Multiple sequence alignment - TraesCS2D01G061900

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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 TraesCS2D01G061900 chr2D 100.000 3243 0 0 1 3243 26036562 26033320 0.000000e+00 5989.0
1 TraesCS2D01G061900 chr2D 89.016 1220 101 12 1120 2328 26469781 26468584 0.000000e+00 1480.0
2 TraesCS2D01G061900 chr2D 86.503 652 57 14 2522 3144 26468533 26467884 0.000000e+00 688.0
3 TraesCS2D01G061900 chr2D 78.462 585 72 26 2687 3243 25654592 25655150 1.860000e-87 333.0
4 TraesCS2D01G061900 chr2D 89.121 239 20 3 907 1140 26470040 26469803 3.160000e-75 292.0
5 TraesCS2D01G061900 chr2D 90.777 206 18 1 408 613 26326951 26327155 1.150000e-69 274.0
6 TraesCS2D01G061900 chr2D 92.857 182 9 2 2183 2360 26034205 26034024 8.920000e-66 261.0
7 TraesCS2D01G061900 chr2D 92.857 182 9 2 2358 2539 26034380 26034203 8.920000e-66 261.0
8 TraesCS2D01G061900 chr2D 88.235 187 14 3 2615 2801 25748057 25747879 1.960000e-52 217.0
9 TraesCS2D01G061900 chr2D 92.466 146 11 0 2358 2503 26468729 26468584 3.280000e-50 209.0
10 TraesCS2D01G061900 chr2B 95.292 2039 75 12 987 3014 41604754 41606782 0.000000e+00 3214.0
11 TraesCS2D01G061900 chr2B 86.479 1494 116 26 907 2328 41417104 41418583 0.000000e+00 1561.0
12 TraesCS2D01G061900 chr2B 92.051 629 38 3 328 950 41604135 41604757 0.000000e+00 874.0
13 TraesCS2D01G061900 chr2B 87.097 651 50 5 2522 3143 41418634 41419279 0.000000e+00 706.0
14 TraesCS2D01G061900 chr2B 93.189 323 19 2 10 332 41598471 41598790 3.790000e-129 472.0
15 TraesCS2D01G061900 chr2B 91.176 238 17 2 860 1096 765917949 765917715 1.450000e-83 320.0
16 TraesCS2D01G061900 chr2B 93.407 182 8 1 2358 2539 41605949 41606126 1.920000e-67 267.0
17 TraesCS2D01G061900 chr2B 92.135 178 14 0 2183 2360 41606124 41606301 5.370000e-63 252.0
18 TraesCS2D01G061900 chr2B 92.466 146 11 0 2358 2503 41418438 41418583 3.280000e-50 209.0
19 TraesCS2D01G061900 chr2B 76.804 388 71 13 1378 1753 41540934 41541314 1.970000e-47 200.0
20 TraesCS2D01G061900 chr2B 74.771 436 62 20 2695 3097 41439579 41439999 5.600000e-33 152.0
21 TraesCS2D01G061900 chr2B 90.625 96 6 2 3093 3185 41607722 41607817 1.220000e-24 124.0
22 TraesCS2D01G061900 chr2B 87.379 103 13 0 3138 3240 41542763 41542865 5.680000e-23 119.0
23 TraesCS2D01G061900 chr2B 84.694 98 12 1 2704 2801 41152333 41152239 9.580000e-16 95.3
24 TraesCS2D01G061900 chr2B 97.674 43 1 0 3201 3243 41607793 41607835 1.250000e-09 75.0
25 TraesCS2D01G061900 chr2A 91.112 1744 120 21 606 2320 28212861 28211124 0.000000e+00 2329.0
26 TraesCS2D01G061900 chr2A 89.779 1223 103 12 1120 2328 28692980 28691766 0.000000e+00 1546.0
27 TraesCS2D01G061900 chr2A 93.148 540 30 3 1 536 28213395 28212859 0.000000e+00 785.0
28 TraesCS2D01G061900 chr2A 87.065 603 45 7 2522 3095 28691715 28691117 0.000000e+00 651.0
29 TraesCS2D01G061900 chr2A 88.953 344 33 4 801 1140 28693340 28692998 1.390000e-113 420.0
30 TraesCS2D01G061900 chr2A 82.609 414 58 5 2733 3139 28209629 28209223 1.430000e-93 353.0
31 TraesCS2D01G061900 chr2A 92.568 148 9 2 2358 2503 28691913 28691766 9.120000e-51 211.0
32 TraesCS2D01G061900 chr2A 87.143 140 10 4 504 638 28693495 28693359 5.600000e-33 152.0
33 TraesCS2D01G061900 chr2A 84.956 113 11 4 3137 3243 28199670 28199558 3.420000e-20 110.0
34 TraesCS2D01G061900 chr2A 86.207 87 11 1 2109 2195 29334762 29334847 3.450000e-15 93.5
35 TraesCS2D01G061900 chr2A 86.207 87 11 1 2109 2195 29350888 29350973 3.450000e-15 93.5
36 TraesCS2D01G061900 chr2A 86.207 87 11 1 2109 2195 29363879 29363964 3.450000e-15 93.5
37 TraesCS2D01G061900 chrUn 90.612 245 22 1 860 1103 22492695 22492451 1.120000e-84 324.0
38 TraesCS2D01G061900 chrUn 87.895 190 23 0 408 597 389442074 389442263 1.170000e-54 224.0
39 TraesCS2D01G061900 chrUn 86.207 87 11 1 2109 2195 333543987 333543902 3.450000e-15 93.5
40 TraesCS2D01G061900 chr7D 85.259 251 28 7 408 651 29934720 29934968 1.930000e-62 250.0
41 TraesCS2D01G061900 chr4A 87.500 176 22 0 408 583 732311149 732311324 1.530000e-48 204.0
42 TraesCS2D01G061900 chr4A 84.184 196 28 2 972 1166 433732881 433733074 1.540000e-43 187.0
43 TraesCS2D01G061900 chr4A 85.556 180 22 3 972 1149 433711670 433711847 5.530000e-43 185.0
44 TraesCS2D01G061900 chr5B 90.780 141 13 0 408 548 672568219 672568079 4.270000e-44 189.0
45 TraesCS2D01G061900 chr7A 86.550 171 22 1 416 586 731059207 731059376 1.540000e-43 187.0
46 TraesCS2D01G061900 chr5A 79.310 174 24 11 1511 1679 435043415 435043249 9.510000e-21 111.0
47 TraesCS2D01G061900 chr1D 91.176 68 6 0 1982 2049 11887894 11887961 3.450000e-15 93.5


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 TraesCS2D01G061900 chr2D 26033320 26036562 3242 True 2170.333333 5989 95.238000 1 3243 3 chr2D.!!$R2 3242
1 TraesCS2D01G061900 chr2D 26467884 26470040 2156 True 667.250000 1480 89.276500 907 3144 4 chr2D.!!$R3 2237
2 TraesCS2D01G061900 chr2D 25654592 25655150 558 False 333.000000 333 78.462000 2687 3243 1 chr2D.!!$F1 556
3 TraesCS2D01G061900 chr2B 41417104 41419279 2175 False 825.333333 1561 88.680667 907 3143 3 chr2B.!!$F3 2236
4 TraesCS2D01G061900 chr2B 41604135 41607835 3700 False 801.000000 3214 93.530667 328 3243 6 chr2B.!!$F5 2915
5 TraesCS2D01G061900 chr2A 28209223 28213395 4172 True 1155.666667 2329 88.956333 1 3139 3 chr2A.!!$R2 3138
6 TraesCS2D01G061900 chr2A 28691117 28693495 2378 True 596.000000 1546 89.101600 504 3095 5 chr2A.!!$R3 2591

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
211 212 0.179166 ACAAGTGTTGCACAAGCGTG 60.179 50.0 0.0 0.0 46.23 5.34 F
325 326 0.249615 TCGGATGTGCTCAGCTATGC 60.250 55.0 0.0 0.0 0.00 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1403 1513 2.818432 CAGAGTGGAGCTGCAAGAAAAT 59.182 45.455 10.44 0.0 34.07 1.82 R
2247 2419 0.706433 ACCATTCACCAGGGCATCTT 59.294 50.000 0.00 0.0 0.00 2.40 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
114 115 1.133199 TGGGTGCCTCTTTCATGGTTT 60.133 47.619 0.00 0.00 0.00 3.27
115 116 1.970640 GGGTGCCTCTTTCATGGTTTT 59.029 47.619 0.00 0.00 0.00 2.43
149 150 6.545504 TCTTCCATGTTCTTTTCTTCTTCG 57.454 37.500 0.00 0.00 0.00 3.79
188 189 2.489722 GCTGTTCATCTTGGTTCCTTCC 59.510 50.000 0.00 0.00 0.00 3.46
206 207 0.453793 CCGGAACAAGTGTTGCACAA 59.546 50.000 14.82 0.00 45.06 3.33
209 210 1.191096 GAACAAGTGTTGCACAAGCG 58.809 50.000 0.42 0.00 46.23 4.68
210 211 0.525761 AACAAGTGTTGCACAAGCGT 59.474 45.000 0.00 0.00 46.23 5.07
211 212 0.179166 ACAAGTGTTGCACAAGCGTG 60.179 50.000 0.00 0.00 46.23 5.34
230 231 3.652274 GTGCGCCGGGTATTTTATAGTA 58.348 45.455 4.18 0.00 0.00 1.82
291 292 1.227645 TGTGTGCTCACCTCAGTGC 60.228 57.895 15.83 0.00 44.16 4.40
320 321 2.172372 CAGCTCGGATGTGCTCAGC 61.172 63.158 0.00 0.00 42.73 4.26
324 325 1.780806 CTCGGATGTGCTCAGCTATG 58.219 55.000 0.00 0.00 0.00 2.23
325 326 0.249615 TCGGATGTGCTCAGCTATGC 60.250 55.000 0.00 0.00 0.00 3.14
326 327 1.554891 CGGATGTGCTCAGCTATGCG 61.555 60.000 12.31 12.31 33.82 4.73
359 364 2.092538 CCATGAGGAACAGAGGAAGCAT 60.093 50.000 0.00 0.00 36.89 3.79
362 367 0.694771 AGGAACAGAGGAAGCATGCA 59.305 50.000 21.98 0.00 0.00 3.96
373 378 2.615912 GGAAGCATGCATAGAGACAACC 59.384 50.000 21.98 0.00 0.00 3.77
399 404 3.827898 GGCGAGGACGTGGGAGAG 61.828 72.222 0.00 0.00 41.98 3.20
446 451 1.300697 GGTCGACAACCTTGAGCGT 60.301 57.895 18.91 0.00 45.45 5.07
455 460 1.241990 ACCTTGAGCGTGTAGAGCGA 61.242 55.000 0.00 0.00 40.04 4.93
531 536 2.842462 ACGAGGTGGAGGTGTGCA 60.842 61.111 0.00 0.00 0.00 4.57
565 570 2.570284 TTGAAGGCTGACGGCGAGA 61.570 57.895 16.62 0.00 42.94 4.04
578 583 2.691522 CGAGATGCGTTCAGTGCG 59.308 61.111 0.00 0.00 34.64 5.34
626 640 4.373116 AGTGTCCGCGATTGCCGT 62.373 61.111 8.23 0.00 41.15 5.68
661 675 4.256920 CGGAAATGTCAGAGAAGAATGGT 58.743 43.478 0.00 0.00 0.00 3.55
763 777 2.039879 GGAGGAAGGGAGCAGTTGTTTA 59.960 50.000 0.00 0.00 0.00 2.01
905 919 7.117812 CCGGTTAATATAGTTCAAATGCGATCT 59.882 37.037 0.00 0.00 0.00 2.75
957 971 3.757745 ATTGAAACCATACGCCGAAAG 57.242 42.857 0.00 0.00 0.00 2.62
996 1011 7.740519 AACATAAATTCGTTATTCTTGCTGC 57.259 32.000 0.00 0.00 29.38 5.25
1111 1133 1.067142 TGCTAGTTTACTGCTGTCGGG 60.067 52.381 0.00 0.00 0.00 5.14
1131 1195 4.277423 CGGGACTTTGTTACACAAGGAAAT 59.723 41.667 5.81 0.00 39.53 2.17
1235 1337 5.833131 ACTTTTATGATGGACACCAACTTGT 59.167 36.000 0.00 0.00 36.95 3.16
1261 1363 2.358615 GCGGCACCAGTCACATCA 60.359 61.111 0.00 0.00 0.00 3.07
1334 1436 5.079689 TGTATGTGCTACGAAAGATCCAA 57.920 39.130 0.00 0.00 32.61 3.53
1386 1496 9.535878 CCATGGATTCTACTAGTTTAGACTTTC 57.464 37.037 5.56 0.00 37.33 2.62
1403 1513 3.071023 ACTTTCGAACCAGTGGATGAAGA 59.929 43.478 18.40 4.87 0.00 2.87
1570 1680 0.261696 AGGCTGGTTTTTGGGTGACT 59.738 50.000 0.00 0.00 0.00 3.41
1611 1742 9.750125 GTCATGTGTATATGTTCTCATGTAGAA 57.250 33.333 9.68 0.00 42.07 2.10
1722 1869 6.899089 TCCATCAATGTACTACATCCAATGT 58.101 36.000 2.05 0.00 46.92 2.71
1830 1977 2.852281 AAACGGGCCCCATTGGACT 61.852 57.895 18.66 0.00 44.39 3.85
1962 2127 6.686630 TCTTAAGGTTTATGTTTGGTGCATG 58.313 36.000 1.85 0.00 0.00 4.06
2073 2240 5.220605 GCGAAAATCATACACAGTAAGACCC 60.221 44.000 0.00 0.00 0.00 4.46
2227 2399 2.799562 CGAACGAATCATGAGGCTAGCA 60.800 50.000 18.24 0.00 0.00 3.49
2228 2400 2.522836 ACGAATCATGAGGCTAGCAG 57.477 50.000 18.24 0.50 0.00 4.24
2230 2402 2.133553 CGAATCATGAGGCTAGCAGTG 58.866 52.381 18.24 9.10 0.00 3.66
2231 2403 2.223900 CGAATCATGAGGCTAGCAGTGA 60.224 50.000 18.24 14.06 0.00 3.41
2232 2404 3.554544 CGAATCATGAGGCTAGCAGTGAT 60.555 47.826 18.24 15.60 0.00 3.06
2233 2405 4.387598 GAATCATGAGGCTAGCAGTGATT 58.612 43.478 23.91 23.91 38.56 2.57
2234 2406 3.189618 TCATGAGGCTAGCAGTGATTG 57.810 47.619 18.24 6.20 0.00 2.67
2235 2407 2.158856 TCATGAGGCTAGCAGTGATTGG 60.159 50.000 18.24 0.00 0.00 3.16
2236 2408 1.279496 TGAGGCTAGCAGTGATTGGT 58.721 50.000 18.24 0.00 41.25 3.67
2237 2409 2.466846 TGAGGCTAGCAGTGATTGGTA 58.533 47.619 18.24 0.00 38.70 3.25
2238 2410 2.837591 TGAGGCTAGCAGTGATTGGTAA 59.162 45.455 18.24 0.00 39.15 2.85
2239 2411 3.198872 GAGGCTAGCAGTGATTGGTAAC 58.801 50.000 18.24 0.00 39.15 2.50
2240 2412 2.840651 AGGCTAGCAGTGATTGGTAACT 59.159 45.455 18.24 0.00 39.15 2.24
2241 2413 2.939103 GGCTAGCAGTGATTGGTAACTG 59.061 50.000 18.24 0.00 45.37 3.16
2242 2414 3.369471 GGCTAGCAGTGATTGGTAACTGA 60.369 47.826 18.24 0.00 45.43 3.41
2243 2415 4.253685 GCTAGCAGTGATTGGTAACTGAA 58.746 43.478 10.63 0.00 45.43 3.02
2244 2416 4.695455 GCTAGCAGTGATTGGTAACTGAAA 59.305 41.667 10.63 0.00 45.43 2.69
2245 2417 5.163814 GCTAGCAGTGATTGGTAACTGAAAG 60.164 44.000 10.63 4.28 45.43 2.62
2246 2418 4.074970 AGCAGTGATTGGTAACTGAAAGG 58.925 43.478 6.98 0.00 45.43 3.11
2247 2419 4.072131 GCAGTGATTGGTAACTGAAAGGA 58.928 43.478 6.98 0.00 45.43 3.36
2248 2420 4.518970 GCAGTGATTGGTAACTGAAAGGAA 59.481 41.667 6.98 0.00 45.43 3.36
2249 2421 5.335191 GCAGTGATTGGTAACTGAAAGGAAG 60.335 44.000 6.98 0.00 45.43 3.46
2250 2422 5.997746 CAGTGATTGGTAACTGAAAGGAAGA 59.002 40.000 0.00 0.00 45.43 2.87
2251 2423 6.656693 CAGTGATTGGTAACTGAAAGGAAGAT 59.343 38.462 0.00 0.00 45.43 2.40
2252 2424 6.656693 AGTGATTGGTAACTGAAAGGAAGATG 59.343 38.462 0.00 0.00 39.30 2.90
2253 2425 5.415701 TGATTGGTAACTGAAAGGAAGATGC 59.584 40.000 0.00 0.00 39.30 3.91
2254 2426 3.686016 TGGTAACTGAAAGGAAGATGCC 58.314 45.455 0.00 0.00 39.30 4.40
2255 2427 3.017442 GGTAACTGAAAGGAAGATGCCC 58.983 50.000 0.00 0.00 39.30 5.36
2256 2428 3.308473 GGTAACTGAAAGGAAGATGCCCT 60.308 47.826 0.00 0.00 39.30 5.19
2257 2429 2.503895 ACTGAAAGGAAGATGCCCTG 57.496 50.000 0.00 0.00 39.30 4.45
2258 2430 1.005215 ACTGAAAGGAAGATGCCCTGG 59.995 52.381 0.00 0.00 39.30 4.45
2259 2431 1.005215 CTGAAAGGAAGATGCCCTGGT 59.995 52.381 0.00 0.00 33.55 4.00
2260 2432 1.272092 TGAAAGGAAGATGCCCTGGTG 60.272 52.381 0.00 0.00 33.55 4.17
2261 2433 1.004745 GAAAGGAAGATGCCCTGGTGA 59.995 52.381 0.00 0.00 33.55 4.02
2262 2434 1.075601 AAGGAAGATGCCCTGGTGAA 58.924 50.000 0.00 0.00 33.55 3.18
2263 2435 1.302907 AGGAAGATGCCCTGGTGAAT 58.697 50.000 0.00 0.00 31.66 2.57
2264 2436 1.064166 AGGAAGATGCCCTGGTGAATG 60.064 52.381 0.00 0.00 31.66 2.67
2265 2437 1.396653 GAAGATGCCCTGGTGAATGG 58.603 55.000 0.00 0.00 0.00 3.16
2266 2438 0.706433 AAGATGCCCTGGTGAATGGT 59.294 50.000 0.00 0.00 0.00 3.55
2267 2439 1.595311 AGATGCCCTGGTGAATGGTA 58.405 50.000 0.00 0.00 0.00 3.25
2268 2440 1.212935 AGATGCCCTGGTGAATGGTAC 59.787 52.381 0.00 0.00 0.00 3.34
2285 2457 5.209818 TGGTACAAGAGTCACTGTTTAGG 57.790 43.478 3.50 0.00 31.92 2.69
2286 2458 4.897076 TGGTACAAGAGTCACTGTTTAGGA 59.103 41.667 3.50 0.00 31.92 2.94
2287 2459 5.221382 TGGTACAAGAGTCACTGTTTAGGAC 60.221 44.000 3.50 0.00 31.92 3.85
2288 2460 5.010820 GGTACAAGAGTCACTGTTTAGGACT 59.989 44.000 3.50 0.00 44.12 3.85
2289 2461 5.615925 ACAAGAGTCACTGTTTAGGACTT 57.384 39.130 0.00 0.00 41.68 3.01
2290 2462 5.990668 ACAAGAGTCACTGTTTAGGACTTT 58.009 37.500 0.00 0.00 41.68 2.66
2291 2463 6.415573 ACAAGAGTCACTGTTTAGGACTTTT 58.584 36.000 0.00 0.00 41.68 2.27
2292 2464 6.719365 CAAGAGTCACTGTTTAGGACTTTTG 58.281 40.000 11.94 11.94 43.02 2.44
2293 2465 5.368989 AGAGTCACTGTTTAGGACTTTTGG 58.631 41.667 0.00 0.00 41.68 3.28
2294 2466 5.104485 AGAGTCACTGTTTAGGACTTTTGGT 60.104 40.000 0.00 0.00 41.68 3.67
2295 2467 4.881850 AGTCACTGTTTAGGACTTTTGGTG 59.118 41.667 0.00 0.00 38.69 4.17
2296 2468 4.638865 GTCACTGTTTAGGACTTTTGGTGT 59.361 41.667 0.00 0.00 0.00 4.16
2297 2469 5.818857 GTCACTGTTTAGGACTTTTGGTGTA 59.181 40.000 0.00 0.00 0.00 2.90
2298 2470 6.018180 GTCACTGTTTAGGACTTTTGGTGTAG 60.018 42.308 0.00 0.00 0.00 2.74
2299 2471 6.053005 CACTGTTTAGGACTTTTGGTGTAGA 58.947 40.000 0.00 0.00 0.00 2.59
2300 2472 6.202954 CACTGTTTAGGACTTTTGGTGTAGAG 59.797 42.308 0.00 0.00 0.00 2.43
2301 2473 6.126854 ACTGTTTAGGACTTTTGGTGTAGAGT 60.127 38.462 0.00 0.00 0.00 3.24
2302 2474 6.053005 TGTTTAGGACTTTTGGTGTAGAGTG 58.947 40.000 0.00 0.00 0.00 3.51
2303 2475 3.771577 AGGACTTTTGGTGTAGAGTGG 57.228 47.619 0.00 0.00 0.00 4.00
2304 2476 3.046374 AGGACTTTTGGTGTAGAGTGGT 58.954 45.455 0.00 0.00 0.00 4.16
2305 2477 3.071167 AGGACTTTTGGTGTAGAGTGGTC 59.929 47.826 0.00 0.00 0.00 4.02
2306 2478 3.181458 GGACTTTTGGTGTAGAGTGGTCA 60.181 47.826 0.00 0.00 0.00 4.02
2307 2479 4.058817 GACTTTTGGTGTAGAGTGGTCAG 58.941 47.826 0.00 0.00 0.00 3.51
2308 2480 3.454812 ACTTTTGGTGTAGAGTGGTCAGT 59.545 43.478 0.00 0.00 0.00 3.41
2309 2481 4.652421 ACTTTTGGTGTAGAGTGGTCAGTA 59.348 41.667 0.00 0.00 0.00 2.74
2310 2482 4.866508 TTTGGTGTAGAGTGGTCAGTAG 57.133 45.455 0.00 0.00 0.00 2.57
2311 2483 2.168496 TGGTGTAGAGTGGTCAGTAGC 58.832 52.381 0.00 0.00 0.00 3.58
2312 2484 2.225041 TGGTGTAGAGTGGTCAGTAGCT 60.225 50.000 0.00 0.00 0.00 3.32
2313 2485 3.009805 TGGTGTAGAGTGGTCAGTAGCTA 59.990 47.826 0.00 0.00 0.00 3.32
2314 2486 3.628487 GGTGTAGAGTGGTCAGTAGCTAG 59.372 52.174 0.00 0.00 0.00 3.42
2315 2487 3.065648 GTGTAGAGTGGTCAGTAGCTAGC 59.934 52.174 6.62 6.62 0.00 3.42
2316 2488 2.818751 AGAGTGGTCAGTAGCTAGCT 57.181 50.000 23.12 23.12 0.00 3.32
2317 2489 3.094484 AGAGTGGTCAGTAGCTAGCTT 57.906 47.619 24.88 1.98 0.00 3.74
2318 2490 2.757868 AGAGTGGTCAGTAGCTAGCTTG 59.242 50.000 24.88 16.41 0.00 4.01
2319 2491 2.755655 GAGTGGTCAGTAGCTAGCTTGA 59.244 50.000 24.88 18.64 0.00 3.02
2320 2492 3.165875 AGTGGTCAGTAGCTAGCTTGAA 58.834 45.455 24.88 1.07 0.00 2.69
2321 2493 3.772025 AGTGGTCAGTAGCTAGCTTGAAT 59.228 43.478 24.88 1.23 0.00 2.57
2322 2494 4.116238 GTGGTCAGTAGCTAGCTTGAATC 58.884 47.826 24.88 16.08 0.00 2.52
2323 2495 3.769300 TGGTCAGTAGCTAGCTTGAATCA 59.231 43.478 24.88 18.21 0.00 2.57
2324 2496 4.142071 TGGTCAGTAGCTAGCTTGAATCAG 60.142 45.833 24.88 6.61 0.00 2.90
2325 2497 3.801594 GTCAGTAGCTAGCTTGAATCAGC 59.198 47.826 24.88 5.46 40.44 4.26
2326 2498 3.448660 TCAGTAGCTAGCTTGAATCAGCA 59.551 43.478 24.88 0.00 42.84 4.41
2327 2499 3.803231 CAGTAGCTAGCTTGAATCAGCAG 59.197 47.826 24.88 0.00 42.84 4.24
2328 2500 3.703556 AGTAGCTAGCTTGAATCAGCAGA 59.296 43.478 24.88 0.00 42.84 4.26
2329 2501 3.182341 AGCTAGCTTGAATCAGCAGAG 57.818 47.619 12.68 5.39 42.84 3.35
2330 2502 2.765135 AGCTAGCTTGAATCAGCAGAGA 59.235 45.455 12.68 0.00 42.84 3.10
2331 2503 3.197333 AGCTAGCTTGAATCAGCAGAGAA 59.803 43.478 12.68 0.00 42.84 2.87
2332 2504 4.128643 GCTAGCTTGAATCAGCAGAGAAT 58.871 43.478 7.70 0.00 42.84 2.40
2333 2505 5.070180 AGCTAGCTTGAATCAGCAGAGAATA 59.930 40.000 12.68 0.00 42.84 1.75
2334 2506 5.757320 GCTAGCTTGAATCAGCAGAGAATAA 59.243 40.000 7.70 0.00 42.84 1.40
2335 2507 6.292811 GCTAGCTTGAATCAGCAGAGAATAAC 60.293 42.308 7.70 0.00 42.84 1.89
2336 2508 5.743117 AGCTTGAATCAGCAGAGAATAACT 58.257 37.500 7.27 0.00 42.84 2.24
2337 2509 6.179040 AGCTTGAATCAGCAGAGAATAACTT 58.821 36.000 7.27 0.00 42.84 2.66
2338 2510 6.658391 AGCTTGAATCAGCAGAGAATAACTTT 59.342 34.615 7.27 0.00 42.84 2.66
2339 2511 7.176340 AGCTTGAATCAGCAGAGAATAACTTTT 59.824 33.333 7.27 0.00 42.84 2.27
2340 2512 8.454106 GCTTGAATCAGCAGAGAATAACTTTTA 58.546 33.333 0.00 0.00 39.83 1.52
2347 2519 9.453572 TCAGCAGAGAATAACTTTTATTGATGT 57.546 29.630 0.00 0.00 0.00 3.06
2354 2526 9.905713 AGAATAACTTTTATTGATGTAGAGCCA 57.094 29.630 0.00 0.00 0.00 4.75
2357 2529 7.944729 AACTTTTATTGATGTAGAGCCATGT 57.055 32.000 0.00 0.00 0.00 3.21
2358 2530 7.559590 ACTTTTATTGATGTAGAGCCATGTC 57.440 36.000 0.00 0.00 0.00 3.06
2359 2531 7.341805 ACTTTTATTGATGTAGAGCCATGTCT 58.658 34.615 0.00 0.00 0.00 3.41
2360 2532 8.486210 ACTTTTATTGATGTAGAGCCATGTCTA 58.514 33.333 0.00 0.00 0.00 2.59
2361 2533 8.893219 TTTTATTGATGTAGAGCCATGTCTAG 57.107 34.615 0.00 0.00 29.38 2.43
2362 2534 7.603180 TTATTGATGTAGAGCCATGTCTAGT 57.397 36.000 0.00 0.00 29.38 2.57
2363 2535 5.939764 TTGATGTAGAGCCATGTCTAGTT 57.060 39.130 0.00 0.00 29.38 2.24
2364 2536 5.521906 TGATGTAGAGCCATGTCTAGTTC 57.478 43.478 0.00 0.00 29.38 3.01
2365 2537 5.204292 TGATGTAGAGCCATGTCTAGTTCT 58.796 41.667 0.00 0.00 29.38 3.01
2366 2538 5.658634 TGATGTAGAGCCATGTCTAGTTCTT 59.341 40.000 0.00 0.00 29.38 2.52
2367 2539 5.584253 TGTAGAGCCATGTCTAGTTCTTC 57.416 43.478 0.00 0.00 29.38 2.87
2368 2540 4.402793 TGTAGAGCCATGTCTAGTTCTTCC 59.597 45.833 0.00 0.00 29.38 3.46
2369 2541 2.428890 AGAGCCATGTCTAGTTCTTCCG 59.571 50.000 0.00 0.00 0.00 4.30
2370 2542 1.482593 AGCCATGTCTAGTTCTTCCGG 59.517 52.381 0.00 0.00 0.00 5.14
2371 2543 1.480954 GCCATGTCTAGTTCTTCCGGA 59.519 52.381 0.00 0.00 0.00 5.14
2372 2544 2.103263 GCCATGTCTAGTTCTTCCGGAT 59.897 50.000 4.15 0.00 0.00 4.18
2373 2545 3.800604 GCCATGTCTAGTTCTTCCGGATC 60.801 52.174 4.15 0.00 0.00 3.36
2374 2546 3.384789 CCATGTCTAGTTCTTCCGGATCA 59.615 47.826 4.15 0.00 0.00 2.92
2375 2547 4.039730 CCATGTCTAGTTCTTCCGGATCAT 59.960 45.833 4.15 0.00 0.00 2.45
2376 2548 5.453903 CCATGTCTAGTTCTTCCGGATCATT 60.454 44.000 4.15 0.00 0.00 2.57
2377 2549 5.677319 TGTCTAGTTCTTCCGGATCATTT 57.323 39.130 4.15 0.00 0.00 2.32
2378 2550 5.419542 TGTCTAGTTCTTCCGGATCATTTG 58.580 41.667 4.15 0.00 0.00 2.32
2379 2551 5.186992 TGTCTAGTTCTTCCGGATCATTTGA 59.813 40.000 4.15 0.00 0.00 2.69
2380 2552 6.127054 TGTCTAGTTCTTCCGGATCATTTGAT 60.127 38.462 4.15 0.00 37.51 2.57
2394 2566 6.908870 ATCATTTGATCGAACGAATCAAGA 57.091 33.333 5.24 1.76 35.95 3.02
2395 2567 6.336514 TCATTTGATCGAACGAATCAAGAG 57.663 37.500 5.24 13.28 35.95 2.85
2396 2568 5.291858 TCATTTGATCGAACGAATCAAGAGG 59.708 40.000 5.24 11.68 35.95 3.69
2397 2569 2.540515 TGATCGAACGAATCAAGAGGC 58.459 47.619 0.12 0.00 0.00 4.70
2398 2570 2.166459 TGATCGAACGAATCAAGAGGCT 59.834 45.455 0.12 0.00 0.00 4.58
2399 2571 3.380320 TGATCGAACGAATCAAGAGGCTA 59.620 43.478 0.12 0.00 0.00 3.93
2400 2572 3.422417 TCGAACGAATCAAGAGGCTAG 57.578 47.619 0.00 0.00 0.00 3.42
2504 2852 3.842007 AGCTAGCTTGAATCAGCAGAT 57.158 42.857 12.68 0.00 42.84 2.90
2517 2865 8.352752 TGAATCAGCAGATAATAACTTGTACG 57.647 34.615 0.00 0.00 33.08 3.67
2518 2866 7.979537 TGAATCAGCAGATAATAACTTGTACGT 59.020 33.333 0.00 0.00 33.08 3.57
2519 2867 9.459640 GAATCAGCAGATAATAACTTGTACGTA 57.540 33.333 0.00 0.00 33.08 3.57
2533 2924 4.644103 TGTACGTATTGAAGTAGAGCCC 57.356 45.455 0.00 0.00 0.00 5.19
2645 3059 0.394565 AGTGAGAGTTGTGTCCTGCC 59.605 55.000 0.00 0.00 0.00 4.85
2741 4346 5.653769 CAGGCAAAAGGATCTTAAGGATGAA 59.346 40.000 1.85 0.00 34.33 2.57
2841 4482 4.284490 TGAGCTCTAGAACCAACTCACAAT 59.716 41.667 16.19 0.00 0.00 2.71
2890 4534 7.424803 TGTACAACACAAATCATCCAAAGAAG 58.575 34.615 0.00 0.00 32.95 2.85
2901 4545 3.726557 TCCAAAGAAGCCAGTCATCAT 57.273 42.857 0.00 0.00 0.00 2.45
2953 4598 2.749621 GCACAACTGAACCCTGAATAGG 59.250 50.000 0.00 0.00 44.18 2.57
2972 4617 6.776887 ATAGGATTTGGTCTCCAAGATCAT 57.223 37.500 16.86 14.40 44.84 2.45
3083 5626 5.049828 ACTAAACAAGCAAATCAAAGCACC 58.950 37.500 0.00 0.00 0.00 5.01
3119 5662 1.269703 AACACGGTCCCACCCTATCC 61.270 60.000 0.00 0.00 33.75 2.59
3166 5709 3.494626 ACTTTCTTGTGCATAGTCGTGTG 59.505 43.478 0.00 0.00 0.00 3.82
3167 5710 2.078849 TCTTGTGCATAGTCGTGTGG 57.921 50.000 0.00 0.00 0.00 4.17
3168 5711 1.343142 TCTTGTGCATAGTCGTGTGGT 59.657 47.619 0.00 0.00 0.00 4.16
3169 5712 2.143122 CTTGTGCATAGTCGTGTGGTT 58.857 47.619 0.00 0.00 0.00 3.67
3170 5713 2.248280 TGTGCATAGTCGTGTGGTTT 57.752 45.000 0.00 0.00 0.00 3.27
3171 5714 2.139917 TGTGCATAGTCGTGTGGTTTC 58.860 47.619 0.00 0.00 0.00 2.78
3172 5715 2.224185 TGTGCATAGTCGTGTGGTTTCT 60.224 45.455 0.00 0.00 0.00 2.52
3173 5716 2.806244 GTGCATAGTCGTGTGGTTTCTT 59.194 45.455 0.00 0.00 0.00 2.52
3174 5717 3.064207 TGCATAGTCGTGTGGTTTCTTC 58.936 45.455 0.00 0.00 0.00 2.87
3175 5718 3.244078 TGCATAGTCGTGTGGTTTCTTCT 60.244 43.478 0.00 0.00 0.00 2.85
3176 5719 3.368236 GCATAGTCGTGTGGTTTCTTCTC 59.632 47.826 0.00 0.00 0.00 2.87
3177 5720 2.528041 AGTCGTGTGGTTTCTTCTCC 57.472 50.000 0.00 0.00 0.00 3.71
3178 5721 1.760613 AGTCGTGTGGTTTCTTCTCCA 59.239 47.619 0.00 0.00 0.00 3.86
3185 5728 3.703001 TGGTTTCTTCTCCACTCCATC 57.297 47.619 0.00 0.00 0.00 3.51
3186 5729 3.251484 TGGTTTCTTCTCCACTCCATCT 58.749 45.455 0.00 0.00 0.00 2.90
3187 5730 3.008375 TGGTTTCTTCTCCACTCCATCTG 59.992 47.826 0.00 0.00 0.00 2.90
3188 5731 3.604582 GTTTCTTCTCCACTCCATCTGG 58.395 50.000 0.00 0.00 0.00 3.86
3189 5732 2.928036 TCTTCTCCACTCCATCTGGA 57.072 50.000 0.00 0.00 43.08 3.86
3210 5790 6.716284 TGGAGATAATACATTGTGTTGTCCA 58.284 36.000 15.88 16.05 28.50 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.254284 ACCTGAGCGAACAGAGGAGG 61.254 60.000 10.13 0.00 39.94 4.30
92 93 0.251297 CCATGAAAGAGGCACCCACA 60.251 55.000 0.00 0.00 0.00 4.17
115 116 9.500785 AAAAGAACATGGAAGAAAACAGAAAAA 57.499 25.926 0.00 0.00 0.00 1.94
121 122 8.066612 AGAAGAAAAGAACATGGAAGAAAACA 57.933 30.769 0.00 0.00 0.00 2.83
132 133 4.998033 GGAGGTCGAAGAAGAAAAGAACAT 59.002 41.667 0.00 0.00 39.69 2.71
134 135 4.633175 AGGAGGTCGAAGAAGAAAAGAAC 58.367 43.478 0.00 0.00 39.69 3.01
149 150 1.683385 AGCAACAGCAAAAAGGAGGTC 59.317 47.619 0.00 0.00 0.00 3.85
206 207 2.855880 TAAAATACCCGGCGCACGCT 62.856 55.000 15.36 0.00 42.52 5.07
209 210 2.486918 ACTATAAAATACCCGGCGCAC 58.513 47.619 10.83 0.00 0.00 5.34
210 211 2.914695 ACTATAAAATACCCGGCGCA 57.085 45.000 10.83 0.00 0.00 6.09
211 212 4.752146 AGATACTATAAAATACCCGGCGC 58.248 43.478 0.00 0.00 0.00 6.53
300 301 3.260483 GAGCACATCCGAGCTGCG 61.260 66.667 0.00 0.00 39.36 5.18
303 304 1.039785 TAGCTGAGCACATCCGAGCT 61.040 55.000 7.39 0.00 42.23 4.09
320 321 3.547095 CAGCGGATCTGCGCATAG 58.453 61.111 20.62 0.00 40.67 2.23
359 364 1.555075 GTCCCAGGTTGTCTCTATGCA 59.445 52.381 0.00 0.00 0.00 3.96
362 367 2.379972 CGAGTCCCAGGTTGTCTCTAT 58.620 52.381 0.00 0.00 0.00 1.98
373 378 3.827898 GTCCTCGCCGAGTCCCAG 61.828 72.222 13.83 0.00 0.00 4.45
399 404 4.790861 GAAGGACGACGACCCCGC 62.791 72.222 12.78 0.00 39.95 6.13
446 451 2.829003 CGGCCTCCTCGCTCTACA 60.829 66.667 0.00 0.00 0.00 2.74
551 556 4.521062 GCATCTCGCCGTCAGCCT 62.521 66.667 0.00 0.00 38.78 4.58
557 562 2.507102 CTGAACGCATCTCGCCGT 60.507 61.111 0.00 0.00 43.23 5.68
565 570 1.019278 CCTTACCGCACTGAACGCAT 61.019 55.000 0.00 0.00 0.00 4.73
578 583 1.792006 CACTCGTTGTCCACCTTACC 58.208 55.000 0.00 0.00 0.00 2.85
661 675 1.596934 GACATCCTTGAGCCCGTCA 59.403 57.895 0.00 0.00 0.00 4.35
853 867 7.918562 GTGTGTTTTGTATACAGATTTGGTGTT 59.081 33.333 5.56 0.00 0.00 3.32
905 919 6.940739 ACTTGCTAAAATCTGAGAGAGCTTA 58.059 36.000 9.04 0.00 0.00 3.09
978 992 4.009675 TCTGGCAGCAAGAATAACGAATT 58.990 39.130 10.34 0.00 0.00 2.17
996 1011 7.227512 GTCTCATAAAATTCTGTACCCATCTGG 59.772 40.741 0.00 0.00 41.37 3.86
1334 1436 9.139174 GCAAGTGTTATAATGCAAAATTACTGT 57.861 29.630 0.00 0.00 38.63 3.55
1386 1496 4.697352 AGAAAATCTTCATCCACTGGTTCG 59.303 41.667 0.00 0.00 33.64 3.95
1403 1513 2.818432 CAGAGTGGAGCTGCAAGAAAAT 59.182 45.455 10.44 0.00 34.07 1.82
1570 1680 4.595781 ACACATGACTCTTACCCCAAAGTA 59.404 41.667 0.00 0.00 0.00 2.24
1611 1742 7.665690 TGCATGTGTAAGTAATTTGTGGAATT 58.334 30.769 0.00 0.00 40.88 2.17
1722 1869 7.226918 TGTTCAAACAACCAACGACATAGAATA 59.773 33.333 0.00 0.00 35.67 1.75
1830 1977 3.430042 AGTGTAGTCACCTCTTCCGTA 57.570 47.619 0.00 0.00 44.83 4.02
1962 2127 3.829948 CAAGGCAATCAACATGAGACAC 58.170 45.455 0.00 0.00 0.00 3.67
2073 2240 5.613358 ATTACACTTTCTTTTCAGAGGCG 57.387 39.130 0.00 0.00 0.00 5.52
2114 2286 6.494835 AGAAATTAAAAATCTGTGGTGCTCCT 59.505 34.615 6.34 0.00 34.23 3.69
2217 2389 1.279496 ACCAATCACTGCTAGCCTCA 58.721 50.000 13.29 0.00 0.00 3.86
2227 2399 6.187727 TCTTCCTTTCAGTTACCAATCACT 57.812 37.500 0.00 0.00 0.00 3.41
2228 2400 6.623767 GCATCTTCCTTTCAGTTACCAATCAC 60.624 42.308 0.00 0.00 0.00 3.06
2230 2402 5.163612 GGCATCTTCCTTTCAGTTACCAATC 60.164 44.000 0.00 0.00 0.00 2.67
2231 2403 4.706962 GGCATCTTCCTTTCAGTTACCAAT 59.293 41.667 0.00 0.00 0.00 3.16
2232 2404 4.079253 GGCATCTTCCTTTCAGTTACCAA 58.921 43.478 0.00 0.00 0.00 3.67
2233 2405 3.561313 GGGCATCTTCCTTTCAGTTACCA 60.561 47.826 0.00 0.00 0.00 3.25
2234 2406 3.017442 GGGCATCTTCCTTTCAGTTACC 58.983 50.000 0.00 0.00 0.00 2.85
2235 2407 3.691609 CAGGGCATCTTCCTTTCAGTTAC 59.308 47.826 0.00 0.00 31.06 2.50
2236 2408 3.308402 CCAGGGCATCTTCCTTTCAGTTA 60.308 47.826 0.00 0.00 31.06 2.24
2237 2409 2.556114 CCAGGGCATCTTCCTTTCAGTT 60.556 50.000 0.00 0.00 31.06 3.16
2238 2410 1.005215 CCAGGGCATCTTCCTTTCAGT 59.995 52.381 0.00 0.00 31.06 3.41
2239 2411 1.005215 ACCAGGGCATCTTCCTTTCAG 59.995 52.381 0.00 0.00 31.06 3.02
2240 2412 1.075601 ACCAGGGCATCTTCCTTTCA 58.924 50.000 0.00 0.00 31.06 2.69
2241 2413 1.004745 TCACCAGGGCATCTTCCTTTC 59.995 52.381 0.00 0.00 31.06 2.62
2242 2414 1.075601 TCACCAGGGCATCTTCCTTT 58.924 50.000 0.00 0.00 31.06 3.11
2243 2415 1.075601 TTCACCAGGGCATCTTCCTT 58.924 50.000 0.00 0.00 31.06 3.36
2244 2416 1.064166 CATTCACCAGGGCATCTTCCT 60.064 52.381 0.00 0.00 34.39 3.36
2245 2417 1.396653 CATTCACCAGGGCATCTTCC 58.603 55.000 0.00 0.00 0.00 3.46
2246 2418 1.341383 ACCATTCACCAGGGCATCTTC 60.341 52.381 0.00 0.00 0.00 2.87
2247 2419 0.706433 ACCATTCACCAGGGCATCTT 59.294 50.000 0.00 0.00 0.00 2.40
2248 2420 1.212935 GTACCATTCACCAGGGCATCT 59.787 52.381 0.00 0.00 0.00 2.90
2249 2421 1.064758 TGTACCATTCACCAGGGCATC 60.065 52.381 0.00 0.00 0.00 3.91
2250 2422 0.998928 TGTACCATTCACCAGGGCAT 59.001 50.000 0.00 0.00 0.00 4.40
2251 2423 0.774276 TTGTACCATTCACCAGGGCA 59.226 50.000 0.00 0.00 0.00 5.36
2252 2424 1.004277 TCTTGTACCATTCACCAGGGC 59.996 52.381 0.00 0.00 0.00 5.19
2253 2425 2.305927 ACTCTTGTACCATTCACCAGGG 59.694 50.000 0.00 0.00 0.00 4.45
2254 2426 3.007940 TGACTCTTGTACCATTCACCAGG 59.992 47.826 0.00 0.00 0.00 4.45
2255 2427 3.997021 GTGACTCTTGTACCATTCACCAG 59.003 47.826 0.00 0.00 0.00 4.00
2256 2428 3.646162 AGTGACTCTTGTACCATTCACCA 59.354 43.478 0.00 0.00 35.06 4.17
2257 2429 3.997021 CAGTGACTCTTGTACCATTCACC 59.003 47.826 0.00 0.00 35.06 4.02
2258 2430 4.632153 ACAGTGACTCTTGTACCATTCAC 58.368 43.478 0.00 0.00 34.78 3.18
2259 2431 4.955811 ACAGTGACTCTTGTACCATTCA 57.044 40.909 0.00 0.00 0.00 2.57
2260 2432 6.369065 CCTAAACAGTGACTCTTGTACCATTC 59.631 42.308 0.00 0.00 0.00 2.67
2261 2433 6.042781 TCCTAAACAGTGACTCTTGTACCATT 59.957 38.462 0.00 0.00 0.00 3.16
2262 2434 5.542635 TCCTAAACAGTGACTCTTGTACCAT 59.457 40.000 0.00 0.00 0.00 3.55
2263 2435 4.897076 TCCTAAACAGTGACTCTTGTACCA 59.103 41.667 0.00 0.00 0.00 3.25
2264 2436 5.010820 AGTCCTAAACAGTGACTCTTGTACC 59.989 44.000 0.00 0.00 34.33 3.34
2265 2437 6.086785 AGTCCTAAACAGTGACTCTTGTAC 57.913 41.667 0.00 0.00 34.33 2.90
2266 2438 6.726490 AAGTCCTAAACAGTGACTCTTGTA 57.274 37.500 0.00 0.00 38.36 2.41
2267 2439 5.615925 AAGTCCTAAACAGTGACTCTTGT 57.384 39.130 0.00 0.00 38.36 3.16
2268 2440 6.238484 CCAAAAGTCCTAAACAGTGACTCTTG 60.238 42.308 0.00 0.00 38.36 3.02
2269 2441 5.823045 CCAAAAGTCCTAAACAGTGACTCTT 59.177 40.000 0.00 0.00 38.36 2.85
2270 2442 5.104485 ACCAAAAGTCCTAAACAGTGACTCT 60.104 40.000 0.00 0.00 38.36 3.24
2271 2443 5.007724 CACCAAAAGTCCTAAACAGTGACTC 59.992 44.000 0.00 0.00 38.36 3.36
2272 2444 4.881850 CACCAAAAGTCCTAAACAGTGACT 59.118 41.667 0.00 0.00 40.94 3.41
2273 2445 4.638865 ACACCAAAAGTCCTAAACAGTGAC 59.361 41.667 0.00 0.00 0.00 3.67
2274 2446 4.850680 ACACCAAAAGTCCTAAACAGTGA 58.149 39.130 0.00 0.00 0.00 3.41
2275 2447 6.053005 TCTACACCAAAAGTCCTAAACAGTG 58.947 40.000 0.00 0.00 0.00 3.66
2276 2448 6.126854 ACTCTACACCAAAAGTCCTAAACAGT 60.127 38.462 0.00 0.00 0.00 3.55
2277 2449 6.202954 CACTCTACACCAAAAGTCCTAAACAG 59.797 42.308 0.00 0.00 0.00 3.16
2278 2450 6.053005 CACTCTACACCAAAAGTCCTAAACA 58.947 40.000 0.00 0.00 0.00 2.83
2279 2451 5.469084 CCACTCTACACCAAAAGTCCTAAAC 59.531 44.000 0.00 0.00 0.00 2.01
2280 2452 5.131475 ACCACTCTACACCAAAAGTCCTAAA 59.869 40.000 0.00 0.00 0.00 1.85
2281 2453 4.657039 ACCACTCTACACCAAAAGTCCTAA 59.343 41.667 0.00 0.00 0.00 2.69
2282 2454 4.228824 ACCACTCTACACCAAAAGTCCTA 58.771 43.478 0.00 0.00 0.00 2.94
2283 2455 3.046374 ACCACTCTACACCAAAAGTCCT 58.954 45.455 0.00 0.00 0.00 3.85
2284 2456 3.181458 TGACCACTCTACACCAAAAGTCC 60.181 47.826 0.00 0.00 0.00 3.85
2285 2457 4.058817 CTGACCACTCTACACCAAAAGTC 58.941 47.826 0.00 0.00 0.00 3.01
2286 2458 3.454812 ACTGACCACTCTACACCAAAAGT 59.545 43.478 0.00 0.00 0.00 2.66
2287 2459 4.073293 ACTGACCACTCTACACCAAAAG 57.927 45.455 0.00 0.00 0.00 2.27
2288 2460 4.502604 GCTACTGACCACTCTACACCAAAA 60.503 45.833 0.00 0.00 0.00 2.44
2289 2461 3.006537 GCTACTGACCACTCTACACCAAA 59.993 47.826 0.00 0.00 0.00 3.28
2290 2462 2.561419 GCTACTGACCACTCTACACCAA 59.439 50.000 0.00 0.00 0.00 3.67
2291 2463 2.168496 GCTACTGACCACTCTACACCA 58.832 52.381 0.00 0.00 0.00 4.17
2292 2464 2.448453 AGCTACTGACCACTCTACACC 58.552 52.381 0.00 0.00 0.00 4.16
2293 2465 3.065648 GCTAGCTACTGACCACTCTACAC 59.934 52.174 7.70 0.00 0.00 2.90
2294 2466 3.054287 AGCTAGCTACTGACCACTCTACA 60.054 47.826 17.69 0.00 0.00 2.74
2295 2467 3.547746 AGCTAGCTACTGACCACTCTAC 58.452 50.000 17.69 0.00 0.00 2.59
2296 2468 3.935818 AGCTAGCTACTGACCACTCTA 57.064 47.619 17.69 0.00 0.00 2.43
2297 2469 2.757868 CAAGCTAGCTACTGACCACTCT 59.242 50.000 19.70 0.00 0.00 3.24
2298 2470 2.755655 TCAAGCTAGCTACTGACCACTC 59.244 50.000 19.70 0.00 0.00 3.51
2299 2471 2.808919 TCAAGCTAGCTACTGACCACT 58.191 47.619 19.70 0.00 0.00 4.00
2300 2472 3.594603 TTCAAGCTAGCTACTGACCAC 57.405 47.619 19.70 0.00 0.00 4.16
2301 2473 3.769300 TGATTCAAGCTAGCTACTGACCA 59.231 43.478 19.70 15.28 0.00 4.02
2302 2474 4.367450 CTGATTCAAGCTAGCTACTGACC 58.633 47.826 19.70 13.06 0.00 4.02
2303 2475 3.801594 GCTGATTCAAGCTAGCTACTGAC 59.198 47.826 19.70 8.67 40.20 3.51
2304 2476 3.448660 TGCTGATTCAAGCTAGCTACTGA 59.551 43.478 19.70 16.36 43.90 3.41
2305 2477 3.790091 TGCTGATTCAAGCTAGCTACTG 58.210 45.455 19.70 14.05 43.90 2.74
2306 2478 3.703556 TCTGCTGATTCAAGCTAGCTACT 59.296 43.478 19.70 0.00 43.90 2.57
2307 2479 4.050553 CTCTGCTGATTCAAGCTAGCTAC 58.949 47.826 19.70 8.10 43.90 3.58
2308 2480 3.956848 TCTCTGCTGATTCAAGCTAGCTA 59.043 43.478 19.70 2.19 43.90 3.32
2309 2481 2.765135 TCTCTGCTGATTCAAGCTAGCT 59.235 45.455 12.68 12.68 43.90 3.32
2310 2482 3.176552 TCTCTGCTGATTCAAGCTAGC 57.823 47.619 6.62 6.62 43.90 3.42
2311 2483 6.985645 AGTTATTCTCTGCTGATTCAAGCTAG 59.014 38.462 0.00 0.00 43.90 3.42
2312 2484 6.882656 AGTTATTCTCTGCTGATTCAAGCTA 58.117 36.000 0.00 0.00 43.90 3.32
2313 2485 5.743117 AGTTATTCTCTGCTGATTCAAGCT 58.257 37.500 0.00 0.00 43.90 3.74
2314 2486 6.434018 AAGTTATTCTCTGCTGATTCAAGC 57.566 37.500 0.00 0.00 43.82 4.01
2321 2493 9.453572 ACATCAATAAAAGTTATTCTCTGCTGA 57.546 29.630 0.00 0.00 0.00 4.26
2328 2500 9.905713 TGGCTCTACATCAATAAAAGTTATTCT 57.094 29.630 0.00 0.00 0.00 2.40
2331 2503 9.632638 ACATGGCTCTACATCAATAAAAGTTAT 57.367 29.630 0.00 0.00 0.00 1.89
2332 2504 9.109393 GACATGGCTCTACATCAATAAAAGTTA 57.891 33.333 0.00 0.00 0.00 2.24
2333 2505 7.831193 AGACATGGCTCTACATCAATAAAAGTT 59.169 33.333 0.00 0.00 0.00 2.66
2334 2506 7.341805 AGACATGGCTCTACATCAATAAAAGT 58.658 34.615 0.00 0.00 0.00 2.66
2335 2507 7.798596 AGACATGGCTCTACATCAATAAAAG 57.201 36.000 0.00 0.00 0.00 2.27
2336 2508 8.486210 ACTAGACATGGCTCTACATCAATAAAA 58.514 33.333 2.95 0.00 0.00 1.52
2337 2509 8.023021 ACTAGACATGGCTCTACATCAATAAA 57.977 34.615 2.95 0.00 0.00 1.40
2338 2510 7.603180 ACTAGACATGGCTCTACATCAATAA 57.397 36.000 2.95 0.00 0.00 1.40
2339 2511 7.507277 AGAACTAGACATGGCTCTACATCAATA 59.493 37.037 2.95 0.00 0.00 1.90
2340 2512 6.326064 AGAACTAGACATGGCTCTACATCAAT 59.674 38.462 2.95 0.00 0.00 2.57
2341 2513 5.658634 AGAACTAGACATGGCTCTACATCAA 59.341 40.000 2.95 0.00 0.00 2.57
2342 2514 5.204292 AGAACTAGACATGGCTCTACATCA 58.796 41.667 2.95 0.00 0.00 3.07
2343 2515 5.782893 AGAACTAGACATGGCTCTACATC 57.217 43.478 2.95 0.00 0.00 3.06
2344 2516 5.069781 GGAAGAACTAGACATGGCTCTACAT 59.930 44.000 2.95 0.00 0.00 2.29
2345 2517 4.402793 GGAAGAACTAGACATGGCTCTACA 59.597 45.833 2.95 0.00 0.00 2.74
2346 2518 4.498345 CGGAAGAACTAGACATGGCTCTAC 60.498 50.000 2.95 0.00 0.00 2.59
2347 2519 3.632604 CGGAAGAACTAGACATGGCTCTA 59.367 47.826 2.95 0.00 0.00 2.43
2348 2520 2.428890 CGGAAGAACTAGACATGGCTCT 59.571 50.000 2.95 0.00 0.00 4.09
2349 2521 2.482142 CCGGAAGAACTAGACATGGCTC 60.482 54.545 2.95 0.00 0.00 4.70
2350 2522 1.482593 CCGGAAGAACTAGACATGGCT 59.517 52.381 6.20 6.20 0.00 4.75
2351 2523 1.480954 TCCGGAAGAACTAGACATGGC 59.519 52.381 0.00 0.00 0.00 4.40
2352 2524 3.384789 TGATCCGGAAGAACTAGACATGG 59.615 47.826 9.01 0.00 0.00 3.66
2353 2525 4.655762 TGATCCGGAAGAACTAGACATG 57.344 45.455 9.01 0.00 0.00 3.21
2354 2526 5.878406 AATGATCCGGAAGAACTAGACAT 57.122 39.130 9.01 0.79 0.00 3.06
2355 2527 5.186992 TCAAATGATCCGGAAGAACTAGACA 59.813 40.000 9.01 0.00 0.00 3.41
2356 2528 5.661458 TCAAATGATCCGGAAGAACTAGAC 58.339 41.667 9.01 0.00 0.00 2.59
2357 2529 5.932619 TCAAATGATCCGGAAGAACTAGA 57.067 39.130 9.01 0.00 0.00 2.43
2358 2530 5.403766 CGATCAAATGATCCGGAAGAACTAG 59.596 44.000 9.01 0.00 46.16 2.57
2359 2531 5.068591 TCGATCAAATGATCCGGAAGAACTA 59.931 40.000 9.01 0.00 46.16 2.24
2360 2532 4.122776 CGATCAAATGATCCGGAAGAACT 58.877 43.478 9.01 0.00 46.16 3.01
2361 2533 4.119862 TCGATCAAATGATCCGGAAGAAC 58.880 43.478 9.01 0.89 46.16 3.01
2362 2534 4.400529 TCGATCAAATGATCCGGAAGAA 57.599 40.909 9.01 0.00 46.16 2.52
2363 2535 4.119862 GTTCGATCAAATGATCCGGAAGA 58.880 43.478 9.01 0.00 46.16 2.87
2364 2536 3.060272 CGTTCGATCAAATGATCCGGAAG 60.060 47.826 9.01 6.49 46.16 3.46
2365 2537 2.863740 CGTTCGATCAAATGATCCGGAA 59.136 45.455 9.01 11.89 46.16 4.30
2366 2538 2.100087 TCGTTCGATCAAATGATCCGGA 59.900 45.455 6.61 6.61 46.16 5.14
2367 2539 2.469826 TCGTTCGATCAAATGATCCGG 58.530 47.619 15.78 0.00 46.16 5.14
2368 2540 4.209080 TGATTCGTTCGATCAAATGATCCG 59.791 41.667 15.78 13.57 46.16 4.18
2369 2541 5.657470 TGATTCGTTCGATCAAATGATCC 57.343 39.130 15.78 3.65 46.16 3.36
2370 2542 6.937457 TCTTGATTCGTTCGATCAAATGATC 58.063 36.000 12.40 12.40 45.60 2.92
2371 2543 6.018425 CCTCTTGATTCGTTCGATCAAATGAT 60.018 38.462 15.03 0.00 34.39 2.45
2372 2544 5.291858 CCTCTTGATTCGTTCGATCAAATGA 59.708 40.000 15.03 0.00 34.39 2.57
2373 2545 5.496387 CCTCTTGATTCGTTCGATCAAATG 58.504 41.667 15.03 11.93 34.39 2.32
2374 2546 4.034510 GCCTCTTGATTCGTTCGATCAAAT 59.965 41.667 15.03 0.00 34.39 2.32
2375 2547 3.370978 GCCTCTTGATTCGTTCGATCAAA 59.629 43.478 15.03 0.00 34.39 2.69
2376 2548 2.930040 GCCTCTTGATTCGTTCGATCAA 59.070 45.455 14.15 14.15 33.77 2.57
2377 2549 2.166459 AGCCTCTTGATTCGTTCGATCA 59.834 45.455 0.00 0.41 0.00 2.92
2378 2550 2.815478 AGCCTCTTGATTCGTTCGATC 58.185 47.619 0.00 0.00 0.00 3.69
2379 2551 2.969628 AGCCTCTTGATTCGTTCGAT 57.030 45.000 0.00 0.00 0.00 3.59
2380 2552 2.479730 GCTAGCCTCTTGATTCGTTCGA 60.480 50.000 2.29 0.00 0.00 3.71
2381 2553 1.855360 GCTAGCCTCTTGATTCGTTCG 59.145 52.381 2.29 0.00 0.00 3.95
2382 2554 2.863137 CTGCTAGCCTCTTGATTCGTTC 59.137 50.000 13.29 0.00 0.00 3.95
2383 2555 2.898705 CTGCTAGCCTCTTGATTCGTT 58.101 47.619 13.29 0.00 0.00 3.85
2384 2556 1.472376 GCTGCTAGCCTCTTGATTCGT 60.472 52.381 13.29 0.00 34.48 3.85
2385 2557 1.216122 GCTGCTAGCCTCTTGATTCG 58.784 55.000 13.29 0.00 34.48 3.34
2386 2558 1.202463 TCGCTGCTAGCCTCTTGATTC 60.202 52.381 13.29 0.00 38.18 2.52
2387 2559 0.826715 TCGCTGCTAGCCTCTTGATT 59.173 50.000 13.29 0.00 38.18 2.57
2388 2560 0.103937 GTCGCTGCTAGCCTCTTGAT 59.896 55.000 13.29 0.00 38.18 2.57
2389 2561 0.967887 AGTCGCTGCTAGCCTCTTGA 60.968 55.000 13.29 0.02 38.18 3.02
2390 2562 0.805322 CAGTCGCTGCTAGCCTCTTG 60.805 60.000 13.29 0.00 38.18 3.02
2391 2563 1.515020 CAGTCGCTGCTAGCCTCTT 59.485 57.895 13.29 0.00 38.18 2.85
2392 2564 2.422231 CCAGTCGCTGCTAGCCTCT 61.422 63.158 13.29 0.46 38.18 3.69
2393 2565 1.384989 TACCAGTCGCTGCTAGCCTC 61.385 60.000 13.29 2.55 38.18 4.70
2394 2566 0.970937 TTACCAGTCGCTGCTAGCCT 60.971 55.000 13.29 0.00 38.18 4.58
2395 2567 0.806492 GTTACCAGTCGCTGCTAGCC 60.806 60.000 13.29 0.00 38.18 3.93
2396 2568 0.173708 AGTTACCAGTCGCTGCTAGC 59.826 55.000 8.10 8.10 38.02 3.42
2397 2569 1.472878 TCAGTTACCAGTCGCTGCTAG 59.527 52.381 0.00 0.00 0.00 3.42
2398 2570 1.541379 TCAGTTACCAGTCGCTGCTA 58.459 50.000 0.00 0.00 0.00 3.49
2399 2571 0.679505 TTCAGTTACCAGTCGCTGCT 59.320 50.000 0.00 0.00 0.00 4.24
2400 2572 1.461127 CTTTCAGTTACCAGTCGCTGC 59.539 52.381 1.84 0.00 0.00 5.25
2516 2864 3.381908 AGACAGGGCTCTACTTCAATACG 59.618 47.826 0.00 0.00 0.00 3.06
2517 2865 4.202172 GGAGACAGGGCTCTACTTCAATAC 60.202 50.000 1.57 0.00 35.26 1.89
2518 2866 3.961408 GGAGACAGGGCTCTACTTCAATA 59.039 47.826 1.57 0.00 35.26 1.90
2519 2867 2.769095 GGAGACAGGGCTCTACTTCAAT 59.231 50.000 1.57 0.00 35.26 2.57
2533 2924 7.391833 GGGCTATTAAAATGGATTAGGAGACAG 59.608 40.741 0.00 0.00 0.00 3.51
2645 3059 2.928116 GCTAAACGGCCTGTACAGTAAG 59.072 50.000 21.18 13.36 0.00 2.34
2658 3072 2.223377 GTCACCAACTCTTGCTAAACGG 59.777 50.000 0.00 0.00 0.00 4.44
2719 3133 6.322201 TGATTCATCCTTAAGATCCTTTTGCC 59.678 38.462 3.36 0.00 30.59 4.52
2890 4534 4.701765 AGACTTGATGTATGATGACTGGC 58.298 43.478 0.00 0.00 0.00 4.85
2953 4598 6.956202 ATTCATGATCTTGGAGACCAAATC 57.044 37.500 8.60 10.19 43.44 2.17
2972 4617 6.378582 GTGCCATCTTTTAGTCGAAAATTCA 58.621 36.000 0.00 0.00 36.44 2.57
3083 5626 4.091945 CCGTGTTGTACTGAACTGATCATG 59.908 45.833 0.00 0.00 37.44 3.07
3119 5662 2.126888 GCGTGCATGACAAACGGG 60.127 61.111 10.93 0.00 37.77 5.28
3166 5709 3.604582 CAGATGGAGTGGAGAAGAAACC 58.395 50.000 0.00 0.00 0.00 3.27
3167 5710 3.261897 TCCAGATGGAGTGGAGAAGAAAC 59.738 47.826 0.00 0.00 39.28 2.78
3168 5711 3.520696 TCCAGATGGAGTGGAGAAGAAA 58.479 45.455 0.00 0.00 39.28 2.52
3169 5712 3.190383 TCCAGATGGAGTGGAGAAGAA 57.810 47.619 0.00 0.00 39.28 2.52
3170 5713 2.928036 TCCAGATGGAGTGGAGAAGA 57.072 50.000 0.00 0.00 39.28 2.87
3180 5723 7.379059 ACACAATGTATTATCTCCAGATGGA 57.621 36.000 0.79 0.79 43.08 3.41
3181 5724 7.500227 ACAACACAATGTATTATCTCCAGATGG 59.500 37.037 0.00 0.00 36.05 3.51
3182 5725 8.442632 ACAACACAATGTATTATCTCCAGATG 57.557 34.615 0.00 0.00 36.05 2.90
3183 5726 7.716998 GGACAACACAATGTATTATCTCCAGAT 59.283 37.037 0.00 0.00 34.58 2.90
3184 5727 7.047891 GGACAACACAATGTATTATCTCCAGA 58.952 38.462 0.00 0.00 32.57 3.86
3185 5728 6.823182 TGGACAACACAATGTATTATCTCCAG 59.177 38.462 0.00 0.00 32.57 3.86
3186 5729 6.716284 TGGACAACACAATGTATTATCTCCA 58.284 36.000 0.00 0.00 32.57 3.86
3202 5745 4.214986 TGAAGTGAAGAAGTGGACAACA 57.785 40.909 0.00 0.00 0.00 3.33
3210 5790 4.926238 CGAGTTAGCATGAAGTGAAGAAGT 59.074 41.667 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.