Multiple sequence alignment - TraesCS3A01G344300

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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 TraesCS3A01G344300 chr3A 100.000 4282 0 0 1386 5667 593704727 593700446 0.000000e+00 7908.0
1 TraesCS3A01G344300 chr3A 100.000 1085 0 0 1 1085 593706112 593705028 0.000000e+00 2004.0
2 TraesCS3A01G344300 chr3D 94.804 2502 84 19 3185 5667 450293910 450291436 0.000000e+00 3858.0
3 TraesCS3A01G344300 chr3D 96.142 1659 47 5 1386 3040 450295671 450294026 0.000000e+00 2693.0
4 TraesCS3A01G344300 chr3D 90.249 441 20 9 662 1085 450296124 450295690 6.420000e-154 555.0
5 TraesCS3A01G344300 chr3D 86.220 537 45 20 52 570 450296709 450296184 6.420000e-154 555.0
6 TraesCS3A01G344300 chr3D 92.308 91 4 2 3106 3196 450294032 450293945 5.960000e-25 126.0
7 TraesCS3A01G344300 chr3D 100.000 32 0 0 8 39 450296740 450296709 6.130000e-05 60.2
8 TraesCS3A01G344300 chr3B 92.100 2519 109 45 3185 5667 592531953 592529489 0.000000e+00 3467.0
9 TraesCS3A01G344300 chr3B 96.805 1659 48 4 1386 3040 592533731 592532074 0.000000e+00 2765.0
10 TraesCS3A01G344300 chr3B 89.498 438 21 11 662 1085 592534176 592533750 1.080000e-146 531.0
11 TraesCS3A01G344300 chr3B 88.506 435 18 19 8 417 592534801 592534374 1.100000e-136 497.0
12 TraesCS3A01G344300 chr3B 86.555 119 14 2 452 570 592534379 592534263 4.610000e-26 130.0
13 TraesCS3A01G344300 chr3B 91.011 89 5 2 3106 3194 592532080 592531995 3.590000e-22 117.0
14 TraesCS3A01G344300 chrUn 97.917 48 1 0 3043 3090 296654909 296654862 3.640000e-12 84.2
15 TraesCS3A01G344300 chrUn 97.917 48 1 0 3043 3090 309531266 309531219 3.640000e-12 84.2
16 TraesCS3A01G344300 chr6D 97.917 48 1 0 3043 3090 468315146 468315099 3.640000e-12 84.2
17 TraesCS3A01G344300 chr6A 97.917 48 1 0 3043 3090 591420724 591420677 3.640000e-12 84.2
18 TraesCS3A01G344300 chr4D 97.917 48 1 0 3043 3090 8826234 8826281 3.640000e-12 84.2
19 TraesCS3A01G344300 chr4D 97.917 48 1 0 3043 3090 286074834 286074787 3.640000e-12 84.2
20 TraesCS3A01G344300 chr4D 97.917 48 1 0 3043 3090 286087496 286087449 3.640000e-12 84.2
21 TraesCS3A01G344300 chr4D 97.917 48 1 0 3043 3090 286127045 286126998 3.640000e-12 84.2
22 TraesCS3A01G344300 chr4B 97.917 48 1 0 3043 3090 207509369 207509416 3.640000e-12 84.2


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 TraesCS3A01G344300 chr3A 593700446 593706112 5666 True 4956.000000 7908 100.000000 1 5667 2 chr3A.!!$R1 5666
1 TraesCS3A01G344300 chr3D 450291436 450296740 5304 True 1307.866667 3858 93.287167 8 5667 6 chr3D.!!$R1 5659
2 TraesCS3A01G344300 chr3B 592529489 592534801 5312 True 1251.166667 3467 90.745833 8 5667 6 chr3B.!!$R1 5659

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
179 194 1.024579 AAGCGGCCGGTGTAAATGAG 61.025 55.000 33.14 0.00 0.00 2.90 F
446 473 1.228583 TCAGCGAGAGGCCCGATAT 60.229 57.895 0.00 0.00 45.17 1.63 F
1980 2065 1.022982 GTAACCTTTTCGCCGGGGAG 61.023 60.000 21.47 12.34 0.00 4.30 F
2971 3061 0.323633 CATGTGTGGGAATCTGGGCA 60.324 55.000 0.00 0.00 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 1957 1.454847 CCCGGAGAGGTCCAGAGAG 60.455 68.421 0.73 0.0 44.18 3.20 R
2274 2359 3.256960 AGGCCGAACACCCACCAT 61.257 61.111 0.00 0.0 0.00 3.55 R
3053 3143 0.102844 CCACACCTTGCCACACTTTG 59.897 55.000 0.00 0.0 0.00 2.77 R
4897 5043 0.763035 ACCGAGGCAATACCCATACC 59.237 55.000 0.00 0.0 40.58 2.73 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
39 40 2.188829 GCACTTGCACTGCTCACCA 61.189 57.895 8.09 0.00 41.59 4.17
179 194 1.024579 AAGCGGCCGGTGTAAATGAG 61.025 55.000 33.14 0.00 0.00 2.90
190 205 3.492337 GTGTAAATGAGGGTTGTTGGGA 58.508 45.455 0.00 0.00 0.00 4.37
249 265 1.807573 CGCGTCAGGAGGAGCTTTC 60.808 63.158 0.00 0.00 0.00 2.62
262 278 2.554462 GGAGCTTTCAAAACCTCCTCAC 59.446 50.000 8.86 0.00 37.64 3.51
269 285 2.158667 TCAAAACCTCCTCACACCCTTC 60.159 50.000 0.00 0.00 0.00 3.46
270 286 1.821088 AAACCTCCTCACACCCTTCT 58.179 50.000 0.00 0.00 0.00 2.85
274 290 2.158608 ACCTCCTCACACCCTTCTTTTG 60.159 50.000 0.00 0.00 0.00 2.44
276 292 1.850345 TCCTCACACCCTTCTTTTGGT 59.150 47.619 0.00 0.00 34.40 3.67
285 301 4.803452 ACCCTTCTTTTGGTGAATGAGAA 58.197 39.130 0.00 0.00 32.36 2.87
371 396 2.603560 GTCTCGCTACAGGCAAATGTAC 59.396 50.000 0.00 0.00 41.91 2.90
372 397 2.232696 TCTCGCTACAGGCAAATGTACA 59.767 45.455 0.00 0.00 41.91 2.90
373 398 2.604914 CTCGCTACAGGCAAATGTACAG 59.395 50.000 0.33 0.00 41.91 2.74
378 403 2.504367 ACAGGCAAATGTACAGTCCAC 58.496 47.619 0.33 0.00 0.00 4.02
379 404 1.812571 CAGGCAAATGTACAGTCCACC 59.187 52.381 0.33 1.38 0.00 4.61
392 419 2.558359 CAGTCCACCCAAACCAAAGATC 59.442 50.000 0.00 0.00 0.00 2.75
393 420 1.539827 GTCCACCCAAACCAAAGATCG 59.460 52.381 0.00 0.00 0.00 3.69
410 437 4.723248 AGATCGAAAACGAAAGGAAATGC 58.277 39.130 0.00 0.00 0.00 3.56
414 441 5.627172 TCGAAAACGAAAGGAAATGCTATG 58.373 37.500 0.00 0.00 0.00 2.23
417 444 4.701956 AACGAAAGGAAATGCTATGTGG 57.298 40.909 0.00 0.00 0.00 4.17
419 446 2.539547 CGAAAGGAAATGCTATGTGGCG 60.540 50.000 0.00 0.00 34.52 5.69
445 472 2.194212 GTCAGCGAGAGGCCCGATA 61.194 63.158 0.00 0.00 45.17 2.92
446 473 1.228583 TCAGCGAGAGGCCCGATAT 60.229 57.895 0.00 0.00 45.17 1.63
450 477 1.546476 AGCGAGAGGCCCGATATAAAG 59.454 52.381 0.00 0.00 45.17 1.85
472 499 6.624352 AGATTGTGAAATCGGGTCATAATG 57.376 37.500 9.41 0.00 37.07 1.90
474 501 2.948979 TGTGAAATCGGGTCATAATGGC 59.051 45.455 0.00 0.00 0.00 4.40
499 532 3.251571 GTCGACGATGGCCCTATTAATC 58.748 50.000 0.00 0.00 0.00 1.75
501 534 2.233922 CGACGATGGCCCTATTAATCCT 59.766 50.000 0.00 0.00 0.00 3.24
523 556 2.639065 GCGTTATCAAGGGGTGAATGA 58.361 47.619 0.00 0.00 40.50 2.57
529 562 1.611491 TCAAGGGGTGAATGAAAACGC 59.389 47.619 0.00 0.00 31.51 4.84
563 596 1.402787 GGTGGCAATCAATCCGGAAT 58.597 50.000 9.01 0.00 0.00 3.01
590 654 8.481492 TCGGAGTATTAACTAATGGTGGATTA 57.519 34.615 0.00 0.00 35.56 1.75
601 665 8.893563 ACTAATGGTGGATTATTTTTCTTCCA 57.106 30.769 0.00 0.00 35.93 3.53
625 689 3.830744 ATAATGGCTGTAACGCACCTA 57.169 42.857 0.00 0.00 0.00 3.08
626 690 2.710096 AATGGCTGTAACGCACCTAT 57.290 45.000 0.00 0.00 0.00 2.57
627 691 3.830744 AATGGCTGTAACGCACCTATA 57.169 42.857 0.00 0.00 0.00 1.31
628 692 2.882927 TGGCTGTAACGCACCTATAG 57.117 50.000 0.00 0.00 0.00 1.31
629 693 2.104967 TGGCTGTAACGCACCTATAGT 58.895 47.619 0.00 0.00 0.00 2.12
630 694 3.289836 TGGCTGTAACGCACCTATAGTA 58.710 45.455 0.00 0.00 0.00 1.82
631 695 3.067180 TGGCTGTAACGCACCTATAGTAC 59.933 47.826 0.00 0.00 0.00 2.73
632 696 3.067180 GGCTGTAACGCACCTATAGTACA 59.933 47.826 0.00 0.00 0.00 2.90
633 697 4.040376 GCTGTAACGCACCTATAGTACAC 58.960 47.826 0.00 0.00 0.00 2.90
634 698 4.439153 GCTGTAACGCACCTATAGTACACA 60.439 45.833 0.00 0.00 0.00 3.72
635 699 5.641783 TGTAACGCACCTATAGTACACAA 57.358 39.130 0.00 0.00 0.00 3.33
636 700 6.023357 TGTAACGCACCTATAGTACACAAA 57.977 37.500 0.00 0.00 0.00 2.83
637 701 6.632909 TGTAACGCACCTATAGTACACAAAT 58.367 36.000 0.00 0.00 0.00 2.32
638 702 7.770201 TGTAACGCACCTATAGTACACAAATA 58.230 34.615 0.00 0.00 0.00 1.40
639 703 8.415553 TGTAACGCACCTATAGTACACAAATAT 58.584 33.333 0.00 0.00 0.00 1.28
640 704 7.941795 AACGCACCTATAGTACACAAATATC 57.058 36.000 0.00 0.00 0.00 1.63
641 705 6.147581 ACGCACCTATAGTACACAAATATCG 58.852 40.000 0.00 0.00 0.00 2.92
642 706 5.571741 CGCACCTATAGTACACAAATATCGG 59.428 44.000 0.00 0.00 0.00 4.18
643 707 6.569035 CGCACCTATAGTACACAAATATCGGA 60.569 42.308 0.00 0.00 0.00 4.55
644 708 6.807230 GCACCTATAGTACACAAATATCGGAG 59.193 42.308 0.00 0.00 0.00 4.63
645 709 7.523380 GCACCTATAGTACACAAATATCGGAGT 60.523 40.741 0.00 0.00 0.00 3.85
646 710 9.006839 CACCTATAGTACACAAATATCGGAGTA 57.993 37.037 0.00 0.00 0.00 2.59
647 711 9.750783 ACCTATAGTACACAAATATCGGAGTAT 57.249 33.333 0.00 0.00 0.00 2.12
660 724 9.720769 AAATATCGGAGTATTAACTAATGGTGG 57.279 33.333 0.00 0.00 35.56 4.61
686 750 3.555527 ATGAGATGAGGTGACCACATG 57.444 47.619 19.20 0.00 0.00 3.21
760 827 8.411991 AGGGAAACAAATCGGAAAAGTTAATA 57.588 30.769 0.00 0.00 0.00 0.98
761 828 8.301720 AGGGAAACAAATCGGAAAAGTTAATAC 58.698 33.333 0.00 0.00 0.00 1.89
789 856 3.446873 CGAATCATTTTGTCCATTCCCCA 59.553 43.478 0.00 0.00 0.00 4.96
985 1070 2.681778 CACTCGCACTCCTCCCCT 60.682 66.667 0.00 0.00 0.00 4.79
1758 1843 2.435059 GCCCACAACGAGCTCTCC 60.435 66.667 12.85 0.00 0.00 3.71
1980 2065 1.022982 GTAACCTTTTCGCCGGGGAG 61.023 60.000 21.47 12.34 0.00 4.30
2529 2614 2.126307 CTGGAGGTGCTCGACGTG 60.126 66.667 0.00 0.00 0.00 4.49
2651 2736 1.246056 GCACAGATTGGGAGCTGCAA 61.246 55.000 7.79 0.00 43.01 4.08
2682 2767 2.742053 TGCACTGTAAGCGAATTTCTCC 59.258 45.455 0.00 0.00 37.60 3.71
2799 2886 4.261614 GGTTGCTTTCAGTTTCCTAGGTTG 60.262 45.833 9.08 4.02 0.00 3.77
2828 2915 4.510340 ACGTTGTAGAAAATGACAGGACAC 59.490 41.667 0.00 0.00 0.00 3.67
2910 3000 1.960040 CTGCTCGTATCCAGTGCCCA 61.960 60.000 0.00 0.00 0.00 5.36
2926 3016 3.440522 GTGCCCAGTTCATTTTCTAGGAC 59.559 47.826 0.00 0.00 0.00 3.85
2934 3024 5.869888 AGTTCATTTTCTAGGACACGCTTAG 59.130 40.000 0.00 0.00 0.00 2.18
2937 3027 6.640518 TCATTTTCTAGGACACGCTTAGAAT 58.359 36.000 0.00 0.00 42.55 2.40
2971 3061 0.323633 CATGTGTGGGAATCTGGGCA 60.324 55.000 0.00 0.00 0.00 5.36
3025 3115 7.418840 AATAGAAAATCTAGCAAGCTGATCG 57.581 36.000 4.53 0.00 31.67 3.69
3027 3117 5.049167 AGAAAATCTAGCAAGCTGATCGAG 58.951 41.667 4.53 0.00 0.00 4.04
3043 3133 7.706281 CTGATCGAGCAAATATAAACTCAGT 57.294 36.000 4.32 0.00 0.00 3.41
3044 3134 8.136057 CTGATCGAGCAAATATAAACTCAGTT 57.864 34.615 4.32 0.00 0.00 3.16
3045 3135 9.249457 CTGATCGAGCAAATATAAACTCAGTTA 57.751 33.333 4.32 0.00 0.00 2.24
3046 3136 9.249457 TGATCGAGCAAATATAAACTCAGTTAG 57.751 33.333 0.00 0.00 0.00 2.34
3047 3137 9.250624 GATCGAGCAAATATAAACTCAGTTAGT 57.749 33.333 0.00 0.00 41.49 2.24
3057 3147 4.900635 AACTCAGTTAGTTGTGGCAAAG 57.099 40.909 0.00 0.00 46.90 2.77
3058 3148 3.886123 ACTCAGTTAGTTGTGGCAAAGT 58.114 40.909 0.00 0.00 33.35 2.66
3059 3149 3.627577 ACTCAGTTAGTTGTGGCAAAGTG 59.372 43.478 0.00 0.00 33.35 3.16
3060 3150 3.616219 TCAGTTAGTTGTGGCAAAGTGT 58.384 40.909 0.00 0.00 0.00 3.55
3061 3151 3.376859 TCAGTTAGTTGTGGCAAAGTGTG 59.623 43.478 0.00 0.00 0.00 3.82
3062 3152 2.687935 AGTTAGTTGTGGCAAAGTGTGG 59.312 45.455 0.00 0.00 0.00 4.17
3069 3159 4.736165 GCAAAGTGTGGCAAGGTG 57.264 55.556 0.00 0.00 0.00 4.00
3070 3160 1.815866 GCAAAGTGTGGCAAGGTGT 59.184 52.632 0.00 0.00 0.00 4.16
3071 3161 0.528249 GCAAAGTGTGGCAAGGTGTG 60.528 55.000 0.00 0.00 0.00 3.82
3072 3162 0.102844 CAAAGTGTGGCAAGGTGTGG 59.897 55.000 0.00 0.00 0.00 4.17
3081 3171 0.881796 GCAAGGTGTGGCTAGAAACC 59.118 55.000 0.00 0.00 0.00 3.27
3082 3172 1.817740 GCAAGGTGTGGCTAGAAACCA 60.818 52.381 0.00 0.00 35.01 3.67
3083 3173 2.582052 CAAGGTGTGGCTAGAAACCAA 58.418 47.619 0.00 0.00 39.39 3.67
3084 3174 2.955660 CAAGGTGTGGCTAGAAACCAAA 59.044 45.455 0.00 0.00 39.39 3.28
3085 3175 2.583143 AGGTGTGGCTAGAAACCAAAC 58.417 47.619 0.00 0.00 43.64 2.93
3086 3176 2.092103 AGGTGTGGCTAGAAACCAAACA 60.092 45.455 9.60 0.00 45.81 2.83
3087 3177 2.293399 GGTGTGGCTAGAAACCAAACAG 59.707 50.000 9.60 0.00 45.81 3.16
3088 3178 1.953686 TGTGGCTAGAAACCAAACAGC 59.046 47.619 0.00 0.00 39.39 4.40
3090 3180 1.911057 GGCTAGAAACCAAACAGCCT 58.089 50.000 3.69 0.00 46.70 4.58
3091 3181 1.541588 GGCTAGAAACCAAACAGCCTG 59.458 52.381 3.69 0.00 46.70 4.85
3092 3182 1.068264 GCTAGAAACCAAACAGCCTGC 60.068 52.381 0.00 0.00 0.00 4.85
3093 3183 2.229792 CTAGAAACCAAACAGCCTGCA 58.770 47.619 0.00 0.00 0.00 4.41
3094 3184 1.035139 AGAAACCAAACAGCCTGCAG 58.965 50.000 6.78 6.78 0.00 4.41
3095 3185 1.032014 GAAACCAAACAGCCTGCAGA 58.968 50.000 17.39 0.00 0.00 4.26
3096 3186 1.615392 GAAACCAAACAGCCTGCAGAT 59.385 47.619 17.39 0.00 0.00 2.90
3097 3187 1.251251 AACCAAACAGCCTGCAGATC 58.749 50.000 17.39 6.56 0.00 2.75
3098 3188 0.957395 ACCAAACAGCCTGCAGATCG 60.957 55.000 17.39 4.90 0.00 3.69
3099 3189 0.674581 CCAAACAGCCTGCAGATCGA 60.675 55.000 17.39 0.00 0.00 3.59
3100 3190 0.725686 CAAACAGCCTGCAGATCGAG 59.274 55.000 17.39 7.47 0.00 4.04
3101 3191 1.023513 AAACAGCCTGCAGATCGAGC 61.024 55.000 17.39 9.76 0.00 5.03
3102 3192 2.176314 AACAGCCTGCAGATCGAGCA 62.176 55.000 17.39 13.92 40.19 4.26
3103 3193 1.449070 CAGCCTGCAGATCGAGCAA 60.449 57.895 17.39 2.50 42.17 3.91
3104 3194 1.022982 CAGCCTGCAGATCGAGCAAA 61.023 55.000 17.39 0.00 42.17 3.68
3140 3230 8.256611 TGTTACTTGATTCTGACTTAATGAGC 57.743 34.615 0.00 0.00 0.00 4.26
3144 3234 6.370994 ACTTGATTCTGACTTAATGAGCACTG 59.629 38.462 0.00 0.00 0.00 3.66
3145 3235 4.633126 TGATTCTGACTTAATGAGCACTGC 59.367 41.667 0.00 0.00 0.00 4.40
3146 3236 3.969287 TCTGACTTAATGAGCACTGCT 57.031 42.857 2.22 2.22 43.88 4.24
3147 3237 4.277515 TCTGACTTAATGAGCACTGCTT 57.722 40.909 4.67 0.00 39.88 3.91
3294 3434 3.859443 CTGTTGATCTCTCCCAGAACAG 58.141 50.000 0.00 0.00 35.47 3.16
3313 3453 2.124570 CTGAATGGGACCCTGCCG 60.125 66.667 13.00 0.00 0.00 5.69
3385 3525 3.137360 ACTTGCTATCAGGAAATCTCCCC 59.863 47.826 0.00 0.00 43.64 4.81
3413 3553 3.527533 CGTTTCTTCGACAATATCCCCA 58.472 45.455 0.00 0.00 0.00 4.96
3418 3558 6.494666 TTCTTCGACAATATCCCCAACTAT 57.505 37.500 0.00 0.00 0.00 2.12
3474 3614 1.880027 GAAGAACAATTCCTGCGGTGT 59.120 47.619 0.00 0.00 0.00 4.16
3475 3615 1.238439 AGAACAATTCCTGCGGTGTG 58.762 50.000 0.00 0.00 0.00 3.82
3529 3669 1.003118 TCCTCATCAAACCCCTTGTCG 59.997 52.381 0.00 0.00 36.34 4.35
3643 3783 2.001812 CCTTCGGAGTGATCACTGTG 57.998 55.000 32.50 22.51 42.66 3.66
4084 4224 1.448540 CCTCCATGAGTGCACGGAC 60.449 63.158 12.01 7.93 30.06 4.79
4303 4443 3.779759 CAGTAAGATCCAGAGTGCACTC 58.220 50.000 34.82 34.82 43.17 3.51
4375 4515 2.873288 GACGTCTACGGCTTCGGT 59.127 61.111 8.70 0.00 45.57 4.69
4450 4590 3.345737 CGTGGTCGTGCTATGTGAT 57.654 52.632 0.00 0.00 0.00 3.06
4451 4591 1.200483 CGTGGTCGTGCTATGTGATC 58.800 55.000 0.00 0.00 0.00 2.92
4457 4597 0.933097 CGTGCTATGTGATCTGGTGC 59.067 55.000 0.00 0.00 0.00 5.01
4502 4642 1.402896 GGAGGACTGCATGGATCCGA 61.403 60.000 7.39 0.00 37.60 4.55
4520 4660 3.112709 GACTGTGCGGCGAGTTCC 61.113 66.667 12.98 0.00 0.00 3.62
4567 4707 3.365265 CTGGGCCTCGTTTGCACC 61.365 66.667 4.53 0.00 0.00 5.01
4618 4758 2.223758 GGGCGAGGTGTTGAGTATACTC 60.224 54.545 23.53 23.53 43.15 2.59
4696 4841 2.277969 TGAACTTTGTTCCGCGTGTAA 58.722 42.857 4.92 0.00 0.00 2.41
4778 4923 2.837498 CGATGGAGTGGTGATGCATTA 58.163 47.619 0.00 0.00 0.00 1.90
4897 5043 5.414360 TGAAACTGTAGCTTATCTCTGCTG 58.586 41.667 0.00 0.00 40.08 4.41
4900 5046 4.537751 ACTGTAGCTTATCTCTGCTGGTA 58.462 43.478 0.00 0.00 40.08 3.25
4912 5058 1.143684 CTGCTGGTATGGGTATTGCCT 59.856 52.381 0.00 0.00 37.43 4.75
4914 5060 1.878102 GCTGGTATGGGTATTGCCTCG 60.878 57.143 0.00 0.00 37.43 4.63
4916 5062 0.763035 GGTATGGGTATTGCCTCGGT 59.237 55.000 0.00 0.00 37.43 4.69
4918 5064 0.107831 TATGGGTATTGCCTCGGTGC 59.892 55.000 0.00 0.00 37.43 5.01
4919 5065 2.516225 GGGTATTGCCTCGGTGCC 60.516 66.667 0.00 0.00 37.43 5.01
4921 5067 3.573491 GTATTGCCTCGGTGCCGC 61.573 66.667 5.64 0.00 39.59 6.53
4922 5068 4.089239 TATTGCCTCGGTGCCGCA 62.089 61.111 5.64 0.00 39.59 5.69
4954 5100 0.462759 CATCTCGGCTCCCCTGAAAC 60.463 60.000 0.00 0.00 0.00 2.78
4972 5118 4.504097 TGAAACGACTGATATCTGATTGCG 59.496 41.667 15.75 13.99 0.00 4.85
4988 5134 4.994852 TGATTGCGTTCTTAGCTAGTTGTT 59.005 37.500 0.00 0.00 35.28 2.83
5005 5151 8.507249 GCTAGTTGTTCTGATAAATGTGACTTT 58.493 33.333 0.00 0.00 0.00 2.66
5169 5335 3.181516 GCAACGACTGTTCTGATTCCATC 60.182 47.826 0.00 0.00 35.72 3.51
5178 5344 7.851228 ACTGTTCTGATTCCATCACTGTAATA 58.149 34.615 0.00 0.00 35.06 0.98
5218 5384 8.595362 TCTGATCCAGTCTAAGTCTATCAAAA 57.405 34.615 0.00 0.00 32.61 2.44
5225 5391 9.307121 CCAGTCTAAGTCTATCAAAACTGTATG 57.693 37.037 0.00 0.00 32.88 2.39
5284 5457 2.759973 CTAGGCCGCTCCAGACCA 60.760 66.667 0.00 0.00 37.29 4.02
5398 5575 3.535629 CTTCTGTGCTCCCACGCCA 62.536 63.158 0.00 0.00 45.04 5.69
5421 5600 4.699522 GCCAGTCGTCACCCCCAC 62.700 72.222 0.00 0.00 0.00 4.61
5449 5628 1.412710 CGGAGGAATTGAATCGAGGGA 59.587 52.381 0.00 0.00 0.00 4.20
5451 5630 2.488952 GAGGAATTGAATCGAGGGAGC 58.511 52.381 0.00 0.00 0.00 4.70
5452 5631 1.141858 AGGAATTGAATCGAGGGAGCC 59.858 52.381 0.00 0.00 0.00 4.70
5453 5632 1.141858 GGAATTGAATCGAGGGAGCCT 59.858 52.381 0.00 0.00 36.03 4.58
5454 5633 2.422093 GGAATTGAATCGAGGGAGCCTT 60.422 50.000 0.00 0.00 31.76 4.35
5455 5634 2.629336 ATTGAATCGAGGGAGCCTTC 57.371 50.000 0.00 0.00 31.76 3.46
5456 5635 1.275666 TTGAATCGAGGGAGCCTTCA 58.724 50.000 0.00 0.00 31.76 3.02
5457 5636 1.275666 TGAATCGAGGGAGCCTTCAA 58.724 50.000 0.00 0.00 31.76 2.69
5458 5637 1.839994 TGAATCGAGGGAGCCTTCAAT 59.160 47.619 0.00 0.00 31.76 2.57
5510 5692 1.301953 CAGTAGCACTGTGCCAGCA 60.302 57.895 27.74 9.29 46.52 4.41
5533 5715 3.991999 GCAGGCAGCATTCACTCA 58.008 55.556 0.00 0.00 44.79 3.41
5534 5716 1.505353 GCAGGCAGCATTCACTCAC 59.495 57.895 0.00 0.00 44.79 3.51
5535 5717 0.959372 GCAGGCAGCATTCACTCACT 60.959 55.000 0.00 0.00 44.79 3.41
5536 5718 1.085091 CAGGCAGCATTCACTCACTC 58.915 55.000 0.00 0.00 0.00 3.51
5541 5723 3.084579 CATTCACTCACTCGCGCC 58.915 61.111 0.00 0.00 0.00 6.53
5584 5766 2.037136 CAGCAAGCGAACCAGGAGG 61.037 63.158 0.00 0.00 42.21 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.710816 ACCTTCAAATTTTGGGCGGA 58.289 45.000 9.18 0.00 0.00 5.54
1 2 2.142319 CAACCTTCAAATTTTGGGCGG 58.858 47.619 9.18 9.26 0.00 6.13
2 3 1.530720 GCAACCTTCAAATTTTGGGCG 59.469 47.619 9.18 1.05 0.00 6.13
3 4 2.290367 GTGCAACCTTCAAATTTTGGGC 59.710 45.455 9.18 5.06 0.00 5.36
4 5 3.807553 AGTGCAACCTTCAAATTTTGGG 58.192 40.909 9.18 6.16 37.80 4.12
5 6 4.496175 GCAAGTGCAACCTTCAAATTTTGG 60.496 41.667 9.18 0.00 41.59 3.28
6 7 4.590226 GCAAGTGCAACCTTCAAATTTTG 58.410 39.130 2.59 2.59 41.59 2.44
179 194 2.212900 GAATGCGCTCCCAACAACCC 62.213 60.000 9.73 0.00 0.00 4.11
190 205 2.415893 GGTTGCTTGTATTGAATGCGCT 60.416 45.455 9.73 0.00 0.00 5.92
249 265 2.158608 AGAAGGGTGTGAGGAGGTTTTG 60.159 50.000 0.00 0.00 0.00 2.44
269 285 6.815142 GGGAATTCATTCTCATTCACCAAAAG 59.185 38.462 7.93 0.00 37.24 2.27
270 286 6.269538 TGGGAATTCATTCTCATTCACCAAAA 59.730 34.615 7.93 0.00 42.05 2.44
280 296 2.083774 GTGCGTGGGAATTCATTCTCA 58.916 47.619 7.93 0.00 44.53 3.27
281 297 1.062587 CGTGCGTGGGAATTCATTCTC 59.937 52.381 7.93 0.00 37.78 2.87
282 298 1.086696 CGTGCGTGGGAATTCATTCT 58.913 50.000 7.93 0.00 37.00 2.40
285 301 3.903783 CCGTGCGTGGGAATTCAT 58.096 55.556 7.93 0.00 0.00 2.57
308 328 1.597663 CAAGCGAACGAAACCACTCTT 59.402 47.619 0.00 0.00 0.00 2.85
371 396 2.065899 TCTTTGGTTTGGGTGGACTG 57.934 50.000 0.00 0.00 0.00 3.51
372 397 2.814097 CGATCTTTGGTTTGGGTGGACT 60.814 50.000 0.00 0.00 0.00 3.85
373 398 1.539827 CGATCTTTGGTTTGGGTGGAC 59.460 52.381 0.00 0.00 0.00 4.02
392 419 5.283717 CACATAGCATTTCCTTTCGTTTTCG 59.716 40.000 0.00 0.00 45.64 3.46
393 420 5.572896 CCACATAGCATTTCCTTTCGTTTTC 59.427 40.000 0.00 0.00 0.00 2.29
432 459 4.177026 CAATCTTTATATCGGGCCTCTCG 58.823 47.826 0.84 0.00 0.00 4.04
442 469 8.378172 TGACCCGATTTCACAATCTTTATATC 57.622 34.615 0.00 0.00 37.27 1.63
445 472 8.746052 TTATGACCCGATTTCACAATCTTTAT 57.254 30.769 0.00 0.00 37.27 1.40
446 473 8.620416 CATTATGACCCGATTTCACAATCTTTA 58.380 33.333 0.00 0.00 37.27 1.85
450 477 5.762045 CCATTATGACCCGATTTCACAATC 58.238 41.667 0.00 0.00 36.20 2.67
490 523 5.643777 CCTTGATAACGCCAGGATTAATAGG 59.356 44.000 0.00 0.00 0.00 2.57
491 524 5.643777 CCCTTGATAACGCCAGGATTAATAG 59.356 44.000 0.00 0.00 0.00 1.73
499 532 0.748005 CACCCCTTGATAACGCCAGG 60.748 60.000 0.00 0.00 0.00 4.45
501 534 0.693622 TTCACCCCTTGATAACGCCA 59.306 50.000 0.00 0.00 32.84 5.69
523 556 4.021807 ACCGATGGAAATTTAAGGCGTTTT 60.022 37.500 0.00 0.00 0.00 2.43
563 596 8.660295 ATCCACCATTAGTTAATACTCCGATA 57.340 34.615 0.00 0.00 35.78 2.92
576 609 8.893563 TGGAAGAAAAATAATCCACCATTAGT 57.106 30.769 0.00 0.00 37.05 2.24
590 654 7.452562 ACAGCCATTATTTGTGGAAGAAAAAT 58.547 30.769 0.00 0.00 39.12 1.82
600 664 3.851403 GTGCGTTACAGCCATTATTTGTG 59.149 43.478 0.00 0.00 36.02 3.33
601 665 3.119637 GGTGCGTTACAGCCATTATTTGT 60.120 43.478 0.00 0.00 41.06 2.83
634 698 9.720769 CCACCATTAGTTAATACTCCGATATTT 57.279 33.333 0.00 0.00 35.78 1.40
635 699 9.096823 TCCACCATTAGTTAATACTCCGATATT 57.903 33.333 0.00 0.00 35.78 1.28
636 700 8.660295 TCCACCATTAGTTAATACTCCGATAT 57.340 34.615 0.00 0.00 35.78 1.63
637 701 7.727186 ACTCCACCATTAGTTAATACTCCGATA 59.273 37.037 0.00 0.00 35.78 2.92
638 702 6.553852 ACTCCACCATTAGTTAATACTCCGAT 59.446 38.462 0.00 0.00 35.78 4.18
639 703 5.895534 ACTCCACCATTAGTTAATACTCCGA 59.104 40.000 0.00 0.00 35.78 4.55
640 704 6.158023 ACTCCACCATTAGTTAATACTCCG 57.842 41.667 0.00 0.00 35.78 4.63
647 711 9.613428 CATCTCATTTACTCCACCATTAGTTAA 57.387 33.333 0.00 0.00 0.00 2.01
648 712 8.988060 TCATCTCATTTACTCCACCATTAGTTA 58.012 33.333 0.00 0.00 0.00 2.24
649 713 7.861629 TCATCTCATTTACTCCACCATTAGTT 58.138 34.615 0.00 0.00 0.00 2.24
650 714 7.419518 CCTCATCTCATTTACTCCACCATTAGT 60.420 40.741 0.00 0.00 0.00 2.24
651 715 6.933521 CCTCATCTCATTTACTCCACCATTAG 59.066 42.308 0.00 0.00 0.00 1.73
652 716 6.386927 ACCTCATCTCATTTACTCCACCATTA 59.613 38.462 0.00 0.00 0.00 1.90
653 717 5.192522 ACCTCATCTCATTTACTCCACCATT 59.807 40.000 0.00 0.00 0.00 3.16
654 718 4.723789 ACCTCATCTCATTTACTCCACCAT 59.276 41.667 0.00 0.00 0.00 3.55
655 719 4.080919 CACCTCATCTCATTTACTCCACCA 60.081 45.833 0.00 0.00 0.00 4.17
656 720 4.162320 TCACCTCATCTCATTTACTCCACC 59.838 45.833 0.00 0.00 0.00 4.61
657 721 5.112686 GTCACCTCATCTCATTTACTCCAC 58.887 45.833 0.00 0.00 0.00 4.02
658 722 4.162320 GGTCACCTCATCTCATTTACTCCA 59.838 45.833 0.00 0.00 0.00 3.86
659 723 4.162320 TGGTCACCTCATCTCATTTACTCC 59.838 45.833 0.00 0.00 0.00 3.85
660 724 5.112686 GTGGTCACCTCATCTCATTTACTC 58.887 45.833 0.00 0.00 0.00 2.59
735 802 6.718522 TTAACTTTTCCGATTTGTTTCCCT 57.281 33.333 0.00 0.00 0.00 4.20
760 827 8.190784 GGAATGGACAAAATGATTCGATTTAGT 58.809 33.333 0.00 0.00 0.00 2.24
761 828 7.649306 GGGAATGGACAAAATGATTCGATTTAG 59.351 37.037 0.00 0.00 0.00 1.85
789 856 4.452825 TGAGCTAGCACGAGTAGAACTAT 58.547 43.478 18.83 0.00 0.00 2.12
850 918 4.876701 TGAACTGTCACCTGTGGC 57.123 55.556 0.00 0.00 35.37 5.01
971 1042 4.779733 GGGAGGGGAGGAGTGCGA 62.780 72.222 0.00 0.00 0.00 5.10
1578 1663 4.089757 CGGGGGAGGGAGAGGGAA 62.090 72.222 0.00 0.00 0.00 3.97
1872 1957 1.454847 CCCGGAGAGGTCCAGAGAG 60.455 68.421 0.73 0.00 44.18 3.20
1989 2074 4.933064 GCCGCCTCTCCGACATCG 62.933 72.222 0.00 0.00 39.44 3.84
2274 2359 3.256960 AGGCCGAACACCCACCAT 61.257 61.111 0.00 0.00 0.00 3.55
2628 2713 2.671070 CTCCCAATCTGTGCCGGT 59.329 61.111 1.90 0.00 0.00 5.28
2651 2736 2.699954 CTTACAGTGCAACGAGGGAAT 58.300 47.619 0.00 0.00 45.86 3.01
2694 2779 2.425312 TGAAGTGTCAAATTTGGTGCGT 59.575 40.909 17.90 6.63 0.00 5.24
2799 2886 4.447724 TGTCATTTTCTACAACGTCTCTGC 59.552 41.667 0.00 0.00 0.00 4.26
2828 2915 6.395629 TCCTAACAGAAAACTAAGACATCGG 58.604 40.000 0.00 0.00 0.00 4.18
2910 3000 4.273148 AGCGTGTCCTAGAAAATGAACT 57.727 40.909 0.00 0.00 0.00 3.01
2926 3016 6.303970 CACATTTGACTTCAATTCTAAGCGTG 59.696 38.462 0.00 0.00 35.55 5.34
2934 3024 5.693104 ACACATGCACATTTGACTTCAATTC 59.307 36.000 3.89 0.00 35.55 2.17
2937 3027 4.361420 CACACATGCACATTTGACTTCAA 58.639 39.130 3.89 0.00 0.00 2.69
2971 3061 7.200778 ACAGTTTGCAAAGTTTGAAACAAAT 57.799 28.000 26.96 17.37 35.28 2.32
3009 3099 2.437200 GCTCGATCAGCTTGCTAGAT 57.563 50.000 0.00 1.45 45.83 1.98
3025 3115 9.760660 CACAACTAACTGAGTTTATATTTGCTC 57.239 33.333 1.97 0.00 46.79 4.26
3027 3117 7.484959 GCCACAACTAACTGAGTTTATATTTGC 59.515 37.037 1.97 0.00 46.79 3.68
3030 3120 8.630054 TTGCCACAACTAACTGAGTTTATATT 57.370 30.769 1.97 0.00 46.79 1.28
3033 3123 6.546034 ACTTTGCCACAACTAACTGAGTTTAT 59.454 34.615 1.97 0.00 46.79 1.40
3034 3124 5.883673 ACTTTGCCACAACTAACTGAGTTTA 59.116 36.000 1.97 0.00 46.79 2.01
3035 3125 4.705023 ACTTTGCCACAACTAACTGAGTTT 59.295 37.500 1.97 0.00 46.79 2.66
3037 3127 3.627577 CACTTTGCCACAACTAACTGAGT 59.372 43.478 0.00 0.00 41.56 3.41
3038 3128 3.627577 ACACTTTGCCACAACTAACTGAG 59.372 43.478 0.00 0.00 0.00 3.35
3039 3129 3.376859 CACACTTTGCCACAACTAACTGA 59.623 43.478 0.00 0.00 0.00 3.41
3040 3130 3.489059 CCACACTTTGCCACAACTAACTG 60.489 47.826 0.00 0.00 0.00 3.16
3041 3131 2.687935 CCACACTTTGCCACAACTAACT 59.312 45.455 0.00 0.00 0.00 2.24
3042 3132 2.798145 GCCACACTTTGCCACAACTAAC 60.798 50.000 0.00 0.00 0.00 2.34
3043 3133 1.407258 GCCACACTTTGCCACAACTAA 59.593 47.619 0.00 0.00 0.00 2.24
3044 3134 1.028905 GCCACACTTTGCCACAACTA 58.971 50.000 0.00 0.00 0.00 2.24
3045 3135 0.969917 TGCCACACTTTGCCACAACT 60.970 50.000 0.00 0.00 0.00 3.16
3046 3136 0.108424 TTGCCACACTTTGCCACAAC 60.108 50.000 0.00 0.00 0.00 3.32
3047 3137 0.175302 CTTGCCACACTTTGCCACAA 59.825 50.000 0.00 0.00 0.00 3.33
3048 3138 1.674764 CCTTGCCACACTTTGCCACA 61.675 55.000 0.00 0.00 0.00 4.17
3049 3139 1.067916 CCTTGCCACACTTTGCCAC 59.932 57.895 0.00 0.00 0.00 5.01
3050 3140 1.381056 ACCTTGCCACACTTTGCCA 60.381 52.632 0.00 0.00 0.00 4.92
3051 3141 1.067916 CACCTTGCCACACTTTGCC 59.932 57.895 0.00 0.00 0.00 4.52
3052 3142 0.528249 CACACCTTGCCACACTTTGC 60.528 55.000 0.00 0.00 0.00 3.68
3053 3143 0.102844 CCACACCTTGCCACACTTTG 59.897 55.000 0.00 0.00 0.00 2.77
3054 3144 1.675720 GCCACACCTTGCCACACTTT 61.676 55.000 0.00 0.00 0.00 2.66
3055 3145 2.127232 GCCACACCTTGCCACACTT 61.127 57.895 0.00 0.00 0.00 3.16
3056 3146 1.705002 TAGCCACACCTTGCCACACT 61.705 55.000 0.00 0.00 0.00 3.55
3057 3147 1.228124 TAGCCACACCTTGCCACAC 60.228 57.895 0.00 0.00 0.00 3.82
3058 3148 1.073025 CTAGCCACACCTTGCCACA 59.927 57.895 0.00 0.00 0.00 4.17
3059 3149 0.250727 TTCTAGCCACACCTTGCCAC 60.251 55.000 0.00 0.00 0.00 5.01
3060 3150 0.476338 TTTCTAGCCACACCTTGCCA 59.524 50.000 0.00 0.00 0.00 4.92
3061 3151 0.881796 GTTTCTAGCCACACCTTGCC 59.118 55.000 0.00 0.00 0.00 4.52
3062 3152 0.881796 GGTTTCTAGCCACACCTTGC 59.118 55.000 0.00 0.00 0.00 4.01
3063 3153 2.270352 TGGTTTCTAGCCACACCTTG 57.730 50.000 0.00 0.00 0.00 3.61
3064 3154 2.956333 GTTTGGTTTCTAGCCACACCTT 59.044 45.455 0.00 0.00 35.46 3.50
3065 3155 2.092103 TGTTTGGTTTCTAGCCACACCT 60.092 45.455 2.81 0.00 36.23 4.00
3066 3156 2.293399 CTGTTTGGTTTCTAGCCACACC 59.707 50.000 2.81 0.00 36.23 4.16
3067 3157 2.287608 GCTGTTTGGTTTCTAGCCACAC 60.288 50.000 0.00 0.00 37.25 3.82
3068 3158 1.953686 GCTGTTTGGTTTCTAGCCACA 59.046 47.619 0.00 0.00 35.46 4.17
3069 3159 2.706555 GCTGTTTGGTTTCTAGCCAC 57.293 50.000 0.00 0.00 35.46 5.01
3072 3162 1.068264 GCAGGCTGTTTGGTTTCTAGC 60.068 52.381 17.16 0.00 0.00 3.42
3073 3163 2.227388 CTGCAGGCTGTTTGGTTTCTAG 59.773 50.000 17.16 0.00 0.00 2.43
3074 3164 2.158682 TCTGCAGGCTGTTTGGTTTCTA 60.159 45.455 17.16 0.00 0.00 2.10
3075 3165 1.035139 CTGCAGGCTGTTTGGTTTCT 58.965 50.000 17.16 0.00 0.00 2.52
3076 3166 1.032014 TCTGCAGGCTGTTTGGTTTC 58.968 50.000 17.16 0.00 0.00 2.78
3077 3167 1.615392 GATCTGCAGGCTGTTTGGTTT 59.385 47.619 17.16 0.00 0.00 3.27
3078 3168 1.251251 GATCTGCAGGCTGTTTGGTT 58.749 50.000 17.16 0.00 0.00 3.67
3079 3169 0.957395 CGATCTGCAGGCTGTTTGGT 60.957 55.000 17.16 2.62 0.00 3.67
3080 3170 0.674581 TCGATCTGCAGGCTGTTTGG 60.675 55.000 17.16 4.27 0.00 3.28
3081 3171 0.725686 CTCGATCTGCAGGCTGTTTG 59.274 55.000 17.16 6.77 0.00 2.93
3082 3172 1.023513 GCTCGATCTGCAGGCTGTTT 61.024 55.000 17.16 0.00 0.00 2.83
3083 3173 1.449246 GCTCGATCTGCAGGCTGTT 60.449 57.895 17.16 0.00 0.00 3.16
3084 3174 2.176314 TTGCTCGATCTGCAGGCTGT 62.176 55.000 17.16 0.00 41.71 4.40
3085 3175 1.022982 TTTGCTCGATCTGCAGGCTG 61.023 55.000 15.13 10.94 41.71 4.85
3086 3176 1.023513 GTTTGCTCGATCTGCAGGCT 61.024 55.000 15.13 0.98 41.71 4.58
3087 3177 1.023513 AGTTTGCTCGATCTGCAGGC 61.024 55.000 15.13 9.50 41.71 4.85
3088 3178 2.299993 TAGTTTGCTCGATCTGCAGG 57.700 50.000 15.13 0.00 41.71 4.85
3089 3179 3.681897 AGTTTAGTTTGCTCGATCTGCAG 59.318 43.478 7.63 7.63 41.71 4.41
3090 3180 3.664107 AGTTTAGTTTGCTCGATCTGCA 58.336 40.909 6.22 6.22 38.80 4.41
3091 3181 4.670227 AAGTTTAGTTTGCTCGATCTGC 57.330 40.909 0.00 0.00 0.00 4.26
3092 3182 7.743104 ACAATAAGTTTAGTTTGCTCGATCTG 58.257 34.615 0.00 0.00 0.00 2.90
3093 3183 7.907214 ACAATAAGTTTAGTTTGCTCGATCT 57.093 32.000 0.00 0.00 0.00 2.75
3094 3184 9.474249 GTAACAATAAGTTTAGTTTGCTCGATC 57.526 33.333 0.00 0.00 41.64 3.69
3095 3185 9.216117 AGTAACAATAAGTTTAGTTTGCTCGAT 57.784 29.630 0.00 0.00 41.64 3.59
3096 3186 8.597662 AGTAACAATAAGTTTAGTTTGCTCGA 57.402 30.769 0.00 0.00 41.64 4.04
3097 3187 9.103048 CAAGTAACAATAAGTTTAGTTTGCTCG 57.897 33.333 0.00 0.00 41.64 5.03
3294 3434 2.440980 GCAGGGTCCCATTCAGCC 60.441 66.667 11.55 0.00 0.00 4.85
3313 3453 2.293170 GGCAGATTAGAAAGCTCCACC 58.707 52.381 0.00 0.00 0.00 4.61
3385 3525 0.934496 TGTCGAAGAAACGGCTGTTG 59.066 50.000 12.68 0.00 39.69 3.33
3413 3553 6.992715 CCGGAATTGTCTGATAGGAAATAGTT 59.007 38.462 0.00 0.00 30.94 2.24
3418 3558 3.541632 GCCGGAATTGTCTGATAGGAAA 58.458 45.455 5.05 0.00 30.94 3.13
3474 3614 2.535485 AATCGGCTTCGGCATGACCA 62.535 55.000 0.00 0.00 43.96 4.02
3475 3615 1.819632 AATCGGCTTCGGCATGACC 60.820 57.895 0.00 0.00 43.96 4.02
3529 3669 1.598701 GGGAGCTTGGTGTGGATTGC 61.599 60.000 0.00 0.00 0.00 3.56
3610 3750 3.346631 GAAGGCAATGGCAGCACCG 62.347 63.158 10.05 0.00 43.94 4.94
3626 3766 2.029918 CAGTCACAGTGATCACTCCGAA 60.030 50.000 25.58 8.82 40.20 4.30
3643 3783 1.299926 ACGACGGTTGAGCACAGTC 60.300 57.895 1.53 0.00 44.67 3.51
4084 4224 3.257393 CATCCAGGAAAGAGTGTTCTCG 58.743 50.000 0.00 0.00 44.65 4.04
4168 4308 4.698201 TGACTTGAGGTTGTAATGGACA 57.302 40.909 0.00 0.00 35.78 4.02
4180 4320 2.342910 GCACATTGCTTGACTTGAGG 57.657 50.000 0.00 0.00 40.96 3.86
4303 4443 2.940890 ATTCTGGCGCCATGTACCCG 62.941 60.000 32.87 16.96 0.00 5.28
4502 4642 2.049063 GAACTCGCCGCACAGTCT 60.049 61.111 0.00 0.00 0.00 3.24
4520 4660 1.072159 GAATGGCCTCCTCCATCGG 59.928 63.158 3.32 0.00 45.64 4.18
4567 4707 4.717629 TTCGACGGCACCTGCGAG 62.718 66.667 0.00 0.00 43.26 5.03
4618 4758 2.701780 CGGACTCCTCACCACCTCG 61.702 68.421 0.00 0.00 0.00 4.63
4696 4841 7.133133 TCTAGTAGAGAAACAAAAACCCAGT 57.867 36.000 0.00 0.00 0.00 4.00
4778 4923 7.315142 CAAACTACAAACTACATGCATTCCAT 58.685 34.615 0.00 0.00 33.39 3.41
4787 4932 8.514330 TTTCAGAACCAAACTACAAACTACAT 57.486 30.769 0.00 0.00 0.00 2.29
4897 5043 0.763035 ACCGAGGCAATACCCATACC 59.237 55.000 0.00 0.00 40.58 2.73
4900 5046 1.152963 GCACCGAGGCAATACCCAT 60.153 57.895 0.00 0.00 40.58 4.00
4921 5067 3.443045 GATGCCGGCCAACCACTG 61.443 66.667 26.77 0.00 34.57 3.66
4922 5068 3.628646 GAGATGCCGGCCAACCACT 62.629 63.158 26.77 13.53 34.57 4.00
4924 5070 4.776322 CGAGATGCCGGCCAACCA 62.776 66.667 26.77 4.49 34.57 3.67
4944 5090 3.384789 CAGATATCAGTCGTTTCAGGGGA 59.615 47.826 5.32 0.00 0.00 4.81
4954 5100 4.294232 AGAACGCAATCAGATATCAGTCG 58.706 43.478 5.32 2.43 0.00 4.18
5005 5151 9.541143 TGTCGAGCAATATATGTAAGAAATCAA 57.459 29.630 0.00 0.00 0.00 2.57
5169 5335 8.378565 AGAAGGGTAATCATGGATATTACAGTG 58.621 37.037 14.36 0.00 40.19 3.66
5178 5344 4.915809 TGGATCAGAAGGGTAATCATGGAT 59.084 41.667 0.00 0.00 0.00 3.41
5218 5384 5.817816 GGCTGCAAATAGTTAGTCATACAGT 59.182 40.000 0.50 0.00 0.00 3.55
5225 5391 3.682858 TCAACGGCTGCAAATAGTTAGTC 59.317 43.478 0.50 0.00 0.00 2.59
5274 5440 2.361737 GCCCCTTTGGTCTGGAGC 60.362 66.667 0.00 0.00 36.04 4.70
5424 5603 1.680338 GATTCAATTCCTCCGGTGGG 58.320 55.000 22.07 15.35 0.00 4.61
5430 5609 2.808567 GCTCCCTCGATTCAATTCCTCC 60.809 54.545 0.00 0.00 0.00 4.30
5449 5628 0.329261 TAGGTGCTGCATTGAAGGCT 59.671 50.000 5.27 0.00 0.00 4.58
5451 5630 1.098050 GGTAGGTGCTGCATTGAAGG 58.902 55.000 5.27 0.00 0.00 3.46
5452 5631 1.825090 TGGTAGGTGCTGCATTGAAG 58.175 50.000 5.27 0.00 0.00 3.02
5453 5632 2.512692 ATGGTAGGTGCTGCATTGAA 57.487 45.000 5.27 0.00 0.00 2.69
5454 5633 2.512692 AATGGTAGGTGCTGCATTGA 57.487 45.000 5.27 0.00 0.00 2.57
5455 5634 3.255725 CAAAATGGTAGGTGCTGCATTG 58.744 45.455 5.27 0.00 0.00 2.82
5456 5635 2.354003 GCAAAATGGTAGGTGCTGCATT 60.354 45.455 5.27 0.00 34.13 3.56
5457 5636 1.205417 GCAAAATGGTAGGTGCTGCAT 59.795 47.619 5.27 0.00 34.13 3.96
5458 5637 0.602562 GCAAAATGGTAGGTGCTGCA 59.397 50.000 0.00 0.00 34.13 4.41
5510 5692 1.980772 GAATGCTGCCTGCTGGGTT 60.981 57.895 12.06 0.00 43.37 4.11


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

AutoCloner maintained by Alex Coulton.