Multiple sequence alignment - TraesCS1A01G005400

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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 TraesCS1A01G005400 chr1A 100.000 3280 0 0 1 3280 3116199 3119478 0.000000e+00 6058.0
1 TraesCS1A01G005400 chr1A 87.709 358 24 9 1292 1629 497899435 497899078 1.830000e-107 399.0
2 TraesCS1A01G005400 chr1A 94.161 137 7 1 1099 1235 398810905 398810770 1.190000e-49 207.0
3 TraesCS1A01G005400 chr1D 86.803 2796 187 81 566 3280 509307 512001 0.000000e+00 2952.0
4 TraesCS1A01G005400 chr1D 83.455 550 49 19 44 558 508657 509199 1.070000e-129 473.0
5 TraesCS1A01G005400 chr1D 85.714 91 12 1 3112 3202 455092859 455092948 9.690000e-16 95.3
6 TraesCS1A01G005400 chr1B 84.766 2862 209 80 566 3280 4219453 4222234 0.000000e+00 2660.0
7 TraesCS1A01G005400 chr1B 80.556 144 20 6 30 168 4218623 4218763 1.610000e-18 104.0
8 TraesCS1A01G005400 chr4A 86.538 676 54 20 982 1629 130525325 130525991 0.000000e+00 710.0
9 TraesCS1A01G005400 chr4A 79.785 465 45 19 1960 2399 731823272 731822832 3.200000e-75 292.0
10 TraesCS1A01G005400 chr2A 86.364 682 50 19 982 1629 174025401 174024729 0.000000e+00 704.0
11 TraesCS1A01G005400 chr6A 85.630 682 55 19 982 1629 531810051 531810723 0.000000e+00 676.0
12 TraesCS1A01G005400 chr3B 87.978 366 33 4 2321 2675 782533261 782532896 3.910000e-114 422.0
13 TraesCS1A01G005400 chr3B 80.000 465 44 20 1960 2399 44082694 44083134 6.880000e-77 298.0
14 TraesCS1A01G005400 chr3B 79.657 467 42 25 1960 2399 43972196 43972636 1.490000e-73 287.0
15 TraesCS1A01G005400 chr3B 79.526 464 44 25 1961 2399 82507955 82507518 1.930000e-72 283.0
16 TraesCS1A01G005400 chr3B 97.436 39 1 0 2798 2836 782532194 782532156 2.110000e-07 67.6
17 TraesCS1A01G005400 chr3B 100.000 29 0 0 655 683 8802223 8802195 2.000000e-03 54.7
18 TraesCS1A01G005400 chr7A 83.459 399 38 16 984 1363 703520838 703520449 2.420000e-91 346.0
19 TraesCS1A01G005400 chr7A 84.444 315 26 12 982 1281 268850306 268850000 4.140000e-74 289.0
20 TraesCS1A01G005400 chr7B 80.000 465 44 18 1960 2399 600816223 600815783 6.880000e-77 298.0
21 TraesCS1A01G005400 chr7B 100.000 39 0 0 2798 2836 637932987 637932949 4.540000e-09 73.1
22 TraesCS1A01G005400 chr6B 80.000 465 44 23 1960 2399 387961427 387960987 6.880000e-77 298.0
23 TraesCS1A01G005400 chr6B 79.570 465 46 20 1960 2399 29303411 29303851 1.490000e-73 287.0
24 TraesCS1A01G005400 chr6B 79.095 464 48 23 1961 2399 220146311 220145872 1.160000e-69 274.0
25 TraesCS1A01G005400 chr2B 80.000 465 44 21 1960 2399 692992108 692992548 6.880000e-77 298.0
26 TraesCS1A01G005400 chr2B 79.355 465 47 23 1960 2399 765321886 765321446 6.930000e-72 281.0
27 TraesCS1A01G005400 chr5B 79.785 465 45 23 1960 2399 58980002 58979562 3.200000e-75 292.0
28 TraesCS1A01G005400 chr5B 79.654 462 46 19 1960 2396 27043566 27043128 4.140000e-74 289.0
29 TraesCS1A01G005400 chr4B 87.379 206 18 3 2321 2518 277740523 277740318 2.550000e-56 230.0
30 TraesCS1A01G005400 chr4B 100.000 39 0 0 2798 2836 277739835 277739797 4.540000e-09 73.1
31 TraesCS1A01G005400 chr2D 86.893 206 19 3 2321 2518 525670292 525670087 1.180000e-54 224.0
32 TraesCS1A01G005400 chr2D 87.000 200 18 3 2321 2512 60275290 60275489 5.510000e-53 219.0
33 TraesCS1A01G005400 chr2D 100.000 39 0 0 2798 2836 525669603 525669565 4.540000e-09 73.1
34 TraesCS1A01G005400 chr5A 94.891 137 6 1 1099 1235 664782985 664783120 2.560000e-51 213.0
35 TraesCS1A01G005400 chr5D 86.500 200 18 4 2321 2512 438252993 438253191 9.220000e-51 211.0
36 TraesCS1A01G005400 chr5D 100.000 39 0 0 2798 2836 438253681 438253719 4.540000e-09 73.1
37 TraesCS1A01G005400 chr7D 85.366 123 10 3 2321 2435 43935295 43935173 1.600000e-23 121.0
38 TraesCS1A01G005400 chr3D 85.366 123 10 3 2321 2435 97256707 97256585 1.600000e-23 121.0
39 TraesCS1A01G005400 chr4D 80.000 130 14 10 2805 2934 122011720 122011603 5.830000e-13 86.1
40 TraesCS1A01G005400 chr3A 86.792 53 7 0 1974 2026 13075851 13075903 3.530000e-05 60.2


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 TraesCS1A01G005400 chr1A 3116199 3119478 3279 False 6058.0 6058 100.000 1 3280 1 chr1A.!!$F1 3279
1 TraesCS1A01G005400 chr1D 508657 512001 3344 False 1712.5 2952 85.129 44 3280 2 chr1D.!!$F2 3236
2 TraesCS1A01G005400 chr1B 4218623 4222234 3611 False 1382.0 2660 82.661 30 3280 2 chr1B.!!$F1 3250
3 TraesCS1A01G005400 chr4A 130525325 130525991 666 False 710.0 710 86.538 982 1629 1 chr4A.!!$F1 647
4 TraesCS1A01G005400 chr2A 174024729 174025401 672 True 704.0 704 86.364 982 1629 1 chr2A.!!$R1 647
5 TraesCS1A01G005400 chr6A 531810051 531810723 672 False 676.0 676 85.630 982 1629 1 chr6A.!!$F1 647
6 TraesCS1A01G005400 chr3B 782532156 782533261 1105 True 244.8 422 92.707 2321 2836 2 chr3B.!!$R3 515

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
558 840 0.028110 GTACATACGGACGGACGGAC 59.972 60.0 6.00 0.0 38.39 4.79 F
1857 2407 0.034059 CGGCTGTTCAGAAGGTGAGT 59.966 55.0 3.84 0.0 36.21 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 2446 0.036875 CTCCCTTCTTCACCACCACC 59.963 60.0 0.0 0.0 0.00 4.61 R
3096 4323 0.105760 ATGAGGTGTTGTGGGCCAAA 60.106 50.0 8.4 0.0 34.07 3.28 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
25 26 8.475331 GAAGAAGAAACATCTATCCGTGTAAA 57.525 34.615 0.00 0.00 0.00 2.01
26 27 8.480643 AAGAAGAAACATCTATCCGTGTAAAG 57.519 34.615 0.00 0.00 0.00 1.85
27 28 7.612677 AGAAGAAACATCTATCCGTGTAAAGT 58.387 34.615 0.00 0.00 0.00 2.66
28 29 7.545965 AGAAGAAACATCTATCCGTGTAAAGTG 59.454 37.037 0.00 0.00 0.00 3.16
39 40 4.128643 CCGTGTAAAGTGTAACAAAGGGA 58.871 43.478 0.00 0.00 41.43 4.20
64 68 6.701841 AGCAGTACGTATGTGGAATATTCTTG 59.298 38.462 14.95 1.20 0.00 3.02
94 100 8.359875 TGTATTTGAATTTTCTTAGCCATCCA 57.640 30.769 0.00 0.00 0.00 3.41
172 348 2.742372 CACGGACGCAAAGGGGAG 60.742 66.667 0.00 0.00 0.00 4.30
185 361 2.112279 AGGGGAGACAACACACCTAA 57.888 50.000 0.00 0.00 38.67 2.69
229 481 0.101759 CCACTGCATATTGCCTGCAC 59.898 55.000 0.00 0.00 44.30 4.57
271 523 2.109126 GGCTGCTTGATCGTGGGAC 61.109 63.158 0.00 0.00 0.00 4.46
300 553 6.949578 AAAGCATTTCCATAACACATTTCG 57.050 33.333 0.00 0.00 27.08 3.46
313 568 3.739300 ACACATTTCGTTGTTACCTCTCG 59.261 43.478 0.00 0.00 0.00 4.04
320 575 3.106672 CGTTGTTACCTCTCGAGCATAC 58.893 50.000 7.81 2.06 0.00 2.39
343 598 3.207778 TGTAGCACACACCAAGGTTTAC 58.792 45.455 0.00 0.00 30.04 2.01
350 605 4.338118 CACACACCAAGGTTTACAATGTCT 59.662 41.667 0.00 0.00 0.00 3.41
352 607 3.317993 ACACCAAGGTTTACAATGTCTGC 59.682 43.478 0.00 0.00 0.00 4.26
376 631 3.272766 GCAAATTGCGGGCCTTATC 57.727 52.632 0.90 0.00 31.71 1.75
378 633 1.021202 CAAATTGCGGGCCTTATCGA 58.979 50.000 0.84 0.00 0.00 3.59
379 634 1.021968 AAATTGCGGGCCTTATCGAC 58.978 50.000 0.84 0.00 0.00 4.20
380 635 0.818040 AATTGCGGGCCTTATCGACC 60.818 55.000 0.84 0.00 0.00 4.79
382 637 2.186602 TTGCGGGCCTTATCGACCAA 62.187 55.000 0.84 0.00 0.00 3.67
383 638 1.227853 GCGGGCCTTATCGACCAAT 60.228 57.895 0.84 0.00 0.00 3.16
384 639 0.818040 GCGGGCCTTATCGACCAATT 60.818 55.000 0.84 0.00 0.00 2.32
386 641 1.602377 CGGGCCTTATCGACCAATTTC 59.398 52.381 0.84 0.00 0.00 2.17
387 642 2.650322 GGGCCTTATCGACCAATTTCA 58.350 47.619 0.84 0.00 0.00 2.69
388 643 2.618709 GGGCCTTATCGACCAATTTCAG 59.381 50.000 0.84 0.00 0.00 3.02
390 645 3.312697 GGCCTTATCGACCAATTTCAGAC 59.687 47.826 0.00 0.00 0.00 3.51
393 648 5.758296 GCCTTATCGACCAATTTCAGACATA 59.242 40.000 0.00 0.00 0.00 2.29
396 651 8.840321 CCTTATCGACCAATTTCAGACATATTT 58.160 33.333 0.00 0.00 0.00 1.40
451 733 0.251121 TCTTGCTGGAATTTGGCCGA 60.251 50.000 0.00 0.00 0.00 5.54
454 736 2.136298 TGCTGGAATTTGGCCGAATA 57.864 45.000 18.96 2.52 0.00 1.75
463 745 4.670896 ATTTGGCCGAATAATTCAAGGG 57.329 40.909 17.19 0.00 0.00 3.95
466 748 4.237976 TGGCCGAATAATTCAAGGGTAA 57.762 40.909 0.00 0.00 0.00 2.85
468 750 5.205056 TGGCCGAATAATTCAAGGGTAAAT 58.795 37.500 0.00 0.00 0.00 1.40
498 780 0.105039 GCCCACCGAGGAATCTACTG 59.895 60.000 0.00 0.00 41.22 2.74
509 791 5.661458 GAGGAATCTACTGGAATTTCGTCA 58.339 41.667 0.00 0.00 32.54 4.35
515 797 9.626045 GAATCTACTGGAATTTCGTCAAAATTT 57.374 29.630 0.00 0.00 45.47 1.82
529 811 4.062293 TCAAAATTTCGGTCGATGTCTGT 58.938 39.130 0.00 0.00 0.00 3.41
535 817 1.536766 TCGGTCGATGTCTGTTTACGT 59.463 47.619 0.00 0.00 0.00 3.57
536 818 2.741517 TCGGTCGATGTCTGTTTACGTA 59.258 45.455 0.00 0.00 0.00 3.57
537 819 2.842485 CGGTCGATGTCTGTTTACGTAC 59.158 50.000 0.00 0.00 0.00 3.67
538 820 3.667695 CGGTCGATGTCTGTTTACGTACA 60.668 47.826 0.00 0.00 0.00 2.90
539 821 3.850273 GGTCGATGTCTGTTTACGTACAG 59.150 47.826 11.51 11.51 45.46 2.74
544 826 6.025896 CGATGTCTGTTTACGTACAGTACAT 58.974 40.000 22.50 22.50 44.62 2.29
558 840 0.028110 GTACATACGGACGGACGGAC 59.972 60.000 6.00 0.00 38.39 4.79
559 841 0.392327 TACATACGGACGGACGGACA 60.392 55.000 6.00 0.00 38.39 4.02
561 843 0.109179 CATACGGACGGACGGACAAA 60.109 55.000 6.00 0.00 38.39 2.83
562 844 0.109132 ATACGGACGGACGGACAAAC 60.109 55.000 6.00 0.00 38.39 2.93
563 845 1.451337 TACGGACGGACGGACAAACA 61.451 55.000 6.00 0.00 38.39 2.83
564 846 2.305127 CGGACGGACGGACAAACAC 61.305 63.158 0.00 0.00 0.00 3.32
584 1044 5.846203 ACACAAAAGAAGAATTGGTCCATG 58.154 37.500 0.00 0.00 0.00 3.66
624 1087 4.081807 AGAGAAAATGAAATGGGCTCTTGC 60.082 41.667 0.00 0.00 38.76 4.01
625 1088 3.579586 AGAAAATGAAATGGGCTCTTGCA 59.420 39.130 0.00 0.00 41.91 4.08
626 1089 4.224370 AGAAAATGAAATGGGCTCTTGCAT 59.776 37.500 0.00 0.00 41.91 3.96
627 1090 4.563140 AAATGAAATGGGCTCTTGCATT 57.437 36.364 0.00 0.00 41.91 3.56
629 1092 1.551430 TGAAATGGGCTCTTGCATTGG 59.449 47.619 0.00 0.00 41.91 3.16
630 1093 1.551883 GAAATGGGCTCTTGCATTGGT 59.448 47.619 0.00 0.00 41.91 3.67
631 1094 2.530460 AATGGGCTCTTGCATTGGTA 57.470 45.000 0.00 0.00 41.91 3.25
632 1095 2.062971 ATGGGCTCTTGCATTGGTAG 57.937 50.000 0.00 0.00 41.91 3.18
633 1096 0.698238 TGGGCTCTTGCATTGGTAGT 59.302 50.000 0.00 0.00 41.91 2.73
635 1098 2.307392 TGGGCTCTTGCATTGGTAGTAA 59.693 45.455 0.00 0.00 41.91 2.24
636 1099 2.683362 GGGCTCTTGCATTGGTAGTAAC 59.317 50.000 0.00 0.00 41.91 2.50
638 1101 4.010349 GGCTCTTGCATTGGTAGTAACTT 58.990 43.478 0.00 0.00 41.91 2.66
639 1102 5.183228 GGCTCTTGCATTGGTAGTAACTTA 58.817 41.667 0.00 0.00 41.91 2.24
640 1103 5.294552 GGCTCTTGCATTGGTAGTAACTTAG 59.705 44.000 0.00 0.00 41.91 2.18
683 1146 4.240096 CATGCTTGTGAAACTTGGAATCC 58.760 43.478 0.00 0.00 38.04 3.01
686 1149 4.405358 TGCTTGTGAAACTTGGAATCCTTT 59.595 37.500 0.00 0.00 38.04 3.11
687 1150 5.104982 TGCTTGTGAAACTTGGAATCCTTTT 60.105 36.000 0.00 0.00 38.04 2.27
689 1152 6.238184 GCTTGTGAAACTTGGAATCCTTTTTG 60.238 38.462 0.00 0.00 38.04 2.44
690 1153 6.537453 TGTGAAACTTGGAATCCTTTTTGA 57.463 33.333 0.00 0.00 38.04 2.69
692 1155 7.390027 TGTGAAACTTGGAATCCTTTTTGAAA 58.610 30.769 0.00 0.00 38.04 2.69
729 1192 6.153680 AGAGTAGGTTGAGATGTTGAGGTAAG 59.846 42.308 0.00 0.00 0.00 2.34
767 1234 3.603965 TGCCCTACCTTCCTTTTTGAA 57.396 42.857 0.00 0.00 0.00 2.69
768 1235 4.126520 TGCCCTACCTTCCTTTTTGAAT 57.873 40.909 0.00 0.00 0.00 2.57
769 1236 4.488770 TGCCCTACCTTCCTTTTTGAATT 58.511 39.130 0.00 0.00 0.00 2.17
770 1237 4.904853 TGCCCTACCTTCCTTTTTGAATTT 59.095 37.500 0.00 0.00 0.00 1.82
771 1238 5.368230 TGCCCTACCTTCCTTTTTGAATTTT 59.632 36.000 0.00 0.00 0.00 1.82
772 1239 5.700832 GCCCTACCTTCCTTTTTGAATTTTG 59.299 40.000 0.00 0.00 0.00 2.44
773 1240 6.463755 GCCCTACCTTCCTTTTTGAATTTTGA 60.464 38.462 0.00 0.00 0.00 2.69
780 1247 4.815846 TCCTTTTTGAATTTTGAGCAAGCC 59.184 37.500 0.00 0.00 0.00 4.35
831 1298 2.129607 CAAGCACAAAACTCATGCACC 58.870 47.619 0.00 0.00 41.97 5.01
832 1299 0.675633 AGCACAAAACTCATGCACCC 59.324 50.000 0.00 0.00 41.97 4.61
833 1300 0.675633 GCACAAAACTCATGCACCCT 59.324 50.000 0.00 0.00 39.23 4.34
834 1301 1.885887 GCACAAAACTCATGCACCCTA 59.114 47.619 0.00 0.00 39.23 3.53
882 1374 6.905776 TCCTCTCCAAGAAATATTCTTCCTCT 59.094 38.462 2.47 0.00 46.62 3.69
888 1380 8.830741 TCCAAGAAATATTCTTCCTCTTCTTCT 58.169 33.333 2.47 0.00 46.62 2.85
911 1406 1.468985 TCTTCTTCCCTCTCAGCTCG 58.531 55.000 0.00 0.00 0.00 5.03
912 1407 1.181786 CTTCTTCCCTCTCAGCTCGT 58.818 55.000 0.00 0.00 0.00 4.18
925 1420 3.462982 TCAGCTCGTCTCTCTAGCTTAG 58.537 50.000 0.00 0.00 41.45 2.18
976 1471 6.973843 TCGTCAAAGCTTATATATACACGGT 58.026 36.000 0.00 0.00 0.00 4.83
1022 1521 2.184113 AGATCATCCCTTCTCCCATCCT 59.816 50.000 0.00 0.00 0.00 3.24
1024 1523 2.130193 TCATCCCTTCTCCCATCCTTG 58.870 52.381 0.00 0.00 0.00 3.61
1025 1524 0.849417 ATCCCTTCTCCCATCCTTGC 59.151 55.000 0.00 0.00 0.00 4.01
1026 1525 1.228510 CCCTTCTCCCATCCTTGCC 59.771 63.158 0.00 0.00 0.00 4.52
1072 1571 6.654122 TCAAGCAAGAAACAAACAAACAAAC 58.346 32.000 0.00 0.00 0.00 2.93
1073 1572 6.258727 TCAAGCAAGAAACAAACAAACAAACA 59.741 30.769 0.00 0.00 0.00 2.83
1087 1586 3.883744 AAACAGAGCTCCACCGCCG 62.884 63.158 10.93 0.00 0.00 6.46
1197 1714 4.749310 CGCCTGCTGGAGTTCGCT 62.749 66.667 14.77 0.00 34.57 4.93
1202 1719 3.426568 GCTGGAGTTCGCTGCCAC 61.427 66.667 0.00 0.00 34.38 5.01
1257 1774 1.043673 GCTACTCCACCCTCATCCGT 61.044 60.000 0.00 0.00 0.00 4.69
1260 1777 2.365105 TCCACCCTCATCCGTCCC 60.365 66.667 0.00 0.00 0.00 4.46
1288 1805 3.041940 CCAACGACGGCAGTGTCC 61.042 66.667 0.00 0.00 35.40 4.02
1289 1806 2.279851 CAACGACGGCAGTGTCCA 60.280 61.111 0.00 0.00 35.40 4.02
1527 2065 2.404995 GGACGACGGTCAGGACGAT 61.405 63.158 9.10 0.00 45.28 3.73
1727 2268 2.743538 CACGCCTAGCAGCAGCAA 60.744 61.111 3.17 0.00 45.49 3.91
1856 2406 1.294659 GCGGCTGTTCAGAAGGTGAG 61.295 60.000 3.84 0.00 36.21 3.51
1857 2407 0.034059 CGGCTGTTCAGAAGGTGAGT 59.966 55.000 3.84 0.00 36.21 3.41
1896 2446 3.953775 AGCACGGGGAAGGTGGTG 61.954 66.667 0.00 0.00 43.77 4.17
1920 2470 1.118965 TGGTGAAGAAGGGAGCGACA 61.119 55.000 0.00 0.00 0.00 4.35
2125 2690 7.760131 ATTTATTCACATTTGCATTCCTTCG 57.240 32.000 0.00 0.00 0.00 3.79
2145 2710 8.071368 TCCTTCGTTCATTTGTAAATTGTACAC 58.929 33.333 0.00 0.00 30.21 2.90
2146 2711 7.858382 CCTTCGTTCATTTGTAAATTGTACACA 59.142 33.333 0.00 0.00 30.21 3.72
2147 2712 8.549777 TTCGTTCATTTGTAAATTGTACACAC 57.450 30.769 0.00 0.00 30.21 3.82
2148 2713 7.133513 TCGTTCATTTGTAAATTGTACACACC 58.866 34.615 0.00 0.00 30.21 4.16
2149 2714 7.012515 TCGTTCATTTGTAAATTGTACACACCT 59.987 33.333 0.00 0.00 30.21 4.00
2150 2715 7.112844 CGTTCATTTGTAAATTGTACACACCTG 59.887 37.037 0.00 0.00 30.21 4.00
2151 2716 7.575414 TCATTTGTAAATTGTACACACCTGT 57.425 32.000 0.00 0.00 0.00 4.00
2152 2717 8.678593 TCATTTGTAAATTGTACACACCTGTA 57.321 30.769 0.00 0.00 0.00 2.74
2153 2718 9.121658 TCATTTGTAAATTGTACACACCTGTAA 57.878 29.630 0.00 0.00 34.53 2.41
2154 2719 9.737427 CATTTGTAAATTGTACACACCTGTAAA 57.263 29.630 0.00 0.00 34.53 2.01
2157 2722 9.737427 TTGTAAATTGTACACACCTGTAAATTG 57.263 29.630 0.00 0.00 34.53 2.32
2158 2723 8.353684 TGTAAATTGTACACACCTGTAAATTGG 58.646 33.333 0.00 0.00 34.53 3.16
2159 2724 4.839668 TTGTACACACCTGTAAATTGGC 57.160 40.909 0.00 0.00 34.53 4.52
2160 2725 4.093472 TGTACACACCTGTAAATTGGCT 57.907 40.909 0.00 0.00 34.53 4.75
2161 2726 5.230323 TGTACACACCTGTAAATTGGCTA 57.770 39.130 0.00 0.00 34.53 3.93
2162 2727 5.242434 TGTACACACCTGTAAATTGGCTAG 58.758 41.667 0.00 0.00 34.53 3.42
2163 2728 3.686016 ACACACCTGTAAATTGGCTAGG 58.314 45.455 0.00 0.00 34.70 3.02
2164 2729 2.423538 CACACCTGTAAATTGGCTAGGC 59.576 50.000 9.85 9.85 31.69 3.93
2165 2730 2.308866 ACACCTGTAAATTGGCTAGGCT 59.691 45.455 18.18 0.00 31.69 4.58
2166 2731 2.684881 CACCTGTAAATTGGCTAGGCTG 59.315 50.000 18.18 0.00 31.69 4.85
2167 2732 2.308866 ACCTGTAAATTGGCTAGGCTGT 59.691 45.455 18.18 2.96 31.69 4.40
2168 2733 2.684881 CCTGTAAATTGGCTAGGCTGTG 59.315 50.000 18.18 0.00 0.00 3.66
2169 2734 3.347216 CTGTAAATTGGCTAGGCTGTGT 58.653 45.455 18.18 3.77 0.00 3.72
2179 2744 4.408921 TGGCTAGGCTGTGTTCATAGTTAT 59.591 41.667 18.18 0.00 0.00 1.89
2184 2749 6.808321 AGGCTGTGTTCATAGTTATCCTTA 57.192 37.500 0.00 0.00 0.00 2.69
2210 2775 5.129634 TCAGGTTTAGTTTGACAGCAATGA 58.870 37.500 0.00 0.00 33.25 2.57
2213 2778 6.364165 CAGGTTTAGTTTGACAGCAATGATTG 59.636 38.462 0.00 0.00 33.25 2.67
2214 2779 6.040842 AGGTTTAGTTTGACAGCAATGATTGT 59.959 34.615 7.05 0.00 33.25 2.71
2226 2791 5.574055 CAGCAATGATTGTTGTAACCATCAC 59.426 40.000 13.01 3.03 41.85 3.06
2236 2801 5.589855 TGTTGTAACCATCACCATCATCATC 59.410 40.000 0.00 0.00 0.00 2.92
2237 2802 5.370875 TGTAACCATCACCATCATCATCA 57.629 39.130 0.00 0.00 0.00 3.07
2238 2803 5.944135 TGTAACCATCACCATCATCATCAT 58.056 37.500 0.00 0.00 0.00 2.45
2307 2898 5.941058 TGCATTTCATTTCATTTGCCTCAAT 59.059 32.000 0.00 0.00 0.00 2.57
2350 2941 6.207417 TCATTCATCTCTGGGTTTCTTGTTTC 59.793 38.462 0.00 0.00 0.00 2.78
2435 3034 6.717084 CCCCTTTGATTCCTACCATAAGAATC 59.283 42.308 5.27 5.27 43.97 2.52
2441 3040 3.845860 TCCTACCATAAGAATCGAGCCT 58.154 45.455 0.00 0.00 0.00 4.58
2472 3075 3.951979 AGAAGCAAGAACAAGAACACG 57.048 42.857 0.00 0.00 0.00 4.49
2490 3094 4.050553 ACACGAATTTGAGGCAATTGTTG 58.949 39.130 7.40 0.00 0.00 3.33
2588 3193 4.937620 TGCAAGATGAGATGTAACCAGTTC 59.062 41.667 0.00 0.00 0.00 3.01
2611 3216 9.141400 GTTCTTGTACAGGAGTAACAAGAATAG 57.859 37.037 24.39 0.06 45.89 1.73
2649 3254 9.646427 TCAATTATTGGTTATGTTTTGTTAGGC 57.354 29.630 5.02 0.00 0.00 3.93
2668 3274 9.890629 TGTTAGGCTATTCATATGGATTGTATC 57.109 33.333 0.69 0.00 0.00 2.24
2671 3277 8.621126 AGGCTATTCATATGGATTGTATCTCT 57.379 34.615 0.69 0.00 0.00 3.10
2672 3278 9.055689 AGGCTATTCATATGGATTGTATCTCTT 57.944 33.333 0.69 0.00 0.00 2.85
2673 3279 9.107177 GGCTATTCATATGGATTGTATCTCTTG 57.893 37.037 0.69 0.00 0.00 3.02
2711 3518 7.891561 TGGAGGTAGTTTTGTTTATTTGATGG 58.108 34.615 0.00 0.00 0.00 3.51
2732 3540 6.139679 TGGTGATTCCTAGGACAAGAAAAT 57.860 37.500 12.22 0.00 37.07 1.82
2741 3549 8.792830 TCCTAGGACAAGAAAATATTGAACAG 57.207 34.615 7.62 0.00 0.00 3.16
2785 3599 4.508124 ACAAGAACAAACGTCTGTCTCATC 59.492 41.667 0.00 0.00 0.00 2.92
2980 4204 2.033492 GCATCAGCTTTGCAACAAACAC 60.033 45.455 12.45 0.00 39.90 3.32
3039 4265 6.250089 GCCAACAACACTTTGATTTCAAAAG 58.750 36.000 7.13 5.66 44.24 2.27
3043 4269 9.311916 CAACAACACTTTGATTTCAAAAGGATA 57.688 29.630 7.13 0.00 44.24 2.59
3103 4330 2.460669 AGATTGTCCATCTTTTGGCCC 58.539 47.619 0.00 0.00 46.01 5.80
3181 4408 4.943093 TCATGTTACAGCAGTATTGTGCAT 59.057 37.500 0.00 0.00 46.60 3.96
3186 4413 4.206477 ACAGCAGTATTGTGCATACAGA 57.794 40.909 0.00 0.00 46.60 3.41
3207 4434 7.004086 ACAGATTGGACCAAGTTCATCTAAAA 58.996 34.615 13.43 0.00 0.00 1.52
3208 4435 7.505585 ACAGATTGGACCAAGTTCATCTAAAAA 59.494 33.333 13.43 0.00 0.00 1.94
3209 4436 8.526147 CAGATTGGACCAAGTTCATCTAAAAAT 58.474 33.333 13.43 0.00 0.00 1.82
3217 4444 7.396339 ACCAAGTTCATCTAAAAATAAGGGTCC 59.604 37.037 0.00 0.00 0.00 4.46
3232 4459 3.267483 AGGGTCCGTGAAAATTACATCG 58.733 45.455 0.00 0.00 0.00 3.84
3233 4460 3.055675 AGGGTCCGTGAAAATTACATCGA 60.056 43.478 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.475331 TTTACACGGATAGATGTTTCTTCTTC 57.525 34.615 0.00 0.00 33.17 2.87
1 2 8.095169 ACTTTACACGGATAGATGTTTCTTCTT 58.905 33.333 0.00 0.00 33.17 2.52
2 3 7.545965 CACTTTACACGGATAGATGTTTCTTCT 59.454 37.037 0.00 0.00 33.17 2.85
3 4 7.331193 ACACTTTACACGGATAGATGTTTCTTC 59.669 37.037 0.00 0.00 33.17 2.87
4 5 7.159372 ACACTTTACACGGATAGATGTTTCTT 58.841 34.615 0.00 0.00 33.17 2.52
5 6 6.698380 ACACTTTACACGGATAGATGTTTCT 58.302 36.000 0.00 0.00 35.90 2.52
6 7 6.963049 ACACTTTACACGGATAGATGTTTC 57.037 37.500 0.00 0.00 0.00 2.78
7 8 7.874016 TGTTACACTTTACACGGATAGATGTTT 59.126 33.333 0.00 0.00 0.00 2.83
8 9 7.380536 TGTTACACTTTACACGGATAGATGTT 58.619 34.615 0.00 0.00 0.00 2.71
9 10 6.927416 TGTTACACTTTACACGGATAGATGT 58.073 36.000 0.00 0.00 0.00 3.06
10 11 7.821595 TTGTTACACTTTACACGGATAGATG 57.178 36.000 0.00 0.00 0.00 2.90
11 12 7.548075 CCTTTGTTACACTTTACACGGATAGAT 59.452 37.037 0.00 0.00 0.00 1.98
12 13 6.869913 CCTTTGTTACACTTTACACGGATAGA 59.130 38.462 0.00 0.00 0.00 1.98
13 14 6.091713 CCCTTTGTTACACTTTACACGGATAG 59.908 42.308 0.00 0.00 0.00 2.08
14 15 5.933463 CCCTTTGTTACACTTTACACGGATA 59.067 40.000 0.00 0.00 0.00 2.59
15 16 4.758165 CCCTTTGTTACACTTTACACGGAT 59.242 41.667 0.00 0.00 0.00 4.18
16 17 4.128643 CCCTTTGTTACACTTTACACGGA 58.871 43.478 0.00 0.00 0.00 4.69
17 18 4.128643 TCCCTTTGTTACACTTTACACGG 58.871 43.478 0.00 0.00 0.00 4.94
18 19 4.319261 GCTCCCTTTGTTACACTTTACACG 60.319 45.833 0.00 0.00 0.00 4.49
19 20 4.577283 TGCTCCCTTTGTTACACTTTACAC 59.423 41.667 0.00 0.00 0.00 2.90
20 21 4.783055 TGCTCCCTTTGTTACACTTTACA 58.217 39.130 0.00 0.00 0.00 2.41
21 22 4.820173 ACTGCTCCCTTTGTTACACTTTAC 59.180 41.667 0.00 0.00 0.00 2.01
22 23 5.043737 ACTGCTCCCTTTGTTACACTTTA 57.956 39.130 0.00 0.00 0.00 1.85
23 24 3.898482 ACTGCTCCCTTTGTTACACTTT 58.102 40.909 0.00 0.00 0.00 2.66
24 25 3.577805 ACTGCTCCCTTTGTTACACTT 57.422 42.857 0.00 0.00 0.00 3.16
25 26 3.554337 CGTACTGCTCCCTTTGTTACACT 60.554 47.826 0.00 0.00 0.00 3.55
26 27 2.735134 CGTACTGCTCCCTTTGTTACAC 59.265 50.000 0.00 0.00 0.00 2.90
27 28 2.366266 ACGTACTGCTCCCTTTGTTACA 59.634 45.455 0.00 0.00 0.00 2.41
28 29 3.036075 ACGTACTGCTCCCTTTGTTAC 57.964 47.619 0.00 0.00 0.00 2.50
39 40 6.406692 AGAATATTCCACATACGTACTGCT 57.593 37.500 11.92 0.00 0.00 4.24
64 68 9.638239 TGGCTAAGAAAATTCAAATACAATGAC 57.362 29.630 0.00 0.00 0.00 3.06
172 348 2.973945 CCTAGCCTTAGGTGTGTTGTC 58.026 52.381 0.00 0.00 41.42 3.18
229 481 0.667993 TGCTGGCCTTGAGTTTTTCG 59.332 50.000 3.32 0.00 0.00 3.46
271 523 6.164876 TGTGTTATGGAAATGCTTTTCATGG 58.835 36.000 22.27 0.00 42.55 3.66
300 553 3.106672 CGTATGCTCGAGAGGTAACAAC 58.893 50.000 18.75 4.15 41.41 3.32
352 607 1.637478 GGCCCGCAATTTGCATGTTG 61.637 55.000 20.56 4.43 45.36 3.33
358 613 0.594796 CGATAAGGCCCGCAATTTGC 60.595 55.000 11.42 11.42 40.69 3.68
361 616 0.818040 GGTCGATAAGGCCCGCAATT 60.818 55.000 0.00 0.00 39.18 2.32
365 620 0.818040 AATTGGTCGATAAGGCCCGC 60.818 55.000 0.00 0.00 46.38 6.13
429 690 1.620323 GGCCAAATTCCAGCAAGACTT 59.380 47.619 0.00 0.00 0.00 3.01
431 692 0.109132 CGGCCAAATTCCAGCAAGAC 60.109 55.000 2.24 0.00 0.00 3.01
433 694 0.602562 TTCGGCCAAATTCCAGCAAG 59.397 50.000 2.24 0.00 0.00 4.01
434 695 1.265236 ATTCGGCCAAATTCCAGCAA 58.735 45.000 2.24 0.00 0.00 3.91
435 696 2.136298 TATTCGGCCAAATTCCAGCA 57.864 45.000 2.24 0.00 0.00 4.41
436 697 3.733443 ATTATTCGGCCAAATTCCAGC 57.267 42.857 2.24 0.00 0.00 4.85
437 698 5.261209 TGAATTATTCGGCCAAATTCCAG 57.739 39.130 19.28 0.00 38.34 3.86
439 700 5.049828 CCTTGAATTATTCGGCCAAATTCC 58.950 41.667 19.28 8.57 38.34 3.01
445 727 2.818751 ACCCTTGAATTATTCGGCCA 57.181 45.000 2.24 0.00 0.00 5.36
454 736 6.150474 CGCCGGAATATATTTACCCTTGAATT 59.850 38.462 5.05 0.00 0.00 2.17
463 745 2.417586 GTGGGCGCCGGAATATATTTAC 59.582 50.000 22.54 1.40 0.00 2.01
466 748 0.322187 GGTGGGCGCCGGAATATATT 60.322 55.000 22.54 0.00 0.00 1.28
468 750 2.745037 GGTGGGCGCCGGAATATA 59.255 61.111 22.54 0.00 0.00 0.86
488 770 6.737254 TTTGACGAAATTCCAGTAGATTCC 57.263 37.500 0.00 0.00 0.00 3.01
498 780 4.319901 CGACCGAAATTTTGACGAAATTCC 59.680 41.667 12.79 0.91 44.98 3.01
509 791 5.432885 AAACAGACATCGACCGAAATTTT 57.567 34.783 0.00 0.00 0.00 1.82
515 797 1.536766 ACGTAAACAGACATCGACCGA 59.463 47.619 0.00 0.00 0.00 4.69
529 811 4.201773 CCGTCCGTATGTACTGTACGTAAA 60.202 45.833 18.68 7.49 42.37 2.01
535 817 1.933181 CGTCCGTCCGTATGTACTGTA 59.067 52.381 0.00 0.00 0.00 2.74
536 818 0.729116 CGTCCGTCCGTATGTACTGT 59.271 55.000 0.00 0.00 0.00 3.55
537 819 0.028505 CCGTCCGTCCGTATGTACTG 59.971 60.000 0.00 0.00 0.00 2.74
538 820 0.107703 TCCGTCCGTCCGTATGTACT 60.108 55.000 0.00 0.00 0.00 2.73
539 821 0.028110 GTCCGTCCGTCCGTATGTAC 59.972 60.000 0.00 0.00 0.00 2.90
544 826 1.285641 GTTTGTCCGTCCGTCCGTA 59.714 57.895 0.00 0.00 0.00 4.02
558 840 6.105333 TGGACCAATTCTTCTTTTGTGTTTG 58.895 36.000 0.00 0.00 0.00 2.93
559 841 6.293004 TGGACCAATTCTTCTTTTGTGTTT 57.707 33.333 0.00 0.00 0.00 2.83
561 843 5.363580 ACATGGACCAATTCTTCTTTTGTGT 59.636 36.000 0.00 0.00 0.00 3.72
562 844 5.693104 CACATGGACCAATTCTTCTTTTGTG 59.307 40.000 0.00 0.34 0.00 3.33
563 845 5.598005 TCACATGGACCAATTCTTCTTTTGT 59.402 36.000 0.00 0.00 0.00 2.83
564 846 6.088016 TCACATGGACCAATTCTTCTTTTG 57.912 37.500 0.00 0.00 0.00 2.44
584 1044 6.884280 TTTCTCTTTTCTTCTTCCCATCAC 57.116 37.500 0.00 0.00 0.00 3.06
624 1087 5.354234 CCACCTTGCTAAGTTACTACCAATG 59.646 44.000 0.00 0.00 0.00 2.82
625 1088 5.249852 TCCACCTTGCTAAGTTACTACCAAT 59.750 40.000 0.00 0.00 0.00 3.16
626 1089 4.594062 TCCACCTTGCTAAGTTACTACCAA 59.406 41.667 0.00 0.00 0.00 3.67
627 1090 4.161876 TCCACCTTGCTAAGTTACTACCA 58.838 43.478 0.00 0.00 0.00 3.25
629 1092 7.985752 ACATTATCCACCTTGCTAAGTTACTAC 59.014 37.037 0.00 0.00 0.00 2.73
630 1093 8.086143 ACATTATCCACCTTGCTAAGTTACTA 57.914 34.615 0.00 0.00 0.00 1.82
631 1094 6.958767 ACATTATCCACCTTGCTAAGTTACT 58.041 36.000 0.00 0.00 0.00 2.24
632 1095 7.120726 ACAACATTATCCACCTTGCTAAGTTAC 59.879 37.037 0.00 0.00 0.00 2.50
633 1096 7.172342 ACAACATTATCCACCTTGCTAAGTTA 58.828 34.615 0.00 0.00 0.00 2.24
635 1098 5.570320 ACAACATTATCCACCTTGCTAAGT 58.430 37.500 0.00 0.00 0.00 2.24
636 1099 6.324819 CAACAACATTATCCACCTTGCTAAG 58.675 40.000 0.00 0.00 0.00 2.18
638 1101 4.157656 GCAACAACATTATCCACCTTGCTA 59.842 41.667 0.00 0.00 31.97 3.49
639 1102 3.056607 GCAACAACATTATCCACCTTGCT 60.057 43.478 0.00 0.00 31.97 3.91
640 1103 3.253230 GCAACAACATTATCCACCTTGC 58.747 45.455 0.00 0.00 0.00 4.01
686 1149 7.939039 ACCTACTCTCTCATGTTGATTTTCAAA 59.061 33.333 0.00 0.00 38.22 2.69
687 1150 7.453393 ACCTACTCTCTCATGTTGATTTTCAA 58.547 34.615 0.00 0.00 33.32 2.69
689 1152 7.604164 TCAACCTACTCTCTCATGTTGATTTTC 59.396 37.037 0.00 0.00 37.69 2.29
690 1153 7.453393 TCAACCTACTCTCTCATGTTGATTTT 58.547 34.615 0.00 0.00 37.69 1.82
692 1155 6.438741 TCTCAACCTACTCTCTCATGTTGATT 59.561 38.462 0.00 0.00 40.64 2.57
709 1172 6.270231 AGTTACTTACCTCAACATCTCAACCT 59.730 38.462 0.00 0.00 0.00 3.50
729 1192 4.941873 AGGGCATGCAAGTAAGTTAGTTAC 59.058 41.667 21.36 1.93 41.39 2.50
739 1206 1.211949 GGAAGGTAGGGCATGCAAGTA 59.788 52.381 21.36 4.34 0.00 2.24
780 1247 0.445436 CAGTGGAAGCAAAGCTAGCG 59.555 55.000 9.55 0.00 38.25 4.26
831 1298 2.119484 TTGCTTGGGGTGGACGTAGG 62.119 60.000 0.00 0.00 0.00 3.18
832 1299 0.953960 GTTGCTTGGGGTGGACGTAG 60.954 60.000 0.00 0.00 0.00 3.51
833 1300 1.071814 GTTGCTTGGGGTGGACGTA 59.928 57.895 0.00 0.00 0.00 3.57
834 1301 2.203294 GTTGCTTGGGGTGGACGT 60.203 61.111 0.00 0.00 0.00 4.34
882 1374 5.841237 TGAGAGGGAAGAAGAAGAAGAAGAA 59.159 40.000 0.00 0.00 0.00 2.52
888 1380 3.513515 GAGCTGAGAGGGAAGAAGAAGAA 59.486 47.826 0.00 0.00 0.00 2.52
911 1406 3.724508 TGCATGCTAAGCTAGAGAGAC 57.275 47.619 20.33 0.00 0.00 3.36
912 1407 4.254402 CATGCATGCTAAGCTAGAGAGA 57.746 45.455 20.33 0.00 0.00 3.10
976 1471 1.681327 GTCGGAGGAGCCTGGTGTA 60.681 63.158 0.00 0.00 0.00 2.90
1022 1521 0.552848 GGATCAATGGAGGAGGGCAA 59.447 55.000 0.00 0.00 0.00 4.52
1024 1523 0.776176 ATGGATCAATGGAGGAGGGC 59.224 55.000 0.00 0.00 0.00 5.19
1025 1524 2.224967 GGAATGGATCAATGGAGGAGGG 60.225 54.545 0.00 0.00 0.00 4.30
1026 1525 2.715336 AGGAATGGATCAATGGAGGAGG 59.285 50.000 0.00 0.00 0.00 4.30
1072 1571 4.504916 CTCGGCGGTGGAGCTCTG 62.505 72.222 14.64 2.63 37.29 3.35
1073 1572 4.742649 TCTCGGCGGTGGAGCTCT 62.743 66.667 14.64 0.00 37.29 4.09
1273 1790 2.279918 GTGGACACTGCCGTCGTT 60.280 61.111 0.00 0.00 36.73 3.85
1274 1791 4.295119 GGTGGACACTGCCGTCGT 62.295 66.667 2.13 0.00 36.73 4.34
1284 1801 2.450243 GAGGAGGGGAGGTGGACA 59.550 66.667 0.00 0.00 0.00 4.02
1518 2050 3.838271 GCCGCCTCATCGTCCTGA 61.838 66.667 0.00 0.00 0.00 3.86
1710 2248 2.743538 TTGCTGCTGCTAGGCGTG 60.744 61.111 17.00 0.00 40.48 5.34
1711 2249 2.743928 GTTGCTGCTGCTAGGCGT 60.744 61.111 17.00 0.00 40.48 5.68
1714 2252 0.953727 TTGTTGTTGCTGCTGCTAGG 59.046 50.000 17.00 0.00 40.48 3.02
1716 2254 1.387539 TGTTGTTGTTGCTGCTGCTA 58.612 45.000 17.00 6.36 40.48 3.49
1718 2256 0.646895 GTTGTTGTTGTTGCTGCTGC 59.353 50.000 8.89 8.89 40.20 5.25
1719 2257 1.655099 GTGTTGTTGTTGTTGCTGCTG 59.345 47.619 0.00 0.00 0.00 4.41
1720 2258 1.732077 CGTGTTGTTGTTGTTGCTGCT 60.732 47.619 0.00 0.00 0.00 4.24
1721 2259 0.639756 CGTGTTGTTGTTGTTGCTGC 59.360 50.000 0.00 0.00 0.00 5.25
1765 2312 4.394078 CGTCGTCGTCTTGGCCGA 62.394 66.667 0.00 0.00 0.00 5.54
1800 2347 1.153127 AGACGGAGGAGTAGGAGCG 60.153 63.158 0.00 0.00 0.00 5.03
1803 2350 0.547075 CAGGAGACGGAGGAGTAGGA 59.453 60.000 0.00 0.00 0.00 2.94
1807 2354 1.680651 CAGCAGGAGACGGAGGAGT 60.681 63.158 0.00 0.00 0.00 3.85
1856 2406 1.139095 CTCTTCCCCGTGCTCGTAC 59.861 63.158 7.47 0.00 35.01 3.67
1857 2407 2.050350 CCTCTTCCCCGTGCTCGTA 61.050 63.158 7.47 0.00 35.01 3.43
1896 2446 0.036875 CTCCCTTCTTCACCACCACC 59.963 60.000 0.00 0.00 0.00 4.61
1920 2470 2.661866 GTCGTCACAGTTGCCGCT 60.662 61.111 0.00 0.00 0.00 5.52
1926 2476 0.868602 CCGTCGTTGTCGTCACAGTT 60.869 55.000 0.00 0.00 38.33 3.16
1929 2479 1.784036 TAGCCGTCGTTGTCGTCACA 61.784 55.000 0.00 0.00 38.33 3.58
2033 2583 7.660617 GTGAGATGAGATGATTGGTTGTATCAT 59.339 37.037 0.00 0.00 43.53 2.45
2034 2584 6.988580 GTGAGATGAGATGATTGGTTGTATCA 59.011 38.462 0.00 0.00 36.53 2.15
2035 2585 6.426328 GGTGAGATGAGATGATTGGTTGTATC 59.574 42.308 0.00 0.00 0.00 2.24
2036 2586 6.126681 TGGTGAGATGAGATGATTGGTTGTAT 60.127 38.462 0.00 0.00 0.00 2.29
2037 2587 5.189539 TGGTGAGATGAGATGATTGGTTGTA 59.810 40.000 0.00 0.00 0.00 2.41
2038 2588 4.019051 TGGTGAGATGAGATGATTGGTTGT 60.019 41.667 0.00 0.00 0.00 3.32
2039 2589 4.334759 GTGGTGAGATGAGATGATTGGTTG 59.665 45.833 0.00 0.00 0.00 3.77
2041 2591 3.779183 AGTGGTGAGATGAGATGATTGGT 59.221 43.478 0.00 0.00 0.00 3.67
2104 2659 5.895636 ACGAAGGAATGCAAATGTGAATA 57.104 34.783 0.00 0.00 0.00 1.75
2110 2675 5.406175 ACAAATGAACGAAGGAATGCAAATG 59.594 36.000 0.00 0.00 0.00 2.32
2125 2690 7.918562 ACAGGTGTGTACAATTTACAAATGAAC 59.081 33.333 0.00 0.00 34.05 3.18
2145 2710 2.684881 CAGCCTAGCCAATTTACAGGTG 59.315 50.000 0.00 0.00 0.00 4.00
2146 2711 2.308866 ACAGCCTAGCCAATTTACAGGT 59.691 45.455 0.00 0.00 0.00 4.00
2147 2712 2.684881 CACAGCCTAGCCAATTTACAGG 59.315 50.000 0.00 0.00 0.00 4.00
2148 2713 3.347216 ACACAGCCTAGCCAATTTACAG 58.653 45.455 0.00 0.00 0.00 2.74
2149 2714 3.433306 ACACAGCCTAGCCAATTTACA 57.567 42.857 0.00 0.00 0.00 2.41
2150 2715 3.756434 TGAACACAGCCTAGCCAATTTAC 59.244 43.478 0.00 0.00 0.00 2.01
2151 2716 4.027674 TGAACACAGCCTAGCCAATTTA 57.972 40.909 0.00 0.00 0.00 1.40
2152 2717 2.875296 TGAACACAGCCTAGCCAATTT 58.125 42.857 0.00 0.00 0.00 1.82
2153 2718 2.584835 TGAACACAGCCTAGCCAATT 57.415 45.000 0.00 0.00 0.00 2.32
2154 2719 2.814805 ATGAACACAGCCTAGCCAAT 57.185 45.000 0.00 0.00 0.00 3.16
2155 2720 2.571653 ACTATGAACACAGCCTAGCCAA 59.428 45.455 0.00 0.00 0.00 4.52
2156 2721 2.187958 ACTATGAACACAGCCTAGCCA 58.812 47.619 0.00 0.00 0.00 4.75
2157 2722 2.990066 ACTATGAACACAGCCTAGCC 57.010 50.000 0.00 0.00 0.00 3.93
2158 2723 4.991687 GGATAACTATGAACACAGCCTAGC 59.008 45.833 0.00 0.00 0.00 3.42
2159 2724 6.412362 AGGATAACTATGAACACAGCCTAG 57.588 41.667 0.00 0.00 0.00 3.02
2160 2725 6.808321 AAGGATAACTATGAACACAGCCTA 57.192 37.500 0.00 0.00 0.00 3.93
2161 2726 5.700402 AAGGATAACTATGAACACAGCCT 57.300 39.130 0.00 0.00 0.00 4.58
2162 2727 7.247929 GTTAAGGATAACTATGAACACAGCC 57.752 40.000 0.00 0.00 38.69 4.85
2179 2744 6.891388 TGTCAAACTAAACCTGAGTTAAGGA 58.109 36.000 0.00 0.00 40.02 3.36
2184 2749 4.523083 TGCTGTCAAACTAAACCTGAGTT 58.477 39.130 0.00 0.00 38.81 3.01
2210 2775 5.951148 TGATGATGGTGATGGTTACAACAAT 59.049 36.000 0.00 0.00 38.46 2.71
2213 2778 5.589855 TGATGATGATGGTGATGGTTACAAC 59.410 40.000 0.00 0.00 0.00 3.32
2214 2779 5.753716 TGATGATGATGGTGATGGTTACAA 58.246 37.500 0.00 0.00 0.00 2.41
2226 2791 8.245491 TGTCTTTTTACAACATGATGATGATGG 58.755 33.333 10.29 0.00 36.83 3.51
2236 2801 7.920151 TGAAATGGACTGTCTTTTTACAACATG 59.080 33.333 7.85 0.00 0.00 3.21
2237 2802 8.006298 TGAAATGGACTGTCTTTTTACAACAT 57.994 30.769 7.85 0.00 0.00 2.71
2238 2803 7.397892 TGAAATGGACTGTCTTTTTACAACA 57.602 32.000 7.85 0.00 0.00 3.33
2282 2847 5.492895 TGAGGCAAATGAAATGAAATGCAT 58.507 33.333 0.00 0.00 39.43 3.96
2283 2848 4.895961 TGAGGCAAATGAAATGAAATGCA 58.104 34.783 0.00 0.00 35.57 3.96
2284 2849 5.866335 TTGAGGCAAATGAAATGAAATGC 57.134 34.783 0.00 0.00 0.00 3.56
2285 2850 7.843490 AGATTGAGGCAAATGAAATGAAATG 57.157 32.000 0.00 0.00 0.00 2.32
2286 2851 9.542462 CATAGATTGAGGCAAATGAAATGAAAT 57.458 29.630 0.00 0.00 0.00 2.17
2288 2853 8.296211 TCATAGATTGAGGCAAATGAAATGAA 57.704 30.769 0.00 0.00 0.00 2.57
2292 2857 8.355169 GCTATTCATAGATTGAGGCAAATGAAA 58.645 33.333 8.79 1.87 34.22 2.69
2293 2858 7.503230 TGCTATTCATAGATTGAGGCAAATGAA 59.497 33.333 7.70 7.70 34.67 2.57
2317 2908 4.583489 ACCCAGAGATGAATGATGAATTGC 59.417 41.667 0.00 0.00 0.00 3.56
2333 2924 4.884164 AGAACAGAAACAAGAAACCCAGAG 59.116 41.667 0.00 0.00 0.00 3.35
2350 2941 4.855715 TCTAACCACTCAGACAGAACAG 57.144 45.455 0.00 0.00 0.00 3.16
2472 3075 5.989551 ACAACAACAATTGCCTCAAATTC 57.010 34.783 5.05 0.00 32.47 2.17
2567 3171 6.652481 ACAAGAACTGGTTACATCTCATCTTG 59.348 38.462 9.43 9.43 44.08 3.02
2588 3193 7.097192 TGCTATTCTTGTTACTCCTGTACAAG 58.903 38.462 0.00 0.00 38.12 3.16
2631 3236 8.588290 ATGAATAGCCTAACAAAACATAACCA 57.412 30.769 0.00 0.00 0.00 3.67
2666 3272 4.973856 TCCAGGAAGGAATCATCAAGAGAT 59.026 41.667 0.00 0.00 45.65 2.75
2668 3274 4.767578 TCCAGGAAGGAATCATCAAGAG 57.232 45.455 0.00 0.00 45.65 2.85
2680 3286 3.790089 ACAAAACTACCTCCAGGAAGG 57.210 47.619 0.00 0.00 42.55 3.46
2694 3501 8.831715 AGGAATCACCATCAAATAAACAAAAC 57.168 30.769 0.00 0.00 42.04 2.43
2699 3506 7.556275 TGTCCTAGGAATCACCATCAAATAAAC 59.444 37.037 14.65 0.00 42.04 2.01
2711 3518 9.396022 TCAATATTTTCTTGTCCTAGGAATCAC 57.604 33.333 14.65 1.66 0.00 3.06
2732 3540 8.031864 TGCTTTTTGTTTTGTCTCTGTTCAATA 58.968 29.630 0.00 0.00 0.00 1.90
2741 3549 6.704512 TGTTCTTGCTTTTTGTTTTGTCTC 57.295 33.333 0.00 0.00 0.00 3.36
2785 3599 0.734889 GCCGATGGTGATGGACAAAG 59.265 55.000 0.00 0.00 0.00 2.77
3039 4265 3.906720 TGTCTGGCCTTGTTAGTATCC 57.093 47.619 3.32 0.00 0.00 2.59
3043 4269 3.577805 ACTTTGTCTGGCCTTGTTAGT 57.422 42.857 3.32 0.00 0.00 2.24
3047 4273 3.290948 TTGTACTTTGTCTGGCCTTGT 57.709 42.857 3.32 0.00 0.00 3.16
3091 4318 1.270252 GGTGTTGTGGGCCAAAAGATG 60.270 52.381 10.07 0.00 34.07 2.90
3096 4323 0.105760 ATGAGGTGTTGTGGGCCAAA 60.106 50.000 8.40 0.00 34.07 3.28
3103 4330 4.566545 TTGTAGCAAATGAGGTGTTGTG 57.433 40.909 0.00 0.00 0.00 3.33
3181 4408 5.762179 AGATGAACTTGGTCCAATCTGTA 57.238 39.130 4.34 0.00 0.00 2.74
3207 4434 6.037830 CGATGTAATTTTCACGGACCCTTATT 59.962 38.462 0.00 0.00 0.00 1.40
3208 4435 5.526111 CGATGTAATTTTCACGGACCCTTAT 59.474 40.000 0.00 0.00 0.00 1.73
3209 4436 4.871557 CGATGTAATTTTCACGGACCCTTA 59.128 41.667 0.00 0.00 0.00 2.69
3217 4444 4.092821 TCTTGGCTCGATGTAATTTTCACG 59.907 41.667 0.00 0.00 0.00 4.35
3232 4459 0.308993 GTGTGCACACTTCTTGGCTC 59.691 55.000 36.77 11.53 43.25 4.70
3233 4460 0.394216 TGTGTGCACACTTCTTGGCT 60.394 50.000 40.79 0.00 46.55 4.75


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

AutoCloner maintained by Alex Coulton.