Multiple sequence alignment - TraesCS7A01G112600

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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 TraesCS7A01G112600 chr7A 100.000 2497 0 0 797 3293 68902086 68899590 0.000000e+00 4612.0
1 TraesCS7A01G112600 chr7A 100.000 604 0 0 1 604 68902882 68902279 0.000000e+00 1116.0
2 TraesCS7A01G112600 chr7A 84.043 564 72 12 1755 2303 68862410 68861850 8.090000e-146 527.0
3 TraesCS7A01G112600 chr7A 84.101 434 44 12 825 1251 68320932 68320517 2.380000e-106 396.0
4 TraesCS7A01G112600 chr7A 90.984 244 19 2 3053 3293 68861681 68861438 3.170000e-85 326.0
5 TraesCS7A01G112600 chr7A 76.949 603 113 22 1167 1765 68863452 68862872 1.470000e-83 320.0
6 TraesCS7A01G112600 chr7A 74.667 225 55 2 1600 1823 68320135 68319912 7.520000e-17 99.0
7 TraesCS7A01G112600 chr7A 90.385 52 5 0 2792 2843 292827504 292827555 5.900000e-08 69.4
8 TraesCS7A01G112600 chr7B 93.592 1904 91 11 797 2689 6375173 6373290 0.000000e+00 2811.0
9 TraesCS7A01G112600 chr7B 80.222 1264 180 41 1048 2303 6181649 6180448 0.000000e+00 885.0
10 TraesCS7A01G112600 chr7B 88.817 617 37 14 1 604 6392144 6391547 0.000000e+00 728.0
11 TraesCS7A01G112600 chr7B 85.160 438 41 12 825 1255 6034847 6034427 8.440000e-116 427.0
12 TraesCS7A01G112600 chr7B 88.525 244 17 6 3053 3293 6180285 6180050 5.380000e-73 285.0
13 TraesCS7A01G112600 chr7B 84.138 145 14 8 2153 2296 7544446 7544582 7.410000e-27 132.0
14 TraesCS7A01G112600 chr7B 81.373 102 18 1 2907 3008 596311024 596311124 7.570000e-12 82.4
15 TraesCS7A01G112600 chr7D 95.471 1678 62 5 1012 2689 64736590 64734927 0.000000e+00 2665.0
16 TraesCS7A01G112600 chr7D 81.358 1325 188 40 1001 2303 64700964 64699677 0.000000e+00 1024.0
17 TraesCS7A01G112600 chr7D 86.313 358 43 6 899 1255 64468251 64467899 5.150000e-103 385.0
18 TraesCS7A01G112600 chr7D 77.134 656 140 8 1624 2277 64467509 64466862 4.010000e-99 372.0
19 TraesCS7A01G112600 chr7D 97.674 43 1 0 111 153 64737350 64737392 1.270000e-09 75.0
20 TraesCS7A01G112600 chr7D 93.182 44 2 1 2802 2845 147822651 147822693 2.740000e-06 63.9
21 TraesCS7A01G112600 chr6B 76.015 1330 248 50 908 2221 43144749 43146023 1.000000e-174 623.0
22 TraesCS7A01G112600 chr6B 76.518 1235 231 40 1000 2221 43090143 43088955 1.300000e-173 619.0
23 TraesCS7A01G112600 chr6B 75.898 1336 249 45 908 2221 42855439 42856723 1.680000e-172 616.0
24 TraesCS7A01G112600 chr6B 75.159 1260 264 34 978 2220 42860624 42861851 6.210000e-152 547.0
25 TraesCS7A01G112600 chr6B 92.308 52 2 2 5 56 503930860 503930811 4.560000e-09 73.1
26 TraesCS7A01G112600 chr6B 100.000 29 0 0 15 43 438383650 438383678 2.000000e-03 54.7
27 TraesCS7A01G112600 chrUn 76.916 1096 216 24 1134 2221 93879956 93881022 3.660000e-164 588.0
28 TraesCS7A01G112600 chrUn 79.737 533 96 10 1692 2221 93939530 93940053 3.100000e-100 375.0
29 TraesCS7A01G112600 chrUn 100.000 28 0 0 2817 2844 176711590 176711563 6.000000e-03 52.8
30 TraesCS7A01G112600 chrUn 100.000 28 0 0 2817 2844 176745789 176745762 6.000000e-03 52.8
31 TraesCS7A01G112600 chr6A 75.389 1349 243 58 901 2221 24705422 24706709 1.330000e-158 569.0
32 TraesCS7A01G112600 chr6A 87.500 48 5 1 15 61 399726543 399726496 2.000000e-03 54.7
33 TraesCS7A01G112600 chr1D 77.976 168 18 6 2842 3008 185069683 185069832 1.630000e-13 87.9
34 TraesCS7A01G112600 chr6D 77.381 168 23 4 2842 3009 95269763 95269611 5.850000e-13 86.1
35 TraesCS7A01G112600 chr6D 97.619 42 1 0 2842 2883 386935118 386935159 4.560000e-09 73.1
36 TraesCS7A01G112600 chr6D 100.000 29 0 0 2880 2908 296676741 296676713 2.000000e-03 54.7
37 TraesCS7A01G112600 chr6D 100.000 29 0 0 2880 2908 386935124 386935152 2.000000e-03 54.7
38 TraesCS7A01G112600 chr4A 82.000 100 18 0 2907 3006 613328051 613327952 5.850000e-13 86.1
39 TraesCS7A01G112600 chr4A 100.000 31 0 0 2880 2910 735604646 735604676 1.280000e-04 58.4
40 TraesCS7A01G112600 chr3A 91.525 59 4 1 2738 2796 744862900 744862843 2.720000e-11 80.5
41 TraesCS7A01G112600 chr3A 93.333 45 3 0 2799 2843 650034985 650035029 2.120000e-07 67.6
42 TraesCS7A01G112600 chr2D 83.529 85 14 0 2907 2991 19617183 19617099 2.720000e-11 80.5
43 TraesCS7A01G112600 chr2D 100.000 42 0 0 2842 2883 383544490 383544449 9.800000e-11 78.7
44 TraesCS7A01G112600 chr2D 87.097 62 5 3 3 61 601609207 601609268 2.120000e-07 67.6
45 TraesCS7A01G112600 chr2D 95.122 41 2 0 2803 2843 527917612 527917652 7.630000e-07 65.8
46 TraesCS7A01G112600 chr1A 100.000 42 0 0 2842 2883 16095858 16095899 9.800000e-11 78.7
47 TraesCS7A01G112600 chr1A 100.000 29 0 0 2880 2908 16095864 16095892 2.000000e-03 54.7
48 TraesCS7A01G112600 chr4D 95.652 46 2 0 2799 2844 499408161 499408116 1.270000e-09 75.0
49 TraesCS7A01G112600 chr1B 76.647 167 18 6 2842 3008 259793562 259793417 4.560000e-09 73.1
50 TraesCS7A01G112600 chr1B 90.000 50 4 1 2799 2847 637371352 637371303 2.740000e-06 63.9
51 TraesCS7A01G112600 chr2B 90.566 53 5 0 4 56 649036762 649036814 1.640000e-08 71.3
52 TraesCS7A01G112600 chr2B 87.500 64 5 3 1 61 731900764 731900827 1.640000e-08 71.3
53 TraesCS7A01G112600 chr5B 100.000 29 0 0 2880 2908 455741721 455741693 2.000000e-03 54.7
54 TraesCS7A01G112600 chr4B 100.000 29 0 0 2880 2908 1321031 1321059 2.000000e-03 54.7
55 TraesCS7A01G112600 chr3B 100.000 28 0 0 2817 2844 713778897 713778924 6.000000e-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 TraesCS7A01G112600 chr7A 68899590 68902882 3292 True 2864.0 4612 100.0000 1 3293 2 chr7A.!!$R3 3292
1 TraesCS7A01G112600 chr7A 68861438 68863452 2014 True 391.0 527 83.9920 1167 3293 3 chr7A.!!$R2 2126
2 TraesCS7A01G112600 chr7A 68319912 68320932 1020 True 247.5 396 79.3840 825 1823 2 chr7A.!!$R1 998
3 TraesCS7A01G112600 chr7B 6373290 6375173 1883 True 2811.0 2811 93.5920 797 2689 1 chr7B.!!$R2 1892
4 TraesCS7A01G112600 chr7B 6391547 6392144 597 True 728.0 728 88.8170 1 604 1 chr7B.!!$R3 603
5 TraesCS7A01G112600 chr7B 6180050 6181649 1599 True 585.0 885 84.3735 1048 3293 2 chr7B.!!$R4 2245
6 TraesCS7A01G112600 chr7D 64734927 64736590 1663 True 2665.0 2665 95.4710 1012 2689 1 chr7D.!!$R2 1677
7 TraesCS7A01G112600 chr7D 64699677 64700964 1287 True 1024.0 1024 81.3580 1001 2303 1 chr7D.!!$R1 1302
8 TraesCS7A01G112600 chr7D 64466862 64468251 1389 True 378.5 385 81.7235 899 2277 2 chr7D.!!$R3 1378
9 TraesCS7A01G112600 chr6B 43144749 43146023 1274 False 623.0 623 76.0150 908 2221 1 chr6B.!!$F1 1313
10 TraesCS7A01G112600 chr6B 43088955 43090143 1188 True 619.0 619 76.5180 1000 2221 1 chr6B.!!$R1 1221
11 TraesCS7A01G112600 chr6B 42855439 42861851 6412 False 581.5 616 75.5285 908 2221 2 chr6B.!!$F3 1313
12 TraesCS7A01G112600 chrUn 93879956 93881022 1066 False 588.0 588 76.9160 1134 2221 1 chrUn.!!$F1 1087
13 TraesCS7A01G112600 chrUn 93939530 93940053 523 False 375.0 375 79.7370 1692 2221 1 chrUn.!!$F2 529
14 TraesCS7A01G112600 chr6A 24705422 24706709 1287 False 569.0 569 75.3890 901 2221 1 chr6A.!!$F1 1320

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
892 909 0.178891 TGGCTCCCAACCTCTCTCTT 60.179 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2476 8351 0.108585 ACTTGCCAGACCATGTTCGT 59.891 50.0 0.0 0.0 0.0 3.85 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
30 31 8.660295 ATGAATTGATGGCATTGATATTACCT 57.340 30.769 0.00 0.00 0.00 3.08
112 113 7.488471 GCGCAAGGTATAGATAATACTTAGGTG 59.512 40.741 0.30 0.00 40.40 4.00
163 164 5.934625 AGACTCACTAATGCTTTGACGATTT 59.065 36.000 0.00 0.00 0.00 2.17
164 165 6.428159 AGACTCACTAATGCTTTGACGATTTT 59.572 34.615 0.00 0.00 0.00 1.82
165 166 6.970484 ACTCACTAATGCTTTGACGATTTTT 58.030 32.000 0.00 0.00 0.00 1.94
166 167 8.094798 ACTCACTAATGCTTTGACGATTTTTA 57.905 30.769 0.00 0.00 0.00 1.52
216 217 3.685139 TCACTGAAGGGATGACAAGAC 57.315 47.619 0.00 0.00 0.00 3.01
219 220 3.750130 CACTGAAGGGATGACAAGACTTG 59.250 47.826 13.77 13.77 0.00 3.16
227 228 4.214332 GGGATGACAAGACTTGAGTTCAAC 59.786 45.833 21.95 12.74 0.00 3.18
229 230 3.857052 TGACAAGACTTGAGTTCAACGT 58.143 40.909 21.95 0.00 0.00 3.99
230 231 3.616821 TGACAAGACTTGAGTTCAACGTG 59.383 43.478 21.95 0.00 0.00 4.49
234 235 2.936498 AGACTTGAGTTCAACGTGTTGG 59.064 45.455 12.43 0.00 40.78 3.77
268 269 8.020819 TGCTTACAAATGAAAGTTAGTACATGC 58.979 33.333 0.00 0.00 0.00 4.06
283 284 2.559998 CATGCCGTATGTGGGTTTTC 57.440 50.000 0.00 0.00 31.92 2.29
284 285 2.091541 CATGCCGTATGTGGGTTTTCT 58.908 47.619 0.00 0.00 31.92 2.52
285 286 2.279935 TGCCGTATGTGGGTTTTCTT 57.720 45.000 0.00 0.00 0.00 2.52
286 287 3.420300 TGCCGTATGTGGGTTTTCTTA 57.580 42.857 0.00 0.00 0.00 2.10
287 288 3.340034 TGCCGTATGTGGGTTTTCTTAG 58.660 45.455 0.00 0.00 0.00 2.18
295 296 9.028185 CGTATGTGGGTTTTCTTAGTAAGATAC 57.972 37.037 13.34 13.41 37.38 2.24
390 400 8.044060 TGACACTGAAAAATATGGATTGTCTC 57.956 34.615 0.00 0.00 0.00 3.36
431 441 4.756642 TGTTGAACTGTCATTCTAGGCTTG 59.243 41.667 0.00 0.00 32.48 4.01
451 461 2.228582 TGGGTTTGACAATGATGCTTCG 59.771 45.455 0.00 0.00 0.00 3.79
540 550 5.220586 GCGCATGCACAATTACTAGTAAGAA 60.221 40.000 19.57 2.46 42.15 2.52
541 551 6.511767 GCGCATGCACAATTACTAGTAAGAAT 60.512 38.462 19.57 4.65 42.15 2.40
847 857 1.081376 CGTCTGCGAAGTCCGAACT 60.081 57.895 0.00 0.00 41.76 3.01
882 899 2.203422 CCAAACCGTGGCTCCCAA 60.203 61.111 0.00 0.00 41.72 4.12
883 900 2.561037 CCAAACCGTGGCTCCCAAC 61.561 63.158 0.00 0.00 41.72 3.77
885 902 2.763645 AAACCGTGGCTCCCAACCT 61.764 57.895 0.00 0.00 34.18 3.50
886 903 2.692273 AAACCGTGGCTCCCAACCTC 62.692 60.000 0.00 0.00 34.18 3.85
887 904 3.322466 CCGTGGCTCCCAACCTCT 61.322 66.667 0.00 0.00 34.18 3.69
891 908 0.907230 GTGGCTCCCAACCTCTCTCT 60.907 60.000 0.00 0.00 34.18 3.10
892 909 0.178891 TGGCTCCCAACCTCTCTCTT 60.179 55.000 0.00 0.00 0.00 2.85
897 917 1.153745 CCAACCTCTCTCTTCGCCG 60.154 63.158 0.00 0.00 0.00 6.46
997 1035 4.541250 ACATTCCTCTCATCTCTCTCCT 57.459 45.455 0.00 0.00 0.00 3.69
1016 1054 2.356432 CCTCCATGGAGCTGATCAAACA 60.356 50.000 32.97 0.00 40.69 2.83
1026 1064 0.179032 TGATCAAACACACGGCCACT 60.179 50.000 2.24 0.00 0.00 4.00
1190 1238 4.473520 CAAGTCCTGGGCGGCGAT 62.474 66.667 12.98 0.00 0.00 4.58
1325 1430 1.519455 CCATCTTCTCCGTGCCGAC 60.519 63.158 0.00 0.00 0.00 4.79
1596 6932 2.793585 CGTTAGCCAGTATTTCGAGCGA 60.794 50.000 0.00 0.00 0.00 4.93
1829 7658 0.757188 CAGTACTCCCCGATCTGCCT 60.757 60.000 0.00 0.00 0.00 4.75
1865 7706 1.271102 GAACTCTCACCTGCTCGAGTT 59.729 52.381 15.13 3.45 46.15 3.01
1890 7731 1.250840 GGGAGGTCATGTTTGTGGGC 61.251 60.000 0.00 0.00 0.00 5.36
1949 7790 0.534412 ATCAGAGGCTTCGAGGTGTG 59.466 55.000 0.00 0.00 0.00 3.82
1955 7796 2.970974 GCTTCGAGGTGTGCAAGCC 61.971 63.158 0.00 0.00 36.11 4.35
2332 8207 3.120792 TGAGTGTAAGTTGCAGTTCGAC 58.879 45.455 2.62 0.00 0.00 4.20
2396 8271 5.359576 TGTTGCTTGTCAAAGGTTTATGAGT 59.640 36.000 0.00 0.00 36.26 3.41
2410 8285 4.574674 TTATGAGTGAAATCCTGTGCCT 57.425 40.909 0.00 0.00 0.00 4.75
2444 8319 2.872858 GCTCAATCGGTCCTTTGTATCC 59.127 50.000 2.43 0.00 0.00 2.59
2460 8335 4.519213 TGTATCCGAAGGGTGGTTTATTG 58.481 43.478 0.00 0.00 44.06 1.90
2555 8430 5.612725 TGATGTGTACTAGCCATTCATGA 57.387 39.130 0.00 0.00 0.00 3.07
2593 8468 3.822735 CCAAACCTCTCTCAAAGCATGAA 59.177 43.478 0.00 0.00 37.67 2.57
2651 8526 4.006319 GTGCTAGCACCTCAAGATTTCTT 58.994 43.478 33.32 0.00 40.79 2.52
2709 8584 9.937175 GATTATAGTTACTGTTCATTTTCCAGC 57.063 33.333 0.00 0.00 0.00 4.85
2710 8585 6.759497 ATAGTTACTGTTCATTTTCCAGCC 57.241 37.500 0.00 0.00 0.00 4.85
2711 8586 4.729868 AGTTACTGTTCATTTTCCAGCCT 58.270 39.130 0.00 0.00 0.00 4.58
2712 8587 5.876357 AGTTACTGTTCATTTTCCAGCCTA 58.124 37.500 0.00 0.00 0.00 3.93
2713 8588 5.705905 AGTTACTGTTCATTTTCCAGCCTAC 59.294 40.000 0.00 0.00 0.00 3.18
2714 8589 4.373156 ACTGTTCATTTTCCAGCCTACT 57.627 40.909 0.00 0.00 0.00 2.57
2715 8590 5.499004 ACTGTTCATTTTCCAGCCTACTA 57.501 39.130 0.00 0.00 0.00 1.82
2716 8591 5.876357 ACTGTTCATTTTCCAGCCTACTAA 58.124 37.500 0.00 0.00 0.00 2.24
2717 8592 5.705905 ACTGTTCATTTTCCAGCCTACTAAC 59.294 40.000 0.00 0.00 0.00 2.34
2718 8593 5.626142 TGTTCATTTTCCAGCCTACTAACA 58.374 37.500 0.00 0.00 0.00 2.41
2719 8594 5.472137 TGTTCATTTTCCAGCCTACTAACAC 59.528 40.000 0.00 0.00 0.00 3.32
2720 8595 5.499004 TCATTTTCCAGCCTACTAACACT 57.501 39.130 0.00 0.00 0.00 3.55
2721 8596 5.876357 TCATTTTCCAGCCTACTAACACTT 58.124 37.500 0.00 0.00 0.00 3.16
2722 8597 5.705441 TCATTTTCCAGCCTACTAACACTTG 59.295 40.000 0.00 0.00 0.00 3.16
2723 8598 4.967084 TTTCCAGCCTACTAACACTTGA 57.033 40.909 0.00 0.00 0.00 3.02
2724 8599 5.499004 TTTCCAGCCTACTAACACTTGAT 57.501 39.130 0.00 0.00 0.00 2.57
2725 8600 6.614694 TTTCCAGCCTACTAACACTTGATA 57.385 37.500 0.00 0.00 0.00 2.15
2726 8601 6.808321 TTCCAGCCTACTAACACTTGATAT 57.192 37.500 0.00 0.00 0.00 1.63
2727 8602 7.907841 TTCCAGCCTACTAACACTTGATATA 57.092 36.000 0.00 0.00 0.00 0.86
2728 8603 8.492415 TTCCAGCCTACTAACACTTGATATAT 57.508 34.615 0.00 0.00 0.00 0.86
2729 8604 9.596308 TTCCAGCCTACTAACACTTGATATATA 57.404 33.333 0.00 0.00 0.00 0.86
2730 8605 9.244292 TCCAGCCTACTAACACTTGATATATAG 57.756 37.037 0.00 0.00 0.00 1.31
2731 8606 8.470805 CCAGCCTACTAACACTTGATATATAGG 58.529 40.741 0.00 0.00 0.00 2.57
2732 8607 9.026121 CAGCCTACTAACACTTGATATATAGGT 57.974 37.037 0.00 0.00 31.21 3.08
2733 8608 9.245481 AGCCTACTAACACTTGATATATAGGTC 57.755 37.037 0.00 0.00 31.21 3.85
2734 8609 8.468399 GCCTACTAACACTTGATATATAGGTCC 58.532 40.741 0.00 0.00 31.21 4.46
2735 8610 9.756571 CCTACTAACACTTGATATATAGGTCCT 57.243 37.037 0.00 0.00 0.00 3.85
2764 8639 3.535280 TTTTTGAGGTTGCCTTTGACC 57.465 42.857 0.00 0.00 31.76 4.02
2765 8640 2.151502 TTTGAGGTTGCCTTTGACCA 57.848 45.000 0.00 0.00 38.42 4.02
2766 8641 2.380064 TTGAGGTTGCCTTTGACCAT 57.620 45.000 0.00 0.00 38.42 3.55
2767 8642 2.380064 TGAGGTTGCCTTTGACCATT 57.620 45.000 0.00 0.00 38.42 3.16
2768 8643 1.962807 TGAGGTTGCCTTTGACCATTG 59.037 47.619 0.00 0.00 38.42 2.82
2769 8644 1.273327 GAGGTTGCCTTTGACCATTGG 59.727 52.381 0.00 0.00 38.42 3.16
2770 8645 1.047801 GGTTGCCTTTGACCATTGGT 58.952 50.000 8.42 8.42 39.44 3.67
2771 8646 2.158385 AGGTTGCCTTTGACCATTGGTA 60.158 45.455 8.70 0.00 38.42 3.25
2772 8647 2.630580 GGTTGCCTTTGACCATTGGTAA 59.369 45.455 8.70 0.00 35.25 2.85
2773 8648 3.306019 GGTTGCCTTTGACCATTGGTAAG 60.306 47.826 8.70 9.68 35.25 2.34
2774 8649 3.517296 TGCCTTTGACCATTGGTAAGA 57.483 42.857 16.66 2.03 35.25 2.10
2775 8650 4.046286 TGCCTTTGACCATTGGTAAGAT 57.954 40.909 16.66 0.00 35.25 2.40
2776 8651 4.415596 TGCCTTTGACCATTGGTAAGATT 58.584 39.130 16.66 0.00 35.25 2.40
2777 8652 5.575157 TGCCTTTGACCATTGGTAAGATTA 58.425 37.500 16.66 3.65 35.25 1.75
2778 8653 6.013379 TGCCTTTGACCATTGGTAAGATTAA 58.987 36.000 16.66 0.00 35.25 1.40
2779 8654 6.667414 TGCCTTTGACCATTGGTAAGATTAAT 59.333 34.615 16.66 0.00 35.25 1.40
2780 8655 7.836685 TGCCTTTGACCATTGGTAAGATTAATA 59.163 33.333 16.66 0.00 35.25 0.98
2781 8656 8.691797 GCCTTTGACCATTGGTAAGATTAATAA 58.308 33.333 16.66 0.00 35.25 1.40
2821 8696 8.958119 TCAAGTTATTACAAAGTTGAGTCACT 57.042 30.769 0.00 0.00 41.57 3.41
2822 8697 9.391006 TCAAGTTATTACAAAGTTGAGTCACTT 57.609 29.630 0.00 0.00 41.57 3.16
2829 8704 6.867662 ACAAAGTTGAGTCACTTATTCTGG 57.132 37.500 0.00 0.00 35.87 3.86
2830 8705 5.765182 ACAAAGTTGAGTCACTTATTCTGGG 59.235 40.000 0.00 0.00 35.87 4.45
2831 8706 5.825593 AAGTTGAGTCACTTATTCTGGGA 57.174 39.130 0.00 0.00 35.10 4.37
2832 8707 5.153950 AGTTGAGTCACTTATTCTGGGAC 57.846 43.478 0.00 0.00 0.00 4.46
2833 8708 3.868757 TGAGTCACTTATTCTGGGACG 57.131 47.619 0.00 0.00 33.84 4.79
2834 8709 2.496070 TGAGTCACTTATTCTGGGACGG 59.504 50.000 0.00 0.00 33.84 4.79
2835 8710 2.758979 GAGTCACTTATTCTGGGACGGA 59.241 50.000 0.00 0.00 45.11 4.69
2845 8720 3.675348 TCTGGGACGGAAGGAGTATAA 57.325 47.619 0.00 0.00 43.00 0.98
2846 8721 3.985127 TCTGGGACGGAAGGAGTATAAA 58.015 45.455 0.00 0.00 43.00 1.40
2847 8722 4.355549 TCTGGGACGGAAGGAGTATAAAA 58.644 43.478 0.00 0.00 43.00 1.52
2848 8723 4.778958 TCTGGGACGGAAGGAGTATAAAAA 59.221 41.667 0.00 0.00 43.00 1.94
2849 8724 5.427481 TCTGGGACGGAAGGAGTATAAAAAT 59.573 40.000 0.00 0.00 43.00 1.82
2850 8725 6.069705 TGGGACGGAAGGAGTATAAAAATT 57.930 37.500 0.00 0.00 0.00 1.82
2851 8726 7.126115 TCTGGGACGGAAGGAGTATAAAAATTA 59.874 37.037 0.00 0.00 43.00 1.40
2852 8727 7.808218 TGGGACGGAAGGAGTATAAAAATTAT 58.192 34.615 0.00 0.00 0.00 1.28
2853 8728 8.936787 TGGGACGGAAGGAGTATAAAAATTATA 58.063 33.333 0.00 0.00 0.00 0.98
2854 8729 9.955102 GGGACGGAAGGAGTATAAAAATTATAT 57.045 33.333 0.00 0.00 0.00 0.86
2910 8785 7.750229 TCATTAGAAACTTCTTTCACATGCT 57.250 32.000 0.00 0.00 38.67 3.79
2911 8786 8.169977 TCATTAGAAACTTCTTTCACATGCTT 57.830 30.769 0.00 0.00 38.67 3.91
2912 8787 8.632679 TCATTAGAAACTTCTTTCACATGCTTT 58.367 29.630 0.00 0.00 38.67 3.51
2913 8788 9.897744 CATTAGAAACTTCTTTCACATGCTTTA 57.102 29.630 0.00 0.00 38.67 1.85
2915 8790 9.897744 TTAGAAACTTCTTTCACATGCTTTATG 57.102 29.630 0.00 0.00 38.67 1.90
2916 8791 7.945134 AGAAACTTCTTTCACATGCTTTATGT 58.055 30.769 0.00 0.00 41.92 2.29
2917 8792 9.066892 AGAAACTTCTTTCACATGCTTTATGTA 57.933 29.630 0.00 0.00 40.32 2.29
2927 8802 5.570262 CATGCTTTATGTAACATGCATGC 57.430 39.130 26.53 11.82 46.74 4.06
2928 8803 4.044336 TGCTTTATGTAACATGCATGCC 57.956 40.909 26.53 14.72 0.00 4.40
2929 8804 3.446516 TGCTTTATGTAACATGCATGCCA 59.553 39.130 26.53 19.64 0.00 4.92
2930 8805 4.099727 TGCTTTATGTAACATGCATGCCAT 59.900 37.500 26.53 24.22 33.39 4.40
2931 8806 5.301298 TGCTTTATGTAACATGCATGCCATA 59.699 36.000 26.53 23.30 31.47 2.74
2932 8807 6.015265 TGCTTTATGTAACATGCATGCCATAT 60.015 34.615 26.53 18.41 31.47 1.78
2933 8808 7.176340 TGCTTTATGTAACATGCATGCCATATA 59.824 33.333 26.53 20.01 31.47 0.86
2934 8809 8.192774 GCTTTATGTAACATGCATGCCATATAT 58.807 33.333 26.53 19.92 31.47 0.86
2943 8818 9.690913 AACATGCATGCCATATATTATTACTCT 57.309 29.630 26.53 0.00 31.47 3.24
2959 8834 9.712305 ATTATTACTCTAAATCATGGTCGAAGG 57.288 33.333 0.00 0.00 0.00 3.46
2960 8835 6.540438 TTACTCTAAATCATGGTCGAAGGT 57.460 37.500 0.00 0.00 0.00 3.50
2961 8836 5.422214 ACTCTAAATCATGGTCGAAGGTT 57.578 39.130 0.00 0.00 0.00 3.50
2962 8837 6.540438 ACTCTAAATCATGGTCGAAGGTTA 57.460 37.500 0.00 0.00 0.00 2.85
2963 8838 6.338937 ACTCTAAATCATGGTCGAAGGTTAC 58.661 40.000 0.00 0.00 0.00 2.50
2964 8839 5.667466 TCTAAATCATGGTCGAAGGTTACC 58.333 41.667 0.00 0.00 36.24 2.85
2965 8840 4.569719 AAATCATGGTCGAAGGTTACCT 57.430 40.909 0.00 0.00 36.67 3.08
2966 8841 3.821421 ATCATGGTCGAAGGTTACCTC 57.179 47.619 3.62 0.00 36.67 3.85
2967 8842 1.475280 TCATGGTCGAAGGTTACCTCG 59.525 52.381 3.62 10.41 36.67 4.63
2968 8843 1.475280 CATGGTCGAAGGTTACCTCGA 59.525 52.381 17.34 17.34 36.67 4.04
2969 8844 1.619654 TGGTCGAAGGTTACCTCGAA 58.380 50.000 20.95 9.37 35.94 3.71
2970 8845 1.962807 TGGTCGAAGGTTACCTCGAAA 59.037 47.619 20.95 13.17 35.94 3.46
2971 8846 2.364970 TGGTCGAAGGTTACCTCGAAAA 59.635 45.455 20.95 12.91 35.94 2.29
2972 8847 3.181467 TGGTCGAAGGTTACCTCGAAAAA 60.181 43.478 20.95 11.14 35.94 1.94
2973 8848 3.185188 GGTCGAAGGTTACCTCGAAAAAC 59.815 47.826 20.95 12.67 35.94 2.43
2974 8849 3.052036 TCGAAGGTTACCTCGAAAAACG 58.948 45.455 18.41 10.41 44.09 3.60
2975 8850 2.796593 CGAAGGTTACCTCGAAAAACGT 59.203 45.455 3.62 0.00 43.13 3.99
2976 8851 3.980775 CGAAGGTTACCTCGAAAAACGTA 59.019 43.478 3.62 0.00 43.13 3.57
2977 8852 4.622740 CGAAGGTTACCTCGAAAAACGTAT 59.377 41.667 3.62 0.00 43.13 3.06
2978 8853 5.119125 CGAAGGTTACCTCGAAAAACGTATT 59.881 40.000 3.62 0.00 43.13 1.89
2979 8854 6.307800 CGAAGGTTACCTCGAAAAACGTATTA 59.692 38.462 3.62 0.00 43.13 0.98
2980 8855 7.461938 CGAAGGTTACCTCGAAAAACGTATTAG 60.462 40.741 3.62 0.00 43.13 1.73
2981 8856 6.101997 AGGTTACCTCGAAAAACGTATTAGG 58.898 40.000 0.00 0.00 43.13 2.69
2982 8857 5.220472 GGTTACCTCGAAAAACGTATTAGGC 60.220 44.000 0.00 0.00 43.13 3.93
2983 8858 3.264947 ACCTCGAAAAACGTATTAGGCC 58.735 45.455 0.00 0.00 43.13 5.19
2984 8859 3.055602 ACCTCGAAAAACGTATTAGGCCT 60.056 43.478 11.78 11.78 43.13 5.19
2985 8860 3.937079 CCTCGAAAAACGTATTAGGCCTT 59.063 43.478 12.58 0.00 43.13 4.35
2986 8861 5.111293 CCTCGAAAAACGTATTAGGCCTTA 58.889 41.667 12.58 0.11 43.13 2.69
2987 8862 5.756833 CCTCGAAAAACGTATTAGGCCTTAT 59.243 40.000 12.58 10.82 43.13 1.73
2988 8863 6.925165 CCTCGAAAAACGTATTAGGCCTTATA 59.075 38.462 12.58 9.49 43.13 0.98
2989 8864 7.601508 CCTCGAAAAACGTATTAGGCCTTATAT 59.398 37.037 12.58 5.16 43.13 0.86
2990 8865 9.630098 CTCGAAAAACGTATTAGGCCTTATATA 57.370 33.333 12.58 4.05 43.13 0.86
3004 8879 8.454859 AGGCCTTATATATTTTGATGGAGAGA 57.545 34.615 0.00 0.00 0.00 3.10
3005 8880 8.547173 AGGCCTTATATATTTTGATGGAGAGAG 58.453 37.037 0.00 0.00 0.00 3.20
3006 8881 8.325046 GGCCTTATATATTTTGATGGAGAGAGT 58.675 37.037 0.00 0.00 0.00 3.24
3014 8889 9.965902 ATATTTTGATGGAGAGAGTAGTTTGTT 57.034 29.630 0.00 0.00 0.00 2.83
3015 8890 7.730364 TTTTGATGGAGAGAGTAGTTTGTTC 57.270 36.000 0.00 0.00 0.00 3.18
3016 8891 6.672266 TTGATGGAGAGAGTAGTTTGTTCT 57.328 37.500 0.00 0.00 0.00 3.01
3017 8892 6.030548 TGATGGAGAGAGTAGTTTGTTCTG 57.969 41.667 0.00 0.00 0.00 3.02
3018 8893 5.540337 TGATGGAGAGAGTAGTTTGTTCTGT 59.460 40.000 0.00 0.00 0.00 3.41
3019 8894 5.455056 TGGAGAGAGTAGTTTGTTCTGTC 57.545 43.478 0.00 0.00 32.26 3.51
3020 8895 4.893524 TGGAGAGAGTAGTTTGTTCTGTCA 59.106 41.667 1.24 0.00 34.07 3.58
3021 8896 5.540337 TGGAGAGAGTAGTTTGTTCTGTCAT 59.460 40.000 1.24 0.00 34.07 3.06
3022 8897 5.866633 GGAGAGAGTAGTTTGTTCTGTCATG 59.133 44.000 0.00 0.00 34.07 3.07
3023 8898 5.788450 AGAGAGTAGTTTGTTCTGTCATGG 58.212 41.667 0.00 0.00 0.00 3.66
3024 8899 5.305644 AGAGAGTAGTTTGTTCTGTCATGGT 59.694 40.000 0.00 0.00 0.00 3.55
3025 8900 5.542779 AGAGTAGTTTGTTCTGTCATGGTC 58.457 41.667 0.00 0.00 0.00 4.02
3026 8901 4.307432 AGTAGTTTGTTCTGTCATGGTCG 58.693 43.478 0.00 0.00 0.00 4.79
3028 8903 0.865111 TTTGTTCTGTCATGGTCGCG 59.135 50.000 0.00 0.00 0.00 5.87
3030 8905 0.246360 TGTTCTGTCATGGTCGCGAT 59.754 50.000 14.06 0.00 0.00 4.58
3033 8908 3.123804 GTTCTGTCATGGTCGCGATAAT 58.876 45.455 14.06 6.35 0.00 1.28
3039 8914 7.320399 TCTGTCATGGTCGCGATAATAATATT 58.680 34.615 14.06 0.00 0.00 1.28
3069 8949 9.683069 CATAGTGCTAGAAGTTCAAATTTTGTT 57.317 29.630 5.50 0.00 0.00 2.83
3098 8979 6.974965 ACAGAGATGGAACTTGAATTTTGTC 58.025 36.000 0.00 0.00 0.00 3.18
3114 8995 6.739331 ATTTTGTCCCAACAGAACCATTTA 57.261 33.333 0.00 0.00 36.57 1.40
3115 8996 5.523438 TTTGTCCCAACAGAACCATTTAC 57.477 39.130 0.00 0.00 36.57 2.01
3117 8998 3.143728 GTCCCAACAGAACCATTTACGT 58.856 45.455 0.00 0.00 0.00 3.57
3127 9008 1.338769 ACCATTTACGTCCAGCAGACC 60.339 52.381 0.00 0.00 43.08 3.85
3131 9012 1.592400 TTACGTCCAGCAGACCGAGG 61.592 60.000 0.00 0.00 43.08 4.63
3132 9013 4.803426 CGTCCAGCAGACCGAGGC 62.803 72.222 1.71 0.00 43.08 4.70
3133 9014 3.695606 GTCCAGCAGACCGAGGCA 61.696 66.667 0.00 0.00 39.84 4.75
3134 9015 2.922503 TCCAGCAGACCGAGGCAA 60.923 61.111 0.00 0.00 0.00 4.52
3135 9016 2.743928 CCAGCAGACCGAGGCAAC 60.744 66.667 0.00 0.00 0.00 4.17
3136 9017 2.031012 CAGCAGACCGAGGCAACA 59.969 61.111 0.00 0.00 41.41 3.33
3137 9018 1.597854 CAGCAGACCGAGGCAACAA 60.598 57.895 0.00 0.00 41.41 2.83
3138 9019 1.598130 AGCAGACCGAGGCAACAAC 60.598 57.895 0.00 0.00 41.41 3.32
3199 9090 5.125367 AGTCCTAACCAAAAACCACTCTT 57.875 39.130 0.00 0.00 0.00 2.85
3208 9099 8.999905 AACCAAAAACCACTCTTATTAGGTAA 57.000 30.769 0.00 0.00 33.15 2.85
3231 9122 0.319383 TGCAATCGCGCAAACCAAAT 60.319 45.000 8.75 0.00 42.97 2.32
3252 9143 8.522830 CCAAATACATTCTACATTGGTCACTTT 58.477 33.333 0.00 0.00 34.12 2.66
3261 9152 3.181480 ACATTGGTCACTTTTTGTTCCGG 60.181 43.478 0.00 0.00 0.00 5.14
3282 9173 5.354234 CCGGTAAAACAGCAATGTAAGAGAT 59.646 40.000 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 5.892160 ATATGATGTGGCATGTATCAAGC 57.108 39.130 13.48 0.00 34.80 4.01
172 173 5.522456 TGCAATGCAGTTTCAGTAAGAAAG 58.478 37.500 2.72 0.00 39.23 2.62
180 181 3.057806 TCAGTGATGCAATGCAGTTTCAG 60.058 43.478 14.98 2.45 43.65 3.02
182 183 3.564235 TCAGTGATGCAATGCAGTTTC 57.436 42.857 14.98 7.23 43.65 2.78
187 188 1.179152 CCCTTCAGTGATGCAATGCA 58.821 50.000 11.44 11.44 44.86 3.96
192 193 1.629861 TGTCATCCCTTCAGTGATGCA 59.370 47.619 0.00 0.00 38.57 3.96
216 217 2.014128 ACCCAACACGTTGAACTCAAG 58.986 47.619 11.46 0.00 42.93 3.02
219 220 1.658994 TCACCCAACACGTTGAACTC 58.341 50.000 11.46 0.00 42.93 3.01
227 228 3.687212 TGTAAGCATTATCACCCAACACG 59.313 43.478 0.00 0.00 30.46 4.49
229 230 6.435591 TCATTTGTAAGCATTATCACCCAACA 59.564 34.615 0.00 0.00 30.46 3.33
230 231 6.862209 TCATTTGTAAGCATTATCACCCAAC 58.138 36.000 0.00 0.00 30.46 3.77
234 235 8.986477 AACTTTCATTTGTAAGCATTATCACC 57.014 30.769 0.00 0.00 30.46 4.02
268 269 6.400568 TCTTACTAAGAAAACCCACATACGG 58.599 40.000 0.00 0.00 33.83 4.02
312 313 5.534207 TCAACTGAACCATGAGCATTTTT 57.466 34.783 0.00 0.00 0.00 1.94
390 400 5.410924 TCAACAACTCGACTCATCCTAATG 58.589 41.667 0.00 0.00 0.00 1.90
394 404 3.322254 AGTTCAACAACTCGACTCATCCT 59.678 43.478 0.00 0.00 38.62 3.24
398 408 3.119280 TGACAGTTCAACAACTCGACTCA 60.119 43.478 0.00 0.00 41.24 3.41
404 414 5.106908 GCCTAGAATGACAGTTCAACAACTC 60.107 44.000 0.00 0.00 41.24 3.01
431 441 2.487762 TCGAAGCATCATTGTCAAACCC 59.512 45.455 0.00 0.00 0.00 4.11
584 594 0.670546 ACCGGTGCTGTTCATCTTCG 60.671 55.000 6.12 0.00 0.00 3.79
801 811 2.068834 TAGAAGGCCCGTCTAAGGAG 57.931 55.000 10.65 0.00 0.00 3.69
872 889 0.907230 AGAGAGAGGTTGGGAGCCAC 60.907 60.000 0.00 0.00 30.78 5.01
879 896 1.153745 CGGCGAAGAGAGAGGTTGG 60.154 63.158 0.00 0.00 0.00 3.77
881 898 0.680061 AAACGGCGAAGAGAGAGGTT 59.320 50.000 16.62 0.00 0.00 3.50
882 899 0.244178 GAAACGGCGAAGAGAGAGGT 59.756 55.000 16.62 0.00 0.00 3.85
883 900 0.458716 GGAAACGGCGAAGAGAGAGG 60.459 60.000 16.62 0.00 0.00 3.69
885 902 0.898789 AGGGAAACGGCGAAGAGAGA 60.899 55.000 16.62 0.00 0.00 3.10
886 903 0.037232 AAGGGAAACGGCGAAGAGAG 60.037 55.000 16.62 0.00 0.00 3.20
887 904 0.320421 CAAGGGAAACGGCGAAGAGA 60.320 55.000 16.62 0.00 0.00 3.10
891 908 0.601841 GAGACAAGGGAAACGGCGAA 60.602 55.000 16.62 0.00 0.00 4.70
892 909 1.005394 GAGACAAGGGAAACGGCGA 60.005 57.895 16.62 0.00 0.00 5.54
897 917 1.014564 CGGAGCGAGACAAGGGAAAC 61.015 60.000 0.00 0.00 0.00 2.78
935 966 0.457851 CAGATGGTGGAGGAGACGAC 59.542 60.000 0.00 0.00 0.00 4.34
936 967 1.323271 GCAGATGGTGGAGGAGACGA 61.323 60.000 0.00 0.00 0.00 4.20
938 969 1.524482 GGCAGATGGTGGAGGAGAC 59.476 63.158 0.00 0.00 0.00 3.36
941 972 3.083349 CCGGCAGATGGTGGAGGA 61.083 66.667 0.00 0.00 0.00 3.71
942 973 4.864334 GCCGGCAGATGGTGGAGG 62.864 72.222 24.80 0.00 0.00 4.30
968 1006 1.444933 TGAGAGGAATGTTGGGGTGT 58.555 50.000 0.00 0.00 0.00 4.16
969 1007 2.240667 AGATGAGAGGAATGTTGGGGTG 59.759 50.000 0.00 0.00 0.00 4.61
970 1008 2.507471 GAGATGAGAGGAATGTTGGGGT 59.493 50.000 0.00 0.00 0.00 4.95
997 1035 2.040145 TGTGTTTGATCAGCTCCATGGA 59.960 45.455 15.27 15.27 0.00 3.41
1016 1054 1.003355 CTTGATGGAGTGGCCGTGT 60.003 57.895 0.00 0.00 40.66 4.49
1026 1064 2.978156 AAAGGGTCTTGCTTGATGGA 57.022 45.000 0.00 0.00 0.00 3.41
1158 1206 1.667830 CTTGCAGACGGAGGCGAAA 60.668 57.895 0.00 0.00 0.00 3.46
1165 1213 2.583441 CCCAGGACTTGCAGACGGA 61.583 63.158 0.00 0.00 0.00 4.69
1190 1238 2.556459 GCTAGCCGCTCGGAGATGA 61.556 63.158 13.11 0.00 37.50 2.92
1865 7706 3.009033 CACAAACATGACCTCCCCTTCTA 59.991 47.826 0.00 0.00 0.00 2.10
1949 7790 2.236382 CGCTCGAGATCAGGCTTGC 61.236 63.158 18.75 0.00 0.00 4.01
1955 7796 1.297967 CGTGACCGCTCGAGATCAG 60.298 63.158 18.75 3.13 33.14 2.90
2332 8207 2.599082 GCATAGAGAAACGGAAGACACG 59.401 50.000 0.00 0.00 37.36 4.49
2396 8271 1.304381 GCCCAGGCACAGGATTTCA 60.304 57.895 3.12 0.00 37.04 2.69
2444 8319 3.150767 TGTTCCAATAAACCACCCTTCG 58.849 45.455 0.00 0.00 0.00 3.79
2460 8335 4.047822 TGTTCGTCATGCAAATTTGTTCC 58.952 39.130 19.03 3.88 0.00 3.62
2476 8351 0.108585 ACTTGCCAGACCATGTTCGT 59.891 50.000 0.00 0.00 0.00 3.85
2477 8352 1.069022 CAACTTGCCAGACCATGTTCG 60.069 52.381 0.00 0.00 32.71 3.95
2555 8430 2.044946 GGCCGCTGGAATTCTGGT 60.045 61.111 5.23 0.00 0.00 4.00
2593 8468 6.670695 ATGGTGTTAAGGATGAAGCTTTTT 57.329 33.333 0.00 0.00 0.00 1.94
2628 8503 3.262915 AGAAATCTTGAGGTGCTAGCACT 59.737 43.478 38.82 27.53 45.52 4.40
2689 8564 4.729868 AGGCTGGAAAATGAACAGTAACT 58.270 39.130 0.00 0.00 34.79 2.24
2690 8565 5.705905 AGTAGGCTGGAAAATGAACAGTAAC 59.294 40.000 0.00 0.00 34.79 2.50
2691 8566 5.876357 AGTAGGCTGGAAAATGAACAGTAA 58.124 37.500 0.00 0.00 34.79 2.24
2692 8567 5.499004 AGTAGGCTGGAAAATGAACAGTA 57.501 39.130 0.00 0.00 34.79 2.74
2693 8568 4.373156 AGTAGGCTGGAAAATGAACAGT 57.627 40.909 0.00 0.00 34.79 3.55
2694 8569 5.705441 TGTTAGTAGGCTGGAAAATGAACAG 59.295 40.000 0.00 0.00 35.40 3.16
2695 8570 5.472137 GTGTTAGTAGGCTGGAAAATGAACA 59.528 40.000 0.00 0.00 0.00 3.18
2696 8571 5.705905 AGTGTTAGTAGGCTGGAAAATGAAC 59.294 40.000 0.00 0.00 0.00 3.18
2697 8572 5.876357 AGTGTTAGTAGGCTGGAAAATGAA 58.124 37.500 0.00 0.00 0.00 2.57
2698 8573 5.499004 AGTGTTAGTAGGCTGGAAAATGA 57.501 39.130 0.00 0.00 0.00 2.57
2699 8574 5.705441 TCAAGTGTTAGTAGGCTGGAAAATG 59.295 40.000 0.00 0.00 0.00 2.32
2700 8575 5.876357 TCAAGTGTTAGTAGGCTGGAAAAT 58.124 37.500 0.00 0.00 0.00 1.82
2701 8576 5.298989 TCAAGTGTTAGTAGGCTGGAAAA 57.701 39.130 0.00 0.00 0.00 2.29
2702 8577 4.967084 TCAAGTGTTAGTAGGCTGGAAA 57.033 40.909 0.00 0.00 0.00 3.13
2703 8578 6.808321 ATATCAAGTGTTAGTAGGCTGGAA 57.192 37.500 0.00 0.00 0.00 3.53
2704 8579 9.244292 CTATATATCAAGTGTTAGTAGGCTGGA 57.756 37.037 0.00 0.00 0.00 3.86
2705 8580 8.470805 CCTATATATCAAGTGTTAGTAGGCTGG 58.529 40.741 0.00 0.00 0.00 4.85
2706 8581 9.026121 ACCTATATATCAAGTGTTAGTAGGCTG 57.974 37.037 0.00 0.00 31.57 4.85
2707 8582 9.245481 GACCTATATATCAAGTGTTAGTAGGCT 57.755 37.037 0.00 0.00 31.57 4.58
2708 8583 8.468399 GGACCTATATATCAAGTGTTAGTAGGC 58.532 40.741 0.00 0.00 31.57 3.93
2709 8584 9.756571 AGGACCTATATATCAAGTGTTAGTAGG 57.243 37.037 0.00 0.00 33.96 3.18
2744 8619 2.834549 TGGTCAAAGGCAACCTCAAAAA 59.165 40.909 0.00 0.00 36.47 1.94
2745 8620 2.461695 TGGTCAAAGGCAACCTCAAAA 58.538 42.857 0.00 0.00 36.47 2.44
2746 8621 2.151502 TGGTCAAAGGCAACCTCAAA 57.848 45.000 0.00 0.00 36.47 2.69
2747 8622 2.364970 CAATGGTCAAAGGCAACCTCAA 59.635 45.455 0.00 0.00 36.47 3.02
2748 8623 1.962807 CAATGGTCAAAGGCAACCTCA 59.037 47.619 0.00 0.00 36.47 3.86
2749 8624 1.273327 CCAATGGTCAAAGGCAACCTC 59.727 52.381 0.00 0.00 36.47 3.85
2750 8625 1.341080 CCAATGGTCAAAGGCAACCT 58.659 50.000 0.00 0.00 36.47 3.50
2751 8626 1.047801 ACCAATGGTCAAAGGCAACC 58.952 50.000 0.00 0.00 36.03 3.77
2752 8627 3.572255 TCTTACCAATGGTCAAAGGCAAC 59.428 43.478 8.82 0.00 37.09 4.17
2753 8628 3.838565 TCTTACCAATGGTCAAAGGCAA 58.161 40.909 8.82 0.00 37.09 4.52
2754 8629 3.517296 TCTTACCAATGGTCAAAGGCA 57.483 42.857 8.82 0.00 37.09 4.75
2755 8630 6.524101 TTAATCTTACCAATGGTCAAAGGC 57.476 37.500 8.82 0.00 37.09 4.35
2795 8670 9.391006 AGTGACTCAACTTTGTAATAACTTGAA 57.609 29.630 0.00 0.00 0.00 2.69
2796 8671 8.958119 AGTGACTCAACTTTGTAATAACTTGA 57.042 30.769 0.00 0.00 0.00 3.02
2803 8678 9.003658 CCAGAATAAGTGACTCAACTTTGTAAT 57.996 33.333 0.00 0.00 40.77 1.89
2804 8679 7.444183 CCCAGAATAAGTGACTCAACTTTGTAA 59.556 37.037 0.00 0.00 40.77 2.41
2805 8680 6.934645 CCCAGAATAAGTGACTCAACTTTGTA 59.065 38.462 0.00 0.00 40.77 2.41
2806 8681 5.765182 CCCAGAATAAGTGACTCAACTTTGT 59.235 40.000 0.00 0.00 40.77 2.83
2807 8682 5.997746 TCCCAGAATAAGTGACTCAACTTTG 59.002 40.000 0.00 0.00 40.77 2.77
2808 8683 5.998363 GTCCCAGAATAAGTGACTCAACTTT 59.002 40.000 0.00 0.00 40.77 2.66
2809 8684 5.552178 GTCCCAGAATAAGTGACTCAACTT 58.448 41.667 0.00 0.00 42.89 2.66
2810 8685 4.322049 CGTCCCAGAATAAGTGACTCAACT 60.322 45.833 0.00 0.00 0.00 3.16
2811 8686 3.927142 CGTCCCAGAATAAGTGACTCAAC 59.073 47.826 0.00 0.00 0.00 3.18
2812 8687 3.056107 CCGTCCCAGAATAAGTGACTCAA 60.056 47.826 0.00 0.00 0.00 3.02
2813 8688 2.496070 CCGTCCCAGAATAAGTGACTCA 59.504 50.000 0.00 0.00 0.00 3.41
2814 8689 2.758979 TCCGTCCCAGAATAAGTGACTC 59.241 50.000 0.00 0.00 0.00 3.36
2815 8690 2.816411 TCCGTCCCAGAATAAGTGACT 58.184 47.619 0.00 0.00 0.00 3.41
2816 8691 3.522553 CTTCCGTCCCAGAATAAGTGAC 58.477 50.000 0.00 0.00 0.00 3.67
2817 8692 2.500098 CCTTCCGTCCCAGAATAAGTGA 59.500 50.000 0.00 0.00 0.00 3.41
2818 8693 2.500098 TCCTTCCGTCCCAGAATAAGTG 59.500 50.000 0.00 0.00 0.00 3.16
2819 8694 2.766828 CTCCTTCCGTCCCAGAATAAGT 59.233 50.000 0.00 0.00 0.00 2.24
2820 8695 2.766828 ACTCCTTCCGTCCCAGAATAAG 59.233 50.000 0.00 0.00 0.00 1.73
2821 8696 2.829023 ACTCCTTCCGTCCCAGAATAA 58.171 47.619 0.00 0.00 0.00 1.40
2822 8697 2.544844 ACTCCTTCCGTCCCAGAATA 57.455 50.000 0.00 0.00 0.00 1.75
2823 8698 2.544844 TACTCCTTCCGTCCCAGAAT 57.455 50.000 0.00 0.00 0.00 2.40
2824 8699 2.544844 ATACTCCTTCCGTCCCAGAA 57.455 50.000 0.00 0.00 0.00 3.02
2825 8700 3.675348 TTATACTCCTTCCGTCCCAGA 57.325 47.619 0.00 0.00 0.00 3.86
2826 8701 4.748277 TTTTATACTCCTTCCGTCCCAG 57.252 45.455 0.00 0.00 0.00 4.45
2827 8702 5.703730 ATTTTTATACTCCTTCCGTCCCA 57.296 39.130 0.00 0.00 0.00 4.37
2828 8703 9.955102 ATATAATTTTTATACTCCTTCCGTCCC 57.045 33.333 0.00 0.00 0.00 4.46
2884 8759 9.453572 AGCATGTGAAAGAAGTTTCTAATGATA 57.546 29.630 13.15 0.00 42.39 2.15
2885 8760 8.345724 AGCATGTGAAAGAAGTTTCTAATGAT 57.654 30.769 13.15 7.43 42.39 2.45
2886 8761 7.750229 AGCATGTGAAAGAAGTTTCTAATGA 57.250 32.000 13.15 0.00 42.39 2.57
2887 8762 8.807667 AAAGCATGTGAAAGAAGTTTCTAATG 57.192 30.769 0.00 4.84 42.39 1.90
2889 8764 9.897744 CATAAAGCATGTGAAAGAAGTTTCTAA 57.102 29.630 0.00 0.00 42.39 2.10
2890 8765 9.066892 ACATAAAGCATGTGAAAGAAGTTTCTA 57.933 29.630 0.00 0.00 46.41 2.10
2891 8766 7.945134 ACATAAAGCATGTGAAAGAAGTTTCT 58.055 30.769 0.00 0.00 46.41 2.52
2906 8781 4.099727 TGGCATGCATGTTACATAAAGCAT 59.900 37.500 26.79 13.54 42.82 3.79
2907 8782 3.446516 TGGCATGCATGTTACATAAAGCA 59.553 39.130 26.79 10.47 36.34 3.91
2908 8783 4.044336 TGGCATGCATGTTACATAAAGC 57.956 40.909 26.79 9.02 0.00 3.51
2917 8792 9.690913 AGAGTAATAATATATGGCATGCATGTT 57.309 29.630 26.79 14.01 0.00 2.71
2933 8808 9.712305 CCTTCGACCATGATTTAGAGTAATAAT 57.288 33.333 0.00 0.00 0.00 1.28
2934 8809 8.701895 ACCTTCGACCATGATTTAGAGTAATAA 58.298 33.333 0.00 0.00 0.00 1.40
2935 8810 8.246430 ACCTTCGACCATGATTTAGAGTAATA 57.754 34.615 0.00 0.00 0.00 0.98
2936 8811 7.125792 ACCTTCGACCATGATTTAGAGTAAT 57.874 36.000 0.00 0.00 0.00 1.89
2937 8812 6.540438 ACCTTCGACCATGATTTAGAGTAA 57.460 37.500 0.00 0.00 0.00 2.24
2938 8813 6.540438 AACCTTCGACCATGATTTAGAGTA 57.460 37.500 0.00 0.00 0.00 2.59
2939 8814 5.422214 AACCTTCGACCATGATTTAGAGT 57.578 39.130 0.00 0.00 0.00 3.24
2940 8815 5.753921 GGTAACCTTCGACCATGATTTAGAG 59.246 44.000 0.00 0.00 35.65 2.43
2941 8816 5.424252 AGGTAACCTTCGACCATGATTTAGA 59.576 40.000 0.00 0.00 38.27 2.10
2942 8817 5.671493 AGGTAACCTTCGACCATGATTTAG 58.329 41.667 0.00 0.00 38.27 1.85
2943 8818 5.667466 GAGGTAACCTTCGACCATGATTTA 58.333 41.667 0.00 0.00 38.27 1.40
2944 8819 4.514401 GAGGTAACCTTCGACCATGATTT 58.486 43.478 0.00 0.00 38.27 2.17
2945 8820 3.430374 CGAGGTAACCTTCGACCATGATT 60.430 47.826 0.00 0.00 38.27 2.57
2946 8821 2.100916 CGAGGTAACCTTCGACCATGAT 59.899 50.000 0.00 0.00 38.27 2.45
2947 8822 1.475280 CGAGGTAACCTTCGACCATGA 59.525 52.381 0.00 0.00 38.27 3.07
2948 8823 1.475280 TCGAGGTAACCTTCGACCATG 59.525 52.381 5.98 0.00 38.27 3.66
2949 8824 1.843368 TCGAGGTAACCTTCGACCAT 58.157 50.000 5.98 0.00 38.27 3.55
2950 8825 1.619654 TTCGAGGTAACCTTCGACCA 58.380 50.000 8.88 0.00 38.27 4.02
2951 8826 2.730550 TTTCGAGGTAACCTTCGACC 57.269 50.000 8.88 0.00 34.72 4.79
2952 8827 3.121227 CGTTTTTCGAGGTAACCTTCGAC 60.121 47.826 8.88 0.21 42.86 4.20
2953 8828 3.052036 CGTTTTTCGAGGTAACCTTCGA 58.948 45.455 5.98 5.98 42.86 3.71
2954 8829 2.796593 ACGTTTTTCGAGGTAACCTTCG 59.203 45.455 0.00 0.00 42.86 3.79
2955 8830 6.471976 AATACGTTTTTCGAGGTAACCTTC 57.528 37.500 0.00 0.00 42.86 3.46
2956 8831 6.591448 CCTAATACGTTTTTCGAGGTAACCTT 59.409 38.462 0.00 0.00 42.86 3.50
2957 8832 6.101997 CCTAATACGTTTTTCGAGGTAACCT 58.898 40.000 0.00 0.00 42.86 3.50
2958 8833 5.220472 GCCTAATACGTTTTTCGAGGTAACC 60.220 44.000 0.00 0.00 42.86 2.85
2959 8834 5.220472 GGCCTAATACGTTTTTCGAGGTAAC 60.220 44.000 0.00 0.00 42.86 2.50
2960 8835 4.869861 GGCCTAATACGTTTTTCGAGGTAA 59.130 41.667 0.00 0.00 42.86 2.85
2961 8836 4.160252 AGGCCTAATACGTTTTTCGAGGTA 59.840 41.667 1.29 0.00 42.86 3.08
2962 8837 3.055602 AGGCCTAATACGTTTTTCGAGGT 60.056 43.478 1.29 0.00 42.86 3.85
2963 8838 3.528532 AGGCCTAATACGTTTTTCGAGG 58.471 45.455 1.29 0.00 42.86 4.63
2964 8839 6.839820 ATAAGGCCTAATACGTTTTTCGAG 57.160 37.500 5.16 0.00 42.86 4.04
2978 8853 9.560860 TCTCTCCATCAAAATATATAAGGCCTA 57.439 33.333 5.16 0.00 0.00 3.93
2979 8854 8.454859 TCTCTCCATCAAAATATATAAGGCCT 57.545 34.615 0.00 0.00 0.00 5.19
2980 8855 8.325046 ACTCTCTCCATCAAAATATATAAGGCC 58.675 37.037 0.00 0.00 0.00 5.19
2988 8863 9.965902 AACAAACTACTCTCTCCATCAAAATAT 57.034 29.630 0.00 0.00 0.00 1.28
2989 8864 9.436957 GAACAAACTACTCTCTCCATCAAAATA 57.563 33.333 0.00 0.00 0.00 1.40
2990 8865 8.160106 AGAACAAACTACTCTCTCCATCAAAAT 58.840 33.333 0.00 0.00 0.00 1.82
2991 8866 7.442364 CAGAACAAACTACTCTCTCCATCAAAA 59.558 37.037 0.00 0.00 0.00 2.44
2992 8867 6.931281 CAGAACAAACTACTCTCTCCATCAAA 59.069 38.462 0.00 0.00 0.00 2.69
2993 8868 6.042093 ACAGAACAAACTACTCTCTCCATCAA 59.958 38.462 0.00 0.00 0.00 2.57
2994 8869 5.540337 ACAGAACAAACTACTCTCTCCATCA 59.460 40.000 0.00 0.00 0.00 3.07
2995 8870 6.031751 ACAGAACAAACTACTCTCTCCATC 57.968 41.667 0.00 0.00 0.00 3.51
2996 8871 5.540337 TGACAGAACAAACTACTCTCTCCAT 59.460 40.000 0.00 0.00 0.00 3.41
2997 8872 4.893524 TGACAGAACAAACTACTCTCTCCA 59.106 41.667 0.00 0.00 0.00 3.86
2998 8873 5.455056 TGACAGAACAAACTACTCTCTCC 57.545 43.478 0.00 0.00 0.00 3.71
2999 8874 5.866633 CCATGACAGAACAAACTACTCTCTC 59.133 44.000 0.00 0.00 0.00 3.20
3000 8875 5.305644 ACCATGACAGAACAAACTACTCTCT 59.694 40.000 0.00 0.00 0.00 3.10
3001 8876 5.542779 ACCATGACAGAACAAACTACTCTC 58.457 41.667 0.00 0.00 0.00 3.20
3002 8877 5.542779 GACCATGACAGAACAAACTACTCT 58.457 41.667 0.00 0.00 0.00 3.24
3003 8878 4.386049 CGACCATGACAGAACAAACTACTC 59.614 45.833 0.00 0.00 0.00 2.59
3004 8879 4.307432 CGACCATGACAGAACAAACTACT 58.693 43.478 0.00 0.00 0.00 2.57
3005 8880 3.120649 GCGACCATGACAGAACAAACTAC 60.121 47.826 0.00 0.00 0.00 2.73
3006 8881 3.064207 GCGACCATGACAGAACAAACTA 58.936 45.455 0.00 0.00 0.00 2.24
3007 8882 1.873591 GCGACCATGACAGAACAAACT 59.126 47.619 0.00 0.00 0.00 2.66
3008 8883 1.398451 CGCGACCATGACAGAACAAAC 60.398 52.381 0.00 0.00 0.00 2.93
3009 8884 0.865111 CGCGACCATGACAGAACAAA 59.135 50.000 0.00 0.00 0.00 2.83
3010 8885 0.032815 TCGCGACCATGACAGAACAA 59.967 50.000 3.71 0.00 0.00 2.83
3011 8886 0.246360 ATCGCGACCATGACAGAACA 59.754 50.000 12.93 0.00 0.00 3.18
3012 8887 2.203800 TATCGCGACCATGACAGAAC 57.796 50.000 12.93 0.00 0.00 3.01
3013 8888 2.951457 TTATCGCGACCATGACAGAA 57.049 45.000 12.93 0.00 0.00 3.02
3014 8889 4.577834 TTATTATCGCGACCATGACAGA 57.422 40.909 12.93 0.00 0.00 3.41
3015 8890 7.525688 AATATTATTATCGCGACCATGACAG 57.474 36.000 12.93 0.00 0.00 3.51
3016 8891 7.899178 AAATATTATTATCGCGACCATGACA 57.101 32.000 12.93 0.00 0.00 3.58
3017 8892 9.685005 GTAAAATATTATTATCGCGACCATGAC 57.315 33.333 12.93 0.00 0.00 3.06
3018 8893 9.425577 TGTAAAATATTATTATCGCGACCATGA 57.574 29.630 12.93 3.28 0.00 3.07
3047 8922 9.677567 TCATAACAAAATTTGAACTTCTAGCAC 57.322 29.630 13.19 0.00 0.00 4.40
3059 8939 9.695526 TTCCATCTCTGTTCATAACAAAATTTG 57.304 29.630 3.89 3.89 41.61 2.32
3069 8949 8.868522 AAATTCAAGTTCCATCTCTGTTCATA 57.131 30.769 0.00 0.00 0.00 2.15
3098 8979 2.486592 GGACGTAAATGGTTCTGTTGGG 59.513 50.000 0.00 0.00 0.00 4.12
3114 8995 3.374402 CCTCGGTCTGCTGGACGT 61.374 66.667 0.00 0.00 45.35 4.34
3115 8996 4.803426 GCCTCGGTCTGCTGGACG 62.803 72.222 4.78 3.62 45.35 4.79
3117 8998 2.922503 TTGCCTCGGTCTGCTGGA 60.923 61.111 0.00 0.00 0.00 3.86
3127 9008 4.436852 GGTGTGTAATATGTTGTTGCCTCG 60.437 45.833 0.00 0.00 0.00 4.63
3131 9012 3.753842 CGGGTGTGTAATATGTTGTTGC 58.246 45.455 0.00 0.00 0.00 4.17
3132 9013 3.189495 TGCGGGTGTGTAATATGTTGTTG 59.811 43.478 0.00 0.00 0.00 3.33
3133 9014 3.189702 GTGCGGGTGTGTAATATGTTGTT 59.810 43.478 0.00 0.00 0.00 2.83
3134 9015 2.745281 GTGCGGGTGTGTAATATGTTGT 59.255 45.455 0.00 0.00 0.00 3.32
3135 9016 2.744741 TGTGCGGGTGTGTAATATGTTG 59.255 45.455 0.00 0.00 0.00 3.33
3136 9017 2.745281 GTGTGCGGGTGTGTAATATGTT 59.255 45.455 0.00 0.00 0.00 2.71
3137 9018 2.289756 TGTGTGCGGGTGTGTAATATGT 60.290 45.455 0.00 0.00 0.00 2.29
3138 9019 2.351455 TGTGTGCGGGTGTGTAATATG 58.649 47.619 0.00 0.00 0.00 1.78
3163 9052 5.432390 TGGTTAGGACTAGGATCTCTACTGT 59.568 44.000 0.00 0.00 0.00 3.55
3199 9090 3.799963 CGCGATTGCACACTTACCTAATA 59.200 43.478 0.00 0.00 42.97 0.98
3208 9099 1.370414 GTTTGCGCGATTGCACACT 60.370 52.632 12.10 0.00 46.25 3.55
3231 9122 8.458573 ACAAAAAGTGACCAATGTAGAATGTA 57.541 30.769 0.00 0.00 0.00 2.29
3252 9143 4.142138 ACATTGCTGTTTTACCGGAACAAA 60.142 37.500 9.46 2.06 36.64 2.83
3261 9152 9.556030 GGTTTATCTCTTACATTGCTGTTTTAC 57.444 33.333 0.00 0.00 36.79 2.01


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

AutoCloner maintained by Alex Coulton.