Multiple sequence alignment - TraesCS1D01G202100

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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 TraesCS1D01G202100 chr1D 100.000 4620 0 0 1 4620 285051625 285056244 0.000000e+00 8532.0
1 TraesCS1D01G202100 chr1B 93.740 1949 86 24 794 2721 387303264 387305197 0.000000e+00 2891.0
2 TraesCS1D01G202100 chr1B 94.710 983 46 4 2789 3767 387305218 387306198 0.000000e+00 1522.0
3 TraesCS1D01G202100 chr1B 94.215 847 36 7 3783 4620 387306262 387307104 0.000000e+00 1280.0
4 TraesCS1D01G202100 chr1B 92.421 818 39 13 1 805 387302439 387303246 0.000000e+00 1146.0
5 TraesCS1D01G202100 chr1B 83.333 114 15 3 3842 3954 387306127 387306237 8.180000e-18 102.0
6 TraesCS1D01G202100 chr1B 94.000 50 3 0 2741 2790 605929087 605929038 4.960000e-10 76.8
7 TraesCS1D01G202100 chr1B 90.385 52 5 0 2740 2791 543504359 543504308 8.290000e-08 69.4
8 TraesCS1D01G202100 chr1A 94.391 1854 69 16 894 2721 356471301 356473145 0.000000e+00 2815.0
9 TraesCS1D01G202100 chr1A 96.301 838 27 3 2792 3626 356473168 356474004 0.000000e+00 1373.0
10 TraesCS1D01G202100 chr1A 93.844 861 38 10 3761 4620 356474144 356474990 0.000000e+00 1282.0
11 TraesCS1D01G202100 chr1A 90.709 818 52 15 1 806 356470384 356471189 0.000000e+00 1068.0
12 TraesCS1D01G202100 chr1A 92.593 108 6 1 3662 3767 356474003 356474110 2.230000e-33 154.0
13 TraesCS1D01G202100 chr1A 85.965 114 13 2 3842 3954 356474038 356474149 8.120000e-23 119.0
14 TraesCS1D01G202100 chr4D 87.324 71 6 1 2720 2790 38288055 38288122 1.380000e-10 78.7
15 TraesCS1D01G202100 chr6D 92.000 50 4 0 2741 2790 48464538 48464587 2.310000e-08 71.3
16 TraesCS1D01G202100 chr4B 93.617 47 3 0 2741 2787 535093380 535093334 2.310000e-08 71.3
17 TraesCS1D01G202100 chr2D 92.000 50 4 0 2741 2790 119819486 119819535 2.310000e-08 71.3
18 TraesCS1D01G202100 chr2B 90.566 53 5 0 2740 2792 1266781 1266833 2.310000e-08 71.3
19 TraesCS1D01G202100 chr3D 88.889 54 6 0 2741 2794 511343481 511343534 2.980000e-07 67.6
20 TraesCS1D01G202100 chr3B 88.889 54 6 0 2741 2794 672866907 672866960 2.980000e-07 67.6


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 TraesCS1D01G202100 chr1D 285051625 285056244 4619 False 8532.000000 8532 100.0000 1 4620 1 chr1D.!!$F1 4619
1 TraesCS1D01G202100 chr1B 387302439 387307104 4665 False 1388.200000 2891 91.6838 1 4620 5 chr1B.!!$F1 4619
2 TraesCS1D01G202100 chr1A 356470384 356474990 4606 False 1135.166667 2815 92.3005 1 4620 6 chr1A.!!$F1 4619

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
855 896 0.040204 CCCAGCCCAGTTCAGGAAAT 59.960 55.000 0.0 0.0 0.0 2.17 F
877 918 0.383231 GCCCAGCCGATTGATGAAAG 59.617 55.000 0.0 0.0 0.0 2.62 F
1652 1716 1.153745 GAGTCACAGCAGTAGGCCG 60.154 63.158 0.0 0.0 46.5 6.13 F
2786 2859 0.708802 AGTTCTTCGGTAGGGAGGGA 59.291 55.000 0.0 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2778 2851 0.119358 AAGCCAACTACTCCCTCCCT 59.881 55.0 0.00 0.00 0.00 4.20 R
2779 2852 0.992695 AAAGCCAACTACTCCCTCCC 59.007 55.0 0.00 0.00 0.00 4.30 R
3132 3248 0.940126 GATAGCCATTGTCGCACTGG 59.060 55.0 10.46 10.46 37.27 4.00 R
3775 3894 0.602562 GCTGTGCAAAATACAGGCCA 59.397 50.0 5.01 0.00 44.36 5.36 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
226 227 0.796312 AAACGGCTCTACATGTTGCG 59.204 50.000 2.30 3.91 0.00 4.85
306 307 1.338655 GGAGCTACCATCCGAGAAGAC 59.661 57.143 0.00 0.00 38.79 3.01
515 516 4.602006 TGAAGCAGACGAATAGAATCGAG 58.398 43.478 3.47 0.00 45.48 4.04
555 556 3.153369 TGATGGTGCCAACTTGTATGT 57.847 42.857 0.00 0.00 0.00 2.29
558 559 1.339610 TGGTGCCAACTTGTATGTTGC 59.660 47.619 5.41 3.07 44.12 4.17
561 562 1.001924 TGCCAACTTGTATGTTGCGTG 60.002 47.619 5.41 0.00 44.12 5.34
594 595 6.616774 TCTTTTGGCAATTTTGGAATGTTC 57.383 33.333 0.00 0.00 0.00 3.18
595 596 6.118170 TCTTTTGGCAATTTTGGAATGTTCA 58.882 32.000 0.00 0.00 0.00 3.18
599 600 5.374921 TGGCAATTTTGGAATGTTCACAAT 58.625 33.333 0.00 0.00 0.00 2.71
612 617 8.755018 GGAATGTTCACAATTGTAAGAGTTTTG 58.245 33.333 11.53 0.00 0.00 2.44
618 623 6.042143 CACAATTGTAAGAGTTTTGGCTGTT 58.958 36.000 11.53 0.00 0.00 3.16
629 634 1.890625 TTGGCTGTTCATGGGCATGC 61.891 55.000 9.90 9.90 38.65 4.06
634 639 2.860009 CTGTTCATGGGCATGCTATCT 58.140 47.619 18.92 0.00 38.65 1.98
640 645 3.842436 TCATGGGCATGCTATCTGTATCT 59.158 43.478 18.92 0.00 38.65 1.98
649 657 7.151308 GCATGCTATCTGTATCTTAGTTGACT 58.849 38.462 11.37 0.00 0.00 3.41
659 667 7.986562 TGTATCTTAGTTGACTAGCAGTACTG 58.013 38.462 18.93 18.93 0.00 2.74
666 674 6.113411 AGTTGACTAGCAGTACTGTGTTTTT 58.887 36.000 23.44 4.36 0.00 1.94
671 679 7.598869 TGACTAGCAGTACTGTGTTTTTATCAG 59.401 37.037 23.44 7.02 35.60 2.90
673 681 4.455877 AGCAGTACTGTGTTTTTATCAGGC 59.544 41.667 23.44 4.45 34.02 4.85
676 684 5.470098 CAGTACTGTGTTTTTATCAGGCAGT 59.530 40.000 15.06 0.00 38.88 4.40
678 686 5.186996 ACTGTGTTTTTATCAGGCAGTTG 57.813 39.130 0.00 0.00 32.62 3.16
679 687 4.644685 ACTGTGTTTTTATCAGGCAGTTGT 59.355 37.500 0.00 0.00 32.62 3.32
680 688 5.127031 ACTGTGTTTTTATCAGGCAGTTGTT 59.873 36.000 0.00 0.00 32.62 2.83
681 689 5.347342 TGTGTTTTTATCAGGCAGTTGTTG 58.653 37.500 0.00 0.00 0.00 3.33
682 690 5.105554 TGTGTTTTTATCAGGCAGTTGTTGT 60.106 36.000 0.00 0.00 0.00 3.32
683 691 5.458779 GTGTTTTTATCAGGCAGTTGTTGTC 59.541 40.000 0.00 0.00 0.00 3.18
684 692 5.359576 TGTTTTTATCAGGCAGTTGTTGTCT 59.640 36.000 0.00 0.00 44.30 3.41
685 693 6.127479 TGTTTTTATCAGGCAGTTGTTGTCTT 60.127 34.615 0.00 0.00 39.12 3.01
686 694 5.437289 TTTATCAGGCAGTTGTTGTCTTG 57.563 39.130 0.00 0.00 39.12 3.02
695 703 5.355071 GGCAGTTGTTGTCTTGATGATGATA 59.645 40.000 0.00 0.00 0.00 2.15
774 787 6.783708 ATGTGTTGTGTTTTTCTTAAGGGA 57.216 33.333 1.85 0.00 0.00 4.20
778 791 7.547370 TGTGTTGTGTTTTTCTTAAGGGAAATG 59.453 33.333 1.85 0.00 35.51 2.32
789 802 5.590259 TCTTAAGGGAAATGTTATCTGCTGC 59.410 40.000 1.85 0.00 0.00 5.25
790 803 3.659183 AGGGAAATGTTATCTGCTGCT 57.341 42.857 0.00 0.00 0.00 4.24
791 804 3.549794 AGGGAAATGTTATCTGCTGCTC 58.450 45.455 0.00 0.00 0.00 4.26
798 811 2.069273 GTTATCTGCTGCTCGTGTTGT 58.931 47.619 0.00 0.00 0.00 3.32
806 819 2.346847 GCTGCTCGTGTTGTAATCTCAG 59.653 50.000 0.00 0.00 0.00 3.35
807 820 3.838120 CTGCTCGTGTTGTAATCTCAGA 58.162 45.455 0.00 0.00 0.00 3.27
808 821 4.237724 CTGCTCGTGTTGTAATCTCAGAA 58.762 43.478 0.00 0.00 0.00 3.02
809 822 4.237724 TGCTCGTGTTGTAATCTCAGAAG 58.762 43.478 0.00 0.00 0.00 2.85
810 823 3.614616 GCTCGTGTTGTAATCTCAGAAGG 59.385 47.826 0.00 0.00 0.00 3.46
811 824 4.618460 GCTCGTGTTGTAATCTCAGAAGGA 60.618 45.833 0.00 0.00 0.00 3.36
812 825 5.462530 TCGTGTTGTAATCTCAGAAGGAA 57.537 39.130 0.00 0.00 0.00 3.36
816 857 6.173339 GTGTTGTAATCTCAGAAGGAATGGA 58.827 40.000 0.00 0.00 0.00 3.41
823 864 7.700022 AATCTCAGAAGGAATGGAAAGAAAG 57.300 36.000 0.00 0.00 0.00 2.62
828 869 6.838612 TCAGAAGGAATGGAAAGAAAGGAAAA 59.161 34.615 0.00 0.00 0.00 2.29
831 872 7.345653 AGAAGGAATGGAAAGAAAGGAAAAACT 59.654 33.333 0.00 0.00 0.00 2.66
833 874 8.547481 AGGAATGGAAAGAAAGGAAAAACTAA 57.453 30.769 0.00 0.00 0.00 2.24
840 881 4.152647 AGAAAGGAAAAACTAAGGCCCAG 58.847 43.478 0.00 0.00 0.00 4.45
854 895 1.460255 CCCAGCCCAGTTCAGGAAA 59.540 57.895 0.00 0.00 0.00 3.13
855 896 0.040204 CCCAGCCCAGTTCAGGAAAT 59.960 55.000 0.00 0.00 0.00 2.17
857 898 2.648059 CCAGCCCAGTTCAGGAAATAG 58.352 52.381 0.00 0.00 0.00 1.73
858 899 2.648059 CAGCCCAGTTCAGGAAATAGG 58.352 52.381 0.00 0.00 0.00 2.57
859 900 1.064389 AGCCCAGTTCAGGAAATAGGC 60.064 52.381 10.25 10.25 39.49 3.93
860 901 2.024306 GCCCAGTTCAGGAAATAGGCC 61.024 57.143 7.54 0.00 32.93 5.19
861 902 1.410224 CCCAGTTCAGGAAATAGGCCC 60.410 57.143 0.00 0.00 0.00 5.80
862 903 1.284785 CCAGTTCAGGAAATAGGCCCA 59.715 52.381 0.00 0.00 0.00 5.36
863 904 2.648059 CAGTTCAGGAAATAGGCCCAG 58.352 52.381 0.00 0.00 0.00 4.45
877 918 0.383231 GCCCAGCCGATTGATGAAAG 59.617 55.000 0.00 0.00 0.00 2.62
878 919 2.018644 GCCCAGCCGATTGATGAAAGA 61.019 52.381 0.00 0.00 0.00 2.52
888 929 5.523188 CCGATTGATGAAAGAGGAAGAAGAG 59.477 44.000 0.00 0.00 0.00 2.85
891 932 5.083533 TGATGAAAGAGGAAGAAGAGAGC 57.916 43.478 0.00 0.00 0.00 4.09
895 942 4.346418 TGAAAGAGGAAGAAGAGAGCAGTT 59.654 41.667 0.00 0.00 0.00 3.16
934 983 4.522114 CATCTACTCTCACACTCAGAGGA 58.478 47.826 1.53 0.00 41.66 3.71
941 990 2.754552 CTCACACTCAGAGGAAGGAGAG 59.245 54.545 1.53 0.00 35.17 3.20
942 991 2.376855 TCACACTCAGAGGAAGGAGAGA 59.623 50.000 1.53 0.00 35.17 3.10
993 1042 3.187700 CACAACCCACGAAGCTAGATAC 58.812 50.000 0.00 0.00 0.00 2.24
1007 1056 3.617531 GCTAGATACATAAGCATGGCGGT 60.618 47.826 0.00 0.00 36.39 5.68
1014 1063 1.836999 TAAGCATGGCGGTCACCAGT 61.837 55.000 0.00 0.00 44.71 4.00
1368 1417 1.407936 CCATGGACTCCGAGTCTGAT 58.592 55.000 24.45 15.35 44.46 2.90
1518 1571 1.825090 TCCACATGGTCATCTTGTGC 58.175 50.000 0.00 0.00 45.03 4.57
1529 1582 4.094294 GGTCATCTTGTGCGCAAATTACTA 59.906 41.667 14.00 0.00 33.73 1.82
1532 1585 4.014847 TCTTGTGCGCAAATTACTATGC 57.985 40.909 14.00 0.00 39.17 3.14
1614 1678 6.778834 TCAAAATCATGACCTGCATATGTT 57.221 33.333 0.00 0.00 34.82 2.71
1615 1679 6.566141 TCAAAATCATGACCTGCATATGTTG 58.434 36.000 0.00 0.00 34.82 3.33
1616 1680 6.153170 TCAAAATCATGACCTGCATATGTTGT 59.847 34.615 0.00 0.00 34.82 3.32
1652 1716 1.153745 GAGTCACAGCAGTAGGCCG 60.154 63.158 0.00 0.00 46.50 6.13
1978 2046 8.181487 TCTTCGTTCTTATCTTCATTAAACCG 57.819 34.615 0.00 0.00 0.00 4.44
1996 2064 5.446260 AACCGGACTTTTGTTATCCCTAT 57.554 39.130 9.46 0.00 0.00 2.57
2001 2069 8.887393 ACCGGACTTTTGTTATCCCTATAATAT 58.113 33.333 9.46 0.00 30.42 1.28
2154 2222 9.342308 CTGAAATCTAGGCCATAACTAAAATCA 57.658 33.333 5.01 0.00 0.00 2.57
2342 2410 9.982291 GTGACGATCAAACAATATTTAAGCTTA 57.018 29.630 0.86 0.86 0.00 3.09
2343 2411 9.982291 TGACGATCAAACAATATTTAAGCTTAC 57.018 29.630 5.45 0.00 0.00 2.34
2344 2412 9.434559 GACGATCAAACAATATTTAAGCTTACC 57.565 33.333 5.45 0.00 0.00 2.85
2345 2413 8.952278 ACGATCAAACAATATTTAAGCTTACCA 58.048 29.630 5.45 0.00 0.00 3.25
2405 2475 9.073475 AGCTGAATGTAACTTTTTGGTAATACA 57.927 29.630 0.00 0.00 0.00 2.29
2525 2595 7.156673 TGAAACTCTTTAGTACTACGCCAATT 58.843 34.615 0.91 0.00 33.75 2.32
2552 2622 9.256228 TGGGTATATGATTACAGTTCTCCTATC 57.744 37.037 0.00 0.00 0.00 2.08
2588 2660 1.871676 GACCCCTCGTTTCTGTGAAAC 59.128 52.381 11.76 11.76 37.35 2.78
2660 2733 8.031277 ACCTTATGAATGATGCTTTTCTTGTTC 58.969 33.333 0.00 0.00 0.00 3.18
2669 2742 5.710513 TGCTTTTCTTGTTCATATGTGCT 57.289 34.783 1.90 0.00 0.00 4.40
2728 2801 9.750783 TTTGACTAGTTGACTATTACTACCTCT 57.249 33.333 0.00 0.00 0.00 3.69
2729 2802 8.734218 TGACTAGTTGACTATTACTACCTCTG 57.266 38.462 0.00 0.00 0.00 3.35
2730 2803 8.327271 TGACTAGTTGACTATTACTACCTCTGT 58.673 37.037 0.00 0.00 0.00 3.41
2731 2804 9.829507 GACTAGTTGACTATTACTACCTCTGTA 57.170 37.037 0.00 0.00 0.00 2.74
2732 2805 9.612066 ACTAGTTGACTATTACTACCTCTGTAC 57.388 37.037 0.00 0.00 0.00 2.90
2733 2806 7.878547 AGTTGACTATTACTACCTCTGTACC 57.121 40.000 0.00 0.00 0.00 3.34
2734 2807 6.541641 AGTTGACTATTACTACCTCTGTACCG 59.458 42.308 0.00 0.00 0.00 4.02
2735 2808 6.239217 TGACTATTACTACCTCTGTACCGA 57.761 41.667 0.00 0.00 0.00 4.69
2736 2809 6.653020 TGACTATTACTACCTCTGTACCGAA 58.347 40.000 0.00 0.00 0.00 4.30
2737 2810 7.112122 TGACTATTACTACCTCTGTACCGAAA 58.888 38.462 0.00 0.00 0.00 3.46
2738 2811 7.776969 TGACTATTACTACCTCTGTACCGAAAT 59.223 37.037 0.00 0.00 0.00 2.17
2739 2812 9.277783 GACTATTACTACCTCTGTACCGAAATA 57.722 37.037 0.00 0.00 0.00 1.40
2740 2813 9.632638 ACTATTACTACCTCTGTACCGAAATAA 57.367 33.333 0.00 0.00 0.00 1.40
2743 2816 8.986477 TTACTACCTCTGTACCGAAATAAAAC 57.014 34.615 0.00 0.00 0.00 2.43
2744 2817 7.237209 ACTACCTCTGTACCGAAATAAAACT 57.763 36.000 0.00 0.00 0.00 2.66
2745 2818 8.353423 ACTACCTCTGTACCGAAATAAAACTA 57.647 34.615 0.00 0.00 0.00 2.24
2746 2819 8.465201 ACTACCTCTGTACCGAAATAAAACTAG 58.535 37.037 0.00 0.00 0.00 2.57
2747 2820 7.237209 ACCTCTGTACCGAAATAAAACTAGT 57.763 36.000 0.00 0.00 0.00 2.57
2748 2821 8.353423 ACCTCTGTACCGAAATAAAACTAGTA 57.647 34.615 0.00 0.00 0.00 1.82
2749 2822 8.246871 ACCTCTGTACCGAAATAAAACTAGTAC 58.753 37.037 0.00 0.00 0.00 2.73
2750 2823 8.246180 CCTCTGTACCGAAATAAAACTAGTACA 58.754 37.037 0.00 0.00 37.01 2.90
2751 2824 9.630098 CTCTGTACCGAAATAAAACTAGTACAA 57.370 33.333 0.00 0.00 38.39 2.41
2752 2825 9.630098 TCTGTACCGAAATAAAACTAGTACAAG 57.370 33.333 0.00 0.00 38.39 3.16
2753 2826 9.415544 CTGTACCGAAATAAAACTAGTACAAGT 57.584 33.333 0.00 0.00 38.39 3.16
2754 2827 9.762933 TGTACCGAAATAAAACTAGTACAAGTT 57.237 29.630 0.00 0.00 41.46 2.66
2756 2829 8.315391 ACCGAAATAAAACTAGTACAAGTTCC 57.685 34.615 0.00 0.00 38.76 3.62
2757 2830 7.388776 ACCGAAATAAAACTAGTACAAGTTCCC 59.611 37.037 0.00 0.00 38.76 3.97
2758 2831 7.148356 CCGAAATAAAACTAGTACAAGTTCCCC 60.148 40.741 0.00 0.00 38.76 4.81
2759 2832 7.148356 CGAAATAAAACTAGTACAAGTTCCCCC 60.148 40.741 0.00 0.00 38.76 5.40
2760 2833 6.707273 ATAAAACTAGTACAAGTTCCCCCA 57.293 37.500 0.00 0.00 38.76 4.96
2761 2834 5.391577 AAAACTAGTACAAGTTCCCCCAA 57.608 39.130 0.00 0.00 38.76 4.12
2762 2835 4.362470 AACTAGTACAAGTTCCCCCAAC 57.638 45.455 0.00 0.00 34.60 3.77
2764 2837 4.755437 ACTAGTACAAGTTCCCCCAACTA 58.245 43.478 0.00 0.00 45.32 2.24
2765 2838 4.529769 ACTAGTACAAGTTCCCCCAACTAC 59.470 45.833 0.00 0.00 45.32 2.73
2766 2839 3.320129 AGTACAAGTTCCCCCAACTACA 58.680 45.455 0.00 0.00 45.32 2.74
2767 2840 3.717913 AGTACAAGTTCCCCCAACTACAA 59.282 43.478 0.00 0.00 45.32 2.41
2768 2841 3.223674 ACAAGTTCCCCCAACTACAAG 57.776 47.619 0.00 0.00 45.32 3.16
2769 2842 2.512476 ACAAGTTCCCCCAACTACAAGT 59.488 45.455 0.00 0.00 45.32 3.16
2770 2843 3.053170 ACAAGTTCCCCCAACTACAAGTT 60.053 43.478 0.00 0.00 45.32 2.66
2771 2844 3.503800 AGTTCCCCCAACTACAAGTTC 57.496 47.619 0.00 0.00 44.13 3.01
2772 2845 3.053826 AGTTCCCCCAACTACAAGTTCT 58.946 45.455 0.00 0.00 44.13 3.01
2773 2846 3.462205 AGTTCCCCCAACTACAAGTTCTT 59.538 43.478 0.00 0.00 44.13 2.52
2774 2847 3.782656 TCCCCCAACTACAAGTTCTTC 57.217 47.619 0.00 0.00 36.03 2.87
2775 2848 2.038033 TCCCCCAACTACAAGTTCTTCG 59.962 50.000 0.00 0.00 36.03 3.79
2776 2849 2.423577 CCCCAACTACAAGTTCTTCGG 58.576 52.381 0.00 0.00 36.03 4.30
2777 2850 2.224450 CCCCAACTACAAGTTCTTCGGT 60.224 50.000 0.00 0.00 36.03 4.69
2778 2851 3.007182 CCCCAACTACAAGTTCTTCGGTA 59.993 47.826 0.00 0.00 36.03 4.02
2779 2852 4.243270 CCCAACTACAAGTTCTTCGGTAG 58.757 47.826 0.00 0.00 36.03 3.18
2780 2853 4.243270 CCAACTACAAGTTCTTCGGTAGG 58.757 47.826 11.80 0.00 36.03 3.18
2781 2854 4.243270 CAACTACAAGTTCTTCGGTAGGG 58.757 47.826 11.80 3.98 36.03 3.53
2782 2855 3.771216 ACTACAAGTTCTTCGGTAGGGA 58.229 45.455 11.80 0.00 37.99 4.20
2783 2856 3.762823 ACTACAAGTTCTTCGGTAGGGAG 59.237 47.826 11.80 0.00 37.99 4.30
2784 2857 1.900486 ACAAGTTCTTCGGTAGGGAGG 59.100 52.381 0.00 0.00 0.00 4.30
2785 2858 1.207329 CAAGTTCTTCGGTAGGGAGGG 59.793 57.143 0.00 0.00 0.00 4.30
2786 2859 0.708802 AGTTCTTCGGTAGGGAGGGA 59.291 55.000 0.00 0.00 0.00 4.20
2787 2860 1.112950 GTTCTTCGGTAGGGAGGGAG 58.887 60.000 0.00 0.00 0.00 4.30
2788 2861 0.708802 TTCTTCGGTAGGGAGGGAGT 59.291 55.000 0.00 0.00 0.00 3.85
2789 2862 1.600058 TCTTCGGTAGGGAGGGAGTA 58.400 55.000 0.00 0.00 0.00 2.59
2823 2937 6.374333 TGAATGCCCTGTTATTTAGTTGACTC 59.626 38.462 0.00 0.00 0.00 3.36
2848 2962 3.975168 TGCCCTCTTCTAGTTTGGTAC 57.025 47.619 0.00 0.00 0.00 3.34
2910 3024 5.514274 TCATGGAACCAGAACAAGTTTTC 57.486 39.130 0.00 0.00 0.00 2.29
2915 3029 4.495844 GGAACCAGAACAAGTTTTCGACAG 60.496 45.833 0.00 0.00 0.00 3.51
3055 3171 3.091545 CCTTGCCATTATGGTGAAGTGT 58.908 45.455 13.28 0.00 40.46 3.55
3090 3206 5.887598 AGCCTTTGCATATCTGTTGATACAA 59.112 36.000 0.00 0.00 41.13 2.41
3259 3375 0.943835 GCGCAAAGGGCAAACGATTT 60.944 50.000 0.30 0.00 45.17 2.17
3460 3576 1.225704 CATGGGTCCTCTTGAGGCC 59.774 63.158 11.61 14.52 0.00 5.19
3629 3745 5.906113 TGAGATATACTAAGCTAGCCTGC 57.094 43.478 12.13 0.00 0.00 4.85
3646 3762 2.352651 CCTGCCAGTCACATGTATTTCG 59.647 50.000 0.00 0.00 0.00 3.46
3673 3789 1.669115 GCAGTCGCTGGAGCTTTCA 60.669 57.895 8.57 0.00 39.32 2.69
3676 3792 0.459237 AGTCGCTGGAGCTTTCATCG 60.459 55.000 7.60 7.60 39.32 3.84
3767 3886 1.615392 GTTCTGGCATTTGACCAAGCT 59.385 47.619 0.00 0.00 36.56 3.74
3769 3888 2.715046 TCTGGCATTTGACCAAGCTAG 58.285 47.619 0.00 0.00 36.56 3.42
3770 3889 1.133790 CTGGCATTTGACCAAGCTAGC 59.866 52.381 6.62 6.62 36.56 3.42
3771 3890 0.457443 GGCATTTGACCAAGCTAGCC 59.543 55.000 12.13 0.00 0.00 3.93
3772 3891 1.467920 GCATTTGACCAAGCTAGCCT 58.532 50.000 12.13 0.00 0.00 4.58
3773 3892 1.403323 GCATTTGACCAAGCTAGCCTC 59.597 52.381 12.13 1.70 0.00 4.70
3775 3894 3.285484 CATTTGACCAAGCTAGCCTCAT 58.715 45.455 12.13 0.00 0.00 2.90
3776 3895 2.408271 TTGACCAAGCTAGCCTCATG 57.592 50.000 12.13 5.79 0.00 3.07
3777 3896 0.543277 TGACCAAGCTAGCCTCATGG 59.457 55.000 19.32 19.32 37.19 3.66
3817 3984 0.236711 CGACTGCTGGAGCTTTTGTG 59.763 55.000 0.00 0.00 42.66 3.33
3821 3988 2.360165 ACTGCTGGAGCTTTTGTGAAAG 59.640 45.455 0.00 0.00 44.10 2.62
3838 4005 5.106475 TGTGAAAGCAAAGACGTAACACTTT 60.106 36.000 0.00 0.00 36.89 2.66
3861 4028 6.385649 TTTTTAGCAGTAGACTTTGTTGGG 57.614 37.500 0.00 0.00 0.00 4.12
3877 4044 2.130272 TGGGCGTTGCATTTGGTATA 57.870 45.000 0.00 0.00 0.00 1.47
3878 4045 2.660572 TGGGCGTTGCATTTGGTATAT 58.339 42.857 0.00 0.00 0.00 0.86
3879 4046 2.360483 TGGGCGTTGCATTTGGTATATG 59.640 45.455 0.00 0.00 0.00 1.78
3880 4047 2.621055 GGGCGTTGCATTTGGTATATGA 59.379 45.455 0.00 0.00 0.00 2.15
3926 4093 3.096489 TGACCAAGCAAATGAAAGCAC 57.904 42.857 0.00 0.00 0.00 4.40
4113 4288 6.333416 TCTGGAACTCTTGATACAATTCTCG 58.667 40.000 0.00 0.00 0.00 4.04
4147 4322 5.178438 CAGTGAAGCATGATCATCTCATCAG 59.822 44.000 4.86 0.00 42.91 2.90
4213 4388 2.604686 ACTCTGAGGCCAAGCGGA 60.605 61.111 5.01 3.35 0.00 5.54
4253 4428 0.401738 TGAGCTCCCAGTTTTCAGGG 59.598 55.000 12.15 0.00 46.51 4.45
4366 4541 6.726379 TGAACCAATTGTCTGACCCAATATA 58.274 36.000 5.17 0.00 32.40 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
226 227 1.003116 GCACGCACATCATCATTCTCC 60.003 52.381 0.00 0.00 0.00 3.71
306 307 3.998099 TCTCAGCTACAGAATCATCCG 57.002 47.619 0.00 0.00 0.00 4.18
345 346 5.526846 CCATCTTTTCTATCTTCACCTGAGC 59.473 44.000 0.00 0.00 0.00 4.26
515 516 0.548510 AAGGGCATTCTGGAGGCTAC 59.451 55.000 0.00 0.00 0.00 3.58
555 556 4.297510 CAAAAGAACAATGGATCACGCAA 58.702 39.130 0.00 0.00 0.00 4.85
558 559 3.244976 GCCAAAAGAACAATGGATCACG 58.755 45.455 0.00 0.00 36.27 4.35
561 562 6.806388 AAATTGCCAAAAGAACAATGGATC 57.194 33.333 0.00 0.00 36.27 3.36
594 595 5.591099 ACAGCCAAAACTCTTACAATTGTG 58.409 37.500 21.42 6.72 0.00 3.33
595 596 5.852282 ACAGCCAAAACTCTTACAATTGT 57.148 34.783 16.68 16.68 0.00 2.71
599 600 5.221224 CCATGAACAGCCAAAACTCTTACAA 60.221 40.000 0.00 0.00 0.00 2.41
612 617 0.752743 TAGCATGCCCATGAACAGCC 60.753 55.000 15.66 0.00 41.20 4.85
618 623 3.842436 AGATACAGATAGCATGCCCATGA 59.158 43.478 15.66 0.00 41.20 3.07
629 634 9.062524 ACTGCTAGTCAACTAAGATACAGATAG 57.937 37.037 0.00 0.00 0.00 2.08
634 639 7.610692 ACAGTACTGCTAGTCAACTAAGATACA 59.389 37.037 22.90 0.00 0.00 2.29
640 645 6.401047 AACACAGTACTGCTAGTCAACTAA 57.599 37.500 22.90 0.00 0.00 2.24
649 657 5.642063 GCCTGATAAAAACACAGTACTGCTA 59.358 40.000 22.90 5.49 0.00 3.49
659 667 5.348164 ACAACAACTGCCTGATAAAAACAC 58.652 37.500 0.00 0.00 0.00 3.32
666 674 4.350368 TCAAGACAACAACTGCCTGATA 57.650 40.909 0.00 0.00 0.00 2.15
671 679 3.503363 TCATCATCAAGACAACAACTGCC 59.497 43.478 0.00 0.00 0.00 4.85
673 681 9.850628 AAATTATCATCATCAAGACAACAACTG 57.149 29.630 0.00 0.00 0.00 3.16
695 703 9.362151 TGTTTTCAAGGGAGTGATTAGTAAATT 57.638 29.630 0.00 0.00 0.00 1.82
747 755 8.842280 CCCTTAAGAAAAACACAACACATAGTA 58.158 33.333 3.36 0.00 0.00 1.82
748 756 7.558444 TCCCTTAAGAAAAACACAACACATAGT 59.442 33.333 3.36 0.00 0.00 2.12
749 757 7.936584 TCCCTTAAGAAAAACACAACACATAG 58.063 34.615 3.36 0.00 0.00 2.23
750 758 7.883391 TCCCTTAAGAAAAACACAACACATA 57.117 32.000 3.36 0.00 0.00 2.29
751 759 6.783708 TCCCTTAAGAAAAACACAACACAT 57.216 33.333 3.36 0.00 0.00 3.21
753 761 7.547722 ACATTTCCCTTAAGAAAAACACAACAC 59.452 33.333 3.36 0.00 39.11 3.32
757 770 9.974980 GATAACATTTCCCTTAAGAAAAACACA 57.025 29.630 3.36 0.00 39.11 3.72
760 773 9.140286 GCAGATAACATTTCCCTTAAGAAAAAC 57.860 33.333 3.36 0.00 39.11 2.43
764 777 6.095440 GCAGCAGATAACATTTCCCTTAAGAA 59.905 38.462 3.36 0.00 0.00 2.52
765 778 5.590259 GCAGCAGATAACATTTCCCTTAAGA 59.410 40.000 3.36 0.00 0.00 2.10
766 779 5.591877 AGCAGCAGATAACATTTCCCTTAAG 59.408 40.000 0.00 0.00 0.00 1.85
769 782 3.950395 GAGCAGCAGATAACATTTCCCTT 59.050 43.478 0.00 0.00 0.00 3.95
770 783 3.549794 GAGCAGCAGATAACATTTCCCT 58.450 45.455 0.00 0.00 0.00 4.20
771 784 2.289002 CGAGCAGCAGATAACATTTCCC 59.711 50.000 0.00 0.00 0.00 3.97
772 785 2.939103 ACGAGCAGCAGATAACATTTCC 59.061 45.455 0.00 0.00 0.00 3.13
774 787 3.338249 ACACGAGCAGCAGATAACATTT 58.662 40.909 0.00 0.00 0.00 2.32
778 791 2.069273 ACAACACGAGCAGCAGATAAC 58.931 47.619 0.00 0.00 0.00 1.89
789 802 5.060662 TCCTTCTGAGATTACAACACGAG 57.939 43.478 0.00 0.00 0.00 4.18
790 803 5.462530 TTCCTTCTGAGATTACAACACGA 57.537 39.130 0.00 0.00 0.00 4.35
791 804 5.063944 CCATTCCTTCTGAGATTACAACACG 59.936 44.000 0.00 0.00 0.00 4.49
798 811 7.831193 CCTTTCTTTCCATTCCTTCTGAGATTA 59.169 37.037 0.00 0.00 0.00 1.75
806 819 7.500992 AGTTTTTCCTTTCTTTCCATTCCTTC 58.499 34.615 0.00 0.00 0.00 3.46
807 820 7.437713 AGTTTTTCCTTTCTTTCCATTCCTT 57.562 32.000 0.00 0.00 0.00 3.36
808 821 8.547481 TTAGTTTTTCCTTTCTTTCCATTCCT 57.453 30.769 0.00 0.00 0.00 3.36
809 822 7.872993 CCTTAGTTTTTCCTTTCTTTCCATTCC 59.127 37.037 0.00 0.00 0.00 3.01
810 823 7.385205 GCCTTAGTTTTTCCTTTCTTTCCATTC 59.615 37.037 0.00 0.00 0.00 2.67
811 824 7.217200 GCCTTAGTTTTTCCTTTCTTTCCATT 58.783 34.615 0.00 0.00 0.00 3.16
812 825 6.239600 GGCCTTAGTTTTTCCTTTCTTTCCAT 60.240 38.462 0.00 0.00 0.00 3.41
816 857 4.966168 TGGGCCTTAGTTTTTCCTTTCTTT 59.034 37.500 4.53 0.00 0.00 2.52
823 864 0.895530 GGCTGGGCCTTAGTTTTTCC 59.104 55.000 4.53 0.00 46.69 3.13
840 881 1.393603 GCCTATTTCCTGAACTGGGC 58.606 55.000 8.47 8.47 39.57 5.36
848 889 4.587056 GGCTGGGCCTATTTCCTG 57.413 61.111 4.53 0.00 46.69 3.86
857 898 1.037030 TTTCATCAATCGGCTGGGCC 61.037 55.000 0.00 0.00 46.75 5.80
858 899 0.383231 CTTTCATCAATCGGCTGGGC 59.617 55.000 0.00 0.00 0.00 5.36
859 900 1.945394 CTCTTTCATCAATCGGCTGGG 59.055 52.381 0.00 0.00 0.00 4.45
860 901 1.945394 CCTCTTTCATCAATCGGCTGG 59.055 52.381 0.00 0.00 0.00 4.85
861 902 2.910199 TCCTCTTTCATCAATCGGCTG 58.090 47.619 0.00 0.00 0.00 4.85
862 903 3.198635 TCTTCCTCTTTCATCAATCGGCT 59.801 43.478 0.00 0.00 0.00 5.52
863 904 3.535561 TCTTCCTCTTTCATCAATCGGC 58.464 45.455 0.00 0.00 0.00 5.54
865 906 6.336566 TCTCTTCTTCCTCTTTCATCAATCG 58.663 40.000 0.00 0.00 0.00 3.34
866 907 6.258507 GCTCTCTTCTTCCTCTTTCATCAATC 59.741 42.308 0.00 0.00 0.00 2.67
867 908 6.114767 GCTCTCTTCTTCCTCTTTCATCAAT 58.885 40.000 0.00 0.00 0.00 2.57
868 909 5.012458 TGCTCTCTTCTTCCTCTTTCATCAA 59.988 40.000 0.00 0.00 0.00 2.57
869 910 4.529769 TGCTCTCTTCTTCCTCTTTCATCA 59.470 41.667 0.00 0.00 0.00 3.07
870 911 5.083533 TGCTCTCTTCTTCCTCTTTCATC 57.916 43.478 0.00 0.00 0.00 2.92
871 912 4.531732 ACTGCTCTCTTCTTCCTCTTTCAT 59.468 41.667 0.00 0.00 0.00 2.57
872 913 3.900601 ACTGCTCTCTTCTTCCTCTTTCA 59.099 43.478 0.00 0.00 0.00 2.69
873 914 4.535526 ACTGCTCTCTTCTTCCTCTTTC 57.464 45.455 0.00 0.00 0.00 2.62
877 918 5.400066 AACTAACTGCTCTCTTCTTCCTC 57.600 43.478 0.00 0.00 0.00 3.71
878 919 6.097696 GGATAACTAACTGCTCTCTTCTTCCT 59.902 42.308 0.00 0.00 0.00 3.36
888 929 5.346181 AAGGAGTGGATAACTAACTGCTC 57.654 43.478 0.00 0.00 41.14 4.26
891 932 5.677319 TGGAAGGAGTGGATAACTAACTG 57.323 43.478 0.00 0.00 40.07 3.16
895 942 6.923670 AGTAGATGGAAGGAGTGGATAACTA 58.076 40.000 0.00 0.00 40.07 2.24
934 983 1.567357 GAGTGCTCCCTTCTCTCCTT 58.433 55.000 0.00 0.00 0.00 3.36
941 990 4.821589 CGGCGGAGTGCTCCCTTC 62.822 72.222 12.20 2.68 46.96 3.46
973 1022 2.829720 TGTATCTAGCTTCGTGGGTTGT 59.170 45.455 0.00 0.00 0.00 3.32
974 1023 3.520290 TGTATCTAGCTTCGTGGGTTG 57.480 47.619 0.00 0.00 0.00 3.77
993 1042 0.747644 TGGTGACCGCCATGCTTATG 60.748 55.000 0.00 0.00 32.81 1.90
1007 1056 4.662961 CGGCACTCGCACTGGTGA 62.663 66.667 4.79 0.00 41.24 4.02
1368 1417 1.404391 GAGTTGACGAAGAGCCGGATA 59.596 52.381 5.05 0.00 0.00 2.59
1518 1571 6.305399 CGAATATTTGGGCATAGTAATTTGCG 59.695 38.462 0.00 0.00 39.78 4.85
1529 1582 7.882791 TGAATACTATCACGAATATTTGGGCAT 59.117 33.333 7.61 2.28 0.00 4.40
1652 1716 9.713740 CAGCAAGATATTGTCTGATAAAAAGAC 57.286 33.333 15.14 0.00 43.62 3.01
1876 1944 3.062234 GCTCGGACCAGAAAATCGTAAAG 59.938 47.826 0.00 0.00 0.00 1.85
2154 2222 7.913674 GAGTTAGTCACTCCATTCAATTCTT 57.086 36.000 0.00 0.00 45.84 2.52
2342 2410 4.632153 CCAATAAGTAGCGAGCTAATGGT 58.368 43.478 6.36 0.00 0.00 3.55
2343 2411 3.433615 GCCAATAAGTAGCGAGCTAATGG 59.566 47.826 6.36 10.79 0.00 3.16
2344 2412 4.310769 AGCCAATAAGTAGCGAGCTAATG 58.689 43.478 6.36 2.21 0.00 1.90
2345 2413 4.608948 AGCCAATAAGTAGCGAGCTAAT 57.391 40.909 6.36 2.51 0.00 1.73
2525 2595 7.931015 AGGAGAACTGTAATCATATACCCAA 57.069 36.000 0.00 0.00 0.00 4.12
2552 2622 2.228822 GGGGTCTGTACAAAATGCACAG 59.771 50.000 0.00 4.66 41.84 3.66
2554 2624 2.488153 GAGGGGTCTGTACAAAATGCAC 59.512 50.000 0.00 0.00 0.00 4.57
2588 2660 9.107177 ACTCAAGACATCAAGCAGAATATTTAG 57.893 33.333 0.00 0.00 0.00 1.85
2610 2683 7.812191 GGTGCAACAAATATCATTACAAACTCA 59.188 33.333 0.00 0.00 39.98 3.41
2660 2733 8.604640 AGAGAGATGAATGTTAAGCACATATG 57.395 34.615 0.00 0.00 46.23 1.78
2721 2794 8.465201 ACTAGTTTTATTTCGGTACAGAGGTAG 58.535 37.037 0.00 0.00 0.00 3.18
2722 2795 8.353423 ACTAGTTTTATTTCGGTACAGAGGTA 57.647 34.615 0.00 0.00 0.00 3.08
2723 2796 7.237209 ACTAGTTTTATTTCGGTACAGAGGT 57.763 36.000 0.00 0.00 0.00 3.85
2724 2797 8.246180 TGTACTAGTTTTATTTCGGTACAGAGG 58.754 37.037 0.00 0.00 34.96 3.69
2725 2798 9.630098 TTGTACTAGTTTTATTTCGGTACAGAG 57.370 33.333 0.00 0.00 39.00 3.35
2726 2799 9.630098 CTTGTACTAGTTTTATTTCGGTACAGA 57.370 33.333 0.00 0.00 39.00 3.41
2727 2800 9.415544 ACTTGTACTAGTTTTATTTCGGTACAG 57.584 33.333 0.00 0.00 39.00 2.74
2728 2801 9.762933 AACTTGTACTAGTTTTATTTCGGTACA 57.237 29.630 15.68 0.00 34.81 2.90
2730 2803 9.423061 GGAACTTGTACTAGTTTTATTTCGGTA 57.577 33.333 21.05 0.00 38.43 4.02
2731 2804 7.388776 GGGAACTTGTACTAGTTTTATTTCGGT 59.611 37.037 21.05 0.00 38.43 4.69
2732 2805 7.148356 GGGGAACTTGTACTAGTTTTATTTCGG 60.148 40.741 21.05 0.00 38.43 4.30
2733 2806 7.148356 GGGGGAACTTGTACTAGTTTTATTTCG 60.148 40.741 21.05 0.00 38.43 3.46
2734 2807 7.666804 TGGGGGAACTTGTACTAGTTTTATTTC 59.333 37.037 21.05 9.41 38.43 2.17
2735 2808 7.528675 TGGGGGAACTTGTACTAGTTTTATTT 58.471 34.615 21.05 0.90 38.43 1.40
2736 2809 7.093965 TGGGGGAACTTGTACTAGTTTTATT 57.906 36.000 21.05 1.60 38.43 1.40
2737 2810 6.707273 TGGGGGAACTTGTACTAGTTTTAT 57.293 37.500 21.05 1.95 38.43 1.40
2738 2811 6.101588 AGTTGGGGGAACTTGTACTAGTTTTA 59.898 38.462 21.05 6.47 42.70 1.52
2739 2812 5.103813 AGTTGGGGGAACTTGTACTAGTTTT 60.104 40.000 21.05 3.00 42.70 2.43
2740 2813 4.414514 AGTTGGGGGAACTTGTACTAGTTT 59.585 41.667 21.05 7.74 42.70 2.66
2741 2814 3.978672 AGTTGGGGGAACTTGTACTAGTT 59.021 43.478 20.40 20.40 42.70 2.24
2742 2815 3.595021 AGTTGGGGGAACTTGTACTAGT 58.405 45.455 3.98 3.98 42.70 2.57
2743 2816 4.529377 TGTAGTTGGGGGAACTTGTACTAG 59.471 45.833 2.56 2.56 42.70 2.57
2744 2817 4.491675 TGTAGTTGGGGGAACTTGTACTA 58.508 43.478 0.00 0.00 42.70 1.82
2745 2818 3.320129 TGTAGTTGGGGGAACTTGTACT 58.680 45.455 0.00 0.00 42.70 2.73
2746 2819 3.775261 TGTAGTTGGGGGAACTTGTAC 57.225 47.619 0.00 0.00 42.70 2.90
2747 2820 3.717913 ACTTGTAGTTGGGGGAACTTGTA 59.282 43.478 0.00 0.00 42.70 2.41
2748 2821 2.512476 ACTTGTAGTTGGGGGAACTTGT 59.488 45.455 0.00 0.00 42.70 3.16
2749 2822 3.223674 ACTTGTAGTTGGGGGAACTTG 57.776 47.619 0.00 0.00 42.70 3.16
2750 2823 3.462205 AGAACTTGTAGTTGGGGGAACTT 59.538 43.478 0.00 0.00 42.70 2.66
2752 2825 3.503800 AGAACTTGTAGTTGGGGGAAC 57.496 47.619 0.00 0.00 38.80 3.62
2753 2826 3.495453 CGAAGAACTTGTAGTTGGGGGAA 60.495 47.826 0.00 0.00 38.80 3.97
2754 2827 2.038033 CGAAGAACTTGTAGTTGGGGGA 59.962 50.000 0.00 0.00 38.80 4.81
2755 2828 2.423577 CGAAGAACTTGTAGTTGGGGG 58.576 52.381 0.00 0.00 38.80 5.40
2756 2829 2.224450 ACCGAAGAACTTGTAGTTGGGG 60.224 50.000 0.00 0.00 38.80 4.96
2757 2830 3.121738 ACCGAAGAACTTGTAGTTGGG 57.878 47.619 0.00 0.00 38.80 4.12
2758 2831 4.243270 CCTACCGAAGAACTTGTAGTTGG 58.757 47.826 0.00 0.00 38.80 3.77
2759 2832 4.021719 TCCCTACCGAAGAACTTGTAGTTG 60.022 45.833 0.00 3.78 38.80 3.16
2760 2833 4.154942 TCCCTACCGAAGAACTTGTAGTT 58.845 43.478 9.54 0.00 41.95 2.24
2761 2834 3.762823 CTCCCTACCGAAGAACTTGTAGT 59.237 47.826 9.54 0.00 30.98 2.73
2762 2835 3.130693 CCTCCCTACCGAAGAACTTGTAG 59.869 52.174 0.00 0.00 0.00 2.74
2763 2836 3.094572 CCTCCCTACCGAAGAACTTGTA 58.905 50.000 0.00 0.00 0.00 2.41
2764 2837 1.900486 CCTCCCTACCGAAGAACTTGT 59.100 52.381 0.00 0.00 0.00 3.16
2765 2838 1.207329 CCCTCCCTACCGAAGAACTTG 59.793 57.143 0.00 0.00 0.00 3.16
2766 2839 1.078324 TCCCTCCCTACCGAAGAACTT 59.922 52.381 0.00 0.00 0.00 2.66
2767 2840 0.708802 TCCCTCCCTACCGAAGAACT 59.291 55.000 0.00 0.00 0.00 3.01
2768 2841 1.112950 CTCCCTCCCTACCGAAGAAC 58.887 60.000 0.00 0.00 0.00 3.01
2769 2842 0.708802 ACTCCCTCCCTACCGAAGAA 59.291 55.000 0.00 0.00 0.00 2.52
2770 2843 1.493871 CTACTCCCTCCCTACCGAAGA 59.506 57.143 0.00 0.00 0.00 2.87
2771 2844 1.214923 ACTACTCCCTCCCTACCGAAG 59.785 57.143 0.00 0.00 0.00 3.79
2772 2845 1.302907 ACTACTCCCTCCCTACCGAA 58.697 55.000 0.00 0.00 0.00 4.30
2773 2846 1.064166 CAACTACTCCCTCCCTACCGA 60.064 57.143 0.00 0.00 0.00 4.69
2774 2847 1.400737 CAACTACTCCCTCCCTACCG 58.599 60.000 0.00 0.00 0.00 4.02
2775 2848 1.790818 CCAACTACTCCCTCCCTACC 58.209 60.000 0.00 0.00 0.00 3.18
2776 2849 1.121378 GCCAACTACTCCCTCCCTAC 58.879 60.000 0.00 0.00 0.00 3.18
2777 2850 1.016415 AGCCAACTACTCCCTCCCTA 58.984 55.000 0.00 0.00 0.00 3.53
2778 2851 0.119358 AAGCCAACTACTCCCTCCCT 59.881 55.000 0.00 0.00 0.00 4.20
2779 2852 0.992695 AAAGCCAACTACTCCCTCCC 59.007 55.000 0.00 0.00 0.00 4.30
2780 2853 1.628846 TCAAAGCCAACTACTCCCTCC 59.371 52.381 0.00 0.00 0.00 4.30
2781 2854 3.418684 TTCAAAGCCAACTACTCCCTC 57.581 47.619 0.00 0.00 0.00 4.30
2782 2855 3.690460 CATTCAAAGCCAACTACTCCCT 58.310 45.455 0.00 0.00 0.00 4.20
2783 2856 2.164422 GCATTCAAAGCCAACTACTCCC 59.836 50.000 0.00 0.00 0.00 4.30
2784 2857 3.494045 GCATTCAAAGCCAACTACTCC 57.506 47.619 0.00 0.00 0.00 3.85
2823 2937 2.939103 CAAACTAGAAGAGGGCATTCCG 59.061 50.000 0.00 0.00 41.52 4.30
2848 2962 2.233922 ACTATTCTTGTCCCACCACTCG 59.766 50.000 0.00 0.00 0.00 4.18
2910 3024 3.951979 AGTTTGACTTTGCTTCTGTCG 57.048 42.857 0.00 0.00 33.81 4.35
2941 3055 9.403583 ACGTAATATTTCAAATACCCATTCTGT 57.596 29.630 0.00 0.00 0.00 3.41
2942 3056 9.663904 CACGTAATATTTCAAATACCCATTCTG 57.336 33.333 0.00 0.00 0.00 3.02
3045 3161 3.207265 ACTATTGCACACACTTCACCA 57.793 42.857 0.00 0.00 0.00 4.17
3090 3206 6.095440 AGTCAAGTCACAAAATGCAACTAGTT 59.905 34.615 1.12 1.12 0.00 2.24
3132 3248 0.940126 GATAGCCATTGTCGCACTGG 59.060 55.000 10.46 10.46 37.27 4.00
3259 3375 2.601067 CTGGTGTTGGGCATGGCA 60.601 61.111 22.06 4.40 0.00 4.92
3629 3745 4.436050 GCTGTTCGAAATACATGTGACTGG 60.436 45.833 9.11 0.00 0.00 4.00
3646 3762 2.358003 AGCGACTGCCTGCTGTTC 60.358 61.111 3.12 0.00 44.31 3.18
3673 3789 7.498900 TGCTAAGGATTACATCATTTGTTCGAT 59.501 33.333 0.00 0.00 39.87 3.59
3676 3792 7.989826 ACTGCTAAGGATTACATCATTTGTTC 58.010 34.615 0.00 0.00 39.87 3.18
3745 3863 2.224018 GCTTGGTCAAATGCCAGAACAA 60.224 45.455 0.00 0.00 39.00 2.83
3750 3869 1.133790 GCTAGCTTGGTCAAATGCCAG 59.866 52.381 7.70 0.00 37.31 4.85
3770 3889 2.101783 TGCAAAATACAGGCCATGAGG 58.898 47.619 5.01 0.00 38.23 3.86
3771 3890 2.492881 TGTGCAAAATACAGGCCATGAG 59.507 45.455 5.01 0.00 0.00 2.90
3772 3891 2.492881 CTGTGCAAAATACAGGCCATGA 59.507 45.455 5.01 0.00 41.36 3.07
3773 3892 2.883574 CTGTGCAAAATACAGGCCATG 58.116 47.619 5.01 2.64 41.36 3.66
3775 3894 0.602562 GCTGTGCAAAATACAGGCCA 59.397 50.000 5.01 0.00 44.36 5.36
3776 3895 0.602562 TGCTGTGCAAAATACAGGCC 59.397 50.000 0.00 0.00 44.36 5.19
3777 3896 2.437200 TTGCTGTGCAAAATACAGGC 57.563 45.000 2.24 1.26 45.96 4.85
3799 3966 1.597742 TCACAAAAGCTCCAGCAGTC 58.402 50.000 0.48 0.00 45.16 3.51
3817 3984 6.864560 AAAAAGTGTTACGTCTTTGCTTTC 57.135 33.333 0.00 0.00 34.67 2.62
3838 4005 5.221165 GCCCAACAAAGTCTACTGCTAAAAA 60.221 40.000 0.00 0.00 0.00 1.94
3861 4028 4.681025 CCAATCATATACCAAATGCAACGC 59.319 41.667 0.00 0.00 0.00 4.84
3877 4044 2.592102 ACACAACAGCTCCCAATCAT 57.408 45.000 0.00 0.00 0.00 2.45
3878 4045 2.158623 AGAACACAACAGCTCCCAATCA 60.159 45.455 0.00 0.00 0.00 2.57
3879 4046 2.227388 CAGAACACAACAGCTCCCAATC 59.773 50.000 0.00 0.00 0.00 2.67
3880 4047 2.233271 CAGAACACAACAGCTCCCAAT 58.767 47.619 0.00 0.00 0.00 3.16
3926 4093 9.265901 CTGGTTAGACTATTTCTATGTTCCATG 57.734 37.037 0.00 0.00 36.65 3.66
4025 4200 7.072454 AGGATTACTGGCTACATTGGATTCTTA 59.928 37.037 0.00 0.00 0.00 2.10
4147 4322 0.796312 CGACTGTTGGTGCCATGTAC 59.204 55.000 0.00 0.00 0.00 2.90
4253 4428 2.768834 GGATTGAAGCTCCGGTGAC 58.231 57.895 7.92 0.00 0.00 3.67
4366 4541 1.428869 CCCTTACCATAGCTGCCTCT 58.571 55.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.