Multiple sequence alignment - TraesCS4A01G260200

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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 TraesCS4A01G260200 chr4A 100.000 5585 0 0 1 5585 572829903 572835487 0.000000e+00 10314.0
1 TraesCS4A01G260200 chr4D 91.919 3403 160 48 1956 5303 30219895 30216553 0.000000e+00 4654.0
2 TraesCS4A01G260200 chr4D 90.196 1938 92 47 36 1952 30221795 30219935 0.000000e+00 2436.0
3 TraesCS4A01G260200 chr4D 86.607 112 14 1 237 347 414999555 414999666 7.600000e-24 122.0
4 TraesCS4A01G260200 chr4B 90.135 2818 188 44 1 2778 43113737 43110970 0.000000e+00 3581.0
5 TraesCS4A01G260200 chr4B 92.277 2538 132 38 2785 5303 43110886 43108394 0.000000e+00 3542.0
6 TraesCS4A01G260200 chr4B 88.293 205 10 6 5339 5543 43108393 43108203 3.360000e-57 233.0
7 TraesCS4A01G260200 chr4B 86.486 111 15 0 237 347 511163702 511163812 7.600000e-24 122.0
8 TraesCS4A01G260200 chr5A 92.632 95 7 0 249 343 174594116 174594022 2.710000e-28 137.0
9 TraesCS4A01G260200 chr3A 91.089 101 9 0 249 349 470095773 470095673 2.710000e-28 137.0
10 TraesCS4A01G260200 chr1D 94.253 87 5 0 254 340 143955556 143955470 3.510000e-27 134.0
11 TraesCS4A01G260200 chr1D 94.286 35 2 0 495 529 279521555 279521589 3.000000e-03 54.7
12 TraesCS4A01G260200 chr2A 91.579 95 7 1 254 347 53078427 53078521 4.540000e-26 130.0
13 TraesCS4A01G260200 chr2A 100.000 33 0 0 496 528 21557983 21557951 1.680000e-05 62.1
14 TraesCS4A01G260200 chr5B 90.625 96 9 0 249 344 166379177 166379082 1.630000e-25 128.0
15 TraesCS4A01G260200 chrUn 76.804 194 35 9 4874 5063 126690809 126690622 3.560000e-17 100.0
16 TraesCS4A01G260200 chrUn 82.979 94 13 3 496 588 31703118 31703209 1.290000e-11 82.4
17 TraesCS4A01G260200 chr2D 73.401 297 60 16 399 680 54888963 54888671 5.960000e-15 93.5
18 TraesCS4A01G260200 chr6D 76.289 194 26 11 496 676 56934716 56934530 9.970000e-13 86.1
19 TraesCS4A01G260200 chr6B 76.623 154 32 4 5282 5433 567477689 567477840 1.290000e-11 82.4
20 TraesCS4A01G260200 chr3B 93.023 43 2 1 496 537 580887841 580887883 1.680000e-05 62.1
21 TraesCS4A01G260200 chr7B 92.308 39 3 0 499 537 464549286 464549248 7.820000e-04 56.5


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 TraesCS4A01G260200 chr4A 572829903 572835487 5584 False 10314 10314 100.0000 1 5585 1 chr4A.!!$F1 5584
1 TraesCS4A01G260200 chr4D 30216553 30221795 5242 True 3545 4654 91.0575 36 5303 2 chr4D.!!$R1 5267
2 TraesCS4A01G260200 chr4B 43108203 43113737 5534 True 2452 3581 90.2350 1 5543 3 chr4B.!!$R1 5542

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
831 846 1.216710 CTCGTCCTCACCTCCTTGC 59.783 63.158 0.00 0.0 0.0 4.01 F
1202 1223 1.081277 ACCCTGACCCTTCCCTCTC 59.919 63.158 0.00 0.0 0.0 3.20 F
1952 1993 1.409427 GACCTCCCCTTGTCACTATCG 59.591 57.143 0.00 0.0 0.0 2.92 F
3479 3681 0.321919 ATCTGTGCACGCATGTTCCT 60.322 50.000 13.13 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 1977 0.325296 AGGCGATAGTGACAAGGGGA 60.325 55.000 0.00 0.0 39.35 4.81 R
2178 2258 1.540267 AGAGAGGACAACAGGACTCG 58.460 55.000 0.00 0.0 35.22 4.18 R
3551 3753 1.667724 GCCACTGCATCACATCAGTAC 59.332 52.381 0.00 0.0 41.19 2.73 R
5097 5311 0.603569 GAAGGCGTCTCAGACTCCAA 59.396 55.000 16.36 0.0 39.62 3.53 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
46 49 6.966021 TGAGACAAAATGTAGCCTACAAAAC 58.034 36.000 8.93 0.00 42.76 2.43
62 65 4.702831 ACAAAACCCACAAATCAATGTCC 58.297 39.130 0.00 0.00 0.00 4.02
64 67 5.600484 ACAAAACCCACAAATCAATGTCCTA 59.400 36.000 0.00 0.00 0.00 2.94
74 77 6.127814 ACAAATCAATGTCCTAGCAAGTCATG 60.128 38.462 0.00 0.00 0.00 3.07
115 118 5.838521 ACTTGTGGACAATTGGGAACTTATT 59.161 36.000 10.83 0.00 35.02 1.40
146 149 3.328505 GCAATGCAACTTGGTAAGCAAT 58.671 40.909 0.00 0.00 40.76 3.56
282 285 2.817538 AAGTGTCACGGTTTTGAACG 57.182 45.000 0.00 0.00 0.00 3.95
293 296 4.395854 ACGGTTTTGAACGAAGGTTAGTTT 59.604 37.500 0.00 0.00 36.24 2.66
340 343 7.289317 ACACTTATTATGGATCGAAGGGAGTAA 59.711 37.037 0.00 0.00 0.00 2.24
381 384 6.708949 AGAAGCCTACTAAACGAAAAATGTCA 59.291 34.615 0.00 0.00 0.00 3.58
397 400 5.640158 AATGTCATCCTAATAACCCCGAA 57.360 39.130 0.00 0.00 0.00 4.30
536 540 7.178805 TGAAATCACATTCATGGAGATTTGGAA 59.821 33.333 19.09 8.49 41.88 3.53
537 541 7.670605 AATCACATTCATGGAGATTTGGAAT 57.329 32.000 0.00 0.00 34.93 3.01
538 542 8.771521 AATCACATTCATGGAGATTTGGAATA 57.228 30.769 0.00 0.00 34.93 1.75
607 613 8.043710 TCTTTTTGAAGTATTTCTTTTTGCCCA 58.956 29.630 0.00 0.00 36.40 5.36
614 620 6.573094 AAGTATTTCTTTTTGCCCAGAGCATC 60.573 38.462 0.00 0.00 41.94 3.91
647 656 5.798125 TTTCATGGAAATTTACAGGCACA 57.202 34.783 10.25 0.00 0.00 4.57
723 738 7.841282 TTTGTCATTTTTAGGGTATTGGTCA 57.159 32.000 0.00 0.00 0.00 4.02
724 739 8.429237 TTTGTCATTTTTAGGGTATTGGTCAT 57.571 30.769 0.00 0.00 0.00 3.06
829 844 1.985116 GCCTCGTCCTCACCTCCTT 60.985 63.158 0.00 0.00 0.00 3.36
830 845 1.893786 CCTCGTCCTCACCTCCTTG 59.106 63.158 0.00 0.00 0.00 3.61
831 846 1.216710 CTCGTCCTCACCTCCTTGC 59.783 63.158 0.00 0.00 0.00 4.01
832 847 1.228894 TCGTCCTCACCTCCTTGCT 60.229 57.895 0.00 0.00 0.00 3.91
835 850 1.853963 GTCCTCACCTCCTTGCTCTA 58.146 55.000 0.00 0.00 0.00 2.43
881 896 1.421646 CCTTCCAGGTTCCAACAGACT 59.578 52.381 0.00 0.00 0.00 3.24
945 960 2.283173 CTTCCCACCACCAAGGCC 60.283 66.667 0.00 0.00 43.14 5.19
1202 1223 1.081277 ACCCTGACCCTTCCCTCTC 59.919 63.158 0.00 0.00 0.00 3.20
1220 1241 2.780094 CCCCAACGCTTTGTGCACA 61.780 57.895 17.42 17.42 43.06 4.57
1296 1324 5.338365 GCTTTGTCTCCAATTATTGAGCTG 58.662 41.667 6.50 0.00 28.80 4.24
1303 1331 2.016318 CAATTATTGAGCTGCCGGTGA 58.984 47.619 1.90 0.00 0.00 4.02
1441 1475 4.349048 TGATATTTGGATCTCCTGTCCCTG 59.651 45.833 0.00 0.00 34.76 4.45
1445 1479 1.909302 TGGATCTCCTGTCCCTGAAAC 59.091 52.381 0.00 0.00 34.76 2.78
1455 1489 4.253685 CTGTCCCTGAAACAATATCGTGT 58.746 43.478 0.00 0.00 0.00 4.49
1456 1490 4.000325 TGTCCCTGAAACAATATCGTGTG 59.000 43.478 0.00 0.00 0.00 3.82
1457 1491 4.250464 GTCCCTGAAACAATATCGTGTGA 58.750 43.478 0.00 0.00 0.00 3.58
1495 1529 2.807676 TGCAGAATTCCCCCTTTTCTC 58.192 47.619 0.65 0.00 0.00 2.87
1511 1545 6.920210 CCCTTTTCTCTGTCAAAAAGTTCATC 59.080 38.462 7.23 0.00 39.66 2.92
1588 1623 8.351495 TGTGATTCTCTTTGTTATTTTTGTGC 57.649 30.769 0.00 0.00 0.00 4.57
1591 1626 6.478512 TTCTCTTTGTTATTTTTGTGCCCT 57.521 33.333 0.00 0.00 0.00 5.19
1629 1664 4.742659 GCGTCAGAGATTCTTCAGTATTCC 59.257 45.833 0.00 0.00 0.00 3.01
1636 1671 7.011295 CAGAGATTCTTCAGTATTCCTCAAAGC 59.989 40.741 0.00 0.00 0.00 3.51
1684 1719 2.093235 GGGTTAGCTCAGTGCAGATTCT 60.093 50.000 0.00 0.00 45.94 2.40
1694 1735 1.694169 GCAGATTCTCCCCCTCCCA 60.694 63.158 0.00 0.00 0.00 4.37
1711 1752 3.371965 TCCCATACCACTGTAGTCTTCC 58.628 50.000 0.00 0.00 0.00 3.46
1896 1937 5.416271 TGGTCCACTGACTAGGTTATTTC 57.584 43.478 0.00 0.00 41.47 2.17
1898 1939 5.487488 TGGTCCACTGACTAGGTTATTTCAT 59.513 40.000 0.00 0.00 41.47 2.57
1921 1962 2.923908 AGGTCTTGGGGTTGGTACATA 58.076 47.619 0.00 0.00 39.30 2.29
1952 1993 1.409427 GACCTCCCCTTGTCACTATCG 59.591 57.143 0.00 0.00 0.00 2.92
1969 2046 1.629043 TCGCCTAGTGTTCTTGACCT 58.371 50.000 0.00 0.00 0.00 3.85
1975 2052 3.244112 CCTAGTGTTCTTGACCTTCCGTT 60.244 47.826 0.00 0.00 0.00 4.44
2016 2093 3.005554 CGGCTCAACATCTTGTCAGAAT 58.994 45.455 0.00 0.00 30.76 2.40
2062 2139 6.547141 TCATTCTCATGTTTCAACTCCAGTTT 59.453 34.615 0.00 0.00 35.83 2.66
2068 2145 6.979817 TCATGTTTCAACTCCAGTTTCAATTG 59.020 34.615 0.00 0.00 35.83 2.32
2090 2167 5.253330 TGTGAACACAGAAAAGAGGTTCTT 58.747 37.500 3.39 0.00 38.82 2.52
2093 2170 5.586243 TGAACACAGAAAAGAGGTTCTTGAG 59.414 40.000 0.00 0.00 36.71 3.02
2165 2245 5.700832 AGACGCAGACATTCAGAACATTTTA 59.299 36.000 0.00 0.00 0.00 1.52
2192 2272 1.374758 CTGCCGAGTCCTGTTGTCC 60.375 63.158 0.00 0.00 0.00 4.02
2212 2292 9.352191 GTTGTCCTCTCTAGAATATGGTACTTA 57.648 37.037 0.00 0.00 0.00 2.24
2264 2345 7.170393 TCTGAGATTCCATCTTCGTCTTTAA 57.830 36.000 0.00 0.00 40.38 1.52
2265 2346 7.786030 TCTGAGATTCCATCTTCGTCTTTAAT 58.214 34.615 0.00 0.00 40.38 1.40
2273 2354 7.748847 TCCATCTTCGTCTTTAATTTGCTAAC 58.251 34.615 0.00 0.00 0.00 2.34
2278 2359 8.832521 TCTTCGTCTTTAATTTGCTAACTTTGA 58.167 29.630 0.00 0.00 0.00 2.69
2395 2483 4.872691 CACACTCACTCCACCTATCAAATC 59.127 45.833 0.00 0.00 0.00 2.17
2492 2580 6.238347 CCCTGCAAAAATTAAACCTTGTCAAC 60.238 38.462 0.00 0.00 0.00 3.18
2494 2582 7.148340 CCTGCAAAAATTAAACCTTGTCAACAA 60.148 33.333 0.00 0.00 0.00 2.83
2502 2590 4.718940 AACCTTGTCAACAACCTTCTTG 57.281 40.909 0.00 0.00 0.00 3.02
2528 2624 8.671028 GTTGTTTTAGTACAAGTCCAAGAGAAA 58.329 33.333 0.00 0.00 38.60 2.52
2529 2625 8.795842 TGTTTTAGTACAAGTCCAAGAGAAAA 57.204 30.769 0.00 0.00 0.00 2.29
2560 2659 4.501058 GGTTTAGGAAGTAGTATCCCGCAG 60.501 50.000 0.00 0.00 37.71 5.18
2593 2692 7.981225 AGCACTTTCACATGAAAAACAGTTTAT 59.019 29.630 8.33 0.00 42.72 1.40
2763 2879 0.682292 TCGTGGATTGGCTGTGTGTA 59.318 50.000 0.00 0.00 0.00 2.90
2778 2894 8.660373 TGGCTGTGTGTAAAAACATTTAAAAAG 58.340 29.630 0.00 0.00 31.49 2.27
2780 2896 9.900264 GCTGTGTGTAAAAACATTTAAAAAGAG 57.100 29.630 0.00 0.00 31.49 2.85
2837 3030 4.956075 GGGGATTGTGAACCTTACATTCAT 59.044 41.667 0.00 0.00 38.31 2.57
3116 3310 2.164624 AGTGGCGTAGATCTCACAAGAC 59.835 50.000 13.12 0.00 33.32 3.01
3156 3350 4.569943 CACACTGCACAGGTAGTCTAAAT 58.430 43.478 2.21 0.00 37.94 1.40
3324 3518 1.949465 ACCCGTTGTTTGACTCAGTC 58.051 50.000 0.00 0.00 0.00 3.51
3333 3527 7.186804 CGTTGTTTGACTCAGTCTTAAATGTT 58.813 34.615 6.33 0.00 33.15 2.71
3334 3528 8.332464 CGTTGTTTGACTCAGTCTTAAATGTTA 58.668 33.333 6.33 0.00 33.15 2.41
3335 3529 9.651718 GTTGTTTGACTCAGTCTTAAATGTTAG 57.348 33.333 6.33 0.00 33.15 2.34
3470 3672 2.654749 TCCTCTACAATCTGTGCACG 57.345 50.000 13.13 7.36 0.00 5.34
3479 3681 0.321919 ATCTGTGCACGCATGTTCCT 60.322 50.000 13.13 0.00 0.00 3.36
3496 3698 4.141181 TGTTCCTTCATATATTGCTGCCCT 60.141 41.667 0.00 0.00 0.00 5.19
3547 3749 8.831550 GTCTAACCTGGATATCTTTTTCATCAC 58.168 37.037 0.00 0.00 0.00 3.06
3551 3753 5.533903 CCTGGATATCTTTTTCATCACTGGG 59.466 44.000 2.05 0.00 0.00 4.45
3681 3883 4.664150 TTTGGCTAGTTTTGAGGTTTGG 57.336 40.909 0.00 0.00 0.00 3.28
3695 3897 4.693566 TGAGGTTTGGCTACATCTTTAACG 59.306 41.667 6.56 0.00 30.56 3.18
3778 3980 1.078709 CATTCGTGCAGATGGTTCGT 58.921 50.000 0.00 0.00 0.00 3.85
3786 3988 4.430007 GTGCAGATGGTTCGTGACTATAA 58.570 43.478 0.00 0.00 28.41 0.98
3992 4195 3.788227 ACTGTACATGGCCTTCTTTCA 57.212 42.857 3.32 0.00 0.00 2.69
3993 4196 4.307032 ACTGTACATGGCCTTCTTTCAT 57.693 40.909 3.32 0.00 0.00 2.57
3995 4198 4.702131 ACTGTACATGGCCTTCTTTCATTC 59.298 41.667 3.32 0.00 0.00 2.67
3998 4201 2.043526 ACATGGCCTTCTTTCATTCCCT 59.956 45.455 3.32 0.00 0.00 4.20
4000 4203 4.264352 ACATGGCCTTCTTTCATTCCCTTA 60.264 41.667 3.32 0.00 0.00 2.69
4001 4204 4.608170 TGGCCTTCTTTCATTCCCTTAT 57.392 40.909 3.32 0.00 0.00 1.73
4002 4205 4.946646 TGGCCTTCTTTCATTCCCTTATT 58.053 39.130 3.32 0.00 0.00 1.40
4003 4206 4.956075 TGGCCTTCTTTCATTCCCTTATTC 59.044 41.667 3.32 0.00 0.00 1.75
4004 4207 5.204292 GGCCTTCTTTCATTCCCTTATTCT 58.796 41.667 0.00 0.00 0.00 2.40
4005 4208 5.658634 GGCCTTCTTTCATTCCCTTATTCTT 59.341 40.000 0.00 0.00 0.00 2.52
4006 4209 6.833933 GGCCTTCTTTCATTCCCTTATTCTTA 59.166 38.462 0.00 0.00 0.00 2.10
4007 4210 7.342026 GGCCTTCTTTCATTCCCTTATTCTTAA 59.658 37.037 0.00 0.00 0.00 1.85
4008 4211 8.918116 GCCTTCTTTCATTCCCTTATTCTTAAT 58.082 33.333 0.00 0.00 0.00 1.40
4161 4364 0.322277 ACATGGCAAGCAGGTGAGAG 60.322 55.000 0.00 0.00 0.00 3.20
4172 4375 2.873245 GCAGGTGAGAGTCAAGCATCAA 60.873 50.000 0.00 0.00 0.00 2.57
4175 4378 4.070716 AGGTGAGAGTCAAGCATCAAAAG 58.929 43.478 0.00 0.00 0.00 2.27
4191 4394 6.073440 GCATCAAAAGCATCAACAATGTTCTT 60.073 34.615 0.00 0.00 37.71 2.52
4192 4395 7.507304 CATCAAAAGCATCAACAATGTTCTTC 58.493 34.615 0.00 0.00 37.71 2.87
4201 4404 7.066766 GCATCAACAATGTTCTTCCTATCTTCT 59.933 37.037 0.00 0.00 37.71 2.85
4203 4406 6.372659 TCAACAATGTTCTTCCTATCTTCTGC 59.627 38.462 0.00 0.00 0.00 4.26
4207 4410 3.782523 TGTTCTTCCTATCTTCTGCCCAT 59.217 43.478 0.00 0.00 0.00 4.00
4221 4424 1.888018 CCCATTGACAGCCAAGCAG 59.112 57.895 0.00 0.00 38.31 4.24
4333 4537 2.426024 GAGCCAAATGATCTGTGCATGT 59.574 45.455 0.00 0.00 0.00 3.21
4338 4542 4.201980 CCAAATGATCTGTGCATGTAGGTG 60.202 45.833 0.00 0.00 0.00 4.00
4401 4605 3.284449 GGTGCGGGCGACTTGTTT 61.284 61.111 0.00 0.00 0.00 2.83
4423 4627 3.698820 GCGGGTTCCTGTACGGGT 61.699 66.667 20.40 0.00 0.00 5.28
4464 4668 2.031163 GAGTGCTGCAAGGTCGGT 59.969 61.111 2.77 0.00 0.00 4.69
4741 4947 5.882557 GCTGGAGGTGAATGAAGAGATAAAA 59.117 40.000 0.00 0.00 0.00 1.52
4742 4948 6.545298 GCTGGAGGTGAATGAAGAGATAAAAT 59.455 38.462 0.00 0.00 0.00 1.82
4743 4949 7.468357 GCTGGAGGTGAATGAAGAGATAAAATG 60.468 40.741 0.00 0.00 0.00 2.32
4790 4998 6.985059 TGCATGTGTCTGAATTTGAATTTGAA 59.015 30.769 0.00 0.00 0.00 2.69
4793 5001 9.419297 CATGTGTCTGAATTTGAATTTGAATCT 57.581 29.630 0.00 0.00 0.00 2.40
4817 5027 6.727824 AAATTCGAACTTCTGACTGGTATG 57.272 37.500 0.00 0.00 0.00 2.39
4832 5042 8.978874 TGACTGGTATGCTAAATGAACATAAT 57.021 30.769 0.00 0.00 0.00 1.28
4833 5043 8.839343 TGACTGGTATGCTAAATGAACATAATG 58.161 33.333 0.00 0.00 0.00 1.90
4842 5052 9.056005 TGCTAAATGAACATAATGGTAGTCATC 57.944 33.333 0.00 0.00 34.44 2.92
4843 5053 9.056005 GCTAAATGAACATAATGGTAGTCATCA 57.944 33.333 0.00 0.00 34.44 3.07
4989 5199 6.824305 ACAACTTGATTGATTAAGGGACAG 57.176 37.500 0.00 0.00 41.23 3.51
5089 5303 2.034066 CCTCCACCGCCAACATGT 59.966 61.111 0.00 0.00 0.00 3.21
5097 5311 1.447838 CGCCAACATGTCCGCTACT 60.448 57.895 13.44 0.00 0.00 2.57
5137 5351 3.160269 CAAGAAGGAAGAACAATGCCCT 58.840 45.455 0.00 0.00 0.00 5.19
5163 5377 2.437895 TCGTCTCCGGCATCGACT 60.438 61.111 0.00 0.00 39.00 4.18
5170 5384 4.193334 CGGCATCGACTCTCGCCA 62.193 66.667 10.91 0.00 45.14 5.69
5172 5386 2.167861 GGCATCGACTCTCGCCAAC 61.168 63.158 6.73 0.00 44.25 3.77
5197 5411 3.662759 AGAACTTTCACCCAGAAACCA 57.337 42.857 0.00 0.00 41.17 3.67
5205 5419 0.106217 ACCCAGAAACCACCCACAAG 60.106 55.000 0.00 0.00 0.00 3.16
5303 5517 5.463286 GTTTTCACCGGGTTTTCGATATTT 58.537 37.500 6.32 0.00 0.00 1.40
5304 5518 4.950434 TTCACCGGGTTTTCGATATTTC 57.050 40.909 6.32 0.00 0.00 2.17
5305 5519 4.210724 TCACCGGGTTTTCGATATTTCT 57.789 40.909 6.32 0.00 0.00 2.52
5306 5520 4.186159 TCACCGGGTTTTCGATATTTCTC 58.814 43.478 6.32 0.00 0.00 2.87
5307 5521 3.000925 CACCGGGTTTTCGATATTTCTCG 59.999 47.826 6.32 0.00 39.99 4.04
5308 5522 3.192466 CCGGGTTTTCGATATTTCTCGT 58.808 45.455 0.00 0.00 39.62 4.18
5309 5523 3.000925 CCGGGTTTTCGATATTTCTCGTG 59.999 47.826 0.00 0.00 39.62 4.35
5310 5524 3.615496 CGGGTTTTCGATATTTCTCGTGT 59.385 43.478 0.00 0.00 39.62 4.49
5311 5525 4.259690 CGGGTTTTCGATATTTCTCGTGTC 60.260 45.833 0.00 0.00 39.62 3.67
5312 5526 4.868734 GGGTTTTCGATATTTCTCGTGTCT 59.131 41.667 0.00 0.00 39.62 3.41
5313 5527 5.350640 GGGTTTTCGATATTTCTCGTGTCTT 59.649 40.000 0.00 0.00 39.62 3.01
5314 5528 6.128363 GGGTTTTCGATATTTCTCGTGTCTTT 60.128 38.462 0.00 0.00 39.62 2.52
5315 5529 6.954297 GGTTTTCGATATTTCTCGTGTCTTTC 59.046 38.462 0.00 0.00 39.62 2.62
5316 5530 7.148623 GGTTTTCGATATTTCTCGTGTCTTTCT 60.149 37.037 0.00 0.00 39.62 2.52
5317 5531 8.857216 GTTTTCGATATTTCTCGTGTCTTTCTA 58.143 33.333 0.00 0.00 39.62 2.10
5318 5532 8.975410 TTTCGATATTTCTCGTGTCTTTCTAA 57.025 30.769 0.00 0.00 39.62 2.10
5319 5533 7.966157 TCGATATTTCTCGTGTCTTTCTAAC 57.034 36.000 0.00 0.00 39.62 2.34
5320 5534 6.685828 TCGATATTTCTCGTGTCTTTCTAACG 59.314 38.462 0.00 0.00 39.62 3.18
5321 5535 6.468319 CGATATTTCTCGTGTCTTTCTAACGT 59.532 38.462 0.00 0.00 38.43 3.99
5322 5536 7.008086 CGATATTTCTCGTGTCTTTCTAACGTT 59.992 37.037 5.88 5.88 38.43 3.99
5323 5537 9.282247 GATATTTCTCGTGTCTTTCTAACGTTA 57.718 33.333 7.94 7.94 38.43 3.18
5324 5538 7.935338 ATTTCTCGTGTCTTTCTAACGTTAA 57.065 32.000 9.68 0.00 38.43 2.01
5325 5539 6.738352 TTCTCGTGTCTTTCTAACGTTAAC 57.262 37.500 9.68 4.88 38.43 2.01
5326 5540 5.215160 TCTCGTGTCTTTCTAACGTTAACC 58.785 41.667 9.68 0.00 38.43 2.85
5327 5541 4.930963 TCGTGTCTTTCTAACGTTAACCA 58.069 39.130 9.68 0.00 38.43 3.67
5328 5542 5.531634 TCGTGTCTTTCTAACGTTAACCAT 58.468 37.500 9.68 0.00 38.43 3.55
5329 5543 5.630680 TCGTGTCTTTCTAACGTTAACCATC 59.369 40.000 9.68 0.20 38.43 3.51
5330 5544 5.164022 CGTGTCTTTCTAACGTTAACCATCC 60.164 44.000 9.68 0.00 32.79 3.51
5331 5545 4.925054 TGTCTTTCTAACGTTAACCATCCG 59.075 41.667 9.68 0.00 0.00 4.18
5332 5546 5.163513 GTCTTTCTAACGTTAACCATCCGA 58.836 41.667 9.68 0.00 0.00 4.55
5333 5547 5.287992 GTCTTTCTAACGTTAACCATCCGAG 59.712 44.000 9.68 0.00 0.00 4.63
5334 5548 5.183713 TCTTTCTAACGTTAACCATCCGAGA 59.816 40.000 9.68 0.00 0.00 4.04
5335 5549 5.389859 TTCTAACGTTAACCATCCGAGAA 57.610 39.130 9.68 4.97 0.00 2.87
5336 5550 5.389859 TCTAACGTTAACCATCCGAGAAA 57.610 39.130 9.68 0.00 0.00 2.52
5337 5551 5.404946 TCTAACGTTAACCATCCGAGAAAG 58.595 41.667 9.68 0.00 0.00 2.62
5349 5563 5.239525 CCATCCGAGAAAGAAGAAAACTTGT 59.760 40.000 0.00 0.00 0.00 3.16
5402 5616 8.837788 ATTTTTGAAAGGAACCAATCAAGATC 57.162 30.769 9.83 0.00 33.71 2.75
5403 5617 6.975196 TTTGAAAGGAACCAATCAAGATCA 57.025 33.333 0.00 0.00 33.71 2.92
5404 5618 5.964958 TGAAAGGAACCAATCAAGATCAC 57.035 39.130 0.00 0.00 0.00 3.06
5405 5619 5.384336 TGAAAGGAACCAATCAAGATCACA 58.616 37.500 0.00 0.00 0.00 3.58
5451 5665 6.083887 AACTTTTGTTGTGCATCAGTGCTTT 61.084 36.000 0.00 0.00 45.60 3.51
5500 5714 5.640218 AGCACAATTGAACAAAATCGTTG 57.360 34.783 13.59 0.00 0.00 4.10
5522 5736 8.261908 CGTTGAAATTCAAAAGAGTGCTAAAAG 58.738 33.333 10.27 0.00 38.22 2.27
5543 5757 7.716799 AAAGATACTTTTAATCCATGCACCA 57.283 32.000 0.00 0.00 0.00 4.17
5544 5758 6.949352 AGATACTTTTAATCCATGCACCAG 57.051 37.500 0.00 0.00 0.00 4.00
5545 5759 6.426587 AGATACTTTTAATCCATGCACCAGT 58.573 36.000 0.00 0.00 0.00 4.00
5546 5760 4.789012 ACTTTTAATCCATGCACCAGTG 57.211 40.909 0.00 0.00 0.00 3.66
5547 5761 4.151883 ACTTTTAATCCATGCACCAGTGT 58.848 39.130 0.00 0.00 0.00 3.55
5548 5762 4.022068 ACTTTTAATCCATGCACCAGTGTG 60.022 41.667 0.00 0.00 45.65 3.82
5549 5763 2.877097 TAATCCATGCACCAGTGTGT 57.123 45.000 0.00 0.00 44.65 3.72
5550 5764 1.250328 AATCCATGCACCAGTGTGTG 58.750 50.000 0.00 7.22 44.65 3.82
5551 5765 0.111061 ATCCATGCACCAGTGTGTGT 59.889 50.000 11.74 0.00 44.65 3.72
5552 5766 0.818852 TCCATGCACCAGTGTGTGTG 60.819 55.000 11.74 4.15 44.65 3.82
5553 5767 1.102809 CCATGCACCAGTGTGTGTGT 61.103 55.000 11.74 1.39 44.65 3.72
5554 5768 0.029700 CATGCACCAGTGTGTGTGTG 59.970 55.000 11.74 3.52 44.65 3.82
5555 5769 0.394216 ATGCACCAGTGTGTGTGTGT 60.394 50.000 11.74 0.00 44.65 3.72
5556 5770 1.304509 TGCACCAGTGTGTGTGTGTG 61.305 55.000 11.74 2.29 44.65 3.82
5557 5771 1.305219 GCACCAGTGTGTGTGTGTGT 61.305 55.000 11.74 0.00 44.65 3.72
5558 5772 0.447406 CACCAGTGTGTGTGTGTGTG 59.553 55.000 4.18 0.00 37.72 3.82
5559 5773 0.036164 ACCAGTGTGTGTGTGTGTGT 59.964 50.000 0.00 0.00 0.00 3.72
5560 5774 0.447406 CCAGTGTGTGTGTGTGTGTG 59.553 55.000 0.00 0.00 0.00 3.82
5561 5775 1.155889 CAGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
5562 5776 1.136000 CAGTGTGTGTGTGTGTGTGTG 60.136 52.381 0.00 0.00 0.00 3.82
5563 5777 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
5564 5778 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
5565 5779 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
5566 5780 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
5567 5781 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
5568 5782 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
5569 5783 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
5570 5784 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
5571 5785 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
5572 5786 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
5573 5787 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
5574 5788 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
5575 5789 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
5576 5790 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
5577 5791 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
5578 5792 2.070028 GTGTGTGTGTGTGTGTGTGTA 58.930 47.619 0.00 0.00 0.00 2.90
5579 5793 2.480802 GTGTGTGTGTGTGTGTGTGTAA 59.519 45.455 0.00 0.00 0.00 2.41
5580 5794 3.058846 GTGTGTGTGTGTGTGTGTGTAAA 60.059 43.478 0.00 0.00 0.00 2.01
5581 5795 3.187432 TGTGTGTGTGTGTGTGTGTAAAG 59.813 43.478 0.00 0.00 0.00 1.85
5582 5796 3.433957 GTGTGTGTGTGTGTGTGTAAAGA 59.566 43.478 0.00 0.00 0.00 2.52
5583 5797 4.094294 GTGTGTGTGTGTGTGTGTAAAGAT 59.906 41.667 0.00 0.00 0.00 2.40
5584 5798 5.292345 GTGTGTGTGTGTGTGTGTAAAGATA 59.708 40.000 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.243060 GGGTTTTGTAGGCTACATTTTGTCT 59.757 40.000 26.71 0.00 38.68 3.41
27 28 5.221342 TGTGGGTTTTGTAGGCTACATTTTG 60.221 40.000 26.71 0.00 38.68 2.44
32 33 3.579534 TTGTGGGTTTTGTAGGCTACA 57.420 42.857 22.96 22.96 36.79 2.74
33 34 4.521256 TGATTTGTGGGTTTTGTAGGCTAC 59.479 41.667 17.76 17.76 0.00 3.58
34 35 4.730966 TGATTTGTGGGTTTTGTAGGCTA 58.269 39.130 0.00 0.00 0.00 3.93
46 49 3.355378 TGCTAGGACATTGATTTGTGGG 58.645 45.455 0.00 0.00 0.00 4.61
115 118 1.075374 AGTTGCATTGCCCACCTCTAA 59.925 47.619 6.12 0.00 0.00 2.10
293 296 6.704493 AGTGTCGCAGTTTTGAACTAAGATTA 59.296 34.615 0.00 0.00 40.46 1.75
353 356 7.860872 ACATTTTTCGTTTAGTAGGCTTCTTTG 59.139 33.333 0.00 0.00 0.00 2.77
381 384 5.703730 TTTGAGTTCGGGGTTATTAGGAT 57.296 39.130 0.00 0.00 0.00 3.24
391 394 1.595093 GGGTGCATTTGAGTTCGGGG 61.595 60.000 0.00 0.00 0.00 5.73
397 400 7.902920 ATTATTCATAAGGGTGCATTTGAGT 57.097 32.000 0.00 0.00 0.00 3.41
472 476 9.881649 TGCAGCCATACAAAAATATAAAAATGA 57.118 25.926 0.00 0.00 0.00 2.57
629 637 6.663093 TGTTCTATGTGCCTGTAAATTTCCAT 59.337 34.615 0.00 0.00 0.00 3.41
630 638 6.007076 TGTTCTATGTGCCTGTAAATTTCCA 58.993 36.000 0.00 0.00 0.00 3.53
829 844 6.827727 GGTTCTCCCTGTTTTATATAGAGCA 58.172 40.000 0.00 0.00 0.00 4.26
1031 1052 1.271127 GGAGGGAGGAAGAAGCTGCT 61.271 60.000 0.00 0.00 0.00 4.24
1032 1053 1.223211 GGAGGGAGGAAGAAGCTGC 59.777 63.158 0.00 0.00 0.00 5.25
1033 1054 1.631071 GGGGAGGGAGGAAGAAGCTG 61.631 65.000 0.00 0.00 0.00 4.24
1034 1055 1.307430 GGGGAGGGAGGAAGAAGCT 60.307 63.158 0.00 0.00 0.00 3.74
1035 1056 2.379459 GGGGGAGGGAGGAAGAAGC 61.379 68.421 0.00 0.00 0.00 3.86
1036 1057 4.074854 GGGGGAGGGAGGAAGAAG 57.925 66.667 0.00 0.00 0.00 2.85
1220 1241 1.226974 CGAGATGAATCACGGCGGT 60.227 57.895 13.24 0.00 37.27 5.68
1327 1360 1.165270 CTTTTAGGCTGAACCCACGG 58.835 55.000 0.00 0.00 40.58 4.94
1441 1475 8.365399 TGAAGGATATCACACGATATTGTTTC 57.635 34.615 4.83 0.00 43.51 2.78
1455 1489 6.779539 TCTGCAATAGAGAGTGAAGGATATCA 59.220 38.462 4.83 0.00 26.42 2.15
1456 1490 7.225784 TCTGCAATAGAGAGTGAAGGATATC 57.774 40.000 0.00 0.00 26.42 1.63
1457 1491 7.609097 TTCTGCAATAGAGAGTGAAGGATAT 57.391 36.000 0.00 0.00 36.61 1.63
1511 1545 1.461127 GCAGGCGAACAGTTCAGTAAG 59.539 52.381 13.82 0.00 0.00 2.34
1588 1623 1.472480 CGCCCACATAACAAAGAAGGG 59.528 52.381 0.00 0.00 37.87 3.95
1591 1626 2.811431 CTGACGCCCACATAACAAAGAA 59.189 45.455 0.00 0.00 0.00 2.52
1636 1671 3.042887 GCCAAAACTAGCAAGTCAAACG 58.957 45.455 0.00 0.00 33.75 3.60
1684 1719 1.004230 CAGTGGTATGGGAGGGGGA 59.996 63.158 0.00 0.00 0.00 4.81
1694 1735 2.766828 GCAGGGAAGACTACAGTGGTAT 59.233 50.000 0.00 0.00 0.00 2.73
1779 1820 4.624882 TCAACAATGAAAGCAACACAACAC 59.375 37.500 0.00 0.00 30.99 3.32
1896 1937 3.169512 ACCAACCCCAAGACCTAAATG 57.830 47.619 0.00 0.00 0.00 2.32
1898 1939 3.054576 TGTACCAACCCCAAGACCTAAA 58.945 45.455 0.00 0.00 0.00 1.85
1921 1962 2.644151 AGGGGAGGTCTGGTACAAAAT 58.356 47.619 0.00 0.00 38.70 1.82
1931 1972 2.753247 GATAGTGACAAGGGGAGGTCT 58.247 52.381 0.00 0.00 35.11 3.85
1936 1977 0.325296 AGGCGATAGTGACAAGGGGA 60.325 55.000 0.00 0.00 39.35 4.81
1952 1993 2.701107 GGAAGGTCAAGAACACTAGGC 58.299 52.381 0.00 0.00 0.00 3.93
1995 2072 2.084610 TCTGACAAGATGTTGAGCCG 57.915 50.000 9.96 0.00 37.10 5.52
2062 2139 5.652014 ACCTCTTTTCTGTGTTCACAATTGA 59.348 36.000 13.59 0.00 0.00 2.57
2068 2145 5.354234 TCAAGAACCTCTTTTCTGTGTTCAC 59.646 40.000 0.00 0.00 38.17 3.18
2090 2167 4.818642 CAGACTCTGCTTCATTTCTCTCA 58.181 43.478 0.00 0.00 0.00 3.27
2178 2258 1.540267 AGAGAGGACAACAGGACTCG 58.460 55.000 0.00 0.00 35.22 4.18
2212 2292 7.827236 TCGTGAAATTATGGTTTCCTAATGAGT 59.173 33.333 0.00 0.00 37.31 3.41
2395 2483 3.383185 GTCCCTCAGTAAGACAGGAGATG 59.617 52.174 0.00 0.00 0.00 2.90
2502 2590 7.781548 TCTCTTGGACTTGTACTAAAACAAC 57.218 36.000 0.00 0.00 35.56 3.32
2528 2624 9.780186 GATACTACTTCCTAAACCAATATGCTT 57.220 33.333 0.00 0.00 0.00 3.91
2529 2625 8.376270 GGATACTACTTCCTAAACCAATATGCT 58.624 37.037 0.00 0.00 0.00 3.79
2622 2721 9.419297 TGTTGACTACAAACACTATATCTTCAC 57.581 33.333 0.00 0.00 37.77 3.18
2705 2819 6.363626 GTGCATGATGTAGAGTCGTAAATAGG 59.636 42.308 0.00 0.00 0.00 2.57
2710 2826 4.983671 AGTGCATGATGTAGAGTCGTAA 57.016 40.909 0.00 0.00 0.00 3.18
2726 2842 5.047590 TCCACGACTCTTAAGAAATAGTGCA 60.048 40.000 17.42 6.64 0.00 4.57
2763 2879 8.977412 TCCCTCAGTCTCTTTTTAAATGTTTTT 58.023 29.630 0.00 0.00 0.00 1.94
2778 2894 5.242838 CCATATCAGTTACTCCCTCAGTCTC 59.757 48.000 0.00 0.00 36.43 3.36
2780 2896 4.262249 GCCATATCAGTTACTCCCTCAGTC 60.262 50.000 0.00 0.00 36.43 3.51
2782 2898 3.643320 TGCCATATCAGTTACTCCCTCAG 59.357 47.826 0.00 0.00 0.00 3.35
2857 3050 5.630061 TGTGATCGCAATACAATTGTCAAG 58.370 37.500 15.85 7.02 0.00 3.02
2872 3065 3.557595 CCTCAAAAGATACCTGTGATCGC 59.442 47.826 0.00 0.00 0.00 4.58
3156 3350 7.382898 GGAATAACATAAAGTTGGCTTTGGAA 58.617 34.615 3.17 0.00 44.00 3.53
3470 3672 5.159209 GCAGCAATATATGAAGGAACATGC 58.841 41.667 0.00 0.00 0.00 4.06
3479 3681 4.279169 GCTTTCAGGGCAGCAATATATGAA 59.721 41.667 0.00 0.00 35.95 2.57
3496 3698 9.979578 ACATACATTTTACAGAATTTGCTTTCA 57.020 25.926 0.00 0.00 0.00 2.69
3535 3737 5.560722 TCAGTACCCAGTGATGAAAAAGA 57.439 39.130 0.00 0.00 0.00 2.52
3547 3749 2.093288 ACTGCATCACATCAGTACCCAG 60.093 50.000 0.00 0.00 41.32 4.45
3551 3753 1.667724 GCCACTGCATCACATCAGTAC 59.332 52.381 0.00 0.00 41.19 2.73
3681 3883 2.901249 TGGGCTCGTTAAAGATGTAGC 58.099 47.619 0.00 0.00 0.00 3.58
3699 3901 7.095144 TGCAAATTAAAATCAACTGAGCAATGG 60.095 33.333 0.00 0.00 0.00 3.16
3778 3980 6.821665 GGGCAATTAGTTGTGACTTATAGTCA 59.178 38.462 5.46 5.46 45.01 3.41
3786 3988 3.508845 ACAGGGCAATTAGTTGTGACT 57.491 42.857 0.00 0.00 37.65 3.41
4035 4238 3.736224 CAGCCCTCCCCTGCACAT 61.736 66.667 0.00 0.00 0.00 3.21
4079 4282 1.985473 TGCAGTGCTTGGACAAGAAT 58.015 45.000 17.60 0.00 40.79 2.40
4161 4364 4.300803 TGTTGATGCTTTTGATGCTTGAC 58.699 39.130 0.00 0.00 0.00 3.18
4172 4375 5.796424 AGGAAGAACATTGTTGATGCTTT 57.204 34.783 6.80 0.00 39.47 3.51
4175 4378 6.690194 AGATAGGAAGAACATTGTTGATGC 57.310 37.500 6.80 0.92 39.47 3.91
4191 4394 3.114606 TGTCAATGGGCAGAAGATAGGA 58.885 45.455 0.00 0.00 0.00 2.94
4192 4395 3.474600 CTGTCAATGGGCAGAAGATAGG 58.525 50.000 0.00 0.00 34.87 2.57
4201 4404 2.277591 GCTTGGCTGTCAATGGGCA 61.278 57.895 0.00 0.00 34.45 5.36
4203 4406 0.896940 ACTGCTTGGCTGTCAATGGG 60.897 55.000 0.00 0.00 35.96 4.00
4207 4410 1.694150 ACTCTACTGCTTGGCTGTCAA 59.306 47.619 5.40 0.00 40.85 3.18
4221 4424 1.136305 TGGTTAGCATCGGCACTCTAC 59.864 52.381 0.00 0.00 44.61 2.59
4250 4454 6.380079 TCTCTCTTTTGCTTCTAGGGAAAT 57.620 37.500 0.00 0.00 0.00 2.17
4251 4455 5.825593 TCTCTCTTTTGCTTCTAGGGAAA 57.174 39.130 0.00 0.00 0.00 3.13
4333 4537 2.589157 CCGGCACCTGAACCACCTA 61.589 63.158 0.00 0.00 0.00 3.08
4338 4542 4.740822 ATGGCCGGCACCTGAACC 62.741 66.667 30.85 8.62 0.00 3.62
4396 4600 2.548295 GGAACCCGCTCGCAAACAA 61.548 57.895 0.00 0.00 0.00 2.83
4401 4605 2.992689 TACAGGAACCCGCTCGCA 60.993 61.111 0.00 0.00 0.00 5.10
4423 4627 2.851045 GGGGAGCCCTTTCACCAA 59.149 61.111 5.38 0.00 40.55 3.67
4464 4668 4.927782 GACCCGCCACTGCACACA 62.928 66.667 0.00 0.00 37.32 3.72
4608 4812 1.252904 CCAATGGGGCTGAACACAGG 61.253 60.000 0.00 0.00 32.85 4.00
4692 4898 0.959553 ATCATCTACGTGCCTACCCG 59.040 55.000 0.00 0.00 0.00 5.28
4705 4911 3.201487 TCACCTCCAGCAAATCATCATCT 59.799 43.478 0.00 0.00 0.00 2.90
4741 4947 7.415989 GCATGATACCACATCAGTTCTTTTCAT 60.416 37.037 0.00 0.00 0.00 2.57
4742 4948 6.127925 GCATGATACCACATCAGTTCTTTTCA 60.128 38.462 0.00 0.00 0.00 2.69
4743 4949 6.127925 TGCATGATACCACATCAGTTCTTTTC 60.128 38.462 0.00 0.00 0.00 2.29
4790 4998 6.702329 ACCAGTCAGAAGTTCGAATTTAGAT 58.298 36.000 5.83 0.00 0.00 1.98
4793 5001 6.312918 GCATACCAGTCAGAAGTTCGAATTTA 59.687 38.462 5.83 0.00 0.00 1.40
4800 5008 6.818644 TCATTTAGCATACCAGTCAGAAGTTC 59.181 38.462 0.00 0.00 0.00 3.01
4804 5012 6.472016 TGTTCATTTAGCATACCAGTCAGAA 58.528 36.000 0.00 0.00 0.00 3.02
4817 5027 9.056005 TGATGACTACCATTATGTTCATTTAGC 57.944 33.333 0.00 0.00 35.17 3.09
4852 5062 9.996554 TGATGAGGTATCGTAATAAACATTGAT 57.003 29.630 0.00 0.00 38.71 2.57
4853 5063 9.825109 TTGATGAGGTATCGTAATAAACATTGA 57.175 29.630 0.00 0.00 38.71 2.57
4856 5066 9.698309 CTCTTGATGAGGTATCGTAATAAACAT 57.302 33.333 0.00 0.00 38.71 2.71
4989 5199 6.645003 GGTCATTGTTGGGTTTTTAGATTGAC 59.355 38.462 0.00 0.00 0.00 3.18
4996 5206 5.677319 TTGTGGTCATTGTTGGGTTTTTA 57.323 34.783 0.00 0.00 0.00 1.52
5089 5303 1.004394 TCTCAGACTCCAAGTAGCGGA 59.996 52.381 0.00 0.00 0.00 5.54
5097 5311 0.603569 GAAGGCGTCTCAGACTCCAA 59.396 55.000 16.36 0.00 39.62 3.53
5163 5377 3.695830 AAGTTCTATTGGTTGGCGAGA 57.304 42.857 0.00 0.00 0.00 4.04
5170 5384 5.319043 TCTGGGTGAAAGTTCTATTGGTT 57.681 39.130 0.00 0.00 0.00 3.67
5172 5386 5.048013 GGTTTCTGGGTGAAAGTTCTATTGG 60.048 44.000 0.00 0.00 44.36 3.16
5197 5411 3.953775 CGGCAGGGACTTGTGGGT 61.954 66.667 0.00 0.00 34.60 4.51
5205 5419 2.359975 CCAAGGTTCGGCAGGGAC 60.360 66.667 0.00 0.00 0.00 4.46
5289 5503 4.868734 AGACACGAGAAATATCGAAAACCC 59.131 41.667 4.27 0.00 45.56 4.11
5303 5517 5.215160 GGTTAACGTTAGAAAGACACGAGA 58.785 41.667 8.23 0.00 37.37 4.04
5304 5518 4.977963 TGGTTAACGTTAGAAAGACACGAG 59.022 41.667 8.23 0.00 37.37 4.18
5305 5519 4.930963 TGGTTAACGTTAGAAAGACACGA 58.069 39.130 8.23 0.00 37.37 4.35
5306 5520 5.164022 GGATGGTTAACGTTAGAAAGACACG 60.164 44.000 8.23 0.00 39.86 4.49
5307 5521 5.164022 CGGATGGTTAACGTTAGAAAGACAC 60.164 44.000 8.23 1.98 0.00 3.67
5308 5522 4.925054 CGGATGGTTAACGTTAGAAAGACA 59.075 41.667 8.23 3.63 0.00 3.41
5309 5523 5.163513 TCGGATGGTTAACGTTAGAAAGAC 58.836 41.667 8.23 3.43 0.00 3.01
5310 5524 5.183713 TCTCGGATGGTTAACGTTAGAAAGA 59.816 40.000 8.23 3.13 0.00 2.52
5311 5525 5.404946 TCTCGGATGGTTAACGTTAGAAAG 58.595 41.667 8.23 0.37 0.00 2.62
5312 5526 5.389859 TCTCGGATGGTTAACGTTAGAAA 57.610 39.130 8.23 0.00 0.00 2.52
5313 5527 5.389859 TTCTCGGATGGTTAACGTTAGAA 57.610 39.130 8.23 4.33 0.00 2.10
5314 5528 5.183713 TCTTTCTCGGATGGTTAACGTTAGA 59.816 40.000 8.23 0.00 0.00 2.10
5315 5529 5.404946 TCTTTCTCGGATGGTTAACGTTAG 58.595 41.667 8.23 0.00 0.00 2.34
5316 5530 5.389859 TCTTTCTCGGATGGTTAACGTTA 57.610 39.130 3.29 3.29 0.00 3.18
5317 5531 4.261578 TCTTTCTCGGATGGTTAACGTT 57.738 40.909 5.88 5.88 0.00 3.99
5318 5532 3.947910 TCTTTCTCGGATGGTTAACGT 57.052 42.857 0.00 0.00 0.00 3.99
5319 5533 4.491676 TCTTCTTTCTCGGATGGTTAACG 58.508 43.478 0.00 0.00 0.00 3.18
5320 5534 6.796705 TTTCTTCTTTCTCGGATGGTTAAC 57.203 37.500 0.00 0.00 0.00 2.01
5321 5535 6.996282 AGTTTTCTTCTTTCTCGGATGGTTAA 59.004 34.615 0.00 0.00 0.00 2.01
5322 5536 6.531021 AGTTTTCTTCTTTCTCGGATGGTTA 58.469 36.000 0.00 0.00 0.00 2.85
5323 5537 5.377478 AGTTTTCTTCTTTCTCGGATGGTT 58.623 37.500 0.00 0.00 0.00 3.67
5324 5538 4.974399 AGTTTTCTTCTTTCTCGGATGGT 58.026 39.130 0.00 0.00 0.00 3.55
5325 5539 5.239525 ACAAGTTTTCTTCTTTCTCGGATGG 59.760 40.000 0.00 0.00 38.17 3.51
5326 5540 6.305693 ACAAGTTTTCTTCTTTCTCGGATG 57.694 37.500 0.00 0.00 38.17 3.51
5327 5541 6.944234 AACAAGTTTTCTTCTTTCTCGGAT 57.056 33.333 0.00 0.00 38.17 4.18
5328 5542 6.753107 AAACAAGTTTTCTTCTTTCTCGGA 57.247 33.333 0.00 0.00 38.17 4.55
5329 5543 7.812309 AAAAACAAGTTTTCTTCTTTCTCGG 57.188 32.000 10.96 0.00 41.45 4.63
5376 5590 9.927668 GATCTTGATTGGTTCCTTTCAAAAATA 57.072 29.630 7.84 0.00 0.00 1.40
5378 5592 7.710475 GTGATCTTGATTGGTTCCTTTCAAAAA 59.290 33.333 0.00 2.49 0.00 1.94
5379 5593 7.147759 TGTGATCTTGATTGGTTCCTTTCAAAA 60.148 33.333 0.00 0.00 0.00 2.44
5380 5594 6.323482 TGTGATCTTGATTGGTTCCTTTCAAA 59.677 34.615 0.00 0.00 0.00 2.69
5381 5595 5.832595 TGTGATCTTGATTGGTTCCTTTCAA 59.167 36.000 0.00 6.77 0.00 2.69
5382 5596 5.384336 TGTGATCTTGATTGGTTCCTTTCA 58.616 37.500 0.00 0.00 0.00 2.69
5383 5597 5.964958 TGTGATCTTGATTGGTTCCTTTC 57.035 39.130 0.00 0.00 0.00 2.62
5384 5598 5.124457 CGATGTGATCTTGATTGGTTCCTTT 59.876 40.000 0.00 0.00 0.00 3.11
5385 5599 4.637534 CGATGTGATCTTGATTGGTTCCTT 59.362 41.667 0.00 0.00 0.00 3.36
5387 5601 4.191544 TCGATGTGATCTTGATTGGTTCC 58.808 43.478 0.00 0.00 0.00 3.62
5388 5602 5.998454 ATCGATGTGATCTTGATTGGTTC 57.002 39.130 0.00 0.00 28.49 3.62
5389 5603 5.882000 TCAATCGATGTGATCTTGATTGGTT 59.118 36.000 17.25 2.83 43.68 3.67
5391 5605 5.996669 TCAATCGATGTGATCTTGATTGG 57.003 39.130 17.25 5.63 43.68 3.16
5392 5606 5.907945 GCTTCAATCGATGTGATCTTGATTG 59.092 40.000 13.59 13.59 44.45 2.67
5393 5607 5.008415 GGCTTCAATCGATGTGATCTTGATT 59.992 40.000 0.00 0.00 35.84 2.57
5394 5608 4.514441 GGCTTCAATCGATGTGATCTTGAT 59.486 41.667 0.00 0.00 35.84 2.57
5395 5609 3.873361 GGCTTCAATCGATGTGATCTTGA 59.127 43.478 0.00 0.00 35.84 3.02
5396 5610 3.624410 TGGCTTCAATCGATGTGATCTTG 59.376 43.478 0.00 0.00 35.84 3.02
5397 5611 3.877559 TGGCTTCAATCGATGTGATCTT 58.122 40.909 0.00 0.00 35.84 2.40
5398 5612 3.548745 TGGCTTCAATCGATGTGATCT 57.451 42.857 0.00 0.00 35.84 2.75
5399 5613 4.621068 TTTGGCTTCAATCGATGTGATC 57.379 40.909 0.00 1.27 35.84 2.92
5400 5614 4.202080 CCATTTGGCTTCAATCGATGTGAT 60.202 41.667 0.00 0.00 39.67 3.06
5401 5615 3.129113 CCATTTGGCTTCAATCGATGTGA 59.871 43.478 0.00 2.35 0.00 3.58
5402 5616 3.129113 TCCATTTGGCTTCAATCGATGTG 59.871 43.478 0.00 0.00 34.44 3.21
5403 5617 3.355378 TCCATTTGGCTTCAATCGATGT 58.645 40.909 0.00 0.00 34.44 3.06
5404 5618 3.794475 GCTCCATTTGGCTTCAATCGATG 60.794 47.826 0.00 0.00 34.44 3.84
5405 5619 2.360165 GCTCCATTTGGCTTCAATCGAT 59.640 45.455 0.00 0.00 34.44 3.59
5442 5656 1.672363 CTTGCACTGTGAAAGCACTGA 59.328 47.619 15.27 0.00 45.36 3.41
5451 5665 0.664224 TACGTCGTCTTGCACTGTGA 59.336 50.000 12.86 0.00 0.00 3.58
5454 5668 0.992072 CCATACGTCGTCTTGCACTG 59.008 55.000 0.00 0.00 0.00 3.66
5522 5736 6.095440 ACACTGGTGCATGGATTAAAAGTATC 59.905 38.462 0.00 0.00 0.00 2.24
5543 5757 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.00 0.00 3.55
5544 5758 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5545 5759 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5546 5760 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5547 5761 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5548 5762 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5549 5763 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5550 5764 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5551 5765 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5552 5766 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5553 5767 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5554 5768 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5555 5769 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5556 5770 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5557 5771 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5558 5772 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5559 5773 2.457366 TACACACACACACACACACA 57.543 45.000 0.00 0.00 0.00 3.72
5560 5774 3.433957 TCTTTACACACACACACACACAC 59.566 43.478 0.00 0.00 0.00 3.82
5561 5775 3.665190 TCTTTACACACACACACACACA 58.335 40.909 0.00 0.00 0.00 3.72
5562 5776 4.875544 ATCTTTACACACACACACACAC 57.124 40.909 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.