Multiple sequence alignment - TraesCS4A01G121900

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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 TraesCS4A01G121900 chr4A 100.000 3997 0 0 1 3997 150656645 150660641 0.000000e+00 7382.0
1 TraesCS4A01G121900 chr4A 88.485 165 13 4 2469 2627 150659038 150659202 1.130000e-45 195.0
2 TraesCS4A01G121900 chr4A 88.485 165 13 4 2394 2558 150659113 150659271 1.130000e-45 195.0
3 TraesCS4A01G121900 chr4A 100.000 97 0 0 3901 3997 150667608 150667704 3.170000e-41 180.0
4 TraesCS4A01G121900 chr4B 93.108 1451 59 16 2394 3822 399037145 399038576 0.000000e+00 2087.0
5 TraesCS4A01G121900 chr4B 94.454 1172 49 11 1467 2627 399036143 399037309 0.000000e+00 1790.0
6 TraesCS4A01G121900 chr4B 86.842 570 38 24 796 1348 399035600 399036149 1.590000e-168 603.0
7 TraesCS4A01G121900 chr4B 90.909 165 9 4 2394 2558 399037220 399037378 2.420000e-52 217.0
8 TraesCS4A01G121900 chr4B 87.805 164 14 4 2470 2627 399037071 399037234 1.900000e-43 187.0
9 TraesCS4A01G121900 chr4B 91.538 130 11 0 1345 1474 626638173 626638044 3.170000e-41 180.0
10 TraesCS4A01G121900 chr4B 88.298 94 8 3 3901 3994 399038819 399038909 4.220000e-20 110.0
11 TraesCS4A01G121900 chr4B 90.769 65 3 1 3845 3909 399038571 399038632 2.560000e-12 84.2
12 TraesCS4A01G121900 chr4D 93.832 843 22 14 1500 2320 322227910 322227076 0.000000e+00 1242.0
13 TraesCS4A01G121900 chr4D 97.202 679 19 0 2348 3026 322227081 322226403 0.000000e+00 1149.0
14 TraesCS4A01G121900 chr4D 92.846 643 26 8 3025 3665 322221181 322220557 0.000000e+00 915.0
15 TraesCS4A01G121900 chr4D 87.788 565 21 20 1 540 322234136 322233595 5.680000e-173 617.0
16 TraesCS4A01G121900 chr4D 90.850 306 24 3 3695 3997 322220565 322220261 1.340000e-109 407.0
17 TraesCS4A01G121900 chr4D 83.127 403 38 20 923 1304 322228322 322227929 1.380000e-89 340.0
18 TraesCS4A01G121900 chr4D 82.429 387 22 20 535 912 322228637 322228288 3.020000e-76 296.0
19 TraesCS4A01G121900 chr4D 90.909 165 9 4 2394 2558 322226960 322226802 2.420000e-52 217.0
20 TraesCS4A01G121900 chr4D 78.223 349 45 16 2263 2611 322227211 322226894 1.130000e-45 195.0
21 TraesCS4A01G121900 chr4D 94.643 56 3 0 2185 2240 322227133 322227078 1.980000e-13 87.9
22 TraesCS4A01G121900 chr3D 93.798 129 8 0 1345 1473 546651737 546651609 1.130000e-45 195.0
23 TraesCS4A01G121900 chr3D 85.799 169 19 4 1337 1501 606951441 606951274 1.480000e-39 174.0
24 TraesCS4A01G121900 chr2D 93.798 129 8 0 1344 1472 164534369 164534241 1.130000e-45 195.0
25 TraesCS4A01G121900 chr5B 91.729 133 11 0 1341 1473 196984212 196984344 6.820000e-43 185.0
26 TraesCS4A01G121900 chr5B 90.977 133 12 0 1342 1474 226429811 226429679 3.170000e-41 180.0
27 TraesCS4A01G121900 chr2B 90.647 139 13 0 1344 1482 526668898 526668760 6.820000e-43 185.0
28 TraesCS4A01G121900 chr7A 91.603 131 11 0 1345 1475 442265755 442265885 8.820000e-42 182.0
29 TraesCS4A01G121900 chr5A 89.286 140 13 2 1340 1478 290115404 290115542 1.480000e-39 174.0
30 TraesCS4A01G121900 chr7B 100.000 28 0 0 3669 3696 539197144 539197171 7.000000e-03 52.8


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 TraesCS4A01G121900 chr4A 150656645 150660641 3996 False 2590.666667 7382 92.323333 1 3997 3 chr4A.!!$F2 3996
1 TraesCS4A01G121900 chr4B 399035600 399038909 3309 False 725.457143 2087 90.312143 796 3994 7 chr4B.!!$F1 3198
2 TraesCS4A01G121900 chr4D 322220261 322221181 920 True 661.000000 915 91.848000 3025 3997 2 chr4D.!!$R2 972
3 TraesCS4A01G121900 chr4D 322233595 322234136 541 True 617.000000 617 87.788000 1 540 1 chr4D.!!$R1 539
4 TraesCS4A01G121900 chr4D 322226403 322228637 2234 True 503.842857 1242 88.623571 535 3026 7 chr4D.!!$R3 2491

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
602 628 0.030235 GTCGTGCCTTTGGTTTGTCC 59.970 55.0 0.0 0.0 0.00 4.02 F
604 630 0.030638 CGTGCCTTTGGTTTGTCCTG 59.969 55.0 0.0 0.0 37.07 3.86 F
638 664 0.035458 CGAGGGAAAGCCTGTTCTGT 59.965 55.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2259 0.119155 ACCCTCCTCTTCCATGACCA 59.881 55.000 0.0 0.0 0.00 4.02 R
2493 2690 3.136123 CCCGCTCCTGCATGGTTG 61.136 66.667 0.0 0.0 39.64 3.77 R
3037 3250 3.242936 GCTACCGTCAAAGCAAAAACTGA 60.243 43.478 0.0 0.0 38.63 3.41 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
38 39 3.784883 CAGAGAGAAACTGCGTTGAAG 57.215 47.619 0.00 0.00 0.00 3.02
39 40 3.126831 CAGAGAGAAACTGCGTTGAAGT 58.873 45.455 0.00 0.00 0.00 3.01
40 41 3.183373 CAGAGAGAAACTGCGTTGAAGTC 59.817 47.826 0.00 0.00 0.00 3.01
41 42 2.476997 GAGAGAAACTGCGTTGAAGTCC 59.523 50.000 0.00 0.00 0.00 3.85
42 43 2.103263 AGAGAAACTGCGTTGAAGTCCT 59.897 45.455 0.00 0.00 0.00 3.85
57 58 6.688073 TGAAGTCCTCTCTCTTTTATTGGT 57.312 37.500 0.00 0.00 0.00 3.67
59 60 4.837972 AGTCCTCTCTCTTTTATTGGTGC 58.162 43.478 0.00 0.00 0.00 5.01
71 72 4.839668 TTATTGGTGCGTAAAGTTTGCT 57.160 36.364 0.00 0.00 0.00 3.91
81 82 1.247567 AAAGTTTGCTCGGTGGGATG 58.752 50.000 0.00 0.00 0.00 3.51
82 83 0.609131 AAGTTTGCTCGGTGGGATGG 60.609 55.000 0.00 0.00 0.00 3.51
83 84 2.046285 GTTTGCTCGGTGGGATGGG 61.046 63.158 0.00 0.00 0.00 4.00
84 85 2.227757 TTTGCTCGGTGGGATGGGA 61.228 57.895 0.00 0.00 0.00 4.37
85 86 1.570857 TTTGCTCGGTGGGATGGGAT 61.571 55.000 0.00 0.00 0.00 3.85
86 87 0.692756 TTGCTCGGTGGGATGGGATA 60.693 55.000 0.00 0.00 0.00 2.59
87 88 1.121407 TGCTCGGTGGGATGGGATAG 61.121 60.000 0.00 0.00 0.00 2.08
92 93 1.807814 GGTGGGATGGGATAGTGACT 58.192 55.000 0.00 0.00 0.00 3.41
102 103 4.091549 TGGGATAGTGACTTAACGGTCTT 58.908 43.478 0.00 0.00 37.16 3.01
107 108 4.189639 AGTGACTTAACGGTCTTGATCC 57.810 45.455 0.00 0.00 37.16 3.36
124 125 2.229675 TCCAGCTCGCTGTGATAATG 57.770 50.000 16.82 1.12 42.15 1.90
130 131 2.157279 GCTCGCTGTGATAATGATCTGC 59.843 50.000 0.00 0.00 32.79 4.26
145 146 0.606401 TCTGCCTGTGCTAAACTGCC 60.606 55.000 0.00 0.00 38.71 4.85
148 149 1.868997 CCTGTGCTAAACTGCCACG 59.131 57.895 0.00 0.00 0.00 4.94
150 151 1.506309 CTGTGCTAAACTGCCACGCA 61.506 55.000 0.00 0.00 36.92 5.24
153 154 1.098129 TGCTAAACTGCCACGCACAA 61.098 50.000 0.00 0.00 33.79 3.33
155 156 1.466950 GCTAAACTGCCACGCACAATA 59.533 47.619 0.00 0.00 33.79 1.90
156 157 2.476185 GCTAAACTGCCACGCACAATAG 60.476 50.000 0.00 0.00 33.79 1.73
157 158 0.240945 AAACTGCCACGCACAATAGC 59.759 50.000 0.00 0.00 33.79 2.97
158 159 0.606401 AACTGCCACGCACAATAGCT 60.606 50.000 0.00 0.00 33.79 3.32
159 160 0.249120 ACTGCCACGCACAATAGCTA 59.751 50.000 0.00 0.00 33.79 3.32
160 161 0.652592 CTGCCACGCACAATAGCTAC 59.347 55.000 0.00 0.00 33.79 3.58
162 163 1.299541 GCCACGCACAATAGCTACAT 58.700 50.000 0.00 0.00 0.00 2.29
180 206 7.978982 AGCTACATGTATGTTGACTGAATTTC 58.021 34.615 5.91 0.00 41.97 2.17
300 326 8.556213 TGTAATGACCCAACAAATCTACTTAC 57.444 34.615 0.00 0.00 0.00 2.34
334 360 5.100344 AGGTTACTGTATGACTCGAGAGA 57.900 43.478 21.68 4.89 39.12 3.10
335 361 4.877251 AGGTTACTGTATGACTCGAGAGAC 59.123 45.833 21.68 11.15 35.39 3.36
336 362 4.634883 GGTTACTGTATGACTCGAGAGACA 59.365 45.833 21.68 15.76 37.49 3.41
337 363 5.123502 GGTTACTGTATGACTCGAGAGACAA 59.876 44.000 21.68 2.33 36.76 3.18
383 409 3.144193 AGGCTCTCGGCGAGGAAG 61.144 66.667 33.93 25.63 42.94 3.46
384 410 3.141488 GGCTCTCGGCGAGGAAGA 61.141 66.667 33.93 16.08 42.94 2.87
385 411 2.711922 GGCTCTCGGCGAGGAAGAA 61.712 63.158 33.93 15.49 42.94 2.52
386 412 1.517475 GCTCTCGGCGAGGAAGAAC 60.517 63.158 33.93 14.85 40.25 3.01
431 457 5.005094 CCAAAATTCAAAATCCACAGCCAT 58.995 37.500 0.00 0.00 0.00 4.40
441 467 1.022735 CCACAGCCATCATCAGAAGC 58.977 55.000 0.00 0.00 0.00 3.86
504 530 1.836604 GGGCCTCCCAAGTTTGCAA 60.837 57.895 0.84 0.00 44.65 4.08
531 557 3.137360 AGGCTCAACTCAACTTTCTTCCT 59.863 43.478 0.00 0.00 0.00 3.36
532 558 4.348168 AGGCTCAACTCAACTTTCTTCCTA 59.652 41.667 0.00 0.00 0.00 2.94
533 559 5.063880 GGCTCAACTCAACTTTCTTCCTAA 58.936 41.667 0.00 0.00 0.00 2.69
574 600 3.066203 TCGGGTGAAAGCAAAAGAGAAAC 59.934 43.478 0.00 0.00 34.77 2.78
576 602 3.066203 GGGTGAAAGCAAAAGAGAAACGA 59.934 43.478 0.00 0.00 34.77 3.85
599 625 1.657181 GCGTCGTGCCTTTGGTTTG 60.657 57.895 0.00 0.00 37.76 2.93
602 628 0.030235 GTCGTGCCTTTGGTTTGTCC 59.970 55.000 0.00 0.00 0.00 4.02
603 629 0.106918 TCGTGCCTTTGGTTTGTCCT 60.107 50.000 0.00 0.00 37.07 3.85
604 630 0.030638 CGTGCCTTTGGTTTGTCCTG 59.969 55.000 0.00 0.00 37.07 3.86
605 631 0.249447 GTGCCTTTGGTTTGTCCTGC 60.249 55.000 0.00 0.00 37.07 4.85
607 633 0.752658 GCCTTTGGTTTGTCCTGCTT 59.247 50.000 0.00 0.00 37.07 3.91
608 634 1.538849 GCCTTTGGTTTGTCCTGCTTG 60.539 52.381 0.00 0.00 37.07 4.01
622 648 3.429141 CTTGTGCAGGCAGGCGAG 61.429 66.667 0.00 0.00 36.28 5.03
627 653 4.722700 GCAGGCAGGCGAGGGAAA 62.723 66.667 0.00 0.00 0.00 3.13
628 654 2.437359 CAGGCAGGCGAGGGAAAG 60.437 66.667 0.00 0.00 0.00 2.62
629 655 4.416738 AGGCAGGCGAGGGAAAGC 62.417 66.667 0.00 0.00 0.00 3.51
635 661 3.579685 GCGAGGGAAAGCCTGTTC 58.420 61.111 0.00 0.00 0.00 3.18
636 662 1.003233 GCGAGGGAAAGCCTGTTCT 60.003 57.895 0.00 0.00 0.00 3.01
637 663 1.301677 GCGAGGGAAAGCCTGTTCTG 61.302 60.000 0.00 0.00 0.00 3.02
638 664 0.035458 CGAGGGAAAGCCTGTTCTGT 59.965 55.000 0.00 0.00 0.00 3.41
639 665 1.543429 CGAGGGAAAGCCTGTTCTGTT 60.543 52.381 0.00 0.00 0.00 3.16
640 666 2.155279 GAGGGAAAGCCTGTTCTGTTC 58.845 52.381 0.00 0.00 0.00 3.18
641 667 1.777272 AGGGAAAGCCTGTTCTGTTCT 59.223 47.619 0.00 0.00 0.00 3.01
642 668 1.882623 GGGAAAGCCTGTTCTGTTCTG 59.117 52.381 0.00 0.00 0.00 3.02
643 669 2.576615 GGAAAGCCTGTTCTGTTCTGT 58.423 47.619 0.00 0.00 0.00 3.41
644 670 2.952310 GGAAAGCCTGTTCTGTTCTGTT 59.048 45.455 0.00 0.00 0.00 3.16
645 671 3.381590 GGAAAGCCTGTTCTGTTCTGTTT 59.618 43.478 0.00 0.00 0.00 2.83
680 706 2.727544 CGCCCACCAACAAACAGG 59.272 61.111 0.00 0.00 0.00 4.00
681 707 1.826054 CGCCCACCAACAAACAGGA 60.826 57.895 0.00 0.00 0.00 3.86
700 726 1.678101 GAGCCCCATTCAATTCCTTCG 59.322 52.381 0.00 0.00 0.00 3.79
753 779 0.932399 GTACCGCGTCTCTCTCTCTC 59.068 60.000 4.92 0.00 0.00 3.20
756 782 0.461163 CCGCGTCTCTCTCTCTCTCA 60.461 60.000 4.92 0.00 0.00 3.27
758 784 1.732941 GCGTCTCTCTCTCTCTCACA 58.267 55.000 0.00 0.00 0.00 3.58
763 789 4.009675 GTCTCTCTCTCTCTCACACACAT 58.990 47.826 0.00 0.00 0.00 3.21
767 793 4.940654 TCTCTCTCTCTCACACACATACAG 59.059 45.833 0.00 0.00 0.00 2.74
779 805 0.458543 ACATACAGACAGCGCTTCGG 60.459 55.000 7.50 12.36 0.00 4.30
860 890 2.767496 CAGCAGGGAGGAGAGGGG 60.767 72.222 0.00 0.00 0.00 4.79
885 915 1.415672 AACCTTGCCAGACGGAAGGA 61.416 55.000 15.84 0.00 39.84 3.36
887 917 1.544825 CCTTGCCAGACGGAAGGAGA 61.545 60.000 4.15 0.00 39.84 3.71
893 923 1.065053 CCAGACGGAAGGAGAGAGAGA 60.065 57.143 0.00 0.00 0.00 3.10
895 925 2.093181 CAGACGGAAGGAGAGAGAGAGA 60.093 54.545 0.00 0.00 0.00 3.10
896 926 2.170607 AGACGGAAGGAGAGAGAGAGAG 59.829 54.545 0.00 0.00 0.00 3.20
900 930 2.158608 GGAAGGAGAGAGAGAGAGGAGG 60.159 59.091 0.00 0.00 0.00 4.30
906 936 0.846693 AGAGAGAGAGGAGGGAGAGC 59.153 60.000 0.00 0.00 0.00 4.09
907 937 0.535102 GAGAGAGAGGAGGGAGAGCG 60.535 65.000 0.00 0.00 0.00 5.03
908 938 0.986019 AGAGAGAGGAGGGAGAGCGA 60.986 60.000 0.00 0.00 0.00 4.93
909 939 0.535102 GAGAGAGGAGGGAGAGCGAG 60.535 65.000 0.00 0.00 0.00 5.03
910 940 0.986019 AGAGAGGAGGGAGAGCGAGA 60.986 60.000 0.00 0.00 0.00 4.04
911 941 0.535102 GAGAGGAGGGAGAGCGAGAG 60.535 65.000 0.00 0.00 0.00 3.20
946 976 4.877773 AGAGAGAGAGAGAGAGAGAGAGT 58.122 47.826 0.00 0.00 0.00 3.24
947 977 5.276440 AGAGAGAGAGAGAGAGAGAGAGTT 58.724 45.833 0.00 0.00 0.00 3.01
949 979 5.738909 AGAGAGAGAGAGAGAGAGAGTTTG 58.261 45.833 0.00 0.00 0.00 2.93
957 987 1.188219 AGAGAGAGTTTGGCAGCGGA 61.188 55.000 0.00 0.00 0.00 5.54
969 999 1.219393 CAGCGGAAGGAAGGAGGAC 59.781 63.158 0.00 0.00 0.00 3.85
970 1000 2.184579 GCGGAAGGAAGGAGGACG 59.815 66.667 0.00 0.00 0.00 4.79
971 1001 2.893398 CGGAAGGAAGGAGGACGG 59.107 66.667 0.00 0.00 0.00 4.79
1122 1182 2.019156 GCTTGCTAATCCACCCACTCC 61.019 57.143 0.00 0.00 0.00 3.85
1146 1238 5.421277 CAACTCTCAATCTCATCTGCTTCT 58.579 41.667 0.00 0.00 0.00 2.85
1216 1308 3.709141 TGAATCTGAATGTATGACCCCGA 59.291 43.478 0.00 0.00 0.00 5.14
1295 1392 5.993748 TCCCCATGTTTTTAACTGAATCC 57.006 39.130 0.00 0.00 0.00 3.01
1304 1407 6.993902 TGTTTTTAACTGAATCCGTTACTCCT 59.006 34.615 0.00 0.00 0.00 3.69
1305 1408 8.149647 TGTTTTTAACTGAATCCGTTACTCCTA 58.850 33.333 0.00 0.00 0.00 2.94
1306 1409 8.992073 GTTTTTAACTGAATCCGTTACTCCTAA 58.008 33.333 0.00 0.00 0.00 2.69
1307 1410 9.729281 TTTTTAACTGAATCCGTTACTCCTAAT 57.271 29.630 0.00 0.00 0.00 1.73
1312 1415 8.480133 ACTGAATCCGTTACTCCTAATATTCT 57.520 34.615 0.00 0.00 0.00 2.40
1360 1463 9.543231 AATATATAAATACTCCCTCCGTCTCAA 57.457 33.333 0.00 0.00 0.00 3.02
1361 1464 7.850935 ATATAAATACTCCCTCCGTCTCAAA 57.149 36.000 0.00 0.00 0.00 2.69
1362 1465 4.903045 AAATACTCCCTCCGTCTCAAAA 57.097 40.909 0.00 0.00 0.00 2.44
1363 1466 5.437191 AAATACTCCCTCCGTCTCAAAAT 57.563 39.130 0.00 0.00 0.00 1.82
1364 1467 5.437191 AATACTCCCTCCGTCTCAAAATT 57.563 39.130 0.00 0.00 0.00 1.82
1365 1468 3.336138 ACTCCCTCCGTCTCAAAATTC 57.664 47.619 0.00 0.00 0.00 2.17
1366 1469 2.907042 ACTCCCTCCGTCTCAAAATTCT 59.093 45.455 0.00 0.00 0.00 2.40
1367 1470 3.328050 ACTCCCTCCGTCTCAAAATTCTT 59.672 43.478 0.00 0.00 0.00 2.52
1368 1471 3.674997 TCCCTCCGTCTCAAAATTCTTG 58.325 45.455 0.00 0.00 0.00 3.02
1369 1472 3.072476 TCCCTCCGTCTCAAAATTCTTGT 59.928 43.478 0.00 0.00 0.00 3.16
1370 1473 3.437049 CCCTCCGTCTCAAAATTCTTGTC 59.563 47.826 0.00 0.00 0.00 3.18
1371 1474 4.319177 CCTCCGTCTCAAAATTCTTGTCT 58.681 43.478 0.00 0.00 0.00 3.41
1372 1475 4.757149 CCTCCGTCTCAAAATTCTTGTCTT 59.243 41.667 0.00 0.00 0.00 3.01
1373 1476 5.932303 CCTCCGTCTCAAAATTCTTGTCTTA 59.068 40.000 0.00 0.00 0.00 2.10
1374 1477 6.128526 CCTCCGTCTCAAAATTCTTGTCTTAC 60.129 42.308 0.00 0.00 0.00 2.34
1375 1478 6.285224 TCCGTCTCAAAATTCTTGTCTTACA 58.715 36.000 0.00 0.00 0.00 2.41
1376 1479 6.934645 TCCGTCTCAAAATTCTTGTCTTACAT 59.065 34.615 0.00 0.00 0.00 2.29
1377 1480 7.444183 TCCGTCTCAAAATTCTTGTCTTACATT 59.556 33.333 0.00 0.00 0.00 2.71
1378 1481 8.076178 CCGTCTCAAAATTCTTGTCTTACATTT 58.924 33.333 0.00 0.00 0.00 2.32
1379 1482 8.895845 CGTCTCAAAATTCTTGTCTTACATTTG 58.104 33.333 0.00 0.00 29.24 2.32
1380 1483 9.736023 GTCTCAAAATTCTTGTCTTACATTTGT 57.264 29.630 0.00 0.00 29.85 2.83
1381 1484 9.950680 TCTCAAAATTCTTGTCTTACATTTGTC 57.049 29.630 0.00 0.00 29.85 3.18
1382 1485 9.734620 CTCAAAATTCTTGTCTTACATTTGTCA 57.265 29.630 0.00 0.00 29.85 3.58
1389 1492 9.959749 TTCTTGTCTTACATTTGTCAAAATACC 57.040 29.630 1.31 0.00 34.14 2.73
1390 1493 8.286800 TCTTGTCTTACATTTGTCAAAATACCG 58.713 33.333 1.31 0.00 34.14 4.02
1391 1494 7.731882 TGTCTTACATTTGTCAAAATACCGA 57.268 32.000 1.31 0.00 34.14 4.69
1392 1495 8.330466 TGTCTTACATTTGTCAAAATACCGAT 57.670 30.769 1.31 0.00 34.14 4.18
1393 1496 8.233868 TGTCTTACATTTGTCAAAATACCGATG 58.766 33.333 1.31 0.00 34.14 3.84
1394 1497 8.234546 GTCTTACATTTGTCAAAATACCGATGT 58.765 33.333 1.31 3.21 34.14 3.06
1395 1498 9.438228 TCTTACATTTGTCAAAATACCGATGTA 57.562 29.630 1.31 2.27 34.14 2.29
1398 1501 8.275015 ACATTTGTCAAAATACCGATGTATCA 57.725 30.769 1.31 0.00 36.65 2.15
1399 1502 8.735315 ACATTTGTCAAAATACCGATGTATCAA 58.265 29.630 1.31 0.00 36.65 2.57
1400 1503 9.225201 CATTTGTCAAAATACCGATGTATCAAG 57.775 33.333 1.31 0.00 36.65 3.02
1401 1504 7.915293 TTGTCAAAATACCGATGTATCAAGT 57.085 32.000 0.00 0.00 36.65 3.16
1402 1505 7.534085 TGTCAAAATACCGATGTATCAAGTC 57.466 36.000 0.00 0.00 36.65 3.01
1403 1506 7.100409 TGTCAAAATACCGATGTATCAAGTCA 58.900 34.615 0.00 0.00 36.65 3.41
1404 1507 7.064134 TGTCAAAATACCGATGTATCAAGTCAC 59.936 37.037 0.00 0.00 36.65 3.67
1405 1508 6.254804 TCAAAATACCGATGTATCAAGTCACG 59.745 38.462 0.00 0.00 36.65 4.35
1406 1509 4.913335 ATACCGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 31.99 4.49
1407 1510 3.587797 ACCGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
1408 1511 3.921677 ACCGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
1409 1512 4.312443 ACCGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
1410 1513 5.472148 ACCGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
1411 1514 5.927689 ACCGATGTATCAAGTCACGTTTTAA 59.072 36.000 0.00 0.00 0.00 1.52
1412 1515 6.592607 ACCGATGTATCAAGTCACGTTTTAAT 59.407 34.615 0.00 0.00 0.00 1.40
1413 1516 7.760794 ACCGATGTATCAAGTCACGTTTTAATA 59.239 33.333 0.00 0.00 0.00 0.98
1414 1517 8.761497 CCGATGTATCAAGTCACGTTTTAATAT 58.239 33.333 0.00 0.00 0.00 1.28
1465 1568 9.801873 TTTAAGACAAGAATTTTGAAACAGAGG 57.198 29.630 7.18 0.00 0.00 3.69
1468 1571 7.710896 AGACAAGAATTTTGAAACAGAGGAAG 58.289 34.615 7.18 0.00 0.00 3.46
1474 1577 9.274206 AGAATTTTGAAACAGAGGAAGTACTAC 57.726 33.333 0.00 0.00 0.00 2.73
1480 1583 4.219264 ACAGAGGAAGTACTACGCTAGT 57.781 45.455 0.00 3.71 42.68 2.57
1484 1587 6.656693 ACAGAGGAAGTACTACGCTAGTTTTA 59.343 38.462 0.00 0.00 40.14 1.52
1490 1593 9.750882 GGAAGTACTACGCTAGTTTTATTTTTG 57.249 33.333 0.00 0.00 40.14 2.44
1493 1596 9.918630 AGTACTACGCTAGTTTTATTTTTGAGA 57.081 29.630 0.00 0.00 40.14 3.27
1563 1669 7.867403 TCTTCCATTTTTGTTAACTGAATCTGC 59.133 33.333 7.22 0.00 0.00 4.26
2137 2259 1.492993 GCCAAGGTGAAGGAGGAGGT 61.493 60.000 0.00 0.00 0.00 3.85
2173 2295 1.485066 GGGTGAGGATATGTCGTTGGT 59.515 52.381 0.00 0.00 0.00 3.67
2399 2521 3.602030 ACCCTCTCCCGACCACCT 61.602 66.667 0.00 0.00 0.00 4.00
2776 2973 0.311165 CCGATGTCGCCGTCTTATCT 59.689 55.000 0.00 0.00 38.18 1.98
2906 3118 4.660938 AGGCCGTTTGCACCTCCC 62.661 66.667 0.00 0.00 43.89 4.30
3037 3250 5.404946 CATTTGCTGTTATTGCTAGCTTGT 58.595 37.500 17.23 4.33 38.25 3.16
3047 3260 3.354089 TGCTAGCTTGTCAGTTTTTGC 57.646 42.857 17.23 0.00 0.00 3.68
3067 3280 2.742589 GCTTTGACGGTAGCTAAGCTTT 59.257 45.455 3.20 0.00 40.44 3.51
3068 3281 3.181519 GCTTTGACGGTAGCTAAGCTTTC 60.182 47.826 3.20 0.00 40.44 2.62
3069 3282 2.273370 TGACGGTAGCTAAGCTTTCG 57.727 50.000 3.20 0.00 40.44 3.46
3070 3283 1.814394 TGACGGTAGCTAAGCTTTCGA 59.186 47.619 3.20 0.00 40.44 3.71
3203 3419 1.909700 TTCTTGTGCCCAGAACCATC 58.090 50.000 0.00 0.00 0.00 3.51
3242 3459 5.240844 GGAATGATTCATGCATGTCTCATGA 59.759 40.000 29.90 15.34 45.91 3.07
3256 3473 9.212641 GCATGTCTCATGATTACTTATGTACAT 57.787 33.333 13.93 13.93 34.98 2.29
3329 3546 7.485810 AGACCACAACAAACCAGTTTTTATAC 58.514 34.615 0.00 0.00 0.00 1.47
3333 3555 8.626526 CCACAACAAACCAGTTTTTATACTAGT 58.373 33.333 0.00 0.00 0.00 2.57
3395 3617 7.295201 CCAATTTCATCAAATCTGTTGCAAAG 58.705 34.615 0.00 1.26 30.37 2.77
3398 3620 5.771153 TCATCAAATCTGTTGCAAAGTGA 57.229 34.783 0.00 0.00 0.00 3.41
3456 3678 2.211279 AAGAGGGCAGGGGTTCCT 59.789 61.111 0.00 0.00 46.26 3.36
3457 3679 0.914417 CAAGAGGGCAGGGGTTCCTA 60.914 60.000 0.00 0.00 42.67 2.94
3458 3680 0.914902 AAGAGGGCAGGGGTTCCTAC 60.915 60.000 0.00 0.00 42.67 3.18
3459 3681 1.615424 GAGGGCAGGGGTTCCTACA 60.615 63.158 0.00 0.00 42.67 2.74
3460 3682 0.988678 GAGGGCAGGGGTTCCTACAT 60.989 60.000 0.00 0.00 42.67 2.29
3461 3683 0.552615 AGGGCAGGGGTTCCTACATT 60.553 55.000 0.00 0.00 42.67 2.71
3562 3784 2.223479 GCCGCACCATTGATTAACGAAT 60.223 45.455 0.00 0.00 0.00 3.34
3580 3802 3.066064 CGAATAATCATGCGAAAACCCCA 59.934 43.478 0.00 0.00 34.89 4.96
3585 3807 0.607620 CATGCGAAAACCCCAACCAT 59.392 50.000 0.00 0.00 0.00 3.55
3592 3814 3.940221 CGAAAACCCCAACCATACGATTA 59.060 43.478 0.00 0.00 0.00 1.75
3607 3829 6.768861 CCATACGATTAATTAAGGGACAACCA 59.231 38.462 3.94 0.00 43.89 3.67
3612 3834 7.830201 ACGATTAATTAAGGGACAACCATACAA 59.170 33.333 3.94 0.00 43.89 2.41
3613 3835 8.679100 CGATTAATTAAGGGACAACCATACAAA 58.321 33.333 3.94 0.00 43.89 2.83
3734 3959 0.879765 TCTCCTTCCGTCACGTCTTC 59.120 55.000 0.00 0.00 0.00 2.87
3785 4011 6.817765 AATTGACGGCTGAGATTTAAAAGA 57.182 33.333 0.00 0.00 0.00 2.52
3787 4013 6.627395 TTGACGGCTGAGATTTAAAAGAAA 57.373 33.333 0.00 0.00 0.00 2.52
3789 4015 5.181245 TGACGGCTGAGATTTAAAAGAAAGG 59.819 40.000 0.00 0.00 0.00 3.11
3790 4016 5.313712 ACGGCTGAGATTTAAAAGAAAGGA 58.686 37.500 0.00 0.00 0.00 3.36
3822 4048 2.365408 AACCTCACGGAAAGATCGAC 57.635 50.000 0.00 0.00 0.00 4.20
3849 4077 1.931551 CGCGTATTCCATGGAACGG 59.068 57.895 30.47 22.45 36.91 4.44
3852 4080 1.741055 GCGTATTCCATGGAACGGTCA 60.741 52.381 30.47 11.86 36.91 4.02
3955 4378 1.508808 AAACCGCGCGCTCCTTTTAA 61.509 50.000 30.48 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 6.467677 CACCAATAAAAGAGAGAGGACTTCA 58.532 40.000 0.00 0.00 0.00 3.02
35 36 5.352846 GCACCAATAAAAGAGAGAGGACTTC 59.647 44.000 0.00 0.00 0.00 3.01
36 37 5.249420 GCACCAATAAAAGAGAGAGGACTT 58.751 41.667 0.00 0.00 0.00 3.01
37 38 4.621747 CGCACCAATAAAAGAGAGAGGACT 60.622 45.833 0.00 0.00 0.00 3.85
38 39 3.619038 CGCACCAATAAAAGAGAGAGGAC 59.381 47.826 0.00 0.00 0.00 3.85
39 40 3.260884 ACGCACCAATAAAAGAGAGAGGA 59.739 43.478 0.00 0.00 0.00 3.71
40 41 3.600388 ACGCACCAATAAAAGAGAGAGG 58.400 45.455 0.00 0.00 0.00 3.69
41 42 6.369065 ACTTTACGCACCAATAAAAGAGAGAG 59.631 38.462 0.00 0.00 32.72 3.20
42 43 6.228258 ACTTTACGCACCAATAAAAGAGAGA 58.772 36.000 0.00 0.00 32.72 3.10
57 58 0.584396 CACCGAGCAAACTTTACGCA 59.416 50.000 0.00 0.00 0.00 5.24
59 60 0.515564 CCCACCGAGCAAACTTTACG 59.484 55.000 0.00 0.00 0.00 3.18
71 72 0.263468 TCACTATCCCATCCCACCGA 59.737 55.000 0.00 0.00 0.00 4.69
81 82 4.159135 TCAAGACCGTTAAGTCACTATCCC 59.841 45.833 0.00 0.00 39.34 3.85
82 83 5.320549 TCAAGACCGTTAAGTCACTATCC 57.679 43.478 0.00 0.00 39.34 2.59
83 84 5.978322 GGATCAAGACCGTTAAGTCACTATC 59.022 44.000 0.00 0.00 39.34 2.08
84 85 5.421056 TGGATCAAGACCGTTAAGTCACTAT 59.579 40.000 0.00 0.00 39.34 2.12
85 86 4.768448 TGGATCAAGACCGTTAAGTCACTA 59.232 41.667 0.00 0.00 39.34 2.74
86 87 3.576982 TGGATCAAGACCGTTAAGTCACT 59.423 43.478 0.00 0.00 39.34 3.41
87 88 3.921677 TGGATCAAGACCGTTAAGTCAC 58.078 45.455 0.00 0.00 39.34 3.67
92 93 2.416836 CGAGCTGGATCAAGACCGTTAA 60.417 50.000 0.00 0.00 0.00 2.01
124 125 1.399791 GCAGTTTAGCACAGGCAGATC 59.600 52.381 0.00 0.00 44.61 2.75
130 131 1.868997 CGTGGCAGTTTAGCACAGG 59.131 57.895 0.00 0.00 35.83 4.00
145 146 4.507756 ACATACATGTAGCTATTGTGCGTG 59.492 41.667 17.80 15.43 39.68 5.34
148 149 6.258727 AGTCAACATACATGTAGCTATTGTGC 59.741 38.462 17.80 9.65 40.80 4.57
150 151 7.555965 TCAGTCAACATACATGTAGCTATTGT 58.444 34.615 11.91 14.44 40.80 2.71
153 154 9.618890 AAATTCAGTCAACATACATGTAGCTAT 57.381 29.630 11.91 0.00 40.80 2.97
155 156 7.826252 AGAAATTCAGTCAACATACATGTAGCT 59.174 33.333 11.91 0.00 40.80 3.32
156 157 7.978982 AGAAATTCAGTCAACATACATGTAGC 58.021 34.615 11.91 0.00 40.80 3.58
180 206 7.602265 CCCACAAAATTGACTTACCCAAATTAG 59.398 37.037 0.00 0.00 0.00 1.73
188 214 5.508994 CCTTCACCCACAAAATTGACTTACC 60.509 44.000 0.00 0.00 0.00 2.85
258 284 5.751509 TCATTACATTAAGATCCAACGGTCG 59.248 40.000 0.00 0.00 0.00 4.79
266 292 7.639113 TTGTTGGGTCATTACATTAAGATCC 57.361 36.000 0.00 0.00 0.00 3.36
318 344 3.488384 GCCTTGTCTCTCGAGTCATACAG 60.488 52.174 13.13 0.90 0.00 2.74
328 354 2.578178 CGAGCGCCTTGTCTCTCG 60.578 66.667 2.29 0.00 41.66 4.04
334 360 0.321298 ACCAAATACGAGCGCCTTGT 60.321 50.000 2.29 2.29 32.27 3.16
335 361 0.096976 CACCAAATACGAGCGCCTTG 59.903 55.000 2.29 0.00 0.00 3.61
336 362 1.024579 CCACCAAATACGAGCGCCTT 61.025 55.000 2.29 0.00 0.00 4.35
337 363 1.449601 CCACCAAATACGAGCGCCT 60.450 57.895 2.29 0.00 0.00 5.52
383 409 2.410262 CGTCTGCATGTTCACTTCGTTC 60.410 50.000 0.00 0.00 0.00 3.95
384 410 1.526887 CGTCTGCATGTTCACTTCGTT 59.473 47.619 0.00 0.00 0.00 3.85
385 411 1.139989 CGTCTGCATGTTCACTTCGT 58.860 50.000 0.00 0.00 0.00 3.85
386 412 1.136529 CACGTCTGCATGTTCACTTCG 60.137 52.381 0.00 0.00 0.00 3.79
431 457 4.321718 CTTTGGTTCTCAGCTTCTGATGA 58.678 43.478 0.00 0.00 39.92 2.92
441 467 2.356535 CCTCCCATCCTTTGGTTCTCAG 60.357 54.545 0.00 0.00 44.83 3.35
504 530 0.475906 AGTTGAGTTGAGCCTGCCTT 59.524 50.000 0.00 0.00 0.00 4.35
531 557 3.184382 TCAGGTCAGGTCAGGTCATTA 57.816 47.619 0.00 0.00 0.00 1.90
532 558 2.030027 TCAGGTCAGGTCAGGTCATT 57.970 50.000 0.00 0.00 0.00 2.57
533 559 2.114616 GATCAGGTCAGGTCAGGTCAT 58.885 52.381 0.00 0.00 0.00 3.06
557 583 5.704888 TGTTTCGTTTCTCTTTTGCTTTCA 58.295 33.333 0.00 0.00 0.00 2.69
574 600 2.101209 AAAGGCACGACGCTGTTTCG 62.101 55.000 0.00 0.00 41.91 3.46
576 602 1.355210 CAAAGGCACGACGCTGTTT 59.645 52.632 0.00 0.00 41.91 2.83
605 631 3.429141 CTCGCCTGCCTGCACAAG 61.429 66.667 0.00 0.00 0.00 3.16
622 648 1.882623 CAGAACAGAACAGGCTTTCCC 59.117 52.381 0.00 0.00 0.00 3.97
623 649 2.576615 ACAGAACAGAACAGGCTTTCC 58.423 47.619 0.00 0.00 0.00 3.13
624 650 4.354587 CAAACAGAACAGAACAGGCTTTC 58.645 43.478 0.00 0.00 0.00 2.62
625 651 3.131046 CCAAACAGAACAGAACAGGCTTT 59.869 43.478 0.00 0.00 0.00 3.51
626 652 2.689983 CCAAACAGAACAGAACAGGCTT 59.310 45.455 0.00 0.00 0.00 4.35
627 653 2.301346 CCAAACAGAACAGAACAGGCT 58.699 47.619 0.00 0.00 0.00 4.58
628 654 1.269257 GCCAAACAGAACAGAACAGGC 60.269 52.381 0.00 0.00 0.00 4.85
629 655 1.002468 CGCCAAACAGAACAGAACAGG 60.002 52.381 0.00 0.00 0.00 4.00
630 656 1.939934 TCGCCAAACAGAACAGAACAG 59.060 47.619 0.00 0.00 0.00 3.16
631 657 1.939934 CTCGCCAAACAGAACAGAACA 59.060 47.619 0.00 0.00 0.00 3.18
632 658 1.264288 CCTCGCCAAACAGAACAGAAC 59.736 52.381 0.00 0.00 0.00 3.01
633 659 1.593196 CCTCGCCAAACAGAACAGAA 58.407 50.000 0.00 0.00 0.00 3.02
634 660 0.250295 CCCTCGCCAAACAGAACAGA 60.250 55.000 0.00 0.00 0.00 3.41
635 661 0.250295 TCCCTCGCCAAACAGAACAG 60.250 55.000 0.00 0.00 0.00 3.16
636 662 0.181587 TTCCCTCGCCAAACAGAACA 59.818 50.000 0.00 0.00 0.00 3.18
637 663 1.314730 TTTCCCTCGCCAAACAGAAC 58.685 50.000 0.00 0.00 0.00 3.01
638 664 1.885887 CATTTCCCTCGCCAAACAGAA 59.114 47.619 0.00 0.00 0.00 3.02
639 665 1.073125 TCATTTCCCTCGCCAAACAGA 59.927 47.619 0.00 0.00 0.00 3.41
640 666 1.533625 TCATTTCCCTCGCCAAACAG 58.466 50.000 0.00 0.00 0.00 3.16
641 667 1.988293 TTCATTTCCCTCGCCAAACA 58.012 45.000 0.00 0.00 0.00 2.83
642 668 2.609491 GGTTTCATTTCCCTCGCCAAAC 60.609 50.000 0.00 0.00 0.00 2.93
643 669 1.616374 GGTTTCATTTCCCTCGCCAAA 59.384 47.619 0.00 0.00 0.00 3.28
644 670 1.253100 GGTTTCATTTCCCTCGCCAA 58.747 50.000 0.00 0.00 0.00 4.52
645 671 0.958382 CGGTTTCATTTCCCTCGCCA 60.958 55.000 0.00 0.00 0.00 5.69
680 706 1.678101 CGAAGGAATTGAATGGGGCTC 59.322 52.381 0.00 0.00 0.00 4.70
681 707 1.005924 ACGAAGGAATTGAATGGGGCT 59.994 47.619 0.00 0.00 0.00 5.19
718 744 1.153529 TACGTTACCGCATGGCAGG 60.154 57.895 0.00 0.00 39.70 4.85
719 745 1.426041 GGTACGTTACCGCATGGCAG 61.426 60.000 0.00 0.00 39.39 4.85
720 746 1.448189 GGTACGTTACCGCATGGCA 60.448 57.895 0.00 0.00 39.39 4.92
721 747 3.402185 GGTACGTTACCGCATGGC 58.598 61.111 0.00 0.00 39.39 4.40
735 761 0.825410 AGAGAGAGAGAGACGCGGTA 59.175 55.000 12.47 0.00 0.00 4.02
753 779 1.988467 CGCTGTCTGTATGTGTGTGAG 59.012 52.381 0.00 0.00 0.00 3.51
756 782 0.318441 AGCGCTGTCTGTATGTGTGT 59.682 50.000 10.39 0.00 0.00 3.72
758 784 1.714794 GAAGCGCTGTCTGTATGTGT 58.285 50.000 12.58 0.00 0.00 3.72
763 789 2.571757 CCCGAAGCGCTGTCTGTA 59.428 61.111 12.58 0.00 0.00 2.74
860 890 1.002011 GTCTGGCAAGGTTCCCCTC 60.002 63.158 0.00 0.00 41.56 4.30
885 915 2.412591 CTCTCCCTCCTCTCTCTCTCT 58.587 57.143 0.00 0.00 0.00 3.10
887 917 0.846693 GCTCTCCCTCCTCTCTCTCT 59.153 60.000 0.00 0.00 0.00 3.10
893 923 1.531748 CTCTCGCTCTCCCTCCTCT 59.468 63.158 0.00 0.00 0.00 3.69
895 925 2.123897 GCTCTCGCTCTCCCTCCT 60.124 66.667 0.00 0.00 0.00 3.69
896 926 3.591835 CGCTCTCGCTCTCCCTCC 61.592 72.222 0.00 0.00 0.00 4.30
914 944 4.936248 CTCTCTCTCTCGCGCGCG 62.936 72.222 44.84 44.84 41.35 6.86
915 945 3.506312 CTCTCTCTCTCTCGCGCGC 62.506 68.421 27.95 23.91 0.00 6.86
916 946 1.821241 CTCTCTCTCTCTCTCGCGCG 61.821 65.000 26.76 26.76 0.00 6.86
917 947 0.529773 TCTCTCTCTCTCTCTCGCGC 60.530 60.000 0.00 0.00 0.00 6.86
918 948 1.067060 TCTCTCTCTCTCTCTCTCGCG 59.933 57.143 0.00 0.00 0.00 5.87
919 949 2.362397 TCTCTCTCTCTCTCTCTCTCGC 59.638 54.545 0.00 0.00 0.00 5.03
920 950 3.885901 TCTCTCTCTCTCTCTCTCTCTCG 59.114 52.174 0.00 0.00 0.00 4.04
946 976 1.603455 CCTTCCTTCCGCTGCCAAA 60.603 57.895 0.00 0.00 0.00 3.28
947 977 2.034066 CCTTCCTTCCGCTGCCAA 59.966 61.111 0.00 0.00 0.00 4.52
949 979 2.124942 CTCCTTCCTTCCGCTGCC 60.125 66.667 0.00 0.00 0.00 4.85
957 987 3.391382 CCGCCGTCCTCCTTCCTT 61.391 66.667 0.00 0.00 0.00 3.36
970 1000 4.798682 TCCTCCCCCTTCTCCGCC 62.799 72.222 0.00 0.00 0.00 6.13
971 1001 3.157949 CTCCTCCCCCTTCTCCGC 61.158 72.222 0.00 0.00 0.00 5.54
1122 1182 4.139859 AGCAGATGAGATTGAGAGTTGG 57.860 45.455 0.00 0.00 0.00 3.77
1146 1238 6.320418 GGAGAAAGTTGGAACCAAAACTAGAA 59.680 38.462 7.89 0.00 35.60 2.10
1295 1392 9.171701 CGAAAGAAGAGAATATTAGGAGTAACG 57.828 37.037 0.00 0.00 0.00 3.18
1335 1438 9.543231 TTTGAGACGGAGGGAGTATTTATATAT 57.457 33.333 0.00 0.00 0.00 0.86
1336 1439 8.945195 TTTGAGACGGAGGGAGTATTTATATA 57.055 34.615 0.00 0.00 0.00 0.86
1338 1441 7.664552 TTTTGAGACGGAGGGAGTATTTATA 57.335 36.000 0.00 0.00 0.00 0.98
1339 1442 6.555463 TTTTGAGACGGAGGGAGTATTTAT 57.445 37.500 0.00 0.00 0.00 1.40
1340 1443 6.555463 ATTTTGAGACGGAGGGAGTATTTA 57.445 37.500 0.00 0.00 0.00 1.40
1341 1444 4.903045 TTTTGAGACGGAGGGAGTATTT 57.097 40.909 0.00 0.00 0.00 1.40
1342 1445 5.189934 AGAATTTTGAGACGGAGGGAGTATT 59.810 40.000 0.00 0.00 0.00 1.89
1344 1447 4.094476 AGAATTTTGAGACGGAGGGAGTA 58.906 43.478 0.00 0.00 0.00 2.59
1345 1448 2.907042 AGAATTTTGAGACGGAGGGAGT 59.093 45.455 0.00 0.00 0.00 3.85
1346 1449 3.618690 AGAATTTTGAGACGGAGGGAG 57.381 47.619 0.00 0.00 0.00 4.30
1347 1450 3.072476 ACAAGAATTTTGAGACGGAGGGA 59.928 43.478 7.18 0.00 0.00 4.20
1348 1451 3.412386 ACAAGAATTTTGAGACGGAGGG 58.588 45.455 7.18 0.00 0.00 4.30
1349 1452 4.319177 AGACAAGAATTTTGAGACGGAGG 58.681 43.478 7.18 0.00 0.00 4.30
1350 1453 5.931441 AAGACAAGAATTTTGAGACGGAG 57.069 39.130 7.18 0.00 0.00 4.63
1351 1454 6.285224 TGTAAGACAAGAATTTTGAGACGGA 58.715 36.000 7.18 0.00 0.00 4.69
1352 1455 6.539649 TGTAAGACAAGAATTTTGAGACGG 57.460 37.500 7.18 0.00 0.00 4.79
1353 1456 8.895845 CAAATGTAAGACAAGAATTTTGAGACG 58.104 33.333 7.18 0.00 29.37 4.18
1354 1457 9.736023 ACAAATGTAAGACAAGAATTTTGAGAC 57.264 29.630 8.74 0.00 31.32 3.36
1355 1458 9.950680 GACAAATGTAAGACAAGAATTTTGAGA 57.049 29.630 8.74 0.00 31.32 3.27
1356 1459 9.734620 TGACAAATGTAAGACAAGAATTTTGAG 57.265 29.630 8.74 0.00 31.32 3.02
1363 1466 9.959749 GGTATTTTGACAAATGTAAGACAAGAA 57.040 29.630 0.50 0.00 34.29 2.52
1364 1467 8.286800 CGGTATTTTGACAAATGTAAGACAAGA 58.713 33.333 0.50 0.00 34.29 3.02
1365 1468 8.286800 TCGGTATTTTGACAAATGTAAGACAAG 58.713 33.333 0.50 0.00 34.29 3.16
1366 1469 8.155821 TCGGTATTTTGACAAATGTAAGACAA 57.844 30.769 0.50 0.00 34.29 3.18
1367 1470 7.731882 TCGGTATTTTGACAAATGTAAGACA 57.268 32.000 0.50 0.00 34.29 3.41
1368 1471 8.234546 ACATCGGTATTTTGACAAATGTAAGAC 58.765 33.333 0.50 0.00 34.29 3.01
1369 1472 8.330466 ACATCGGTATTTTGACAAATGTAAGA 57.670 30.769 0.50 0.57 34.29 2.10
1372 1475 9.384764 TGATACATCGGTATTTTGACAAATGTA 57.615 29.630 0.50 6.16 40.28 2.29
1373 1476 8.275015 TGATACATCGGTATTTTGACAAATGT 57.725 30.769 0.50 4.11 40.28 2.71
1374 1477 9.225201 CTTGATACATCGGTATTTTGACAAATG 57.775 33.333 0.50 0.00 40.28 2.32
1375 1478 8.956426 ACTTGATACATCGGTATTTTGACAAAT 58.044 29.630 0.50 0.00 40.28 2.32
1376 1479 8.330466 ACTTGATACATCGGTATTTTGACAAA 57.670 30.769 0.00 0.00 40.28 2.83
1377 1480 7.604545 TGACTTGATACATCGGTATTTTGACAA 59.395 33.333 0.00 0.00 40.28 3.18
1378 1481 7.064134 GTGACTTGATACATCGGTATTTTGACA 59.936 37.037 0.00 0.00 40.28 3.58
1379 1482 7.399523 GTGACTTGATACATCGGTATTTTGAC 58.600 38.462 0.00 0.00 40.28 3.18
1380 1483 6.254804 CGTGACTTGATACATCGGTATTTTGA 59.745 38.462 0.00 0.00 40.28 2.69
1381 1484 6.035650 ACGTGACTTGATACATCGGTATTTTG 59.964 38.462 0.00 0.00 40.28 2.44
1382 1485 6.103997 ACGTGACTTGATACATCGGTATTTT 58.896 36.000 0.00 0.00 40.28 1.82
1383 1486 5.657474 ACGTGACTTGATACATCGGTATTT 58.343 37.500 0.00 0.00 40.28 1.40
1384 1487 5.258456 ACGTGACTTGATACATCGGTATT 57.742 39.130 0.00 0.00 40.28 1.89
1385 1488 4.913335 ACGTGACTTGATACATCGGTAT 57.087 40.909 0.00 0.00 42.86 2.73
1386 1489 4.707030 AACGTGACTTGATACATCGGTA 57.293 40.909 0.00 0.00 0.00 4.02
1387 1490 3.587797 AACGTGACTTGATACATCGGT 57.412 42.857 0.00 0.00 0.00 4.69
1388 1491 4.921470 AAAACGTGACTTGATACATCGG 57.079 40.909 0.00 0.00 0.00 4.18
1439 1542 9.801873 CCTCTGTTTCAAAATTCTTGTCTTAAA 57.198 29.630 0.00 0.00 0.00 1.52
1440 1543 9.184523 TCCTCTGTTTCAAAATTCTTGTCTTAA 57.815 29.630 0.00 0.00 0.00 1.85
1441 1544 8.746052 TCCTCTGTTTCAAAATTCTTGTCTTA 57.254 30.769 0.00 0.00 0.00 2.10
1442 1545 7.645058 TCCTCTGTTTCAAAATTCTTGTCTT 57.355 32.000 0.00 0.00 0.00 3.01
1443 1546 7.340487 ACTTCCTCTGTTTCAAAATTCTTGTCT 59.660 33.333 0.00 0.00 0.00 3.41
1444 1547 7.484140 ACTTCCTCTGTTTCAAAATTCTTGTC 58.516 34.615 0.00 0.00 0.00 3.18
1445 1548 7.410120 ACTTCCTCTGTTTCAAAATTCTTGT 57.590 32.000 0.00 0.00 0.00 3.16
1446 1549 8.624776 AGTACTTCCTCTGTTTCAAAATTCTTG 58.375 33.333 0.00 0.00 0.00 3.02
1447 1550 8.753497 AGTACTTCCTCTGTTTCAAAATTCTT 57.247 30.769 0.00 0.00 0.00 2.52
1448 1551 9.274206 GTAGTACTTCCTCTGTTTCAAAATTCT 57.726 33.333 0.00 0.00 0.00 2.40
1449 1552 8.221766 CGTAGTACTTCCTCTGTTTCAAAATTC 58.778 37.037 0.00 0.00 0.00 2.17
1450 1553 7.307811 GCGTAGTACTTCCTCTGTTTCAAAATT 60.308 37.037 0.00 0.00 0.00 1.82
1451 1554 6.147328 GCGTAGTACTTCCTCTGTTTCAAAAT 59.853 38.462 0.00 0.00 0.00 1.82
1452 1555 5.464389 GCGTAGTACTTCCTCTGTTTCAAAA 59.536 40.000 0.00 0.00 0.00 2.44
1453 1556 4.986659 GCGTAGTACTTCCTCTGTTTCAAA 59.013 41.667 0.00 0.00 0.00 2.69
1454 1557 4.280174 AGCGTAGTACTTCCTCTGTTTCAA 59.720 41.667 0.00 0.00 0.00 2.69
1455 1558 3.825014 AGCGTAGTACTTCCTCTGTTTCA 59.175 43.478 0.00 0.00 0.00 2.69
1456 1559 4.437772 AGCGTAGTACTTCCTCTGTTTC 57.562 45.455 0.00 0.00 0.00 2.78
1457 1560 5.008980 ACTAGCGTAGTACTTCCTCTGTTT 58.991 41.667 0.00 0.00 37.23 2.83
1458 1561 4.587891 ACTAGCGTAGTACTTCCTCTGTT 58.412 43.478 0.00 0.00 37.23 3.16
1459 1562 4.219264 ACTAGCGTAGTACTTCCTCTGT 57.781 45.455 0.00 0.00 37.23 3.41
1460 1563 5.564048 AAACTAGCGTAGTACTTCCTCTG 57.436 43.478 0.00 0.00 38.26 3.35
1461 1564 7.878547 ATAAAACTAGCGTAGTACTTCCTCT 57.121 36.000 0.00 0.00 38.26 3.69
1462 1565 8.923609 AAATAAAACTAGCGTAGTACTTCCTC 57.076 34.615 0.00 0.00 38.26 3.71
1463 1566 9.716531 AAAAATAAAACTAGCGTAGTACTTCCT 57.283 29.630 0.00 0.00 38.26 3.36
1464 1567 9.750882 CAAAAATAAAACTAGCGTAGTACTTCC 57.249 33.333 0.00 0.00 38.26 3.46
1608 1720 3.452627 AGGAGAGGGAACACATCACATAC 59.547 47.826 0.00 0.00 32.04 2.39
1622 1734 3.898509 CGCGCAGAGAGGAGAGGG 61.899 72.222 8.75 0.00 0.00 4.30
2137 2259 0.119155 ACCCTCCTCTTCCATGACCA 59.881 55.000 0.00 0.00 0.00 4.02
2493 2690 3.136123 CCCGCTCCTGCATGGTTG 61.136 66.667 0.00 0.00 39.64 3.77
3037 3250 3.242936 GCTACCGTCAAAGCAAAAACTGA 60.243 43.478 0.00 0.00 38.63 3.41
3047 3260 3.060895 CGAAAGCTTAGCTACCGTCAAAG 59.939 47.826 7.32 0.00 38.25 2.77
3067 3280 2.998670 CACCGTGTAGTAACTCTCTCGA 59.001 50.000 0.00 0.00 0.00 4.04
3068 3281 2.998670 TCACCGTGTAGTAACTCTCTCG 59.001 50.000 0.00 0.00 0.00 4.04
3069 3282 3.181522 CGTCACCGTGTAGTAACTCTCTC 60.182 52.174 0.00 0.00 0.00 3.20
3070 3283 2.740981 CGTCACCGTGTAGTAACTCTCT 59.259 50.000 0.00 0.00 0.00 3.10
3203 3419 6.717997 TGAATCATTCCAATATCCCACTGATG 59.282 38.462 0.00 0.00 34.76 3.07
3256 3473 2.413837 GCTAGTGCGGAAAGAAAGTGA 58.586 47.619 0.00 0.00 0.00 3.41
3277 3494 3.300066 CGCGAACAAAACTTTGACGTTTC 60.300 43.478 0.00 2.09 40.55 2.78
3329 3546 7.860918 TGGACGGAATAGCATATACTACTAG 57.139 40.000 0.00 0.00 0.00 2.57
3333 3555 6.492429 ACACTTGGACGGAATAGCATATACTA 59.508 38.462 0.00 0.00 0.00 1.82
3334 3556 5.304614 ACACTTGGACGGAATAGCATATACT 59.695 40.000 0.00 0.00 0.00 2.12
3335 3557 5.405571 CACACTTGGACGGAATAGCATATAC 59.594 44.000 0.00 0.00 0.00 1.47
3336 3558 5.069914 ACACACTTGGACGGAATAGCATATA 59.930 40.000 0.00 0.00 0.00 0.86
3337 3559 4.141711 ACACACTTGGACGGAATAGCATAT 60.142 41.667 0.00 0.00 0.00 1.78
3395 3617 4.978083 AGATCCAAAGCATTGTCATCAC 57.022 40.909 11.36 0.00 34.60 3.06
3398 3620 7.893124 AATAGAAGATCCAAAGCATTGTCAT 57.107 32.000 0.43 0.00 34.60 3.06
3562 3784 2.494073 GGTTGGGGTTTTCGCATGATTA 59.506 45.455 0.00 0.00 38.15 1.75
3567 3789 1.822371 GTATGGTTGGGGTTTTCGCAT 59.178 47.619 0.00 0.00 38.15 4.73
3580 3802 7.283807 GGTTGTCCCTTAATTAATCGTATGGTT 59.716 37.037 0.00 0.00 0.00 3.67
3585 3807 8.484575 TGTATGGTTGTCCCTTAATTAATCGTA 58.515 33.333 0.00 0.00 0.00 3.43
3706 3931 4.380655 CGTGACGGAAGGAGAACTAAGAAT 60.381 45.833 0.00 0.00 0.00 2.40
3785 4011 7.174426 CGTGAGGTTACCTTTAAAATCTCCTTT 59.826 37.037 4.99 0.00 31.76 3.11
3787 4013 6.171213 CGTGAGGTTACCTTTAAAATCTCCT 58.829 40.000 4.99 0.00 31.76 3.69
3822 4048 2.733593 GAATACGCGCTAGGCCGG 60.734 66.667 5.73 0.00 38.94 6.13
3849 4077 1.079503 GCAGGAACGGATCAGTTGAC 58.920 55.000 16.23 8.67 34.00 3.18
3852 4080 2.270352 TTTGCAGGAACGGATCAGTT 57.730 45.000 11.21 11.21 36.99 3.16


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

AutoCloner maintained by Alex Coulton.