Multiple sequence alignment - TraesCS4D01G297500

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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 TraesCS4D01G297500 chr4D 100.000 2668 0 0 1 2668 466407497 466410164 0.000000e+00 4927.0
1 TraesCS4D01G297500 chr4D 98.131 428 3 5 2122 2548 466409207 466409630 0.000000e+00 741.0
2 TraesCS4D01G297500 chr4D 98.131 428 3 5 1711 2134 466409618 466410044 0.000000e+00 741.0
3 TraesCS4D01G297500 chr4D 95.484 310 14 0 1 310 493808166 493807857 1.840000e-136 496.0
4 TraesCS4D01G297500 chr4D 98.106 264 5 0 1 264 323554929 323554666 6.730000e-126 460.0
5 TraesCS4D01G297500 chr4D 92.835 321 10 1 301 621 493807899 493807592 1.130000e-123 453.0
6 TraesCS4D01G297500 chr7D 97.577 1362 27 2 299 1659 16031685 16030329 0.000000e+00 2327.0
7 TraesCS4D01G297500 chr7D 97.455 1100 27 1 561 1659 484418691 484419790 0.000000e+00 1875.0
8 TraesCS4D01G297500 chr7D 95.692 441 10 5 1659 2099 11768700 11769131 0.000000e+00 701.0
9 TraesCS4D01G297500 chr7D 90.128 547 22 8 2122 2668 11768752 11769266 0.000000e+00 682.0
10 TraesCS4D01G297500 chr7D 89.959 488 14 6 1658 2134 99721738 99722201 4.920000e-167 597.0
11 TraesCS4D01G297500 chr7D 88.955 507 20 8 2122 2618 99721791 99722271 6.360000e-166 593.0
12 TraesCS4D01G297500 chr7D 97.419 310 8 0 1 310 16031950 16031641 1.820000e-146 529.0
13 TraesCS4D01G297500 chr7D 98.596 285 3 1 1657 1940 489502222 489502506 1.100000e-138 503.0
14 TraesCS4D01G297500 chr7D 95.298 319 9 6 2351 2668 85625665 85625978 3.970000e-138 501.0
15 TraesCS4D01G297500 chr7D 95.268 317 12 3 2353 2668 508244800 508244486 1.430000e-137 499.0
16 TraesCS4D01G297500 chr7D 95.431 197 5 3 1939 2134 85625665 85625858 7.170000e-81 311.0
17 TraesCS4D01G297500 chr6D 97.504 1362 30 3 299 1659 402837304 402835946 0.000000e+00 2324.0
18 TraesCS4D01G297500 chr6D 83.039 1191 169 17 472 1658 174380169 174379008 0.000000e+00 1050.0
19 TraesCS4D01G297500 chr6D 97.097 310 9 0 1 310 402837569 402837260 8.460000e-145 523.0
20 TraesCS4D01G297500 chr6D 98.940 283 2 1 1659 1940 124088217 124087935 3.070000e-139 505.0
21 TraesCS4D01G297500 chr6D 87.817 197 11 4 1938 2134 441376254 441376071 4.470000e-53 219.0
22 TraesCS4D01G297500 chr6D 85.000 200 14 8 1941 2134 74631873 74631684 3.510000e-44 189.0
23 TraesCS4D01G297500 chr6D 91.729 133 5 5 2006 2134 470253413 470253543 2.110000e-41 180.0
24 TraesCS4D01G297500 chr2D 96.405 1363 47 2 299 1659 642120427 642119065 0.000000e+00 2244.0
25 TraesCS4D01G297500 chr2D 97.742 310 7 0 1 310 642120692 642120383 3.910000e-148 534.0
26 TraesCS4D01G297500 chr2D 97.458 236 4 2 2119 2352 491592862 491592627 4.140000e-108 401.0
27 TraesCS4D01G297500 chr3D 97.343 1129 25 3 533 1659 105445188 105446313 0.000000e+00 1914.0
28 TraesCS4D01G297500 chr3D 97.917 1104 22 1 557 1659 239582364 239581261 0.000000e+00 1910.0
29 TraesCS4D01G297500 chr3D 94.192 551 25 6 2122 2668 558471060 558471607 0.000000e+00 833.0
30 TraesCS4D01G297500 chr3D 95.625 480 15 4 1660 2134 558471009 558471487 0.000000e+00 765.0
31 TraesCS4D01G297500 chr3D 91.257 549 27 4 2122 2668 550295201 550294672 0.000000e+00 728.0
32 TraesCS4D01G297500 chr3D 96.235 425 11 5 1679 2099 20305183 20305606 0.000000e+00 691.0
33 TraesCS4D01G297500 chr3D 91.875 480 15 5 1660 2134 550295252 550294792 0.000000e+00 649.0
34 TraesCS4D01G297500 chr3D 91.631 466 15 5 2122 2585 20305215 20305658 8.110000e-175 623.0
35 TraesCS4D01G297500 chr3D 94.953 317 12 3 2353 2668 547719358 547719045 6.630000e-136 494.0
36 TraesCS4D01G297500 chr1D 97.634 1099 25 1 562 1659 59121549 59120451 0.000000e+00 1884.0
37 TraesCS4D01G297500 chr1D 97.366 1101 28 1 560 1659 89557377 89556277 0.000000e+00 1871.0
38 TraesCS4D01G297500 chr1D 97.097 310 9 0 1 310 197525126 197525435 8.460000e-145 523.0
39 TraesCS4D01G297500 chr1D 95.312 320 12 2 2350 2668 382627532 382627849 3.070000e-139 505.0
40 TraesCS4D01G297500 chr1D 95.000 200 5 4 1938 2134 382627532 382627729 2.580000e-80 309.0
41 TraesCS4D01G297500 chr1D 89.286 196 8 4 1940 2134 356769172 356769355 1.600000e-57 233.0
42 TraesCS4D01G297500 chr5D 97.361 1099 28 1 562 1659 12216676 12217774 0.000000e+00 1868.0
43 TraesCS4D01G297500 chr5D 91.985 549 19 7 2122 2668 392936374 392936899 0.000000e+00 747.0
44 TraesCS4D01G297500 chr5D 91.807 476 19 10 1660 2134 392936323 392936779 0.000000e+00 645.0
45 TraesCS4D01G297500 chr5D 95.611 319 12 2 2350 2668 83324236 83324552 6.590000e-141 510.0
46 TraesCS4D01G297500 chr5D 97.458 236 4 2 2119 2352 151357721 151357486 4.140000e-108 401.0
47 TraesCS4D01G297500 chr5D 95.960 198 6 2 1938 2134 83324236 83324432 1.190000e-83 320.0
48 TraesCS4D01G297500 chr2A 84.017 1683 222 30 1 1658 364472208 364473868 0.000000e+00 1574.0
49 TraesCS4D01G297500 chr2A 95.455 44 2 0 371 414 364472516 364472559 1.330000e-08 71.3
50 TraesCS4D01G297500 chr5A 83.234 1682 237 25 1 1659 664583483 664581824 0.000000e+00 1502.0
51 TraesCS4D01G297500 chr5B 93.986 981 46 5 371 1351 616965304 616964337 0.000000e+00 1472.0
52 TraesCS4D01G297500 chr5B 93.722 223 9 3 1 222 616966730 616966512 1.980000e-86 329.0
53 TraesCS4D01G297500 chrUn 92.326 430 10 5 1659 2088 89754500 89754906 8.230000e-165 590.0
54 TraesCS4D01G297500 chrUn 94.536 366 10 4 2137 2502 89754551 89754906 8.340000e-155 556.0
55 TraesCS4D01G297500 chrUn 88.722 133 10 4 2006 2134 104913561 104913692 9.890000e-35 158.0
56 TraesCS4D01G297500 chrUn 91.919 99 6 2 2038 2134 29801894 29801992 1.290000e-28 137.0
57 TraesCS4D01G297500 chrUn 87.611 113 12 2 2022 2134 253776795 253776685 2.160000e-26 130.0
58 TraesCS4D01G297500 chrUn 87.611 113 12 2 2022 2134 347003118 347003008 2.160000e-26 130.0
59 TraesCS4D01G297500 chrUn 93.182 88 5 1 2047 2134 437581988 437582074 7.750000e-26 128.0
60 TraesCS4D01G297500 chrUn 98.413 63 0 1 1941 2002 90672445 90672383 2.810000e-20 110.0


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 TraesCS4D01G297500 chr4D 466407497 466410164 2667 False 2136.333333 4927 98.7540 1 2668 3 chr4D.!!$F1 2667
1 TraesCS4D01G297500 chr4D 493807592 493808166 574 True 474.500000 496 94.1595 1 621 2 chr4D.!!$R2 620
2 TraesCS4D01G297500 chr7D 484418691 484419790 1099 False 1875.000000 1875 97.4550 561 1659 1 chr7D.!!$F1 1098
3 TraesCS4D01G297500 chr7D 16030329 16031950 1621 True 1428.000000 2327 97.4980 1 1659 2 chr7D.!!$R2 1658
4 TraesCS4D01G297500 chr7D 11768700 11769266 566 False 691.500000 701 92.9100 1659 2668 2 chr7D.!!$F3 1009
5 TraesCS4D01G297500 chr7D 99721738 99722271 533 False 595.000000 597 89.4570 1658 2618 2 chr7D.!!$F5 960
6 TraesCS4D01G297500 chr6D 402835946 402837569 1623 True 1423.500000 2324 97.3005 1 1659 2 chr6D.!!$R5 1658
7 TraesCS4D01G297500 chr6D 174379008 174380169 1161 True 1050.000000 1050 83.0390 472 1658 1 chr6D.!!$R3 1186
8 TraesCS4D01G297500 chr2D 642119065 642120692 1627 True 1389.000000 2244 97.0735 1 1659 2 chr2D.!!$R2 1658
9 TraesCS4D01G297500 chr3D 105445188 105446313 1125 False 1914.000000 1914 97.3430 533 1659 1 chr3D.!!$F1 1126
10 TraesCS4D01G297500 chr3D 239581261 239582364 1103 True 1910.000000 1910 97.9170 557 1659 1 chr3D.!!$R1 1102
11 TraesCS4D01G297500 chr3D 558471009 558471607 598 False 799.000000 833 94.9085 1660 2668 2 chr3D.!!$F3 1008
12 TraesCS4D01G297500 chr3D 550294672 550295252 580 True 688.500000 728 91.5660 1660 2668 2 chr3D.!!$R3 1008
13 TraesCS4D01G297500 chr1D 59120451 59121549 1098 True 1884.000000 1884 97.6340 562 1659 1 chr1D.!!$R1 1097
14 TraesCS4D01G297500 chr1D 89556277 89557377 1100 True 1871.000000 1871 97.3660 560 1659 1 chr1D.!!$R2 1099
15 TraesCS4D01G297500 chr5D 12216676 12217774 1098 False 1868.000000 1868 97.3610 562 1659 1 chr5D.!!$F1 1097
16 TraesCS4D01G297500 chr5D 392936323 392936899 576 False 696.000000 747 91.8960 1660 2668 2 chr5D.!!$F3 1008
17 TraesCS4D01G297500 chr2A 364472208 364473868 1660 False 822.650000 1574 89.7360 1 1658 2 chr2A.!!$F1 1657
18 TraesCS4D01G297500 chr5A 664581824 664583483 1659 True 1502.000000 1502 83.2340 1 1659 1 chr5A.!!$R1 1658
19 TraesCS4D01G297500 chr5B 616964337 616966730 2393 True 900.500000 1472 93.8540 1 1351 2 chr5B.!!$R1 1350

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
328 388 0.042708 CTTCCGATCAATTGCGCTCG 60.043 55.0 9.73 8.37 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2272 3473 0.036875 GCACCTGGGTATAGATGGCC 59.963 60.0 0.0 0.0 0.0 5.36 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
208 210 0.882474 GTCTCCCGATCGATCCGATT 59.118 55.000 18.66 0.00 47.00 3.34
222 282 4.496336 GATTGCTCTGCCCCGCCT 62.496 66.667 0.00 0.00 0.00 5.52
317 377 3.143338 GGCCTCTCCCTTCCGATC 58.857 66.667 0.00 0.00 0.00 3.69
318 378 1.762460 GGCCTCTCCCTTCCGATCA 60.762 63.158 0.00 0.00 0.00 2.92
319 379 1.338136 GGCCTCTCCCTTCCGATCAA 61.338 60.000 0.00 0.00 0.00 2.57
320 380 0.761802 GCCTCTCCCTTCCGATCAAT 59.238 55.000 0.00 0.00 0.00 2.57
321 381 1.141858 GCCTCTCCCTTCCGATCAATT 59.858 52.381 0.00 0.00 0.00 2.32
322 382 2.843701 CCTCTCCCTTCCGATCAATTG 58.156 52.381 0.00 0.00 0.00 2.32
323 383 2.216898 CTCTCCCTTCCGATCAATTGC 58.783 52.381 0.00 0.00 0.00 3.56
324 384 0.940126 CTCCCTTCCGATCAATTGCG 59.060 55.000 0.00 0.00 0.00 4.85
325 385 1.095228 TCCCTTCCGATCAATTGCGC 61.095 55.000 0.00 0.00 0.00 6.09
326 386 1.097547 CCCTTCCGATCAATTGCGCT 61.098 55.000 9.73 0.00 0.00 5.92
327 387 0.305922 CCTTCCGATCAATTGCGCTC 59.694 55.000 9.73 0.00 0.00 5.03
328 388 0.042708 CTTCCGATCAATTGCGCTCG 60.043 55.000 9.73 8.37 0.00 5.03
329 389 2.035617 TTCCGATCAATTGCGCTCGC 62.036 55.000 9.73 7.38 42.35 5.03
330 390 2.052766 CGATCAATTGCGCTCGCC 60.053 61.111 9.73 0.00 41.09 5.54
331 391 2.329339 GATCAATTGCGCTCGCCC 59.671 61.111 9.73 0.00 41.09 6.13
332 392 3.512287 GATCAATTGCGCTCGCCCG 62.512 63.158 9.73 0.00 41.09 6.13
607 1801 1.598130 GTTGCTGTCCCTCGCTGTT 60.598 57.895 0.00 0.00 0.00 3.16
627 1821 3.536956 TCGGTGATCTTTGATGGTACC 57.463 47.619 4.43 4.43 0.00 3.34
724 1918 4.034258 GCTGTCCGTCACGTCCGA 62.034 66.667 5.76 0.00 0.00 4.55
740 1934 2.674754 GATTCCTCCGGTTGCCCA 59.325 61.111 0.00 0.00 0.00 5.36
969 2163 1.268079 GTTCTGCCTCAGTTTGCTTCC 59.732 52.381 0.00 0.00 32.61 3.46
1008 2202 5.485353 TCCTATTGTCTTTCAGATGTGGACT 59.515 40.000 0.00 0.00 0.00 3.85
1010 2204 6.656693 CCTATTGTCTTTCAGATGTGGACTTT 59.343 38.462 0.00 0.00 0.00 2.66
1669 2865 1.135083 CACGGCTTCACACTACTAGGG 60.135 57.143 0.00 0.00 0.00 3.53
2086 3287 6.839134 TCTTAATCTCTGGTCACTATGGCTTA 59.161 38.462 0.00 0.00 0.00 3.09
2087 3288 5.957771 AATCTCTGGTCACTATGGCTTAA 57.042 39.130 0.00 0.00 0.00 1.85
2089 3290 5.537300 TCTCTGGTCACTATGGCTTAATC 57.463 43.478 0.00 0.00 0.00 1.75
2090 3291 5.211973 TCTCTGGTCACTATGGCTTAATCT 58.788 41.667 0.00 0.00 0.00 2.40
2091 3292 5.303078 TCTCTGGTCACTATGGCTTAATCTC 59.697 44.000 0.00 0.00 0.00 2.75
2092 3293 4.962362 TCTGGTCACTATGGCTTAATCTCA 59.038 41.667 0.00 0.00 0.00 3.27
2093 3294 5.069648 TCTGGTCACTATGGCTTAATCTCAG 59.930 44.000 0.00 0.00 0.00 3.35
2094 3295 4.101585 TGGTCACTATGGCTTAATCTCAGG 59.898 45.833 0.00 0.00 0.00 3.86
2095 3296 4.101741 GGTCACTATGGCTTAATCTCAGGT 59.898 45.833 0.00 0.00 0.00 4.00
2096 3297 5.293560 GTCACTATGGCTTAATCTCAGGTC 58.706 45.833 0.00 0.00 0.00 3.85
2097 3298 4.962362 TCACTATGGCTTAATCTCAGGTCA 59.038 41.667 0.00 0.00 0.00 4.02
2098 3299 5.425217 TCACTATGGCTTAATCTCAGGTCAA 59.575 40.000 0.00 0.00 0.00 3.18
2099 3300 6.100279 TCACTATGGCTTAATCTCAGGTCAAT 59.900 38.462 0.00 0.00 0.00 2.57
2100 3301 7.290014 TCACTATGGCTTAATCTCAGGTCAATA 59.710 37.037 0.00 0.00 0.00 1.90
2101 3302 8.099537 CACTATGGCTTAATCTCAGGTCAATAT 58.900 37.037 0.00 0.00 0.00 1.28
2102 3303 8.099537 ACTATGGCTTAATCTCAGGTCAATATG 58.900 37.037 0.00 0.00 0.00 1.78
2103 3304 5.065914 TGGCTTAATCTCAGGTCAATATGC 58.934 41.667 0.00 0.00 0.00 3.14
2104 3305 5.163163 TGGCTTAATCTCAGGTCAATATGCT 60.163 40.000 0.00 0.00 0.00 3.79
2105 3306 5.767168 GGCTTAATCTCAGGTCAATATGCTT 59.233 40.000 0.00 0.00 0.00 3.91
2106 3307 6.936900 GGCTTAATCTCAGGTCAATATGCTTA 59.063 38.462 0.00 0.00 0.00 3.09
2107 3308 7.445402 GGCTTAATCTCAGGTCAATATGCTTAA 59.555 37.037 0.00 0.00 0.00 1.85
2108 3309 9.007901 GCTTAATCTCAGGTCAATATGCTTAAT 57.992 33.333 0.00 0.00 0.00 1.40
2112 3313 8.985315 ATCTCAGGTCAATATGCTTAATTTCA 57.015 30.769 0.00 0.00 0.00 2.69
2113 3314 8.806429 TCTCAGGTCAATATGCTTAATTTCAA 57.194 30.769 0.00 0.00 0.00 2.69
2114 3315 8.896744 TCTCAGGTCAATATGCTTAATTTCAAG 58.103 33.333 0.00 0.00 0.00 3.02
2115 3316 8.579850 TCAGGTCAATATGCTTAATTTCAAGT 57.420 30.769 0.00 0.00 0.00 3.16
2116 3317 8.677300 TCAGGTCAATATGCTTAATTTCAAGTC 58.323 33.333 0.00 0.00 0.00 3.01
2117 3318 8.461222 CAGGTCAATATGCTTAATTTCAAGTCA 58.539 33.333 0.00 0.00 0.00 3.41
2118 3319 9.023962 AGGTCAATATGCTTAATTTCAAGTCAA 57.976 29.630 0.00 0.00 0.00 3.18
2119 3320 9.638239 GGTCAATATGCTTAATTTCAAGTCAAA 57.362 29.630 0.00 0.00 0.00 2.69
2123 3324 6.875926 ATGCTTAATTTCAAGTCAAATCGC 57.124 33.333 0.00 0.00 0.00 4.58
2124 3325 5.767269 TGCTTAATTTCAAGTCAAATCGCA 58.233 33.333 0.00 0.00 0.00 5.10
2125 3326 5.629020 TGCTTAATTTCAAGTCAAATCGCAC 59.371 36.000 0.00 0.00 0.00 5.34
2126 3327 5.858581 GCTTAATTTCAAGTCAAATCGCACT 59.141 36.000 0.00 0.00 0.00 4.40
2127 3328 7.021196 GCTTAATTTCAAGTCAAATCGCACTA 58.979 34.615 0.00 0.00 0.00 2.74
2128 3329 7.537306 GCTTAATTTCAAGTCAAATCGCACTAA 59.463 33.333 0.00 0.00 0.00 2.24
2129 3330 8.948853 TTAATTTCAAGTCAAATCGCACTAAG 57.051 30.769 0.00 0.00 0.00 2.18
2130 3331 6.560253 ATTTCAAGTCAAATCGCACTAAGT 57.440 33.333 0.00 0.00 0.00 2.24
2131 3332 4.990543 TCAAGTCAAATCGCACTAAGTG 57.009 40.909 0.00 0.00 36.51 3.16
2132 3333 3.745975 TCAAGTCAAATCGCACTAAGTGG 59.254 43.478 0.00 0.00 33.64 4.00
2133 3334 3.402628 AGTCAAATCGCACTAAGTGGT 57.597 42.857 0.00 0.00 33.64 4.16
2134 3335 3.067106 AGTCAAATCGCACTAAGTGGTG 58.933 45.455 0.00 0.00 39.91 4.17
2151 3352 4.536687 GCGCCATTAGTGCCACGC 62.537 66.667 0.00 0.00 46.76 5.34
2152 3353 3.876198 CGCCATTAGTGCCACGCC 61.876 66.667 0.00 0.00 0.00 5.68
2153 3354 2.749839 GCCATTAGTGCCACGCCA 60.750 61.111 0.00 0.00 0.00 5.69
2154 3355 2.120909 GCCATTAGTGCCACGCCAT 61.121 57.895 0.00 0.00 0.00 4.40
2155 3356 1.666209 GCCATTAGTGCCACGCCATT 61.666 55.000 0.00 0.00 0.00 3.16
2156 3357 1.674359 CCATTAGTGCCACGCCATTA 58.326 50.000 0.00 0.00 0.00 1.90
2157 3358 1.603802 CCATTAGTGCCACGCCATTAG 59.396 52.381 0.00 0.00 0.00 1.73
2158 3359 2.288666 CATTAGTGCCACGCCATTAGT 58.711 47.619 0.00 0.00 0.00 2.24
2159 3360 3.462982 CATTAGTGCCACGCCATTAGTA 58.537 45.455 0.00 0.00 0.00 1.82
2160 3361 3.830744 TTAGTGCCACGCCATTAGTAT 57.169 42.857 0.00 0.00 0.00 2.12
2161 3362 4.940905 TTAGTGCCACGCCATTAGTATA 57.059 40.909 0.00 0.00 0.00 1.47
2162 3363 5.477607 TTAGTGCCACGCCATTAGTATAT 57.522 39.130 0.00 0.00 0.00 0.86
2163 3364 4.351874 AGTGCCACGCCATTAGTATATT 57.648 40.909 0.00 0.00 0.00 1.28
2164 3365 4.714632 AGTGCCACGCCATTAGTATATTT 58.285 39.130 0.00 0.00 0.00 1.40
2165 3366 5.130350 AGTGCCACGCCATTAGTATATTTT 58.870 37.500 0.00 0.00 0.00 1.82
2166 3367 6.292923 AGTGCCACGCCATTAGTATATTTTA 58.707 36.000 0.00 0.00 0.00 1.52
2167 3368 6.204108 AGTGCCACGCCATTAGTATATTTTAC 59.796 38.462 0.00 0.00 0.00 2.01
2168 3369 6.204108 GTGCCACGCCATTAGTATATTTTACT 59.796 38.462 0.00 0.00 0.00 2.24
2169 3370 7.385752 GTGCCACGCCATTAGTATATTTTACTA 59.614 37.037 0.00 0.00 0.00 1.82
2170 3371 7.932491 TGCCACGCCATTAGTATATTTTACTAA 59.068 33.333 8.55 8.55 42.18 2.24
2171 3372 8.943002 GCCACGCCATTAGTATATTTTACTAAT 58.057 33.333 11.52 11.52 46.06 1.73
2179 3380 6.796705 AGTATATTTTACTAATGGCGCACC 57.203 37.500 10.83 0.00 0.00 5.01
2193 3394 4.301505 CACCACTAGTGCGCCATT 57.698 55.556 17.86 0.00 40.28 3.16
2194 3395 3.451793 CACCACTAGTGCGCCATTA 57.548 52.632 17.86 0.00 40.28 1.90
2195 3396 1.290203 CACCACTAGTGCGCCATTAG 58.710 55.000 17.86 6.66 40.28 1.73
2196 3397 0.902531 ACCACTAGTGCGCCATTAGT 59.097 50.000 17.86 7.36 37.38 2.24
2197 3398 2.104967 ACCACTAGTGCGCCATTAGTA 58.895 47.619 17.86 0.00 35.29 1.82
2198 3399 2.698797 ACCACTAGTGCGCCATTAGTAT 59.301 45.455 17.86 0.00 35.29 2.12
2199 3400 3.243771 ACCACTAGTGCGCCATTAGTATC 60.244 47.826 17.86 0.00 35.29 2.24
2200 3401 3.005897 CCACTAGTGCGCCATTAGTATCT 59.994 47.826 17.86 0.00 35.29 1.98
2201 3402 3.983988 CACTAGTGCGCCATTAGTATCTG 59.016 47.826 10.54 0.00 35.29 2.90
2202 3403 2.533266 AGTGCGCCATTAGTATCTGG 57.467 50.000 4.18 0.00 35.53 3.86
2203 3404 1.762957 AGTGCGCCATTAGTATCTGGT 59.237 47.619 4.18 0.00 34.86 4.00
2204 3405 2.963101 AGTGCGCCATTAGTATCTGGTA 59.037 45.455 4.18 0.00 34.86 3.25
2205 3406 3.578716 AGTGCGCCATTAGTATCTGGTAT 59.421 43.478 4.18 0.00 34.86 2.73
2206 3407 4.770531 AGTGCGCCATTAGTATCTGGTATA 59.229 41.667 4.18 0.00 34.86 1.47
2207 3408 4.863131 GTGCGCCATTAGTATCTGGTATAC 59.137 45.833 4.18 0.00 34.86 1.47
2208 3409 4.770531 TGCGCCATTAGTATCTGGTATACT 59.229 41.667 4.18 3.40 38.32 2.12
2209 3410 5.947566 TGCGCCATTAGTATCTGGTATACTA 59.052 40.000 4.18 0.00 36.38 1.82
2210 3411 6.434965 TGCGCCATTAGTATCTGGTATACTAA 59.565 38.462 16.03 16.03 45.52 2.24
2217 3418 8.625786 TTAGTATCTGGTATACTAATGACGCA 57.374 34.615 11.67 0.00 40.28 5.24
2218 3419 6.910995 AGTATCTGGTATACTAATGACGCAC 58.089 40.000 2.25 0.00 33.45 5.34
2219 3420 4.579454 TCTGGTATACTAATGACGCACC 57.421 45.455 2.25 0.00 0.00 5.01
2220 3421 3.319972 TCTGGTATACTAATGACGCACCC 59.680 47.826 2.25 0.00 0.00 4.61
2221 3422 2.366266 TGGTATACTAATGACGCACCCC 59.634 50.000 2.25 0.00 0.00 4.95
2222 3423 2.366266 GGTATACTAATGACGCACCCCA 59.634 50.000 2.25 0.00 0.00 4.96
2223 3424 2.910688 ATACTAATGACGCACCCCAG 57.089 50.000 0.00 0.00 0.00 4.45
2224 3425 1.855295 TACTAATGACGCACCCCAGA 58.145 50.000 0.00 0.00 0.00 3.86
2225 3426 1.204146 ACTAATGACGCACCCCAGAT 58.796 50.000 0.00 0.00 0.00 2.90
2226 3427 1.134401 ACTAATGACGCACCCCAGATG 60.134 52.381 0.00 0.00 0.00 2.90
2227 3428 0.463654 TAATGACGCACCCCAGATGC 60.464 55.000 0.00 0.00 39.81 3.91
2233 3434 2.440796 CACCCCAGATGCGCCATT 60.441 61.111 4.18 0.00 0.00 3.16
2234 3435 1.152984 CACCCCAGATGCGCCATTA 60.153 57.895 4.18 0.00 0.00 1.90
2235 3436 1.149174 ACCCCAGATGCGCCATTAG 59.851 57.895 4.18 0.00 0.00 1.73
2236 3437 1.149174 CCCCAGATGCGCCATTAGT 59.851 57.895 4.18 0.00 0.00 2.24
2237 3438 0.396435 CCCCAGATGCGCCATTAGTA 59.604 55.000 4.18 0.00 0.00 1.82
2238 3439 1.003580 CCCCAGATGCGCCATTAGTAT 59.996 52.381 4.18 0.00 0.00 2.12
2239 3440 2.236146 CCCCAGATGCGCCATTAGTATA 59.764 50.000 4.18 0.00 0.00 1.47
2240 3441 3.118261 CCCCAGATGCGCCATTAGTATAT 60.118 47.826 4.18 0.00 0.00 0.86
2241 3442 4.100963 CCCCAGATGCGCCATTAGTATATA 59.899 45.833 4.18 0.00 0.00 0.86
2242 3443 5.050490 CCCAGATGCGCCATTAGTATATAC 58.950 45.833 4.18 4.60 0.00 1.47
2243 3444 5.395214 CCCAGATGCGCCATTAGTATATACA 60.395 44.000 15.18 0.00 0.00 2.29
2244 3445 6.106003 CCAGATGCGCCATTAGTATATACAA 58.894 40.000 15.18 7.71 0.00 2.41
2245 3446 6.036083 CCAGATGCGCCATTAGTATATACAAC 59.964 42.308 15.18 0.00 0.00 3.32
2246 3447 6.589907 CAGATGCGCCATTAGTATATACAACA 59.410 38.462 15.18 0.00 0.00 3.33
2247 3448 6.813649 AGATGCGCCATTAGTATATACAACAG 59.186 38.462 15.18 2.65 0.00 3.16
2248 3449 5.849510 TGCGCCATTAGTATATACAACAGT 58.150 37.500 15.18 0.00 0.00 3.55
2249 3450 5.694458 TGCGCCATTAGTATATACAACAGTG 59.306 40.000 15.18 7.23 0.00 3.66
2250 3451 5.389516 GCGCCATTAGTATATACAACAGTGC 60.390 44.000 15.18 12.45 0.00 4.40
2251 3452 5.164090 CGCCATTAGTATATACAACAGTGCG 60.164 44.000 15.18 15.59 0.00 5.34
2252 3453 5.389516 GCCATTAGTATATACAACAGTGCGC 60.390 44.000 15.18 0.00 0.00 6.09
2253 3454 5.120208 CCATTAGTATATACAACAGTGCGCC 59.880 44.000 15.18 0.00 0.00 6.53
2254 3455 3.812156 AGTATATACAACAGTGCGCCA 57.188 42.857 15.18 0.00 0.00 5.69
2255 3456 4.336889 AGTATATACAACAGTGCGCCAT 57.663 40.909 15.18 0.00 0.00 4.40
2256 3457 4.703897 AGTATATACAACAGTGCGCCATT 58.296 39.130 15.18 0.00 0.00 3.16
2257 3458 5.849510 AGTATATACAACAGTGCGCCATTA 58.150 37.500 15.18 0.00 0.00 1.90
2258 3459 5.926542 AGTATATACAACAGTGCGCCATTAG 59.073 40.000 15.18 0.00 0.00 1.73
2259 3460 2.465860 TACAACAGTGCGCCATTAGT 57.534 45.000 4.18 0.00 0.00 2.24
2260 3461 2.465860 ACAACAGTGCGCCATTAGTA 57.534 45.000 4.18 0.00 0.00 1.82
2261 3462 2.985896 ACAACAGTGCGCCATTAGTAT 58.014 42.857 4.18 0.00 0.00 2.12
2262 3463 2.677836 ACAACAGTGCGCCATTAGTATG 59.322 45.455 4.18 0.00 0.00 2.39
2263 3464 1.299541 ACAGTGCGCCATTAGTATGC 58.700 50.000 4.18 0.00 0.00 3.14
2264 3465 0.588252 CAGTGCGCCATTAGTATGCC 59.412 55.000 4.18 0.00 0.00 4.40
2265 3466 0.469917 AGTGCGCCATTAGTATGCCT 59.530 50.000 4.18 0.00 0.00 4.75
2266 3467 0.868406 GTGCGCCATTAGTATGCCTC 59.132 55.000 4.18 0.00 0.00 4.70
2267 3468 0.250295 TGCGCCATTAGTATGCCTCC 60.250 55.000 4.18 0.00 0.00 4.30
2268 3469 0.955919 GCGCCATTAGTATGCCTCCC 60.956 60.000 0.00 0.00 0.00 4.30
2269 3470 0.396435 CGCCATTAGTATGCCTCCCA 59.604 55.000 0.00 0.00 0.00 4.37
2270 3471 1.609061 CGCCATTAGTATGCCTCCCAG 60.609 57.143 0.00 0.00 0.00 4.45
2271 3472 1.271597 GCCATTAGTATGCCTCCCAGG 60.272 57.143 0.00 0.00 38.80 4.45
2272 3473 1.352352 CCATTAGTATGCCTCCCAGGG 59.648 57.143 0.00 0.00 35.37 4.45
2273 3474 1.352352 CATTAGTATGCCTCCCAGGGG 59.648 57.143 5.33 0.92 35.37 4.79
2280 3481 2.290393 CCTCCCAGGGGCCATCTA 59.710 66.667 5.33 0.00 34.68 1.98
2281 3482 1.151721 CCTCCCAGGGGCCATCTAT 60.152 63.158 5.33 0.00 34.68 1.98
2282 3483 0.119155 CCTCCCAGGGGCCATCTATA 59.881 60.000 5.33 0.00 34.68 1.31
2283 3484 1.280457 CTCCCAGGGGCCATCTATAC 58.720 60.000 5.33 0.00 34.68 1.47
2284 3485 0.178873 TCCCAGGGGCCATCTATACC 60.179 60.000 5.33 0.00 34.68 2.73
2285 3486 1.208165 CCCAGGGGCCATCTATACCC 61.208 65.000 4.39 0.00 43.69 3.69
2286 3487 0.475632 CCAGGGGCCATCTATACCCA 60.476 60.000 4.39 0.00 46.21 4.51
2287 3488 0.987294 CAGGGGCCATCTATACCCAG 59.013 60.000 4.39 0.00 46.21 4.45
2288 3489 0.178861 AGGGGCCATCTATACCCAGG 60.179 60.000 4.39 0.00 46.21 4.45
2289 3490 0.475828 GGGGCCATCTATACCCAGGT 60.476 60.000 4.39 0.00 46.21 4.00
2290 3491 0.693049 GGGCCATCTATACCCAGGTG 59.307 60.000 4.39 0.00 43.64 4.00
2291 3492 0.036875 GGCCATCTATACCCAGGTGC 59.963 60.000 0.00 0.00 0.00 5.01
2292 3493 1.059913 GCCATCTATACCCAGGTGCT 58.940 55.000 0.00 0.00 0.00 4.40
2293 3494 1.421646 GCCATCTATACCCAGGTGCTT 59.578 52.381 0.00 0.00 0.00 3.91
2294 3495 2.158608 GCCATCTATACCCAGGTGCTTT 60.159 50.000 0.00 0.00 0.00 3.51
2295 3496 3.480470 CCATCTATACCCAGGTGCTTTG 58.520 50.000 0.00 0.00 0.00 2.77
2296 3497 3.480470 CATCTATACCCAGGTGCTTTGG 58.520 50.000 0.00 0.00 35.41 3.28
2297 3498 1.211949 TCTATACCCAGGTGCTTTGGC 59.788 52.381 0.00 0.00 34.26 4.52
2315 3516 2.105323 GCATACTAATGGCGCACAAC 57.895 50.000 10.83 0.00 33.38 3.32
2316 3517 1.400142 GCATACTAATGGCGCACAACA 59.600 47.619 10.83 0.00 33.38 3.33
2317 3518 2.159448 GCATACTAATGGCGCACAACAA 60.159 45.455 10.83 0.00 33.38 2.83
2318 3519 3.425404 CATACTAATGGCGCACAACAAC 58.575 45.455 10.83 0.00 0.00 3.32
2319 3520 1.313772 ACTAATGGCGCACAACAACA 58.686 45.000 10.83 0.00 0.00 3.33
2320 3521 1.266718 ACTAATGGCGCACAACAACAG 59.733 47.619 10.83 2.09 0.00 3.16
2321 3522 0.595588 TAATGGCGCACAACAACAGG 59.404 50.000 10.83 0.00 0.00 4.00
2322 3523 1.106351 AATGGCGCACAACAACAGGA 61.106 50.000 10.83 0.00 0.00 3.86
2323 3524 0.895100 ATGGCGCACAACAACAGGAT 60.895 50.000 10.83 0.00 0.00 3.24
2324 3525 1.081242 GGCGCACAACAACAGGATG 60.081 57.895 10.83 0.00 46.00 3.51
2325 3526 1.730547 GCGCACAACAACAGGATGC 60.731 57.895 0.30 0.00 42.53 3.91
2326 3527 4.539152 GCACAACAACAGGATGCG 57.461 55.556 0.00 0.00 42.53 4.73
2327 3528 1.730547 GCACAACAACAGGATGCGC 60.731 57.895 0.00 0.00 42.53 6.09
2328 3529 1.081242 CACAACAACAGGATGCGCC 60.081 57.895 4.18 0.00 42.53 6.53
2329 3530 1.528076 ACAACAACAGGATGCGCCA 60.528 52.632 4.18 0.00 42.53 5.69
2330 3531 0.895100 ACAACAACAGGATGCGCCAT 60.895 50.000 4.18 0.00 42.53 4.40
2331 3532 0.244450 CAACAACAGGATGCGCCATT 59.756 50.000 4.18 0.00 42.53 3.16
2332 3533 1.472082 CAACAACAGGATGCGCCATTA 59.528 47.619 4.18 0.00 42.53 1.90
2333 3534 1.382522 ACAACAGGATGCGCCATTAG 58.617 50.000 4.18 0.00 42.53 1.73
2334 3535 1.340017 ACAACAGGATGCGCCATTAGT 60.340 47.619 4.18 0.00 42.53 2.24
2335 3536 2.093181 ACAACAGGATGCGCCATTAGTA 60.093 45.455 4.18 0.00 42.53 1.82
2336 3537 2.942376 CAACAGGATGCGCCATTAGTAA 59.058 45.455 4.18 0.00 42.53 2.24
2337 3538 2.561569 ACAGGATGCGCCATTAGTAAC 58.438 47.619 4.18 0.00 42.53 2.50
2338 3539 2.170607 ACAGGATGCGCCATTAGTAACT 59.829 45.455 4.18 0.00 42.53 2.24
2339 3540 3.206150 CAGGATGCGCCATTAGTAACTT 58.794 45.455 4.18 0.00 40.02 2.66
2340 3541 3.248602 CAGGATGCGCCATTAGTAACTTC 59.751 47.826 4.18 0.00 40.02 3.01
2341 3542 2.221055 GGATGCGCCATTAGTAACTTCG 59.779 50.000 4.18 0.00 36.34 3.79
2342 3543 1.647346 TGCGCCATTAGTAACTTCGG 58.353 50.000 4.18 0.00 0.00 4.30
2343 3544 0.303796 GCGCCATTAGTAACTTCGGC 59.696 55.000 0.00 0.00 36.16 5.54
2344 3545 1.647346 CGCCATTAGTAACTTCGGCA 58.353 50.000 12.43 0.00 39.56 5.69
2345 3546 2.210116 CGCCATTAGTAACTTCGGCAT 58.790 47.619 12.43 0.00 39.56 4.40
2346 3547 3.386486 CGCCATTAGTAACTTCGGCATA 58.614 45.455 12.43 0.00 39.56 3.14
2347 3548 3.183775 CGCCATTAGTAACTTCGGCATAC 59.816 47.826 12.43 0.00 39.56 2.39
2348 3549 4.377897 GCCATTAGTAACTTCGGCATACT 58.622 43.478 8.76 0.00 39.38 2.12
2349 3550 5.535333 GCCATTAGTAACTTCGGCATACTA 58.465 41.667 8.76 0.00 39.38 1.82
2350 3551 5.987347 GCCATTAGTAACTTCGGCATACTAA 59.013 40.000 6.98 6.98 42.85 2.24
2351 3552 6.649557 GCCATTAGTAACTTCGGCATACTAAT 59.350 38.462 10.20 10.20 46.23 1.73
2352 3553 7.172703 GCCATTAGTAACTTCGGCATACTAATT 59.827 37.037 12.38 0.00 44.45 1.40
2353 3554 9.052759 CCATTAGTAACTTCGGCATACTAATTT 57.947 33.333 12.38 0.00 44.45 1.82
2496 3697 8.792830 TTTTTCTTAATCTCTGGTCACTATGG 57.207 34.615 0.00 0.00 0.00 2.74
2585 3806 2.043115 TCACCCATCCTCACACTACTCT 59.957 50.000 0.00 0.00 0.00 3.24
2591 3812 1.639108 TCCTCACACTACTCTAGCCCA 59.361 52.381 0.00 0.00 0.00 5.36
2659 3880 7.584108 TCACTTAACAGCAACTTGTTGATATG 58.416 34.615 16.57 12.85 41.18 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 1.453155 GGATCAATGCCACGAGTTGT 58.547 50.000 0.00 0.00 0.00 3.32
66 67 3.028969 GCAGGAGCGGATCAATGC 58.971 61.111 6.88 6.88 35.71 3.56
307 367 1.097547 AGCGCAATTGATCGGAAGGG 61.098 55.000 11.47 0.00 0.00 3.95
308 368 0.305922 GAGCGCAATTGATCGGAAGG 59.694 55.000 11.47 0.00 0.00 3.46
309 369 0.042708 CGAGCGCAATTGATCGGAAG 60.043 55.000 11.47 0.00 0.00 3.46
310 370 2.005995 CGAGCGCAATTGATCGGAA 58.994 52.632 11.47 0.00 0.00 4.30
311 371 2.525248 GCGAGCGCAATTGATCGGA 61.525 57.895 21.72 0.00 41.49 4.55
312 372 2.052766 GCGAGCGCAATTGATCGG 60.053 61.111 21.72 6.21 41.49 4.18
313 373 2.052766 GGCGAGCGCAATTGATCG 60.053 61.111 17.16 15.46 44.11 3.69
314 374 2.329339 GGGCGAGCGCAATTGATC 59.671 61.111 17.16 2.70 44.11 2.92
315 375 3.576356 CGGGCGAGCGCAATTGAT 61.576 61.111 17.16 0.00 44.11 2.57
333 393 3.607661 GATCGGTCGGGAGAGGCC 61.608 72.222 0.00 0.00 41.26 5.19
334 394 3.967335 CGATCGGTCGGGAGAGGC 61.967 72.222 11.03 0.00 44.00 4.70
345 405 4.505217 GTGCAAGTGCGCGATCGG 62.505 66.667 18.30 8.23 45.83 4.18
357 417 1.301716 GAGCGAACCAGGAGTGCAA 60.302 57.895 0.00 0.00 0.00 4.08
607 1801 2.835156 TGGTACCATCAAAGATCACCGA 59.165 45.455 11.60 0.00 0.00 4.69
627 1821 3.569701 AGCCAGTGAACTTGGTGTAATTG 59.430 43.478 0.00 0.00 0.00 2.32
740 1934 1.076923 AGTGGAGTCGGCGGAGTAT 60.077 57.895 7.21 0.00 0.00 2.12
969 2163 4.184629 CAATAGGAAGACCCAGAAACTCG 58.815 47.826 0.00 0.00 37.41 4.18
1008 2202 2.923655 CTCATAGCGCTGACGAAGAAAA 59.076 45.455 22.90 0.00 43.93 2.29
1010 2204 1.799181 GCTCATAGCGCTGACGAAGAA 60.799 52.381 22.90 0.00 43.93 2.52
1771 2967 1.762957 ACCAGATACTAATGGCGCACT 59.237 47.619 10.83 0.00 40.45 4.40
2086 3287 9.412460 TGAAATTAAGCATATTGACCTGAGATT 57.588 29.630 0.00 0.00 0.00 2.40
2087 3288 8.985315 TGAAATTAAGCATATTGACCTGAGAT 57.015 30.769 0.00 0.00 0.00 2.75
2089 3290 8.680903 ACTTGAAATTAAGCATATTGACCTGAG 58.319 33.333 0.00 0.00 0.00 3.35
2090 3291 8.579850 ACTTGAAATTAAGCATATTGACCTGA 57.420 30.769 0.00 0.00 0.00 3.86
2091 3292 8.461222 TGACTTGAAATTAAGCATATTGACCTG 58.539 33.333 0.00 0.00 0.00 4.00
2092 3293 8.579850 TGACTTGAAATTAAGCATATTGACCT 57.420 30.769 0.00 0.00 0.00 3.85
2093 3294 9.638239 TTTGACTTGAAATTAAGCATATTGACC 57.362 29.630 0.00 0.00 0.00 4.02
2097 3298 9.023967 GCGATTTGACTTGAAATTAAGCATATT 57.976 29.630 0.00 0.00 0.00 1.28
2098 3299 8.190122 TGCGATTTGACTTGAAATTAAGCATAT 58.810 29.630 0.00 0.00 31.59 1.78
2099 3300 7.484641 GTGCGATTTGACTTGAAATTAAGCATA 59.515 33.333 0.00 0.00 35.27 3.14
2100 3301 6.308766 GTGCGATTTGACTTGAAATTAAGCAT 59.691 34.615 0.00 0.00 35.27 3.79
2101 3302 5.629020 GTGCGATTTGACTTGAAATTAAGCA 59.371 36.000 0.00 0.00 32.84 3.91
2102 3303 5.858581 AGTGCGATTTGACTTGAAATTAAGC 59.141 36.000 0.00 0.00 0.00 3.09
2103 3304 8.948853 TTAGTGCGATTTGACTTGAAATTAAG 57.051 30.769 0.00 0.00 0.00 1.85
2104 3305 8.564574 ACTTAGTGCGATTTGACTTGAAATTAA 58.435 29.630 0.00 0.00 0.00 1.40
2105 3306 8.015087 CACTTAGTGCGATTTGACTTGAAATTA 58.985 33.333 0.00 0.00 0.00 1.40
2106 3307 6.857964 CACTTAGTGCGATTTGACTTGAAATT 59.142 34.615 0.00 0.00 0.00 1.82
2107 3308 6.373779 CACTTAGTGCGATTTGACTTGAAAT 58.626 36.000 0.00 0.00 0.00 2.17
2108 3309 5.277779 CCACTTAGTGCGATTTGACTTGAAA 60.278 40.000 6.88 0.00 31.34 2.69
2109 3310 4.213270 CCACTTAGTGCGATTTGACTTGAA 59.787 41.667 6.88 0.00 31.34 2.69
2110 3311 3.745975 CCACTTAGTGCGATTTGACTTGA 59.254 43.478 6.88 0.00 31.34 3.02
2111 3312 3.498397 ACCACTTAGTGCGATTTGACTTG 59.502 43.478 6.88 0.00 31.34 3.16
2112 3313 3.498397 CACCACTTAGTGCGATTTGACTT 59.502 43.478 6.88 0.00 31.34 3.01
2113 3314 3.067106 CACCACTTAGTGCGATTTGACT 58.933 45.455 6.88 0.00 31.34 3.41
2114 3315 3.455619 CACCACTTAGTGCGATTTGAC 57.544 47.619 6.88 0.00 31.34 3.18
2137 3338 1.603802 CTAATGGCGTGGCACTAATGG 59.396 52.381 16.72 0.12 0.00 3.16
2138 3339 2.288666 ACTAATGGCGTGGCACTAATG 58.711 47.619 16.72 0.53 0.00 1.90
2139 3340 2.710096 ACTAATGGCGTGGCACTAAT 57.290 45.000 16.72 3.44 0.00 1.73
2140 3341 3.830744 ATACTAATGGCGTGGCACTAA 57.169 42.857 16.72 0.89 0.00 2.24
2141 3342 5.477607 AATATACTAATGGCGTGGCACTA 57.522 39.130 16.72 2.20 0.00 2.74
2142 3343 4.351874 AATATACTAATGGCGTGGCACT 57.648 40.909 16.72 0.00 0.00 4.40
2143 3344 5.432885 AAAATATACTAATGGCGTGGCAC 57.567 39.130 7.79 7.79 0.00 5.01
2144 3345 6.292923 AGTAAAATATACTAATGGCGTGGCA 58.707 36.000 0.00 0.00 0.00 4.92
2145 3346 6.796705 AGTAAAATATACTAATGGCGTGGC 57.203 37.500 0.00 0.00 0.00 5.01
2153 3354 8.943002 GGTGCGCCATTAGTAAAATATACTAAT 58.057 33.333 12.58 12.73 46.06 1.73
2154 3355 7.932491 TGGTGCGCCATTAGTAAAATATACTAA 59.068 33.333 16.89 9.72 42.18 2.24
2155 3356 7.443477 TGGTGCGCCATTAGTAAAATATACTA 58.557 34.615 16.89 0.00 40.46 1.82
2156 3357 6.292923 TGGTGCGCCATTAGTAAAATATACT 58.707 36.000 16.89 0.00 40.46 2.12
2157 3358 6.548441 TGGTGCGCCATTAGTAAAATATAC 57.452 37.500 16.89 0.00 40.46 1.47
2177 3378 0.902531 ACTAATGGCGCACTAGTGGT 59.097 50.000 23.95 8.05 0.00 4.16
2178 3379 2.882927 TACTAATGGCGCACTAGTGG 57.117 50.000 23.95 14.74 0.00 4.00
2179 3380 3.983988 CAGATACTAATGGCGCACTAGTG 59.016 47.826 18.93 18.93 0.00 2.74
2180 3381 3.005897 CCAGATACTAATGGCGCACTAGT 59.994 47.826 10.83 14.49 0.00 2.57
2181 3382 3.005897 ACCAGATACTAATGGCGCACTAG 59.994 47.826 10.83 8.92 40.45 2.57
2182 3383 2.963101 ACCAGATACTAATGGCGCACTA 59.037 45.455 10.83 0.00 40.45 2.74
2183 3384 1.762957 ACCAGATACTAATGGCGCACT 59.237 47.619 10.83 0.00 40.45 4.40
2184 3385 2.240493 ACCAGATACTAATGGCGCAC 57.760 50.000 10.83 0.00 40.45 5.34
2185 3386 4.770531 AGTATACCAGATACTAATGGCGCA 59.229 41.667 10.83 0.00 40.45 6.09
2186 3387 5.326200 AGTATACCAGATACTAATGGCGC 57.674 43.478 0.00 0.00 40.45 6.53
2192 3393 8.509690 GTGCGTCATTAGTATACCAGATACTAA 58.490 37.037 15.81 15.81 45.52 2.24
2193 3394 7.120285 GGTGCGTCATTAGTATACCAGATACTA 59.880 40.741 0.00 1.20 36.38 1.82
2194 3395 6.072064 GGTGCGTCATTAGTATACCAGATACT 60.072 42.308 0.00 2.98 38.32 2.12
2195 3396 6.091437 GGTGCGTCATTAGTATACCAGATAC 58.909 44.000 0.00 0.00 0.00 2.24
2196 3397 5.184479 GGGTGCGTCATTAGTATACCAGATA 59.816 44.000 0.00 0.00 0.00 1.98
2197 3398 4.021368 GGGTGCGTCATTAGTATACCAGAT 60.021 45.833 0.00 0.00 0.00 2.90
2198 3399 3.319972 GGGTGCGTCATTAGTATACCAGA 59.680 47.826 0.00 0.00 0.00 3.86
2199 3400 3.554337 GGGGTGCGTCATTAGTATACCAG 60.554 52.174 0.00 0.00 0.00 4.00
2200 3401 2.366266 GGGGTGCGTCATTAGTATACCA 59.634 50.000 0.00 0.00 0.00 3.25
2201 3402 2.366266 TGGGGTGCGTCATTAGTATACC 59.634 50.000 0.00 0.00 0.00 2.73
2202 3403 3.319972 TCTGGGGTGCGTCATTAGTATAC 59.680 47.826 0.00 0.00 0.00 1.47
2203 3404 3.568443 TCTGGGGTGCGTCATTAGTATA 58.432 45.455 0.00 0.00 0.00 1.47
2204 3405 2.394632 TCTGGGGTGCGTCATTAGTAT 58.605 47.619 0.00 0.00 0.00 2.12
2205 3406 1.855295 TCTGGGGTGCGTCATTAGTA 58.145 50.000 0.00 0.00 0.00 1.82
2206 3407 1.134401 CATCTGGGGTGCGTCATTAGT 60.134 52.381 0.00 0.00 0.00 2.24
2207 3408 1.586422 CATCTGGGGTGCGTCATTAG 58.414 55.000 0.00 0.00 0.00 1.73
2208 3409 0.463654 GCATCTGGGGTGCGTCATTA 60.464 55.000 0.00 0.00 32.29 1.90
2209 3410 1.750399 GCATCTGGGGTGCGTCATT 60.750 57.895 0.00 0.00 32.29 2.57
2210 3411 2.124570 GCATCTGGGGTGCGTCAT 60.125 61.111 0.00 0.00 32.29 3.06
2216 3417 1.152984 TAATGGCGCATCTGGGGTG 60.153 57.895 10.83 0.00 0.00 4.61
2217 3418 1.149174 CTAATGGCGCATCTGGGGT 59.851 57.895 10.83 0.00 0.00 4.95
2218 3419 0.396435 TACTAATGGCGCATCTGGGG 59.604 55.000 10.83 0.00 0.00 4.96
2219 3420 2.479566 ATACTAATGGCGCATCTGGG 57.520 50.000 10.83 0.00 0.00 4.45
2220 3421 5.660460 TGTATATACTAATGGCGCATCTGG 58.340 41.667 10.83 0.00 0.00 3.86
2221 3422 6.589907 TGTTGTATATACTAATGGCGCATCTG 59.410 38.462 10.83 0.00 0.00 2.90
2222 3423 6.697395 TGTTGTATATACTAATGGCGCATCT 58.303 36.000 10.83 0.00 0.00 2.90
2223 3424 6.590292 ACTGTTGTATATACTAATGGCGCATC 59.410 38.462 10.83 0.00 0.00 3.91
2224 3425 6.368791 CACTGTTGTATATACTAATGGCGCAT 59.631 38.462 10.83 0.00 0.00 4.73
2225 3426 5.694458 CACTGTTGTATATACTAATGGCGCA 59.306 40.000 10.83 0.00 0.00 6.09
2226 3427 5.389516 GCACTGTTGTATATACTAATGGCGC 60.390 44.000 13.89 0.00 0.00 6.53
2227 3428 5.164090 CGCACTGTTGTATATACTAATGGCG 60.164 44.000 13.89 15.85 0.00 5.69
2228 3429 5.389516 GCGCACTGTTGTATATACTAATGGC 60.390 44.000 13.89 9.36 0.00 4.40
2229 3430 5.120208 GGCGCACTGTTGTATATACTAATGG 59.880 44.000 10.83 3.48 0.00 3.16
2230 3431 5.694458 TGGCGCACTGTTGTATATACTAATG 59.306 40.000 10.83 7.13 0.00 1.90
2231 3432 5.849510 TGGCGCACTGTTGTATATACTAAT 58.150 37.500 10.83 0.00 0.00 1.73
2232 3433 5.265350 TGGCGCACTGTTGTATATACTAA 57.735 39.130 10.83 4.42 0.00 2.24
2233 3434 4.922471 TGGCGCACTGTTGTATATACTA 57.078 40.909 10.83 3.68 0.00 1.82
2234 3435 3.812156 TGGCGCACTGTTGTATATACT 57.188 42.857 10.83 0.00 0.00 2.12
2235 3436 5.694910 ACTAATGGCGCACTGTTGTATATAC 59.305 40.000 10.83 5.89 0.00 1.47
2236 3437 5.849510 ACTAATGGCGCACTGTTGTATATA 58.150 37.500 10.83 0.00 0.00 0.86
2237 3438 4.703897 ACTAATGGCGCACTGTTGTATAT 58.296 39.130 10.83 0.00 0.00 0.86
2238 3439 4.131649 ACTAATGGCGCACTGTTGTATA 57.868 40.909 10.83 0.00 0.00 1.47
2239 3440 2.985896 ACTAATGGCGCACTGTTGTAT 58.014 42.857 10.83 0.00 0.00 2.29
2240 3441 2.465860 ACTAATGGCGCACTGTTGTA 57.534 45.000 10.83 0.00 0.00 2.41
2241 3442 2.465860 TACTAATGGCGCACTGTTGT 57.534 45.000 10.83 2.95 0.00 3.32
2242 3443 2.539547 GCATACTAATGGCGCACTGTTG 60.540 50.000 10.83 0.00 33.38 3.33
2243 3444 1.670811 GCATACTAATGGCGCACTGTT 59.329 47.619 10.83 0.00 33.38 3.16
2244 3445 1.299541 GCATACTAATGGCGCACTGT 58.700 50.000 10.83 2.73 33.38 3.55
2252 3453 1.352352 CCCTGGGAGGCATACTAATGG 59.648 57.143 7.01 0.00 32.73 3.16
2253 3454 1.352352 CCCCTGGGAGGCATACTAATG 59.648 57.143 16.20 0.00 37.50 1.90
2254 3455 1.747444 CCCCTGGGAGGCATACTAAT 58.253 55.000 16.20 0.00 37.50 1.73
2255 3456 3.257627 CCCCTGGGAGGCATACTAA 57.742 57.895 16.20 0.00 37.50 2.24
2263 3464 0.119155 TATAGATGGCCCCTGGGAGG 59.881 60.000 16.20 0.00 37.50 4.30
2264 3465 1.280457 GTATAGATGGCCCCTGGGAG 58.720 60.000 16.20 5.50 37.50 4.30
2265 3466 0.178873 GGTATAGATGGCCCCTGGGA 60.179 60.000 16.20 0.00 37.50 4.37
2266 3467 1.208165 GGGTATAGATGGCCCCTGGG 61.208 65.000 5.50 5.50 36.46 4.45
2267 3468 0.475632 TGGGTATAGATGGCCCCTGG 60.476 60.000 0.00 0.00 41.66 4.45
2268 3469 0.987294 CTGGGTATAGATGGCCCCTG 59.013 60.000 0.00 0.00 41.66 4.45
2269 3470 0.178861 CCTGGGTATAGATGGCCCCT 60.179 60.000 0.00 0.00 41.66 4.79
2270 3471 0.475828 ACCTGGGTATAGATGGCCCC 60.476 60.000 0.00 0.00 41.66 5.80
2271 3472 0.693049 CACCTGGGTATAGATGGCCC 59.307 60.000 0.00 0.00 42.64 5.80
2272 3473 0.036875 GCACCTGGGTATAGATGGCC 59.963 60.000 0.00 0.00 0.00 5.36
2273 3474 1.059913 AGCACCTGGGTATAGATGGC 58.940 55.000 0.00 0.00 0.00 4.40
2274 3475 3.480470 CAAAGCACCTGGGTATAGATGG 58.520 50.000 0.00 0.00 0.00 3.51
2275 3476 3.480470 CCAAAGCACCTGGGTATAGATG 58.520 50.000 0.00 0.00 0.00 2.90
2276 3477 2.158608 GCCAAAGCACCTGGGTATAGAT 60.159 50.000 0.00 0.00 39.53 1.98
2277 3478 1.211949 GCCAAAGCACCTGGGTATAGA 59.788 52.381 0.00 0.00 39.53 1.98
2278 3479 1.064758 TGCCAAAGCACCTGGGTATAG 60.065 52.381 0.00 0.00 46.52 1.31
2279 3480 0.995803 TGCCAAAGCACCTGGGTATA 59.004 50.000 0.00 0.00 46.52 1.47
2280 3481 1.773635 TGCCAAAGCACCTGGGTAT 59.226 52.632 0.00 0.00 46.52 2.73
2281 3482 3.256082 TGCCAAAGCACCTGGGTA 58.744 55.556 0.00 0.00 46.52 3.69
2290 3491 1.600413 GCGCCATTAGTATGCCAAAGC 60.600 52.381 0.00 0.00 40.48 3.51
2291 3492 1.675483 TGCGCCATTAGTATGCCAAAG 59.325 47.619 4.18 0.00 0.00 2.77
2292 3493 1.403679 GTGCGCCATTAGTATGCCAAA 59.596 47.619 4.18 0.00 0.00 3.28
2293 3494 1.021202 GTGCGCCATTAGTATGCCAA 58.979 50.000 4.18 0.00 0.00 4.52
2294 3495 0.107459 TGTGCGCCATTAGTATGCCA 60.107 50.000 4.18 0.00 0.00 4.92
2295 3496 1.021202 TTGTGCGCCATTAGTATGCC 58.979 50.000 4.18 0.00 0.00 4.40
2296 3497 1.400142 TGTTGTGCGCCATTAGTATGC 59.600 47.619 4.18 0.00 0.00 3.14
2297 3498 3.120025 TGTTGTTGTGCGCCATTAGTATG 60.120 43.478 4.18 0.00 0.00 2.39
2298 3499 3.078097 TGTTGTTGTGCGCCATTAGTAT 58.922 40.909 4.18 0.00 0.00 2.12
2299 3500 2.482336 CTGTTGTTGTGCGCCATTAGTA 59.518 45.455 4.18 0.00 0.00 1.82
2300 3501 1.266718 CTGTTGTTGTGCGCCATTAGT 59.733 47.619 4.18 0.00 0.00 2.24
2301 3502 1.401409 CCTGTTGTTGTGCGCCATTAG 60.401 52.381 4.18 0.00 0.00 1.73
2302 3503 0.595588 CCTGTTGTTGTGCGCCATTA 59.404 50.000 4.18 0.00 0.00 1.90
2303 3504 1.106351 TCCTGTTGTTGTGCGCCATT 61.106 50.000 4.18 0.00 0.00 3.16
2304 3505 0.895100 ATCCTGTTGTTGTGCGCCAT 60.895 50.000 4.18 0.00 0.00 4.40
2305 3506 1.528076 ATCCTGTTGTTGTGCGCCA 60.528 52.632 4.18 0.00 0.00 5.69
2306 3507 1.081242 CATCCTGTTGTTGTGCGCC 60.081 57.895 4.18 0.00 0.00 6.53
2307 3508 1.730547 GCATCCTGTTGTTGTGCGC 60.731 57.895 0.00 0.00 0.00 6.09
2308 3509 4.539152 GCATCCTGTTGTTGTGCG 57.461 55.556 0.00 0.00 0.00 5.34
2309 3510 1.730547 GCGCATCCTGTTGTTGTGC 60.731 57.895 0.30 0.00 41.44 4.57
2310 3511 1.081242 GGCGCATCCTGTTGTTGTG 60.081 57.895 10.83 0.00 0.00 3.33
2311 3512 0.895100 ATGGCGCATCCTGTTGTTGT 60.895 50.000 10.83 0.00 35.26 3.32
2312 3513 0.244450 AATGGCGCATCCTGTTGTTG 59.756 50.000 10.83 0.00 35.26 3.33
2313 3514 1.745087 CTAATGGCGCATCCTGTTGTT 59.255 47.619 10.83 0.00 35.26 2.83
2314 3515 1.340017 ACTAATGGCGCATCCTGTTGT 60.340 47.619 10.83 0.00 35.26 3.32
2315 3516 1.382522 ACTAATGGCGCATCCTGTTG 58.617 50.000 10.83 0.00 35.26 3.33
2316 3517 2.943033 GTTACTAATGGCGCATCCTGTT 59.057 45.455 10.83 0.00 35.26 3.16
2317 3518 2.170607 AGTTACTAATGGCGCATCCTGT 59.829 45.455 10.83 4.70 35.26 4.00
2318 3519 2.838736 AGTTACTAATGGCGCATCCTG 58.161 47.619 10.83 0.00 35.26 3.86
2319 3520 3.467803 GAAGTTACTAATGGCGCATCCT 58.532 45.455 10.83 0.00 35.26 3.24
2320 3521 2.221055 CGAAGTTACTAATGGCGCATCC 59.779 50.000 10.83 0.00 0.00 3.51
2321 3522 2.221055 CCGAAGTTACTAATGGCGCATC 59.779 50.000 10.83 0.00 0.00 3.91
2322 3523 2.210116 CCGAAGTTACTAATGGCGCAT 58.790 47.619 10.83 0.00 0.00 4.73
2323 3524 1.647346 CCGAAGTTACTAATGGCGCA 58.353 50.000 10.83 0.00 0.00 6.09
2324 3525 0.303796 GCCGAAGTTACTAATGGCGC 59.696 55.000 0.00 0.00 32.14 6.53
2325 3526 1.647346 TGCCGAAGTTACTAATGGCG 58.353 50.000 14.62 2.53 45.34 5.69
2326 3527 4.377897 AGTATGCCGAAGTTACTAATGGC 58.622 43.478 13.29 13.29 42.76 4.40
2327 3528 8.603242 AATTAGTATGCCGAAGTTACTAATGG 57.397 34.615 12.72 0.00 43.35 3.16
2471 3672 7.336931 GCCATAGTGACCAGAGATTAAGAAAAA 59.663 37.037 0.00 0.00 0.00 1.94
2472 3673 6.823689 GCCATAGTGACCAGAGATTAAGAAAA 59.176 38.462 0.00 0.00 0.00 2.29
2473 3674 6.156949 AGCCATAGTGACCAGAGATTAAGAAA 59.843 38.462 0.00 0.00 0.00 2.52
2474 3675 5.663106 AGCCATAGTGACCAGAGATTAAGAA 59.337 40.000 0.00 0.00 0.00 2.52
2475 3676 5.211973 AGCCATAGTGACCAGAGATTAAGA 58.788 41.667 0.00 0.00 0.00 2.10
2476 3677 5.543507 AGCCATAGTGACCAGAGATTAAG 57.456 43.478 0.00 0.00 0.00 1.85
2477 3678 5.957771 AAGCCATAGTGACCAGAGATTAA 57.042 39.130 0.00 0.00 0.00 1.40
2478 3679 7.510685 AGATTAAGCCATAGTGACCAGAGATTA 59.489 37.037 0.00 0.00 0.00 1.75
2479 3680 5.957771 TTAAGCCATAGTGACCAGAGATT 57.042 39.130 0.00 0.00 0.00 2.40
2480 3681 5.843421 AGATTAAGCCATAGTGACCAGAGAT 59.157 40.000 0.00 0.00 0.00 2.75
2481 3682 5.211973 AGATTAAGCCATAGTGACCAGAGA 58.788 41.667 0.00 0.00 0.00 3.10
2482 3683 5.069648 TGAGATTAAGCCATAGTGACCAGAG 59.930 44.000 0.00 0.00 0.00 3.35
2483 3684 4.962362 TGAGATTAAGCCATAGTGACCAGA 59.038 41.667 0.00 0.00 0.00 3.86
2484 3685 5.282055 TGAGATTAAGCCATAGTGACCAG 57.718 43.478 0.00 0.00 0.00 4.00
2485 3686 4.101585 CCTGAGATTAAGCCATAGTGACCA 59.898 45.833 0.00 0.00 0.00 4.02
2486 3687 4.101741 ACCTGAGATTAAGCCATAGTGACC 59.898 45.833 0.00 0.00 0.00 4.02
2487 3688 5.163405 TGACCTGAGATTAAGCCATAGTGAC 60.163 44.000 0.00 0.00 0.00 3.67
2488 3689 4.962362 TGACCTGAGATTAAGCCATAGTGA 59.038 41.667 0.00 0.00 0.00 3.41
2489 3690 5.282055 TGACCTGAGATTAAGCCATAGTG 57.718 43.478 0.00 0.00 0.00 2.74
2490 3691 5.957771 TTGACCTGAGATTAAGCCATAGT 57.042 39.130 0.00 0.00 0.00 2.12
2491 3692 7.065563 GCATATTGACCTGAGATTAAGCCATAG 59.934 40.741 0.00 0.00 0.00 2.23
2492 3693 6.881065 GCATATTGACCTGAGATTAAGCCATA 59.119 38.462 0.00 0.00 0.00 2.74
2493 3694 5.709164 GCATATTGACCTGAGATTAAGCCAT 59.291 40.000 0.00 0.00 0.00 4.40
2494 3695 5.065914 GCATATTGACCTGAGATTAAGCCA 58.934 41.667 0.00 0.00 0.00 4.75
2495 3696 5.312079 AGCATATTGACCTGAGATTAAGCC 58.688 41.667 0.00 0.00 0.00 4.35
2496 3697 6.874288 AAGCATATTGACCTGAGATTAAGC 57.126 37.500 0.00 0.00 0.00 3.09
2585 3806 0.323629 AGTTAAGCGTGCTTGGGCTA 59.676 50.000 16.98 0.00 38.88 3.93


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

AutoCloner maintained by Alex Coulton.