Multiple sequence alignment - TraesCS3A01G252200

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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 TraesCS3A01G252200 chr3A 100.000 3161 0 0 1 3161 472790170 472793330 0.000000e+00 5838.0
1 TraesCS3A01G252200 chr3B 91.409 2363 109 40 1 2339 452461348 452463640 0.000000e+00 3153.0
2 TraesCS3A01G252200 chr3B 86.643 277 30 5 2530 2801 214266403 214266129 1.840000e-77 300.0
3 TraesCS3A01G252200 chr3B 86.380 279 32 4 2531 2803 365498066 365497788 1.840000e-77 300.0
4 TraesCS3A01G252200 chr3B 81.191 319 50 8 1666 1981 362054314 362054003 6.770000e-62 248.0
5 TraesCS3A01G252200 chr3B 88.889 207 9 9 2965 3161 452464131 452464333 3.150000e-60 243.0
6 TraesCS3A01G252200 chr3B 98.077 52 1 0 2452 2503 452463892 452463943 1.210000e-14 91.6
7 TraesCS3A01G252200 chr3B 100.000 41 0 0 2358 2398 452463637 452463677 3.380000e-10 76.8
8 TraesCS3A01G252200 chr3D 94.404 1787 57 19 628 2399 354072850 354074608 0.000000e+00 2706.0
9 TraesCS3A01G252200 chr3D 85.256 624 42 23 1 599 354072264 354072862 5.840000e-167 597.0
10 TraesCS3A01G252200 chr3D 88.235 204 5 3 2965 3158 354074966 354075160 3.170000e-55 226.0
11 TraesCS3A01G252200 chr7A 87.636 275 26 6 2534 2801 80496730 80496457 2.370000e-81 313.0
12 TraesCS3A01G252200 chr4D 87.365 277 28 4 2533 2803 28409046 28408771 8.510000e-81 311.0
13 TraesCS3A01G252200 chr7B 86.786 280 29 5 2532 2804 573115267 573114989 3.960000e-79 305.0
14 TraesCS3A01G252200 chr7B 86.738 279 31 3 2532 2804 727336797 727337075 3.960000e-79 305.0
15 TraesCS3A01G252200 chr7B 86.477 281 32 4 2529 2803 747970870 747970590 1.420000e-78 303.0
16 TraesCS3A01G252200 chr5A 86.572 283 28 4 2532 2804 524905370 524905652 1.420000e-78 303.0
17 TraesCS3A01G252200 chr5B 86.331 278 33 2 2531 2803 660343326 660343049 6.630000e-77 298.0
18 TraesCS3A01G252200 chr1D 81.034 348 39 18 1655 1977 447550955 447551300 5.230000e-63 252.0
19 TraesCS3A01G252200 chr1A 80.912 351 40 17 1655 1980 543635058 543635406 5.230000e-63 252.0
20 TraesCS3A01G252200 chr1B 79.052 401 47 24 1604 1980 613021405 613021792 1.130000e-59 241.0


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 TraesCS3A01G252200 chr3A 472790170 472793330 3160 False 5838.000000 5838 100.000000 1 3161 1 chr3A.!!$F1 3160
1 TraesCS3A01G252200 chr3B 452461348 452464333 2985 False 891.100000 3153 94.593750 1 3161 4 chr3B.!!$F1 3160
2 TraesCS3A01G252200 chr3D 354072264 354075160 2896 False 1176.333333 2706 89.298333 1 3158 3 chr3D.!!$F1 3157

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
378 403 0.385751 CATCTCACGGTATGGCGAGT 59.614 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2344 2421 0.321034 TCTCACGCTGCAGCTGAATT 60.321 50.0 34.22 11.97 39.32 2.17 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
43 44 7.225725 ACACAGGTAGGTCTACATCTATCTAC 58.774 42.308 9.94 0.00 37.78 2.59
122 124 0.881796 GTAGCTTGCTTGGTTGGGTC 59.118 55.000 0.00 0.00 0.00 4.46
124 126 0.771127 AGCTTGCTTGGTTGGGTCTA 59.229 50.000 0.00 0.00 0.00 2.59
125 127 1.355720 AGCTTGCTTGGTTGGGTCTAT 59.644 47.619 0.00 0.00 0.00 1.98
126 128 1.474077 GCTTGCTTGGTTGGGTCTATG 59.526 52.381 0.00 0.00 0.00 2.23
140 143 6.855763 TGGGTCTATGCATGAAGAAATTTT 57.144 33.333 10.16 0.00 0.00 1.82
198 201 3.381949 CTTATTCCAGGTCGATCGAACC 58.618 50.000 28.75 24.66 30.85 3.62
199 202 0.464452 ATTCCAGGTCGATCGAACCC 59.536 55.000 28.75 21.52 30.85 4.11
200 203 1.940883 TTCCAGGTCGATCGAACCCG 61.941 60.000 28.75 19.83 30.85 5.28
201 204 2.582498 CAGGTCGATCGAACCCGC 60.582 66.667 28.75 11.69 35.37 6.13
202 205 2.754658 AGGTCGATCGAACCCGCT 60.755 61.111 28.75 8.26 35.37 5.52
203 206 2.582498 GGTCGATCGAACCCGCTG 60.582 66.667 22.68 0.00 35.37 5.18
204 207 3.255379 GTCGATCGAACCCGCTGC 61.255 66.667 21.31 0.27 35.37 5.25
205 208 4.847516 TCGATCGAACCCGCTGCG 62.848 66.667 16.99 16.34 35.37 5.18
271 282 3.972227 CTGACCAAGGAGTTGCCG 58.028 61.111 0.00 0.00 43.43 5.69
378 403 0.385751 CATCTCACGGTATGGCGAGT 59.614 55.000 0.00 0.00 0.00 4.18
458 494 6.697892 CACTTAATCAGGCTGCTTAGTACTAC 59.302 42.308 10.34 0.00 0.00 2.73
460 496 4.927978 ATCAGGCTGCTTAGTACTACTG 57.072 45.455 10.34 5.90 0.00 2.74
461 497 3.964411 TCAGGCTGCTTAGTACTACTGA 58.036 45.455 10.34 12.30 0.00 3.41
462 498 3.948473 TCAGGCTGCTTAGTACTACTGAG 59.052 47.826 10.34 5.43 35.21 3.35
463 499 3.697045 CAGGCTGCTTAGTACTACTGAGT 59.303 47.826 0.00 0.00 34.65 3.41
483 519 7.986320 ACTGAGTAGTAGTACAGTGTACCATAG 59.014 40.741 26.22 16.04 41.16 2.23
530 566 3.864186 GGCCGGCGGGGTGTAATA 61.864 66.667 29.48 0.00 38.44 0.98
531 567 2.190048 GCCGGCGGGGTGTAATAA 59.810 61.111 29.48 0.00 38.44 1.40
532 568 2.182181 GCCGGCGGGGTGTAATAAC 61.182 63.158 29.48 2.10 38.44 1.89
533 569 1.524393 CCGGCGGGGTGTAATAACC 60.524 63.158 20.56 0.00 39.71 2.85
536 572 1.538849 CGGCGGGGTGTAATAACCTAC 60.539 57.143 0.00 0.00 40.35 3.18
578 616 2.300433 ACATGTGCATGGCAATACGAT 58.700 42.857 15.52 0.00 41.47 3.73
579 617 2.291465 ACATGTGCATGGCAATACGATC 59.709 45.455 15.52 0.00 41.47 3.69
580 618 0.936600 TGTGCATGGCAATACGATCG 59.063 50.000 14.88 14.88 41.47 3.69
581 619 1.217001 GTGCATGGCAATACGATCGA 58.783 50.000 24.34 5.87 41.47 3.59
585 623 2.408704 GCATGGCAATACGATCGAGTAC 59.591 50.000 24.34 6.74 0.00 2.73
603 641 7.933396 TCGAGTACGATTTTGTAGATTATGGA 58.067 34.615 0.00 0.00 43.81 3.41
604 642 7.859377 TCGAGTACGATTTTGTAGATTATGGAC 59.141 37.037 0.00 0.00 43.81 4.02
605 643 7.149176 CGAGTACGATTTTGTAGATTATGGACG 60.149 40.741 0.00 0.00 42.66 4.79
606 644 5.652744 ACGATTTTGTAGATTATGGACGC 57.347 39.130 0.00 0.00 0.00 5.19
607 645 5.113383 ACGATTTTGTAGATTATGGACGCA 58.887 37.500 0.00 0.00 0.00 5.24
608 646 5.758296 ACGATTTTGTAGATTATGGACGCAT 59.242 36.000 0.00 0.00 0.00 4.73
609 647 6.073369 CGATTTTGTAGATTATGGACGCATG 58.927 40.000 0.00 0.00 0.00 4.06
610 648 6.292865 CGATTTTGTAGATTATGGACGCATGT 60.293 38.462 0.00 0.00 0.00 3.21
613 651 4.765273 TGTAGATTATGGACGCATGTTGT 58.235 39.130 0.00 0.00 0.00 3.32
614 652 4.570369 TGTAGATTATGGACGCATGTTGTG 59.430 41.667 0.00 0.00 0.00 3.33
615 653 2.945008 AGATTATGGACGCATGTTGTGG 59.055 45.455 0.00 0.00 30.87 4.17
626 668 2.614057 GCATGTTGTGGTATGTAGAGGC 59.386 50.000 0.00 0.00 0.00 4.70
638 680 3.784701 TGTAGAGGCGATTCTTGAGAC 57.215 47.619 0.00 0.00 0.00 3.36
689 731 2.215196 CGGTGTAATTATGGGGTTCGG 58.785 52.381 0.00 0.00 0.00 4.30
744 786 0.621082 TTGTCCGCCCATCAATACCA 59.379 50.000 0.00 0.00 0.00 3.25
848 892 0.841961 TCCCTCCTCCTCGATCGTAA 59.158 55.000 15.94 0.86 0.00 3.18
851 895 2.553466 CCCTCCTCCTCGATCGTAATCT 60.553 54.545 15.94 0.00 0.00 2.40
852 896 2.745281 CCTCCTCCTCGATCGTAATCTC 59.255 54.545 15.94 0.00 0.00 2.75
853 897 3.403968 CTCCTCCTCGATCGTAATCTCA 58.596 50.000 15.94 0.00 0.00 3.27
874 919 8.120140 TCTCATCATTCATAGTATCACTCTGG 57.880 38.462 0.00 0.00 0.00 3.86
911 958 6.128715 CGAGAATAATATGCTGACGCTTTCAT 60.129 38.462 0.00 0.00 36.97 2.57
917 964 3.592898 TGCTGACGCTTTCATTCTCTA 57.407 42.857 0.00 0.00 36.97 2.43
919 966 4.507710 TGCTGACGCTTTCATTCTCTATT 58.492 39.130 0.00 0.00 36.97 1.73
920 967 5.660460 TGCTGACGCTTTCATTCTCTATTA 58.340 37.500 0.00 0.00 36.97 0.98
921 968 6.283694 TGCTGACGCTTTCATTCTCTATTAT 58.716 36.000 0.00 0.00 36.97 1.28
922 969 6.201615 TGCTGACGCTTTCATTCTCTATTATG 59.798 38.462 0.00 0.00 36.97 1.90
980 1031 1.619332 GGATAGTTAGCTTCTCCCGGG 59.381 57.143 16.85 16.85 0.00 5.73
981 1032 1.001068 GATAGTTAGCTTCTCCCGGGC 59.999 57.143 18.49 2.86 0.00 6.13
982 1033 1.389609 TAGTTAGCTTCTCCCGGGCG 61.390 60.000 18.49 10.95 0.00 6.13
983 1034 3.467226 TTAGCTTCTCCCGGGCGG 61.467 66.667 18.49 11.61 0.00 6.13
1428 1479 3.047877 AACAACTACAGCGGCGGC 61.048 61.111 9.78 8.43 40.37 6.53
1455 1506 1.154150 CCACGACGTAACCGAGGTC 60.154 63.158 0.00 0.00 39.19 3.85
1521 1575 1.348538 CGATTACGTCGGCACAGCAA 61.349 55.000 0.00 0.00 46.47 3.91
1743 1809 0.911769 CCATGAGGCCAGTGAACCTA 59.088 55.000 5.01 0.00 36.05 3.08
1884 1950 2.507992 CTGCAGAAGCTCGTCCCG 60.508 66.667 8.42 0.00 42.74 5.14
1983 2049 0.392595 CGCTGGAAACCCTAGGAACC 60.393 60.000 11.48 8.33 0.00 3.62
1986 2052 1.004394 CTGGAAACCCTAGGAACCACC 59.996 57.143 11.48 7.62 39.35 4.61
1987 2053 1.069775 GGAAACCCTAGGAACCACCA 58.930 55.000 11.48 0.00 42.04 4.17
1988 2054 1.004394 GGAAACCCTAGGAACCACCAG 59.996 57.143 11.48 0.00 42.04 4.00
1989 2055 0.404426 AAACCCTAGGAACCACCAGC 59.596 55.000 11.48 0.00 42.04 4.85
2038 2110 2.746277 CCAGCACGGGCAGGTTAC 60.746 66.667 14.57 0.00 41.48 2.50
2039 2111 2.031919 CAGCACGGGCAGGTTACA 59.968 61.111 14.57 0.00 44.61 2.41
2040 2112 2.034879 CAGCACGGGCAGGTTACAG 61.035 63.158 14.57 0.00 44.61 2.74
2305 2382 1.790623 CGTCGTGTACTTTTGTCCAGG 59.209 52.381 0.00 0.00 0.00 4.45
2324 2401 7.996066 TGTCCAGGATTAATTAATTTGGATCGA 59.004 33.333 29.17 20.39 39.59 3.59
2344 2421 3.120385 CGCTGCATCGTGGAAGCA 61.120 61.111 0.88 0.00 35.04 3.91
2351 2428 1.796617 GCATCGTGGAAGCAATTCAGC 60.797 52.381 0.00 0.00 0.00 4.26
2500 2738 1.444042 TGGCGTGCATGCAAAATCG 60.444 52.632 30.79 22.09 36.28 3.34
2501 2739 1.444212 GGCGTGCATGCAAAATCGT 60.444 52.632 30.79 0.00 36.28 3.73
2502 2740 0.179176 GGCGTGCATGCAAAATCGTA 60.179 50.000 30.79 0.00 36.28 3.43
2503 2741 0.907171 GCGTGCATGCAAAATCGTAC 59.093 50.000 24.58 6.26 34.15 3.67
2504 2742 1.465689 GCGTGCATGCAAAATCGTACT 60.466 47.619 24.58 0.00 34.15 2.73
2505 2743 2.222931 GCGTGCATGCAAAATCGTACTA 60.223 45.455 24.58 0.00 34.15 1.82
2516 2754 5.972382 GCAAAATCGTACTAGTAGTGAGAGG 59.028 44.000 13.29 0.00 0.00 3.69
2517 2755 6.404513 GCAAAATCGTACTAGTAGTGAGAGGT 60.405 42.308 13.29 2.45 0.00 3.85
2527 2765 4.742012 AGTAGTGAGAGGTTCTCTTCCAA 58.258 43.478 7.52 0.00 43.73 3.53
2539 2777 3.922171 CTCTTCCAAGAGTTAGGGCAT 57.078 47.619 8.02 0.00 45.84 4.40
2540 2778 3.539604 CTCTTCCAAGAGTTAGGGCATG 58.460 50.000 8.02 0.00 45.84 4.06
2541 2779 2.912956 TCTTCCAAGAGTTAGGGCATGT 59.087 45.455 0.00 0.00 0.00 3.21
2542 2780 4.101114 TCTTCCAAGAGTTAGGGCATGTA 58.899 43.478 0.00 0.00 0.00 2.29
2543 2781 4.162320 TCTTCCAAGAGTTAGGGCATGTAG 59.838 45.833 0.00 0.00 0.00 2.74
2544 2782 3.719871 TCCAAGAGTTAGGGCATGTAGA 58.280 45.455 0.00 0.00 0.00 2.59
2545 2783 4.101114 TCCAAGAGTTAGGGCATGTAGAA 58.899 43.478 0.00 0.00 0.00 2.10
2546 2784 4.721776 TCCAAGAGTTAGGGCATGTAGAAT 59.278 41.667 0.00 0.00 0.00 2.40
2547 2785 4.818546 CCAAGAGTTAGGGCATGTAGAATG 59.181 45.833 0.00 0.00 0.00 2.67
2548 2786 4.696479 AGAGTTAGGGCATGTAGAATGG 57.304 45.455 0.00 0.00 0.00 3.16
2549 2787 4.040755 AGAGTTAGGGCATGTAGAATGGT 58.959 43.478 0.00 0.00 0.00 3.55
2550 2788 4.475016 AGAGTTAGGGCATGTAGAATGGTT 59.525 41.667 0.00 0.00 0.00 3.67
2551 2789 4.526970 AGTTAGGGCATGTAGAATGGTTG 58.473 43.478 0.00 0.00 0.00 3.77
2552 2790 4.227300 AGTTAGGGCATGTAGAATGGTTGA 59.773 41.667 0.00 0.00 0.00 3.18
2553 2791 3.959495 AGGGCATGTAGAATGGTTGAT 57.041 42.857 0.00 0.00 0.00 2.57
2554 2792 6.101150 AGTTAGGGCATGTAGAATGGTTGATA 59.899 38.462 0.00 0.00 0.00 2.15
2555 2793 5.387113 AGGGCATGTAGAATGGTTGATAA 57.613 39.130 0.00 0.00 0.00 1.75
2556 2794 5.765510 AGGGCATGTAGAATGGTTGATAAA 58.234 37.500 0.00 0.00 0.00 1.40
2557 2795 6.194235 AGGGCATGTAGAATGGTTGATAAAA 58.806 36.000 0.00 0.00 0.00 1.52
2558 2796 6.840705 AGGGCATGTAGAATGGTTGATAAAAT 59.159 34.615 0.00 0.00 0.00 1.82
2559 2797 8.004215 AGGGCATGTAGAATGGTTGATAAAATA 58.996 33.333 0.00 0.00 0.00 1.40
2560 2798 8.637986 GGGCATGTAGAATGGTTGATAAAATAA 58.362 33.333 0.00 0.00 0.00 1.40
2625 2863 8.854614 ATGTCTATAATGGGTCATCTTTTAGC 57.145 34.615 0.00 0.00 0.00 3.09
2626 2864 7.801104 TGTCTATAATGGGTCATCTTTTAGCA 58.199 34.615 0.00 0.00 0.00 3.49
2627 2865 8.439971 TGTCTATAATGGGTCATCTTTTAGCAT 58.560 33.333 0.00 0.00 0.00 3.79
2628 2866 9.289782 GTCTATAATGGGTCATCTTTTAGCATT 57.710 33.333 0.00 0.00 0.00 3.56
2633 2871 8.773033 AATGGGTCATCTTTTAGCATTATCTT 57.227 30.769 0.00 0.00 0.00 2.40
2634 2872 7.807977 TGGGTCATCTTTTAGCATTATCTTC 57.192 36.000 0.00 0.00 0.00 2.87
2635 2873 7.345691 TGGGTCATCTTTTAGCATTATCTTCA 58.654 34.615 0.00 0.00 0.00 3.02
2636 2874 7.833682 TGGGTCATCTTTTAGCATTATCTTCAA 59.166 33.333 0.00 0.00 0.00 2.69
2637 2875 8.854117 GGGTCATCTTTTAGCATTATCTTCAAT 58.146 33.333 0.00 0.00 0.00 2.57
2667 2905 8.950403 AGCTATTTTTAAAAACGTGATGAGAC 57.050 30.769 15.35 0.00 0.00 3.36
2668 2906 8.564574 AGCTATTTTTAAAAACGTGATGAGACA 58.435 29.630 15.35 0.00 0.00 3.41
2669 2907 9.176181 GCTATTTTTAAAAACGTGATGAGACAA 57.824 29.630 15.35 0.00 0.00 3.18
2674 2912 8.918961 TTTAAAAACGTGATGAGACAAATTGT 57.081 26.923 0.00 0.00 0.00 2.71
2675 2913 6.810888 AAAAACGTGATGAGACAAATTGTG 57.189 33.333 2.20 0.00 0.00 3.33
2676 2914 3.542712 ACGTGATGAGACAAATTGTGC 57.457 42.857 2.20 0.00 0.00 4.57
2677 2915 3.141398 ACGTGATGAGACAAATTGTGCT 58.859 40.909 2.20 0.36 0.00 4.40
2678 2916 4.314961 ACGTGATGAGACAAATTGTGCTA 58.685 39.130 2.20 0.00 0.00 3.49
2679 2917 4.754618 ACGTGATGAGACAAATTGTGCTAA 59.245 37.500 2.20 0.00 0.00 3.09
2680 2918 5.106948 ACGTGATGAGACAAATTGTGCTAAG 60.107 40.000 2.20 0.00 0.00 2.18
2681 2919 5.120674 CGTGATGAGACAAATTGTGCTAAGA 59.879 40.000 2.20 0.00 0.00 2.10
2682 2920 6.541086 GTGATGAGACAAATTGTGCTAAGAG 58.459 40.000 2.20 0.00 0.00 2.85
2683 2921 6.369890 GTGATGAGACAAATTGTGCTAAGAGA 59.630 38.462 2.20 0.00 0.00 3.10
2684 2922 7.065563 GTGATGAGACAAATTGTGCTAAGAGAT 59.934 37.037 2.20 0.00 0.00 2.75
2685 2923 6.732531 TGAGACAAATTGTGCTAAGAGATG 57.267 37.500 2.20 0.00 0.00 2.90
2686 2924 6.466812 TGAGACAAATTGTGCTAAGAGATGA 58.533 36.000 2.20 0.00 0.00 2.92
2687 2925 7.108194 TGAGACAAATTGTGCTAAGAGATGAT 58.892 34.615 2.20 0.00 0.00 2.45
2688 2926 7.279536 TGAGACAAATTGTGCTAAGAGATGATC 59.720 37.037 2.20 0.00 0.00 2.92
2689 2927 7.337167 AGACAAATTGTGCTAAGAGATGATCT 58.663 34.615 2.20 0.00 41.27 2.75
2690 2928 7.495279 AGACAAATTGTGCTAAGAGATGATCTC 59.505 37.037 14.47 14.47 43.70 2.75
2749 2987 9.799106 TTTTTATGATTTCTCTCTTCTTCACCT 57.201 29.630 0.00 0.00 0.00 4.00
2750 2988 9.442047 TTTTATGATTTCTCTCTTCTTCACCTC 57.558 33.333 0.00 0.00 0.00 3.85
2751 2989 6.617782 ATGATTTCTCTCTTCTTCACCTCA 57.382 37.500 0.00 0.00 0.00 3.86
2752 2990 6.617782 TGATTTCTCTCTTCTTCACCTCAT 57.382 37.500 0.00 0.00 0.00 2.90
2753 2991 6.638610 TGATTTCTCTCTTCTTCACCTCATC 58.361 40.000 0.00 0.00 0.00 2.92
2754 2992 6.212187 TGATTTCTCTCTTCTTCACCTCATCA 59.788 38.462 0.00 0.00 0.00 3.07
2755 2993 6.617782 TTTCTCTCTTCTTCACCTCATCAT 57.382 37.500 0.00 0.00 0.00 2.45
2756 2994 6.617782 TTCTCTCTTCTTCACCTCATCATT 57.382 37.500 0.00 0.00 0.00 2.57
2757 2995 6.617782 TCTCTCTTCTTCACCTCATCATTT 57.382 37.500 0.00 0.00 0.00 2.32
2758 2996 7.724490 TCTCTCTTCTTCACCTCATCATTTA 57.276 36.000 0.00 0.00 0.00 1.40
2759 2997 8.316497 TCTCTCTTCTTCACCTCATCATTTAT 57.684 34.615 0.00 0.00 0.00 1.40
2760 2998 8.420222 TCTCTCTTCTTCACCTCATCATTTATC 58.580 37.037 0.00 0.00 0.00 1.75
2761 2999 7.504403 TCTCTTCTTCACCTCATCATTTATCC 58.496 38.462 0.00 0.00 0.00 2.59
2762 3000 7.346698 TCTCTTCTTCACCTCATCATTTATCCT 59.653 37.037 0.00 0.00 0.00 3.24
2763 3001 8.553085 TCTTCTTCACCTCATCATTTATCCTA 57.447 34.615 0.00 0.00 0.00 2.94
2764 3002 8.424918 TCTTCTTCACCTCATCATTTATCCTAC 58.575 37.037 0.00 0.00 0.00 3.18
2765 3003 7.675161 TCTTCACCTCATCATTTATCCTACA 57.325 36.000 0.00 0.00 0.00 2.74
2766 3004 8.267620 TCTTCACCTCATCATTTATCCTACAT 57.732 34.615 0.00 0.00 0.00 2.29
2767 3005 8.152898 TCTTCACCTCATCATTTATCCTACATG 58.847 37.037 0.00 0.00 0.00 3.21
2768 3006 6.772605 TCACCTCATCATTTATCCTACATGG 58.227 40.000 0.00 0.00 37.10 3.66
2769 3007 5.413833 CACCTCATCATTTATCCTACATGGC 59.586 44.000 0.00 0.00 35.26 4.40
2770 3008 5.073554 ACCTCATCATTTATCCTACATGGCA 59.926 40.000 0.00 0.00 35.26 4.92
2771 3009 6.185511 CCTCATCATTTATCCTACATGGCAT 58.814 40.000 0.00 0.00 35.26 4.40
2772 3010 6.662234 CCTCATCATTTATCCTACATGGCATT 59.338 38.462 0.00 0.00 35.26 3.56
2773 3011 7.148120 CCTCATCATTTATCCTACATGGCATTC 60.148 40.741 0.00 0.00 35.26 2.67
2774 3012 6.372381 TCATCATTTATCCTACATGGCATTCG 59.628 38.462 0.00 0.00 35.26 3.34
2775 3013 5.620206 TCATTTATCCTACATGGCATTCGT 58.380 37.500 0.00 0.00 35.26 3.85
2776 3014 6.764379 TCATTTATCCTACATGGCATTCGTA 58.236 36.000 0.00 0.00 35.26 3.43
2777 3015 7.220740 TCATTTATCCTACATGGCATTCGTAA 58.779 34.615 0.00 0.00 35.26 3.18
2778 3016 7.387673 TCATTTATCCTACATGGCATTCGTAAG 59.612 37.037 0.00 0.00 35.26 2.34
2779 3017 4.955811 ATCCTACATGGCATTCGTAAGA 57.044 40.909 0.00 0.00 39.67 2.10
2780 3018 4.955811 TCCTACATGGCATTCGTAAGAT 57.044 40.909 0.00 0.00 40.70 2.40
2781 3019 6.605471 ATCCTACATGGCATTCGTAAGATA 57.395 37.500 0.00 0.00 40.70 1.98
2782 3020 6.413783 TCCTACATGGCATTCGTAAGATAA 57.586 37.500 0.00 0.00 40.70 1.75
2783 3021 6.822442 TCCTACATGGCATTCGTAAGATAAA 58.178 36.000 0.00 0.00 40.70 1.40
2784 3022 7.276658 TCCTACATGGCATTCGTAAGATAAAA 58.723 34.615 0.00 0.00 40.70 1.52
2785 3023 7.225931 TCCTACATGGCATTCGTAAGATAAAAC 59.774 37.037 0.00 0.00 40.70 2.43
2797 3035 7.690228 TCGTAAGATAAAACCATTGTACATGC 58.310 34.615 0.00 0.00 45.01 4.06
2798 3036 6.910433 CGTAAGATAAAACCATTGTACATGCC 59.090 38.462 0.00 0.00 43.02 4.40
2799 3037 5.852282 AGATAAAACCATTGTACATGCCC 57.148 39.130 0.00 0.00 0.00 5.36
2800 3038 5.518865 AGATAAAACCATTGTACATGCCCT 58.481 37.500 0.00 0.00 0.00 5.19
2801 3039 5.957774 AGATAAAACCATTGTACATGCCCTT 59.042 36.000 0.00 0.00 0.00 3.95
2846 3120 2.260844 AACCCTACATGCATGGATCG 57.739 50.000 29.41 16.39 0.00 3.69
2848 3122 1.490490 ACCCTACATGCATGGATCGTT 59.510 47.619 29.41 10.82 0.00 3.85
2856 3130 1.612950 TGCATGGATCGTTTGTTTGCT 59.387 42.857 0.00 0.00 0.00 3.91
2894 3168 4.183865 CGTCATGATACTCACACAATGGT 58.816 43.478 0.00 0.00 0.00 3.55
2907 3181 3.941483 ACACAATGGTTGAGCTAGCATAC 59.059 43.478 18.83 11.11 35.33 2.39
2912 3186 3.021695 TGGTTGAGCTAGCATACGTACT 58.978 45.455 18.83 0.00 0.00 2.73
2915 3189 5.125900 TGGTTGAGCTAGCATACGTACTAAA 59.874 40.000 18.83 0.00 0.00 1.85
2916 3190 6.183360 TGGTTGAGCTAGCATACGTACTAAAT 60.183 38.462 18.83 0.00 0.00 1.40
2917 3191 7.013559 TGGTTGAGCTAGCATACGTACTAAATA 59.986 37.037 18.83 0.00 0.00 1.40
2918 3192 7.325579 GGTTGAGCTAGCATACGTACTAAATAC 59.674 40.741 18.83 0.00 0.00 1.89
2920 3194 8.162878 TGAGCTAGCATACGTACTAAATACTT 57.837 34.615 18.83 0.00 0.00 2.24
2921 3195 9.276590 TGAGCTAGCATACGTACTAAATACTTA 57.723 33.333 18.83 0.00 0.00 2.24
2956 3230 9.698309 ATGATTGTATCTAGTATTTCTGAACGG 57.302 33.333 0.00 0.00 0.00 4.44
2957 3231 8.909923 TGATTGTATCTAGTATTTCTGAACGGA 58.090 33.333 0.00 0.00 0.00 4.69
2958 3232 9.915629 GATTGTATCTAGTATTTCTGAACGGAT 57.084 33.333 0.00 0.00 0.00 4.18
2959 3233 9.915629 ATTGTATCTAGTATTTCTGAACGGATC 57.084 33.333 0.00 0.00 0.00 3.36
2960 3234 8.459911 TGTATCTAGTATTTCTGAACGGATCA 57.540 34.615 0.00 0.00 36.38 2.92
2961 3235 9.078990 TGTATCTAGTATTTCTGAACGGATCAT 57.921 33.333 0.00 0.00 37.44 2.45
2962 3236 9.347934 GTATCTAGTATTTCTGAACGGATCATG 57.652 37.037 0.00 0.00 37.44 3.07
2963 3237 6.749139 TCTAGTATTTCTGAACGGATCATGG 58.251 40.000 0.00 0.00 37.44 3.66
2966 3240 7.303182 AGTATTTCTGAACGGATCATGGATA 57.697 36.000 0.00 0.00 37.44 2.59
3000 3274 6.483640 GCATAGGAGGTTAGTTTAGAATGGTG 59.516 42.308 0.00 0.00 0.00 4.17
3004 3278 5.823045 GGAGGTTAGTTTAGAATGGTGATGG 59.177 44.000 0.00 0.00 0.00 3.51
3005 3279 5.755849 AGGTTAGTTTAGAATGGTGATGGG 58.244 41.667 0.00 0.00 0.00 4.00
3062 3346 5.686159 ATGATTTCTTCCGCTCAATCATC 57.314 39.130 0.00 0.00 40.72 2.92
3078 3362 1.136110 TCATCGTCCGATTGCTTGCTA 59.864 47.619 0.00 0.00 31.62 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.633418 AGATGTAGACCTACCTGTGTCC 58.367 50.000 4.88 0.00 35.26 4.02
43 44 4.866508 TTGAAGTACTAGACACTGTGGG 57.133 45.455 13.09 2.19 0.00 4.61
140 143 1.000955 GACCTCGAGCCAACAAGAAGA 59.999 52.381 6.99 0.00 0.00 2.87
148 151 2.650116 GCCTGAGACCTCGAGCCAA 61.650 63.158 6.99 0.00 0.00 4.52
205 208 3.991536 GACCAAGGCCGAGAGACGC 62.992 68.421 0.00 0.00 41.07 5.19
409 434 5.753438 GTGCATGCATTTGCTACTAGTACTA 59.247 40.000 25.64 1.89 43.18 1.82
410 435 4.572389 GTGCATGCATTTGCTACTAGTACT 59.428 41.667 25.64 0.00 43.18 2.73
411 436 4.332543 TGTGCATGCATTTGCTACTAGTAC 59.667 41.667 25.64 5.93 43.18 2.73
414 439 3.376234 AGTGTGCATGCATTTGCTACTAG 59.624 43.478 25.64 0.00 43.18 2.57
499 535 1.806247 GCCGGCCTCAAATATTTTGCC 60.806 52.381 18.11 17.43 35.55 4.52
530 566 8.877195 TCTTTATGTGAAAAGTAGGAGTAGGTT 58.123 33.333 0.00 0.00 37.65 3.50
531 567 8.431910 TCTTTATGTGAAAAGTAGGAGTAGGT 57.568 34.615 0.00 0.00 37.65 3.08
579 617 7.149176 CGTCCATAATCTACAAAATCGTACTCG 60.149 40.741 0.00 0.00 38.55 4.18
580 618 7.358187 GCGTCCATAATCTACAAAATCGTACTC 60.358 40.741 0.00 0.00 0.00 2.59
581 619 6.420008 GCGTCCATAATCTACAAAATCGTACT 59.580 38.462 0.00 0.00 0.00 2.73
585 623 5.651172 TGCGTCCATAATCTACAAAATCG 57.349 39.130 0.00 0.00 0.00 3.34
597 635 2.192664 ACCACAACATGCGTCCATAA 57.807 45.000 0.00 0.00 0.00 1.90
599 637 2.016318 CATACCACAACATGCGTCCAT 58.984 47.619 0.00 0.00 0.00 3.41
600 638 1.271108 ACATACCACAACATGCGTCCA 60.271 47.619 0.00 0.00 0.00 4.02
601 639 1.448985 ACATACCACAACATGCGTCC 58.551 50.000 0.00 0.00 0.00 4.79
602 640 3.517602 TCTACATACCACAACATGCGTC 58.482 45.455 0.00 0.00 0.00 5.19
603 641 3.521560 CTCTACATACCACAACATGCGT 58.478 45.455 0.00 0.00 0.00 5.24
604 642 2.866156 CCTCTACATACCACAACATGCG 59.134 50.000 0.00 0.00 0.00 4.73
605 643 2.614057 GCCTCTACATACCACAACATGC 59.386 50.000 0.00 0.00 0.00 4.06
606 644 2.866156 CGCCTCTACATACCACAACATG 59.134 50.000 0.00 0.00 0.00 3.21
607 645 2.764010 TCGCCTCTACATACCACAACAT 59.236 45.455 0.00 0.00 0.00 2.71
608 646 2.172679 TCGCCTCTACATACCACAACA 58.827 47.619 0.00 0.00 0.00 3.33
609 647 2.953466 TCGCCTCTACATACCACAAC 57.047 50.000 0.00 0.00 0.00 3.32
610 648 3.704566 AGAATCGCCTCTACATACCACAA 59.295 43.478 0.00 0.00 0.00 3.33
613 651 3.958147 TCAAGAATCGCCTCTACATACCA 59.042 43.478 0.00 0.00 0.00 3.25
614 652 4.278669 TCTCAAGAATCGCCTCTACATACC 59.721 45.833 0.00 0.00 0.00 2.73
615 653 5.009210 AGTCTCAAGAATCGCCTCTACATAC 59.991 44.000 0.00 0.00 0.00 2.39
626 668 6.197364 ACTTACTACCAGTCTCAAGAATCG 57.803 41.667 0.00 0.00 0.00 3.34
638 680 5.006552 GCACTACTCTACGACTTACTACCAG 59.993 48.000 0.00 0.00 0.00 4.00
689 731 1.137282 GGAGAGAAACCGGAGATGTCC 59.863 57.143 9.46 4.73 39.88 4.02
848 892 8.751242 CCAGAGTGATACTATGAATGATGAGAT 58.249 37.037 5.25 0.00 39.66 2.75
851 895 6.496218 AGCCAGAGTGATACTATGAATGATGA 59.504 38.462 5.25 0.00 39.66 2.92
852 896 6.699366 AGCCAGAGTGATACTATGAATGATG 58.301 40.000 5.25 0.00 39.66 3.07
853 897 6.931790 AGCCAGAGTGATACTATGAATGAT 57.068 37.500 5.25 0.00 39.66 2.45
874 919 7.278868 AGCATATTATTCTCGGCTGTAAATAGC 59.721 37.037 0.00 0.00 42.94 2.97
901 948 7.378995 ACGTACATAATAGAGAATGAAAGCGTC 59.621 37.037 0.00 0.00 0.00 5.19
911 958 4.617959 GGCTGCACGTACATAATAGAGAA 58.382 43.478 0.50 0.00 0.00 2.87
917 964 3.752796 ACGGCTGCACGTACATAAT 57.247 47.368 13.14 0.00 46.58 1.28
961 1008 1.001068 GCCCGGGAGAAGCTAACTATC 59.999 57.143 29.31 0.00 0.00 2.08
962 1009 1.049402 GCCCGGGAGAAGCTAACTAT 58.951 55.000 29.31 0.00 0.00 2.12
990 1041 4.147322 GTGTCCATCGCCGCAACG 62.147 66.667 0.00 0.00 0.00 4.10
991 1042 3.799755 GGTGTCCATCGCCGCAAC 61.800 66.667 0.00 0.00 36.95 4.17
1056 1107 4.834453 CTGAGCTGGCTCGCAGGG 62.834 72.222 16.33 2.62 45.48 4.45
1184 1235 1.269465 GGCCGTTATTAGTCGAGTCCC 60.269 57.143 0.00 0.00 0.00 4.46
1185 1236 1.269465 GGGCCGTTATTAGTCGAGTCC 60.269 57.143 0.00 0.00 0.00 3.85
1186 1237 1.598924 CGGGCCGTTATTAGTCGAGTC 60.599 57.143 19.97 0.00 0.00 3.36
1187 1238 0.383231 CGGGCCGTTATTAGTCGAGT 59.617 55.000 19.97 0.00 0.00 4.18
1188 1239 0.938168 GCGGGCCGTTATTAGTCGAG 60.938 60.000 28.82 0.00 0.00 4.04
1189 1240 1.066257 GCGGGCCGTTATTAGTCGA 59.934 57.895 28.82 0.00 0.00 4.20
1190 1241 1.066918 AGCGGGCCGTTATTAGTCG 59.933 57.895 28.82 0.00 0.00 4.18
1191 1242 0.878961 CCAGCGGGCCGTTATTAGTC 60.879 60.000 28.82 7.88 0.00 2.59
1192 1243 1.145377 CCAGCGGGCCGTTATTAGT 59.855 57.895 28.82 0.49 0.00 2.24
1212 1263 1.377333 GACCCCCGAGCCAAAGAAG 60.377 63.158 0.00 0.00 0.00 2.85
1576 1630 2.686816 GCTTTGTGCCGGCGTGTAT 61.687 57.895 23.90 0.00 35.15 2.29
1729 1795 0.977395 GTGACTAGGTTCACTGGCCT 59.023 55.000 3.32 0.00 42.36 5.19
1884 1950 3.797353 TCCATCTTGCTCCCGCCC 61.797 66.667 0.00 0.00 34.43 6.13
2040 2112 5.551760 AATAATGCTGCTGTGAGTGTAAC 57.448 39.130 0.00 0.00 0.00 2.50
2324 2401 1.522355 CTTCCACGATGCAGCGGAT 60.522 57.895 29.52 5.29 35.12 4.18
2344 2421 0.321034 TCTCACGCTGCAGCTGAATT 60.321 50.000 34.22 11.97 39.32 2.17
2351 2428 0.865218 GTCTCGATCTCACGCTGCAG 60.865 60.000 10.11 10.11 0.00 4.41
2445 2539 4.323485 CCAGGCACTTTGATTCTACCAGTA 60.323 45.833 0.00 0.00 34.60 2.74
2446 2540 3.560025 CCAGGCACTTTGATTCTACCAGT 60.560 47.826 0.00 0.00 34.60 4.00
2448 2542 2.290896 CCCAGGCACTTTGATTCTACCA 60.291 50.000 0.00 0.00 34.60 3.25
2449 2543 2.026262 TCCCAGGCACTTTGATTCTACC 60.026 50.000 0.00 0.00 34.60 3.18
2450 2544 3.010420 GTCCCAGGCACTTTGATTCTAC 58.990 50.000 0.00 0.00 34.60 2.59
2493 2731 7.086230 ACCTCTCACTACTAGTACGATTTTG 57.914 40.000 0.00 0.00 0.00 2.44
2500 2738 6.539826 GGAAGAGAACCTCTCACTACTAGTAC 59.460 46.154 0.00 0.00 45.73 2.73
2501 2739 6.215023 TGGAAGAGAACCTCTCACTACTAGTA 59.785 42.308 1.89 1.89 45.73 1.82
2502 2740 5.014333 TGGAAGAGAACCTCTCACTACTAGT 59.986 44.000 0.00 0.00 45.73 2.57
2503 2741 5.502079 TGGAAGAGAACCTCTCACTACTAG 58.498 45.833 6.45 0.00 45.73 2.57
2504 2742 5.516059 TGGAAGAGAACCTCTCACTACTA 57.484 43.478 6.45 0.00 45.73 1.82
2505 2743 4.390129 TGGAAGAGAACCTCTCACTACT 57.610 45.455 6.45 0.00 45.73 2.57
2527 2765 4.040755 ACCATTCTACATGCCCTAACTCT 58.959 43.478 0.00 0.00 0.00 3.24
2532 2770 6.508030 TTATCAACCATTCTACATGCCCTA 57.492 37.500 0.00 0.00 0.00 3.53
2533 2771 3.959495 ATCAACCATTCTACATGCCCT 57.041 42.857 0.00 0.00 0.00 5.19
2534 2772 6.463995 TTTTATCAACCATTCTACATGCCC 57.536 37.500 0.00 0.00 0.00 5.36
2599 2837 9.944376 GCTAAAAGATGACCCATTATAGACATA 57.056 33.333 0.00 0.00 0.00 2.29
2600 2838 8.439971 TGCTAAAAGATGACCCATTATAGACAT 58.560 33.333 0.00 0.00 0.00 3.06
2601 2839 7.801104 TGCTAAAAGATGACCCATTATAGACA 58.199 34.615 0.00 0.00 0.00 3.41
2602 2840 8.854614 ATGCTAAAAGATGACCCATTATAGAC 57.145 34.615 0.00 0.00 0.00 2.59
2607 2845 9.866655 AAGATAATGCTAAAAGATGACCCATTA 57.133 29.630 0.00 0.00 0.00 1.90
2608 2846 8.773033 AAGATAATGCTAAAAGATGACCCATT 57.227 30.769 0.00 0.00 0.00 3.16
2609 2847 8.000709 TGAAGATAATGCTAAAAGATGACCCAT 58.999 33.333 0.00 0.00 0.00 4.00
2610 2848 7.345691 TGAAGATAATGCTAAAAGATGACCCA 58.654 34.615 0.00 0.00 0.00 4.51
2611 2849 7.807977 TGAAGATAATGCTAAAAGATGACCC 57.192 36.000 0.00 0.00 0.00 4.46
2642 2880 8.564574 TGTCTCATCACGTTTTTAAAAATAGCT 58.435 29.630 16.02 0.00 0.00 3.32
2643 2881 8.722342 TGTCTCATCACGTTTTTAAAAATAGC 57.278 30.769 16.02 3.55 0.00 2.97
2648 2886 9.360093 ACAATTTGTCTCATCACGTTTTTAAAA 57.640 25.926 0.00 0.00 0.00 1.52
2649 2887 8.802856 CACAATTTGTCTCATCACGTTTTTAAA 58.197 29.630 0.00 0.00 0.00 1.52
2650 2888 7.043722 GCACAATTTGTCTCATCACGTTTTTAA 60.044 33.333 0.00 0.00 0.00 1.52
2651 2889 6.416455 GCACAATTTGTCTCATCACGTTTTTA 59.584 34.615 0.00 0.00 0.00 1.52
2652 2890 5.231991 GCACAATTTGTCTCATCACGTTTTT 59.768 36.000 0.00 0.00 0.00 1.94
2653 2891 4.739716 GCACAATTTGTCTCATCACGTTTT 59.260 37.500 0.00 0.00 0.00 2.43
2654 2892 4.036734 AGCACAATTTGTCTCATCACGTTT 59.963 37.500 0.00 0.00 0.00 3.60
2655 2893 3.565482 AGCACAATTTGTCTCATCACGTT 59.435 39.130 0.00 0.00 0.00 3.99
2656 2894 3.141398 AGCACAATTTGTCTCATCACGT 58.859 40.909 0.00 0.00 0.00 4.49
2657 2895 3.818961 AGCACAATTTGTCTCATCACG 57.181 42.857 0.00 0.00 0.00 4.35
2658 2896 6.369890 TCTCTTAGCACAATTTGTCTCATCAC 59.630 38.462 0.00 0.00 0.00 3.06
2659 2897 6.466812 TCTCTTAGCACAATTTGTCTCATCA 58.533 36.000 0.00 0.00 0.00 3.07
2660 2898 6.974932 TCTCTTAGCACAATTTGTCTCATC 57.025 37.500 0.00 0.00 0.00 2.92
2661 2899 7.108194 TCATCTCTTAGCACAATTTGTCTCAT 58.892 34.615 0.00 0.00 0.00 2.90
2662 2900 6.466812 TCATCTCTTAGCACAATTTGTCTCA 58.533 36.000 0.00 0.00 0.00 3.27
2663 2901 6.974932 TCATCTCTTAGCACAATTTGTCTC 57.025 37.500 0.00 0.00 0.00 3.36
2664 2902 7.337167 AGATCATCTCTTAGCACAATTTGTCT 58.663 34.615 0.00 3.34 0.00 3.41
2665 2903 7.551035 AGATCATCTCTTAGCACAATTTGTC 57.449 36.000 0.00 0.00 0.00 3.18
2666 2904 7.551035 GAGATCATCTCTTAGCACAATTTGT 57.449 36.000 7.48 0.00 40.30 2.83
2723 2961 9.799106 AGGTGAAGAAGAGAGAAATCATAAAAA 57.201 29.630 0.00 0.00 0.00 1.94
2724 2962 9.442047 GAGGTGAAGAAGAGAGAAATCATAAAA 57.558 33.333 0.00 0.00 0.00 1.52
2725 2963 8.597167 TGAGGTGAAGAAGAGAGAAATCATAAA 58.403 33.333 0.00 0.00 0.00 1.40
2726 2964 8.138928 TGAGGTGAAGAAGAGAGAAATCATAA 57.861 34.615 0.00 0.00 0.00 1.90
2727 2965 7.724490 TGAGGTGAAGAAGAGAGAAATCATA 57.276 36.000 0.00 0.00 0.00 2.15
2728 2966 6.617782 TGAGGTGAAGAAGAGAGAAATCAT 57.382 37.500 0.00 0.00 0.00 2.45
2729 2967 6.212187 TGATGAGGTGAAGAAGAGAGAAATCA 59.788 38.462 0.00 0.00 0.00 2.57
2730 2968 6.638610 TGATGAGGTGAAGAAGAGAGAAATC 58.361 40.000 0.00 0.00 0.00 2.17
2731 2969 6.617782 TGATGAGGTGAAGAAGAGAGAAAT 57.382 37.500 0.00 0.00 0.00 2.17
2732 2970 6.617782 ATGATGAGGTGAAGAAGAGAGAAA 57.382 37.500 0.00 0.00 0.00 2.52
2733 2971 6.617782 AATGATGAGGTGAAGAAGAGAGAA 57.382 37.500 0.00 0.00 0.00 2.87
2734 2972 6.617782 AAATGATGAGGTGAAGAAGAGAGA 57.382 37.500 0.00 0.00 0.00 3.10
2735 2973 7.656948 GGATAAATGATGAGGTGAAGAAGAGAG 59.343 40.741 0.00 0.00 0.00 3.20
2736 2974 7.346698 AGGATAAATGATGAGGTGAAGAAGAGA 59.653 37.037 0.00 0.00 0.00 3.10
2737 2975 7.507829 AGGATAAATGATGAGGTGAAGAAGAG 58.492 38.462 0.00 0.00 0.00 2.85
2738 2976 7.443302 AGGATAAATGATGAGGTGAAGAAGA 57.557 36.000 0.00 0.00 0.00 2.87
2739 2977 8.206867 TGTAGGATAAATGATGAGGTGAAGAAG 58.793 37.037 0.00 0.00 0.00 2.85
2740 2978 8.089625 TGTAGGATAAATGATGAGGTGAAGAA 57.910 34.615 0.00 0.00 0.00 2.52
2741 2979 7.675161 TGTAGGATAAATGATGAGGTGAAGA 57.325 36.000 0.00 0.00 0.00 2.87
2742 2980 7.389884 CCATGTAGGATAAATGATGAGGTGAAG 59.610 40.741 0.00 0.00 38.63 3.02
2743 2981 7.226441 CCATGTAGGATAAATGATGAGGTGAA 58.774 38.462 0.00 0.00 38.63 3.18
2744 2982 6.745190 GCCATGTAGGATAAATGATGAGGTGA 60.745 42.308 0.00 0.00 38.63 4.02
2745 2983 5.413833 GCCATGTAGGATAAATGATGAGGTG 59.586 44.000 0.00 0.00 38.63 4.00
2746 2984 5.073554 TGCCATGTAGGATAAATGATGAGGT 59.926 40.000 0.00 0.00 38.63 3.85
2747 2985 5.563592 TGCCATGTAGGATAAATGATGAGG 58.436 41.667 0.00 0.00 38.63 3.86
2748 2986 7.413767 CGAATGCCATGTAGGATAAATGATGAG 60.414 40.741 0.00 0.00 38.63 2.90
2749 2987 6.372381 CGAATGCCATGTAGGATAAATGATGA 59.628 38.462 0.00 0.00 38.63 2.92
2750 2988 6.149973 ACGAATGCCATGTAGGATAAATGATG 59.850 38.462 0.00 0.00 38.63 3.07
2751 2989 6.240894 ACGAATGCCATGTAGGATAAATGAT 58.759 36.000 0.00 0.00 38.63 2.45
2752 2990 5.620206 ACGAATGCCATGTAGGATAAATGA 58.380 37.500 0.00 0.00 38.63 2.57
2753 2991 5.947228 ACGAATGCCATGTAGGATAAATG 57.053 39.130 0.00 0.00 41.22 2.32
2754 2992 7.450074 TCTTACGAATGCCATGTAGGATAAAT 58.550 34.615 0.00 0.00 41.22 1.40
2755 2993 6.822442 TCTTACGAATGCCATGTAGGATAAA 58.178 36.000 0.00 0.00 41.22 1.40
2756 2994 6.413783 TCTTACGAATGCCATGTAGGATAA 57.586 37.500 0.00 0.00 41.22 1.75
2757 2995 6.605471 ATCTTACGAATGCCATGTAGGATA 57.395 37.500 0.00 0.00 41.22 2.59
2758 2996 4.955811 TCTTACGAATGCCATGTAGGAT 57.044 40.909 0.00 0.00 41.22 3.24
2759 2997 4.955811 ATCTTACGAATGCCATGTAGGA 57.044 40.909 0.00 0.00 41.22 2.94
2760 2998 7.352739 GTTTTATCTTACGAATGCCATGTAGG 58.647 38.462 0.00 0.00 41.84 3.18
2761 2999 7.011950 TGGTTTTATCTTACGAATGCCATGTAG 59.988 37.037 0.00 0.00 0.00 2.74
2762 3000 6.824196 TGGTTTTATCTTACGAATGCCATGTA 59.176 34.615 0.00 0.00 0.00 2.29
2763 3001 5.650266 TGGTTTTATCTTACGAATGCCATGT 59.350 36.000 0.00 0.00 0.00 3.21
2764 3002 6.130298 TGGTTTTATCTTACGAATGCCATG 57.870 37.500 0.00 0.00 0.00 3.66
2765 3003 6.959639 ATGGTTTTATCTTACGAATGCCAT 57.040 33.333 0.00 0.00 0.00 4.40
2766 3004 6.151985 ACAATGGTTTTATCTTACGAATGCCA 59.848 34.615 0.00 0.00 0.00 4.92
2767 3005 6.560711 ACAATGGTTTTATCTTACGAATGCC 58.439 36.000 0.00 0.00 0.00 4.40
2768 3006 8.178964 TGTACAATGGTTTTATCTTACGAATGC 58.821 33.333 0.00 0.00 0.00 3.56
2771 3009 8.178964 GCATGTACAATGGTTTTATCTTACGAA 58.821 33.333 0.00 0.00 0.00 3.85
2772 3010 7.201661 GGCATGTACAATGGTTTTATCTTACGA 60.202 37.037 0.00 0.00 0.00 3.43
2773 3011 6.910433 GGCATGTACAATGGTTTTATCTTACG 59.090 38.462 0.00 0.00 0.00 3.18
2774 3012 7.068226 AGGGCATGTACAATGGTTTTATCTTAC 59.932 37.037 0.00 0.00 0.00 2.34
2775 3013 7.122715 AGGGCATGTACAATGGTTTTATCTTA 58.877 34.615 0.00 0.00 0.00 2.10
2776 3014 5.957774 AGGGCATGTACAATGGTTTTATCTT 59.042 36.000 0.00 0.00 0.00 2.40
2777 3015 5.518865 AGGGCATGTACAATGGTTTTATCT 58.481 37.500 0.00 0.00 0.00 1.98
2778 3016 5.852282 AGGGCATGTACAATGGTTTTATC 57.148 39.130 0.00 0.00 0.00 1.75
2779 3017 7.912778 ATAAGGGCATGTACAATGGTTTTAT 57.087 32.000 0.00 0.00 0.00 1.40
2780 3018 9.073475 GATATAAGGGCATGTACAATGGTTTTA 57.927 33.333 0.00 0.00 0.00 1.52
2781 3019 7.015195 GGATATAAGGGCATGTACAATGGTTTT 59.985 37.037 0.00 0.00 0.00 2.43
2782 3020 6.493458 GGATATAAGGGCATGTACAATGGTTT 59.507 38.462 0.00 0.00 0.00 3.27
2783 3021 6.010219 GGATATAAGGGCATGTACAATGGTT 58.990 40.000 0.00 0.00 0.00 3.67
2784 3022 5.313240 AGGATATAAGGGCATGTACAATGGT 59.687 40.000 0.00 0.00 0.00 3.55
2785 3023 5.819991 AGGATATAAGGGCATGTACAATGG 58.180 41.667 0.00 0.00 0.00 3.16
2786 3024 8.862325 TTTAGGATATAAGGGCATGTACAATG 57.138 34.615 0.00 0.12 0.00 2.82
2816 3054 8.318412 CCATGCATGTAGGGTTTAGTATATGTA 58.682 37.037 24.58 0.00 0.00 2.29
2818 3056 7.394016 TCCATGCATGTAGGGTTTAGTATATG 58.606 38.462 24.58 3.85 0.00 1.78
2820 3058 7.568128 ATCCATGCATGTAGGGTTTAGTATA 57.432 36.000 24.58 0.00 0.00 1.47
2821 3059 5.904984 TCCATGCATGTAGGGTTTAGTAT 57.095 39.130 24.58 0.00 0.00 2.12
2822 3060 5.510690 CGATCCATGCATGTAGGGTTTAGTA 60.511 44.000 24.58 0.00 0.00 1.82
2831 3105 4.621068 AACAAACGATCCATGCATGTAG 57.379 40.909 24.58 14.51 0.00 2.74
2879 3153 4.292186 AGCTCAACCATTGTGTGAGTAT 57.708 40.909 12.74 3.35 0.00 2.12
2880 3154 3.769739 AGCTCAACCATTGTGTGAGTA 57.230 42.857 12.74 0.00 0.00 2.59
2894 3168 8.162878 AGTATTTAGTACGTATGCTAGCTCAA 57.837 34.615 17.23 0.00 38.38 3.02
2930 3204 9.698309 CCGTTCAGAAATACTAGATACAATCAT 57.302 33.333 0.00 0.00 0.00 2.45
2931 3205 8.909923 TCCGTTCAGAAATACTAGATACAATCA 58.090 33.333 0.00 0.00 0.00 2.57
2932 3206 9.915629 ATCCGTTCAGAAATACTAGATACAATC 57.084 33.333 0.00 0.00 0.00 2.67
2933 3207 9.915629 GATCCGTTCAGAAATACTAGATACAAT 57.084 33.333 0.00 0.00 0.00 2.71
2934 3208 8.909923 TGATCCGTTCAGAAATACTAGATACAA 58.090 33.333 0.00 0.00 0.00 2.41
2935 3209 8.459911 TGATCCGTTCAGAAATACTAGATACA 57.540 34.615 0.00 0.00 0.00 2.29
2936 3210 9.347934 CATGATCCGTTCAGAAATACTAGATAC 57.652 37.037 0.00 0.00 37.89 2.24
2937 3211 8.523658 CCATGATCCGTTCAGAAATACTAGATA 58.476 37.037 0.00 0.00 37.89 1.98
2938 3212 7.233553 TCCATGATCCGTTCAGAAATACTAGAT 59.766 37.037 0.00 0.00 37.89 1.98
2939 3213 6.549736 TCCATGATCCGTTCAGAAATACTAGA 59.450 38.462 0.00 0.00 37.89 2.43
2940 3214 6.749139 TCCATGATCCGTTCAGAAATACTAG 58.251 40.000 0.00 0.00 37.89 2.57
2941 3215 6.724893 TCCATGATCCGTTCAGAAATACTA 57.275 37.500 0.00 0.00 37.89 1.82
2942 3216 5.614324 TCCATGATCCGTTCAGAAATACT 57.386 39.130 0.00 0.00 37.89 2.12
2943 3217 8.553459 AATATCCATGATCCGTTCAGAAATAC 57.447 34.615 0.00 0.00 37.89 1.89
2950 3224 9.764363 GCTATTATAATATCCATGATCCGTTCA 57.236 33.333 5.64 0.00 39.12 3.18
2951 3225 9.764363 TGCTATTATAATATCCATGATCCGTTC 57.236 33.333 5.64 0.00 0.00 3.95
3000 3274 5.114081 ACGCTTTACATAGTTACACCCATC 58.886 41.667 0.00 0.00 0.00 3.51
3004 3278 9.305925 AGTATAAACGCTTTACATAGTTACACC 57.694 33.333 0.00 0.00 0.00 4.16
3062 3346 0.370273 GTGTAGCAAGCAATCGGACG 59.630 55.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.