Multiple sequence alignment - TraesCS3D01G465800

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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 TraesCS3D01G465800 chr3D 100.000 3933 0 0 1 3933 569554066 569557998 0.000000e+00 7263.0
1 TraesCS3D01G465800 chr3D 100.000 32 0 0 3127 3158 305317149 305317118 4.240000e-05 60.2
2 TraesCS3D01G465800 chr3A 89.598 2913 168 67 1085 3933 700580535 700583376 0.000000e+00 3576.0
3 TraesCS3D01G465800 chr3A 92.835 321 19 3 1 320 700580153 700580470 2.770000e-126 462.0
4 TraesCS3D01G465800 chr3A 85.342 307 28 2 1 306 701867791 701868081 6.390000e-78 302.0
5 TraesCS3D01G465800 chr3B 91.532 1677 105 15 992 2660 756129038 756127391 0.000000e+00 2276.0
6 TraesCS3D01G465800 chr3B 90.574 679 56 6 1 678 756131622 756130951 0.000000e+00 893.0
7 TraesCS3D01G465800 chr3B 90.533 338 22 4 3596 3933 756126300 756125973 4.670000e-119 438.0
8 TraesCS3D01G465800 chr3B 97.619 42 1 0 907 948 756129081 756129040 5.450000e-09 73.1
9 TraesCS3D01G465800 chr3B 100.000 28 0 0 949 976 756129049 756129022 7.000000e-03 52.8
10 TraesCS3D01G465800 chrUn 93.072 1429 74 9 1309 2730 40896998 40895588 0.000000e+00 2067.0
11 TraesCS3D01G465800 chrUn 93.274 788 38 6 1872 2657 255359103 255359877 0.000000e+00 1147.0
12 TraesCS3D01G465800 chrUn 90.722 679 54 7 1 678 255356140 255356810 0.000000e+00 896.0
13 TraesCS3D01G465800 chrUn 89.051 548 42 9 992 1534 255358578 255359112 0.000000e+00 664.0
14 TraesCS3D01G465800 chrUn 89.645 338 25 4 3596 3933 255360969 255361296 4.700000e-114 422.0
15 TraesCS3D01G465800 chrUn 90.079 252 19 1 998 1249 41053975 41053730 4.900000e-84 322.0
16 TraesCS3D01G465800 chrUn 97.917 48 1 0 2759 2806 40895589 40895542 2.520000e-12 84.2
17 TraesCS3D01G465800 chrUn 100.000 39 0 0 907 945 255358535 255358573 5.450000e-09 73.1
18 TraesCS3D01G465800 chrUn 100.000 28 0 0 3131 3158 112185222 112185195 7.000000e-03 52.8
19 TraesCS3D01G465800 chr5A 93.274 788 38 6 1875 2660 42269978 42269204 0.000000e+00 1147.0
20 TraesCS3D01G465800 chr5A 90.722 679 54 7 1 678 42272944 42272274 0.000000e+00 896.0
21 TraesCS3D01G465800 chr5A 89.051 548 42 9 992 1534 42270506 42269972 0.000000e+00 664.0
22 TraesCS3D01G465800 chr5A 89.645 338 25 4 3596 3933 42268115 42267788 4.700000e-114 422.0
23 TraesCS3D01G465800 chr5A 97.619 42 1 0 907 948 42270549 42270508 5.450000e-09 73.1
24 TraesCS3D01G465800 chr1B 88.342 772 71 8 1966 2736 320105745 320104992 0.000000e+00 909.0
25 TraesCS3D01G465800 chr1B 84.082 779 92 14 992 1756 320106988 320106228 0.000000e+00 723.0
26 TraesCS3D01G465800 chr1B 83.430 344 53 2 335 678 343950672 343951011 2.280000e-82 316.0
27 TraesCS3D01G465800 chr1B 83.019 265 21 9 992 1248 321040274 321040026 6.620000e-53 219.0
28 TraesCS3D01G465800 chr1B 82.243 107 14 4 1817 1918 320106189 320106083 1.950000e-13 87.9
29 TraesCS3D01G465800 chr7D 84.286 350 51 1 329 678 497044309 497043964 4.870000e-89 339.0
30 TraesCS3D01G465800 chr7B 84.000 350 52 1 329 678 572030058 572030403 2.260000e-87 333.0
31 TraesCS3D01G465800 chr7A 83.143 350 55 2 329 678 20689761 20690106 2.280000e-82 316.0
32 TraesCS3D01G465800 chr7A 91.837 49 1 2 3118 3163 641268466 641268514 9.120000e-07 65.8
33 TraesCS3D01G465800 chr5D 83.090 343 53 2 336 678 347476265 347476602 1.370000e-79 307.0
34 TraesCS3D01G465800 chr4A 82.000 350 59 1 329 678 681923288 681923633 1.070000e-75 294.0
35 TraesCS3D01G465800 chr5B 93.182 44 2 1 3121 3163 145476124 145476081 3.280000e-06 63.9
36 TraesCS3D01G465800 chr2D 97.222 36 1 0 3124 3159 18889305 18889340 1.180000e-05 62.1
37 TraesCS3D01G465800 chr2D 97.222 36 1 0 3124 3159 18993274 18993309 1.180000e-05 62.1
38 TraesCS3D01G465800 chr1D 100.000 33 0 0 3130 3162 493057423 493057455 1.180000e-05 62.1
39 TraesCS3D01G465800 chr6A 91.304 46 1 2 3126 3171 304930340 304930298 4.240000e-05 60.2


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 TraesCS3D01G465800 chr3D 569554066 569557998 3932 False 7263.00 7263 100.0000 1 3933 1 chr3D.!!$F1 3932
1 TraesCS3D01G465800 chr3A 700580153 700583376 3223 False 2019.00 3576 91.2165 1 3933 2 chr3A.!!$F2 3932
2 TraesCS3D01G465800 chr3B 756125973 756131622 5649 True 746.58 2276 94.0516 1 3933 5 chr3B.!!$R1 3932
3 TraesCS3D01G465800 chrUn 40895542 40896998 1456 True 1075.60 2067 95.4945 1309 2806 2 chrUn.!!$R3 1497
4 TraesCS3D01G465800 chrUn 255356140 255361296 5156 False 640.42 1147 92.5384 1 3933 5 chrUn.!!$F1 3932
5 TraesCS3D01G465800 chr5A 42267788 42272944 5156 True 640.42 1147 92.0622 1 3933 5 chr5A.!!$R1 3932
6 TraesCS3D01G465800 chr1B 320104992 320106988 1996 True 573.30 909 84.8890 992 2736 3 chr1B.!!$R2 1744

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
614 616 0.035439 TTCGAGCATCAGGGGAAACC 60.035 55.0 0.00 0.0 43.53 3.27 F
778 1152 0.035534 AGCATGCCATGTAACGGTGA 60.036 50.0 15.66 0.0 0.00 4.02 F
833 1207 0.177373 CCTACCTTGCTTCGGTACCC 59.823 60.0 6.25 0.0 35.98 3.69 F
1042 2710 0.240145 CCACAGTCGTCGTTGCTCTA 59.760 55.0 0.00 0.0 0.00 2.43 F
1156 2836 0.744414 CACGCCCATCCGAGTTTGAT 60.744 55.0 0.00 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 3219 1.140852 TGGCAGGAAGTATAGCGCATT 59.859 47.619 11.47 0.00 0.00 3.56 R
2745 4818 1.153449 CCCCTATTGAAGCGCACGA 60.153 57.895 11.47 3.21 0.00 4.35 R
2829 5327 5.712152 ACAATCCTTTGACCAATGTCTTC 57.288 39.130 0.00 0.00 42.28 2.87 R
2875 5373 0.468771 AGCTGGAGTGGCAAAGCTTT 60.469 50.000 5.69 5.69 43.33 3.51 R
3144 5665 1.091537 ATTCCCGTTGTAATGCACGG 58.908 50.000 4.30 4.30 39.63 4.94 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
35 36 2.043953 GACCCTTGGATGGTGGCC 60.044 66.667 0.00 0.00 35.85 5.36
66 67 4.980805 GACGGCTTGGCGTGTGGA 62.981 66.667 25.75 0.00 0.00 4.02
79 80 1.130373 CGTGTGGATCCCATTTCGTTG 59.870 52.381 9.90 0.00 35.28 4.10
86 87 2.762535 TCCCATTTCGTTGTCTCTCC 57.237 50.000 0.00 0.00 0.00 3.71
193 195 1.979809 TCATTGGTAGGTCCCCACAT 58.020 50.000 0.00 0.00 34.77 3.21
225 227 4.269183 TCTGGTCTCTGATGAACTCTCTC 58.731 47.826 0.00 0.00 0.00 3.20
226 228 4.018506 TCTGGTCTCTGATGAACTCTCTCT 60.019 45.833 0.00 0.00 0.00 3.10
238 240 3.012934 ACTCTCTCTCTTAGGAGGTGC 57.987 52.381 1.52 0.00 39.86 5.01
257 259 1.908340 CTGCTGCTGAGGGGTAGCTT 61.908 60.000 0.00 0.00 43.54 3.74
266 268 2.267961 GGGTAGCTTGGTCCCACG 59.732 66.667 0.00 0.00 40.79 4.94
285 287 2.679837 ACGGCAATGCATAGAACAAGAG 59.320 45.455 7.79 0.00 0.00 2.85
298 300 1.742308 ACAAGAGTAGGGGCTTTGGA 58.258 50.000 0.00 0.00 0.00 3.53
308 310 1.272704 GGGGCTTTGGATTTCCTCACT 60.273 52.381 0.00 0.00 36.82 3.41
324 326 2.234661 CTCACTGGTGCCTCTCATTACA 59.765 50.000 0.00 0.00 0.00 2.41
325 327 2.234661 TCACTGGTGCCTCTCATTACAG 59.765 50.000 0.00 0.00 33.16 2.74
327 329 2.639839 ACTGGTGCCTCTCATTACAGTT 59.360 45.455 0.00 0.00 35.17 3.16
331 333 3.369471 GGTGCCTCTCATTACAGTTAGCA 60.369 47.826 0.00 0.00 0.00 3.49
396 398 1.221021 GTGCCTCCTTTAGGGTCGG 59.779 63.158 0.00 0.00 46.65 4.79
399 401 1.689582 CCTCCTTTAGGGTCGGGCT 60.690 63.158 0.00 0.00 42.32 5.19
411 413 4.803908 CGGGCTTGGCTCCCCTTC 62.804 72.222 6.22 0.00 40.75 3.46
413 415 3.342477 GGCTTGGCTCCCCTTCCT 61.342 66.667 0.00 0.00 0.00 3.36
414 416 2.044551 GCTTGGCTCCCCTTCCTG 60.045 66.667 0.00 0.00 0.00 3.86
415 417 2.044551 CTTGGCTCCCCTTCCTGC 60.045 66.667 0.00 0.00 0.00 4.85
416 418 2.858476 TTGGCTCCCCTTCCTGCA 60.858 61.111 0.00 0.00 0.00 4.41
417 419 2.220786 CTTGGCTCCCCTTCCTGCAT 62.221 60.000 0.00 0.00 0.00 3.96
431 433 0.520404 CTGCATGCAGTCACAGTTCC 59.480 55.000 34.76 0.00 39.10 3.62
432 434 0.890542 TGCATGCAGTCACAGTTCCC 60.891 55.000 18.46 0.00 0.00 3.97
434 436 1.672356 ATGCAGTCACAGTTCCCGC 60.672 57.895 0.00 0.00 0.00 6.13
456 458 3.004315 CCTATGCTCGACTTCCTCTTCTC 59.996 52.174 0.00 0.00 0.00 2.87
457 459 1.178276 TGCTCGACTTCCTCTTCTCC 58.822 55.000 0.00 0.00 0.00 3.71
469 471 0.098905 TCTTCTCCGATTCGTGCTCG 59.901 55.000 5.20 0.81 38.55 5.03
509 511 2.432146 GGAATTTGGCCAGGGAGAAATC 59.568 50.000 5.11 0.00 0.00 2.17
534 536 1.274703 ATCCTGTGTTGGGAGCGGAT 61.275 55.000 0.00 0.00 36.21 4.18
567 569 1.511613 CTATCCCCTTCTTGGAGGCA 58.488 55.000 0.00 0.00 38.35 4.75
570 572 0.332632 TCCCCTTCTTGGAGGCATTG 59.667 55.000 0.00 0.00 38.35 2.82
586 588 2.503331 CATTGCCATGGCCGTTATCTA 58.497 47.619 33.44 9.85 41.09 1.98
588 590 4.260985 CATTGCCATGGCCGTTATCTATA 58.739 43.478 33.44 8.21 41.09 1.31
606 608 1.403814 TACCCCTCTTCGAGCATCAG 58.596 55.000 0.00 0.00 33.17 2.90
614 616 0.035439 TTCGAGCATCAGGGGAAACC 60.035 55.000 0.00 0.00 43.53 3.27
642 644 3.455910 TCTGGTTTTCAGGATCGGATGAT 59.544 43.478 0.00 0.00 43.53 2.45
654 656 2.537560 GGATGATGACGGCGCCTTG 61.538 63.158 26.68 12.89 0.00 3.61
659 661 4.980805 TGACGGCGCCTTGGTGTC 62.981 66.667 26.68 23.07 0.00 3.67
696 1069 2.087646 GCCAAAAAGCCAACAAACCAA 58.912 42.857 0.00 0.00 0.00 3.67
712 1085 6.712276 ACAAACCAAAACAAAACCCATCTAA 58.288 32.000 0.00 0.00 0.00 2.10
716 1089 6.953101 ACCAAAACAAAACCCATCTAAAACT 58.047 32.000 0.00 0.00 0.00 2.66
728 1101 4.212636 CCATCTAAAACTCGAAAACACGGT 59.787 41.667 0.00 0.00 0.00 4.83
732 1105 4.541085 AAAACTCGAAAACACGGTAAGG 57.459 40.909 0.00 0.00 0.00 2.69
760 1134 2.969628 AATCCTAAGTGAGCGTCCAG 57.030 50.000 0.00 0.00 0.00 3.86
777 1151 0.099259 CAGCATGCCATGTAACGGTG 59.901 55.000 15.66 0.00 0.00 4.94
778 1152 0.035534 AGCATGCCATGTAACGGTGA 60.036 50.000 15.66 0.00 0.00 4.02
789 1163 2.523184 TAACGGTGACTGAGAGCGCG 62.523 60.000 0.00 0.00 37.85 6.86
794 1168 2.510238 GACTGAGAGCGCGCCATT 60.510 61.111 30.33 14.08 0.00 3.16
795 1169 2.510238 ACTGAGAGCGCGCCATTC 60.510 61.111 30.33 22.46 0.00 2.67
796 1170 2.202851 CTGAGAGCGCGCCATTCT 60.203 61.111 30.33 24.48 0.00 2.40
797 1171 2.202797 TGAGAGCGCGCCATTCTC 60.203 61.111 30.91 30.91 38.23 2.87
798 1172 2.202797 GAGAGCGCGCCATTCTCA 60.203 61.111 31.94 0.00 37.78 3.27
799 1173 1.811266 GAGAGCGCGCCATTCTCAA 60.811 57.895 31.94 0.00 37.78 3.02
801 1175 0.745845 AGAGCGCGCCATTCTCAATT 60.746 50.000 30.33 4.23 0.00 2.32
802 1176 0.316524 GAGCGCGCCATTCTCAATTC 60.317 55.000 30.33 10.97 0.00 2.17
803 1177 1.298638 GCGCGCCATTCTCAATTCC 60.299 57.895 23.24 0.00 0.00 3.01
807 1181 1.473258 CGCCATTCTCAATTCCCCAA 58.527 50.000 0.00 0.00 0.00 4.12
808 1182 1.824230 CGCCATTCTCAATTCCCCAAA 59.176 47.619 0.00 0.00 0.00 3.28
809 1183 2.417243 CGCCATTCTCAATTCCCCAAAC 60.417 50.000 0.00 0.00 0.00 2.93
811 1185 3.368739 GCCATTCTCAATTCCCCAAACTG 60.369 47.826 0.00 0.00 0.00 3.16
833 1207 0.177373 CCTACCTTGCTTCGGTACCC 59.823 60.000 6.25 0.00 35.98 3.69
870 1244 1.672030 CCACACATTGGCTCTGCGA 60.672 57.895 0.00 0.00 39.07 5.10
871 1245 1.642037 CCACACATTGGCTCTGCGAG 61.642 60.000 0.00 1.80 39.07 5.03
954 2622 2.785921 CGAGACGGACAGAGACGG 59.214 66.667 0.00 0.00 0.00 4.79
955 2623 2.486042 GAGACGGACAGAGACGGC 59.514 66.667 0.00 0.00 38.71 5.68
956 2624 3.053849 GAGACGGACAGAGACGGCC 62.054 68.421 0.00 0.00 39.40 6.13
957 2625 3.371063 GACGGACAGAGACGGCCA 61.371 66.667 2.24 0.00 30.28 5.36
958 2626 3.628280 GACGGACAGAGACGGCCAC 62.628 68.421 2.24 0.00 30.28 5.01
960 2628 4.436998 GGACAGAGACGGCCACGG 62.437 72.222 2.24 0.00 46.48 4.94
961 2629 3.371063 GACAGAGACGGCCACGGA 61.371 66.667 2.24 0.00 46.48 4.69
962 2630 2.680352 ACAGAGACGGCCACGGAT 60.680 61.111 2.24 0.00 46.48 4.18
963 2631 2.105128 CAGAGACGGCCACGGATC 59.895 66.667 2.24 0.00 46.48 3.36
964 2632 2.043852 AGAGACGGCCACGGATCT 60.044 61.111 2.24 0.00 46.48 2.75
965 2633 2.105128 GAGACGGCCACGGATCTG 59.895 66.667 2.24 0.00 46.48 2.90
966 2634 3.432051 GAGACGGCCACGGATCTGG 62.432 68.421 2.24 1.15 46.48 3.86
967 2635 3.771160 GACGGCCACGGATCTGGT 61.771 66.667 2.24 0.00 46.48 4.00
968 2636 3.718210 GACGGCCACGGATCTGGTC 62.718 68.421 2.24 0.57 46.48 4.02
969 2637 4.530857 CGGCCACGGATCTGGTCC 62.531 72.222 2.24 0.00 44.10 4.46
980 2648 4.408182 GGATCTGGTCCATATATTCCCG 57.592 50.000 1.02 0.00 46.96 5.14
981 2649 4.030913 GGATCTGGTCCATATATTCCCGA 58.969 47.826 1.02 0.00 46.96 5.14
982 2650 4.469945 GGATCTGGTCCATATATTCCCGAA 59.530 45.833 1.02 0.00 46.96 4.30
983 2651 5.045869 GGATCTGGTCCATATATTCCCGAAA 60.046 44.000 1.02 0.00 46.96 3.46
984 2652 5.897851 TCTGGTCCATATATTCCCGAAAA 57.102 39.130 0.00 0.00 0.00 2.29
985 2653 6.255294 TCTGGTCCATATATTCCCGAAAAA 57.745 37.500 0.00 0.00 0.00 1.94
1030 2698 2.733593 GGTGACGACGCCACAGTC 60.734 66.667 16.22 0.00 45.14 3.51
1037 2705 2.645510 GACGCCACAGTCGTCGTTG 61.646 63.158 0.00 0.00 45.19 4.10
1038 2706 4.059459 CGCCACAGTCGTCGTTGC 62.059 66.667 0.00 0.00 0.00 4.17
1039 2707 2.661866 GCCACAGTCGTCGTTGCT 60.662 61.111 0.00 0.00 0.00 3.91
1040 2708 2.658707 GCCACAGTCGTCGTTGCTC 61.659 63.158 0.00 0.00 0.00 4.26
1041 2709 1.007271 CCACAGTCGTCGTTGCTCT 60.007 57.895 0.00 0.00 0.00 4.09
1042 2710 0.240145 CCACAGTCGTCGTTGCTCTA 59.760 55.000 0.00 0.00 0.00 2.43
1045 2713 1.132643 ACAGTCGTCGTTGCTCTATCC 59.867 52.381 0.00 0.00 0.00 2.59
1047 2715 1.816835 AGTCGTCGTTGCTCTATCCAA 59.183 47.619 0.00 0.00 0.00 3.53
1049 2717 3.119101 AGTCGTCGTTGCTCTATCCAATT 60.119 43.478 0.00 0.00 0.00 2.32
1053 2721 6.018994 GTCGTCGTTGCTCTATCCAATTAATT 60.019 38.462 0.00 0.00 0.00 1.40
1156 2836 0.744414 CACGCCCATCCGAGTTTGAT 60.744 55.000 0.00 0.00 0.00 2.57
1240 2920 3.364549 AGTTCTGGATCAGGACAGAGAG 58.635 50.000 8.81 0.00 42.11 3.20
1249 2929 2.647299 TCAGGACAGAGAGGAGAAGACT 59.353 50.000 0.00 0.00 0.00 3.24
1257 2937 3.212275 GGAGAAGACTCGCCTCCC 58.788 66.667 0.00 0.00 43.44 4.30
1349 3035 1.284198 ACCCTAGTAAGAGCCTCGACA 59.716 52.381 3.18 0.00 0.00 4.35
1382 3071 4.511527 CAGGGATATTCGGGATTCAGATG 58.488 47.826 0.00 0.00 0.00 2.90
1483 3176 4.139786 TCTTTTGCAATCTGCTCACTTCT 58.860 39.130 0.00 0.00 45.31 2.85
1507 3200 5.966853 TTTTTCATTTCCTTTTCCCCAGT 57.033 34.783 0.00 0.00 0.00 4.00
1576 3276 2.763039 TGCTCTCATTATCCTCACCCA 58.237 47.619 0.00 0.00 0.00 4.51
1589 3289 0.896923 TCACCCAATGCTGCAATTCC 59.103 50.000 6.36 0.00 0.00 3.01
1717 3426 4.080975 TCCCGGAACTATATTTTTCACCGT 60.081 41.667 0.73 0.00 37.87 4.83
1734 3443 1.446272 GTTCCAGGGAGAACGCTCG 60.446 63.158 0.00 0.00 42.25 5.03
1772 3484 8.035394 TGGTAATTCTACACTCTTTCTTAGCAG 58.965 37.037 0.00 0.00 0.00 4.24
1790 3503 9.317936 TCTTAGCAGTCTACATGATTAATTGTG 57.682 33.333 0.00 2.15 0.00 3.33
1825 3555 2.749621 CAACTGTAGGTCTCCATTTGCC 59.250 50.000 0.00 0.00 0.00 4.52
1831 3561 1.177401 GGTCTCCATTTGCCTTGGTC 58.823 55.000 0.00 0.00 35.64 4.02
1873 3641 4.331992 TCCGTTTGTGTTTGTTATGAACGA 59.668 37.500 7.22 0.00 40.32 3.85
2090 4156 7.088905 GGCTGCCTGATTGAAATTGATATAAG 58.911 38.462 12.43 0.00 0.00 1.73
2265 4331 5.234543 GGCAACTATAGACCTCGATTTTGTC 59.765 44.000 6.78 0.00 0.00 3.18
2608 4681 6.173339 GGGTCTGTAATCACTGAAAGAATGA 58.827 40.000 0.00 0.00 37.43 2.57
2733 4806 5.924825 AGGACAAGTGTTCGACAATTACTAC 59.075 40.000 0.00 0.00 33.79 2.73
2829 5327 1.750193 AATGCCCATGTGACTTACGG 58.250 50.000 0.00 0.00 0.00 4.02
2871 5369 7.009540 GGATTGTTTTCATCGCATTAGGAAAAG 59.990 37.037 0.00 0.00 39.13 2.27
2875 5373 3.342719 TCATCGCATTAGGAAAAGCACA 58.657 40.909 0.00 0.00 29.75 4.57
2908 5406 2.097038 CAGCTCGGAGTTGGCTTCG 61.097 63.158 13.40 0.00 44.82 3.79
2997 5495 8.887036 TGTTCACTTGTAGCGAATATATGAAT 57.113 30.769 0.00 0.00 0.00 2.57
3006 5504 9.045223 TGTAGCGAATATATGAATCCATATTGC 57.955 33.333 3.62 6.52 41.83 3.56
3075 5573 1.814772 CGCTCCTGCCTCCCTATGAG 61.815 65.000 0.00 0.00 41.07 2.90
3076 5574 2.056985 CTCCTGCCTCCCTATGAGC 58.943 63.158 0.00 0.00 39.98 4.26
3079 5577 1.479368 CCTGCCTCCCTATGAGCCTC 61.479 65.000 0.00 0.00 39.98 4.70
3080 5578 1.460305 TGCCTCCCTATGAGCCTCC 60.460 63.158 0.00 0.00 39.98 4.30
3081 5579 2.220586 GCCTCCCTATGAGCCTCCC 61.221 68.421 0.00 0.00 39.98 4.30
3082 5580 1.551358 CCTCCCTATGAGCCTCCCT 59.449 63.158 0.00 0.00 39.98 4.20
3083 5581 0.787084 CCTCCCTATGAGCCTCCCTA 59.213 60.000 0.00 0.00 39.98 3.53
3084 5582 1.364328 CCTCCCTATGAGCCTCCCTAT 59.636 57.143 0.00 0.00 39.98 2.57
3085 5583 2.465813 CTCCCTATGAGCCTCCCTATG 58.534 57.143 0.00 0.00 33.47 2.23
3086 5584 2.043664 CTCCCTATGAGCCTCCCTATGA 59.956 54.545 0.00 0.00 33.47 2.15
3087 5585 2.183679 CCCTATGAGCCTCCCTATGAC 58.816 57.143 0.00 0.00 0.00 3.06
3088 5586 2.493500 CCCTATGAGCCTCCCTATGACA 60.494 54.545 0.00 0.00 0.00 3.58
3089 5587 2.564947 CCTATGAGCCTCCCTATGACAC 59.435 54.545 0.00 0.00 0.00 3.67
3090 5588 2.485966 ATGAGCCTCCCTATGACACT 57.514 50.000 0.00 0.00 0.00 3.55
3091 5589 1.781786 TGAGCCTCCCTATGACACTC 58.218 55.000 0.00 0.00 0.00 3.51
3092 5590 1.007118 TGAGCCTCCCTATGACACTCA 59.993 52.381 0.00 0.00 30.87 3.41
3093 5591 2.324541 GAGCCTCCCTATGACACTCAT 58.675 52.381 0.00 0.00 40.72 2.90
3094 5592 2.298729 GAGCCTCCCTATGACACTCATC 59.701 54.545 0.00 0.00 38.26 2.92
3095 5593 1.346068 GCCTCCCTATGACACTCATCC 59.654 57.143 0.00 0.00 38.26 3.51
3096 5594 2.969628 CCTCCCTATGACACTCATCCT 58.030 52.381 0.00 0.00 38.26 3.24
3103 5601 4.458989 CCTATGACACTCATCCTCTCTAGC 59.541 50.000 0.00 0.00 38.26 3.42
3134 5655 9.790389 CTTCCTCGCCTATTATGTAAATACTAG 57.210 37.037 0.00 0.00 0.00 2.57
3173 5694 8.687242 TGCATTACAACGGGAATGAAAATTATA 58.313 29.630 3.89 0.00 35.46 0.98
3314 5836 5.591099 TCGGTATTATTAAGTCACGGGTTC 58.409 41.667 0.00 0.00 0.00 3.62
3323 5845 1.617357 AGTCACGGGTTCACTTAGTCC 59.383 52.381 0.00 0.00 0.00 3.85
3350 5872 0.951558 ATTTTCCGCGCATATCACCC 59.048 50.000 8.75 0.00 0.00 4.61
3381 5903 2.798680 CTCAACGTAATCAGGTCGAGG 58.201 52.381 0.00 0.00 0.00 4.63
3391 5913 1.822990 TCAGGTCGAGGGTTCACATAC 59.177 52.381 0.00 0.00 0.00 2.39
3392 5914 1.548719 CAGGTCGAGGGTTCACATACA 59.451 52.381 0.00 0.00 0.00 2.29
3394 5916 1.625616 GTCGAGGGTTCACATACACG 58.374 55.000 0.00 0.00 0.00 4.49
3401 5932 2.159572 GGGTTCACATACACGCATTCAC 60.160 50.000 0.00 0.00 0.00 3.18
3411 5942 1.588404 CACGCATTCACGTAGGTCATC 59.412 52.381 0.00 0.00 46.34 2.92
3412 5943 1.209128 CGCATTCACGTAGGTCATCC 58.791 55.000 0.00 0.00 0.00 3.51
3456 5987 3.689649 CACACATTTAACCACTAGGCTCC 59.310 47.826 0.00 0.00 39.06 4.70
3485 6017 2.350522 CCTCTTTGTCCACCTCGAATG 58.649 52.381 0.00 0.00 0.00 2.67
3563 6095 9.896645 ACTCATATATGATTCTCTCTCTCTCTC 57.103 37.037 15.71 0.00 36.02 3.20
3568 6100 6.760440 ATGATTCTCTCTCTCTCTCTCTCT 57.240 41.667 0.00 0.00 0.00 3.10
3569 6101 6.166984 TGATTCTCTCTCTCTCTCTCTCTC 57.833 45.833 0.00 0.00 0.00 3.20
3570 6102 5.901853 TGATTCTCTCTCTCTCTCTCTCTCT 59.098 44.000 0.00 0.00 0.00 3.10
3574 6106 2.370189 CTCTCTCTCTCTCTCTCTCCCC 59.630 59.091 0.00 0.00 0.00 4.81
3591 6123 6.277044 TCTCTCCCCTAAATAATTTATGGGGG 59.723 42.308 21.17 21.96 46.93 5.40
3618 6337 2.702270 ATTCTGGGGCCTTGTTCTTT 57.298 45.000 0.84 0.00 0.00 2.52
3620 6339 1.703411 TCTGGGGCCTTGTTCTTTTG 58.297 50.000 0.84 0.00 0.00 2.44
3624 6343 2.016165 GGCCTTGTTCTTTTGCGCG 61.016 57.895 0.00 0.00 0.00 6.86
3658 6377 1.964223 CATCTACGCCCCTGAGTACAT 59.036 52.381 0.00 0.00 0.00 2.29
3670 6389 4.825634 CCCTGAGTACATATACCTTCGACA 59.174 45.833 0.00 0.00 30.88 4.35
3689 6408 1.566703 CAGGGTCTAGACTCCAGAGGA 59.433 57.143 19.44 0.00 30.26 3.71
3714 6433 5.029973 ACTATGGGTATGAGAGGGCTATT 57.970 43.478 0.00 0.00 0.00 1.73
3722 6441 4.803329 ATGAGAGGGCTATTGTGGAAAT 57.197 40.909 0.00 0.00 0.00 2.17
3739 6458 1.293062 AATGGCAGGTGTGGAGATCT 58.707 50.000 0.00 0.00 0.00 2.75
3799 6518 0.321298 GCTCGAGGTGGCCTTTTGTA 60.321 55.000 15.58 0.00 31.76 2.41
3810 6529 5.007682 GTGGCCTTTTGTACATAAGAGGAA 58.992 41.667 22.89 6.98 34.69 3.36
3819 6538 9.691362 TTTTGTACATAAGAGGAAATTTTCTGC 57.309 29.630 2.93 0.00 0.00 4.26
3837 6556 4.641645 CGCACAGGGGAAGCACCA 62.642 66.667 2.58 0.00 41.20 4.17
3838 6557 2.985847 GCACAGGGGAAGCACCAC 60.986 66.667 2.58 0.00 43.70 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.738389 GCCGTCAATAACCCCACATG 59.262 55.000 0.00 0.00 0.00 3.21
66 67 2.571653 TGGAGAGACAACGAAATGGGAT 59.428 45.455 0.00 0.00 0.00 3.85
79 80 6.523840 AGCTTTGAAGATATGATGGAGAGAC 58.476 40.000 0.00 0.00 0.00 3.36
86 87 5.752472 ACGTGAGAGCTTTGAAGATATGATG 59.248 40.000 0.00 0.00 0.00 3.07
193 195 2.432874 TCAGAGACCAGAAAACGTTCCA 59.567 45.455 0.00 0.00 33.92 3.53
199 201 5.546526 AGAGTTCATCAGAGACCAGAAAAC 58.453 41.667 0.00 0.00 0.00 2.43
225 227 0.461693 GCAGCAGCACCTCCTAAGAG 60.462 60.000 0.00 0.00 41.58 2.85
226 228 0.906756 AGCAGCAGCACCTCCTAAGA 60.907 55.000 3.17 0.00 45.49 2.10
238 240 1.908340 AAGCTACCCCTCAGCAGCAG 61.908 60.000 0.00 0.00 41.66 4.24
257 259 2.203549 TATGCATTGCCGTGGGACCA 62.204 55.000 3.54 0.00 0.00 4.02
266 268 4.274459 CCTACTCTTGTTCTATGCATTGCC 59.726 45.833 3.54 0.00 0.00 4.52
285 287 2.025321 TGAGGAAATCCAAAGCCCCTAC 60.025 50.000 1.67 0.00 38.89 3.18
298 300 1.280421 GAGAGGCACCAGTGAGGAAAT 59.720 52.381 0.99 0.00 41.22 2.17
308 310 3.369471 GCTAACTGTAATGAGAGGCACCA 60.369 47.826 0.00 0.00 0.00 4.17
324 326 1.602377 GACAAGGTTGCGTTGCTAACT 59.398 47.619 2.06 0.00 31.96 2.24
325 327 1.334689 GGACAAGGTTGCGTTGCTAAC 60.335 52.381 2.06 0.00 33.25 2.34
327 329 0.107831 AGGACAAGGTTGCGTTGCTA 59.892 50.000 2.06 0.00 33.25 3.49
331 333 0.250338 GAGGAGGACAAGGTTGCGTT 60.250 55.000 0.00 0.00 0.00 4.84
376 378 1.221021 GACCCTAAAGGAGGCACCG 59.779 63.158 0.00 0.00 45.17 4.94
396 398 3.342477 AGGAAGGGGAGCCAAGCC 61.342 66.667 0.00 0.00 0.00 4.35
399 401 2.240918 ATGCAGGAAGGGGAGCCAA 61.241 57.895 0.00 0.00 0.00 4.52
413 415 0.890542 GGGAACTGTGACTGCATGCA 60.891 55.000 21.29 21.29 0.00 3.96
414 416 1.878775 GGGAACTGTGACTGCATGC 59.121 57.895 11.82 11.82 0.00 4.06
415 417 1.915614 GCGGGAACTGTGACTGCATG 61.916 60.000 9.97 0.00 36.53 4.06
416 418 1.672356 GCGGGAACTGTGACTGCAT 60.672 57.895 9.97 0.00 36.53 3.96
417 419 2.280797 GCGGGAACTGTGACTGCA 60.281 61.111 9.97 0.00 36.53 4.41
434 436 2.955660 AGAAGAGGAAGTCGAGCATAGG 59.044 50.000 0.00 0.00 0.00 2.57
457 459 2.589492 GCCATCCGAGCACGAATCG 61.589 63.158 4.70 0.00 42.66 3.34
469 471 1.450531 CGAGCAATCCCAAGCCATCC 61.451 60.000 0.00 0.00 0.00 3.51
472 474 2.045045 CCGAGCAATCCCAAGCCA 60.045 61.111 0.00 0.00 0.00 4.75
509 511 2.751436 CCAACACAGGATGCGGGG 60.751 66.667 0.00 0.00 42.53 5.73
511 513 1.746615 CTCCCAACACAGGATGCGG 60.747 63.158 0.00 0.00 42.53 5.69
513 515 2.401766 CGCTCCCAACACAGGATGC 61.402 63.158 0.00 0.00 42.53 3.91
543 545 4.142632 CTCCAAGAAGGGGATAGCACCC 62.143 59.091 0.00 0.00 42.25 4.61
567 569 2.949177 TAGATAACGGCCATGGCAAT 57.051 45.000 36.56 23.11 44.11 3.56
570 572 2.629051 GGTATAGATAACGGCCATGGC 58.371 52.381 29.47 29.47 41.06 4.40
614 616 3.430929 CGATCCTGAAAACCAGACCTAGG 60.431 52.174 7.41 7.41 45.78 3.02
642 644 4.980805 GACACCAAGGCGCCGTCA 62.981 66.667 23.20 0.00 0.00 4.35
654 656 1.004918 CACCAAGGAGGACGACACC 60.005 63.158 0.00 0.00 41.22 4.16
683 1056 3.504134 GGTTTTGTTTTGGTTTGTTGGCT 59.496 39.130 0.00 0.00 0.00 4.75
696 1069 6.702716 TCGAGTTTTAGATGGGTTTTGTTT 57.297 33.333 0.00 0.00 0.00 2.83
712 1085 3.795877 TCCTTACCGTGTTTTCGAGTTT 58.204 40.909 0.00 0.00 0.00 2.66
740 1114 2.678190 GCTGGACGCTCACTTAGGATTT 60.678 50.000 0.00 0.00 35.14 2.17
741 1115 1.134670 GCTGGACGCTCACTTAGGATT 60.135 52.381 0.00 0.00 35.14 3.01
742 1116 0.461961 GCTGGACGCTCACTTAGGAT 59.538 55.000 0.00 0.00 35.14 3.24
760 1134 0.098728 GTCACCGTTACATGGCATGC 59.901 55.000 26.70 9.90 0.00 4.06
777 1151 2.510238 AATGGCGCGCTCTCAGTC 60.510 61.111 32.29 12.98 0.00 3.51
778 1152 2.510238 GAATGGCGCGCTCTCAGT 60.510 61.111 32.29 19.96 0.00 3.41
789 1163 2.833943 AGTTTGGGGAATTGAGAATGGC 59.166 45.455 0.00 0.00 0.00 4.40
794 1168 2.225017 GGGTCAGTTTGGGGAATTGAGA 60.225 50.000 0.00 0.00 35.03 3.27
795 1169 2.171003 GGGTCAGTTTGGGGAATTGAG 58.829 52.381 0.00 0.00 35.03 3.02
796 1170 1.786441 AGGGTCAGTTTGGGGAATTGA 59.214 47.619 0.00 0.00 32.28 2.57
797 1171 2.309136 AGGGTCAGTTTGGGGAATTG 57.691 50.000 0.00 0.00 0.00 2.32
798 1172 2.042569 GGTAGGGTCAGTTTGGGGAATT 59.957 50.000 0.00 0.00 0.00 2.17
799 1173 1.639108 GGTAGGGTCAGTTTGGGGAAT 59.361 52.381 0.00 0.00 0.00 3.01
801 1175 0.195096 AGGTAGGGTCAGTTTGGGGA 59.805 55.000 0.00 0.00 0.00 4.81
802 1176 1.073098 AAGGTAGGGTCAGTTTGGGG 58.927 55.000 0.00 0.00 0.00 4.96
803 1177 1.886655 GCAAGGTAGGGTCAGTTTGGG 60.887 57.143 0.00 0.00 0.00 4.12
807 1181 1.002087 CGAAGCAAGGTAGGGTCAGTT 59.998 52.381 0.00 0.00 0.00 3.16
808 1182 0.608640 CGAAGCAAGGTAGGGTCAGT 59.391 55.000 0.00 0.00 0.00 3.41
809 1183 0.108138 CCGAAGCAAGGTAGGGTCAG 60.108 60.000 0.00 0.00 0.00 3.51
811 1185 1.134877 GTACCGAAGCAAGGTAGGGTC 60.135 57.143 5.40 0.00 44.09 4.46
884 1266 6.469782 AATCAAGCCTCTCTGTTTCAAAAA 57.530 33.333 0.00 0.00 0.00 1.94
885 1267 6.469782 AAATCAAGCCTCTCTGTTTCAAAA 57.530 33.333 0.00 0.00 0.00 2.44
886 1268 6.469782 AAAATCAAGCCTCTCTGTTTCAAA 57.530 33.333 0.00 0.00 0.00 2.69
887 1269 6.469782 AAAAATCAAGCCTCTCTGTTTCAA 57.530 33.333 0.00 0.00 0.00 2.69
945 2613 2.680352 ATCCGTGGCCGTCTCTGT 60.680 61.111 0.00 0.00 0.00 3.41
948 2616 2.105128 CAGATCCGTGGCCGTCTC 59.895 66.667 0.00 0.00 0.00 3.36
949 2617 3.461773 CCAGATCCGTGGCCGTCT 61.462 66.667 0.00 0.00 0.00 4.18
950 2618 3.718210 GACCAGATCCGTGGCCGTC 62.718 68.421 0.00 0.00 41.90 4.79
951 2619 3.771160 GACCAGATCCGTGGCCGT 61.771 66.667 0.00 0.00 41.90 5.68
952 2620 4.530857 GGACCAGATCCGTGGCCG 62.531 72.222 0.00 0.00 41.90 6.13
960 2628 5.677319 TTCGGGAATATATGGACCAGATC 57.323 43.478 4.49 0.00 0.00 2.75
961 2629 6.448369 TTTTCGGGAATATATGGACCAGAT 57.552 37.500 6.86 6.86 0.00 2.90
962 2630 5.897851 TTTTCGGGAATATATGGACCAGA 57.102 39.130 0.00 0.00 0.00 3.86
1027 2695 1.460504 TGGATAGAGCAACGACGACT 58.539 50.000 0.00 0.00 0.00 4.18
1028 2696 2.273370 TTGGATAGAGCAACGACGAC 57.727 50.000 0.00 0.00 0.00 4.34
1029 2697 3.520290 AATTGGATAGAGCAACGACGA 57.480 42.857 0.00 0.00 0.00 4.20
1030 2698 5.907197 ATTAATTGGATAGAGCAACGACG 57.093 39.130 0.00 0.00 0.00 5.12
1031 2699 6.293462 GGGAATTAATTGGATAGAGCAACGAC 60.293 42.308 5.17 0.00 0.00 4.34
1032 2700 5.763204 GGGAATTAATTGGATAGAGCAACGA 59.237 40.000 5.17 0.00 0.00 3.85
1033 2701 5.530915 TGGGAATTAATTGGATAGAGCAACG 59.469 40.000 5.17 0.00 0.00 4.10
1034 2702 6.959639 TGGGAATTAATTGGATAGAGCAAC 57.040 37.500 5.17 0.00 0.00 4.17
1037 2705 6.153510 GGGATTGGGAATTAATTGGATAGAGC 59.846 42.308 5.17 0.00 0.00 4.09
1038 2706 6.665248 GGGGATTGGGAATTAATTGGATAGAG 59.335 42.308 5.17 0.00 0.00 2.43
1039 2707 6.561294 GGGGATTGGGAATTAATTGGATAGA 58.439 40.000 5.17 0.00 0.00 1.98
1040 2708 5.418840 CGGGGATTGGGAATTAATTGGATAG 59.581 44.000 5.17 0.00 0.00 2.08
1041 2709 5.162925 ACGGGGATTGGGAATTAATTGGATA 60.163 40.000 5.17 0.00 0.00 2.59
1042 2710 4.159557 CGGGGATTGGGAATTAATTGGAT 58.840 43.478 5.17 0.00 0.00 3.41
1045 2713 3.704061 ACACGGGGATTGGGAATTAATTG 59.296 43.478 5.17 0.00 0.00 2.32
1047 2715 3.053245 TGACACGGGGATTGGGAATTAAT 60.053 43.478 0.00 0.00 0.00 1.40
1049 2717 1.916874 TGACACGGGGATTGGGAATTA 59.083 47.619 0.00 0.00 0.00 1.40
1053 2721 0.478942 TTTTGACACGGGGATTGGGA 59.521 50.000 0.00 0.00 0.00 4.37
1098 2778 0.687354 ACCTTCTGTTGCGTCCATCT 59.313 50.000 0.00 0.00 0.00 2.90
1141 2821 3.696051 ACATGAAATCAAACTCGGATGGG 59.304 43.478 0.00 0.00 0.00 4.00
1156 2836 1.606994 CCCTCGTCGGTGAACATGAAA 60.607 52.381 0.00 0.00 0.00 2.69
1240 2920 1.682684 TGGGAGGCGAGTCTTCTCC 60.683 63.158 16.06 16.06 44.64 3.71
1307 2993 1.827399 ATCTGTTTGTCCGGCCGAGT 61.827 55.000 30.73 1.88 0.00 4.18
1367 3053 4.510167 AAAGGTCATCTGAATCCCGAAT 57.490 40.909 0.00 0.00 0.00 3.34
1382 3071 2.076863 CTGTCGGATCCACAAAAGGTC 58.923 52.381 13.41 0.00 0.00 3.85
1520 3219 1.140852 TGGCAGGAAGTATAGCGCATT 59.859 47.619 11.47 0.00 0.00 3.56
1576 3276 1.972795 ACACCAAGGAATTGCAGCATT 59.027 42.857 0.00 0.00 0.00 3.56
1589 3289 6.159988 TGTAAAACTGGACAAAAACACCAAG 58.840 36.000 0.00 0.00 33.14 3.61
1717 3426 1.595993 CTCGAGCGTTCTCCCTGGAA 61.596 60.000 0.00 0.00 35.94 3.53
1734 3443 4.226113 AGAATTACCACGTCGATAGCTC 57.774 45.455 0.00 0.00 0.00 4.09
1772 3484 7.051623 TGTACCCCACAATTAATCATGTAGAC 58.948 38.462 0.00 0.00 32.95 2.59
1788 3500 6.317893 CCTACAGTTGATTAAATGTACCCCAC 59.682 42.308 6.44 0.00 42.67 4.61
1790 3503 6.420638 ACCTACAGTTGATTAAATGTACCCC 58.579 40.000 6.44 0.00 42.67 4.95
1825 3555 8.553459 ACAGAAATATAGTGTTCTTGACCAAG 57.447 34.615 3.47 3.47 39.71 3.61
1831 3561 7.596749 AACGGACAGAAATATAGTGTTCTTG 57.403 36.000 0.00 0.00 31.66 3.02
2090 4156 1.753073 CAACATCCTTGCCCTTGATCC 59.247 52.381 0.00 0.00 0.00 3.36
2211 4277 5.007332 ACCTTTACGAACAACATGTGTCTTC 59.993 40.000 0.00 0.00 40.60 2.87
2421 4494 7.012515 AGTCTATACATAGTGTATCGCCTATGC 59.987 40.741 5.92 0.00 42.16 3.14
2422 4495 8.439993 AGTCTATACATAGTGTATCGCCTATG 57.560 38.462 5.92 0.00 42.16 2.23
2423 4496 9.111613 GAAGTCTATACATAGTGTATCGCCTAT 57.888 37.037 5.92 0.00 42.16 2.57
2424 4497 8.098912 TGAAGTCTATACATAGTGTATCGCCTA 58.901 37.037 5.92 0.00 42.16 3.93
2425 4498 6.940867 TGAAGTCTATACATAGTGTATCGCCT 59.059 38.462 5.92 0.00 42.16 5.52
2426 4499 7.142306 TGAAGTCTATACATAGTGTATCGCC 57.858 40.000 5.92 0.00 42.16 5.54
2427 4500 7.698550 CCATGAAGTCTATACATAGTGTATCGC 59.301 40.741 5.92 0.00 42.16 4.58
2510 4583 3.535561 CTCCATTGCTGAATCGGTAAGT 58.464 45.455 0.00 0.00 0.00 2.24
2540 4613 6.626302 TGGTTGACCAAAAGACTTTAACAAG 58.374 36.000 0.00 0.00 44.35 3.16
2617 4690 9.883142 TCCAAAACTTCAAAACTGACAATAATT 57.117 25.926 0.00 0.00 0.00 1.40
2710 4783 5.924825 AGTAGTAATTGTCGAACACTTGTCC 59.075 40.000 0.00 0.00 0.00 4.02
2745 4818 1.153449 CCCCTATTGAAGCGCACGA 60.153 57.895 11.47 3.21 0.00 4.35
2829 5327 5.712152 ACAATCCTTTGACCAATGTCTTC 57.288 39.130 0.00 0.00 42.28 2.87
2871 5369 0.598419 GGAGTGGCAAAGCTTTGTGC 60.598 55.000 33.47 24.18 40.24 4.57
2875 5373 0.468771 AGCTGGAGTGGCAAAGCTTT 60.469 50.000 5.69 5.69 43.33 3.51
2908 5406 4.372656 GAGTTATCCATCCACTGTGCTAC 58.627 47.826 1.29 0.00 0.00 3.58
2997 5495 4.858850 AGTCACCTCAAATGCAATATGGA 58.141 39.130 0.00 0.00 0.00 3.41
3006 5504 6.102663 AGAATCTTACGAGTCACCTCAAATG 58.897 40.000 0.00 0.00 36.74 2.32
3034 5532 4.394729 GGGAGTAACACATGTTTCCAGAA 58.605 43.478 14.52 0.00 36.91 3.02
3075 5573 1.346068 GGATGAGTGTCATAGGGAGGC 59.654 57.143 0.00 0.00 37.20 4.70
3076 5574 2.896685 GAGGATGAGTGTCATAGGGAGG 59.103 54.545 0.00 0.00 37.20 4.30
3079 5577 3.843422 AGAGAGGATGAGTGTCATAGGG 58.157 50.000 0.00 0.00 37.20 3.53
3080 5578 4.458989 GCTAGAGAGGATGAGTGTCATAGG 59.541 50.000 0.00 0.00 37.20 2.57
3081 5579 4.154015 CGCTAGAGAGGATGAGTGTCATAG 59.846 50.000 0.00 0.00 37.20 2.23
3082 5580 4.068599 CGCTAGAGAGGATGAGTGTCATA 58.931 47.826 0.00 0.00 37.20 2.15
3083 5581 2.884012 CGCTAGAGAGGATGAGTGTCAT 59.116 50.000 0.00 0.00 40.34 3.06
3084 5582 2.092914 TCGCTAGAGAGGATGAGTGTCA 60.093 50.000 0.00 0.00 0.00 3.58
3085 5583 2.566913 TCGCTAGAGAGGATGAGTGTC 58.433 52.381 0.00 0.00 0.00 3.67
3086 5584 2.719531 TCGCTAGAGAGGATGAGTGT 57.280 50.000 0.00 0.00 0.00 3.55
3087 5585 2.487762 GGATCGCTAGAGAGGATGAGTG 59.512 54.545 1.80 0.00 0.00 3.51
3088 5586 2.375174 AGGATCGCTAGAGAGGATGAGT 59.625 50.000 1.80 0.00 0.00 3.41
3089 5587 3.071874 AGGATCGCTAGAGAGGATGAG 57.928 52.381 1.80 0.00 0.00 2.90
3090 5588 3.417101 GAAGGATCGCTAGAGAGGATGA 58.583 50.000 1.80 0.00 0.00 2.92
3091 5589 2.491693 GGAAGGATCGCTAGAGAGGATG 59.508 54.545 1.80 0.00 0.00 3.51
3092 5590 2.378547 AGGAAGGATCGCTAGAGAGGAT 59.621 50.000 1.80 0.00 0.00 3.24
3093 5591 1.777878 AGGAAGGATCGCTAGAGAGGA 59.222 52.381 1.80 0.00 0.00 3.71
3094 5592 2.159382 GAGGAAGGATCGCTAGAGAGG 58.841 57.143 1.80 0.00 0.00 3.69
3095 5593 1.804151 CGAGGAAGGATCGCTAGAGAG 59.196 57.143 1.80 0.00 32.81 3.20
3096 5594 1.885560 CGAGGAAGGATCGCTAGAGA 58.114 55.000 0.00 0.00 32.81 3.10
3103 5601 3.193691 ACATAATAGGCGAGGAAGGATCG 59.806 47.826 0.00 0.00 43.00 3.69
3144 5665 1.091537 ATTCCCGTTGTAATGCACGG 58.908 50.000 4.30 4.30 39.63 4.94
3146 5667 3.840890 TTCATTCCCGTTGTAATGCAC 57.159 42.857 0.00 0.00 33.91 4.57
3173 5694 9.985730 TTCATTTTCATTAAATTTGAGTGCTCT 57.014 25.926 0.00 0.00 34.19 4.09
3314 5836 6.402226 GCGGAAAATACAGAAAGGACTAAGTG 60.402 42.308 0.00 0.00 0.00 3.16
3323 5845 2.892373 TGCGCGGAAAATACAGAAAG 57.108 45.000 8.83 0.00 0.00 2.62
3350 5872 2.203800 TACGTTGAGCATAAGAGCCG 57.796 50.000 0.00 0.00 34.23 5.52
3381 5903 2.473868 CGTGAATGCGTGTATGTGAACC 60.474 50.000 0.00 0.00 0.00 3.62
3391 5913 1.588404 GATGACCTACGTGAATGCGTG 59.412 52.381 0.00 0.00 45.33 5.34
3394 5916 1.209128 CGGATGACCTACGTGAATGC 58.791 55.000 0.00 0.00 0.00 3.56
3401 5932 1.244816 TATGAGCCGGATGACCTACG 58.755 55.000 5.05 0.00 0.00 3.51
3411 5942 2.353889 GCAATATGAGCATATGAGCCGG 59.646 50.000 6.97 0.00 34.45 6.13
3412 5943 3.004862 TGCAATATGAGCATATGAGCCG 58.995 45.455 6.97 4.14 37.02 5.52
3456 5987 2.291741 GTGGACAAAGAGGCTTGTGAAG 59.708 50.000 0.00 0.00 39.63 3.02
3485 6017 7.665559 TCATATATTTGGATTAGTTGGACAGCC 59.334 37.037 0.00 0.00 0.00 4.85
3545 6077 6.558014 AGAGAGAGAGAGAGAGAGAGAATCAT 59.442 42.308 0.00 0.00 37.82 2.45
3547 6079 6.418057 AGAGAGAGAGAGAGAGAGAGAATC 57.582 45.833 0.00 0.00 0.00 2.52
3548 6080 5.306678 GGAGAGAGAGAGAGAGAGAGAGAAT 59.693 48.000 0.00 0.00 0.00 2.40
3550 6082 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
3552 6084 3.309296 GGGAGAGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
3556 6088 2.587060 AGGGGAGAGAGAGAGAGAGA 57.413 55.000 0.00 0.00 0.00 3.10
3574 6106 8.950007 TTTAGGAGCCCCCATAAATTATTTAG 57.050 34.615 3.73 0.00 37.41 1.85
3591 6123 0.553333 AGGCCCCAGAATTTAGGAGC 59.447 55.000 0.00 0.00 0.00 4.70
3624 6343 0.179100 TAGATGAGCAGGTTCAGCGC 60.179 55.000 0.00 0.00 38.47 5.92
3658 6377 4.411540 AGTCTAGACCCTGTCGAAGGTATA 59.588 45.833 19.38 8.24 45.78 1.47
3670 6389 1.567175 GTCCTCTGGAGTCTAGACCCT 59.433 57.143 19.38 1.31 29.39 4.34
3689 6408 2.706190 GCCCTCTCATACCCATAGTTGT 59.294 50.000 0.00 0.00 0.00 3.32
3714 6433 0.827089 CCACACCTGCCATTTCCACA 60.827 55.000 0.00 0.00 0.00 4.17
3722 6441 2.290847 GAGATCTCCACACCTGCCA 58.709 57.895 12.00 0.00 0.00 4.92
3799 6518 4.142381 GCGGCAGAAAATTTCCTCTTATGT 60.142 41.667 1.57 0.00 0.00 2.29
3826 6545 1.669999 GCATGATGTGGTGCTTCCCC 61.670 60.000 0.00 0.00 38.30 4.81
3836 6555 2.831366 GCGCCTCCTGCATGATGTG 61.831 63.158 0.00 3.97 41.33 3.21
3837 6556 2.515523 GCGCCTCCTGCATGATGT 60.516 61.111 0.00 0.00 41.33 3.06
3838 6557 1.659622 TTTGCGCCTCCTGCATGATG 61.660 55.000 4.18 0.00 42.84 3.07
3908 6627 7.446106 TCCATTGTGGTACCTAGACATTAAT 57.554 36.000 14.36 0.00 39.03 1.40
3909 6628 6.877668 TCCATTGTGGTACCTAGACATTAA 57.122 37.500 14.36 0.00 39.03 1.40


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

AutoCloner maintained by Alex Coulton.