Multiple sequence alignment - TraesCS1A01G063500

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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 TraesCS1A01G063500 chr1A 100.000 1824 0 0 1523 3346 44407409 44405586 0.000000e+00 3369.0
1 TraesCS1A01G063500 chr1A 100.000 1332 0 0 1 1332 44408931 44407600 0.000000e+00 2460.0
2 TraesCS1A01G063500 chr1A 100.000 72 0 0 2644 2715 44406217 44406146 2.090000e-27 134.0
3 TraesCS1A01G063500 chr1A 100.000 72 0 0 2715 2786 44406288 44406217 2.090000e-27 134.0
4 TraesCS1A01G063500 chr1D 90.484 1156 60 17 1550 2682 44642261 44641133 0.000000e+00 1480.0
5 TraesCS1A01G063500 chr1D 87.653 899 68 22 444 1331 44643425 44642559 0.000000e+00 1005.0
6 TraesCS1A01G063500 chr1D 82.118 425 32 22 1 406 44643825 44643426 1.160000e-84 324.0
7 TraesCS1A01G063500 chr1D 87.111 225 24 2 2419 2641 44640930 44640709 1.990000e-62 250.0
8 TraesCS1A01G063500 chr1D 92.683 164 10 2 2746 2907 44641127 44640964 5.580000e-58 235.0
9 TraesCS1A01G063500 chr1D 89.831 59 3 1 1274 1332 422493062 422493117 4.630000e-09 73.1
10 TraesCS1A01G063500 chr1B 84.400 1359 117 40 2 1332 63961512 63960221 0.000000e+00 1247.0
11 TraesCS1A01G063500 chr1B 94.492 817 30 9 1914 2715 63959463 63958647 0.000000e+00 1245.0
12 TraesCS1A01G063500 chr1B 92.344 627 32 2 2715 3339 63958720 63958108 0.000000e+00 878.0
13 TraesCS1A01G063500 chr1B 92.308 325 19 3 1550 1869 63959788 63959465 1.090000e-124 457.0
14 TraesCS1A01G063500 chr1B 94.737 190 6 2 3157 3346 63944359 63944174 3.270000e-75 292.0
15 TraesCS1A01G063500 chr1B 94.737 190 6 2 3157 3346 63951349 63951164 3.270000e-75 292.0
16 TraesCS1A01G063500 chr1B 94.211 190 7 2 3157 3346 63936814 63936629 1.520000e-73 287.0
17 TraesCS1A01G063500 chr1B 82.000 150 15 3 1580 1717 22738292 22738441 2.110000e-22 117.0
18 TraesCS1A01G063500 chr3A 90.212 848 64 12 1851 2682 391489859 391490703 0.000000e+00 1088.0
19 TraesCS1A01G063500 chr3A 88.199 161 12 4 2746 2905 391490712 391490866 5.700000e-43 185.0
20 TraesCS1A01G063500 chr3A 96.078 51 2 0 1185 1235 108218485 108218435 2.140000e-12 84.2
21 TraesCS1A01G063500 chr3A 97.436 39 1 0 2715 2753 391490665 391490703 2.150000e-07 67.6
22 TraesCS1A01G063500 chr3D 89.517 849 73 9 1851 2685 297466412 297465566 0.000000e+00 1061.0
23 TraesCS1A01G063500 chr3D 88.272 162 13 3 2746 2905 297465563 297465406 4.410000e-44 189.0
24 TraesCS1A01G063500 chr3D 94.118 51 3 0 1185 1235 493419547 493419597 9.950000e-11 78.7
25 TraesCS1A01G063500 chr3B 89.610 847 66 12 1851 2682 391873778 391872939 0.000000e+00 1057.0
26 TraesCS1A01G063500 chr3B 87.500 160 15 2 2746 2905 391872930 391872776 2.650000e-41 180.0
27 TraesCS1A01G063500 chr3B 97.436 39 1 0 2715 2753 391872977 391872939 2.150000e-07 67.6
28 TraesCS1A01G063500 chrUn 94.737 190 6 2 3157 3346 339391380 339391565 3.270000e-75 292.0
29 TraesCS1A01G063500 chrUn 94.737 190 6 2 3157 3346 352526103 352526288 3.270000e-75 292.0
30 TraesCS1A01G063500 chrUn 94.737 190 6 2 3157 3346 403970600 403970785 3.270000e-75 292.0
31 TraesCS1A01G063500 chr2A 86.486 148 17 2 1185 1332 728718428 728718572 3.460000e-35 159.0
32 TraesCS1A01G063500 chr7A 86.207 145 17 2 1188 1332 546937276 546937135 1.610000e-33 154.0
33 TraesCS1A01G063500 chr7B 82.667 150 14 3 1580 1717 594730362 594730511 4.530000e-24 122.0
34 TraesCS1A01G063500 chr6A 79.781 183 19 6 1552 1717 65262502 65262683 2.110000e-22 117.0
35 TraesCS1A01G063500 chr6B 81.333 150 16 3 1580 1717 151488265 151488414 9.810000e-21 111.0
36 TraesCS1A01G063500 chr2D 90.244 82 8 0 3260 3341 24901106 24901187 1.270000e-19 108.0
37 TraesCS1A01G063500 chr2D 95.833 48 2 0 1188 1235 532378474 532378427 9.950000e-11 78.7
38 TraesCS1A01G063500 chr2D 77.206 136 20 9 3214 3346 24900959 24901086 5.990000e-08 69.4
39 TraesCS1A01G063500 chr2B 90.244 82 8 0 3260 3341 253786420 253786339 1.270000e-19 108.0
40 TraesCS1A01G063500 chr2B 90.000 50 3 2 3214 3261 253786578 253786529 2.790000e-06 63.9
41 TraesCS1A01G063500 chr7D 95.833 48 2 0 1188 1235 485653114 485653067 9.950000e-11 78.7
42 TraesCS1A01G063500 chr7D 91.525 59 2 1 1274 1332 597516398 597516343 9.950000e-11 78.7
43 TraesCS1A01G063500 chr7D 89.831 59 3 1 1274 1332 27355185 27355130 4.630000e-09 73.1
44 TraesCS1A01G063500 chr7D 89.831 59 3 1 1274 1332 228138051 228137996 4.630000e-09 73.1
45 TraesCS1A01G063500 chr5D 94.118 51 3 0 1185 1235 545794047 545794097 9.950000e-11 78.7
46 TraesCS1A01G063500 chr4B 89.831 59 3 1 1274 1332 20348514 20348459 4.630000e-09 73.1


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 TraesCS1A01G063500 chr1A 44405586 44408931 3345 True 1524.250000 3369 100.000000 1 3346 4 chr1A.!!$R1 3345
1 TraesCS1A01G063500 chr1D 44640709 44643825 3116 True 658.800000 1480 88.009800 1 2907 5 chr1D.!!$R1 2906
2 TraesCS1A01G063500 chr1B 63958108 63961512 3404 True 956.750000 1247 90.886000 2 3339 4 chr1B.!!$R4 3337
3 TraesCS1A01G063500 chr3A 391489859 391490866 1007 False 446.866667 1088 91.949000 1851 2905 3 chr3A.!!$F1 1054
4 TraesCS1A01G063500 chr3D 297465406 297466412 1006 True 625.000000 1061 88.894500 1851 2905 2 chr3D.!!$R1 1054
5 TraesCS1A01G063500 chr3B 391872776 391873778 1002 True 434.866667 1057 91.515333 1851 2905 3 chr3B.!!$R1 1054

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
657 711 0.107897 TTCCCGTTCGATGATGTGGG 60.108 55.0 0.0 0.0 38.02 4.61 F
1150 1214 0.103208 CGCTCCCAGGTACTAGCTTG 59.897 60.0 0.0 0.0 35.57 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 1589 0.107897 ACACGCAGACAACCAGTTCA 60.108 50.0 0.0 0.0 0.00 3.18 R
2703 3229 0.399233 AGATAGGAGGACCAGGTGGC 60.399 60.0 0.0 0.0 39.32 5.01 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
52 53 7.807977 ATCATTATCACCAACATAGACCAAC 57.192 36.000 0.00 0.00 0.00 3.77
71 72 3.410631 ACACATACAACCATCAACCGA 57.589 42.857 0.00 0.00 0.00 4.69
85 86 0.397564 AACCGACAATACAACCGGGT 59.602 50.000 6.32 0.00 45.63 5.28
87 88 1.022451 CCGACAATACAACCGGGTGG 61.022 60.000 26.30 8.35 38.42 4.61
151 164 5.305128 TGTGGCTGAAGAATTTTTGGAAGAT 59.695 36.000 0.00 0.00 0.00 2.40
154 167 6.707161 TGGCTGAAGAATTTTTGGAAGATTTG 59.293 34.615 0.00 0.00 0.00 2.32
181 194 9.574516 AGATTACCTTAATAATTTGGCTACTGG 57.425 33.333 0.00 0.00 0.00 4.00
186 199 8.282256 ACCTTAATAATTTGGCTACTGGAGAAT 58.718 33.333 0.00 0.00 0.00 2.40
209 222 4.150627 TGCTCGTTTTCTTCAAATCTCGAG 59.849 41.667 5.93 5.93 38.77 4.04
220 233 7.085116 TCTTCAAATCTCGAGTTCAGTAAGAC 58.915 38.462 13.13 0.00 0.00 3.01
230 243 6.073167 TCGAGTTCAGTAAGACTAGTGAGTTG 60.073 42.308 0.00 0.00 38.45 3.16
268 281 4.100189 AGCTATGTAAACCTAGAGTGCAGG 59.900 45.833 0.00 0.00 39.25 4.85
406 427 7.108847 AGGATCTGATCTTCCTTGTAGTTTTG 58.891 38.462 16.61 0.00 39.36 2.44
414 435 6.721318 TCTTCCTTGTAGTTTTGCCAGATAT 58.279 36.000 0.00 0.00 0.00 1.63
421 448 6.582636 TGTAGTTTTGCCAGATATACAGGAG 58.417 40.000 0.00 0.00 0.00 3.69
430 457 5.542779 CCAGATATACAGGAGGCTTGTTAC 58.457 45.833 0.00 0.00 0.00 2.50
433 460 6.648310 CAGATATACAGGAGGCTTGTTACATG 59.352 42.308 0.00 0.00 0.00 3.21
437 464 5.435686 ACAGGAGGCTTGTTACATGATTA 57.564 39.130 0.00 0.00 0.00 1.75
440 467 7.749666 ACAGGAGGCTTGTTACATGATTATAT 58.250 34.615 0.00 0.00 0.00 0.86
568 612 4.173924 GAGCAGGGCAGGGAGAGC 62.174 72.222 0.00 0.00 0.00 4.09
569 613 4.737476 AGCAGGGCAGGGAGAGCT 62.737 66.667 0.00 0.00 0.00 4.09
588 639 2.423898 CCTCCCGCCGTAGATGTGT 61.424 63.158 0.00 0.00 0.00 3.72
657 711 0.107897 TTCCCGTTCGATGATGTGGG 60.108 55.000 0.00 0.00 38.02 4.61
695 749 3.459063 GCCTTCGGCGGGAGTAGT 61.459 66.667 7.21 0.00 39.62 2.73
703 757 1.221021 GCGGGAGTAGTTGGGGAAG 59.779 63.158 0.00 0.00 0.00 3.46
704 758 1.905512 CGGGAGTAGTTGGGGAAGG 59.094 63.158 0.00 0.00 0.00 3.46
705 759 1.623542 CGGGAGTAGTTGGGGAAGGG 61.624 65.000 0.00 0.00 0.00 3.95
706 760 0.253020 GGGAGTAGTTGGGGAAGGGA 60.253 60.000 0.00 0.00 0.00 4.20
707 761 1.665137 GGAGTAGTTGGGGAAGGGAA 58.335 55.000 0.00 0.00 0.00 3.97
708 762 1.560146 GGAGTAGTTGGGGAAGGGAAG 59.440 57.143 0.00 0.00 0.00 3.46
717 772 1.544151 GGAAGGGAAGGGAAGGGGT 60.544 63.158 0.00 0.00 0.00 4.95
789 848 3.462199 GATAGGCGGGAGTGGTGGC 62.462 68.421 0.00 0.00 0.00 5.01
795 854 4.351054 GGGAGTGGTGGCCTGGTG 62.351 72.222 3.32 0.00 0.00 4.17
796 855 4.351054 GGAGTGGTGGCCTGGTGG 62.351 72.222 3.32 0.00 0.00 4.61
822 881 0.915364 GTGGCTTGAAGGAGGAGGAT 59.085 55.000 0.00 0.00 0.00 3.24
865 924 1.207329 ACGAGGGACCTCTTTGCATAC 59.793 52.381 15.83 0.00 40.69 2.39
871 930 3.019564 GGACCTCTTTGCATACAAGCAT 58.980 45.455 0.00 0.00 45.19 3.79
876 935 2.760092 TCTTTGCATACAAGCATTCCCC 59.240 45.455 0.00 0.00 45.19 4.81
884 943 1.551883 ACAAGCATTCCCCTCATTTGC 59.448 47.619 0.00 0.00 0.00 3.68
889 948 2.364632 CATTCCCCTCATTTGCGTGTA 58.635 47.619 0.00 0.00 0.00 2.90
909 970 2.960957 CTACGGATCCCAGCACTGCG 62.961 65.000 6.06 0.00 0.00 5.18
926 987 1.302366 GCGATCTGTGCCATTCATCA 58.698 50.000 0.00 0.00 0.00 3.07
943 1004 2.869101 TCATCAATCCAACGGTCCAA 57.131 45.000 0.00 0.00 0.00 3.53
950 1011 2.549282 CAACGGTCCAACTTCGCG 59.451 61.111 0.00 0.00 0.00 5.87
952 1013 1.522130 AACGGTCCAACTTCGCGTT 60.522 52.632 5.77 0.00 35.88 4.84
963 1024 5.080068 CCAACTTCGCGTTTTCTATTTCTC 58.920 41.667 5.77 0.00 32.27 2.87
965 1026 4.312443 ACTTCGCGTTTTCTATTTCTCCA 58.688 39.130 5.77 0.00 0.00 3.86
968 1029 4.755411 TCGCGTTTTCTATTTCTCCATCT 58.245 39.130 5.77 0.00 0.00 2.90
972 1033 6.481984 GCGTTTTCTATTTCTCCATCTTCAG 58.518 40.000 0.00 0.00 0.00 3.02
1075 1139 2.686106 GGAGCCCCTTCACCCGTA 60.686 66.667 0.00 0.00 0.00 4.02
1080 1144 1.987855 CCCCTTCACCCGTAGCTCA 60.988 63.158 0.00 0.00 0.00 4.26
1089 1153 3.066190 CGTAGCTCACCCCCGTCA 61.066 66.667 0.00 0.00 0.00 4.35
1092 1156 3.572447 TAGCTCACCCCCGTCACGA 62.572 63.158 0.00 0.00 0.00 4.35
1099 1163 2.430244 CCCCGTCACGAGTTCACG 60.430 66.667 0.00 0.00 39.31 4.35
1118 1182 1.384502 TCGCCTCCTCCAATCCCAT 60.385 57.895 0.00 0.00 0.00 4.00
1121 1185 1.152368 CCTCCTCCAATCCCATGCC 59.848 63.158 0.00 0.00 0.00 4.40
1145 1209 2.443390 GCCCGCTCCCAGGTACTA 60.443 66.667 0.00 0.00 36.02 1.82
1146 1210 2.499827 GCCCGCTCCCAGGTACTAG 61.500 68.421 0.00 0.00 36.02 2.57
1147 1211 2.499827 CCCGCTCCCAGGTACTAGC 61.500 68.421 0.00 0.00 36.02 3.42
1148 1212 1.455959 CCGCTCCCAGGTACTAGCT 60.456 63.158 0.00 0.00 35.57 3.32
1149 1213 1.043673 CCGCTCCCAGGTACTAGCTT 61.044 60.000 0.00 0.00 35.57 3.74
1150 1214 0.103208 CGCTCCCAGGTACTAGCTTG 59.897 60.000 0.00 0.00 35.57 4.01
1161 1225 0.695347 ACTAGCTTGCTTCTTGCCCT 59.305 50.000 0.00 0.00 42.00 5.19
1182 1246 1.615124 TCGGATTCAGCTCCCCCAA 60.615 57.895 0.00 0.00 31.04 4.12
1226 1290 0.535780 TTGTGTGCTCTCCTTGCAGG 60.536 55.000 0.00 0.00 41.41 4.85
1237 1301 2.530151 TTGCAGGAGCCTGAGGGT 60.530 61.111 20.29 1.18 46.30 4.34
1243 1307 0.622665 AGGAGCCTGAGGGTTTCATG 59.377 55.000 4.00 0.00 34.68 3.07
1268 1332 1.135489 CGTAGGCGACTGTATGTGTGT 60.135 52.381 0.00 0.00 43.88 3.72
1271 1335 1.635663 GGCGACTGTATGTGTGTGCC 61.636 60.000 0.00 0.00 0.00 5.01
1295 1359 4.754667 GGCGAGGTTGGTCCGGAC 62.755 72.222 27.04 27.04 41.99 4.79
1296 1360 3.998672 GCGAGGTTGGTCCGGACA 61.999 66.667 34.40 18.59 41.99 4.02
1591 2042 4.002982 AGATCACTTGTTGAATGCGCTTA 58.997 39.130 9.73 0.00 37.92 3.09
1628 2079 7.081349 TCCAGTTCAAATACAAATGCTAAACG 58.919 34.615 0.00 0.00 0.00 3.60
1652 2103 6.362551 CGTATCATAGACGATGTACCTTTTGG 59.637 42.308 0.00 0.00 42.98 3.28
1722 2173 6.205270 CCACATAATACTCATGCAGCAATGTA 59.795 38.462 0.00 3.56 0.00 2.29
1724 2175 6.994496 ACATAATACTCATGCAGCAATGTACT 59.006 34.615 0.00 0.00 0.00 2.73
1862 2319 8.284557 TGAAATCACACTTTGAAATTGAATCG 57.715 30.769 2.14 0.00 37.92 3.34
1871 2371 7.007725 CACTTTGAAATTGAATCGTCATACTGC 59.992 37.037 0.00 0.00 32.48 4.40
1910 2410 9.290988 TGTCTAGAATGGCTTTAAAACAACATA 57.709 29.630 0.00 0.00 0.00 2.29
1977 2477 3.668447 TCCTAGAAGAAGCTTGCTTGTG 58.332 45.455 12.92 0.00 0.00 3.33
1978 2478 3.324846 TCCTAGAAGAAGCTTGCTTGTGA 59.675 43.478 12.92 0.00 0.00 3.58
2496 3007 5.799213 AGCAGCTTACTCAGTTCATAACTT 58.201 37.500 0.00 0.00 40.46 2.66
2502 3013 7.041098 AGCTTACTCAGTTCATAACTTGGTTTG 60.041 37.037 0.00 0.00 40.46 2.93
2516 3027 6.160576 ACTTGGTTTGTATGCACTCAAATT 57.839 33.333 17.15 0.00 36.25 1.82
2629 3142 6.654582 TGGCACTAATTGTATGATATTCGCAT 59.345 34.615 0.00 0.00 0.00 4.73
2647 3170 6.156748 TCGCATTGTATACACATTACTCCT 57.843 37.500 4.68 0.00 33.76 3.69
2682 3208 5.702670 TCTTGATTGTCTGGAACATCACTTC 59.297 40.000 0.00 0.00 37.82 3.01
2683 3209 5.233083 TGATTGTCTGGAACATCACTTCT 57.767 39.130 0.00 0.00 37.82 2.85
2684 3210 5.240891 TGATTGTCTGGAACATCACTTCTC 58.759 41.667 0.00 0.00 37.82 2.87
2685 3211 4.963318 TTGTCTGGAACATCACTTCTCT 57.037 40.909 0.00 0.00 37.82 3.10
2686 3212 4.527509 TGTCTGGAACATCACTTCTCTC 57.472 45.455 0.00 0.00 38.20 3.20
2687 3213 4.155709 TGTCTGGAACATCACTTCTCTCT 58.844 43.478 0.00 0.00 38.20 3.10
2688 3214 4.590647 TGTCTGGAACATCACTTCTCTCTT 59.409 41.667 0.00 0.00 38.20 2.85
2689 3215 4.928615 GTCTGGAACATCACTTCTCTCTTG 59.071 45.833 0.00 0.00 38.20 3.02
2690 3216 4.590647 TCTGGAACATCACTTCTCTCTTGT 59.409 41.667 0.00 0.00 38.20 3.16
2691 3217 5.070981 TCTGGAACATCACTTCTCTCTTGTT 59.929 40.000 0.00 0.00 38.20 2.83
2692 3218 5.300752 TGGAACATCACTTCTCTCTTGTTC 58.699 41.667 5.31 5.31 41.21 3.18
2693 3219 5.070981 TGGAACATCACTTCTCTCTTGTTCT 59.929 40.000 11.87 0.00 41.50 3.01
2694 3220 5.994668 GGAACATCACTTCTCTCTTGTTCTT 59.005 40.000 11.87 0.00 41.50 2.52
2695 3221 6.147000 GGAACATCACTTCTCTCTTGTTCTTC 59.853 42.308 11.87 0.00 41.50 2.87
2696 3222 5.546526 ACATCACTTCTCTCTTGTTCTTCC 58.453 41.667 0.00 0.00 0.00 3.46
2697 3223 5.306678 ACATCACTTCTCTCTTGTTCTTCCT 59.693 40.000 0.00 0.00 0.00 3.36
2698 3224 5.461032 TCACTTCTCTCTTGTTCTTCCTC 57.539 43.478 0.00 0.00 0.00 3.71
2699 3225 5.144100 TCACTTCTCTCTTGTTCTTCCTCT 58.856 41.667 0.00 0.00 0.00 3.69
2700 3226 5.600484 TCACTTCTCTCTTGTTCTTCCTCTT 59.400 40.000 0.00 0.00 0.00 2.85
2701 3227 6.098982 TCACTTCTCTCTTGTTCTTCCTCTTT 59.901 38.462 0.00 0.00 0.00 2.52
2702 3228 6.202570 CACTTCTCTCTTGTTCTTCCTCTTTG 59.797 42.308 0.00 0.00 0.00 2.77
2703 3229 5.220710 TCTCTCTTGTTCTTCCTCTTTGG 57.779 43.478 0.00 0.00 37.10 3.28
2704 3230 3.744660 TCTCTTGTTCTTCCTCTTTGGC 58.255 45.455 0.00 0.00 35.26 4.52
2705 3231 2.816672 CTCTTGTTCTTCCTCTTTGGCC 59.183 50.000 0.00 0.00 35.26 5.36
2706 3232 2.174639 TCTTGTTCTTCCTCTTTGGCCA 59.825 45.455 0.00 0.00 35.26 5.36
2707 3233 1.981256 TGTTCTTCCTCTTTGGCCAC 58.019 50.000 3.88 0.00 35.26 5.01
2708 3234 1.248486 GTTCTTCCTCTTTGGCCACC 58.752 55.000 3.88 0.00 35.26 4.61
2709 3235 1.149101 TTCTTCCTCTTTGGCCACCT 58.851 50.000 3.88 0.00 35.26 4.00
2710 3236 0.401738 TCTTCCTCTTTGGCCACCTG 59.598 55.000 3.88 0.00 35.26 4.00
2711 3237 0.610232 CTTCCTCTTTGGCCACCTGG 60.610 60.000 3.88 5.86 35.26 4.45
2712 3238 1.360393 TTCCTCTTTGGCCACCTGGT 61.360 55.000 3.88 0.00 37.57 4.00
2713 3239 1.303643 CCTCTTTGGCCACCTGGTC 60.304 63.158 3.88 0.00 41.09 4.02
2714 3240 1.303643 CTCTTTGGCCACCTGGTCC 60.304 63.158 3.88 0.00 39.61 4.46
2715 3241 1.774217 TCTTTGGCCACCTGGTCCT 60.774 57.895 3.88 0.00 39.61 3.85
2716 3242 1.303643 CTTTGGCCACCTGGTCCTC 60.304 63.158 3.88 0.00 39.61 3.71
2717 3243 2.771328 CTTTGGCCACCTGGTCCTCC 62.771 65.000 3.88 0.00 39.61 4.30
2718 3244 3.810687 TTGGCCACCTGGTCCTCCT 62.811 63.158 3.88 0.00 39.61 3.69
2719 3245 2.040606 GGCCACCTGGTCCTCCTA 59.959 66.667 0.00 0.00 37.57 2.94
2720 3246 1.384643 GGCCACCTGGTCCTCCTAT 60.385 63.158 0.00 0.00 37.57 2.57
2721 3247 1.411651 GGCCACCTGGTCCTCCTATC 61.412 65.000 0.00 0.00 37.57 2.08
2722 3248 0.399233 GCCACCTGGTCCTCCTATCT 60.399 60.000 0.00 0.00 37.57 1.98
2723 3249 1.972207 GCCACCTGGTCCTCCTATCTT 60.972 57.143 0.00 0.00 37.57 2.40
2724 3250 1.765314 CCACCTGGTCCTCCTATCTTG 59.235 57.143 0.00 0.00 34.23 3.02
2725 3251 1.139853 CACCTGGTCCTCCTATCTTGC 59.860 57.143 0.00 0.00 34.23 4.01
2726 3252 1.008938 ACCTGGTCCTCCTATCTTGCT 59.991 52.381 0.00 0.00 34.23 3.91
2727 3253 1.415659 CCTGGTCCTCCTATCTTGCTG 59.584 57.143 0.00 0.00 34.23 4.41
2728 3254 2.392662 CTGGTCCTCCTATCTTGCTGA 58.607 52.381 0.00 0.00 34.23 4.26
2729 3255 2.971330 CTGGTCCTCCTATCTTGCTGAT 59.029 50.000 0.00 0.00 39.11 2.90
2730 3256 2.968574 TGGTCCTCCTATCTTGCTGATC 59.031 50.000 0.00 0.00 36.65 2.92
2731 3257 3.238597 GGTCCTCCTATCTTGCTGATCT 58.761 50.000 0.00 0.00 36.65 2.75
2732 3258 3.645687 GGTCCTCCTATCTTGCTGATCTT 59.354 47.826 0.00 0.00 36.65 2.40
2733 3259 4.502950 GGTCCTCCTATCTTGCTGATCTTG 60.503 50.000 0.00 0.00 36.65 3.02
2734 3260 4.343526 GTCCTCCTATCTTGCTGATCTTGA 59.656 45.833 0.00 0.00 36.65 3.02
2735 3261 5.011943 GTCCTCCTATCTTGCTGATCTTGAT 59.988 44.000 0.00 0.00 36.65 2.57
2736 3262 5.605908 TCCTCCTATCTTGCTGATCTTGATT 59.394 40.000 0.00 0.00 36.65 2.57
2737 3263 5.701750 CCTCCTATCTTGCTGATCTTGATTG 59.298 44.000 0.00 0.00 36.65 2.67
2738 3264 6.244552 TCCTATCTTGCTGATCTTGATTGT 57.755 37.500 0.00 0.00 36.65 2.71
2739 3265 6.286758 TCCTATCTTGCTGATCTTGATTGTC 58.713 40.000 0.00 0.00 36.65 3.18
2740 3266 6.099413 TCCTATCTTGCTGATCTTGATTGTCT 59.901 38.462 0.00 0.00 36.65 3.41
2741 3267 6.203145 CCTATCTTGCTGATCTTGATTGTCTG 59.797 42.308 0.00 0.00 36.65 3.51
2742 3268 4.259356 TCTTGCTGATCTTGATTGTCTGG 58.741 43.478 0.00 0.00 0.00 3.86
2743 3269 3.986996 TGCTGATCTTGATTGTCTGGA 57.013 42.857 0.00 0.00 0.00 3.86
2744 3270 4.290711 TGCTGATCTTGATTGTCTGGAA 57.709 40.909 0.00 0.00 0.00 3.53
2745 3271 4.005650 TGCTGATCTTGATTGTCTGGAAC 58.994 43.478 0.00 0.00 0.00 3.62
2746 3272 4.005650 GCTGATCTTGATTGTCTGGAACA 58.994 43.478 0.00 0.00 35.59 3.18
2747 3273 4.639310 GCTGATCTTGATTGTCTGGAACAT 59.361 41.667 0.00 0.00 37.82 2.71
2748 3274 5.220815 GCTGATCTTGATTGTCTGGAACATC 60.221 44.000 0.00 0.00 37.82 3.06
2749 3275 5.807909 TGATCTTGATTGTCTGGAACATCA 58.192 37.500 0.00 0.00 37.82 3.07
2750 3276 5.645067 TGATCTTGATTGTCTGGAACATCAC 59.355 40.000 0.00 0.00 37.82 3.06
2961 3500 3.835395 GGCTACCAGAATATGCTACTCCT 59.165 47.826 0.00 0.00 0.00 3.69
2986 3525 7.036829 TGTTGAAATGCAGATGGAATTACATG 58.963 34.615 8.22 0.00 0.00 3.21
2990 3529 7.285858 TGAAATGCAGATGGAATTACATGATCA 59.714 33.333 8.22 0.00 0.00 2.92
2991 3530 6.819397 ATGCAGATGGAATTACATGATCAG 57.181 37.500 8.22 0.00 0.00 2.90
2999 3538 7.991084 TGGAATTACATGATCAGATGGATTC 57.009 36.000 0.00 9.55 36.00 2.52
3011 3550 3.762288 CAGATGGATTCATATGCAAGGGG 59.238 47.826 0.00 0.00 36.07 4.79
3050 3589 7.640597 TGCACAAGTAGACTACATACATACT 57.359 36.000 14.95 0.00 0.00 2.12
3080 3619 7.389607 GGCAGGTCTATACTTGTTAAAGTTTCA 59.610 37.037 0.00 0.00 44.47 2.69
3145 3684 6.765989 CGGACCTATAATTTCCAGTTGATGAA 59.234 38.462 0.00 0.00 0.00 2.57
3172 3711 5.741982 GGAACCGAATCATTTACCAATTTCG 59.258 40.000 0.00 0.00 34.47 3.46
3180 3719 4.709397 TCATTTACCAATTTCGATGGGCTT 59.291 37.500 8.36 0.00 42.48 4.35
3249 3788 3.751698 GCACCAGTCCTTTTTAGTACAGG 59.248 47.826 0.00 0.00 0.00 4.00
3281 3820 5.932303 GGTAAGACTCTTTGCAGTTCATGTA 59.068 40.000 0.00 0.00 0.00 2.29
3311 3850 8.650490 ACCCAAAACAATATAATGATCCATTCC 58.350 33.333 0.00 0.00 35.54 3.01
3334 3873 5.916883 CCTAAAACTCTTTGCAGTTCATGTG 59.083 40.000 0.00 0.00 35.45 3.21
3339 3878 5.821204 ACTCTTTGCAGTTCATGTGTAAAC 58.179 37.500 0.00 0.00 0.00 2.01
3340 3879 5.181690 TCTTTGCAGTTCATGTGTAAACC 57.818 39.130 0.00 0.00 0.00 3.27
3341 3880 4.037446 TCTTTGCAGTTCATGTGTAAACCC 59.963 41.667 0.00 0.00 0.00 4.11
3342 3881 2.937519 TGCAGTTCATGTGTAAACCCA 58.062 42.857 0.00 0.00 0.00 4.51
3343 3882 3.291584 TGCAGTTCATGTGTAAACCCAA 58.708 40.909 0.00 0.00 0.00 4.12
3344 3883 3.701542 TGCAGTTCATGTGTAAACCCAAA 59.298 39.130 0.00 0.00 0.00 3.28
3345 3884 4.160439 TGCAGTTCATGTGTAAACCCAAAA 59.840 37.500 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.572255 GGTTGATGGTTGTATGTGTTGGT 59.428 43.478 0.00 0.00 0.00 3.67
52 53 3.070748 TGTCGGTTGATGGTTGTATGTG 58.929 45.455 0.00 0.00 0.00 3.21
71 72 0.891904 GCACCACCCGGTTGTATTGT 60.892 55.000 0.00 0.00 46.31 2.71
161 174 8.571336 CATTCTCCAGTAGCCAAATTATTAAGG 58.429 37.037 0.00 0.00 0.00 2.69
168 181 3.950395 GAGCATTCTCCAGTAGCCAAATT 59.050 43.478 0.00 0.00 33.19 1.82
169 182 3.549794 GAGCATTCTCCAGTAGCCAAAT 58.450 45.455 0.00 0.00 33.19 2.32
170 183 2.677902 CGAGCATTCTCCAGTAGCCAAA 60.678 50.000 0.00 0.00 35.94 3.28
181 194 6.606768 AGATTTGAAGAAAACGAGCATTCTC 58.393 36.000 0.00 0.00 34.90 2.87
186 199 4.055360 TCGAGATTTGAAGAAAACGAGCA 58.945 39.130 0.00 0.00 0.00 4.26
209 222 6.328641 TCCAACTCACTAGTCTTACTGAAC 57.671 41.667 0.00 0.00 33.75 3.18
220 233 6.127925 TGCTTATTTTGCATCCAACTCACTAG 60.128 38.462 0.00 0.00 35.31 2.57
230 243 5.192327 ACATAGCTGCTTATTTTGCATCC 57.808 39.130 7.79 0.00 39.86 3.51
268 281 4.253685 TGAAACAGCCTGTTACATAGCTC 58.746 43.478 11.10 3.45 40.14 4.09
300 318 6.849085 ATTTAGTGTTGTATCCATGGCAAA 57.151 33.333 6.96 0.00 0.00 3.68
324 342 9.315363 TGATATTGTTTAACACCCAACCTATTT 57.685 29.630 0.00 0.00 0.00 1.40
325 343 8.887264 TGATATTGTTTAACACCCAACCTATT 57.113 30.769 0.00 0.00 0.00 1.73
326 344 9.487442 AATGATATTGTTTAACACCCAACCTAT 57.513 29.630 0.00 0.00 0.00 2.57
327 345 8.887264 AATGATATTGTTTAACACCCAACCTA 57.113 30.769 0.00 0.00 0.00 3.08
328 346 7.790782 AATGATATTGTTTAACACCCAACCT 57.209 32.000 0.00 0.00 0.00 3.50
329 347 9.744468 GATAATGATATTGTTTAACACCCAACC 57.256 33.333 0.00 0.00 0.00 3.77
406 427 2.370189 ACAAGCCTCCTGTATATCTGGC 59.630 50.000 0.00 0.00 40.54 4.85
414 435 5.435686 AATCATGTAACAAGCCTCCTGTA 57.564 39.130 0.00 0.00 0.00 2.74
421 448 7.819644 TGATGCATATAATCATGTAACAAGCC 58.180 34.615 0.00 0.00 0.00 4.35
437 464 8.866970 TGTTAATACATGACCATGATGCATAT 57.133 30.769 16.07 1.54 41.20 1.78
551 595 4.173924 GCTCTCCCTGCCCTGCTC 62.174 72.222 0.00 0.00 0.00 4.26
552 596 4.737476 AGCTCTCCCTGCCCTGCT 62.737 66.667 0.00 0.00 0.00 4.24
553 597 4.173924 GAGCTCTCCCTGCCCTGC 62.174 72.222 6.43 0.00 0.00 4.85
554 598 3.478274 GGAGCTCTCCCTGCCCTG 61.478 72.222 14.64 0.00 43.94 4.45
564 608 4.124943 TACGGCGGGAGGAGCTCT 62.125 66.667 14.64 0.00 34.52 4.09
568 612 1.828660 ACATCTACGGCGGGAGGAG 60.829 63.158 19.60 11.20 0.00 3.69
569 613 2.125326 CACATCTACGGCGGGAGGA 61.125 63.158 19.60 9.20 0.00 3.71
571 615 1.065928 GACACATCTACGGCGGGAG 59.934 63.158 13.24 8.43 0.00 4.30
572 616 2.767445 CGACACATCTACGGCGGGA 61.767 63.158 13.24 9.73 0.00 5.14
644 698 2.189257 CGGCCCCACATCATCGAA 59.811 61.111 0.00 0.00 0.00 3.71
695 749 1.146544 CCTTCCCTTCCCTTCCCCAA 61.147 60.000 0.00 0.00 0.00 4.12
703 757 4.426313 CGCACCCCTTCCCTTCCC 62.426 72.222 0.00 0.00 0.00 3.97
705 759 3.569200 AAGCGCACCCCTTCCCTTC 62.569 63.158 11.47 0.00 0.00 3.46
706 760 3.580319 AAGCGCACCCCTTCCCTT 61.580 61.111 11.47 0.00 0.00 3.95
707 761 4.351054 CAAGCGCACCCCTTCCCT 62.351 66.667 11.47 0.00 0.00 4.20
717 772 2.202878 GATCTACGGCCAAGCGCA 60.203 61.111 11.47 0.00 40.31 6.09
727 782 1.659954 GCGCTGCTCCAGATCTACG 60.660 63.158 0.00 0.00 32.44 3.51
789 848 1.978617 GCCACAATCACCCACCAGG 60.979 63.158 0.00 0.00 43.78 4.45
790 849 0.540365 AAGCCACAATCACCCACCAG 60.540 55.000 0.00 0.00 0.00 4.00
791 850 0.827089 CAAGCCACAATCACCCACCA 60.827 55.000 0.00 0.00 0.00 4.17
792 851 0.539438 TCAAGCCACAATCACCCACC 60.539 55.000 0.00 0.00 0.00 4.61
793 852 1.270550 CTTCAAGCCACAATCACCCAC 59.729 52.381 0.00 0.00 0.00 4.61
794 853 1.619654 CTTCAAGCCACAATCACCCA 58.380 50.000 0.00 0.00 0.00 4.51
795 854 0.890683 CCTTCAAGCCACAATCACCC 59.109 55.000 0.00 0.00 0.00 4.61
796 855 1.815003 CTCCTTCAAGCCACAATCACC 59.185 52.381 0.00 0.00 0.00 4.02
822 881 0.825425 TGGTGAATTTGCTTCCGCCA 60.825 50.000 0.00 0.00 36.30 5.69
865 924 1.470285 CGCAAATGAGGGGAATGCTTG 60.470 52.381 0.00 0.00 34.93 4.01
871 930 1.349688 AGTACACGCAAATGAGGGGAA 59.650 47.619 0.00 0.00 0.00 3.97
889 948 1.961180 GCAGTGCTGGGATCCGTAGT 61.961 60.000 8.18 0.00 0.00 2.73
926 987 2.879103 AGTTGGACCGTTGGATTGAT 57.121 45.000 0.00 0.00 0.00 2.57
943 1004 4.312443 TGGAGAAATAGAAAACGCGAAGT 58.688 39.130 15.93 0.00 0.00 3.01
950 1011 7.607991 TGGACTGAAGATGGAGAAATAGAAAAC 59.392 37.037 0.00 0.00 0.00 2.43
952 1013 7.257790 TGGACTGAAGATGGAGAAATAGAAA 57.742 36.000 0.00 0.00 0.00 2.52
963 1024 3.641434 ACTGGATTGGACTGAAGATGG 57.359 47.619 0.00 0.00 0.00 3.51
965 1026 3.135530 GGCTACTGGATTGGACTGAAGAT 59.864 47.826 0.00 0.00 0.00 2.40
968 1029 2.027192 GTGGCTACTGGATTGGACTGAA 60.027 50.000 0.00 0.00 0.00 3.02
972 1033 0.462047 CGGTGGCTACTGGATTGGAC 60.462 60.000 0.05 0.00 0.00 4.02
1075 1139 4.988716 TCGTGACGGGGGTGAGCT 62.989 66.667 4.70 0.00 0.00 4.09
1080 1144 2.522436 TGAACTCGTGACGGGGGT 60.522 61.111 10.58 0.00 0.00 4.95
1089 1153 2.254651 GAGGCGACGTGAACTCGT 59.745 61.111 0.00 1.71 46.88 4.18
1092 1156 2.637383 GGAGGAGGCGACGTGAACT 61.637 63.158 0.00 0.00 0.00 3.01
1099 1163 1.700042 ATGGGATTGGAGGAGGCGAC 61.700 60.000 0.00 0.00 0.00 5.19
1133 1197 1.490574 AGCAAGCTAGTACCTGGGAG 58.509 55.000 0.00 0.00 0.00 4.30
1150 1214 0.678048 ATCCGACAAGGGCAAGAAGC 60.678 55.000 0.00 0.00 41.52 3.86
1161 1225 1.602237 GGGGAGCTGAATCCGACAA 59.398 57.895 0.00 0.00 40.56 3.18
1182 1246 1.067212 CCTTATTAGCTCAGGCGTCGT 59.933 52.381 0.00 0.00 44.37 4.34
1226 1290 1.743996 GACATGAAACCCTCAGGCTC 58.256 55.000 0.00 0.00 39.53 4.70
1237 1301 0.522626 TCGCCTACGACGACATGAAA 59.477 50.000 0.00 0.00 45.12 2.69
1258 1322 0.321564 GGAGCAGGCACACACATACA 60.322 55.000 0.00 0.00 0.00 2.29
1522 1586 0.798776 CGCAGACAACCAGTTCATCC 59.201 55.000 0.00 0.00 0.00 3.51
1523 1587 1.195448 CACGCAGACAACCAGTTCATC 59.805 52.381 0.00 0.00 0.00 2.92
1524 1588 1.229428 CACGCAGACAACCAGTTCAT 58.771 50.000 0.00 0.00 0.00 2.57
1525 1589 0.107897 ACACGCAGACAACCAGTTCA 60.108 50.000 0.00 0.00 0.00 3.18
1526 1590 1.014352 AACACGCAGACAACCAGTTC 58.986 50.000 0.00 0.00 0.00 3.01
1527 1591 0.732571 CAACACGCAGACAACCAGTT 59.267 50.000 0.00 0.00 0.00 3.16
1528 1592 1.714899 GCAACACGCAGACAACCAGT 61.715 55.000 0.00 0.00 41.79 4.00
1529 1593 1.009675 GCAACACGCAGACAACCAG 60.010 57.895 0.00 0.00 41.79 4.00
1530 1594 2.477176 GGCAACACGCAGACAACCA 61.477 57.895 0.00 0.00 45.17 3.67
1531 1595 2.186826 AGGCAACACGCAGACAACC 61.187 57.895 0.00 0.00 45.17 3.77
1532 1596 1.009675 CAGGCAACACGCAGACAAC 60.010 57.895 0.00 0.00 45.17 3.32
1537 1601 2.354074 AAAAGGCAGGCAACACGCAG 62.354 55.000 0.00 0.00 45.17 5.18
1591 2042 7.560991 TGTATTTGAACTGGAATAGGATTGCAT 59.439 33.333 0.00 0.00 0.00 3.96
1602 2053 7.593273 CGTTTAGCATTTGTATTTGAACTGGAA 59.407 33.333 0.00 0.00 0.00 3.53
1628 2079 6.645415 CCCAAAAGGTACATCGTCTATGATAC 59.355 42.308 0.00 0.00 39.07 2.24
1638 2089 7.681862 ACTGAAAGAACCCAAAAGGTACATCG 61.682 42.308 0.00 0.00 44.08 3.84
1652 2103 7.520131 GCCTAAAAGTACAAGACTGAAAGAACC 60.520 40.741 0.00 0.00 38.87 3.62
1722 2173 4.494484 GTTTGTGCCAAGTTTTGAAGAGT 58.506 39.130 0.00 0.00 0.00 3.24
1724 2175 3.259374 TGGTTTGTGCCAAGTTTTGAAGA 59.741 39.130 0.00 0.00 35.25 2.87
1862 2319 3.793559 ACAGGTTAATCCGCAGTATGAC 58.206 45.455 0.00 0.00 39.17 3.06
1871 2371 5.523916 CCATTCTAGACAACAGGTTAATCCG 59.476 44.000 0.00 0.00 41.99 4.18
1910 2410 8.985315 TTCCTGCAATATCAGATAAGAAACAT 57.015 30.769 0.00 0.00 36.19 2.71
1921 2421 6.317140 TCAAAACTAGCTTCCTGCAATATCAG 59.683 38.462 0.00 0.00 45.94 2.90
1977 2477 9.490663 GCATCACATTTAGTACATGTAAACTTC 57.509 33.333 7.25 0.00 32.88 3.01
1978 2478 9.008965 TGCATCACATTTAGTACATGTAAACTT 57.991 29.630 7.25 0.00 32.88 2.66
2413 2922 9.431887 GTCTACAAGGTTCAAATAGTCAATGTA 57.568 33.333 0.00 0.00 0.00 2.29
2496 3007 5.528043 ACAATTTGAGTGCATACAAACCA 57.472 34.783 18.48 3.33 38.50 3.67
2516 3027 6.215495 TCTGGTATCGTGAATTGTGATACA 57.785 37.500 16.82 7.68 43.90 2.29
2568 3079 9.769093 AGCAACAATGTATCGTTTTTCTATAAC 57.231 29.630 0.00 0.00 0.00 1.89
2629 3142 8.924303 AGCAAGATAGGAGTAATGTGTATACAA 58.076 33.333 7.25 0.00 40.84 2.41
2641 3154 7.070447 ACAATCAAGATCAGCAAGATAGGAGTA 59.930 37.037 0.00 0.00 37.00 2.59
2647 3170 6.053650 CCAGACAATCAAGATCAGCAAGATA 58.946 40.000 0.00 0.00 37.00 1.98
2682 3208 3.750652 GCCAAAGAGGAAGAACAAGAGAG 59.249 47.826 0.00 0.00 41.22 3.20
2683 3209 3.496870 GGCCAAAGAGGAAGAACAAGAGA 60.497 47.826 0.00 0.00 41.22 3.10
2684 3210 2.816672 GGCCAAAGAGGAAGAACAAGAG 59.183 50.000 0.00 0.00 41.22 2.85
2685 3211 2.174639 TGGCCAAAGAGGAAGAACAAGA 59.825 45.455 0.61 0.00 41.22 3.02
2686 3212 2.294512 GTGGCCAAAGAGGAAGAACAAG 59.705 50.000 7.24 0.00 41.22 3.16
2687 3213 2.306847 GTGGCCAAAGAGGAAGAACAA 58.693 47.619 7.24 0.00 41.22 2.83
2688 3214 1.478654 GGTGGCCAAAGAGGAAGAACA 60.479 52.381 7.24 0.00 41.22 3.18
2689 3215 1.202940 AGGTGGCCAAAGAGGAAGAAC 60.203 52.381 7.24 0.00 41.22 3.01
2690 3216 1.149101 AGGTGGCCAAAGAGGAAGAA 58.851 50.000 7.24 0.00 41.22 2.52
2691 3217 0.401738 CAGGTGGCCAAAGAGGAAGA 59.598 55.000 7.24 0.00 41.22 2.87
2692 3218 0.610232 CCAGGTGGCCAAAGAGGAAG 60.610 60.000 7.24 0.00 41.22 3.46
2693 3219 1.360393 ACCAGGTGGCCAAAGAGGAA 61.360 55.000 7.24 0.00 40.02 3.36
2694 3220 1.774217 ACCAGGTGGCCAAAGAGGA 60.774 57.895 7.24 0.00 40.02 3.71
2695 3221 1.303643 GACCAGGTGGCCAAAGAGG 60.304 63.158 7.24 10.35 39.32 3.69
2696 3222 1.303643 GGACCAGGTGGCCAAAGAG 60.304 63.158 7.24 0.00 39.32 2.85
2697 3223 1.774217 AGGACCAGGTGGCCAAAGA 60.774 57.895 7.24 0.00 39.32 2.52
2698 3224 1.303643 GAGGACCAGGTGGCCAAAG 60.304 63.158 7.24 0.00 39.32 2.77
2699 3225 2.840753 GGAGGACCAGGTGGCCAAA 61.841 63.158 7.24 0.00 39.32 3.28
2700 3226 2.409984 TAGGAGGACCAGGTGGCCAA 62.410 60.000 7.24 0.00 39.32 4.52
2701 3227 2.194951 ATAGGAGGACCAGGTGGCCA 62.195 60.000 0.00 0.00 39.32 5.36
2702 3228 1.384643 ATAGGAGGACCAGGTGGCC 60.385 63.158 0.00 0.00 39.32 5.36
2703 3229 0.399233 AGATAGGAGGACCAGGTGGC 60.399 60.000 0.00 0.00 39.32 5.01
2704 3230 1.765314 CAAGATAGGAGGACCAGGTGG 59.235 57.143 0.00 0.00 38.94 4.61
2705 3231 1.139853 GCAAGATAGGAGGACCAGGTG 59.860 57.143 0.00 0.00 38.94 4.00
2706 3232 1.008938 AGCAAGATAGGAGGACCAGGT 59.991 52.381 0.00 0.00 38.94 4.00
2707 3233 1.415659 CAGCAAGATAGGAGGACCAGG 59.584 57.143 0.00 0.00 38.94 4.45
2708 3234 2.392662 TCAGCAAGATAGGAGGACCAG 58.607 52.381 0.00 0.00 38.94 4.00
2709 3235 2.550277 TCAGCAAGATAGGAGGACCA 57.450 50.000 0.00 0.00 38.94 4.02
2710 3236 3.238597 AGATCAGCAAGATAGGAGGACC 58.761 50.000 0.00 0.00 37.00 4.46
2711 3237 4.343526 TCAAGATCAGCAAGATAGGAGGAC 59.656 45.833 0.00 0.00 37.00 3.85
2712 3238 4.550669 TCAAGATCAGCAAGATAGGAGGA 58.449 43.478 0.00 0.00 37.00 3.71
2713 3239 4.952071 TCAAGATCAGCAAGATAGGAGG 57.048 45.455 0.00 0.00 37.00 4.30
2714 3240 6.289834 ACAATCAAGATCAGCAAGATAGGAG 58.710 40.000 0.00 0.00 37.00 3.69
2715 3241 6.099413 AGACAATCAAGATCAGCAAGATAGGA 59.901 38.462 0.00 0.00 37.00 2.94
2716 3242 6.203145 CAGACAATCAAGATCAGCAAGATAGG 59.797 42.308 0.00 0.00 37.00 2.57
2717 3243 6.203145 CCAGACAATCAAGATCAGCAAGATAG 59.797 42.308 0.00 0.00 37.00 2.08
2718 3244 6.053650 CCAGACAATCAAGATCAGCAAGATA 58.946 40.000 0.00 0.00 37.00 1.98
2719 3245 4.882427 CCAGACAATCAAGATCAGCAAGAT 59.118 41.667 0.00 0.00 40.48 2.40
2720 3246 4.019950 TCCAGACAATCAAGATCAGCAAGA 60.020 41.667 0.00 0.00 0.00 3.02
2721 3247 4.259356 TCCAGACAATCAAGATCAGCAAG 58.741 43.478 0.00 0.00 0.00 4.01
2722 3248 4.290711 TCCAGACAATCAAGATCAGCAA 57.709 40.909 0.00 0.00 0.00 3.91
2723 3249 3.986996 TCCAGACAATCAAGATCAGCA 57.013 42.857 0.00 0.00 0.00 4.41
2724 3250 4.005650 TGTTCCAGACAATCAAGATCAGC 58.994 43.478 0.00 0.00 34.69 4.26
2725 3251 5.878669 TGATGTTCCAGACAATCAAGATCAG 59.121 40.000 0.00 0.00 42.62 2.90
2726 3252 5.645067 GTGATGTTCCAGACAATCAAGATCA 59.355 40.000 0.00 0.00 42.62 2.92
2727 3253 5.879223 AGTGATGTTCCAGACAATCAAGATC 59.121 40.000 0.00 0.00 42.62 2.75
2728 3254 5.813383 AGTGATGTTCCAGACAATCAAGAT 58.187 37.500 0.00 0.00 42.62 2.40
2729 3255 5.233083 AGTGATGTTCCAGACAATCAAGA 57.767 39.130 0.00 0.00 42.62 3.02
2730 3256 5.704515 AGAAGTGATGTTCCAGACAATCAAG 59.295 40.000 0.00 0.00 42.62 3.02
2731 3257 5.624159 AGAAGTGATGTTCCAGACAATCAA 58.376 37.500 0.00 0.00 42.62 2.57
2732 3258 5.012458 AGAGAAGTGATGTTCCAGACAATCA 59.988 40.000 0.00 0.00 42.62 2.57
2733 3259 5.486526 AGAGAAGTGATGTTCCAGACAATC 58.513 41.667 0.00 0.00 42.62 2.67
2734 3260 5.248020 AGAGAGAAGTGATGTTCCAGACAAT 59.752 40.000 0.00 0.00 42.62 2.71
2735 3261 4.590647 AGAGAGAAGTGATGTTCCAGACAA 59.409 41.667 0.00 0.00 42.62 3.18
2736 3262 4.155709 AGAGAGAAGTGATGTTCCAGACA 58.844 43.478 0.00 0.00 43.71 3.41
2737 3263 4.799564 AGAGAGAAGTGATGTTCCAGAC 57.200 45.455 0.00 0.00 0.00 3.51
2738 3264 4.590647 ACAAGAGAGAAGTGATGTTCCAGA 59.409 41.667 0.00 0.00 0.00 3.86
2739 3265 4.892433 ACAAGAGAGAAGTGATGTTCCAG 58.108 43.478 0.00 0.00 0.00 3.86
2740 3266 4.963318 ACAAGAGAGAAGTGATGTTCCA 57.037 40.909 0.00 0.00 0.00 3.53
2741 3267 5.546526 AGAACAAGAGAGAAGTGATGTTCC 58.453 41.667 11.55 0.00 44.67 3.62
2742 3268 6.147000 GGAAGAACAAGAGAGAAGTGATGTTC 59.853 42.308 8.06 8.06 44.19 3.18
2743 3269 5.994668 GGAAGAACAAGAGAGAAGTGATGTT 59.005 40.000 0.00 0.00 34.01 2.71
2744 3270 5.306678 AGGAAGAACAAGAGAGAAGTGATGT 59.693 40.000 0.00 0.00 0.00 3.06
2745 3271 5.792741 AGGAAGAACAAGAGAGAAGTGATG 58.207 41.667 0.00 0.00 0.00 3.07
2746 3272 5.779771 AGAGGAAGAACAAGAGAGAAGTGAT 59.220 40.000 0.00 0.00 0.00 3.06
2747 3273 5.144100 AGAGGAAGAACAAGAGAGAAGTGA 58.856 41.667 0.00 0.00 0.00 3.41
2748 3274 5.467035 AGAGGAAGAACAAGAGAGAAGTG 57.533 43.478 0.00 0.00 0.00 3.16
2749 3275 6.287525 CAAAGAGGAAGAACAAGAGAGAAGT 58.712 40.000 0.00 0.00 0.00 3.01
2750 3276 5.700373 CCAAAGAGGAAGAACAAGAGAGAAG 59.300 44.000 0.00 0.00 41.22 2.85
2961 3500 6.587206 TGTAATTCCATCTGCATTTCAACA 57.413 33.333 0.00 0.00 0.00 3.33
2986 3525 5.357314 CCCTTGCATATGAATCCATCTGATC 59.643 44.000 6.97 0.00 34.31 2.92
2990 3529 3.659195 TCCCCTTGCATATGAATCCATCT 59.341 43.478 6.97 0.00 34.31 2.90
2991 3530 4.038271 TCCCCTTGCATATGAATCCATC 57.962 45.455 6.97 0.00 34.31 3.51
2999 3538 0.852842 TCCCCTTCCCCTTGCATATG 59.147 55.000 0.00 0.00 0.00 1.78
3011 3550 3.959535 TGTGCATTCATTTTCCCCTTC 57.040 42.857 0.00 0.00 0.00 3.46
3050 3589 8.599792 ACTTTAACAAGTATAGACCTGCCTTAA 58.400 33.333 0.00 0.00 41.81 1.85
3080 3619 2.584608 GCCGCCTACACTGACCAT 59.415 61.111 0.00 0.00 0.00 3.55
3120 3659 6.288294 TCATCAACTGGAAATTATAGGTCCG 58.712 40.000 0.00 0.00 33.87 4.79
3145 3684 6.850752 ATTGGTAAATGATTCGGTTCCTTT 57.149 33.333 0.00 0.00 0.00 3.11
3172 3711 8.736244 TGTTTTACTATCTTTGTTAAGCCCATC 58.264 33.333 0.00 0.00 0.00 3.51
3204 3743 0.167689 CTTGCTTCGCTGGAAAGAGC 59.832 55.000 0.00 0.00 35.46 4.09
3249 3788 6.150140 ACTGCAAAGAGTCTTACCATGATTTC 59.850 38.462 5.65 0.00 0.00 2.17
3262 3801 7.244192 GGTTTATACATGAACTGCAAAGAGTC 58.756 38.462 0.00 0.00 0.00 3.36
3305 3844 5.712152 ACTGCAAAGAGTTTTAGGAATGG 57.288 39.130 0.00 0.00 0.00 3.16
3311 3850 6.498304 ACACATGAACTGCAAAGAGTTTTAG 58.502 36.000 0.00 0.00 36.27 1.85


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

AutoCloner maintained by Alex Coulton.