Multiple sequence alignment - TraesCS5B01G044800

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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 TraesCS5B01G044800 chr5B 100.000 4277 0 0 1 4277 50280750 50276474 0.000000e+00 7899.0
1 TraesCS5B01G044800 chr5B 98.837 602 7 0 1 602 576230041 576229440 0.000000e+00 1074.0
2 TraesCS5B01G044800 chr5B 98.505 602 9 0 1 602 115866369 115865768 0.000000e+00 1062.0
3 TraesCS5B01G044800 chr5B 86.339 183 25 0 1052 1234 50279639 50279457 2.610000e-47 200.0
4 TraesCS5B01G044800 chr5B 86.339 183 25 0 1112 1294 50279699 50279517 2.610000e-47 200.0
5 TraesCS5B01G044800 chr5B 82.812 128 22 0 1052 1179 50279579 50279452 9.720000e-22 115.0
6 TraesCS5B01G044800 chr5B 82.812 128 22 0 1172 1299 50279699 50279572 9.720000e-22 115.0
7 TraesCS5B01G044800 chr5B 90.323 62 6 0 3883 3944 639558154 639558093 9.860000e-12 82.4
8 TraesCS5B01G044800 chr5D 92.896 2731 83 23 812 3496 47301949 47299284 0.000000e+00 3866.0
9 TraesCS5B01G044800 chr5D 87.733 375 13 4 3935 4277 47298715 47298342 1.430000e-109 407.0
10 TraesCS5B01G044800 chr5D 94.538 238 5 6 3495 3724 47299170 47298933 1.130000e-95 361.0
11 TraesCS5B01G044800 chr5D 87.552 241 7 11 602 819 47303714 47303474 1.530000e-64 257.0
12 TraesCS5B01G044800 chr5D 84.581 227 31 4 1074 1299 47301756 47301533 5.570000e-54 222.0
13 TraesCS5B01G044800 chr5D 95.588 136 6 0 1052 1187 47301660 47301525 7.200000e-53 219.0
14 TraesCS5B01G044800 chr5D 82.353 136 12 7 993 1126 47301650 47301525 1.630000e-19 108.0
15 TraesCS5B01G044800 chr5D 88.060 67 6 2 3883 3948 10367291 10367226 1.280000e-10 78.7
16 TraesCS5B01G044800 chr4A 98.502 601 9 0 2 602 511237790 511238390 0.000000e+00 1061.0
17 TraesCS5B01G044800 chr4A 76.471 238 44 11 4044 4272 661172428 661172662 7.510000e-23 119.0
18 TraesCS5B01G044800 chr3B 98.339 602 10 0 2 603 120572493 120573094 0.000000e+00 1057.0
19 TraesCS5B01G044800 chr3B 98.336 601 8 1 1 599 23715553 23714953 0.000000e+00 1053.0
20 TraesCS5B01G044800 chr7A 97.712 612 12 2 2 611 22373111 22373722 0.000000e+00 1051.0
21 TraesCS5B01G044800 chr7B 98.010 603 12 0 1 603 504951109 504951711 0.000000e+00 1048.0
22 TraesCS5B01G044800 chr7B 77.824 239 34 18 4046 4271 529200609 529200841 3.470000e-26 130.0
23 TraesCS5B01G044800 chr6B 97.841 602 13 0 1 602 665534125 665534726 0.000000e+00 1040.0
24 TraesCS5B01G044800 chr6B 89.062 64 7 0 3883 3946 333176060 333175997 3.550000e-11 80.5
25 TraesCS5B01G044800 chr6A 97.993 598 12 0 2 599 207819173 207818576 0.000000e+00 1038.0
26 TraesCS5B01G044800 chr6A 76.316 190 30 14 3524 3707 226066380 226066200 2.120000e-13 87.9
27 TraesCS5B01G044800 chr2B 76.676 373 48 23 3935 4277 732968774 732969137 2.050000e-38 171.0
28 TraesCS5B01G044800 chr2B 77.130 223 39 11 4045 4257 373907721 373907941 7.510000e-23 119.0
29 TraesCS5B01G044800 chr2B 78.022 182 25 10 3715 3882 444962005 444962185 2.720000e-17 100.0
30 TraesCS5B01G044800 chr3D 79.710 207 31 11 4079 4277 44219432 44219229 5.770000e-29 139.0
31 TraesCS5B01G044800 chr5A 77.778 243 41 12 4045 4277 52879576 52879815 2.070000e-28 137.0
32 TraesCS5B01G044800 chr5A 77.328 247 35 16 4046 4277 633101287 633101047 4.490000e-25 126.0
33 TraesCS5B01G044800 chr6D 78.922 204 33 10 4082 4277 62147674 62147875 3.470000e-26 130.0
34 TraesCS5B01G044800 chr1B 92.063 63 5 0 3883 3945 151118168 151118106 5.890000e-14 89.8
35 TraesCS5B01G044800 chr1B 92.063 63 5 0 3883 3945 151135047 151134985 5.890000e-14 89.8
36 TraesCS5B01G044800 chr1B 92.063 63 5 0 3883 3945 152360572 152360634 5.890000e-14 89.8
37 TraesCS5B01G044800 chr1B 96.154 52 2 0 3896 3947 108209420 108209369 7.620000e-13 86.1
38 TraesCS5B01G044800 chr1B 90.476 63 6 0 3883 3945 134955432 134955370 2.740000e-12 84.2
39 TraesCS5B01G044800 chr1B 91.525 59 4 1 3887 3945 312920615 312920558 3.550000e-11 80.5
40 TraesCS5B01G044800 chrUn 84.375 64 10 0 3539 3602 327609113 327609050 3.570000e-06 63.9
41 TraesCS5B01G044800 chrUn 84.375 64 10 0 3539 3602 349882530 349882467 3.570000e-06 63.9
42 TraesCS5B01G044800 chrUn 84.375 64 10 0 3539 3602 382294075 382294012 3.570000e-06 63.9


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 TraesCS5B01G044800 chr5B 50276474 50280750 4276 True 1705.800000 7899 87.660400 1 4277 5 chr5B.!!$R4 4276
1 TraesCS5B01G044800 chr5B 576229440 576230041 601 True 1074.000000 1074 98.837000 1 602 1 chr5B.!!$R2 601
2 TraesCS5B01G044800 chr5B 115865768 115866369 601 True 1062.000000 1062 98.505000 1 602 1 chr5B.!!$R1 601
3 TraesCS5B01G044800 chr5D 47298342 47303714 5372 True 777.142857 3866 89.320143 602 4277 7 chr5D.!!$R2 3675
4 TraesCS5B01G044800 chr4A 511237790 511238390 600 False 1061.000000 1061 98.502000 2 602 1 chr4A.!!$F1 600
5 TraesCS5B01G044800 chr3B 120572493 120573094 601 False 1057.000000 1057 98.339000 2 603 1 chr3B.!!$F1 601
6 TraesCS5B01G044800 chr3B 23714953 23715553 600 True 1053.000000 1053 98.336000 1 599 1 chr3B.!!$R1 598
7 TraesCS5B01G044800 chr7A 22373111 22373722 611 False 1051.000000 1051 97.712000 2 611 1 chr7A.!!$F1 609
8 TraesCS5B01G044800 chr7B 504951109 504951711 602 False 1048.000000 1048 98.010000 1 603 1 chr7B.!!$F1 602
9 TraesCS5B01G044800 chr6B 665534125 665534726 601 False 1040.000000 1040 97.841000 1 602 1 chr6B.!!$F1 601
10 TraesCS5B01G044800 chr6A 207818576 207819173 597 True 1038.000000 1038 97.993000 2 599 1 chr6A.!!$R1 597

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
730 751 1.110442 TATTTTTGCATCTGGCCGGG 58.890 50.0 12.87 0.0 43.89 5.73 F
1622 3188 0.251832 AGGACAGTGTGGTCGAGGAT 60.252 55.0 0.00 0.0 38.70 3.24 F
1690 3256 0.179062 ACTGCAGAGATCCGGCATTC 60.179 55.0 23.35 0.0 44.59 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 3256 0.094730 GATCGCCCAAACGTTCTTCG 59.905 55.0 0.0 3.58 46.00 3.79 R
3223 4817 0.179026 CTCATGTCCCCAGCATCCTG 60.179 60.0 0.0 0.00 38.85 3.86 R
3649 5367 0.391661 TCGCATCACTCAAAGAGGCC 60.392 55.0 0.0 0.00 39.44 5.19 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
630 633 2.435586 CCAAGTGAGGCGCTCCTG 60.436 66.667 7.64 1.21 44.46 3.86
685 688 5.292101 GGTCTAGGAATTGAATTGACGAGTG 59.708 44.000 0.00 0.00 0.00 3.51
686 689 6.100004 GTCTAGGAATTGAATTGACGAGTGA 58.900 40.000 0.00 0.00 0.00 3.41
687 690 6.254589 GTCTAGGAATTGAATTGACGAGTGAG 59.745 42.308 0.00 0.00 0.00 3.51
688 691 5.152623 AGGAATTGAATTGACGAGTGAGA 57.847 39.130 0.00 0.00 0.00 3.27
691 694 7.504403 AGGAATTGAATTGACGAGTGAGATAT 58.496 34.615 0.00 0.00 0.00 1.63
692 695 8.642432 AGGAATTGAATTGACGAGTGAGATATA 58.358 33.333 0.00 0.00 0.00 0.86
693 696 8.920665 GGAATTGAATTGACGAGTGAGATATAG 58.079 37.037 0.00 0.00 0.00 1.31
694 697 9.684448 GAATTGAATTGACGAGTGAGATATAGA 57.316 33.333 0.00 0.00 0.00 1.98
695 698 9.689976 AATTGAATTGACGAGTGAGATATAGAG 57.310 33.333 0.00 0.00 0.00 2.43
730 751 1.110442 TATTTTTGCATCTGGCCGGG 58.890 50.000 12.87 0.00 43.89 5.73
877 2434 3.522731 CCTCCGAGTCGCTCCCTG 61.523 72.222 7.12 0.00 0.00 4.45
1030 2587 2.590645 CGAGGACCTCCCGAGAGA 59.409 66.667 16.13 0.00 43.39 3.10
1031 2588 1.820481 CGAGGACCTCCCGAGAGAC 60.820 68.421 16.13 0.00 43.39 3.36
1032 2589 1.610873 GAGGACCTCCCGAGAGACT 59.389 63.158 10.74 0.00 43.39 3.24
1033 2590 0.464916 GAGGACCTCCCGAGAGACTC 60.465 65.000 10.74 0.00 43.39 3.36
1034 2591 1.454295 GGACCTCCCGAGAGACTCC 60.454 68.421 0.00 0.00 43.39 3.85
1035 2592 1.610873 GACCTCCCGAGAGACTCCT 59.389 63.158 0.00 0.00 43.39 3.69
1036 2593 0.750182 GACCTCCCGAGAGACTCCTG 60.750 65.000 0.00 0.00 43.39 3.86
1037 2594 1.208844 ACCTCCCGAGAGACTCCTGA 61.209 60.000 0.00 0.00 43.39 3.86
1038 2595 0.465460 CCTCCCGAGAGACTCCTGAG 60.465 65.000 0.00 0.53 43.39 3.35
1039 2596 0.544223 CTCCCGAGAGACTCCTGAGA 59.456 60.000 0.22 0.00 43.39 3.27
1040 2597 0.544223 TCCCGAGAGACTCCTGAGAG 59.456 60.000 0.22 0.00 46.36 3.20
1041 2598 1.101049 CCCGAGAGACTCCTGAGAGC 61.101 65.000 0.22 0.00 44.65 4.09
1050 2607 3.385384 CCTGAGAGCTCCACCGCA 61.385 66.667 10.93 0.45 0.00 5.69
1051 2608 2.729479 CCTGAGAGCTCCACCGCAT 61.729 63.158 10.93 0.00 0.00 4.73
1064 2621 3.499737 CGCATCCACGGCTTCCAC 61.500 66.667 0.00 0.00 0.00 4.02
1124 2681 4.135153 CAGCTCCACGACCTCCCG 62.135 72.222 0.00 0.00 0.00 5.14
1154 2711 4.003788 CCACGCCAGGACCTTCGT 62.004 66.667 11.63 11.63 35.35 3.85
1184 2741 3.775654 CAGCTCCACGACCTCCCC 61.776 72.222 0.00 0.00 0.00 4.81
1289 2855 3.522731 CCCAGAGACGGCCGAGAG 61.523 72.222 35.90 16.00 0.00 3.20
1290 2856 2.752238 CCAGAGACGGCCGAGAGT 60.752 66.667 35.90 9.58 0.00 3.24
1291 2857 2.344203 CCAGAGACGGCCGAGAGTT 61.344 63.158 35.90 9.07 0.00 3.01
1292 2858 1.137825 CAGAGACGGCCGAGAGTTC 59.862 63.158 35.90 19.11 0.00 3.01
1293 2859 2.047443 AGAGACGGCCGAGAGTTCC 61.047 63.158 35.90 12.15 0.00 3.62
1294 2860 2.282958 AGACGGCCGAGAGTTCCA 60.283 61.111 35.90 0.00 0.00 3.53
1295 2861 2.126031 GACGGCCGAGAGTTCCAC 60.126 66.667 35.90 7.18 0.00 4.02
1296 2862 2.600769 ACGGCCGAGAGTTCCACT 60.601 61.111 35.90 0.68 0.00 4.00
1297 2863 1.303888 ACGGCCGAGAGTTCCACTA 60.304 57.895 35.90 0.00 0.00 2.74
1298 2864 1.139095 CGGCCGAGAGTTCCACTAC 59.861 63.158 24.07 0.00 0.00 2.73
1299 2865 1.139095 GGCCGAGAGTTCCACTACG 59.861 63.158 0.00 0.00 0.00 3.51
1300 2866 1.593296 GGCCGAGAGTTCCACTACGT 61.593 60.000 0.00 0.00 0.00 3.57
1301 2867 1.089920 GCCGAGAGTTCCACTACGTA 58.910 55.000 0.00 0.00 0.00 3.57
1342 2908 4.941873 AGGGTACGAATCACAAATCCTTTC 59.058 41.667 0.00 0.00 0.00 2.62
1345 2911 5.411669 GGTACGAATCACAAATCCTTTCTGT 59.588 40.000 0.00 0.00 0.00 3.41
1350 2916 6.566197 AATCACAAATCCTTTCTGTCTGTC 57.434 37.500 0.00 0.00 0.00 3.51
1478 3044 2.315011 GAGATCGTTAGCTCAGATGCG 58.685 52.381 0.00 0.00 38.07 4.73
1492 3058 4.172625 TGCGGTGCATGTTCCTTT 57.827 50.000 0.00 0.00 31.71 3.11
1493 3059 1.956043 TGCGGTGCATGTTCCTTTC 59.044 52.632 0.00 0.00 31.71 2.62
1494 3060 0.821301 TGCGGTGCATGTTCCTTTCA 60.821 50.000 0.00 0.00 31.71 2.69
1495 3061 0.527565 GCGGTGCATGTTCCTTTCAT 59.472 50.000 0.00 0.00 0.00 2.57
1496 3062 1.733389 GCGGTGCATGTTCCTTTCATG 60.733 52.381 0.00 0.00 43.58 3.07
1497 3063 1.135315 CGGTGCATGTTCCTTTCATGG 60.135 52.381 7.78 0.00 41.77 3.66
1498 3064 1.895131 GGTGCATGTTCCTTTCATGGT 59.105 47.619 7.78 0.00 41.77 3.55
1499 3065 2.299867 GGTGCATGTTCCTTTCATGGTT 59.700 45.455 7.78 0.00 41.77 3.67
1500 3066 3.244181 GGTGCATGTTCCTTTCATGGTTT 60.244 43.478 7.78 0.00 41.77 3.27
1501 3067 4.021544 GGTGCATGTTCCTTTCATGGTTTA 60.022 41.667 7.78 0.00 41.77 2.01
1502 3068 5.163513 GTGCATGTTCCTTTCATGGTTTAG 58.836 41.667 7.78 0.00 41.77 1.85
1503 3069 4.176271 GCATGTTCCTTTCATGGTTTAGC 58.824 43.478 7.78 0.00 41.77 3.09
1504 3070 4.747810 CATGTTCCTTTCATGGTTTAGCC 58.252 43.478 0.00 0.00 38.97 3.93
1505 3071 4.112634 TGTTCCTTTCATGGTTTAGCCT 57.887 40.909 0.00 0.00 38.35 4.58
1506 3072 4.479158 TGTTCCTTTCATGGTTTAGCCTT 58.521 39.130 0.00 0.00 38.35 4.35
1507 3073 4.280677 TGTTCCTTTCATGGTTTAGCCTTG 59.719 41.667 0.00 0.00 42.09 3.61
1563 3129 1.135373 ACGGAGATCTTGCACACTACG 60.135 52.381 0.00 10.34 41.66 3.51
1622 3188 0.251832 AGGACAGTGTGGTCGAGGAT 60.252 55.000 0.00 0.00 38.70 3.24
1656 3222 6.690194 ATCAGATAACAAACTTGCTGGATC 57.310 37.500 0.00 0.00 0.00 3.36
1690 3256 0.179062 ACTGCAGAGATCCGGCATTC 60.179 55.000 23.35 0.00 44.59 2.67
1712 3278 0.673644 AGAACGTTTGGGCGATCCTG 60.674 55.000 0.46 0.00 34.83 3.86
1760 3326 3.531538 ACACAGGAATGCGGTAGTATTG 58.468 45.455 0.00 0.00 32.81 1.90
1818 3403 2.093341 GGTTGTGAAGCGGGTATCCTTA 60.093 50.000 0.00 0.00 0.00 2.69
1954 3539 3.480470 CATGTGGATGGATGTCTTACCC 58.520 50.000 0.00 0.00 0.00 3.69
1955 3540 2.845659 TGTGGATGGATGTCTTACCCT 58.154 47.619 0.00 0.00 0.00 4.34
1956 3541 2.771943 TGTGGATGGATGTCTTACCCTC 59.228 50.000 0.00 0.00 0.00 4.30
1957 3542 3.041946 GTGGATGGATGTCTTACCCTCT 58.958 50.000 0.00 0.00 0.00 3.69
1958 3543 3.456277 GTGGATGGATGTCTTACCCTCTT 59.544 47.826 0.00 0.00 0.00 2.85
2050 3635 7.444183 GGCATACTAATGTAACAGCTTATTGGA 59.556 37.037 0.00 0.00 35.38 3.53
2062 3647 3.507622 AGCTTATTGGAGCCAACAAAGTC 59.492 43.478 19.35 14.32 43.74 3.01
2136 3728 7.759489 TTTGCTGTAATTCTGTTGGTAGATT 57.241 32.000 0.00 0.00 0.00 2.40
2226 3818 7.122055 TCCAGGGTTGTATCAAAATCACATTAC 59.878 37.037 0.00 0.00 0.00 1.89
2278 3870 7.028926 TGTTTAGTTTTATTTGTCGCCAAGA 57.971 32.000 0.00 0.00 0.00 3.02
2291 3883 1.197721 CGCCAAGAATGTGAACCTGAC 59.802 52.381 0.00 0.00 0.00 3.51
2292 3884 2.229792 GCCAAGAATGTGAACCTGACA 58.770 47.619 0.00 0.00 0.00 3.58
2296 3888 4.155462 CCAAGAATGTGAACCTGACAGATG 59.845 45.833 3.32 0.00 0.00 2.90
2311 3903 8.051535 ACCTGACAGATGTCTGATTTAATGATT 58.948 33.333 16.41 0.00 46.59 2.57
2483 4077 3.328931 ACTCCATGGCTCTTCTTGAAGAA 59.671 43.478 6.96 7.49 32.50 2.52
2511 4105 6.980397 CAGGAAATGCATTAGTTAATGTTCCC 59.020 38.462 13.39 11.92 41.96 3.97
2525 4119 9.212593 AGTTAATGTTCCCCATATTTAGCATTT 57.787 29.630 0.00 0.00 31.97 2.32
2526 4120 9.476202 GTTAATGTTCCCCATATTTAGCATTTC 57.524 33.333 0.00 0.00 31.97 2.17
2599 4193 1.228245 GGAGCAACTGGGCACTCAA 60.228 57.895 0.00 0.00 35.83 3.02
2639 4233 0.890542 GGATTGAGCAGTGTGGCACA 60.891 55.000 17.96 17.96 36.74 4.57
2649 4243 3.885297 GCAGTGTGGCACATATTTAGGAT 59.115 43.478 24.95 0.00 44.52 3.24
2735 4329 4.337145 AGAGTCAGTCTCCGACATTAGTT 58.663 43.478 0.00 0.00 43.71 2.24
2744 4338 3.270027 TCCGACATTAGTTGCTTGGATG 58.730 45.455 0.00 0.00 0.00 3.51
2804 4398 1.154225 CGCGAACATGGTGAAAGGC 60.154 57.895 0.00 0.00 0.00 4.35
2807 4401 1.851021 CGAACATGGTGAAAGGCGCA 61.851 55.000 10.83 0.00 0.00 6.09
2822 4416 1.534595 GGCGCATCAGGTTTATGCTTG 60.535 52.381 10.83 0.00 46.05 4.01
2866 4460 1.141254 CATCATGGAGAGGCAAGAGCT 59.859 52.381 0.00 0.00 41.70 4.09
2918 4512 4.453480 AGAAAACCCATCTTCTGTTCCA 57.547 40.909 0.00 0.00 30.67 3.53
2930 4524 2.054799 TCTGTTCCAAGGCTAGTGGTT 58.945 47.619 5.18 0.00 37.43 3.67
2933 4527 1.880027 GTTCCAAGGCTAGTGGTTGTG 59.120 52.381 5.18 0.00 37.43 3.33
2961 4555 4.007659 ACTTGAAGAGGTTTGTTTCGTGT 58.992 39.130 0.00 0.00 0.00 4.49
2967 4561 1.063469 AGGTTTGTTTCGTGTTGAGCG 59.937 47.619 0.00 0.00 0.00 5.03
2973 4567 0.512518 TTTCGTGTTGAGCGATGCAG 59.487 50.000 0.00 0.00 38.21 4.41
2982 4576 6.564686 CGTGTTGAGCGATGCAGAATATTATT 60.565 38.462 0.00 0.00 0.00 1.40
3048 4642 3.840666 AGCTGGAGGAAGTATTGAGTGAA 59.159 43.478 0.00 0.00 0.00 3.18
3058 4652 4.521146 AGTATTGAGTGAATGGAAGGCAG 58.479 43.478 0.00 0.00 0.00 4.85
3066 4660 0.749454 AATGGAAGGCAGCGATCACC 60.749 55.000 0.00 0.00 0.00 4.02
3081 4675 3.732169 CGATCACCGCGCTATCTATTGAT 60.732 47.826 5.56 2.49 36.74 2.57
3089 4683 3.923461 GCGCTATCTATTGATGTGAGTCC 59.077 47.826 0.00 0.00 34.32 3.85
3104 4698 0.617413 AGTCCAGACATGCCCTTCAG 59.383 55.000 0.00 0.00 0.00 3.02
3135 4729 1.208614 GTGCTTTGAGCGGCTTGAG 59.791 57.895 2.97 3.93 46.26 3.02
3165 4759 3.794475 GCTTGCAAGCGCTGAATATGATT 60.794 43.478 33.75 0.00 42.88 2.57
3178 4772 4.098349 TGAATATGATTCAAGCAGGCCAAC 59.902 41.667 5.01 0.00 0.00 3.77
3179 4773 1.927487 ATGATTCAAGCAGGCCAACA 58.073 45.000 5.01 0.00 0.00 3.33
3217 4811 2.603473 AGTACCTGCGTGCCCAGA 60.603 61.111 0.00 0.00 34.77 3.86
3292 4886 4.416738 GAGCCCCAGACCAGCACC 62.417 72.222 0.00 0.00 0.00 5.01
3321 4916 5.610552 GCATGACTTGCGACGAAATAGATAC 60.611 44.000 0.00 0.00 42.54 2.24
3373 4968 7.222000 AGAGCTAGTAGTATGGATGCTTTAC 57.778 40.000 0.00 0.00 0.00 2.01
3374 4969 6.778069 AGAGCTAGTAGTATGGATGCTTTACA 59.222 38.462 0.00 0.00 0.00 2.41
3392 4987 2.941453 CATAGGAGTACTGTGTGCGT 57.059 50.000 0.00 0.00 33.99 5.24
3423 5026 5.505159 GGTTTGCTAACTGTTTGACACCTAC 60.505 44.000 10.80 3.10 34.59 3.18
3427 5030 4.091509 GCTAACTGTTTGACACCTACGATG 59.908 45.833 6.17 0.00 0.00 3.84
3478 5081 2.698855 TCTGTGCTCTTAATCCTGCC 57.301 50.000 0.00 0.00 0.00 4.85
3508 5226 9.614792 GACACATAGAAATAGTTTGGAAGGTAT 57.385 33.333 0.00 0.00 0.00 2.73
3649 5367 6.246420 AGCTGCTTTTCTTGTGTTGTATAG 57.754 37.500 0.00 0.00 0.00 1.31
3667 5387 0.392193 AGGCCTCTTTGAGTGATGCG 60.392 55.000 0.00 0.00 0.00 4.73
3689 5409 2.365293 ACAGGCCCATTGTCTTGTTTTC 59.635 45.455 0.00 0.00 0.00 2.29
3709 5432 7.116233 TGTTTTCTTTTCTTTTCTTGTGTGCTC 59.884 33.333 0.00 0.00 0.00 4.26
3711 5434 2.755836 TTCTTTTCTTGTGTGCTCGC 57.244 45.000 0.00 0.00 0.00 5.03
3712 5435 1.662517 TCTTTTCTTGTGTGCTCGCA 58.337 45.000 0.00 0.00 0.00 5.10
3713 5436 1.599071 TCTTTTCTTGTGTGCTCGCAG 59.401 47.619 1.92 0.00 35.43 5.18
3727 5493 2.711924 GCAGCAGCGCCATCTAAC 59.288 61.111 2.29 0.00 0.00 2.34
3741 5507 2.789203 CTAACGAACTGGCGCTCGC 61.789 63.158 15.63 5.60 38.64 5.03
3742 5508 3.561217 TAACGAACTGGCGCTCGCA 62.561 57.895 15.63 0.57 44.11 5.10
3821 5597 7.496346 TTACAAGACCAGGATTAGAACTCAT 57.504 36.000 0.00 0.00 0.00 2.90
3838 5614 3.189287 ACTCATGCCGTTTGCTTCTAAAG 59.811 43.478 0.00 0.00 42.00 1.85
3865 5641 2.426024 CGGCTAACCACTAGAGCTAACA 59.574 50.000 0.00 0.00 36.43 2.41
3866 5642 3.068307 CGGCTAACCACTAGAGCTAACAT 59.932 47.826 0.00 0.00 36.43 2.71
3867 5643 4.441634 CGGCTAACCACTAGAGCTAACATT 60.442 45.833 0.00 0.00 36.43 2.71
3868 5644 4.811557 GGCTAACCACTAGAGCTAACATTG 59.188 45.833 0.00 0.00 36.43 2.82
3869 5645 4.271291 GCTAACCACTAGAGCTAACATTGC 59.729 45.833 0.00 0.00 33.28 3.56
3873 5649 4.878397 ACCACTAGAGCTAACATTGCATTC 59.122 41.667 0.00 0.00 0.00 2.67
3878 5654 5.306532 AGAGCTAACATTGCATTCTGTTG 57.693 39.130 15.97 9.53 36.34 3.33
3879 5655 4.763793 AGAGCTAACATTGCATTCTGTTGT 59.236 37.500 15.97 4.97 36.34 3.32
3880 5656 5.939883 AGAGCTAACATTGCATTCTGTTGTA 59.060 36.000 15.97 1.70 36.34 2.41
3881 5657 6.093219 AGAGCTAACATTGCATTCTGTTGTAG 59.907 38.462 15.97 9.80 36.34 2.74
3882 5658 4.795278 GCTAACATTGCATTCTGTTGTAGC 59.205 41.667 15.97 14.09 36.34 3.58
3883 5659 5.392380 GCTAACATTGCATTCTGTTGTAGCT 60.392 40.000 15.97 0.00 35.53 3.32
3885 5661 4.801891 ACATTGCATTCTGTTGTAGCTTG 58.198 39.130 0.00 0.00 0.00 4.01
3886 5662 4.520111 ACATTGCATTCTGTTGTAGCTTGA 59.480 37.500 0.00 0.00 0.00 3.02
3887 5663 5.184479 ACATTGCATTCTGTTGTAGCTTGAT 59.816 36.000 0.00 0.00 0.00 2.57
3888 5664 6.375174 ACATTGCATTCTGTTGTAGCTTGATA 59.625 34.615 0.00 0.00 0.00 2.15
3890 5666 5.491070 TGCATTCTGTTGTAGCTTGATACT 58.509 37.500 0.00 0.00 0.00 2.12
3891 5667 5.582269 TGCATTCTGTTGTAGCTTGATACTC 59.418 40.000 0.00 0.00 0.00 2.59
3892 5668 5.007136 GCATTCTGTTGTAGCTTGATACTCC 59.993 44.000 0.00 0.00 0.00 3.85
3893 5669 4.737855 TCTGTTGTAGCTTGATACTCCC 57.262 45.455 0.00 0.00 0.00 4.30
3894 5670 4.353777 TCTGTTGTAGCTTGATACTCCCT 58.646 43.478 0.00 0.00 0.00 4.20
3895 5671 4.777896 TCTGTTGTAGCTTGATACTCCCTT 59.222 41.667 0.00 0.00 0.00 3.95
3896 5672 5.248477 TCTGTTGTAGCTTGATACTCCCTTT 59.752 40.000 0.00 0.00 0.00 3.11
3897 5673 6.439375 TCTGTTGTAGCTTGATACTCCCTTTA 59.561 38.462 0.00 0.00 0.00 1.85
3898 5674 6.640518 TGTTGTAGCTTGATACTCCCTTTAG 58.359 40.000 0.00 0.00 0.00 1.85
3899 5675 6.212791 TGTTGTAGCTTGATACTCCCTTTAGT 59.787 38.462 0.00 0.00 0.00 2.24
3900 5676 7.398047 TGTTGTAGCTTGATACTCCCTTTAGTA 59.602 37.037 0.00 0.00 36.44 1.82
3901 5677 7.344095 TGTAGCTTGATACTCCCTTTAGTAC 57.656 40.000 0.00 0.00 34.87 2.73
3902 5678 6.893554 TGTAGCTTGATACTCCCTTTAGTACA 59.106 38.462 0.00 0.00 34.87 2.90
3903 5679 6.869206 AGCTTGATACTCCCTTTAGTACAA 57.131 37.500 0.00 0.00 34.87 2.41
3904 5680 7.253905 AGCTTGATACTCCCTTTAGTACAAA 57.746 36.000 0.00 0.00 34.87 2.83
3905 5681 7.331791 AGCTTGATACTCCCTTTAGTACAAAG 58.668 38.462 0.00 3.45 34.87 2.77
3906 5682 7.038231 AGCTTGATACTCCCTTTAGTACAAAGT 60.038 37.037 13.29 0.00 34.87 2.66
3907 5683 7.606839 GCTTGATACTCCCTTTAGTACAAAGTT 59.393 37.037 13.29 2.75 34.87 2.66
3908 5684 8.842358 TTGATACTCCCTTTAGTACAAAGTTG 57.158 34.615 13.29 0.00 34.87 3.16
3909 5685 8.197592 TGATACTCCCTTTAGTACAAAGTTGA 57.802 34.615 13.29 9.83 34.87 3.18
3910 5686 8.311836 TGATACTCCCTTTAGTACAAAGTTGAG 58.688 37.037 19.18 19.18 34.87 3.02
3911 5687 6.496144 ACTCCCTTTAGTACAAAGTTGAGT 57.504 37.500 19.88 19.88 34.99 3.41
3912 5688 6.522946 ACTCCCTTTAGTACAAAGTTGAGTC 58.477 40.000 19.88 0.00 34.89 3.36
3913 5689 6.099269 ACTCCCTTTAGTACAAAGTTGAGTCA 59.901 38.462 19.88 0.00 34.89 3.41
3914 5690 7.074653 TCCCTTTAGTACAAAGTTGAGTCAT 57.925 36.000 13.29 0.00 0.00 3.06
3915 5691 7.159372 TCCCTTTAGTACAAAGTTGAGTCATC 58.841 38.462 13.29 0.00 0.00 2.92
3916 5692 7.016268 TCCCTTTAGTACAAAGTTGAGTCATCT 59.984 37.037 13.29 0.00 0.00 2.90
3917 5693 8.311836 CCCTTTAGTACAAAGTTGAGTCATCTA 58.688 37.037 4.14 0.00 0.00 1.98
3918 5694 9.877178 CCTTTAGTACAAAGTTGAGTCATCTAT 57.123 33.333 4.14 0.00 0.00 1.98
3923 5699 9.778741 AGTACAAAGTTGAGTCATCTATTTTGA 57.221 29.630 15.99 3.46 38.91 2.69
3926 5702 9.736023 ACAAAGTTGAGTCATCTATTTTGAAAC 57.264 29.630 15.99 0.00 38.91 2.78
3927 5703 8.895845 CAAAGTTGAGTCATCTATTTTGAAACG 58.104 33.333 4.14 0.00 38.91 3.60
3928 5704 7.133891 AGTTGAGTCATCTATTTTGAAACGG 57.866 36.000 1.70 0.00 0.00 4.44
3929 5705 6.934645 AGTTGAGTCATCTATTTTGAAACGGA 59.065 34.615 1.70 0.00 0.00 4.69
3930 5706 6.968131 TGAGTCATCTATTTTGAAACGGAG 57.032 37.500 0.00 0.00 0.00 4.63
3931 5707 5.874810 TGAGTCATCTATTTTGAAACGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
3932 5708 5.186198 AGTCATCTATTTTGAAACGGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
3933 5709 5.045869 AGTCATCTATTTTGAAACGGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
3957 5733 7.758528 GGAATAGTTATTAACGACGATATGGCT 59.241 37.037 0.00 0.00 36.23 4.75
4049 5839 9.952188 TCACGTATTCAACACAAATAATGAAAA 57.048 25.926 0.00 0.00 35.62 2.29
4120 5928 5.961272 AGTTTGGAAAAAGTTCACGTGAAT 58.039 33.333 31.81 17.09 36.33 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 120 3.925913 CAGCCCCGTCAACATTAATTTTG 59.074 43.478 7.85 7.85 0.00 2.44
176 179 2.040544 CCATCCTGGTCACGGCAAC 61.041 63.158 0.00 0.00 31.35 4.17
614 617 3.123620 GCAGGAGCGCCTCACTTG 61.124 66.667 5.80 0.00 44.80 3.16
685 688 8.819643 AATCGGTTTTTGCTACTCTATATCTC 57.180 34.615 0.00 0.00 0.00 2.75
692 695 9.191995 CAAAAATAAATCGGTTTTTGCTACTCT 57.808 29.630 0.00 0.00 43.81 3.24
712 733 0.614415 TCCCGGCCAGATGCAAAAAT 60.614 50.000 2.24 0.00 43.89 1.82
788 809 1.072505 CCAACCTACCAACCGCTGT 59.927 57.895 0.00 0.00 0.00 4.40
791 812 0.594602 GAAACCAACCTACCAACCGC 59.405 55.000 0.00 0.00 0.00 5.68
793 814 2.235891 CAGGAAACCAACCTACCAACC 58.764 52.381 0.00 0.00 35.84 3.77
1030 2587 1.680651 CGGTGGAGCTCTCAGGAGT 60.681 63.158 14.64 0.00 41.38 3.85
1031 2588 3.074999 GCGGTGGAGCTCTCAGGAG 62.075 68.421 14.64 5.61 42.18 3.69
1032 2589 3.071206 GCGGTGGAGCTCTCAGGA 61.071 66.667 14.64 0.00 0.00 3.86
1033 2590 2.641439 GATGCGGTGGAGCTCTCAGG 62.641 65.000 14.64 6.30 38.13 3.86
1034 2591 1.227205 GATGCGGTGGAGCTCTCAG 60.227 63.158 14.64 9.15 38.13 3.35
1035 2592 2.725312 GGATGCGGTGGAGCTCTCA 61.725 63.158 14.64 7.25 38.13 3.27
1036 2593 2.107953 GGATGCGGTGGAGCTCTC 59.892 66.667 14.64 7.27 38.13 3.20
1037 2594 2.685017 TGGATGCGGTGGAGCTCT 60.685 61.111 14.64 0.00 38.13 4.09
1038 2595 2.512515 GTGGATGCGGTGGAGCTC 60.513 66.667 4.71 4.71 38.13 4.09
1039 2596 4.457496 CGTGGATGCGGTGGAGCT 62.457 66.667 0.00 0.00 38.13 4.09
1050 2607 3.000819 TCCGTGGAAGCCGTGGAT 61.001 61.111 0.00 0.00 0.00 3.41
1051 2608 3.691342 CTCCGTGGAAGCCGTGGA 61.691 66.667 0.00 0.00 0.00 4.02
1096 2653 4.500116 GGAGCTGTCGGGCGTCTC 62.500 72.222 0.00 0.00 37.29 3.36
1135 2692 3.637273 GAAGGTCCTGGCGTGGGT 61.637 66.667 0.00 0.00 0.00 4.51
1139 2696 4.003788 CCACGAAGGTCCTGGCGT 62.004 66.667 12.82 12.82 37.48 5.68
1289 2855 0.108472 GGGCCTGTACGTAGTGGAAC 60.108 60.000 15.57 8.46 45.73 3.62
1290 2856 1.597797 CGGGCCTGTACGTAGTGGAA 61.598 60.000 15.57 0.00 45.73 3.53
1291 2857 2.048023 CGGGCCTGTACGTAGTGGA 61.048 63.158 15.57 0.00 45.73 4.02
1292 2858 2.493030 CGGGCCTGTACGTAGTGG 59.507 66.667 2.29 2.19 45.73 4.00
1293 2859 2.202703 GCGGGCCTGTACGTAGTG 60.203 66.667 14.55 0.00 45.73 2.74
1295 2861 4.217159 GGGCGGGCCTGTACGTAG 62.217 72.222 14.55 0.00 36.10 3.51
1342 2908 4.372656 AGAAAGAAAGAACCGACAGACAG 58.627 43.478 0.00 0.00 0.00 3.51
1345 2911 5.671493 AGAAAGAAAGAAAGAACCGACAGA 58.329 37.500 0.00 0.00 0.00 3.41
1350 2916 3.968724 CGCAAGAAAGAAAGAAAGAACCG 59.031 43.478 0.00 0.00 43.02 4.44
1437 3003 6.393897 TCTCCAGGAGATGTCCCTAAAATAT 58.606 40.000 15.98 0.00 45.26 1.28
1478 3044 1.895131 ACCATGAAAGGAACATGCACC 59.105 47.619 0.00 0.00 42.31 5.01
1484 3050 4.112634 AGGCTAAACCATGAAAGGAACA 57.887 40.909 0.00 0.00 43.14 3.18
1488 3054 4.335416 TCTCAAGGCTAAACCATGAAAGG 58.665 43.478 0.00 0.00 45.24 3.11
1489 3055 5.964958 TTCTCAAGGCTAAACCATGAAAG 57.035 39.130 0.00 0.00 45.24 2.62
1490 3056 5.010617 GGTTTCTCAAGGCTAAACCATGAAA 59.989 40.000 19.86 7.77 45.24 2.69
1491 3057 4.522789 GGTTTCTCAAGGCTAAACCATGAA 59.477 41.667 19.86 2.89 45.24 2.57
1496 3062 1.199327 GCGGTTTCTCAAGGCTAAACC 59.801 52.381 16.35 16.35 45.64 3.27
1497 3063 2.095718 CAGCGGTTTCTCAAGGCTAAAC 60.096 50.000 2.66 2.66 31.72 2.01
1498 3064 2.151202 CAGCGGTTTCTCAAGGCTAAA 58.849 47.619 0.00 0.00 31.72 1.85
1499 3065 1.071699 ACAGCGGTTTCTCAAGGCTAA 59.928 47.619 0.00 0.00 31.72 3.09
1500 3066 0.685097 ACAGCGGTTTCTCAAGGCTA 59.315 50.000 0.00 0.00 31.72 3.93
1501 3067 0.179018 AACAGCGGTTTCTCAAGGCT 60.179 50.000 0.00 0.00 31.83 4.58
1502 3068 1.464997 CTAACAGCGGTTTCTCAAGGC 59.535 52.381 7.73 0.00 38.45 4.35
1503 3069 2.737252 GTCTAACAGCGGTTTCTCAAGG 59.263 50.000 7.73 0.00 38.45 3.61
1504 3070 3.654414 AGTCTAACAGCGGTTTCTCAAG 58.346 45.455 7.73 0.00 38.45 3.02
1505 3071 3.746045 AGTCTAACAGCGGTTTCTCAA 57.254 42.857 7.73 0.00 38.45 3.02
1506 3072 3.554337 GGAAGTCTAACAGCGGTTTCTCA 60.554 47.826 7.73 0.00 38.45 3.27
1507 3073 2.994578 GGAAGTCTAACAGCGGTTTCTC 59.005 50.000 7.73 0.00 38.45 2.87
1563 3129 4.192317 AGGATACGCTTGATGGTTTTCTC 58.808 43.478 0.00 0.00 46.39 2.87
1622 3188 9.793259 AAGTTTGTTATCTGATTTTGGAGTAGA 57.207 29.630 0.00 0.00 0.00 2.59
1656 3222 1.754803 TGCAGTCTTATCCCTACACCG 59.245 52.381 0.00 0.00 0.00 4.94
1690 3256 0.094730 GATCGCCCAAACGTTCTTCG 59.905 55.000 0.00 3.58 46.00 3.79
1712 3278 2.192175 CCCGACATTACCAGGGCC 59.808 66.667 0.00 0.00 37.07 5.80
1818 3403 2.043526 AGAAAACATCCCAATCTGCCCT 59.956 45.455 0.00 0.00 0.00 5.19
1939 3524 6.926630 AGATAAGAGGGTAAGACATCCATC 57.073 41.667 0.00 0.00 35.15 3.51
2050 3635 0.537143 TGGATGCGACTTTGTTGGCT 60.537 50.000 0.00 0.00 0.00 4.75
2136 3728 8.621532 AATTCACAGCTCATCTAACAAACTAA 57.378 30.769 0.00 0.00 0.00 2.24
2311 3903 9.904198 TCCTTCATCTGTTATTTGTAATCATCA 57.096 29.630 0.00 0.00 0.00 3.07
2333 3925 5.045578 AGCACAAATATACCTGACACTCCTT 60.046 40.000 0.00 0.00 0.00 3.36
2334 3926 4.471386 AGCACAAATATACCTGACACTCCT 59.529 41.667 0.00 0.00 0.00 3.69
2335 3927 4.770795 AGCACAAATATACCTGACACTCC 58.229 43.478 0.00 0.00 0.00 3.85
2483 4077 9.807649 GAACATTAACTAATGCATTTCCTGAAT 57.192 29.630 18.75 8.55 45.24 2.57
2511 4105 7.013083 AGCTTCAGTCAGAAATGCTAAATATGG 59.987 37.037 0.00 0.00 36.37 2.74
2599 4193 2.133641 GCCCCAGTTTGTGCAAGGT 61.134 57.895 0.00 0.00 0.00 3.50
2639 4233 9.066842 AGATATGCTTCCCAAGATCCTAAATAT 57.933 33.333 0.00 0.00 0.00 1.28
2649 4243 2.707791 CCCTCAGATATGCTTCCCAAGA 59.292 50.000 0.00 0.00 0.00 3.02
2735 4329 4.764771 GCCCCAGCCATCCAAGCA 62.765 66.667 0.00 0.00 0.00 3.91
2786 4380 1.154225 GCCTTTCACCATGTTCGCG 60.154 57.895 0.00 0.00 0.00 5.87
2789 4383 0.527565 ATGCGCCTTTCACCATGTTC 59.472 50.000 4.18 0.00 0.00 3.18
2807 4401 3.091633 ACCAGCAAGCATAAACCTGAT 57.908 42.857 0.00 0.00 0.00 2.90
2918 4512 1.002544 GAGCTCACAACCACTAGCCTT 59.997 52.381 9.40 0.00 35.54 4.35
2933 4527 3.471680 ACAAACCTCTTCAAGTGAGCTC 58.528 45.455 6.82 6.82 0.00 4.09
2961 4555 9.002600 ACATAAATAATATTCTGCATCGCTCAA 57.997 29.630 0.00 0.00 0.00 3.02
2982 4576 6.202516 TGACACACAGATCGTCATACATAA 57.797 37.500 0.00 0.00 34.83 1.90
3048 4642 1.153086 GGTGATCGCTGCCTTCCAT 60.153 57.895 6.18 0.00 0.00 3.41
3066 4660 3.569548 ACTCACATCAATAGATAGCGCG 58.430 45.455 0.00 0.00 31.88 6.86
3081 4675 0.837691 AGGGCATGTCTGGACTCACA 60.838 55.000 0.00 0.00 0.00 3.58
3089 4683 1.642037 CGTGCTGAAGGGCATGTCTG 61.642 60.000 0.00 0.00 44.34 3.51
3107 4701 2.170985 CAAAGCACTCGTTCGCCG 59.829 61.111 0.00 0.00 38.13 6.46
3135 4729 4.584688 GCTTGCAAGCCATCCAAC 57.415 55.556 36.21 10.24 46.20 3.77
3153 4747 3.305199 GGCCTGCTTGAATCATATTCAGC 60.305 47.826 0.00 12.87 0.00 4.26
3155 4749 3.900971 TGGCCTGCTTGAATCATATTCA 58.099 40.909 3.32 0.00 0.00 2.57
3165 4759 2.804986 TCATATGTTGGCCTGCTTGA 57.195 45.000 3.32 0.00 0.00 3.02
3178 4772 3.557185 TCAGCACGCTTTAGCTTCATATG 59.443 43.478 0.00 0.00 39.50 1.78
3179 4773 3.797039 TCAGCACGCTTTAGCTTCATAT 58.203 40.909 0.00 0.00 39.50 1.78
3223 4817 0.179026 CTCATGTCCCCAGCATCCTG 60.179 60.000 0.00 0.00 38.85 3.86
3271 4865 2.976490 GCTGGTCTGGGGCTCATGT 61.976 63.158 0.00 0.00 0.00 3.21
3284 4878 2.268920 CATGCTACCGGTGCTGGT 59.731 61.111 19.93 7.91 46.26 4.00
3321 4916 6.952773 AGTGCTACCTTCTCTTCTATACTG 57.047 41.667 0.00 0.00 0.00 2.74
3373 4968 2.941453 ACGCACACAGTACTCCTATG 57.059 50.000 0.00 0.00 0.00 2.23
3374 4969 4.461781 ACTTAACGCACACAGTACTCCTAT 59.538 41.667 0.00 0.00 0.00 2.57
3392 4987 5.652891 TCAAACAGTTAGCAAACCCACTTAA 59.347 36.000 0.00 0.00 36.15 1.85
3423 5026 1.190984 GCACGATCATAGCACACATCG 59.809 52.381 0.00 6.59 43.06 3.84
3478 5081 5.803461 TCCAAACTATTTCTATGTGTCGACG 59.197 40.000 11.62 0.00 0.00 5.12
3508 5226 5.187772 TCAAAGTAATCTAGAAGCTGGCTCA 59.812 40.000 0.00 0.00 0.00 4.26
3649 5367 0.391661 TCGCATCACTCAAAGAGGCC 60.392 55.000 0.00 0.00 39.44 5.19
3667 5387 1.620822 AACAAGACAATGGGCCTGTC 58.379 50.000 16.05 16.05 42.95 3.51
3689 5409 3.483558 GCGAGCACACAAGAAAAGAAAAG 59.516 43.478 0.00 0.00 0.00 2.27
3711 5434 1.083806 TTCGTTAGATGGCGCTGCTG 61.084 55.000 7.64 0.00 0.00 4.41
3712 5435 1.084370 GTTCGTTAGATGGCGCTGCT 61.084 55.000 7.64 4.82 0.00 4.24
3713 5436 1.084370 AGTTCGTTAGATGGCGCTGC 61.084 55.000 7.64 0.00 0.00 5.25
3764 5530 4.539083 TTGTCCGCTGGCACGTGT 62.539 61.111 18.38 0.00 0.00 4.49
3794 5569 8.383175 TGAGTTCTAATCCTGGTCTTGTAATTT 58.617 33.333 0.00 0.00 0.00 1.82
3838 5614 0.528684 CTAGTGGTTAGCCGAGCAGC 60.529 60.000 0.00 0.00 37.67 5.25
3840 5616 1.103803 CTCTAGTGGTTAGCCGAGCA 58.896 55.000 0.00 0.00 37.67 4.26
3841 5617 0.249114 GCTCTAGTGGTTAGCCGAGC 60.249 60.000 7.31 7.31 37.36 5.03
3865 5641 5.909621 ATCAAGCTACAACAGAATGCAAT 57.090 34.783 0.00 0.00 42.53 3.56
3866 5642 5.939883 AGTATCAAGCTACAACAGAATGCAA 59.060 36.000 0.00 0.00 42.53 4.08
3867 5643 5.491070 AGTATCAAGCTACAACAGAATGCA 58.509 37.500 0.00 0.00 42.53 3.96
3868 5644 5.007136 GGAGTATCAAGCTACAACAGAATGC 59.993 44.000 0.00 0.00 36.43 3.56
3869 5645 5.525378 GGGAGTATCAAGCTACAACAGAATG 59.475 44.000 0.00 0.00 39.00 2.67
3873 5649 4.744795 AGGGAGTATCAAGCTACAACAG 57.255 45.455 0.00 0.00 36.25 3.16
3878 5654 7.344095 TGTACTAAAGGGAGTATCAAGCTAC 57.656 40.000 0.00 0.00 36.25 3.58
3879 5655 7.966339 TTGTACTAAAGGGAGTATCAAGCTA 57.034 36.000 0.00 0.00 36.25 3.32
3880 5656 6.869206 TTGTACTAAAGGGAGTATCAAGCT 57.131 37.500 0.00 0.00 36.25 3.74
3881 5657 7.104290 ACTTTGTACTAAAGGGAGTATCAAGC 58.896 38.462 16.79 0.00 36.25 4.01
3882 5658 8.936864 CAACTTTGTACTAAAGGGAGTATCAAG 58.063 37.037 16.79 0.00 36.25 3.02
3883 5659 8.653191 TCAACTTTGTACTAAAGGGAGTATCAA 58.347 33.333 16.79 0.00 36.25 2.57
3885 5661 8.312564 ACTCAACTTTGTACTAAAGGGAGTATC 58.687 37.037 24.79 0.00 40.68 2.24
3886 5662 8.203681 ACTCAACTTTGTACTAAAGGGAGTAT 57.796 34.615 24.79 14.25 40.68 2.12
3887 5663 7.288389 TGACTCAACTTTGTACTAAAGGGAGTA 59.712 37.037 25.33 18.34 41.58 2.59
3888 5664 6.099269 TGACTCAACTTTGTACTAAAGGGAGT 59.901 38.462 25.43 25.43 42.84 3.85
3890 5666 6.488769 TGACTCAACTTTGTACTAAAGGGA 57.511 37.500 16.79 13.49 0.00 4.20
3891 5667 7.162082 AGATGACTCAACTTTGTACTAAAGGG 58.838 38.462 16.79 11.13 0.00 3.95
3892 5668 9.877178 ATAGATGACTCAACTTTGTACTAAAGG 57.123 33.333 16.79 0.00 0.00 3.11
3897 5673 9.778741 TCAAAATAGATGACTCAACTTTGTACT 57.221 29.630 0.00 0.00 0.00 2.73
3900 5676 9.736023 GTTTCAAAATAGATGACTCAACTTTGT 57.264 29.630 0.00 0.00 0.00 2.83
3901 5677 8.895845 CGTTTCAAAATAGATGACTCAACTTTG 58.104 33.333 0.00 0.00 0.00 2.77
3902 5678 8.076178 CCGTTTCAAAATAGATGACTCAACTTT 58.924 33.333 0.00 0.00 0.00 2.66
3903 5679 7.444183 TCCGTTTCAAAATAGATGACTCAACTT 59.556 33.333 0.00 0.00 0.00 2.66
3904 5680 6.934645 TCCGTTTCAAAATAGATGACTCAACT 59.065 34.615 0.00 0.00 0.00 3.16
3905 5681 7.129109 TCCGTTTCAAAATAGATGACTCAAC 57.871 36.000 0.00 0.00 0.00 3.18
3906 5682 6.371548 CCTCCGTTTCAAAATAGATGACTCAA 59.628 38.462 0.00 0.00 0.00 3.02
3907 5683 5.874810 CCTCCGTTTCAAAATAGATGACTCA 59.125 40.000 0.00 0.00 0.00 3.41
3908 5684 5.294552 CCCTCCGTTTCAAAATAGATGACTC 59.705 44.000 0.00 0.00 0.00 3.36
3909 5685 5.045869 TCCCTCCGTTTCAAAATAGATGACT 60.046 40.000 0.00 0.00 0.00 3.41
3910 5686 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
3911 5687 5.429681 TCCCTCCGTTTCAAAATAGATGA 57.570 39.130 0.00 0.00 0.00 2.92
3912 5688 6.699575 ATTCCCTCCGTTTCAAAATAGATG 57.300 37.500 0.00 0.00 0.00 2.90
3913 5689 7.574607 ACTATTCCCTCCGTTTCAAAATAGAT 58.425 34.615 0.00 0.00 32.32 1.98
3914 5690 6.954232 ACTATTCCCTCCGTTTCAAAATAGA 58.046 36.000 0.00 0.00 32.32 1.98
3915 5691 7.625828 AACTATTCCCTCCGTTTCAAAATAG 57.374 36.000 0.00 0.00 33.52 1.73
3916 5692 9.689501 AATAACTATTCCCTCCGTTTCAAAATA 57.310 29.630 0.00 0.00 0.00 1.40
3917 5693 8.589701 AATAACTATTCCCTCCGTTTCAAAAT 57.410 30.769 0.00 0.00 0.00 1.82
3918 5694 9.517868 TTAATAACTATTCCCTCCGTTTCAAAA 57.482 29.630 0.00 0.00 0.00 2.44
3919 5695 8.949177 GTTAATAACTATTCCCTCCGTTTCAAA 58.051 33.333 0.00 0.00 0.00 2.69
3920 5696 7.278424 CGTTAATAACTATTCCCTCCGTTTCAA 59.722 37.037 1.42 0.00 0.00 2.69
3921 5697 6.757947 CGTTAATAACTATTCCCTCCGTTTCA 59.242 38.462 1.42 0.00 0.00 2.69
3922 5698 6.980397 TCGTTAATAACTATTCCCTCCGTTTC 59.020 38.462 1.42 0.00 0.00 2.78
3923 5699 6.758416 GTCGTTAATAACTATTCCCTCCGTTT 59.242 38.462 1.42 0.00 0.00 3.60
3924 5700 6.276091 GTCGTTAATAACTATTCCCTCCGTT 58.724 40.000 1.42 0.00 0.00 4.44
3925 5701 5.506317 CGTCGTTAATAACTATTCCCTCCGT 60.506 44.000 1.42 0.00 0.00 4.69
3926 5702 4.913924 CGTCGTTAATAACTATTCCCTCCG 59.086 45.833 1.42 0.00 0.00 4.63
3927 5703 6.076981 TCGTCGTTAATAACTATTCCCTCC 57.923 41.667 1.42 0.00 0.00 4.30
3928 5704 9.286946 CATATCGTCGTTAATAACTATTCCCTC 57.713 37.037 1.42 0.00 0.00 4.30
3929 5705 8.248945 CCATATCGTCGTTAATAACTATTCCCT 58.751 37.037 1.42 0.00 0.00 4.20
3930 5706 7.009907 GCCATATCGTCGTTAATAACTATTCCC 59.990 40.741 1.42 0.00 0.00 3.97
3931 5707 7.758528 AGCCATATCGTCGTTAATAACTATTCC 59.241 37.037 1.42 0.00 0.00 3.01
3932 5708 8.684973 AGCCATATCGTCGTTAATAACTATTC 57.315 34.615 1.42 0.00 0.00 1.75
3933 5709 8.922676 CAAGCCATATCGTCGTTAATAACTATT 58.077 33.333 1.42 0.00 0.00 1.73
4085 5875 8.126871 ACTTTTTCCAAACTCGCTAAATTTTC 57.873 30.769 0.00 0.00 0.00 2.29
4088 5878 7.222031 GTGAACTTTTTCCAAACTCGCTAAATT 59.778 33.333 0.00 0.00 0.00 1.82
4095 5885 3.783943 CACGTGAACTTTTTCCAAACTCG 59.216 43.478 10.90 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.