Multiple sequence alignment - TraesCS5A01G053300

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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 TraesCS5A01G053300 chr5A 100.000 2261 0 0 1 2261 48368868 48371128 0.000000e+00 4176
1 TraesCS5A01G053300 chr5A 100.000 685 0 0 2489 3173 48371356 48372040 0.000000e+00 1266
2 TraesCS5A01G053300 chr5A 84.524 504 65 6 55 552 502438627 502439123 1.320000e-133 486
3 TraesCS5A01G053300 chr5A 81.107 307 48 8 55 354 423011406 423011103 1.470000e-58 237
4 TraesCS5A01G053300 chr5D 94.101 1373 66 5 883 2254 59938659 59940017 0.000000e+00 2073
5 TraesCS5A01G053300 chr5D 93.750 304 12 2 2867 3170 59940756 59941052 1.740000e-122 449
6 TraesCS5A01G053300 chr5D 93.048 187 13 0 2489 2675 59940031 59940217 1.120000e-69 274
7 TraesCS5A01G053300 chr5D 88.789 223 11 6 618 835 59938418 59938631 8.730000e-66 261
8 TraesCS5A01G053300 chr5B 93.050 1036 56 12 886 1920 70805951 70804931 0.000000e+00 1500
9 TraesCS5A01G053300 chr5B 92.021 188 14 1 1911 2098 70804814 70804628 2.430000e-66 263
10 TraesCS5A01G053300 chr5B 92.814 167 8 4 2096 2258 70804547 70804381 4.090000e-59 239
11 TraesCS5A01G053300 chr5B 91.837 147 10 2 2734 2879 366076659 366076804 1.490000e-48 204
12 TraesCS5A01G053300 chr5B 92.000 125 9 1 2489 2612 70804371 70804247 1.170000e-39 174
13 TraesCS5A01G053300 chr4B 86.535 505 60 4 55 552 72974636 72975139 1.660000e-152 549
14 TraesCS5A01G053300 chr4B 85.193 493 56 9 55 531 640110448 640110939 1.020000e-134 490
15 TraesCS5A01G053300 chr4B 80.533 375 60 9 188 552 94939983 94940354 3.120000e-70 276
16 TraesCS5A01G053300 chr4B 94.286 140 8 0 2728 2867 99436907 99437046 6.890000e-52 215
17 TraesCS5A01G053300 chr4B 94.161 137 8 0 2734 2870 63765693 63765829 3.210000e-50 209
18 TraesCS5A01G053300 chr4B 94.495 109 6 0 2947 3055 672482 672590 5.440000e-38 169
19 TraesCS5A01G053300 chr4B 88.172 93 9 2 3017 3109 672591 672681 3.350000e-20 110
20 TraesCS5A01G053300 chr6B 85.827 508 59 8 55 554 182354709 182354207 7.800000e-146 527
21 TraesCS5A01G053300 chr6B 83.673 343 39 7 56 383 594660503 594660163 1.110000e-79 307
22 TraesCS5A01G053300 chr6B 93.793 145 6 3 2737 2880 660665888 660666030 6.890000e-52 215
23 TraesCS5A01G053300 chr2B 85.573 506 67 2 55 554 88247169 88247674 2.800000e-145 525
24 TraesCS5A01G053300 chr1D 85.119 504 66 5 55 552 472335945 472335445 1.020000e-139 507
25 TraesCS5A01G053300 chr1D 93.571 140 9 0 2728 2867 294126271 294126132 3.210000e-50 209
26 TraesCS5A01G053300 chr2D 83.205 518 66 12 57 556 629436105 629435591 3.730000e-124 455
27 TraesCS5A01G053300 chr2D 82.295 305 43 6 55 351 591300015 591300316 1.460000e-63 254
28 TraesCS5A01G053300 chr2D 93.836 146 8 1 2734 2879 619720543 619720687 5.330000e-53 219
29 TraesCS5A01G053300 chr4A 83.074 514 70 6 55 552 532109986 532109474 4.830000e-123 451
30 TraesCS5A01G053300 chr4A 91.724 145 12 0 2737 2881 236198096 236198240 5.370000e-48 202
31 TraesCS5A01G053300 chr1B 84.915 411 43 8 153 555 469979960 469979561 6.380000e-107 398
32 TraesCS5A01G053300 chr1B 83.292 407 54 9 153 552 531695441 531695840 2.330000e-96 363
33 TraesCS5A01G053300 chr1B 85.990 207 22 3 55 255 618408520 618408725 6.890000e-52 215
34 TraesCS5A01G053300 chr1B 93.525 139 9 0 2736 2874 372226510 372226372 1.150000e-49 207
35 TraesCS5A01G053300 chr6D 87.119 295 38 0 55 349 383250428 383250134 5.070000e-88 335
36 TraesCS5A01G053300 chr6D 71.618 1057 230 47 1076 2104 432876381 432877395 3.180000e-55 226
37 TraesCS5A01G053300 chr7B 96.094 128 5 0 2736 2863 126893248 126893121 3.210000e-50 209


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 TraesCS5A01G053300 chr5A 48368868 48372040 3172 False 2721.00 4176 100.00000 1 3173 2 chr5A.!!$F2 3172
1 TraesCS5A01G053300 chr5D 59938418 59941052 2634 False 764.25 2073 92.42200 618 3170 4 chr5D.!!$F1 2552
2 TraesCS5A01G053300 chr5B 70804247 70805951 1704 True 544.00 1500 92.47125 886 2612 4 chr5B.!!$R1 1726
3 TraesCS5A01G053300 chr4B 72974636 72975139 503 False 549.00 549 86.53500 55 552 1 chr4B.!!$F2 497
4 TraesCS5A01G053300 chr6B 182354207 182354709 502 True 527.00 527 85.82700 55 554 1 chr6B.!!$R1 499
5 TraesCS5A01G053300 chr2B 88247169 88247674 505 False 525.00 525 85.57300 55 554 1 chr2B.!!$F1 499
6 TraesCS5A01G053300 chr1D 472335445 472335945 500 True 507.00 507 85.11900 55 552 1 chr1D.!!$R2 497
7 TraesCS5A01G053300 chr2D 629435591 629436105 514 True 455.00 455 83.20500 57 556 1 chr2D.!!$R1 499
8 TraesCS5A01G053300 chr4A 532109474 532109986 512 True 451.00 451 83.07400 55 552 1 chr4A.!!$R1 497
9 TraesCS5A01G053300 chr6D 432876381 432877395 1014 False 226.00 226 71.61800 1076 2104 1 chr6D.!!$F1 1028

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
861 884 0.179134 CGGGTTGCGGTCAAAAACAA 60.179 50.0 0.0 0.0 33.37 2.83 F
1699 1732 0.308993 GAACACACTCTGCTGGTTGC 59.691 55.0 0.0 0.0 43.25 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 1849 0.386113 CTAAGGCTACCGTCCTCTGC 59.614 60.0 0.0 0.0 32.45 4.26 R
2735 2983 1.180029 TTTTCGGACGGAGGGAGTAG 58.820 55.0 0.0 0.0 0.00 2.57 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
19 20 1.560505 GGACAAATGGCCATGTTCCT 58.439 50.000 21.63 0.00 44.76 3.36
20 21 2.733956 GGACAAATGGCCATGTTCCTA 58.266 47.619 21.63 0.00 44.76 2.94
21 22 2.427095 GGACAAATGGCCATGTTCCTAC 59.573 50.000 21.63 7.41 44.76 3.18
22 23 3.356290 GACAAATGGCCATGTTCCTACT 58.644 45.455 21.63 0.00 0.00 2.57
23 24 4.523083 GACAAATGGCCATGTTCCTACTA 58.477 43.478 21.63 0.00 0.00 1.82
24 25 4.526970 ACAAATGGCCATGTTCCTACTAG 58.473 43.478 21.63 1.03 0.00 2.57
25 26 4.018415 ACAAATGGCCATGTTCCTACTAGT 60.018 41.667 21.63 1.76 0.00 2.57
26 27 3.845781 ATGGCCATGTTCCTACTAGTG 57.154 47.619 20.04 0.00 0.00 2.74
27 28 2.546899 TGGCCATGTTCCTACTAGTGT 58.453 47.619 0.00 0.00 0.00 3.55
28 29 2.500098 TGGCCATGTTCCTACTAGTGTC 59.500 50.000 0.00 0.00 0.00 3.67
29 30 2.500098 GGCCATGTTCCTACTAGTGTCA 59.500 50.000 5.39 0.00 0.00 3.58
30 31 3.134804 GGCCATGTTCCTACTAGTGTCAT 59.865 47.826 5.39 0.51 0.00 3.06
31 32 4.344102 GGCCATGTTCCTACTAGTGTCATA 59.656 45.833 5.39 0.00 0.00 2.15
32 33 5.012148 GGCCATGTTCCTACTAGTGTCATAT 59.988 44.000 5.39 0.00 0.00 1.78
33 34 6.464465 GGCCATGTTCCTACTAGTGTCATATT 60.464 42.308 5.39 0.00 0.00 1.28
34 35 6.425114 GCCATGTTCCTACTAGTGTCATATTG 59.575 42.308 5.39 0.00 0.00 1.90
35 36 7.686859 GCCATGTTCCTACTAGTGTCATATTGA 60.687 40.741 5.39 0.00 0.00 2.57
36 37 7.869937 CCATGTTCCTACTAGTGTCATATTGAG 59.130 40.741 5.39 0.00 0.00 3.02
37 38 7.348080 TGTTCCTACTAGTGTCATATTGAGG 57.652 40.000 5.39 0.60 0.00 3.86
38 39 6.183360 TGTTCCTACTAGTGTCATATTGAGGC 60.183 42.308 5.39 0.00 0.00 4.70
39 40 4.519350 TCCTACTAGTGTCATATTGAGGCG 59.481 45.833 5.39 0.00 0.00 5.52
40 41 4.278669 CCTACTAGTGTCATATTGAGGCGT 59.721 45.833 5.39 0.00 0.00 5.68
41 42 4.737855 ACTAGTGTCATATTGAGGCGTT 57.262 40.909 0.00 0.00 0.00 4.84
42 43 5.086104 ACTAGTGTCATATTGAGGCGTTT 57.914 39.130 0.00 0.00 0.00 3.60
43 44 4.870426 ACTAGTGTCATATTGAGGCGTTTG 59.130 41.667 0.00 0.00 0.00 2.93
44 45 3.009723 AGTGTCATATTGAGGCGTTTGG 58.990 45.455 0.00 0.00 0.00 3.28
45 46 3.006940 GTGTCATATTGAGGCGTTTGGA 58.993 45.455 0.00 0.00 0.00 3.53
46 47 3.006940 TGTCATATTGAGGCGTTTGGAC 58.993 45.455 0.00 0.00 0.00 4.02
87 88 2.431683 GCAAGGAGCAGGACCACA 59.568 61.111 0.00 0.00 44.79 4.17
95 96 2.665000 CAGGACCACATGCTCCGT 59.335 61.111 0.00 0.00 0.00 4.69
168 169 3.733960 CCAGCTCCGACGACGACA 61.734 66.667 9.28 0.00 42.66 4.35
209 210 2.610859 ACGGAGGAGGGGCACAAT 60.611 61.111 0.00 0.00 0.00 2.71
220 221 4.083600 GCACAATCGCGCCGACAA 62.084 61.111 0.00 0.00 39.18 3.18
245 253 4.483243 GGGCCGGCGAGGAAATGA 62.483 66.667 22.54 0.00 45.00 2.57
266 274 3.703001 TGATTTCCTTCGCTCTTCCTT 57.297 42.857 0.00 0.00 0.00 3.36
276 284 5.412904 CCTTCGCTCTTCCTTGTTCTATTTT 59.587 40.000 0.00 0.00 0.00 1.82
324 341 2.539338 GCACTGTCCGCCGTTGAAA 61.539 57.895 0.00 0.00 0.00 2.69
369 386 4.080807 TGTCCGGCTAATCCAATGAACTAA 60.081 41.667 0.00 0.00 34.01 2.24
424 441 4.986034 TGAATTGCATGCTTTTGAGACTTG 59.014 37.500 20.33 0.00 0.00 3.16
474 491 0.185901 AATATGAGGCATGCCCGGTT 59.814 50.000 33.14 15.20 39.21 4.44
516 534 2.622011 GCATCCGTGGGCGTTTGAA 61.622 57.895 0.00 0.00 36.15 2.69
519 537 2.119484 ATCCGTGGGCGTTTGAAGGA 62.119 55.000 0.00 0.00 36.15 3.36
560 578 4.837896 CAGTAGATGCTCTAATCACCGA 57.162 45.455 0.00 0.00 29.58 4.69
561 579 5.188327 CAGTAGATGCTCTAATCACCGAA 57.812 43.478 0.00 0.00 29.58 4.30
562 580 5.218885 CAGTAGATGCTCTAATCACCGAAG 58.781 45.833 0.00 0.00 29.58 3.79
563 581 3.104843 AGATGCTCTAATCACCGAAGC 57.895 47.619 0.00 0.00 0.00 3.86
564 582 2.697751 AGATGCTCTAATCACCGAAGCT 59.302 45.455 0.00 0.00 0.00 3.74
565 583 3.891977 AGATGCTCTAATCACCGAAGCTA 59.108 43.478 0.00 0.00 0.00 3.32
566 584 4.342378 AGATGCTCTAATCACCGAAGCTAA 59.658 41.667 0.00 0.00 0.00 3.09
567 585 4.046938 TGCTCTAATCACCGAAGCTAAG 57.953 45.455 0.00 0.00 0.00 2.18
568 586 2.797719 GCTCTAATCACCGAAGCTAAGC 59.202 50.000 0.00 0.00 0.00 3.09
569 587 3.046390 CTCTAATCACCGAAGCTAAGCG 58.954 50.000 0.00 0.00 0.00 4.68
570 588 1.523095 CTAATCACCGAAGCTAAGCGC 59.477 52.381 0.00 0.00 39.57 5.92
571 589 1.421410 AATCACCGAAGCTAAGCGCG 61.421 55.000 0.00 0.00 45.59 6.86
572 590 2.558554 ATCACCGAAGCTAAGCGCGT 62.559 55.000 8.43 0.00 45.59 6.01
573 591 2.506438 ACCGAAGCTAAGCGCGTC 60.506 61.111 8.43 0.00 45.59 5.19
574 592 2.202623 CCGAAGCTAAGCGCGTCT 60.203 61.111 8.43 1.94 43.72 4.18
575 593 2.224885 CCGAAGCTAAGCGCGTCTC 61.225 63.158 8.43 0.00 43.72 3.36
576 594 2.224885 CGAAGCTAAGCGCGTCTCC 61.225 63.158 8.43 0.00 43.72 3.71
577 595 1.878975 GAAGCTAAGCGCGTCTCCC 60.879 63.158 8.43 0.00 42.79 4.30
578 596 2.286127 GAAGCTAAGCGCGTCTCCCT 62.286 60.000 8.43 0.00 42.79 4.20
579 597 2.278923 GCTAAGCGCGTCTCCCTC 60.279 66.667 8.43 0.00 0.00 4.30
580 598 2.024871 CTAAGCGCGTCTCCCTCG 59.975 66.667 8.43 0.00 0.00 4.63
581 599 3.471244 CTAAGCGCGTCTCCCTCGG 62.471 68.421 8.43 0.00 0.00 4.63
584 602 4.736896 GCGCGTCTCCCTCGGTTT 62.737 66.667 8.43 0.00 0.00 3.27
585 603 2.048503 CGCGTCTCCCTCGGTTTT 60.049 61.111 0.00 0.00 0.00 2.43
586 604 2.380410 CGCGTCTCCCTCGGTTTTG 61.380 63.158 0.00 0.00 0.00 2.44
587 605 1.301479 GCGTCTCCCTCGGTTTTGT 60.301 57.895 0.00 0.00 0.00 2.83
588 606 0.883370 GCGTCTCCCTCGGTTTTGTT 60.883 55.000 0.00 0.00 0.00 2.83
589 607 1.589803 CGTCTCCCTCGGTTTTGTTT 58.410 50.000 0.00 0.00 0.00 2.83
590 608 1.263217 CGTCTCCCTCGGTTTTGTTTG 59.737 52.381 0.00 0.00 0.00 2.93
591 609 2.294979 GTCTCCCTCGGTTTTGTTTGT 58.705 47.619 0.00 0.00 0.00 2.83
592 610 2.032924 GTCTCCCTCGGTTTTGTTTGTG 59.967 50.000 0.00 0.00 0.00 3.33
593 611 1.336755 CTCCCTCGGTTTTGTTTGTGG 59.663 52.381 0.00 0.00 0.00 4.17
594 612 1.064611 TCCCTCGGTTTTGTTTGTGGA 60.065 47.619 0.00 0.00 0.00 4.02
595 613 1.751924 CCCTCGGTTTTGTTTGTGGAA 59.248 47.619 0.00 0.00 0.00 3.53
596 614 2.166664 CCCTCGGTTTTGTTTGTGGAAA 59.833 45.455 0.00 0.00 0.00 3.13
597 615 3.368531 CCCTCGGTTTTGTTTGTGGAAAA 60.369 43.478 0.00 0.00 0.00 2.29
598 616 4.438148 CCTCGGTTTTGTTTGTGGAAAAT 58.562 39.130 0.00 0.00 0.00 1.82
599 617 4.269844 CCTCGGTTTTGTTTGTGGAAAATG 59.730 41.667 0.00 0.00 0.00 2.32
600 618 4.184629 TCGGTTTTGTTTGTGGAAAATGG 58.815 39.130 0.00 0.00 0.00 3.16
601 619 3.311048 CGGTTTTGTTTGTGGAAAATGGG 59.689 43.478 0.00 0.00 0.00 4.00
602 620 4.265893 GGTTTTGTTTGTGGAAAATGGGT 58.734 39.130 0.00 0.00 0.00 4.51
603 621 4.334203 GGTTTTGTTTGTGGAAAATGGGTC 59.666 41.667 0.00 0.00 0.00 4.46
604 622 3.828875 TTGTTTGTGGAAAATGGGTCC 57.171 42.857 0.00 0.00 35.55 4.46
605 623 2.043227 TGTTTGTGGAAAATGGGTCCC 58.957 47.619 0.00 0.00 33.89 4.46
606 624 1.346395 GTTTGTGGAAAATGGGTCCCC 59.654 52.381 5.13 0.00 33.89 4.81
635 653 0.250640 AGCAAAGCTGGGTCTCTGTG 60.251 55.000 0.00 0.00 37.57 3.66
644 662 4.411540 AGCTGGGTCTCTGTGAATCATATT 59.588 41.667 0.00 0.00 0.00 1.28
669 687 3.425422 GCATCCGGCAGCCTAAAG 58.575 61.111 10.54 0.00 43.97 1.85
685 703 5.814783 GCCTAAAGCAATCTTGAGTACATG 58.185 41.667 0.00 0.00 42.97 3.21
705 723 9.453572 GTACATGTTCCCATCATCATTACATAT 57.546 33.333 2.30 0.00 0.00 1.78
714 732 8.229811 CCCATCATCATTACATATTGTTACACG 58.770 37.037 0.00 0.00 0.00 4.49
724 742 5.461078 ACATATTGTTACACGATTAGCGGTC 59.539 40.000 0.00 0.00 46.49 4.79
778 801 4.280436 TCATCCACGGTCATAAACTGTT 57.720 40.909 0.00 0.00 45.54 3.16
782 805 5.427036 TCCACGGTCATAAACTGTTTTTC 57.573 39.130 11.48 0.54 45.54 2.29
784 807 5.591067 TCCACGGTCATAAACTGTTTTTCTT 59.409 36.000 11.48 0.00 45.54 2.52
785 808 6.095720 TCCACGGTCATAAACTGTTTTTCTTT 59.904 34.615 11.48 0.00 45.54 2.52
786 809 6.754675 CCACGGTCATAAACTGTTTTTCTTTT 59.245 34.615 11.48 0.00 45.54 2.27
787 810 7.276878 CCACGGTCATAAACTGTTTTTCTTTTT 59.723 33.333 11.48 0.00 45.54 1.94
835 858 2.224314 GCTTCTTCGTCCAGGAAACTTG 59.776 50.000 0.00 0.00 40.21 3.16
836 859 3.728845 CTTCTTCGTCCAGGAAACTTGA 58.271 45.455 0.00 0.00 40.21 3.02
837 860 3.386768 TCTTCGTCCAGGAAACTTGAG 57.613 47.619 0.00 0.00 40.21 3.02
838 861 2.963101 TCTTCGTCCAGGAAACTTGAGA 59.037 45.455 0.00 0.00 40.21 3.27
839 862 3.386726 TCTTCGTCCAGGAAACTTGAGAA 59.613 43.478 0.00 0.00 40.21 2.87
841 864 3.926616 TCGTCCAGGAAACTTGAGAATC 58.073 45.455 0.00 0.00 40.21 2.52
842 865 3.003480 CGTCCAGGAAACTTGAGAATCC 58.997 50.000 0.00 0.00 40.21 3.01
843 866 3.003480 GTCCAGGAAACTTGAGAATCCG 58.997 50.000 0.00 0.00 40.21 4.18
844 867 2.027192 TCCAGGAAACTTGAGAATCCGG 60.027 50.000 0.00 0.00 40.21 5.14
846 869 1.985895 AGGAAACTTGAGAATCCGGGT 59.014 47.619 0.00 0.00 37.44 5.28
847 870 2.375509 AGGAAACTTGAGAATCCGGGTT 59.624 45.455 0.00 0.00 37.44 4.11
848 871 2.488153 GGAAACTTGAGAATCCGGGTTG 59.512 50.000 3.59 0.00 0.00 3.77
849 872 1.534729 AACTTGAGAATCCGGGTTGC 58.465 50.000 3.59 0.00 0.00 4.17
850 873 0.673644 ACTTGAGAATCCGGGTTGCG 60.674 55.000 3.59 0.00 0.00 4.85
851 874 1.369091 CTTGAGAATCCGGGTTGCGG 61.369 60.000 3.59 0.00 0.00 5.69
852 875 2.119484 TTGAGAATCCGGGTTGCGGT 62.119 55.000 3.59 0.00 0.00 5.68
853 876 1.814169 GAGAATCCGGGTTGCGGTC 60.814 63.158 3.59 0.00 0.00 4.79
854 877 2.046700 GAATCCGGGTTGCGGTCA 60.047 61.111 3.59 0.00 0.00 4.02
855 878 1.673009 GAATCCGGGTTGCGGTCAA 60.673 57.895 3.59 0.00 0.00 3.18
856 879 1.228306 AATCCGGGTTGCGGTCAAA 60.228 52.632 0.00 0.00 33.37 2.69
858 881 0.824182 ATCCGGGTTGCGGTCAAAAA 60.824 50.000 0.00 0.00 33.37 1.94
859 882 1.299544 CCGGGTTGCGGTCAAAAAC 60.300 57.895 0.00 0.00 33.37 2.43
861 884 0.179134 CGGGTTGCGGTCAAAAACAA 60.179 50.000 0.00 0.00 33.37 2.83
863 886 2.347731 GGGTTGCGGTCAAAAACAAAA 58.652 42.857 0.00 0.00 33.37 2.44
865 888 3.242576 GGGTTGCGGTCAAAAACAAAATG 60.243 43.478 0.00 0.00 33.37 2.32
866 889 3.372514 GGTTGCGGTCAAAAACAAAATGT 59.627 39.130 0.00 0.00 33.37 2.71
867 890 4.330313 GTTGCGGTCAAAAACAAAATGTG 58.670 39.130 0.00 0.00 33.37 3.21
868 891 2.932614 TGCGGTCAAAAACAAAATGTGG 59.067 40.909 0.00 0.00 0.00 4.17
869 892 2.933260 GCGGTCAAAAACAAAATGTGGT 59.067 40.909 0.00 0.00 0.00 4.16
870 893 3.000825 GCGGTCAAAAACAAAATGTGGTC 59.999 43.478 0.00 0.00 0.00 4.02
871 894 4.177026 CGGTCAAAAACAAAATGTGGTCA 58.823 39.130 0.00 0.00 0.00 4.02
872 895 4.627467 CGGTCAAAAACAAAATGTGGTCAA 59.373 37.500 0.00 0.00 0.00 3.18
873 896 5.120830 CGGTCAAAAACAAAATGTGGTCAAA 59.879 36.000 0.00 0.00 0.00 2.69
874 897 6.347725 CGGTCAAAAACAAAATGTGGTCAAAA 60.348 34.615 0.00 0.00 0.00 2.44
875 898 7.363431 GGTCAAAAACAAAATGTGGTCAAAAA 58.637 30.769 0.00 0.00 0.00 1.94
913 936 0.591170 AGGCATCAACAACCGAAACG 59.409 50.000 0.00 0.00 0.00 3.60
918 941 3.429543 GCATCAACAACCGAAACGTACTA 59.570 43.478 0.00 0.00 0.00 1.82
997 1021 1.359475 GTCCAGCCGTAGATCCGAC 59.641 63.158 0.00 0.00 0.00 4.79
998 1022 1.826921 TCCAGCCGTAGATCCGACC 60.827 63.158 0.00 0.00 0.00 4.79
1098 1122 3.473647 CTCCCTCCGCAGCCATCA 61.474 66.667 0.00 0.00 0.00 3.07
1241 1265 0.602905 AACTACAGCAGGAACCACGC 60.603 55.000 0.00 0.00 0.00 5.34
1461 1491 2.542896 GACGACGACAACAACGGC 59.457 61.111 0.00 0.00 35.25 5.68
1540 1573 1.522580 GATTGCCTCTCGAGCCCAC 60.523 63.158 7.81 0.00 0.00 4.61
1570 1603 3.791928 CTGATCTCCGTCGGACGCG 62.792 68.421 24.26 17.01 40.91 6.01
1699 1732 0.308993 GAACACACTCTGCTGGTTGC 59.691 55.000 0.00 0.00 43.25 4.17
1807 1843 4.425520 CGACTATTGGTCTCTTCAACTCC 58.574 47.826 0.00 0.00 42.44 3.85
1813 1849 0.390472 GTCTCTTCAACTCCTGCGGG 60.390 60.000 4.71 4.71 0.00 6.13
1815 1851 2.032528 CTTCAACTCCTGCGGGCA 59.967 61.111 6.73 0.00 0.00 5.36
1872 1908 3.179830 GCAGAAGCTGAGCATTCAATTG 58.820 45.455 7.39 0.00 37.91 2.32
2048 2209 4.563184 GTCTACGATGATTGGTGACTTCAC 59.437 45.833 0.34 0.34 45.72 3.18
2243 2491 8.487176 CCTTCTTGTTGTAATGTTTTTATGTGC 58.513 33.333 0.00 0.00 0.00 4.57
2255 2503 6.740110 TGTTTTTATGTGCTTACGGTTCAAT 58.260 32.000 0.00 0.00 0.00 2.57
2258 2506 5.950758 TTATGTGCTTACGGTTCAATTGT 57.049 34.783 5.13 0.00 0.00 2.71
2259 2507 3.617540 TGTGCTTACGGTTCAATTGTG 57.382 42.857 5.13 0.00 0.00 3.33
2521 2769 9.706691 TTAAGTTGTTATTTTGTTTGTTGGTCA 57.293 25.926 0.00 0.00 0.00 4.02
2523 2771 6.312672 AGTTGTTATTTTGTTTGTTGGTCAGC 59.687 34.615 0.00 0.00 0.00 4.26
2603 2851 6.671614 TGAATAAAACTATTAGGGCACGTG 57.328 37.500 12.28 12.28 0.00 4.49
2668 2916 8.660295 TTACTAGGTTGGAACAGAGAGAAATA 57.340 34.615 0.00 0.00 42.39 1.40
2675 2923 7.230712 GGTTGGAACAGAGAGAAATAGGAAAAA 59.769 37.037 0.00 0.00 42.39 1.94
2677 2925 7.518188 TGGAACAGAGAGAAATAGGAAAAAGT 58.482 34.615 0.00 0.00 0.00 2.66
2680 2928 8.753497 AACAGAGAGAAATAGGAAAAAGTGTT 57.247 30.769 0.00 0.00 0.00 3.32
2681 2929 8.753497 ACAGAGAGAAATAGGAAAAAGTGTTT 57.247 30.769 0.00 0.00 0.00 2.83
2682 2930 8.624776 ACAGAGAGAAATAGGAAAAAGTGTTTG 58.375 33.333 0.00 0.00 0.00 2.93
2683 2931 8.624776 CAGAGAGAAATAGGAAAAAGTGTTTGT 58.375 33.333 0.00 0.00 0.00 2.83
2684 2932 8.841300 AGAGAGAAATAGGAAAAAGTGTTTGTC 58.159 33.333 0.00 0.00 0.00 3.18
2685 2933 8.753497 AGAGAAATAGGAAAAAGTGTTTGTCT 57.247 30.769 0.00 0.00 0.00 3.41
2686 2934 8.841300 AGAGAAATAGGAAAAAGTGTTTGTCTC 58.159 33.333 0.00 0.00 27.20 3.36
2687 2935 8.753497 AGAAATAGGAAAAAGTGTTTGTCTCT 57.247 30.769 0.00 0.00 0.00 3.10
2688 2936 8.841300 AGAAATAGGAAAAAGTGTTTGTCTCTC 58.159 33.333 0.00 0.00 0.00 3.20
2689 2937 8.753497 AAATAGGAAAAAGTGTTTGTCTCTCT 57.247 30.769 0.00 0.00 0.00 3.10
2690 2938 8.753497 AATAGGAAAAAGTGTTTGTCTCTCTT 57.247 30.769 0.00 0.00 0.00 2.85
2691 2939 9.847224 AATAGGAAAAAGTGTTTGTCTCTCTTA 57.153 29.630 0.00 0.00 0.00 2.10
2692 2940 7.555306 AGGAAAAAGTGTTTGTCTCTCTTAC 57.445 36.000 0.00 0.00 0.00 2.34
2693 2941 7.339482 AGGAAAAAGTGTTTGTCTCTCTTACT 58.661 34.615 0.00 0.00 0.00 2.24
2694 2942 8.483758 AGGAAAAAGTGTTTGTCTCTCTTACTA 58.516 33.333 0.00 0.00 0.00 1.82
2695 2943 9.106070 GGAAAAAGTGTTTGTCTCTCTTACTAA 57.894 33.333 0.00 0.00 0.00 2.24
2697 2945 8.664211 AAAAGTGTTTGTCTCTCTTACTAAGG 57.336 34.615 0.00 0.00 0.00 2.69
2698 2946 7.598759 AAGTGTTTGTCTCTCTTACTAAGGA 57.401 36.000 0.00 0.00 0.00 3.36
2699 2947 7.598759 AGTGTTTGTCTCTCTTACTAAGGAA 57.401 36.000 0.00 0.00 0.00 3.36
2700 2948 7.662897 AGTGTTTGTCTCTCTTACTAAGGAAG 58.337 38.462 0.00 0.00 0.00 3.46
2701 2949 7.506261 AGTGTTTGTCTCTCTTACTAAGGAAGA 59.494 37.037 0.00 0.00 0.00 2.87
2702 2950 7.595875 GTGTTTGTCTCTCTTACTAAGGAAGAC 59.404 40.741 16.76 16.76 39.15 3.01
2703 2951 7.287005 TGTTTGTCTCTCTTACTAAGGAAGACA 59.713 37.037 19.72 19.72 42.86 3.41
2704 2952 7.834881 TTGTCTCTCTTACTAAGGAAGACAA 57.165 36.000 24.86 24.86 46.24 3.18
2705 2953 7.834881 TGTCTCTCTTACTAAGGAAGACAAA 57.165 36.000 20.56 8.35 42.26 2.83
2706 2954 7.887381 TGTCTCTCTTACTAAGGAAGACAAAG 58.113 38.462 20.56 5.35 42.26 2.77
2707 2955 7.724506 TGTCTCTCTTACTAAGGAAGACAAAGA 59.275 37.037 20.56 7.03 42.26 2.52
2708 2956 8.024865 GTCTCTCTTACTAAGGAAGACAAAGAC 58.975 40.741 17.78 11.27 38.84 3.01
2709 2957 7.724506 TCTCTCTTACTAAGGAAGACAAAGACA 59.275 37.037 0.00 0.00 0.00 3.41
2710 2958 8.246430 TCTCTTACTAAGGAAGACAAAGACAA 57.754 34.615 0.00 0.00 0.00 3.18
2711 2959 8.871125 TCTCTTACTAAGGAAGACAAAGACAAT 58.129 33.333 0.00 0.00 0.00 2.71
2712 2960 9.495572 CTCTTACTAAGGAAGACAAAGACAATT 57.504 33.333 0.00 0.00 0.00 2.32
2713 2961 9.490379 TCTTACTAAGGAAGACAAAGACAATTC 57.510 33.333 0.00 0.00 0.00 2.17
2735 2983 9.545105 AATTCTCTCTATTGTCAAGATGTCATC 57.455 33.333 4.52 4.52 0.00 2.92
2750 2998 0.179026 TCATCTACTCCCTCCGTCCG 60.179 60.000 0.00 0.00 0.00 4.79
2752 3000 0.549950 ATCTACTCCCTCCGTCCGAA 59.450 55.000 0.00 0.00 0.00 4.30
2757 3005 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2758 3006 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2759 3007 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2760 3008 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2761 3009 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2762 3010 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2763 3011 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2764 3012 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2765 3013 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2766 3014 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2767 3015 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2768 3016 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2769 3017 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2771 3019 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2772 3020 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
2774 3022 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
2783 3031 9.170734 CTTGTCATCAAAATGGATAGAAAGAGA 57.829 33.333 0.00 0.00 33.42 3.10
2784 3032 9.690913 TTGTCATCAAAATGGATAGAAAGAGAT 57.309 29.630 0.00 0.00 33.42 2.75
2785 3033 9.117183 TGTCATCAAAATGGATAGAAAGAGATG 57.883 33.333 0.00 0.00 33.42 2.90
2786 3034 9.118300 GTCATCAAAATGGATAGAAAGAGATGT 57.882 33.333 0.00 0.00 33.42 3.06
2817 3065 9.717942 AGAACTAAAATACATCTAGATGCATCC 57.282 33.333 28.86 5.58 42.39 3.51
2819 3067 9.717942 AACTAAAATACATCTAGATGCATCCTC 57.282 33.333 28.86 0.00 42.39 3.71
2820 3068 9.099071 ACTAAAATACATCTAGATGCATCCTCT 57.901 33.333 28.86 12.73 42.39 3.69
2821 3069 9.941325 CTAAAATACATCTAGATGCATCCTCTT 57.059 33.333 28.86 16.05 42.39 2.85
2823 3071 9.638176 AAAATACATCTAGATGCATCCTCTTTT 57.362 29.630 28.86 17.04 42.39 2.27
2827 3075 7.393216 ACATCTAGATGCATCCTCTTTTATCC 58.607 38.462 28.86 0.00 42.39 2.59
2828 3076 7.016957 ACATCTAGATGCATCCTCTTTTATCCA 59.983 37.037 28.86 0.00 42.39 3.41
2829 3077 7.565190 TCTAGATGCATCCTCTTTTATCCAT 57.435 36.000 23.06 2.35 0.00 3.41
2830 3078 7.982252 TCTAGATGCATCCTCTTTTATCCATT 58.018 34.615 23.06 1.91 0.00 3.16
2833 3081 7.723324 AGATGCATCCTCTTTTATCCATTTTG 58.277 34.615 23.06 0.00 0.00 2.44
2838 3086 7.650903 GCATCCTCTTTTATCCATTTTGATGAC 59.349 37.037 0.00 0.00 0.00 3.06
2839 3087 8.689061 CATCCTCTTTTATCCATTTTGATGACA 58.311 33.333 0.00 0.00 0.00 3.58
2853 3482 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2854 3483 3.193903 TGATGACAAGTATTTCCGGACGA 59.806 43.478 1.83 0.00 0.00 4.20
2860 3489 2.181975 AGTATTTCCGGACGAAGGGAA 58.818 47.619 1.83 0.00 40.44 3.97
2863 3492 4.591924 AGTATTTCCGGACGAAGGGAATAT 59.408 41.667 1.83 8.25 40.32 1.28
2864 3493 5.776716 AGTATTTCCGGACGAAGGGAATATA 59.223 40.000 1.83 7.60 40.32 0.86
2865 3494 5.757099 ATTTCCGGACGAAGGGAATATAT 57.243 39.130 1.83 0.00 41.67 0.86
2925 3554 8.619146 ATCTTATGAACATGCAAACATTTACG 57.381 30.769 0.00 0.00 32.87 3.18
2926 3555 7.589395 TCTTATGAACATGCAAACATTTACGT 58.411 30.769 0.00 0.00 32.87 3.57
2927 3556 8.079203 TCTTATGAACATGCAAACATTTACGTT 58.921 29.630 0.00 0.00 32.87 3.99
3065 3694 0.179124 TTGTTGGGCAACGTTTGAGC 60.179 50.000 0.00 0.00 43.94 4.26
3077 3706 4.602340 ACGTTTGAGCGGGAATATATCT 57.398 40.909 0.00 0.00 35.98 1.98
3078 3707 5.717078 ACGTTTGAGCGGGAATATATCTA 57.283 39.130 0.00 0.00 35.98 1.98
3079 3708 5.467705 ACGTTTGAGCGGGAATATATCTAC 58.532 41.667 0.00 0.00 35.98 2.59
3080 3709 5.010314 ACGTTTGAGCGGGAATATATCTACA 59.990 40.000 0.00 0.00 35.98 2.74
3082 3711 6.590292 CGTTTGAGCGGGAATATATCTACATT 59.410 38.462 0.00 0.00 0.00 2.71
3083 3712 7.117812 CGTTTGAGCGGGAATATATCTACATTT 59.882 37.037 0.00 0.00 0.00 2.32
3160 3789 8.822652 TCAATGCACACTATATTATGAGACAG 57.177 34.615 0.00 0.00 0.00 3.51
3170 3799 9.653516 ACTATATTATGAGACAGAGGGGATATG 57.346 37.037 0.00 0.00 0.00 1.78
3171 3800 9.874195 CTATATTATGAGACAGAGGGGATATGA 57.126 37.037 0.00 0.00 0.00 2.15
3172 3801 8.780616 ATATTATGAGACAGAGGGGATATGAG 57.219 38.462 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.560505 AGGAACATGGCCATTTGTCC 58.439 50.000 23.34 23.34 0.00 4.02
1 2 3.356290 AGTAGGAACATGGCCATTTGTC 58.644 45.455 17.92 13.25 0.00 3.18
2 3 3.456380 AGTAGGAACATGGCCATTTGT 57.544 42.857 17.92 11.45 0.00 2.83
3 4 4.336433 CACTAGTAGGAACATGGCCATTTG 59.664 45.833 17.92 10.65 0.00 2.32
4 5 4.018415 ACACTAGTAGGAACATGGCCATTT 60.018 41.667 17.92 13.92 0.00 2.32
5 6 3.523564 ACACTAGTAGGAACATGGCCATT 59.476 43.478 17.92 2.49 0.00 3.16
6 7 3.115390 ACACTAGTAGGAACATGGCCAT 58.885 45.455 14.09 14.09 0.00 4.40
7 8 2.500098 GACACTAGTAGGAACATGGCCA 59.500 50.000 8.56 8.56 0.00 5.36
8 9 2.500098 TGACACTAGTAGGAACATGGCC 59.500 50.000 0.00 0.00 0.00 5.36
9 10 3.887621 TGACACTAGTAGGAACATGGC 57.112 47.619 1.45 0.00 0.00 4.40
10 11 7.726216 TCAATATGACACTAGTAGGAACATGG 58.274 38.462 1.45 0.41 0.00 3.66
11 12 7.869937 CCTCAATATGACACTAGTAGGAACATG 59.130 40.741 1.45 0.00 0.00 3.21
12 13 7.472100 GCCTCAATATGACACTAGTAGGAACAT 60.472 40.741 6.71 6.35 0.00 2.71
13 14 6.183360 GCCTCAATATGACACTAGTAGGAACA 60.183 42.308 6.71 0.00 0.00 3.18
14 15 6.217294 GCCTCAATATGACACTAGTAGGAAC 58.783 44.000 6.71 0.00 0.00 3.62
15 16 5.009710 CGCCTCAATATGACACTAGTAGGAA 59.990 44.000 6.71 0.00 0.00 3.36
16 17 4.519350 CGCCTCAATATGACACTAGTAGGA 59.481 45.833 6.71 0.00 0.00 2.94
17 18 4.278669 ACGCCTCAATATGACACTAGTAGG 59.721 45.833 1.45 0.00 0.00 3.18
18 19 5.440234 ACGCCTCAATATGACACTAGTAG 57.560 43.478 0.00 0.00 0.00 2.57
19 20 5.847111 AACGCCTCAATATGACACTAGTA 57.153 39.130 0.00 0.00 0.00 1.82
20 21 4.737855 AACGCCTCAATATGACACTAGT 57.262 40.909 0.00 0.00 0.00 2.57
21 22 4.271049 CCAAACGCCTCAATATGACACTAG 59.729 45.833 0.00 0.00 0.00 2.57
22 23 4.081365 TCCAAACGCCTCAATATGACACTA 60.081 41.667 0.00 0.00 0.00 2.74
23 24 3.009723 CCAAACGCCTCAATATGACACT 58.990 45.455 0.00 0.00 0.00 3.55
24 25 3.006940 TCCAAACGCCTCAATATGACAC 58.993 45.455 0.00 0.00 0.00 3.67
25 26 3.006940 GTCCAAACGCCTCAATATGACA 58.993 45.455 0.00 0.00 0.00 3.58
26 27 2.030457 CGTCCAAACGCCTCAATATGAC 59.970 50.000 0.00 0.00 42.82 3.06
27 28 2.276201 CGTCCAAACGCCTCAATATGA 58.724 47.619 0.00 0.00 42.82 2.15
28 29 2.737467 CGTCCAAACGCCTCAATATG 57.263 50.000 0.00 0.00 42.82 1.78
39 40 1.838568 GCCTTGGTCGACGTCCAAAC 61.839 60.000 23.41 16.15 43.16 2.93
40 41 1.595929 GCCTTGGTCGACGTCCAAA 60.596 57.895 23.41 10.62 43.16 3.28
41 42 2.029964 GCCTTGGTCGACGTCCAA 59.970 61.111 22.24 22.24 41.84 3.53
42 43 4.351938 CGCCTTGGTCGACGTCCA 62.352 66.667 10.58 9.85 0.00 4.02
70 71 1.001641 ATGTGGTCCTGCTCCTTGC 60.002 57.895 0.00 0.00 43.25 4.01
85 86 1.219124 CACAGCCTACGGAGCATGT 59.781 57.895 0.00 0.00 0.00 3.21
87 88 1.680522 CCTCACAGCCTACGGAGCAT 61.681 60.000 0.00 0.00 0.00 3.79
95 96 0.618680 ACCTCATGCCTCACAGCCTA 60.619 55.000 0.00 0.00 0.00 3.93
121 122 1.332686 CGTCCGTCATATCCAAGTCGA 59.667 52.381 0.00 0.00 0.00 4.20
209 210 4.287781 TTCTGGTTGTCGGCGCGA 62.288 61.111 12.10 0.00 0.00 5.87
245 253 3.922171 AGGAAGAGCGAAGGAAATCAT 57.078 42.857 0.00 0.00 0.00 2.45
255 263 8.561738 AATAAAAATAGAACAAGGAAGAGCGA 57.438 30.769 0.00 0.00 0.00 4.93
293 310 4.216257 GCGGACAGTGCAAATCCATAATAT 59.784 41.667 11.56 0.00 32.35 1.28
296 313 1.742831 GCGGACAGTGCAAATCCATAA 59.257 47.619 11.56 0.00 32.35 1.90
324 341 7.161773 ACAAAAGAAACATGATTCATCGGAT 57.838 32.000 16.93 0.00 0.00 4.18
412 429 4.631813 CCCTCGTATTCCAAGTCTCAAAAG 59.368 45.833 0.00 0.00 0.00 2.27
421 438 0.870307 CGCGTCCCTCGTATTCCAAG 60.870 60.000 0.00 0.00 42.13 3.61
424 441 1.008767 CTCGCGTCCCTCGTATTCC 60.009 63.158 5.77 0.00 42.13 3.01
500 518 1.674322 CCTTCAAACGCCCACGGAT 60.674 57.895 0.00 0.00 46.04 4.18
505 523 1.376683 CCGATCCTTCAAACGCCCA 60.377 57.895 0.00 0.00 0.00 5.36
516 534 2.810400 CGTATTGGGCAAATCCGATCCT 60.810 50.000 0.00 0.00 33.21 3.24
519 537 1.604604 CCGTATTGGGCAAATCCGAT 58.395 50.000 0.61 0.00 35.24 4.18
556 574 2.506438 GACGCGCTTAGCTTCGGT 60.506 61.111 5.73 3.92 45.59 4.69
559 577 1.878975 GGGAGACGCGCTTAGCTTC 60.879 63.158 5.73 0.00 45.59 3.86
560 578 2.184579 GGGAGACGCGCTTAGCTT 59.815 61.111 5.73 0.00 45.59 3.74
561 579 2.756283 AGGGAGACGCGCTTAGCT 60.756 61.111 5.73 0.00 45.59 3.32
562 580 2.278923 GAGGGAGACGCGCTTAGC 60.279 66.667 5.73 0.00 40.28 3.09
563 581 2.024871 CGAGGGAGACGCGCTTAG 59.975 66.667 5.73 0.00 40.28 2.18
564 582 3.515286 CCGAGGGAGACGCGCTTA 61.515 66.667 5.73 0.00 41.29 3.09
567 585 4.736896 AAACCGAGGGAGACGCGC 62.737 66.667 5.73 0.00 41.29 6.86
568 586 2.048503 AAAACCGAGGGAGACGCG 60.049 61.111 3.53 3.53 42.34 6.01
569 587 0.883370 AACAAAACCGAGGGAGACGC 60.883 55.000 0.00 0.00 0.00 5.19
570 588 1.263217 CAAACAAAACCGAGGGAGACG 59.737 52.381 0.00 0.00 0.00 4.18
571 589 2.032924 CACAAACAAAACCGAGGGAGAC 59.967 50.000 0.00 0.00 0.00 3.36
572 590 2.294074 CACAAACAAAACCGAGGGAGA 58.706 47.619 0.00 0.00 0.00 3.71
573 591 1.336755 CCACAAACAAAACCGAGGGAG 59.663 52.381 0.00 0.00 0.00 4.30
574 592 1.064611 TCCACAAACAAAACCGAGGGA 60.065 47.619 0.00 0.00 0.00 4.20
575 593 1.394618 TCCACAAACAAAACCGAGGG 58.605 50.000 0.00 0.00 0.00 4.30
576 594 3.512033 TTTCCACAAACAAAACCGAGG 57.488 42.857 0.00 0.00 0.00 4.63
577 595 4.269844 CCATTTTCCACAAACAAAACCGAG 59.730 41.667 0.00 0.00 0.00 4.63
578 596 4.184629 CCATTTTCCACAAACAAAACCGA 58.815 39.130 0.00 0.00 0.00 4.69
579 597 3.311048 CCCATTTTCCACAAACAAAACCG 59.689 43.478 0.00 0.00 0.00 4.44
580 598 4.265893 ACCCATTTTCCACAAACAAAACC 58.734 39.130 0.00 0.00 0.00 3.27
581 599 4.334203 GGACCCATTTTCCACAAACAAAAC 59.666 41.667 0.00 0.00 32.82 2.43
582 600 4.518249 GGACCCATTTTCCACAAACAAAA 58.482 39.130 0.00 0.00 32.82 2.44
583 601 3.118223 GGGACCCATTTTCCACAAACAAA 60.118 43.478 5.33 0.00 34.45 2.83
584 602 2.436173 GGGACCCATTTTCCACAAACAA 59.564 45.455 5.33 0.00 34.45 2.83
585 603 2.043227 GGGACCCATTTTCCACAAACA 58.957 47.619 5.33 0.00 34.45 2.83
586 604 2.831685 GGGACCCATTTTCCACAAAC 57.168 50.000 5.33 0.00 34.45 2.93
601 619 3.367395 GCTTTGCTGACTTATTTGGGGAC 60.367 47.826 0.00 0.00 0.00 4.46
602 620 2.825532 GCTTTGCTGACTTATTTGGGGA 59.174 45.455 0.00 0.00 0.00 4.81
603 621 2.827921 AGCTTTGCTGACTTATTTGGGG 59.172 45.455 0.00 0.00 37.57 4.96
616 634 0.250640 CACAGAGACCCAGCTTTGCT 60.251 55.000 0.00 0.00 40.77 3.91
635 653 5.352569 CCGGATGCTACTTGGAATATGATTC 59.647 44.000 0.00 0.00 0.00 2.52
644 662 1.522092 CTGCCGGATGCTACTTGGA 59.478 57.895 5.05 0.00 42.00 3.53
662 680 5.355350 ACATGTACTCAAGATTGCTTTAGGC 59.645 40.000 0.00 0.00 42.22 3.93
664 682 7.414540 GGGAACATGTACTCAAGATTGCTTTAG 60.415 40.741 0.00 0.00 32.77 1.85
665 683 6.374333 GGGAACATGTACTCAAGATTGCTTTA 59.626 38.462 0.00 0.00 30.14 1.85
667 685 4.702131 GGGAACATGTACTCAAGATTGCTT 59.298 41.667 0.00 0.00 33.74 3.91
668 686 4.263462 TGGGAACATGTACTCAAGATTGCT 60.263 41.667 0.00 0.00 33.40 3.91
669 687 4.009675 TGGGAACATGTACTCAAGATTGC 58.990 43.478 0.00 0.00 33.40 3.56
705 723 3.057386 TGAGACCGCTAATCGTGTAACAA 60.057 43.478 0.00 0.00 35.74 2.83
714 732 4.192317 AGGTTCATTTGAGACCGCTAATC 58.808 43.478 6.39 0.00 0.00 1.75
724 742 4.568152 ACAAAACCGAGGTTCATTTGAG 57.432 40.909 19.09 5.00 37.35 3.02
785 808 6.095720 AGTTTATGACCGTTGGTTCTCAAAAA 59.904 34.615 0.00 0.00 35.25 1.94
786 809 5.591067 AGTTTATGACCGTTGGTTCTCAAAA 59.409 36.000 0.00 0.00 35.25 2.44
787 810 5.008217 CAGTTTATGACCGTTGGTTCTCAAA 59.992 40.000 0.00 0.00 35.25 2.69
788 811 4.513692 CAGTTTATGACCGTTGGTTCTCAA 59.486 41.667 0.00 0.00 35.25 3.02
789 812 4.062293 CAGTTTATGACCGTTGGTTCTCA 58.938 43.478 0.00 0.00 35.25 3.27
790 813 4.062991 ACAGTTTATGACCGTTGGTTCTC 58.937 43.478 0.00 0.00 35.25 2.87
842 865 0.179134 TTGTTTTTGACCGCAACCCG 60.179 50.000 0.00 0.00 32.79 5.28
843 866 2.011540 TTTGTTTTTGACCGCAACCC 57.988 45.000 0.00 0.00 32.79 4.11
844 867 3.372514 ACATTTTGTTTTTGACCGCAACC 59.627 39.130 0.00 0.00 32.79 3.77
846 869 3.372206 CCACATTTTGTTTTTGACCGCAA 59.628 39.130 0.00 0.00 0.00 4.85
847 870 2.932614 CCACATTTTGTTTTTGACCGCA 59.067 40.909 0.00 0.00 0.00 5.69
848 871 2.933260 ACCACATTTTGTTTTTGACCGC 59.067 40.909 0.00 0.00 0.00 5.68
849 872 4.177026 TGACCACATTTTGTTTTTGACCG 58.823 39.130 0.00 0.00 0.00 4.79
850 873 6.487689 TTTGACCACATTTTGTTTTTGACC 57.512 33.333 0.00 0.00 0.00 4.02
884 907 2.995283 TGTTGATGCCTGGATTCTCAG 58.005 47.619 0.00 0.00 34.70 3.35
913 936 8.178313 CCGTTAGAAAAGGTGTAGTACTAGTAC 58.822 40.741 23.03 23.03 36.35 2.73
918 941 5.184671 CCTCCGTTAGAAAAGGTGTAGTACT 59.815 44.000 0.00 0.00 0.00 2.73
1098 1122 2.439104 GGAGAGGCGAGGGAGCAAT 61.439 63.158 0.00 0.00 39.27 3.56
1241 1265 3.771160 CGAGGACGGGGGTGAAGG 61.771 72.222 0.00 0.00 35.72 3.46
1315 1345 1.801913 CGAAGTTCCACTCCTCGCG 60.802 63.158 0.00 0.00 0.00 5.87
1453 1483 3.317449 GGTACCTCTTGCCGTTGTT 57.683 52.632 4.06 0.00 0.00 2.83
1461 1491 2.813908 GCGTGCCGGTACCTCTTG 60.814 66.667 17.62 3.56 0.00 3.02
1540 1573 1.407989 GGAGATCAGGGCCACTTTGAG 60.408 57.143 6.18 0.00 0.00 3.02
1699 1732 1.811266 CGAGGATGACGCACCCAAG 60.811 63.158 0.00 0.00 0.00 3.61
1813 1849 0.386113 CTAAGGCTACCGTCCTCTGC 59.614 60.000 0.00 0.00 32.45 4.26
1815 1851 1.565288 AGTCTAAGGCTACCGTCCTCT 59.435 52.381 0.00 0.00 32.45 3.69
1872 1908 2.797177 AGCTCAATTTCCTCTCCCAC 57.203 50.000 0.00 0.00 0.00 4.61
2048 2209 1.519455 GTCGGCTCAATCTGGACCG 60.519 63.158 0.00 0.00 45.15 4.79
2050 2211 2.167861 GCGTCGGCTCAATCTGGAC 61.168 63.158 0.00 0.00 35.83 4.02
2184 2432 8.160521 TGTAACCGAAATCATTCTCAGAAAAA 57.839 30.769 0.00 0.00 33.17 1.94
2188 2436 7.606073 TCAAATGTAACCGAAATCATTCTCAGA 59.394 33.333 0.00 0.00 33.17 3.27
2195 2443 8.519799 AAGGTATCAAATGTAACCGAAATCAT 57.480 30.769 0.00 0.00 37.09 2.45
2232 2480 7.168469 ACAATTGAACCGTAAGCACATAAAAAC 59.832 33.333 13.59 0.00 0.00 2.43
2502 2750 6.039616 TCAGCTGACCAACAAACAAAATAAC 58.960 36.000 13.74 0.00 0.00 1.89
2521 2769 6.228995 CAAGTACATCACCATATGATCAGCT 58.771 40.000 3.65 0.00 45.52 4.24
2523 2771 6.228995 AGCAAGTACATCACCATATGATCAG 58.771 40.000 3.65 0.00 45.52 2.90
2545 2793 8.561738 TTTAGTATAGCCCAATAATAGCAAGC 57.438 34.615 0.00 0.00 0.00 4.01
2645 2893 6.155393 CCTATTTCTCTCTGTTCCAACCTAGT 59.845 42.308 0.00 0.00 0.00 2.57
2668 2916 7.339482 AGTAAGAGAGACAAACACTTTTTCCT 58.661 34.615 0.00 0.00 0.00 3.36
2675 2923 7.506261 TCTTCCTTAGTAAGAGAGACAAACACT 59.494 37.037 11.66 0.00 0.00 3.55
2677 2925 7.287005 TGTCTTCCTTAGTAAGAGAGACAAACA 59.713 37.037 27.83 16.03 42.13 2.83
2680 2928 7.834881 TTGTCTTCCTTAGTAAGAGAGACAA 57.165 36.000 31.36 31.36 46.11 3.18
2681 2929 7.724506 TCTTTGTCTTCCTTAGTAAGAGAGACA 59.275 37.037 27.05 27.05 42.73 3.41
2682 2930 8.024865 GTCTTTGTCTTCCTTAGTAAGAGAGAC 58.975 40.741 24.25 24.25 39.04 3.36
2683 2931 7.724506 TGTCTTTGTCTTCCTTAGTAAGAGAGA 59.275 37.037 11.66 10.49 33.75 3.10
2684 2932 7.887381 TGTCTTTGTCTTCCTTAGTAAGAGAG 58.113 38.462 11.66 8.47 33.75 3.20
2685 2933 7.834881 TGTCTTTGTCTTCCTTAGTAAGAGA 57.165 36.000 11.66 4.49 33.75 3.10
2686 2934 9.495572 AATTGTCTTTGTCTTCCTTAGTAAGAG 57.504 33.333 11.66 2.08 33.75 2.85
2687 2935 9.490379 GAATTGTCTTTGTCTTCCTTAGTAAGA 57.510 33.333 11.66 0.00 0.00 2.10
2688 2936 9.495572 AGAATTGTCTTTGTCTTCCTTAGTAAG 57.504 33.333 2.65 2.65 0.00 2.34
2689 2937 9.490379 GAGAATTGTCTTTGTCTTCCTTAGTAA 57.510 33.333 0.00 0.00 32.80 2.24
2690 2938 8.871125 AGAGAATTGTCTTTGTCTTCCTTAGTA 58.129 33.333 0.00 0.00 32.80 1.82
2691 2939 7.740805 AGAGAATTGTCTTTGTCTTCCTTAGT 58.259 34.615 0.00 0.00 32.80 2.24
2692 2940 8.093927 AGAGAGAATTGTCTTTGTCTTCCTTAG 58.906 37.037 6.56 0.00 32.80 2.18
2693 2941 7.967908 AGAGAGAATTGTCTTTGTCTTCCTTA 58.032 34.615 6.56 0.00 32.80 2.69
2694 2942 6.836242 AGAGAGAATTGTCTTTGTCTTCCTT 58.164 36.000 6.56 0.00 32.80 3.36
2695 2943 6.432403 AGAGAGAATTGTCTTTGTCTTCCT 57.568 37.500 6.56 0.00 32.80 3.36
2696 2944 8.663911 CAATAGAGAGAATTGTCTTTGTCTTCC 58.336 37.037 6.56 0.00 32.80 3.46
2697 2945 9.213799 ACAATAGAGAGAATTGTCTTTGTCTTC 57.786 33.333 12.86 0.00 42.45 2.87
2708 2956 8.713737 TGACATCTTGACAATAGAGAGAATTG 57.286 34.615 0.00 0.00 39.68 2.32
2709 2957 9.545105 GATGACATCTTGACAATAGAGAGAATT 57.455 33.333 8.25 0.00 0.00 2.17
2710 2958 8.926374 AGATGACATCTTGACAATAGAGAGAAT 58.074 33.333 12.37 0.00 35.76 2.40
2711 2959 8.303780 AGATGACATCTTGACAATAGAGAGAA 57.696 34.615 12.37 0.00 35.76 2.87
2712 2960 7.894753 AGATGACATCTTGACAATAGAGAGA 57.105 36.000 12.37 0.00 35.76 3.10
2713 2961 8.849168 AGTAGATGACATCTTGACAATAGAGAG 58.151 37.037 22.63 0.00 40.76 3.20
2735 2983 1.180029 TTTTCGGACGGAGGGAGTAG 58.820 55.000 0.00 0.00 0.00 2.57
2757 3005 9.170734 TCTCTTTCTATCCATTTTGATGACAAG 57.829 33.333 0.00 0.00 37.32 3.16
2758 3006 9.690913 ATCTCTTTCTATCCATTTTGATGACAA 57.309 29.630 0.00 0.00 0.00 3.18
2759 3007 9.117183 CATCTCTTTCTATCCATTTTGATGACA 57.883 33.333 0.00 0.00 32.05 3.58
2760 3008 9.118300 ACATCTCTTTCTATCCATTTTGATGAC 57.882 33.333 0.00 0.00 33.85 3.06
2792 3040 9.717942 AGGATGCATCTAGATGTATTTTAGTTC 57.282 33.333 29.66 18.97 42.77 3.01
2793 3041 9.717942 GAGGATGCATCTAGATGTATTTTAGTT 57.282 33.333 29.66 12.78 42.77 2.24
2794 3042 9.099071 AGAGGATGCATCTAGATGTATTTTAGT 57.901 33.333 29.66 16.49 42.77 2.24
2795 3043 9.941325 AAGAGGATGCATCTAGATGTATTTTAG 57.059 33.333 29.66 7.72 42.77 1.85
2797 3045 9.638176 AAAAGAGGATGCATCTAGATGTATTTT 57.362 29.630 29.66 23.53 42.77 1.82
2801 3049 8.535335 GGATAAAAGAGGATGCATCTAGATGTA 58.465 37.037 28.92 26.27 40.80 2.29
2803 3051 7.392418 TGGATAAAAGAGGATGCATCTAGATG 58.608 38.462 25.64 25.64 41.60 2.90
2804 3052 7.565190 TGGATAAAAGAGGATGCATCTAGAT 57.435 36.000 25.28 9.93 0.00 1.98
2806 3054 8.632906 AAATGGATAAAAGAGGATGCATCTAG 57.367 34.615 25.28 0.00 33.50 2.43
2807 3055 8.853126 CAAAATGGATAAAAGAGGATGCATCTA 58.147 33.333 25.28 9.84 33.50 1.98
2808 3056 7.562454 TCAAAATGGATAAAAGAGGATGCATCT 59.438 33.333 25.28 12.03 33.50 2.90
2811 3059 7.342541 TCATCAAAATGGATAAAAGAGGATGCA 59.657 33.333 0.00 0.00 33.42 3.96
2812 3060 7.650903 GTCATCAAAATGGATAAAAGAGGATGC 59.349 37.037 0.00 0.00 33.42 3.91
2813 3061 8.689061 TGTCATCAAAATGGATAAAAGAGGATG 58.311 33.333 0.00 0.00 33.42 3.51
2814 3062 8.827832 TGTCATCAAAATGGATAAAAGAGGAT 57.172 30.769 0.00 0.00 33.42 3.24
2815 3063 8.648698 TTGTCATCAAAATGGATAAAAGAGGA 57.351 30.769 0.00 0.00 33.42 3.71
2816 3064 8.526147 ACTTGTCATCAAAATGGATAAAAGAGG 58.474 33.333 0.00 0.00 33.42 3.69
2823 3071 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
2824 3072 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
2825 3073 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
2827 3075 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2828 3076 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2829 3077 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2830 3078 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2833 3081 3.777478 TCGTCCGGAAATACTTGTCATC 58.223 45.455 5.23 0.00 0.00 2.92
2838 3086 2.093869 TCCCTTCGTCCGGAAATACTTG 60.094 50.000 5.23 0.00 33.34 3.16
2839 3087 2.181975 TCCCTTCGTCCGGAAATACTT 58.818 47.619 5.23 0.00 33.34 2.24
2844 3092 4.345837 ACATATATTCCCTTCGTCCGGAAA 59.654 41.667 5.23 0.00 41.39 3.13
2845 3093 3.899360 ACATATATTCCCTTCGTCCGGAA 59.101 43.478 5.23 0.00 42.24 4.30
2847 3095 3.955650 ACATATATTCCCTTCGTCCGG 57.044 47.619 0.00 0.00 0.00 5.14
2971 3600 5.247862 TGCATGTCATTTTGCTAGAGAAGA 58.752 37.500 0.00 0.00 39.60 2.87
2979 3608 2.739913 GTGCAATGCATGTCATTTTGCT 59.260 40.909 12.38 0.00 42.48 3.91
3009 3638 2.622064 AGGATGGTTGATAAGACGGC 57.378 50.000 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.