Multiple sequence alignment - TraesCS5A01G526200

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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 TraesCS5A01G526200 chr5A 100.000 5533 0 0 1 5533 687147907 687153439 0.000000e+00 10218.0
1 TraesCS5A01G526200 chr5A 74.597 496 97 18 4547 5035 687160380 687160853 2.030000e-44 191.0
2 TraesCS5A01G526200 chr4D 88.072 5642 337 162 11 5533 502707500 502712924 0.000000e+00 6381.0
3 TraesCS5A01G526200 chr4D 75.203 617 117 21 4471 5081 502725705 502726291 5.500000e-65 259.0
4 TraesCS5A01G526200 chr4D 100.000 34 0 0 496 529 502707942 502707975 4.630000e-06 63.9
5 TraesCS5A01G526200 chr4B 91.850 1914 107 22 1449 3341 647623176 647625061 0.000000e+00 2625.0
6 TraesCS5A01G526200 chr4B 90.048 1045 78 13 409 1450 647622113 647623134 0.000000e+00 1330.0
7 TraesCS5A01G526200 chr4B 82.688 1421 154 47 4136 5533 647625884 647627235 0.000000e+00 1177.0
8 TraesCS5A01G526200 chr4B 84.658 717 48 30 3363 4029 647625115 647625819 0.000000e+00 658.0
9 TraesCS5A01G526200 chr4B 81.250 432 37 17 11 419 647621668 647622078 5.380000e-80 309.0
10 TraesCS5A01G526200 chr2B 79.608 868 163 7 2220 3083 446081469 446082326 1.320000e-170 610.0
11 TraesCS5A01G526200 chr2A 79.237 891 169 10 2198 3083 508031538 508032417 1.700000e-169 606.0
12 TraesCS5A01G526200 chr2D 78.989 890 173 7 2198 3083 375593904 375594783 3.690000e-166 595.0
13 TraesCS5A01G526200 chr7D 83.200 125 17 4 2948 3070 4794787 4794909 1.630000e-20 111.0
14 TraesCS5A01G526200 chr4A 82.400 125 18 4 2948 3070 738888589 738888467 7.580000e-19 106.0
15 TraesCS5A01G526200 chr3A 84.112 107 16 1 2234 2339 17226112 17226006 9.810000e-18 102.0
16 TraesCS5A01G526200 chr6B 89.062 64 7 0 2220 2283 18593673 18593736 4.590000e-11 80.5


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 TraesCS5A01G526200 chr5A 687147907 687153439 5532 False 10218.0 10218 100.0000 1 5533 1 chr5A.!!$F1 5532
1 TraesCS5A01G526200 chr4D 502707500 502712924 5424 False 6381.0 6381 88.0720 11 5533 1 chr4D.!!$F1 5522
2 TraesCS5A01G526200 chr4D 502725705 502726291 586 False 259.0 259 75.2030 4471 5081 1 chr4D.!!$F3 610
3 TraesCS5A01G526200 chr4B 647621668 647627235 5567 False 1219.8 2625 86.0988 11 5533 5 chr4B.!!$F1 5522
4 TraesCS5A01G526200 chr2B 446081469 446082326 857 False 610.0 610 79.6080 2220 3083 1 chr2B.!!$F1 863
5 TraesCS5A01G526200 chr2A 508031538 508032417 879 False 606.0 606 79.2370 2198 3083 1 chr2A.!!$F1 885
6 TraesCS5A01G526200 chr2D 375593904 375594783 879 False 595.0 595 78.9890 2198 3083 1 chr2D.!!$F1 885

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
972 1112 0.033894 GTCTCCCCCTCTCTCGTCTT 60.034 60.000 0.00 0.0 0.00 3.01 F
973 1113 0.256464 TCTCCCCCTCTCTCGTCTTC 59.744 60.000 0.00 0.0 0.00 2.87 F
1023 1170 0.392595 GGACTCCGAAATGGGTGGTC 60.393 60.000 0.00 0.0 38.76 4.02 F
1140 1287 0.400525 CCTCCATTCTCAGCCCCCTA 60.401 60.000 0.00 0.0 0.00 3.53 F
1715 1911 1.003003 TGCCACGAATCATGGTTCAGA 59.997 47.619 18.55 0.0 39.63 3.27 F
3201 3453 0.035458 GGAAGATATGGCTGGACCCG 59.965 60.000 0.00 0.0 37.83 5.28 F
4171 4527 0.117140 ACAGGTCATCTCTCACCCCA 59.883 55.000 0.00 0.0 32.45 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2331 1.200760 AGGCCATCCTACACACTGCA 61.201 55.000 5.01 0.00 42.06 4.41 R
2196 2434 1.818674 GTGGCCCTGTATGTTCCAAAG 59.181 52.381 0.00 0.00 0.00 2.77 R
2251 2489 2.044352 GCGCCCTTGGGGTTGTAT 60.044 61.111 7.91 0.00 46.51 2.29 R
3104 3345 2.697229 ACTCGAGATTGAGGATGATGCA 59.303 45.455 21.68 0.00 40.39 3.96 R
3620 3916 0.810648 TTGATGGACGATTTGCAGGC 59.189 50.000 0.00 0.00 0.00 4.85 R
4432 4788 0.023732 CACGTAAAGATGCGCGTCTG 59.976 55.000 31.62 20.94 38.30 3.51 R
5455 5864 0.107897 ACAGTGCAGTTCGTTGTGGA 60.108 50.000 0.00 0.00 0.00 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.752198 TTCCCTCCACTGTCCAACG 59.248 57.895 0.00 0.00 0.00 4.10
19 20 0.761323 TTCCCTCCACTGTCCAACGA 60.761 55.000 0.00 0.00 0.00 3.85
20 21 0.761323 TCCCTCCACTGTCCAACGAA 60.761 55.000 0.00 0.00 0.00 3.85
24 25 1.726791 CTCCACTGTCCAACGAAATCG 59.273 52.381 0.48 0.48 46.33 3.34
54 55 4.040461 TGGATTTAATTTGACCGGCCAAAA 59.960 37.500 20.18 9.51 39.20 2.44
55 56 4.629634 GGATTTAATTTGACCGGCCAAAAG 59.370 41.667 20.18 0.00 39.20 2.27
56 57 3.669251 TTAATTTGACCGGCCAAAAGG 57.331 42.857 20.18 0.00 39.20 3.11
57 58 0.684535 AATTTGACCGGCCAAAAGGG 59.315 50.000 20.18 0.00 39.20 3.95
79 80 2.615493 CCAAATGAGGCCTGAACGTACT 60.615 50.000 12.00 0.00 0.00 2.73
125 134 4.141620 TGTTTCTTCTCCTGAGCTTGTTCT 60.142 41.667 0.00 0.00 0.00 3.01
175 184 3.845781 GGATTCTCCTGAGCATTACCA 57.154 47.619 0.00 0.00 32.53 3.25
182 191 4.943705 TCTCCTGAGCATTACCACATTTTC 59.056 41.667 0.00 0.00 0.00 2.29
183 192 4.016444 TCCTGAGCATTACCACATTTTCC 58.984 43.478 0.00 0.00 0.00 3.13
199 208 6.210584 CACATTTTCCCCACAGTTAAATAGGT 59.789 38.462 0.00 0.00 0.00 3.08
222 239 3.545624 CCGAAACCATCTACTACGAGTCG 60.546 52.174 11.85 11.85 0.00 4.18
244 261 2.227626 GAGACTTTTCTCTTGGCCTTGC 59.772 50.000 3.32 0.00 44.54 4.01
253 270 1.834896 TCTTGGCCTTGCGGTAGAATA 59.165 47.619 3.32 0.00 0.00 1.75
255 272 1.200519 TGGCCTTGCGGTAGAATACT 58.799 50.000 3.32 0.00 42.51 2.12
256 273 2.390696 TGGCCTTGCGGTAGAATACTA 58.609 47.619 3.32 0.00 42.51 1.82
257 274 2.364324 TGGCCTTGCGGTAGAATACTAG 59.636 50.000 3.32 0.00 42.51 2.57
258 275 2.626743 GGCCTTGCGGTAGAATACTAGA 59.373 50.000 0.00 0.00 42.51 2.43
259 276 3.069158 GGCCTTGCGGTAGAATACTAGAA 59.931 47.826 0.00 0.00 42.51 2.10
260 277 4.262506 GGCCTTGCGGTAGAATACTAGAAT 60.263 45.833 0.00 0.00 42.51 2.40
261 278 5.298347 GCCTTGCGGTAGAATACTAGAATT 58.702 41.667 0.00 0.00 42.51 2.17
262 279 5.405873 GCCTTGCGGTAGAATACTAGAATTC 59.594 44.000 0.00 0.00 42.51 2.17
263 280 6.739008 GCCTTGCGGTAGAATACTAGAATTCT 60.739 42.308 13.56 13.56 45.79 2.40
294 311 5.304357 TCATCTTGGATATTTCTCCGTGCTA 59.696 40.000 0.00 0.00 38.21 3.49
295 312 5.201713 TCTTGGATATTTCTCCGTGCTAG 57.798 43.478 0.00 0.00 38.21 3.42
296 313 4.649674 TCTTGGATATTTCTCCGTGCTAGT 59.350 41.667 0.00 0.00 38.21 2.57
384 408 1.335324 GCAAGACATGTTGGTGCAGTC 60.335 52.381 18.89 0.00 35.28 3.51
450 522 5.068987 TGCAGTGTCTAATTTCTGGCTTTTT 59.931 36.000 0.00 0.00 0.00 1.94
455 527 5.080068 GTCTAATTTCTGGCTTTTTCGACG 58.920 41.667 0.00 0.00 0.00 5.12
537 657 4.025979 CGACAGTCAAGTTTTGTACACTCC 60.026 45.833 0.00 0.00 0.00 3.85
582 702 4.273148 ACACAGCTTTACCGAGAAAGAT 57.727 40.909 11.76 4.06 38.48 2.40
587 707 8.038944 ACACAGCTTTACCGAGAAAGATATTAA 58.961 33.333 11.76 0.00 38.48 1.40
596 716 8.050778 ACCGAGAAAGATATTAACATTGCAAA 57.949 30.769 1.71 0.00 0.00 3.68
673 807 8.932945 ACTATTTAGTACCGTCGATATCGATA 57.067 34.615 29.00 15.74 41.87 2.92
674 808 9.539825 ACTATTTAGTACCGTCGATATCGATAT 57.460 33.333 29.00 17.77 41.87 1.63
758 893 4.461198 CCTTGTAAACTTGACCCTTGACT 58.539 43.478 0.00 0.00 0.00 3.41
791 931 4.392138 GGTGCCACTTTTCTCATACAGTAC 59.608 45.833 0.00 0.00 0.00 2.73
794 934 6.204882 GTGCCACTTTTCTCATACAGTACTTT 59.795 38.462 0.00 0.00 0.00 2.66
795 935 6.204688 TGCCACTTTTCTCATACAGTACTTTG 59.795 38.462 0.00 0.00 0.00 2.77
796 936 6.426937 GCCACTTTTCTCATACAGTACTTTGA 59.573 38.462 0.00 0.00 0.00 2.69
838 978 4.576216 TCGGTTGCAAAATTCTAAGCAA 57.424 36.364 0.00 0.00 43.90 3.91
962 1102 1.617181 ATCCATCCCTGTCTCCCCCT 61.617 60.000 0.00 0.00 0.00 4.79
963 1103 1.768077 CCATCCCTGTCTCCCCCTC 60.768 68.421 0.00 0.00 0.00 4.30
964 1104 1.316266 CATCCCTGTCTCCCCCTCT 59.684 63.158 0.00 0.00 0.00 3.69
965 1105 0.762461 CATCCCTGTCTCCCCCTCTC 60.762 65.000 0.00 0.00 0.00 3.20
966 1106 0.933791 ATCCCTGTCTCCCCCTCTCT 60.934 60.000 0.00 0.00 0.00 3.10
967 1107 1.075600 CCCTGTCTCCCCCTCTCTC 60.076 68.421 0.00 0.00 0.00 3.20
968 1108 1.454847 CCTGTCTCCCCCTCTCTCG 60.455 68.421 0.00 0.00 0.00 4.04
969 1109 1.304952 CTGTCTCCCCCTCTCTCGT 59.695 63.158 0.00 0.00 0.00 4.18
970 1110 0.750182 CTGTCTCCCCCTCTCTCGTC 60.750 65.000 0.00 0.00 0.00 4.20
971 1111 1.208844 TGTCTCCCCCTCTCTCGTCT 61.209 60.000 0.00 0.00 0.00 4.18
972 1112 0.033894 GTCTCCCCCTCTCTCGTCTT 60.034 60.000 0.00 0.00 0.00 3.01
973 1113 0.256464 TCTCCCCCTCTCTCGTCTTC 59.744 60.000 0.00 0.00 0.00 2.87
1006 1153 2.681064 GCAAGCAGGCAATGGGGA 60.681 61.111 0.00 0.00 0.00 4.81
1023 1170 0.392595 GGACTCCGAAATGGGTGGTC 60.393 60.000 0.00 0.00 38.76 4.02
1140 1287 0.400525 CCTCCATTCTCAGCCCCCTA 60.401 60.000 0.00 0.00 0.00 3.53
1197 1344 8.994226 ATGAACTGGATCAACGGTAAGATACCA 61.994 40.741 7.29 8.06 39.75 3.25
1230 1381 4.562347 GCTGGACTTGTCTGAATCTTCTCA 60.562 45.833 0.61 0.00 0.00 3.27
1240 1391 6.317140 TGTCTGAATCTTCTCATGTTTATGCC 59.683 38.462 0.00 0.00 34.21 4.40
1242 1393 5.759059 TGAATCTTCTCATGTTTATGCCCT 58.241 37.500 0.00 0.00 34.21 5.19
1256 1407 1.743252 GCCCTGCTCCGTCTTCAAG 60.743 63.158 0.00 0.00 0.00 3.02
1265 1416 5.070685 TGCTCCGTCTTCAAGCTAGATATA 58.929 41.667 0.00 0.00 36.96 0.86
1282 1433 9.849166 GCTAGATATAGCTCTCGTTCTTAAATT 57.151 33.333 12.13 0.00 39.84 1.82
1288 1439 5.542779 AGCTCTCGTTCTTAAATTCACACT 58.457 37.500 0.00 0.00 0.00 3.55
1291 1442 6.292919 GCTCTCGTTCTTAAATTCACACTTGT 60.293 38.462 0.00 0.00 0.00 3.16
1296 1447 8.653338 TCGTTCTTAAATTCACACTTGTATAGC 58.347 33.333 0.00 0.00 0.00 2.97
1297 1448 7.903431 CGTTCTTAAATTCACACTTGTATAGCC 59.097 37.037 0.00 0.00 0.00 3.93
1300 1451 8.318412 TCTTAAATTCACACTTGTATAGCCAGA 58.682 33.333 0.00 0.00 0.00 3.86
1301 1452 8.856153 TTAAATTCACACTTGTATAGCCAGAA 57.144 30.769 0.00 0.00 0.00 3.02
1302 1453 6.992063 AATTCACACTTGTATAGCCAGAAG 57.008 37.500 0.00 0.00 0.00 2.85
1303 1454 5.483685 TTCACACTTGTATAGCCAGAAGT 57.516 39.130 0.00 0.00 32.62 3.01
1332 1483 1.174783 GTCAGGCCGTAGACAGAGAA 58.825 55.000 17.55 0.00 34.93 2.87
1368 1519 4.825546 AATGCCGATGCTGATTTTAGAG 57.174 40.909 0.00 0.00 38.71 2.43
1376 1527 5.106555 CGATGCTGATTTTAGAGGTGTGTTT 60.107 40.000 0.00 0.00 0.00 2.83
1382 1533 7.639113 TGATTTTAGAGGTGTGTTTTGTTCT 57.361 32.000 0.00 0.00 0.00 3.01
1404 1555 1.101049 CATGGGGGCGGATACAACAC 61.101 60.000 0.00 0.00 0.00 3.32
1567 1762 4.448732 GCGTCAAAATTGATGGCTTTCTTT 59.551 37.500 15.18 0.00 42.91 2.52
1568 1763 5.388786 GCGTCAAAATTGATGGCTTTCTTTC 60.389 40.000 15.18 0.00 42.91 2.62
1598 1793 2.173519 CCGTGTTAGTTAGGGAGTCCA 58.826 52.381 12.30 0.00 34.83 4.02
1635 1830 9.144298 TCTTCTTCTAGTTCCTTGAGAAAAGTA 57.856 33.333 0.00 0.00 35.85 2.24
1639 1834 8.707796 TTCTAGTTCCTTGAGAAAAGTAGAGA 57.292 34.615 0.00 0.00 35.85 3.10
1642 1837 6.169800 AGTTCCTTGAGAAAAGTAGAGATGC 58.830 40.000 0.00 0.00 35.85 3.91
1644 1839 6.114187 TCCTTGAGAAAAGTAGAGATGCAA 57.886 37.500 0.00 0.00 0.00 4.08
1655 1850 6.793492 AGTAGAGATGCAAGTTCAAAGTTC 57.207 37.500 0.00 0.00 0.00 3.01
1675 1871 2.576317 GCAGTAGCCGACGACGAC 60.576 66.667 9.28 0.00 42.66 4.34
1706 1902 1.026182 GCTCACCATGCCACGAATCA 61.026 55.000 0.00 0.00 0.00 2.57
1708 1904 1.332686 CTCACCATGCCACGAATCATG 59.667 52.381 0.00 0.00 39.67 3.07
1714 1910 1.452110 TGCCACGAATCATGGTTCAG 58.548 50.000 18.55 12.96 39.63 3.02
1715 1911 1.003003 TGCCACGAATCATGGTTCAGA 59.997 47.619 18.55 0.00 39.63 3.27
1811 2007 8.928270 TGTTTACTAGAGCTTATTGTAAGAGC 57.072 34.615 0.00 0.00 36.68 4.09
1925 2121 1.174078 TGGTACGACTTCTGCGACCA 61.174 55.000 0.00 0.00 36.95 4.02
2035 2232 6.017400 TCAGAGCATCAAAGACCAAATTTC 57.983 37.500 0.00 0.00 37.82 2.17
2148 2386 2.013400 TCGACAACATGCAACTTGTGT 58.987 42.857 15.14 0.65 30.59 3.72
2149 2387 2.421775 TCGACAACATGCAACTTGTGTT 59.578 40.909 15.14 6.92 36.57 3.32
2150 2388 3.623510 TCGACAACATGCAACTTGTGTTA 59.376 39.130 15.14 0.93 34.55 2.41
2151 2389 3.723764 CGACAACATGCAACTTGTGTTAC 59.276 43.478 15.14 6.72 34.55 2.50
2152 2390 4.495679 CGACAACATGCAACTTGTGTTACT 60.496 41.667 15.14 0.00 34.55 2.24
2153 2391 4.671377 ACAACATGCAACTTGTGTTACTG 58.329 39.130 10.69 0.05 34.55 2.74
2154 2392 4.157656 ACAACATGCAACTTGTGTTACTGT 59.842 37.500 10.69 0.60 34.55 3.55
2155 2393 4.981806 ACATGCAACTTGTGTTACTGTT 57.018 36.364 0.00 0.00 34.60 3.16
2156 2394 6.127869 ACAACATGCAACTTGTGTTACTGTTA 60.128 34.615 10.69 0.00 34.55 2.41
2157 2395 6.060028 ACATGCAACTTGTGTTACTGTTAG 57.940 37.500 0.00 0.00 34.60 2.34
2158 2396 4.545823 TGCAACTTGTGTTACTGTTAGC 57.454 40.909 0.00 0.00 34.60 3.09
2159 2397 3.942115 TGCAACTTGTGTTACTGTTAGCA 59.058 39.130 0.00 0.00 34.60 3.49
2160 2398 4.201871 TGCAACTTGTGTTACTGTTAGCAC 60.202 41.667 0.00 0.00 39.30 4.40
2161 2399 4.035208 GCAACTTGTGTTACTGTTAGCACT 59.965 41.667 9.32 0.00 39.51 4.40
2196 2434 3.795561 CATGTTTGAGACGTGGTTCTC 57.204 47.619 0.00 0.00 40.82 2.87
2251 2489 3.263369 TGGTACCACCTCTTCTACCAA 57.737 47.619 11.60 0.00 39.58 3.67
3079 3320 4.290622 GGATGGGCCGGCATCCAT 62.291 66.667 31.21 30.84 44.99 3.41
3104 3345 2.367486 GTCCTTACTACGTGCTCCTCT 58.633 52.381 0.00 0.00 0.00 3.69
3110 3351 0.457443 CTACGTGCTCCTCTGCATCA 59.543 55.000 0.00 0.00 45.23 3.07
3111 3352 1.068281 CTACGTGCTCCTCTGCATCAT 59.932 52.381 0.00 0.00 45.23 2.45
3115 3356 0.757512 TGCTCCTCTGCATCATCCTC 59.242 55.000 0.00 0.00 38.12 3.71
3117 3358 1.140452 GCTCCTCTGCATCATCCTCAA 59.860 52.381 0.00 0.00 0.00 3.02
3118 3359 2.224572 GCTCCTCTGCATCATCCTCAAT 60.225 50.000 0.00 0.00 0.00 2.57
3126 3367 3.133542 TGCATCATCCTCAATCTCGAGTT 59.866 43.478 13.13 0.15 0.00 3.01
3128 3369 5.163416 TGCATCATCCTCAATCTCGAGTTAA 60.163 40.000 13.13 0.00 0.00 2.01
3129 3370 5.931146 GCATCATCCTCAATCTCGAGTTAAT 59.069 40.000 13.13 0.00 0.00 1.40
3130 3371 6.426328 GCATCATCCTCAATCTCGAGTTAATT 59.574 38.462 13.13 1.92 0.00 1.40
3132 3373 9.481340 CATCATCCTCAATCTCGAGTTAATTAA 57.519 33.333 13.13 0.00 0.00 1.40
3134 3375 8.696374 TCATCCTCAATCTCGAGTTAATTAAGT 58.304 33.333 13.13 5.20 0.00 2.24
3135 3376 8.759641 CATCCTCAATCTCGAGTTAATTAAGTG 58.240 37.037 13.13 0.53 0.00 3.16
3136 3377 6.757010 TCCTCAATCTCGAGTTAATTAAGTGC 59.243 38.462 13.13 2.23 0.00 4.40
3137 3378 6.535150 CCTCAATCTCGAGTTAATTAAGTGCA 59.465 38.462 13.13 0.00 0.00 4.57
3138 3379 7.225538 CCTCAATCTCGAGTTAATTAAGTGCAT 59.774 37.037 13.13 0.00 0.00 3.96
3140 3381 7.549134 TCAATCTCGAGTTAATTAAGTGCATGT 59.451 33.333 13.13 0.00 0.00 3.21
3141 3382 7.849804 ATCTCGAGTTAATTAAGTGCATGTT 57.150 32.000 13.13 0.00 0.00 2.71
3142 3383 7.667043 TCTCGAGTTAATTAAGTGCATGTTT 57.333 32.000 13.13 0.00 0.00 2.83
3201 3453 0.035458 GGAAGATATGGCTGGACCCG 59.965 60.000 0.00 0.00 37.83 5.28
3243 3495 2.765807 CCGGTGGAGGAGCTGGAT 60.766 66.667 0.00 0.00 0.00 3.41
3264 3516 2.360852 CTGAGGGGCAAGGCTGTG 60.361 66.667 0.00 0.00 0.00 3.66
3291 3543 0.249911 GTGACAAGGTCGTCAAGCCT 60.250 55.000 0.00 0.00 46.99 4.58
3555 3848 1.071857 ACTCTCGTTTTCAACCTCCCC 59.928 52.381 0.00 0.00 0.00 4.81
3556 3849 1.348036 CTCTCGTTTTCAACCTCCCCT 59.652 52.381 0.00 0.00 0.00 4.79
3557 3850 1.346722 TCTCGTTTTCAACCTCCCCTC 59.653 52.381 0.00 0.00 0.00 4.30
3558 3851 1.071699 CTCGTTTTCAACCTCCCCTCA 59.928 52.381 0.00 0.00 0.00 3.86
3559 3852 1.702957 TCGTTTTCAACCTCCCCTCAT 59.297 47.619 0.00 0.00 0.00 2.90
3560 3853 2.907696 TCGTTTTCAACCTCCCCTCATA 59.092 45.455 0.00 0.00 0.00 2.15
3561 3854 3.007635 CGTTTTCAACCTCCCCTCATAC 58.992 50.000 0.00 0.00 0.00 2.39
3562 3855 3.307480 CGTTTTCAACCTCCCCTCATACT 60.307 47.826 0.00 0.00 0.00 2.12
3563 3856 4.081309 CGTTTTCAACCTCCCCTCATACTA 60.081 45.833 0.00 0.00 0.00 1.82
3564 3857 5.183969 GTTTTCAACCTCCCCTCATACTAC 58.816 45.833 0.00 0.00 0.00 2.73
3565 3858 4.348020 TTCAACCTCCCCTCATACTACT 57.652 45.455 0.00 0.00 0.00 2.57
3566 3859 4.348020 TCAACCTCCCCTCATACTACTT 57.652 45.455 0.00 0.00 0.00 2.24
3616 3912 4.215399 TCACCACGATTTGAATGGTCTTTC 59.785 41.667 0.00 0.00 45.11 2.62
3620 3916 3.122948 ACGATTTGAATGGTCTTTCGTCG 59.877 43.478 0.00 12.44 35.55 5.12
3624 3920 0.721718 GAATGGTCTTTCGTCGCCTG 59.278 55.000 0.00 0.00 0.00 4.85
3743 4081 5.221461 CCCTGGCTAATACTTATCGACTTGT 60.221 44.000 0.00 0.00 0.00 3.16
3791 4138 3.474570 GAGGTGCCGAGCCTGGAT 61.475 66.667 0.00 0.00 36.29 3.41
3839 4186 3.406361 AACGACGCGCAGAAGCTG 61.406 61.111 5.73 0.00 39.10 4.24
3906 4253 1.614824 CTCTGGGTCCTGGCCTCTT 60.615 63.158 3.32 0.00 0.00 2.85
3907 4254 1.613630 TCTGGGTCCTGGCCTCTTC 60.614 63.158 3.32 0.00 0.00 2.87
4016 4363 4.949856 ACCAAGTATGATTTCACCACATCC 59.050 41.667 0.00 0.00 0.00 3.51
4021 4368 4.598036 ATGATTTCACCACATCCCTCTT 57.402 40.909 0.00 0.00 0.00 2.85
4024 4371 3.874383 TTTCACCACATCCCTCTTTCA 57.126 42.857 0.00 0.00 0.00 2.69
4025 4372 4.387026 TTTCACCACATCCCTCTTTCAT 57.613 40.909 0.00 0.00 0.00 2.57
4031 4384 2.131023 ACATCCCTCTTTCATCTCCCC 58.869 52.381 0.00 0.00 0.00 4.81
4041 4394 4.223923 TCTTTCATCTCCCCTCAACTTCTC 59.776 45.833 0.00 0.00 0.00 2.87
4043 4396 2.834549 TCATCTCCCCTCAACTTCTCAC 59.165 50.000 0.00 0.00 0.00 3.51
4044 4397 2.704190 TCTCCCCTCAACTTCTCACT 57.296 50.000 0.00 0.00 0.00 3.41
4045 4398 2.977808 TCTCCCCTCAACTTCTCACTT 58.022 47.619 0.00 0.00 0.00 3.16
4046 4399 2.634940 TCTCCCCTCAACTTCTCACTTG 59.365 50.000 0.00 0.00 0.00 3.16
4047 4400 2.634940 CTCCCCTCAACTTCTCACTTGA 59.365 50.000 0.00 0.00 0.00 3.02
4048 4401 3.251484 TCCCCTCAACTTCTCACTTGAT 58.749 45.455 0.00 0.00 0.00 2.57
4049 4402 3.008375 TCCCCTCAACTTCTCACTTGATG 59.992 47.826 0.00 0.00 0.00 3.07
4050 4403 3.008375 CCCCTCAACTTCTCACTTGATGA 59.992 47.826 0.00 0.00 35.45 2.92
4051 4404 4.324099 CCCCTCAACTTCTCACTTGATGAT 60.324 45.833 0.00 0.00 36.48 2.45
4088 4441 9.605275 TCCATAGATTTCAAGTGTAAATGAGAG 57.395 33.333 0.00 0.00 0.00 3.20
4092 4445 7.461749 AGATTTCAAGTGTAAATGAGAGGGAA 58.538 34.615 0.00 0.00 0.00 3.97
4094 4447 9.396022 GATTTCAAGTGTAAATGAGAGGGAATA 57.604 33.333 0.00 0.00 0.00 1.75
4171 4527 0.117140 ACAGGTCATCTCTCACCCCA 59.883 55.000 0.00 0.00 32.45 4.96
4246 4602 5.394663 CGGGAAGATCTCTTTGAGAAGCTTA 60.395 44.000 0.00 0.00 42.27 3.09
4289 4645 6.898041 TGTAACATCATTTTGACTAGTGCAC 58.102 36.000 9.40 9.40 0.00 4.57
4337 4693 8.879342 ATTTTTCATTGACCAACGTTGATTTA 57.121 26.923 29.35 12.07 0.00 1.40
4432 4788 1.669115 CATCCATGGCGATCGGGAC 60.669 63.158 18.30 0.00 31.04 4.46
4454 4810 3.650183 CGCGCATCTTTACGTGTTT 57.350 47.368 8.75 0.00 35.20 2.83
4465 4821 2.898729 TACGTGTTTAACAACGGGGA 57.101 45.000 18.41 6.38 35.40 4.81
4466 4822 1.298602 ACGTGTTTAACAACGGGGAC 58.701 50.000 18.41 0.00 35.40 4.46
4496 4852 0.250597 AGGTGTCCAAACTAACGGCC 60.251 55.000 0.00 0.00 0.00 6.13
4583 4939 8.670135 TCGAGAGTTTAAGTTTTTGTTGAATGA 58.330 29.630 0.00 0.00 0.00 2.57
4677 5037 8.500773 TGGTTAGAGAAATTTGTTGTACGATTC 58.499 33.333 0.00 0.00 0.00 2.52
4692 5052 6.683715 TGTACGATTCATAGTTTCTGTCACA 58.316 36.000 0.00 0.00 0.00 3.58
4728 5088 2.019249 CATGATCATCCCACGCTGTTT 58.981 47.619 4.86 0.00 0.00 2.83
4730 5090 2.083774 TGATCATCCCACGCTGTTTTC 58.916 47.619 0.00 0.00 0.00 2.29
4732 5092 2.198827 TCATCCCACGCTGTTTTCAT 57.801 45.000 0.00 0.00 0.00 2.57
4784 5147 6.692486 TCTTTCCACTGATCTCTCTTTGTAC 58.308 40.000 0.00 0.00 0.00 2.90
4788 5151 6.246163 TCCACTGATCTCTCTTTGTACTGTA 58.754 40.000 0.00 0.00 0.00 2.74
4791 5158 7.337184 CCACTGATCTCTCTTTGTACTGTAGTA 59.663 40.741 0.00 0.00 0.00 1.82
4817 5184 3.128415 ACGGATGAGATCGATGATGCTAG 59.872 47.826 0.54 0.00 0.00 3.42
4836 5203 2.025155 AGTCTGACTCAACTGTGACGT 58.975 47.619 4.06 0.00 0.00 4.34
4905 5303 2.028112 GGCACTCCTTGTATGAGTCACA 60.028 50.000 0.00 0.00 41.02 3.58
4906 5304 3.257393 GCACTCCTTGTATGAGTCACAG 58.743 50.000 0.00 0.00 41.02 3.66
4908 5306 2.234908 ACTCCTTGTATGAGTCACAGGC 59.765 50.000 0.00 0.00 38.71 4.85
4909 5307 2.499289 CTCCTTGTATGAGTCACAGGCT 59.501 50.000 0.00 0.00 0.00 4.58
4910 5308 2.497675 TCCTTGTATGAGTCACAGGCTC 59.502 50.000 0.00 0.00 0.00 4.70
4911 5309 2.234661 CCTTGTATGAGTCACAGGCTCA 59.765 50.000 3.58 3.58 45.59 4.26
4934 5333 2.092753 GGGAGCAATGGATCTCTTCACA 60.093 50.000 0.00 0.00 0.00 3.58
4972 5371 3.451141 TTGGTCAAACAGAAACATGGC 57.549 42.857 0.00 0.00 0.00 4.40
4974 5373 1.336755 GGTCAAACAGAAACATGGCGT 59.663 47.619 0.00 0.00 0.00 5.68
4977 5376 3.250040 GTCAAACAGAAACATGGCGTACT 59.750 43.478 0.00 0.00 0.00 2.73
4981 5380 3.067106 ACAGAAACATGGCGTACTCTTG 58.933 45.455 0.00 0.00 0.00 3.02
4991 5390 3.314080 TGGCGTACTCTTGTTCCTTTTTG 59.686 43.478 0.00 0.00 0.00 2.44
4993 5392 4.201980 GGCGTACTCTTGTTCCTTTTTGTT 60.202 41.667 0.00 0.00 0.00 2.83
5039 5441 4.025040 AGTGAAAGAAGGATGCACATGA 57.975 40.909 0.00 0.00 32.16 3.07
5044 5446 1.002430 AGAAGGATGCACATGACACGT 59.998 47.619 0.00 0.00 0.00 4.49
5093 5495 3.004752 ACCAGTGGTGCAGATTATTCC 57.995 47.619 15.86 0.00 32.98 3.01
5096 5498 4.019174 CCAGTGGTGCAGATTATTCCTTT 58.981 43.478 0.00 0.00 0.00 3.11
5098 5500 5.393461 CCAGTGGTGCAGATTATTCCTTTTC 60.393 44.000 0.00 0.00 0.00 2.29
5099 5501 5.416952 CAGTGGTGCAGATTATTCCTTTTCT 59.583 40.000 0.00 0.00 0.00 2.52
5185 5592 5.106673 GGAATCTCGAAAAAGGTTAGTGGTG 60.107 44.000 0.00 0.00 0.00 4.17
5308 5717 6.715347 AAAGCTTATGTTGTCCTGAAAAGT 57.285 33.333 0.00 0.00 0.00 2.66
5309 5718 6.715347 AAGCTTATGTTGTCCTGAAAAGTT 57.285 33.333 0.00 0.00 0.00 2.66
5317 5726 8.691661 ATGTTGTCCTGAAAAGTTGTACTATT 57.308 30.769 0.00 0.00 0.00 1.73
5474 5883 0.107897 TCCACAACGAACTGCACTGT 60.108 50.000 0.00 0.00 0.00 3.55
5488 5897 1.003545 GCACTGTACTGCACAACACTG 60.004 52.381 2.40 0.00 36.48 3.66
5490 5899 3.453424 CACTGTACTGCACAACACTGTA 58.547 45.455 0.00 0.00 36.48 2.74
5491 5900 3.868661 CACTGTACTGCACAACACTGTAA 59.131 43.478 0.00 0.00 36.48 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.761323 TTCGTTGGACAGTGGAGGGA 60.761 55.000 0.00 0.00 0.00 4.20
2 3 0.107831 TTTCGTTGGACAGTGGAGGG 59.892 55.000 0.00 0.00 0.00 4.30
4 5 1.726791 CGATTTCGTTGGACAGTGGAG 59.273 52.381 0.00 0.00 34.11 3.86
5 6 1.341852 TCGATTTCGTTGGACAGTGGA 59.658 47.619 0.00 0.00 40.80 4.02
7 8 2.155732 CACTCGATTTCGTTGGACAGTG 59.844 50.000 0.00 1.94 40.80 3.66
9 10 1.126846 GCACTCGATTTCGTTGGACAG 59.873 52.381 0.00 0.00 40.80 3.51
10 11 1.144969 GCACTCGATTTCGTTGGACA 58.855 50.000 0.00 0.00 40.80 4.02
11 12 1.429463 AGCACTCGATTTCGTTGGAC 58.571 50.000 0.00 0.00 40.80 4.02
12 13 1.798223 CAAGCACTCGATTTCGTTGGA 59.202 47.619 0.00 0.00 40.80 3.53
13 14 1.135972 CCAAGCACTCGATTTCGTTGG 60.136 52.381 0.00 2.82 40.80 3.77
14 15 1.798223 TCCAAGCACTCGATTTCGTTG 59.202 47.619 0.00 0.64 40.80 4.10
15 16 2.163818 TCCAAGCACTCGATTTCGTT 57.836 45.000 0.00 0.00 40.80 3.85
16 17 2.386661 ATCCAAGCACTCGATTTCGT 57.613 45.000 0.00 0.00 40.80 3.85
17 18 3.747099 AAATCCAAGCACTCGATTTCG 57.253 42.857 0.00 0.00 32.12 3.46
18 19 7.754924 TCAAATTAAATCCAAGCACTCGATTTC 59.245 33.333 8.25 0.00 37.40 2.17
19 20 7.542130 GTCAAATTAAATCCAAGCACTCGATTT 59.458 33.333 9.38 9.38 39.10 2.17
20 21 7.029563 GTCAAATTAAATCCAAGCACTCGATT 58.970 34.615 0.00 0.00 0.00 3.34
24 25 5.095490 CGGTCAAATTAAATCCAAGCACTC 58.905 41.667 0.00 0.00 0.00 3.51
58 59 1.737793 GTACGTTCAGGCCTCATTTGG 59.262 52.381 0.00 0.00 0.00 3.28
59 60 2.673368 GAGTACGTTCAGGCCTCATTTG 59.327 50.000 0.00 0.00 0.00 2.32
60 61 2.567615 AGAGTACGTTCAGGCCTCATTT 59.432 45.455 0.00 0.00 0.00 2.32
61 62 2.180276 AGAGTACGTTCAGGCCTCATT 58.820 47.619 0.00 0.00 0.00 2.57
62 63 1.853963 AGAGTACGTTCAGGCCTCAT 58.146 50.000 0.00 0.00 0.00 2.90
63 64 1.272490 CAAGAGTACGTTCAGGCCTCA 59.728 52.381 0.00 0.00 0.00 3.86
68 69 4.188247 TCAATCCAAGAGTACGTTCAGG 57.812 45.455 0.00 0.00 0.00 3.86
79 80 7.484975 ACAAAAACGTGTAAATCAATCCAAGA 58.515 30.769 0.00 0.00 0.00 3.02
125 134 1.633432 AGTCCCCCGTTGATTTCATCA 59.367 47.619 0.00 0.00 37.55 3.07
137 146 1.626825 TCCTTACAAGAAAGTCCCCCG 59.373 52.381 0.00 0.00 0.00 5.73
174 183 6.210584 ACCTATTTAACTGTGGGGAAAATGTG 59.789 38.462 0.00 0.00 0.00 3.21
175 184 6.319715 ACCTATTTAACTGTGGGGAAAATGT 58.680 36.000 0.00 0.00 0.00 2.71
182 191 2.502538 TCGGACCTATTTAACTGTGGGG 59.497 50.000 0.00 0.00 0.00 4.96
183 192 3.899052 TCGGACCTATTTAACTGTGGG 57.101 47.619 0.00 0.00 0.00 4.61
199 208 3.614092 ACTCGTAGTAGATGGTTTCGGA 58.386 45.455 0.00 0.00 0.00 4.55
244 261 8.167605 TGAAGGAGAATTCTAGTATTCTACCG 57.832 38.462 23.66 0.00 43.61 4.02
253 270 7.346698 TCCAAGATGATGAAGGAGAATTCTAGT 59.653 37.037 8.25 0.00 0.00 2.57
255 272 7.681259 TCCAAGATGATGAAGGAGAATTCTA 57.319 36.000 8.25 0.00 0.00 2.10
256 273 6.572182 TCCAAGATGATGAAGGAGAATTCT 57.428 37.500 7.95 7.95 0.00 2.40
257 274 9.517868 AATATCCAAGATGATGAAGGAGAATTC 57.482 33.333 0.00 0.00 0.00 2.17
258 275 9.878737 AAATATCCAAGATGATGAAGGAGAATT 57.121 29.630 0.00 0.00 0.00 2.17
259 276 9.517868 GAAATATCCAAGATGATGAAGGAGAAT 57.482 33.333 0.00 0.00 0.00 2.40
260 277 8.721479 AGAAATATCCAAGATGATGAAGGAGAA 58.279 33.333 0.00 0.00 0.00 2.87
261 278 8.272659 AGAAATATCCAAGATGATGAAGGAGA 57.727 34.615 0.00 0.00 0.00 3.71
262 279 7.607223 GGAGAAATATCCAAGATGATGAAGGAG 59.393 40.741 0.00 0.00 39.34 3.69
263 280 7.456725 GGAGAAATATCCAAGATGATGAAGGA 58.543 38.462 0.00 0.00 39.34 3.36
272 289 4.696479 AGCACGGAGAAATATCCAAGAT 57.304 40.909 0.00 0.00 39.53 2.40
294 311 3.368427 CCCTGTCGTGTCATTGTCATACT 60.368 47.826 0.00 0.00 0.00 2.12
295 312 2.930040 CCCTGTCGTGTCATTGTCATAC 59.070 50.000 0.00 0.00 0.00 2.39
296 313 2.676750 GCCCTGTCGTGTCATTGTCATA 60.677 50.000 0.00 0.00 0.00 2.15
330 347 3.299503 AGCCAGAACATTCAACTTGGTT 58.700 40.909 0.00 0.00 0.00 3.67
384 408 6.441093 TTCATGCAGCTAAGTTATTTCCAG 57.559 37.500 0.00 0.00 0.00 3.86
435 507 4.066490 TCCGTCGAAAAAGCCAGAAATTA 58.934 39.130 0.00 0.00 0.00 1.40
450 522 4.380841 AACATTAGCAATACTCCGTCGA 57.619 40.909 0.00 0.00 0.00 4.20
455 527 8.296713 TGAAAACTCAAACATTAGCAATACTCC 58.703 33.333 0.00 0.00 0.00 3.85
468 540 2.948979 ACGGAGCATGAAAACTCAAACA 59.051 40.909 0.00 0.00 34.48 2.83
469 541 3.626028 ACGGAGCATGAAAACTCAAAC 57.374 42.857 0.00 0.00 34.48 2.93
474 546 5.670485 TGTCATATACGGAGCATGAAAACT 58.330 37.500 0.00 0.00 30.85 2.66
475 547 5.984233 TGTCATATACGGAGCATGAAAAC 57.016 39.130 0.00 0.00 30.85 2.43
537 657 6.569179 TTTATTCCCTTCCGAAGTTTTCAG 57.431 37.500 7.37 0.00 0.00 3.02
673 807 8.190784 ACTTTGATCGAGTTTGTCAAGAAAAAT 58.809 29.630 0.00 0.00 33.82 1.82
674 808 7.535139 ACTTTGATCGAGTTTGTCAAGAAAAA 58.465 30.769 0.00 0.00 33.82 1.94
675 809 7.083875 ACTTTGATCGAGTTTGTCAAGAAAA 57.916 32.000 0.00 0.00 33.82 2.29
676 810 6.677781 ACTTTGATCGAGTTTGTCAAGAAA 57.322 33.333 0.00 0.00 33.82 2.52
677 811 6.677781 AACTTTGATCGAGTTTGTCAAGAA 57.322 33.333 8.12 0.00 33.76 2.52
678 812 7.780008 TTAACTTTGATCGAGTTTGTCAAGA 57.220 32.000 16.48 0.00 38.28 3.02
679 813 8.835467 TTTTAACTTTGATCGAGTTTGTCAAG 57.165 30.769 16.48 0.00 38.28 3.02
680 814 9.796120 ATTTTTAACTTTGATCGAGTTTGTCAA 57.204 25.926 16.48 5.51 38.28 3.18
681 815 9.232082 CATTTTTAACTTTGATCGAGTTTGTCA 57.768 29.630 16.48 0.39 38.28 3.58
682 816 9.233232 ACATTTTTAACTTTGATCGAGTTTGTC 57.767 29.630 16.48 0.00 38.28 3.18
683 817 9.581099 AACATTTTTAACTTTGATCGAGTTTGT 57.419 25.926 16.48 12.29 38.28 2.83
722 857 7.524717 AGTTTACAAGGCATAGTTTGATTGT 57.475 32.000 8.75 8.75 39.06 2.71
726 861 6.016610 GGTCAAGTTTACAAGGCATAGTTTGA 60.017 38.462 0.00 0.00 0.00 2.69
791 931 5.717038 ATCGGCAGTTTTGTTTTTCAAAG 57.283 34.783 0.00 0.00 45.14 2.77
794 934 4.748892 TCAATCGGCAGTTTTGTTTTTCA 58.251 34.783 0.00 0.00 0.00 2.69
795 935 5.387342 CGATCAATCGGCAGTTTTGTTTTTC 60.387 40.000 4.48 0.00 45.93 2.29
796 936 4.444056 CGATCAATCGGCAGTTTTGTTTTT 59.556 37.500 4.48 0.00 45.93 1.94
838 978 1.692148 CGCATGTGATTGGCGTACGT 61.692 55.000 17.90 0.00 45.27 3.57
962 1102 3.010361 AGTTAAGAGGGGAAGACGAGAGA 59.990 47.826 0.00 0.00 0.00 3.10
963 1103 3.129638 CAGTTAAGAGGGGAAGACGAGAG 59.870 52.174 0.00 0.00 0.00 3.20
964 1104 3.090037 CAGTTAAGAGGGGAAGACGAGA 58.910 50.000 0.00 0.00 0.00 4.04
965 1105 2.417515 GCAGTTAAGAGGGGAAGACGAG 60.418 54.545 0.00 0.00 0.00 4.18
966 1106 1.549170 GCAGTTAAGAGGGGAAGACGA 59.451 52.381 0.00 0.00 0.00 4.20
967 1107 1.275291 TGCAGTTAAGAGGGGAAGACG 59.725 52.381 0.00 0.00 0.00 4.18
968 1108 3.339141 CTTGCAGTTAAGAGGGGAAGAC 58.661 50.000 0.00 0.00 31.30 3.01
969 1109 2.290323 GCTTGCAGTTAAGAGGGGAAGA 60.290 50.000 0.00 0.00 31.30 2.87
970 1110 2.087646 GCTTGCAGTTAAGAGGGGAAG 58.912 52.381 0.00 0.00 0.00 3.46
971 1111 1.423541 TGCTTGCAGTTAAGAGGGGAA 59.576 47.619 0.00 0.00 0.00 3.97
972 1112 1.064003 TGCTTGCAGTTAAGAGGGGA 58.936 50.000 0.00 0.00 0.00 4.81
973 1113 1.815003 CTTGCTTGCAGTTAAGAGGGG 59.185 52.381 0.00 0.00 0.00 4.79
996 1143 0.395724 ATTTCGGAGTCCCCATTGCC 60.396 55.000 2.80 0.00 34.14 4.52
997 1144 0.740737 CATTTCGGAGTCCCCATTGC 59.259 55.000 2.80 0.00 34.14 3.56
998 1145 1.392589 CCATTTCGGAGTCCCCATTG 58.607 55.000 2.80 0.00 36.56 2.82
999 1146 0.258774 CCCATTTCGGAGTCCCCATT 59.741 55.000 2.80 0.00 36.56 3.16
1006 1153 1.295423 CGACCACCCATTTCGGAGT 59.705 57.895 0.00 0.00 36.56 3.85
1068 1215 2.892640 CTCCGGCGGACTTCATGA 59.107 61.111 27.46 1.18 0.00 3.07
1140 1287 4.371417 TGGTAGCCCGTCCGGAGT 62.371 66.667 3.06 0.00 37.50 3.85
1197 1344 1.133976 ACAAGTCCAGCAAGAGCAGTT 60.134 47.619 0.00 0.00 45.49 3.16
1230 1381 0.255890 ACGGAGCAGGGCATAAACAT 59.744 50.000 0.00 0.00 0.00 2.71
1240 1391 0.532573 TAGCTTGAAGACGGAGCAGG 59.467 55.000 0.00 0.00 38.85 4.85
1242 1393 1.545841 TCTAGCTTGAAGACGGAGCA 58.454 50.000 0.00 0.00 38.85 4.26
1265 1416 5.542779 AGTGTGAATTTAAGAACGAGAGCT 58.457 37.500 0.00 0.00 0.00 4.09
1282 1433 4.081642 GGACTTCTGGCTATACAAGTGTGA 60.082 45.833 0.00 0.00 0.00 3.58
1288 1439 4.530553 TGTTCTGGACTTCTGGCTATACAA 59.469 41.667 0.00 0.00 0.00 2.41
1291 1442 4.716784 ACATGTTCTGGACTTCTGGCTATA 59.283 41.667 0.00 0.00 0.00 1.31
1295 1446 2.079925 GACATGTTCTGGACTTCTGGC 58.920 52.381 0.00 0.00 0.00 4.85
1296 1447 3.332919 CTGACATGTTCTGGACTTCTGG 58.667 50.000 0.00 0.00 0.00 3.86
1297 1448 3.332919 CCTGACATGTTCTGGACTTCTG 58.667 50.000 0.00 0.00 44.46 3.02
1300 1451 1.271597 GGCCTGACATGTTCTGGACTT 60.272 52.381 18.64 0.00 46.05 3.01
1301 1452 0.326264 GGCCTGACATGTTCTGGACT 59.674 55.000 18.64 0.00 46.05 3.85
1302 1453 1.021390 CGGCCTGACATGTTCTGGAC 61.021 60.000 18.64 16.14 46.07 4.02
1303 1454 1.296392 CGGCCTGACATGTTCTGGA 59.704 57.895 18.64 0.00 44.46 3.86
1332 1483 3.007506 TCGGCATTACGGATGGACATATT 59.992 43.478 3.66 0.00 36.21 1.28
1368 1519 3.490761 CCCATGACAGAACAAAACACACC 60.491 47.826 0.00 0.00 0.00 4.16
1376 1527 1.303236 CGCCCCCATGACAGAACAA 60.303 57.895 0.00 0.00 0.00 2.83
1382 1533 1.275421 TTGTATCCGCCCCCATGACA 61.275 55.000 0.00 0.00 0.00 3.58
1404 1555 3.329386 CAGACCTATGTGTTGTCTGTGG 58.671 50.000 10.01 0.00 46.85 4.17
1480 1674 4.528920 ACACTTGGCTACAAACTAACCAA 58.471 39.130 0.00 0.00 38.04 3.67
1567 1762 1.338864 ACTAACACGGCGAGAGAGAGA 60.339 52.381 16.62 0.00 0.00 3.10
1568 1763 1.088306 ACTAACACGGCGAGAGAGAG 58.912 55.000 16.62 5.32 0.00 3.20
1598 1793 4.967036 ACTAGAAGAAGAAAACAGCTGCT 58.033 39.130 15.27 0.00 0.00 4.24
1635 1830 4.450419 CGAGAACTTTGAACTTGCATCTCT 59.550 41.667 5.41 0.00 32.02 3.10
1639 1834 2.618241 TGCGAGAACTTTGAACTTGCAT 59.382 40.909 0.00 0.00 43.32 3.96
1642 1837 3.951979 ACTGCGAGAACTTTGAACTTG 57.048 42.857 0.00 0.00 0.00 3.16
1644 1839 3.060602 GCTACTGCGAGAACTTTGAACT 58.939 45.455 0.00 0.00 0.00 3.01
1655 1850 2.277373 GTCGTCGGCTACTGCGAG 60.277 66.667 0.00 0.00 40.82 5.03
1808 2004 6.072452 ACAAGTTAATTAGAACCAAGCAGCTC 60.072 38.462 0.00 0.00 0.00 4.09
1809 2005 5.770162 ACAAGTTAATTAGAACCAAGCAGCT 59.230 36.000 0.00 0.00 0.00 4.24
1810 2006 6.013842 ACAAGTTAATTAGAACCAAGCAGC 57.986 37.500 0.00 0.00 0.00 5.25
1811 2007 8.871686 AAAACAAGTTAATTAGAACCAAGCAG 57.128 30.769 0.00 0.00 0.00 4.24
1881 2077 4.512198 TCGGATCTAGAGTCGATGAGTTTC 59.488 45.833 13.87 0.00 0.00 2.78
1896 2092 4.275196 CAGAAGTCGTACCATTCGGATCTA 59.725 45.833 0.00 0.00 35.59 1.98
1925 2121 6.926630 AGACAGAGACAAGTAGAGGAAATT 57.073 37.500 0.00 0.00 0.00 1.82
2005 2202 7.365497 TGGTCTTTGATGCTCTGATAATCTA 57.635 36.000 0.00 0.00 0.00 1.98
2018 2215 7.775397 ACAAACTGAAATTTGGTCTTTGATG 57.225 32.000 0.00 0.00 42.74 3.07
2098 2331 1.200760 AGGCCATCCTACACACTGCA 61.201 55.000 5.01 0.00 42.06 4.41
2106 2339 5.622460 CGATAGTATCACAAGGCCATCCTAC 60.622 48.000 5.01 0.00 43.40 3.18
2148 2386 4.537135 AGCTGCTAAGTGCTAACAGTAA 57.463 40.909 0.00 0.00 43.37 2.24
2149 2387 4.440250 GCTAGCTGCTAAGTGCTAACAGTA 60.440 45.833 11.02 0.00 40.65 2.74
2150 2388 3.677424 GCTAGCTGCTAAGTGCTAACAGT 60.677 47.826 11.02 0.00 40.65 3.55
2151 2389 2.863137 GCTAGCTGCTAAGTGCTAACAG 59.137 50.000 11.02 0.00 40.65 3.16
2152 2390 2.893637 GCTAGCTGCTAAGTGCTAACA 58.106 47.619 11.02 0.00 40.65 2.41
2194 2432 2.290896 TGGCCCTGTATGTTCCAAAGAG 60.291 50.000 0.00 0.00 0.00 2.85
2196 2434 1.818674 GTGGCCCTGTATGTTCCAAAG 59.181 52.381 0.00 0.00 0.00 2.77
2251 2489 2.044352 GCGCCCTTGGGGTTGTAT 60.044 61.111 7.91 0.00 46.51 2.29
2350 2588 3.006728 TGGTCGGTGGGGATGGAC 61.007 66.667 0.00 0.00 0.00 4.02
3104 3345 2.697229 ACTCGAGATTGAGGATGATGCA 59.303 45.455 21.68 0.00 40.39 3.96
3110 3351 7.439655 GCACTTAATTAACTCGAGATTGAGGAT 59.560 37.037 21.68 0.19 40.39 3.24
3111 3352 6.757010 GCACTTAATTAACTCGAGATTGAGGA 59.243 38.462 21.68 0.00 40.39 3.71
3115 3356 7.688372 ACATGCACTTAATTAACTCGAGATTG 58.312 34.615 21.68 1.43 0.00 2.67
3117 3358 7.849804 AACATGCACTTAATTAACTCGAGAT 57.150 32.000 21.68 10.50 0.00 2.75
3118 3359 7.667043 AAACATGCACTTAATTAACTCGAGA 57.333 32.000 21.68 0.00 0.00 4.04
3126 3367 9.979578 AATCAGTTCAAAACATGCACTTAATTA 57.020 25.926 0.00 0.00 32.90 1.40
3128 3369 7.385752 CCAATCAGTTCAAAACATGCACTTAAT 59.614 33.333 0.00 0.00 32.90 1.40
3129 3370 6.700960 CCAATCAGTTCAAAACATGCACTTAA 59.299 34.615 0.00 0.00 32.90 1.85
3130 3371 6.183360 ACCAATCAGTTCAAAACATGCACTTA 60.183 34.615 0.00 0.00 32.90 2.24
3132 3373 4.099881 ACCAATCAGTTCAAAACATGCACT 59.900 37.500 0.00 0.00 35.80 4.40
3134 3375 4.669206 ACCAATCAGTTCAAAACATGCA 57.331 36.364 0.00 0.00 0.00 3.96
3135 3376 4.810491 ACAACCAATCAGTTCAAAACATGC 59.190 37.500 0.00 0.00 0.00 4.06
3136 3377 5.276963 GCACAACCAATCAGTTCAAAACATG 60.277 40.000 0.00 0.00 0.00 3.21
3137 3378 4.810491 GCACAACCAATCAGTTCAAAACAT 59.190 37.500 0.00 0.00 0.00 2.71
3138 3379 4.081752 AGCACAACCAATCAGTTCAAAACA 60.082 37.500 0.00 0.00 0.00 2.83
3140 3381 4.431809 CAGCACAACCAATCAGTTCAAAA 58.568 39.130 0.00 0.00 0.00 2.44
3141 3382 3.737663 GCAGCACAACCAATCAGTTCAAA 60.738 43.478 0.00 0.00 0.00 2.69
3142 3383 2.223782 GCAGCACAACCAATCAGTTCAA 60.224 45.455 0.00 0.00 0.00 2.69
3228 3480 1.828768 CTGATCCAGCTCCTCCACC 59.171 63.158 0.00 0.00 0.00 4.61
3243 3495 4.039092 GCCTTGCCCCTCAGCTGA 62.039 66.667 17.19 17.19 0.00 4.26
3264 3516 1.668151 GACCTTGTCACCCACGCTC 60.668 63.158 0.00 0.00 32.09 5.03
3291 3543 1.228245 GACCTCAAAGTGCTGGCCA 60.228 57.895 4.71 4.71 0.00 5.36
3559 3852 8.717821 GCAGATGTGTGAATGTAAAAAGTAGTA 58.282 33.333 0.00 0.00 0.00 1.82
3560 3853 7.228507 TGCAGATGTGTGAATGTAAAAAGTAGT 59.771 33.333 0.00 0.00 0.00 2.73
3561 3854 7.584108 TGCAGATGTGTGAATGTAAAAAGTAG 58.416 34.615 0.00 0.00 0.00 2.57
3562 3855 7.503521 TGCAGATGTGTGAATGTAAAAAGTA 57.496 32.000 0.00 0.00 0.00 2.24
3563 3856 6.389830 TGCAGATGTGTGAATGTAAAAAGT 57.610 33.333 0.00 0.00 0.00 2.66
3564 3857 7.085746 TGATGCAGATGTGTGAATGTAAAAAG 58.914 34.615 0.00 0.00 0.00 2.27
3565 3858 6.979465 TGATGCAGATGTGTGAATGTAAAAA 58.021 32.000 0.00 0.00 0.00 1.94
3566 3859 6.572167 TGATGCAGATGTGTGAATGTAAAA 57.428 33.333 0.00 0.00 0.00 1.52
3616 3912 2.395690 GACGATTTGCAGGCGACG 59.604 61.111 11.10 0.00 0.00 5.12
3620 3916 0.810648 TTGATGGACGATTTGCAGGC 59.189 50.000 0.00 0.00 0.00 4.85
3624 3920 1.670811 ACGGATTGATGGACGATTTGC 59.329 47.619 0.00 0.00 0.00 3.68
3743 4081 3.194861 CTCCACGTCAGACTGTCAAAAA 58.805 45.455 10.88 0.00 0.00 1.94
3839 4186 2.785258 GCGTTCTTCATCCCGCAC 59.215 61.111 0.00 0.00 45.12 5.34
3906 4253 1.535444 TCTTCTCGGCCAGGTTGGA 60.535 57.895 2.24 0.00 40.96 3.53
3907 4254 1.376037 GTCTTCTCGGCCAGGTTGG 60.376 63.158 2.24 0.00 41.55 3.77
4016 4363 2.843113 AGTTGAGGGGAGATGAAAGAGG 59.157 50.000 0.00 0.00 0.00 3.69
4021 4368 3.261897 GTGAGAAGTTGAGGGGAGATGAA 59.738 47.826 0.00 0.00 0.00 2.57
4024 4371 3.197927 AGTGAGAAGTTGAGGGGAGAT 57.802 47.619 0.00 0.00 0.00 2.75
4025 4372 2.634940 CAAGTGAGAAGTTGAGGGGAGA 59.365 50.000 0.00 0.00 0.00 3.71
4031 4384 7.770201 TCTCTATCATCAAGTGAGAAGTTGAG 58.230 38.462 2.76 0.00 40.92 3.02
4041 4394 6.814043 TGGACAGATTCTCTATCATCAAGTG 58.186 40.000 0.00 0.00 35.59 3.16
4043 4396 9.022884 TCTATGGACAGATTCTCTATCATCAAG 57.977 37.037 0.00 0.00 35.59 3.02
4044 4397 8.946797 TCTATGGACAGATTCTCTATCATCAA 57.053 34.615 0.00 0.00 35.59 2.57
4045 4398 9.544579 AATCTATGGACAGATTCTCTATCATCA 57.455 33.333 0.00 0.00 40.47 3.07
4048 4401 9.372189 TGAAATCTATGGACAGATTCTCTATCA 57.628 33.333 0.00 0.00 43.01 2.15
4051 4404 9.206690 ACTTGAAATCTATGGACAGATTCTCTA 57.793 33.333 0.00 0.00 43.01 2.43
4122 4475 9.676195 CACAAAAGAAACAAAAAGAAAATGGTT 57.324 25.926 0.00 0.00 0.00 3.67
4130 4483 4.623595 GTCGGCACAAAAGAAACAAAAAGA 59.376 37.500 0.00 0.00 0.00 2.52
4137 4490 1.404035 ACCTGTCGGCACAAAAGAAAC 59.596 47.619 0.00 0.00 29.82 2.78
4171 4527 4.504858 CAAAAGTCGGCTTGTATAGACCT 58.495 43.478 1.40 0.00 34.71 3.85
4216 4572 3.386078 TCAAAGAGATCTTCCCGGATGAG 59.614 47.826 0.73 0.00 34.61 2.90
4219 4575 3.647636 TCTCAAAGAGATCTTCCCGGAT 58.352 45.455 0.73 0.00 33.35 4.18
4318 4674 7.636259 AAACATAAATCAACGTTGGTCAATG 57.364 32.000 27.02 25.19 0.00 2.82
4319 4675 7.923344 TGAAAACATAAATCAACGTTGGTCAAT 59.077 29.630 27.02 14.51 0.00 2.57
4432 4788 0.023732 CACGTAAAGATGCGCGTCTG 59.976 55.000 31.62 20.94 38.30 3.51
4472 4828 3.188460 CCGTTAGTTTGGACACCTTGATG 59.812 47.826 0.00 0.00 0.00 3.07
4514 4870 2.953648 TGCTTAGGCACCATTCATCATG 59.046 45.455 0.00 0.00 44.28 3.07
4677 5037 6.364976 TCGTACAACATGTGACAGAAACTATG 59.635 38.462 0.00 0.00 0.00 2.23
4692 5052 8.559536 GGATGATCATGTTTATTCGTACAACAT 58.440 33.333 14.30 3.37 40.94 2.71
4714 5074 3.270027 TCTATGAAAACAGCGTGGGATG 58.730 45.455 0.00 0.00 35.16 3.51
4773 5136 6.967767 CCGTTGATACTACAGTACAAAGAGAG 59.032 42.308 0.00 0.00 32.72 3.20
4784 5147 5.179555 TCGATCTCATCCGTTGATACTACAG 59.820 44.000 0.00 0.00 32.72 2.74
4788 5151 4.762251 TCATCGATCTCATCCGTTGATACT 59.238 41.667 0.00 0.00 32.72 2.12
4791 5158 4.492611 CATCATCGATCTCATCCGTTGAT 58.507 43.478 0.00 0.00 42.43 2.57
4817 5184 2.120232 CACGTCACAGTTGAGTCAGAC 58.880 52.381 0.00 0.00 30.10 3.51
4898 5296 0.177604 CTCCCATGAGCCTGTGACTC 59.822 60.000 0.00 0.00 34.62 3.36
4908 5306 2.372504 AGAGATCCATTGCTCCCATGAG 59.627 50.000 0.00 0.00 41.84 2.90
4909 5307 2.415624 AGAGATCCATTGCTCCCATGA 58.584 47.619 0.00 0.00 0.00 3.07
4910 5308 2.953284 AGAGATCCATTGCTCCCATG 57.047 50.000 0.00 0.00 0.00 3.66
4911 5309 2.781757 TGAAGAGATCCATTGCTCCCAT 59.218 45.455 0.00 0.00 0.00 4.00
4926 5325 4.363138 GCCAAAAGAAGGTTTGTGAAGAG 58.637 43.478 0.00 0.00 36.87 2.85
4934 5333 3.201930 ACCAAATGGCCAAAAGAAGGTTT 59.798 39.130 10.96 0.00 39.32 3.27
4972 5371 9.590088 GTATTAACAAAAAGGAACAAGAGTACG 57.410 33.333 0.00 0.00 0.00 3.67
5009 5411 9.937175 GTGCATCCTTCTTTCACTATTTATAAC 57.063 33.333 0.00 0.00 0.00 1.89
5028 5430 1.003545 GCATACGTGTCATGTGCATCC 60.004 52.381 8.00 0.00 35.93 3.51
5044 5446 2.866156 GCATAGAAGCTTGTCGTGCATA 59.134 45.455 21.54 0.00 35.45 3.14
5120 5527 3.311596 GGCATGTCAGTAACGGTTAATCC 59.688 47.826 1.47 0.00 0.00 3.01
5168 5575 2.578786 ACCCACCACTAACCTTTTTCG 58.421 47.619 0.00 0.00 0.00 3.46
5185 5592 4.189231 CACTACCAGTACTGCATAAACCC 58.811 47.826 17.86 0.00 0.00 4.11
5317 5726 6.070251 TCACCTGGAGATCATAAGCTTTACAA 60.070 38.462 3.20 0.00 0.00 2.41
5425 5834 0.655733 CCGGCCGTCACACATTTATC 59.344 55.000 26.12 0.00 0.00 1.75
5439 5848 4.270376 GATGCAATTCGGCCGGCC 62.270 66.667 36.69 36.69 0.00 6.13
5440 5849 4.270376 GGATGCAATTCGGCCGGC 62.270 66.667 27.83 21.18 0.00 6.13
5441 5850 2.828095 TGGATGCAATTCGGCCGG 60.828 61.111 27.83 10.44 0.00 6.13
5455 5864 0.107897 ACAGTGCAGTTCGTTGTGGA 60.108 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.