Multiple sequence alignment - TraesCS6D01G390000

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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 TraesCS6D01G390000 chr6D 100.000 4318 0 0 1 4318 465097337 465101654 0.000000e+00 7974
1 TraesCS6D01G390000 chr6A 90.791 1618 77 30 2112 3695 611806857 611808436 0.000000e+00 2097
2 TraesCS6D01G390000 chr6A 85.364 1305 108 41 838 2116 611805581 611806828 0.000000e+00 1275
3 TraesCS6D01G390000 chr6A 87.224 407 31 10 3920 4318 611809004 611809397 1.100000e-120 444
4 TraesCS6D01G390000 chr6A 88.983 118 7 4 3700 3811 611808484 611808601 1.620000e-29 141
5 TraesCS6D01G390000 chr6B 92.251 1226 59 15 2112 3320 709219579 709218373 0.000000e+00 1705
6 TraesCS6D01G390000 chr6B 83.431 1533 106 43 642 2115 709221052 709219609 0.000000e+00 1288
7 TraesCS6D01G390000 chr6B 85.016 634 87 7 12 640 337877428 337876798 4.710000e-179 638
8 TraesCS6D01G390000 chr6B 88.353 249 12 6 3354 3585 709218371 709218123 2.540000e-72 283
9 TraesCS6D01G390000 chr2D 96.885 642 19 1 1 641 260959636 260960277 0.000000e+00 1074
10 TraesCS6D01G390000 chr7D 96.220 635 23 1 8 641 632454532 632453898 0.000000e+00 1038
11 TraesCS6D01G390000 chr3D 96.801 594 18 1 49 641 609572702 609573295 0.000000e+00 990
12 TraesCS6D01G390000 chr7A 93.887 638 38 1 5 641 47427305 47426668 0.000000e+00 961
13 TraesCS6D01G390000 chr7A 91.038 636 56 1 7 641 91433713 91434348 0.000000e+00 857
14 TraesCS6D01G390000 chr4B 92.947 638 44 1 5 641 25553807 25554444 0.000000e+00 928
15 TraesCS6D01G390000 chr2B 92.151 637 49 1 5 640 621244458 621245094 0.000000e+00 898
16 TraesCS6D01G390000 chr7B 87.578 644 71 6 5 640 616433673 616433031 0.000000e+00 737


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 TraesCS6D01G390000 chr6D 465097337 465101654 4317 False 7974.00 7974 100.000000 1 4318 1 chr6D.!!$F1 4317
1 TraesCS6D01G390000 chr6A 611805581 611809397 3816 False 989.25 2097 88.090500 838 4318 4 chr6A.!!$F1 3480
2 TraesCS6D01G390000 chr6B 709218123 709221052 2929 True 1092.00 1705 88.011667 642 3585 3 chr6B.!!$R2 2943
3 TraesCS6D01G390000 chr6B 337876798 337877428 630 True 638.00 638 85.016000 12 640 1 chr6B.!!$R1 628
4 TraesCS6D01G390000 chr2D 260959636 260960277 641 False 1074.00 1074 96.885000 1 641 1 chr2D.!!$F1 640
5 TraesCS6D01G390000 chr7D 632453898 632454532 634 True 1038.00 1038 96.220000 8 641 1 chr7D.!!$R1 633
6 TraesCS6D01G390000 chr3D 609572702 609573295 593 False 990.00 990 96.801000 49 641 1 chr3D.!!$F1 592
7 TraesCS6D01G390000 chr7A 47426668 47427305 637 True 961.00 961 93.887000 5 641 1 chr7A.!!$R1 636
8 TraesCS6D01G390000 chr7A 91433713 91434348 635 False 857.00 857 91.038000 7 641 1 chr7A.!!$F1 634
9 TraesCS6D01G390000 chr4B 25553807 25554444 637 False 928.00 928 92.947000 5 641 1 chr4B.!!$F1 636
10 TraesCS6D01G390000 chr2B 621244458 621245094 636 False 898.00 898 92.151000 5 640 1 chr2B.!!$F1 635
11 TraesCS6D01G390000 chr7B 616433031 616433673 642 True 737.00 737 87.578000 5 640 1 chr7B.!!$R1 635

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
962 1005 0.105039 GTGGATAAGAGAGTGCCCCG 59.895 60.0 0.00 0.0 0.00 5.73 F
1446 1518 0.107017 ATGCTGGCCATTAGCTTCGT 60.107 50.0 5.51 0.0 43.05 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2162 0.729116 ATGCGAATCTGAACTTGCGG 59.271 50.0 0.0 0.0 0.0 5.69 R
3330 3490 0.257039 ACCATCCACTGAATGCCCTC 59.743 55.0 0.0 0.0 0.0 4.30 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
649 660 2.000825 TAACCTGCACCTGGGCACAA 62.001 55.000 5.85 0.00 39.25 3.33
656 667 0.827089 CACCTGGGCACAATTGTGGA 60.827 55.000 33.56 4.70 45.72 4.02
689 700 1.608590 ACAACCCATTTCTTCTGTGCG 59.391 47.619 0.00 0.00 0.00 5.34
703 714 3.067106 TCTGTGCGTGGAAAGAAATCTC 58.933 45.455 0.00 0.00 0.00 2.75
708 719 2.095718 GCGTGGAAAGAAATCTCACCAC 60.096 50.000 19.77 19.77 42.75 4.16
709 720 3.403038 CGTGGAAAGAAATCTCACCACT 58.597 45.455 23.51 0.00 43.34 4.00
710 721 3.187227 CGTGGAAAGAAATCTCACCACTG 59.813 47.826 23.51 17.41 43.34 3.66
711 722 3.503748 GTGGAAAGAAATCTCACCACTGG 59.496 47.826 21.20 0.00 42.81 4.00
712 723 2.489722 GGAAAGAAATCTCACCACTGGC 59.510 50.000 0.00 0.00 0.00 4.85
713 724 1.813513 AAGAAATCTCACCACTGGCG 58.186 50.000 0.00 0.00 0.00 5.69
714 725 0.687354 AGAAATCTCACCACTGGCGT 59.313 50.000 0.00 0.00 0.00 5.68
718 729 1.195115 ATCTCACCACTGGCGTACAT 58.805 50.000 0.00 0.00 0.00 2.29
738 760 5.556355 CATGCAATGTATCACTTGTCACT 57.444 39.130 0.00 0.00 40.20 3.41
740 762 6.712549 CATGCAATGTATCACTTGTCACTAG 58.287 40.000 0.00 0.00 40.20 2.57
750 772 3.056250 CACTTGTCACTAGCAGAGGACAT 60.056 47.826 0.00 0.00 36.12 3.06
758 780 0.252421 AGCAGAGGACATGGGAGTGA 60.252 55.000 0.00 0.00 0.00 3.41
759 781 0.835941 GCAGAGGACATGGGAGTGAT 59.164 55.000 0.00 0.00 0.00 3.06
762 784 3.570540 CAGAGGACATGGGAGTGATCTA 58.429 50.000 0.00 0.00 0.00 1.98
857 898 3.541632 ACAGTTGACGGCCCATATTAAG 58.458 45.455 0.00 0.00 0.00 1.85
861 902 1.069513 TGACGGCCCATATTAAGACCG 59.930 52.381 0.00 0.00 45.86 4.79
894 936 1.228063 CCCAGAGCCCATCCGAATG 60.228 63.158 0.00 0.00 0.00 2.67
900 942 2.194056 CCCATCCGAATGCTGCCT 59.806 61.111 0.00 0.00 0.00 4.75
962 1005 0.105039 GTGGATAAGAGAGTGCCCCG 59.895 60.000 0.00 0.00 0.00 5.73
1079 1138 2.840102 CGCCTTCTCCTCCCCGAT 60.840 66.667 0.00 0.00 0.00 4.18
1092 1151 3.917760 CCGATCCGCCTCCAGACC 61.918 72.222 0.00 0.00 0.00 3.85
1125 1184 2.264480 CTGGTCATCGTCGCCCAA 59.736 61.111 0.00 0.00 0.00 4.12
1181 1240 4.400251 CCGTCACTCCCCCTCCCT 62.400 72.222 0.00 0.00 0.00 4.20
1183 1242 1.918800 CGTCACTCCCCCTCCCTTT 60.919 63.158 0.00 0.00 0.00 3.11
1196 1255 4.840680 CCCCTCCCTTTCAATTCTTCTTTT 59.159 41.667 0.00 0.00 0.00 2.27
1203 1262 7.014615 TCCCTTTCAATTCTTCTTTTCTGAAGG 59.985 37.037 4.71 0.00 42.54 3.46
1221 1280 2.815722 GCATTCGCCTCCGTAGATC 58.184 57.895 0.00 0.00 35.54 2.75
1258 1317 2.226912 CGGCAGGATAGTAGTAGTGCTC 59.773 54.545 0.00 0.00 0.00 4.26
1263 1322 2.226912 GGATAGTAGTAGTGCTCCGCAG 59.773 54.545 0.00 0.00 40.08 5.18
1265 1324 1.384525 AGTAGTAGTGCTCCGCAGAG 58.615 55.000 0.00 0.00 40.08 3.35
1280 1339 1.801025 GCAGAGGCTCGAGCTAGTTTC 60.801 57.143 34.46 22.58 41.70 2.78
1336 1395 7.148507 GGAAAAATGTATCTGACAGACTGACAG 60.149 40.741 23.65 23.65 42.79 3.51
1341 1400 2.937519 TCTGACAGACTGACAGACACT 58.062 47.619 26.80 2.79 42.42 3.55
1342 1401 4.086706 TCTGACAGACTGACAGACACTA 57.913 45.455 26.80 10.39 42.42 2.74
1343 1402 4.657013 TCTGACAGACTGACAGACACTAT 58.343 43.478 26.80 0.00 42.42 2.12
1344 1403 4.457257 TCTGACAGACTGACAGACACTATG 59.543 45.833 26.80 6.82 42.42 2.23
1353 1412 6.582636 ACTGACAGACACTATGAAGAAACAA 58.417 36.000 10.08 0.00 0.00 2.83
1354 1413 6.480320 ACTGACAGACACTATGAAGAAACAAC 59.520 38.462 10.08 0.00 0.00 3.32
1366 1425 3.896648 AGAAACAACAGTAATGTGGCG 57.103 42.857 0.00 0.00 0.00 5.69
1368 1427 3.003275 AGAAACAACAGTAATGTGGCGTG 59.997 43.478 0.00 0.00 0.00 5.34
1372 1431 1.722011 ACAGTAATGTGGCGTGCTAC 58.278 50.000 0.00 0.93 0.00 3.58
1373 1432 1.275291 ACAGTAATGTGGCGTGCTACT 59.725 47.619 9.76 0.00 0.00 2.57
1378 1437 1.119684 ATGTGGCGTGCTACTATCCA 58.880 50.000 9.76 0.00 0.00 3.41
1430 1502 1.268265 GCCACGGAAAATCGAAATGC 58.732 50.000 0.00 0.00 0.00 3.56
1446 1518 0.107017 ATGCTGGCCATTAGCTTCGT 60.107 50.000 5.51 0.00 43.05 3.85
1447 1519 1.026182 TGCTGGCCATTAGCTTCGTG 61.026 55.000 5.51 0.00 43.05 4.35
1448 1520 1.723870 CTGGCCATTAGCTTCGTGC 59.276 57.895 5.51 0.00 43.05 5.34
1487 1559 3.181521 GCAACTGTTTCTGTTTGTTTGGC 60.182 43.478 0.00 0.00 0.00 4.52
1488 1560 2.874849 ACTGTTTCTGTTTGTTTGGCG 58.125 42.857 0.00 0.00 0.00 5.69
1489 1561 1.587946 CTGTTTCTGTTTGTTTGGCGC 59.412 47.619 0.00 0.00 0.00 6.53
1490 1562 0.927537 GTTTCTGTTTGTTTGGCGCC 59.072 50.000 22.73 22.73 0.00 6.53
1491 1563 0.820871 TTTCTGTTTGTTTGGCGCCT 59.179 45.000 29.70 0.00 0.00 5.52
1492 1564 0.820871 TTCTGTTTGTTTGGCGCCTT 59.179 45.000 29.70 0.00 0.00 4.35
1493 1565 0.820871 TCTGTTTGTTTGGCGCCTTT 59.179 45.000 29.70 0.00 0.00 3.11
1494 1566 1.202359 TCTGTTTGTTTGGCGCCTTTC 60.202 47.619 29.70 17.26 0.00 2.62
1495 1567 0.526524 TGTTTGTTTGGCGCCTTTCG 60.527 50.000 29.70 0.00 42.12 3.46
1619 1700 7.496529 TGATTTGTTAGTTATAGCAGATGGC 57.503 36.000 0.00 0.00 45.30 4.40
1640 1721 0.598065 GAAGGCACAGCGGTTTGATT 59.402 50.000 4.68 0.00 0.00 2.57
1641 1722 0.314935 AAGGCACAGCGGTTTGATTG 59.685 50.000 4.68 0.00 0.00 2.67
1644 1725 2.800096 CACAGCGGTTTGATTGTGC 58.200 52.632 0.00 0.00 35.11 4.57
1646 1727 2.082366 CAGCGGTTTGATTGTGCGC 61.082 57.895 0.00 0.00 0.00 6.09
1650 1731 2.050533 GTTTGATTGTGCGCGGCA 60.051 55.556 8.83 3.20 35.60 5.69
1652 1733 1.066422 TTTGATTGTGCGCGGCAAA 59.934 47.368 18.57 13.15 41.47 3.68
1664 1745 2.950673 GGCAAATGCGACCGACAA 59.049 55.556 0.00 0.00 43.26 3.18
1677 1774 1.344837 CGACAACGTGCCATCATCG 59.655 57.895 0.00 0.00 34.56 3.84
1723 1828 3.507233 TGGTTCTGATGCTGTTTCATTCC 59.493 43.478 0.00 0.00 0.00 3.01
1740 1845 1.039068 TCCATTGGTTTGGTGCTGTG 58.961 50.000 1.86 0.00 38.01 3.66
1788 1893 2.293170 GAGATAAGTGGCAAGAAGGGC 58.707 52.381 0.00 0.00 0.00 5.19
1892 1997 0.109226 AAGTAACGTCTCTGCCTCGC 60.109 55.000 0.00 0.00 0.00 5.03
1982 2087 1.661821 CGATAGGCAGCGGCACTAC 60.662 63.158 11.88 4.58 43.71 2.73
2028 2133 1.633561 CGTGAACTGCTCATCGATGT 58.366 50.000 24.09 4.40 36.14 3.06
2036 2141 1.878734 TGCTCATCGATGTGTTTTGCA 59.121 42.857 24.09 19.89 0.00 4.08
2037 2142 2.095617 TGCTCATCGATGTGTTTTGCAG 60.096 45.455 24.09 12.80 0.00 4.41
2038 2143 2.095567 GCTCATCGATGTGTTTTGCAGT 60.096 45.455 24.09 0.00 0.00 4.40
2057 2162 3.126343 CAGTAGTATGTTTTTCCCGTGCC 59.874 47.826 0.00 0.00 0.00 5.01
2073 2178 1.298157 TGCCCGCAAGTTCAGATTCG 61.298 55.000 0.00 0.00 0.00 3.34
2097 2202 5.339177 CATTGCGTAATAATTCAGTGGCAA 58.661 37.500 0.00 8.09 42.46 4.52
2200 2339 5.208463 TGCTTGTTTTAAGGGATGGTTTC 57.792 39.130 0.00 0.00 0.00 2.78
2236 2375 1.970640 GAAGGCTGGGTTGGTTTTCAT 59.029 47.619 0.00 0.00 0.00 2.57
2331 2481 1.956477 GGCAATGTTCAGTCTGGTGTT 59.044 47.619 0.00 0.00 0.00 3.32
2417 2567 1.753649 CAGGAGAGAATCGAGGCTGAA 59.246 52.381 0.00 0.00 42.67 3.02
2432 2582 3.653352 AGGCTGAAAAGAAGAGGGTAAGT 59.347 43.478 0.00 0.00 0.00 2.24
2456 2606 7.499232 AGTGAATACTGTATATGTTTGAAGGCC 59.501 37.037 0.00 0.00 35.34 5.19
2471 2621 8.087750 TGTTTGAAGGCCTGATAACAAAAATAG 58.912 33.333 19.02 0.00 0.00 1.73
2533 2683 4.151417 CAACGCTTGCGGATTTGG 57.849 55.556 19.19 0.00 0.00 3.28
2543 2693 4.697352 GCTTGCGGATTTGGTCATATATCT 59.303 41.667 0.00 0.00 0.00 1.98
2853 3012 5.411669 ACTCCGGAATCATTTTGTACTTGAC 59.588 40.000 5.23 0.00 0.00 3.18
2985 3144 2.802816 AGTTGCACAGTTTCATCGTCTC 59.197 45.455 0.00 0.00 0.00 3.36
2986 3145 2.524569 TGCACAGTTTCATCGTCTCA 57.475 45.000 0.00 0.00 0.00 3.27
2987 3146 2.135139 TGCACAGTTTCATCGTCTCAC 58.865 47.619 0.00 0.00 0.00 3.51
2988 3147 2.135139 GCACAGTTTCATCGTCTCACA 58.865 47.619 0.00 0.00 0.00 3.58
2989 3148 2.096713 GCACAGTTTCATCGTCTCACAC 60.097 50.000 0.00 0.00 0.00 3.82
2990 3149 3.123050 CACAGTTTCATCGTCTCACACA 58.877 45.455 0.00 0.00 0.00 3.72
2991 3150 3.742882 CACAGTTTCATCGTCTCACACAT 59.257 43.478 0.00 0.00 0.00 3.21
2992 3151 4.212004 CACAGTTTCATCGTCTCACACATT 59.788 41.667 0.00 0.00 0.00 2.71
2996 3155 5.406780 AGTTTCATCGTCTCACACATTTCTC 59.593 40.000 0.00 0.00 0.00 2.87
3007 3166 4.878971 TCACACATTTCTCGTTTTCTCCAA 59.121 37.500 0.00 0.00 0.00 3.53
3009 3168 5.853282 CACACATTTCTCGTTTTCTCCAATC 59.147 40.000 0.00 0.00 0.00 2.67
3096 3255 3.064207 CAAGTCGCAGCTTAACAGGTAA 58.936 45.455 0.00 0.00 0.00 2.85
3126 3286 3.876914 TCCTTTCAAGTGTGTACAGCAAG 59.123 43.478 0.00 0.00 0.00 4.01
3131 3291 2.332063 AGTGTGTACAGCAAGCAACT 57.668 45.000 0.00 0.00 0.00 3.16
3146 3306 5.644644 CAAGCAACTAAACTTCCCATCATC 58.355 41.667 0.00 0.00 0.00 2.92
3150 3310 3.782046 ACTAAACTTCCCATCATCGTCG 58.218 45.455 0.00 0.00 0.00 5.12
3151 3311 1.369625 AAACTTCCCATCATCGTCGC 58.630 50.000 0.00 0.00 0.00 5.19
3152 3312 0.537188 AACTTCCCATCATCGTCGCT 59.463 50.000 0.00 0.00 0.00 4.93
3153 3313 0.537188 ACTTCCCATCATCGTCGCTT 59.463 50.000 0.00 0.00 0.00 4.68
3154 3314 1.212616 CTTCCCATCATCGTCGCTTC 58.787 55.000 0.00 0.00 0.00 3.86
3155 3315 0.527600 TTCCCATCATCGTCGCTTCG 60.528 55.000 0.00 0.00 0.00 3.79
3156 3316 2.589492 CCCATCATCGTCGCTTCGC 61.589 63.158 0.00 0.00 0.00 4.70
3157 3317 1.589993 CCATCATCGTCGCTTCGCT 60.590 57.895 0.00 0.00 0.00 4.93
3158 3318 1.148157 CCATCATCGTCGCTTCGCTT 61.148 55.000 0.00 0.00 0.00 4.68
3159 3319 1.477105 CATCATCGTCGCTTCGCTTA 58.523 50.000 0.00 0.00 0.00 3.09
3160 3320 1.188138 CATCATCGTCGCTTCGCTTAC 59.812 52.381 0.00 0.00 0.00 2.34
3161 3321 0.860203 TCATCGTCGCTTCGCTTACG 60.860 55.000 0.00 0.00 37.09 3.18
3173 3333 3.955771 TCGCTTACGGGCAAATTAATC 57.044 42.857 0.00 0.00 40.63 1.75
3203 3363 1.276989 TGGAAACCATGTAGGGACGTC 59.723 52.381 7.13 7.13 43.89 4.34
3251 3411 2.905880 CGCGAGGTCGGGGAGTAT 60.906 66.667 0.00 0.00 46.57 2.12
3254 3414 1.673808 GCGAGGTCGGGGAGTATGTT 61.674 60.000 0.89 0.00 40.23 2.71
3278 3438 0.692419 AGATCAAGCTCCACCCCGAT 60.692 55.000 0.00 0.00 0.00 4.18
3324 3484 1.090052 GTATGCCAAGTGAGCCGGTC 61.090 60.000 1.90 0.00 0.00 4.79
3330 3490 3.883744 AAGTGAGCCGGTCGCAAGG 62.884 63.158 13.32 0.00 41.38 3.61
3333 3493 4.821589 GAGCCGGTCGCAAGGAGG 62.822 72.222 1.90 0.00 41.38 4.30
3352 3512 1.386533 GGCATTCAGTGGATGGTGAG 58.613 55.000 13.46 0.00 0.00 3.51
3374 3536 4.013728 GGTCTGATCTCGCCATATACTCT 58.986 47.826 0.00 0.00 0.00 3.24
3463 3632 5.454755 GGCCTTGTATACATTAGGAGAAGCA 60.455 44.000 22.61 0.00 0.00 3.91
3584 3771 1.333177 GCTATCCTCGTCATGGTCCT 58.667 55.000 0.00 0.00 0.00 3.85
3585 3772 1.689273 GCTATCCTCGTCATGGTCCTT 59.311 52.381 0.00 0.00 0.00 3.36
3586 3773 2.103263 GCTATCCTCGTCATGGTCCTTT 59.897 50.000 0.00 0.00 0.00 3.11
3622 3809 3.632333 TCCTCGTCATGATCCTACTTGT 58.368 45.455 0.00 0.00 0.00 3.16
3625 3812 5.833667 TCCTCGTCATGATCCTACTTGTATT 59.166 40.000 0.00 0.00 0.00 1.89
3628 3815 6.273071 TCGTCATGATCCTACTTGTATTGTG 58.727 40.000 0.00 0.00 0.00 3.33
3634 3821 7.247456 TGATCCTACTTGTATTGTGTAACCA 57.753 36.000 0.00 0.00 34.36 3.67
3636 3823 7.604927 TGATCCTACTTGTATTGTGTAACCAAC 59.395 37.037 0.00 0.00 34.36 3.77
3637 3824 7.069877 TCCTACTTGTATTGTGTAACCAACT 57.930 36.000 0.00 0.00 34.36 3.16
3638 3825 7.156673 TCCTACTTGTATTGTGTAACCAACTC 58.843 38.462 0.00 0.00 34.36 3.01
3695 3884 2.030562 AAAGAGGCACACGTCGGG 59.969 61.111 0.00 0.00 35.81 5.14
3698 3887 4.309950 GAGGCACACGTCGGGGTT 62.310 66.667 0.00 0.00 0.00 4.11
3740 3972 3.396260 TCCGACCAGGAGTTGTTTTAG 57.604 47.619 0.00 0.00 45.98 1.85
3741 3973 2.038033 TCCGACCAGGAGTTGTTTTAGG 59.962 50.000 0.00 0.00 45.98 2.69
3844 4422 4.839706 ATGCCCGGCCCATTGTCC 62.840 66.667 7.03 0.00 0.00 4.02
3865 4444 3.131478 GACATTTGGGGCGTCCGG 61.131 66.667 0.00 0.00 38.76 5.14
3873 4452 3.152400 GGGCGTCCGGTAGGTGAT 61.152 66.667 0.00 0.00 39.05 3.06
3874 4453 2.106332 GGCGTCCGGTAGGTGATG 59.894 66.667 0.00 0.00 39.05 3.07
3875 4454 2.718073 GGCGTCCGGTAGGTGATGT 61.718 63.158 0.00 0.00 39.05 3.06
3876 4455 1.518572 GCGTCCGGTAGGTGATGTG 60.519 63.158 0.00 0.00 39.05 3.21
3877 4456 1.518572 CGTCCGGTAGGTGATGTGC 60.519 63.158 0.00 0.00 39.05 4.57
3878 4457 1.594833 GTCCGGTAGGTGATGTGCA 59.405 57.895 0.00 0.00 39.05 4.57
3879 4458 0.739813 GTCCGGTAGGTGATGTGCAC 60.740 60.000 10.75 10.75 46.98 4.57
3880 4459 0.902984 TCCGGTAGGTGATGTGCACT 60.903 55.000 19.41 3.19 46.86 4.40
3881 4460 0.740868 CCGGTAGGTGATGTGCACTG 60.741 60.000 19.41 0.00 46.86 3.66
3882 4461 1.361668 CGGTAGGTGATGTGCACTGC 61.362 60.000 19.41 10.38 46.86 4.40
3883 4462 0.321564 GGTAGGTGATGTGCACTGCA 60.322 55.000 19.41 13.00 46.86 4.41
3884 4463 1.081892 GTAGGTGATGTGCACTGCAG 58.918 55.000 19.41 13.48 46.86 4.41
3885 4464 0.036105 TAGGTGATGTGCACTGCAGG 60.036 55.000 19.93 8.27 46.86 4.85
3886 4465 1.601759 GGTGATGTGCACTGCAGGT 60.602 57.895 19.93 0.24 46.86 4.00
3887 4466 0.321564 GGTGATGTGCACTGCAGGTA 60.322 55.000 19.93 3.66 46.86 3.08
3888 4467 0.798776 GTGATGTGCACTGCAGGTAC 59.201 55.000 19.93 16.18 44.27 3.34
3889 4468 0.396060 TGATGTGCACTGCAGGTACA 59.604 50.000 19.93 20.92 40.08 2.90
3890 4469 0.798776 GATGTGCACTGCAGGTACAC 59.201 55.000 21.65 21.85 40.08 2.90
3891 4470 0.397941 ATGTGCACTGCAGGTACACT 59.602 50.000 26.18 15.02 41.46 3.55
3892 4471 0.180171 TGTGCACTGCAGGTACACTT 59.820 50.000 26.18 1.82 41.46 3.16
3893 4472 1.414550 TGTGCACTGCAGGTACACTTA 59.585 47.619 26.18 12.26 41.46 2.24
3894 4473 2.069273 GTGCACTGCAGGTACACTTAG 58.931 52.381 19.93 0.00 40.08 2.18
3895 4474 1.079503 GCACTGCAGGTACACTTAGC 58.920 55.000 19.93 3.88 0.00 3.09
3896 4475 1.726853 CACTGCAGGTACACTTAGCC 58.273 55.000 19.93 0.00 0.00 3.93
3897 4476 1.276421 CACTGCAGGTACACTTAGCCT 59.724 52.381 19.93 0.00 0.00 4.58
3898 4477 1.978580 ACTGCAGGTACACTTAGCCTT 59.021 47.619 19.93 0.00 0.00 4.35
3899 4478 2.372172 ACTGCAGGTACACTTAGCCTTT 59.628 45.455 19.93 0.00 0.00 3.11
3900 4479 3.003480 CTGCAGGTACACTTAGCCTTTC 58.997 50.000 5.57 0.00 0.00 2.62
3901 4480 2.637872 TGCAGGTACACTTAGCCTTTCT 59.362 45.455 0.00 0.00 0.00 2.52
3902 4481 3.072476 TGCAGGTACACTTAGCCTTTCTT 59.928 43.478 0.00 0.00 0.00 2.52
3903 4482 4.072839 GCAGGTACACTTAGCCTTTCTTT 58.927 43.478 0.00 0.00 0.00 2.52
3904 4483 4.083271 GCAGGTACACTTAGCCTTTCTTTG 60.083 45.833 0.00 0.00 0.00 2.77
3905 4484 5.063880 CAGGTACACTTAGCCTTTCTTTGT 58.936 41.667 0.00 0.00 0.00 2.83
3906 4485 5.179555 CAGGTACACTTAGCCTTTCTTTGTC 59.820 44.000 0.00 0.00 0.00 3.18
3907 4486 5.071923 AGGTACACTTAGCCTTTCTTTGTCT 59.928 40.000 0.00 0.00 0.00 3.41
3908 4487 5.179555 GGTACACTTAGCCTTTCTTTGTCTG 59.820 44.000 0.00 0.00 0.00 3.51
3909 4488 4.137543 ACACTTAGCCTTTCTTTGTCTGG 58.862 43.478 0.00 0.00 0.00 3.86
3910 4489 4.137543 CACTTAGCCTTTCTTTGTCTGGT 58.862 43.478 0.00 0.00 0.00 4.00
3911 4490 5.163237 ACACTTAGCCTTTCTTTGTCTGGTA 60.163 40.000 0.00 0.00 0.00 3.25
3912 4491 5.179555 CACTTAGCCTTTCTTTGTCTGGTAC 59.820 44.000 0.00 0.00 0.00 3.34
3913 4492 3.857157 AGCCTTTCTTTGTCTGGTACA 57.143 42.857 0.00 0.00 35.88 2.90
3943 4522 1.882623 GCATTGCAGATACCCTTAGCC 59.117 52.381 3.15 0.00 0.00 3.93
3944 4523 2.487986 GCATTGCAGATACCCTTAGCCT 60.488 50.000 3.15 0.00 0.00 4.58
3947 4526 3.560636 TGCAGATACCCTTAGCCTTTC 57.439 47.619 0.00 0.00 0.00 2.62
3951 4530 4.336713 GCAGATACCCTTAGCCTTTCTTTG 59.663 45.833 0.00 0.00 0.00 2.77
3953 4532 5.586643 CAGATACCCTTAGCCTTTCTTTGTC 59.413 44.000 0.00 0.00 0.00 3.18
3995 4575 8.421249 AGACTGGGTTTCATTGATTTATTTCA 57.579 30.769 0.00 0.00 0.00 2.69
4036 4616 2.217429 TTTTTGCCGCTTTCACTTCC 57.783 45.000 0.00 0.00 0.00 3.46
4052 4632 6.110411 TCACTTCCGGTTCTTTCTTTCTAT 57.890 37.500 0.00 0.00 0.00 1.98
4158 4743 8.377681 AGTGACAACATATAAAAATACACGACG 58.622 33.333 0.00 0.00 0.00 5.12
4171 4756 2.223745 ACACGACGGGCATTACTTTTT 58.776 42.857 0.00 0.00 0.00 1.94
4175 4760 5.213675 CACGACGGGCATTACTTTTTAAAA 58.786 37.500 0.00 0.00 0.00 1.52
4177 4762 6.363896 CACGACGGGCATTACTTTTTAAAATT 59.636 34.615 0.55 0.00 0.00 1.82
4178 4763 6.583427 ACGACGGGCATTACTTTTTAAAATTC 59.417 34.615 0.55 0.00 0.00 2.17
4179 4764 6.583050 CGACGGGCATTACTTTTTAAAATTCA 59.417 34.615 0.55 0.00 0.00 2.57
4180 4765 7.274686 CGACGGGCATTACTTTTTAAAATTCAT 59.725 33.333 0.55 0.00 0.00 2.57
4181 4766 8.250538 ACGGGCATTACTTTTTAAAATTCATG 57.749 30.769 0.55 4.02 0.00 3.07
4182 4767 8.091449 ACGGGCATTACTTTTTAAAATTCATGA 58.909 29.630 0.55 0.00 0.00 3.07
4183 4768 8.930760 CGGGCATTACTTTTTAAAATTCATGAA 58.069 29.630 11.26 11.26 0.00 2.57
4214 4799 6.392354 TCTGAAATCCATGAACATCTTTTGC 58.608 36.000 0.00 0.00 0.00 3.68
4215 4800 6.209986 TCTGAAATCCATGAACATCTTTTGCT 59.790 34.615 0.00 0.00 0.00 3.91
4218 4803 5.831702 ATCCATGAACATCTTTTGCTCTC 57.168 39.130 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 2.733218 CCGCGTCTTCGTTCTGCA 60.733 61.111 4.92 0.00 39.49 4.41
457 467 2.756760 CCTTGCCTAAGGTACGTCTACA 59.243 50.000 0.00 0.00 46.92 2.74
659 670 0.033366 AATGGGTTGTTTGCTTCGGC 59.967 50.000 0.00 0.00 42.19 5.54
673 684 0.523072 CCACGCACAGAAGAAATGGG 59.477 55.000 0.00 0.00 0.00 4.00
689 700 3.503748 CCAGTGGTGAGATTTCTTTCCAC 59.496 47.826 18.75 18.75 43.50 4.02
703 714 1.233950 TTGCATGTACGCCAGTGGTG 61.234 55.000 21.37 21.37 39.41 4.17
718 729 4.631377 GCTAGTGACAAGTGATACATTGCA 59.369 41.667 0.00 0.00 0.00 4.08
725 747 4.399618 GTCCTCTGCTAGTGACAAGTGATA 59.600 45.833 0.00 0.00 0.00 2.15
738 760 1.007118 TCACTCCCATGTCCTCTGCTA 59.993 52.381 0.00 0.00 0.00 3.49
740 762 0.835941 ATCACTCCCATGTCCTCTGC 59.164 55.000 0.00 0.00 0.00 4.26
750 772 8.059461 TCACTAGTCTTTTATAGATCACTCCCA 58.941 37.037 0.00 0.00 34.79 4.37
762 784 9.877178 AGATTGTCGAAATCACTAGTCTTTTAT 57.123 29.630 17.03 0.00 0.00 1.40
889 931 4.121691 CCTCAGAGGCAGCATTCG 57.878 61.111 2.60 0.00 0.00 3.34
900 942 1.483415 GTATACGGTTTGGGCCTCAGA 59.517 52.381 4.53 0.00 0.00 3.27
1104 1163 2.951745 GCGACGATGACCAGCGAG 60.952 66.667 14.73 8.73 43.75 5.03
1125 1184 0.984995 GGTACTTCTTGACCCTGCCT 59.015 55.000 0.00 0.00 0.00 4.75
1157 1216 2.675772 GGGAGTGACGGACGGACT 60.676 66.667 0.00 0.00 0.00 3.85
1181 1240 7.111247 TGCCTTCAGAAAAGAAGAATTGAAA 57.889 32.000 5.34 0.00 46.18 2.69
1183 1242 6.906157 ATGCCTTCAGAAAAGAAGAATTGA 57.094 33.333 5.34 0.00 46.18 2.57
1203 1262 1.004277 CGATCTACGGAGGCGAATGC 61.004 60.000 5.07 0.00 38.25 3.56
1221 1280 1.423845 CCGATTTTGAGCCGTTCCG 59.576 57.895 0.00 0.00 0.00 4.30
1227 1286 1.876156 CTATCCTGCCGATTTTGAGCC 59.124 52.381 0.00 0.00 31.92 4.70
1228 1287 2.565841 ACTATCCTGCCGATTTTGAGC 58.434 47.619 0.00 0.00 31.92 4.26
1231 1290 5.692204 CACTACTACTATCCTGCCGATTTTG 59.308 44.000 0.00 0.00 31.92 2.44
1258 1317 3.192954 CTAGCTCGAGCCTCTGCGG 62.193 68.421 32.94 11.82 44.33 5.69
1263 1322 3.818773 AGATAGAAACTAGCTCGAGCCTC 59.181 47.826 32.94 20.35 43.38 4.70
1265 1324 4.577834 AAGATAGAAACTAGCTCGAGCC 57.422 45.455 32.94 16.86 43.38 4.70
1280 1339 3.873910 ACAATGTCACCGGGAAAGATAG 58.126 45.455 6.32 0.00 0.00 2.08
1336 1395 8.774586 ACATTACTGTTGTTTCTTCATAGTGTC 58.225 33.333 0.00 0.00 28.70 3.67
1337 1396 8.559536 CACATTACTGTTGTTTCTTCATAGTGT 58.440 33.333 0.00 0.00 31.62 3.55
1338 1397 8.017373 CCACATTACTGTTGTTTCTTCATAGTG 58.983 37.037 0.00 0.00 31.62 2.74
1339 1398 7.308589 GCCACATTACTGTTGTTTCTTCATAGT 60.309 37.037 0.00 0.00 31.62 2.12
1341 1400 6.348132 CGCCACATTACTGTTGTTTCTTCATA 60.348 38.462 0.00 0.00 31.62 2.15
1342 1401 5.562696 CGCCACATTACTGTTGTTTCTTCAT 60.563 40.000 0.00 0.00 31.62 2.57
1343 1402 4.260990 CGCCACATTACTGTTGTTTCTTCA 60.261 41.667 0.00 0.00 31.62 3.02
1344 1403 4.219033 CGCCACATTACTGTTGTTTCTTC 58.781 43.478 0.00 0.00 31.62 2.87
1353 1412 1.275291 AGTAGCACGCCACATTACTGT 59.725 47.619 0.00 0.00 35.44 3.55
1354 1413 2.010145 AGTAGCACGCCACATTACTG 57.990 50.000 0.00 0.00 0.00 2.74
1366 1425 1.002087 CGGGGGAATGGATAGTAGCAC 59.998 57.143 0.00 0.00 0.00 4.40
1368 1427 0.036294 GCGGGGGAATGGATAGTAGC 60.036 60.000 0.00 0.00 0.00 3.58
1372 1431 0.987294 ATGAGCGGGGGAATGGATAG 59.013 55.000 0.00 0.00 0.00 2.08
1373 1432 0.984230 GATGAGCGGGGGAATGGATA 59.016 55.000 0.00 0.00 0.00 2.59
1430 1502 1.723870 GCACGAAGCTAATGGCCAG 59.276 57.895 13.05 0.00 43.05 4.85
1489 1561 2.202810 GCGAGGAGAGGCGAAAGG 60.203 66.667 0.00 0.00 0.00 3.11
1490 1562 1.518133 CAGCGAGGAGAGGCGAAAG 60.518 63.158 0.00 0.00 0.00 2.62
1491 1563 2.573869 CAGCGAGGAGAGGCGAAA 59.426 61.111 0.00 0.00 0.00 3.46
1492 1564 4.135153 GCAGCGAGGAGAGGCGAA 62.135 66.667 0.00 0.00 0.00 4.70
1494 1566 4.869440 CAGCAGCGAGGAGAGGCG 62.869 72.222 0.00 0.00 0.00 5.52
1496 1568 4.527583 GGCAGCAGCGAGGAGAGG 62.528 72.222 0.00 0.00 43.41 3.69
1497 1569 2.074230 CTAGGCAGCAGCGAGGAGAG 62.074 65.000 0.00 0.00 43.41 3.20
1498 1570 2.043953 TAGGCAGCAGCGAGGAGA 60.044 61.111 0.00 0.00 43.41 3.71
1499 1571 2.074230 CTCTAGGCAGCAGCGAGGAG 62.074 65.000 0.00 0.00 43.41 3.69
1500 1572 2.043953 TCTAGGCAGCAGCGAGGA 60.044 61.111 0.00 0.00 43.41 3.71
1501 1573 1.103987 TACTCTAGGCAGCAGCGAGG 61.104 60.000 8.82 0.95 43.41 4.63
1502 1574 0.310543 CTACTCTAGGCAGCAGCGAG 59.689 60.000 0.00 3.51 43.41 5.03
1619 1700 1.165907 TCAAACCGCTGTGCCTTCAG 61.166 55.000 0.00 0.00 38.35 3.02
1623 1704 0.823356 ACAATCAAACCGCTGTGCCT 60.823 50.000 0.00 0.00 0.00 4.75
1630 1711 3.165318 CGCGCACAATCAAACCGC 61.165 61.111 8.75 0.00 41.10 5.68
1633 1714 1.211818 TTTGCCGCGCACAATCAAAC 61.212 50.000 8.75 0.00 38.71 2.93
1646 1727 2.960512 TTGTCGGTCGCATTTGCCG 61.961 57.895 0.00 0.00 46.12 5.69
1650 1731 1.567537 CACGTTGTCGGTCGCATTT 59.432 52.632 0.00 0.00 41.85 2.32
1652 1733 3.411351 GCACGTTGTCGGTCGCAT 61.411 61.111 0.00 0.00 41.85 4.73
1656 1737 1.019278 ATGATGGCACGTTGTCGGTC 61.019 55.000 0.00 0.00 41.85 4.79
1659 1740 1.344837 CGATGATGGCACGTTGTCG 59.655 57.895 0.00 0.00 43.34 4.35
1723 1828 2.030007 CCTACACAGCACCAAACCAATG 60.030 50.000 0.00 0.00 0.00 2.82
1740 1845 5.824904 TGTCGTCCTTAAGTATGACCTAC 57.175 43.478 15.49 9.45 0.00 3.18
1788 1893 1.516386 CCGGACCTTCATCGTGTCG 60.516 63.158 0.00 0.00 0.00 4.35
1892 1997 2.281761 AGGCAAACGAGTGCAGGG 60.282 61.111 15.12 0.00 46.81 4.45
1995 2100 5.088739 GCAGTTCACGGATAAGAAAACATG 58.911 41.667 0.00 0.00 0.00 3.21
2002 2107 3.489229 CGATGAGCAGTTCACGGATAAGA 60.489 47.826 0.00 0.00 38.99 2.10
2028 2133 6.508777 GGGAAAAACATACTACTGCAAAACA 58.491 36.000 0.00 0.00 0.00 2.83
2036 2141 3.340928 GGCACGGGAAAAACATACTACT 58.659 45.455 0.00 0.00 0.00 2.57
2037 2142 2.421073 GGGCACGGGAAAAACATACTAC 59.579 50.000 0.00 0.00 0.00 2.73
2038 2143 2.713877 GGGCACGGGAAAAACATACTA 58.286 47.619 0.00 0.00 0.00 1.82
2057 2162 0.729116 ATGCGAATCTGAACTTGCGG 59.271 50.000 0.00 0.00 0.00 5.69
2073 2178 3.730715 GCCACTGAATTATTACGCAATGC 59.269 43.478 0.00 0.00 0.00 3.56
2110 2215 7.225725 TGCTTTTCCCAATCTTGATCAAAATT 58.774 30.769 9.88 5.31 0.00 1.82
2116 2254 5.397142 AACTGCTTTTCCCAATCTTGATC 57.603 39.130 0.00 0.00 0.00 2.92
2119 2257 8.087750 TGTATTAAACTGCTTTTCCCAATCTTG 58.912 33.333 0.00 0.00 0.00 3.02
2200 2339 6.258160 CCAGCCTTCAGAAAATAAATGTACG 58.742 40.000 0.00 0.00 0.00 3.67
2313 2463 6.559810 TGTTTAAACACCAGACTGAACATTG 58.440 36.000 17.01 0.00 33.17 2.82
2350 2500 5.036117 AGAAGCAGAGGACACAAACTTAA 57.964 39.130 0.00 0.00 0.00 1.85
2360 2510 2.175878 TGCAAAGAGAAGCAGAGGAC 57.824 50.000 0.00 0.00 35.51 3.85
2417 2567 7.317722 ACAGTATTCACTTACCCTCTTCTTT 57.682 36.000 0.00 0.00 30.46 2.52
2432 2582 7.498900 CAGGCCTTCAAACATATACAGTATTCA 59.501 37.037 0.00 0.00 0.00 2.57
2456 2606 9.643693 AAACTGCAATCCTATTTTTGTTATCAG 57.356 29.630 0.00 0.00 0.00 2.90
2471 2621 4.701956 TGCTAAGCTTAAACTGCAATCC 57.298 40.909 13.89 0.00 0.00 3.01
2521 2671 6.808008 AAGATATATGACCAAATCCGCAAG 57.192 37.500 0.00 0.00 0.00 4.01
2785 2944 5.376854 ACAAGAATGTGGTGTGCTAAATC 57.623 39.130 0.00 0.00 38.69 2.17
2823 2982 6.834168 ACAAAATGATTCCGGAGTTTATGT 57.166 33.333 3.34 2.95 0.00 2.29
2853 3012 3.935828 GCTGTGCCTCTTCTTTTACCTAG 59.064 47.826 0.00 0.00 0.00 3.02
2969 3128 3.123050 TGTGTGAGACGATGAAACTGTG 58.877 45.455 0.00 0.00 0.00 3.66
2973 3132 5.597813 AGAAATGTGTGAGACGATGAAAC 57.402 39.130 0.00 0.00 0.00 2.78
2985 3144 4.811555 TGGAGAAAACGAGAAATGTGTG 57.188 40.909 0.00 0.00 0.00 3.82
2986 3145 5.048713 GGATTGGAGAAAACGAGAAATGTGT 60.049 40.000 0.00 0.00 0.00 3.72
2987 3146 5.048782 TGGATTGGAGAAAACGAGAAATGTG 60.049 40.000 0.00 0.00 0.00 3.21
2988 3147 5.048713 GTGGATTGGAGAAAACGAGAAATGT 60.049 40.000 0.00 0.00 0.00 2.71
2989 3148 5.048782 TGTGGATTGGAGAAAACGAGAAATG 60.049 40.000 0.00 0.00 0.00 2.32
2990 3149 5.070001 TGTGGATTGGAGAAAACGAGAAAT 58.930 37.500 0.00 0.00 0.00 2.17
2991 3150 4.456535 TGTGGATTGGAGAAAACGAGAAA 58.543 39.130 0.00 0.00 0.00 2.52
2992 3151 4.079980 TGTGGATTGGAGAAAACGAGAA 57.920 40.909 0.00 0.00 0.00 2.87
2996 3155 3.347216 AGGATGTGGATTGGAGAAAACG 58.653 45.455 0.00 0.00 0.00 3.60
3007 3166 4.521146 GAAATGTGTGAGAGGATGTGGAT 58.479 43.478 0.00 0.00 0.00 3.41
3009 3168 3.012518 GGAAATGTGTGAGAGGATGTGG 58.987 50.000 0.00 0.00 0.00 4.17
3096 3255 4.536765 ACACACTTGAAAGGAAGGATTGT 58.463 39.130 0.00 0.00 0.00 2.71
3126 3286 3.689649 ACGATGATGGGAAGTTTAGTTGC 59.310 43.478 0.00 0.00 0.00 4.17
3131 3291 2.167693 AGCGACGATGATGGGAAGTTTA 59.832 45.455 0.00 0.00 0.00 2.01
3151 3311 3.750639 TTAATTTGCCCGTAAGCGAAG 57.249 42.857 0.00 0.00 39.47 3.79
3152 3312 3.690139 TGATTAATTTGCCCGTAAGCGAA 59.310 39.130 0.00 0.00 40.38 4.70
3153 3313 3.064271 GTGATTAATTTGCCCGTAAGCGA 59.936 43.478 0.00 0.00 41.33 4.93
3154 3314 3.064820 AGTGATTAATTTGCCCGTAAGCG 59.935 43.478 0.00 0.00 34.65 4.68
3155 3315 4.095782 TCAGTGATTAATTTGCCCGTAAGC 59.904 41.667 0.00 0.00 0.00 3.09
3156 3316 5.811399 TCAGTGATTAATTTGCCCGTAAG 57.189 39.130 0.00 0.00 0.00 2.34
3157 3317 5.106078 GGTTCAGTGATTAATTTGCCCGTAA 60.106 40.000 0.00 0.00 0.00 3.18
3158 3318 4.396790 GGTTCAGTGATTAATTTGCCCGTA 59.603 41.667 0.00 0.00 0.00 4.02
3159 3319 3.192633 GGTTCAGTGATTAATTTGCCCGT 59.807 43.478 0.00 0.00 0.00 5.28
3160 3320 3.730662 CGGTTCAGTGATTAATTTGCCCG 60.731 47.826 0.00 1.88 0.00 6.13
3161 3321 3.192633 ACGGTTCAGTGATTAATTTGCCC 59.807 43.478 0.00 0.00 0.00 5.36
3173 3333 1.266718 CATGGTTTCCACGGTTCAGTG 59.733 52.381 0.00 0.00 41.53 3.66
3203 3363 4.680237 TCCACCAGCCGCTTGTCG 62.680 66.667 0.00 0.00 38.08 4.35
3251 3411 0.391661 GGAGCTTGATCTCCGCAACA 60.392 55.000 0.00 0.00 42.74 3.33
3278 3438 1.451504 CCTCACCTTGGCTGTGACA 59.548 57.895 1.82 0.00 37.80 3.58
3324 3484 1.377725 ACTGAATGCCCTCCTTGCG 60.378 57.895 0.00 0.00 0.00 4.85
3330 3490 0.257039 ACCATCCACTGAATGCCCTC 59.743 55.000 0.00 0.00 0.00 4.30
3333 3493 1.386533 CTCACCATCCACTGAATGCC 58.613 55.000 0.00 0.00 0.00 4.40
3334 3494 1.340405 ACCTCACCATCCACTGAATGC 60.340 52.381 0.00 0.00 0.00 3.56
3352 3512 4.013728 AGAGTATATGGCGAGATCAGACC 58.986 47.826 0.00 0.00 0.00 3.85
3374 3536 2.358582 CACAACAGTTGCAGGATGTTCA 59.641 45.455 13.56 0.00 39.31 3.18
3597 3784 1.123928 AGGATCATGACGAGGAACCC 58.876 55.000 0.00 0.00 0.00 4.11
3622 3809 5.204409 ACACTCGAGTTGGTTACACAATA 57.796 39.130 17.26 0.00 32.24 1.90
3625 3812 3.633525 AGTACACTCGAGTTGGTTACACA 59.366 43.478 17.26 0.00 0.00 3.72
3628 3815 8.152309 AGATATAGTACACTCGAGTTGGTTAC 57.848 38.462 17.26 14.12 0.00 2.50
3634 3821 7.507829 ACAGGTAGATATAGTACACTCGAGTT 58.492 38.462 17.26 10.23 0.00 3.01
3636 3823 9.656040 ATTACAGGTAGATATAGTACACTCGAG 57.344 37.037 11.84 11.84 0.00 4.04
3706 3938 0.895530 GTCGGAGGTGAGGTCAATGA 59.104 55.000 0.00 0.00 0.00 2.57
3765 3997 7.067859 ACACCGAGCACTTTTATAGTACATAGA 59.932 37.037 0.00 0.00 34.56 1.98
3766 3998 7.201145 ACACCGAGCACTTTTATAGTACATAG 58.799 38.462 0.00 0.00 34.56 2.23
3782 4020 1.407656 AACAAGGAGGACACCGAGCA 61.408 55.000 0.00 0.00 34.73 4.26
3783 4021 0.250338 AAACAAGGAGGACACCGAGC 60.250 55.000 0.00 0.00 34.73 5.03
3859 4438 1.518572 GCACATCACCTACCGGACG 60.519 63.158 9.46 0.00 0.00 4.79
3865 4444 1.081892 CTGCAGTGCACATCACCTAC 58.918 55.000 21.04 0.00 46.81 3.18
3871 4450 3.231734 TGTACCTGCAGTGCACATC 57.768 52.632 21.04 10.50 36.01 3.06
3875 4454 1.608025 GCTAAGTGTACCTGCAGTGCA 60.608 52.381 18.58 18.58 38.94 4.57
3876 4455 1.079503 GCTAAGTGTACCTGCAGTGC 58.920 55.000 13.81 8.58 0.00 4.40
3877 4456 1.276421 AGGCTAAGTGTACCTGCAGTG 59.724 52.381 13.81 6.81 30.82 3.66
3878 4457 1.645710 AGGCTAAGTGTACCTGCAGT 58.354 50.000 13.81 3.45 30.82 4.40
3879 4458 2.770164 AAGGCTAAGTGTACCTGCAG 57.230 50.000 6.78 6.78 32.92 4.41
3880 4459 2.637872 AGAAAGGCTAAGTGTACCTGCA 59.362 45.455 0.00 0.00 32.92 4.41
3881 4460 3.336138 AGAAAGGCTAAGTGTACCTGC 57.664 47.619 0.00 0.00 32.92 4.85
3882 4461 5.063880 ACAAAGAAAGGCTAAGTGTACCTG 58.936 41.667 0.00 0.00 32.92 4.00
3883 4462 5.071923 AGACAAAGAAAGGCTAAGTGTACCT 59.928 40.000 0.00 0.00 34.45 3.08
3884 4463 5.179555 CAGACAAAGAAAGGCTAAGTGTACC 59.820 44.000 0.00 0.00 0.00 3.34
3885 4464 5.179555 CCAGACAAAGAAAGGCTAAGTGTAC 59.820 44.000 0.00 0.00 0.00 2.90
3886 4465 5.163237 ACCAGACAAAGAAAGGCTAAGTGTA 60.163 40.000 0.00 0.00 0.00 2.90
3887 4466 4.137543 CCAGACAAAGAAAGGCTAAGTGT 58.862 43.478 0.00 0.00 0.00 3.55
3888 4467 4.137543 ACCAGACAAAGAAAGGCTAAGTG 58.862 43.478 0.00 0.00 0.00 3.16
3889 4468 4.439253 ACCAGACAAAGAAAGGCTAAGT 57.561 40.909 0.00 0.00 0.00 2.24
3890 4469 5.305585 TGTACCAGACAAAGAAAGGCTAAG 58.694 41.667 0.00 0.00 34.15 2.18
3891 4470 5.163237 ACTGTACCAGACAAAGAAAGGCTAA 60.163 40.000 0.00 0.00 37.70 3.09
3892 4471 4.347000 ACTGTACCAGACAAAGAAAGGCTA 59.653 41.667 0.00 0.00 37.70 3.93
3893 4472 3.136626 ACTGTACCAGACAAAGAAAGGCT 59.863 43.478 0.00 0.00 37.70 4.58
3894 4473 3.477530 ACTGTACCAGACAAAGAAAGGC 58.522 45.455 0.00 0.00 37.70 4.35
3895 4474 6.464222 TCATACTGTACCAGACAAAGAAAGG 58.536 40.000 0.00 0.00 37.70 3.11
3896 4475 7.604164 ACATCATACTGTACCAGACAAAGAAAG 59.396 37.037 0.00 0.00 37.70 2.62
3897 4476 7.387673 CACATCATACTGTACCAGACAAAGAAA 59.612 37.037 0.00 0.00 37.70 2.52
3898 4477 6.873605 CACATCATACTGTACCAGACAAAGAA 59.126 38.462 0.00 0.00 37.70 2.52
3899 4478 6.398095 CACATCATACTGTACCAGACAAAGA 58.602 40.000 0.00 0.00 37.70 2.52
3900 4479 5.063944 GCACATCATACTGTACCAGACAAAG 59.936 44.000 0.00 0.00 37.70 2.77
3901 4480 4.935205 GCACATCATACTGTACCAGACAAA 59.065 41.667 0.00 0.00 37.70 2.83
3902 4481 4.020662 TGCACATCATACTGTACCAGACAA 60.021 41.667 0.00 0.00 37.70 3.18
3903 4482 3.513515 TGCACATCATACTGTACCAGACA 59.486 43.478 0.00 0.00 35.18 3.41
3904 4483 4.123497 TGCACATCATACTGTACCAGAC 57.877 45.455 0.00 0.00 35.18 3.51
3905 4484 5.118286 CAATGCACATCATACTGTACCAGA 58.882 41.667 0.00 0.00 34.33 3.86
3906 4485 4.260907 GCAATGCACATCATACTGTACCAG 60.261 45.833 0.00 0.00 34.33 4.00
3907 4486 3.627123 GCAATGCACATCATACTGTACCA 59.373 43.478 0.00 0.00 34.33 3.25
3908 4487 3.627123 TGCAATGCACATCATACTGTACC 59.373 43.478 2.72 0.00 34.33 3.34
3909 4488 4.571984 TCTGCAATGCACATCATACTGTAC 59.428 41.667 2.72 0.00 34.33 2.90
3910 4489 4.768583 TCTGCAATGCACATCATACTGTA 58.231 39.130 2.72 0.00 34.33 2.74
3911 4490 3.613030 TCTGCAATGCACATCATACTGT 58.387 40.909 2.72 0.00 34.33 3.55
3912 4491 4.830826 ATCTGCAATGCACATCATACTG 57.169 40.909 2.72 0.00 34.33 2.74
3913 4492 4.758674 GGTATCTGCAATGCACATCATACT 59.241 41.667 2.72 0.00 34.33 2.12
3914 4493 4.083110 GGGTATCTGCAATGCACATCATAC 60.083 45.833 2.72 8.32 34.33 2.39
3915 4494 4.074259 GGGTATCTGCAATGCACATCATA 58.926 43.478 2.72 0.00 34.33 2.15
3916 4495 2.889045 GGGTATCTGCAATGCACATCAT 59.111 45.455 2.72 0.00 36.87 2.45
3917 4496 2.092267 AGGGTATCTGCAATGCACATCA 60.092 45.455 2.72 0.00 33.79 3.07
3918 4497 2.579873 AGGGTATCTGCAATGCACATC 58.420 47.619 2.72 0.00 33.79 3.06
3943 4522 4.684703 CCGTACTGTACCAGACAAAGAAAG 59.315 45.833 12.08 0.00 37.70 2.62
3944 4523 4.341806 TCCGTACTGTACCAGACAAAGAAA 59.658 41.667 12.08 0.00 37.70 2.52
3947 4526 3.928727 TCCGTACTGTACCAGACAAAG 57.071 47.619 12.08 0.00 37.70 2.77
3951 4530 4.880696 AGTCTTATCCGTACTGTACCAGAC 59.119 45.833 12.08 13.70 35.18 3.51
3953 4532 4.036498 CCAGTCTTATCCGTACTGTACCAG 59.964 50.000 12.08 4.58 39.17 4.00
3965 4545 7.410120 AAATCAATGAAACCCAGTCTTATCC 57.590 36.000 0.00 0.00 0.00 2.59
3972 4552 8.193953 ACTGAAATAAATCAATGAAACCCAGT 57.806 30.769 0.00 0.00 0.00 4.00
3994 4574 7.872113 AAAATCAGCTCCCTATAGAAAACTG 57.128 36.000 0.00 4.14 0.00 3.16
4022 4602 2.183858 GAACCGGAAGTGAAAGCGGC 62.184 60.000 9.46 0.00 0.00 6.53
4025 4605 2.879026 AGAAAGAACCGGAAGTGAAAGC 59.121 45.455 9.46 0.00 0.00 3.51
4035 4615 9.569167 GGAAATAAAATAGAAAGAAAGAACCGG 57.431 33.333 0.00 0.00 0.00 5.28
4144 4727 5.177326 AGTAATGCCCGTCGTGTATTTTTA 58.823 37.500 0.00 0.00 0.00 1.52
4155 4740 7.876896 TGAATTTTAAAAAGTAATGCCCGTC 57.123 32.000 4.44 0.00 0.00 4.79
4186 4771 9.835389 AAAAGATGTTCATGGATTTCAGAAAAA 57.165 25.926 0.00 0.00 0.00 1.94
4187 4772 9.263538 CAAAAGATGTTCATGGATTTCAGAAAA 57.736 29.630 0.00 0.00 0.00 2.29
4188 4773 7.385752 GCAAAAGATGTTCATGGATTTCAGAAA 59.614 33.333 0.00 0.00 0.00 2.52
4189 4774 6.869913 GCAAAAGATGTTCATGGATTTCAGAA 59.130 34.615 0.00 0.00 0.00 3.02
4190 4775 6.209986 AGCAAAAGATGTTCATGGATTTCAGA 59.790 34.615 0.00 0.00 0.00 3.27
4191 4776 6.395629 AGCAAAAGATGTTCATGGATTTCAG 58.604 36.000 0.00 0.00 0.00 3.02
4199 4784 6.190954 TCATGAGAGCAAAAGATGTTCATG 57.809 37.500 0.00 5.46 41.36 3.07
4200 4785 7.406031 AATCATGAGAGCAAAAGATGTTCAT 57.594 32.000 0.09 0.00 41.36 2.57


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

AutoCloner maintained by Alex Coulton.