Multiple sequence alignment - TraesCS5A01G494300

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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 TraesCS5A01G494300 chr5A 100.000 2922 0 0 1 2922 663074075 663076996 0.000000e+00 5397
1 TraesCS5A01G494300 chr6B 87.851 2066 216 24 1 2055 610805865 610807906 0.000000e+00 2392
2 TraesCS5A01G494300 chr6B 83.819 1236 175 20 822 2047 103963362 103964582 0.000000e+00 1151
3 TraesCS5A01G494300 chr7A 94.819 1544 60 6 1097 2624 171878764 171877225 0.000000e+00 2390
4 TraesCS5A01G494300 chr7A 88.030 1980 218 14 1 1976 255889372 255887408 0.000000e+00 2326
5 TraesCS5A01G494300 chr7A 85.324 1942 271 12 3 1938 88959661 88957728 0.000000e+00 1995
6 TraesCS5A01G494300 chr7A 85.170 1942 274 12 3 1938 722320039 722318106 0.000000e+00 1978
7 TraesCS5A01G494300 chr7A 86.770 1678 204 13 361 2033 32589644 32587980 0.000000e+00 1853
8 TraesCS5A01G494300 chr1A 87.694 2064 222 20 1 2055 184936439 184934399 0.000000e+00 2375
9 TraesCS5A01G494300 chr7B 87.349 2063 229 22 1 2055 574510876 574512914 0.000000e+00 2335
10 TraesCS5A01G494300 chrUn 94.695 1395 54 6 1097 2475 386814551 386813161 0.000000e+00 2148
11 TraesCS5A01G494300 chrUn 94.519 967 33 6 1674 2624 342998812 342997850 0.000000e+00 1474
12 TraesCS5A01G494300 chrUn 86.465 1123 140 10 822 1939 98277487 98276372 0.000000e+00 1221
13 TraesCS5A01G494300 chrUn 89.275 979 93 11 1 973 445250997 445251969 0.000000e+00 1216
14 TraesCS5A01G494300 chr2A 93.632 1005 35 10 1755 2748 539234737 539233751 0.000000e+00 1474
15 TraesCS5A01G494300 chr3A 82.879 1431 202 25 7 1430 47783913 47785307 0.000000e+00 1245
16 TraesCS5A01G494300 chr6A 86.007 1122 144 9 822 1939 53257554 53256442 0.000000e+00 1190
17 TraesCS5A01G494300 chr6A 94.886 176 9 0 2747 2922 525818768 525818943 2.870000e-70 276
18 TraesCS5A01G494300 chr6D 87.897 1008 88 9 1448 2442 292304150 292305136 0.000000e+00 1155
19 TraesCS5A01G494300 chr6D 94.737 190 6 1 2304 2493 7212590 7212405 2.850000e-75 292
20 TraesCS5A01G494300 chr6D 96.479 142 5 0 2608 2749 7212409 7212268 4.870000e-58 235
21 TraesCS5A01G494300 chr5D 87.244 439 50 3 2317 2749 475169447 475169885 2.020000e-136 496
22 TraesCS5A01G494300 chr5D 95.429 175 6 2 2750 2922 19424 19250 7.980000e-71 278
23 TraesCS5A01G494300 chr7D 95.480 177 7 1 2747 2922 440958796 440958972 6.170000e-72 281
24 TraesCS5A01G494300 chr7D 94.944 178 7 2 2747 2922 227520390 227520567 7.980000e-71 278
25 TraesCS5A01G494300 chr7D 95.429 175 6 2 2750 2922 588439796 588439622 7.980000e-71 278
26 TraesCS5A01G494300 chr2D 95.954 173 6 1 2747 2918 608971695 608971867 2.220000e-71 279
27 TraesCS5A01G494300 chr2D 94.944 178 7 2 2747 2922 552232290 552232467 7.980000e-71 278
28 TraesCS5A01G494300 chr4D 95.429 175 6 2 2750 2922 136251464 136251290 7.980000e-71 278
29 TraesCS5A01G494300 chr1D 94.915 177 8 1 2747 2922 334176872 334176696 2.870000e-70 276


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 TraesCS5A01G494300 chr5A 663074075 663076996 2921 False 5397 5397 100.000 1 2922 1 chr5A.!!$F1 2921
1 TraesCS5A01G494300 chr6B 610805865 610807906 2041 False 2392 2392 87.851 1 2055 1 chr6B.!!$F2 2054
2 TraesCS5A01G494300 chr6B 103963362 103964582 1220 False 1151 1151 83.819 822 2047 1 chr6B.!!$F1 1225
3 TraesCS5A01G494300 chr7A 171877225 171878764 1539 True 2390 2390 94.819 1097 2624 1 chr7A.!!$R3 1527
4 TraesCS5A01G494300 chr7A 255887408 255889372 1964 True 2326 2326 88.030 1 1976 1 chr7A.!!$R4 1975
5 TraesCS5A01G494300 chr7A 88957728 88959661 1933 True 1995 1995 85.324 3 1938 1 chr7A.!!$R2 1935
6 TraesCS5A01G494300 chr7A 722318106 722320039 1933 True 1978 1978 85.170 3 1938 1 chr7A.!!$R5 1935
7 TraesCS5A01G494300 chr7A 32587980 32589644 1664 True 1853 1853 86.770 361 2033 1 chr7A.!!$R1 1672
8 TraesCS5A01G494300 chr1A 184934399 184936439 2040 True 2375 2375 87.694 1 2055 1 chr1A.!!$R1 2054
9 TraesCS5A01G494300 chr7B 574510876 574512914 2038 False 2335 2335 87.349 1 2055 1 chr7B.!!$F1 2054
10 TraesCS5A01G494300 chrUn 386813161 386814551 1390 True 2148 2148 94.695 1097 2475 1 chrUn.!!$R3 1378
11 TraesCS5A01G494300 chrUn 342997850 342998812 962 True 1474 1474 94.519 1674 2624 1 chrUn.!!$R2 950
12 TraesCS5A01G494300 chrUn 98276372 98277487 1115 True 1221 1221 86.465 822 1939 1 chrUn.!!$R1 1117
13 TraesCS5A01G494300 chrUn 445250997 445251969 972 False 1216 1216 89.275 1 973 1 chrUn.!!$F1 972
14 TraesCS5A01G494300 chr2A 539233751 539234737 986 True 1474 1474 93.632 1755 2748 1 chr2A.!!$R1 993
15 TraesCS5A01G494300 chr3A 47783913 47785307 1394 False 1245 1245 82.879 7 1430 1 chr3A.!!$F1 1423
16 TraesCS5A01G494300 chr6A 53256442 53257554 1112 True 1190 1190 86.007 822 1939 1 chr6A.!!$R1 1117
17 TraesCS5A01G494300 chr6D 292304150 292305136 986 False 1155 1155 87.897 1448 2442 1 chr6D.!!$F1 994

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
384 387 0.302890 CGGATTGCTCAAGATGCGAC 59.697 55.0 0.0 0.0 39.08 5.19 F
638 641 0.323302 TGTGGAAAGCGTGGATAGCA 59.677 50.0 0.0 0.0 37.01 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 1686 1.901591 TTCTCCTGCTTTGCTTCCAG 58.098 50.000 0.0 0.0 0.0 3.86 R
2548 2600 3.194968 TGGGAGTTATTGAGGAGACGTTC 59.805 47.826 0.0 0.0 0.0 3.95 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
61 62 4.554036 GCGGCTGATGGGAGGGTC 62.554 72.222 0.00 0.00 0.00 4.46
72 73 0.688087 GGGAGGGTCCTTCGAGATGT 60.688 60.000 0.00 0.00 36.57 3.06
81 82 5.646360 GGGTCCTTCGAGATGTTTTATCAAA 59.354 40.000 0.00 0.00 0.00 2.69
95 96 8.321650 TGTTTTATCAAAATCAAATGGCCTTC 57.678 30.769 3.32 0.00 32.22 3.46
122 123 5.329191 TCCTCGGGGTAAGAGATAATACA 57.671 43.478 0.00 0.00 37.93 2.29
145 146 7.406799 CAAAAATGGTCCATGTTTGTTAGAC 57.593 36.000 29.01 0.00 41.52 2.59
146 147 6.723298 AAAATGGTCCATGTTTGTTAGACA 57.277 33.333 4.74 0.00 0.00 3.41
152 153 8.675705 TGGTCCATGTTTGTTAGACATATATG 57.324 34.615 11.29 11.29 36.04 1.78
179 180 7.973402 TGTATACATAGCTGACAAACCCATAT 58.027 34.615 0.08 0.00 0.00 1.78
180 181 7.877612 TGTATACATAGCTGACAAACCCATATG 59.122 37.037 0.08 0.00 0.00 1.78
183 184 6.055588 ACATAGCTGACAAACCCATATGTAC 58.944 40.000 0.00 0.00 32.25 2.90
189 190 5.306394 TGACAAACCCATATGTACGTTTCA 58.694 37.500 0.00 0.00 0.00 2.69
341 344 2.124983 ATGCCGCATTCGTCAGCT 60.125 55.556 0.00 0.00 0.00 4.24
354 357 6.676456 GCATTCGTCAGCTAGAAATGTGATTT 60.676 38.462 0.00 0.00 34.64 2.17
384 387 0.302890 CGGATTGCTCAAGATGCGAC 59.697 55.000 0.00 0.00 39.08 5.19
401 404 2.673833 CGACGGGCTATCATTAGGAAC 58.326 52.381 0.00 0.00 0.00 3.62
464 467 8.818141 TTCTAGTATGCTGCTATATTCACAAC 57.182 34.615 0.00 0.00 0.00 3.32
482 485 6.224584 TCACAACCTGATACGACAACAAATA 58.775 36.000 0.00 0.00 0.00 1.40
500 503 3.526931 ATACGTGTTGATCCCTGTGAG 57.473 47.619 0.00 0.00 0.00 3.51
526 529 8.246871 GCAATATCTAGATGAGTACATGCTACA 58.753 37.037 15.79 0.00 36.82 2.74
533 536 4.456280 TGAGTACATGCTACACCTTCAG 57.544 45.455 0.00 0.00 0.00 3.02
544 547 0.887836 CACCTTCAGCAGCAGCAAGA 60.888 55.000 3.17 0.00 45.49 3.02
546 549 1.174783 CCTTCAGCAGCAGCAAGAAT 58.825 50.000 3.17 0.00 45.49 2.40
555 558 3.188873 GCAGCAGCAAGAATATGAGGATC 59.811 47.826 0.00 0.00 41.58 3.36
578 581 3.007940 TCATTCAGTCCACCGAAACATCT 59.992 43.478 0.00 0.00 0.00 2.90
610 613 6.098409 TGGACTGAGAAAAGAGACAAGTTAGT 59.902 38.462 0.00 0.00 0.00 2.24
629 632 4.164822 AGTTGATGAAATGTGGAAAGCG 57.835 40.909 0.00 0.00 0.00 4.68
638 641 0.323302 TGTGGAAAGCGTGGATAGCA 59.677 50.000 0.00 0.00 37.01 3.49
671 675 8.906693 CAAGATCGTTGATACATGTAGTACATC 58.093 37.037 13.00 5.22 36.53 3.06
694 698 7.900782 TCTTTAGTTGTAGGACATTAAGTGC 57.099 36.000 0.00 0.00 39.14 4.40
712 716 6.579666 AAGTGCTTGTTCATCAACATATGT 57.420 33.333 1.41 1.41 42.28 2.29
721 725 6.433716 TGTTCATCAACATATGTGTGTCCAAT 59.566 34.615 9.63 0.00 37.61 3.16
726 730 7.465353 TCAACATATGTGTGTCCAATCATTT 57.535 32.000 9.63 0.00 38.92 2.32
730 734 8.125978 ACATATGTGTGTCCAATCATTTTTCT 57.874 30.769 7.78 0.00 37.14 2.52
734 738 5.523188 TGTGTGTCCAATCATTTTTCTTTGC 59.477 36.000 0.00 0.00 0.00 3.68
758 762 7.148086 TGCTATTTGTTTTCTCCCATATGTCAC 60.148 37.037 1.24 0.00 0.00 3.67
762 766 5.003160 TGTTTTCTCCCATATGTCACAGTG 58.997 41.667 1.24 0.00 0.00 3.66
773 777 6.127647 CCATATGTCACAGTGGCTTATGTTTT 60.128 38.462 27.12 3.69 37.99 2.43
775 779 5.940192 TGTCACAGTGGCTTATGTTTTAG 57.060 39.130 6.72 0.00 0.00 1.85
781 785 7.023575 CACAGTGGCTTATGTTTTAGTTCATC 58.976 38.462 0.00 0.00 0.00 2.92
786 790 7.335924 GTGGCTTATGTTTTAGTTCATCCACTA 59.664 37.037 0.00 0.00 35.48 2.74
807 811 9.083422 CCACTATTCTGTAATGATAGGAGAGAA 57.917 37.037 0.00 0.00 0.00 2.87
924 930 2.856222 ACCAAGTCAAAGGAGAGCAAG 58.144 47.619 0.00 0.00 0.00 4.01
927 933 3.633986 CCAAGTCAAAGGAGAGCAAGTTT 59.366 43.478 0.00 0.00 0.00 2.66
928 934 4.498682 CCAAGTCAAAGGAGAGCAAGTTTG 60.499 45.833 0.00 0.00 0.00 2.93
987 994 6.127423 CGGAGGAGGAGAAGTTACTTATTGAA 60.127 42.308 0.00 0.00 0.00 2.69
1074 1081 3.313526 CCTACATTGAGAAGGAAATGGCG 59.686 47.826 0.00 0.00 37.96 5.69
1222 1230 7.405292 TGATGAGAAGAAAATGGTAACTGGAT 58.595 34.615 0.00 0.00 37.61 3.41
1257 1265 1.678970 GGGCTGGGCAAAGGTACAG 60.679 63.158 0.00 0.00 0.00 2.74
1258 1266 1.074951 GGCTGGGCAAAGGTACAGT 59.925 57.895 0.00 0.00 33.62 3.55
1259 1267 0.326927 GGCTGGGCAAAGGTACAGTA 59.673 55.000 0.00 0.00 33.62 2.74
1260 1268 1.064685 GGCTGGGCAAAGGTACAGTAT 60.065 52.381 0.00 0.00 33.62 2.12
1261 1269 2.171870 GGCTGGGCAAAGGTACAGTATA 59.828 50.000 0.00 0.00 33.62 1.47
1262 1270 3.181443 GGCTGGGCAAAGGTACAGTATAT 60.181 47.826 0.00 0.00 33.62 0.86
1263 1271 4.461198 GCTGGGCAAAGGTACAGTATATT 58.539 43.478 0.00 0.00 33.62 1.28
1264 1272 4.515567 GCTGGGCAAAGGTACAGTATATTC 59.484 45.833 0.00 0.00 33.62 1.75
1265 1273 5.680619 CTGGGCAAAGGTACAGTATATTCA 58.319 41.667 0.00 0.00 0.00 2.57
1266 1274 6.260700 TGGGCAAAGGTACAGTATATTCAT 57.739 37.500 0.00 0.00 0.00 2.57
1267 1275 6.668645 TGGGCAAAGGTACAGTATATTCATT 58.331 36.000 0.00 0.00 0.00 2.57
1268 1276 6.770785 TGGGCAAAGGTACAGTATATTCATTC 59.229 38.462 0.00 0.00 0.00 2.67
1269 1277 6.770785 GGGCAAAGGTACAGTATATTCATTCA 59.229 38.462 0.00 0.00 0.00 2.57
1270 1278 7.041098 GGGCAAAGGTACAGTATATTCATTCAG 60.041 40.741 0.00 0.00 0.00 3.02
1316 1338 8.015087 TGTTTCATGTGATTTTCGATTGTACTC 58.985 33.333 0.00 0.00 0.00 2.59
1446 1473 4.288626 TGATTTGGCTAAAGGAGGTAGTGT 59.711 41.667 0.65 0.00 0.00 3.55
1516 1544 3.510360 AGACACAACCTACTAGCGAACAT 59.490 43.478 0.00 0.00 0.00 2.71
1547 1578 7.053316 GAGAATCTTCCTGAATCTCATGAGA 57.947 40.000 27.03 27.03 46.08 3.27
1560 1591 1.691976 TCATGAGAACACGAACCCACT 59.308 47.619 0.00 0.00 0.00 4.00
1595 1626 3.321111 GCCTGGTCGGAAGAGAACATATA 59.679 47.826 0.00 0.00 43.49 0.86
1596 1627 4.021016 GCCTGGTCGGAAGAGAACATATAT 60.021 45.833 0.00 0.00 43.49 0.86
1655 1686 5.405269 GTGTCCAATACAATTGCAAAGTTCC 59.595 40.000 1.71 0.00 40.63 3.62
1664 1695 1.774110 TGCAAAGTTCCTGGAAGCAA 58.226 45.000 16.05 3.52 0.00 3.91
1864 1897 7.308951 GGAAAGACCGAACTTTTCATCCAATTA 60.309 37.037 7.87 0.00 39.71 1.40
1976 2011 9.565090 GGTAGTTTAATATTTTTAGGTCGGGAT 57.435 33.333 0.00 0.00 0.00 3.85
2175 2223 1.067516 GCTATGAATTGCAATGGCGGT 59.932 47.619 13.82 0.00 45.35 5.68
2303 2355 8.862091 ATCCTATTTAGGCCACTAAGCTATAT 57.138 34.615 5.01 0.00 43.31 0.86
2304 2356 9.953429 ATCCTATTTAGGCCACTAAGCTATATA 57.047 33.333 5.01 0.00 43.31 0.86
2305 2357 9.953429 TCCTATTTAGGCCACTAAGCTATATAT 57.047 33.333 5.01 0.00 43.31 0.86
2313 2365 8.968969 AGGCCACTAAGCTATATATACACTTAC 58.031 37.037 5.01 0.52 0.00 2.34
2493 2545 6.904498 TGTACTGACCGTCATTTTATTTTGG 58.096 36.000 0.62 0.00 0.00 3.28
2495 2547 4.173256 CTGACCGTCATTTTATTTTGGCC 58.827 43.478 0.62 0.00 0.00 5.36
2496 2548 3.829601 TGACCGTCATTTTATTTTGGCCT 59.170 39.130 3.32 0.00 0.00 5.19
2548 2600 2.930040 CAAGGCTGGTTCGTACATACTG 59.070 50.000 0.00 0.00 0.00 2.74
2648 2700 1.951209 ATTCCCATCCCAACCCAAAC 58.049 50.000 0.00 0.00 0.00 2.93
2679 2731 3.315880 GACTAGTAGTCCACTCCCCAT 57.684 52.381 18.10 0.00 39.28 4.00
2691 2743 2.780010 CACTCCCCATGTCTTATCCCTT 59.220 50.000 0.00 0.00 0.00 3.95
2707 2759 0.256177 CCTTAGCCAACTCCCCCTTC 59.744 60.000 0.00 0.00 0.00 3.46
2725 2777 1.851304 TCAAAACTCCCATGCCCATC 58.149 50.000 0.00 0.00 0.00 3.51
2736 2788 0.032813 ATGCCCATCCCCTCAAACTG 60.033 55.000 0.00 0.00 0.00 3.16
2744 2796 0.389025 CCCCTCAAACTGCCAAACAC 59.611 55.000 0.00 0.00 0.00 3.32
2748 2800 0.100325 TCAAACTGCCAAACACGCTG 59.900 50.000 0.00 0.00 0.00 5.18
2749 2801 1.226945 AAACTGCCAAACACGCTGC 60.227 52.632 0.00 0.00 0.00 5.25
2750 2802 1.666209 AAACTGCCAAACACGCTGCT 61.666 50.000 0.00 0.00 0.00 4.24
2751 2803 0.817634 AACTGCCAAACACGCTGCTA 60.818 50.000 0.00 0.00 0.00 3.49
2752 2804 1.207593 CTGCCAAACACGCTGCTAC 59.792 57.895 0.00 0.00 0.00 3.58
2753 2805 1.227823 TGCCAAACACGCTGCTACT 60.228 52.632 0.00 0.00 0.00 2.57
2754 2806 0.034198 TGCCAAACACGCTGCTACTA 59.966 50.000 0.00 0.00 0.00 1.82
2755 2807 0.442699 GCCAAACACGCTGCTACTAC 59.557 55.000 0.00 0.00 0.00 2.73
2756 2808 1.790755 CCAAACACGCTGCTACTACA 58.209 50.000 0.00 0.00 0.00 2.74
2757 2809 2.346803 CCAAACACGCTGCTACTACAT 58.653 47.619 0.00 0.00 0.00 2.29
2758 2810 2.094258 CCAAACACGCTGCTACTACATG 59.906 50.000 0.00 0.00 0.00 3.21
2759 2811 2.010145 AACACGCTGCTACTACATGG 57.990 50.000 0.00 0.00 0.00 3.66
2760 2812 1.182667 ACACGCTGCTACTACATGGA 58.817 50.000 0.00 0.00 0.00 3.41
2761 2813 1.548719 ACACGCTGCTACTACATGGAA 59.451 47.619 0.00 0.00 0.00 3.53
2762 2814 2.196749 CACGCTGCTACTACATGGAAG 58.803 52.381 0.00 0.00 0.00 3.46
2763 2815 1.137086 ACGCTGCTACTACATGGAAGG 59.863 52.381 0.00 0.00 0.00 3.46
2764 2816 1.539065 CGCTGCTACTACATGGAAGGG 60.539 57.143 0.00 0.00 0.00 3.95
2765 2817 1.202698 GCTGCTACTACATGGAAGGGG 60.203 57.143 0.00 0.00 0.00 4.79
2766 2818 1.417890 CTGCTACTACATGGAAGGGGG 59.582 57.143 0.00 0.00 0.00 5.40
2767 2819 1.009060 TGCTACTACATGGAAGGGGGA 59.991 52.381 0.00 0.00 0.00 4.81
2768 2820 2.124411 GCTACTACATGGAAGGGGGAA 58.876 52.381 0.00 0.00 0.00 3.97
2769 2821 2.508300 GCTACTACATGGAAGGGGGAAA 59.492 50.000 0.00 0.00 0.00 3.13
2770 2822 3.138468 GCTACTACATGGAAGGGGGAAAT 59.862 47.826 0.00 0.00 0.00 2.17
2771 2823 3.953542 ACTACATGGAAGGGGGAAATC 57.046 47.619 0.00 0.00 0.00 2.17
2772 2824 2.514160 ACTACATGGAAGGGGGAAATCC 59.486 50.000 0.00 0.00 0.00 3.01
2773 2825 1.698874 ACATGGAAGGGGGAAATCCT 58.301 50.000 0.00 0.00 34.24 3.24
2774 2826 2.871796 ACATGGAAGGGGGAAATCCTA 58.128 47.619 0.00 0.00 33.58 2.94
2775 2827 2.514160 ACATGGAAGGGGGAAATCCTAC 59.486 50.000 0.00 0.00 33.58 3.18
2776 2828 2.680439 TGGAAGGGGGAAATCCTACT 57.320 50.000 0.00 0.00 33.58 2.57
2777 2829 2.488836 TGGAAGGGGGAAATCCTACTC 58.511 52.381 0.00 0.00 33.58 2.59
2778 2830 1.775459 GGAAGGGGGAAATCCTACTCC 59.225 57.143 0.00 0.00 33.58 3.85
2782 2834 2.926539 GGGAAATCCTACTCCCGGT 58.073 57.895 0.00 0.00 42.03 5.28
2783 2835 0.468648 GGGAAATCCTACTCCCGGTG 59.531 60.000 0.00 0.00 42.03 4.94
2784 2836 0.468648 GGAAATCCTACTCCCGGTGG 59.531 60.000 0.00 0.00 0.00 4.61
2785 2837 0.468648 GAAATCCTACTCCCGGTGGG 59.531 60.000 0.00 0.00 46.39 4.61
2795 2847 2.663196 CCGGTGGGAACAGGACTC 59.337 66.667 0.00 0.00 44.46 3.36
2796 2848 2.663196 CGGTGGGAACAGGACTCC 59.337 66.667 0.00 0.00 44.46 3.85
2801 2853 3.404773 GGAACAGGACTCCCAGGG 58.595 66.667 0.00 0.00 33.88 4.45
2802 2854 2.671682 GAACAGGACTCCCAGGGC 59.328 66.667 0.00 0.00 33.88 5.19
2803 2855 3.316573 GAACAGGACTCCCAGGGCG 62.317 68.421 0.00 0.00 33.88 6.13
2813 2865 3.923864 CCAGGGCGCGCCATAGTA 61.924 66.667 46.88 0.00 37.98 1.82
2814 2866 2.356313 CAGGGCGCGCCATAGTAG 60.356 66.667 46.88 27.65 37.98 2.57
2815 2867 2.520982 AGGGCGCGCCATAGTAGA 60.521 61.111 46.88 0.00 37.98 2.59
2816 2868 2.049063 GGGCGCGCCATAGTAGAG 60.049 66.667 46.88 0.00 37.98 2.43
2817 2869 2.049063 GGCGCGCCATAGTAGAGG 60.049 66.667 43.55 0.00 35.81 3.69
2818 2870 2.049063 GCGCGCCATAGTAGAGGG 60.049 66.667 23.24 0.00 0.00 4.30
2819 2871 2.857744 GCGCGCCATAGTAGAGGGT 61.858 63.158 23.24 0.00 0.00 4.34
2820 2872 1.286260 CGCGCCATAGTAGAGGGTC 59.714 63.158 0.00 0.00 0.00 4.46
2821 2873 1.286260 GCGCCATAGTAGAGGGTCG 59.714 63.158 0.00 0.00 33.51 4.79
2822 2874 1.957562 CGCCATAGTAGAGGGTCGG 59.042 63.158 0.00 0.00 0.00 4.79
2823 2875 1.666580 GCCATAGTAGAGGGTCGGC 59.333 63.158 0.00 0.00 0.00 5.54
2824 2876 1.817911 GCCATAGTAGAGGGTCGGCC 61.818 65.000 0.00 0.00 31.76 6.13
2840 2892 3.700350 CCCTCCCCCTCCTCCACT 61.700 72.222 0.00 0.00 0.00 4.00
2841 2893 2.041405 CCTCCCCCTCCTCCACTC 60.041 72.222 0.00 0.00 0.00 3.51
2842 2894 2.041405 CTCCCCCTCCTCCACTCC 60.041 72.222 0.00 0.00 0.00 3.85
2843 2895 2.540910 TCCCCCTCCTCCACTCCT 60.541 66.667 0.00 0.00 0.00 3.69
2844 2896 2.184631 TCCCCCTCCTCCACTCCTT 61.185 63.158 0.00 0.00 0.00 3.36
2845 2897 1.229984 CCCCCTCCTCCACTCCTTT 60.230 63.158 0.00 0.00 0.00 3.11
2846 2898 0.044244 CCCCCTCCTCCACTCCTTTA 59.956 60.000 0.00 0.00 0.00 1.85
2847 2899 1.345526 CCCCCTCCTCCACTCCTTTAT 60.346 57.143 0.00 0.00 0.00 1.40
2848 2900 2.090153 CCCCCTCCTCCACTCCTTTATA 60.090 54.545 0.00 0.00 0.00 0.98
2849 2901 3.441658 CCCCCTCCTCCACTCCTTTATAT 60.442 52.174 0.00 0.00 0.00 0.86
2850 2902 4.202901 CCCCCTCCTCCACTCCTTTATATA 60.203 50.000 0.00 0.00 0.00 0.86
2851 2903 4.778427 CCCCTCCTCCACTCCTTTATATAC 59.222 50.000 0.00 0.00 0.00 1.47
2852 2904 5.403512 CCCTCCTCCACTCCTTTATATACA 58.596 45.833 0.00 0.00 0.00 2.29
2853 2905 5.482175 CCCTCCTCCACTCCTTTATATACAG 59.518 48.000 0.00 0.00 0.00 2.74
2854 2906 5.482175 CCTCCTCCACTCCTTTATATACAGG 59.518 48.000 8.45 8.45 0.00 4.00
2855 2907 5.403512 TCCTCCACTCCTTTATATACAGGG 58.596 45.833 13.81 8.05 0.00 4.45
2856 2908 4.532521 CCTCCACTCCTTTATATACAGGGG 59.467 50.000 12.55 12.55 36.61 4.79
2857 2909 5.403512 CTCCACTCCTTTATATACAGGGGA 58.596 45.833 19.78 14.08 33.77 4.81
2858 2910 5.403512 TCCACTCCTTTATATACAGGGGAG 58.596 45.833 19.78 12.48 43.99 4.30
2859 2911 4.532521 CCACTCCTTTATATACAGGGGAGG 59.467 50.000 19.78 17.10 43.06 4.30
2860 2912 4.532521 CACTCCTTTATATACAGGGGAGGG 59.467 50.000 19.78 12.61 43.06 4.30
2861 2913 4.104831 CTCCTTTATATACAGGGGAGGGG 58.895 52.174 8.95 0.00 37.33 4.79
2862 2914 3.181388 TCCTTTATATACAGGGGAGGGGG 60.181 52.174 13.81 0.00 0.00 5.40
2863 2915 2.354261 TTATATACAGGGGAGGGGGC 57.646 55.000 0.00 0.00 0.00 5.80
2864 2916 1.181731 TATATACAGGGGAGGGGGCA 58.818 55.000 0.00 0.00 0.00 5.36
2865 2917 0.475828 ATATACAGGGGAGGGGGCAC 60.476 60.000 0.00 0.00 0.00 5.01
2878 2930 4.637771 GGCACCCCATAGACACAC 57.362 61.111 0.00 0.00 0.00 3.82
2879 2931 1.682849 GGCACCCCATAGACACACA 59.317 57.895 0.00 0.00 0.00 3.72
2880 2932 0.037590 GGCACCCCATAGACACACAA 59.962 55.000 0.00 0.00 0.00 3.33
2881 2933 1.453155 GCACCCCATAGACACACAAG 58.547 55.000 0.00 0.00 0.00 3.16
2882 2934 1.271379 GCACCCCATAGACACACAAGT 60.271 52.381 0.00 0.00 0.00 3.16
2883 2935 2.814097 GCACCCCATAGACACACAAGTT 60.814 50.000 0.00 0.00 0.00 2.66
2884 2936 2.813754 CACCCCATAGACACACAAGTTG 59.186 50.000 0.00 0.00 0.00 3.16
2885 2937 2.708861 ACCCCATAGACACACAAGTTGA 59.291 45.455 10.54 0.00 0.00 3.18
2886 2938 3.330701 ACCCCATAGACACACAAGTTGAT 59.669 43.478 10.54 0.00 0.00 2.57
2887 2939 3.941483 CCCCATAGACACACAAGTTGATC 59.059 47.826 10.54 1.78 0.00 2.92
2888 2940 4.565444 CCCCATAGACACACAAGTTGATCA 60.565 45.833 10.54 0.00 0.00 2.92
2889 2941 5.188434 CCCATAGACACACAAGTTGATCAT 58.812 41.667 10.54 0.00 0.00 2.45
2890 2942 5.649395 CCCATAGACACACAAGTTGATCATT 59.351 40.000 10.54 0.00 0.00 2.57
2891 2943 6.403964 CCCATAGACACACAAGTTGATCATTG 60.404 42.308 10.54 7.38 0.00 2.82
2892 2944 6.372381 CCATAGACACACAAGTTGATCATTGA 59.628 38.462 14.50 0.00 0.00 2.57
2893 2945 7.066645 CCATAGACACACAAGTTGATCATTGAT 59.933 37.037 14.50 0.00 0.00 2.57
2894 2946 6.492007 AGACACACAAGTTGATCATTGATC 57.508 37.500 17.97 17.97 39.31 2.92
2895 2947 6.236409 AGACACACAAGTTGATCATTGATCT 58.764 36.000 23.49 4.89 39.56 2.75
2896 2948 6.370994 AGACACACAAGTTGATCATTGATCTC 59.629 38.462 23.49 16.98 39.56 2.75
2897 2949 6.236409 ACACACAAGTTGATCATTGATCTCT 58.764 36.000 23.49 18.51 39.56 3.10
2898 2950 6.713903 ACACACAAGTTGATCATTGATCTCTT 59.286 34.615 23.49 21.92 39.56 2.85
2899 2951 7.879677 ACACACAAGTTGATCATTGATCTCTTA 59.120 33.333 23.49 4.56 39.56 2.10
2900 2952 8.388853 CACACAAGTTGATCATTGATCTCTTAG 58.611 37.037 23.49 20.95 39.56 2.18
2901 2953 7.065563 ACACAAGTTGATCATTGATCTCTTAGC 59.934 37.037 23.49 8.75 39.56 3.09
2902 2954 6.541641 ACAAGTTGATCATTGATCTCTTAGCC 59.458 38.462 23.49 7.19 39.56 3.93
2903 2955 5.295950 AGTTGATCATTGATCTCTTAGCCG 58.704 41.667 23.49 0.00 39.56 5.52
2904 2956 4.944619 TGATCATTGATCTCTTAGCCGT 57.055 40.909 23.49 0.00 39.56 5.68
2905 2957 4.625028 TGATCATTGATCTCTTAGCCGTG 58.375 43.478 23.49 0.00 39.56 4.94
2906 2958 4.100035 TGATCATTGATCTCTTAGCCGTGT 59.900 41.667 23.49 0.00 39.56 4.49
2907 2959 3.785486 TCATTGATCTCTTAGCCGTGTG 58.215 45.455 0.00 0.00 0.00 3.82
2908 2960 2.010145 TTGATCTCTTAGCCGTGTGC 57.990 50.000 0.00 0.00 41.71 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.691219 GCAGATCCTTCCCAACCCA 59.309 57.895 0.00 0.00 0.00 4.51
61 62 9.624697 TTTGATTTTGATAAAACATCTCGAAGG 57.375 29.630 0.00 0.00 32.37 3.46
72 73 7.607223 CCTGAAGGCCATTTGATTTTGATAAAA 59.393 33.333 5.01 0.00 34.41 1.52
81 82 2.833943 GGAACCTGAAGGCCATTTGATT 59.166 45.455 5.01 0.00 39.32 2.57
95 96 0.824759 CTCTTACCCCGAGGAACCTG 59.175 60.000 0.00 0.00 36.73 4.00
122 123 7.118496 TGTCTAACAAACATGGACCATTTTT 57.882 32.000 12.02 12.02 0.00 1.94
152 153 5.878116 TGGGTTTGTCAGCTATGTATACAAC 59.122 40.000 10.14 2.92 30.28 3.32
165 166 5.410132 TGAAACGTACATATGGGTTTGTCAG 59.590 40.000 19.78 1.28 33.13 3.51
179 180 4.155099 CACCCTATGCAATTGAAACGTACA 59.845 41.667 10.34 0.00 0.00 2.90
180 181 4.658071 CACCCTATGCAATTGAAACGTAC 58.342 43.478 10.34 0.00 0.00 3.67
328 331 2.604914 ACATTTCTAGCTGACGAATGCG 59.395 45.455 0.00 0.00 44.79 4.73
341 344 7.764443 CCGAAAGTCCTCTAAATCACATTTCTA 59.236 37.037 0.00 0.00 33.82 2.10
354 357 3.096852 TGAGCAATCCGAAAGTCCTCTA 58.903 45.455 0.00 0.00 0.00 2.43
384 387 1.003233 GGGGTTCCTAATGATAGCCCG 59.997 57.143 0.00 0.00 33.20 6.13
401 404 8.217799 TGTGTATCAAAAGGATAATAAGAGGGG 58.782 37.037 0.00 0.00 40.11 4.79
445 448 6.173427 TCAGGTTGTGAATATAGCAGCATA 57.827 37.500 0.00 0.00 29.64 3.14
464 467 4.624024 ACACGTATTTGTTGTCGTATCAGG 59.376 41.667 0.00 0.00 35.13 3.86
482 485 0.320771 GCTCACAGGGATCAACACGT 60.321 55.000 0.00 0.00 0.00 4.49
500 503 8.246871 TGTAGCATGTACTCATCTAGATATTGC 58.753 37.037 4.54 7.13 31.15 3.56
526 529 0.179009 TTCTTGCTGCTGCTGAAGGT 60.179 50.000 17.00 0.00 40.48 3.50
533 536 2.569059 TCCTCATATTCTTGCTGCTGC 58.431 47.619 8.89 8.89 40.20 5.25
555 558 2.766313 TGTTTCGGTGGACTGAATGAG 58.234 47.619 1.89 0.00 40.57 2.90
610 613 3.305267 CCACGCTTTCCACATTTCATCAA 60.305 43.478 0.00 0.00 0.00 2.57
629 632 5.122396 ACGATCTTGTCTTTTTGCTATCCAC 59.878 40.000 0.00 0.00 0.00 4.02
638 641 8.099364 ACATGTATCAACGATCTTGTCTTTTT 57.901 30.769 0.00 0.00 0.00 1.94
671 675 7.907214 AGCACTTAATGTCCTACAACTAAAG 57.093 36.000 0.00 0.00 0.00 1.85
691 695 5.570206 CACACATATGTTGATGAACAAGCAC 59.430 40.000 5.37 0.00 45.23 4.40
694 698 6.072563 TGGACACACATATGTTGATGAACAAG 60.073 38.462 18.72 0.00 45.23 3.16
702 706 7.465353 AAATGATTGGACACACATATGTTGA 57.535 32.000 18.72 3.66 36.72 3.18
712 716 5.916318 AGCAAAGAAAAATGATTGGACACA 58.084 33.333 0.00 0.00 0.00 3.72
726 730 7.118496 TGGGAGAAAACAAATAGCAAAGAAA 57.882 32.000 0.00 0.00 0.00 2.52
730 734 8.133024 ACATATGGGAGAAAACAAATAGCAAA 57.867 30.769 7.80 0.00 0.00 3.68
734 738 8.279970 TGTGACATATGGGAGAAAACAAATAG 57.720 34.615 7.80 0.00 0.00 1.73
758 762 6.150976 TGGATGAACTAAAACATAAGCCACTG 59.849 38.462 0.00 0.00 0.00 3.66
762 766 6.759497 AGTGGATGAACTAAAACATAAGCC 57.241 37.500 0.00 0.00 0.00 4.35
775 779 9.429359 CCTATCATTACAGAATAGTGGATGAAC 57.571 37.037 0.00 0.00 32.77 3.18
781 785 8.642935 TCTCTCCTATCATTACAGAATAGTGG 57.357 38.462 0.00 0.00 0.00 4.00
924 930 5.095691 TGTCTCTCTTTTTCGATGCAAAC 57.904 39.130 0.00 0.00 0.00 2.93
927 933 4.631131 TCTTGTCTCTCTTTTTCGATGCA 58.369 39.130 0.00 0.00 0.00 3.96
928 934 4.926238 TCTCTTGTCTCTCTTTTTCGATGC 59.074 41.667 0.00 0.00 0.00 3.91
1074 1081 5.665459 AGATCAGCATGTGGTAGTACTTTC 58.335 41.667 0.00 0.00 37.40 2.62
1137 1144 8.993121 TCTAGAACATAAGAAAGTTGCTTCTTG 58.007 33.333 0.00 2.37 43.77 3.02
1177 1184 2.352561 TCCCATCCAAACCCACTAGA 57.647 50.000 0.00 0.00 0.00 2.43
1178 1185 2.509548 TCATCCCATCCAAACCCACTAG 59.490 50.000 0.00 0.00 0.00 2.57
1222 1230 4.533815 CAGCCCATATACGTCTCCCTATA 58.466 47.826 0.00 0.00 0.00 1.31
1286 1296 6.695292 ATCGAAAATCACATGAAACAAAGC 57.305 33.333 0.00 0.00 0.00 3.51
1367 1394 4.809193 ACCATAGGCTTCATGTAGAGAGA 58.191 43.478 3.14 0.00 0.00 3.10
1446 1473 6.101296 AGTTTCTTCTTCTCCAGGACCTTTAA 59.899 38.462 0.00 0.00 0.00 1.52
1516 1544 2.269023 TCAGGAAGATTCTCCTTGGCA 58.731 47.619 2.91 0.00 43.76 4.92
1560 1591 2.185387 GACCAGGCCTAGAACTACCAA 58.815 52.381 3.98 0.00 0.00 3.67
1595 1626 5.190677 TGACTCAAGTGCATCATCATCAAT 58.809 37.500 0.00 0.00 0.00 2.57
1596 1627 4.581868 TGACTCAAGTGCATCATCATCAA 58.418 39.130 0.00 0.00 0.00 2.57
1655 1686 1.901591 TTCTCCTGCTTTGCTTCCAG 58.098 50.000 0.00 0.00 0.00 3.86
1864 1897 4.385825 ACACCACTTTGTAATCATCACGT 58.614 39.130 0.00 0.00 0.00 4.49
2091 2129 7.344612 TGTTTATACAGCTCTCCAGGAGAATTA 59.655 37.037 20.32 9.09 44.45 1.40
2236 2288 3.772572 TGATAGTTTTGACATCTCCCCGA 59.227 43.478 0.00 0.00 0.00 5.14
2426 2478 8.995027 ATACAAACAGATTATCCCTTGCATTA 57.005 30.769 0.00 0.00 0.00 1.90
2548 2600 3.194968 TGGGAGTTATTGAGGAGACGTTC 59.805 47.826 0.00 0.00 0.00 3.95
2648 2700 3.465871 GACTACTAGTCCTAGTCCCACG 58.534 54.545 10.15 0.00 44.58 4.94
2674 2726 2.040412 GGCTAAGGGATAAGACATGGGG 59.960 54.545 0.00 0.00 0.00 4.96
2679 2731 3.454812 GGAGTTGGCTAAGGGATAAGACA 59.545 47.826 0.00 0.00 0.00 3.41
2691 2743 1.451449 TTTGAAGGGGGAGTTGGCTA 58.549 50.000 0.00 0.00 0.00 3.93
2707 2759 0.826062 GGATGGGCATGGGAGTTTTG 59.174 55.000 0.00 0.00 0.00 2.44
2725 2777 0.389025 GTGTTTGGCAGTTTGAGGGG 59.611 55.000 0.00 0.00 0.00 4.79
2736 2788 0.442699 GTAGTAGCAGCGTGTTTGGC 59.557 55.000 0.00 0.00 0.00 4.52
2744 2796 1.539065 CCCTTCCATGTAGTAGCAGCG 60.539 57.143 0.00 0.00 0.00 5.18
2748 2800 1.802553 TCCCCCTTCCATGTAGTAGC 58.197 55.000 0.00 0.00 0.00 3.58
2749 2801 4.202472 GGATTTCCCCCTTCCATGTAGTAG 60.202 50.000 0.00 0.00 0.00 2.57
2750 2802 3.720002 GGATTTCCCCCTTCCATGTAGTA 59.280 47.826 0.00 0.00 0.00 1.82
2751 2803 2.514160 GGATTTCCCCCTTCCATGTAGT 59.486 50.000 0.00 0.00 0.00 2.73
2752 2804 2.785857 AGGATTTCCCCCTTCCATGTAG 59.214 50.000 0.00 0.00 36.42 2.74
2753 2805 2.871796 AGGATTTCCCCCTTCCATGTA 58.128 47.619 0.00 0.00 36.42 2.29
2754 2806 1.698874 AGGATTTCCCCCTTCCATGT 58.301 50.000 0.00 0.00 36.42 3.21
2755 2807 2.785857 AGTAGGATTTCCCCCTTCCATG 59.214 50.000 0.00 0.00 35.30 3.66
2756 2808 3.056832 GAGTAGGATTTCCCCCTTCCAT 58.943 50.000 0.00 0.00 35.30 3.41
2757 2809 2.488836 GAGTAGGATTTCCCCCTTCCA 58.511 52.381 0.00 0.00 35.30 3.53
2758 2810 1.775459 GGAGTAGGATTTCCCCCTTCC 59.225 57.143 0.00 0.00 35.30 3.46
2759 2811 1.775459 GGGAGTAGGATTTCCCCCTTC 59.225 57.143 0.00 0.00 46.15 3.46
2760 2812 1.908643 GGGAGTAGGATTTCCCCCTT 58.091 55.000 0.00 0.00 46.15 3.95
2761 2813 3.676953 GGGAGTAGGATTTCCCCCT 57.323 57.895 0.00 0.00 46.15 4.79
2765 2817 0.468648 CCACCGGGAGTAGGATTTCC 59.531 60.000 6.32 0.00 35.59 3.13
2777 2829 2.928396 AGTCCTGTTCCCACCGGG 60.928 66.667 6.32 0.00 46.11 5.73
2778 2830 2.663196 GAGTCCTGTTCCCACCGG 59.337 66.667 0.00 0.00 0.00 5.28
2779 2831 2.663196 GGAGTCCTGTTCCCACCG 59.337 66.667 0.41 0.00 0.00 4.94
2784 2836 2.972819 GCCCTGGGAGTCCTGTTCC 61.973 68.421 19.27 0.00 0.00 3.62
2785 2837 2.671682 GCCCTGGGAGTCCTGTTC 59.328 66.667 19.27 0.00 0.00 3.18
2786 2838 3.322466 CGCCCTGGGAGTCCTGTT 61.322 66.667 19.27 0.00 0.00 3.16
2796 2848 3.865929 CTACTATGGCGCGCCCTGG 62.866 68.421 44.42 37.49 34.56 4.45
2797 2849 2.356313 CTACTATGGCGCGCCCTG 60.356 66.667 44.42 33.73 34.56 4.45
2798 2850 2.520982 TCTACTATGGCGCGCCCT 60.521 61.111 44.42 37.34 34.56 5.19
2799 2851 2.049063 CTCTACTATGGCGCGCCC 60.049 66.667 44.42 27.83 34.56 6.13
2800 2852 2.049063 CCTCTACTATGGCGCGCC 60.049 66.667 42.35 42.35 0.00 6.53
2801 2853 2.049063 CCCTCTACTATGGCGCGC 60.049 66.667 25.94 25.94 0.00 6.86
2802 2854 1.286260 GACCCTCTACTATGGCGCG 59.714 63.158 0.00 0.00 0.00 6.86
2803 2855 1.286260 CGACCCTCTACTATGGCGC 59.714 63.158 0.00 0.00 0.00 6.53
2804 2856 1.957562 CCGACCCTCTACTATGGCG 59.042 63.158 0.00 0.00 0.00 5.69
2805 2857 1.666580 GCCGACCCTCTACTATGGC 59.333 63.158 0.00 0.00 0.00 4.40
2806 2858 2.352817 GGCCGACCCTCTACTATGG 58.647 63.158 0.00 0.00 0.00 2.74
2823 2875 3.700350 AGTGGAGGAGGGGGAGGG 61.700 72.222 0.00 0.00 0.00 4.30
2824 2876 2.041405 GAGTGGAGGAGGGGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
2825 2877 2.041405 GGAGTGGAGGAGGGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
2826 2878 1.761780 AAAGGAGTGGAGGAGGGGGA 61.762 60.000 0.00 0.00 0.00 4.81
2827 2879 0.044244 TAAAGGAGTGGAGGAGGGGG 59.956 60.000 0.00 0.00 0.00 5.40
2828 2880 2.198334 ATAAAGGAGTGGAGGAGGGG 57.802 55.000 0.00 0.00 0.00 4.79
2829 2881 5.403512 TGTATATAAAGGAGTGGAGGAGGG 58.596 45.833 0.00 0.00 0.00 4.30
2830 2882 5.482175 CCTGTATATAAAGGAGTGGAGGAGG 59.518 48.000 13.20 0.00 35.40 4.30
2831 2883 5.482175 CCCTGTATATAAAGGAGTGGAGGAG 59.518 48.000 19.32 0.00 35.40 3.69
2832 2884 5.403512 CCCTGTATATAAAGGAGTGGAGGA 58.596 45.833 19.32 0.00 35.40 3.71
2833 2885 4.532521 CCCCTGTATATAAAGGAGTGGAGG 59.467 50.000 19.32 7.73 35.40 4.30
2834 2886 5.403512 TCCCCTGTATATAAAGGAGTGGAG 58.596 45.833 19.32 2.62 35.40 3.86
2835 2887 5.403512 CTCCCCTGTATATAAAGGAGTGGA 58.596 45.833 19.32 15.43 36.87 4.02
2836 2888 4.532521 CCTCCCCTGTATATAAAGGAGTGG 59.467 50.000 19.32 12.84 39.43 4.00
2837 2889 4.532521 CCCTCCCCTGTATATAAAGGAGTG 59.467 50.000 19.32 7.88 39.43 3.51
2838 2890 4.452363 CCCCTCCCCTGTATATAAAGGAGT 60.452 50.000 19.32 0.00 39.43 3.85
2839 2891 4.104831 CCCCTCCCCTGTATATAAAGGAG 58.895 52.174 19.32 7.33 40.51 3.69
2840 2892 3.181388 CCCCCTCCCCTGTATATAAAGGA 60.181 52.174 19.32 5.95 35.40 3.36
2841 2893 3.190439 CCCCCTCCCCTGTATATAAAGG 58.810 54.545 11.67 11.67 0.00 3.11
2842 2894 2.576648 GCCCCCTCCCCTGTATATAAAG 59.423 54.545 0.00 0.00 0.00 1.85
2843 2895 2.089292 TGCCCCCTCCCCTGTATATAAA 60.089 50.000 0.00 0.00 0.00 1.40
2844 2896 1.514893 TGCCCCCTCCCCTGTATATAA 59.485 52.381 0.00 0.00 0.00 0.98
2845 2897 1.181731 TGCCCCCTCCCCTGTATATA 58.818 55.000 0.00 0.00 0.00 0.86
2846 2898 0.475828 GTGCCCCCTCCCCTGTATAT 60.476 60.000 0.00 0.00 0.00 0.86
2847 2899 1.074014 GTGCCCCCTCCCCTGTATA 60.074 63.158 0.00 0.00 0.00 1.47
2848 2900 2.368329 GTGCCCCCTCCCCTGTAT 60.368 66.667 0.00 0.00 0.00 2.29
2849 2901 4.752594 GGTGCCCCCTCCCCTGTA 62.753 72.222 0.00 0.00 0.00 2.74
2860 2912 1.077716 GTGTGTCTATGGGGTGCCC 60.078 63.158 0.00 0.00 45.71 5.36
2861 2913 0.037590 TTGTGTGTCTATGGGGTGCC 59.962 55.000 0.00 0.00 0.00 5.01
2862 2914 1.271379 ACTTGTGTGTCTATGGGGTGC 60.271 52.381 0.00 0.00 0.00 5.01
2863 2915 2.813754 CAACTTGTGTGTCTATGGGGTG 59.186 50.000 0.00 0.00 0.00 4.61
2864 2916 2.708861 TCAACTTGTGTGTCTATGGGGT 59.291 45.455 0.00 0.00 0.00 4.95
2865 2917 3.417069 TCAACTTGTGTGTCTATGGGG 57.583 47.619 0.00 0.00 0.00 4.96
2866 2918 4.578871 TGATCAACTTGTGTGTCTATGGG 58.421 43.478 0.00 0.00 0.00 4.00
2867 2919 6.372381 TCAATGATCAACTTGTGTGTCTATGG 59.628 38.462 0.00 0.00 0.00 2.74
2868 2920 7.368480 TCAATGATCAACTTGTGTGTCTATG 57.632 36.000 0.00 0.00 0.00 2.23
2869 2921 8.045507 AGATCAATGATCAACTTGTGTGTCTAT 58.954 33.333 23.41 0.00 41.12 1.98
2870 2922 7.389232 AGATCAATGATCAACTTGTGTGTCTA 58.611 34.615 23.41 0.00 41.12 2.59
2871 2923 6.236409 AGATCAATGATCAACTTGTGTGTCT 58.764 36.000 23.41 0.00 41.12 3.41
2872 2924 6.370994 AGAGATCAATGATCAACTTGTGTGTC 59.629 38.462 23.41 9.28 41.12 3.67
2873 2925 6.236409 AGAGATCAATGATCAACTTGTGTGT 58.764 36.000 23.41 0.33 41.12 3.72
2874 2926 6.738832 AGAGATCAATGATCAACTTGTGTG 57.261 37.500 23.41 0.00 41.12 3.82
2875 2927 7.065563 GCTAAGAGATCAATGATCAACTTGTGT 59.934 37.037 28.10 15.50 41.12 3.72
2876 2928 7.408123 GCTAAGAGATCAATGATCAACTTGTG 58.592 38.462 28.10 23.32 41.12 3.33
2877 2929 6.541641 GGCTAAGAGATCAATGATCAACTTGT 59.458 38.462 28.10 16.19 41.12 3.16
2878 2930 6.292757 CGGCTAAGAGATCAATGATCAACTTG 60.293 42.308 28.10 22.07 41.12 3.16
2879 2931 5.757320 CGGCTAAGAGATCAATGATCAACTT 59.243 40.000 25.67 25.67 41.12 2.66
2880 2932 5.163364 ACGGCTAAGAGATCAATGATCAACT 60.163 40.000 23.41 18.16 41.12 3.16
2881 2933 5.050499 CACGGCTAAGAGATCAATGATCAAC 60.050 44.000 23.41 16.46 41.12 3.18
2882 2934 5.052481 CACGGCTAAGAGATCAATGATCAA 58.948 41.667 23.41 6.70 41.12 2.57
2883 2935 4.100035 ACACGGCTAAGAGATCAATGATCA 59.900 41.667 23.41 0.00 41.12 2.92
2884 2936 4.447054 CACACGGCTAAGAGATCAATGATC 59.553 45.833 15.01 15.01 39.17 2.92
2885 2937 4.375272 CACACGGCTAAGAGATCAATGAT 58.625 43.478 0.00 0.00 0.00 2.45
2886 2938 3.785486 CACACGGCTAAGAGATCAATGA 58.215 45.455 0.00 0.00 0.00 2.57
2887 2939 2.286294 GCACACGGCTAAGAGATCAATG 59.714 50.000 0.00 0.00 40.25 2.82
2888 2940 2.555199 GCACACGGCTAAGAGATCAAT 58.445 47.619 0.00 0.00 40.25 2.57
2889 2941 1.735700 CGCACACGGCTAAGAGATCAA 60.736 52.381 0.00 0.00 41.67 2.57
2890 2942 0.179137 CGCACACGGCTAAGAGATCA 60.179 55.000 0.00 0.00 41.67 2.92
2891 2943 2.582959 CGCACACGGCTAAGAGATC 58.417 57.895 0.00 0.00 41.67 2.75
2892 2944 4.814900 CGCACACGGCTAAGAGAT 57.185 55.556 0.00 0.00 41.67 2.75


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

AutoCloner maintained by Alex Coulton.