Multiple sequence alignment - TraesCS7D01G029800

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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 TraesCS7D01G029800 chr7D 100.000 3269 0 0 1 3269 15321234 15324502 0.000000e+00 6037.0
1 TraesCS7D01G029800 chr7D 87.337 537 57 7 2 535 15202854 15203382 3.610000e-169 604.0
2 TraesCS7D01G029800 chr7D 81.481 594 80 16 1725 2302 573827010 573826431 8.260000e-126 460.0
3 TraesCS7D01G029800 chr7D 80.280 644 83 22 1753 2371 573696936 573696312 2.310000e-121 446.0
4 TraesCS7D01G029800 chr7D 76.800 250 41 14 1093 1339 573697665 573697430 1.230000e-24 124.0
5 TraesCS7D01G029800 chr7A 87.700 1626 146 26 1675 3269 14619234 14620836 0.000000e+00 1845.0
6 TraesCS7D01G029800 chr7A 80.176 681 88 26 1723 2375 663533673 663533012 1.780000e-127 466.0
7 TraesCS7D01G029800 chr7A 86.243 378 26 14 1009 1377 14618506 14618866 1.420000e-103 387.0
8 TraesCS7D01G029800 chr7A 91.707 205 17 0 2688 2892 318138990 318139194 5.340000e-73 285.0
9 TraesCS7D01G029800 chr7A 93.671 158 8 1 2183 2338 318138831 318138988 5.450000e-58 235.0
10 TraesCS7D01G029800 chr4A 89.239 920 84 11 1711 2620 720516329 720515415 0.000000e+00 1136.0
11 TraesCS7D01G029800 chr4A 89.634 656 52 8 2605 3259 720515394 720514754 0.000000e+00 821.0
12 TraesCS7D01G029800 chr4A 93.110 537 35 2 7 541 719620107 719620643 0.000000e+00 785.0
13 TraesCS7D01G029800 chr4A 92.804 542 37 2 2 541 719581788 719582329 0.000000e+00 784.0
14 TraesCS7D01G029800 chr4A 92.251 542 40 2 2 541 719659214 719659755 0.000000e+00 767.0
15 TraesCS7D01G029800 chr4A 81.285 887 91 29 541 1377 720517666 720516805 0.000000e+00 649.0
16 TraesCS7D01G029800 chr4A 87.384 539 57 7 2 537 719575549 719576079 2.790000e-170 608.0
17 TraesCS7D01G029800 chr4A 87.132 544 60 6 2 541 720519077 720518540 2.790000e-170 608.0
18 TraesCS7D01G029800 chr4A 87.199 539 58 7 2 537 719613861 719614391 1.300000e-168 603.0
19 TraesCS7D01G029800 chr4A 86.447 546 63 6 2 544 720539941 720539404 3.630000e-164 588.0
20 TraesCS7D01G029800 chr4A 83.221 298 34 8 2976 3269 720363966 720363681 3.240000e-65 259.0
21 TraesCS7D01G029800 chr4A 83.772 228 21 5 837 1052 720519599 720519376 5.530000e-48 202.0
22 TraesCS7D01G029800 chr4A 76.115 381 48 16 738 1085 719626773 719627143 3.380000e-35 159.0
23 TraesCS7D01G029800 chr4A 75.718 383 46 17 738 1085 719588021 719588391 7.310000e-32 148.0
24 TraesCS7D01G029800 chrUn 87.316 544 59 6 2 541 268669409 268668872 5.990000e-172 614.0
25 TraesCS7D01G029800 chrUn 83.772 228 21 5 837 1052 268669931 268669708 5.530000e-48 202.0
26 TraesCS7D01G029800 chr7B 81.081 592 83 17 1725 2302 632658249 632657673 2.310000e-121 446.0
27 TraesCS7D01G029800 chr7B 79.173 677 98 24 1722 2375 632494041 632493385 2.330000e-116 429.0
28 TraesCS7D01G029800 chr7B 92.683 205 15 0 2688 2892 121187159 121187363 2.470000e-76 296.0
29 TraesCS7D01G029800 chr7B 92.405 158 10 1 2183 2338 121187000 121187157 1.180000e-54 224.0
30 TraesCS7D01G029800 chr7B 78.819 288 48 7 1206 1489 697909371 697909649 7.210000e-42 182.0
31 TraesCS7D01G029800 chr5B 91.827 208 17 0 2691 2898 566110926 566110719 1.150000e-74 291.0
32 TraesCS7D01G029800 chr6A 94.074 135 8 0 2758 2892 230442338 230442472 4.280000e-49 206.0
33 TraesCS7D01G029800 chr3A 89.933 149 14 1 2745 2892 338206881 338207029 1.200000e-44 191.0
34 TraesCS7D01G029800 chr3A 80.347 173 32 1 1282 1452 443957824 443957996 2.650000e-26 130.0
35 TraesCS7D01G029800 chr4B 78.746 287 48 6 1206 1489 99087135 99086859 2.590000e-41 180.0
36 TraesCS7D01G029800 chr3B 78.671 286 49 9 1206 1489 706497190 706496915 2.590000e-41 180.0
37 TraesCS7D01G029800 chr3D 78.467 274 46 8 1282 1552 31197759 31198022 2.020000e-37 167.0
38 TraesCS7D01G029800 chr1A 77.455 275 48 8 1282 1552 530578344 530578608 5.650000e-33 152.0
39 TraesCS7D01G029800 chr2B 83.654 104 16 1 1282 1384 608561954 608562057 2.680000e-16 97.1
40 TraesCS7D01G029800 chr2B 90.141 71 6 1 2822 2892 8504234 8504303 1.250000e-14 91.6


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 TraesCS7D01G029800 chr7D 15321234 15324502 3268 False 6037.0 6037 100.0000 1 3269 1 chr7D.!!$F2 3268
1 TraesCS7D01G029800 chr7D 15202854 15203382 528 False 604.0 604 87.3370 2 535 1 chr7D.!!$F1 533
2 TraesCS7D01G029800 chr7D 573826431 573827010 579 True 460.0 460 81.4810 1725 2302 1 chr7D.!!$R1 577
3 TraesCS7D01G029800 chr7D 573696312 573697665 1353 True 285.0 446 78.5400 1093 2371 2 chr7D.!!$R2 1278
4 TraesCS7D01G029800 chr7A 14618506 14620836 2330 False 1116.0 1845 86.9715 1009 3269 2 chr7A.!!$F1 2260
5 TraesCS7D01G029800 chr7A 663533012 663533673 661 True 466.0 466 80.1760 1723 2375 1 chr7A.!!$R1 652
6 TraesCS7D01G029800 chr4A 719620107 719620643 536 False 785.0 785 93.1100 7 541 1 chr4A.!!$F5 534
7 TraesCS7D01G029800 chr4A 719581788 719582329 541 False 784.0 784 92.8040 2 541 1 chr4A.!!$F2 539
8 TraesCS7D01G029800 chr4A 719659214 719659755 541 False 767.0 767 92.2510 2 541 1 chr4A.!!$F7 539
9 TraesCS7D01G029800 chr4A 720514754 720519599 4845 True 683.2 1136 86.2124 2 3259 5 chr4A.!!$R3 3257
10 TraesCS7D01G029800 chr4A 719575549 719576079 530 False 608.0 608 87.3840 2 537 1 chr4A.!!$F1 535
11 TraesCS7D01G029800 chr4A 719613861 719614391 530 False 603.0 603 87.1990 2 537 1 chr4A.!!$F4 535
12 TraesCS7D01G029800 chr4A 720539404 720539941 537 True 588.0 588 86.4470 2 544 1 chr4A.!!$R2 542
13 TraesCS7D01G029800 chrUn 268668872 268669931 1059 True 408.0 614 85.5440 2 1052 2 chrUn.!!$R1 1050
14 TraesCS7D01G029800 chr7B 632657673 632658249 576 True 446.0 446 81.0810 1725 2302 1 chr7B.!!$R2 577
15 TraesCS7D01G029800 chr7B 632493385 632494041 656 True 429.0 429 79.1730 1722 2375 1 chr7B.!!$R1 653

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
627 2031 0.107654 AAGTTGGCCGAGCTATCACC 60.108 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2419 4301 0.609681 TTGCAGCCATCAGATGTGCA 60.61 50.0 19.81 19.81 39.53 4.57 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
46 568 6.317893 CACAGATGATTGATGGAGATGAACAA 59.682 38.462 0.00 0.00 0.00 2.83
57 579 3.243839 GGAGATGAACAAAGCCTGCAAAA 60.244 43.478 0.00 0.00 0.00 2.44
102 627 9.531412 TGTAAAATAAAACATCGTTACGACATG 57.469 29.630 10.39 8.28 39.18 3.21
113 638 2.596904 TACGACATGGCCTAAAGCTC 57.403 50.000 3.32 0.00 43.05 4.09
147 673 1.401905 GCATCGGAAAAGACACATCCC 59.598 52.381 0.00 0.00 0.00 3.85
158 684 6.484364 AAAGACACATCCCATTTGTTTCTT 57.516 33.333 0.66 0.66 42.76 2.52
171 697 3.586470 TGTTTCTTTGTGCCCTAAGGA 57.414 42.857 0.00 0.00 33.47 3.36
175 701 3.806949 TCTTTGTGCCCTAAGGACATT 57.193 42.857 0.00 0.00 33.47 2.71
232 758 4.868171 TGCACTTACTATCACGTTCATTCC 59.132 41.667 0.00 0.00 0.00 3.01
334 861 2.035321 TGCAAATGAAAACCTTCGGTCC 59.965 45.455 0.00 0.00 33.12 4.46
573 1977 3.948719 GACCCCTCGGCAACACCA 61.949 66.667 0.00 0.00 39.03 4.17
576 1980 4.641645 CCCTCGGCAACACCAGCA 62.642 66.667 0.00 0.00 39.03 4.41
578 1982 2.591429 CTCGGCAACACCAGCACA 60.591 61.111 0.00 0.00 39.03 4.57
592 1996 2.590007 CACAGCCGGGCATCTAGC 60.590 66.667 23.09 0.00 44.65 3.42
609 2013 3.781307 CGTCGATGGGCCCTGGAA 61.781 66.667 25.70 1.52 0.00 3.53
614 2018 1.380380 GATGGGCCCTGGAAGTTGG 60.380 63.158 25.70 0.00 0.00 3.77
622 2026 1.596934 CTGGAAGTTGGCCGAGCTA 59.403 57.895 0.00 0.00 0.00 3.32
627 2031 0.107654 AAGTTGGCCGAGCTATCACC 60.108 55.000 0.00 0.00 0.00 4.02
639 2043 3.943479 TATCACCACACACCGCGCC 62.943 63.158 0.00 0.00 0.00 6.53
651 2055 3.199190 CGCGCCCGAGCCAATTTA 61.199 61.111 0.00 0.00 36.29 1.40
658 2062 2.427095 GCCCGAGCCAATTTATTTGAGT 59.573 45.455 0.00 0.00 37.53 3.41
660 2064 4.097286 GCCCGAGCCAATTTATTTGAGTAA 59.903 41.667 0.00 0.00 37.53 2.24
665 2069 6.523201 CGAGCCAATTTATTTGAGTAACACAC 59.477 38.462 0.00 0.00 37.53 3.82
666 2070 7.283625 AGCCAATTTATTTGAGTAACACACA 57.716 32.000 0.00 0.00 37.53 3.72
668 2072 8.028938 AGCCAATTTATTTGAGTAACACACATC 58.971 33.333 0.00 0.00 37.53 3.06
712 2116 1.133823 ACATTGTCACTGTTGAGGGCA 60.134 47.619 0.00 0.00 30.10 5.36
718 2122 1.211703 TCACTGTTGAGGGCAGTCAAA 59.788 47.619 3.35 0.00 44.43 2.69
724 2137 3.130340 TGTTGAGGGCAGTCAAAGAAAAC 59.870 43.478 3.35 0.00 38.17 2.43
735 2148 6.083630 CAGTCAAAGAAAACAAACACTTCGA 58.916 36.000 0.00 0.00 0.00 3.71
736 2149 6.249260 CAGTCAAAGAAAACAAACACTTCGAG 59.751 38.462 0.00 0.00 0.00 4.04
752 2165 1.833630 TCGAGATCAATGGGCTCAAGT 59.166 47.619 0.00 0.00 0.00 3.16
753 2166 2.159043 TCGAGATCAATGGGCTCAAGTC 60.159 50.000 0.00 0.00 0.00 3.01
763 2177 2.581354 CTCAAGTCTCAGGGCCGG 59.419 66.667 0.00 0.00 0.00 6.13
764 2178 3.672295 CTCAAGTCTCAGGGCCGGC 62.672 68.421 21.18 21.18 0.00 6.13
765 2179 3.710722 CAAGTCTCAGGGCCGGCT 61.711 66.667 28.56 3.74 0.00 5.52
792 2207 0.819666 GAAATCGCCCCATCCACTCC 60.820 60.000 0.00 0.00 0.00 3.85
810 2225 2.544359 CATCGGCGCGATAAACCG 59.456 61.111 12.10 13.79 45.19 4.44
831 2250 4.237724 CGCAGGAAAGAAAAGGAAAATCC 58.762 43.478 0.00 0.00 36.58 3.01
832 2251 4.569943 GCAGGAAAGAAAAGGAAAATCCC 58.430 43.478 0.00 0.00 37.19 3.85
833 2252 4.040339 GCAGGAAAGAAAAGGAAAATCCCA 59.960 41.667 0.00 0.00 37.19 4.37
834 2253 5.454613 GCAGGAAAGAAAAGGAAAATCCCAA 60.455 40.000 0.00 0.00 37.19 4.12
835 2254 6.226052 CAGGAAAGAAAAGGAAAATCCCAAG 58.774 40.000 0.00 0.00 37.19 3.61
836 2255 4.997395 GGAAAGAAAAGGAAAATCCCAAGC 59.003 41.667 0.00 0.00 37.19 4.01
875 2294 3.937706 CGCAATTCTCACCTCTGAATCTT 59.062 43.478 0.00 0.00 32.43 2.40
910 2332 0.470833 ACAGCACAGGTCAGTCTCCT 60.471 55.000 0.00 0.00 35.45 3.69
920 2343 0.851332 TCAGTCTCCTCTCCCTCCCA 60.851 60.000 0.00 0.00 0.00 4.37
948 2377 1.449778 GTCGCCCTAGGGTTCAAGC 60.450 63.158 28.96 12.31 37.65 4.01
952 2381 1.915983 CCCTAGGGTTCAAGCTCCC 59.084 63.158 20.88 0.00 43.71 4.30
953 2382 1.636769 CCCTAGGGTTCAAGCTCCCC 61.637 65.000 20.88 3.83 44.40 4.81
957 2386 3.007581 GGGTTCAAGCTCCCCTAGA 57.992 57.895 0.00 0.00 37.89 2.43
958 2387 1.512735 GGGTTCAAGCTCCCCTAGAT 58.487 55.000 0.00 0.00 37.89 1.98
959 2388 1.418264 GGGTTCAAGCTCCCCTAGATC 59.582 57.143 0.00 0.00 37.89 2.75
960 2389 1.418264 GGTTCAAGCTCCCCTAGATCC 59.582 57.143 0.00 0.00 0.00 3.36
961 2390 2.403561 GTTCAAGCTCCCCTAGATCCT 58.596 52.381 0.00 0.00 0.00 3.24
962 2391 2.367241 GTTCAAGCTCCCCTAGATCCTC 59.633 54.545 0.00 0.00 0.00 3.71
963 2392 1.133009 TCAAGCTCCCCTAGATCCTCC 60.133 57.143 0.00 0.00 0.00 4.30
964 2393 0.192315 AAGCTCCCCTAGATCCTCCC 59.808 60.000 0.00 0.00 0.00 4.30
965 2394 1.608046 GCTCCCCTAGATCCTCCCG 60.608 68.421 0.00 0.00 0.00 5.14
966 2395 1.608046 CTCCCCTAGATCCTCCCGC 60.608 68.421 0.00 0.00 0.00 6.13
967 2396 2.992114 CCCCTAGATCCTCCCGCG 60.992 72.222 0.00 0.00 0.00 6.46
968 2397 2.203509 CCCTAGATCCTCCCGCGT 60.204 66.667 4.92 0.00 0.00 6.01
969 2398 2.269529 CCCTAGATCCTCCCGCGTC 61.270 68.421 4.92 0.00 0.00 5.19
970 2399 2.269529 CCTAGATCCTCCCGCGTCC 61.270 68.421 4.92 0.00 0.00 4.79
971 2400 2.203451 TAGATCCTCCCGCGTCCC 60.203 66.667 4.92 0.00 0.00 4.46
972 2401 2.978298 CTAGATCCTCCCGCGTCCCA 62.978 65.000 4.92 0.00 0.00 4.37
973 2402 4.222847 GATCCTCCCGCGTCCCAC 62.223 72.222 4.92 0.00 0.00 4.61
1061 2514 2.546795 GCCGTGATCTGATTCCTCGAAT 60.547 50.000 0.00 0.00 34.71 3.34
1064 2517 3.738282 CGTGATCTGATTCCTCGAATTCC 59.262 47.826 0.00 0.00 31.89 3.01
1148 2616 2.528818 CCAGTCCCTCACCAAGGCA 61.529 63.158 0.00 0.00 44.71 4.75
1203 2671 4.426736 TTCGTTTTCTTTCCCCAGTACT 57.573 40.909 0.00 0.00 0.00 2.73
1204 2672 3.999046 TCGTTTTCTTTCCCCAGTACTC 58.001 45.455 0.00 0.00 0.00 2.59
1257 2728 2.271800 GGGTTACTGATGTGCTTCTCG 58.728 52.381 0.00 0.00 0.00 4.04
1258 2729 2.094182 GGGTTACTGATGTGCTTCTCGA 60.094 50.000 0.00 0.00 0.00 4.04
1259 2730 2.924290 GGTTACTGATGTGCTTCTCGAC 59.076 50.000 0.00 0.00 0.00 4.20
1260 2731 3.367498 GGTTACTGATGTGCTTCTCGACT 60.367 47.826 0.00 0.00 0.00 4.18
1261 2732 4.238514 GTTACTGATGTGCTTCTCGACTT 58.761 43.478 0.00 0.00 0.00 3.01
1262 2733 2.953020 ACTGATGTGCTTCTCGACTTC 58.047 47.619 0.00 0.00 0.00 3.01
1263 2734 2.560542 ACTGATGTGCTTCTCGACTTCT 59.439 45.455 0.00 0.00 0.00 2.85
1264 2735 3.178267 CTGATGTGCTTCTCGACTTCTC 58.822 50.000 0.00 0.00 0.00 2.87
1308 2791 3.641986 GTGGTTTTCGCCGTCGCA 61.642 61.111 0.00 0.00 35.26 5.10
1341 2824 5.800438 GGTTCAGGTAATTTTCGATGCTTTC 59.200 40.000 0.00 0.00 0.00 2.62
1343 2826 4.094294 TCAGGTAATTTTCGATGCTTTCCG 59.906 41.667 0.00 0.00 0.00 4.30
1345 2828 2.939460 AATTTTCGATGCTTTCCGGG 57.061 45.000 0.00 0.00 0.00 5.73
1347 2830 0.037017 TTTTCGATGCTTTCCGGGGA 59.963 50.000 0.00 0.00 0.00 4.81
1348 2831 0.675522 TTTCGATGCTTTCCGGGGAC 60.676 55.000 0.00 0.00 0.00 4.46
1349 2832 1.550130 TTCGATGCTTTCCGGGGACT 61.550 55.000 0.00 0.00 0.00 3.85
1377 2866 3.939740 CCTGATTTGGGATGGAGAAGA 57.060 47.619 0.00 0.00 0.00 2.87
1410 2982 7.155328 ACTGAGTTTAGGATATTCATTAGGCG 58.845 38.462 0.00 0.00 0.00 5.52
1411 2983 7.062749 TGAGTTTAGGATATTCATTAGGCGT 57.937 36.000 0.00 0.00 0.00 5.68
1413 2985 7.062749 AGTTTAGGATATTCATTAGGCGTCA 57.937 36.000 0.00 0.00 0.00 4.35
1414 2986 7.680730 AGTTTAGGATATTCATTAGGCGTCAT 58.319 34.615 0.00 0.00 0.00 3.06
1415 2987 8.812972 AGTTTAGGATATTCATTAGGCGTCATA 58.187 33.333 0.00 0.00 0.00 2.15
1416 2988 9.088512 GTTTAGGATATTCATTAGGCGTCATAG 57.911 37.037 0.00 0.00 0.00 2.23
1435 3010 4.547859 GCCATAGCTGGTGGTCTG 57.452 61.111 17.98 0.00 45.10 3.51
1441 3016 2.231716 TAGCTGGTGGTCTGCTAGAA 57.768 50.000 0.00 0.00 46.65 2.10
1446 3021 3.739519 GCTGGTGGTCTGCTAGAACTATG 60.740 52.174 0.00 0.00 37.35 2.23
1447 3022 2.168521 TGGTGGTCTGCTAGAACTATGC 59.831 50.000 0.00 0.00 31.84 3.14
1456 3031 4.697514 TGCTAGAACTATGCACTGATTCC 58.302 43.478 0.00 0.00 0.00 3.01
1459 3034 5.178996 GCTAGAACTATGCACTGATTCCATG 59.821 44.000 0.00 0.00 0.00 3.66
1461 3036 3.939740 ACTATGCACTGATTCCATGGT 57.060 42.857 12.58 0.00 0.00 3.55
1466 3042 1.771565 CACTGATTCCATGGTGGCAT 58.228 50.000 12.58 0.00 37.47 4.40
1467 3043 1.407618 CACTGATTCCATGGTGGCATG 59.592 52.381 12.58 1.07 37.47 4.06
1476 3052 2.435422 CATGGTGGCATGTGTCTTGTA 58.565 47.619 0.00 0.00 0.00 2.41
1479 3055 1.133025 GGTGGCATGTGTCTTGTATGC 59.867 52.381 0.00 0.00 44.81 3.14
1482 3058 3.057315 GTGGCATGTGTCTTGTATGCTTT 60.057 43.478 0.00 0.00 44.88 3.51
1489 3065 7.967854 GCATGTGTCTTGTATGCTTTTTATACA 59.032 33.333 0.00 0.00 42.84 2.29
1510 3086 6.829229 ACAAGATTTCATCATCTTTCAGCA 57.171 33.333 0.00 0.00 40.86 4.41
1511 3087 6.853720 ACAAGATTTCATCATCTTTCAGCAG 58.146 36.000 0.00 0.00 40.86 4.24
1516 3099 3.007635 TCATCATCTTTCAGCAGCAGTG 58.992 45.455 0.00 0.00 0.00 3.66
1533 3222 0.032540 GTGGGCTTTCAGGTTGCAAG 59.967 55.000 0.00 0.00 0.00 4.01
1552 3241 5.118990 GCAAGAATCTGATGCACCTAGTAA 58.881 41.667 2.32 0.00 39.81 2.24
1553 3242 5.007136 GCAAGAATCTGATGCACCTAGTAAC 59.993 44.000 2.32 0.00 39.81 2.50
1554 3243 5.939764 AGAATCTGATGCACCTAGTAACA 57.060 39.130 0.00 0.00 0.00 2.41
1555 3244 5.911752 AGAATCTGATGCACCTAGTAACAG 58.088 41.667 0.00 0.00 0.00 3.16
1557 3246 4.456280 TCTGATGCACCTAGTAACAGTG 57.544 45.455 0.00 0.00 34.58 3.66
1562 3251 3.227614 TGCACCTAGTAACAGTGTCTGA 58.772 45.455 0.00 0.00 35.18 3.27
1563 3252 3.832490 TGCACCTAGTAACAGTGTCTGAT 59.168 43.478 0.00 0.00 35.18 2.90
1565 3254 5.656859 TGCACCTAGTAACAGTGTCTGATAT 59.343 40.000 0.00 0.00 35.18 1.63
1566 3255 5.980116 GCACCTAGTAACAGTGTCTGATATG 59.020 44.000 0.00 0.00 35.18 1.78
1598 3410 1.028905 TTCTTTGGTTCGGGCACTTG 58.971 50.000 0.00 0.00 0.00 3.16
1599 3411 0.106918 TCTTTGGTTCGGGCACTTGT 60.107 50.000 0.00 0.00 0.00 3.16
1602 3414 0.457851 TTGGTTCGGGCACTTGTTTG 59.542 50.000 0.00 0.00 0.00 2.93
1604 3416 0.248866 GGTTCGGGCACTTGTTTGTG 60.249 55.000 0.00 0.00 40.62 3.33
1614 3426 2.679837 CACTTGTTTGTGCTGACTGACT 59.320 45.455 0.00 0.00 0.00 3.41
1618 3430 2.419673 TGTTTGTGCTGACTGACTGTTG 59.580 45.455 0.00 0.00 0.00 3.33
1629 3441 2.107204 ACTGACTGTTGGCCAGATTCTT 59.893 45.455 5.11 0.00 44.49 2.52
1637 3452 2.811410 TGGCCAGATTCTTTCAGCAAT 58.189 42.857 0.00 0.00 0.00 3.56
1651 3466 3.423749 TCAGCAATTTCCATCTGAGCAA 58.576 40.909 0.00 0.00 32.43 3.91
1652 3467 3.827876 TCAGCAATTTCCATCTGAGCAAA 59.172 39.130 0.00 0.00 32.43 3.68
1663 3479 6.913170 TCCATCTGAGCAAATGTTTTTACTC 58.087 36.000 0.00 0.00 36.26 2.59
1673 3489 1.606668 TGTTTTTACTCGCTGGCCTTG 59.393 47.619 3.32 0.00 0.00 3.61
1700 3550 4.798882 CCCCCTAGTTGCAATATAAACCA 58.201 43.478 0.59 0.00 0.00 3.67
1705 3555 5.536161 CCTAGTTGCAATATAAACCATGGCT 59.464 40.000 13.04 0.00 0.00 4.75
1706 3556 5.937975 AGTTGCAATATAAACCATGGCTT 57.062 34.783 13.04 8.96 0.00 4.35
1707 3557 5.663456 AGTTGCAATATAAACCATGGCTTG 58.337 37.500 13.04 7.43 0.00 4.01
1718 3568 1.133823 CCATGGCTTGGTATGGTAGCA 60.134 52.381 11.13 0.00 40.99 3.49
1737 3587 1.000506 CACAGAGCCATTTGCAAGCTT 59.999 47.619 12.39 0.00 44.83 3.74
1882 3734 5.778241 GGAATTTCTTTCTTTTACCCCTCCA 59.222 40.000 0.00 0.00 34.56 3.86
1887 3739 5.570320 TCTTTCTTTTACCCCTCCAGATTG 58.430 41.667 0.00 0.00 0.00 2.67
1888 3740 5.312178 TCTTTCTTTTACCCCTCCAGATTGA 59.688 40.000 0.00 0.00 0.00 2.57
1894 3746 2.566746 ACCCCTCCAGATTGAGTTCAT 58.433 47.619 0.00 0.00 0.00 2.57
1895 3747 2.922283 ACCCCTCCAGATTGAGTTCATT 59.078 45.455 0.00 0.00 0.00 2.57
1916 3768 5.620738 TTCTTCCTTGTCTCCAGGATATG 57.379 43.478 0.00 0.00 0.00 1.78
1958 3813 5.049267 TGTTTTTACAGTTTGCCTCCGTATC 60.049 40.000 0.00 0.00 0.00 2.24
2013 3868 8.868635 GGTAACTATACTTCCACTGTTACATC 57.131 38.462 13.38 0.00 40.51 3.06
2014 3869 8.472413 GGTAACTATACTTCCACTGTTACATCA 58.528 37.037 13.38 0.00 40.51 3.07
2016 3871 8.948631 AACTATACTTCCACTGTTACATCATG 57.051 34.615 0.00 0.00 0.00 3.07
2032 3898 9.369904 GTTACATCATGCAAATTATTCTTTGGT 57.630 29.630 0.00 0.00 36.76 3.67
2036 3903 8.937884 CATCATGCAAATTATTCTTTGGTTTCA 58.062 29.630 0.00 0.00 36.76 2.69
2052 3919 6.849085 TGGTTTCAGGCATAACATTGTATT 57.151 33.333 0.00 0.00 0.00 1.89
2055 3922 7.178274 TGGTTTCAGGCATAACATTGTATTTCT 59.822 33.333 0.00 0.00 0.00 2.52
2088 3957 0.044244 AGGATCTTCCCCCGGAAAGA 59.956 55.000 0.73 9.77 41.54 2.52
2188 4057 3.433615 ACAAGCTGTCGAGATTTTGTAGC 59.566 43.478 9.23 0.00 0.00 3.58
2338 4220 5.316987 ACAACTTATTTGAGGGAGTGAAGG 58.683 41.667 0.00 0.00 38.73 3.46
2340 4222 3.589288 ACTTATTTGAGGGAGTGAAGGCT 59.411 43.478 0.00 0.00 0.00 4.58
2345 4227 1.614824 AGGGAGTGAAGGCTGGGAG 60.615 63.158 0.00 0.00 0.00 4.30
2391 4273 0.179023 TTCACACCTGATGCTGTGCA 60.179 50.000 0.00 0.00 44.86 4.57
2420 4302 7.883229 AAAATTTAAGGGACGTGCTTAAATG 57.117 32.000 23.78 0.00 40.32 2.32
2421 4303 4.428615 TTTAAGGGACGTGCTTAAATGC 57.571 40.909 7.11 0.00 30.54 3.56
2422 4304 1.904287 AAGGGACGTGCTTAAATGCA 58.096 45.000 7.11 0.00 41.05 3.96
2446 4329 0.174617 TGATGGCTGCAATGCACATG 59.825 50.000 14.73 2.50 33.79 3.21
2450 4333 0.249322 GGCTGCAATGCACATGGATC 60.249 55.000 2.72 0.00 33.79 3.36
2479 4363 7.516198 AACCTGAATTCAGATATGGCATAAC 57.484 36.000 32.49 9.06 46.59 1.89
2494 4378 2.476185 GCATAACGCTTGTAGCCAACAG 60.476 50.000 0.00 0.00 39.87 3.16
2518 4403 5.235186 GCGAAATATGAGATACAGCTTGTGT 59.765 40.000 0.00 0.00 43.86 3.72
2521 4406 7.848051 CGAAATATGAGATACAGCTTGTGTTTC 59.152 37.037 0.00 0.00 40.94 2.78
2522 4407 8.565896 AAATATGAGATACAGCTTGTGTTTCA 57.434 30.769 8.03 8.03 39.05 2.69
2529 4414 2.033299 ACAGCTTGTGTTTCATGGAACG 59.967 45.455 12.26 0.00 34.94 3.95
2531 4416 2.687935 AGCTTGTGTTTCATGGAACGTT 59.312 40.909 12.26 0.00 32.18 3.99
2532 4417 2.788786 GCTTGTGTTTCATGGAACGTTG 59.211 45.455 5.00 3.92 32.18 4.10
2543 4430 2.210116 TGGAACGTTGCAACTCTCTTC 58.790 47.619 26.09 18.69 0.00 2.87
2556 4444 3.439154 ACTCTCTTCAGGCTGATTGAGA 58.561 45.455 30.87 30.87 35.52 3.27
2557 4445 4.049546 CTCTCTTCAGGCTGATTGAGAG 57.950 50.000 35.96 35.96 42.31 3.20
2564 4452 4.573900 TCAGGCTGATTGAGAGAGAAAAC 58.426 43.478 14.43 0.00 0.00 2.43
2574 4462 4.899502 TGAGAGAGAAAACCTCAATCCAC 58.100 43.478 0.00 0.00 44.40 4.02
2578 4466 5.072329 AGAGAGAAAACCTCAATCCACTGAA 59.928 40.000 0.00 0.00 44.40 3.02
2584 4472 8.328758 AGAAAACCTCAATCCACTGAACATATA 58.671 33.333 0.00 0.00 0.00 0.86
2594 4482 9.866655 AATCCACTGAACATATATTGTACCAAT 57.133 29.630 0.00 0.00 37.68 3.16
2602 4490 9.355215 GAACATATATTGTACCAATAGTCCTCG 57.645 37.037 3.40 0.00 37.68 4.63
2603 4491 7.321153 ACATATATTGTACCAATAGTCCTCGC 58.679 38.462 3.40 0.00 36.57 5.03
2633 4557 3.008375 TCTGAAGTTGCAAGACCAGCTAT 59.992 43.478 0.00 0.00 0.00 2.97
2648 4572 4.263506 ACCAGCTATACATTAGCATTCCCC 60.264 45.833 7.31 0.00 42.68 4.81
2657 4581 3.513909 TTAGCATTCCCCCATCTCATG 57.486 47.619 0.00 0.00 0.00 3.07
2661 4585 2.767960 GCATTCCCCCATCTCATGTTTT 59.232 45.455 0.00 0.00 0.00 2.43
2662 4586 3.431207 GCATTCCCCCATCTCATGTTTTG 60.431 47.826 0.00 0.00 0.00 2.44
2665 4589 5.464588 TTCCCCCATCTCATGTTTTGATA 57.535 39.130 0.00 0.00 32.72 2.15
2667 4591 5.836705 TCCCCCATCTCATGTTTTGATAAA 58.163 37.500 0.00 0.00 32.72 1.40
2715 4639 7.095649 GGCTTATTGTTTGTTTGGAAGACAATC 60.096 37.037 3.58 0.00 40.34 2.67
2742 4666 4.326826 ACCACTTGACATCACAGTAATGG 58.673 43.478 0.00 0.00 0.00 3.16
2745 4669 5.240891 CACTTGACATCACAGTAATGGTCT 58.759 41.667 0.00 0.00 0.00 3.85
2821 4746 8.436046 AAAATATTCACACTGCAATTTTGTGT 57.564 26.923 13.91 9.37 44.52 3.72
2827 4753 5.287274 TCACACTGCAATTTTGTGTTTAACG 59.713 36.000 5.98 0.00 42.19 3.18
2878 4804 6.513180 ACACCTACAAGTATCCATGATTACG 58.487 40.000 0.00 0.00 0.00 3.18
2888 4814 4.123497 TCCATGATTACGAAGACCAGTG 57.877 45.455 0.00 0.00 0.00 3.66
2919 4845 3.242349 GCATTCTCTCATCAGAACTTGCG 60.242 47.826 0.00 0.00 35.18 4.85
2924 4850 3.320626 TCTCATCAGAACTTGCGAACAG 58.679 45.455 0.00 0.00 0.00 3.16
2994 4920 1.400846 GATGAACACATGCTGCTCTGG 59.599 52.381 0.00 0.00 0.00 3.86
3070 4996 5.403766 CAGAGTAGTTAGTGTTTGCAGTCAG 59.596 44.000 0.00 0.00 0.00 3.51
3071 4997 5.302059 AGAGTAGTTAGTGTTTGCAGTCAGA 59.698 40.000 0.00 0.00 0.00 3.27
3075 5001 4.332819 AGTTAGTGTTTGCAGTCAGACAAC 59.667 41.667 2.66 0.00 38.76 3.32
3125 5051 4.263727 TGCAATGTTGTGGGGTAGTAGAAT 60.264 41.667 0.00 0.00 0.00 2.40
3134 5060 5.781306 TGTGGGGTAGTAGAATTCAACACTA 59.219 40.000 8.44 9.00 0.00 2.74
3143 5069 7.217200 AGTAGAATTCAACACTAAGCACTGAA 58.783 34.615 8.44 0.00 0.00 3.02
3153 5079 4.210120 CACTAAGCACTGAACTCTGAACAC 59.790 45.833 0.00 0.00 0.00 3.32
3163 5089 2.205074 ACTCTGAACACTGAAACAGCG 58.795 47.619 0.00 0.00 34.37 5.18
3165 5091 3.062763 CTCTGAACACTGAAACAGCGAT 58.937 45.455 0.00 0.00 34.37 4.58
3173 5099 5.720202 ACACTGAAACAGCGATAAGTATCA 58.280 37.500 0.00 0.00 34.37 2.15
3176 5102 7.334421 ACACTGAAACAGCGATAAGTATCAATT 59.666 33.333 0.00 0.00 34.37 2.32
3177 5103 7.637519 CACTGAAACAGCGATAAGTATCAATTG 59.362 37.037 0.00 0.00 34.37 2.32
3178 5104 7.549134 ACTGAAACAGCGATAAGTATCAATTGA 59.451 33.333 11.26 11.26 34.37 2.57
3179 5105 8.437360 TGAAACAGCGATAAGTATCAATTGAT 57.563 30.769 23.75 23.75 38.51 2.57
3180 5106 8.892723 TGAAACAGCGATAAGTATCAATTGATT 58.107 29.630 25.26 11.67 36.05 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.443879 TCTGTGATCTTTGTTTACATTGCAGTA 59.556 33.333 0.00 0.00 0.00 2.74
46 568 2.071778 TTCCACTCTTTTGCAGGCTT 57.928 45.000 0.00 0.00 0.00 4.35
76 601 9.531412 CATGTCGTAACGATGTTTTATTTTACA 57.469 29.630 0.00 0.00 38.42 2.41
77 602 8.991810 CCATGTCGTAACGATGTTTTATTTTAC 58.008 33.333 0.00 0.00 38.42 2.01
78 603 7.693120 GCCATGTCGTAACGATGTTTTATTTTA 59.307 33.333 0.00 0.00 38.42 1.52
79 604 6.525280 GCCATGTCGTAACGATGTTTTATTTT 59.475 34.615 0.00 0.00 38.42 1.82
85 610 1.735571 GGCCATGTCGTAACGATGTTT 59.264 47.619 0.00 0.00 38.42 2.83
102 627 2.770232 TGGTTACCTAGAGCTTTAGGCC 59.230 50.000 26.30 20.09 43.36 5.19
113 638 2.169769 TCCGATGCCTTTGGTTACCTAG 59.830 50.000 2.07 0.00 0.00 3.02
147 673 4.990426 CCTTAGGGCACAAAGAAACAAATG 59.010 41.667 0.00 0.00 0.00 2.32
158 684 3.517296 TTGAATGTCCTTAGGGCACAA 57.483 42.857 8.09 6.24 0.00 3.33
171 697 3.242969 GCACGATGCAGATGATTGAATGT 60.243 43.478 0.00 0.00 44.26 2.71
175 701 0.932399 CGCACGATGCAGATGATTGA 59.068 50.000 9.95 0.00 45.36 2.57
232 758 1.020861 TGCAAGCGAGGTGCATACAG 61.021 55.000 4.23 0.00 46.76 2.74
573 1977 3.083349 TAGATGCCCGGCTGTGCT 61.083 61.111 11.61 5.17 0.00 4.40
576 1980 4.227134 CGCTAGATGCCCGGCTGT 62.227 66.667 11.61 0.00 38.78 4.40
578 1982 3.917760 GACGCTAGATGCCCGGCT 61.918 66.667 11.61 0.00 38.78 5.52
592 1996 3.740128 CTTCCAGGGCCCATCGACG 62.740 68.421 27.56 9.72 0.00 5.12
597 2001 2.772924 CCAACTTCCAGGGCCCAT 59.227 61.111 27.56 6.18 0.00 4.00
609 2013 1.264749 TGGTGATAGCTCGGCCAACT 61.265 55.000 2.24 0.00 0.00 3.16
614 2018 1.084370 GTGTGTGGTGATAGCTCGGC 61.084 60.000 0.00 0.00 0.00 5.54
639 2043 6.027749 GTGTTACTCAAATAAATTGGCTCGG 58.972 40.000 0.00 0.00 39.62 4.63
640 2044 6.523201 GTGTGTTACTCAAATAAATTGGCTCG 59.477 38.462 0.00 0.00 39.62 5.03
684 2088 5.056480 TCAACAGTGACAATGTGTTCCTAG 58.944 41.667 9.64 0.00 32.01 3.02
692 2096 1.133823 TGCCCTCAACAGTGACAATGT 60.134 47.619 1.98 1.98 0.00 2.71
712 2116 6.148811 TCTCGAAGTGTTTGTTTTCTTTGACT 59.851 34.615 0.00 0.00 0.00 3.41
718 2122 6.677781 TTGATCTCGAAGTGTTTGTTTTCT 57.322 33.333 0.00 0.00 0.00 2.52
724 2137 3.426695 GCCCATTGATCTCGAAGTGTTTG 60.427 47.826 0.00 0.00 0.00 2.93
735 2148 2.842496 TGAGACTTGAGCCCATTGATCT 59.158 45.455 0.00 0.00 0.00 2.75
736 2149 3.204526 CTGAGACTTGAGCCCATTGATC 58.795 50.000 0.00 0.00 0.00 2.92
792 2207 2.935955 GGTTTATCGCGCCGATGG 59.064 61.111 20.06 0.00 46.43 3.51
802 2217 4.457949 TCCTTTTCTTTCCTGCGGTTTATC 59.542 41.667 0.00 0.00 0.00 1.75
810 2225 4.040339 TGGGATTTTCCTTTTCTTTCCTGC 59.960 41.667 0.00 0.00 36.57 4.85
822 2241 1.625315 GCTTTGGCTTGGGATTTTCCT 59.375 47.619 0.00 0.00 34.38 3.36
823 2242 2.099141 GCTTTGGCTTGGGATTTTCC 57.901 50.000 0.00 0.00 33.63 3.13
857 2276 3.736433 CGCGAAGATTCAGAGGTGAGAAT 60.736 47.826 0.00 0.00 37.19 2.40
875 2294 2.127496 GTGAAGACGACGACGCGA 60.127 61.111 15.93 0.00 43.96 5.87
910 2332 1.063341 CAGAGATCTGTGGGAGGGAGA 60.063 57.143 12.01 0.00 39.09 3.71
930 2353 1.449778 GCTTGAACCCTAGGGCGAC 60.450 63.158 28.88 18.67 39.32 5.19
948 2377 1.608046 GCGGGAGGATCTAGGGGAG 60.608 68.421 0.00 0.00 33.73 4.30
952 2381 2.269529 GGACGCGGGAGGATCTAGG 61.270 68.421 12.47 0.00 33.73 3.02
953 2382 2.269529 GGGACGCGGGAGGATCTAG 61.270 68.421 12.47 0.00 33.73 2.43
954 2383 2.203451 GGGACGCGGGAGGATCTA 60.203 66.667 12.47 0.00 33.73 1.98
955 2384 4.458829 TGGGACGCGGGAGGATCT 62.459 66.667 12.47 0.00 33.73 2.75
956 2385 4.222847 GTGGGACGCGGGAGGATC 62.223 72.222 12.47 0.00 0.00 3.36
967 2396 4.035102 GAGGGTGCAGGGTGGGAC 62.035 72.222 0.00 0.00 0.00 4.46
974 2403 3.732849 GAAGGGGGAGGGTGCAGG 61.733 72.222 0.00 0.00 0.00 4.85
975 2404 3.732849 GGAAGGGGGAGGGTGCAG 61.733 72.222 0.00 0.00 0.00 4.41
978 2407 4.371231 AGGGGAAGGGGGAGGGTG 62.371 72.222 0.00 0.00 0.00 4.61
979 2408 4.040198 GAGGGGAAGGGGGAGGGT 62.040 72.222 0.00 0.00 0.00 4.34
980 2409 4.845307 GGAGGGGAAGGGGGAGGG 62.845 77.778 0.00 0.00 0.00 4.30
1061 2514 2.888594 CTTCGAGCTGGTAAATCGGAA 58.111 47.619 0.00 0.00 37.08 4.30
1064 2517 0.572590 CGCTTCGAGCTGGTAAATCG 59.427 55.000 0.00 0.00 39.60 3.34
1068 2521 2.577059 CCCGCTTCGAGCTGGTAA 59.423 61.111 0.00 0.00 40.25 2.85
1203 2671 3.259064 CGGCAGAGGAAAGAAAATACGA 58.741 45.455 0.00 0.00 0.00 3.43
1204 2672 2.223044 GCGGCAGAGGAAAGAAAATACG 60.223 50.000 0.00 0.00 0.00 3.06
1231 2702 1.078426 ACATCAGTAACCCGGCAGC 60.078 57.895 0.00 0.00 0.00 5.25
1335 2818 4.388499 GCGAGTCCCCGGAAAGCA 62.388 66.667 0.73 0.00 0.00 3.91
1347 2830 1.448540 CAAATCAGGGCTCGCGAGT 60.449 57.895 34.46 14.96 0.00 4.18
1348 2831 2.176273 CCAAATCAGGGCTCGCGAG 61.176 63.158 31.37 31.37 0.00 5.03
1349 2832 2.125147 CCAAATCAGGGCTCGCGA 60.125 61.111 9.26 9.26 0.00 5.87
1357 2846 3.201708 ACTCTTCTCCATCCCAAATCAGG 59.798 47.826 0.00 0.00 0.00 3.86
1377 2866 9.368416 TGAATATCCTAAACTCAGTATGCTACT 57.632 33.333 0.00 0.00 40.28 2.57
1390 2962 7.907214 ATGACGCCTAATGAATATCCTAAAC 57.093 36.000 0.00 0.00 0.00 2.01
1394 2966 5.665459 GCTATGACGCCTAATGAATATCCT 58.335 41.667 0.00 0.00 0.00 3.24
1395 2967 4.504461 CGCTATGACGCCTAATGAATATCC 59.496 45.833 0.00 0.00 0.00 2.59
1396 2968 5.627802 CGCTATGACGCCTAATGAATATC 57.372 43.478 0.00 0.00 0.00 1.63
1409 2981 1.010935 CCAGCTATGGCGCTATGACG 61.011 60.000 17.43 5.88 40.52 4.35
1410 2982 2.832931 CCAGCTATGGCGCTATGAC 58.167 57.895 17.43 8.10 40.52 3.06
1424 2999 0.610687 AGTTCTAGCAGACCACCAGC 59.389 55.000 0.00 0.00 0.00 4.85
1431 3006 4.377839 TCAGTGCATAGTTCTAGCAGAC 57.622 45.455 0.00 0.00 39.21 3.51
1435 3010 4.697514 TGGAATCAGTGCATAGTTCTAGC 58.302 43.478 0.00 0.00 0.00 3.42
1441 3016 3.548770 CACCATGGAATCAGTGCATAGT 58.451 45.455 21.47 0.00 35.84 2.12
1446 3021 0.966875 TGCCACCATGGAATCAGTGC 60.967 55.000 21.47 9.95 40.96 4.40
1447 3022 1.407618 CATGCCACCATGGAATCAGTG 59.592 52.381 21.47 4.57 44.07 3.66
1459 3034 1.133025 GCATACAAGACACATGCCACC 59.867 52.381 0.00 0.00 39.30 4.61
1461 3036 2.495155 AGCATACAAGACACATGCCA 57.505 45.000 0.00 0.00 44.90 4.92
1489 3065 5.417894 TGCTGCTGAAAGATGATGAAATCTT 59.582 36.000 0.00 0.00 46.52 2.40
1491 3067 5.163642 ACTGCTGCTGAAAGATGATGAAATC 60.164 40.000 13.69 0.00 39.70 2.17
1497 3073 2.366533 CCACTGCTGCTGAAAGATGAT 58.633 47.619 13.69 0.00 34.07 2.45
1498 3074 1.612462 CCCACTGCTGCTGAAAGATGA 60.612 52.381 13.69 0.00 34.07 2.92
1499 3075 0.809385 CCCACTGCTGCTGAAAGATG 59.191 55.000 13.69 0.67 34.07 2.90
1502 3078 2.960170 GCCCACTGCTGCTGAAAG 59.040 61.111 13.69 0.00 36.87 2.62
1511 3087 1.662044 CAACCTGAAAGCCCACTGC 59.338 57.895 0.00 0.00 41.71 4.40
1516 3099 1.039856 TTCTTGCAACCTGAAAGCCC 58.960 50.000 0.00 0.00 32.94 5.19
1521 3210 3.192001 GCATCAGATTCTTGCAACCTGAA 59.808 43.478 15.50 10.05 37.41 3.02
1533 3222 5.521735 CACTGTTACTAGGTGCATCAGATTC 59.478 44.000 0.00 0.00 0.00 2.52
1552 3241 3.243234 GCTAGACGCATATCAGACACTGT 60.243 47.826 0.00 0.00 38.92 3.55
1553 3242 3.304257 GCTAGACGCATATCAGACACTG 58.696 50.000 0.00 0.00 38.92 3.66
1554 3243 2.294791 GGCTAGACGCATATCAGACACT 59.705 50.000 0.00 0.00 41.67 3.55
1555 3244 2.034685 TGGCTAGACGCATATCAGACAC 59.965 50.000 0.00 0.00 41.67 3.67
1557 3246 2.034685 TGTGGCTAGACGCATATCAGAC 59.965 50.000 8.04 0.00 41.67 3.51
1562 3251 4.342862 AAGAATGTGGCTAGACGCATAT 57.657 40.909 24.67 13.80 40.44 1.78
1563 3252 3.819564 AAGAATGTGGCTAGACGCATA 57.180 42.857 24.67 0.00 40.44 3.14
1565 3254 2.076100 CAAAGAATGTGGCTAGACGCA 58.924 47.619 15.61 15.61 41.67 5.24
1566 3255 1.398390 CCAAAGAATGTGGCTAGACGC 59.602 52.381 0.85 0.85 36.10 5.19
1577 3389 1.247567 AGTGCCCGAACCAAAGAATG 58.752 50.000 0.00 0.00 0.00 2.67
1584 3396 0.681564 ACAAACAAGTGCCCGAACCA 60.682 50.000 0.00 0.00 0.00 3.67
1598 3410 2.223340 CCAACAGTCAGTCAGCACAAAC 60.223 50.000 0.00 0.00 0.00 2.93
1599 3411 2.016318 CCAACAGTCAGTCAGCACAAA 58.984 47.619 0.00 0.00 0.00 2.83
1602 3414 1.510480 GGCCAACAGTCAGTCAGCAC 61.510 60.000 0.00 0.00 31.63 4.40
1604 3416 1.227943 TGGCCAACAGTCAGTCAGC 60.228 57.895 0.61 0.00 0.00 4.26
1614 3426 1.888512 GCTGAAAGAATCTGGCCAACA 59.111 47.619 7.01 0.00 34.07 3.33
1618 3430 3.881937 AATTGCTGAAAGAATCTGGCC 57.118 42.857 0.00 0.00 34.07 5.36
1629 3441 3.423749 TGCTCAGATGGAAATTGCTGAA 58.576 40.909 0.00 0.00 36.99 3.02
1637 3452 7.725251 AGTAAAAACATTTGCTCAGATGGAAA 58.275 30.769 5.56 0.00 0.00 3.13
1651 3466 2.514803 AGGCCAGCGAGTAAAAACATT 58.485 42.857 5.01 0.00 0.00 2.71
1652 3467 2.200373 AGGCCAGCGAGTAAAAACAT 57.800 45.000 5.01 0.00 0.00 2.71
1700 3550 1.563879 TGTGCTACCATACCAAGCCAT 59.436 47.619 0.00 0.00 35.33 4.40
1705 3555 1.209504 GGCTCTGTGCTACCATACCAA 59.790 52.381 1.44 0.00 42.39 3.67
1706 3556 0.830648 GGCTCTGTGCTACCATACCA 59.169 55.000 1.44 0.00 42.39 3.25
1707 3557 0.830648 TGGCTCTGTGCTACCATACC 59.169 55.000 1.44 0.00 42.39 2.73
1708 3558 2.918712 ATGGCTCTGTGCTACCATAC 57.081 50.000 1.44 0.00 41.10 2.39
1709 3559 3.544684 CAAATGGCTCTGTGCTACCATA 58.455 45.455 1.44 0.00 42.06 2.74
1718 3568 1.271656 GAAGCTTGCAAATGGCTCTGT 59.728 47.619 2.10 0.00 45.15 3.41
1737 3587 3.691118 GCCACATACAAGAGCATTTCAGA 59.309 43.478 0.00 0.00 0.00 3.27
1882 3734 6.777782 AGACAAGGAAGAATGAACTCAATCT 58.222 36.000 0.00 0.00 37.70 2.40
1887 3739 4.899502 TGGAGACAAGGAAGAATGAACTC 58.100 43.478 0.00 0.00 37.44 3.01
1888 3740 4.263243 CCTGGAGACAAGGAAGAATGAACT 60.263 45.833 0.00 0.00 42.06 3.01
1894 3746 5.032846 ACATATCCTGGAGACAAGGAAGAA 58.967 41.667 1.52 0.00 42.06 2.52
1895 3747 4.624913 ACATATCCTGGAGACAAGGAAGA 58.375 43.478 1.52 0.00 42.06 2.87
1941 3796 0.981183 TGGATACGGAGGCAAACTGT 59.019 50.000 0.00 0.00 42.51 3.55
1958 3813 3.181487 CCTTGTTGTCCTTGTTGACTTGG 60.181 47.826 0.00 0.00 36.21 3.61
1995 3850 5.744171 TGCATGATGTAACAGTGGAAGTAT 58.256 37.500 0.00 0.00 0.00 2.12
2010 3865 8.937884 TGAAACCAAAGAATAATTTGCATGATG 58.062 29.630 0.00 0.00 38.57 3.07
2011 3866 9.158233 CTGAAACCAAAGAATAATTTGCATGAT 57.842 29.630 0.00 0.00 38.57 2.45
2013 3868 7.624764 GCCTGAAACCAAAGAATAATTTGCATG 60.625 37.037 0.00 0.00 38.57 4.06
2014 3869 6.372381 GCCTGAAACCAAAGAATAATTTGCAT 59.628 34.615 0.00 0.00 38.57 3.96
2016 3871 5.700373 TGCCTGAAACCAAAGAATAATTTGC 59.300 36.000 0.00 0.00 38.57 3.68
2052 3919 6.244552 AGATCCTGCAGATGATGTTTAGAA 57.755 37.500 17.39 0.00 34.42 2.10
2055 3922 5.371526 GGAAGATCCTGCAGATGATGTTTA 58.628 41.667 17.39 0.00 34.42 2.01
2188 4057 5.562506 TGACAGTCTTAGACATTAGGACG 57.437 43.478 15.23 0.00 34.60 4.79
2316 4192 4.156739 GCCTTCACTCCCTCAAATAAGTTG 59.843 45.833 0.00 0.00 38.71 3.16
2377 4259 1.985473 TTTTCTGCACAGCATCAGGT 58.015 45.000 0.00 0.00 38.13 4.00
2400 4282 3.821600 TGCATTTAAGCACGTCCCTTAAA 59.178 39.130 22.69 22.69 44.29 1.52
2401 4283 3.413327 TGCATTTAAGCACGTCCCTTAA 58.587 40.909 11.81 11.81 40.11 1.85
2402 4284 3.060736 TGCATTTAAGCACGTCCCTTA 57.939 42.857 2.02 2.02 40.11 2.69
2419 4301 0.609681 TTGCAGCCATCAGATGTGCA 60.610 50.000 19.81 19.81 39.53 4.57
2420 4302 0.744874 ATTGCAGCCATCAGATGTGC 59.255 50.000 15.89 15.89 34.10 4.57
2421 4303 1.536072 GCATTGCAGCCATCAGATGTG 60.536 52.381 9.64 3.37 0.00 3.21
2422 4304 0.744874 GCATTGCAGCCATCAGATGT 59.255 50.000 9.64 0.00 0.00 3.06
2423 4305 0.744281 TGCATTGCAGCCATCAGATG 59.256 50.000 7.38 3.04 33.32 2.90
2424 4306 0.744874 GTGCATTGCAGCCATCAGAT 59.255 50.000 12.53 0.00 40.08 2.90
2473 4357 1.466950 TGTTGGCTACAAGCGTTATGC 59.533 47.619 0.00 0.00 43.62 3.14
2479 4363 1.565156 TTCGCTGTTGGCTACAAGCG 61.565 55.000 26.08 26.08 46.35 4.68
2494 4378 5.235186 ACACAAGCTGTATCTCATATTTCGC 59.765 40.000 0.00 0.00 0.00 4.70
2496 4380 8.668353 TGAAACACAAGCTGTATCTCATATTTC 58.332 33.333 0.00 0.00 30.51 2.17
2503 4388 4.937620 TCCATGAAACACAAGCTGTATCTC 59.062 41.667 0.00 0.00 30.51 2.75
2518 4403 2.948979 AGAGTTGCAACGTTCCATGAAA 59.051 40.909 23.21 0.00 0.00 2.69
2521 4406 2.146342 AGAGAGTTGCAACGTTCCATG 58.854 47.619 23.21 0.00 0.00 3.66
2522 4407 2.550830 AGAGAGTTGCAACGTTCCAT 57.449 45.000 23.21 5.14 0.00 3.41
2529 4414 1.534595 CAGCCTGAAGAGAGTTGCAAC 59.465 52.381 22.17 22.17 0.00 4.17
2531 4416 1.051008 TCAGCCTGAAGAGAGTTGCA 58.949 50.000 0.00 0.00 0.00 4.08
2532 4417 2.399916 ATCAGCCTGAAGAGAGTTGC 57.600 50.000 0.00 0.00 0.00 4.17
2543 4430 3.688673 GGTTTTCTCTCTCAATCAGCCTG 59.311 47.826 0.00 0.00 0.00 4.85
2556 4444 4.982241 TCAGTGGATTGAGGTTTTCTCT 57.018 40.909 0.00 0.00 42.86 3.10
2557 4445 4.821805 TGTTCAGTGGATTGAGGTTTTCTC 59.178 41.667 0.00 0.00 42.74 2.87
2564 4452 8.993121 GTACAATATATGTTCAGTGGATTGAGG 58.007 37.037 0.00 0.00 43.63 3.86
2594 4482 1.688735 CAGATTGGATGGCGAGGACTA 59.311 52.381 0.00 0.00 0.00 2.59
2602 4490 1.820519 TGCAACTTCAGATTGGATGGC 59.179 47.619 0.00 0.00 0.00 4.40
2603 4491 3.760151 TCTTGCAACTTCAGATTGGATGG 59.240 43.478 0.00 0.00 0.00 3.51
2633 4557 3.980022 TGAGATGGGGGAATGCTAATGTA 59.020 43.478 0.00 0.00 0.00 2.29
2661 4585 9.950680 GAAGACACAAGAAGAAAATGTTTATCA 57.049 29.630 0.00 0.00 0.00 2.15
2662 4586 9.950680 TGAAGACACAAGAAGAAAATGTTTATC 57.049 29.630 0.00 0.00 0.00 1.75
2665 4589 7.260603 CCTGAAGACACAAGAAGAAAATGTTT 58.739 34.615 0.00 0.00 0.00 2.83
2667 4591 5.221126 GCCTGAAGACACAAGAAGAAAATGT 60.221 40.000 0.00 0.00 0.00 2.71
2673 4597 3.845781 AAGCCTGAAGACACAAGAAGA 57.154 42.857 0.00 0.00 0.00 2.87
2685 4609 5.860941 TCCAAACAAACAATAAGCCTGAA 57.139 34.783 0.00 0.00 0.00 3.02
2715 4639 2.810274 CTGTGATGTCAAGTGGTTCTGG 59.190 50.000 0.00 0.00 0.00 3.86
2718 4642 5.106555 CCATTACTGTGATGTCAAGTGGTTC 60.107 44.000 11.06 0.00 0.00 3.62
2800 4725 8.812329 GTTAAACACAAAATTGCAGTGTGAATA 58.188 29.630 21.46 13.55 44.99 1.75
2821 4746 3.278668 TGAGTGTTGGGTTCCGTTAAA 57.721 42.857 0.00 0.00 0.00 1.52
2827 4753 4.003648 CTGAGTATTGAGTGTTGGGTTCC 58.996 47.826 0.00 0.00 0.00 3.62
2878 4804 3.664107 TGCTAATGTGTCACTGGTCTTC 58.336 45.455 4.27 0.00 0.00 2.87
2888 4814 6.279123 TCTGATGAGAGAATGCTAATGTGTC 58.721 40.000 0.00 0.00 0.00 3.67
3033 4959 9.639601 CACTAACTACTCTGTTAATGTGAATGA 57.360 33.333 0.00 0.00 33.86 2.57
3034 4960 9.424319 ACACTAACTACTCTGTTAATGTGAATG 57.576 33.333 11.19 0.00 40.06 2.67
3035 4961 9.998106 AACACTAACTACTCTGTTAATGTGAAT 57.002 29.630 11.19 1.88 40.47 2.57
3036 4962 9.826574 AAACACTAACTACTCTGTTAATGTGAA 57.173 29.630 11.19 0.00 40.47 3.18
3037 4963 9.256477 CAAACACTAACTACTCTGTTAATGTGA 57.744 33.333 11.19 0.00 40.47 3.58
3038 4964 8.009974 GCAAACACTAACTACTCTGTTAATGTG 58.990 37.037 2.98 4.52 40.47 3.21
3039 4965 7.713507 TGCAAACACTAACTACTCTGTTAATGT 59.286 33.333 0.00 0.00 42.27 2.71
3040 4966 8.083462 TGCAAACACTAACTACTCTGTTAATG 57.917 34.615 0.00 0.00 36.22 1.90
3041 4967 7.931948 ACTGCAAACACTAACTACTCTGTTAAT 59.068 33.333 0.00 0.00 32.80 1.40
3042 4968 7.270047 ACTGCAAACACTAACTACTCTGTTAA 58.730 34.615 0.00 0.00 32.80 2.01
3043 4969 6.812998 ACTGCAAACACTAACTACTCTGTTA 58.187 36.000 0.00 0.00 0.00 2.41
3101 5027 1.909700 ACTACCCCACAACATTGCAG 58.090 50.000 0.00 0.00 0.00 4.41
3125 5051 4.811024 CAGAGTTCAGTGCTTAGTGTTGAA 59.189 41.667 0.00 0.00 0.00 2.69
3134 5060 3.118629 TCAGTGTTCAGAGTTCAGTGCTT 60.119 43.478 0.00 0.00 33.95 3.91
3143 5069 2.159099 TCGCTGTTTCAGTGTTCAGAGT 60.159 45.455 9.57 0.00 41.99 3.24
3153 5079 7.909267 TCAATTGATACTTATCGCTGTTTCAG 58.091 34.615 3.38 0.00 35.48 3.02
3178 5104 8.518702 GCCTTCTTCAATTTGAGACTTAGAAAT 58.481 33.333 10.23 0.00 0.00 2.17
3179 5105 7.040409 GGCCTTCTTCAATTTGAGACTTAGAAA 60.040 37.037 10.23 0.00 0.00 2.52
3180 5106 6.431234 GGCCTTCTTCAATTTGAGACTTAGAA 59.569 38.462 0.00 9.14 0.00 2.10
3191 5117 6.842807 AGATGGATATTGGCCTTCTTCAATTT 59.157 34.615 3.32 0.00 36.77 1.82
3193 5119 5.961897 AGATGGATATTGGCCTTCTTCAAT 58.038 37.500 3.32 0.00 36.77 2.57


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

AutoCloner maintained by Alex Coulton.