Multiple sequence alignment - TraesCS7A01G049200

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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 TraesCS7A01G049200 chr7A 100.000 5061 0 0 1 5061 22948885 22943825 0.000000e+00 9347
1 TraesCS7A01G049200 chr7A 93.768 706 23 1 1 706 44759206 44759890 0.000000e+00 1040
2 TraesCS7A01G049200 chr7A 97.732 529 12 0 1 529 438476419 438475891 0.000000e+00 911
3 TraesCS7A01G049200 chr7A 96.491 171 5 1 541 710 628239489 628239659 1.070000e-71 281
4 TraesCS7A01G049200 chr7A 95.322 171 7 1 541 710 628238143 628237973 2.320000e-68 270
5 TraesCS7A01G049200 chr7A 94.949 99 3 2 4632 4730 22944160 22944064 2.440000e-33 154
6 TraesCS7A01G049200 chr7A 94.949 99 3 2 4726 4822 22944254 22944156 2.440000e-33 154
7 TraesCS7A01G049200 chr7D 93.753 1793 84 17 2959 4730 22594101 22592316 0.000000e+00 2665
8 TraesCS7A01G049200 chr7D 93.180 1569 85 17 1228 2786 22595682 22594126 0.000000e+00 2285
9 TraesCS7A01G049200 chr7D 91.622 370 7 8 708 1055 22596367 22596000 1.640000e-134 490
10 TraesCS7A01G049200 chr7D 85.106 376 15 15 4726 5061 22592414 22592040 3.750000e-91 346
11 TraesCS7A01G049200 chr4A 91.620 1957 111 30 2818 4730 705518982 705517035 0.000000e+00 2656
12 TraesCS7A01G049200 chr4A 93.243 1036 60 6 1761 2786 705520141 705519106 0.000000e+00 1517
13 TraesCS7A01G049200 chr4A 90.060 503 41 5 215 709 719139696 719140197 1.190000e-180 643
14 TraesCS7A01G049200 chr4A 83.366 505 60 18 1252 1749 705520722 705520235 3.590000e-121 446
15 TraesCS7A01G049200 chr4A 85.411 377 13 17 4726 5061 705517133 705516758 2.240000e-93 353
16 TraesCS7A01G049200 chr4A 89.773 264 6 7 811 1061 705521391 705521136 8.180000e-83 318
17 TraesCS7A01G049200 chr3A 96.100 718 17 6 1 708 34526289 34527005 0.000000e+00 1160
18 TraesCS7A01G049200 chr3A 94.561 717 29 5 1 708 663364310 663365025 0.000000e+00 1099
19 TraesCS7A01G049200 chr3A 92.157 714 27 8 1 705 676759267 676758574 0.000000e+00 981
20 TraesCS7A01G049200 chr3A 93.523 633 30 6 1 624 658635526 658636156 0.000000e+00 931
21 TraesCS7A01G049200 chr6A 94.476 706 17 2 1 705 87498483 87497799 0.000000e+00 1068
22 TraesCS7A01G049200 chr5A 93.653 709 21 4 1 707 556585575 556586261 0.000000e+00 1038
23 TraesCS7A01G049200 chr5A 93.635 707 22 3 1 706 201396662 201397346 0.000000e+00 1035
24 TraesCS7A01G049200 chr5A 93.839 633 28 6 1 624 17564421 17563791 0.000000e+00 942
25 TraesCS7A01G049200 chr5A 94.857 175 7 2 541 713 17563844 17563670 6.460000e-69 272
26 TraesCS7A01G049200 chr1A 94.184 619 25 6 3 613 397748831 397749446 0.000000e+00 933
27 TraesCS7A01G049200 chr1A 87.059 425 43 11 293 708 493930658 493931079 2.130000e-128 470
28 TraesCS7A01G049200 chr3B 90.400 500 37 7 215 708 741363000 741363494 0.000000e+00 647
29 TraesCS7A01G049200 chr5D 89.773 88 9 0 1442 1529 361213455 361213368 4.140000e-21 113


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 TraesCS7A01G049200 chr7A 22943825 22948885 5060 True 9347.0 9347 100.00000 1 5061 1 chr7A.!!$R1 5060
1 TraesCS7A01G049200 chr7A 44759206 44759890 684 False 1040.0 1040 93.76800 1 706 1 chr7A.!!$F1 705
2 TraesCS7A01G049200 chr7A 438475891 438476419 528 True 911.0 911 97.73200 1 529 1 chr7A.!!$R2 528
3 TraesCS7A01G049200 chr7D 22592040 22596367 4327 True 1446.5 2665 90.91525 708 5061 4 chr7D.!!$R1 4353
4 TraesCS7A01G049200 chr4A 705516758 705521391 4633 True 1058.0 2656 88.68260 811 5061 5 chr4A.!!$R1 4250
5 TraesCS7A01G049200 chr4A 719139696 719140197 501 False 643.0 643 90.06000 215 709 1 chr4A.!!$F1 494
6 TraesCS7A01G049200 chr3A 34526289 34527005 716 False 1160.0 1160 96.10000 1 708 1 chr3A.!!$F1 707
7 TraesCS7A01G049200 chr3A 663364310 663365025 715 False 1099.0 1099 94.56100 1 708 1 chr3A.!!$F3 707
8 TraesCS7A01G049200 chr3A 676758574 676759267 693 True 981.0 981 92.15700 1 705 1 chr3A.!!$R1 704
9 TraesCS7A01G049200 chr3A 658635526 658636156 630 False 931.0 931 93.52300 1 624 1 chr3A.!!$F2 623
10 TraesCS7A01G049200 chr6A 87497799 87498483 684 True 1068.0 1068 94.47600 1 705 1 chr6A.!!$R1 704
11 TraesCS7A01G049200 chr5A 556585575 556586261 686 False 1038.0 1038 93.65300 1 707 1 chr5A.!!$F2 706
12 TraesCS7A01G049200 chr5A 201396662 201397346 684 False 1035.0 1035 93.63500 1 706 1 chr5A.!!$F1 705
13 TraesCS7A01G049200 chr5A 17563670 17564421 751 True 607.0 942 94.34800 1 713 2 chr5A.!!$R1 712
14 TraesCS7A01G049200 chr1A 397748831 397749446 615 False 933.0 933 94.18400 3 613 1 chr1A.!!$F1 610

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
536 539 0.241213 GGACTCTTTGGCTTTTCGGC 59.759 55.0 0.00 0.0 38.97 5.54 F
1250 1479 0.315788 CTCGCATCTCGTCTCGTCTG 60.316 60.0 0.00 0.0 39.67 3.51 F
1415 1723 0.040499 TCCTGGCCCATGTTTTACCC 59.960 55.0 0.00 0.0 0.00 3.69 F
1416 1724 0.041090 CCTGGCCCATGTTTTACCCT 59.959 55.0 0.00 0.0 0.00 4.34 F
1838 2234 0.101759 ATGGCGCTGACATGCAAATC 59.898 50.0 7.64 0.0 25.61 2.17 F
3645 4152 0.324645 GTTGCATCCCCCAGACCATT 60.325 55.0 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1343 1651 0.464373 TCCAGCATTTCCAGCGATCC 60.464 55.0 0.00 0.00 37.01 3.36 R
2559 2962 0.037877 AAAGCTGCCAGTGCTCAGAT 59.962 50.0 12.93 5.43 40.22 2.90 R
2928 3428 2.428890 CCGGACTTCTCATCAGCTACTT 59.571 50.0 0.00 0.00 0.00 2.24 R
3324 3827 6.648192 TCAACAATTGTTCCCTGTTCAAATT 58.352 32.0 20.85 0.00 35.83 1.82 R
3771 4280 0.450319 TAAATATGAATGCGCGCGCG 60.450 50.0 45.73 45.73 45.51 6.86 R
4804 5348 0.036858 GGAGGAGCTTGAGTGGTGAC 60.037 60.0 0.00 0.00 0.00 3.67 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
145 146 3.849951 GCGGGAGAGAATGGCGGA 61.850 66.667 0.00 0.00 0.00 5.54
169 170 5.786121 AAGAAAATGGAGGGAGAGAATGA 57.214 39.130 0.00 0.00 0.00 2.57
288 289 4.701956 ACAAAGTCACAAAGAACCAGTG 57.298 40.909 0.00 0.00 34.67 3.66
534 537 1.897560 AGGGACTCTTTGGCTTTTCG 58.102 50.000 0.00 0.00 0.00 3.46
535 538 0.881796 GGGACTCTTTGGCTTTTCGG 59.118 55.000 0.00 0.00 0.00 4.30
536 539 0.241213 GGACTCTTTGGCTTTTCGGC 59.759 55.000 0.00 0.00 38.97 5.54
545 548 3.678921 GCTTTTCGGCCAACCTTTT 57.321 47.368 2.24 0.00 0.00 2.27
546 549 1.948104 GCTTTTCGGCCAACCTTTTT 58.052 45.000 2.24 0.00 0.00 1.94
547 550 1.597195 GCTTTTCGGCCAACCTTTTTG 59.403 47.619 2.24 0.00 0.00 2.44
548 551 2.740256 GCTTTTCGGCCAACCTTTTTGA 60.740 45.455 2.24 0.00 0.00 2.69
658 720 8.950007 ACTTTTGATTTTTCTCCATTAGGGTA 57.050 30.769 0.00 0.00 38.11 3.69
743 805 4.063689 TGTTAATTTCGTCAGGCCGTTTA 58.936 39.130 0.00 0.00 0.00 2.01
939 1007 2.283809 CCCACCCGATCCCTCTCT 59.716 66.667 0.00 0.00 0.00 3.10
1096 1180 4.150454 CCTCCGCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
1097 1181 2.520741 CTCCGCCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
1098 1182 4.144727 TCCGCCTCCTCCTCCTCC 62.145 72.222 0.00 0.00 0.00 4.30
1099 1183 4.150454 CCGCCTCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
1100 1184 2.520741 CGCCTCCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
1101 1185 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
1102 1186 2.710826 GCCTCCTCCTCCTCCTCCT 61.711 68.421 0.00 0.00 0.00 3.69
1103 1187 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1104 1188 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1105 1189 2.015726 TCCTCCTCCTCCTCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
1106 1190 2.612251 CTCCTCCTCCTCCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
1107 1191 3.036959 TCCTCCTCCTCCTCCCCC 61.037 72.222 0.00 0.00 0.00 5.40
1108 1192 4.548513 CCTCCTCCTCCTCCCCCG 62.549 77.778 0.00 0.00 0.00 5.73
1109 1193 4.548513 CTCCTCCTCCTCCCCCGG 62.549 77.778 0.00 0.00 0.00 5.73
1134 1218 4.873129 CCGGCGGTGGTCGAGATG 62.873 72.222 19.97 0.00 46.20 2.90
1135 1219 4.873129 CGGCGGTGGTCGAGATGG 62.873 72.222 0.00 0.00 46.20 3.51
1138 1222 3.461773 CGGTGGTCGAGATGGCCT 61.462 66.667 3.32 0.00 42.43 5.19
1139 1223 2.501610 GGTGGTCGAGATGGCCTC 59.498 66.667 3.32 0.00 38.55 4.70
1146 1230 2.280052 GAGATGGCCTCGCTGCTC 60.280 66.667 3.32 0.00 31.32 4.26
1147 1231 3.805891 GAGATGGCCTCGCTGCTCC 62.806 68.421 3.32 0.00 31.32 4.70
1174 1258 4.752879 GCAACTACGCGCCCCTCA 62.753 66.667 5.73 0.00 0.00 3.86
1175 1259 2.509336 CAACTACGCGCCCCTCAG 60.509 66.667 5.73 0.00 0.00 3.35
1176 1260 4.452733 AACTACGCGCCCCTCAGC 62.453 66.667 5.73 0.00 0.00 4.26
1185 1269 4.436998 CCCCTCAGCACCGACGAC 62.437 72.222 0.00 0.00 0.00 4.34
1186 1270 4.436998 CCCTCAGCACCGACGACC 62.437 72.222 0.00 0.00 0.00 4.79
1187 1271 4.436998 CCTCAGCACCGACGACCC 62.437 72.222 0.00 0.00 0.00 4.46
1188 1272 4.436998 CTCAGCACCGACGACCCC 62.437 72.222 0.00 0.00 0.00 4.95
1189 1273 4.988716 TCAGCACCGACGACCCCT 62.989 66.667 0.00 0.00 0.00 4.79
1190 1274 4.436998 CAGCACCGACGACCCCTC 62.437 72.222 0.00 0.00 0.00 4.30
1204 1288 4.787280 CCTCCGCCTCCTCCAGGT 62.787 72.222 0.00 0.00 45.61 4.00
1205 1289 3.151022 CTCCGCCTCCTCCAGGTC 61.151 72.222 0.00 0.00 45.61 3.85
1206 1290 3.965026 CTCCGCCTCCTCCAGGTCA 62.965 68.421 0.00 0.00 45.61 4.02
1207 1291 3.775654 CCGCCTCCTCCAGGTCAC 61.776 72.222 0.00 0.00 45.61 3.67
1208 1292 3.775654 CGCCTCCTCCAGGTCACC 61.776 72.222 0.00 0.00 45.61 4.02
1209 1293 3.403558 GCCTCCTCCAGGTCACCC 61.404 72.222 0.00 0.00 45.61 4.61
1210 1294 3.077556 CCTCCTCCAGGTCACCCG 61.078 72.222 0.00 0.00 37.53 5.28
1211 1295 3.077556 CTCCTCCAGGTCACCCGG 61.078 72.222 0.00 0.00 36.34 5.73
1244 1473 2.835431 CCCCCTCGCATCTCGTCT 60.835 66.667 0.00 0.00 39.67 4.18
1247 1476 2.473760 CCCTCGCATCTCGTCTCGT 61.474 63.158 0.00 0.00 39.67 4.18
1248 1477 1.010574 CCTCGCATCTCGTCTCGTC 60.011 63.158 0.00 0.00 39.67 4.20
1249 1478 1.433053 CCTCGCATCTCGTCTCGTCT 61.433 60.000 0.00 0.00 39.67 4.18
1250 1479 0.315788 CTCGCATCTCGTCTCGTCTG 60.316 60.000 0.00 0.00 39.67 3.51
1308 1616 3.821881 CGTAGCTAGGTAGTCACGC 57.178 57.895 0.86 0.00 0.00 5.34
1328 1636 1.365633 GCGGGGTTGTCAAATTGCA 59.634 52.632 0.00 0.00 0.00 4.08
1329 1637 0.943835 GCGGGGTTGTCAAATTGCAC 60.944 55.000 0.00 0.00 0.00 4.57
1330 1638 0.673437 CGGGGTTGTCAAATTGCACT 59.327 50.000 0.00 0.00 0.00 4.40
1389 1697 1.072331 ACCACCAGACTTGTCCATCAC 59.928 52.381 0.00 0.00 0.00 3.06
1408 1716 0.692419 CCTAGTCTCCTGGCCCATGT 60.692 60.000 0.00 0.00 0.00 3.21
1409 1717 1.207791 CTAGTCTCCTGGCCCATGTT 58.792 55.000 0.00 0.00 0.00 2.71
1410 1718 1.561542 CTAGTCTCCTGGCCCATGTTT 59.438 52.381 0.00 0.00 0.00 2.83
1411 1719 0.779997 AGTCTCCTGGCCCATGTTTT 59.220 50.000 0.00 0.00 0.00 2.43
1412 1720 1.992557 AGTCTCCTGGCCCATGTTTTA 59.007 47.619 0.00 0.00 0.00 1.52
1414 1722 1.005450 TCTCCTGGCCCATGTTTTACC 59.995 52.381 0.00 0.00 0.00 2.85
1415 1723 0.040499 TCCTGGCCCATGTTTTACCC 59.960 55.000 0.00 0.00 0.00 3.69
1416 1724 0.041090 CCTGGCCCATGTTTTACCCT 59.959 55.000 0.00 0.00 0.00 4.34
1418 1726 1.550072 CTGGCCCATGTTTTACCCTTG 59.450 52.381 0.00 0.00 0.00 3.61
1449 1758 9.811995 ACATTAGCTAGTTATTTCGAACATGTA 57.188 29.630 0.00 0.00 0.00 2.29
1468 1777 4.191544 TGTACATCAGCTAATTGACCTGC 58.808 43.478 0.00 0.00 0.00 4.85
1479 1788 3.959495 ATTGACCTGCCCATCAGTTAT 57.041 42.857 0.00 0.00 41.25 1.89
1498 1807 7.565398 TCAGTTATTCTGATCTAAGCTACCCTT 59.435 37.037 0.00 0.00 46.77 3.95
1520 1829 1.924524 GTGCGTTAGCTAATTCGAGCA 59.075 47.619 17.76 16.12 45.43 4.26
1580 1890 4.790766 GCAATTGGTATCTTGATTGGAGCG 60.791 45.833 7.72 0.00 31.78 5.03
1590 1900 0.318784 GATTGGAGCGCTACGGTAGG 60.319 60.000 16.43 8.03 37.83 3.18
1595 1905 1.726533 GAGCGCTACGGTAGGAAGCT 61.727 60.000 11.50 10.90 37.83 3.74
1605 1915 1.481363 GGTAGGAAGCTACCTGACACC 59.519 57.143 0.00 0.00 44.41 4.16
1617 1927 2.048127 GACACCGACAGCAGGGTC 60.048 66.667 0.00 0.00 33.23 4.46
1691 2005 4.439289 GGATCTTTCGGGCTCATTTTCTTG 60.439 45.833 0.00 0.00 0.00 3.02
1800 2196 3.118261 AGCACTTTCTTGGACTTCTGACA 60.118 43.478 0.00 0.00 0.00 3.58
1802 2198 4.096382 GCACTTTCTTGGACTTCTGACAAA 59.904 41.667 0.00 0.00 0.00 2.83
1820 2216 6.348498 TGACAAATGATCAGATCAACGGTAT 58.652 36.000 17.24 1.54 43.50 2.73
1824 2220 2.061773 GATCAGATCAACGGTATGGCG 58.938 52.381 5.44 0.00 0.00 5.69
1834 2230 1.819208 GGTATGGCGCTGACATGCA 60.819 57.895 7.64 0.00 35.36 3.96
1836 2232 0.451383 GTATGGCGCTGACATGCAAA 59.549 50.000 7.64 0.00 33.85 3.68
1838 2234 0.101759 ATGGCGCTGACATGCAAATC 59.898 50.000 7.64 0.00 25.61 2.17
1839 2235 0.961857 TGGCGCTGACATGCAAATCT 60.962 50.000 7.64 0.00 0.00 2.40
1856 2252 4.357918 AATCTTGTTGTGCAGTAGAGGT 57.642 40.909 0.00 0.00 0.00 3.85
2030 2426 2.417933 AGCAATTGAGATTCTCACGCAC 59.582 45.455 23.50 13.04 40.46 5.34
2039 2435 3.128764 AGATTCTCACGCACGAGATAACA 59.871 43.478 3.10 0.00 41.58 2.41
2173 2569 9.155975 CTTTATGTATTAACAGACACAAGAGCT 57.844 33.333 0.00 0.00 39.49 4.09
2213 2612 0.971959 TGCTGATGGACCAAATGCCC 60.972 55.000 0.00 0.00 0.00 5.36
2347 2747 3.507622 GCCACTCTGCCTTAAGATGTTTT 59.492 43.478 3.36 0.00 0.00 2.43
2515 2915 1.135083 AGGATGTGGTACGCTTTCTCG 60.135 52.381 0.00 0.00 40.97 4.04
2559 2962 4.799678 TCTTTTTCGTGAAGTTGTTTGCA 58.200 34.783 0.00 0.00 0.00 4.08
2764 3171 3.904136 AAATTGAGAACACAGAAGGCG 57.096 42.857 0.00 0.00 0.00 5.52
2775 3182 2.851824 CACAGAAGGCGAAAACAACAAC 59.148 45.455 0.00 0.00 0.00 3.32
2795 3214 5.163468 ACAACCACACAATTAGTTGCATTGA 60.163 36.000 4.06 0.00 42.61 2.57
2799 3218 7.665690 ACCACACAATTAGTTGCATTGATTTA 58.334 30.769 4.06 0.00 38.96 1.40
2812 3231 8.408601 GTTGCATTGATTTAGGTCATTAGTCAT 58.591 33.333 0.00 0.00 0.00 3.06
2814 3233 9.056005 TGCATTGATTTAGGTCATTAGTCATAC 57.944 33.333 0.00 0.00 0.00 2.39
2832 3331 6.207417 AGTCATACAGGTTTGAACTTTGGATG 59.793 38.462 13.29 13.29 36.75 3.51
2836 3335 6.144078 ACAGGTTTGAACTTTGGATGTAAC 57.856 37.500 0.00 0.00 0.00 2.50
2837 3336 5.212194 CAGGTTTGAACTTTGGATGTAACG 58.788 41.667 0.00 0.00 0.00 3.18
2838 3337 5.008217 CAGGTTTGAACTTTGGATGTAACGA 59.992 40.000 0.00 0.00 0.00 3.85
2839 3338 5.238650 AGGTTTGAACTTTGGATGTAACGAG 59.761 40.000 0.00 0.00 0.00 4.18
2868 3368 8.268878 ACTTTATAGAAGAGGCTAATGACCAT 57.731 34.615 0.00 0.00 0.00 3.55
2888 3388 5.222547 ACCATGGTTTCCCCTAAAATCTTCT 60.223 40.000 13.00 0.00 0.00 2.85
2889 3389 5.127682 CCATGGTTTCCCCTAAAATCTTCTG 59.872 44.000 2.57 0.00 0.00 3.02
2908 3408 8.754991 TCTTCTGAGTCTATTTACTTAGGGAG 57.245 38.462 0.00 0.00 34.68 4.30
2910 3410 9.629878 CTTCTGAGTCTATTTACTTAGGGAGTA 57.370 37.037 0.00 0.00 39.86 2.59
2928 3428 7.069986 AGGGAGTAGCTAAACTGATTATGAGA 58.930 38.462 0.00 0.00 0.00 3.27
2948 3448 3.380004 AGAAGTAGCTGATGAGAAGTCCG 59.620 47.826 0.00 0.00 0.00 4.79
2963 3463 5.627135 AGAAGTCCGGGAAACTCATTAAAA 58.373 37.500 0.00 0.00 0.00 1.52
3156 3659 3.760684 ACTGATGCCCTGAAATTCACTTC 59.239 43.478 0.00 0.00 0.00 3.01
3169 3672 8.125978 TGAAATTCACTTCCATTATCTGCTTT 57.874 30.769 0.00 0.00 0.00 3.51
3256 3759 9.246670 TCTTGTGATTGATCAGGTATGAAAATT 57.753 29.630 0.00 0.00 39.39 1.82
3288 3791 7.404671 AATTGGGTCATTGATGGTAAGTTAC 57.595 36.000 4.32 4.32 0.00 2.50
3290 3793 4.020039 TGGGTCATTGATGGTAAGTTACGT 60.020 41.667 6.94 0.00 0.00 3.57
3308 3811 8.164058 AGTTACGTTAACTAGTTCAGACTTCT 57.836 34.615 12.39 2.51 46.53 2.85
3421 3924 6.129194 GCTATAAACAGTTGCAAAAGGTTTCG 60.129 38.462 20.77 14.27 36.28 3.46
3500 4006 4.789012 ACCATAATTTTGCCACACTCTG 57.211 40.909 0.00 0.00 0.00 3.35
3645 4152 0.324645 GTTGCATCCCCCAGACCATT 60.325 55.000 0.00 0.00 0.00 3.16
3648 4155 0.846693 GCATCCCCCAGACCATTAGT 59.153 55.000 0.00 0.00 0.00 2.24
3653 4160 4.562934 TCCCCCAGACCATTAGTATGTA 57.437 45.455 0.00 0.00 35.86 2.29
3709 4218 5.670792 TTTTCGGCCAGAGACTAGATTTA 57.329 39.130 2.24 0.00 0.00 1.40
3713 4222 6.045072 TCGGCCAGAGACTAGATTTAAAAA 57.955 37.500 2.24 0.00 0.00 1.94
3752 4261 5.992217 ACCTCAAGTACTTGCTTTTACTCTG 59.008 40.000 27.49 3.74 40.24 3.35
3754 4263 6.073548 CCTCAAGTACTTGCTTTTACTCTGTG 60.074 42.308 27.49 3.11 40.24 3.66
3756 4265 6.257849 TCAAGTACTTGCTTTTACTCTGTGTG 59.742 38.462 27.49 2.09 40.24 3.82
3758 4267 4.882671 ACTTGCTTTTACTCTGTGTGTG 57.117 40.909 0.00 0.00 0.00 3.82
3760 4269 4.094887 ACTTGCTTTTACTCTGTGTGTGTG 59.905 41.667 0.00 0.00 0.00 3.82
3762 4271 3.373748 TGCTTTTACTCTGTGTGTGTGTG 59.626 43.478 0.00 0.00 0.00 3.82
3764 4273 4.727734 GCTTTTACTCTGTGTGTGTGTGTG 60.728 45.833 0.00 0.00 0.00 3.82
3765 4274 3.603158 TTACTCTGTGTGTGTGTGTGT 57.397 42.857 0.00 0.00 0.00 3.72
3766 4275 1.725641 ACTCTGTGTGTGTGTGTGTG 58.274 50.000 0.00 0.00 0.00 3.82
3768 4277 1.394572 CTCTGTGTGTGTGTGTGTGTG 59.605 52.381 0.00 0.00 0.00 3.82
3769 4278 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
3770 4279 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3771 4280 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
3772 4281 1.225991 GTGTGTGTGTGTGTGTGCG 60.226 57.895 0.00 0.00 0.00 5.34
3773 4282 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
3774 4283 3.858989 TGTGTGTGTGTGTGCGCG 61.859 61.111 0.00 0.00 0.00 6.86
3797 4316 3.547813 CGCGCATTCATATTTAACTGCCA 60.548 43.478 8.75 0.00 0.00 4.92
3855 4375 2.685897 GTGTTTCACCTGCAACACCTTA 59.314 45.455 9.11 0.00 43.18 2.69
3856 4376 3.317993 GTGTTTCACCTGCAACACCTTAT 59.682 43.478 9.11 0.00 43.18 1.73
3857 4377 4.517453 GTGTTTCACCTGCAACACCTTATA 59.483 41.667 9.11 0.00 43.18 0.98
3858 4378 5.183140 GTGTTTCACCTGCAACACCTTATAT 59.817 40.000 9.11 0.00 43.18 0.86
3863 4383 6.894682 TCACCTGCAACACCTTATATTATCA 58.105 36.000 0.00 0.00 0.00 2.15
3891 4411 7.178097 AGAGCTTCTGCAAAGGAAGAAAAATAT 59.822 33.333 16.12 0.00 38.24 1.28
3916 4436 4.586618 CGTCAGTCCCTGAAGCTG 57.413 61.111 0.00 0.00 42.46 4.24
4064 4584 7.502120 TTGAAGAAGATCCTTTTCTGACTTG 57.498 36.000 0.00 0.00 35.20 3.16
4069 4589 1.149101 TCCTTTTCTGACTTGGCCCT 58.851 50.000 0.00 0.00 0.00 5.19
4075 4595 1.734655 TCTGACTTGGCCCTCTCTTT 58.265 50.000 0.00 0.00 0.00 2.52
4076 4596 2.902608 TCTGACTTGGCCCTCTCTTTA 58.097 47.619 0.00 0.00 0.00 1.85
4078 4598 3.198635 TCTGACTTGGCCCTCTCTTTATG 59.801 47.826 0.00 0.00 0.00 1.90
4079 4599 2.239654 TGACTTGGCCCTCTCTTTATGG 59.760 50.000 0.00 0.00 0.00 2.74
4097 4629 0.534203 GGACGCCTTCCAAGTGAACA 60.534 55.000 0.00 0.00 45.10 3.18
4116 4648 7.688372 GTGAACACCATTCACATATACTCTTG 58.312 38.462 13.53 0.00 45.89 3.02
4125 4657 6.860790 TCACATATACTCTTGTGTGGGTAA 57.139 37.500 4.73 0.00 42.95 2.85
4127 4659 7.272244 TCACATATACTCTTGTGTGGGTAATG 58.728 38.462 4.73 0.00 42.95 1.90
4146 4678 4.221422 ACTGTGCAGTGCCGTCGT 62.221 61.111 13.72 1.52 40.75 4.34
4157 4690 1.131826 GCCGTCGTGTTGGAATTCG 59.868 57.895 0.00 0.00 0.00 3.34
4160 4693 1.355971 CGTCGTGTTGGAATTCGGAT 58.644 50.000 0.00 0.00 0.00 4.18
4165 4698 2.936498 CGTGTTGGAATTCGGATAAGCT 59.064 45.455 0.00 0.00 0.00 3.74
4258 4791 2.365635 TGGGCCAGTAGCTCCCTC 60.366 66.667 0.00 0.00 43.71 4.30
4259 4792 3.164977 GGGCCAGTAGCTCCCTCC 61.165 72.222 4.39 0.00 43.05 4.30
4371 4907 2.113986 AGTTCACACCTGCCTGCC 59.886 61.111 0.00 0.00 0.00 4.85
4468 5004 4.550076 AAATAGCTTCACTCTCTGTGCT 57.450 40.909 0.00 0.00 45.81 4.40
4580 5123 4.689612 TGCTTTCTAAGGTCTTGTCTGT 57.310 40.909 0.00 0.00 0.00 3.41
4640 5184 0.106868 TCGGCCGATTCTCCTGTAGA 60.107 55.000 27.28 0.00 0.00 2.59
4680 5224 5.070180 TGCAATGTGGATTTTTCCTTCTTCA 59.930 36.000 0.00 0.00 0.00 3.02
4711 5255 3.857854 GCACGCCGATGCTGTCAG 61.858 66.667 0.00 0.00 42.62 3.51
4712 5256 3.190849 CACGCCGATGCTGTCAGG 61.191 66.667 1.14 0.00 34.43 3.86
4713 5257 3.695606 ACGCCGATGCTGTCAGGT 61.696 61.111 1.14 0.00 34.43 4.00
4714 5258 2.887568 CGCCGATGCTGTCAGGTC 60.888 66.667 1.14 0.00 34.43 3.85
4715 5259 2.265739 GCCGATGCTGTCAGGTCA 59.734 61.111 1.14 0.00 33.53 4.02
4716 5260 2.103042 GCCGATGCTGTCAGGTCAC 61.103 63.158 1.14 0.00 33.53 3.67
4717 5261 1.448540 CCGATGCTGTCAGGTCACC 60.449 63.158 1.14 0.00 0.00 4.02
4718 5262 1.293179 CGATGCTGTCAGGTCACCA 59.707 57.895 0.00 0.00 0.00 4.17
4719 5263 1.016130 CGATGCTGTCAGGTCACCAC 61.016 60.000 0.00 0.00 0.00 4.16
4720 5264 0.322975 GATGCTGTCAGGTCACCACT 59.677 55.000 0.00 0.00 0.00 4.00
4721 5265 0.322975 ATGCTGTCAGGTCACCACTC 59.677 55.000 0.00 0.00 0.00 3.51
4722 5266 1.048160 TGCTGTCAGGTCACCACTCA 61.048 55.000 0.00 0.00 0.00 3.41
4723 5267 0.106708 GCTGTCAGGTCACCACTCAA 59.893 55.000 0.00 0.00 0.00 3.02
4724 5268 1.875576 GCTGTCAGGTCACCACTCAAG 60.876 57.143 0.00 0.00 0.00 3.02
4725 5269 0.106708 TGTCAGGTCACCACTCAAGC 59.893 55.000 0.00 0.00 0.00 4.01
4726 5270 0.394565 GTCAGGTCACCACTCAAGCT 59.605 55.000 0.00 0.00 0.00 3.74
4727 5271 0.681733 TCAGGTCACCACTCAAGCTC 59.318 55.000 0.00 0.00 0.00 4.09
4728 5272 0.321122 CAGGTCACCACTCAAGCTCC 60.321 60.000 0.00 0.00 0.00 4.70
4729 5273 0.472734 AGGTCACCACTCAAGCTCCT 60.473 55.000 0.00 0.00 0.00 3.69
4730 5274 0.321122 GGTCACCACTCAAGCTCCTG 60.321 60.000 0.00 0.00 0.00 3.86
4731 5275 0.394565 GTCACCACTCAAGCTCCTGT 59.605 55.000 0.00 0.00 0.00 4.00
4732 5276 1.618837 GTCACCACTCAAGCTCCTGTA 59.381 52.381 0.00 0.00 0.00 2.74
4733 5277 1.895798 TCACCACTCAAGCTCCTGTAG 59.104 52.381 0.00 0.00 0.00 2.74
4734 5278 1.895798 CACCACTCAAGCTCCTGTAGA 59.104 52.381 0.00 0.00 0.00 2.59
4735 5279 2.094286 CACCACTCAAGCTCCTGTAGAG 60.094 54.545 0.00 0.00 46.29 2.43
4736 5280 2.175202 CCACTCAAGCTCCTGTAGAGT 58.825 52.381 0.00 0.00 45.21 3.24
4737 5281 3.229276 CACTCAAGCTCCTGTAGAGTG 57.771 52.381 6.50 6.50 46.75 3.51
4738 5282 2.175202 ACTCAAGCTCCTGTAGAGTGG 58.825 52.381 0.00 0.00 45.21 4.00
4739 5283 2.175202 CTCAAGCTCCTGTAGAGTGGT 58.825 52.381 0.00 0.00 45.21 4.16
4740 5284 2.564947 CTCAAGCTCCTGTAGAGTGGTT 59.435 50.000 0.00 0.00 45.21 3.67
4741 5285 2.563179 TCAAGCTCCTGTAGAGTGGTTC 59.437 50.000 0.00 0.00 45.21 3.62
4742 5286 2.300152 CAAGCTCCTGTAGAGTGGTTCA 59.700 50.000 0.00 0.00 45.21 3.18
4743 5287 1.896465 AGCTCCTGTAGAGTGGTTCAC 59.104 52.381 0.00 0.00 45.21 3.18
4753 5297 2.254546 AGTGGTTCACTCGAAATGCA 57.745 45.000 0.00 0.00 41.21 3.96
4754 5298 2.571212 AGTGGTTCACTCGAAATGCAA 58.429 42.857 0.00 0.00 41.21 4.08
4755 5299 3.149196 AGTGGTTCACTCGAAATGCAAT 58.851 40.909 0.00 0.00 41.21 3.56
4756 5300 3.058016 AGTGGTTCACTCGAAATGCAATG 60.058 43.478 0.00 0.00 41.21 2.82
4757 5301 2.228582 TGGTTCACTCGAAATGCAATGG 59.771 45.455 0.00 0.00 31.43 3.16
4758 5302 2.415893 GGTTCACTCGAAATGCAATGGG 60.416 50.000 0.00 0.00 31.43 4.00
4759 5303 1.462616 TCACTCGAAATGCAATGGGG 58.537 50.000 0.00 0.00 0.00 4.96
4760 5304 1.004161 TCACTCGAAATGCAATGGGGA 59.996 47.619 0.00 0.00 0.00 4.81
4761 5305 2.026641 CACTCGAAATGCAATGGGGAT 58.973 47.619 0.00 0.00 0.00 3.85
4762 5306 2.428171 CACTCGAAATGCAATGGGGATT 59.572 45.455 0.00 0.00 39.48 3.01
4764 5308 3.515104 ACTCGAAATGCAATGGGGATTTT 59.485 39.130 0.00 0.00 46.08 1.82
4765 5309 4.114794 CTCGAAATGCAATGGGGATTTTC 58.885 43.478 0.00 0.00 46.08 2.29
4766 5310 3.118811 TCGAAATGCAATGGGGATTTTCC 60.119 43.478 0.00 0.00 46.08 3.13
4767 5311 3.118665 CGAAATGCAATGGGGATTTTCCT 60.119 43.478 0.00 0.00 46.08 3.36
4768 5312 4.623647 CGAAATGCAATGGGGATTTTCCTT 60.624 41.667 0.00 0.00 46.08 3.36
4769 5313 4.492494 AATGCAATGGGGATTTTCCTTC 57.508 40.909 0.00 0.00 33.19 3.46
4770 5314 3.188880 TGCAATGGGGATTTTCCTTCT 57.811 42.857 0.00 0.00 36.57 2.85
4771 5315 3.519667 TGCAATGGGGATTTTCCTTCTT 58.480 40.909 0.00 0.00 36.57 2.52
4772 5316 3.515104 TGCAATGGGGATTTTCCTTCTTC 59.485 43.478 0.00 0.00 36.57 2.87
4773 5317 3.771479 GCAATGGGGATTTTCCTTCTTCT 59.229 43.478 0.00 0.00 36.57 2.85
4774 5318 4.223700 GCAATGGGGATTTTCCTTCTTCTT 59.776 41.667 0.00 0.00 36.57 2.52
4775 5319 5.280164 GCAATGGGGATTTTCCTTCTTCTTT 60.280 40.000 0.00 0.00 36.57 2.52
4776 5320 6.745190 GCAATGGGGATTTTCCTTCTTCTTTT 60.745 38.462 0.00 0.00 36.57 2.27
4777 5321 7.226441 CAATGGGGATTTTCCTTCTTCTTTTT 58.774 34.615 0.00 0.00 36.57 1.94
4778 5322 6.419484 TGGGGATTTTCCTTCTTCTTTTTC 57.581 37.500 0.00 0.00 36.57 2.29
4779 5323 5.902431 TGGGGATTTTCCTTCTTCTTTTTCA 59.098 36.000 0.00 0.00 36.57 2.69
4780 5324 6.041979 TGGGGATTTTCCTTCTTCTTTTTCAG 59.958 38.462 0.00 0.00 36.57 3.02
4781 5325 6.459066 GGGATTTTCCTTCTTCTTTTTCAGG 58.541 40.000 0.00 0.00 36.57 3.86
4782 5326 6.042093 GGGATTTTCCTTCTTCTTTTTCAGGT 59.958 38.462 0.00 0.00 36.57 4.00
4783 5327 7.419057 GGGATTTTCCTTCTTCTTTTTCAGGTT 60.419 37.037 0.00 0.00 36.57 3.50
4784 5328 7.653713 GGATTTTCCTTCTTCTTTTTCAGGTTC 59.346 37.037 0.00 0.00 32.53 3.62
4785 5329 5.751243 TTCCTTCTTCTTTTTCAGGTTCG 57.249 39.130 0.00 0.00 0.00 3.95
4786 5330 4.134563 TCCTTCTTCTTTTTCAGGTTCGG 58.865 43.478 0.00 0.00 0.00 4.30
4787 5331 3.304726 CCTTCTTCTTTTTCAGGTTCGGC 60.305 47.826 0.00 0.00 0.00 5.54
4788 5332 2.925724 TCTTCTTTTTCAGGTTCGGCA 58.074 42.857 0.00 0.00 0.00 5.69
4789 5333 2.616842 TCTTCTTTTTCAGGTTCGGCAC 59.383 45.455 0.00 0.00 0.00 5.01
4804 5348 3.190849 CACGCCGATGCTGTCAGG 61.191 66.667 1.14 0.00 34.43 3.86
4842 5386 4.711980 ACGATCTCGGCGATTGTC 57.288 55.556 11.27 8.12 41.94 3.18
4843 5387 1.298413 ACGATCTCGGCGATTGTCG 60.298 57.895 26.02 26.02 41.94 4.35
4867 5436 2.644992 GTTTGTCTGCCCGGCTTG 59.355 61.111 11.61 3.78 0.00 4.01
4937 5513 1.412710 GATCTGAGCGGACCACCATTA 59.587 52.381 0.00 0.00 35.59 1.90
5007 5583 1.661463 TCTTCTTGCCCTCACCTCAT 58.339 50.000 0.00 0.00 0.00 2.90
5058 5647 2.398554 CCGCGGCAGCATTTGTACT 61.399 57.895 14.67 0.00 45.49 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 6.435591 GTCATTCTCTCCCTCCATTTTCTTTT 59.564 38.462 0.00 0.00 0.00 2.27
169 170 2.943033 CTCCCGCCATTTTATTTCTCGT 59.057 45.455 0.00 0.00 0.00 4.18
529 532 2.418884 GGTCAAAAAGGTTGGCCGAAAA 60.419 45.455 0.00 0.00 40.50 2.29
530 533 1.137282 GGTCAAAAAGGTTGGCCGAAA 59.863 47.619 0.00 0.00 40.50 3.46
531 534 0.747852 GGTCAAAAAGGTTGGCCGAA 59.252 50.000 0.00 0.00 40.50 4.30
532 535 0.395862 TGGTCAAAAAGGTTGGCCGA 60.396 50.000 0.00 0.00 46.71 5.54
533 536 0.461961 TTGGTCAAAAAGGTTGGCCG 59.538 50.000 0.00 0.00 46.71 6.13
534 537 1.484653 AGTTGGTCAAAAAGGTTGGCC 59.515 47.619 0.00 0.00 44.14 5.36
535 538 2.093711 ACAGTTGGTCAAAAAGGTTGGC 60.094 45.455 0.00 0.00 0.00 4.52
536 539 3.885724 ACAGTTGGTCAAAAAGGTTGG 57.114 42.857 0.00 0.00 0.00 3.77
537 540 3.932089 CCAACAGTTGGTCAAAAAGGTTG 59.068 43.478 22.74 0.00 45.93 3.77
538 541 4.200838 CCAACAGTTGGTCAAAAAGGTT 57.799 40.909 22.74 0.00 45.93 3.50
539 542 3.885724 CCAACAGTTGGTCAAAAAGGT 57.114 42.857 22.74 0.00 45.93 3.50
706 768 7.807907 ACGAAATTAACAAGAGCAACTAATTGG 59.192 33.333 0.00 0.00 36.23 3.16
718 780 2.739913 CGGCCTGACGAAATTAACAAGA 59.260 45.455 0.00 0.00 35.47 3.02
721 783 2.172851 ACGGCCTGACGAAATTAACA 57.827 45.000 0.00 0.00 37.61 2.41
1079 1163 4.150454 AGGAGGAGGAGGCGGAGG 62.150 72.222 0.00 0.00 0.00 4.30
1080 1164 2.520741 GAGGAGGAGGAGGCGGAG 60.521 72.222 0.00 0.00 0.00 4.63
1081 1165 4.144727 GGAGGAGGAGGAGGCGGA 62.145 72.222 0.00 0.00 0.00 5.54
1082 1166 4.150454 AGGAGGAGGAGGAGGCGG 62.150 72.222 0.00 0.00 0.00 6.13
1083 1167 2.520741 GAGGAGGAGGAGGAGGCG 60.521 72.222 0.00 0.00 0.00 5.52
1084 1168 2.123033 GGAGGAGGAGGAGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
1085 1169 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1086 1170 1.541672 GGAGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
1087 1171 2.015726 GGGAGGAGGAGGAGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
1088 1172 2.612251 GGGAGGAGGAGGAGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
1089 1173 2.612251 GGGGAGGAGGAGGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
1090 1174 3.036959 GGGGGAGGAGGAGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
1091 1175 4.548513 CGGGGGAGGAGGAGGAGG 62.549 77.778 0.00 0.00 0.00 4.30
1092 1176 4.548513 CCGGGGGAGGAGGAGGAG 62.549 77.778 0.00 0.00 0.00 3.69
1117 1201 4.873129 CATCTCGACCACCGCCGG 62.873 72.222 0.00 0.00 38.37 6.13
1118 1202 4.873129 CCATCTCGACCACCGCCG 62.873 72.222 0.00 0.00 38.37 6.46
1121 1205 3.432051 GAGGCCATCTCGACCACCG 62.432 68.421 5.01 0.00 40.25 4.94
1122 1206 2.501610 GAGGCCATCTCGACCACC 59.498 66.667 5.01 0.00 32.18 4.61
1129 1213 2.280052 GAGCAGCGAGGCCATCTC 60.280 66.667 5.01 0.00 39.10 2.75
1130 1214 3.859414 GGAGCAGCGAGGCCATCT 61.859 66.667 5.01 0.00 0.00 2.90
1157 1241 4.752879 TGAGGGGCGCGTAGTTGC 62.753 66.667 8.43 0.00 0.00 4.17
1158 1242 2.509336 CTGAGGGGCGCGTAGTTG 60.509 66.667 8.43 0.00 0.00 3.16
1159 1243 4.452733 GCTGAGGGGCGCGTAGTT 62.453 66.667 8.43 0.00 0.00 2.24
1168 1252 4.436998 GTCGTCGGTGCTGAGGGG 62.437 72.222 0.00 0.00 0.00 4.79
1169 1253 4.436998 GGTCGTCGGTGCTGAGGG 62.437 72.222 0.00 0.00 0.00 4.30
1170 1254 4.436998 GGGTCGTCGGTGCTGAGG 62.437 72.222 0.00 0.00 0.00 3.86
1171 1255 4.436998 GGGGTCGTCGGTGCTGAG 62.437 72.222 0.00 0.00 0.00 3.35
1172 1256 4.988716 AGGGGTCGTCGGTGCTGA 62.989 66.667 0.00 0.00 0.00 4.26
1173 1257 4.436998 GAGGGGTCGTCGGTGCTG 62.437 72.222 0.00 0.00 0.00 4.41
1220 1304 4.888325 ATGCGAGGGGGAGGGGAG 62.888 72.222 0.00 0.00 0.00 4.30
1221 1305 4.880426 GATGCGAGGGGGAGGGGA 62.880 72.222 0.00 0.00 0.00 4.81
1222 1306 4.888325 AGATGCGAGGGGGAGGGG 62.888 72.222 0.00 0.00 0.00 4.79
1223 1307 3.237741 GAGATGCGAGGGGGAGGG 61.238 72.222 0.00 0.00 0.00 4.30
1224 1308 3.610669 CGAGATGCGAGGGGGAGG 61.611 72.222 0.00 0.00 44.57 4.30
1225 1309 2.835431 ACGAGATGCGAGGGGGAG 60.835 66.667 0.00 0.00 44.57 4.30
1226 1310 2.833582 GACGAGATGCGAGGGGGA 60.834 66.667 0.00 0.00 44.57 4.81
1244 1473 2.283676 GGGGGTGAGGTCAGACGA 60.284 66.667 0.00 0.00 0.00 4.20
1247 1476 1.000019 CTACGGGGGTGAGGTCAGA 60.000 63.158 0.00 0.00 0.00 3.27
1248 1477 1.000019 TCTACGGGGGTGAGGTCAG 60.000 63.158 0.00 0.00 0.00 3.51
1249 1478 1.000019 CTCTACGGGGGTGAGGTCA 60.000 63.158 0.00 0.00 0.00 4.02
1250 1479 1.036481 GTCTCTACGGGGGTGAGGTC 61.036 65.000 0.00 0.00 0.00 3.85
1286 1594 1.261089 GTGACTACCTAGCTACGCTCG 59.739 57.143 0.00 0.00 40.44 5.03
1308 1616 1.080839 CAATTTGACAACCCCGCGG 60.081 57.895 21.04 21.04 0.00 6.46
1343 1651 0.464373 TCCAGCATTTCCAGCGATCC 60.464 55.000 0.00 0.00 37.01 3.36
1389 1697 0.692419 ACATGGGCCAGGAGACTAGG 60.692 60.000 27.05 0.00 40.21 3.02
1408 1716 9.039165 ACTAGCTAATGTACTACAAGGGTAAAA 57.961 33.333 0.00 0.00 0.00 1.52
1409 1717 8.599624 ACTAGCTAATGTACTACAAGGGTAAA 57.400 34.615 0.00 0.00 0.00 2.01
1410 1718 8.599624 AACTAGCTAATGTACTACAAGGGTAA 57.400 34.615 0.00 0.00 0.00 2.85
1411 1719 9.872684 ATAACTAGCTAATGTACTACAAGGGTA 57.127 33.333 0.00 0.00 0.00 3.69
1412 1720 8.779096 ATAACTAGCTAATGTACTACAAGGGT 57.221 34.615 0.00 0.00 0.00 4.34
1443 1752 5.994250 AGGTCAATTAGCTGATGTACATGT 58.006 37.500 14.43 2.69 33.68 3.21
1479 1788 5.734720 CACAAAGGGTAGCTTAGATCAGAA 58.265 41.667 0.00 0.00 0.00 3.02
1498 1807 2.347452 GCTCGAATTAGCTAACGCACAA 59.653 45.455 8.70 0.00 39.50 3.33
1529 1838 2.104253 GTACCGGTGAACATGGCCG 61.104 63.158 19.93 11.55 44.55 6.13
1534 1843 1.354101 TTCCCAGTACCGGTGAACAT 58.646 50.000 19.93 0.00 0.00 2.71
1535 1844 1.129917 TTTCCCAGTACCGGTGAACA 58.870 50.000 19.93 0.00 0.00 3.18
1538 1847 0.616371 CCATTTCCCAGTACCGGTGA 59.384 55.000 19.93 1.50 0.00 4.02
1590 1900 0.601558 TGTCGGTGTCAGGTAGCTTC 59.398 55.000 0.00 0.00 0.00 3.86
1595 1905 1.532604 CCTGCTGTCGGTGTCAGGTA 61.533 60.000 0.00 0.00 40.79 3.08
1617 1927 5.634896 AGCTTTTCAAGACAATGCTATTCG 58.365 37.500 0.00 0.00 33.95 3.34
1691 2005 3.119316 TCAACTTCTCCTCTCAAGCGATC 60.119 47.826 0.00 0.00 0.00 3.69
1800 2196 4.516698 GCCATACCGTTGATCTGATCATTT 59.483 41.667 20.16 8.23 39.39 2.32
1802 2198 3.668447 GCCATACCGTTGATCTGATCAT 58.332 45.455 20.16 8.70 39.39 2.45
1815 2211 2.885676 GCATGTCAGCGCCATACCG 61.886 63.158 2.29 0.00 0.00 4.02
1820 2216 0.961857 AGATTTGCATGTCAGCGCCA 60.962 50.000 2.29 0.00 37.31 5.69
1824 2220 3.427528 CACAACAAGATTTGCATGTCAGC 59.572 43.478 0.00 0.00 33.42 4.26
1834 2230 4.516698 CACCTCTACTGCACAACAAGATTT 59.483 41.667 0.00 0.00 0.00 2.17
1836 2232 3.668447 CACCTCTACTGCACAACAAGAT 58.332 45.455 0.00 0.00 0.00 2.40
1838 2234 1.532868 GCACCTCTACTGCACAACAAG 59.467 52.381 0.00 0.00 34.56 3.16
1839 2235 1.593196 GCACCTCTACTGCACAACAA 58.407 50.000 0.00 0.00 34.56 2.83
1877 2273 1.729267 AAACATCCACCCAGGCTGGT 61.729 55.000 30.68 16.76 37.84 4.00
1895 2291 3.380320 TGTTCGCAGATATCTCTTCGGAA 59.620 43.478 1.03 0.00 38.47 4.30
2030 2426 3.129462 TCTTCAGCAGGTCTGTTATCTCG 59.871 47.826 0.00 0.00 43.32 4.04
2137 2533 1.986882 ATACATAAAGCAGCAGGGGC 58.013 50.000 0.00 0.00 41.61 5.80
2147 2543 9.155975 AGCTCTTGTGTCTGTTAATACATAAAG 57.844 33.333 0.00 0.00 32.86 1.85
2173 2569 5.473162 AGCACAAACATTCATAGCAGTTACA 59.527 36.000 0.00 0.00 0.00 2.41
2213 2612 2.341257 ACGCTGCAGATAACAGTGAAG 58.659 47.619 20.43 0.00 46.26 3.02
2347 2747 2.224079 GCACAAGCGTCTGAATTTCTGA 59.776 45.455 2.19 2.19 0.00 3.27
2404 2804 2.136298 TGCCCCTGAAATCGCATTTA 57.864 45.000 0.00 0.00 31.47 1.40
2515 2915 9.708092 AAAGAGTCTATGGTAAGTAAAGACAAC 57.292 33.333 0.00 0.00 39.20 3.32
2559 2962 0.037877 AAAGCTGCCAGTGCTCAGAT 59.962 50.000 12.93 5.43 40.22 2.90
2598 3001 7.278646 TGTCAAATTCATACAGCTGACATACTC 59.721 37.037 23.35 0.89 38.52 2.59
2603 3008 6.207221 ACAATGTCAAATTCATACAGCTGACA 59.793 34.615 23.35 10.67 45.06 3.58
2691 3097 3.068024 GTGAAGCATTCCAGTGAAAACCA 59.932 43.478 0.00 0.00 46.93 3.67
2698 3104 3.405831 TCTGAAGTGAAGCATTCCAGTG 58.594 45.455 0.00 0.00 46.93 3.66
2764 3171 7.452231 CAACTAATTGTGTGGTTGTTGTTTTC 58.548 34.615 0.00 0.00 35.67 2.29
2775 3182 7.276218 CCTAAATCAATGCAACTAATTGTGTGG 59.724 37.037 0.00 0.00 38.17 4.17
2795 3214 9.396022 CAAACCTGTATGACTAATGACCTAAAT 57.604 33.333 0.00 0.00 0.00 1.40
2799 3218 6.620877 TCAAACCTGTATGACTAATGACCT 57.379 37.500 0.00 0.00 0.00 3.85
2812 3231 6.017770 CGTTACATCCAAAGTTCAAACCTGTA 60.018 38.462 0.00 0.00 0.00 2.74
2814 3233 5.008217 TCGTTACATCCAAAGTTCAAACCTG 59.992 40.000 0.00 0.00 0.00 4.00
2832 3331 9.824534 GCCTCTTCTATAAAGTATACTCGTTAC 57.175 37.037 5.70 0.00 0.00 2.50
2849 3349 4.298626 ACCATGGTCATTAGCCTCTTCTA 58.701 43.478 13.00 0.00 0.00 2.10
2854 3354 2.952310 GGAAACCATGGTCATTAGCCTC 59.048 50.000 20.07 4.95 0.00 4.70
2888 3388 7.584532 AGCTACTCCCTAAGTAAATAGACTCA 58.415 38.462 0.00 0.00 39.98 3.41
2889 3389 9.571816 TTAGCTACTCCCTAAGTAAATAGACTC 57.428 37.037 0.00 0.00 39.98 3.36
2908 3408 9.187455 GCTACTTCTCATAATCAGTTTAGCTAC 57.813 37.037 0.00 0.00 0.00 3.58
2910 3410 7.925483 CAGCTACTTCTCATAATCAGTTTAGCT 59.075 37.037 0.00 0.00 33.38 3.32
2928 3428 2.428890 CCGGACTTCTCATCAGCTACTT 59.571 50.000 0.00 0.00 0.00 2.24
3156 3659 6.930722 ACCTTCAAACAAAAAGCAGATAATGG 59.069 34.615 0.00 0.00 0.00 3.16
3256 3759 7.410174 ACCATCAATGACCCAATTAAGTTAGA 58.590 34.615 0.00 0.00 0.00 2.10
3324 3827 6.648192 TCAACAATTGTTCCCTGTTCAAATT 58.352 32.000 20.85 0.00 35.83 1.82
3421 3924 1.682344 GGCAAATGGGGGTGAGGAC 60.682 63.158 0.00 0.00 0.00 3.85
3608 4115 4.142447 TGCAACTTTAAACACGTGGCTAAA 60.142 37.500 21.57 19.30 0.00 1.85
3645 4152 9.391006 CTTTTTACTGGATGCCTTTACATACTA 57.609 33.333 0.00 0.00 31.64 1.82
3648 4155 9.742144 TTACTTTTTACTGGATGCCTTTACATA 57.258 29.630 0.00 0.00 0.00 2.29
3653 4160 8.261522 TGTTTTTACTTTTTACTGGATGCCTTT 58.738 29.630 0.00 0.00 0.00 3.11
3691 4198 6.927294 ATTTTTAAATCTAGTCTCTGGCCG 57.073 37.500 0.00 0.00 0.00 6.13
3709 4218 9.958180 CTTGAGGTAAATTTGGGGATTATTTTT 57.042 29.630 0.00 0.00 0.00 1.94
3713 4222 8.566109 AGTACTTGAGGTAAATTTGGGGATTAT 58.434 33.333 0.00 0.00 31.56 1.28
3721 4230 8.871686 AAAAGCAAGTACTTGAGGTAAATTTG 57.128 30.769 34.43 8.91 42.93 2.32
3752 4261 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
3754 4263 1.225991 CGCACACACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
3756 4265 2.277247 GCGCACACACACACACAC 60.277 61.111 0.30 0.00 0.00 3.82
3771 4280 0.450319 TAAATATGAATGCGCGCGCG 60.450 50.000 45.73 45.73 45.51 6.86
3772 4281 1.378807 GTTAAATATGAATGCGCGCGC 59.621 47.619 45.02 45.02 42.35 6.86
3773 4282 2.647036 CAGTTAAATATGAATGCGCGCG 59.353 45.455 28.44 28.44 0.00 6.86
3774 4283 2.401720 GCAGTTAAATATGAATGCGCGC 59.598 45.455 27.26 27.26 0.00 6.86
3775 4284 2.973224 GGCAGTTAAATATGAATGCGCG 59.027 45.455 0.00 0.00 34.54 6.86
3797 4316 5.712917 TGGGTTTCTTTAAATTATGTCGGCT 59.287 36.000 0.00 0.00 0.00 5.52
3848 4368 9.553064 CAGAAGCTCTTTGATAATATAAGGTGT 57.447 33.333 0.00 0.00 0.00 4.16
3855 4375 7.776969 TCCTTTGCAGAAGCTCTTTGATAATAT 59.223 33.333 0.00 0.00 42.74 1.28
3856 4376 7.112122 TCCTTTGCAGAAGCTCTTTGATAATA 58.888 34.615 0.00 0.00 42.74 0.98
3857 4377 5.948162 TCCTTTGCAGAAGCTCTTTGATAAT 59.052 36.000 0.00 0.00 42.74 1.28
3858 4378 5.316167 TCCTTTGCAGAAGCTCTTTGATAA 58.684 37.500 0.00 0.00 42.74 1.75
3863 4383 3.825328 TCTTCCTTTGCAGAAGCTCTTT 58.175 40.909 8.86 0.00 40.48 2.52
3891 4411 1.000771 AGGGACTGACGCTAGCTCA 60.001 57.895 13.93 13.85 40.01 4.26
3914 4434 4.813161 CAGACCAACATATTAGACTGCCAG 59.187 45.833 0.00 0.00 0.00 4.85
3916 4436 5.023533 TCAGACCAACATATTAGACTGCC 57.976 43.478 0.00 0.00 0.00 4.85
4064 4584 0.533085 GCGTCCATAAAGAGAGGGCC 60.533 60.000 0.00 0.00 0.00 5.80
4069 4589 2.981859 GGAAGGCGTCCATAAAGAGA 57.018 50.000 14.94 0.00 46.97 3.10
4079 4599 0.586802 GTGTTCACTTGGAAGGCGTC 59.413 55.000 0.00 0.00 35.82 5.19
4116 4648 1.165270 GCACAGTCCATTACCCACAC 58.835 55.000 0.00 0.00 0.00 3.82
4125 4657 2.359107 CGGCACTGCACAGTCCAT 60.359 61.111 2.82 0.00 40.20 3.41
4127 4659 3.044305 GACGGCACTGCACAGTCC 61.044 66.667 2.82 4.98 40.20 3.85
4146 4678 2.682856 GCAGCTTATCCGAATTCCAACA 59.317 45.455 0.00 0.00 0.00 3.33
4249 4782 0.710588 TGGAAGACTGGAGGGAGCTA 59.289 55.000 0.00 0.00 0.00 3.32
4371 4907 1.669115 CCTGGTTGCTCCACGACAG 60.669 63.158 0.00 0.00 41.93 3.51
4468 5004 8.589701 TTCAATACCTAGACAGAATAGTGACA 57.410 34.615 0.00 0.00 0.00 3.58
4580 5123 5.104527 CCATATTGAAGGGGACACAGTTAGA 60.105 44.000 0.00 0.00 0.00 2.10
4625 5169 2.379972 ACCACTCTACAGGAGAATCGG 58.620 52.381 0.00 0.00 44.45 4.18
4640 5184 2.363306 TGCATTTCCAGTGAACCACT 57.637 45.000 0.00 0.00 46.51 4.00
4680 5224 1.852067 GCGTGCCGACACCTGAAAAT 61.852 55.000 0.00 0.00 44.40 1.82
4703 5247 1.048160 TGAGTGGTGACCTGACAGCA 61.048 55.000 2.11 0.00 44.20 4.41
4704 5248 0.106708 TTGAGTGGTGACCTGACAGC 59.893 55.000 2.11 0.00 38.53 4.40
4705 5249 1.875576 GCTTGAGTGGTGACCTGACAG 60.876 57.143 2.11 0.00 0.00 3.51
4706 5250 0.106708 GCTTGAGTGGTGACCTGACA 59.893 55.000 2.11 0.00 0.00 3.58
4707 5251 0.394565 AGCTTGAGTGGTGACCTGAC 59.605 55.000 2.11 0.00 0.00 3.51
4708 5252 0.681733 GAGCTTGAGTGGTGACCTGA 59.318 55.000 2.11 0.00 0.00 3.86
4709 5253 0.321122 GGAGCTTGAGTGGTGACCTG 60.321 60.000 2.11 0.00 0.00 4.00
4710 5254 0.472734 AGGAGCTTGAGTGGTGACCT 60.473 55.000 2.11 0.00 0.00 3.85
4711 5255 0.321122 CAGGAGCTTGAGTGGTGACC 60.321 60.000 0.00 0.00 0.00 4.02
4712 5256 0.394565 ACAGGAGCTTGAGTGGTGAC 59.605 55.000 0.00 0.00 0.00 3.67
4713 5257 1.895798 CTACAGGAGCTTGAGTGGTGA 59.104 52.381 0.00 0.00 0.00 4.02
4714 5258 1.895798 TCTACAGGAGCTTGAGTGGTG 59.104 52.381 0.00 0.00 0.00 4.17
4715 5259 2.175202 CTCTACAGGAGCTTGAGTGGT 58.825 52.381 0.00 0.00 35.08 4.16
4716 5260 2.094286 CACTCTACAGGAGCTTGAGTGG 60.094 54.545 12.06 6.68 46.16 4.00
4717 5261 3.229276 CACTCTACAGGAGCTTGAGTG 57.771 52.381 6.98 6.98 45.48 3.51
4718 5262 2.175202 CCACTCTACAGGAGCTTGAGT 58.825 52.381 0.00 0.00 45.48 3.41
4719 5263 2.175202 ACCACTCTACAGGAGCTTGAG 58.825 52.381 0.00 0.00 45.48 3.02
4720 5264 2.310779 ACCACTCTACAGGAGCTTGA 57.689 50.000 0.00 0.00 45.48 3.02
4721 5265 2.300152 TGAACCACTCTACAGGAGCTTG 59.700 50.000 0.00 0.00 45.48 4.01
4722 5266 2.300437 GTGAACCACTCTACAGGAGCTT 59.700 50.000 0.00 0.00 45.48 3.74
4723 5267 1.896465 GTGAACCACTCTACAGGAGCT 59.104 52.381 0.00 0.00 45.48 4.09
4724 5268 1.896465 AGTGAACCACTCTACAGGAGC 59.104 52.381 0.00 0.00 41.21 4.70
4735 5279 3.236816 CATTGCATTTCGAGTGAACCAC 58.763 45.455 4.29 0.00 32.71 4.16
4736 5280 2.228582 CCATTGCATTTCGAGTGAACCA 59.771 45.455 4.29 0.00 32.71 3.67
4737 5281 2.415893 CCCATTGCATTTCGAGTGAACC 60.416 50.000 4.29 0.00 32.71 3.62
4738 5282 2.415893 CCCCATTGCATTTCGAGTGAAC 60.416 50.000 4.29 0.00 32.71 3.18
4739 5283 1.818060 CCCCATTGCATTTCGAGTGAA 59.182 47.619 4.29 0.00 0.00 3.18
4740 5284 1.004161 TCCCCATTGCATTTCGAGTGA 59.996 47.619 4.29 0.00 0.00 3.41
4741 5285 1.462616 TCCCCATTGCATTTCGAGTG 58.537 50.000 0.00 0.00 0.00 3.51
4742 5286 2.442236 ATCCCCATTGCATTTCGAGT 57.558 45.000 0.00 0.00 0.00 4.18
4743 5287 3.806625 AAATCCCCATTGCATTTCGAG 57.193 42.857 0.00 0.00 0.00 4.04
4744 5288 3.118811 GGAAAATCCCCATTGCATTTCGA 60.119 43.478 0.00 0.00 0.00 3.71
4745 5289 3.118665 AGGAAAATCCCCATTGCATTTCG 60.119 43.478 0.00 0.00 37.19 3.46
4746 5290 4.492494 AGGAAAATCCCCATTGCATTTC 57.508 40.909 0.00 0.00 37.19 2.17
4747 5291 4.537288 AGAAGGAAAATCCCCATTGCATTT 59.463 37.500 0.00 0.00 37.19 2.32
4748 5292 4.106324 AGAAGGAAAATCCCCATTGCATT 58.894 39.130 0.00 0.00 37.19 3.56
4749 5293 3.727948 AGAAGGAAAATCCCCATTGCAT 58.272 40.909 0.00 0.00 37.19 3.96
4750 5294 3.188880 AGAAGGAAAATCCCCATTGCA 57.811 42.857 0.00 0.00 37.19 4.08
4751 5295 3.771479 AGAAGAAGGAAAATCCCCATTGC 59.229 43.478 0.00 0.00 37.19 3.56
4752 5296 6.364568 AAAGAAGAAGGAAAATCCCCATTG 57.635 37.500 0.00 0.00 37.19 2.82
4753 5297 7.072328 TGAAAAAGAAGAAGGAAAATCCCCATT 59.928 33.333 0.00 0.00 37.19 3.16
4754 5298 6.558394 TGAAAAAGAAGAAGGAAAATCCCCAT 59.442 34.615 0.00 0.00 37.19 4.00
4755 5299 5.902431 TGAAAAAGAAGAAGGAAAATCCCCA 59.098 36.000 0.00 0.00 37.19 4.96
4756 5300 6.419484 TGAAAAAGAAGAAGGAAAATCCCC 57.581 37.500 0.00 0.00 37.19 4.81
4757 5301 6.042093 ACCTGAAAAAGAAGAAGGAAAATCCC 59.958 38.462 0.00 0.00 37.19 3.85
4758 5302 7.055667 ACCTGAAAAAGAAGAAGGAAAATCC 57.944 36.000 0.00 0.00 36.58 3.01
4759 5303 7.379797 CGAACCTGAAAAAGAAGAAGGAAAATC 59.620 37.037 0.00 0.00 0.00 2.17
4760 5304 7.203218 CGAACCTGAAAAAGAAGAAGGAAAAT 58.797 34.615 0.00 0.00 0.00 1.82
4761 5305 6.405397 CCGAACCTGAAAAAGAAGAAGGAAAA 60.405 38.462 0.00 0.00 0.00 2.29
4762 5306 5.067283 CCGAACCTGAAAAAGAAGAAGGAAA 59.933 40.000 0.00 0.00 0.00 3.13
4763 5307 4.578928 CCGAACCTGAAAAAGAAGAAGGAA 59.421 41.667 0.00 0.00 0.00 3.36
4764 5308 4.134563 CCGAACCTGAAAAAGAAGAAGGA 58.865 43.478 0.00 0.00 0.00 3.36
4765 5309 3.304726 GCCGAACCTGAAAAAGAAGAAGG 60.305 47.826 0.00 0.00 0.00 3.46
4766 5310 3.315191 TGCCGAACCTGAAAAAGAAGAAG 59.685 43.478 0.00 0.00 0.00 2.85
4767 5311 3.066203 GTGCCGAACCTGAAAAAGAAGAA 59.934 43.478 0.00 0.00 0.00 2.52
4768 5312 2.616842 GTGCCGAACCTGAAAAAGAAGA 59.383 45.455 0.00 0.00 0.00 2.87
4769 5313 2.602217 CGTGCCGAACCTGAAAAAGAAG 60.602 50.000 0.00 0.00 0.00 2.85
4770 5314 1.332375 CGTGCCGAACCTGAAAAAGAA 59.668 47.619 0.00 0.00 0.00 2.52
4771 5315 0.941542 CGTGCCGAACCTGAAAAAGA 59.058 50.000 0.00 0.00 0.00 2.52
4772 5316 0.660300 GCGTGCCGAACCTGAAAAAG 60.660 55.000 0.00 0.00 0.00 2.27
4773 5317 1.357334 GCGTGCCGAACCTGAAAAA 59.643 52.632 0.00 0.00 0.00 1.94
4774 5318 2.548295 GGCGTGCCGAACCTGAAAA 61.548 57.895 0.00 0.00 0.00 2.29
4775 5319 2.975799 GGCGTGCCGAACCTGAAA 60.976 61.111 0.00 0.00 0.00 2.69
4790 5334 2.103042 GTGACCTGACAGCATCGGC 61.103 63.158 0.00 0.00 41.61 5.54
4791 5335 1.448540 GGTGACCTGACAGCATCGG 60.449 63.158 0.00 0.00 38.05 4.18
4792 5336 1.016130 GTGGTGACCTGACAGCATCG 61.016 60.000 2.11 0.00 46.96 3.84
4793 5337 0.322975 AGTGGTGACCTGACAGCATC 59.677 55.000 2.11 0.00 46.96 3.91
4794 5338 0.322975 GAGTGGTGACCTGACAGCAT 59.677 55.000 2.11 0.00 46.96 3.79
4804 5348 0.036858 GGAGGAGCTTGAGTGGTGAC 60.037 60.000 0.00 0.00 0.00 3.67
4837 5381 2.675075 CAAACCCCCGGCGACAAT 60.675 61.111 9.30 0.00 0.00 2.71
4838 5382 4.192453 ACAAACCCCCGGCGACAA 62.192 61.111 9.30 0.00 0.00 3.18
4839 5383 4.629523 GACAAACCCCCGGCGACA 62.630 66.667 9.30 0.00 0.00 4.35
4840 5384 4.324991 AGACAAACCCCCGGCGAC 62.325 66.667 9.30 0.00 0.00 5.19
4937 5513 2.286197 GGGGCTGGGGGAGTAGTT 60.286 66.667 0.00 0.00 0.00 2.24
5007 5583 1.781025 CGGTCAAAACGAGGCAGCAA 61.781 55.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.