0.00 39.88 2.69
4498 5820 6.317893 GGTAGAGGTTGAGTTTGAACTTTGAA 59.682 38.462 0.00 0.00 39.88 2.69
4780 6313 1.198637 GTGCTGCTCTGTTTTGCCTAG 59.801 52.381 0.00 0.00 0.00 3.02
5082 6766 7.189693 TGTGTAACTGAAGCTCATTAAACTG 57.810 36.000 0.00 0.00 38.04 3.16
5087 6776 5.181748 ACTGAAGCTCATTAAACTGCTAGG 58.818 41.667 0.00 0.00 35.09 3.02
5103 6792 3.774766 TGCTAGGTCATTCATACACACCT 59.225 43.478 0.00 0.00 40.67 4.00
5225 6922 2.618442 CTCTGGAAGCTGGGATCTTC 57.382 55.000 0.00 0.00 39.26 2.87
5300 7008 3.332919 CTCACGGGATGATGATGATTCC 58.667 50.000 0.00 0.00 36.48 3.01
5332 7040 0.736325 AGGAGACGCCGAATTCAACG 60.736 55.000 13.77 13.77 43.43 4.10
5336 7044 1.005394 ACGCCGAATTCAACGACCT 60.005 52.632 20.26 0.00 0.00 3.85
5391 7104 2.553602 TGGCAGCAAGAACACAATGTAG 59.446 45.455 0.00 0.00 0.00 2.74
5400 7113 4.136796 AGAACACAATGTAGAGCAAGCAA 58.863 39.130 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.132502 CCAAAGGGCTTCAAAGGAATTTTT 58.867 37.500 0.00 0.00 31.34 1.94
14 15 4.165950 ACCAAAGGGCTTCAAAGGAATTTT 59.834 37.500 0.00 0.00 37.90 1.82
15 16 3.716353 ACCAAAGGGCTTCAAAGGAATTT 59.284 39.130 0.00 0.00 37.90 1.82
16 17 3.317406 ACCAAAGGGCTTCAAAGGAATT 58.683 40.909 0.00 0.00 37.90 2.17
17 18 2.976440 ACCAAAGGGCTTCAAAGGAAT 58.024 42.857 0.00 0.00 37.90 3.01
18 19 2.470057 ACCAAAGGGCTTCAAAGGAA 57.530 45.000 0.00 0.00 37.90 3.36
19 20 2.433970 CAAACCAAAGGGCTTCAAAGGA 59.566 45.455 0.00 0.00 37.90 3.36
20 21 2.170397 ACAAACCAAAGGGCTTCAAAGG 59.830 45.455 0.00 0.00 37.90 3.11
21 22 3.541996 ACAAACCAAAGGGCTTCAAAG 57.458 42.857 0.00 0.00 37.90 2.77
22 23 4.282496 TCTACAAACCAAAGGGCTTCAAA 58.718 39.130 0.00 0.00 37.90 2.69
23 24 3.904717 TCTACAAACCAAAGGGCTTCAA 58.095 40.909 0.00 0.00 37.90 2.69
24 25 3.586470 TCTACAAACCAAAGGGCTTCA 57.414 42.857 0.00 0.00 37.90 3.02
25 26 4.929819 TTTCTACAAACCAAAGGGCTTC 57.070 40.909 0.00 0.00 37.90 3.86
26 27 4.040339 CCATTTCTACAAACCAAAGGGCTT 59.960 41.667 0.00 0.00 37.90 4.35
27 28 3.578282 CCATTTCTACAAACCAAAGGGCT 59.422 43.478 0.00 0.00 37.90 5.19
28 29 3.576550 TCCATTTCTACAAACCAAAGGGC 59.423 43.478 0.00 0.00 37.90 5.19
29 30 6.358974 AATCCATTTCTACAAACCAAAGGG 57.641 37.500 0.00 0.00 41.29 3.95
30 31 6.211384 AGGAATCCATTTCTACAAACCAAAGG 59.789 38.462 0.61 0.00 34.56 3.11
31 32 7.232118 AGGAATCCATTTCTACAAACCAAAG 57.768 36.000 0.61 0.00 34.56 2.77
32 33 8.893563 ATAGGAATCCATTTCTACAAACCAAA 57.106 30.769 0.61 0.00 30.99 3.28
33 34 8.893563 AATAGGAATCCATTTCTACAAACCAA 57.106 30.769 0.61 0.00 30.99 3.67
34 35 7.559897 GGAATAGGAATCCATTTCTACAAACCA 59.440 37.037 0.61 0.00 36.92 3.67
35 36 7.780271 AGGAATAGGAATCCATTTCTACAAACC 59.220 37.037 0.61 0.00 39.55 3.27
36 37 8.753497 AGGAATAGGAATCCATTTCTACAAAC 57.247 34.615 0.61 0.00 39.55 2.93
39 40 9.170890 ACATAGGAATAGGAATCCATTTCTACA 57.829 33.333 0.61 0.00 39.55 2.74
42 43 9.621239 TCTACATAGGAATAGGAATCCATTTCT 57.379 33.333 0.61 6.31 39.55 2.52
98 99 8.635765 TTCATTGAGTCTAGGCTAATGTTTTT 57.364 30.769 18.08 0.00 32.22 1.94
99 100 8.635765 TTTCATTGAGTCTAGGCTAATGTTTT 57.364 30.769 18.08 0.00 32.22 2.43
100 101 8.635765 TTTTCATTGAGTCTAGGCTAATGTTT 57.364 30.769 18.08 0.00 32.22 2.83
101 102 8.635765 TTTTTCATTGAGTCTAGGCTAATGTT 57.364 30.769 18.08 0.00 32.22 2.71
141 142 9.288576 TGTAGAGAAAGAAATGTCATTTGATGT 57.711 29.630 15.52 0.00 31.47 3.06
142 143 9.770503 CTGTAGAGAAAGAAATGTCATTTGATG 57.229 33.333 15.52 0.00 31.47 3.07
143 144 8.954350 CCTGTAGAGAAAGAAATGTCATTTGAT 58.046 33.333 15.52 1.50 31.47 2.57
144 145 7.939039 ACCTGTAGAGAAAGAAATGTCATTTGA 59.061 33.333 15.52 0.00 31.47 2.69
145 146 8.103948 ACCTGTAGAGAAAGAAATGTCATTTG 57.896 34.615 15.52 0.00 31.47 2.32
146 147 9.965902 ATACCTGTAGAGAAAGAAATGTCATTT 57.034 29.630 10.63 10.63 34.64 2.32
147 148 9.606631 GATACCTGTAGAGAAAGAAATGTCATT 57.393 33.333 0.00 0.00 0.00 2.57
148 149 8.762645 TGATACCTGTAGAGAAAGAAATGTCAT 58.237 33.333 0.00 0.00 0.00 3.06
149 150 8.134202 TGATACCTGTAGAGAAAGAAATGTCA 57.866 34.615 0.00 0.00 0.00 3.58
150 151 9.606631 ATTGATACCTGTAGAGAAAGAAATGTC 57.393 33.333 0.00 0.00 0.00 3.06
151 152 9.606631 GATTGATACCTGTAGAGAAAGAAATGT 57.393 33.333 0.00 0.00 0.00 2.71
152 153 9.829507 AGATTGATACCTGTAGAGAAAGAAATG 57.170 33.333 0.00 0.00 0.00 2.32
154 155 9.035890 TGAGATTGATACCTGTAGAGAAAGAAA 57.964 33.333 0.00 0.00 0.00 2.52
155 156 8.470805 GTGAGATTGATACCTGTAGAGAAAGAA 58.529 37.037 0.00 0.00 0.00 2.52
156 157 7.836685 AGTGAGATTGATACCTGTAGAGAAAGA 59.163 37.037 0.00 0.00 0.00 2.52
157 158 8.006298 AGTGAGATTGATACCTGTAGAGAAAG 57.994 38.462 0.00 0.00 0.00 2.62
158 159 7.962995 AGTGAGATTGATACCTGTAGAGAAA 57.037 36.000 0.00 0.00 0.00 2.52
159 160 7.615757 TGAAGTGAGATTGATACCTGTAGAGAA 59.384 37.037 0.00 0.00 0.00 2.87
160 161 7.119387 TGAAGTGAGATTGATACCTGTAGAGA 58.881 38.462 0.00 0.00 0.00 3.10
161 162 7.340122 TGAAGTGAGATTGATACCTGTAGAG 57.660 40.000 0.00 0.00 0.00 2.43
162 163 7.904558 ATGAAGTGAGATTGATACCTGTAGA 57.095 36.000 0.00 0.00 0.00 2.59
163 164 9.636879 CATATGAAGTGAGATTGATACCTGTAG 57.363 37.037 0.00 0.00 0.00 2.74
164 165 9.367160 TCATATGAAGTGAGATTGATACCTGTA 57.633 33.333 1.98 0.00 0.00 2.74
165 166 8.255111 TCATATGAAGTGAGATTGATACCTGT 57.745 34.615 1.98 0.00 0.00 4.00
166 167 9.722184 AATCATATGAAGTGAGATTGATACCTG 57.278 33.333 9.99 0.00 0.00 4.00
172 173 9.465199 TGGAAAAATCATATGAAGTGAGATTGA 57.535 29.630 9.99 0.00 0.00 2.57
176 177 8.192774 GCAATGGAAAAATCATATGAAGTGAGA 58.807 33.333 9.99 0.00 0.00 3.27
177 178 8.195436 AGCAATGGAAAAATCATATGAAGTGAG 58.805 33.333 9.99 0.00 0.00 3.51
178 179 8.070034 AGCAATGGAAAAATCATATGAAGTGA 57.930 30.769 9.99 0.00 0.00 3.41
179 180 9.976511 ATAGCAATGGAAAAATCATATGAAGTG 57.023 29.630 9.99 2.05 0.00 3.16
193 194 9.881773 AGGATAGGAATTTTATAGCAATGGAAA 57.118 29.630 0.00 0.00 0.00 3.13
195 196 9.959721 GTAGGATAGGAATTTTATAGCAATGGA 57.040 33.333 0.00 0.00 0.00 3.41
196 197 9.739276 TGTAGGATAGGAATTTTATAGCAATGG 57.261 33.333 0.00 0.00 0.00 3.16
200 201 9.569122 GGTTTGTAGGATAGGAATTTTATAGCA 57.431 33.333 0.00 0.00 0.00 3.49
201 202 9.569122 TGGTTTGTAGGATAGGAATTTTATAGC 57.431 33.333 0.00 0.00 0.00 2.97
206 207 9.996554 CTTTTTGGTTTGTAGGATAGGAATTTT 57.003 29.630 0.00 0.00 0.00 1.82
207 208 9.374711 TCTTTTTGGTTTGTAGGATAGGAATTT 57.625 29.630 0.00 0.00 0.00 1.82
208 209 8.950007 TCTTTTTGGTTTGTAGGATAGGAATT 57.050 30.769 0.00 0.00 0.00 2.17
209 210 7.615757 CCTCTTTTTGGTTTGTAGGATAGGAAT 59.384 37.037 0.00 0.00 0.00 3.01
210 211 6.946009 CCTCTTTTTGGTTTGTAGGATAGGAA 59.054 38.462 0.00 0.00 0.00 3.36
211 212 6.481643 CCTCTTTTTGGTTTGTAGGATAGGA 58.518 40.000 0.00 0.00 0.00 2.94
212 213 5.125578 GCCTCTTTTTGGTTTGTAGGATAGG 59.874 44.000 0.00 0.00 0.00 2.57
213 214 5.946377 AGCCTCTTTTTGGTTTGTAGGATAG 59.054 40.000 0.00 0.00 0.00 2.08
214 215 5.887754 AGCCTCTTTTTGGTTTGTAGGATA 58.112 37.500 0.00 0.00 0.00 2.59
215 216 4.740902 AGCCTCTTTTTGGTTTGTAGGAT 58.259 39.130 0.00 0.00 0.00 3.24
216 217 4.178956 AGCCTCTTTTTGGTTTGTAGGA 57.821 40.909 0.00 0.00 0.00 2.94
217 218 5.048013 CCTTAGCCTCTTTTTGGTTTGTAGG 60.048 44.000 0.00 0.00 0.00 3.18
218 219 5.564848 GCCTTAGCCTCTTTTTGGTTTGTAG 60.565 44.000 0.00 0.00 0.00 2.74
219 220 4.279922 GCCTTAGCCTCTTTTTGGTTTGTA 59.720 41.667 0.00 0.00 0.00 2.41
220 221 3.069586 GCCTTAGCCTCTTTTTGGTTTGT 59.930 43.478 0.00 0.00 0.00 2.83
221 222 3.653344 GCCTTAGCCTCTTTTTGGTTTG 58.347 45.455 0.00 0.00 0.00 2.93
266 267 9.667107 CTGAGGTTCTGAAATACTATGGTTTTA 57.333 33.333 0.00 0.00 0.00 1.52
284 285 6.205658 GCCCATCTATTGAAATACTGAGGTTC 59.794 42.308 0.00 0.00 0.00 3.62
349 352 2.298163 ACCTCGGCGGTATTATCGAAAT 59.702 45.455 7.21 0.00 46.73 2.17
392 395 6.169094 TCTGTGCAAACCAAAGAAAATTGAA 58.831 32.000 0.00 0.00 34.82 2.69
396 399 6.114767 ACAATCTGTGCAAACCAAAGAAAAT 58.885 32.000 0.00 0.00 41.09 1.82
444 459 4.807834 CACAAGCTGATCGATGAGTGTAAT 59.192 41.667 13.56 0.00 0.00 1.89
483 498 3.467803 AGAGAACATGCCCGTATAAAGC 58.532 45.455 0.00 0.00 0.00 3.51
484 499 4.058817 GGAGAGAACATGCCCGTATAAAG 58.941 47.826 0.00 0.00 0.00 1.85
485 500 3.709653 AGGAGAGAACATGCCCGTATAAA 59.290 43.478 0.00 0.00 0.00 1.40
486 501 3.305720 AGGAGAGAACATGCCCGTATAA 58.694 45.455 0.00 0.00 0.00 0.98
488 503 1.794714 AGGAGAGAACATGCCCGTAT 58.205 50.000 0.00 0.00 0.00 3.06
585 614 0.950836 CCGGCTGAAAACACATGTCA 59.049 50.000 0.00 0.00 0.00 3.58
826 928 6.732896 TTGGGAGCCAAAGTATTTTTGTAA 57.267 33.333 0.00 0.00 40.92 2.41
870 981 4.367023 TGTATATCCCGCCGCCGC 62.367 66.667 0.00 0.00 0.00 6.53
871 982 2.126071 CTGTATATCCCGCCGCCG 60.126 66.667 0.00 0.00 0.00 6.46
872 983 1.215647 CTCTGTATATCCCGCCGCC 59.784 63.158 0.00 0.00 0.00 6.13
873 984 1.446272 GCTCTGTATATCCCGCCGC 60.446 63.158 0.00 0.00 0.00 6.53
874 985 1.215647 GGCTCTGTATATCCCGCCG 59.784 63.158 0.00 0.00 0.00 6.46
875 986 1.215647 CGGCTCTGTATATCCCGCC 59.784 63.158 0.00 0.00 31.87 6.13
876 987 0.601558 TTCGGCTCTGTATATCCCGC 59.398 55.000 0.00 0.00 38.85 6.13
877 988 2.492088 TGATTCGGCTCTGTATATCCCG 59.508 50.000 0.00 0.00 40.25 5.14
878 989 3.511934 ACTGATTCGGCTCTGTATATCCC 59.488 47.826 0.00 0.00 0.00 3.85
879 990 4.218635 TGACTGATTCGGCTCTGTATATCC 59.781 45.833 0.00 0.00 0.00 2.59
880 991 5.378292 TGACTGATTCGGCTCTGTATATC 57.622 43.478 0.00 0.00 0.00 1.63
881 992 5.791336 TTGACTGATTCGGCTCTGTATAT 57.209 39.130 0.00 0.00 0.00 0.86
882 993 5.359860 TCTTTGACTGATTCGGCTCTGTATA 59.640 40.000 0.00 0.00 0.00 1.47
883 994 4.160439 TCTTTGACTGATTCGGCTCTGTAT 59.840 41.667 0.00 0.00 0.00 2.29
884 995 3.509967 TCTTTGACTGATTCGGCTCTGTA 59.490 43.478 0.00 0.00 0.00 2.74
885 996 2.300152 TCTTTGACTGATTCGGCTCTGT 59.700 45.455 0.00 0.00 0.00 3.41
886 997 2.928757 CTCTTTGACTGATTCGGCTCTG 59.071 50.000 0.00 0.00 0.00 3.35
887 998 2.093764 CCTCTTTGACTGATTCGGCTCT 60.094 50.000 0.00 0.00 0.00 4.09
888 999 2.275318 CCTCTTTGACTGATTCGGCTC 58.725 52.381 0.00 0.00 0.00 4.70
889 1000 1.625818 ACCTCTTTGACTGATTCGGCT 59.374 47.619 0.00 0.00 0.00 5.52
894 1005 5.073428 GGGAAGAAACCTCTTTGACTGATT 58.927 41.667 0.00 0.00 42.19 2.57
910 1021 2.902457 GCGGAAGGGTGGGGAAGAA 61.902 63.158 0.00 0.00 0.00 2.52
930 1041 2.516909 GGTTTGGGGGTGGAACGA 59.483 61.111 0.00 0.00 38.12 3.85
931 1042 2.599281 GGGTTTGGGGGTGGAACG 60.599 66.667 0.00 0.00 38.12 3.95
932 1043 2.203728 GGGGTTTGGGGGTGGAAC 60.204 66.667 0.00 0.00 0.00 3.62
933 1044 2.333462 TTGGGGTTTGGGGGTGGAA 61.333 57.895 0.00 0.00 0.00 3.53
953 1064 2.203640 TGCGTGGAGTGGGAGAGT 60.204 61.111 0.00 0.00 0.00 3.24
957 1068 4.954118 AGGGTGCGTGGAGTGGGA 62.954 66.667 0.00 0.00 0.00 4.37
960 1071 4.394712 GGGAGGGTGCGTGGAGTG 62.395 72.222 0.00 0.00 0.00 3.51
961 1072 4.640690 AGGGAGGGTGCGTGGAGT 62.641 66.667 0.00 0.00 0.00 3.85
962 1073 3.775654 GAGGGAGGGTGCGTGGAG 61.776 72.222 0.00 0.00 0.00 3.86
969 1080 3.465403 CAGGAGCGAGGGAGGGTG 61.465 72.222 0.00 0.00 0.00 4.61
1047 1166 1.940613 GAATCCGATGGTGTGGTAAGC 59.059 52.381 0.00 0.00 0.00 3.09
1108 1237 2.359850 ATCAATGCGTGTGGCCGT 60.360 55.556 0.00 0.00 42.61 5.68
1109 1238 2.108514 AGATCAATGCGTGTGGCCG 61.109 57.895 0.00 0.00 42.61 6.13
1110 1239 1.430632 CAGATCAATGCGTGTGGCC 59.569 57.895 0.00 0.00 42.61 5.36
1111 1240 1.226491 GCAGATCAATGCGTGTGGC 60.226 57.895 0.00 0.00 43.96 5.01
1181 1334 0.249073 CATGGAGACGACGGATGGTC 60.249 60.000 0.00 0.00 42.48 4.02
1222 1378 0.693049 GAGGGGAACTCAAGAGGCAA 59.307 55.000 1.73 0.00 45.85 4.52
1223 1379 2.377136 GAGGGGAACTCAAGAGGCA 58.623 57.895 1.73 0.00 45.85 4.75
1421 1588 4.587584 TTTACGAAACCCCCAAATTGAC 57.412 40.909 0.00 0.00 0.00 3.18
1433 1600 7.968405 AGAACAAGCCATGATTATTTACGAAAC 59.032 33.333 0.00 0.00 0.00 2.78
1438 1605 5.909610 GCGAGAACAAGCCATGATTATTTAC 59.090 40.000 0.00 0.00 0.00 2.01
1502 1675 1.601171 CTTCCACCTCTCCCTGCTG 59.399 63.158 0.00 0.00 0.00 4.41
1604 1801 2.494870 ACCCAGATCATTCAAAGCAAGC 59.505 45.455 0.00 0.00 0.00 4.01
1627 1824 3.054508 TGGGGAAATGATGCCAATTTTCC 60.055 43.478 5.00 5.00 42.44 3.13
1659 1883 2.887151 ACTTCCTGACCCAAATGGAG 57.113 50.000 0.00 0.00 37.39 3.86
1733 1999 5.145059 GGCGCTTTGTTCTAGAAGTTAAAC 58.855 41.667 7.64 0.00 0.00 2.01
1760 2026 1.590932 AGCAGCATAATTCGCCAGAG 58.409 50.000 0.00 0.00 0.00 3.35
1919 2192 4.082571 GCATACAAAAGCTGGACAGATTGT 60.083 41.667 16.81 16.81 37.11 2.71
1935 2208 7.936496 TGACTAAGAAAATCATGGCATACAA 57.064 32.000 0.00 0.00 0.00 2.41
2054 2332 8.873144 TGTAGACATCAGATATCATGGAAATCA 58.127 33.333 5.32 0.00 0.00 2.57
2128 2406 1.751924 CCTCACTAGTCACCTGCTACC 59.248 57.143 0.00 0.00 0.00 3.18
2306 2776 6.375736 ACTCGATTTCTAGAGAAGATGACACA 59.624 38.462 0.00 0.00 37.87 3.72
2436 2943 1.960689 TGATCACGACCACAGTTCTCA 59.039 47.619 0.00 0.00 0.00 3.27
2566 3075 2.070783 GCCAGCAAAATGTCACAATGG 58.929 47.619 0.00 0.00 0.00 3.16
2567 3076 2.070783 GGCCAGCAAAATGTCACAATG 58.929 47.619 0.00 0.00 0.00 2.82
2604 3235 6.015027 ACAGCTGTATACGATTCAGGATAC 57.985 41.667 20.16 4.78 0.00 2.24
2616 3247 4.324267 AGACCAAACCAACAGCTGTATAC 58.676 43.478 22.01 4.68 0.00 1.47
2632 3263 3.592427 ACCCTACTAGAGACTGAGACCAA 59.408 47.826 0.00 0.00 0.00 3.67
2672 3303 5.244402 ACCAGACAAATGCATTCAAGATCAA 59.756 36.000 13.38 0.00 0.00 2.57
2720 3358 7.673641 TGCATTACCCTTCAAATTAATCCAT 57.326 32.000 0.00 0.00 0.00 3.41
2750 3389 5.559148 AGTCTAATGAGATCAACCCCATC 57.441 43.478 0.00 0.00 33.14 3.51
2767 3406 5.299531 CCGGTCATAAGATCTGACAAGTCTA 59.700 44.000 13.70 0.00 43.85 2.59
2789 3428 7.495934 ACAAGTTTGATATTCTCCATCTAACCG 59.504 37.037 0.00 2.49 38.25 4.44
2944 3598 8.920665 GCTATGTTGTCAGTCATTCATAGATAC 58.079 37.037 16.61 0.00 40.00 2.24
2945 3599 8.090831 GGCTATGTTGTCAGTCATTCATAGATA 58.909 37.037 16.61 0.00 40.00 1.98
2976 3633 8.995027 TTGATAAATATAAACATCAGGGCTGT 57.005 30.769 0.00 0.00 0.00 4.40
3302 4017 4.411013 AGATCGTATCTGATCCCATGACA 58.589 43.478 0.00 0.00 44.74 3.58
3551 4267 5.064558 TCGTAAACCTTTGCCTTCACAATA 58.935 37.500 0.00 0.00 0.00 1.90
3950 5005 1.180029 GCATGTGCATCCCACTTCTT 58.820 50.000 0.00 0.00 44.92 2.52
4037 5092 3.250040 CGGAAACCTTTACCTTCACACTG 59.750 47.826 0.00 0.00 0.00 3.66
4253 5555 2.736682 CTGTCCGGGCTTAAACGCG 61.737 63.158 7.97 3.53 44.69 6.01
4266 5568 4.322080 TGATATCGTCAATGGTCTGTCC 57.678 45.455 0.00 0.00 32.78 4.02
4377 5679 0.107410 AGAACAAGGGTGCACGAACA 60.107 50.000 11.45 0.00 0.00 3.18
5082 6766 4.408182 AGGTGTGTATGAATGACCTAGC 57.592 45.455 0.00 0.00 35.19 3.42
5087 6776 3.134804 AGGCCTAGGTGTGTATGAATGAC 59.865 47.826 1.29 0.00 0.00 3.06
5300 7008 2.670414 GCGTCTCCTGATTTCAGTCAAG 59.330 50.000 6.81 2.19 42.27 3.02
5332 7040 4.755629 GGGTAGAGTTTCAGTTTCAAGGTC 59.244 45.833 0.00 0.00 0.00 3.85
5336 7044 4.994852 CGATGGGTAGAGTTTCAGTTTCAA 59.005 41.667 0.00 0.00 0.00 2.69
5372 7080 3.669023 GCTCTACATTGTGTTCTTGCTGC 60.669 47.826 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.