Multiple sequence alignment - TraesCS4A01G149200

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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 TraesCS4A01G149200 chr4A 100.000 4088 0 0 1 4088 284628380 284632467 0.000000e+00 7550
1 TraesCS4A01G149200 chr4D 93.575 2459 84 21 775 3184 185798342 185795909 0.000000e+00 3598
2 TraesCS4A01G149200 chr4D 91.892 185 14 1 3182 3366 185795598 185795415 1.460000e-64 257
3 TraesCS4A01G149200 chr4B 95.768 1205 40 7 1978 3174 340997827 340999028 0.000000e+00 1932
4 TraesCS4A01G149200 chr4B 91.939 1253 55 11 773 1984 340990934 340992181 0.000000e+00 1712
5 TraesCS4A01G149200 chr4B 89.069 247 16 7 3183 3429 340999537 340999772 3.090000e-76 296
6 TraesCS4A01G149200 chr7A 95.166 724 26 5 1 719 111954227 111954946 0.000000e+00 1134
7 TraesCS4A01G149200 chr7A 90.093 535 26 9 3525 4033 365399098 365399631 0.000000e+00 669
8 TraesCS4A01G149200 chr6B 90.339 590 32 9 3524 4088 467114920 467114331 0.000000e+00 750
9 TraesCS4A01G149200 chr3D 91.045 536 20 12 3524 4033 52000899 52000366 0.000000e+00 699
10 TraesCS4A01G149200 chr3D 82.461 382 37 16 1 362 572147425 572147054 1.430000e-79 307
11 TraesCS4A01G149200 chr2A 90.841 535 22 8 3525 4033 487931643 487932176 0.000000e+00 691
12 TraesCS4A01G149200 chr2A 90.299 536 24 5 3524 4033 444003457 444003990 0.000000e+00 676
13 TraesCS4A01G149200 chrUn 90.467 535 24 11 3525 4033 104494204 104493671 0.000000e+00 680
14 TraesCS4A01G149200 chr6D 90.582 361 22 6 3526 3878 43961300 43960944 6.190000e-128 468
15 TraesCS4A01G149200 chr5A 88.462 364 28 9 3524 3878 135036748 135037106 1.050000e-115 427
16 TraesCS4A01G149200 chr1D 88.187 364 28 9 3525 3878 16281204 16281562 1.760000e-113 420
17 TraesCS4A01G149200 chr3A 80.000 375 52 11 1 362 411373678 411374042 5.240000e-64 255


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 TraesCS4A01G149200 chr4A 284628380 284632467 4087 False 7550.0 7550 100.0000 1 4088 1 chr4A.!!$F1 4087
1 TraesCS4A01G149200 chr4D 185795415 185798342 2927 True 1927.5 3598 92.7335 775 3366 2 chr4D.!!$R1 2591
2 TraesCS4A01G149200 chr4B 340990934 340992181 1247 False 1712.0 1712 91.9390 773 1984 1 chr4B.!!$F1 1211
3 TraesCS4A01G149200 chr4B 340997827 340999772 1945 False 1114.0 1932 92.4185 1978 3429 2 chr4B.!!$F2 1451
4 TraesCS4A01G149200 chr7A 111954227 111954946 719 False 1134.0 1134 95.1660 1 719 1 chr7A.!!$F1 718
5 TraesCS4A01G149200 chr7A 365399098 365399631 533 False 669.0 669 90.0930 3525 4033 1 chr7A.!!$F2 508
6 TraesCS4A01G149200 chr6B 467114331 467114920 589 True 750.0 750 90.3390 3524 4088 1 chr6B.!!$R1 564
7 TraesCS4A01G149200 chr3D 52000366 52000899 533 True 699.0 699 91.0450 3524 4033 1 chr3D.!!$R1 509
8 TraesCS4A01G149200 chr2A 487931643 487932176 533 False 691.0 691 90.8410 3525 4033 1 chr2A.!!$F2 508
9 TraesCS4A01G149200 chr2A 444003457 444003990 533 False 676.0 676 90.2990 3524 4033 1 chr2A.!!$F1 509
10 TraesCS4A01G149200 chrUn 104493671 104494204 533 True 680.0 680 90.4670 3525 4033 1 chrUn.!!$R1 508

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
252 254 0.040246 GTCGCTATCTACTCCGGCAC 60.040 60.0 0.00 0.00 0.00 5.01 F
1225 1231 0.404426 CCCTTCCTTTTCTCCCGGTT 59.596 55.0 0.00 0.00 0.00 4.44 F
1964 2010 0.602106 CGGCGATCAGATTCTGGCAT 60.602 55.0 13.59 0.82 31.51 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 1991 0.602106 ATGCCAGAATCTGATCGCCG 60.602 55.0 12.53 0.00 32.44 6.46 R
2631 2681 0.538118 AATGTGCCACATGAATGGGC 59.462 50.0 11.79 7.60 37.97 5.36 R
3438 4067 0.039035 AAAACCTCTGCCCGGCAATA 59.961 50.0 14.45 3.68 38.41 1.90 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
54 55 3.904339 GGATATTTGTCTAGCTGGAGGGA 59.096 47.826 0.00 0.00 0.00 4.20
96 97 0.170339 GGGCGTCTGTAATTTGGCAC 59.830 55.000 0.00 0.00 0.00 5.01
170 171 0.456312 CGACTGGGCGTCTGTAGTTC 60.456 60.000 0.00 0.00 40.59 3.01
181 182 1.616865 TCTGTAGTTCCCTGAACCGTG 59.383 52.381 3.47 0.00 42.85 4.94
202 203 3.314080 TGAAACCACGTCCTTCACAAATC 59.686 43.478 0.00 0.00 0.00 2.17
252 254 0.040246 GTCGCTATCTACTCCGGCAC 60.040 60.000 0.00 0.00 0.00 5.01
307 309 1.589803 TCGATAGATGCCTCGAACGA 58.410 50.000 1.09 1.09 40.64 3.85
313 315 0.579156 GATGCCTCGAACGAATGAGC 59.421 55.000 0.00 0.73 0.00 4.26
522 524 1.135546 CGCTGTCGTCAGTCTCTTCAT 60.136 52.381 11.28 0.00 43.05 2.57
523 525 2.257894 GCTGTCGTCAGTCTCTTCATG 58.742 52.381 11.28 0.00 43.05 3.07
537 539 1.209504 CTTCATGCTCGGAAGGGGTAA 59.790 52.381 0.00 0.00 38.44 2.85
549 551 3.381335 GAAGGGGTAACTGATGGAGGTA 58.619 50.000 0.00 0.00 0.00 3.08
596 601 8.863872 AATGGCGTAATTTTAGAAGGCTATAT 57.136 30.769 0.00 0.00 0.00 0.86
598 603 8.997621 TGGCGTAATTTTAGAAGGCTATATAG 57.002 34.615 5.30 5.30 0.00 1.31
600 605 9.085250 GGCGTAATTTTAGAAGGCTATATAGAC 57.915 37.037 14.16 11.02 0.00 2.59
601 606 9.635520 GCGTAATTTTAGAAGGCTATATAGACA 57.364 33.333 18.02 0.00 32.29 3.41
686 691 4.153655 TCGTTGCTATAGATAGTAGCCGTG 59.846 45.833 3.21 0.00 43.00 4.94
691 696 7.698506 TGCTATAGATAGTAGCCGTGTAAAT 57.301 36.000 3.21 0.00 43.00 1.40
707 712 6.183360 CCGTGTAAATTAATGTACATGCCCTT 60.183 38.462 24.24 4.18 36.37 3.95
709 714 8.564574 CGTGTAAATTAATGTACATGCCCTTAT 58.435 33.333 20.17 0.00 33.05 1.73
714 719 9.860650 AAATTAATGTACATGCCCTTATAGACA 57.139 29.630 9.63 0.00 0.00 3.41
715 720 9.507329 AATTAATGTACATGCCCTTATAGACAG 57.493 33.333 9.63 0.00 0.00 3.51
716 721 4.336889 TGTACATGCCCTTATAGACAGC 57.663 45.455 0.00 0.00 0.00 4.40
717 722 3.967326 TGTACATGCCCTTATAGACAGCT 59.033 43.478 0.00 0.00 0.00 4.24
718 723 3.482156 ACATGCCCTTATAGACAGCTG 57.518 47.619 13.48 13.48 0.00 4.24
719 724 3.041211 ACATGCCCTTATAGACAGCTGA 58.959 45.455 23.35 0.00 0.00 4.26
720 725 3.455910 ACATGCCCTTATAGACAGCTGAA 59.544 43.478 23.35 5.62 0.00 3.02
721 726 4.103785 ACATGCCCTTATAGACAGCTGAAT 59.896 41.667 23.35 12.95 0.00 2.57
722 727 5.307976 ACATGCCCTTATAGACAGCTGAATA 59.692 40.000 23.35 12.78 0.00 1.75
723 728 5.474578 TGCCCTTATAGACAGCTGAATAG 57.525 43.478 23.35 8.20 0.00 1.73
724 729 5.147767 TGCCCTTATAGACAGCTGAATAGA 58.852 41.667 23.35 6.95 0.00 1.98
725 730 5.011125 TGCCCTTATAGACAGCTGAATAGAC 59.989 44.000 23.35 4.36 0.00 2.59
726 731 5.011125 GCCCTTATAGACAGCTGAATAGACA 59.989 44.000 23.35 0.00 0.00 3.41
727 732 6.451393 CCCTTATAGACAGCTGAATAGACAC 58.549 44.000 23.35 1.23 0.00 3.67
728 733 6.266558 CCCTTATAGACAGCTGAATAGACACT 59.733 42.308 23.35 8.36 0.00 3.55
729 734 7.144661 CCTTATAGACAGCTGAATAGACACTG 58.855 42.308 23.35 1.17 0.00 3.66
730 735 7.201866 CCTTATAGACAGCTGAATAGACACTGT 60.202 40.741 23.35 6.98 43.93 3.55
731 736 4.881019 AGACAGCTGAATAGACACTGTT 57.119 40.909 23.35 0.00 41.45 3.16
732 737 4.564041 AGACAGCTGAATAGACACTGTTG 58.436 43.478 23.35 0.00 41.45 3.33
733 738 4.039730 AGACAGCTGAATAGACACTGTTGT 59.960 41.667 23.35 0.00 41.45 3.32
734 739 5.243954 AGACAGCTGAATAGACACTGTTGTA 59.756 40.000 23.35 0.00 41.45 2.41
735 740 5.230942 ACAGCTGAATAGACACTGTTGTAC 58.769 41.667 23.35 0.00 38.38 2.90
736 741 5.221441 ACAGCTGAATAGACACTGTTGTACA 60.221 40.000 23.35 0.00 38.38 2.90
737 742 5.871524 CAGCTGAATAGACACTGTTGTACAT 59.128 40.000 8.42 0.00 35.47 2.29
738 743 6.035435 CAGCTGAATAGACACTGTTGTACATC 59.965 42.308 8.42 0.00 35.47 3.06
739 744 5.292101 GCTGAATAGACACTGTTGTACATCC 59.708 44.000 0.00 0.00 35.47 3.51
740 745 6.605471 TGAATAGACACTGTTGTACATCCT 57.395 37.500 0.00 0.00 35.47 3.24
741 746 6.631016 TGAATAGACACTGTTGTACATCCTC 58.369 40.000 0.00 0.00 35.47 3.71
742 747 6.437477 TGAATAGACACTGTTGTACATCCTCT 59.563 38.462 0.00 0.00 35.47 3.69
743 748 7.614192 TGAATAGACACTGTTGTACATCCTCTA 59.386 37.037 0.00 0.00 35.47 2.43
744 749 7.956328 ATAGACACTGTTGTACATCCTCTAA 57.044 36.000 0.00 0.00 35.47 2.10
745 750 6.665992 AGACACTGTTGTACATCCTCTAAA 57.334 37.500 0.00 0.00 35.47 1.85
746 751 7.246171 AGACACTGTTGTACATCCTCTAAAT 57.754 36.000 0.00 0.00 35.47 1.40
747 752 8.362464 AGACACTGTTGTACATCCTCTAAATA 57.638 34.615 0.00 0.00 35.47 1.40
748 753 8.251721 AGACACTGTTGTACATCCTCTAAATAC 58.748 37.037 0.00 0.00 35.47 1.89
749 754 8.135382 ACACTGTTGTACATCCTCTAAATACT 57.865 34.615 0.00 0.00 32.60 2.12
750 755 8.594550 ACACTGTTGTACATCCTCTAAATACTT 58.405 33.333 0.00 0.00 32.60 2.24
751 756 9.436957 CACTGTTGTACATCCTCTAAATACTTT 57.563 33.333 0.00 0.00 0.00 2.66
752 757 9.654663 ACTGTTGTACATCCTCTAAATACTTTC 57.345 33.333 0.00 0.00 0.00 2.62
753 758 8.697846 TGTTGTACATCCTCTAAATACTTTCG 57.302 34.615 0.00 0.00 0.00 3.46
754 759 7.762615 TGTTGTACATCCTCTAAATACTTTCGG 59.237 37.037 0.00 0.00 0.00 4.30
755 760 6.812998 TGTACATCCTCTAAATACTTTCGGG 58.187 40.000 0.00 0.00 0.00 5.14
756 761 5.291905 ACATCCTCTAAATACTTTCGGGG 57.708 43.478 0.00 0.00 0.00 5.73
757 762 4.720273 ACATCCTCTAAATACTTTCGGGGT 59.280 41.667 0.00 0.00 0.00 4.95
758 763 5.163332 ACATCCTCTAAATACTTTCGGGGTC 60.163 44.000 0.00 0.00 0.00 4.46
759 764 3.708121 TCCTCTAAATACTTTCGGGGTCC 59.292 47.826 0.00 0.00 0.00 4.46
769 774 4.904466 CGGGGTCCGTTAGAGTTG 57.096 61.111 0.00 0.00 42.73 3.16
770 775 1.447314 CGGGGTCCGTTAGAGTTGC 60.447 63.158 0.00 0.00 42.73 4.17
771 776 1.885163 CGGGGTCCGTTAGAGTTGCT 61.885 60.000 0.00 0.00 42.73 3.91
782 787 2.217510 AGAGTTGCTCTAAGGGACGA 57.782 50.000 0.00 0.00 39.28 4.20
817 822 7.097087 GCTGTTTCACACAAAAACAAAACAAAG 60.097 33.333 3.38 0.00 43.78 2.77
818 823 7.974675 TGTTTCACACAAAAACAAAACAAAGA 58.025 26.923 0.00 0.00 42.09 2.52
819 824 8.450964 TGTTTCACACAAAAACAAAACAAAGAA 58.549 25.926 0.00 0.00 42.09 2.52
820 825 9.278734 GTTTCACACAAAAACAAAACAAAGAAA 57.721 25.926 0.00 0.00 36.76 2.52
822 827 9.657121 TTCACACAAAAACAAAACAAAGAAATC 57.343 25.926 0.00 0.00 0.00 2.17
823 828 8.286097 TCACACAAAAACAAAACAAAGAAATCC 58.714 29.630 0.00 0.00 0.00 3.01
824 829 7.268023 CACACAAAAACAAAACAAAGAAATCCG 59.732 33.333 0.00 0.00 0.00 4.18
833 838 2.621526 ACAAAGAAATCCGCCGAGTTTT 59.378 40.909 0.00 0.00 0.00 2.43
913 918 3.085533 GCCTTTTCCTTCTTCCTTCTCC 58.914 50.000 0.00 0.00 0.00 3.71
928 933 1.267121 TCTCCCTTTCCTCCACGAAG 58.733 55.000 0.00 0.00 0.00 3.79
995 1001 0.909623 GTTCGGATTTGAGGGAGGGA 59.090 55.000 0.00 0.00 0.00 4.20
1042 1048 1.142060 TGTGGTTTCTCATGTTCCCGT 59.858 47.619 0.00 0.00 0.00 5.28
1225 1231 0.404426 CCCTTCCTTTTCTCCCGGTT 59.596 55.000 0.00 0.00 0.00 4.44
1249 1255 3.565482 GGATGCTAGAATCCGAATTTGCA 59.435 43.478 14.36 0.00 36.99 4.08
1256 1262 4.442706 AGAATCCGAATTTGCACGACTAT 58.557 39.130 0.00 0.00 0.00 2.12
1284 1290 4.793071 CTCTTGCTGGTATACTCAGATCG 58.207 47.826 19.53 9.82 34.36 3.69
1409 1415 7.237887 AGAGGGTTAGGAGATACAAAAGAGTTT 59.762 37.037 0.00 0.00 0.00 2.66
1469 1480 2.166459 CGATCTTGGTTGCCTCTGTAGA 59.834 50.000 0.00 0.00 0.00 2.59
1510 1521 2.353011 CCATGGGCATGTGAACACTTTC 60.353 50.000 2.85 0.00 37.11 2.62
1590 1601 4.932200 GCCTATCTTACATGTCACTATGCC 59.068 45.833 0.00 0.00 0.00 4.40
1609 1620 1.414181 CCGACTTGCTGAGGATGGTAT 59.586 52.381 0.00 0.00 0.00 2.73
1613 1635 3.378512 ACTTGCTGAGGATGGTATCTCA 58.621 45.455 0.00 0.00 37.65 3.27
1639 1661 9.495382 AATCCAGACTAGTAGTAAAAGGAGAAT 57.505 33.333 1.88 0.00 0.00 2.40
1676 1698 6.207614 AGCAGGAACTTTTTGATCTACTTTCC 59.792 38.462 0.00 0.00 34.60 3.13
1919 1965 1.350071 TGCCCATTTCCAATTGCACT 58.650 45.000 0.00 0.00 0.00 4.40
1941 1987 2.235016 TGGTGCCAGTATTGACCAAAC 58.765 47.619 0.00 0.00 35.51 2.93
1945 1991 2.625790 TGCCAGTATTGACCAAACCAAC 59.374 45.455 0.00 0.00 0.00 3.77
1949 1995 0.875728 TATTGACCAAACCAACGGCG 59.124 50.000 4.80 4.80 0.00 6.46
1964 2010 0.602106 CGGCGATCAGATTCTGGCAT 60.602 55.000 13.59 0.82 31.51 4.40
2003 2049 1.259609 CAAACACATCCATGCCACCT 58.740 50.000 0.00 0.00 0.00 4.00
2011 2057 2.133281 TCCATGCCACCTGAAATCAG 57.867 50.000 3.37 3.37 43.40 2.90
2099 2145 2.795329 AGCCCAACTATCCTTGTGTTG 58.205 47.619 0.00 0.00 40.26 3.33
2108 2154 5.815581 ACTATCCTTGTGTTGATAAGCCAA 58.184 37.500 0.00 0.00 0.00 4.52
2140 2186 8.816640 TTTAATCATTTGCCTTTCTTCAAGTC 57.183 30.769 0.00 0.00 0.00 3.01
2178 2224 5.962031 TGCTTATTCCTAGACCAGGTCTAAA 59.038 40.000 26.59 19.98 43.36 1.85
2252 2299 4.104383 TCACTTGCTTCCTGGAAAGATT 57.896 40.909 10.86 0.00 0.00 2.40
2279 2326 1.001293 TCTGACTGCCACAGCTTAGTG 59.999 52.381 0.00 0.00 40.80 2.74
2333 2380 4.020928 TGGACTGGTAGCAAAATTCGTCTA 60.021 41.667 8.91 1.86 0.00 2.59
2337 2384 4.513442 TGGTAGCAAAATTCGTCTAGCAT 58.487 39.130 0.00 0.00 35.44 3.79
2455 2502 4.505390 CCATTCTTTGGCAGGTTTGGATTT 60.505 41.667 0.00 0.00 39.09 2.17
2534 2581 5.720371 TCGTCCATGACCAATTTTTGATT 57.280 34.783 0.00 0.00 0.00 2.57
2578 2625 2.888834 ACCAAACATGCCTTTGTGTC 57.111 45.000 7.72 0.00 30.33 3.67
2631 2681 4.827284 ACTTGACTTATGGAGGTTGTTTGG 59.173 41.667 0.00 0.00 0.00 3.28
2822 2872 0.108992 GTAATCGACAGCACCGACCA 60.109 55.000 0.00 0.00 38.97 4.02
2877 2927 1.202110 CGGTTGATTCAGCATGCAGAC 60.202 52.381 21.98 7.11 34.76 3.51
2907 2957 1.380403 CGGTGGTCCTTGTGTTTGCA 61.380 55.000 0.00 0.00 0.00 4.08
3009 3059 2.464459 GCACATACAGGCCTCGTGC 61.464 63.158 23.02 23.02 45.25 5.34
3143 3197 1.384191 GGAGGCAGGATGGGTTTGT 59.616 57.895 0.00 0.00 35.86 2.83
3150 3204 2.365293 GCAGGATGGGTTTGTTTGTTCT 59.635 45.455 0.00 0.00 35.86 3.01
3205 3834 2.364324 TGTGAGAACTGTGTACTCCCAC 59.636 50.000 0.00 0.00 35.86 4.61
3206 3835 1.968493 TGAGAACTGTGTACTCCCACC 59.032 52.381 0.00 0.00 34.35 4.61
3224 3853 5.763204 TCCCACCGATCTGAATATAAAAAGC 59.237 40.000 0.00 0.00 0.00 3.51
3237 3866 8.728833 TGAATATAAAAAGCCAAATTTGCAAGG 58.271 29.630 12.92 0.00 0.00 3.61
3248 3877 4.395959 AATTTGCAAGGCATCTGTATGG 57.604 40.909 0.00 0.00 38.76 2.74
3272 3901 7.394641 TGGTCAGATCGACTATATGCTTCTAAT 59.605 37.037 14.42 0.00 44.70 1.73
3300 3929 4.142315 ACGACATTACATAGGCTACAACGT 60.142 41.667 0.00 0.00 0.00 3.99
3355 3984 2.557924 TCATGAAGTTGGCGATTGCTTT 59.442 40.909 4.59 0.00 42.25 3.51
3356 3985 2.704725 TGAAGTTGGCGATTGCTTTC 57.295 45.000 4.59 5.23 42.25 2.62
3361 3990 2.821969 AGTTGGCGATTGCTTTCTCATT 59.178 40.909 4.59 0.00 42.25 2.57
3362 3991 3.256631 AGTTGGCGATTGCTTTCTCATTT 59.743 39.130 4.59 0.00 42.25 2.32
3363 3992 4.458989 AGTTGGCGATTGCTTTCTCATTTA 59.541 37.500 4.59 0.00 42.25 1.40
3364 3993 4.621068 TGGCGATTGCTTTCTCATTTAG 57.379 40.909 4.59 0.00 42.25 1.85
3365 3994 3.378112 TGGCGATTGCTTTCTCATTTAGG 59.622 43.478 4.59 0.00 42.25 2.69
3366 3995 3.366719 GCGATTGCTTTCTCATTTAGGC 58.633 45.455 0.00 0.00 38.39 3.93
3367 3996 3.065925 GCGATTGCTTTCTCATTTAGGCT 59.934 43.478 0.00 0.00 38.39 4.58
3368 3997 4.273480 GCGATTGCTTTCTCATTTAGGCTA 59.727 41.667 0.00 0.00 38.39 3.93
3369 3998 5.559799 GCGATTGCTTTCTCATTTAGGCTAG 60.560 44.000 0.00 0.00 38.39 3.42
3370 3999 5.559799 CGATTGCTTTCTCATTTAGGCTAGC 60.560 44.000 6.04 6.04 0.00 3.42
3371 4000 4.494091 TGCTTTCTCATTTAGGCTAGCT 57.506 40.909 15.72 3.22 0.00 3.32
3384 4013 2.108250 AGGCTAGCTTAGGAGAGGAGAG 59.892 54.545 15.72 0.00 0.00 3.20
3398 4027 1.492993 GGAGAGGCCTGTTTGGAGGT 61.493 60.000 12.00 0.00 38.35 3.85
3414 4043 3.325425 TGGAGGTGAATCGTAGGTTTTCA 59.675 43.478 1.31 1.31 0.00 2.69
3415 4044 4.202377 TGGAGGTGAATCGTAGGTTTTCAA 60.202 41.667 5.55 0.00 31.66 2.69
3429 4058 8.344098 CGTAGGTTTTCAACTTTGGTATTTACA 58.656 33.333 0.00 0.00 0.00 2.41
3432 4061 8.919145 AGGTTTTCAACTTTGGTATTTACATCA 58.081 29.630 0.00 0.00 0.00 3.07
3433 4062 9.535878 GGTTTTCAACTTTGGTATTTACATCAA 57.464 29.630 0.00 0.00 0.00 2.57
3445 4074 8.349245 TGGTATTTACATCAAATTCTATTGCCG 58.651 33.333 0.00 0.00 37.93 5.69
3446 4075 7.807907 GGTATTTACATCAAATTCTATTGCCGG 59.192 37.037 0.00 0.00 37.93 6.13
3447 4076 5.766150 TTACATCAAATTCTATTGCCGGG 57.234 39.130 2.18 0.00 0.00 5.73
3448 4077 2.362077 ACATCAAATTCTATTGCCGGGC 59.638 45.455 13.32 13.32 0.00 6.13
3449 4078 2.136298 TCAAATTCTATTGCCGGGCA 57.864 45.000 19.77 19.77 36.47 5.36
3450 4079 2.023673 TCAAATTCTATTGCCGGGCAG 58.976 47.619 22.59 11.18 40.61 4.85
3451 4080 2.023673 CAAATTCTATTGCCGGGCAGA 58.976 47.619 22.59 13.53 40.61 4.26
3452 4081 1.972872 AATTCTATTGCCGGGCAGAG 58.027 50.000 22.59 21.70 40.61 3.35
3453 4082 0.109342 ATTCTATTGCCGGGCAGAGG 59.891 55.000 22.59 15.08 40.61 3.69
3454 4083 1.271840 TTCTATTGCCGGGCAGAGGT 61.272 55.000 22.59 11.99 40.61 3.85
3455 4084 1.224592 CTATTGCCGGGCAGAGGTT 59.775 57.895 22.59 8.53 40.61 3.50
3456 4085 0.394352 CTATTGCCGGGCAGAGGTTT 60.394 55.000 22.59 6.82 40.61 3.27
3457 4086 0.039035 TATTGCCGGGCAGAGGTTTT 59.961 50.000 22.59 5.14 40.61 2.43
3458 4087 0.831711 ATTGCCGGGCAGAGGTTTTT 60.832 50.000 22.59 0.00 40.61 1.94
3478 4107 5.957842 TTTTTCCTGCGATAAACACTCAT 57.042 34.783 0.00 0.00 0.00 2.90
3479 4108 5.957842 TTTTCCTGCGATAAACACTCATT 57.042 34.783 0.00 0.00 0.00 2.57
3480 4109 4.944962 TTCCTGCGATAAACACTCATTG 57.055 40.909 0.00 0.00 0.00 2.82
3481 4110 2.677836 TCCTGCGATAAACACTCATTGC 59.322 45.455 0.00 0.00 32.98 3.56
3482 4111 2.537529 CCTGCGATAAACACTCATTGCG 60.538 50.000 0.00 0.00 34.77 4.85
3483 4112 2.073056 TGCGATAAACACTCATTGCGT 58.927 42.857 0.00 0.00 34.77 5.24
3484 4113 2.093625 TGCGATAAACACTCATTGCGTC 59.906 45.455 0.00 0.00 34.77 5.19
3485 4114 2.348666 GCGATAAACACTCATTGCGTCT 59.651 45.455 0.00 0.00 0.00 4.18
3486 4115 3.542291 GCGATAAACACTCATTGCGTCTC 60.542 47.826 0.00 0.00 0.00 3.36
3487 4116 3.612423 CGATAAACACTCATTGCGTCTCA 59.388 43.478 0.00 0.00 0.00 3.27
3488 4117 4.091365 CGATAAACACTCATTGCGTCTCAA 59.909 41.667 0.00 0.00 39.32 3.02
3489 4118 5.389411 CGATAAACACTCATTGCGTCTCAAA 60.389 40.000 0.00 0.00 38.34 2.69
3490 4119 4.630894 AAACACTCATTGCGTCTCAAAA 57.369 36.364 0.00 0.00 38.34 2.44
3491 4120 4.836125 AACACTCATTGCGTCTCAAAAT 57.164 36.364 0.00 0.00 38.34 1.82
3492 4121 4.836125 ACACTCATTGCGTCTCAAAATT 57.164 36.364 0.00 0.00 38.34 1.82
3493 4122 4.539870 ACACTCATTGCGTCTCAAAATTG 58.460 39.130 0.00 0.00 38.34 2.32
3494 4123 4.036734 ACACTCATTGCGTCTCAAAATTGT 59.963 37.500 0.00 0.00 38.34 2.71
3495 4124 5.238432 ACACTCATTGCGTCTCAAAATTGTA 59.762 36.000 0.00 0.00 38.34 2.41
3496 4125 5.791974 CACTCATTGCGTCTCAAAATTGTAG 59.208 40.000 0.00 0.00 38.34 2.74
3497 4126 5.106555 ACTCATTGCGTCTCAAAATTGTAGG 60.107 40.000 0.00 0.00 38.34 3.18
3498 4127 5.000591 TCATTGCGTCTCAAAATTGTAGGA 58.999 37.500 0.00 0.00 38.34 2.94
3499 4128 5.647658 TCATTGCGTCTCAAAATTGTAGGAT 59.352 36.000 0.00 0.00 38.34 3.24
3500 4129 5.957842 TTGCGTCTCAAAATTGTAGGATT 57.042 34.783 0.00 0.00 0.00 3.01
3501 4130 5.295431 TGCGTCTCAAAATTGTAGGATTG 57.705 39.130 0.00 0.00 0.00 2.67
3502 4131 4.155826 TGCGTCTCAAAATTGTAGGATTGG 59.844 41.667 0.00 0.00 0.00 3.16
3503 4132 4.156008 GCGTCTCAAAATTGTAGGATTGGT 59.844 41.667 0.00 0.00 0.00 3.67
3504 4133 5.631026 CGTCTCAAAATTGTAGGATTGGTG 58.369 41.667 0.00 0.00 0.00 4.17
3505 4134 5.411361 CGTCTCAAAATTGTAGGATTGGTGA 59.589 40.000 0.00 0.00 0.00 4.02
3506 4135 6.072728 CGTCTCAAAATTGTAGGATTGGTGAA 60.073 38.462 0.00 0.00 0.00 3.18
3507 4136 7.521423 CGTCTCAAAATTGTAGGATTGGTGAAA 60.521 37.037 0.00 0.00 0.00 2.69
3508 4137 7.809806 GTCTCAAAATTGTAGGATTGGTGAAAG 59.190 37.037 0.00 0.00 0.00 2.62
3509 4138 7.505585 TCTCAAAATTGTAGGATTGGTGAAAGT 59.494 33.333 0.00 0.00 0.00 2.66
3510 4139 7.432869 TCAAAATTGTAGGATTGGTGAAAGTG 58.567 34.615 0.00 0.00 0.00 3.16
3511 4140 6.976934 AAATTGTAGGATTGGTGAAAGTGT 57.023 33.333 0.00 0.00 0.00 3.55
3512 4141 8.356657 CAAAATTGTAGGATTGGTGAAAGTGTA 58.643 33.333 0.00 0.00 0.00 2.90
3513 4142 8.650143 AAATTGTAGGATTGGTGAAAGTGTAT 57.350 30.769 0.00 0.00 0.00 2.29
3514 4143 9.747898 AAATTGTAGGATTGGTGAAAGTGTATA 57.252 29.630 0.00 0.00 0.00 1.47
3515 4144 9.920946 AATTGTAGGATTGGTGAAAGTGTATAT 57.079 29.630 0.00 0.00 0.00 0.86
3516 4145 9.920946 ATTGTAGGATTGGTGAAAGTGTATATT 57.079 29.630 0.00 0.00 0.00 1.28
3522 4151 9.227777 GGATTGGTGAAAGTGTATATTATACCC 57.772 37.037 10.59 0.49 0.00 3.69
3826 4458 4.412199 TCCCTTCCCTCTGTACAATAATGG 59.588 45.833 0.00 0.00 0.00 3.16
3867 4499 3.240069 GCAGCATCAGTACAAAGCAAAG 58.760 45.455 0.00 0.00 0.00 2.77
3878 4510 5.867174 AGTACAAAGCAAAGACCAACAAAAC 59.133 36.000 0.00 0.00 0.00 2.43
3998 4654 2.552743 GGAAAAACGGGTGAGAAAGGAG 59.447 50.000 0.00 0.00 0.00 3.69
4013 4669 6.440647 TGAGAAAGGAGCTATTTACCTGAGAA 59.559 38.462 0.00 0.00 34.03 2.87
4073 4729 7.643569 ATTGTGGCAATACATGAGTTTATGA 57.356 32.000 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 6.187682 CCTTCTTCTCTCTCCTAGTTCTCTT 58.812 44.000 0.00 0.00 0.00 2.85
96 97 2.607668 TTCCAGCGCTATCGACCGTG 62.608 60.000 10.99 0.00 38.10 4.94
170 171 2.327228 GTGGTTTCACGGTTCAGGG 58.673 57.895 0.00 0.00 33.87 4.45
181 182 3.304458 GGATTTGTGAAGGACGTGGTTTC 60.304 47.826 0.00 0.00 0.00 2.78
202 203 3.316283 CAAAACATGTTCCGTGGATTGG 58.684 45.455 12.39 0.00 0.00 3.16
406 408 4.938080 AGCACCTACGTGAATCTAATCAG 58.062 43.478 0.00 0.00 43.14 2.90
522 524 0.543410 TCAGTTACCCCTTCCGAGCA 60.543 55.000 0.00 0.00 0.00 4.26
523 525 0.831307 ATCAGTTACCCCTTCCGAGC 59.169 55.000 0.00 0.00 0.00 5.03
537 539 7.639062 ATTATTCCAATCTACCTCCATCAGT 57.361 36.000 0.00 0.00 0.00 3.41
627 632 3.573967 CAGACAATAGGCAAAACACCCTT 59.426 43.478 0.00 0.00 32.65 3.95
632 637 6.371548 GTCATCTACAGACAATAGGCAAAACA 59.628 38.462 0.00 0.00 36.06 2.83
638 643 4.045104 CACGTCATCTACAGACAATAGGC 58.955 47.826 0.00 0.00 35.77 3.93
676 681 9.251792 CATGTACATTAATTTACACGGCTACTA 57.748 33.333 14.98 0.00 31.09 1.82
691 696 6.934645 GCTGTCTATAAGGGCATGTACATTAA 59.065 38.462 5.37 0.00 0.00 1.40
707 712 7.122799 ACAACAGTGTCTATTCAGCTGTCTATA 59.877 37.037 14.67 9.26 39.19 1.31
709 714 5.243954 ACAACAGTGTCTATTCAGCTGTCTA 59.756 40.000 14.67 5.76 39.19 2.59
710 715 4.039730 ACAACAGTGTCTATTCAGCTGTCT 59.960 41.667 14.67 4.80 39.19 3.41
711 716 4.310769 ACAACAGTGTCTATTCAGCTGTC 58.689 43.478 14.67 0.00 39.19 3.51
712 717 4.342862 ACAACAGTGTCTATTCAGCTGT 57.657 40.909 14.67 0.00 41.51 4.40
713 718 5.230182 TGTACAACAGTGTCTATTCAGCTG 58.770 41.667 7.63 7.63 39.30 4.24
714 719 5.468540 TGTACAACAGTGTCTATTCAGCT 57.531 39.130 0.00 0.00 39.30 4.24
715 720 5.292101 GGATGTACAACAGTGTCTATTCAGC 59.708 44.000 0.00 0.00 39.30 4.26
716 721 6.634805 AGGATGTACAACAGTGTCTATTCAG 58.365 40.000 0.00 0.00 39.30 3.02
717 722 6.437477 AGAGGATGTACAACAGTGTCTATTCA 59.563 38.462 0.00 0.00 39.30 2.57
718 723 6.868622 AGAGGATGTACAACAGTGTCTATTC 58.131 40.000 0.00 0.00 39.30 1.75
719 724 6.859112 AGAGGATGTACAACAGTGTCTATT 57.141 37.500 0.00 0.00 39.30 1.73
720 725 7.956328 TTAGAGGATGTACAACAGTGTCTAT 57.044 36.000 0.00 0.00 39.30 1.98
721 726 7.770366 TTTAGAGGATGTACAACAGTGTCTA 57.230 36.000 0.00 0.17 39.30 2.59
722 727 6.665992 TTTAGAGGATGTACAACAGTGTCT 57.334 37.500 0.00 1.11 39.30 3.41
723 728 8.251721 AGTATTTAGAGGATGTACAACAGTGTC 58.748 37.037 0.00 0.00 39.30 3.67
724 729 8.135382 AGTATTTAGAGGATGTACAACAGTGT 57.865 34.615 0.00 0.00 42.09 3.55
725 730 9.436957 AAAGTATTTAGAGGATGTACAACAGTG 57.563 33.333 0.00 0.00 35.86 3.66
726 731 9.654663 GAAAGTATTTAGAGGATGTACAACAGT 57.345 33.333 0.00 0.00 39.27 3.55
727 732 8.808529 CGAAAGTATTTAGAGGATGTACAACAG 58.191 37.037 0.00 0.00 39.27 3.16
728 733 7.762615 CCGAAAGTATTTAGAGGATGTACAACA 59.237 37.037 0.00 0.00 39.27 3.33
729 734 7.224167 CCCGAAAGTATTTAGAGGATGTACAAC 59.776 40.741 0.00 0.00 39.27 3.32
730 735 7.270047 CCCGAAAGTATTTAGAGGATGTACAA 58.730 38.462 0.00 0.00 39.27 2.41
731 736 6.183360 CCCCGAAAGTATTTAGAGGATGTACA 60.183 42.308 0.00 0.00 39.27 2.90
732 737 6.183360 ACCCCGAAAGTATTTAGAGGATGTAC 60.183 42.308 0.00 0.00 39.27 2.90
733 738 5.901276 ACCCCGAAAGTATTTAGAGGATGTA 59.099 40.000 0.00 0.00 39.27 2.29
734 739 4.720273 ACCCCGAAAGTATTTAGAGGATGT 59.280 41.667 0.00 0.00 39.27 3.06
735 740 5.291905 ACCCCGAAAGTATTTAGAGGATG 57.708 43.478 0.00 0.00 39.27 3.51
736 741 4.347292 GGACCCCGAAAGTATTTAGAGGAT 59.653 45.833 0.00 0.00 39.27 3.24
737 742 3.708121 GGACCCCGAAAGTATTTAGAGGA 59.292 47.826 0.00 0.00 39.27 3.71
738 743 4.069300 GGACCCCGAAAGTATTTAGAGG 57.931 50.000 0.00 0.00 39.27 3.69
753 758 0.108281 GAGCAACTCTAACGGACCCC 60.108 60.000 0.00 0.00 0.00 4.95
754 759 0.896226 AGAGCAACTCTAACGGACCC 59.104 55.000 0.00 0.00 39.28 4.46
755 760 3.429135 CCTTAGAGCAACTCTAACGGACC 60.429 52.174 18.33 0.00 44.85 4.46
756 761 3.429135 CCCTTAGAGCAACTCTAACGGAC 60.429 52.174 19.46 0.00 44.85 4.79
757 762 2.758979 CCCTTAGAGCAACTCTAACGGA 59.241 50.000 19.46 1.63 44.85 4.69
758 763 2.758979 TCCCTTAGAGCAACTCTAACGG 59.241 50.000 18.68 18.68 44.85 4.44
759 764 3.731264 CGTCCCTTAGAGCAACTCTAACG 60.731 52.174 11.99 11.14 44.85 3.18
760 765 3.442977 TCGTCCCTTAGAGCAACTCTAAC 59.557 47.826 11.99 4.16 44.85 2.34
761 766 3.442977 GTCGTCCCTTAGAGCAACTCTAA 59.557 47.826 14.56 14.56 46.70 2.10
762 767 3.015327 GTCGTCCCTTAGAGCAACTCTA 58.985 50.000 0.16 0.16 41.50 2.43
763 768 1.819903 GTCGTCCCTTAGAGCAACTCT 59.180 52.381 2.23 2.23 43.83 3.24
764 769 1.544691 TGTCGTCCCTTAGAGCAACTC 59.455 52.381 0.00 0.00 0.00 3.01
765 770 1.629043 TGTCGTCCCTTAGAGCAACT 58.371 50.000 0.00 0.00 0.00 3.16
766 771 2.450609 TTGTCGTCCCTTAGAGCAAC 57.549 50.000 0.00 0.00 0.00 4.17
767 772 3.596214 GATTTGTCGTCCCTTAGAGCAA 58.404 45.455 0.00 0.00 0.00 3.91
768 773 2.093658 GGATTTGTCGTCCCTTAGAGCA 60.094 50.000 0.00 0.00 0.00 4.26
769 774 2.168728 AGGATTTGTCGTCCCTTAGAGC 59.831 50.000 0.00 0.00 36.36 4.09
770 775 3.786635 CAGGATTTGTCGTCCCTTAGAG 58.213 50.000 0.00 0.00 36.36 2.43
771 776 2.093658 GCAGGATTTGTCGTCCCTTAGA 60.094 50.000 0.00 0.00 36.36 2.10
817 822 2.225727 AGACAAAAACTCGGCGGATTTC 59.774 45.455 7.21 0.00 0.00 2.17
818 823 2.227194 AGACAAAAACTCGGCGGATTT 58.773 42.857 7.21 5.18 0.00 2.17
819 824 1.892209 AGACAAAAACTCGGCGGATT 58.108 45.000 7.21 0.00 0.00 3.01
820 825 1.535462 CAAGACAAAAACTCGGCGGAT 59.465 47.619 7.21 0.00 0.00 4.18
821 826 0.941542 CAAGACAAAAACTCGGCGGA 59.058 50.000 7.21 0.00 0.00 5.54
822 827 0.040425 CCAAGACAAAAACTCGGCGG 60.040 55.000 7.21 0.00 0.00 6.13
823 828 0.661020 ACCAAGACAAAAACTCGGCG 59.339 50.000 0.00 0.00 0.00 6.46
824 829 2.727777 GAACCAAGACAAAAACTCGGC 58.272 47.619 0.00 0.00 0.00 5.54
833 838 1.541670 GGCTGTACCGAACCAAGACAA 60.542 52.381 0.00 0.00 0.00 3.18
892 897 3.085533 GGAGAAGGAAGAAGGAAAAGGC 58.914 50.000 0.00 0.00 0.00 4.35
913 918 1.741770 CGGCTTCGTGGAGGAAAGG 60.742 63.158 0.00 0.00 0.00 3.11
928 933 0.320050 GGAGAGGAGATTGGATCGGC 59.680 60.000 0.00 0.00 0.00 5.54
980 986 1.923148 TCCTTTCCCTCCCTCAAATCC 59.077 52.381 0.00 0.00 0.00 3.01
995 1001 2.316586 ATCCACGCCCCCATCCTTT 61.317 57.895 0.00 0.00 0.00 3.11
1042 1048 2.496070 CCACGATCTTGTACTCCTTGGA 59.504 50.000 0.00 0.00 0.00 3.53
1140 1146 2.281484 ACGTTGCTGCCGATGGTT 60.281 55.556 5.34 0.00 0.00 3.67
1225 1231 4.036734 GCAAATTCGGATTCTAGCATCCAA 59.963 41.667 19.67 13.29 42.88 3.53
1249 1255 4.122776 CCAGCAAGAGCAAATATAGTCGT 58.877 43.478 0.00 0.00 45.49 4.34
1256 1262 6.098266 TCTGAGTATACCAGCAAGAGCAAATA 59.902 38.462 13.53 0.00 45.49 1.40
1374 1380 1.123928 CCTAACCCTCTTGCCGAGAT 58.876 55.000 1.97 0.00 42.62 2.75
1409 1415 6.204882 GCTGCTAGAACTAGGAAGAAACAAAA 59.795 38.462 10.30 0.00 33.11 2.44
1469 1480 3.699538 TGGAGCTATGAACGTACACAGAT 59.300 43.478 0.00 0.00 0.00 2.90
1510 1521 5.116074 GGAATTCATTATCTGCAATTTCGCG 59.884 40.000 7.93 0.00 33.35 5.87
1590 1601 2.363680 AGATACCATCCTCAGCAAGTCG 59.636 50.000 0.00 0.00 0.00 4.18
1609 1620 8.114102 TCCTTTTACTACTAGTCTGGATTGAGA 58.886 37.037 0.00 0.00 0.00 3.27
1613 1635 8.896722 TTCTCCTTTTACTACTAGTCTGGATT 57.103 34.615 0.00 0.00 0.00 3.01
1839 1861 4.093743 TCTGGACATGGCGGTATATATGT 58.906 43.478 0.00 0.00 36.54 2.29
1842 1864 5.554437 TTTTCTGGACATGGCGGTATATA 57.446 39.130 0.00 0.00 0.00 0.86
1848 1870 1.818060 TCAATTTTCTGGACATGGCGG 59.182 47.619 0.00 0.00 0.00 6.13
1849 1871 3.574284 TTCAATTTTCTGGACATGGCG 57.426 42.857 0.00 0.00 0.00 5.69
1919 1965 2.666272 TGGTCAATACTGGCACCAAA 57.334 45.000 0.00 0.00 35.93 3.28
1941 1987 0.933097 CAGAATCTGATCGCCGTTGG 59.067 55.000 3.77 0.00 32.44 3.77
1945 1991 0.602106 ATGCCAGAATCTGATCGCCG 60.602 55.000 12.53 0.00 32.44 6.46
1949 1995 3.057456 GCCAATCATGCCAGAATCTGATC 60.057 47.826 12.53 3.78 32.44 2.92
1964 2010 3.157733 TTGGTGCCCAGGCCAATCA 62.158 57.895 5.01 0.00 39.57 2.57
2034 2080 3.070590 ACCGGCAAGTACTAAGTTTGAGT 59.929 43.478 0.00 0.00 0.00 3.41
2140 2186 7.856145 AGGAATAAGCAAGTGAAGTCTTATG 57.144 36.000 0.00 0.00 33.49 1.90
2178 2224 9.959721 AAATTATAAGTATGACAACTCACCACT 57.040 29.630 0.00 0.00 29.85 4.00
2200 2247 5.484998 AGATTGCTGGGATTTGTGGTAAATT 59.515 36.000 0.00 0.00 0.00 1.82
2252 2299 1.241315 TGTGGCAGTCAGACGATCGA 61.241 55.000 24.34 0.00 0.00 3.59
2279 2326 8.515414 AGAAAATGTTAGGCACTATCAAGTTTC 58.485 33.333 14.93 14.93 42.88 2.78
2333 2380 5.142061 TCATGAAATTTGACAAGCATGCT 57.858 34.783 16.30 16.30 34.64 3.79
2337 2384 7.040494 TCTGTTTTCATGAAATTTGACAAGCA 58.960 30.769 21.10 5.43 0.00 3.91
2437 2484 2.145536 GCAAATCCAAACCTGCCAAAG 58.854 47.619 0.00 0.00 0.00 2.77
2543 2590 6.222038 TGTTTGGTTTTGTTTGTGCCTATA 57.778 33.333 0.00 0.00 0.00 1.31
2546 2593 3.409026 TGTTTGGTTTTGTTTGTGCCT 57.591 38.095 0.00 0.00 0.00 4.75
2578 2625 2.320805 CAGAATGTGCAACTTCCACG 57.679 50.000 6.01 0.00 38.04 4.94
2631 2681 0.538118 AATGTGCCACATGAATGGGC 59.462 50.000 11.79 7.60 37.97 5.36
2822 2872 3.480505 TGATGATGTTGATCCGAGCAT 57.519 42.857 0.00 0.00 0.00 3.79
2877 2927 1.164041 GGACCACCGTGTTGTCAAGG 61.164 60.000 9.33 0.00 46.08 3.61
2907 2957 3.795688 TCCTTGAGATCCTGCTTGTTT 57.204 42.857 0.00 0.00 0.00 2.83
3009 3059 2.202797 CCCTCACCAGTGATCGCG 60.203 66.667 0.00 0.00 39.13 5.87
3078 3128 1.824230 TGTTTTTGTGGTCAGCTTGCT 59.176 42.857 0.00 0.00 0.00 3.91
3143 3197 2.428890 ACACCGAAATGGCAAGAACAAA 59.571 40.909 0.00 0.00 43.94 2.83
3150 3204 6.692486 ACATAAATAAACACCGAAATGGCAA 58.308 32.000 0.00 0.00 43.94 4.52
3180 3234 5.483937 TGGGAGTACACAGTTCTCACATATT 59.516 40.000 4.86 0.00 38.19 1.28
3205 3834 9.533253 AAATTTGGCTTTTTATATTCAGATCGG 57.467 29.630 0.00 0.00 0.00 4.18
3224 3853 3.048337 ACAGATGCCTTGCAAATTTGG 57.952 42.857 19.47 4.17 43.62 3.28
3272 3901 7.279750 TGTAGCCTATGTAATGTCGTGAATA 57.720 36.000 0.00 0.00 0.00 1.75
3286 3915 2.554806 TGTCGACGTTGTAGCCTATG 57.445 50.000 11.62 0.00 0.00 2.23
3300 3929 6.262193 TCCGCATACATCTTATTATGTCGA 57.738 37.500 0.00 0.00 40.52 4.20
3355 3984 5.706447 TCTCCTAAGCTAGCCTAAATGAGA 58.294 41.667 12.13 12.37 0.00 3.27
3356 3985 5.047377 CCTCTCCTAAGCTAGCCTAAATGAG 60.047 48.000 12.13 12.36 0.00 2.90
3361 3990 3.722627 TCTCCTCTCCTAAGCTAGCCTAA 59.277 47.826 12.13 0.00 0.00 2.69
3362 3991 3.328357 TCTCCTCTCCTAAGCTAGCCTA 58.672 50.000 12.13 1.14 0.00 3.93
3363 3992 2.108250 CTCTCCTCTCCTAAGCTAGCCT 59.892 54.545 12.13 0.00 0.00 4.58
3364 3993 2.514803 CTCTCCTCTCCTAAGCTAGCC 58.485 57.143 12.13 0.00 0.00 3.93
3365 3994 2.514803 CCTCTCCTCTCCTAAGCTAGC 58.485 57.143 6.62 6.62 0.00 3.42
3366 3995 2.514803 GCCTCTCCTCTCCTAAGCTAG 58.485 57.143 0.00 0.00 0.00 3.42
3367 3996 1.146152 GGCCTCTCCTCTCCTAAGCTA 59.854 57.143 0.00 0.00 0.00 3.32
3368 3997 0.105709 GGCCTCTCCTCTCCTAAGCT 60.106 60.000 0.00 0.00 0.00 3.74
3369 3998 0.105709 AGGCCTCTCCTCTCCTAAGC 60.106 60.000 0.00 0.00 43.20 3.09
3370 3999 1.063266 ACAGGCCTCTCCTCTCCTAAG 60.063 57.143 0.00 0.00 45.52 2.18
3371 4000 1.011595 ACAGGCCTCTCCTCTCCTAA 58.988 55.000 0.00 0.00 45.52 2.69
3384 4013 1.177401 GATTCACCTCCAAACAGGCC 58.823 55.000 0.00 0.00 36.98 5.19
3429 4058 2.624838 CTGCCCGGCAATAGAATTTGAT 59.375 45.455 14.45 0.00 38.41 2.57
3430 4059 2.023673 CTGCCCGGCAATAGAATTTGA 58.976 47.619 14.45 0.00 38.41 2.69
3431 4060 2.023673 TCTGCCCGGCAATAGAATTTG 58.976 47.619 14.45 0.00 38.41 2.32
3432 4061 2.301346 CTCTGCCCGGCAATAGAATTT 58.699 47.619 14.45 0.00 38.41 1.82
3433 4062 1.477558 CCTCTGCCCGGCAATAGAATT 60.478 52.381 14.45 0.00 38.41 2.17
3434 4063 0.109342 CCTCTGCCCGGCAATAGAAT 59.891 55.000 14.45 0.00 38.41 2.40
3435 4064 1.271840 ACCTCTGCCCGGCAATAGAA 61.272 55.000 14.45 0.00 38.41 2.10
3436 4065 1.271840 AACCTCTGCCCGGCAATAGA 61.272 55.000 14.45 6.61 38.41 1.98
3437 4066 0.394352 AAACCTCTGCCCGGCAATAG 60.394 55.000 14.45 13.36 38.41 1.73
3438 4067 0.039035 AAAACCTCTGCCCGGCAATA 59.961 50.000 14.45 3.68 38.41 1.90
3439 4068 0.831711 AAAAACCTCTGCCCGGCAAT 60.832 50.000 14.45 0.00 38.41 3.56
3440 4069 1.456705 AAAAACCTCTGCCCGGCAA 60.457 52.632 14.45 3.92 38.41 4.52
3441 4070 2.197324 AAAAACCTCTGCCCGGCA 59.803 55.556 12.67 12.67 36.92 5.69
3456 4085 5.957842 ATGAGTGTTTATCGCAGGAAAAA 57.042 34.783 0.00 0.00 0.00 1.94
3457 4086 5.698832 CAATGAGTGTTTATCGCAGGAAAA 58.301 37.500 0.00 0.00 0.00 2.29
3458 4087 4.379394 GCAATGAGTGTTTATCGCAGGAAA 60.379 41.667 0.00 0.00 0.00 3.13
3459 4088 3.126858 GCAATGAGTGTTTATCGCAGGAA 59.873 43.478 0.00 0.00 0.00 3.36
3460 4089 2.677836 GCAATGAGTGTTTATCGCAGGA 59.322 45.455 0.00 0.00 0.00 3.86
3461 4090 2.537529 CGCAATGAGTGTTTATCGCAGG 60.538 50.000 0.00 0.00 0.00 4.85
3462 4091 2.094258 ACGCAATGAGTGTTTATCGCAG 59.906 45.455 0.00 0.00 37.83 5.18
3463 4092 2.073056 ACGCAATGAGTGTTTATCGCA 58.927 42.857 0.00 0.00 37.83 5.10
3464 4093 2.348666 AGACGCAATGAGTGTTTATCGC 59.651 45.455 0.00 0.00 42.04 4.58
3465 4094 3.612423 TGAGACGCAATGAGTGTTTATCG 59.388 43.478 0.00 0.00 42.04 2.92
3466 4095 5.530519 TTGAGACGCAATGAGTGTTTATC 57.469 39.130 0.00 0.00 42.04 1.75
3467 4096 5.940192 TTTGAGACGCAATGAGTGTTTAT 57.060 34.783 0.00 0.00 42.04 1.40
3468 4097 5.743026 TTTTGAGACGCAATGAGTGTTTA 57.257 34.783 0.00 0.00 42.04 2.01
3469 4098 4.630894 TTTTGAGACGCAATGAGTGTTT 57.369 36.364 0.00 0.00 42.04 2.83
3470 4099 4.836125 ATTTTGAGACGCAATGAGTGTT 57.164 36.364 0.00 0.00 42.04 3.32
3471 4100 4.036734 ACAATTTTGAGACGCAATGAGTGT 59.963 37.500 0.00 0.00 45.36 3.55
3472 4101 4.539870 ACAATTTTGAGACGCAATGAGTG 58.460 39.130 0.00 0.00 36.15 3.51
3473 4102 4.836125 ACAATTTTGAGACGCAATGAGT 57.164 36.364 0.00 0.00 36.15 3.41
3474 4103 5.122239 TCCTACAATTTTGAGACGCAATGAG 59.878 40.000 0.00 0.00 36.15 2.90
3475 4104 5.000591 TCCTACAATTTTGAGACGCAATGA 58.999 37.500 0.00 0.00 36.15 2.57
3476 4105 5.295431 TCCTACAATTTTGAGACGCAATG 57.705 39.130 0.00 0.00 36.15 2.82
3477 4106 6.324819 CAATCCTACAATTTTGAGACGCAAT 58.675 36.000 0.00 0.00 36.15 3.56
3478 4107 5.335583 CCAATCCTACAATTTTGAGACGCAA 60.336 40.000 0.00 0.00 33.88 4.85
3479 4108 4.155826 CCAATCCTACAATTTTGAGACGCA 59.844 41.667 0.00 0.00 0.00 5.24
3480 4109 4.156008 ACCAATCCTACAATTTTGAGACGC 59.844 41.667 0.00 0.00 0.00 5.19
3481 4110 5.411361 TCACCAATCCTACAATTTTGAGACG 59.589 40.000 0.00 0.00 0.00 4.18
3482 4111 6.817765 TCACCAATCCTACAATTTTGAGAC 57.182 37.500 0.00 0.00 0.00 3.36
3483 4112 7.505585 ACTTTCACCAATCCTACAATTTTGAGA 59.494 33.333 0.00 0.00 0.00 3.27
3484 4113 7.596248 CACTTTCACCAATCCTACAATTTTGAG 59.404 37.037 0.00 0.00 0.00 3.02
3485 4114 7.069331 ACACTTTCACCAATCCTACAATTTTGA 59.931 33.333 0.00 0.00 0.00 2.69
3486 4115 7.209475 ACACTTTCACCAATCCTACAATTTTG 58.791 34.615 0.00 0.00 0.00 2.44
3487 4116 7.360113 ACACTTTCACCAATCCTACAATTTT 57.640 32.000 0.00 0.00 0.00 1.82
3488 4117 6.976934 ACACTTTCACCAATCCTACAATTT 57.023 33.333 0.00 0.00 0.00 1.82
3489 4118 9.920946 ATATACACTTTCACCAATCCTACAATT 57.079 29.630 0.00 0.00 0.00 2.32
3490 4119 9.920946 AATATACACTTTCACCAATCCTACAAT 57.079 29.630 0.00 0.00 0.00 2.71
3496 4125 9.227777 GGGTATAATATACACTTTCACCAATCC 57.772 37.037 11.98 0.00 0.00 3.01
3507 4136 9.818270 TGTGCTAGTAAGGGTATAATATACACT 57.182 33.333 9.27 9.27 31.48 3.55
3512 4141 9.449719 GCATTTGTGCTAGTAAGGGTATAATAT 57.550 33.333 0.00 0.00 0.00 1.28
3513 4142 7.881232 GGCATTTGTGCTAGTAAGGGTATAATA 59.119 37.037 0.07 0.00 34.73 0.98
3514 4143 6.715264 GGCATTTGTGCTAGTAAGGGTATAAT 59.285 38.462 0.07 0.00 34.73 1.28
3515 4144 6.059484 GGCATTTGTGCTAGTAAGGGTATAA 58.941 40.000 0.07 0.00 34.73 0.98
3516 4145 5.455612 GGGCATTTGTGCTAGTAAGGGTATA 60.456 44.000 0.07 0.00 34.73 1.47
3517 4146 4.461198 GGCATTTGTGCTAGTAAGGGTAT 58.539 43.478 0.07 0.00 34.73 2.73
3518 4147 3.371166 GGGCATTTGTGCTAGTAAGGGTA 60.371 47.826 0.07 0.00 34.73 3.69
3519 4148 2.620627 GGGCATTTGTGCTAGTAAGGGT 60.621 50.000 0.07 0.00 34.73 4.34
3520 4149 2.024414 GGGCATTTGTGCTAGTAAGGG 58.976 52.381 0.07 0.00 34.73 3.95
3521 4150 2.722094 TGGGCATTTGTGCTAGTAAGG 58.278 47.619 0.07 0.00 34.73 2.69
3522 4151 3.489738 GCATGGGCATTTGTGCTAGTAAG 60.490 47.826 0.00 0.00 40.72 2.34
3626 4258 9.337396 AGACTGAACTAAAACATGTTGATGTAA 57.663 29.630 12.82 3.32 42.30 2.41
3699 4331 5.977129 GGTTGTTGTGATGGAAAGTTAACAG 59.023 40.000 8.61 0.00 0.00 3.16
3787 4419 1.118838 GGGACAGTGAGAGAGATGGG 58.881 60.000 0.00 0.00 0.00 4.00
3826 4458 3.189285 GCCATTATTTGTGTGATGGTGC 58.811 45.455 0.00 0.00 40.87 5.01
3867 4499 7.337150 CATGACAATACATGTTTTGTTGGTC 57.663 36.000 27.97 18.56 44.12 4.02
4047 4703 9.353431 TCATAAACTCATGTATTGCCACAATAT 57.647 29.630 3.54 0.00 30.84 1.28


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

AutoCloner maintained by Alex Coulton.