Multiple sequence alignment - TraesCS4A01G281000

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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 TraesCS4A01G281000 chr4A 100.000 2731 0 0 1 2731 589471934 589474664 0.000000e+00 5044.0
1 TraesCS4A01G281000 chr4D 90.102 1374 49 35 4 1317 13097992 13096646 0.000000e+00 1703.0
2 TraesCS4A01G281000 chr4D 87.608 807 27 26 1453 2243 13096568 13095819 0.000000e+00 869.0
3 TraesCS4A01G281000 chr4D 82.937 504 38 25 2251 2731 13095463 13094985 7.040000e-111 411.0
4 TraesCS4A01G281000 chr4D 93.182 44 3 0 1384 1427 75264119 75264076 6.310000e-07 65.8
5 TraesCS4A01G281000 chr4B 88.995 1363 66 24 1 1342 23706995 23705696 0.000000e+00 1609.0
6 TraesCS4A01G281000 chr4B 87.840 699 36 24 1564 2252 23705543 23704884 0.000000e+00 774.0
7 TraesCS4A01G281000 chr4B 87.905 463 22 17 2279 2731 23695121 23694683 5.210000e-142 514.0
8 TraesCS4A01G281000 chr4B 87.500 56 6 1 1368 1422 411715100 411715155 2.270000e-06 63.9
9 TraesCS4A01G281000 chr3D 95.745 47 2 0 1381 1427 129018220 129018174 2.920000e-10 76.8
10 TraesCS4A01G281000 chr3A 95.349 43 2 0 1384 1426 117319698 117319656 4.880000e-08 69.4
11 TraesCS4A01G281000 chr3A 97.500 40 1 0 1381 1420 140812695 140812734 4.880000e-08 69.4
12 TraesCS4A01G281000 chr6B 90.196 51 4 1 1383 1433 85383720 85383769 6.310000e-07 65.8
13 TraesCS4A01G281000 chr5D 97.368 38 1 0 1383 1420 28479991 28480028 6.310000e-07 65.8
14 TraesCS4A01G281000 chr6A 91.489 47 3 1 1374 1420 25691298 25691343 2.270000e-06 63.9
15 TraesCS4A01G281000 chr5B 87.719 57 4 2 1381 1434 6399752 6399696 2.270000e-06 63.9


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 TraesCS4A01G281000 chr4A 589471934 589474664 2730 False 5044.000000 5044 100.000000 1 2731 1 chr4A.!!$F1 2730
1 TraesCS4A01G281000 chr4D 13094985 13097992 3007 True 994.333333 1703 86.882333 4 2731 3 chr4D.!!$R2 2727
2 TraesCS4A01G281000 chr4B 23704884 23706995 2111 True 1191.500000 1609 88.417500 1 2252 2 chr4B.!!$R2 2251

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
965 1028 0.534652 CCTGATCTAGCTTGCAGCCC 60.535 60.0 0.0 0.0 43.77 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2208 0.179702 TGATAGCAGGCTCAGCTTGG 59.82 55.0 11.3 0.0 43.25 3.61 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
186 188 2.557452 GGGGAAGAAGCAAAGGGAATGA 60.557 50.000 0.00 0.00 0.00 2.57
232 234 3.859414 GCTCCCCTGCTCGCTGAT 61.859 66.667 0.00 0.00 0.00 2.90
233 235 2.502492 GCTCCCCTGCTCGCTGATA 61.502 63.158 0.00 0.00 0.00 2.15
234 236 1.365633 CTCCCCTGCTCGCTGATAC 59.634 63.158 0.00 0.00 0.00 2.24
235 237 2.028190 CCCCTGCTCGCTGATACG 59.972 66.667 0.00 0.00 0.00 3.06
236 238 2.490148 CCCCTGCTCGCTGATACGA 61.490 63.158 0.00 0.00 40.36 3.43
246 250 0.933796 GCTGATACGAGCTTGGCTTC 59.066 55.000 5.79 0.00 39.88 3.86
247 251 1.576356 CTGATACGAGCTTGGCTTCC 58.424 55.000 5.79 0.00 39.88 3.46
311 315 3.636764 GGTGGAATCATTGGAACCATACC 59.363 47.826 0.00 0.00 36.47 2.73
312 316 4.277476 GTGGAATCATTGGAACCATACCA 58.723 43.478 0.00 0.00 36.47 3.25
313 317 4.895297 GTGGAATCATTGGAACCATACCAT 59.105 41.667 0.00 0.00 36.47 3.55
314 318 6.068010 GTGGAATCATTGGAACCATACCATA 58.932 40.000 0.00 0.00 36.47 2.74
315 319 6.016276 GTGGAATCATTGGAACCATACCATAC 60.016 42.308 0.00 0.00 36.47 2.39
318 322 4.956085 TCATTGGAACCATACCATACTCG 58.044 43.478 0.00 0.00 37.26 4.18
322 326 2.288886 GGAACCATACCATACTCGCTCC 60.289 54.545 0.00 0.00 0.00 4.70
336 348 2.871022 CTCGCTCCAAGAATCATCCTTG 59.129 50.000 0.00 0.00 40.37 3.61
338 350 2.652590 GCTCCAAGAATCATCCTTGCT 58.347 47.619 0.00 0.00 39.60 3.91
389 403 2.315925 TAGTGCATGCTAAGTGGAGC 57.684 50.000 20.33 0.00 43.16 4.70
436 450 9.555727 GCTAGATAGATAATCTACTCTACCCAG 57.444 40.741 0.00 0.00 43.45 4.45
454 468 0.771755 AGTTTGGAACCTCCCTGTCC 59.228 55.000 0.00 0.00 35.03 4.02
743 777 4.585162 GCTAGGACCATAGTATCACACACT 59.415 45.833 0.00 0.00 0.00 3.55
843 897 1.406614 CCATCACCTCCTCTTCAGCAC 60.407 57.143 0.00 0.00 0.00 4.40
848 911 1.078567 CTCCTCTTCAGCACCAGGC 60.079 63.158 0.00 0.00 45.30 4.85
863 926 4.477975 GGCGGAGGAGACGTCGTG 62.478 72.222 10.46 0.00 34.16 4.35
865 928 3.054503 CGGAGGAGACGTCGTGGT 61.055 66.667 10.46 0.00 0.00 4.16
960 1023 2.167281 TCAGTCACCTGATCTAGCTTGC 59.833 50.000 0.00 0.00 42.80 4.01
965 1028 0.534652 CCTGATCTAGCTTGCAGCCC 60.535 60.000 0.00 0.00 43.77 5.19
977 1041 2.359107 CAGCCCGCAGAAGCAAGA 60.359 61.111 0.00 0.00 42.27 3.02
1164 1239 3.406200 CAGGCTGCCACCCTAGCT 61.406 66.667 22.65 0.00 39.80 3.32
1282 1357 0.868406 GCCCGATCCGATTCACAATC 59.132 55.000 0.00 0.00 34.52 2.67
1310 1386 3.190744 TGTTACTCGTGTCATCTCTGGTC 59.809 47.826 0.00 0.00 0.00 4.02
1317 1393 3.654414 GTGTCATCTCTGGTCGTTCTTT 58.346 45.455 0.00 0.00 0.00 2.52
1324 1408 4.404640 TCTCTGGTCGTTCTTTCTTCCTA 58.595 43.478 0.00 0.00 0.00 2.94
1325 1409 4.831155 TCTCTGGTCGTTCTTTCTTCCTAA 59.169 41.667 0.00 0.00 0.00 2.69
1328 1412 5.756833 TCTGGTCGTTCTTTCTTCCTAAAAC 59.243 40.000 0.00 0.00 0.00 2.43
1331 1415 5.441543 GTCGTTCTTTCTTCCTAAAACTGC 58.558 41.667 0.00 0.00 0.00 4.40
1339 1423 1.132640 CCTAAAACTGCGCTCGTGC 59.867 57.895 9.73 0.00 0.00 5.34
1342 1426 1.724623 CTAAAACTGCGCTCGTGCTTA 59.275 47.619 9.73 6.94 36.97 3.09
1343 1427 0.512952 AAAACTGCGCTCGTGCTTAG 59.487 50.000 9.73 7.91 36.97 2.18
1344 1428 0.600255 AAACTGCGCTCGTGCTTAGT 60.600 50.000 9.73 8.52 35.55 2.24
1357 1441 6.623331 GCTCGTGCTTAGTTTACTTCTCTAGT 60.623 42.308 1.41 0.00 37.25 2.57
1359 1443 7.972527 TCGTGCTTAGTTTACTTCTCTAGTAG 58.027 38.462 0.00 0.00 40.35 2.57
1361 1445 7.904461 CGTGCTTAGTTTACTTCTCTAGTAGAC 59.096 40.741 0.00 0.00 42.12 2.59
1370 1454 9.598517 TTTACTTCTCTAGTAGACTAGTGCTAC 57.401 37.037 14.79 17.70 44.74 3.58
1372 1456 6.384886 ACTTCTCTAGTAGACTAGTGCTACCT 59.615 42.308 19.98 13.68 44.74 3.08
1373 1457 6.409524 TCTCTAGTAGACTAGTGCTACCTC 57.590 45.833 19.98 0.00 44.74 3.85
1374 1458 6.138263 TCTCTAGTAGACTAGTGCTACCTCT 58.862 44.000 19.98 6.19 44.74 3.69
1375 1459 6.041182 TCTCTAGTAGACTAGTGCTACCTCTG 59.959 46.154 19.98 12.85 44.74 3.35
1377 1461 5.954153 AGTAGACTAGTGCTACCTCTGTA 57.046 43.478 19.98 0.00 39.17 2.74
1378 1462 5.673514 AGTAGACTAGTGCTACCTCTGTAC 58.326 45.833 19.98 0.00 39.17 2.90
1381 1465 3.622630 ACTAGTGCTACCTCTGTACCAG 58.377 50.000 0.00 0.00 0.00 4.00
1382 1466 2.901338 AGTGCTACCTCTGTACCAGA 57.099 50.000 0.00 0.00 38.25 3.86
1384 1468 3.714144 AGTGCTACCTCTGTACCAGATT 58.286 45.455 0.00 0.00 39.92 2.40
1385 1469 4.097418 AGTGCTACCTCTGTACCAGATTT 58.903 43.478 0.00 0.00 39.92 2.17
1386 1470 4.081420 AGTGCTACCTCTGTACCAGATTTG 60.081 45.833 0.00 0.00 39.92 2.32
1387 1471 4.081642 GTGCTACCTCTGTACCAGATTTGA 60.082 45.833 0.00 0.00 39.92 2.69
1388 1472 4.530553 TGCTACCTCTGTACCAGATTTGAA 59.469 41.667 0.00 0.00 39.92 2.69
1389 1473 4.870991 GCTACCTCTGTACCAGATTTGAAC 59.129 45.833 0.00 0.00 39.92 3.18
1390 1474 5.337652 GCTACCTCTGTACCAGATTTGAACT 60.338 44.000 0.00 0.00 39.92 3.01
1391 1475 4.899502 ACCTCTGTACCAGATTTGAACTG 58.100 43.478 0.00 0.00 39.92 3.16
1392 1476 3.686726 CCTCTGTACCAGATTTGAACTGC 59.313 47.826 0.00 0.00 39.92 4.40
1393 1477 4.318332 CTCTGTACCAGATTTGAACTGCA 58.682 43.478 0.00 0.00 39.92 4.41
1394 1478 4.713553 TCTGTACCAGATTTGAACTGCAA 58.286 39.130 0.00 0.00 35.39 4.08
1409 1493 9.522804 TTTGAACTGCAAAAACGTCTTATATTT 57.477 25.926 0.00 0.00 43.18 1.40
1410 1494 9.522804 TTGAACTGCAAAAACGTCTTATATTTT 57.477 25.926 0.00 0.00 32.46 1.82
1411 1495 8.963130 TGAACTGCAAAAACGTCTTATATTTTG 58.037 29.630 13.82 13.82 42.66 2.44
1412 1496 9.176181 GAACTGCAAAAACGTCTTATATTTTGA 57.824 29.630 19.73 8.16 42.48 2.69
1413 1497 9.691362 AACTGCAAAAACGTCTTATATTTTGAT 57.309 25.926 19.73 6.17 42.48 2.57
1416 1500 9.268255 TGCAAAAACGTCTTATATTTTGATACG 57.732 29.630 19.73 0.00 42.48 3.06
1417 1501 9.480538 GCAAAAACGTCTTATATTTTGATACGA 57.519 29.630 19.73 0.00 42.48 3.43
1451 1535 7.224522 AGAACTTCTAACGTATAACCACACT 57.775 36.000 0.00 0.00 0.00 3.55
1520 1630 6.798315 ACTGCTAATGCTAATAATGCAGAG 57.202 37.500 17.15 0.00 46.23 3.35
1536 1655 2.082231 CAGAGCCATATAGCATGCACC 58.918 52.381 21.98 0.00 34.23 5.01
1546 1665 6.295292 CCATATAGCATGCACCTACTCAGTTA 60.295 42.308 21.98 0.00 0.00 2.24
1596 1715 2.356278 GCTGGTCCCCTGCATCAA 59.644 61.111 7.20 0.00 45.75 2.57
1597 1716 1.751927 GCTGGTCCCCTGCATCAAG 60.752 63.158 7.20 0.00 45.75 3.02
1598 1717 1.751927 CTGGTCCCCTGCATCAAGC 60.752 63.158 0.00 0.00 45.96 4.01
1752 1876 0.247460 CAGGACAGGAGCAATCACGA 59.753 55.000 0.00 0.00 0.00 4.35
1769 1893 1.797964 CGAAAACCGTCGATCAATGC 58.202 50.000 0.00 0.00 43.86 3.56
1780 1904 1.202498 CGATCAATGCTGAGAGGCTCA 60.202 52.381 18.26 0.00 38.25 4.26
1781 1905 2.740904 CGATCAATGCTGAGAGGCTCAA 60.741 50.000 18.26 3.35 40.18 3.02
1977 2108 2.027460 CACCGTGGTTGCTTTGGC 59.973 61.111 0.00 0.00 39.26 4.52
2007 2141 5.184711 GCTTTGTTCTCCTCTCTTGATGAT 58.815 41.667 0.00 0.00 0.00 2.45
2079 2213 2.549332 GAGCACTCCAACTCCAAGC 58.451 57.895 0.00 0.00 0.00 4.01
2080 2214 0.036022 GAGCACTCCAACTCCAAGCT 59.964 55.000 0.00 0.00 0.00 3.74
2081 2215 0.250640 AGCACTCCAACTCCAAGCTG 60.251 55.000 0.00 0.00 0.00 4.24
2082 2216 0.250467 GCACTCCAACTCCAAGCTGA 60.250 55.000 0.00 0.00 0.00 4.26
2083 2217 1.805869 CACTCCAACTCCAAGCTGAG 58.194 55.000 0.00 0.00 38.37 3.35
2084 2218 0.036022 ACTCCAACTCCAAGCTGAGC 59.964 55.000 0.00 0.00 35.72 4.26
2085 2219 0.676151 CTCCAACTCCAAGCTGAGCC 60.676 60.000 0.00 0.00 35.72 4.70
2086 2220 1.130054 TCCAACTCCAAGCTGAGCCT 61.130 55.000 0.00 0.00 35.72 4.58
2087 2221 0.959372 CCAACTCCAAGCTGAGCCTG 60.959 60.000 0.00 0.00 35.72 4.85
2088 2222 1.303155 AACTCCAAGCTGAGCCTGC 60.303 57.895 0.00 0.00 35.72 4.85
2089 2223 1.776975 AACTCCAAGCTGAGCCTGCT 61.777 55.000 0.00 0.00 40.24 4.24
2090 2224 0.906756 ACTCCAAGCTGAGCCTGCTA 60.907 55.000 0.00 0.00 37.67 3.49
2091 2225 0.469070 CTCCAAGCTGAGCCTGCTAT 59.531 55.000 0.00 0.00 37.67 2.97
2092 2226 0.467384 TCCAAGCTGAGCCTGCTATC 59.533 55.000 0.00 0.00 37.67 2.08
2093 2227 0.179702 CCAAGCTGAGCCTGCTATCA 59.820 55.000 0.00 0.00 37.67 2.15
2094 2228 1.297664 CAAGCTGAGCCTGCTATCAC 58.702 55.000 0.00 0.00 37.67 3.06
2095 2229 1.134461 CAAGCTGAGCCTGCTATCACT 60.134 52.381 0.00 0.00 37.67 3.41
2096 2230 2.079170 AGCTGAGCCTGCTATCACTA 57.921 50.000 0.00 0.00 36.91 2.74
2097 2231 1.686052 AGCTGAGCCTGCTATCACTAC 59.314 52.381 0.00 0.00 36.91 2.73
2098 2232 1.686052 GCTGAGCCTGCTATCACTACT 59.314 52.381 0.00 0.00 0.00 2.57
2099 2233 2.288152 GCTGAGCCTGCTATCACTACTC 60.288 54.545 0.00 0.00 0.00 2.59
2100 2234 2.954989 CTGAGCCTGCTATCACTACTCA 59.045 50.000 0.00 0.00 0.00 3.41
2101 2235 2.690497 TGAGCCTGCTATCACTACTCAC 59.310 50.000 0.00 0.00 0.00 3.51
2102 2236 2.955660 GAGCCTGCTATCACTACTCACT 59.044 50.000 0.00 0.00 0.00 3.41
2103 2237 3.370104 AGCCTGCTATCACTACTCACTT 58.630 45.455 0.00 0.00 0.00 3.16
2104 2238 3.383185 AGCCTGCTATCACTACTCACTTC 59.617 47.826 0.00 0.00 0.00 3.01
2105 2239 3.131223 GCCTGCTATCACTACTCACTTCA 59.869 47.826 0.00 0.00 0.00 3.02
2114 2250 4.036852 TCACTACTCACTTCACTCACACAG 59.963 45.833 0.00 0.00 0.00 3.66
2135 2271 6.091986 CACAGAGAGTAAAGCTCAAAGATTCC 59.908 42.308 0.00 0.00 46.47 3.01
2147 2283 2.154567 AAGATTCCTGGCATGCACAT 57.845 45.000 21.36 2.96 0.00 3.21
2148 2284 2.154567 AGATTCCTGGCATGCACATT 57.845 45.000 21.36 0.00 0.00 2.71
2150 2286 2.429610 AGATTCCTGGCATGCACATTTC 59.570 45.455 21.36 8.69 0.00 2.17
2151 2287 0.527113 TTCCTGGCATGCACATTTCG 59.473 50.000 21.36 3.43 0.00 3.46
2152 2288 0.322366 TCCTGGCATGCACATTTCGA 60.322 50.000 21.36 1.43 0.00 3.71
2153 2289 0.742505 CCTGGCATGCACATTTCGAT 59.257 50.000 21.36 0.00 0.00 3.59
2154 2290 1.135527 CCTGGCATGCACATTTCGATT 59.864 47.619 21.36 0.00 0.00 3.34
2155 2291 2.456989 CTGGCATGCACATTTCGATTC 58.543 47.619 21.36 0.00 0.00 2.52
2157 2293 3.277715 TGGCATGCACATTTCGATTCTA 58.722 40.909 21.36 0.00 0.00 2.10
2158 2294 3.065233 TGGCATGCACATTTCGATTCTAC 59.935 43.478 21.36 0.00 0.00 2.59
2161 2297 4.553547 GCATGCACATTTCGATTCTACTCC 60.554 45.833 14.21 0.00 0.00 3.85
2162 2298 4.471904 TGCACATTTCGATTCTACTCCT 57.528 40.909 0.00 0.00 0.00 3.69
2191 2327 2.611292 GCTTTCAGTCTTCCCGATGATG 59.389 50.000 0.00 0.00 0.00 3.07
2193 2329 3.981071 TTCAGTCTTCCCGATGATGTT 57.019 42.857 0.00 0.00 0.00 2.71
2195 2331 5.414789 TTCAGTCTTCCCGATGATGTTTA 57.585 39.130 0.00 0.00 0.00 2.01
2196 2332 5.414789 TCAGTCTTCCCGATGATGTTTAA 57.585 39.130 0.00 0.00 0.00 1.52
2197 2333 5.989477 TCAGTCTTCCCGATGATGTTTAAT 58.011 37.500 0.00 0.00 0.00 1.40
2199 2335 7.561251 TCAGTCTTCCCGATGATGTTTAATAA 58.439 34.615 0.00 0.00 0.00 1.40
2200 2336 8.210946 TCAGTCTTCCCGATGATGTTTAATAAT 58.789 33.333 0.00 0.00 0.00 1.28
2204 2341 6.892658 TCCCGATGATGTTTAATAATTGGG 57.107 37.500 2.41 2.41 41.64 4.12
2240 2377 3.885297 TGCTTTCAAAGGACTCAAAGGAG 59.115 43.478 0.00 0.00 46.96 3.69
2259 2744 5.138276 AGGAGTACTAACAAGTGACTGACA 58.862 41.667 0.00 0.00 0.00 3.58
2283 2768 3.431233 CACTCTCTGCACACACTTACATG 59.569 47.826 0.00 0.00 0.00 3.21
2320 2805 4.685169 ACAACCATCAACGATCAATCAC 57.315 40.909 0.00 0.00 0.00 3.06
2321 2806 4.071423 ACAACCATCAACGATCAATCACA 58.929 39.130 0.00 0.00 0.00 3.58
2322 2807 4.518590 ACAACCATCAACGATCAATCACAA 59.481 37.500 0.00 0.00 0.00 3.33
2331 2816 3.383505 ACGATCAATCACAATACTCCGGA 59.616 43.478 2.93 2.93 0.00 5.14
2336 2821 4.808895 TCAATCACAATACTCCGGAATTCG 59.191 41.667 5.23 0.00 38.88 3.34
2338 2823 4.041740 TCACAATACTCCGGAATTCGAG 57.958 45.455 5.23 8.36 42.43 4.04
2339 2824 3.697542 TCACAATACTCCGGAATTCGAGA 59.302 43.478 5.23 6.62 42.43 4.04
2340 2825 4.341235 TCACAATACTCCGGAATTCGAGAT 59.659 41.667 5.23 4.36 42.43 2.75
2341 2826 4.445718 CACAATACTCCGGAATTCGAGATG 59.554 45.833 5.23 12.41 42.43 2.90
2342 2827 2.795175 TACTCCGGAATTCGAGATGC 57.205 50.000 5.23 0.00 42.43 3.91
2343 2828 1.115467 ACTCCGGAATTCGAGATGCT 58.885 50.000 5.23 0.00 42.43 3.79
2344 2829 1.202463 ACTCCGGAATTCGAGATGCTG 60.202 52.381 5.23 0.00 42.43 4.41
2345 2830 0.104855 TCCGGAATTCGAGATGCTGG 59.895 55.000 0.00 6.97 42.43 4.85
2346 2831 0.882042 CCGGAATTCGAGATGCTGGG 60.882 60.000 0.00 0.00 42.43 4.45
2357 2842 3.813606 ATGCTGGGGTGCAGTGCAA 62.814 57.895 21.67 2.72 46.71 4.08
2358 2843 3.225798 GCTGGGGTGCAGTGCAAA 61.226 61.111 21.67 5.12 41.47 3.68
2359 2844 2.730094 CTGGGGTGCAGTGCAAAC 59.270 61.111 21.67 15.74 41.47 2.93
2360 2845 3.198236 CTGGGGTGCAGTGCAAACG 62.198 63.158 21.67 3.06 41.47 3.60
2362 2847 2.781158 GGGGTGCAGTGCAAACGTT 61.781 57.895 21.67 0.00 41.47 3.99
2365 2850 1.061887 GTGCAGTGCAAACGTTCGT 59.938 52.632 21.67 0.00 41.47 3.85
2369 2867 1.656429 GCAGTGCAAACGTTCGTGTAG 60.656 52.381 11.09 0.00 0.00 2.74
2380 2878 2.413765 CGTTCGTGTAGGTGTAGGTGAG 60.414 54.545 0.00 0.00 0.00 3.51
2387 2885 4.040095 GTGTAGGTGTAGGTGAGGTTCTTT 59.960 45.833 0.00 0.00 0.00 2.52
2400 2898 2.031683 AGGTTCTTTTCACGCAGAAACG 59.968 45.455 3.40 2.80 45.48 3.60
2401 2899 2.372350 GTTCTTTTCACGCAGAAACGG 58.628 47.619 3.40 1.44 45.48 4.44
2423 2921 1.683025 CAGGGTGCATGGAATGGCA 60.683 57.895 0.00 0.00 46.86 4.92
2426 2924 0.971959 GGGTGCATGGAATGGCAAGA 60.972 55.000 0.00 0.00 46.86 3.02
2427 2925 0.458669 GGTGCATGGAATGGCAAGAG 59.541 55.000 0.00 0.00 46.86 2.85
2428 2926 0.458669 GTGCATGGAATGGCAAGAGG 59.541 55.000 0.00 0.00 46.86 3.69
2429 2927 0.040058 TGCATGGAATGGCAAGAGGT 59.960 50.000 0.00 0.00 46.86 3.85
2430 2928 1.284491 TGCATGGAATGGCAAGAGGTA 59.716 47.619 0.00 0.00 46.86 3.08
2431 2929 1.952296 GCATGGAATGGCAAGAGGTAG 59.048 52.381 0.00 0.00 46.86 3.18
2443 2941 2.681778 AGGTAGCAGAGTGCCGCT 60.682 61.111 0.00 0.00 46.52 5.52
2452 2950 1.068250 GAGTGCCGCTAGACCCATC 59.932 63.158 0.00 0.00 0.00 3.51
2453 2951 1.381872 AGTGCCGCTAGACCCATCT 60.382 57.895 0.00 0.00 39.15 2.90
2454 2952 1.068250 GTGCCGCTAGACCCATCTC 59.932 63.158 0.00 0.00 36.29 2.75
2455 2953 1.381191 TGCCGCTAGACCCATCTCA 60.381 57.895 0.00 0.00 36.29 3.27
2456 2954 1.068250 GCCGCTAGACCCATCTCAC 59.932 63.158 0.00 0.00 36.29 3.51
2457 2955 1.742768 CCGCTAGACCCATCTCACC 59.257 63.158 0.00 0.00 36.29 4.02
2458 2956 1.742768 CGCTAGACCCATCTCACCC 59.257 63.158 0.00 0.00 36.29 4.61
2459 2957 1.043116 CGCTAGACCCATCTCACCCA 61.043 60.000 0.00 0.00 36.29 4.51
2460 2958 0.466124 GCTAGACCCATCTCACCCAC 59.534 60.000 0.00 0.00 36.29 4.61
2461 2959 1.866015 CTAGACCCATCTCACCCACA 58.134 55.000 0.00 0.00 36.29 4.17
2462 2960 2.402564 CTAGACCCATCTCACCCACAT 58.597 52.381 0.00 0.00 36.29 3.21
2463 2961 0.914644 AGACCCATCTCACCCACATG 59.085 55.000 0.00 0.00 0.00 3.21
2464 2962 0.749454 GACCCATCTCACCCACATGC 60.749 60.000 0.00 0.00 0.00 4.06
2465 2963 1.303948 CCCATCTCACCCACATGCA 59.696 57.895 0.00 0.00 0.00 3.96
2466 2964 1.033746 CCCATCTCACCCACATGCAC 61.034 60.000 0.00 0.00 0.00 4.57
2496 2994 1.372499 GGCAACGTCGTCACTGCTA 60.372 57.895 17.40 0.00 35.13 3.49
2499 2997 1.080705 AACGTCGTCACTGCTAGGC 60.081 57.895 0.00 0.00 0.00 3.93
2516 3014 1.226660 GCGATTTCATGGTTGGCCG 60.227 57.895 0.00 0.00 37.67 6.13
2533 3031 1.727022 CGCGCCACTTCTTTTGCAG 60.727 57.895 0.00 0.00 0.00 4.41
2546 3044 0.106769 TTTGCAGGCAGACACAAGGA 60.107 50.000 0.00 0.00 0.00 3.36
2551 3049 1.197430 AGGCAGACACAAGGAGGAGG 61.197 60.000 0.00 0.00 0.00 4.30
2552 3050 1.194781 GGCAGACACAAGGAGGAGGA 61.195 60.000 0.00 0.00 0.00 3.71
2555 3053 0.907230 AGACACAAGGAGGAGGAGCC 60.907 60.000 0.00 0.00 0.00 4.70
2556 3054 2.232298 GACACAAGGAGGAGGAGCCG 62.232 65.000 0.00 0.00 43.43 5.52
2561 3059 4.292178 GGAGGAGGAGCCGCATCG 62.292 72.222 0.00 0.00 43.43 3.84
2568 3066 1.153549 GGAGCCGCATCGTCTCTTT 60.154 57.895 0.00 0.00 0.00 2.52
2581 3079 3.119459 TCGTCTCTTTGCTCGCTTTATCT 60.119 43.478 0.00 0.00 0.00 1.98
2582 3080 3.614616 CGTCTCTTTGCTCGCTTTATCTT 59.385 43.478 0.00 0.00 0.00 2.40
2585 3083 6.018542 GTCTCTTTGCTCGCTTTATCTTTTC 58.981 40.000 0.00 0.00 0.00 2.29
2625 3129 1.626654 CGAGACGCGCATTTTGAGGT 61.627 55.000 5.73 0.00 0.00 3.85
2674 3178 0.389426 GCCTTGAACCTCGCTACGAA 60.389 55.000 0.00 0.00 34.74 3.85
2718 3222 3.945434 CGATGCATGGCGACCTGC 61.945 66.667 12.09 12.09 45.38 4.85
2728 3232 1.098050 GGCGACCTGCTGATTTGATT 58.902 50.000 0.00 0.00 45.43 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 188 1.276622 GTGGTGGTCATCAGGTAGGT 58.723 55.000 0.00 0.00 0.00 3.08
230 232 0.466124 AGGGAAGCCAAGCTCGTATC 59.534 55.000 0.00 0.00 38.25 2.24
231 233 0.466124 GAGGGAAGCCAAGCTCGTAT 59.534 55.000 0.00 0.00 38.25 3.06
232 234 0.902984 TGAGGGAAGCCAAGCTCGTA 60.903 55.000 0.00 0.00 38.25 3.43
233 235 2.217038 TGAGGGAAGCCAAGCTCGT 61.217 57.895 0.00 0.00 38.25 4.18
234 236 1.743252 GTGAGGGAAGCCAAGCTCG 60.743 63.158 0.00 0.00 38.25 5.03
235 237 0.034670 ATGTGAGGGAAGCCAAGCTC 60.035 55.000 0.00 0.00 38.25 4.09
236 238 0.034670 GATGTGAGGGAAGCCAAGCT 60.035 55.000 0.00 0.00 42.56 3.74
237 239 0.322816 TGATGTGAGGGAAGCCAAGC 60.323 55.000 0.00 0.00 0.00 4.01
239 241 0.770499 TGTGATGTGAGGGAAGCCAA 59.230 50.000 0.00 0.00 0.00 4.52
240 242 0.994247 ATGTGATGTGAGGGAAGCCA 59.006 50.000 0.00 0.00 0.00 4.75
241 243 1.340405 ACATGTGATGTGAGGGAAGCC 60.340 52.381 0.00 0.00 43.01 4.35
246 250 1.091771 GGCGACATGTGATGTGAGGG 61.092 60.000 1.15 0.00 45.03 4.30
247 251 1.423721 CGGCGACATGTGATGTGAGG 61.424 60.000 1.15 0.00 45.03 3.86
311 315 3.993081 GGATGATTCTTGGAGCGAGTATG 59.007 47.826 0.00 0.00 0.00 2.39
312 316 3.900601 AGGATGATTCTTGGAGCGAGTAT 59.099 43.478 0.00 0.00 0.00 2.12
313 317 3.300388 AGGATGATTCTTGGAGCGAGTA 58.700 45.455 0.00 0.00 0.00 2.59
314 318 2.114616 AGGATGATTCTTGGAGCGAGT 58.885 47.619 0.00 0.00 0.00 4.18
315 319 2.871022 CAAGGATGATTCTTGGAGCGAG 59.129 50.000 5.53 0.00 38.26 5.03
318 322 2.652590 AGCAAGGATGATTCTTGGAGC 58.347 47.619 14.94 1.09 41.21 4.70
336 348 8.608844 ATTGATACTACTATGGTTGCTTTAGC 57.391 34.615 0.00 0.00 42.50 3.09
389 403 2.517875 GCATGCAGGGCCCTACTG 60.518 66.667 28.13 22.22 38.95 2.74
436 450 0.771755 AGGACAGGGAGGTTCCAAAC 59.228 55.000 0.00 0.00 38.64 2.93
472 486 7.813148 TCAGCCTACGTATAAATAGCAGAATTC 59.187 37.037 0.00 0.00 0.00 2.17
582 605 1.068281 CAGCAGATAGAGATGTGGCGT 59.932 52.381 0.00 0.00 0.00 5.68
684 714 7.001674 AGTATGGTCTTCTACTCTATCTGGTG 58.998 42.308 0.00 0.00 0.00 4.17
686 716 9.747898 AATAGTATGGTCTTCTACTCTATCTGG 57.252 37.037 0.00 0.00 30.98 3.86
691 721 9.887629 CCGATAATAGTATGGTCTTCTACTCTA 57.112 37.037 0.00 0.00 30.98 2.43
692 722 7.337436 GCCGATAATAGTATGGTCTTCTACTCT 59.663 40.741 0.00 0.00 30.98 3.24
693 723 7.120873 TGCCGATAATAGTATGGTCTTCTACTC 59.879 40.741 0.00 0.00 30.98 2.59
694 724 6.946583 TGCCGATAATAGTATGGTCTTCTACT 59.053 38.462 0.00 0.00 33.02 2.57
695 725 7.154435 TGCCGATAATAGTATGGTCTTCTAC 57.846 40.000 0.00 0.00 0.00 2.59
743 777 4.105754 TGGAAGAAGAGAGAGTGAGTGA 57.894 45.455 0.00 0.00 0.00 3.41
843 897 3.827898 GACGTCTCCTCCGCCTGG 61.828 72.222 8.70 0.00 0.00 4.45
848 911 1.742880 TACCACGACGTCTCCTCCG 60.743 63.158 14.70 1.85 0.00 4.63
863 926 0.110192 GCTTGCTTCGCACAAGTACC 60.110 55.000 11.73 0.00 45.09 3.34
865 928 2.337583 CTAGCTTGCTTCGCACAAGTA 58.662 47.619 0.00 0.00 45.09 2.24
959 1022 4.112341 CTTGCTTCTGCGGGCTGC 62.112 66.667 12.43 12.43 43.34 5.25
960 1023 1.919956 CTTCTTGCTTCTGCGGGCTG 61.920 60.000 0.00 0.00 43.34 4.85
965 1028 1.462670 GGACTTCTTCTTGCTTCTGCG 59.537 52.381 0.00 0.00 43.34 5.18
977 1041 1.188219 TCGCTCTGGCTGGACTTCTT 61.188 55.000 0.00 0.00 36.09 2.52
1016 1088 1.300465 CTGATCCGGCATCGACCAG 60.300 63.158 0.00 0.00 39.00 4.00
1210 1285 0.536915 GGATCCTCCAATGCAGCTCC 60.537 60.000 3.84 0.00 36.28 4.70
1282 1357 4.669318 AGATGACACGAGTAACAATACCG 58.331 43.478 0.00 0.00 34.18 4.02
1296 1372 3.305398 AAGAACGACCAGAGATGACAC 57.695 47.619 0.00 0.00 0.00 3.67
1298 1374 4.181309 AGAAAGAACGACCAGAGATGAC 57.819 45.455 0.00 0.00 0.00 3.06
1310 1386 4.455124 CGCAGTTTTAGGAAGAAAGAACG 58.545 43.478 0.00 0.00 0.00 3.95
1317 1393 1.000506 ACGAGCGCAGTTTTAGGAAGA 59.999 47.619 11.47 0.00 0.00 2.87
1325 1409 3.631993 AAACTAAGCACGAGCGCAGTTT 61.632 45.455 23.48 23.48 45.90 2.66
1331 1415 9.672633 ACTAGAGAAGTAAACTAAGCACGAGCG 62.673 44.444 0.00 0.00 40.87 5.03
1342 1426 8.323567 AGCACTAGTCTACTAGAGAAGTAAACT 58.676 37.037 21.12 4.20 46.80 2.66
1343 1427 8.496707 AGCACTAGTCTACTAGAGAAGTAAAC 57.503 38.462 21.12 2.29 46.80 2.01
1344 1428 9.598517 GTAGCACTAGTCTACTAGAGAAGTAAA 57.401 37.037 21.12 0.00 46.80 2.01
1357 1441 5.033589 GGTACAGAGGTAGCACTAGTCTA 57.966 47.826 0.00 0.00 45.18 2.59
1374 1458 5.843673 TTTTGCAGTTCAAATCTGGTACA 57.156 34.783 0.00 0.00 43.53 2.90
1375 1459 5.173131 CGTTTTTGCAGTTCAAATCTGGTAC 59.827 40.000 0.00 0.00 43.53 3.34
1377 1461 4.111916 CGTTTTTGCAGTTCAAATCTGGT 58.888 39.130 0.00 0.00 43.53 4.00
1378 1462 4.111916 ACGTTTTTGCAGTTCAAATCTGG 58.888 39.130 0.00 0.00 43.53 3.86
1381 1465 5.949233 AAGACGTTTTTGCAGTTCAAATC 57.051 34.783 0.00 0.00 43.53 2.17
1382 1466 9.691362 AATATAAGACGTTTTTGCAGTTCAAAT 57.309 25.926 0.00 0.00 43.53 2.32
1384 1468 9.522804 AAAATATAAGACGTTTTTGCAGTTCAA 57.477 25.926 0.00 0.00 0.00 2.69
1385 1469 8.963130 CAAAATATAAGACGTTTTTGCAGTTCA 58.037 29.630 7.67 0.00 33.75 3.18
1386 1470 9.176181 TCAAAATATAAGACGTTTTTGCAGTTC 57.824 29.630 13.47 0.00 38.38 3.01
1387 1471 9.691362 ATCAAAATATAAGACGTTTTTGCAGTT 57.309 25.926 13.47 0.00 38.38 3.16
1390 1474 9.268255 CGTATCAAAATATAAGACGTTTTTGCA 57.732 29.630 13.47 6.02 38.38 4.08
1391 1475 9.480538 TCGTATCAAAATATAAGACGTTTTTGC 57.519 29.630 13.47 2.95 38.38 3.68
1413 1497 9.979270 CGTTAGAAGTTCTATACTTTCTTCGTA 57.021 33.333 13.34 0.00 47.00 3.43
1414 1498 8.510505 ACGTTAGAAGTTCTATACTTTCTTCGT 58.489 33.333 13.34 9.77 47.00 3.85
1415 1499 8.892887 ACGTTAGAAGTTCTATACTTTCTTCG 57.107 34.615 13.34 9.29 47.00 3.79
1425 1509 8.964772 AGTGTGGTTATACGTTAGAAGTTCTAT 58.035 33.333 13.34 2.14 0.00 1.98
1426 1510 8.340618 AGTGTGGTTATACGTTAGAAGTTCTA 57.659 34.615 8.59 8.59 0.00 2.10
1427 1511 7.224522 AGTGTGGTTATACGTTAGAAGTTCT 57.775 36.000 10.87 10.87 0.00 3.01
1428 1512 7.880059 AAGTGTGGTTATACGTTAGAAGTTC 57.120 36.000 0.00 0.00 0.00 3.01
1429 1513 7.712205 ACAAAGTGTGGTTATACGTTAGAAGTT 59.288 33.333 0.00 0.00 0.00 2.66
1430 1514 7.212274 ACAAAGTGTGGTTATACGTTAGAAGT 58.788 34.615 0.00 0.00 0.00 3.01
1431 1515 7.647907 ACAAAGTGTGGTTATACGTTAGAAG 57.352 36.000 0.00 0.00 0.00 2.85
1432 1516 8.359642 AGTACAAAGTGTGGTTATACGTTAGAA 58.640 33.333 0.00 0.00 0.00 2.10
1433 1517 7.809331 CAGTACAAAGTGTGGTTATACGTTAGA 59.191 37.037 0.00 0.00 0.00 2.10
1434 1518 7.596248 ACAGTACAAAGTGTGGTTATACGTTAG 59.404 37.037 0.00 0.00 37.88 2.34
1435 1519 7.432869 ACAGTACAAAGTGTGGTTATACGTTA 58.567 34.615 0.00 0.00 37.88 3.18
1436 1520 6.282930 ACAGTACAAAGTGTGGTTATACGTT 58.717 36.000 0.00 0.00 37.88 3.99
1437 1521 5.846203 ACAGTACAAAGTGTGGTTATACGT 58.154 37.500 0.00 0.00 37.88 3.57
1438 1522 7.872163 TTACAGTACAAAGTGTGGTTATACG 57.128 36.000 0.00 0.00 39.65 3.06
1441 1525 9.181061 AGTTTTTACAGTACAAAGTGTGGTTAT 57.819 29.630 0.00 0.00 39.65 1.89
1502 1612 9.551734 CTATATGGCTCTGCATTATTAGCATTA 57.448 33.333 0.00 0.00 41.82 1.90
1520 1630 3.265791 GAGTAGGTGCATGCTATATGGC 58.734 50.000 20.33 3.73 0.00 4.40
1560 1679 3.330110 CAGCCAGAGGATCCTTCCATATT 59.670 47.826 17.42 0.00 45.30 1.28
1561 1680 2.911636 CAGCCAGAGGATCCTTCCATAT 59.088 50.000 17.42 0.00 45.30 1.78
1562 1681 2.333069 CAGCCAGAGGATCCTTCCATA 58.667 52.381 17.42 0.00 45.30 2.74
1596 1715 1.107538 GTCTGCATGGCCATGATGCT 61.108 55.000 43.18 9.52 45.45 3.79
1597 1716 1.107538 AGTCTGCATGGCCATGATGC 61.108 55.000 43.18 32.05 45.45 3.91
1598 1717 1.399714 AAGTCTGCATGGCCATGATG 58.600 50.000 43.18 32.56 41.20 3.07
1599 1718 2.579873 GTAAGTCTGCATGGCCATGAT 58.420 47.619 43.18 24.09 41.20 2.45
1600 1719 1.408683 GGTAAGTCTGCATGGCCATGA 60.409 52.381 43.18 27.76 41.20 3.07
1601 1720 1.027357 GGTAAGTCTGCATGGCCATG 58.973 55.000 36.80 36.80 41.60 3.66
1602 1721 0.921896 AGGTAAGTCTGCATGGCCAT 59.078 50.000 14.09 14.09 0.00 4.40
1666 1785 5.426504 TGAAAAAGCAAACACATCATGGTT 58.573 33.333 0.00 0.00 39.53 3.67
1752 1876 2.416547 CTCAGCATTGATCGACGGTTTT 59.583 45.455 0.00 0.00 31.68 2.43
1760 1884 1.202498 TGAGCCTCTCAGCATTGATCG 60.202 52.381 0.00 0.00 35.39 3.69
1780 1904 2.431601 GTGCTCTGCTCGCTCGTT 60.432 61.111 0.00 0.00 0.00 3.85
1781 1905 3.674523 TGTGCTCTGCTCGCTCGT 61.675 61.111 0.00 0.00 0.00 4.18
1850 1974 0.322816 ACCATCATGAGCACCACCAC 60.323 55.000 0.09 0.00 0.00 4.16
2074 2208 0.179702 TGATAGCAGGCTCAGCTTGG 59.820 55.000 11.30 0.00 43.25 3.61
2075 2209 1.134461 AGTGATAGCAGGCTCAGCTTG 60.134 52.381 3.92 3.92 43.25 4.01
2076 2210 1.202330 AGTGATAGCAGGCTCAGCTT 58.798 50.000 4.54 0.00 43.25 3.74
2077 2211 1.686052 GTAGTGATAGCAGGCTCAGCT 59.314 52.381 4.64 4.64 45.77 4.24
2078 2212 1.686052 AGTAGTGATAGCAGGCTCAGC 59.314 52.381 0.00 0.00 0.00 4.26
2079 2213 2.954989 TGAGTAGTGATAGCAGGCTCAG 59.045 50.000 0.00 0.00 0.00 3.35
2080 2214 2.690497 GTGAGTAGTGATAGCAGGCTCA 59.310 50.000 0.00 5.34 0.00 4.26
2081 2215 2.955660 AGTGAGTAGTGATAGCAGGCTC 59.044 50.000 0.00 0.00 0.00 4.70
2082 2216 3.025322 AGTGAGTAGTGATAGCAGGCT 57.975 47.619 0.00 0.00 0.00 4.58
2083 2217 3.131223 TGAAGTGAGTAGTGATAGCAGGC 59.869 47.826 0.00 0.00 0.00 4.85
2084 2218 4.400884 AGTGAAGTGAGTAGTGATAGCAGG 59.599 45.833 0.00 0.00 0.00 4.85
2085 2219 5.124617 TGAGTGAAGTGAGTAGTGATAGCAG 59.875 44.000 0.00 0.00 0.00 4.24
2086 2220 5.010282 TGAGTGAAGTGAGTAGTGATAGCA 58.990 41.667 0.00 0.00 0.00 3.49
2087 2221 5.106118 TGTGAGTGAAGTGAGTAGTGATAGC 60.106 44.000 0.00 0.00 0.00 2.97
2088 2222 6.072452 TGTGTGAGTGAAGTGAGTAGTGATAG 60.072 42.308 0.00 0.00 0.00 2.08
2089 2223 5.768164 TGTGTGAGTGAAGTGAGTAGTGATA 59.232 40.000 0.00 0.00 0.00 2.15
2090 2224 4.584743 TGTGTGAGTGAAGTGAGTAGTGAT 59.415 41.667 0.00 0.00 0.00 3.06
2091 2225 3.951680 TGTGTGAGTGAAGTGAGTAGTGA 59.048 43.478 0.00 0.00 0.00 3.41
2092 2226 4.036852 TCTGTGTGAGTGAAGTGAGTAGTG 59.963 45.833 0.00 0.00 0.00 2.74
2093 2227 4.207955 TCTGTGTGAGTGAAGTGAGTAGT 58.792 43.478 0.00 0.00 0.00 2.73
2094 2228 4.517075 TCTCTGTGTGAGTGAAGTGAGTAG 59.483 45.833 0.00 0.00 43.13 2.57
2095 2229 4.461198 TCTCTGTGTGAGTGAAGTGAGTA 58.539 43.478 0.00 0.00 43.13 2.59
2096 2230 3.291584 TCTCTGTGTGAGTGAAGTGAGT 58.708 45.455 0.00 0.00 43.13 3.41
2097 2231 3.317711 ACTCTCTGTGTGAGTGAAGTGAG 59.682 47.826 2.11 0.00 42.46 3.51
2098 2232 3.291584 ACTCTCTGTGTGAGTGAAGTGA 58.708 45.455 2.11 0.00 42.46 3.41
2099 2233 3.724508 ACTCTCTGTGTGAGTGAAGTG 57.275 47.619 2.11 0.00 42.46 3.16
2100 2234 5.837437 CTTTACTCTCTGTGTGAGTGAAGT 58.163 41.667 17.96 5.92 45.22 3.01
2102 2236 4.342378 AGCTTTACTCTCTGTGTGAGTGAA 59.658 41.667 11.15 8.81 43.66 3.18
2103 2237 3.891977 AGCTTTACTCTCTGTGTGAGTGA 59.108 43.478 11.15 2.37 43.66 3.41
2104 2238 4.233789 GAGCTTTACTCTCTGTGTGAGTG 58.766 47.826 11.15 1.22 43.66 3.51
2105 2239 3.891977 TGAGCTTTACTCTCTGTGTGAGT 59.108 43.478 7.32 7.32 46.41 3.41
2114 2250 5.584251 CCAGGAATCTTTGAGCTTTACTCTC 59.416 44.000 0.00 0.00 46.41 3.20
2135 2271 2.098607 AGAATCGAAATGTGCATGCCAG 59.901 45.455 16.68 1.39 0.00 4.85
2147 2283 8.921353 AGCTAATAGTAGGAGTAGAATCGAAA 57.079 34.615 0.00 0.00 0.00 3.46
2148 2284 8.921353 AAGCTAATAGTAGGAGTAGAATCGAA 57.079 34.615 0.00 0.00 0.00 3.71
2150 2286 8.784994 TGAAAGCTAATAGTAGGAGTAGAATCG 58.215 37.037 0.00 0.00 0.00 3.34
2152 2288 9.649316 ACTGAAAGCTAATAGTAGGAGTAGAAT 57.351 33.333 0.00 0.00 37.60 2.40
2153 2289 9.122779 GACTGAAAGCTAATAGTAGGAGTAGAA 57.877 37.037 0.00 0.00 37.60 2.10
2154 2290 8.496088 AGACTGAAAGCTAATAGTAGGAGTAGA 58.504 37.037 0.00 0.00 37.60 2.59
2155 2291 8.685838 AGACTGAAAGCTAATAGTAGGAGTAG 57.314 38.462 0.00 0.00 37.60 2.57
2157 2293 7.068962 GGAAGACTGAAAGCTAATAGTAGGAGT 59.931 40.741 0.00 0.00 37.60 3.85
2158 2294 7.430441 GGAAGACTGAAAGCTAATAGTAGGAG 58.570 42.308 0.00 0.00 37.60 3.69
2161 2297 6.039493 TCGGGAAGACTGAAAGCTAATAGTAG 59.961 42.308 0.00 0.00 37.60 2.57
2162 2298 5.889853 TCGGGAAGACTGAAAGCTAATAGTA 59.110 40.000 0.00 0.00 37.60 1.82
2177 2313 8.076178 CCAATTATTAAACATCATCGGGAAGAC 58.924 37.037 0.00 0.00 0.00 3.01
2191 2327 6.019398 GCAAACATACGGCCCAATTATTAAAC 60.019 38.462 0.00 0.00 0.00 2.01
2193 2329 5.127194 TGCAAACATACGGCCCAATTATTAA 59.873 36.000 0.00 0.00 0.00 1.40
2195 2331 3.449018 TGCAAACATACGGCCCAATTATT 59.551 39.130 0.00 0.00 0.00 1.40
2196 2332 3.027412 TGCAAACATACGGCCCAATTAT 58.973 40.909 0.00 0.00 0.00 1.28
2197 2333 2.447443 TGCAAACATACGGCCCAATTA 58.553 42.857 0.00 0.00 0.00 1.40
2199 2335 1.136695 CATGCAAACATACGGCCCAAT 59.863 47.619 0.00 0.00 33.67 3.16
2200 2336 0.529833 CATGCAAACATACGGCCCAA 59.470 50.000 0.00 0.00 33.67 4.12
2204 2341 1.919918 GAAAGCATGCAAACATACGGC 59.080 47.619 21.98 0.00 33.67 5.68
2240 2377 4.743644 GTGGTGTCAGTCACTTGTTAGTAC 59.256 45.833 0.00 0.00 45.50 2.73
2243 2380 4.051922 GAGTGGTGTCAGTCACTTGTTAG 58.948 47.826 9.37 0.00 43.41 2.34
2245 2382 2.501723 AGAGTGGTGTCAGTCACTTGTT 59.498 45.455 9.37 0.00 43.41 2.83
2247 2384 2.363680 AGAGAGTGGTGTCAGTCACTTG 59.636 50.000 9.37 0.00 43.41 3.16
2248 2385 2.363680 CAGAGAGTGGTGTCAGTCACTT 59.636 50.000 9.37 2.26 43.41 3.16
2259 2744 0.833287 AAGTGTGTGCAGAGAGTGGT 59.167 50.000 0.00 0.00 0.00 4.16
2261 2746 3.097877 TGTAAGTGTGTGCAGAGAGTG 57.902 47.619 0.00 0.00 0.00 3.51
2263 2748 3.431233 CACATGTAAGTGTGTGCAGAGAG 59.569 47.826 0.00 0.00 43.43 3.20
2264 2749 3.392882 CACATGTAAGTGTGTGCAGAGA 58.607 45.455 0.00 0.00 43.43 3.10
2283 2768 5.458041 TGGTTGTTACTAGGAGTACACAC 57.542 43.478 0.00 0.00 28.93 3.82
2286 2771 6.570957 CGTTGATGGTTGTTACTAGGAGTACA 60.571 42.308 0.00 0.00 28.93 2.90
2292 2777 5.416083 TGATCGTTGATGGTTGTTACTAGG 58.584 41.667 0.00 0.00 0.00 3.02
2320 2805 3.430218 GCATCTCGAATTCCGGAGTATTG 59.570 47.826 3.34 0.00 39.14 1.90
2321 2806 3.322254 AGCATCTCGAATTCCGGAGTATT 59.678 43.478 3.34 1.91 39.14 1.89
2322 2807 2.894126 AGCATCTCGAATTCCGGAGTAT 59.106 45.455 3.34 0.00 39.14 2.12
2331 2816 0.749454 GCACCCCAGCATCTCGAATT 60.749 55.000 0.00 0.00 0.00 2.17
2336 2821 1.748122 CACTGCACCCCAGCATCTC 60.748 63.158 0.00 0.00 45.78 2.75
2338 2823 3.446570 GCACTGCACCCCAGCATC 61.447 66.667 0.00 0.00 45.78 3.91
2339 2824 3.813606 TTGCACTGCACCCCAGCAT 62.814 57.895 2.26 0.00 45.78 3.79
2340 2825 4.519612 TTGCACTGCACCCCAGCA 62.520 61.111 2.26 0.00 45.78 4.41
2341 2826 3.225798 TTTGCACTGCACCCCAGC 61.226 61.111 2.26 0.00 45.78 4.85
2343 2828 3.215568 CGTTTGCACTGCACCCCA 61.216 61.111 2.26 0.00 38.71 4.96
2344 2829 2.677573 GAACGTTTGCACTGCACCCC 62.678 60.000 2.26 0.00 38.71 4.95
2345 2830 1.299089 GAACGTTTGCACTGCACCC 60.299 57.895 2.26 0.00 38.71 4.61
2346 2831 1.654137 CGAACGTTTGCACTGCACC 60.654 57.895 2.26 0.00 38.71 5.01
2357 2842 1.956477 ACCTACACCTACACGAACGTT 59.044 47.619 0.00 0.00 0.00 3.99
2358 2843 1.267806 CACCTACACCTACACGAACGT 59.732 52.381 0.00 0.00 0.00 3.99
2359 2844 1.536766 TCACCTACACCTACACGAACG 59.463 52.381 0.00 0.00 0.00 3.95
2360 2845 2.094854 CCTCACCTACACCTACACGAAC 60.095 54.545 0.00 0.00 0.00 3.95
2362 2847 1.074405 ACCTCACCTACACCTACACGA 59.926 52.381 0.00 0.00 0.00 4.35
2365 2850 3.537795 AGAACCTCACCTACACCTACA 57.462 47.619 0.00 0.00 0.00 2.74
2369 2867 3.813724 GTGAAAAGAACCTCACCTACACC 59.186 47.826 0.00 0.00 36.72 4.16
2380 2878 2.372350 CGTTTCTGCGTGAAAAGAACC 58.628 47.619 10.65 0.00 45.10 3.62
2387 2885 1.959226 GCTCCCGTTTCTGCGTGAA 60.959 57.895 0.00 0.00 0.00 3.18
2400 2898 2.578586 ATTCCATGCACCCTGCTCCC 62.579 60.000 0.00 0.00 45.31 4.30
2401 2899 1.076485 ATTCCATGCACCCTGCTCC 60.076 57.895 0.00 0.00 45.31 4.70
2418 2916 1.209019 CACTCTGCTACCTCTTGCCAT 59.791 52.381 0.00 0.00 0.00 4.40
2420 2918 0.742635 GCACTCTGCTACCTCTTGCC 60.743 60.000 0.00 0.00 40.96 4.52
2423 2921 1.893786 CGGCACTCTGCTACCTCTT 59.106 57.895 0.00 0.00 44.28 2.85
2431 2929 2.202810 GGTCTAGCGGCACTCTGC 60.203 66.667 1.45 0.00 44.91 4.26
2443 2941 2.118679 CATGTGGGTGAGATGGGTCTA 58.881 52.381 0.00 0.00 33.97 2.59
2452 2950 0.250858 TCAAGGTGCATGTGGGTGAG 60.251 55.000 0.00 0.00 0.00 3.51
2453 2951 0.405198 ATCAAGGTGCATGTGGGTGA 59.595 50.000 0.00 0.00 0.00 4.02
2454 2952 2.127271 TATCAAGGTGCATGTGGGTG 57.873 50.000 0.00 0.00 0.00 4.61
2455 2953 2.446435 GTTATCAAGGTGCATGTGGGT 58.554 47.619 0.00 0.00 0.00 4.51
2456 2954 1.750778 GGTTATCAAGGTGCATGTGGG 59.249 52.381 0.00 0.00 0.00 4.61
2457 2955 1.401552 CGGTTATCAAGGTGCATGTGG 59.598 52.381 0.00 0.00 0.00 4.17
2458 2956 1.401552 CCGGTTATCAAGGTGCATGTG 59.598 52.381 0.00 0.00 0.00 3.21
2459 2957 1.681780 CCCGGTTATCAAGGTGCATGT 60.682 52.381 0.00 0.00 0.00 3.21
2460 2958 1.024271 CCCGGTTATCAAGGTGCATG 58.976 55.000 0.00 0.00 0.00 4.06
2461 2959 0.751643 GCCCGGTTATCAAGGTGCAT 60.752 55.000 0.00 0.00 0.00 3.96
2462 2960 1.377987 GCCCGGTTATCAAGGTGCA 60.378 57.895 0.00 0.00 0.00 4.57
2463 2961 0.963355 TTGCCCGGTTATCAAGGTGC 60.963 55.000 0.00 0.00 0.00 5.01
2464 2962 0.808755 GTTGCCCGGTTATCAAGGTG 59.191 55.000 0.00 0.00 0.00 4.00
2465 2963 0.675522 CGTTGCCCGGTTATCAAGGT 60.676 55.000 0.00 0.00 0.00 3.50
2466 2964 0.675522 ACGTTGCCCGGTTATCAAGG 60.676 55.000 0.00 7.34 42.24 3.61
2496 2994 1.322538 GGCCAACCATGAAATCGCCT 61.323 55.000 0.00 0.00 35.26 5.52
2499 2997 1.226660 GCGGCCAACCATGAAATCG 60.227 57.895 2.24 0.00 34.57 3.34
2516 3014 1.372128 CCTGCAAAAGAAGTGGCGC 60.372 57.895 0.00 0.00 0.00 6.53
2533 3031 1.194781 TCCTCCTCCTTGTGTCTGCC 61.195 60.000 0.00 0.00 0.00 4.85
2546 3044 3.532155 GACGATGCGGCTCCTCCT 61.532 66.667 0.00 0.00 0.00 3.69
2555 3053 1.627943 CGAGCAAAGAGACGATGCG 59.372 57.895 0.00 0.00 44.60 4.73
2556 3054 1.080995 AGCGAGCAAAGAGACGATGC 61.081 55.000 0.00 0.00 40.34 3.91
2561 3059 5.538067 AAAGATAAAGCGAGCAAAGAGAC 57.462 39.130 0.00 0.00 0.00 3.36
2568 3066 5.237815 TCAAGAGAAAAGATAAAGCGAGCA 58.762 37.500 0.00 0.00 0.00 4.26
2581 3079 2.247790 GCGGCAGCTCAAGAGAAAA 58.752 52.632 0.00 0.00 41.01 2.29
2582 3080 3.972227 GCGGCAGCTCAAGAGAAA 58.028 55.556 0.00 0.00 41.01 2.52
2603 3107 0.941936 TCAAAATGCGCGTCTCGACA 60.942 50.000 8.43 0.00 41.67 4.35
2604 3108 0.246912 CTCAAAATGCGCGTCTCGAC 60.247 55.000 8.43 0.00 41.67 4.20
2625 3129 1.447140 GCCATGCAGACGTACGGAA 60.447 57.895 21.06 0.00 0.00 4.30
2653 3157 1.295423 GTAGCGAGGTTCAAGGCCA 59.705 57.895 5.01 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.