Multiple sequence alignment - TraesCS2B01G294000

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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 TraesCS2B01G294000 chr2B 100.000 5597 0 0 1 5597 410186544 410180948 0.000000e+00 10336.0
1 TraesCS2B01G294000 chr2A 95.772 3169 113 11 871 4033 456499875 456496722 0.000000e+00 5090.0
2 TraesCS2B01G294000 chr2A 94.310 1195 42 7 4031 5213 456496640 456495460 0.000000e+00 1807.0
3 TraesCS2B01G294000 chr2A 89.937 159 16 0 5324 5482 695287349 695287191 7.350000e-49 206.0
4 TraesCS2B01G294000 chr2A 89.744 78 7 1 5247 5324 703037759 703037683 1.280000e-16 99.0
5 TraesCS2B01G294000 chr2A 100.000 33 0 0 5482 5514 456495224 456495192 1.680000e-05 62.1
6 TraesCS2B01G294000 chr2A 100.000 30 0 0 4658 4687 158458207 158458236 7.830000e-04 56.5
7 TraesCS2B01G294000 chr2D 91.993 1636 79 18 3637 5256 344970591 344968992 0.000000e+00 2248.0
8 TraesCS2B01G294000 chr2D 95.681 1042 39 5 867 1906 344973341 344972304 0.000000e+00 1670.0
9 TraesCS2B01G294000 chr2D 91.252 663 45 7 2473 3132 344971869 344971217 0.000000e+00 891.0
10 TraesCS2B01G294000 chr2D 90.400 375 20 2 2107 2476 344972295 344971932 3.920000e-131 479.0
11 TraesCS2B01G294000 chr2D 86.269 386 34 9 3178 3550 344971130 344970751 8.730000e-108 401.0
12 TraesCS2B01G294000 chr2D 89.720 107 9 2 3509 3614 344970761 344970656 9.780000e-28 135.0
13 TraesCS2B01G294000 chr1B 99.301 858 6 0 1 858 289303016 289302159 0.000000e+00 1552.0
14 TraesCS2B01G294000 chr1B 97.216 862 20 3 1 858 666939627 666938766 0.000000e+00 1456.0
15 TraesCS2B01G294000 chr1B 95.775 71 3 0 5254 5324 54888228 54888298 1.270000e-21 115.0
16 TraesCS2B01G294000 chr1B 94.444 72 4 0 5250 5321 632028900 632028971 1.650000e-20 111.0
17 TraesCS2B01G294000 chr1A 98.836 859 10 0 1 859 375612170 375611312 0.000000e+00 1531.0
18 TraesCS2B01G294000 chr1A 89.744 156 16 0 5324 5479 569341824 569341669 3.420000e-47 200.0
19 TraesCS2B01G294000 chr1A 95.775 71 3 0 5254 5324 447735998 447735928 1.270000e-21 115.0
20 TraesCS2B01G294000 chr5B 98.718 858 11 0 1 858 361490584 361491441 0.000000e+00 1524.0
21 TraesCS2B01G294000 chr5B 96.129 155 6 0 5325 5479 437912113 437912267 2.590000e-63 254.0
22 TraesCS2B01G294000 chr4B 98.601 858 11 1 1 858 145515406 145514550 0.000000e+00 1517.0
23 TraesCS2B01G294000 chr4B 89.744 156 16 0 5324 5479 398126313 398126468 3.420000e-47 200.0
24 TraesCS2B01G294000 chr4B 89.744 156 16 0 5324 5479 398161222 398161377 3.420000e-47 200.0
25 TraesCS2B01G294000 chr4B 89.744 156 16 0 5324 5479 398195984 398196139 3.420000e-47 200.0
26 TraesCS2B01G294000 chr3B 96.644 864 24 4 1 859 466385486 466384623 0.000000e+00 1430.0
27 TraesCS2B01G294000 chr3B 90.323 155 15 0 5325 5479 432599375 432599529 2.640000e-48 204.0
28 TraesCS2B01G294000 chr4D 96.000 875 17 8 1 858 81336071 81336944 0.000000e+00 1406.0
29 TraesCS2B01G294000 chr7D 86.185 637 66 11 238 853 535549506 535550141 0.000000e+00 669.0
30 TraesCS2B01G294000 chr7D 95.833 72 3 0 5253 5324 20289131 20289060 3.540000e-22 117.0
31 TraesCS2B01G294000 chr7D 86.076 79 11 0 5243 5321 618410137 618410215 9.990000e-13 86.1
32 TraesCS2B01G294000 chr7B 84.181 354 50 4 393 740 577244828 577245181 6.950000e-89 339.0
33 TraesCS2B01G294000 chr7B 89.671 213 19 3 30 240 577278409 577278620 9.240000e-68 268.0
34 TraesCS2B01G294000 chr7B 89.202 213 20 3 30 240 577235545 577235756 4.300000e-66 263.0
35 TraesCS2B01G294000 chr7B 100.000 28 0 0 4660 4687 362043394 362043421 1.000000e-02 52.8
36 TraesCS2B01G294000 chr3A 89.744 156 16 0 5324 5479 601354661 601354816 3.420000e-47 200.0
37 TraesCS2B01G294000 chr3A 87.500 168 21 0 5324 5491 101441790 101441623 1.590000e-45 195.0
38 TraesCS2B01G294000 chr4A 78.481 237 30 17 5253 5480 523305995 523306219 9.780000e-28 135.0
39 TraesCS2B01G294000 chr5D 98.507 67 1 0 5253 5319 74113432 74113366 9.850000e-23 119.0
40 TraesCS2B01G294000 chr6D 94.595 74 4 0 5251 5324 27318259 27318186 1.270000e-21 115.0
41 TraesCS2B01G294000 chr6D 95.714 70 3 0 5255 5324 448338187 448338118 4.580000e-21 113.0
42 TraesCS2B01G294000 chr3D 95.714 70 3 0 5255 5324 313719247 313719178 4.580000e-21 113.0
43 TraesCS2B01G294000 chr7A 89.873 79 8 0 5246 5324 628401749 628401671 9.920000e-18 102.0
44 TraesCS2B01G294000 chr5A 89.873 79 8 0 5243 5321 523613588 523613666 9.920000e-18 102.0
45 TraesCS2B01G294000 chrUn 92.857 56 2 2 818 873 360690264 360690211 4.650000e-11 80.5
46 TraesCS2B01G294000 chr6B 92.683 41 3 0 4660 4700 140363012 140362972 6.060000e-05 60.2


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 TraesCS2B01G294000 chr2B 410180948 410186544 5596 True 10336.000000 10336 100.000000 1 5597 1 chr2B.!!$R1 5596
1 TraesCS2B01G294000 chr2A 456495192 456499875 4683 True 2319.700000 5090 96.694000 871 5514 3 chr2A.!!$R3 4643
2 TraesCS2B01G294000 chr2D 344968992 344973341 4349 True 970.666667 2248 90.885833 867 5256 6 chr2D.!!$R1 4389
3 TraesCS2B01G294000 chr1B 289302159 289303016 857 True 1552.000000 1552 99.301000 1 858 1 chr1B.!!$R1 857
4 TraesCS2B01G294000 chr1B 666938766 666939627 861 True 1456.000000 1456 97.216000 1 858 1 chr1B.!!$R2 857
5 TraesCS2B01G294000 chr1A 375611312 375612170 858 True 1531.000000 1531 98.836000 1 859 1 chr1A.!!$R1 858
6 TraesCS2B01G294000 chr5B 361490584 361491441 857 False 1524.000000 1524 98.718000 1 858 1 chr5B.!!$F1 857
7 TraesCS2B01G294000 chr4B 145514550 145515406 856 True 1517.000000 1517 98.601000 1 858 1 chr4B.!!$R1 857
8 TraesCS2B01G294000 chr3B 466384623 466385486 863 True 1430.000000 1430 96.644000 1 859 1 chr3B.!!$R1 858
9 TraesCS2B01G294000 chr4D 81336071 81336944 873 False 1406.000000 1406 96.000000 1 858 1 chr4D.!!$F1 857
10 TraesCS2B01G294000 chr7D 535549506 535550141 635 False 669.000000 669 86.185000 238 853 1 chr7D.!!$F1 615

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
535 550 0.036164 CTTGATGTCCCGTGACCCAA 59.964 55.0 0.00 0.0 41.01 4.12 F
1603 1634 0.698238 TGGTTATCAGCTTGGGTGCT 59.302 50.0 0.00 0.0 45.18 4.40 F
2091 2122 1.015109 TATGACTCCGACTCAGCGAC 58.985 55.0 0.00 0.0 0.00 5.19 F
3618 3807 0.878523 TGCTGGTATTATGACGCGCC 60.879 55.0 5.73 0.0 0.00 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 1719 0.035458 GAGGTAGTGGCAGTGCAAGT 59.965 55.0 18.61 11.73 0.0 3.16 R
2809 2913 1.356527 GCCCGTGCCGTAACTAACAG 61.357 60.0 0.00 0.00 0.0 3.16 R
3738 3969 2.420058 AAGCAGTAATTCCCCTTCGG 57.580 50.0 0.00 0.00 0.0 4.30 R
5453 5803 0.108329 CTCCGTCCGCCAATAAGTGT 60.108 55.0 0.00 0.00 0.0 3.55 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
535 550 0.036164 CTTGATGTCCCGTGACCCAA 59.964 55.000 0.00 0.00 41.01 4.12
859 888 2.750712 GCACGGGCAATTTTCCTAGTAA 59.249 45.455 3.77 0.00 40.72 2.24
860 889 3.191791 GCACGGGCAATTTTCCTAGTAAA 59.808 43.478 3.77 0.00 40.72 2.01
861 890 4.142249 GCACGGGCAATTTTCCTAGTAAAT 60.142 41.667 3.77 0.00 40.72 1.40
862 891 5.066764 GCACGGGCAATTTTCCTAGTAAATA 59.933 40.000 3.77 0.00 40.72 1.40
863 892 6.404954 GCACGGGCAATTTTCCTAGTAAATAA 60.405 38.462 3.77 0.00 40.72 1.40
864 893 7.540299 CACGGGCAATTTTCCTAGTAAATAAA 58.460 34.615 0.00 0.00 0.00 1.40
865 894 7.700656 CACGGGCAATTTTCCTAGTAAATAAAG 59.299 37.037 0.00 0.00 0.00 1.85
986 1016 0.961753 GTCAGGTTCCAAGCCCAAAG 59.038 55.000 0.00 0.00 0.00 2.77
1056 1086 2.519302 AAGCAGCACAAACCCGCT 60.519 55.556 0.00 0.00 39.66 5.52
1151 1181 2.130073 GAGCAGGACCAAACCAACGC 62.130 60.000 0.00 0.00 0.00 4.84
1200 1230 2.741092 GGTGGCGTCCTCTTGTCA 59.259 61.111 0.00 0.00 0.00 3.58
1236 1266 2.262915 CGGCAGCTCGAGTTCCTT 59.737 61.111 15.13 0.00 0.00 3.36
1329 1359 2.476619 CACATTCAGACGAACCACTGTC 59.523 50.000 0.00 0.00 35.84 3.51
1356 1387 1.672881 CCTGTCCAATTCGATTCAGCC 59.327 52.381 0.00 0.00 0.00 4.85
1369 1400 3.492309 CGATTCAGCCTGTCTCTATGCTT 60.492 47.826 0.00 0.00 30.08 3.91
1377 1408 1.135139 TGTCTCTATGCTTGTCTCGCC 59.865 52.381 0.00 0.00 0.00 5.54
1395 1426 1.940613 GCCGTAAGTGTTGGATGGATC 59.059 52.381 0.00 0.00 0.00 3.36
1408 1439 8.689972 GTGTTGGATGGATCATAAAAGATTTCT 58.310 33.333 0.00 0.00 0.00 2.52
1546 1577 0.839853 AGCTCTGTGAGGGGAAGCTT 60.840 55.000 0.00 0.00 0.00 3.74
1603 1634 0.698238 TGGTTATCAGCTTGGGTGCT 59.302 50.000 0.00 0.00 45.18 4.40
1649 1680 6.653989 AGGTAGCTGCTGTTATGATACTTTT 58.346 36.000 13.43 0.00 0.00 2.27
1654 1685 8.115490 AGCTGCTGTTATGATACTTTTTCTTT 57.885 30.769 0.00 0.00 0.00 2.52
1678 1709 7.697352 TTGAAACTGCTGTTGTTATGAATTG 57.303 32.000 9.95 0.00 36.39 2.32
1688 1719 4.961435 TGTTATGAATTGAATCGCTGCA 57.039 36.364 0.00 0.00 0.00 4.41
1705 1736 1.856265 GCACTTGCACTGCCACTACC 61.856 60.000 4.44 0.00 41.59 3.18
1716 1747 2.480419 CTGCCACTACCTCGTTTTGAAG 59.520 50.000 0.00 0.00 0.00 3.02
1717 1748 2.158871 TGCCACTACCTCGTTTTGAAGT 60.159 45.455 0.00 0.00 0.00 3.01
1723 1754 7.095270 CCACTACCTCGTTTTGAAGTACTATT 58.905 38.462 0.00 0.00 0.00 1.73
1803 1834 3.658757 GCTGTTGCCCTGTTTTCATAA 57.341 42.857 0.00 0.00 0.00 1.90
1811 1842 4.165779 GCCCTGTTTTCATAACATCAACG 58.834 43.478 0.00 0.00 0.00 4.10
1936 1967 8.644619 CACATTGAAAATTTTCTGTAGCATCAG 58.355 33.333 26.73 9.98 38.02 2.90
1953 1984 4.506654 GCATCAGGCTATTGCATTTTTCTG 59.493 41.667 14.05 0.00 41.91 3.02
1980 2011 2.848691 CTGTACACCCGTACCCAAAAA 58.151 47.619 0.00 0.00 46.33 1.94
2054 2085 3.437049 GCTACCAAGATTTTTGAGTCGCT 59.563 43.478 0.00 0.00 0.00 4.93
2091 2122 1.015109 TATGACTCCGACTCAGCGAC 58.985 55.000 0.00 0.00 0.00 5.19
2129 2160 1.062587 CAATTAGCTTCCCAAGTCGCG 59.937 52.381 0.00 0.00 0.00 5.87
2272 2308 2.246719 ATGCTCTACCTCGATTTGGC 57.753 50.000 0.00 0.00 0.00 4.52
2275 2311 1.405526 GCTCTACCTCGATTTGGCACA 60.406 52.381 0.00 0.00 0.00 4.57
2420 2456 7.178983 TGCCATTGTTCTAATTCTTTTGGAGAT 59.821 33.333 0.00 0.00 33.49 2.75
2551 2653 3.437049 GCTCAACCATAGTTTCACAGGAC 59.563 47.826 0.00 0.00 32.45 3.85
2617 2719 2.396590 TATGACGCCTTTTCTCACCC 57.603 50.000 0.00 0.00 0.00 4.61
2686 2788 1.865865 GTGTTGTGTGAGACCGTCAT 58.134 50.000 0.40 0.00 37.56 3.06
2710 2812 2.295602 GCTCGGTTTGGAGGGGGTA 61.296 63.158 0.00 0.00 34.56 3.69
2859 2963 7.615365 TGATTTATTTTCTTGGCCTCATACTGT 59.385 33.333 3.32 0.00 0.00 3.55
2908 3012 5.121611 TGTGCTAATTTTCACATGTAGGTCG 59.878 40.000 0.00 0.00 38.18 4.79
3019 3123 7.860373 TGTCTTTATGTTTAATCAGCACACAAC 59.140 33.333 0.00 0.00 0.00 3.32
3238 3385 9.299963 TGTTTATTGTTGCAGCATATATTGTTC 57.700 29.630 3.36 0.00 0.00 3.18
3332 3483 1.409064 TGCAAATTTTGGTACGGCACA 59.591 42.857 10.96 0.00 0.00 4.57
3349 3500 5.356751 ACGGCACATTTGATTTATAGCTTGA 59.643 36.000 0.00 0.00 0.00 3.02
3431 3583 1.089920 AGCGTGGCAAGATTTAGCAG 58.910 50.000 4.11 0.00 0.00 4.24
3441 3598 7.119262 GTGGCAAGATTTAGCAGAAGTTAAGTA 59.881 37.037 0.00 0.00 0.00 2.24
3617 3806 1.148310 ATGCTGGTATTATGACGCGC 58.852 50.000 5.73 0.00 0.00 6.86
3618 3807 0.878523 TGCTGGTATTATGACGCGCC 60.879 55.000 5.73 0.00 0.00 6.53
3619 3808 0.878523 GCTGGTATTATGACGCGCCA 60.879 55.000 5.73 0.00 0.00 5.69
3662 3893 2.664402 ATTGTCTGCTTCCCAACAGT 57.336 45.000 0.00 0.00 35.37 3.55
3738 3969 8.743099 GTTGTTTTAGACATTAGAGTTTGTTGC 58.257 33.333 0.00 0.00 38.26 4.17
3803 4034 1.973515 AGTCATGGAGAACTGACAGCA 59.026 47.619 1.25 0.00 43.35 4.41
3854 4085 2.223157 TGTTGCATACTTTATTCGCCGC 60.223 45.455 0.00 0.00 0.00 6.53
3972 4203 9.469807 CGAAGCATGGGATATTATATCTTCTAC 57.530 37.037 11.46 1.04 0.00 2.59
3973 4204 9.469807 GAAGCATGGGATATTATATCTTCTACG 57.530 37.037 11.46 0.00 0.00 3.51
4028 4259 7.906160 TCTAAGAACACTTGTTTTTCTTCTCG 58.094 34.615 1.42 0.00 39.66 4.04
4098 4413 4.341520 AGAAGTTGACTGAACTCTTACCGT 59.658 41.667 0.00 0.00 44.68 4.83
4099 4414 5.533903 AGAAGTTGACTGAACTCTTACCGTA 59.466 40.000 0.00 0.00 44.68 4.02
4100 4415 5.779529 AGTTGACTGAACTCTTACCGTAA 57.220 39.130 0.00 0.00 41.37 3.18
4101 4416 6.152932 AGTTGACTGAACTCTTACCGTAAA 57.847 37.500 0.00 0.00 41.37 2.01
4102 4417 6.756221 AGTTGACTGAACTCTTACCGTAAAT 58.244 36.000 0.00 0.00 41.37 1.40
4103 4418 7.889469 AGTTGACTGAACTCTTACCGTAAATA 58.111 34.615 0.00 0.00 41.37 1.40
4104 4419 7.811713 AGTTGACTGAACTCTTACCGTAAATAC 59.188 37.037 0.00 0.00 41.37 1.89
4141 4463 3.758554 GAGGAAAAGATTGCCTGCTGTTA 59.241 43.478 0.00 0.00 30.70 2.41
4263 4596 8.339344 TGCTTGTTCATTTCTTGATCAGAATA 57.661 30.769 0.00 0.00 41.42 1.75
4338 4671 2.659063 CGACATGCAGAGGGACCCA 61.659 63.158 14.60 0.00 0.00 4.51
4396 4729 4.571984 GGTACCACTTACGTCAACAACTTT 59.428 41.667 7.15 0.00 0.00 2.66
4415 4748 6.259550 ACTTTGGACATTCAGAAATGCTAC 57.740 37.500 0.00 0.00 45.16 3.58
4452 4785 9.166173 TGCCATCTCCATCTTATTATATTTTCG 57.834 33.333 0.00 0.00 0.00 3.46
4545 4878 5.028375 GGCGACACAAGAATATGCTTTTAC 58.972 41.667 0.00 0.00 0.00 2.01
4636 4969 2.680577 GTGTCCCAAGTACACTTACCG 58.319 52.381 0.00 0.00 43.13 4.02
4668 5001 2.300437 GCGGCAAGATATTACTCCCTCT 59.700 50.000 0.00 0.00 0.00 3.69
4670 5003 3.306364 CGGCAAGATATTACTCCCTCTGG 60.306 52.174 0.00 0.00 0.00 3.86
4702 5035 5.560966 AGTGTCGTTGTTTCAGTTCAAAT 57.439 34.783 0.00 0.00 0.00 2.32
4727 5061 1.173913 GGAATTTTGGTCGGGTGAGG 58.826 55.000 0.00 0.00 0.00 3.86
4767 5101 3.192422 TGCGATTTTCCAATGTACCTTGG 59.808 43.478 20.51 20.51 45.91 3.61
4769 5103 3.428862 CGATTTTCCAATGTACCTTGGCC 60.429 47.826 21.44 0.00 44.48 5.36
4817 5151 6.015603 TGCAAGACATACAATGTTTCCATGAA 60.016 34.615 0.00 0.00 45.03 2.57
4843 5177 0.313672 GCTGCGGTGTTGGAATTCAA 59.686 50.000 7.93 0.00 0.00 2.69
4844 5178 1.269517 GCTGCGGTGTTGGAATTCAAA 60.270 47.619 7.93 0.00 37.08 2.69
4845 5179 2.664916 CTGCGGTGTTGGAATTCAAAG 58.335 47.619 7.93 0.00 37.08 2.77
4846 5180 2.293122 CTGCGGTGTTGGAATTCAAAGA 59.707 45.455 7.93 0.00 37.08 2.52
4847 5181 2.690497 TGCGGTGTTGGAATTCAAAGAA 59.310 40.909 7.93 0.00 37.08 2.52
4848 5182 3.320541 TGCGGTGTTGGAATTCAAAGAAT 59.679 39.130 7.93 0.00 37.08 2.40
4849 5183 4.202202 TGCGGTGTTGGAATTCAAAGAATT 60.202 37.500 7.93 4.77 37.08 2.17
4850 5184 4.385748 GCGGTGTTGGAATTCAAAGAATTC 59.614 41.667 19.19 19.19 37.08 2.17
4851 5185 5.527951 CGGTGTTGGAATTCAAAGAATTCA 58.472 37.500 25.20 13.86 38.15 2.57
4852 5186 6.158598 CGGTGTTGGAATTCAAAGAATTCAT 58.841 36.000 25.20 0.00 38.15 2.57
4853 5187 7.312154 CGGTGTTGGAATTCAAAGAATTCATA 58.688 34.615 25.20 15.29 38.15 2.15
4896 5230 7.778083 TCGTGAACTCAAGCTAGGATATTTAA 58.222 34.615 0.00 0.00 0.00 1.52
5102 5436 3.093814 TCCAGTTACAAGGTATGCGAGA 58.906 45.455 0.00 0.00 0.00 4.04
5213 5548 4.020218 TGATTTCTGACGAGTTGGATTCCT 60.020 41.667 3.95 0.00 0.00 3.36
5214 5549 5.186992 TGATTTCTGACGAGTTGGATTCCTA 59.813 40.000 3.95 0.00 0.00 2.94
5215 5550 4.720649 TTCTGACGAGTTGGATTCCTAG 57.279 45.455 3.95 0.00 0.00 3.02
5216 5551 2.427453 TCTGACGAGTTGGATTCCTAGC 59.573 50.000 3.95 0.00 0.00 3.42
5217 5552 1.480954 TGACGAGTTGGATTCCTAGCC 59.519 52.381 3.95 0.00 0.00 3.93
5256 5606 3.067320 GCAAGCCCATTCTTCCTTCATAC 59.933 47.826 0.00 0.00 0.00 2.39
5258 5608 4.429854 AGCCCATTCTTCCTTCATACTC 57.570 45.455 0.00 0.00 0.00 2.59
5259 5609 3.137360 AGCCCATTCTTCCTTCATACTCC 59.863 47.826 0.00 0.00 0.00 3.85
5261 5611 3.718956 CCCATTCTTCCTTCATACTCCCT 59.281 47.826 0.00 0.00 0.00 4.20
5264 5614 2.667470 TCTTCCTTCATACTCCCTCCG 58.333 52.381 0.00 0.00 0.00 4.63
5265 5615 2.024273 TCTTCCTTCATACTCCCTCCGT 60.024 50.000 0.00 0.00 0.00 4.69
5266 5616 2.068834 TCCTTCATACTCCCTCCGTC 57.931 55.000 0.00 0.00 0.00 4.79
5267 5617 1.041437 CCTTCATACTCCCTCCGTCC 58.959 60.000 0.00 0.00 0.00 4.79
5268 5618 0.669077 CTTCATACTCCCTCCGTCCG 59.331 60.000 0.00 0.00 0.00 4.79
5269 5619 0.033796 TTCATACTCCCTCCGTCCGT 60.034 55.000 0.00 0.00 0.00 4.69
5270 5620 0.750546 TCATACTCCCTCCGTCCGTG 60.751 60.000 0.00 0.00 0.00 4.94
5272 5622 0.033796 ATACTCCCTCCGTCCGTGAA 60.034 55.000 0.00 0.00 0.00 3.18
5273 5623 0.033796 TACTCCCTCCGTCCGTGAAT 60.034 55.000 0.00 0.00 0.00 2.57
5277 5627 0.822164 CCCTCCGTCCGTGAATAAGT 59.178 55.000 0.00 0.00 0.00 2.24
5278 5628 1.470979 CCCTCCGTCCGTGAATAAGTG 60.471 57.143 0.00 0.00 0.00 3.16
5279 5629 1.203994 CCTCCGTCCGTGAATAAGTGT 59.796 52.381 0.00 0.00 0.00 3.55
5280 5630 2.424601 CCTCCGTCCGTGAATAAGTGTA 59.575 50.000 0.00 0.00 0.00 2.90
5284 5634 3.795101 CCGTCCGTGAATAAGTGTACATC 59.205 47.826 0.00 0.00 0.00 3.06
5285 5635 4.439700 CCGTCCGTGAATAAGTGTACATCT 60.440 45.833 0.00 0.00 0.00 2.90
5286 5636 5.220912 CCGTCCGTGAATAAGTGTACATCTA 60.221 44.000 0.00 0.00 0.00 1.98
5287 5637 6.260377 CGTCCGTGAATAAGTGTACATCTAA 58.740 40.000 0.00 0.00 0.00 2.10
5288 5638 6.916387 CGTCCGTGAATAAGTGTACATCTAAT 59.084 38.462 0.00 0.00 0.00 1.73
5290 5640 9.095065 GTCCGTGAATAAGTGTACATCTAATTT 57.905 33.333 0.00 0.00 0.00 1.82
5387 5737 7.662604 TGTATCAATCTGATGTCATGTATGC 57.337 36.000 0.00 0.00 37.70 3.14
5388 5738 7.447594 TGTATCAATCTGATGTCATGTATGCT 58.552 34.615 0.00 0.00 37.70 3.79
5389 5739 8.587608 TGTATCAATCTGATGTCATGTATGCTA 58.412 33.333 0.00 0.00 37.70 3.49
5391 5741 7.059202 TCAATCTGATGTCATGTATGCTACT 57.941 36.000 0.00 0.00 0.00 2.57
5392 5742 8.181904 TCAATCTGATGTCATGTATGCTACTA 57.818 34.615 0.00 0.00 0.00 1.82
5393 5743 8.810041 TCAATCTGATGTCATGTATGCTACTAT 58.190 33.333 0.00 0.00 0.00 2.12
5394 5744 9.433153 CAATCTGATGTCATGTATGCTACTATT 57.567 33.333 0.00 0.00 0.00 1.73
5396 5746 8.414629 TCTGATGTCATGTATGCTACTATTCT 57.585 34.615 0.00 0.00 0.00 2.40
5398 5748 8.414629 TGATGTCATGTATGCTACTATTCTCT 57.585 34.615 0.00 0.00 0.00 3.10
5399 5749 8.864087 TGATGTCATGTATGCTACTATTCTCTT 58.136 33.333 0.00 0.00 0.00 2.85
5400 5750 9.352784 GATGTCATGTATGCTACTATTCTCTTC 57.647 37.037 0.00 0.00 0.00 2.87
5401 5751 8.470657 TGTCATGTATGCTACTATTCTCTTCT 57.529 34.615 0.00 0.00 0.00 2.85
5402 5752 9.574516 TGTCATGTATGCTACTATTCTCTTCTA 57.425 33.333 0.00 0.00 0.00 2.10
5465 5815 7.891183 AAAGCTAGATATACACTTATTGGCG 57.109 36.000 0.00 0.00 0.00 5.69
5466 5816 5.967088 AGCTAGATATACACTTATTGGCGG 58.033 41.667 0.00 0.00 0.00 6.13
5467 5817 5.715279 AGCTAGATATACACTTATTGGCGGA 59.285 40.000 0.00 0.00 0.00 5.54
5468 5818 5.805994 GCTAGATATACACTTATTGGCGGAC 59.194 44.000 0.00 0.00 0.00 4.79
5469 5819 4.806330 AGATATACACTTATTGGCGGACG 58.194 43.478 0.00 0.00 0.00 4.79
5470 5820 2.234300 ATACACTTATTGGCGGACGG 57.766 50.000 0.00 0.00 0.00 4.79
5471 5821 1.184431 TACACTTATTGGCGGACGGA 58.816 50.000 0.00 0.00 0.00 4.69
5472 5822 0.108329 ACACTTATTGGCGGACGGAG 60.108 55.000 0.00 0.00 0.00 4.63
5473 5823 0.810031 CACTTATTGGCGGACGGAGG 60.810 60.000 0.00 0.00 0.00 4.30
5474 5824 1.227556 CTTATTGGCGGACGGAGGG 60.228 63.158 0.00 0.00 0.00 4.30
5475 5825 1.682451 CTTATTGGCGGACGGAGGGA 61.682 60.000 0.00 0.00 0.00 4.20
5476 5826 1.682451 TTATTGGCGGACGGAGGGAG 61.682 60.000 0.00 0.00 0.00 4.30
5477 5827 2.866523 TATTGGCGGACGGAGGGAGT 62.867 60.000 0.00 0.00 0.00 3.85
5478 5828 2.866523 ATTGGCGGACGGAGGGAGTA 62.867 60.000 0.00 0.00 0.00 2.59
5479 5829 3.217743 GGCGGACGGAGGGAGTAG 61.218 72.222 0.00 0.00 0.00 2.57
5480 5830 2.439883 GCGGACGGAGGGAGTAGT 60.440 66.667 0.00 0.00 0.00 2.73
5526 5876 9.895138 TTAATACTAAATTTAGTCAGGTGTCCC 57.105 33.333 29.47 0.00 42.66 4.46
5527 5877 5.836024 ACTAAATTTAGTCAGGTGTCCCA 57.164 39.130 22.49 0.00 39.72 4.37
5528 5878 6.195600 ACTAAATTTAGTCAGGTGTCCCAA 57.804 37.500 22.49 0.00 39.72 4.12
5529 5879 6.607019 ACTAAATTTAGTCAGGTGTCCCAAA 58.393 36.000 22.49 0.00 39.72 3.28
5530 5880 5.784578 AAATTTAGTCAGGTGTCCCAAAC 57.215 39.130 0.00 0.00 0.00 2.93
5531 5881 2.943036 TTAGTCAGGTGTCCCAAACC 57.057 50.000 0.00 0.00 38.03 3.27
5532 5882 1.061546 TAGTCAGGTGTCCCAAACCC 58.938 55.000 0.00 0.00 38.57 4.11
5533 5883 1.599797 GTCAGGTGTCCCAAACCCG 60.600 63.158 0.00 0.00 38.57 5.28
5534 5884 2.983592 CAGGTGTCCCAAACCCGC 60.984 66.667 0.00 0.00 38.57 6.13
5535 5885 4.280019 AGGTGTCCCAAACCCGCC 62.280 66.667 0.00 0.00 38.57 6.13
5536 5886 4.280019 GGTGTCCCAAACCCGCCT 62.280 66.667 0.00 0.00 0.00 5.52
5537 5887 2.671963 GTGTCCCAAACCCGCCTC 60.672 66.667 0.00 0.00 0.00 4.70
5538 5888 3.172106 TGTCCCAAACCCGCCTCA 61.172 61.111 0.00 0.00 0.00 3.86
5539 5889 2.114411 GTCCCAAACCCGCCTCAA 59.886 61.111 0.00 0.00 0.00 3.02
5540 5890 1.529713 GTCCCAAACCCGCCTCAAA 60.530 57.895 0.00 0.00 0.00 2.69
5541 5891 1.529713 TCCCAAACCCGCCTCAAAC 60.530 57.895 0.00 0.00 0.00 2.93
5542 5892 2.642700 CCAAACCCGCCTCAAACG 59.357 61.111 0.00 0.00 0.00 3.60
5543 5893 2.190841 CCAAACCCGCCTCAAACGT 61.191 57.895 0.00 0.00 0.00 3.99
5544 5894 1.730451 CCAAACCCGCCTCAAACGTT 61.730 55.000 0.00 0.00 0.00 3.99
5545 5895 0.317519 CAAACCCGCCTCAAACGTTC 60.318 55.000 0.00 0.00 0.00 3.95
5546 5896 1.778027 AAACCCGCCTCAAACGTTCG 61.778 55.000 0.00 0.00 0.00 3.95
5547 5897 3.419759 CCCGCCTCAAACGTTCGG 61.420 66.667 16.12 16.12 39.79 4.30
5548 5898 3.419759 CCGCCTCAAACGTTCGGG 61.420 66.667 15.46 12.12 36.73 5.14
5549 5899 2.663852 CGCCTCAAACGTTCGGGT 60.664 61.111 0.00 0.00 0.00 5.28
5550 5900 2.943653 GCCTCAAACGTTCGGGTG 59.056 61.111 0.00 0.00 0.00 4.61
5551 5901 2.613506 GCCTCAAACGTTCGGGTGG 61.614 63.158 0.00 6.30 0.00 4.61
5552 5902 1.070105 CCTCAAACGTTCGGGTGGA 59.930 57.895 0.00 0.00 0.00 4.02
5553 5903 1.226030 CCTCAAACGTTCGGGTGGAC 61.226 60.000 0.00 0.00 0.00 4.02
5554 5904 0.249741 CTCAAACGTTCGGGTGGACT 60.250 55.000 0.00 0.00 0.00 3.85
5555 5905 0.531090 TCAAACGTTCGGGTGGACTG 60.531 55.000 0.00 0.00 0.00 3.51
5556 5906 1.890510 AAACGTTCGGGTGGACTGC 60.891 57.895 0.00 0.00 0.00 4.40
5557 5907 2.319890 AAACGTTCGGGTGGACTGCT 62.320 55.000 0.00 0.00 0.00 4.24
5558 5908 2.432628 CGTTCGGGTGGACTGCTC 60.433 66.667 0.00 0.00 0.00 4.26
5559 5909 2.432628 GTTCGGGTGGACTGCTCG 60.433 66.667 0.00 0.00 0.00 5.03
5560 5910 3.691342 TTCGGGTGGACTGCTCGG 61.691 66.667 0.00 0.00 0.00 4.63
5561 5911 4.988716 TCGGGTGGACTGCTCGGT 62.989 66.667 0.00 0.00 0.00 4.69
5562 5912 4.436998 CGGGTGGACTGCTCGGTC 62.437 72.222 0.29 0.29 35.66 4.79
5563 5913 3.311110 GGGTGGACTGCTCGGTCA 61.311 66.667 10.63 0.00 37.91 4.02
5564 5914 2.048127 GGTGGACTGCTCGGTCAC 60.048 66.667 10.63 6.93 37.91 3.67
5565 5915 2.734591 GTGGACTGCTCGGTCACA 59.265 61.111 10.63 4.13 37.91 3.58
5566 5916 1.069090 GTGGACTGCTCGGTCACAA 59.931 57.895 10.63 0.00 37.91 3.33
5567 5917 0.531974 GTGGACTGCTCGGTCACAAA 60.532 55.000 10.63 0.00 37.91 2.83
5568 5918 0.179234 TGGACTGCTCGGTCACAAAA 59.821 50.000 10.63 0.00 37.91 2.44
5569 5919 1.305201 GGACTGCTCGGTCACAAAAA 58.695 50.000 10.63 0.00 37.91 1.94
5570 5920 1.880027 GGACTGCTCGGTCACAAAAAT 59.120 47.619 10.63 0.00 37.91 1.82
5571 5921 2.095718 GGACTGCTCGGTCACAAAAATC 60.096 50.000 10.63 0.00 37.91 2.17
5572 5922 1.880027 ACTGCTCGGTCACAAAAATCC 59.120 47.619 0.00 0.00 0.00 3.01
5573 5923 1.879380 CTGCTCGGTCACAAAAATCCA 59.121 47.619 0.00 0.00 0.00 3.41
5574 5924 2.293122 CTGCTCGGTCACAAAAATCCAA 59.707 45.455 0.00 0.00 0.00 3.53
5575 5925 2.890311 TGCTCGGTCACAAAAATCCAAT 59.110 40.909 0.00 0.00 0.00 3.16
5576 5926 3.057596 TGCTCGGTCACAAAAATCCAATC 60.058 43.478 0.00 0.00 0.00 2.67
5577 5927 3.673323 GCTCGGTCACAAAAATCCAATCC 60.673 47.826 0.00 0.00 0.00 3.01
5578 5928 3.491342 TCGGTCACAAAAATCCAATCCA 58.509 40.909 0.00 0.00 0.00 3.41
5579 5929 3.505680 TCGGTCACAAAAATCCAATCCAG 59.494 43.478 0.00 0.00 0.00 3.86
5580 5930 3.505680 CGGTCACAAAAATCCAATCCAGA 59.494 43.478 0.00 0.00 0.00 3.86
5581 5931 4.615912 CGGTCACAAAAATCCAATCCAGAC 60.616 45.833 0.00 0.00 0.00 3.51
5582 5932 4.524328 GGTCACAAAAATCCAATCCAGACT 59.476 41.667 0.00 0.00 0.00 3.24
5583 5933 5.464168 GTCACAAAAATCCAATCCAGACTG 58.536 41.667 0.00 0.00 0.00 3.51
5584 5934 4.523943 TCACAAAAATCCAATCCAGACTGG 59.476 41.667 15.99 15.99 39.43 4.00
5585 5935 3.259123 ACAAAAATCCAATCCAGACTGGC 59.741 43.478 17.33 0.00 37.47 4.85
5586 5936 3.463048 AAAATCCAATCCAGACTGGCT 57.537 42.857 17.33 3.93 37.47 4.75
5587 5937 2.725221 AATCCAATCCAGACTGGCTC 57.275 50.000 17.33 0.00 37.47 4.70
5588 5938 0.842635 ATCCAATCCAGACTGGCTCC 59.157 55.000 17.33 0.00 37.47 4.70
5589 5939 0.252881 TCCAATCCAGACTGGCTCCT 60.253 55.000 17.33 0.00 37.47 3.69
5590 5940 0.622665 CCAATCCAGACTGGCTCCTT 59.377 55.000 17.33 4.79 37.47 3.36
5591 5941 1.839994 CCAATCCAGACTGGCTCCTTA 59.160 52.381 17.33 0.00 37.47 2.69
5592 5942 2.239654 CCAATCCAGACTGGCTCCTTAA 59.760 50.000 17.33 0.00 37.47 1.85
5593 5943 3.308402 CCAATCCAGACTGGCTCCTTAAA 60.308 47.826 17.33 0.00 37.47 1.52
5594 5944 3.636153 ATCCAGACTGGCTCCTTAAAC 57.364 47.619 17.33 0.00 37.47 2.01
5595 5945 1.275291 TCCAGACTGGCTCCTTAAACG 59.725 52.381 17.33 0.00 37.47 3.60
5596 5946 1.676014 CCAGACTGGCTCCTTAAACGG 60.676 57.143 8.99 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 189 9.981114 ACAAACTAAAAGACCATAAAATTCAGG 57.019 29.630 0.00 0.00 0.00 3.86
535 550 2.649816 AGGGTTAGCCAGTTCAAGGAAT 59.350 45.455 2.44 0.00 36.17 3.01
746 767 8.455903 CATGTCCATGTCCTCTATTTTAACAT 57.544 34.615 0.00 0.00 34.23 2.71
864 893 9.207868 ACAGCTACTCCTCTTATATTTCTTTCT 57.792 33.333 0.00 0.00 0.00 2.52
865 894 9.255304 CACAGCTACTCCTCTTATATTTCTTTC 57.745 37.037 0.00 0.00 0.00 2.62
917 947 7.977853 GGGTTTAGTTCTAGTATGTTCGATTGA 59.022 37.037 0.00 0.00 0.00 2.57
919 949 8.075761 AGGGTTTAGTTCTAGTATGTTCGATT 57.924 34.615 0.00 0.00 0.00 3.34
986 1016 2.717044 GCCATTTTGGGGGTACGGC 61.717 63.158 0.00 0.00 38.19 5.68
1056 1086 0.535335 ATTTCACGGCGAGGCTCTTA 59.465 50.000 16.62 0.00 0.00 2.10
1236 1266 4.482684 CGCTCGAAGCTGCGGAGA 62.483 66.667 15.70 0.00 43.61 3.71
1329 1359 1.077716 GAATTGGACAGGACCCGGG 60.078 63.158 22.25 22.25 0.00 5.73
1356 1387 2.458951 GCGAGACAAGCATAGAGACAG 58.541 52.381 0.00 0.00 34.19 3.51
1369 1400 0.319211 CCAACACTTACGGCGAGACA 60.319 55.000 16.62 0.00 0.00 3.41
1377 1408 6.918892 TTTATGATCCATCCAACACTTACG 57.081 37.500 0.00 0.00 0.00 3.18
1395 1426 5.755813 CAGCGGATCCAGAAATCTTTTATG 58.244 41.667 13.41 0.00 0.00 1.90
1546 1577 0.459899 CATCGATCGACCCCTCAACA 59.540 55.000 22.06 0.00 0.00 3.33
1603 1634 2.759535 CAGAAGCTCCAGTGATCTCAGA 59.240 50.000 0.00 0.00 0.00 3.27
1649 1680 7.542890 TCATAACAACAGCAGTTTCAAAAGAA 58.457 30.769 0.00 0.00 35.28 2.52
1654 1685 7.487484 TCAATTCATAACAACAGCAGTTTCAA 58.513 30.769 0.00 0.00 35.28 2.69
1688 1719 0.035458 GAGGTAGTGGCAGTGCAAGT 59.965 55.000 18.61 11.73 0.00 3.16
1705 1736 6.399669 CGTCCACAATAGTACTTCAAAACGAG 60.400 42.308 0.00 0.00 0.00 4.18
1716 1747 7.012138 TCTGATAGTTCTCGTCCACAATAGTAC 59.988 40.741 0.00 0.00 0.00 2.73
1717 1748 7.052248 TCTGATAGTTCTCGTCCACAATAGTA 58.948 38.462 0.00 0.00 0.00 1.82
1723 1754 4.079970 ACTTCTGATAGTTCTCGTCCACA 58.920 43.478 0.00 0.00 0.00 4.17
1803 1834 3.818773 CCCTAGAAACCAAACGTTGATGT 59.181 43.478 0.00 0.00 33.93 3.06
1811 1842 5.387788 TCTTTAACCCCCTAGAAACCAAAC 58.612 41.667 0.00 0.00 0.00 2.93
1936 1967 4.454728 TGACCAGAAAAATGCAATAGCC 57.545 40.909 0.00 0.00 41.13 3.93
1946 1977 3.568007 GGTGTACAGCATGACCAGAAAAA 59.432 43.478 19.87 0.00 39.69 1.94
1953 1984 0.533491 TACGGGTGTACAGCATGACC 59.467 55.000 25.23 8.31 39.69 4.02
1980 2011 2.024655 ACTGAAGATGGATGCACCCATT 60.025 45.455 15.69 0.00 46.34 3.16
2017 2048 1.488527 GTAGCAACCCTAGCGATTCG 58.511 55.000 0.62 0.62 37.01 3.34
2018 2049 1.138266 TGGTAGCAACCCTAGCGATTC 59.862 52.381 0.00 0.00 46.16 2.52
2091 2122 4.872357 TCGACTAGGCCCGACTAG 57.128 61.111 0.00 2.89 44.71 2.57
2153 2184 4.202212 GGTAGCAACCAATGGTTTTGAGTT 60.202 41.667 16.07 4.91 44.33 3.01
2272 2308 6.041511 TGTGGTTTCTTTCAACATCAATGTG 58.958 36.000 0.00 0.00 41.61 3.21
2275 2311 6.638610 TGTTGTGGTTTCTTTCAACATCAAT 58.361 32.000 5.64 0.00 42.96 2.57
2308 2344 8.199449 AGGTTGCAGATATCACAAAAATAATGG 58.801 33.333 11.47 0.00 0.00 3.16
2420 2456 5.278758 GCTACTTTTTGCCAAACAGGTCATA 60.279 40.000 8.12 0.00 40.61 2.15
2526 2628 3.325870 TGTGAAACTATGGTTGAGCTCG 58.674 45.455 9.64 0.00 38.04 5.03
2551 2653 1.965754 GCTCACCCTGCCACCTAGAG 61.966 65.000 0.00 0.00 0.00 2.43
2617 2719 3.149981 GGGAGAAACAAGACTGGGAAAG 58.850 50.000 0.00 0.00 0.00 2.62
2686 2788 3.234630 CTCCAAACCGAGCCACCGA 62.235 63.158 0.00 0.00 0.00 4.69
2710 2812 8.677148 TGTGACTAAGAGCATTAAGTTTTCTT 57.323 30.769 0.00 0.00 43.24 2.52
2809 2913 1.356527 GCCCGTGCCGTAACTAACAG 61.357 60.000 0.00 0.00 0.00 3.16
2815 2919 1.743995 AGAATGCCCGTGCCGTAAC 60.744 57.895 0.00 0.00 36.33 2.50
2908 3012 6.750775 ATTAACTCGATCTTTAAGTAGCGC 57.249 37.500 0.00 0.00 0.00 5.92
2965 3069 4.227538 CAGACAAAAGCTTGAGCATTCAG 58.772 43.478 0.00 0.00 45.16 3.02
3019 3123 4.386867 TCCACCAAATACTAAGCTCTCG 57.613 45.455 0.00 0.00 0.00 4.04
3102 3206 6.048732 TGAATCACAGCACTTCCAACTATA 57.951 37.500 0.00 0.00 0.00 1.31
3187 3332 4.840716 AATGCTCTGTTCTGAGGAAGAT 57.159 40.909 5.25 0.00 37.91 2.40
3238 3385 5.467035 TTGCAAAAATAGGAGGGAAAGTG 57.533 39.130 0.00 0.00 0.00 3.16
3349 3500 4.261614 GCACTTGCCTTAGCTTAGTTTTGT 60.262 41.667 0.00 0.00 40.80 2.83
3431 3583 7.891183 ACAGTCATGTGTCATACTTAACTTC 57.109 36.000 0.00 0.00 38.57 3.01
3662 3893 7.223777 GCTTTGTCAGCCAACTTTTTATTGTTA 59.776 33.333 0.00 0.00 43.65 2.41
3738 3969 2.420058 AAGCAGTAATTCCCCTTCGG 57.580 50.000 0.00 0.00 0.00 4.30
4102 4417 9.986157 TCTTTTCCTCCACTAGACTATTTAGTA 57.014 33.333 0.00 0.00 36.50 1.82
4103 4418 8.896722 TCTTTTCCTCCACTAGACTATTTAGT 57.103 34.615 0.00 0.00 39.71 2.24
4141 4463 9.467258 CTTGACAAAAGAATGACAATGTACATT 57.533 29.630 15.47 15.47 39.06 2.71
4263 4596 7.530426 AGCTTCCATGTCAATTAGTTTCTTT 57.470 32.000 0.00 0.00 0.00 2.52
4303 4636 5.220416 GCATGTCGAGTACCACTAATTTCAC 60.220 44.000 0.00 0.00 0.00 3.18
4338 4671 9.401873 GGTAGCGTAAACAAATTAAATGACTTT 57.598 29.630 0.00 0.00 0.00 2.66
4396 4729 4.096833 GCATGTAGCATTTCTGAATGTCCA 59.903 41.667 0.00 0.00 43.67 4.02
4452 4785 3.848019 CGTTGCTGCATCAAAAGTGATAC 59.152 43.478 4.23 0.00 42.88 2.24
4545 4878 2.483876 TCTTTCTCAGAAACAGCACCG 58.516 47.619 0.00 0.00 0.00 4.94
4636 4969 0.459585 TCTTGCCGCCAACTACGATC 60.460 55.000 0.00 0.00 0.00 3.69
4668 5001 4.200874 ACAACGACACTTATTTTGGACCA 58.799 39.130 0.00 0.00 0.00 4.02
4670 5003 6.259638 TGAAACAACGACACTTATTTTGGAC 58.740 36.000 0.00 0.00 0.00 4.02
4702 5035 1.004979 CCCGACCAAAATTCCTACCCA 59.995 52.381 0.00 0.00 0.00 4.51
4727 5061 5.116069 TCGCAACCAAAACTCCTAATTTC 57.884 39.130 0.00 0.00 0.00 2.17
4767 5101 2.791170 CTCATTCAGCAAGGAGGGC 58.209 57.895 0.00 0.00 36.88 5.19
4817 5151 1.447317 CCAACACCGCAGCTTCAGTT 61.447 55.000 0.00 0.00 0.00 3.16
4853 5187 9.436957 AGTTCACGAGTTTTCATTAGTTGATAT 57.563 29.630 0.00 0.00 33.34 1.63
4873 5207 9.036671 GTCTTAAATATCCTAGCTTGAGTTCAC 57.963 37.037 0.00 0.00 0.00 3.18
4896 5230 1.133136 ACACCACTACACAGGAGGTCT 60.133 52.381 0.00 0.00 33.47 3.85
4959 5293 4.556523 GCTTACGAGTAGTAAAAGGTGTCG 59.443 45.833 0.00 0.00 43.96 4.35
4963 5297 5.473066 TTGGCTTACGAGTAGTAAAAGGT 57.527 39.130 0.00 0.00 43.96 3.50
5009 5343 3.848272 ATAAAACCAGCCACAATGACG 57.152 42.857 0.00 0.00 0.00 4.35
5102 5436 2.923605 GCGAATGCAGCAACACATTCTT 60.924 45.455 0.00 0.00 46.43 2.52
5213 5548 4.465660 TGCTTTGGCTAATTTGATTGGCTA 59.534 37.500 8.55 0.68 44.92 3.93
5214 5549 3.261390 TGCTTTGGCTAATTTGATTGGCT 59.739 39.130 8.55 0.00 44.92 4.75
5215 5550 3.598299 TGCTTTGGCTAATTTGATTGGC 58.402 40.909 0.96 0.96 44.84 4.52
5216 5551 4.093850 GCTTGCTTTGGCTAATTTGATTGG 59.906 41.667 0.00 0.00 39.59 3.16
5217 5552 4.093850 GGCTTGCTTTGGCTAATTTGATTG 59.906 41.667 0.00 0.00 39.59 2.67
5256 5606 1.067212 CTTATTCACGGACGGAGGGAG 59.933 57.143 0.00 0.00 0.00 4.30
5258 5608 0.822164 ACTTATTCACGGACGGAGGG 59.178 55.000 0.00 0.00 0.00 4.30
5259 5609 1.203994 ACACTTATTCACGGACGGAGG 59.796 52.381 0.00 0.00 0.00 4.30
5261 5611 2.819019 TGTACACTTATTCACGGACGGA 59.181 45.455 0.00 0.00 0.00 4.69
5264 5614 8.644318 AATTAGATGTACACTTATTCACGGAC 57.356 34.615 0.00 0.00 0.00 4.79
5265 5615 9.661563 AAAATTAGATGTACACTTATTCACGGA 57.338 29.630 0.00 0.00 0.00 4.69
5361 5711 8.727910 GCATACATGACATCAGATTGATACATT 58.272 33.333 0.00 0.00 34.28 2.71
5362 5712 8.101419 AGCATACATGACATCAGATTGATACAT 58.899 33.333 0.00 0.00 34.28 2.29
5363 5713 7.447594 AGCATACATGACATCAGATTGATACA 58.552 34.615 0.00 0.00 34.28 2.29
5365 5715 8.810041 AGTAGCATACATGACATCAGATTGATA 58.190 33.333 0.00 0.00 46.26 2.15
5366 5716 7.677892 AGTAGCATACATGACATCAGATTGAT 58.322 34.615 0.00 0.00 46.26 2.57
5367 5717 7.059202 AGTAGCATACATGACATCAGATTGA 57.941 36.000 0.00 0.00 46.26 2.57
5368 5718 8.999220 ATAGTAGCATACATGACATCAGATTG 57.001 34.615 0.00 0.00 46.26 2.67
5369 5719 9.650539 GAATAGTAGCATACATGACATCAGATT 57.349 33.333 0.00 0.00 46.26 2.40
5372 5722 8.522003 AGAGAATAGTAGCATACATGACATCAG 58.478 37.037 0.00 0.00 46.26 2.90
5373 5723 8.414629 AGAGAATAGTAGCATACATGACATCA 57.585 34.615 0.00 0.00 46.26 3.07
5374 5724 9.352784 GAAGAGAATAGTAGCATACATGACATC 57.647 37.037 0.00 0.00 46.26 3.06
5375 5725 9.087871 AGAAGAGAATAGTAGCATACATGACAT 57.912 33.333 0.00 0.00 46.26 3.06
5376 5726 8.470657 AGAAGAGAATAGTAGCATACATGACA 57.529 34.615 0.00 0.00 46.26 3.58
5439 5789 9.419297 CGCCAATAAGTGTATATCTAGCTTTTA 57.581 33.333 0.00 0.00 0.00 1.52
5440 5790 7.387948 CCGCCAATAAGTGTATATCTAGCTTTT 59.612 37.037 0.00 0.00 0.00 2.27
5441 5791 6.874134 CCGCCAATAAGTGTATATCTAGCTTT 59.126 38.462 0.00 0.00 0.00 3.51
5442 5792 6.210784 TCCGCCAATAAGTGTATATCTAGCTT 59.789 38.462 0.00 0.00 0.00 3.74
5443 5793 5.715279 TCCGCCAATAAGTGTATATCTAGCT 59.285 40.000 0.00 0.00 0.00 3.32
5444 5794 5.805994 GTCCGCCAATAAGTGTATATCTAGC 59.194 44.000 0.00 0.00 0.00 3.42
5445 5795 6.028368 CGTCCGCCAATAAGTGTATATCTAG 58.972 44.000 0.00 0.00 0.00 2.43
5446 5796 5.106038 CCGTCCGCCAATAAGTGTATATCTA 60.106 44.000 0.00 0.00 0.00 1.98
5447 5797 4.321750 CCGTCCGCCAATAAGTGTATATCT 60.322 45.833 0.00 0.00 0.00 1.98
5448 5798 3.924686 CCGTCCGCCAATAAGTGTATATC 59.075 47.826 0.00 0.00 0.00 1.63
5449 5799 3.575256 TCCGTCCGCCAATAAGTGTATAT 59.425 43.478 0.00 0.00 0.00 0.86
5450 5800 2.957680 TCCGTCCGCCAATAAGTGTATA 59.042 45.455 0.00 0.00 0.00 1.47
5451 5801 1.758280 TCCGTCCGCCAATAAGTGTAT 59.242 47.619 0.00 0.00 0.00 2.29
5452 5802 1.135527 CTCCGTCCGCCAATAAGTGTA 59.864 52.381 0.00 0.00 0.00 2.90
5453 5803 0.108329 CTCCGTCCGCCAATAAGTGT 60.108 55.000 0.00 0.00 0.00 3.55
5454 5804 0.810031 CCTCCGTCCGCCAATAAGTG 60.810 60.000 0.00 0.00 0.00 3.16
5455 5805 1.520666 CCTCCGTCCGCCAATAAGT 59.479 57.895 0.00 0.00 0.00 2.24
5456 5806 1.227556 CCCTCCGTCCGCCAATAAG 60.228 63.158 0.00 0.00 0.00 1.73
5457 5807 1.682451 CTCCCTCCGTCCGCCAATAA 61.682 60.000 0.00 0.00 0.00 1.40
5458 5808 2.042741 TCCCTCCGTCCGCCAATA 60.043 61.111 0.00 0.00 0.00 1.90
5459 5809 2.866523 TACTCCCTCCGTCCGCCAAT 62.867 60.000 0.00 0.00 0.00 3.16
5460 5810 3.588817 TACTCCCTCCGTCCGCCAA 62.589 63.158 0.00 0.00 0.00 4.52
5461 5811 4.051167 TACTCCCTCCGTCCGCCA 62.051 66.667 0.00 0.00 0.00 5.69
5462 5812 3.217743 CTACTCCCTCCGTCCGCC 61.218 72.222 0.00 0.00 0.00 6.13
5463 5813 0.749454 TAACTACTCCCTCCGTCCGC 60.749 60.000 0.00 0.00 0.00 5.54
5464 5814 1.403323 GTTAACTACTCCCTCCGTCCG 59.597 57.143 0.00 0.00 0.00 4.79
5465 5815 2.450476 TGTTAACTACTCCCTCCGTCC 58.550 52.381 7.22 0.00 0.00 4.79
5466 5816 3.446516 ACATGTTAACTACTCCCTCCGTC 59.553 47.826 7.22 0.00 0.00 4.79
5467 5817 3.438183 ACATGTTAACTACTCCCTCCGT 58.562 45.455 7.22 0.00 0.00 4.69
5468 5818 4.467198 AACATGTTAACTACTCCCTCCG 57.533 45.455 9.97 0.00 0.00 4.63
5469 5819 6.148976 GTCAAAACATGTTAACTACTCCCTCC 59.851 42.308 12.39 0.00 0.00 4.30
5470 5820 6.708949 TGTCAAAACATGTTAACTACTCCCTC 59.291 38.462 12.39 0.00 0.00 4.30
5471 5821 6.485648 GTGTCAAAACATGTTAACTACTCCCT 59.514 38.462 12.39 0.00 37.81 4.20
5472 5822 6.261381 TGTGTCAAAACATGTTAACTACTCCC 59.739 38.462 12.39 2.56 37.81 4.30
5473 5823 7.012044 AGTGTGTCAAAACATGTTAACTACTCC 59.988 37.037 12.39 4.62 37.81 3.85
5474 5824 7.916552 AGTGTGTCAAAACATGTTAACTACTC 58.083 34.615 12.39 9.32 37.81 2.59
5475 5825 7.859325 AGTGTGTCAAAACATGTTAACTACT 57.141 32.000 12.39 14.38 37.81 2.57
5476 5826 8.905103 AAAGTGTGTCAAAACATGTTAACTAC 57.095 30.769 12.39 12.74 37.81 2.73
5514 5864 1.844130 GGGTTTGGGACACCTGACT 59.156 57.895 0.00 0.00 39.29 3.41
5515 5865 1.599797 CGGGTTTGGGACACCTGAC 60.600 63.158 0.00 0.00 42.69 3.51
5516 5866 2.833227 CGGGTTTGGGACACCTGA 59.167 61.111 0.00 0.00 42.69 3.86
5517 5867 2.983592 GCGGGTTTGGGACACCTG 60.984 66.667 0.00 0.00 42.91 4.00
5518 5868 4.280019 GGCGGGTTTGGGACACCT 62.280 66.667 0.00 0.00 39.29 4.00
5519 5869 4.280019 AGGCGGGTTTGGGACACC 62.280 66.667 0.00 0.00 39.29 4.16
5520 5870 2.671963 GAGGCGGGTTTGGGACAC 60.672 66.667 0.00 0.00 39.29 3.67
5521 5871 2.285889 TTTGAGGCGGGTTTGGGACA 62.286 55.000 0.00 0.00 0.00 4.02
5522 5872 1.529713 TTTGAGGCGGGTTTGGGAC 60.530 57.895 0.00 0.00 0.00 4.46
5523 5873 1.529713 GTTTGAGGCGGGTTTGGGA 60.530 57.895 0.00 0.00 0.00 4.37
5524 5874 2.914908 CGTTTGAGGCGGGTTTGGG 61.915 63.158 0.00 0.00 0.00 4.12
5525 5875 1.730451 AACGTTTGAGGCGGGTTTGG 61.730 55.000 0.00 0.00 0.00 3.28
5526 5876 0.317519 GAACGTTTGAGGCGGGTTTG 60.318 55.000 0.46 0.00 0.00 2.93
5527 5877 1.778027 CGAACGTTTGAGGCGGGTTT 61.778 55.000 10.16 0.00 0.00 3.27
5528 5878 2.248835 CGAACGTTTGAGGCGGGTT 61.249 57.895 10.16 0.00 0.00 4.11
5529 5879 2.663852 CGAACGTTTGAGGCGGGT 60.664 61.111 10.16 0.00 0.00 5.28
5530 5880 3.419759 CCGAACGTTTGAGGCGGG 61.420 66.667 17.38 0.00 38.40 6.13
5531 5881 3.419759 CCCGAACGTTTGAGGCGG 61.420 66.667 17.38 16.67 41.53 6.13
5532 5882 2.663852 ACCCGAACGTTTGAGGCG 60.664 61.111 17.38 8.20 0.00 5.52
5533 5883 2.613506 CCACCCGAACGTTTGAGGC 61.614 63.158 17.38 0.00 0.00 4.70
5534 5884 1.070105 TCCACCCGAACGTTTGAGG 59.930 57.895 17.38 17.14 0.00 3.86
5535 5885 0.249741 AGTCCACCCGAACGTTTGAG 60.250 55.000 17.38 6.28 0.00 3.02
5536 5886 0.531090 CAGTCCACCCGAACGTTTGA 60.531 55.000 17.38 0.00 0.00 2.69
5537 5887 1.938861 CAGTCCACCCGAACGTTTG 59.061 57.895 8.68 8.68 0.00 2.93
5538 5888 1.890510 GCAGTCCACCCGAACGTTT 60.891 57.895 0.46 0.00 0.00 3.60
5539 5889 2.280592 GCAGTCCACCCGAACGTT 60.281 61.111 0.00 0.00 0.00 3.99
5540 5890 3.222354 GAGCAGTCCACCCGAACGT 62.222 63.158 0.00 0.00 0.00 3.99
5541 5891 2.432628 GAGCAGTCCACCCGAACG 60.433 66.667 0.00 0.00 0.00 3.95
5542 5892 2.432628 CGAGCAGTCCACCCGAAC 60.433 66.667 0.00 0.00 0.00 3.95
5543 5893 3.691342 CCGAGCAGTCCACCCGAA 61.691 66.667 0.00 0.00 0.00 4.30
5544 5894 4.988716 ACCGAGCAGTCCACCCGA 62.989 66.667 0.00 0.00 0.00 5.14
5545 5895 4.436998 GACCGAGCAGTCCACCCG 62.437 72.222 0.00 0.00 0.00 5.28
5546 5896 3.311110 TGACCGAGCAGTCCACCC 61.311 66.667 0.00 0.00 35.83 4.61
5547 5897 2.048127 GTGACCGAGCAGTCCACC 60.048 66.667 0.00 0.00 35.83 4.61
5548 5898 0.531974 TTTGTGACCGAGCAGTCCAC 60.532 55.000 0.00 0.00 35.83 4.02
5549 5899 0.179234 TTTTGTGACCGAGCAGTCCA 59.821 50.000 0.00 0.00 35.83 4.02
5550 5900 1.305201 TTTTTGTGACCGAGCAGTCC 58.695 50.000 0.00 0.00 35.83 3.85
5551 5901 2.095718 GGATTTTTGTGACCGAGCAGTC 60.096 50.000 0.00 0.00 37.28 3.51
5552 5902 1.880027 GGATTTTTGTGACCGAGCAGT 59.120 47.619 0.00 0.00 0.00 4.40
5553 5903 1.879380 TGGATTTTTGTGACCGAGCAG 59.121 47.619 0.00 0.00 0.00 4.24
5554 5904 1.974265 TGGATTTTTGTGACCGAGCA 58.026 45.000 0.00 0.00 0.00 4.26
5555 5905 3.501950 GATTGGATTTTTGTGACCGAGC 58.498 45.455 0.00 0.00 0.00 5.03
5556 5906 3.505680 TGGATTGGATTTTTGTGACCGAG 59.494 43.478 0.00 0.00 0.00 4.63
5557 5907 3.491342 TGGATTGGATTTTTGTGACCGA 58.509 40.909 0.00 0.00 0.00 4.69
5558 5908 3.505680 TCTGGATTGGATTTTTGTGACCG 59.494 43.478 0.00 0.00 0.00 4.79
5559 5909 4.524328 AGTCTGGATTGGATTTTTGTGACC 59.476 41.667 0.00 0.00 0.00 4.02
5560 5910 5.464168 CAGTCTGGATTGGATTTTTGTGAC 58.536 41.667 0.00 0.00 0.00 3.67
5561 5911 4.523943 CCAGTCTGGATTGGATTTTTGTGA 59.476 41.667 14.26 0.00 40.96 3.58
5562 5912 4.813027 CCAGTCTGGATTGGATTTTTGTG 58.187 43.478 14.26 0.00 40.96 3.33
5563 5913 3.259123 GCCAGTCTGGATTGGATTTTTGT 59.741 43.478 23.77 0.00 40.96 2.83
5564 5914 3.512724 AGCCAGTCTGGATTGGATTTTTG 59.487 43.478 23.77 0.00 40.96 2.44
5565 5915 3.766051 GAGCCAGTCTGGATTGGATTTTT 59.234 43.478 23.77 0.00 35.51 1.94
5566 5916 3.359950 GAGCCAGTCTGGATTGGATTTT 58.640 45.455 23.77 0.00 35.51 1.82
5567 5917 2.357569 GGAGCCAGTCTGGATTGGATTT 60.358 50.000 23.77 1.30 35.51 2.17
5568 5918 1.213926 GGAGCCAGTCTGGATTGGATT 59.786 52.381 23.77 3.46 35.51 3.01
5569 5919 0.842635 GGAGCCAGTCTGGATTGGAT 59.157 55.000 23.77 9.22 35.51 3.41
5570 5920 0.252881 AGGAGCCAGTCTGGATTGGA 60.253 55.000 23.77 0.00 35.51 3.53
5571 5921 0.622665 AAGGAGCCAGTCTGGATTGG 59.377 55.000 23.77 7.63 35.51 3.16
5572 5922 3.634397 TTAAGGAGCCAGTCTGGATTG 57.366 47.619 23.77 0.00 35.51 2.67
5573 5923 3.619979 CGTTTAAGGAGCCAGTCTGGATT 60.620 47.826 23.77 9.57 35.51 3.01
5574 5924 2.093447 CGTTTAAGGAGCCAGTCTGGAT 60.093 50.000 23.77 17.55 39.95 3.41
5575 5925 1.275291 CGTTTAAGGAGCCAGTCTGGA 59.725 52.381 23.77 0.00 40.96 3.86
5576 5926 1.676014 CCGTTTAAGGAGCCAGTCTGG 60.676 57.143 15.15 15.15 41.55 3.86
5577 5927 1.726853 CCGTTTAAGGAGCCAGTCTG 58.273 55.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.