Multiple sequence alignment - TraesCS2D01G227500

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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 TraesCS2D01G227500 chr2D 100.000 3446 0 0 1 3446 196226134 196222689 0.000000e+00 6364
1 TraesCS2D01G227500 chr2D 80.309 518 88 10 1589 2099 196131002 196130492 2.910000e-101 379
2 TraesCS2D01G227500 chr2D 87.580 314 37 2 2266 2578 196130314 196130002 2.940000e-96 363
3 TraesCS2D01G227500 chr2D 89.161 286 31 0 2264 2549 196002536 196002821 1.370000e-94 357
4 TraesCS2D01G227500 chr2D 85.460 337 41 4 2269 2598 195422202 195421867 1.060000e-90 344
5 TraesCS2D01G227500 chr2D 100.000 176 0 0 3821 3996 196222314 196222139 3.850000e-85 326
6 TraesCS2D01G227500 chr2D 77.593 482 92 12 1589 2063 195995614 195996086 1.090000e-70 278
7 TraesCS2D01G227500 chr2D 82.067 329 46 8 3089 3406 196147029 196146703 6.580000e-68 268
8 TraesCS2D01G227500 chr2D 93.277 119 5 2 674 789 488891955 488892073 5.310000e-39 172
9 TraesCS2D01G227500 chr2A 93.312 2467 119 19 1010 3444 211710784 211708332 0.000000e+00 3600
10 TraesCS2D01G227500 chr2A 84.777 381 52 6 2266 2644 211694091 211693715 1.050000e-100 377
11 TraesCS2D01G227500 chr2A 80.077 522 82 17 1589 2099 211695167 211694657 6.310000e-98 368
12 TraesCS2D01G227500 chr2A 86.350 337 38 4 2269 2598 210750117 210749782 1.060000e-95 361
13 TraesCS2D01G227500 chr2A 87.762 286 35 0 2264 2549 211483526 211483811 6.400000e-88 335
14 TraesCS2D01G227500 chr2A 88.811 143 12 2 673 811 409123441 409123299 5.310000e-39 172
15 TraesCS2D01G227500 chr2B 94.208 2072 71 13 897 2947 252977937 252975894 0.000000e+00 3116
16 TraesCS2D01G227500 chr2B 87.311 331 40 2 2269 2598 251770503 251770174 1.050000e-100 377
17 TraesCS2D01G227500 chr2B 89.123 285 29 2 3093 3375 252961650 252961366 1.770000e-93 353
18 TraesCS2D01G227500 chr2B 93.571 140 8 1 2957 3096 252975657 252975519 1.460000e-49 207
19 TraesCS2D01G227500 chr2B 96.667 90 1 2 3842 3931 252961307 252961220 8.950000e-32 148
20 TraesCS2D01G227500 chr2B 95.402 87 2 1 787 873 252978184 252978100 1.940000e-28 137
21 TraesCS2D01G227500 chr5D 90.421 689 41 10 1 672 473442649 473441969 0.000000e+00 883
22 TraesCS2D01G227500 chr5D 78.838 482 91 10 1589 2063 565786302 565785825 8.340000e-82 315
23 TraesCS2D01G227500 chr5D 87.109 256 21 5 428 672 41072974 41073228 3.040000e-71 279
24 TraesCS2D01G227500 chr5D 88.584 219 12 3 466 672 407375686 407375469 1.840000e-63 254
25 TraesCS2D01G227500 chr5D 77.273 308 63 6 1738 2040 510058794 510059099 1.480000e-39 174
26 TraesCS2D01G227500 chr5D 79.310 203 37 5 1843 2041 93862237 93862036 1.940000e-28 137
27 TraesCS2D01G227500 chr5D 74.204 314 64 13 1738 2041 3636465 3636771 9.070000e-22 115
28 TraesCS2D01G227500 chr5D 77.720 193 35 7 2269 2457 93861916 93861728 1.170000e-20 111
29 TraesCS2D01G227500 chr5D 78.750 160 33 1 2269 2428 503049613 503049771 5.460000e-19 106
30 TraesCS2D01G227500 chr5D 83.929 112 10 4 3842 3945 556896792 556896681 2.540000e-17 100
31 TraesCS2D01G227500 chrUn 89.513 677 50 13 4 674 12271180 12271841 0.000000e+00 837
32 TraesCS2D01G227500 chrUn 79.098 488 87 14 1585 2063 67470192 67469711 4.980000e-84 322
33 TraesCS2D01G227500 chr1D 92.665 559 25 5 129 672 463580377 463579820 0.000000e+00 791
34 TraesCS2D01G227500 chr1D 79.747 316 57 7 1730 2040 485555096 485555409 5.200000e-54 222
35 TraesCS2D01G227500 chr1D 94.643 112 3 1 674 782 370560985 370561096 1.910000e-38 171
36 TraesCS2D01G227500 chr1D 92.500 120 5 2 674 789 436967883 436967764 6.870000e-38 169
37 TraesCS2D01G227500 chr1B 87.706 667 54 19 30 675 398836359 398835700 0.000000e+00 752
38 TraesCS2D01G227500 chr1B 87.984 516 54 4 1 510 22647757 22648270 1.590000e-168 603
39 TraesCS2D01G227500 chr1B 79.114 316 59 7 1730 2040 676074663 676074976 1.130000e-50 211
40 TraesCS2D01G227500 chr1B 94.643 112 3 1 674 782 437695520 437695631 1.910000e-38 171
41 TraesCS2D01G227500 chr3D 86.763 695 66 17 1 673 485206071 485205381 0.000000e+00 750
42 TraesCS2D01G227500 chr3D 84.943 704 69 17 1 672 372446382 372445684 0.000000e+00 678
43 TraesCS2D01G227500 chr3D 83.679 723 66 18 1 675 486068590 486067872 5.630000e-178 634
44 TraesCS2D01G227500 chr3D 81.522 184 28 3 2267 2447 462073443 462073623 3.220000e-31 147
45 TraesCS2D01G227500 chr4D 84.561 706 69 18 1 672 496109690 496108991 0.000000e+00 664
46 TraesCS2D01G227500 chr4D 90.875 263 13 1 418 669 5715227 5714965 3.820000e-90 342
47 TraesCS2D01G227500 chr4D 93.277 119 5 1 674 789 184610191 184610309 5.310000e-39 172
48 TraesCS2D01G227500 chr6B 84.280 528 55 10 163 672 561643270 561643787 1.290000e-134 490
49 TraesCS2D01G227500 chr6B 92.920 113 5 1 673 782 591765694 591765806 1.150000e-35 161
50 TraesCS2D01G227500 chr7A 88.968 281 31 0 2269 2549 680628883 680628603 8.220000e-92 348
51 TraesCS2D01G227500 chr7A 93.694 111 6 1 673 782 64133036 64133146 8.880000e-37 165
52 TraesCS2D01G227500 chr4A 78.468 483 91 12 1589 2063 607309662 607310139 1.800000e-78 303
53 TraesCS2D01G227500 chr4A 89.552 134 8 4 673 802 62265470 62265339 8.880000e-37 165
54 TraesCS2D01G227500 chr4A 87.500 112 6 2 3842 3945 605420721 605420610 5.420000e-24 122
55 TraesCS2D01G227500 chr6A 94.928 138 7 0 537 674 444578296 444578159 2.420000e-52 217
56 TraesCS2D01G227500 chr5B 75.691 362 75 12 1687 2040 641043138 641043494 6.870000e-38 169
57 TraesCS2D01G227500 chr5B 78.818 203 38 5 1843 2041 98845546 98845345 9.010000e-27 132
58 TraesCS2D01G227500 chr5B 77.487 191 39 4 2269 2457 98845226 98845038 1.170000e-20 111
59 TraesCS2D01G227500 chr5B 75.481 208 49 2 2269 2475 5066191 5065985 2.540000e-17 100
60 TraesCS2D01G227500 chr3A 81.319 182 28 3 2269 2447 604569639 604569817 4.160000e-30 143
61 TraesCS2D01G227500 chr7D 78.155 206 34 8 1843 2041 610420779 610420578 1.950000e-23 121
62 TraesCS2D01G227500 chr5A 77.720 193 35 7 2269 2457 87416734 87416546 1.170000e-20 111


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 TraesCS2D01G227500 chr2D 196222139 196226134 3995 True 3345.000000 6364 100.000000 1 3996 2 chr2D.!!$R4 3995
1 TraesCS2D01G227500 chr2D 196130002 196131002 1000 True 371.000000 379 83.944500 1589 2578 2 chr2D.!!$R3 989
2 TraesCS2D01G227500 chr2A 211708332 211710784 2452 True 3600.000000 3600 93.312000 1010 3444 1 chr2A.!!$R2 2434
3 TraesCS2D01G227500 chr2A 211693715 211695167 1452 True 372.500000 377 82.427000 1589 2644 2 chr2A.!!$R4 1055
4 TraesCS2D01G227500 chr2B 252975519 252978184 2665 True 1153.333333 3116 94.393667 787 3096 3 chr2B.!!$R3 2309
5 TraesCS2D01G227500 chr5D 473441969 473442649 680 True 883.000000 883 90.421000 1 672 1 chr5D.!!$R2 671
6 TraesCS2D01G227500 chrUn 12271180 12271841 661 False 837.000000 837 89.513000 4 674 1 chrUn.!!$F1 670
7 TraesCS2D01G227500 chr1D 463579820 463580377 557 True 791.000000 791 92.665000 129 672 1 chr1D.!!$R2 543
8 TraesCS2D01G227500 chr1B 398835700 398836359 659 True 752.000000 752 87.706000 30 675 1 chr1B.!!$R1 645
9 TraesCS2D01G227500 chr1B 22647757 22648270 513 False 603.000000 603 87.984000 1 510 1 chr1B.!!$F1 509
10 TraesCS2D01G227500 chr3D 485205381 485206071 690 True 750.000000 750 86.763000 1 673 1 chr3D.!!$R2 672
11 TraesCS2D01G227500 chr3D 372445684 372446382 698 True 678.000000 678 84.943000 1 672 1 chr3D.!!$R1 671
12 TraesCS2D01G227500 chr3D 486067872 486068590 718 True 634.000000 634 83.679000 1 675 1 chr3D.!!$R3 674
13 TraesCS2D01G227500 chr4D 496108991 496109690 699 True 664.000000 664 84.561000 1 672 1 chr4D.!!$R2 671
14 TraesCS2D01G227500 chr6B 561643270 561643787 517 False 490.000000 490 84.280000 163 672 1 chr6B.!!$F1 509

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
245 253 0.040499 AGCTTCTCGTCCTCTCCCTT 59.960 55.0 0.00 0.0 0.00 3.95 F
1423 1642 0.037882 CTCAGAAGCTGGACGAAGCA 60.038 55.0 11.06 0.0 46.08 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1716 0.031585 TTCTTGACGGACGACCACAG 59.968 55.0 4.48 0.0 35.59 3.66 R
3250 4225 0.319083 ATCAGGGTTGCGTCGTGTTA 59.681 50.0 0.00 0.0 0.00 2.41 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
112 114 4.322349 GCTAGATGCATCTAACCCACCTAG 60.322 50.000 30.96 20.95 38.80 3.02
125 128 3.985452 ACCCACCTAGAAAAACTAACCCT 59.015 43.478 0.00 0.00 0.00 4.34
126 129 4.042560 ACCCACCTAGAAAAACTAACCCTC 59.957 45.833 0.00 0.00 0.00 4.30
127 130 4.567116 CCCACCTAGAAAAACTAACCCTCC 60.567 50.000 0.00 0.00 0.00 4.30
161 164 6.315642 GTGCTTATTTGGGTTAGTTCTCCTAC 59.684 42.308 0.00 0.00 0.00 3.18
170 174 1.546961 AGTTCTCCTACGGACCACTG 58.453 55.000 0.00 0.00 0.00 3.66
212 220 0.107017 CATCCCGCAACAGATCCCTT 60.107 55.000 0.00 0.00 0.00 3.95
245 253 0.040499 AGCTTCTCGTCCTCTCCCTT 59.960 55.000 0.00 0.00 0.00 3.95
296 304 4.944372 CCGTATCCGCACTCCCGC 62.944 72.222 0.00 0.00 0.00 6.13
326 337 3.851184 AGCCCCGCCCTATCCTCT 61.851 66.667 0.00 0.00 0.00 3.69
564 610 6.889301 AGTCAAATGATTGAGAAAGAGCAA 57.111 33.333 0.00 0.00 45.88 3.91
675 754 4.740902 AGAGTATTCAAACAGGGCCTTTT 58.259 39.130 1.32 0.00 0.00 2.27
676 755 5.147767 AGAGTATTCAAACAGGGCCTTTTT 58.852 37.500 11.86 11.86 0.00 1.94
698 777 7.712204 TTTTTGGATGGGTTAGAATCTAACC 57.288 36.000 33.35 33.35 44.64 2.85
709 788 8.489990 GGTTAGAATCTAACCCAAACTAACTC 57.510 38.462 31.93 10.30 40.71 3.01
710 789 8.319881 GGTTAGAATCTAACCCAAACTAACTCT 58.680 37.037 31.93 0.00 40.71 3.24
711 790 9.368674 GTTAGAATCTAACCCAAACTAACTCTC 57.631 37.037 19.55 0.00 36.82 3.20
712 791 6.948589 AGAATCTAACCCAAACTAACTCTCC 58.051 40.000 0.00 0.00 0.00 3.71
713 792 6.731448 AGAATCTAACCCAAACTAACTCTCCT 59.269 38.462 0.00 0.00 0.00 3.69
714 793 5.740290 TCTAACCCAAACTAACTCTCCTG 57.260 43.478 0.00 0.00 0.00 3.86
715 794 5.152934 TCTAACCCAAACTAACTCTCCTGT 58.847 41.667 0.00 0.00 0.00 4.00
716 795 4.790718 AACCCAAACTAACTCTCCTGTT 57.209 40.909 0.00 0.00 0.00 3.16
717 796 4.790718 ACCCAAACTAACTCTCCTGTTT 57.209 40.909 0.00 0.00 33.56 2.83
718 797 4.461198 ACCCAAACTAACTCTCCTGTTTG 58.539 43.478 9.59 9.59 44.90 2.93
724 803 8.567285 CAAACTAACTCTCCTGTTTGGATATT 57.433 34.615 8.90 0.00 45.16 1.28
725 804 9.014297 CAAACTAACTCTCCTGTTTGGATATTT 57.986 33.333 8.90 0.00 45.16 1.40
726 805 9.588096 AAACTAACTCTCCTGTTTGGATATTTT 57.412 29.630 0.00 0.00 45.16 1.82
727 806 9.588096 AACTAACTCTCCTGTTTGGATATTTTT 57.412 29.630 0.00 0.00 45.16 1.94
730 809 8.581253 AACTCTCCTGTTTGGATATTTTTAGG 57.419 34.615 0.00 0.00 45.16 2.69
731 810 7.699878 ACTCTCCTGTTTGGATATTTTTAGGT 58.300 34.615 0.00 0.00 45.16 3.08
732 811 8.170730 ACTCTCCTGTTTGGATATTTTTAGGTT 58.829 33.333 0.00 0.00 45.16 3.50
733 812 9.681062 CTCTCCTGTTTGGATATTTTTAGGTTA 57.319 33.333 0.00 0.00 45.16 2.85
734 813 9.681062 TCTCCTGTTTGGATATTTTTAGGTTAG 57.319 33.333 0.00 0.00 45.16 2.34
735 814 9.462606 CTCCTGTTTGGATATTTTTAGGTTAGT 57.537 33.333 0.00 0.00 45.16 2.24
736 815 9.816787 TCCTGTTTGGATATTTTTAGGTTAGTT 57.183 29.630 0.00 0.00 40.56 2.24
756 835 6.704289 AGTTAAGTCCAAACTAACCCAAAC 57.296 37.500 0.00 0.00 35.44 2.93
757 836 6.429151 AGTTAAGTCCAAACTAACCCAAACT 58.571 36.000 0.00 0.00 35.44 2.66
758 837 7.576403 AGTTAAGTCCAAACTAACCCAAACTA 58.424 34.615 0.00 0.00 35.44 2.24
759 838 8.054572 AGTTAAGTCCAAACTAACCCAAACTAA 58.945 33.333 0.00 0.00 35.44 2.24
760 839 6.704289 AAGTCCAAACTAACCCAAACTAAC 57.296 37.500 0.00 0.00 33.48 2.34
761 840 6.009908 AGTCCAAACTAACCCAAACTAACT 57.990 37.500 0.00 0.00 32.59 2.24
762 841 6.060136 AGTCCAAACTAACCCAAACTAACTC 58.940 40.000 0.00 0.00 32.59 3.01
763 842 6.060136 GTCCAAACTAACCCAAACTAACTCT 58.940 40.000 0.00 0.00 0.00 3.24
764 843 7.071572 AGTCCAAACTAACCCAAACTAACTCTA 59.928 37.037 0.00 0.00 32.59 2.43
765 844 7.716560 GTCCAAACTAACCCAAACTAACTCTAA 59.283 37.037 0.00 0.00 0.00 2.10
766 845 7.716560 TCCAAACTAACCCAAACTAACTCTAAC 59.283 37.037 0.00 0.00 0.00 2.34
767 846 7.040892 CCAAACTAACCCAAACTAACTCTAACC 60.041 40.741 0.00 0.00 0.00 2.85
768 847 6.119240 ACTAACCCAAACTAACTCTAACCC 57.881 41.667 0.00 0.00 0.00 4.11
769 848 5.608015 ACTAACCCAAACTAACTCTAACCCA 59.392 40.000 0.00 0.00 0.00 4.51
770 849 5.594199 AACCCAAACTAACTCTAACCCAT 57.406 39.130 0.00 0.00 0.00 4.00
771 850 4.918588 ACCCAAACTAACTCTAACCCATG 58.081 43.478 0.00 0.00 0.00 3.66
772 851 4.263771 ACCCAAACTAACTCTAACCCATGG 60.264 45.833 4.14 4.14 0.00 3.66
773 852 4.018779 CCCAAACTAACTCTAACCCATGGA 60.019 45.833 15.22 0.00 0.00 3.41
774 853 5.340027 CCCAAACTAACTCTAACCCATGGAT 60.340 44.000 15.22 4.04 0.00 3.41
775 854 5.823045 CCAAACTAACTCTAACCCATGGATC 59.177 44.000 15.22 0.00 0.00 3.36
776 855 5.632034 AACTAACTCTAACCCATGGATCC 57.368 43.478 15.22 4.20 0.00 3.36
777 856 4.631234 ACTAACTCTAACCCATGGATCCA 58.369 43.478 18.88 18.88 0.00 3.41
778 857 5.036916 ACTAACTCTAACCCATGGATCCAA 58.963 41.667 20.67 1.96 0.00 3.53
779 858 4.946160 AACTCTAACCCATGGATCCAAA 57.054 40.909 20.67 0.00 0.00 3.28
780 859 4.236527 ACTCTAACCCATGGATCCAAAC 57.763 45.455 20.67 0.00 0.00 2.93
781 860 3.591527 ACTCTAACCCATGGATCCAAACA 59.408 43.478 20.67 0.00 0.00 2.83
782 861 4.230502 ACTCTAACCCATGGATCCAAACAT 59.769 41.667 20.67 7.08 0.00 2.71
783 862 4.535781 TCTAACCCATGGATCCAAACATG 58.464 43.478 20.67 12.42 43.07 3.21
784 863 2.925966 ACCCATGGATCCAAACATGT 57.074 45.000 20.67 9.10 42.15 3.21
785 864 2.738743 ACCCATGGATCCAAACATGTC 58.261 47.619 20.67 0.00 42.15 3.06
789 868 4.472496 CCATGGATCCAAACATGTCCATA 58.528 43.478 20.67 0.00 46.79 2.74
854 933 1.124477 GGCTTTCTTTTCGACGTCTCG 59.876 52.381 14.70 1.54 41.65 4.04
855 934 1.460428 GCTTTCTTTTCGACGTCTCGC 60.460 52.381 14.70 0.00 39.96 5.03
864 943 1.153997 GACGTCTCGCTTCCAGGAC 60.154 63.158 8.70 0.00 0.00 3.85
892 1090 1.946267 CCAGACGGTGGTTTTTCGG 59.054 57.895 0.00 0.00 42.17 4.30
893 1091 0.816421 CCAGACGGTGGTTTTTCGGT 60.816 55.000 0.00 0.00 42.17 4.69
895 1093 0.533531 AGACGGTGGTTTTTCGGTCC 60.534 55.000 0.00 0.00 35.50 4.46
903 1121 0.794473 GTTTTTCGGTCCTACCAGCG 59.206 55.000 0.00 0.00 38.47 5.18
1049 1268 1.683943 CCACGGCATTGATGGATCTT 58.316 50.000 0.00 0.00 35.33 2.40
1270 1489 0.866061 CGAACGCTCGTCATCCGAAT 60.866 55.000 0.00 0.00 46.75 3.34
1274 1493 0.936764 CGCTCGTCATCCGAATCCAG 60.937 60.000 0.00 0.00 46.75 3.86
1349 1568 4.704103 TCCTGCAGGCTCGACCCT 62.704 66.667 28.91 0.00 40.58 4.34
1423 1642 0.037882 CTCAGAAGCTGGACGAAGCA 60.038 55.000 11.06 0.00 46.08 3.91
1472 1691 3.676742 GATGTCTTCGACGGCGTC 58.323 61.111 29.06 29.06 38.98 5.19
1481 1700 3.676742 GACGGCGTCGATGTCTTC 58.323 61.111 25.42 3.59 40.11 2.87
1512 1737 1.829096 TTCCTGTGGTCGTCCGTCA 60.829 57.895 0.00 0.00 36.30 4.35
1544 1769 0.673956 GAGGCGGAGGAGGAAACAAC 60.674 60.000 0.00 0.00 0.00 3.32
1562 1787 0.841289 ACAAGTCCAAGAACGGGGAA 59.159 50.000 0.00 0.00 34.34 3.97
1747 1972 4.127744 CCACCATCACCCCGCCAT 62.128 66.667 0.00 0.00 0.00 4.40
2187 2419 3.368323 GGAGGTAATTACGGACGTTTCCA 60.368 47.826 9.46 0.00 43.00 3.53
2196 2428 0.951558 GGACGTTTCCACTGCATTGT 59.048 50.000 3.14 0.00 42.30 2.71
2212 2444 6.430925 ACTGCATTGTTGTGTGAACATAGTAT 59.569 34.615 0.00 0.00 0.00 2.12
2213 2445 7.040478 ACTGCATTGTTGTGTGAACATAGTATT 60.040 33.333 0.00 0.00 0.00 1.89
2214 2446 8.329203 TGCATTGTTGTGTGAACATAGTATTA 57.671 30.769 0.00 0.00 0.00 0.98
2215 2447 8.233868 TGCATTGTTGTGTGAACATAGTATTAC 58.766 33.333 0.00 0.00 0.00 1.89
2216 2448 7.425309 GCATTGTTGTGTGAACATAGTATTACG 59.575 37.037 0.00 0.00 0.00 3.18
2324 3040 2.599281 TCGACCAGTGGCGAGGAA 60.599 61.111 20.17 3.56 30.64 3.36
2480 3196 3.308705 GTCGACGACCACCCCCTT 61.309 66.667 17.25 0.00 0.00 3.95
2572 3288 1.079819 CCAATGAGCCTGACGTCGT 60.080 57.895 11.62 0.00 0.00 4.34
2613 3329 5.022787 AGTTCCTCATAGAGAAGAAGCAGT 58.977 41.667 0.00 0.00 0.00 4.40
2730 3469 4.506886 AGGAATTAGCCGATCTAACGAG 57.493 45.455 0.00 0.00 39.86 4.18
2759 3498 3.119316 TGTTTTGCAAATGTCTCGTGGTT 60.119 39.130 13.65 0.00 0.00 3.67
2779 3518 3.430333 TGCATTATCACATTGCTGCAG 57.570 42.857 10.11 10.11 37.28 4.41
2798 3537 8.090831 TGCTGCAGGATTATTATTACTACTCTG 58.909 37.037 17.12 0.00 0.00 3.35
2799 3538 8.307483 GCTGCAGGATTATTATTACTACTCTGA 58.693 37.037 17.12 0.00 0.00 3.27
2858 3597 7.558161 TCGATCTTTGATCAATGTTATGCTT 57.442 32.000 17.97 0.00 0.00 3.91
2892 3631 5.125097 ACTGATGCATAGCTTCTTTTTCTGG 59.875 40.000 0.00 0.00 34.46 3.86
2952 3691 3.703001 TTAGTTGGGAGGAAGAAGCTG 57.297 47.619 0.00 0.00 0.00 4.24
2955 3920 2.175715 AGTTGGGAGGAAGAAGCTGTTT 59.824 45.455 0.00 0.00 0.00 2.83
3078 4045 1.609061 CCACACTGCTGGTTGAGTAGG 60.609 57.143 0.00 0.00 38.68 3.18
3102 4069 5.830000 AAAAACTATTGGCTTACGGATCC 57.170 39.130 0.00 0.00 0.00 3.36
3117 4084 1.889829 GGATCCTATCGAGAGGTGGTG 59.110 57.143 24.73 0.00 37.88 4.17
3137 4111 3.630312 GTGGCCACTAGAACAAAGAACAA 59.370 43.478 29.12 0.00 0.00 2.83
3165 4140 0.385390 AGTTTTTGGGCTGCTCAACG 59.615 50.000 15.73 0.00 0.00 4.10
3169 4144 3.772853 TTGGGCTGCTCAACGCACT 62.773 57.895 11.63 0.00 45.47 4.40
3232 4207 1.782028 GCCAACCTCACGTCCAACAC 61.782 60.000 0.00 0.00 0.00 3.32
3255 4230 3.121544 GCCTACGATACTTGCCTAACAC 58.878 50.000 0.00 0.00 0.00 3.32
3258 4233 2.872370 ACGATACTTGCCTAACACGAC 58.128 47.619 0.00 0.00 0.00 4.34
3272 4247 0.740868 CACGACGCAACCCTGATCAT 60.741 55.000 0.00 0.00 0.00 2.45
3274 4249 1.202417 ACGACGCAACCCTGATCATAG 60.202 52.381 0.00 0.00 0.00 2.23
3281 4256 4.573900 GCAACCCTGATCATAGATCGATT 58.426 43.478 0.00 0.00 0.00 3.34
3349 4325 7.117236 CACGACTCATAACAAAGCCTAAACTTA 59.883 37.037 0.00 0.00 0.00 2.24
3353 4329 7.095355 ACTCATAACAAAGCCTAAACTTACACG 60.095 37.037 0.00 0.00 0.00 4.49
3363 4339 6.040878 GCCTAAACTTACACGTGATACAGAT 58.959 40.000 25.01 0.00 0.00 2.90
3366 4342 9.577110 CCTAAACTTACACGTGATACAGATTTA 57.423 33.333 25.01 14.48 0.00 1.40
3413 4389 3.826524 TGGAACATAAACTTGCCACTCA 58.173 40.909 0.00 0.00 0.00 3.41
3414 4390 4.211125 TGGAACATAAACTTGCCACTCAA 58.789 39.130 0.00 0.00 0.00 3.02
3424 4400 5.590530 ACTTGCCACTCAAACATAAAACA 57.409 34.783 0.00 0.00 33.65 2.83
3426 4402 7.283625 ACTTGCCACTCAAACATAAAACATA 57.716 32.000 0.00 0.00 33.65 2.29
3838 4814 1.153549 AACTCCAATCCTCTCGCGC 60.154 57.895 0.00 0.00 0.00 6.86
3839 4815 1.888436 AACTCCAATCCTCTCGCGCA 61.888 55.000 8.75 0.00 0.00 6.09
3840 4816 1.068753 CTCCAATCCTCTCGCGCAT 59.931 57.895 8.75 0.00 0.00 4.73
3841 4817 0.943359 CTCCAATCCTCTCGCGCATC 60.943 60.000 8.75 0.00 0.00 3.91
3842 4818 1.068753 CCAATCCTCTCGCGCATCT 59.931 57.895 8.75 0.00 0.00 2.90
3843 4819 0.531532 CCAATCCTCTCGCGCATCTT 60.532 55.000 8.75 0.00 0.00 2.40
3844 4820 0.857935 CAATCCTCTCGCGCATCTTC 59.142 55.000 8.75 0.00 0.00 2.87
3845 4821 0.461548 AATCCTCTCGCGCATCTTCA 59.538 50.000 8.75 0.00 0.00 3.02
3846 4822 0.249238 ATCCTCTCGCGCATCTTCAC 60.249 55.000 8.75 0.00 0.00 3.18
3847 4823 1.880340 CCTCTCGCGCATCTTCACC 60.880 63.158 8.75 0.00 0.00 4.02
3848 4824 1.880340 CTCTCGCGCATCTTCACCC 60.880 63.158 8.75 0.00 0.00 4.61
3849 4825 2.185350 CTCGCGCATCTTCACCCT 59.815 61.111 8.75 0.00 0.00 4.34
3850 4826 1.448540 CTCGCGCATCTTCACCCTT 60.449 57.895 8.75 0.00 0.00 3.95
3851 4827 1.424493 CTCGCGCATCTTCACCCTTC 61.424 60.000 8.75 0.00 0.00 3.46
3852 4828 2.464459 CGCGCATCTTCACCCTTCC 61.464 63.158 8.75 0.00 0.00 3.46
3853 4829 1.377202 GCGCATCTTCACCCTTCCA 60.377 57.895 0.30 0.00 0.00 3.53
3854 4830 0.960364 GCGCATCTTCACCCTTCCAA 60.960 55.000 0.30 0.00 0.00 3.53
3855 4831 1.089920 CGCATCTTCACCCTTCCAAG 58.910 55.000 0.00 0.00 0.00 3.61
3856 4832 1.611673 CGCATCTTCACCCTTCCAAGT 60.612 52.381 0.00 0.00 0.00 3.16
3857 4833 1.815003 GCATCTTCACCCTTCCAAGTG 59.185 52.381 0.00 0.00 35.24 3.16
3858 4834 2.553028 GCATCTTCACCCTTCCAAGTGA 60.553 50.000 0.00 0.00 41.13 3.41
3859 4835 2.930826 TCTTCACCCTTCCAAGTGAC 57.069 50.000 0.00 0.00 42.49 3.67
3860 4836 2.408565 TCTTCACCCTTCCAAGTGACT 58.591 47.619 0.00 0.00 42.49 3.41
3861 4837 2.777692 TCTTCACCCTTCCAAGTGACTT 59.222 45.455 0.00 0.00 42.49 3.01
3862 4838 2.638480 TCACCCTTCCAAGTGACTTG 57.362 50.000 18.04 18.04 38.07 3.16
3877 4853 7.456253 CAAGTGACTTGGTCAAAATATCTACG 58.544 38.462 17.27 0.00 44.49 3.51
3878 4854 6.931838 AGTGACTTGGTCAAAATATCTACGA 58.068 36.000 1.77 0.00 44.49 3.43
3879 4855 7.036220 AGTGACTTGGTCAAAATATCTACGAG 58.964 38.462 1.77 0.00 44.49 4.18
3880 4856 6.812160 GTGACTTGGTCAAAATATCTACGAGT 59.188 38.462 1.77 0.00 44.49 4.18
3881 4857 7.331193 GTGACTTGGTCAAAATATCTACGAGTT 59.669 37.037 1.77 0.00 44.49 3.01
3882 4858 7.330946 TGACTTGGTCAAAATATCTACGAGTTG 59.669 37.037 0.00 0.00 39.78 3.16
3883 4859 7.383687 ACTTGGTCAAAATATCTACGAGTTGA 58.616 34.615 0.00 0.00 0.00 3.18
3884 4860 8.041323 ACTTGGTCAAAATATCTACGAGTTGAT 58.959 33.333 5.60 5.60 0.00 2.57
3885 4861 8.420374 TTGGTCAAAATATCTACGAGTTGATC 57.580 34.615 3.64 0.00 0.00 2.92
3896 4872 3.852471 CGAGTTGATCGTTTGTGTTCA 57.148 42.857 0.00 0.00 46.62 3.18
3897 4873 4.190304 CGAGTTGATCGTTTGTGTTCAA 57.810 40.909 0.00 0.00 46.62 2.69
3898 4874 3.960002 CGAGTTGATCGTTTGTGTTCAAC 59.040 43.478 6.55 6.55 46.62 3.18
3899 4875 4.493382 CGAGTTGATCGTTTGTGTTCAACA 60.493 41.667 14.79 0.00 46.51 3.33
3900 4876 5.499139 AGTTGATCGTTTGTGTTCAACAT 57.501 34.783 14.79 0.95 46.51 2.71
3901 4877 5.510671 AGTTGATCGTTTGTGTTCAACATC 58.489 37.500 14.79 0.00 46.51 3.06
3902 4878 4.481930 TGATCGTTTGTGTTCAACATCC 57.518 40.909 0.00 0.00 38.99 3.51
3903 4879 3.879892 TGATCGTTTGTGTTCAACATCCA 59.120 39.130 0.00 0.00 38.99 3.41
3904 4880 3.684103 TCGTTTGTGTTCAACATCCAC 57.316 42.857 0.00 0.00 38.99 4.02
3905 4881 2.356382 TCGTTTGTGTTCAACATCCACC 59.644 45.455 0.00 0.00 38.99 4.61
3906 4882 2.357637 CGTTTGTGTTCAACATCCACCT 59.642 45.455 0.00 0.00 38.99 4.00
3907 4883 3.181491 CGTTTGTGTTCAACATCCACCTT 60.181 43.478 0.00 0.00 38.99 3.50
3908 4884 4.676723 CGTTTGTGTTCAACATCCACCTTT 60.677 41.667 0.00 0.00 38.99 3.11
3909 4885 4.647424 TTGTGTTCAACATCCACCTTTC 57.353 40.909 0.00 0.00 38.99 2.62
3910 4886 2.955660 TGTGTTCAACATCCACCTTTCC 59.044 45.455 0.00 0.00 32.36 3.13
3911 4887 3.222603 GTGTTCAACATCCACCTTTCCT 58.777 45.455 0.00 0.00 0.00 3.36
3912 4888 3.636764 GTGTTCAACATCCACCTTTCCTT 59.363 43.478 0.00 0.00 0.00 3.36
3913 4889 3.888930 TGTTCAACATCCACCTTTCCTTC 59.111 43.478 0.00 0.00 0.00 3.46
3914 4890 4.145052 GTTCAACATCCACCTTTCCTTCT 58.855 43.478 0.00 0.00 0.00 2.85
3915 4891 4.453480 TCAACATCCACCTTTCCTTCTT 57.547 40.909 0.00 0.00 0.00 2.52
3916 4892 4.398319 TCAACATCCACCTTTCCTTCTTC 58.602 43.478 0.00 0.00 0.00 2.87
3917 4893 3.441500 ACATCCACCTTTCCTTCTTCC 57.558 47.619 0.00 0.00 0.00 3.46
3918 4894 2.716424 ACATCCACCTTTCCTTCTTCCA 59.284 45.455 0.00 0.00 0.00 3.53
3919 4895 2.951229 TCCACCTTTCCTTCTTCCAC 57.049 50.000 0.00 0.00 0.00 4.02
3920 4896 2.131854 TCCACCTTTCCTTCTTCCACA 58.868 47.619 0.00 0.00 0.00 4.17
3921 4897 2.158667 TCCACCTTTCCTTCTTCCACAC 60.159 50.000 0.00 0.00 0.00 3.82
3922 4898 2.422803 CCACCTTTCCTTCTTCCACACA 60.423 50.000 0.00 0.00 0.00 3.72
3923 4899 3.287222 CACCTTTCCTTCTTCCACACAA 58.713 45.455 0.00 0.00 0.00 3.33
3924 4900 3.891366 CACCTTTCCTTCTTCCACACAAT 59.109 43.478 0.00 0.00 0.00 2.71
3925 4901 4.022849 CACCTTTCCTTCTTCCACACAATC 60.023 45.833 0.00 0.00 0.00 2.67
3926 4902 4.141158 ACCTTTCCTTCTTCCACACAATCT 60.141 41.667 0.00 0.00 0.00 2.40
3927 4903 4.457257 CCTTTCCTTCTTCCACACAATCTC 59.543 45.833 0.00 0.00 0.00 2.75
3928 4904 4.982241 TTCCTTCTTCCACACAATCTCT 57.018 40.909 0.00 0.00 0.00 3.10
3929 4905 6.433847 TTTCCTTCTTCCACACAATCTCTA 57.566 37.500 0.00 0.00 0.00 2.43
3930 4906 6.433847 TTCCTTCTTCCACACAATCTCTAA 57.566 37.500 0.00 0.00 0.00 2.10
3931 4907 6.627087 TCCTTCTTCCACACAATCTCTAAT 57.373 37.500 0.00 0.00 0.00 1.73
3932 4908 7.733773 TCCTTCTTCCACACAATCTCTAATA 57.266 36.000 0.00 0.00 0.00 0.98
3933 4909 8.324191 TCCTTCTTCCACACAATCTCTAATAT 57.676 34.615 0.00 0.00 0.00 1.28
3934 4910 9.434275 TCCTTCTTCCACACAATCTCTAATATA 57.566 33.333 0.00 0.00 0.00 0.86
3935 4911 9.703892 CCTTCTTCCACACAATCTCTAATATAG 57.296 37.037 0.00 0.00 0.00 1.31
3938 4914 8.642432 TCTTCCACACAATCTCTAATATAGTGG 58.358 37.037 0.00 0.00 43.94 4.00
3939 4915 7.914427 TCCACACAATCTCTAATATAGTGGT 57.086 36.000 0.00 0.00 43.28 4.16
3940 4916 9.429109 TTCCACACAATCTCTAATATAGTGGTA 57.571 33.333 0.00 0.00 43.28 3.25
3941 4917 8.857098 TCCACACAATCTCTAATATAGTGGTAC 58.143 37.037 0.00 0.00 43.28 3.34
3942 4918 8.861086 CCACACAATCTCTAATATAGTGGTACT 58.139 37.037 0.00 0.00 39.21 2.73
3960 4936 7.657761 AGTGGTACTTTATATCTATGTGCTTGC 59.342 37.037 0.00 0.00 0.00 4.01
3961 4937 7.657761 GTGGTACTTTATATCTATGTGCTTGCT 59.342 37.037 0.00 0.00 0.00 3.91
3962 4938 7.657354 TGGTACTTTATATCTATGTGCTTGCTG 59.343 37.037 0.00 0.00 0.00 4.41
3963 4939 6.551385 ACTTTATATCTATGTGCTTGCTGC 57.449 37.500 0.00 0.00 43.25 5.25
3964 4940 5.471456 ACTTTATATCTATGTGCTTGCTGCC 59.529 40.000 0.00 0.00 42.00 4.85
3965 4941 3.497103 ATATCTATGTGCTTGCTGCCA 57.503 42.857 0.00 0.00 42.00 4.92
3966 4942 2.359981 ATCTATGTGCTTGCTGCCAT 57.640 45.000 0.00 0.00 42.00 4.40
3967 4943 1.671979 TCTATGTGCTTGCTGCCATC 58.328 50.000 0.00 0.00 42.00 3.51
3968 4944 1.065272 TCTATGTGCTTGCTGCCATCA 60.065 47.619 0.00 0.00 42.00 3.07
3969 4945 1.954382 CTATGTGCTTGCTGCCATCAT 59.046 47.619 0.00 0.00 42.00 2.45
3970 4946 0.459899 ATGTGCTTGCTGCCATCATG 59.540 50.000 0.00 0.00 42.00 3.07
3971 4947 0.609681 TGTGCTTGCTGCCATCATGA 60.610 50.000 0.00 0.00 42.00 3.07
3972 4948 0.744874 GTGCTTGCTGCCATCATGAT 59.255 50.000 1.18 1.18 42.00 2.45
3973 4949 1.136305 GTGCTTGCTGCCATCATGATT 59.864 47.619 5.16 0.00 42.00 2.57
3974 4950 2.359848 GTGCTTGCTGCCATCATGATTA 59.640 45.455 5.16 0.00 42.00 1.75
3975 4951 3.025262 TGCTTGCTGCCATCATGATTAA 58.975 40.909 5.16 0.00 42.00 1.40
3976 4952 3.181484 TGCTTGCTGCCATCATGATTAAC 60.181 43.478 5.16 0.00 42.00 2.01
3977 4953 3.067742 GCTTGCTGCCATCATGATTAACT 59.932 43.478 5.16 0.00 35.15 2.24
3978 4954 4.607955 CTTGCTGCCATCATGATTAACTG 58.392 43.478 5.16 3.96 0.00 3.16
3979 4955 2.953648 TGCTGCCATCATGATTAACTGG 59.046 45.455 5.16 6.70 0.00 4.00
3980 4956 3.216800 GCTGCCATCATGATTAACTGGA 58.783 45.455 15.10 1.66 0.00 3.86
3981 4957 3.825014 GCTGCCATCATGATTAACTGGAT 59.175 43.478 15.10 0.00 0.00 3.41
3982 4958 4.280174 GCTGCCATCATGATTAACTGGATT 59.720 41.667 15.10 0.00 0.00 3.01
3983 4959 5.564259 GCTGCCATCATGATTAACTGGATTC 60.564 44.000 15.10 0.17 0.00 2.52
3984 4960 5.698104 TGCCATCATGATTAACTGGATTCT 58.302 37.500 15.10 0.00 0.00 2.40
3985 4961 6.131264 TGCCATCATGATTAACTGGATTCTT 58.869 36.000 15.10 0.00 0.00 2.52
3986 4962 6.040054 TGCCATCATGATTAACTGGATTCTTG 59.960 38.462 15.10 0.00 0.00 3.02
3987 4963 6.444633 CCATCATGATTAACTGGATTCTTGC 58.555 40.000 5.16 0.00 0.00 4.01
3988 4964 6.040054 CCATCATGATTAACTGGATTCTTGCA 59.960 38.462 5.16 0.00 0.00 4.08
3989 4965 6.441093 TCATGATTAACTGGATTCTTGCAC 57.559 37.500 0.00 0.00 0.00 4.57
3990 4966 5.945191 TCATGATTAACTGGATTCTTGCACA 59.055 36.000 0.00 0.00 0.00 4.57
3991 4967 6.433716 TCATGATTAACTGGATTCTTGCACAA 59.566 34.615 0.00 0.00 0.00 3.33
3992 4968 6.647334 TGATTAACTGGATTCTTGCACAAA 57.353 33.333 0.00 0.00 0.00 2.83
3993 4969 6.680810 TGATTAACTGGATTCTTGCACAAAG 58.319 36.000 0.00 0.00 37.22 2.77
3994 4970 6.489700 TGATTAACTGGATTCTTGCACAAAGA 59.510 34.615 0.00 0.00 43.37 2.52
3995 4971 6.899393 TTAACTGGATTCTTGCACAAAGAT 57.101 33.333 0.00 0.00 44.46 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 114 4.981812 TCTTGGAGGAGGGTTAGTTTTTC 58.018 43.478 0.00 0.00 0.00 2.29
127 130 3.019564 CCCAAATAAGCACCTCTTGGAG 58.980 50.000 0.73 0.00 39.12 3.86
194 202 0.181350 GAAGGGATCTGTTGCGGGAT 59.819 55.000 0.00 0.00 0.00 3.85
212 220 1.971357 AGAAGCTTCGAGAAAGTGGGA 59.029 47.619 20.43 0.00 37.31 4.37
245 253 3.071206 GCAGTGCGAGAGGGAGGA 61.071 66.667 0.00 0.00 0.00 3.71
326 337 2.524887 ACGAGGGGGTTGGAACGA 60.525 61.111 0.00 0.00 0.00 3.85
510 526 1.825281 GCCCTGACTGAGAGCTGTGT 61.825 60.000 0.00 0.00 0.00 3.72
564 610 7.721399 GGATGACAGGGTTAGATTGACAATAAT 59.279 37.037 0.00 0.00 0.00 1.28
684 763 8.319881 AGAGTTAGTTTGGGTTAGATTCTAACC 58.680 37.037 33.74 33.74 44.64 2.85
685 764 9.368674 GAGAGTTAGTTTGGGTTAGATTCTAAC 57.631 37.037 22.88 22.88 37.25 2.34
686 765 8.537858 GGAGAGTTAGTTTGGGTTAGATTCTAA 58.462 37.037 1.90 1.90 0.00 2.10
687 766 7.899709 AGGAGAGTTAGTTTGGGTTAGATTCTA 59.100 37.037 0.00 0.00 0.00 2.10
688 767 6.731448 AGGAGAGTTAGTTTGGGTTAGATTCT 59.269 38.462 0.00 0.00 0.00 2.40
689 768 6.819146 CAGGAGAGTTAGTTTGGGTTAGATTC 59.181 42.308 0.00 0.00 0.00 2.52
690 769 6.272558 ACAGGAGAGTTAGTTTGGGTTAGATT 59.727 38.462 0.00 0.00 0.00 2.40
691 770 5.785940 ACAGGAGAGTTAGTTTGGGTTAGAT 59.214 40.000 0.00 0.00 0.00 1.98
692 771 5.152934 ACAGGAGAGTTAGTTTGGGTTAGA 58.847 41.667 0.00 0.00 0.00 2.10
693 772 5.485209 ACAGGAGAGTTAGTTTGGGTTAG 57.515 43.478 0.00 0.00 0.00 2.34
694 773 5.899631 AACAGGAGAGTTAGTTTGGGTTA 57.100 39.130 0.00 0.00 0.00 2.85
695 774 4.790718 AACAGGAGAGTTAGTTTGGGTT 57.209 40.909 0.00 0.00 0.00 4.11
696 775 4.461198 CAAACAGGAGAGTTAGTTTGGGT 58.539 43.478 8.55 0.00 44.17 4.51
731 810 8.054572 AGTTTGGGTTAGTTTGGACTTAACTAA 58.945 33.333 0.00 0.00 42.63 2.24
732 811 7.576403 AGTTTGGGTTAGTTTGGACTTAACTA 58.424 34.615 0.00 0.00 37.12 2.24
733 812 6.429151 AGTTTGGGTTAGTTTGGACTTAACT 58.571 36.000 0.00 0.00 39.13 2.24
734 813 6.704289 AGTTTGGGTTAGTTTGGACTTAAC 57.296 37.500 0.00 0.00 37.33 2.01
735 814 8.054572 AGTTAGTTTGGGTTAGTTTGGACTTAA 58.945 33.333 0.00 0.00 37.33 1.85
736 815 7.576403 AGTTAGTTTGGGTTAGTTTGGACTTA 58.424 34.615 0.00 0.00 37.33 2.24
737 816 6.429151 AGTTAGTTTGGGTTAGTTTGGACTT 58.571 36.000 0.00 0.00 37.33 3.01
738 817 6.009908 AGTTAGTTTGGGTTAGTTTGGACT 57.990 37.500 0.00 0.00 39.97 3.85
739 818 6.060136 AGAGTTAGTTTGGGTTAGTTTGGAC 58.940 40.000 0.00 0.00 0.00 4.02
740 819 6.256643 AGAGTTAGTTTGGGTTAGTTTGGA 57.743 37.500 0.00 0.00 0.00 3.53
741 820 7.040892 GGTTAGAGTTAGTTTGGGTTAGTTTGG 60.041 40.741 0.00 0.00 0.00 3.28
742 821 7.040892 GGGTTAGAGTTAGTTTGGGTTAGTTTG 60.041 40.741 0.00 0.00 0.00 2.93
743 822 7.000472 GGGTTAGAGTTAGTTTGGGTTAGTTT 59.000 38.462 0.00 0.00 0.00 2.66
744 823 6.101588 TGGGTTAGAGTTAGTTTGGGTTAGTT 59.898 38.462 0.00 0.00 0.00 2.24
745 824 5.608015 TGGGTTAGAGTTAGTTTGGGTTAGT 59.392 40.000 0.00 0.00 0.00 2.24
746 825 6.117975 TGGGTTAGAGTTAGTTTGGGTTAG 57.882 41.667 0.00 0.00 0.00 2.34
747 826 6.478129 CATGGGTTAGAGTTAGTTTGGGTTA 58.522 40.000 0.00 0.00 0.00 2.85
748 827 5.321927 CATGGGTTAGAGTTAGTTTGGGTT 58.678 41.667 0.00 0.00 0.00 4.11
749 828 4.263771 CCATGGGTTAGAGTTAGTTTGGGT 60.264 45.833 2.85 0.00 0.00 4.51
750 829 4.018779 TCCATGGGTTAGAGTTAGTTTGGG 60.019 45.833 13.02 0.00 0.00 4.12
751 830 5.174037 TCCATGGGTTAGAGTTAGTTTGG 57.826 43.478 13.02 0.00 0.00 3.28
752 831 5.823045 GGATCCATGGGTTAGAGTTAGTTTG 59.177 44.000 13.02 0.00 0.00 2.93
753 832 5.491078 TGGATCCATGGGTTAGAGTTAGTTT 59.509 40.000 11.44 0.00 0.00 2.66
754 833 5.036916 TGGATCCATGGGTTAGAGTTAGTT 58.963 41.667 11.44 0.00 0.00 2.24
755 834 4.631234 TGGATCCATGGGTTAGAGTTAGT 58.369 43.478 11.44 0.00 0.00 2.24
756 835 5.630415 TTGGATCCATGGGTTAGAGTTAG 57.370 43.478 17.06 0.00 0.00 2.34
757 836 5.251932 TGTTTGGATCCATGGGTTAGAGTTA 59.748 40.000 17.06 0.00 0.00 2.24
758 837 4.044065 TGTTTGGATCCATGGGTTAGAGTT 59.956 41.667 17.06 0.00 0.00 3.01
759 838 3.591527 TGTTTGGATCCATGGGTTAGAGT 59.408 43.478 17.06 0.00 0.00 3.24
760 839 4.235079 TGTTTGGATCCATGGGTTAGAG 57.765 45.455 17.06 0.00 0.00 2.43
761 840 4.017591 ACATGTTTGGATCCATGGGTTAGA 60.018 41.667 17.06 0.00 42.15 2.10
762 841 4.280819 ACATGTTTGGATCCATGGGTTAG 58.719 43.478 17.06 5.49 42.15 2.34
763 842 4.277476 GACATGTTTGGATCCATGGGTTA 58.723 43.478 17.06 0.00 42.15 2.85
764 843 3.099141 GACATGTTTGGATCCATGGGTT 58.901 45.455 17.06 0.00 42.15 4.11
765 844 2.624029 GGACATGTTTGGATCCATGGGT 60.624 50.000 17.06 3.70 42.15 4.51
766 845 2.034124 GGACATGTTTGGATCCATGGG 58.966 52.381 17.06 6.57 42.15 4.00
767 846 2.737544 TGGACATGTTTGGATCCATGG 58.262 47.619 17.06 4.97 42.15 3.66
770 849 4.860802 ACTATGGACATGTTTGGATCCA 57.139 40.909 11.44 11.44 45.12 3.41
771 850 5.505173 CAACTATGGACATGTTTGGATCC 57.495 43.478 4.20 4.20 0.00 3.36
789 868 1.000283 CTTCGTGACTGAGCTCCAACT 60.000 52.381 12.15 0.00 0.00 3.16
854 933 0.108585 TCACACTTGGTCCTGGAAGC 59.891 55.000 0.00 0.00 0.00 3.86
855 934 1.543429 GGTCACACTTGGTCCTGGAAG 60.543 57.143 0.00 0.00 0.00 3.46
864 943 4.361253 CCGTCTGGTCACACTTGG 57.639 61.111 0.00 0.00 0.00 3.61
891 1089 4.509737 GGACGCGCTGGTAGGACC 62.510 72.222 5.73 0.00 39.22 4.46
892 1090 3.755628 TGGACGCGCTGGTAGGAC 61.756 66.667 5.73 0.00 0.00 3.85
893 1091 3.755628 GTGGACGCGCTGGTAGGA 61.756 66.667 5.73 0.00 0.00 2.94
895 1093 2.167219 CATGTGGACGCGCTGGTAG 61.167 63.158 5.73 0.00 0.00 3.18
903 1121 2.255252 GTGTTGCCATGTGGACGC 59.745 61.111 2.55 0.00 37.39 5.19
1423 1642 1.604378 CCGGGCTCAATGAAGAGGT 59.396 57.895 0.00 0.00 36.15 3.85
1464 1683 3.676742 GAAGACATCGACGCCGTC 58.323 61.111 7.29 7.29 37.05 4.79
1497 1716 0.031585 TTCTTGACGGACGACCACAG 59.968 55.000 4.48 0.00 35.59 3.66
1512 1737 0.531200 CCGCCTCCGTTAGTCTTCTT 59.469 55.000 0.00 0.00 0.00 2.52
1526 1751 1.375326 GTTGTTTCCTCCTCCGCCT 59.625 57.895 0.00 0.00 0.00 5.52
1544 1769 2.084546 GATTCCCCGTTCTTGGACTTG 58.915 52.381 0.00 0.00 0.00 3.16
1569 1794 3.760035 GAGCAGGAACTCGGCGGA 61.760 66.667 7.21 0.00 41.48 5.54
1922 2147 1.557099 AGATGTTGTAGCGGAGGTGA 58.443 50.000 0.00 0.00 40.22 4.02
1992 2220 1.429463 GACTTGTCGGACATGGTGAC 58.571 55.000 22.96 2.41 0.00 3.67
2187 2419 4.580167 ACTATGTTCACACAACAATGCAGT 59.420 37.500 0.00 0.00 36.16 4.40
2196 2428 7.829725 AGGTACGTAATACTATGTTCACACAA 58.170 34.615 0.00 0.00 33.38 3.33
2212 2444 6.971726 ATGGACATTGAGATAGGTACGTAA 57.028 37.500 0.00 0.00 0.00 3.18
2213 2445 7.668469 ACATATGGACATTGAGATAGGTACGTA 59.332 37.037 7.80 0.00 0.00 3.57
2214 2446 6.493802 ACATATGGACATTGAGATAGGTACGT 59.506 38.462 7.80 0.00 0.00 3.57
2215 2447 6.925211 ACATATGGACATTGAGATAGGTACG 58.075 40.000 7.80 0.00 0.00 3.67
2216 2448 8.367911 TGAACATATGGACATTGAGATAGGTAC 58.632 37.037 7.80 0.00 0.00 3.34
2328 3044 3.634397 ATTGGTGGTGAAGACGATGAT 57.366 42.857 0.00 0.00 0.00 2.45
2480 3196 2.500098 CAGTTCCTGTATCTCCGGGAAA 59.500 50.000 0.00 0.00 39.20 3.13
2613 3329 1.942776 TCCTCCATCTTGCTCTGTCA 58.057 50.000 0.00 0.00 0.00 3.58
2759 3498 2.100087 CCTGCAGCAATGTGATAATGCA 59.900 45.455 8.66 0.00 42.45 3.96
2798 3537 4.560035 GTGCACAAATGATGCTACACATTC 59.440 41.667 13.17 0.00 43.77 2.67
2799 3538 4.022155 TGTGCACAAATGATGCTACACATT 60.022 37.500 19.28 0.00 43.77 2.71
2952 3691 3.242518 GCCAAGGCTCGTAAAATCAAAC 58.757 45.455 3.29 0.00 38.26 2.93
2955 3920 1.459450 GGCCAAGGCTCGTAAAATCA 58.541 50.000 11.40 0.00 41.60 2.57
3058 4025 1.609061 CCTACTCAACCAGCAGTGTGG 60.609 57.143 9.41 9.41 44.01 4.17
3102 4069 1.043116 TGGCCACCACCTCTCGATAG 61.043 60.000 0.00 0.00 0.00 2.08
3117 4084 4.578928 TCTTTGTTCTTTGTTCTAGTGGCC 59.421 41.667 0.00 0.00 0.00 5.36
3137 4111 3.430790 GCAGCCCAAAAACTTTCTGTCTT 60.431 43.478 0.00 0.00 0.00 3.01
3216 4191 4.431035 CGTGTTGGACGTGAGGTT 57.569 55.556 0.00 0.00 43.50 3.50
3232 4207 4.338327 GGCAAGTATCGTAGGCCG 57.662 61.111 0.00 0.00 34.56 6.13
3250 4225 0.319083 ATCAGGGTTGCGTCGTGTTA 59.681 50.000 0.00 0.00 0.00 2.41
3255 4230 1.067060 TCTATGATCAGGGTTGCGTCG 59.933 52.381 0.09 0.00 0.00 5.12
3258 4233 2.029918 TCGATCTATGATCAGGGTTGCG 60.030 50.000 0.09 1.09 0.00 4.85
3272 4247 6.177610 AGGCAAGTTTAAACCAATCGATCTA 58.822 36.000 14.72 0.00 0.00 1.98
3274 4249 5.310720 AGGCAAGTTTAAACCAATCGATC 57.689 39.130 14.72 0.00 0.00 3.69
3281 4256 6.779860 AGAGATAGAAGGCAAGTTTAAACCA 58.220 36.000 14.72 0.00 0.00 3.67
3385 4361 7.779798 AGTGGCAAGTTTATGTTCCATGTATAT 59.220 33.333 0.00 0.00 0.00 0.86
3820 4796 1.153549 GCGCGAGAGGATTGGAGTT 60.154 57.895 12.10 0.00 0.00 3.01
3821 4797 1.680522 ATGCGCGAGAGGATTGGAGT 61.681 55.000 12.10 0.00 0.00 3.85
3822 4798 0.943359 GATGCGCGAGAGGATTGGAG 60.943 60.000 12.10 0.00 0.00 3.86
3823 4799 1.068083 GATGCGCGAGAGGATTGGA 59.932 57.895 12.10 0.00 0.00 3.53
3824 4800 0.531532 AAGATGCGCGAGAGGATTGG 60.532 55.000 12.10 0.00 0.00 3.16
3825 4801 0.857935 GAAGATGCGCGAGAGGATTG 59.142 55.000 12.10 0.00 0.00 2.67
3826 4802 0.461548 TGAAGATGCGCGAGAGGATT 59.538 50.000 12.10 0.00 0.00 3.01
3827 4803 0.249238 GTGAAGATGCGCGAGAGGAT 60.249 55.000 12.10 0.00 0.00 3.24
3828 4804 1.139734 GTGAAGATGCGCGAGAGGA 59.860 57.895 12.10 0.00 0.00 3.71
3829 4805 1.880340 GGTGAAGATGCGCGAGAGG 60.880 63.158 12.10 0.00 0.00 3.69
3830 4806 1.880340 GGGTGAAGATGCGCGAGAG 60.880 63.158 12.10 0.00 0.00 3.20
3831 4807 1.888436 AAGGGTGAAGATGCGCGAGA 61.888 55.000 12.10 0.00 0.00 4.04
3832 4808 1.424493 GAAGGGTGAAGATGCGCGAG 61.424 60.000 12.10 0.00 0.00 5.03
3833 4809 1.447838 GAAGGGTGAAGATGCGCGA 60.448 57.895 12.10 0.00 0.00 5.87
3834 4810 2.464459 GGAAGGGTGAAGATGCGCG 61.464 63.158 0.00 0.00 0.00 6.86
3835 4811 0.960364 TTGGAAGGGTGAAGATGCGC 60.960 55.000 0.00 0.00 0.00 6.09
3836 4812 1.089920 CTTGGAAGGGTGAAGATGCG 58.910 55.000 0.00 0.00 0.00 4.73
3837 4813 1.815003 CACTTGGAAGGGTGAAGATGC 59.185 52.381 0.00 0.00 35.69 3.91
3838 4814 3.077359 GTCACTTGGAAGGGTGAAGATG 58.923 50.000 0.00 0.00 42.88 2.90
3839 4815 2.982488 AGTCACTTGGAAGGGTGAAGAT 59.018 45.455 0.00 0.00 42.88 2.40
3840 4816 2.408565 AGTCACTTGGAAGGGTGAAGA 58.591 47.619 0.00 0.00 42.88 2.87
3841 4817 2.880890 CAAGTCACTTGGAAGGGTGAAG 59.119 50.000 9.96 0.00 42.88 3.02
3842 4818 2.930950 CAAGTCACTTGGAAGGGTGAA 58.069 47.619 9.96 0.00 42.88 3.18
3843 4819 2.638480 CAAGTCACTTGGAAGGGTGA 57.362 50.000 9.96 0.00 37.77 4.02
3852 4828 7.330946 TCGTAGATATTTTGACCAAGTCACTTG 59.669 37.037 10.91 10.91 42.60 3.16
3853 4829 7.383687 TCGTAGATATTTTGACCAAGTCACTT 58.616 34.615 0.00 0.00 42.60 3.16
3854 4830 6.931838 TCGTAGATATTTTGACCAAGTCACT 58.068 36.000 0.00 0.00 42.60 3.41
3855 4831 6.812160 ACTCGTAGATATTTTGACCAAGTCAC 59.188 38.462 0.00 0.00 38.01 3.67
3856 4832 6.931838 ACTCGTAGATATTTTGACCAAGTCA 58.068 36.000 0.00 0.00 36.91 3.41
3857 4833 7.544566 TCAACTCGTAGATATTTTGACCAAGTC 59.455 37.037 0.00 0.00 33.89 3.01
3858 4834 7.383687 TCAACTCGTAGATATTTTGACCAAGT 58.616 34.615 0.00 0.00 33.89 3.16
3859 4835 7.827819 TCAACTCGTAGATATTTTGACCAAG 57.172 36.000 0.00 0.00 33.89 3.61
3860 4836 7.222031 CGATCAACTCGTAGATATTTTGACCAA 59.778 37.037 0.00 0.00 42.56 3.67
3861 4837 6.695713 CGATCAACTCGTAGATATTTTGACCA 59.304 38.462 0.00 0.00 42.56 4.02
3862 4838 7.095024 CGATCAACTCGTAGATATTTTGACC 57.905 40.000 0.00 0.00 42.56 4.02
3880 4856 4.336713 TGGATGTTGAACACAAACGATCAA 59.663 37.500 0.00 0.00 39.50 2.57
3881 4857 3.879892 TGGATGTTGAACACAAACGATCA 59.120 39.130 0.00 0.00 39.50 2.92
3882 4858 4.219033 GTGGATGTTGAACACAAACGATC 58.781 43.478 0.00 0.00 39.50 3.69
3883 4859 3.004315 GGTGGATGTTGAACACAAACGAT 59.996 43.478 0.00 0.00 39.50 3.73
3884 4860 2.356382 GGTGGATGTTGAACACAAACGA 59.644 45.455 0.00 0.00 39.50 3.85
3885 4861 2.357637 AGGTGGATGTTGAACACAAACG 59.642 45.455 0.00 0.00 39.50 3.60
3886 4862 4.385358 AAGGTGGATGTTGAACACAAAC 57.615 40.909 0.00 0.00 39.50 2.93
3887 4863 4.142049 GGAAAGGTGGATGTTGAACACAAA 60.142 41.667 0.00 0.00 39.50 2.83
3888 4864 3.383185 GGAAAGGTGGATGTTGAACACAA 59.617 43.478 0.00 0.00 39.50 3.33
3889 4865 2.955660 GGAAAGGTGGATGTTGAACACA 59.044 45.455 0.00 0.00 40.71 3.72
3890 4866 3.222603 AGGAAAGGTGGATGTTGAACAC 58.777 45.455 0.00 0.00 0.00 3.32
3891 4867 3.593442 AGGAAAGGTGGATGTTGAACA 57.407 42.857 0.00 0.00 0.00 3.18
3892 4868 4.145052 AGAAGGAAAGGTGGATGTTGAAC 58.855 43.478 0.00 0.00 0.00 3.18
3893 4869 4.453480 AGAAGGAAAGGTGGATGTTGAA 57.547 40.909 0.00 0.00 0.00 2.69
3894 4870 4.398319 GAAGAAGGAAAGGTGGATGTTGA 58.602 43.478 0.00 0.00 0.00 3.18
3895 4871 3.507622 GGAAGAAGGAAAGGTGGATGTTG 59.492 47.826 0.00 0.00 0.00 3.33
3896 4872 3.140144 TGGAAGAAGGAAAGGTGGATGTT 59.860 43.478 0.00 0.00 0.00 2.71
3897 4873 2.716424 TGGAAGAAGGAAAGGTGGATGT 59.284 45.455 0.00 0.00 0.00 3.06
3898 4874 3.084786 GTGGAAGAAGGAAAGGTGGATG 58.915 50.000 0.00 0.00 0.00 3.51
3899 4875 2.716424 TGTGGAAGAAGGAAAGGTGGAT 59.284 45.455 0.00 0.00 0.00 3.41
3900 4876 2.131854 TGTGGAAGAAGGAAAGGTGGA 58.868 47.619 0.00 0.00 0.00 4.02
3901 4877 2.230660 GTGTGGAAGAAGGAAAGGTGG 58.769 52.381 0.00 0.00 0.00 4.61
3902 4878 2.930950 TGTGTGGAAGAAGGAAAGGTG 58.069 47.619 0.00 0.00 0.00 4.00
3903 4879 3.662759 TTGTGTGGAAGAAGGAAAGGT 57.337 42.857 0.00 0.00 0.00 3.50
3904 4880 4.401925 AGATTGTGTGGAAGAAGGAAAGG 58.598 43.478 0.00 0.00 0.00 3.11
3905 4881 5.312079 AGAGATTGTGTGGAAGAAGGAAAG 58.688 41.667 0.00 0.00 0.00 2.62
3906 4882 5.310409 AGAGATTGTGTGGAAGAAGGAAA 57.690 39.130 0.00 0.00 0.00 3.13
3907 4883 4.982241 AGAGATTGTGTGGAAGAAGGAA 57.018 40.909 0.00 0.00 0.00 3.36
3908 4884 6.627087 ATTAGAGATTGTGTGGAAGAAGGA 57.373 37.500 0.00 0.00 0.00 3.36
3909 4885 9.703892 CTATATTAGAGATTGTGTGGAAGAAGG 57.296 37.037 0.00 0.00 0.00 3.46
3912 4888 8.642432 CCACTATATTAGAGATTGTGTGGAAGA 58.358 37.037 0.00 0.00 43.39 2.87
3913 4889 8.424918 ACCACTATATTAGAGATTGTGTGGAAG 58.575 37.037 14.13 0.00 43.39 3.46
3914 4890 8.319057 ACCACTATATTAGAGATTGTGTGGAA 57.681 34.615 14.13 0.00 43.39 3.53
3915 4891 7.914427 ACCACTATATTAGAGATTGTGTGGA 57.086 36.000 14.13 0.00 43.39 4.02
3916 4892 8.861086 AGTACCACTATATTAGAGATTGTGTGG 58.139 37.037 0.00 0.00 45.38 4.17
3934 4910 7.657761 GCAAGCACATAGATATAAAGTACCACT 59.342 37.037 0.00 0.00 0.00 4.00
3935 4911 7.657761 AGCAAGCACATAGATATAAAGTACCAC 59.342 37.037 0.00 0.00 0.00 4.16
3936 4912 7.657354 CAGCAAGCACATAGATATAAAGTACCA 59.343 37.037 0.00 0.00 0.00 3.25
3937 4913 7.360438 GCAGCAAGCACATAGATATAAAGTACC 60.360 40.741 0.00 0.00 44.79 3.34
3938 4914 7.513968 GCAGCAAGCACATAGATATAAAGTAC 58.486 38.462 0.00 0.00 44.79 2.73
3939 4915 7.658179 GCAGCAAGCACATAGATATAAAGTA 57.342 36.000 0.00 0.00 44.79 2.24
3940 4916 6.551385 GCAGCAAGCACATAGATATAAAGT 57.449 37.500 0.00 0.00 44.79 2.66
3955 4931 3.067742 AGTTAATCATGATGGCAGCAAGC 59.932 43.478 10.46 0.00 44.65 4.01
3956 4932 4.499188 CCAGTTAATCATGATGGCAGCAAG 60.499 45.833 10.46 5.34 0.00 4.01
3957 4933 3.382227 CCAGTTAATCATGATGGCAGCAA 59.618 43.478 10.46 0.00 0.00 3.91
3958 4934 2.953648 CCAGTTAATCATGATGGCAGCA 59.046 45.455 8.33 8.33 0.00 4.41
3959 4935 3.216800 TCCAGTTAATCATGATGGCAGC 58.783 45.455 9.46 0.00 0.00 5.25
3960 4936 5.768662 AGAATCCAGTTAATCATGATGGCAG 59.231 40.000 9.46 0.00 0.00 4.85
3961 4937 5.698104 AGAATCCAGTTAATCATGATGGCA 58.302 37.500 9.46 0.00 0.00 4.92
3962 4938 6.444633 CAAGAATCCAGTTAATCATGATGGC 58.555 40.000 9.46 2.75 0.00 4.40
3963 4939 6.040054 TGCAAGAATCCAGTTAATCATGATGG 59.960 38.462 9.46 7.49 0.00 3.51
3964 4940 6.916387 GTGCAAGAATCCAGTTAATCATGATG 59.084 38.462 9.46 0.00 0.00 3.07
3965 4941 6.604396 TGTGCAAGAATCCAGTTAATCATGAT 59.396 34.615 1.18 1.18 0.00 2.45
3966 4942 5.945191 TGTGCAAGAATCCAGTTAATCATGA 59.055 36.000 0.00 0.00 0.00 3.07
3967 4943 6.198650 TGTGCAAGAATCCAGTTAATCATG 57.801 37.500 0.00 0.00 0.00 3.07
3968 4944 6.839124 TTGTGCAAGAATCCAGTTAATCAT 57.161 33.333 0.00 0.00 0.00 2.45
3969 4945 6.489700 TCTTTGTGCAAGAATCCAGTTAATCA 59.510 34.615 0.00 0.00 38.68 2.57
3970 4946 6.913170 TCTTTGTGCAAGAATCCAGTTAATC 58.087 36.000 0.00 0.00 38.68 1.75
3971 4947 6.899393 TCTTTGTGCAAGAATCCAGTTAAT 57.101 33.333 0.00 0.00 38.68 1.40
3972 4948 6.899393 ATCTTTGTGCAAGAATCCAGTTAA 57.101 33.333 0.00 0.00 45.06 2.01


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

AutoCloner maintained by Alex Coulton.