Multiple sequence alignment - TraesCS2B01G490500

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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 TraesCS2B01G490500 chr2B 100.000 4759 0 0 1 4759 688243651 688238893 0.000000e+00 8789.0
1 TraesCS2B01G490500 chr2B 86.582 1021 103 24 2929 3926 688376331 688375322 0.000000e+00 1096.0
2 TraesCS2B01G490500 chr2B 84.763 1096 103 24 741 1832 688377363 688376328 0.000000e+00 1040.0
3 TraesCS2B01G490500 chr2B 96.462 537 18 1 3855 4391 790049585 790049050 0.000000e+00 885.0
4 TraesCS2B01G490500 chr2B 86.325 234 25 4 405 632 688377998 688377766 1.020000e-61 248.0
5 TraesCS2B01G490500 chr2B 92.683 41 2 1 1851 1891 688241763 688241724 1.850000e-04 58.4
6 TraesCS2B01G490500 chr2B 92.683 41 2 1 1889 1928 688241801 688241761 1.850000e-04 58.4
7 TraesCS2B01G490500 chr2A 93.898 2540 101 25 2259 4759 711883122 711880598 0.000000e+00 3783.0
8 TraesCS2B01G490500 chr2A 92.284 972 53 9 741 1711 711884816 711883866 0.000000e+00 1360.0
9 TraesCS2B01G490500 chr2A 85.714 1148 114 22 691 1832 711942720 711941617 0.000000e+00 1166.0
10 TraesCS2B01G490500 chr2A 84.713 1027 116 27 2929 3926 711941620 711940606 0.000000e+00 989.0
11 TraesCS2B01G490500 chr2A 94.638 373 20 0 1891 2263 711883529 711883157 3.190000e-161 579.0
12 TraesCS2B01G490500 chr2A 94.681 188 10 0 1704 1891 711883679 711883492 4.660000e-75 292.0
13 TraesCS2B01G490500 chr2A 85.572 201 18 6 405 595 711953531 711953332 2.900000e-47 200.0
14 TraesCS2B01G490500 chr2A 79.290 169 16 9 70 237 711886018 711885868 3.030000e-17 100.0
15 TraesCS2B01G490500 chr2A 97.368 38 1 0 4041 4078 711881261 711881224 1.110000e-06 65.8
16 TraesCS2B01G490500 chr2D 88.645 1092 112 11 741 1830 572684601 572683520 0.000000e+00 1319.0
17 TraesCS2B01G490500 chr2D 86.119 1059 101 16 755 1808 572697018 572696001 0.000000e+00 1099.0
18 TraesCS2B01G490500 chr2D 85.170 998 116 19 2929 3904 572695552 572694565 0.000000e+00 994.0
19 TraesCS2B01G490500 chr2D 91.789 341 26 2 2930 3269 572683519 572683180 1.550000e-129 473.0
20 TraesCS2B01G490500 chr2D 78.912 294 39 11 1836 2118 62282863 62282582 1.360000e-40 178.0
21 TraesCS2B01G490500 chr1B 83.550 231 34 4 1891 2118 299455864 299455635 3.730000e-51 213.0
22 TraesCS2B01G490500 chr5D 83.193 238 30 7 1891 2118 370751250 370751487 4.830000e-50 209.0
23 TraesCS2B01G490500 chr5D 97.222 36 1 0 1849 1884 370751245 370751280 1.430000e-05 62.1
24 TraesCS2B01G490500 chrUn 81.466 232 37 6 1891 2118 51921940 51922169 8.130000e-43 185.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G490500 chr2B 688238893 688243651 4758 True 2968.600000 8789 95.1220 1 4759 3 chr2B.!!$R2 4758
1 TraesCS2B01G490500 chr2B 790049050 790049585 535 True 885.000000 885 96.4620 3855 4391 1 chr2B.!!$R1 536
2 TraesCS2B01G490500 chr2B 688375322 688377998 2676 True 794.666667 1096 85.8900 405 3926 3 chr2B.!!$R3 3521
3 TraesCS2B01G490500 chr2A 711940606 711942720 2114 True 1077.500000 1166 85.2135 691 3926 2 chr2A.!!$R3 3235
4 TraesCS2B01G490500 chr2A 711880598 711886018 5420 True 1029.966667 3783 92.0265 70 4759 6 chr2A.!!$R2 4689
5 TraesCS2B01G490500 chr2D 572694565 572697018 2453 True 1046.500000 1099 85.6445 755 3904 2 chr2D.!!$R3 3149
6 TraesCS2B01G490500 chr2D 572683180 572684601 1421 True 896.000000 1319 90.2170 741 3269 2 chr2D.!!$R2 2528

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
962 1628 0.468226 CTAAGCCATAGGACGCCCAA 59.532 55.0 0.00 0.00 33.88 4.12 F
1515 2195 0.033208 ATTCCCAATGCCACCACGAT 60.033 50.0 0.00 0.00 0.00 3.73 F
1650 2330 0.459489 GTGCTGTCAACAAAGGCCAA 59.541 50.0 5.01 0.00 0.00 4.52 F
2607 3951 0.459759 GGGCAGAGCTTGTACGGTAC 60.460 60.0 11.33 11.33 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2566 3910 0.741221 GGATGGACGTCCTGTTCTGC 60.741 60.000 33.39 15.01 35.32 4.26 R
2621 3979 1.375908 CTGTTCGCCTAGCTTGCCA 60.376 57.895 0.00 0.00 0.00 4.92 R
2782 4140 2.271821 CCACGCATCCCATGACCA 59.728 61.111 0.00 0.00 0.00 4.02 R
4568 5999 0.826256 CATGCCATGCCTGCCATAGT 60.826 55.000 0.00 0.00 31.47 2.12 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
39 40 4.851179 CCTCGCCCGCCTAAACCC 62.851 72.222 0.00 0.00 0.00 4.11
40 41 4.851179 CTCGCCCGCCTAAACCCC 62.851 72.222 0.00 0.00 0.00 4.95
42 43 4.851179 CGCCCGCCTAAACCCCTC 62.851 72.222 0.00 0.00 0.00 4.30
43 44 4.501285 GCCCGCCTAAACCCCTCC 62.501 72.222 0.00 0.00 0.00 4.30
44 45 3.805497 CCCGCCTAAACCCCTCCC 61.805 72.222 0.00 0.00 0.00 4.30
45 46 3.805497 CCGCCTAAACCCCTCCCC 61.805 72.222 0.00 0.00 0.00 4.81
46 47 3.805497 CGCCTAAACCCCTCCCCC 61.805 72.222 0.00 0.00 0.00 5.40
47 48 2.286962 GCCTAAACCCCTCCCCCT 60.287 66.667 0.00 0.00 0.00 4.79
48 49 2.384433 GCCTAAACCCCTCCCCCTC 61.384 68.421 0.00 0.00 0.00 4.30
49 50 1.696674 CCTAAACCCCTCCCCCTCC 60.697 68.421 0.00 0.00 0.00 4.30
50 51 1.696674 CTAAACCCCTCCCCCTCCC 60.697 68.421 0.00 0.00 0.00 4.30
51 52 3.292460 TAAACCCCTCCCCCTCCCC 62.292 68.421 0.00 0.00 0.00 4.81
57 58 4.024984 CTCCCCCTCCCCACAGGA 62.025 72.222 0.00 0.00 44.91 3.86
58 59 3.547737 TCCCCCTCCCCACAGGAA 61.548 66.667 0.00 0.00 46.94 3.36
59 60 2.534272 CCCCCTCCCCACAGGAAA 60.534 66.667 0.00 0.00 46.94 3.13
60 61 2.763902 CCCCTCCCCACAGGAAAC 59.236 66.667 0.00 0.00 46.94 2.78
61 62 2.763902 CCCTCCCCACAGGAAACC 59.236 66.667 0.00 0.00 46.94 3.27
62 63 1.852626 CCCTCCCCACAGGAAACCT 60.853 63.158 0.00 0.00 46.94 3.50
63 64 1.685820 CCTCCCCACAGGAAACCTC 59.314 63.158 0.00 0.00 46.94 3.85
64 65 0.842467 CCTCCCCACAGGAAACCTCT 60.842 60.000 0.00 0.00 46.94 3.69
65 66 0.615850 CTCCCCACAGGAAACCTCTC 59.384 60.000 0.00 0.00 46.94 3.20
66 67 1.192146 TCCCCACAGGAAACCTCTCG 61.192 60.000 0.00 0.00 43.78 4.04
67 68 1.376037 CCCACAGGAAACCTCTCGC 60.376 63.158 0.00 0.00 33.47 5.03
68 69 1.738099 CCACAGGAAACCTCTCGCG 60.738 63.158 0.00 0.00 0.00 5.87
69 70 2.048127 ACAGGAAACCTCTCGCGC 60.048 61.111 0.00 0.00 0.00 6.86
70 71 3.181967 CAGGAAACCTCTCGCGCG 61.182 66.667 26.76 26.76 0.00 6.86
104 105 0.969409 CCGTTCCCCTTCTACCTCGT 60.969 60.000 0.00 0.00 0.00 4.18
127 128 4.090588 CCCTGCCGTTTCCGCCTA 62.091 66.667 0.00 0.00 0.00 3.93
128 129 2.511600 CCTGCCGTTTCCGCCTAG 60.512 66.667 0.00 0.00 0.00 3.02
138 139 3.771160 CCGCCTAGTCCGCAACCT 61.771 66.667 0.00 0.00 0.00 3.50
143 144 1.745489 CTAGTCCGCAACCTTGGGC 60.745 63.158 0.00 0.00 39.52 5.36
147 148 2.262292 CCGCAACCTTGGGCATTG 59.738 61.111 0.00 0.00 39.52 2.82
154 155 2.877786 CAACCTTGGGCATTGGTTTTTC 59.122 45.455 4.85 0.00 41.57 2.29
155 156 1.419762 ACCTTGGGCATTGGTTTTTCC 59.580 47.619 0.00 0.00 0.00 3.13
156 157 1.419387 CCTTGGGCATTGGTTTTTCCA 59.581 47.619 0.00 0.00 45.60 3.53
196 197 2.159572 CGTTCATTCCGGGTTTGCTTAG 60.160 50.000 0.00 0.00 0.00 2.18
198 199 3.149005 TCATTCCGGGTTTGCTTAGTT 57.851 42.857 0.00 0.00 0.00 2.24
207 208 4.083484 CGGGTTTGCTTAGTTCCAAACTAG 60.083 45.833 13.73 0.00 46.09 2.57
208 209 4.321008 GGGTTTGCTTAGTTCCAAACTAGC 60.321 45.833 13.73 11.21 46.09 3.42
211 212 3.939066 TGCTTAGTTCCAAACTAGCCTC 58.061 45.455 13.62 3.04 44.22 4.70
237 238 1.134068 GCACCTTCTAGATTGGGGTCC 60.134 57.143 13.88 0.00 0.00 4.46
238 239 1.490910 CACCTTCTAGATTGGGGTCCC 59.509 57.143 14.42 0.00 0.00 4.46
249 250 3.728373 GGGTCCCAGTCCGCCATT 61.728 66.667 1.78 0.00 0.00 3.16
250 251 2.124695 GGTCCCAGTCCGCCATTC 60.125 66.667 0.00 0.00 0.00 2.67
251 252 2.124695 GTCCCAGTCCGCCATTCC 60.125 66.667 0.00 0.00 0.00 3.01
252 253 3.407967 TCCCAGTCCGCCATTCCC 61.408 66.667 0.00 0.00 0.00 3.97
254 255 4.506255 CCAGTCCGCCATTCCCCC 62.506 72.222 0.00 0.00 0.00 5.40
255 256 3.727258 CAGTCCGCCATTCCCCCA 61.727 66.667 0.00 0.00 0.00 4.96
256 257 2.938798 AGTCCGCCATTCCCCCAA 60.939 61.111 0.00 0.00 0.00 4.12
257 258 2.036572 GTCCGCCATTCCCCCAAA 59.963 61.111 0.00 0.00 0.00 3.28
258 259 2.036572 TCCGCCATTCCCCCAAAC 59.963 61.111 0.00 0.00 0.00 2.93
259 260 2.037208 CCGCCATTCCCCCAAACT 59.963 61.111 0.00 0.00 0.00 2.66
260 261 2.350458 CCGCCATTCCCCCAAACTG 61.350 63.158 0.00 0.00 0.00 3.16
261 262 1.304052 CGCCATTCCCCCAAACTGA 60.304 57.895 0.00 0.00 0.00 3.41
262 263 1.315257 CGCCATTCCCCCAAACTGAG 61.315 60.000 0.00 0.00 0.00 3.35
267 268 0.930726 TTCCCCCAAACTGAGGTGTT 59.069 50.000 0.00 0.00 0.00 3.32
268 269 1.822425 TCCCCCAAACTGAGGTGTTA 58.178 50.000 0.00 0.00 0.00 2.41
269 270 2.354328 TCCCCCAAACTGAGGTGTTAT 58.646 47.619 0.00 0.00 0.00 1.89
271 272 3.141272 TCCCCCAAACTGAGGTGTTATTT 59.859 43.478 0.00 0.00 0.00 1.40
272 273 3.901222 CCCCCAAACTGAGGTGTTATTTT 59.099 43.478 0.00 0.00 0.00 1.82
273 274 4.346709 CCCCCAAACTGAGGTGTTATTTTT 59.653 41.667 0.00 0.00 0.00 1.94
311 337 1.274167 CGGTGGGAGTACTTTGTAGCA 59.726 52.381 0.00 0.00 0.00 3.49
321 347 5.542779 AGTACTTTGTAGCAGTTCAAGGAG 58.457 41.667 0.00 0.00 0.00 3.69
327 353 4.973168 TGTAGCAGTTCAAGGAGTTGATT 58.027 39.130 0.00 0.00 42.41 2.57
328 354 5.376625 TGTAGCAGTTCAAGGAGTTGATTT 58.623 37.500 0.00 0.00 42.41 2.17
334 360 7.449704 AGCAGTTCAAGGAGTTGATTTTAGAAT 59.550 33.333 0.00 0.00 42.41 2.40
378 418 8.550376 TGATTTTTCTACACCTACGTTGTTAAC 58.450 33.333 0.00 0.00 0.00 2.01
380 420 7.467557 TTTTCTACACCTACGTTGTTAACTG 57.532 36.000 7.22 0.00 0.00 3.16
384 424 5.723492 ACACCTACGTTGTTAACTGAAAC 57.277 39.130 7.22 2.37 0.00 2.78
385 425 5.177326 ACACCTACGTTGTTAACTGAAACA 58.823 37.500 7.22 0.00 37.58 2.83
386 426 5.063817 ACACCTACGTTGTTAACTGAAACAC 59.936 40.000 7.22 0.00 39.02 3.32
387 427 4.268405 ACCTACGTTGTTAACTGAAACACG 59.732 41.667 7.22 7.99 39.02 4.49
388 428 4.503734 CCTACGTTGTTAACTGAAACACGA 59.496 41.667 7.22 0.00 39.02 4.35
389 429 5.176223 CCTACGTTGTTAACTGAAACACGAT 59.824 40.000 7.22 1.23 39.02 3.73
390 430 6.363088 CCTACGTTGTTAACTGAAACACGATA 59.637 38.462 7.22 2.10 39.02 2.92
391 431 6.586868 ACGTTGTTAACTGAAACACGATAA 57.413 33.333 7.22 0.00 39.02 1.75
394 434 8.124199 ACGTTGTTAACTGAAACACGATAAAAT 58.876 29.630 7.22 0.00 39.02 1.82
412 452 5.998454 AAAATATGCTCTGGACATTCTCG 57.002 39.130 0.00 0.00 0.00 4.04
424 464 4.391140 GACATTCTCGAAGTCCACAAAC 57.609 45.455 0.00 0.00 0.00 2.93
432 472 3.119388 TCGAAGTCCACAAACCTATACGG 60.119 47.826 0.00 0.00 39.35 4.02
442 482 2.592102 ACCTATACGGCGATTCCCTA 57.408 50.000 16.62 0.00 35.61 3.53
459 504 4.624913 TCCCTAGACCATTCTTGATCTGT 58.375 43.478 0.00 0.00 32.75 3.41
461 506 4.444022 CCCTAGACCATTCTTGATCTGTGG 60.444 50.000 0.00 0.00 32.75 4.17
477 522 3.820467 TCTGTGGACAACATGGTCAATTC 59.180 43.478 0.00 0.00 38.39 2.17
500 546 3.802862 AGAGGATAACCGCTCGAGA 57.197 52.632 18.75 0.00 42.44 4.04
516 562 5.895636 CTCGAGAGCCATAATAGACAGAT 57.104 43.478 6.58 0.00 0.00 2.90
520 566 5.149973 AGAGCCATAATAGACAGATGCTG 57.850 43.478 0.00 0.00 37.52 4.41
522 568 5.306419 AGAGCCATAATAGACAGATGCTGAA 59.694 40.000 0.82 0.00 35.18 3.02
528 574 7.119407 CCATAATAGACAGATGCTGAATTGGAG 59.881 40.741 0.82 0.00 35.18 3.86
577 881 7.279615 TCTGTTGTTCTATATTGGTATGGTGG 58.720 38.462 0.00 0.00 0.00 4.61
589 893 2.356741 GGTATGGTGGCATGGTTGTACT 60.357 50.000 0.00 0.00 0.00 2.73
621 925 3.544244 GCGTTCAGCGATAAATGGAAGTC 60.544 47.826 0.00 0.00 44.77 3.01
627 931 6.403049 TCAGCGATAAATGGAAGTCTGTTTA 58.597 36.000 0.00 0.00 0.00 2.01
632 936 8.798153 GCGATAAATGGAAGTCTGTTTAAAATG 58.202 33.333 0.00 0.00 0.00 2.32
637 941 9.643693 AAATGGAAGTCTGTTTAAAATGCATAG 57.356 29.630 0.00 0.00 0.00 2.23
672 1172 6.889301 TCTCTAAATAGTACCCCGTACATG 57.111 41.667 4.86 0.00 41.03 3.21
706 1206 6.044682 GCTAATGAGTTCATTCAAAATGGGG 58.955 40.000 10.43 0.00 44.67 4.96
709 1209 5.975693 TGAGTTCATTCAAAATGGGGTAC 57.024 39.130 0.19 0.00 0.00 3.34
716 1216 6.022315 TCATTCAAAATGGGGTACTTGGATT 58.978 36.000 0.00 0.00 0.00 3.01
720 1220 8.442660 TTCAAAATGGGGTACTTGGATTTATT 57.557 30.769 0.00 0.00 0.00 1.40
725 1225 3.889538 GGGGTACTTGGATTTATTGGCTC 59.110 47.826 0.00 0.00 0.00 4.70
732 1232 7.814264 ACTTGGATTTATTGGCTCTCTTATG 57.186 36.000 0.00 0.00 0.00 1.90
737 1400 6.376581 GGATTTATTGGCTCTCTTATGGATGG 59.623 42.308 0.00 0.00 0.00 3.51
738 1401 6.514012 TTTATTGGCTCTCTTATGGATGGA 57.486 37.500 0.00 0.00 0.00 3.41
739 1402 6.708885 TTATTGGCTCTCTTATGGATGGAT 57.291 37.500 0.00 0.00 0.00 3.41
751 1414 9.091784 CTCTTATGGATGGATTTGTATGTATCG 57.908 37.037 0.00 0.00 0.00 2.92
753 1416 9.219603 CTTATGGATGGATTTGTATGTATCGTT 57.780 33.333 0.00 0.00 0.00 3.85
778 1441 5.200368 CCACATTAGAACTGGCAGTTTTT 57.800 39.130 31.60 24.04 38.80 1.94
789 1452 6.280855 ACTGGCAGTTTTTACTTCAAACTT 57.719 33.333 15.88 0.00 41.58 2.66
792 1455 6.930731 TGGCAGTTTTTACTTCAAACTTTCT 58.069 32.000 0.00 0.00 41.58 2.52
866 1531 5.979517 GCTCAAAGCTTTTGTACTGTGAAAT 59.020 36.000 9.53 0.00 38.45 2.17
892 1557 7.978414 TCAAGTCATTGACTCTTTGCTATCTAG 59.022 37.037 19.23 0.00 42.59 2.43
958 1624 3.060602 GTTCATCTAAGCCATAGGACGC 58.939 50.000 0.00 0.00 32.09 5.19
962 1628 0.468226 CTAAGCCATAGGACGCCCAA 59.532 55.000 0.00 0.00 33.88 4.12
973 1639 2.169561 AGGACGCCCAATTTGTTTGTTT 59.830 40.909 0.00 0.00 33.15 2.83
995 1663 2.812358 TTCTAAGCACGCTTCTGACA 57.188 45.000 7.71 0.00 37.47 3.58
1003 1671 6.935763 TAAGCACGCTTCTGACACAAAATGT 61.936 40.000 7.71 0.00 39.82 2.71
1091 1759 1.830279 CCACATGCTGGATTGTCACT 58.170 50.000 8.20 0.00 43.95 3.41
1152 1820 6.030228 CCTTTTCTCAACAAGTGTTCAAGAC 58.970 40.000 5.64 0.00 35.83 3.01
1515 2195 0.033208 ATTCCCAATGCCACCACGAT 60.033 50.000 0.00 0.00 0.00 3.73
1650 2330 0.459489 GTGCTGTCAACAAAGGCCAA 59.541 50.000 5.01 0.00 0.00 4.52
1728 2603 7.721286 TCCATACTACTAGTAAGTAAGCGTC 57.279 40.000 3.76 0.00 37.75 5.19
1853 3157 4.216411 TGGGTTGTTTGGATAGCTAGTC 57.784 45.455 0.00 0.00 0.00 2.59
1866 3170 6.547880 TGGATAGCTAGTCTTTAGAGAACCAG 59.452 42.308 0.00 0.00 32.66 4.00
1867 3171 6.548251 GGATAGCTAGTCTTTAGAGAACCAGT 59.452 42.308 0.00 0.00 32.66 4.00
1868 3172 7.068962 GGATAGCTAGTCTTTAGAGAACCAGTT 59.931 40.741 0.00 0.00 32.66 3.16
1869 3173 9.122779 GATAGCTAGTCTTTAGAGAACCAGTTA 57.877 37.037 0.00 0.00 32.66 2.24
1870 3174 7.399245 AGCTAGTCTTTAGAGAACCAGTTAG 57.601 40.000 0.00 0.00 32.66 2.34
1871 3175 6.037726 GCTAGTCTTTAGAGAACCAGTTAGC 58.962 44.000 0.00 0.00 32.66 3.09
1872 3176 6.127563 GCTAGTCTTTAGAGAACCAGTTAGCT 60.128 42.308 0.00 0.00 32.66 3.32
1873 3177 7.067251 GCTAGTCTTTAGAGAACCAGTTAGCTA 59.933 40.741 0.00 0.00 32.66 3.32
1874 3178 7.964666 AGTCTTTAGAGAACCAGTTAGCTAT 57.035 36.000 0.00 0.00 32.66 2.97
1876 3180 9.476928 AGTCTTTAGAGAACCAGTTAGCTATAA 57.523 33.333 0.00 0.00 32.66 0.98
1879 3183 8.922058 TTTAGAGAACCAGTTAGCTATAAACG 57.078 34.615 0.00 0.00 32.00 3.60
1880 3184 6.527057 AGAGAACCAGTTAGCTATAAACGT 57.473 37.500 0.00 0.00 32.00 3.99
1881 3185 6.331061 AGAGAACCAGTTAGCTATAAACGTG 58.669 40.000 0.00 0.00 32.00 4.49
1882 3186 6.034161 AGAACCAGTTAGCTATAAACGTGT 57.966 37.500 0.00 0.00 32.00 4.49
1883 3187 6.461640 AGAACCAGTTAGCTATAAACGTGTT 58.538 36.000 0.00 1.34 32.14 3.32
1884 3188 6.589139 AGAACCAGTTAGCTATAAACGTGTTC 59.411 38.462 18.17 18.17 39.65 3.18
1885 3189 5.786311 ACCAGTTAGCTATAAACGTGTTCA 58.214 37.500 0.00 0.00 32.00 3.18
1886 3190 5.867716 ACCAGTTAGCTATAAACGTGTTCAG 59.132 40.000 0.00 0.00 32.00 3.02
1887 3191 5.291128 CCAGTTAGCTATAAACGTGTTCAGG 59.709 44.000 0.00 0.00 32.00 3.86
1888 3192 6.097356 CAGTTAGCTATAAACGTGTTCAGGA 58.903 40.000 0.00 0.00 32.00 3.86
1889 3193 6.253727 CAGTTAGCTATAAACGTGTTCAGGAG 59.746 42.308 0.00 0.00 32.00 3.69
1890 3194 4.803098 AGCTATAAACGTGTTCAGGAGT 57.197 40.909 0.00 0.00 0.00 3.85
1891 3195 5.148651 AGCTATAAACGTGTTCAGGAGTT 57.851 39.130 0.00 0.00 0.00 3.01
1892 3196 5.548406 AGCTATAAACGTGTTCAGGAGTTT 58.452 37.500 0.00 3.69 39.68 2.66
1893 3197 5.995897 AGCTATAAACGTGTTCAGGAGTTTT 59.004 36.000 0.00 0.00 37.83 2.43
1894 3198 7.156673 AGCTATAAACGTGTTCAGGAGTTTTA 58.843 34.615 0.00 0.00 37.83 1.52
1895 3199 7.331193 AGCTATAAACGTGTTCAGGAGTTTTAG 59.669 37.037 0.00 2.73 37.83 1.85
1896 3200 7.330208 GCTATAAACGTGTTCAGGAGTTTTAGA 59.670 37.037 0.00 0.00 37.83 2.10
1897 3201 5.986004 AAACGTGTTCAGGAGTTTTAGAG 57.014 39.130 0.00 0.00 33.59 2.43
1898 3202 4.931661 ACGTGTTCAGGAGTTTTAGAGA 57.068 40.909 0.00 0.00 0.00 3.10
1899 3203 5.272283 ACGTGTTCAGGAGTTTTAGAGAA 57.728 39.130 0.00 0.00 0.00 2.87
1900 3204 5.048507 ACGTGTTCAGGAGTTTTAGAGAAC 58.951 41.667 0.00 0.00 36.73 3.01
1901 3205 4.448060 CGTGTTCAGGAGTTTTAGAGAACC 59.552 45.833 0.00 0.00 35.68 3.62
1902 3206 5.365619 GTGTTCAGGAGTTTTAGAGAACCA 58.634 41.667 0.00 0.00 35.68 3.67
1903 3207 5.467063 GTGTTCAGGAGTTTTAGAGAACCAG 59.533 44.000 0.00 0.00 35.68 4.00
1916 3220 8.922058 TTTAGAGAACCAGTTAGCTATAAACG 57.078 34.615 0.00 0.00 32.00 3.60
1944 3248 7.704789 TTCGGAGTCTAACAAACTAAAACTC 57.295 36.000 0.00 0.00 0.00 3.01
2009 3313 5.878669 GGTTCTCGTAATACCCAAAATCTGT 59.121 40.000 0.00 0.00 0.00 3.41
2072 3376 4.149922 GCGTTTTAGAAAAATGGGTCTTGC 59.850 41.667 6.50 0.00 0.00 4.01
2173 3477 2.410060 ACGCGACAGAACGTCACA 59.590 55.556 15.93 0.00 45.70 3.58
2216 3520 1.134367 GTGGCGACTATGCTCTGTACA 59.866 52.381 0.00 0.00 34.52 2.90
2221 3525 2.035193 CGACTATGCTCTGTACAGCCAT 59.965 50.000 23.36 23.36 38.80 4.40
2230 3534 2.158682 TCTGTACAGCCATGTTGTTGGT 60.159 45.455 18.45 0.00 41.01 3.67
2256 3560 2.623450 TAGTCCTGCCGACCTCCCT 61.623 63.158 0.00 0.00 43.08 4.20
2257 3561 2.856039 TAGTCCTGCCGACCTCCCTG 62.856 65.000 0.00 0.00 43.08 4.45
2286 3629 0.895559 CCACACTTTTCCTCCAGCCC 60.896 60.000 0.00 0.00 0.00 5.19
2389 3732 0.520404 CGCTGCCTGGATATTGATGC 59.480 55.000 0.00 0.00 0.00 3.91
2431 3774 4.059459 CACACTGGACGCGTTCGC 62.059 66.667 15.53 7.14 39.84 4.70
2487 3830 1.374758 GTGCTGGGAGGACGAGTTG 60.375 63.158 0.00 0.00 0.00 3.16
2521 3865 3.047877 GCGCCGTTACTGCTGGTT 61.048 61.111 0.00 0.00 0.00 3.67
2551 3895 5.628193 CACCGATATCACGTTGGTATAAGAC 59.372 44.000 3.12 0.00 32.00 3.01
2555 3899 4.707030 ATCACGTTGGTATAAGACGACA 57.293 40.909 9.81 0.00 39.85 4.35
2577 3921 3.050275 GGCCACGCAGAACAGGAC 61.050 66.667 0.00 0.00 0.00 3.85
2605 3949 2.663196 GGGCAGAGCTTGTACGGT 59.337 61.111 0.00 0.00 0.00 4.83
2607 3951 0.459759 GGGCAGAGCTTGTACGGTAC 60.460 60.000 11.33 11.33 0.00 3.34
2621 3979 3.042059 ACGGTACAGGGATGTAGGAAT 57.958 47.619 0.00 0.00 0.00 3.01
2760 4118 0.687354 AGCTTGGAGGTCGTCAATGT 59.313 50.000 0.00 0.00 0.00 2.71
2782 4140 8.593945 ATGTCTAGTTTGAGAAAGAGAGAGAT 57.406 34.615 0.00 0.00 0.00 2.75
2820 4178 5.699001 GTGGGGTATCAAAACATGTTTTTCC 59.301 40.000 29.42 25.22 40.45 3.13
2897 4255 9.724839 CAACTAAAAACTCGTTTTCTAAATCCA 57.275 29.630 8.09 0.00 41.45 3.41
2902 4260 3.744426 ACTCGTTTTCTAAATCCACGTGG 59.256 43.478 29.26 29.26 32.65 4.94
2917 4275 3.741344 CCACGTGGCTTATACTTGCTATC 59.259 47.826 24.02 0.00 0.00 2.08
2993 4351 4.399303 ACTTCCATTACTACTGGCATTTGC 59.601 41.667 0.00 0.00 41.14 3.68
3227 4585 3.350219 AAAGCACTTCATACCATCGGT 57.650 42.857 0.00 0.00 40.16 4.69
3410 4813 3.433740 GGTTCTGGGAATATGAGGACCAC 60.434 52.174 0.00 0.00 0.00 4.16
3944 5359 1.207791 CCTACTGTGGGAGCTGGATT 58.792 55.000 3.81 0.00 0.00 3.01
3972 5387 8.532186 TGATATTTACCCTTGCATTAACATGT 57.468 30.769 0.00 0.00 32.28 3.21
4127 5553 5.360999 GGCATTAGGAAAGAAAACCTAGCAT 59.639 40.000 0.00 0.00 39.48 3.79
4151 5577 9.056005 CATTGTTTGTAGTAGCATGGTATATGT 57.944 33.333 8.06 0.00 0.00 2.29
4256 5682 4.100707 TGTAACGTGTGCTCCTATACAC 57.899 45.455 0.00 0.00 42.77 2.90
4261 5687 2.713011 GTGTGCTCCTATACACGTACG 58.287 52.381 15.01 15.01 39.71 3.67
4307 5735 3.889196 TTCTCGGGAACAATTTCGTTG 57.111 42.857 0.00 0.00 43.64 4.10
4440 5870 8.628280 ACTTTGTTACCTTACGGAGATATAGTC 58.372 37.037 0.00 0.00 0.00 2.59
4466 5896 5.065218 AGCAAAAATGATACCTACGCAAGAG 59.935 40.000 0.00 0.00 43.62 2.85
4467 5897 5.730568 GCAAAAATGATACCTACGCAAGAGG 60.731 44.000 0.00 0.00 43.62 3.69
4534 5965 5.048991 GGTTTCCACTGTTATGGTACTTGTG 60.049 44.000 0.00 0.00 40.95 3.33
4568 5999 4.520874 TGCTCGGATAAAATGTTTTGTGGA 59.479 37.500 1.16 0.00 0.00 4.02
4583 6014 0.820891 GTGGACTATGGCAGGCATGG 60.821 60.000 19.63 18.62 31.57 3.66
4591 6022 3.534056 GCAGGCATGGCATGGTCC 61.534 66.667 27.48 20.49 40.87 4.46
4592 6023 2.277737 CAGGCATGGCATGGTCCT 59.722 61.111 27.48 22.28 36.65 3.85
4593 6024 2.125326 CAGGCATGGCATGGTCCTG 61.125 63.158 28.28 28.28 36.65 3.86
4594 6025 2.276409 GGCATGGCATGGTCCTGA 59.724 61.111 27.48 0.00 0.00 3.86
4595 6026 1.152610 GGCATGGCATGGTCCTGAT 60.153 57.895 27.48 0.00 0.00 2.90
4596 6027 1.177256 GGCATGGCATGGTCCTGATC 61.177 60.000 27.48 9.03 0.00 2.92
4597 6028 0.178998 GCATGGCATGGTCCTGATCT 60.179 55.000 27.48 0.00 0.00 2.75
4598 6029 1.605753 CATGGCATGGTCCTGATCTG 58.394 55.000 19.80 0.00 0.00 2.90
4599 6030 1.133884 CATGGCATGGTCCTGATCTGT 60.134 52.381 19.80 0.00 0.00 3.41
4600 6031 0.994247 TGGCATGGTCCTGATCTGTT 59.006 50.000 0.00 0.00 0.00 3.16
4607 6038 2.038952 TGGTCCTGATCTGTTTCCAGTG 59.961 50.000 0.00 0.00 39.82 3.66
4656 6087 5.163663 GGTCTGATCAGTTAGACAGACTCTG 60.164 48.000 21.92 4.36 45.04 3.35
4657 6088 4.946772 TCTGATCAGTTAGACAGACTCTGG 59.053 45.833 21.92 0.00 35.51 3.86
4658 6089 4.667573 TGATCAGTTAGACAGACTCTGGT 58.332 43.478 10.86 0.20 35.51 4.00
4662 6095 5.382616 TCAGTTAGACAGACTCTGGTGTTA 58.617 41.667 10.86 0.00 35.51 2.41
4686 6119 5.565592 TTAGCGTCTCCGTAAATTGTAGA 57.434 39.130 0.00 0.00 36.15 2.59
4698 6131 7.699391 TCCGTAAATTGTAGAGTAGTCATTTCG 59.301 37.037 0.00 4.07 0.00 3.46
4699 6132 7.487189 CCGTAAATTGTAGAGTAGTCATTTCGT 59.513 37.037 0.00 0.00 0.00 3.85
4701 6134 9.953825 GTAAATTGTAGAGTAGTCATTTCGTTG 57.046 33.333 0.00 0.00 0.00 4.10
4702 6135 8.827177 AAATTGTAGAGTAGTCATTTCGTTGA 57.173 30.769 0.00 0.00 0.00 3.18
4703 6136 8.467402 AATTGTAGAGTAGTCATTTCGTTGAG 57.533 34.615 0.00 0.00 0.00 3.02
4704 6137 5.399858 TGTAGAGTAGTCATTTCGTTGAGC 58.600 41.667 0.00 0.00 0.00 4.26
4708 6144 5.406780 AGAGTAGTCATTTCGTTGAGCTTTG 59.593 40.000 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.851179 GGGTTTAGGCGGGCGAGG 62.851 72.222 0.00 0.00 0.00 4.63
23 24 4.851179 GGGGTTTAGGCGGGCGAG 62.851 72.222 0.00 0.00 0.00 5.03
25 26 4.851179 GAGGGGTTTAGGCGGGCG 62.851 72.222 0.00 0.00 0.00 6.13
26 27 4.501285 GGAGGGGTTTAGGCGGGC 62.501 72.222 0.00 0.00 0.00 6.13
27 28 3.805497 GGGAGGGGTTTAGGCGGG 61.805 72.222 0.00 0.00 0.00 6.13
28 29 3.805497 GGGGAGGGGTTTAGGCGG 61.805 72.222 0.00 0.00 0.00 6.13
29 30 3.805497 GGGGGAGGGGTTTAGGCG 61.805 72.222 0.00 0.00 0.00 5.52
30 31 2.286962 AGGGGGAGGGGTTTAGGC 60.287 66.667 0.00 0.00 0.00 3.93
31 32 1.696674 GGAGGGGGAGGGGTTTAGG 60.697 68.421 0.00 0.00 0.00 2.69
32 33 1.696674 GGGAGGGGGAGGGGTTTAG 60.697 68.421 0.00 0.00 0.00 1.85
33 34 2.462605 GGGAGGGGGAGGGGTTTA 59.537 66.667 0.00 0.00 0.00 2.01
34 35 4.714711 GGGGAGGGGGAGGGGTTT 62.715 72.222 0.00 0.00 0.00 3.27
40 41 3.579451 TTCCTGTGGGGAGGGGGAG 62.579 68.421 0.00 0.00 46.01 4.30
41 42 3.135716 TTTCCTGTGGGGAGGGGGA 62.136 63.158 0.00 0.00 46.01 4.81
42 43 2.534272 TTTCCTGTGGGGAGGGGG 60.534 66.667 0.00 0.00 46.01 5.40
43 44 2.763902 GTTTCCTGTGGGGAGGGG 59.236 66.667 0.00 0.00 46.01 4.79
44 45 1.852626 AGGTTTCCTGTGGGGAGGG 60.853 63.158 0.00 0.00 46.01 4.30
45 46 0.842467 AGAGGTTTCCTGTGGGGAGG 60.842 60.000 0.00 0.00 46.01 4.30
46 47 0.615850 GAGAGGTTTCCTGTGGGGAG 59.384 60.000 0.00 0.00 46.01 4.30
47 48 1.192146 CGAGAGGTTTCCTGTGGGGA 61.192 60.000 0.00 0.00 43.41 4.81
48 49 1.296715 CGAGAGGTTTCCTGTGGGG 59.703 63.158 0.00 0.00 31.76 4.96
49 50 1.376037 GCGAGAGGTTTCCTGTGGG 60.376 63.158 0.00 0.00 31.76 4.61
50 51 1.738099 CGCGAGAGGTTTCCTGTGG 60.738 63.158 0.00 0.00 31.76 4.17
51 52 2.383527 GCGCGAGAGGTTTCCTGTG 61.384 63.158 12.10 0.00 31.76 3.66
52 53 2.048127 GCGCGAGAGGTTTCCTGT 60.048 61.111 12.10 0.00 31.76 4.00
53 54 3.181967 CGCGCGAGAGGTTTCCTG 61.182 66.667 28.94 0.00 31.76 3.86
78 79 4.796495 AAGGGGAACGGCGATGGC 62.796 66.667 16.62 0.00 38.90 4.40
79 80 1.682451 TAGAAGGGGAACGGCGATGG 61.682 60.000 16.62 0.00 0.00 3.51
80 81 0.529992 GTAGAAGGGGAACGGCGATG 60.530 60.000 16.62 0.00 0.00 3.84
81 82 1.683418 GGTAGAAGGGGAACGGCGAT 61.683 60.000 16.62 0.00 0.00 4.58
88 89 1.318158 GCGACGAGGTAGAAGGGGAA 61.318 60.000 0.00 0.00 0.00 3.97
89 90 1.751927 GCGACGAGGTAGAAGGGGA 60.752 63.158 0.00 0.00 0.00 4.81
119 120 2.263540 GTTGCGGACTAGGCGGAA 59.736 61.111 7.45 0.00 0.00 4.30
120 121 3.766691 GGTTGCGGACTAGGCGGA 61.767 66.667 7.45 0.00 0.00 5.54
121 122 3.310860 AAGGTTGCGGACTAGGCGG 62.311 63.158 0.00 0.00 0.00 6.13
122 123 2.100631 CAAGGTTGCGGACTAGGCG 61.101 63.158 0.00 0.00 0.00 5.52
123 124 1.745489 CCAAGGTTGCGGACTAGGC 60.745 63.158 0.00 0.00 0.00 3.93
124 125 1.078426 CCCAAGGTTGCGGACTAGG 60.078 63.158 0.00 0.00 0.00 3.02
125 126 1.745489 GCCCAAGGTTGCGGACTAG 60.745 63.158 0.00 0.00 0.00 2.57
126 127 1.847798 ATGCCCAAGGTTGCGGACTA 61.848 55.000 2.45 0.00 0.00 2.59
127 128 2.713531 AATGCCCAAGGTTGCGGACT 62.714 55.000 2.45 0.00 0.00 3.85
128 129 2.275380 AATGCCCAAGGTTGCGGAC 61.275 57.895 2.45 0.00 0.00 4.79
158 159 1.377536 ACGGAAGCTCGTAGGAGTAC 58.622 55.000 13.65 5.89 41.98 2.73
159 160 2.012673 GAACGGAAGCTCGTAGGAGTA 58.987 52.381 13.65 0.00 43.07 2.59
160 161 0.810016 GAACGGAAGCTCGTAGGAGT 59.190 55.000 13.65 0.00 43.07 3.85
161 162 0.809385 TGAACGGAAGCTCGTAGGAG 59.191 55.000 8.10 8.10 43.07 3.69
162 163 1.471119 ATGAACGGAAGCTCGTAGGA 58.529 50.000 0.39 0.00 43.07 2.94
163 164 2.194271 GAATGAACGGAAGCTCGTAGG 58.806 52.381 0.39 0.00 43.07 3.18
164 165 2.194271 GGAATGAACGGAAGCTCGTAG 58.806 52.381 0.39 0.00 43.07 3.51
196 197 3.154589 CGGGAGGCTAGTTTGGAAC 57.845 57.895 0.00 0.00 0.00 3.62
211 212 2.311688 AATCTAGAAGGTGCGCCGGG 62.312 60.000 11.42 0.80 40.50 5.73
217 218 1.134068 GGACCCCAATCTAGAAGGTGC 60.134 57.143 10.77 10.01 0.00 5.01
219 220 1.082194 TGGGACCCCAATCTAGAAGGT 59.918 52.381 8.45 9.56 44.12 3.50
237 238 4.506255 GGGGGAATGGCGGACTGG 62.506 72.222 0.00 0.00 0.00 4.00
238 239 2.779742 TTTGGGGGAATGGCGGACTG 62.780 60.000 0.00 0.00 0.00 3.51
242 243 2.037208 AGTTTGGGGGAATGGCGG 59.963 61.111 0.00 0.00 0.00 6.13
245 246 0.409484 ACCTCAGTTTGGGGGAATGG 59.591 55.000 0.00 0.00 44.22 3.16
246 247 1.203050 ACACCTCAGTTTGGGGGAATG 60.203 52.381 0.00 0.00 44.22 2.67
247 248 1.158007 ACACCTCAGTTTGGGGGAAT 58.842 50.000 0.00 0.00 44.22 3.01
248 249 0.930726 AACACCTCAGTTTGGGGGAA 59.069 50.000 0.00 0.00 44.22 3.97
249 250 1.822425 TAACACCTCAGTTTGGGGGA 58.178 50.000 0.00 0.00 44.22 4.81
250 251 2.899303 ATAACACCTCAGTTTGGGGG 57.101 50.000 0.00 0.00 44.22 5.40
251 252 5.545063 AAAAATAACACCTCAGTTTGGGG 57.455 39.130 0.00 0.00 45.84 4.96
280 281 1.843368 CTCCCACCGTACAAGGAGTA 58.157 55.000 8.58 0.00 40.91 2.59
281 282 2.667348 CTCCCACCGTACAAGGAGT 58.333 57.895 8.58 0.00 40.91 3.85
283 284 1.076024 AGTACTCCCACCGTACAAGGA 59.924 52.381 0.00 0.00 39.66 3.36
285 286 3.243975 ACAAAGTACTCCCACCGTACAAG 60.244 47.826 0.00 0.00 39.66 3.16
286 287 2.699846 ACAAAGTACTCCCACCGTACAA 59.300 45.455 0.00 0.00 39.66 2.41
287 288 2.318908 ACAAAGTACTCCCACCGTACA 58.681 47.619 0.00 0.00 39.66 2.90
288 289 3.674410 GCTACAAAGTACTCCCACCGTAC 60.674 52.174 0.00 0.00 37.96 3.67
289 290 2.493278 GCTACAAAGTACTCCCACCGTA 59.507 50.000 0.00 0.00 0.00 4.02
290 291 1.274447 GCTACAAAGTACTCCCACCGT 59.726 52.381 0.00 0.00 0.00 4.83
291 292 1.274167 TGCTACAAAGTACTCCCACCG 59.726 52.381 0.00 0.00 0.00 4.94
311 337 8.924511 TGATTCTAAAATCAACTCCTTGAACT 57.075 30.769 0.00 0.00 46.41 3.01
367 407 7.691430 TTATCGTGTTTCAGTTAACAACGTA 57.309 32.000 8.61 1.95 39.54 3.57
369 409 7.879962 TTTTATCGTGTTTCAGTTAACAACG 57.120 32.000 8.61 7.78 39.54 4.10
378 418 7.011389 TCCAGAGCATATTTTATCGTGTTTCAG 59.989 37.037 0.00 0.00 0.00 3.02
380 420 7.126398 GTCCAGAGCATATTTTATCGTGTTTC 58.874 38.462 0.00 0.00 0.00 2.78
384 424 6.791887 ATGTCCAGAGCATATTTTATCGTG 57.208 37.500 0.00 0.00 0.00 4.35
385 425 7.220030 AGAATGTCCAGAGCATATTTTATCGT 58.780 34.615 0.00 0.00 0.00 3.73
386 426 7.411264 CGAGAATGTCCAGAGCATATTTTATCG 60.411 40.741 0.00 0.00 0.00 2.92
387 427 7.600375 TCGAGAATGTCCAGAGCATATTTTATC 59.400 37.037 0.00 0.00 0.00 1.75
388 428 7.445121 TCGAGAATGTCCAGAGCATATTTTAT 58.555 34.615 0.00 0.00 0.00 1.40
389 429 6.816136 TCGAGAATGTCCAGAGCATATTTTA 58.184 36.000 0.00 0.00 0.00 1.52
390 430 5.674525 TCGAGAATGTCCAGAGCATATTTT 58.325 37.500 0.00 0.00 0.00 1.82
391 431 5.282055 TCGAGAATGTCCAGAGCATATTT 57.718 39.130 0.00 0.00 0.00 1.40
394 434 3.701542 ACTTCGAGAATGTCCAGAGCATA 59.298 43.478 0.00 0.00 0.00 3.14
412 452 2.934553 GCCGTATAGGTTTGTGGACTTC 59.065 50.000 0.00 0.00 43.70 3.01
424 464 2.422832 GTCTAGGGAATCGCCGTATAGG 59.577 54.545 0.00 0.00 44.97 2.57
432 472 3.134458 CAAGAATGGTCTAGGGAATCGC 58.866 50.000 0.00 0.00 32.16 4.58
459 504 4.892345 TCAAAGAATTGACCATGTTGTCCA 59.108 37.500 0.00 0.00 40.59 4.02
461 506 6.317789 TCTCAAAGAATTGACCATGTTGTC 57.682 37.500 0.00 0.00 40.59 3.18
477 522 2.099263 TCGAGCGGTTATCCTCTCAAAG 59.901 50.000 9.85 0.00 43.52 2.77
495 541 4.082517 GCATCTGTCTATTATGGCTCTCGA 60.083 45.833 0.00 0.00 0.00 4.04
500 546 5.557576 TTCAGCATCTGTCTATTATGGCT 57.442 39.130 0.00 0.00 32.61 4.75
512 558 2.431954 ACCCTCCAATTCAGCATCTG 57.568 50.000 0.00 0.00 0.00 2.90
515 561 2.208872 ACCTACCCTCCAATTCAGCAT 58.791 47.619 0.00 0.00 0.00 3.79
516 562 1.668826 ACCTACCCTCCAATTCAGCA 58.331 50.000 0.00 0.00 0.00 4.41
520 566 3.555966 CATCCAACCTACCCTCCAATTC 58.444 50.000 0.00 0.00 0.00 2.17
522 568 1.852965 CCATCCAACCTACCCTCCAAT 59.147 52.381 0.00 0.00 0.00 3.16
528 574 0.546598 CTGACCCATCCAACCTACCC 59.453 60.000 0.00 0.00 0.00 3.69
589 893 0.512518 CGCTGAACGCATGACTGAAA 59.487 50.000 0.00 0.00 39.08 2.69
613 917 8.353423 ACTATGCATTTTAAACAGACTTCCAT 57.647 30.769 3.54 0.00 0.00 3.41
644 952 6.610075 ACGGGGTACTATTTAGAGAACAAA 57.390 37.500 0.00 0.00 0.00 2.83
650 958 5.537674 ACCATGTACGGGGTACTATTTAGAG 59.462 44.000 6.48 0.00 39.49 2.43
657 965 4.405358 CCTAAAACCATGTACGGGGTACTA 59.595 45.833 8.51 3.56 39.49 1.82
663 971 1.741145 GCACCTAAAACCATGTACGGG 59.259 52.381 2.04 2.04 0.00 5.28
672 1172 6.759497 ATGAACTCATTAGCACCTAAAACC 57.241 37.500 0.00 0.00 31.37 3.27
706 1206 8.778358 CATAAGAGAGCCAATAAATCCAAGTAC 58.222 37.037 0.00 0.00 0.00 2.73
709 1209 7.000472 TCCATAAGAGAGCCAATAAATCCAAG 59.000 38.462 0.00 0.00 0.00 3.61
716 1216 6.708885 ATCCATCCATAAGAGAGCCAATAA 57.291 37.500 0.00 0.00 0.00 1.40
720 1220 4.166725 ACAAATCCATCCATAAGAGAGCCA 59.833 41.667 0.00 0.00 0.00 4.75
725 1225 9.091784 CGATACATACAAATCCATCCATAAGAG 57.908 37.037 0.00 0.00 0.00 2.85
732 1232 6.142817 GCAAACGATACATACAAATCCATCC 58.857 40.000 0.00 0.00 0.00 3.51
737 1400 5.874831 TGTGGCAAACGATACATACAAATC 58.125 37.500 0.00 0.00 0.00 2.17
738 1401 5.888691 TGTGGCAAACGATACATACAAAT 57.111 34.783 0.00 0.00 0.00 2.32
739 1402 5.888691 ATGTGGCAAACGATACATACAAA 57.111 34.783 0.00 0.00 32.41 2.83
778 1441 6.049149 CAGTCAGGTCAGAAAGTTTGAAGTA 58.951 40.000 0.00 0.00 0.00 2.24
792 1455 5.133221 TCGATTCTGATATCAGTCAGGTCA 58.867 41.667 27.80 8.09 44.51 4.02
818 1483 5.468592 TGGAAAGCACGAAACGTAATACTA 58.531 37.500 0.00 0.00 38.32 1.82
820 1485 4.634991 CTGGAAAGCACGAAACGTAATAC 58.365 43.478 0.00 0.00 38.32 1.89
823 1488 1.262151 GCTGGAAAGCACGAAACGTAA 59.738 47.619 0.00 0.00 38.32 3.18
824 1489 0.863144 GCTGGAAAGCACGAAACGTA 59.137 50.000 0.00 0.00 38.32 3.57
825 1490 0.814010 AGCTGGAAAGCACGAAACGT 60.814 50.000 0.00 0.00 42.36 3.99
826 1491 0.110644 GAGCTGGAAAGCACGAAACG 60.111 55.000 0.00 0.00 37.25 3.60
827 1492 0.944386 TGAGCTGGAAAGCACGAAAC 59.056 50.000 0.00 0.00 37.25 2.78
845 1510 7.489113 ACTTGATTTCACAGTACAAAAGCTTTG 59.511 33.333 13.54 9.55 0.00 2.77
849 1514 6.494842 TGACTTGATTTCACAGTACAAAAGC 58.505 36.000 0.00 0.00 0.00 3.51
866 1531 6.705302 AGATAGCAAAGAGTCAATGACTTGA 58.295 36.000 17.79 0.00 43.53 3.02
902 1568 5.750067 GCCTGCATCAATAAAACAACCATAG 59.250 40.000 0.00 0.00 0.00 2.23
903 1569 5.659463 GCCTGCATCAATAAAACAACCATA 58.341 37.500 0.00 0.00 0.00 2.74
904 1570 4.506758 GCCTGCATCAATAAAACAACCAT 58.493 39.130 0.00 0.00 0.00 3.55
958 1624 9.050601 TGCTTAGAATTAAACAAACAAATTGGG 57.949 29.630 0.00 0.00 43.66 4.12
962 1628 7.651704 AGCGTGCTTAGAATTAAACAAACAAAT 59.348 29.630 0.00 0.00 0.00 2.32
973 1639 4.625742 GTGTCAGAAGCGTGCTTAGAATTA 59.374 41.667 7.15 0.00 36.26 1.40
995 1663 3.983344 GCGAAGAAGCAATGACATTTTGT 59.017 39.130 0.00 0.00 37.05 2.83
1003 1671 3.752747 TGATTGAAGCGAAGAAGCAATGA 59.247 39.130 0.00 0.00 40.15 2.57
1091 1759 5.350504 TTTTGGATCAAGCAACTTTCCAA 57.649 34.783 8.68 8.68 38.09 3.53
1152 1820 0.235665 CACTGTGCAAACTAGCCGTG 59.764 55.000 0.00 0.00 0.00 4.94
1155 1823 1.207593 CGCACTGTGCAAACTAGCC 59.792 57.895 29.86 0.17 45.36 3.93
1173 1841 2.952310 GGAAATACATGAACCCAGGCTC 59.048 50.000 0.00 0.00 0.00 4.70
1515 2195 3.640029 GACTAATGTGAAGGGACGGGATA 59.360 47.826 0.00 0.00 0.00 2.59
1650 2330 8.658499 ACTGAACAAATAGACTTACTTTCGTT 57.342 30.769 0.00 0.00 0.00 3.85
1746 2621 8.715191 AACTTACAAAATGCACAAGATTTTCA 57.285 26.923 0.00 0.00 31.96 2.69
1853 3157 9.021863 CGTTTATAGCTAACTGGTTCTCTAAAG 57.978 37.037 0.00 0.00 0.00 1.85
1866 3170 6.098017 ACTCCTGAACACGTTTATAGCTAAC 58.902 40.000 0.00 0.00 0.00 2.34
1867 3171 6.276832 ACTCCTGAACACGTTTATAGCTAA 57.723 37.500 0.00 0.00 0.00 3.09
1868 3172 5.909621 ACTCCTGAACACGTTTATAGCTA 57.090 39.130 0.00 0.00 0.00 3.32
1869 3173 4.803098 ACTCCTGAACACGTTTATAGCT 57.197 40.909 0.00 0.00 0.00 3.32
1870 3174 5.857822 AAACTCCTGAACACGTTTATAGC 57.142 39.130 0.00 0.00 0.00 2.97
1871 3175 8.752766 TCTAAAACTCCTGAACACGTTTATAG 57.247 34.615 0.00 0.00 0.00 1.31
1872 3176 8.579006 TCTCTAAAACTCCTGAACACGTTTATA 58.421 33.333 0.00 0.00 0.00 0.98
1873 3177 7.439381 TCTCTAAAACTCCTGAACACGTTTAT 58.561 34.615 0.00 0.00 0.00 1.40
1874 3178 6.808829 TCTCTAAAACTCCTGAACACGTTTA 58.191 36.000 0.00 0.00 0.00 2.01
1875 3179 5.667466 TCTCTAAAACTCCTGAACACGTTT 58.333 37.500 0.00 0.00 0.00 3.60
1876 3180 5.272283 TCTCTAAAACTCCTGAACACGTT 57.728 39.130 0.00 0.00 0.00 3.99
1877 3181 4.931661 TCTCTAAAACTCCTGAACACGT 57.068 40.909 0.00 0.00 0.00 4.49
1878 3182 4.448060 GGTTCTCTAAAACTCCTGAACACG 59.552 45.833 0.00 0.00 36.50 4.49
1879 3183 5.365619 TGGTTCTCTAAAACTCCTGAACAC 58.634 41.667 0.00 0.00 36.50 3.32
1880 3184 5.130477 ACTGGTTCTCTAAAACTCCTGAACA 59.870 40.000 0.00 0.00 36.50 3.18
1881 3185 5.612351 ACTGGTTCTCTAAAACTCCTGAAC 58.388 41.667 0.00 0.00 34.74 3.18
1882 3186 5.888982 ACTGGTTCTCTAAAACTCCTGAA 57.111 39.130 0.00 0.00 0.00 3.02
1883 3187 5.888982 AACTGGTTCTCTAAAACTCCTGA 57.111 39.130 0.00 0.00 0.00 3.86
1884 3188 5.639931 GCTAACTGGTTCTCTAAAACTCCTG 59.360 44.000 0.00 0.00 0.00 3.86
1885 3189 5.544562 AGCTAACTGGTTCTCTAAAACTCCT 59.455 40.000 0.00 0.00 0.00 3.69
1886 3190 5.795972 AGCTAACTGGTTCTCTAAAACTCC 58.204 41.667 0.00 0.00 0.00 3.85
1890 3194 9.362539 CGTTTATAGCTAACTGGTTCTCTAAAA 57.637 33.333 0.00 0.00 0.00 1.52
1891 3195 8.526147 ACGTTTATAGCTAACTGGTTCTCTAAA 58.474 33.333 0.00 0.00 0.00 1.85
1892 3196 7.972277 CACGTTTATAGCTAACTGGTTCTCTAA 59.028 37.037 0.00 0.00 0.00 2.10
1893 3197 7.121759 ACACGTTTATAGCTAACTGGTTCTCTA 59.878 37.037 0.00 0.00 0.00 2.43
1894 3198 6.071503 ACACGTTTATAGCTAACTGGTTCTCT 60.072 38.462 0.00 0.00 0.00 3.10
1895 3199 6.098017 ACACGTTTATAGCTAACTGGTTCTC 58.902 40.000 0.00 0.00 0.00 2.87
1896 3200 6.034161 ACACGTTTATAGCTAACTGGTTCT 57.966 37.500 0.00 0.00 0.00 3.01
1897 3201 6.716898 AACACGTTTATAGCTAACTGGTTC 57.283 37.500 0.00 0.00 0.00 3.62
1898 3202 6.128742 CGAAACACGTTTATAGCTAACTGGTT 60.129 38.462 0.00 0.00 37.22 3.67
1899 3203 5.346822 CGAAACACGTTTATAGCTAACTGGT 59.653 40.000 0.00 0.00 37.22 4.00
1900 3204 5.220340 CCGAAACACGTTTATAGCTAACTGG 60.220 44.000 0.00 0.00 40.78 4.00
1901 3205 5.574055 TCCGAAACACGTTTATAGCTAACTG 59.426 40.000 0.00 0.00 40.78 3.16
1902 3206 5.713025 TCCGAAACACGTTTATAGCTAACT 58.287 37.500 0.00 0.00 40.78 2.24
1903 3207 5.574443 ACTCCGAAACACGTTTATAGCTAAC 59.426 40.000 0.00 0.00 40.78 2.34
1916 3220 6.833342 TTAGTTTGTTAGACTCCGAAACAC 57.167 37.500 0.00 0.00 33.10 3.32
1944 3248 5.888161 AGGATTAGTTAGATTGCCCAAACAG 59.112 40.000 0.00 0.00 0.00 3.16
1953 3257 8.908786 TGCTTATCCAAGGATTAGTTAGATTG 57.091 34.615 14.52 0.00 34.76 2.67
2016 3320 1.066002 ACGTCTCGGAGTCGTTTTTCA 59.934 47.619 21.40 0.00 37.69 2.69
2025 3329 0.935196 GCACAAAAACGTCTCGGAGT 59.065 50.000 4.69 0.00 0.00 3.85
2100 3404 1.827969 CCAGAAGACGTTCCTCTCCAT 59.172 52.381 0.00 0.00 32.48 3.41
2107 3411 3.119096 GGCGCCAGAAGACGTTCC 61.119 66.667 24.80 0.00 32.48 3.62
2197 3501 1.405463 CTGTACAGAGCATAGTCGCCA 59.595 52.381 18.45 0.00 0.00 5.69
2216 3520 1.956477 GAAGTCACCAACAACATGGCT 59.044 47.619 0.00 0.00 44.75 4.75
2221 3525 3.530265 ACTACGAAGTCACCAACAACA 57.470 42.857 0.00 0.00 43.93 3.33
2271 3614 2.757077 CGGGGCTGGAGGAAAAGT 59.243 61.111 0.00 0.00 0.00 2.66
2389 3732 1.012086 CAACGCTGGACATCCATGAG 58.988 55.000 0.00 0.92 46.46 2.90
2404 3747 3.286751 CCAGTGTGCCCCACAACG 61.287 66.667 0.00 0.00 46.28 4.10
2431 3774 2.024871 CGAGCGAGGTCCTTAGCG 59.975 66.667 12.74 4.67 34.34 4.26
2505 3848 2.726691 CGAACCAGCAGTAACGGCG 61.727 63.158 4.80 4.80 36.08 6.46
2521 3865 5.622611 CCAACGTGATATCGGTGCTACGA 62.623 52.174 15.42 5.82 45.60 3.43
2566 3910 0.741221 GGATGGACGTCCTGTTCTGC 60.741 60.000 33.39 15.01 35.32 4.26
2572 3916 3.849951 CCGGGGATGGACGTCCTG 61.850 72.222 33.39 13.81 38.38 3.86
2605 3949 2.770447 TGCCATTCCTACATCCCTGTA 58.230 47.619 0.00 0.00 36.79 2.74
2607 3951 2.579873 CTTGCCATTCCTACATCCCTG 58.420 52.381 0.00 0.00 0.00 4.45
2621 3979 1.375908 CTGTTCGCCTAGCTTGCCA 60.376 57.895 0.00 0.00 0.00 4.92
2679 4037 4.135153 CTGCTCCACTCGGGTCGG 62.135 72.222 0.00 0.00 38.11 4.79
2760 4118 6.951198 ACCATCTCTCTCTTTCTCAAACTAGA 59.049 38.462 0.00 0.00 0.00 2.43
2782 4140 2.271821 CCACGCATCCCATGACCA 59.728 61.111 0.00 0.00 0.00 4.02
2875 4233 7.851963 CACGTGGATTTAGAAAACGAGTTTTTA 59.148 33.333 7.95 7.13 42.26 1.52
2897 4255 3.386726 TGGATAGCAAGTATAAGCCACGT 59.613 43.478 0.00 0.00 0.00 4.49
2902 4260 6.094881 TGGTTGTTTGGATAGCAAGTATAAGC 59.905 38.462 0.00 0.00 0.00 3.09
2917 4275 6.877611 AGATAACACTTAGTGGTTGTTTGG 57.122 37.500 17.21 0.00 37.94 3.28
2993 4351 2.391389 GGAGTTTGGCGGCTTCGAG 61.391 63.158 11.43 0.00 35.61 4.04
3036 4394 6.420604 GGCCATCAAATCGTTTTACATTATGG 59.579 38.462 0.00 0.00 34.58 2.74
3410 4813 3.189285 CACTTGGCCACTTCAACAAAAG 58.811 45.455 3.88 0.00 0.00 2.27
3457 4862 4.406456 ACTGGGACTGCAAAAATGATACA 58.594 39.130 0.00 0.00 0.00 2.29
3904 5319 2.035066 GGCTTTCACTGACAAATGCAGT 59.965 45.455 0.00 0.00 46.86 4.40
3972 5387 4.288626 ACCTGGCAATAGTTTTCTACCTGA 59.711 41.667 0.00 0.00 35.02 3.86
4127 5553 8.261522 TGACATATACCATGCTACTACAAACAA 58.738 33.333 0.00 0.00 0.00 2.83
4151 5577 7.653647 AGCGTAGGTTCAAACAATTTTAATGA 58.346 30.769 0.00 0.00 27.67 2.57
4256 5682 6.145048 ACAAAGACTAAACTGAAATCCGTACG 59.855 38.462 8.69 8.69 0.00 3.67
4261 5687 8.603242 TGACTACAAAGACTAAACTGAAATCC 57.397 34.615 0.00 0.00 0.00 3.01
4398 5826 4.060205 ACAAAGTAAGGTAATGAACGCGT 58.940 39.130 5.58 5.58 0.00 6.01
4399 5827 4.657075 ACAAAGTAAGGTAATGAACGCG 57.343 40.909 3.53 3.53 0.00 6.01
4428 5856 5.991606 TCATTTTTGCTGGACTATATCTCCG 59.008 40.000 0.00 0.00 0.00 4.63
4440 5870 3.376859 TGCGTAGGTATCATTTTTGCTGG 59.623 43.478 0.00 0.00 0.00 4.85
4466 5896 3.763057 AGGGTCAACCAATACAAAGACC 58.237 45.455 0.89 0.00 43.89 3.85
4467 5897 5.528870 CAAAGGGTCAACCAATACAAAGAC 58.471 41.667 0.89 0.00 43.89 3.01
4515 5946 4.280436 TCCACAAGTACCATAACAGTGG 57.720 45.455 0.00 0.00 43.54 4.00
4534 5965 1.523758 ATCCGAGCAGTGTTTGTTCC 58.476 50.000 0.00 0.00 33.85 3.62
4545 5976 4.520874 TCCACAAAACATTTTATCCGAGCA 59.479 37.500 0.00 0.00 0.00 4.26
4568 5999 0.826256 CATGCCATGCCTGCCATAGT 60.826 55.000 0.00 0.00 31.47 2.12
4583 6014 2.019984 GGAAACAGATCAGGACCATGC 58.980 52.381 0.00 0.00 0.00 4.06
4597 6028 1.827789 GCTGCACCCACTGGAAACA 60.828 57.895 0.00 0.00 39.59 2.83
4598 6029 1.518903 GAGCTGCACCCACTGGAAAC 61.519 60.000 1.02 0.00 34.81 2.78
4599 6030 1.228245 GAGCTGCACCCACTGGAAA 60.228 57.895 1.02 0.00 34.81 3.13
4600 6031 2.431683 GAGCTGCACCCACTGGAA 59.568 61.111 1.02 0.00 34.81 3.53
4607 6038 2.592993 TAGTGTGGGAGCTGCACCC 61.593 63.158 25.95 25.95 46.87 4.61
4686 6119 5.057149 ACAAAGCTCAACGAAATGACTACT 58.943 37.500 0.00 0.00 0.00 2.57
4702 6135 5.123502 CAGAACAGAGCATCAATACAAAGCT 59.876 40.000 0.00 0.00 37.82 3.74
4703 6136 5.106396 ACAGAACAGAGCATCAATACAAAGC 60.106 40.000 0.00 0.00 37.82 3.51
4704 6137 6.492007 ACAGAACAGAGCATCAATACAAAG 57.508 37.500 0.00 0.00 37.82 2.77
4708 6144 8.125448 GGATAAAACAGAACAGAGCATCAATAC 58.875 37.037 0.00 0.00 37.82 1.89


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

AutoCloner maintained by Alex Coulton.