Multiple sequence alignment - TraesCS2A01G345800

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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 TraesCS2A01G345800 chr2A 100.000 5721 0 0 1 5721 584061908 584067628 0.000000e+00 10565
1 TraesCS2A01G345800 chr2B 94.154 4379 154 43 778 5128 518513499 518517803 0.000000e+00 6575
2 TraesCS2A01G345800 chr2B 86.933 727 92 3 28 753 518512068 518512792 0.000000e+00 813
3 TraesCS2A01G345800 chr2B 94.194 310 15 3 5413 5721 518518112 518518419 2.410000e-128 470
4 TraesCS2A01G345800 chr2B 94.366 213 12 0 5126 5338 518517906 518518118 1.540000e-85 327
5 TraesCS2A01G345800 chr2D 91.944 3637 184 49 111 3711 440607322 440610885 0.000000e+00 4992
6 TraesCS2A01G345800 chr2D 97.711 830 15 4 3933 4760 440610890 440611717 0.000000e+00 1424
7 TraesCS2A01G345800 chr2D 91.684 493 31 6 4858 5348 440612123 440612607 0.000000e+00 675
8 TraesCS2A01G345800 chr2D 95.238 189 8 1 5445 5633 440612640 440612827 1.210000e-76 298
9 TraesCS2A01G345800 chr2D 98.958 96 1 0 5626 5721 440614932 440615027 7.620000e-39 172


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 TraesCS2A01G345800 chr2A 584061908 584067628 5720 False 10565.00 10565 100.00000 1 5721 1 chr2A.!!$F1 5720
1 TraesCS2A01G345800 chr2B 518512068 518518419 6351 False 2046.25 6575 92.41175 28 5721 4 chr2B.!!$F1 5693
2 TraesCS2A01G345800 chr2D 440607322 440615027 7705 False 1512.20 4992 95.10700 111 5721 5 chr2D.!!$F1 5610

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
22 23 0.036732 TGCTCAAGGCCGTCTGATTT 59.963 50.000 0.0 0.0 40.92 2.17 F
929 1628 0.108963 ATCGCTACTACTCCTCGGCT 59.891 55.000 0.0 0.0 0.00 5.52 F
1588 2298 0.038892 GGTCATGTTGCTTGGCTGTG 60.039 55.000 0.0 0.0 0.00 3.66 F
2356 3071 0.390735 AAGCGTGCCCTTACTTACCG 60.391 55.000 0.0 0.0 0.00 4.02 F
3147 3867 1.133009 AGGAGCGAGATACCAATCCCT 60.133 52.381 0.0 0.0 31.98 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1141 1840 0.241481 GGGCGAGTGGAGATATCGAC 59.759 60.000 0.00 0.00 43.77 4.20 R
2459 3174 1.615392 GGAGAATTTTGCAGTGTGGCT 59.385 47.619 0.00 0.00 34.04 4.75 R
3073 3793 0.169009 GCGAGGCTCCAATGTTCAAC 59.831 55.000 9.32 0.00 0.00 3.18 R
4272 5005 0.529378 CCCCTGCTTTCATGAACTGC 59.471 55.000 19.84 19.84 0.00 4.40 R
4798 5533 0.601841 AACTAACTCGCCCACCAACG 60.602 55.000 0.00 0.00 0.00 4.10 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 2.925170 AGGTGCTCAAGGCCGTCT 60.925 61.111 0.00 0.00 40.92 4.18
18 19 2.743928 GGTGCTCAAGGCCGTCTG 60.744 66.667 0.00 0.00 40.92 3.51
19 20 2.343758 GTGCTCAAGGCCGTCTGA 59.656 61.111 0.00 0.52 40.92 3.27
20 21 1.078848 GTGCTCAAGGCCGTCTGAT 60.079 57.895 0.00 0.00 40.92 2.90
21 22 0.674895 GTGCTCAAGGCCGTCTGATT 60.675 55.000 0.00 0.00 40.92 2.57
22 23 0.036732 TGCTCAAGGCCGTCTGATTT 59.963 50.000 0.00 0.00 40.92 2.17
23 24 0.449388 GCTCAAGGCCGTCTGATTTG 59.551 55.000 0.00 0.00 34.27 2.32
24 25 0.449388 CTCAAGGCCGTCTGATTTGC 59.551 55.000 0.00 0.00 0.00 3.68
25 26 0.250684 TCAAGGCCGTCTGATTTGCA 60.251 50.000 0.00 0.00 0.00 4.08
26 27 0.813184 CAAGGCCGTCTGATTTGCAT 59.187 50.000 0.00 0.00 0.00 3.96
27 28 1.098050 AAGGCCGTCTGATTTGCATC 58.902 50.000 0.00 0.00 0.00 3.91
28 29 0.254178 AGGCCGTCTGATTTGCATCT 59.746 50.000 0.00 0.00 0.00 2.90
29 30 1.098050 GGCCGTCTGATTTGCATCTT 58.902 50.000 0.00 0.00 0.00 2.40
30 31 2.092968 AGGCCGTCTGATTTGCATCTTA 60.093 45.455 0.00 0.00 0.00 2.10
31 32 2.289002 GGCCGTCTGATTTGCATCTTAG 59.711 50.000 0.00 0.00 0.00 2.18
32 33 2.286654 GCCGTCTGATTTGCATCTTAGC 60.287 50.000 0.00 0.00 0.00 3.09
37 38 2.539688 CTGATTTGCATCTTAGCGCGTA 59.460 45.455 8.43 0.00 37.31 4.42
48 49 1.024046 TAGCGCGTAACAGTCGGGTA 61.024 55.000 8.43 0.00 41.86 3.69
62 63 1.001760 GGGTAGTCAGAGAGGGCCA 59.998 63.158 6.18 0.00 0.00 5.36
67 68 0.324738 AGTCAGAGAGGGCCATTCGA 60.325 55.000 6.18 2.33 0.00 3.71
73 74 0.760945 AGAGGGCCATTCGACTAGGG 60.761 60.000 6.18 0.00 0.00 3.53
107 108 0.541863 GTGATGGATGAGGTCGGGTT 59.458 55.000 0.00 0.00 0.00 4.11
160 161 4.697756 TTCGCTCGCCCCAACCAG 62.698 66.667 0.00 0.00 0.00 4.00
220 221 1.001631 TCGAAGAGGGCCATCTGGA 59.998 57.895 22.78 18.33 37.39 3.86
236 237 4.119556 TCTGGACAGAGATCCCGATAAT 57.880 45.455 0.00 0.00 38.06 1.28
252 253 3.495100 CGATAATAAGAGGCCAGCTGGTT 60.495 47.826 32.81 21.79 37.57 3.67
295 296 1.401018 GCGGTTTTGAAGGATGTTCGG 60.401 52.381 0.00 0.00 0.00 4.30
306 307 6.703319 TGAAGGATGTTCGGTATTTAAGACA 58.297 36.000 0.00 0.00 0.00 3.41
311 312 6.691388 GGATGTTCGGTATTTAAGACAATTGC 59.309 38.462 5.05 0.00 0.00 3.56
312 313 6.561737 TGTTCGGTATTTAAGACAATTGCA 57.438 33.333 5.05 0.00 0.00 4.08
353 354 5.726397 TGTTTTAGGCTACACGTCATACAT 58.274 37.500 0.00 0.00 0.00 2.29
363 364 2.028763 CACGTCATACATAACGCACACC 59.971 50.000 0.00 0.00 42.47 4.16
366 367 1.205179 TCATACATAACGCACACCGGT 59.795 47.619 0.00 0.00 42.52 5.28
387 388 0.243907 TTCCTCTCGCTTCGTCTTGG 59.756 55.000 0.00 0.00 0.00 3.61
417 418 0.659957 CTAGATCGCCTTTTGCCTGC 59.340 55.000 0.00 0.00 36.24 4.85
419 420 1.028868 AGATCGCCTTTTGCCTGCTC 61.029 55.000 0.00 0.00 36.24 4.26
423 424 3.752339 CCTTTTGCCTGCTCCCGC 61.752 66.667 0.00 0.00 0.00 6.13
424 425 2.985282 CTTTTGCCTGCTCCCGCA 60.985 61.111 0.00 0.00 45.60 5.69
447 449 1.724018 CGACAGTCGAACACGTCTACC 60.724 57.143 18.63 0.00 43.74 3.18
489 491 1.817099 CGCATCCTGCCCTGTTCTC 60.817 63.158 0.00 0.00 41.12 2.87
504 506 2.305635 TGTTCTCTGGCCTCAATAAGCA 59.694 45.455 3.32 0.00 0.00 3.91
516 518 5.737922 GCCTCAATAAGCATGCAATTCATCA 60.738 40.000 21.98 2.59 31.79 3.07
521 523 8.147704 TCAATAAGCATGCAATTCATCATCAAT 58.852 29.630 21.98 0.00 31.79 2.57
526 528 5.516090 CATGCAATTCATCATCAATCGACA 58.484 37.500 0.00 0.00 31.79 4.35
558 560 0.838987 TTCGGGTGGGTAGCTCCTTT 60.839 55.000 0.00 0.00 36.25 3.11
562 564 0.400594 GGTGGGTAGCTCCTTTGTGT 59.599 55.000 0.00 0.00 36.25 3.72
586 589 6.000891 TCGTGTTCTCTTCCATTTGAAATG 57.999 37.500 10.84 10.84 31.06 2.32
587 590 5.530915 TCGTGTTCTCTTCCATTTGAAATGT 59.469 36.000 15.93 0.00 31.06 2.71
613 616 3.408851 GTTTCGTCGCCGTGGTCC 61.409 66.667 0.00 0.00 35.01 4.46
625 628 2.033448 TGGTCCACCATTGCCGTC 59.967 61.111 0.00 0.00 42.01 4.79
676 679 0.391661 ATCGCGATCCTTTGTGCACT 60.392 50.000 17.62 0.00 0.00 4.40
870 1569 4.894784 TCCAAGAGCTCTAACGAAAATGT 58.105 39.130 18.59 0.00 0.00 2.71
919 1618 6.261603 TGAATCTAAACTCGGAATCGCTACTA 59.738 38.462 0.00 0.00 36.13 1.82
928 1627 0.953003 AATCGCTACTACTCCTCGGC 59.047 55.000 0.00 0.00 0.00 5.54
929 1628 0.108963 ATCGCTACTACTCCTCGGCT 59.891 55.000 0.00 0.00 0.00 5.52
930 1629 0.532417 TCGCTACTACTCCTCGGCTC 60.532 60.000 0.00 0.00 0.00 4.70
931 1630 0.814410 CGCTACTACTCCTCGGCTCA 60.814 60.000 0.00 0.00 0.00 4.26
932 1631 0.664224 GCTACTACTCCTCGGCTCAC 59.336 60.000 0.00 0.00 0.00 3.51
933 1632 1.310904 CTACTACTCCTCGGCTCACC 58.689 60.000 0.00 0.00 0.00 4.02
934 1633 0.622136 TACTACTCCTCGGCTCACCA 59.378 55.000 0.00 0.00 34.57 4.17
954 1653 1.347097 CTGATGTCACCGACACGCTG 61.347 60.000 0.00 0.00 45.65 5.18
1202 1901 1.520666 CGAATAAGGTGACGCCCCT 59.479 57.895 0.08 0.00 38.26 4.79
1212 1911 1.299976 GACGCCCCTCAACCTGATT 59.700 57.895 0.00 0.00 0.00 2.57
1255 1954 0.324943 TGCCCTCTACTGCCTTCAAC 59.675 55.000 0.00 0.00 0.00 3.18
1268 1974 3.008375 TGCCTTCAACTATTCTGTGCTCT 59.992 43.478 0.00 0.00 0.00 4.09
1304 2010 3.951680 TGTGCGATTACTGAGATCTGGTA 59.048 43.478 0.00 0.11 0.00 3.25
1333 2039 3.410631 TTTTCCTATTGAGGTGTGCGA 57.589 42.857 0.00 0.00 44.19 5.10
1335 2041 3.627395 TTCCTATTGAGGTGTGCGATT 57.373 42.857 0.00 0.00 44.19 3.34
1336 2042 4.746535 TTCCTATTGAGGTGTGCGATTA 57.253 40.909 0.00 0.00 44.19 1.75
1337 2043 4.955811 TCCTATTGAGGTGTGCGATTAT 57.044 40.909 0.00 0.00 44.19 1.28
1338 2044 6.413783 TTCCTATTGAGGTGTGCGATTATA 57.586 37.500 0.00 0.00 44.19 0.98
1339 2045 6.605471 TCCTATTGAGGTGTGCGATTATAT 57.395 37.500 0.00 0.00 44.19 0.86
1340 2046 7.004555 TCCTATTGAGGTGTGCGATTATATT 57.995 36.000 0.00 0.00 44.19 1.28
1341 2047 6.873605 TCCTATTGAGGTGTGCGATTATATTG 59.126 38.462 0.00 0.00 44.19 1.90
1342 2048 6.873605 CCTATTGAGGTGTGCGATTATATTGA 59.126 38.462 0.00 0.00 38.16 2.57
1343 2049 5.984233 TTGAGGTGTGCGATTATATTGAC 57.016 39.130 0.00 0.00 0.00 3.18
1344 2050 4.377021 TGAGGTGTGCGATTATATTGACC 58.623 43.478 0.00 0.00 0.00 4.02
1345 2051 4.100963 TGAGGTGTGCGATTATATTGACCT 59.899 41.667 0.00 0.00 35.24 3.85
1348 2054 4.449068 GGTGTGCGATTATATTGACCTCTG 59.551 45.833 0.00 0.00 0.00 3.35
1356 2062 5.537300 TTATATTGACCTCTGCACTCTCC 57.463 43.478 0.00 0.00 0.00 3.71
1388 2094 4.347607 AGTAGAAATTCATTTGCTGCCCT 58.652 39.130 0.00 0.00 0.00 5.19
1392 2098 0.616679 ATTCATTTGCTGCCCTGCCT 60.617 50.000 0.00 0.00 0.00 4.75
1393 2099 1.252904 TTCATTTGCTGCCCTGCCTC 61.253 55.000 0.00 0.00 0.00 4.70
1394 2100 1.681327 CATTTGCTGCCCTGCCTCT 60.681 57.895 0.00 0.00 0.00 3.69
1395 2101 0.394762 CATTTGCTGCCCTGCCTCTA 60.395 55.000 0.00 0.00 0.00 2.43
1396 2102 0.106819 ATTTGCTGCCCTGCCTCTAG 60.107 55.000 0.00 0.00 0.00 2.43
1397 2103 2.202236 TTTGCTGCCCTGCCTCTAGG 62.202 60.000 0.00 0.00 37.59 3.02
1460 2166 2.105006 AATGCAGTTCACTCGAGCAT 57.895 45.000 13.61 6.27 46.86 3.79
1468 2174 0.817654 TCACTCGAGCATCCATCGTT 59.182 50.000 13.61 0.00 40.95 3.85
1481 2187 4.582701 TCCATCGTTTGCTTGATTGTTT 57.417 36.364 0.00 0.00 0.00 2.83
1494 2200 5.351189 GCTTGATTGTTTGGTGTGAACTTTT 59.649 36.000 0.00 0.00 0.00 2.27
1498 2204 8.472683 TGATTGTTTGGTGTGAACTTTTAAAG 57.527 30.769 2.81 2.81 0.00 1.85
1516 2222 3.942130 AAGTTGGTTATGCTTGCTTCC 57.058 42.857 0.00 0.00 0.00 3.46
1540 2246 3.062639 GTGGCAATGTAGATGTTCGAGTG 59.937 47.826 0.00 0.00 0.00 3.51
1578 2288 4.279169 ACTGATTTCTGGTTGGTCATGTTG 59.721 41.667 0.00 0.00 0.00 3.33
1588 2298 0.038892 GGTCATGTTGCTTGGCTGTG 60.039 55.000 0.00 0.00 0.00 3.66
1632 2343 8.256356 ACTGAATATCTTATAGAACTGCTGGT 57.744 34.615 0.00 0.00 0.00 4.00
1650 2361 4.675510 CTGGTGAAATGGCAATGTACATC 58.324 43.478 9.23 0.00 0.00 3.06
1662 2373 1.200519 TGTACATCCACTGGTAGGCC 58.799 55.000 0.00 0.00 0.00 5.19
1670 2381 1.545582 CCACTGGTAGGCCATTGTTTG 59.454 52.381 5.01 0.00 45.05 2.93
1673 2384 3.069443 CACTGGTAGGCCATTGTTTGTTT 59.931 43.478 5.01 0.00 45.05 2.83
1674 2385 3.709141 ACTGGTAGGCCATTGTTTGTTTT 59.291 39.130 5.01 0.00 45.05 2.43
1681 2392 4.401837 AGGCCATTGTTTGTTTTGCAATTT 59.598 33.333 5.01 0.00 36.89 1.82
1682 2393 4.503370 GGCCATTGTTTGTTTTGCAATTTG 59.497 37.500 0.00 0.00 36.89 2.32
1760 2471 6.538945 TGTTGTGACTAGATTGCTATGGTA 57.461 37.500 0.00 0.00 0.00 3.25
1763 2474 8.700973 TGTTGTGACTAGATTGCTATGGTATAA 58.299 33.333 0.00 0.00 0.00 0.98
1764 2475 9.712305 GTTGTGACTAGATTGCTATGGTATAAT 57.288 33.333 0.00 0.00 0.00 1.28
1877 2590 2.243602 ACAGCAAACAAAGGGCAATG 57.756 45.000 0.00 0.00 0.00 2.82
2257 2972 5.047802 AGTTTTGGTATCTGAATGGTTGCAG 60.048 40.000 0.00 0.00 0.00 4.41
2260 2975 3.019564 GGTATCTGAATGGTTGCAGCTT 58.980 45.455 0.00 0.00 32.27 3.74
2289 3004 8.706521 TCAGTCTGTACTCTGTACACTATAGAT 58.293 37.037 6.78 0.00 31.97 1.98
2356 3071 0.390735 AAGCGTGCCCTTACTTACCG 60.391 55.000 0.00 0.00 0.00 4.02
2418 3133 9.964354 TTGCATGACCTCATTATAAATAGCTAT 57.036 29.630 0.00 0.00 33.61 2.97
2918 3633 4.079844 TGCATGGTCCTATTCTTCCATTGA 60.080 41.667 0.00 0.00 38.43 2.57
2955 3670 5.673337 TTTTGGAGTCTGAAGATTTGACG 57.327 39.130 0.00 0.00 36.01 4.35
3073 3793 1.905215 AGGACAGACATGAACCTGGAG 59.095 52.381 0.00 0.00 36.19 3.86
3120 3840 1.407979 GATGGGAAAGCATTGGAGCAG 59.592 52.381 0.00 0.00 36.85 4.24
3147 3867 1.133009 AGGAGCGAGATACCAATCCCT 60.133 52.381 0.00 0.00 31.98 4.20
3178 3898 4.466726 GTCCACATAGGTCTGTTACTTCCT 59.533 45.833 0.00 0.00 39.02 3.36
3208 3928 5.414144 TGTGACATCTGTTGTTGTTCTTTGA 59.586 36.000 0.00 0.00 39.18 2.69
3248 3968 8.106247 AGATTCCTATATCGTCTTGACTTCTC 57.894 38.462 0.00 0.00 0.00 2.87
3281 4001 7.280205 TCACTTTCTGGTGTCTTTAAACTCTTC 59.720 37.037 0.00 0.00 38.28 2.87
3316 4049 8.755696 TGGCAATACATTTTCTGTTAATCAAC 57.244 30.769 0.00 0.00 39.39 3.18
3610 4343 9.350357 CATGATGGAGAAAGTTGTTCATTTTAG 57.650 33.333 0.00 0.00 0.00 1.85
3612 4345 9.300681 TGATGGAGAAAGTTGTTCATTTTAGAT 57.699 29.630 0.00 0.00 0.00 1.98
3742 4475 3.113260 ACTAGTGTGGACTGCAGTTTC 57.887 47.619 22.65 16.60 33.21 2.78
3751 4484 3.182967 GGACTGCAGTTTCGATACAGAG 58.817 50.000 22.65 3.65 32.67 3.35
3770 4503 4.991687 CAGAGGACAGGTCTGTTTTTCTAC 59.008 45.833 5.02 0.00 45.05 2.59
3781 4514 6.643770 GGTCTGTTTTTCTACGAGTGATTGTA 59.356 38.462 0.00 0.00 0.00 2.41
3862 4595 7.973048 ATCGTATGGTACCATAATAGGATGT 57.027 36.000 31.64 9.19 40.15 3.06
3915 4648 6.635641 TCGCGTGTTTATCAACATAGATACTC 59.364 38.462 5.77 0.00 44.85 2.59
4035 4768 2.158900 GCCTATGCAGATGGTGTACAGT 60.159 50.000 0.00 0.00 37.47 3.55
4206 4939 4.104102 AGAATGACCTTGGTTGGTGAAGTA 59.896 41.667 0.00 0.00 41.00 2.24
4317 5051 4.374689 TGGGAAAATGTTGTGCTAGGTA 57.625 40.909 0.00 0.00 0.00 3.08
4373 5107 7.170828 GTGGTGTTTTCTCTGTTTCTTGTTTTT 59.829 33.333 0.00 0.00 0.00 1.94
4469 5204 9.836864 AATAATATGATGCTAACAGAACTGTGA 57.163 29.630 8.25 0.00 44.13 3.58
4772 5507 7.484324 GCAGAGCATTCTTTCAGTATTCTTTTC 59.516 37.037 0.00 0.00 0.00 2.29
4783 5518 8.483307 TTCAGTATTCTTTTCGGTACATAACC 57.517 34.615 0.00 0.00 45.77 2.85
4836 5571 9.444600 AGTTAGTTTATTGTCATACGAATTGGT 57.555 29.630 0.00 0.00 0.00 3.67
4872 5915 4.142315 GCACTTTCACATCATGCCACTTAT 60.142 41.667 0.00 0.00 0.00 1.73
4889 5932 7.990314 TGCCACTTATTCTGTTGTATGCTTATA 59.010 33.333 0.00 0.00 0.00 0.98
4974 6018 9.190858 CTATGCTGATGTTCTAATCTTGTACTC 57.809 37.037 0.00 0.00 0.00 2.59
4975 6019 6.341316 TGCTGATGTTCTAATCTTGTACTCC 58.659 40.000 0.00 0.00 0.00 3.85
4976 6020 6.155221 TGCTGATGTTCTAATCTTGTACTCCT 59.845 38.462 0.00 0.00 0.00 3.69
4977 6021 7.342026 TGCTGATGTTCTAATCTTGTACTCCTA 59.658 37.037 0.00 0.00 0.00 2.94
4982 6026 5.776173 TCTAATCTTGTACTCCTAGCTGC 57.224 43.478 0.00 0.00 0.00 5.25
4992 6036 3.370104 ACTCCTAGCTGCAACAGATACT 58.630 45.455 1.02 0.00 32.44 2.12
5020 6064 5.529060 ACTCTTGTGTTTCTTGATGTTCCTC 59.471 40.000 0.00 0.00 0.00 3.71
5060 6104 5.741011 AGCAATTCGTGGGAGAAAAGTATA 58.259 37.500 0.00 0.00 33.43 1.47
5153 6302 3.449018 TGAGAGGTGTTCAGATAAGAGGC 59.551 47.826 0.00 0.00 0.00 4.70
5184 6333 3.002348 GGTAGTTTTCATATGCACTCCGC 59.998 47.826 0.00 0.00 42.89 5.54
5223 6372 2.982488 ACCTCTCATCCAAACACCTTCT 59.018 45.455 0.00 0.00 0.00 2.85
5229 6378 4.906618 TCATCCAAACACCTTCTAAGACC 58.093 43.478 0.00 0.00 0.00 3.85
5235 6384 5.368989 CAAACACCTTCTAAGACCAAGACT 58.631 41.667 0.00 0.00 0.00 3.24
5240 6389 8.431910 ACACCTTCTAAGACCAAGACTTATTA 57.568 34.615 0.00 0.00 30.96 0.98
5336 6485 5.067936 CGTCATCTTGACCTATTCCTACAGT 59.932 44.000 2.26 0.00 44.20 3.55
5363 6512 6.706055 TTTTTGCGAGATCAACAGTACTAG 57.294 37.500 0.00 0.00 0.00 2.57
5364 6513 5.386958 TTTGCGAGATCAACAGTACTAGT 57.613 39.130 0.00 0.00 0.00 2.57
5365 6514 5.386958 TTGCGAGATCAACAGTACTAGTT 57.613 39.130 0.00 0.00 0.00 2.24
5366 6515 5.386958 TGCGAGATCAACAGTACTAGTTT 57.613 39.130 0.00 0.00 0.00 2.66
5367 6516 6.505044 TGCGAGATCAACAGTACTAGTTTA 57.495 37.500 0.00 0.00 0.00 2.01
5370 6519 7.701078 TGCGAGATCAACAGTACTAGTTTATTC 59.299 37.037 0.00 0.71 0.00 1.75
5371 6520 7.167801 GCGAGATCAACAGTACTAGTTTATTCC 59.832 40.741 0.00 0.00 0.00 3.01
5372 6521 8.188799 CGAGATCAACAGTACTAGTTTATTCCA 58.811 37.037 0.00 0.00 0.00 3.53
5373 6522 9.871238 GAGATCAACAGTACTAGTTTATTCCAA 57.129 33.333 0.00 0.00 0.00 3.53
5377 6526 9.280174 TCAACAGTACTAGTTTATTCCAAAAGG 57.720 33.333 0.00 0.00 0.00 3.11
5378 6527 9.063615 CAACAGTACTAGTTTATTCCAAAAGGT 57.936 33.333 0.00 0.00 0.00 3.50
5379 6528 9.636789 AACAGTACTAGTTTATTCCAAAAGGTT 57.363 29.630 0.00 0.00 0.00 3.50
5382 6531 9.955102 AGTACTAGTTTATTCCAAAAGGTTAGG 57.045 33.333 0.00 0.00 0.00 2.69
5383 6532 9.170734 GTACTAGTTTATTCCAAAAGGTTAGGG 57.829 37.037 0.00 0.00 0.00 3.53
5384 6533 5.995565 AGTTTATTCCAAAAGGTTAGGGC 57.004 39.130 0.00 0.00 0.00 5.19
5385 6534 5.651303 AGTTTATTCCAAAAGGTTAGGGCT 58.349 37.500 0.00 0.00 0.00 5.19
5386 6535 6.796648 AGTTTATTCCAAAAGGTTAGGGCTA 58.203 36.000 0.00 0.00 0.00 3.93
5387 6536 6.662234 AGTTTATTCCAAAAGGTTAGGGCTAC 59.338 38.462 0.00 0.00 0.00 3.58
5388 6537 4.668138 ATTCCAAAAGGTTAGGGCTACA 57.332 40.909 0.00 0.00 0.00 2.74
5389 6538 4.456662 TTCCAAAAGGTTAGGGCTACAA 57.543 40.909 0.00 0.00 0.00 2.41
5390 6539 4.668138 TCCAAAAGGTTAGGGCTACAAT 57.332 40.909 0.00 0.00 0.00 2.71
5391 6540 4.595986 TCCAAAAGGTTAGGGCTACAATC 58.404 43.478 0.00 0.00 0.00 2.67
5392 6541 3.699538 CCAAAAGGTTAGGGCTACAATCC 59.300 47.826 0.00 0.00 0.00 3.01
5393 6542 4.340617 CAAAAGGTTAGGGCTACAATCCA 58.659 43.478 0.00 0.00 0.00 3.41
5394 6543 4.668138 AAAGGTTAGGGCTACAATCCAA 57.332 40.909 0.00 0.00 0.00 3.53
5395 6544 3.933861 AGGTTAGGGCTACAATCCAAG 57.066 47.619 0.00 0.00 0.00 3.61
5396 6545 2.509964 AGGTTAGGGCTACAATCCAAGG 59.490 50.000 0.00 0.00 0.00 3.61
5397 6546 2.422945 GGTTAGGGCTACAATCCAAGGG 60.423 54.545 0.00 0.00 0.00 3.95
5398 6547 0.843984 TAGGGCTACAATCCAAGGGC 59.156 55.000 0.00 0.00 0.00 5.19
5399 6548 1.214305 AGGGCTACAATCCAAGGGCA 61.214 55.000 0.00 0.00 0.00 5.36
5400 6549 0.324275 GGGCTACAATCCAAGGGCAA 60.324 55.000 0.00 0.00 0.00 4.52
5401 6550 1.106285 GGCTACAATCCAAGGGCAAG 58.894 55.000 0.00 0.00 0.00 4.01
5402 6551 1.340991 GGCTACAATCCAAGGGCAAGA 60.341 52.381 0.00 0.00 0.00 3.02
5403 6552 2.019984 GCTACAATCCAAGGGCAAGAG 58.980 52.381 0.00 0.00 0.00 2.85
5404 6553 2.619074 GCTACAATCCAAGGGCAAGAGT 60.619 50.000 0.00 0.00 0.00 3.24
5405 6554 2.683211 ACAATCCAAGGGCAAGAGTT 57.317 45.000 0.00 0.00 0.00 3.01
5406 6555 2.519013 ACAATCCAAGGGCAAGAGTTC 58.481 47.619 0.00 0.00 0.00 3.01
5407 6556 2.108952 ACAATCCAAGGGCAAGAGTTCT 59.891 45.455 0.00 0.00 0.00 3.01
5408 6557 3.160269 CAATCCAAGGGCAAGAGTTCTT 58.840 45.455 0.00 0.00 36.45 2.52
5409 6558 2.568623 TCCAAGGGCAAGAGTTCTTC 57.431 50.000 0.00 0.00 33.11 2.87
5410 6559 1.774254 TCCAAGGGCAAGAGTTCTTCA 59.226 47.619 0.00 0.00 33.11 3.02
5411 6560 2.174639 TCCAAGGGCAAGAGTTCTTCAA 59.825 45.455 0.00 0.00 33.11 2.69
5412 6561 3.160269 CCAAGGGCAAGAGTTCTTCAAT 58.840 45.455 0.00 0.00 33.11 2.57
5413 6562 4.042809 TCCAAGGGCAAGAGTTCTTCAATA 59.957 41.667 0.00 0.00 33.11 1.90
5414 6563 4.156739 CCAAGGGCAAGAGTTCTTCAATAC 59.843 45.833 0.00 0.00 33.11 1.89
5415 6564 4.640771 AGGGCAAGAGTTCTTCAATACA 57.359 40.909 0.00 0.00 33.11 2.29
5416 6565 5.184892 AGGGCAAGAGTTCTTCAATACAT 57.815 39.130 0.00 0.00 33.11 2.29
5417 6566 4.946157 AGGGCAAGAGTTCTTCAATACATG 59.054 41.667 0.00 0.00 33.11 3.21
5428 6577 6.544928 TCTTCAATACATGGACTTGAGCTA 57.455 37.500 0.00 0.00 31.11 3.32
5442 6591 5.368145 ACTTGAGCTATTTCAACTCACACA 58.632 37.500 0.00 0.00 40.03 3.72
5491 6640 1.679139 TGGCAAGTGTTGTTCTCTGG 58.321 50.000 0.00 0.00 0.00 3.86
5567 6716 6.093495 GGTTCCTTGTGATTACGATGATCAAA 59.907 38.462 0.00 0.00 35.46 2.69
5583 6732 9.919348 CGATGATCAAAACATTTTTGTTTTCTT 57.081 25.926 12.51 5.04 46.44 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.925170 AGACGGCCTTGAGCACCT 60.925 61.111 0.00 0.00 46.50 4.00
1 2 2.527951 ATCAGACGGCCTTGAGCACC 62.528 60.000 0.00 0.00 46.50 5.01
2 3 0.674895 AATCAGACGGCCTTGAGCAC 60.675 55.000 0.00 0.00 46.50 4.40
3 4 0.036732 AAATCAGACGGCCTTGAGCA 59.963 50.000 0.00 0.00 46.50 4.26
5 6 0.449388 GCAAATCAGACGGCCTTGAG 59.551 55.000 0.00 0.00 0.00 3.02
6 7 0.250684 TGCAAATCAGACGGCCTTGA 60.251 50.000 0.00 2.16 0.00 3.02
7 8 0.813184 ATGCAAATCAGACGGCCTTG 59.187 50.000 0.00 0.00 0.00 3.61
8 9 1.098050 GATGCAAATCAGACGGCCTT 58.902 50.000 0.00 0.00 0.00 4.35
9 10 0.254178 AGATGCAAATCAGACGGCCT 59.746 50.000 0.00 0.00 0.00 5.19
10 11 1.098050 AAGATGCAAATCAGACGGCC 58.902 50.000 0.00 0.00 0.00 6.13
11 12 2.286654 GCTAAGATGCAAATCAGACGGC 60.287 50.000 0.00 0.00 0.00 5.68
12 13 2.033407 CGCTAAGATGCAAATCAGACGG 60.033 50.000 0.00 0.00 0.00 4.79
13 14 2.598439 GCGCTAAGATGCAAATCAGACG 60.598 50.000 0.00 0.00 0.00 4.18
14 15 2.598439 CGCGCTAAGATGCAAATCAGAC 60.598 50.000 5.56 0.00 0.00 3.51
15 16 1.594397 CGCGCTAAGATGCAAATCAGA 59.406 47.619 5.56 0.00 0.00 3.27
16 17 1.328680 ACGCGCTAAGATGCAAATCAG 59.671 47.619 5.73 0.00 0.00 2.90
17 18 1.368641 ACGCGCTAAGATGCAAATCA 58.631 45.000 5.73 0.00 0.00 2.57
18 19 3.242284 TGTTACGCGCTAAGATGCAAATC 60.242 43.478 5.73 0.00 0.00 2.17
19 20 2.675844 TGTTACGCGCTAAGATGCAAAT 59.324 40.909 5.73 0.00 0.00 2.32
20 21 2.070028 TGTTACGCGCTAAGATGCAAA 58.930 42.857 5.73 0.00 0.00 3.68
21 22 1.658596 CTGTTACGCGCTAAGATGCAA 59.341 47.619 5.73 0.00 0.00 4.08
22 23 1.277326 CTGTTACGCGCTAAGATGCA 58.723 50.000 5.73 0.00 0.00 3.96
23 24 1.255600 GACTGTTACGCGCTAAGATGC 59.744 52.381 5.73 0.00 0.00 3.91
24 25 1.513178 CGACTGTTACGCGCTAAGATG 59.487 52.381 5.73 0.00 0.00 2.90
25 26 1.533338 CCGACTGTTACGCGCTAAGAT 60.533 52.381 5.73 0.00 0.00 2.40
26 27 0.179181 CCGACTGTTACGCGCTAAGA 60.179 55.000 5.73 2.02 0.00 2.10
27 28 1.138047 CCCGACTGTTACGCGCTAAG 61.138 60.000 5.73 0.90 0.00 2.18
28 29 1.153978 CCCGACTGTTACGCGCTAA 60.154 57.895 5.73 1.01 0.00 3.09
29 30 1.024046 TACCCGACTGTTACGCGCTA 61.024 55.000 5.73 0.00 0.00 4.26
30 31 2.262471 CTACCCGACTGTTACGCGCT 62.262 60.000 5.73 0.00 0.00 5.92
31 32 1.870901 CTACCCGACTGTTACGCGC 60.871 63.158 5.73 0.00 0.00 6.86
32 33 0.522076 GACTACCCGACTGTTACGCG 60.522 60.000 3.53 3.53 0.00 6.01
37 38 2.438411 CTCTCTGACTACCCGACTGTT 58.562 52.381 0.00 0.00 0.00 3.16
48 49 0.324738 TCGAATGGCCCTCTCTGACT 60.325 55.000 0.00 0.00 0.00 3.41
81 82 1.226688 CTCATCCATCACGCGTCGT 60.227 57.895 9.86 0.00 42.36 4.34
88 89 0.541863 AACCCGACCTCATCCATCAC 59.458 55.000 0.00 0.00 0.00 3.06
89 90 0.830648 GAACCCGACCTCATCCATCA 59.169 55.000 0.00 0.00 0.00 3.07
107 108 0.598419 CGATGAATGCTAGCAGGCGA 60.598 55.000 23.89 7.25 34.52 5.54
152 153 4.700448 TGCATGGGCCTGGTTGGG 62.700 66.667 4.53 0.00 40.13 4.12
220 221 4.464597 GCCTCTTATTATCGGGATCTCTGT 59.535 45.833 0.00 0.00 0.00 3.41
224 225 3.772025 CTGGCCTCTTATTATCGGGATCT 59.228 47.826 3.32 0.00 0.00 2.75
236 237 0.615331 CTGAACCAGCTGGCCTCTTA 59.385 55.000 33.06 13.04 39.32 2.10
252 253 1.148273 GGATATGGTTGGCCGCTGA 59.852 57.895 0.00 0.00 37.67 4.26
282 283 6.703319 TGTCTTAAATACCGAACATCCTTCA 58.297 36.000 0.00 0.00 0.00 3.02
306 307 7.336931 ACAACGAACTTATAGGAAGATGCAATT 59.663 33.333 0.00 0.00 0.00 2.32
312 313 9.379791 CCTAAAACAACGAACTTATAGGAAGAT 57.620 33.333 0.00 0.00 32.25 2.40
353 354 1.005867 GGAAGACCGGTGTGCGTTA 60.006 57.895 14.63 0.00 0.00 3.18
363 364 1.226435 CGAAGCGAGAGGAAGACCG 60.226 63.158 0.00 0.00 41.83 4.79
366 367 1.200252 CAAGACGAAGCGAGAGGAAGA 59.800 52.381 0.00 0.00 0.00 2.87
399 400 0.253044 AGCAGGCAAAAGGCGATCTA 59.747 50.000 0.00 0.00 46.16 1.98
417 418 2.372690 CGACTGTCGTTTGCGGGAG 61.373 63.158 21.30 0.00 38.89 4.30
419 420 1.952133 TTCGACTGTCGTTTGCGGG 60.952 57.895 27.16 0.00 41.35 6.13
423 424 0.918619 ACGTGTTCGACTGTCGTTTG 59.081 50.000 27.16 16.47 41.35 2.93
424 425 1.194495 GACGTGTTCGACTGTCGTTT 58.806 50.000 27.16 8.50 41.35 3.60
425 426 0.379669 AGACGTGTTCGACTGTCGTT 59.620 50.000 27.16 8.18 41.35 3.85
489 491 1.395635 TGCATGCTTATTGAGGCCAG 58.604 50.000 20.33 0.00 0.00 4.85
504 506 5.761165 TGTCGATTGATGATGAATTGCAT 57.239 34.783 0.00 0.00 40.77 3.96
558 560 2.971660 TGGAAGAGAACACGAACACA 57.028 45.000 0.00 0.00 0.00 3.72
562 564 6.039270 ACATTTCAAATGGAAGAGAACACGAA 59.961 34.615 14.70 0.00 36.72 3.85
586 589 4.405173 GACGAAACGGCGCGACAC 62.405 66.667 14.85 0.00 33.86 3.67
651 654 1.066143 ACAAAGGATCGCGATGGTCTT 60.066 47.619 29.09 21.92 0.00 3.01
793 1488 2.084546 GAGCATCACCAACAGTTACCC 58.915 52.381 0.00 0.00 33.17 3.69
837 1534 5.520748 AGAGCTCTTGGAATTTTTAGGGA 57.479 39.130 11.45 0.00 0.00 4.20
844 1543 6.877611 TTTTCGTTAGAGCTCTTGGAATTT 57.122 33.333 23.84 0.00 0.00 1.82
870 1569 1.149361 ACGCGCAGAGAACAAAACGA 61.149 50.000 5.73 0.00 0.00 3.85
919 1618 2.118513 AGTGGTGAGCCGAGGAGT 59.881 61.111 0.00 0.00 37.67 3.85
928 1627 0.603065 TCGGTGACATCAGTGGTGAG 59.397 55.000 11.21 0.00 35.66 3.51
929 1628 0.317160 GTCGGTGACATCAGTGGTGA 59.683 55.000 11.21 0.00 37.02 4.02
930 1629 0.033366 TGTCGGTGACATCAGTGGTG 59.967 55.000 0.57 0.57 37.67 4.17
931 1630 0.033504 GTGTCGGTGACATCAGTGGT 59.966 55.000 2.62 0.00 44.63 4.16
932 1631 1.008875 CGTGTCGGTGACATCAGTGG 61.009 60.000 2.62 0.00 44.63 4.00
933 1632 1.617755 GCGTGTCGGTGACATCAGTG 61.618 60.000 2.62 0.00 44.63 3.66
934 1633 1.372997 GCGTGTCGGTGACATCAGT 60.373 57.895 2.62 0.00 44.63 3.41
1141 1840 0.241481 GGGCGAGTGGAGATATCGAC 59.759 60.000 0.00 0.00 43.77 4.20
1184 1883 0.529992 GAGGGGCGTCACCTTATTCG 60.530 60.000 2.09 0.00 38.79 3.34
1186 1885 0.988832 TTGAGGGGCGTCACCTTATT 59.011 50.000 2.09 0.00 38.79 1.40
1187 1886 0.252197 GTTGAGGGGCGTCACCTTAT 59.748 55.000 2.09 0.00 38.79 1.73
1188 1887 1.675219 GTTGAGGGGCGTCACCTTA 59.325 57.895 2.09 0.00 38.79 2.69
1202 1901 8.203485 GCCCAATAATCATAAAAATCAGGTTGA 58.797 33.333 0.00 0.00 0.00 3.18
1212 1911 5.893255 AGACAGCAGCCCAATAATCATAAAA 59.107 36.000 0.00 0.00 0.00 1.52
1268 1974 2.282110 CACACCCCGACAATGCCA 60.282 61.111 0.00 0.00 0.00 4.92
1273 1979 0.671163 GTAATCGCACACCCCGACAA 60.671 55.000 0.00 0.00 37.56 3.18
1318 2024 7.148573 GGTCAATATAATCGCACACCTCAATAG 60.149 40.741 0.00 0.00 0.00 1.73
1319 2025 6.649141 GGTCAATATAATCGCACACCTCAATA 59.351 38.462 0.00 0.00 0.00 1.90
1320 2026 5.470098 GGTCAATATAATCGCACACCTCAAT 59.530 40.000 0.00 0.00 0.00 2.57
1322 2028 4.100963 AGGTCAATATAATCGCACACCTCA 59.899 41.667 0.00 0.00 0.00 3.86
1323 2029 4.632153 AGGTCAATATAATCGCACACCTC 58.368 43.478 0.00 0.00 0.00 3.85
1324 2030 4.345257 AGAGGTCAATATAATCGCACACCT 59.655 41.667 0.00 0.00 35.65 4.00
1325 2031 4.449068 CAGAGGTCAATATAATCGCACACC 59.551 45.833 0.00 0.00 0.00 4.16
1326 2032 4.084328 GCAGAGGTCAATATAATCGCACAC 60.084 45.833 0.00 0.00 0.00 3.82
1327 2033 4.058124 GCAGAGGTCAATATAATCGCACA 58.942 43.478 0.00 0.00 0.00 4.57
1328 2034 4.058124 TGCAGAGGTCAATATAATCGCAC 58.942 43.478 0.00 0.00 0.00 5.34
1330 2036 4.310769 AGTGCAGAGGTCAATATAATCGC 58.689 43.478 0.00 0.00 0.00 4.58
1331 2037 5.777802 AGAGTGCAGAGGTCAATATAATCG 58.222 41.667 0.00 0.00 0.00 3.34
1332 2038 6.162777 GGAGAGTGCAGAGGTCAATATAATC 58.837 44.000 0.00 0.00 0.00 1.75
1333 2039 5.279206 CGGAGAGTGCAGAGGTCAATATAAT 60.279 44.000 0.00 0.00 0.00 1.28
1335 2041 3.570125 CGGAGAGTGCAGAGGTCAATATA 59.430 47.826 0.00 0.00 0.00 0.86
1336 2042 2.363680 CGGAGAGTGCAGAGGTCAATAT 59.636 50.000 0.00 0.00 0.00 1.28
1337 2043 1.751351 CGGAGAGTGCAGAGGTCAATA 59.249 52.381 0.00 0.00 0.00 1.90
1338 2044 0.534412 CGGAGAGTGCAGAGGTCAAT 59.466 55.000 0.00 0.00 0.00 2.57
1339 2045 0.539669 TCGGAGAGTGCAGAGGTCAA 60.540 55.000 0.00 0.00 0.00 3.18
1340 2046 0.323816 ATCGGAGAGTGCAGAGGTCA 60.324 55.000 0.00 0.00 43.63 4.02
1341 2047 0.820871 AATCGGAGAGTGCAGAGGTC 59.179 55.000 0.00 0.00 43.63 3.85
1342 2048 2.983512 AATCGGAGAGTGCAGAGGT 58.016 52.632 0.00 0.00 43.63 3.85
1356 2062 5.998454 ATGAATTTCTACTCTGCCAATCG 57.002 39.130 0.00 0.00 0.00 3.34
1397 2103 1.528129 AGCACTTGAAGGCAGTAAGC 58.472 50.000 8.07 0.00 44.65 3.09
1398 2104 3.141398 TCAAGCACTTGAAGGCAGTAAG 58.859 45.455 10.58 0.00 45.56 2.34
1399 2105 3.207265 TCAAGCACTTGAAGGCAGTAA 57.793 42.857 10.58 0.00 45.56 2.24
1460 2166 4.297510 CAAACAATCAAGCAAACGATGGA 58.702 39.130 0.00 0.00 0.00 3.41
1468 2174 4.081752 AGTTCACACCAAACAATCAAGCAA 60.082 37.500 0.00 0.00 0.00 3.91
1494 2200 5.048083 CAGGAAGCAAGCATAACCAACTTTA 60.048 40.000 0.00 0.00 0.00 1.85
1498 2204 2.558359 ACAGGAAGCAAGCATAACCAAC 59.442 45.455 0.00 0.00 0.00 3.77
1516 2222 3.261580 TCGAACATCTACATTGCCACAG 58.738 45.455 0.00 0.00 0.00 3.66
1540 2246 7.020010 CAGAAATCAGTGTTCTGCAATTAGAC 58.980 38.462 9.75 0.00 43.94 2.59
1578 2288 0.322456 TATGACCACCACAGCCAAGC 60.322 55.000 0.00 0.00 0.00 4.01
1622 2332 0.961019 TGCCATTTCACCAGCAGTTC 59.039 50.000 0.00 0.00 0.00 3.01
1632 2343 4.158209 CAGTGGATGTACATTGCCATTTCA 59.842 41.667 16.86 0.00 32.26 2.69
1760 2471 9.729281 AGCAAATCAACTTGAAATCCAAATTAT 57.271 25.926 0.00 0.00 33.76 1.28
1763 2474 7.520937 GCAAGCAAATCAACTTGAAATCCAAAT 60.521 33.333 6.91 0.00 44.89 2.32
1764 2475 6.238429 GCAAGCAAATCAACTTGAAATCCAAA 60.238 34.615 6.91 0.00 44.89 3.28
1877 2590 2.092968 TGTCCATGGAACCTGTAGATGC 60.093 50.000 18.20 0.00 0.00 3.91
2218 2933 5.373222 ACCAAAACTACAGCAATAGTGTGA 58.627 37.500 1.04 0.00 35.53 3.58
2257 2972 3.983741 ACAGAGTACAGACTGACAAAGC 58.016 45.455 10.08 0.00 35.45 3.51
2260 2975 5.131067 AGTGTACAGAGTACAGACTGACAA 58.869 41.667 10.08 0.00 35.45 3.18
2373 3088 8.233868 TCATGCAACAACATTACATAGTACAAC 58.766 33.333 0.00 0.00 0.00 3.32
2418 3133 7.454260 ACTCAGCAATATGTATCGACTATCA 57.546 36.000 0.00 0.00 0.00 2.15
2459 3174 1.615392 GGAGAATTTTGCAGTGTGGCT 59.385 47.619 0.00 0.00 34.04 4.75
2714 3429 3.111098 GCCGTATTGTCCAGTTACTACG 58.889 50.000 0.00 0.00 33.61 3.51
2930 3645 7.117812 TCGTCAAATCTTCAGACTCCAAAATAC 59.882 37.037 0.00 0.00 0.00 1.89
2931 3646 7.158697 TCGTCAAATCTTCAGACTCCAAAATA 58.841 34.615 0.00 0.00 0.00 1.40
2932 3647 5.997746 TCGTCAAATCTTCAGACTCCAAAAT 59.002 36.000 0.00 0.00 0.00 1.82
2942 3657 6.201806 AGTGAAAGAACTCGTCAAATCTTCAG 59.798 38.462 0.00 0.00 31.20 3.02
3073 3793 0.169009 GCGAGGCTCCAATGTTCAAC 59.831 55.000 9.32 0.00 0.00 3.18
3120 3840 1.273886 GGTATCTCGCTCCTCCATTCC 59.726 57.143 0.00 0.00 0.00 3.01
3178 3898 5.125356 ACAACAACAGATGTCACATGAAGA 58.875 37.500 0.00 0.00 42.99 2.87
3248 3968 1.931172 ACACCAGAAAGTGAAACGTCG 59.069 47.619 0.00 0.00 45.86 5.12
3252 3972 7.535997 AGTTTAAAGACACCAGAAAGTGAAAC 58.464 34.615 0.00 0.00 40.34 2.78
3316 4049 8.055279 TGCCCAGAACTTATTCTTCAAAATAG 57.945 34.615 0.00 0.00 42.91 1.73
3322 4055 5.241403 TCTTGCCCAGAACTTATTCTTCA 57.759 39.130 0.00 0.00 42.91 3.02
3407 4140 6.543465 CCTGATGCAAAATAGTAGGTCATGAA 59.457 38.462 0.00 0.00 0.00 2.57
3610 4343 7.148356 TGCAATAAACTGATCTGAGTTGACATC 60.148 37.037 6.60 0.00 36.28 3.06
3612 4345 5.997129 TGCAATAAACTGATCTGAGTTGACA 59.003 36.000 6.60 5.72 36.28 3.58
3690 4423 4.035675 GGTGAAGCATGCTAGGTATTCAAC 59.964 45.833 23.00 18.34 0.00 3.18
3742 4475 2.370349 ACAGACCTGTCCTCTGTATCG 58.630 52.381 0.00 0.00 45.35 2.92
3751 4484 3.986277 TCGTAGAAAAACAGACCTGTCC 58.014 45.455 2.84 0.00 44.13 4.02
3770 4503 7.226720 AGGGCATTAACTATTTACAATCACTCG 59.773 37.037 0.00 0.00 0.00 4.18
3781 4514 8.686334 CAATTGACTGTAGGGCATTAACTATTT 58.314 33.333 0.00 0.00 30.17 1.40
3813 4546 6.662414 TGATAGATTTTTCACTAAGTGCCG 57.338 37.500 0.00 0.00 32.98 5.69
4035 4768 8.680039 TTTCATCATCAAGCATGTATACATCA 57.320 30.769 15.60 0.00 33.61 3.07
4206 4939 4.827284 AGTGTCTCCAAATTGAACCGAAAT 59.173 37.500 0.00 0.00 0.00 2.17
4267 5000 4.374399 CCTGCTTTCATGAACTGCTTTTT 58.626 39.130 24.20 0.00 0.00 1.94
4269 5002 2.298163 CCCTGCTTTCATGAACTGCTTT 59.702 45.455 24.20 0.00 0.00 3.51
4272 5005 0.529378 CCCCTGCTTTCATGAACTGC 59.471 55.000 19.84 19.84 0.00 4.40
4273 5006 2.205022 TCCCCTGCTTTCATGAACTG 57.795 50.000 7.89 5.48 0.00 3.16
4274 5007 2.108952 ACTTCCCCTGCTTTCATGAACT 59.891 45.455 7.89 0.00 0.00 3.01
4275 5008 2.519013 ACTTCCCCTGCTTTCATGAAC 58.481 47.619 7.89 0.00 0.00 3.18
4373 5107 9.424319 CTCTGTGTATTAAGAGCAGAACTTAAA 57.576 33.333 0.00 0.00 41.17 1.52
4488 5223 5.559035 CGCAATTCAAGATTTACGGATCCTC 60.559 44.000 10.75 0.00 0.00 3.71
4491 5226 4.963953 CACGCAATTCAAGATTTACGGATC 59.036 41.667 0.00 0.00 0.00 3.36
4494 5229 3.425404 CCACGCAATTCAAGATTTACGG 58.575 45.455 0.00 0.00 0.00 4.02
4503 5238 3.365465 CGATAACAACCCACGCAATTCAA 60.365 43.478 0.00 0.00 0.00 2.69
4798 5533 0.601841 AACTAACTCGCCCACCAACG 60.602 55.000 0.00 0.00 0.00 4.10
4806 5541 5.745294 TCGTATGACAATAAACTAACTCGCC 59.255 40.000 0.00 0.00 0.00 5.54
4836 5571 2.028658 TGAAAGTGCACAACAAAGCCAA 60.029 40.909 21.04 0.00 0.00 4.52
4872 5915 7.148154 ACCGCAAAATATAAGCATACAACAGAA 60.148 33.333 0.00 0.00 0.00 3.02
4889 5932 7.551262 TCTGTGATGTAAGTATAACCGCAAAAT 59.449 33.333 0.00 0.00 0.00 1.82
4907 5950 6.591448 TGTGTAAAGTGAGCTATTCTGTGATG 59.409 38.462 0.00 0.00 0.00 3.07
4974 6018 4.399004 AGAAGTATCTGTTGCAGCTAGG 57.601 45.455 1.17 0.00 33.59 3.02
4975 6019 6.039270 AGAGTAGAAGTATCTGTTGCAGCTAG 59.961 42.308 1.17 0.00 37.10 3.42
4976 6020 5.888724 AGAGTAGAAGTATCTGTTGCAGCTA 59.111 40.000 1.17 0.00 37.10 3.32
4977 6021 4.709397 AGAGTAGAAGTATCTGTTGCAGCT 59.291 41.667 1.17 0.00 37.10 4.24
4982 6026 8.594881 AAACACAAGAGTAGAAGTATCTGTTG 57.405 34.615 0.00 0.00 38.07 3.33
4992 6036 7.226720 GGAACATCAAGAAACACAAGAGTAGAA 59.773 37.037 0.00 0.00 0.00 2.10
5020 6064 7.653713 ACGAATTGCTATGTACTCCAAGAATAG 59.346 37.037 0.00 0.00 0.00 1.73
5060 6104 4.809426 GTGGCTAGCAGTATTTCGTACAAT 59.191 41.667 18.24 0.00 35.67 2.71
5150 6299 1.562672 AAACTACCTGCCGGATGCCT 61.563 55.000 5.05 0.00 40.16 4.75
5153 6302 2.107950 TGAAAACTACCTGCCGGATG 57.892 50.000 5.05 0.00 0.00 3.51
5184 6333 6.934645 TGAGAGGTGTTTCTGGTTAACTAATG 59.065 38.462 5.42 0.00 0.00 1.90
5229 6378 8.203485 AGAGGCTTGAGAGAATAATAAGTCTTG 58.797 37.037 0.00 0.00 33.84 3.02
5235 6384 6.126940 ACTGCAGAGGCTTGAGAGAATAATAA 60.127 38.462 23.35 0.00 41.91 1.40
5240 6389 1.907936 ACTGCAGAGGCTTGAGAGAAT 59.092 47.619 23.35 0.00 41.91 2.40
5345 6494 7.167801 GGAATAAACTAGTACTGTTGATCTCGC 59.832 40.741 5.39 0.00 0.00 5.03
5346 6495 8.188799 TGGAATAAACTAGTACTGTTGATCTCG 58.811 37.037 5.39 0.00 0.00 4.04
5347 6496 9.871238 TTGGAATAAACTAGTACTGTTGATCTC 57.129 33.333 5.39 7.17 0.00 2.75
5351 6500 9.280174 CCTTTTGGAATAAACTAGTACTGTTGA 57.720 33.333 5.39 1.86 44.07 3.18
5352 6501 9.063615 ACCTTTTGGAATAAACTAGTACTGTTG 57.936 33.333 5.39 0.00 44.07 3.33
5353 6502 9.636789 AACCTTTTGGAATAAACTAGTACTGTT 57.363 29.630 5.39 5.31 44.07 3.16
5356 6505 9.955102 CCTAACCTTTTGGAATAAACTAGTACT 57.045 33.333 0.00 0.00 44.07 2.73
5357 6506 9.170734 CCCTAACCTTTTGGAATAAACTAGTAC 57.829 37.037 0.00 0.00 44.07 2.73
5358 6507 7.830697 GCCCTAACCTTTTGGAATAAACTAGTA 59.169 37.037 0.00 0.00 44.07 1.82
5359 6508 6.662234 GCCCTAACCTTTTGGAATAAACTAGT 59.338 38.462 0.00 0.00 44.07 2.57
5360 6509 6.890268 AGCCCTAACCTTTTGGAATAAACTAG 59.110 38.462 0.00 0.00 44.07 2.57
5361 6510 6.796648 AGCCCTAACCTTTTGGAATAAACTA 58.203 36.000 0.00 0.00 44.07 2.24
5362 6511 5.651303 AGCCCTAACCTTTTGGAATAAACT 58.349 37.500 0.00 0.00 44.07 2.66
5363 6512 5.995565 AGCCCTAACCTTTTGGAATAAAC 57.004 39.130 0.00 0.00 44.07 2.01
5364 6513 6.553857 TGTAGCCCTAACCTTTTGGAATAAA 58.446 36.000 0.00 0.00 44.07 1.40
5365 6514 6.142259 TGTAGCCCTAACCTTTTGGAATAA 57.858 37.500 0.00 0.00 44.07 1.40
5366 6515 5.782677 TGTAGCCCTAACCTTTTGGAATA 57.217 39.130 0.00 0.00 44.07 1.75
5367 6516 4.668138 TGTAGCCCTAACCTTTTGGAAT 57.332 40.909 0.00 0.00 44.07 3.01
5371 6520 4.340617 TGGATTGTAGCCCTAACCTTTTG 58.659 43.478 0.00 0.00 0.00 2.44
5372 6521 4.668138 TGGATTGTAGCCCTAACCTTTT 57.332 40.909 0.00 0.00 0.00 2.27
5373 6522 4.569865 CCTTGGATTGTAGCCCTAACCTTT 60.570 45.833 0.00 0.00 0.00 3.11
5374 6523 3.053619 CCTTGGATTGTAGCCCTAACCTT 60.054 47.826 0.00 0.00 0.00 3.50
5375 6524 2.509964 CCTTGGATTGTAGCCCTAACCT 59.490 50.000 0.00 0.00 0.00 3.50
5376 6525 2.422945 CCCTTGGATTGTAGCCCTAACC 60.423 54.545 0.00 0.00 0.00 2.85
5377 6526 2.932261 CCCTTGGATTGTAGCCCTAAC 58.068 52.381 0.00 0.00 0.00 2.34
5378 6527 1.214424 GCCCTTGGATTGTAGCCCTAA 59.786 52.381 0.00 0.00 0.00 2.69
5379 6528 0.843984 GCCCTTGGATTGTAGCCCTA 59.156 55.000 0.00 0.00 0.00 3.53
5380 6529 1.214305 TGCCCTTGGATTGTAGCCCT 61.214 55.000 0.00 0.00 0.00 5.19
5381 6530 0.324275 TTGCCCTTGGATTGTAGCCC 60.324 55.000 0.00 0.00 0.00 5.19
5382 6531 1.106285 CTTGCCCTTGGATTGTAGCC 58.894 55.000 0.00 0.00 0.00 3.93
5383 6532 2.019984 CTCTTGCCCTTGGATTGTAGC 58.980 52.381 0.00 0.00 0.00 3.58
5384 6533 3.356529 ACTCTTGCCCTTGGATTGTAG 57.643 47.619 0.00 0.00 0.00 2.74
5385 6534 3.330701 AGAACTCTTGCCCTTGGATTGTA 59.669 43.478 0.00 0.00 0.00 2.41
5386 6535 2.108952 AGAACTCTTGCCCTTGGATTGT 59.891 45.455 0.00 0.00 0.00 2.71
5387 6536 2.800250 AGAACTCTTGCCCTTGGATTG 58.200 47.619 0.00 0.00 0.00 2.67
5388 6537 3.181429 TGAAGAACTCTTGCCCTTGGATT 60.181 43.478 0.00 0.00 36.11 3.01
5389 6538 2.376518 TGAAGAACTCTTGCCCTTGGAT 59.623 45.455 0.00 0.00 36.11 3.41
5390 6539 1.774254 TGAAGAACTCTTGCCCTTGGA 59.226 47.619 0.00 0.00 36.11 3.53
5391 6540 2.276732 TGAAGAACTCTTGCCCTTGG 57.723 50.000 0.00 0.00 36.11 3.61
5392 6541 4.761739 TGTATTGAAGAACTCTTGCCCTTG 59.238 41.667 0.00 0.00 36.11 3.61
5393 6542 4.985538 TGTATTGAAGAACTCTTGCCCTT 58.014 39.130 0.00 0.00 36.11 3.95
5394 6543 4.640771 TGTATTGAAGAACTCTTGCCCT 57.359 40.909 0.00 0.00 36.11 5.19
5395 6544 4.096984 CCATGTATTGAAGAACTCTTGCCC 59.903 45.833 0.00 0.00 36.11 5.36
5396 6545 4.943705 TCCATGTATTGAAGAACTCTTGCC 59.056 41.667 0.00 0.00 36.11 4.52
5397 6546 5.645497 AGTCCATGTATTGAAGAACTCTTGC 59.355 40.000 0.00 0.00 36.11 4.01
5398 6547 7.388776 TCAAGTCCATGTATTGAAGAACTCTTG 59.611 37.037 0.00 0.00 36.11 3.02
5399 6548 7.453393 TCAAGTCCATGTATTGAAGAACTCTT 58.547 34.615 2.90 0.00 39.23 2.85
5400 6549 7.009179 TCAAGTCCATGTATTGAAGAACTCT 57.991 36.000 2.90 0.00 30.33 3.24
5401 6550 6.183360 GCTCAAGTCCATGTATTGAAGAACTC 60.183 42.308 6.11 0.00 32.87 3.01
5402 6551 5.645497 GCTCAAGTCCATGTATTGAAGAACT 59.355 40.000 6.11 0.00 32.87 3.01
5403 6552 5.645497 AGCTCAAGTCCATGTATTGAAGAAC 59.355 40.000 6.11 0.00 32.87 3.01
5404 6553 5.809001 AGCTCAAGTCCATGTATTGAAGAA 58.191 37.500 6.11 0.00 32.87 2.52
5405 6554 5.426689 AGCTCAAGTCCATGTATTGAAGA 57.573 39.130 6.11 0.00 32.87 2.87
5406 6555 7.798596 AATAGCTCAAGTCCATGTATTGAAG 57.201 36.000 0.00 3.20 32.87 3.02
5407 6556 7.828717 TGAAATAGCTCAAGTCCATGTATTGAA 59.171 33.333 0.00 0.00 32.87 2.69
5408 6557 7.337938 TGAAATAGCTCAAGTCCATGTATTGA 58.662 34.615 0.00 0.00 0.00 2.57
5409 6558 7.558161 TGAAATAGCTCAAGTCCATGTATTG 57.442 36.000 0.00 0.00 0.00 1.90
5410 6559 7.831193 AGTTGAAATAGCTCAAGTCCATGTATT 59.169 33.333 0.00 0.00 34.53 1.89
5411 6560 7.341805 AGTTGAAATAGCTCAAGTCCATGTAT 58.658 34.615 0.00 0.00 34.53 2.29
5412 6561 6.711277 AGTTGAAATAGCTCAAGTCCATGTA 58.289 36.000 0.00 0.00 34.53 2.29
5413 6562 5.564550 AGTTGAAATAGCTCAAGTCCATGT 58.435 37.500 0.00 0.00 34.53 3.21
5414 6563 6.116680 GAGTTGAAATAGCTCAAGTCCATG 57.883 41.667 9.16 0.00 44.69 3.66
5428 6577 5.437060 AGGTGTAACTGTGTGAGTTGAAAT 58.563 37.500 0.00 0.00 45.05 2.17
5442 6591 2.260822 AGGCATGTGAGAGGTGTAACT 58.739 47.619 0.00 0.00 36.74 2.24
5567 6716 8.994170 TCGAAGGAAAAAGAAAACAAAAATGTT 58.006 25.926 0.00 0.00 0.00 2.71
5583 6732 2.504367 CTCCCAGCTTTCGAAGGAAAA 58.496 47.619 12.00 0.00 41.38 2.29


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

AutoCloner maintained by Alex Coulton.