Multiple sequence alignment - TraesCS3B01G335900

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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 TraesCS3B01G335900 chr3B 100.000 4516 0 0 1 4516 542166264 542161749 0.000000e+00 8340.0
1 TraesCS3B01G335900 chr3B 97.294 739 19 1 1 738 781445717 781446455 0.000000e+00 1253.0
2 TraesCS3B01G335900 chr3B 95.907 733 30 0 1 733 225697523 225696791 0.000000e+00 1188.0
3 TraesCS3B01G335900 chr3B 80.720 389 43 21 3259 3641 763312001 763311639 1.600000e-69 274.0
4 TraesCS3B01G335900 chr3B 87.156 109 3 2 4259 4358 818161752 818161646 3.690000e-21 113.0
5 TraesCS3B01G335900 chr3A 91.895 2369 139 23 770 3102 534531268 534533619 0.000000e+00 3262.0
6 TraesCS3B01G335900 chr3A 89.150 553 27 19 3194 3723 534533661 534534203 0.000000e+00 658.0
7 TraesCS3B01G335900 chr3A 87.172 343 30 8 3724 4064 730343991 730343661 1.190000e-100 377.0
8 TraesCS3B01G335900 chr3D 90.992 2420 158 26 768 3150 415655527 415653131 0.000000e+00 3206.0
9 TraesCS3B01G335900 chr3D 88.587 552 33 17 3194 3723 415653119 415652576 1.060000e-180 643.0
10 TraesCS3B01G335900 chr3D 100.000 32 0 0 4482 4513 377879708 377879739 4.880000e-05 60.2
11 TraesCS3B01G335900 chr6B 98.367 735 12 0 1 735 197570809 197571543 0.000000e+00 1291.0
12 TraesCS3B01G335900 chr2B 96.892 740 22 1 1 739 514411566 514410827 0.000000e+00 1238.0
13 TraesCS3B01G335900 chr1B 96.065 737 28 1 1 737 433773586 433772851 0.000000e+00 1199.0
14 TraesCS3B01G335900 chr1B 80.463 389 45 20 3259 3641 668457776 668458139 7.450000e-68 268.0
15 TraesCS3B01G335900 chr1B 95.522 67 2 1 4448 4513 475493365 475493299 6.180000e-19 106.0
16 TraesCS3B01G335900 chr1B 97.297 37 0 1 4259 4295 555134305 555134340 1.360000e-05 62.1
17 TraesCS3B01G335900 chr4A 95.929 737 28 1 1 735 279601573 279602309 0.000000e+00 1194.0
18 TraesCS3B01G335900 chr4A 95.510 735 31 2 1 734 81633177 81633910 0.000000e+00 1173.0
19 TraesCS3B01G335900 chr7B 95.907 733 30 0 1 733 217885120 217884388 0.000000e+00 1188.0
20 TraesCS3B01G335900 chr7B 84.211 133 8 6 4242 4364 666583030 666583159 2.850000e-22 117.0
21 TraesCS3B01G335900 chr7B 97.436 39 1 0 4259 4297 727871157 727871195 2.920000e-07 67.6
22 TraesCS3B01G335900 chr6A 95.777 734 30 1 1 734 399139040 399139772 0.000000e+00 1182.0
23 TraesCS3B01G335900 chr6A 86.337 344 45 2 3721 4064 584913464 584913805 1.530000e-99 374.0
24 TraesCS3B01G335900 chr6A 85.833 120 5 3 4259 4366 28664039 28664158 2.850000e-22 117.0
25 TraesCS3B01G335900 chr6A 86.325 117 4 3 4259 4366 593560130 593560243 2.850000e-22 117.0
26 TraesCS3B01G335900 chr6A 93.421 76 4 1 4439 4513 584914452 584914527 1.330000e-20 111.0
27 TraesCS3B01G335900 chr7D 94.082 490 26 1 2191 2680 6141958 6141472 0.000000e+00 741.0
28 TraesCS3B01G335900 chr7D 92.199 423 26 3 2612 3030 6141475 6141056 3.890000e-165 592.0
29 TraesCS3B01G335900 chr7D 86.116 569 30 15 3194 3723 6140885 6140327 6.560000e-158 568.0
30 TraesCS3B01G335900 chr7D 88.372 344 33 4 3724 4064 630820638 630820299 1.510000e-109 407.0
31 TraesCS3B01G335900 chr7D 98.077 52 1 0 803 854 6142287 6142236 1.730000e-14 91.6
32 TraesCS3B01G335900 chr5A 87.077 650 44 14 1321 1962 54731625 54731008 0.000000e+00 699.0
33 TraesCS3B01G335900 chr5A 96.784 342 8 2 3724 4064 12225856 12225517 6.560000e-158 568.0
34 TraesCS3B01G335900 chr5A 96.907 194 5 1 4065 4258 12225485 12225293 1.570000e-84 324.0
35 TraesCS3B01G335900 chr5A 99.286 140 1 0 4377 4516 12225292 12225153 2.090000e-63 254.0
36 TraesCS3B01G335900 chrUn 95.489 266 4 1 4259 4516 397984496 397984761 6.990000e-113 418.0
37 TraesCS3B01G335900 chrUn 95.113 266 5 1 4259 4516 183178361 183178626 3.250000e-111 412.0
38 TraesCS3B01G335900 chr4B 87.283 346 31 8 3721 4064 618333920 618334254 2.550000e-102 383.0
39 TraesCS3B01G335900 chr4B 100.000 38 0 0 4258 4295 87937938 87937901 2.250000e-08 71.3
40 TraesCS3B01G335900 chr5B 80.463 389 42 23 3259 3641 106549183 106548823 2.680000e-67 267.0
41 TraesCS3B01G335900 chr1D 88.034 117 5 2 4259 4366 481924931 481924815 3.670000e-26 130.0
42 TraesCS3B01G335900 chr1A 80.800 125 5 5 4259 4366 571678552 571678430 3.740000e-11 80.5


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 TraesCS3B01G335900 chr3B 542161749 542166264 4515 True 8340.00 8340 100.0000 1 4516 1 chr3B.!!$R2 4515
1 TraesCS3B01G335900 chr3B 781445717 781446455 738 False 1253.00 1253 97.2940 1 738 1 chr3B.!!$F1 737
2 TraesCS3B01G335900 chr3B 225696791 225697523 732 True 1188.00 1188 95.9070 1 733 1 chr3B.!!$R1 732
3 TraesCS3B01G335900 chr3A 534531268 534534203 2935 False 1960.00 3262 90.5225 770 3723 2 chr3A.!!$F1 2953
4 TraesCS3B01G335900 chr3D 415652576 415655527 2951 True 1924.50 3206 89.7895 768 3723 2 chr3D.!!$R1 2955
5 TraesCS3B01G335900 chr6B 197570809 197571543 734 False 1291.00 1291 98.3670 1 735 1 chr6B.!!$F1 734
6 TraesCS3B01G335900 chr2B 514410827 514411566 739 True 1238.00 1238 96.8920 1 739 1 chr2B.!!$R1 738
7 TraesCS3B01G335900 chr1B 433772851 433773586 735 True 1199.00 1199 96.0650 1 737 1 chr1B.!!$R1 736
8 TraesCS3B01G335900 chr4A 279601573 279602309 736 False 1194.00 1194 95.9290 1 735 1 chr4A.!!$F2 734
9 TraesCS3B01G335900 chr4A 81633177 81633910 733 False 1173.00 1173 95.5100 1 734 1 chr4A.!!$F1 733
10 TraesCS3B01G335900 chr7B 217884388 217885120 732 True 1188.00 1188 95.9070 1 733 1 chr7B.!!$R1 732
11 TraesCS3B01G335900 chr6A 399139040 399139772 732 False 1182.00 1182 95.7770 1 734 1 chr6A.!!$F2 733
12 TraesCS3B01G335900 chr6A 584913464 584914527 1063 False 242.50 374 89.8790 3721 4513 2 chr6A.!!$F4 792
13 TraesCS3B01G335900 chr7D 6140327 6142287 1960 True 498.15 741 92.6185 803 3723 4 chr7D.!!$R2 2920
14 TraesCS3B01G335900 chr5A 54731008 54731625 617 True 699.00 699 87.0770 1321 1962 1 chr5A.!!$R1 641
15 TraesCS3B01G335900 chr5A 12225153 12225856 703 True 382.00 568 97.6590 3724 4516 3 chr5A.!!$R2 792

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
973 999 0.252513 TCCCTTTCCCGATCAGTCCA 60.253 55.0 0.0 0.0 0.00 4.02 F
975 1001 0.460284 CCTTTCCCGATCAGTCCACG 60.460 60.0 0.0 0.0 0.00 4.94 F
2802 2926 0.032815 GGATAGCTCAAGACGGAGGC 59.967 60.0 0.0 0.0 35.41 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2783 2907 0.032815 GCCTCCGTCTTGAGCTATCC 59.967 60.0 0.00 0.0 0.00 2.59 R
2853 2977 0.318784 ACACGCTTCCTCGAAGACAC 60.319 55.0 5.58 0.0 41.71 3.67 R
4289 4812 0.039165 CTTTTCTCCAAAGCCACGGC 60.039 55.0 0.00 0.0 35.66 5.68 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
103 104 9.821240 ACATTACCTTTATGGGCATATCATTTA 57.179 29.630 0.00 0.00 41.11 1.40
623 627 4.099380 GTTTTGGTCAAACGGTCAAAGA 57.901 40.909 0.00 0.00 35.64 2.52
655 659 4.082190 GGGACCTCAATGGAAAAAGTAAGC 60.082 45.833 0.00 0.00 39.71 3.09
712 716 6.707273 AACCCATAAGTAGGAACCAACTAA 57.293 37.500 0.00 0.00 0.00 2.24
758 762 5.416271 AAAATACTACACAGGATCCACGT 57.584 39.130 15.82 7.85 0.00 4.49
759 763 4.650754 AATACTACACAGGATCCACGTC 57.349 45.455 15.82 0.00 0.00 4.34
760 764 2.217510 ACTACACAGGATCCACGTCT 57.782 50.000 15.82 0.77 0.00 4.18
761 765 2.093106 ACTACACAGGATCCACGTCTC 58.907 52.381 15.82 0.00 0.00 3.36
762 766 2.092323 CTACACAGGATCCACGTCTCA 58.908 52.381 15.82 0.00 0.00 3.27
763 767 0.891373 ACACAGGATCCACGTCTCAG 59.109 55.000 15.82 1.47 0.00 3.35
764 768 1.177401 CACAGGATCCACGTCTCAGA 58.823 55.000 15.82 0.00 0.00 3.27
765 769 1.133982 CACAGGATCCACGTCTCAGAG 59.866 57.143 15.82 0.00 0.00 3.35
766 770 0.743688 CAGGATCCACGTCTCAGAGG 59.256 60.000 15.82 0.00 0.00 3.69
776 780 0.390472 GTCTCAGAGGAAACGCAGGG 60.390 60.000 0.00 0.00 0.00 4.45
870 879 4.303993 CCCAACGGTCGGTTCGGT 62.304 66.667 0.00 0.00 36.49 4.69
876 885 2.570181 GGTCGGTTCGGTCGATGT 59.430 61.111 0.00 0.00 38.93 3.06
879 888 0.864797 GTCGGTTCGGTCGATGTAGC 60.865 60.000 0.00 0.00 38.93 3.58
920 929 3.753283 ATATCCCCTTCCTTCCTTCCT 57.247 47.619 0.00 0.00 0.00 3.36
921 930 2.385263 ATCCCCTTCCTTCCTTCCTT 57.615 50.000 0.00 0.00 0.00 3.36
922 931 1.670059 TCCCCTTCCTTCCTTCCTTC 58.330 55.000 0.00 0.00 0.00 3.46
923 932 0.626382 CCCCTTCCTTCCTTCCTTCC 59.374 60.000 0.00 0.00 0.00 3.46
972 998 0.466124 CTCCCTTTCCCGATCAGTCC 59.534 60.000 0.00 0.00 0.00 3.85
973 999 0.252513 TCCCTTTCCCGATCAGTCCA 60.253 55.000 0.00 0.00 0.00 4.02
975 1001 0.460284 CCTTTCCCGATCAGTCCACG 60.460 60.000 0.00 0.00 0.00 4.94
1010 1036 4.569180 CGCCGCCATGGATTCCCT 62.569 66.667 18.40 0.00 42.00 4.20
1025 1051 2.498726 CCTCAAGCGAGCTCTCCC 59.501 66.667 12.85 0.00 38.00 4.30
1026 1052 2.498726 CTCAAGCGAGCTCTCCCC 59.501 66.667 12.85 0.00 31.00 4.81
1027 1053 3.077556 TCAAGCGAGCTCTCCCCC 61.078 66.667 12.85 0.00 0.00 5.40
1028 1054 3.393970 CAAGCGAGCTCTCCCCCA 61.394 66.667 12.85 0.00 0.00 4.96
1029 1055 2.607750 AAGCGAGCTCTCCCCCAA 60.608 61.111 12.85 0.00 0.00 4.12
1030 1056 2.664081 AAGCGAGCTCTCCCCCAAG 61.664 63.158 12.85 0.00 0.00 3.61
1044 1070 2.384828 CCCCAAGCCCAAGGTAAATAC 58.615 52.381 0.00 0.00 0.00 1.89
1045 1071 2.021457 CCCAAGCCCAAGGTAAATACG 58.979 52.381 0.00 0.00 0.00 3.06
1066 1092 3.052329 GGATCCTCTCCTTGATTTCCCT 58.948 50.000 3.84 0.00 41.29 4.20
1068 1094 2.482494 TCCTCTCCTTGATTTCCCTCC 58.518 52.381 0.00 0.00 0.00 4.30
1070 1096 2.578021 CCTCTCCTTGATTTCCCTCCAA 59.422 50.000 0.00 0.00 0.00 3.53
1076 1103 3.897505 CCTTGATTTCCCTCCAACTTGTT 59.102 43.478 0.00 0.00 0.00 2.83
1100 1127 4.127171 GCTGCTTCCTTAATTGATCCGTA 58.873 43.478 0.00 0.00 0.00 4.02
1101 1128 4.757149 GCTGCTTCCTTAATTGATCCGTAT 59.243 41.667 0.00 0.00 0.00 3.06
1102 1129 5.239525 GCTGCTTCCTTAATTGATCCGTATT 59.760 40.000 0.00 0.00 0.00 1.89
1104 1131 7.041372 GCTGCTTCCTTAATTGATCCGTATTTA 60.041 37.037 0.00 0.00 0.00 1.40
1105 1132 8.918202 TGCTTCCTTAATTGATCCGTATTTAT 57.082 30.769 0.00 0.00 0.00 1.40
1141 1174 3.618750 AGGTTCCCCGCGACGAAA 61.619 61.111 8.23 0.00 35.12 3.46
1148 1181 4.367023 CCGCGACGAAACCCCAGA 62.367 66.667 8.23 0.00 0.00 3.86
1340 1382 1.135523 GACGTACGACCCGAAGACC 59.864 63.158 24.41 0.00 0.00 3.85
1596 1644 2.099431 CGACTGCTGCTGCTTCTCC 61.099 63.158 17.00 1.33 40.48 3.71
1660 1716 1.497161 GCTCCCTTCCCTGCTACTAA 58.503 55.000 0.00 0.00 0.00 2.24
1705 1761 2.437651 TCGGATTGAATGGGAGCATGTA 59.562 45.455 0.00 0.00 0.00 2.29
1751 1807 0.612732 CTCTGCTGGGGCCAATTCAA 60.613 55.000 4.39 0.00 37.74 2.69
1766 1822 5.217393 CCAATTCAATATGAACATGAGGCG 58.783 41.667 0.00 0.00 39.45 5.52
1790 1846 5.010719 GGATATAGATCAAACTGTGGTCGGA 59.989 44.000 0.00 0.00 42.76 4.55
1876 1932 3.227614 CAATGATGGGAATGGCAGATGA 58.772 45.455 0.00 0.00 0.00 2.92
1952 2008 4.154918 AGCGAGATTTTGGATGTTCTGAAC 59.845 41.667 13.49 13.49 0.00 3.18
1982 2038 1.070758 GGGATAGGCGAGCTGAAATCA 59.929 52.381 0.00 0.00 0.00 2.57
2056 2112 1.448540 CGGGTGGAGATGTCACTGC 60.449 63.158 0.00 0.00 35.61 4.40
2059 2115 1.023513 GGTGGAGATGTCACTGCAGC 61.024 60.000 15.27 0.00 45.60 5.25
2101 2157 2.547211 GCGATGATTTGGATGAGGACAG 59.453 50.000 0.00 0.00 0.00 3.51
2244 2303 6.149640 GGGTTTGGAAAGTGAGAAGTTAGATC 59.850 42.308 0.00 0.00 0.00 2.75
2253 2312 9.784531 AAAGTGAGAAGTTAGATCAAGAATTCA 57.215 29.630 8.44 0.00 0.00 2.57
2322 2381 6.376864 TGTTGATATGGTGAAAATACTGTGGG 59.623 38.462 0.00 0.00 0.00 4.61
2363 2422 0.815095 TGAAGATGCTGGCATGCTTG 59.185 50.000 18.92 11.63 36.70 4.01
2396 2455 4.037446 GGCCTTGTGACTGTTATGTTCAAA 59.963 41.667 0.00 0.00 0.00 2.69
2457 2516 2.811431 CAACGTATGCCTTCAGTTCCAA 59.189 45.455 0.00 0.00 0.00 3.53
2498 2557 1.867233 GCTCCACATAATACTGTGCCG 59.133 52.381 0.00 0.00 44.16 5.69
2555 2614 1.021202 TTGTGCCCAAACAAGAGTCG 58.979 50.000 0.00 0.00 35.16 4.18
2576 2635 2.753446 GCCTGCTTGGAGCTTCCC 60.753 66.667 1.29 0.00 42.97 3.97
2577 2636 2.044551 CCTGCTTGGAGCTTCCCC 60.045 66.667 1.29 0.00 42.97 4.81
2682 2806 1.379916 CAAGAGGATGGTGGTGGCA 59.620 57.895 0.00 0.00 0.00 4.92
2709 2833 1.762957 GGGCTTCAGATGGCAGTACTA 59.237 52.381 11.49 0.00 0.00 1.82
2783 2907 3.502920 AGAGTTCTCGTTTGTAGATGCG 58.497 45.455 0.00 0.00 0.00 4.73
2802 2926 0.032815 GGATAGCTCAAGACGGAGGC 59.967 60.000 0.00 0.00 35.41 4.70
2828 2952 3.192001 TCAAAGACTCAATTCAGCATGGC 59.808 43.478 0.00 0.00 36.16 4.40
2922 3046 1.342474 TGCAAACCCCTGGTCTTCAAA 60.342 47.619 0.00 0.00 33.12 2.69
2946 3072 6.974965 ACAGCAAGAAAGAAGGTAAATTCTG 58.025 36.000 0.00 0.00 39.47 3.02
2958 3084 8.633561 AGAAGGTAAATTCTGGTTTCTTTTCAG 58.366 33.333 0.00 0.00 38.12 3.02
2963 3089 6.790232 AATTCTGGTTTCTTTTCAGGACAA 57.210 33.333 0.00 0.00 0.00 3.18
2988 3114 2.219458 TGGCATTGCATTTTTGTGTGG 58.781 42.857 11.39 0.00 0.00 4.17
3010 3138 4.063689 GGAAGTGAGTGCATCATATGAGG 58.936 47.826 12.98 12.98 40.92 3.86
3039 3224 8.668510 TCCTCTCTAGAATTACATTGCATTTC 57.331 34.615 0.00 0.00 0.00 2.17
3048 3233 7.816031 AGAATTACATTGCATTTCAGTTCCTTG 59.184 33.333 0.00 0.00 0.00 3.61
3049 3234 6.647334 TTACATTGCATTTCAGTTCCTTGA 57.353 33.333 0.00 0.00 0.00 3.02
3057 3242 6.042143 GCATTTCAGTTCCTTGAAAAGTGAA 58.958 36.000 5.41 2.79 46.63 3.18
3122 3308 4.097892 CCTATGGGTGTGTTATTTTCTGCC 59.902 45.833 0.00 0.00 0.00 4.85
3128 3314 5.867174 GGGTGTGTTATTTTCTGCCAATTAC 59.133 40.000 0.00 0.00 0.00 1.89
3150 3336 8.876275 TTACACAGGTACACAAAAGTAGTTAG 57.124 34.615 0.00 0.00 0.00 2.34
3151 3337 5.756833 ACACAGGTACACAAAAGTAGTTAGC 59.243 40.000 0.00 0.00 0.00 3.09
3152 3338 5.989777 CACAGGTACACAAAAGTAGTTAGCT 59.010 40.000 0.00 0.00 0.00 3.32
3153 3339 6.482308 CACAGGTACACAAAAGTAGTTAGCTT 59.518 38.462 0.00 0.00 0.00 3.74
3154 3340 7.654520 CACAGGTACACAAAAGTAGTTAGCTTA 59.345 37.037 0.00 0.00 0.00 3.09
3155 3341 8.206189 ACAGGTACACAAAAGTAGTTAGCTTAA 58.794 33.333 0.00 0.00 0.00 1.85
3157 3343 9.216117 AGGTACACAAAAGTAGTTAGCTTAATG 57.784 33.333 0.00 0.00 0.00 1.90
3158 3344 8.996271 GGTACACAAAAGTAGTTAGCTTAATGT 58.004 33.333 0.00 0.00 31.02 2.71
3159 3345 9.807386 GTACACAAAAGTAGTTAGCTTAATGTG 57.193 33.333 15.74 15.74 42.76 3.21
3160 3346 7.360361 ACACAAAAGTAGTTAGCTTAATGTGC 58.640 34.615 16.58 0.00 41.91 4.57
3161 3347 7.012894 ACACAAAAGTAGTTAGCTTAATGTGCA 59.987 33.333 16.58 0.00 41.91 4.57
3162 3348 8.023128 CACAAAAGTAGTTAGCTTAATGTGCAT 58.977 33.333 0.00 0.00 37.24 3.96
3163 3349 8.576442 ACAAAAGTAGTTAGCTTAATGTGCATT 58.424 29.630 0.00 2.83 30.31 3.56
3164 3350 9.065871 CAAAAGTAGTTAGCTTAATGTGCATTC 57.934 33.333 0.00 0.00 32.50 2.67
3165 3351 7.921786 AAGTAGTTAGCTTAATGTGCATTCA 57.078 32.000 0.00 0.00 32.50 2.57
3166 3352 7.308782 AGTAGTTAGCTTAATGTGCATTCAC 57.691 36.000 0.00 0.00 43.40 3.18
3167 3353 5.221891 AGTTAGCTTAATGTGCATTCACG 57.778 39.130 0.00 0.00 46.01 4.35
3168 3354 2.549633 AGCTTAATGTGCATTCACGC 57.450 45.000 0.18 3.45 46.01 5.34
3169 3355 1.811965 AGCTTAATGTGCATTCACGCA 59.188 42.857 0.18 0.00 46.01 5.24
3170 3356 2.159476 AGCTTAATGTGCATTCACGCAG 60.159 45.455 0.18 0.00 46.01 5.18
3171 3357 2.789208 CTTAATGTGCATTCACGCAGG 58.211 47.619 0.18 0.00 46.01 4.85
3172 3358 1.093972 TAATGTGCATTCACGCAGGG 58.906 50.000 0.18 0.00 46.01 4.45
3173 3359 1.597797 AATGTGCATTCACGCAGGGG 61.598 55.000 0.00 0.00 46.01 4.79
3174 3360 2.359850 GTGCATTCACGCAGGGGA 60.360 61.111 0.00 0.00 44.05 4.81
3175 3361 1.971167 GTGCATTCACGCAGGGGAA 60.971 57.895 0.00 0.00 44.05 3.97
3176 3362 1.675310 TGCATTCACGCAGGGGAAG 60.675 57.895 0.00 0.00 36.86 3.46
3177 3363 1.675641 GCATTCACGCAGGGGAAGT 60.676 57.895 0.00 0.00 0.00 3.01
3178 3364 1.926511 GCATTCACGCAGGGGAAGTG 61.927 60.000 0.00 0.00 37.24 3.16
3179 3365 0.606401 CATTCACGCAGGGGAAGTGT 60.606 55.000 0.00 0.00 37.20 3.55
3180 3366 0.981183 ATTCACGCAGGGGAAGTGTA 59.019 50.000 0.00 0.00 37.20 2.90
3181 3367 0.759959 TTCACGCAGGGGAAGTGTAA 59.240 50.000 0.00 0.00 37.20 2.41
3182 3368 0.981183 TCACGCAGGGGAAGTGTAAT 59.019 50.000 0.00 0.00 37.20 1.89
3183 3369 1.086696 CACGCAGGGGAAGTGTAATG 58.913 55.000 0.00 0.00 0.00 1.90
3184 3370 0.981183 ACGCAGGGGAAGTGTAATGA 59.019 50.000 0.00 0.00 0.00 2.57
3185 3371 1.338769 ACGCAGGGGAAGTGTAATGAC 60.339 52.381 0.00 0.00 0.00 3.06
3186 3372 1.066143 CGCAGGGGAAGTGTAATGACT 60.066 52.381 0.00 0.00 0.00 3.41
3187 3373 2.359900 GCAGGGGAAGTGTAATGACTG 58.640 52.381 0.00 0.00 0.00 3.51
3188 3374 2.941415 GCAGGGGAAGTGTAATGACTGG 60.941 54.545 0.00 0.00 0.00 4.00
3189 3375 2.305927 CAGGGGAAGTGTAATGACTGGT 59.694 50.000 0.00 0.00 0.00 4.00
3190 3376 2.305927 AGGGGAAGTGTAATGACTGGTG 59.694 50.000 0.00 0.00 0.00 4.17
3191 3377 2.618045 GGGGAAGTGTAATGACTGGTGG 60.618 54.545 0.00 0.00 0.00 4.61
3192 3378 2.039879 GGGAAGTGTAATGACTGGTGGT 59.960 50.000 0.00 0.00 0.00 4.16
3234 3422 9.028185 CCACTATTATGATATGTGACATCATCG 57.972 37.037 0.00 0.00 41.21 3.84
3246 3434 4.627467 GTGACATCATCGTTGCTAGTCTTT 59.373 41.667 11.37 0.00 0.00 2.52
3295 3499 9.639601 TGAAAATAAATTAAACACACACACACA 57.360 25.926 0.00 0.00 0.00 3.72
3296 3500 9.894439 GAAAATAAATTAAACACACACACACAC 57.106 29.630 0.00 0.00 0.00 3.82
3297 3501 8.988064 AAATAAATTAAACACACACACACACA 57.012 26.923 0.00 0.00 0.00 3.72
3298 3502 7.979115 ATAAATTAAACACACACACACACAC 57.021 32.000 0.00 0.00 0.00 3.82
3299 3503 5.378292 AATTAAACACACACACACACACA 57.622 34.783 0.00 0.00 0.00 3.72
3352 3563 4.279169 CCATTATGCCCCAGACATTAAGTG 59.721 45.833 0.00 0.00 0.00 3.16
3354 3565 5.702065 TTATGCCCCAGACATTAAGTGTA 57.298 39.130 0.00 0.00 42.36 2.90
3375 3586 7.232534 AGTGTATTTTCATGCTTTTAGTTCCCA 59.767 33.333 0.00 0.00 0.00 4.37
3435 3667 7.297936 TGTTATTCTGTTCAACAGGAGACTA 57.702 36.000 17.71 0.00 45.94 2.59
3624 3861 5.708230 TGTAACCCAACGATGCTTAGATTTT 59.292 36.000 0.00 0.00 0.00 1.82
3626 3863 4.331968 ACCCAACGATGCTTAGATTTTGA 58.668 39.130 0.00 0.00 0.00 2.69
3657 3894 6.685657 AGCTGTAACAGGTTAACTAGTGTAC 58.314 40.000 5.42 0.00 39.27 2.90
3658 3895 6.492772 AGCTGTAACAGGTTAACTAGTGTACT 59.507 38.462 5.42 0.00 39.27 2.73
3943 4182 0.329261 TTGGGGGAGCATGTTCAGAG 59.671 55.000 11.93 0.00 0.00 3.35
3952 4191 5.046448 GGGAGCATGTTCAGAGAGATATGAT 60.046 44.000 11.93 0.00 0.00 2.45
4038 4278 8.691661 ATGACTGTATTTTTAGACACTTTGGT 57.308 30.769 0.00 0.00 0.00 3.67
4068 4339 9.546909 GACAAAGATTGTACACTAATCATGTTG 57.453 33.333 13.92 12.72 45.52 3.33
4116 4639 1.826720 GCCCTCAGCAAAATCATTGGA 59.173 47.619 0.00 0.00 42.97 3.53
4180 4703 4.729881 AGAATGCCCTTACCAATACCCTTA 59.270 41.667 0.00 0.00 0.00 2.69
4260 4783 1.271840 ATGCGGAGAACTAGGGCCAA 61.272 55.000 6.18 0.00 0.00 4.52
4261 4784 1.449778 GCGGAGAACTAGGGCCAAC 60.450 63.158 6.18 0.00 0.00 3.77
4262 4785 1.153628 CGGAGAACTAGGGCCAACG 60.154 63.158 6.18 0.00 0.00 4.10
4263 4786 1.221021 GGAGAACTAGGGCCAACGG 59.779 63.158 6.18 0.00 0.00 4.44
4282 4805 2.203209 GGAGCTATGTTGGGGCCG 60.203 66.667 0.00 0.00 0.00 6.13
4283 4806 2.742116 GGAGCTATGTTGGGGCCGA 61.742 63.158 0.00 0.00 0.00 5.54
4285 4808 2.203209 GCTATGTTGGGGCCGAGG 60.203 66.667 0.00 0.00 0.00 4.63
4286 4809 2.510906 CTATGTTGGGGCCGAGGG 59.489 66.667 0.00 0.00 0.00 4.30
4287 4810 3.093835 TATGTTGGGGCCGAGGGG 61.094 66.667 0.00 0.00 0.00 4.79
4305 4828 2.282180 GGCCGTGGCTTTGGAGAA 60.282 61.111 11.25 0.00 41.60 2.87
4306 4829 1.901464 GGCCGTGGCTTTGGAGAAA 60.901 57.895 11.25 0.00 41.60 2.52
4307 4830 1.460273 GGCCGTGGCTTTGGAGAAAA 61.460 55.000 11.25 0.00 41.60 2.29
4320 4843 7.219484 CTTTGGAGAAAAGCCTGAAGAATTA 57.781 36.000 0.00 0.00 38.99 1.40
4322 4845 7.781324 TTGGAGAAAAGCCTGAAGAATTATT 57.219 32.000 0.00 0.00 0.00 1.40
4323 4846 7.781324 TGGAGAAAAGCCTGAAGAATTATTT 57.219 32.000 0.00 0.00 0.00 1.40
4325 4848 8.650490 TGGAGAAAAGCCTGAAGAATTATTTTT 58.350 29.630 0.00 0.00 0.00 1.94
4344 4925 3.524095 TTTTGAAGGGCCAAGATGAGA 57.476 42.857 6.18 0.00 0.00 3.27
4347 4928 2.199208 TGAAGGGCCAAGATGAGATGA 58.801 47.619 6.18 0.00 0.00 2.92
4352 4933 4.617593 AGGGCCAAGATGAGATGAAAAAT 58.382 39.130 6.18 0.00 0.00 1.82
4355 4936 5.508657 GGGCCAAGATGAGATGAAAAATAGC 60.509 44.000 4.39 0.00 0.00 2.97
4357 4938 5.301298 GCCAAGATGAGATGAAAAATAGCCT 59.699 40.000 0.00 0.00 0.00 4.58
4360 4941 8.255905 CCAAGATGAGATGAAAAATAGCCTTTT 58.744 33.333 0.00 0.00 0.00 2.27
4363 4944 5.723295 TGAGATGAAAAATAGCCTTTTGCC 58.277 37.500 0.00 0.00 42.71 4.52
4364 4945 5.089970 AGATGAAAAATAGCCTTTTGCCC 57.910 39.130 0.00 0.00 42.71 5.36
4365 4946 3.694043 TGAAAAATAGCCTTTTGCCCC 57.306 42.857 0.00 0.00 42.71 5.80
4366 4947 2.975489 TGAAAAATAGCCTTTTGCCCCA 59.025 40.909 0.00 0.00 42.71 4.96
4367 4948 3.586618 TGAAAAATAGCCTTTTGCCCCAT 59.413 39.130 0.00 0.00 42.71 4.00
4368 4949 4.780021 TGAAAAATAGCCTTTTGCCCCATA 59.220 37.500 0.00 0.00 42.71 2.74
4369 4950 5.249393 TGAAAAATAGCCTTTTGCCCCATAA 59.751 36.000 0.00 0.00 42.71 1.90
4370 4951 4.753516 AAATAGCCTTTTGCCCCATAAC 57.246 40.909 0.00 0.00 42.71 1.89
4371 4952 2.909504 TAGCCTTTTGCCCCATAACA 57.090 45.000 0.00 0.00 42.71 2.41
4372 4953 2.022718 AGCCTTTTGCCCCATAACAA 57.977 45.000 0.00 0.00 42.71 2.83
4373 4954 1.901833 AGCCTTTTGCCCCATAACAAG 59.098 47.619 0.00 0.00 42.71 3.16
4374 4955 1.066215 GCCTTTTGCCCCATAACAAGG 60.066 52.381 0.00 0.00 34.94 3.61
4375 4956 2.256306 CCTTTTGCCCCATAACAAGGT 58.744 47.619 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 3.290710 ACAATGCTTTTGTCCTGACTGT 58.709 40.909 0.00 0.00 0.00 3.55
623 627 1.134280 CATTGAGGTCCCTCGAATGCT 60.134 52.381 17.60 0.00 45.48 3.79
655 659 0.723790 CGAGCTTGCTCAGTTTTGCG 60.724 55.000 20.59 3.03 0.00 4.85
696 700 6.768641 TTTACCCTTAGTTGGTTCCTACTT 57.231 37.500 10.70 0.00 37.31 2.24
697 701 6.768641 TTTTACCCTTAGTTGGTTCCTACT 57.231 37.500 10.34 10.34 37.31 2.57
712 716 3.906846 TGGGACAATTGCATTTTTACCCT 59.093 39.130 19.07 0.00 36.20 4.34
739 743 3.884091 GAGACGTGGATCCTGTGTAGTAT 59.116 47.826 14.23 1.32 0.00 2.12
740 744 3.276857 GAGACGTGGATCCTGTGTAGTA 58.723 50.000 14.23 0.00 0.00 1.82
741 745 2.093106 GAGACGTGGATCCTGTGTAGT 58.907 52.381 14.23 3.82 0.00 2.73
742 746 2.092323 TGAGACGTGGATCCTGTGTAG 58.908 52.381 14.23 0.54 0.00 2.74
743 747 2.092323 CTGAGACGTGGATCCTGTGTA 58.908 52.381 14.23 0.00 0.00 2.90
744 748 0.891373 CTGAGACGTGGATCCTGTGT 59.109 55.000 14.23 10.11 0.00 3.72
745 749 1.133982 CTCTGAGACGTGGATCCTGTG 59.866 57.143 14.23 5.11 0.00 3.66
746 750 1.468985 CTCTGAGACGTGGATCCTGT 58.531 55.000 14.23 11.65 0.00 4.00
747 751 0.743688 CCTCTGAGACGTGGATCCTG 59.256 60.000 14.23 8.18 0.00 3.86
748 752 0.626382 TCCTCTGAGACGTGGATCCT 59.374 55.000 14.23 0.00 0.00 3.24
749 753 1.475403 TTCCTCTGAGACGTGGATCC 58.525 55.000 4.20 4.20 0.00 3.36
750 754 2.732597 CGTTTCCTCTGAGACGTGGATC 60.733 54.545 6.17 0.00 42.38 3.36
751 755 1.202582 CGTTTCCTCTGAGACGTGGAT 59.797 52.381 6.17 0.00 42.38 3.41
752 756 0.596577 CGTTTCCTCTGAGACGTGGA 59.403 55.000 6.17 0.00 42.38 4.02
753 757 3.108521 CGTTTCCTCTGAGACGTGG 57.891 57.895 6.17 0.00 42.38 4.94
757 761 0.390472 CCCTGCGTTTCCTCTGAGAC 60.390 60.000 6.17 0.00 0.00 3.36
758 762 0.832135 ACCCTGCGTTTCCTCTGAGA 60.832 55.000 6.17 0.00 0.00 3.27
759 763 0.390472 GACCCTGCGTTTCCTCTGAG 60.390 60.000 0.00 0.00 0.00 3.35
760 764 1.671742 GACCCTGCGTTTCCTCTGA 59.328 57.895 0.00 0.00 0.00 3.27
761 765 1.376037 GGACCCTGCGTTTCCTCTG 60.376 63.158 0.00 0.00 0.00 3.35
762 766 1.831652 CTGGACCCTGCGTTTCCTCT 61.832 60.000 0.00 0.00 0.00 3.69
763 767 1.376037 CTGGACCCTGCGTTTCCTC 60.376 63.158 0.00 0.00 0.00 3.71
764 768 2.750350 CTGGACCCTGCGTTTCCT 59.250 61.111 0.00 0.00 0.00 3.36
765 769 3.056328 GCTGGACCCTGCGTTTCC 61.056 66.667 2.19 0.00 0.00 3.13
766 770 3.056328 GGCTGGACCCTGCGTTTC 61.056 66.667 11.01 0.00 40.98 2.78
776 780 0.818040 ACGTGTTTCCTTGGCTGGAC 60.818 55.000 0.00 0.00 35.58 4.02
870 879 0.742505 ATTCGAACCGGCTACATCGA 59.257 50.000 0.00 7.10 42.01 3.59
920 929 4.667935 TTGGGGGAGGCGGAGGAA 62.668 66.667 0.00 0.00 0.00 3.36
921 930 3.962530 ATTTGGGGGAGGCGGAGGA 62.963 63.158 0.00 0.00 0.00 3.71
922 931 3.420482 ATTTGGGGGAGGCGGAGG 61.420 66.667 0.00 0.00 0.00 4.30
923 932 2.193248 GATTTGGGGGAGGCGGAG 59.807 66.667 0.00 0.00 0.00 4.63
1008 1034 2.498726 GGGAGAGCTCGCTTGAGG 59.501 66.667 17.35 0.00 40.26 3.86
1010 1036 3.077556 GGGGGAGAGCTCGCTTGA 61.078 66.667 17.35 0.00 41.61 3.02
1025 1051 2.021457 CGTATTTACCTTGGGCTTGGG 58.979 52.381 0.00 0.00 0.00 4.12
1026 1052 2.021457 CCGTATTTACCTTGGGCTTGG 58.979 52.381 0.00 0.00 0.00 3.61
1027 1053 2.993937 TCCGTATTTACCTTGGGCTTG 58.006 47.619 0.00 0.00 0.00 4.01
1028 1054 3.434596 GGATCCGTATTTACCTTGGGCTT 60.435 47.826 0.00 0.00 0.00 4.35
1029 1055 2.105993 GGATCCGTATTTACCTTGGGCT 59.894 50.000 0.00 0.00 0.00 5.19
1030 1056 2.105993 AGGATCCGTATTTACCTTGGGC 59.894 50.000 5.98 0.00 0.00 5.36
1066 1092 1.408702 GGAAGCAGCAAACAAGTTGGA 59.591 47.619 7.96 0.00 37.73 3.53
1068 1094 2.877043 AGGAAGCAGCAAACAAGTTG 57.123 45.000 0.00 0.00 40.50 3.16
1070 1096 5.068987 TCAATTAAGGAAGCAGCAAACAAGT 59.931 36.000 0.00 0.00 0.00 3.16
1076 1103 3.378112 CGGATCAATTAAGGAAGCAGCAA 59.622 43.478 0.00 0.00 0.00 3.91
1100 1127 6.868622 TGGCCGCATAAGTAAACAAATAAAT 58.131 32.000 0.00 0.00 0.00 1.40
1101 1128 6.268825 TGGCCGCATAAGTAAACAAATAAA 57.731 33.333 0.00 0.00 0.00 1.40
1102 1129 5.163602 CCTGGCCGCATAAGTAAACAAATAA 60.164 40.000 0.00 0.00 0.00 1.40
1104 1131 3.130340 CCTGGCCGCATAAGTAAACAAAT 59.870 43.478 0.00 0.00 0.00 2.32
1105 1132 2.490115 CCTGGCCGCATAAGTAAACAAA 59.510 45.455 0.00 0.00 0.00 2.83
1112 1145 1.077716 GGAACCTGGCCGCATAAGT 60.078 57.895 0.00 0.00 0.00 2.24
1113 1146 3.827634 GGAACCTGGCCGCATAAG 58.172 61.111 0.00 0.00 0.00 1.73
1141 1174 2.693864 CCTCCATGGCTCTGGGGT 60.694 66.667 6.96 0.00 34.71 4.95
1340 1382 3.773630 CGCGGCGTGGTGTAGTTG 61.774 66.667 15.36 0.00 0.00 3.16
1529 1574 2.607750 GGCACCACCTCCTCCTCA 60.608 66.667 0.00 0.00 34.51 3.86
1596 1644 4.154347 GAGGCAGGCCGAGGACAG 62.154 72.222 4.37 0.00 41.95 3.51
1660 1716 4.697352 CGAAACTGATGGGTTCTTCTGAAT 59.303 41.667 0.00 0.00 39.36 2.57
1705 1761 1.404181 CCTCGTGAACACCGACATCAT 60.404 52.381 0.00 0.00 0.00 2.45
1751 1807 7.288621 TGATCTATATCCGCCTCATGTTCATAT 59.711 37.037 0.00 0.00 0.00 1.78
1766 1822 5.010719 TCCGACCACAGTTTGATCTATATCC 59.989 44.000 0.00 0.00 0.00 2.59
1790 1846 6.176183 CAAAAGGATACCATCTTCACTGTCT 58.824 40.000 0.00 0.00 37.17 3.41
1876 1932 1.839424 GAAGGCAACATTAGGGCAGT 58.161 50.000 0.00 0.00 41.41 4.40
1952 2008 1.613925 TCGCCTATCCCAGAATCTTCG 59.386 52.381 0.00 0.00 0.00 3.79
1982 2038 2.188994 GGCCTCATGCTCGCTTCT 59.811 61.111 0.00 0.00 40.92 2.85
2056 2112 2.646121 GTGGAACCAAAGGGAGCTG 58.354 57.895 0.00 0.00 38.05 4.24
2195 2251 3.855255 TCATCACTCACCACCTTCAAA 57.145 42.857 0.00 0.00 0.00 2.69
2196 2252 5.491070 CTTATCATCACTCACCACCTTCAA 58.509 41.667 0.00 0.00 0.00 2.69
2363 2422 0.819259 TCACAAGGCCTGCAACAGAC 60.819 55.000 5.69 0.00 32.44 3.51
2396 2455 4.720273 ACCTTACGAGACCTTTGGGAATAT 59.280 41.667 0.00 0.00 36.25 1.28
2555 2614 1.303155 AAGCTCCAAGCAGGCAGAC 60.303 57.895 1.29 0.00 45.56 3.51
2682 2806 2.105766 GCCATCTGAAGCCCTTTCAAT 58.894 47.619 0.00 0.00 44.84 2.57
2709 2833 7.289549 TGATCTGTCAGTATCTTTCTGATCCAT 59.710 37.037 0.00 0.00 42.63 3.41
2771 2895 3.717707 TGAGCTATCCGCATCTACAAAC 58.282 45.455 0.00 0.00 42.61 2.93
2777 2901 1.000827 CGTCTTGAGCTATCCGCATCT 60.001 52.381 0.00 0.00 42.61 2.90
2783 2907 0.032815 GCCTCCGTCTTGAGCTATCC 59.967 60.000 0.00 0.00 0.00 2.59
2802 2926 3.817084 TGCTGAATTGAGTCTTTGACAGG 59.183 43.478 0.00 0.00 34.60 4.00
2828 2952 1.442184 CTGAACCGTGACGTCTCCG 60.442 63.158 17.92 17.69 40.83 4.63
2853 2977 0.318784 ACACGCTTCCTCGAAGACAC 60.319 55.000 5.58 0.00 41.71 3.67
2922 3046 6.015940 CCAGAATTTACCTTCTTTCTTGCTGT 60.016 38.462 0.00 0.00 33.18 4.40
2946 3072 5.580691 CCAAAAGTTGTCCTGAAAAGAAACC 59.419 40.000 0.00 0.00 0.00 3.27
2958 3084 2.237393 TGCAATGCCAAAAGTTGTCC 57.763 45.000 1.53 0.00 0.00 4.02
2963 3089 4.398673 ACACAAAAATGCAATGCCAAAAGT 59.601 33.333 1.53 0.00 0.00 2.66
2988 3114 4.063689 CCTCATATGATGCACTCACTTCC 58.936 47.826 5.72 0.00 36.48 3.46
3010 3138 7.382110 TGCAATGTAATTCTAGAGAGGATAGC 58.618 38.462 0.00 0.00 31.22 2.97
3011 3139 9.941325 AATGCAATGTAATTCTAGAGAGGATAG 57.059 33.333 0.00 0.00 31.22 2.08
3018 3146 9.713740 GAACTGAAATGCAATGTAATTCTAGAG 57.286 33.333 0.00 0.00 31.22 2.43
3027 3155 6.647334 TTCAAGGAACTGAAATGCAATGTA 57.353 33.333 0.00 0.00 40.86 2.29
3039 3224 9.801873 TTCTAAAATTCACTTTTCAAGGAACTG 57.198 29.630 0.00 0.00 37.19 3.16
3073 3258 6.460399 GCCAGAAAACATGTTTGGTGTAAGTA 60.460 38.462 23.93 0.00 32.36 2.24
3122 3308 8.149973 ACTACTTTTGTGTACCTGTGTAATTG 57.850 34.615 0.00 0.00 0.00 2.32
3128 3314 5.989777 AGCTAACTACTTTTGTGTACCTGTG 59.010 40.000 0.00 0.00 0.00 3.66
3150 3336 2.179589 CTGCGTGAATGCACATTAAGC 58.820 47.619 4.29 0.00 45.41 3.09
3151 3337 2.478370 CCCTGCGTGAATGCACATTAAG 60.478 50.000 4.29 0.00 45.41 1.85
3152 3338 1.472082 CCCTGCGTGAATGCACATTAA 59.528 47.619 4.29 0.00 45.41 1.40
3153 3339 1.093972 CCCTGCGTGAATGCACATTA 58.906 50.000 4.29 0.00 45.41 1.90
3154 3340 1.597797 CCCCTGCGTGAATGCACATT 61.598 55.000 4.29 0.00 45.41 2.71
3155 3341 2.048023 CCCCTGCGTGAATGCACAT 61.048 57.895 4.29 0.00 45.41 3.21
3157 3343 1.926511 CTTCCCCTGCGTGAATGCAC 61.927 60.000 0.00 0.00 40.62 4.57
3158 3344 1.675310 CTTCCCCTGCGTGAATGCA 60.675 57.895 0.00 0.00 43.95 3.96
3159 3345 1.675641 ACTTCCCCTGCGTGAATGC 60.676 57.895 0.00 0.00 0.00 3.56
3160 3346 0.606401 ACACTTCCCCTGCGTGAATG 60.606 55.000 0.00 0.00 33.13 2.67
3161 3347 0.981183 TACACTTCCCCTGCGTGAAT 59.019 50.000 0.00 0.00 33.13 2.57
3162 3348 0.759959 TTACACTTCCCCTGCGTGAA 59.240 50.000 0.00 0.00 33.13 3.18
3163 3349 0.981183 ATTACACTTCCCCTGCGTGA 59.019 50.000 0.00 0.00 33.13 4.35
3164 3350 1.086696 CATTACACTTCCCCTGCGTG 58.913 55.000 0.00 0.00 34.92 5.34
3165 3351 0.981183 TCATTACACTTCCCCTGCGT 59.019 50.000 0.00 0.00 0.00 5.24
3166 3352 1.066143 AGTCATTACACTTCCCCTGCG 60.066 52.381 0.00 0.00 0.00 5.18
3167 3353 2.359900 CAGTCATTACACTTCCCCTGC 58.640 52.381 0.00 0.00 0.00 4.85
3168 3354 2.305927 ACCAGTCATTACACTTCCCCTG 59.694 50.000 0.00 0.00 0.00 4.45
3169 3355 2.305927 CACCAGTCATTACACTTCCCCT 59.694 50.000 0.00 0.00 0.00 4.79
3170 3356 2.618045 CCACCAGTCATTACACTTCCCC 60.618 54.545 0.00 0.00 0.00 4.81
3171 3357 2.039879 ACCACCAGTCATTACACTTCCC 59.960 50.000 0.00 0.00 0.00 3.97
3172 3358 3.335579 GACCACCAGTCATTACACTTCC 58.664 50.000 0.00 0.00 45.55 3.46
3183 3369 4.393062 CACTAATGTGAATGACCACCAGTC 59.607 45.833 0.00 0.00 46.55 3.51
3184 3370 4.326826 CACTAATGTGAATGACCACCAGT 58.673 43.478 0.00 0.00 46.55 4.00
3185 3371 3.691118 CCACTAATGTGAATGACCACCAG 59.309 47.826 0.00 0.00 46.55 4.00
3186 3372 3.684908 CCACTAATGTGAATGACCACCA 58.315 45.455 0.00 0.00 46.55 4.17
3187 3373 2.423538 GCCACTAATGTGAATGACCACC 59.576 50.000 0.00 0.00 46.55 4.61
3188 3374 2.423538 GGCCACTAATGTGAATGACCAC 59.576 50.000 0.00 0.00 46.55 4.16
3189 3375 2.040947 TGGCCACTAATGTGAATGACCA 59.959 45.455 0.00 0.00 46.55 4.02
3190 3376 2.423538 GTGGCCACTAATGTGAATGACC 59.576 50.000 29.12 0.00 46.55 4.02
3191 3377 3.347216 AGTGGCCACTAATGTGAATGAC 58.653 45.455 37.12 4.11 46.55 3.06
3192 3378 3.719268 AGTGGCCACTAATGTGAATGA 57.281 42.857 37.12 0.00 46.55 2.57
3234 3422 7.717568 TGGATCAGACTATAAAGACTAGCAAC 58.282 38.462 0.00 0.00 0.00 4.17
3284 3488 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3285 3489 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
3286 3490 1.136000 CACTGTGTGTGTGTGTGTGTG 60.136 52.381 0.00 0.00 41.53 3.82
3288 3492 3.973923 CACTGTGTGTGTGTGTGTG 57.026 52.632 0.00 0.00 41.53 3.82
3295 3499 6.965702 AGATAAATCTGAAGCACTGTGTGTGT 60.966 38.462 9.86 0.00 41.17 3.72
3296 3500 5.410746 AGATAAATCTGAAGCACTGTGTGTG 59.589 40.000 9.86 0.00 41.62 3.82
3297 3501 5.555017 AGATAAATCTGAAGCACTGTGTGT 58.445 37.500 9.86 0.00 35.42 3.72
3298 3502 6.492007 AAGATAAATCTGAAGCACTGTGTG 57.508 37.500 9.86 0.00 37.19 3.82
3299 3503 8.043113 TGATAAGATAAATCTGAAGCACTGTGT 58.957 33.333 9.86 0.00 37.19 3.72
3352 3563 7.328493 GTGTGGGAACTAAAAGCATGAAAATAC 59.672 37.037 0.00 0.00 0.00 1.89
3354 3565 6.183360 TGTGTGGGAACTAAAAGCATGAAAAT 60.183 34.615 0.00 0.00 0.00 1.82
3369 3580 1.334869 CTTGAAGCACTGTGTGGGAAC 59.665 52.381 9.86 0.00 33.64 3.62
3375 3586 1.755179 ACAAGCTTGAAGCACTGTGT 58.245 45.000 32.50 13.87 45.56 3.72
3435 3667 3.645687 ACCTTCTCTTCTTCTGCTCTTGT 59.354 43.478 0.00 0.00 0.00 3.16
3617 3854 7.102993 TGTTACAGCTACAGCATCAAAATCTA 58.897 34.615 3.70 0.00 45.16 1.98
3624 3861 2.567169 ACCTGTTACAGCTACAGCATCA 59.433 45.455 6.88 0.00 45.16 3.07
3626 3863 3.703001 AACCTGTTACAGCTACAGCAT 57.297 42.857 6.88 0.00 45.16 3.79
3657 3894 2.287788 CCAAACACACTGCAAGCCTTAG 60.288 50.000 0.00 0.00 37.60 2.18
3658 3895 1.680735 CCAAACACACTGCAAGCCTTA 59.319 47.619 0.00 0.00 37.60 2.69
3917 4156 2.906568 ACATGCTCCCCCAAATCTTTT 58.093 42.857 0.00 0.00 0.00 2.27
3918 4157 2.629017 ACATGCTCCCCCAAATCTTT 57.371 45.000 0.00 0.00 0.00 2.52
4116 4639 6.375455 AGAGTCTGATGGCGATAAATTTGTTT 59.625 34.615 0.00 0.00 0.00 2.83
4245 4768 1.221021 CCGTTGGCCCTAGTTCTCC 59.779 63.158 0.00 0.00 0.00 3.71
4260 4783 2.186903 CCAACATAGCTCCGCCGT 59.813 61.111 0.00 0.00 0.00 5.68
4261 4784 2.588877 CCCAACATAGCTCCGCCG 60.589 66.667 0.00 0.00 0.00 6.46
4262 4785 2.203209 CCCCAACATAGCTCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
4263 4786 2.902343 GCCCCAACATAGCTCCGC 60.902 66.667 0.00 0.00 0.00 5.54
4265 4788 2.203209 CGGCCCCAACATAGCTCC 60.203 66.667 0.00 0.00 0.00 4.70
4266 4789 1.227674 CTCGGCCCCAACATAGCTC 60.228 63.158 0.00 0.00 0.00 4.09
4267 4790 2.746375 CCTCGGCCCCAACATAGCT 61.746 63.158 0.00 0.00 0.00 3.32
4268 4791 2.203209 CCTCGGCCCCAACATAGC 60.203 66.667 0.00 0.00 0.00 2.97
4269 4792 2.510906 CCCTCGGCCCCAACATAG 59.489 66.667 0.00 0.00 0.00 2.23
4287 4810 3.860930 TTCTCCAAAGCCACGGCCC 62.861 63.158 3.95 0.00 43.17 5.80
4288 4811 1.460273 TTTTCTCCAAAGCCACGGCC 61.460 55.000 3.95 0.00 43.17 6.13
4289 4812 0.039165 CTTTTCTCCAAAGCCACGGC 60.039 55.000 0.00 0.00 35.66 5.68
4296 4819 5.718724 ATTCTTCAGGCTTTTCTCCAAAG 57.281 39.130 0.00 0.00 44.44 2.77
4297 4820 7.781324 ATAATTCTTCAGGCTTTTCTCCAAA 57.219 32.000 0.00 0.00 0.00 3.28
4299 4822 7.781324 AAATAATTCTTCAGGCTTTTCTCCA 57.219 32.000 0.00 0.00 0.00 3.86
4323 4846 3.843422 TCTCATCTTGGCCCTTCAAAAA 58.157 40.909 0.00 0.00 0.00 1.94
4325 4848 3.010472 TCATCTCATCTTGGCCCTTCAAA 59.990 43.478 0.00 0.00 0.00 2.69
4326 4849 2.577563 TCATCTCATCTTGGCCCTTCAA 59.422 45.455 0.00 0.00 0.00 2.69
4327 4850 2.199208 TCATCTCATCTTGGCCCTTCA 58.801 47.619 0.00 0.00 0.00 3.02
4328 4851 3.287867 TTCATCTCATCTTGGCCCTTC 57.712 47.619 0.00 0.00 0.00 3.46
4329 4852 3.744940 TTTCATCTCATCTTGGCCCTT 57.255 42.857 0.00 0.00 0.00 3.95
4331 4854 5.508657 GCTATTTTTCATCTCATCTTGGCCC 60.509 44.000 0.00 0.00 0.00 5.80
4334 4915 6.956202 AGGCTATTTTTCATCTCATCTTGG 57.044 37.500 0.00 0.00 0.00 3.61
4335 4916 9.084164 CAAAAGGCTATTTTTCATCTCATCTTG 57.916 33.333 0.00 0.00 0.00 3.02
4340 4921 5.337491 GGGCAAAAGGCTATTTTTCATCTCA 60.337 40.000 0.00 0.00 44.01 3.27
4341 4922 5.111989 GGGCAAAAGGCTATTTTTCATCTC 58.888 41.667 0.00 0.00 44.01 2.75
4342 4923 4.080919 GGGGCAAAAGGCTATTTTTCATCT 60.081 41.667 0.00 0.00 44.01 2.90
4343 4924 4.191544 GGGGCAAAAGGCTATTTTTCATC 58.808 43.478 0.00 0.00 44.01 2.92
4344 4925 3.586618 TGGGGCAAAAGGCTATTTTTCAT 59.413 39.130 0.00 0.00 44.01 2.57
4347 4928 5.013599 TGTTATGGGGCAAAAGGCTATTTTT 59.986 36.000 0.00 0.00 44.01 1.94
4352 4933 2.909504 TGTTATGGGGCAAAAGGCTA 57.090 45.000 0.00 0.00 44.01 3.93
4355 4936 2.256306 ACCTTGTTATGGGGCAAAAGG 58.744 47.619 0.00 0.00 40.04 3.11
4357 4938 6.098982 CCATTATACCTTGTTATGGGGCAAAA 59.901 38.462 0.00 0.00 33.66 2.44
4360 4941 4.417183 TCCATTATACCTTGTTATGGGGCA 59.583 41.667 0.00 0.00 37.07 5.36


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

AutoCloner maintained by Alex Coulton.