Multiple sequence alignment - TraesCS7A01G287000

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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 TraesCS7A01G287000 chr7A 100.000 3819 0 0 3086 6904 339753906 339750088 0.000000e+00 7053.0
1 TraesCS7A01G287000 chr7A 100.000 2718 0 0 1 2718 339756991 339754274 0.000000e+00 5020.0
2 TraesCS7A01G287000 chr7A 95.958 1534 49 11 1137 2665 339895526 339894001 0.000000e+00 2477.0
3 TraesCS7A01G287000 chr7A 97.790 1267 24 2 3088 4352 339893747 339892483 0.000000e+00 2182.0
4 TraesCS7A01G287000 chr7A 98.171 656 9 2 4486 5141 339892486 339891834 0.000000e+00 1142.0
5 TraesCS7A01G287000 chr7A 89.369 555 34 9 1 537 339896610 339896063 0.000000e+00 675.0
6 TraesCS7A01G287000 chr7A 87.187 359 8 6 523 880 339895992 339895671 2.350000e-99 374.0
7 TraesCS7A01G287000 chr7A 96.396 222 6 1 933 1152 339895676 339895455 1.420000e-96 364.0
8 TraesCS7A01G287000 chr7A 93.750 96 6 0 6809 6904 10383495 10383400 2.010000e-30 145.0
9 TraesCS7A01G287000 chr7A 97.059 34 1 0 6665 6698 904374 904341 2.690000e-04 58.4
10 TraesCS7A01G287000 chr7D 97.548 2936 43 9 3088 6019 294047027 294049937 0.000000e+00 4996.0
11 TraesCS7A01G287000 chr7D 95.364 1100 30 5 1158 2239 294045866 294046962 0.000000e+00 1729.0
12 TraesCS7A01G287000 chr7D 98.025 405 8 0 6017 6421 294050200 294050604 0.000000e+00 704.0
13 TraesCS7A01G287000 chr7D 94.688 433 12 4 722 1152 294045497 294045920 0.000000e+00 662.0
14 TraesCS7A01G287000 chr7D 90.708 226 14 3 6421 6646 294050654 294050872 1.880000e-75 294.0
15 TraesCS7A01G287000 chr7B 97.726 1715 34 5 4709 6421 358498319 358496608 0.000000e+00 2946.0
16 TraesCS7A01G287000 chr7B 98.419 1645 20 2 3090 4728 358500147 358498503 0.000000e+00 2889.0
17 TraesCS7A01G287000 chr7B 94.342 813 25 5 1160 1955 358501811 358501003 0.000000e+00 1227.0
18 TraesCS7A01G287000 chr7B 93.211 707 26 11 1975 2680 358500860 358500175 0.000000e+00 1020.0
19 TraesCS7A01G287000 chr7B 92.037 427 10 4 728 1152 358502163 358501759 4.640000e-161 579.0
20 TraesCS7A01G287000 chr7B 98.765 81 0 1 6421 6500 358496558 358496478 7.220000e-30 143.0
21 TraesCS7A01G287000 chr7B 85.315 143 16 4 6498 6638 594214533 594214672 7.220000e-30 143.0
22 TraesCS7A01G287000 chr5B 85.996 557 54 9 1 537 700954418 700953866 6.010000e-160 575.0
23 TraesCS7A01G287000 chr5B 83.831 569 54 14 1 537 292173371 292172809 2.220000e-139 507.0
24 TraesCS7A01G287000 chr5B 82.374 556 42 23 2 537 326882338 326881819 3.820000e-117 433.0
25 TraesCS7A01G287000 chr5B 93.035 201 10 3 523 721 700953782 700953584 2.440000e-74 291.0
26 TraesCS7A01G287000 chr5B 90.769 195 14 3 528 722 326881747 326881557 2.470000e-64 257.0
27 TraesCS7A01G287000 chr5B 87.374 198 22 3 526 722 292172738 292172543 2.510000e-54 224.0
28 TraesCS7A01G287000 chr1B 85.821 536 49 10 22 538 560036658 560036131 1.690000e-150 544.0
29 TraesCS7A01G287000 chr1B 84.232 501 52 12 56 537 684117035 684116543 4.880000e-126 462.0
30 TraesCS7A01G287000 chr1B 92.462 199 13 2 524 722 684116465 684116269 4.080000e-72 283.0
31 TraesCS7A01G287000 chr1B 85.492 193 22 6 533 721 175404154 175404344 5.460000e-46 196.0
32 TraesCS7A01G287000 chr2D 86.264 182 22 3 541 721 476702357 476702178 1.960000e-45 195.0
33 TraesCS7A01G287000 chr2D 88.667 150 15 2 6497 6646 533780297 533780150 1.530000e-41 182.0
34 TraesCS7A01G287000 chr2D 89.831 118 8 3 3723 3837 351973346 351973462 1.550000e-31 148.0
35 TraesCS7A01G287000 chr2D 84.000 150 20 3 6498 6646 630131403 630131549 2.600000e-29 141.0
36 TraesCS7A01G287000 chr2D 89.041 73 7 1 309 381 54126141 54126212 9.540000e-14 89.8
37 TraesCS7A01G287000 chr3D 83.173 208 29 6 533 736 440699275 440699480 1.180000e-42 185.0
38 TraesCS7A01G287000 chr3D 86.885 122 15 1 3726 3847 124516094 124515974 1.210000e-27 135.0
39 TraesCS7A01G287000 chr2A 83.744 203 21 12 523 718 393001528 393001725 1.530000e-41 182.0
40 TraesCS7A01G287000 chr2A 84.667 150 17 4 6500 6646 193449775 193449629 2.010000e-30 145.0
41 TraesCS7A01G287000 chr2A 88.983 118 9 3 3723 3837 469789677 469789793 7.220000e-30 143.0
42 TraesCS7A01G287000 chr2A 88.136 118 11 3 3726 3841 205917600 205917716 3.360000e-28 137.0
43 TraesCS7A01G287000 chr3B 87.586 145 12 4 6502 6646 142248117 142248255 5.540000e-36 163.0
44 TraesCS7A01G287000 chr3B 86.000 150 16 5 6499 6646 173123259 173123405 9.270000e-34 156.0
45 TraesCS7A01G287000 chr3B 87.302 126 14 2 3726 3851 178386658 178386535 7.220000e-30 143.0
46 TraesCS7A01G287000 chr6D 85.811 148 15 3 6499 6646 1486633 1486492 1.200000e-32 152.0
47 TraesCS7A01G287000 chr6D 100.000 31 0 0 6057 6087 29151241 29151211 2.690000e-04 58.4
48 TraesCS7A01G287000 chr6B 85.235 149 19 2 6498 6646 70877370 70877515 4.310000e-32 150.0
49 TraesCS7A01G287000 chr3A 87.705 122 14 1 3726 3847 131755338 131755218 2.600000e-29 141.0
50 TraesCS7A01G287000 chr4D 92.708 96 7 0 6809 6904 361393968 361394063 9.340000e-29 139.0
51 TraesCS7A01G287000 chr5D 91.489 94 8 0 6811 6904 113795867 113795960 5.620000e-26 130.0
52 TraesCS7A01G287000 chr5D 79.861 144 27 2 309 452 118174665 118174806 3.410000e-18 104.0
53 TraesCS7A01G287000 chr1A 94.286 35 1 1 6662 6696 383827052 383827085 1.300000e-02 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 TraesCS7A01G287000 chr7A 339750088 339756991 6903 True 6036.500000 7053 100.000000 1 6904 2 chr7A.!!$R3 6903
1 TraesCS7A01G287000 chr7A 339891834 339896610 4776 True 1202.333333 2477 94.145167 1 5141 6 chr7A.!!$R4 5140
2 TraesCS7A01G287000 chr7D 294045497 294050872 5375 False 1677.000000 4996 95.266600 722 6646 5 chr7D.!!$F1 5924
3 TraesCS7A01G287000 chr7B 358496478 358502163 5685 True 1467.333333 2946 95.750000 728 6500 6 chr7B.!!$R1 5772
4 TraesCS7A01G287000 chr5B 700953584 700954418 834 True 433.000000 575 89.515500 1 721 2 chr5B.!!$R3 720
5 TraesCS7A01G287000 chr5B 292172543 292173371 828 True 365.500000 507 85.602500 1 722 2 chr5B.!!$R1 721
6 TraesCS7A01G287000 chr5B 326881557 326882338 781 True 345.000000 433 86.571500 2 722 2 chr5B.!!$R2 720
7 TraesCS7A01G287000 chr1B 560036131 560036658 527 True 544.000000 544 85.821000 22 538 1 chr1B.!!$R1 516
8 TraesCS7A01G287000 chr1B 684116269 684117035 766 True 372.500000 462 88.347000 56 722 2 chr1B.!!$R2 666

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
360 403 0.958822 ACCAAGTTCCGAAACATGCC 59.041 50.000 0.00 0.00 37.88 4.40 F
1116 1297 0.178935 CCTCCTCATCCTCCTCCTCC 60.179 65.000 0.00 0.00 0.00 4.30 F
1254 1435 0.252467 CTGACTTCTCCCTCCCACCT 60.252 60.000 0.00 0.00 0.00 4.00 F
2473 2799 0.900647 CTGGACCGAGGTGAAGAGGT 60.901 60.000 0.00 0.00 40.11 3.85 F
2680 3008 0.033405 ATCGAGGGGAACGAGGAAGA 60.033 55.000 0.00 0.00 42.81 2.87 F
2705 3033 0.564767 GACGATTACGAAGCGAACCG 59.435 55.000 11.17 0.00 44.20 4.44 F
2715 3043 2.395690 GCGAACCGCGATTGACAG 59.604 61.111 8.23 0.00 44.55 3.51 F
4472 4808 1.202452 ACTTGCTGAAGGTTGCAAAGC 60.202 47.619 12.19 12.19 46.55 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 1687 1.706287 CGACGGAGAGCGACATCTGA 61.706 60.000 0.00 0.00 0.00 3.27 R
2450 2776 0.101399 CTTCACCTCGGTCCAGATCG 59.899 60.000 0.00 0.00 36.00 3.69 R
2627 2955 0.903454 AGCTAGTTGGGCCTGTACGT 60.903 55.000 4.53 0.00 0.00 3.57 R
4049 4385 4.016444 AGCTGGAAACAACTCAAACTTCA 58.984 39.130 0.00 0.00 42.06 3.02 R
4314 4650 6.644592 GCACAAATCTACAAATGGTTAAGCAA 59.355 34.615 12.00 0.00 0.00 3.91 R
4472 4808 7.833786 TCAAATCCAGGAAGATCTTCAAATTG 58.166 34.615 31.29 24.05 41.20 2.32 R
4836 5376 9.559732 CCTTCATAGGATGATAAACATAACACA 57.440 33.333 0.00 0.00 45.05 3.72 R
6529 7388 3.186909 CATCGACTGAGGCATAACGAAA 58.813 45.455 0.00 0.00 33.77 3.46 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
37 39 5.163622 CCCGAGCACAATTTAAGACATGATT 60.164 40.000 0.00 0.00 0.00 2.57
38 40 6.324819 CCGAGCACAATTTAAGACATGATTT 58.675 36.000 0.00 0.00 0.00 2.17
256 297 6.573664 TCCATAACTCAAACATTGTTCCAG 57.426 37.500 1.83 4.55 0.00 3.86
276 317 6.985117 TCCAGAATTCTGACCAAATTTTGAG 58.015 36.000 32.49 13.59 46.59 3.02
287 328 9.865321 CTGACCAAATTTTGAGAATGACAATAT 57.135 29.630 10.72 0.00 0.00 1.28
360 403 0.958822 ACCAAGTTCCGAAACATGCC 59.041 50.000 0.00 0.00 37.88 4.40
401 444 8.591312 TCTGAACAGCTTTTGAAAATTTTAACG 58.409 29.630 2.75 0.00 0.00 3.18
632 811 1.064952 CCGGAGTTGCTCAAACGTTTT 59.935 47.619 11.66 0.00 44.04 2.43
779 958 1.329599 AGAAACGACGCACAAGGAAAC 59.670 47.619 0.00 0.00 0.00 2.78
1098 1279 2.131067 CCTCCTCTCCGCCTCTTCC 61.131 68.421 0.00 0.00 0.00 3.46
1099 1280 1.076339 CTCCTCTCCGCCTCTTCCT 60.076 63.158 0.00 0.00 0.00 3.36
1100 1281 1.076632 TCCTCTCCGCCTCTTCCTC 60.077 63.158 0.00 0.00 0.00 3.71
1101 1282 2.131067 CCTCTCCGCCTCTTCCTCC 61.131 68.421 0.00 0.00 0.00 4.30
1102 1283 1.076339 CTCTCCGCCTCTTCCTCCT 60.076 63.158 0.00 0.00 0.00 3.69
1103 1284 1.076632 TCTCCGCCTCTTCCTCCTC 60.077 63.158 0.00 0.00 0.00 3.71
1104 1285 1.380515 CTCCGCCTCTTCCTCCTCA 60.381 63.158 0.00 0.00 0.00 3.86
1105 1286 0.758685 CTCCGCCTCTTCCTCCTCAT 60.759 60.000 0.00 0.00 0.00 2.90
1106 1287 0.757188 TCCGCCTCTTCCTCCTCATC 60.757 60.000 0.00 0.00 0.00 2.92
1107 1288 1.745264 CGCCTCTTCCTCCTCATCC 59.255 63.158 0.00 0.00 0.00 3.51
1108 1289 0.758685 CGCCTCTTCCTCCTCATCCT 60.759 60.000 0.00 0.00 0.00 3.24
1109 1290 1.047801 GCCTCTTCCTCCTCATCCTC 58.952 60.000 0.00 0.00 0.00 3.71
1110 1291 1.715785 CCTCTTCCTCCTCATCCTCC 58.284 60.000 0.00 0.00 0.00 4.30
1111 1292 1.220236 CCTCTTCCTCCTCATCCTCCT 59.780 57.143 0.00 0.00 0.00 3.69
1112 1293 2.597455 CTCTTCCTCCTCATCCTCCTC 58.403 57.143 0.00 0.00 0.00 3.71
1113 1294 1.219213 TCTTCCTCCTCATCCTCCTCC 59.781 57.143 0.00 0.00 0.00 4.30
1114 1295 1.220236 CTTCCTCCTCATCCTCCTCCT 59.780 57.143 0.00 0.00 0.00 3.69
1115 1296 0.856982 TCCTCCTCATCCTCCTCCTC 59.143 60.000 0.00 0.00 0.00 3.71
1116 1297 0.178935 CCTCCTCATCCTCCTCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
1117 1298 0.539438 CTCCTCATCCTCCTCCTCCG 60.539 65.000 0.00 0.00 0.00 4.63
1118 1299 2.206536 CCTCATCCTCCTCCTCCGC 61.207 68.421 0.00 0.00 0.00 5.54
1119 1300 2.123251 TCATCCTCCTCCTCCGCC 60.123 66.667 0.00 0.00 0.00 6.13
1120 1301 3.610669 CATCCTCCTCCTCCGCCG 61.611 72.222 0.00 0.00 0.00 6.46
1137 1318 4.925861 GCTGCCGCCTCCTCATCC 62.926 72.222 0.00 0.00 0.00 3.51
1138 1319 3.160047 CTGCCGCCTCCTCATCCT 61.160 66.667 0.00 0.00 0.00 3.24
1139 1320 3.157252 TGCCGCCTCCTCATCCTC 61.157 66.667 0.00 0.00 0.00 3.71
1140 1321 3.934962 GCCGCCTCCTCATCCTCC 61.935 72.222 0.00 0.00 0.00 4.30
1141 1322 2.123077 CCGCCTCCTCATCCTCCT 60.123 66.667 0.00 0.00 0.00 3.69
1142 1323 2.206536 CCGCCTCCTCATCCTCCTC 61.207 68.421 0.00 0.00 0.00 3.71
1143 1324 2.206536 CGCCTCCTCATCCTCCTCC 61.207 68.421 0.00 0.00 0.00 4.30
1144 1325 1.235696 GCCTCCTCATCCTCCTCCT 59.764 63.158 0.00 0.00 0.00 3.69
1145 1326 0.831711 GCCTCCTCATCCTCCTCCTC 60.832 65.000 0.00 0.00 0.00 3.71
1146 1327 0.178935 CCTCCTCATCCTCCTCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
1147 1328 0.539438 CTCCTCATCCTCCTCCTCCG 60.539 65.000 0.00 0.00 0.00 4.63
1148 1329 2.206536 CCTCATCCTCCTCCTCCGC 61.207 68.421 0.00 0.00 0.00 5.54
1149 1330 2.123251 TCATCCTCCTCCTCCGCC 60.123 66.667 0.00 0.00 0.00 6.13
1150 1331 3.610669 CATCCTCCTCCTCCGCCG 61.611 72.222 0.00 0.00 0.00 6.46
1254 1435 0.252467 CTGACTTCTCCCTCCCACCT 60.252 60.000 0.00 0.00 0.00 4.00
1506 1687 1.022903 AGGAGGTCAGGAAGGAGGAT 58.977 55.000 0.00 0.00 0.00 3.24
1647 1829 8.707938 TTGTCAATACTAGATCTTGTGACATG 57.292 34.615 21.09 14.08 34.42 3.21
1686 1885 2.501261 GGGCGAAACTAAACCTCTTGT 58.499 47.619 0.00 0.00 0.00 3.16
1939 2139 4.993028 TGTATTTGAGGTACCAAAAGGCT 58.007 39.130 15.94 2.72 39.20 4.58
2184 2510 7.380536 TCAAGAGTTAATTACCACGTATGTGT 58.619 34.615 13.91 5.10 44.92 3.72
2217 2543 6.300354 ACAGTTCATTTGAAAACTACTCGG 57.700 37.500 0.00 0.00 34.05 4.63
2450 2776 2.159170 GCATCCCTAGGTCATCTATCGC 60.159 54.545 8.29 0.00 0.00 4.58
2473 2799 0.900647 CTGGACCGAGGTGAAGAGGT 60.901 60.000 0.00 0.00 40.11 3.85
2556 2884 8.280258 TGGATCCTGATTGATAGGTTATTCTT 57.720 34.615 14.23 0.00 36.67 2.52
2616 2944 4.137543 GACTAGGCCCAATGACCTATTTG 58.862 47.826 0.00 0.00 37.88 2.32
2627 2955 6.150976 CCAATGACCTATTTGTTAAGTGCAGA 59.849 38.462 0.00 0.00 0.00 4.26
2674 3002 3.884350 CGCGATCGAGGGGAACGA 61.884 66.667 21.57 0.00 42.88 3.85
2677 3005 1.822613 CGATCGAGGGGAACGAGGA 60.823 63.158 10.26 0.00 42.88 3.71
2680 3008 0.033405 ATCGAGGGGAACGAGGAAGA 60.033 55.000 0.00 0.00 42.81 2.87
2681 3009 0.964358 TCGAGGGGAACGAGGAAGAC 60.964 60.000 0.00 0.00 34.85 3.01
2682 3010 1.511768 GAGGGGAACGAGGAAGACG 59.488 63.158 0.00 0.00 0.00 4.18
2685 3013 1.064166 AGGGGAACGAGGAAGACGATA 60.064 52.381 0.00 0.00 34.70 2.92
2687 3015 2.295885 GGGAACGAGGAAGACGATAGA 58.704 52.381 0.00 0.00 41.38 1.98
2688 3016 2.033174 GGGAACGAGGAAGACGATAGAC 59.967 54.545 0.00 0.00 41.38 2.59
2690 3018 2.306341 ACGAGGAAGACGATAGACGA 57.694 50.000 0.00 0.00 45.77 4.20
2691 3019 2.836262 ACGAGGAAGACGATAGACGAT 58.164 47.619 0.00 0.00 45.77 3.73
2692 3020 3.204526 ACGAGGAAGACGATAGACGATT 58.795 45.455 0.00 0.00 45.77 3.34
2693 3021 4.375272 ACGAGGAAGACGATAGACGATTA 58.625 43.478 0.00 0.00 45.77 1.75
2694 3022 4.210955 ACGAGGAAGACGATAGACGATTAC 59.789 45.833 0.00 0.00 45.77 1.89
2695 3023 4.663639 CGAGGAAGACGATAGACGATTACG 60.664 50.000 0.00 0.00 45.77 3.18
2696 3024 4.375272 AGGAAGACGATAGACGATTACGA 58.625 43.478 0.00 0.00 45.77 3.43
2697 3025 4.813161 AGGAAGACGATAGACGATTACGAA 59.187 41.667 0.00 0.00 45.77 3.85
2698 3026 5.050227 AGGAAGACGATAGACGATTACGAAG 60.050 44.000 0.00 0.00 45.77 3.79
2699 3027 4.131202 AGACGATAGACGATTACGAAGC 57.869 45.455 0.00 0.00 45.77 3.86
2700 3028 2.895204 GACGATAGACGATTACGAAGCG 59.105 50.000 0.00 0.00 45.77 4.68
2701 3029 2.541346 ACGATAGACGATTACGAAGCGA 59.459 45.455 11.17 0.00 45.77 4.93
2702 3030 3.001634 ACGATAGACGATTACGAAGCGAA 59.998 43.478 11.17 0.00 45.77 4.70
2703 3031 3.354343 CGATAGACGATTACGAAGCGAAC 59.646 47.826 11.17 5.96 44.35 3.95
2704 3032 1.905449 AGACGATTACGAAGCGAACC 58.095 50.000 11.17 2.34 44.20 3.62
2705 3033 0.564767 GACGATTACGAAGCGAACCG 59.435 55.000 11.17 0.00 44.20 4.44
2715 3043 2.395690 GCGAACCGCGATTGACAG 59.604 61.111 8.23 0.00 44.55 3.51
2716 3044 2.395690 CGAACCGCGATTGACAGC 59.604 61.111 8.23 0.00 44.57 4.40
2717 3045 2.785258 GAACCGCGATTGACAGCC 59.215 61.111 8.23 0.00 0.00 4.85
3208 3538 8.995027 TGGTTTGAGATGCCATTTATTACTAT 57.005 30.769 0.00 0.00 0.00 2.12
3777 4111 6.515200 GCTCAAACGGATTAGATCTAGCACTA 60.515 42.308 2.02 0.00 0.00 2.74
4314 4650 5.363562 TCTCAAGGTCATGATAAGCACAT 57.636 39.130 0.00 0.00 0.00 3.21
4472 4808 1.202452 ACTTGCTGAAGGTTGCAAAGC 60.202 47.619 12.19 12.19 46.55 3.51
4836 5376 9.696917 GTTTTGTAGATTGAAATGTCCATCTTT 57.303 29.630 4.86 0.00 37.43 2.52
5073 5615 7.954788 AAACACTTGTTTTTCTTTGTTGCTA 57.045 28.000 1.35 0.00 45.07 3.49
5126 5668 8.941977 CACTATGTTTGGTTGCTAAGTAATACA 58.058 33.333 0.00 0.00 0.00 2.29
5429 5971 1.946768 TGGCGCTCCTTTAATATGTGC 59.053 47.619 7.64 0.00 0.00 4.57
6010 6553 9.750125 GAAATGGTAGAAAGATTCAAAAAGTGT 57.250 29.630 0.00 0.00 0.00 3.55
6030 6838 8.798859 AAGTGTGCAGTTAATATTCTCTCAAT 57.201 30.769 0.00 0.00 0.00 2.57
6055 6863 7.974482 ACTTTGCTACCGAAGTAAATAGTTT 57.026 32.000 2.51 0.00 42.56 2.66
6065 6873 7.760340 ACCGAAGTAAATAGTTTTGCAAAAACA 59.240 29.630 25.40 16.23 32.81 2.83
6068 6876 9.777843 GAAGTAAATAGTTTTGCAAAAACATCG 57.222 29.630 25.40 0.00 32.81 3.84
6521 7380 4.051922 ACAGTTTTGCTAAGTCTCAGTCG 58.948 43.478 0.00 0.00 0.00 4.18
6539 7398 4.027295 CAGTCGACTGAGATTTCGTTATGC 60.027 45.833 36.73 0.00 46.59 3.14
6546 7405 4.433615 TGAGATTTCGTTATGCCTCAGTC 58.566 43.478 0.00 0.00 0.00 3.51
6554 7413 3.612717 CGTTATGCCTCAGTCGATGCTAT 60.613 47.826 0.00 0.00 34.21 2.97
6555 7414 4.310769 GTTATGCCTCAGTCGATGCTATT 58.689 43.478 0.00 0.00 34.21 1.73
6562 7421 4.878397 CCTCAGTCGATGCTATTTTCCTTT 59.122 41.667 0.00 0.00 0.00 3.11
6563 7422 5.220739 CCTCAGTCGATGCTATTTTCCTTTG 60.221 44.000 0.00 0.00 0.00 2.77
6646 7505 6.321690 ACATAGTATACCACTTGACTGAGACC 59.678 42.308 0.00 0.00 38.80 3.85
6647 7506 4.936802 AGTATACCACTTGACTGAGACCT 58.063 43.478 0.00 0.00 31.59 3.85
6648 7507 6.075949 AGTATACCACTTGACTGAGACCTA 57.924 41.667 0.00 0.00 31.59 3.08
6649 7508 6.123651 AGTATACCACTTGACTGAGACCTAG 58.876 44.000 0.00 0.00 31.59 3.02
6650 7509 1.896465 ACCACTTGACTGAGACCTAGC 59.104 52.381 0.00 0.00 0.00 3.42
6651 7510 1.205893 CCACTTGACTGAGACCTAGCC 59.794 57.143 0.00 0.00 0.00 3.93
6652 7511 1.895798 CACTTGACTGAGACCTAGCCA 59.104 52.381 0.00 0.00 0.00 4.75
6653 7512 1.896465 ACTTGACTGAGACCTAGCCAC 59.104 52.381 0.00 0.00 0.00 5.01
6654 7513 1.895798 CTTGACTGAGACCTAGCCACA 59.104 52.381 0.00 0.00 0.00 4.17
6655 7514 1.257743 TGACTGAGACCTAGCCACAC 58.742 55.000 0.00 0.00 0.00 3.82
6656 7515 0.533032 GACTGAGACCTAGCCACACC 59.467 60.000 0.00 0.00 0.00 4.16
6657 7516 0.115349 ACTGAGACCTAGCCACACCT 59.885 55.000 0.00 0.00 0.00 4.00
6658 7517 1.270907 CTGAGACCTAGCCACACCTT 58.729 55.000 0.00 0.00 0.00 3.50
6659 7518 1.625818 CTGAGACCTAGCCACACCTTT 59.374 52.381 0.00 0.00 0.00 3.11
6660 7519 1.347707 TGAGACCTAGCCACACCTTTG 59.652 52.381 0.00 0.00 0.00 2.77
6661 7520 1.348036 GAGACCTAGCCACACCTTTGT 59.652 52.381 0.00 0.00 35.84 2.83
6662 7521 1.774856 AGACCTAGCCACACCTTTGTT 59.225 47.619 0.00 0.00 31.66 2.83
6663 7522 2.976882 AGACCTAGCCACACCTTTGTTA 59.023 45.455 0.00 0.00 31.66 2.41
6664 7523 3.393278 AGACCTAGCCACACCTTTGTTAA 59.607 43.478 0.00 0.00 31.66 2.01
6665 7524 4.139038 GACCTAGCCACACCTTTGTTAAA 58.861 43.478 0.00 0.00 31.66 1.52
6666 7525 4.538738 ACCTAGCCACACCTTTGTTAAAA 58.461 39.130 0.00 0.00 31.66 1.52
6667 7526 5.144832 ACCTAGCCACACCTTTGTTAAAAT 58.855 37.500 0.00 0.00 31.66 1.82
6668 7527 5.243060 ACCTAGCCACACCTTTGTTAAAATC 59.757 40.000 0.00 0.00 31.66 2.17
6669 7528 5.476945 CCTAGCCACACCTTTGTTAAAATCT 59.523 40.000 0.00 0.00 31.66 2.40
6670 7529 6.657541 CCTAGCCACACCTTTGTTAAAATCTA 59.342 38.462 0.00 0.00 31.66 1.98
6671 7530 7.339466 CCTAGCCACACCTTTGTTAAAATCTAT 59.661 37.037 0.00 0.00 31.66 1.98
6672 7531 9.391006 CTAGCCACACCTTTGTTAAAATCTATA 57.609 33.333 0.00 0.00 31.66 1.31
6673 7532 8.823220 AGCCACACCTTTGTTAAAATCTATAT 57.177 30.769 0.00 0.00 31.66 0.86
6674 7533 8.903820 AGCCACACCTTTGTTAAAATCTATATC 58.096 33.333 0.00 0.00 31.66 1.63
6675 7534 8.903820 GCCACACCTTTGTTAAAATCTATATCT 58.096 33.333 0.00 0.00 31.66 1.98
6710 7569 9.274206 ACCTAACATTAAAGAACAGAGTCTTTC 57.726 33.333 3.57 0.00 42.88 2.62
6711 7570 9.273016 CCTAACATTAAAGAACAGAGTCTTTCA 57.727 33.333 13.84 0.00 42.88 2.69
6721 7580 9.784531 AAGAACAGAGTCTTTCATATTTCTTCA 57.215 29.630 13.84 0.00 34.03 3.02
6722 7581 9.956640 AGAACAGAGTCTTTCATATTTCTTCAT 57.043 29.630 13.84 0.00 0.00 2.57
6774 7633 9.906660 TTTGTGTAAACCTCAAATATTGATGTC 57.093 29.630 2.28 0.00 37.51 3.06
6775 7634 8.862325 TGTGTAAACCTCAAATATTGATGTCT 57.138 30.769 2.28 0.00 37.51 3.41
6776 7635 8.729756 TGTGTAAACCTCAAATATTGATGTCTG 58.270 33.333 2.28 0.00 37.51 3.51
6777 7636 8.946085 GTGTAAACCTCAAATATTGATGTCTGA 58.054 33.333 2.28 0.00 37.51 3.27
6778 7637 9.166173 TGTAAACCTCAAATATTGATGTCTGAG 57.834 33.333 5.84 5.84 37.51 3.35
6779 7638 9.383519 GTAAACCTCAAATATTGATGTCTGAGA 57.616 33.333 12.23 0.00 37.51 3.27
6781 7640 9.471702 AAACCTCAAATATTGATGTCTGAGATT 57.528 29.630 12.23 1.40 37.51 2.40
6782 7641 9.471702 AACCTCAAATATTGATGTCTGAGATTT 57.528 29.630 12.23 4.72 37.51 2.17
6815 7674 9.778741 AGACATGTAATCTGTTTCTACAAAAGA 57.221 29.630 0.00 0.00 32.92 2.52
6829 7688 8.746052 TTCTACAAAAGAAATCCAGAAACTCA 57.254 30.769 0.00 0.00 41.35 3.41
6830 7689 8.924511 TCTACAAAAGAAATCCAGAAACTCAT 57.075 30.769 0.00 0.00 0.00 2.90
6831 7690 8.786898 TCTACAAAAGAAATCCAGAAACTCATG 58.213 33.333 0.00 0.00 0.00 3.07
6832 7691 6.218746 ACAAAAGAAATCCAGAAACTCATGC 58.781 36.000 0.00 0.00 0.00 4.06
6833 7692 6.041296 ACAAAAGAAATCCAGAAACTCATGCT 59.959 34.615 0.00 0.00 0.00 3.79
6834 7693 7.231317 ACAAAAGAAATCCAGAAACTCATGCTA 59.769 33.333 0.00 0.00 0.00 3.49
6835 7694 7.765695 AAAGAAATCCAGAAACTCATGCTAA 57.234 32.000 0.00 0.00 0.00 3.09
6836 7695 6.998968 AGAAATCCAGAAACTCATGCTAAG 57.001 37.500 0.00 0.00 0.00 2.18
6837 7696 5.884792 AGAAATCCAGAAACTCATGCTAAGG 59.115 40.000 0.00 0.00 0.00 2.69
6838 7697 5.441718 AATCCAGAAACTCATGCTAAGGA 57.558 39.130 0.00 0.00 0.00 3.36
6839 7698 4.908601 TCCAGAAACTCATGCTAAGGAA 57.091 40.909 0.00 0.00 0.00 3.36
6840 7699 5.241403 TCCAGAAACTCATGCTAAGGAAA 57.759 39.130 0.00 0.00 0.00 3.13
6841 7700 5.819991 TCCAGAAACTCATGCTAAGGAAAT 58.180 37.500 0.00 0.00 0.00 2.17
6842 7701 6.957631 TCCAGAAACTCATGCTAAGGAAATA 58.042 36.000 0.00 0.00 0.00 1.40
6843 7702 7.402054 TCCAGAAACTCATGCTAAGGAAATAA 58.598 34.615 0.00 0.00 0.00 1.40
6844 7703 7.888021 TCCAGAAACTCATGCTAAGGAAATAAA 59.112 33.333 0.00 0.00 0.00 1.40
6845 7704 8.522830 CCAGAAACTCATGCTAAGGAAATAAAA 58.477 33.333 0.00 0.00 0.00 1.52
6846 7705 9.346725 CAGAAACTCATGCTAAGGAAATAAAAC 57.653 33.333 0.00 0.00 0.00 2.43
6847 7706 8.523658 AGAAACTCATGCTAAGGAAATAAAACC 58.476 33.333 0.00 0.00 0.00 3.27
6848 7707 6.775594 ACTCATGCTAAGGAAATAAAACCC 57.224 37.500 0.00 0.00 0.00 4.11
6849 7708 6.252995 ACTCATGCTAAGGAAATAAAACCCA 58.747 36.000 0.00 0.00 0.00 4.51
6850 7709 6.152831 ACTCATGCTAAGGAAATAAAACCCAC 59.847 38.462 0.00 0.00 0.00 4.61
6851 7710 5.124776 TCATGCTAAGGAAATAAAACCCACG 59.875 40.000 0.00 0.00 0.00 4.94
6852 7711 4.400120 TGCTAAGGAAATAAAACCCACGT 58.600 39.130 0.00 0.00 0.00 4.49
6853 7712 4.456566 TGCTAAGGAAATAAAACCCACGTC 59.543 41.667 0.00 0.00 0.00 4.34
6854 7713 4.436451 GCTAAGGAAATAAAACCCACGTCG 60.436 45.833 0.00 0.00 0.00 5.12
6855 7714 3.130280 AGGAAATAAAACCCACGTCGT 57.870 42.857 0.00 0.00 0.00 4.34
6856 7715 3.069289 AGGAAATAAAACCCACGTCGTC 58.931 45.455 0.00 0.00 0.00 4.20
6857 7716 3.069289 GGAAATAAAACCCACGTCGTCT 58.931 45.455 0.00 0.00 0.00 4.18
6858 7717 3.124128 GGAAATAAAACCCACGTCGTCTC 59.876 47.826 0.00 0.00 0.00 3.36
6859 7718 3.672767 AATAAAACCCACGTCGTCTCT 57.327 42.857 0.00 0.00 0.00 3.10
6860 7719 4.789012 AATAAAACCCACGTCGTCTCTA 57.211 40.909 0.00 0.00 0.00 2.43
6861 7720 4.789012 ATAAAACCCACGTCGTCTCTAA 57.211 40.909 0.00 0.00 0.00 2.10
6862 7721 3.457610 AAAACCCACGTCGTCTCTAAA 57.542 42.857 0.00 0.00 0.00 1.85
6863 7722 3.672767 AAACCCACGTCGTCTCTAAAT 57.327 42.857 0.00 0.00 0.00 1.40
6864 7723 3.672767 AACCCACGTCGTCTCTAAATT 57.327 42.857 0.00 0.00 0.00 1.82
6865 7724 4.789012 AACCCACGTCGTCTCTAAATTA 57.211 40.909 0.00 0.00 0.00 1.40
6866 7725 4.367386 ACCCACGTCGTCTCTAAATTAG 57.633 45.455 0.00 0.00 0.00 1.73
6867 7726 4.012374 ACCCACGTCGTCTCTAAATTAGA 58.988 43.478 2.44 2.44 0.00 2.10
6868 7727 4.643784 ACCCACGTCGTCTCTAAATTAGAT 59.356 41.667 2.87 0.00 33.66 1.98
6869 7728 5.213675 CCCACGTCGTCTCTAAATTAGATC 58.786 45.833 2.87 0.12 33.66 2.75
6870 7729 4.904724 CCACGTCGTCTCTAAATTAGATCG 59.095 45.833 15.95 15.95 33.66 3.69
6871 7730 5.277202 CCACGTCGTCTCTAAATTAGATCGA 60.277 44.000 18.73 18.73 38.08 3.59
6872 7731 6.364261 CACGTCGTCTCTAAATTAGATCGAT 58.636 40.000 22.48 0.00 40.34 3.59
6873 7732 6.301137 CACGTCGTCTCTAAATTAGATCGATG 59.699 42.308 27.44 27.44 44.17 3.84
6874 7733 5.281842 CGTCGTCTCTAAATTAGATCGATGC 59.718 44.000 22.94 15.34 40.34 3.91
6875 7734 5.569823 GTCGTCTCTAAATTAGATCGATGCC 59.430 44.000 22.48 12.91 40.34 4.40
6876 7735 5.473846 TCGTCTCTAAATTAGATCGATGCCT 59.526 40.000 18.73 0.00 36.72 4.75
6877 7736 5.797934 CGTCTCTAAATTAGATCGATGCCTC 59.202 44.000 0.54 0.00 35.57 4.70
6878 7737 6.096695 GTCTCTAAATTAGATCGATGCCTCC 58.903 44.000 0.54 0.00 33.66 4.30
6879 7738 5.775195 TCTCTAAATTAGATCGATGCCTCCA 59.225 40.000 0.54 0.00 33.66 3.86
6880 7739 6.030548 TCTAAATTAGATCGATGCCTCCAG 57.969 41.667 0.54 0.00 0.00 3.86
6881 7740 4.963318 AAATTAGATCGATGCCTCCAGA 57.037 40.909 0.54 0.00 0.00 3.86
6882 7741 5.495926 AAATTAGATCGATGCCTCCAGAT 57.504 39.130 0.54 0.00 0.00 2.90
6883 7742 5.495926 AATTAGATCGATGCCTCCAGATT 57.504 39.130 0.54 0.00 0.00 2.40
6884 7743 2.835580 AGATCGATGCCTCCAGATTG 57.164 50.000 0.54 0.00 0.00 2.67
6885 7744 1.347050 AGATCGATGCCTCCAGATTGG 59.653 52.381 0.54 0.00 39.43 3.16
6886 7745 1.071385 GATCGATGCCTCCAGATTGGT 59.929 52.381 0.54 0.00 39.03 3.67
6887 7746 0.178767 TCGATGCCTCCAGATTGGTG 59.821 55.000 0.00 0.00 39.03 4.17
6888 7747 0.107508 CGATGCCTCCAGATTGGTGT 60.108 55.000 0.00 0.00 39.03 4.16
6889 7748 1.679944 CGATGCCTCCAGATTGGTGTT 60.680 52.381 0.00 0.00 39.03 3.32
6890 7749 2.019984 GATGCCTCCAGATTGGTGTTC 58.980 52.381 0.00 0.00 39.03 3.18
6891 7750 0.321564 TGCCTCCAGATTGGTGTTCG 60.322 55.000 0.00 0.00 39.03 3.95
6892 7751 0.321653 GCCTCCAGATTGGTGTTCGT 60.322 55.000 0.00 0.00 39.03 3.85
6893 7752 1.882352 GCCTCCAGATTGGTGTTCGTT 60.882 52.381 0.00 0.00 39.03 3.85
6894 7753 2.504367 CCTCCAGATTGGTGTTCGTTT 58.496 47.619 0.00 0.00 39.03 3.60
6895 7754 2.484264 CCTCCAGATTGGTGTTCGTTTC 59.516 50.000 0.00 0.00 39.03 2.78
6896 7755 2.484264 CTCCAGATTGGTGTTCGTTTCC 59.516 50.000 0.00 0.00 39.03 3.13
6897 7756 2.158740 TCCAGATTGGTGTTCGTTTCCA 60.159 45.455 0.00 0.00 39.03 3.53
6898 7757 2.819608 CCAGATTGGTGTTCGTTTCCAT 59.180 45.455 0.00 0.00 31.35 3.41
6899 7758 4.006989 CCAGATTGGTGTTCGTTTCCATA 58.993 43.478 0.00 0.00 31.35 2.74
6900 7759 4.640201 CCAGATTGGTGTTCGTTTCCATAT 59.360 41.667 0.00 0.00 31.35 1.78
6901 7760 5.820423 CCAGATTGGTGTTCGTTTCCATATA 59.180 40.000 0.00 0.00 31.35 0.86
6902 7761 6.486657 CCAGATTGGTGTTCGTTTCCATATAT 59.513 38.462 0.00 0.00 31.35 0.86
6903 7762 7.659799 CCAGATTGGTGTTCGTTTCCATATATA 59.340 37.037 0.00 0.00 31.35 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
256 297 8.919661 GTCATTCTCAAAATTTGGTCAGAATTC 58.080 33.333 14.56 0.00 29.94 2.17
360 403 6.536224 AGCTGTTCAGATTTTCAAAAAGTTGG 59.464 34.615 3.84 0.00 35.29 3.77
466 527 7.095816 CGGACTTCAAACTTTGTTCTTGTTTTT 60.096 33.333 1.44 0.00 32.42 1.94
684 863 1.355210 CTCGTTGCGGCAAGTTGTT 59.645 52.632 16.97 0.00 0.00 2.83
779 958 2.654749 TATGTCTCACCTCAAGCGTG 57.345 50.000 0.00 0.00 0.00 5.34
1098 1279 0.539438 CGGAGGAGGAGGATGAGGAG 60.539 65.000 0.00 0.00 0.00 3.69
1099 1280 1.539165 CGGAGGAGGAGGATGAGGA 59.461 63.158 0.00 0.00 0.00 3.71
1100 1281 2.206536 GCGGAGGAGGAGGATGAGG 61.207 68.421 0.00 0.00 0.00 3.86
1101 1282 2.206536 GGCGGAGGAGGAGGATGAG 61.207 68.421 0.00 0.00 0.00 2.90
1102 1283 2.123251 GGCGGAGGAGGAGGATGA 60.123 66.667 0.00 0.00 0.00 2.92
1103 1284 3.610669 CGGCGGAGGAGGAGGATG 61.611 72.222 0.00 0.00 0.00 3.51
1120 1301 4.925861 GGATGAGGAGGCGGCAGC 62.926 72.222 13.08 0.00 44.18 5.25
1121 1302 3.160047 AGGATGAGGAGGCGGCAG 61.160 66.667 13.08 0.00 0.00 4.85
1122 1303 3.157252 GAGGATGAGGAGGCGGCA 61.157 66.667 13.08 0.00 0.00 5.69
1123 1304 3.934962 GGAGGATGAGGAGGCGGC 61.935 72.222 0.00 0.00 0.00 6.53
1124 1305 2.123077 AGGAGGATGAGGAGGCGG 60.123 66.667 0.00 0.00 0.00 6.13
1125 1306 2.206536 GGAGGAGGATGAGGAGGCG 61.207 68.421 0.00 0.00 0.00 5.52
1126 1307 0.831711 GAGGAGGAGGATGAGGAGGC 60.832 65.000 0.00 0.00 0.00 4.70
1127 1308 0.178935 GGAGGAGGAGGATGAGGAGG 60.179 65.000 0.00 0.00 0.00 4.30
1128 1309 0.539438 CGGAGGAGGAGGATGAGGAG 60.539 65.000 0.00 0.00 0.00 3.69
1129 1310 1.539165 CGGAGGAGGAGGATGAGGA 59.461 63.158 0.00 0.00 0.00 3.71
1130 1311 2.206536 GCGGAGGAGGAGGATGAGG 61.207 68.421 0.00 0.00 0.00 3.86
1131 1312 2.206536 GGCGGAGGAGGAGGATGAG 61.207 68.421 0.00 0.00 0.00 2.90
1132 1313 2.123251 GGCGGAGGAGGAGGATGA 60.123 66.667 0.00 0.00 0.00 2.92
1133 1314 3.610669 CGGCGGAGGAGGAGGATG 61.611 72.222 0.00 0.00 0.00 3.51
1150 1331 4.925861 GGATGAGGAGGCGGCAGC 62.926 72.222 13.08 0.00 44.18 5.25
1151 1332 3.160047 AGGATGAGGAGGCGGCAG 61.160 66.667 13.08 0.00 0.00 4.85
1152 1333 3.157252 GAGGATGAGGAGGCGGCA 61.157 66.667 13.08 0.00 0.00 5.69
1153 1334 3.934962 GGAGGATGAGGAGGCGGC 61.935 72.222 0.00 0.00 0.00 6.53
1154 1335 2.123077 AGGAGGATGAGGAGGCGG 60.123 66.667 0.00 0.00 0.00 6.13
1155 1336 2.206536 GGAGGAGGATGAGGAGGCG 61.207 68.421 0.00 0.00 0.00 5.52
1156 1337 0.831711 GAGGAGGAGGATGAGGAGGC 60.832 65.000 0.00 0.00 0.00 4.70
1157 1338 0.178935 GGAGGAGGAGGATGAGGAGG 60.179 65.000 0.00 0.00 0.00 4.30
1254 1435 2.766651 GCTGGGGATGGGTCCGTA 60.767 66.667 0.00 0.00 46.09 4.02
1305 1486 3.582780 GTCGAATCGGACCTTACAAAGT 58.417 45.455 1.76 0.00 0.00 2.66
1506 1687 1.706287 CGACGGAGAGCGACATCTGA 61.706 60.000 0.00 0.00 0.00 3.27
1631 1813 3.041211 TCCCCCATGTCACAAGATCTAG 58.959 50.000 0.00 0.00 0.00 2.43
1647 1829 2.041922 GAGCCCCCAAAATCCCCC 60.042 66.667 0.00 0.00 0.00 5.40
2157 2482 8.879759 CACATACGTGGTAATTAACTCTTGATT 58.120 33.333 0.00 0.00 39.64 2.57
2179 2505 4.206375 TGAACTGTTCAATGACCACACAT 58.794 39.130 20.14 0.00 36.59 3.21
2184 2510 6.462552 TTCAAATGAACTGTTCAATGACCA 57.537 33.333 27.66 18.30 43.95 4.02
2217 2543 4.184629 ACGGAGATGTTTTAGATGCTGAC 58.815 43.478 0.00 0.00 0.00 3.51
2258 2584 6.685527 TTAATAATGATGTTTGTAGCGCCA 57.314 33.333 2.29 0.00 0.00 5.69
2386 2712 2.638480 TGCAAGCAGTAAGACTTGGT 57.362 45.000 0.00 0.00 42.82 3.67
2450 2776 0.101399 CTTCACCTCGGTCCAGATCG 59.899 60.000 0.00 0.00 36.00 3.69
2473 2799 2.670251 CAAACCTAACGCCCGCCA 60.670 61.111 0.00 0.00 0.00 5.69
2482 2808 2.161410 GCATCACGCATGTCAAACCTAA 59.839 45.455 0.00 0.00 41.79 2.69
2570 2898 6.654161 TCGAAGTGATAATAGCTACTACCCTC 59.346 42.308 0.00 0.00 0.00 4.30
2616 2944 1.725164 GCCTGTACGTCTGCACTTAAC 59.275 52.381 0.00 0.00 0.00 2.01
2627 2955 0.903454 AGCTAGTTGGGCCTGTACGT 60.903 55.000 4.53 0.00 0.00 3.57
2670 2998 2.625737 TCGTCTATCGTCTTCCTCGTT 58.374 47.619 0.00 0.00 40.80 3.85
2674 3002 4.375272 TCGTAATCGTCTATCGTCTTCCT 58.625 43.478 0.00 0.00 40.80 3.36
2677 3005 4.525686 GCTTCGTAATCGTCTATCGTCTT 58.474 43.478 0.00 0.00 40.80 3.01
2680 3008 2.541346 TCGCTTCGTAATCGTCTATCGT 59.459 45.455 0.00 0.00 40.80 3.73
2681 3009 3.165031 TCGCTTCGTAATCGTCTATCG 57.835 47.619 0.00 0.00 41.41 2.92
2682 3010 3.663105 GGTTCGCTTCGTAATCGTCTATC 59.337 47.826 0.00 0.00 38.33 2.08
2685 3013 1.792993 CGGTTCGCTTCGTAATCGTCT 60.793 52.381 0.00 0.00 38.33 4.18
2687 3015 2.645411 CGGTTCGCTTCGTAATCGT 58.355 52.632 0.00 0.00 38.33 3.73
2699 3027 2.395690 GCTGTCAATCGCGGTTCG 59.604 61.111 0.00 0.00 40.15 3.95
2700 3028 2.785258 GGCTGTCAATCGCGGTTC 59.215 61.111 0.00 0.00 0.00 3.62
3085 3413 2.637872 TCTCTCCCCTTTGTACCAAGTG 59.362 50.000 6.01 0.00 0.00 3.16
3086 3414 2.986050 TCTCTCCCCTTTGTACCAAGT 58.014 47.619 6.01 0.00 0.00 3.16
3095 3423 6.722328 AGTTTCGAAATTATCTCTCCCCTTT 58.278 36.000 14.69 0.00 0.00 3.11
3208 3538 6.379988 TGAATGGCTCATGTTACTCTAGTACA 59.620 38.462 0.00 0.00 0.00 2.90
3438 3768 6.313519 AGGAAACTTAAGGCATCACTATGA 57.686 37.500 7.53 0.00 37.44 2.15
4049 4385 4.016444 AGCTGGAAACAACTCAAACTTCA 58.984 39.130 0.00 0.00 42.06 3.02
4314 4650 6.644592 GCACAAATCTACAAATGGTTAAGCAA 59.355 34.615 12.00 0.00 0.00 3.91
4472 4808 7.833786 TCAAATCCAGGAAGATCTTCAAATTG 58.166 34.615 31.29 24.05 41.20 2.32
4836 5376 9.559732 CCTTCATAGGATGATAAACATAACACA 57.440 33.333 0.00 0.00 45.05 3.72
5073 5615 6.962182 TCACAAGATCCTGGATTCAGTTTAT 58.038 36.000 11.17 0.00 39.31 1.40
5126 5668 7.472334 AGGAGAGCACAAACAATCATTAATT 57.528 32.000 0.00 0.00 0.00 1.40
5141 5683 3.685272 GCAAGTACCTAAAAGGAGAGCAC 59.315 47.826 0.00 0.00 37.67 4.40
6030 6838 9.492973 AAAACTATTTACTTCGGTAGCAAAGTA 57.507 29.630 1.34 1.34 37.02 2.24
6521 7380 4.433615 TGAGGCATAACGAAATCTCAGTC 58.566 43.478 0.00 0.00 0.00 3.51
6529 7388 3.186909 CATCGACTGAGGCATAACGAAA 58.813 45.455 0.00 0.00 33.77 3.46
6539 7398 4.065321 AGGAAAATAGCATCGACTGAGG 57.935 45.455 0.00 0.00 0.00 3.86
6608 7467 9.880157 GTGGTATACTATGTAAGAACAAAAGGA 57.120 33.333 2.25 0.00 39.58 3.36
6609 7468 9.886132 AGTGGTATACTATGTAAGAACAAAAGG 57.114 33.333 2.25 0.00 38.04 3.11
6646 7505 6.575162 AGATTTTAACAAAGGTGTGGCTAG 57.425 37.500 0.00 0.00 38.27 3.42
6647 7506 9.914834 ATATAGATTTTAACAAAGGTGTGGCTA 57.085 29.630 0.00 0.00 38.27 3.93
6648 7507 8.823220 ATATAGATTTTAACAAAGGTGTGGCT 57.177 30.769 0.00 0.00 38.27 4.75
6649 7508 8.903820 AGATATAGATTTTAACAAAGGTGTGGC 58.096 33.333 0.00 0.00 38.27 5.01
6684 7543 9.274206 GAAAGACTCTGTTCTTTAATGTTAGGT 57.726 33.333 6.90 0.00 44.27 3.08
6685 7544 9.273016 TGAAAGACTCTGTTCTTTAATGTTAGG 57.727 33.333 6.90 0.00 44.27 2.69
6695 7554 9.784531 TGAAGAAATATGAAAGACTCTGTTCTT 57.215 29.630 0.00 0.00 37.44 2.52
6696 7555 9.956640 ATGAAGAAATATGAAAGACTCTGTTCT 57.043 29.630 0.00 0.00 0.00 3.01
6789 7648 9.778741 TCTTTTGTAGAAACAGATTACATGTCT 57.221 29.630 0.00 0.00 36.83 3.41
6804 7663 8.746052 TGAGTTTCTGGATTTCTTTTGTAGAA 57.254 30.769 0.00 0.00 41.11 2.10
6805 7664 8.786898 CATGAGTTTCTGGATTTCTTTTGTAGA 58.213 33.333 0.00 0.00 0.00 2.59
6806 7665 7.540055 GCATGAGTTTCTGGATTTCTTTTGTAG 59.460 37.037 0.00 0.00 0.00 2.74
6807 7666 7.231317 AGCATGAGTTTCTGGATTTCTTTTGTA 59.769 33.333 0.00 0.00 0.00 2.41
6808 7667 6.041296 AGCATGAGTTTCTGGATTTCTTTTGT 59.959 34.615 0.00 0.00 0.00 2.83
6809 7668 6.453092 AGCATGAGTTTCTGGATTTCTTTTG 58.547 36.000 0.00 0.00 0.00 2.44
6810 7669 6.661304 AGCATGAGTTTCTGGATTTCTTTT 57.339 33.333 0.00 0.00 0.00 2.27
6811 7670 7.094032 CCTTAGCATGAGTTTCTGGATTTCTTT 60.094 37.037 0.00 0.00 0.00 2.52
6812 7671 6.376581 CCTTAGCATGAGTTTCTGGATTTCTT 59.623 38.462 0.00 0.00 0.00 2.52
6813 7672 5.884792 CCTTAGCATGAGTTTCTGGATTTCT 59.115 40.000 0.00 0.00 0.00 2.52
6814 7673 5.882557 TCCTTAGCATGAGTTTCTGGATTTC 59.117 40.000 0.00 0.00 0.00 2.17
6815 7674 5.819991 TCCTTAGCATGAGTTTCTGGATTT 58.180 37.500 0.00 0.00 0.00 2.17
6816 7675 5.441718 TCCTTAGCATGAGTTTCTGGATT 57.558 39.130 0.00 0.00 0.00 3.01
6817 7676 5.441718 TTCCTTAGCATGAGTTTCTGGAT 57.558 39.130 0.00 0.00 0.00 3.41
6818 7677 4.908601 TTCCTTAGCATGAGTTTCTGGA 57.091 40.909 0.00 0.00 0.00 3.86
6819 7678 7.630242 TTATTTCCTTAGCATGAGTTTCTGG 57.370 36.000 0.00 0.00 0.00 3.86
6820 7679 9.346725 GTTTTATTTCCTTAGCATGAGTTTCTG 57.653 33.333 0.00 0.00 0.00 3.02
6821 7680 8.523658 GGTTTTATTTCCTTAGCATGAGTTTCT 58.476 33.333 0.00 0.00 0.00 2.52
6822 7681 7.759886 GGGTTTTATTTCCTTAGCATGAGTTTC 59.240 37.037 0.00 0.00 0.00 2.78
6823 7682 7.234577 TGGGTTTTATTTCCTTAGCATGAGTTT 59.765 33.333 0.00 0.00 0.00 2.66
6824 7683 6.723977 TGGGTTTTATTTCCTTAGCATGAGTT 59.276 34.615 0.00 0.00 0.00 3.01
6825 7684 6.152831 GTGGGTTTTATTTCCTTAGCATGAGT 59.847 38.462 0.00 0.00 0.00 3.41
6826 7685 6.564328 GTGGGTTTTATTTCCTTAGCATGAG 58.436 40.000 0.00 0.00 0.00 2.90
6827 7686 5.124776 CGTGGGTTTTATTTCCTTAGCATGA 59.875 40.000 0.00 0.00 0.00 3.07
6828 7687 5.105917 ACGTGGGTTTTATTTCCTTAGCATG 60.106 40.000 0.00 0.00 0.00 4.06
6829 7688 5.014202 ACGTGGGTTTTATTTCCTTAGCAT 58.986 37.500 0.00 0.00 0.00 3.79
6830 7689 4.400120 ACGTGGGTTTTATTTCCTTAGCA 58.600 39.130 0.00 0.00 0.00 3.49
6831 7690 4.436451 CGACGTGGGTTTTATTTCCTTAGC 60.436 45.833 0.00 0.00 0.00 3.09
6832 7691 4.692155 ACGACGTGGGTTTTATTTCCTTAG 59.308 41.667 0.00 0.00 0.00 2.18
6833 7692 4.640364 ACGACGTGGGTTTTATTTCCTTA 58.360 39.130 0.00 0.00 0.00 2.69
6834 7693 3.479489 ACGACGTGGGTTTTATTTCCTT 58.521 40.909 0.00 0.00 0.00 3.36
6835 7694 3.069289 GACGACGTGGGTTTTATTTCCT 58.931 45.455 4.58 0.00 0.00 3.36
6836 7695 3.069289 AGACGACGTGGGTTTTATTTCC 58.931 45.455 4.58 0.00 0.00 3.13
6837 7696 3.992427 AGAGACGACGTGGGTTTTATTTC 59.008 43.478 4.58 0.00 0.00 2.17
6838 7697 3.999046 AGAGACGACGTGGGTTTTATTT 58.001 40.909 4.58 0.00 0.00 1.40
6839 7698 3.672767 AGAGACGACGTGGGTTTTATT 57.327 42.857 4.58 0.00 0.00 1.40
6840 7699 4.789012 TTAGAGACGACGTGGGTTTTAT 57.211 40.909 4.58 0.00 0.00 1.40
6841 7700 4.582701 TTTAGAGACGACGTGGGTTTTA 57.417 40.909 4.58 0.00 0.00 1.52
6842 7701 3.457610 TTTAGAGACGACGTGGGTTTT 57.542 42.857 4.58 0.00 0.00 2.43
6843 7702 3.672767 ATTTAGAGACGACGTGGGTTT 57.327 42.857 4.58 0.00 0.00 3.27
6844 7703 3.672767 AATTTAGAGACGACGTGGGTT 57.327 42.857 4.58 0.00 0.00 4.11
6845 7704 4.012374 TCTAATTTAGAGACGACGTGGGT 58.988 43.478 4.58 0.00 0.00 4.51
6846 7705 4.627611 TCTAATTTAGAGACGACGTGGG 57.372 45.455 4.58 0.00 0.00 4.61
6847 7706 4.904724 CGATCTAATTTAGAGACGACGTGG 59.095 45.833 20.85 0.00 39.26 4.94
6848 7707 5.735324 TCGATCTAATTTAGAGACGACGTG 58.265 41.667 22.57 0.00 40.11 4.49
6849 7708 5.980698 TCGATCTAATTTAGAGACGACGT 57.019 39.130 22.57 0.00 40.11 4.34
6850 7709 5.281842 GCATCGATCTAATTTAGAGACGACG 59.718 44.000 25.80 22.12 43.99 5.12
6851 7710 5.569823 GGCATCGATCTAATTTAGAGACGAC 59.430 44.000 25.80 18.88 43.99 4.34
6852 7711 5.473846 AGGCATCGATCTAATTTAGAGACGA 59.526 40.000 25.63 25.63 44.65 4.20
6853 7712 5.704888 AGGCATCGATCTAATTTAGAGACG 58.295 41.667 20.07 20.07 38.38 4.18
6854 7713 6.096695 GGAGGCATCGATCTAATTTAGAGAC 58.903 44.000 11.56 7.53 38.38 3.36
6855 7714 5.775195 TGGAGGCATCGATCTAATTTAGAGA 59.225 40.000 11.56 5.32 38.38 3.10
6856 7715 6.030548 TGGAGGCATCGATCTAATTTAGAG 57.969 41.667 11.56 0.25 38.38 2.43
6857 7716 5.775195 TCTGGAGGCATCGATCTAATTTAGA 59.225 40.000 8.53 8.53 39.50 2.10
6858 7717 6.030548 TCTGGAGGCATCGATCTAATTTAG 57.969 41.667 0.00 0.00 0.00 1.85
6859 7718 6.611613 ATCTGGAGGCATCGATCTAATTTA 57.388 37.500 0.00 0.00 0.00 1.40
6860 7719 4.963318 TCTGGAGGCATCGATCTAATTT 57.037 40.909 0.00 0.00 0.00 1.82
6861 7720 5.243981 CAATCTGGAGGCATCGATCTAATT 58.756 41.667 0.00 0.00 0.00 1.40
6862 7721 4.323333 CCAATCTGGAGGCATCGATCTAAT 60.323 45.833 0.00 0.00 40.96 1.73
6863 7722 3.007290 CCAATCTGGAGGCATCGATCTAA 59.993 47.826 0.00 0.00 40.96 2.10
6864 7723 2.564504 CCAATCTGGAGGCATCGATCTA 59.435 50.000 0.00 0.00 40.96 1.98
6865 7724 1.347050 CCAATCTGGAGGCATCGATCT 59.653 52.381 0.00 0.00 40.96 2.75
6866 7725 1.071385 ACCAATCTGGAGGCATCGATC 59.929 52.381 0.00 0.00 40.96 3.69
6867 7726 1.135094 ACCAATCTGGAGGCATCGAT 58.865 50.000 0.00 0.00 40.96 3.59
6868 7727 0.178767 CACCAATCTGGAGGCATCGA 59.821 55.000 0.00 0.00 40.96 3.59
6869 7728 0.107508 ACACCAATCTGGAGGCATCG 60.108 55.000 0.00 0.00 40.96 3.84
6870 7729 2.019984 GAACACCAATCTGGAGGCATC 58.980 52.381 0.00 0.00 40.96 3.91
6871 7730 1.679944 CGAACACCAATCTGGAGGCAT 60.680 52.381 0.00 0.00 40.96 4.40
6872 7731 0.321564 CGAACACCAATCTGGAGGCA 60.322 55.000 0.00 0.00 40.96 4.75
6873 7732 0.321653 ACGAACACCAATCTGGAGGC 60.322 55.000 0.00 0.00 40.96 4.70
6874 7733 2.185004 AACGAACACCAATCTGGAGG 57.815 50.000 0.00 0.00 40.96 4.30
6875 7734 2.484264 GGAAACGAACACCAATCTGGAG 59.516 50.000 0.00 0.00 40.96 3.86
6876 7735 2.158740 TGGAAACGAACACCAATCTGGA 60.159 45.455 0.00 0.00 40.96 3.86
6877 7736 2.226330 TGGAAACGAACACCAATCTGG 58.774 47.619 0.00 0.00 45.02 3.86
6878 7737 5.818136 ATATGGAAACGAACACCAATCTG 57.182 39.130 0.00 0.00 37.24 2.90


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

AutoCloner maintained by Alex Coulton.