Multiple sequence alignment - TraesCS5A01G157800

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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 TraesCS5A01G157800 chr5A 100.000 5031 0 0 1 5031 338225446 338230476 0.000000e+00 9291.0
1 TraesCS5A01G157800 chr5D 93.428 3256 139 23 831 4046 254826728 254829948 0.000000e+00 4758.0
2 TraesCS5A01G157800 chr5D 95.308 959 35 4 4077 5031 254829951 254830903 0.000000e+00 1513.0
3 TraesCS5A01G157800 chr5B 93.111 3266 140 33 831 4046 287800580 287797350 0.000000e+00 4706.0
4 TraesCS5A01G157800 chr5B 95.729 960 26 5 4077 5031 287797347 287796398 0.000000e+00 1531.0
5 TraesCS5A01G157800 chr2B 98.507 670 10 0 1 670 89528062 89528731 0.000000e+00 1182.0
6 TraesCS5A01G157800 chr2B 97.910 670 13 1 3 672 250057848 250057180 0.000000e+00 1158.0
7 TraesCS5A01G157800 chr2B 88.421 285 23 5 1094 1378 653684688 653684962 8.070000e-88 335.0
8 TraesCS5A01G157800 chr2B 92.511 227 10 3 1364 1583 653685953 653686179 8.130000e-83 318.0
9 TraesCS5A01G157800 chr2A 98.063 671 13 0 1 671 716908462 716907792 0.000000e+00 1168.0
10 TraesCS5A01G157800 chr3A 97.914 671 13 1 1 671 344148179 344148848 0.000000e+00 1160.0
11 TraesCS5A01G157800 chr3A 97.619 672 16 0 4 675 633902721 633902050 0.000000e+00 1153.0
12 TraesCS5A01G157800 chr3A 93.333 150 10 0 682 831 193604132 193604281 6.560000e-54 222.0
13 TraesCS5A01G157800 chr1B 97.904 668 13 1 4 670 649979433 649978766 0.000000e+00 1155.0
14 TraesCS5A01G157800 chr7B 97.210 681 16 3 1 681 220147626 220146949 0.000000e+00 1149.0
15 TraesCS5A01G157800 chr7B 97.474 673 14 3 1 671 132144081 132144752 0.000000e+00 1146.0
16 TraesCS5A01G157800 chr7B 91.183 431 25 6 1157 1587 439316839 439316422 1.570000e-159 573.0
17 TraesCS5A01G157800 chr7B 100.000 29 0 0 1095 1123 439316872 439316844 3.000000e-03 54.7
18 TraesCS5A01G157800 chr3B 97.317 671 17 1 1 671 375225488 375226157 0.000000e+00 1138.0
19 TraesCS5A01G157800 chr2D 91.767 498 33 6 1096 1587 628363513 628364008 0.000000e+00 686.0
20 TraesCS5A01G157800 chr6B 90.303 495 40 4 1089 1583 505328754 505328268 4.250000e-180 641.0
21 TraesCS5A01G157800 chr4B 88.940 434 31 7 1154 1587 68649645 68650061 2.080000e-143 520.0
22 TraesCS5A01G157800 chr4B 97.143 35 0 1 1089 1123 68649610 68649643 1.960000e-04 58.4


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 TraesCS5A01G157800 chr5A 338225446 338230476 5030 False 9291.0 9291 100.000 1 5031 1 chr5A.!!$F1 5030
1 TraesCS5A01G157800 chr5D 254826728 254830903 4175 False 3135.5 4758 94.368 831 5031 2 chr5D.!!$F1 4200
2 TraesCS5A01G157800 chr5B 287796398 287800580 4182 True 3118.5 4706 94.420 831 5031 2 chr5B.!!$R1 4200
3 TraesCS5A01G157800 chr2B 89528062 89528731 669 False 1182.0 1182 98.507 1 670 1 chr2B.!!$F1 669
4 TraesCS5A01G157800 chr2B 250057180 250057848 668 True 1158.0 1158 97.910 3 672 1 chr2B.!!$R1 669
5 TraesCS5A01G157800 chr2B 653684688 653686179 1491 False 326.5 335 90.466 1094 1583 2 chr2B.!!$F2 489
6 TraesCS5A01G157800 chr2A 716907792 716908462 670 True 1168.0 1168 98.063 1 671 1 chr2A.!!$R1 670
7 TraesCS5A01G157800 chr3A 344148179 344148848 669 False 1160.0 1160 97.914 1 671 1 chr3A.!!$F2 670
8 TraesCS5A01G157800 chr3A 633902050 633902721 671 True 1153.0 1153 97.619 4 675 1 chr3A.!!$R1 671
9 TraesCS5A01G157800 chr1B 649978766 649979433 667 True 1155.0 1155 97.904 4 670 1 chr1B.!!$R1 666
10 TraesCS5A01G157800 chr7B 220146949 220147626 677 True 1149.0 1149 97.210 1 681 1 chr7B.!!$R1 680
11 TraesCS5A01G157800 chr7B 132144081 132144752 671 False 1146.0 1146 97.474 1 671 1 chr7B.!!$F1 670
12 TraesCS5A01G157800 chr3B 375225488 375226157 669 False 1138.0 1138 97.317 1 671 1 chr3B.!!$F1 670

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
699 703 0.039437 ACGGAAGTACTCTGCACACG 60.039 55.0 0.00 0.0 46.88 4.49 F
729 733 0.041135 GACGAGATCCGGACGATGTC 60.041 60.0 18.64 14.8 43.93 3.06 F
799 803 0.179073 ATCCATCGTCCAGCTTTCGG 60.179 55.0 0.00 0.0 0.00 4.30 F
2749 3823 0.036765 TAACTCCGGCAGCGACAAAT 60.037 50.0 0.00 0.0 0.00 2.32 F
2960 4034 0.179936 GCTGGAATGGGAGAGAGTGG 59.820 60.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 3128 0.742281 CACTAGCGCTGCATTCCAGT 60.742 55.000 22.90 10.9 43.71 4.00 R
2721 3792 1.003718 GCCGGAGTTACCTTGCAGT 60.004 57.895 5.05 0.0 35.24 4.40 R
2761 3835 0.377554 AGACATCGTCATCGTCGGTC 59.622 55.000 0.00 0.0 38.33 4.79 R
3898 4975 0.612744 GCTCTTCTTCCTCCTGCTGT 59.387 55.000 0.00 0.0 0.00 4.40 R
4860 5943 0.901580 CCCATGGCAGCAAGGACTTT 60.902 55.000 6.09 0.0 0.00 2.66 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
55 56 5.338632 TCTTACAGGATAGTCCCTCAAACA 58.661 41.667 0.00 0.00 37.19 2.83
238 241 0.712380 AGGAGGCAATTTGGGGATGT 59.288 50.000 0.00 0.00 0.00 3.06
341 344 3.547054 AGTCAGTTACACAAAACGGGA 57.453 42.857 0.00 0.00 34.46 5.14
530 533 4.341806 TCAACTCCCTTTAGTGTACAACGA 59.658 41.667 0.00 0.00 0.00 3.85
569 572 2.267961 CCGGCCGCTCCTAAACTT 59.732 61.111 22.85 0.00 0.00 2.66
672 676 1.875576 CGCCAGCTAGATTGGTCCATC 60.876 57.143 13.38 0.00 38.02 3.51
675 679 3.686691 GCCAGCTAGATTGGTCCATCTTT 60.687 47.826 13.38 0.00 38.02 2.52
676 680 3.881688 CCAGCTAGATTGGTCCATCTTTG 59.118 47.826 8.54 6.33 0.00 2.77
677 681 4.521146 CAGCTAGATTGGTCCATCTTTGT 58.479 43.478 8.54 0.00 0.00 2.83
678 682 5.396772 CCAGCTAGATTGGTCCATCTTTGTA 60.397 44.000 8.54 0.00 0.00 2.41
679 683 6.294473 CAGCTAGATTGGTCCATCTTTGTAT 58.706 40.000 8.54 0.00 0.00 2.29
680 684 7.445121 CAGCTAGATTGGTCCATCTTTGTATA 58.555 38.462 8.54 0.00 0.00 1.47
681 685 7.386299 CAGCTAGATTGGTCCATCTTTGTATAC 59.614 40.741 8.54 0.00 0.00 1.47
682 686 6.366332 GCTAGATTGGTCCATCTTTGTATACG 59.634 42.308 8.54 0.00 0.00 3.06
683 687 5.611374 AGATTGGTCCATCTTTGTATACGG 58.389 41.667 0.00 0.00 0.00 4.02
684 688 5.365605 AGATTGGTCCATCTTTGTATACGGA 59.634 40.000 0.00 0.00 0.00 4.69
685 689 5.423704 TTGGTCCATCTTTGTATACGGAA 57.576 39.130 0.00 0.00 0.00 4.30
686 690 5.018539 TGGTCCATCTTTGTATACGGAAG 57.981 43.478 10.86 10.86 0.00 3.46
698 702 3.888093 ACGGAAGTACTCTGCACAC 57.112 52.632 0.00 0.00 46.88 3.82
699 703 0.039437 ACGGAAGTACTCTGCACACG 60.039 55.000 0.00 0.00 46.88 4.49
700 704 0.240145 CGGAAGTACTCTGCACACGA 59.760 55.000 0.00 0.00 0.00 4.35
701 705 1.699343 GGAAGTACTCTGCACACGAC 58.301 55.000 0.00 0.00 0.00 4.34
702 706 1.669211 GGAAGTACTCTGCACACGACC 60.669 57.143 0.00 0.00 0.00 4.79
703 707 0.039437 AAGTACTCTGCACACGACCG 60.039 55.000 0.00 0.00 0.00 4.79
704 708 1.170919 AGTACTCTGCACACGACCGT 61.171 55.000 0.00 0.00 0.00 4.83
716 720 2.571757 GACCGTGCATGGACGAGA 59.428 61.111 36.93 0.00 42.10 4.04
717 721 1.141881 GACCGTGCATGGACGAGAT 59.858 57.895 36.93 23.01 42.10 2.75
718 722 0.872021 GACCGTGCATGGACGAGATC 60.872 60.000 36.93 26.12 42.10 2.75
726 730 3.747266 GGACGAGATCCGGACGAT 58.253 61.111 18.64 2.13 43.93 3.73
727 731 1.283181 GGACGAGATCCGGACGATG 59.717 63.158 18.64 6.97 43.93 3.84
728 732 1.445716 GGACGAGATCCGGACGATGT 61.446 60.000 18.64 10.15 43.93 3.06
729 733 0.041135 GACGAGATCCGGACGATGTC 60.041 60.000 18.64 14.80 43.93 3.06
742 746 3.518590 GACGATGTCCATCTTAAACGGT 58.481 45.455 5.79 0.00 35.72 4.83
743 747 3.259064 ACGATGTCCATCTTAAACGGTG 58.741 45.455 5.79 0.00 35.72 4.94
744 748 2.030457 CGATGTCCATCTTAAACGGTGC 59.970 50.000 5.79 0.00 35.72 5.01
745 749 2.851263 TGTCCATCTTAAACGGTGCT 57.149 45.000 0.00 0.00 0.00 4.40
746 750 3.965379 TGTCCATCTTAAACGGTGCTA 57.035 42.857 0.00 0.00 0.00 3.49
747 751 4.274602 TGTCCATCTTAAACGGTGCTAA 57.725 40.909 0.00 0.00 0.00 3.09
748 752 4.839121 TGTCCATCTTAAACGGTGCTAAT 58.161 39.130 0.00 0.00 0.00 1.73
749 753 5.250200 TGTCCATCTTAAACGGTGCTAATT 58.750 37.500 0.00 0.00 0.00 1.40
750 754 5.708230 TGTCCATCTTAAACGGTGCTAATTT 59.292 36.000 0.00 0.00 0.00 1.82
751 755 6.027749 GTCCATCTTAAACGGTGCTAATTTG 58.972 40.000 0.00 0.00 0.00 2.32
752 756 4.798387 CCATCTTAAACGGTGCTAATTTGC 59.202 41.667 4.83 4.83 0.00 3.68
753 757 5.393027 CCATCTTAAACGGTGCTAATTTGCT 60.393 40.000 12.99 0.00 0.00 3.91
754 758 6.183360 CCATCTTAAACGGTGCTAATTTGCTA 60.183 38.462 12.99 0.00 0.00 3.49
755 759 6.804770 TCTTAAACGGTGCTAATTTGCTAA 57.195 33.333 12.99 1.99 0.00 3.09
756 760 7.204496 TCTTAAACGGTGCTAATTTGCTAAA 57.796 32.000 12.99 0.00 0.00 1.85
757 761 7.649973 TCTTAAACGGTGCTAATTTGCTAAAA 58.350 30.769 12.99 0.00 0.00 1.52
758 762 8.136165 TCTTAAACGGTGCTAATTTGCTAAAAA 58.864 29.630 12.99 0.00 0.00 1.94
780 784 7.514784 AAAATGCTATCCATCGATGATTTGA 57.485 32.000 26.86 15.07 31.43 2.69
781 785 7.698506 AAATGCTATCCATCGATGATTTGAT 57.301 32.000 26.86 20.45 31.43 2.57
782 786 6.922247 ATGCTATCCATCGATGATTTGATC 57.078 37.500 26.86 9.79 0.00 2.92
783 787 5.181009 TGCTATCCATCGATGATTTGATCC 58.819 41.667 26.86 13.94 0.00 3.36
784 788 5.181009 GCTATCCATCGATGATTTGATCCA 58.819 41.667 26.86 5.94 0.00 3.41
785 789 5.821470 GCTATCCATCGATGATTTGATCCAT 59.179 40.000 26.86 3.14 0.00 3.41
786 790 6.018098 GCTATCCATCGATGATTTGATCCATC 60.018 42.308 26.86 7.02 36.67 3.51
793 797 2.564771 TGATTTGATCCATCGTCCAGC 58.435 47.619 0.00 0.00 0.00 4.85
794 798 2.171237 TGATTTGATCCATCGTCCAGCT 59.829 45.455 0.00 0.00 0.00 4.24
795 799 2.787473 TTTGATCCATCGTCCAGCTT 57.213 45.000 0.00 0.00 0.00 3.74
796 800 2.787473 TTGATCCATCGTCCAGCTTT 57.213 45.000 0.00 0.00 0.00 3.51
797 801 2.315925 TGATCCATCGTCCAGCTTTC 57.684 50.000 0.00 0.00 0.00 2.62
798 802 1.212616 GATCCATCGTCCAGCTTTCG 58.787 55.000 0.00 0.00 0.00 3.46
799 803 0.179073 ATCCATCGTCCAGCTTTCGG 60.179 55.000 0.00 0.00 0.00 4.30
800 804 2.464459 CCATCGTCCAGCTTTCGGC 61.464 63.158 0.00 0.00 42.19 5.54
809 813 4.625800 GCTTTCGGCTGGAGATGT 57.374 55.556 0.00 0.00 38.06 3.06
810 814 2.093216 GCTTTCGGCTGGAGATGTG 58.907 57.895 0.00 0.00 38.06 3.21
811 815 0.674895 GCTTTCGGCTGGAGATGTGT 60.675 55.000 0.00 0.00 38.06 3.72
812 816 1.363744 CTTTCGGCTGGAGATGTGTC 58.636 55.000 0.00 0.00 0.00 3.67
813 817 0.389817 TTTCGGCTGGAGATGTGTCG 60.390 55.000 0.00 0.00 0.00 4.35
814 818 1.532604 TTCGGCTGGAGATGTGTCGT 61.533 55.000 0.00 0.00 0.00 4.34
815 819 1.517257 CGGCTGGAGATGTGTCGTC 60.517 63.158 0.00 0.00 0.00 4.20
816 820 1.893786 GGCTGGAGATGTGTCGTCT 59.106 57.895 0.00 0.00 31.77 4.18
817 821 0.179124 GGCTGGAGATGTGTCGTCTC 60.179 60.000 9.65 9.65 43.52 3.36
818 822 0.814457 GCTGGAGATGTGTCGTCTCT 59.186 55.000 15.51 0.00 43.68 3.10
819 823 1.468908 GCTGGAGATGTGTCGTCTCTG 60.469 57.143 15.51 11.13 43.68 3.35
820 824 1.815613 CTGGAGATGTGTCGTCTCTGT 59.184 52.381 15.51 0.00 43.68 3.41
821 825 3.010420 CTGGAGATGTGTCGTCTCTGTA 58.990 50.000 15.51 5.49 43.68 2.74
822 826 3.010420 TGGAGATGTGTCGTCTCTGTAG 58.990 50.000 15.51 0.00 43.68 2.74
823 827 2.223386 GGAGATGTGTCGTCTCTGTAGC 60.223 54.545 15.51 0.00 43.68 3.58
824 828 2.420372 GAGATGTGTCGTCTCTGTAGCA 59.580 50.000 10.57 0.00 41.69 3.49
825 829 2.162608 AGATGTGTCGTCTCTGTAGCAC 59.837 50.000 0.00 0.00 0.00 4.40
826 830 1.605753 TGTGTCGTCTCTGTAGCACT 58.394 50.000 0.00 0.00 0.00 4.40
827 831 1.266989 TGTGTCGTCTCTGTAGCACTG 59.733 52.381 0.00 0.00 0.00 3.66
828 832 0.241213 TGTCGTCTCTGTAGCACTGC 59.759 55.000 0.00 0.00 0.00 4.40
829 833 0.523966 GTCGTCTCTGTAGCACTGCT 59.476 55.000 8.95 8.95 43.41 4.24
958 962 1.349627 CAATGACGACCTCATGCGC 59.650 57.895 0.00 0.00 38.82 6.09
959 963 2.167219 AATGACGACCTCATGCGCG 61.167 57.895 0.00 0.00 38.82 6.86
1026 1036 0.548682 ACCCACCAAGCTCTCCATCT 60.549 55.000 0.00 0.00 0.00 2.90
1052 1062 1.392853 CTTCTCACTTCGCATGCACTC 59.607 52.381 19.57 0.00 0.00 3.51
1913 2941 1.473677 GGCCGCCGTTAAGGTAATTTT 59.526 47.619 0.00 0.00 43.70 1.82
1914 2942 2.521996 GCCGCCGTTAAGGTAATTTTG 58.478 47.619 0.00 0.00 43.70 2.44
1940 2968 2.797156 ACGATCGTGCATGAGAATAAGC 59.203 45.455 22.06 0.00 0.00 3.09
1999 3031 7.153985 TGTCATGCGTATCATAGATTCATTCA 58.846 34.615 0.00 0.00 33.19 2.57
2093 3125 3.009033 TGCCAAAAGTAGACCAGCACTAT 59.991 43.478 0.00 0.00 0.00 2.12
2094 3126 3.375299 GCCAAAAGTAGACCAGCACTATG 59.625 47.826 0.00 0.00 0.00 2.23
2095 3127 3.375299 CCAAAAGTAGACCAGCACTATGC 59.625 47.826 0.00 0.00 45.46 3.14
2246 3317 2.184385 CGGATCTGGTACGTACACAC 57.816 55.000 26.02 10.43 0.00 3.82
2267 3338 7.606456 ACACACGATGAACTAAACTTGGATTAT 59.394 33.333 0.00 0.00 0.00 1.28
2268 3339 8.116753 CACACGATGAACTAAACTTGGATTATC 58.883 37.037 0.00 0.00 0.00 1.75
2560 3631 2.480419 GACCAAGACGACCATCAACAAG 59.520 50.000 0.00 0.00 0.00 3.16
2581 3652 5.981088 AGCAATCACCATTAATGTTGACA 57.019 34.783 16.86 0.00 31.92 3.58
2583 3654 6.757237 AGCAATCACCATTAATGTTGACAAA 58.243 32.000 16.86 0.00 31.92 2.83
2667 3738 0.687427 TCCATGCATCTCCTCCGTCA 60.687 55.000 0.00 0.00 0.00 4.35
2695 3766 2.045536 CAGCAGTTGGCCTCCTCC 60.046 66.667 3.32 0.00 46.50 4.30
2721 3792 2.496070 CGGATCAGACCAAGACTACCAA 59.504 50.000 0.00 0.00 0.00 3.67
2747 3821 1.373748 GTAACTCCGGCAGCGACAA 60.374 57.895 0.00 0.00 0.00 3.18
2748 3822 0.947180 GTAACTCCGGCAGCGACAAA 60.947 55.000 0.00 0.00 0.00 2.83
2749 3823 0.036765 TAACTCCGGCAGCGACAAAT 60.037 50.000 0.00 0.00 0.00 2.32
2755 3829 2.099062 GCAGCGACAAATGCCGAG 59.901 61.111 0.00 0.00 36.41 4.63
2758 3832 1.091771 CAGCGACAAATGCCGAGGAT 61.092 55.000 0.00 0.00 0.00 3.24
2761 3835 0.301687 CGACAAATGCCGAGGATTCG 59.698 55.000 0.00 0.00 46.29 3.34
2776 3850 3.803886 TCGACCGACGATGACGAT 58.196 55.556 0.00 0.00 46.45 3.73
2778 3852 1.062047 CGACCGACGATGACGATGT 59.938 57.895 0.00 0.00 45.77 3.06
2800 3874 4.011023 TCTTCTACCTGTCCGAAGAAGAG 58.989 47.826 9.04 0.00 39.91 2.85
2806 3880 1.474879 CTGTCCGAAGAAGAGGAGGAC 59.525 57.143 6.03 6.03 38.52 3.85
2811 3885 2.085320 CGAAGAAGAGGAGGACGAAGA 58.915 52.381 0.00 0.00 0.00 2.87
2812 3886 2.096819 CGAAGAAGAGGAGGACGAAGAG 59.903 54.545 0.00 0.00 0.00 2.85
2814 3888 1.356398 AGAAGAGGAGGACGAAGAGGT 59.644 52.381 0.00 0.00 0.00 3.85
2818 3892 2.018515 GAGGAGGACGAAGAGGTACAG 58.981 57.143 0.00 0.00 0.00 2.74
2827 3901 0.838122 AAGAGGTACAGGCCAGCAGT 60.838 55.000 5.01 0.00 0.00 4.40
2842 3916 4.000331 CAGCAGTGGAGAAGAAGAAGAA 58.000 45.455 0.00 0.00 0.00 2.52
2843 3917 3.995705 CAGCAGTGGAGAAGAAGAAGAAG 59.004 47.826 0.00 0.00 0.00 2.85
2844 3918 3.007831 AGCAGTGGAGAAGAAGAAGAAGG 59.992 47.826 0.00 0.00 0.00 3.46
2845 3919 3.244387 GCAGTGGAGAAGAAGAAGAAGGT 60.244 47.826 0.00 0.00 0.00 3.50
2847 3921 4.039730 CAGTGGAGAAGAAGAAGAAGGTCA 59.960 45.833 0.00 0.00 0.00 4.02
2848 3922 4.656112 AGTGGAGAAGAAGAAGAAGGTCAA 59.344 41.667 0.00 0.00 0.00 3.18
2849 3923 5.309282 AGTGGAGAAGAAGAAGAAGGTCAAT 59.691 40.000 0.00 0.00 0.00 2.57
2860 3934 5.537674 AGAAGAAGGTCAATTGCAAGAACAT 59.462 36.000 4.94 0.00 0.00 2.71
2862 3936 3.947910 AGGTCAATTGCAAGAACATGG 57.052 42.857 4.94 0.00 0.00 3.66
2890 3964 3.737559 AATAAGACTGGCCACATGGAA 57.262 42.857 0.00 0.00 37.39 3.53
2896 3970 0.888736 CTGGCCACATGGAAACGACA 60.889 55.000 0.00 0.00 37.39 4.35
2909 3983 1.813513 AACGACATCCAAGAAGCAGG 58.186 50.000 0.00 0.00 0.00 4.85
2914 3988 3.269178 GACATCCAAGAAGCAGGAGAAG 58.731 50.000 0.00 0.00 37.34 2.85
2915 3989 2.909006 ACATCCAAGAAGCAGGAGAAGA 59.091 45.455 0.00 0.00 37.34 2.87
2916 3990 3.328931 ACATCCAAGAAGCAGGAGAAGAA 59.671 43.478 0.00 0.00 37.34 2.52
2956 4030 1.694169 GGGGCTGGAATGGGAGAGA 60.694 63.158 0.00 0.00 0.00 3.10
2960 4034 0.179936 GCTGGAATGGGAGAGAGTGG 59.820 60.000 0.00 0.00 0.00 4.00
3166 4240 4.087892 GGCTGCCTCCTCTCGCAA 62.088 66.667 12.43 0.00 33.87 4.85
3229 4303 1.218316 GATCGTCCTCGCCACCTTT 59.782 57.895 0.00 0.00 36.96 3.11
3259 4333 3.289834 CATGCATACGGCCCTGCC 61.290 66.667 14.94 0.00 46.75 4.85
3482 4556 3.226242 AGTGCGTGGTTGGACTCA 58.774 55.556 0.00 0.00 35.41 3.41
3711 4785 0.456142 CGAGCCGTTCTCATCGACAA 60.456 55.000 0.00 0.00 41.98 3.18
3719 4793 3.989698 CTCATCGACAACGCCGGCT 62.990 63.158 26.68 4.89 39.58 5.52
3799 4876 2.583520 GCACTGCTGGAGGAGGAG 59.416 66.667 0.14 0.00 45.56 3.69
3800 4877 3.028921 GCACTGCTGGAGGAGGAGG 62.029 68.421 0.14 0.00 44.38 4.30
3801 4878 1.305633 CACTGCTGGAGGAGGAGGA 60.306 63.158 0.14 0.00 44.38 3.71
3838 4915 1.812571 GGCAAAGGAATCTTCTGCGAA 59.187 47.619 0.00 0.00 33.76 4.70
3841 4918 3.376546 GCAAAGGAATCTTCTGCGAAGAT 59.623 43.478 20.72 20.72 38.55 2.40
3855 4932 1.869754 CGAAGATATGGCGGTGGTCAG 60.870 57.143 0.00 0.00 0.00 3.51
3874 4951 3.008517 TCCTTCCTCGGCCATGCA 61.009 61.111 2.24 0.00 0.00 3.96
3898 4975 2.188829 GGCACTGTCACAGCAGCAA 61.189 57.895 20.72 0.00 39.96 3.91
3902 4979 1.281960 CTGTCACAGCAGCAACAGC 59.718 57.895 0.00 0.00 33.42 4.40
3961 5038 0.607620 CGATTGGGTTTTGCATGGGT 59.392 50.000 0.00 0.00 0.00 4.51
4041 5118 1.153568 GTCGCTGATGCTGCCTACA 60.154 57.895 0.00 0.00 36.97 2.74
4046 5123 2.564771 GCTGATGCTGCCTACATTGTA 58.435 47.619 0.00 0.00 36.03 2.41
4048 5125 3.801698 CTGATGCTGCCTACATTGTACT 58.198 45.455 0.00 0.00 0.00 2.73
4049 5126 4.740634 GCTGATGCTGCCTACATTGTACTA 60.741 45.833 0.00 0.00 36.03 1.82
4050 5127 5.545588 CTGATGCTGCCTACATTGTACTAT 58.454 41.667 0.00 0.00 0.00 2.12
4051 5128 5.299949 TGATGCTGCCTACATTGTACTATG 58.700 41.667 14.63 14.63 0.00 2.23
4052 5129 3.466836 TGCTGCCTACATTGTACTATGC 58.533 45.455 15.90 4.17 0.00 3.14
4053 5130 3.134623 TGCTGCCTACATTGTACTATGCT 59.865 43.478 15.90 7.24 0.00 3.79
4054 5131 3.743396 GCTGCCTACATTGTACTATGCTC 59.257 47.826 15.90 4.95 0.00 4.26
4055 5132 3.977427 TGCCTACATTGTACTATGCTCG 58.023 45.455 15.90 5.69 0.00 5.03
4056 5133 3.634910 TGCCTACATTGTACTATGCTCGA 59.365 43.478 15.90 0.68 0.00 4.04
4057 5134 4.280929 TGCCTACATTGTACTATGCTCGAT 59.719 41.667 15.90 0.73 0.00 3.59
4058 5135 5.221441 TGCCTACATTGTACTATGCTCGATT 60.221 40.000 15.90 0.08 0.00 3.34
4059 5136 5.346281 GCCTACATTGTACTATGCTCGATTC 59.654 44.000 15.90 0.00 0.00 2.52
4060 5137 6.682746 CCTACATTGTACTATGCTCGATTCT 58.317 40.000 15.90 0.00 0.00 2.40
4061 5138 6.804295 CCTACATTGTACTATGCTCGATTCTC 59.196 42.308 15.90 0.00 0.00 2.87
4062 5139 6.149129 ACATTGTACTATGCTCGATTCTCA 57.851 37.500 15.90 0.00 0.00 3.27
4063 5140 6.573434 ACATTGTACTATGCTCGATTCTCAA 58.427 36.000 15.90 0.00 0.00 3.02
4064 5141 6.477033 ACATTGTACTATGCTCGATTCTCAAC 59.523 38.462 15.90 0.00 0.00 3.18
4065 5142 5.576447 TGTACTATGCTCGATTCTCAACA 57.424 39.130 0.00 0.00 0.00 3.33
4066 5143 5.340803 TGTACTATGCTCGATTCTCAACAC 58.659 41.667 0.00 0.00 0.00 3.32
4067 5144 4.456280 ACTATGCTCGATTCTCAACACA 57.544 40.909 0.00 0.00 0.00 3.72
4068 5145 4.820897 ACTATGCTCGATTCTCAACACAA 58.179 39.130 0.00 0.00 0.00 3.33
4069 5146 5.237815 ACTATGCTCGATTCTCAACACAAA 58.762 37.500 0.00 0.00 0.00 2.83
4070 5147 5.700832 ACTATGCTCGATTCTCAACACAAAA 59.299 36.000 0.00 0.00 0.00 2.44
4071 5148 4.891627 TGCTCGATTCTCAACACAAAAA 57.108 36.364 0.00 0.00 0.00 1.94
4125 5205 1.020437 TGCACTGCATTGTTCAACGA 58.980 45.000 5.89 0.00 31.71 3.85
4129 5209 3.061006 GCACTGCATTGTTCAACGAAAAG 60.061 43.478 5.89 0.00 0.00 2.27
4131 5211 4.797868 CACTGCATTGTTCAACGAAAAGAA 59.202 37.500 0.00 0.00 0.00 2.52
4142 5222 7.272515 TGTTCAACGAAAAGAAAAACACTCATC 59.727 33.333 0.00 0.00 0.00 2.92
4246 5326 5.070446 TGCTACAACTCAGAGGAAGAGAAAA 59.930 40.000 1.53 0.00 36.91 2.29
4247 5327 5.992217 GCTACAACTCAGAGGAAGAGAAAAA 59.008 40.000 1.53 0.00 36.91 1.94
4348 5429 5.789643 AATAAAATACATGGCCGCATCTT 57.210 34.783 0.00 0.00 0.00 2.40
4673 5754 8.735692 TTGCTCAAAATCTTCCAAAAGAATTT 57.264 26.923 0.00 0.00 44.49 1.82
4729 5810 6.166984 TGCAAATTGAACAGGGTGATTAAA 57.833 33.333 0.00 0.00 0.00 1.52
4983 6066 3.157949 TCCACGTCCTGGTGCACA 61.158 61.111 20.43 3.92 41.52 4.57
5004 6087 1.617740 GCACGCACTCATTTTAAGCC 58.382 50.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 0.317479 GTGTGAGCCTCTACAACCGT 59.683 55.000 0.00 0.00 0.00 4.83
238 241 6.614694 TGCAGTTTTTCTCTATGGTACCTA 57.385 37.500 14.36 0.00 0.00 3.08
419 422 4.811969 TTAAGATCCGCTTTCACCACTA 57.188 40.909 0.00 0.00 38.05 2.74
506 509 5.011329 TCGTTGTACACTAAAGGGAGTTGAT 59.989 40.000 0.00 0.00 0.00 2.57
530 533 4.129380 GTGGAAAAGGTAAGTACGTGGTT 58.871 43.478 0.00 0.00 0.00 3.67
563 566 9.843334 CATATTAAAAACGCCAGGTAAAGTTTA 57.157 29.630 0.00 0.00 35.99 2.01
569 572 4.201930 CCGCATATTAAAAACGCCAGGTAA 60.202 41.667 0.00 0.00 0.00 2.85
672 676 5.515626 GTGCAGAGTACTTCCGTATACAAAG 59.484 44.000 11.57 11.57 0.00 2.77
675 679 4.011698 TGTGCAGAGTACTTCCGTATACA 58.988 43.478 3.32 0.00 0.00 2.29
676 680 4.349501 GTGTGCAGAGTACTTCCGTATAC 58.650 47.826 0.00 0.00 0.00 1.47
677 681 3.064408 CGTGTGCAGAGTACTTCCGTATA 59.936 47.826 0.00 0.00 0.00 1.47
678 682 2.159421 CGTGTGCAGAGTACTTCCGTAT 60.159 50.000 0.00 0.00 0.00 3.06
679 683 1.198408 CGTGTGCAGAGTACTTCCGTA 59.802 52.381 0.00 0.00 0.00 4.02
680 684 0.039437 CGTGTGCAGAGTACTTCCGT 60.039 55.000 0.00 0.00 0.00 4.69
681 685 0.240145 TCGTGTGCAGAGTACTTCCG 59.760 55.000 0.00 0.00 0.00 4.30
682 686 1.669211 GGTCGTGTGCAGAGTACTTCC 60.669 57.143 0.00 0.00 0.00 3.46
683 687 1.699343 GGTCGTGTGCAGAGTACTTC 58.301 55.000 0.00 0.00 0.00 3.01
684 688 0.039437 CGGTCGTGTGCAGAGTACTT 60.039 55.000 0.00 0.00 0.00 2.24
685 689 1.170919 ACGGTCGTGTGCAGAGTACT 61.171 55.000 0.00 0.00 0.00 2.73
686 690 1.002250 CACGGTCGTGTGCAGAGTAC 61.002 60.000 14.51 0.00 40.91 2.73
687 691 1.284715 CACGGTCGTGTGCAGAGTA 59.715 57.895 14.51 0.00 40.91 2.59
688 692 2.027605 CACGGTCGTGTGCAGAGT 59.972 61.111 14.51 0.00 40.91 3.24
694 698 2.356913 TCCATGCACGGTCGTGTG 60.357 61.111 21.94 14.18 46.90 3.82
695 699 2.357034 GTCCATGCACGGTCGTGT 60.357 61.111 21.94 3.38 46.90 4.49
697 701 3.626680 CTCGTCCATGCACGGTCGT 62.627 63.158 17.34 0.00 40.35 4.34
698 702 2.613739 ATCTCGTCCATGCACGGTCG 62.614 60.000 12.21 12.21 40.35 4.79
699 703 0.872021 GATCTCGTCCATGCACGGTC 60.872 60.000 9.72 2.06 40.35 4.79
700 704 1.141881 GATCTCGTCCATGCACGGT 59.858 57.895 9.72 0.00 40.35 4.83
701 705 1.592669 GGATCTCGTCCATGCACGG 60.593 63.158 9.72 0.00 46.96 4.94
702 706 4.018609 GGATCTCGTCCATGCACG 57.981 61.111 1.77 1.77 46.96 5.34
709 713 1.283181 CATCGTCCGGATCTCGTCC 59.717 63.158 7.81 0.00 44.10 4.79
710 714 0.041135 GACATCGTCCGGATCTCGTC 60.041 60.000 7.81 9.35 37.11 4.20
711 715 1.445716 GGACATCGTCCGGATCTCGT 61.446 60.000 7.81 2.91 43.14 4.18
712 716 1.283181 GGACATCGTCCGGATCTCG 59.717 63.158 7.81 7.09 43.14 4.04
721 725 3.306166 CACCGTTTAAGATGGACATCGTC 59.694 47.826 4.06 0.00 42.48 4.20
722 726 3.259064 CACCGTTTAAGATGGACATCGT 58.741 45.455 6.65 6.34 42.48 3.73
723 727 2.030457 GCACCGTTTAAGATGGACATCG 59.970 50.000 6.65 0.00 42.48 3.84
724 728 3.270877 AGCACCGTTTAAGATGGACATC 58.729 45.455 4.15 4.15 37.88 3.06
725 729 3.350219 AGCACCGTTTAAGATGGACAT 57.650 42.857 0.00 0.00 37.88 3.06
726 730 2.851263 AGCACCGTTTAAGATGGACA 57.149 45.000 0.00 0.00 37.88 4.02
727 731 5.813080 AATTAGCACCGTTTAAGATGGAC 57.187 39.130 0.00 0.00 37.88 4.02
728 732 5.392595 GCAAATTAGCACCGTTTAAGATGGA 60.393 40.000 0.00 0.00 37.88 3.41
729 733 4.798387 GCAAATTAGCACCGTTTAAGATGG 59.202 41.667 0.00 0.00 40.53 3.51
730 734 5.640732 AGCAAATTAGCACCGTTTAAGATG 58.359 37.500 0.00 0.00 36.85 2.90
731 735 5.897377 AGCAAATTAGCACCGTTTAAGAT 57.103 34.783 0.00 0.00 36.85 2.40
732 736 6.804770 TTAGCAAATTAGCACCGTTTAAGA 57.195 33.333 0.00 0.00 36.85 2.10
733 737 7.861176 TTTTAGCAAATTAGCACCGTTTAAG 57.139 32.000 0.00 0.00 36.85 1.85
755 759 7.944061 TCAAATCATCGATGGATAGCATTTTT 58.056 30.769 24.61 8.40 0.00 1.94
756 760 7.514784 TCAAATCATCGATGGATAGCATTTT 57.485 32.000 24.61 9.27 0.00 1.82
757 761 7.148120 GGATCAAATCATCGATGGATAGCATTT 60.148 37.037 24.61 17.55 0.00 2.32
758 762 6.318144 GGATCAAATCATCGATGGATAGCATT 59.682 38.462 24.61 12.88 0.00 3.56
759 763 5.821470 GGATCAAATCATCGATGGATAGCAT 59.179 40.000 24.61 7.35 0.00 3.79
760 764 5.181009 GGATCAAATCATCGATGGATAGCA 58.819 41.667 24.61 5.10 0.00 3.49
761 765 5.181009 TGGATCAAATCATCGATGGATAGC 58.819 41.667 24.61 9.21 0.00 2.97
762 766 7.479897 GATGGATCAAATCATCGATGGATAG 57.520 40.000 24.61 12.86 31.83 2.08
771 775 3.188048 GCTGGACGATGGATCAAATCATC 59.812 47.826 8.01 4.57 37.12 2.92
772 776 3.144506 GCTGGACGATGGATCAAATCAT 58.855 45.455 8.01 0.00 0.00 2.45
773 777 2.171237 AGCTGGACGATGGATCAAATCA 59.829 45.455 8.01 0.00 0.00 2.57
774 778 2.843701 AGCTGGACGATGGATCAAATC 58.156 47.619 0.00 0.00 0.00 2.17
775 779 3.287867 AAGCTGGACGATGGATCAAAT 57.712 42.857 0.00 0.00 0.00 2.32
776 780 2.787473 AAGCTGGACGATGGATCAAA 57.213 45.000 0.00 0.00 0.00 2.69
777 781 2.632377 GAAAGCTGGACGATGGATCAA 58.368 47.619 0.00 0.00 0.00 2.57
778 782 1.471501 CGAAAGCTGGACGATGGATCA 60.472 52.381 0.00 0.00 0.00 2.92
779 783 1.212616 CGAAAGCTGGACGATGGATC 58.787 55.000 0.00 0.00 0.00 3.36
780 784 0.179073 CCGAAAGCTGGACGATGGAT 60.179 55.000 8.61 0.00 0.00 3.41
781 785 1.218047 CCGAAAGCTGGACGATGGA 59.782 57.895 8.61 0.00 0.00 3.41
782 786 2.464459 GCCGAAAGCTGGACGATGG 61.464 63.158 8.61 0.00 38.99 3.51
783 787 3.093278 GCCGAAAGCTGGACGATG 58.907 61.111 8.61 0.00 38.99 3.84
792 796 0.674895 ACACATCTCCAGCCGAAAGC 60.675 55.000 0.00 0.00 44.25 3.51
793 797 1.363744 GACACATCTCCAGCCGAAAG 58.636 55.000 0.00 0.00 0.00 2.62
794 798 0.389817 CGACACATCTCCAGCCGAAA 60.390 55.000 0.00 0.00 0.00 3.46
795 799 1.215382 CGACACATCTCCAGCCGAA 59.785 57.895 0.00 0.00 0.00 4.30
796 800 1.934220 GACGACACATCTCCAGCCGA 61.934 60.000 0.00 0.00 0.00 5.54
797 801 1.517257 GACGACACATCTCCAGCCG 60.517 63.158 0.00 0.00 0.00 5.52
798 802 0.179124 GAGACGACACATCTCCAGCC 60.179 60.000 0.00 0.00 37.26 4.85
799 803 0.814457 AGAGACGACACATCTCCAGC 59.186 55.000 0.00 0.00 43.15 4.85
800 804 1.815613 ACAGAGACGACACATCTCCAG 59.184 52.381 0.00 0.00 43.15 3.86
801 805 1.911057 ACAGAGACGACACATCTCCA 58.089 50.000 0.00 0.00 43.15 3.86
802 806 2.223386 GCTACAGAGACGACACATCTCC 60.223 54.545 0.00 0.00 43.15 3.71
803 807 2.420372 TGCTACAGAGACGACACATCTC 59.580 50.000 0.00 0.00 42.57 2.75
804 808 2.162608 GTGCTACAGAGACGACACATCT 59.837 50.000 0.00 0.00 0.00 2.90
805 809 2.162608 AGTGCTACAGAGACGACACATC 59.837 50.000 0.00 0.00 0.00 3.06
806 810 2.095008 CAGTGCTACAGAGACGACACAT 60.095 50.000 0.00 0.00 0.00 3.21
807 811 1.266989 CAGTGCTACAGAGACGACACA 59.733 52.381 0.00 0.00 0.00 3.72
808 812 1.970447 CAGTGCTACAGAGACGACAC 58.030 55.000 0.00 0.00 0.00 3.67
809 813 0.241213 GCAGTGCTACAGAGACGACA 59.759 55.000 8.18 0.00 0.00 4.35
810 814 0.523966 AGCAGTGCTACAGAGACGAC 59.476 55.000 18.11 0.00 36.99 4.34
811 815 0.805614 GAGCAGTGCTACAGAGACGA 59.194 55.000 19.77 0.00 39.88 4.20
812 816 0.522286 CGAGCAGTGCTACAGAGACG 60.522 60.000 19.77 11.74 39.88 4.18
813 817 0.800300 GCGAGCAGTGCTACAGAGAC 60.800 60.000 19.77 2.29 39.88 3.36
814 818 1.244019 TGCGAGCAGTGCTACAGAGA 61.244 55.000 19.77 0.62 39.88 3.10
815 819 0.801451 CTGCGAGCAGTGCTACAGAG 60.801 60.000 30.53 16.61 42.11 3.35
816 820 1.213799 CTGCGAGCAGTGCTACAGA 59.786 57.895 30.53 12.04 42.11 3.41
817 821 2.451167 GCTGCGAGCAGTGCTACAG 61.451 63.158 30.17 30.17 45.24 2.74
818 822 2.433145 GCTGCGAGCAGTGCTACA 60.433 61.111 19.77 18.07 45.24 2.74
827 831 0.302890 GTGACATACATGCTGCGAGC 59.697 55.000 0.00 1.70 42.82 5.03
828 832 1.643880 TGTGACATACATGCTGCGAG 58.356 50.000 0.00 0.00 33.42 5.03
829 833 3.830679 TGTGACATACATGCTGCGA 57.169 47.368 0.00 0.00 33.42 5.10
839 843 2.483538 CGTCAGCCATGGATGTGACATA 60.484 50.000 28.29 6.29 39.46 2.29
1026 1036 0.666374 TGCGAAGTGAGAAGACGACA 59.334 50.000 0.00 0.00 0.00 4.35
1059 1069 2.050895 ATTCTCGGCTCGATCGCG 60.051 61.111 11.09 5.24 34.61 5.87
1060 1070 2.018866 CCATTCTCGGCTCGATCGC 61.019 63.158 11.09 0.00 34.61 4.58
1062 1072 1.666234 GCCCATTCTCGGCTCGATC 60.666 63.158 0.00 0.00 43.48 3.69
1069 1079 2.908940 GGCCATGCCCATTCTCGG 60.909 66.667 0.00 0.00 44.06 4.63
1085 1098 0.995728 GTTGTTGTTGTTGGTTGCGG 59.004 50.000 0.00 0.00 0.00 5.69
1086 1099 0.637738 CGTTGTTGTTGTTGGTTGCG 59.362 50.000 0.00 0.00 0.00 4.85
1091 1104 1.544686 GCTCACGTTGTTGTTGTTGG 58.455 50.000 0.00 0.00 0.00 3.77
1242 1258 4.687215 GTGAGGTGGCGCTGCAGA 62.687 66.667 20.43 0.00 0.00 4.26
1246 1262 2.743928 GAAGGTGAGGTGGCGCTG 60.744 66.667 7.64 0.00 0.00 5.18
1803 2831 4.554363 CGCCGCCGTCTACCAGAG 62.554 72.222 0.00 0.00 0.00 3.35
1913 2941 3.580731 TCTCATGCACGATCGTTAAACA 58.419 40.909 20.14 14.65 0.00 2.83
1914 2942 4.577687 TTCTCATGCACGATCGTTAAAC 57.422 40.909 20.14 9.13 0.00 2.01
1940 2968 8.330302 CCACTTTGCTAAAAAGAAAGATTTGTG 58.670 33.333 4.91 0.00 32.18 3.33
1958 2986 1.270274 TGACATGCATGACCACTTTGC 59.730 47.619 32.75 10.13 0.00 3.68
1999 3031 8.381636 AGCAGGAATTTAGCACTAGATATGAAT 58.618 33.333 0.00 0.00 0.00 2.57
2096 3128 0.742281 CACTAGCGCTGCATTCCAGT 60.742 55.000 22.90 10.90 43.71 4.00
2097 3129 2.012237 CACTAGCGCTGCATTCCAG 58.988 57.895 22.90 10.14 44.67 3.86
2098 3130 2.108514 GCACTAGCGCTGCATTCCA 61.109 57.895 22.90 0.00 34.56 3.53
2099 3131 2.711924 GCACTAGCGCTGCATTCC 59.288 61.111 22.90 0.00 34.56 3.01
2242 3313 5.862924 ATCCAAGTTTAGTTCATCGTGTG 57.137 39.130 0.00 0.00 0.00 3.82
2244 3315 8.116753 GTGATAATCCAAGTTTAGTTCATCGTG 58.883 37.037 0.00 0.00 0.00 4.35
2246 3317 8.196802 TGTGATAATCCAAGTTTAGTTCATCG 57.803 34.615 0.00 0.00 0.00 3.84
2434 3505 2.281970 TCCAACCAGCTGCTGCAG 60.282 61.111 24.80 24.80 42.74 4.41
2581 3652 2.532531 ACGTCGTCATCGTATCGTTT 57.467 45.000 0.00 0.00 39.78 3.60
2583 3654 1.129251 ACAACGTCGTCATCGTATCGT 59.871 47.619 0.00 0.00 40.69 3.73
2667 3738 3.518552 AACTGCTGCAGGGTGCCAT 62.519 57.895 31.00 7.70 44.23 4.40
2695 3766 1.123077 TCTTGGTCTGATCCGGATGG 58.877 55.000 24.82 14.50 0.00 3.51
2721 3792 1.003718 GCCGGAGTTACCTTGCAGT 60.004 57.895 5.05 0.00 35.24 4.40
2761 3835 0.377554 AGACATCGTCATCGTCGGTC 59.622 55.000 0.00 0.00 38.33 4.79
2768 3842 4.498345 GGACAGGTAGAAGACATCGTCATC 60.498 50.000 0.00 0.00 34.60 2.92
2769 3843 3.381908 GGACAGGTAGAAGACATCGTCAT 59.618 47.826 0.00 0.00 34.60 3.06
2770 3844 2.753452 GGACAGGTAGAAGACATCGTCA 59.247 50.000 0.00 0.00 34.60 4.35
2776 3850 3.150458 TCTTCGGACAGGTAGAAGACA 57.850 47.619 12.75 0.00 43.53 3.41
2778 3852 4.011023 CTCTTCTTCGGACAGGTAGAAGA 58.989 47.826 14.91 14.91 46.15 2.87
2800 3874 1.104630 CCTGTACCTCTTCGTCCTCC 58.895 60.000 0.00 0.00 0.00 4.30
2806 3880 1.153549 GCTGGCCTGTACCTCTTCG 60.154 63.158 11.69 0.00 0.00 3.79
2811 3885 2.596851 CCACTGCTGGCCTGTACCT 61.597 63.158 11.69 0.00 0.00 3.08
2812 3886 2.045926 CCACTGCTGGCCTGTACC 60.046 66.667 11.69 0.00 0.00 3.34
2814 3888 0.835971 TTCTCCACTGCTGGCCTGTA 60.836 55.000 11.69 5.82 37.49 2.74
2818 3892 0.676151 CTTCTTCTCCACTGCTGGCC 60.676 60.000 0.00 0.00 37.49 5.36
2827 3901 5.832539 ATTGACCTTCTTCTTCTTCTCCA 57.167 39.130 0.00 0.00 0.00 3.86
2842 3916 2.564062 CCCATGTTCTTGCAATTGACCT 59.436 45.455 10.34 0.00 0.00 3.85
2843 3917 2.354003 CCCCATGTTCTTGCAATTGACC 60.354 50.000 10.34 0.00 0.00 4.02
2844 3918 2.932187 GCCCCATGTTCTTGCAATTGAC 60.932 50.000 10.34 1.02 0.00 3.18
2845 3919 1.275856 GCCCCATGTTCTTGCAATTGA 59.724 47.619 10.34 0.00 0.00 2.57
2847 3921 0.247185 CGCCCCATGTTCTTGCAATT 59.753 50.000 0.00 0.00 0.00 2.32
2848 3922 1.892338 CGCCCCATGTTCTTGCAAT 59.108 52.632 0.00 0.00 0.00 3.56
2849 3923 2.929903 GCGCCCCATGTTCTTGCAA 61.930 57.895 0.00 0.00 0.00 4.08
2860 3934 0.679640 CAGTCTTATTTGGCGCCCCA 60.680 55.000 26.77 11.16 40.06 4.96
2862 3936 2.106844 CCAGTCTTATTTGGCGCCC 58.893 57.895 26.77 5.30 0.00 6.13
2882 3956 3.073678 TCTTGGATGTCGTTTCCATGTG 58.926 45.455 12.78 5.54 42.69 3.21
2890 3964 1.347707 TCCTGCTTCTTGGATGTCGTT 59.652 47.619 0.00 0.00 0.00 3.85
2896 3970 3.843027 TCTTCTTCTCCTGCTTCTTGGAT 59.157 43.478 0.00 0.00 0.00 3.41
2909 3983 2.349912 GCCACACGCTTTTCTTCTTCTC 60.350 50.000 0.00 0.00 0.00 2.87
3079 4153 4.082523 ACGGCCCATGTGGAGTCG 62.083 66.667 11.27 11.27 38.70 4.18
3130 4204 1.153647 CAGCACGCCATAGACGGAA 60.154 57.895 0.00 0.00 34.00 4.30
3166 4240 3.320879 CTCCATGAGGTGCGGCTGT 62.321 63.158 0.00 0.00 35.89 4.40
3229 4303 3.129502 GCATGGCTGCGCTTGAGA 61.130 61.111 9.73 0.00 38.92 3.27
3334 4408 1.142748 CTCCACGAGCCTGGTGATC 59.857 63.158 8.57 0.00 37.60 2.92
3481 4555 3.036084 GCTGACGACGTGGGTGTG 61.036 66.667 4.58 0.00 0.00 3.82
3482 4556 4.640855 CGCTGACGACGTGGGTGT 62.641 66.667 4.58 0.00 43.93 4.16
3515 4589 2.255554 CTTGTGCTGCTGCTGCTG 59.744 61.111 27.67 16.73 40.48 4.41
3592 4666 1.576421 CGCCAGCCACAGAAAGTTC 59.424 57.895 0.00 0.00 0.00 3.01
3698 4772 1.683790 CCGGCGTTGTCGATGAGAAC 61.684 60.000 6.01 0.00 39.71 3.01
3700 4774 2.180769 CCGGCGTTGTCGATGAGA 59.819 61.111 6.01 0.00 39.71 3.27
3739 4813 1.016130 CGTGGAAGCGCTTCATGTCT 61.016 55.000 41.60 14.05 41.20 3.41
3772 4846 2.285969 AGCAGTGCCTCCAGGGAT 60.286 61.111 12.58 0.00 38.01 3.85
3799 4876 2.126031 GCCTCAAGGTCGACGTCC 60.126 66.667 11.73 2.65 37.57 4.79
3800 4877 2.126031 GGCCTCAAGGTCGACGTC 60.126 66.667 11.73 5.18 37.57 4.34
3838 4915 0.691078 ACCTGACCACCGCCATATCT 60.691 55.000 0.00 0.00 0.00 1.98
3841 4918 2.363975 GGACCTGACCACCGCCATA 61.364 63.158 0.00 0.00 0.00 2.74
3855 4932 2.190578 CATGGCCGAGGAAGGACC 59.809 66.667 0.00 0.00 39.00 4.46
3874 4951 1.757306 CTGTGACAGTGCCTCCCTT 59.243 57.895 4.01 0.00 0.00 3.95
3898 4975 0.612744 GCTCTTCTTCCTCCTGCTGT 59.387 55.000 0.00 0.00 0.00 4.40
3902 4979 2.614987 CCAACTGCTCTTCTTCCTCCTG 60.615 54.545 0.00 0.00 0.00 3.86
3961 5038 2.169978 CTGTGCCTCCTTCATCATCTCA 59.830 50.000 0.00 0.00 0.00 3.27
4012 5089 1.115467 ATCAGCGACTAGGTTGGAGG 58.885 55.000 0.00 0.00 0.00 4.30
4041 5118 6.477033 GTGTTGAGAATCGAGCATAGTACAAT 59.523 38.462 0.00 0.00 38.61 2.71
4046 5123 4.456280 TGTGTTGAGAATCGAGCATAGT 57.544 40.909 0.00 0.00 38.61 2.12
4048 5125 6.552859 TTTTTGTGTTGAGAATCGAGCATA 57.447 33.333 0.00 0.00 38.61 3.14
4049 5126 5.437289 TTTTTGTGTTGAGAATCGAGCAT 57.563 34.783 0.00 0.00 38.61 3.79
4050 5127 4.891627 TTTTTGTGTTGAGAATCGAGCA 57.108 36.364 0.00 0.00 38.61 4.26
4071 5148 9.672673 AAGATGTACATGAGCATAGTACTTTTT 57.327 29.630 14.43 12.00 39.02 1.94
4073 5150 9.751542 GTAAGATGTACATGAGCATAGTACTTT 57.248 33.333 14.43 0.00 39.02 2.66
4074 5151 9.137459 AGTAAGATGTACATGAGCATAGTACTT 57.863 33.333 14.43 8.50 39.02 2.24
4075 5152 8.698973 AGTAAGATGTACATGAGCATAGTACT 57.301 34.615 14.43 0.00 39.02 2.73
4084 5161 8.706936 GTGCATTGATAGTAAGATGTACATGAG 58.293 37.037 14.43 0.00 35.87 2.90
4123 5203 8.979574 AGTAGTAGATGAGTGTTTTTCTTTTCG 58.020 33.333 0.00 0.00 0.00 3.46
4131 5211 9.862371 CTGTTGATAGTAGTAGATGAGTGTTTT 57.138 33.333 0.00 0.00 0.00 2.43
4142 5222 7.761704 ACATTTGCTGTCTGTTGATAGTAGTAG 59.238 37.037 0.00 0.00 34.46 2.57
4246 5326 2.484264 GTGCGTTCCATTGTAGCTCTTT 59.516 45.455 0.00 0.00 0.00 2.52
4247 5327 2.076863 GTGCGTTCCATTGTAGCTCTT 58.923 47.619 0.00 0.00 0.00 2.85
4328 5409 5.451242 GGAAAAGATGCGGCCATGTATTTTA 60.451 40.000 2.24 0.00 0.00 1.52
4329 5410 4.432712 GAAAAGATGCGGCCATGTATTTT 58.567 39.130 2.24 4.03 0.00 1.82
4330 5411 3.181476 GGAAAAGATGCGGCCATGTATTT 60.181 43.478 2.24 0.00 0.00 1.40
4397 5478 1.133790 GCAGACCAGCTAAATGGCTTG 59.866 52.381 0.00 0.00 44.80 4.01
4673 5754 2.049959 CATTTTCAATCGTGTTGCGCA 58.950 42.857 5.66 5.66 41.07 6.09
4860 5943 0.901580 CCCATGGCAGCAAGGACTTT 60.902 55.000 6.09 0.00 0.00 2.66
4861 5944 1.304713 CCCATGGCAGCAAGGACTT 60.305 57.895 6.09 0.00 0.00 3.01
4862 5945 2.357836 CCCATGGCAGCAAGGACT 59.642 61.111 6.09 0.00 0.00 3.85
4983 6066 1.399727 GCTTAAAATGAGTGCGTGCGT 60.400 47.619 0.00 0.00 0.00 5.24
5004 6087 0.334676 TGGTCCTTATTGCCTTGGGG 59.665 55.000 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.