Multiple sequence alignment - TraesCS7D01G536000

Loading Multiple Alignment...

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 TraesCS7D01G536000 chr7D 100.000 4468 0 0 1 4468 627435382 627430915 0.000000e+00 8251
1 TraesCS7D01G536000 chr7D 89.266 177 6 5 1476 1641 636513724 636513898 4.530000e-50 209
2 TraesCS7D01G536000 chr7D 87.097 155 11 2 3125 3270 195416796 195416642 2.760000e-37 167
3 TraesCS7D01G536000 chr7D 97.647 85 1 1 1315 1399 350791320 350791403 1.300000e-30 145
4 TraesCS7D01G536000 chr7A 90.631 4024 165 82 1 3922 723308509 723304596 0.000000e+00 5147
5 TraesCS7D01G536000 chr7A 92.683 328 15 3 1594 1914 712320666 712320991 8.750000e-127 464
6 TraesCS7D01G536000 chr7A 92.378 328 15 5 1594 1914 724282258 724282582 4.070000e-125 459
7 TraesCS7D01G536000 chr7A 92.073 328 17 3 1594 1914 637066464 637066789 1.890000e-123 453
8 TraesCS7D01G536000 chr7A 93.564 202 9 2 2083 2281 724282585 724282785 9.400000e-77 298
9 TraesCS7D01G536000 chr7A 93.069 202 10 2 2083 2281 637066792 637066992 4.370000e-75 292
10 TraesCS7D01G536000 chr7A 83.183 333 24 12 4132 4449 723304444 723304129 4.400000e-70 276
11 TraesCS7D01G536000 chr7A 92.233 103 4 3 3940 4041 723304544 723304445 4.660000e-30 143
12 TraesCS7D01G536000 chr7B 89.371 2211 114 56 1805 3932 728836703 728834531 0.000000e+00 2669
13 TraesCS7D01G536000 chr7B 91.217 945 42 18 890 1802 728837787 728836852 0.000000e+00 1247
14 TraesCS7D01G536000 chr7B 90.352 881 45 20 1 863 728838643 728837785 0.000000e+00 1120
15 TraesCS7D01G536000 chr7B 85.100 349 20 17 3605 3932 701398299 701398636 1.200000e-85 327
16 TraesCS7D01G536000 chr7B 78.287 327 35 14 4172 4466 728834371 728834049 1.280000e-40 178
17 TraesCS7D01G536000 chr7B 88.742 151 8 2 3125 3266 164619558 164619708 4.590000e-40 176
18 TraesCS7D01G536000 chr7B 92.157 102 2 2 3940 4035 701398692 701398793 6.030000e-29 139
19 TraesCS7D01G536000 chr7B 92.157 102 2 2 3940 4035 728834481 728834380 6.030000e-29 139
20 TraesCS7D01G536000 chr7B 77.338 278 20 15 4169 4404 701398799 701399075 1.690000e-24 124
21 TraesCS7D01G536000 chr1A 87.231 603 36 20 1327 1914 199209352 199208776 0.000000e+00 649
22 TraesCS7D01G536000 chr1A 84.989 453 52 8 2133 2582 189659095 189658656 3.170000e-121 446
23 TraesCS7D01G536000 chr1A 81.562 461 63 12 2131 2582 243093717 243093270 1.180000e-95 361
24 TraesCS7D01G536000 chr1A 86.452 155 12 2 3125 3270 488677484 488677330 1.290000e-35 161
25 TraesCS7D01G536000 chr5D 87.196 453 40 9 2133 2582 430747992 430748429 2.400000e-137 499
26 TraesCS7D01G536000 chr5D 96.471 85 2 1 1315 1399 178105193 178105276 6.030000e-29 139
27 TraesCS7D01G536000 chr5A 92.378 328 16 3 1594 1914 178827548 178827223 4.070000e-125 459
28 TraesCS7D01G536000 chr5A 92.073 328 17 3 1594 1914 568932069 568932394 1.890000e-123 453
29 TraesCS7D01G536000 chr5A 93.662 284 15 2 1632 1914 568912671 568912952 5.340000e-114 422
30 TraesCS7D01G536000 chr5A 81.818 462 60 12 2131 2582 573739674 573740121 2.540000e-97 366
31 TraesCS7D01G536000 chr5A 93.467 199 9 2 2086 2281 178827217 178827020 4.370000e-75 292
32 TraesCS7D01G536000 chr5A 88.028 142 8 5 3138 3270 326341575 326341716 4.630000e-35 159
33 TraesCS7D01G536000 chr5A 85.806 155 13 2 3125 3270 622169317 622169471 5.980000e-34 156
34 TraesCS7D01G536000 chr5A 88.136 118 5 7 3162 3270 132181052 132181169 1.010000e-26 132
35 TraesCS7D01G536000 chrUn 91.317 334 20 4 1587 1913 151562116 151562447 8.820000e-122 448
36 TraesCS7D01G536000 chrUn 91.018 334 21 3 1587 1913 146624171 146624502 4.100000e-120 442
37 TraesCS7D01G536000 chrUn 93.970 199 8 2 2086 2281 170964678 170964481 9.400000e-77 298
38 TraesCS7D01G536000 chrUn 93.069 202 10 2 2083 2281 146624506 146624706 4.370000e-75 292
39 TraesCS7D01G536000 chrUn 93.069 202 10 2 2083 2281 151562451 151562651 4.370000e-75 292
40 TraesCS7D01G536000 chr3D 87.887 355 12 15 1315 1659 596006368 596006701 5.420000e-104 388
41 TraesCS7D01G536000 chr3D 96.471 85 2 1 1315 1399 19402704 19402787 6.030000e-29 139
42 TraesCS7D01G536000 chr3D 96.471 85 2 1 1315 1399 409591447 409591364 6.030000e-29 139
43 TraesCS7D01G536000 chr6A 82.251 462 58 14 2131 2582 119185835 119185388 1.170000e-100 377
44 TraesCS7D01G536000 chr6A 78.358 268 29 13 2991 3250 426298700 426298454 3.600000e-31 147
45 TraesCS7D01G536000 chr3B 80.440 455 56 11 2131 2582 167208554 167208978 2.590000e-82 316
46 TraesCS7D01G536000 chr5B 93.564 202 9 2 2083 2281 382084 382284 9.400000e-77 298
47 TraesCS7D01G536000 chr4B 83.429 350 29 15 3605 3932 626990216 626990558 9.400000e-77 298
48 TraesCS7D01G536000 chr4B 87.324 142 9 4 3138 3270 346916622 346916763 2.150000e-33 154
49 TraesCS7D01G536000 chr4B 91.176 102 3 2 3940 4035 626990609 626990710 2.800000e-27 134
50 TraesCS7D01G536000 chr4B 76.978 278 21 14 4169 4404 626990716 626990992 7.850000e-23 119
51 TraesCS7D01G536000 chr2D 82.773 238 32 3 3023 3251 648900421 648900658 2.110000e-48 204
52 TraesCS7D01G536000 chr2D 96.471 85 2 1 1315 1399 617454301 617454384 6.030000e-29 139
53 TraesCS7D01G536000 chr3A 87.097 155 11 3 3125 3270 142213279 142213433 2.760000e-37 167
54 TraesCS7D01G536000 chr2B 86.577 149 11 5 3127 3266 633595448 633595596 5.980000e-34 156
55 TraesCS7D01G536000 chr1D 95.294 85 3 1 1315 1399 26748027 26748110 2.800000e-27 134


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 TraesCS7D01G536000 chr7D 627430915 627435382 4467 True 8251.000000 8251 100.000000 1 4468 1 chr7D.!!$R2 4467
1 TraesCS7D01G536000 chr7A 723304129 723308509 4380 True 1855.333333 5147 88.682333 1 4449 3 chr7A.!!$R1 4448
2 TraesCS7D01G536000 chr7A 724282258 724282785 527 False 378.500000 459 92.971000 1594 2281 2 chr7A.!!$F3 687
3 TraesCS7D01G536000 chr7A 637066464 637066992 528 False 372.500000 453 92.571000 1594 2281 2 chr7A.!!$F2 687
4 TraesCS7D01G536000 chr7B 728834049 728838643 4594 True 1070.600000 2669 88.276800 1 4466 5 chr7B.!!$R1 4465
5 TraesCS7D01G536000 chr1A 199208776 199209352 576 True 649.000000 649 87.231000 1327 1914 1 chr1A.!!$R2 587
6 TraesCS7D01G536000 chr5A 178827020 178827548 528 True 375.500000 459 92.922500 1594 2281 2 chr5A.!!$R1 687
7 TraesCS7D01G536000 chrUn 151562116 151562651 535 False 370.000000 448 92.193000 1587 2281 2 chrUn.!!$F2 694
8 TraesCS7D01G536000 chrUn 146624171 146624706 535 False 367.000000 442 92.043500 1587 2281 2 chrUn.!!$F1 694

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
391 430 0.464036 TTCTTGGATCGACGGATGGG 59.536 55.0 0.00 0.0 31.51 4.00 F
1188 1265 0.179009 CAATCCACCGATCCATGGCT 60.179 55.0 6.96 0.0 35.81 4.75 F
2250 2544 0.397564 TGGAACCCCGGTCAAGTTAC 59.602 55.0 0.00 0.0 34.29 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2387 0.175760 CGGTGTCCTCCATGTCGATT 59.824 55.0 0.00 0.00 0.00 3.34 R
2846 3151 0.888619 TTCAAGCCTGTCGACGATCT 59.111 50.0 11.62 4.28 0.00 2.75 R
4109 4532 0.240945 GCCATGAAGTTGGTCGGTTG 59.759 55.0 0.00 0.00 39.11 3.77 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
88 89 2.594592 GCCAGCCCACACGTTTCT 60.595 61.111 0.00 0.00 0.00 2.52
193 195 2.605535 TTATCTCGCCCCTGCCTCCT 62.606 60.000 0.00 0.00 0.00 3.69
371 410 3.031660 CCGTCACGGTAGCTTCTTC 57.968 57.895 8.54 0.00 42.73 2.87
372 411 0.526662 CCGTCACGGTAGCTTCTTCT 59.473 55.000 8.54 0.00 42.73 2.85
373 412 1.067776 CCGTCACGGTAGCTTCTTCTT 60.068 52.381 8.54 0.00 42.73 2.52
374 413 2.251893 CGTCACGGTAGCTTCTTCTTC 58.748 52.381 0.00 0.00 0.00 2.87
375 414 2.095161 CGTCACGGTAGCTTCTTCTTCT 60.095 50.000 0.00 0.00 0.00 2.85
376 415 3.612004 CGTCACGGTAGCTTCTTCTTCTT 60.612 47.826 0.00 0.00 0.00 2.52
377 416 3.675698 GTCACGGTAGCTTCTTCTTCTTG 59.324 47.826 0.00 0.00 0.00 3.02
378 417 2.996621 CACGGTAGCTTCTTCTTCTTGG 59.003 50.000 0.00 0.00 0.00 3.61
379 418 2.897969 ACGGTAGCTTCTTCTTCTTGGA 59.102 45.455 0.00 0.00 0.00 3.53
380 419 3.515901 ACGGTAGCTTCTTCTTCTTGGAT 59.484 43.478 0.00 0.00 0.00 3.41
381 420 4.116238 CGGTAGCTTCTTCTTCTTGGATC 58.884 47.826 0.00 0.00 0.00 3.36
384 423 3.855858 AGCTTCTTCTTCTTGGATCGAC 58.144 45.455 0.00 0.00 0.00 4.20
391 430 0.464036 TTCTTGGATCGACGGATGGG 59.536 55.000 0.00 0.00 31.51 4.00
392 431 1.595382 CTTGGATCGACGGATGGGC 60.595 63.158 0.00 0.00 31.51 5.36
417 456 2.764637 CTTGAACGGGGTTGAGGGGG 62.765 65.000 0.00 0.00 0.00 5.40
422 461 4.295199 GGGGTTGAGGGGGCGTTT 62.295 66.667 0.00 0.00 0.00 3.60
423 462 2.675423 GGGTTGAGGGGGCGTTTC 60.675 66.667 0.00 0.00 0.00 2.78
424 463 2.434774 GGTTGAGGGGGCGTTTCT 59.565 61.111 0.00 0.00 0.00 2.52
425 464 1.228459 GGTTGAGGGGGCGTTTCTT 60.228 57.895 0.00 0.00 0.00 2.52
426 465 1.524008 GGTTGAGGGGGCGTTTCTTG 61.524 60.000 0.00 0.00 0.00 3.02
498 543 4.228097 CGGATTTGGCGCTGCGAG 62.228 66.667 28.07 0.00 0.00 5.03
499 544 4.543084 GGATTTGGCGCTGCGAGC 62.543 66.667 28.07 8.79 38.02 5.03
500 545 3.503363 GATTTGGCGCTGCGAGCT 61.503 61.111 28.07 4.41 39.60 4.09
501 546 3.446175 GATTTGGCGCTGCGAGCTC 62.446 63.158 28.07 2.73 39.60 4.09
502 547 3.965539 ATTTGGCGCTGCGAGCTCT 62.966 57.895 28.07 3.48 39.60 4.09
625 670 2.749839 TTGCGGCGGATCTTTGGG 60.750 61.111 9.78 0.00 0.00 4.12
626 671 4.794648 TGCGGCGGATCTTTGGGG 62.795 66.667 9.78 0.00 0.00 4.96
722 767 4.182132 CAGAGTTCCAGCTGCTCG 57.818 61.111 8.66 0.00 34.69 5.03
773 819 1.213182 GGTTTCTTCCTGGATCTCCCC 59.787 57.143 0.00 0.00 34.29 4.81
774 820 1.134371 GTTTCTTCCTGGATCTCCCCG 60.134 57.143 0.00 0.00 34.29 5.73
780 826 4.458829 TGGATCTCCCCGGCGAGT 62.459 66.667 15.64 3.67 34.29 4.18
781 827 3.607661 GGATCTCCCCGGCGAGTC 61.608 72.222 15.64 11.85 0.00 3.36
823 895 1.153706 GGGTTTCGGATTCGCGAGA 60.154 57.895 9.59 0.00 39.20 4.04
827 899 2.095372 GGTTTCGGATTCGCGAGATTTT 59.905 45.455 9.59 0.00 41.60 1.82
863 935 2.800250 CCAAATCCAGAGTTCTTGGCT 58.200 47.619 0.00 0.00 30.84 4.75
923 995 3.230976 ACCAAAAGATCCCGCTTTTTCT 58.769 40.909 0.00 0.00 43.50 2.52
924 996 3.641436 ACCAAAAGATCCCGCTTTTTCTT 59.359 39.130 0.00 0.00 43.50 2.52
925 997 4.237724 CCAAAAGATCCCGCTTTTTCTTC 58.762 43.478 0.00 0.00 43.50 2.87
961 1036 5.505654 GCGTTTCCTCTGTTTCTGAATTTGA 60.506 40.000 0.00 0.00 0.00 2.69
962 1037 6.672147 CGTTTCCTCTGTTTCTGAATTTGAT 58.328 36.000 0.00 0.00 0.00 2.57
967 1042 9.533253 TTCCTCTGTTTCTGAATTTGATTTTTC 57.467 29.630 0.00 0.00 0.00 2.29
969 1044 8.146412 CCTCTGTTTCTGAATTTGATTTTTCCT 58.854 33.333 0.00 0.00 0.00 3.36
971 1046 8.143835 TCTGTTTCTGAATTTGATTTTTCCTCC 58.856 33.333 0.00 0.00 0.00 4.30
1029 1106 1.320344 TGAGATCCGAGAACCACCGG 61.320 60.000 0.00 0.00 46.57 5.28
1156 1233 4.785453 CCGTCAGCAAGAGGGGCC 62.785 72.222 0.00 0.00 46.26 5.80
1188 1265 0.179009 CAATCCACCGATCCATGGCT 60.179 55.000 6.96 0.00 35.81 4.75
1200 1277 2.091541 TCCATGGCTGAATTTCGAACC 58.908 47.619 6.96 0.00 0.00 3.62
1400 1489 6.511605 GCAACTAAAAATCCTTGCTGTTTTGG 60.512 38.462 0.00 0.00 36.81 3.28
1428 1517 0.754587 TGGGTGTGCATTGCTGTTCA 60.755 50.000 10.49 1.76 0.00 3.18
1449 1538 7.942341 TGTTCATACCTCTGTACTTTCCAATTT 59.058 33.333 0.00 0.00 0.00 1.82
1451 1540 6.374333 TCATACCTCTGTACTTTCCAATTTGC 59.626 38.462 0.00 0.00 0.00 3.68
1466 1557 4.142924 CCAATTTGCGCAAATTTTAGGACC 60.143 41.667 43.13 0.00 45.67 4.46
1471 1562 3.242518 GCGCAAATTTTAGGACCTGTTC 58.757 45.455 0.30 0.00 0.00 3.18
1535 1627 7.882179 TCTGCGTTTGCTATCAGTTAGATATA 58.118 34.615 0.00 0.00 43.34 0.86
1536 1628 8.523658 TCTGCGTTTGCTATCAGTTAGATATAT 58.476 33.333 0.00 0.00 43.34 0.86
1590 1689 7.606456 GGTTTGAATTACTACACCTGAATCTGA 59.394 37.037 0.00 0.00 0.00 3.27
1603 1705 5.105877 ACCTGAATCTGAAGATTTGCACATG 60.106 40.000 6.98 0.00 44.14 3.21
1651 1759 6.207417 GCATGCCAAATCTTGTACTATATGGT 59.793 38.462 6.36 0.00 0.00 3.55
1698 1810 4.195416 AGTTCTAGCAGATTTAGGCAAGC 58.805 43.478 0.00 0.00 0.00 4.01
1700 1812 3.535561 TCTAGCAGATTTAGGCAAGCAC 58.464 45.455 0.00 0.00 0.00 4.40
1775 1887 7.502226 TGATATCAATGTAGGTTCAATTGGGTC 59.498 37.037 1.98 0.00 0.00 4.46
1780 1892 3.585289 TGTAGGTTCAATTGGGTCAGCTA 59.415 43.478 5.42 4.48 0.00 3.32
1847 1999 5.300286 CCTTGTTTGAACCAAGAATCTGAGT 59.700 40.000 3.90 0.00 0.00 3.41
1924 2181 0.894141 GCAGTGAGAGGCAGAAGAGA 59.106 55.000 0.00 0.00 0.00 3.10
1939 2196 1.818642 AGAGAAATGCTGACACTGCC 58.181 50.000 0.00 0.00 0.00 4.85
1943 2200 1.200948 GAAATGCTGACACTGCCTTCC 59.799 52.381 0.00 0.00 0.00 3.46
2014 2271 4.371855 TGAGATGGTAAGCAGAGTAACG 57.628 45.455 0.00 0.00 0.00 3.18
2093 2384 3.009363 TCCAGATGACCAATGAGCTCAAA 59.991 43.478 22.50 0.00 0.00 2.69
2096 2387 4.698780 CAGATGACCAATGAGCTCAAAGAA 59.301 41.667 22.50 5.08 0.00 2.52
2221 2515 4.246712 TCTACAGAAGGACCGAGGTAAT 57.753 45.455 0.00 0.00 0.00 1.89
2250 2544 0.397564 TGGAACCCCGGTCAAGTTAC 59.602 55.000 0.00 0.00 34.29 2.50
2287 2584 1.208052 CTGACCTGACCTGGTATGGTG 59.792 57.143 22.71 9.73 41.00 4.17
2288 2585 1.203250 TGACCTGACCTGGTATGGTGA 60.203 52.381 22.71 14.65 41.00 4.02
2444 2741 0.824109 TTCGATGCTCGGTGGATTCT 59.176 50.000 5.87 0.00 40.88 2.40
2504 2804 6.650427 AAGTTCTTAGAAACCCCAATGTTC 57.350 37.500 0.00 0.00 0.00 3.18
2520 2822 1.955778 TGTTCTTGTCCAATGCAGGTG 59.044 47.619 0.00 0.00 0.00 4.00
2547 2849 1.983224 GCTGGAGCTACTGGGTGAA 59.017 57.895 4.83 0.00 38.21 3.18
2601 2903 2.620234 CCTGGCCAGGGAGAATGTA 58.380 57.895 40.24 0.00 44.87 2.29
2846 3151 3.181329 TGGTAATTCTGCAGGAGAGGAA 58.819 45.455 15.13 0.00 30.18 3.36
2850 3155 4.420522 AATTCTGCAGGAGAGGAAGATC 57.579 45.455 15.13 0.00 30.18 2.75
2853 3158 1.066908 CTGCAGGAGAGGAAGATCGTC 59.933 57.143 5.57 0.00 0.00 4.20
2886 3191 4.908601 ATTCAACATGTCAGTCCCTACA 57.091 40.909 0.00 0.00 0.00 2.74
2889 3194 0.895530 ACATGTCAGTCCCTACACCG 59.104 55.000 0.00 0.00 0.00 4.94
2945 3250 4.223923 AGGGTCTGACAAGAAGGTAAGATG 59.776 45.833 10.38 0.00 31.01 2.90
2947 3252 5.104735 GGGTCTGACAAGAAGGTAAGATGAT 60.105 44.000 10.38 0.00 31.01 2.45
2950 3255 6.699642 GTCTGACAAGAAGGTAAGATGATAGC 59.300 42.308 2.24 0.00 31.01 2.97
2951 3256 6.609212 TCTGACAAGAAGGTAAGATGATAGCT 59.391 38.462 0.00 0.00 35.23 3.32
2952 3257 6.810911 TGACAAGAAGGTAAGATGATAGCTC 58.189 40.000 0.00 0.00 32.69 4.09
2954 3259 5.361285 ACAAGAAGGTAAGATGATAGCTCGT 59.639 40.000 0.00 0.00 32.69 4.18
2955 3260 6.546403 ACAAGAAGGTAAGATGATAGCTCGTA 59.454 38.462 0.00 0.00 32.69 3.43
2956 3261 7.068348 ACAAGAAGGTAAGATGATAGCTCGTAA 59.932 37.037 0.00 0.00 32.69 3.18
2958 3263 5.708877 AGGTAAGATGATAGCTCGTAACC 57.291 43.478 0.00 0.00 0.00 2.85
2959 3264 5.386924 AGGTAAGATGATAGCTCGTAACCT 58.613 41.667 0.00 0.00 0.00 3.50
2960 3265 5.834204 AGGTAAGATGATAGCTCGTAACCTT 59.166 40.000 0.00 0.00 29.88 3.50
2961 3266 5.921408 GGTAAGATGATAGCTCGTAACCTTG 59.079 44.000 0.00 0.00 0.00 3.61
2964 3269 3.438297 TGATAGCTCGTAACCTTGCTC 57.562 47.619 0.00 0.00 37.02 4.26
2965 3270 2.100916 TGATAGCTCGTAACCTTGCTCC 59.899 50.000 0.00 0.00 37.02 4.70
2966 3271 1.848652 TAGCTCGTAACCTTGCTCCT 58.151 50.000 0.00 0.00 37.02 3.69
2967 3272 0.247736 AGCTCGTAACCTTGCTCCTG 59.752 55.000 0.00 0.00 0.00 3.86
2968 3273 1.362406 GCTCGTAACCTTGCTCCTGC 61.362 60.000 0.00 0.00 40.20 4.85
2982 3287 4.645535 TGCTCCTGCAGAATTACCATATC 58.354 43.478 17.39 0.00 45.31 1.63
2983 3288 4.006319 GCTCCTGCAGAATTACCATATCC 58.994 47.826 17.39 0.00 39.41 2.59
2984 3289 4.263243 GCTCCTGCAGAATTACCATATCCT 60.263 45.833 17.39 0.00 39.41 3.24
2985 3290 5.046304 GCTCCTGCAGAATTACCATATCCTA 60.046 44.000 17.39 0.00 39.41 2.94
2986 3291 6.360370 TCCTGCAGAATTACCATATCCTAC 57.640 41.667 17.39 0.00 0.00 3.18
3074 3389 1.323412 TCCTAATCGAGCTCAGCCTC 58.677 55.000 15.40 0.00 0.00 4.70
3220 3535 4.186926 TCTGAAGAACAGCTCATGTATGC 58.813 43.478 0.00 0.00 43.00 3.14
3229 3544 2.489329 AGCTCATGTATGCAAACACACC 59.511 45.455 0.00 0.00 30.75 4.16
3252 3573 4.023707 CACTGTCTTTCATTCAGACCAACC 60.024 45.833 0.00 0.00 40.12 3.77
3254 3575 4.531854 TGTCTTTCATTCAGACCAACCAA 58.468 39.130 0.00 0.00 40.12 3.67
3269 3590 3.885297 CCAACCAACTTTCAGTGAGTGAT 59.115 43.478 0.00 0.00 34.17 3.06
3270 3591 4.261322 CCAACCAACTTTCAGTGAGTGATG 60.261 45.833 0.00 0.00 34.17 3.07
3271 3592 4.156455 ACCAACTTTCAGTGAGTGATGT 57.844 40.909 0.00 0.00 34.17 3.06
3272 3593 3.879295 ACCAACTTTCAGTGAGTGATGTG 59.121 43.478 0.00 0.00 34.17 3.21
3273 3594 4.129380 CCAACTTTCAGTGAGTGATGTGA 58.871 43.478 0.00 0.00 34.17 3.58
3274 3595 4.758674 CCAACTTTCAGTGAGTGATGTGAT 59.241 41.667 0.00 0.00 34.17 3.06
3312 3636 1.529244 GGCTGTTTGGCTCACTGGT 60.529 57.895 0.00 0.00 38.32 4.00
3529 3865 2.417933 ACTGCTAAAAAGATGCGAGCTG 59.582 45.455 0.00 0.00 37.88 4.24
3598 3940 7.230747 TGATGAGATTTACACCAAGGAAGAAA 58.769 34.615 0.00 0.00 0.00 2.52
3625 3967 2.961669 AACGTTCGATGTTGGCCGC 61.962 57.895 0.00 0.00 0.00 6.53
3668 4015 8.838365 ACTACTCTCTCGGTATAACTTAACATG 58.162 37.037 0.00 0.00 0.00 3.21
3675 4022 5.535783 TCGGTATAACTTAACATGGATCCGA 59.464 40.000 7.39 0.00 39.62 4.55
3754 4116 9.906660 TGGAATGTGTTGTGTATTTAATTCTTC 57.093 29.630 0.00 0.00 0.00 2.87
3790 4152 3.826524 TGATGACACCTACCTGCAAAAA 58.173 40.909 0.00 0.00 0.00 1.94
3875 4249 7.437713 TGATTATTGATCTTGTCCTGGTAGT 57.562 36.000 0.00 0.00 35.69 2.73
3877 4251 8.642432 TGATTATTGATCTTGTCCTGGTAGTAG 58.358 37.037 0.00 0.00 35.69 2.57
3878 4252 4.737855 TTGATCTTGTCCTGGTAGTAGC 57.262 45.455 0.00 0.00 0.00 3.58
3879 4253 3.708451 TGATCTTGTCCTGGTAGTAGCA 58.292 45.455 1.44 1.44 0.00 3.49
3886 4260 4.832248 TGTCCTGGTAGTAGCAAAATCTG 58.168 43.478 3.25 0.00 0.00 2.90
3891 4265 8.202137 GTCCTGGTAGTAGCAAAATCTGTAATA 58.798 37.037 3.25 0.00 0.00 0.98
3892 4266 8.202137 TCCTGGTAGTAGCAAAATCTGTAATAC 58.798 37.037 3.25 0.00 0.00 1.89
3922 4296 4.692155 GCCCCAGAATTTGAAATTTGACTG 59.308 41.667 4.46 7.56 0.00 3.51
3923 4297 5.511202 GCCCCAGAATTTGAAATTTGACTGA 60.511 40.000 15.36 0.00 0.00 3.41
3924 4298 5.928264 CCCCAGAATTTGAAATTTGACTGAC 59.072 40.000 15.36 0.00 0.00 3.51
3926 4300 7.212274 CCCAGAATTTGAAATTTGACTGACTT 58.788 34.615 15.36 0.00 0.00 3.01
3927 4301 7.170320 CCCAGAATTTGAAATTTGACTGACTTG 59.830 37.037 15.36 3.60 0.00 3.16
3928 4302 7.922278 CCAGAATTTGAAATTTGACTGACTTGA 59.078 33.333 15.36 0.00 0.00 3.02
3976 4395 4.816048 AATAAAAGGGGAGGGAAGATCC 57.184 45.455 0.00 0.00 35.99 3.36
4042 4465 7.756395 AACTTGTACTAGTAAGCAGTACTGA 57.244 36.000 27.08 2.48 45.64 3.41
4043 4466 7.143514 ACTTGTACTAGTAAGCAGTACTGAC 57.856 40.000 27.08 15.38 45.64 3.51
4044 4467 6.713903 ACTTGTACTAGTAAGCAGTACTGACA 59.286 38.462 27.08 14.64 45.64 3.58
4045 4468 7.230108 ACTTGTACTAGTAAGCAGTACTGACAA 59.770 37.037 27.08 20.23 45.64 3.18
4046 4469 7.142306 TGTACTAGTAAGCAGTACTGACAAG 57.858 40.000 27.08 14.81 45.64 3.16
4047 4470 5.646577 ACTAGTAAGCAGTACTGACAAGG 57.353 43.478 27.08 11.17 43.24 3.61
4048 4471 5.078256 ACTAGTAAGCAGTACTGACAAGGT 58.922 41.667 27.08 11.76 43.24 3.50
4049 4472 6.243900 ACTAGTAAGCAGTACTGACAAGGTA 58.756 40.000 27.08 8.72 43.24 3.08
4050 4473 5.388408 AGTAAGCAGTACTGACAAGGTAC 57.612 43.478 27.08 15.71 41.75 3.34
4060 4483 7.732996 AGTACTGACAAGGTACTGTAATTTGT 58.267 34.615 14.38 14.38 45.29 2.83
4061 4484 6.861065 ACTGACAAGGTACTGTAATTTGTG 57.139 37.500 17.61 10.16 40.86 3.33
4062 4485 6.588204 ACTGACAAGGTACTGTAATTTGTGA 58.412 36.000 17.61 11.44 40.86 3.58
4063 4486 7.051623 ACTGACAAGGTACTGTAATTTGTGAA 58.948 34.615 17.61 8.86 40.86 3.18
4064 4487 7.012044 ACTGACAAGGTACTGTAATTTGTGAAC 59.988 37.037 17.61 8.41 40.86 3.18
4065 4488 7.051623 TGACAAGGTACTGTAATTTGTGAACT 58.948 34.615 17.61 0.14 40.86 3.01
4066 4489 7.554835 TGACAAGGTACTGTAATTTGTGAACTT 59.445 33.333 17.61 0.00 40.86 2.66
4067 4490 8.967664 ACAAGGTACTGTAATTTGTGAACTTA 57.032 30.769 13.95 0.00 40.86 2.24
4068 4491 9.569122 ACAAGGTACTGTAATTTGTGAACTTAT 57.431 29.630 13.95 0.00 40.86 1.73
4070 4493 9.787435 AAGGTACTGTAATTTGTGAACTTATCA 57.213 29.630 0.00 0.00 40.86 2.15
4071 4494 9.787435 AGGTACTGTAATTTGTGAACTTATCAA 57.213 29.630 0.00 0.00 37.18 2.57
4073 4496 9.543018 GTACTGTAATTTGTGAACTTATCAAGC 57.457 33.333 0.00 0.00 40.50 4.01
4074 4497 7.593825 ACTGTAATTTGTGAACTTATCAAGCC 58.406 34.615 0.00 0.00 40.50 4.35
4075 4498 7.448469 ACTGTAATTTGTGAACTTATCAAGCCT 59.552 33.333 0.00 0.00 40.50 4.58
4076 4499 7.592938 TGTAATTTGTGAACTTATCAAGCCTG 58.407 34.615 0.00 0.00 40.50 4.85
4077 4500 6.655078 AATTTGTGAACTTATCAAGCCTGT 57.345 33.333 0.00 0.00 40.50 4.00
4078 4501 5.437289 TTTGTGAACTTATCAAGCCTGTG 57.563 39.130 0.00 0.00 40.50 3.66
4079 4502 3.411446 TGTGAACTTATCAAGCCTGTGG 58.589 45.455 0.00 0.00 40.50 4.17
4080 4503 3.072330 TGTGAACTTATCAAGCCTGTGGA 59.928 43.478 0.00 0.00 40.50 4.02
4081 4504 4.263462 TGTGAACTTATCAAGCCTGTGGAT 60.263 41.667 0.00 0.00 40.50 3.41
4082 4505 5.045942 TGTGAACTTATCAAGCCTGTGGATA 60.046 40.000 0.00 0.00 40.50 2.59
4083 4506 6.058183 GTGAACTTATCAAGCCTGTGGATAT 58.942 40.000 0.00 0.00 40.50 1.63
4084 4507 6.017605 GTGAACTTATCAAGCCTGTGGATATG 60.018 42.308 0.00 0.00 40.50 1.78
4085 4508 5.894298 ACTTATCAAGCCTGTGGATATGA 57.106 39.130 0.00 0.00 0.00 2.15
4086 4509 6.252599 ACTTATCAAGCCTGTGGATATGAA 57.747 37.500 0.00 0.00 0.00 2.57
4087 4510 6.845908 ACTTATCAAGCCTGTGGATATGAAT 58.154 36.000 0.00 0.00 0.00 2.57
4088 4511 6.939163 ACTTATCAAGCCTGTGGATATGAATC 59.061 38.462 0.00 0.00 0.00 2.52
4089 4512 5.579753 ATCAAGCCTGTGGATATGAATCT 57.420 39.130 0.00 0.00 32.29 2.40
4090 4513 4.965814 TCAAGCCTGTGGATATGAATCTC 58.034 43.478 0.00 0.00 32.29 2.75
4091 4514 4.657504 TCAAGCCTGTGGATATGAATCTCT 59.342 41.667 0.00 0.00 32.29 3.10
4092 4515 5.131642 TCAAGCCTGTGGATATGAATCTCTT 59.868 40.000 0.00 0.00 32.29 2.85
4093 4516 4.970711 AGCCTGTGGATATGAATCTCTTG 58.029 43.478 0.00 0.00 32.29 3.02
4094 4517 3.501445 GCCTGTGGATATGAATCTCTTGC 59.499 47.826 0.00 0.00 32.29 4.01
4095 4518 4.711399 CCTGTGGATATGAATCTCTTGCA 58.289 43.478 0.00 0.00 32.29 4.08
4096 4519 5.128205 CCTGTGGATATGAATCTCTTGCAA 58.872 41.667 0.00 0.00 32.29 4.08
4097 4520 5.238868 CCTGTGGATATGAATCTCTTGCAAG 59.761 44.000 20.81 20.81 32.29 4.01
4098 4521 5.993055 TGTGGATATGAATCTCTTGCAAGA 58.007 37.500 26.87 26.87 32.29 3.02
4099 4522 6.598503 TGTGGATATGAATCTCTTGCAAGAT 58.401 36.000 28.57 15.06 37.61 2.40
4100 4523 6.709397 TGTGGATATGAATCTCTTGCAAGATC 59.291 38.462 28.57 22.54 34.90 2.75
4101 4524 6.935771 GTGGATATGAATCTCTTGCAAGATCT 59.064 38.462 28.57 16.14 34.90 2.75
4102 4525 6.935208 TGGATATGAATCTCTTGCAAGATCTG 59.065 38.462 28.57 17.51 34.90 2.90
4103 4526 6.372103 GGATATGAATCTCTTGCAAGATCTGG 59.628 42.308 28.57 17.15 34.90 3.86
4104 4527 4.831674 TGAATCTCTTGCAAGATCTGGA 57.168 40.909 28.57 21.59 34.90 3.86
4105 4528 5.169992 TGAATCTCTTGCAAGATCTGGAA 57.830 39.130 28.57 11.04 34.90 3.53
4106 4529 5.752650 TGAATCTCTTGCAAGATCTGGAAT 58.247 37.500 28.57 15.50 34.90 3.01
4107 4530 5.589050 TGAATCTCTTGCAAGATCTGGAATG 59.411 40.000 28.57 14.68 34.90 2.67
4108 4531 4.564782 TCTCTTGCAAGATCTGGAATGT 57.435 40.909 28.57 0.00 34.49 2.71
4109 4532 4.511527 TCTCTTGCAAGATCTGGAATGTC 58.488 43.478 28.57 0.00 34.49 3.06
4110 4533 4.019950 TCTCTTGCAAGATCTGGAATGTCA 60.020 41.667 28.57 2.59 34.49 3.58
4111 4534 4.654915 TCTTGCAAGATCTGGAATGTCAA 58.345 39.130 25.16 0.00 34.49 3.18
4112 4535 4.456911 TCTTGCAAGATCTGGAATGTCAAC 59.543 41.667 25.16 0.00 34.49 3.18
4113 4536 3.084039 TGCAAGATCTGGAATGTCAACC 58.916 45.455 0.00 0.00 0.00 3.77
4114 4537 2.096496 GCAAGATCTGGAATGTCAACCG 59.904 50.000 0.00 0.00 0.00 4.44
4115 4538 3.599343 CAAGATCTGGAATGTCAACCGA 58.401 45.455 0.00 0.00 0.00 4.69
4116 4539 3.252974 AGATCTGGAATGTCAACCGAC 57.747 47.619 0.00 0.00 42.93 4.79
4117 4540 2.093447 AGATCTGGAATGTCAACCGACC 60.093 50.000 0.00 0.00 41.85 4.79
4118 4541 1.052617 TCTGGAATGTCAACCGACCA 58.947 50.000 0.00 0.00 41.85 4.02
4119 4542 1.418264 TCTGGAATGTCAACCGACCAA 59.582 47.619 0.00 0.00 41.85 3.67
4120 4543 1.535462 CTGGAATGTCAACCGACCAAC 59.465 52.381 0.00 0.00 41.85 3.77
4121 4544 1.142060 TGGAATGTCAACCGACCAACT 59.858 47.619 0.00 0.00 41.85 3.16
4122 4545 2.227194 GGAATGTCAACCGACCAACTT 58.773 47.619 0.00 0.00 41.85 2.66
4123 4546 2.225727 GGAATGTCAACCGACCAACTTC 59.774 50.000 0.00 0.00 41.85 3.01
4124 4547 2.631160 ATGTCAACCGACCAACTTCA 57.369 45.000 0.00 0.00 41.85 3.02
4125 4548 2.631160 TGTCAACCGACCAACTTCAT 57.369 45.000 0.00 0.00 41.85 2.57
4126 4549 2.217750 TGTCAACCGACCAACTTCATG 58.782 47.619 0.00 0.00 41.85 3.07
4127 4550 1.535462 GTCAACCGACCAACTTCATGG 59.465 52.381 0.00 0.00 46.38 3.66
4128 4551 0.240945 CAACCGACCAACTTCATGGC 59.759 55.000 0.00 0.00 44.75 4.40
4129 4552 0.893727 AACCGACCAACTTCATGGCC 60.894 55.000 0.00 0.00 44.75 5.36
4130 4553 2.046285 CCGACCAACTTCATGGCCC 61.046 63.158 0.00 0.00 44.75 5.80
4159 4582 4.387598 TGCCAAATTTGAATTCCCTGTTG 58.612 39.130 19.86 2.94 0.00 3.33
4165 4588 5.750352 ATTTGAATTCCCTGTTGAGCATT 57.250 34.783 2.27 0.00 0.00 3.56
4179 4602 5.236911 TGTTGAGCATTTTTGAATTTCCTGC 59.763 36.000 0.00 0.00 0.00 4.85
4187 4610 7.520292 GCATTTTTGAATTTCCTGCTAGCAAAA 60.520 33.333 19.86 17.16 33.52 2.44
4221 4655 3.007831 TGGTCCCAGAATTCAAATTTGGC 59.992 43.478 17.90 5.87 31.26 4.52
4222 4656 3.599343 GTCCCAGAATTCAAATTTGGCC 58.401 45.455 17.90 0.00 31.26 5.36
4223 4657 3.261643 GTCCCAGAATTCAAATTTGGCCT 59.738 43.478 17.90 7.37 31.26 5.19
4224 4658 3.261390 TCCCAGAATTCAAATTTGGCCTG 59.739 43.478 17.90 16.77 31.26 4.85
4225 4659 3.008266 CCCAGAATTCAAATTTGGCCTGT 59.992 43.478 17.90 0.00 31.26 4.00
4226 4660 4.505390 CCCAGAATTCAAATTTGGCCTGTT 60.505 41.667 17.90 6.30 31.26 3.16
4227 4661 4.692155 CCAGAATTCAAATTTGGCCTGTTC 59.308 41.667 17.90 13.54 0.00 3.18
4228 4662 5.511888 CCAGAATTCAAATTTGGCCTGTTCT 60.512 40.000 17.90 15.17 0.00 3.01
4229 4663 5.993441 CAGAATTCAAATTTGGCCTGTTCTT 59.007 36.000 17.90 1.35 0.00 2.52
4230 4664 5.993441 AGAATTCAAATTTGGCCTGTTCTTG 59.007 36.000 17.90 1.48 0.00 3.02
4231 4665 3.749665 TCAAATTTGGCCTGTTCTTGG 57.250 42.857 17.90 0.00 0.00 3.61
4232 4666 3.303938 TCAAATTTGGCCTGTTCTTGGA 58.696 40.909 17.90 0.00 0.00 3.53
4258 4692 4.524714 TGAATTCAAATTTAGCGTGGGGAA 59.475 37.500 5.45 0.00 0.00 3.97
4260 4694 9.821062 TTGAATTCAAATTTAGCGTGGGGAACC 62.821 40.741 18.45 0.00 41.61 3.62
4275 4709 3.793819 GGAACCCACTACCCAGTAAAA 57.206 47.619 0.00 0.00 32.21 1.52
4276 4710 3.682696 GGAACCCACTACCCAGTAAAAG 58.317 50.000 0.00 0.00 32.21 2.27
4277 4711 3.560668 GGAACCCACTACCCAGTAAAAGG 60.561 52.174 0.00 0.00 32.21 3.11
4278 4712 2.709966 ACCCACTACCCAGTAAAAGGT 58.290 47.619 0.00 0.00 40.31 3.50
4279 4713 2.374170 ACCCACTACCCAGTAAAAGGTG 59.626 50.000 0.00 0.00 36.88 4.00
4280 4714 2.290705 CCCACTACCCAGTAAAAGGTGG 60.291 54.545 0.00 0.00 41.40 4.61
4281 4715 2.433436 CACTACCCAGTAAAAGGTGGC 58.567 52.381 0.00 0.00 38.13 5.01
4287 4749 2.618045 CCCAGTAAAAGGTGGCACTAGG 60.618 54.545 18.45 7.71 31.85 3.02
4383 4870 5.974108 AGGCATTGTAATTCGTGTAGTACT 58.026 37.500 0.00 0.00 0.00 2.73
4384 4871 7.104043 AGGCATTGTAATTCGTGTAGTACTA 57.896 36.000 0.00 0.00 0.00 1.82
4385 4872 6.976925 AGGCATTGTAATTCGTGTAGTACTAC 59.023 38.462 23.58 23.58 36.63 2.73
4450 4937 5.046663 GGAATGCCAAGGAAAATTAACAGGA 60.047 40.000 0.00 0.00 0.00 3.86
4466 4953 1.066573 CAGGATTCGCTTCACTCCACT 60.067 52.381 0.00 0.00 0.00 4.00
4467 4954 2.166459 CAGGATTCGCTTCACTCCACTA 59.834 50.000 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 156 1.649271 AAATAGGGGCCTGCCTGAGG 61.649 60.000 10.64 0.00 46.13 3.86
193 195 1.073008 ATGGGGATTGGGATCGGGA 60.073 57.895 0.00 0.00 32.84 5.14
363 402 3.674682 CGTCGATCCAAGAAGAAGAAGCT 60.675 47.826 0.00 0.00 0.00 3.74
365 404 3.119459 TCCGTCGATCCAAGAAGAAGAAG 60.119 47.826 0.00 0.00 0.00 2.85
371 410 1.539065 CCCATCCGTCGATCCAAGAAG 60.539 57.143 0.00 0.00 0.00 2.85
372 411 0.464036 CCCATCCGTCGATCCAAGAA 59.536 55.000 0.00 0.00 0.00 2.52
373 412 2.028125 GCCCATCCGTCGATCCAAGA 62.028 60.000 0.00 0.00 0.00 3.02
374 413 1.595382 GCCCATCCGTCGATCCAAG 60.595 63.158 0.00 0.00 0.00 3.61
375 414 2.504032 GCCCATCCGTCGATCCAA 59.496 61.111 0.00 0.00 0.00 3.53
376 415 3.911698 CGCCCATCCGTCGATCCA 61.912 66.667 0.00 0.00 0.00 3.41
384 423 3.864686 CAAGAACGCGCCCATCCG 61.865 66.667 5.73 0.00 0.00 4.18
417 456 4.495828 GTCAAGAACAAGAACAAGAAACGC 59.504 41.667 0.00 0.00 0.00 4.84
421 460 3.625764 CCCGTCAAGAACAAGAACAAGAA 59.374 43.478 0.00 0.00 0.00 2.52
422 461 3.118555 TCCCGTCAAGAACAAGAACAAGA 60.119 43.478 0.00 0.00 0.00 3.02
423 462 3.202906 TCCCGTCAAGAACAAGAACAAG 58.797 45.455 0.00 0.00 0.00 3.16
424 463 3.269538 TCCCGTCAAGAACAAGAACAA 57.730 42.857 0.00 0.00 0.00 2.83
425 464 2.992124 TCCCGTCAAGAACAAGAACA 57.008 45.000 0.00 0.00 0.00 3.18
426 465 2.484264 CCATCCCGTCAAGAACAAGAAC 59.516 50.000 0.00 0.00 0.00 3.01
592 637 0.318699 GCAAGAACGCCAAAGAACCC 60.319 55.000 0.00 0.00 0.00 4.11
625 670 1.602605 CAAGAACAACCGGGACCCC 60.603 63.158 6.32 0.00 0.00 4.95
626 671 2.265904 GCAAGAACAACCGGGACCC 61.266 63.158 6.32 0.00 0.00 4.46
705 750 0.037882 TTCGAGCAGCTGGAACTCTG 60.038 55.000 15.36 9.86 34.02 3.35
773 819 4.208686 GCCCTACTGGACTCGCCG 62.209 72.222 0.00 0.00 40.66 6.46
774 820 4.208686 CGCCCTACTGGACTCGCC 62.209 72.222 0.00 0.00 35.39 5.54
777 823 0.896226 AAGAACGCCCTACTGGACTC 59.104 55.000 0.00 0.00 35.39 3.36
780 826 1.192146 AGCAAGAACGCCCTACTGGA 61.192 55.000 0.00 0.00 35.39 3.86
781 827 0.741221 GAGCAAGAACGCCCTACTGG 60.741 60.000 0.00 0.00 37.09 4.00
823 895 2.233676 GGCCAAGAAACCGATGGAAAAT 59.766 45.455 0.00 0.00 36.27 1.82
827 899 0.111446 TTGGCCAAGAAACCGATGGA 59.889 50.000 16.05 0.00 36.27 3.41
923 995 0.605319 AAACGCATCCGCAGAAGGAA 60.605 50.000 0.00 0.00 44.50 3.36
924 996 1.003839 AAACGCATCCGCAGAAGGA 60.004 52.632 0.00 0.00 45.54 3.36
925 997 1.425428 GAAACGCATCCGCAGAAGG 59.575 57.895 0.00 0.00 38.40 3.46
971 1046 0.111253 AAGAGGAAACCCTGCACCAG 59.889 55.000 0.00 0.00 33.25 4.00
1156 1233 1.467734 GTGGATTGCTCACTCTTGCAG 59.532 52.381 0.00 0.00 40.46 4.41
1314 1403 2.485122 GCGGCGAATTTCCTGGTG 59.515 61.111 12.98 0.00 0.00 4.17
1381 1470 6.048509 CAGTACCAAAACAGCAAGGATTTTT 58.951 36.000 0.00 0.00 0.00 1.94
1400 1489 2.185004 ATGCACACCCAAGACAGTAC 57.815 50.000 0.00 0.00 0.00 2.73
1428 1517 5.354234 CGCAAATTGGAAAGTACAGAGGTAT 59.646 40.000 0.00 0.00 0.00 2.73
1449 1538 2.235016 ACAGGTCCTAAAATTTGCGCA 58.765 42.857 5.66 5.66 0.00 6.09
1451 1540 3.488489 CGAACAGGTCCTAAAATTTGCG 58.512 45.455 0.00 0.00 0.00 4.85
1466 1557 4.201851 CCAGCATCTAAATTCACCGAACAG 60.202 45.833 0.00 0.00 0.00 3.16
1471 1562 2.917933 TCCCAGCATCTAAATTCACCG 58.082 47.619 0.00 0.00 0.00 4.94
1546 1638 1.611006 ACCATACGCAATTTGTGTGCA 59.389 42.857 22.52 6.90 41.73 4.57
1670 1779 9.494271 TTGCCTAAATCTGCTAGAACTATATTG 57.506 33.333 0.00 0.00 0.00 1.90
1775 1887 6.709397 TGCAGAAGATGGAAAATCTATAGCTG 59.291 38.462 0.00 0.00 0.00 4.24
1847 1999 9.268268 CTTGAGTTGACACAGTTACCTATTTTA 57.732 33.333 0.00 0.00 0.00 1.52
1860 2012 6.713762 AATTCAAATCCTTGAGTTGACACA 57.286 33.333 6.48 0.00 44.35 3.72
1861 2013 9.696917 AATAAATTCAAATCCTTGAGTTGACAC 57.303 29.630 6.48 0.00 44.35 3.67
1924 2181 1.251251 GGAAGGCAGTGTCAGCATTT 58.749 50.000 0.00 0.00 35.98 2.32
1939 2196 2.775911 TGTCTGAAGGAGCATGGAAG 57.224 50.000 0.00 0.00 0.00 3.46
1943 2200 2.562635 CTCCATGTCTGAAGGAGCATG 58.437 52.381 8.54 4.29 42.13 4.06
2037 2328 3.608707 GCATGGATGATGAGCGATGAAAC 60.609 47.826 0.00 0.00 33.31 2.78
2093 2384 2.093447 GGTGTCCTCCATGTCGATTTCT 60.093 50.000 0.00 0.00 0.00 2.52
2096 2387 0.175760 CGGTGTCCTCCATGTCGATT 59.824 55.000 0.00 0.00 0.00 3.34
2221 2515 1.340600 CCGGGGTTCCAAGCAGATAAA 60.341 52.381 0.00 0.00 0.00 1.40
2250 2544 1.344438 TCAGGCACACAACTCTGTAGG 59.656 52.381 0.00 0.00 33.22 3.18
2395 2692 2.191128 ACCTCAATCAGCCAGTCAAC 57.809 50.000 0.00 0.00 0.00 3.18
2444 2741 8.696374 AGCATACTAAGATAAGACTACTTTGCA 58.304 33.333 0.00 0.00 37.53 4.08
2532 2834 3.553109 GGTTTCACCCAGTAGCTCC 57.447 57.895 0.00 0.00 30.04 4.70
2544 2846 1.843851 ACAGTGAGGAACAGGGTTTCA 59.156 47.619 0.00 0.00 0.00 2.69
2547 2849 3.201266 TGTTTACAGTGAGGAACAGGGTT 59.799 43.478 0.00 0.00 0.00 4.11
2598 2900 0.905357 GGAGCTTCTTCCTGGCTACA 59.095 55.000 0.00 0.00 36.95 2.74
2601 2903 1.989620 CTGGAGCTTCTTCCTGGCT 59.010 57.895 0.00 0.00 38.12 4.75
2752 3054 4.112716 TCGACGAAAGGTGTATGCATAA 57.887 40.909 8.28 0.00 0.00 1.90
2756 3058 2.034842 CGAATCGACGAAAGGTGTATGC 60.035 50.000 0.00 0.00 35.09 3.14
2758 3060 3.770263 TCGAATCGACGAAAGGTGTAT 57.230 42.857 0.00 0.00 39.34 2.29
2846 3151 0.888619 TTCAAGCCTGTCGACGATCT 59.111 50.000 11.62 4.28 0.00 2.75
2850 3155 1.428448 TGAATTCAAGCCTGTCGACG 58.572 50.000 11.62 5.76 0.00 5.12
2853 3158 3.058016 ACATGTTGAATTCAAGCCTGTCG 60.058 43.478 21.05 8.26 36.39 4.35
2886 3191 2.093973 CCTTCTCATGAAGCAGTACGGT 60.094 50.000 0.00 0.00 46.13 4.83
2889 3194 3.935828 GGAACCTTCTCATGAAGCAGTAC 59.064 47.826 0.00 0.00 46.13 2.73
2945 3250 2.362717 AGGAGCAAGGTTACGAGCTATC 59.637 50.000 0.00 0.00 37.48 2.08
2947 3252 1.476891 CAGGAGCAAGGTTACGAGCTA 59.523 52.381 0.00 0.00 37.48 3.32
2950 3255 2.755929 GCAGGAGCAAGGTTACGAG 58.244 57.895 0.00 0.00 41.58 4.18
2961 3266 4.006319 GGATATGGTAATTCTGCAGGAGC 58.994 47.826 15.13 7.41 42.57 4.70
2964 3269 6.365970 AGTAGGATATGGTAATTCTGCAGG 57.634 41.667 15.13 0.00 0.00 4.85
2965 3270 8.753133 TCATAGTAGGATATGGTAATTCTGCAG 58.247 37.037 7.63 7.63 34.51 4.41
2966 3271 8.664669 TCATAGTAGGATATGGTAATTCTGCA 57.335 34.615 0.00 0.00 34.51 4.41
2967 3272 8.754080 ACTCATAGTAGGATATGGTAATTCTGC 58.246 37.037 0.00 0.00 34.51 4.26
2969 3274 8.754080 GCACTCATAGTAGGATATGGTAATTCT 58.246 37.037 0.00 0.00 34.51 2.40
2970 3275 8.531982 TGCACTCATAGTAGGATATGGTAATTC 58.468 37.037 0.00 0.00 34.51 2.17
2971 3276 8.435931 TGCACTCATAGTAGGATATGGTAATT 57.564 34.615 0.00 0.00 34.51 1.40
2972 3277 8.615360 ATGCACTCATAGTAGGATATGGTAAT 57.385 34.615 0.00 0.00 34.51 1.89
2973 3278 8.314021 CAATGCACTCATAGTAGGATATGGTAA 58.686 37.037 0.00 0.00 34.51 2.85
2974 3279 7.579531 GCAATGCACTCATAGTAGGATATGGTA 60.580 40.741 0.00 0.00 34.51 3.25
2975 3280 6.705302 CAATGCACTCATAGTAGGATATGGT 58.295 40.000 0.00 0.00 34.51 3.55
2977 3282 6.404708 AGCAATGCACTCATAGTAGGATATG 58.595 40.000 8.35 0.00 34.96 1.78
2978 3283 6.617782 AGCAATGCACTCATAGTAGGATAT 57.382 37.500 8.35 0.00 31.46 1.63
2980 3285 4.970860 AGCAATGCACTCATAGTAGGAT 57.029 40.909 8.35 0.00 31.46 3.24
2982 3287 4.194640 ACAAGCAATGCACTCATAGTAGG 58.805 43.478 8.35 0.00 31.46 3.18
2983 3288 5.006455 CAGACAAGCAATGCACTCATAGTAG 59.994 44.000 8.35 0.00 31.46 2.57
2984 3289 4.872124 CAGACAAGCAATGCACTCATAGTA 59.128 41.667 8.35 0.00 31.46 1.82
2985 3290 3.688185 CAGACAAGCAATGCACTCATAGT 59.312 43.478 8.35 0.00 31.46 2.12
2986 3291 3.937079 TCAGACAAGCAATGCACTCATAG 59.063 43.478 8.35 0.00 31.46 2.23
3074 3389 2.544480 TGAGCATCTTGTAGTCGACG 57.456 50.000 10.46 0.00 34.92 5.12
3229 3544 4.023707 GGTTGGTCTGAATGAAAGACAGTG 60.024 45.833 5.97 0.00 44.86 3.66
3269 3590 5.411361 GTGTGAGTAACAAAGGCATATCACA 59.589 40.000 0.00 0.00 41.57 3.58
3270 3591 5.445939 CGTGTGAGTAACAAAGGCATATCAC 60.446 44.000 0.00 0.00 41.57 3.06
3271 3592 4.629634 CGTGTGAGTAACAAAGGCATATCA 59.370 41.667 0.00 0.00 41.57 2.15
3272 3593 4.034048 CCGTGTGAGTAACAAAGGCATATC 59.966 45.833 0.00 0.00 41.57 1.63
3273 3594 3.938963 CCGTGTGAGTAACAAAGGCATAT 59.061 43.478 0.00 0.00 41.57 1.78
3274 3595 3.331150 CCGTGTGAGTAACAAAGGCATA 58.669 45.455 0.00 0.00 41.57 3.14
3529 3865 2.027653 CCACCACCTCTTCCTCTTCTTC 60.028 54.545 0.00 0.00 0.00 2.87
3598 3940 0.246635 CATCGAACGTTGGTCTCCCT 59.753 55.000 5.00 0.00 0.00 4.20
3645 3992 6.832384 TCCATGTTAAGTTATACCGAGAGAGT 59.168 38.462 0.00 0.00 0.00 3.24
3668 4015 1.033574 ACTCAACTCGGATCGGATCC 58.966 55.000 24.29 24.29 46.22 3.36
3675 4022 3.809832 CACAAACTCAACTCAACTCGGAT 59.190 43.478 0.00 0.00 0.00 4.18
3754 4116 3.093574 GTCATCATCGCACAACAAATCG 58.906 45.455 0.00 0.00 0.00 3.34
3875 4249 7.447238 GGCCCAATAGTATTACAGATTTTGCTA 59.553 37.037 0.00 0.00 0.00 3.49
3877 4251 6.447162 GGCCCAATAGTATTACAGATTTTGC 58.553 40.000 0.00 1.58 0.00 3.68
3878 4252 6.015434 GGGGCCCAATAGTATTACAGATTTTG 60.015 42.308 26.86 0.00 0.00 2.44
3879 4253 6.075315 GGGGCCCAATAGTATTACAGATTTT 58.925 40.000 26.86 0.00 0.00 1.82
3886 4260 4.717279 TTCTGGGGCCCAATAGTATTAC 57.283 45.455 28.43 1.60 30.80 1.89
3891 4265 2.314549 TCAAATTCTGGGGCCCAATAGT 59.685 45.455 28.43 13.78 30.80 2.12
3892 4266 3.030873 TCAAATTCTGGGGCCCAATAG 57.969 47.619 28.43 18.48 30.80 1.73
3894 4268 2.340721 TTCAAATTCTGGGGCCCAAT 57.659 45.000 28.43 15.93 30.80 3.16
3958 4375 0.919710 CGGATCTTCCCTCCCCTTTT 59.080 55.000 0.00 0.00 31.13 2.27
3976 4395 3.588955 TCACACATCCATCTTCACTTCG 58.411 45.455 0.00 0.00 0.00 3.79
4042 4465 7.875327 AAGTTCACAAATTACAGTACCTTGT 57.125 32.000 0.00 1.94 35.09 3.16
4044 4467 9.787435 TGATAAGTTCACAAATTACAGTACCTT 57.213 29.630 0.00 0.00 0.00 3.50
4045 4468 9.787435 TTGATAAGTTCACAAATTACAGTACCT 57.213 29.630 0.00 0.00 32.84 3.08
4047 4470 9.543018 GCTTGATAAGTTCACAAATTACAGTAC 57.457 33.333 0.00 0.00 32.84 2.73
4048 4471 8.726988 GGCTTGATAAGTTCACAAATTACAGTA 58.273 33.333 0.00 0.00 32.84 2.74
4049 4472 7.448469 AGGCTTGATAAGTTCACAAATTACAGT 59.552 33.333 0.00 0.00 32.84 3.55
4050 4473 7.752239 CAGGCTTGATAAGTTCACAAATTACAG 59.248 37.037 0.00 0.00 32.84 2.74
4051 4474 7.230510 ACAGGCTTGATAAGTTCACAAATTACA 59.769 33.333 1.40 0.00 32.84 2.41
4052 4475 7.538678 CACAGGCTTGATAAGTTCACAAATTAC 59.461 37.037 1.40 0.00 32.84 1.89
4053 4476 7.309133 CCACAGGCTTGATAAGTTCACAAATTA 60.309 37.037 1.40 0.00 32.84 1.40
4054 4477 6.449698 CACAGGCTTGATAAGTTCACAAATT 58.550 36.000 1.40 0.00 32.84 1.82
4055 4478 5.047802 CCACAGGCTTGATAAGTTCACAAAT 60.048 40.000 1.40 0.00 32.84 2.32
4056 4479 4.278170 CCACAGGCTTGATAAGTTCACAAA 59.722 41.667 1.40 0.00 32.84 2.83
4057 4480 3.820467 CCACAGGCTTGATAAGTTCACAA 59.180 43.478 1.40 0.00 32.84 3.33
4058 4481 3.072330 TCCACAGGCTTGATAAGTTCACA 59.928 43.478 1.40 0.00 32.84 3.58
4059 4482 3.674997 TCCACAGGCTTGATAAGTTCAC 58.325 45.455 1.40 0.00 32.84 3.18
4060 4483 4.574674 ATCCACAGGCTTGATAAGTTCA 57.425 40.909 1.40 0.00 0.00 3.18
4061 4484 6.291377 TCATATCCACAGGCTTGATAAGTTC 58.709 40.000 1.40 0.00 0.00 3.01
4062 4485 6.252599 TCATATCCACAGGCTTGATAAGTT 57.747 37.500 1.40 0.00 0.00 2.66
4063 4486 5.894298 TCATATCCACAGGCTTGATAAGT 57.106 39.130 1.40 0.00 0.00 2.24
4064 4487 7.166851 AGATTCATATCCACAGGCTTGATAAG 58.833 38.462 1.40 0.32 0.00 1.73
4065 4488 7.016957 AGAGATTCATATCCACAGGCTTGATAA 59.983 37.037 1.40 0.00 0.00 1.75
4066 4489 6.499699 AGAGATTCATATCCACAGGCTTGATA 59.500 38.462 1.40 0.00 0.00 2.15
4067 4490 5.310068 AGAGATTCATATCCACAGGCTTGAT 59.690 40.000 1.40 0.00 0.00 2.57
4068 4491 4.657504 AGAGATTCATATCCACAGGCTTGA 59.342 41.667 1.40 0.00 0.00 3.02
4069 4492 4.970711 AGAGATTCATATCCACAGGCTTG 58.029 43.478 0.00 0.00 0.00 4.01
4070 4493 5.374921 CAAGAGATTCATATCCACAGGCTT 58.625 41.667 0.00 0.00 0.00 4.35
4071 4494 4.746089 GCAAGAGATTCATATCCACAGGCT 60.746 45.833 0.00 0.00 0.00 4.58
4072 4495 3.501445 GCAAGAGATTCATATCCACAGGC 59.499 47.826 0.00 0.00 0.00 4.85
4073 4496 4.711399 TGCAAGAGATTCATATCCACAGG 58.289 43.478 0.00 0.00 0.00 4.00
4074 4497 6.053650 TCTTGCAAGAGATTCATATCCACAG 58.946 40.000 25.16 0.00 0.00 3.66
4075 4498 5.993055 TCTTGCAAGAGATTCATATCCACA 58.007 37.500 25.16 0.00 0.00 4.17
4076 4499 6.935771 AGATCTTGCAAGAGATTCATATCCAC 59.064 38.462 31.14 10.65 38.66 4.02
4077 4500 6.935208 CAGATCTTGCAAGAGATTCATATCCA 59.065 38.462 31.14 6.69 38.66 3.41
4078 4501 6.372103 CCAGATCTTGCAAGAGATTCATATCC 59.628 42.308 31.14 11.50 38.66 2.59
4079 4502 7.160049 TCCAGATCTTGCAAGAGATTCATATC 58.840 38.462 31.14 21.19 38.66 1.63
4080 4503 7.075851 TCCAGATCTTGCAAGAGATTCATAT 57.924 36.000 31.14 14.30 38.66 1.78
4081 4504 6.490241 TCCAGATCTTGCAAGAGATTCATA 57.510 37.500 31.14 12.65 38.66 2.15
4082 4505 5.369409 TCCAGATCTTGCAAGAGATTCAT 57.631 39.130 31.14 15.76 38.66 2.57
4083 4506 4.831674 TCCAGATCTTGCAAGAGATTCA 57.168 40.909 31.14 14.30 38.66 2.57
4084 4507 5.589452 ACATTCCAGATCTTGCAAGAGATTC 59.411 40.000 31.14 23.79 38.66 2.52
4085 4508 5.507637 ACATTCCAGATCTTGCAAGAGATT 58.492 37.500 31.14 17.23 38.66 2.40
4086 4509 5.113446 ACATTCCAGATCTTGCAAGAGAT 57.887 39.130 31.14 20.32 38.66 2.75
4087 4510 4.019950 TGACATTCCAGATCTTGCAAGAGA 60.020 41.667 31.14 20.87 38.66 3.10
4088 4511 4.259356 TGACATTCCAGATCTTGCAAGAG 58.741 43.478 31.14 19.03 38.66 2.85
4089 4512 4.290711 TGACATTCCAGATCTTGCAAGA 57.709 40.909 30.23 30.23 39.78 3.02
4090 4513 4.380233 GGTTGACATTCCAGATCTTGCAAG 60.380 45.833 20.81 20.81 0.00 4.01
4091 4514 3.507233 GGTTGACATTCCAGATCTTGCAA 59.493 43.478 0.00 0.00 0.00 4.08
4092 4515 3.084039 GGTTGACATTCCAGATCTTGCA 58.916 45.455 0.00 0.00 0.00 4.08
4093 4516 2.096496 CGGTTGACATTCCAGATCTTGC 59.904 50.000 0.00 0.00 0.00 4.01
4094 4517 3.372206 GTCGGTTGACATTCCAGATCTTG 59.628 47.826 0.00 0.00 44.82 3.02
4095 4518 3.600388 GTCGGTTGACATTCCAGATCTT 58.400 45.455 0.00 0.00 44.82 2.40
4096 4519 3.252974 GTCGGTTGACATTCCAGATCT 57.747 47.619 0.00 0.00 44.82 2.75
4107 4530 1.535462 CCATGAAGTTGGTCGGTTGAC 59.465 52.381 0.00 0.00 44.72 3.18
4108 4531 1.890876 CCATGAAGTTGGTCGGTTGA 58.109 50.000 0.00 0.00 31.74 3.18
4109 4532 0.240945 GCCATGAAGTTGGTCGGTTG 59.759 55.000 0.00 0.00 39.11 3.77
4110 4533 0.893727 GGCCATGAAGTTGGTCGGTT 60.894 55.000 0.00 0.00 39.11 4.44
4111 4534 1.303317 GGCCATGAAGTTGGTCGGT 60.303 57.895 0.00 0.00 39.11 4.69
4112 4535 2.046285 GGGCCATGAAGTTGGTCGG 61.046 63.158 4.39 0.00 42.55 4.79
4113 4536 0.680921 ATGGGCCATGAAGTTGGTCG 60.681 55.000 20.49 0.00 42.55 4.79
4114 4537 1.560505 AATGGGCCATGAAGTTGGTC 58.439 50.000 22.01 0.00 40.82 4.02
4115 4538 1.624813 CAAATGGGCCATGAAGTTGGT 59.375 47.619 22.01 0.00 39.11 3.67
4116 4539 1.901159 TCAAATGGGCCATGAAGTTGG 59.099 47.619 22.01 1.76 39.94 3.77
4117 4540 3.527533 CATCAAATGGGCCATGAAGTTG 58.472 45.455 22.01 19.86 0.00 3.16
4118 4541 2.093341 GCATCAAATGGGCCATGAAGTT 60.093 45.455 22.01 7.66 0.00 2.66
4119 4542 1.483415 GCATCAAATGGGCCATGAAGT 59.517 47.619 22.01 0.00 0.00 3.01
4120 4543 1.202604 GGCATCAAATGGGCCATGAAG 60.203 52.381 22.01 13.72 46.92 3.02
4121 4544 0.831966 GGCATCAAATGGGCCATGAA 59.168 50.000 22.01 9.05 46.92 2.57
4122 4545 2.518772 GGCATCAAATGGGCCATGA 58.481 52.632 22.01 16.50 46.92 3.07
4150 4573 5.549742 ATTCAAAAATGCTCAACAGGGAA 57.450 34.783 0.00 0.00 0.00 3.97
4159 4582 5.290400 GCTAGCAGGAAATTCAAAAATGCTC 59.710 40.000 10.63 0.00 41.33 4.26
4165 4588 7.385752 CAGATTTTGCTAGCAGGAAATTCAAAA 59.614 33.333 22.22 15.37 37.94 2.44
4187 4610 4.524802 TCTGGGACCATTATTTGCAGAT 57.475 40.909 0.00 0.00 0.00 2.90
4258 4692 2.374170 CACCTTTTACTGGGTAGTGGGT 59.626 50.000 0.00 0.00 37.78 4.51
4260 4694 2.878526 GCCACCTTTTACTGGGTAGTGG 60.879 54.545 0.00 0.00 44.85 4.00
4261 4695 2.224670 TGCCACCTTTTACTGGGTAGTG 60.225 50.000 0.00 0.00 37.78 2.74
4262 4696 2.059490 TGCCACCTTTTACTGGGTAGT 58.941 47.619 0.00 0.00 40.99 2.73
4263 4697 2.039879 AGTGCCACCTTTTACTGGGTAG 59.960 50.000 0.00 0.00 34.07 3.18
4264 4698 2.059490 AGTGCCACCTTTTACTGGGTA 58.941 47.619 0.00 0.00 34.07 3.69
4265 4699 0.850784 AGTGCCACCTTTTACTGGGT 59.149 50.000 0.00 0.00 36.07 4.51
4267 4701 2.304761 TCCTAGTGCCACCTTTTACTGG 59.695 50.000 0.00 0.00 0.00 4.00
4268 4702 3.335579 GTCCTAGTGCCACCTTTTACTG 58.664 50.000 0.00 0.00 0.00 2.74
4270 4704 2.039348 TGGTCCTAGTGCCACCTTTTAC 59.961 50.000 0.00 0.00 0.00 2.01
4272 4706 1.145571 TGGTCCTAGTGCCACCTTTT 58.854 50.000 0.00 0.00 0.00 2.27
4273 4707 1.073923 CTTGGTCCTAGTGCCACCTTT 59.926 52.381 2.39 0.00 34.02 3.11
4274 4708 0.693049 CTTGGTCCTAGTGCCACCTT 59.307 55.000 2.39 0.00 34.02 3.50
4275 4709 0.473886 ACTTGGTCCTAGTGCCACCT 60.474 55.000 5.07 0.00 34.02 4.00
4276 4710 1.207329 CTACTTGGTCCTAGTGCCACC 59.793 57.143 15.37 0.00 34.02 4.61
4277 4711 1.207329 CCTACTTGGTCCTAGTGCCAC 59.793 57.143 15.37 0.00 34.02 5.01
4278 4712 1.078159 TCCTACTTGGTCCTAGTGCCA 59.922 52.381 15.37 0.00 37.07 4.92
4279 4713 1.757699 CTCCTACTTGGTCCTAGTGCC 59.242 57.143 15.37 0.00 37.07 5.01
4280 4714 1.757699 CCTCCTACTTGGTCCTAGTGC 59.242 57.143 15.37 0.00 37.07 4.40
4281 4715 3.383698 TCCTCCTACTTGGTCCTAGTG 57.616 52.381 15.37 6.18 37.07 2.74
4287 4749 2.436173 CCCAGATTCCTCCTACTTGGTC 59.564 54.545 0.00 0.00 37.07 4.02
4383 4870 7.418337 TTCATATCTACAGGCTTGACAAGTA 57.582 36.000 16.39 1.44 0.00 2.24
4384 4871 5.939764 TCATATCTACAGGCTTGACAAGT 57.060 39.130 16.39 0.25 0.00 3.16
4385 4872 7.215789 AGATTCATATCTACAGGCTTGACAAG 58.784 38.462 11.02 11.02 39.36 3.16
4413 4900 2.429250 TGGCATTCCAGATCTTGCAATG 59.571 45.455 16.78 13.87 37.47 2.82


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

AutoCloner maintained by Alex Coulton.