Multiple sequence alignment - TraesCS2D01G203100

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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 TraesCS2D01G203100 chr2D 100.000 7422 0 0 1 7422 155457120 155449699 0.000000e+00 13706.0
1 TraesCS2D01G203100 chr2D 82.568 2025 297 28 4397 6401 1607931 1609919 0.000000e+00 1733.0
2 TraesCS2D01G203100 chr2D 84.583 1187 142 28 1176 2334 1602008 1603181 0.000000e+00 1140.0
3 TraesCS2D01G203100 chr2D 85.590 576 77 4 2537 3108 1605966 1606539 3.830000e-167 599.0
4 TraesCS2D01G203100 chr2D 79.596 495 78 20 1162 1648 11068239 11067760 4.290000e-87 333.0
5 TraesCS2D01G203100 chr2A 94.826 3537 129 19 3903 7422 144859109 144862608 0.000000e+00 5469.0
6 TraesCS2D01G203100 chr2A 95.375 1254 46 4 1102 2346 144855078 144856328 0.000000e+00 1984.0
7 TraesCS2D01G203100 chr2A 95.148 845 35 3 2348 3192 144857429 144858267 0.000000e+00 1328.0
8 TraesCS2D01G203100 chr2A 83.983 949 121 22 2325 3257 634149 633216 0.000000e+00 881.0
9 TraesCS2D01G203100 chr2A 92.512 601 41 3 3193 3790 144858309 144858908 0.000000e+00 857.0
10 TraesCS2D01G203100 chr2A 80.628 924 113 20 1378 2262 635141 634245 0.000000e+00 654.0
11 TraesCS2D01G203100 chr2A 86.062 452 50 6 6503 6947 9109839 9110284 2.420000e-129 473.0
12 TraesCS2D01G203100 chr2A 81.457 453 70 5 6503 6947 9396428 9395982 7.080000e-95 359.0
13 TraesCS2D01G203100 chr2A 81.236 453 71 5 6503 6947 9848905 9848459 3.290000e-93 353.0
14 TraesCS2D01G203100 chr2A 94.030 134 5 3 3788 3919 144858942 144859074 4.540000e-47 200.0
15 TraesCS2D01G203100 chr2B 96.752 3110 73 16 1102 4194 212583264 212580166 0.000000e+00 5158.0
16 TraesCS2D01G203100 chr2B 98.815 2278 27 0 4222 6499 212580170 212577893 0.000000e+00 4058.0
17 TraesCS2D01G203100 chr2B 84.341 2184 291 28 4080 6244 10386556 10388707 0.000000e+00 2091.0
18 TraesCS2D01G203100 chr2B 84.693 1385 212 0 4503 5887 10616598 10617982 0.000000e+00 1384.0
19 TraesCS2D01G203100 chr2B 81.768 1629 261 20 4793 6398 10660723 10662338 0.000000e+00 1330.0
20 TraesCS2D01G203100 chr2B 95.219 732 17 3 6542 7256 212576912 212576182 0.000000e+00 1142.0
21 TraesCS2D01G203100 chr2B 84.139 1179 133 21 1176 2327 10382898 10384049 0.000000e+00 1092.0
22 TraesCS2D01G203100 chr2B 80.000 1140 174 35 1177 2304 10613283 10614380 0.000000e+00 793.0
23 TraesCS2D01G203100 chr2B 83.550 693 108 3 2412 3098 10385136 10385828 1.750000e-180 643.0
24 TraesCS2D01G203100 chr2B 79.499 639 117 10 2473 3102 10614962 10615595 6.830000e-120 442.0
25 TraesCS2D01G203100 chr2B 82.889 450 63 6 6503 6947 13130253 13130693 6.980000e-105 392.0
26 TraesCS2D01G203100 chr2B 94.253 174 8 2 7249 7422 212574522 212574351 1.590000e-66 265.0
27 TraesCS2D01G203100 chr2B 75.338 296 71 2 5518 5812 748514740 748515034 2.790000e-29 141.0
28 TraesCS2D01G203100 chr2B 100.000 43 0 0 6503 6545 212577065 212577023 6.170000e-11 80.5
29 TraesCS2D01G203100 chr1D 88.359 859 96 3 1 858 220417139 220416284 0.000000e+00 1029.0
30 TraesCS2D01G203100 chr7D 87.340 861 98 8 2 855 421170828 421171684 0.000000e+00 976.0
31 TraesCS2D01G203100 chr7D 86.842 836 98 8 12 842 465570096 465570924 0.000000e+00 924.0
32 TraesCS2D01G203100 chr7D 86.030 859 115 5 2 859 369148365 369149219 0.000000e+00 917.0
33 TraesCS2D01G203100 chr7D 85.229 853 116 8 1 849 497566246 497565400 0.000000e+00 869.0
34 TraesCS2D01G203100 chr7D 75.064 1171 246 31 4665 5812 571260563 571259416 3.090000e-138 503.0
35 TraesCS2D01G203100 chr7D 77.682 811 158 17 4918 5718 633595828 633596625 2.420000e-129 473.0
36 TraesCS2D01G203100 chr7D 77.297 185 32 7 6061 6236 621298376 621298559 4.740000e-17 100.0
37 TraesCS2D01G203100 chr1A 85.848 855 109 6 2 855 284154202 284153359 0.000000e+00 898.0
38 TraesCS2D01G203100 chr7B 85.714 861 109 11 2 858 457783018 457782168 0.000000e+00 896.0
39 TraesCS2D01G203100 chr7B 85.250 861 116 8 3 858 181356513 181355659 0.000000e+00 876.0
40 TraesCS2D01G203100 chr7B 75.893 784 143 24 4654 5417 750066758 750067515 7.080000e-95 359.0
41 TraesCS2D01G203100 chr7B 77.273 176 32 5 6066 6234 718834597 718834423 6.130000e-16 97.1
42 TraesCS2D01G203100 chr7B 74.370 238 46 10 2539 2770 718837888 718837660 3.690000e-13 87.9
43 TraesCS2D01G203100 chr3B 85.116 860 113 12 1 855 683011443 683012292 0.000000e+00 865.0
44 TraesCS2D01G203100 chr3B 86.207 58 3 4 3787 3843 673847775 673847722 2.890000e-04 58.4
45 TraesCS2D01G203100 chrUn 100.000 408 0 0 5128 5535 477940217 477939810 0.000000e+00 754.0
46 TraesCS2D01G203100 chr7A 74.896 1207 267 26 4623 5811 716418020 716419208 1.100000e-142 518.0
47 TraesCS2D01G203100 chr7A 75.291 1117 231 28 4649 5741 733341948 733340853 6.690000e-135 492.0
48 TraesCS2D01G203100 chr7A 77.174 184 34 5 6061 6236 716424165 716424348 4.740000e-17 100.0
49 TraesCS2D01G203100 chr7A 76.757 185 37 4 6056 6234 716419393 716419577 1.700000e-16 99.0
50 TraesCS2D01G203100 chr7A 92.105 38 3 0 4784 4821 271625783 271625746 4.000000e-03 54.7
51 TraesCS2D01G203100 chr4D 81.474 475 58 18 1175 1644 64730202 64729753 5.470000e-96 363.0
52 TraesCS2D01G203100 chr4D 78.300 447 82 8 6508 6947 464205883 464205445 2.640000e-69 274.0
53 TraesCS2D01G203100 chr4D 73.795 477 103 18 2610 3078 64728496 64728034 1.280000e-37 169.0
54 TraesCS2D01G203100 chr4B 81.450 469 57 19 1175 1638 95343531 95343974 2.550000e-94 357.0
55 TraesCS2D01G203100 chr4B 75.738 474 99 14 2610 3078 95345954 95346416 2.690000e-54 224.0
56 TraesCS2D01G203100 chr4A 81.450 469 57 19 1175 1638 531236898 531237341 2.550000e-94 357.0
57 TraesCS2D01G203100 chr3A 80.676 207 29 8 848 1049 88199694 88199894 4.640000e-32 150.0
58 TraesCS2D01G203100 chr6D 80.000 205 37 4 866 1068 423033561 423033359 1.670000e-31 148.0


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 TraesCS2D01G203100 chr2D 155449699 155457120 7421 True 13706.000000 13706 100.000000 1 7422 1 chr2D.!!$R2 7421
1 TraesCS2D01G203100 chr2D 1602008 1609919 7911 False 1157.333333 1733 84.247000 1176 6401 3 chr2D.!!$F1 5225
2 TraesCS2D01G203100 chr2A 144855078 144862608 7530 False 1967.600000 5469 94.378200 1102 7422 5 chr2A.!!$F2 6320
3 TraesCS2D01G203100 chr2A 633216 635141 1925 True 767.500000 881 82.305500 1378 3257 2 chr2A.!!$R3 1879
4 TraesCS2D01G203100 chr2B 212574351 212583264 8913 True 2140.700000 5158 97.007800 1102 7422 5 chr2B.!!$R1 6320
5 TraesCS2D01G203100 chr2B 10660723 10662338 1615 False 1330.000000 1330 81.768000 4793 6398 1 chr2B.!!$F1 1605
6 TraesCS2D01G203100 chr2B 10382898 10388707 5809 False 1275.333333 2091 84.010000 1176 6244 3 chr2B.!!$F4 5068
7 TraesCS2D01G203100 chr2B 10613283 10617982 4699 False 873.000000 1384 81.397333 1177 5887 3 chr2B.!!$F5 4710
8 TraesCS2D01G203100 chr1D 220416284 220417139 855 True 1029.000000 1029 88.359000 1 858 1 chr1D.!!$R1 857
9 TraesCS2D01G203100 chr7D 421170828 421171684 856 False 976.000000 976 87.340000 2 855 1 chr7D.!!$F2 853
10 TraesCS2D01G203100 chr7D 465570096 465570924 828 False 924.000000 924 86.842000 12 842 1 chr7D.!!$F3 830
11 TraesCS2D01G203100 chr7D 369148365 369149219 854 False 917.000000 917 86.030000 2 859 1 chr7D.!!$F1 857
12 TraesCS2D01G203100 chr7D 497565400 497566246 846 True 869.000000 869 85.229000 1 849 1 chr7D.!!$R1 848
13 TraesCS2D01G203100 chr7D 571259416 571260563 1147 True 503.000000 503 75.064000 4665 5812 1 chr7D.!!$R2 1147
14 TraesCS2D01G203100 chr7D 633595828 633596625 797 False 473.000000 473 77.682000 4918 5718 1 chr7D.!!$F5 800
15 TraesCS2D01G203100 chr1A 284153359 284154202 843 True 898.000000 898 85.848000 2 855 1 chr1A.!!$R1 853
16 TraesCS2D01G203100 chr7B 457782168 457783018 850 True 896.000000 896 85.714000 2 858 1 chr7B.!!$R2 856
17 TraesCS2D01G203100 chr7B 181355659 181356513 854 True 876.000000 876 85.250000 3 858 1 chr7B.!!$R1 855
18 TraesCS2D01G203100 chr7B 750066758 750067515 757 False 359.000000 359 75.893000 4654 5417 1 chr7B.!!$F1 763
19 TraesCS2D01G203100 chr3B 683011443 683012292 849 False 865.000000 865 85.116000 1 855 1 chr3B.!!$F1 854
20 TraesCS2D01G203100 chr7A 733340853 733341948 1095 True 492.000000 492 75.291000 4649 5741 1 chr7A.!!$R2 1092
21 TraesCS2D01G203100 chr7A 716418020 716419577 1557 False 308.500000 518 75.826500 4623 6234 2 chr7A.!!$F2 1611
22 TraesCS2D01G203100 chr4D 64728034 64730202 2168 True 266.000000 363 77.634500 1175 3078 2 chr4D.!!$R2 1903
23 TraesCS2D01G203100 chr4B 95343531 95346416 2885 False 290.500000 357 78.594000 1175 3078 2 chr4B.!!$F1 1903

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
984 1006 0.098728 AATTGGCGCGCACTGATTAC 59.901 50.000 34.42 13.35 0.00 1.89 F
989 1011 0.373370 GCGCGCACTGATTACATGAA 59.627 50.000 29.10 0.00 0.00 2.57 F
1095 1117 0.744414 GCGGATTTGCCAGCTGTAGA 60.744 55.000 13.81 0.00 35.94 2.59 F
1972 2076 0.179089 CGGCTCAGTTCTATGCAGCT 60.179 55.000 0.00 0.00 0.00 4.24 F
1984 2088 0.326427 ATGCAGCTTCCTCCTCTCCT 60.326 55.000 0.00 0.00 0.00 3.69 F
2832 7697 1.338769 ACTTGTGTACGATGGGAAGCC 60.339 52.381 0.00 0.00 0.00 4.35 F
3446 8646 3.266510 TCACTGGAATGTGCTATCCAC 57.733 47.619 0.00 0.00 40.74 4.02 F
6258 12381 1.068895 CTCAAGGCTGATCTCATCGCT 59.931 52.381 0.00 0.00 0.00 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1943 2047 0.759346 AACTGAGCCGTCAAAGACCT 59.241 50.000 0.00 0.00 30.14 3.85 R
1972 2076 1.380515 CTCGCCAGGAGAGGAGGAA 60.381 63.158 12.38 0.00 46.23 3.36 R
2194 2307 1.483415 GCTACCTCGAATTGGTGGGTA 59.517 52.381 12.41 12.04 38.42 3.69 R
3450 8650 0.881118 GACCGCAACAACATCCACAT 59.119 50.000 0.00 0.00 0.00 3.21 R
3523 8723 2.674852 CTGGAACGTCAACATGATCCAG 59.325 50.000 12.80 12.80 41.79 3.86 R
4010 9308 1.271108 TGTTGCTGCGGGAATCAGTTA 60.271 47.619 1.67 0.00 34.21 2.24 R
6313 12436 1.027255 TCAGGACGAAGAGGCTCTCG 61.027 60.000 24.70 24.70 35.36 4.04 R
7375 16122 2.458592 ATAAGCAAAGCAATCGACGC 57.541 45.000 0.36 0.36 0.00 5.19 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 47 2.818169 GGTGGATATGAGGGCGCCA 61.818 63.158 30.85 8.42 0.00 5.69
78 79 4.308458 CGTCGGACCCAACAGCCA 62.308 66.667 1.91 0.00 0.00 4.75
125 127 0.402861 ACCAAACCCTTCCTCCTCCA 60.403 55.000 0.00 0.00 0.00 3.86
206 208 3.706373 CCTCACCACCAGTCCCGG 61.706 72.222 0.00 0.00 0.00 5.73
217 219 2.125961 AGTCCCGGTCCATCGCTAC 61.126 63.158 0.00 0.00 0.00 3.58
360 370 2.757508 CAGCGAGAGAGGGAGGCA 60.758 66.667 0.00 0.00 0.00 4.75
402 419 0.798776 CGAACATGGTGGAGCAGTTC 59.201 55.000 0.00 0.00 36.22 3.01
413 430 1.304879 AGCAGTTCTCTCCTCCGCT 60.305 57.895 0.00 0.00 0.00 5.52
495 512 1.909302 GTTGGGACAGAGGAGGATTCA 59.091 52.381 0.00 0.00 42.39 2.57
702 724 7.011389 CGATCAGATTTTTGCATAGACCACTAA 59.989 37.037 0.00 0.00 32.04 2.24
707 729 9.193806 AGATTTTTGCATAGACCACTAATTCAT 57.806 29.630 0.00 0.00 32.04 2.57
748 770 7.225784 TGTTTGCAAACCATAATCATGTAGT 57.774 32.000 33.33 0.00 38.11 2.73
759 781 6.366332 CCATAATCATGTAGTAGGCGTTCTTC 59.634 42.308 0.00 0.00 0.00 2.87
789 811 6.831868 ACATGATCAATGACAATGAAGATCCA 59.168 34.615 12.30 0.00 38.72 3.41
820 842 1.215423 AGTATGAATTGGAGGCCACCC 59.785 52.381 17.45 12.02 30.78 4.61
837 859 1.079888 CCCCGCATTTGAAGTTGGC 60.080 57.895 0.00 0.00 0.00 4.52
855 877 3.732212 TGGCACAATATCCGATCTCAAG 58.268 45.455 0.00 0.00 31.92 3.02
859 881 4.321718 CACAATATCCGATCTCAAGCCAT 58.678 43.478 0.00 0.00 0.00 4.40
860 882 4.391216 CACAATATCCGATCTCAAGCCATC 59.609 45.833 0.00 0.00 0.00 3.51
861 883 3.902881 ATATCCGATCTCAAGCCATCC 57.097 47.619 0.00 0.00 0.00 3.51
862 884 1.427809 ATCCGATCTCAAGCCATCCA 58.572 50.000 0.00 0.00 0.00 3.41
863 885 1.427809 TCCGATCTCAAGCCATCCAT 58.572 50.000 0.00 0.00 0.00 3.41
864 886 1.345741 TCCGATCTCAAGCCATCCATC 59.654 52.381 0.00 0.00 0.00 3.51
865 887 1.071228 CCGATCTCAAGCCATCCATCA 59.929 52.381 0.00 0.00 0.00 3.07
866 888 2.141517 CGATCTCAAGCCATCCATCAC 58.858 52.381 0.00 0.00 0.00 3.06
867 889 2.141517 GATCTCAAGCCATCCATCACG 58.858 52.381 0.00 0.00 0.00 4.35
868 890 0.462581 TCTCAAGCCATCCATCACGC 60.463 55.000 0.00 0.00 0.00 5.34
869 891 0.463295 CTCAAGCCATCCATCACGCT 60.463 55.000 0.00 0.00 0.00 5.07
870 892 0.462581 TCAAGCCATCCATCACGCTC 60.463 55.000 0.00 0.00 0.00 5.03
871 893 1.522355 AAGCCATCCATCACGCTCG 60.522 57.895 0.00 0.00 0.00 5.03
872 894 2.930385 AAGCCATCCATCACGCTCGG 62.930 60.000 0.00 0.00 0.00 4.63
873 895 2.814604 CCATCCATCACGCTCGGA 59.185 61.111 0.00 0.00 0.00 4.55
874 896 1.592669 CCATCCATCACGCTCGGAC 60.593 63.158 0.00 0.00 0.00 4.79
875 897 1.141665 CATCCATCACGCTCGGACA 59.858 57.895 0.00 0.00 0.00 4.02
876 898 0.249615 CATCCATCACGCTCGGACAT 60.250 55.000 0.00 0.00 0.00 3.06
877 899 0.465705 ATCCATCACGCTCGGACATT 59.534 50.000 0.00 0.00 0.00 2.71
878 900 0.460109 TCCATCACGCTCGGACATTG 60.460 55.000 0.00 0.00 0.00 2.82
879 901 0.460109 CCATCACGCTCGGACATTGA 60.460 55.000 0.00 0.00 0.00 2.57
880 902 1.358877 CATCACGCTCGGACATTGAA 58.641 50.000 0.00 0.00 0.00 2.69
881 903 1.935873 CATCACGCTCGGACATTGAAT 59.064 47.619 0.00 0.00 0.00 2.57
882 904 2.093306 TCACGCTCGGACATTGAATT 57.907 45.000 0.00 0.00 0.00 2.17
883 905 1.999735 TCACGCTCGGACATTGAATTC 59.000 47.619 0.00 0.00 0.00 2.17
884 906 1.731709 CACGCTCGGACATTGAATTCA 59.268 47.619 3.38 3.38 0.00 2.57
885 907 2.352651 CACGCTCGGACATTGAATTCAT 59.647 45.455 9.40 0.00 0.00 2.57
886 908 3.009723 ACGCTCGGACATTGAATTCATT 58.990 40.909 9.40 2.66 0.00 2.57
887 909 3.440173 ACGCTCGGACATTGAATTCATTT 59.560 39.130 9.40 0.00 0.00 2.32
888 910 4.082787 ACGCTCGGACATTGAATTCATTTT 60.083 37.500 9.40 0.00 0.00 1.82
889 911 4.263677 CGCTCGGACATTGAATTCATTTTG 59.736 41.667 9.40 10.02 0.00 2.44
890 912 4.563976 GCTCGGACATTGAATTCATTTTGG 59.436 41.667 9.40 0.31 0.00 3.28
891 913 4.493547 TCGGACATTGAATTCATTTTGGC 58.506 39.130 9.40 9.60 0.00 4.52
892 914 4.021632 TCGGACATTGAATTCATTTTGGCA 60.022 37.500 9.40 0.00 0.00 4.92
893 915 4.871557 CGGACATTGAATTCATTTTGGCAT 59.128 37.500 9.40 0.00 0.00 4.40
894 916 5.220510 CGGACATTGAATTCATTTTGGCATG 60.221 40.000 9.40 10.33 0.00 4.06
895 917 5.644636 GGACATTGAATTCATTTTGGCATGT 59.355 36.000 15.94 15.94 0.00 3.21
896 918 6.183360 GGACATTGAATTCATTTTGGCATGTC 60.183 38.462 25.44 25.44 34.51 3.06
897 919 5.644636 ACATTGAATTCATTTTGGCATGTCC 59.355 36.000 9.40 0.00 0.00 4.02
898 920 3.847542 TGAATTCATTTTGGCATGTCCG 58.152 40.909 3.38 0.00 37.80 4.79
899 921 2.965572 ATTCATTTTGGCATGTCCGG 57.034 45.000 0.00 0.00 37.80 5.14
900 922 1.626686 TTCATTTTGGCATGTCCGGT 58.373 45.000 0.00 0.00 37.80 5.28
901 923 1.626686 TCATTTTGGCATGTCCGGTT 58.373 45.000 0.00 0.00 37.80 4.44
902 924 1.967066 TCATTTTGGCATGTCCGGTTT 59.033 42.857 0.00 0.00 37.80 3.27
903 925 2.067766 CATTTTGGCATGTCCGGTTTG 58.932 47.619 0.00 0.00 37.80 2.93
904 926 1.115467 TTTTGGCATGTCCGGTTTGT 58.885 45.000 0.00 0.00 37.80 2.83
905 927 1.115467 TTTGGCATGTCCGGTTTGTT 58.885 45.000 0.00 0.00 37.80 2.83
906 928 1.982660 TTGGCATGTCCGGTTTGTTA 58.017 45.000 0.00 0.00 37.80 2.41
907 929 1.982660 TGGCATGTCCGGTTTGTTAA 58.017 45.000 0.00 0.00 37.80 2.01
908 930 2.307768 TGGCATGTCCGGTTTGTTAAA 58.692 42.857 0.00 0.00 37.80 1.52
909 931 2.894126 TGGCATGTCCGGTTTGTTAAAT 59.106 40.909 0.00 0.00 37.80 1.40
910 932 3.322254 TGGCATGTCCGGTTTGTTAAATT 59.678 39.130 0.00 0.00 37.80 1.82
911 933 4.523173 TGGCATGTCCGGTTTGTTAAATTA 59.477 37.500 0.00 0.00 37.80 1.40
912 934 5.186021 TGGCATGTCCGGTTTGTTAAATTAT 59.814 36.000 0.00 0.00 37.80 1.28
913 935 6.377429 TGGCATGTCCGGTTTGTTAAATTATA 59.623 34.615 0.00 0.00 37.80 0.98
914 936 7.093902 TGGCATGTCCGGTTTGTTAAATTATAA 60.094 33.333 0.00 0.00 37.80 0.98
915 937 7.923878 GGCATGTCCGGTTTGTTAAATTATAAT 59.076 33.333 0.00 0.00 0.00 1.28
916 938 9.308318 GCATGTCCGGTTTGTTAAATTATAATT 57.692 29.630 4.81 4.81 0.00 1.40
919 941 9.141400 TGTCCGGTTTGTTAAATTATAATTTGC 57.859 29.630 26.61 20.18 38.90 3.68
920 942 9.361315 GTCCGGTTTGTTAAATTATAATTTGCT 57.639 29.630 26.61 9.29 38.90 3.91
921 943 9.930693 TCCGGTTTGTTAAATTATAATTTGCTT 57.069 25.926 26.61 8.98 38.90 3.91
932 954 8.953507 AATTATAATTTGCTTTGCTTTGTTGC 57.046 26.923 4.81 0.00 0.00 4.17
933 955 3.322230 AATTTGCTTTGCTTTGTTGCG 57.678 38.095 0.00 0.00 35.36 4.85
934 956 2.001812 TTTGCTTTGCTTTGTTGCGA 57.998 40.000 0.00 0.00 35.36 5.10
935 957 2.001812 TTGCTTTGCTTTGTTGCGAA 57.998 40.000 0.00 0.00 35.32 4.70
936 958 2.222007 TGCTTTGCTTTGTTGCGAAT 57.778 40.000 0.00 0.00 35.96 3.34
937 959 2.548875 TGCTTTGCTTTGTTGCGAATT 58.451 38.095 0.00 0.00 35.96 2.17
938 960 3.711086 TGCTTTGCTTTGTTGCGAATTA 58.289 36.364 0.00 0.00 35.96 1.40
939 961 4.305769 TGCTTTGCTTTGTTGCGAATTAT 58.694 34.783 0.00 0.00 35.96 1.28
940 962 4.749099 TGCTTTGCTTTGTTGCGAATTATT 59.251 33.333 0.00 0.00 35.96 1.40
941 963 5.074791 GCTTTGCTTTGTTGCGAATTATTG 58.925 37.500 0.00 0.00 35.96 1.90
942 964 5.107530 GCTTTGCTTTGTTGCGAATTATTGA 60.108 36.000 0.00 0.00 35.96 2.57
943 965 6.563753 GCTTTGCTTTGTTGCGAATTATTGAA 60.564 34.615 0.00 0.00 35.96 2.69
944 966 7.418840 TTTGCTTTGTTGCGAATTATTGAAT 57.581 28.000 0.00 0.00 31.98 2.57
945 967 7.418840 TTGCTTTGTTGCGAATTATTGAATT 57.581 28.000 0.00 0.00 38.00 2.17
946 968 8.526218 TTGCTTTGTTGCGAATTATTGAATTA 57.474 26.923 0.00 0.00 35.33 1.40
947 969 8.526218 TGCTTTGTTGCGAATTATTGAATTAA 57.474 26.923 0.00 0.00 35.33 1.40
948 970 8.646356 TGCTTTGTTGCGAATTATTGAATTAAG 58.354 29.630 0.00 0.00 35.33 1.85
949 971 8.859156 GCTTTGTTGCGAATTATTGAATTAAGA 58.141 29.630 0.00 0.00 35.33 2.10
973 995 9.840427 AGATAATTTGTATTGTATAATTGGCGC 57.160 29.630 0.00 0.00 0.00 6.53
974 996 6.984740 AATTTGTATTGTATAATTGGCGCG 57.015 33.333 0.00 0.00 0.00 6.86
975 997 3.529634 TGTATTGTATAATTGGCGCGC 57.470 42.857 25.94 25.94 0.00 6.86
976 998 2.872858 TGTATTGTATAATTGGCGCGCA 59.127 40.909 34.42 14.59 0.00 6.09
977 999 2.399396 ATTGTATAATTGGCGCGCAC 57.601 45.000 34.42 22.27 0.00 5.34
978 1000 1.374560 TTGTATAATTGGCGCGCACT 58.625 45.000 34.42 15.76 0.00 4.40
979 1001 0.655208 TGTATAATTGGCGCGCACTG 59.345 50.000 34.42 0.00 0.00 3.66
980 1002 0.934496 GTATAATTGGCGCGCACTGA 59.066 50.000 34.42 15.37 0.00 3.41
981 1003 1.531149 GTATAATTGGCGCGCACTGAT 59.469 47.619 34.42 20.00 0.00 2.90
982 1004 1.024271 ATAATTGGCGCGCACTGATT 58.976 45.000 34.42 25.08 0.00 2.57
983 1005 1.657822 TAATTGGCGCGCACTGATTA 58.342 45.000 34.42 24.11 0.00 1.75
984 1006 0.098728 AATTGGCGCGCACTGATTAC 59.901 50.000 34.42 13.35 0.00 1.89
985 1007 1.024046 ATTGGCGCGCACTGATTACA 61.024 50.000 34.42 16.12 0.00 2.41
986 1008 1.024046 TTGGCGCGCACTGATTACAT 61.024 50.000 34.42 0.00 0.00 2.29
987 1009 1.010797 GGCGCGCACTGATTACATG 60.011 57.895 34.42 0.00 0.00 3.21
988 1010 1.428370 GGCGCGCACTGATTACATGA 61.428 55.000 34.42 0.00 0.00 3.07
989 1011 0.373370 GCGCGCACTGATTACATGAA 59.627 50.000 29.10 0.00 0.00 2.57
990 1012 1.003545 GCGCGCACTGATTACATGAAT 60.004 47.619 29.10 0.00 0.00 2.57
991 1013 2.539547 GCGCGCACTGATTACATGAATT 60.540 45.455 29.10 0.00 0.00 2.17
992 1014 3.683989 CGCGCACTGATTACATGAATTT 58.316 40.909 8.75 0.00 0.00 1.82
993 1015 3.479590 CGCGCACTGATTACATGAATTTG 59.520 43.478 8.75 0.00 0.00 2.32
994 1016 4.661125 GCGCACTGATTACATGAATTTGA 58.339 39.130 0.30 0.00 0.00 2.69
995 1017 4.731961 GCGCACTGATTACATGAATTTGAG 59.268 41.667 0.30 0.00 0.00 3.02
996 1018 5.268544 CGCACTGATTACATGAATTTGAGG 58.731 41.667 0.00 0.00 0.00 3.86
997 1019 5.065090 CGCACTGATTACATGAATTTGAGGA 59.935 40.000 0.00 0.00 0.00 3.71
998 1020 6.238566 CGCACTGATTACATGAATTTGAGGAT 60.239 38.462 0.00 0.00 0.00 3.24
999 1021 7.137426 GCACTGATTACATGAATTTGAGGATC 58.863 38.462 0.00 0.00 0.00 3.36
1017 1039 8.217131 TGAGGATCACAATTTTGAGATATGTG 57.783 34.615 0.23 0.00 42.56 3.21
1018 1040 7.283807 TGAGGATCACAATTTTGAGATATGTGG 59.716 37.037 0.23 0.00 42.56 4.17
1019 1041 7.348815 AGGATCACAATTTTGAGATATGTGGA 58.651 34.615 0.23 0.00 41.23 4.02
1020 1042 8.003044 AGGATCACAATTTTGAGATATGTGGAT 58.997 33.333 0.23 0.00 41.23 3.41
1021 1043 8.080417 GGATCACAATTTTGAGATATGTGGATG 58.920 37.037 0.23 0.00 41.23 3.51
1022 1044 8.756486 ATCACAATTTTGAGATATGTGGATGA 57.244 30.769 0.23 0.00 41.23 2.92
1023 1045 8.217131 TCACAATTTTGAGATATGTGGATGAG 57.783 34.615 4.58 0.00 41.23 2.90
1024 1046 7.830697 TCACAATTTTGAGATATGTGGATGAGT 59.169 33.333 4.58 0.00 41.23 3.41
1025 1047 9.112725 CACAATTTTGAGATATGTGGATGAGTA 57.887 33.333 0.00 0.00 38.13 2.59
1026 1048 9.334947 ACAATTTTGAGATATGTGGATGAGTAG 57.665 33.333 0.00 0.00 0.00 2.57
1027 1049 9.334947 CAATTTTGAGATATGTGGATGAGTAGT 57.665 33.333 0.00 0.00 0.00 2.73
1028 1050 8.899427 ATTTTGAGATATGTGGATGAGTAGTG 57.101 34.615 0.00 0.00 0.00 2.74
1029 1051 7.423844 TTTGAGATATGTGGATGAGTAGTGT 57.576 36.000 0.00 0.00 0.00 3.55
1030 1052 8.533569 TTTGAGATATGTGGATGAGTAGTGTA 57.466 34.615 0.00 0.00 0.00 2.90
1031 1053 8.533569 TTGAGATATGTGGATGAGTAGTGTAA 57.466 34.615 0.00 0.00 0.00 2.41
1032 1054 8.712228 TGAGATATGTGGATGAGTAGTGTAAT 57.288 34.615 0.00 0.00 0.00 1.89
1033 1055 9.807921 TGAGATATGTGGATGAGTAGTGTAATA 57.192 33.333 0.00 0.00 0.00 0.98
1040 1062 9.025041 TGTGGATGAGTAGTGTAATATATGAGG 57.975 37.037 0.00 0.00 0.00 3.86
1041 1063 8.470805 GTGGATGAGTAGTGTAATATATGAGGG 58.529 40.741 0.00 0.00 0.00 4.30
1042 1064 7.619698 TGGATGAGTAGTGTAATATATGAGGGG 59.380 40.741 0.00 0.00 0.00 4.79
1043 1065 6.852420 TGAGTAGTGTAATATATGAGGGGC 57.148 41.667 0.00 0.00 0.00 5.80
1044 1066 5.720041 TGAGTAGTGTAATATATGAGGGGCC 59.280 44.000 0.00 0.00 0.00 5.80
1045 1067 4.710375 AGTAGTGTAATATATGAGGGGCCG 59.290 45.833 0.00 0.00 0.00 6.13
1046 1068 2.838202 AGTGTAATATATGAGGGGCCGG 59.162 50.000 0.00 0.00 0.00 6.13
1047 1069 1.557832 TGTAATATATGAGGGGCCGGC 59.442 52.381 21.18 21.18 0.00 6.13
1048 1070 0.828022 TAATATATGAGGGGCCGGCG 59.172 55.000 22.54 0.00 0.00 6.46
1049 1071 1.910580 AATATATGAGGGGCCGGCGG 61.911 60.000 24.35 24.35 0.00 6.13
1071 1093 4.842091 GTCCACGGACGCGCGTAT 62.842 66.667 37.91 21.77 35.30 3.06
1072 1094 3.201297 TCCACGGACGCGCGTATA 61.201 61.111 37.91 14.59 0.00 1.47
1073 1095 2.724721 CCACGGACGCGCGTATAG 60.725 66.667 37.91 29.42 0.00 1.31
1074 1096 2.724721 CACGGACGCGCGTATAGG 60.725 66.667 37.91 25.43 0.00 2.57
1075 1097 3.957535 ACGGACGCGCGTATAGGG 61.958 66.667 37.91 23.63 0.00 3.53
1076 1098 4.695231 CGGACGCGCGTATAGGGG 62.695 72.222 37.91 16.93 0.00 4.79
1084 1106 2.540145 GCGTATAGGGGCGGATTTG 58.460 57.895 0.00 0.00 0.00 2.32
1085 1107 1.574702 GCGTATAGGGGCGGATTTGC 61.575 60.000 0.00 0.00 0.00 3.68
1093 1115 3.903783 GCGGATTTGCCAGCTGTA 58.096 55.556 13.81 0.00 35.94 2.74
1094 1116 1.723870 GCGGATTTGCCAGCTGTAG 59.276 57.895 13.81 0.00 35.94 2.74
1095 1117 0.744414 GCGGATTTGCCAGCTGTAGA 60.744 55.000 13.81 0.00 35.94 2.59
1096 1118 1.959042 CGGATTTGCCAGCTGTAGAT 58.041 50.000 13.81 1.91 35.94 1.98
1097 1119 1.600957 CGGATTTGCCAGCTGTAGATG 59.399 52.381 13.81 0.00 35.94 2.90
1098 1120 2.742856 CGGATTTGCCAGCTGTAGATGA 60.743 50.000 13.81 0.00 35.94 2.92
1099 1121 3.484407 GGATTTGCCAGCTGTAGATGAT 58.516 45.455 13.81 0.00 36.34 2.45
1100 1122 3.501445 GGATTTGCCAGCTGTAGATGATC 59.499 47.826 13.81 8.01 36.34 2.92
1116 1138 3.680642 TGATCTAATTGAAAGCAGCGC 57.319 42.857 0.00 0.00 0.00 5.92
1681 1746 1.078143 GGTTTCCTCCTGCGATGCT 60.078 57.895 0.00 0.00 0.00 3.79
1731 1796 2.158957 TCTTCGAGGCGGCATTTAGAAT 60.159 45.455 13.08 0.00 0.00 2.40
1943 2047 0.834261 TGATCCCCACCAGTTCGTCA 60.834 55.000 0.00 0.00 0.00 4.35
1972 2076 0.179089 CGGCTCAGTTCTATGCAGCT 60.179 55.000 0.00 0.00 0.00 4.24
1973 2077 1.741732 CGGCTCAGTTCTATGCAGCTT 60.742 52.381 0.00 0.00 0.00 3.74
1984 2088 0.326427 ATGCAGCTTCCTCCTCTCCT 60.326 55.000 0.00 0.00 0.00 3.69
2194 2307 1.384989 GCAGCTGCATCATCTTGCCT 61.385 55.000 33.36 0.00 42.06 4.75
2832 7697 1.338769 ACTTGTGTACGATGGGAAGCC 60.339 52.381 0.00 0.00 0.00 4.35
3446 8646 3.266510 TCACTGGAATGTGCTATCCAC 57.733 47.619 0.00 0.00 40.74 4.02
4083 9381 8.911918 ATGTAGTAAATGTTGTTACTGTTCCA 57.088 30.769 7.66 1.38 42.82 3.53
4336 9979 5.642063 TGCTTGTGCTACCTAAATAGTGAAC 59.358 40.000 0.00 0.00 40.48 3.18
6258 12381 1.068895 CTCAAGGCTGATCTCATCGCT 59.931 52.381 0.00 0.00 0.00 4.93
6307 12430 5.253330 AGAAACCTGTTGTGAAGTTTGAGA 58.747 37.500 0.00 0.00 32.80 3.27
6351 12475 2.576191 TGATAGTTTGGGAGGTCAAGGG 59.424 50.000 0.00 0.00 0.00 3.95
6431 12555 0.190815 AAACATCAAACCTGGGGCCT 59.809 50.000 0.84 0.00 0.00 5.19
6457 12581 0.973632 TCCACAGCGGTCACATTAGT 59.026 50.000 0.00 0.00 35.57 2.24
6499 12623 5.601313 TCCTAAGATTAGCGGGTGTCTTAAT 59.399 40.000 13.86 0.00 34.01 1.40
6500 12624 6.099269 TCCTAAGATTAGCGGGTGTCTTAATT 59.901 38.462 13.86 0.00 34.01 1.40
6548 13610 7.364522 TGATTGAGACATTAGTTGTACAAGC 57.635 36.000 8.98 4.38 39.18 4.01
6652 13714 5.010282 ACATGCGGAGAGGTTTCTTTTAAT 58.990 37.500 0.00 0.00 32.53 1.40
6722 13784 8.679288 GAACATTAAGGTTCATTCTCAACATG 57.321 34.615 24.08 0.00 45.07 3.21
6764 13826 2.504367 ACAAGTGTACCTGGCACATTC 58.496 47.619 2.51 0.00 38.20 2.67
6840 13902 2.554344 GGTCTACACTCCCAAATGCCAA 60.554 50.000 0.00 0.00 0.00 4.52
6907 13969 6.850752 AAAATAGGTTTCACCGATCCAAAT 57.149 33.333 0.00 0.00 44.90 2.32
7031 14093 3.537337 TCCCTTTTGTCCTCCCAGATTA 58.463 45.455 0.00 0.00 0.00 1.75
7091 14153 5.334879 GGAAAGCAACTGTAGTAACACCATG 60.335 44.000 0.00 0.00 0.00 3.66
7224 14303 2.039787 TGCCGGTGAGGGGTATGA 59.960 61.111 1.90 0.00 41.48 2.15
7267 16013 5.405269 GGTTTGATTATGTGGTTTGTTCTGC 59.595 40.000 0.00 0.00 0.00 4.26
7278 16024 3.243401 GGTTTGTTCTGCGAGGTTTCAAT 60.243 43.478 0.00 0.00 0.00 2.57
7279 16025 4.359706 GTTTGTTCTGCGAGGTTTCAATT 58.640 39.130 0.00 0.00 0.00 2.32
7375 16122 3.152341 AGAGCTGTTCCTGGTTTGATTG 58.848 45.455 0.00 0.00 0.00 2.67
7376 16123 1.615392 AGCTGTTCCTGGTTTGATTGC 59.385 47.619 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 3.953775 CGGTGGGGTCTGGCTGTT 61.954 66.667 0.00 0.00 0.00 3.16
78 79 2.275380 GCAATTTGCGGTGGGGTCT 61.275 57.895 5.49 0.00 31.71 3.85
136 138 2.265904 GGCACGGGAAAGGTTGGAC 61.266 63.158 0.00 0.00 0.00 4.02
206 208 1.065701 ACGACATCTGTAGCGATGGAC 59.934 52.381 5.85 0.00 43.92 4.02
217 219 2.202797 CGGGCTGGACGACATCTG 60.203 66.667 0.00 0.00 0.00 2.90
311 321 3.871248 AACTTCCGGGCGACGTTCC 62.871 63.158 0.00 0.00 42.24 3.62
370 387 3.119096 GTTCGAACCTCCCTGCGC 61.119 66.667 17.68 0.00 0.00 6.09
433 450 4.207281 CGGCGCTCGGATGGAAGA 62.207 66.667 7.64 0.00 34.75 2.87
702 724 6.334989 ACATTCATCATGTGCGAAAATGAAT 58.665 32.000 0.00 9.54 45.12 2.57
707 729 4.150274 GCAAACATTCATCATGTGCGAAAA 59.850 37.500 0.00 0.00 46.23 2.29
726 748 7.416213 GCCTACTACATGATTATGGTTTGCAAA 60.416 37.037 8.05 8.05 38.66 3.68
759 781 6.354039 TCATTGTCATTGATCATGTTCGAG 57.646 37.500 0.00 0.00 34.06 4.04
789 811 4.019681 TCCAATTCATACTCCACTTCGGTT 60.020 41.667 0.00 0.00 35.57 4.44
820 842 0.667184 GTGCCAACTTCAAATGCGGG 60.667 55.000 0.00 0.00 0.00 6.13
837 859 3.732212 TGGCTTGAGATCGGATATTGTG 58.268 45.455 0.00 0.00 0.00 3.33
855 877 2.969238 CCGAGCGTGATGGATGGC 60.969 66.667 0.00 0.00 0.00 4.40
859 881 0.460109 CAATGTCCGAGCGTGATGGA 60.460 55.000 0.00 0.00 0.00 3.41
860 882 0.460109 TCAATGTCCGAGCGTGATGG 60.460 55.000 0.00 0.00 0.00 3.51
861 883 1.358877 TTCAATGTCCGAGCGTGATG 58.641 50.000 0.00 0.00 0.00 3.07
862 884 2.315925 ATTCAATGTCCGAGCGTGAT 57.684 45.000 0.00 0.00 0.00 3.06
863 885 1.999735 GAATTCAATGTCCGAGCGTGA 59.000 47.619 0.00 0.00 0.00 4.35
864 886 1.731709 TGAATTCAATGTCCGAGCGTG 59.268 47.619 5.45 0.00 0.00 5.34
865 887 2.093306 TGAATTCAATGTCCGAGCGT 57.907 45.000 5.45 0.00 0.00 5.07
866 888 3.680642 AATGAATTCAATGTCCGAGCG 57.319 42.857 13.09 0.00 0.00 5.03
867 889 4.563976 CCAAAATGAATTCAATGTCCGAGC 59.436 41.667 13.09 0.00 0.00 5.03
868 890 4.563976 GCCAAAATGAATTCAATGTCCGAG 59.436 41.667 13.09 1.20 0.00 4.63
869 891 4.021632 TGCCAAAATGAATTCAATGTCCGA 60.022 37.500 13.09 0.00 0.00 4.55
870 892 4.244066 TGCCAAAATGAATTCAATGTCCG 58.756 39.130 13.09 0.15 0.00 4.79
871 893 5.644636 ACATGCCAAAATGAATTCAATGTCC 59.355 36.000 13.09 6.30 0.00 4.02
872 894 6.183360 GGACATGCCAAAATGAATTCAATGTC 60.183 38.462 25.44 25.44 36.34 3.06
873 895 5.644636 GGACATGCCAAAATGAATTCAATGT 59.355 36.000 13.09 14.83 36.34 2.71
874 896 5.220510 CGGACATGCCAAAATGAATTCAATG 60.221 40.000 13.09 11.76 35.94 2.82
875 897 4.871557 CGGACATGCCAAAATGAATTCAAT 59.128 37.500 13.09 0.02 35.94 2.57
876 898 4.244066 CGGACATGCCAAAATGAATTCAA 58.756 39.130 13.09 0.00 35.94 2.69
877 899 3.368220 CCGGACATGCCAAAATGAATTCA 60.368 43.478 11.26 11.26 35.94 2.57
878 900 3.189285 CCGGACATGCCAAAATGAATTC 58.811 45.455 0.00 0.00 35.94 2.17
879 901 2.566724 ACCGGACATGCCAAAATGAATT 59.433 40.909 9.46 0.00 35.94 2.17
880 902 2.178580 ACCGGACATGCCAAAATGAAT 58.821 42.857 9.46 0.00 35.94 2.57
881 903 1.626686 ACCGGACATGCCAAAATGAA 58.373 45.000 9.46 0.00 35.94 2.57
882 904 1.626686 AACCGGACATGCCAAAATGA 58.373 45.000 9.46 0.00 35.94 2.57
883 905 2.067766 CAAACCGGACATGCCAAAATG 58.932 47.619 9.46 0.00 35.94 2.32
884 906 1.691434 ACAAACCGGACATGCCAAAAT 59.309 42.857 9.46 0.00 35.94 1.82
885 907 1.115467 ACAAACCGGACATGCCAAAA 58.885 45.000 9.46 0.00 35.94 2.44
886 908 1.115467 AACAAACCGGACATGCCAAA 58.885 45.000 9.46 0.00 35.94 3.28
887 909 1.982660 TAACAAACCGGACATGCCAA 58.017 45.000 9.46 0.00 35.94 4.52
888 910 1.982660 TTAACAAACCGGACATGCCA 58.017 45.000 9.46 0.00 35.94 4.92
889 911 3.586100 ATTTAACAAACCGGACATGCC 57.414 42.857 9.46 0.00 0.00 4.40
890 912 8.865590 ATTATAATTTAACAAACCGGACATGC 57.134 30.769 9.46 0.00 0.00 4.06
893 915 9.141400 GCAAATTATAATTTAACAAACCGGACA 57.859 29.630 20.32 0.00 36.52 4.02
894 916 9.361315 AGCAAATTATAATTTAACAAACCGGAC 57.639 29.630 20.32 4.99 36.52 4.79
895 917 9.930693 AAGCAAATTATAATTTAACAAACCGGA 57.069 25.926 20.32 0.00 36.52 5.14
906 928 9.396938 GCAACAAAGCAAAGCAAATTATAATTT 57.603 25.926 16.15 16.15 39.07 1.82
907 929 7.745594 CGCAACAAAGCAAAGCAAATTATAATT 59.254 29.630 4.81 4.81 0.00 1.40
908 930 7.117523 TCGCAACAAAGCAAAGCAAATTATAAT 59.882 29.630 0.00 0.00 0.00 1.28
909 931 6.422100 TCGCAACAAAGCAAAGCAAATTATAA 59.578 30.769 0.00 0.00 0.00 0.98
910 932 5.923114 TCGCAACAAAGCAAAGCAAATTATA 59.077 32.000 0.00 0.00 0.00 0.98
911 933 4.749099 TCGCAACAAAGCAAAGCAAATTAT 59.251 33.333 0.00 0.00 0.00 1.28
912 934 4.115516 TCGCAACAAAGCAAAGCAAATTA 58.884 34.783 0.00 0.00 0.00 1.40
913 935 2.935201 TCGCAACAAAGCAAAGCAAATT 59.065 36.364 0.00 0.00 0.00 1.82
914 936 2.548875 TCGCAACAAAGCAAAGCAAAT 58.451 38.095 0.00 0.00 0.00 2.32
915 937 2.001812 TCGCAACAAAGCAAAGCAAA 57.998 40.000 0.00 0.00 0.00 3.68
916 938 2.001812 TTCGCAACAAAGCAAAGCAA 57.998 40.000 0.00 0.00 0.00 3.91
917 939 2.222007 ATTCGCAACAAAGCAAAGCA 57.778 40.000 0.00 0.00 0.00 3.91
918 940 4.908966 ATAATTCGCAACAAAGCAAAGC 57.091 36.364 0.00 0.00 0.00 3.51
919 941 6.450845 TCAATAATTCGCAACAAAGCAAAG 57.549 33.333 0.00 0.00 0.00 2.77
920 942 6.834959 TTCAATAATTCGCAACAAAGCAAA 57.165 29.167 0.00 0.00 0.00 3.68
921 943 7.418840 AATTCAATAATTCGCAACAAAGCAA 57.581 28.000 0.00 0.00 28.88 3.91
922 944 8.526218 TTAATTCAATAATTCGCAACAAAGCA 57.474 26.923 0.00 0.00 36.67 3.91
923 945 8.859156 TCTTAATTCAATAATTCGCAACAAAGC 58.141 29.630 0.00 0.00 36.67 3.51
947 969 9.840427 GCGCCAATTATACAATACAAATTATCT 57.160 29.630 0.00 0.00 0.00 1.98
948 970 8.785101 CGCGCCAATTATACAATACAAATTATC 58.215 33.333 0.00 0.00 0.00 1.75
949 971 7.272515 GCGCGCCAATTATACAATACAAATTAT 59.727 33.333 23.24 0.00 0.00 1.28
950 972 6.579292 GCGCGCCAATTATACAATACAAATTA 59.421 34.615 23.24 0.00 0.00 1.40
951 973 5.401079 GCGCGCCAATTATACAATACAAATT 59.599 36.000 23.24 0.00 0.00 1.82
952 974 4.915085 GCGCGCCAATTATACAATACAAAT 59.085 37.500 23.24 0.00 0.00 2.32
953 975 4.201920 TGCGCGCCAATTATACAATACAAA 60.202 37.500 30.77 0.00 0.00 2.83
954 976 3.312697 TGCGCGCCAATTATACAATACAA 59.687 39.130 30.77 0.00 0.00 2.41
955 977 2.872858 TGCGCGCCAATTATACAATACA 59.127 40.909 30.77 0.00 0.00 2.29
956 978 3.059188 AGTGCGCGCCAATTATACAATAC 60.059 43.478 30.77 14.97 0.00 1.89
957 979 3.059257 CAGTGCGCGCCAATTATACAATA 60.059 43.478 30.77 0.71 0.00 1.90
958 980 1.946768 AGTGCGCGCCAATTATACAAT 59.053 42.857 30.77 1.77 0.00 2.71
959 981 1.063321 CAGTGCGCGCCAATTATACAA 59.937 47.619 30.77 1.61 0.00 2.41
960 982 0.655208 CAGTGCGCGCCAATTATACA 59.345 50.000 30.77 2.53 0.00 2.29
961 983 0.934496 TCAGTGCGCGCCAATTATAC 59.066 50.000 30.77 18.16 0.00 1.47
962 984 1.877637 ATCAGTGCGCGCCAATTATA 58.122 45.000 30.77 4.37 0.00 0.98
963 985 1.024271 AATCAGTGCGCGCCAATTAT 58.976 45.000 30.77 12.83 0.00 1.28
964 986 1.329292 GTAATCAGTGCGCGCCAATTA 59.671 47.619 30.77 21.48 0.00 1.40
965 987 0.098728 GTAATCAGTGCGCGCCAATT 59.901 50.000 30.77 22.46 0.00 2.32
966 988 1.024046 TGTAATCAGTGCGCGCCAAT 61.024 50.000 30.77 13.36 0.00 3.16
967 989 1.024046 ATGTAATCAGTGCGCGCCAA 61.024 50.000 30.77 8.12 0.00 4.52
968 990 1.449423 ATGTAATCAGTGCGCGCCA 60.449 52.632 30.77 16.96 0.00 5.69
969 991 1.010797 CATGTAATCAGTGCGCGCC 60.011 57.895 30.77 19.97 0.00 6.53
970 992 0.373370 TTCATGTAATCAGTGCGCGC 59.627 50.000 27.26 27.26 0.00 6.86
971 993 3.323729 AATTCATGTAATCAGTGCGCG 57.676 42.857 0.00 0.00 0.00 6.86
972 994 4.661125 TCAAATTCATGTAATCAGTGCGC 58.339 39.130 0.00 0.00 0.00 6.09
973 995 5.065090 TCCTCAAATTCATGTAATCAGTGCG 59.935 40.000 0.00 0.00 0.00 5.34
974 996 6.441093 TCCTCAAATTCATGTAATCAGTGC 57.559 37.500 0.00 0.00 0.00 4.40
975 997 8.127327 GTGATCCTCAAATTCATGTAATCAGTG 58.873 37.037 0.00 0.00 0.00 3.66
976 998 7.830697 TGTGATCCTCAAATTCATGTAATCAGT 59.169 33.333 0.00 0.00 0.00 3.41
977 999 8.217131 TGTGATCCTCAAATTCATGTAATCAG 57.783 34.615 0.00 0.00 0.00 2.90
978 1000 8.578448 TTGTGATCCTCAAATTCATGTAATCA 57.422 30.769 0.00 0.00 0.00 2.57
982 1004 9.642327 CAAAATTGTGATCCTCAAATTCATGTA 57.358 29.630 0.00 0.00 0.00 2.29
983 1005 8.369424 TCAAAATTGTGATCCTCAAATTCATGT 58.631 29.630 0.00 0.00 0.00 3.21
984 1006 8.766000 TCAAAATTGTGATCCTCAAATTCATG 57.234 30.769 0.00 0.00 0.00 3.07
985 1007 8.809066 TCTCAAAATTGTGATCCTCAAATTCAT 58.191 29.630 0.00 0.00 0.00 2.57
986 1008 8.180706 TCTCAAAATTGTGATCCTCAAATTCA 57.819 30.769 0.00 0.00 0.00 2.57
990 1012 9.246670 ACATATCTCAAAATTGTGATCCTCAAA 57.753 29.630 12.48 0.00 40.59 2.69
991 1013 8.680001 CACATATCTCAAAATTGTGATCCTCAA 58.320 33.333 12.48 3.53 40.59 3.02
992 1014 7.283807 CCACATATCTCAAAATTGTGATCCTCA 59.716 37.037 12.48 0.00 40.59 3.86
993 1015 7.500227 TCCACATATCTCAAAATTGTGATCCTC 59.500 37.037 12.48 0.00 40.59 3.71
994 1016 7.348815 TCCACATATCTCAAAATTGTGATCCT 58.651 34.615 12.48 2.17 40.59 3.24
995 1017 7.572523 TCCACATATCTCAAAATTGTGATCC 57.427 36.000 12.48 0.00 40.59 3.36
996 1018 8.843262 TCATCCACATATCTCAAAATTGTGATC 58.157 33.333 12.48 0.00 40.59 2.92
997 1019 8.756486 TCATCCACATATCTCAAAATTGTGAT 57.244 30.769 13.37 13.37 42.21 3.06
998 1020 7.830697 ACTCATCCACATATCTCAAAATTGTGA 59.169 33.333 0.00 0.00 39.98 3.58
999 1021 7.993101 ACTCATCCACATATCTCAAAATTGTG 58.007 34.615 0.00 0.00 37.90 3.33
1000 1022 9.334947 CTACTCATCCACATATCTCAAAATTGT 57.665 33.333 0.00 0.00 0.00 2.71
1001 1023 9.334947 ACTACTCATCCACATATCTCAAAATTG 57.665 33.333 0.00 0.00 0.00 2.32
1002 1024 9.334947 CACTACTCATCCACATATCTCAAAATT 57.665 33.333 0.00 0.00 0.00 1.82
1003 1025 8.489489 ACACTACTCATCCACATATCTCAAAAT 58.511 33.333 0.00 0.00 0.00 1.82
1004 1026 7.851228 ACACTACTCATCCACATATCTCAAAA 58.149 34.615 0.00 0.00 0.00 2.44
1005 1027 7.423844 ACACTACTCATCCACATATCTCAAA 57.576 36.000 0.00 0.00 0.00 2.69
1006 1028 8.533569 TTACACTACTCATCCACATATCTCAA 57.466 34.615 0.00 0.00 0.00 3.02
1007 1029 8.712228 ATTACACTACTCATCCACATATCTCA 57.288 34.615 0.00 0.00 0.00 3.27
1014 1036 9.025041 CCTCATATATTACACTACTCATCCACA 57.975 37.037 0.00 0.00 0.00 4.17
1015 1037 8.470805 CCCTCATATATTACACTACTCATCCAC 58.529 40.741 0.00 0.00 0.00 4.02
1016 1038 7.619698 CCCCTCATATATTACACTACTCATCCA 59.380 40.741 0.00 0.00 0.00 3.41
1017 1039 7.418025 GCCCCTCATATATTACACTACTCATCC 60.418 44.444 0.00 0.00 0.00 3.51
1018 1040 7.418025 GGCCCCTCATATATTACACTACTCATC 60.418 44.444 0.00 0.00 0.00 2.92
1019 1041 6.384305 GGCCCCTCATATATTACACTACTCAT 59.616 42.308 0.00 0.00 0.00 2.90
1020 1042 5.720041 GGCCCCTCATATATTACACTACTCA 59.280 44.000 0.00 0.00 0.00 3.41
1021 1043 5.163540 CGGCCCCTCATATATTACACTACTC 60.164 48.000 0.00 0.00 0.00 2.59
1022 1044 4.710375 CGGCCCCTCATATATTACACTACT 59.290 45.833 0.00 0.00 0.00 2.57
1023 1045 4.142004 CCGGCCCCTCATATATTACACTAC 60.142 50.000 0.00 0.00 0.00 2.73
1024 1046 4.028131 CCGGCCCCTCATATATTACACTA 58.972 47.826 0.00 0.00 0.00 2.74
1025 1047 2.838202 CCGGCCCCTCATATATTACACT 59.162 50.000 0.00 0.00 0.00 3.55
1026 1048 2.679930 GCCGGCCCCTCATATATTACAC 60.680 54.545 18.11 0.00 0.00 2.90
1027 1049 1.557832 GCCGGCCCCTCATATATTACA 59.442 52.381 18.11 0.00 0.00 2.41
1028 1050 1.472728 CGCCGGCCCCTCATATATTAC 60.473 57.143 23.46 0.00 0.00 1.89
1029 1051 0.828022 CGCCGGCCCCTCATATATTA 59.172 55.000 23.46 0.00 0.00 0.98
1030 1052 1.602237 CGCCGGCCCCTCATATATT 59.398 57.895 23.46 0.00 0.00 1.28
1031 1053 2.367202 CCGCCGGCCCCTCATATAT 61.367 63.158 23.46 0.00 0.00 0.86
1032 1054 3.000819 CCGCCGGCCCCTCATATA 61.001 66.667 23.46 0.00 0.00 0.86
1046 1068 4.832608 GTCCGTGGACATCCCCGC 62.833 72.222 14.10 0.00 44.02 6.13
1047 1069 4.508128 CGTCCGTGGACATCCCCG 62.508 72.222 18.54 0.00 44.77 5.73
1048 1070 4.832608 GCGTCCGTGGACATCCCC 62.833 72.222 18.54 0.00 44.77 4.81
1058 1080 3.957535 CCCTATACGCGCGTCCGT 61.958 66.667 41.35 27.32 44.62 4.69
1059 1081 4.695231 CCCCTATACGCGCGTCCG 62.695 72.222 41.35 26.53 37.57 4.79
1064 1086 3.584868 AATCCGCCCCTATACGCGC 62.585 63.158 5.73 0.00 46.88 6.86
1066 1088 1.574702 GCAAATCCGCCCCTATACGC 61.575 60.000 0.00 0.00 0.00 4.42
1067 1089 2.540145 GCAAATCCGCCCCTATACG 58.460 57.895 0.00 0.00 0.00 3.06
1076 1098 0.744414 TCTACAGCTGGCAAATCCGC 60.744 55.000 19.93 0.00 37.80 5.54
1077 1099 1.600957 CATCTACAGCTGGCAAATCCG 59.399 52.381 19.93 0.00 37.80 4.18
1078 1100 2.923121 TCATCTACAGCTGGCAAATCC 58.077 47.619 19.93 0.00 0.00 3.01
1079 1101 4.387598 AGATCATCTACAGCTGGCAAATC 58.612 43.478 19.93 12.34 0.00 2.17
1080 1102 4.434545 AGATCATCTACAGCTGGCAAAT 57.565 40.909 19.93 3.50 0.00 2.32
1081 1103 3.920231 AGATCATCTACAGCTGGCAAA 57.080 42.857 19.93 0.33 0.00 3.68
1082 1104 5.557576 ATTAGATCATCTACAGCTGGCAA 57.442 39.130 19.93 2.35 0.00 4.52
1083 1105 5.070847 TCAATTAGATCATCTACAGCTGGCA 59.929 40.000 19.93 4.23 0.00 4.92
1084 1106 5.545588 TCAATTAGATCATCTACAGCTGGC 58.454 41.667 19.93 0.00 0.00 4.85
1085 1107 7.307870 GCTTTCAATTAGATCATCTACAGCTGG 60.308 40.741 19.93 0.36 0.00 4.85
1086 1108 7.226128 TGCTTTCAATTAGATCATCTACAGCTG 59.774 37.037 13.48 13.48 0.00 4.24
1087 1109 7.278135 TGCTTTCAATTAGATCATCTACAGCT 58.722 34.615 0.00 0.00 0.00 4.24
1088 1110 7.488187 TGCTTTCAATTAGATCATCTACAGC 57.512 36.000 0.00 0.00 0.00 4.40
1089 1111 7.569043 CGCTGCTTTCAATTAGATCATCTACAG 60.569 40.741 0.00 0.00 0.00 2.74
1090 1112 6.201615 CGCTGCTTTCAATTAGATCATCTACA 59.798 38.462 0.00 0.00 0.00 2.74
1091 1113 6.588552 CGCTGCTTTCAATTAGATCATCTAC 58.411 40.000 0.00 0.00 0.00 2.59
1092 1114 5.178252 GCGCTGCTTTCAATTAGATCATCTA 59.822 40.000 0.00 0.00 0.00 1.98
1093 1115 4.024218 GCGCTGCTTTCAATTAGATCATCT 60.024 41.667 0.00 0.00 0.00 2.90
1094 1116 4.217497 GCGCTGCTTTCAATTAGATCATC 58.783 43.478 0.00 0.00 0.00 2.92
1095 1117 3.303593 CGCGCTGCTTTCAATTAGATCAT 60.304 43.478 5.56 0.00 0.00 2.45
1096 1118 2.030823 CGCGCTGCTTTCAATTAGATCA 59.969 45.455 5.56 0.00 0.00 2.92
1097 1119 2.285220 TCGCGCTGCTTTCAATTAGATC 59.715 45.455 5.56 0.00 0.00 2.75
1098 1120 2.279741 TCGCGCTGCTTTCAATTAGAT 58.720 42.857 5.56 0.00 0.00 1.98
1099 1121 1.660607 CTCGCGCTGCTTTCAATTAGA 59.339 47.619 5.56 0.00 0.00 2.10
1100 1122 1.267732 CCTCGCGCTGCTTTCAATTAG 60.268 52.381 5.56 0.00 0.00 1.73
1116 1138 3.695060 ACCACATACTACTTCACTCCTCG 59.305 47.826 0.00 0.00 0.00 4.63
1665 1730 0.391661 GACAGCATCGCAGGAGGAAA 60.392 55.000 0.00 0.00 0.00 3.13
1695 1760 0.884704 GAAGAGCCTGTTGAACGCCA 60.885 55.000 0.00 0.00 0.00 5.69
1747 1824 3.325753 GGGAGCAGCTGGGTGAGT 61.326 66.667 17.12 0.00 0.00 3.41
1943 2047 0.759346 AACTGAGCCGTCAAAGACCT 59.241 50.000 0.00 0.00 30.14 3.85
1972 2076 1.380515 CTCGCCAGGAGAGGAGGAA 60.381 63.158 12.38 0.00 46.23 3.36
1973 2077 2.277072 CTCGCCAGGAGAGGAGGA 59.723 66.667 12.38 0.00 46.23 3.71
2052 2165 2.236395 TCGAAATCCTTGAGGGGTTCTC 59.764 50.000 0.00 0.00 37.45 2.87
2194 2307 1.483415 GCTACCTCGAATTGGTGGGTA 59.517 52.381 12.41 12.04 38.42 3.69
2832 7697 2.346803 ACACTCGACAATGGGATTTCG 58.653 47.619 0.00 0.00 0.00 3.46
3127 7992 4.348168 ACATACAAGGAACTGGACAGAAGT 59.652 41.667 6.29 0.00 40.86 3.01
3170 8035 5.692613 ATAAAATACGAGGAGAGGAGTCG 57.307 43.478 0.00 0.00 39.63 4.18
3446 8646 1.725611 CGCAACAACATCCACATCACG 60.726 52.381 0.00 0.00 0.00 4.35
3450 8650 0.881118 GACCGCAACAACATCCACAT 59.119 50.000 0.00 0.00 0.00 3.21
3523 8723 2.674852 CTGGAACGTCAACATGATCCAG 59.325 50.000 12.80 12.80 41.79 3.86
4010 9308 1.271108 TGTTGCTGCGGGAATCAGTTA 60.271 47.619 1.67 0.00 34.21 2.24
4214 9853 3.785887 AGGTGTGACCCCATGTATTACAT 59.214 43.478 3.40 3.40 39.75 2.29
6307 12430 2.161030 ACGAAGAGGCTCTCGTAGTTT 58.839 47.619 28.19 10.53 37.03 2.66
6313 12436 1.027255 TCAGGACGAAGAGGCTCTCG 61.027 60.000 24.70 24.70 35.36 4.04
6351 12475 3.763897 ACCAGCAACAAGATTAATGACCC 59.236 43.478 0.00 0.00 0.00 4.46
6431 12555 2.563620 TGTGACCGCTGTGGAAGTATAA 59.436 45.455 15.34 0.00 42.00 0.98
6457 12581 7.857456 TCTTAGGATAACTAATTGCCAAGTGA 58.143 34.615 0.00 0.00 40.71 3.41
6499 12623 6.779860 AGAAGGAATTGCCAAGTCTAACTAA 58.220 36.000 4.76 0.00 40.02 2.24
6500 12624 6.374417 AGAAGGAATTGCCAAGTCTAACTA 57.626 37.500 4.76 0.00 40.02 2.24
6548 13610 5.761726 TGCTTTGATCCACTTAGCATGATAG 59.238 40.000 0.00 0.00 36.96 2.08
6652 13714 2.840511 TGGACAAGGGGCTAAGATACA 58.159 47.619 0.00 0.00 0.00 2.29
6721 13783 1.795872 CAACAAATACACTCGCGGACA 59.204 47.619 6.13 0.00 0.00 4.02
6722 13784 1.463528 GCAACAAATACACTCGCGGAC 60.464 52.381 6.13 0.00 0.00 4.79
6764 13826 2.948979 TGACTTTGCCAAGGTGTTACAG 59.051 45.455 0.00 0.00 33.82 2.74
6840 13902 4.973168 TGAGCTGTACCTTTTCAAGACAT 58.027 39.130 0.00 0.00 0.00 3.06
6907 13969 4.833380 AGTAGACTTCAAACACTAGCCTGA 59.167 41.667 0.00 0.00 0.00 3.86
7031 14093 2.497273 GCCTTGCTATTCAACCATGGTT 59.503 45.455 24.86 24.86 39.13 3.67
7091 14153 7.604545 AGAAGTTCTTCAAAGCTACAACTATCC 59.395 37.037 13.85 0.00 0.00 2.59
7375 16122 2.458592 ATAAGCAAAGCAATCGACGC 57.541 45.000 0.36 0.36 0.00 5.19
7376 16123 7.436536 AAATAAATAAGCAAAGCAATCGACG 57.563 32.000 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.