Multiple sequence alignment - TraesCS4D01G069200

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 TraesCS4D01G069200 chr4D 100.000 4453 0 0 1 4453 44741220 44745672 0.000000e+00 8224.0
1 TraesCS4D01G069200 chr4D 78.092 283 42 12 92 369 19147910 19148177 1.280000e-35 161.0
2 TraesCS4D01G069200 chr4A 89.385 3740 218 67 441 4091 554929934 554926285 0.000000e+00 4542.0
3 TraesCS4D01G069200 chr4B 93.314 2423 97 25 1368 3771 64694103 64696479 0.000000e+00 3517.0
4 TraesCS4D01G069200 chr4B 89.114 643 28 9 743 1357 64693432 64694060 0.000000e+00 761.0
5 TraesCS4D01G069200 chr4B 82.726 631 57 24 3832 4453 64696495 64697082 8.540000e-142 514.0
6 TraesCS4D01G069200 chr4B 82.812 192 19 10 556 747 64692292 64692469 4.610000e-35 159.0
7 TraesCS4D01G069200 chr5D 79.262 569 92 17 1 550 395771270 395770709 1.510000e-99 374.0
8 TraesCS4D01G069200 chr2A 80.752 452 65 14 1 436 52273972 52273527 2.570000e-87 333.0
9 TraesCS4D01G069200 chr6D 82.507 383 44 16 3551 3922 173902628 173902998 9.300000e-82 315.0
10 TraesCS4D01G069200 chr2B 82.206 399 39 14 9 391 505936143 505935761 9.300000e-82 315.0
11 TraesCS4D01G069200 chr6A 75.718 383 57 28 130 490 53886065 53886433 4.610000e-35 159.0
12 TraesCS4D01G069200 chr7A 80.556 180 22 10 142 319 536158965 536158797 4.680000e-25 126.0
13 TraesCS4D01G069200 chr3B 88.158 76 9 0 137 212 252329231 252329306 1.710000e-14 91.6
14 TraesCS4D01G069200 chr7D 100.000 31 0 0 157 187 179949485 179949515 1.730000e-04 58.4


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 TraesCS4D01G069200 chr4D 44741220 44745672 4452 False 8224.00 8224 100.0000 1 4453 1 chr4D.!!$F2 4452
1 TraesCS4D01G069200 chr4A 554926285 554929934 3649 True 4542.00 4542 89.3850 441 4091 1 chr4A.!!$R1 3650
2 TraesCS4D01G069200 chr4B 64692292 64697082 4790 False 1237.75 3517 86.9915 556 4453 4 chr4B.!!$F1 3897
3 TraesCS4D01G069200 chr5D 395770709 395771270 561 True 374.00 374 79.2620 1 550 1 chr5D.!!$R1 549

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
55 56 0.460284 CGGGACTTGGACGGAGATTG 60.460 60.0 0.00 0.00 0.00 2.67 F
1273 2310 0.039798 GCGCTGATCCGTAATCCGTA 60.040 55.0 0.00 0.00 33.01 4.02 F
1924 2993 0.166814 GTGAAGGCGCTGTTCATGAC 59.833 55.0 22.71 10.97 36.35 3.06 F
2173 3257 0.179129 GCCAATGCCGAAACAGATGG 60.179 55.0 0.00 0.00 34.93 3.51 F
2318 3402 0.179156 CATTGCAGCCCGACATTCAC 60.179 55.0 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 2455 0.317160 AGCCGTCGAATTCAGTCACA 59.683 50.0 6.22 0.0 0.0 3.58 R
2129 3213 0.102481 TCGCCGAACAGCCTAAGATC 59.898 55.0 0.00 0.0 0.0 2.75 R
3163 4261 0.874390 TTTGCCTTTAGTCAGCGCAG 59.126 50.0 11.47 0.0 0.0 5.18 R
3373 4471 0.976641 TCGAGAGGGTGCTGTGAAAT 59.023 50.0 0.00 0.0 0.0 2.17 R
4257 5377 0.106419 TTTCCCATTGATACCCGGCC 60.106 55.0 0.00 0.0 0.0 6.13 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
17 18 2.919043 GCCGATGGGATGGAACCT 59.081 61.111 0.00 0.00 34.06 3.50
18 19 1.526917 GCCGATGGGATGGAACCTG 60.527 63.158 0.00 0.00 34.06 4.00
21 22 1.152673 GATGGGATGGAACCTGGCC 60.153 63.158 0.00 0.00 0.00 5.36
37 38 2.672996 CCTTGGTTGGGCAGTCCG 60.673 66.667 0.00 0.00 38.76 4.79
42 43 3.637273 GTTGGGCAGTCCGGGACT 61.637 66.667 23.90 23.90 44.44 3.85
53 54 3.617368 CGGGACTTGGACGGAGAT 58.383 61.111 0.00 0.00 0.00 2.75
54 55 1.898154 CGGGACTTGGACGGAGATT 59.102 57.895 0.00 0.00 0.00 2.40
55 56 0.460284 CGGGACTTGGACGGAGATTG 60.460 60.000 0.00 0.00 0.00 2.67
58 59 1.002087 GGACTTGGACGGAGATTGTGT 59.998 52.381 0.00 0.00 0.00 3.72
60 61 1.336887 ACTTGGACGGAGATTGTGTCG 60.337 52.381 0.00 0.00 33.45 4.35
72 73 3.406361 GTGTCGTGCACGCCTGAG 61.406 66.667 33.63 7.65 38.45 3.35
113 122 1.450211 CCACGGGAAGAGGTTGTGT 59.550 57.895 0.00 0.00 0.00 3.72
117 126 0.974383 CGGGAAGAGGTTGTGTAGGT 59.026 55.000 0.00 0.00 0.00 3.08
118 127 1.337823 CGGGAAGAGGTTGTGTAGGTG 60.338 57.143 0.00 0.00 0.00 4.00
120 129 1.610886 GGAAGAGGTTGTGTAGGTGCC 60.611 57.143 0.00 0.00 0.00 5.01
189 198 2.055042 ACCTCTAGCAGCCACCTCG 61.055 63.158 0.00 0.00 0.00 4.63
236 245 1.451747 GAGGACGAGTAGGACGGCT 60.452 63.158 0.00 0.00 38.92 5.52
241 250 1.355916 CGAGTAGGACGGCTGCTAC 59.644 63.158 0.00 0.00 40.73 3.58
258 267 2.745884 CGGAAGTCAATGGCGGCA 60.746 61.111 16.34 16.34 0.00 5.69
259 268 2.114670 CGGAAGTCAATGGCGGCAT 61.115 57.895 20.18 20.18 0.00 4.40
260 269 1.729881 GGAAGTCAATGGCGGCATC 59.270 57.895 25.97 12.95 0.00 3.91
261 270 1.353103 GAAGTCAATGGCGGCATCG 59.647 57.895 25.97 15.16 39.81 3.84
262 271 1.078497 AAGTCAATGGCGGCATCGA 60.078 52.632 25.97 17.65 39.00 3.59
338 347 4.481368 TTAATGTGGTGAACTCGGCTAT 57.519 40.909 0.00 0.00 0.00 2.97
354 375 4.093703 TCGGCTATTGTGGACGTTTTAATG 59.906 41.667 0.00 0.00 0.00 1.90
418 439 7.504924 AATTTGAAGTCTGAATAAACGGACA 57.495 32.000 0.00 0.00 45.39 4.02
433 454 1.586154 GGACAGTTTGGGATGTGGCG 61.586 60.000 0.00 0.00 0.00 5.69
436 457 2.282887 GTTTGGGATGTGGCGGGT 60.283 61.111 0.00 0.00 0.00 5.28
438 459 2.835049 TTTGGGATGTGGCGGGTCA 61.835 57.895 0.00 0.00 0.00 4.02
439 460 3.561120 TTGGGATGTGGCGGGTCAC 62.561 63.158 0.00 0.00 38.09 3.67
444 465 3.567579 ATGTGGCGGGTCACTTGGG 62.568 63.158 4.92 0.00 38.40 4.12
494 515 2.566824 GGACATGTCCGTTTGCCAT 58.433 52.632 28.52 0.00 40.36 4.40
500 521 2.799126 TGTCCGTTTGCCATCCTTAT 57.201 45.000 0.00 0.00 0.00 1.73
525 546 2.465855 ACAAAATCCAAACGAAACGGC 58.534 42.857 0.00 0.00 0.00 5.68
526 547 2.100087 ACAAAATCCAAACGAAACGGCT 59.900 40.909 0.00 0.00 0.00 5.52
538 562 2.660552 ACGGCTCGTTTGTGGTCG 60.661 61.111 0.00 0.00 36.35 4.79
575 599 4.038402 CCCTTACGAGTTAATCCCGTGTAT 59.962 45.833 0.00 0.00 37.69 2.29
627 661 5.303589 TCATAGTCGGTTTGGGTAATCTAGG 59.696 44.000 0.00 0.00 0.00 3.02
637 671 8.657712 GGTTTGGGTAATCTAGGTTCATACTAT 58.342 37.037 0.00 0.00 0.00 2.12
693 730 2.509111 TGCGTGCACATCTAGCCG 60.509 61.111 18.64 0.61 0.00 5.52
725 762 1.895231 ACGGCCGGGTTTCACTTTC 60.895 57.895 31.76 0.00 0.00 2.62
726 763 1.894756 CGGCCGGGTTTCACTTTCA 60.895 57.895 20.10 0.00 0.00 2.69
727 764 1.658114 GGCCGGGTTTCACTTTCAC 59.342 57.895 2.18 0.00 0.00 3.18
777 1781 6.038603 GCATCTCTTTATTTACTGCCACATCA 59.961 38.462 0.00 0.00 0.00 3.07
842 1846 1.536907 TCCAACGGCTAGTTCCCCA 60.537 57.895 0.00 0.00 42.02 4.96
896 1900 3.730761 CAACTCGCCACAGCCAGC 61.731 66.667 0.00 0.00 34.57 4.85
1163 2191 1.660560 TTCTGCCTCCGCGTAGGTAC 61.661 60.000 19.70 3.94 41.99 3.34
1266 2303 3.592814 CCTCGGCGCTGATCCGTA 61.593 66.667 21.31 0.00 46.49 4.02
1268 2305 1.007271 CTCGGCGCTGATCCGTAAT 60.007 57.895 21.31 0.00 46.49 1.89
1270 2307 2.022129 CGGCGCTGATCCGTAATCC 61.022 63.158 11.90 0.00 41.85 3.01
1271 2308 2.022129 GGCGCTGATCCGTAATCCG 61.022 63.158 7.64 0.00 33.01 4.18
1272 2309 1.299926 GCGCTGATCCGTAATCCGT 60.300 57.895 0.00 0.00 33.01 4.69
1273 2310 0.039798 GCGCTGATCCGTAATCCGTA 60.040 55.000 0.00 0.00 33.01 4.02
1274 2311 1.682982 CGCTGATCCGTAATCCGTAC 58.317 55.000 0.00 0.00 33.01 3.67
1275 2312 1.665161 CGCTGATCCGTAATCCGTACC 60.665 57.143 0.00 0.00 33.01 3.34
1280 2317 1.305201 TCCGTAATCCGTACCCGTAC 58.695 55.000 0.00 0.00 33.66 3.67
1306 2343 1.986757 AGGCTGCGACCAGAGTCAT 60.987 57.895 0.00 0.00 43.73 3.06
1357 2394 1.014352 GCTTCGTCATGCGGGTAATT 58.986 50.000 9.16 0.00 41.72 1.40
1360 2397 1.647346 TCGTCATGCGGGTAATTCAC 58.353 50.000 9.16 0.00 41.72 3.18
1361 2398 1.206132 TCGTCATGCGGGTAATTCACT 59.794 47.619 9.16 0.00 41.72 3.41
1362 2399 1.327460 CGTCATGCGGGTAATTCACTG 59.673 52.381 2.16 0.00 36.85 3.66
1363 2400 1.064060 GTCATGCGGGTAATTCACTGC 59.936 52.381 6.24 6.24 0.00 4.40
1365 2402 2.169561 TCATGCGGGTAATTCACTGCTA 59.830 45.455 12.61 2.67 32.09 3.49
1366 2403 2.772077 TGCGGGTAATTCACTGCTAA 57.228 45.000 12.61 0.00 32.09 3.09
1386 2455 6.149308 TGCTAATTCTCGTGTTTGATTGATGT 59.851 34.615 0.00 0.00 0.00 3.06
1517 2586 1.875813 GAGGTGCGCGTCTCTGATG 60.876 63.158 18.63 0.00 0.00 3.07
1525 2594 2.603110 GCGCGTCTCTGATGTGAATTTA 59.397 45.455 8.43 0.00 31.49 1.40
1540 2609 5.028375 GTGAATTTATTTCCTTTCTCGCCG 58.972 41.667 0.00 0.00 33.04 6.46
1600 2669 4.148825 GACCCCGTGCAGCTCGAT 62.149 66.667 18.26 3.38 0.00 3.59
1622 2691 2.677228 CCGAAATGCCCCCACTCT 59.323 61.111 0.00 0.00 0.00 3.24
1854 2923 1.674057 CCCTTCCTCAGCGTGAAGT 59.326 57.895 0.00 0.00 36.98 3.01
1924 2993 0.166814 GTGAAGGCGCTGTTCATGAC 59.833 55.000 22.71 10.97 36.35 3.06
2129 3213 4.197750 CAAGGAGTGGGAAGAAGATGATG 58.802 47.826 0.00 0.00 0.00 3.07
2130 3214 3.729108 AGGAGTGGGAAGAAGATGATGA 58.271 45.455 0.00 0.00 0.00 2.92
2131 3215 4.305524 AGGAGTGGGAAGAAGATGATGAT 58.694 43.478 0.00 0.00 0.00 2.45
2173 3257 0.179129 GCCAATGCCGAAACAGATGG 60.179 55.000 0.00 0.00 34.93 3.51
2174 3258 0.457035 CCAATGCCGAAACAGATGGG 59.543 55.000 0.00 0.00 30.56 4.00
2222 3306 2.508891 CGCGGATGAGAACTCGTGC 61.509 63.158 0.00 3.59 34.18 5.34
2270 3354 1.351017 CAAGAACCCAAGGAGGTGCTA 59.649 52.381 0.00 0.00 45.97 3.49
2318 3402 0.179156 CATTGCAGCCCGACATTCAC 60.179 55.000 0.00 0.00 0.00 3.18
2409 3496 0.662619 TGAAAACAGCAAGCAGTCGG 59.337 50.000 0.00 0.00 0.00 4.79
2410 3497 0.944386 GAAAACAGCAAGCAGTCGGA 59.056 50.000 0.00 0.00 0.00 4.55
2411 3498 0.947244 AAAACAGCAAGCAGTCGGAG 59.053 50.000 0.00 0.00 0.00 4.63
2419 3506 1.048601 AAGCAGTCGGAGGAGAACAA 58.951 50.000 0.00 0.00 0.00 2.83
2435 3522 4.515361 AGAACAATGAGAATGCTCCTCAG 58.485 43.478 0.00 0.00 43.07 3.35
2493 3583 2.017049 CATGGTTTAGCTGTGGGTAGC 58.983 52.381 0.00 0.00 44.01 3.58
2515 3605 4.580167 GCATATGGTGAACCTGAAATGCTA 59.420 41.667 4.56 0.00 35.97 3.49
2526 3616 5.815581 ACCTGAAATGCTACCATGACTAAA 58.184 37.500 0.00 0.00 0.00 1.85
2650 3740 3.322828 AGTTATGATTGCATTGCATCCCC 59.677 43.478 12.95 2.99 38.76 4.81
2673 3763 4.190772 CCATTGCTTGTTTTTGTGAAGGT 58.809 39.130 0.00 0.00 0.00 3.50
2791 3882 0.674895 GAGAAGAACGCCATGCCAGT 60.675 55.000 0.00 0.00 0.00 4.00
2801 3892 2.014068 GCCATGCCAGTACTGAAGGAC 61.014 57.143 24.68 11.37 0.00 3.85
2810 3901 5.623824 GCCAGTACTGAAGGACGAAAATAGA 60.624 44.000 24.68 0.00 0.00 1.98
2815 3906 4.217983 ACTGAAGGACGAAAATAGACGAGT 59.782 41.667 0.00 0.00 0.00 4.18
2816 3907 4.482386 TGAAGGACGAAAATAGACGAGTG 58.518 43.478 0.00 0.00 0.00 3.51
2817 3908 4.216902 TGAAGGACGAAAATAGACGAGTGA 59.783 41.667 0.00 0.00 0.00 3.41
2901 3995 6.092670 CCTGTGGTTACTCATTGTTCTATGTG 59.907 42.308 0.00 0.00 0.00 3.21
2963 4057 5.852282 TGGAAAGGAAAGAGAAAAACTGG 57.148 39.130 0.00 0.00 0.00 4.00
2993 4087 1.074405 AGAAGCAGGTGAGCATTTCCA 59.926 47.619 0.00 0.00 36.85 3.53
3000 4094 1.457346 GTGAGCATTTCCAGGTCCAG 58.543 55.000 0.00 0.00 32.75 3.86
3010 4104 6.127366 GCATTTCCAGGTCCAGATCAATTTAA 60.127 38.462 0.00 0.00 0.00 1.52
3046 4140 4.924305 AGAAACACACATGCTGAATTGT 57.076 36.364 0.00 0.00 0.00 2.71
3054 4152 3.427528 CACATGCTGAATTGTTTGTCTGC 59.572 43.478 0.00 0.00 38.70 4.26
3233 4331 5.754890 GTCATCAACAAGAACAGCCAAAATT 59.245 36.000 0.00 0.00 0.00 1.82
3263 4361 4.057406 TGCAAAACCAAATCAGTTCCTG 57.943 40.909 0.00 0.00 0.00 3.86
3264 4362 3.450457 TGCAAAACCAAATCAGTTCCTGT 59.550 39.130 0.00 0.00 32.61 4.00
3342 4440 9.888878 ATGATATCTTTTCATTTTAGCACATCG 57.111 29.630 3.98 0.00 29.55 3.84
3343 4441 8.892723 TGATATCTTTTCATTTTAGCACATCGT 58.107 29.630 3.98 0.00 0.00 3.73
3344 4442 9.162793 GATATCTTTTCATTTTAGCACATCGTG 57.837 33.333 0.00 0.00 36.51 4.35
3345 4443 6.552859 TCTTTTCATTTTAGCACATCGTGA 57.447 33.333 0.00 0.00 35.23 4.35
3346 4444 7.144722 TCTTTTCATTTTAGCACATCGTGAT 57.855 32.000 0.00 0.00 35.23 3.06
3347 4445 8.262715 TCTTTTCATTTTAGCACATCGTGATA 57.737 30.769 0.00 0.00 35.23 2.15
3348 4446 8.892723 TCTTTTCATTTTAGCACATCGTGATAT 58.107 29.630 0.00 0.00 34.38 1.63
3349 4447 9.162793 CTTTTCATTTTAGCACATCGTGATATC 57.837 33.333 0.00 0.00 34.38 1.63
3350 4448 8.437360 TTTCATTTTAGCACATCGTGATATCT 57.563 30.769 3.98 0.00 34.38 1.98
3351 4449 8.437360 TTCATTTTAGCACATCGTGATATCTT 57.563 30.769 3.98 0.00 34.38 2.40
3352 4450 8.437360 TCATTTTAGCACATCGTGATATCTTT 57.563 30.769 3.98 0.00 34.38 2.52
3353 4451 8.892723 TCATTTTAGCACATCGTGATATCTTTT 58.107 29.630 3.98 0.00 34.38 2.27
3354 4452 9.162793 CATTTTAGCACATCGTGATATCTTTTC 57.837 33.333 3.98 0.00 34.38 2.29
3363 4461 7.557719 ACATCGTGATATCTTTTCATTTCCCTT 59.442 33.333 3.98 0.00 0.00 3.95
3373 4471 6.379703 TCTTTTCATTTCCCTTTGTTCAGTGA 59.620 34.615 0.00 0.00 0.00 3.41
3432 4530 1.003118 CCTCGGTGAAAACATCCAGGA 59.997 52.381 0.00 0.00 0.00 3.86
3517 4616 2.106338 TGTCTGCTCCATCCAAAAGACA 59.894 45.455 0.00 0.00 41.14 3.41
3520 4619 3.008330 CTGCTCCATCCAAAAGACAGAG 58.992 50.000 0.00 0.00 32.45 3.35
3579 4678 9.090692 GTTTTGTCAACTAGAAGTGTACACTAA 57.909 33.333 28.13 15.59 41.58 2.24
3580 4679 8.867112 TTTGTCAACTAGAAGTGTACACTAAG 57.133 34.615 28.13 24.49 41.58 2.18
3604 4703 2.840753 GGGGTTGGCCAGGAACTCA 61.841 63.158 5.11 0.00 34.60 3.41
3605 4704 1.603739 GGGTTGGCCAGGAACTCAC 60.604 63.158 5.11 0.00 34.60 3.51
3606 4705 1.456287 GGTTGGCCAGGAACTCACT 59.544 57.895 5.11 0.00 34.60 3.41
3607 4706 0.606673 GGTTGGCCAGGAACTCACTC 60.607 60.000 5.11 0.00 34.60 3.51
3796 4896 6.626302 TGGTTTTCTGAGTTTTGTTAACTGG 58.374 36.000 7.22 0.00 0.00 4.00
3869 4971 6.777580 AGTTTCCTTGTTTCTGTACCATGAAT 59.222 34.615 0.00 0.00 0.00 2.57
3968 5082 8.909708 TGAAAATCTGTAGTGAAACACAAAAG 57.090 30.769 4.75 0.00 41.43 2.27
3970 5084 9.997482 GAAAATCTGTAGTGAAACACAAAAGTA 57.003 29.630 4.75 0.00 41.43 2.24
3975 5089 7.065324 TCTGTAGTGAAACACAAAAGTACAAGG 59.935 37.037 0.00 0.00 41.43 3.61
3997 5115 8.846211 CAAGGAAGTTAAGAATTGTGTTCCTTA 58.154 33.333 15.45 1.33 43.62 2.69
4040 5158 7.973388 TCCAAACACAATAACTGTTCTTGAAAG 59.027 33.333 20.98 13.70 35.47 2.62
4041 5159 7.254084 CCAAACACAATAACTGTTCTTGAAAGC 60.254 37.037 20.98 0.00 35.47 3.51
4077 5195 3.700538 TGGAGGTCCCATTCAATTTGAG 58.299 45.455 0.00 0.00 40.82 3.02
4086 5204 5.779771 TCCCATTCAATTTGAGCCTTAAACT 59.220 36.000 0.00 0.00 0.00 2.66
4096 5214 3.199946 TGAGCCTTAAACTCCATACCTGG 59.800 47.826 0.00 0.00 44.64 4.45
4117 5235 8.772250 ACCTGGATATAAACATGGATATCGATT 58.228 33.333 1.71 0.00 36.35 3.34
4118 5236 9.618890 CCTGGATATAAACATGGATATCGATTT 57.381 33.333 1.71 0.00 36.35 2.17
4163 5283 0.874390 AACTGCACACAATAGCACCG 59.126 50.000 0.00 0.00 36.62 4.94
4175 5295 6.989759 ACACAATAGCACCGATATGAACAATA 59.010 34.615 0.00 0.00 0.00 1.90
4199 5319 6.915544 TTGCTGATTTACAAATTTTGCACA 57.084 29.167 9.04 2.62 32.40 4.57
4200 5320 6.284475 TGCTGATTTACAAATTTTGCACAC 57.716 33.333 9.04 0.00 0.00 3.82
4201 5321 5.814188 TGCTGATTTACAAATTTTGCACACA 59.186 32.000 9.04 3.53 0.00 3.72
4202 5322 6.314648 TGCTGATTTACAAATTTTGCACACAA 59.685 30.769 9.04 0.00 0.00 3.33
4203 5323 6.847289 GCTGATTTACAAATTTTGCACACAAG 59.153 34.615 9.04 2.84 37.04 3.16
4204 5324 7.465781 GCTGATTTACAAATTTTGCACACAAGT 60.466 33.333 9.04 0.00 37.04 3.16
4205 5325 8.932945 TGATTTACAAATTTTGCACACAAGTA 57.067 26.923 9.04 0.00 37.04 2.24
4206 5326 9.029243 TGATTTACAAATTTTGCACACAAGTAG 57.971 29.630 9.04 0.00 37.04 2.57
4207 5327 6.820470 TTACAAATTTTGCACACAAGTAGC 57.180 33.333 9.04 0.00 37.04 3.58
4208 5328 4.753233 ACAAATTTTGCACACAAGTAGCA 58.247 34.783 9.04 0.00 37.04 3.49
4212 5332 2.036958 TTGCACACAAGTAGCACACT 57.963 45.000 0.00 0.00 38.11 3.55
4215 5335 3.325870 TGCACACAAGTAGCACACTATC 58.674 45.455 0.00 0.00 36.04 2.08
4219 5339 4.749598 CACACAAGTAGCACACTATCACAA 59.250 41.667 0.00 0.00 36.04 3.33
4229 5349 7.400599 AGCACACTATCACAATTGATCAAAT 57.599 32.000 13.09 0.02 41.87 2.32
4239 5359 8.058667 TCACAATTGATCAAATGATTGCTAGT 57.941 30.769 26.44 2.32 36.45 2.57
4245 5365 5.711506 TGATCAAATGATTGCTAGTTGGTGT 59.288 36.000 0.00 0.00 36.45 4.16
4249 5369 6.488344 TCAAATGATTGCTAGTTGGTGTAACA 59.512 34.615 0.00 0.00 37.82 2.41
4251 5371 6.892658 ATGATTGCTAGTTGGTGTAACAAA 57.107 33.333 0.00 0.00 41.88 2.83
4254 5374 7.721402 TGATTGCTAGTTGGTGTAACAAATTT 58.279 30.769 0.00 0.00 41.88 1.82
4255 5375 7.865385 TGATTGCTAGTTGGTGTAACAAATTTC 59.135 33.333 0.00 0.00 41.88 2.17
4256 5376 6.701145 TGCTAGTTGGTGTAACAAATTTCA 57.299 33.333 0.00 0.00 41.88 2.69
4257 5377 6.734137 TGCTAGTTGGTGTAACAAATTTCAG 58.266 36.000 0.00 0.00 41.88 3.02
4258 5378 6.149633 GCTAGTTGGTGTAACAAATTTCAGG 58.850 40.000 0.00 0.00 41.88 3.86
4277 5397 1.480498 GGCCGGGTATCAATGGGAAAT 60.480 52.381 2.18 0.00 0.00 2.17
4280 5400 3.506067 GCCGGGTATCAATGGGAAATAAG 59.494 47.826 2.18 0.00 0.00 1.73
4286 5406 5.891551 GGTATCAATGGGAAATAAGGTGTGT 59.108 40.000 0.00 0.00 0.00 3.72
4304 5424 6.151144 AGGTGTGTTGTAATAAAGAATCTGCC 59.849 38.462 0.00 0.00 0.00 4.85
4340 5460 5.003160 TGCCATATTGACATGGTACTATGC 58.997 41.667 18.24 11.76 46.21 3.14
4341 5461 5.003160 GCCATATTGACATGGTACTATGCA 58.997 41.667 18.24 13.96 46.21 3.96
4343 5463 6.403964 GCCATATTGACATGGTACTATGCATG 60.404 42.308 18.24 12.64 46.21 4.06
4357 5477 7.540745 GGTACTATGCATGTTAACCAAAGTTTG 59.459 37.037 10.16 8.73 37.42 2.93
4383 5503 8.322091 GGTATCTGTATATGCTGGGTATTTCTT 58.678 37.037 0.00 0.00 0.00 2.52
4392 5512 6.584185 TGCTGGGTATTTCTTTTTCCTTAC 57.416 37.500 0.00 0.00 0.00 2.34
4393 5513 6.311735 TGCTGGGTATTTCTTTTTCCTTACT 58.688 36.000 0.00 0.00 0.00 2.24
4394 5514 7.463431 TGCTGGGTATTTCTTTTTCCTTACTA 58.537 34.615 0.00 0.00 0.00 1.82
4395 5515 8.113462 TGCTGGGTATTTCTTTTTCCTTACTAT 58.887 33.333 0.00 0.00 0.00 2.12
4396 5516 9.623000 GCTGGGTATTTCTTTTTCCTTACTATA 57.377 33.333 0.00 0.00 0.00 1.31
4425 5545 6.597672 ACACATCAGAAGTTGTTTGTAGAACA 59.402 34.615 0.00 0.00 30.29 3.18
4432 5552 2.949644 GTTGTTTGTAGAACACCTGCCT 59.050 45.455 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.672996 CCGGACTGCCCAACCAAG 60.673 66.667 0.00 0.00 34.14 3.61
27 28 3.636231 CAAGTCCCGGACTGCCCA 61.636 66.667 21.15 0.00 42.59 5.36
36 37 0.460284 CAATCTCCGTCCAAGTCCCG 60.460 60.000 0.00 0.00 0.00 5.14
37 38 0.613777 ACAATCTCCGTCCAAGTCCC 59.386 55.000 0.00 0.00 0.00 4.46
40 41 1.336887 CGACACAATCTCCGTCCAAGT 60.337 52.381 0.00 0.00 0.00 3.16
42 43 0.677288 ACGACACAATCTCCGTCCAA 59.323 50.000 0.00 0.00 0.00 3.53
58 59 4.662961 CACCTCAGGCGTGCACGA 62.663 66.667 41.19 20.37 43.02 4.35
60 61 4.314440 TCCACCTCAGGCGTGCAC 62.314 66.667 6.82 6.82 0.00 4.57
93 102 2.742372 CAACCTCTTCCCGTGGCG 60.742 66.667 0.00 0.00 0.00 5.69
98 107 0.974383 ACCTACACAACCTCTTCCCG 59.026 55.000 0.00 0.00 0.00 5.14
189 198 1.354506 CCGGTGAGGTCGACGTATC 59.645 63.158 11.30 8.78 34.51 2.24
200 209 3.103911 GTTGTCGTCGCCGGTGAG 61.104 66.667 20.25 12.76 33.95 3.51
205 214 4.394078 TCCTCGTTGTCGTCGCCG 62.394 66.667 0.00 0.00 38.33 6.46
214 223 0.096628 CGTCCTACTCGTCCTCGTTG 59.903 60.000 0.00 0.00 38.33 4.10
215 224 1.023513 CCGTCCTACTCGTCCTCGTT 61.024 60.000 0.00 0.00 38.33 3.85
216 225 1.449246 CCGTCCTACTCGTCCTCGT 60.449 63.158 0.00 0.00 38.33 4.18
217 226 2.821688 GCCGTCCTACTCGTCCTCG 61.822 68.421 0.00 0.00 38.55 4.63
220 229 2.799371 CAGCCGTCCTACTCGTCC 59.201 66.667 0.00 0.00 0.00 4.79
236 245 0.739462 CGCCATTGACTTCCGTAGCA 60.739 55.000 0.00 0.00 0.00 3.49
241 250 2.051804 GATGCCGCCATTGACTTCCG 62.052 60.000 0.00 0.00 0.00 4.30
247 256 2.889988 CGTCGATGCCGCCATTGA 60.890 61.111 0.00 0.00 39.11 2.57
260 269 2.978598 GATAAGGGTCGTCGCCGTCG 62.979 65.000 0.00 0.00 35.01 5.12
261 270 1.298938 GATAAGGGTCGTCGCCGTC 60.299 63.158 2.24 0.00 35.01 4.79
262 271 0.464373 TAGATAAGGGTCGTCGCCGT 60.464 55.000 0.00 0.00 35.01 5.68
325 334 2.000447 GTCCACAATAGCCGAGTTCAC 59.000 52.381 0.00 0.00 0.00 3.18
332 341 4.142773 ACATTAAAACGTCCACAATAGCCG 60.143 41.667 0.00 0.00 0.00 5.52
389 410 9.672086 CCGTTTATTCAGACTTCAAATTTAACA 57.328 29.630 0.00 0.00 0.00 2.41
390 411 9.887406 TCCGTTTATTCAGACTTCAAATTTAAC 57.113 29.630 0.00 0.00 0.00 2.01
391 412 9.887406 GTCCGTTTATTCAGACTTCAAATTTAA 57.113 29.630 0.00 0.00 0.00 1.52
392 413 9.058174 TGTCCGTTTATTCAGACTTCAAATTTA 57.942 29.630 0.00 0.00 0.00 1.40
397 418 5.607477 ACTGTCCGTTTATTCAGACTTCAA 58.393 37.500 0.00 0.00 0.00 2.69
399 420 6.363473 CAAACTGTCCGTTTATTCAGACTTC 58.637 40.000 0.00 0.00 43.75 3.01
405 426 4.088056 TCCCAAACTGTCCGTTTATTCA 57.912 40.909 0.00 0.00 43.75 2.57
406 427 4.457949 ACATCCCAAACTGTCCGTTTATTC 59.542 41.667 0.00 0.00 43.75 1.75
413 434 1.586154 GCCACATCCCAAACTGTCCG 61.586 60.000 0.00 0.00 0.00 4.79
418 439 2.035626 CCCGCCACATCCCAAACT 59.964 61.111 0.00 0.00 0.00 2.66
426 447 2.034066 CCAAGTGACCCGCCACAT 59.966 61.111 0.00 0.00 39.42 3.21
476 497 2.566824 ATGGCAAACGGACATGTCC 58.433 52.632 31.59 31.59 46.05 4.02
507 528 2.603652 CGAGCCGTTTCGTTTGGATTTT 60.604 45.455 0.00 0.00 35.91 1.82
525 546 0.586319 AATGCACGACCACAAACGAG 59.414 50.000 0.00 0.00 0.00 4.18
526 547 0.306228 CAATGCACGACCACAAACGA 59.694 50.000 0.00 0.00 0.00 3.85
533 557 0.602638 GTGACTCCAATGCACGACCA 60.603 55.000 0.00 0.00 0.00 4.02
538 562 2.084546 GTAAGGGTGACTCCAATGCAC 58.915 52.381 0.00 0.00 38.11 4.57
575 599 0.097499 CTACACGGACACGCATACGA 59.903 55.000 0.00 0.00 46.04 3.43
601 627 2.945447 TACCCAAACCGACTATGACG 57.055 50.000 0.00 0.00 0.00 4.35
693 730 2.202756 CCGTGCGGAGTAGAAGGC 60.203 66.667 4.35 0.00 37.50 4.35
722 759 2.281208 CCGGGCGTGAAGGTGAAA 60.281 61.111 0.00 0.00 0.00 2.69
726 763 2.509651 TAACACCGGGCGTGAAGGT 61.510 57.895 6.32 0.00 46.20 3.50
727 764 2.030958 GTAACACCGGGCGTGAAGG 61.031 63.158 6.32 0.00 46.20 3.46
777 1781 4.509580 AAACCGTGGGCCGTTGGT 62.510 61.111 8.21 8.21 35.90 3.67
897 1901 4.340246 TGGGCTGTGGCTGCTCTG 62.340 66.667 0.00 0.00 38.73 3.35
898 1902 4.341783 GTGGGCTGTGGCTGCTCT 62.342 66.667 0.00 0.00 38.73 4.09
899 1903 4.648626 TGTGGGCTGTGGCTGCTC 62.649 66.667 0.00 0.00 38.73 4.26
926 1930 1.078759 GCGTCGGAGATGGTGTTCTG 61.079 60.000 0.00 0.00 45.11 3.02
929 1933 2.264794 GGCGTCGGAGATGGTGTT 59.735 61.111 0.00 0.00 45.11 3.32
1163 2191 2.918712 AAGGGTAGAGGATGATTGCG 57.081 50.000 0.00 0.00 0.00 4.85
1217 2254 1.751351 TCTTTGCGTCTCAGATCCGAT 59.249 47.619 0.00 0.00 0.00 4.18
1221 2258 1.996191 GGTGTCTTTGCGTCTCAGATC 59.004 52.381 0.00 0.00 0.00 2.75
1271 2308 1.668047 GCCTGCATATCGTACGGGTAC 60.668 57.143 16.52 2.45 32.07 3.34
1272 2309 0.599558 GCCTGCATATCGTACGGGTA 59.400 55.000 16.52 9.45 32.07 3.69
1273 2310 1.113517 AGCCTGCATATCGTACGGGT 61.114 55.000 16.52 7.37 32.07 5.28
1274 2311 0.667487 CAGCCTGCATATCGTACGGG 60.667 60.000 16.52 7.77 0.00 5.28
1275 2312 1.284982 GCAGCCTGCATATCGTACGG 61.285 60.000 16.52 0.00 44.26 4.02
1280 2317 2.313172 GGTCGCAGCCTGCATATCG 61.313 63.158 18.21 0.00 45.36 2.92
1357 2394 4.627058 TCAAACACGAGAATTAGCAGTGA 58.373 39.130 0.00 0.00 36.71 3.41
1360 2397 6.169419 TCAATCAAACACGAGAATTAGCAG 57.831 37.500 0.00 0.00 0.00 4.24
1361 2398 6.149308 ACATCAATCAAACACGAGAATTAGCA 59.851 34.615 0.00 0.00 0.00 3.49
1362 2399 6.467047 CACATCAATCAAACACGAGAATTAGC 59.533 38.462 0.00 0.00 0.00 3.09
1363 2400 7.479603 CACACATCAATCAAACACGAGAATTAG 59.520 37.037 0.00 0.00 0.00 1.73
1365 2402 6.017192 TCACACATCAATCAAACACGAGAATT 60.017 34.615 0.00 0.00 0.00 2.17
1366 2403 5.469760 TCACACATCAATCAAACACGAGAAT 59.530 36.000 0.00 0.00 0.00 2.40
1386 2455 0.317160 AGCCGTCGAATTCAGTCACA 59.683 50.000 6.22 0.00 0.00 3.58
1517 2586 5.028375 CGGCGAGAAAGGAAATAAATTCAC 58.972 41.667 0.00 0.00 39.98 3.18
1525 2594 1.749258 GGCCGGCGAGAAAGGAAAT 60.749 57.895 22.54 0.00 0.00 2.17
1646 2715 2.202987 CTCAGCCTGGTCATCCGC 60.203 66.667 0.00 0.00 36.30 5.54
1854 2923 2.686106 GACCGGCCCCTTCTGGTA 60.686 66.667 0.00 0.00 45.35 3.25
1924 2993 1.376037 GTCTCCTTCTTGGGCGTGG 60.376 63.158 0.00 0.00 36.20 4.94
2089 3158 1.153667 GGCTCCTGCACTCTCTTCG 60.154 63.158 0.00 0.00 41.91 3.79
2129 3213 0.102481 TCGCCGAACAGCCTAAGATC 59.898 55.000 0.00 0.00 0.00 2.75
2130 3214 0.535335 TTCGCCGAACAGCCTAAGAT 59.465 50.000 0.00 0.00 0.00 2.40
2131 3215 0.319083 TTTCGCCGAACAGCCTAAGA 59.681 50.000 0.00 0.00 0.00 2.10
2173 3257 4.735358 GGCCACTTCGGTTCCCCC 62.735 72.222 0.00 0.00 36.97 5.40
2222 3306 2.010817 GCGCCTTGCAGTTCGTTTG 61.011 57.895 0.00 0.00 45.45 2.93
2270 3354 1.553690 CCTCAACCCGTGATCCCTGT 61.554 60.000 0.00 0.00 35.07 4.00
2318 3402 1.153823 ATTCTCCTTGTCGTCGCCG 60.154 57.895 0.00 0.00 0.00 6.46
2409 3496 3.876320 GGAGCATTCTCATTGTTCTCCTC 59.124 47.826 0.00 0.00 41.13 3.71
2410 3497 3.522750 AGGAGCATTCTCATTGTTCTCCT 59.477 43.478 2.32 2.32 42.79 3.69
2411 3498 3.876320 GAGGAGCATTCTCATTGTTCTCC 59.124 47.826 0.00 0.00 41.13 3.71
2419 3506 3.113824 ACCTTCTGAGGAGCATTCTCAT 58.886 45.455 0.00 0.00 46.74 2.90
2435 3522 4.240175 ACGTCAGAGTTTCAGTACCTTC 57.760 45.455 0.00 0.00 0.00 3.46
2493 3583 5.009010 GGTAGCATTTCAGGTTCACCATATG 59.991 44.000 0.00 0.00 38.89 1.78
2515 3605 2.094675 GCACCTGCATTTAGTCATGGT 58.905 47.619 0.00 0.00 41.59 3.55
2526 3616 1.547372 CTGCCTTTTAAGCACCTGCAT 59.453 47.619 0.00 0.00 45.16 3.96
2650 3740 3.560896 CCTTCACAAAAACAAGCAATGGG 59.439 43.478 0.00 0.00 0.00 4.00
2652 3742 5.799681 AACCTTCACAAAAACAAGCAATG 57.200 34.783 0.00 0.00 0.00 2.82
2653 3743 6.816134 AAAACCTTCACAAAAACAAGCAAT 57.184 29.167 0.00 0.00 0.00 3.56
2673 3763 4.677779 GCCTTTCAGCAACTGAGTGAAAAA 60.678 41.667 0.00 0.00 41.75 1.94
2791 3882 5.413833 ACTCGTCTATTTTCGTCCTTCAGTA 59.586 40.000 0.00 0.00 0.00 2.74
2801 3892 5.043903 ACCATCATCACTCGTCTATTTTCG 58.956 41.667 0.00 0.00 0.00 3.46
2810 3901 4.801330 TCAACTTACCATCATCACTCGT 57.199 40.909 0.00 0.00 0.00 4.18
2815 3906 6.070021 ACTCCTGATTCAACTTACCATCATCA 60.070 38.462 0.00 0.00 0.00 3.07
2816 3907 6.259608 CACTCCTGATTCAACTTACCATCATC 59.740 42.308 0.00 0.00 0.00 2.92
2817 3908 6.118170 CACTCCTGATTCAACTTACCATCAT 58.882 40.000 0.00 0.00 0.00 2.45
2901 3995 1.329906 GCTGCATCACATCACAGTAGC 59.670 52.381 0.00 0.00 32.65 3.58
2963 4057 2.684843 CCTGCTTCTCGCCACAAGC 61.685 63.158 0.00 0.00 44.55 4.01
2993 4087 5.203528 CCACCATTAAATTGATCTGGACCT 58.796 41.667 2.17 0.00 0.00 3.85
3010 4104 6.547880 TGTGTGTTTCTAAATTGTACCACCAT 59.452 34.615 0.00 0.00 0.00 3.55
3046 4140 1.340088 ATGCAACATGGGCAGACAAA 58.660 45.000 17.51 0.00 45.68 2.83
3054 4152 3.824133 TCCTCTGAATATGCAACATGGG 58.176 45.455 0.00 0.00 0.00 4.00
3163 4261 0.874390 TTTGCCTTTAGTCAGCGCAG 59.126 50.000 11.47 0.00 0.00 5.18
3164 4262 1.001815 GTTTTGCCTTTAGTCAGCGCA 60.002 47.619 11.47 0.00 0.00 6.09
3165 4263 1.666023 GGTTTTGCCTTTAGTCAGCGC 60.666 52.381 0.00 0.00 0.00 5.92
3166 4264 1.399727 CGGTTTTGCCTTTAGTCAGCG 60.400 52.381 0.00 0.00 34.25 5.18
3167 4265 1.607148 ACGGTTTTGCCTTTAGTCAGC 59.393 47.619 0.00 0.00 34.25 4.26
3168 4266 4.312443 TCTACGGTTTTGCCTTTAGTCAG 58.688 43.478 0.00 0.00 34.25 3.51
3233 4331 5.734720 TGATTTGGTTTTGCAAACCTTGTA 58.265 33.333 22.78 4.11 40.88 2.41
3263 4361 8.576442 TGTAAATTCAGAAATTCAGAAAGGGAC 58.424 33.333 4.96 2.99 33.93 4.46
3264 4362 8.576442 GTGTAAATTCAGAAATTCAGAAAGGGA 58.424 33.333 4.96 0.00 33.93 4.20
3329 4427 8.892723 TGAAAAGATATCACGATGTGCTAAAAT 58.107 29.630 5.32 0.00 32.98 1.82
3330 4428 8.262715 TGAAAAGATATCACGATGTGCTAAAA 57.737 30.769 5.32 0.00 32.98 1.52
3331 4429 7.841915 TGAAAAGATATCACGATGTGCTAAA 57.158 32.000 5.32 0.00 32.98 1.85
3332 4430 8.437360 AATGAAAAGATATCACGATGTGCTAA 57.563 30.769 5.32 0.00 32.98 3.09
3333 4431 8.437360 AAATGAAAAGATATCACGATGTGCTA 57.563 30.769 5.32 0.00 32.98 3.49
3334 4432 6.932356 AATGAAAAGATATCACGATGTGCT 57.068 33.333 5.32 0.00 32.98 4.40
3335 4433 6.634436 GGAAATGAAAAGATATCACGATGTGC 59.366 38.462 5.32 0.00 32.98 4.57
3336 4434 7.012704 AGGGAAATGAAAAGATATCACGATGTG 59.987 37.037 5.32 0.00 34.45 3.21
3337 4435 7.056635 AGGGAAATGAAAAGATATCACGATGT 58.943 34.615 5.32 0.00 0.00 3.06
3338 4436 7.502120 AGGGAAATGAAAAGATATCACGATG 57.498 36.000 5.32 0.00 0.00 3.84
3339 4437 8.408601 CAAAGGGAAATGAAAAGATATCACGAT 58.591 33.333 5.32 0.00 0.00 3.73
3340 4438 7.393234 ACAAAGGGAAATGAAAAGATATCACGA 59.607 33.333 5.32 0.00 0.00 4.35
3341 4439 7.538575 ACAAAGGGAAATGAAAAGATATCACG 58.461 34.615 5.32 0.00 0.00 4.35
3342 4440 9.358872 GAACAAAGGGAAATGAAAAGATATCAC 57.641 33.333 5.32 0.00 0.00 3.06
3343 4441 9.087871 TGAACAAAGGGAAATGAAAAGATATCA 57.912 29.630 5.32 0.00 0.00 2.15
3344 4442 9.578439 CTGAACAAAGGGAAATGAAAAGATATC 57.422 33.333 0.00 0.00 0.00 1.63
3345 4443 9.093458 ACTGAACAAAGGGAAATGAAAAGATAT 57.907 29.630 0.00 0.00 0.00 1.63
3346 4444 8.359642 CACTGAACAAAGGGAAATGAAAAGATA 58.640 33.333 0.00 0.00 0.00 1.98
3347 4445 7.069826 TCACTGAACAAAGGGAAATGAAAAGAT 59.930 33.333 0.00 0.00 0.00 2.40
3348 4446 6.379703 TCACTGAACAAAGGGAAATGAAAAGA 59.620 34.615 0.00 0.00 0.00 2.52
3349 4447 6.572519 TCACTGAACAAAGGGAAATGAAAAG 58.427 36.000 0.00 0.00 0.00 2.27
3350 4448 6.537453 TCACTGAACAAAGGGAAATGAAAA 57.463 33.333 0.00 0.00 0.00 2.29
3351 4449 6.729690 ATCACTGAACAAAGGGAAATGAAA 57.270 33.333 0.00 0.00 32.08 2.69
3352 4450 6.729690 AATCACTGAACAAAGGGAAATGAA 57.270 33.333 0.00 0.00 32.08 2.57
3353 4451 6.323482 TGAAATCACTGAACAAAGGGAAATGA 59.677 34.615 0.00 0.00 32.08 2.57
3354 4452 6.421801 GTGAAATCACTGAACAAAGGGAAATG 59.578 38.462 6.30 0.00 43.25 2.32
3373 4471 0.976641 TCGAGAGGGTGCTGTGAAAT 59.023 50.000 0.00 0.00 0.00 2.17
3517 4616 2.290916 CGACGCCATAGATACACACTCT 59.709 50.000 0.00 0.00 0.00 3.24
3520 4619 2.768833 TCGACGCCATAGATACACAC 57.231 50.000 0.00 0.00 0.00 3.82
3796 4896 3.489785 CAGAAACAGACGGTACACACTTC 59.510 47.826 0.00 0.00 0.00 3.01
3808 4908 4.117685 ACGGTTTGAGTACAGAAACAGAC 58.882 43.478 19.44 7.55 0.00 3.51
3869 4971 9.748708 CAAAAGAATTTCACCTATCTCACAAAA 57.251 29.630 0.00 0.00 37.28 2.44
3968 5082 8.074370 GGAACACAATTCTTAACTTCCTTGTAC 58.926 37.037 0.00 0.00 0.00 2.90
3970 5084 6.833933 AGGAACACAATTCTTAACTTCCTTGT 59.166 34.615 0.00 0.00 33.71 3.16
3997 5115 8.474025 TGTGTTTGGATTTCACAATTTCTAACT 58.526 29.630 0.00 0.00 38.80 2.24
4021 5139 6.371809 TTCGCTTTCAAGAACAGTTATTGT 57.628 33.333 18.04 0.00 43.45 2.71
4024 5142 7.595130 GGAATTTTCGCTTTCAAGAACAGTTAT 59.405 33.333 0.00 0.00 0.00 1.89
4025 5143 6.915843 GGAATTTTCGCTTTCAAGAACAGTTA 59.084 34.615 0.00 0.00 0.00 2.24
4026 5144 5.748630 GGAATTTTCGCTTTCAAGAACAGTT 59.251 36.000 0.00 0.00 0.00 3.16
4040 5158 5.181433 GGACCTCCATATTAGGAATTTTCGC 59.819 44.000 7.71 0.00 37.20 4.70
4041 5159 5.705905 GGGACCTCCATATTAGGAATTTTCG 59.294 44.000 7.71 0.00 37.20 3.46
4066 5184 6.916360 TGGAGTTTAAGGCTCAAATTGAAT 57.084 33.333 0.00 0.00 34.83 2.57
4175 5295 7.012138 TGTGTGCAAAATTTGTAAATCAGCAAT 59.988 29.630 7.60 0.00 33.93 3.56
4195 5315 3.123621 GTGATAGTGTGCTACTTGTGTGC 59.876 47.826 0.00 0.00 40.89 4.57
4198 5318 6.147656 TCAATTGTGATAGTGTGCTACTTGTG 59.852 38.462 5.13 0.00 40.89 3.33
4199 5319 6.230472 TCAATTGTGATAGTGTGCTACTTGT 58.770 36.000 5.13 0.00 40.89 3.16
4200 5320 6.726258 TCAATTGTGATAGTGTGCTACTTG 57.274 37.500 5.13 0.00 40.89 3.16
4201 5321 7.105588 TGATCAATTGTGATAGTGTGCTACTT 58.894 34.615 5.13 0.00 44.83 2.24
4202 5322 6.643388 TGATCAATTGTGATAGTGTGCTACT 58.357 36.000 5.13 0.12 44.83 2.57
4203 5323 6.908870 TGATCAATTGTGATAGTGTGCTAC 57.091 37.500 5.13 0.00 44.83 3.58
4204 5324 7.920160 TTTGATCAATTGTGATAGTGTGCTA 57.080 32.000 9.40 0.00 44.83 3.49
4205 5325 6.822667 TTTGATCAATTGTGATAGTGTGCT 57.177 33.333 9.40 0.00 44.83 4.40
4206 5326 7.252708 TCATTTGATCAATTGTGATAGTGTGC 58.747 34.615 22.99 0.00 44.83 4.57
4207 5327 9.797556 AATCATTTGATCAATTGTGATAGTGTG 57.202 29.630 22.99 0.82 44.83 3.82
4208 5328 9.797556 CAATCATTTGATCAATTGTGATAGTGT 57.202 29.630 22.99 10.59 44.83 3.55
4215 5335 8.592155 CAACTAGCAATCATTTGATCAATTGTG 58.408 33.333 22.99 17.72 34.60 3.33
4219 5339 7.093640 ACACCAACTAGCAATCATTTGATCAAT 60.094 33.333 9.40 0.00 34.60 2.57
4229 5349 6.892658 ATTTGTTACACCAACTAGCAATCA 57.107 33.333 0.00 0.00 38.05 2.57
4239 5359 3.243569 CGGCCTGAAATTTGTTACACCAA 60.244 43.478 0.00 0.00 0.00 3.67
4245 5365 2.296073 ACCCGGCCTGAAATTTGTTA 57.704 45.000 0.00 0.00 0.00 2.41
4249 5369 2.818751 TGATACCCGGCCTGAAATTT 57.181 45.000 0.00 0.00 0.00 1.82
4251 5371 2.586425 CATTGATACCCGGCCTGAAAT 58.414 47.619 0.00 0.00 0.00 2.17
4254 5374 1.705002 CCCATTGATACCCGGCCTGA 61.705 60.000 0.00 0.00 0.00 3.86
4255 5375 1.228245 CCCATTGATACCCGGCCTG 60.228 63.158 0.00 0.00 0.00 4.85
4256 5376 0.991355 TTCCCATTGATACCCGGCCT 60.991 55.000 0.00 0.00 0.00 5.19
4257 5377 0.106419 TTTCCCATTGATACCCGGCC 60.106 55.000 0.00 0.00 0.00 6.13
4258 5378 1.995376 ATTTCCCATTGATACCCGGC 58.005 50.000 0.00 0.00 0.00 6.13
4277 5397 8.726988 GCAGATTCTTTATTACAACACACCTTA 58.273 33.333 0.00 0.00 0.00 2.69
4280 5400 6.322491 GGCAGATTCTTTATTACAACACACC 58.678 40.000 0.00 0.00 0.00 4.16
4286 5406 5.509498 AGCAGGGCAGATTCTTTATTACAA 58.491 37.500 0.00 0.00 0.00 2.41
4304 5424 4.763279 TCAATATGGCATTGACATAGCAGG 59.237 41.667 16.95 7.13 36.93 4.85
4357 5477 7.852263 AGAAATACCCAGCATATACAGATACC 58.148 38.462 0.00 0.00 0.00 2.73
4360 5480 9.646522 AAAAAGAAATACCCAGCATATACAGAT 57.353 29.630 0.00 0.00 0.00 2.90
4363 5483 8.058847 AGGAAAAAGAAATACCCAGCATATACA 58.941 33.333 0.00 0.00 0.00 2.29
4391 5511 9.561069 AAACAACTTCTGATGTGTTCTTATAGT 57.439 29.630 0.00 0.00 29.49 2.12
4392 5512 9.817365 CAAACAACTTCTGATGTGTTCTTATAG 57.183 33.333 0.00 0.00 29.49 1.31
4393 5513 9.337396 ACAAACAACTTCTGATGTGTTCTTATA 57.663 29.630 0.00 0.00 30.79 0.98
4394 5514 8.225603 ACAAACAACTTCTGATGTGTTCTTAT 57.774 30.769 0.00 0.00 30.79 1.73
4395 5515 7.624360 ACAAACAACTTCTGATGTGTTCTTA 57.376 32.000 0.00 0.00 30.79 2.10
4396 5516 6.515272 ACAAACAACTTCTGATGTGTTCTT 57.485 33.333 0.00 0.00 30.79 2.52
4397 5517 7.047891 TCTACAAACAACTTCTGATGTGTTCT 58.952 34.615 0.00 0.00 33.05 3.01
4398 5518 7.246674 TCTACAAACAACTTCTGATGTGTTC 57.753 36.000 0.00 0.00 33.05 3.18
4425 5545 1.474332 TTTCGAACCGGTAGGCAGGT 61.474 55.000 8.00 0.00 45.04 4.00


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

AutoCloner maintained by Alex Coulton.